Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_001660
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 186609
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Found at i:3604 original size:14 final size:14
Alignment explanation
Indices: 3571--3606 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
3561 GCTGTCAGAG
3571 AAAAAAAACTGACA
1 AAAAAAAACTGACA
**
3585 GGAAAAAACTGACA
1 AAAAAAAACTGACA
3599 AAAAAAAA
1 AAAAAAAA
3607 TAGAAAAAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.72, C:0.11, G:0.11, T:0.06
Consensus pattern (14 bp):
AAAAAAAACTGACA
Left flanking sequence: Indices 3071 -- 3570
ACCCCATCATTATTTCCTTTTTTGTAACATGGGATTTCATGCCATAACTGTTATTTGTATTTTAG
TGTTTATTGGCGCTGTTGGAAAATCTGCACAGATTGGATTGCATACTTGGTTACCCGATGCAATG
GAGGGTTTTATAATATTTGAGGGCTCTCATGTGCCATTAGGTACATTCCAACAATCTCACTGTAT
GCTGGAATCGTCGACCAAATGAGAGTCCCTATCGGAAAAATATCTCATTTTGACCAATCAGCAGG
AAACCTATTAGGGTCAAATCCACCCGGCGAAGTCAAGGCCGAAGGAGCTCTATAGGATCCCCAGA
GACTGTACGTAAGACCTCTTGTTCGAAATTGAATCTCTCCCGAACCTGCTGGCCCAAAGGGCACG
AAGACCAGAGGGAGGGCCCGGAGGGCAGGGGACTTTGTTTGTCTGACAGGGCCCTGGACTGTCAG
ACAAACAAGGAAAAAAACTGAAAAAAAAGGCCCCGGCTGTCAGAG
Right flanking sequence: Indices 3607 -- 4106
TAGAAAAAAACAGAGCAGAAACTTATAAGTTTTTGGAAAAATCTATATTTTTGGCGTCAAGTCTA
TTCATGTATGAAAGAAAAACCACATCTTAGTTTTTAAGGCCACAGCGGCCATCCATAAGACTATT
GGGAGAGCCTATATTTCATAAGTGGAAGATCCAGTCCCTACTCTTGCCAAAGGTAGACTCACCAA
CCAATTACCCAATGCTGTGGAAAAAAATATATATATTTTCCGGCCTTGTGAAATCGTAAAAGGTT
ATGCGAGAGTAGCCCACTCCAGTATCCGCTTTGATTCATGCAGCTACTATGGTAACAGCAGGCGT
TTTTATGATAGCAAGGTGCTCCCCTTTATTTGAATACTCACCCAATGCTTTGATTGTTATTACTT
TTGTAGGCGCTATGACGTCATTCTTCGCGGCAACCACCGGAATATTACAAAACGATTTAAAAAGG
GTTATAGCTTATTCAACTTGTAGTCAGTTAGGCTATATGATCTTT
Found at i:6328 original size:13 final size:14
Alignment explanation
Indices: 6301--6331 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
6291 TCTATTATCC
*
6301 AAAAACTGACAAAA
1 AAAAACAGACAAAA
6315 AAAAACAGACAAAA
1 AAAAACAGACAAAA
6329 AAA
1 AAA
6332 GGGCAAAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.77, C:0.13, G:0.06, T:0.03
Consensus pattern (14 bp):
AAAAACAGACAAAA
Left flanking sequence: Indices 5801 -- 6300
TTATGACCTGGTTGATATATACCATCAATAGGCATGGAGCGAGCAACGTACGTTCATGCCGTTCG
CCATTTGCGGAGCTCAGGTGCCAATGGTTAGTTGCTGGTTGACAAGGACCGAAAGAGTCTCCGAT
TCGCCAGTACAGAACCTCATCTTAAATACAAGAAAACCGGCTTGCTTCATACTTTTGGGTTACCC
CCCCCCACCGGGGAGGGTAAATGAACCCCCCTCAACAGAGCTTCTTGCACATGCTAAGGTCTCCG
TGTTCGTTGCCGAACAAGAATGAGTGCAATGCCTTTGCACAGAAATGGACTTGTGCTTTTTCTCG
TGCGGGACGGTCACTCGATGAAAATAATAAACTTAATTCGCCAAAAACAGACCGGGTCAACAGAT
TTTTAGTATCAAATGCTAATTCTTTGCTTTAGGCCATTATTGTATTGGCATTTTTTATAATAATT
AGATTAGCACATCCTGATTTCATTATGAATAACTATCTATTATCC
Right flanking sequence: Indices 6332 -- 6831
GGGCAAAAACTTGCTTAACAAGCGGAGGCCTAGGCCCGTAGGGCAGCGCTACGGGCCTTTTCGCA
GCATATATATTTTTCGCAGCAAAAATATATATATATTTTTTTCGGGATTTCTAGGAAAAAGAGTA
AACGTATATGTTACAAGTTTTAGCTCCATTTTATTCCAATTTAAGTGGTCTTATTTTGCTTCCTT
TGCTAGGAAGCCTTATTATTTTGGTGATCCCGAATTCAAGAGTACGTCTGATACGAGGTATCACA
ATTTGGACCTCTTTGATTACTTTTTTATATTCTCTTTTTTTTTGGATACGCTTTGAGAATGATAC
AGCAAAATTTCAGTTTGTGGAAACTATTCGATGGCTTCCGTATTCAAATATCAATTTTTATATAG
GTATAGATGGTATCTCTTTATTCTTTGTGATCTTGACCACGTTTTTAACTCCTATTTGCATTCTT
GTTGGCTTTTATAGCGTCAAAAGTTATAAAAAAGAATATATGATA
Found at i:6426 original size:20 final size:18
Alignment explanation
Indices: 6389--6424 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
6379 GCTACGGGCC
*
6389 TTTTCGCAGCATATATAT
1 TTTTCGCAGCAAATATAT
*
6407 TTTTCGCAGCAAAAATAT
1 TTTTCGCAGCAAATATAT
6425 ATATATATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.33, C:0.17, G:0.11, T:0.39
Consensus pattern (18 bp):
TTTTCGCAGCAAATATAT
Left flanking sequence: Indices 5889 -- 6388
ATGGTTAGTTGCTGGTTGACAAGGACCGAAAGAGTCTCCGATTCGCCAGTACAGAACCTCATCTT
AAATACAAGAAAACCGGCTTGCTTCATACTTTTGGGTTACCCCCCCCCACCGGGGAGGGTAAATG
AACCCCCCTCAACAGAGCTTCTTGCACATGCTAAGGTCTCCGTGTTCGTTGCCGAACAAGAATGA
GTGCAATGCCTTTGCACAGAAATGGACTTGTGCTTTTTCTCGTGCGGGACGGTCACTCGATGAAA
ATAATAAACTTAATTCGCCAAAAACAGACCGGGTCAACAGATTTTTAGTATCAAATGCTAATTCT
TTGCTTTAGGCCATTATTGTATTGGCATTTTTTATAATAATTAGATTAGCACATCCTGATTTCAT
TATGAATAACTATCTATTATCCAAAAACTGACAAAAAAAAACAGACAAAAAAAGGGCAAAAACTT
GCTTAACAAGCGGAGGCCTAGGCCCGTAGGGCAGCGCTACGGGCC
Right flanking sequence: Indices 6425 -- 6924
ATATATATTTTTTTCGGGATTTCTAGGAAAAAGAGTAAACGTATATGTTACAAGTTTTAGCTCCA
TTTTATTCCAATTTAAGTGGTCTTATTTTGCTTCCTTTGCTAGGAAGCCTTATTATTTTGGTGAT
CCCGAATTCAAGAGTACGTCTGATACGAGGTATCACAATTTGGACCTCTTTGATTACTTTTTTAT
ATTCTCTTTTTTTTTGGATACGCTTTGAGAATGATACAGCAAAATTTCAGTTTGTGGAAACTATT
CGATGGCTTCCGTATTCAAATATCAATTTTTATATAGGTATAGATGGTATCTCTTTATTCTTTGT
GATCTTGACCACGTTTTTAACTCCTATTTGCATTCTTGTTGGCTTTTATAGCGTCAAAAGTTATA
AAAAAGAATATATGATAGCGTTTTTCATTTGTGAATCTTTCCTAATTGCTGTGTTTTGCTCACTC
GATCTTTTAATCTTTTACGTTTTTTTTGAAAGCGTGTTAATTCCC
Found at i:14685 original size:27 final size:27
Alignment explanation
Indices: 14655--14795 Score: 79
Period size: 27 Copynumber: 5.1 Consensus size: 27
14645 GTTATATATA
*
14655 TATATATATACGAAACTTCAGTTTCTG
1 TATATGTATACGAAACTTCAGTTTCTG
**** * * * *
14682 TATATGTATATTCTATTTGAAGTTATATA
1 TATATGTATACGAAACTT-CAGTT-TCTG
* *
14711 TATATATATACGAAACTTTAGTTTCTG
1 TATATGTATACGAAACTTCAGTTTCTG
* * ** *
14738 TATATGTATAGGCTATTTTCAATTAT-T-
1 TATATGTATACG-AAACTTCAGTT-TCTG
14765 TATATGTATACGAAACTTCAGTTTCGTG
1 TATATGTATACGAAACTTCAGTTTC-TG
14793 TAT
1 TAT
14796 TCTATATGAT
Statistics
Matches: 77, Mismatches: 30, Indels: 13
0.64 0.25 0.11
Matches are distributed among these distances:
25 1 0.01
26 7 0.09
27 36 0.47
28 18 0.23
29 15 0.19
ACGTcount: A:0.32, C:0.10, G:0.12, T:0.46
Consensus pattern (27 bp):
TATATGTATACGAAACTTCAGTTTCTG
Left flanking sequence: Indices 14155 -- 14654
TAACAGCCGGCAGCACGACATTCGCGGTTGCTGGATGATCGCCGATGTGAGCTGTCACATAACCC
CGATCTACAAAATGTTCTACAAATTGCTTTCTCATTGAAAACCTCAAAAGAACCGCAAAGGCTAT
AATTAAGCCTAGAACGTATCAACTGCAAACTGCGCAGACTATTTATAAATAAATGAAAGGCTCAG
AAAAGTCCAGTACGCGCTGTCGTTCCGCGTACGAAAATAAAAACATAAACGTGTACAATACGCGG
CCTAAATTGGGCACTCCGAAGAAATGAATAACTTTCAAACAAAATTTGAGGGTAATCACATAAGT
ATAATAAACGCGGATTAGCGCATAAAAGCCTCCGACTGCTGCAACTAGATAGTAACTTCAGCGGC
TTCTTTCCATAAATTCTTTCAACTTGCACCTCGACAACGAATGTGAAAAGCGATTATATAAACGA
AACTTCAGTTTCTGTATATGTATATGCTATTTGAAGTTATATATA
Right flanking sequence: Indices 14796 -- 15295
TCTATATGATATAACAAGTCCTATATGCTATGCGTTATGCCGCACTCTGCGCCACGCCCCGGGGC
CGTCTTAGGCTTCTGAGAACCAATAACACGTAAACTATGTAAAACTAAAGTAAATCAATATACAA
AAAACACGAATTATAATTTCCTCCAAAATAGTTTTTAATACAAAATTCATTATATTTCGTCGTGT
GTTGAACCAGATCAAAACCAAGAAAACGCAAAGCAAAAAAAAATATATATATTTTTTTTTCGTTT
TATTCTATTGGACTCTTTCAGCCTTCATTCGCGATGCGAATAAAGCGGGAGAGAAGAAAGAAGCA
AGCTTCTCCGGATTTCACTCTTTTTTTGCGAAGTGGTTAGTAATGTACTGCATTCTTAGCTCAGT
TGGATAGAGCAACAACCTTCTAAGTTGAAGGTCACAGGTTCAAATCCTGTAGAATGCGTAAAGTG
CACAATGAATAATATATACCAACGGTAATCCTTCTACTTGTTTAA
Found at i:14715 original size:56 final size:56
Alignment explanation
Indices: 14599--14803 Score: 283
Period size: 56 Copynumber: 3.7 Consensus size: 56
14589 GAAAAGCGAT
*
14599 TATATAAACGAAACTTCAGTTTCTGTATATGTATATGCTATTTGAAGTTATATATATA
1 TATATATACGAAACTTCAGTTTCTGTATATGTATATGCTATTTGAAG-T-TATATATA
*
14657 TATATATACGAAACTTCAGTTTCTGTATATGTATATTCTATTTGAAGTTATATATA
1 TATATATACGAAACTTCAGTTTCTGTATATGTATATGCTATTTGAAGTTATATATA
* * *
14713 TATATATACGAAACTTTAGTTTCTGTATATGTATAGGCTATTTTCAA-TTAT-T-TA
1 TATATATACGAAACTTCAGTTTCTGTATATGTATATGCTA-TTTGAAGTTATATATA
* *
14767 TATGTATACGAAACTTCAGTTTCGTGTAT-TCTATATG
1 TATATATACGAAACTTCAGTTTC-TGTATATGTATATG
14804 ATATAACAAG
Statistics
Matches: 135, Mismatches: 10, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
54 29 0.21
55 6 0.04
56 49 0.36
57 6 0.04
58 45 0.33
ACGTcount: A:0.33, C:0.10, G:0.12, T:0.45
Consensus pattern (56 bp):
TATATATACGAAACTTCAGTTTCTGTATATGTATATGCTATTTGAAGTTATATATA
Left flanking sequence: Indices 14099 -- 14598
TTGATGGCCTGCCCCTAGTCGAGTCCTCTATCAAATAATACAACTATCAAATAATATAACAGCCG
GCAGCACGACATTCGCGGTTGCTGGATGATCGCCGATGTGAGCTGTCACATAACCCCGATCTACA
AAATGTTCTACAAATTGCTTTCTCATTGAAAACCTCAAAAGAACCGCAAAGGCTATAATTAAGCC
TAGAACGTATCAACTGCAAACTGCGCAGACTATTTATAAATAAATGAAAGGCTCAGAAAAGTCCA
GTACGCGCTGTCGTTCCGCGTACGAAAATAAAAACATAAACGTGTACAATACGCGGCCTAAATTG
GGCACTCCGAAGAAATGAATAACTTTCAAACAAAATTTGAGGGTAATCACATAAGTATAATAAAC
GCGGATTAGCGCATAAAAGCCTCCGACTGCTGCAACTAGATAGTAACTTCAGCGGCTTCTTTCCA
TAAATTCTTTCAACTTGCACCTCGACAACGAATGTGAAAAGCGAT
Right flanking sequence: Indices 14804 -- 15303
ATATAACAAGTCCTATATGCTATGCGTTATGCCGCACTCTGCGCCACGCCCCGGGGCCGTCTTAG
GCTTCTGAGAACCAATAACACGTAAACTATGTAAAACTAAAGTAAATCAATATACAAAAAACACG
AATTATAATTTCCTCCAAAATAGTTTTTAATACAAAATTCATTATATTTCGTCGTGTGTTGAACC
AGATCAAAACCAAGAAAACGCAAAGCAAAAAAAAATATATATATTTTTTTTTCGTTTTATTCTAT
TGGACTCTTTCAGCCTTCATTCGCGATGCGAATAAAGCGGGAGAGAAGAAAGAAGCAAGCTTCTC
CGGATTTCACTCTTTTTTTGCGAAGTGGTTAGTAATGTACTGCATTCTTAGCTCAGTTGGATAGA
GCAACAACCTTCTAAGTTGAAGGTCACAGGTTCAAATCCTGTAGAATGCGTAAAGTGCACAATGA
ATAATATATACCAACGGTAATCCTTCTACTTGTTTAATTAGTATA
Found at i:36342 original size:24 final size:24
Alignment explanation
Indices: 36315--36360 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
36305 TCCGATGAAT
* *
36315 GATACTTTATAATGCAATTACAAC
1 GATACTTGAAAATGCAATTACAAC
36339 GATACTTGAAAATGCAATTACA
1 GATACTTGAAAATGCAATTACA
36361 TAATAAATTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.43, C:0.15, G:0.11, T:0.30
Consensus pattern (24 bp):
GATACTTGAAAATGCAATTACAAC
Left flanking sequence: Indices 35815 -- 36314
CGAGCTGACTTGCCCGGCCCCTGACATAGCTCAGGGAAAGGCTGGGGTGAATCCTCTTTCCTCAT
GGGCCTCTGAAGAGCTAGTAGAAGGGGCATATGTTGGAGTCCACATGGATAAAGGGCCGGGAACC
CCAAAGAAGTCTACTTCGGATCCTTAAAAGTCAAATTACCAAAGGGATAACAACTATTAGGAAGT
TCCTGCCCTTTTATTACAAACCGATGGGAGGATCATTCCCGTAAGCTACAAGGACTCTTTGAATT
CTGTCAAGCGTGCTGTTAGGGAAAAGAAGGCCGTGGGTCCCTGCCTTTTATTACCATATTTATCT
ATGAGAATTCATCGGATTCAGCCTTTATCTATCTATGGGGGTTCTTCCTTATTTATCTATAATGA
TTCTTCATTTCTCTATGATTATTCAAGGCTATGGACGGAAACGAGCTATTCATCATGGAATTACA
TAGTTAATAGCATAACTGGAAAATTCATCGTATATTCCGATGAAT
Right flanking sequence: Indices 36361 -- 36860
TAATAAATTGCATTTTTAAGCAAATTAATAAGGCGGACAATGACCGACTTGGACTCTTCCGGACT
TGAGCGAACGTATAAAGGCTGAAAAACTAATACACGTCCGTGAGGCCAAAAATATCTTTTTTTCT
TCTTAGCCTTTTTTATTAATGTTGATTAATCAAATCCTAAGCATTAATATAATATTATTTGGGGG
AGCCAAGGTGTAGCGCAATCTGGTAGCGCGTCTGCCTTGGGCGCAGAAAGTTACAGGTTCAAATC
CTGTCACCTTGAATCAAAATCGGAGTCAACTAAAAAGATGAAAATAAATCGACCGTTATCACCTC
ACCTTACCATCTATAAGCCACAGCTTACTTCGACGTTTTCTATTTTTCATAGAATATCCGGGGCT
TTCTTGGCCACTATGGTTTTGTTTAGTATTCTTTTTTTTAAAATAGGTGATCTTAGCCTTACGTT
TTATCATTTTTACCAGTATTTTTTTTTTTTAACTTTCTATTTGAA
Found at i:37991 original size:21 final size:21
Alignment explanation
Indices: 37967--38007 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
37957 CAAAATGAGA
37967 AAAAGTATGAGCTGGATAAAT
1 AAAAGTATGAGCTGGATAAAT
37988 AAAAGTATGAGCTGGATAAA
1 AAAAGTATGAGCTGGATAAA
38008 GGAAAGTTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.49, C:0.05, G:0.24, T:0.22
Consensus pattern (21 bp):
AAAAGTATGAGCTGGATAAAT
Left flanking sequence: Indices 37467 -- 37966
AAAAATAGTCATTGTGTTTATAATAATCTACTATCGATTAAGACGCGATTTTTTTGTGTTTCAAA
CTACCGAAAATTCACAAAAAATAAGAACGTGGGATTTGATATTGAGTAAGCTCCGGGATGCTATT
CAACAACAGTTGGCCGACTACAGGGAGAATATTGAAGAGTTTATAGGGCCTTTTGTAAATAAACT
ATCAAACAAATCCTCAGTGACCTTCCCGTTTTTTACACAAAAAAGGTCTTATTATGCTTCAGCTG
CAAGAGAAACACCCGGTGGTGGATCTGCCGCTAGAGCCGGTAATTCTGTGGTACAGTGGGCAACT
GATTGGGCCTAGTCAAATTTTTTGGGAACCCTGCCGTCTATTGCTGTCATTGTAGGCGGGGCGGG
GTTTTTCGGTTATCAAATATATGACAATGAGCGTTTTCACGCTCGAAAAGACCGAGCCCTGGACC
AAAAAGATGAAGAGCTTGCCCAAAAAAAGCTGGGCCAAAATGAGA
Right flanking sequence: Indices 38008 -- 38507
GGAAAGTTTGAGTACGAAAAGTCGAAAAAAGGGAGGCCATGGAAGATCTTAACGCCCCGACTCCG
GAGGATGCACAGTAAGAATTTCTTCAAAAGCCTGGAGGACTTTCAGCCGTAGGAGCTCATAACAA
ACCAATGGGCCTTTTGAGCCTACGGCCGAGCGGGATACGTTGAATATCTTCGATTTCTTTTTTTC
ATTTTTCTAACGGAAAGAGCAGCGCTACGCGCCTGGCTTTGTTGTTTTAGCCAAAACTAATCTTT
TTTTAGCTATTACCTTGTCTATTACTATGTTTTCATACGCAGGAATACCCCGTTAGCTGGATTTT
GTAGCAAATTCTATTTGTTTTTTGCCGCTTTAGGCTGTGGGGCCTACTTACTAGCTTTAATAGGA
GTAGTTACTAGCGTTATCAGTTGTTTTTATTATATACGCTTTGTGAAAATAATGGATTTTGATAC
ACTTAAAACATGGATTTTATATAAACCCATGGATCGTGAAAAATC
Found at i:38013 original size:21 final size:21
Alignment explanation
Indices: 37967--38019 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
37957 CAAAATGAGA
*
37967 AAAAGTATGAGCTGGATAAAT
1 AAAAGTATGAGCTGGATAAAG
37988 AAAAGTATGAGCTGGATAAAG
1 AAAAGTATGAGCTGGATAAAG
* *
38009 GAAAGTTTGAG
1 AAAAGTATGAG
38020 TACGAAAAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.45, C:0.04, G:0.28, T:0.23
Consensus pattern (21 bp):
AAAAGTATGAGCTGGATAAAG
Left flanking sequence: Indices 37467 -- 37966
AAAAATAGTCATTGTGTTTATAATAATCTACTATCGATTAAGACGCGATTTTTTTGTGTTTCAAA
CTACCGAAAATTCACAAAAAATAAGAACGTGGGATTTGATATTGAGTAAGCTCCGGGATGCTATT
CAACAACAGTTGGCCGACTACAGGGAGAATATTGAAGAGTTTATAGGGCCTTTTGTAAATAAACT
ATCAAACAAATCCTCAGTGACCTTCCCGTTTTTTACACAAAAAAGGTCTTATTATGCTTCAGCTG
CAAGAGAAACACCCGGTGGTGGATCTGCCGCTAGAGCCGGTAATTCTGTGGTACAGTGGGCAACT
GATTGGGCCTAGTCAAATTTTTTGGGAACCCTGCCGTCTATTGCTGTCATTGTAGGCGGGGCGGG
GTTTTTCGGTTATCAAATATATGACAATGAGCGTTTTCACGCTCGAAAAGACCGAGCCCTGGACC
AAAAAGATGAAGAGCTTGCCCAAAAAAAGCTGGGCCAAAATGAGA
Right flanking sequence: Indices 38020 -- 38519
TACGAAAAGTCGAAAAAAGGGAGGCCATGGAAGATCTTAACGCCCCGACTCCGGAGGATGCACAG
TAAGAATTTCTTCAAAAGCCTGGAGGACTTTCAGCCGTAGGAGCTCATAACAAACCAATGGGCCT
TTTGAGCCTACGGCCGAGCGGGATACGTTGAATATCTTCGATTTCTTTTTTTCATTTTTCTAACG
GAAAGAGCAGCGCTACGCGCCTGGCTTTGTTGTTTTAGCCAAAACTAATCTTTTTTTAGCTATTA
CCTTGTCTATTACTATGTTTTCATACGCAGGAATACCCCGTTAGCTGGATTTTGTAGCAAATTCT
ATTTGTTTTTTGCCGCTTTAGGCTGTGGGGCCTACTTACTAGCTTTAATAGGAGTAGTTACTAGC
GTTATCAGTTGTTTTTATTATATACGCTTTGTGAAAATAATGGATTTTGATACACTTAAAACATG
GATTTTATATAAACCCATGGATCGTGAAAAATCGTTACTACTAGC
Found at i:43829 original size:76 final size:76
Alignment explanation
Indices: 43742--43894 Score: 229
Period size: 76 Copynumber: 2.0 Consensus size: 76
43732 TTTTTCTTTT
*
43742 TTTTCCATTTTTTTCAATAAAAATTCTTATTTCATA-TTGTATTATCGTACTTTAATA-CTTCAT
1 TTTTCCATTTTTTTCAATAAAAATTCTTATTTCATACTT-TATTATCGTAATTTAATATC-TCAT
43805 ATACGATGCATCA
64 ATACGATGCATCA
* * *
43818 TTTTCTATTTTTTTCAATAAAAATTGTTATTTTATACTTTATTATCGTAATTTAATATCTCATAT
1 TTTTCCATTTTTTTCAATAAAAATTCTTATTTCATACTTTATTATCGTAATTTAATATCTCATAT
*
43883 ATGATGCATCA
66 ACGATGCATCA
43894 T
1 T
43895 CAAACCGTTT
Statistics
Matches: 70, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
76 67 0.96
77 3 0.04
ACGTcount: A:0.31, C:0.13, G:0.05, T:0.51
Consensus pattern (76 bp):
TTTTCCATTTTTTTCAATAAAAATTCTTATTTCATACTTTATTATCGTAATTTAATATCTCATAT
ACGATGCATCA
Left flanking sequence: Indices 43242 -- 43741
GATGGTTTAGCGACGACCCACTTTTAGATGCCCTTATATATTAATGATAAGAAATATATAAGGGT
TTCACTTTCATACATATTGGCCTGAAGAACGAAAATGCTAGTCGCTATACAGCGACGAAGCAAAT
ACGCTTCGCGTATCCCGAGTTCGAAAACCGACAGTGTAACGTGTCATTTCATAAGGGCAGGAGTA
ACCGTCCTGGCATCTGGCAAGTGTATGGATCGAACCGCCGGTCGAGCCCTCAGAGATCGGGAATA
ATTTCCTCTGACCCGGGTCCAGAGTGAAAAGATAATAAAAAGAAAATAGATATCGGCCATCCTGT
CCCTGTTAATAATGGAAACGCTACGCTTCTCAAGTACTAGGTTCCCGCCGCCAGCACCACGTCTA
CAAAAGAACGGCGGCCGACCCAGCGCGGAAGGCGAAGGTATTGTTTCCTGTCTGTCGTCGTAGAC
GGCTAATTGTCGTAGACGCTTAGCCGTCTACCCAGTTTTTCTTTT
Right flanking sequence: Indices 43895 -- 44394
CAAACCGTTTTAGTTCTAAAAATCTTGAAAAATGCGTTTCAAAATTTTGAAACTACATGAAAATT
TGTTTAAAAAGATCCAATTCTACTAATGGTTTCAAATTTACTAAATTAGTAATATCCATCAATAA
AGCCCAAAATTATGCAGGCACAGGTAATGAAAACGAAGTGTAATGTCTTTTACGGAATAATTAAA
AATAGAACTCCCCGAGTAGTGATACCAATTTCAAAAATAAACTATAGACAGATCCCAGGCATATT
TTCTAAATATAGTTCGAGAGGATTTGCTATAGGTGTAACCTCGGATATCTCGCCTGTGTTACTGG
GAAAGGCGACGGATTTCTCTCTATTTCTTTCTTTTGGAAATACTGAGACCGTATTTTCATTGCGG
CTGCGGTCGACTTTTTCGAATTTGCCGCGGCTTCCAATAATGACTTTTTAGAGGGTTCATTACCC
TGGGACGGTTTAGTTCTTTGTAACAGGAGGGCCGCGCCCCAATTT
Found at i:48439 original size:24 final size:24
Alignment explanation
Indices: 48407--48466 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
48397 TTCCTTTTTT
* *
48407 TGTCTGACAGTCCCCCTGGGGCCC
1 TGTCAGACAGTCCCCCAGGGGCCC
* *
48431 TGTCGGACAGTCCCCCAGGGGCCT
1 TGTCAGACAGTCCCCCAGGGGCCC
48455 TGTCAGACAGTC
1 TGTCAGACAGTC
48467 GCGGGCCCCA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.13, C:0.37, G:0.30, T:0.20
Consensus pattern (24 bp):
TGTCAGACAGTCCCCCAGGGGCCC
Left flanking sequence: Indices 47907 -- 48406
GTTTTATGGCTTCTGTTGCGCGGCTTGTATTTTTATTCTGCAATTCGAACCAATCCCAATTGACT
TTAAAGGGCCCTTTATGCTTTATTATAGTACAAACCCCTTTTTCATTTCATTTTACCCAATGCAG
GTTCAACTGGAGACGCTGGCGGAGGCCTTTCCGTCACTGCAGATTCCGTATCAGTATAATAGTAG
GACTCTGTTCGAATAAACGGATACATATGAATCCGTGCGTGAGCGGTGACCGCCGCATCAATTTG
AACTGTAACGTTTAAAACAACTTTTTTCTTTATAAGACTCCCCTCTACCACAGCTGCATGTCTCA
GGACATCCGGAGACTGATCGCCCATCACCTGCATTTCATCAAGATAGGTTATTAAAAAACGTTCC
ATATCCAATTTGTGGAAACTCAAAATGCGGTAACACTAATCTTTCCGATTTTTCCTAAAACCCTG
TCAGTTTTTTTCTTTTTTTGAAAGCATCGATTTTTTTCCTTTTTT
Right flanking sequence: Indices 48467 -- 48966
GCGGGCCCCACCCTTCAAACTCCACCACACTATACAATTTATCTAAGATGTACAATTATATGTAT
TATACCCGAAATCATCAACAACCAAAAAATACAATGTCTTTTTTTTGTAATGAATCATCGTAGAT
AATTTATTACTTTTGGGGAAATAGCTTAGTGGTTTATAGCGCTGGTCTGTCAAGCCAGAAGTCGC
GGGTTCAAATCCCGTTTTTCCCGGTGAAACTTTAATTCAATTATAAAACCCAGTTCATCAAGATA
TATATATTTTTTTCCGAAAAAAGCAGCTTAGATAAGCTTTTTTTTAAGCTTCGGCATACTGGCGG
AGCTCTTACACCCCGCATCCTCCGCGCATATGCCGAAGCCAAGGTAATCAAAAATATTTTTTTTT
TTGGAGGTATGGCTGAGTGGTTGAAAGCATTGGTTTGCTAAATCAGTGCGACAAGAAACTGTGCA
ATGTAATGTGGTTCAATTCCACAGGACGTAACCCCCGTCCTACCC
Found at i:70131 original size:27 final size:27
Alignment explanation
Indices: 70101--70156 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
70091 ATAAACACTC
*
70101 ATGCAAAAAAAGCACGGTATTACTAAT
1 ATGCAAAAAAAACACGGTATTACTAAT
* *
70128 ATGCAAAAAAAACACTGTATTACTTAT
1 ATGCAAAAAAAACACGGTATTACTAAT
70155 AT
1 AT
70157 TCAATCAACT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.48, C:0.14, G:0.11, T:0.27
Consensus pattern (27 bp):
ATGCAAAAAAAACACGGTATTACTAAT
Left flanking sequence: Indices 69601 -- 70100
AAAATAAATCATGTCATATATTTTAGGAACTAATTTAAATTCCAATAAACAAGTAAAAATTGCCT
TAACTCGAATCTTTGGAATTGGCCCTAAAAAGGCAATTCAAGTTTGTGATCAATTAGGCCTCAGC
GATACCATTAAGGTTAATAAGTTAACTAAGTATCAATTTGACCAAATTCTAAAAATAATAAGTCA
AAATTATTTAGTTGATTCAGAATTGAAGAGAGTCATTCAGAGAGACATCAAACGATTAATTAGTA
TTGGTTGTTATCGTGGGTTTCGCCATAATGCAGGATTGCCCTTACGCGGCCAACGAACTCATACT
AATGCTAAGACTTGTCGCAAATTAAGATACGTTTCGATTAGAAGTTGATAAAAAATTTATATATT
TTTTTTCAGTTTGTACAAAATATCTTTGTAATTAGTAAACGGATTAGATGGATCATAAAAAAACA
AAATCGATGATATCAAACAACACCAAAAACATTCAATAAACACTC
Right flanking sequence: Indices 70157 -- 70656
TCAATCAACTTTTGGTAATACAATTATTACTTTAACAGATTATAACGGAAATACAAAAACTTGGT
CCTCCTCAGGTTCAGTGGGGTTTAAGGGATCTCGTCGCTCAACCAATTATGCTGCTCAAGCAACT
GCAGAAAATGCCGCGCGAGTTGCCATTCAACTTGGATTTAAGTTTGTTGAAGTGAGAATAAAAGG
ATTAGGTTATGGAAAGGAATCTTCACTACGTGGTTTAAAACTAGGAGGTCTTATTATTACCAAAA
TTCGCGATGTAACCCCAACGCCACATAATGGATGCCGACCCCCTAAAAAACGTCGTGTTTAAATA
TCATCATAAAGTCCTATGTCATCATAAAATGGTAAATTGAGGTTCAAGAGTAAACAAAATTTTTC
TAGGGTCCGAAGGAGACTTCTTTGGCTTTACAGGGCTTAACCCTTCTTTCGTAAAGGCAAAGAAG
GAAATCTACAAGCCATGTCTGGCCTTCGGCCTTCGGACCCACAAA
Found at i:73770 original size:52 final size:52
Alignment explanation
Indices: 73692--73797 Score: 212
Period size: 52 Copynumber: 2.0 Consensus size: 52
73682 GGAATTCCTC
73692 TGGTGCTTGAAGAGTACCTCCGGGCATTTGCTCTGCAAGAGCAAATAGCTGT
1 TGGTGCTTGAAGAGTACCTCCGGGCATTTGCTCTGCAAGAGCAAATAGCTGT
73744 TGGTGCTTGAAGAGTACCTCCGGGCATTTGCTCTGCAAGAGCAAATAGCTGT
1 TGGTGCTTGAAGAGTACCTCCGGGCATTTGCTCTGCAAGAGCAAATAGCTGT
73796 TG
1 TG
73798 AGCTAGCGCC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 54 1.00
ACGTcount: A:0.23, C:0.21, G:0.29, T:0.27
Consensus pattern (52 bp):
TGGTGCTTGAAGAGTACCTCCGGGCATTTGCTCTGCAAGAGCAAATAGCTGT
Left flanking sequence: Indices 73192 -- 73691
AGTTGGAGGGATGCTTGTTGGAGAGCTCTAATTTTAGCGTACCTGACTTCCATTTACTTCTTTCC
TATTCTTGGTTCTTTTCCCCGAGTGTTAAAAGATCAAGTGGATTTTGGGTATATTCCTACTGTGT
GTATTTTGCTATACGTAATTTTTCTCTTTTTTTTTGACAGTTACAGGAAAAGTCTTTTTACTACG
GCTCTCACACATTCTTTTTGGCTCTAATATTTTCCAATACCTGTTATTTCAATGTATTTCCATGG
ATCAATTATTCAAGGAGTCCGTTTTGATGTCCTTAATTATAGGATTTAACTTAGGACAGCTGTTT
GGTTTAGTTTTTTTTTTAAACCATGGATTTCTTCGTGATGTTCTATTCCGGGGCTTGTTTGCGTT
CGTCATAGTATATTTTAAGTTAAGGCGCATACTCAACGGACCGGCACAAGGTTCAAATTTATTGA
CCGATGCCCTGGAGGGCGAAGGGCTTCCACCGGAGGGAATTCCTC
Right flanking sequence: Indices 73798 -- 74297
AGCTAGCGCCAATACCTAACCATTATCCCAGGAAATCAGATGTGCTGTTTGGTAACTTTTATAAG
ACCAGCTGCCACTTCCATACTACTCCCCACGGAAATAAACCTTCTAAGGTTATATACCCACCGGG
CACTACATTTGGTAGTAGCATAAAAGGGTGCCCCGAACGGCTCGGGTATCGGTGGCTGACTACAT
TAAGTCTCAACCTATAGAACATAAAGACCGTGGTGGGGGCGACAGCCGCGGCCGTGGGGAGCGCG
GGCTACCGCAAAGTCGAGTTAGATAAAGCGAAGGCTGCTAACGAGGCAGCTCATACCCGCTAATG
GCTTGAAGTGGCAGAAGCTTAAAATAAGCATTTGGAGCCAACAACGCGATTATCTTAATAATAAT
GGAACACGCGCGGAACAGGAACTAAAGGATGCTATACCGCACGATGAGTAACTTGCGCGTAACAG
GGGGTTTGGCTCTACAGTAAAATACGGGGCCAACAAATGGGAATC
Found at i:94513 original size:16 final size:16
Alignment explanation
Indices: 94492--94525 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
94482 CTTTAGTCGC
94492 GCGCTCCAACCGTAAA
1 GCGCTCCAACCGTAAA
*
94508 GCGCTCCAATCGTAAA
1 GCGCTCCAACCGTAAA
94524 GC
1 GC
94526 CCAAGGAGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.29, C:0.35, G:0.21, T:0.15
Consensus pattern (16 bp):
GCGCTCCAACCGTAAA
Left flanking sequence: Indices 93992 -- 94491
AGACCGGGTACAATCTTGGATCTCATTATCAAGCAGATGGAGCGCGATAGCTTTTTCGATAAATC
AGCGGTCCGAGCTGCCGCTTACTCCGCGATGCTTGGGGGGTTTGTAACGCGATGATCGCAGCTAT
TTTAGAATCAAAACAAAAAGGGATAGGGATCAAAAAATGAATGACTTCAAGTCTTTGCCTGACTT
CCATAATAGGCTTTAAAAGGCTAAAGAAGTGGCAGAGTGTCTCACATTCCGGACTTGAGGAAGGC
TGCCAAGGCCCTGCTTCTACGAATAGTACCTTCAGTCTTACGAATTTTCTCTTATAGCCGAAGCC
ACCATTCGGCTGAGGGAGATGGTGCGCAGCACTTGACCAGAGGAAGAGCGCTTGTAGAAAGAAGG
GTCGAGTTTCCGAAGGACCGAGAGGTCGGAAATGGCTTTACGATTTCCGCACACGAAGACACTTC
TAAAAATGGCTGAGAAAAGAAGGCACCTAGTGTTTCTTTAGTCGC
Right flanking sequence: Indices 94526 -- 95025
CCAAGGAGTGCGGCCATTTATCTCTTGAATATTTTAAGACTTTTGTCTTACCCCTGGTGAGTTTA
TTACGTAATTTTATGGATAATACAAGATGACCAATCTTTCGGTTATGCCATTACTACGTAATTTA
TTTTGGTCACAATAAAAAAAAAGCCAACAAATATGAGAATTTATCTAATTGGTCTTGTCGCTAAG
ATACTTGGAATTATAATACCCCTGTTACTGGGTGTCGCGTTCTTAGTACTAGCAGAACGAAAAGT
CATGGCGTCTATGCAAAGAAGAAAAGGACCGAACGTAGTCGGCATTTTAGGATTGTTACAACCTT
TAGCAGATGGTTTGAAGCTCATGATAAAAGAGCCCATTTTGCCTAGTAGCGCGAATATTTTTATT
TTTCTAATGGCACCCGTTCTGACGTTTACACTGGCTTTGTGCGCTTGGGCTGTGATCCCTTTCGA
TTATGGCATGGTTTTTTCAGATTTAAATATTGGGGTTTTGTATCT
Found at i:98692 original size:15 final size:15
Alignment explanation
Indices: 98672--98703 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
98662 ACTTGTTTCT
*
98672 ATGATAGCATATGCC
1 ATGATAGCATACGCC
98687 ATGATAGCATACGCC
1 ATGATAGCATACGCC
98702 AT
1 AT
98704 TACGTCTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (15 bp):
ATGATAGCATACGCC
Left flanking sequence: Indices 98172 -- 98671
CCTGAAGGCCTGCCGGCCTTGGGCTTTCGGCGGAGGGCTTTGGCCTTCGGCTTCGGCCTTGGGCA
GCAGGCCTGCTGCTTGTGGGTCTAGCCGGCCTAAGGCATATAGCCAGCGGAAGGCTGTCCTTGAA
TGACTGGGTTTTTACAAGCCCTCCAGCATTTGAAGCACGGGAGCTCGCCGGAAGTTTCTATTTTC
ATTTGAAACAAAAGCCAAAAAGAGTAGTTTATTATATGAATTTGTACTTTTTCATCTGGTTACCC
ATTTTGTTTTGGTTCTATTGCCTAAGCTAATCTACTGGCCCCCATAACACCCCTATTTTAAAGCC
CGTGGGTCGTCACGGCAAGCATAGTTTTCTATTTAATAGATCACTGGGTAAACACGGATTCCGCT
TTTTTGTCCTTTTGCAAAACTAGATTCTTTCAGTACTATTTGTATTATTCCCTCTCCGGCTGGAG
GAATGGTTACGGGATAACTATTACGGGAGATTTATACTTGTTTCT
Right flanking sequence: Indices 98704 -- 99203
TACGTCTTTATTTGTTGAATCCGGGGGACAAAAGGAAGTTATTCATATATATAGCATCAGTTTAC
TATATAAGACTCAGATATAAAATTCTAAATGATAATCCACTCAAATTTTATAGAGCTTATAAGGA
TTCTTGGGGCGCAGGCGGTTTGAATAATGCCAACCGCACCCTTGAAAATCCTTTGGATTTAAGTG
GCAACCGGATACCCAAACGTAACATGAGGAGCTGTAGGATAGCAAACGCAGCGCCTAACCCTGCC
CCGGAAACATTGTCAGCCACCGCTACGGGTACGGGCAGACTAGCCCCGCAGTTGTGGCTGGAGGG
GCGGTCAACATTGTAACCACTAAGATGATCGCGAACTCAAACGAAGAAATCCAAAAGTAAAAAAT
GGCGCTGAAGGAATATCAACAAAATTTGGCCAATATGGCGTGGCATTAGAGCTTAAAATGAAACC
GTCTAAGCACACGGAGACAAGTTAGCACAATTTACTTGAGGACGC
Found at i:100508 original size:10 final size:10
Alignment explanation
Indices: 100493--100518 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
100483 AGAGATATAG
100493 ATATATCTAT
1 ATATATCTAT
100503 ATATATCTAT
1 ATATATCTAT
100513 ATATAT
1 ATATAT
100519 AGAATTTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (10 bp):
ATATATCTAT
Left flanking sequence: Indices 99993 -- 100492
AGCATTGCTAAATGACTAAATTTCGTTAATATGACTAAATTCCGAGGATTTGTAGATAAATATAG
ATAATTAATACTCTGGAATCCTCATCGCTAATGACACCTTCGCGAAATGACGCATATTTAGCTAA
TATGACTAAACTTGTTGAGGATCTGTAGTATAATATAATACCCTTTAATATGGAATTAAAGGGTC
GGGAAGGGAATATATAATAGAATTATATATGGAATATGGAATAATTCTATAGAATTAAAAAGGGT
TAATCAATTAAATGAAAATAAATAGAATAAATTAATAAATTCATAAATAAAAGAAATTCAAATAT
ATATATATATATATTTATATATAATAGAAGAAATGCATAAATAAAATAGATTCTATTATTTATAG
AAGAGACTTTTCAATCCATGTTTATTCTTCGCTCATCTTCCAAAAGAAAATGAGCTACTATTTTT
CTTCTTCGAAGAAGAGGATGAGCTGCAATAGATATAGAGATATAG
Right flanking sequence: Indices 100519 -- 101018
AGAATTTATAAGTCAGGGAAGATAGCCTTGACCTCTAACCTTTGAGGATACTGAAGGCCTAGATC
TTCTCCTACTTGGGTTACCATGTTCTTGAGATCTGTTATATAGGCCTCTAGTTTTTTTTCGGGAA
CGTCCAAAGACTTCCATCATGGAAGTGACATAGGAACTCCGGGCGGGGTTCATGGCACTTCTCAT
AGAACCTTAGGGACGCTTCCGCCAGGAGTCCAAACAAATAGGACTGAAGATAGGAAGCATAGACC
GAGGAGAAACGTATTTTCGGTTACGCAGTACGTACGGCCTCTAGGTCCTGTAAGCATCTTGTCCT
TATGCAGTTTGTAAACGGTGTCCGCTATATTCCGAAGATCAAGAATTCTATTTGTTTGTTGGAGG
GCGAAGAACTTGGTTTTGTCGGACACCACAAAACCAAAATACTGTCCGACAAAACAAAAGCCACT
TATGACCTCTACAGCCTTGGCATACCTTTTAGGATAATCTGGCAA
Found at i:127875 original size:21 final size:22
Alignment explanation
Indices: 127843--127885 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
127833 TTAAAGTAAG
127843 AAAAACCACTAC-AAAGAAACA
1 AAAAACCACTACTAAAGAAACA
*
127864 AAAAATCC-CTACTACAGAAACA
1 AAAAA-CCACTACTAAAGAAACA
127886 TATGAGCCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.60, C:0.26, G:0.05, T:0.09
Consensus pattern (22 bp):
AAAAACCACTACTAAAGAAACA
Left flanking sequence: Indices 127343 -- 127842
ATAAAAATCCCTTCAGCTTTCCTTGTCTTAGTAAATGAAAACTCTTCATCTTTGAAAACTCGGGC
AAACCGTCCCAAAGGTGCGTAGCGGAAGTAAAGGAAGGTATACGGGCATAGATTGGAAAAAGATA
TGATAGATACATAAAATATGACATTGTCATCAAATATACAAATAGAACTCGAAGGAATGCCAAAT
ACAGGAAGGGGTAGGCGGGGCAGGCTGGCGCCTACCCCGAAAAAGAGGGCCTGGCTCGGTAAAGT
CCCTAACTACAACTTTCGGGGCGGGCTCCGCCCTATAAGGACTAGGTCTGTATAGGGCGGAGCAG
GTCAGTGCTTAAGTTGCACAAATTGCTAAGACGTCTAAATGCTTTCCTTGATAGCTGGAAGTTCT
TCAAAAGTATGAAATGCCGGAGGGCTTGGGACCATCCATTCAAGTGTCGTTGAATTCTGTTCAAC
AGCCCAAGGACTTGGAGCACACTTGTTTTCACTAGTTAAAGTAAG
Right flanking sequence: Indices 127886 -- 128385
TATGAGCCAAAACTACTAAAGGCATTCCATCCAGCGTAAGCATCTGGATAATCAGGAATGCGACG
TGGCATACCTGCAAGCGGTTTTTTCCTTATTTATCAAATGTTAATGGATTGTGACTAAATATTTT
TCCTTTGTAAACTTCATCTGAAATTAGTCTTTTAGACTTTTCAGTGTGTTTAAATTCCAATGTTG
AATCAGTTCTTTTATTGATATTAAGAACTGGTTTATAAAGATCTAAATAGTACTGTTCTCGAGCT
AAATAATCCTTTTTAGTAATAGTACCTGTTGAACCACATAACTCAATAATAACTAAACTAAAATT
GTCATGACCATATTTCCAAATAGAATTCTAAATATATTTGTTATCAGATAATTTAGAAGGGTGAT
AGTATTCAGCAAGTCTATCGCTTTATTTATAACCACTACCTACATATTGTTTACTATTAACTAAA
TTATGCCAAAGATAGATTCCAGTTTTCGTTAGATAATCAGAAACG
Found at i:129650 original size:13 final size:13
Alignment explanation
Indices: 129632--129664 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
129622 GTATCTGCCC
129632 TTTTTTTGTCAGT
1 TTTTTTTGTCAGT
129645 TTTTTTTGTCAGT
1 TTTTTTTGTCAGT
129658 TTTTTTT
1 TTTTTTT
129665 CCCTTTTTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.06, C:0.06, G:0.12, T:0.76
Consensus pattern (13 bp):
TTTTTTTGTCAGT
Left flanking sequence: Indices 129132 -- 129631
ATAAAGCAAAAACGGCTCCCATAGAAAGAACATAATGGAAATGTGCAACCACATAATAAGTCAAC
TTTCCCTAGATATTTTCATATCTACTTGGACTATATCATCACTCCGTCGATCCTACTATTGACCA
ACAGATGTGTTTGGCCTATAGTCTCTGAGAATCCTACTCCCCATAAAGCGCAAAGGCCGTAGGGC
CCGAAGGTTCCGAAGGAGGCTTTTTTGGCTTGTAAGGGCCCTTCGGGCCTCTCCCGTTGGTCTCG
GGGAAAGCCCGGAAATCGTAAATTTCCGGAACGTCCGCCCTTTTCTGACAGTGCCCCGACCTGTC
GGACAGTCGCACGCCCTCCGGCCCTTTTTTTTGAGTTTGGTTTCCGGCGGATTGTCCATTTCAGT
AGATTTTAGATCTACGTCATACTTAGGATTATTACTGAAGCCCAAGGAAGGCCGTAGGCCGCAGC
TGAAGCCCGGAAAACGTAAAGCCAGAAACTTCACCGTATCTGCCC
Right flanking sequence: Indices 129665 -- 130164
CCCTTTTTTGTCTGACAGTACCTCGCCCTACGCGCGAAACGTTACGGCCTCCGGCCCGTAAATCG
TCAAGCCGTTTCCGCCCGTAGGTACAAAGAGCCGAAGACCAGAAATGGCTTGACGATTTACGCGC
ACGATATTTAGTCAGCGCTACGCGCGTAGCGCATAAACTTAACAGTTTATGGCCCCGCAGGTATA
CCCCCCGATAGGTTATAGGCCCGGAGGTCCATAGGCCCGGGGGGCATAAAGGGTTTTACTATTTA
CGGGTTTACGTTTTCTGGGCGCCTTCGGCGCCGGAGCGCAAAAAATATATTTTTTTTGCTTGCTT
CTTCTCTCGACCTTTTTTCGCTTGCGAATGAAGTGAAAGGCCTCTAGTACTCAAGTCTTTAGGAA
TTTCCCGCATACAGCCAAATTTAGCCATGACACTTTTGCACAGGCTAAAGCCCCTTTTTGTTTTT
ATAAAAAGCTGATATGAATTTATGAAATTGTAACAACTTCTCTCC
Found at i:132468 original size:11 final size:11
Alignment explanation
Indices: 132450--132491 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
132440 GTAATTGCCC
132450 TTTTTTTTCTG
1 TTTTTTTTCTG
*
132461 TGTTTTTTT-TT
1 T-TTTTTTTCTG
*
132472 TTTTTTTTCAG
1 TTTTTTTTCTG
132483 TTTTTTTTC
1 TTTTTTTTC
132492 CCTTTTTTGT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
10 7 0.27
11 12 0.46
12 7 0.27
ACGTcount: A:0.02, C:0.07, G:0.07, T:0.83
Consensus pattern (11 bp):
TTTTTTTTCTG
Left flanking sequence: Indices 131950 -- 132449
TACTTCACAGCTTATATATCCAGCCTTTTCAATGGAAAAACCTCCATCCCAGCTAACCCATTTTG
AAATTGATCCTCATCATTCCTTGTTTCAATAGGAAATGCGCTGCGTGTAGTCTCTGAGGATCCTT
CACCTGTTTGTAAAGTCAAAATATTTGTTTCATTCATTTACATTTTTTTTTTTGAAGTTTCCTGC
TGATTGTGCATTGCCTATAGAACTGAAGATCTAATTCAGATCTATATATAAGCTTTTCACAGGTT
CGGGCGTAAAAAAAGAGATTTTTTCGCGCACTTATGAACCGAGTACTTAATGGCATTTAGCCTTT
CCAGCAAATAGCGGCATTATTCAATTTGGGATTGCTCTCAAATGCGGCCATCCTGTGGTTATTTT
TTGACCGAAGAACCAAAAAAGATGCTGGTATAAAATGGGATCCCCGCCACCAGCAGGATCAAAAA
AGGTTGTATTAAAGTTTCTATCAGTTAATAACATGGTAATTGCCC
Right flanking sequence: Indices 132492 -- 132991
CCTTTTTTGTCTGACAGTCCTGGGGCCTTGTCGGACAGTATTTTGGTTTTATGGTGTCCGACAAG
ACAAAGCCCGGGGCTCTGTCTGACAAAAAAAGTGCTTACACCGGAAACTAATATTTTTTTTCATG
CCCGGCGTGGTTTTGGACTATATCTTCATCTCTTTCTATTCATACCTGCTTTGATGCGCACAATT
TAAGCAAACTCCGCATTGGTCAGATGTGGTTTGTGTAAGATCATGTCATAGATGCATCGCCAGTC
ACGCCAATCCGCGGCTTTTGCCCGAGGAAAGGCATCAAAGTAAGCAACCACATGGCATGCCTGCC
TGCCATGCTGCATGTGCGACTACGCCAATTTACTCTAGAAGCACTAACCTTGTAAAGTATAACTT
GTGCCCCAATTTGCTCAAGCGTCGGTCTAGTATCTATTTTCGTTTGTTTCTGCAGCTTACTCTAT
TCTAGCTCAAACGAAATGGAAACGCGCCAATATCTACTGGATATG
Found at i:132478 original size:22 final size:21
Alignment explanation
Indices: 132450--132490 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
132440 GTAATTGCCC
*
132450 TTTTTTTTCTGTGTTTTTTTTT
1 TTTTTTTTCAGT-TTTTTTTTT
132472 TTTTTTTTCAGTTTTTTTT
1 TTTTTTTTCAGTTTTTTTT
132491 CCCTTTTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.02, C:0.05, G:0.07, T:0.85
Consensus pattern (21 bp):
TTTTTTTTCAGTTTTTTTTTT
Left flanking sequence: Indices 131950 -- 132449
TACTTCACAGCTTATATATCCAGCCTTTTCAATGGAAAAACCTCCATCCCAGCTAACCCATTTTG
AAATTGATCCTCATCATTCCTTGTTTCAATAGGAAATGCGCTGCGTGTAGTCTCTGAGGATCCTT
CACCTGTTTGTAAAGTCAAAATATTTGTTTCATTCATTTACATTTTTTTTTTTGAAGTTTCCTGC
TGATTGTGCATTGCCTATAGAACTGAAGATCTAATTCAGATCTATATATAAGCTTTTCACAGGTT
CGGGCGTAAAAAAAGAGATTTTTTCGCGCACTTATGAACCGAGTACTTAATGGCATTTAGCCTTT
CCAGCAAATAGCGGCATTATTCAATTTGGGATTGCTCTCAAATGCGGCCATCCTGTGGTTATTTT
TTGACCGAAGAACCAAAAAAGATGCTGGTATAAAATGGGATCCCCGCCACCAGCAGGATCAAAAA
AGGTTGTATTAAAGTTTCTATCAGTTAATAACATGGTAATTGCCC
Right flanking sequence: Indices 132491 -- 132990
CCCTTTTTTGTCTGACAGTCCTGGGGCCTTGTCGGACAGTATTTTGGTTTTATGGTGTCCGACAA
GACAAAGCCCGGGGCTCTGTCTGACAAAAAAAGTGCTTACACCGGAAACTAATATTTTTTTTCAT
GCCCGGCGTGGTTTTGGACTATATCTTCATCTCTTTCTATTCATACCTGCTTTGATGCGCACAAT
TTAAGCAAACTCCGCATTGGTCAGATGTGGTTTGTGTAAGATCATGTCATAGATGCATCGCCAGT
CACGCCAATCCGCGGCTTTTGCCCGAGGAAAGGCATCAAAGTAAGCAACCACATGGCATGCCTGC
CTGCCATGCTGCATGTGCGACTACGCCAATTTACTCTAGAAGCACTAACCTTGTAAAGTATAACT
TGTGCCCCAATTTGCTCAAGCGTCGGTCTAGTATCTATTTTCGTTTGTTTCTGCAGCTTACTCTA
TTCTAGCTCAAACGAAATGGAAACGCGCCAATATCTACTGGATAT
Found at i:165273 original size:25 final size:25
Alignment explanation
Indices: 165238--165285 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
165228 AGGCCCCGCG
* * *
165238 ACTGTCTGACAGGGCTCCTGGGGAA
1 ACTGTCAGACAGGCCCCCTGGGGAA
165263 ACTGTCAGACAGGCCCCCTGGGG
1 ACTGTCAGACAGGCCCCCTGGGG
165286 GCCCTGTCAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.19, C:0.29, G:0.35, T:0.17
Consensus pattern (25 bp):
ACTGTCAGACAGGCCCCCTGGGGAA
Left flanking sequence: Indices 164738 -- 165237
GTTTATTCTCTGAACTTTCATTTCCATAATCATTGAATATTAGGTTTATTATTGTTTGCTTCAAG
CTTAAGAGCTGATTACAAAAAGGATGGATGTCTGAGCGGTTGAAAGAGTCGGTCTTGAAAACCGA
AGTATTGAGAATACCGGGGGTTCGAATCCCTCTCCATCCGTGAGTATGTTAATGAGTTAACTGCA
TTCTCTTCAATGCGTTTTCCCGAACCCTAGGGCTCTTTGGGCACTCGACCTATAAGGAGAGGGTC
GAGCCGCCTCTGGTGTTCGTGCACGGAAATCGTCAAGCCATTTCTCGTTCGGCCTTCGGACGGCC
CGAAGGATACTGCTTTGGCTTTCCGAAAAAAGGGCGCAGAAACTTTCCAGTATCTGCCCGCAGGC
ACGTAATGCGAAGACAAAAGGCCCCCGGACTTTTTTGTCTAACTGACAAAGCCCCGGACTTTGTT
GTGTCGGACACCACAAAACAAAATACTGTCCGACAAGGCCCCGCG
Right flanking sequence: Indices 165286 -- 165785
GCCCTGTCAGACAAAAAAAGGCCAAAAACCGATGCTTTCAAAAAAAACTGATTTACCTAAAATAG
TTTTTTTTCCTGCGATACAAAAACTAATTGAACCAATTCCAACTTGTACGGATAGAGGGACTCGA
ACCCCCACGAACATTATGGTCACCAGAACCTAAACCTGGCATGTCTACCAATTCCATCATATCCG
CCAACCCTTGAAGTTATACAATCACTAGGCCTTGGATAAAGAAAAAATATAGAAAAAAGCGAAGT
GAAAAAAACTATTTTAGGCACGTAGTACTCGACCCGATAAGGGAGAGGGGTAGAAAAATCTATAT
TTTTTGCCGCTACGCGCCTTCTTTCTCAGCCATTTCTAGAAGCGTCGGACCTACGGGCAGAAAGG
GTTTAGCTGCGCCCTAACGTTCAGCTAATGCAAGTTGAGTCACGAAGTGACAATCGTAGAAAAAT
CTTTATAATGTCATTACAAAGTAATTGCATGCTTTGCTCAAGCCA
Found at i:168026 original size:18 final size:18
Alignment explanation
Indices: 168003--168046 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
167993 GAGGCGCGAA
168003 GACCAAAGAGAGACACTC
1 GACCAAAGAGAGACACTC
*
168021 GACCAAAGCGAGACACTC
1 GACCAAAGAGAGACACTC
168039 GACCAAAG
1 GACCAAAG
168047 GAAGAGAGCC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.43, C:0.30, G:0.23, T:0.05
Consensus pattern (18 bp):
GACCAAAGAGAGACACTC
Left flanking sequence: Indices 167503 -- 168002
TAAGGCAAACAAAGCAATAGCTTCAGTTAAAGCAAAACCTAAAATGGCATAACCAAATAATTGCT
TAGCCAATGATGGATTTCGCGCAACAGAATTAATCAAAGAATACCGATAGGGTTATTCCCCCCGG
TCAGAACCACACGTGCAAGTTTCCCTGCATGTGGCTCGTCCATGGCAATTTCTTCAGCTTTTGTG
GCTTGGCCGTATAAGCGCTACTAGCCCTCCTTACACCGGGACGCGCGACTACTGTGCAATTCCCC
CTCCCTGCACCTTGTAACTAAGTCATTGTAGGCATAGCGTGATCCGCTTTCTTGATTTGGCTATG
GTTGCCCTAGCAAGAGCGCCGAGACCGGGATATAAGGTCTCAAGTGATACAGTTAAAGCTGCAAA
AAAAATTTTGAACTAGTCTAAATGGCTGATAAAGAAGGGTCCGCAGGTTGGAAATGGCTTTACGA
TTTCCACGCGCGAGTGCTAAAGGGAGAAGAGGGGAGAGGCGCGAA
Right flanking sequence: Indices 168047 -- 168546
GAAGAGAGCCTAAACATATTTTTTTTGTCGGAGGCGCGGGATAGAGCCTTTTGTTGTGAGTAGTC
TGTCCGCTCTATCCACGCCACTCCATCACAGGGTTCCTCGAATATAGTCACCTGACTCCATAATA
TGGTTCCTCGAGTATAGTAACCTGACTGAACCTAGTAGCGTGGAACTTTCCTGTAGTTTTTAGAG
AGGTGGGGTAGTATAGTGACGCTACCTCCTTGCCTTTTTCTGTGATTCGCAGGTTTGGACCAAAC
TTGAGTAAAGCAGCTTTGGCTGACCGTAGGCCGTGTTTTCTGGCCAAGGTTAGCGCGCAGGACTT
TTTATAGATGGACACAACTTTCCACAGGGAAGAGCGCTTGTTCACAAATGAATAGTAGTTAACAA
TGCCGCGTATCACCGATGAGAAGTGGATAACAATGTGTTTGTCCCCTGAGGAAACCAATCGTGGA
TTGGAGGTTGCTCGAGCTAAGCCCTTGGCGTTTTTTTTTCGCGTA
Found at i:171658 original size:21 final size:17
Alignment explanation
Indices: 171615--171651 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
171605 ATATTCAAAC
171615 ATTTTGATTGAACATAT
1 ATTTTGATTGAACATAT
171632 ATTTTGATTGAACATAT
1 ATTTTGATTGAACATAT
171649 ATT
1 ATT
171652 GCATTTGGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.35, C:0.05, G:0.11, T:0.49
Consensus pattern (17 bp):
ATTTTGATTGAACATAT
Left flanking sequence: Indices 171115 -- 171614
TACAACCTCGCCGTCGGTCAACTCTTTGGCTTTTTATTCCAAATCACAATAATAAATGACGTGAC
CGAAAGGATAACCAAGTAAGCCCGAGAAAACCCTCGGTCTTGCTATACTTATATGGAACCATCGA
AGAAGTTATACATACCATGAGTTGGGCTATTTGACTGGCTATATCTTGGAAATCCTTAGTATTCG
CAAGAGAAACCCAAAGGTATCGCCTACTTGTTCCGTGATGTTGTGAAAATCGATGTTTCCGCGTA
GAATAAGCGGTGGTGGGGCGAAGACTACGGCCCTAAAGGGTTCGGGTCGAGCACTACGTGCCTTC
AATCTACAAGCCCTCTCCCGTTGGTCTTCGTCCCCCTCGGGGCCTTCTCCCGCTCCCCGCGCACT
CCGTGCCTATGGGTCCGAAGGAAACTTTCTTTGGCTTTACGAAAGAAGGACCTGAAGGGCGCGAG
ACTATAGGGAGAGGTTTCTTTTTCTTTTTTACGTAATATTCAAAC
Right flanking sequence: Indices 171652 -- 172151
GCATTTGGTAATGTTCGATATAATAAAAACTATGGAATCCCCGGGATTCCGAATCGACAACAGCT
TCAATAAAACGAAGTAGGTAGCAATGACCATCATATATGAAAAAATGGAGCTCCTTCCACAAGGT
TAAACTAAGTAAAAGGGGATAAATGGCTATCAAATACCAATCGGTAGTTGAATATGTTGCTGTAT
TCTACACATTTTCGAGGTGATATTAAAAAATGATGTCATAAAAACAGTCTGTTGGTAAAATTGAG
TCATATTAATGGTTGTGACAAAGTGTTTTTGGCTTACGCCAATCTTGTTGTTTTTCATATTTTTT
TTATTTTGGTTCAAAAAGTATAAGAAATGGCTAAGTAACATAAGGGTAATGTATTGGATTGCAAA
TCCTATAAAGATGGTTCGAATCCGTCCTTAGCCTACTTTACGATTCTATTGTTCCTGGAAATAAC
CTATTATCTAATAAGTACAAAGATCTTAACCACCCTTTAGACTTA
Found at i:186310 original size:22 final size:21
Alignment explanation
Indices: 186283--186324 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
186273 GTATAGTCTA
186283 CGAAAAAATATATATTTTTTTG
1 CGAAAAAATATAT-TTTTTTTG
* *
186305 CGAAAATATATCTTTTTTTT
1 CGAAAAAATATATTTTTTTT
186325 ACATAAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.36, C:0.07, G:0.07, T:0.50
Consensus pattern (21 bp):
CGAAAAAATATATTTTTTTTG
Left flanking sequence: Indices 185783 -- 186282
CCTCCTGCATAGGTAGCGTTTAGTTAGGCAGGGCTCAAGTACTAGCCTAGGATAGCAAGGGTCAA
AAAATTTTTTGGTGGCTGAGACCATACATAGTTGTACAAGGTACTATCCGCGTCTTACCATGAAC
TGCTCCGGGCGGTTAAATTGATAAATTTTATATAAGTGGATTGATTCACTACAGCAGAATTGGGG
GGCTGGCCACCACTGGGTTTCTCAGCGCCTTGTATCATTAATCTAGTCCCTAGGGGAGCCCGGCG
CTACGCGAACAAAAAAAAATATTTTTTTTGTTTTGCATGTTTTTAGCACTCCCTCGGCAGGGTCC
AAGGGGACTTTGTTTTGTCAGACACCACAATAGTAAAATACTGTCCGACAAAACAAAGGGCTAAA
GCCTTTCGGCCCGAAAGTCGACCCGATCGCAGCCTCTAAGCTCTTTGCCTTTTTTTTACAAGAAA
GTGCAATCCTCCGCAATTTCACAAAAAACTTTAGAGTATAGTCTA
Right flanking sequence: Indices 186325 -- 186609
ACATAAATATTCAAGCTAACGGAGGAGGGCCGCAGGCAAAATAAAATATATATTTTATGACAAAA
TAAAAATATTTTAGTTTTTCGGCGAATAACGGGATTCGAACCCGTGTTTTCAGAGCCACAATCTG
CAACTTTAACCCCTAAGTTATATCCGCCCTTATTTATAAATAAGATACTCGCTATCGGATTCGAA
CCGATATTCCATTAGAAACAGATTTTGAGTCTGCCGTGTTTGCCGTTCCACCAAGCGAGTCTTGG
CTTTTATTAGGAATAGATTGAAAAT
Done.