Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_069588
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: 519026
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Found at i:24045 original size:30 final size:30
Alignment explanation
Indices: 24009--24110 Score: 123
Period size: 30 Copynumber: 3.4 Consensus size: 30
23999 TCATAGGTCT
24009 AGGGTACGGTACCGCGATAAAAGGGTGTCG
1 AGGGTACGGTACCGCGATAAAAGGGTGTCG
** * *
24039 AGGGTACGGTAGGGCGATACAAGGTGGGTCG
1 AGGGTACGGTACCGCGATAAAAGG-GTGTCG
* *
24070 AGCGTACGGCACCGCGATAAAAGGGTGTCG
1 AGGGTACGGTACCGCGATAAAAGGGTGTCG
* *
24100 ATGGTAGGGTA
1 AGGGTACGGTA
24111 GGGTAGTGTT
Statistics
Matches: 57, Mismatches: 14, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
30 33 0.58
31 24 0.42
ACGTcount: A:0.25, C:0.16, G:0.42, T:0.17
Consensus pattern (30 bp):
AGGGTACGGTACCGCGATAAAAGGGTGTCG
Left flanking sequence: Indices 23509 -- 24008
GTTAAGGCAATTCGGACTTGTTCATCGGGAAGTAATCTAGCTCCTGAGATATATAACATTCTTGA
TCCTTCTCTTTTCCTGGTCTTCTCGGCTGGAATCTACAATGGTTGTCTCCCGAGGTCAGATGAAA
TTGAAAACAATAGATATAACAAGGAAAAGCCGAGCACAAAAGAAGATCTTTTCTCTTCTCTTCTC
ATAGATCAAGAAGGTCGGATAAAGGCGGGCTCCTTCTCTCTCGCCTATACGGAATGTTGGGACAC
TTGAACTTTCTCTTATCCACGGACAAATTCGACGAAAGAGCTCTTTCTATGTTCTAGTACTGGAA
GGAAGCTAGGGTAGAACGTTGTTATCTATGATATTTCTAGTTCAGTTAAATTGCTGGCGAGTGAT
ATAGTCTTGGGTTTGAAAGGGTCAATCATAGTTCGAGGGTACGGTACCGCGATAAAAGAAAGGTG
TATGTGTTTTCTGAACCATGTCAAGCAAGGGAAAATCATAGGTCT
Right flanking sequence: Indices 24111 -- 24610
GGGTAGTGTTGGGTAGGGGTATACAAGGGTGTCTAAGGAGCGTACTGTACTGACTCAAGGTTTAT
CCTCACGATACCTATTTGATACTACTATACGCCGTACATATTGTAATCGGGTTGTTCATGATGAT
GAAATGGTACCTGAGCTTTGTCATGCACTAGATATTTTATATGTCAAATTACGAGAACAAAATCT
TCTTACTGATTTTACACCTGATCAGCTCAATGCACTGAAAGATAATATAATATCTCGTCAATATC
AATTCTCTCCGATCCCAGTACGTATTATACCTTTAGTAGAGGAGGAGGAATATCATAGACTCAAT
CCTCCTCAGTACAATGTTATACAAGCTAGTTGGCATATTCCTAATTATCGATTATTCTTGTTGAT
GAAGTTGGAAGATTGCTTAATATTGCAAGCTTTCGCATTATATATGTTGCATGATAACATACAAT
CGATTTTGGAACGCAAGATTGAGCATGTTATGTCATTTGATAATG
Found at i:34810 original size:34 final size:34
Alignment explanation
Indices: 34772--34849 Score: 84
Period size: 34 Copynumber: 2.3 Consensus size: 34
34762 CCATCTCCCT
* *
34772 TCTATTCGACGAGTATAAGTAGAATCTCTTACCA
1 TCTATTCGACGAGTATAAATAGAATATCTTACCA
* * * * * *
34806 TCTATTCCAAGAGTCTAAATTGATTATCTTCCCA
1 TCTATTCGACGAGTATAAATAGAATATCTTACCA
34840 TCTATTCGAC
1 TCTATTCGAC
34850 ACTTCAAGGA
Statistics
Matches: 34, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.29, C:0.23, G:0.12, T:0.36
Consensus pattern (34 bp):
TCTATTCGACGAGTATAAATAGAATATCTTACCA
Left flanking sequence: Indices 34272 -- 34771
TAAATAAGTAGCTTAATCGATAGGAAAAGCACCTCTTGTCGGCGGGCATAGGACTTGATAGCTTC
ACTAGGCATGAAAGGAAAGTAGTCGTAGTCAGGGTAGGGTCAAGCACGCCAAAGAAGAGCGGATA
ATTAGTCAGTAACAAGTTTGATAAGTTGTTGAATTGCTTATCTAGGAATAAGTAGTAGTAGAAGT
AGATGGGATTGTAGAATCCGTTCCATATCCTGCCTCAGTAGTAGGTGTTGAGAGTGGTTGTTTGT
TGGTCCTTACGAAGAATTTGCATGTTGTAAGGAAAGCTATAATCAAGGACTTTCTCTAAAGTGTT
CTTAATAGGAAACATACACCAGTCCATAAGATAAGAATAGTGAAAGTTTGGTTACCAACTTCTTC
CATACCTTTCGAAGAAGACTTTAGTACATTTTGAGTATCTAAAGCCACTTCTTGAAGAATAGAAT
TAGTAGCATTACCAAGAGTAGAACTAGGCAACCATCCATCTCCCT
Right flanking sequence: Indices 34850 -- 35349
ACTTCAAGGAAGGCATCTACGACTGGCGTCTCATCCTATTTCCAATATTCTATCTACTGATGATG
CATCACTTCATATGTTGAACACGTCTCGTTGCTTCAAAAAGTTCCCACCTTGGTTGGCTTTGTTG
TCAGTGAAAAGGGACGCTTTACGTGAATATTGCTATAGACCAATGTTCCAACTACATCAATAACT
AACGATGAACTGGACATTCTTCCTCTACGAATGAATCAGAGGTGATCTCCATTTGCTTTTTCACC
GGCGGGTTGCTGGAACAGAGATTCCTGCACTATGATAGGATAGGTATGACTGACATCACATCAAA
TTCTGAAAGAACTTCTCCCAAACCACAGAGAAGTCACTCGACCTTCGGATCATCAAGTACCGAAT
AAGTCGACGTCAGGCAGTTGGGTATGTACATTTTCTGAATGGAATTGGAAAGAATGCGCACATTC
CATATGTGACACACGACCCCCATTTTGATGTAATTTGCCTTTTCT
Found at i:78725 original size:42 final size:44
Alignment explanation
Indices: 78640--78741 Score: 145
Period size: 42 Copynumber: 2.4 Consensus size: 44
78630 TGAGTAGGAA
* * *
78640 CATAATCAAGAGGGTCTATAGGTCGGGATAGAGAAAGACCTGCT
1 CATAGTCAAGAGGGTCTATAGCTCGGGAGAGAGAAAGACCTGCT
* *
78684 CATAGTCAAGAGGGTCT-T-GCTCGGGAGATAGAAAGATCTGCT
1 CATAGTCAAGAGGGTCTATAGCTCGGGAGAGAGAAAGACCTGCT
78726 CATAGTCAAGAGGGTC
1 CATAGTCAAGAGGGTC
78742 ACAAAGTCTA
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
42 36 0.68
43 1 0.02
44 16 0.30
ACGTcount: A:0.31, C:0.17, G:0.30, T:0.22
Consensus pattern (44 bp):
CATAGTCAAGAGGGTCTATAGCTCGGGAGAGAGAAAGACCTGCT
Left flanking sequence: Indices 78140 -- 78639
TGCATCCCAATGCAAATCGGCTCCCCGCGAGAAAAGGCCCTTTGCAGGGTAAAAGAAAGGGAGAT
CAACATCAAGGATGAGGGAAGTGCGGTAGGGTCTTCGAACTCAAGGAACTGCAAAAGGGAACCGC
TAATTGCTTGATCTGCGGCTCTTGCCTCTGCATTTGGATTTGTGCGCGGAATAGTCTTCGCAAAG
GACATATCAGAGACAAGTGTTGGATTCCCAAACGCAAAAGAAGTGGAGTCAATAGTTGGATGGGA
ATCTTTGTTGTGGTTGATGAGCGGAAGAATGAACAAGGAAGAAAGAATGTGAAGTGCTGCAGGGG
CTCACCCATATCCCGACATCTTCATCTAGCGAGTACTTCTATTATCAGGCTGAAACCACCGGTGC
TACGAGAAAGAAAGAAAAGACTGCCTTGCCTCTGAAGCTAGTATATTTTCTACCTCCCAATGATG
TTCCCGGGAAGAGAAAACGCAAGCCAAACTCTTTGTGAGTAGGAA
Right flanking sequence: Indices 78742 -- 79241
ACAAAGTCTAAGTACCTGCTGTTATATCTCTTTCTCTCTGTCAGTCTTCTTCTTTTGATCTGGCA
CTTCTAAGCATCCATCTGATTAATAAAGCAAGCACCTCCTATTCTTGATTCCATGTTTTAAGGTC
TGATATCTGAGGTCTCCGGTACTTGATTGAAGTGAAGTGAAGGACTCTCCTCATTGAAAAGTACC
ATTTGATAAAGCACTTGCTGAAGAAGGAATAGGAAAAGTACAAGGAAGTTGAACTCCTCACTCTG
GATGTCTATCTAATTAGTCTGTAGATTCCTCCCTTCCTTGTTCTACTTGTCAACTCAAAAGAAGA
AGAGGCCTCTTCATTGCTAGTCTTTACAGCCCCCTTGGAAAGGCTGTCATCTATCCAAGTCTCAC
TCTCCTTCCCCTGGCCCCATCTCACTGCCGAGCTCTTGATGGAGTTATATTCACTCTGTAGAACT
CTCTTCGACTTACTCTTGAATCGAAAAAGTACCTCCTTATATTTC
Found at i:81121 original size:31 final size:31
Alignment explanation
Indices: 81064--81123 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
81054 TGTATTGAAA
* *
81064 AGCATTGAGAGTAAGTAAGAGGGAGGAAGTC
1 AGCATTGAGAGTAAATAAGAGAGAGGAAGTC
*
81095 AGCATTGATAGTAAATAAGTA-AGAGGAAG
1 AGCATTGAGAGTAAATAAG-AGAGAGGAAG
81124 CATTGGTTGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 24 0.96
32 1 0.04
ACGTcount: A:0.43, C:0.05, G:0.33, T:0.18
Consensus pattern (31 bp):
AGCATTGAGAGTAAATAAGAGAGAGGAAGTC
Left flanking sequence: Indices 80564 -- 81063
TGTTTGGGTGAAGTTAGAAAGGTATGACATTGAGAGTCCAAAAGCGATCTTAGTAGAATGTTTTT
CTCCCCCACTCACTGGATAGGTACCCCCAGTCGTACGAAGGAATAGGAAGAGAAGAATGAAATCA
AAGAAGAAGAAAGAGAAGTGAGAGGGTTAGCAGTTTTGTCCACTCTCTATTTACCAGCTCCCTAA
TAAGCTGTTCATTACTGCTCCAGTGACAAGTCGATTACGAAGATTAGATTAGGCAGATGAATGAT
GGGACCAATATAAGAGATGACTGACTATTGGAGTGATTTCGGTGTTGATATTGGAGAATGTTTGA
CTATGTCTTCCTTATACTTCTTCATTCTACTAGCTCTTAGTATGCCTGTCACTTTCTTAGACTTC
TTAGGGACTCCTTGAAAAGCAAGTATCACCTCTTTCTTATCCTTTATAGGTCTATGTATGTATTC
CACGTCCTGATACTTCTTATTATCCGGATAGGCGGTGTATTGAAA
Right flanking sequence: Indices 81124 -- 81623
CATTGGTTGAATAGTAAGAGGACGCATTGATAGTAAGTAACTGTCGGCCTTGCCTTGATAGCTGT
AAGCATTGATATTTCAATAACTGGGGTGAAATGTAGAAGTTGAACTCCCTTCCACTTAATAAGAT
AAATAGGCACCTGTTGAAAAGGAGCACTTTCCGTCCTCAGTCTTGAACTAGCTAGGAAGCCTCTG
TCCATGTATACCCGATTCGTATTATTTTCGTGGATAGCTAACTAAAGTCAACTCCACTCCTTTGC
CCTTGTTCTGGGCTTTCGACCTCATTAACTCCACTGGCTTCCACTTCTTCTGATCTTTCTACCTC
ACTAAGTCAACTGCAAAAGGAGAAGTTTCACTCTGTTGAATGAGCCTACCAAGTGCGCCGGGTCG
AAGACGAGAAAGAAAGGAAGGTGACGAAGTCAAGGGGCTACACAATCCTATGGATTGGAATCTTG
ATCAGAACTCACCTCAGGTCGAAAAGAAGGATGCAGACATGTTGC
Found at i:124396 original size:13 final size:13
Alignment explanation
Indices: 124378--124402 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
124368 TATGGCAAAG
124378 AACAAGAAGAAAA
1 AACAAGAAGAAAA
124391 AACAAGAAGAAA
1 AACAAGAAGAAA
124403 TTTGTCCAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.76, C:0.08, G:0.16, T:0.00
Consensus pattern (13 bp):
AACAAGAAGAAAA
Left flanking sequence: Indices 123878 -- 124377
GCGACGTACTTCAAATGAGAGTTCCAAAATCCTAACTCATCTACCGAGGAAATCAGTCATTGTCC
TTTTACTAAGTCAGCGGTGTCTTCATTCCGAAAATTCAGGTTTCCGCGGAAATAAGTCAATCCCG
ATTTGCTAAGTAAATTGGCTAACCATATCCAAAAATCTTGTCTCATATACCGGGACAATCACTCA
GCCCCGATTTCCCTCAGTAAACGGTCAAACCATATCCGAAAATCTTGTCTCATCTATCGGGAAAA
GTAGTATCGAATTGGTATTTCACTATGCACACATCGTCAAAGGGAGGTCGTTCAAGAAGTCAGTG
CTTCGAATACTTTCATCCACTTGTCAATTCTTTGTGTCAGACTCACTCGTCAATTCTGTGTGATT
GAATTTTGCACTGATAAGGTGTGACTTATTGGATGTATCTTGCTCATTCATCTGTGTAAGAATTT
GGAATTCCTCTTCCAACTCGTCCCAAAATGGGCGTTATGGCAAAG
Right flanking sequence: Indices 124403 -- 124902
TTTGTCCAATAGTAACAAAAGGTGCCTCTACAGGTTGACATCCGATCCAACCTAGTAGTAAGCAA
TCTGCCAAAAGCAACCAAAATATTCCTTGGTAAATGGGTCGAAAACTTGAACTACGCACATACAT
ACTTGGAAAAAAAGGTAAAGCCAAGAGAGATATAAAAACTAGTGCTATTGCGGCTACACCTCCCG
CTTTGTCAGGTATACTGCGAAGAATGGCATAGATCGGTAGGAAATACCATTCCGGCACAATATGA
GGCGGGGTGGACATCGGATTAGCAGGTATATAATTGTCGGGATGCCCCAAAACATTAGGAGCATA
AAAAATCCAAATGGAAAAAAAGATAGCAAAAGCTACCCAACCTACTAGATCCTTGACATAAAAAT
AAGGGTAAAAAGAAATTTTATCCATCTCTGAATGTACCCCCAATGGATTATTTGATCCATATTGA
TGCAATGCGGCCAGATGAAGAAGACTGGCGCCTACTAAAAGAAAG
Found at i:175572 original size:22 final size:22
Alignment explanation
Indices: 175516--175588 Score: 83
Period size: 22 Copynumber: 3.3 Consensus size: 22
175506 CAGGTCTAGT
* * *
175516 AGAAGGAGCAGTGGTTACCGGA
1 AGAAGGATCAGTTGTTAGCGGA
* *
175538 AGAAAGATCAGTTGTTAGCAGA
1 AGAAGGATCAGTTGTTAGCGGA
* *
175560 AGAAGGATCAGTTCTTAGTGGA
1 AGAAGGATCAGTTGTTAGCGGA
175582 AGAAGGA
1 AGAAGGA
175589 GCACTTCTTT
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.37, C:0.10, G:0.34, T:0.19
Consensus pattern (22 bp):
AGAAGGATCAGTTGTTAGCGGA
Left flanking sequence: Indices 175016 -- 175515
AGAAAAGAGTGCTTCCTCTTATGCTGGTGCTCGAGACGTTATACCAATATCCTCTTCTGGTACTC
TCAAGGCCTCATCTCCTCTATCGAGAGCTAGTCTGAGAGTCCTTCGCTCCTTATCATCTCAACTG
CTGTCCTCAAGGCCTCATGTTGAAAGGGGCTCCCTCTCTGCTCTCTTAGTATAACCTAGCTATTA
CTGCCAGGAGAGAACGCAAGCAGGCTAGGATATACTAGACTCTATGACTTGTGTGAAGCATAGCT
GGATGTAGCTAGTGAACTTGTTGATAAGTCAAGAGCGACATCCCTGTAAATTGTTCGTCTAGGTC
TTTCGCGCCGATGCTGTCTTCGGCCTTTTCCTGACTTTAGCCGTTCAATCTCCCTGCTTCTTCCA
ACAAGATTCCGCGCCGGTGTATTCTCTTTCGTCGAGAAGTAATCTGAATGTAGTGTCCGCAAGGA
AGTGGAATTCACTCAATGGTTAGGTTGCGGTGCTACAGGTCTAGT
Right flanking sequence: Indices 175589 -- 176088
GCACTTCTTTCTTTTGACTTTGATTGATGCCTATCGAAAAAAAGGAGAAGCGAGGGTGCCTGATT
CTGGAAGATTCGAATCAGATCTGACCATACTATATCAAGTAAGCGCTTTTCACACCTTACCTGAA
CTGAACACCTACCCAATTGAGCTTTTTGACCTCAGTCTTGTTTCTGACCCCTTTTTGATAAGCAA
GATGGTAGGTGAGGTGGGCACAAACACTGGCACATTCCAATCGCACATCTCTCGTAGATATTCAA
AAAGAGTTATTCACCACCATGAGAGTCTTTCTTCTGCACGGTACACGCACGACACACATCGATCT
GGAGCAAGGTCGTTCGAGCTGGATTCTTTGGTAAGTGATTGGCTTAATGCCGGCGCTTTCAAACT
ACCACGAGATATGAGTTTATGCAACTTCGACGAATATTAACGATAGAGCCGAGTGAAAAGATGAC
CATAGCCGAACAGCCGGCGATTGAGGCGACAAGCATTGGTTCGAA
Found at i:217133 original size:22 final size:22
Alignment explanation
Indices: 217077--217135 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 22
217067 GGACCAATCC
* *
217077 CCGAGTTTCCAACCCTCAGTAT
1 CCGAGTTTCCAACCGTCAGGAT
** **
217099 CCCTGTTGACAACCGTCAGGAT
1 CCGAGTTTCCAACCGTCAGGAT
217121 CCGAGTTTCCAACCG
1 CCGAGTTTCCAACCG
217136 GGAGGAACCT
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.22, C:0.36, G:0.19, T:0.24
Consensus pattern (22 bp):
CCGAGTTTCCAACCGTCAGGAT
Left flanking sequence: Indices 216577 -- 217076
AATAGTTTCCGTTGCCAAATTCAATTCAATGAGTAATTCAAAGGAGAAATAATTGTTGAGGAGAT
ACTAACAACTCCTGGTAAACGGGCGGACTAAGAGAACAAAGCCGCTTCTTCAACACAGACGGCTC
ATTCTTTTCCCCGCATGAAAAACAAAAAAAGAACCATGAAACTCTGACATACGATATTCCTCAAG
ATACCCTTCCTCAAGAAACTGTTTAGCAAGTTGGGCCTCTGCAAGAAAAGAGAAGACACACCAAA
AACTAGGTTAGAGCTCTGGGTCGACCAACATCAAAAGAGAGGAATAGAGATAAACAAGATGGACC
TCTGGATGGATCTAGTGCAGGAAGAGAGATATTCATCAAAGCCGATTTCCTCTGCGGCAGTGGTA
CAACACTCTTCTTATTATATACGTTATTGATGTTTCGGAGAAAGTCGAGTGAATTCCCTCAATAG
TGAAAGAGGAAAAAAAAAAGGAAGTAGCTTTGATAGGACCAATCC
Right flanking sequence: Indices 217136 -- 217635
GGAGGAACCTTCGTTTCCCACAGATTGGTACCTTTGTTTATCAACGATGACCTTGAACACCCGGG
TACCCCCTACCTCAAACCCTTGTTTCAGTGTTGAGGAATGAATCGTACATCCTTTGATGAAGATG
ACATGACACCTTTCGAGGAGAAGTAGGCAGAGCGGTACAATCAGGCTAGCCAGTCAGGGCGGTCT
TTGGATTGACCAGCAAGTGGGAGCTGTAAGGCAGGAAAGGGTGTGGTGCAGGCTGCTTTCGGTTG
GAGACATGGCTGCTTAGCCTCAGCTTAATGCCTTTATTGCAATCATTGAGTGAAGGTTTTCTGCT
ACAAGAAATTGTTGAAAGTTACATAAAGACAAAGTGTCAGTTATGTCAGTCATTCCAAATGAGAA
GCCCCGCCCGCTTTGTGACATCAATTTGAAAGAGTGACCAGAGACTTTTGAAAGGTGAACTGATG
CTACCTTACTGTCCTTGCCAGGTCTTTATTTCACACAACTAGGGA
Found at i:244925 original size:19 final size:19
Alignment explanation
Indices: 244897--244934 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
244887 CCCCAATCAC
*
244897 CCTTAGCCCACGTAATAAT
1 CCTTAACCCACGTAATAAT
244916 CCTTAACCCACGTAATAAT
1 CCTTAACCCACGTAATAAT
244935 GACGATACGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.34, C:0.32, G:0.08, T:0.26
Consensus pattern (19 bp):
CCTTAACCCACGTAATAAT
Left flanking sequence: Indices 244397 -- 244896
GCATCTGATGCCAATACAGACTCCGATGTCTAAATCAATCAAGTCTTTTCGTCCCCCCCTCTTTC
GTATACAAACTCTTCCTCTTCTTGATGCTTGTTTAGGGCTCGATAGTCTATGCATAGCCATAGGC
TCCAATCGTGCTTCTTCAAACCGAGGTTGTAGACACGTGCGTCGATCCAGGGAATCTCTACGACC
ACGAACCGTACAGAGGATAGGCTGGCGATCCGATGGACCCCAACTAACATAGCTCATTATGTAGA
TTCACCCCCCCAACACCCACCCGGGTCTAGGGATGGCAAATCTAGGAGAGGATCAACTACTATCT
TGCTTAGGGAGGAAATCGAGGGATGGACTGTCACGATTAGGGTTACCCCTATTTTCAAATGAAAG
GAGGAAGAAAGAGAATAAAGGAAACTTAGTTGCTTAAGAACTAAGCCAACTCTCACTTTCTATTT
GATTGAGAGTCAAATCCCATCACTCTTGGGAAATCCCCCAATCAC
Right flanking sequence: Indices 244935 -- 245434
GACGATACGTGTCACCAACTAATTAATCCAACTAGGTTATTGACAAGTTTGAATTAACCTCAAAA
CAAAAACTCGCTTCCATCGTCGGTTGTTACTTCCTTGCAGTAATTGAGATATGTTTTCCTTACAC
GTTCCTATCAGCCGGTACTCCATCTAGGCGGGCTGAACTAACCCCCCAGCAGCCGCCCCAGTTGT
TATTTCAAACAAGATCTGTATCGGTTCTTTCCTCCTTACAGAACGGTAGTAATGGCAATCCAAGG
AACTGGAATGGGCGAAAGAAGAGCTCTTCTACTCGATCGATTGTGTTCTCTCTGTATTTCATAAC
CTCGAGAGATTCTCGCACGAGCTAAACAATGGAAAAGAAAGACTTCTCTTGTTCCCGGATCAGGG
CATCAAAAGGGGCCCACCTTTCCCAGTTTCATAGTAGTTAGACCCACTCGTCGACCTCTTCTCGG
CGGAGTATCCATACAACTGAGGAAGTTGCAAATCAAGTTCTCAAA
Found at i:282212 original size:19 final size:19
Alignment explanation
Indices: 282176--282218 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
282166 TTGAGATTGG
*
282176 AAGGACTGCTCTACAACTC
1 AAGGACTGCTCTACAACTA
*
282195 AAGGGCTGCTCGTA-AACTA
1 AAGGACTGCTC-TACAACTA
282214 AAGGA
1 AAGGA
282219 ATGAGGTTAC
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
19 18 0.90
20 2 0.10
ACGTcount: A:0.35, C:0.23, G:0.23, T:0.19
Consensus pattern (19 bp):
AAGGACTGCTCTACAACTA
Left flanking sequence: Indices 281676 -- 282175
GTTGACTCAGTCTATGAGAATCCGCTTCTTAGTGTTCCTATTAGTCAGAGAGAGGTGGAATCAAT
TCAACGCCGAATCATGACCGGTCAATATGTGTTCTTGCCATTGAATGTGAAGTTCGTTAATAAGA
ATGATCCCACTTCTCAAGAGCCGGAAATTAGATGGGGATATTGGCCTACTGAGATAATGGTTTCG
ACTGATTATTGTGTAGATCCGGATGTCTCAATGCTCTAGCTTACCTGGTACTTGAGTAGGCTGTC
TCAATGCCCTACCAACTCTCATCTTCCAACTAGCTTCTTCTTTTGTTTGACAGGACAGGGAGTTG
ACTGTAGCAAGGGGCATTCATCCTACCAAGCTGAACGGAGTTCTTGGAATGGCTAGAGACAGACT
CTAGATATAGAGCTAGGACTGAGACTTCCTCTTTCTTCTTAATAGGGCATACTCCTTCTATTCAT
TGCCTGCTTTTCCTTTATGGACTGCAGGAAGCTACTTGAGATTGG
Right flanking sequence: Indices 282219 -- 282718
ATGAGGTTACCTACTTAGGGACGTTGAGATTGAAAGAAATGAAAATGGATTGTCGGACTTTTTAT
ACACAAACTCCGAAACCACCTCTCATTTCATCTATCAATTGAAATCTTTCTTAACCATACGATGA
TTTGAGTCATTGCGATTCAAAAAGTATGGACGGGAGATCGACGTAGTTTGTTGAGACCTTTCTTT
CACTGTAAACAGTTACCGGGTCCTCTAGAGTTGGGACTGAGGTAGTGACTCGCTCATATGCAAGA
GACTTAGTAGTTGAGACGAAGCGAATCCCTAGCTCTTCCACTCAAAGGTAGCCAAAGCAAAGAAA
GAGACGTATGAAAGCCTGCCCCGCCCCAATCGAGACTAGCGAACAAAGGAAAGACTCAATTACCT
GCTTGATGGATCCCCCCTTGATGAGAAGGAAGATAAGTGAAGTGGAAGACAGGGGAATAGCATTG
AATTGAATACAGTAATTCCACTGTCCTTGAAAGCAAGAGTTGTCA
Found at i:299949 original size:30 final size:30
Alignment explanation
Indices: 299913--299969 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
299903 CGACTTTAGT
*
299913 CTGGTAAGACCTTTGCTTTAGACGAGCCTC
1 CTGGTAAGACCCTTGCTTTAGACGAGCCTC
*
299943 CTGGTAAGACCCTTGCTTTCGACGAGC
1 CTGGTAAGACCCTTGCTTTAGACGAGC
299970 ATCAAATTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.19, C:0.28, G:0.25, T:0.28
Consensus pattern (30 bp):
CTGGTAAGACCCTTGCTTTAGACGAGCCTC
Left flanking sequence: Indices 299413 -- 299912
TGATCAGAGGATTGAAGAGAGAATGCAAGAGATAGTATATAGAGGAGACGGGGCTATCAGGTAGC
CTTTGGTTCCGCCTTCTTGTGAGGAGGATTTTCGTTATTCGAATACATACGGACAAGCTATAAGG
AATTCATTCCACTTATATTCTTGCTAAATTGGACTCTGATACCACACTTATCGGCTCTATTGGCC
TCCTGGCGAGTTTCTCCTTCTTTGTTGGTTTGTATTCGCCGGGCTGTATAAGTCAGTAGTCCTAG
CGAGTGCCCAACTATTTGTCTGATCGTGCTTCTTTGTCTTTTCACTGAATTTGTTCTGTAACGTC
ATATCAAGCCCTTGAATACCCGGTTCTCTATCAAAGTCTAGCAAATGTCTTCTAGCTCTATTTTG
ATTAATAAAGACTAATCGGAATGGATAGAAATGGTACGAAAGAGTAGGACGAGCTCTCAAGCAAG
GACCTGTAACCTCTTCTTAGATGCGCCGGACCCCTCGACTTTAGT
Right flanking sequence: Indices 299970 -- 300469
ATCAAATTGATGAGCGGGAAAGACATCAGATTGTACGCGTGAGGGGAGCTAGTTCTGTTCCCCAT
GCTGGCGCCGGGAGGAGAATCCGACCAGAAGGGCCGGGGAGAGAATCCAACCAATAAGAGGTGCT
TCACTAGACTGAATGACTTTATATTGCTATGCAACGGAAATGAGCTTCCTTTCGACCCAAACCCG
CTATTGGTAAAACGATTCGAATAAGGTCTGGGGAGAGCCAGAGGTATCAAGAGTAAAGGCCAGAG
AGAACACTGAAATTCAAGGCCGAGGAAATCCTTCTATCGTAGCTACTCCCTACGGGGCAAGAAGG
GCTGGCTCTTGTTTGCGAGCTTTATTGGAGCGGAGTTTCCTGGTACCATCTAATCTACCCTTATT
GTACGAATTCCCTTATTGCAGACAAGAACTTTTTTTTCCTGGTCCTTTTGCCCCGGATACTCCAG
TTCCCATGTACCCTTATACTCATGCGGGGGTAGACTAGACTTCTT
Found at i:317088 original size:7 final size:7
Alignment explanation
Indices: 317076--317101 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
317066 TACCTGATTA
317076 GGGTGCC
1 GGGTGCC
317083 GGGTGCC
1 GGGTGCC
317090 GGGTGCC
1 GGGTGCC
317097 GGGTG
1 GGGTG
317102 AATTGGCCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.00, C:0.23, G:0.62, T:0.15
Consensus pattern (7 bp):
GGGTGCC
Left flanking sequence: Indices 316576 -- 317075
ATCGGCTGAGGCTGCTAACTTCTCCTTCAGTTCCAAAACAGTCTTCTGCAGACCAGTTTTCGCCT
CAAGAAGGGAATTGACCATACCGCTCATCCCTCTCTTTCTTCAGTTGGGCAAATTGGGCATCCCT
CTCCTGAACAGCTTGACTCAGGTCATCCCTTTCCCCAGCTAACTTCTGGTTCTTTTCAACCTCTT
GAAATGAAACAACAGGACTAATTTGAGCAGCACTCTCTGCTAACACCTTATCAAGCTCAAACAGA
GAAAGAAAGCACCATCAACCATTATCACTACCAGTTAGAACAATTCAAAAAGGGGTAATGGGGAA
GGATTAGGGTACCTGGGCCAGAGAATCAGATGAGGCAGCCCTTTCTCTCTGGTTCGAAGCCGCAG
CTGGGGGGAGGGGCATCTTGACCCTGCGCGCACCAATAGGCATCACCAGAATAAGTCCAATTTAT
CCCCTCACTGGTAGAATGGAAAAAATGAGGAGAGTTACCTGATTA
Right flanking sequence: Indices 317102 -- 317601
AATTGGCCAAGCCAAGAAGGGTCCTTCTCAGACCTAGCGAGCTTTCCTTTCCTTTGTCTCCAGCG
CCCAGATCTGACCTTCGTCAAGTCAAGCCCTGTCTCCCTCCGGGAAGGTGCGGAGCTTGGAGAAA
ATACGAGCGGTGTCGTTGAAAACACGAAGCATGGGAAGGCGTTAAACGTCCCATTCGGGCCACGA
ATGTAGCTGCCCATGGAGCGAATGTTATGAACTGATACGCCAATTCCTCTGGCTGATTTGCTAAT
GACCGCACATTCCTTCAGAGTGTCATAGATGCCCTCAATGCTATCCTCTTTCACTCATTTGACTA
AACTTTCCCAAGCCATTGAAAAGAATCAGCTATTGGTACTTGCTTATTCAAGCGGTGAATGCCAG
GGATTTGCCCAAAGCATAAGGAGAAATCCCATGAGGAGGTCGGTCAGATGCCAATTCACAACGAG
TCTATTCTAATCGGAGGAAAAGAAGGAGATCCCATAGCTTTCTGA
Found at i:403936 original size:22 final size:22
Alignment explanation
Indices: 403880--403952 Score: 83
Period size: 22 Copynumber: 3.3 Consensus size: 22
403870 CAGGTCTAGT
* * *
403880 AGAAGGAGCAGTGGTTACCGGA
1 AGAAGGATCAGTTGTTAGCGGA
* *
403902 AGAAAGATCAGTTGTTAGCAGA
1 AGAAGGATCAGTTGTTAGCGGA
* *
403924 AGAAGGATCAGTTCTTAGTGGA
1 AGAAGGATCAGTTGTTAGCGGA
403946 AGAAGGA
1 AGAAGGA
403953 GCACTTCTTT
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.37, C:0.10, G:0.34, T:0.19
Consensus pattern (22 bp):
AGAAGGATCAGTTGTTAGCGGA
Left flanking sequence: Indices 403380 -- 403879
AGAAAAGAGTGCTTCCTCTTATGCTGGTGCTCGAGACGTTATACCAATATCCTCTTCTGGTACTC
TCAAGGCCTCATCTCCTCTATCGAGAGCTAGTCTGAGAGTCCTTCGCTCCTTATCATCTCAACTG
CTGTCCTCAAGGCCTCATGTTGAAAGGGGCTCCCTCTCTGCTCTCTTAGTATAACCTAGCTATTA
CTGCCAGGAGAGAACGCAAGCAGGCTAGGATATACTAGACTCTATGACTTGTGTGAAGCATAGCT
GGATGTAGCTAGTGAACTTGTTGATAAGTCAAGAGCGACATCCCTGTAAATTGTTCGTCTAGGTC
TTTCGCGCCGATGCTGTCTTCGGCCTTTTCCTGACTTTAGCCGTTCAATCTCCCTGCTTCTTCCA
ACAAGATTCCGCGCCGGTGTATTCTCTTTCGTCGAGAAGTAATCTGAATGTAGTGTCCGCAAGGA
AGTGGAATTCACTCAATGGTTAGGTTGCGGTGCTACAGGTCTAGT
Right flanking sequence: Indices 403953 -- 404452
GCACTTCTTTCTTTTGACTTTGATTGATGCCTATCGAAAAAAAGGAGAAGCGAGGGTGCCTGATT
CTGGAAGATTCGAATCAGATCTGACCATACTATATCAAGTAAGCGCTTTTCACACCTTACCTGAA
CTGAACACCTACCCAATTGAGCTTTTTGACCTCAGTCTTGTTTCTGACCCCTTTTTGATAAGCAA
GATGGTAGGTGAGGTGGGCACAAACACTGGCACATTCCAATCGCACATCTCTCGTAGATATTCAA
AAAGAGTTATTCACCACCATGAGAGTCTTTCTTCTGCACGGTACACGCACGACACACATCGATCT
GGAGCAAGGTCGTTCGAGCTGGATTCTTTGGTAAGTGATTGGCTTAATGCCGGCGCTTTCAAACT
ACCACGAGATATGAGTTTATGCAACTTCGACGAATATTAACGATAGAGCCGAGTGAAAAGATGAC
CATAGCCGAACAGCCGGCGATTGAGGCGACAAGCATTGGTTCGAA
Found at i:416992 original size:30 final size:31
Alignment explanation
Indices: 416958--417016 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
416948 GTGGGCTTGC
416958 TGCGGCTCAGCG-CTCA-ATCTGTCTTTCTGG
1 TGCGGCTCAGCGCCT-ATATCTGTCTTTCTGG
*
416988 TGCGGCTGAGCGCCTATATCTGTCTTTCT
1 TGCGGCTCAGCGCCTATATCTGTCTTTCT
417017 TTCATTTCCT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 12 0.46
31 14 0.54
ACGTcount: A:0.10, C:0.29, G:0.25, T:0.36
Consensus pattern (31 bp):
TGCGGCTCAGCGCCTATATCTGTCTTTCTGG
Left flanking sequence: Indices 416458 -- 416957
TCCTTACCCCGAGATAGAACCTCGTGCCCCTGGCCCCTCATCAGTAGGGCGTAATTCCTACTATG
CATATCTATATATCTCTTCTTTGGTTCTACGCTTCTCAAAAGTCTCATTTCTTTCCAGAGTACTG
TATTTCAGGGCTGAGCCTAGTAAGATGAAAAGGGACGATCCATAAATACGTACTGAAATCAGTTT
TGAGCTCTCTCACCCTTCGGAACTACTCACCGAGAGTCTATCGGAACTCTTACTACTTTCCAAAA
GAATTCGACAACTAGAGACCTAAGGAATAGCGATCACATTTCTCGTAAATCAGAAAAGAAATCCA
TAGCCCACACAAAAACAACCACCAAAGCTACGCGACGCGGCTGCGGCATCATAAGCACTACTACC
AGGCAATACTCCTGTTGAGTAATCACATTATCAAGAATGGGACTTTAAGCAAATGAGTTTTCACA
GGCAGTGTTTGGTCTTCTTTGTGTTTCCTTCCAATGTGGGCTTGC
Right flanking sequence: Indices 417017 -- 417516
TTCATTTCCTAAAAGGTTTGTCTCCTGATGACGGTCGATGTGGATCCCGTCCTTCAATTGTCTTC
CCCCTAACGTGAGCCTAATGAAAGAACCGAGACAGTGAATTTATGAAAGAAGGACAGAAATAAGT
GGTAAGTGCATCCAGTGTAAGTTGAGACTTTCTTTCTTCCTAGTGGAACTCTCTTTTCATTCCCT
TTCTTTCGGACAGTGTAGCAAGAGTGTATAGCCTAGGCTTTTTGAATCTAAATCATAGGACAGGA
CGTAATACTCCAGTATGGAAGAAAATCTATTAGAATAATGACGTCGGACTCAGCTCCTCTACGAA
AGAGTCCCACATTTTTCTCTATACCAATATACTACTCAGTCTTTGTCTTCCCCAGTCGGCGCTAT
TTTGAGAAGTTCGATTACTAGCAGTCACAGAAAAAGTCAAGTGAGAATAGACCGAAAAGCGTGGG
TCTTGAATTTTCTCAGGCAAGTAAGATTTCAAAGTATTAGATAAT
Found at i:417012 original size:31 final size:30
Alignment explanation
Indices: 416958--417016 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 30
416948 GTGGGCTTGC
416958 TGCGGCTCAGCGCTCAATCTGTCTTTCTGG
1 TGCGGCTCAGCGCTCAATCTGTCTTTCTGG
*
416988 TGCGGCTGAGCGC-CTATATCTGTCTTTCT
1 TGCGGCTCAGCGCTC-A-ATCTGTCTTTCT
417017 TTCATTTCCT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 1 0.04
30 13 0.50
31 12 0.46
ACGTcount: A:0.10, C:0.29, G:0.25, T:0.36
Consensus pattern (30 bp):
TGCGGCTCAGCGCTCAATCTGTCTTTCTGG
Left flanking sequence: Indices 416458 -- 416957
TCCTTACCCCGAGATAGAACCTCGTGCCCCTGGCCCCTCATCAGTAGGGCGTAATTCCTACTATG
CATATCTATATATCTCTTCTTTGGTTCTACGCTTCTCAAAAGTCTCATTTCTTTCCAGAGTACTG
TATTTCAGGGCTGAGCCTAGTAAGATGAAAAGGGACGATCCATAAATACGTACTGAAATCAGTTT
TGAGCTCTCTCACCCTTCGGAACTACTCACCGAGAGTCTATCGGAACTCTTACTACTTTCCAAAA
GAATTCGACAACTAGAGACCTAAGGAATAGCGATCACATTTCTCGTAAATCAGAAAAGAAATCCA
TAGCCCACACAAAAACAACCACCAAAGCTACGCGACGCGGCTGCGGCATCATAAGCACTACTACC
AGGCAATACTCCTGTTGAGTAATCACATTATCAAGAATGGGACTTTAAGCAAATGAGTTTTCACA
GGCAGTGTTTGGTCTTCTTTGTGTTTCCTTCCAATGTGGGCTTGC
Right flanking sequence: Indices 417017 -- 417516
TTCATTTCCTAAAAGGTTTGTCTCCTGATGACGGTCGATGTGGATCCCGTCCTTCAATTGTCTTC
CCCCTAACGTGAGCCTAATGAAAGAACCGAGACAGTGAATTTATGAAAGAAGGACAGAAATAAGT
GGTAAGTGCATCCAGTGTAAGTTGAGACTTTCTTTCTTCCTAGTGGAACTCTCTTTTCATTCCCT
TTCTTTCGGACAGTGTAGCAAGAGTGTATAGCCTAGGCTTTTTGAATCTAAATCATAGGACAGGA
CGTAATACTCCAGTATGGAAGAAAATCTATTAGAATAATGACGTCGGACTCAGCTCCTCTACGAA
AGAGTCCCACATTTTTCTCTATACCAATATACTACTCAGTCTTTGTCTTCCCCAGTCGGCGCTAT
TTTGAGAAGTTCGATTACTAGCAGTCACAGAAAAAGTCAAGTGAGAATAGACCGAAAAGCGTGGG
TCTTGAATTTTCTCAGGCAAGTAAGATTTCAAAGTATTAGATAAT
Found at i:490368 original size:52 final size:52
Alignment explanation
Indices: 490290--490392 Score: 197
Period size: 52 Copynumber: 2.0 Consensus size: 52
490280 AGGAGATAAG
*
490290 ACAGACTAACTCGATAAGGCAGGTAGCTGAGCTTAGACCCAAGAGCAATGAA
1 ACAGACTAACTCGATAAGGCAGGTAGCTGAGCCTAGACCCAAGAGCAATGAA
490342 ACAGACTAACTCGATAAGGCAGGTAGCTGAGCCTAGACCCAAGAGCAATGA
1 ACAGACTAACTCGATAAGGCAGGTAGCTGAGCCTAGACCCAAGAGCAATGA
490393 GGTGTATTGA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.38, C:0.22, G:0.25, T:0.15
Consensus pattern (52 bp):
ACAGACTAACTCGATAAGGCAGGTAGCTGAGCCTAGACCCAAGAGCAATGAA
Left flanking sequence: Indices 489790 -- 490289
TCTCTACCAATTTGTGAATCAAGATTTTGGTTTATTGATCTTTGTCGGTGTATGGTGGTGTCAAG
TCCTTTTGAAGAAATCGTACTCTATCCGTCTCAACCGACTCGTTGATTCTCAAATTATTACGACG
GGAGAGGCACTATTGTACGTTGAAGCCCTTCACCTTCATTATACGTGAGTTGCTAAGCAAGCTTT
CCTTCCGTTCGCTAGTGAGGAGGAATTGAGTTGTGGATTCACATCATGTGCATTCAAGCATATAG
CTTAGTACCAACTAGTACGGATTTTGACTCTACCTCGAGAAGCAGAACAAAGGCACTGAGACTTA
GGGCAGTGATCATATCCCAAAGACAAGAGATAGAGTGATCATATCCCATAGACAACAGCCAGATT
GAATAGAGAAGTCGGGCATCCAGGGCAGTTAGCTGGGCCGAGAAGGTGTGCATTCCGGGAAGGTA
GCTGAACCTAGAGCCCTGAAACATGAGACAGATTGAGGAGATAAG
Right flanking sequence: Indices 490393 -- 490892
GGTGTATTGAGATAAGTTTCTCATTCATCCCAATTTGAGAAAAAGAGCTAACCGAAGCACTCCAT
AACCAAGAGACAGATCAAGAGGGATACAGCAACAGGAGGGGTTCTACTTTATTTGATCCCGTGGT
AAAGAAAGAGTGGATGTCTCTCTGCCTCCACCGCCCGCCCTTGGCCTCGAAGTTCTGATGAGCAC
TGCTGCCTTCTCGTGTGGAAGATGATTTCCTTTTCCAATACCTGAAGGCACTTGCCAAGTTTGAC
TTATAGACTGGTAGAAAAGAAGGAATTTCCACTGTTATATATTGGAATTCTCGTCAGCTTTTTGA
GGTCATTCATGAGCCCACGTAACACACTAAGACTTCCTTTCTCTTGGCCTTGCTTATTCAACTAG
GAAGCAAGTGAAGTGACGGGGCGGTCTTTGTCACGAAGGCTCTAAGCAAGTTCACTCAGCTGACA
GGCTACTTGGAGTATGAGCACTTACCGCTAGCCCTAAAAGCGATA
Done.