Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_044768
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: 389709
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Found at i:14893 original size:22 final size:22
Alignment explanation
Indices: 14853--14896 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
14843 TATAAATCAA
*
14853 ATATAGATGAGTAATTCAAAGT
1 ATATAGATGAGTAAATCAAAGT
14875 ATATAGATGA-TGAAATCAAAGT
1 ATATAGATGAGT-AAATCAAAGT
14897 CAGTCGTCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 1 0.05
22 19 0.95
ACGTcount: A:0.48, C:0.05, G:0.18, T:0.30
Consensus pattern (22 bp):
ATATAGATGAGTAAATCAAAGT
Left flanking sequence: Indices 14353 -- 14852
CTATCCGAGTGAGTCCCAGTCTGGGAGAAGGGGGGGCCATCTGTTTCAGAAGGTCCGAAGATTCA
TTTCAAAAAACAGGAATGTCAGAGCAGTTAGTCCGCATGTCCCTAACTACCTTGTTCCTGATTGG
ATTGCTTTCTTAGTGTGGCATCTTTTTGTTCGCTGTCCACTGGTGATATTATCATATCATATATA
AATGTAGATAGAGAAAGAGGCTAAGCTAAGCCTACGTAACGCTATGGGAACAGCTTTTTTTGTCC
GCTTTCAGCTATGCTATATAGATGCGCTACCTTGTGAAAGAAAACATCATATGTAAGTAAGTAGC
ATCTAGAATAGAATCCAGAGCTGCTAAGAAAAAAAAAAAAATATTTAGAGAAAGAGGCTATAAAC
CATTGAATTGTGTCGATTCGAGCTAGCTTCAGGTCTTCTTCAATCAGAAAGTCATGCCTTTTCAC
TATAGTAAGGGATTCGATCCATATCACAAAACATATATAAATCAA
Right flanking sequence: Indices 14897 -- 15396
CAGTCGTCTATCAGTTATGGAGTTGAGAGTCACCTTTGTTGCTTCTTTTGTCTCCTACGGTTATG
CTAAGATATATTAAAATGTGCATTCAACCTATATTTCCCCTTTTCTATTGTACAGATGCCTATTC
ATTTCTGCGTAAAGCTCCCCCTTTCCTTTCTTCAAATATCTCATTTCTCAGTCTTGACTACTTCG
GGCACGGCGCGCAACGGAACAGAAAATGAAAGCAAAGAAATCTAGCCTCGTATTCCAAATAATCG
ACCAAGGAATGAAGGGATCCGTTTTGATAGATCCCGTTTTGGCTTTCATATGGCAGATGGTCCGG
TGCCTTTTCATATATGTAATGATGGCGCCCTAGGATTACACACCACGCAAGGCGGGCAAAGCCAT
TCAAATTTCACTACCTAACGGAGGAGCGTGATAACCTCTTTGTAATAAAGGAATTCATTCACCCT
TTCCATCGGCTAGGAACAGTTGTTTGGATTGGACATACGTCACAG
Found at i:16500 original size:14 final size:14
Alignment explanation
Indices: 16481--16508 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
16471 CCATCCCTTC
16481 TTCTCGAATATGTA
1 TTCTCGAATATGTA
16495 TTCTCGAATATGTA
1 TTCTCGAATATGTA
16509 CTCTTATTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (14 bp):
TTCTCGAATATGTA
Left flanking sequence: Indices 15981 -- 16480
AACCTTTTATTTGCTGTGATCTCGATCCTGTTCCGATTCGGATTTCCTTTTGTAGTGGATAGCAT
CCCCTTATTGTCTTCACTAGCGTTTTCTTTTTATGTCCCGGAGCAGTCGCCTTATTCAAAACTAT
AACGATTATAGCTGCTGTACAAGAAATAGATTATATTAGTAGTAAACTATAAGACTTTTGCTTCT
AATATTGAAAATGAAGCTTCATCTCTTACCTGCGGATTTTAGTGCTTTTGAAGTGCATCTCGCGG
CCAACAAGCTCTAGTGACTGCCTCGATCAAAAGCCCTTAACCTCCTTCCTATTTGAGGATGATAC
CCGGGAACAATCCTAGATCAATGAAAGCAACCGAAGCATAGCAAGGGGAGCTTTAGCTTCTTCAT
CATGTCATTCTTCTGCTAGATGAGCCCATAAGCAATCGTAGGGCTTCCAAGCCCGACTATACTAG
ATTGGACCCTTCTGTATCTACTCTACAGAAAATAACCATCCCTTC
Right flanking sequence: Indices 16509 -- 17008
CTCTTATTTCATAGAAATGAACCATCTCGCCTTTCTCTACGCTGCCCGGTTCGTCAGGAAGGTAG
ACAATTACCACATAATAAGCAAGCAAGGCCTCATCCTCGGGTAGCATTCATCGGTGGTAGGGTGG
CGTCCCTGAAATAATAACTCTTTAATAGGCACCGCCTCGTCGAAGAAAGATATCTATTGAGTATG
TTCGCGATTCCTCTTCTTTACTCCTCCTTACTTGAAGATTGAACCTCAAAACTCTTTTATTTCGA
CCTCTATTAAGCTAGTTTTACAGGGTGATCCTGACTAAACCAAAGTACCGTGACTCAAGGGGCAT
GATCGCAAGGCCGAATCTTTTAATGTAGGGACTTCACCAGACCCGAACTTATCCTCTTAACTATG
AGTCGCCATCTTCAATTTTCTTTGTAGCCGATATCTTTCCTCCGCACCTACAAGGAGCTATATGC
ACCTCTTGTCTAATTGATCACAAGTCAAGGAAGAAGAATCTCTGG
Found at i:43624 original size:26 final size:26
Alignment explanation
Indices: 43588--43687 Score: 200
Period size: 26 Copynumber: 3.8 Consensus size: 26
43578 CTCGCTCGAC
43588 TGAAAGGAACGAAGTAGCTTGATTGA
1 TGAAAGGAACGAAGTAGCTTGATTGA
43614 TGAAAGGAACGAAGTAGCTTGATTGA
1 TGAAAGGAACGAAGTAGCTTGATTGA
43640 TGAAAGGAACGAAGTAGCTTGATTGA
1 TGAAAGGAACGAAGTAGCTTGATTGA
43666 TGAAAGGAACGAAGTAGCTTGA
1 TGAAAGGAACGAAGTAGCTTGA
43688 CCGCGGGCGC
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 74 1.00
ACGTcount: A:0.39, C:0.08, G:0.31, T:0.22
Consensus pattern (26 bp):
TGAAAGGAACGAAGTAGCTTGATTGA
Left flanking sequence: Indices 43088 -- 43587
GGATGCCCAACATGAGCAGTTCCACCTGAAGCACCGGCTAAGTGAATGGAAAAAAGATAAGCAGT
TGACGAGGCACAAGGGCGGGTGTAGCTGATTGTACTTCCTCTCTGCCAGACCCAACCCTAAAACT
AATAAAAAGAAAAGAAAGGGGAATCAGAATACATTTCCTCGAGCAAGCAAATCAAGAAAAGACTC
ACCCTTGCCATGGGCGATAGCGGCTATGTCTAAGCAGCTGCTTTCCCATTCATTCCATAGGTAAG
TCTTATTTTTTGCTGTAAACGAAGAAGGAATGATTCAATATCATATCATAAAAGACCTAGATGCT
CTAGCTCCAAGAAAAGACTAAGAAAACTCCTTAAAAAGAGAAGAGTCAATCCTCAGCGTCGGATT
CTTCTTATGCTGATTGACCTAGCCGTGCGTTTCCAACTGTTATGACTGGGAGCTAGGCGCTATTT
AGCCCTCCATTTCTAAAGCAAGCAGGGGAGCTAGACTCGCTCGAC
Right flanking sequence: Indices 43688 -- 44187
CCGCGGGCGCAGGGAAAGGAGAGGGAGTCACCGAAGAGAAAAAATAAAGGTTCAAGACAATGAAA
AATATAAACGCAGGAAGGAAAAAAAGTCAAGTATGTAATCTAGCAGTCATGAGAGCAGGTTAGAG
GCAAGCCGACCTAACCAACCTACGATATATAGTAACCGACCTACGAATATAACTTTGGGTTAGGT
TGAAAAGTCTAGTTGGAAAAACAGATCAATCGCATCCCAAAGGGTCAAGGGCTGAGTTGCACATT
CTATTTTGGCCTCTTTTCTTAAGTAGAATGAAATGTTCGGCCTAATCTATGATATTGTGATTATG
TTACTGTTATTTGGTCTTTTTCAAGCTTCCCAGAGTTGTCCTTCAGCAAGCAATTATAGGGGTTG
AAGGGGTACCCTTCTAGGTCGTCGCTTTAGTGGTCTAATTTCGGTCTTTTTACGTTATGGAGTTT
ACTCACTTCTTTTTTATATTATTAGAGTTGAGTCTGGTATCGATA
Found at i:43859 original size:21 final size:20
Alignment explanation
Indices: 43829--43868 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
43819 CAAGCCGACC
43829 TAACCAACCTACGATATATAG
1 TAACCAACCTACGA-ATATAG
*
43850 TAACCGACCTACGAATATA
1 TAACCAACCTACGAATATA
43869 ACTTTGGGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.42, C:0.25, G:0.10, T:0.23
Consensus pattern (20 bp):
TAACCAACCTACGAATATAG
Left flanking sequence: Indices 43329 -- 43828
CATTCATTCCATAGGTAAGTCTTATTTTTTGCTGTAAACGAAGAAGGAATGATTCAATATCATAT
CATAAAAGACCTAGATGCTCTAGCTCCAAGAAAAGACTAAGAAAACTCCTTAAAAAGAGAAGAGT
CAATCCTCAGCGTCGGATTCTTCTTATGCTGATTGACCTAGCCGTGCGTTTCCAACTGTTATGAC
TGGGAGCTAGGCGCTATTTAGCCCTCCATTTCTAAAGCAAGCAGGGGAGCTAGACTCGCTCGACT
GAAAGGAACGAAGTAGCTTGATTGATGAAAGGAACGAAGTAGCTTGATTGATGAAAGGAACGAAG
TAGCTTGATTGATGAAAGGAACGAAGTAGCTTGACCGCGGGCGCAGGGAAAGGAGAGGGAGTCAC
CGAAGAGAAAAAATAAAGGTTCAAGACAATGAAAAATATAAACGCAGGAAGGAAAAAAAGTCAAG
TATGTAATCTAGCAGTCATGAGAGCAGGTTAGAGGCAAGCCGACC
Right flanking sequence: Indices 43869 -- 44368
ACTTTGGGTTAGGTTGAAAAGTCTAGTTGGAAAAACAGATCAATCGCATCCCAAAGGGTCAAGGG
CTGAGTTGCACATTCTATTTTGGCCTCTTTTCTTAAGTAGAATGAAATGTTCGGCCTAATCTATG
ATATTGTGATTATGTTACTGTTATTTGGTCTTTTTCAAGCTTCCCAGAGTTGTCCTTCAGCAAGC
AATTATAGGGGTTGAAGGGGTACCCTTCTAGGTCGTCGCTTTAGTGGTCTAATTTCGGTCTTTTT
ACGTTATGGAGTTTACTCACTTCTTTTTTATATTATTAGAGTTGAGTCTGGTATCGATAGATTGG
CAACCTCTAGGGTACAAGCCCCTCCAGGTACACATATATGGGCTCTAATCCCAGGTTAAACTATC
CAGTCGAACTACGTAATCAAATAATCCATGGAAGACAGGGGTTGATCGAGTTTTTTACCCTTTCT
CGTTTTTGGGTATAGGCTGATAGTTAGGCGGTGACTCACGTATCC
Found at i:46771 original size:2 final size:2
Alignment explanation
Indices: 46764--46793 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
46754 TTAATAGTAT
*
46764 TA TA TA TA TA TA TA GA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
46794 ATACTATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Left flanking sequence: Indices 46264 -- 46763
AACTCAACTTACAAGGGCTAGAAATGGAGAGGATGAAGCAAAGCCAAGAGGAAGCCTAAGCAAGT
GAAACTCTCGCGAATAGGAGAAGAAGTCTATCAGCTCAAACTGAGAAAGAGGGGTGCAAACGGGG
AACCACTTACACCGCCCTTTACTCTCTAACTAAGAAACGCGAGGAGTCTTCGGCAAAGCAACTCA
AGACGGAGGTACACAGCTCGGAGCGGATGGTTGGTGTATCCCTTTTTTTCTTTTTTAGCAATTTC
ACTTTCAGAGGACTAAACGACAAAGCCTGGTCCCTCAAAAATCTCTCTTTTAAGGTTTATAGCAT
TCTATCTAATATCGACCGGATGCTTTTGATCACCCATTAATGGAAAACCTTTTTGGGGGGCTTCC
ACCTTACACACGGAAGATTGGATTGCCTGAATCACGAGTAAAGAAAAGGTGCTAAGACACTTATA
ATTTATTCTATTTTTAGGTCGATTTGAAGAAGAAATTAATAGTAT
Right flanking sequence: Indices 46794 -- 47293
ATACTATTTTTATGCACATAAGGAGGGAACCATATGAGAGGAAAATCACTGTTGAGGATCTACCA
AAGAAGCGGTCTATGGACCTTCGTCTTCTCCATGGCGTTGCTTACGGACACTCTTGGTTTGGTAG
ATGGGGGTACAGGTTCTGCCAAGGAAGCTTCGGCGTCACAGAACACAATTATGAAAGAGCACTGG
AGATTCTTAGCTCATTACAACAACCAGAGCAGCCCTCCAGATCAAGCACCCGATGAAGGAAAAGT
CTGTGAGTTATAGGAAGTTCACTACTGTTATTACTCACATGGATAGCAGATGGCCTAAAAGAAGA
CTAGAGTTTGCAGCGGAAGTGATTGTGAACGCATTGCAAGAAAAGAAAGAGATAGTTCTTCAGTC
CCTTTCATCAGCAGCTCTAGTTCCTGGAGTTGATGTTAGCAATGATGTGCTTTATCTGTATGAGC
ATGTGCTGCTAGGATACCCAGAATCAGAGTTGGTGGAGTTGGCTA
Found at i:81813 original size:18 final size:19
Alignment explanation
Indices: 81773--81816 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
81763 ACGCGTGCGA
* * *
81773 GTAGTAGTAGAGGTAAGTG
1 GTAGTAGTAGACGAAAGTC
81792 GTAGTAGT-GACGAAAGTC
1 GTAGTAGTAGACGAAAGTC
81810 GTAGTAG
1 GTAGTAG
81817 GTGTCTCCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 14 0.64
19 8 0.36
ACGTcount: A:0.32, C:0.05, G:0.39, T:0.25
Consensus pattern (19 bp):
GTAGTAGTAGACGAAAGTC
Left flanking sequence: Indices 81273 -- 81772
TAGTATATGGTGATATCAAACTCGAAAGCCCGAACACAAGCAAGCTTACCTTTAAGTCATCAGAG
GAAAAACCCGACGATCCAGAGCAGCGGGTGGGGAAGTCCAGTAGCCAAAAGATATGAACTCGCTT
TAAAGATCAGGGGATCTAGCTAGAACCAAAATAGGAGACTTTTGGTCCGGTACGGAATTTATTTC
CATATCCTGCATATAGAGAGGAAAGGAGAAGGGGCGGAATTCTAGACCGATTATCCCACGCAGTA
ATAGGCATACCACTCCCAGTCTCGCTAAGTTGTCGTTCCTACGGCCTCTGGAGAGCATGAAAACG
CTAGTTCAGCTGCTCACATAGCGTCGGACGAGTGGTTTTAGCCTTTCAAAAAGTGATTTCAACTA
AAGTCTTGAGTGAAGTGCGTTAGCCCCTTAAGCTGTAGTCTAATAAGAATCTAGCTATTGTACTT
TCTATCTCCAGTAACAAAGAGGAATAGGAAGCTGTACGCGTGCGA
Right flanking sequence: Indices 81817 -- 82316
GTGTCTCCTTTCCCAAAGTCTTAGTAGTTGTACGAAGGCCAGTATTTAAGAAAATGTAATTGGCA
GGAGGTCTCATCTCTCTTGTTCCTAGACCGAAGTCTCCTATTAAGAGATCAGTCTTCATCCTTTC
CAATACGAACCTTTAGCTCAAGCTGGAGGATAAAAAGAATATTATTATTACGGGATATCCCTCTT
GTTCTATTGTATTCCCTCAGGCTGTAATGCCTATAGTTCCAACTGCCTTTCACTCTTCTTCTCTG
AATATATTATATTCTAGCTACCTTTCTCCGGCTAACGCGTATCCGTTTTCTTGTACTTATCAACT
GTTTGTCGAGATTGGCTTGGTCTTCCGCTACGCCCCTAAGCACTAGAAATGTCAGAAGCAAAATC
GTAACGTAGAAAAGAGAGGAAAAAAGAAGACAGACAGACTGAAGGCGATGGCTGGGAGGCGTGGT
TTACGAACGGTCCCGACTAACTAAAGTAAATTATCTTCCTATGAT
Found at i:87887 original size:21 final size:21
Alignment explanation
Indices: 87863--87904 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
87853 CTTCTTCCAC
87863 TTCTCTTTCTTGTGGTAGTCG
1 TTCTCTTTCTTGTGGTAGTCG
87884 TTCTCTTTCTTGTGGTAGTCG
1 TTCTCTTTCTTGTGGTAGTCG
87905 AATGAGGAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.05, C:0.19, G:0.24, T:0.52
Consensus pattern (21 bp):
TTCTCTTTCTTGTGGTAGTCG
Left flanking sequence: Indices 87363 -- 87862
ATCACCTATATAACACGAAAGGAAGAAAAAAGCAGGGAATACAAGCATTACGGGGAGTTTAAAAA
AAGAATATGAATATGACTCTTCTCAACTCAAGTCAAGCGAAGCGTAGTGAGGGGAAGAACTACTA
GAGAAAGGCTAAGCGAAGTTCTTCTCCAAATAGGTAAAACTCTTGGTAAACCTATTAAAATTGAT
ACCGGTTAAGTACATTAACAAGTAAGCAAGTAAACTACCTTCAATCCACTAGTATAAGAAAGACG
GTGACGAAAGTTGTCACAAATAAAACCTACTTCAACTGAAGGGTGATAAATCAGCCGTACTCTTT
CCCAATCCATGCTATCTATGGCGTGTAGAAATACACCAGCTGTAACCGACCAATACCTACAAATG
CATCTCAAGTAATTTGAGTTATTTTATTAGGCGGGGACAGGATTCGAACCTGCAGTCTTCAGGTC
ATGAGCCTGATGAGTCGACCAATTCCTCTACCCCGCTTCTTCCAC
Right flanking sequence: Indices 87905 -- 88404
AATGAGGAAGTATGTTGCGGCAACTAAAGAGTTATCGAGACTGACCGCAATTGCAGTAAGAGTTT
GACTTTCTTTCAGTTATGTAAAGTTGTTTAGTACGAGATCGCTTCACACCTCGCGGTGCTTACAC
CTCTCGCCTATCGAAGTTCTGTTCTAAAACCTCTTCCGAGAACTTGTATAGAGAAGGATTTCCCG
CAGAGCTGCAGTTCTTCCATACCAACTTAGCTGCCCGGCGCTGCTATTGGCATAACAACCGGTAC
ACCATAGGTTGGCCCAACCCAGTCCTCTCGTACTAGGGTTGGCTCCTCGCAGTTCTCCCTTTAAC
ACCAACGGTAGATAGGAACCGAACTGTCTCACGACGTTCTAAACCCAACTCACGTACCACTTGAA
TCGGCGAACAACCGAACCCTTGGGACCTTCTTCAACCCCAGGATGTGATGAGTCGACATCGAGGT
GCCAAACGACTCCGTCGATAAGAGCTCTTGGGAGTCATCAGCCTG
Found at i:89305 original size:18 final size:18
Alignment explanation
Indices: 89284--89326 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
89274 CAACCTTGTT
89284 GACTATGACAACAG-TCGC
1 GACTATGA-AACAGATCGC
89302 GACTAT-AAACAGACTCGC
1 GACTATGAAACAGA-TCGC
89320 GACTATG
1 GACTATG
89327 GCAGGGCGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 5 0.23
17 1 0.05
18 16 0.73
ACGTcount: A:0.35, C:0.26, G:0.21, T:0.19
Consensus pattern (18 bp):
GACTATGAAACAGATCGC
Left flanking sequence: Indices 88784 -- 89283
TACCGTCTAGCCGTTGGTACTCCGCATCTTCACGGAGAATTCAATTTCACCGGGTCCATGTCGGA
GACAGCGGGGCAGTCGTTACACCATTCGTGCAGGTCGCTACTTATGCGACAAGGAATTTCGCTAC
CTTAGGACAGTTAGAGTTACTGCCGCCGTTTACCGGGGCTTCCATTCAAAGCTTATAACACTTCT
CCTTCCGACCTTCCAGCACCGGGCAGGTGTCAGACTCTATACATCGTGTTACCACTTAGCAGAGT
CCTGTGTTTTTAATAAACAGTCGCTACCCCCTGGTATGTGCCGCTTTCCTAATCAAAAGATAGGA
GAGCACCCCTTCTCCCGAAGTTACGGGGTCATTTTGCCGAGTTCCTTCGACATGGTTCTCTCAAG
CGCCCTAGTATACTCTACTTGTTCACCTGTGTCGGTTTGGGGTACGGTCAGTTCACCGGGAGGAT
CGCCCTCCCAATTCGAAGTTTTTTCCTGGAAGTTTCAACCTTGTT
Right flanking sequence: Indices 89327 -- 89826
GCAGGGCGGTACGCTCTGCTCTCTCGCGACCCCTACTCTAATCAAAAGACTAAGGGCCCCTTAGG
TCGCCAAACTACGACGAGAGTTTCGCCTTTTGAAGCGCCAGTCGCGTAGGGCGACCGGGCCAGGC
CGAGTCAGAAAGGCTTTGATGACTCAAGGTTCATATTAGGGAAAGGAGAGTGAGGGGAAGAGGGG
GCAGCCCTCGGCCCGATCATCCAATTCGCTCCAACAGATAGGCATGGTTCTGTAGTCAAAGCAAC
TTCGTCACTTTCGTGTACCCATCGGACGGCAGCCCTTTCGGGGGTTCCTTAGGGACCGATTCACT
CTGCGTAGATTGACTGAACGCAGAAAGCCTTCCACTGGCAGGCGATCGTGTTTTTCACAGGATTT
ATCGTTACTCATGTCAGCATTCTCACTTCTGATATCTCCAGGTGTTGTCACCAAAAACCTTCCCC
GATTGACAGAACGTTCCGCTACTGACACTTGAAAAAGAAGCTTTC
Found at i:130847 original size:25 final size:25
Alignment explanation
Indices: 130809--130858 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
130799 TTCCCTACTT
** *
130809 CTGTACTTGGTTGCCTGTCTCTAAG
1 CTGTACTTCCTTGCCTGTATCTAAG
130834 CTGTACTTCCTTGCCTGTATCTAAG
1 CTGTACTTCCTTGCCTGTATCTAAG
130859 TAGGTACGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.14, C:0.26, G:0.20, T:0.40
Consensus pattern (25 bp):
CTGTACTTCCTTGCCTGTATCTAAG
Left flanking sequence: Indices 130309 -- 130808
GCTCGTTCGCTAAAGTCCTGTCTGCCTGCCCGTTGATTCAGTACGTTCCTATCCCCTTGGGAAGT
TTGATCAATCTTCCTCTCCCTCTCCCTTTGGTCGAGCAAGTAACCTCCCTTCTCCCCAAAGGTCG
AGTGAGTCCCTACCTTCGATGCCCATTTGTTGATTAATCTGGGGCGGTATTCATCCCCGGCTTTG
GTGCCTTTCCTCGCCCTCTTTCATTTGGTAATACCCTTTGATTGACTGCATTTGCTTATCCTGGT
ATATAGGTAGTGAACTTCTGTCCTGTCGTATTGTCCTTATTGAGTTATCCTAGCAAGAATCCCCC
ATCGACTAAGAAAGCTATGTATTGATTACTATAAGAAGGAAGCCCCGCTATCTATCTCTGCTTTC
CTGTCTTCCTATCTTTCTGCCTATCTGTCTTTCCTCTTTCTGCTTTGTCTTTCTCGCTGTCGGTA
GAGATTAGTATTTCCTAAGTTGTCTGAGGCTGAGCTTCCCTACTT
Right flanking sequence: Indices 130859 -- 131358
TAGGTACGTCTCGCTTCGCTCCTCATTTCCTTGCCGTCTTTCAATTCTGACTATTGAGAAATATC
CATGAGTCTGTCCCCCCGCGAGTAAATAAGCTAACCTTGGCTTCCCCTTCGACTGAGGCGGACTT
GAGCCTAGTTATTGACTTCCTGAACCTTAAACAAGTTATCAAAGAAGTGGATTTGCTCACAGCTT
CTCCTTCGTTCCTAGACCAACAGCTTAGCTTACCTTAGCCCAGCCGTACGTCCTACTGCTTACCT
TAGCCCAACCATAGGTCCTACAGCTTCGATGGCAGAATGATTGACCGGGCCGCTTGGCCCACTTG
AACTAGCAGCCCTACCTGCTGCCGTACCTGTCTGTGAATGAACTTCTGGATATTCACCTACCAAC
ACAACCCGGGCCACGCCGGGACTTTCTTTATCCATTCAATCAAACTAGGGAAGTGGTTAGAGAAG
CAGTAGCTGCTATGCGAGTTAGATCGGTCAAGTTTTGATGTAGAT
Found at i:131117 original size:30 final size:30
Alignment explanation
Indices: 131080--131144 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 30
131070 CCAACAGCTT
* *
131080 AGCTTACCTTAGCCCAGCCGTACGTCCTAC
1 AGCTTACCTTAGCCCAACCATACGTCCTAC
* *
131110 TGCTTACCTTAGCCCAACCATAGGTCCTAC
1 AGCTTACCTTAGCCCAACCATACGTCCTAC
131140 AGCTT
1 AGCTT
131145 CGATGGCAGA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.22, C:0.37, G:0.15, T:0.26
Consensus pattern (30 bp):
AGCTTACCTTAGCCCAACCATACGTCCTAC
Left flanking sequence: Indices 130580 -- 131079
GAACTTCTGTCCTGTCGTATTGTCCTTATTGAGTTATCCTAGCAAGAATCCCCCATCGACTAAGA
AAGCTATGTATTGATTACTATAAGAAGGAAGCCCCGCTATCTATCTCTGCTTTCCTGTCTTCCTA
TCTTTCTGCCTATCTGTCTTTCCTCTTTCTGCTTTGTCTTTCTCGCTGTCGGTAGAGATTAGTAT
TTCCTAAGTTGTCTGAGGCTGAGCTTCCCTACTTCTGTACTTGGTTGCCTGTCTCTAAGCTGTAC
TTCCTTGCCTGTATCTAAGTAGGTACGTCTCGCTTCGCTCCTCATTTCCTTGCCGTCTTTCAATT
CTGACTATTGAGAAATATCCATGAGTCTGTCCCCCCGCGAGTAAATAAGCTAACCTTGGCTTCCC
CTTCGACTGAGGCGGACTTGAGCCTAGTTATTGACTTCCTGAACCTTAAACAAGTTATCAAAGAA
GTGGATTTGCTCACAGCTTCTCCTTCGTTCCTAGACCAACAGCTT
Right flanking sequence: Indices 131145 -- 131644
CGATGGCAGAATGATTGACCGGGCCGCTTGGCCCACTTGAACTAGCAGCCCTACCTGCTGCCGTA
CCTGTCTGTGAATGAACTTCTGGATATTCACCTACCAACACAACCCGGGCCACGCCGGGACTTTC
TTTATCCATTCAATCAAACTAGGGAAGTGGTTAGAGAAGCAGTAGCTGCTATGCGAGTTAGATCG
GTCAAGTTTTGATGTAGATATAGTCGCCCTCTTCTCTATGTCATAAAGTCGCTTATAATTAATGG
TTGTTCACTTCAGATGTGATACGTTGTTCACTTCGGATGTGGTGGATGAACCCTGATCGATGCGG
TTCAGGCCGTTTGATTGAACTACGCTAAGCTGAGACTTTCTCTTGTGCTTCGGGCGATCATAGTG
GATTTGATAATAGAAATAGCGAGCGGTCCGCCTTCCTTCTTCGCCTTTTCAATTTCAAGTAATGA
TAGGACTCATGGGCCAAAAGGATATTGTCTTGAATTTGTCTTTCA
Found at i:137705 original size:22 final size:23
Alignment explanation
Indices: 137666--137711 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
137656 CTTTGAGACT
**
137666 TTCTTCTCTTTGCTAGAAT-CGC
1 TTCTTCTCTTTGAAAGAATGCGC
137688 TTCTTCTCTTTGAAAGAATGCGC
1 TTCTTCTCTTTGAAAGAATGCGC
137711 T
1 T
137712 GTGATCTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.17, C:0.24, G:0.15, T:0.43
Consensus pattern (23 bp):
TTCTTCTCTTTGAAAGAATGCGC
Left flanking sequence: Indices 137166 -- 137665
CGGAAAGGAATGGAATTTCTTTAAGCTTCACTCCGCTATCAGACTAGTTGCGAAGCGTTGGGATA
ACTAAAGTGGAATATGCCTCAACTAGTTGCCCAGGATGAGGCCATTGCAGCCACTAGCACGGCCA
AGTCACCAACCTATGGCTCCGGGGAAGCCGGCAGGGAGGAAGGATGATAATCCAACCAAAGGAAT
TAGCCACTCGTTCTATCAATAGGCGCCGTGGGCCTATGAGCTTCTGGGCCTGTACGATTTCCTGT
CCTCAACAGTTCAAAACGCTTGACACTGAGAGCTTTGGTGAATATTTTGCCTTTTGGTTATGGAG
TCTTTCCTTCCTTCCAAGCCGCTTTCAAAGCAGTAGGCAGTCTCTTCTTTCTTCTTATACGGTAG
CCAGTCTTTTTTAGAATGGTTGAATAGAGCCTCCCTTCTGTCTCCCAGTCTGTCTTATAAGAAGA
TAGTAGTAAGTCAGTTGTAGGTTTACGAATGGCTTCTTTGAGACT
Right flanking sequence: Indices 137712 -- 138211
GTGATCTTTTCAAGTTCATCCTAGCTATCATCTCAATCATTCTTCATTCACTTCGAGCCCTCGGG
TAGTTTTCTCATCCAGGAGAGTCGTCTTAGAGGCGGTCTCCTCCCTGTCCTTCTTAGATGGTATC
CTCTCTGTCCTTCCCCTTTCCCGGACTCGAGAACCCCTGAAGCGCACTGGAAGCATCTCAAGGAA
AAGAGAGAAGTCAAATATCGTAGGCTTTAGATAAGATTCCCTAGTAGATAGCTAAGCTAAGAGAG
TGCTCCGGAAGAGCTAATATTCAAAATTCTTTCCCTTTCTTTCACCGAGGAGGCTAACTAGATAG
ATGGTGGGTCTAAGGAAGAGAAGAATATGAGCTATATTTTCATCCCCTTTCAGTTCCTTTCCTTA
TCCTTAGAACAGTAGGGTTTGAAGCTGGCAAAGTCAATCAATCCAGCAGTCAAAGGGGCAAGTGC
AGTCACTCAACCAACGCCTTTCAAGCAATATCTTAAGTAGGGGTA
Found at i:169591 original size:47 final size:46
Alignment explanation
Indices: 169505--169596 Score: 123
Period size: 47 Copynumber: 2.0 Consensus size: 46
169495 GAAGAGAATT
169505 TAAGATAATACCTTTACACTCCTTTAGCAGTTACCAACAAAACAAAC
1 TAAGATAATACCTTTACACTCCTTTAGCAGTTACCAAC-AAACAAAC
* * * *
169552 TAAGATAATAGCTTTACACTGCTTTAGCGGCTTA-GAACAAACAAA
1 TAAGATAATACCTTTACACTCCTTTAGCAG-TTACCAACAAACAAA
169597 TTGGATTAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
46 7 0.17
47 30 0.75
48 3 0.08
ACGTcount: A:0.41, C:0.22, G:0.11, T:0.26
Consensus pattern (46 bp):
TAAGATAATACCTTTACACTCCTTTAGCAGTTACCAACAAACAAAC
Left flanking sequence: Indices 169005 -- 169504
AGCAACACGCCCCCCAATCACGCTGCCTGTGTGAACAAACAAACTTTGCACAACCAGCTTTAGCA
GTTCCGCCTAATCGATCGCTGTGAAGTAAGTAGTTCTGCTGGCAGACCGTTTCGTGTTTGTTGTA
TAACGGGAGGAAGAGGCGCTTGCGAACCCCTTACTACCACGAAGTGGTGTTCTTCGTTGTAGTAT
GTAAGAAATGTGACCCAAAATGCTTCTTGTTTTTGACAAAGGAGTTCCAACGTTTCCAAAACGCT
TCCCCGCGGGCGGGCCCAAGCTTAGTCCACTACTCAACTCAGGTTAGCAGGTGCTCGTGCATAAT
GAAGCCGACCCCCACTACTGAAGCAGAACCACCCCAGAACGGGATTTACATTAGCTTTTCACCGC
GGGGGAACTGATAAACGCTTATGGGAACAAAGATTAAAGATTAGGTATTGATTAGAGAAAGAAAG
AAATAAAAAAACTTAGTTACATAGATTAACATTTAGAAGAGAATT
Right flanking sequence: Indices 169597 -- 170096
TTGGATTAAAATTAGAAAGATTTTACTTTGCGTCGATCAACAAAAAAGAGACAAAAGGCGGCGAA
TCTAAGATAAACATTTGTCGGAGAATCCGCTGAAGTAGCTCTTTTGATATAGCCTCTCTATGGGG
GAAACAATAAGATGAGTACTTTGGGTACTTCTTTTTAAAATTATTGCATGTCATTCATATAGACT
CTATACCACTAAAGCAACCAAGCAAGAAGCTGACCAAGCCGAAGGGCTAAGACTTTTTCAACAGG
CGCTAACCGATTCCAAAGATTCGAAAGCGAAAGCGGTTCCCTCATAAGCAAGTAAGAATGCTTTC
ACCCCCCGGAATCACATCCAGATAAGGAAGCTTGTCAGGTAATAGCATTTGGTAGTCTATCTCAT
CCGAACAACTTGGAATGTGCTCATCAAAATTAGGGCTTATTTCGTTTTGCAGGTATCACCCGGAG
GCAGCTAAACGGCGATTTCTCTGATAGCAACCGGGATACAAATAA
Found at i:179262 original size:19 final size:19
Alignment explanation
Indices: 179238--179275 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
179228 GGAGTTTCCA
*
179238 GCAGTAACCCCAAAGGGTT
1 GCAGTAACACCAAAGGGTT
179257 GCAGTAACACCAAAGGGTT
1 GCAGTAACACCAAAGGGTT
179276 TCAGATTCCG
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:0.24, G:0.26, T:0.16
Consensus pattern (19 bp):
GCAGTAACACCAAAGGGTT
Left flanking sequence: Indices 178738 -- 179237
CTCGTTCCTAGGAACTCAGTAACGTGGCCAGTAAGTCAGCGAGCATTGAGGCAGGCAGACAGATA
TTATTAACTGCTTTAAGTCGGTAAGGCAAGGAAGGCGGATTTCACCGATCATTCCTACTTGACGC
TTTGGACGAGTATTTTCAAAACCTTAGTTCACTATCATTAAGGGAACTTCTTGGATCGCCGCTTT
GAGTCTTGTCTTAAGGCGACGGAAGGCAGAAGAGGGAAAGTCGCTCCTTAAATACGAGGAGTTTC
AAGAACCCGGCTGATCAGTGTTCTGTTACTAATATGTTGATGACTTCGGCCAGTTCCTCGGTTAA
GTTGCTTAGCATAATTGGTAACTACATGGTGTTGCTGCTATGGCCCTGGAGAGAGATTCCTACTT
ATACCGGGCAGCTCTACCAGCACTAAATTCCCTTCTTTCCGACCAGGACGTATGTTTCTTTAGCT
TGTATATCCTCTTACCATGCAGAGTTATATGTTCAGGAGTTTCCA
Right flanking sequence: Indices 179276 -- 179775
TCAGATTCCGGACTGATCTCGTAGTCGGCTAGCTCATTCGAGCGTATCTCGTTTGGCCTCTTTTT
CTCACCCTTACCTTTCCATTTCAAGCTTCATATCCTACTAATAGCCCCCCTTGTCGTTGAATCTC
TTGTAGAAACCACCATTGAATAAAATCAAAGGGTTAGTCTTCTTTGATAGAGGAAAGGTTGAATG
CTGCCCCCTTCCTCTGACCCCGAATCATTCTTTCAACCTTCGGCCAGGCGCCTAACTAACCTAAA
AATTCGGAAGCTCCTGAAGATCTGACCGAAATCGGATTTACTTTTCGCGCCAGATTTGTTGAATG
GCCTAGGAGTGAAGTTCAAGGGCTTGGCTTTTTGGCTCAGATTCCGTATCGGCTGTTTGTTCATC
AAGCCTATTCTCGAGCCTATATCTACTCTCTTTTCTTTTAGAGGCGTACCTCTCCACGAGATCGA
ACACTTTACCAAGGATTGAATCCAAAAGCAAGAACTCGGTTGACA
Found at i:183013 original size:14 final size:14
Alignment explanation
Indices: 182994--183020 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
182984 CAGCTTATCG
182994 TTAGAACGCTTTCA
1 TTAGAACGCTTTCA
183008 TTAGAACGCTTTC
1 TTAGAACGCTTTC
183021 TCGCGGGCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.37
Consensus pattern (14 bp):
TTAGAACGCTTTCA
Left flanking sequence: Indices 182494 -- 182993
GCGGGGACAGAGAAGGATAACCTCTTTGAAAAGGACAGAGCCGCTTGGCCGCTACTTACACATCT
GGAGTTCCGGACTGAACTACGGAACGGAATTCAAGGGCTGGGCTTAGAAGCCCCTTAGATAGCAC
TTCCTCTATGAATAGAAGAGATTTTCTTTCTAGTAGAGCTCATCACGACCATCATAACCTAACTC
CAGGACTGCTACGGGCACTGATCCTTCTATTTTCTATTCAAAGTTTCGTTTCTCCTGTTGAATGT
AGTTTCTCCGGAAGCGAGCTACTGACTAGCGGCAATCGGGACGGAGAGAAGACTAGAAAACTCCG
GAAGGCGCTAACAAACCGACTCTGCTTACCTACTGAGCCCTTGAACACTGAATCCTATACTATAG
AAATGGCATTTGACCCACTTCCTTCAGCTTGCCTAAACCGTCGGTAGCGAAGGGGAAGGGTCGGT
CTGTCATTCTGTCCTGAGAGTTTAGTAAGGACTTTCAGCTTATCG
Right flanking sequence: Indices 183021 -- 183520
TCGCGGGCAAGGATAGCTGTCCAGGGCTTTCGTCTCGGGGTAGCAACCGAATCTTAGAAAAGCGC
AGACGGGATTAGTGGGAAGGGCTTGGTCGATAGAGATTGCTTTTTCTTTAGAATCCCTATGGAAT
TGGGCGAGGAACCCTCTTCTACTCATTCATGGGCTAGGCTACTCAAGGGTTGCTGACTCTGATAT
TGATTCTCAAAGTGGGCATCCTCCAGCTGGGTCTCTAGTCTTTCTCATGTATTCACTTTCACTTT
CAGCAAAGAGGTTTCAAGCAATCGAAGGAGCAATCCGTGGCAGCTCAGCTCGCTTCTCACCCTAG
TTACACAGTCCTCTTTTTTAGGAAGAATAAGAAAAATCTTACCTCCGTTTTCAAGTTTCAGTCTT
TCCAGTGGGCAAGCGAGTTTCCCTCTTACTTAAGTAAGAGTAAGCTCCCATCGAAGGTAATTTAT
TATTCTCAGGCGAAGGGGAAGAACAAGCAGCGAAACGGTAATAGG
Found at i:184268 original size:18 final size:17
Alignment explanation
Indices: 184241--184281 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
184231 GGTTTTACTT
* *
184241 TCTTTCAGGGTTTGACC
1 TCTTTAAGGGTTTAACC
184258 TCGTTTAAGGGTTTAACC
1 TC-TTTAAGGGTTTAACC
184276 TCTTTA
1 TCTTTA
184282 TGTAATTGGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.17, C:0.20, G:0.20, T:0.44
Consensus pattern (17 bp):
TCTTTAAGGGTTTAACC
Left flanking sequence: Indices 183741 -- 184240
AGCGATACTAAAAATTAGGCAAAAGCAGAACTAGAACTCGAATTCTTCGCCCCTCCCCTTGTACC
AAGAAGCAAGTTCAAAACAGAAGGATAATGGGCTCGTCTATTATAAGTTATTAGTTGACGGGGCT
ATCTCAGATATCTCGAGTAAGGAAACGGGCTTGATGGGGAAACATAATCGATTTCATAGGAAGAC
GTGCGCCAATCCACTTCTTTTCGAACGGTGAAGAAGGAGAATCGAATAAGTCAAGGCGGTTCGCT
TCCTCTGCTCTGGCAGCTCCTTCAGCTAGCAAGCTATGTTGGTTGGGACATTTCCAATCTCCACC
GGCTATTAGTAATCGCCGTTTGTTCTCTCTTCTCGTTTGGGATCAAAAAGAAATGAGTCCTTTGC
CCTTCTCTGGGCCTCGTCCGCCATGGGCGAGTAGCTACATCTTCTTTACAAGTTAGCTCGCAAAG
CGGGCTGGATTGAATCCATAGTCTTACATTTAAGTGGTTTTACTT
Right flanking sequence: Indices 184282 -- 184781
TGTAATTGGTTAATTGAAAGGAAGGGGATGTAATGAGGTAAAATACAGTTGGTTAACCTTGTTCC
TCATTCCCTGGCTGCTCTGCTATTGTCTGATTTCTGGTCTTCTATTCTAATAACAAGTTCCATCC
ATGATTACTCTATTTCGAAAGTTGTGCTTACAGTCCGATCCTATCGTTCGAAATCATCCCATTTT
CGTAGGTCCGTCCTATTCCGACTCGATCGCTCCACCTTTCGAGGGTCGAGTTCGTGTTCACGGCT
CCGACTCGGTCTGTCCTGTGACCAGTCGTATGCCGCTTCCGTTCCATACACGTACCCGTGGTTGG
CGTGCTCAAGCACCCCTTTGGTTTCGTGTGAACAAGAGTCCCATTTCTTCTGCTCTTCCGGGTAG
TCAAATTTATATCCAGGATCCGGATACAGGTGACAAAGCTGTGCTGACTTATGGCTTCTCTCGTT
GGATACCTTACGCGATCAGGAGGTCCCAGCTTCCGTTCGTGCTTT
Found at i:227840 original size:19 final size:21
Alignment explanation
Indices: 227806--227868 Score: 117
Period size: 21 Copynumber: 3.0 Consensus size: 21
227796 AGAAAGGGTC
227806 CATAGGCTTCTCTCTCAAGAA
1 CATAGGCTTCTCTCTCAAGAA
*
227827 CATAGGGTTCTCTCTCAAGAA
1 CATAGGCTTCTCTCTCAAGAA
227848 CATAGGCTTCTCTCTCAAGAA
1 CATAGGCTTCTCTCTCAAGAA
227869 AGCGGGTCTT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.29
Consensus pattern (21 bp):
CATAGGCTTCTCTCTCAAGAA
Left flanking sequence: Indices 227306 -- 227805
ATTTTCTCGTTCATGATCTCTAATCCTTTGAGTAGATTGGGCAGGGGTAAGACTATGCACATAGC
TTCGGTTCCGTCTTGTTTGCCAAGGAGATATGGTTGCTTTTCCTTCTTCAGTAGGCTTTCCCGCA
GGTTCGGTTACAGATAGGATACGCGGGTCAAAGGGAAGGCTTGAGTTCAGAGACGAAGTTGGCTT
TGAAGGGACAAACTTTCAGACAGTTCCTTACTTTCTATTCTCTAATCTCTCGCTTCCGACTCCTA
TATTGAAACTCTAAGGTACGAAACTATATATTTAGTCTCTGTCCCGGACTACACAAATTCCATAA
ACCCCGTGTTTTTTGATGCAAATTGTGTCAAGAGAGTAGTTTCCGCAAGATATTCCATAGGTGGA
TTTAAGCGGAAGATCTGCGTGATCTGATCTTTCTTGAGGACTAGTAACTGGTCCTGTAGCTAGAA
GTCCCCATGAGCTCCCTCAATTCCTATTGAGATTGAGAAAGGGTC
Right flanking sequence: Indices 227869 -- 228368
AGCGGGTCTTAGTGGGTAGTATAGTGCCGTTCAAGCGTACTCCCTGCGGGTAGGGTCTAATACCC
CTTATTGGCATGAGGAACTGGGCTCCCAATTCTTCATCCTCCTTTTTGAGCTGTAAGACCAGGCA
AGGGATCCCGCTTAGTGGGTTCGAGTTCAGTAACAGAACCTCCTAGCCTGCCCTTTTTTAATAGA
TATCTAGGGTTGTCGGCACCCTTCCTCTCCCTCTCCCTACCTTTGGTCGAGCTAGTAAACTTCCT
CAACTGGAGAGGGAAGAATAAGCTGCAAAGCTCTGCTGGTGAATAGCAGATGATGCTCGATTAGG
TATGCCAATCCGGCTGAAGGCGCGTGTCTGATGTTTCGGTAGGATGTTGCTATGTCCGCTTTCAG
CCCGTAAATCGAAGGCTGTTCTTCCCATAAGGGGGATGACGTTATAGGGTTAAAATTAAAGAATC
TTATAGGTGGAACTAGACATCGAATAAATATTCGTGCATCTCCTA
Found at i:233179 original size:15 final size:16
Alignment explanation
Indices: 233137--233179 Score: 52
Period size: 18 Copynumber: 2.6 Consensus size: 16
233127 TCCTACCTTA
233137 ACAGTCGATCATGCGCTC
1 ACAGTCGATCATGCG--C
*
233155 ACACTCGATCATGCG-
1 ACAGTCGATCATGCGC
233170 ACAGTCGATC
1 ACAGTCGATC
233180 TGTCCATCCG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 9 0.39
18 14 0.61
ACGTcount: A:0.26, C:0.33, G:0.21, T:0.21
Consensus pattern (16 bp):
ACAGTCGATCATGCGC
Left flanking sequence: Indices 232637 -- 233136
GCCACATAAGAAGCTTTTATTGACCTTTTTTGCCTTTCCTCCGTCTTCGTCACCTGATGACTTTC
CTGCTTTACTTTGTCGGCTTTGGTAGGGTGGTAGCATGTCCTTTAGCAAGGCTAGGCACCTTCCT
TAAAGGAGGCAGCATCCGATCTTTAGCATCCTAGCCAGGGAAATCCCCAAATCGCGAGTCCGGGG
CATATACTTTTTCTTTATCCCCCAGAGAATCCGACAAGAAAGAAGATAAAATAAAGTACATATAT
ATGGGCAAGATCCATATTCCATTTCTAACAGTTCCTTACTTTCTATTCTCTAATCTCGTATGGCA
GCTTTCAGTCTCATCTTCAGTTTCGGGACATTGTTCCTATGCCTCTTTGAAGTGAAGCCCTTATA
TCGAATGATTCAAGACATTTGATTTTATAATAGAAATGAGAGGACAGCCGAATTGACAGAAAATA
GTCTGAACTTGTTGATCAACTCTCTTTGTTGAAGGTCCTACCTTA
Right flanking sequence: Indices 233180 -- 233679
TGTCCATCCGACTACATTCACTGGGGGGTGAGGTTGTCCAATTTCAATTATGTGCCGCTCGTTGA
CATCTAGTTTCCATTGCCGGTGTGAGAGATCTTCCTTCGGTTCTAGTCAAGTATGGCAGCTTGAG
GTCTCCTATTTAACTTTCACCAGCCATTGGGAACTCAAATAAACTTTCATTTAACGGCAGGCGAG
AAAGGTTCTGAAAGAAAGAAAGGTAGAAGGGGGGTTTGCTCCCGTTTCGGGGTTCTCTTGTGGAC
TGGCTGTTGACTGGCCTTTGCCTGGGGAGAAAACCGGTGCTTTTAGCTTAAACGGATTTTAACTG
GATCGGAGCCTTTCGGAAATCCTCCCTTTTTGGCTTCACTTGAGCGGTTGACGCAATCCAAGAGG
AAGAGGAAGCTAAACCCGTGCTGACGAATAACCAAACCCCTTAATTCGTCGAGTAAAGTAAATAG
GGAAGGTATAGGTTTGCTATGAATGACCCAGTATCGAATACAGGT
Found at i:244208 original size:20 final size:22
Alignment explanation
Indices: 244183--244223 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
244173 GCCGGACTCC
244183 TTGTACCAG-CT-TTCCTTATA
1 TTGTACCAGTCTCTTCCTTATA
*
244203 TTGTACCTGTCTCTTCCTTAT
1 TTGTACCAGTCTCTTCCTTAT
244224 TCGGATGAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
21 2 0.11
22 8 0.44
ACGTcount: A:0.15, C:0.27, G:0.10, T:0.49
Consensus pattern (22 bp):
TTGTACCAGTCTCTTCCTTATA
Left flanking sequence: Indices 243683 -- 244182
TCGAGCCGGGTAACCCATTGGTACTATCTTCCCCTTGCTCGACTTGGCCCGGCGAAGTTCCTTGG
CTAGCCCATTTTTATTTGTAAGAGGTGGTAGACGTCCAGGGATAGGAATCGCTCCTTTCGGGTCG
GTTCCTTGGCCGAGGGGGTCCTGTCATCATGGGTAGTGAATGGGGTTGAATGAAGCCGGGATCCG
CGGACATCAATACATCGATTCTACGGCAGTTTTTCTTCGTTCTATCGCTACTTCGAAACCGCTCT
AAGTTCTTTTCTTTGCCAAGCGGCTTTTAATTTGTAAAAGGCCTCGTATAAGGGGTAAAGTGAAG
AGGGAGTAGGAGCTAACCATAGTGATATGAATGTCCGATCTACTTCTATATGCAAGTAGAACGTG
GGTGCTCCCTTTGCCTGCTGACCCGAAAATTACCAATACGAACTTGTCGGGTTAGGCTAGGCTGT
GTTGCTTGATGAAAGAAGCTGATCTGGGTGGTTCAGCCGGACTCC
Right flanking sequence: Indices 244224 -- 244723
TCGGATGAAGGTGAGTGGCAAAGTATGGTTCAACTAAGGAGTAGGTCGTCCTATCTGATGGAGCG
GATAATGATCAAATTATTTTGTTCTTACTTGGGCTGCGGGAAGTCTCTCTCATGCCGTGCTATTG
CTCCTGATGTGGTAGTGGACCTGCTTTGTCCTTAAAAAATATATATATAAGGGCTTCCGTTTATG
GTTGGGATCAATTACCGTTGGAGGTGACTCTAGTGACAAATTTATCTGTACGCTCAATCGCCGCT
AAGGGCTCGCTGTATTCTTCAGAGTTGTGAAAGTGGGTTGTTCAAAGGGGATCTACAAGCTGGAT
GAGTTCAGAATCCCGCGAAGTCAGGTTCGGAATGGAAGTCTATCTAATATAAATAGGCTAGCTCG
CCCGACCATAAAGAGCAACACTCGCCAGGCGTGTAACAAGACTAGGAAGAGGCCTCAGCCTCAAT
CTATATGGTGAAAAGGTCTTGCTGAAAAGCTCTTCGAGGTAAGTA
Found at i:314733 original size:17 final size:17
Alignment explanation
Indices: 314711--314747 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
314701 GCACAGATTC
*
314711 CCTATAAATAAAAATTT
1 CCTATAAAGAAAAATTT
*
314728 CCTATAAAGAAAGATTT
1 CCTATAAAGAAAAATTT
314745 CCT
1 CCT
314748 CTCTTCCCCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.46, C:0.16, G:0.05, T:0.32
Consensus pattern (17 bp):
CCTATAAAGAAAAATTT
Left flanking sequence: Indices 314211 -- 314710
TTTCATCTCTTATTGCTCCAGCTCCTAAGGAATGAGATTAGCTTGATTACGCACCAGATTTACTT
TTAGTTACTGAAAGCGCTGATGAACGATCTTCCTTATTTTAGGATGCAACTCGGATTCCTCCTTC
ACGGCTTGAAGCCGGATAGCTTGAAGCTTAAGGGCTCTCGGAATTCCCTTTCAAGCTTTCTCGAG
TCACCCTAACGTAACGGCTAAGAGAACTTGGCTAACTTCGATCAATTCCACGACTTTCCATCCTT
CTTGTGTTGTGAGAGTTTCAGATTAAGGGGATGCGAGTCATCAGTTCTTTCCTCCTAGTCTAGGC
TTTAGGCCTGATAGTTCATTCTCGAGGATCACTGAACTTGGCTTACTTCTTACTGAATGCCGTAC
TTAGAGTTATCCCACTCGGGGTGAGCTCTTAGCGATTAGTCAGTCCGGGTCCAGCTAGTCTTGCA
CTTTCAGACCGGTCCTTCAAACAAAGGCTTAGTAAGCACAGATTC
Right flanking sequence: Indices 314748 -- 315247
CTCTTCCCCAGAATTAGAATGCTTTCCTTAGCTAATACTGATTGATTCACCGCATCTTCTCGTTC
ATTACATTAGGAGATCTAACCAAGCACTCGAAATGCGACATTGACTAAAGAAGGTAGACAAAAAG
GCAAACTAGAGAAAAAGCCAAGCTGACTGAATTAAATATGTAAGCGGATTGGTGTGGAACTAGAT
CCTCTGTTAGAGTTACAGTTGTTGTGTAGCCGGGTTCACCCCCAATGATACGAAGGGCTAGCTTT
GCTACCCGAAAAGGCTACTTGCTTGCGGGACCCTTTCGTTTTCGAGTTTGCCCATACTTTTTGTT
TGAACAGATATTATGTTAGTGTTCCGTCTTAGGTCGAAAAGAAAAAAGAATTGCGTAAATAACTC
GTCAGAGTCACGATCTACTAAAAGGCAAGTAGCTTGATTGGTTCGAATCCAATTCGTGAGATGGT
TTCTTTTCTTCTTTTTTTCCGGTATGCCGCTCCGCGAACAAGGAG
Found at i:352878 original size:19 final size:19
Alignment explanation
Indices: 352842--352896 Score: 62
Period size: 17 Copynumber: 3.0 Consensus size: 19
352832 ACTAAAGGGG
*
352842 TTATGAGTTAGAAG-AGTTA
1 TTATGAGTTA-TAGCAGTTA
352861 TTATGAGTTATAGCAG-T-
1 TTATGAGTTATAGCAGTTA
*
352878 TTAAGAGTTATAGCAGTTA
1 TTATGAGTTATAGCAGTTA
352897 GGGAGTTATG
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
17 15 0.48
18 4 0.13
19 12 0.39
ACGTcount: A:0.35, C:0.04, G:0.24, T:0.38
Consensus pattern (19 bp):
TTATGAGTTATAGCAGTTA
Left flanking sequence: Indices 352342 -- 352841
AAAGTTAGGGGAGCAGTGTAACTGCCATCAACTCCTATAACTCTTTTCCTTAAGTTTAGGTTAGT
TCCCTCTTAATTAGGTATTCTGCAGAGTTCCGACCTAGAACTCCCTTATAAACTAGAAAGCTAAC
TCGAACTCGTAACTCAATTAATTTAAGTTACAGGTATGATAAATATAAGTTACTGTTATTAGGCA
CATCCTTCTTTCTTGTCCTTGTTGGGGAATCCTATATCTTTTAAGAAAAAAGAAGTTTTAAGTCC
TCTCCTTTGCAGTCGAGTTACTTTATTCCTCATAGCTTCACTCTTTTCTTTTAGTTCCCTACGGG
GTTAAGTTAAAGTCTTATTATTATTGATATTCCCCCTACGGGGAGGTTACCGTTATTATTATTAA
TAGAATTCTAATTAGTTACCAGTAAAGTATTATTAGGTATTAAAAGTCTTTTTAGTTAGGGGTGT
AACTGGGGGGTCTGGGGGCACTCCCCCGGAACTAAACTAAAGGGG
Right flanking sequence: Indices 352897 -- 353396
GGGAGTTATGAGTTGCTAATTGTCATTCTCTTTAGTTCCCTACGGGGTAGTTACAGGTATGATAA
ATATAAATCTTAGTTACCGGTATTAGAAATATAAGTAATATAAATATATTGGTAGTTACAGATAT
TCTTAATTTGGTGGAACTGGGGGGTCTGGCGCAGTGTAACTGCCCCCGGAACTGGTTTAAAGAAG
AGTTAATTGTCTTAATCTTTAGAAACTAATAGCTAGAAAAACAGGCTATTCCATCTAAGGCATAA
CATGAACCGAGGAATCCAACCAAATAGGAATGAATAGGCATGTGGGAACAGCATTGCTTGCATTG
ATTCAATTGATTTGAAGCGGCGGTTATACTATACATACAGACATAGTTTTCACTAGGGGTTTTTA
CCGAGTTGGTCACAAGCCCGTCAGAAGCAACCTCAGCAGAAAGCCACTCTTCCAGAGTCTCGTCC
ATCGTCTGCTTAGGCGACTATTTAATAGCCTTTAGATCTGCCTGT
Found at i:383178 original size:39 final size:39
Alignment explanation
Indices: 383121--383199 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
383111 CCCATCCTTC
* *
383121 AATATCATGATTGGGTCGACCAGGCCAGATCATGAGTGA
1 AATATCATGATCGAGTCGACCAGGCCAGATCATGAGTGA
383160 AATATCATGATCGAGTCGACCAGGCCAGATCATGAGTGA
1 AATATCATGATCGAGTCGACCAGGCCAGATCATGAGTGA
383199 A
1 A
383200 TAGAAAATCG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.22
Consensus pattern (39 bp):
AATATCATGATCGAGTCGACCAGGCCAGATCATGAGTGA
Left flanking sequence: Indices 382621 -- 383120
CTCTCAGCGATTCTTTTCTCCGCTAATCACCCCCGCCCGATCGATTTTGTAAGATCGGCTAATTC
AAAAGGGTTAATCTGGTCCGAAGTTGTCGGAACGACTCGTTTGCTTTATCGAACAAAGCTTGATT
AGGGTAGGGGTCTTGGTTGGCCCCCTATTTTCAACCATTACAGCTGGCGTCGACCAGCTTTGCGA
TACGGACGGACACGAAGAAGAACGCAGGCAGCGGAAATGCAAAAGAGAAGAGCAAAGATTCCCGA
CCCAGAGCATGTTATTGACTCAACCACAAATCTGTTGAATGAAGGTAGCTTGCTTACTCTCAGCC
ACTAGTTAGAAGGAAATCCCTTGACTTCGCTTATGCCCTTATGGCCCTTATGCAGTACAGAAAGC
AAGTGAGGCGGGCTAAGATTCCATTCGAAGTAAGGTAACAGGATTCGATGTTGCACCATCTTCAA
CTCTTCTCTGGATCCGGAGTTTTTCGAGAAAAGGTCCCATCCTTC
Right flanking sequence: Indices 383200 -- 383699
TAGAAAATCGAAAACGTACATAGCTGTTCCAGCCGAAATACTTGGAATAATTCTACCACTTCTAC
TAGGAGTAGCCTTTTTAGTGCTAGCTGAACGTAAAGTAATGGCTTTTGTGCAACGTCGAAAGGGT
CCTGATGTAGTGGGATCGTTCGGATTGTTACAACCTCTAGCAGATGGTTTGAAATTGATTCTAAA
AGAACCTATTTCACCAAGTAGTGCTAATTTCTCCCTTTTTAGAATGGCTCCAGTGACTACATTTA
TGTTAAGTCTGGTTGCTCGGGCCGTTGTACCTTTTGATTATGGTATGGTATTGTCAGATTCGAAC
ATAGGGCTACTTTATTTGTTTGCCATATCTTCGCTAGGTGTTTATGGAATTATTATAGCAGGTTG
GTCTAGTAATTAGGGGGCGGCCGTTCGGTCGCCTATGATACTAGGACCAATAGGTCAAAAATGGG
TTTGTGCCGCAGGTGTTGAACGATCCACTCTACACAGGTGTGGGC
Done.