Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_065039
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: 493958
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Found at i:24548 original size:32 final size:32
Alignment explanation
Indices: 24507--24572 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
24497 CATCTATTTT
*
24507 CATTGTTCAACTCTTTGACAACACGAAAAAAC
1 CATTGTTCAACTATTTGACAACACGAAAAAAC
*
24539 CATTGTTCAACTATTTGACAACATGAAAAAAC
1 CATTGTTCAACTATTTGACAACACGAAAAAAC
24571 CA
1 CA
24573 AAAGCTCTGC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.42, C:0.23, G:0.09, T:0.26
Consensus pattern (32 bp):
CATTGTTCAACTATTTGACAACACGAAAAAAC
Left flanking sequence: Indices 24007 -- 24506
TTGGGCTGTTCGCCCATTAAAGCGGTACGTGAGCTGGGTTCAGAACGTCGTGAGACAGTTCGGTC
CATATCCGGTGTGGGCGTTAGAGCATTGAGAGGACCTTTCCCTAGTACGAGAGGACCGGGAAGGA
CGCACCTCTGGTGTACCAGTTATCGTGCCCACGGTAAACGCTGGGTAGCCAAGTGCGGAGCGGAT
AACTGCTGAAAGCATCTAAGTAGTAAGCCCACCCCAAGATGAGTGCTCTCCTATTCCGACTTCCC
CAGAGCCTCCGGTAGCACAGCCGAGACAGCGACGGGTTCTCTGCCCCTGCGGGGATGGAGCGACA
GAAGTTTTGAGAATTCAAGAGAAGGTCACGGCGAGACGAGCCGTTTATCATTACGATAGGTGTCA
AGTGGAAGTGCAGTGATGTATGCAGCTGAGGCATCCTAACAGACCGCTTAGGCTTGAACCTTGTT
CCTACATGACCCGATCAATTCGATCAGGCACTCGCCATCTATTTT
Right flanking sequence: Indices 24573 -- 25072
AAAGCTCTGCCCTCCCTCTCTATCTATCCAAGGGATGGAAGGGCAGAGGCCTTTGGTGTCCCCTC
CAGTCAAGAATTGGGGCCTCACAATCACTAGCCAATATGTTTTTCTCTCATGCCTTTCTTCGTTC
ATGGTTCGATATTCTGGTGTCCTAGGCGTAGAGGAACCACACCAATCCATCCCGAACTTGGTGGT
TAAACTCTACTGCGGTGACGATACTGTAGGGGAGGGCCTGCGGAAAAATAGCTCGACGCCAGGAT
GATAAAAAGCTTAACACCCCCCATTCTTATTACTTTTTCAATATGAAAAAGAAAAAAAAAATGAA
AAGGTCGTCTTATTCAAAACCCCAATCATGACACCCCTTCTCTCCCACTTCACACCTCGGAACGC
ACCGTTCTTATAGAGATAAACGCGCTTTCACATCTTCTTAACCCGAAATGGCCGGGGAGAGGACA
GGTTCCTTTTTTTGAGGGTACTCCCGGGTGGAGACGGGGTGGGGC
Found at i:123432 original size:30 final size:30
Alignment explanation
Indices: 123393--123450 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
123383 ATCGACTTGC
123393 TACTACAATCCGTATCGA-AACTAGAATCCG
1 TACTACAATCCGTA-CGATAACTAGAATCCG
* * *
123423 TACTGCAATCGGTACTATAACTAGAATC
1 TACTACAATCCGTACGATAACTAGAATC
123451 GCTATCGGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 2 0.08
30 22 0.92
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (30 bp):
TACTACAATCCGTACGATAACTAGAATCCG
Left flanking sequence: Indices 122893 -- 123392
CTAACCTTCGTCCCCGTCAACCTCTATTTCATCAACCGAAAAAGGAAAGTCAAATACAGATGAAG
GAGAAGCGGCTTGGCCGACGAGAGGAGGGAGTGGTGACCCCTCTACTGACCTCGAGACAAACTTG
ACAGCTATGCTTGACCGACGGTGGCTCCGATCAAGGCAAGGAGAGACTCAGAGAAGAAAGACAAA
TCGACTATCGACTTCTTTGACAATCTCCATTGCCCGGAGGAGGTGAATCAGAGGGAGAGATAGCC
CTCGCTAAGAGTCTCGGTGTCTACATTGCGGATATTTTTCCTATAATAAATCCGCTAAAAGCCCT
AAAAAGAAGAGTTAAAAGCGTGTTTATGAAACCCATAGCGTGTTGGTATTACACGTACCTTAAAA
TCAAGATTCTCGTAAGATAAGATGACAATCAAAGCCTTTTCTCCTTGAGGGTTTACTCTAGCACT
AGCCTCTAAAACTCTAGGAAGACGGGTAAGAGGAAATCGACTTGC
Right flanking sequence: Indices 123451 -- 123950
GCTATCGGTATCGTATCGGAATCGAATCAAACACGAATTTTATCAAAAAACTTCTTTATCGGTAA
GGAGACCCACTTTCCCACATCTCCTTTCCCCTATTGCTAGGGGCCTCACCCAAGATTGGATTACA
AGTTATTCCTTTCTTTACGAGATTCAGCTACAGACAATTCTATAACCGATGATTGAGCTCGCTGT
CCCTAGAACTATGTAAGCTGAGATGTGAAATTCTACCTTCGAACTGAGAACCAAGAACTTTCTTT
GTCACCCCGAACGGGCATTTTTCGGGGAGTAGCACTCGAAGAGAAGTTCATTTTTGTTCTTACAG
TCTCAGATGGACATGAAAAAAAAATGTCTCTTTCCCCATGTCAGTTGCTTGCCTTGCTACTGCTA
TGCTTCCTTCCTCCAACTCTGTCACTTCCTTTTCATTCAGTTGAATGGAGGCCGAAGGACTGGTA
CTTTATTATCTACAACCTATTTTTTAAGAATAAAATAAGTTGTTA
Found at i:143986 original size:18 final size:18
Alignment explanation
Indices: 143948--143987 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
143938 TAGAATGCCA
* *
143948 GCTTGATTCGGTGTCACC
1 GCTTGATTCGGTGTAAAC
143966 GCTTGATTCGGTGTAAAC
1 GCTTGATTCGGTGTAAAC
143984 GCTT
1 GCTT
143988 ATGTCAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.15, C:0.23, G:0.28, T:0.35
Consensus pattern (18 bp):
GCTTGATTCGGTGTAAAC
Left flanking sequence: Indices 143448 -- 143947
TTTTCAAAAGTCGAACGTGGCTCATGAAGATTTAAACGATCCATAAAGTCGTTTAGGAATTCAAG
AGCTTCCGGTCTTATAGATCCTTCAGGAAAGGGGGAGTCACTCAATATTTGAGTGAGACGCGCAG
TCGGCTCGCTCACCAACAAATTAGAAAGCTGATCCACCAAATTCGCCTTCAATTCCATAACTGCA
ATTTCAAAGAGCTCATTGCTCATGGTATTACAGTAATGCTCAATGGTAAGAGTTTGGTTGAGAAA
GCCTCTTACTAAGGTTTCGTATTCACCCAAGTTGAGTTGCGGGGGCAATCCCTCAATCATGCGGT
TCTCTAGAATTCGGATACGAGCAAAGAGTTCTAGCTCCATCTCGAAGTTTAGGATACGAAACTGA
TCCACAACGTCTACAGGGATTCCATTATGATTAGGGGCGTTATTCTCATTAGGTAGTAAAGGATG
CTCGTCATGGAAATTCTCAGCAGGATTTATTGAATTAGAATGCCA
Right flanking sequence: Indices 143988 -- 144487
ATGTCAGAAACATAATTCCAAACGGATATGTCTGTGGAAGGCCAGTATCCGAAGAAAAAATAGAA
TATATTAATATATAAGTAAGCGATCAAAAGTCGAAAGATTGGTCGAAGAAAGAAAAAGGTGTAAA
GCAACGAATTACGTAAGAATCGATGAGGAGATAAGGGGCGAAGGATAGTCATGAGACTTTTTTTA
TTAAGTTTATTCGCTCTATTCGAAGAGCGGCATACCGAAAAAAAGAAGCCCTTATCGGATTTGAA
CCGATGATTGAAGCCTATTTCTTAGGTTAGGGCGTTTAAAGAAAAAGCGTGACACAGACTCCGGG
AAGACAACGTTCGACTTGCATGTGTTAAGCATATAGCTAGCCTTAAACTAAGCCAAGGGCTTGTC
CCTTGACCTATCGGTCAAGTTACTTCGTCCCTTTACCGCCCTTGCCCATTTTCTTCTTTCAAAAG
GCCAGGAAAGGAATCAGTGCCAAGCTTAAGAGCTGATTCAATAGC
Found at i:176100 original size:20 final size:21
Alignment explanation
Indices: 176075--176115 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
176065 GCTGAAGGTA
176075 TTTGATTTCATCTTC-TATAC
1 TTTGATTTCATCTTCATATAC
*
176095 TTTGATTTCGTCTTCATATAC
1 TTTGATTTCATCTTCATATAC
176116 CTTTAGGGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.20, C:0.20, G:0.07, T:0.54
Consensus pattern (21 bp):
TTTGATTTCATCTTCATATAC
Left flanking sequence: Indices 175575 -- 176074
ATAGGTATGTATCCCTACCCCCGCTGACCAATGGTAATGGTATCCCACAACCTCCGATTTCAATC
GAAAAACCATCAAATGATCGAGATCAATACCACCGCCTCTCCCTTCTTCTCTCTTCAATTACCGA
GACCCATACATAAGAATATGATCAGTGAAGTAAAATACCATTTTACTCTATGTAATTCTATCTGG
TAATGATTGGATTCGGTTCCACACCTTTATACTAGGAGATTATAGGCGCAGCTTCCTGCCTTACC
AGTGAAAGTCCCGCCTAACCAATTGCGAACTCGTCCGACCAATTGAGTTTACCTAGCATACGTAT
GTTGAACATAATAATTCATTGATCCAGCAATGGCAGCGAAGTAGCATCAGTATCTAGTAGAAGGG
CGTCCTACTTGAGGTAGATAGCTTAACTGAACACAAACTGAAAGTATCAACTTCACACGCATCGA
GATGAGACTCGAAGTCTTGAATGCAAACCGGGAGAGCTGAAGGTA
Right flanking sequence: Indices 176116 -- 176615
CTTTAGGGAACATAAAGAAGAAGAAAAGTTTACTATCAATTATCCACCAACTCTATAAAAAGACT
AAACCAGCGCAAACTGCGGGCATGCATTAATGGAAGAACGGATCTCATCCCCAGAAGCAATTAAG
GCGAATCAAAGAGAGAAATTGTTGATACAGCCGCCCACTAAGCACTAAGATGCACCGCCCACAGA
AAGTTCTCCAATTGAGTTTGAGACGAACAGCGAGCTATCGCAAAGTCTCCCACCACAACCACGGA
GGAAGAACCGAAGTATGCCGCTTTTACCGAGCTCGAACCTTCCCAAGGGAGACGACTAGATTTAT
CGACCTAGACCCATCCGATCTGTTTCAGTCTAATATATGGAATAGAAACCGTCACATCCTTGGGC
TAGGAGAATCACTACAGGCAGAGTCGGGCAAGTAAGTAGCAAAGCTACCCAGGTTGCCTAGCCTA
AGCATAAACAAAAGAATAGTGTAGAACAATCAGCAAACTTAGCTC
Found at i:210510 original size:14 final size:14
Alignment explanation
Indices: 210479--210515 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
210469 CTGGCTTCCA
210479 GGAGCTG-CA-CCT
1 GGAGCTGACACCCT
*
210491 GAAGCTGACACCCT
1 GGAGCTGACACCCT
210505 GGAGCTGACAC
1 GGAGCTGACAC
210516 TTCCAGTTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
12 6 0.29
13 2 0.10
14 13 0.62
ACGTcount: A:0.24, C:0.32, G:0.30, T:0.14
Consensus pattern (14 bp):
GGAGCTGACACCCT
Left flanking sequence: Indices 209979 -- 210478
TCCACATAGGGGCACAGATTCAGGCAGCCAGACGATAAGGCTTTGGGAAAAAGACCTTCCTTTTA
AAGGATCAAATCCCAAGGTATTCGACCAGGCATTCCACCAGACATTCGCGGAGACATCGATTCTC
GGAGATCCATCCGCTCTTCGGGCAGATATTGATTTATTCTAAAACTCTTCCATAGTGGCTTAGCC
GACCTTCTAGCTACACCTTCGAGACCGTCTTCTCTTTGAAGACTGGATCACCACCTTCTACCCTC
TGGTTTACAGAAGCTTTATCGCTACCAGAGACTGAAGGAAAAAGGAAGTTATACCGGCGATTTAC
CAGGCCTTCAGGTGCCCATTGGACTGATTGATCATATCTTCAGGATATACCTTCTGGTGCTGCAC
TTGCGGACATATTCTTTAAACAAAGGGGCACTACTCTGTCGGTCGGGGGATGACCCCTCCCTTCA
TCGCTACACCTGCTTTACGTCTGGCTTGCTACCTTCTGGCTTCCA
Right flanking sequence: Indices 210516 -- 211015
TTCCAGTTGACAAACAGCAGCTGAGCGAGCTACTCGAGCTACACTTTCGAACTCTTCGAAATTCT
CTCATTTAGTTAGGATGCCCCTTACCTTAGCCGGACAGGCTTCTAGCTCTAGCATTGATTCCAAA
TCGAAATCTTGGAACAAATTCTTTTGATTGAATGATTGAAACTCATCCGAAAAACGTGATCCTCG
GCGCATATCCCTCTACCTATGAGCAGTCCGAACAGGCTTTCATGGTTGGCTTACTAGGGAATCCT
ATACCAGTTTTTTTTACCAGAACGAAAGGCTTACACCCCTCTCTACAACCACTAATACGAGATTC
TTTTGGGAATAGATCACACGATCCCACGCACTCTCACTCTCACAGGATATCTATCAAGAGGTATC
TTCGGGGGAAGTACACACCTGTCGCGTTTAATGCACATCAAGACCGGTTGGCTATCTGTTGTCGC
GTTTAGTGTACATTCGAGAGGAGGTTTCGCGGCAAGTGTACATTG
Found at i:273499 original size:15 final size:15
Alignment explanation
Indices: 273479--273514 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
273469 GACGTATTTG
*
273479 AAATAAAAAAATATA
1 AAATAAAAAAATAAA
*
273494 AAATAATAAAATAAA
1 AAATAAAAAAATAAA
273509 AAATAA
1 AAATAA
273515 GGGGTGGCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (15 bp):
AAATAAAAAAATAAA
Left flanking sequence: Indices 272979 -- 273478
TTTTTTTAAGTAAAAAAAAAGCACGTGACATCGGCTTGATGGAAGAAGGGCTATTGGTGCTTTAC
TCAGTTAGATTTATAACAGATATGGGACTAAGAAGTATTGTCTCTAAAGTAAGTGAAGTGAACCA
CGGGTGTGGTGCACGAACGGATTGTCTTTACAATGGGATGGTAAGGAACGTACGCCAAGCTGGCT
CCCGGTTGCGCAAAAAGCGGCAGGGAGCCTGCATTGCCGGGTGTGACTTACCTTACCTAAAGGAA
GTACCGTTAACACTCCCCGCCCAACTCCCCAGAATTGCCCTGTCGTCGTTCAAAGAGCAGAGCTC
GTCTATCCTTCTAGTTCTGCTTAGACGTAAGATTCGATAAAGAGGGTTTAGAAGTAGAGTGACGG
ATTGTTCTAATTCTGAAATGAGTTGCTTTCCCGTGGATTGGTTTGTGTGAGCAAGGAAGGTAAAA
TTATTCCCAATAATTTGACGATAAAAAAGTCGTCTGACGTATTTG
Right flanking sequence: Indices 273515 -- 274014
GGGGTGGCTTAGCTACCTTTAGAAAGAATTTAAGAGATTAATTGCCATGCTTCCGTTAATAGGTA
GAGTATACAAATTAGTACAAGCTGCTGTTGAAAACCGTTACGAGTATCCTTCTCACCCGATCTCT
GATAAGAGTGGTTCTAGCAGTAAGGTTAAGCTTAAGCTTATATGCTCTGAAAGAGGACCTAGTAC
ATTCATTAGAGTTGAAAAGGGTAAACCCGGCGTTGTACTAAAGTATAACCGAAACATAAAGGCGG
GTTCCGAGCTGACGGGTACAGGAGTGCATCCAATCCAAGCCTGGAAGGATTTAATAGGCGTGCAT
GACTTTTTGTCAACTCTCCAAAAAGAGGGATTTGCAAGTCTAGTTAAGGAAACATATAAAAAGAA
AAAGAACATCCTCCATTCGATGGATATTTCCACGCTGCGAGGTATCGAAGCGGGGGGTATGATTA
CAGCTCTGGCTATTGGGATTACAGTATGGGGAGAGATCACCTTAG
Found at i:308492 original size:19 final size:19
Alignment explanation
Indices: 308468--308506 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
308458 AAGCATTAAG
308468 AACAACCTAT-TATGCGACA
1 AACAACCTATCT-TGCGACA
308487 AACAACCTATCTTGCGACA
1 AACAACCTATCTTGCGACA
308506 A
1 A
308507 CCTATTATGC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 18 0.95
20 1 0.05
ACGTcount: A:0.41, C:0.28, G:0.10, T:0.21
Consensus pattern (19 bp):
AACAACCTATCTTGCGACA
Left flanking sequence: Indices 307968 -- 308467
AGGGGATCATTGCATTTTAAAGCAGCGCGTTAAAGCCTATAAGAGAAGAGCTTTTAATAATGAAA
TAGGCACGTAAACGTAAAGACGGGTAGGCTAAGATCTTCTCCTTCACTGTTCATAATATGCTATT
ATGCGATTAAGAACAACCTATTATGCGATCGGAATAAGGGCAATTAAATTCGAAAAGTACTAGTA
AAGATCACAGACACTATAGGGAAAATAAGTAACAAAAATTAAAGGAACAAAAAAAAGACAAAAAG
AACAAAAGAGAAATACAGACAACAAATAAGGGTGTTCAGGTTACAGCGGGTAAGGCTACGGGTTA
AAAACTAACCCTAAAAATAGAGAATCCCCAAGAAGCCGGACCTCTATACATATGAGTACGCAGTG
CGTCAATAACCTCATTATTGGTATAGAGGAAGTAACCACAATCCTTATGTTGGCACAACGGACTT
AGAGTTATCCCTATTTACCGCATTTGATAGCTTGAAAGCATTAAG
Right flanking sequence: Indices 308507 -- 309006
CCTATTATGCGACATCCTAGTTCTCTAACACCTGATTATGCGACACCTATCTTGCGACAACCTAT
TTCAAAATAGCGTAAGAGAGGTAACAACCGATTTTGCGATCATTATTTACCGCATTTGATAGCTT
GAAAGCAAAAGAGAGGTAACAACCGATTTTGCGATCATTTCTTTATTTGATAGCTTGAAAGCAAA
AGAGAGGGGTATACTCCAAGATTCTATTATCCTCCAAGATCATATTAACATACAACACTCGGATG
TAACATAGCGCAACTAGGGAGAATTCGGTCAGCTCCACGCCAATCTTAATGAAAAGTTGGTGACT
TCAGTTCATACAAAGAACAGAAGGACTGCACTAAAAAATAATTAAAAAAAGAAAATAACAAACAA
TGATAACAATATCAAATAAGAACAACCTATCGACTTTCGGAATAAGGGCAATTAAATTCGAATTC
AAACTTAGGGCCTTTAGCCTTCAGCAAAGAAATTGTGAACCGCCC
Found at i:308506 original size:15 final size:15
Alignment explanation
Indices: 308469--308572 Score: 65
Period size: 15 Copynumber: 6.7 Consensus size: 15
308459 AGCATTAAGA
308469 ACAACCTATTATGCG
1 ACAACCTATTATGCG
308484 ACAAACAACCTATCT-TGCG
1 ----ACAACCTAT-TATGCG
308503 ACAACCTATTATGCG
1 ACAACCTATTATGCG
* * *
308518 ACATCCTAGTTCT-CT
1 ACAACCTA-TTATGCG
308533 A-ACACCTGATTATGCG
1 ACA-ACCT-ATTATGCG
308549 AC-ACCTATCT-TGCG
1 ACAACCTAT-TATGCG
308563 ACAACCTATT
1 ACAACCTATT
308573 TCAAAATAGC
Statistics
Matches: 70, Mismatches: 6, Indels: 23
0.71 0.06 0.23
Matches are distributed among these distances:
14 11 0.16
15 39 0.56
16 6 0.09
19 13 0.19
20 1 0.01
ACGTcount: A:0.31, C:0.30, G:0.12, T:0.28
Consensus pattern (15 bp):
ACAACCTATTATGCG
Left flanking sequence: Indices 307969 -- 308468
GGGGATCATTGCATTTTAAAGCAGCGCGTTAAAGCCTATAAGAGAAGAGCTTTTAATAATGAAAT
AGGCACGTAAACGTAAAGACGGGTAGGCTAAGATCTTCTCCTTCACTGTTCATAATATGCTATTA
TGCGATTAAGAACAACCTATTATGCGATCGGAATAAGGGCAATTAAATTCGAAAAGTACTAGTAA
AGATCACAGACACTATAGGGAAAATAAGTAACAAAAATTAAAGGAACAAAAAAAAGACAAAAAGA
ACAAAAGAGAAATACAGACAACAAATAAGGGTGTTCAGGTTACAGCGGGTAAGGCTACGGGTTAA
AAACTAACCCTAAAAATAGAGAATCCCCAAGAAGCCGGACCTCTATACATATGAGTACGCAGTGC
GTCAATAACCTCATTATTGGTATAGAGGAAGTAACCACAATCCTTATGTTGGCACAACGGACTTA
GAGTTATCCCTATTTACCGCATTTGATAGCTTGAAAGCATTAAGA
Right flanking sequence: Indices 308573 -- 309072
TCAAAATAGCGTAAGAGAGGTAACAACCGATTTTGCGATCATTATTTACCGCATTTGATAGCTTG
AAAGCAAAAGAGAGGTAACAACCGATTTTGCGATCATTTCTTTATTTGATAGCTTGAAAGCAAAA
GAGAGGGGTATACTCCAAGATTCTATTATCCTCCAAGATCATATTAACATACAACACTCGGATGT
AACATAGCGCAACTAGGGAGAATTCGGTCAGCTCCACGCCAATCTTAATGAAAAGTTGGTGACTT
CAGTTCATACAAAGAACAGAAGGACTGCACTAAAAAATAATTAAAAAAAGAAAATAACAAACAAT
GATAACAATATCAAATAAGAACAACCTATCGACTTTCGGAATAAGGGCAATTAAATTCGAATTCA
AACTTAGGGCCTTTAGCCTTCAGCAAAGAAATTGTGAACCGCCCTGACCAGGGCGTCTTCAATAA
TCTTCCAACAGTGAGAGTCAAAAAAAAAAGACCTGGGAATCCATC
Found at i:308654 original size:60 final size:56
Alignment explanation
Indices: 308585--308708 Score: 187
Period size: 60 Copynumber: 2.1 Consensus size: 56
308575 AAAATAGCGT
308585 AAGAGAGGTAACAACCGATTTTGCGATCATTAT-TTACCGCATTTGATAGCTTGAAAGCAA
1 AAGAGAGGTAACAACCGATTTTGCGATCATT-TCTT----CATTTGATAGCTTGAAAGCAA
*
308645 AAGAGAGGTAACAACCGATTTTGCGATCATTTCTTTATTTGATAGCTTGAAAGCAA
1 AAGAGAGGTAACAACCGATTTTGCGATCATTTCTTCATTTGATAGCTTGAAAGCAA
308701 AAGAGAGG
1 AAGAGAGG
308709 GGTATACTCC
Statistics
Matches: 62, Mismatches: 1, Indels: 6
0.90 0.01 0.09
Matches are distributed among these distances:
56 28 0.45
59 1 0.02
60 33 0.53
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (56 bp):
AAGAGAGGTAACAACCGATTTTGCGATCATTTCTTCATTTGATAGCTTGAAAGCAA
Left flanking sequence: Indices 308085 -- 308584
ATAATATGCTATTATGCGATTAAGAACAACCTATTATGCGATCGGAATAAGGGCAATTAAATTCG
AAAAGTACTAGTAAAGATCACAGACACTATAGGGAAAATAAGTAACAAAAATTAAAGGAACAAAA
AAAAGACAAAAAGAACAAAAGAGAAATACAGACAACAAATAAGGGTGTTCAGGTTACAGCGGGTA
AGGCTACGGGTTAAAAACTAACCCTAAAAATAGAGAATCCCCAAGAAGCCGGACCTCTATACATA
TGAGTACGCAGTGCGTCAATAACCTCATTATTGGTATAGAGGAAGTAACCACAATCCTTATGTTG
GCACAACGGACTTAGAGTTATCCCTATTTACCGCATTTGATAGCTTGAAAGCATTAAGAACAACC
TATTATGCGACAAACAACCTATCTTGCGACAACCTATTATGCGACATCCTAGTTCTCTAACACCT
GATTATGCGACACCTATCTTGCGACAACCTATTTCAAAATAGCGT
Right flanking sequence: Indices 308709 -- 309208
GGTATACTCCAAGATTCTATTATCCTCCAAGATCATATTAACATACAACACTCGGATGTAACATA
GCGCAACTAGGGAGAATTCGGTCAGCTCCACGCCAATCTTAATGAAAAGTTGGTGACTTCAGTTC
ATACAAAGAACAGAAGGACTGCACTAAAAAATAATTAAAAAAAGAAAATAACAAACAATGATAAC
AATATCAAATAAGAACAACCTATCGACTTTCGGAATAAGGGCAATTAAATTCGAATTCAAACTTA
GGGCCTTTAGCCTTCAGCAAAGAAATTGTGAACCGCCCTGACCAGGGCGTCTTCAATAATCTTCC
AACAGTGAGAGTCAAAAAAAAAAGACCTGGGAATCCATCAATTGTTAGGATAGGGGAGGCACAGC
CCCCAACCAAGGGAGTGGTTACATCCAGTATGTCCCCCCGGCATGCTGCCCCGGGGCCGGAATGC
GGTAGGGTGCTCAAGCTAACGGCAAGGAGTGATTCACAATAAAAT
Found at i:335240 original size:18 final size:18
Alignment explanation
Indices: 335217--335254 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
335207 ATCACTAACT
**
335217 AATACTAATCTAATAGAA
1 AATACTAATAGAATAGAA
335235 AATACTAATAGAATAGAA
1 AATACTAATAGAATAGAA
335253 AA
1 AA
335255 GAACTGTCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.61, C:0.08, G:0.08, T:0.24
Consensus pattern (18 bp):
AATACTAATAGAATAGAA
Left flanking sequence: Indices 334717 -- 335216
TTCTTGCGCCAAAGATCTTACCATTTCCGAAGGAACTGGAGTTACATCTCTTTTCCATTTCCATT
CAAGAGTTCTTATGTGTTTTCACGCCCCTTTGAGACCCCGAAAAATGGACAAATTCCTTTTCTTA
GGAACACATACAAGATGCGTCACTACAAAAAGGATAATGGTAACCCCACCATTAATTACTTCATT
TATGAATTTCATAGTAATAGAAATACATGTCCTACCGAGACAGAATTTGTAACTTGCTATCCTCT
TGCCTAACAGGCAAAGATTGACCTCCGTGGAAAGGATGATTCATTCAGATCGACATGAGAGTCCA
ACTACATTGCATTGCCAGAATCCATGTTGTATATTTGAAAGAGGTTGACCTCCTTGCTTCTCTCA
TGGTACAATCCTCTTCCCGCCGAGCCCCCCGGTCCACAGAGACAAAATGTGGGACTGATGCCAAC
AGTTCATCACGGAAGAAAGGACTCACTAAGCCGGGATCACTAACT
Right flanking sequence: Indices 335255 -- 335754
GAACTGTCTTTTCTGTATACTTTCCCCGGTTCCGTTGCTACCGCGGGCTTTACGCAATCGATCGG
ATTATATAGATATCCCTTCAACAAACATAGGTCATCGAAAGGATCTCGGAGACCCACCAAAGCAC
GAAAGCCAGAATCTTTTCGATTCTGCTACCTTGAGCTATCCTCCTACCTGCGCCCTAACGATCAT
ACCCACTTGAGCTTTCTTTGTCCGGCTTTCAGTCTCTAACTACTTCTTTCCCCGGTTCGTAGGTA
TAGTGCCTGGTGCTAACTCCCGTCTTTTCTTTCATCCGTTCAGCTAAACGCCCTTAGCTAAAGGG
TATTTCATTAACAGGATTATCCCATTGCTGACTCGCTCATTCTTTCTTAACAGCTAGTACTTTTT
TCTGGACACAATCCAAAGATCTTGTTAAGGGACTGCTAGACGGTCTTTTTAAGACATTTCAGATT
CCGGGGAAACGATAGTGCCAGTGATGAGAGATTCGATCTAAGCGG
Found at i:400240 original size:18 final size:18
Alignment explanation
Indices: 400200--400242 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
400190 ACCGCCCTGC
400200 CATAGTCGCGAGTCTGTTT
1 CATAGTCGCGAG-CTGTTT
400219 -ATAGTCGCGA-CTGTTGT
1 CATAGTCGCGAGCTGTT-T
400236 CATAGTC
1 CATAGTC
400243 AACAAGGTTG
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:0.19, C:0.21, G:0.26, T:0.35
Consensus pattern (18 bp):
CATAGTCGCGAGCTGTTT
Left flanking sequence: Indices 399700 -- 400199
CCGAAAGGGCTGCCGTCCGATGGGTACACGAAAGTGACGAAGTTGCTTTGACTACAGAACCATGC
CTGTCTGTTGGAGCGAATTGGATGATCGGGCCGAGGGCTGCCCCCTCTTCCCCTCACTCTCCTTT
CCCTAACGCTGCGCGCCTTGAGTCATCAAAGCCTTTCTGACTCGGCCTGGCCCGGTCGCCCTACG
CGACTGGCGCTTCAAAAGGCGAAACTCTCGTCGTAGTTTGGCGACCTAAGGGGCGGACACTTTTT
GTTAGGCGAAGACTCTGAAGTGGGCGAACACTCGGCCCAGCGGGCGAACATGCCGGGCTCCGGCT
CCGCGCACCTGCTGACACCTTTCGAAGCACTTTCGTCTGTGCGCTTTAGTTTTAGAATGTGTCGT
TCAGCGTCACGAGTCTACAAGCCTTTCTCATTTCAGTGCTCGCCCTTAGTAGGGCCTTTAGTCTT
TTGATTCGAGTAGGGGTAGCGAGAGAGCAGAGCGTACCGCCCTGC
Right flanking sequence: Indices 400243 -- 400742
AACAAGGTTGAAACTTCCAGGAAAAAACTTCGAATTGGGAGGGCGATCCTCCCGGTGAACTGACC
GTACCCCAAACCGACACAGGTGAACAAGTAGAGTATACTAGGGCGCTTGAGAGAACCATGTCGAA
GGAACTCGGCAAAATGACCCCGTAACTTCGGGAGAAGGGGTGCTCTCCTATCTTTTGATTAGGAA
AGCGGCACATACCAGGGGGTAGCGACTGTTTATTAAAAACACAGGACTCTGCTAAGTGGTAACAC
GATGTATAGAGTCTGACACCTGCCCGGTGCTGGAAGGTCGGAAGGAGAAGTGTTAGTTGCTTTGA
ATGGAAGCCCCGGTAAACGGCGGCAGTAACTCTAACTGTCCTAAGGTAGCGAAATTCCTTGTCGC
ATAAGTAGCGACCTGCACGAATGGTGTAACGACTGCCCCGCTGTCTCCGACATGGACCCGGTGAA
ATTGAATTCTCCGTGAAGATGCGGAGTACCAACGGCTAGACGGTA
Found at i:409207 original size:6 final size:6
Alignment explanation
Indices: 409196--409220 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
409186 AAATTAAATC
409196 AAAGAA AAAGAA AAAGAA AAAGAA A
1 AAAGAA AAAGAA AAAGAA AAAGAA A
409221 CCAAAGGAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAGAA
Left flanking sequence: Indices 408696 -- 409195
CATCTGCCTTTCTTTTCGCCTCAACGCGGGCAAGATTATATTCGTTAGAGTCGCTAGCTCTTCTT
TCTCTTTTCACGAATCCTAGTTACTTGGCACTAGGAGTTGTCTAATCAAAAGGCGTAAGCGCAGC
AGTTAGAATTTCATCCGCATCTGTTGTCGTAAGGGCAGTAGGTCTTGGTCCTTGAGTAAGTCCGG
GATCAGCATGTGATTAGTTCGAGGCGCTAGCTGTACTAGTTGGAGTAGGAGTAGCAGTGGTGGTA
CTTACTTTCGTTCTTTGGTGGTGTATCTTATTTAAGTATCCCGTCTGCTTTTGTTTAAGGAAGGA
ATAAAATAAAGGCAGCTATTGGACTGCTCTCCCTGGCTAGAGGGGATAACTCTTAACTAACTAAC
AAGGCTAGCCTAGCGAAGTCACTTCTGGATTCACTTCTTTTTTGAGTTTGAGTGCACACCCGCGT
AAATGGATTTTGGGGTTCAAACCCAGCCCCAGGCTAAATTAAATC
Right flanking sequence: Indices 409221 -- 409720
CCAAAGGAACCTGATGGGTAAGAACACAAAGATTTAAAGTCATTTCTTCAAATTGCTCTCCATTT
CTAAGTTCATAGCCTTCGCGGTAGCTTCATCGATATTACCTACCAAATAAAAGGCCTGTTCAGGA
AGACCATCTAATTCTCCGGAAAGGATCAATTGAAACCCTCTAATGGTTTCTGCTAGACCAACATA
TTTCCCTGGAGAACCGGTAAATACTTCTGCTACAAAAAAAGGTTGTGATAAGAAACGCTCAATTT
TTCGCGCTCTTGCTACGGTTAAACGATCCTCTTCGGATAATTCGTCCAACCCAAGGATAGCTATA
ATGTCCTGAAGCTCTTTGTAACGTTGTAAAGTTTGCTTAACTCTTTGCGCAATTTCATAATGTTC
CTCACCAACGATCCGAGGTTGAAGCATGGTTGATGTTGAATCTAAAGGATCTACTGCTGGATAGA
TCCCTTTGGCAGCTAATCCTCTTGATAGTACGGTAGTAGCATCTA
Found at i:456634 original size:18 final size:18
Alignment explanation
Indices: 456597--456686 Score: 132
Period size: 18 Copynumber: 5.2 Consensus size: 18
456587 AAGGTTTTCT
456597 TATTGATGATA-T--CGA
1 TATTGATGATAGTGACGA
*
456612 CATTGATGATAGTGACGA
1 TATTGATGATAGTGACGA
456630 TATTGATGATAGTGACGA
1 TATTGATGATAGTGACGA
*
456648 TATTGATGCTAGTGACGA
1 TATTGATGATAGTGACGA
*
456666 TATTGATGCTAGTGACGA
1 TATTGATGATAGTGACGA
456684 TAT
1 TAT
456687 CGATCGTGAC
Statistics
Matches: 69, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
15 10 0.14
16 1 0.01
18 58 0.84
ACGTcount: A:0.31, C:0.09, G:0.26, T:0.34
Consensus pattern (18 bp):
TATTGATGATAGTGACGA
Left flanking sequence: Indices 456097 -- 456596
TCTTGCTGGGACCTCTGCAGCCCCTCAAATCCATGCAACTTTTTACATTCGATGGATACCGCCAG
ACTTCGGTTGGTCCAAACTGAACACGGATGGATCCTCCTCTGGAAACCCTGGACCAGGCAGCGCT
GGTGGTGTTCTACGGGATCATATGGGCAAATGGATCATTGGATTCTCCAGGAAATGAACTTGTAC
AAGACGTGTACAAGCTGAACTCATAGCACTTAGAGATGGGTTGATAATGGCTCAAGCGCAAAATA
TCCTAAAACTAGAGATCAATGTTGATTCCCAAGTTGTGATTTCGCTCATCAACAAGAGTCCTCAT
TCAAGATATTCTGTTATCCTCGATGACTGCAGATGGTTGCTATCCCAAATCCCAATGGTGAAGAT
CCTGCATACCTACAGAGAAAGCAAGTCAGTTGCAGATGCCATGGCAAAGAATAGAAGAGACCCAT
CATTACGGTATTTCTGAACATGGATAACAAGCCTAAAGGTTTTCT
Right flanking sequence: Indices 456687 -- 457186
CGATCGTGACCTTGATACGGAGCTGGAGCTGCTAACTATGATGAATGCACTAACTATGGATATGA
TGTCGGAAATAGACCGATTTTATATCACCCTTCAATTCGAATTAGCAAAAGCAATGTCTCCTTGC
ATAATATGGATTCCAAACATTCATGATCTGGATGTGAATGAGTCGAATTACTTATCCCTCGGTCT
ATTAGTGAACCATCTCTCCAGGGATTGTGAAAGATGTTCCACTAGAAATATTCTTGTTATTGCTT
CGACTCATATTCCCCAAAAAGTGGATCCCGCTCTAATAGCTCCGAATAAATTAAATACGTGCATT
AAGATACGAAGGCTTCTTATTCCACAACAACGAAAGCACTTTTTCACTCTTTCATATACTAGGGG
ATTTCACTTGGAAAAGAAAATGTTCCATACTAATGGATTCGGGTCCATAACCATGGGTTCCAATG
CACGAGATCTTGTAGCACTTACCAATGAGGCTCTATCGATTAGTA
Found at i:456640 original size:9 final size:9
Alignment explanation
Indices: 456613--456673 Score: 59
Period size: 9 Copynumber: 6.8 Consensus size: 9
456603 TGATATCGAC
456613 ATTGATGAT
1 ATTGATGAT
* *
456622 AGTGACGAT
1 ATTGATGAT
456631 ATTGATGAT
1 ATTGATGAT
* *
456640 AGTGACGAT
1 ATTGATGAT
*
456649 ATTGATGCT
1 ATTGATGAT
* *
456658 AGTGACGAT
1 ATTGATGAT
456667 ATTGATG
1 ATTGATG
456674 CTAGTGACGA
Statistics
Matches: 38, Mismatches: 14, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
9 38 1.00
ACGTcount: A:0.31, C:0.07, G:0.28, T:0.34
Consensus pattern (9 bp):
ATTGATGAT
Left flanking sequence: Indices 456113 -- 456612
GCAGCCCCTCAAATCCATGCAACTTTTTACATTCGATGGATACCGCCAGACTTCGGTTGGTCCAA
ACTGAACACGGATGGATCCTCCTCTGGAAACCCTGGACCAGGCAGCGCTGGTGGTGTTCTACGGG
ATCATATGGGCAAATGGATCATTGGATTCTCCAGGAAATGAACTTGTACAAGACGTGTACAAGCT
GAACTCATAGCACTTAGAGATGGGTTGATAATGGCTCAAGCGCAAAATATCCTAAAACTAGAGAT
CAATGTTGATTCCCAAGTTGTGATTTCGCTCATCAACAAGAGTCCTCATTCAAGATATTCTGTTA
TCCTCGATGACTGCAGATGGTTGCTATCCCAAATCCCAATGGTGAAGATCCTGCATACCTACAGA
GAAAGCAAGTCAGTTGCAGATGCCATGGCAAAGAATAGAAGAGACCCATCATTACGGTATTTCTG
AACATGGATAACAAGCCTAAAGGTTTTCTTATTGATGATATCGAC
Right flanking sequence: Indices 456674 -- 457173
CTAGTGACGATATCGATCGTGACCTTGATACGGAGCTGGAGCTGCTAACTATGATGAATGCACTA
ACTATGGATATGATGTCGGAAATAGACCGATTTTATATCACCCTTCAATTCGAATTAGCAAAAGC
AATGTCTCCTTGCATAATATGGATTCCAAACATTCATGATCTGGATGTGAATGAGTCGAATTACT
TATCCCTCGGTCTATTAGTGAACCATCTCTCCAGGGATTGTGAAAGATGTTCCACTAGAAATATT
CTTGTTATTGCTTCGACTCATATTCCCCAAAAAGTGGATCCCGCTCTAATAGCTCCGAATAAATT
AAATACGTGCATTAAGATACGAAGGCTTCTTATTCCACAACAACGAAAGCACTTTTTCACTCTTT
CATATACTAGGGGATTTCACTTGGAAAAGAAAATGTTCCATACTAATGGATTCGGGTCCATAACC
ATGGGTTCCAATGCACGAGATCTTGTAGCACTTACCAATGAGGCT
Done.