Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_029809
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: 365190
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.27
Found at i:88141 original size:18 final size:19
Alignment explanation
Indices: 88120--88157 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
88110 AGGCGAAGTC
*
88120 GGTTCAGTAG-TCTCAGTA
1 GGTTCAGTAGAGCTCAGTA
*
88138 GGTTCCGTAGAGCTCAGTA
1 GGTTCAGTAGAGCTCAGTA
88157 G
1 G
88158 TGGAGTGCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.21, C:0.18, G:0.32, T:0.29
Consensus pattern (19 bp):
GGTTCAGTAGAGCTCAGTA
Left flanking sequence: Indices 87620 -- 88119
CTAGAATGAAACTATCGACGAGGATATAGAAGGTGACATGATGGAATTCTCTTTTTTCTGCAACT
GCTTCGTTTGCCTCGGGAGGGAGTACGAAAGAAAGACTTCTTGGAAGACAGGGCCTTTCTTCAAT
CTAAGCTCAAAACGGAAACTATTGAAATAGAAGAGAAGTAAGGACGATGGTGGAGTGAAAAAGAA
AAGGCTGAGTTAAGGAGGAACAAGGTAGCCGTACGGTAAGAGTTCTGGAGGCAAGCGAAGCCAAC
GACGGAGTTGGAAAAGGAGAGACGAGAGGTAAAAAAAAAGGAGTCTTAGATAGCTAACGGAAGGG
TAGCGTTAGCTAACAATACTAGAGGTCAATTCATAAAAGGGGAAACGAACACTAACGGAAAATAA
ATAAAAAAAATATAATTCAGTTAAAAGCGAATAAGTCGAAGTTTTGTTTCAAATCCAAGAAGTCA
AGTTCCATGGGCCAAATCAAATAAGGATTTTTAGTAGGCGAAGTC
Right flanking sequence: Indices 88158 -- 88657
TGGAGTGCATCAGTTCAGGAATCAAGCCTTTGAATCTAATAGGGCAGGGCCCAGAAAGATAGTAA
GTAGCGAAAGGTGGTGGAGACATTTAATATCCAATCCAAGAGCCAAATAGAAAGTCAAGATGAAG
GATAAACAGAGGAGAGCAGGCCAACGAAGTAGTAATCGAGTGATCGGCAAGCTGACCCTACAAGG
AATTCGTCAAGGGTCAAAAGGAGAAGACCTAAGAGCGGTGAAACTATGGCATATCCTCTATAGCT
CAAAGGTAGGTTGTAGGTTTTCAATCGATTAGGTAAGCTTGTCGTTCTCAAACCAGTAGCAAAAC
GGAATCAAGCAGAGCAGCTTCCGGAGAACCCGAGGAGAGCGGTGAAACAACGTAGACGTATCTTA
TATATATTGACTGAGAAAGAATTTCAGATACTAAGGCTTCGCTTTCCGGGCTACTGCTAGCCGAG
CTTGGAACAATAAGGTTACTCACCAACTTATTAGAAGCCATCTCC
Found at i:120658 original size:11 final size:11
Alignment explanation
Indices: 120638--120670 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
120628 TAGCATTTTC
*
120638 TATTATATTAG
1 TATTAGATTAG
120649 TATTAGATTAG
1 TATTAGATTAG
120660 TATTAG-TTAG
1 TATTAGATTAG
120670 T
1 T
120671 GATCTCGGCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
10 5 0.24
11 16 0.76
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (11 bp):
TATTAGATTAG
Left flanking sequence: Indices 120138 -- 120637
GCCATAGGTTTGATCCTGTAGAATCTGACTCATTTTATCATTGAGCGAAAGGTACGAAATAAATC
AGATTGATTTTTCGATCAAAAGTACTATGTTATGTGAAATCTTCGGTTTTTTTCTCTTTCTCTAT
CCCTATCCCGTAGGTACAGCGTTTGAATCAATAGAGAACCTTTTCTTCTGTATAAATGTATCTGT
ATAAATCGATATTATTACATTCCAATTCCTTCCCGATACCTCCCAAGGAAAATCCCGAATTGGAT
CCCAAATTGACGGGTTAGTGTGAGCTTATCCATGCGGTTATGCACTCTTCGAATAGGAATCCATT
TTCTGAAAGATCCTGGCTTTCGTGCTTTGGTGGGTCTCCGAGATCCTTTCGATGACCTATGTTGT
GTTGAAGGGATATCTATATGATCCGATCGATTGCGTAAAGCCCGCGGTAGCAACGGAACCGGGGA
AAGTATACAGAAAAGACAGTTCTTTTCTATTATATTAGCATTTTC
Right flanking sequence: Indices 120671 -- 121170
GATCTCGGCTCAGTGAGTCCTTTCTTCCATGATGAACTGTTGGCACCAGTCCTACATTTTGTCTC
TGTGGACCGAGGAGAAAGGGGGTTCAGCGGGAAGAGGATTGTAACATGAGAGAAGCAAGGGGGTC
AACCTCTTTCAAATATACAACATGGATTCTGGCAATGCAATGTAGTTGGACTCTCATGTCGATCC
GAATGAATCATCCTTTCCACGGAGGGAAATCTTTGCCTGCTAGGCAAGAGGATAGCAAGTTACAA
ATTCTGGCTCGGTAGGACATGTATTTCTATTACTATGAAATTCATAAATGAAGTAGTTAATGGTG
GGGTTACCATTATCCTTTTTGTAGTGACGAATCTTGGAATGCGTTCCTAAGAAAAGGAATTTGTA
CATTTTTCGGGGTCTCGAAGGGGCGTGGAAACACATAAGAACTCTTGAATGGAAATGGAAAAGAG
ATGTAACTCCAGTTCCTTCGGAAATGGTAAGATCTTTGGCGCAAG
Found at i:121538 original size:25 final size:25
Alignment explanation
Indices: 121504--121556 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
121494 TTCTCGACCC
121504 TTTGCCTTAGGATTAGTCAGTTCTA
1 TTTGCCTTAGGATTAGTCAGTTCTA
121529 TTTGCCTTAGGATTAGTCAGTTCTA
1 TTTGCCTTAGGATTAGTCAGTTCTA
121554 TTT
1 TTT
121557 CTCTCGATGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.19, C:0.15, G:0.19, T:0.47
Consensus pattern (25 bp):
TTTGCCTTAGGATTAGTCAGTTCTA
Left flanking sequence: Indices 121004 -- 121503
ATTATCCTTTTTGTAGTGACGAATCTTGGAATGCGTTCCTAAGAAAAGGAATTTGTACATTTTTC
GGGGTCTCGAAGGGGCGTGGAAACACATAAGAACTCTTGAATGGAAATGGAAAAGAGATGTAACT
CCAGTTCCTTCGGAAATGGTAAGATCTTTGGCGCAAGAAGAAGGAGTTGATCCGTATCATCTTGA
CTTGGTTCTGATTTCTCTATTTTTTTTAAGAATACCGAGTCGGGCTCTTCTCCTACCCGTATCGA
ATAGAACATGCTGAGCCAAATCTTCTTCATGTAAAACCTGCTTGCTTTATTTAGATCGGGAAAAT
CGTACGGTTTTATGAAACCATGTGCTATGGCTCGAATCCGTAGTCAATCCTATTTCCGATAGGAA
CAGTTGACAATTGAATCCAATTTTTCCCATTATTTTCGTATCCGTAATAGTGCGAAAAGAAGGCC
CGACTCCAAGTTGTTCAAGAATAGTGGCGTTGAGTTTCTCGACCC
Right flanking sequence: Indices 121557 -- 122056
CTCTCGATGGGGGGCAAGGGAAGGGATATAACTCAGCGGTAGAGTGTCACCTTGACGTGGTGGAA
GTCATCAGTTCGAGCCTGATTATCCCTAAACCCGATTATCCCTAAACCCAATGTGAGTTTTTCTA
TTTTTACTTGCCCCCCCGCCGTGATCGAATGAGAATGGATAAGAGGCTCGTGGGATTGACGTGAG
GGGGTAGGGATGGCTATATTTCTGGGACTCGAACCTCCACGCTCTTTTGAAGCTTAATACTCTCA
TCTAAGAGAAAGAGTTTCCCAAAGGGCTTTTATCTTAGAGCCCGCCTAAAACAAGATGAGAATGA
GAAAAAGGGAGGCATAGAGGCAATCTTTTCGGCTTCGCTCCTCGCTTTTGTTCAATTATAAATAA
AAAACCACTTTGATGGAGATTTGTAGCATCATTCAAGTAAATACAGATTGAGATCGTAGAAACAT
GAGCTTGTGATATAGCTACACCTAATTCCGGACCGGTTAATGCAA
Found at i:121660 original size:16 final size:16
Alignment explanation
Indices: 121639--121670 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
121629 GTTCGAGCCT
121639 GATTATCCCTAAACCC
1 GATTATCCCTAAACCC
121655 GATTATCCCTAAACCC
1 GATTATCCCTAAACCC
121671 AATGTGAGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.38, G:0.06, T:0.25
Consensus pattern (16 bp):
GATTATCCCTAAACCC
Left flanking sequence: Indices 121139 -- 121638
TCCTTCGGAAATGGTAAGATCTTTGGCGCAAGAAGAAGGAGTTGATCCGTATCATCTTGACTTGG
TTCTGATTTCTCTATTTTTTTTAAGAATACCGAGTCGGGCTCTTCTCCTACCCGTATCGAATAGA
ACATGCTGAGCCAAATCTTCTTCATGTAAAACCTGCTTGCTTTATTTAGATCGGGAAAATCGTAC
GGTTTTATGAAACCATGTGCTATGGCTCGAATCCGTAGTCAATCCTATTTCCGATAGGAACAGTT
GACAATTGAATCCAATTTTTCCCATTATTTTCGTATCCGTAATAGTGCGAAAAGAAGGCCCGACT
CCAAGTTGTTCAAGAATAGTGGCGTTGAGTTTCTCGACCCTTTGCCTTAGGATTAGTCAGTTCTA
TTTGCCTTAGGATTAGTCAGTTCTATTTCTCTCGATGGGGGGCAAGGGAAGGGATATAACTCAGC
GGTAGAGTGTCACCTTGACGTGGTGGAAGTCATCAGTTCGAGCCT
Right flanking sequence: Indices 121671 -- 122170
AATGTGAGTTTTTCTATTTTTACTTGCCCCCCCGCCGTGATCGAATGAGAATGGATAAGAGGCTC
GTGGGATTGACGTGAGGGGGTAGGGATGGCTATATTTCTGGGACTCGAACCTCCACGCTCTTTTG
AAGCTTAATACTCTCATCTAAGAGAAAGAGTTTCCCAAAGGGCTTTTATCTTAGAGCCCGCCTAA
AACAAGATGAGAATGAGAAAAAGGGAGGCATAGAGGCAATCTTTTCGGCTTCGCTCCTCGCTTTT
GTTCAATTATAAATAAAAAACCACTTTGATGGAGATTTGTAGCATCATTCAAGTAAATACAGATT
GAGATCGTAGAAACATGAGCTTGTGATATAGCTACACCTAATTCCGGACCGGTTAATGCAAGAAC
TATAAATAAAGGACCAGGATCTCCTATAAAAAAGAAAATATCATTCATACATAGCATAGTCCAAG
CGAACCCACTTAAAATCTTTACTGAACTATGACCGGCCATCATAT
Found at i:131004 original size:14 final size:14
Alignment explanation
Indices: 130985--131015 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
130975 TCTGACCCAT
*
130985 AAGACCGATTAAGG
1 AAGACCAATTAAGG
130999 AAGACCAATTAAGG
1 AAGACCAATTAAGG
131013 AAG
1 AAG
131016 GGGAACTAAT
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:0.48, C:0.13, G:0.26, T:0.13
Consensus pattern (14 bp):
AAGACCAATTAAGG
Left flanking sequence: Indices 130485 -- 130984
AGTCTAATCATCCCTCCTTTCTCCGAACTGTGGAGCAAGCGTGGAATATCCGAGTTGAGGGCAAC
CCCATGTTCAAAGTGGTCCAAAAGCTTAAAGCGGTCAAAGAGGCGCTGAAAAGTTAGAACGTTAC
CACCTTTGGCAAAATAGATGAAAGAAGCCAGGCTACATAAGACTCTCTAGGAATGGACAGAAGAG
GCTACGGGATTCGCACACTAGCAGGGCCAATCAGCGAGACTTTTACAAAAAGACTTAACAAGGAA
TTGACTGAATAGGACACGAGTGGGTCCTTTCAAGCCTATGTGACCAATGCACTTATGCTGCCTTC
ACTCAAACACTTTCAAAGAAGCAAGGGGAAGAGTTAAATACTGAAATCGATTCACTAAGCTAGCT
TAACTCTTAAACTACTTGAACTAGAGGAGCGGTACGAGCTACTAATAGGCTTACTACAAAAGAAA
AGGCTATTTGATATCCTTTTTAAAGGCTCAAGTACTCTGACCCAT
Right flanking sequence: Indices 131016 -- 131515
GGGAACTAATTCCAGATATCGATTAACTGCTTGCCAACCTATCCCTAGACCGATGGATTGACCTG
TTGACCAGGCAGGAATACCAATACTAATTGCGACAGGAGAGACCGATAGAGTTGAACAGACAGCT
GACAGCTCGCGATTGAGAGACTTTCTATCCAGTTGTGCTTTCAGTTCAATAACTTCATCCTCTAT
CACTTTAGCATCATTTCGAAGTCTGGATATCTCTTCCCCTCCCTTTCTCGGTGCTTCTCAATGCC
TTTCTATCCTTAACAGCTCCTCTTTCTGTTTTGCCATTTCATTAAGCCATGCCCTTAGGTTTTGA
TAAGGGTTTTCCATTTTTCCTATTCAAATTTGAGTAGTTTGTCCGAACATAGTCCGATTGTGCCT
TCCGGAGTCTCTGGAGTCATCCTGAGGACTTTACCAAAAATAGAGGCGAACTCTTCCCATAAGGC
CCTTGCAATGCAGTCTATCAATGGCCCATATGACATTTATCTGTA
Found at i:142439 original size:39 final size:39
Alignment explanation
Indices: 142396--142474 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
142386 CCCATCCTTC
*
142396 AATATCATGATTGGGTCGAGCAGGCCAGATCATGAGTGA
1 AATATCATGATCGGGTCGAGCAGGCCAGATCATGAGTGA
142435 AATATCATGATCGGGTCGAGCAGGCCAGATCATGAGTGA
1 AATATCATGATCGGGTCGAGCAGGCCAGATCATGAGTGA
142474 A
1 A
142475 TAGAAAATCG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.32, C:0.16, G:0.30, T:0.22
Consensus pattern (39 bp):
AATATCATGATCGGGTCGAGCAGGCCAGATCATGAGTGA
Left flanking sequence: Indices 141896 -- 142395
ATAGTATAATCTATCTCTCAGCGATTCTTTTCTCCGCTAATCACCCCTTCCCAACCAGCCCGCCC
GATCGATTTTGTAAGATCGGCTAATTCAAAAGGGTTAATCTGGTCCGAGTCGGAACGAATCGTTT
GCTTTATCGAACAAAGCTTTATTAGGGGTCTTGGTTGGCCCCCTATTTTCAACCATTACAGCTGG
CGTCGACCAGCTTTGCGATACGGACGGACACGAAGAAGAACGCAGGCAGCGGAAATGCAAAAGAG
AAGAGCAAAGATTCCCGACCCAGAGCATGTTATTGACTCAACCACAAATCTGTTGAATGAAGGTA
GCTACTCTCAGCCACTAGTTAGAAGGAAACCCCTTGACTTCGCTTATGCCCTTATGCAGTAAAGC
AAGTGAGGCGGGCTAAGATTCCATTCGAAGTAACGTAACAGGATTCGATGTTGCACCATCTTCAA
CTCTTCTCTGGATCCGGAGTTTTTCGAGAAAAGGTCCCATCCTTC
Right flanking sequence: Indices 142475 -- 142974
TAGAAAATCGAAAACGTACATAGCTGTTCCAGCGGAAATACTTGGAATAATTCTACCACTTCTAC
TAGGAGTAGCCTTTTTAGTGCTAGCTGAACGTAAAGTAATGGCTTTTGTGCAACGTCGAAAGGGT
CCTGATGTAGTGGGATCATTCGGATTGTTACAACCTCTAGCAGATGGTTTGAAATTGATTCTAAA
AGAACCTATTTCACCAAGTAGTGCTAATTTCTCCCTTTTTAGAATGGCTCCAGTGACTACATTTA
TGTTAAGTCTGGTCGCTTGGGCCGTTGTACCTTTTGATTATGGTATGGTATTGTCAGATTCGAAC
ATAGGGCTACTTTATTTGTTTGCCATATCTTCGCTAGGTGTTTATGGAATTATTATAGCAGGTTG
GTCTAGTAATTAGGGGGCGGCCGTTCGGTCGCCTATGATACTAGGACCAATAGGTCAAAAATGGG
TTTGTGCCGCAGGTGTTGAACGATCTACTCTACACAGGTGTGGGC
Found at i:148117 original size:17 final size:18
Alignment explanation
Indices: 148095--148128 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
148085 TAACCTGCCT
148095 TTAGAG-TTACAGAGGGG
1 TTAGAGCTTACAGAGGGG
*
148112 TTAGAGCTTAGAGAGGG
1 TTAGAGCTTACAGAGGG
148129 TCGCCCCTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.29, C:0.06, G:0.41, T:0.24
Consensus pattern (18 bp):
TTAGAGCTTACAGAGGGG
Left flanking sequence: Indices 147595 -- 148094
GAAGAACCCTCCACGAATTTTCGATAGTAGTTGACTAATCCAAGGAAGGAGTGATGCGAAGAATA
GCTTTCTTTCGTACCCATTCACAAGAAAGAAGGGTCTCAAGCAGTGTGTTCATGGTCACTCATAA
CATAGGATTTTCGGCATATTTTCATAGTCCAATAGCGGAGGGAAGTTTTCTATTCTCTTTATCTC
GATCGTGCAGGAATTACAACCGATATGCGACAATTTCAACATAAGAGATAGGAAATGTCGCAGAT
GCGCTGCTAGCTTAACTCACTTACCAAACTGACCAAACTCCGGAACTTATCTGGAATCTAAAGTC
CGAGGCTTGGGATATTCTAAGGACCCTAAGGGCTAAGGACTAGAGAAGAGGGCTAAGCCTAAGGG
ATAGGGAAGACGGGTTCTATTAAGTCTAGTCTTAGAGGTTAGTTTTCTCTTGACTTTAGGAGCTA
GCTGCGCCTGACTGATTTCAGGCTATAACAGGTCCTAACCTGCCT
Right flanking sequence: Indices 148129 -- 148628
TCGCCCCTTACTCCATTCCTTAATCAGAGGAATTGCGGCATTTCGGTTGTTGGTCAGTTGGTATT
TAGGTCCTGTAAAAAGGGGCGTAGCGAATGACTCACTTCTTTGTCTCCATCCTAACCTCATAGTT
ATGAGATATAGAGAAATTCATTCAACTGAAAAAGTCATTGCTACTTCAGCTAGCGGATGGTTTTC
TCTGAATTCCACCCCGCTTTGGTACTTCATCCCGTCGGTACATTGCTACATTCTGTTACAAGGGC
AGTCTCATTTCTGGCTCTAAGACTGCAATTGACTGCTTGAACCCGCTGGCGAATTCCGTCACCCA
CTTTCCCCATCACTTTGGCTTAGTGTGCATAGCCTTCCTTTTGCCTTCGGGTGGATAGATGCCTA
TTTAAATTTAACCTCCCATCAACGTTCCCCTAGGTTGACGAAGTCTCCCTATGTATTCTAATCTT
TCTCTAAACACAAGAGCTAACTATATATCCGGAGTAGTATCTAAA
Found at i:182231 original size:17 final size:17
Alignment explanation
Indices: 182188--182233 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
182178 GCAGTAAATG
*
182188 GAATAAACTAAGCAAGA
1 GAATAAACTAACCAAGA
*
182205 G-ATCAACTAACCAAGA
1 GAATAAACTAACCAAGA
*
182221 GAATGAACTAACC
1 GAATAAACTAACC
182234 CCAAGGGATG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 14 0.56
17 11 0.44
ACGTcount: A:0.52, C:0.20, G:0.15, T:0.13
Consensus pattern (17 bp):
GAATAAACTAACCAAGA
Left flanking sequence: Indices 181688 -- 182187
AAGCAGGAGTAGTCCTATCTGCCTAGAAGGATTCGATAAAGAGAATGTGAGTGGGCAGGAGATCA
ATAGACACAGAAAGAGAAGAGCAAAAGGAGCAGAAGGCACTCAGTTGTTTATGTGAAATCAAGGA
GCAGCAGGTTACACTTTGACACTTTCCCGAAGAGAGCTCAAAGCAATAAGATGAAAGATGAAAAA
TGCTAGTAGATGAAAGATGGGATGAGATGCTAGCCTTAGCGCAGAAGATCAATCATTGAGCCTTA
GGCCACTACCGAGCAGCAATGGAGGATCATAACACTTGAGAGAGGATCCCCACTTGAAAAGGCGG
AGACAATACCTCTTCTCTTGTTGCGACAAATCGAGTTTCAAAAGCCCTTTTCTCAATCCAATTTT
CAGGCACACCAGTCAAAGAGCCATCGGACCCATGAAAGTCCCCTTCTTTTACTAATATACAAGGG
CTTTGCCAGGATGTCTTTCATCAAGCAAAAGAGGGGCAGTAAATG
Right flanking sequence: Indices 182234 -- 182733
CCAAGGGATGATCTCGGATTGAAAGTCCAAGGGAGTATGATCCCAATAAAGATAGGATGGATTGT
CAGGAATGGTAGATGGAGCAAGGGTGCATTGCAGGCTTAAAACACGACACAAGTAGGACGCGCTG
AGGCCGAGCTTTCCTCTACTACTCATTGGAGCTAGCATACGAAATTTCCCGTTGAAGGGTTCAAC
TATCAGGGCGGCCATTGCGAGCGATATTCACTTTCAAGAGTCATCGAGCCTACGCCTATTTCATT
ACTCTCGAAGAGCTCATCAAACAAACAAAGAGCTAAGGGATGAGAAAAGGAGGAGGTGGAATTTC
AACTAGAACATTTATTACAACATCTTACAACACTTAATATTACAGAAAATGACAGAGAATTCGGT
AAGGGGATAGAAGCACATCCTGCACCCGATATGTCAAAGCAGCTTGAAGCCCTGCAACTCGCGCA
TACTGATGAAAGGGAAAAAGCAGGCCAATTCACACATCTTCCGCA
Found at i:219904 original size:15 final size:15
Alignment explanation
Indices: 219884--219912 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
219874 CTATGACTTC
219884 TTACTCTTTTTCTTT
1 TTACTCTTTTTCTTT
219899 TTACTCTTTTTCTT
1 TTACTCTTTTTCTT
219913 CTTAGAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.07, C:0.21, G:0.00, T:0.72
Consensus pattern (15 bp):
TTACTCTTTTTCTTT
Left flanking sequence: Indices 219384 -- 219883
GCAGGAGTAACTAAGCGCTTTATTGAAAGGAAGAATTCTTAGATCCCGGGAGTCATAGTGAGTAG
GCACTAGATTGAACGAGAAGGATGGAAGTGAATGAGCGACCTTTGCATATTCGTGTAATGCCGAG
GGCTTTCTCCGGATAAGATGTCTAAACCTGGGGTGAAGATTTATTAAATCTTATCTAGAATAAAA
ACATATAATAGAAGTAATTAATCAAATATAAACTACAATAATACTAGTAACATGCATATAATAGT
ACATAATAATAAAATACTGAGACCCTTTCTTTGAACCTTGTCAATGCTGGAACTTTCAAAAACAC
ATTATATAAAATCCCATTAGTTTCAAATCTATACTTATCTCGTAAGTGAGGGTAATGAATGGTAT
CCCATACAACGGATATATGCTCACGAGTGAAAAATGACATTGATGTATCGCCTATAAGACTCATC
GTTATCCAATTTCGTGGTTAGCTTCTTTTTCTAGCCTATGACTTC
Right flanking sequence: Indices 219913 -- 220412
CTTAGAATTAGGCTGCTTCTTTGCATTGGCCTTCTTTCCCTTTGGTTTATTAACCTTCTTGTCCT
GAGTAGGTGGTTCTACTTCCTCAGTAAGAGTGTGCTTCACTGGCACCTCAGAAGGCTTAGCAGCA
GACAATGATTGAATCTCTTCATCCTTTGATTGAATCTCATCATCCTTTTTAGCAAGTTCAGACAT
CAGACTATCAATATAAGTATAATATATATTCTCTTTCTCCTCAAAGAGCTTCTGCTGGAGCATCA
ATTCATATTTGATAATAGTGCTTTCATGACCAGCGAAGTCTATTACATTCTTTGGAAGTGTGTCT
ACCCAAACATTCTTATCATCATAGACTGGTTCCCTTTTTGTAGCCACTTTTGATCCAAGTTGGAA
TTGGAATTCCTTTTTGGCTATGTTTAGGGTATGCCAATCAATTTTAAAGAAAGACTGCAAGGTTA
TCTTCTCTGTTAGAGACGTATCGGCGTATTGCCCCATAAACCATT
Found at i:220074 original size:21 final size:21
Alignment explanation
Indices: 220048--220090 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
220038 CAGCAGACAA
*
220048 TGATTGAATCTCTTCATCCTT
1 TGATTGAATCTCATCATCCTT
220069 TGATTGAATCTCATCATCCTT
1 TGATTGAATCTCATCATCCTT
220090 T
1 T
220091 TTAGCAAGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.21, C:0.23, G:0.09, T:0.47
Consensus pattern (21 bp):
TGATTGAATCTCATCATCCTT
Left flanking sequence: Indices 219548 -- 220047
GAAGATTTATTAAATCTTATCTAGAATAAAAACATATAATAGAAGTAATTAATCAAATATAAACT
ACAATAATACTAGTAACATGCATATAATAGTACATAATAATAAAATACTGAGACCCTTTCTTTGA
ACCTTGTCAATGCTGGAACTTTCAAAAACACATTATATAAAATCCCATTAGTTTCAAATCTATAC
TTATCTCGTAAGTGAGGGTAATGAATGGTATCCCATACAACGGATATATGCTCACGAGTGAAAAA
TGACATTGATGTATCGCCTATAAGACTCATCGTTATCCAATTTCGTGGTTAGCTTCTTTTTCTAG
CCTATGACTTCTTACTCTTTTTCTTTTTACTCTTTTTCTTCTTAGAATTAGGCTGCTTCTTTGCA
TTGGCCTTCTTTCCCTTTGGTTTATTAACCTTCTTGTCCTGAGTAGGTGGTTCTACTTCCTCAGT
AAGAGTGTGCTTCACTGGCACCTCAGAAGGCTTAGCAGCAGACAA
Right flanking sequence: Indices 220091 -- 220590
TTAGCAAGTTCAGACATCAGACTATCAATATAAGTATAATATATATTCTCTTTCTCCTCAAAGAG
CTTCTGCTGGAGCATCAATTCATATTTGATAATAGTGCTTTCATGACCAGCGAAGTCTATTACAT
TCTTTGGAAGTGTGTCTACCCAAACATTCTTATCATCATAGACTGGTTCCCTTTTTGTAGCCACT
TTTGATCCAAGTTGGAATTGGAATTCCTTTTTGGCTATGTTTAGGGTATGCCAATCAATTTTAAA
GAAAGACTGCAAGGTTATCTTCTCTGTTAGAGACGTATCGGCGTATTGCCCCATAAACCATTCAA
CATTGACCTTATCTTTAGCAGGACCCTTGTGCTTAACAATATCACCATGACATTCAGTTAATAAG
GTATAACTCTTAGGTGCTAAGAAGATACCAGTCTTTACAAAGTGTTCTAGCTTTAACTTACCCAA
TTCAGTGGAAGAGACTTCTTCTTCAGGAAGAGGGCTTCCTAGAAT
Found at i:281997 original size:2 final size:2
Alignment explanation
Indices: 281984--282030 Score: 51
Period size: 2 Copynumber: 24.0 Consensus size: 2
281974 TTTTTCTATC
* * *
281984 TA TA TC TA TA TA TA TA TA -A TA TA TA TA TA TA GA TA GA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
282025 GA TA TA
1 TA TA TA
282031 GATACAAGAG
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.02, G:0.06, T:0.43
Consensus pattern (2 bp):
TA
Left flanking sequence: Indices 281484 -- 281983
ATGCATCAGTGTACTGTCATGATCACATATTAGCTCGATTTTCTTGACGGCTTGAAGGCGAGGCC
GCCTATTTCTTAGGGCAAAAGGCGCTCCCCCCTCCTAACTCCTTACACTTCTCCCAGGGACAGGG
ACTACGGCTTGACCTTCGGGGAAGAACTCCGTGGGACCCCTCTCCTTCTAGGGCGCCTAGATAGT
GAAAGGTTATCCCTTTGCAACGCTGGAAGCTAAGCAAAGTAACGAAGCTGGCTGACTACGCTCGA
GCAGAGCTCAGGCCCGGAGGTGGTGGCTGAACTCGCCGCAGAGTTCAGGAGCGAGCAAGACTCTC
TTGGTGAATGCAATAAGAATCGGCTGCTTGCCGCAGCAGAGTGCTTTGCCCATGCTGCTATCCGC
CGCCGAAGCGCTCAAGGGATTCGTGCTTGGATGTCGAGATCAGGGGACTCTATCCAATCCATGTG
GCGAAATCCATTTGTGGTGGAACAAACTCAATCTATTTTTCTATC
Right flanking sequence: Indices 282031 -- 282530
GATACAAGAGATCGGCCCCGAAGCAAGCAAGGTATGGTGGGTGCCAGCTACTTTCACTTGTTAGG
AGTAGGGGCTGAAAAGAGCTCTTTGTATAGGTTGGGTTTGCTGGGCTTTGATGCTTTGCTTACCT
TATTATTAGAGAAAGGGGAAGGTTTGATAAAGGAGCTTTTAAGCCCTTTTGCTGGATTGTCGGTC
CGCAGCCCCGCCCTATAGAATGAATAAGGAGAGGCCTATTGATGACCGAGCCACTCTTATACTAC
TCCTTACTTCACCCCCCTTGTTTGTCACTTAAAGGGCGAAGTCGCTGAAGCGAGTCTAAAGGCCA
AAGAGTGCTCTTTGAACGCTACTACGCATCCTTACTAATAGTATAGTGTAAGTAAGGTAGGTTTG
GGTATAGCAGGACTTGAACCTGCGACCATTAGGTTAAAAGCCCAATGCTCTACCAACTGAGCTAT
ACACCCCCAAAAAAAGTTAGTAGTACATAAGGATTGGTGCGGAAA
Found at i:282029 original size:16 final size:16
Alignment explanation
Indices: 282004--282034 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
281994 TATATATAAT
*
282004 ATATATATATAGATAG
1 ATATAGATATAGATAG
282020 ATATAGATATAGATA
1 ATATAGATATAGATA
282035 CAAGAGATCG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.13, T:0.35
Consensus pattern (16 bp):
ATATAGATATAGATAG
Left flanking sequence: Indices 281504 -- 282003
GATCACATATTAGCTCGATTTTCTTGACGGCTTGAAGGCGAGGCCGCCTATTTCTTAGGGCAAAA
GGCGCTCCCCCCTCCTAACTCCTTACACTTCTCCCAGGGACAGGGACTACGGCTTGACCTTCGGG
GAAGAACTCCGTGGGACCCCTCTCCTTCTAGGGCGCCTAGATAGTGAAAGGTTATCCCTTTGCAA
CGCTGGAAGCTAAGCAAAGTAACGAAGCTGGCTGACTACGCTCGAGCAGAGCTCAGGCCCGGAGG
TGGTGGCTGAACTCGCCGCAGAGTTCAGGAGCGAGCAAGACTCTCTTGGTGAATGCAATAAGAAT
CGGCTGCTTGCCGCAGCAGAGTGCTTTGCCCATGCTGCTATCCGCCGCCGAAGCGCTCAAGGGAT
TCGTGCTTGGATGTCGAGATCAGGGGACTCTATCCAATCCATGTGGCGAAATCCATTTGTGGTGG
AACAAACTCAATCTATTTTTCTATCTATATCTATATATATATAAT
Right flanking sequence: Indices 282035 -- 282534
CAAGAGATCGGCCCCGAAGCAAGCAAGGTATGGTGGGTGCCAGCTACTTTCACTTGTTAGGAGTA
GGGGCTGAAAAGAGCTCTTTGTATAGGTTGGGTTTGCTGGGCTTTGATGCTTTGCTTACCTTATT
ATTAGAGAAAGGGGAAGGTTTGATAAAGGAGCTTTTAAGCCCTTTTGCTGGATTGTCGGTCCGCA
GCCCCGCCCTATAGAATGAATAAGGAGAGGCCTATTGATGACCGAGCCACTCTTATACTACTCCT
TACTTCACCCCCCTTGTTTGTCACTTAAAGGGCGAAGTCGCTGAAGCGAGTCTAAAGGCCAAAGA
GTGCTCTTTGAACGCTACTACGCATCCTTACTAATAGTATAGTGTAAGTAAGGTAGGTTTGGGTA
TAGCAGGACTTGAACCTGCGACCATTAGGTTAAAAGCCCAATGCTCTACCAACTGAGCTATACAC
CCCCAAAAAAAGTTAGTAGTACATAAGGATTGGTGCGGAAAAGAA
Found at i:328424 original size:14 final size:14
Alignment explanation
Indices: 328397--328430 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
328387 TATCTATCTT
328397 CTATAAGATATAAAG
1 CTAT-AGATATAAAG
*
328412 CTATAGATCTAAAG
1 CTATAGATATAAAG
328426 CTATA
1 CTATA
328431 TATTTAGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.29
Consensus pattern (14 bp):
CTATAGATATAAAG
Left flanking sequence: Indices 327897 -- 328396
AAGAAAGCATTCCTTAGCTAACAGTAGTGCTTTTAACACTCTCTTGCCGCTGCTAGTTAATCTGT
TGGAGGGAAGCTGCTAACTGTGAAGGATGCTTTGACCGACAATGCCGATTCCTAATTAGTGAGCG
GAGCCTGGTCTGGGATCAAATGAATCCCTTCTTTCTATTAATAGGAAGTTACTTGCATAAAGAGA
GCGGATGTCCCGGAGTTAGACAAGTGACAGGTAGAGCTAATAGAGCTAAAGGAAACTAGATCTGT
AGAAGGAAACCTCCGAGAAGTGTCGATTGTATGTAAGAAAGAAGTATGCATCCTCCCGGACACCC
AATCCCTTCTGACCCATGAGTTTGGGCATGTTCCGAACTTAGCTATTCGGGAAACAGGTATTAGG
TATTGGATTCCGCTTGAACTAATAGACAGAGGGGCCGACTATCTGGATCTGGTTCGAATCTGTAC
TGGATTGACTGTCCAAGCTATATAGCTGATAAGCTTATCTATCTT
Right flanking sequence: Indices 328431 -- 328930
TATTTAGAATAGATATGCTTTGAAAGGTTTACAATTATTGTTGGGGACTGAAATGGTACAGAATA
CCCTTTAGGGAATTAGAAAGAATTCCAATCAGAATCCAAGTATGAATGCCCGCTTTAACTTCTAG
CTTTGAAAGACCGGGAACCTTGTCCGGAGCTGGCATGACTGTACGAGTTCCTTTCCTATTTTTAC
ACAAAGAGCTTTTTCTATTTAATATAATTAGGAAAGATTGGCTTCATTCCCCTTCTCTTCCTCAA
ATCCCACACTCGCCTACTTAGTTAGGTCAATCAGTTCCTTGACTGATGCCATACTTCACTAATTC
AGTCTTTTCTATTTGGCCTTAAAGAGCAATAGACTCTTCCTAGTGTAGCAGCTAAGACGATTCGT
TCAAAGCAAAGATGGGTGCCTCCCACGCTTCCTCCTGTTCTCCTTCGATAAGTGCCTAAGCTCAG
TCTTTGTCTTGATGAATGCTAGATTTCTAAACAAGAAGGGGAAGG
Found at i:342334 original size:18 final size:18
Alignment explanation
Indices: 342313--342355 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
342303 CAACCTTGTT
* *
342313 GACTATGACAACAGTCGC
1 GACTATGAAAACACTCGC
* *
342331 GACTATAAAAAGACTCGC
1 GACTATGAAAACACTCGC
342349 GACTATG
1 GACTATG
342356 GCAGGTCGGT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.37, C:0.23, G:0.21, T:0.19
Consensus pattern (18 bp):
GACTATGAAAACACTCGC
Left flanking sequence: Indices 341813 -- 342312
TACCGTCTAGCCGTTGGTACTCCGCATCTTCACGGAGAATTCAATTTCACCGGGTCCATGTCGGA
GACAGCGGGGCAGTCGTTACACCATTCGTGCAGGTCGCTACTTATGCGACAAGGAATTTCGCTAC
CTTAGGACAGTTAGAGTTACTGCCGCCGTTTACCGGGGCTTCCATTCAAAGCTTATAACACTTCT
CCTTCCGACCTTCCAGCACCGGGCAGGTGTCAGACTCTATACATCGTGTTACCACTTAGCAGAGT
CCTGTGTTTTTAATAAACAGTCGCTACCCCCTGGTATGTGCCGCTTTCCTAATCAAAAGATAGGA
GAGCACCCCTTCTCCCGAAGTTACGGGGTCATTTTGCCGAGTTCCTTCGACATGGTTCTCTCAAG
CGCCCTAGTATACTCTACTTGTTCACCTGTGTCGGTTTGGGGTACGGTCAGTTCACCGGGAGGAT
CGCCCTCCCAATTCGAAGTTTTTTCCTGGAAGTTTCAACCTTGTT
Right flanking sequence: Indices 342356 -- 342855
GCAGGTCGGTACGCTCTGCTCTCTCGCGACCCCTACTCTAATCAAAAGACTAAAGGCCCCTTACC
TTAGGTCGCCAAACAAACTACGACGAGAGTTTCGCCTTTTGAAGCGCCAGTCGCGTAGGGCGACC
GGGCCAGGCCGAGTCAGAAAGGCTTTGATGACTCAAGGTTCATATTAGGGAAAGGAGAGTGAGGG
GAAGAGGGGGCAGCCCTCGGCCCGATCATCCAATTCGCTCCAACGGACAGGCATGGTTCTGTAGT
CAAAGCAACTTCGTCACTTTCGTGTACCCATCGGACGGCAGCCCTTTCGGGGGTTCCTTAGGGAC
CGATTCACTCTGCGTAGATTGACTGAACGCAGAAAGCCTTCCACTGGCAGGCGATCGTGTTTTTC
ACAGGATTTCTCGTTACTCATGTCAGCATTCTCACTTCTGATATCTCCAGGTGTTGTCACCAAAA
ACCTTCCCCGATTGACAGAACGTTCCGCTACTGACACTTGAAAAA
Found at i:358236 original size:20 final size:20
Alignment explanation
Indices: 358207--358246 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
358197 ATTCTTTTTC
* *
358207 TAAATTAAATAGAGTAAGTA
1 TAAATGAAATAGAGAAAGTA
358227 TAAATGAAATAGAGAAAGTA
1 TAAATGAAATAGAGAAAGTA
358247 AAAAAAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.57, C:0.00, G:0.17, T:0.25
Consensus pattern (20 bp):
TAAATGAAATAGAGAAAGTA
Left flanking sequence: Indices 357707 -- 358206
TGTATTAACATATACTGTATTAACATAGTAGTAGAAAGAGTACCACGCTGCATCTGGACTTCAAA
CGATTTAGCTTTAACCCTGTTAACGGTCCCACATTATTGGTTGATAGAGAATCAAAGTAGATTTA
CCAATGAATCACGAAATGCTATGGTTCTTAAATATGGTTTCTTAATGTATTCAGAAGTAATTCGC
GGAATCGTGCACCTTTTCGAGTTATAACGAAAAAAAGTGCAGTTGGTTGGATCCAGCCTATTCTT
GAAATAAACAACTCGCACACACTCCCTTTCCAAAAAAAAATCAATACACCAAAGACTACACTTAG
ATTTATTGGATTTGTTGCTAACGGTATTAAACCCGAAACTCCCGGCGAATGGCCAATAACCCAAG
GAAAGGAAAGAATCGGTTACATTTTTCATATGATCTCCTCTTCTCTTTCTTATTCTTATAGATAG
ACTAATTATCTATTTATCTATATTTTTTTTATTCTATTCTTTTTC
Right flanking sequence: Indices 358247 -- 358746
AAAAAAAATATATATATTGATTTATAATCCCACTTGGCGAGTATGCCACTATCACGTGGCGATAC
CAGTGCCTACTTTTGTTGACGTTAAAATGCTCTGGTCTTGACGAAATAAAACCAGCCCACCCCCA
ATTTCATTCTTAGAGATAGTTGAAGAGAGTTGCACTTAAGATGATTAAGCACTGCCATCCAAGCA
ACTGAAAAGTTGGCCGATCGCATCATTTTTACACTAATCGGAGAGAAAGTCATGAATCCGCACTT
TTTTAGCGAACTCAAGAACCCCTGATTTAGAAATGAATGATTTTTTTCTAAATCAGAAAGAATCT
GCTTGTACACACTCGCCACCGCGGAATCTCCGATGACGATATCATCGCCAAGGATAGCGTATGCG
GTAAACTTACGACCCGGGTAAACTCTGTCTGCATACAACCACACCAATATAGGGTGAGATAGGGC
AGGGAAAAGAAAACCCAGAGGTTGCCCAGCGCGGAACCGAACAAA
Found at i:364785 original size:12 final size:12
Alignment explanation
Indices: 364768--364817 Score: 82
Period size: 12 Copynumber: 4.2 Consensus size: 12
364758 GGCGGAGCCG
364768 GTACCTCAACCA
1 GTACCTCAACCA
364780 GTACCTCAACCA
1 GTACCTCAACCA
*
364792 GTACCTCAACCG
1 GTACCTCAACCA
*
364804 GTACCACAACCA
1 GTACCTCAACCA
364816 GT
1 GT
364818 TGTTATCCCA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 35 1.00
ACGTcount: A:0.32, C:0.40, G:0.12, T:0.16
Consensus pattern (12 bp):
GTACCTCAACCA
Left flanking sequence: Indices 364268 -- 364767
TTTCTCCCATTCGTTTTGTTGGTCAACAACCAACCGGCTACTCATACTCAAACAAAGTCTTTTTG
CTTTTTTGAGCAAGAAGTGGAACTACAGTCCTGAAATTTAAAATGTTTTGGTCCAACAGCCCACT
TGATAATTTTTCCATTCTCCCATCTGGATACTTTTTTATGGAACTTACTCCAGTCCAAGTTCCTT
TTGAATCCCCCCCAGAAATCAGTCGATTTTTTGACAACGGCCCATACCCATACTTATCTTTCATA
TTCTTAGTATTTTTTACGACAGTCTTTTCACAGACAGAAAGGTTCGAAACTCAAGAGTTCGAAGA
AAAGAAATATGAGTTTCTTGTCCCTTTACTTTATTTATTTATAATAATACATTGTAACTTTACCA
TGGGTATGGGTTTTCAAGGTTCTAAGATCTCCTTGTGCGAGGGATTAAACGCCTTCTCCCCGCCA
AGTCCAGTTCTTCCTGAACCGATGCTTCCCCCCGAGGCGGAGCCG
Right flanking sequence: Indices 364818 -- 365190
TGTTATCCCACAATTGGACCCGCCTCTTATCTGGGATGACTCCAGAAGTAGAATCCTTTATAGCC
GATTTCTACTTCTGGACCTGGGTAACCCTACCGACCTACAGCGAATGGTATCTATTATAGATGCC
CAAGTTAGGGTGGAACGCGCTGTCGAAGCTGCCTTGGTGGAGGATGGATTTAGGCCAAATTCCAT
TCTAGCCCACTACGGAGAAATTAGAGGCCTTCTACATTCTCCGGCAGGGCGGCTTTTGACTGAAC
ACACTGTGCACTCGTACCTGAATCAGATAAGGTTGGAAGGAACGCGCCAAAGCGTTCCCTATCGG
CGAATTCTTAGAGCCGTCCAAGCGAATAATCTCCTTTTAGAACGCTAA
Done.