Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_029317
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: 644437
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.28
Found at i:6166 original size:28 final size:28
Alignment explanation
Indices: 6098--6154 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
6088 CAACTACCGA
6098 TATCTATTAATATCTTTTCTTATAATGT
1 TATCTATTAATATCTTTTCTTATAATGT
6126 TATCTATTAATATCTTTTCTTATAATGT
1 TATCTATTAATATCTTTTCTTATAATGT
6154 T
1 T
6155 GTTGTTAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.28, C:0.11, G:0.04, T:0.58
Consensus pattern (28 bp):
TATCTATTAATATCTTTTCTTATAATGT
Left flanking sequence: Indices 5598 -- 6097
TTCACGCAAATCCGAAGAAGTTATCACGGACGAGCCACATGCAGGGAAACTTGCACGTGTGGTTC
TGGCCGGGCTTTCCTGAGGTATCTAATAACCTTGCTTCTGCTCGCCGCTGGCGCACCTCTCCTAA
CTATTGCCCATTTATTCTGGAATAATTTTTTTAGGAGGGACAATTTTACATATTTCTGCCAAATC
CTTCTATTATTAAGTACGGCTGGTACCATTTCGATGTGTTTCGATTCTTCCGAACAAGAGAGGTT
TGATGCTTTTGAATTCATTGTATTAATTCTACTTCCTACTCGCAGTATGCTCTTTATGATCTCGG
CTCATGATTCAATTGCCATGTATTTAGCTATTGAGCCTCAAAGTTTATGTTTTTATGTGATCGCA
GCATCAAAAAGAAAGTCTGAATTTTCCACGGAAGCCGGCTCGAAATATTTGATCTTAGGTGCATT
TCCCTCTGGAATCTTATTGTTTGGGTACGACCGGACAACTACCGA
Right flanking sequence: Indices 6155 -- 6654
GTTGTTAAATATATATATCGTAAACTACCGGATCGGGTATTACTTAGATGTGAAACTTGCAGACC
TCATTGGTTGTGATATTGATCGTCACGGGGGGAACGAAATCTAAGAATATATAGACTTGTAGAGA
CCCTCTATGTAGTTGTCTATCTAGGGCGATCGATCTACATCTTTCCCCATAGCCCTGGGGCTGTG
TCTCGATCTCCTACGTGCGAAATCTGAGGGACTAGTTCCTATGGAGATTCCCCTTGGTCTAATTC
CACGCCTTATGACGTTTCGAAAAGGGAGTCGGTGTGGCGTAAAGTGAAGATCACGGGAAGTAGAG
AAGAATTCCCTTTCTGGGGTATTCCGAAGGTGTAACCTAGACAACGAAAAAGGGGCCCGATACTT
CAACTAGAAGAGCGACCAGTTGGTTCACCAAACCCCGACCCAGCGTTACACGTTTTCCAGGTCCG
AAGGGATCCAGTGCCCAATTACCGACTCCTCCCGGAATTGCGTTA
Found at i:37060 original size:15 final size:16
Alignment explanation
Indices: 37030--37062 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
37020 TTCTATTCTA
*
37030 ATTATAGGATTCTATT
1 ATTATAGGATTATATT
37046 ATTATA-GATTATATT
1 ATTATAGGATTATATT
37061 AT
1 AT
37063 ATATTATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.36, C:0.03, G:0.09, T:0.52
Consensus pattern (16 bp):
ATTATAGGATTATATT
Left flanking sequence: Indices 36530 -- 37029
GCAAGTTCAGTCTTTTCAGGGCGAGCTGACCGCAGAAACCGTAGACTTCCATGATGAACCCACCT
TAGCCACCTCCGATCAGACAGAAAGATGCGATCGTTAGAGATTCGACGATTCCCGGTTGGACCTA
TTCAAGCGATTGAACGAGATACTCGACAACTAGAAAGACGCACTTGAATACTGAATGCTATGAGG
AGAAAGAATGACTATCACCAACCATAAAGACGATAAAAGAAGGCACTCCCGTTCCCCCGAAATCA
TCTTCTGTGCGTGGTTATCCAATCATGATGTGGTAGGCTTAGTAGGGCTCGAACCTACAATCTAA
CCGTTATGAGCGGTACGTTTCAACCAATTAAACTATAAGCCCCTACAGATCTCTACATGCAATTC
GCTCACTTCGGGAAGAGCGGACGGAAGGCGACGGGGAGGCCTTTGCTCTATCTGCTTCTTCCTCT
TCTCAGGAATGAAGAATTAGATAAAAAAAAATGGATTCTATTCTA
Right flanking sequence: Indices 37063 -- 37562
ATATTATATATATAATATTCTATATCTATTATTAGAATGAATAATATAATTAAGCAAGCGGCCCT
TTTGCGACTCAAACTGCCGGTACGCTTTCCGGCTCGCAACGACTCAAACGGGCGGAGGCTCTCTA
TTTGCTTGCACTGCCGGCTGTTCGCCTTTAGTTAGAAGTAGAAGTCGCTCTTTGCCCCACACTTC
TAAAAAAGTATGGATTAATTCAGTAAGAAAAAAAAAACTTGGTTACGGGAACCGAAGGTTAGGCC
GACTACTTACTTTCTCCTTACCCTTAACAGGATTGTCTCCTACCGATCGAGGAAAGGCTTAGAAT
CCATGCTTTGACCGGTAATGTCCAATCTAAGAACGTCTTGTGCCTTTTCCTGGGCCCCCTTCATT
CTGACTTAGCTAATTCAATTCTTTCTATTTCTAATGGGCTTATACTTTTTTCTATATCCCCCGAG
AAAAGAAAGTCCTGCTATATCTAATGTATTTTTTCCAGGACCGCT
Found at i:45833 original size:14 final size:14
Alignment explanation
Indices: 45814--45842 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
45804 TTACTAATAT
45814 AATATAGAATATAA
1 AATATAGAATATAA
45828 AATATAGAATATAA
1 AATATAGAATATAA
45842 A
1 A
45843 GGAGGAGGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.66, C:0.00, G:0.07, T:0.28
Consensus pattern (14 bp):
AATATAGAATATAA
Left flanking sequence: Indices 45314 -- 45813
CCGTGAAGTCTCCCTTTGGACTAAGAAATCGGCACAGAGTAGAATCGAACTGATGTAATGGGCGG
AACGCTCCCCTACCGATGCCTTAGGCCCAAAAAAGCTTTCTTTTTCCTCAGGGGAGACCAGGAGC
CATTGATTGAATCCTTCGAGCTAGTCGGCGAAGGGACCAATGAGTATGATAGAATAGATAGGAAT
GCCAGAGCGTCAATGAAATTCATGTTTTCCGGTTCTCCATTTATGAATAGAAAAGGTCTTGAAGC
CCAAAATCAAGTTTTTTTGGAAAGGAGTAAAGTCAGGCTTTCTTCAACATCTGTACTTGATCTAA
CCCTTTCTTTTGCTTGACTTTCGTTTTCAATAAGGCTACCCTATCGCGATAGACCACCTTACTCA
AATAGGGGGCATCTCGGGCATTGAAAGCAAGGAGACTGGAAAGGGCTGAGGTAAGGGATCGTGAG
CCATAAGCAGCAAGCACAGTATTCAAGTAAAGGCCTTACTAATAT
Right flanking sequence: Indices 45843 -- 46342
GGAGGAGGATTTGGATCAAGCTCATATTACTATCACATTACTATGTTAGGAGATAAAAGCCATTC
AATCCCCGGGAGCTCTTTTTCCCTAAAGCGAACGGTCTACTCAAGCTCAAGAAAAGTAGAAGTTG
TGCAGCAAGTCGGGACTTCAATTCCTATCGTATCAGTTCGAGACAGTCAATTGTATCCCCCTCGA
CGCGAGGCCATCCAAAAGAATGAAGACGAGCTCACCCTGCAAGAAAACGGATGCAACAAGCAACG
ATTGAGCAGGGCGAATCCCTTACCCGGAGTCAAAATGCGCTGCGATCTAGCCTCTCTTGGCGCAC
CTACCTAATAGATAGAGATAAAGCTGAGGTAAGTAGTTAACTGACTAGTGCTTCCAGTCCAACAA
GTCTCCTATTTCCGAGTGAATTAGCAAGAGCACGACCCGCGACCTGTTATTCAGCGACATAAGAC
TTTTGTCGCCTAATCTTCCATTCCCCTCTACCTATGAGCTCCCAA
Found at i:94100 original size:13 final size:13
Alignment explanation
Indices: 94082--94107 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
94072 TCCTGCGAGC
94082 TTAGTTTATGAAT
1 TTAGTTTATGAAT
94095 TTAGTTTATGAAT
1 TTAGTTTATGAAT
94108 AATGCAGCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.15, T:0.54
Consensus pattern (13 bp):
TTAGTTTATGAAT
Left flanking sequence: Indices 93582 -- 94081
AAGAATAGACGGAGACGAGACGTACGATTGAAATCACGTTTATGAAAGCAATGGCTCTTAGCCGA
CTAAGATGACCACATAGTGGTATACTACTTCACGTAATTCACGTAATTTTCCACTTTACCACTAT
CAGACTAGACCGGAGCTTTTGAATAGGGCTTTGAGGATAAAAAGACTAGCCGGAAAGCCATTCCC
CTGCTTGCGACCGCTGGACCACTTGGAATGATGGAAAAGAGAGTACAGAGAGCATTCCATATGGG
GCTTCCCATCGGGGCTACCATTTTATCAGGCCCGATCGAGGTTCTCTTCTTTCCCGTTCATATGA
AAAAGACCTGCAATGCTAATCTCGTTAGGCCACCCGAACCCATCGAACCGGAGTTAGATAGGTGA
AAAGATAACAAGACAACACCTGCCTATATCGCTCCTGTCTAAGCGAGCGAGACTTTTTCCATTGA
TATTTCCATATCATGTAGCGAGACTCCACTTTAGATCCTGCGAGC
Right flanking sequence: Indices 94108 -- 94607
AATGCAGCAATCGTAGGGTCGACAGTACCGGTGGGCTTTGAGCTACCAGAGCAAGGAGATAGAGC
TTGAGCTTTTCCTTCATGGACCAAGGCGACTCTCGTTAGCTCTACTTGGGCTTAGTGCGATTCGA
AACTGGGATTTTTTCTAGCCCGAAGAACGAACAAAGACAACAAGGAGCGACTGATAAGGAGCGGT
TCAAGCTTTCTGGCCATTCCAACTGCCTCCATTATTCTACTTTTTAAGCGCCATAAGCAGCCAAG
CATAGTGGTTCGCTCAAGCAATGGAGTTTGCGAAACTTCCGTTCCGGTAGTCCTTAACGCAAGGA
AATAGTAAGATCAGACCCTCGAATTCGATTACACACAAGCTGCCAAGTAAGCTCTCGAAAGAGCT
ACCTCAGAATGAAAGCTACATCAATCCAAAGGAATTCAATCCGTTATATCTCCACCTCGTAAAGC
CGTAACAGCATCGACTCATTAATGCGCCCTCAAGGGGCAGCCTAT
Found at i:115539 original size:12 final size:12
Alignment explanation
Indices: 115524--115549 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
115514 TTTAATCGAT
115524 GCTTTTGTCAAG
1 GCTTTTGTCAAG
115536 GCTTTTGTCAAG
1 GCTTTTGTCAAG
115548 GC
1 GC
115550 GGCTCCTCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.19, G:0.27, T:0.38
Consensus pattern (12 bp):
GCTTTTGTCAAG
Left flanking sequence: Indices 115024 -- 115523
GAGAGGTCTTTCGGCTTGGACATGACGTTTGCTTGATATTGGGCGGAGTGGGCTTTGTTTGCTGC
TTTGCAGAGACTAGGCTAGGCCACGTGAATTGACCTCACCCATCACATCATCTTGGGAAGCTCCT
CCCTCCTCAACAAGCTCCACCTCCAGAATATCTAGAACCGTTTGGGATTGGACTAGATTGGTTCA
CTCAATATCCTATATAAAGGAGAAAGGGCCAAATCATATATAATGATATAATTGAAATTAAAGTT
ATGGACTCATTTTATAGATATGTTTATGTCTTATCAAGAAGCCCAAAAACTCTTTGATCTCTATA
CTTTAGAAGAGTTGAGGAATTTCCTGGAGCTCTTTCTTTCCATTTCTTTTCTGGTGTAAAACCCT
CCCTATCAATACTTCCTTGCTATTCATTGACAAGAGTTGTAGGGACAAAAATGAGTAATCGAACC
CCTTAGACCCTTTTGCATACTTCGATCTACAAGGCTTTAATCGAT
Right flanking sequence: Indices 115550 -- 116049
GGCTCCTCATATGAAATCCTGAAAAATAGAAATAGCCCATAAAATGACAGCCATCAAAAGGCCTA
AGTCCATATTCTAGCCTCGGTCTGTCCAAATTCAGCGGTCTCTACCCAAGTAGCTCTGGCCCATG
ATCCAAGGGACCTGCAACCAGTTAATCATTCTTTCTTTATTTTCCAACCACTCGGGCAATCATGC
TTGTTTTATCTTCCAACCAATCCCTTTGATTCCGTTTCTGCAGCAGTATATAATCTCGGTCCCTT
ACCTTGATGCCTACAGCTCAATCTTTTTTACAGTGATGGCAATAATATGCGAAATACTGTTTTTT
CTTTTTCTTGGGTTGTTTCTGAATGGCATCATAGCTACACGAGGGAAAGCGATGCTGCCCACTCT
GCCGGGGGCCGCTTTCTTCCCCTCAAAAATGCCAGTTCCACCATCAGGGCCCAGCAAGCAGCATA
ATTCTGTTCCGAGGCTGCGTTTCATTCCAGCACCAGTAGTATATG
Found at i:124192 original size:14 final size:14
Alignment explanation
Indices: 124175--124202 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
124165 GAACCACTAA
124175 CTATAAAGATAAAG
1 CTATAAAGATAAAG
124189 CTATAAAGATAAAG
1 CTATAAAGATAAAG
124203 GAGGTGACTG
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:0.57, C:0.07, G:0.14, T:0.21
Consensus pattern (14 bp):
CTATAAAGATAAAG
Left flanking sequence: Indices 123675 -- 124174
AGGAAGAAACTCCATAACATAAGGGGGAAAGCTCCACTCCTACTCCACCTAAGTTGAATCCAGTG
AAGAAGACTGGAACCTGAAAAGGCATCTTTTTCAACACTTTGATTAGTGTAACTACAAACCGCAT
TCTAGCAGCCCTAAAAAAAGAATCTCTAGCGAAGCTGTCAACTCAACCTAAGGAAAGCGATCCGC
TAGTCTAATCTATTCTCTGCTTTCGAGCAGTGAATTCCGGCCAGTCAACTTAGATGTCACTGGAC
TGGGCAAAAGCCCTTCAGTCAGCTTAGATACCGCTCCTGCTGCGTAAGATAATGTTGTAGAGGAG
TTTGTTGTCCTCAACGTTGACCGATTTCAAGAAGAGTCTAATCTAACGGGTCAAATCAAGTCAGT
TTTTCATTGACCTTAGAAGATGATTTCTTTTCCCCGAAATCCAGTACTGTCGAAAAAACAAAATA
AAAATCTAAAAAGAAAATGGAAAGAAACTAAGATAGAACCACTAA
Right flanking sequence: Indices 124203 -- 124702
GAGGTGACTGTAAAGGTCTCCGACCGAGGCTTTCATAGAAAGGAGCTTCGGTGTCACACTGGTCT
GGGCTTGTAGGGGCACCAGAAGCGGGTCTAGAGCCTGCTTCACACCCAAATCTCTTTTTGGACAC
GGACACTCAAATAAATAAAGCGTGCCCAACACCAACGTACAAGACAGATGCCAGGGCAATGAACC
ATAACCCCATTCAATATGGTTCCGACCTGCCTTGAAGCAGGAAGAGGAGCACCCGGGAAGGAGGA
CTAAGGATCTAATCTTCCCCAAGAGGGGAGAATAGGAAAGCAAAGGCTAAGGCAGGGGATCGGAT
TGAGCACTTTCATTCTTCCGGCGGAATCAAAGACATACCTCGATGCCCAGAATAAGGAAATAGAT
TCTTTATCCGCCTTCCTTAATGAAGACGAGGATTTTTAACTACTCGTATCAGCTCAACCAGTTGG
AATATCCCTTGATCTCGTATCCGTTGGTCAAGATTAGGAAAGTTT
Found at i:137276 original size:15 final size:15
Alignment explanation
Indices: 137256--137285 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
137246 AGGTTATAGC
137256 CTTTTATTTTACTTA
1 CTTTTATTTTACTTA
137271 CTTTTATTTTACTTA
1 CTTTTATTTTACTTA
137286 TTCAATTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.13, G:0.00, T:0.67
Consensus pattern (15 bp):
CTTTTATTTTACTTA
Left flanking sequence: Indices 136756 -- 137255
CTCATAAACCCAATAAAAAAAGTTTCACCCAGGTATACATATCCTTAGCTTGCGCCCTATTTGAG
ACTAAGGCAGGGAACCCTGTCCTATCACCTTTATCAAATCCCTAGCTCTATTCCTTAGTGCAACT
GTCCTATTCCTACCATGGAAATATCTATATTTCTTTTGTTCTATAGTTTCGGATAGAAAAGCGGA
CGGTATCATATATGAAGAAAGAGATTTAAAAGCCATAAGTCGTGCTAGCAACAGTCTTACTGTCT
TGGCTCCTTTGCCCCGGTCTTTTCTTTTTATAAAGTAGCACGTTCCTCTACGAAGGTGCGTTTTA
GGCCACGGTAGCAAGTGTTCTGTAAGGAGCTGTGGGACTAAAAGGCTTATGCTTATCGAGCCCTT
AATTAAGAGGAAGATGTGATTTAGTTTTCCCTGTTTTTCGCAAGTTAATCAGAATCGGCAAGATC
CCCTCTTGTTCTTGCTGCTTGGGAAGAGCAGGAAGAGGTTATAGC
Right flanking sequence: Indices 137286 -- 137785
TTCAATTTAAATCGCAAAAAGATGGATGGGCCAAATTGAACAAATCAATTTGCCTGTGCTATCGG
GCTACTCAGCTTCAAATCCTTCACGCTCCTTGGGATGCCTTACAGTCAGGGAATCACGAAGATGA
AACTAGACTCCTTTTTTGCAGTACCTTCGGTTGAGGTGCATTTATGATTTAATCCAAAGCCTGAG
CCTCTGAACAACCTGATGAATCGCGTTAAATGTGCTTTTCTGGCGTCTTTGAGTTTATGTTATGA
GTTGATCCTAGTTCATAGTAAGTAGAAGGTGTTACGGGTCGGCCTCGGGAATTCGAGGAGCTACT
GACGTTAAGCGTTAAGATTGGACTGCTCTTGGGGGAACAGCTTAGTCCATCTTCAACTCCTAGCA
TGAAAGTGAAAGTCTCAATCCCAGTTCCATATTAAGAAAGTAGACGGACAGAACTCCCCGACCTT
GTTAGGACCCCTTCGGATTGGTCCTCTTCTAGTCGAGTAAGGTGC
Found at i:138899 original size:20 final size:20
Alignment explanation
Indices: 138874--138912 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
138864 AGGTAACTCG
138874 AGAGTA-GAAAGAACTAGAAT
1 AGAGTATGAAAGAAC-AGAAT
*
138894 AGAGTATGACAGAACAGAA
1 AGAGTATGAAAGAACAGAA
138913 CCAGTAGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.54, C:0.08, G:0.26, T:0.13
Consensus pattern (20 bp):
AGAGTATGAAAGAACAGAAT
Left flanking sequence: Indices 138374 -- 138873
TCTTCTTTCCCCGTTGTGAAAGGAGTTGGTTCCGTAGTTTTAGAATTCGGCTGATCCCAAGTACT
CCATCTCCATCATTGCATATTTTTATATAGAAAGTAAAGAAGAAAAGGCATAACCAGAAGAATTG
TGTAAAATAAGTGAATTTATCCAGTTGAGGCATGATTGATTTTTTAAAAAGGATTCCCTCCAGAC
AGCTTAACTCCGTCAAGCCTGTACGAGTAAACAATAGATAAGGTTTGCTTGTTGGTTGTTGACCA
ACAGAAAGCATGGGATGCCCCACAACAAATAGATGGGAGCAGGAAATCTTTATCATTCGGCGTAG
TGCAGCTTATATAGAATAGAAGGGGCAAAGCGCTGTTCGTGGCACAGCTTTCTTATATTACGATA
TTTTCATTGATCGTAGCTAATTAGGTGGCAACAACCGAAGAAGCAGAAGAAGTAGCTGCTACCGC
TTCGTGGGCTTCTTCTTTTTCTGAGTCTGCTCGAAAGGTAACTCG
Right flanking sequence: Indices 138913 -- 139412
CCAGTAGCTTTGAGCTTTCACGTGTTTCAGCTCTTGTTCACAATCCAGTTGCTATTGAATCAGCG
TAAGGAGATGCCGATGAGGGTACAAGAAAAGAATGAGCTTTTGTTCAGAGCTTGAATCAGAATAT
CCTTCAGTAACTCCAGGATTCCCCTGGTAGGGCATACAGGACATACCAGGTGAGAAGTTCGGGCG
GAAAGATAGATCGAGTTTACTTTACCCTCTTGATTGACTTTCACTTTAGGACTGAAAGATAGCAA
AGGAAATGGCAGCAGTGCTTTATATATTAGGTCTTCGTTGATCACTTCTGCTTAATTTAAGCACT
TCTCTTTCGAAACCTAGAAAGCGAGAAAGAGAAGAGTCAGTTCTTGTGAACGACTCCGATGCTCT
TTCTATTTAAGAAGATGGAGGAATAAGCGATGCTGCTAAGATCCGCAGTCGATTTAGCTCTTGAG
GGAAGGGAAAGGCGGACTTTAATTTGATGGGCTTTTAGGACTGGC
Found at i:144497 original size:13 final size:13
Alignment explanation
Indices: 144479--144507 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
144469 GGATGAGTAT
144479 AAGAATGAATTAC
1 AAGAATGAATTAC
144492 AAGAATGAATTAC
1 AAGAATGAATTAC
144505 AAG
1 AAG
144508 GGGTATAGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.55, C:0.07, G:0.17, T:0.21
Consensus pattern (13 bp):
AAGAATGAATTAC
Left flanking sequence: Indices 143979 -- 144478
CGCCTGACCCACTTTCCACTGTGAACCTGCGCCGACACAAGACACAACCGCAGCAGTTCGACGGA
GAGCATGGTTCCTCCTCCTCACGAAATGGATTTTCAGTTCTTTGCCTCGGGTCAGCGGATGGTCA
GGGGACAGGTAATTACATTAACTAACAAAGCGAAATGGATAGGGATAGCTCGCTTACTACCTTCT
GGTCTCATCCAGCGTCTACAAGCGGAGAATTAGTTATAGCGTAGGGGTGGAAAAGAGGAAGAGTG
CCCGCTAGAATCTTCTTTCACATCCATCTTTCTGCGTCAAAGCTTTATGTTTGCCGCCCATTCTT
ATTCATCATACGACACGAGAAAGACAAAACGAATATCACAAGTAGAGTGAAAAGCATAATCTAAC
CTAGATGGGAATCCGAAGACAAAAGTTGGAATCTAAATCCGTTGAAGACAAAGAATACTGCGTGG
AAGCCATTGGATTTTCAAGATGTAGATGCGAAACCGGATGAGTAT
Right flanking sequence: Indices 144508 -- 145007
GGGTATAGACGTATGACTAGACTATGTTTTATAAATTGATACAACTTCTGAATTGAAGGCTCTGG
CAAGAGTTCGTGAATAGTCGACGTAAACAGATAAGAAAGAAGGATTCTAATTCTAGGCCAACCGG
CCCTAACTGATAGGGGTATTGGTCTTCTTTACCAATGTTTGGTAAAAAAGTTATATTGTACCCGA
CCTGTTCGGATATGTGTTAGAGTCGATAGGAGGTTCCCTCCCGAACTCGATCAAAATAAGGACGG
ACGAATATGTTTTGTAAATCTCTCACTGGAGCATCCTCAGGAAAAGGTGTAAGTGAAGGAGTTGC
CCGATCCCGAAGAAATTCACATACTCTCTTTATCCTCAGAGTTCTTAATGGCTTTAGTAAGGAAA
GTCTTAAAACCAGCCTGCCGTTTGGTCTTGTTCTTCCCTCTATGCCAAGATAAATCGAAAGGAGA
AATCTTGAGATCCCCGGTAGCGGGAGGACCCATTAGAGCTGCAAG
Found at i:166988 original size:13 final size:13
Alignment explanation
Indices: 166970--166995 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
166960 AAGGAGTTTT
166970 CTCGTATTCTGTA
1 CTCGTATTCTGTA
166983 CTCGTATTCTGTA
1 CTCGTATTCTGTA
166996 TTAGCTCCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.23, G:0.15, T:0.46
Consensus pattern (13 bp):
CTCGTATTCTGTA
Left flanking sequence: Indices 166470 -- 166969
ATGCGGCACACATGCTCTGAAGCGTGCTTTTACGCTCGATGATTCCCTCTTCAAGGTGTGTTCAG
TTAGAACGTTAAAAAGAAAGAGAGCGTTCAAGTTCAGGTGGTCGAATGCATTTTTCTGTACTGTA
GCAGGAATGGCTTTCCTGGGCCCTACTTTGTTTATGTATGCGTACGTGTAAACGCATTTACTTTC
TCTGACTCTGAGGGTAAATTGACTTCGGGAGCGGTAACGGATTTTCTCGATACTAAGTTTGCCGG
AAAGCACTTCACGTATAAGAGCTTGGGTCCCCGTATCCTTTGTTTGCCTTTTTACCTTCGGTAGG
AAACCATTATGGAAAGTGATCACACGAAAAGCAAAAAAGCGCTCTTCCTTCCGGCTTCTGGAAAG
ACTTGAGCCGATAGACGAACATTGGTCAATTTCAATTAAAGGTCGGCTACTAATTACAATTGTTG
GATTGAAAGCATCTCTCTTTCCGATTTCGTTTTCGAAGGAGTTTT
Right flanking sequence: Indices 166996 -- 167495
TTAGCTCCTTCCACGAATGAATAAGGTAAGGCTTCGATCTTTCGCTTTTGAGTTCGTCCGGAAGC
TCTAGTATGAGCCGGTGATTCCAGTCCGTCTCGGATGGAACTCCCACCTAAAAGGTCGTCTCTTG
TCGAACATCTCACCCAAGCGCTAGGTAATCCAATTTGGAGCATCGGTACTCGCCAGAGTTACAAG
TCGTTAAGCGACGCGAAAGAGTTGATCCATCGGATTGGGATTAGCCAGTCTTTGAGCTAGCCCTA
ATTGAATCTACCAAATAGGCAAATAGGCTAAAGAAGGGAAGCACCAACCATTCATTTGTCGAATC
GAAAGCTTCGCCTACGACGTAACTCAGCGCGGTAAGCTCCATTTTGCTGGCGCTTGTTTAATTTA
AAGTGGTACGGTATCCCCATACTTTTCTAACTAAGTCAATTGAAAATGACATCGGCTAGTGAGCA
AACGAGCTTCCGAATTGGATCAAAGCCAAGAACCGAGGCGAGGTC
Found at i:207302 original size:14 final size:14
Alignment explanation
Indices: 207285--207313 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
207275 GACTACATCC
207285 ATCTATCCTACCTA
1 ATCTATCCTACCTA
207299 ATCTATCCTACCTA
1 ATCTATCCTACCTA
207313 A
1 A
207314 ACAGTAAGCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.31, C:0.34, G:0.00, T:0.34
Consensus pattern (14 bp):
ATCTATCCTACCTA
Left flanking sequence: Indices 206785 -- 207284
GAACAAATACTATTTATTAGCTTAGCCGGGAGAATCTAGTCATTTAGTCAGTTCATAACAATCTC
TGTAAAGCAAGGGGCAAAGCTTCTACGACAGCTTCTCCCTCATGTCATGTAGTCGTCGGCCTTCC
CGACGCCCCCCCTTCGTCGCTTCTGGCTAAGCATCTTTCGGCGGAGGAAAGGAGGCGACTAGTCG
CTTCTGGCGAAGCTGCGAGCCTACCCTGCCTACTTAAATAGCTTACGCTTACTCAGCCTAGTCTA
CTAAAAGAGGGCTACAGCAAGCAACGAAGTTGCCTTTGTTTGTTGTGGGTCGCGCCTCGCCGTAG
GCACTGAATGAATGAAATGAGTGGAGATCTTCCTTCCTCCTTTCAAATAACCAAGAACTTCGTTG
GTACTAGTGGCGAAGAAAAATCTTACCCCAAAAAAAGCAACTCGGAACCTAAAGAGAAGAGAGTT
CAGTCTACAAGAAGCTGGCAGAGCTTTAGCCATTGGACTACATCC
Right flanking sequence: Indices 207314 -- 207813
ACAGTAAGCCTTTTCTTGTTCGTTCTTCGAGCTAGTGGAGTCCTTCCGGCTAATGAAGATACTAC
TCCAGTCTTCCCATTCATTCACAGTGGATCCTTCCTTTTCCCTAAGAATTGAACGAACCAAGTTC
ACCTATACGAGAGTGAAGAATAAAACCCTACAATCAACTTCCCACTTTTGATGTCCCACGATTCT
GCTAGTTTAGAAACTAAAGAGAAAAACAGGCGTCAGAAAAGCGATAACTCAAAATTCTCCCCAAG
TAGGATTTGAACCTACGACCAGTCAGTTAACAGCCGACCGCTCTACCACTGAGCTACTGAGGAAG
AACTCCCTTAAGGAAGCCGACTCTCGTTCTTTGGACCAACCTATGACCGGGTTCGTCACTCTTTT
TTTTTCCCTTGATTGAAAGAGGCTAAGCGCGGTACATTGAGTAAAGGGAGGATTTGCTACATCGC
TACATCGGGCGGTGGGTGGCCCCTTCGAGAGTTGCGGGTCCTTGC
Found at i:383768 original size:24 final size:24
Alignment explanation
Indices: 383741--383788 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
383731 AACTTGCAAA
*
383741 CATAACCAGGCAGTGAGGTATCTT
1 CATAACCAGGCAGTGAGGAATCTT
* *
383765 CATACCCAGGCGGTGAGGAATCTT
1 CATAACCAGGCAGTGAGGAATCTT
383789 AAGGGGAGGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (24 bp):
CATAACCAGGCAGTGAGGAATCTT
Left flanking sequence: Indices 383241 -- 383740
GGCCAAATCAGGTCTTGTAATATACTGCAGGGCTCCAACGATGCTTCTGTACAGAGATGGATTAT
GAAATGGAGTAGAAGAGACTGCAGCAGAGGACTGATTTTAAAGTTAATTGGAGAAGAGCAGGGCT
TACAATTCAGCATAGCAGCTCTCTGGAGGAGATCCAACGCATATTTTTGCTGTGTTAAAAAAAGT
CCACGATCATTCTTGTCTTGAGTACCTCAATGCCAAGAAAATAGTTCAAGTTCCCGAGGTTCTTT
ATAGCGGAGCACTTAATTCAGTGATTAGAGTGGAGATATAAGAGGTATCACTGCCAGTTATAATA
ATATCATCCACATAAACCGCAAGAATTGTAGTTCGCAAACTGTTAGTTTGAATAAATAACGAGGA
ATCACTACGGCTCATAAGAAAGCCTTTACTGATTAAAAAGCTATAAAACTTATCATACCAAGCGC
GTGATGCCTGTTTAAGACCATACAATGCTTTCTGCAACTTGCAAA
Right flanking sequence: Indices 383789 -- 384288
AAGGGGAGGGGTTGGTAGTGAAGGGAAGTCCAGGGCTGTGTCTGATCAGCTTACTGGGAGAATTC
CAGGCGAGGGAGTATTGGTAAGGTTATGGAGGAAAGAGGAAATAGGATTTTGGGCATCTCTCGTT
GCTTCGGATGTTTATGAGAAAGAAGCTTCTCACAGATATTGACTTTTAGATAGATACCAGCATCG
TATCTTAATTAGCAGTTTCTTGAACTTGGTTGCACTCGTAAAGCAGCTTAAGAGAGCAACGAAAG
ACGGAGCGGTGATATTTCATGACTAGCAAGTGGAGGATCATTCCAGGCTCTAATTCAGTCTCTGA
TGGCGTAGCTGATGTGTCATGCTAGGAAGCTGAGCTAGGGCATTTCTTCTTTCGGTTTAAGTGTT
GTGAAAACCCTCCTCTCCGCTTCTGGCAGCATAGAAGGAAGCTTGGGGGAAAGGTCTAAGTGCAA
GCATTGAGTCAAACTGATTCAGGTATAGCAATGTAGTTCTTGTCT
Found at i:422092 original size:13 final size:13
Alignment explanation
Indices: 422070--422104 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
422060 ATCAGACAAT
422070 AATAAGAATAATA
1 AATAAGAATAATA
*
422083 AATAATAATAATA
1 AATAAGAATAATA
422096 AA-AAGAATA
1 AATAAGAATA
422105 TTCATGAGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 6 0.30
13 14 0.70
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.23
Consensus pattern (13 bp):
AATAAGAATAATA
Left flanking sequence: Indices 421570 -- 422069
AGACAATCACAGATTCAGACAATGAGTAAATACTAAACCCGCAAAAGGAAGCCTGCCCTATGATT
ACCAACCTCCGTAGTCTTTGTTGGGAACGTCAAGATAGGAATAAGGAAGCACCAAAAGGACCCCA
GGTTGCTCTGTTCACCCAAGCAATACGTCATCAAGGTGTAAATAGAGTCAGCTCACTTTCAAGCA
AATCAACAAAATAACTTATAGTAAAAGGAAACCAGATAAACATGACAATAGTCTTTCGACGCAAA
ATTCACATAGATAAGAGCAAGAGAACAAGATTCACAATATTTCAAGAGAACCCACACAAAAAAGG
GAACGGGATACCGTTATATTGGGTCAAGGTTTGCACACTCCAACTCCCACTCTCAATGCCTTTAT
TTAGGTCAAGCTCCAACAGGTAGATTACACTAAAAGAAATCCACTCAGACACCTTTTTCACTTAT
TTCTTTTGAGAAAGACATTTTCATATACTGGTTCAATCAGACAAT
Right flanking sequence: Indices 422105 -- 422604
TTCATGAGGATGTTGAAGATTTATTCACATCTTTATTAGAGCAAGGGTTGATCGAGCTTCCCGAA
CCTAAGAGACCGGATGAGGTGGGACGAGTAGGAGATCCCAAATACTGTAATTCCATCGGGTTATT
TGTCATCCGATAGATTATTGTTGAGTTCTTAAAGTGAAAAAAGTTTGAAAATGATGGTGTCATTG
AAATAGACCCTCCTAAGCAACCTGTGGTCACTTCAAATGCTTGTAATAGTTGGAGATATTCTTTG
CCCGATAGCTGAGATCTCGCCAAGCATAGCCTATATCTAGATCTAGTTCTAGCACCGGAAGAGCA
ATTTCAGAGGATCTCACAAAATATGATGAAAGATATATTCAAGGAGAATGGAGCACTCGTGTTAG
CCAAAGGAGTAGGGAAGTCTGGTTTGGGCAACTCCTTATACTGAGACTTGCAAGAGCCGGTGGAA
AAAAATCCTTATGATCCGGTAGAAGCTGGAGCTGTGGAAAATCAA
Found at i:522081 original size:15 final size:15
Alignment explanation
Indices: 522061--522091 Score: 53
Period size: 15 Copynumber: 2.0 Consensus size: 15
522051 ATAAAAAATA
522061 TAAAAAAGAAAAAGGC
1 TAAAAAA-AAAAAGGC
522077 TAAAAAAAAAAAGGC
1 TAAAAAAAAAAAGGC
522092 ACTCATCAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.71, C:0.06, G:0.16, T:0.06
Consensus pattern (15 bp):
TAAAAAAAAAAAGGC
Left flanking sequence: Indices 521561 -- 522060
AGGCTGGGCTGCGTACTTTTCGGCGCCCACCTTTTCTTTAGGTGTTGGGGCAAGCCCCAGGAAAG
TCTAGGTTGGCTCCCAGCTCCATCTCGGTCGGCATCCTGCTCTCGAGGGAATGGAGTCCTGGAGC
GAACTACTCATTGCTGTCTTGCCCAAGGAAGGGCATTTGGAACATTCTTTTTAGGGAGGGAAAAC
GTGGTTGACAAGCCACTTCGAGGAGGCGACTGGAGTGCTTTCATCAAATAATGCATGTGGGCTGA
GCCATTCCCATCCCGACGTGGTGGCCCGATTCGGCCTGGCCTGGTCGGGAAGAGATTCACATAGA
GACAGACTACTGTTATCTGGGAATATCTTTCTATGTTAGCTAGCGGGGGCGGGCTTTGCTTTCCT
ATGGTAGTCCCGCGGCGGCCTCTGACCGTCCGTCCCGTCTCATCTTGATTTGGCTATACTTGTAT
GTAGCCAGCCATGTTAGCTTCACATGAGAGCCTTTATAAAAAATA
Right flanking sequence: Indices 522092 -- 522591
ACTCATCAGTCGGCCCCTTTCCTATTCAGCCTTGCCACCTCTCCAGTTAAGAGAATAGGTCCCGC
GGCCGCCCGCCTGAATCTATACTAGCTGCCACGCACGACCCGAACGATTTCAGCGCCCCTCTCCA
GATAAGAAGCAAAGCGTGCCATCACCTACAGCCCTTTCCTCTGCCGGGGACTTCCATGAAATGAA
AACGGGCGGCATCGTCGTATGCTCGACATTTGTTGCCCTGGTTTATACCCCGGAGTACTCCTATG
GCCGATCTGTCACCCAACCTCCTTAAACAACCTAAAGGCTTGGCCCCGTTCCGTTTGGAGTTGGA
GAATGGGCCTTATGGCACGGCTTAGTCAGTTATTCTCGCAGATAAGATTCGGACCGCCACTTCTC
TGAAAGCATGGTTTTTGCCTCCCTCCTTGGAGTTCGTCCATTCGTTGGGCGATCCCTTGCTCTCA
CGTTCGAGTGTTTGCTCGTCGTTTAGGCCGGTGAGTGAGATTTCT
Found at i:561243 original size:19 final size:19
Alignment explanation
Indices: 561219--561257 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
561209 CAAAGAGCTG
561219 TTTTCTTTCTTGCTT-TGTT
1 TTTTC-TTCTTGCTTCTGTT
*
561238 TTTTCTTGTTGCTTCTGTT
1 TTTTCTTCTTGCTTCTGTT
561257 T
1 T
561258 GGGCTTGCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.00, C:0.15, G:0.13, T:0.72
Consensus pattern (19 bp):
TTTTCTTCTTGCTTCTGTT
Left flanking sequence: Indices 560719 -- 561218
TTCTCCATCCGCCCGCCAGCAGCAGGGGGGTTCGATTCCCGTTATACGCGATGTGGCGAAGAAAA
GCGCTTGTTATTTGCGGAAAGGAAGAAGTCATCCCTCTTGCTGGAGGAAACTACCTTTCTATCCT
TCTCCTGCCCCTCTCAGTTGGAAAAAGGGCTTTCGACTTTCCCTAATCTCCTTTGCTCCCTAATC
CATTCCCGGTGCCATTCAACTATCTGACAATAGAGTATCTAAGTCAAAGCTGTTCCCGGGTTCAG
GTGAAGAATGTTAGAAAGACTCTCATGAAAAAAACCTCTAACTTGGTTCGAGTGGCTGATAGCTG
CTTATCGCTCCTGTCCAGTCATCTTAGTCCATGGCTTCTGTTTCATGCTTGGTTGATGGAAGACA
GCTTTGAGTGCCGTTACTTTCCCCCTCCATGCTTGAAGTTCATTCCTCCGTTGTGCTTTGTCTGT
CATCTTCTTTCTTCCCTTCCTCGGGCACAGTAAGACAAAGAGCTG
Right flanking sequence: Indices 561258 -- 561757
GGGCTTGCTCCTCTGTTATCCCTGACTCCCTAAACTTAATGAATGAAGGAAGGGTCTCCGCTCCT
TACCCTATCGGGCAAGTGGCTTACACTCCTTGCTTGCTTTCATCCTGCTTTTAGTGCCGCTTGCT
TGCTCGAAGGAGGGGCTACCGCTCTTTAACCTCGTCGGTAAAGCGGCTTGAATAGGACTTTCCCT
ATTTTCATTGGCCTTTTCTTCGATGTCAATGTGCTCAGGTCCTTTCTTTGCCCCTTCCCTTGGGT
TGGGCTCTCCCTCAAATGCCCTTTCCCTTCGTTATCTCTACATGAGTGAAACTCAAGCACTCGAA
TATCAGTAGATTAGCGTCACGCCAACGCAACTCTCAAACCATCGGCGAGAGGAGAGTAGGTCCGG
CTATGACTTTCATAGGAACCGTTGGGCCACTATGTCATAGTGAGAGTAGGGACCCATCCCATATG
ACTCAGAGTCAAAGAAAGCTCTTAGCCTCCGACCAGTGAAGATCA
Found at i:597309 original size:28 final size:28
Alignment explanation
Indices: 597277--597334 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
597267 TTATCAAAGT
597277 TAGGACAGATGTACAAGGTCTTTCTTTA
1 TAGGACAGATGTACAAGGTCTTTCTTTA
597305 TAGGACAGATGTACAAGGTCTTTCTTTA
1 TAGGACAGATGTACAAGGTCTTTCTTTA
597333 TA
1 TA
597335 TTGAAAAGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (28 bp):
TAGGACAGATGTACAAGGTCTTTCTTTA
Left flanking sequence: Indices 596777 -- 597276
GATCGGATGGCGTGTGTTCTGAGTTCAAGCACGTAAAATGGTACAACAAATCCATAGCGTCCGTT
GGCTCTATATCCGTTAGAGTTTTTGTAACCCGATTAATCTAATATAGGGGGATAGGTTGCTTGCA
AGACGGATGCTGCAAAGAAAGCCTCTTTTATTTAGTCGGAAATCAAAGTATGTACGAGCATCAGC
GAGGGTCGATGCTTTCTTAGAGATGTTAGGGGTTCTATTAAAAGCCAGTCTTACAGGATAAAAAA
AGTCTTACCGAGTGTGACCAGCCAGTTCCAGCAGAAGTCCAATCAGACTATCGGATGTGACGTGG
AAGCTTTCCTTTATTAAAAGAAATACATTTACCGGGATGTCTTTTCCAATCTCCCAGATCCTATC
AACATTAACCCATGCAGTAGGCCCATTTTTTTTCTCTTTAAGGTGGAGCTCATCAAGCCCGAAAG
CCAATACCCGCGGAAGTAAAGTATGTATTCCAGTGTTATCAAAGT
Right flanking sequence: Indices 597335 -- 597834
TTGAAAAGTTCTATTAGTAAGCCAGTTTGAAAAGTTTTTGATCTACGCAAGGCAAGCCAGCTTCA
GTAAGACAGTAGTGGCAGACCAAAAAGGAAGAGTGGATTGGCAGGTTTTCCAGTTAGTGGAGAAT
CCATTCAAATTCATATTAGAAAATTGGATTCTCTTTCTTATTATAGGTAATTTCTCTTCCACCTT
CCTAGCCTTCTTCTAGCTATTTTACTCTCAACTCTAAAGGAAATCAATGTATATATTAGCGCTTG
ACCTAGATGGATAACTCCCACTAAAATAAATCTATGTCTTATCTGATCCTTCTGCTTGCCTAAAA
TCTGACGCCTAAGAGACTGCCACGAAGGCGAATTCAATGCGGGTACTTTTTATGCTTGGAATGAA
ACTACTGGAATGACTCCTACAATGCCAAGAGGGGGAAACTACCTTTATCACAGGTTTGTGCTTAC
TTAAGATCCATATCAAAAGCTTTCAGCTATCCCACTTGCTTACCT
Done.