Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_072122
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: 257378
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Found at i:141245 original size:30 final size:30
Alignment explanation
Indices: 141211--141287 Score: 136
Period size: 30 Copynumber: 2.6 Consensus size: 30
141201 TCCAATCAAA
141211 AGGAAAGTATAAAGCTCGACCAATAGGGAG
1 AGGAAAGTATAAAGCTCGACCAATAGGGAG
141241 AGGAAAGTATAAAGCTCGACCAATAGGGAG
1 AGGAAAGTATAAAGCTCGACCAATAGGGAG
* *
141271 AGGAAAGAACAAAGCTC
1 AGGAAAGTATAAAGCTC
141288 AATCAAGTCG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 45 1.00
ACGTcount: A:0.45, C:0.14, G:0.29, T:0.12
Consensus pattern (30 bp):
AGGAAAGTATAAAGCTCGACCAATAGGGAG
Left flanking sequence: Indices 140711 -- 141210
GAGAAGGGAGTGAACGGGCGACGGCTTGCCCCGATAAGTGGGATGCAGGATCCGCAACAGCAGTT
ATAACATATTTTCCTTGACTTAATGTGAACTAGGGCGGATACCTTGGCCGGATAACTAGGATTCA
GATCTTTTCTAAGACAGGTCTCCTGAACGAAGGATTCCCTCGCCTTGAGATTGAAGTGAGCTTTC
TGAGACTAAAGACCACAGGATAGGAGACTTGGGAAACTACTTCTTAAACTTGTAAAAGAAGAAAG
GTTTGGGAGACAAACCCCAAATGCGCTTTAAAAAGCCTTGTGCCCCATTGATGGAAGTGAGCTTG
AAGAGGCGCCTTCTAATAAGTGGGGAAATGTATTCATTTGAGTCAATCTCTTTCCTAAAATCCTT
CTTTAGCAAAACAAGATATTAGGTTACGCTGGCAGACTCCCCTGTCCATTTACAGATCAGACTAT
GTCAACTCAGCCAGTAACAGGGTATTAGGGTTAATTCCAATCAAA
Right flanking sequence: Indices 141288 -- 141787
AATCAAGTCGGTTGAAGGAATATTCCAGTCAAAGGCCCAAGGGTAAGTTAACTGCCGCTTATTAC
TTAGTTTCCTGGCTTAACTCTTGCCGGGCACGGGCAGCAAAACAAGAATCGGTGCCAGAGATGCA
GGTTAGCTAAATGCTCTTAACACGCTTACATCGATATCCTTACTTTTAAAGTATAGCATCTCTCT
CTCCCATAGGAAGAAAGAAGCACTGTCATAACTCATCTAACAAGTAACCCCCCTACTAATATCCC
TTAAGCTAAGAAGCCCGAAGAGGTCACATCCACATGTGAAAGACTAAGACTTTCATTCCTGATTA
GCTAACTCTTTAGTAAAAGAAAGAGAAGAAAGACAGCTAATTAGCCTATTAGTCTAATAGCTGTT
TATGAACCTCTATCAAGTCTTATGAGCAAAGTCTGGGATGTCGTATCCACCTCTTCTGACTGGGA
ATAACAAGCCTAGGTGAGCAAGAGGAGCTGAAAGAGAGGGCCTAA
Found at i:155534 original size:27 final size:27
Alignment explanation
Indices: 155504--155566 Score: 90
Period size: 27 Copynumber: 2.3 Consensus size: 27
155494 AAATAACGAA
155504 TAATGAAACAATTCATATATTGACTAT
1 TAATGAAACAATTCATATATTGACTAT
****
155531 TAATGAATTGTTTCATATATTGACTAT
1 TAATGAAACAATTCATATATTGACTAT
155558 TAATGAAAC
1 TAATGAAAC
155567 CTGGCAAAAC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.40
Consensus pattern (27 bp):
TAATGAAACAATTCATATATTGACTAT
Left flanking sequence: Indices 155004 -- 155503
GCGCATAAAAAAGGGCTGGCCCGTCAAAAGCCCGGTTCCTTCGCGAATGAAGTTCAGAATCAACA
AGGGTTCGTAGAACGAAGGAAGTGTACAACTGGGGCGCAGCCCCACTTTTTTGTTCGTAACGAGG
GAGAGATAGGATAGAGTTCTTCACGAAGTTCGAGACAAAGGAATAAAAAAAAGTTTCTCGAAGGC
CTCCTCGTTTTGAGACATTATTGCTTTGGGGTCGACCCCCGTAACAAAGAAAAAATCCATAAAAA
CTTGGGATCCGACACCATGATAAAATACTACCCTCATGATTAGACCATGTCCCTGAGATTTGATA
AAAGAAAGGTGCATTAGCGGTTAATACGTTGTAATTGGATAAGTTATTAGGAATATGACGGAACG
AAAGACCAAGGAAAGAAAGAAGAATGCACCATAATGCGGGTGCTTTTCCAAAAACTTCTCTTTTT
TTCTTTTTGCAAATGAATGCAAGGAAAAGACCCGGAAATAACGAA
Right flanking sequence: Indices 155567 -- 156066
CTGGCAAAACGAATCAGATACCTATTTGAACAGCGGCGAGCTTTCTTTCTAATGCACATGATTGG
CTGCTACCCTTTCCCAACCCATATGATATGGTAAGGGATGGGATGCTATGATTAGTCTCACGAAC
GGGGCTAAGCCCTTTGTCAGTAGAGGAAATTCCAGGTAAGTATCAGTCTTCAGTCTGAGGAAGTG
GATGGAAGGATGTGACCCCTTGCTTTTGACTTTGCTGTTGTTGTTGATTAGTCTAGCGCAAGGCT
TTGATGAATTCGCGGATGTTATTTGATCAGGAATGGGACTGAGAGAGCTAGCCCTGATTCCGTCT
TTATTGACCGAGTAGCTGGACAAAGAACAAAGGAACGAGACCTATCTCACTAATCCGGACTCGTT
CGATTAATGGTGTTGCTGTCAGCCCTGTTCCTAGAGATCTGGGATGGAGGGACGCAAGAAAAGTA
GGAATAGGAATGAACAGCAAATCCAATAGTTAGAGTAGGGTTAAG
Found at i:176606 original size:18 final size:18
Alignment explanation
Indices: 176583--176619 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
176573 GCAGCTGATA
176583 CTTCAAGTATATCCTTAT
1 CTTCAAGTATATCCTTAT
176601 CTTCAAGTATATCCTTAT
1 CTTCAAGTATATCCTTAT
176619 C
1 C
176620 CAAGAGTAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.24, G:0.05, T:0.43
Consensus pattern (18 bp):
CTTCAAGTATATCCTTAT
Left flanking sequence: Indices 176083 -- 176582
GGTTTGCCTTCGTTCCTTGGCTTCCCTTCGGCATTTAAAGAGTGGAGTTATTCCCCTTCCTTAGG
TAGCCGGGAAGAGTTTTTTCACTAGTTTTCTAGAAAGCATTGATTCTATAATTAGCATTTTTGAG
TCATCCTCGAAATGAATATATAAATAGCCCTTAAGCTCATTGAGCATGTGCATGTATACGTCTTG
TATTTGACCATCGGGGTGAGGAAGAAGATTCGTTTTCACTGCCATATCCGTGTTTAGCAATAAAT
AACTCATGATCTGATAAGCACTTGAGGATGCATCTTGAGATATGGCTTCTTCCTTATATTCTTCC
ATTCTATCGTTAGACGCACACAGGGCCTTTGAAATGAACTGAAAAGGATCACTGGCACCTTTCAC
AAAGCTTATTAAAGACTCATCGGAAGAATAGATCAAACTCTTCTTTGACTTAACCCATTCAAGCG
CTTTCTCGTAGTTATTGAATTTTTTATATTTAAAGGCAGCTGATA
Right flanking sequence: Indices 176620 -- 177119
CAAGAGTAGGCTCTCATCTTGATTCCCTTTCTCAAATACTATGAGACTTCTTGCTAAATCCCGCT
CATGAAAATGAAAGATTCCTGATCGATAGATTCTACCCCTAAAATCCATAAAGGCAGGGAGATAA
AAGACATAATCCTCGTATGCAGAGGCTAAACTAATGATTGATTCTTCAAACATAGCCACTTGCAT
CTCATTAGATAATTGTTGAAAGAGAGATCCTAGGGTAAAAATACTATAGATGCAAGATATATAAG
GGGAGTCAATTCTTTCTTTTTTGACATTTTTTTCATCTTTGAATTATTAATGAACCCACCCTATT
CATCGATTCTATGTGATCTACTCTTTCGATCAAGCGTGAGTTCTATTACAAGATATGAATCCCCC
CTTTTTTGTGATTCAGGGTTTAGCCTCTGATCCTACAAAGAATACATAAATAGAATAAGACTGTT
TCGAATTTGAATAAGGAAATACTCATTTTTTTTTTCAGATATCTT
Found at i:176627 original size:18 final size:17
Alignment explanation
Indices: 176585--176623 Score: 62
Period size: 18 Copynumber: 2.3 Consensus size: 17
176575 AGCTGATACT
176585 TCAAGTATATCCTTATC
1 TCAAGTATATCCTTATC
176602 TTCAAGTATATCCTTATC
1 -TCAAGTATATCCTTATC
176620 -CAAG
1 TCAAG
176624 AGTAGGCTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 4 0.19
18 17 0.81
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (17 bp):
TCAAGTATATCCTTATC
Left flanking sequence: Indices 176085 -- 176584
TTTGCCTTCGTTCCTTGGCTTCCCTTCGGCATTTAAAGAGTGGAGTTATTCCCCTTCCTTAGGTA
GCCGGGAAGAGTTTTTTCACTAGTTTTCTAGAAAGCATTGATTCTATAATTAGCATTTTTGAGTC
ATCCTCGAAATGAATATATAAATAGCCCTTAAGCTCATTGAGCATGTGCATGTATACGTCTTGTA
TTTGACCATCGGGGTGAGGAAGAAGATTCGTTTTCACTGCCATATCCGTGTTTAGCAATAAATAA
CTCATGATCTGATAAGCACTTGAGGATGCATCTTGAGATATGGCTTCTTCCTTATATTCTTCCAT
TCTATCGTTAGACGCACACAGGGCCTTTGAAATGAACTGAAAAGGATCACTGGCACCTTTCACAA
AGCTTATTAAAGACTCATCGGAAGAATAGATCAAACTCTTCTTTGACTTAACCCATTCAAGCGCT
TTCTCGTAGTTATTGAATTTTTTATATTTAAAGGCAGCTGATACT
Right flanking sequence: Indices 176624 -- 177123
AGTAGGCTCTCATCTTGATTCCCTTTCTCAAATACTATGAGACTTCTTGCTAAATCCCGCTCATG
AAAATGAAAGATTCCTGATCGATAGATTCTACCCCTAAAATCCATAAAGGCAGGGAGATAAAAGA
CATAATCCTCGTATGCAGAGGCTAAACTAATGATTGATTCTTCAAACATAGCCACTTGCATCTCA
TTAGATAATTGTTGAAAGAGAGATCCTAGGGTAAAAATACTATAGATGCAAGATATATAAGGGGA
GTCAATTCTTTCTTTTTTGACATTTTTTTCATCTTTGAATTATTAATGAACCCACCCTATTCATC
GATTCTATGTGATCTACTCTTTCGATCAAGCGTGAGTTCTATTACAAGATATGAATCCCCCCTTT
TTTGTGATTCAGGGTTTAGCCTCTGATCCTACAAAGAATACATAAATAGAATAAGACTGTTTCGA
ATTTGAATAAGGAAATACTCATTTTTTTTTTCAGATATCTTAATT
Found at i:248069 original size:18 final size:18
Alignment explanation
Indices: 248043--248078 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
248033 CCCTTGAAAG
* *
248043 GATCTAATCTATCCACTT
1 GATCGAATCGATCCACTT
248061 GATCGAATCGATCCACTT
1 GATCGAATCGATCCACTT
248079 CTGTAACAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.28, C:0.28, G:0.11, T:0.33
Consensus pattern (18 bp):
GATCGAATCGATCCACTT
Left flanking sequence: Indices 247543 -- 248042
AGGAGATTCTCTCCCCCAACGGTCTCTTAGGCCGATACTAACCCGCTACAACTGGACGAAACTCC
CTCGGACGCCTGGGACTCAACAACCCCCCCGGAATCTCCCACTTATTATAAGGCGGAATTTCATG
CATTGGATGCGGCACCCTCATGTTAACTAATGACTTTCGTTCAGGCACAGGAAATGTAATAGAAA
TTCCATATGAATCTTCCATTCTGACTTACTTTCAAAGGAATTTCCTTTTTAGGTGTCCTATATGC
AATTTAAAGTCTTACCTTTATAAGGTAGCTAAGAGCTAAGGCTACTCTGTCCTTTCCTATCAAGA
GCTCAAACAAGTACTTTTTAAGAAAAGGTTAACTCATAAGCTAAGGCCGGGCCAAGGCTTAATAA
AATGGCCAGACGTTGATCCATCTCTTTCACGAGTGACCCATTCTTTACTCAAAAGCTCCGCTTCT
TTGATTCCTTTTTAGTCGTTCACTTGACATAGACTCCCTTGAAAG
Right flanking sequence: Indices 248079 -- 248578
CTGTAACAACTCTAAGTCAAAAGAAGAGCTAACTCAGAAGAGAGTCAGACCTACTTGTGAAAGAA
AGTCAATCGACTGGGCAAAGGAAGAAAGGAATATAAGGCATAACCACTTTAAGAGGTTCTATTTG
ACAAAAGTAGTTAAAAGGAAATCGCGAGTTCGAGGACCTTGCTGTATGATTTTCCTAAGGGGGCG
GCAAACAAGAGATTTCGTGCTATAAAGTCGGCCGTATGGGCTAGCAAAGCTATGTTGTCAGGGAG
GCAGGTATCGGAGTCCCAGCGGGGTGGACATTCAAAGGCCAACTATTTAGAAAACGTGAGTTCCG
GGTCCCTCAAATCGAATGAGTGATTTAGACGCTTAACTGCTCCCGTAAGCTCTTATCCAGTCTAG
GAAGAAGCAAGCAAAAAGGCTGCTATGCCGGAGTGGAGAGCCTAGCTGCAAGCTGAGGAAGACTC
TCTCAATAGGGCGGGCTTCCCTCTTCATCGATCTTATTACTAGAC
Done.