Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_026974
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: 107215
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Found at i:1159 original size:2 final size:2
Alignment explanation
Indices: 1152--1176 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1142 TAGTATAGAC
1152 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1177 TGGCTAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Left flanking sequence: Indices 652 -- 1151
GGTGTATAGCTTAATTGGTAGAGCATTAGGCTTTTAACTTAATGGTCGCAGGTTCAAGTCCTGCT
ATACCCAAATGTTTTTATAGAAGTTCCCCAGGCAGTTCATATGCACATCAAAATATACATTGTAC
GTTGACTCGTCTAGTACGATTAATTACGTTAAACTAAAATATATATATATTTTTTATGTCTTTAT
GGCCGCTCACGCCCTTTTTTTTTCTTTGCGAGAAAAGGCCGCGGGCCTCTAATCTAAGCTTAGAG
TGGGTGGAGAGAACGTCGCAGCGTTTGATGCGGCTCTGAAAAGATAGAAGTTAAGTAGGTGTTAC
CAACTACTTAACTATTTAACTTCTCTATATTATACAATCTGCAGCAATCCTGCATTCTGCAATTA
AGGAGTTGTTTGATAGCAACTGTGAATAACAGTATAGATATAGATATTTTCATAAAATAAATAAA
TAGCTTATTTATTATTGGCCAAATACATAATATTTTAGTATAGAC
Right flanking sequence: Indices 1177 -- 1676
TGGCTAATAATGCCGTATTGATTGTTGTTTCATTAAAGCTAATTGCTGTTGGAATAAAGGCTCTA
GTAAACTAGAAGTCTCGATTACATGTGCCGCGTTTTGCGCTTTTCGGACAGCATTGCTGGAGCTG
CCAACATGAAGAGCGGATTCCCGTTATTTTCCCCGTTATTTTCAAAATCCTAAGTAATCTACGTC
ACCGTCAACATTAATTCATGAGATATGCGTCTCTTTCATTAATTATCTAAATTATGCCAACCTAT
CTTATGAAAGCCAGCCCGGCAGTATAATATAATAAATACTGGCTCGCTCGCGTATATTCCCACAT
TCATTCGTCAAATCAGGCAATCTCTATTGAATAAAAGAGAAGATATGATAATAAATTGAATAAGA
AGCTTCCGAGTACGCAAATGGTAGGAATACGCCAGAAGTATTGGCAACCTAGAAATAGGCCGGCA
AAAGGTACAAGAATAGCATGTCGCCATTAGCTGTGTTATGGCATT
Found at i:29822 original size:14 final size:14
Alignment explanation
Indices: 29803--29830 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
29793 GCAACAAAAA
29803 TTAGATATATTTGC
1 TTAGATATATTTGC
29817 TTAGATATATTTGC
1 TTAGATATATTTGC
29831 CGTTTTCTTT
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:0.07, G:0.14, T:0.50
Consensus pattern (14 bp):
TTAGATATATTTGC
Left flanking sequence: Indices 29303 -- 29802
GCACAGAAGAACATAATAATTCCGGAAGTATATACTTTGGATAATTCTAGAAAAAAACCTAGATC
CCACAATAAATGACGAATTCCATTACTCATATGATAGCACAAGGCCAATAAACTGAAATTGACTA
CGCTTGAGATCAACCAATGGGAATAGAAAGTGAAAGAAAAAGCGTACCGGTAAAGATAATAAGAA
GTAAGGTTAAGATCGCCTATTTTCAGAGAAAGAATACTAGAAAAAACCATAATGGATAGAGTCAA
ACTTCGGTAGCAAGTTATGATTAACTCCTGCCTACTAAGTGCTCTCCGAACCGTACGTGATAGTC
TTCCATCATACGGCTCACTAACTCTCCTAATCCAACTCATAGGAGACGGGCTCCATTGACTGCGG
CTCGTCGGGTGCCTGGCCTTCCCGGCTATTGATTGGATTATCAATGGCACTGGATGTATCATCAT
ATATAATGTATTAACATTTTGATGTTAATTAGGGCGCAACAAAAA
Right flanking sequence: Indices 29831 -- 30330
CGTTTTCTTTTTTGAGTTTTGGAGAGTAAAACCTGCCAGACTAGGCAGGTGCATAGACCCCTTCG
CCTTTTACTTAATCTGCAAGTTTCCCGTTTACACGGTTCTTTCAGGATCGGGCAGGTACTATGGG
TCCTCTGACTTCCAACTCGGACCATAGTGTACGGTTGGATCTCGCCGATATCACCTGTGAGCTAT
AGCGCCTAAGATGTCGTTTAGTTCTCTGTCCCCATTAAATTTAAATTAATTTGGGTAATCTGCTT
CCATGCGTAAAAATATATCTATTTTTTTTCGTCCTTACCGTTCTTAGCCGCCAGCGGGCTGAAAG
CATAACAGTGTTCGTTCGTGCGATTCCCCGCGTGCATTTTTTCTGCACTGGTTCGCCGTACTAAC
TACTAACTATAGGGCAGGCTGACCCGAAAAGAACTGCGATTCTGCTTTATCATCTCATGCTAAAT
GAAATATATATATATATATTTCATTTAGCAAGCGCCAGCGGACTC
Found at i:41864 original size:81 final size:81
Alignment explanation
Indices: 41729--41877 Score: 255
Period size: 81 Copynumber: 1.8 Consensus size: 81
41719 TAAATACTCG
*
41729 CTATCGGATTCGAACCGATAACCCATAGGAACAGATTTTGAGACTGCCGTGTTTACCATTTTCAC
1 CTATCGGATTCGAACCGATAACCCATAGGAACAGATTTTAAGACTGCCGTGTTTACCATTTTCAC
41794 CAAGCGAGTATGCTCA
66 CAAGCGAGTATGCTCA
* *
41810 CTATCGGACTT-GAACCGATAACCCATAGGAACAGATTTTAAGTCTGTCGTGTTTACCATTTTCA
1 CTATCGGA-TTCGAACCGATAACCCATAGGAACAGATTTTAAGACTGCCGTGTTTACCATTTTCA
41874 CCAA
65 CCAA
41878 ATGAGCTTAG
Statistics
Matches: 64, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
81 62 0.97
82 2 0.03
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (81 bp):
CTATCGGATTCGAACCGATAACCCATAGGAACAGATTTTAAGACTGCCGTGTTTACCATTTTCAC
CAAGCGAGTATGCTCA
Left flanking sequence: Indices 41229 -- 41728
CTTCAATCTACTTTAGTCAATCATATGGATATAAAAAAAGCGGCTAATTTAGAAATAACATCAGT
ATTTCAACAACTTTTTGAGCTCATTTTTTACCCATATAATTCTTTATGTTCTTGTTTGAACAAGC
CAATTTGTGCTTCATCCACTATACAAGAAAAGACGCAAGGAGGGTTACTTAGTCACCAGAGGATA
ACCACTTAGTAACTTGGGTCCCCACTTTGCCAATTAAAGCCTGCGGCTTTATTGACAGAACTGGG
GACCCAAGTTTGTAGCGAACCTTTTTTTTTTAATATTTCGGGAAACCCCCCAAAAATATTAAAAA
TATTTTTTGCTGCGAAAAACAGCGTCCTCAAAAATTGTAAAGATTTAAACTAATGGATGATTTGT
TTTTTTGGCGAATAACGGGATTCGAACCCGTGTTTTCAAATTCACAATCTGACACTTTCACCTAT
TAAGTTATACTCGCCCTTTTTCCAATTTAGACATTTAAATACTCG
Right flanking sequence: Indices 41878 -- 42377
ATGAGCTTAGGGAAGCGAAGCGCAGAGTGGAAACACAATCTTTTTGTTTCGTTTTATTTTCGCCA
TTTTATTTTATAGACATCCCCGGCTTATTCCGGCTCGGCTGGACCTGCGGCATTTTCTCAAATAT
TTGAAAAATCTATAGTCCCTTGTCTTAAGGTGTGTAGAGACTCCTTTTTTATTGATTTATACTAG
TCTATCTTAGATCCGAGATAGTGCCGAAAAAATGATTCAATTTCATCTAACCACGGTTGCCTTGG
CAATGGCAATTACTCTTATACGATATGCAGAATACTCCAAAACCTCTATTTATTCTATTTAGAAC
TAAAAGAAGATAACTAAAAGAAGATAATGCTTTTTCATAAAAAAATCATAAAGTGCAAAGATTCA
AATTTTGAGCTTTGTTTTACGTAGTTTTGCCATCTATATAATATAATATAGTAAGAAAGTTGGCG
AGGAATTAAAAAAAATATATATATATATATTTTTTTTTTTATTCT
Found at i:42219 original size:14 final size:14
Alignment explanation
Indices: 42200--42229 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
42190 TTCTATTTAG
42200 AACTAAAAGAAGAT
1 AACTAAAAGAAGAT
42214 AACTAAAAGAAGAT
1 AACTAAAAGAAGAT
42228 AA
1 AA
42230 TGCTTTTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.67, C:0.07, G:0.13, T:0.13
Consensus pattern (14 bp):
AACTAAAAGAAGAT
Left flanking sequence: Indices 41700 -- 42199
TTTTTCCAATTTAGACATTTAAATACTCGCTATCGGATTCGAACCGATAACCCATAGGAACAGAT
TTTGAGACTGCCGTGTTTACCATTTTCACCAAGCGAGTATGCTCACTATCGGACTTGAACCGATA
ACCCATAGGAACAGATTTTAAGTCTGTCGTGTTTACCATTTTCACCAAATGAGCTTAGGGAAGCG
AAGCGCAGAGTGGAAACACAATCTTTTTGTTTCGTTTTATTTTCGCCATTTTATTTTATAGACAT
CCCCGGCTTATTCCGGCTCGGCTGGACCTGCGGCATTTTCTCAAATATTTGAAAAATCTATAGTC
CCTTGTCTTAAGGTGTGTAGAGACTCCTTTTTTATTGATTTATACTAGTCTATCTTAGATCCGAG
ATAGTGCCGAAAAAATGATTCAATTTCATCTAACCACGGTTGCCTTGGCAATGGCAATTACTCTT
ATACGATATGCAGAATACTCCAAAACCTCTATTTATTCTATTTAG
Right flanking sequence: Indices 42230 -- 42729
TGCTTTTTCATAAAAAAATCATAAAGTGCAAAGATTCAAATTTTGAGCTTTGTTTTACGTAGTTT
TGCCATCTATATAATATAATATAGTAAGAAAGTTGGCGAGGAATTAAAAAAAATATATATATATA
TATTTTTTTTTTTATTCTGTGGTCCTGCAATTGTACTTAAAGCTAAGGGCCGCAGCCCCCTATTT
CCTATTGTCCTCGTCAATTAAATAAAGGCTTCGTTTGGCCAGGGGGTCATTCTTCCCCCCCGCTG
AATTGCCTCGCGAACAAAAAAATAAATATTTTTTTTCTCCGCCTTATTATTTTTTTATTATTTAA
ATGGCCTCATGAGCTTTTACCAAGCAAAATATTGATTGCATAAGCCATCGGCTTCTACAAAGACC
GATAAAGTGATAACAGCAGCGTAACCAAGGTTGTTCCGCCCACTGCGCGCAAAAAAAGAATTTTT
TTGCGGCACTTAGTAAAACAAAATTTTGACACTCCTTGCAGATGT
Found at i:54945 original size:11 final size:11
Alignment explanation
Indices: 54929--54953 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
54919 AAGGCAGGGG
54929 CGCGCTGCAGC
1 CGCGCTGCAGC
54940 CGCGCTGCAGC
1 CGCGCTGCAGC
54951 CGC
1 CGC
54954 TTCTTTATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.48, G:0.36, T:0.08
Consensus pattern (11 bp):
CGCGCTGCAGC
Left flanking sequence: Indices 54429 -- 54928
TTACTAGTGTTATCAGTTGTTTTTATTATATACGCTTTGTCAAAATCATTTATTCTGATACACCT
AAAAAATGGATTCTATATAAAACAATGGATCGTGAAAAATCCTTACTACTAGCAATTACTTTATT
CTTCATTACTTTTTTCTCTTTATACCCTTCTCCCCTATTCTTAGTCACCCATCAAATGGCACTAA
GTCTATCTTTCTAAGCCGCTGGCTGCAACGCCGGCGCACCAATGACTCTCCGTACCGTTTCCCAT
CATTTGTTATGCAAATAATGTGGGCACAGCGAATAATGTGGGCGCCAGCCTTCGACCTGTAGCGC
CAAGCCCACCGCACCCACCGCAGCGCGAGGCCGCTCTCCCATCGGCCTGGCATACATTTTAAGCG
GAAAAAGGGACTTGAACCCTCAACCTCAGCCTTGGCAAGGCTATACTCTACCATTAAGCTATTTC
CGCAGCACGATAATAAAAAAGTAACAAGGGTCCGAAAGGCAGGGG
Right flanking sequence: Indices 54954 -- 55453
TTCTTTATTACCAATAAGAAGGGCTGTATTCTCTACAAAAAGTAAGAAGGCTTCTTTATTACCAG
TAAGAAGGGCAGCCTCGCTGCAGCCGCTTCTTTATTATTAGATGTATTATCTTAGTAAACCATGC
TTGGAAAGATTCGAACTCTCAACCCCCAAATCCGTAGTTTGGTGCTCTATCCGATTGAGCTACAA
GCATAAATTTCTTAAGCACTACGTGTCATGTAGGCTGCATTATTACAAAGAAAAAACATATATAT
ATGAAAAAAGAATAGCAGTTCGGGCAGCATTTTATAGAGATTAGTATTACCGTATTGCATTATTT
TAAGTATGCCTTCTGTGACTGCACTGTGTAGTCAACATCCGCAGTTACGTGCATTACTAACGTAA
TTAAGTTCGAATGTTGATTCGATTAGATTAGATTAGATTAGCTTGCGTTTTTACTGCTAAAATAG
ATATATATATATATTTTGTTTTCTCACCTAATTTATCCGAAAAGG
Found at i:62560 original size:11 final size:11
Alignment explanation
Indices: 62546--62580 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
62536 TTAAGCTTAA
*
62546 ATTTTTTTTCT
1 ATTTTTTTTCG
62557 ATTTTTTTTCG
1 ATTTTTTTTCG
*
62568 ATTTTTATTCG
1 ATTTTTTTTCG
62579 AT
1 AT
62581 AATGAGCTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.14, C:0.09, G:0.06, T:0.71
Consensus pattern (11 bp):
ATTTTTTTTCG
Left flanking sequence: Indices 62046 -- 62545
AATCAAAGCCAAGTGGTTTTTCCATTATATGAATAATCCACAAGTTGCATAATCTGCTACTTTGA
ATCCCTTTAAGCATTGTATTGGTTTAACTGTGTGTTTCCAAGAGGTTGATTATACTTATTAAAGC
AAATAACCAAAGCCTTTGTAGGCTCTGTTTTTTACATATTATGGGCACATGGTTAACGGGAGATT
AATACTGATCATGTAGAACAGATTCAGTTGTGCGAAGCACTTATAATGCATTATGCAGCGTGTTT
AGTTTGCTTGTAGTCATCAAGCTACGTGCGTAGGCGGATAAACTGGCTACACTCGATTGCTTCGC
CTGTGGCTTCGTCCATAGCACGTGCCAGTCACCGTTCCGCGATTTGCCAGTGAGGAACGCAGCCC
CGGGGCCCGCTTTTTCTTCAAAAAGGAACGCCCTATTTTAATTTTATTTGGCAGGCTTAATTCCC
AAACTGAAGGCCCAGGGGCCCTTTTTACTCAAGAATTAAGCTTAA
Right flanking sequence: Indices 62581 -- 63080
AATGAGCTCTGAAAAAAAAAGTGGGTAAATTTGGGCCTGAAGCGGGGTGGCTTGGCAAAATAAAT
AAATATATATATATATGCCGCACTATGCGGTCTGGTGCTCTCAGCGTTAAAATCATCAGCAATGG
CGTCAGAGTTTCCATAGTACAATGAATTGGAAGTGAAACAATCAGTTTTTTTCATCATTATACAG
TTATGGTACGAACTGGGTCTTCATAAAAAAAAAATATTTTTTTTGGTTTATGTCATCATAGTTGT
TCAATTATGCTAGTTTCGAATACCAAACAAGAGCCGCGTGCTTGAAAATCTTGCAAGCACTTTGA
GGGGGAGTATTTATTTCGAAGGCTTAAGTTCGACTCAATAAGAGCGATGTTTGGGGATAATTTAT
GATATATGACTTGCTTTCATCAAGCATGTTGCGTGATTACTGAAGCTTTCTCTGCCCAACATAAT
GACCTATAATTATTTTAAAAAGCTTACTCTATCTATTGGGCCCTT
Found at i:85605 original size:22 final size:22
Alignment explanation
Indices: 85577--85620 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
85567 GGCGCTTAGA
*
85577 GGCTGCAAGTGATGAATGTGTG
1 GGCTGCAAATGATGAATGTGTG
* *
85599 GGCTGCAAATTATGCATGTGTG
1 GGCTGCAAATGATGAATGTGTG
85621 AGCGTTAACA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.23, C:0.11, G:0.36, T:0.30
Consensus pattern (22 bp):
GGCTGCAAATGATGAATGTGTG
Left flanking sequence: Indices 85077 -- 85576
TCGTCAAAAATTTACACAGAGCTTCTTAGCAACTCATTAAGTTTAAAAAAATTCAACTAAAAAAA
AATTTTCAGGCCGCTGGTTTTGTTTCCGTGCTTCCGGGTGGAGGGTGAAAGCGGCCAGGGCGCAG
CCAATTTTTTTTTTTTTCGCCCTCTGGCTACGCCCCTAGTAAGGCTTCGTCATACGAGCGGAGCT
CAAACCCCTCCATCCCCACATTAACAACATGTAGATTTGGAGAAAACAGGAACGCAACAAAACAT
TAACAAAATCGGGCCAGGAACGCTTATTTGTAGAATGTACTATTTGTAGGTTCTGTAGGTTTTTA
CTGCGTAGATGATATTATTAGATATTATTTACGTATGGCGTAGCCGGCAAAGATAACTGGGTGAC
CCAGATTAACTATGGCCTTCGCCTCTAATGCATCTGGCTCTAATCTATTAATCTCGCGCTTAGAT
AGATTAATGCATCAGTCTGGCGCTTTTCACTTTCTGGCGCTTAGA
Right flanking sequence: Indices 85621 -- 86120
AGCGTTAACAAAAACAATATATATTACATGGCTCCAGTCGTCTCAAGTCTATTGCTCCGCAACAA
TTTTTAAAATGAATCAATCATCGAAAATGATTGATAGCTACCTGCACCAAATTATGGCTGGTGTA
ATCAGGAGAAAAGGGATTCGAACCCTTAACCTGTGGTTTTGGAGACCATTGTTCTACCATTGGAA
CTATTCTCCTAAAAAAAAGTGGTTCTTGGTTTATGGAATTTGCACCTATTTGTGTCTATTTAGTA
ATAAGTTTGCTATTTTCTTTGATCTTAATCGGCGTTTCCTTTCTATTTGCTTCTTCTTCTAATCT
GGCTTATCCAGAGAAATTGTCAGCTTACGAATGCGGTTTTGATCCTTTTGATGATGCCAGAAGTC
GTTTTGATATACGATTTTATCTCGTTTCTATTTTATTTATTATATTTGATTTGGAAGTCACCTTT
TTATTTCCTTGGGCAGTTTCTCTTAACAAGATTGGTTTGTTCGGA
Done.