Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_031390
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: 104785
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Found at i:2427 original size:25 final size:25
Alignment explanation
Indices: 2393--2441 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
2383 GGGCGCAACA
2393 TATATTATATTATATATTGCCGCGT
1 TATATTATATTATATATTGCCGCGT
2418 TATATTATATTATATATTGCCGCG
1 TATATTATATTATATATTGCCGCG
2442 CCCCTTCAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.47
Consensus pattern (25 bp):
TATATTATATTATATATTGCCGCGT
Left flanking sequence: Indices 1893 -- 2392
CTAAAGTCTCTGGATATTGAAGACCAGTTATTTTCCCTATCCAATAGTAGAATCCTGCAAATAAA
GCAAAAACAGCTCCCATAGAAAGAACATAATGGAAATGTGCAACCACATAATAAGTATCATGTAG
AGCGATGTCCAGCCCAGAATTGGCCAATACTATTCCAGTGAGAGTAGAGTAGGTGCCCTTACTCG
CGTGGGGCCAATTTTGGGTTTCCCTTGCGCTTTTAGTGCACCTCTCTCGTAACCGTACATGATAG
TTTTCCCATCATACGGCTTGCCCGCGCGTTTAATTCTCTCACGACTTGGCACGGGTTTCATAGCC
TGTACCGACGTGTCGAACGAGGTTGCGGTGCCTCTCCGGTTTCCTTTTTTTCCCTCTGAGTTTAT
CTTTTCGATCGAAGAGAGAGAGCCCGAAGAAGTATTTTCCGTGGTCGGCTCTCTCGTGCTCGAGC
TTGGCAAGTGTAGCCAGAGAATAACGCGGCAGCAAGGGCGCAACA
Right flanking sequence: Indices 2442 -- 2941
CCCCTTCAACAACTTTCTCAGTTTCATGAGCTTTTAGTCTGGTCATCATCTCGTTTATCTGTGAG
ATGTTCTTGTCGAGTTGGCTCAACTTGCGCTGCTATTGTTGTGTCCTCTTTATTGGTCCGGATTT
GTTGACTAGGCATCTGGTATCGTCCAGTATAGATCTGCCGCGTAGCCTTTTGAAAAGAGGCGTAG
CGGGACCAAGCTTTTTGGTTGGGGTTTTCCAACATACTTGTGTGCTCTTCTTGTCTTGGTTCGGA
CTTCTATAACTGCAGAACACCAGAAAGTCACCTCTGACTTAATTCCGAGTTCCTTTCCCTGGAAA
ATGATGTTGATATATCACTTCTGGAGAAGCCTGCGGCCTCTTGTTTTAATCCGTCCCATTGTAGT
TGTAAGGCGTTTGCTTTTTTTAGTATGATTAGAGTGCGAACACAGCCGCTCCTGATGACGAGTTT
CATTTCATTTGTTAATTGGTAGAACTTATCAACGAACGAATAGTA
Found at i:18183 original size:21 final size:22
Alignment explanation
Indices: 18148--18190 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
18138 CTTTCTGTAG
* *
18148 TGTACTTTGTTTTTTATTATTT
1 TGTACATTGTTTTTTATCATTT
18170 TGTACATT-TTTTTTATCATTT
1 TGTACATTGTTTTTTATCATTT
18191 AAATATAGGC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.16, C:0.07, G:0.07, T:0.70
Consensus pattern (22 bp):
TGTACATTGTTTTTTATCATTT
Left flanking sequence: Indices 17648 -- 18147
CCGAAGAAGAGAAGCCTTCGGCCCTGCCAATGAATCATTTTTTTGTTTCAATTTTGAGTTTTTTT
ATCTTGTATTCTTTTCTTCTTTAAAGCAAAATCCTAAAAACAAATAGAGCAGATGGTCCAACTAC
AGAACTTTTTTTTTTTTCTTATGTTTATGGTTGTGCTTTGTGGTACGGCAGCACCCATACTATTT
CAATGGTTGGTAAGTAGAGATGTTCCCACAGGTGCTCCTTTTTCTCATGGTACTATAATACCTAT
TTTTACCTCTTTATTATTGCTTCTAGTTCATGTACATTCCAGGGGATTCATACGCTCTATGGAGA
AAACAGAAAGGATAGTTTTGGTAAAAGCAAAACGCATTTTATTACTCAACATAATTGAAAAAAGC
TCCCCAAAAACTAGAGCTAAAAATGCATTTTTTTTCTTCTTTTTTTTTTTTTCGAATTTTTTTAT
TTTTAAATTTATGGGAGACTTGTCATATTTAGAATCTTTCTGTAG
Right flanking sequence: Indices 18191 -- 18690
AAATATAGGCGCGATACGTGGGCAAACGAGGAGCGTAGGCTTGGAATGGAAGAGAAAAGAAAACC
GCGTAAGCGGGCACAGAGAAGAAAGCGCCAAGCGCTTTGTTGGCCTGACAGAAAAAAGAAACAAA
GAAATAAAAAGAAAGAAAACTTTTCCTTTTTATTTCTTTCAAATAAATCCAAAATATTTTTGATT
TATTTGCTGCAATTTTCAAAAACCTTCGGCTTCAACGAGAAAACCAAAATTTTGGCTTTTTATTC
TCTGCTTGCTTTTTTGCAAGCTTATTCTTTCGTCCTTGAAAATATTTGGAATAGATTTTTTATTG
TTCGCGCCTTACCGAAAAGACTGATGGATGTTGGTCATGACTTTCGAAAAGTTCCCATGACTATG
AAAATTTCACATGGAGGAGTTTGCATCTTTATTATGGGTGTTATTCTGTCGTGCGACCCGGCAGC
TTATGCGCGACCATCTCGTGTTTAAGCTCACGCCATGTGGGCGTG
Found at i:18593 original size:19 final size:20
Alignment explanation
Indices: 18551--18593 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
18541 GGATGTTGGT
* *
18551 CATGACTTTCGAAAAGTTCC
1 CATGACTATCGAAAAGTTCA
*
18571 CATGACTAT-GAAAATTTCA
1 CATGACTATCGAAAAGTTCA
18590 CATG
1 CATG
18594 GAGGAGTTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (20 bp):
CATGACTATCGAAAAGTTCA
Left flanking sequence: Indices 18051 -- 18550
GAGCTAAAAATGCATTTTTTTTCTTCTTTTTTTTTTTTTCGAATTTTTTTATTTTTAAATTTATG
GGAGACTTGTCATATTTAGAATCTTTCTGTAGTGTACTTTGTTTTTTATTATTTTGTACATTTTT
TTTATCATTTAAATATAGGCGCGATACGTGGGCAAACGAGGAGCGTAGGCTTGGAATGGAAGAGA
AAAGAAAACCGCGTAAGCGGGCACAGAGAAGAAAGCGCCAAGCGCTTTGTTGGCCTGACAGAAAA
AAGAAACAAAGAAATAAAAAGAAAGAAAACTTTTCCTTTTTATTTCTTTCAAATAAATCCAAAAT
ATTTTTGATTTATTTGCTGCAATTTTCAAAAACCTTCGGCTTCAACGAGAAAACCAAAATTTTGG
CTTTTTATTCTCTGCTTGCTTTTTTGCAAGCTTATTCTTTCGTCCTTGAAAATATTTGGAATAGA
TTTTTTATTGTTCGCGCCTTACCGAAAAGACTGATGGATGTTGGT
Right flanking sequence: Indices 18594 -- 19093
GAGGAGTTTGCATCTTTATTATGGGTGTTATTCTGTCGTGCGACCCGGCAGCTTATGCGCGACCA
TCTCGTGTTTAAGCTCACGCCATGTGGGCGTGAACTCTGGTTGAATTCGGGTTCTAAATCCCGCC
GCTGAGATGCTCAGTCGACTCTTGAACCTTGATAGGAAGACGGCTTCTTCTCAAATTAGTGCAAG
AGGTTCAAGGACTTAGGATGAACTTAATGTGAATGGGTATAAGCTTCGCTGCTCAAAAACACCCA
GTATTGACCACACTGAGAGACTTGCCAATGGCAATGCCAGGCCGCGGGTAACGCTAGTTGGCTCC
CAGGCGTTAAGCATTCCTAACAATACGGAAAAAGAGGTCGTGATGATATTCATCTACGTTCGTAC
TGTTCCTCGTGGAGTAAATCTCACATCCAAAAATCTAACCAGGGAACGGAATAATTCCCATTAAG
TTCCAGTAAAACTGGCAGGCCAGCCGGGCCGTAAGCTAGTGGGAA
Found at i:41407 original size:81 final size:81
Alignment explanation
Indices: 41272--41421 Score: 257
Period size: 81 Copynumber: 1.9 Consensus size: 81
41262 AAAATACTCG
*
41272 CTATCGGATTCGAACCGATAACCCATAGGAACAGATTTTGAGACTGCCGTGTTTACCATTTTCAC
1 CTATCGGATTCGAACCGATAACCCATAGGAACAGATTTTAAGACTGCCGTGTTTACCATTTTCAC
41337 CAAGCGAGTATGCTCA
66 CAAGCGAGTATGCTCA
* *
41353 CTATCGGACTT-GAACCGATAACCCATAGGAACAGATTTTAAGTCTGTCGTGTTTACCATTTTCA
1 CTATCGGA-TTCGAACCGATAACCCATAGGAACAGATTTTAAGACTGCCGTGTTTACCATTTTCA
41417 CCAAG
65 CCAAG
41422 TGAGCTTAAG
Statistics
Matches: 65, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
81 63 0.97
82 2 0.03
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.29
Consensus pattern (81 bp):
CTATCGGATTCGAACCGATAACCCATAGGAACAGATTTTAAGACTGCCGTGTTTACCATTTTCAC
CAAGCGAGTATGCTCA
Left flanking sequence: Indices 40772 -- 41271
CAACTTCAATCTACTTTAGTCAATCATATGGATATAAAAAAAGCGGCTAATTTGGAAATAACATC
AGTATTTCAACAACTTTTTGAGCTCATTTTTCACCCATATAATTCTTTATGTTTTTGTTTGAACA
AGCCAATTTATGCTTCACCCACTATACAAGAAAAGACGCAAGGAGGGTTACTTAGTCACCAGAGG
ATAACCACTTAGTAACTAACTTGGGCCCCCACTTTGCCAATTAAGGCCGCAGGCTTTAGTAACAG
AACTGGGGCGCGTAGTTTATAGCGAAGCTTTTTTTTTTTAATATTTGGGGAAATCCCCCAAAAAT
ATTTTTTGTTGCGAAAAGCAGCGCCCTCGAAGATTGTAAAGATTTAAGCTAATGGATGATTTGTT
TTTTTGGCGAATAACGGGATTTGAACCCGTGTTTTCAAATTCACAATCTGACACTTTCACCTATT
AAGTTATACTCGCCCTTTTTTTCAATTCAGACATTAAAATACTCG
Right flanking sequence: Indices 41422 -- 41921
TGAGCTTAAGGAAACGAAGCGCAGAATGGAAACACAATCTTTTTGTTTCGTTTTCTTTTTGTTAT
TTCATTTTATAGACATCTCCGGCTTATCCCGGCTCGGCTGAATCTGCGGCGTTTTTTCAAATATT
TGAAAAATCTATAGTCCTCTGTCTTAAGGTGTGTAGAGACTCCTTTTTCATTGATTTATACCAGT
CTATCTTAGATCCGAGATAGTGCCGAAAAAATGATTCAATTTAATCTAACCATGGTTGCCTTGGC
AATGGCAATGACTTTTATACAATATGCAGAATACTCCAAAACCTGTATTTAGAACTAAAAGAAAA
TAATGCTTTTTTAGAAAAAAATCATAAAGTGCAAAGGTTAAAATTTTGAGCTTTGTTTTACGTAG
TTTTGCCATCTATATAATAGAATATAGTAGAAAATAATAAGTTGGCGAGGAAGTAAAAATATATA
TATATATCTATAGATATATATATATTTTTTTTTTATTCTGTGGAT
Found at i:63300 original size:14 final size:14
Alignment explanation
Indices: 63281--63308 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
63271 TCTTCGTTTT
63281 TATAAGATATGAAG
1 TATAAGATATGAAG
63295 TATAAGATATGAAG
1 TATAAGATATGAAG
63309 GTATTTTTGT
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:0.50, C:0.00, G:0.21, T:0.29
Consensus pattern (14 bp):
TATAAGATATGAAG
Left flanking sequence: Indices 62781 -- 63280
AGAGGCTGTTAAGATAGCTGCTAATGCCATAGGCGCGTTTACTGCGGCGGGGTACTTGGTTGTAC
GTGCACAATTTAAATAGAGCGAATGCATTAGAATTGTAAGAAAAAAGCCTAAAATTGAAAAAGCT
AAAGTTCAATTATAAGGTACTTATTAATGAAGCTAAAAACACGGATCAGCTTTTGGAAGAAATTG
AAGAGCGTTAAATGAAAGAAATTAAGGCTTGTTGGTTGGGTAGTAAAAAAAATGAGTACTGATGA
AGAATGAACAGCCACGTCTAGATGATGCTGTTTAGCGTGTAGTAGAAGCTAAATACAACAAGCTG
CAAGCTAAGGGTAAGGGTCTTCGCGCGACAAGATTCGAGATCAGTATGCGGAACAAACGACCATA
AAAGAAAGGCCACGAGTATCATAGGCAGACCTTCAACAGGCACCTAAAAAAAAATTACCACCTAA
ATTATCTATTAAGTACCCTGTCCCAAACGCAAACTTCTTCGTTTT
Right flanking sequence: Indices 63309 -- 63808
GTATTTTTGTTTCTCGAAGAGCCATCGGGAACTTAGGTTCTTTTATTTATCGAGTTTCGCAAGTA
TATCTTTCTTAAGATCTAAATCCTATTAATTTGAACGTAGAGTTGTATGATGCGAAACTATCACT
TACGGGGTGGGTTTAATCTTAGATTTTTTTATTTTCTGAGTTTTTATGGGATTATTATCGCGGGT
TTGTCTATCCTAATGGGCGTCTAACAAAAAAATCGATTTTTTTGTTGGTTGGCCCTTTTGTGGGG
CCTGTTGAAGGGCCGAAGTAGTTCTGAAAAAAACAAGAATATACCAAATGAGTTTGAAAAATACA
TGGCTATTTCCAATTGGTTATTGTGACGCTGCGGAACCTTGGCAATTAGGATTTCAAGACGCAGC
AACACCTATGATGCAAGGAATAATTGAGTGCGCCTAGATATATCATCACGGTTGCAGAGCTCTGC
TCCAACTCTGCCATATCTGCTCGAGCTGGCTATCGCCAGGATGTG
Found at i:104647 original size:10 final size:10
Alignment explanation
Indices: 104632--104657 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
104622 TCTTCTTATA
104632 AATAATCTTT
1 AATAATCTTT
104642 AATAATCTTT
1 AATAATCTTT
104652 AATAAT
1 AATAAT
104658 GCATAGCTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (10 bp):
AATAATCTTT
Left flanking sequence: Indices 104132 -- 104631
TCTATCGGGGGGGGGGGAGTTGTGCATCATAGGTACCTTCTTATTGCTGCGAAGGGCGATATGAA
AATAACCCCCCTATCCAACCTCATTCTGTTGCGCGAAATCCATCATTGGCTAAGCAATTATTTGG
TTATGCCATCTTAGGTTTCGCTTTAACAGAAGCTATTGCTTTGTTTGCCTTAATGATGGCCTTTT
TGATCTTATTTGTTTTTTAATTTTTTGGTGCTGCGATTTTTTGGGAAAAAAACTATATTTTGGCC
GCACCCTATTGGCTTTGCGAATAGGGCTGCGCCCAAAAAATCTAGATTTTTTGGCACCTTAGGGC
CGAACGATTAGTACGTTCGAGCCCTTCACCACTTGCTACCAAAAGCATAAGCGTAAAAAAACTGA
ACTGACAAAGATTTTAACCTTAAAGGCTCATTGGATAAAAAAAGAAGCAGGACAAATATATCTAT
ATATATATTTTTTTTTCTTTTTTAGCTGCTTCACTTCTTCTTATA
Right flanking sequence: Indices 104658 -- 104785
GCATAGCTTCGCGTGCTTTTCGATTGATGATGGGACCGAAGACGAAAGGCGCGAAGCGGCCGCGG
GTCTAGATTCTCGTTTTTTCGGCCGCGCGCCTGCGGCGGCCCTCGGTCGTTGTTAACTTACCA
Done.