Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_031391
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: 104638
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Found at i:18700 original size:19 final size:20
Alignment explanation
Indices: 18658--18700 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
18648 GGATGTTGGT
* *
18658 CATGACTTTCGAAAAGTTCC
1 CATGACTATCGAAAAGTTCA
*
18678 CATGACTAT-GAAAATTTCA
1 CATGACTATCGAAAAGTTCA
18697 CATG
1 CATG
18701 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 18158 -- 18657
GAGCTAAAAATGCATTTTTTTTCTTTTTTTTTTTTTTTTCGAATTTTTTTATTTTTAAATTTATG
GGAGACTTGTCATATTTAGAATCTTTCTGTAGTGTGCTTTGTTTTTTATTATTTTGTACATTTTT
TTTATCATTTAAATATAGGCGCGATACGTGGGCAAACGAGGAGCGTAGGCTTGGAATGGAAGAGA
AAAGAAAACCGCGTAAGCGGGCACAGAGAAGAAAGCGCCAAGCGCTTTGTTGGCCTGACAGAAAA
AAGAAACAAAGAAATAAAAAGAAAGAAAATTTTTCCTTTTTATTTCTTTCAAATAAATCAAAAAT
ATTTTTGATTTATTTGCTGCAATTTTCAAAAACCTTCGGCTTCAACGAGAAAAGCAAAATTTTTG
CTTTTTATTCTCTGCTTGCTTTTTTGCAAGCTTATTCTTTCGTCCTTGAAAATATTTGGAATAGA
TTTTTTATTGTTCGCGCCTTACCGAAAAGACTGATGGATGTTGGT
Right flanking sequence: Indices 18701 -- 19200
GAGGAGTTTGCATCTTTATTATGGGTGTTATTCTGTCGTGCGACCCGGCAGCTTATGCGCGACCA
TCTCGTGTTTAAGCTCACGCCATGTGGGCGTGAACTCTGGTTGAATTCGGGTTCTAAATCCCGCC
GCTGAGATGCTCAGTCGACTCTTGAACCTTGATAGGAAGACGGCTTCTTCCCAAATTAGTGCAAG
AGGTTCAAGGACTTAGGATGAACTTAATGTGAATGGGTATAAGCTTCGCTGCTCAAAAACACCCA
GTATTGACCACACTGAGAGGCTTGCCAATGGCAAAAAAGGCCGCGGGTAACGCTAGTTGGCAAAA
TGGCGTTAAGCATTCCTAACAATACGGAAAAAGAGGTCGTGATGATATTCATCTACGTTCGTACT
GTTCCTCGTGGAGTAAATCTCACATCCAAAAATCTAACCAGGGAACGGAATAATTCCCATTAAGT
TCCAGTAAAACTGGCAGGCCAGCCGGGCCGTAAGCTAGTGGGAAC
Found at i:41378 original size:81 final size:81
Alignment explanation
Indices: 41243--41392 Score: 257
Period size: 81 Copynumber: 1.9 Consensus size: 81
41233 AAAATACTCG
*
41243 CTATCGGATTCGAACCGATAACCCATAGGAACAGATTTTGAGACTGCCGTGTTTACCATTTTCAC
1 CTATCGGATTCGAACCGATAACCCATAGGAACAGATTTTAAGACTGCCGTGTTTACCATTTTCAC
41308 CAAGCGAGTATGCTCA
66 CAAGCGAGTATGCTCA
* *
41324 CTATCGGACTT-GAACCGATAACCCATAGGAACAGATTTTAAGTCTGTCGTGTTTACCATTTTCA
1 CTATCGGA-TTCGAACCGATAACCCATAGGAACAGATTTTAAGACTGCCGTGTTTACCATTTTCA
41388 CCAAG
65 CCAAG
41393 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 40743 -- 41242
CAACTTCAATCTACTTTAGTCAATCATATGGATATAAAAAAAGCGGCTAATTTGGAAATAACATC
AGTATTTCAACAACTTTTTGAGCTCATTTTTCACCCATATAATTCTTTATGTTTTTGTTTGAACA
AGCCAATTTATGCTTCACCCACTATACAAGAAAAGACGCAAGGAGGGTTACTTAGTCACCAGAGG
ATAACCACTTAGTAACTAACTTGGGCCCCCACTTTGCCAATTAAGGCCGCAGGCTTTATTAACAG
AACTGGGGCGCGTAGTTTATAGCGAAGCTTTTTTTTTTTAATATTTTGGGAAATCCCCCAAAAAT
ATTTTTTGTTGCGAAAAGCAGCGCCCTCGAAGATTGTAAAGATTTAAGCTAATGGATGATTTGTT
TTTTTGGCGAATAACGGGATTTGAACCCGTGTTTTCAAATTCACAATCTGACACTTTCACCTATT
AAGTTATACTCGCCCTTTTTTTCAATTCAGACATTAAAATACTCG
Right flanking sequence: Indices 41393 -- 41892
TGAGCTTAAGGAAACGAAGCGCAGAATGGAAACACAATCTTTTTGTTTCGTTTTCTTTTTGCTAT
TTCATTTTATAGACATCTCCGGCTTATCCCGGCTCGGCTGAATCTGCGGCGTTTTTTCAAATATT
TGAAAAATCTATAGTCCTCTGTCTTAAGGTGTGTAGAGACTCCTTTTTCATTGATTTATACCAGT
CTATCTTAGATCCGAGATAGTGCCGAAAAAATGATTCAATTTAATCTAACCATGGTTGCCTTGGC
AATGGCAATGACTTTTATACAATATGCAGAATACTCCAAAACCTCTATTTAGAACTAAAAGAAAA
TAATGCTTTTTTATAAAAAAATCATAAAGTGCAAAGGTTAAAATTTTGAGCTTTGTTTTACGTAG
TTTTGCCATCTATATAATAGAATATAGTAGAAAATAATAAGTTGGCGAGGAAGTAAAAATATGTA
TCTATATCTATAGATATATATATATTTTTTTTTTATTTTGTGGAT
Found at i:63248 original size:14 final size:14
Alignment explanation
Indices: 63229--63256 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
63219 TCTTCGTTTT
63229 TATAAGATATGAAG
1 TATAAGATATGAAG
63243 TATAAGATATGAAG
1 TATAAGATATGAAG
63257 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 62729 -- 63228
AACAAAGACCTGGAGAGGCTGTTAAGATAGCTGCTAATGCCATAGGCGCTTTTACTGCGGCGGGG
TACTTGGTTGTACGTGCACAATTTAAATTTAAATAGAGCGAATGCATTAGAATTGTAAGAAAAAA
GCCTAAAATTGAAAAAGCTAAAGTTCAATTATAAGGTATTTATTAATGAAGCTAAAAACACGGAT
CAGCTTTTGGAACAAATTGAAGAGCGTTAAATGAAAGAAATTAAGGCTTGTTGGTTGGGTAGTAA
AAAAAATGAGTACTGATGAAGAATGAACAGCCACGTCTAGATGATGCTGTTTAGCGTGTAGTAGA
AGCTAAATACAACAAGCTGCAAGCTAACTTCGCGCGACAAGATTCGAGCGGAACAAACGACCATA
AAAGAAAGGCCACGAGTATCATAGGCAGACCTTCAACAGGCACCTAAAAAAAAATTACCACCTAA
ATTATCTATTAAGTACCCTGTCCCAAACGCAAACTTCTTCGTTTT
Right flanking sequence: Indices 63257 -- 63756
GTATTTTTGTTTCTCGAAGAGCCATCGGGAACTTAGGTTCTTTTATTTATCGAGTTTCGCAAGTA
TATCTTTCTTAGGATCTAAATCCTATTAATTTGAACGTAGAGTTGTATGATGCGAAACTATCACT
TACGGGGTGGGTTTAATCTTAGATTTTTTTATTTTCTGAGTTTTTATGGGATTATTATCGCGGGT
TTGTCTATCCTAATGGGCGTCTAACAAAAAAATCAATTTTTTTGTTGGTTGGCCCTTTTGTGGGG
CCTGTTGAAGGGCCGAAGTAGTTCTGAAAAAAACAAGAATATACCAAATGAGTTTGAAAAATACA
TGGCTATTTCCAATTGGTTATTGTGACGCTGCGGAACCTTGGCAATTAGGATTTCAAGACGCAGC
AACACCTATGATGCAAGGAATAATTGAGTGCGCCTAGATATATCATCACGGTTGCAGAGCTCTGC
TCCAACTCTGCCATATCTGCTCGAGCTGGCTATCGCCAGGATGTG
Found at i:104622 original size:10 final size:10
Alignment explanation
Indices: 104607--104632 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
104597 TCTTCTTATA
104607 AATAATCTTT
1 AATAATCTTT
104617 AATAATCTTT
1 AATAATCTTT
104627 AATAAT
1 AATAAT
104633 GCATAG
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 104107 -- 104606
TTCTATCGGGGGGGGGGAGTTGTGCATCATAGGTACCTTCTTATTGCTGCGAAGGGCGATATGAA
AATAACCCCCCTATCCAACCTCATTCTGTTGCGCGAAATCCATCATTGGCTAAGCAATTATTTGG
TTATGCCATCTTAGGTTTCGCTTTAACAGAAGCTATTGCTTTGTTTGCCTTAATGATGGCCTTTT
TGATCTTATTTGTTTTTTAATTTTTTGGTGCTGCGATTTTTTGGGAAAAAAACTATATTTTGGCC
GCACCCTATTGGCTTTGCGAATAGGGCTGCGCCCAAAAAATCTAGATTTTTTGGCACCTTAGGGC
CGAACGATTAGTACGTTCGAGCCCTTCACCACTTGCTACCAAAAGCATAAGCGTAAAAAAACTGA
ACTGACAAAGATTTTAACCTTAAAGGCTCATTGGATAAAAAAAGAAGCAGGACAAATATATCTAT
ATATATATTTTTTTTTCTTTTTTAGCTGCTTCACTTCTTCTTATA
Right flanking sequence: Indices 104633 -- 104638
GCATAG
Done.