Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_047462
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: 106827
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Found at i:1467 original size:16 final size:16
Alignment explanation
Indices: 1411--1458 Score: 87
Period size: 16 Copynumber: 3.0 Consensus size: 16
1401 AGTGCTCTTC
*
1411 ATTTATAGTATTTTTT
1 ATTTATATTATTTTTT
1427 ATTTATATTATTTTTT
1 ATTTATATTATTTTTT
1443 ATTTATATTATTTTTT
1 ATTTATATTATTTTTT
1459 TTTTTTATTG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (16 bp):
ATTTATATTATTTTTT
Left flanking sequence: Indices 911 -- 1410
CTCACGCCCTTTTCTTTCTTTGTGAGAAAAGGCCGCGGGCCTGTAATCTAAGCTCAAATAGTTCA
AAACACAAAAAGAGAAGTTACAAGAAGATTTCGAGCTTAGATTGAGCAAAGAGAACACCGCAGCC
TTTGATGCGGCTCTGAAAAGAGAGAAGTTAAGTAGGTGTTACCAACTACTATTCCCATTTAATTT
CTTTATATTATACAATCTGCAGCAATCCTGCAGTTAAGGAGTTGTTTGGTAACAACTGTGAATAA
CAGTATAGATATAGATATCTCTTTATATTTAGCTCCCGCAAATTAATTAATATCTATGATTTTTC
TATGAAGAGCGGATTCCCGTTATTTTCAAGTTCCGCCAGTAATCTACGTCACCGTCAACATTAAT
TATCTATCTGTCTTTTTCATTAATTATCTAAATTATGCCAACCTATCTTATGAAACCCGGCCCAG
CAATATAATAAGTACTGGCGACACGATTGAGAAGCAGTGCTCTTC
Right flanking sequence: Indices 1459 -- 1958
TTTTTTATTGGTCATTTATTAAAAATTTTCTGTAGTTTGAAGCTCGGCCCTGGTTCTTGTTAAAG
CGAGTAGTAATTTCTGCTGTTTGTTTGATAGCTTATTTGTTCTACGCTCTTTCATGCACTGTATG
CGGAGTGCTCCTTTAATATCAATGAATATGTCAGAAGCATTGGCAACCTATACATTATTGCCATA
ACTGTTCAAATATCTGTCCTCGTTATTTAATTGTTTTTTTTTTCTTAGTATAATAAATTGAGTTG
CCATATTCCAATTAATTGATAAATTGATTACATTAAATTCATAATTAGTTTTGGCGGCCGAAGGC
CCTTGTTAAATTAATATCTTTTTGCCATTACTTTTTGGGGTGAGGCGGGGCTCCGCCCCCCAATG
GACTAAGTCCTTAGAGGGCAGAGCGGGTAAGTGCTTAAGTGGCACCATCTGCTAAGACGTCTAAA
TGCTTTCTTTAATAACCGGAAGTTCTGAAAAAGTGTGAAATGCCG
Found at i:16331 original size:14 final size:16
Alignment explanation
Indices: 16312--16343 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
16302 GCTATTTCAC
16312 TTTATT-TTT-TTTTT
1 TTTATTATTTCTTTTT
16326 TTTATTATTTCTTTTT
1 TTTATTATTTCTTTTT
16342 TT
1 TT
16344 GGTATTTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.38
15 3 0.19
16 7 0.44
ACGTcount: A:0.09, C:0.03, G:0.00, T:0.88
Consensus pattern (16 bp):
TTTATTATTTCTTTTT
Left flanking sequence: Indices 15812 -- 16311
TTAATTAATATACCAATAATTAAATTTTCTGTAAACTGGTGGAATACATTGCATCAACCTTCCAG
CATTAGCCAATTTGGTACTTCAATACATATTTCTATGCTCATTCCAATCCTGTTAATTCTTATTA
GCTTCCTTTGTTTAAGTGGGATTTTTTTTATTTTGGAAACACGTCAAATTATTTTATCTTTTTCT
AGTTTTTCTGTAAAAAGTCAAATAGATCCGCAAAACAACAATAGAAAACAGGTTTTTTTTTATAC
AAACAATAAATCAAGCAAAAGCACCTAAGGAAAGGTGGACTTTTCTTGAGTTTAAGCAAGTTGTT
CAAAGCTTTATAAGAAGCAAAGCAACGCTCTGCGTTAAAAAACGCAAAAAAATATATTTTTTTTG
CCAATTATAAGCAAAATTTACTGAAATGTATAATGAATTGGGCCATTATTTTTTAGTACTGAGTA
TTTTCGTTGCATTAACTTACAACAAAAGACCTGCGGCTATTTCAC
Right flanking sequence: Indices 16344 -- 16843
GGTATTTTGTTTTGTTATATTTCTTCTGATTTTTCTAATTATAATGTATTTATTAACTCAAATGC
TAATGCGCCTTTATTTTATAAAATATCAGGAACATGGTCTAATCATGAGGGCAGTTTGTTATTAT
GGTGTTGGATCTTAAGTTTCTATGGATTTTTTTTGGGTCATCGGGTTCGACCCTGCAATGTTTCA
AAACGAGGGCGCAGCAAAAATATATTTTTTTTTCGCAGACCGCTTGTGGCTTTTCGCTCTGCTTT
CTTTATAAAGAAAGAGAATAAACAATTCAGACATCATTTGTTGCAGAACCTGTTTGGTACCATAA
ATCATAAAAGCTCCCTCAAGAGCCAATCCAAAGCGGCGCCCTCAGGTATCGTTCAAGAGCCCTTA
AATAAAAAGTTAAAAGATAGTGCAAATGCAAAAGAAAATAAAAGGTCCATAAGGCTTAAAAAATG
GAAAGAGTTGAAAAAAAAAAAATCTAGATTTTTTTTTTTGCTTTA
Found at i:19193 original size:19 final size:20
Alignment explanation
Indices: 19151--19193 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
19141 GGATGTTGAT
* *
19151 CATGACTTTCGAAAAGTTCC
1 CATGACTATCGAAAAGTTCA
*
19171 CATGACTAT-GAAAATTTCA
1 CATGACTATCGAAAAGTTCA
19190 CATG
1 CATG
19194 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 18651 -- 19150
GAGCTAAAAATGCATTTTTTTTCTTTTTTATTTTTATTTTTAATTTCTTTATTTTTAAATTTATG
GGAGACTTGTCATATTTAGAATCTTTCTGTGGTGTGCTTTGTTTTTTATTATTTTGTACATTTTT
TTTATTATTTAAATATAAACGCGATACGTGGGCAAACAAGGAGCGTAAGCTTAAAATAGAAAAAG
AAATAAAAACGCGTAAGCGGGCACAGAGAAGAAAGCGCCAAGCGCTTTGTTGGCCTAACAGAAAA
AAGAAACAAAGAAATAAAAAGAAAGAAAATTTTTACTTTTTATTTCTTTCAAATAAATCAAAAAT
ATTTTTGATTTATTTGCTGCAATTTTCAAAAACCTTCGGCTTCAACGAAAAAGCAAAAATTTTGG
CTTTTTATTCTCTGCTTGCTTTTTCGCAAGCTTATTCTTTCGTCCTTGAAAATATTTGGAATAGA
TTTTTTATTGTTCGTGCTTTACCAAAAAGACTGATGGATGTTGAT
Right flanking sequence: Indices 19194 -- 19693
GAGGAGTTTGCATCTTTATTATGGGTGTTATTCTGTCGTGCGACCCGGCAGCTTATGCGCGACCA
TCTCGTGTTTAAGCTCACGCCATGTGGGCGTGAACTCTGGTTGAATTCGGGTTCTAAATCCCGCC
GCTGAGATGCTCAGTCGACTCTTGAACCTTAATAGGAAGACGGCTTCTTCCCAAATTAGTGCAAA
AGGTTCAAGGACTTAGGATGAACTTAATGTGAATGGGTATAAGCTTCGCTGCTCAAAAACACCCA
GTATTGACCACACTGAGAGACTTGCCAATGGCAAGAAAGGCCGCGGGTAACGCTAGTTGGCGAAA
TGGCGTTAAGCATTCCTAGCAATACGGAAAGAGAGGTCGTGATGATATCATCTACGTTCGTACTG
TTCCTCGTGGAGTAAATCTCACATCCAAAAATCTAACCAGGGAACGGAATAATTCCCATTAAGTT
CCAGTAAAACTGGCAGGCCAGCCGGGCCGTAAGCTAGTGGGAACA
Found at i:30206 original size:12 final size:12
Alignment explanation
Indices: 30189--30213 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
30179 AAATGAAATA
30189 TATATATATATT
1 TATATATATATT
30201 TATATATATATT
1 TATATATATATT
30213 T
1 T
30214 CATTTAGCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TATATATATATT
Left flanking sequence: Indices 29689 -- 30188
TCATCATATATAATGTATTAACATCTTGATGTTAATAGGGCGCAACAAAAAATAGATATATTTGC
CGTTTTCTTTTTTGAGTTTTGGAGAGTAAAACCTGCCAGACTAGGCAGGTGCATAGACCCCTTCG
CCTTTTATTTAATCCGCAAGTTTCCTGTTTACACGGTTCTTTTAGGATCAAGCAGGTACTATGGG
TCCTCTGACTTCCAACTCAAACCATAGTGTATGGTTGGATCTCGCCGATATCACCTGTGAGCTAT
AGCGCTTGAGATGTCGTTTAGTTCTCTGTCCCCATTACTTTGGGTAATCTGCTTTCATGCGTAAA
AATATATCTATTTTTTTATTGTCCTTACCGTTCTTAGCCGCCAGCAGGCTGAAAGCATAACAGTG
TTCGTTCGTGCGATTCCCCGCGTGCATTTTTTTCGTACTAGTTCGCTGTAGGGTAGGCTGACCCG
AAAAGAACTGCGATTCTGCTTTATCATCTCATGCTAAATGAAATA
Right flanking sequence: Indices 30214 -- 30713
CATTTAGCAAGCGCCAGCGGACTCGCGGAGGATTATTGAGTAGGCCGATAAACTAGCCGACAGCC
GACGAATATCTCCTTTATCGCTGTTTCTGTGGTATGCTTCCTTTCTTTTGTTATTGGGTAAGCTC
TGAGCTCTTTGAGCAGTAGTGCCTTTATTGTAATCACAAGTGATCTAACGGCCGCCCCTAAGAAA
GCCCCAGAAATTCTATGAAAAATAGAAAGAGTAGAAGTAAGCTGTGGCTTATAAATGGTAAGATG
AGGTGATAAGGGTCGATTGATTTTCATGTTTTTAGTTGACTTTAATTTTGATTCAAGGTGACAGG
ATTTGAACCTATGACCCTCTGTACCCAAAACAGATGCGCTACCAGACTGCGCTACACCTTGGCTG
ATGTTCCCTAATGAATATTTGATAAATGCTTAAATTGTTATTAAGCAACATACAAAAAGAACTAA
AACTAATAAAAAAAACTATATTTTTAACGCTACTGAAAAAAAGCA
Found at i:38330 original size:23 final size:23
Alignment explanation
Indices: 38294--38338 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
38284 TGCTAATACG
*
38294 AAAAATAAACAAAAAAACTAAAA
1 AAAAAGAAACAAAAAAACTAAAA
* *
38317 AAAAAGAAATAAAAATACTAAA
1 AAAAAGAAACAAAAAAACTAAA
38339 GTGAGCACTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.80, C:0.07, G:0.02, T:0.11
Consensus pattern (23 bp):
AAAAAGAAACAAAAAAACTAAAA
Left flanking sequence: Indices 37794 -- 38293
GGACTCAGTGAAATTGAACTCTCCGTGAAGATGCGGAGTACCAACGGCTAGACGGTAAGACCCCG
TGCACCTTTACTATAGCTTTGCAGTGATAACCTTGATTGAATGTGTAGGATAGGTGGGAGGTGGT
GACGTTGCACGTCACCACCAATCTTGAAATACCACTCTTTCGTCTAAGGATGTCTAACTGCCGAA
ACAGAGGCGGGACACTGCATGGTGGTTAGTTTATCTGGGGCGGATGCCTTTAAGTAAGGGGCGCT
TGGATGGTAACATCCCAGGCTAATCTGGCTATATGCTGAAATCTCCATTTCTTGGACAATCAGCA
GGGAAGGCTGAAAAAAGCCACTGCGAAAAATTTATTTGGCTCCCTCAACGACTGCATGCCAGGTA
TCCAATGCAATAATGATTGGATAATGATACAGTCTGAACTTCCAGTAAACTGGAAGCCTAAAGCA
CTGTTCACTACAAAACAATGATAGGACATTCAAACTGCTAATACG
Right flanking sequence: Indices 38339 -- 38838
GTGAGCACTTCGATTAAATCAAATACAACGACAAGTATGTTGCAGAGTGGATGAACATAATTGCC
CAAAGAGTAACGGAGGTGTGCGAAGGTAGGCTCGAGCTGATATTATGACAGCTTTAGAGCGTAAT
GGTAGAAGCCTGCCTGACTGTGAGACTTACCAGTCGAACAGAGACGAAAGTCGGCCATAGTGATC
CGGGAGTCCCGTGTGGAAGGGCTCTCGCTCAACGGATCAAAGGTACGCCGGGGATAACAGGCTGA
TGACTCCCAAGAGCTCTTATCGACGGAGTCGTTTGGCACCTCGATGTCGACTCATCACATCCTGG
GGTTGAAGAAGGTCCCAAGGGTTCGGTTGTTCGCCGATGAAAGTGGTACGTGAGTTGGGTTTAGA
ACGTCGTGAGACAGTTCGGTTCCTATCTACCGTTGGTGTTTAAAAGAGAACTGCGAGAAGCCAAC
CCTAGTACGAGAGGACTGGGTTGGGTCAACCTATGGTGTACCGGT
Found at i:42310 original size:81 final size:81
Alignment explanation
Indices: 42175--42324 Score: 257
Period size: 81 Copynumber: 1.9 Consensus size: 81
42165 AAAATACTCG
*
42175 CTATCGGATTCGAACCGATAACCCATAGGAACAGATTTTGAGACTGCCGTGTTTACCATTTTCAC
1 CTATCGGATTCGAACCGATAACCCATAGGAACAGATTTTAAGACTGCCGTGTTTACCATTTTCAC
42240 CAAGCGAGTATGCTCA
66 CAAGCGAGTATGCTCA
* *
42256 CTATCGGACTT-GAACCGATAACCCATAGGAACAGATTTTAAGTCTGTCGTGTTTACCATTTTCA
1 CTATCGGA-TTCGAACCGATAACCCATAGGAACAGATTTTAAGACTGCCGTGTTTACCATTTTCA
42320 CCAAG
65 CCAAG
42325 TGAGCTTAGG
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 41675 -- 42174
CGGACAACTTCAATCTACTTTAATCAATCATATGGATATAAAAAAAGCAGCTAATTTAGAAATAA
CATCAGTATTTCAACAACTTTTTGAGCTCATTTTTTACCCATATAATTCTTTATGTTTTTGTTTG
AATAAGCCAATTTATGCTTCATCCACTATACAAGAAAAGACGCAAGGAGGTTTACTTAGTCACCA
GAGGATAACCACTTAGTAACTTGGGCCCTCACTTTGCCAATTAAGGTCATAAGCTTTATTAACAG
AACTGGGGCGCGTAGTTTATAGCGAAGCTTTTTTTTTTTAATATTTTGGGAAATCCCTTAAAAAT
ATTTTTTGCTGCGAAAAGCAGCGCCCTCGAAGATTGTAAAGATTTAAGCTAATGGATGATTTGTT
TTTTTGGCGAATAACGGGATTTGAACCCGTGTTTTCAAATTCACAATCTGACACTTTCACCTATT
AAGTTATACTCGCCCTTTCTTTCAATTCAGACATTAAAATACTCG
Right flanking sequence: Indices 42325 -- 42824
TGAGCTTAGGGAAGCGAAGCGCAGAGTGGAAACACAATCTTTTTGTTTCGTTTTATTTTTGCTAT
TCTATTTTATAGACATCTTTGGTTTATTCCGGCTCGGCTGAATCTGCGGCATTTTTTCAAATATT
TGAAAAATCTATAGTCCTCTGTCTTAAGGTGTGTAGAGACTCCTTTTTTATTGATTTATATCAGT
CTATCTTAGATCCGAGATAGTGCCGAAAAAATGATTCAATTTAATCTAGCCATGGTTGCCTTGGT
AATGGTAATGATTTTTATACAATATGCAGAATACTCCAAAACCTCTATTTAGAACTAAAAGAAGA
TAATGCTTTTTTATAAAAAAATCATAAAGTGCAAAGGTTAAAATTTTGAGCTTTGTTTTACGTAG
TTTTGCTATCTATATAATATAATATAATAGGAAATAATAAGTTGGCGAGGAAGTAAAAATATATA
TATATCTATATATATATATATTTTTTTTTTTTATTTTGTGGTCTT
Found at i:88210 original size:14 final size:14
Alignment explanation
Indices: 88191--88217 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
88181 GGAACCGAAA
88191 AATTTTCTATATAG
1 AATTTTCTATATAG
88205 AATTTTCTATATA
1 AATTTTCTATATA
88218 AAATATCATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.07, G:0.04, T:0.52
Consensus pattern (14 bp):
AATTTTCTATATAG
Left flanking sequence: Indices 87691 -- 88190
GTAGCCAGTAGAATGGAAAGATCCCGATGAATCATCTACGATGATTCATTATGTTTGGGAAAATA
GCTTAGTTGGTTAGAGTGCTGGTCTGTCACGCCAGAAGTCGCGGGTTCAAATCCCGTTTTTCCCG
GTAATTTTCTAATTTAAAAATGAATTATTATAAAATCAGTTTAGAAAGAGAGATATATATCTCTC
TTTATGAACTGGTAACTGAATCAGTTAAAAATTTTTTTTTTATTAAAATATGGCCAAAAAAGCAT
GCGATATAATATGATTCAATTTTACAGGGCGTAGCCCCTATCCTACCTGCGTTAAAAGTAATCCT
GAGGTGTAAAACTTTAAGGATAATATAATAATGGTTAAGATTACATACTGAGCTAATGCTAGAAT
AAAAAAATAAAAAAAAAAATTATGCTATGCAGATGAATAGTGCAAAGAACTAATACAAAGACCTT
GTCAAAAAGAATCTAAGATCTTAATCGGTGTTGGCGGAACCGAAA
Right flanking sequence: Indices 88218 -- 88717
AAATATCATAGGTTAAGGATTGGATTAGCGCCCCGAGTTGTTCAATTATAGCGGGAAGCCAGCGG
TGAAAAGGGCGAAGCTCTCTTATGATGAGATAGAAAGATTTACTGCGCCTTATTTGCTCTGCTCT
TTAAAAATAGCGCTATTTAATATAGCAGTTCCCACTGAAAGAAGGACATCTAATAATAAAAATAA
GATACCCTAGCAAAACAAGTAAGCATAAGCTTATAAAAGTGTCGAACAGACCGCAGGGCCGAAGG
CTTCTTACACTTAACTTCTCACAATATACATAGGACATCTTCTAGTAGCCAATAAGTCAAACATT
ACTTCTGCGGGTTAACATGGTTAATAGGTTGCGTAAGTCGTATGTGGGCGCAAAGCGCAGCACGT
GTGGTTCTAACCGGAAGAGAAAACATGAAAGGGCCCGCCCATCCTGACAAATACAACAATACTGT
ATCCTGGGTTCAAATCCCATTTTCTCTATAGGGGACGTAGTTCAA
Done.