Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_029452
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: 106795
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Found at i:19051 original size:19 final size:20
Alignment explanation
Indices: 19009--19051 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
18999 GGATGTTGGT
* *
19009 CATGACTTTCGAAAAGTTCC
1 CATGACTATCGAAAAGTTCA
*
19029 CATGACTAT-GAAAATTTCA
1 CATGACTATCGAAAAGTTCA
19048 CATG
1 CATG
19052 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 18509 -- 19008
GAGCTAAAAATGCATTTTTTTTCTTTTTTATTTTCATTTTCAATTTTTTTATTTTCAAATTTATG
GGAGACTTGTCATATTTAGAATCTTTCTGTGGTGTGCTTTGTTTTTTATTATTTTGTACTTTTTT
TTTATCATCTAAATATAGGCGCGATACGTGGGCAAACAAGGAGCGTAGGCTTGAAATAAAAAAAA
AAATAAAACCGCGTAAGCGGGCACAGAGAACAAAGCGCCAAGCGCTTTGTTGGCCTAACGAAAAA
AAGAAACAAAGAAATAAAAATAAAGAAAATTTTTCCTTTTTATTTCTTTCAAATAAATCAAAAAT
ATTTTTGATTTATTTGCTGCAATTTTTAAAAACCTTCGGCTTCAACGAAAAAGCAAAAATTTTGA
CTTTTTATTCTCTGCTTGCTTTTTCGCAAGCTTATTCTTCCGTCCCTGAAAATATTTGGAATAGA
TTTTTTATTGTTCGCGCCTTACCAAAAAGACTGATGGATGTTGGT
Right flanking sequence: Indices 19052 -- 19551
GAGGAGTTTGCATCTTTATTATGGGTGTTATTTTGTCGTGCGACCCTGCAGCTTATGCGCGACTA
TCTCGTGTTTAAGCTCACGCCATGTAGGCGTGAACTCTGGTTGAATTCGGGTTCTCAATCCCGCC
GCTGAGATGCTCAGTCGACTCTTGAACCTTGATAGGAAGACGGCTTCTTCCTAAATTAGTGCAAA
AGGTTCAAGGACTTAGGATGAACTTAATGTGAATGGGTATAAGCTTCGCTGCTCAAAAACACCCA
GTATTGACCACACTGAGAGACTTGCCAATGGCAAGAAAGGCCGCGGGTAACGCTAGTTGGCGAAA
TGGCGTTAAGCATTCCTAGCGATACGGAAAAAGAGGTCGTGATGATATCATCTACGTTCGTACTG
TTCTTCGTGGAGTAAATCTCACATCCAAAAATCTAACCAGGGAACGGGATAATTCCCATTAAGTT
CCAGTAAAACTGGCAGGCCAGCCGGGCCGTAAGCTAGTGGGAACA
Found at i:41616 original size:81 final size:81
Alignment explanation
Indices: 41481--41629 Score: 255
Period size: 81 Copynumber: 1.8 Consensus size: 81
41471 AAAATACTCG
*
41481 CTATCGGATTCGAACCGATAACCCATAGGAACAGATTTTGAGACTGCCGTGTTTACCATTTTCAC
1 CTATCGGATTCGAACCGATAACCCATAGGAACAGATTTTAAGACTGCCGTGTTTACCATTTTCAC
41546 CAAGCGAGTATGCTCA
66 CAAGCGAGTATGCTCA
* *
41562 CTATCGGACTT-GAACCGATAACCCATAGGAACAGATTTTAAGTCTGTCGTGTTTACCATTTTCA
1 CTATCGGA-TTCGAACCGATAACCCATAGGAACAGATTTTAAGACTGCCGTGTTTACCATTTTCA
41626 CCAA
65 CCAA
41630 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 40981 -- 41480
CTTCAATCTACTTTAGTCAATCATATGGATATAAAAAAAGCGGCTAATTTAGAAATAACATCAGT
ATTTCAACAACTTTTTGAGCTCATTTTTTACCCATATAATTCTTTATGTTCTTGTTTGAACAAGC
CAATTTGTGCTTCATCCACTATACAAGAAAAGACGCAAGGAGGGTTACTTAGTCACCAGAGGATA
ACCACTTAGTAACTTGGGTCCCCACTTTGCCAATTAAAGCCTGCGGCTTTATTGACAGAACTGGG
GCGCGTAGTTTGTAGCGAACCTTTTTTTTTTAATATTTCGGGAATCCCCCCAAAAATATTAAAAA
TATTTTTTGCTGCGAAAAACAGCGTCCTCAAAAATTGTAAAGATTTAAACTAATGGATGATTTGT
TTTTTTGGCGAATAACGGGATTCGAACCCGTGTTTTCAAATTCACAATCTGACACTTTCACCTAT
TAAGTTATACTAGACCTTTTTCCAATTTAGACATTAAAATACTCG
Right flanking sequence: Indices 41630 -- 42129
ATGAGCTTAGGGAAGCGAAGCGCAGAGTGGAAACACAATCTTTTTGTTTCGTTTTATTTTCGCCA
TTTTATTTTATAGACATCCCCGGCTTATTCCGGCTCGGCTGGACCTGCGGCATTTTTTCAAATAT
TTGAAAAATCTATAGTCCCTTGTCTTAAGGTGTGTAGAGACTCCTTTTTTATTGATTTATACTAG
TCTATCTTAGATCCGAGATAGTGCCGAAAAAATGATTCAATTTCATCTAACCACGGTTGCCTTGG
CAATGGCAATTACTCTTATACGATATGCAGAATACTCCAAAACCTCTATTTATTCTATTTAGAAC
TAAAAGAAGATAATGCTTTTTTATAAAAAAATCATAAAGTGCAAAGATTCAAATTTTGAGCTTTG
TTTTACGTAGTTTTGCCATCTATATAATATAATATAGTAAGAAATAATAAGTTGGCGAGGAATTA
AAAAAAAATATATATATATATTTTTTTTTTTATTCTGTGGTCCTG
Found at i:54707 original size:11 final size:11
Alignment explanation
Indices: 54691--54715 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
54681 AAGGCAGGGG
54691 CGCGCTGCAGC
1 CGCGCTGCAGC
54702 CGCGCTGCAGC
1 CGCGCTGCAGC
54713 CGC
1 CGC
54716 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 54191 -- 54690
TAGCCTTAATAGGAGTTGTTACTAGTGTTATCAGTTGTTTTTATTATATACGCTTTGTCAAAATC
ATGTATTTTGATACACCTAAAAAATGGATTCTATATAAAACAATGGATCGTGAAAAATCCTTACT
ACTAGCAATTACTTTATTCTTCATTACTTTTTTCTTTTTATACCCTTCTCCCCTATTCTTAGTCA
CCCATCAAATGGCACTAAGTCTATCTTTCTAAGCCGCTGGCTGCAACGCCGGCGCACCAATGACT
CTCCGTACCGTTTCCCATCATTTGTTATGCGAATAATGTGGGCGCCAGCCTTCGGCCTGTCGCGC
CAAGCCCACCGCACCCACCGCAGCGCGAGGCTGCCCTCCCATCGGCCTGGCATACATTTTAAGCG
GAAAAAGGGACTTGAACCCTCAACCTCAGCCTTGGCAAGGCTATACTCTACCATTAAGCTATTTC
CGCAGCACAATAATAAAAAAGTAACAAGGGTCCGAAAGGCAGGGG
Right flanking sequence: Indices 54716 -- 55215
TTCTTTATTACCAATAAGAAGGGCAGCCTCGCTGCAGCCGCTTCTTTATTATCAGATGTATTATC
TTAGTAAACCATGCTTGGAAAGATTCGAACTCTCAACCCCCAAATCCGTAGTTTGGTGCTCTATC
CGATTGAGCTACAAGCATAAATTTCTTAAGCACTACGTGTCATGTAGGCTCCATTATTACAAAGA
AAAAACATATATATATGAAAAAAGAATAGCAGTTCGGGCAGCATTTTCTAGAGAATAGTATTACC
GTATTGCATTATTTTAAGTATGCCTTCTGTGACTGCACTGTGTAGTCAACATCCGCAGTTACGTG
CATTACTAACGTAATTAAGTTCGAATGTTGATTCGATTAGATTAGATTAGCTTGCGTTTTTACTG
CTAAAATAGATATATATATATATTTTGTTTTCTCACCTAATTTATCCGAAAAGGGGAAATGCAGA
CGCTATTTTATTAAAGGTCGCTCTTGATGTAATGTTCAACAGGTA
Found at i:78012 original size:16 final size:16
Alignment explanation
Indices: 77991--78022 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
77981 AATTATCATT
77991 ATATATTATGGTGTTG
1 ATATATTATGGTGTTG
78007 ATATATTATGGTGTTG
1 ATATATTATGGTGTTG
78023 GCATGGCAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (16 bp):
ATATATTATGGTGTTG
Left flanking sequence: Indices 77491 -- 77990
CTGGATCAAACGAAGTTTATCTGGCTATAGTTTACAAGAGATTTTGACCAACAGATTAAAATATA
AAATAAAAGGAGAGGTTTTGCGCTGTGGTATCTTTCTACCAAATTTATTGGAGCTTACGCCCTGA
CTAAATAAGTTGTAGTAGAAGAGGTTATTATGGCCCAGGCGTGCCGCCGTCTTCTCTGTTCCATC
AATTTTGTTTCGTCTATCTCTTTATGAATCTGCTGAGATTTTGCTGATTCCACATCAGATCCAGC
TACGGCGCAAAAAACGTCTATGCCTAGAACGTATCAATTAGCTACTTTTATGCGCAGATTTATTA
TACTGGGAATTTTTCTAGCGGGCATATCTAATAGTTTTTTTGGTTTCGCTGGTCTTATTATAGCA
AGCGCGTAATCATCCGAACAGTTGTCGTCTACTGTTTCCATTAAATTTGATGATTTACCACATTG
CAAAATTTAATTGACTTCGTTAAGTCTTCCCTAAAAATTATCATT
Right flanking sequence: Indices 78023 -- 78522
GCATGGCAGCGGCTATCAAAAAAGTTGTTTCTGGTATTAGAACCCCAGTCATCGAGGCTTTTGTA
GCTTCTACAGCAATGACGGCCTATAGCAAAATAAAGTAAGTCATAGAGGCGTCTCAAAGCTTAAT
AAGTACGGCAATGCCCGGGCGACCGGCCTGCCCAATATCGTGCCCACATATATGCGCGGAAATAA
TATGATATGAGCTGTTGGTGTACCGCCCAGCGAAGAAGCTTATCCCGGCCGAGTAACCGCTCCTG
TAGACAGCCAGGATGAGTTAGCAATAGCACGGCGCGCCTCCGGCTTTACTTGATAACGAATCGGT
TAGAGCTTTACACGTATAGCGCCTTCGGCCCTTGGCGAGTTCACGGAATATATACTGTTTTTTCA
GCTTATTTCAGTTTTTCGTATATTTCTATTTTACTTAATTGACGGTTTAGAAGAGATGCCATGAA
AAAGTTTCATAGCATAGTCTCAAGATACAATATAACACGTAGAAG
Found at i:85440 original size:22 final size:22
Alignment explanation
Indices: 85412--85455 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
85402 GGCGCTTAGA
*
85412 GGCTGCAAGTGATGAATGTGTG
1 GGCTGCAAATGATGAATGTGTG
* *
85434 GGCTGCAAATTATGCATGTGTG
1 GGCTGCAAATGATGAATGTGTG
85456 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 84912 -- 85411
TGTCCACCCTTTACACAGAGAGTAGTAGCAACTCATTCAGTTTAAAAAAATTCAACTAAAAAAAA
ATTTTCAGGCCGCTGGTTTTGTTTCCGTGCTTCCGGGTGGAGGGTGAAAGCGGCCAGGGCGCAGC
CAATTTTTTTTTTTTTCGCCCTCTGGCTACGCCCCTAGTAAGGCTTCGTCATACGAGCGGAGCTC
GAAACCCCTCCATCCCCACATTAACAACATGTAGATTTGGAGAAAACAGGAACGCAACAAAACAT
TAACAAAATCGGGCCAGGAACGCTTATTTGTAGAATGTACTATTTGTAGGTTCTGTAGGTTTTTA
CTGCGTAGACGATATTATTAGATATTATTTACGTATGGCGTAGCCGGCAAAGATAACTGGGTGAC
CCAGATTAACTATGGCCTTCGCCTCTAATGCATCTGGCCCTAATCTATTAATCTCGCGCTTAGAT
AGATTAATGCATCAGTCTGGCGCTTTTCACTTTCTGGCGCTTAGA
Right flanking sequence: Indices 85456 -- 85955
AGCGTTAACAAAAACAATATATATTACATGGCTCCAGTCGTCTCAAGTCTATTGCTCCGCAACAA
TTTTTAAAATGAATCAATCATCGAAAATGATTGATAGCTACCTGCACCAAATTATGGCTGGTGTA
ATCAGGAGAAAAGGGATTCGAACCCTTAACCTGTGGTTTTGGAGACCATTGTTCTACCATTGGAA
CTATTCTCCTAAAAAAAAAAGTGGTTCTTGGTTTATGGAATTTGCACCTATTTGTGTCTATTTAG
TAATAAGTTTGCTATTTTCTTTGATCTTAATCGGCGTTTCCTTTCTATTTGCTTCTTCTTCTAAT
TTGGCTTATCCAGAGAAATTGTCAGCTTACGAATGCGGTTTTGATCCTTTTGATGATGCCAGAAG
TCGTTTTGATATACGATTTTATCTCGTTTCTATTTTATTTATTATATTTGATTTGGAAGTCACCT
TTCATTCGCTGTGCGAACCCTCCCAGCCGCTTTTTTGGGCTTCCC
Done.