Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: MZ328723
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: 260164
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Found at i:9824 original size:20 final size:20
Alignment explanation
Indices: 9791--9835 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
9781 TTTTTTATTA
* *
9791 TATTATTGTTTATAGAATAT
1 TATTATTATATATAGAATAT
* *
9811 TATTATTATATATATATTAT
1 TATTATTATATATAGAATAT
9831 TATTA
1 TATTA
9836 ATAAAATGAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (20 bp):
TATTATTATATATAGAATAT
Left flanking sequence: Indices 9291 -- 9790
AAGACTTAAGGCTTTCGCTATCGCTCTTCGCCTAAAGCCGTAACTTCGCTCTTCGATCCTTCGCG
CTATCGCAAGAATATAGCGATCGAAGAGCTATCGCTCAGCTGCTTCGCGTTTATAAATATAAAGC
CGTATTGCCCGAAGGGGGCATGCTGCAAAAGCGTAGGTGGGTGATAAGCGTAGGAGGCGTGCCCG
AAGGGCAGCGGCAGCAGTGTGGTTCCAGGTGCCCGTCGCTAGATTGAGATCTGCAGGGCGGCGGG
GACTTCGACTGCCTTGTATCAGGTGAAGAGAAGAGGGTGGTAGGCTTAGTAGGGCTCGAACCTAC
AATATAACCGTTATGAGCGGTACGTTTCAACCAATTAAACTATAAGCCCCTACGGATCTCTACAT
GCAATTCACTCACTTCGGGAAGAGCGGACGGAAAGAGGAGGCCTTTGCTCTATCTGCTTCTTCCT
CTTCCCAGGAATGAACATTTGGATAAAAAAAGGAATTTTTTATTA
Right flanking sequence: Indices 9836 -- 10335
ATAAAATGATAAAAATAGAATAGAATTAAGTTCTATTAGCCCTTTCGCGACTCAAACTGCCGGTA
CGCTTTCCGGCTCGCAATGGCTCAAACGGGCGGGGGCTCTCTATTTGCTTGCAATGCCGGTTCTT
CGCCTTTAGTTAGAAGTAGAAGTAGAGGGCGCCATTTGCCCCACACTTCATAAAAAGTAGAAGTG
AGAAAGAAAAACTTGGTTACGGGAACGGCCGACTACTTTAGTATAGCTACACCTAGAAAAGGGTT
TTCCTACCCCTTCTCCTTTCTGTCAATGTTGCCAATTCCCAGAATACTAATATACCCTCGTGTAT
ACAGTTGTCCAACTACTTTCTTCCTCCGACTTATTTAGTAACTTCCGGCTTCCCCACTTCCGCAT
CTGTCGTATTCGGGAGAGCTTGCTTCGTAGCGGAGCATTTAGCAATGCCAGCAGCCTGGTGAGGG
CTGGCTGTCTGGGGACAGGTTAAGGCAGGGCCTGCTGGGCTTGCT
Found at i:9827 original size:17 final size:18
Alignment explanation
Indices: 9789--9835 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
9779 AATTTTTTAT
*
9789 TATATTATTGTT-TATAG
1 TATATTATTATTATATAG
*
9806 AATATTATTATTATATA-
1 TATATTATTATTATATAG
9823 TATATTATTATTA
1 TATATTATTATTA
9836 ATAAAATGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
17 22 0.85
18 4 0.15
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.57
Consensus pattern (18 bp):
TATATTATTATTATATAG
Left flanking sequence: Indices 9289 -- 9788
ATAAGACTTAAGGCTTTCGCTATCGCTCTTCGCCTAAAGCCGTAACTTCGCTCTTCGATCCTTCG
CGCTATCGCAAGAATATAGCGATCGAAGAGCTATCGCTCAGCTGCTTCGCGTTTATAAATATAAA
GCCGTATTGCCCGAAGGGGGCATGCTGCAAAAGCGTAGGTGGGTGATAAGCGTAGGAGGCGTGCC
CGAAGGGCAGCGGCAGCAGTGTGGTTCCAGGTGCCCGTCGCTAGATTGAGATCTGCAGGGCGGCG
GGGACTTCGACTGCCTTGTATCAGGTGAAGAGAAGAGGGTGGTAGGCTTAGTAGGGCTCGAACCT
ACAATATAACCGTTATGAGCGGTACGTTTCAACCAATTAAACTATAAGCCCCTACGGATCTCTAC
ATGCAATTCACTCACTTCGGGAAGAGCGGACGGAAAGAGGAGGCCTTTGCTCTATCTGCTTCTTC
CTCTTCCCAGGAATGAACATTTGGATAAAAAAAGGAATTTTTTAT
Right flanking sequence: Indices 9836 -- 10335
ATAAAATGATAAAAATAGAATAGAATTAAGTTCTATTAGCCCTTTCGCGACTCAAACTGCCGGTA
CGCTTTCCGGCTCGCAATGGCTCAAACGGGCGGGGGCTCTCTATTTGCTTGCAATGCCGGTTCTT
CGCCTTTAGTTAGAAGTAGAAGTAGAGGGCGCCATTTGCCCCACACTTCATAAAAAGTAGAAGTG
AGAAAGAAAAACTTGGTTACGGGAACGGCCGACTACTTTAGTATAGCTACACCTAGAAAAGGGTT
TTCCTACCCCTTCTCCTTTCTGTCAATGTTGCCAATTCCCAGAATACTAATATACCCTCGTGTAT
ACAGTTGTCCAACTACTTTCTTCCTCCGACTTATTTAGTAACTTCCGGCTTCCCCACTTCCGCAT
CTGTCGTATTCGGGAGAGCTTGCTTCGTAGCGGAGCATTTAGCAATGCCAGCAGCCTGGTGAGGG
CTGGCTGTCTGGGGACAGGTTAAGGCAGGGCCTGCTGGGCTTGCT
Found at i:67370 original size:8 final size:8
Alignment explanation
Indices: 67357--67381 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
67347 CGACTCTATT
67357 CTATTAGC
1 CTATTAGC
67365 CTATTAGC
1 CTATTAGC
67373 CTATTAGC
1 CTATTAGC
67381 C
1 C
67382 ATAGGCGTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.28, G:0.12, T:0.36
Consensus pattern (8 bp):
CTATTAGC
Left flanking sequence: Indices 66857 -- 67356
CGCTTTCTTTCTTCGACGTGAGGCGCTCTCCCTTTACTGAAAGCAAGTAATGAATAAAAACAGGA
GTAGATTGTAATAAGAACGGGATTGATTGCACGCACCGGATCACCTCTACTTTCAAGTTCTGCTT
CGGGGATACTTTTGTTCAAATGCCATAATAAATCGAACAAAGCCGTAGCTATAGATCAGGGATCG
GAATGTAAGTACTTGTAACAATAGTCACCTCCTTCCACAGGTCGAGATAGGGCTCTCTGAGATAG
GCTACCATCAAAAGAGCGCAGAGCTCAGCTAAAACATTAACGAGAACATAGACTATAACACAAAA
CTCACTTAGCGAGAGAACATCTGCTTTCTTTCTTGGAATCATGAGTTTGCAATCGAGAGGGAGCT
TGCAAAGCTGCTCAATCATAGAGAGGCAAGAAGGGGGAATGGAATAAAGTAGGCTATAGTGACGC
TAGGGCCTAGTCGGCTTCAACCATCAAAGCAATTTCGACTCTATT
Right flanking sequence: Indices 67382 -- 67881
ATAGGCGTAGGAATGGCGTGCTGAGAGAAGACCCCACTTACTAATTCTTTATGCATGGATGCAGG
AAGAGCCAACTGCTTTCTTTGGGATCAGCGCTTAGGGTACAATCTATTTCTTAGAATTCGAACAA
CCGAGTTTCTTAATAAAGAGAAGTTGGGGACATAGTCAACCTCCTACTATAAGAGCGATTCCCTG
GGACCGGAAGGGGAAAGATTCAATCTTGAAAGACTGAGCCCCCGGCTAGCAAGATCGGGAGGTTT
AGTGTCCTCTTAAGAAGGAATACCCCACTTCTGGGGTCAGCTTCGATCACGAGGAGAGAAGAGCG
GACCATTGAAAGTCTCAATTCCTATCCGCCTAAGACCGCCTAAGGCAATGGCAATTTCAAATCCA
ACGATTTATTTACCTACGAATCTGCTATTACGCAATTCAACCCTTCTCTGCTGTTGGATGCGCAA
AACAACCTATTCCCCTTTCCGACGACTCGGTGACCTTTGACACGT
Found at i:110719 original size:16 final size:16
Alignment explanation
Indices: 110698--110733 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
110688 TATGCGTATC
110698 TTGGTGGTCGTTACTT
1 TTGGTGGTCGTTACTT
110714 TTGGTGGTCGTTACTT
1 TTGGTGGTCGTTACTT
110730 TTGG
1 TTGG
110734 CTGACTCCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.06, C:0.11, G:0.33, T:0.50
Consensus pattern (16 bp):
TTGGTGGTCGTTACTT
Left flanking sequence: Indices 110198 -- 110697
CCATCAGCTCCTCTCGTAGATCGGTGCGGTTTTACGAAGCGTCTAAGCACAGTTCACTCGCGTTG
ATCAATCAAGAGGGTTGCCGCCACTCCTTAAGGTTACCTGTTGTATCGTACACTTCTTGCATTAT
TTCCCACGCTTCATACCCCCCTCTTTTAAGATAAGGTAAAGGGCCAGGCATGGTGGGGTAGGAGC
ATCCAGTCGGCAAATCTTTTTTTGGCTTGACCAAGAAGTCTTATGTCCTACGAGTCGCACGGCGT
TTTAACCGAAAGAACTTCTTGCGCAATTCATGCCTTTCTGTTTTTATGACCAGAAATTGTTTCTT
TATTTCCATTTCAAATTGTTCTCTGGACTTTTTATCAATATGAGGTGATCGTAACACAGTATATA
AGACTCGTGATTCAGGCAATCCAATCTTCCGTGTGTAAGGCGGAAGCCCCCAAAAAGGGTTTTCA
AAAAATGGGTGATCAAAAGCAAAAGATCGAATCACTATGCGTATC
Right flanking sequence: Indices 110734 -- 111233
CTGACTCCTCTTCCTCTTACTATTAATCAGATTCCTATTAATCAGAAGCATCCAGCGGCGCCACG
CCGCCGGCTTAGAATTGGATTAATGAAATTCTAAGGGCTAAGGCTCCCTTCCACCGATTTACTTC
TCTTTTGATCAGACGCCAGACCTTGCTATCGGGATAAAAGACCCCAGGCCGTCTTTTCCGCCTTT
TGATTTTAAAGAATTCTCTTGTCTTATTTATTTCCGAGATGCATTCTTCTTTTTTCGGATGATTC
CCACCCTCTACAATCTCTTTTATTTGAGTGAGGATCTCAGCGCCTTCCTATTTGAGACCGCCGAA
GCATCTTTCTCTGCCTTTTTCCGCTCAAGAATGGCTTTTATGCGATCAGGCTCTTTTTCGTAATA
GACGTCTTCAGCCGGTTGAGGGGGGGAGCCTCAGGCGGGGGGCCGTTGAGATCCGGAATAGACGA
GCCGACACCGCCTCCGACGGGGAGACGAAATCCTTCCATGGCCGA
Found at i:239478 original size:9 final size:9
Alignment explanation
Indices: 239464--239489 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
239454 CGGACGAGCA
239464 CGTGCCCCC
1 CGTGCCCCC
239473 CGTGCCCCC
1 CGTGCCCCC
239482 CGTGCCCC
1 CGTGCCCC
239490 AAGAAGATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.00, C:0.65, G:0.23, T:0.12
Consensus pattern (9 bp):
CGTGCCCCC
Left flanking sequence: Indices 238964 -- 239463
TCCTATATTCATAAAAAGCGCGCGAACTCGTTTTTGGCTCGAAAAAGTTCTTTGTATACAAAGGA
CTGTTCAGCATTCGGAGAATGTAGTTGTTGTAGCTTCGTTTCAAGCATTTGGATAGAATATTCCC
CCCCGCGTGGGGGTGTCAAGAAGTTTCGTATGAGCAACATACGATGGTTATCCCAGCATGCGTTA
GGAGATATTTGTGACATTTGGGTTATAATATCCCCTTTCAGTCGGAAGACCTGCGCAACCTCCTC
ATCAGTGGTCTCTTTGGTTCCACCCAGCCGATTAATAAGAAGACGTGTTCTTATAGTCTCTATAA
CATCGTGCTGCGTAGGCTCAGGAGGCAATGTGTAGATGTGTGGGGCTTGAGGATTCTGGGGTTGG
ATAACTTCTTCCTCCTGGGGATTAGCAGGAGGGTTAGAAGGACCAACTTCTTCCCCTGGGGAAGC
CACTGGATTACCGTGCGTCACTGGTGGTTGGTTTACGGACGAGCA
Right flanking sequence: Indices 239490 -- 239989
AAGAAGATTCGAGAAGTATATCGATATCCCGGGTGTCCTCTCTCGTGGTTTCTCTTGAATCAGCC
ATCATGTGGATTTCCGAGGGCGAGACCCAGGCAATGAAGGCCGCGTTAAGGGCCAAATTGAGCGC
AAGAGCCAGATTGCCTGAAAATAATTTAAAACATATATGCGATATCGCTTGTCTGATGAGATAAA
AAGTGAATTTTTCAATTAACAGATACATATCAATCCAATCAAATAAATGGTGCATTGACAAAAGA
ACAATAAAGATAAAGCATAAGCGGGTAAATACGGAAAAAAGAAAGAAGCTCTTCATTTCGGGAAC
GTATAATGTCGGAGAAATTCAAATGAAAAAAAGTAGGAAGGTAGATGTTAAACCTTCGATCAATC
GATGAAACTAGCTGTGATGCTGCTGTTTCTGGATCAGCAGCGGGAATTGGCACAAGTTCAATTGG
CTCCCCAACCGAAACGAATGCAGCGGTCCCAGTAAACCGAATCAC
Done.