Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021305.1 Corchorus olitorius cultivar O-4 contig21338, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 9910
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:1833 original size:40 final size:40
Alignment explanation
Indices: 1789--1868 Score: 106
Period size: 40 Copynumber: 2.0 Consensus size: 40
1779 ACTGTTTTAT
** *
1789 TTTATAAGTTCTTTTAAAAAAATTCAGTCAAGAAATAAAA
1 TTTATAAGCGCTTTTAAAAAAATTCAGTCAAGAAAAAAAA
* * *
1829 TTTATAAGCGCTTTTAAGAAAATTTAGTTAAGAAAAAAAA
1 TTTATAAGCGCTTTTAAAAAAATTCAGTCAAGAAAAAAAA
1869 AAGTCATTAG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.50, C:0.06, G:0.10, T:0.34
Consensus pattern (40 bp):
TTTATAAGCGCTTTTAAAAAAATTCAGTCAAGAAAAAAAA
Found at i:2274 original size:4 final size:4
Alignment explanation
Indices: 2265--2292 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
2255 AAAATTAATA
2265 GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT
2293 ATAATGTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
GTAT
Found at i:6097 original size:66 final size:66
Alignment explanation
Indices: 6025--6162 Score: 267
Period size: 66 Copynumber: 2.1 Consensus size: 66
6015 CTCATTTAGA
*
6025 TGTTTGGGCATGCATAGAGATTTATTTGAATTGTTTTGAATTGTAATGAGATTTCACTGGGGGGT
1 TGTTTGGGCATGCATAGAGATTTATTTGAATTGATTTGAATTGTAATGAGATTTCACTGGGGGGT
6090 T
66 T
6091 TGTTTGGGCATGCATAGAGATTTATTTGAATTGATTTGAATTGTAATGAGATTTCACTGGGGGGT
1 TGTTTGGGCATGCATAGAGATTTATTTGAATTGATTTGAATTGTAATGAGATTTCACTGGGGGGT
6156 T
66 T
6157 TGTTTG
1 TGTTTG
6163 TTGGGGAAGG
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
66 71 1.00
ACGTcount: A:0.22, C:0.06, G:0.29, T:0.43
Consensus pattern (66 bp):
TGTTTGGGCATGCATAGAGATTTATTTGAATTGATTTGAATTGTAATGAGATTTCACTGGGGGGT
T
Found at i:6327 original size:78 final size:78
Alignment explanation
Indices: 6226--6371 Score: 274
Period size: 78 Copynumber: 1.9 Consensus size: 78
6216 CATGTAGCGG
*
6226 TGTATGGGTATTATGTGCGTTTGTATTTAGATGTTTGGGCATGCATAGAGATTTATTTGAATTGA
1 TGTACGGGTATTATGTGCGTTTGTATTTAGATGTTTGGGCATGCATAGAGATTTATTTGAATTGA
6291 TTTGAATTGTAAT
66 TTTGAATTGTAAT
*
6304 TGTACGGGTATTCTGTGCGTTTGTATTTAGATGTTTGGGCATGCATAGAGATTTATTTGAATTGA
1 TGTACGGGTATTATGTGCGTTTGTATTTAGATGTTTGGGCATGCATAGAGATTTATTTGAATTGA
6369 TTT
66 TTT
6372 CACTGGGGGG
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
78 66 1.00
ACGTcount: A:0.23, C:0.05, G:0.26, T:0.46
Consensus pattern (78 bp):
TGTACGGGTATTATGTGCGTTTGTATTTAGATGTTTGGGCATGCATAGAGATTTATTTGAATTGA
TTTGAATTGTAAT
Found at i:7519 original size:437 final size:434
Alignment explanation
Indices: 6725--7710 Score: 1122
Period size: 437 Copynumber: 2.2 Consensus size: 434
6715 TTGAAACATG
* * *
6725 AAAATTAGCTTTTAAG-TCTTTCATGAAAGTTGTAGATAATAAAATTACCTTTTAATAGACACTT
1 AAAATTAGCTTTTGAGTTC-TTCATGAAAGTTGTAGATCATGAAATTACCTTTTAATAGACACTT
* * * *
6789 GAATTACCTTAATTGGACAAATAGAACAAAGAAAATTAAAAAAAAAAGAAGCGTTAAATCGAATA
65 GAATTAACTTAATCGGACAAAT--AA-AAA-AAAA-TAAAAAAAATA-AAGCGTTAAACCGAATA
* * *
6854 AGATAGAATTTGTAAATGACTAAGTAGCATAAAATAGAAAAGTATGAGGGTCATTTGATAACTAA
124 AGATAGAATTTGTAAAGGACTAAGTAGCATAAAATAGAAAAATATGAGGGTCATTTGATAAATAA
* * * * *
6919 TTCAAATAAGAAAATATTTCTTAATGGATATCTTAAAACATAATAATTCCCTATTGAACCCTTAA
189 TCCAAATAAAAAAATAGTTCTTAATGGAGATCTTAAAACATAATAATTCCCTATTAAACCCTTAA
* * * ** *
6984 AGAAACTCGTAGATCAAATTAACTTTCGGGTTCTTCATGAAAGTCGTTGATCATACAGTAACCTT
254 AGAAACTCGTAGATCAAATTAACTTTAGGGTCCTTCATGAAAGTCCTAAATCATACAATAACCTT
* * * *** * * *
7049 TTAACCGACATTTGAATAACCTTAATTGGACATGTGGATCGAAAATTATATGGTATTTAATAGAC
319 TTAACCGACACTTCAATAACCTTAATCGGACATGTGGAAAAAAAATTATACGATATTAAATAGAC
* * * * * * *
7114 CAATAATCGAAACGACCAAATTTAGGAAGCATTTTTTTAAATTAAAAAATA
384 CAACAATCAAAACCACAAAATTTAGGAAGCATTTATATAAATCAAAAAATA
* *
7165 AAAATTTGCTTTTGAGTTCTTCATGAAAGTTGTAGATCATGAAATTACCTTTTAATAGACACATG
1 AAAATTAGCTTTTGAGTTCTTCATGAAAGTTGTAGATCATGAAATTACCTTTTAATAGACACTTG
* * * *
7230 AATCAACTTAATCGGACAGATAAAACAAAAATAAAAAAAATAAATC-TT-ACCCGTTAGATTAAG
66 AATTAACTTAATCGGACAAATAAAA-AAAAATAAAAAAAATAAAGCGTTAAACCG--A-A-TAAG
* * *
7293 ATAGAATTTGTAAAGGACTAAGTAGTATAAAGTAGAAAAATATGAGTGTCATTTGATAAATAATC
126 ATAGAATTTGTAAAGGACTAAGTAGCATAAAATAGAAAAATATGAGGGTCATTTGATAAATAATC
* * * * * * *
7358 CAAATAAAAAAATGGTTGTTAATGGAGATCTTGAAGCATTAA-AATTCCCTTTTAAACCCTTCAT
191 CAAATAAAAAAATAGTTCTTAATGGAGATCTTAAAACA-TAATAATTCCCTATTAAACCCTTAAA
* * *
7422 GAAACTCGTAGATCAAATTTAGC-TTAGGGTCCTTCATGAAAGTCCTAAATTATGCAATAACCTT
255 GAAACTCGTAGATCAAA-TTAACTTTAGGGTCCTTCATGAAAGTCCTAAATCATACAATAACCTT
* *
7486 TTAACTGACACTTCAATAA-CTTCAATCGGACATGTGGAAAAAAAATTATACGATATTAAATTGA
319 TTAACCGACACTTCAATAACCTT-AATCGGACATGTGGAAAAAAAATTATACGATATTAAATAGA
** * * * *
7550 CCGGCAATCAAAACCACAAAATTTCGGAAGTATTTATATAAATCAAAACATT
383 CCAACAATCAAAACCACAAAATTTAGGAAGCATTTATATAAATCAAAAAATA
* * * * * *
7602 AAAATTGGCTTTTGAGTTCTTCATGAAAATTATAGATCATGAAATTATCTTTAAATAGATACTTG
1 AAAATTAGCTTTTGAGTTCTTCATGAAAGTTGTAGATCATGAAATTACCTTTTAATAGACACTTG
* *
7667 AATTATCTTAATCGGACAAATTGAAAAAAAAA-AACAAAAATAAA
66 AATTAACTTAATCGGACAAA-T-AAAAAAAAATAAAAAAAATAAA
7711 AGCCAACGCG
Statistics
Matches: 460, Mismatches: 75, Indels: 25
0.82 0.13 0.04
Matches are distributed among these distances:
433 3 0.01
434 2 0.00
435 4 0.01
436 14 0.03
437 341 0.74
438 16 0.03
439 4 0.01
440 74 0.16
441 2 0.00
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.31
Consensus pattern (434 bp):
AAAATTAGCTTTTGAGTTCTTCATGAAAGTTGTAGATCATGAAATTACCTTTTAATAGACACTTG
AATTAACTTAATCGGACAAATAAAAAAAAATAAAAAAAATAAAGCGTTAAACCGAATAAGATAGA
ATTTGTAAAGGACTAAGTAGCATAAAATAGAAAAATATGAGGGTCATTTGATAAATAATCCAAAT
AAAAAAATAGTTCTTAATGGAGATCTTAAAACATAATAATTCCCTATTAAACCCTTAAAGAAACT
CGTAGATCAAATTAACTTTAGGGTCCTTCATGAAAGTCCTAAATCATACAATAACCTTTTAACCG
ACACTTCAATAACCTTAATCGGACATGTGGAAAAAAAATTATACGATATTAAATAGACCAACAAT
CAAAACCACAAAATTTAGGAAGCATTTATATAAATCAAAAAATA
Done.