Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019798.1 Corchorus olitorius cultivar O-4 contig19831, 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: 58518
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:31678 original size:437 final size:438
Alignment explanation
Indices: 30851--31710 Score: 1120
Period size: 437 Copynumber: 2.0 Consensus size: 438
30841 TTAAATCGAA
* * * * *
30851 TAAGATAAAATTTGTGAATGACTAAGTAGCATAAAATAGAAAAGTATGAGGGTCATTTGATAACT
1 TAAGATAAAATTTGTAAAGGACTAAGTAGCATAAAATAGAAAAATATGAGAGTCATTTGATAAAT
* * * *
30916 AATTCAAATAAGAAAATAGTTCTTAATGGATATCTTAAAATATAAAAATTCACTTTTGAACCCTT
66 AATCCAAATAAGAAAATAGTTCTTAATGGAGATCTTAAAACATAAAAATTCACTTTTAAACCCTT
* * * * *
30981 AATGAAACTCGTAGATCAAATTAACTTTCGGTTTCTTCATGAAAGACGTAGATCATACAGTAACC
131 AATGAAACTCGTAGATCAAATTAACTTTCGGGTCCCTCATGAAAGACGTAAATCATACAATAACC
* * * * * *
31046 TTTTAACCAACACTTGAATAACTTTAATTGGACATGTGGATCGAAAATTATATGGTATTAAATAG
196 TTTTAACCAACACTTCAATAACTTCAATCGGACATGTGGATCAAAAATTATACGATATTAAATAG
* * * * * * *
31111 ACCAACAATCGAAACGACCAAATTTAGGAAGCATTTTTTTGAATTAAAACATAAAAATTTGCTTT
261 ACCAACAATCAAAACCACAAAATTTAGGAAGCATTTTTCTAAATCAAAACATAAAAATTGGCTTT
* *
31176 TGAGTTCTTCATGAAAGTTGTAGAGCATGAAATTACCTTTTAATAGACACATGAATCAACTTAAT
326 TGAGTTCTTCATGAAAATTGTAGAGCATGAAATTACCTTTTAACAGACACATGAATCAACTTAAT
* *
31241 CGGACATATAGAACAAAAAATAAAAAAAATAAATCTTAAACGTTAGAT
391 CGGACAAATAGAAAAAAAAATAAAAAAAATAAATCTTAAACGTTAGAT
* *
31289 TAAGATAGAATTTGTAAAGGA-TAAGTAGTA-AAAAGTAGAAAAATATGAGAGTCATTTGATAAA
1 TAAGATAAAATTTGTAAAGGACTAAGTAGCATAAAA-TAGAAAAATATGAGAGTCATTTGATAAA
* * * * *
31352 TAATCCAAATGAGAAAAT-GTTTGTTAATGGAGATCTTGAAGCATAAAAATTCCCTTTTAAACCC
65 TAATCCAAATAAGAAAATAG-TTCTTAATGGAGATCTTAAAACATAAAAATTCACTTTTAAACCC
* * * * **
31416 TTCATGAAATTCGTAGATCAAATTTAGCTTTCGGGTCCCTCATGAAAGTCGTAAATCATGTAATA
129 TTAATGAAACTCGTAGATCAAA-TTAACTTTCGGGTCCCTCATGAAAGACGTAAATCATACAATA
**
31481 ACCTTTTAACTGACACTTCAATAACTTCAATCGGACATGTGGA-CAAAAAATTATACGATATTAA
193 ACCTTTTAACCAACACTTCAATAACTTCAATCGGACATGTGGATC-AAAAATTATACGATATTAA
** * *
31545 ACT-GACCGGCAATCAAAACCACAAAATTTCGGAAGCATTTTTCTAAATCAAAACATTAAAATTG
257 A-TAGACCAACAATCAAAACCACAAAATTTAGGAAGCATTTTTCTAAATCAAAACATAAAAATTG
* * * * *
31609 GCTTTTGAGTTC-TCATGAAAATTGTAGATCATGAAATTATCTTTTAACAGACACTTGAATTACC
321 GCTTTTGAGTTCTTCATGAAAATTGTAGAGCATGAAATTACCTTTTAACAGACACATGAATCAAC
* *
31673 TTAATCGGACAAATTGAAAAAAAAATAAAAGAAATAAA
386 TTAATCGGACAAATAGAAAAAAAAATAAAAAAAATAAA
31711 AGCCAACGCG
Statistics
Matches: 360, Mismatches: 57, Indels: 11
0.84 0.13 0.03
Matches are distributed among these distances:
436 5 0.01
437 186 0.52
438 168 0.47
439 1 0.00
ACGTcount: A:0.42, C:0.13, G:0.14, T:0.30
Consensus pattern (438 bp):
TAAGATAAAATTTGTAAAGGACTAAGTAGCATAAAATAGAAAAATATGAGAGTCATTTGATAAAT
AATCCAAATAAGAAAATAGTTCTTAATGGAGATCTTAAAACATAAAAATTCACTTTTAAACCCTT
AATGAAACTCGTAGATCAAATTAACTTTCGGGTCCCTCATGAAAGACGTAAATCATACAATAACC
TTTTAACCAACACTTCAATAACTTCAATCGGACATGTGGATCAAAAATTATACGATATTAAATAG
ACCAACAATCAAAACCACAAAATTTAGGAAGCATTTTTCTAAATCAAAACATAAAAATTGGCTTT
TGAGTTCTTCATGAAAATTGTAGAGCATGAAATTACCTTTTAACAGACACATGAATCAACTTAAT
CGGACAAATAGAAAAAAAAATAAAAAAAATAAATCTTAAACGTTAGAT
Found at i:42444 original size:3 final size:3
Alignment explanation
Indices: 42436--42466 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
42426 GGTGTTCTTA
42436 AAG AAG AAG AAG AAG AAG AAG AAG -AG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
42467 AAAAAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:48749 original size:71 final size:71
Alignment explanation
Indices: 48633--48778 Score: 256
Period size: 71 Copynumber: 2.1 Consensus size: 71
48623 ACTCGTTGAG
* * * *
48633 CACCACACAACTGTCTTGGGTCAAACAGGTCGTGTGACCACTTCACAAGCAGATAAGGGAAAGAT
1 CACCACACAACTGCCTTGGGTCAAACAAGTCGCGTGACCACTTCACAAGCAAATAAGGGAAAGAT
48698 GTCGAC
66 GTCGAC
48704 CACCACACAACTGCCTTGGGTCAAACAAGTCGCGTGACCACTTCACAAGCAAATAAGGGAAAGAT
1 CACCACACAACTGCCTTGGGTCAAACAAGTCGCGTGACCACTTCACAAGCAAATAAGGGAAAGAT
48769 GTCGAC
66 GTCGAC
48775 CACC
1 CACC
48779 CTAAGCTTAC
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
71 71 1.00
ACGTcount: A:0.34, C:0.28, G:0.22, T:0.16
Consensus pattern (71 bp):
CACCACACAACTGCCTTGGGTCAAACAAGTCGCGTGACCACTTCACAAGCAAATAAGGGAAAGAT
GTCGAC
Found at i:50401 original size:14 final size:14
Alignment explanation
Indices: 50382--50409 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
50372 AATTGGTTTA
50382 ACCATTGGGTCGAT
1 ACCATTGGGTCGAT
50396 ACCATTGGGTCGAT
1 ACCATTGGGTCGAT
50410 CAGGTTAAGG
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:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (14 bp):
ACCATTGGGTCGAT
Found at i:58368 original size:228 final size:228
Alignment explanation
Indices: 57957--58518 Score: 655
Period size: 228 Copynumber: 2.5 Consensus size: 228
57947 AGCTTAGATA
* * * * * *
57957 CCACCACGAAGGCGAAGGA-CAAGATGCAGAGTGGACTCCTTCTGGATGTTATAATCGGCAAGAG
1 CCACCACGAAGACGCAGAACCAA-ATGAAGAGTCGACTCCTTCTGGATGTTATAATCAGCAAGAG
* * * * * *
58021 TTCTCCCATCTTCCAGCTGCTTACCAGCAAAAATCAACCTCTGCTGGTCAGGTGGGATCCCTTCC
65 TCCTCCCATCTTCAAGCTGCTTACCAGCAAAAATCAACCTCTGCTGATCAGGAGGAATACCTTCC
* * * * *
58086 TTGTCTTGAATCTTTGCCTTGACATTATCAATGGTGTCTGAACTCTCGACCTCCAAAGTGATGGT
130 TTATCTTGAATCTTTGCCTTCACATTATCAATGGTATCTGAACTCTCAACCTCCAAAGTGATAGT
*
58151 CTTTCCAGTTAAG-GTTTTAACAAAGATCTGCATC
195 CTTTCCAG-TAAGAGTCTTAACAAAGATCTGCATC
* * * * * *
58185 CCACCACGCAGACGCA-ACACCAAGTGAAGGGTCGACTCCTTCTGGATATTATAGTCAGCCAA-T
1 CCACCACGAAGACGCAGA-ACCAAATGAAGAGTCGACTCCTTCTGGATGTTATAATCAG-CAAGA
* * * * * * *
58248 GTCCTCCCATCTTCAAGCTGCTTGCCAGCAAAGATGAGCCTTTGTTGATCTGGAGGAATACCTTC
64 GTCCTCCCATCTTCAAGCTGCTTACCAGCAAAAATCAACCTCTGCTGATCAGGAGGAATACCTTC
* * * *
58313 CTTATCTTGAATTTTTGCCTTCACGTTATCAATGGTATCTGAGCTTTCAACCTCCAAAGTGATAG
129 CTTATCTTGAATCTTTGCCTTCACATTATCAATGGTATCTGAACTCTCAACCTCCAAAGTGATAG
* * *
58378 TCTTTCCAGTCAGAGTCTTGACAAAGATCTGCATT
194 TCTTTCCAGTAAGAGTCTTAACAAAGATCTGCATC
* * *
58413 CCACCACGAAGACGGAGAACCAAATGGAGAGTCGACTCCTTCTGAATGTTATAATCAGCAAGAGT
1 CCACCACGAAGACGCAGAACCAAATGAAGAGTCGACTCCTTCTGGATGTTATAATCAGCAAGAGT
* * * *
58478 CCTTCCATCTTCAAGCTGTTTTCCAGCAAAAATCAATCTCT
66 CCTCCCATCTTCAAGCTGCTTACCAGCAAAAATCAACCTCT
Statistics
Matches: 273, Mismatches: 55, Indels: 12
0.80 0.16 0.04
Matches are distributed among these distances:
227 6 0.02
228 260 0.95
229 7 0.03
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.28
Consensus pattern (228 bp):
CCACCACGAAGACGCAGAACCAAATGAAGAGTCGACTCCTTCTGGATGTTATAATCAGCAAGAGT
CCTCCCATCTTCAAGCTGCTTACCAGCAAAAATCAACCTCTGCTGATCAGGAGGAATACCTTCCT
TATCTTGAATCTTTGCCTTCACATTATCAATGGTATCTGAACTCTCAACCTCCAAAGTGATAGTC
TTTCCAGTAAGAGTCTTAACAAAGATCTGCATC
Done.