Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021082.1 Corchorus olitorius cultivar O-4 contig21115, 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: 21453
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:1749 original size:31 final size:31
Alignment explanation
Indices: 1702--1867 Score: 152
Period size: 31 Copynumber: 5.4 Consensus size: 31
1692 TTTGTCCACG
** * **
1702 TGGCATGCCATGTGTCAGTTTTTGAAACACA
1 TGGCATGCCACATGTCACTTTTTGGTACACA
*
1733 TGGCATGCCACATGTCACTTTTGGGTACACA
1 TGGCATGCCACATGTCACTTTTTGGTACACA
* ** *
1764 TGGCGTGATACATGTCACTTTTTGGTACACG
1 TGGCATGCCACATGTCACTTTTTGGTACACA
* * * *
1795 TGGCGTGCCTCATGTCGCTTTTTGGTACACG
1 TGGCATGCCACATGTCACTTTTTGGTACACA
* * ** **
1826 TGGCGTGCTACATGTTGCTTTTTGGTACATG
1 TGGCATGCCACATGTCACTTTTTGGTACACA
1857 TGGCATGCCAC
1 TGGCATGCCAC
1868 GTCGAACACC
Statistics
Matches: 114, Mismatches: 21, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 114 1.00
ACGTcount: A:0.18, C:0.22, G:0.26, T:0.34
Consensus pattern (31 bp):
TGGCATGCCACATGTCACTTTTTGGTACACA
Found at i:1786 original size:62 final size:62
Alignment explanation
Indices: 1714--1867 Score: 191
Period size: 62 Copynumber: 2.5 Consensus size: 62
1704 GCATGCCATG
* ** *
1714 TGTCAGTTTTTGAAACACATGGCATGCCACATGTCACTTTTGGGTACACATGGCGTGATACA
1 TGTCACTTTTTGGTACACGTGGCATGCCACATGTCACTTTTGGGTACACATGGCGTGATACA
* * * * * *
1776 TGTCACTTTTTGGTACACGTGGCGTGCCTCATGTCGCTTTTTGGTACACGTGGCGTGCTACA
1 TGTCACTTTTTGGTACACGTGGCATGCCACATGTCACTTTTGGGTACACATGGCGTGATACA
** *
1838 TGTTGCTTTTTGGTACATGTGGCATGCCAC
1 TGTCACTTTTTGGTACACGTGGCATGCCAC
1868 GTCGAACACC
Statistics
Matches: 77, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
62 77 1.00
ACGTcount: A:0.18, C:0.22, G:0.25, T:0.34
Consensus pattern (62 bp):
TGTCACTTTTTGGTACACGTGGCATGCCACATGTCACTTTTGGGTACACATGGCGTGATACA
Found at i:15403 original size:54 final size:54
Alignment explanation
Indices: 15318--15426 Score: 193
Period size: 54 Copynumber: 2.0 Consensus size: 54
15308 CACGCCCTAA
15318 ACTAAATCCTAACAGGTGTACTAATGCAGTTCCAACCGTCTACTAGATTCAAGT
1 ACTAAATCCTAACAGGTGTACTAATGCAGTTCCAACCGTCTACTAGATTCAAGT
*
15372 ACTAAATCCTAACAGGTGTACTAAT-CTAGTTCCAATCGTCTACTAGATTCAAGT
1 ACTAAATCCTAACAGGTGTACTAATGC-AGTTCCAACCGTCTACTAGATTCAAGT
15426 A
1 A
15427 ACCCGTTGCT
Statistics
Matches: 53, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
53 1 0.02
54 52 0.98
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.29
Consensus pattern (54 bp):
ACTAAATCCTAACAGGTGTACTAATGCAGTTCCAACCGTCTACTAGATTCAAGT
Found at i:16226 original size:108 final size:108
Alignment explanation
Indices: 16037--16255 Score: 402
Period size: 108 Copynumber: 2.0 Consensus size: 108
16027 GCTGGTGAAA
*
16037 TTGTGAGCCCAAAAGGAAGTTAAGCCCACGTGACATCTCCAAAGTTCAGCCCTTTGATTTCCGCA
1 TTGTGAGCCCAAAAGGAAGTTAAACCCACGTGACATCTCCAAAGTTCAGCCCTTTGATTTCCGCA
** *
16102 GCCTGTTTCGACCCTGATAAGGTCGAGTTCGACCCGCTCCAGG
66 AACTGTTTCGACCCTGATAAGGTCGAGTTCGACACGCTCCAGG
16145 TTGTGAGCCCAAAAGGAAGTTAAACCCACGTGACATCTCCAAAGTTCAGCCCTTTGATTTCCGCA
1 TTGTGAGCCCAAAAGGAAGTTAAACCCACGTGACATCTCCAAAGTTCAGCCCTTTGATTTCCGCA
16210 AACTGTTTCGACCCTGATAAGGTCGAGTTCGACACGCTCCAGG
66 AACTGTTTCGACCCTGATAAGGTCGAGTTCGACACGCTCCAGG
16253 TTG
1 TTG
16256 AAATAGGAAA
Statistics
Matches: 107, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
108 107 1.00
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (108 bp):
TTGTGAGCCCAAAAGGAAGTTAAACCCACGTGACATCTCCAAAGTTCAGCCCTTTGATTTCCGCA
AACTGTTTCGACCCTGATAAGGTCGAGTTCGACACGCTCCAGG
Found at i:17683 original size:446 final size:443
Alignment explanation
Indices: 16594--17683 Score: 1111
Period size: 446 Copynumber: 2.4 Consensus size: 443
16584 GATCTTTGTT
* * * * * * **** * *
16594 AATCGGACATTTGGATAAAAAATAATATGATATTATATAGATTGTCAATCGAAAATCACAATATT
1 AATCGGACGTGTGGAAAAAAAATTATACGATATTAAATAGACCAACAATC-AAAACCACAAAATT
* * *
16659 TCAAAAGCATTTTTTAGAATTGAAATATAAAAATT-AGCTTTTGAGTCTTTTATGGAAATTGTAG
65 TCAGAAGCATTTTTTAGAATTGAAATAT-AAAATTGA-CTTTTGAGTCTTTAATGAAAATTGTAG
* * * * * * *
16723 ATCATAAAATTACCTTTTAATAGATACCTGAATTACCTTAATTGGAC-AA-ATAGAACAA-AGAA
128 ATCATGAAATTACCTTTTAATAGACACATGAATCACCTTAATTGGACAAATATAAAAAAATAAAA
* * * *
16785 AATAAAAAAATGAAGTGTTAAATCGAGTAAGATAGAATTTGTAAAGGACTAAGTAGGATAAAATA
193 AATAAAAAAATAAAGTCTTAAATCGAGTAAGATAGAATATGTAAAGAACTAAGTAGGATAAAATA
* * *
16850 GAAAAGTATAAGGGTGATTTGATAACTAATTCAAATAAGAAAATATTTGTTAATTAATGGAGATC
258 GAAAAGTATAAGGGTCATTTGATAAATAATCCAAATAAGAAAATA-TTGTTAATTAATGGAGATC
* * *
16915 TTGAAACATAAAAAATTTCCTTTCGAATCCTTCATGGAACTCGTAGATCAAATTAACTTTCGGGT
322 TTAAAACATAAAAAATTTCCTTTCGAACCCTTCATGAAACTCGTAGATCAAATTAACTTTCGGGT
* * * * * * *
16980 TCTTAATGAAAGTCGTAGATTATACGATAACCTTTTAACCGACACTTGAATAACTTT
387 CCTTAATGAAAGTCGTAAATCATACAATAACCTCTTAACCGACACTTCAATAACTTC
* *** * * * * *
17037 AATTGGACGTGTGGATCGAAAATTATATGGTATTAAATAGACCAACAATCGAAACGACCAAATTT
1 AATCGGACGTGTGGAAAAAAAATTATACGATATTAAATAGACCAACAATCAAAACCACAAAATTT
* * * * * * *
17102 -AGGAAGCCTTTTTTTTTTGAGTTGACATA-AAAATTG-CTTTTGAGTCTTTCACGAAAGTTGTA
66 CA-GAAG-C--ATTTTTTAGAATTGAAATATAAAATTGACTTTTGAGTCTTTAATGAAAATTGTA
* * *
17164 GATCATGAAATTACCTTTTAATAGACACATGAATCAACTTAATTGTACAAATAGAACAAAGAAT-
127 GATCATGAAATTACCTTTTAATAGACACATGAATCACCTTAATTGGACAAATATAA-AAA-AATA
* *
17228 AATAATAAAAAAA-AAACG-CTTAAA-CGTTAGATTAAGATAGAATATGTAAAGAACTAAGTAGT
190 AAAAATAAAAAAATAAA-GTCTTAAATCG--AG--TAAGATAGAATATGTAAAGAACTAAGTAGG
* * **
17290 ATAAAGTAGAAAAGTATGAGGGTCATTTGATAAATAATCCAAATAA-AAAA-A-TGTTTGTTAAT
250 ATAAAATAGAAAAGTATAAGGGTCATTTGATAAATAATCCAAATAAGAAAATATTGTTAATTAAT
* * * *
17352 GGAGATGTTAAAACAT-AAAAA-TTCCATTTTGAACCCTTCTTGAAACTCGTAGATCAAATTTAG
315 GGAGATCTTAAAACATAAAAAATTTCC-TTTCGAACCCTTCATGAAACTCGTAGATCAAA-TTAA
* * *
17415 TTTTCGGGTCCTTCATGAAAGTCGTAAATCATGCAATAACCTCTTAACCGACACTTCAATAACTT
378 CTTTCGGGTCCTTAATGAAAGTCGTAAATCATACAATAACCTCTTAACCGACACTTCAATAACTT
17480 C
443 C
**
17481 AATCGGA-GATGTGGAAAAAAAAATTTATACGATATTAAATTA-ACCGGCAATCAAAACCACAAA
1 AATCGGACG-TGTGG-AAAAAAAA-TTATACGATATTAAA-TAGACCAACAATCAAAACCACAAA
* ** * *
17544 ATTTCAGAAGCATGTTTTAGAATCAAAATATTAAAATTGACTTCTGAGT-TCTAAATGAAAATTG
62 ATTTCAGAAGCATTTTTTAGAATTGAAATA-TAAAATTGACTTTTGAGTCT-TTAATGAAAATTG
* *
17608 TAGATCATGAAATTACCTTTTAATAGACACTTGAATCACCTTAATCGGACAAATATAAAAAAATA
125 TAGATCATGAAATTACCTTTTAATAGACACATGAATCACCTTAATTGGACAAATATAAAAAAATA
17673 CAAAAATAAAA
190 -AAAAATAAAA
17684 GCCAACGCGT
Statistics
Matches: 524, Mismatches: 95, Indels: 53
0.78 0.14 0.08
Matches are distributed among these distances:
441 1 0.00
442 81 0.15
443 93 0.18
444 100 0.19
445 41 0.08
446 133 0.25
447 7 0.01
448 68 0.13
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.31
Consensus pattern (443 bp):
AATCGGACGTGTGGAAAAAAAATTATACGATATTAAATAGACCAACAATCAAAACCACAAAATTT
CAGAAGCATTTTTTAGAATTGAAATATAAAATTGACTTTTGAGTCTTTAATGAAAATTGTAGATC
ATGAAATTACCTTTTAATAGACACATGAATCACCTTAATTGGACAAATATAAAAAAATAAAAAAT
AAAAAAATAAAGTCTTAAATCGAGTAAGATAGAATATGTAAAGAACTAAGTAGGATAAAATAGAA
AAGTATAAGGGTCATTTGATAAATAATCCAAATAAGAAAATATTGTTAATTAATGGAGATCTTAA
AACATAAAAAATTTCCTTTCGAACCCTTCATGAAACTCGTAGATCAAATTAACTTTCGGGTCCTT
AATGAAAGTCGTAAATCATACAATAACCTCTTAACCGACACTTCAATAACTTC
Done.