Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014736.1 Corchorus olitorius cultivar O-4 contig14769, 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: 14053
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:6164 original size:685 final size:674
Alignment explanation
Indices: 4671--7274 Score: 3002
Period size: 685 Copynumber: 3.9 Consensus size: 674
4661 AAAATTTAGC
* * * * * *
4671 CGAAATCGTGTTCTAACCATCACTGTTTTTGGCTAAAAACTCGTTCTGGAGTGCCGGCTCAATTT
1 CGAAATCGTATACTAACTATCAC-GTTTTTGGCTAAAAACGCGTTCCGGAGTCCCGGCTCAATTT
* * *
4736 TGCAGGATTTTTGGCACAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATGTCAGCCACA
65 TGCATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCCACA
* * * *
4801 TTGGATATAAGGATTTGTTTTTACGAGCATCTCAATCTTGTTTTGATTTAATTATAAATTAATTC
130 TTGTATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAAAAATTAATTC
* * * *
4866 GG-AAACAAATGGAAAAACGATATTAGAAGCGTGAAAAGCCCATCAATCTTTTTGGCATTGAATT
195 GGAAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGGCCGTCAATCTTTTTGGCGTTGAATT
* * *
4930 ATATATTTTTTTCTAAATATTTCGCAAAAAATTGAGAAAAAAACTTTTCGGGTCAGTTTTTAGCC
260 ATATA-TTTTTTCTGAATATTTTGCAAAAAATTGAGAAAAAAACTTTTC-GGTAAGTTTTTAGCC
* * *
4995 GAATTCGTGTACTGTTA-CATCACGGTTTTCGGCTAAAAACGCGTTTCGGGGCCCCGACTCAGTT
323 GAA-ACATGTAC--TAACCATCACGGTTTT-GGCTAAAAACGCGTTTC--GGCCCCGACTCAGTT
* * * * *
5059 TTGCATTATTTTTGGCAGAAAGAATCCTTGAAATATCTATATTCATCTGACCAAGTCTAAGCCAC
382 TTGAATTATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCAC
** *
5124 AATGGATTTAAGGATTTGTTGGTACGAGCATCTGAA-CTTTGTTTCAATTTAATTAATTAGAAAT
447 AATGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTTGTTTCGA--T--TTAATTAGAAAT
* *
5188 AAATTTG-AAAAAAAGGAAAAACGATATTAGAAATGTGAAAACCCCTTCAATTCTTTTTGGCGTT
508 AAATTCGAAAAAAAAGGAAAAACGATATTAGAAGTGTGAAAACCCCTTCAATTCTTTTTGGCGTT
* *
5252 GAATTATATATTAGATTTAAGTATTGTGGCAAAAAATTGAGGAAAAACTTTTCAGGTCAATTTTT
573 GAATTATATATTAGATCTGAGTATTGTGGCAAAAAATTGAGGAAAAACTTTTCAGGTCAATTTTT
* *
5317 GCAAAATTTTAGTCGAAATCGTCCATTTTTTTCCCAA
638 GCAAAATTTTAGTCGAAATAGTACATTTTTTTCCCAA
* * *
5354 CGAAATCGTATACTAACTATCACGTTTTTTTTTGCCTAAAAACGCGTTCCGGAGTCTCTGCTCAA
1 CGAAATCGTATACTAACTATCACG----TTTTTGGCTAAAAACGCGTTCCGGAGTCCCGGCTCAA
* * ** *
5419 TTTCGCATGATTTTTGGCGCAGAGACTTTTTGAAATATCTATATTCATCGAACCAAATCTCAACC
62 TTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCC
** * * *
5484 ACATTGTATATAAAAATTTGTTTTTATGAGTATCTGAATCTTATTTCGATTTAATTAAAAATTAA
127 ACATTGTATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAAAAATTAA
* *
5549 TTCGGAAAAAAAATTGGAAAAACGATATTAGAAGCGTCAAAAGGCTGTCAATCTTTTTGGCGTTG
192 TTCGGAAAAAAAA-TGGAAAAACGATATTAGAAGCGTGAAAAGGCCGTCAATCTTTTTGGCGTTG
5614 AATTATATATTTTTT-TGAATATTTTGCAAAAAATTGAGAAAAAAACTTTTCAGGTAAGTTTTTA
256 AATTATATATTTTTTCTGAATATTTTGCAAAAAATTGAGAAAAAAACTTTTC-GGTAAGTTTTTA
* *
5678 GCCGAAACCATGTACTAACCATCACGGCTTTTGGCTAAAAACGAGTTTCATGGCCCCTACTCAGT
320 GCCGAAA-CATGTACTAACCATCACGG-TTTTGGCTAAAAACGCGTTTC--GGCCCCGACTCAGT
* * *
5743 TTTGAATGATTTTTTGCAGAAAGACTCCTTGAAATACCTATATTCATCTAACCAAATCTCAGCCA
381 TTTGAATTATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCA
* * *
5808 CAATGGATTTAAGGATTTGTTTTTATGAGTATCTGAATCTTTGTCTCGATTTAATTAGAAATAAA
446 CAATGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTTGTTTCGATTTAATTAGAAATAAA
* *
5873 TTCGGAAAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAACCCCTTCAATTCTTTCTTGGTGT
511 TTC-G-AAAAAAAA-GGAAAAACGATATTAGAAGTGTGAAAACCCCTTCAATTCTTT-TTGGCGT
* * * *
5938 TGAATTATATATTAGATCTGAGTATTGTGGCAAAAACTTGAAGAAAAACTTTCCGGGTCAATTTT
572 TGAATTATATATTAGATCTGAGTATTGTGGCAAAAAATTGAGGAAAAACTTTTCAGGTCAATTTT
* *
6003 TGCAAAATTTTAGCCGAAATAGTATACTTTTTTTCCCAA
637 TGCAAAATTTTAGTCGAAATAGTACA-TTTTTTTCCCAA
* * * *
6042 CGAAATCGTATACTAAGTATCACAGTTTTTGGCAAAAAACGCGTCCCGGAATCCCGGCTCAATTT
1 CGAAATCGTATACTAACTATCAC-GTTTTTGGCTAAAAACGCGTTCCGGAGTCCCGGCTCAATTT
* * * *
6107 TGCTTGATTTTTGGCGTAAAGACTCCTTGAAATAGT-TATGTTCATCGAACAAAATCTCAGCCAC
65 TGCATGATTTTTGGCGCAAAGACTCCTTGAAATA-TCTATATTCATCGAACCAAATCTCAGCCAC
* * *
6171 ATTGTATATAAGGTTTTGTTTTTACGAGCATCCGAATCTTGTTTCGATTTAATTACAAATTAATT
129 ATTGTATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAAAAATTAATT
* * * *
6236 TGGAAAAAAAATGGAAAAACGATATTAGAATCTTGAAAAGGCCGTCAATCTTTTCGGCGTTGAAT
194 CGGAAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGGCCGTCAATCTTTTTGGCGTTGAAT
* * *
6301 AATATATTTTTTCTGAATATTTTGCAAAAAAATTGAG--AAAAACTTTTCGAGTTAGTTTCTAGC
259 TATATATTTTTTCTGAATATTTTGC-AAAAAATTGAGAAAAAAACTTTTCG-GTAAGTTTTTAGC
* * * * ** *
6364 CGAAATAGTGTACTAACCATCACGATTTTTGGCTAAAAATGCG-TTCGGATCCCGGTTCAATTTT
322 CGAAACA-TGTACTAACCATCACG-GTTTTGGCTAAAAACGCGTTTCGG-CCCCGACTCAGTTTT
* * * * * *
6428 AAATTAATTATGGCAGAAAGTCTCCTTCAAATATCTATATTCATCTAACAAAATCTCAGCCACAA
384 GAATTATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACAA
* *
6493 TGGATTTAAGAATTTGTTTTTACGAGCATCTTAATCTTTGTTTCGATTTAATTAGAAATAAATTC
449 TGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTTGTTTCGATTTAATTAGAAATAAATTC
* * * *
6558 TAAAAAAAAGGAAAAACGATATT-GAAAGTGTGAAAAACCCTTCAATT-TTTTTGGCATTAAATT
514 GAAAAAAAAGGAAAAACGATATTAG-AAGTGTGAAAACCCCTTCAATTCTTTTTGGCGTTGAATT
* ***
6621 ATATTTTTTTTCTGAGTATTGT-GCAAAAAATTGAGGAAAAACTTTTCAGGTC-ATTTTTCGCAA
578 ATATATTAGATCTGAGTATTGTGGCAAAAAATTGAGGAAAAACTTTTCAGGTCAATTTTT-GCAA
6684 AATTTTAGTCG----A--A-A------T-----
642 AATTTTAGTCGAAATAGTACATTTTTTTCCCAA
* ** *
6699 CG---T-G-----T--C-ATCACGATTTTTGACTAAAAACGCGTTCCGGATCCCTGGCTCAATTT
1 CGAAATCGTATACTAACTATCACG-TTTTTGGCTAAAAACGCGTTCCGGAGTCCCGGCTCAATTT
** *
6752 TGCATGATTTTTGGCATAAAGACTCCTTGAAATAT-TCATATTCATCGAACCAAATGTCAGCCAC
65 TGCATGATTTTTGGCGCAAAGACTCCTTGAAATATCT-ATATTCATCGAACCAAATCTCAGCCAC
* * * *
6816 GTTGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCAATTTAATTAGAAATTAATT
129 ATTGTATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAAAAATTAATT
* * *
6881 CGG-AAAAAAATGGGAAAACGATATTAGAAGCGTGAAAAGGCTGTCAATATTTTTGGCGTTGAAT
194 CGGAAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGGCCGTCAATCTTTTTGGCGTTGAAT
* * * * *
6945 TATATATTTTTTCTGAGTATTGTGTCAAAAAATCGAG-AATAAACGTTTCGGGTAAGTTTTTAGC
259 TATATATTTTTTCTGAATATTTTG-CAAAAAATTGAGAAAAAAACTTTTC-GGTAAGTTTTTAGC
** * * * * * * * * *
7009 CGAAATTGTGTACTAATCGTCACGATTTTTGACTAAAAACGCATTCCCGGGCCACGGCTCTGTTT
322 CGAAA-CATGTACTAACCATCACG-GTTTTGGCTAAAAACGCGTT-TC-GGCCCCGACTCAGTTT
* * ** * * * *
7074 TGCATGATTTTTGGC-GCCGAGACTCCTTGAAATATCTTTATTCATCTAATCAAATCTCAACCTC
383 TGAATTATTTTTGGCAG-AAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCAC
* * *
7138 ATTGGATTTAAGGATTTGTTTTTACGTGCATCTGAAT-TTTGTTTCGATTTAATTAGAAATTAAT
447 AATGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTTGTTTCGATTTAATTAGAAA-TAAA
* * * * ** ** *
7202 TTAGAAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCACCAA-TCTTTTTGGCGTTCA
511 TTCGAAAAAAA-AGGAAAAACGATATTAGAAGTGTGAAAACCCCTTCAATTCTTTTTGGCGTTGA
7266 ATTATATAT
575 ATTATATAT
7275 ATTTTATGAG
Statistics
Matches: 1663, Mismatches: 218, Indels: 115
0.83 0.11 0.06
Matches are distributed among these distances:
644 89 0.05
645 212 0.13
646 26 0.02
647 104 0.06
648 51 0.03
653 1 0.00
654 1 0.00
657 2 0.00
662 1 0.00
669 1 0.00
670 1 0.00
672 1 0.00
675 6 0.00
676 40 0.02
677 28 0.02
678 4 0.00
679 34 0.02
680 8 0.00
681 2 0.00
682 144 0.09
683 26 0.02
684 121 0.07
685 300 0.18
686 271 0.16
687 99 0.06
688 89 0.05
689 1 0.00
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.35
Consensus pattern (674 bp):
CGAAATCGTATACTAACTATCACGTTTTTGGCTAAAAACGCGTTCCGGAGTCCCGGCTCAATTTT
GCATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCCACAT
TGTATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAAAAATTAATTCG
GAAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGGCCGTCAATCTTTTTGGCGTTGAATTA
TATATTTTTTCTGAATATTTTGCAAAAAATTGAGAAAAAAACTTTTCGGTAAGTTTTTAGCCGAA
ACATGTACTAACCATCACGGTTTTGGCTAAAAACGCGTTTCGGCCCCGACTCAGTTTTGAATTAT
TTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACAATGGATTT
AAGGATTTGTTTTTACGAGCATCTGAATCTTTGTTTCGATTTAATTAGAAATAAATTCGAAAAAA
AAGGAAAAACGATATTAGAAGTGTGAAAACCCCTTCAATTCTTTTTGGCGTTGAATTATATATTA
GATCTGAGTATTGTGGCAAAAAATTGAGGAAAAACTTTTCAGGTCAATTTTTGCAAAATTTTAGT
CGAAATAGTACATTTTTTTCCCAA
Found at i:12110 original size:23 final size:23
Alignment explanation
Indices: 12080--12126 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
12070 ACCTTGGCTG
12080 CTACCAAGCCTTAGAAGTAATTC
1 CTACCAAGCCTTAGAAGTAATTC
*
12103 CTACCAAGCCTTGGAAGTAATTC
1 CTACCAAGCCTTAGAAGTAATTC
12126 C
1 C
12127 AATATGGGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.26
Consensus pattern (23 bp):
CTACCAAGCCTTAGAAGTAATTC
Done.