Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017586.1 Corchorus olitorius cultivar O-4 contig17619, 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: 34940
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:416 original size:2 final size:2
Alignment explanation
Indices: 409--437 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
399 AAATAATGGA
409 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
438 CACACACACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:7642 original size:2 final size:2
Alignment explanation
Indices: 7635--7674 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
7625 AGTATGCTAC
* *
7635 AT AT AT AT TT AT AT TT AT A- AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
7675 ATTAATGGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:23766 original size:9 final size:9
Alignment explanation
Indices: 23749--23792 Score: 52
Period size: 9 Copynumber: 4.9 Consensus size: 9
23739 ACAGCAATTG
*
23749 CAGCGACAA
1 CAGCCACAA
*
23758 CAGTCACAA
1 CAGCCACAA
*
23767 CAGCCACAG
1 CAGCCACAA
23776 CAGCCACAA
1 CAGCCACAA
*
23785 CAACCACA
1 CAGCCACA
23793 GCAACAGCCA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.43, C:0.41, G:0.14, T:0.02
Consensus pattern (9 bp):
CAGCCACAA
Found at i:29855 original size:2 final size:2
Alignment explanation
Indices: 29850--29880 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
29840 ACACACACAC
*
29850 AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
29881 GTGATGCATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:32423 original size:332 final size:333
Alignment explanation
Indices: 31552--34940 Score: 4774
Period size: 334 Copynumber: 10.2 Consensus size: 333
31542 TCAGTTTTAC
* *
31552 CCGAAATCGTGTACTAACCATCACGATTTTTGGCTGAAAACGCGTTCCGGGGCCCCGGCTCAGTT
1 CCGAAATCGTGTACTAAACATCACGATTCTTGGCTGAAAACGCGTTCCGGGGCCCCGGCTCAGTT
* * *
31617 TTGCTTGATTTTTAGCGCCAAGACTCATTGAATTATCCT-TATTCATCATTCCAAATCTCAGCCA
66 TTGCATGATTTTTGGCGCCAAGACTCATTGAATTAT-CTATATTCATCATCCCAAATCTCAGCCA
*
31681 CGTTGGATAAAGGGATTTGATTTTACGAGCATTTGAATCATGTTTCGATTTAATCGGAAATT--T
130 CCTTGGATAAAGGGATTTGATTTTACGAGCATTTGAATCATGTTTCGATTTAATCGGAAATTAAT
** *
31744 T---------TTTTAAAAAATTATATTAGAAGCGTGGAAAGCCCTTCAATCTTTTTGGCGTTGAA
195 TCGGAAAAAATTAAAAAAAATGATATTAGAAGCGTGGAAAGCCCTTCAATCTTTTTGGCGTTGAA
* * * * *
31800 TTATATATTTTTTACGAGTATCGCGGTTAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCA
260 ATATATATTTTTCACGAGTATTGCGGTCAAAAATTGGGGAAAAATCTTTCGGGTCAATTTTTGCA
31865 AAATTTTTG
325 AAATTTTTG
* * * * * *
31874 CCTAAATCGTGTAC-CATCA-CATGATTCTTGGCTGAAAACGCGTTCCGGGGCCCCAGATCAGTT
1 CCGAAATCGTGTACTAAACATCACGATTCTTGGCTGAAAACGCGTTCCGGGGCCCCGGCTCAGTT
* * *
31937 TTGCATGATATTTGGC-CAAAAGACTCATTGAATTATCTATATTCATCATCCCAATTCTCAGCCA
66 TTGCATGATTTTTGGCGC-CAAGACTCATTGAATTATCTATATTCATCATCCCAAATCTCAGCCA
*
32001 CCTTGGATTTAA-GGATTTGATTTTACGAGCATTTGAATCATGTTTCGATTTAATCGGAAATTAA
130 CCTTGGA-TAAAGGGATTTGATTTTACGAGCATTTGAATCATGTTTCGATTTAATCGGAAATTAA
*
32065 TTC-GCAAAAATTAAAAAAACAATGATATTAGAAGCGTGGAAAGCCCTTCAATCTTTTTGGCGTT
194 TTCGGAAAAAATT-AAAAAA-AATGATATTAGAAGCGTGGAAAGCCCTTCAATCTTTTTGGCGTT
* *
32129 GAAATATATATTTTTCACGAGTATTGCGATCAAAAATTGGGGAAAAATCTTTCAGGTCAATTTTT
257 GAAATATATATTTTTCACGAGTATTGCGGTCAAAAATTGGGGAAAAATCTTTCGGGTCAATTTTT
32194 GCAAAATTTTTG
322 GCAAAATTTTTG
* * * **
32206 TCGAAATCGTGTACTAAACATCACTATTCTTGGCTGAAAACGCGTTCCTGGATCCCGGCTCAGTT
1 CCGAAATCGTGTACTAAACATCACGATTCTTGGCTGAAAACGCGTTCCGGGGCCCCGGCTCAGTT
* *
32271 TTGCTTGATTTTTGGCGCCAAGACTCATTGAATTATCTATATTCATCATCCCAAATCTCAACCAC
66 TTGCATGATTTTTGGCGCCAAGACTCATTGAATTATCTATATTCATCATCCCAAATCTCAGCCAC
32336 CTTGGATAAAGGGATTTGATTTTACGAGCATTTGAATCATGTTTCGATTTAATCGGAAATTAATT
131 CTTGGATAAAGGGATTTGATTTTACGAGCATTTGAATCATGTTTCGATTTAATCGGAAATTAATT
* * *
32401 CGGAAAAAATT-AAAAAAATGATATTAGAAGCGTGGAAAGCCCTTGAATCTTTTTGGCATTGAAT
196 CGGAAAAAATTAAAAAAAATGATATTAGAAGCGTGGAAAGCCCTTCAATCTTTTTGGCGTTGAAA
* ** *
32465 TATATATTTTTTACGCTTATTGCGGTTAAAAATTGGGGAAAAATCTTTCGGGTCAATTTTTGCAA
261 TATATATTTTTCACGAGTATTGCGGTCAAAAATTGGGGAAAAATCTTTCGGGTCAATTTTTGCAA
32530 AATTTTTG
326 AATTTTTG
* * * * *
32538 CTGAAATCGTGTACTAAACATCACGATTCTTGGATGAAAACGAGTTTCGGGGCCCCAGCTCAGTT
1 CCGAAATCGTGTACTAAACATCACGATTCTTGGCTGAAAACGCGTTCCGGGGCCCCGGCTCAGTT
* * * * *
32603 TTGCATGATTTTTGGC-CAAAAGGCTCATTGAATTATCTATATTCATCATCCCAATTCTTAGCTA
66 TTGCATGATTTTTGGCGC-CAAGACTCATTGAATTATCTATATTCATCATCCCAAATCTCAGCCA
* *
32667 CCTTGGATTTAA-GGATTTGATTTTACGAGCATTTGAATCATGTTTCGATTTAATCGGAATTTAA
130 CCTTGGA-TAAAGGGATTTGATTTTACGAGCATTTGAATCATGTTTCGATTTAATCGGAAATTAA
* *
32731 TTCGCAAAAAATTAAAAAAACAATGATATTAGAAGCGTGGAAAACCCTTCAAATCTTTTTGGCGT
194 TTCGGAAAAAATT-AAAAAA-AATGATATTAGAAGCGTGGAAAGCCCTTC-AATCTTTTTGGCGT
* * * *
32796 TGAAATAAATATTTTTCACGAGTATTGCGGTAAAAAATTAGGGAAATATCTTTCGGGTCAATTTT
256 TGAAATATATATTTTTCACGAGTATTGCGGTCAAAAATTGGGGAAAAATCTTTCGGGTCAATTTT
*
32861 TCCAAAATTTTTG
321 TGCAAAATTTTTG
* * * *
32874 TCGAATTCGTGTACTAAACATCACGATTCTTGGTTGAAAACGCGTTACGGGGCCCCGGCTCAGTT
1 CCGAAATCGTGTACTAAACATCACGATTCTTGGCTGAAAACGCGTTCCGGGGCCCCGGCTCAGTT
* * *
32939 TTGCTTGATTTTTGGCGCCAAGGCT-AGTTGAATTATCTATATTCATCATCCAAAATCTCAGCCA
66 TTGCATGATTTTTGGCGCCAAGACTCA-TTGAATTATCTATATTCATCATCCCAAATCTCAGCCA
** * **
33003 CCTTGGAT-TTGAGGATTTGATTTTACGAGCATTTGAATCATGTTTCAATTTAATCCAAAATTAA
130 CCTTGGATAAAG-GGATTTGATTTTACGAGCATTTGAATCATGTTTCGATTTAATCGGAAATTAA
* * *
33067 TTCGG-AAAAA-TAAAAAAAATGATATTAGAAGCGTGCAAAGCCCTTCAATCCTTTTGGCATTGA
194 TTCGGAAAAAATTAAAAAAAATGATATTAGAAGCGTGGAAAGCCCTTCAATCTTTTTGGCGTTGA
* * * * * *
33130 ATTATTTATTATTT-ACGAATATTGCGGTTAAAAATTGAGGAAAAATCTTTCGAGTCAATTTTTG
259 AATATATATT-TTTCACGAGTATTGCGGTCAAAAATTGGGGAAAAATCTTTCGGGTCAATTTTTG
33194 CAAAATTTTTG
323 CAAAATTTTTG
* * * **
33205 CCGAAATCATGTAC-AAACAATCACGATTTTTGGCTGAAAACGCGTTCCGGGTCCCCGATTCAGT
1 CCGAAATCGTGTACTAAAC-ATCACGATTCTTGGCTGAAAACGCGTTCCGGGGCCCCGGCTCAGT
* * * *
33269 TCTGCTTGATTTTTTGGCGTCAAGACTCATTGAATTATCCT-TATTCATCATTCCAAATCTCAGC
65 TTTGCATGA-TTTTTGGCGCCAAGACTCATTGAATTAT-CTATATTCATCATCCCAAATCTCAGC
*
33333 CACGTTGGATAAAGGGATTTGATTTTACGAGCATTTGAATCATGTTTCGATTTAATCGGAAATTA
128 CACCTTGGATAAAGGGATTTGATTTTACGAGCATTTGAATCATGTTTCGATTTAATCGGAAATTA
* * *
33398 ATTCGG-AAAAATTACAAAAAATGATATTAGAAGCGTGGAAAGCCCATCAATCTTTTTGGCATTG
193 ATTCGGAAAAAATTAAAAAAAATGATATTAGAAGCGTGGAAAGCCCTTCAATCTTTTTGGCGTTG
* *
33462 AATTATATATTTTT-ACGAGTATTGAGGGT-AAAAATTGGGGAAAAATCTTTCGGGTCAATTTTT
258 AAATATATATTTTTCACGAGTATTG-CGGTCAAAAATTGGGGAAAAATCTTTCGGGTCAATTTTT
33525 GCAAAATTTTTG
322 GCAAAATTTTTG
* * *
33537 CCGATATCGTGTACTAAACATCACGATTCTTGGATGAAAACGCGTTTCGGGGCCCCGGCTCAGTT
1 CCGAAATCGTGTACTAAACATCACGATTCTTGGCTGAAAACGCGTTCCGGGGCCCCGGCTCAGTT
* *
33602 TTGCATGATTTTTGGC-CAAAAGACTCATTGAATTATCTATATTCATCATCCCAATTCTCAGCCA
66 TTGCATGATTTTTGGCGC-CAAGACTCATTGAATTATCTATATTCATCATCCCAAATCTCAGCCA
* *
33666 CCTTGGATTTAA-GGATTTGATTTTACGAGCATTTGACA-CATGTTTTGATTTAATCGGAAATTA
130 CCTTGGA-TAAAGGGATTTGATTTTACGAGCATTTGA-ATCATGTTTCGATTTAATCGGAAATTA
** * ** *
33729 ATTCACAAAAAATTTAAAAAACAATGATATTAAAAGCGTGGAAAGCCCTTCAAAATTTTTGGCGA
193 ATTCGGAAAAAA-TTAAAAAA-AATGATATTAGAAGCGTGGAAAGCCCTTCAATCTTTTTGGCGT
* *
33794 TGAAATATATATTTTTCACGAGTATTGCGATCAAAAATTAGGGAAAAATCTTTCGGGTCAATTTT
256 TGAAATATATATTTTTCACGAGTATTGCGGTCAAAAATTGGGGAAAAATCTTTCGGGTCAATTTT
33859 TGCAAAATTTTTG
321 TGCAAAATTTTTG
* * *
33872 CCGAAATCGTGTACTAAAAATCACGATT-TTCGTCTGAAAACGCGTTCCGGGGCCTCGGCTCAGT
1 CCGAAATCGTGTACTAAACATCACGATTCTT-GGCTGAAAACGCGTTCCGGGGCCCCGGCTCAGT
* * *
33936 TTTGCATGATTTTTGTCGCCAAGACTCATTGAATTATCTATATTCATCATTCCAAATCTCAACCA
65 TTTGCATGATTTTTGGCGCCAAGACTCATTGAATTATCTATATTCATCATCCCAAATCTCAGCCA
* * *
34001 CGTTGGATAAAGGGAATTGATTTTACGAGCATTTGAATCATTTTTCGATTTAATCGGAAATTAAT
130 CCTTGGATAAAGGGATTTGATTTTACGAGCATTTGAATCATGTTTCGATTTAATCGGAAATTAAT
*
34066 TCGGAAAAAAATTAAAACAAATGATATTAGAAGCGTGGAAAGCCCTTCAATCTTTTTGGCGTTGA
195 TCGG-AAAAAATTAAAAAAAATGATATTAGAAGCGTGGAAAGCCCTTCAATCTTTTTGGCGTTGA
* * *
34131 AATATATATTTTT-ACGAGTATTGAGGGCAAAAATTGGGTAAAAATCTTTCGGGTCAATTTTTGC
259 AATATATATTTTTCACGAGTATTGCGGTCAAAAATTGGGGAAAAATCTTTCGGGTCAATTTTTGC
34195 AAAATTTTTTG
324 AAAA-TTTTTG
* *
34206 CTGAAATCGTGTACTAAACATCACGATTCTTGGCTGAAAACGGGTTCCGGGGCCCCGGCTCAGTT
1 CCGAAATCGTGTACTAAACATCACGATTCTTGGCTGAAAACGCGTTCCGGGGCCCCGGCTCAGTT
* * *
34271 TTGCTTGATTTTTGGTGCCAAGACTCATTGAATTATCCT-TATTCATCATTCCAAATCTCAGCCA
66 TTGCATGATTTTTGGCGCCAAGACTCATTGAATTAT-CTATATTCATCATCCCAAATCTCAGCCA
*
34335 CGTTGGATAAAGGGATTTGATTTTACGAGCATTTGAATCATGTTTCGATTTAATCGGAAATTAAT
130 CCTTGGATAAAGGGATTTGATTTTACGAGCATTTGAATCATGTTTCGATTTAATCGGAAATTAAT
* *
34400 TCGGAAAAAATTAAAAAAAATGATATTAGAAGCGTGGAAAGCCCTTGAATCTTTTTGGCATTGAA
195 TCGGAAAAAATTAAAAAAAATGATATTAGAAGCGTGGAAAGCCCTTCAATCTTTTTGGCGTTGAA
* * *
34465 TTATATATTTTTTACGAGTATTGCGGTTAAAAATTAGGGGAAAAATCTTTCGGGTCAATTTTTGC
260 ATATATATTTTTCACGAGTATTGCGGTCAAAAATT-GGGGAAAAATCTTTCGGGTCAATTTTTGC
34530 AAAATTTTTG
324 AAAATTTTTG
* * * * *
34540 CCGAAATCGTGTACTAAACATCACGATTCTTGGATGAAAATGTGATT-CGGGGCCCCAGCTTAGT
1 CCGAAATCGTGTACTAAACATCACGATTCTTGGCTGAAAACGCG-TTCCGGGGCCCCGGCTCAGT
* * *
34604 TTTGCATGATTTTTGGC-CAAAAGA-TACATTGAATTATCTATATTCATCATCCTAATTCTCAGC
65 TTTGCATGATTTTTGGCGC-CAAGACT-CATTGAATTATCTATATTCATCATCCCAAATCTCAGC
* *
34667 CACCTTGGATTTAA-GGATTTGATTTTACGAGCATTTGACA-CATGTTTTGATTTAATCGGAAAT
128 CACCTTGGA-TAAAGGGATTTGATTTTACGAGCATTTGA-ATCATGTTTCGATTTAATCGGAAAT
* *
34730 TAATTCGCAAAAAATTAAAAAACAATGATATTAGAAGCGTGGAAAGCCCTTCAATGTTTTTGGCG
191 TAATTCGGAAAAAATTAAAAAA-AATGATATTAGAAGCGTGGAAAGCCCTTCAATCTTTTTGGCG
* * *
34795 TTGAAATATATATTTTTCACGAGTATTGCGATCAAAAATTAGGGAAAAATCTTTCGGGTTAATTT
255 TTGAAATATATATTTTTCACGAGTATTGCGGTCAAAAATTGGGGAAAAATCTTTCGGGTCAATTT
34860 TTGCAAAATTTTTG
320 TTGCAAAATTTTTG
* * * * * *
34874 TCGAAACCGTGTACT-AACAATTACGATTTTTGGCTGAAAACGCGTTCCGGGACCCCGACTCAGT
1 CCGAAATCGTGTACTAAAC-ATCACGATTCTTGGCTGAAAACGCGTTCCGGGGCCCCGGCTCAGT
34938 TTT
65 TTT
Statistics
Matches: 2740, Mismatches: 260, Indels: 122
0.88 0.08 0.04
Matches are distributed among these distances:
319 3 0.00
320 149 0.05
321 6 0.00
322 15 0.01
330 8 0.00
331 245 0.09
332 683 0.25
333 224 0.08
334 755 0.28
335 391 0.14
336 260 0.09
337 1 0.00
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Consensus pattern (333 bp):
CCGAAATCGTGTACTAAACATCACGATTCTTGGCTGAAAACGCGTTCCGGGGCCCCGGCTCAGTT
TTGCATGATTTTTGGCGCCAAGACTCATTGAATTATCTATATTCATCATCCCAAATCTCAGCCAC
CTTGGATAAAGGGATTTGATTTTACGAGCATTTGAATCATGTTTCGATTTAATCGGAAATTAATT
CGGAAAAAATTAAAAAAAATGATATTAGAAGCGTGGAAAGCCCTTCAATCTTTTTGGCGTTGAAA
TATATATTTTTCACGAGTATTGCGGTCAAAAATTGGGGAAAAATCTTTCGGGTCAATTTTTGCAA
AATTTTTG
Done.