Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005534.1 Corchorus capsularis cultivar CVL-1 contig05552, 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: 2267
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.36
Found at i:875 original size:326 final size:319
Alignment explanation
Indices: 5--2126 Score: 1834
Period size: 326 Copynumber: 6.5 Consensus size: 319
1 GCAT
* * * * * *
5 AAAGACTCCTT-ATGATATCTATATTCATCTAACCAAATCTCAGACACGTTGGATTTAAGGATTT
1 AAAGACTTCTTGATAATATATATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGAATTT
* * * *
69 CTTTTTACGAGCATCTCAATCTTATTTCAATTTAATT-GTAAA-TAATTTCGGGAAAAAATGGAA
66 GTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAG-AAATTAA-TTC-GGAAAAAATGGAA
* * * * ** * * *
132 AAACGATATTA-AA-ATTGTGAAAAACACGTTTAA-CCTTTTGTCTTTGAATTAAATATTTTTTC
128 AAACGATATTAGAAGCTTG-AAAAAAC-CCTTCAATATTTTTGGCGTTGAATTATATATTTTTTC
* ** *
194 CAAGTATTGTGGCAAAAAATTGAGGAAAAACCTTTCGGGTCAGTTTTTGCAAAATTTTAGCTGAA
191 TAAGTATTGTGGCAAAAAATTGA-GAAAAAATTTTC-GGTCAG----T------TTTTAGCCGAA
* * *
259 ATCGTGTACTAACCATCACGGTTTTTGGCTAAAAAAGCGTTTCGGGGCTCCGG-CTTAATTTTGC
244 ATCGTGTACTAACCATCACGGTTTTTGGCT-AAAACGCGTTTCGGGGCT-CGGACTCAGTTTTGC
*
323 ATGATTTTTGGCAG
307 A-GATTTTTGGCAA
*
337 AAAGACTTCTTGA-AATATATATATTCATCTAACCAAATCGCAGCCACATTGGATTTAAGAATTT
1 AAAGACTTCTTGATAATATATATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGAATTT
* *
401 GTTTTTATGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAATGCAAAAA
66 GTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAATG--GAAA
* * * * ** * * * * *
466 AATGATATGAGAAGCGTG--ACAATTCTTCAATGTTTTTTTGCGTT-AGTTTATTTAGTTTTTCT
129 AACGATATTAGAAGCTTGAAAAAACCCTTCAAT-ATTTTTGGCGTTGA-ATTATATATTTTTTCT
* * * *
528 TAGTATTGTGGCGAGAAATTGAGAATAAAATTTTCAGGTCAGTTTTTAGCCGAAAATGGTGTACT
192 AAGTATTGTGGCAAAAAATTGAGAA-AAAATTTTC-GGTCAGTTTTTAGCCG-AAATCGTGTACT
* * * * ** *
593 AACCATCACGGTTTCTGGATAAAACTTCATTTCGGGGCTCGGGTTCAGTTTTGCATGATTTTTTG
254 AACCATCACGGTTTTTGGCTAAAAC-GCGTTTCGGGGCTCGGACTCAGTTTTGCA-GATTTTTGG
658 CAA
317 CAA
* * *
661 AAAGGGCTTCTTGA-AATATATATATTCTTCTAAGCAAAATCTCAGCCACATTGGATTTAAGAAT
1 AAA-GACTTCTTGATAATATATATATTCATCTAA-CCAAATCTCAGCCACATTGGATTTAAGAAT
*
725 TTGTTTTTACGAGCAACTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAACAATGGAA
64 TTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAA-AATGGAA
* * * *
790 AAACGATATTAGAAGCTTGAAAAAACCTTTCAATATTTTTGGCGTTGAATTATATATCTTTTATG
128 AAACGATATTAGAAGCTTGAAAAAACCCTTCAATATTTTTGGCGTTGAATTATATATTTTTTCTA
* * * *
855 AGTATTATAGCAAAAAATTGAGAAAAAAATTTTTCGAGCCAGTTTTTAGCCGAAATCATGTACTA
193 AGTATTGTGGCAAAAAATTGAG-AAAAAA-TTTTCG-GTCAGTTTTTAGCCGAAATCGTGTACTA
* * * * *
920 ACCATCACTGTTTTTGGCTAAAAACGCGTTTCAGGGC-CTTGAATCAGTTTTGCGAGGTTTTTGG
255 ACCATCACGGTTTTTGGCT-AAAACGCGTTTCGGGGCTC-GGACTCAGTTTTGC-AGATTTTTGG
**
984 CGT
317 CAA
* * * * * *
987 AAAGACTCCTT-ATGATATCTATATTCATCTAACCAAATCTCAGACACGTTGGATTTAAGGATTT
1 AAAGACTTCTTGATAATATATATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGAATTT
* * * * *
1051 CTTTTTACGAGCATCTCAATCTTATTTCAATTTAATTGGAAA-TAATTTCGGGAAAAAAAATGGA
66 GTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAA-TTC-GG--AAAAAATGGA
** * * *
1115 AAAACGATATTA-AAAATGTG-AAAAACCCATT-AA-ACTTTTTGTCTTTGAATTAAATATTTTT
127 AAAACGATATTAGAAGCT-TGAAAAAACCC-TTCAATA-TTTTTGGCGTTGAATTATATATTTTT
* * * *
1176 TCCAACTATTGTGGCAAAAAATTGAGGAAAAACTTTTCGGGTCAGTTTTTGCAAAATTTTAGCCA
189 TCTAAGTATTGTGGCAAAAAATTGA-GAAAAAATTTTC-GGTCAG----T------TTTTAGCCG
* * *
1241 AAATCGTATACTAACCATCACGGTTTTTGGCTTAAAACGCGTTTCGCGGCTCCGG-CTCA----A
242 AAATCGTGTACTAACCATCACGGTTTTTGGC-TAAAACGCGTTTCGGGGCT-CGGACTCAGTTTT
*
1301 GC--ATTTTTGGCAG
305 GCAGATTTTTGGCAA
*
1314 AAAGACTTCTTGA-AATATATATATTCATCTAACCAAATCGCAGCCACAATTGGATTTAAGAATT
1 AAAGACTTCTTGATAATATATATATTCATCTAACCAAATCTCAGCCAC-ATTGGATTTAAGAATT
* *
1378 TGTTTTTATGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGG-AAAAATGCCAAA
65 TGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAATG--GAA
* * * * * *
1442 AAATGATATTAGAAGCGTG-AAAAACCCTTCAATGTTTTTTGCGTT-AATTTATTTAGTTTTTCT
128 AAACGATATTAGAAGCTTGAAAAAACCCTTCAATATTTTTGGCGTTGAA-TTATATATTTTTTCT
* * *
1505 TAGTATTGTGGCGAAAAATTGAGAATAAAATTTTCAGGTAAGTTTTTAGCCGAAATCGTGTACTA
192 AAGTATTGTGGCAAAAAATTGAGAA-AAAATTTTC-GGTCAGTTTTTAGCCGAAATCGTGTACTA
* * * * * * *
1570 ACCATCTCGGTTTCTGGCTAAAACTGCATTTCGTGGCTCAGACTCAGTTTTGCATTATTTTTTGC
255 ACCATCACGGTTTTTGGCTAAAAC-GCGTTTCGGGGCTCGGACTCAGTTTTGCA-GATTTTTGGC
1635 AA
318 AA
*
1637 AAAGACTTCTTGAATTATATATATATATATATATATATATATTCATTTAACCAAATCTCAGCCAC
1 AAAGACTTCTTG----------------ATA-ATATATATATTCATCTAACCAAATCTCAGCCAC
1702 ATTGGATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATT
49 ATTGGATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATT
* * * *
1767 CGGAAAATAATGGAAAAACGATATTAGAAGCGTG-AAAAACCCGTCAATCTTTTTGGTGTTGAAT
114 CGGAAAA-AATGGAAAAACGATATTAGAAGCTTGAAAAAACCCTTCAATATTTTTGGCGTTGAAT
* * * * * * * *
1831 TATATGTTTTTTATGAGTAGTATAGCAAAAAATTGAGAAAAAAATTTTCGAGCCAGTTTTTAGCG
178 TATATATTTTTTCTAAGTATTGTGGCAAAAAATTGAG-AAAAAATTTTCG-GTCAGTTTTTAGCC
* * *
1896 GAAATCATGTACTAACCATCACGATTTTTGGCTAAAAACGCGTTTCGGGGC-CTTGACTCAGTTC
241 GAAATCGTGTACTAACCATCACGGTTTTTGGCT-AAAACGCGTTTCGGGGCTC-GGACTCAGTT-
* *
1960 TGTG-AGGTTTTTGGCAT
303 T-TGCAGATTTTTGGCAA
* * * * * * *
1977 AAAGACTCCTT-ATGATATCTATATTTATCTAACCAAATCTCAGACACGTTGGATTTAAGGATTT
1 AAAGACTTCTTGATAATATATATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGAATTT
* * * * *
2041 CTTTTTACGAGCATCTCAATCTTATTTCAATTTAATT-GTAAA-TAATTTCGGGAAAAATGGAAA
66 GTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAG-AAATTAA-TTCGGAAAAAATGGAAA
*
2104 AACGATATTAAAAG-TGTGAAAAA
129 AACGATATTAGAAGCT-TGAAAAA
2127 CACATTAAAA
Statistics
Matches: 1468, Mismatches: 223, Indels: 208
0.77 0.12 0.11
Matches are distributed among these distances:
315 8 0.01
316 51 0.03
320 2 0.00
321 27 0.02
322 93 0.06
323 41 0.03
324 148 0.10
325 136 0.09
326 283 0.19
327 97 0.07
328 56 0.04
329 4 0.00
330 2 0.00
331 14 0.01
332 100 0.07
333 66 0.04
334 56 0.04
335 4 0.00
336 1 0.00
339 3 0.00
340 225 0.15
341 45 0.03
342 6 0.00
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.36
Consensus pattern (319 bp):
AAAGACTTCTTGATAATATATATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGAATTT
GTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAATGGAAAAA
CGATATTAGAAGCTTGAAAAAACCCTTCAATATTTTTGGCGTTGAATTATATATTTTTTCTAAGT
ATTGTGGCAAAAAATTGAGAAAAAATTTTCGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATC
ACGGTTTTTGGCTAAAACGCGTTTCGGGGCTCGGACTCAGTTTTGCAGATTTTTGGCAA
Found at i:1659 original size:2 final size:2
Alignment explanation
Indices: 1652--1678 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1642 CTTCTTGAAT
1652 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1679 TCATTTAACC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.