Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019411.1 Corchorus olitorius cultivar O-4 contig19444, 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: 4721
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32
Found at i:813 original size:323 final size:321
Alignment explanation
Indices: 1--1251 Score: 1695
Period size: 321 Copynumber: 3.9 Consensus size: 321
* * *
1 AACTGACCTGAAAAGTTTTTTCTCAATTTTCTTGACACAATACTTAAAAATAATATATAATTCAA
1 AACTGACCCGAAAAG-TTTTTCTCAATTTTCTTGCCACAATACTTAAAAACAATATATAATTCAA
* *
66 CGCCAAAAAGATTAAAGGATTTTTCACGCTT-TCAATATCATTTTCCAACTTTTTTCCGACTTAA
65 CGCCAAAAAGATTAAAGGTTTTTTCACGCTTCT-AATATCATTTTCCAACTTTTTTCCGAATTAA
* * * *
130 CTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACTAATCCTTAAATCCAACGTGTCA
129 TTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAACGTGGCT
* * *
195 GAGATTTTGTTAGATGAATATAGATATTTCAAGGAGTCTTTGCGCCCAAAATCATGTAAAACTAA
194 GAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAACTAA
* *
260 CACGGGCTCCAGAACGCGTTTTTAGCCAAAACCCGTGATGGTTAGTACACGATTTCGTCTAAA
259 CTCGGGCTCCAGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGTCTAAA
* * *
323 AACTAACCCGAAAAGTTTTCCTCAATTTTCTTGCCACAATATTTATAAAA-AATATATAATTCAA
1 AACTGACCCGAAAAGTTTTTCTCAATTTTCTTGCCACAATACTTA-AAAACAATATATAATTCAA
* *
387 TGCCAAAAAGATTAAAGGTTTTTTCACGCTTCTAATATCATTTTCCAACTTTTCTCCGAATTAAT
65 CGCCAAAAAGATTAAAGGTTTTTTCACGCTTCTAATATCATTTTCCAACTTTTTTCCGAATTAAT
*
452 TTCTATTTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAACGTGGCTG
130 TTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAACGTGGCTG
* * * *
517 AGATTTGGTTTGATGAATATAGATATTTCGAGGAGTCTTTGCGTCAAAAATCATGTAAAAACTAA
195 AGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATG-CAAAACTAA
* * * *
582 CTCGGGCTCCGGAAAGCGTTTTTAGCCAAAAACTGTGATGGTTAGTACACGATTTCGGCTAAA
259 CTCGGGCTCCAGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGTCTAAA
* * * *
645 ACCTGACCCGAAAAGTTTTTCGTCAATTTTCTTGCCACAAAACTTATGAAA-AATAAATAATTCA
1 AACTGACCCGAAAAGTTTTTC-TCAATTTTCTTGCCACAATACTTA-AAAACAATATATAATTCA
* *
709 ATGCCAAAAAGATTAAAAGG-TTTTTCACGTTTCTAATATCATTTTTCCAACTTTTTTCCGAATT
64 ACGCCAAAAAGATT-AAAGGTTTTTTCACGCTTCTAATATCA-TTTTCCAACTTTTTTCCGAATT
* * * * *
773 AATTACAAATT-AATTGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATGCAATGTGG
127 AATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAACGTGG
* * *
837 CTGAGATTTGGTTAGATGATTATAGATATTTCAAGGAG----T-C-CCAAGAA-CATGCAAAATT
192 CTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAACT
* * *
895 GAGC-CGGGCTCCAGAATGCGTTTTTAGCCAAAAAACCGTGATGATTAGTACACGATTTCGTCTA
257 -AACTCGGGCTCCAGAACGCGTTTTTAGCC-AAAAACCGTGATGGTTAGTACACGATTTCGTCTA
959 AA
320 AA
* ** *
961 AACTGACCCGAAAAGTTTTTCTAAATTTT-TT-TAACAATACTTAGAAACAATATATAATTCAAC
1 AACTGACCCGAAAAGTTTTTCTCAATTTTCTTGCCACAATACTTAAAAACAATATATAATTCAAC
* * *
1024 ACCGAAAAGATTAAAGGTTTTTTCAAGCTTCTAAATATCATTTTTCCAACTTTTTTCCGAATTAA
66 GCCAAAAAGATTAAAGGTTTTTTCACGCTTCT-AATATCA-TTTTCCAACTTTTTTCCGAATTAA
* ** ** * *
1089 TTTCTAATTAAATCGAAACAATATTCAGATGCTTTTAAAAACAAATTTTTAAATTCAATGTGGCT
129 TTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAACGTGGCT
* * * *
1154 GAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTGCGCCCACAATCATGCAAAATTGA
194 GAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAACTAA
* * *
1219 GTCTGGCTCCAGAACGCGGTTTTAGCCAAAAAC
259 CTCGGGCTCCAGAACGCGTTTTTAGCCAAAAAC
1252 GATTTCGGCT
Statistics
Matches: 826, Mismatches: 83, Indels: 41
0.87 0.09 0.04
Matches are distributed among these distances:
312 9 0.01
313 44 0.05
314 41 0.05
315 118 0.14
316 59 0.07
317 5 0.01
318 1 0.00
319 2 0.00
320 1 0.00
321 221 0.27
322 134 0.16
323 157 0.19
324 34 0.04
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.33
Consensus pattern (321 bp):
AACTGACCCGAAAAGTTTTTCTCAATTTTCTTGCCACAATACTTAAAAACAATATATAATTCAAC
GCCAAAAAGATTAAAGGTTTTTTCACGCTTCTAATATCATTTTCCAACTTTTTTCCGAATTAATT
TCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAACGTGGCTGA
GATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAACTAACT
CGGGCTCCAGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGTCTAAA
Found at i:2002 original size:323 final size:324
Alignment explanation
Indices: 1556--2230 Score: 896
Period size: 323 Copynumber: 2.1 Consensus size: 324
1546 AAAATTTTGC
* * * * *
1556 AAAAATTGACACG-AAAGTTTTCCCTC-ATTTTTTTACCACACTACTCAGAAAAAATATATAATT
1 AAAAACTGACCCGAAAACTTTTTCCTCAATTTTTTTACCACAATACTCAGAAAAAATATATAATT
* *
1619 CAACGCCAAAAAGATTAAAGGTTTTTTCACGCTTCTAATATCATTTTTCCAACTTTTTTCCGAAT
66 CAACGCCAAAAAGATTAAAGGGTTTTTCACACTTCTAATATCATTTTTCCAACTTTTTTCCGAAT
* * *
1684 TAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAACGTG
131 TAATTTCCAATTAAATCGAAACAAGAATCAGATGCTCGTAAAAACAAATCCTCAAATCCAACGTG
* * * * *
1749 TCTGAAATTTTGTTAGATGAATATAGATATTCCAAGGAGTCTTTGCGCCCAAAATCCTGTAAAAC
196 GCTGAAATTTGGTTAGATGAATATAGATATTCCAAGGAATCTTTGCACCCAAAATCATG-AAAAC
* * * * * *
1814 T-GAGC-CGGACTCCGGAAGGCGTTTTTT-GC-CAAAAACCGTGATGGTTTGTACTCGATTTCGA
260 TGGAGCTAGG-CTCCGGAAAGCGTTTTTTCGCAAAAAAACAGTGATGGTTAGTACACGATTTCG-
1875 CT
323 CT
* * * * *
1877 AAAAACTGACCCGAAAACTTTTTCCTCAATTTTTTTGCCACAATACTTATAGAAAATATATTATT
1 AAAAACTGACCCGAAAACTTTTTCCTCAATTTTTTTACCACAATACTCAGAAAAAATATATAATT
* * * *
1942 GAACGCCAAAAAGATTTAAGGGTTTTTCACACTTTTAATATCATTTTTCCAACTTTTTTCCTAAT
66 CAACGCCAAAAAGATTAAAGGGTTTTTCACACTTCTAATATCATTTTTCCAACTTTTTTCCGAAT
* * * *
2007 TAATTTCCAATTAAATCGAAACAAGAATCAGATGCTCGTAAAAATAAGTTCTCAAATCCAATGTG
131 TAATTTCCAATTAAATCGAAACAAGAATCAGATGCTCGTAAAAACAAATCCTCAAATCCAACGTG
* * * * *
2072 GCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAATCTTTGCATCCAAAATCATGCAAATT
196 GCTGAAATTTGGTTAGATGAATATAGATATTCCAAGGAATCTTTGCACCCAAAATCATGAAAACT
2137 GGAGCTAGGCTCCGGAAAGCGTTTTTTCGCAAAAAAAACAGTGATGGTTAGTACACGATTTCGCT
261 GGAGCTAGGCTCCGGAAAGCGTTTTTTCGC-AAAAAAACAGTGATGGTTAGTACACGATTTCGCT
*
2202 AAAAACTGATCCGAAAAACTTTTT-CTCAA
1 AAAAACTGACCCG-AAAACTTTTTCCTCAA
2231 CCTTTATTAC
Statistics
Matches: 306, Mismatches: 40, Indels: 12
0.85 0.11 0.03
Matches are distributed among these distances:
321 11 0.04
322 15 0.05
323 220 0.72
324 4 0.01
325 19 0.06
326 37 0.12
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33
Consensus pattern (324 bp):
AAAAACTGACCCGAAAACTTTTTCCTCAATTTTTTTACCACAATACTCAGAAAAAATATATAATT
CAACGCCAAAAAGATTAAAGGGTTTTTCACACTTCTAATATCATTTTTCCAACTTTTTTCCGAAT
TAATTTCCAATTAAATCGAAACAAGAATCAGATGCTCGTAAAAACAAATCCTCAAATCCAACGTG
GCTGAAATTTGGTTAGATGAATATAGATATTCCAAGGAATCTTTGCACCCAAAATCATGAAAACT
GGAGCTAGGCTCCGGAAAGCGTTTTTTCGCAAAAAAACAGTGATGGTTAGTACACGATTTCGCT
Done.