Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010127.1 Corchorus capsularis cultivar CVL-1 contig10148, 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: 21624
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Found at i:5749 original size:128 final size:127
Alignment explanation
Indices: 5521--5774 Score: 454
Period size: 128 Copynumber: 2.0 Consensus size: 127
5511 GGGCACGTGC
*
5521 CCCCACTCAAATCCAATTGTCCCTTAATCATGTAGTAAAATGTTTTTTATATATTTTGTTTTTTT
1 CCCCACTCAAATCCAATTGTCCCTTAATCATGTAGTAAAATGTTTTTTATATATTTTATTTTTTT
* *
5586 TATTGTGCCCCCACTATTGAGTAAAAAAAATTGTGCCCCGTAGAAGAATTCACTTAAGACTG
66 TATTGTGCCCCCACTATTGAGTAAAAAAAACTGTGCCCCATAGAAGAATTCACTTAAGACTG
5648 CCCCACTCAAATCCAATTGTCCCTTAATCATGTAGTAAAATGTTTTTTTATATATTTTATTTTTT
1 CCCCACTCAAATCCAATTGTCCCTTAATCATGTAGTAAAATG-TTTTTTATATATTTTATTTTTT
* *
5713 TTATTGTGCCCCCACTATTGAGTAAAAAAAACTGTGCCTCATAGAAGAATTCACTTCAGACT
65 TTATTGTGCCCCCACTATTGAGTAAAAAAAACTGTGCCCCATAGAAGAATTCACTTAAGACT
5775 CAAAACAAAA
Statistics
Matches: 121, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
127 42 0.35
128 79 0.65
ACGTcount: A:0.30, C:0.20, G:0.11, T:0.38
Consensus pattern (127 bp):
CCCCACTCAAATCCAATTGTCCCTTAATCATGTAGTAAAATGTTTTTTATATATTTTATTTTTTT
TATTGTGCCCCCACTATTGAGTAAAAAAAACTGTGCCCCATAGAAGAATTCACTTAAGACTG
Found at i:11199 original size:18 final size:18
Alignment explanation
Indices: 11157--11192 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
11147 CATATTTGCG
11157 AAGTATGTAATATGTACA
1 AAGTATGTAATATGTACA
11175 AAGTATGTAATATGTACA
1 AAGTATGTAATATGTACA
11193 TGATATGATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.06, G:0.17, T:0.33
Consensus pattern (18 bp):
AAGTATGTAATATGTACA
Found at i:15493 original size:279 final size:274
Alignment explanation
Indices: 14975--15516 Score: 840
Period size: 279 Copynumber: 2.0 Consensus size: 274
14965 CCTAAACCTA
* * ** *
14975 GGTAGGCCTACAGGCTGTTTAACGATACTGGCACATCAAAGACTCATACAAGAAGTAATTTCAGT
1 GGTAGGCCTACAGGCTGTATAACAATACTGGCACATCAAAGACAAATACAAGAAATAATTTCAGT
* * * *
15040 TATAGGACCCATAGAATCAACATAATTCTAGAAGGATAAATAGCAGGGGAAAAAATCCTATGTGA
66 TATAGGAACCATAGAATCAACATAATTCTAGAAGGAGAAATAGCAGGGCAAAAAATACTATGTGA
15105 AAGGAGTAGGAAATGAACTGCCATAAGCACCAAGAAAAACGAAAACCCAAATTAGGTTGAAAGCG
131 AAGGAGTAGGAAATGAACTGCCATAAGCACCAAGAAAAACGAAAACCCAAATTAGGTTGAAAGCG
*
15170 AAGGCAAAACAAAGGAGAAAGGCCCTAGATTCTCAAGAAATGCGCAATACTTAAAGCATAATCTC
196 AAGGCAAAACAAAGGAGAAAGGCCCTAGATTATCAAGAAATGCGCAATACTTAAAGCATAATCTC
15235 AACCAGCCTTTGTG
261 AACCAGCCTTTGTG
15249 GGTAGGCCTACAGGCTG-ATAACAATACTGGCACATCAAAGACAAATACAAGAAATAATTTCAGT
1 GGTAGGCCTACAGGCTGTATAACAATACTGGCACATCAAAGACAAATACAAGAAATAATTTCAGT
* *
15313 TATAGGATACC-TAGAATCAACATAATTCTGGAAGGAGATATAGCAGGAGCCAAAACAA-ACTAA
66 TATAGGA-ACCATAGAATCAACATAATTCTAGAAGGAGAAATAGCAGG-G-CAAAA-AATACT-A
* * *
15376 TGTGAAAGGAGTAGGAAATGAACTGCTATATGCACCCTCAAGAAAACCGAAAACCCAAATTAGGT
126 TGTGAAAGGAGTAGGAAATGAACTGCCATAAGCA--C-CAAGAAAAACGAAAACCCAAATTAGGT
15441 TGAAAGC-ATAGGCAAAACAAAGGAGAAAGGCCCTAGATTATCAAGAAATGCGCAATACTTAAAG
188 TGAAAGCGA-AGGCAAAACAAAGGAGAAAGGCCCTAGATTATCAAGAAATGCGCAATACTTAAAG
15505 CATAATCTCAAC
252 CATAATCTCAAC
15517 ATCCTATCAC
Statistics
Matches: 244, Mismatches: 15, Indels: 13
0.90 0.06 0.05
Matches are distributed among these distances:
273 82 0.34
274 20 0.08
275 6 0.02
276 35 0.14
278 2 0.01
279 99 0.41
ACGTcount: A:0.43, C:0.18, G:0.20, T:0.19
Consensus pattern (274 bp):
GGTAGGCCTACAGGCTGTATAACAATACTGGCACATCAAAGACAAATACAAGAAATAATTTCAGT
TATAGGAACCATAGAATCAACATAATTCTAGAAGGAGAAATAGCAGGGCAAAAAATACTATGTGA
AAGGAGTAGGAAATGAACTGCCATAAGCACCAAGAAAAACGAAAACCCAAATTAGGTTGAAAGCG
AAGGCAAAACAAAGGAGAAAGGCCCTAGATTATCAAGAAATGCGCAATACTTAAAGCATAATCTC
AACCAGCCTTTGTG
Found at i:18089 original size:4 final size:4
Alignment explanation
Indices: 18082--18128 Score: 94
Period size: 4 Copynumber: 11.8 Consensus size: 4
18072 AAGCATACAT
18082 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
18129 TATATATATA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 43 1.00
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:20493 original size:17 final size:18
Alignment explanation
Indices: 20455--20494 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
20445 ATTTTGGTGG
*
20455 TATTTTATATATTATATTA
1 TATTATATATATTATA-TA
20474 TATTATATATATTATA-A
1 TATTATATATATTATATA
20491 TATT
1 TATT
20495 CTGAAAGTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 5 0.25
19 15 0.75
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TATTATATATATTATATA
Done.