Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015152.1 Corchorus olitorius cultivar O-4 contig15185, 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: 9193
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Found at i:905 original size:421 final size:419
Alignment explanation
Indices: 1--934 Score: 1674
Period size: 421 Copynumber: 2.2 Consensus size: 419
1 TGGTAAGTATCTAAATTTAAGATATCATTATGATAGAATTTACTAAGTTGTGACTATATTAGT-G
1 TGGTAAGTATCTAAATTTAAGATATCATTATGATAGAATTTACTAAGTTGTGACTATATTAGTGG
65 --G---T--T-G-TGATATGGTGAGACAATCTCACCTAAACTAGTTTTGAGATTTGATTAATTTG
66 TTGTTCTCATAGCTGATATGGTGAGACAATCTCACCTAAACTAGTTTTGAGATTTGATTAATTTG
121 GGAATTGAGTGGCGGCCACTCTAAATAAAAAGAAAAAAAACTATTATTAATATAACACATACTTT
131 GGAATTGAGTGGCGGCCACTCTAAATAAAAAGAAAAAAAACTATTATTAATATAACACATACTTT
* *
186 TTCTATCCATAATATTCGAATCGGAAAATTTTCTTAAAATTGACATTATACTAGTAAGTGGCAAG
196 TTCTATCCATAATATTCGAATCGGAAAATTTTCTTAAAATCGACATTATACTAGCAAGTGGCAAG
*
251 CTACTTAAGGGATAAATTATTAGACAGAACTGTTTTACCATGTCAGGCATGAAACCAACCACAAA
261 CTACTTAAGGGATAAATTATTAGACAGAACTGTCTTACCATGTCAGGCATGAAACCAACCACAAA
* *
316 TTGTACCACATCACATAAAAAAAATCAATTCCTAAAATTTAAACAGAATTTTAGTCCAAAATTTA
326 TTGTACCAAATCACATAAAAAAAATCAATTCCTAAAATTTAAACAGAATGTTAGTCCAAAATTTA
381 ACCCCATTTGGAAATAAACGATGCGGAAA
391 ACCCCATTTGGAAATAAACGATGCGGAAA
* * *
410 TGGTAAGTATCTAAATTTAAGGTGTCATTATGATAGAATTTACTAAGTTGTGACTACATTAGTGG
1 TGGTAAGTATCTAAATTTAAGATATCATTATGATAGAATTTACTAAGTTGTGACTATATTAGTGG
475 TTGTTCTCATAGCTGATATGGTGAGACAATCTCACCTAAACTAGTTTTGAGATTTGATTAATTTG
66 TTGTTCTCATAGCTGATATGGTGAGACAATCTCACCTAAACTAGTTTTGAGATTTGATTAATTTG
*
540 GGAATTGAGTGGCGGCCACTCTAAATAAAAA-AAAAAAAACTATTATTAGTATAACACATACTTT
131 GGAATTGAGTGGCGGCCACTCTAAATAAAAAGAAAAAAAACTATTATTAATATAACACATACTTT
604 TTCTATATCCATAATATTCGAATCGGAAAATTTTCTTAAAATCGACATTATACTAGCAAGTGGCA
196 TTC--TATCCATAATATTCGAATCGGAAAATTTTCTTAAAATCGACATTATACTAGCAAGTGGCA
669 AGCTACTTAAGGGATAAATTATTAGACAGAACTGTCTTACCATGTCAGGCATGAAACCAACCACA
259 AGCTACTTAAGGGATAAATTATTAGACAGAACTGTCTTACCATGTCAGGCATGAAACCAACCACA
*
734 AATTGTACCAAATCACATAAAAAAAAATCAATTCCTAAAATTTAAACAGAATGTTAGTCCAAGAT
324 AATTGTACCAAATCACAT-AAAAAAAATCAATTCCTAAAATTTAAACAGAATGTTAGTCCAAAAT
799 TTAACCCCATTTGGAAATAAACGATGCGGAAA
388 TTAACCCCATTTGGAAATAAACGATGCGGAAA
831 TGGTAAGTATCTAAATTTAAGATATCATTATGATAGAATTTACTAAGTTGTGACTATATTAGTGG
1 TGGTAAGTATCTAAATTTAAGATATCATTATGATAGAATTTACTAAGTTGTGACTATATTAGTGG
896 TTGTTCTCATAGCTGATATGGTGAGACAATCTCACCTAA
66 TTGTTCTCATAGCTGATATGGTGAGACAATCTCACCTAA
935 TAATTTCTCT
Statistics
Matches: 499, Mismatches: 13, Indels: 14
0.95 0.02 0.03
Matches are distributed among these distances:
409 60 0.12
410 1 0.00
412 1 0.00
415 1 0.00
417 1 0.00
418 36 0.07
419 83 0.17
420 139 0.28
421 177 0.35
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.32
Consensus pattern (419 bp):
TGGTAAGTATCTAAATTTAAGATATCATTATGATAGAATTTACTAAGTTGTGACTATATTAGTGG
TTGTTCTCATAGCTGATATGGTGAGACAATCTCACCTAAACTAGTTTTGAGATTTGATTAATTTG
GGAATTGAGTGGCGGCCACTCTAAATAAAAAGAAAAAAAACTATTATTAATATAACACATACTTT
TTCTATCCATAATATTCGAATCGGAAAATTTTCTTAAAATCGACATTATACTAGCAAGTGGCAAG
CTACTTAAGGGATAAATTATTAGACAGAACTGTCTTACCATGTCAGGCATGAAACCAACCACAAA
TTGTACCAAATCACATAAAAAAAATCAATTCCTAAAATTTAAACAGAATGTTAGTCCAAAATTTA
ACCCCATTTGGAAATAAACGATGCGGAAA
Found at i:2202 original size:48 final size:48
Alignment explanation
Indices: 2121--2216 Score: 129
Period size: 48 Copynumber: 2.0 Consensus size: 48
2111 TTAACTAAGG
* * * *
2121 TTTCTATTCAAGTCTTATGAATGTCGAGAATAGGTATTGTAAGAGCTT
1 TTTCCATTCAAGTCTTATGAATGTCAAAAATAGGTATTGGAAGAGCTT
* * *
2169 TTTCCATTCGAGTCTTGTGAATGTCAAAAATAGGTATTGGGAGAGCTT
1 TTTCCATTCAAGTCTTATGAATGTCAAAAATAGGTATTGGAAGAGCTT
2217 CTCCAAATGG
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
48 41 1.00
ACGTcount: A:0.28, C:0.11, G:0.23, T:0.38
Consensus pattern (48 bp):
TTTCCATTCAAGTCTTATGAATGTCAAAAATAGGTATTGGAAGAGCTT
Found at i:2949 original size:3 final size:3
Alignment explanation
Indices: 2941--2969 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
2931 CCTGGTCAGT
2941 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
2970 GAACATTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:4528 original size:20 final size:20
Alignment explanation
Indices: 4503--4541 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
4493 GCCATGTCAT
4503 GCCACATCAGCAATTTTTGG
1 GCCACATCAGCAATTTTTGG
**
4523 GCCACATTTGCAATTTTTG
1 GCCACATCAGCAATTTTTG
4542 ACAACCGAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.23, C:0.23, G:0.18, T:0.36
Consensus pattern (20 bp):
GCCACATCAGCAATTTTTGG
Found at i:9156 original size:59 final size:57
Alignment explanation
Indices: 9058--9171 Score: 158
Period size: 59 Copynumber: 1.9 Consensus size: 57
9048 ATTAATCAAA
*
9058 TATCAAGTGACATGTTCTTTATTAGATGCATTAAAAAAGACGTTTTCGGACCGAGACT
1 TATCAAGTGACATGTTCTTTATTAGATGCA-TAAAAAAGACGTTTTAGGACCGAGACT
* *
9116 TATCGAAGTGACATGTTTTTTTATTAGATGTC-TAAGAAAGACGTTTTAGGACCGAG
1 TATC-AAGTGACATG-TTCTTTATTAGATG-CATAAAAAAGACGTTTTAGGACCGAG
9172 GCATGATGCT
Statistics
Matches: 50, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
58 4 0.08
59 32 0.64
60 13 0.26
61 1 0.02
ACGTcount: A:0.32, C:0.13, G:0.21, T:0.34
Consensus pattern (57 bp):
TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAGACGTTTTAGGACCGAGACT
Done.