Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007930.1 Corchorus capsularis cultivar CVL-1 contig07951, 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: 13959
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Found at i:849 original size:27 final size:27
Alignment explanation
Indices: 811--869 Score: 91
Period size: 27 Copynumber: 2.2 Consensus size: 27
801 TATTTCTAGA
*
811 AAACAAGGGAAAGAGACAATTAAAAAG
1 AAACAAGAGAAAGAGACAATTAAAAAG
*
838 AAACAAGAGAAAGGGACAATTAAAAAG
1 AAACAAGAGAAAGAGACAATTAAAAAG
*
865 GAACA
1 AAACA
870 GAGGGAGTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.63, C:0.08, G:0.22, T:0.07
Consensus pattern (27 bp):
AAACAAGAGAAAGAGACAATTAAAAAG
Found at i:3356 original size:16 final size:15
Alignment explanation
Indices: 3337--3410 Score: 59
Period size: 15 Copynumber: 5.1 Consensus size: 15
3327 AAGAATGTAT
3337 TTTTTTAAAGGATTTA
1 TTTTTT-AAGGATTTA
*
3353 TTTTTGAAGGA--TA
1 TTTTTTAAGGATTTA
* *
3366 ---TTTAAGAATGTA
1 TTTTTTAAGGATTTA
3378 TTTTTTAAAGGATTTA
1 TTTTTT-AAGGATTTA
*
3394 TTTTTTAAGGATATA
1 TTTTTTAAGGATTTA
3409 TT
1 TT
3411 ATAGATAATA
Statistics
Matches: 46, Mismatches: 6, Indels: 13
0.71 0.09 0.20
Matches are distributed among these distances:
10 6 0.13
12 2 0.04
13 2 0.04
15 18 0.39
16 18 0.39
ACGTcount: A:0.32, C:0.00, G:0.15, T:0.53
Consensus pattern (15 bp):
TTTTTTAAGGATTTA
Found at i:3394 original size:41 final size:42
Alignment explanation
Indices: 3314--3407 Score: 172
Period size: 41 Copynumber: 2.3 Consensus size: 42
3304 TTCTCCATTG
3314 TTGAAGGATATTTAAGAATGTATTTTTTTAAAGGATTTATTT
1 TTGAAGGATATTTAAGAATGTATTTTTTTAAAGGATTTATTT
3356 TTGAAGGATATTTAAGAATGTA-TTTTTTAAAGGATTTATTT
1 TTGAAGGATATTTAAGAATGTATTTTTTTAAAGGATTTATTT
*
3397 TTTAAGGATAT
1 TTGAAGGATAT
3408 ATTATAGATA
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 29 0.57
42 22 0.43
ACGTcount: A:0.34, C:0.00, G:0.17, T:0.49
Consensus pattern (42 bp):
TTGAAGGATATTTAAGAATGTATTTTTTTAAAGGATTTATTT
Found at i:10943 original size:329 final size:329
Alignment explanation
Indices: 10345--11005 Score: 1295
Period size: 329 Copynumber: 2.0 Consensus size: 329
10335 AAATTAGCTT
10345 TTGAGTTCTTCATGAAAGTTGTAGACCATGAAATTACCATTTAAGGGACACTTGAATCACCTTAA
1 TTGAGTTCTTCATGAAAGTTGTAGACCATGAAATTACCATTTAAGGGACACTTGAATCACCTTAA
10410 TCGGACAAATAAAACTAAAATTAAATAAGTAAAATTGAAGCGTTAGATCAAATAAATTAGAATTT
66 TCGGACAAATAAAACTAAAATTAAATAAGTAAAATTGAAGCGTTAGATCAAATAAATTAGAATTT
*
10475 GTAAAGGACTAAGTAGGATAACATTTAAAACTATGAGGGTTATTTGATAAATAAAAAAATATATT
131 GTAAAGAACTAAGTAGGATAACATTTAAAACTATGAGGGTTATTTGATAAATAAAAAAATATATT
*
10540 TGTTGGTGGAGGTGGGCCCATTAAGGGTAATTTTTGGCAAAGTTCCGAAAATGCCCTTAGCAATT
196 TGTTGGTGGAGGTGGGCCCATTAAGGGTAATTTTTGGCAAAGTTCCGAAAATACCCTTAGCAATT
10605 TTCCTAAATAACAAAATAACCAAGTATGATATGACTAAAATACCTTCTGCTCTTCGTTCAATGTG
261 TTCCTAAATAACAAAATAACCAAGTATGATATGACTAAAATACCTTCTGCTCTTCGTTCAATGTG
10670 ATGA
326 ATGA
10674 TTGAGTTCTTCATGAAAGTTGTAGACCATGAAATTACCATTTAAGGGACACTTGAATCACCTTAA
1 TTGAGTTCTTCATGAAAGTTGTAGACCATGAAATTACCATTTAAGGGACACTTGAATCACCTTAA
10739 TCGGACAAATAAAACTAAAATTAAATAAGTAAAATTGAAGCGTTAGATCAAATAAATTAGAATTT
66 TCGGACAAATAAAACTAAAATTAAATAAGTAAAATTGAAGCGTTAGATCAAATAAATTAGAATTT
*
10804 GTAAAGAACTAAGTAGGATAACGTTTAAAACTATGAGGGTTATTTGATAAATAAAAAAATATATT
131 GTAAAGAACTAAGTAGGATAACATTTAAAACTATGAGGGTTATTTGATAAATAAAAAAATATATT
10869 TGTTGGTGGAGGTGGGCCCATTAAGGGTAATTTTTGGCAAAGTTCCGAAAATACCCTTAGCAATT
196 TGTTGGTGGAGGTGGGCCCATTAAGGGTAATTTTTGGCAAAGTTCCGAAAATACCCTTAGCAATT
10934 TTCCTAAATAACAAAATAACCAAGTATGATATGACTAAAATACCTTCTGCTCTTCGTTCAATGTG
261 TTCCTAAATAACAAAATAACCAAGTATGATATGACTAAAATACCTTCTGCTCTTCGTTCAATGTG
10999 ATGA
326 ATGA
11003 TTG
1 TTG
11006 GGTTAGAAAT
Statistics
Matches: 329, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
329 329 1.00
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.31
Consensus pattern (329 bp):
TTGAGTTCTTCATGAAAGTTGTAGACCATGAAATTACCATTTAAGGGACACTTGAATCACCTTAA
TCGGACAAATAAAACTAAAATTAAATAAGTAAAATTGAAGCGTTAGATCAAATAAATTAGAATTT
GTAAAGAACTAAGTAGGATAACATTTAAAACTATGAGGGTTATTTGATAAATAAAAAAATATATT
TGTTGGTGGAGGTGGGCCCATTAAGGGTAATTTTTGGCAAAGTTCCGAAAATACCCTTAGCAATT
TTCCTAAATAACAAAATAACCAAGTATGATATGACTAAAATACCTTCTGCTCTTCGTTCAATGTG
ATGA
Found at i:12603 original size:16 final size:16
Alignment explanation
Indices: 12582--12614 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
12572 TGAAATATCA
*
12582 AAATCTATATATCTAT
1 AAATCTATAGATCTAT
12598 AAATCTATAGATCTAT
1 AAATCTATAGATCTAT
12614 A
1 A
12615 CAATATATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.45, C:0.12, G:0.03, T:0.39
Consensus pattern (16 bp):
AAATCTATAGATCTAT
Found at i:13818 original size:16 final size:16
Alignment explanation
Indices: 13797--13830 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
13787 CAATTTTCTT
*
13797 AAGACTTACAAGTTAC
1 AAGACTCACAAGTTAC
13813 AAGACTCACAAGTTAC
1 AAGACTCACAAGTTAC
13829 AA
1 AA
13831 CATATGTAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.47, C:0.21, G:0.12, T:0.21
Consensus pattern (16 bp):
AAGACTCACAAGTTAC
Done.