Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012102.1 Corchorus olitorius cultivar O-4 contig12135, 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: 23574
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Found at i:2644 original size:6 final size:6
Alignment explanation
Indices: 2620--2653 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
2610 TTCTAAATGC
2620 TTTT-T TTTTCT TATTTCT TTTTCT TTTTCT TTTT
1 TTTTCT TTTTCT T-TTTCT TTTTCT TTTTCT TTTT
2654 TCTTCTTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
5 4 0.15
6 17 0.63
7 6 0.22
ACGTcount: A:0.03, C:0.12, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTCT
Found at i:2648 original size:19 final size:18
Alignment explanation
Indices: 2620--2657 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
2610 TTCTAAATGC
2620 TTTTTTTTTCTTATTTCT
1 TTTTTTTTTCTTATTTCT
*
2638 TTTTCTTTTTCTTTTTTCT
1 TTTT-TTTTTCTTATTTCT
2657 T
1 T
2658 CTTATTTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.84
Consensus pattern (18 bp):
TTTTTTTTTCTTATTTCT
Found at i:2654 original size:13 final size:14
Alignment explanation
Indices: 2623--2657 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
2613 TAAATGCTTT
2623 TTTTTTCTTATTTC
1 TTTTTTCTTATTTC
2637 -TTTTTCTT-TTTC
1 TTTTTTCTTATTTC
2649 TTTTTTCTT
1 TTTTTTCTT
2658 CTTATTTTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 4 0.20
13 16 0.80
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTTTTCTTATTTC
Found at i:2665 original size:19 final size:19
Alignment explanation
Indices: 2624--2666 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
2614 AAATGCTTTT
* *
2624 TTTTTCTTATTTCTTTTTC
1 TTTTTCTTATTTCTTCTTA
*
2643 TTTTTCTTTTTTCTTCTTA
1 TTTTTCTTATTTCTTCTTA
2662 TTTTT
1 TTTTT
2667 GTGTTTGGGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.05, C:0.14, G:0.00, T:0.81
Consensus pattern (19 bp):
TTTTTCTTATTTCTTCTTA
Found at i:13340 original size:93 final size:93
Alignment explanation
Indices: 13238--13422 Score: 289
Period size: 93 Copynumber: 2.0 Consensus size: 93
13228 GCTTTTTAAT
* *
13238 TAAATTAGTAATATAGTAAAAATAAAATAGGTATAAAGATATTAGATTTAATTAAATAAAAATAG
1 TAAAATAGTAAAATAGTAAAAATAAAATAGGTATAAAGATATTAGATTTAATTAAATAAAAATAG
***
13303 AGTTTTTAGTTTTGTAAAACTATAAAAG
66 AGTTTTTAGTTGACTAAAACTATAAAAG
* * *
13331 TAAAATAGTAAAATGGTAAAAATAAAATAGTTATAAGGATATTAGATTTAATTAAATAAAAATAG
1 TAAAATAGTAAAATAGTAAAAATAAAATAGGTATAAAGATATTAGATTTAATTAAATAAAAATAG
*
13396 AGTTTTTTGTTGACTAAAACTATAAAA
66 AGTTTTTAGTTGACTAAAACTATAAAA
13423 ATTTAAATAA
Statistics
Matches: 83, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 83 1.00
ACGTcount: A:0.52, C:0.02, G:0.12, T:0.35
Consensus pattern (93 bp):
TAAAATAGTAAAATAGTAAAAATAAAATAGGTATAAAGATATTAGATTTAATTAAATAAAAATAG
AGTTTTTAGTTGACTAAAACTATAAAAG
Found at i:13341 original size:22 final size:22
Alignment explanation
Indices: 13316--13361 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
13306 TTTTAGTTTT
*
13316 GTAAAACT-ATAAAAGTAAAATA
1 GTAAAA-TGATAAAAATAAAATA
*
13338 GTAAAATGGTAAAAATAAAATA
1 GTAAAATGATAAAAATAAAATA
13360 GT
1 GT
13362 TATAAGGATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 20 0.95
ACGTcount: A:0.61, C:0.02, G:0.13, T:0.24
Consensus pattern (22 bp):
GTAAAATGATAAAAATAAAATA
Found at i:13503 original size:31 final size:31
Alignment explanation
Indices: 13458--13519 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
13448 ATATTCAAAA
* *
13458 AATAAGGGTGTAATAGGCGATTCAAAAGTTT
1 AATAAAGGTATAATAGGCGATTCAAAAGTTT
*
13489 AATAAAGGTATAATAGGCGATTCAAATGTTT
1 AATAAAGGTATAATAGGCGATTCAAAAGTTT
13520 TACAAAACTC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.40, C:0.06, G:0.23, T:0.31
Consensus pattern (31 bp):
AATAAAGGTATAATAGGCGATTCAAAAGTTT
Found at i:13970 original size:26 final size:26
Alignment explanation
Indices: 13927--13976 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
13917 TGGGTCCTAC
*
13927 TAGCCATTATAGTGATTTTTATTAGG
1 TAGCCATTATAGTCATTTTTATTAGG
13953 TAGCCATTATCA-TCATTTTTATTA
1 TAGCCATTAT-AGTCATTTTTATTA
13977 CTATCATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 21 0.95
27 1 0.05
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.48
Consensus pattern (26 bp):
TAGCCATTATAGTCATTTTTATTAGG
Found at i:14010 original size:13 final size:13
Alignment explanation
Indices: 13959--14014 Score: 51
Period size: 13 Copynumber: 4.2 Consensus size: 13
13949 TAGGTAGCCA
13959 TTATC-ATCATTT
1 TTATCTATCATTT
13971 TTATTACTATCATTT
1 TTA-T-CTATCATTT
* ** *
13986 TTTTAGAACATTT
1 TTATCTATCATTT
13999 TTATCTATCATTT
1 TTATCTATCATTT
14012 TTA
1 TTA
14015 AAGAGTCAAA
Statistics
Matches: 33, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
12 3 0.09
13 19 0.58
14 2 0.06
15 9 0.27
ACGTcount: A:0.27, C:0.12, G:0.02, T:0.59
Consensus pattern (13 bp):
TTATCTATCATTT
Found at i:20586 original size:18 final size:19
Alignment explanation
Indices: 20554--20589 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
20544 TAACTAGTAA
*
20554 TAATAAATAATACTAATAT
1 TAATAAATAACACTAATAT
20573 TAAT-AATAACACTAATA
1 TAATAAATAACACTAATA
20590 ATTATTATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.33
Consensus pattern (19 bp):
TAATAAATAACACTAATAT
Found at i:21187 original size:2 final size:2
Alignment explanation
Indices: 21180--21214 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
21170 TATCCTTTAC
21180 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
21215 AGACATAAGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:21438 original size:2 final size:2
Alignment explanation
Indices: 21431--21460 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
21421 TTTCTAATTA
*
21431 AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
21461 TACAACACAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Done.