Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013711.1 Corchorus capsularis cultivar CVL-1 contig13732, 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: 48335
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:228 original size:12 final size:12
Alignment explanation
Indices: 211--246 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
201 AAATTAATAC
*
211 TATATATATATA
1 TATATATCTATA
223 TATATATCTATA
1 TATATATCTATA
*
235 TCTATATCTATA
1 TATATATCTATA
247 CTAATTATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (12 bp):
TATATATCTATA
Found at i:368 original size:20 final size:20
Alignment explanation
Indices: 329--370 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
319 AAAATAAAAT
*
329 AAAACTACCCATTTTAGATA
1 AAAACTACCCATTATAGATA
349 AAAACTACCCA-TATAGGATA
1 AAAACTACCCATTATA-GATA
369 AA
1 AA
371 TATAATATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 3 0.15
20 17 0.85
ACGTcount: A:0.50, C:0.19, G:0.07, T:0.24
Consensus pattern (20 bp):
AAAACTACCCATTATAGATA
Found at i:1210 original size:2 final size:2
Alignment explanation
Indices: 1203--1230 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1193 GAAACATGAC
1203 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1231 GTTTCTATTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:7713 original size:2 final size:2
Alignment explanation
Indices: 7706--7730 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
7696 AGGAAGCATA
7706 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 A
7731 ATTCAGTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:8725 original size:26 final size:22
Alignment explanation
Indices: 8668--8713 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
8658 GGTACAAAAC
8668 TACATTACCATTTTTTTATATA
1 TACATTACCATTTTTTTATATA
8690 TACATTACCATTTTTTTATATA
1 TACATTACCATTTTTTTATATA
8712 TA
1 TA
8714 TCTGCATTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.33, C:0.13, G:0.00, T:0.54
Consensus pattern (22 bp):
TACATTACCATTTTTTTATATA
Found at i:9054 original size:59 final size:60
Alignment explanation
Indices: 8979--9137 Score: 180
Period size: 59 Copynumber: 2.7 Consensus size: 60
8969 TGACGCCAGG
** * *
8979 CCCTTATTTGAGCATTTTCGATAATGTTAGGCCCTTATTTGACCAAATTAAAAG-ATGAGA
1 CCCTTATTTGAGCATTTTCGATAACATTAGACCCTTATTTGACCAAATTAAAAGAACGA-A
* * *
9039 -CCTTATTTGAGCATTTTCGGTAACATTAGACCCTTATTTGGCTAAATTAAAAGAACGAA
1 CCCTTATTTGAGCATTTTCGATAACATTAGACCCTTATTTGACCAAATTAAAAGAACGAA
* * * *
9098 CCCTTATTTAAGCATTTTGGCA-AATATTAAACCCTTATTT
1 CCCTTATTTGAGCATTTTCG-ATAACATTAGACCCTTATTT
9138 AAGCAATTAA
Statistics
Matches: 84, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
59 48 0.57
60 36 0.43
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (60 bp):
CCCTTATTTGAGCATTTTCGATAACATTAGACCCTTATTTGACCAAATTAAAAGAACGAA
Found at i:9076 original size:31 final size:31
Alignment explanation
Indices: 8979--9078 Score: 89
Period size: 31 Copynumber: 3.3 Consensus size: 31
8969 TGACGCCAGG
** *
8979 CCCTTATTTGAGCATTTTCGATAATGTTAGG
1 CCCTTATTTGAGCATTTTCGATAACATTAGA
* ** * * *
9010 CCCTTATTTGACCAAATT--AAAAGATGAGA
1 CCCTTATTTGAGCATTTTCGATAACATTAGA
*
9039 -CCTTATTTGAGCATTTTCGGTAACATTAGA
1 CCCTTATTTGAGCATTTTCGATAACATTAGA
9069 CCCTTATTTG
1 CCCTTATTTG
9079 GCTAAATTAA
Statistics
Matches: 51, Mismatches: 15, Indels: 6
0.71 0.21 0.08
Matches are distributed among these distances:
28 14 0.27
29 6 0.12
30 7 0.14
31 24 0.47
ACGTcount: A:0.28, C:0.18, G:0.16, T:0.38
Consensus pattern (31 bp):
CCCTTATTTGAGCATTTTCGATAACATTAGA
Found at i:32661 original size:20 final size:20
Alignment explanation
Indices: 32633--32671 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
32623 TTTGATCACC
*
32633 AAATTTTAAAAACTAATAGA
1 AAATCTTAAAAACTAATAGA
*
32653 AAATCTTAAAAGCTAATAG
1 AAATCTTAAAAACTAATAG
32672 CTTGCTCAGA
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:0.56, C:0.08, G:0.08, T:0.28
Consensus pattern (20 bp):
AAATCTTAAAAACTAATAGA
Found at i:32892 original size:16 final size:16
Alignment explanation
Indices: 32871--32906 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
32861 ATGACAAATA
32871 TAATCATAACGTGTAC
1 TAATCATAACGTGTAC
32887 TAATCATAACGTGTAC
1 TAATCATAACGTGTAC
32903 TAAT
1 TAAT
32907 AGTTTTGTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.33
Consensus pattern (16 bp):
TAATCATAACGTGTAC
Found at i:34550 original size:2 final size:2
Alignment explanation
Indices: 34543--34576 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
34533 TCTTTGGGAA
*
34543 AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
34577 TAGACAATGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:37936 original size:1 final size:1
Alignment explanation
Indices: 37930--37969 Score: 80
Period size: 1 Copynumber: 40.0 Consensus size: 1
37920 CGGACAAGTC
37930 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
37970 GTTGCAGAGG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 39 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Done.