Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016082.1 Corchorus olitorius cultivar O-4 contig16115, 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: 36606
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:12 original size:1 final size:1
Alignment explanation
Indices: 7--52 Score: 74
Period size: 1 Copynumber: 46.0 Consensus size: 1
1 AAAAGT
* *
7 AAAAAAAAAGAAAAAAAAAATAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
53 CTAAATGAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
1 41 1.00
ACGTcount: A:0.96, C:0.00, G:0.02, T:0.02
Consensus pattern (1 bp):
A
Found at i:16 original size:11 final size:10
Alignment explanation
Indices: 1--52 Score: 65
Period size: 10 Copynumber: 5.3 Consensus size: 10
1 AAAAGTAAAAA
1 AAAAG-AAAAA
12 AAAAGAAAAA
1 AAAAGAAAAA
22 AAAA-ATAAAA
1 AAAAGA-AAAA
32 AAAA-AAAAA
1 AAAAGAAAAA
41 AAAA-AAAAA
1 AAAAGAAAAA
50 AAA
1 AAA
53 CTAAATGAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
9 17 0.43
10 18 0.45
11 5 0.12
ACGTcount: A:0.92, C:0.00, G:0.04, T:0.04
Consensus pattern (10 bp):
AAAAGAAAAA
Found at i:32552 original size:46 final size:46
Alignment explanation
Indices: 32499--32591 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
32489 TAATGCAGTT
32499 TCCGTAATATTTTTTCACAAATAAAATGCATTGTTAGTCATAACCC
1 TCCGTAATATTTTTTCACAAATAAAATGCATTGTTAGTCATAACCC
32545 TCCGTAATATTTTTTCACAAATAAAATGCATTGTTAGTCATAACCC
1 TCCGTAATATTTTTTCACAAATAAAATGCATTGTTAGTCATAACCC
32591 T
1 T
32592 AGTTTTGTCT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.34, C:0.19, G:0.09, T:0.38
Consensus pattern (46 bp):
TCCGTAATATTTTTTCACAAATAAAATGCATTGTTAGTCATAACCC
Found at i:34791 original size:20 final size:20
Alignment explanation
Indices: 34768--34805 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
34758 GGTGGTTGAG
34768 TTTTATAGTTG-TAAAATTCA
1 TTTT-TAGTTGATAAAATTCA
*
34788 TTTTTTGTTGATAAAATT
1 TTTTTAGTTGATAAAATT
34806 GTAACGTGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.32, C:0.03, G:0.11, T:0.55
Consensus pattern (20 bp):
TTTTTAGTTGATAAAATTCA
Found at i:35651 original size:121 final size:120
Alignment explanation
Indices: 35437--35678 Score: 466
Period size: 121 Copynumber: 2.0 Consensus size: 120
35427 CTCTTCTAAA
*
35437 GTGTGTAGCATTTAAACAAAAACTAAGTTTACTCTCTTCTTCATATGGACATGAAAGGCCTGAAA
1 GTGTGTAGCATTTAAACAAAAACTAAGTTTACTCTCTTCTTCATATGGACATGAAAGGCCTAAAA
35502 GAGGTTACAATTCTAGATAATTAAGGGGGGATAGGATTTTATTATAACATTTATGT
66 GAGGTTACAATTCTAGATAATTAAGGGGGGATAGGA-TTTATTATAACATTTATGT
35558 GTGTGTAGCATTTAAACAAAAACTAAGTTTACTCTCTTCTTCATATGGACATGAAAGGCCTAAAA
1 GTGTGTAGCATTTAAACAAAAACTAAGTTTACTCTCTTCTTCATATGGACATGAAAGGCCTAAAA
35623 GAGGTTACAATTCTAGATAATTAAGGGGGGATAGGATTTATTATAACATTTATGT
66 GAGGTTACAATTCTAGATAATTAAGGGGGGATAGGATTTATTATAACATTTATGT
35678 G
1 G
35679 AAAGGAAAGG
Statistics
Matches: 120, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
120 20 0.17
121 100 0.83
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (120 bp):
GTGTGTAGCATTTAAACAAAAACTAAGTTTACTCTCTTCTTCATATGGACATGAAAGGCCTAAAA
GAGGTTACAATTCTAGATAATTAAGGGGGGATAGGATTTATTATAACATTTATGT
Found at i:35940 original size:122 final size:122
Alignment explanation
Indices: 35723--35968 Score: 474
Period size: 122 Copynumber: 2.0 Consensus size: 122
35713 GTAAGAAACT
35723 AACCTAGGGTCTTCTTAGTAATTTGACAAGTGAGAAAAGACAGAAAATGACAAAAAAAGTTCAAA
1 AACCTAGGGTCTTCTTAGTAATTTGACAAGTGAGAAAAGACAGAAAATGACAAAAAAAGTTCAAA
*
35788 TGGAGCATCCTCATCGATTCTCAAAAGGGACATTTGGTAAATTCCCTGGGTCTTTCA
66 TGGAGCATCCTCATCGATTCTCAAAAGGGACATTTGGTAAATTCCCTAGGTCTTTCA
35845 AACCTAGGGTCTTCTTAGTAATTTGACAAGTGAGAAAAGACAGAAAATGACAAAAAAAGTTCAAA
1 AACCTAGGGTCTTCTTAGTAATTTGACAAGTGAGAAAAGACAGAAAATGACAAAAAAAGTTCAAA
*
35910 TGGAGTATCCTCATCGATTCTCAAAAGGGACATTTGGTAAATTCCCTAGGTCTTTCA
66 TGGAGCATCCTCATCGATTCTCAAAAGGGACATTTGGTAAATTCCCTAGGTCTTTCA
35967 AA
1 AA
35969 TAATATTTAG
Statistics
Matches: 122, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
122 122 1.00
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.26
Consensus pattern (122 bp):
AACCTAGGGTCTTCTTAGTAATTTGACAAGTGAGAAAAGACAGAAAATGACAAAAAAAGTTCAAA
TGGAGCATCCTCATCGATTCTCAAAAGGGACATTTGGTAAATTCCCTAGGTCTTTCA
Found at i:35986 original size:2 final size:2
Alignment explanation
Indices: 35979--36015 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
35969 TAATATTTAG
35979 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
36016 TTCCAAACTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.