Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012577.1 Corchorus capsularis cultivar CVL-1 contig12598, 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: 28117
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Found at i:793 original size:9 final size:9
Alignment explanation
Indices: 781--814 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
771 TTGCCCTAGC
781 TAGTTTAGT
1 TAGTTTAGT
790 TAGTTTAGT
1 TAGTTTAGT
*
799 TAGTTTAGC
1 TAGTTTAGT
808 TAGTTTA
1 TAGTTTA
815 ATAGATCCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.24, C:0.03, G:0.21, T:0.53
Consensus pattern (9 bp):
TAGTTTAGT
Found at i:1235 original size:5 final size:5
Alignment explanation
Indices: 1225--1255 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
1215 CAAAAGCAAA
1225 CCAAG CCAAG CCAAG CCAAG CCAAG CCAAG C
1 CCAAG CCAAG CCAAG CCAAG CCAAG CCAAG C
1256 AAGAAGAAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.39, C:0.42, G:0.19, T:0.00
Consensus pattern (5 bp):
CCAAG
Found at i:9577 original size:2 final size:2
Alignment explanation
Indices: 9565--9622 Score: 63
Period size: 2 Copynumber: 31.0 Consensus size: 2
9555 TTCTAAAATT
9565 TA TA T- TA TA TA TA TA TA TA TA -A TA TA TCA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA
*
9605 -A AA TA TA TA T- TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA
9623 AAATTATAAA
Statistics
Matches: 49, Mismatches: 1, Indels: 12
0.79 0.02 0.19
Matches are distributed among these distances:
1 5 0.10
2 42 0.86
3 2 0.04
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:9589 original size:7 final size:7
Alignment explanation
Indices: 9565--9620 Score: 67
Period size: 7 Copynumber: 7.9 Consensus size: 7
9555 TTCTAAAATT
*
9565 TATATTA
1 TATATAA
9572 TATATATA
1 TATATA-A
9580 TATATAA
1 TATATAA
*
9587 TATATCA
1 TATATAA
9594 TATATAA
1 TATATAA
*
9601 TATAAAA
1 TATATAA
*
9608 TATATAT
1 TATATAA
9615 TATATA
1 TATATA
9621 TAAAATTATA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
7 35 0.83
8 7 0.17
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (7 bp):
TATATAA
Found at i:10208 original size:28 final size:26
Alignment explanation
Indices: 10151--10211 Score: 81
Period size: 24 Copynumber: 2.3 Consensus size: 26
10141 AATATTGTTA
*
10151 AAGAGGTTGGTTGAGATTAAAATTGG
1 AAGAGTTTGGTTGAGATTAAAATTGG
10177 --GAGTTTGGTTGAGATTAAAATTGG
1 AAGAGTTTGGTTGAGATTAAAATTGG
10201 TTAAGAGTTTG
1 --AAGAGTTTG
10212 TCTAAAAGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
24 23 0.77
28 7 0.23
ACGTcount: A:0.31, C:0.00, G:0.33, T:0.36
Consensus pattern (26 bp):
AAGAGTTTGGTTGAGATTAAAATTGG
Found at i:13882 original size:21 final size:22
Alignment explanation
Indices: 13834--13884 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 22
13824 GCGTCAGAGA
*
13834 TATGGGGGCCAAGTTCCACCAT
1 TATGGGGCCCAAGTTCCACCAT
*
13856 T-CGGGGCCCAAGTTCCACC-T
1 TATGGGGCCCAAGTTCCACCAT
13876 TATGGGGCC
1 TATGGGGCC
13885 GCCCAACCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 2 0.08
21 22 0.88
22 1 0.04
ACGTcount: A:0.18, C:0.31, G:0.29, T:0.22
Consensus pattern (22 bp):
TATGGGGCCCAAGTTCCACCAT
Found at i:17377 original size:15 final size:16
Alignment explanation
Indices: 17357--17390 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
17347 GATTGATTTC
*
17357 TTAGTTA-ATTTACTT
1 TTAGTTAGATTTAATT
17372 TTAGTTAGATTTAATT
1 TTAGTTAGATTTAATT
17388 TTA
1 TTA
17391 ATTTTTCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.29, C:0.03, G:0.09, T:0.59
Consensus pattern (16 bp):
TTAGTTAGATTTAATT
Found at i:25750 original size:21 final size:21
Alignment explanation
Indices: 25726--25774 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
25716 CAGCTGGGGG
* * *
25726 CCCATGTGGTATGCTTGGCGC
1 CCCATGTGGTATGCCTCGCGA
*
25747 CCCATGTGGTTTGCCTCGCGA
1 CCCATGTGGTATGCCTCGCGA
25768 CCCATGT
1 CCCATGT
25775 CCTCCAGTGC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.10, C:0.33, G:0.29, T:0.29
Consensus pattern (21 bp):
CCCATGTGGTATGCCTCGCGA
Found at i:26739 original size:19 final size:20
Alignment explanation
Indices: 26723--26768 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
26713 CCTTGCTATA
26723 TAATGAAAA-TTTTGCTAAG
1 TAATGAAAATTTTTGCTAAG
*
26742 TATTGAAAATTTTTGCTAAG
1 TAATGAAAATTTTTGCTAAG
26762 TAATGAA
1 TAATGAA
26769 GGGAAACTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 8 0.33
20 16 0.67
ACGTcount: A:0.41, C:0.04, G:0.15, T:0.39
Consensus pattern (20 bp):
TAATGAAAATTTTTGCTAAG
Found at i:27308 original size:47 final size:45
Alignment explanation
Indices: 27173--27332 Score: 214
Period size: 45 Copynumber: 3.5 Consensus size: 45
27163 AAACCAAGTT
* **
27173 TGTTCAAACTAAACTAAAACAGCCATGAAAGACTATTTGAAACCA
1 TGTTCAAACTAAACTAAAATAGCCATGAAAGACTATTTGTTACCA
* *
27218 TGTTCAAACTAAAATCAAATAGCCATGAAAGACTATTTGTTACCA
1 TGTTCAAACTAAACTAAAATAGCCATGAAAGACTATTTGTTACCA
* *
27263 TGTTCAAACTAAACTAAAAATAGCCAATTAAAGACTATTTGTTACCT
1 TGTTCAAACTAAACT-AAAATAGCC-ATGAAAGACTATTTGTTACCA
* *
27310 TGTTCAAAATAAAC-AAAACAGCC
1 TGTTCAAACTAAACTAAAATAGCC
27333 TATAGCAGCA
Statistics
Matches: 102, Mismatches: 11, Indels: 4
0.87 0.09 0.03
Matches are distributed among these distances:
45 62 0.61
46 8 0.08
47 32 0.31
ACGTcount: A:0.45, C:0.19, G:0.10, T:0.26
Consensus pattern (45 bp):
TGTTCAAACTAAACTAAAATAGCCATGAAAGACTATTTGTTACCA
Done.