Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016503.1 Corchorus capsularis cultivar CVL-1 contig16524, 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: 58334
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:9 original size:2 final size:2
Alignment explanation
Indices: 3--67 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
1 CA
3 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
45 TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC T
68 TTTTCCCACA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:3366 original size:21 final size:21
Alignment explanation
Indices: 3320--3369 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
3310 AGAATTCCTC
* *
3320 TTTGGGCTATAAGACATCCGA
1 TTTGGGCTATAAGAAATCAGA
*
3341 GTTGGGCT-TAGAGAAATCAGA
1 TTTGGGCTATA-AGAAATCAGA
3362 TTTGGGCT
1 TTTGGGCT
3370 GGGCTTCTAG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 2 0.08
21 22 0.92
ACGTcount: A:0.26, C:0.14, G:0.30, T:0.30
Consensus pattern (21 bp):
TTTGGGCTATAAGAAATCAGA
Found at i:10234 original size:43 final size:43
Alignment explanation
Indices: 10186--10273 Score: 176
Period size: 43 Copynumber: 2.0 Consensus size: 43
10176 TGTTTCAATG
10186 ATCAGATCAACCCGAATAGTCGATGCTTGGGATTGGAGTATTT
1 ATCAGATCAACCCGAATAGTCGATGCTTGGGATTGGAGTATTT
10229 ATCAGATCAACCCGAATAGTCGATGCTTGGGATTGGAGTATTT
1 ATCAGATCAACCCGAATAGTCGATGCTTGGGATTGGAGTATTT
10272 AT
1 AT
10274 TTATCTTGTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (43 bp):
ATCAGATCAACCCGAATAGTCGATGCTTGGGATTGGAGTATTT
Found at i:11848 original size:22 final size:22
Alignment explanation
Indices: 11617--11993 Score: 183
Period size: 22 Copynumber: 17.0 Consensus size: 22
11607 TCAAGTCTAC
11617 AGGTTATCAAAATTT-ATAGTG
1 AGGTTATCAAAATTTCATAGTG
* * * *
11638 TGATTACCAAAATTTCATTGTG
1 AGGTTATCAAAATTTCATAGTG
* * **
11660 ATGTCATCAAAA-TTCATAGAA
1 AGGTTATCAAAATTTCATAGTG
*
11681 AGGTTATCAAAATTTCATGGTG
1 AGGTTATCAAAATTTCATAGTG
* * * * *
11703 AGATTAACGAAATTCCATAAGGG
1 AGGTTATCAAAATTTCAT-AGTG
* * * *
11726 A-GTTATTAACATTTGATAGGG
1 AGGTTATCAAAATTTCATAGTG
* *
11747 AAGTTATCAAAATTTCATAAT-
1 AGGTTATCAAAATTTCATAGTG
*
11768 ATGGTTATCAAAATTTTATAGTG
1 A-GGTTATCAAAATTTCATAGTG
*** **
11791 TACCATATCAACCTTTCACTA-TG
1 -AGGTTATCAAAATTTCA-TAGTG
* **
11814 TGGTTATTGAAATTTCATAGTG
1 AGGTTATCAAAATTTCATAGTG
* **
11836 AGGTCATCAAAATTAATTTCATACAG
1 AGGTTATC--AA--AATTTCATAGTG
*
11862 AGGTTATCACAATTTCATAGTG
1 AGGTTATCAAAATTTCATAGTG
* * *
11884 TGGGTTATCAAAATTTAAGAGTG
1 -AGGTTATCAAAATTTCATAGTG
* * * *
11907 TGGTTTTTAAAATATCATAGTG
1 AGGTTATCAAAATTTCATAGTG
* *
11929 TA-GTTATCAAAATTTCACAGGG
1 -AGGTTATCAAAATTTCATAGTG
* * * *
11951 AGGCTATCACAATTT-TTAAGGG
1 AGGTTATCAAAATTTCAT-AGTG
*
11973 AGATTATCAAAATTTCATAGT
1 AGGTTATCAAAATTTCATAGT
11994 AAGACTATGT
Statistics
Matches: 251, Mismatches: 87, Indels: 35
0.67 0.23 0.09
Matches are distributed among these distances:
21 37 0.15
22 158 0.63
23 34 0.14
24 5 0.02
26 17 0.07
ACGTcount: A:0.36, C:0.11, G:0.17, T:0.36
Consensus pattern (22 bp):
AGGTTATCAAAATTTCATAGTG
Found at i:11864 original size:26 final size:26
Alignment explanation
Indices: 11824--11875 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
11814 TGGTTATTGA
**
11824 AATTTCATAGTGAGGTCATCAAAATT
1 AATTTCATACAGAGGTCATCAAAATT
* *
11850 AATTTCATACAGAGGTTATCACAATT
1 AATTTCATACAGAGGTCATCAAAATT
11876 TCATAGTGTG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.35
Consensus pattern (26 bp):
AATTTCATACAGAGGTCATCAAAATT
Found at i:19677 original size:15 final size:16
Alignment explanation
Indices: 19657--19690 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
19647 GATTGCTCTC
*
19657 TTAGTTA-ATTTACTT
1 TTAGTTAGATTTAATT
19672 TTAGTTAGATTTAATT
1 TTAGTTAGATTTAATT
19688 TTA
1 TTA
19691 AATTCTTCTT
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:36000 original size:2 final size:2
Alignment explanation
Indices: 35995--36035 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
35985 TTTCTATACC
35995 TA TA TA TA T- TA TA T- TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
36034 TA
1 TA
36036 ATGACAATCC
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
1 3 0.08
2 33 0.92
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:40446 original size:138 final size:138
Alignment explanation
Indices: 40198--40474 Score: 554
Period size: 138 Copynumber: 2.0 Consensus size: 138
40188 TTTACTCTTT
40198 CTGTTTCAAAGATCAAATAAATAAAAAACTATTAACATGATGAACACCACGAACAACTTTCTCCA
1 CTGTTTCAAAGATCAAATAAATAAAAAACTATTAACATGATGAACACCACGAACAACTTTCTCCA
40263 ACCACCATGGGAATCACTGTCAACACCACCGCCACCCACCATAAATACCACCAACACCGGCACTA
66 ACCACCATGGGAATCACTGTCAACACCACCGCCACCCACCATAAATACCACCAACACCGGCACTA
40328 AAAATTCC
131 AAAATTCC
40336 CTGTTTCAAAGATCAAATAAATAAAAAACTATTAACATGATGAACACCACGAACAACTTTCTCCA
1 CTGTTTCAAAGATCAAATAAATAAAAAACTATTAACATGATGAACACCACGAACAACTTTCTCCA
40401 ACCACCATGGGAATCACTGTCAACACCACCGCCACCCACCATAAATACCACCAACACCGGCACTA
66 ACCACCATGGGAATCACTGTCAACACCACCGCCACCCACCATAAATACCACCAACACCGGCACTA
40466 AAAATTCC
131 AAAATTCC
40474 C
1 C
40475 AAAGCTCACA
Statistics
Matches: 139, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
138 139 1.00
ACGTcount: A:0.41, C:0.32, G:0.09, T:0.18
Consensus pattern (138 bp):
CTGTTTCAAAGATCAAATAAATAAAAAACTATTAACATGATGAACACCACGAACAACTTTCTCCA
ACCACCATGGGAATCACTGTCAACACCACCGCCACCCACCATAAATACCACCAACACCGGCACTA
AAAATTCC
Found at i:48448 original size:25 final size:26
Alignment explanation
Indices: 48403--48453 Score: 95
Period size: 25 Copynumber: 2.0 Consensus size: 26
48393 ATATAGATTC
48403 TAACATATTCAAAATCTGAATAAGAA
1 TAACATATTCAAAATCTGAATAAGAA
48429 TAACATATTC-AAATCTGAATAAGAA
1 TAACATATTCAAAATCTGAATAAGAA
48454 AGAGGAGTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 15 0.60
26 10 0.40
ACGTcount: A:0.53, C:0.12, G:0.08, T:0.27
Consensus pattern (26 bp):
TAACATATTCAAAATCTGAATAAGAA
Found at i:51593 original size:7 final size:7
Alignment explanation
Indices: 51566--51602 Score: 53
Period size: 7 Copynumber: 5.7 Consensus size: 7
51556 TCATTATGCT
51566 TATAATA
1 TATAATA
51573 -ATAATA
1 TATAATA
51579 -AT-ATA
1 TATAATA
51584 TATAATA
1 TATAATA
51591 TATAATA
1 TATAATA
51598 TATAA
1 TATAA
51603 GTCTGTATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 3 0.11
6 10 0.36
7 15 0.54
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (7 bp):
TATAATA
Found at i:51595 original size:16 final size:15
Alignment explanation
Indices: 51566--51601 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
51556 TCATTATGCT
51566 TATA-ATAATAATAA
1 TATATATAATAATAA
51580 TATATATAATATATAA
1 TATATATAATA-ATAA
51596 TATATA
1 TATATA
51602 AGTCTGTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 4 0.20
15 6 0.30
16 10 0.50
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
TATATATAATAATAA
Done.