Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009071.1 Corchorus capsularis cultivar CVL-1 contig09092, 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: 7925
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Found at i:208 original size:13 final size:14
Alignment explanation
Indices: 188--219 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
178 TTGGATTTAA
*
188 ATTTTTTATAAATT
1 ATTTTTAATAAATT
202 ATTTTTAATAAATT
1 ATTTTTAATAAATT
216 ATTT
1 ATTT
220 AATTCAACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
ATTTTTAATAAATT
Found at i:511 original size:2 final size:2
Alignment explanation
Indices: 504--533 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
494 TCGAGTTGAG
504 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
534 AAATAATTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:965 original size:22 final size:22
Alignment explanation
Indices: 937--982 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
927 AAAAAGGGTG
937 TTGCTAAACACCGCCCCAGTTT
1 TTGCTAAACACCGCCCCAGTTT
*
959 TTGCTAAACACCGCCCCATTTT
1 TTGCTAAACACCGCCCCAGTTT
981 TT
1 TT
983 ACACTTTTGC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.22, C:0.35, G:0.11, T:0.33
Consensus pattern (22 bp):
TTGCTAAACACCGCCCCAGTTT
Found at i:1306 original size:30 final size:30
Alignment explanation
Indices: 1272--1344 Score: 146
Period size: 30 Copynumber: 2.4 Consensus size: 30
1262 AGAAGAGCTA
1272 GGATGCGCACAAGTTGATTTGAGCAAGGAG
1 GGATGCGCACAAGTTGATTTGAGCAAGGAG
1302 GGATGCGCACAAGTTGATTTGAGCAAGGAG
1 GGATGCGCACAAGTTGATTTGAGCAAGGAG
1332 GGATGCGCACAAG
1 GGATGCGCACAAG
1345 AGGAATCAAG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.30, C:0.15, G:0.37, T:0.18
Consensus pattern (30 bp):
GGATGCGCACAAGTTGATTTGAGCAAGGAG
Found at i:1520 original size:19 final size:20
Alignment explanation
Indices: 1485--1525 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
1475 GCTTGAAGAC
1485 CATTGAAGATCAATTGGAGAG
1 CATTGAAGATCAATTGGA-AG
1506 CATTGAAG-T-AATTGGAAG
1 CATTGAAGATCAATTGGAAG
1524 CA
1 CA
1526 AGAATATTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 4 0.20
19 7 0.35
20 1 0.05
21 8 0.40
ACGTcount: A:0.39, C:0.10, G:0.27, T:0.24
Consensus pattern (20 bp):
CATTGAAGATCAATTGGAAG
Found at i:5600 original size:26 final size:26
Alignment explanation
Indices: 5565--5625 Score: 88
Period size: 26 Copynumber: 2.3 Consensus size: 26
5555 TTTTATTTCT
*
5565 TGATTACCATTTTTTACTCTTTGTAC
1 TGATTACCATTTTTTACTCTTTTTAC
*
5591 TGATTACCA-TATTTACTCTTTTTTAC
1 TGATTACCATTTTTTACTC-TTTTTAC
5617 TGATTACCA
1 TGATTACCA
5626 ATCATATTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
25 8 0.25
26 24 0.75
ACGTcount: A:0.23, C:0.20, G:0.07, T:0.51
Consensus pattern (26 bp):
TGATTACCATTTTTTACTCTTTTTAC
Found at i:5719 original size:27 final size:25
Alignment explanation
Indices: 5674--5805 Score: 131
Period size: 27 Copynumber: 4.9 Consensus size: 25
5664 TACTCTTTTT
* *
5674 TACCATTTTTACCCCTTTTTACTGAA
1 TACCATTTTTACTCTTTTTTACTG-A
5700 TACCACTTTTTACTCTTTTTTACTGA
1 TACCA-TTTTTACTCTTTTTTACTGA
* *
5726 TCACCATTTCTTACTCTTTATTACTAA
1 T-ACCATTT-TTACTCTTTTTTACTGA
5753 TTACTC-TCTTTTACTCTTTTTTACTGA
1 -TAC-CAT-TTTTACTCTTTTTTACTGA
5780 TCACCATTTTTTACTCATTTTTTACT
1 T-ACCA-TTTTTACTC-TTTTTTACT
5806 CTTTTTACTG
Statistics
Matches: 90, Mismatches: 6, Indels: 18
0.79 0.05 0.16
Matches are distributed among these distances:
26 12 0.13
27 64 0.71
28 14 0.16
ACGTcount: A:0.20, C:0.24, G:0.02, T:0.53
Consensus pattern (25 bp):
TACCATTTTTACTCTTTTTTACTGA
Found at i:5805 original size:65 final size:65
Alignment explanation
Indices: 5730--5860 Score: 174
Period size: 65 Copynumber: 2.0 Consensus size: 65
5720 TACTGATCAC
* * **
5730 CATTTCTTACTCTTTATTACTAATTACTCTCTT-TTACTCTTTTTTACTGATCACCATTTTTTAC
1 CATTTCTTACTCTTT-TTACTAATTACTCTCTTCTTACCCTTTTTAACTGATCACCACATTTTAC
5794 T
65 T
* * * *
5795 CATTTTTTACTCTTTTTACTGATTACTCTTTTCTTACCCTTTTTAACTGATTACCACATTTTACT
1 CATTTCTTACTCTTTTTACTAATTACTCTCTTCTTACCCTTTTTAACTGATCACCACATTTTACT
5860 C
1 C
5861 TTCTTCTTTT
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
64 15 0.26
65 42 0.74
ACGTcount: A:0.20, C:0.24, G:0.02, T:0.54
Consensus pattern (65 bp):
CATTTCTTACTCTTTTTACTAATTACTCTCTTCTTACCCTTTTTAACTGATCACCACATTTTACT
Found at i:5820 original size:27 final size:28
Alignment explanation
Indices: 5790--5862 Score: 89
Period size: 27 Copynumber: 2.7 Consensus size: 28
5780 TCACCATTTT
5790 TTACTCATTTTTTACTCTTTTT-ACTGA
1 TTACTCATTTTTTACTCTTTTTAACTGA
*
5817 TTACTC-TTTTCTTACCCTTTTTAACTGA
1 TTACTCATTTT-TTACTCTTTTTAACTGA
**
5845 TTAC-CACATTTTACTCTT
1 TTACTCATTTTTTACTCTT
5863 CTTCTTTTTC
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
26 4 0.10
27 24 0.62
28 11 0.28
ACGTcount: A:0.19, C:0.23, G:0.03, T:0.55
Consensus pattern (28 bp):
TTACTCATTTTTTACTCTTTTTAACTGA
Found at i:5971 original size:24 final size:23
Alignment explanation
Indices: 5922--6330 Score: 91
Period size: 22 Copynumber: 18.1 Consensus size: 23
5912 CTGACTATCA
* *
5922 TTTTACTCTTTACTGATTATTTT
1 TTTTACTCTTTACTGATTACTAT
* *
5945 TTTTACTTTTTTATTGATTACTA-
1 TTTTAC-TCTTTACTGATTACTAT
*
5968 TTTTATTC-TTACTGATTACCATCATT
1 TTTTACTCTTTACTGATTA-C-T-A-T
* **
5994 TTTTGAACT-TGATTACAGATTAC-CC
1 TTTT--ACTCT--TTACTGATTACTAT
*
6019 TTTTACT-TTTACTGATTACCA-
1 TTTTACTCTTTACTGATTACTAT
* *
6040 TTTTACTCTTTACTAATTACCA-
1 TTTTACTCTTTACTGATTACTAT
* * *
6062 TCTTAC-CTTTTACAGA-TAC-CT
1 TTTTACTC-TTTACTGATTACTAT
* *
6083 TTTTACTTTTTACTGATTAC-CT
1 TTTTACTCTTTACTGATTACTAT
* *
6105 TTTTACTTTTTTTACTGTTTACTAT
1 TTTTAC--TCTTTACTGATTACTAT
* * **
6130 TATTACT-ATTACTCTTTACTGAT
1 TTTTACTCTTTACTGATTACT-AT
* * *
6153 TATCACTTACTCTTTACTAATTGCCA-
1 T-T---TTACTCTTTACTGATTACTAT
* * * * *
6179 TTGTACCCATTACTGACTAC-CT
1 TTTTACTCTTTACTGATTACTAT
* *
6201 TTTTACTTTTTACTGATTACCA-
1 TTTTACTCTTTACTGATTACTAT
6223 --TTACT-TCTTACTGATTACTA-
1 TTTTACTCT-TTACTGATTACTAT
*
6243 --TTACTCTTTACTGATTACCA-
1 TTTTACTCTTTACTGATTACTAT
* * * * *
6263 TATTGCTTTTTACTAATTACCA-
1 TTTTACTCTTTACTGATTACTAT
6285 TTTTAC-CTTTTACTGATTA-TCAT
1 TTTTACTC-TTTACTGATTACT-AT
*
6308 TATT--T-TTTACTGATTACTAT
1 TTTTACTCTTTACTGATTACTAT
6328 TTT
1 TTT
6331 ACTATTTGAA
Statistics
Matches: 292, Mismatches: 57, Indels: 77
0.69 0.13 0.18
Matches are distributed among these distances:
19 1 0.00
20 49 0.17
21 44 0.15
22 107 0.37
23 23 0.08
24 26 0.09
25 11 0.04
26 5 0.02
27 6 0.02
28 10 0.03
29 1 0.00
30 9 0.03
ACGTcount: A:0.23, C:0.19, G:0.05, T:0.53
Consensus pattern (23 bp):
TTTTACTCTTTACTGATTACTAT
Found at i:6058 original size:22 final size:22
Alignment explanation
Indices: 6006--6333 Score: 196
Period size: 22 Copynumber: 14.9 Consensus size: 22
5996 TTGAACTTGA
* *
6006 TTACAGATTACCCTTTTACT-T
1 TTACTGATTACCATTTTACTCT
6027 TTACTGATTACCATTTTACTCT
1 TTACTGATTACCATTTTACTCT
* *
6049 TTACTAATTACCATCTTAC-CTT
1 TTACTGATTACCATTTTACTC-T
* * *
6071 TTACAGA-TACCTTTTTACTTT
1 TTACTGATTACCATTTTACTCT
* *
6092 TTACTGATTACCTTTTTACTTTTT
1 TTACTGATTACCATTTTAC--TCT
* *
6116 TTACTGTTTACTATTATTACTATTACTCT
1 TTACTGATTAC---CA-T--T-TTACTCT
* *
6145 TTACTGATTATCA-CTTACTCT
1 TTACTGATTACCATTTTACTCT
* * * * *
6166 TTACTAATTGCCATTGTACCCA
1 TTACTGATTACCATTTTACTCT
* * *
6188 TTACTGACTACCTTTTTACTTT
1 TTACTGATTACCATTTTACTCT
6210 TTACTGATTACCA--TTACT-T
1 TTACTGATTACCATTTTACTCT
*
6229 CTTACTGATTA-C-TATTACTCT
1 -TTACTGATTACCATTTTACTCT
* * *
6250 TTACTGATTACCATATTGCTTT
1 TTACTGATTACCATTTTACTCT
*
6272 TTACTAATTACCATTTTAC-CTT
1 TTACTGATTACCATTTTACTC-T
*
6294 TTACTGATTATCATTATT--T-T
1 TTACTGATTACCATT-TTACTCT
*
6314 TTACTGATTACTATTTTACT
1 TTACTGATTACCATTTTACT
6334 ATTTGAATTT
Statistics
Matches: 237, Mismatches: 45, Indels: 50
0.71 0.14 0.15
Matches are distributed among these distances:
19 4 0.02
20 44 0.19
21 55 0.23
22 101 0.43
23 2 0.01
24 13 0.05
26 1 0.00
28 1 0.00
29 11 0.05
30 1 0.00
31 4 0.02
ACGTcount: A:0.24, C:0.21, G:0.05, T:0.51
Consensus pattern (22 bp):
TTACTGATTACCATTTTACTCT
Found at i:6228 original size:20 final size:20
Alignment explanation
Indices: 6203--6324 Score: 136
Period size: 20 Copynumber: 5.9 Consensus size: 20
6193 GACTACCTTT
6203 TTACTTTTTACTGATTACCA
1 TTACTTTTTACTGATTACCA
* *
6223 TTACTTCTTACTGATTACTA
1 TTACTTTTTACTGATTACCA
*
6243 TTACTCTTTACTGATTACCATA
1 TTACTTTTTACTGATTACC--A
* *
6265 TTGCTTTTTACTAATTACCA
1 TTACTTTTTACTGATTACCA
* *
6285 TTTTACCTTTTACTGATTATCA
1 --TTACTTTTTACTGATTACCA
*
6307 TTATTTTTTACTGATTAC
1 TTACTTTTTACTGATTAC
6325 TATTTTACTA
Statistics
Matches: 83, Mismatches: 15, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
20 50 0.60
22 33 0.40
ACGTcount: A:0.25, C:0.19, G:0.05, T:0.52
Consensus pattern (20 bp):
TTACTTTTTACTGATTACCA
Found at i:6236 original size:42 final size:41
Alignment explanation
Indices: 6188--6333 Score: 150
Period size: 42 Copynumber: 3.5 Consensus size: 41
6178 ATTGTACCCA
* *
6188 TTACTGACTACCTTTTTACTTTTTACTGATTACCATTACTTC
1 TTACTGATTA-CTTTTTACTTTTTACTGATTACCATTACTTT
* * *
6230 TTACTGATTAC-TATTACTCTTTACTGATTACCATATTGCTTT
1 TTACTGATTACTTTTTACTTTTTACTGATTACC--ATTACTTT
* * * * *
6272 TTACTAATTACCATTTTACCTTTTACTGATTATCATTATTTT
1 TTACTGATTA-CTTTTTACTTTTTACTGATTACCATTACTTT
6314 TTACTGATTACTATTTTACT
1 TTACTGATTACT-TTTTACT
6334 ATTTGAATTT
Statistics
Matches: 84, Mismatches: 15, Indels: 10
0.77 0.14 0.09
Matches are distributed among these distances:
40 19 0.23
41 2 0.02
42 45 0.54
43 1 0.01
44 17 0.20
ACGTcount: A:0.24, C:0.19, G:0.05, T:0.52
Consensus pattern (41 bp):
TTACTGATTACTTTTTACTTTTTACTGATTACCATTACTTT
Found at i:6408 original size:30 final size:30
Alignment explanation
Indices: 6372--6440 Score: 120
Period size: 30 Copynumber: 2.3 Consensus size: 30
6362 TTTACTCTTT
6372 ACTGATTGCTTTTTCTTATTGAACTTAATC
1 ACTGATTGCTTTTTCTTATTGAACTTAATC
* *
6402 ACTGATTACTTTTTCTTATTGAACTTAATT
1 ACTGATTGCTTTTTCTTATTGAACTTAATC
6432 ACTGATTGC
1 ACTGATTGC
6441 CCTTTTTACT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.25, C:0.16, G:0.10, T:0.49
Consensus pattern (30 bp):
ACTGATTGCTTTTTCTTATTGAACTTAATC
Found at i:7454 original size:16 final size:15
Alignment explanation
Indices: 7433--7505 Score: 110
Period size: 16 Copynumber: 4.7 Consensus size: 15
7423 GACAATTGGG
7433 CGGGTTCGGGATTTTT
1 CGGGTTCGGG-TTTTT
7449 CGGGTTCGGGTTTTTT
1 CGGGTTCGGG-TTTTT
*
7465 CGGGTTCGGGTATTT
1 CGGGTTCGGGTTTTT
7480 CGGGTTCGGGTATTTT
1 CGGGTTCGGGT-TTTT
7496 CGGGTTCGGG
1 CGGGTTCGGG
7506 CTCGGATCGG
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
15 15 0.28
16 38 0.72
ACGTcount: A:0.04, C:0.14, G:0.41, T:0.41
Consensus pattern (15 bp):
CGGGTTCGGGTTTTT
Found at i:7472 original size:6 final size:6
Alignment explanation
Indices: 7463--7542 Score: 56
Period size: 6 Copynumber: 12.5 Consensus size: 6
7453 TTCGGGTTTT
*
7463 TTCGGG TTCGGG TATTTCGGG TTCGGG TATTTTCGGG TTCGGG CTC-GG
1 TTCGGG TTCGGG ---TTCGGG TTCGGG ---T-TCGGG TTCGGG TTCGGG
* *
7511 ATCGGG TTCGGG TCCGGG -TCGGG TTCGGG TTC
1 TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG TTC
7543 ACTTTCGATA
Statistics
Matches: 60, Mismatches: 5, Indels: 18
0.72 0.06 0.22
Matches are distributed among these distances:
5 8 0.13
6 39 0.65
7 1 0.02
9 7 0.12
10 5 0.08
ACGTcount: A:0.04, C:0.19, G:0.44, T:0.34
Consensus pattern (6 bp):
TTCGGG
Found at i:7484 original size:31 final size:32
Alignment explanation
Indices: 7433--7505 Score: 121
Period size: 31 Copynumber: 2.3 Consensus size: 32
7423 GACAATTGGG
* *
7433 CGGGTTCGGGATTTTTCGGGTTCGGGTTTTTT
1 CGGGTTCGGGATATTTCGGGTTCGGGTATTTT
7465 CGGGTTCGGG-TATTTCGGGTTCGGGTATTTT
1 CGGGTTCGGGATATTTCGGGTTCGGGTATTTT
7496 CGGGTTCGGG
1 CGGGTTCGGG
7506 CTCGGATCGG
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
31 29 0.74
32 10 0.26
ACGTcount: A:0.04, C:0.14, G:0.41, T:0.41
Consensus pattern (32 bp):
CGGGTTCGGGATATTTCGGGTTCGGGTATTTT
Found at i:7517 original size:17 final size:17
Alignment explanation
Indices: 7495--7540 Score: 67
Period size: 17 Copynumber: 2.7 Consensus size: 17
7485 TCGGGTATTT
7495 TCGGGTTCGGG-CTCGGA
1 TCGGGTTCGGGTC-CGGA
*
7512 TCGGGTTCGGGTCCGGG
1 TCGGGTTCGGGTCCGGA
7529 TCGGGTTCGGGT
1 TCGGGTTCGGGT
7541 TCACTTTCGA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 26 0.96
18 1 0.04
ACGTcount: A:0.02, C:0.22, G:0.50, T:0.26
Consensus pattern (17 bp):
TCGGGTTCGGGTCCGGA
Done.