Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014567.1 Corchorus capsularis cultivar CVL-1 contig14588, 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: 43251
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.31
Found at i:3444 original size:16 final size:16
Alignment explanation
Indices: 3425--3499 Score: 89
Period size: 16 Copynumber: 4.7 Consensus size: 16
3415 CCCGAACCCG
*
3425 CCCGAACCCGAAATTA
1 CCCGAACCCGAAAATA
3441 CCCGAACCCGAAAATA
1 CCCGAACCCGAAAATA
* *
3457 CCCGGACCCGAGACA-A
1 CCCGAACCCGA-AAATA
*
3473 CCCGATCCCGAAAATA
1 CCCGAACCCGAAAATA
*
3489 CGCGAACCCGA
1 CCCGAACCCGA
3500 GACAACCCGA
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
15 2 0.04
16 45 0.92
17 2 0.04
ACGTcount: A:0.36, C:0.40, G:0.17, T:0.07
Consensus pattern (16 bp):
CCCGAACCCGAAAATA
Found at i:3466 original size:32 final size:32
Alignment explanation
Indices: 3425--3515 Score: 110
Period size: 32 Copynumber: 2.8 Consensus size: 32
3415 CCCGAACCCG
**
3425 CCCGAACCCGAAATTACCCGAACCCGAAAATA
1 CCCGAACCCGAAACAACCCGAACCCGAAAATA
* * *
3457 CCCGGACCCGAGACAACCCGATCCCGAAAATA
1 CCCGAACCCGAAACAACCCGAACCCGAAAATA
* * *
3489 CGCGAACCCGAGACAACCCGAGCCCGA
1 CCCGAACCCGAAACAACCCGAACCCGA
3516 GATCAAAATA
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 51 1.00
ACGTcount: A:0.35, C:0.41, G:0.19, T:0.05
Consensus pattern (32 bp):
CCCGAACCCGAAACAACCCGAACCCGAAAATA
Found at i:3508 original size:48 final size:48
Alignment explanation
Indices: 3425--3517 Score: 118
Period size: 48 Copynumber: 1.9 Consensus size: 48
3415 CCCGAACCCG
*
3425 CCCGAACCCGAAATTACCCGAACCCGAAAATACCCG-GACCCGAGACAA
1 CCCGAACCCGAAAATACCCGAACCCGAAAATACCCGAG-CCCGAGACAA
* * *
3473 CCCGATCCCGAAAATACGCGAACCCGAGACA-ACCCGAGCCCGAGA
1 CCCGAACCCGAAAATACCCGAACCCGA-AAATACCCGAGCCCGAGA
3518 TCAAAATAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
48 36 0.92
49 3 0.08
ACGTcount: A:0.35, C:0.40, G:0.19, T:0.05
Consensus pattern (48 bp):
CCCGAACCCGAAAATACCCGAACCCGAAAATACCCGAGCCCGAGACAA
Found at i:3514 original size:16 final size:16
Alignment explanation
Indices: 3425--3517 Score: 73
Period size: 16 Copynumber: 5.8 Consensus size: 16
3415 CCCGAACCCG
* **
3425 CCCGAACCCGAAATTA
1 CCCGAACCCGAGACAA
*
3441 CCCGAACCCGA-AAATA
1 CCCGAACCCGAGACA-A
*
3457 CCCGGACCCGAGACAA
1 CCCGAACCCGAGACAA
* *
3473 CCCGATCCCGA-AAATA
1 CCCGAACCCGAGACA-A
*
3489 CGCGAACCCGAGACAA
1 CCCGAACCCGAGACAA
*
3505 CCCGAGCCCGAGA
1 CCCGAACCCGAGA
3518 TCAAAATAAT
Statistics
Matches: 61, Mismatches: 12, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
15 3 0.05
16 54 0.89
17 4 0.07
ACGTcount: A:0.35, C:0.40, G:0.19, T:0.05
Consensus pattern (16 bp):
CCCGAACCCGAGACAA
Found at i:4286 original size:9 final size:9
Alignment explanation
Indices: 4272--4311 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
4262 CCCGATCCGG
4272 CCCGAAATA
1 CCCGAAATA
4281 CCCG--A-A
1 CCCGAAATA
4287 CCCGAAATA
1 CCCGAAATA
4296 CCCGAAAATA
1 CCCG-AAATA
4306 CCCGAA
1 CCCGAA
4312 CCCGAAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
6 5 0.19
7 1 0.04
8 1 0.04
9 11 0.41
10 9 0.33
ACGTcount: A:0.42, C:0.38, G:0.12, T:0.07
Consensus pattern (9 bp):
CCCGAAATA
Found at i:4292 original size:15 final size:15
Alignment explanation
Indices: 4272--4331 Score: 67
Period size: 16 Copynumber: 4.3 Consensus size: 15
4262 CCCGATCCGG
4272 CCCGAAATACCCGAA
1 CCCGAAATACCCGAA
4287 CCCGAAATACCCG-A
1 CCCGAAATACCCGAA
4301 ----AAATACCCGAA
1 CCCGAAATACCCGAA
*
4312 CCCGAAAATATCCGAA
1 CCCG-AAATACCCGAA
4328 CCCG
1 CCCG
4332 CCCAATTGCC
Statistics
Matches: 38, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
10 9 0.24
11 1 0.03
14 1 0.03
15 13 0.34
16 14 0.37
ACGTcount: A:0.40, C:0.38, G:0.13, T:0.08
Consensus pattern (15 bp):
CCCGAAATACCCGAA
Found at i:4304 original size:25 final size:26
Alignment explanation
Indices: 4272--4327 Score: 89
Period size: 25 Copynumber: 2.2 Consensus size: 26
4262 CCCGATCCGG
4272 CCCG-AAATACCCGAACCCG-AAATA
1 CCCGAAAATACCCGAACCCGAAAATA
4296 CCCGAAAATACCCGAACCCGAAAATA
1 CCCGAAAATACCCGAACCCGAAAATA
*
4322 TCCGAA
1 CCCGAA
4328 CCCGCCCAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
24 4 0.14
25 15 0.52
26 10 0.34
ACGTcount: A:0.43, C:0.36, G:0.12, T:0.09
Consensus pattern (26 bp):
CCCGAAAATACCCGAACCCGAAAATA
Found at i:15230 original size:65 final size:65
Alignment explanation
Indices: 15039--15239 Score: 233
Period size: 68 Copynumber: 3.0 Consensus size: 65
15029 TAAAGTAAAA
* * * * *
15039 TCACATCCTTTTTGTTCTTAACAAAACTATAGTAGCAATGTTTAGTTCTTAAAAAATATAACTAG
1 TCACA-CCTTTTTGTTCTT--CAAAAATTTAGTAGTAATGATTAGTTCTTAAAACATATAACTAG
15104 CTT
63 CTT
* *
15107 TCACACCTTTTTGTTATTAAAAAATTTAGTACTAGTAATGATTAGTTCTTAAAACATATAACTAG
1 TCACACCTTTTTGTTCTTCAAAAATTTAG---TAGTAATGATTAGTTCTTAAAACATATAACTAG
15172 CTT
63 CTT
* * * *
15175 TCATACTTTTTTGTTCTTCCAAAAATTTAGT-GTAATGATTAGTTCTTCAAACATATAATTAGCT
1 TCACACCTTTTTGTTCTT-CAAAAATTTAGTAGTAATGATTAGTTCTTAAAACATATAACTAGCT
15239 T
65 T
15240 ATAATCGTGG
Statistics
Matches: 116, Mismatches: 13, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
65 40 0.34
66 1 0.01
67 12 0.10
68 53 0.46
69 10 0.09
ACGTcount: A:0.34, C:0.14, G:0.09, T:0.42
Consensus pattern (65 bp):
TCACACCTTTTTGTTCTTCAAAAATTTAGTAGTAATGATTAGTTCTTAAAACATATAACTAGCTT
Found at i:20306 original size:7 final size:7
Alignment explanation
Indices: 20294--20320 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
20284 TCTCTCTTTC
20294 ACTCTCG
1 ACTCTCG
20301 ACTCTCG
1 ACTCTCG
20308 ACTCTCG
1 ACTCTCG
20315 ACTCTC
1 ACTCTC
20321 TCTTTCAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.44, G:0.11, T:0.30
Consensus pattern (7 bp):
ACTCTCG
Found at i:23702 original size:2 final size:2
Alignment explanation
Indices: 23692--23728 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
23682 TATGGAGTAT
23692 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
23729 CTAGTCATCA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:29545 original size:16 final size:17
Alignment explanation
Indices: 29514--29553 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
29504 CTACGACGAT
*
29514 GACAAATTCTGAAAAAA
1 GACAATTTCTGAAAAAA
29531 GACAATTTCTGAAAAAA
1 GACAATTTCTGAAAAAA
29548 GACAAT
1 GACAAT
29554 CTCATCATGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.55, C:0.12, G:0.12, T:0.20
Consensus pattern (17 bp):
GACAATTTCTGAAAAAA
Found at i:31159 original size:72 final size:72
Alignment explanation
Indices: 31077--31213 Score: 222
Period size: 72 Copynumber: 1.9 Consensus size: 72
31067 CCCATCAAGA
* *
31077 TCAATTTTTGACAATCTAAAAATTTCAGCAGAAAA-TTTCGCATCAAAACTAGAATCCCACAAAC
1 TCAATTTTTGACAACCTAAAAACTTCAGCAGAAAACTTT-GCATCAAAACTAGAATCCCACAAAC
31141 CTTCAAAG
65 CTTCAAAG
* *
31149 TCAATTTTTGACAACCTCAAGACTTCAGCAGAAAACTTTGCATCAAAACTAGAATCCCACAAACC
1 TCAATTTTTGACAACCTAAAAACTTCAGCAGAAAACTTTGCATCAAAACTAGAATCCCACAAACC
31214 AAGACCTTCA
Statistics
Matches: 60, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
72 57 0.95
73 3 0.05
ACGTcount: A:0.42, C:0.25, G:0.09, T:0.25
Consensus pattern (72 bp):
TCAATTTTTGACAACCTAAAAACTTCAGCAGAAAACTTTGCATCAAAACTAGAATCCCACAAACC
TTCAAAG
Found at i:37585 original size:15 final size:15
Alignment explanation
Indices: 37561--37591 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
37551 ATAAAGGACT
37561 ACTTTCAAACTCTCA
1 ACTTTCAAACTCTCA
*
37576 ACTTTGAAACTCTCA
1 ACTTTCAAACTCTCA
37591 A
1 A
37592 TAGCCTCATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.29, G:0.03, T:0.32
Consensus pattern (15 bp):
ACTTTCAAACTCTCA
Found at i:40804 original size:33 final size:33
Alignment explanation
Indices: 40739--40804 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
40729 ATTTCATCTT
* * *
40739 TTACTTAAAAGATTTAATCTTTATTTACAAAAA
1 TTACTTAAAAGATTCAATCTTTAATTAAAAAAA
40772 TTACTTAAAAG-TTCAATCTTTAAATTAAAAAAA
1 TTACTTAAAAGATTCAATCTTT-AATTAAAAAAA
40805 AAATTCAATC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 9 0.31
33 20 0.69
ACGTcount: A:0.48, C:0.09, G:0.03, T:0.39
Consensus pattern (33 bp):
TTACTTAAAAGATTCAATCTTTAATTAAAAAAA
Found at i:40868 original size:51 final size:51
Alignment explanation
Indices: 40803--40940 Score: 181
Period size: 51 Copynumber: 2.7 Consensus size: 51
40793 AAATTAAAAA
* * *
40803 AAAAATTCAATCTTTATTCACAAATTACTTTAAAGATTTAATTTTTCAACT
1 AAAAATTCAATCTTTATTTACAAATTACTTAAAAGATTTAATCTTTCAACT
* * *
40854 AAAAACTCAATCTTTATTTACAAATTACTTAAAAG-CTTAATCTTTCAATT
1 AAAAATTCAATCTTTATTTACAAATTACTTAAAAGATTTAATCTTTCAACT
* * *
40904 AAAAGTTC-ATCTCTATTTACAAATTACTTGAAAGATT
1 AAAAATTCAATCTTTATTTACAAATTACTTAAAAGATT
40941 CATCTTCTAA
Statistics
Matches: 75, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
49 24 0.32
50 19 0.25
51 32 0.43
ACGTcount: A:0.41, C:0.14, G:0.04, T:0.41
Consensus pattern (51 bp):
AAAAATTCAATCTTTATTTACAAATTACTTAAAAGATTTAATCTTTCAACT
Found at i:40946 original size:49 final size:50
Alignment explanation
Indices: 40725--40997 Score: 207
Period size: 49 Copynumber: 5.3 Consensus size: 50
40715 CACATCATTC
* * * *
40725 AAAGATTTCATCTTTTACTTAAAAGATTTAATCTTTATTTACAAAAATTACTTA
1 AAAGA-TTAATCTTTCAATTAAAA-ATTCAATCTTTATTTAC--AAATTACTTA
* * *
40779 AAAG-TTCAATCTTTAAATTAAAAAAAAAATTCAATCTTTATTCACAAATTACTTT
1 AAAGATT-AATCTTTCAATT-----AAAAATTCAATCTTTATTTACAAATTACTTA
* * *
40834 AAAGATTTAATTTTTCAACTAAAAACTCAATCTTTATTTACAAATTACTTA
1 AAAGA-TTAATCTTTCAATTAAAAATTCAATCTTTATTTACAAATTACTTA
* * * *
40885 AAAGCTTAATCTTTCAATTAAAAGTTC-ATCTCTATTTACAAATTACTTG
1 AAAGATTAATCTTTCAATTAAAAATTCAATCTTTATTTACAAATTACTTA
* * * *
40934 AAAGATTCATC-TTCTAATT-AAAATCCCA-CTTTTATTTACAAATCACTTTA
1 AAAGATTAATCTTTC-AATTAAAAATTCAATC-TTTATTTACAAATTAC-TTA
40984 AAA-ATTCAATCTTT
1 AAAGATT-AATCTTT
40998 ATATACAAAT
Statistics
Matches: 178, Mismatches: 27, Indels: 31
0.75 0.11 0.13
Matches are distributed among these distances:
48 9 0.05
49 51 0.29
50 26 0.15
51 34 0.19
52 2 0.01
53 9 0.05
54 4 0.02
55 13 0.07
56 9 0.05
57 17 0.10
58 4 0.02
ACGTcount: A:0.41, C:0.15, G:0.03, T:0.41
Consensus pattern (50 bp):
AAAGATTAATCTTTCAATTAAAAATTCAATCTTTATTTACAAATTACTTA
Done.