Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009392.1 Corchorus capsularis cultivar CVL-1 contig09413, 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: 14544
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.31
Found at i:3208 original size:20 final size:21
Alignment explanation
Indices: 3170--3208 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
3160 TAGAAAATAA
*
3170 GGTAAAAATGCATATAAAAGT
1 GGTAAAAATGCATAGAAAAGT
*
3191 GGTAAAAA-GTATAGAAAA
1 GGTAAAAATGCATAGAAAA
3209 TAGCCATAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.56, C:0.03, G:0.21, T:0.21
Consensus pattern (21 bp):
GGTAAAAATGCATAGAAAAGT
Found at i:4075 original size:40 final size:39
Alignment explanation
Indices: 3982--4126 Score: 188
Period size: 38 Copynumber: 3.7 Consensus size: 39
3972 AAGAAGTCCC
* * *
3982 AAAGTTGA-TTGGAAACAAGTCATCTTTCAACAATCATCG
1 AAAGTTGACTT-GAAACAGGTCATCTTTCAGCAATAATCG
* *
4021 -AAGTTGACTAGAAACAGGTCACCTTTCAGCAATAATCG
1 AAAGTTGACTTGAAACAGGTCATCTTTCAGCAATAATCG
*
4059 AAAAGTTGACTTGAAACAGGTCATCTTTCAGCAATATTC-
1 -AAAGTTGACTTGAAACAGGTCATCTTTCAGCAATAATCG
*
4098 AAAGTTGACTGGAAACAGGTCATCTTTCA
1 AAAGTTGACTTGAAACAGGTCATCTTTCA
4127 AGTTATCAGA
Statistics
Matches: 94, Mismatches: 9, Indels: 7
0.85 0.08 0.06
Matches are distributed among these distances:
38 59 0.63
39 1 0.01
40 34 0.36
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.28
Consensus pattern (39 bp):
AAAGTTGACTTGAAACAGGTCATCTTTCAGCAATAATCG
Found at i:4113 original size:78 final size:78
Alignment explanation
Indices: 3982--4126 Score: 213
Period size: 78 Copynumber: 1.9 Consensus size: 78
3972 AAGAAGTCCC
*
3982 AAAGTTGATTGGAAACAAGTCATCTTTCAACAATCATCGAAGTTGACTAGAAACAGGTCACCTTT
1 AAAGTTGATTGGAAACAAGTCATCTTTCAACAATCATCAAAGTTGACTAGAAACAGGTCACCTTT
4047 CAGCAATAATCGA
66 CAGCAATAATCGA
* * * *
4060 AAAGTTGACTT-GAAACAGGTCATCTTTCAGCAAT-ATTCAAAGTTGACTGGAAACAGGTCATCT
1 AAAGTTGA-TTGGAAACAAGTCATCTTTCAACAATCA-TCAAAGTTGACTAGAAACAGGTCACCT
4123 TTCA
64 TTCA
4127 AGTTATCAGA
Statistics
Matches: 60, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
77 1 0.02
78 57 0.95
79 2 0.03
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.28
Consensus pattern (78 bp):
AAAGTTGATTGGAAACAAGTCATCTTTCAACAATCATCAAAGTTGACTAGAAACAGGTCACCTTT
CAGCAATAATCGA
Found at i:4210 original size:39 final size:39
Alignment explanation
Indices: 4162--4336 Score: 153
Period size: 39 Copynumber: 4.6 Consensus size: 39
4152 TATCAAAGTT
*
4162 GACTAGAAACAGGTCATCTTTCAACAAGTTATCAAGATC
1 GACTGGAAACAGGTCATCTTTCAACAAGTTATCAAGATC
* * * **
4201 GTCTGGAAACATGTCATCTTTCAGCAA-TTATC-TTA-C
1 GACTGGAAACAGGTCATCTTTCAACAAGTTATCAAGATC
* * * * * * * *
4237 GATTGGAAACTGGTCGTCTTTCAGC-ACTTAT-TAGTTTT
1 GACTGGAAACAGGTCATCTTTCAACAAGTTATCAAG-ATC
* *
4275 GACTGGAAATAGGTAATCTTTCAACAAGTTATCAAGATC
1 GACTGGAAACAGGTCATCTTTCAACAAGTTATCAAGATC
*
4314 GACTGGAAACATGTCATCTTTCA
1 GACTGGAAACAGGTCATCTTTCA
4337 GCAGTTTTCA
Statistics
Matches: 102, Mismatches: 28, Indels: 12
0.72 0.20 0.08
Matches are distributed among these distances:
35 1 0.01
36 25 0.25
37 1 0.01
38 24 0.24
39 49 0.48
40 2 0.02
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (39 bp):
GACTGGAAACAGGTCATCTTTCAACAAGTTATCAAGATC
Found at i:4402 original size:34 final size:34
Alignment explanation
Indices: 4364--4473 Score: 193
Period size: 34 Copynumber: 3.2 Consensus size: 34
4354 CCAAGCGGCG
4364 CATTTCAACAACTTTTCAATTTACAACTTTACAA
1 CATTTCAACAACTTTTCAATTTACAACTTTACAA
*
4398 CATTTCAACAACTTTTCAATTTACAACTTTATAA
1 CATTTCAACAACTTTTCAATTTACAACTTTACAA
* *
4432 CATTTCAACAACTTTTCAATTTACAACTTTTCAG
1 CATTTCAACAACTTTTCAATTTACAACTTTACAA
4466 CATTTCAA
1 CATTTCAA
4474 TTTACAACTT
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 72 1.00
ACGTcount: A:0.36, C:0.23, G:0.01, T:0.40
Consensus pattern (34 bp):
CATTTCAACAACTTTTCAATTTACAACTTTACAA
Found at i:4474 original size:57 final size:57
Alignment explanation
Indices: 4391--4530 Score: 208
Period size: 57 Copynumber: 2.4 Consensus size: 57
4381 AATTTACAAC
* *
4391 TTTACAACATTTCAACAACTTTTCAATTTACAACTTTATAACATTTCAACAACTTTTCAA
1 TTTACAAC-TTT--ACAACATTTCAATTTACAACTTTACAACATTTCAACAACTTTTCAA
* * *
4451 TTTACAACTTTTCAGCATTTCAATTTACAACTTTACAGCATTTCAACAACTTTTCAA
1 TTTACAACTTTACAACATTTCAATTTACAACTTTACAACATTTCAACAACTTTTCAA
4508 TTTACAACTTTACAACATTTCAA
1 TTTACAACTTTACAACATTTCAA
4531 CAACTTTTCA
Statistics
Matches: 73, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
57 62 0.85
59 3 0.04
60 8 0.11
ACGTcount: A:0.36, C:0.22, G:0.01, T:0.40
Consensus pattern (57 bp):
TTTACAACTTTACAACATTTCAATTTACAACTTTACAACATTTCAACAACTTTTCAA
Found at i:4506 original size:34 final size:34
Alignment explanation
Indices: 4468--4566 Score: 162
Period size: 34 Copynumber: 2.9 Consensus size: 34
4458 CTTTTCAGCA
4468 TTTCAATTTACAACTTTACAGCATTTCAACAACT
1 TTTCAATTTACAACTTTACAGCATTTCAACAACT
*
4502 TTTCAATTTACAACTTTACAACATTTCAACAACT
1 TTTCAATTTACAACTTTACAGCATTTCAACAACT
*
4536 TTTCAGAATTTACAACTTTTCAGCATTTCAA
1 TTTC--AATTTACAACTTTACAGCATTTCAA
4567 TTCACAACTT
Statistics
Matches: 60, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
34 37 0.62
36 23 0.38
ACGTcount: A:0.35, C:0.22, G:0.03, T:0.39
Consensus pattern (34 bp):
TTTCAATTTACAACTTTACAGCATTTCAACAACT
Found at i:4532 original size:91 final size:92
Alignment explanation
Indices: 4377--4596 Score: 361
Period size: 91 Copynumber: 2.4 Consensus size: 92
4367 TTCAACAACT
* *
4377 TTTCAATTTACAACTTTACAACATTTCAACAACTTTTCAATTTACAACTTTATAACATTTCAACA
1 TTTCAATTTACAACTTTACAGCATTTCAACAACTTTTCAATTTACAACTTTACAACATTTCAACA
4442 ACTTTTC-AATTTACAACTTTTCAGCA
66 ACTTTTCAAATTTACAACTTTTCAGCA
4468 TTTCAATTTACAACTTTACAGCATTTCAACAACTTTTCAATTTACAACTTTACAACATTTCAACA
1 TTTCAATTTACAACTTTACAGCATTTCAACAACTTTTCAATTTACAACTTTACAACATTTCAACA
4533 ACTTTTCAGAATTTACAACTTTTCAGCA
66 ACTTTTCA-AATTTACAACTTTTCAGCA
* ** * *
4561 TTTCAATTCACAACTTTTGAGCATTCCATCAACTTT
1 TTTCAATTTACAACTTTACAGCATTTCAACAACTTT
4597 ACAGTTTTCG
Statistics
Matches: 120, Mismatches: 7, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
91 70 0.58
93 50 0.42
ACGTcount: A:0.35, C:0.23, G:0.03, T:0.40
Consensus pattern (92 bp):
TTTCAATTTACAACTTTACAGCATTTCAACAACTTTTCAATTTACAACTTTACAACATTTCAACA
ACTTTTCAAATTTACAACTTTTCAGCA
Found at i:4578 original size:23 final size:23
Alignment explanation
Indices: 4377--4585 Score: 136
Period size: 23 Copynumber: 9.1 Consensus size: 23
4367 TTCAACAACT
* *
4377 TTTCAATTTACAACTTTACAACA
1 TTTCAATTTACAACTTTTCAGCA
4400 TTTC-A---ACAACTTTTCA--A
1 TTTCAATTTACAACTTTTCAGCA
* * *
4417 TTTACAACTTTATAACATTTCAACAA
1 TTT-CAA-TTTACAACTTTTCAGC-A
4443 CTTTTCAATTTACAACTTTTCAGCA
1 --TTTCAATTTACAACTTTTCAGCA
*
4468 TTTCAATTTACAACTTTACAGCA
1 TTTCAATTTACAACTTTTCAGCA
4491 TTTC-A---ACAACTTTTCA--A
1 TTTCAATTTACAACTTTTCAGCA
* *
4508 TTTACAACTTTACAACATTTCAACAA
1 TTT-CAA-TTTACAACTTTTCAGC-A
4534 CTTTTCAGAATTTACAACTTTTCAGCA
1 --TTTC--AATTTACAACTTTTCAGCA
* *
4561 TTTCAATTCACAACTTTTGAGCA
1 TTTCAATTTACAACTTTTCAGCA
4584 TT
1 TT
4586 CCATCAACTT
Statistics
Matches: 149, Mismatches: 13, Indels: 48
0.71 0.06 0.23
Matches are distributed among these distances:
17 8 0.05
18 2 0.01
19 22 0.15
22 2 0.01
23 68 0.46
25 5 0.03
26 15 0.10
27 5 0.03
28 20 0.13
29 2 0.01
ACGTcount: A:0.35, C:0.22, G:0.03, T:0.40
Consensus pattern (23 bp):
TTTCAATTTACAACTTTTCAGCA
Found at i:6879 original size:13 final size:11
Alignment explanation
Indices: 6846--6884 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
6836 AGTAATATCG
*
6846 AAAAATATCAA
1 AAAAATATAAA
6857 AAAAATATAAA
1 AAAAATATAAA
6868 AAAAATA-AATA
1 AAAAATATAA-A
6879 AAAAAT
1 AAAAAT
6885 TTCGACCAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
10 2 0.08
11 24 0.92
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (11 bp):
AAAAATATAAA
Found at i:8476 original size:33 final size:32
Alignment explanation
Indices: 8394--8477 Score: 87
Period size: 33 Copynumber: 2.5 Consensus size: 32
8384 TTGCAAAGAG
* *
8394 TGTTTTAGATGTTGTTTGCGATGATACTAAACC
1 TGTTTTAG-TGTTGTTTGCAATGACACTAAACC
* * * *
8427 TAATTTGAGTGCTGTTTGCAATGACACTAAATC
1 T-GTTTTAGTGTTGTTTGCAATGACACTAAACC
8460 TGTTTTAAGTGTTGTTTG
1 TGTTTT-AGTGTTGTTTG
8478 TGATGAAAAC
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
32 3 0.08
33 32 0.80
34 5 0.12
ACGTcount: A:0.24, C:0.11, G:0.21, T:0.44
Consensus pattern (32 bp):
TGTTTTAGTGTTGTTTGCAATGACACTAAACC
Found at i:8530 original size:33 final size:33
Alignment explanation
Indices: 8493--8598 Score: 169
Period size: 33 Copynumber: 3.2 Consensus size: 33
8483 AAAACAAATA
8493 TGTTTTGGTTGATCATAGCATTGCAAATAATTC
1 TGTTTTGGTTGATCATAGCATTGCAAATAATTC
*
8526 TGTTTTGGTTGATCATAGCATTGCAAATAATTT
1 TGTTTTGGTTGATCATAGCATTGCAAATAATTC
* * *
8559 TGTTTTGGTTGATTATAGAATT-AAAATAATTC
1 TGTTTTGGTTGATCATAGCATTGCAAATAATTC
8591 TGTTTTGG
1 TGTTTTGG
8599 GTGAAAAGAA
Statistics
Matches: 68, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
32 16 0.24
33 52 0.76
ACGTcount: A:0.27, C:0.08, G:0.19, T:0.46
Consensus pattern (33 bp):
TGTTTTGGTTGATCATAGCATTGCAAATAATTC
Found at i:11489 original size:12 final size:12
Alignment explanation
Indices: 11458--11497 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
11448 CATGACCGGC
11458 CAACGCATGGAG
1 CAACGCATGGAG
**
11470 CATTGCATGGAG
1 CAACGCATGGAG
*
11482 CAACGCATGGGG
1 CAACGCATGGAG
11494 CAAC
1 CAAC
11498 CGACCACAAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.30, C:0.25, G:0.33, T:0.12
Consensus pattern (12 bp):
CAACGCATGGAG
Done.