Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014756.1 Corchorus capsularis cultivar CVL-1 contig14777, 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: 45140
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.31
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1428 original size:40 final size:43
Alignment explanation
Indices: 1316--1430 Score: 157
Period size: 44 Copynumber: 2.7 Consensus size: 43
1306 ACATTTCCAA
* *
1316 TTTAAGTAATTCCAAAAGAAGATTTTGGAAAACAAAGATTTTC
1 TTTAAGAAATTTCAAAAGAAGATTTTGGAAAACAAAGATTTTC
*
1359 TTTCAAGTAATTTCAAAAGAAGATTTTGGAAAACAAA-AGTTTT-
1 TTT-AAGAAATTTCAAAAGAAGATTTTGGAAAACAAAGA-TTTTC
1402 TTT-AGAAATTT-AAAAGAAGATTTTGGAAA
1 TTTAAGAAATTTCAAAAGAAGATTTTGGAAA
1431 TTAATAAAAT
Statistics
Matches: 68, Mismatches: 2, Indels: 7
0.88 0.03 0.09
Matches are distributed among these distances:
40 18 0.26
41 7 0.10
43 7 0.10
44 36 0.53
ACGTcount: A:0.45, C:0.06, G:0.15, T:0.34
Consensus pattern (43 bp):
TTTAAGAAATTTCAAAAGAAGATTTTGGAAAACAAAGATTTTC
Found at i:1434 original size:20 final size:20
Alignment explanation
Indices: 1373--1434 Score: 54
Period size: 20 Copynumber: 3.1 Consensus size: 20
1363 AAGTAATTTC
**
1373 AAAAGAAGATTTTGGAAAAC
1 AAAAGAAGATTTTGGAAATT
*** *
1393 AAAAG-TTTTTTTAGAAATTT
1 AAAAGAAGATTTTGGAAA-TT
1413 AAAAGAAGATTTTGGAAATT
1 AAAAGAAGATTTTGGAAATT
1433 AA
1 AA
1435 TAAAATTGGA
Statistics
Matches: 30, Mismatches: 10, Indels: 4
0.68 0.23 0.09
Matches are distributed among these distances:
19 8 0.27
20 14 0.47
21 8 0.27
ACGTcount: A:0.50, C:0.02, G:0.16, T:0.32
Consensus pattern (20 bp):
AAAAGAAGATTTTGGAAATT
Found at i:2488 original size:19 final size:18
Alignment explanation
Indices: 2464--2499 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
2454 TGAAGATTTA
2464 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
2483 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
2500 ATTATTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:3848 original size:21 final size:21
Alignment explanation
Indices: 3824--3872 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
3814 ATAGATTAGA
* *
3824 TTTAATTTACTTTGCTTTGTT
1 TTTAATTTAATTTGCTTTCTT
*
3845 TTTAGTTTAATTTGCTTTCTT
1 TTTAATTTAATTTGCTTTCTT
*
3866 TATAATT
1 TTTAATT
3873 AATCTTTTTA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.18, C:0.08, G:0.08, T:0.65
Consensus pattern (21 bp):
TTTAATTTAATTTGCTTTCTT
Found at i:5807 original size:12 final size:12
Alignment explanation
Indices: 5786--5826 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
5776 TTTACTAACA
5786 TTTTAATTTTCT
1 TTTTAATTTTCT
*
5798 TTTTAGTTTTCT
1 TTTTAATTTTCT
**
5810 TTTTCTTTTTCT
1 TTTTAATTTTCT
5822 TTTTA
1 TTTTA
5827 TGATTTCAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.10, C:0.10, G:0.02, T:0.78
Consensus pattern (12 bp):
TTTTAATTTTCT
Found at i:5812 original size:5 final size:6
Alignment explanation
Indices: 5792--5825 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
5782 AACATTTTAA
**
5792 TTTTCT TTTTAG TTTTCT TTTTCT TTTTCT TTTT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTT
5826 ATGATTTCAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.03, C:0.12, G:0.03, T:0.82
Consensus pattern (6 bp):
TTTTCT
Found at i:6346 original size:21 final size:21
Alignment explanation
Indices: 6317--6357 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
6307 TATGACTCAT
6317 ATGCCTTGAA-TGCTATGATTG
1 ATGCCTTGAATTGCT-TGATTG
*
6338 ATGCTTTGAATTGCTTGATT
1 ATGCCTTGAATTGCTTGATT
6358 TGTTTGATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.22, C:0.12, G:0.22, T:0.44
Consensus pattern (21 bp):
ATGCCTTGAATTGCTTGATTG
Found at i:7953 original size:19 final size:18
Alignment explanation
Indices: 7929--7964 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
7919 TGAAGATTTA
7929 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
7948 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
7965 ATTATTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:14385 original size:30 final size:30
Alignment explanation
Indices: 14329--14388 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
14319 AAAGGAGAGG
* *
14329 ATGGAATCGCAAAGTATTATGAAGATGCCA
1 ATGGAATCGCAAAGCATCATGAAGATGCCA
* *
14359 ATGGAATCGCAAAGCCTCATGGAGATGCCA
1 ATGGAATCGCAAAGCATCATGAAGATGCCA
14389 TTAAGATGCC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.37, C:0.18, G:0.25, T:0.20
Consensus pattern (30 bp):
ATGGAATCGCAAAGCATCATGAAGATGCCA
Found at i:15277 original size:17 final size:17
Alignment explanation
Indices: 15257--15341 Score: 72
Period size: 16 Copynumber: 5.2 Consensus size: 17
15247 GACTTAAGTC
*
15257 GGGTTCGAGTTAAATTT
1 GGGTTCGGGTTAAATTT
* *
15274 GGGTT-GGGTT-GATTC
1 GGGTTCGGGTTAAATTT
15289 GGGTTCGGGTTAAATTT
1 GGGTTCGGGTTAAATTT
* *
15306 GGG-TCGGGTT-GATTC
1 GGGTTCGGGTTAAATTT
*
15321 CGGTTCGGG-TAAATTTT
1 GGGTTCGGGTTAAA-TTT
15338 GGGT
1 GGGT
15342 CAGGTTAATT
Statistics
Matches: 52, Mismatches: 11, Indels: 10
0.71 0.15 0.14
Matches are distributed among these distances:
15 14 0.27
16 22 0.42
17 16 0.31
ACGTcount: A:0.14, C:0.08, G:0.39, T:0.39
Consensus pattern (17 bp):
GGGTTCGGGTTAAATTT
Found at i:15301 original size:32 final size:32
Alignment explanation
Indices: 15255--15361 Score: 144
Period size: 32 Copynumber: 3.3 Consensus size: 32
15245 CGGACTTAAG
* *
15255 TCGGGTTCGAGTTAAATTTGGGTTGGGTTGAT
1 TCGGGTTCGGGTTAAATTTGGGTCGGGTTGAT
15287 TCGGGTTCGGGTTAAATTTGGGTCGGGTTGAT
1 TCGGGTTCGGGTTAAATTTGGGTCGGGTTGAT
* * *
15319 TCCGGTTCGGG-TAAATTTTGGGTCAGGTTAAT
1 TCGGGTTCGGGTTAAA-TTTGGGTCGGGTTGAT
*
15351 TCGAGTTCGGG
1 TCGGGTTCGGG
15362 CTCGGGTTGG
Statistics
Matches: 67, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
31 4 0.06
32 63 0.94
ACGTcount: A:0.15, C:0.10, G:0.37, T:0.37
Consensus pattern (32 bp):
TCGGGTTCGGGTTAAATTTGGGTCGGGTTGAT
Found at i:15536 original size:20 final size:20
Alignment explanation
Indices: 15503--15541 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
15493 CATAGATGAA
*
15503 ATTTTCAGAAATTATTATTT
1 ATTTTCAGAAATTAGTATTT
15523 ATTTTCA-AATATTAGTATT
1 ATTTTCAGAA-ATTAGTATT
15542 GAATTCAGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.54
Consensus pattern (20 bp):
ATTTTCAGAAATTAGTATTT
Found at i:15574 original size:22 final size:21
Alignment explanation
Indices: 15549--15609 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 21
15539 ATTGAATTCA
15549 GGTTTTTTTAGGTTCGGGTTCG
1 GGTTTTTTT-GGTTCGGGTTCG
*
15571 GG---TTTT--TTCGGGTTCA
1 GGTTTTTTTGGTTCGGGTTCG
15587 GGTTTTTTTGGGTTCGGGTTCG
1 GGTTTTTTT-GGTTCGGGTTCG
15609 G
1 G
15610 ACGGGTCAGG
Statistics
Matches: 31, Mismatches: 2, Indels: 12
0.69 0.04 0.27
Matches are distributed among these distances:
16 11 0.35
19 8 0.26
22 12 0.39
ACGTcount: A:0.03, C:0.10, G:0.38, T:0.49
Consensus pattern (21 bp):
GGTTTTTTTGGTTCGGGTTCG
Found at i:15580 original size:16 final size:16
Alignment explanation
Indices: 15561--15606 Score: 74
Period size: 16 Copynumber: 2.9 Consensus size: 16
15551 TTTTTTTAGG
15561 TTCGGGTTCGGGTTTT
1 TTCGGGTTCGGGTTTT
*
15577 TTCGGGTTCAGGTTTT
1 TTCGGGTTCGGGTTTT
*
15593 TTTGGGTTCGGGTT
1 TTCGGGTTCGGGTT
15607 CGGACGGGTC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.02, C:0.11, G:0.37, T:0.50
Consensus pattern (16 bp):
TTCGGGTTCGGGTTTT
Found at i:20993 original size:67 final size:67
Alignment explanation
Indices: 20885--21021 Score: 247
Period size: 67 Copynumber: 2.0 Consensus size: 67
20875 AATCAAAACC
*
20885 ATGTCAAGATCGGAATACATTAGTAAAAGGAAGAATAAAAAGGGGAAAAAGAAGAAATACAGAAT
1 ATGTCAAGATCGAAATACATTAGTAAAAGGAAGAATAAAAAGGGGAAAAAGAAGAAATACAGAAT
20950 GA
66 GA
* *
20952 ATGTCAAGATCGAAATACATTAGTAAAATGAAGAATAAAAAGGGGAAAAAGAAGTAATACAGAAT
1 ATGTCAAGATCGAAATACATTAGTAAAAGGAAGAATAAAAAGGGGAAAAAGAAGAAATACAGAAT
21017 GA
66 GA
21019 ATG
1 ATG
21022 AATCCGGAGA
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
67 67 1.00
ACGTcount: A:0.55, C:0.06, G:0.23, T:0.17
Consensus pattern (67 bp):
ATGTCAAGATCGAAATACATTAGTAAAAGGAAGAATAAAAAGGGGAAAAAGAAGAAATACAGAAT
GA
Found at i:29635 original size:21 final size:22
Alignment explanation
Indices: 29599--29640 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
29589 CATCTGATTC
*
29599 AGTTCGACCTTTTTCGGGGTCG
1 AGTTCGACCCTTTTCGGGGTCG
29621 AGTTC-ACCCTTTTCGGGGTC
1 AGTTCGACCCTTTTCGGGGTC
29641 AAGATAGGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.10, C:0.26, G:0.29, T:0.36
Consensus pattern (22 bp):
AGTTCGACCCTTTTCGGGGTCG
Found at i:35421 original size:30 final size:30
Alignment explanation
Indices: 35385--35449 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
35375 CACTTGACCA
35385 GCCATCGCATGGAGCAACCG-GCTACAACCG
1 GCCATCGCATGGAGCAACCGCGC-ACAACCG
* *
35415 GCCATCGCATGGGGCATCCGCGCACAACCG
1 GCCATCGCATGGAGCAACCGCGCACAACCG
35445 GCCAT
1 GCCAT
35450 TTGATCCTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 30 0.94
31 2 0.06
ACGTcount: A:0.23, C:0.38, G:0.28, T:0.11
Consensus pattern (30 bp):
GCCATCGCATGGAGCAACCGCGCACAACCG
Found at i:42421 original size:14 final size:14
Alignment explanation
Indices: 42404--42433 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
42394 TTTAAGTTTC
42404 AAGGACTTAATTGA
1 AAGGACTTAATTGA
*
42418 AAGGACTTATTTGA
1 AAGGACTTAATTGA
42432 AA
1 AA
42434 ATAAATTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.07, G:0.20, T:0.30
Consensus pattern (14 bp):
AAGGACTTAATTGA
Done.