Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024444.1 Corchorus olitorius cultivar O-4 contig24477, 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: 41182
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:11030 original size:21 final size:22
Alignment explanation
Indices: 10977--11030 Score: 67
Period size: 23 Copynumber: 2.5 Consensus size: 22
10967 TTAGCTATTT
10977 GTCGACAATTTGCTTCTACTTGA
1 GTCGACAATTTGCTTCTA-TTGA
*
11000 GTCGATAATTTGCTTCCT-TTG-
1 GTCGACAATTTGCTT-CTATTGA
11021 GTCGACAATT
1 GTCGACAATT
11031 CCCTAGTCGA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 9 0.32
22 3 0.11
23 14 0.50
24 2 0.07
ACGTcount: A:0.20, C:0.20, G:0.19, T:0.41
Consensus pattern (22 bp):
GTCGACAATTTGCTTCTATTGA
Found at i:11615 original size:14 final size:14
Alignment explanation
Indices: 11598--11639 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
11588 CGGCTGCTGG
*
11598 TGCTGGGGCGGCCT
1 TGCTGGGGCAGCCT
*
11612 TGCT-GGGCAGCTT
1 TGCTGGGGCAGCCT
11625 TG-TGGGGCAGCCT
1 TGCTGGGGCAGCCT
11638 TG
1 TG
11640 ATGCTGCTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
12 1 0.04
13 19 0.79
14 4 0.17
ACGTcount: A:0.05, C:0.24, G:0.45, T:0.26
Consensus pattern (14 bp):
TGCTGGGGCAGCCT
Found at i:18489 original size:22 final size:21
Alignment explanation
Indices: 18437--18490 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 21
18427 GCTTCTTGGA
18437 AATAATTCTTC-AATGATCTTC
1 AATAA-TCTTCAAATGATCTTC
*
18458 -A-AATCTTCAAATTATCTTC
1 AATAATCTTCAAATGATCTTC
18477 AATAAGTCTTCAAA
1 AATAA-TCTTCAAA
18491 CATGAATTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 5 0.18
19 11 0.39
20 2 0.07
21 2 0.07
22 8 0.29
ACGTcount: A:0.39, C:0.19, G:0.04, T:0.39
Consensus pattern (21 bp):
AATAATCTTCAAATGATCTTC
Found at i:27545 original size:14 final size:14
Alignment explanation
Indices: 27515--27564 Score: 50
Period size: 13 Copynumber: 3.6 Consensus size: 14
27505 TGCCATGAGC
*
27515 AAAAGCAAAAAACAA
1 AAAAG-AAAAAAGAA
**
27530 AAAA-ACTAAAGAA
1 AAAAGAAAAAAGAA
27543 AAAAGAAAAAAG-A
1 AAAAGAAAAAAGAA
27556 AAAAGAAAA
1 AAAAGAAAA
27565 CGAAAGCAAC
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
13 20 0.69
14 5 0.17
15 4 0.14
ACGTcount: A:0.82, C:0.06, G:0.10, T:0.02
Consensus pattern (14 bp):
AAAAGAAAAAAGAA
Found at i:27547 original size:7 final size:7
Alignment explanation
Indices: 27515--27564 Score: 50
Period size: 7 Copynumber: 7.3 Consensus size: 7
27505 TGCCATGAGC
27515 AAAAGCAA
1 AAAAG-AA
*
27523 AAAACAA
1 AAAAGAA
*
27530 AAAA-AC
1 AAAAGAA
*
27536 TAAAGAA
1 AAAAGAA
27543 AAAAGAA
1 AAAAGAA
27550 AAAAG-A
1 AAAAGAA
27556 AAAAGAA
1 AAAAGAA
27563 AA
1 AA
27565 CGAAAGCAAC
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
6 10 0.29
7 21 0.60
8 4 0.11
ACGTcount: A:0.82, C:0.06, G:0.10, T:0.02
Consensus pattern (7 bp):
AAAAGAA
Found at i:27560 original size:20 final size:20
Alignment explanation
Indices: 27514--27564 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
27504 TTGCCATGAG
27514 CAAAAGCAAAAAACAAAAAAA
1 CAAAAG-AAAAAACAAAAAAA
* *
27535 CTAAAGAAAAAAGAAAAAAGA
1 CAAAAGAAAAAACAAAAAA-A
27556 -AAAAGAAAA
1 CAAAAGAAAA
27565 CGAAAGCAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 20 0.77
21 6 0.23
ACGTcount: A:0.80, C:0.08, G:0.10, T:0.02
Consensus pattern (20 bp):
CAAAAGAAAAAACAAAAAAA
Found at i:30489 original size:68 final size:68
Alignment explanation
Indices: 30380--30533 Score: 290
Period size: 68 Copynumber: 2.3 Consensus size: 68
30370 GAAAAATAAA
*
30380 TAATGCACCTAATACTTTAAAACTAAACTTGGATTGTATGAATGGTTAGTTATGCCTTTTGGATT
1 TAATGCACCTAGTACTTTAAAACTAAACTTGGATTGTATGAATGGTTAGTTATGCCTTTTGGATT
30445 GAC
66 GAC
*
30448 TAATGCACATAGTACTTTAAAACTAAACTTGGATTGTATGAATGGTTAGTTATGCCTTTTGGATT
1 TAATGCACCTAGTACTTTAAAACTAAACTTGGATTGTATGAATGGTTAGTTATGCCTTTTGGATT
30513 GAC
66 GAC
30516 TAATGCACCTAGTACTTT
1 TAATGCACCTAGTACTTT
30534 TATGAGGCTA
Statistics
Matches: 83, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
68 83 1.00
ACGTcount: A:0.31, C:0.14, G:0.18, T:0.38
Consensus pattern (68 bp):
TAATGCACCTAGTACTTTAAAACTAAACTTGGATTGTATGAATGGTTAGTTATGCCTTTTGGATT
GAC
Found at i:31014 original size:16 final size:16
Alignment explanation
Indices: 30995--31064 Score: 72
Period size: 16 Copynumber: 4.4 Consensus size: 16
30985 TTTGGGTACT
30995 CGAACCCAAAATAACC
1 CGAACCCAAAATAACC
* *
31011 CGAATCC-AAACAACC
1 CGAACCCAAAATAACC
*
31026 CGAACCCGAAAA-GACC
1 CGAACCC-AAAATAACC
* *
31042 TGAACCCAAAATGACC
1 CGAACCCAAAATAACC
31058 CGAACCC
1 CGAACCC
31065 GATCAACCCA
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
15 17 0.38
16 25 0.56
17 3 0.07
ACGTcount: A:0.44, C:0.39, G:0.11, T:0.06
Consensus pattern (16 bp):
CGAACCCAAAATAACC
Found at i:34643 original size:2 final size:2
Alignment explanation
Indices: 34626--34659 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
34616 CAAAATAATC
* *
34626 AT AT AC AT AC AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
34660 GAAATAATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:36321 original size:32 final size:32
Alignment explanation
Indices: 36285--36346 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
36275 AATTATTTAA
36285 TTTGTGTTAGTTGGAAATTAAAATCTTCTTTC
1 TTTGTGTTAGTTGGAAATTAAAATCTTCTTTC
*
36317 TTTGTGTTAGTTGGAAGTTAAAATCTTCTT
1 TTTGTGTTAGTTGGAAATTAAAATCTTCTT
36347 AAATATAAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.24, C:0.08, G:0.18, T:0.50
Consensus pattern (32 bp):
TTTGTGTTAGTTGGAAATTAAAATCTTCTTTC
Found at i:36551 original size:54 final size:50
Alignment explanation
Indices: 36469--36572 Score: 145
Period size: 51 Copynumber: 2.0 Consensus size: 50
36459 TTATACTATC
*
36469 AAATTAAATATGATAGGAATAATAATAATAATAAACTTTAACTATGTTTACATG
1 AAATTAAATATGATAGG---AATAATAATAATAAACCTTAACTATG-TTACATG
* *
36523 AAATTAAATGTGATTGGAATAATAATAATAAACCTTAACTATGTTACATG
1 AAATTAAATATGATAGGAATAATAATAATAAACCTTAACTATGTTACATG
36573 GTCATATAAC
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
50 7 0.15
51 25 0.53
54 15 0.32
ACGTcount: A:0.48, C:0.07, G:0.11, T:0.35
Consensus pattern (50 bp):
AAATTAAATATGATAGGAATAATAATAATAAACCTTAACTATGTTACATG
Found at i:37399 original size:84 final size:84
Alignment explanation
Indices: 37210--37388 Score: 270
Period size: 84 Copynumber: 2.1 Consensus size: 84
37200 TAATGACCCG
* *
37210 TGACCCGAAACCGAAAACCCGAGGCTCAAACCAGAAATTATCCGAACCGCATGACCCAAAACCGA
1 TGACCAGAACCCGAAAACCCGAGGCTCAAACCAGAAATTATCCGAACCGCATGACCCAAAACCGA
37275 AAACAACCCAACCCAGAAT
66 AAACAACCCAACCCAGAAT
* * * *
37294 TGACCAGAACCCGAAAACCCGAGGCTCAAACCCGATATTATTCGAACCGCATGA-CCGAAACCGA
1 TGACCAGAACCCGAAAACCCGAGGCTCAAACCAGAAATTATCCGAACCGCATGACCCAAAACCGA
* *
37358 AAGCGACCCAACCCAGAAT
66 AAACAACCCAACCCAGAAT
*
37377 TGACCGGAACCC
1 TGACCAGAACCC
37389 AAATGACCCG
Statistics
Matches: 86, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
83 37 0.43
84 49 0.57
ACGTcount: A:0.39, C:0.35, G:0.17, T:0.09
Consensus pattern (84 bp):
TGACCAGAACCCGAAAACCCGAGGCTCAAACCAGAAATTATCCGAACCGCATGACCCAAAACCGA
AAACAACCCAACCCAGAAT
Found at i:37506 original size:14 final size:14
Alignment explanation
Indices: 37473--37511 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 14
37463 AACTTTTCTT
37473 AACCCGAAACTGACCC
1 AACCC-AAA-TGACCC
*
37489 AACCCAAATGACCG
1 AACCCAAATGACCC
37503 AACCCAAAT
1 AACCCAAAT
37512 CCAACCCGAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 14 0.64
15 3 0.14
16 5 0.23
ACGTcount: A:0.44, C:0.38, G:0.10, T:0.08
Consensus pattern (14 bp):
AACCCAAATGACCC
Done.