Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008061.1 Corchorus capsularis cultivar CVL-1 contig08082, 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: 19906
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:7501 original size:19 final size:19
Alignment explanation
Indices: 7479--7535 Score: 59
Period size: 19 Copynumber: 3.1 Consensus size: 19
7469 CTCCCTCTCA
7479 TTCAAATTAAGTGCAACAT
1 TTCAAATTAAGTGCAACAT
*
7498 TTCAAGATT---TGCAGTCA-
1 TTCAA-ATTAAGTGCA-ACAT
7515 TTCAAATTAAGTGCAACAT
1 TTCAAATTAAGTGCAACAT
7534 TT
1 TT
7536 ATAAAATTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 12
0.68 0.05 0.27
Matches are distributed among these distances:
16 3 0.10
17 9 0.30
18 4 0.13
19 11 0.37
20 3 0.10
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (19 bp):
TTCAAATTAAGTGCAACAT
Found at i:7534 original size:18 final size:18
Alignment explanation
Indices: 7477--7534 Score: 59
Period size: 17 Copynumber: 3.2 Consensus size: 18
7467 TACTCCCTCT
7477 CATTCAAATTAAGTGCAA
1 CATTCAAATTAAGTGCAA
*
7495 CATTTCAAGATT---TGCAGT
1 CA-TTCAA-ATTAAGTGCA-A
7513 CATTCAAATTAAGTGCAA
1 CATTCAAATTAAGTGCAA
7531 CATT
1 CATT
7535 TATAAAATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
16 3 0.09
17 9 0.28
18 8 0.25
19 9 0.28
20 3 0.09
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (18 bp):
CATTCAAATTAAGTGCAA
Found at i:11500 original size:45 final size:45
Alignment explanation
Indices: 11449--11548 Score: 155
Period size: 45 Copynumber: 2.2 Consensus size: 45
11439 CTTCCAACAT
* * *
11449 ATAATTAAGAGATATTAGATGCTATAAAAGTGAAATTAAAAAATA
1 ATAATTAAGAGATATTAGATGCTATAAAAGTAAAAGTAAAAAAGA
*
11494 ATAATTAAGAGATATTAGATGCTATAAAATTAAAAGTAAAAAAGA
1 ATAATTAAGAGATATTAGATGCTATAAAAGTAAAAGTAAAAAAGA
*
11539 AAAATTAAGA
1 ATAATTAAGA
11549 CTTAAGAGAT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 50 1.00
ACGTcount: A:0.58, C:0.02, G:0.13, T:0.27
Consensus pattern (45 bp):
ATAATTAAGAGATATTAGATGCTATAAAAGTAAAAGTAAAAAAGA
Found at i:12766 original size:135 final size:135
Alignment explanation
Indices: 12524--12774 Score: 493
Period size: 135 Copynumber: 1.9 Consensus size: 135
12514 TTCCTTTTTT
12524 TTTTATTTGAACAAAATTTATAACTACTACTCCTAATTTTAGGCTATGTAGACTTTATTAGACGT
1 TTTTATTTGAACAAAATTTATAACTACTACTCCTAATTTTAGGCTATGTAGACTTTATTAGACGT
*
12589 TAGAGAGACCTCACAGGCCACGCCTGGCCGAGATTGGTCTTGTTAACAAAGAAATGCCTAGGGTT
66 TAGAGAGACCTCACAGGCCACGCCTAGCCGAGATTGGTCTTGTTAACAAAGAAATGCCTAGGGTT
12654 TTATC
131 TTATC
12659 TTTTATTTGAACAAAATTTATAACTACTACTCCTAATTTTAGGCTATGTAGACTTTATTAGACGT
1 TTTTATTTGAACAAAATTTATAACTACTACTCCTAATTTTAGGCTATGTAGACTTTATTAGACGT
12724 TAGAGAGACCTCACAGGCCACGCCTAGCCGAGATTGGTCTTGTTAACAAAG
66 TAGAGAGACCTCACAGGCCACGCCTAGCCGAGATTGGTCTTGTTAACAAAG
12775 TCTAAAAAAC
Statistics
Matches: 115, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
135 115 1.00
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (135 bp):
TTTTATTTGAACAAAATTTATAACTACTACTCCTAATTTTAGGCTATGTAGACTTTATTAGACGT
TAGAGAGACCTCACAGGCCACGCCTAGCCGAGATTGGTCTTGTTAACAAAGAAATGCCTAGGGTT
TTATC
Found at i:15783 original size:94 final size:94
Alignment explanation
Indices: 15622--15798 Score: 300
Period size: 94 Copynumber: 1.9 Consensus size: 94
15612 CAGAGAAATT
15622 AAAATTGGAATTCTGCTGAAATTTCATGGTATAGGTGTGAAATCCATGTTTGCTACTAGTAAATT
1 AAAATTGGAATTCTGCTGAAATTTCATGGTATAGGTGTGAAATCCATGTTTGCTACTAGTAAATT
*
15687 TTACACAAAATTAATTAGCAACCTTTAGA
66 TTACAAAAAATTAATTAGCAACCTTTAGA
* * * *
15716 AAAATTGGATTTCTGCTGAAATTTCATGTTATAGGTGTGAAATCCATGTTTGCTGCTAGTTAATT
1 AAAATTGGAATTCTGCTGAAATTTCATGGTATAGGTGTGAAATCCATGTTTGCTACTAGTAAATT
*
15781 TTACAAAAAATTATTTAG
66 TTACAAAAAATTAATTAG
15799 TAACAAGAGA
Statistics
Matches: 77, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
94 77 1.00
ACGTcount: A:0.34, C:0.11, G:0.16, T:0.38
Consensus pattern (94 bp):
AAAATTGGAATTCTGCTGAAATTTCATGGTATAGGTGTGAAATCCATGTTTGCTACTAGTAAATT
TTACAAAAAATTAATTAGCAACCTTTAGA
Found at i:17087 original size:35 final size:35
Alignment explanation
Indices: 17047--17119 Score: 128
Period size: 35 Copynumber: 2.1 Consensus size: 35
17037 TAGTTCGCGT
*
17047 AGATGTGGTGAATTAGTAACCAAATAAAGAACAGA
1 AGATGTGGAGAATTAGTAACCAAATAAAGAACAGA
*
17082 AGATGTGGAGAATTAGTAACCAAATAAAGCACAGA
1 AGATGTGGAGAATTAGTAACCAAATAAAGAACAGA
17117 AGA
1 AGA
17120 CAGTGAATCA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.49, C:0.10, G:0.23, T:0.18
Consensus pattern (35 bp):
AGATGTGGAGAATTAGTAACCAAATAAAGAACAGA
Found at i:18458 original size:13 final size:13
Alignment explanation
Indices: 18440--18465 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
18430 TTTCAAAAAA
18440 AAACTAATTAATT
1 AAACTAATTAATT
18453 AAACTAATTAATT
1 AAACTAATTAATT
18466 TTATTCCTGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (13 bp):
AAACTAATTAATT
Found at i:19389 original size:13 final size:13
Alignment explanation
Indices: 19368--19404 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
19358 AATAATTCTT
19368 TTTGACCCTCCAA
1 TTTGACCCTCCAA
*
19381 TTTGTCCCTCCAA
1 TTTGACCCTCCAA
*
19394 CTTGACCCTCC
1 TTTGACCCTCC
19405 TAATAATTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.16, C:0.43, G:0.08, T:0.32
Consensus pattern (13 bp):
TTTGACCCTCCAA
Found at i:19866 original size:54 final size:54
Alignment explanation
Indices: 19783--19891 Score: 209
Period size: 54 Copynumber: 2.0 Consensus size: 54
19773 TGACTTATGA
*
19783 AGCCTTACACTTATATATTGTAATGGCTATGCACTTGTATTCAAATATTTATAT
1 AGCCTTACACTTATATATTGTAATCGCTATGCACTTGTATTCAAATATTTATAT
19837 AGCCTTACACTTATATATTGTAATCGCTATGCACTTGTATTCAAATATTTATAT
1 AGCCTTACACTTATATATTGTAATCGCTATGCACTTGTATTCAAATATTTATAT
19891 A
1 A
19892 TATATAAAAA
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.32, C:0.16, G:0.10, T:0.42
Consensus pattern (54 bp):
AGCCTTACACTTATATATTGTAATCGCTATGCACTTGTATTCAAATATTTATAT
Done.