Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012036.1 Corchorus capsularis cultivar CVL-1 contig12057, 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: 59332
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:237 original size:8 final size:8
Alignment explanation
Indices: 224--266 Score: 52
Period size: 8 Copynumber: 5.4 Consensus size: 8
214 AAATAACCCG
224 TAAGTATT
1 TAAGTATT
232 TAAGTATT
1 TAAGTATT
*
240 TACA-AATT
1 TA-AGTATT
*
248 CAAGTATT
1 TAAGTATT
256 TAAGTATT
1 TAAGTATT
264 TAA
1 TAA
267 ATTTCTAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
7 1 0.03
8 27 0.93
9 1 0.03
ACGTcount: A:0.42, C:0.05, G:0.09, T:0.44
Consensus pattern (8 bp):
TAAGTATT
Found at i:1399 original size:12 final size:12
Alignment explanation
Indices: 1382--1410 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
1372 TATTCAATAA
1382 TAATAAACATTT
1 TAATAAACATTT
1394 TAAT-AACATTT
1 TAATAAACATTT
1405 TAATAA
1 TAATAA
1411 TAAAATATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (12 bp):
TAATAAACATTT
Found at i:1484 original size:12 final size:12
Alignment explanation
Indices: 1469--1496 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1459 ATATATATAT
1469 ATATTATTAAAA
1 ATATTATTAAAA
1481 ATATTATTAAAA
1 ATATTATTAAAA
1493 ATAT
1 ATAT
1497 ATAGGTACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (12 bp):
ATATTATTAAAA
Found at i:2770 original size:21 final size:21
Alignment explanation
Indices: 2744--2792 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
2734 TTGATTAATT
* *
2744 ATTTTTTTAATAATATTTTTA
1 ATTTTTTTAATAAAATTTTAA
**
2765 ATTTTTTTTGTAAAATTTTAA
1 ATTTTTTTAATAAAATTTTAA
2786 ATTTTTT
1 ATTTTTT
2793 GACATGACAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (21 bp):
ATTTTTTTAATAAAATTTTAA
Found at i:13912 original size:54 final size:54
Alignment explanation
Indices: 13806--13913 Score: 153
Period size: 54 Copynumber: 2.0 Consensus size: 54
13796 TGAGTTTCAG
* * *
13806 GAAACAAAAGAGTTGCTAATCAAGGAACGTGAAGCTGCAAAGATCATGGCTGAA
1 GAAACAAAAGACTTGCTAATCAAGGAACATGAAGCTGCAAAGAACATGGCTGAA
* * * *
13860 GAAACAAAGGACTTGCTAATGAAGGAACATGAAGCTGCAAAGAACGTTGCTGAA
1 GAAACAAAAGACTTGCTAATCAAGGAACATGAAGCTGCAAAGAACATGGCTGAA
13914 CAGGTTCCCG
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
54 47 1.00
ACGTcount: A:0.43, C:0.15, G:0.26, T:0.17
Consensus pattern (54 bp):
GAAACAAAAGACTTGCTAATCAAGGAACATGAAGCTGCAAAGAACATGGCTGAA
Found at i:22713 original size:32 final size:33
Alignment explanation
Indices: 22656--22719 Score: 112
Period size: 32 Copynumber: 1.9 Consensus size: 33
22646 CTTAGCATGG
22656 ATCTTGCGGTTCTTAATTTTGCATGGATCTTGGC
1 ATCTTGCGGTTCTT-ATTTTGCATGGATCTTGGC
22690 ATCTTGCGGTTCTT-TTTTGCATGGATCTTG
1 ATCTTGCGGTTCTTATTTTGCATGGATCTTG
22720 CACTTCTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 16 0.53
34 14 0.47
ACGTcount: A:0.12, C:0.17, G:0.23, T:0.47
Consensus pattern (33 bp):
ATCTTGCGGTTCTTATTTTGCATGGATCTTGGC
Found at i:26254 original size:31 final size:30
Alignment explanation
Indices: 26219--26281 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 30
26209 TTATGTTTTA
26219 TTAATTATCTTAAA-CTAATTTTAACCTAATT
1 TTAATTATC--AAACCTAATTTTAACCTAATT
26250 TTAATTATCAAATCCTAATTTTAACCTAATT
1 TTAATTATCAAA-CCTAATTTTAACCTAATT
26281 T
1 T
26282 CTATGTAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
29 3 0.10
31 27 0.90
ACGTcount: A:0.38, C:0.14, G:0.00, T:0.48
Consensus pattern (30 bp):
TTAATTATCAAACCTAATTTTAACCTAATT
Found at i:35473 original size:20 final size:20
Alignment explanation
Indices: 35448--35488 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
35438 AGGAAATAAA
*
35448 TTAAATTCAGATTTAGCCCC
1 TTAAATCCAGATTTAGCCCC
*
35468 TTAAATCCAGGTTTAGCCCC
1 TTAAATCCAGATTTAGCCCC
35488 T
1 T
35489 AGTTATAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.12, T:0.34
Consensus pattern (20 bp):
TTAAATCCAGATTTAGCCCC
Found at i:36111 original size:23 final size:24
Alignment explanation
Indices: 36078--36123 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
36068 TTTTTCAGGG
36078 CACAATATATATTG-TTTAATGGAC
1 CACAATATATA-TGATTTAATGGAC
36102 CACAA-ATATATGATTTAATGGA
1 CACAATATATATGATTTAATGGA
36124 AGAAATGGCC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 2 0.10
23 14 0.67
24 5 0.24
ACGTcount: A:0.41, C:0.11, G:0.13, T:0.35
Consensus pattern (24 bp):
CACAATATATATGATTTAATGGAC
Found at i:36756 original size:15 final size:15
Alignment explanation
Indices: 36736--36786 Score: 63
Period size: 15 Copynumber: 3.5 Consensus size: 15
36726 GAGGCTGAGA
36736 TTTGAAAAAGT-TTGG
1 TTTGAAAAAGTGTT-G
36751 TTTGAAAGAAGTGTT-
1 TTTGAAA-AAGTGTTG
36766 TTTG-AAAAGTGTTG
1 TTTGAAAAAGTGTTG
36780 TTTGAAA
1 TTTGAAA
36787 TTGCAGCTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
13 7 0.22
14 6 0.19
15 13 0.41
16 4 0.12
17 2 0.06
ACGTcount: A:0.33, C:0.00, G:0.25, T:0.41
Consensus pattern (15 bp):
TTTGAAAAAGTGTTG
Found at i:53076 original size:20 final size:20
Alignment explanation
Indices: 53051--53088 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
53041 AGCTTATTTT
*
53051 CCATTAGCAAATTACTTAGA
1 CCATTAACAAATTACTTAGA
*
53071 CCATTAATAAATTACTTA
1 CCATTAACAAATTACTTA
53089 ACACCGTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.18, G:0.05, T:0.34
Consensus pattern (20 bp):
CCATTAACAAATTACTTAGA
Found at i:54567 original size:70 final size:70
Alignment explanation
Indices: 54454--54592 Score: 226
Period size: 70 Copynumber: 2.0 Consensus size: 70
54444 TACTTATAAT
* *
54454 TTAATTTTGTATTAGGGTTTAATGCTCTTGGATTTTTGGTAAAACAAAGATCAGAGAATT-ATTG
1 TTAATTTTGTATTAGGGTTTAATGCTCTTAGATTTTTGGTAAAACAAAGATCAAAGAATTAATT-
54518 CCCACC
65 CCCACC
* *
54524 TTAATTTTGTTTTAGGGTTTTATGCTCTTAGATTTTTGGTAAAACAAAGATCAAAGAATTAATTC
1 TTAATTTTGTATTAGGGTTTAATGCTCTTAGATTTTTGGTAAAACAAAGATCAAAGAATTAATTC
54589 CCAC
66 CCAC
54593 ACGTTGCCAA
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
70 61 0.95
71 3 0.05
ACGTcount: A:0.31, C:0.12, G:0.17, T:0.40
Consensus pattern (70 bp):
TTAATTTTGTATTAGGGTTTAATGCTCTTAGATTTTTGGTAAAACAAAGATCAAAGAATTAATTC
CCACC
Done.