Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011702.1 Corchorus capsularis cultivar CVL-1 contig11723, 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: 35854
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:342 original size:14 final size:14
Alignment explanation
Indices: 323--354 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
313 TTTTTTTCTC
323 AAAAAAAAAAAAAG
1 AAAAAAAAAAAAAG
*
337 AAAAAAAAAAAAGG
1 AAAAAAAAAAAAAG
351 AAAA
1 AAAA
355 GAGCATCATC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAAAG
Found at i:6570 original size:13 final size:12
Alignment explanation
Indices: 6540--6582 Score: 68
Period size: 12 Copynumber: 3.5 Consensus size: 12
6530 CATCGATATC
6540 TCGATATATCCG
1 TCGATATATCCG
6552 TCGATATATCCG
1 TCGATATATCCG
*
6564 TTCGATATATCCA
1 -TCGATATATCCG
6577 TCGATA
1 TCGATA
6583 CCTGTATTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
12 18 0.62
13 11 0.38
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (12 bp):
TCGATATATCCG
Found at i:14308 original size:2 final size:2
Alignment explanation
Indices: 14301--14325 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
14291 TGGGTTTGCT
14301 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
14326 TGGATTTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:14831 original size:35 final size:36
Alignment explanation
Indices: 14739--14842 Score: 113
Period size: 35 Copynumber: 2.9 Consensus size: 36
14729 AAATTAGTAT
* ***
14739 TATGAAAGTTTCTGCTAAATTGAATAAAACA-AAAA
1 TATGAAAGCTTCTGCTAAATTGAATAAGTTAGAAAA
*
14774 TAATGAAAGCTTTCTGCTAAATTGAATAAGTTAGCAAA
1 T-ATGAAAGC-TTCTGCTAAATTGAATAAGTTAGAAAA
**
14812 T-TGAAAGCTTCTGCTAAATTGTTTAAGTTAG
1 TATGAAAGCTTCTGCTAAATTGAATAAGTTAG
14843 TAATGTTTAA
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
35 22 0.37
36 14 0.24
37 19 0.32
38 4 0.07
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.34
Consensus pattern (36 bp):
TATGAAAGCTTCTGCTAAATTGAATAAGTTAGAAAA
Found at i:14832 original size:18 final size:18
Alignment explanation
Indices: 14777--14832 Score: 55
Period size: 17 Copynumber: 3.1 Consensus size: 18
14767 ACAAAAATAA
14777 TGAAAGCTTTCTGCTAAAT
1 TGAAAGC-TTCTGCTAAAT
*
14796 TGAATAAG-TT-AGC-AAAT
1 TG-A-AAGCTTCTGCTAAAT
14813 TGAAAGCTTCTGCTAAAT
1 TGAAAGCTTCTGCTAAAT
14831 TG
1 TG
14833 TTTAAGTTAG
Statistics
Matches: 30, Mismatches: 2, Indels: 11
0.70 0.05 0.26
Matches are distributed among these distances:
15 3 0.10
16 3 0.10
17 8 0.27
18 8 0.27
19 4 0.13
20 1 0.03
21 3 0.10
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.34
Consensus pattern (18 bp):
TGAAAGCTTCTGCTAAAT
Found at i:14880 original size:18 final size:18
Alignment explanation
Indices: 14857--14905 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
14847 GTTTAAACTG
*
14857 ATTAAGCAAG-AAAATTGA
1 ATTAAGCAAGTAAAA-GGA
*
14875 ATTAAGTAAGTAAAAGGA
1 ATTAAGCAAGTAAAAGGA
14893 ATTAAGCAAGTAA
1 ATTAAGCAAGTAA
14906 TTGATTAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
18 23 0.85
19 4 0.15
ACGTcount: A:0.55, C:0.04, G:0.18, T:0.22
Consensus pattern (18 bp):
ATTAAGCAAGTAAAAGGA
Found at i:18324 original size:2 final size:2
Alignment explanation
Indices: 18317--18345 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
18307 AATATAACTT
18317 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
18346 TTATTATTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:23550 original size:175 final size:175
Alignment explanation
Indices: 23273--23601 Score: 552
Period size: 175 Copynumber: 1.9 Consensus size: 175
23263 GGATTATTTA
* *
23273 TTAAATGATCCTCATACTTTTATAATTTATGCTATTTAATCCTTACAATTATATGTTGGACGATT
1 TTAAATGATCCTCATACTTTTATAATTTATACTATTTAATCCTTACAATTATAGGTTGGACGATT
* * * * *
23338 GAATGTTTCGGCTTTAATTGTTTTTTTTTTCTATTTGATCGATCAAGGTGATTTAGGTGTCTATT
66 GAATGTTTCGGCTTTAATTCTTTTATTTTTCTATTTGACCGATCAAGGTGATTCAAGTGTCTATT
*
23403 TAAAGGTAATTTCATGGTCTACAATCATTTTTTTTGTTGGATTAT
131 TAAAGGTAATTCCATGGTCTACAATCATTTTTTTTGTTGGATTAT
*
23448 TTAAATGATCCTCATACTTTTATAATTTATACTATTTAATCACTTACAATTATGGGTTGGACGAT
1 TTAAATGATCCTCATACTTTTATAATTTATACTATTTAATC-CTTACAATTATAGGTTGGACGAT
*
23513 TGAATGTTTCGGCTTTAATTCTTTTATTTTT-TATTTGACCGATTAAGGTGATTCAAGTGTCTAT
65 TGAATGTTTCGGCTTTAATTCTTTTATTTTTCTATTTGACCGATCAAGGTGATTCAAGTGTCTAT
23577 TTAAAGGTAATTCCATGGTCTACAA
130 TTAAAGGTAATTCCATGGTCTACAA
23602 CTTTCATGAA
Statistics
Matches: 143, Mismatches: 10, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
175 93 0.65
176 50 0.35
ACGTcount: A:0.27, C:0.12, G:0.15, T:0.47
Consensus pattern (175 bp):
TTAAATGATCCTCATACTTTTATAATTTATACTATTTAATCCTTACAATTATAGGTTGGACGATT
GAATGTTTCGGCTTTAATTCTTTTATTTTTCTATTTGACCGATCAAGGTGATTCAAGTGTCTATT
TAAAGGTAATTCCATGGTCTACAATCATTTTTTTTGTTGGATTAT
Found at i:25701 original size:31 final size:31
Alignment explanation
Indices: 25666--25731 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 31
25656 AACTTTATGT
* *
25666 TTTCCGATTGTACCCTTATT-TTTAAAATATA
1 TTTCCAATTGTACCCTT-TTCTTTAAAACATA
25697 TTTCCAATTGTACCCTTTTCTTTAAAACATA
1 TTTCCAATTGTACCCTTTTCTTTAAAACATA
25728 TTTC
1 TTTC
25732 TAAATTTCCA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 2 0.06
31 30 0.94
ACGTcount: A:0.27, C:0.20, G:0.05, T:0.48
Consensus pattern (31 bp):
TTTCCAATTGTACCCTTTTCTTTAAAACATA
Found at i:26065 original size:19 final size:20
Alignment explanation
Indices: 26038--26075 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
26028 TACTATTATT
26038 TTTTGAATTT-AATATTTTAC
1 TTTTGAATTTCAAT-TTTTAC
26058 TTTT-AATTTCAATTTTTA
1 TTTTGAATTTCAATTTTTA
26076 AATGTCAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTGAATTTCAATTTTTAC
Found at i:26254 original size:22 final size:22
Alignment explanation
Indices: 26174--26254 Score: 74
Period size: 22 Copynumber: 3.6 Consensus size: 22
26164 TCACTTGTTC
**
26174 AAAATTTCATAGCG-TGGTTACC
1 AAAATTTCATAG-GTTGGTTATT
*
26196 AAAATTTCATAGGATCAGGTTATT
1 AAAATTTCATAGG-T-TGGTTATT
* *
26220 AAAATCTCTTAGGTTGGTTATT
1 AAAATTTCATAGGTTGGTTATT
*
26242 GAAATTTCATAGG
1 AAAATTTCATAGG
26255 ACGGTTAATT
Statistics
Matches: 47, Mismatches: 9, Indels: 6
0.76 0.15 0.10
Matches are distributed among these distances:
21 1 0.02
22 29 0.62
23 1 0.02
24 16 0.34
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (22 bp):
AAAATTTCATAGGTTGGTTATT
Found at i:26409 original size:44 final size:44
Alignment explanation
Indices: 26297--26436 Score: 112
Period size: 44 Copynumber: 3.2 Consensus size: 44
26287 ATCAAAGAGA
* * *
26297 TTATCAAAATGTCA-TAGCGAGCTTAT-AAGAATTTCATAGTG-TGG
1 TTATCAAAATTTCATTAG-GAGGTTATCAA-AATTTCATA-TGAAGG
* * * *
26341 TTAACAAAATTTCATTAGGAGGTTA-CTAATATTTCATGTGGAGG
1 TTATCAAAATTTCATTAGGAGGTTATC-AAAATTTCATATGAAGG
* *
26385 TTATCAAAATTTTA-TAGTGTGGTTATCAAAATTTCATATGAAGG
1 TTATCAAAATTTCATTAG-GAGGTTATCAAAATTTCATATGAAGG
26429 TTAT-AAAA
1 TTATCAAAA
26437 GTCTCAATTT
Statistics
Matches: 78, Mismatches: 12, Indels: 13
0.76 0.12 0.13
Matches are distributed among these distances:
43 9 0.12
44 63 0.81
45 6 0.08
ACGTcount: A:0.36, C:0.09, G:0.18, T:0.37
Consensus pattern (44 bp):
TTATCAAAATTTCATTAGGAGGTTATCAAAATTTCATATGAAGG
Found at i:26432 original size:22 final size:21
Alignment explanation
Indices: 26297--26436 Score: 97
Period size: 22 Copynumber: 6.4 Consensus size: 21
26287 ATCAAAGAGA
* * *
26297 TTATCAAAATGTCATAGCGAGC
1 TTATCAAAATTTCATA-TGAGG
*
26319 TTAT-AAGAATTTCATAGTGTGG
1 TTATCAA-AATTTCATA-TGAGG
* *
26341 TTAACAAAATTTCATTAGGAGG
1 TTATCAAAATTTCA-TATGAGG
* *
26363 TTA-CTAATATTTCATGTGGAGG
1 TTATC-AAAATTTCATAT-GAGG
* *
26385 TTATCAAAATTTTATAGTGTGG
1 TTATCAAAATTTCATA-TGAGG
26407 TTATCAAAATTTCATATGAAGG
1 TTATCAAAATTTCATATG-AGG
26429 TTAT-AAAA
1 TTATCAAAA
26437 GTCTCAATTT
Statistics
Matches: 94, Mismatches: 16, Indels: 17
0.74 0.13 0.13
Matches are distributed among these distances:
21 10 0.11
22 78 0.83
23 6 0.06
ACGTcount: A:0.36, C:0.09, G:0.18, T:0.37
Consensus pattern (21 bp):
TTATCAAAATTTCATATGAGG
Found at i:26735 original size:22 final size:22
Alignment explanation
Indices: 26707--27268 Score: 165
Period size: 22 Copynumber: 25.7 Consensus size: 22
26697 TCAGGGAGGA
26707 TATCAAAATTTCATATGAAGGT
1 TATCAAAATTTCATATGAAGGT
**
26729 TATCAAAATTTCATAGTTTA-GT
1 TATCAAAATTTCATA-TGAAGGT
* * * *
26751 TTTCAAAATTTCACAAGAGGGT
1 TATCAAAATTTCATATGAAGGT
* * *
26773 TTTCAAAATTTCATA-GTATGT
1 TATCAAAATTTCATATGAAGGT
* * * *
26794 AGATCAAGATTTCATAGGGAGGT
1 -TATCAAAATTTCATATGAAGGT
* *
26817 TAACAAAATTTCATAATTAA-GT
1 TATCAAAATTTCAT-ATGAAGGT
** ** *
26839 TATCAAAAAATCATCGGGAGGT
1 TATCAAAATTTCATATGAAGGT
*
26861 TATCAAAA--T--T-TGTA-GT
1 TATCAAAATTTCATATGAAGGT
* * **
26877 TATCAAGATTTCATAAGAAATT
1 TATCAAAATTTCATATGAAGGT
* * *
26899 TATCAAAATTTTATAGGGAGGTT
1 TATCAAAATTTCATATGAAGG-T
* * *
26922 TATCAAAATTTTATAGGAAGATT
1 TATCAAAATTTCATATGAAG-GT
*
26945 TATCAAAATTTCATA-GCGAGGT
1 TATCAAAATTTCATATG-AAGGT
* * *
26967 TATCACAATTTCATAGTG-TGAT
1 TATCAAAATTTCATA-TGAAGGT
* * *
26989 TATCAAAATTTCAGAGTG-TGAT
1 TATCAAAATTTCATA-TGAAGGT
* *
27011 TACCAACAA-TTCATATGGAGGT
1 TATCAA-AATTTCATATGAAGGT
* * * * *
27033 TTTTAAATTTTCATAACG-TGGT
1 TATCAAAATTTCAT-ATGAAGGT
* ** *
27055 TATCAATATAACATATGGAGGT
1 TATCAAAATTTCATATGAAGGT
* * **
27077 TATCAACATCTCATAGTGTTGGT
1 TATCAAAATTTCATA-TGAAGGT
27100 TATCAAAATTTCAT-TGGGAA-GT
1 TATCAAAATTTCATAT--GAAGGT
27122 TATCAAAATTTCATATTG-AGGT
1 TATCAAAATTTCATA-TGAAGGT
* * * *
27144 CT-TCAAAATTCCTTAAGGAGGT
1 -TATCAAAATTTCATATGAAGGT
* ** *
27166 TAACCGAATTTCATAAGAAGGT
1 TATCAAAATTTCATATGAAGGT
** * **
27188 TAAGAAAAATTT-GTAAAAAGGT
1 T-ATCAAAATTTCATATGAAGGT
* * * **
27210 TCTCGAAATTCCATAATG-TCGT
1 TATCAAAATTTCAT-ATGAAGGT
* **
27232 TATTAAAATTTCATAAAAAGGT
1 TATCAAAATTTCATATGAAGGT
27254 TATCAAAATTTCATA
1 TATCAAAATTTCATA
27269 ATGGGGTCAT
Statistics
Matches: 392, Mismatches: 113, Indels: 70
0.68 0.20 0.12
Matches are distributed among these distances:
16 9 0.02
17 2 0.01
18 2 0.01
20 2 0.01
21 21 0.05
22 279 0.71
23 75 0.19
24 2 0.01
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (22 bp):
TATCAAAATTTCATATGAAGGT
Found at i:29519 original size:19 final size:18
Alignment explanation
Indices: 29485--29523 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 18
29475 TCATGAGCTG
29485 ATATAATATTATTATATC
1 ATATAATATTATTATATC
29503 ATAT-ATATATATATATATC
1 ATATAATAT-TAT-TATATC
29522 AT
1 AT
29524 TAAAAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 4 0.21
18 7 0.37
19 8 0.42
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (18 bp):
ATATAATATTATTATATC
Found at i:30463 original size:18 final size:16
Alignment explanation
Indices: 30429--30459 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
30419 AAACTATTCT
*
30429 TTTTAAATATAAATTA
1 TTTTAAAAATAAATTA
30445 TTTTAAAAATAAATT
1 TTTTAAAAATAAATT
30460 TTATATCAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TTTTAAAAATAAATTA
Found at i:34894 original size:17 final size:17
Alignment explanation
Indices: 34872--34919 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
34862 GAGACACATA
34872 AAAAATCAAGAATACCC
1 AAAAATCAAGAATACCC
* * *
34889 AAAAATCCGATAATACCG
1 AAAAAT-CAAGAATACCC
34907 AAAAATTCAAGAA
1 AAAAA-TCAAGAA
34920 AAAAACTGAA
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
17 6 0.25
18 17 0.71
19 1 0.04
ACGTcount: A:0.58, C:0.19, G:0.08, T:0.15
Consensus pattern (17 bp):
AAAAATCAAGAATACCC
Found at i:35847 original size:25 final size:26
Alignment explanation
Indices: 35800--35848 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
35790 GAACAAGGGA
*
35800 AAAAGTAAAAAATAATAATAAAACCT
1 AAAAGTAAAAAATAATAAAAAAACCT
35826 AAAA-TAATAAAA-AATAAAAAAAC
1 AAAAGTAA-AAAATAATAAAAAAAC
35849 TTAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 13 0.62
26 8 0.38
ACGTcount: A:0.76, C:0.06, G:0.02, T:0.16
Consensus pattern (26 bp):
AAAAGTAAAAAATAATAAAAAAACCT
Done.