Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011020.1 Corchorus capsularis cultivar CVL-1 contig11041, 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: 18379
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Found at i:1807 original size:5 final size:5
Alignment explanation
Indices: 1797--1836 Score: 73
Period size: 5 Copynumber: 8.2 Consensus size: 5
1787 TATATATATA
1797 TCTAG TCTAG TCTAG TCTA- TCTAG TCTAG TCTAG TCTAG T
1 TCTAG TCTAG TCTAG TCTAG TCTAG TCTAG TCTAG TCTAG T
1837 ATAATAAAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 4 0.12
5 30 0.88
ACGTcount: A:0.20, C:0.20, G:0.17, T:0.42
Consensus pattern (5 bp):
TCTAG
Found at i:1819 original size:19 final size:19
Alignment explanation
Indices: 1795--1834 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
1785 TATATATATA
1795 TATCTAGTCTAGTCTAGTC
1 TATCTAGTCTAGTCTAGTC
1814 TATCTAGTCTAGTCTAGTC
1 TATCTAGTCTAGTCTAGTC
1833 TA
1 TA
1835 GTATAATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.23, C:0.20, G:0.15, T:0.42
Consensus pattern (19 bp):
TATCTAGTCTAGTCTAGTC
Found at i:3520 original size:30 final size:31
Alignment explanation
Indices: 3465--3529 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
3455 AACCTTTATA
*
3465 ATTTTCAATTGTATCTTTATTTTTAAAACAT
1 ATTTTCAATTGTATCCTTATTTTTAAAACAT
*
3496 ATTTTCAATTGTATCCTT-TTTTTAAAGCAT
1 ATTTTCAATTGTATCCTTATTTTTAAAACAT
3526 ATTT
1 ATTT
3530 CTAAATTGCA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 15 0.47
31 17 0.53
ACGTcount: A:0.29, C:0.11, G:0.05, T:0.55
Consensus pattern (31 bp):
ATTTTCAATTGTATCCTTATTTTTAAAACAT
Found at i:3537 original size:31 final size:31
Alignment explanation
Indices: 3465--3537 Score: 94
Period size: 31 Copynumber: 2.4 Consensus size: 31
3455 AACCTTTATA
* *
3465 ATTTTCAATTGTATCTTTATTTTTAAAACAT
1 ATTTTAAATTGTATCCTTATTTTTAAAACAT
* *
3496 ATTTTCAATTGTATCCTT-TTTTTAAAGCAT
1 ATTTTAAATTGTATCCTTATTTTTAAAACAT
3526 ATTTCTAAATTG
1 ATTT-TAAATTG
3538 CAATTACTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
30 15 0.39
31 23 0.61
ACGTcount: A:0.30, C:0.11, G:0.05, T:0.53
Consensus pattern (31 bp):
ATTTTAAATTGTATCCTTATTTTTAAAACAT
Found at i:3996 original size:22 final size:22
Alignment explanation
Indices: 3968--4015 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
3958 CTTTGCAGAT
*
3968 TATCAAAATTTCATAGTGTGAC
1 TATCAAAATTTCATAATGTGAC
*
3990 TATCAAAATTTCATAATGTGAT
1 TATCAAAATTTCATAATGTGAC
4012 TATC
1 TATC
4016 CAACAAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (22 bp):
TATCAAAATTTCATAATGTGAC
Found at i:4088 original size:22 final size:22
Alignment explanation
Indices: 3964--4091 Score: 64
Period size: 22 Copynumber: 5.6 Consensus size: 22
3954 ATCACTTTGC
*
3964 AGATTATCAAAATTTCATAGTG
1 AGATTAACAAAATTTCATAGTG
* * *
3986 TGACTATCAAAATTTCATAATGTG
1 AGATTAACAAAATTTCAT-A-GTG
* * *
4010 ATTATCCAACAAAAATTTCATAG-A
1 A-GAT-TAAC-AAAATTTCATAGTG
* *
4034 AG-GTAATCAAAATTTGAT-GTTG
1 AGATTAA-CAAAATTTCATAG-TG
* * *
4056 TGCTTATCAAAATTTCATAGTG
1 AGATTAACAAAATTTCATAGTG
4078 AGATTAACAAAATT
1 AGATTAACAAAATT
4092 CTATAAGGAA
Statistics
Matches: 76, Mismatches: 20, Indels: 20
0.66 0.17 0.17
Matches are distributed among these distances:
20 1 0.01
21 11 0.14
22 41 0.54
23 4 0.05
24 4 0.05
25 2 0.03
26 3 0.04
27 10 0.13
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.35
Consensus pattern (22 bp):
AGATTAACAAAATTTCATAGTG
Found at i:4339 original size:22 final size:21
Alignment explanation
Indices: 4255--4348 Score: 66
Period size: 22 Copynumber: 4.3 Consensus size: 21
4245 GGTTATTACT
* * *
4255 ATTTTATAGTGTAGTTATCAA
1 ATTTCATAGTGTGGGTATCAA
*
4276 AGTTTCATAATGT-GGTAATCAAA
1 A-TTTCATAGTGTGGGT-ATC-AA
* *
4299 ATTTAATAG-GATGGTTATCGAA
1 ATTTCATAGTG-TGGGTATC-AA
4321 ATTTCATAGTGTGGGTATCAA
1 ATTTCATAGTGTGGGTATCAA
4342 AGTTTCA
1 A-TTTCA
4349 CAGGCATTAG
Statistics
Matches: 57, Mismatches: 9, Indels: 13
0.72 0.11 0.16
Matches are distributed among these distances:
21 7 0.12
22 44 0.77
23 6 0.11
ACGTcount: A:0.34, C:0.07, G:0.19, T:0.39
Consensus pattern (21 bp):
ATTTCATAGTGTGGGTATCAA
Found at i:5350 original size:2 final size:2
Alignment explanation
Indices: 5343--5368 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5333 CTAAGACTAG
5343 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
5369 CATTTTTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6098 original size:15 final size:15
Alignment explanation
Indices: 6066--6095 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
6056 TAAATTTCAA
6066 TAAAATAAAATATAT
1 TAAAATAAAATATAT
6081 TAAAATAAAA-ATAT
1 TAAAATAAAATATAT
6095 T
1 T
6096 TAATTTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
TAAAATAAAATATAT
Found at i:8696 original size:2 final size:2
Alignment explanation
Indices: 8689--8718 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
8679 ATAAGCCAAT
*
8689 TA TA TA TA TA TA TA TA TA TA TA GA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
8719 GTTATATGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:12977 original size:108 final size:109
Alignment explanation
Indices: 12740--13034 Score: 450
Period size: 108 Copynumber: 2.7 Consensus size: 109
12730 ACTATTATAG
* *
12740 TTTTATTCTACTAGAAACTCTATTTTTATTCAATTAAATTAAATCTAATATCTTTATAATTACTT
1 TTTTATTCTACTAAAAACTCTA---TT-TTC-ATTTAATTAAATCTAATATCTTTATAATTACTT
12805 TATTTTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
61 TATTTTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
12854 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
*
12919 TTACCAAAAAA-TTGGATATATTAAAATTTTTTCTAATATACAA
66 TTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
* **
12962 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAAT-TCAATATTTTATATATATTTTTTTA
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCT-AATATCTT-TATA-ATTACTTTA
13026 TTTTTACCA
63 TTTTTACCA
13035 TTTTAATTTA
Statistics
Matches: 172, Mismatches: 6, Indels: 10
0.91 0.03 0.05
Matches are distributed among these distances:
107 1 0.01
108 77 0.45
109 52 0.30
110 19 0.11
111 2 0.01
114 21 0.12
ACGTcount: A:0.37, C:0.11, G:0.02, T:0.50
Consensus pattern (109 bp):
TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
TTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
Found at i:15469 original size:19 final size:19
Alignment explanation
Indices: 15436--15485 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
15426 TTATGGAGTA
15436 ATCAAAATTTCAGGGAGGAT
1 ATCAAAATTT-AGGGAGGAT
15456 ATCAAAATTTAGGGAGGAT
1 ATCAAAATTTAGGGAGGAT
*
15475 ATCAAATTTTA
1 ATCAAAATTTA
15486 TATGAAGGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 19 0.66
20 10 0.34
ACGTcount: A:0.42, C:0.08, G:0.20, T:0.30
Consensus pattern (19 bp):
ATCAAAATTTAGGGAGGAT
Found at i:15676 original size:23 final size:23
Alignment explanation
Indices: 15436--15751 Score: 152
Period size: 22 Copynumber: 14.5 Consensus size: 23
15426 TTATGGAGTA
*
15436 ATCAAAATTTC--AGGGAGG-AT
1 ATCAAAATTTCATAGGGAGGTTT
*
15456 ATCAAAA-TT--TAGGGAGG-AT
1 ATCAAAATTTCATAGGGAGGTTT
* * *
15475 ATC-AAATTTTATATGAAGG-TT
1 ATCAAAATTTCATAGGGAGGTTT
**
15496 ATCAAAATTTCATAGTTTA-GTTT
1 ATCAAAATTTCATAG-GGAGGTTT
* *
15519 -TCAAAATTTCATAAGCAGG-TT
1 ATCAAAATTTCATAGGGAGGTTT
* * * **
15540 ATCAAAATTTCAGA-GTATGTAG
1 ATCAAAATTTCATAGGGAGGTTT
*
15562 ATCAAAATTTCATAGGGA-GATT
1 ATCAAAATTTCATAGGGAGGTTT
* **
15584 AACAAAATTTCATAATGA-GTTT
1 ATCAAAATTTCATAGGGAGGTTT
* ** *
15606 ATAAAAAAATCATAGGGTA-G-AT
1 ATCAAAATTTCATAGGG-AGGTTT
* * * *
15628 ATCAAGATTTCATAAGAAAG-TT
1 ATCAAAATTTCATAGGGAGGTTT
*
15650 ATCAAAATTTTATAGGGAGGTTT
1 ATCAAAATTTCATAGGGAGGTTT
* *
15673 ATCAAAACTTT-ATAGGAAGATTT
1 ATCAAAA-TTTCATAGGGAGGTTT
*
15696 ATCAAAATTTCATAGCGAGG-TT
1 ATCAAAATTTCATAGGGAGGTTT
* * * *
15718 ATCACAATTTCATAGTG-TGATT
1 ATCAAAATTTCATAGGGAGGTTT
15740 ATCAAAATTTCA
1 ATCAAAATTTCA
15752 GAATGTGATT
Statistics
Matches: 227, Mismatches: 52, Indels: 32
0.73 0.17 0.10
Matches are distributed among these distances:
18 3 0.01
19 16 0.07
20 7 0.03
21 18 0.08
22 141 0.62
23 39 0.17
24 3 0.01
ACGTcount: A:0.41, C:0.09, G:0.16, T:0.34
Consensus pattern (23 bp):
ATCAAAATTTCATAGGGAGGTTT
Found at i:15751 original size:44 final size:45
Alignment explanation
Indices: 15431--15751 Score: 208
Period size: 44 Copynumber: 7.4 Consensus size: 45
15421 TTTTATTATG
* * *
15431 GAGTAATCAAAATTTC--AGGGAGGATATCAAAA-TT--TAGGGA
1 GAGTTATCAAAATTTCATAGGGAGGTTATCAAAATTTCATAGTGA
* * * * *
15471 G-GATATC-AAATTTTATATGAAGGTTATCAAAATTTCATAGT-T
1 GAGTTATCAAAATTTCATAGGGAGGTTATCAAAATTTCATAGTGA
* * * * *
15513 TAGTTTTCAAAATTTCATAAGCAGGTTATCAAAATTTCAGAGT-A
1 GAGTTATCAAAATTTCATAGGGAGGTTATCAAAATTTCATAGTGA
* * *
15557 TGTAG--ATCAAAATTTCATAGGGAGATTAACAAAATTTCATAATGA
1 -G-AGTTATCAAAATTTCATAGGGAGGTTATCAAAATTTCATAGTGA
* * ** * * *
15602 G-TTTATAAAAAAATCATAGGGTA-GATATCAAGATTTCATA-AGA
1 GAGTTATCAAAATTTCATAGGG-AGGTTATCAAAATTTCATAGTGA
* *
15645 AAGTTATCAAAATTTTATAGGGAGGTTTATCAAAACTTT-ATAG-GAA
1 GAGTTATCAAAATTTCATAGGGAGG-TTATCAAAA-TTTCATAGTG-A
* * * *
15691 GATTTATCAAAATTTCATAGCGAGGTTATCACAATTTCATAGTGT
1 GAGTTATCAAAATTTCATAGGGAGGTTATCAAAATTTCATAGTGA
15736 GA-TTATCAAAATTTCA
1 GAGTTATCAAAATTTCA
15752 GAATGTGATT
Statistics
Matches: 213, Mismatches: 47, Indels: 38
0.71 0.16 0.13
Matches are distributed among these distances:
38 6 0.03
39 4 0.02
40 14 0.07
41 2 0.01
43 10 0.05
44 122 0.57
45 27 0.13
46 28 0.13
ACGTcount: A:0.41, C:0.09, G:0.16, T:0.34
Consensus pattern (45 bp):
GAGTTATCAAAATTTCATAGGGAGGTTATCAAAATTTCATAGTGA
Found at i:15758 original size:22 final size:22
Alignment explanation
Indices: 15716--15762 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
15706 CATAGCGAGG
* * *
15716 TTATCACAATTTCATAGTGTGA
1 TTATCAAAATTTCAGAATGTGA
15738 TTATCAAAATTTCAGAATGTGA
1 TTATCAAAATTTCAGAATGTGA
15760 TTA
1 TTA
15763 CTAACAATTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.40
Consensus pattern (22 bp):
TTATCAAAATTTCAGAATGTGA
Found at i:15941 original size:22 final size:22
Alignment explanation
Indices: 15913--15961 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
15903 TTCCTTAGGG
* *
15913 AGGTTAACAAAATTTCATAAGA
1 AGGTTAAAAAAATTTCATAAAA
*
15935 AGGTTAAAAAAATTTTATAAAA
1 AGGTTAAAAAAATTTCATAAAA
15957 AGGTT
1 AGGTT
15962 CTCGAAATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.51, C:0.04, G:0.14, T:0.31
Consensus pattern (22 bp):
AGGTTAAAAAAATTTCATAAAA
Found at i:17850 original size:2 final size:2
Alignment explanation
Indices: 17843--17906 Score: 69
Period size: 2 Copynumber: 33.0 Consensus size: 2
17833 TACTATAGTC
** * *
17843 TA TA TA TA TA TA TA TA TA TA TA TA TA TA CC TA TA TT TA AA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
17884 TT TA -A TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA
17907 ATTAAAAAAA
Statistics
Matches: 51, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
1 2 0.04
2 49 0.96
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:17918 original size:34 final size:36
Alignment explanation
Indices: 17852--17927 Score: 102
Period size: 36 Copynumber: 2.2 Consensus size: 36
17842 CTATATATAT
* ***
17852 ATATATATATATATATATACCTATATTTAAATTTTA
1 ATATATATATATATATATACATATAAAAAAATTTTA
17888 ATATATATATATATATATA-AT-TAAAAAAATTTTA
1 ATATATATATATATATATACATATAAAAAAATTTTA
17922 ATATAT
1 ATATAT
17928 GTTTTATAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
34 16 0.44
35 1 0.03
36 19 0.53
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (36 bp):
ATATATATATATATATATACATATAAAAAAATTTTA
Done.