Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009188.1 Corchorus capsularis cultivar CVL-1 contig09209, 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: 65772
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:28453 original size:21 final size:22
Alignment explanation
Indices: 28406--28454 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 22
28396 GATTGCACTT
28406 GAAAAAAATAGGAAAACAAAA-
1 GAAAAAAATAGGAAAACAAAAG
* * *
28427 GAAAAAAAAAGGAAAGCAAATG
1 GAAAAAAATAGGAAAACAAAAG
28449 GAAAAA
1 GAAAAA
28455 GGGGACAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 18 0.75
22 6 0.25
ACGTcount: A:0.73, C:0.04, G:0.18, T:0.04
Consensus pattern (22 bp):
GAAAAAAATAGGAAAACAAAAG
Found at i:30934 original size:27 final size:27
Alignment explanation
Indices: 30904--30956 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
30894 TCTGGAAAAC
30904 AAGGGAAAGAGACAATTAAAAAGGAAT
1 AAGGGAAAGAGACAATTAAAAAGGAAT
* *
30931 AAGGGAAATAGATAATTAAAAAGGAA
1 AAGGGAAAGAGACAATTAAAAAGGAA
30957 CAGAAGGAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.60, C:0.02, G:0.25, T:0.13
Consensus pattern (27 bp):
AAGGGAAAGAGACAATTAAAAAGGAAT
Found at i:37237 original size:17 final size:17
Alignment explanation
Indices: 37215--37248 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
37205 AGGTTAAATA
37215 TAACATCATGAAACTGG
1 TAACATCATGAAACTGG
37232 TAACATCATGAAACTGG
1 TAACATCATGAAACTGG
37249 GCTTACTTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.24
Consensus pattern (17 bp):
TAACATCATGAAACTGG
Found at i:38922 original size:31 final size:31
Alignment explanation
Indices: 38887--39054 Score: 160
Period size: 31 Copynumber: 5.4 Consensus size: 31
38877 CTTTTTGTGT
*
38887 ACGTGGCATACCATGTGTCACTTTCTGGTAC
1 ACGTGGCATACCATGTGTCACTTTTTGGTAC
** * *
38918 ACGTGGCATGTCATATGTCATTTTTTGGTAC
1 ACGTGGCATACCATGTGTCACTTTTTGGTAC
** * *
38949 ACGTGGTGTGA-CATGCGTCATTTTTTGGTAC
1 ACGTGGCAT-ACCATGTGTCACTTTTTGGTAC
* *
38980 ACGTGGCGTGA-CACGTGTCACTTTTTGGTAC
1 ACGTGGCAT-ACCATGTGTCACTTTTTGGTAC
* * * *
39011 ATGTGGCGTGCCATGTGTCACTTTTTGGTAT
1 ACGTGGCATACCATGTGTCACTTTTTGGTAC
*
39042 ACATGGCATACCA
1 ACGTGGCATACCA
39055 CGTTGGACAT
Statistics
Matches: 113, Mismatches: 22, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
31 113 1.00
ACGTcount: A:0.18, C:0.20, G:0.26, T:0.36
Consensus pattern (31 bp):
ACGTGGCATACCATGTGTCACTTTTTGGTAC
Found at i:38978 original size:62 final size:62
Alignment explanation
Indices: 38898--39050 Score: 189
Period size: 62 Copynumber: 2.5 Consensus size: 62
38888 CGTGGCATAC
* * * * *
38898 CATGTGTCACTTTCTGGTACACGTGGCATGTCATATGTCATTTTTTGGTACACGTGGTGTGA
1 CATGTGTCACTTTTTGGTACACGTGGCATGACACATGTCACTTTTTGGTACACGTGGCGTGA
* * * * * *
38960 CATGCGTCATTTTTTGGTACACGTGGCGTGACACGTGTCACTTTTTGGTACATGTGGCGTGC
1 CATGTGTCACTTTTTGGTACACGTGGCATGACACATGTCACTTTTTGGTACACGTGGCGTGA
* *
39022 CATGTGTCACTTTTTGGTATACATGGCAT
1 CATGTGTCACTTTTTGGTACACGTGGCAT
39051 ACCACGTTGG
Statistics
Matches: 75, Mismatches: 16, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
62 75 1.00
ACGTcount: A:0.17, C:0.19, G:0.26, T:0.38
Consensus pattern (62 bp):
CATGTGTCACTTTTTGGTACACGTGGCATGACACATGTCACTTTTTGGTACACGTGGCGTGA
Found at i:39057 original size:62 final size:61
Alignment explanation
Indices: 38887--39057 Score: 180
Period size: 62 Copynumber: 2.8 Consensus size: 61
38877 CTTTTTGTGT
* * * * ** *
38887 ACGTGGCATACCATGTGTCACTTTCTGGTACACGTGGCATGTCATATGTCATTTTTTGGTAC
1 ACGTGGCGTGCCATGTGTCACTTTTTGGTACACGTGGCAT-ACACGTGTCACTTTTTGGTAC
* * * * *
38949 ACGTGGTGTGACATGCGTCATTTTTTGGTACACGTGGCGTGACACGTGTCACTTTTTGGTAC
1 ACGTGGCGTGCCATGTGTCACTTTTTGGTACACGTGGCAT-ACACGTGTCACTTTTTGGTAC
* * *
39011 ATGTGGCGTGCCATGTGTCACTTTTTGGTATACATGGCATACCACGT
1 ACGTGGCGTGCCATGTGTCACTTTTTGGTACACGTGGCATA-CACGT
39058 TGGACATCGT
Statistics
Matches: 88, Mismatches: 20, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
61 1 0.01
62 87 0.99
ACGTcount: A:0.18, C:0.20, G:0.26, T:0.36
Consensus pattern (61 bp):
ACGTGGCGTGCCATGTGTCACTTTTTGGTACACGTGGCATACACGTGTCACTTTTTGGTAC
Found at i:42766 original size:12 final size:11
Alignment explanation
Indices: 42748--42787 Score: 62
Period size: 12 Copynumber: 3.5 Consensus size: 11
42738 AAGAGCTTCC
42748 TTTTTTTCTTT
1 TTTTTTTCTTT
42759 TCTTTTTTCTTT
1 T-TTTTTTCTTT
42771 TTTTTTTCTTT
1 TTTTTTTCTTT
42782 GTTTTT
1 -TTTTT
42788 CAATACATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
11 11 0.41
12 16 0.59
ACGTcount: A:0.00, C:0.10, G:0.03, T:0.88
Consensus pattern (11 bp):
TTTTTTTCTTT
Found at i:42775 original size:11 final size:11
Alignment explanation
Indices: 42748--42787 Score: 62
Period size: 11 Copynumber: 3.5 Consensus size: 11
42738 AAGAGCTTCC
42748 TTTTTTTCTTT
1 TTTTTTTCTTT
42759 TCTTTTTTCTTT
1 T-TTTTTTCTTT
42771 TTTTTTTCTTT
1 TTTTTTTCTTT
*
42782 GTTTTT
1 TTTTTT
42788 CAATACATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
11 16 0.59
12 11 0.41
ACGTcount: A:0.00, C:0.10, G:0.03, T:0.88
Consensus pattern (11 bp):
TTTTTTTCTTT
Found at i:50117 original size:14 final size:14
Alignment explanation
Indices: 50098--50125 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
50088 TTTTTATGTC
50098 TATGTATGTATATA
1 TATGTATGTATATA
50112 TATGTATGTATATA
1 TATGTATGTATATA
50126 AGTTTTGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (14 bp):
TATGTATGTATATA
Found at i:50382 original size:3 final size:3
Alignment explanation
Indices: 50367--50427 Score: 88
Period size: 3 Copynumber: 20.3 Consensus size: 3
50357 CAGTTATGAT
*
50367 TTA TTA CTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
50414 TTA TAA TATA TTA T
1 TTA TTA T-TA TTA T
50428 AAGTATCGAA
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
2 2 0.04
3 48 0.92
4 2 0.04
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:54952 original size:1 final size:1
Alignment explanation
Indices: 54946--54971 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
54936 GAATTTGAAG
54946 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
54972 CAAGGGAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:59035 original size:31 final size:31
Alignment explanation
Indices: 59000--59059 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
58990 ACGTTTTTCG
59000 ATTGTATCCTTATTTTTAAAACATATTTCCA
1 ATTGTATCCTTATTTTTAAAACATATTTCCA
*
59031 ATTGTATCCTTTTTTTTAAAACATATTTC
1 ATTGTATCCTTATTTTTAAAACATATTTC
59060 TAAATTGTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.30, C:0.15, G:0.03, T:0.52
Consensus pattern (31 bp):
ATTGTATCCTTATTTTTAAAACATATTTCCA
Found at i:59414 original size:38 final size:38
Alignment explanation
Indices: 59371--59443 Score: 110
Period size: 38 Copynumber: 1.9 Consensus size: 38
59361 ATATAATGTG
*
59371 ATTATCAAAAAATCATAGGGAGGTTATCAAAATTTGTA
1 ATTATCAAAAAATCATAAGGAGGTTATCAAAATTTGTA
* **
59409 ATTATCAAGATTTCATAAGGAGGTTATCAAAATTT
1 ATTATCAAAAAATCATAAGGAGGTTATCAAAATTT
59444 TATAGGGAGC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 31 1.00
ACGTcount: A:0.42, C:0.08, G:0.15, T:0.34
Consensus pattern (38 bp):
ATTATCAAAAAATCATAAGGAGGTTATCAAAATTTGTA
Found at i:59438 original size:22 final size:22
Alignment explanation
Indices: 59331--59519 Score: 97
Period size: 22 Copynumber: 8.6 Consensus size: 22
59321 TGGTCCAATT
* *
59331 TCAAAATTTCAAAACGAGGTTA
1 TCAAAATTTCATAAGGAGGTTA
* * *
59353 TCAAAATTAT-ATAATGTGATTA
1 TCAAAATT-TCATAAGGAGGTTA
** *
59375 TCAAAAAATCATAGGGAGGTTA
1 TCAAAATTTCATAAGGAGGTTA
*
59397 TCAAAATTT-GT-A--A--TTA
1 TCAAAATTTCATAAGGAGGTTA
*
59413 TCAAGATTTCATAAGGAGGTTA
1 TCAAAATTTCATAAGGAGGTTA
* *
59435 TCAAAATTTTATAGGGAGCTAGGTTTA
1 TCAAAATTTCATA---AG-GAGG-TTA
* *
59462 TCAAAATTTTAT-AGTAAGGTTTA
1 TCAAAATTTCATAAG-GAGG-TTA
* * *
59485 TCACAATTTCATAATGTGGTTA
1 TCAAAATTTCATAAGGAGGTTA
59507 TCAAAATTTCATA
1 TCAAAATTTCATA
59520 GTGTAATTAC
Statistics
Matches: 126, Mismatches: 27, Indels: 28
0.70 0.15 0.15
Matches are distributed among these distances:
16 11 0.09
17 1 0.01
18 2 0.02
20 1 0.01
21 2 0.02
22 66 0.52
23 22 0.17
24 1 0.01
25 2 0.02
26 3 0.02
27 15 0.12
ACGTcount: A:0.40, C:0.09, G:0.15, T:0.36
Consensus pattern (22 bp):
TCAAAATTTCATAAGGAGGTTA
Found at i:59482 original size:23 final size:23
Alignment explanation
Indices: 59455--59521 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 23
59445 ATAGGGAGCT
*
59455 AGGTTTATCAAAATTTTATAGTA
1 AGGTTTATCAAAATTTCATAGTA
* * *
59478 AGGTTTATCACAATTTCATAATG
1 AGGTTTATCAAAATTTCATAGTA
*
59501 TGG-TTATCAAAATTTCATAGT
1 AGGTTTATCAAAATTTCATAGT
59522 GTAATTACTG
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
22 16 0.43
23 21 0.57
ACGTcount: A:0.36, C:0.09, G:0.13, T:0.42
Consensus pattern (23 bp):
AGGTTTATCAAAATTTCATAGTA
Found at i:59800 original size:62 final size:62
Alignment explanation
Indices: 59734--59885 Score: 259
Period size: 62 Copynumber: 2.5 Consensus size: 62
59724 TTGTTATTGA
59734 AATTTCATAGGAAGGTTATCAAAATTTCATAAGGACGTCATAAAAAATAGTGTAATTATCAT
1 AATTTCATAGGAAGGTTATCAAAATTTCATAAGGACGTCATAAAAAATAGTGTAATTATCAT
* * *
59796 AATTTCATAGGAATGTTATCAAAATTTCATAAGGATGTTATAAAAAATAGTGTAATTATCAT
1 AATTTCATAGGAAGGTTATCAAAATTTCATAAGGACGTCATAAAAAATAGTGTAATTATCAT
* *
59858 AATTTAATAGGAAGGTTATCATAATTTC
1 AATTTCATAGGAAGGTTATCAAAATTTC
59886 GTATGAATAT
Statistics
Matches: 84, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
62 84 1.00
ACGTcount: A:0.43, C:0.08, G:0.14, T:0.36
Consensus pattern (62 bp):
AATTTCATAGGAAGGTTATCAAAATTTCATAAGGACGTCATAAAAAATAGTGTAATTATCAT
Found at i:59814 original size:22 final size:22
Alignment explanation
Indices: 59789--59885 Score: 73
Period size: 22 Copynumber: 4.6 Consensus size: 22
59779 AATAGTGTAA
59789 TTATCATAATTTCATAGGAATG
1 TTATCATAATTTCATAGGAATG
*
59811 TTATCAAAATTTCATAAGG-ATG
1 TTATCATAATTTCAT-AGGAATG
**
59833 TTAT-A-AA--AAATAGTGTAA--
1 TTATCATAATTTCATAG-G-AATG
* *
59851 TTATCATAATTTAATAGGAAGG
1 TTATCATAATTTCATAGGAATG
59873 TTATCATAATTTC
1 TTATCATAATTTC
59886 GTATGAATAT
Statistics
Matches: 60, Mismatches: 5, Indels: 20
0.71 0.06 0.24
Matches are distributed among these distances:
17 2 0.03
18 7 0.12
19 1 0.02
20 7 0.12
21 2 0.03
22 38 0.63
23 3 0.05
ACGTcount: A:0.41, C:0.07, G:0.12, T:0.39
Consensus pattern (22 bp):
TTATCATAATTTCATAGGAATG
Found at i:64097 original size:29 final size:28
Alignment explanation
Indices: 64081--64160 Score: 115
Period size: 30 Copynumber: 2.7 Consensus size: 28
64071 TTCTTTAATT
64081 AATTAATTAATACTACTATTTTTTAGGAG
1 AATTAATTAATACTACTATTTTTTA-GAG
64110 AATTAATTAATACTACTATTTTTTTAGGAG
1 AATTAATTAATACTACTA-TTTTTTA-GAG
*
64140 AATTAATATACTACTACTATT
1 AATTAAT-TAATACTACTATT
64161 AATATCAATA
Statistics
Matches: 48, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
29 18 0.38
30 20 0.42
31 10 0.21
ACGTcount: A:0.39, C:0.09, G:0.07, T:0.45
Consensus pattern (28 bp):
AATTAATTAATACTACTATTTTTTAGAG
Found at i:64135 original size:30 final size:30
Alignment explanation
Indices: 64081--64160 Score: 135
Period size: 29 Copynumber: 2.7 Consensus size: 30
64071 TTCTTTAATT
64081 AATTAATTAATACTACTA-TTTTTTAGGAG
1 AATTAATTAATACTACTATTTTTTTAGGAG
64110 AATTAATTAATACTACTATTTTTTTAGGAG
1 AATTAATTAATACTACTATTTTTTTAGGAG
*
64140 AATTAATATACTACTACTATT
1 AATTAAT-TAATACTACTATT
64161 AATATCAATA
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
29 18 0.38
30 18 0.38
31 12 0.25
ACGTcount: A:0.39, C:0.09, G:0.07, T:0.45
Consensus pattern (30 bp):
AATTAATTAATACTACTATTTTTTTAGGAG
Found at i:65268 original size:2 final size:2
Alignment explanation
Indices: 65261--65295 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
65251 TTTTATCCTT
65261 TA TA TA 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 TA TA TA T
65296 TCTTGTAATC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.