Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007153.1 Corchorus capsularis cultivar CVL-1 contig07174, 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: 61761
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:8496 original size:12 final size:12
Alignment explanation
Indices: 8464--8499 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
8454 TTCCTTCTCC
8464 CCTCTGTTATTT
1 CCTCTGTTATTT
8476 -C-CT-TTATTT
1 CCTCTGTTATTT
8485 CCTCTGTTATTT
1 CCTCTGTTATTT
8497 CCT
1 CCT
8500 TGCTTCCCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 6
0.78 0.00 0.22
Matches are distributed among these distances:
9 6 0.29
10 3 0.14
11 3 0.14
12 9 0.43
ACGTcount: A:0.08, C:0.28, G:0.06, T:0.58
Consensus pattern (12 bp):
CCTCTGTTATTT
Found at i:8656 original size:66 final size:66
Alignment explanation
Indices: 8583--8711 Score: 190
Period size: 66 Copynumber: 2.0 Consensus size: 66
8573 AAATTAACGG
* *
8583 CAACAGAGGGTTAGAGATC-T-CGCGTTTGTTGTTTTTTTATCAAGGGAGAGCTTGAGCTTGGCA
1 CAACAGAGGGTTAGAGATCTTGCGAGTTTGTTG--TTTTTATCAAAGGAGAGCTTGAGCTTGGCA
8646 CGA
64 CGA
* *
8649 CAACAGAGGGTTGGAGATCTTGCGAGTTTGTTGTTTTTATCAAAGGAGAGTTTGAGCTTGGCA
1 CAACAGAGGGTTAGAGATCTTGCGAGTTTGTTGTTTTTATCAAAGGAGAGCTTGAGCTTGGCA
8712 AGGTTGTCAA
Statistics
Matches: 57, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
66 46 0.81
67 1 0.02
68 10 0.18
ACGTcount: A:0.23, C:0.13, G:0.31, T:0.33
Consensus pattern (66 bp):
CAACAGAGGGTTAGAGATCTTGCGAGTTTGTTGTTTTTATCAAAGGAGAGCTTGAGCTTGGCACG
A
Found at i:9510 original size:12 final size:12
Alignment explanation
Indices: 9490--9527 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
9480 CATTTGGTTT
*
9490 AAGAAGAAGAAG
1 AAGATGAAGAAG
*
9502 AAGATGAAGATG
1 AAGATGAAGAAG
9514 AAGATGAAGAAG
1 AAGATGAAGAAG
9526 AA
1 AA
9528 AAACCCTAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.61, C:0.00, G:0.32, T:0.08
Consensus pattern (12 bp):
AAGATGAAGAAG
Found at i:10094 original size:29 final size:29
Alignment explanation
Indices: 10059--10169 Score: 128
Period size: 29 Copynumber: 4.0 Consensus size: 29
10049 GCGGCATGCC
10059 ACGTGTCACTTTTTGGTACACGTGGCGTG
1 ACGTGTCACTTTTTGGTACACGTGGCGTG
*
10088 ACGTGTCACTTTTTGGTACATGTGGC---
1 ACGTGTCACTTTTTGGTACACGTGGCGTG
*
10114 AC--G--ACTTTTTGGTACATGTGGCGTG
1 ACGTGTCACTTTTTGGTACACGTGGCGTG
*
10139 CCACATGTCACTTTTTGGTACACGTGGCGTG
1 --ACGTGTCACTTTTTGGTACACGTGGCGTG
10170 TCACGTCAAA
Statistics
Matches: 71, Mismatches: 2, Indels: 16
0.80 0.02 0.18
Matches are distributed among these distances:
22 19 0.27
24 1 0.01
26 2 0.03
27 2 0.03
29 26 0.37
31 21 0.30
ACGTcount: A:0.15, C:0.21, G:0.29, T:0.35
Consensus pattern (29 bp):
ACGTGTCACTTTTTGGTACACGTGGCGTG
Found at i:10125 original size:51 final size:52
Alignment explanation
Indices: 10066--10166 Score: 159
Period size: 53 Copynumber: 1.9 Consensus size: 52
10056 GCCACGTGTC
* *
10066 ACTTTTTGGTACACGTGGCGTG-ACGTGTCACTTTTTGGTACATGTGGCACG
1 ACTTTTTGGTACACGTGGCGTGCACATGTCACTTTTTGGTACACGTGGCACG
*
10117 ACTTTTTGGTACATGTGGCGTGCCACATGTCACTTTTTGGTACACGTGGC
1 ACTTTTTGGTACACGTGGCGTG-CACATGTCACTTTTTGGTACACGTGGC
10167 GTGTCACGTC
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
51 21 0.47
53 24 0.53
ACGTcount: A:0.16, C:0.21, G:0.28, T:0.36
Consensus pattern (52 bp):
ACTTTTTGGTACACGTGGCGTGCACATGTCACTTTTTGGTACACGTGGCACG
Found at i:12021 original size:19 final size:19
Alignment explanation
Indices: 11997--12033 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
11987 TCACAGTCCA
* *
11997 ATTTTTCGATCCACACTTG
1 ATTTTTCCATCCAAACTTG
12016 ATTTTTCCATCCAAACTT
1 ATTTTTCCATCCAAACTT
12034 CTTCTTCCTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.24, C:0.27, G:0.05, T:0.43
Consensus pattern (19 bp):
ATTTTTCCATCCAAACTTG
Found at i:20421 original size:2 final size:2
Alignment explanation
Indices: 20414--20453 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
20404 TGATTTTGCA
20414 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20454 TCTAAATAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30205 original size:26 final size:26
Alignment explanation
Indices: 30126--30206 Score: 66
Period size: 26 Copynumber: 3.3 Consensus size: 26
30116 CAATGGCATT
* *
30126 TAATTAAGGGTAGTTTAGTAATTGAC
1 TAATTAAGGATATTTTAGTAATTGAC
* *
30152 TAATTAA-GAT-TTAT-G-AACT-A-
1 TAATTAAGGATATTTTAGTAATTGAC
30172 TAATATTAAGGATATTTTAGTAATTGAC
1 T-A-ATTAAGGATATTTTAGTAATTGAC
30200 TAATTAA
1 TAATTAA
30207 ATATTAAGGG
Statistics
Matches: 41, Mismatches: 6, Indels: 16
0.65 0.10 0.25
Matches are distributed among these distances:
20 1 0.02
21 2 0.05
22 8 0.20
23 4 0.10
24 5 0.12
25 3 0.07
26 15 0.37
27 2 0.05
28 1 0.02
ACGTcount: A:0.41, C:0.04, G:0.15, T:0.41
Consensus pattern (26 bp):
TAATTAAGGATATTTTAGTAATTGAC
Found at i:30215 original size:33 final size:33
Alignment explanation
Indices: 30173--30239 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
30163 TATGAACTAT
30173 AATATTAAGGATATTTTAGTAATTGACTAATTA
1 AATATTAAGGATATTTTAGTAATTGACTAATTA
* *
30206 AATATTAAGGGTATTTTAGTAATTGATTAATTA
1 AATATTAAGGATATTTTAGTAATTGACTAATTA
30239 A
1 A
30240 GATTTATAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.42, C:0.01, G:0.13, T:0.43
Consensus pattern (33 bp):
AATATTAAGGATATTTTAGTAATTGACTAATTA
Found at i:30331 original size:86 final size:86
Alignment explanation
Indices: 30128--30292 Score: 241
Period size: 81 Copynumber: 2.0 Consensus size: 86
30118 ATGGCATTTA
* * * *
30128 ATTAAGGGTAGTTTAGTAATTGACTAATTAAGATTTAT-GA--ACT--ATAATATTAAGGATATT
1 ATTAAGGGTATTTTAGTAATTGAGTAACTAAGATTTATAAACTACTCCATAATATTAAGGATATT
30188 TTAGTAATTGACTAATTAAAT
66 TTAGTAATTGACTAATTAAAT
* *
30209 ATTAAGGGTATTTTAGTAATTGATTAATTAAGATTTATAAACTACTCCATAATATTAAGGATATT
1 ATTAAGGGTATTTTAGTAATTGAGTAACTAAGATTTATAAACTACTCCATAATATTAAGGATATT
30274 TTAGTAATTGACTAATTAA
66 TTAGTAATTGACTAATTAA
30293 GATTTTTGAG
Statistics
Matches: 76, Mismatches: 3, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
81 36 0.47
82 1 0.01
84 3 0.04
86 36 0.47
ACGTcount: A:0.41, C:0.05, G:0.13, T:0.41
Consensus pattern (86 bp):
ATTAAGGGTATTTTAGTAATTGAGTAACTAAGATTTATAAACTACTCCATAATATTAAGGATATT
TTAGTAATTGACTAATTAAAT
Found at i:32767 original size:109 final size:109
Alignment explanation
Indices: 32625--33008 Score: 603
Period size: 109 Copynumber: 3.5 Consensus size: 109
32615 AAAATATATA
*
32625 TATAAA-ATATT-GAATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAG
1 TATAAAGATATTAG-ATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATCAG
* * *
32688 AAAAATTTTTAATATATCCAAAATTTT-TGGTAAAAATAAAGTAAT
65 AAAAAATTTTAGTATATCC-AAATTTTGTGGTAAAAGTAAAGTAAT
*
32733 TATAAAGATACTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATCAGA
1 TATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATCAGA
32798 AAAAATTTTAGTATATCCAAATTTTGTGGTAAAAGTAAAGTAAT
66 AAAAATTTTAGTATATCCAAATTTTGTGGTAAAAGTAAAGTAAT
*
32842 TATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATCGGA
1 TATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATCAGA
32907 AAAAATTTTAGTATATCCAAATTTTGTGGTAAAAGTAAAGTAAT
66 AAAAATTTTAGTATATCCAAATTTTGTGGTAAAAGTAAAGTAAT
* * *
32951 TATAAAGATATTAGATTTAATTTAATTGAATAAAAATAGAGTTTCTAGTAAAATAAAA
1 TATAAAGATATTAGATTTAA-TT-A---AATGAAAATAGAGTTTTTAGTAGAATAAAA
33009 CTATAATAGT
Statistics
Matches: 258, Mismatches: 10, Indels: 10
0.93 0.04 0.04
Matches are distributed among these distances:
108 13 0.05
109 214 0.83
110 3 0.01
111 1 0.00
114 27 0.10
ACGTcount: A:0.48, C:0.03, G:0.12, T:0.37
Consensus pattern (109 bp):
TATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATCAGA
AAAAATTTTAGTATATCCAAATTTTGTGGTAAAAGTAAAGTAAT
Found at i:42794 original size:18 final size:19
Alignment explanation
Indices: 42771--42808 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
42761 GAAATAGGAT
42771 TTCAAATCCAACAGA-AGA
1 TTCAAATCCAACAGATAGA
*
42789 TTCAAATTCAACAGATAGA
1 TTCAAATCCAACAGATAGA
42808 T
1 T
42809 AGGATAAATC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.47, C:0.18, G:0.11, T:0.24
Consensus pattern (19 bp):
TTCAAATCCAACAGATAGA
Found at i:44632 original size:12 final size:13
Alignment explanation
Indices: 44615--44643 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
44605 CGATACCTCC
44615 ATATATCCG-TCG
1 ATATATCCGTTCG
44627 ATATATCCGTTCG
1 ATATATCCGTTCG
44640 ATAT
1 ATAT
44644 CTGTATTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.38
Consensus pattern (13 bp):
ATATATCCGTTCG
Found at i:46858 original size:22 final size:22
Alignment explanation
Indices: 46828--46876 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
46818 GCCGCTCCTC
*
46828 TCTCCCCTTCTCCCTCTCTAGT
1 TCTCGCCTTCTCCCTCTCTAGT
46850 TCTCGCCTTCTCCCTCTCTAGT
1 TCTCGCCTTCTCCCTCTCTAGT
46872 TCTCG
1 TCTCG
46877 TTGGTGTTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.04, C:0.47, G:0.08, T:0.41
Consensus pattern (22 bp):
TCTCGCCTTCTCCCTCTCTAGT
Found at i:47021 original size:25 final size:26
Alignment explanation
Indices: 46993--47070 Score: 97
Period size: 28 Copynumber: 3.0 Consensus size: 26
46983 GTTTTATTTG
*
46993 AGTTTGTTTTGAGTCGGTTT-GAGTC
1 AGTTTGTTTTGAGTCAGTTTCGAGTC
*
47018 AGTTT-TTTTTAGTCAGTTTCGAGTC
1 AGTTTGTTTTGAGTCAGTTTCGAGTC
*
47043 AGTTTGTTTTTTTAGTCAGTTTCGAGTC
1 AGTTTG--TTTTGAGTCAGTTTCGAGTC
47071 TAGTCTCAGT
Statistics
Matches: 47, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
24 12 0.26
25 15 0.32
28 20 0.43
ACGTcount: A:0.14, C:0.10, G:0.24, T:0.51
Consensus pattern (26 bp):
AGTTTGTTTTGAGTCAGTTTCGAGTC
Found at i:47048 original size:35 final size:36
Alignment explanation
Indices: 46979--47048 Score: 88
Period size: 35 Copynumber: 2.0 Consensus size: 36
46969 TACAGATCTG
** * *
46979 GTCAGTTTTATTTGAGTTTGTTTTGAGTCGGTTTGA
1 GTCAGTTTTATTTGAGTCAGTTTCGAGTCAGTTTGA
*
47015 GTCAGTTTT-TTTTAGTCAGTTTCGAGTCAGTTTG
1 GTCAGTTTTATTTGAGTCAGTTTCGAGTCAGTTTG
47049 TTTTTTTAGT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
35 20 0.69
36 9 0.31
ACGTcount: A:0.14, C:0.09, G:0.26, T:0.51
Consensus pattern (36 bp):
GTCAGTTTTATTTGAGTCAGTTTCGAGTCAGTTTGA
Found at i:53899 original size:2 final size:2
Alignment explanation
Indices: 53887--53927 Score: 66
Period size: 2 Copynumber: 20.5 Consensus size: 2
53877 ATACATCTTT
53887 TA TA TA CTA TA TA -A 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 TA TA TA T
53928 CAATACTTAC
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 1 0.03
2 34 0.92
3 2 0.05
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:53955 original size:11 final size:11
Alignment explanation
Indices: 53939--53964 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
53929 AATACTTACT
53939 TACTTTATTTA
1 TACTTTATTTA
53950 TACTTTATTTA
1 TACTTTATTTA
53961 TACT
1 TACT
53965 AGGTAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.27, C:0.12, G:0.00, T:0.62
Consensus pattern (11 bp):
TACTTTATTTA
Found at i:55045 original size:11 final size:11
Alignment explanation
Indices: 54999--55047 Score: 59
Period size: 11 Copynumber: 4.5 Consensus size: 11
54989 ATCTTACCTA
54999 TATATATTTA-
1 TATATATTTAT
55009 TATAT-TATTAT
1 TATATAT-TTAT
55020 TAT-TATTATAT
1 TATATATT-TAT
55031 TATATATTTAT
1 TATATATTTAT
55042 TATATA
1 TATATA
55048 ATACTAGCAT
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
9 1 0.03
10 10 0.29
11 19 0.56
12 4 0.12
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (11 bp):
TATATATTTAT
Found at i:56128 original size:15 final size:14
Alignment explanation
Indices: 56097--56146 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
56087 TTTATCCTAA
56097 TTTT-AAAAATCAC-
1 TTTTCAAAAAT-ACT
56110 TTTTCAAAAATACTT
1 TTTTCAAAAATAC-T
**
56125 TTTTCAAACGTACT
1 TTTTCAAAAATACT
56139 TTTTCAAA
1 TTTTCAAA
56147 GCACAACCTC
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
13 6 0.19
14 15 0.47
15 11 0.34
ACGTcount: A:0.38, C:0.16, G:0.02, T:0.44
Consensus pattern (14 bp):
TTTTCAAAAATACT
Found at i:57456 original size:39 final size:39
Alignment explanation
Indices: 57393--57467 Score: 114
Period size: 39 Copynumber: 1.9 Consensus size: 39
57383 TTTGTCTCAC
*
57393 TTTATATAGGCTTTATTCCCTTCTATGTATGTGTGACAG
1 TTTATATAGGCTTTATTCCCTTCTATATATGTGTGACAG
* * *
57432 TTTATATGGGCTTTGTTCCTTTCTATATATGTGTGA
1 TTTATATAGGCTTTATTCCCTTCTATATATGTGTGA
57468 TTAGTTAGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 32 1.00
ACGTcount: A:0.19, C:0.13, G:0.19, T:0.49
Consensus pattern (39 bp):
TTTATATAGGCTTTATTCCCTTCTATATATGTGTGACAG
Done.