Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006981.1 Corchorus capsularis cultivar CVL-1 contig07002, 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: 54556
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Found at i:1471 original size:78 final size:74
Alignment explanation
Indices: 1318--1530 Score: 310
Period size: 78 Copynumber: 2.9 Consensus size: 74
1308 TTGTTTAGGT
* *
1318 TTTTA-TAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATAT-CTT-T-A-T
1 TTTTACTA-TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACT
1378 AATTATTTTA
65 AATTATTTTA
1388 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTA
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTA
*
1453 TTATATTTTACCA
66 AT-TATTTT---A
*
1466 TTTTACTATTTTACTCAACTAAAAACTCAATTTTTATATAATTAAATCTAATATCCTTATAACTA
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTA
1531 CTAGTCTTCG
Statistics
Matches: 130, Mismatches: 4, Indels: 10
0.90 0.03 0.07
Matches are distributed among these distances:
70 49 0.38
71 5 0.04
72 1 0.01
73 1 0.01
74 3 0.02
75 6 0.05
78 65 0.50
ACGTcount: A:0.38, C:0.13, G:0.00, T:0.48
Consensus pattern (74 bp):
TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTA
ATTATTTTA
Found at i:2456 original size:109 final size:109
Alignment explanation
Indices: 2327--2601 Score: 455
Period size: 109 Copynumber: 2.5 Consensus size: 109
2317 AAAAAAATTA
2327 TATAAA-ATATT-GAATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAG
1 TATAAAGATATTAG-ATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAG
2390 AAAAAATTTTAATATATCCAAATTTTTTGGTAAAAATAAAGTAAT
65 AAAAAATTTTAATATATCCAAATTTTTTGGTAAAAATAAAGTAAT
2435 TATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAGA
1 TATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAGA
*
2500 AAAAATTTTAGTATATCCAAATTTTTTGGTAAAAATAAAGTAAT
66 AAAAATTTTAATATATCCAAATTTTTTGGTAAAAATAAAGTAAT
* *
2544 TATAAAGATATTAGATTTAATTTAATTGAATAAAAATAGAGTTTCTAGTAGAATAAAA
1 TATAAAGATATTAGATTTAA-TT-A---AATGAAAATAGAGTTTTTAGTAGAATAAAA
2602 CTATAATAGT
Statistics
Matches: 157, Mismatches: 3, Indels: 8
0.93 0.02 0.05
Matches are distributed among these distances:
108 6 0.04
109 119 0.76
110 3 0.02
111 1 0.01
114 28 0.18
ACGTcount: A:0.49, C:0.02, G:0.11, T:0.38
Consensus pattern (109 bp):
TATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAGA
AAAAATTTTAATATATCCAAATTTTTTGGTAAAAATAAAGTAAT
Found at i:4564 original size:20 final size:20
Alignment explanation
Indices: 4536--4573 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
4526 ATCAACTTCT
4536 GCCACGTCATCCGTTGACCC
1 GCCACGTCATCCGTTGACCC
* *
4556 GCCATGTCATTCGTTGAC
1 GCCACGTCATCCGTTGAC
4574 TACCACGTCA
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:0.16, C:0.37, G:0.21, T:0.26
Consensus pattern (20 bp):
GCCACGTCATCCGTTGACCC
Found at i:5933 original size:28 final size:28
Alignment explanation
Indices: 5902--5959 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 28
5892 CGATTACAAT
*
5902 TTCTGTCCTTGACCTGTTTGGTCCCGTA
1 TTCTGTCCTTGACCTGCTTGGTCCCGTA
* *
5930 TTCTGTCCTTGACTTGCTTGGTCTCGTA
1 TTCTGTCCTTGACCTGCTTGGTCCCGTA
5958 TT
1 TT
5960 TGACTCTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.07, C:0.26, G:0.21, T:0.47
Consensus pattern (28 bp):
TTCTGTCCTTGACCTGCTTGGTCCCGTA
Found at i:14729 original size:24 final size:25
Alignment explanation
Indices: 14681--14729 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
14671 TTATTTTCCA
*
14681 TCAAACTTCAAACTTTTCAATTCTC
1 TCAAACTTCAAACTTTTCAAATCTC
*
14706 TCAACCTTCAAAC-TTTCAAATCTC
1 TCAAACTTCAAACTTTTCAAATCTC
14730 AATCATTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 10 0.45
25 12 0.55
ACGTcount: A:0.33, C:0.31, G:0.00, T:0.37
Consensus pattern (25 bp):
TCAAACTTCAAACTTTTCAAATCTC
Found at i:17943 original size:51 final size:51
Alignment explanation
Indices: 17879--17979 Score: 184
Period size: 51 Copynumber: 2.0 Consensus size: 51
17869 TGCTTAGCCT
17879 TGTTATGTCTTATAACTATATATGCTGCTTTATCAATGGCTTCTTTATGTC
1 TGTTATGTCTTATAACTATATATGCTGCTTTATCAATGGCTTCTTTATGTC
* *
17930 TGTTATGTGTTATAACTGTATATGCTGCTTTATCAATGGCTTCTTTATGT
1 TGTTATGTCTTATAACTATATATGCTGCTTTATCAATGGCTTCTTTATGT
17980 TGCTCACATT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.21, C:0.14, G:0.16, T:0.50
Consensus pattern (51 bp):
TGTTATGTCTTATAACTATATATGCTGCTTTATCAATGGCTTCTTTATGTC
Found at i:22374 original size:8 final size:8
Alignment explanation
Indices: 22363--22388 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
22353 CGCACACACA
22363 CACACATG
1 CACACATG
22371 CACACATG
1 CACACATG
22379 CACACATG
1 CACACATG
22387 CA
1 CA
22389 TCTGATATCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.38, C:0.38, G:0.12, T:0.12
Consensus pattern (8 bp):
CACACATG
Found at i:22375 original size:16 final size:16
Alignment explanation
Indices: 22354--22388 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
22344 CTCTATGCGC
22354 GCACACACACACACAT
1 GCACACACACACACAT
**
22370 GCACACATGCACACAT
1 GCACACACACACACAT
22386 GCA
1 GCA
22389 TCTGATATCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.40, C:0.40, G:0.11, T:0.09
Consensus pattern (16 bp):
GCACACACACACACAT
Found at i:26746 original size:6 final size:6
Alignment explanation
Indices: 26735--26772 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
26725 CGCCAGCACT
26735 TGTCTC TGTCTC TGTCTC TGTCTC TGTCTC TGTCTC TG
1 TGTCTC TGTCTC TGTCTC TGTCTC TGTCTC TGTCTC TG
26773 ATCCTTTAGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.00, C:0.32, G:0.18, T:0.50
Consensus pattern (6 bp):
TGTCTC
Found at i:31821 original size:17 final size:17
Alignment explanation
Indices: 31799--31835 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
31789 TTTGTTTGGT
31799 TGAGGGGTA-GAGATGGG
1 TGAGGGGTAGGA-ATGGG
31816 TGAGGGGTAGGAATGGG
1 TGAGGGGTAGGAATGGG
31833 TGA
1 TGA
31836 TTACTACCCC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 17 0.89
18 2 0.11
ACGTcount: A:0.24, C:0.00, G:0.57, T:0.19
Consensus pattern (17 bp):
TGAGGGGTAGGAATGGG
Found at i:36752 original size:245 final size:245
Alignment explanation
Indices: 36437--36881 Score: 836
Period size: 245 Copynumber: 1.8 Consensus size: 245
36427 GCTTGTTGCT
*
36437 TGTGGCCCTAGATGTGTTCTTCAACATGATAGGCCATTTTGTTTCGGTTGTTGCTGTTTGCCCTA
1 TGTGGCCCTAGATGTGTTCTTCAACATGATAGGCCATTTTGTTTCGGTTGTTGCTATTTGCCCTA
* *
36502 CACTTGAGTGGGAGTAATATATCTCCCATTGGTCAGTCCTGAGTTGGTTGTGTCTTTGTATTCAA
66 CACTTGAGTGGGAGTAATATATCTACCATTGGTCAGTCCTGAGTTGGTTGTGTATTTGTATTCAA
* *
36567 GTTGGTTCTTGTTATCTAACACTTTTTTGTTAGATGTCATTCTCTACCATATGAACATGATATAA
131 GTTGGTTCTTGTTATCTAACACTTTGTTGTTAGATGCCATTCTCTACCATATGAACATGATATAA
36632 TGAAGCTTGGGCTGTTTGATAAACCATTGAATATTTTCAAACCATTGAAA
196 TGAAGCTTGGGCTGTTTGATAAACCATTGAATATTTTCAAACCATTGAAA
36682 TGTGGCCCTAGATGTGTTCTTCAACATGATAGGCCATTTTGTTTCGGTTGTTGCTATTTGCCCTA
1 TGTGGCCCTAGATGTGTTCTTCAACATGATAGGCCATTTTGTTTCGGTTGTTGCTATTTGCCCTA
36747 CACTTGAGTGGGAGTAATATATCTACCATTGGTCAGTCCTGAGTTGGTTGTGTATTTGTATTCAA
66 CACTTGAGTGGGAGTAATATATCTACCATTGGTCAGTCCTGAGTTGGTTGTGTATTTGTATTCAA
*
36812 GTTGGTTCTTGTTATCTAACACTTTGTTGTTAGATGCCATTCTCTACCATATGAACATGATATAT
131 GTTGGTTCTTGTTATCTAACACTTTGTTGTTAGATGCCATTCTCTACCATATGAACATGATATAA
36877 TGAAG
196 TGAAG
36882 TTTGTGGAAT
Statistics
Matches: 194, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
245 194 1.00
ACGTcount: A:0.22, C:0.17, G:0.21, T:0.40
Consensus pattern (245 bp):
TGTGGCCCTAGATGTGTTCTTCAACATGATAGGCCATTTTGTTTCGGTTGTTGCTATTTGCCCTA
CACTTGAGTGGGAGTAATATATCTACCATTGGTCAGTCCTGAGTTGGTTGTGTATTTGTATTCAA
GTTGGTTCTTGTTATCTAACACTTTGTTGTTAGATGCCATTCTCTACCATATGAACATGATATAA
TGAAGCTTGGGCTGTTTGATAAACCATTGAATATTTTCAAACCATTGAAA
Found at i:40145 original size:29 final size:29
Alignment explanation
Indices: 40112--40173 Score: 106
Period size: 29 Copynumber: 2.1 Consensus size: 29
40102 ATTGCTTGGC
*
40112 TGGTAAGGATTTTCAATAATTGGAAAACA
1 TGGTAAGGATTTTCAATAATTGAAAAACA
*
40141 TGGTAAGGATTTTCAATAGTTGAAAAACA
1 TGGTAAGGATTTTCAATAATTGAAAAACA
40170 TGGT
1 TGGT
40174 TTATATTATG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.39, C:0.06, G:0.23, T:0.32
Consensus pattern (29 bp):
TGGTAAGGATTTTCAATAATTGAAAAACA
Found at i:44183 original size:32 final size:32
Alignment explanation
Indices: 44147--44213 Score: 116
Period size: 32 Copynumber: 2.1 Consensus size: 32
44137 AATGCGAATT
44147 GTAATTTTATTCCAGATTAATCAGTAATCAAG
1 GTAATTTTATTCCAGATTAATCAGTAATCAAG
* *
44179 GTAATTTTATTCCAGATTAGTCAGTAGTCAAG
1 GTAATTTTATTCCAGATTAATCAGTAATCAAG
44211 GTA
1 GTA
44214 TCGGATGGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.37
Consensus pattern (32 bp):
GTAATTTTATTCCAGATTAATCAGTAATCAAG
Found at i:44457 original size:14 final size:14
Alignment explanation
Indices: 44438--44464 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
44428 TAAAAATAAC
44438 AATTATAAACTTTG
1 AATTATAAACTTTG
44452 AATTATAAACTTT
1 AATTATAAACTTT
44465 TTAGCACATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.44
Consensus pattern (14 bp):
AATTATAAACTTTG
Found at i:54060 original size:43 final size:43
Alignment explanation
Indices: 53999--54084 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
53989 TTAAATTCCA
53999 TTCACAACGTTAATCCAAGTCCGAGATAGACCCATTCACCAGC
1 TTCACAACGTTAATCCAAGTCCGAGATAGACCCATTCACCAGC
54042 TTCACAACGTTAATCCAAGTCCGAGATAGACCCATTCACCAGC
1 TTCACAACGTTAATCCAAGTCCGAGATAGACCCATTCACCAGC
54085 AACATGAGGA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.33, C:0.33, G:0.14, T:0.21
Consensus pattern (43 bp):
TTCACAACGTTAATCCAAGTCCGAGATAGACCCATTCACCAGC
Found at i:54169 original size:2 final size:2
Alignment explanation
Indices: 54162--54195 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
54152 ATTATATTGC
54162 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
54196 GGAGTCAAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.