Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007201.1 Corchorus capsularis cultivar CVL-1 contig07222, 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: 85058
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.32
Found at i:1145 original size:18 final size:19
Alignment explanation
Indices: 1122--1161 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
1112 CTAAATTTAA
1122 TTTCGACAC-AATTTTTTT
1 TTTCGACACAAATTTTTTT
1140 TTTCGACACAAATTTTTTT
1 TTTCGACACAAATTTTTTT
1159 TTT
1 TTT
1162 TTTAGAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.23, C:0.15, G:0.05, T:0.57
Consensus pattern (19 bp):
TTTCGACACAAATTTTTTT
Found at i:1173 original size:21 final size:22
Alignment explanation
Indices: 1133--1173 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1123 TTCGACACAA
* *
1133 TTTTTTTTTTCGACACAAATTT
1 TTTTTTTTTTAGACAAAAATTT
1155 TTTTTTTTTTAGA-AAAAAT
1 TTTTTTTTTTAGACAAAAAT
1174 GGAAAACAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.29, C:0.07, G:0.05, T:0.59
Consensus pattern (22 bp):
TTTTTTTTTTAGACAAAAATTT
Found at i:2456 original size:10 final size:10
Alignment explanation
Indices: 2441--2466 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
2431 GAGGACTCTA
2441 GAATTTTCTG
1 GAATTTTCTG
2451 GAATTTTCTG
1 GAATTTTCTG
2461 GAATTT
1 GAATTT
2467 GGCAGCAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.23, C:0.08, G:0.19, T:0.50
Consensus pattern (10 bp):
GAATTTTCTG
Found at i:3124 original size:2 final size:2
Alignment explanation
Indices: 3117--3147 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
3107 AAGTCTATTT
3117 TA TA TA TA TA TA TA TA TA TA TA TA TA GTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
3148 AATCAGAGAC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:8309 original size:30 final size:30
Alignment explanation
Indices: 8269--8326 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
8259 AGCTTCTCCT
*
8269 TGCTATTTGAAGTAGGATTTGCGATTCCCA
1 TGCTACTTGAAGTAGGATTTGCGATTCCCA
* *
8299 TGCTACTTGAATTAGGGTTTGCGATTCC
1 TGCTACTTGAAGTAGGATTTGCGATTCC
8327 TCCTCCTTCT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.21, C:0.17, G:0.24, T:0.38
Consensus pattern (30 bp):
TGCTACTTGAAGTAGGATTTGCGATTCCCA
Found at i:10436 original size:42 final size:42
Alignment explanation
Indices: 10383--10468 Score: 136
Period size: 42 Copynumber: 2.0 Consensus size: 42
10373 ATACATGGGA
* * * *
10383 CATCGCACGGGCTATCGGACGGGCCATCCGGCCACAACCGGC
1 CATCACACGGGCTAACGCACGGACCATCCGGCCACAACCGGC
10425 CATCACACGGGCTAACGCACGGACCATCCGGCCACAACCGGC
1 CATCACACGGGCTAACGCACGGACCATCCGGCCACAACCGGC
10467 CA
1 CA
10469 CTTGATCCTT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.23, C:0.42, G:0.27, T:0.08
Consensus pattern (42 bp):
CATCACACGGGCTAACGCACGGACCATCCGGCCACAACCGGC
Found at i:25280 original size:27 final size:27
Alignment explanation
Indices: 25250--25324 Score: 87
Period size: 27 Copynumber: 2.7 Consensus size: 27
25240 AGGGTCACCT
*
25250 AGGGGCATTTCGGTCATTTTTACATTC
1 AGGGGCATTTTGGTCATTTTTACATTC
* * * *
25277 AGGGGCATTTTTGTCATTCTTGCATTT
1 AGGGGCATTTTGGTCATTTTTACATTC
25304 AGGGGGGCATTTTGGTCATTT
1 A--GGGGCATTTTGGTCATTT
25325 GGTCCCTTTA
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
27 23 0.59
29 16 0.41
ACGTcount: A:0.16, C:0.15, G:0.27, T:0.43
Consensus pattern (27 bp):
AGGGGCATTTTGGTCATTTTTACATTC
Found at i:29573 original size:5 final size:5
Alignment explanation
Indices: 29563--29600 Score: 76
Period size: 5 Copynumber: 7.6 Consensus size: 5
29553 TATAAAGAAG
29563 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
29601 TTTAAACTAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:30295 original size:33 final size:33
Alignment explanation
Indices: 30253--30365 Score: 181
Period size: 33 Copynumber: 3.4 Consensus size: 33
30243 AGCCGCGCAA
* **
30253 CACCGGCCACATGATTCGGGGATGCCCGGCCAC
1 CACCGGCCACATGACTCGGCCATGCCCGGCCAC
*
30286 CACCGGCCACGTGACTCGGCCATGCCCGGCCAC
1 CACCGGCCACATGACTCGGCCATGCCCGGCCAC
30319 CACCGGCCACATGACTCGGCCATGCCCGGCCAC
1 CACCGGCCACATGACTCGGCCATGCCCGGCCAC
*
30352 AACCGGCCACATGA
1 CACCGGCCACATGA
30366 TCCTTTAACT
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
33 74 1.00
ACGTcount: A:0.19, C:0.44, G:0.27, T:0.10
Consensus pattern (33 bp):
CACCGGCCACATGACTCGGCCATGCCCGGCCAC
Found at i:33456 original size:33 final size:33
Alignment explanation
Indices: 33419--33499 Score: 108
Period size: 33 Copynumber: 2.5 Consensus size: 33
33409 AGCCGCGCAA
* *
33419 CACCGGCCACATGATTCGGAGATGCCCGGCCAC
1 CACCGGCCACATGATTCGGACATGCCCGACCAC
* *
33452 CACCGGCCACATGACTCGGCCATGCCCGACCAC
1 CACCGGCCACATGATTCGGACATGCCCGACCAC
* *
33485 AACCGGCCTCATGAT
1 CACCGGCCACATGAT
33500 CCATTAACTA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.22, C:0.42, G:0.23, T:0.12
Consensus pattern (33 bp):
CACCGGCCACATGATTCGGACATGCCCGACCAC
Found at i:35379 original size:33 final size:33
Alignment explanation
Indices: 35342--35458 Score: 139
Period size: 33 Copynumber: 3.5 Consensus size: 33
35332 CGACTTGGAG
*
35342 ATGCCCGACCA-ACACCGGTCACGCGACATGACC
1 ATGCCCGGCCACA-ACCGGTCACGCGACATGACC
* *
35375 ATGCCTGGCCACAACCGGCCACGCGACATGACC
1 ATGCCCGGCCACAACCGGTCACGCGACATGACC
** *
35408 ATGCCCGGCCACAACCGGTCACATGAC-TCGGCC
1 ATGCCCGGCCACAACCGGTCACGCGACAT-GACC
*
35441 AAGCCCGGCCACAACCGG
1 ATGCCCGGCCACAACCGG
35459 CCACATGATC
Statistics
Matches: 73, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
32 1 0.01
33 71 0.97
34 1 0.01
ACGTcount: A:0.25, C:0.43, G:0.24, T:0.09
Consensus pattern (33 bp):
ATGCCCGGCCACAACCGGTCACGCGACATGACC
Found at i:38997 original size:30 final size:32
Alignment explanation
Indices: 38916--38997 Score: 98
Period size: 33 Copynumber: 2.6 Consensus size: 32
38906 TCGCATGGGG
*
38916 CAACCGGCCACAACCGGCCATCGATTGGCGCAC
1 CAACCGGACACAACCGGCCATCGATTGGCG-AC
*
38949 CAACCGGCCACAACCGGCCATCGATTGG-G-C
1 CAACCGGACACAACCGGCCATCGATTGGCGAC
*
38979 CATCCGGACA-AGACCGGCC
1 CAACCGGACACA-ACCGGCC
38998 TTTTGATCCT
Statistics
Matches: 46, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
29 1 0.02
30 16 0.35
32 1 0.02
33 28 0.61
ACGTcount: A:0.24, C:0.41, G:0.26, T:0.09
Consensus pattern (32 bp):
CAACCGGACACAACCGGCCATCGATTGGCGAC
Found at i:42891 original size:33 final size:33
Alignment explanation
Indices: 42865--43018 Score: 195
Period size: 33 Copynumber: 4.7 Consensus size: 33
42855 CGACTTGGAG
*
42865 ATGCCCGGCCA-ACACCGGTCACGCGACATGACC
1 ATGCCCGGCCACA-ACCGGCCACGCGACATGACC
*
42898 ATGCCCAGCCACAACCGGCCACGCGACATGACC
1 ATGCCCGGCCACAACCGGCCACGCGACATGACC
*
42931 ATGCTCGGCCACAACCGGCCACGCGACATGACC
1 ATGCCCGGCCACAACCGGCCACGCGACATGACC
* ** *
42964 ATGCCCGGCCACAACCGGTCACATGAC-TCGGCC
1 ATGCCCGGCCACAACCGGCCACGCGACAT-GACC
* *
42997 AAGCCCGGCCACAACCAGCCAC
1 ATGCCCGGCCACAACCGGCCAC
43019 ATGATCCTTT
Statistics
Matches: 107, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
32 1 0.01
33 105 0.98
34 1 0.01
ACGTcount: A:0.25, C:0.44, G:0.23, T:0.08
Consensus pattern (33 bp):
ATGCCCGGCCACAACCGGCCACGCGACATGACC
Found at i:47131 original size:33 final size:33
Alignment explanation
Indices: 47088--47190 Score: 127
Period size: 33 Copynumber: 3.1 Consensus size: 33
47078 CGAGTGACAA
* * *
47088 GCCATGCGACTTGGAGAAGCCCGGCCAACACCG
1 GCCACGCGACTTGGAGATGTCCGGCCAACACCG
* *
47121 GCCACGCGACTGGGAGATGTCCGGCCATCACCG
1 GCCACGCGACTTGGAGATGTCCGGCCAACACCG
* *
47154 GCCACGCGACATGGACATGTCCGGCC-ACAACCG
1 GCCACGCGACTTGGAGATGTCCGGCCAAC-ACCG
47187 GCCA
1 GCCA
47191 TCGCTTGGCG
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
32 1 0.02
33 59 0.98
ACGTcount: A:0.22, C:0.38, G:0.30, T:0.10
Consensus pattern (33 bp):
GCCACGCGACTTGGAGATGTCCGGCCAACACCG
Found at i:48263 original size:11 final size:10
Alignment explanation
Indices: 48238--48271 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
48228 TAGTTATATC
*
48238 AAAAAATATA
1 AAAAAATAAA
48248 AAAAAATAAA
1 AAAAAATAAA
48258 ATAAAAATAAA
1 A-AAAAATAAA
48269 AAA
1 AAA
48272 TTTTTCGACC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 12 0.55
11 10 0.45
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (10 bp):
AAAAAATAAA
Found at i:61823 original size:13 final size:13
Alignment explanation
Indices: 61805--61832 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
61795 GGTGACATCG
61805 GCATGGCATGGGT
1 GCATGGCATGGGT
61818 GCATGGCATGGGT
1 GCATGGCATGGGT
61831 GC
1 GC
61833 TGTCCGCGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.18, G:0.46, T:0.21
Consensus pattern (13 bp):
GCATGGCATGGGT
Found at i:69303 original size:46 final size:46
Alignment explanation
Indices: 69253--69348 Score: 192
Period size: 46 Copynumber: 2.1 Consensus size: 46
69243 TTGAGGATTT
69253 TTGGATTATTTATATGGGAATATATTCAGCCCATATAAACCTATAA
1 TTGGATTATTTATATGGGAATATATTCAGCCCATATAAACCTATAA
69299 TTGGATTATTTATATGGGAATATATTCAGCCCATATAAACCTATAA
1 TTGGATTATTTATATGGGAATATATTCAGCCCATATAAACCTATAA
69345 TTGG
1 TTGG
69349 GAATATATCC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 50 1.00
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (46 bp):
TTGGATTATTTATATGGGAATATATTCAGCCCATATAAACCTATAA
Done.