Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010667.1 Corchorus capsularis cultivar CVL-1 contig10688, 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: 12433
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Found at i:580 original size:12 final size:12
Alignment explanation
Indices: 560--591 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
550 GCCGCGCAAC
*
560 ACCGCCCACATG
1 ACCGGCCACATG
572 ACCGGCCACATG
1 ACCGGCCACATG
584 ACCGGCCA
1 ACCGGCCA
592 TCGCATGCGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.25, C:0.47, G:0.22, T:0.06
Consensus pattern (12 bp):
ACCGGCCACATG
Found at i:3101 original size:21 final size:21
Alignment explanation
Indices: 3075--3116 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
3065 AGCACAAGTG
*
3075 ACCGGCCATGCGACTTGGAGA
1 ACCGGCCACGCGACTTGGAGA
*
3096 ACCGGCCACGTGACTTGGAGA
1 ACCGGCCACGCGACTTGGAGA
3117 TGCCCGCGCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.29, G:0.33, T:0.14
Consensus pattern (21 bp):
ACCGGCCACGCGACTTGGAGA
Found at i:3133 original size:33 final size:32
Alignment explanation
Indices: 3096--3202 Score: 124
Period size: 33 Copynumber: 3.2 Consensus size: 32
3086 GACTTGGAGA
* *
3096 ACCGGCCACGTGACTTGGAGATGCCCGCGCAAC
1 ACCGGCCACGCGACATGGAGATGCCCG-GCAAC
* *
3129 ACCGGCCATGCGACATGGAGATGCCCGGCCATC
1 ACCGGCCACGCGACATGGAGATGCCCGG-CAAC
* * *
3162 ACCGGCCACGCGACATGGACATGTCCGGCCAC
1 ACCGGCCACGCGACATGGAGATGCCCGGCAAC
3194 TACCGGCCA
1 -ACCGGCCA
3203 TCGCTTGGCG
Statistics
Matches: 63, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
32 3 0.05
33 60 0.95
ACGTcount: A:0.21, C:0.38, G:0.29, T:0.11
Consensus pattern (32 bp):
ACCGGCCACGCGACATGGAGATGCCCGGCAAC
Found at i:4191 original size:17 final size:17
Alignment explanation
Indices: 4166--4199 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
4156 CACCCTTCTT
4166 GAAAATTCAAAAATTCA
1 GAAAATTCAAAAATTCA
*
4183 GAAACTTCAAAAATTCA
1 GAAAATTCAAAAATTCA
4200 TAGCCGATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.56, C:0.15, G:0.06, T:0.24
Consensus pattern (17 bp):
GAAAATTCAAAAATTCA
Found at i:8192 original size:14 final size:14
Alignment explanation
Indices: 8173--8200 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
8163 AGAGCTTTCC
8173 TTATTTTTTTTATT
1 TTATTTTTTTTATT
8187 TTATTTTTTTTATT
1 TTATTTTTTTTATT
8201 CAAATTTTTT
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:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (14 bp):
TTATTTTTTTTATT
Found at i:9193 original size:23 final size:23
Alignment explanation
Indices: 9144--9197 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 23
9134 GTGGCCGGTT
*
9144 GTGGCCGGGCATGGCCGAGTCAT
1 GTGGCCGGGCATGGCCGAGTCAC
*
9167 GTGGCCGGGCATGGCC-ATGTCGC
1 GTGGCCGGGCATGGCCGA-GTCAC
9190 GTGGCCGG
1 GTGGCCGG
9198 TGATGGTCGG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 1 0.04
23 27 0.96
ACGTcount: A:0.09, C:0.28, G:0.46, T:0.17
Consensus pattern (23 bp):
GTGGCCGGGCATGGCCGAGTCAC
Found at i:9209 original size:33 final size:33
Alignment explanation
Indices: 9172--9263 Score: 123
Period size: 33 Copynumber: 2.8 Consensus size: 33
9162 GTCATGTGGC
**
9172 CGGGCATGGCCATGTCGCGTGGCCGGTGATG-G
1 CGGGCATCTCCATGTCGCGTGGCCGGTGATGCG
* *
9204 TCGGGCATCTCCATGTCGCATGGCCGGTGTTGCG
1 -CGGGCATCTCCATGTCGCGTGGCCGGTGATGCG
*
9238 CGGGCATCTCCAAGTCGCGTGGCCGG
1 CGGGCATCTCCATGTCGCGTGGCCGG
9264 ATCTCCAAGT
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
33 51 0.98
34 1 0.02
ACGTcount: A:0.10, C:0.29, G:0.40, T:0.21
Consensus pattern (33 bp):
CGGGCATCTCCATGTCGCGTGGCCGGTGATGCG
Found at i:9269 original size:21 final size:21
Alignment explanation
Indices: 9243--9282 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
9233 TTGCGCGGGC
*
9243 ATCTCCAAGTCGCGTGGCCGG
1 ATCTCCAAGTCGCATGGCCGG
9264 ATCTCCAAGTCGCATGGCC
1 ATCTCCAAGTCGCATGGCC
9283 TGTCACTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.35, G:0.28, T:0.20
Consensus pattern (21 bp):
ATCTCCAAGTCGCATGGCCGG
Found at i:10372 original size:20 final size:21
Alignment explanation
Indices: 10347--10395 Score: 82
Period size: 20 Copynumber: 2.4 Consensus size: 21
10337 GACTAAAAAA
10347 TCGTGTTTAGTCGTGTCGTG-
1 TCGTGTTTAGTCGTGTCGTGT
*
10367 TCGTGTTTATTCGTGTCGTGT
1 TCGTGTTTAGTCGTGTCGTGT
10388 TCGTGTTT
1 TCGTGTTT
10396 GGCCATATAC
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
20 19 0.70
21 8 0.30
ACGTcount: A:0.04, C:0.14, G:0.31, T:0.51
Consensus pattern (21 bp):
TCGTGTTTAGTCGTGTCGTGT
Found at i:10444 original size:12 final size:12
Alignment explanation
Indices: 10427--10454 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
10417 ACATGTTTAT
10427 ACGACACGAAAC
1 ACGACACGAAAC
10439 ACGACACGAAAC
1 ACGACACGAAAC
10451 ACGA
1 ACGA
10455 ATTGCCAGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.50, C:0.32, G:0.18, T:0.00
Consensus pattern (12 bp):
ACGACACGAAAC
Found at i:10721 original size:13 final size:13
Alignment explanation
Indices: 10705--10729 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
10695 CTTTAATTGC
10705 TTTCTTTTTAATT
1 TTTCTTTTTAATT
10718 TTTCTTTTTAAT
1 TTTCTTTTTAAT
10730 CCCCTGTTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTCTTTTTAATT
Found at i:11370 original size:33 final size:33
Alignment explanation
Indices: 11333--11439 Score: 126
Period size: 33 Copynumber: 3.2 Consensus size: 33
11323 AGCACTAGTG
** *
11333 ACCGGCCATACGACTTGGAGAAGTCCGGCCAAC
1 ACCGGCCACGCGACTTGGAGATGTCCGGCCAAC
* * *
11366 ACCGGCCACGTGACTCGGAGATGCCCGGCCAAC
1 ACCGGCCACGCGACTTGGAGATGTCCGGCCAAC
* *
11399 ACCGGCCACGCGACATGGACATGTCCGGCC-AC
1 ACCGGCCACGCGACTTGGAGATGTCCGGCCAAC
11431 AACCGGCCA
1 -ACCGGCCA
11440 TCGCTAGGCG
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
32 2 0.03
33 60 0.97
ACGTcount: A:0.24, C:0.38, G:0.28, T:0.09
Consensus pattern (33 bp):
ACCGGCCACGCGACTTGGAGATGTCCGGCCAAC
Done.