Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007889.1 Corchorus capsularis cultivar CVL-1 contig07910, 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: 36618
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:1234 original size:69 final size:69
Alignment explanation
Indices: 1123--1258 Score: 254
Period size: 69 Copynumber: 2.0 Consensus size: 69
1113 TAGATACACC
*
1123 TCATTTCTATATTCTATTCTCTCTGAAGTAATAAGAAATTCTCTCTAATTTTTCTCTCTATATTG
1 TCATTTCTATATTCTATTCTCTCTGAAATAATAAGAAATTCTCTCTAATTTTTCTCTCTATATTG
1188 ATAA
66 ATAA
*
1192 TCATTTCTGTATTCTATTCTCTCTGAAATAATAAGAAATTCTCTCTAATTTTTCTCTCTATATTG
1 TCATTTCTATATTCTATTCTCTCTGAAATAATAAGAAATTCTCTCTAATTTTTCTCTCTATATTG
1257 AT
66 AT
1259 GATGTAAGAA
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
69 65 1.00
ACGTcount: A:0.28, C:0.18, G:0.06, T:0.49
Consensus pattern (69 bp):
TCATTTCTATATTCTATTCTCTCTGAAATAATAAGAAATTCTCTCTAATTTTTCTCTCTATATTG
ATAA
Found at i:1249 original size:35 final size:35
Alignment explanation
Indices: 1139--1250 Score: 115
Period size: 35 Copynumber: 3.2 Consensus size: 35
1129 CTATATTCTA
*
1139 TTCTCTCTGAAGTAATAAGAAATTCTCTCTAATTT
1 TTCTCTCTGAAATAATAAGAAATTCTCTCTAATTT
* * ** *
1174 TTCTCTCT-ATATTGATAA-TCATT-TCTGT-ATTCT
1 TTCTCTCTGA-AATAATAAGAAATTCTCTCTAATT-T
1207 ATTCTCTCTGAAATAATAAGAAATTCTCTCTAATTT
1 -TTCTCTCTGAAATAATAAGAAATTCTCTCTAATTT
1243 TTCTCTCT
1 TTCTCTCT
1251 ATATTGATGA
Statistics
Matches: 60, Mismatches: 10, Indels: 14
0.71 0.12 0.17
Matches are distributed among these distances:
32 3 0.05
33 5 0.08
34 18 0.30
35 26 0.43
36 5 0.08
37 3 0.05
ACGTcount: A:0.28, C:0.19, G:0.06, T:0.47
Consensus pattern (35 bp):
TTCTCTCTGAAATAATAAGAAATTCTCTCTAATTT
Found at i:1341 original size:31 final size:31
Alignment explanation
Indices: 1303--1366 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
1293 TTCTCACTTC
1303 TCATGAATCCAAATACGAGATACTATCACAA
1 TCATGAATCCAAATACGAGATACTATCACAA
1334 TCATGAATCCAAATACGAGATACTATCACAA
1 TCATGAATCCAAATACGAGATACTATCACAA
1365 TC
1 TC
1367 TTGATGGCCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.44, C:0.23, G:0.09, T:0.23
Consensus pattern (31 bp):
TCATGAATCCAAATACGAGATACTATCACAA
Found at i:8306 original size:60 final size:60
Alignment explanation
Indices: 8229--8349 Score: 197
Period size: 60 Copynumber: 2.0 Consensus size: 60
8219 ATTTCAAGCC
* *
8229 TATTAAGGCATGATTTATTTGTTTTAATAGAGATAAGTGTTAATTTAGGCTTTTAACAGG
1 TATTAAGACATGATTTATTTGTTTTAATAGAGACAAGTGTTAATTTAGGCTTTTAACAGG
* * *
8289 TATTAAGACATGGTTTATTTGTTTTAATAGAGACAGGTGTTAATTTAGTCTTTTAACAGG
1 TATTAAGACATGATTTATTTGTTTTAATAGAGACAAGTGTTAATTTAGGCTTTTAACAGG
8349 T
1 T
8350 GAATTTGGCA
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 56 1.00
ACGTcount: A:0.31, C:0.06, G:0.20, T:0.44
Consensus pattern (60 bp):
TATTAAGACATGATTTATTTGTTTTAATAGAGACAAGTGTTAATTTAGGCTTTTAACAGG
Found at i:13039 original size:16 final size:16
Alignment explanation
Indices: 13020--13089 Score: 63
Period size: 15 Copynumber: 4.5 Consensus size: 16
13010 AAAAAATCTG
* *
13020 AACCCGATAAAGCTCA
1 AACCCGAAAAAACTCA
13036 AACCCGAAAAAAC-CA
1 AACCCGAAAAAACTCA
* *
13051 AAACCGAAAAATCT-A
1 AACCCGAAAAAACTCA
* * *
13066 AATCCGATAAAACTCG
1 AACCCGAAAAAACTCA
13082 AACCCGAA
1 AACCCGAA
13090 CCTGAAAAAA
Statistics
Matches: 42, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
15 25 0.60
16 17 0.40
ACGTcount: A:0.51, C:0.29, G:0.10, T:0.10
Consensus pattern (16 bp):
AACCCGAAAAAACTCA
Found at i:13072 original size:15 final size:15
Alignment explanation
Indices: 13011--13077 Score: 53
Period size: 15 Copynumber: 4.3 Consensus size: 15
13001 CCGAACCCAA
*
13011 AAAAATCTGAACCCG
1 AAAAATCTAAACCCG
* *
13026 ATAAAGCTCAAACCCG
1 AAAAATCT-AAACCCG
* * *
13042 AAAAAACCAAAACCG
1 AAAAATCTAAACCCG
*
13057 AAAAATCTAAATCCG
1 AAAAATCTAAACCCG
13072 ATAAAA
1 A-AAAA
13078 CTCGAACCCG
Statistics
Matches: 40, Mismatches: 10, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
15 25 0.62
16 15 0.38
ACGTcount: A:0.55, C:0.24, G:0.09, T:0.12
Consensus pattern (15 bp):
AAAAATCTAAACCCG
Found at i:13350 original size:16 final size:16
Alignment explanation
Indices: 13329--13383 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
13319 AACCTGAATC
13329 AACCTGACCCAAATTT
1 AACCTGACCCAAATTT
* ** *
13345 AACCTGAACCTGATTC
1 AACCTGACCCAAATTT
*
13361 AACCTGACCAAAATTT
1 AACCTGACCCAAATTT
13377 AACCTGA
1 AACCTGA
13384 TCTGACTCAA
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.38, C:0.29, G:0.09, T:0.24
Consensus pattern (16 bp):
AACCTGACCCAAATTT
Found at i:13354 original size:32 final size:32
Alignment explanation
Indices: 13318--13383 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
13308 AAATGGATCC
*
13318 GAACCTGAATCAACCTGACCCAAATTTAACCT
1 GAACCTGAATCAACCTGACCAAAATTTAACCT
*
13350 GAACCTGATTCAACCTGACCAAAATTTAACCT
1 GAACCTGAATCAACCTGACCAAAATTTAACCT
13382 GA
1 GA
13384 TCTGACTCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.38, C:0.29, G:0.11, T:0.23
Consensus pattern (32 bp):
GAACCTGAATCAACCTGACCAAAATTTAACCT
Found at i:13420 original size:39 final size:39
Alignment explanation
Indices: 13377--13470 Score: 125
Period size: 39 Copynumber: 2.4 Consensus size: 39
13367 ACCAAAATTT
* * ** *
13377 AACCTGATCTGACTCAAGTCTGAACTAAAAAATGACCTG
1 AACCTGACCTGACTCAAATCCAAACCAAAAAATGACCTG
13416 AACCTGACCTGACTCAAATCCAAACCAAAAAATGACCTG
1 AACCTGACCTGACTCAAATCCAAACCAAAAAATGACCTG
**
13455 AACCCAACCTGACTCA
1 AACCTGACCTGACTCA
13471 CCCGATTACC
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 48 1.00
ACGTcount: A:0.40, C:0.30, G:0.12, T:0.18
Consensus pattern (39 bp):
AACCTGACCTGACTCAAATCCAAACCAAAAAATGACCTG
Found at i:18082 original size:12 final size:12
Alignment explanation
Indices: 18048--18089 Score: 66
Period size: 12 Copynumber: 3.4 Consensus size: 12
18038 ACAGACAATA
18048 ACAAACAGCAGC
1 ACAAACAGCAGC
*
18060 AACAGACAGCAGC
1 -ACAAACAGCAGC
18073 ACAAACAGCAGC
1 ACAAACAGCAGC
18085 ACAAA
1 ACAAA
18090 TTGCATTACG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
12 16 0.59
13 11 0.41
ACGTcount: A:0.52, C:0.31, G:0.17, T:0.00
Consensus pattern (12 bp):
ACAAACAGCAGC
Found at i:25066 original size:13 final size:13
Alignment explanation
Indices: 25045--25078 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
25035 TATAAAGTCC
*
25045 AAAAGGAAAAAAA
1 AAAAAGAAAAAAA
*
25058 AAAAAGAAAAAGA
1 AAAAAGAAAAAAA
25071 AAAAAGAA
1 AAAAAGAA
25079 TACCCTGCCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (13 bp):
AAAAAGAAAAAAA
Found at i:33244 original size:2 final size:2
Alignment explanation
Indices: 33237--33266 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
33227 CAATACAATA
33237 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
33267 GCATCATTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:36480 original size:21 final size:21
Alignment explanation
Indices: 36437--36480 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
36427 ATAAATGGGG
*
36437 TTGCTAAATACCGCCCTAGTT
1 TTGCTAAATACCGCCCCAGTT
*
36458 TTGCTAAATACCGCCCCATTT
1 TTGCTAAATACCGCCCCAGTT
36479 TT
1 TT
36481 TTACACTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.30, G:0.11, T:0.36
Consensus pattern (21 bp):
TTGCTAAATACCGCCCCAGTT
Found at i:36500 original size:15 final size:16
Alignment explanation
Indices: 36479--36523 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 16
36469 CGCCCCATTT
*
36479 TTTTACACTTTTGCCC
1 TTTTACACTTTTACCC
36495 -TTTACA-TTTTACCC
1 TTTTACACTTTTACCC
36509 TTTCTACACTTTTAC
1 TTT-TACACTTTTAC
36524 ACTGAGTCTC
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 7 0.28
15 8 0.32
16 4 0.16
17 6 0.24
ACGTcount: A:0.18, C:0.29, G:0.02, T:0.51
Consensus pattern (16 bp):
TTTTACACTTTTACCC
Done.