Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006751.1 Corchorus capsularis cultivar CVL-1 contig06772, 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: 31611
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Found at i:244 original size:16 final size:16
Alignment explanation
Indices: 223--255 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
213 GGAAGAAGAC
223 GACAAGTGAGCTACTG
1 GACAAGTGAGCTACTG
*
239 GACAAGTGAGCTGCTG
1 GACAAGTGAGCTACTG
255 G
1 G
256 TTTGGATGTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.27, C:0.18, G:0.36, T:0.18
Consensus pattern (16 bp):
GACAAGTGAGCTACTG
Found at i:1089 original size:21 final size:20
Alignment explanation
Indices: 1063--1106 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 20
1053 ACCTGTTTAT
*
1063 GATAAGTATGGCGAGGAGGAA
1 GATAAGTATGACGAGGA-GAA
1084 GATAAGTATGACGAGGAGAA
1 GATAAGTATGACGAGGAGAA
1104 GAT
1 GAT
1107 TCTGATTTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.41, C:0.05, G:0.39, T:0.16
Consensus pattern (20 bp):
GATAAGTATGACGAGGAGAA
Found at i:1158 original size:30 final size:30
Alignment explanation
Indices: 1097--1160 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
1087 AAGTATGACG
* * * *
1097 AGGAGAAGATTCTGATTTCTTTGTTTGTGA
1 AGGAGAACAATCTGATTTCCTTGCTTGTGA
1127 AGGAGAACAATCTGATTTCCTT-CTTGATGA
1 AGGAGAACAATCTGATTTCCTTGCTTG-TGA
1157 AGGA
1 AGGA
1161 TTTGTTTGTG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 3 0.10
30 26 0.90
ACGTcount: A:0.28, C:0.11, G:0.25, T:0.36
Consensus pattern (30 bp):
AGGAGAACAATCTGATTTCCTTGCTTGTGA
Found at i:1499 original size:16 final size:16
Alignment explanation
Indices: 1478--1510 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1468 GGAAGAAGAC
1478 GACAAGTGAGCTACTG
1 GACAAGTGAGCTACTG
*
1494 GACAAGTGAGCTGCTG
1 GACAAGTGAGCTACTG
1510 G
1 G
1511 TTTGGATGTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.27, C:0.18, G:0.36, T:0.18
Consensus pattern (16 bp):
GACAAGTGAGCTACTG
Found at i:19095 original size:30 final size:30
Alignment explanation
Indices: 19054--19116 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
19044 TTCTGCATAA
19054 CATGATTGTTCGCACCATTGTTGTTTGCAC
1 CATGATTGTTCGCACCATTGTTGTTTGCAC
* *
19084 CATGGTTGTTCGCACCATTGTTGTTTGCGC
1 CATGATTGTTCGCACCATTGTTGTTTGCAC
19114 CAT
1 CAT
19117 TCTCCCTAGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.14, C:0.24, G:0.22, T:0.40
Consensus pattern (30 bp):
CATGATTGTTCGCACCATTGTTGTTTGCAC
Found at i:19116 original size:15 final size:15
Alignment explanation
Indices: 19059--19117 Score: 82
Period size: 15 Copynumber: 3.9 Consensus size: 15
19049 CATAACATGA
*
19059 TTGTTCGCACCATTG
1 TTGTTTGCACCATTG
*
19074 TTGTTTGCACCATGG
1 TTGTTTGCACCATTG
*
19089 TTGTTCGCACCATTG
1 TTGTTTGCACCATTG
*
19104 TTGTTTGCGCCATT
1 TTGTTTGCACCATT
19118 CTCCCTAGCA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 38 1.00
ACGTcount: A:0.12, C:0.24, G:0.22, T:0.42
Consensus pattern (15 bp):
TTGTTTGCACCATTG
Found at i:29303 original size:24 final size:24
Alignment explanation
Indices: 29276--29325 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
29266 AAAATGTCCA
29276 ATTTTTGCTAATCAAATTAATGAG
1 ATTTTTGCTAATCAAATTAATGAG
29300 ATTTTTGCTAATCAAATTAATGAG
1 ATTTTTGCTAATCAAATTAATGAG
29324 AT
1 AT
29326 AATAAGAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.38, C:0.08, G:0.12, T:0.42
Consensus pattern (24 bp):
ATTTTTGCTAATCAAATTAATGAG
Found at i:30939 original size:14 final size:14
Alignment explanation
Indices: 30920--30963 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
30910 GCATGTTAAA
30920 TTGATATAATTTTT
1 TTGATATAATTTTT
30934 TTGATATAATTTTT
1 TTGATATAATTTTT
*
30948 TTGA-A-ATTTTTT
1 TTGATATAATTTTT
30960 TTGA
1 TTGA
30964 AAATTTTGAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
12 10 0.34
13 1 0.03
14 18 0.62
ACGTcount: A:0.27, C:0.00, G:0.09, T:0.64
Consensus pattern (14 bp):
TTGATATAATTTTT
Done.