Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006213.1 Corchorus capsularis cultivar CVL-1 contig06232, 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: 7993
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Found at i:1349 original size:19 final size:20
Alignment explanation
Indices: 1327--1366 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1317 TTTAAAAATT
1327 CAAAA-TAAAATAAAAACTA
1 CAAAATTAAAATAAAAACTA
* *
1346 CAAAATTTAGATAAAAACTA
1 CAAAATTAAAATAAAAACTA
1366 C
1 C
1367 CCATTATACT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.65, C:0.12, G:0.03, T:0.20
Consensus pattern (20 bp):
CAAAATTAAAATAAAAACTA
Found at i:1429 original size:13 final size:13
Alignment explanation
Indices: 1407--1438 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
1397 TATTATAAGA
1407 TAAATATAATATT
1 TAAATATAATATT
*
1420 TAAATTTAATATT
1 TAAATATAATATT
1433 TAAATA
1 TAAATA
1439 AATTATATCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
TAAATATAATATT
Found at i:1527 original size:3 final size:3
Alignment explanation
Indices: 1519--1574 Score: 60
Period size: 3 Copynumber: 19.0 Consensus size: 3
1509 CTTTGTCTTG
** * * *
1519 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA TTT TTA TTA TTA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1566 TAA TAA TAA
1 TAA TAA TAA
1575 CTGAATTATA
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
2 2 0.04
3 46 0.96
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (3 bp):
TAA
Found at i:2437 original size:2 final size:2
Alignment explanation
Indices: 2430--2457 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2420 ACCCCAAAGC
2430 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2458 ACATAAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3892 original size:6 final size:6
Alignment explanation
Indices: 3881--3943 Score: 72
Period size: 6 Copynumber: 10.2 Consensus size: 6
3871 TTTGAATAAA
* * * *
3881 ATTAAT ATTAAT AATAAA ATTAAT ATTAAT AAATTAAT ATTAAT AATAAA
1 ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT --ATTAAT ATTAAT ATTAAT
3931 ATTAAT ATTAAT A
1 ATTAAT ATTAAT A
3944 AATTAGTTAT
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
6 41 0.87
8 6 0.13
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (6 bp):
ATTAAT
Found at i:3898 original size:18 final size:18
Alignment explanation
Indices: 3875--3944 Score: 112
Period size: 18 Copynumber: 4.1 Consensus size: 18
3865 AACTAATTTG
3875 AATAAAATTAATATTAAT
1 AATAAAATTAATATTAAT
3893 AATAAAATTAATA-T--T
1 AATAAAATTAATATTAAT
3908 AAT-AAATTAATATTAAT
1 AATAAAATTAATATTAAT
3925 AATAAAATTAATATTAAT
1 AATAAAATTAATATTAAT
3943 AA
1 AA
3945 ATTAGTTATA
Statistics
Matches: 48, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
14 9 0.19
15 5 0.10
17 5 0.10
18 29 0.60
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
AATAAAATTAATATTAAT
Found at i:3916 original size:32 final size:32
Alignment explanation
Indices: 3879--3948 Score: 140
Period size: 32 Copynumber: 2.2 Consensus size: 32
3869 AATTTGAATA
3879 AAATTAATATTAATAATAAAATTAATATTAAT
1 AAATTAATATTAATAATAAAATTAATATTAAT
3911 AAATTAATATTAATAATAAAATTAATATTAAT
1 AAATTAATATTAATAATAAAATTAATATTAAT
3943 AAATTA
1 AAATTA
3949 GTTATAAAGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (32 bp):
AAATTAATATTAATAATAAAATTAATATTAAT
Found at i:6157 original size:16 final size:16
Alignment explanation
Indices: 6136--6195 Score: 86
Period size: 16 Copynumber: 3.8 Consensus size: 16
6126 CCGACCTGGG
*
6136 CCCGAAGCCGAAAATA
1 CCCGAACCCGAAAATA
*
6152 CCCGAACCCGATAGA-A
1 CCCGAACCCGA-AAATA
6168 CCCGAACCCGAAAATA
1 CCCGAACCCGAAAATA
6184 CCCGAACCCGAA
1 CCCGAACCCGAA
6196 CCCGCCCAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
15 2 0.05
16 35 0.90
17 2 0.05
ACGTcount: A:0.40, C:0.38, G:0.17, T:0.05
Consensus pattern (16 bp):
CCCGAACCCGAAAATA
Found at i:6884 original size:63 final size:63
Alignment explanation
Indices: 6807--6932 Score: 252
Period size: 63 Copynumber: 2.0 Consensus size: 63
6797 ACAGTTTCGT
6807 TTTATCTTGCTTTGAGAGGTTGTGTACATAGTTAATAGTTTTCATTGTAGTATGTCAAAGACC
1 TTTATCTTGCTTTGAGAGGTTGTGTACATAGTTAATAGTTTTCATTGTAGTATGTCAAAGACC
6870 TTTATCTTGCTTTGAGAGGTTGTGTACATAGTTAATAGTTTTCATTGTAGTATGTCAAAGACC
1 TTTATCTTGCTTTGAGAGGTTGTGTACATAGTTAATAGTTTTCATTGTAGTATGTCAAAGACC
6933 GATGTTAGGG
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 63 1.00
ACGTcount: A:0.25, C:0.11, G:0.21, T:0.43
Consensus pattern (63 bp):
TTTATCTTGCTTTGAGAGGTTGTGTACATAGTTAATAGTTTTCATTGTAGTATGTCAAAGACC
Done.