Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013218.1 Corchorus capsularis cultivar CVL-1 contig13239, 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: 40429
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:422 original size:16 final size:16
Alignment explanation
Indices: 389--422 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
379 TTATTACATA
*
389 TATATATATATATATT
1 TATATATATAAATATT
*
405 TATATATATAAATGTT
1 TATATATATAAATATT
421 TA
1 TA
423 ATACTTCGTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
TATATATATAAATATT
Found at i:1092 original size:3 final size:3
Alignment explanation
Indices: 1084--1110 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1074 TAACTACATA
1084 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1111 AATCTTAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:3766 original size:27 final size:27
Alignment explanation
Indices: 3736--3788 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
3726 TCTTGGCCAC
**
3736 GTTTTCCATCTTCTTTCATCTTCTCAT
1 GTTTTCCATCTTCCCTCATCTTCTCAT
*
3763 GTTTTCCGTCTTCCCTCATCTTCTCA
1 GTTTTCCATCTTCCCTCATCTTCTCA
3789 GCTCACCCTG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.09, C:0.34, G:0.06, T:0.51
Consensus pattern (27 bp):
GTTTTCCATCTTCCCTCATCTTCTCAT
Found at i:7986 original size:27 final size:27
Alignment explanation
Indices: 7954--8009 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
7944 TATTCTTGGC
7954 CACGTTTTCCATCTT-CCTTCATCTTCT
1 CACGTTTTCCATCTTCCCTT-ATCTTCT
* *
7981 CACGTTTTTCGTCTTCCCTTATCTTCT
1 CACGTTTTCCATCTTCCCTTATCTTCT
8008 CA
1 CA
8010 GCTCACCCTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 22 0.85
28 4 0.15
ACGTcount: A:0.11, C:0.36, G:0.05, T:0.48
Consensus pattern (27 bp):
CACGTTTTCCATCTTCCCTTATCTTCT
Found at i:9230 original size:21 final size:22
Alignment explanation
Indices: 9188--9230 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
9178 GGTGTGTATG
*
9188 TGTGATTGTTTGGTTTGGTAGA
1 TGTGATTGTTTAGTTTGGTAGA
*
9210 TGTGATTG-TTAGTTTGTTAGA
1 TGTGATTGTTTAGTTTGGTAGA
9231 GACCGAGCGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.16, C:0.00, G:0.33, T:0.51
Consensus pattern (22 bp):
TGTGATTGTTTAGTTTGGTAGA
Found at i:10265 original size:21 final size:22
Alignment explanation
Indices: 10223--10265 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
10213 GGTGTGTATG
*
10223 TGTGATTGTTTGGTTTGGTAGA
1 TGTGATTGTTTAGTTTGGTAGA
*
10245 TGTGATTG-TTAGTTTGTTAGA
1 TGTGATTGTTTAGTTTGGTAGA
10266 GACCGAGCGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.16, C:0.00, G:0.33, T:0.51
Consensus pattern (22 bp):
TGTGATTGTTTAGTTTGGTAGA
Found at i:10296 original size:25 final size:25
Alignment explanation
Indices: 10262--10311 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
10252 GTTAGTTTGT
*
10262 TAGAGACCGAGCGAGAGTGCTCAAA
1 TAGAGACCGAGCGAAAGTGCTCAAA
10287 TAGAGACCGAGCGAAAGTGCTCAAA
1 TAGAGACCGAGCGAAAGTGCTCAAA
10312 ATTGTTTGGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.38, C:0.20, G:0.30, T:0.12
Consensus pattern (25 bp):
TAGAGACCGAGCGAAAGTGCTCAAA
Found at i:10542 original size:25 final size:25
Alignment explanation
Indices: 10514--10563 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
10504 TTCCGCTTGC
10514 ATGATGAATTTGATAGATTATAGTT
1 ATGATGAATTTGATAGATTATAGTT
10539 ATGATGAATTTGATAGATTATAGTT
1 ATGATGAATTTGATAGATTATAGTT
10564 TGGGATATCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.20, T:0.44
Consensus pattern (25 bp):
ATGATGAATTTGATAGATTATAGTT
Found at i:23743 original size:23 final size:23
Alignment explanation
Indices: 23717--23762 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
23707 TGCTATAGCA
23717 TTTCAAATTCCATTTTCCATTTT
1 TTTCAAATTCCATTTTCCATTTT
23740 TTTCAAATTCCATTTTCCATTTT
1 TTTCAAATTCCATTTTCCATTTT
23763 GCTTAGCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.22, C:0.22, G:0.00, T:0.57
Consensus pattern (23 bp):
TTTCAAATTCCATTTTCCATTTT
Found at i:36816 original size:65 final size:65
Alignment explanation
Indices: 36712--36841 Score: 260
Period size: 65 Copynumber: 2.0 Consensus size: 65
36702 AACAAATTTC
36712 CAAGAAATTTGTGATACGGTAAAGATTCATAATGTTACTAATGAAGCAATTCGTTTGCGTTTGTT
1 CAAGAAATTTGTGATACGGTAAAGATTCATAATGTTACTAATGAAGCAATTCGTTTGCGTTTGTT
36777 CAAGAAATTTGTGATACGGTAAAGATTCATAATGTTACTAATGAAGCAATTCGTTTGCGTTTGTT
1 CAAGAAATTTGTGATACGGTAAAGATTCATAATGTTACTAATGAAGCAATTCGTTTGCGTTTGTT
36842 TCCTTTTTCT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 65 1.00
ACGTcount: A:0.32, C:0.11, G:0.20, T:0.37
Consensus pattern (65 bp):
CAAGAAATTTGTGATACGGTAAAGATTCATAATGTTACTAATGAAGCAATTCGTTTGCGTTTGTT
Found at i:38020 original size:30 final size:32
Alignment explanation
Indices: 37978--38067 Score: 93
Period size: 30 Copynumber: 3.0 Consensus size: 32
37968 TTGAGAAGTT
37978 TGGTAAGG-TTGTGAAAGTTGA-GAAAAAGAA
1 TGGTAAGGTTTGTGAAAGTTGACGAAAAAGAA
* * *
38008 TGGT-AGGTTTGTGAGAA-TTGAGGAAGATG-A
1 TGGTAAGGTTTGTGA-AAGTTGACGAAAAAGAA
*
38038 TGGTAAGGTTTG-GAAAGTTGACGAGAAAGA
1 TGGTAAGGTTTGTGAAAGTTGACGAAAAAGA
38068 TGAGGAAAAG
Statistics
Matches: 48, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
29 5 0.10
30 29 0.60
31 14 0.29
ACGTcount: A:0.37, C:0.01, G:0.37, T:0.26
Consensus pattern (32 bp):
TGGTAAGGTTTGTGAAAGTTGACGAAAAAGAA
Done.