Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013116.1 Corchorus capsularis cultivar CVL-1 contig13137, 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: 12412
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:1102 original size:13 final size:14
Alignment explanation
Indices: 1073--1108 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
1063 GGTATACAAA
1073 TTTTTATTTTGCCT
1 TTTTTATTTTGCCT
1087 TTTTTATTTTG--T
1 TTTTTATTTTGCCT
1099 TTTTT-TTTTG
1 TTTTTATTTTG
1109 AAGATGAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 5 0.23
12 6 0.27
14 11 0.50
ACGTcount: A:0.06, C:0.06, G:0.08, T:0.81
Consensus pattern (14 bp):
TTTTTATTTTGCCT
Found at i:3116 original size:16 final size:15
Alignment explanation
Indices: 3092--3152 Score: 59
Period size: 16 Copynumber: 3.9 Consensus size: 15
3082 GCTTAAGTCA
*
3092 GGTCGGGTTGAATTTG
1 GGTCAGGTT-AATTTG
*
3108 GGTCAGGTTAATTCG
1 GGTCAGGTTAATTTG
**
3123 GGTTTGGGTTGAATTTG
1 GG-TCAGGTT-AATTTG
3140 GGTCAGGTTAATT
1 GGTCAGGTTAATT
3153 CGGATTTGGG
Statistics
Matches: 36, Mismatches: 7, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
15 11 0.31
16 18 0.50
17 7 0.19
ACGTcount: A:0.16, C:0.07, G:0.38, T:0.39
Consensus pattern (15 bp):
GGTCAGGTTAATTTG
Found at i:3137 original size:32 final size:32
Alignment explanation
Indices: 3096--3174 Score: 131
Period size: 32 Copynumber: 2.5 Consensus size: 32
3086 AAGTCAGGTC
*
3096 GGGTTGAATTTGGGTCAGGTTAATTCGGGTTT
1 GGGTTGAATTTGGGTCAGGTTAATTCGGATTT
3128 GGGTTGAATTTGGGTCAGGTTAATTCGGATTT
1 GGGTTGAATTTGGGTCAGGTTAATTCGGATTT
* *
3160 GGGTTCAGTTTGGGT
1 GGGTTGAATTTGGGT
3175 TTTGGCCAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 44 1.00
ACGTcount: A:0.15, C:0.06, G:0.38, T:0.41
Consensus pattern (32 bp):
GGGTTGAATTTGGGTCAGGTTAATTCGGATTT
Found at i:3365 original size:16 final size:16
Alignment explanation
Indices: 3320--3365 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
3310 AATTTTCAGA
*
3320 TTCGGATTCGGGTTTT
1 TTCGGATTCGGATTTT
* * *
3336 TTTGGGTTCTGATTTT
1 TTCGGATTCGGATTTT
3352 TTCGGATTCGGATT
1 TTCGGATTCGGATT
3366 CAGGCGGGTT
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.09, C:0.11, G:0.28, T:0.52
Consensus pattern (16 bp):
TTCGGATTCGGATTTT
Found at i:3407 original size:32 final size:32
Alignment explanation
Indices: 3371--3444 Score: 130
Period size: 32 Copynumber: 2.3 Consensus size: 32
3361 GGATTCAGGC
*
3371 GGGTTCAGGTATTTGACTTTTTCTGGTCAATT
1 GGGTTCAGGTATTTGACTTTTTCTGATCAATT
*
3403 GGGTTCAGGTATTTGATTTTTTCTGATCAATT
1 GGGTTCAGGTATTTGACTTTTTCTGATCAATT
3435 GGGTTCAGGT
1 GGGTTCAGGT
3445 CGGGTTTGGG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.16, C:0.11, G:0.27, T:0.46
Consensus pattern (32 bp):
GGGTTCAGGTATTTGACTTTTTCTGATCAATT
Found at i:3455 original size:17 final size:18
Alignment explanation
Indices: 3433--3469 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
3423 TTCTGATCAA
3433 TTGGGTTCAGG-TCGGGT
1 TTGGGTTCAGGTTCGGGT
*
3450 TTGGGTTCGGGTTCGGGT
1 TTGGGTTCAGGTTCGGGT
3468 TT
1 TT
3470 TCAGACGAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.03, C:0.11, G:0.46, T:0.41
Consensus pattern (18 bp):
TTGGGTTCAGGTTCGGGT
Found at i:6761 original size:14 final size:14
Alignment explanation
Indices: 6742--6768 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
6732 TTATTGAATT
6742 AAATAATAATTATC
1 AAATAATAATTATC
6756 AAATAATAATTAT
1 AAATAATAATTAT
6769 TTTCCAATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (14 bp):
AAATAATAATTATC
Found at i:6991 original size:48 final size:48
Alignment explanation
Indices: 6935--7053 Score: 238
Period size: 48 Copynumber: 2.5 Consensus size: 48
6925 AGAACATATA
6935 TGTAAATTGAGCTATCAACATTACCTTTCACACTTTTTTAGCCTCAAG
1 TGTAAATTGAGCTATCAACATTACCTTTCACACTTTTTTAGCCTCAAG
6983 TGTAAATTGAGCTATCAACATTACCTTTCACACTTTTTTAGCCTCAAG
1 TGTAAATTGAGCTATCAACATTACCTTTCACACTTTTTTAGCCTCAAG
7031 TGTAAATTGAGCTATCAACATTA
1 TGTAAATTGAGCTATCAACATTA
7054 TGCGACCTAA
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 71 1.00
ACGTcount: A:0.31, C:0.21, G:0.11, T:0.37
Consensus pattern (48 bp):
TGTAAATTGAGCTATCAACATTACCTTTCACACTTTTTTAGCCTCAAG
Found at i:10813 original size:22 final size:23
Alignment explanation
Indices: 10780--10827 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
10770 GGAAATCCGC
10780 TTTTGATAAAAATCAAGACTTGT
1 TTTTGATAAAAATCAAGACTTGT
10803 TTTTGATAAAAATCAAGACTTGT
1 TTTTGATAAAAATCAAGACTTGT
10826 TT
1 TT
10828 GGTACTTGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.38, C:0.08, G:0.12, T:0.42
Consensus pattern (23 bp):
TTTTGATAAAAATCAAGACTTGT
Found at i:11559 original size:11 final size:12
Alignment explanation
Indices: 11543--11571 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
11533 TCAAAATTTT
11543 AACCGAC-AAAA
1 AACCGACTAAAA
11554 AACCGACTAAAA
1 AACCGACTAAAA
11566 AACCGA
1 AACCGA
11572 AAACCGACCG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 7 0.41
12 10 0.59
ACGTcount: A:0.59, C:0.28, G:0.10, T:0.03
Consensus pattern (12 bp):
AACCGACTAAAA
Done.