Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015818.1 Corchorus capsularis cultivar CVL-1 contig15839, 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: 7333
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.30
Found at i:788 original size:14 final size:14
Alignment explanation
Indices: 771--821 Score: 93
Period size: 14 Copynumber: 3.6 Consensus size: 14
761 TAGGTTTTAC
771 AAATTAGGGACATG
1 AAATTAGGGACATG
785 AAATTAGGGACATG
1 AAATTAGGGACATG
*
799 AAATTAGGGACAGG
1 AAATTAGGGACATG
813 AAATTAGGG
1 AAATTAGGG
822 TTACGCCCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
14 36 1.00
ACGTcount: A:0.43, C:0.06, G:0.31, T:0.20
Consensus pattern (14 bp):
AAATTAGGGACATG
Found at i:898 original size:6 final size:6
Alignment explanation
Indices: 880--941 Score: 72
Period size: 6 Copynumber: 10.5 Consensus size: 6
870 GAACTCACGG
* * * * *
880 AAGGAA AAAGAA AAGG-A AATGAA AAGTAA AATGAA AAGTAA AAGGAA
1 AAGGAA AAGGAA AAGGAA AAGGAA AAGGAA AAGGAA AAGGAA AAGGAA
927 AAGGAA AAGGAA AAG
1 AAGGAA AAGGAA AAG
942 AACTTACTGT
Statistics
Matches: 45, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
5 4 0.09
6 41 0.91
ACGTcount: A:0.68, C:0.00, G:0.26, T:0.06
Consensus pattern (6 bp):
AAGGAA
Found at i:1570 original size:206 final size:205
Alignment explanation
Indices: 1208--1584 Score: 623
Period size: 206 Copynumber: 1.8 Consensus size: 205
1198 GAATTTTTTT
** * *
1208 AGTCGAACTGGGGGCCTTGTTGGGGGCGAAGTCGGTGCCCAGTCAGGACAGTGACTTCGCCCTGA
1 AGTCGAACTGGGGGCCCGGTTGGGGGCGAAGTCGGCGCCCAGTCAGCACAGTGACTTCGCCCTGA
*
1273 TTTAAGTATCCAACTGGGCTCCCAGGTGAGGGGTAACTGGGGTCCCAAATGGACTTCACCAAATA
66 TTTAAGTATCCAACTGGGCTCCCAGCTGAGGGGTAACTGGGGTCCCAAATGGACTTCACCAAATA
1338 GCGGCGTCTAGCTTAATGAGACGCCGCTAAATAGTGGCGTTAAAATCGTCAGACGCCGCTCTTTG
131 GCGGCGTCTAGCTTAATGAGACGCCGCTAAATAGTGGCGTTAAAATCGTCAGACGCCGCTCTTTG
1403 AGAATTACAA
196 AGAATTACAA
*
1413 AGTCGAACTGGGGGCCCGGTTGGGGGCGAAGTCGGCGCCCAGTCAGCACAGTGACTTCGCCCTTA
1 AGTCGAACTGGGGGCCCGGTTGGGGGCGAAGTCGGCGCCCAGTCAGCACAGTGACTTCGCCCTGA
1478 TTTAAGGT-TCCAACCTGGGCTCCCAGCTGAGGGGTAACTGGGGTCCCAAATGGACTTCACCAAA
66 TTTAA-GTATCCAA-CTGGGCTCCCAGCTGAGGGGTAACTGGGGTCCCAAATGGACTTCACCAAA
* * * *
1542 TAGCGGCGTTTTGTTTCATTG-GACGCCGCTAAATAGTGGCGTT
129 TAGCGGCGTCTAGCTT-AATGAGACGCCGCTAAATAGTGGCGTT
1585 TTGTTCATTA
Statistics
Matches: 159, Mismatches: 10, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
205 70 0.44
206 86 0.54
207 3 0.02
ACGTcount: A:0.22, C:0.24, G:0.31, T:0.23
Consensus pattern (205 bp):
AGTCGAACTGGGGGCCCGGTTGGGGGCGAAGTCGGCGCCCAGTCAGCACAGTGACTTCGCCCTGA
TTTAAGTATCCAACTGGGCTCCCAGCTGAGGGGTAACTGGGGTCCCAAATGGACTTCACCAAATA
GCGGCGTCTAGCTTAATGAGACGCCGCTAAATAGTGGCGTTAAAATCGTCAGACGCCGCTCTTTG
AGAATTACAA
Found at i:1599 original size:32 final size:33
Alignment explanation
Indices: 1539--1604 Score: 107
Period size: 32 Copynumber: 2.0 Consensus size: 33
1529 GGACTTCACC
*
1539 AAATAGCGGCGTTTTGTTTCATTGGACGCCGCT
1 AAATAGCGGCGTTTTGTTTCATTAGACGCCGCT
*
1572 AAATAGTGGCGTTTTG-TTCATTAGACGCCGCT
1 AAATAGCGGCGTTTTGTTTCATTAGACGCCGCT
1604 A
1 A
1605 TTTTGCTGCA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 16 0.52
33 15 0.48
ACGTcount: A:0.21, C:0.20, G:0.26, T:0.33
Consensus pattern (33 bp):
AAATAGCGGCGTTTTGTTTCATTAGACGCCGCT
Found at i:2950 original size:29 final size:31
Alignment explanation
Indices: 2906--2968 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 31
2896 TTTCTTCAAG
* *
2906 TCCATTATAAGTCCTT-GGCACTTCATTCCC
1 TCCATGATAAGTCCTTGGGCACATCATTCCC
*
2936 TCCATGATAA-TCCTTGGGCGCATCATTCCC
1 TCCATGATAAGTCCTTGGGCACATCATTCCC
2966 TCC
1 TCC
2969 CCCTTGAAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 5 0.17
30 24 0.83
ACGTcount: A:0.19, C:0.35, G:0.13, T:0.33
Consensus pattern (31 bp):
TCCATGATAAGTCCTTGGGCACATCATTCCC
Found at i:3703 original size:5 final size:5
Alignment explanation
Indices: 3690--3730 Score: 66
Period size: 5 Copynumber: 8.4 Consensus size: 5
3680 TCTGGTCGAA
*
3690 ATTTT ATTTC ATTTT ATTTT ATTTT ATTTT ATTTT -TTTT AT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT AT
3731 ATTTTTCGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
4 4 0.12
5 29 0.88
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (5 bp):
ATTTT
Found at i:4514 original size:17 final size:19
Alignment explanation
Indices: 4492--4527 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
4482 CCAATGTCTT
4492 CTAAACTAA-ATA-AATAA
1 CTAAACTAAGATAGAATAA
4509 CTAAACTAAGATAGAATAA
1 CTAAACTAAGATAGAATAA
4528 AGGCCTCAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
18 3 0.18
19 5 0.29
ACGTcount: A:0.61, C:0.11, G:0.06, T:0.22
Consensus pattern (19 bp):
CTAAACTAAGATAGAATAA
Found at i:6315 original size:15 final size:16
Alignment explanation
Indices: 6278--6474 Score: 147
Period size: 16 Copynumber: 12.6 Consensus size: 16
6268 TAGACAGTTT
6278 TTTCGGGTCATTCGGG
1 TTTCGGGTCATTCGGG
6294 TTTCGGGTCA-TCTGGG
1 TTTCGGGTCATTC-GGG
*
6310 -TTCGGGTTATTCGGG
1 TTTCGGGTCATTCGGG
* *
6325 TCTCGGGTTATTCGGG
1 TTTCGGGTCATTCGGG
* * * *
6341 TCTCGGATCCTACGGG
1 TTTCGGGTCATTCGGG
*
6357 TTTCGGGTCATTCGGA
1 TTTCGGGTCATTCGGG
* *
6373 TCTCGGGTCATACGGG
1 TTTCGGGTCATTCGGG
*
6389 TTTCGGATCATTCGGG
1 TTTCGGGTCATTCGGG
* *
6405 TCTCGGGTC-TACCGGG
1 TTTCGGGTCAT-TCGGG
* ****
6421 TCTCGGGTTGGGCGGG
1 TTTCGGGTCATTCGGG
6437 -TTCGGGTC-TT--GG
1 TTTCGGGTCATTCGGG
* *
6449 CTTCGGGTCACTCGGG
1 TTTCGGGTCATTCGGG
6465 TTTCGGGTCA
1 TTTCGGGTCA
6475 ATTGGGTCAG
Statistics
Matches: 143, Mismatches: 29, Indels: 18
0.75 0.15 0.09
Matches are distributed among these distances:
12 2 0.01
13 8 0.06
14 1 0.01
15 20 0.14
16 112 0.78
ACGTcount: A:0.08, C:0.22, G:0.38, T:0.33
Consensus pattern (16 bp):
TTTCGGGTCATTCGGG
Found at i:6425 original size:48 final size:48
Alignment explanation
Indices: 6280--6428 Score: 171
Period size: 48 Copynumber: 3.1 Consensus size: 48
6270 GACAGTTTTT
*
6280 TCGGGTCATTCGGGTTTCGGGTCA-TCTGGGTTCGGGT-TATTCGGGTC
1 TCGGGTCATTCGGGTTTCGGATCATTC-GGGTTCGGGTCTATTCGGGTC
* * * * *
6327 TCGGGTTATTCGGGTCTCGGATCCTACGGGTTTCGGGTC-ATTCGGATC
1 TCGGGTCATTCGGGTTTCGGATCATTCGGG-TTCGGGTCTATTCGGGTC
* *
6375 TCGGGTCATACGGGTTTCGGATCATTCGGGTCTCGGGTCTA-CCGGGTC
1 TCGGGTCATTCGGGTTTCGGATCATTCGGGT-TCGGGTCTATTCGGGTC
6423 TCGGGT
1 TCGGGT
6429 TGGGCGGGTT
Statistics
Matches: 84, Mismatches: 13, Indels: 9
0.79 0.12 0.08
Matches are distributed among these distances:
47 24 0.29
48 59 0.70
49 1 0.01
ACGTcount: A:0.09, C:0.22, G:0.36, T:0.33
Consensus pattern (48 bp):
TCGGGTCATTCGGGTTTCGGATCATTCGGGTTCGGGTCTATTCGGGTC
Found at i:6700 original size:42 final size:42
Alignment explanation
Indices: 6653--6734 Score: 155
Period size: 42 Copynumber: 2.0 Consensus size: 42
6643 TTGATATTAA
6653 TTTTGAATATTAAATACATAATTAATTATCATGTGCGGTAAG
1 TTTTGAATATTAAATACATAATTAATTATCATGTGCGGTAAG
*
6695 TTTTGAATATTAAATACATAATTAATTATCATGTGGGGTA
1 TTTTGAATATTAAATACATAATTAATTATCATGTGCGGTA
6735 TGTGTCAACA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.38, C:0.06, G:0.15, T:0.41
Consensus pattern (42 bp):
TTTTGAATATTAAATACATAATTAATTATCATGTGCGGTAAG
Found at i:7255 original size:22 final size:23
Alignment explanation
Indices: 7225--7270 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
7215 TTTTAGTTTA
7225 TAATATTCTCGGGTCATTCGGGT
1 TAATATTCTCGGGTCATTCGGGT
**
7248 TAAT-TTCTCGGGTTTTTCGGGT
1 TAATATTCTCGGGTCATTCGGGT
7270 T
1 T
7271 TCGGGTCATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.13, C:0.15, G:0.26, T:0.46
Consensus pattern (23 bp):
TAATATTCTCGGGTCATTCGGGT
Found at i:7276 original size:16 final size:16
Alignment explanation
Indices: 7255--7333 Score: 79
Period size: 16 Copynumber: 4.9 Consensus size: 16
7245 GGTTAATTTC
*
7255 TCGGGTTTTTCGGGTT
1 TCGGGTTATTCGGGTT
* * * *
7271 TCGGGTCATACAGGTC
1 TCGGGTTATTCGGGTT
*
7287 TCGGGTCATTCGGGTT
1 TCGGGTTATTCGGGTT
7303 TCGGGTTA-TCTGGGTT
1 TCGGGTTATTC-GGGTT
*
7319 ACGGGTTATTCGGGT
1 TCGGGTTATTCGGGT
Statistics
Matches: 51, Mismatches: 10, Indels: 4
0.78 0.15 0.06
Matches are distributed among these distances:
15 2 0.04
16 47 0.92
17 2 0.04
ACGTcount: A:0.09, C:0.16, G:0.37, T:0.38
Consensus pattern (16 bp):
TCGGGTTATTCGGGTT
Found at i:7330 original size:32 final size:32
Alignment explanation
Indices: 7253--7333 Score: 94
Period size: 32 Copynumber: 2.5 Consensus size: 32
7243 CGGGTTAATT
*
7253 TCTCGGGTTTTTCGGGTTTCGGGTCATACAGG
1 TCTCGGGTTATTCGGGTTTCGGGTCATACAGG
* * *
7285 TCTCGGGTCATTCGGGTTTCGGGTTAT-CTGGG
1 TCTCGGGTTATTCGGGTTTCGGGTCATAC-AGG
7317 T-TACGGGTTATTCGGGT
1 TCT-CGGGTTATTCGGGT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
31 2 0.05
32 40 0.95
ACGTcount: A:0.09, C:0.17, G:0.36, T:0.38
Consensus pattern (32 bp):
TCTCGGGTTATTCGGGTTTCGGGTCATACAGG
Done.