Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016353.1 Corchorus capsularis cultivar CVL-1 contig16374, 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: 13784
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Found at i:414 original size:30 final size:30
Alignment explanation
Indices: 374--430 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
364 ATTCGTATCA
* *
374 AATGATGCGCCCAAGGA-TTATCATGGAGGG
1 AATGAAGCG-CCAAGGACTTATAATGGAGGG
404 AATGAAGCGCCAAGGACTTATAATGGA
1 AATGAAGCGCCAAGGACTTATAATGGA
431 CTTGAAGACA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 7 0.29
30 17 0.71
ACGTcount: A:0.35, C:0.16, G:0.30, T:0.19
Consensus pattern (30 bp):
AATGAAGCGCCAAGGACTTATAATGGAGGG
Found at i:1479 original size:8 final size:8
Alignment explanation
Indices: 1466--1499 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
1456 CACCTTCTTG
1466 AAAAATTC
1 AAAAATTC
1474 AAAAATTC
1 AAAAATTC
*
1482 AGAAACTTC
1 A-AAAATTC
1491 AAAAATTC
1 AAAAATTC
1499 A
1 A
1500 TAGACGATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.59, C:0.15, G:0.03, T:0.24
Consensus pattern (8 bp):
AAAAATTC
Found at i:2363 original size:30 final size:30
Alignment explanation
Indices: 2327--2385 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
2317 CAAGGGGGAG
* *
2327 GGAATGATGCGCCCAAGGA-TTATCATGGAA
1 GGAATGAAGCG-CCAAGGACTTATAATGGAA
2357 GGAATGAAGCGCCAAGGACTTATAATGGA
1 GGAATGAAGCGCCAAGGACTTATAATGGA
2386 CTTGAAGACA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 7 0.27
30 19 0.73
ACGTcount: A:0.36, C:0.15, G:0.31, T:0.19
Consensus pattern (30 bp):
GGAATGAAGCGCCAAGGACTTATAATGGAA
Found at i:3994 original size:11 final size:11
Alignment explanation
Indices: 3978--4003 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
3968 CGAAAAATAT
3978 AAAAAATTAAA
1 AAAAAATTAAA
3989 AAAAAATTAAA
1 AAAAAATTAAA
4000 AAAA
1 AAAA
4004 TTTAGACCAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (11 bp):
AAAAAATTAAA
Found at i:6750 original size:33 final size:33
Alignment explanation
Indices: 6670--6767 Score: 110
Period size: 33 Copynumber: 3.0 Consensus size: 33
6660 AAGGATCATA
* **
6670 TGGCCGGTTGTGGCCGGGCATGGCCGA-GTCATG
1 TGGCCGGGTGTGGCCGGGCATGGCC-ATGTCGCG
6703 TGGCCGGGTGTGGCCGGGCATGGCCATGTCGCG
1 TGGCCGGGTGTGGCCGGGCATGGCCATGTCGCG
* **
6736 TGGTC-GGTGATGGCCGGGCATCTCCATGTCGC
1 TGGCCGGGTG-TGGCCGGGCATGGCCATGTCGC
6768 ACGGCCGGTG
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
32 5 0.09
33 52 0.91
ACGTcount: A:0.08, C:0.27, G:0.44, T:0.21
Consensus pattern (33 bp):
TGGCCGGGTGTGGCCGGGCATGGCCATGTCGCG
Found at i:6777 original size:33 final size:32
Alignment explanation
Indices: 6704--6800 Score: 95
Period size: 33 Copynumber: 2.9 Consensus size: 32
6694 CGAGTCATGT
** **
6704 GGCCGGGTGTGGCCGGGCATGGCCATGTCGCGT
1 GGCC-GGTGTGGCCGGGCATCTCCATGTCGCAC
*
6737 GGTCGGTGATGGCCGGGCATCTCCATGTCGCAC
1 GGCCGGTG-TGGCCGGGCATCTCCATGTCGCAC
* * *
6770 GGCCGGTGTTGCGCAGGCATCTCCAAGTCGC
1 GGCCGGTGTGGC-CGGGCATCTCCATGTCGC
6801 GTGGCCTGAT
Statistics
Matches: 53, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
32 7 0.13
33 46 0.87
ACGTcount: A:0.10, C:0.30, G:0.40, T:0.20
Consensus pattern (32 bp):
GGCCGGTGTGGCCGGGCATCTCCATGTCGCAC
Found at i:6814 original size:21 final size:21
Alignment explanation
Indices: 6788--6827 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
6778 TTGCGCAGGC
*
6788 ATCTCCAAGTCGCGTGGCCTG
1 ATCTCCAAGTCGCATGGCCTG
6809 ATCTCCAAGTCGCATGGCC
1 ATCTCCAAGTCGCATGGCC
6828 GGTCACTTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.35, G:0.25, T:0.23
Consensus pattern (21 bp):
ATCTCCAAGTCGCATGGCCTG
Found at i:11355 original size:9 final size:8
Alignment explanation
Indices: 11321--11354 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
11311 GAATCGACTA
11321 TGAATTTT
1 TGAATTTT
*
11329 TGAAGTTTC
1 TGAA-TTTT
11338 TGAATTTT
1 TGAATTTT
11346 TGAATTTT
1 TGAATTTT
11354 T
1 T
11355 TTAAGAAGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.24, C:0.03, G:0.15, T:0.59
Consensus pattern (8 bp):
TGAATTTT
Found at i:12174 original size:33 final size:33
Alignment explanation
Indices: 12132--12223 Score: 116
Period size: 33 Copynumber: 2.8 Consensus size: 33
12122 AGCTAAAGGA
*
12132 TCATATGGCCGGTTGTGGCCGGGCATGGCCGAG
1 TCATATGGCCGGGTGTGGCCGGGCATGGCCGAG
*
12165 TCATGTGGCCGGGTGTGGCCGGGCATGGCC-ATG
1 TCATATGGCCGGGTGTGGCCGGGCATGGCCGA-G
**
12198 TCGCATGGCC-GGTGATGGCCGGGCAT
1 TCATATGGCCGGGTG-TGGCCGGGCAT
12224 CTCCAAGTCG
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
32 5 0.10
33 47 0.90
ACGTcount: A:0.11, C:0.25, G:0.43, T:0.21
Consensus pattern (33 bp):
TCATATGGCCGGGTGTGGCCGGGCATGGCCGAG
Found at i:12234 original size:33 final size:32
Alignment explanation
Indices: 12136--12242 Score: 106
Period size: 33 Copynumber: 3.2 Consensus size: 32
12126 AAAGGATCAT
* * **
12136 ATGGCCGGTTGTGGCCGGGCATGGCCGAGTCAT
1 ATGGCCGG-TGTGGCCGGGCATCGCCAAGTCGC
* * *
12169 GTGGCCGGGTGTGGCCGGGCATGGCCATGTCGC
1 ATGGCC-GGTGTGGCCGGGCATCGCCAAGTCGC
*
12202 ATGGCCGGTGATGGCCGGGCATCTCCAAGTCGC
1 ATGGCCGGTG-TGGCCGGGCATCGCCAAGTCGC
*
12235 GTGGCCGG
1 ATGGCCGG
12243 ATCTCCAAGT
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
32 4 0.06
33 56 0.90
34 2 0.03
ACGTcount: A:0.10, C:0.27, G:0.44, T:0.19
Consensus pattern (32 bp):
ATGGCCGGTGTGGCCGGGCATCGCCAAGTCGC
Found at i:12248 original size:21 final size:22
Alignment explanation
Indices: 12212--12263 Score: 79
Period size: 21 Copynumber: 2.4 Consensus size: 22
12202 ATGGCCGGTG
12212 ATGGCCGGGCATCTCCAAGTCGC
1 ATGGCC-GGCATCTCCAAGTCGC
*
12235 GTGGCCGG-ATCTCCAAGTCGC
1 ATGGCCGGCATCTCCAAGTCGC
12256 ATGGCCGG
1 ATGGCCGG
12264 TCACTTGTGC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 20 0.74
22 2 0.07
23 5 0.19
ACGTcount: A:0.15, C:0.33, G:0.35, T:0.17
Consensus pattern (22 bp):
ATGGCCGGCATCTCCAAGTCGC
Done.