Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01001948.1 Corchorus capsularis cultivar CVL-1 contig01950, 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: 3240
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.37
Found at i:1485 original size:15 final size:15
Alignment explanation
Indices: 1461--1532 Score: 54
Period size: 11 Copynumber: 5.4 Consensus size: 15
1451 AAATTACTTA
1461 GTTT-ATTAGTTTAT
1 GTTTAATTAGTTTAT
1475 GTTTAATTAG--TA-
1 GTTTAATTAGTTTAT
*
1487 -TTTAATTATTTTAT
1 GTTTAATTAGTTTAT
*
1501 GATTAATTAG--TA-
1 GTTTAATTAGTTTAT
1513 -TTTAATTAGTTTAT
1 GTTTAATTAGTTTAT
*
1527 GATTAA
1 GTTTAA
1533 AATGAAGGAA
Statistics
Matches: 44, Mismatches: 5, Indels: 17
0.67 0.08 0.26
Matches are distributed among these distances:
11 16 0.36
13 8 0.18
14 4 0.09
15 16 0.36
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (15 bp):
GTTTAATTAGTTTAT
Found at i:1494 original size:26 final size:26
Alignment explanation
Indices: 1465--1532 Score: 118
Period size: 26 Copynumber: 2.6 Consensus size: 26
1455 TACTTAGTTT
*
1465 ATTAGTTTATGTTTAATTAGTATTTA
1 ATTAGTTTATGATTAATTAGTATTTA
*
1491 ATTATTTTATGATTAATTAGTATTTA
1 ATTAGTTTATGATTAATTAGTATTTA
1517 ATTAGTTTATGATTAA
1 ATTAGTTTATGATTAA
1533 AATGAAGGAA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.56
Consensus pattern (26 bp):
ATTAGTTTATGATTAATTAGTATTTA
Found at i:2336 original size:31 final size:34
Alignment explanation
Indices: 2298--2359 Score: 94
Period size: 31 Copynumber: 1.9 Consensus size: 34
2288 TCAGGTTGGG
2298 TTTGGGTTCGGG-TT-A-TCGGATTCGGGTTATT
1 TTTGGGTTCGGGCTTGAGTCGGATTCGGGTTATT
*
2329 TTTGGGTTCGGGCTTGAGTCGGGTTCGGGTT
1 TTTGGGTTCGGGCTTGAGTCGGATTCGGGTT
2360 GGATTTGGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
31 12 0.44
32 2 0.07
33 1 0.04
34 12 0.44
ACGTcount: A:0.06, C:0.11, G:0.40, T:0.42
Consensus pattern (34 bp):
TTTGGGTTCGGGCTTGAGTCGGATTCGGGTTATT
Found at i:2403 original size:31 final size:32
Alignment explanation
Indices: 2347--2448 Score: 170
Period size: 32 Copynumber: 3.2 Consensus size: 32
2337 CGGGCTTGAG
*
2347 TCGGGTTCGGGTTGGATTTGGGTCAGGTTAAT
1 TCGGGTTCGGGTTGAATTTGGGTCAGGTTAAT
*
2379 TCGGGTTCGGGTT-AATTTGAGTCAGGTTAAT
1 TCGGGTTCGGGTTGAATTTGGGTCAGGTTAAT
*
2410 TCGGGTTCGGGTTGAATTTGGGTCAGATTAAT
1 TCGGGTTCGGGTTGAATTTGGGTCAGGTTAAT
2442 TCGGGTT
1 TCGGGTT
2449 TAGGTTCTGT
Statistics
Matches: 65, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
31 29 0.45
32 36 0.55
ACGTcount: A:0.16, C:0.10, G:0.36, T:0.38
Consensus pattern (32 bp):
TCGGGTTCGGGTTGAATTTGGGTCAGGTTAAT
Found at i:2408 original size:15 final size:15
Alignment explanation
Indices: 2362--2447 Score: 82
Period size: 15 Copynumber: 5.5 Consensus size: 15
2352 TTCGGGTTGG
2362 ATTTGGGTCAGGTTA
1 ATTTGGGTCAGGTTA
* *
2377 ATTCGGGTTCGGGTTA
1 ATTTGGG-TCAGGTTA
*
2393 ATTTGAGTCAGGTTA
1 ATTTGGGTCAGGTTA
* *
2408 ATTCGGGTTCGGGTTGA
1 ATTTGGG-TCAGGTT-A
*
2425 ATTTGGGTCAGATTA
1 ATTTGGGTCAGGTTA
*
2440 ATTCGGGT
1 ATTTGGGT
2448 TTAGGTTCTG
Statistics
Matches: 56, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
15 26 0.46
16 23 0.41
17 7 0.12
ACGTcount: A:0.19, C:0.09, G:0.34, T:0.38
Consensus pattern (15 bp):
ATTTGGGTCAGGTTA
Found at i:2603 original size:16 final size:16
Alignment explanation
Indices: 2595--2687 Score: 123
Period size: 16 Copynumber: 5.8 Consensus size: 16
2585 TCGGATTCGG
*
2595 GTTTTTTCGGATTTGA
1 GTTTTTTCGGGTTTGA
* *
2611 GCTTTTTCGGGTTTGG
1 GTTTTTTCGGGTTTGA
2627 GTTTTTTCGGGTTTGA
1 GTTTTTTCGGGTTTGA
* *
2643 GTTTTTTCGGGTTCGT
1 GTTTTTTCGGGTTTGA
2659 GTTTTTTCGGGTTTGA
1 GTTTTTTCGGGTTTGA
**
2675 ACTTTTTCGGGTT
1 GTTTTTTCGGGTT
2688 CGTATTCGTG
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 66 1.00
ACGTcount: A:0.05, C:0.10, G:0.30, T:0.55
Consensus pattern (16 bp):
GTTTTTTCGGGTTTGA
Found at i:2690 original size:32 final size:32
Alignment explanation
Indices: 2582--2689 Score: 162
Period size: 32 Copynumber: 3.4 Consensus size: 32
2572 ATTTTCATAA
* *
2582 TTTTCGGATTCGGGTTTTTTCGGATTTGAGCT
1 TTTTCGGGTTCGGGTTTTTTCGGGTTTGAGCT
* *
2614 TTTTCGGGTTTGGGTTTTTTCGGGTTTGAGTT
1 TTTTCGGGTTCGGGTTTTTTCGGGTTTGAGCT
* *
2646 TTTTCGGGTTCGTGTTTTTTCGGGTTTGAACT
1 TTTTCGGGTTCGGGTTTTTTCGGGTTTGAGCT
2678 TTTTCGGGTTCG
1 TTTTCGGGTTCG
2690 TATTCGTGTT
Statistics
Matches: 68, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 68 1.00
ACGTcount: A:0.06, C:0.11, G:0.31, T:0.53
Consensus pattern (32 bp):
TTTTCGGGTTCGGGTTTTTTCGGGTTTGAGCT
Done.