Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011583.1 Corchorus capsularis cultivar CVL-1 contig11604, 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: 14536
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Found at i:533 original size:17 final size:17
Alignment explanation
Indices: 511--549 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
501 AAATTGAATA
**
511 TTTTTATTTTAATATAT
1 TTTTTATTGAAATATAT
*
528 TTTTTATTGAAATTTAT
1 TTTTTATTGAAATATAT
545 TTTTT
1 TTTTT
550 TAATAATAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.72
Consensus pattern (17 bp):
TTTTTATTGAAATATAT
Found at i:1454 original size:13 final size:14
Alignment explanation
Indices: 1431--1466 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1421 TTTTTTTTAT
1431 TATTAAAAAAATGAA
1 TATTAAAAAAA-GAA
1446 T-TTAAAAAAAGAA
1 TATTAAAAAAAGAA
1459 TATTAAAA
1 TATTAAAA
1467 TTAAAATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 4 0.20
14 15 0.75
15 1 0.05
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.28
Consensus pattern (14 bp):
TATTAAAAAAAGAA
Found at i:1935 original size:15 final size:15
Alignment explanation
Indices: 1900--1928 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1890 TGACCGACCC
1900 CGAATTAACCCGAAT
1 CGAATTAACCCGAAT
1915 CGAATTAACCCGAA
1 CGAATTAACCCGAA
1929 CTCAATTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.28, G:0.14, T:0.17
Consensus pattern (15 bp):
CGAATTAACCCGAAT
Found at i:2793 original size:30 final size:31
Alignment explanation
Indices: 2730--2807 Score: 97
Period size: 30 Copynumber: 2.5 Consensus size: 31
2720 AAAAGAGGCT
* *
2730 TGCTCAAATAAGGGTCCAATATTTGCGAAAA
1 TGCTCAAATAAGGGTCCAATATTTACAAAAA
*
2761 TGCTCAAATCAA-GGTCTAAT-TTTACAAAAA
1 TGCTCAAAT-AAGGGTCCAATATTTACAAAAA
*
2791 TGCTCAAATATGGGTCC
1 TGCTCAAATAAGGGTCC
2808 GAATGAAAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
29 1 0.03
30 21 0.52
31 16 0.40
32 2 0.05
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28
Consensus pattern (31 bp):
TGCTCAAATAAGGGTCCAATATTTACAAAAA
Found at i:3070 original size:53 final size:57
Alignment explanation
Indices: 2969--3076 Score: 143
Period size: 53 Copynumber: 2.0 Consensus size: 57
2959 ATTTGAACAT
* * * *
2969 TTTTTTTTCTTTAGATCCTTATTTGAGTATTTTCGCAAACATTGGGCCCTGATTTCA
1 TTTTTTTTCTTTAGATCCTTATGTGAGCATTTTCGCAAACATTAGGCCCTAATTTCA
*
3026 TTTTTTTTCTTTAGA-CC-T-TGT-AGCATTTTCGCAAACGTTAGGCCCTAATTT
1 TTTTTTTTCTTTAGATCCTTATGTGAGCATTTTCGCAAACATTAGGCCCTAATTT
3077 AAGCAATTAG
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
53 26 0.57
54 2 0.04
55 1 0.02
56 2 0.04
57 15 0.33
ACGTcount: A:0.19, C:0.19, G:0.14, T:0.48
Consensus pattern (57 bp):
TTTTTTTTCTTTAGATCCTTATGTGAGCATTTTCGCAAACATTAGGCCCTAATTTCA
Found at i:5365 original size:4 final size:4
Alignment explanation
Indices: 5358--5427 Score: 70
Period size: 4 Copynumber: 17.8 Consensus size: 4
5348 ACACACACAA
* * *
5358 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATCT ATAT CTAT ATCT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
* * * *
5406 CTAT CTAT A-AT CTAT ATCT ATA
1 ATAT ATAT ATAT ATAT ATAT ATA
5428 GGTGGTAATT
Statistics
Matches: 53, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
3 2 0.04
4 51 0.96
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.49
Consensus pattern (4 bp):
ATAT
Found at i:5367 original size:6 final size:6
Alignment explanation
Indices: 5358--5427 Score: 70
Period size: 6 Copynumber: 11.8 Consensus size: 6
5348 ACACACACAA
* * *
5358 ATATAT ATATAT ATATAT ATATAT ATATAT CTATAT CTATAT CTATAT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT
* * * *
5406 CTATCT ATA-AT CTATAT CTATA
1 ATATAT ATATAT ATATAT ATATA
5428 GGTGGTAATT
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
5 3 0.05
6 55 0.95
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.49
Consensus pattern (6 bp):
ATATAT
Found at i:7631 original size:84 final size:83
Alignment explanation
Indices: 7516--7672 Score: 271
Period size: 84 Copynumber: 1.9 Consensus size: 83
7506 TTATATATTC
7516 AATTAAATCTAATTCTTTATAACTATTTTATTTTTACCA-TTTTACTATTTTAATTAAAAAAACT
1 AATTAAATCTAATTCTTTATAACTATTTTATTTTTACCATTTTTACTATTTTAATT-AAAAAACT
7580 TAGATATATTAGAATTTTT
65 TAGATATATTAGAATTTTT
* *
7599 AATTAAATCTAATCTCTTTATAACTATTTTATTTTTACCATTTTTACTATTTTAATTACATAACT
1 AATTAAATCTAAT-TCTTTATAACTATTTTATTTTTACCATTTTTACTATTTTAATTAAAAAACT
7664 TAGATATAT
65 TAGATATAT
7673 ATATATATAT
Statistics
Matches: 70, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
83 13 0.19
84 41 0.59
85 16 0.23
ACGTcount: A:0.37, C:0.10, G:0.02, T:0.51
Consensus pattern (83 bp):
AATTAAATCTAATTCTTTATAACTATTTTATTTTTACCATTTTTACTATTTTAATTAAAAAACTT
AGATATATTAGAATTTTT
Found at i:8481 original size:2 final size:2
Alignment explanation
Indices: 8474--8518 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
8464 ATTACAAGGC
* *
8474 AT AT AT AT AT AT AT AC AT AT AT AT AT AC AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
8516 AT A
1 AT A
8519 AAAGTACAAG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Done.