Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014210.1 Corchorus capsularis cultivar CVL-1 contig14231, 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: 21340
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.30
Found at i:1208 original size:28 final size:28
Alignment explanation
Indices: 1135--1208 Score: 73
Period size: 28 Copynumber: 2.6 Consensus size: 28
1125 AAGTAACTTG
*
1135 GAAAATAAAAAG-TAAGGAAAAATTAAC
1 GAAAATAAAAAGATAAAGAAAAATTAAC
* *
1162 TAAACTAAAAATTGA-AAAGAAAAA-TAAC
1 GAAAATAAAAA--GATAAAGAAAAATTAAC
1190 GAAAATATAAAAGATAAAG
1 GAAAATA-AAAAGATAAAG
1209 GTAAGAAATT
Statistics
Matches: 37, Mismatches: 5, Indels: 9
0.73 0.10 0.18
Matches are distributed among these distances:
27 11 0.30
28 13 0.35
29 13 0.35
ACGTcount: A:0.68, C:0.04, G:0.12, T:0.16
Consensus pattern (28 bp):
GAAAATAAAAAGATAAAGAAAAATTAAC
Found at i:2870 original size:20 final size:21
Alignment explanation
Indices: 2845--2883 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2835 ACTAGCGCTG
2845 GGCG-CCCATGTGGTTTGCTT
1 GGCGCCCCATGTGGTTTGCTT
*
2865 GGCGCCCCATGTTGTTTGC
1 GGCGCCCCATGTGGTTTGC
2884 CTCGTGACCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.05, C:0.28, G:0.33, T:0.33
Consensus pattern (21 bp):
GGCGCCCCATGTGGTTTGCTT
Found at i:7138 original size:30 final size:30
Alignment explanation
Indices: 7102--7160 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
7092 GGGTTCTAAA
* *
7102 GGCATCTCCATGCGGCTTTGCGATTCCATT
1 GGCATCTCCATGAGACTTTGCGATTCCATT
* *
7132 GGCATCTTCATGAGACTTTGGGATTCCAT
1 GGCATCTCCATGAGACTTTGCGATTCCAT
7161 CCTCTCCTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.17, C:0.25, G:0.24, T:0.34
Consensus pattern (30 bp):
GGCATCTCCATGAGACTTTGCGATTCCATT
Found at i:8131 original size:21 final size:20
Alignment explanation
Indices: 8092--8136 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
8082 AATTATCAAT
* *
8092 TAAAAAGAAAGCAATTAAAC
1 TAAAAACAAAGCAAGTAAAC
*
8112 TAAAAACAAAGCAAAGTAAAT
1 TAAAAACAAAGC-AAGTAAAC
8133 TAAA
1 TAAA
8137 TATAAATCTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.67, C:0.09, G:0.09, T:0.16
Consensus pattern (20 bp):
TAAAAACAAAGCAAGTAAAC
Found at i:9493 original size:22 final size:21
Alignment explanation
Indices: 9463--9521 Score: 61
Period size: 19 Copynumber: 2.9 Consensus size: 21
9453 AATTCTTGCT
*
9463 TCTTGAAATAATTCTTCAATAA
1 TCTTCAAATAA-TCTTCAATAA
*
9485 TCTTC--A-AATCTTCAAATTA
1 TCTTCAAATAATCTTC-AATAA
9504 TCTTCAAATAATCTTCAA
1 TCTTCAAATAATCTTCAA
9522 ACACGAACTT
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
18 5 0.16
19 11 0.35
20 1 0.03
21 3 0.10
22 11 0.35
ACGTcount: A:0.39, C:0.19, G:0.02, T:0.41
Consensus pattern (21 bp):
TCTTCAAATAATCTTCAATAA
Found at i:9522 original size:11 final size:11
Alignment explanation
Indices: 9463--9522 Score: 65
Period size: 11 Copynumber: 5.7 Consensus size: 11
9453 AATTCTTGCT
*
9463 TCTTGAAATAA
1 TCTTCAAATAA
9474 TTCTTC-AATAA
1 -TCTTCAAATAA
9485 TCTTC--A-AA
1 TCTTCAAATAA
*
9493 TCTTCAAATTA
1 TCTTCAAATAA
9504 TCTTCAAATAA
1 TCTTCAAATAA
9515 TCTTCAAA
1 TCTTCAAA
9523 CACGAACTTC
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
8 7 0.17
9 1 0.02
10 6 0.14
11 24 0.57
12 4 0.10
ACGTcount: A:0.40, C:0.18, G:0.02, T:0.40
Consensus pattern (11 bp):
TCTTCAAATAA
Found at i:14855 original size:22 final size:20
Alignment explanation
Indices: 14828--14870 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 20
14818 TTTCAAATTA
14828 ACGCAAACCCTAATTTTTTTTT
1 ACGCAAA-CCT-ATTTTTTTTT
*
14850 ACGCAAACCTTTTTTTTTTT
1 ACGCAAACCTATTTTTTTTT
14870 A
1 A
14871 GAACAAACAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 10 0.50
21 3 0.15
22 7 0.35
ACGTcount: A:0.26, C:0.21, G:0.05, T:0.49
Consensus pattern (20 bp):
ACGCAAACCTATTTTTTTTT
Found at i:16549 original size:11 final size:11
Alignment explanation
Indices: 16509--16549 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
16499 AATTCTTGCT
*
16509 TCTTGAAATAA
1 TCTTCAAATAA
16520 TTCTTC-AATAA
1 -TCTTCAAATAA
16531 TCTTCAAATAA
1 TCTTCAAATAA
16542 TCTTCAAA
1 TCTTCAAA
16550 CACGAACTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
10 5 0.19
11 18 0.67
12 4 0.15
ACGTcount: A:0.41, C:0.17, G:0.02, T:0.39
Consensus pattern (11 bp):
TCTTCAAATAA
Done.