Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01004770.1 Corchorus capsularis cultivar CVL-1 contig04788, 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: 11930
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Found at i:1500 original size:29 final size:31
Alignment explanation
Indices: 1474--1540 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
1464 GATCAATTTG
* *
1474 GGATCTAACGTTTCA-GAAACG-CCAATTCA
1 GGATATAACGTTACATGAAACGACCAATTCA
*
1503 GGATATAACGTTACATGAAACGACCAAATCA
1 GGATATAACGTTACATGAAACGACCAATTCA
1534 GGATATA
1 GGATATA
1541 TTTAGACGGA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 13 0.39
30 6 0.18
31 14 0.42
ACGTcount: A:0.40, C:0.19, G:0.18, T:0.22
Consensus pattern (31 bp):
GGATATAACGTTACATGAAACGACCAATTCA
Found at i:5884 original size:12 final size:12
Alignment explanation
Indices: 5867--5914 Score: 71
Period size: 12 Copynumber: 4.0 Consensus size: 12
5857 CTTGTTCCCC
5867 ACCTTCATCATT
1 ACCTTCATCATT
5879 ACCTTCATCATT
1 ACCTTCATCATT
5891 -CACTTCATCATT
1 AC-CTTCATCATT
*
5903 TCCTTCATCATT
1 ACCTTCATCATT
5915 GCAATTGTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
11 1 0.03
12 32 0.94
13 1 0.03
ACGTcount: A:0.23, C:0.33, G:0.00, T:0.44
Consensus pattern (12 bp):
ACCTTCATCATT
Found at i:5901 original size:24 final size:24
Alignment explanation
Indices: 5869--5914 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
5859 TGTTCCCCAC
5869 CTTCATCATTACCTTCATCATTCA
1 CTTCATCATTACCTTCATCATTCA
*
5893 CTTCATCATTTCCTTCATCATT
1 CTTCATCATTACCTTCATCATT
5915 GCAATTGTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.22, C:0.33, G:0.00, T:0.46
Consensus pattern (24 bp):
CTTCATCATTACCTTCATCATTCA
Found at i:7151 original size:30 final size:29
Alignment explanation
Indices: 7116--7172 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
7106 TGATTTTGGT
* *
7116 CGTTTCATGTAACGTTATATCTTAAATTCG
1 CGTTTC-TGAAACGTTATATCCTAAATTCG
*
7146 CGTTTCTGAAATGTTATATCCTAAATT
1 CGTTTCTGAAACGTTATATCCTAAATT
7173 AATCCGCACG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 18 0.75
30 6 0.25
ACGTcount: A:0.28, C:0.16, G:0.12, T:0.44
Consensus pattern (29 bp):
CGTTTCTGAAACGTTATATCCTAAATTCG
Found at i:8477 original size:22 final size:21
Alignment explanation
Indices: 8449--8493 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
8439 AAAGGGCTGA
8449 ATTTAATTAAATAATAATTATT
1 ATTTAATT-AATAATAATTATT
* *
8471 ATTTAATTAATTATTATTATT
1 ATTTAATTAATAATAATTATT
8492 AT
1 AT
8494 CAAGTTAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
ATTTAATTAATAATAATTATT
Found at i:8503 original size:21 final size:18
Alignment explanation
Indices: 8455--8491 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
8445 CTGAATTTAA
* *
8455 TTAAATAATAATTATTAT
1 TTAATTAATTATTATTAT
8473 TTAATTAATTATTATTAT
1 TTAATTAATTATTATTAT
8491 T
1 T
8492 ATCAAGTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TTAATTAATTATTATTAT
Found at i:11586 original size:21 final size:21
Alignment explanation
Indices: 11560--11603 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
11550 AAAAATTGGA
11560 TTGCTAAAT-ACCGCCCCATTT
1 TTGCT-AATCACCGCCCCATTT
* *
11581 TTGCTATTCACCGTCCCATTT
1 TTGCTAATCACCGCCCCATTT
11602 TT
1 TT
11604 TACGCTTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.18, C:0.32, G:0.09, T:0.41
Consensus pattern (21 bp):
TTGCTAATCACCGCCCCATTT
Found at i:11915 original size:32 final size:33
Alignment explanation
Indices: 11843--11916 Score: 114
Period size: 33 Copynumber: 2.3 Consensus size: 33
11833 CCACGGCGAA
*
11843 GCCGCCCCACTGGGACGGCTTCACCATAAACAG
1 GCCGCCCCACTGGGACAGCTTCACCATAAACAG
* *
11876 GCCGCCCCACTGGGGCAGCTTCACCATGAA-AG
1 GCCGCCCCACTGGGACAGCTTCACCATAAACAG
11908 GCCGCCCCA
1 GCCGCCCCA
11917 TGAGAGCGGC
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
32 11 0.29
33 27 0.71
ACGTcount: A:0.22, C:0.42, G:0.26, T:0.11
Consensus pattern (33 bp):
GCCGCCCCACTGGGACAGCTTCACCATAAACAG
Done.