Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007504.1 Corchorus capsularis cultivar CVL-1 contig07525, 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: 30127
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:2202 original size:18 final size:18
Alignment explanation
Indices: 2056--2195 Score: 163
Period size: 18 Copynumber: 7.8 Consensus size: 18
2046 AAGTGTGGCA
* *
2056 ACTTGGTGCGGTGCGGCC
1 ACTTGGTGTGGTGCGACC
* *
2074 ACTAGGTGTGGTGCGATC
1 ACTTGGTGTGGTGCGACC
2092 ACTTGGTGTGGTGCGACC
1 ACTTGGTGTGGTGCGACC
*
2110 ACTTGGTGTGGTGCAACC
1 ACTTGGTGTGGTGCGACC
* *
2128 ACTGGGTGTGGTGCGTCC
1 ACTTGGTGTGGTGCGACC
* * **
2146 ATTTGGTATGGTGCGGTC
1 ACTTGGTGTGGTGCGACC
2164 ACTTGGTGTGGTGCGACC
1 ACTTGGTGTGGTGCGACC
* *
2182 ATTTGGTATGGTGC
1 ACTTGGTGTGGTGC
2196 AGCCATTGGG
Statistics
Matches: 101, Mismatches: 21, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 101 1.00
ACGTcount: A:0.11, C:0.19, G:0.39, T:0.30
Consensus pattern (18 bp):
ACTTGGTGTGGTGCGACC
Found at i:2208 original size:36 final size:36
Alignment explanation
Indices: 2096--2210 Score: 151
Period size: 36 Copynumber: 3.2 Consensus size: 36
2086 GCGATCACTT
* * * *
2096 GGTGTGGTGCGACCACTTGGTGTGGTGCAACCACTG
1 GGTGTGGTGCGACCATTTGGTATGGTGCAGCCATTG
* * *
2132 GGTGTGGTGCGTCCATTTGGTATGGTGCGGTCACTT-
1 GGTGTGGTGCGACCATTTGGTATGGTGCAGCCA-TTG
2168 GGTGTGGTGCGACCATTTGGTATGGTGCAGCCATTG
1 GGTGTGGTGCGACCATTTGGTATGGTGCAGCCATTG
2204 GGTGTGG
1 GGTGTGG
2211 CGCCATTTGT
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
35 2 0.03
36 64 0.96
37 1 0.01
ACGTcount: A:0.11, C:0.17, G:0.41, T:0.30
Consensus pattern (36 bp):
GGTGTGGTGCGACCATTTGGTATGGTGCAGCCATTG
Found at i:13768 original size:10 final size:10
Alignment explanation
Indices: 13753--13778 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
13743 AATTTAATAT
13753 GGATATTTAC
1 GGATATTTAC
13763 GGATATTTAC
1 GGATATTTAC
13773 GGATAT
1 GGATAT
13779 ATCGAGATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.31, C:0.08, G:0.23, T:0.38
Consensus pattern (10 bp):
GGATATTTAC
Found at i:20766 original size:18 final size:16
Alignment explanation
Indices: 20743--20787 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 16
20733 ACAGAGGAAG
20743 AAAGAAAGAAAAAAGAA
1 AAAGAAA-AAAAAAGAA
*
20760 TAAAGAATAAAAAAATAA
1 -AAAGAA-AAAAAAAGAA
20778 AAAGAAAAAA
1 AAAGAAAAAA
20788 GACACGTTAC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 4 0.16
17 6 0.24
18 14 0.56
19 1 0.04
ACGTcount: A:0.82, C:0.00, G:0.11, T:0.07
Consensus pattern (16 bp):
AAAGAAAAAAAAAGAA
Found at i:21089 original size:19 final size:20
Alignment explanation
Indices: 21065--21102 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
21055 TTGAAGATTT
21065 CTTGAAG-ATAATTTGAAGA
1 CTTGAAGAATAATTTGAAGA
*
21084 CTTGAAGAATTATTTGAAG
1 CTTGAAGAATAATTTGAAG
21103 GAGCAAGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.39, C:0.05, G:0.21, T:0.34
Consensus pattern (20 bp):
CTTGAAGAATAATTTGAAGA
Found at i:23600 original size:13 final size:13
Alignment explanation
Indices: 23582--23606 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
23572 TTAAATAAAT
23582 TGAATAGAGAATA
1 TGAATAGAGAATA
23595 TGAATAGAGAAT
1 TGAATAGAGAAT
23607 TCAATTTCTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.00, G:0.24, T:0.24
Consensus pattern (13 bp):
TGAATAGAGAATA
Found at i:24926 original size:43 final size:44
Alignment explanation
Indices: 24877--24965 Score: 153
Period size: 44 Copynumber: 2.0 Consensus size: 44
24867 TCTATCAGGG
*
24877 CATAGTTTTGTGAAGTGAACT-GTTAAATATTAGGATTAGAATT
1 CATAGTTTTGTGAAGTGAACTAATTAAATATTAGGATTAGAATT
*
24920 CATAGTTTTGTGAAGTGAACTAATTACATATTAGGATTAGAATT
1 CATAGTTTTGTGAAGTGAACTAATTAAATATTAGGATTAGAATT
24964 CA
1 CA
24966 ATTCGTTGGT
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
43 21 0.49
44 22 0.51
ACGTcount: A:0.36, C:0.07, G:0.19, T:0.38
Consensus pattern (44 bp):
CATAGTTTTGTGAAGTGAACTAATTAAATATTAGGATTAGAATT
Done.