Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015484.1 Corchorus capsularis cultivar CVL-1 contig15505, 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: 9029
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.30
Found at i:1534 original size:28 final size:28
Alignment explanation
Indices: 1481--1534 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
1471 AAACTAATGT
* * *
1481 AGAGCAAGAAAATTTTACCATTAAAAAA
1 AGAGCAACAAAATTTTACAATAAAAAAA
1509 AGAGCAACAAAA-TTTACAATAAAAAA
1 AGAGCAACAAAATTTTACAATAAAAAA
1535 GCTGATTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 12 0.52
28 11 0.48
ACGTcount: A:0.61, C:0.11, G:0.09, T:0.19
Consensus pattern (28 bp):
AGAGCAACAAAATTTTACAATAAAAAAA
Found at i:3323 original size:25 final size:25
Alignment explanation
Indices: 3295--3385 Score: 119
Period size: 25 Copynumber: 3.6 Consensus size: 25
3285 CAGCCTATGT
* *
3295 GTTTTCTAAACGCAAGCACATGCTC
1 GTTTGCTAAACGCAAGCACAGGCTC
*
3320 GTTTTCTAAACGCAAGCACAGGCTC
1 GTTTGCTAAACGCAAGCACAGGCTC
* **
3345 GTTTGCTCAACGCAAGCGTAGGCTC
1 GTTTGCTAAACGCAAGCACAGGCTC
*
3370 GTTTGCCAAACGCAAG
1 GTTTGCTAAACGCAAG
3386 AACATGAGCG
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 59 1.00
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.24
Consensus pattern (25 bp):
GTTTGCTAAACGCAAGCACAGGCTC
Found at i:4932 original size:15 final size:15
Alignment explanation
Indices: 4906--4999 Score: 80
Period size: 15 Copynumber: 5.9 Consensus size: 15
4896 AAATTGGCAT
*
4906 CGTTTCAGAAACAAC
1 CGTTGCAGAAACAAC
*
4921 CGTTGCAAAAACATCATC
1 CGTTGCAGAAACA--A-C
*
4939 CATTGCAGAAACAAC
1 CGTTGCAGAAACAAC
*
4954 CGTTGCAAAAACATCATC
1 CGTTGCAGAAACA--A-C
*
4972 CATTGCAGAAACAAC
1 CGTTGCAGAAACAAC
*
4987 CGGTGCAGAAACA
1 CGTTGCAGAAACA
5000 CCCTTTTAAA
Statistics
Matches: 63, Mismatches: 10, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
15 35 0.56
16 2 0.03
17 2 0.03
18 24 0.38
ACGTcount: A:0.41, C:0.27, G:0.15, T:0.17
Consensus pattern (15 bp):
CGTTGCAGAAACAAC
Found at i:4948 original size:33 final size:33
Alignment explanation
Indices: 4911--4999 Score: 160
Period size: 33 Copynumber: 2.7 Consensus size: 33
4901 GGCATCGTTT
4911 CAGAAACAACCGTTGCAAAAACATCATCCATTG
1 CAGAAACAACCGTTGCAAAAACATCATCCATTG
4944 CAGAAACAACCGTTGCAAAAACATCATCCATTG
1 CAGAAACAACCGTTGCAAAAACATCATCCATTG
* *
4977 CAGAAACAACCGGTGCAGAAACA
1 CAGAAACAACCGTTGCAAAAACA
5000 CCCTTTTAAA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 54 1.00
ACGTcount: A:0.44, C:0.27, G:0.15, T:0.15
Consensus pattern (33 bp):
CAGAAACAACCGTTGCAAAAACATCATCCATTG
Found at i:4950 original size:18 final size:18
Alignment explanation
Indices: 4923--4984 Score: 76
Period size: 18 Copynumber: 3.6 Consensus size: 18
4913 GAAACAACCG
4923 TTGCAAAAACATCATCCA
1 TTGCAAAAACATCATCCA
* *
4941 TTGCAGAAACA--A-CCG
1 TTGCAAAAACATCATCCA
4956 TTGCAAAAACATCATCCA
1 TTGCAAAAACATCATCCA
*
4974 TTGCAGAAACA
1 TTGCAAAAACA
4985 ACCGGTGCAG
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
15 12 0.33
16 1 0.03
17 1 0.03
18 22 0.61
ACGTcount: A:0.44, C:0.26, G:0.11, T:0.19
Consensus pattern (18 bp):
TTGCAAAAACATCATCCA
Found at i:7603 original size:25 final size:25
Alignment explanation
Indices: 7575--7665 Score: 121
Period size: 25 Copynumber: 3.6 Consensus size: 25
7565 CAGCCTATGT
7575 GTTTTCTAAACGCAAGCACAGGCTC
1 GTTTTCTAAACGCAAGCACAGGCTC
7600 GTTTTCTAAACGCAAGCACAGGCTC
1 GTTTTCTAAACGCAAGCACAGGCTC
* **
7625 GTTTGT-TCAACGCAAGCGTAGGCTC
1 GTTT-TCTAAACGCAAGCACAGGCTC
* *
7650 GTTTGCCAAACGCAAG
1 GTTTTCTAAACGCAAG
7666 AACATGAGCG
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
25 57 0.98
26 1 0.02
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.24
Consensus pattern (25 bp):
GTTTTCTAAACGCAAGCACAGGCTC
Found at i:7678 original size:50 final size:50
Alignment explanation
Indices: 7583--7678 Score: 120
Period size: 50 Copynumber: 1.9 Consensus size: 50
7573 GTGTTTTCTA
* * * **
7583 AACGCAAGCACAGGCTCGTTTTCTAAACGCAAGCACAGGCTCGTTTGTTC
1 AACGCAAGCACAGGCTCGTTTGCCAAACGCAAGAACAGGAGCGTTTGTTC
** *
7633 AACGCAAGCGTAGGCTCGTTTGCCAAACGCAAGAACATGAGCGTTT
1 AACGCAAGCACAGGCTCGTTTGCCAAACGCAAGAACAGGAGCGTTT
7679 ACCCAGTGCA
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
50 38 1.00
ACGTcount: A:0.28, C:0.26, G:0.24, T:0.22
Consensus pattern (50 bp):
AACGCAAGCACAGGCTCGTTTGCCAAACGCAAGAACAGGAGCGTTTGTTC
Done.