Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015439.1 Corchorus capsularis cultivar CVL-1 contig15460, 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: 26166
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Found at i:779 original size:12 final size:12
Alignment explanation
Indices: 764--795 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
754 TCGCATGCGA
764 TGGCCGGTCATG
1 TGGCCGGTCATG
*
776 TGGCCGGACATG
1 TGGCCGGTCATG
788 TGGCCGGT
1 TGGCCGGT
796 GTTGCACGGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.09, C:0.25, G:0.44, T:0.22
Consensus pattern (12 bp):
TGGCCGGTCATG
Found at i:3405 original size:12 final size:12
Alignment explanation
Indices: 3390--3421 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
3380 TCGCATGCGA
3390 TGGCCGGTCATG
1 TGGCCGGTCATG
*
3402 TGGCCGGACATG
1 TGGCCGGTCATG
3414 TGGCCGGT
1 TGGCCGGT
3422 GTTGCACGGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.09, C:0.25, G:0.44, T:0.22
Consensus pattern (12 bp):
TGGCCGGTCATG
Found at i:9274 original size:30 final size:30
Alignment explanation
Indices: 9239--9299 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
9229 ATCACAAGGA
*
9239 CCATCGCATGGGACAACCG-GCCACAACCGG
1 CCATCGCAAGGGACAACCGCG-CACAACCGG
* *
9269 CCATCGCAAGGGGCATCCGCGCACAACCGG
1 CCATCGCAAGGGACAACCGCGCACAACCGG
9299 C
1 C
9300 TAATGGACCC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 26 0.96
31 1 0.04
ACGTcount: A:0.25, C:0.41, G:0.28, T:0.07
Consensus pattern (30 bp):
CCATCGCAAGGGACAACCGCGCACAACCGG
Found at i:10720 original size:25 final size:25
Alignment explanation
Indices: 10665--10720 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
10655 GAATCAGTGT
*
10665 GTTTTTTAGAAAGAGAAAAATGAGC
1 GTTTTTTAGAAAGAGAAAAATGAGA
* **
10690 GATTTTT-GATAAGAGAGTAATGAGA
1 GTTTTTTAGA-AAGAGAAAAATGAGA
10715 GTTTTT
1 GTTTTT
10721 CTTCCAGTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
24 2 0.08
25 23 0.92
ACGTcount: A:0.38, C:0.02, G:0.25, T:0.36
Consensus pattern (25 bp):
GTTTTTTAGAAAGAGAAAAATGAGA
Found at i:12968 original size:19 final size:19
Alignment explanation
Indices: 12944--12984 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
12934 GGGGGCTACC
12944 GAAAACTGAAAAGCTGTTG
1 GAAAACTGAAAAGCTGTTG
* *
12963 GAAAACTGATAAGTTGTTG
1 GAAAACTGAAAAGCTGTTG
12982 GAA
1 GAA
12985 TCCCCCCTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.41, C:0.07, G:0.27, T:0.24
Consensus pattern (19 bp):
GAAAACTGAAAAGCTGTTG
Found at i:13058 original size:38 final size:38
Alignment explanation
Indices: 13007--13156 Score: 142
Period size: 38 Copynumber: 4.0 Consensus size: 38
12997 AGAAACCGAA
* * *
13007 AACTGCTGAAAGATGACATGTTTCTAGTCGATCTTGAT
1 AACTGCTGAAAGATGACCTGTTTCCAGTCAATCTTGAT
* * *
13045 AACTGTTGAAAGATCACCTGTTTCCAGTCAAACTTGAT
1 AACTGCTGAAAGATGACCTGTTTCCAGTCAATCTTGAT
* * * * * **
13083 AAGTGTTGAAAGACGACCTGTTTCCAATC-GT-AAGAT
1 AACTGCTGAAAGATGACCTGTTTCCAGTCAATCTTGAT
* * *
13119 AATTGCTGAAACATGACCTGTTTCTAGTCAATCTTGAT
1 AACTGCTGAAAGATGACCTGTTTCCAGTCAATCTTGAT
13157 GACCTGTTTC
Statistics
Matches: 87, Mismatches: 23, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
36 26 0.30
37 1 0.01
38 60 0.69
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.33
Consensus pattern (38 bp):
AACTGCTGAAAGATGACCTGTTTCCAGTCAATCTTGAT
Found at i:13195 original size:60 final size:60
Alignment explanation
Indices: 13097--13209 Score: 190
Period size: 60 Copynumber: 1.9 Consensus size: 60
13087 GTTGAAAGAC
* *
13097 GACCTGTTTCCAATCGTAAGATAATTGCTGAAACATGACCTGTTTCTAGTCAATCTTGAT
1 GACCTGTTTCCAATCGAAAGATAATTGCTGAAACATGACCTGTTTCCAGTCAATCTTGAT
* *
13157 GACCTGTTTCCAGTCGAAAGATAATTGCTGAAAGATGACCTGTTTCCAGTCAA
1 GACCTGTTTCCAATCGAAAGATAATTGCTGAAACATGACCTGTTTCCAGTCAA
13210 CTTTAATAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 49 1.00
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (60 bp):
GACCTGTTTCCAATCGAAAGATAATTGCTGAAACATGACCTGTTTCCAGTCAATCTTGAT
Found at i:22007 original size:20 final size:19
Alignment explanation
Indices: 21982--22026 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
21972 AATAAACTCC
*
21982 ATAATACCACAAACTACTGA
1 ATAATACCACAAACT-CCGA
*
22002 ATAATACCATAAACTCCGA
1 ATAATACCACAAACTCCGA
22021 ATAATA
1 ATAATA
22027 ACATAATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.51, C:0.22, G:0.04, T:0.22
Consensus pattern (19 bp):
ATAATACCACAAACTCCGA
Found at i:22024 original size:19 final size:19
Alignment explanation
Indices: 21973--22032 Score: 70
Period size: 19 Copynumber: 3.2 Consensus size: 19
21963 GTTCTGAAAA
21973 ATAAACTCC--ATAATACC
1 ATAAACTCCGAATAATACC
* *
21990 ACAAACTACTGAATAATACC
1 ATAAACT-CCGAATAATACC
*
22010 ATAAACTCCGAATAATAAC
1 ATAAACTCCGAATAATACC
22029 ATAA
1 ATAA
22033 TTAAACACAT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
17 6 0.17
18 1 0.03
19 14 0.40
20 14 0.40
ACGTcount: A:0.52, C:0.23, G:0.03, T:0.22
Consensus pattern (19 bp):
ATAAACTCCGAATAATACC
Done.