Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009341.1 Corchorus capsularis cultivar CVL-1 contig09362, 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: 14934
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--39 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
40 CACACTAATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3969 original size:32 final size:32
Alignment explanation
Indices: 3928--3988 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
3918 AGTTTAGCAA
*
3928 ATTGCACATGTAGAATTAAAGGGTTGATACAG
1 ATTGCACATGTAGAATTAAAGGGCTGATACAG
* *
3960 ATTGCACATGTGGGATTAAAGGGCTGATA
1 ATTGCACATGTAGAATTAAAGGGCTGATA
3989 TTAAATACAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.34, C:0.10, G:0.28, T:0.28
Consensus pattern (32 bp):
ATTGCACATGTAGAATTAAAGGGCTGATACAG
Found at i:4530 original size:16 final size:16
Alignment explanation
Indices: 4511--4542 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
4501 ATATTCTTGG
4511 GTTATTCAAGTTTCGA
1 GTTATTCAAGTTTCGA
*
4527 GTTATTCGAGTTTCGA
1 GTTATTCAAGTTTCGA
4543 ATCATCCGAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.22, C:0.12, G:0.22, T:0.44
Consensus pattern (16 bp):
GTTATTCAAGTTTCGA
Found at i:4552 original size:16 final size:16
Alignment explanation
Indices: 4519--4562 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
4509 GGGTTATTCA
* * *
4519 AGTTTCGAGTTATTCG
1 AGTTTCGAATCATCCG
4535 AGTTTCGAATCATCCG
1 AGTTTCGAATCATCCG
*
4551 AGTCTCGAATCA
1 AGTTTCGAATCA
4563 CGAGTCATTC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.34
Consensus pattern (16 bp):
AGTTTCGAATCATCCG
Found at i:5002 original size:27 final size:27
Alignment explanation
Indices: 4972--5025 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
4962 GAGAACTACA
*
4972 CTAGTAAAACACGTTTTCCCTCAAACG
1 CTAGCAAAACACGTTTTCCCTCAAACG
* *
4999 CTAGCAAAATACGTTTTCCTTCAAACG
1 CTAGCAAAACACGTTTTCCCTCAAACG
5026 TGTTTTCTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.33, C:0.28, G:0.11, T:0.28
Consensus pattern (27 bp):
CTAGCAAAACACGTTTTCCCTCAAACG
Found at i:5498 original size:26 final size:26
Alignment explanation
Indices: 5461--5510 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
5451 GAAAACGTGT
*
5461 TTGAGGGGAAACATATTTTGCTAGCG
1 TTGAGGGAAAACATATTTTGCTAGCG
*
5487 TTGAGGGAAAACATGTTTTGCTAG
1 TTGAGGGAAAACATATTTTGCTAG
5511 TGTAGTTCTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.28, C:0.10, G:0.30, T:0.32
Consensus pattern (26 bp):
TTGAGGGAAAACATATTTTGCTAGCG
Found at i:12939 original size:16 final size:16
Alignment explanation
Indices: 12914--12945 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
12904 TCTTCTCCAT
12914 ATTCTATTGTCTTTTC
1 ATTCTATTGTCTTTTC
*
12930 ATTCTCTTGTCTTTTC
1 ATTCTATTGTCTTTTC
12946 CATACTTCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.09, C:0.22, G:0.06, T:0.62
Consensus pattern (16 bp):
ATTCTATTGTCTTTTC
Found at i:13636 original size:14 final size:15
Alignment explanation
Indices: 13611--13639 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
13601 AAAATAAGTG
13611 TTCAAAAGTTTATAA
1 TTCAAAAGTTTATAA
13626 TTCAAAA-TTTATAA
1 TTCAAAAGTTTATAA
13640 GTATTATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.48, C:0.07, G:0.03, T:0.41
Consensus pattern (15 bp):
TTCAAAAGTTTATAA
Found at i:14770 original size:20 final size:21
Alignment explanation
Indices: 14744--14788 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
14734 CAAAAATTAT
*
14744 AAAAAGGGGGCGATATTTAGC
1 AAAAGGGGGGCGATATTTAGC
* *
14765 AAAAGGGGGGCGGTGTTTAGC
1 AAAAGGGGGGCGATATTTAGC
14786 AAA
1 AAA
14789 CCCCTCAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.36, C:0.09, G:0.38, T:0.18
Consensus pattern (21 bp):
AAAAGGGGGGCGATATTTAGC
Done.