Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007356.1 Corchorus capsularis cultivar CVL-1 contig07377, 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: 17897
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:5726 original size:30 final size:30
Alignment explanation
Indices: 5663--5728 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
5653 TGCCTTTGGA
* * * *
5663 GAAGGAGAAGATTCTGATTTCTTTGTTTGT
1 GAAGGAGAACAATCTGATTTCCTTGCTTGT
5693 GAAGGAGAACAATCTGATTTCCTT-CTTGAT
1 GAAGGAGAACAATCTGATTTCCTTGCTTG-T
5723 GAAGGA
1 GAAGGA
5729 TTTGTTTGTG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 3 0.10
30 28 0.90
ACGTcount: A:0.29, C:0.11, G:0.26, T:0.35
Consensus pattern (30 bp):
GAAGGAGAACAATCTGATTTCCTTGCTTGT
Found at i:7894 original size:48 final size:48
Alignment explanation
Indices: 7841--7938 Score: 178
Period size: 48 Copynumber: 2.0 Consensus size: 48
7831 TCAAGCAAGT
7841 TGAACCATTTTTAGTCTGTTTTACAAAGTACATGGCAATGACACGCAA
1 TGAACCATTTTTAGTCTGTTTTACAAAGTACATGGCAATGACACGCAA
* *
7889 TGAACCATTTTTAGTCTGTTTTACAAAGTACATGGCAATGATAGGCAA
1 TGAACCATTTTTAGTCTGTTTTACAAAGTACATGGCAATGACACGCAA
7937 TG
1 TG
7939 GATAATGCCA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (48 bp):
TGAACCATTTTTAGTCTGTTTTACAAAGTACATGGCAATGACACGCAA
Found at i:8967 original size:16 final size:16
Alignment explanation
Indices: 8942--9032 Score: 85
Period size: 16 Copynumber: 5.7 Consensus size: 16
8932 GAACCCGCCT
*
8942 GAACCTGAAAAAATCC
1 GAACCCGAAAAAATCC
8958 GAACCCGAAAAAGAT-C
1 GAACCCGAAAAA-ATCC
* * *
8974 AAATCCGAAAAAACCC
1 GAACCCGAAAAAATCC
* *
8990 GAACCCGAAAAAGTTC
1 GAACCCGAAAAAATCC
* *
9006 AAACCCGAAAAAACCC
1 GAACCCGAAAAAATCC
*
9022 GAATCCGAAAA
1 GAACCCGAAAA
9033 TTTATGAAAA
Statistics
Matches: 58, Mismatches: 15, Indels: 4
0.75 0.19 0.05
Matches are distributed among these distances:
15 1 0.02
16 55 0.95
17 2 0.03
ACGTcount: A:0.52, C:0.27, G:0.13, T:0.08
Consensus pattern (16 bp):
GAACCCGAAAAAATCC
Found at i:8984 original size:32 final size:32
Alignment explanation
Indices: 8943--9032 Score: 135
Period size: 32 Copynumber: 2.8 Consensus size: 32
8933 AACCCGCCTG
* *
8943 AACCTGAAAAAATCCGAACCCGAAAAAGATCA
1 AACCCGAAAAAACCCGAACCCGAAAAAGATCA
* *
8975 AATCCGAAAAAACCCGAACCCGAAAAAGTTCA
1 AACCCGAAAAAACCCGAACCCGAAAAAGATCA
*
9007 AACCCGAAAAAACCCGAATCCGAAAA
1 AACCCGAAAAAACCCGAACCCGAAAA
9033 TTTATGAAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 52 1.00
ACGTcount: A:0.52, C:0.28, G:0.12, T:0.08
Consensus pattern (32 bp):
AACCCGAAAAAACCCGAACCCGAAAAAGATCA
Found at i:9222 original size:17 final size:15
Alignment explanation
Indices: 9199--9248 Score: 55
Period size: 17 Copynumber: 3.1 Consensus size: 15
9189 GAATTAACAT
9199 GACCCAAATTCATCCC
1 GACCCAAATTCAT-CC
* *
9215 GAACCCAAATTAATCT
1 G-ACCCAAATTCATCC
9231 GACCCAAATTCAATCC
1 GACCCAAATTC-ATCC
9247 GA
1 GA
9249 ATCCGATTCA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 9 0.32
16 8 0.29
17 11 0.39
ACGTcount: A:0.38, C:0.34, G:0.08, T:0.20
Consensus pattern (15 bp):
GACCCAAATTCATCC
Found at i:10076 original size:2 final size:2
Alignment explanation
Indices: 10069--10100 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
10059 TAAATGCATC
10069 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10101 TAAATGTTAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13406 original size:30 final size:30
Alignment explanation
Indices: 13370--13432 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 30
13360 TCTTCAAGGG
13370 GGAGGGAATGATGCGCCCAAGG-CTTATCAT
1 GGAGGGAATGATGCG-CCAAGGACTTATCAT
13400 GGAGGGAATGATGCGCCAAGGACTTATCAT
1 GGAGGGAATGATGCGCCAAGGACTTATCAT
13430 GGA
1 GGA
13433 CTTGAAGATG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 6 0.19
30 26 0.81
ACGTcount: A:0.29, C:0.17, G:0.35, T:0.19
Consensus pattern (30 bp):
GGAGGGAATGATGCGCCAAGGACTTATCAT
Done.