Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006744.1 Corchorus capsularis cultivar CVL-1 contig06765, 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: 10714
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:1061 original size:21 final size:21
Alignment explanation
Indices: 1037--1086 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
1027 TTGATGATGC
*
1037 TTTTATATAAAACAACTTTT-
1 TTTTATATAAAAAAACTTTTG
* *
1057 TTTTTTCAAAAAAAAACTTTTG
1 TTTTAT-ATAAAAAAACTTTTG
1079 TTTTATAT
1 TTTTATAT
1087 TATTTCTTTT
Statistics
Matches: 23, Mismatches: 5, Indels: 3
0.74 0.16 0.10
Matches are distributed among these distances:
20 5 0.22
21 13 0.57
22 5 0.22
ACGTcount: A:0.38, C:0.08, G:0.02, T:0.52
Consensus pattern (21 bp):
TTTTATATAAAAAAACTTTTG
Found at i:4548 original size:33 final size:33
Alignment explanation
Indices: 4470--4574 Score: 113
Period size: 33 Copynumber: 3.2 Consensus size: 33
4460 TTGCAAAGAG
* * *
4470 TGTTTTAGATGTTGTTTGCGATGATACTAAACC
1 TGTTTTAGGTGTTGTTTGCGATGAAACTAAATC
** *
4503 TAATTT-GAGTGTTGTTTGCGATGACACTAAATC
1 TGTTTTAG-GTGTTGTTTGCGATGAAACTAAATC
** *
4536 TGTTTTAGGTGTTGTTTGTAATGAAACAAAATC
1 TGTTTTAGGTGTTGTTTGCGATGAAACTAAATC
4569 TGTTTT
1 TGTTTT
4575 GGATGCTAAT
Statistics
Matches: 59, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
32 1 0.02
33 57 0.97
34 1 0.02
ACGTcount: A:0.26, C:0.10, G:0.21, T:0.44
Consensus pattern (33 bp):
TGTTTTAGGTGTTGTTTGCGATGAAACTAAATC
Found at i:8677 original size:2 final size:2
Alignment explanation
Indices: 8672--8722 Score: 59
Period size: 2 Copynumber: 25.5 Consensus size: 2
8662 ATATATCAAC
* *
8672 AT AT AT AT AT AT AT AT TT AT AT CA- AC 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 AT AT AT AT AT
*
8714 TT AT AT AT A
1 AT AT AT AT A
8723 CAGTTGCATA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
1 1 0.02
2 40 0.95
3 1 0.02
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:8680 original size:14 final size:14
Alignment explanation
Indices: 8661--8707 Score: 62
Period size: 14 Copynumber: 3.5 Consensus size: 14
8651 TCAGCATCAT
8661 TATATATCAACATA
1 TATATATCAACATA
*
8675 TATATAT--ATATA
1 TATATATCAACATA
*
8687 TTTATATCAACATA
1 TATATATCAACATA
8701 TATATAT
1 TATATAT
8708 ATATATTTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
12 10 0.37
14 17 0.63
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.45
Consensus pattern (14 bp):
TATATATCAACATA
Found at i:8692 original size:26 final size:26
Alignment explanation
Indices: 8663--8719 Score: 114
Period size: 26 Copynumber: 2.2 Consensus size: 26
8653 AGCATCATTA
8663 TATATCAACATATATATATATATATT
1 TATATCAACATATATATATATATATT
8689 TATATCAACATATATATATATATATT
1 TATATCAACATATATATATATATATT
8715 TATAT
1 TATAT
8720 ATACAGTTGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.47
Consensus pattern (26 bp):
TATATCAACATATATATATATATATT
Found at i:8920 original size:13 final size:13
Alignment explanation
Indices: 8891--8933 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
8881 ACTATTTACT
8891 TTAATTTTGC--A
1 TTAATTTTGCATA
8902 -TAATTTTGCATA
1 TTAATTTTGCATA
*
8914 TTAATTTTGTATA
1 TTAATTTTGCATA
8927 TTAATTT
1 TTAATTT
8934 CAAATGAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
10 9 0.32
12 1 0.04
13 18 0.64
ACGTcount: A:0.30, C:0.05, G:0.07, T:0.58
Consensus pattern (13 bp):
TTAATTTTGCATA
Done.