Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014768.1 Corchorus olitorius cultivar O-4 contig14801, 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: 24968
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Found at i:7262 original size:21 final size:24
Alignment explanation
Indices: 7208--7286 Score: 82
Period size: 22 Copynumber: 3.5 Consensus size: 24
7198 TTAGTAATTA
7208 AATATATATTATTTATTTATTT--T
1 AATATATATTA-TTATTTATTTAAT
*
7231 AA-ACT-CATTATTA-TTATTTAA-
1 AATA-TATATTATTATTTATTTAAT
7252 AATATAT-TTATTATTTATTTAAT
1 AATATATATTATTATTTATTTAAT
7275 AATATATATTAT
1 AATATATATTAT
7287 ATCTAAGATA
Statistics
Matches: 46, Mismatches: 2, Indels: 15
0.73 0.03 0.24
Matches are distributed among these distances:
20 6 0.13
21 12 0.26
22 14 0.30
23 10 0.22
24 4 0.09
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (24 bp):
AATATATATTATTATTTATTTAAT
Found at i:9432 original size:29 final size:28
Alignment explanation
Indices: 9400--9455 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 28
9390 TTCAAATTGC
* *
9400 AAGTTCAATGGGTAAAATGTCCAAAATTA
1 AAGTTCAAGGGGCAAAATGT-CAAAATTA
* *
9429 AAGTTTAGGGGGCAAAATGTCAAAATT
1 AAGTTCAAGGGGCAAAATGTCAAAATT
9456 GTACAAATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
28 7 0.30
29 16 0.70
ACGTcount: A:0.43, C:0.09, G:0.21, T:0.27
Consensus pattern (28 bp):
AAGTTCAAGGGGCAAAATGTCAAAATTA
Found at i:11049 original size:16 final size:18
Alignment explanation
Indices: 11037--11096 Score: 67
Period size: 18 Copynumber: 3.6 Consensus size: 18
11027 TGGTTTGGCC
11037 ACGTGGCATTTTGGTCCG
1 ACGTGGCATTTTGGTCCG
*
11055 ATGTGGCA--TT-G-CC-
1 ACGTGGCATTTTGGTCCG
11068 ACGTGGCATTTTTGGTCCG
1 ACGTGGCA-TTTTGGTCCG
11087 ACGTGGCATT
1 ACGTGGCATT
11097 GACATGTCAG
Statistics
Matches: 34, Mismatches: 2, Indels: 12
0.71 0.04 0.25
Matches are distributed among these distances:
13 7 0.21
14 2 0.06
15 1 0.03
16 4 0.12
17 1 0.03
18 11 0.32
19 8 0.24
ACGTcount: A:0.13, C:0.22, G:0.32, T:0.33
Consensus pattern (18 bp):
ACGTGGCATTTTGGTCCG
Found at i:11069 original size:31 final size:32
Alignment explanation
Indices: 11034--11097 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
11024 TCTTGGTTTG
*
11034 GCCACGTGGCA-TTTTGGTCCGATGTGGCATT
1 GCCACGTGGCATTTTTGGTCCGACGTGGCATT
11065 GCCACGTGGCATTTTTGGTCCGACGTGGCATT
1 GCCACGTGGCATTTTTGGTCCGACGTGGCATT
11097 G
1 G
11098 ACATGTCAGC
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 11 0.35
32 20 0.65
ACGTcount: A:0.12, C:0.23, G:0.33, T:0.31
Consensus pattern (32 bp):
GCCACGTGGCATTTTTGGTCCGACGTGGCATT
Found at i:14179 original size:30 final size:29
Alignment explanation
Indices: 14112--14181 Score: 106
Period size: 29 Copynumber: 2.4 Consensus size: 29
14102 ACTTGTAACG
* *
14112 TTTGGACGTTTT-GCCCCTGAACTTCAAT
1 TTTGGACATTTTAACCCCTGAACTTCAAT
14140 TTTGGACATTTTAACCCCTGAACTTCAAT
1 TTTGGACATTTTAACCCCTGAACTTCAAT
14169 TTTGGGACATTTT
1 TTT-GGACATTTT
14182 GCTCCCTCAG
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
28 11 0.29
29 18 0.47
30 9 0.24
ACGTcount: A:0.21, C:0.21, G:0.16, T:0.41
Consensus pattern (29 bp):
TTTGGACATTTTAACCCCTGAACTTCAAT
Found at i:14378 original size:29 final size:30
Alignment explanation
Indices: 14336--14396 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 30
14326 GTAAAACGTC
* *
14336 CCAAAATTGAAGTTCATG-GGACAAAATGT
1 CCAAAATTAAAGTTCACGAGGACAAAATGT
*
14365 CCAAAATTAAAGTTCACGAGGGCAAAATGT
1 CCAAAATTAAAGTTCACGAGGACAAAATGT
14395 CC
1 CC
14397 CGTTGCAAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 16 0.57
30 12 0.43
ACGTcount: A:0.41, C:0.18, G:0.20, T:0.21
Consensus pattern (30 bp):
CCAAAATTAAAGTTCACGAGGACAAAATGT
Found at i:24574 original size:29 final size:29
Alignment explanation
Indices: 24537--24609 Score: 137
Period size: 29 Copynumber: 2.5 Consensus size: 29
24527 AGAAAAAAGA
*
24537 TCAATTTAGTCCCTCCATTATCAAATCTG
1 TCAATTTAGTCCCTCCATTATCAAATATG
24566 TCAATTTAGTCCCTCCATTATCAAATATG
1 TCAATTTAGTCCCTCCATTATCAAATATG
24595 TCAATTTAGTCCCTC
1 TCAATTTAGTCCCTC
24610 TACTATTGAA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.27, C:0.27, G:0.07, T:0.38
Consensus pattern (29 bp):
TCAATTTAGTCCCTCCATTATCAAATATG
Done.