Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015187.1 Corchorus olitorius cultivar O-4 contig15220, 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: 20141
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Found at i:2018 original size:26 final size:25
Alignment explanation
Indices: 1989--2050 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 25
1979 TTATAGCTTT
1989 TCAAATTTAGATGGGCTTCTATATTG
1 TCAAA-TTAGATGGGCTTCTATATTG
*
2015 TC-AA--A-ATTGGCTTCTATATTG
1 TCAAATTAGATGGGCTTCTATATTG
2036 TCAAAACTTAGATGG
1 TC-AAA-TTAGATGG
2051 TTTGATTGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 11
0.68 0.05 0.27
Matches are distributed among these distances:
21 17 0.61
22 1 0.04
23 2 0.07
25 2 0.07
26 3 0.11
27 3 0.11
ACGTcount: A:0.31, C:0.13, G:0.18, T:0.39
Consensus pattern (25 bp):
TCAAATTAGATGGGCTTCTATATTG
Found at i:2028 original size:21 final size:21
Alignment explanation
Indices: 2002--2041 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
1992 AATTTAGATG
2002 GGCTTCTATATTGTCAAAATT
1 GGCTTCTATATTGTCAAAATT
2023 GGCTTCTATATTGTCAAAA
1 GGCTTCTATATTGTCAAAA
2042 CTTAGATGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (21 bp):
GGCTTCTATATTGTCAAAATT
Found at i:9672 original size:38 final size:40
Alignment explanation
Indices: 9617--9696 Score: 128
Period size: 38 Copynumber: 2.0 Consensus size: 40
9607 TTTAATTCCT
9617 ATGTAATATATATAATAACTAAAATACTTACATT-ATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
* *
9656 ATGTAATA-CTATAATAACTGAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
9695 AT
1 AT
9697 TCTTAGGTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
38 23 0.61
39 15 0.39
ACGTcount: A:0.50, C:0.09, G:0.04, T:0.38
Consensus pattern (40 bp):
ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
Found at i:9691 original size:21 final size:21
Alignment explanation
Indices: 9629--9691 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 21
9619 GTAATATATA
*
9629 TAATAACTAAAATACTTACAT
1 TAATAACTGAAATACTTACAT
* * *
9650 TATTAAATGTAATAC-T--A-
1 TAATAACTGAAATACTTACAT
9667 TAATAACTGAAATACTTACAT
1 TAATAACTGAAATACTTACAT
9688 TAAT
1 TAAT
9692 TAAATTCTTA
Statistics
Matches: 31, Mismatches: 7, Indels: 8
0.67 0.15 0.17
Matches are distributed among these distances:
17 12 0.39
18 2 0.06
20 2 0.06
21 15 0.48
ACGTcount: A:0.49, C:0.11, G:0.03, T:0.37
Consensus pattern (21 bp):
TAATAACTGAAATACTTACAT
Found at i:9723 original size:25 final size:24
Alignment explanation
Indices: 9687--9733 Score: 85
Period size: 25 Copynumber: 1.9 Consensus size: 24
9677 AATACTTACA
9687 TTAATTAAATTCTTAGGTATTTTT
1 TTAATTAAATTCTTAGGTATTTTT
9711 TTAATTCAAATTCTTAGGTATTT
1 TTAATT-AAATTCTTAGGTATTT
9734 GTGCAAACGT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.30, C:0.06, G:0.09, T:0.55
Consensus pattern (24 bp):
TTAATTAAATTCTTAGGTATTTTT
Found at i:13567 original size:29 final size:29
Alignment explanation
Indices: 13534--13595 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 29
13524 CTCTACTTGT
* *
13534 AGAATAGGAATTATGGCGATATACCATGA
1 AGAATAAGAATCATGGCGATATACCATGA
*
13563 AGAATAAGAATCATGGCGATATGCCATGA
1 AGAATAAGAATCATGGCGATATACCATGA
13592 AGAA
1 AGAA
13596 CAACCACCTG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.44, C:0.11, G:0.24, T:0.21
Consensus pattern (29 bp):
AGAATAAGAATCATGGCGATATACCATGA
Done.