Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016234.1 Corchorus capsularis cultivar CVL-1 contig16255, 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: 28443
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:1017 original size:26 final size:26
Alignment explanation
Indices: 939--1028 Score: 87
Period size: 26 Copynumber: 3.6 Consensus size: 26
929 GCACTCTGCA
*
939 TTAGGCATCAACATTCGCATTAATAG
1 TTAGGCATCAGCATTCGCATTAATAG
* * *** *
965 TTAGACATTAGCA---GCATTCGCAT
1 TTAGGCATCAGCATTCGCATTAATAG
988 TTAGGCATCAGCATTCGCATTAATAG
1 TTAGGCATCAGCATTCGCATTAATAG
*
1014 TTAGGCATTAGCATT
1 TTAGGCATCAGCATT
1029 AGCAGTTTGG
Statistics
Matches: 47, Mismatches: 14, Indels: 6
0.70 0.21 0.09
Matches are distributed among these distances:
23 17 0.36
26 30 0.64
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Consensus pattern (26 bp):
TTAGGCATCAGCATTCGCATTAATAG
Found at i:1035 original size:20 final size:20
Alignment explanation
Indices: 998--1043 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
988 TTAGGCATCA
* *
998 GCATTCGCATTAATAGTTAG
1 GCATTAGCATTAACAGTTAG
* *
1018 GCATTAGCATTAGCAGTTTG
1 GCATTAGCATTAACAGTTAG
1038 GCATTA
1 GCATTA
1044 TCTTATATGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.28, C:0.15, G:0.22, T:0.35
Consensus pattern (20 bp):
GCATTAGCATTAACAGTTAG
Found at i:4345 original size:29 final size:29
Alignment explanation
Indices: 4312--4405 Score: 134
Period size: 29 Copynumber: 3.1 Consensus size: 29
4302 CAAGTTTTTA
*
4312 AAGTTTTCAATTTAGGGAAAGATCCCACC
1 AAGTTTTCAATTTAGGGAAAGATCCCATC
*
4341 AAGTTTTTTTAAATTTAGGGAAAGATCCCATC
1 AAG---TTTTCAATTTAGGGAAAGATCCCATC
*
4373 AAATTTTCAATTTAGGGAAAGATCCCATC
1 AAGTTTTCAATTTAGGGAAAGATCCCATC
4402 AAGT
1 AAGT
4406 CTTCGGAGTT
Statistics
Matches: 57, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
29 31 0.54
32 26 0.46
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (29 bp):
AAGTTTTCAATTTAGGGAAAGATCCCATC
Found at i:4468 original size:38 final size:38
Alignment explanation
Indices: 4371--4461 Score: 123
Period size: 38 Copynumber: 2.4 Consensus size: 38
4361 AAAGATCCCA
4371 TCAAA-TTTTCAATTTAGGGAAAGATCCCATCAAGTCT
1 TCAAAGTTTTCAATTTAGGGAAAGATCCCATCAAGTCT
** * *
4408 TCGGAGTTTTCAATTTAGGGAAAGAT-CCATCCAGTTT
1 TCAAAGTTTTCAATTTAGGGAAAGATCCCATCAAGTCT
4445 TCAAAGTTTTTCAATTT
1 TCAAAG-TTTTCAATTT
4462 CAGGAAATAT
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
37 16 0.35
38 30 0.65
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.37
Consensus pattern (38 bp):
TCAAAGTTTTCAATTTAGGGAAAGATCCCATCAAGTCT
Found at i:5747 original size:21 final size:20
Alignment explanation
Indices: 5708--5752 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
5698 AAAGATCAAT
* *
5708 TAAAAAGAAAGCAATTAAAC
1 TAAAAACAAAGCAAGTAAAC
*
5728 TAAAAACAAAGCAAAGTAAAT
1 TAAAAACAAAGC-AAGTAAAC
5749 TAAA
1 TAAA
5753 TCTAAATCTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.67, C:0.09, G:0.09, T:0.16
Consensus pattern (20 bp):
TAAAAACAAAGCAAGTAAAC
Found at i:7135 original size:30 final size:30
Alignment explanation
Indices: 7079--7135 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
7069 CAGTTATTGT
*
7079 TTCTTGAAATAATTCTTCAATTATCTTAAA
1 TTCTTGAAATAATTCTTCAATAATCTTAAA
7109 TTCTTGAAACT-A-TCTTCAATAAATCTT
1 TTCTTGAAA-TAATTCTTCAAT-AATCTT
7136 CAAACACGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
29 8 0.33
30 15 0.62
31 1 0.04
ACGTcount: A:0.35, C:0.16, G:0.04, T:0.46
Consensus pattern (30 bp):
TTCTTGAAATAATTCTTCAATAATCTTAAA
Found at i:7608 original size:10 final size:10
Alignment explanation
Indices: 7593--7620 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
7583 TAAATTAAAA
7593 AGATAATTAG
1 AGATAATTAG
7603 AGATAATTAG
1 AGATAATTAG
7613 AGATAATT
1 AGATAATT
7621 TCTTAATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.18, T:0.32
Consensus pattern (10 bp):
AGATAATTAG
Found at i:8384 original size:15 final size:15
Alignment explanation
Indices: 8366--8396 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
8356 TAAGTTTCAG
8366 GGACTTAATTGAAAA
1 GGACTTAATTGAAAA
*
8381 GGACTTATTTGAAAA
1 GGACTTAATTGAAAA
8396 G
1 G
8397 AAAAGAAATC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.06, G:0.23, T:0.29
Consensus pattern (15 bp):
GGACTTAATTGAAAA
Found at i:19659 original size:19 final size:18
Alignment explanation
Indices: 19635--19670 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
19625 TGAAGATTTC
19635 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
19654 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
19671 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Done.