Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013986.1 Corchorus capsularis cultivar CVL-1 contig14007, 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: 25218
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.34
Found at i:989 original size:25 final size:27
Alignment explanation
Indices: 937--989 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
927 TTACTCAACT
**
937 AAAAACTCTATTTTTATTTTTCTGTAA
1 AAAAACTCTATTTTTATTTTAATGTAA
964 AAAAACTCTATTTTTA-TTTAAT-TAA
1 AAAAACTCTATTTTTATTTTAATGTAA
989 A
1 A
990 TCTAATATCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 4 0.17
26 4 0.17
27 16 0.67
ACGTcount: A:0.40, C:0.09, G:0.02, T:0.49
Consensus pattern (27 bp):
AAAAACTCTATTTTTATTTTAATGTAA
Found at i:3918 original size:15 final size:16
Alignment explanation
Indices: 3896--3933 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
3886 CGCTCAAATG
3896 TCGGGTC-ATTTGGGT
1 TCGGGTCAATTTGGGT
* *
3911 TTGGGTCAATTTTGGT
1 TCGGGTCAATTTGGGT
3927 TCGGGTC
1 TCGGGTC
3934 TTTTTCAGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.08, C:0.13, G:0.37, T:0.42
Consensus pattern (16 bp):
TCGGGTCAATTTGGGT
Found at i:6022 original size:1 final size:1
Alignment explanation
Indices: 6016--6041 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
6006 ATTTGGACCC
6016 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
6042 CTTTCCTTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:7706 original size:35 final size:35
Alignment explanation
Indices: 7671--7737 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
7661 TGAGCAAGCA
* *
7671 AAACGTGGTGAGTTGAGA-GCAAATTGTGGAGAGC
1 AAACGTGGTGAATTGAGAGGAAAATTGTGGAGAGC
* *
7705 AATCGTGGTGAATTGTGAGGAAAATTGTGGAGA
1 AAACGTGGTGAATTGAGAGGAAAATTGTGGAGA
7738 AGAGCAAAGC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 15 0.54
35 13 0.46
ACGTcount: A:0.33, C:0.06, G:0.37, T:0.24
Consensus pattern (35 bp):
AAACGTGGTGAATTGAGAGGAAAATTGTGGAGAGC
Found at i:14646 original size:32 final size:32
Alignment explanation
Indices: 14610--14759 Score: 241
Period size: 32 Copynumber: 4.7 Consensus size: 32
14600 GAACCCGCCC
* *
14610 GACCCGAGACCCGAGTGACCCGCAACCCAGAT
1 GACCCGAGACCCGAATGACCCGTAACCCAGAT
14642 GACCCGAGACCCGAATGACCCGTAACCCAGAT
1 GACCCGAGACCCGAATGACCCGTAACCCAGAT
14674 GACCCGAGACCCGAATGACCCGTAACCCAGAT
1 GACCCGAGACCCGAATGACCCGTAACCCAGAT
*
14706 GACCCGAAACCCGAATGACCCGTAACCC-GAGT
1 GACCCGAGACCCGAATGACCCGTAACCCAGA-T
14738 GACCCGAGACCC-ATATGACCCG
1 GACCCGAGACCCGA-ATGACCCG
14760 AAACTTGAAT
Statistics
Matches: 112, Mismatches: 4, Indels: 4
0.93 0.03 0.03
Matches are distributed among these distances:
31 3 0.03
32 109 0.97
ACGTcount: A:0.30, C:0.39, G:0.23, T:0.09
Consensus pattern (32 bp):
GACCCGAGACCCGAATGACCCGTAACCCAGAT
Found at i:14756 original size:16 final size:15
Alignment explanation
Indices: 14595--14761 Score: 144
Period size: 16 Copynumber: 10.5 Consensus size: 15
14585 AAAAGTAAAC
***
14595 GACCCGAACCCGCCC
1 GACCCGAACCCGAAT
*
14610 GACCCGAGACCCGAGT
1 GACCCGA-ACCCGAAT
14626 GACCCGCAACCC-AGAT
1 GACCCG-AACCCGA-AT
14642 GACCCGAGACCCGAAT
1 GACCCGA-ACCCGAAT
14658 GACCCGTAACCC-AGAT
1 GACCCG-AACCCGA-AT
14674 GACCCGAGACCCGAAT
1 GACCCGA-ACCCGAAT
14690 GACCCGTAACCC-AGAT
1 GACCCG-AACCCGA-AT
14706 GACCCGAAACCCGAAT
1 GACCCG-AACCCGAAT
*
14722 GACCCGTAACCCGAGT
1 GACCCG-AACCCGAAT
14738 GACCCGAGACCC-ATAT
1 GACCCGA-ACCCGA-AT
14754 GACCCGAA
1 GACCCGAA
14762 ACTTGAATAA
Statistics
Matches: 130, Mismatches: 8, Indels: 28
0.78 0.05 0.17
Matches are distributed among these distances:
15 15 0.12
16 109 0.84
17 6 0.05
ACGTcount: A:0.30, C:0.40, G:0.22, T:0.08
Consensus pattern (15 bp):
GACCCGAACCCGAAT
Found at i:15248 original size:57 final size:58
Alignment explanation
Indices: 15165--15278 Score: 176
Period size: 57 Copynumber: 2.0 Consensus size: 58
15155 ATGGATCAAG
15165 GGAAAAAATAACAAAAAGGGTGCCTGATAACCAAAAGACGATTGACGTTTTGATTGCC
1 GGAAAAAATAACAAAAAGGGTGCCTGATAACCAAAAGACGATTGACGTTTTGATTGCC
* * * * *
15223 GGAAAATATAAC-ATAAGGGTGCCTGATAACCAAGAGATGATTGATGTTTTGATTGC
1 GGAAAAAATAACAAAAAGGGTGCCTGATAACCAAAAGACGATTGACGTTTTGATTGC
15279 AAGACCTAGC
Statistics
Matches: 51, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
57 40 0.78
58 11 0.22
ACGTcount: A:0.39, C:0.13, G:0.24, T:0.25
Consensus pattern (58 bp):
GGAAAAAATAACAAAAAGGGTGCCTGATAACCAAAAGACGATTGACGTTTTGATTGCC
Found at i:21638 original size:50 final size:49
Alignment explanation
Indices: 21583--21685 Score: 172
Period size: 50 Copynumber: 2.1 Consensus size: 49
21573 TTTCTTTTGA
*
21583 CATATATACACTTTTAAAAGATGTTAAATATCA-ATTCGTGTGACAATTAT
1 CATATATACACTTTTAAAAGATGTTAAATA--AGATTCATGTGACAATTAT
21633 CATATATACACTTTTAAAAGATGTTAAATAAGATTCATGTGACAATTAT
1 CATATATACACTTTTAAAAGATGTTAAATAAGATTCATGTGACAATTAT
21682 CATA
1 CATA
21686 ATATGGAGGA
Statistics
Matches: 51, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
48 1 0.02
49 20 0.39
50 30 0.59
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.37
Consensus pattern (49 bp):
CATATATACACTTTTAAAAGATGTTAAATAAGATTCATGTGACAATTAT
Found at i:23595 original size:23 final size:23
Alignment explanation
Indices: 23569--23613 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
23559 ATCTTATTCC
*
23569 CTCTGTTTCTCACCTCTTCCTCT
1 CTCTGTTTCTCACCTCCTCCTCT
* *
23592 CTCTGTTTGTCATCTCCTCCTC
1 CTCTGTTTCTCACCTCCTCCTC
23614 CTATTTCTCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.04, C:0.42, G:0.07, T:0.47
Consensus pattern (23 bp):
CTCTGTTTCTCACCTCCTCCTCT
Done.