Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023216.1 Corchorus olitorius cultivar O-4 contig23249, 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: 12188
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Found at i:47 original size:20 final size:20
Alignment explanation
Indices: 22--62 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
12 TCAACTACAA
22 TTTTTTACTTGATTTATTAT
1 TTTTTTACTTGATTTATTAT
42 TTTTTTACTTGATTTATTAT
1 TTTTTTACTTGATTTATTAT
62 T
1 T
63 CCAAAAGGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.20, C:0.05, G:0.05, T:0.71
Consensus pattern (20 bp):
TTTTTTACTTGATTTATTAT
Found at i:935 original size:201 final size:201
Alignment explanation
Indices: 561--961 Score: 684
Period size: 201 Copynumber: 2.0 Consensus size: 201
551 TTAATAACTT
*
561 TATCGATGATGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAGA
1 TATCAATGATGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAGA
* *
626 TACAACACATTATTATTATATATAAAACTATACCAAAAAAAGTAGTTGAACATTAGTGGTTGATT
66 TACAACACATTACTATTATATATAAAACTATACAAAAAAAAGTAGTTGAACATTAGTGGTTGATT
*
691 TATTAAATTAAATTAGATCAATGTCAAACAAAATTTTAAAATTATAAAA-GATATTAAAGATCCG
131 TATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAATGATATT-AAGATCCG
755 ATTTATA
195 ATTTATA
*
762 TATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAGA
1 TATCAATGATGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAGA
827 TACAACACATTACTATTATATATATAGAACTATACAAAAAAAAAG-AGTTGAACATTAGTGGTTG
66 TACAACACATTACTATTATATATA-A-AACTATAC-AAAAAAAAGTAGTTGAACATTAGTGGTTG
*
891 ATTTATTAAATTAAATTAGGTCAATGTC-AAC-AAATTTCAAAATTATAAAATGATATTAAGATC
128 ATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAATGATATTAAGATC
954 CGATTTAT
193 CGATTTAT
962 TTATTATTAA
Statistics
Matches: 190, Mismatches: 6, Indels: 8
0.93 0.03 0.04
Matches are distributed among these distances:
201 118 0.62
202 10 0.05
203 54 0.28
204 8 0.04
ACGTcount: A:0.44, C:0.08, G:0.12, T:0.36
Consensus pattern (201 bp):
TATCAATGATGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAGA
TACAACACATTACTATTATATATAAAACTATACAAAAAAAAGTAGTTGAACATTAGTGGTTGATT
TATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAATGATATTAAGATCCGA
TTTATA
Found at i:1123 original size:40 final size:40
Alignment explanation
Indices: 1079--1160 Score: 121
Period size: 40 Copynumber: 2.0 Consensus size: 40
1069 ATACCTAAAA
1079 ATTTAATTAATGTAAGTATTTCAATTATTATAGTAT-TTAC
1 ATTTAATTAATGTAAGTATTTCAATTATTATA-TATATTAC
* * *
1119 ATTTAATTAATTTAAGTATTTTAGTTATTATATATATTAC
1 ATTTAATTAATGTAAGTATTTCAATTATTATATATATTAC
1159 AT
1 AT
1161 AGGAATTAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
39 3 0.08
40 35 0.92
ACGTcount: A:0.38, C:0.04, G:0.06, T:0.52
Consensus pattern (40 bp):
ATTTAATTAATGTAAGTATTTCAATTATTATATATATTAC
Found at i:5182 original size:31 final size:31
Alignment explanation
Indices: 5147--5311 Score: 108
Period size: 31 Copynumber: 5.5 Consensus size: 31
5137 GCTAATTTGT
5147 TCAAATAAGGGCCTAATGTTTGCCAAAATGC
1 TCAAATAAGGGCCTAATGTTTGCCAAAATGC
** * * * **
5178 TCAAATAAGGGTATAGTCTTT--TAATTTGGC
1 TCAAATAAGGGCCTAATGTTTGCCAAAAT-GC
* *
5208 -CAAATAAAGGCCTAACGTTTGCCAAAATGC
1 TCAAATAAGGGCCTAATGTTTGCCAAAATGC
** ** * * **
5238 TCAAATAAGGGTTTGGTCTTT--TAATTTGGC
1 TCAAATAAGGGCCTAATGTTTGCCAAAAT-GC
*
5268 -CAAATAAGGGCCTAATGTTTGCCAAAATGT
1 TCAAATAAGGGCCTAATGTTTGCCAAAATGC
5298 TCAAATAAGGGCCT
1 TCAAATAAGGGCCT
5312 GGTGTCGAAA
Statistics
Matches: 91, Mismatches: 35, Indels: 16
0.64 0.25 0.11
Matches are distributed among these distances:
29 35 0.38
30 7 0.08
31 49 0.54
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.30
Consensus pattern (31 bp):
TCAAATAAGGGCCTAATGTTTGCCAAAATGC
Found at i:5232 original size:60 final size:60
Alignment explanation
Indices: 5139--5308 Score: 277
Period size: 60 Copynumber: 2.8 Consensus size: 60
5129 TATTTACGGC
**
5139 TAATTTGTTCAAATAAGGGCCTAATGTTTGCCAAAATGCTCAAATAAGGGTATAGTCTTT
1 TAATTTGGCCAAATAAGGGCCTAATGTTTGCCAAAATGCTCAAATAAGGGTATAGTCTTT
* * * *
5199 TAATTTGGCCAAATAAAGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGTTTGGTCTTT
1 TAATTTGGCCAAATAAGGGCCTAATGTTTGCCAAAATGCTCAAATAAGGGTATAGTCTTT
*
5259 TAATTTGGCCAAATAAGGGCCTAATGTTTGCCAAAATGTTCAAATAAGGG
1 TAATTTGGCCAAATAAGGGCCTAATGTTTGCCAAAATGCTCAAATAAGGG
5309 CCTGGTGTCG
Statistics
Matches: 101, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 101 1.00
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.32
Consensus pattern (60 bp):
TAATTTGGCCAAATAAGGGCCTAATGTTTGCCAAAATGCTCAAATAAGGGTATAGTCTTT
Found at i:5391 original size:31 final size:31
Alignment explanation
Indices: 5353--5485 Score: 114
Period size: 31 Copynumber: 4.4 Consensus size: 31
5343 TGACGCCAGA
*
5353 CCCTTATTTTAGCATTTTCGATAACATTAGG
1 CCCTTATTTGAGCATTTTCGATAACATTAGG
** * *
5384 CCCTTATTTG-GCCAAATT--AAAAGATT-GG
1 CCCTTATTTGAG-CATTTTCGATAACATTAGG
**
5412 CCCCTTATTTGAGCATTTTCGATAATGTTAGG
1 -CCCTTATTTGAGCATTTTCGATAACATTAGG
* *
5444 CCCTTATTTGAGCATTTTGGCA-AACGTTAGG
1 CCCTTATTTGAGCATTTTCG-ATAACATTAGG
*
5475 TCCTTATTTGA
1 CCCTTATTTGA
5486 ACAATTATCC
Statistics
Matches: 82, Mismatches: 13, Indels: 14
0.75 0.12 0.13
Matches are distributed among these distances:
28 2 0.02
29 20 0.24
30 2 0.02
31 55 0.67
32 3 0.04
ACGTcount: A:0.25, C:0.19, G:0.17, T:0.39
Consensus pattern (31 bp):
CCCTTATTTGAGCATTTTCGATAACATTAGG
Found at i:8000 original size:42 final size:43
Alignment explanation
Indices: 7949--8042 Score: 147
Period size: 45 Copynumber: 2.2 Consensus size: 43
7939 AGTACATTAC
*
7949 CTAA-ATTCTACT-CCATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACTCCCATCTCTAGATAATTCATCAAAATAAAG
7990 CTAATATTCTACTCCCCCATCTCTAGATAATTCATCAAAATAAAG
1 CTAATATTCTACT--CCCATCTCTAGATAATTCATCAAAATAAAG
8035 CTAATATT
1 CTAATATT
8043 GATTGTTGCT
Statistics
Matches: 48, Mismatches: 1, Indels: 4
0.91 0.02 0.08
Matches are distributed among these distances:
41 4 0.08
42 8 0.17
45 36 0.75
ACGTcount: A:0.38, C:0.23, G:0.05, T:0.33
Consensus pattern (43 bp):
CTAATATTCTACTCCCATCTCTAGATAATTCATCAAAATAAAG
Found at i:9554 original size:16 final size:16
Alignment explanation
Indices: 9529--9560 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
9519 CACCCTTCTA
9529 TTATTAAACTGGTCTC
1 TTATTAAACTGGTCTC
*
9545 TTATTGAACTGGTCTC
1 TTATTAAACTGGTCTC
9561 GAGGAGGGAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.22, C:0.19, G:0.16, T:0.44
Consensus pattern (16 bp):
TTATTAAACTGGTCTC
Done.