Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011181.1 Corchorus olitorius cultivar O-4 contig11214, 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: 30697
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:3664 original size:2 final size:2
Alignment explanation
Indices: 3659--3696 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
3649 CTAATTCTTT
3659 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3697 GGCCGCATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:7265 original size:10 final size:10
Alignment explanation
Indices: 7252--7286 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
7242 GTAGGACTTA
7252 AAAAGTAAAG
1 AAAAGTAAAG
*
7262 AAAAGAAAAG
1 AAAAGTAAAG
7272 AAAAAGTAAAG
1 -AAAAGTAAAG
7283 AAAA
1 AAAA
7287 TATACCCTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.77, C:0.00, G:0.17, T:0.06
Consensus pattern (10 bp):
AAAAGTAAAG
Found at i:7276 original size:11 final size:11
Alignment explanation
Indices: 7251--7286 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
7241 GGTAGGACTT
7251 AAAAAGTAAAG
1 AAAAAGTAAAG
*
7262 -AAAAGAAAAG
1 AAAAAGTAAAG
7272 AAAAAGTAAAG
1 AAAAAGTAAAG
7283 AAAA
1 AAAA
7287 TATACCCTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
10 9 0.41
11 13 0.59
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.06
Consensus pattern (11 bp):
AAAAAGTAAAG
Found at i:12855 original size:2 final size:2
Alignment explanation
Indices: 12848--12879 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
12838 AATTTAAAGC
12848 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12880 GAGCTGAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13933 original size:19 final size:18
Alignment explanation
Indices: 13909--13958 Score: 75
Period size: 18 Copynumber: 2.7 Consensus size: 18
13899 TTGATGGGCC
13909 AAAAAAAAGAAAAGAAAG
1 AAAAAAAAGAAAAGAAAG
13927 AAAAAAAAGAAAAAGAAAG
1 AAAAAAAAG-AAAAGAAAG
13946 AAAGAAAAA-AAAA
1 AAA-AAAAAGAAAA
13959 ACGTATCGAC
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
18 13 0.43
19 12 0.40
20 5 0.17
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (18 bp):
AAAAAAAAGAAAAGAAAG
Found at i:13945 original size:23 final size:24
Alignment explanation
Indices: 13912--13957 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 24
13902 ATGGGCCAAA
13912 AAAAAGAAAAGAAAGAAAAAAAAG
1 AAAAAGAAAAGAAAGAAAAAAAAG
13936 AAAAAG-AAAGAAAGAAAAAAAA
1 AAAAAGAAAAGAAAGAAAAAAAA
13958 AACGTATCGA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 16 0.73
24 6 0.27
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (24 bp):
AAAAAGAAAAGAAAGAAAAAAAAG
Found at i:13959 original size:19 final size:18
Alignment explanation
Indices: 13909--13959 Score: 75
Period size: 19 Copynumber: 2.7 Consensus size: 18
13899 TTGATGGGCC
*
13909 AAAAAAAAGAAAAGAAAG
1 AAAAAAAAAAAAAGAAAG
13927 AAAAAAAAGAAAAAGAAAG
1 AAAAAAAA-AAAAAGAAAG
13946 AAAGAAAAAAAAAA
1 AAA-AAAAAAAAAA
13960 CGTATCGACT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 8 0.27
19 17 0.57
20 5 0.17
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (18 bp):
AAAAAAAAAAAAAGAAAG
Found at i:27512 original size:14 final size:14
Alignment explanation
Indices: 27475--27517 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
27465 TCTGAGTTTG
27475 TTTTTGAGTCAGTT
1 TTTTTGAGTCAGTT
*** *
27489 TGAGTCAGTCAGTT
1 TTTTTGAGTCAGTT
27503 TTTTTGAGTCAGTT
1 TTTTTGAGTCAGTT
27517 T
1 T
27518 CGAGTCTAGT
Statistics
Matches: 21, Mismatches: 8, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.16, C:0.09, G:0.23, T:0.51
Consensus pattern (14 bp):
TTTTTGAGTCAGTT
Found at i:28251 original size:15 final size:15
Alignment explanation
Indices: 28231--28260 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
28221 AATCCATGAC
28231 TGCTCTAATCATTTG
1 TGCTCTAATCATTTG
*
28246 TGCTCTAATCCTTTG
1 TGCTCTAATCATTTG
28261 AGTCTTTGCG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.23, G:0.13, T:0.47
Consensus pattern (15 bp):
TGCTCTAATCATTTG
Found at i:28635 original size:36 final size:36
Alignment explanation
Indices: 28595--28668 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
28585 TCGCTCTATA
28595 TGGGATTATTGCATGAAATCCAACTTAGACAGTTAT
1 TGGGATTATTGCATGAAATCCAACTTAGACAGTTAT
28631 TGGGATTATTGCATGAAATCCAACTTAGACAGTTAT
1 TGGGATTATTGCATGAAATCCAACTTAGACAGTTAT
28667 TG
1 TG
28669 AGTTATGCTC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.34
Consensus pattern (36 bp):
TGGGATTATTGCATGAAATCCAACTTAGACAGTTAT
Done.