Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024281.1 Corchorus olitorius cultivar O-4 contig24314, 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: 22692
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:3363 original size:21 final size:21
Alignment explanation
Indices: 3313--3357 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
3303 GTGACACTGC
* *
3313 CCACCTGGGTTCTCAAGCAAA
1 CCACATGGGTGCTCAAGCAAA
*
3334 CCACATGGGTGCTCAAGGAAA
1 CCACATGGGTGCTCAAGCAAA
3355 CCA
1 CCA
3358 TGTGGGCGCC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.31, G:0.22, T:0.16
Consensus pattern (21 bp):
CCACATGGGTGCTCAAGCAAA
Found at i:4685 original size:26 final size:26
Alignment explanation
Indices: 4656--4707 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
4646 TTTTCTCAAA
*
4656 CTATTTTCTTAATCTCTAGTTTAATT
1 CTATTTTATTAATCTCTAGTTTAATT
** *
4682 CTATTTTATTGTTTTCTAGTTTAATT
1 CTATTTTATTAATCTCTAGTTTAATT
4708 TGCCTATTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.21, C:0.12, G:0.06, T:0.62
Consensus pattern (26 bp):
CTATTTTATTAATCTCTAGTTTAATT
Found at i:5004 original size:10 final size:9
Alignment explanation
Indices: 4956--5012 Score: 50
Period size: 10 Copynumber: 6.4 Consensus size: 9
4946 ATTTCTTACC
*
4956 CTTATCTTT
1 CTTATTTTT
4965 -TTA-TTTT
1 CTTATTTTT
4972 CGTTATTTTT
1 C-TTATTTTT
4982 CTT-TTTCTT
1 CTTATTT-TT
4991 -TTATTTTT
1 CTTATTTTT
4999 CGTTATTTTT
1 C-TTATTTTT
5009 CTTA
1 CTTA
5013 CTTACTTTTA
Statistics
Matches: 40, Mismatches: 1, Indels: 14
0.73 0.02 0.25
Matches are distributed among these distances:
7 3 0.08
8 10 0.25
9 13 0.32
10 14 0.35
ACGTcount: A:0.11, C:0.12, G:0.04, T:0.74
Consensus pattern (9 bp):
CTTATTTTT
Found at i:13571 original size:26 final size:26
Alignment explanation
Indices: 13542--13593 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
13532 TTTTCTCAAA
*
13542 CTATTTTCTTAATCTCTAGTTTAATT
1 CTATTTTATTAATCTCTAGTTTAATT
** *
13568 CTATTTTATTGTTTTCTAGTTTAATT
1 CTATTTTATTAATCTCTAGTTTAATT
13594 TGCCTATTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.21, C:0.12, G:0.06, T:0.62
Consensus pattern (26 bp):
CTATTTTATTAATCTCTAGTTTAATT
Found at i:16728 original size:3 final size:3
Alignment explanation
Indices: 16720--16794 Score: 150
Period size: 3 Copynumber: 25.0 Consensus size: 3
16710 ATACACACAA
16720 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
16768 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
16795 TAAGAAAGGA
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 72 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:19757 original size:15 final size:15
Alignment explanation
Indices: 19727--19768 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
19717 TTACTTTGCT
19727 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
19743 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
*
19758 TTGCTTTCTGT
1 TTGTTTTCTGT
19769 CAACCTCTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.12, C:0.10, G:0.14, T:0.64
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:20129 original size:38 final size:33
Alignment explanation
Indices: 20081--20155 Score: 105
Period size: 33 Copynumber: 2.1 Consensus size: 33
20071 GCGTTTTTAA
20081 TTTTTTGTGTTTTGCGTCTTTTTGAAAAAAAAAAAAAT
1 TTTTTTGTGTTTTGCGTC-----GAAAAAAAAAAAAAT
20119 TTTTTTGTGTTTTGCGTCGAAAAAAAAAAAAAT
1 TTTTTTGTGTTTTGCGTCGAAAAAAAAAAAAAT
20152 TTTT
1 TTTT
20156 GCGTCATAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
33 19 0.51
38 18 0.49
ACGTcount: A:0.35, C:0.05, G:0.13, T:0.47
Consensus pattern (33 bp):
TTTTTTGTGTTTTGCGTCGAAAAAAAAAAAAAT
Found at i:20167 original size:26 final size:26
Alignment explanation
Indices: 20138--20206 Score: 75
Period size: 26 Copynumber: 2.6 Consensus size: 26
20128 TTTTGCGTCG
*
20138 AAAAAAAAAAAAATTTTTGCGTCATA
1 AAAAAAAAAAAAATTTTGGCGTCATA
*****
20164 AAAAAAAATTTTGTTTTGGCGTCATA
1 AAAAAAAAAAAAATTTTGGCGTCATA
20190 AATAAAAAAAAAAATTT
1 AA-AAAAAAAAAAATTT
20207 CTTGTTCTTG
Statistics
Matches: 31, Mismatches: 11, Indels: 1
0.72 0.26 0.02
Matches are distributed among these distances:
26 22 0.71
27 9 0.29
ACGTcount: A:0.55, C:0.06, G:0.09, T:0.30
Consensus pattern (26 bp):
AAAAAAAAAAAAATTTTGGCGTCATA
Found at i:20212 original size:34 final size:34
Alignment explanation
Indices: 20163--20243 Score: 96
Period size: 34 Copynumber: 2.4 Consensus size: 34
20153 TTTGCGTCAT
20163 AAAAAAAAA-TT-TTGTT-TTGGCGTCATAAATAA
1 AAAAAAAAATTTCTTGTTCTT-GCGTCATAAATAA
** * *
20195 AAAAAAAAATTTCTTGTTCTTGCGTTTTTATTAA
1 AAAAAAAAATTTCTTGTTCTTGCGTCATAAATAA
20229 AAAAAAAAATTTCTT
1 AAAAAAAAATTTCTT
20244 TATTTTCTGT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
32 9 0.21
33 2 0.05
34 29 0.69
35 2 0.05
ACGTcount: A:0.44, C:0.07, G:0.09, T:0.40
Consensus pattern (34 bp):
AAAAAAAAATTTCTTGTTCTTGCGTCATAAATAA
Done.