Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016366.1 Corchorus olitorius cultivar O-4 contig16399, 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: 26353
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Found at i:1727 original size:3 final size:3
Alignment explanation
Indices: 1719--1765 Score: 58
Period size: 3 Copynumber: 15.0 Consensus size: 3
1709 GCCATCTCCG
* *
1719 CCA CCA CCA CCA CCA CCG CCG CCAA CTCA CCA CCA CCA CCA CCA CCA
1 CCA CCA CCA CCA CCA CCA CCA CC-A C-CA CCA CCA CCA CCA CCA CCA
1766 TCATCAAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
3 36 0.90
4 3 0.08
5 1 0.03
ACGTcount: A:0.30, C:0.64, G:0.04, T:0.02
Consensus pattern (3 bp):
CCA
Found at i:4666 original size:15 final size:15
Alignment explanation
Indices: 4646--4675 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
4636 TTTGGAGGGT
4646 TTCTTCTTCTTCTTA
1 TTCTTCTTCTTCTTA
4661 TTCTTCTTCTTCTTA
1 TTCTTCTTCTTCTTA
4676 CATTTCTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.07, C:0.27, G:0.00, T:0.67
Consensus pattern (15 bp):
TTCTTCTTCTTCTTA
Found at i:10978 original size:19 final size:20
Alignment explanation
Indices: 10948--11011 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 20
10938 TTGACACTGT
10948 TTAGCAACTGTACAGATGAGA
1 TTAGC-ACTGTACAGATGAGA
* *
10969 TTA-CACTGTACATATTAGA
1 TTAGCACTGTACAGATGAGA
* *
10988 TTAGGTACTATACAGATGAGA
1 TTA-GCACTGTACAGATGAGA
11009 TTA
1 TTA
11012 TTAGAGTAGC
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
19 16 0.46
20 1 0.03
21 18 0.51
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (20 bp):
TTAGCACTGTACAGATGAGA
Found at i:12896 original size:12 final size:12
Alignment explanation
Indices: 12879--12905 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
12869 GTTAACATGC
12879 TATTTTTTTTCT
1 TATTTTTTTTCT
12891 TATTTTTTTTCT
1 TATTTTTTTTCT
12903 TAT
1 TAT
12906 GATGGAATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.11, C:0.07, G:0.00, T:0.81
Consensus pattern (12 bp):
TATTTTTTTTCT
Found at i:16912 original size:32 final size:31
Alignment explanation
Indices: 16845--16915 Score: 79
Period size: 32 Copynumber: 2.3 Consensus size: 31
16835 GCCTTGGTCT
* *
16845 TGCCACGTGGCATTTTGATCCAACATGGCAT
1 TGCCACGTGGCATTTTGATCCAACATGACAA
* * * *
16876 TGCCACGTGTCATTTTTGGTCCGACGTGACAA
1 TGCCACGTGGCA-TTTTGATCCAACATGACAA
16908 TGCCACGT
1 TGCCACGT
16916 CAGCAATACC
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
31 11 0.33
32 22 0.67
ACGTcount: A:0.20, C:0.27, G:0.24, T:0.30
Consensus pattern (31 bp):
TGCCACGTGGCATTTTGATCCAACATGACAA
Found at i:18712 original size:2 final size:2
Alignment explanation
Indices: 18662--18695 Score: 59
Period size: 2 Copynumber: 16.5 Consensus size: 2
18652 GGATTTTGTG
18662 AT AT GAT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
18696 GTAGAAATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:19460 original size:15 final size:15
Alignment explanation
Indices: 19440--19469 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
19430 ACAGTTCTCC
19440 GACGAAAAAGAAGAA
1 GACGAAAAAGAAGAA
*
19455 GACGAAGAAGAAGAA
1 GACGAAAAAGAAGAA
19470 TCTTCCACCA
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:0.63, C:0.07, G:0.30, T:0.00
Consensus pattern (15 bp):
GACGAAAAAGAAGAA
Found at i:20827 original size:18 final size:18
Alignment explanation
Indices: 20804--20846 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
20794 CTCTAATGTA
20804 TTTTTTCAAGTATCTAAT
1 TTTTTTCAAGTATCTAAT
20822 TTTTTTCAAGTATCTAAT
1 TTTTTTCAAGTATCTAAT
20840 TTTTTTC
1 TTTTTTC
20847 TTTTTTGGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.23, C:0.12, G:0.05, T:0.60
Consensus pattern (18 bp):
TTTTTTCAAGTATCTAAT
Done.