Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018511.1 Corchorus olitorius cultivar O-4 contig18544, 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: 27552
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Found at i:2060 original size:49 final size:47
Alignment explanation
Indices: 1955--2060 Score: 142
Period size: 49 Copynumber: 2.2 Consensus size: 47
1945 AAAACAATTT
* *
1955 TTTACATTTCCTGCACTTTTTCTCAATTTTTACAATAAAATTGAACC
1 TTTACTTTTCCTGCACTTTTTCTCAATTTTTACAATAAAATTGAACA
* *
2002 TTTATTTTTCCTCGCACCTTTTTCTCAATTTTTA-AGATAAAATTGAATA
1 TTTACTTTTCCT-GCA-CTTTTTCTCAATTTTTACA-ATAAAATTGAACA
2051 TTTACTTTTC
1 TTTACTTTTC
2061 ATTGCTCTTT
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
47 10 0.20
48 4 0.08
49 37 0.73
ACGTcount: A:0.27, C:0.19, G:0.05, T:0.49
Consensus pattern (47 bp):
TTTACTTTTCCTGCACTTTTTCTCAATTTTTACAATAAAATTGAACA
Found at i:6579 original size:29 final size:31
Alignment explanation
Indices: 6534--6606 Score: 89
Period size: 29 Copynumber: 2.4 Consensus size: 31
6524 ACAATCTTGC
**
6534 AAGTAGAGGGATTAAATTGA-TCATTTT-T-T
1 AAGTAGAGGGACCAAATTGATTC-TTTTGTGT
*
6563 TAGTAGAGGGACCAAATTGATTCTTTTGTGT
1 AAGTAGAGGGACCAAATTGATTCTTTTGTGT
6594 AAGTAGAGGGACC
1 AAGTAGAGGGACC
6607 TCCCAGGTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
29 21 0.57
30 3 0.08
31 13 0.35
ACGTcount: A:0.32, C:0.08, G:0.26, T:0.34
Consensus pattern (31 bp):
AAGTAGAGGGACCAAATTGATTCTTTTGTGT
Found at i:8428 original size:29 final size:29
Alignment explanation
Indices: 8391--8461 Score: 142
Period size: 29 Copynumber: 2.4 Consensus size: 29
8381 TATAATTATC
8391 AAATCTCACTATTTTTAAATTTAAAATTA
1 AAATCTCACTATTTTTAAATTTAAAATTA
8420 AAATCTCACTATTTTTAAATTTAAAATTA
1 AAATCTCACTATTTTTAAATTTAAAATTA
8449 AAATCTCACTATT
1 AAATCTCACTATT
8462 AGTATATGGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.44, C:0.13, G:0.00, T:0.44
Consensus pattern (29 bp):
AAATCTCACTATTTTTAAATTTAAAATTA
Found at i:24879 original size:6 final size:6
Alignment explanation
Indices: 24865--24924 Score: 63
Period size: 6 Copynumber: 10.2 Consensus size: 6
24855 TTTCCTTTAG
*
24865 TTTTGT TTTTAT TTTTCGT ATTTTGT TTTTGT TTTT-T TTTTG- TTTT-T
1 TTTTGT TTTTGT TTTT-GT -TTTTGT TTTTGT TTTTGT TTTTGT TTTTGT
*
24912 TTGTGT TTTTGT T
1 TTTTGT TTTTGT T
24925 AATTTTGCAG
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
5 12 0.27
6 26 0.58
7 3 0.07
8 4 0.09
ACGTcount: A:0.03, C:0.02, G:0.13, T:0.82
Consensus pattern (6 bp):
TTTTGT
Found at i:24892 original size:25 final size:22
Alignment explanation
Indices: 24864--24921 Score: 64
Period size: 26 Copynumber: 2.5 Consensus size: 22
24854 CTTTCCTTTA
24864 GTTTTGTTTTTATTTTTCGTATTTT
1 GTTTTGTTTTT-TTTTT-GT-TTTT
24889 GTTTTTGTTTTTTTTTTGTTTTT
1 G-TTTTGTTTTTTTTTTGTTTTT
*
24912 -TTGTGTTTTT
1 GTTTTGTTTTT
24922 GTTAATTTTG
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
21 9 0.29
23 4 0.13
24 2 0.06
25 6 0.19
26 10 0.32
ACGTcount: A:0.03, C:0.02, G:0.14, T:0.81
Consensus pattern (22 bp):
GTTTTGTTTTTTTTTTGTTTTT
Found at i:24901 original size:8 final size:8
Alignment explanation
Indices: 24885--24924 Score: 53
Period size: 8 Copynumber: 4.9 Consensus size: 8
24875 ATTTTTCGTA
24885 TTTTGTTT
1 TTTTGTTT
*
24893 TTGTTTTTT
1 TT-TTGTTT
24902 TTTTGTTT
1 TTTTGTTT
*
24910 TTTTGTGT
1 TTTTGTTT
24918 TTTTGTT
1 TTTTGTT
24925 AATTTTGCAG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
8 20 0.74
9 7 0.26
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (8 bp):
TTTTGTTT
Done.