Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021297.1 Corchorus olitorius cultivar O-4 contig21330, 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: 10696
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:354 original size:15 final size:15
Alignment explanation
Indices: 324--365 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
314 TTACTTTGCT
324 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
340 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
*
355 TTGCTTTCTGT
1 TTGTTTTCTGT
366 CAATCTCTGT
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:3897 original size:10 final size:9
Alignment explanation
Indices: 3854--3911 Score: 50
Period size: 10 Copynumber: 6.4 Consensus size: 9
3844 TAAAAGTAAC
3854 TAAGAAAAA
1 TAAGAAAAA
*
3863 TAAACAAAAA
1 T-AAGAAAAA
3873 TAA-AAGAAA
1 TAAGAA-AAA
3882 -AAGAAAAA
1 TAAGAAAAA
3890 TAACGAAAAA
1 TAA-GAAAAA
*
3900 TAA-AAAGA
1 TAAGAAAAA
3908 TAAG
1 TAAG
3912 GGTAAGAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
8 14 0.34
9 10 0.24
10 17 0.41
ACGTcount: A:0.76, C:0.03, G:0.10, T:0.10
Consensus pattern (9 bp):
TAAGAAAAA
Found at i:3897 original size:16 final size:17
Alignment explanation
Indices: 3868--3905 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
3858 AAAAATAAAC
3868 AAAAATAAAAGAAAAAG
1 AAAAATAAAAGAAAAAG
* *
3885 AAAAAT-AACGAAAAAT
1 AAAAATAAAAGAAAAAG
3901 AAAAA
1 AAAAA
3906 GATAAGGGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.82, C:0.03, G:0.08, T:0.08
Consensus pattern (17 bp):
AAAAATAAAAGAAAAAG
Found at i:5463 original size:34 final size:38
Alignment explanation
Indices: 5418--5495 Score: 92
Period size: 37 Copynumber: 2.2 Consensus size: 38
5408 GAGGGTTTTC
5418 TTAATTATTTT-C-T-AGTTTATTCATTGCTTTCTTA-
1 TTAATTATTTTCCTTAAGTTTATTCATTGCTTTCTTAG
* * * *
5452 TTAATTGTTTTCCTTAATTTTCTTGATTGCTTTCTTAG
1 TTAATTATTTTCCTTAAGTTTATTCATTGCTTTCTTAG
5490 TTAATT
1 TTAATT
5496 TTACTTGTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
34 10 0.28
35 1 0.03
36 1 0.03
37 18 0.50
38 6 0.17
ACGTcount: A:0.19, C:0.12, G:0.08, T:0.62
Consensus pattern (38 bp):
TTAATTATTTTCCTTAAGTTTATTCATTGCTTTCTTAG
Found at i:5730 original size:11 final size:11
Alignment explanation
Indices: 5714--5740 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
5704 TGTGAATTAT
5714 TTTTCTTTTTC
1 TTTTCTTTTTC
5725 TTTTCTTTTTC
1 TTTTCTTTTTC
5736 TTTTC
1 TTTTC
5741 CTATTTGATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (11 bp):
TTTTCTTTTTC
Found at i:9282 original size:11 final size:11
Alignment explanation
Indices: 9266--9313 Score: 50
Period size: 11 Copynumber: 4.7 Consensus size: 11
9256 AAAGTTCGTG
9266 TTTGAAGACCA
1 TTTGAAGACCA
**
9277 TTTGAAGATAA
1 TTTGAAGACCA
9288 TTTGAAGA-C-
1 TTTGAAGACCA
9297 -TTGAAGACCA
1 TTTGAAGACCA
9307 -TTGAAGA
1 TTTGAAGA
9314 TTTATTTCAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
8 7 0.22
9 1 0.03
10 7 0.22
11 17 0.53
ACGTcount: A:0.40, C:0.10, G:0.21, T:0.29
Consensus pattern (11 bp):
TTTGAAGACCA
Done.