Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018654.1 Corchorus olitorius cultivar O-4 contig18687, 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: 7307
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:40 original size:18 final size:17
Alignment explanation
Indices: 17--67 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 17
7 AGTTCAATTT
17 ATTTTTCAAAAAAAGTG
1 ATTTTTCAAAAAAAGTG
34 AATTTTTCAAAAAAAAGTG
1 -ATTTTTC-AAAAAAAGTG
*
53 ATTGTTTTAAAAAAA
1 ATT-TTTCAAAAAAA
68 TTGGTTTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
18 17 0.57
19 13 0.43
ACGTcount: A:0.51, C:0.04, G:0.10, T:0.35
Consensus pattern (17 bp):
ATTTTTCAAAAAAAGTG
Found at i:46 original size:19 final size:18
Alignment explanation
Indices: 17--67 Score: 68
Period size: 19 Copynumber: 2.8 Consensus size: 18
7 AGTTCAATTT
17 ATTTTTC-AAAAAAAGTG
1 ATTTTTCAAAAAAAAGTG
34 AATTTTTCAAAAAAAAGTG
1 -ATTTTTCAAAAAAAAGTG
*
53 ATTGTTTTAAAAAAA
1 ATT-TTTCAAAAAAA
68 TTGGTTTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 10 0.33
19 20 0.67
ACGTcount: A:0.51, C:0.04, G:0.10, T:0.35
Consensus pattern (18 bp):
ATTTTTCAAAAAAAAGTG
Found at i:77 original size:17 final size:18
Alignment explanation
Indices: 19--85 Score: 57
Period size: 18 Copynumber: 3.6 Consensus size: 18
9 TTCAATTTAT
19 TTTTCAAAAAAAGTGAATT-
1 TTTT-AAAAAAAGTG-ATTG
*
38 TTTCAAAAAAAAGTGATTG
1 TTT-TAAAAAAAGTGATTG
* *
57 TTTTAAAAAAATTGGTT-
1 TTTTAAAAAAAGTGATTG
74 TTTTAATAAAAA
1 TTTTAA-AAAAA
86 AAACCGAAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
17 6 0.15
18 19 0.46
19 16 0.39
ACGTcount: A:0.48, C:0.03, G:0.10, T:0.39
Consensus pattern (18 bp):
TTTTAAAAAAAGTGATTG
Found at i:150 original size:17 final size:18
Alignment explanation
Indices: 111--151 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 18
101 TTTTTAGGTC
111 AAAAAATAATTTTTTGAA
1 AAAAAATAATTTTTTGAA
129 AAAAAAT-ATTTTTT-AA
1 AAAAAATAATTTTTTGAA
145 ATAAAAA
1 A-AAAAA
152 AAGGTGAGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.14
17 12 0.55
18 7 0.32
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (18 bp):
AAAAAATAATTTTTTGAA
Found at i:152 original size:18 final size:18
Alignment explanation
Indices: 111--152 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
101 TTTTTAGGTC
*
111 AAAAAATAATTTTTTGAA
1 AAAAAATAATTTTTTAAA
129 AAAAAAT-ATTTTTTAAA
1 AAAAAATAATTTTTTAAA
146 TAAAAAA
1 -AAAAAA
153 AGGTGAGTGC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (18 bp):
AAAAAATAATTTTTTAAA
Found at i:1411 original size:19 final size:18
Alignment explanation
Indices: 1374--1418 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
1364 TTAAATTTAT
1374 TAATTATTTATTAAATAA
1 TAATTATTTATTAAATAA
1392 TAATTATTT-TTCAGAATAA
1 TAATTATTTATT-A-AATAA
*
1411 TTATTATT
1 TAATTATT
1419 AATATTCCCC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 2 0.08
18 10 0.42
19 12 0.50
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (18 bp):
TAATTATTTATTAAATAA
Done.