Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_137 ID=scaffold_137-JGI_221_v2.0
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: 50853
ACGTcount: A:0.07, C:0.04, G:0.04, T:0.07
Warning! 39626 characters in sequence are not A, C, G, or T
Found at i:916 original size:20 final size:20
Alignment explanation
Indices: 891--937 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
881 AGCTCATTTC
*
891 CAGCTCACTTGAGCTCAAGT
1 CAGCTCACTTGAGATCAAGT
* *
911 CAGCTCATTTGAGATCAATT
1 CAGCTCACTTGAGATCAAGT
931 CAGCTCA
1 CAGCTCA
938 ATTTTAACCC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.28
Consensus pattern (20 bp):
CAGCTCACTTGAGATCAAGT
Found at i:2517 original size:14 final size:15
Alignment explanation
Indices: 2489--2528 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
2479 AAAAAAAAGA
2489 AAAAAAAGAAGTGAGC
1 AAAAAAA-AAGTGAGC
*
2505 AAAAAAAAA-TGAGT
1 AAAAAAAAAGTGAGC
2519 AAAAAAAAAG
1 AAAAAAAAAG
2529 AAGAAAAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 13 0.59
15 2 0.09
16 7 0.32
ACGTcount: A:0.72, C:0.03, G:0.17, T:0.07
Consensus pattern (15 bp):
AAAAAAAAAGTGAGC
Found at i:2544 original size:13 final size:13
Alignment explanation
Indices: 2479--2544 Score: 55
Period size: 13 Copynumber: 4.9 Consensus size: 13
2469 AAAAAATTCG
2479 AAAAAAAAGAA-A
1 AAAAAAAAGAAGA
* *
2491 AAAAAGAAGTGAGCA
1 AAAAAAAAG-AAG-A
2506 AAAAAAAATG-AGTA
1 AAAAAAAA-GAAG-A
2520 AAAAAAAAGAAGA
1 AAAAAAAAGAAGA
*
2533 AAAAAGAAGAAG
1 AAAAAAAAGAAG
2545 TGAAAAGTCT
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
12 8 0.18
13 14 0.32
14 13 0.30
15 8 0.18
16 1 0.02
ACGTcount: A:0.76, C:0.02, G:0.18, T:0.05
Consensus pattern (13 bp):
AAAAAAAAGAAGA
Found at i:3752 original size:15 final size:14
Alignment explanation
Indices: 3732--3779 Score: 60
Period size: 15 Copynumber: 3.3 Consensus size: 14
3722 NNNNNNNNNN
3732 TGAAAAGAAATCGAG
1 TGAAAAGAAA-CGAG
*
3747 TGAAAAGAAAAGAG
1 TGAAAAGAAACGAG
*
3761 TCGCAAAGAAACGAG
1 T-GAAAAGAAACGAG
3776 TGAA
1 TGAA
3780 GAAAGCAAGC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
14 6 0.21
15 22 0.79
ACGTcount: A:0.54, C:0.08, G:0.27, T:0.10
Consensus pattern (14 bp):
TGAAAAGAAACGAG
Found at i:6346 original size:8 final size:9
Alignment explanation
Indices: 6328--6354 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
6318 AATCAGATTC
6328 AAAAATAAA
1 AAAAATAAA
6337 AAAAATAAA
1 AAAAATAAA
6346 AAAAATAAA
1 AAAAATAAA
6355 GGAGGAATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (9 bp):
AAAAATAAA
Found at i:50719 original size:8 final size:9
Alignment explanation
Indices: 50691--50723 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
50681 GTCCCGCAAA
50691 AAAATAAGTC
1 AAAA-AAGTC
50701 AAAAAAGTC
1 AAAAAAGTC
50710 AAAAAA-TC
1 AAAAAAGTC
50718 AAAAAA
1 AAAAAA
50724 ATACGAAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 8 0.35
9 11 0.48
10 4 0.17
ACGTcount: A:0.73, C:0.09, G:0.06, T:0.12
Consensus pattern (9 bp):
AAAAAAGTC
Done.