Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga02g00319.F1
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: 2972
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.28
Found at i:2389 original size:117 final size:117
Alignment explanation
Indices: 2217--2439 Score: 374
Period size: 117 Copynumber: 1.9 Consensus size: 117
2207 GGTGGCTGCA
* *
2217 GTGGTTGTGGCGCTGGATGTGGAAACGTGGTGAAGAGTGGTGGTTGTGGTAGTGGTTGCGGCAGT
1 GTGGTTGTGGCGCTGGATGTGGAAACATGGTGAAGAGTGGTGGCTGTGGTAGTGGTTGCGGCAGT
*
2282 GGATGTGGGGGTGGTTGTGGAAGCATAGTGAATAGCGGCAGCTGCGGTGCCG
66 GGATGCGGGGGTGGTTGTGGAAGCATAGTGAATAGCGGCAGCTGCGGTGCCG
* * **
2334 GTGGTTGTGGTGCTGGATGTGGAAACATGGTGAAGAGTGGTGGCTGTGGTGGTGGTTGCGGGGGT
1 GTGGTTGTGGCGCTGGATGTGGAAACATGGTGAAGAGTGGTGGCTGTGGTAGTGGTTGCGGCAGT
*
2399 GGGTGCGGGGGTGGTTGTGGAAGCATAGTGAATAGCGGCAG
66 GGATGCGGGGGTGGTTGTGGAAGCATAGTGAATAGCGGCAG
2440 TTGTGGCTCT
Statistics
Matches: 98, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
117 98 1.00
ACGTcount: A:0.15, C:0.09, G:0.50, T:0.26
Consensus pattern (117 bp):
GTGGTTGTGGCGCTGGATGTGGAAACATGGTGAAGAGTGGTGGCTGTGGTAGTGGTTGCGGCAGT
GGATGCGGGGGTGGTTGTGGAAGCATAGTGAATAGCGGCAGCTGCGGTGCCG
Found at i:2399 original size:12 final size:12
Alignment explanation
Indices: 2384--2415 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
2374 TGGCTGTGGT
2384 GGTGGTTGCGGG
1 GGTGGTTGCGGG
*
2396 GGTGGGTGCGGG
1 GGTGGTTGCGGG
2408 GGTGGTTG
1 GGTGGTTG
2416 TGGAAGCATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.00, C:0.06, G:0.69, T:0.25
Consensus pattern (12 bp):
GGTGGTTGCGGG
Found at i:2549 original size:9 final size:9
Alignment explanation
Indices: 2535--2581 Score: 64
Period size: 9 Copynumber: 5.6 Consensus size: 9
2525 GGTTGTGGCG
2535 GTGGCGGTT
1 GTGGCGGTT
2544 GTGGCGGTT
1 GTGGCGGTT
2553 GTGGC-G--
1 GTGGCGGTT
2559 GTGGCGGTT
1 GTGGCGGTT
*
2568 GTGGTGGTT
1 GTGGCGGTT
2577 GTGGC
1 GTGGC
2582 AGTGGGTGTG
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
6 5 0.15
7 1 0.03
8 1 0.03
9 26 0.79
ACGTcount: A:0.00, C:0.11, G:0.57, T:0.32
Consensus pattern (9 bp):
GTGGCGGTT
Found at i:2557 original size:24 final size:24
Alignment explanation
Indices: 2525--2586 Score: 106
Period size: 24 Copynumber: 2.6 Consensus size: 24
2515 GGAGAACAGT
2525 GGTTGTGGCGGTGGCGGTTGTGGC
1 GGTTGTGGCGGTGGCGGTTGTGGC
*
2549 GGTTGTGGCGGTGGCGGTTGTGGT
1 GGTTGTGGCGGTGGCGGTTGTGGC
*
2573 GGTTGTGGCAGTGG
1 GGTTGTGGCGGTGG
2587 GTGTGGCAAC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.02, C:0.10, G:0.58, T:0.31
Consensus pattern (24 bp):
GGTTGTGGCGGTGGCGGTTGTGGC
Found at i:2872 original size:27 final size:27
Alignment explanation
Indices: 2842--2895 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
2832 GATTCTGGCT
*
2842 TTGCATATCTATTTTCCTTCAAAAATA
1 TTGCATATCTATTTTCCTTAAAAAATA
2869 TTGCATATCTATTTTCCTTAAAAAATA
1 TTGCATATCTATTTTCCTTAAAAAATA
2896 AACTTTCCTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.35, C:0.17, G:0.04, T:0.44
Consensus pattern (27 bp):
TTGCATATCTATTTTCCTTAAAAAATA
Done.