Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga02g00132.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: 5035
ACGTcount: A:0.37, C:0.15, G:0.28, T:0.21
Found at i:85 original size:6 final size:7
Alignment explanation
Indices: 74--106 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
64 AATAATATTT
74 TAAAAAA
1 TAAAAAA
81 TAAAAAA
1 TAAAAAA
88 TAAAAAA
1 TAAAAAA
95 T-AAAAA
1 TAAAAAA
101 TAAAAA
1 TAAAAA
107 CTCTCTCAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 6 0.24
7 19 0.76
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (7 bp):
TAAAAAA
Found at i:93 original size:14 final size:13
Alignment explanation
Indices: 74--106 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
64 AATAATATTT
74 TAAAAAATAAAAAA
1 TAAAAAAT-AAAAA
88 TAAAAAATAAAAA
1 TAAAAAATAAAAA
101 TAAAAA
1 TAAAAA
107 CTCTCTCAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 11 0.58
14 8 0.42
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (13 bp):
TAAAAAATAAAAA
Found at i:2278 original size:39 final size:39
Alignment explanation
Indices: 2235--2870 Score: 787
Period size: 39 Copynumber: 16.2 Consensus size: 39
2225 TGTTCAGCAG
*
2235 GAAGAGAAAGAGAAGAAATTGAAGGAAGCTCATGAACGA
1 GAAGAGAAAGAGAAGAAATTGAAGGAAGCTCGTGAACGA
** * *
2274 GAAGAGAGAAG-GAAGAAAGAGAAGGAGGCACGTGAACTAGAAGA
1 GAAGAGA-AAGAGAAGAAATTGAAGGAAGCTCGTGAAC-----GA
*
2318 GAAAGAGAAGGAGAAGAAATTGAAGGAAGCTCGTGAACGA
1 G-AAGAGAAAGAGAAGAAATTGAAGGAAGCTCGTGAACGA
* * * * *
2358 GAAGAGAATGAGAAGAGATTGAGGGAGGATCGTGAACGA
1 GAAGAGAAAGAGAAGAAATTGAAGGAAGCTCGTGAACGA
*
2397 GAAGAGATAGAGAAGAAATTGAAGGAAGCTCGTGAACGA
1 GAAGAGAAAGAGAAGAAATTGAAGGAAGCTCGTGAACGA
* * * * * *
2436 GAAGAGAATGAGAAGAGATTGAGGGAGGCTTGTGAGCGA
1 GAAGAGAAAGAGAAGAAATTGAAGGAAGCTCGTGAACGA
* * *
2475 GAAGAGAAAGAGAAGAAA--G-AGGAGGCACATGAACGA
1 GAAGAGAAAGAGAAGAAATTGAAGGAAGCTCGTGAACGA
2511 GAAGAGAAAGAGAAGAAATTGAAGGAAGCTCGTGAACGA
1 GAAGAGAAAGAGAAGAAATTGAAGGAAGCTCGTGAACGA
2550 GAAGAGAAAGAGAAGAAATTGAAGGAAGCTCGTGAACGA
1 GAAGAGAAAGAGAAGAAATTGAAGGAAGCTCGTGAACGA
* * *
2589 GAAGAGAATGAGAGGAGATTGAAGGAAGCTCGTGAACGA
1 GAAGAGAAAGAGAAGAAATTGAAGGAAGCTCGTGAACGA
* * **
2628 GAAGAGAATGAGAAGAGATTGAAGGAAATTCGTGAACGA
1 GAAGAGAAAGAGAAGAAATTGAAGGAAGCTCGTGAACGA
** *
2667 GAAGAGAAAGAGAAGAAAGAGAAGG-AGGTACGTGAACGA
1 GAAGAGAAAGAGAAGAAATTGAAGGAAGCT-CGTGAACGA
* *
2706 GAAGAGAAAGAGAAGAAATTGAAAGAAGCTCGTGAACAA
1 GAAGAGAAAGAGAAGAAATTGAAGGAAGCTCGTGAACGA
* *
2745 GAAGAGAATGAGAAGAGATTGAAGGAAGCTCGTGAACGA
1 GAAGAGAAAGAGAAGAAATTGAAGGAAGCTCGTGAACGA
* * * *
2784 GAAGAGAATGAGAAGAGATTGAAGGAAGCTTGTGAACAA
1 GAAGAGAAAGAGAAGAAATTGAAGGAAGCTCGTGAACGA
* * *
2823 GAAGAGAATGATAAGAGATTGAAGGAAGCTCGTGAACGA
1 GAAGAGAAAGAGAAGAAATTGAAGGAAGCTCGTGAACGA
2862 GAAGAGAAA
1 GAAGAGAAA
2871 TTGAAGGAAG
Statistics
Matches: 519, Mismatches: 65, Indels: 26
0.85 0.11 0.04
Matches are distributed among these distances:
36 30 0.06
37 1 0.00
38 3 0.01
39 443 0.85
40 9 0.02
44 5 0.01
45 28 0.05
ACGTcount: A:0.47, C:0.07, G:0.35, T:0.11
Consensus pattern (39 bp):
GAAGAGAAAGAGAAGAAATTGAAGGAAGCTCGTGAACGA
Found at i:2280 original size:78 final size:73
Alignment explanation
Indices: 2235--2974 Score: 492
Period size: 78 Copynumber: 9.7 Consensus size: 73
2225 TGTTCAGCAG
* * *
2235 GAAGAGAAAGAGAAGAAATTGAAGGAAGCTCATGAACGAGAAGAGAGAAGGAAGAAAGAGAAGGA
1 GAAGAGAAAGAGAAGAAATTGAAGGAAGCTCGTGAACGAG-A-AGAGAATG-AGAAAGTG-AGGA
* *
2300 GGCACGTGAACTAGAAGA
62 GGC-TGTG----AG-CGA
*
2318 GAAAGAGAAGGAGAAGAAATTGAAGGAAGCTCGTGAACGAGAAGAGAATGAGAAGAGATTGAGGG
1 G-AAGAGAAAGAGAAGAAATTGAAGGAAGCTCGTGAACGAGAAGAGAATGAGAA-AG--TGA-GG
* *
2383 AGGATCGTGAACGA
61 AGGCT-GTGAGCGA
*
2397 GAAGAGATAGAGAAGAAATTGAAGGAAGCTCGTGAACGAGAAGAGAATGAGAAGAGATTGAGGGA
1 GAAGAGAAAGAGAAGAAATTGAAGGAAGCTCGTGAACGAGAAGAGAATGAGAA-AG--TGA-GGA
2462 GGCTTGTGAGCGA
62 GGC-TGTGAGCGA
* * * * *
2475 GAAGAGAAAGAGAAGAAA--G-AGGAGGCACATGAACGAGAAGAGAAAGAGAAGAAATTGAAGGA
1 GAAGAGAAAGAGAAGAAATTGAAGGAAGCTCGTGAACGAGAAGAG-AA-TG-AGAAAGTG-AGGA
* *
2537 AGCTCGTGAACGA
62 GGCT-GTGAGCGA
*
2550 GAAGAGAAAGAGAAGAAATTGAAGGAAGCTCGTGAACGAGAAGAGAATGAGAGGAGATTGAAGGA
1 GAAGAGAAAGAGAAGAAATTGAAGGAAGCTCGTGAACGAGAAGAGAATGAGA--A-AGTG-AGGA
* *
2615 AGCTCGTGAACGA
62 GGCT-GTGAGCGA
* * ** * *
2628 GAAGAGAATGAGAAGAGATTGAAGGAAATTCGTGAACGAGAAGAGAAAGAGAAGAAAGAGAAGGA
1 GAAGAGAAAGAGAAGAAATTGAAGGAAGCTCGTGAACGAGAAGAG-AA-TG-AGAAAGTG-AGGA
*
2693 GG-TACGTGAACGA
62 GGCT--GTGAGCGA
* *
2706 GAAGAGAAAGAGAAGAAATTGAAAGAAGCTCGTGAACAAGAAGAGAATGAGAAGAGATTGAAGGA
1 GAAGAGAAAGAGAAGAAATTGAAGGAAGCTCGTGAACGAGAAGAGAATGAGAA-AG--TG-AGGA
* *
2771 AGCTCGTGAACGA
62 GGCT-GTGAGCGA
* * * * *
2784 GAAGAGAATGAGAAGAGATTGAAGGAAGCTTGTGAACAAGAAGAGAATGATAAGAGATTGAAGGA
1 GAAGAGAAAGAGAAGAAATTGAAGGAAGCTCGTGAACGAGAAGAGAATGAGAA-AG--TG-AGGA
*
2849 AGCTCGT----GA
62 GGCT-GTGAGCGA
* *
2858 -ACGAG--A-AG-AGAAATTGAAGGAAGCTTGTGAACGAGAAGAGAA--AG--AG-GAGGAGGCA
1 GAAGAGAAAGAGAAGAAATTGAAGGAAGCTCGTGAACGAGAAGAGAATGAGAAAGTGAGGAGGC-
* *
2913 CGTGAACGA
65 TGTGAGCGA
* ** * * *
2922 GAAGAGAAAGAGAGGAAAGAGAAGGAGGCACGTGAACTAGAAGA-AAGTGAGAA
1 GAAGAGAAAGAGAAGAAATTGAAGGAAGCTCGTGAACGAGAAGAGAA-TGAGAA
2975 GATATGGAGA
Statistics
Matches: 555, Mismatches: 61, Indels: 92
0.78 0.09 0.13
Matches are distributed among these distances:
60 8 0.01
61 1 0.00
64 4 0.01
65 4 0.01
67 2 0.00
68 4 0.01
69 56 0.10
70 2 0.00
71 2 0.00
73 4 0.01
74 3 0.01
75 59 0.11
76 8 0.01
77 9 0.02
78 314 0.57
79 8 0.01
80 2 0.00
81 7 0.01
82 9 0.02
83 3 0.01
84 46 0.08
ACGTcount: A:0.47, C:0.07, G:0.36, T:0.11
Consensus pattern (73 bp):
GAAGAGAAAGAGAAGAAATTGAAGGAAGCTCGTGAACGAGAAGAGAATGAGAAAGTGAGGAGGCT
GTGAGCGA
Found at i:2875 original size:30 final size:30
Alignment explanation
Indices: 2840--2930 Score: 128
Period size: 30 Copynumber: 3.0 Consensus size: 30
2830 ATGATAAGAG
2840 ATTGAAGGAAGCTCGTGAACGAGAAGAGAA
1 ATTGAAGGAAGCTCGTGAACGAGAAGAGAA
*
2870 ATTGAAGGAAGCTTGTGAACGAGAAGAGAA
1 ATTGAAGGAAGCTCGTGAACGAGAAGAGAA
** * * *
2900 AGAGGAGGAGGCACGTGAACGAGAAGAGAA
1 ATTGAAGGAAGCTCGTGAACGAGAAGAGAA
2930 A
1 A
2931 GAGAGGAAAG
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 54 1.00
ACGTcount: A:0.44, C:0.09, G:0.36, T:0.11
Consensus pattern (30 bp):
ATTGAAGGAAGCTCGTGAACGAGAAGAGAA
Done.