Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Cotton_A_01598
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: 6158
ACGTcount: A:0.35, C:0.16, G:0.28, T:0.21
Found at i:2135 original size:39 final size:39
Alignment explanation
Indices: 2092--2727 Score: 787
Period size: 39 Copynumber: 16.2 Consensus size: 39
2082 TGTTCAGCAG
*
2092 GAAGAGAAAGAGAAGAAATTGAAGGAAGCTCATGAACGA
1 GAAGAGAAAGAGAAGAAATTGAAGGAAGCTCGTGAACGA
** * *
2131 GAAGAGAGAAG-GAAGAAAGAGAAGGAGGCACGTGAACTAGAAGA
1 GAAGAGA-AAGAGAAGAAATTGAAGGAAGCTCGTGAAC-----GA
*
2175 GAAAGAGAAGGAGAAGAAATTGAAGGAAGCTCGTGAACGA
1 G-AAGAGAAAGAGAAGAAATTGAAGGAAGCTCGTGAACGA
* * * * *
2215 GAAGAGAATGAGAAGAGATTGAGGGAGGATCGTGAACGA
1 GAAGAGAAAGAGAAGAAATTGAAGGAAGCTCGTGAACGA
*
2254 GAAGAGATAGAGAAGAAATTGAAGGAAGCTCGTGAACGA
1 GAAGAGAAAGAGAAGAAATTGAAGGAAGCTCGTGAACGA
* * * * * *
2293 GAAGAGAATGAGAAGAGATTGAGGGAGGCTTGTGAGCGA
1 GAAGAGAAAGAGAAGAAATTGAAGGAAGCTCGTGAACGA
* * *
2332 GAAGAGAAAGAGAAGAAA--G-AGGAGGCACATGAACGA
1 GAAGAGAAAGAGAAGAAATTGAAGGAAGCTCGTGAACGA
2368 GAAGAGAAAGAGAAGAAATTGAAGGAAGCTCGTGAACGA
1 GAAGAGAAAGAGAAGAAATTGAAGGAAGCTCGTGAACGA
2407 GAAGAGAAAGAGAAGAAATTGAAGGAAGCTCGTGAACGA
1 GAAGAGAAAGAGAAGAAATTGAAGGAAGCTCGTGAACGA
* * *
2446 GAAGAGAATGAGAGGAGATTGAAGGAAGCTCGTGAACGA
1 GAAGAGAAAGAGAAGAAATTGAAGGAAGCTCGTGAACGA
* * **
2485 GAAGAGAATGAGAAGAGATTGAAGGAAATTCGTGAACGA
1 GAAGAGAAAGAGAAGAAATTGAAGGAAGCTCGTGAACGA
** *
2524 GAAGAGAAAGAGAAGAAAGAGAAGG-AGGTACGTGAACGA
1 GAAGAGAAAGAGAAGAAATTGAAGGAAGCT-CGTGAACGA
* *
2563 GAAGAGAAAGAGAAGAAATTGAAAGAAGCTCGTGAACAA
1 GAAGAGAAAGAGAAGAAATTGAAGGAAGCTCGTGAACGA
* *
2602 GAAGAGAATGAGAAGAGATTGAAGGAAGCTCGTGAACGA
1 GAAGAGAAAGAGAAGAAATTGAAGGAAGCTCGTGAACGA
* * * *
2641 GAAGAGAATGAGAAGAGATTGAAGGAAGCTTGTGAACAA
1 GAAGAGAAAGAGAAGAAATTGAAGGAAGCTCGTGAACGA
* * *
2680 GAAGAGAATGATAAGAGATTGAAGGAAGCTCGTGAACGA
1 GAAGAGAAAGAGAAGAAATTGAAGGAAGCTCGTGAACGA
2719 GAAGAGAAA
1 GAAGAGAAA
2728 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:2137 original size:78 final size:73
Alignment explanation
Indices: 2092--2831 Score: 492
Period size: 78 Copynumber: 9.7 Consensus size: 73
2082 TGTTCAGCAG
* * *
2092 GAAGAGAAAGAGAAGAAATTGAAGGAAGCTCATGAACGAGAAGAGAGAAGGAAGAAAGAGAAGGA
1 GAAGAGAAAGAGAAGAAATTGAAGGAAGCTCGTGAACGAG-A-AGAGAATG-AGAAAGTG-AGGA
* *
2157 GGCACGTGAACTAGAAGA
62 GGC-TGTG----AG-CGA
*
2175 GAAAGAGAAGGAGAAGAAATTGAAGGAAGCTCGTGAACGAGAAGAGAATGAGAAGAGATTGAGGG
1 G-AAGAGAAAGAGAAGAAATTGAAGGAAGCTCGTGAACGAGAAGAGAATGAGAA-AG--TGA-GG
* *
2240 AGGATCGTGAACGA
61 AGGCT-GTGAGCGA
*
2254 GAAGAGATAGAGAAGAAATTGAAGGAAGCTCGTGAACGAGAAGAGAATGAGAAGAGATTGAGGGA
1 GAAGAGAAAGAGAAGAAATTGAAGGAAGCTCGTGAACGAGAAGAGAATGAGAA-AG--TGA-GGA
2319 GGCTTGTGAGCGA
62 GGC-TGTGAGCGA
* * * * *
2332 GAAGAGAAAGAGAAGAAA--G-AGGAGGCACATGAACGAGAAGAGAAAGAGAAGAAATTGAAGGA
1 GAAGAGAAAGAGAAGAAATTGAAGGAAGCTCGTGAACGAGAAGAG-AA-TG-AGAAAGTG-AGGA
* *
2394 AGCTCGTGAACGA
62 GGCT-GTGAGCGA
*
2407 GAAGAGAAAGAGAAGAAATTGAAGGAAGCTCGTGAACGAGAAGAGAATGAGAGGAGATTGAAGGA
1 GAAGAGAAAGAGAAGAAATTGAAGGAAGCTCGTGAACGAGAAGAGAATGAGA--A-AGTG-AGGA
* *
2472 AGCTCGTGAACGA
62 GGCT-GTGAGCGA
* * ** * *
2485 GAAGAGAATGAGAAGAGATTGAAGGAAATTCGTGAACGAGAAGAGAAAGAGAAGAAAGAGAAGGA
1 GAAGAGAAAGAGAAGAAATTGAAGGAAGCTCGTGAACGAGAAGAG-AA-TG-AGAAAGTG-AGGA
*
2550 GG-TACGTGAACGA
62 GGCT--GTGAGCGA
* *
2563 GAAGAGAAAGAGAAGAAATTGAAAGAAGCTCGTGAACAAGAAGAGAATGAGAAGAGATTGAAGGA
1 GAAGAGAAAGAGAAGAAATTGAAGGAAGCTCGTGAACGAGAAGAGAATGAGAA-AG--TG-AGGA
* *
2628 AGCTCGTGAACGA
62 GGCT-GTGAGCGA
* * * * *
2641 GAAGAGAATGAGAAGAGATTGAAGGAAGCTTGTGAACAAGAAGAGAATGATAAGAGATTGAAGGA
1 GAAGAGAAAGAGAAGAAATTGAAGGAAGCTCGTGAACGAGAAGAGAATGAGAA-AG--TG-AGGA
*
2706 AGCTCGT----GA
62 GGCT-GTGAGCGA
* *
2715 -ACGAG--A-AG-AGAAATTGAAGGAAGCTTGTGAACGAGAAGAGAA--AG--AG-GAGGAGGCA
1 GAAGAGAAAGAGAAGAAATTGAAGGAAGCTCGTGAACGAGAAGAGAATGAGAAAGTGAGGAGGC-
* *
2770 CGTGAACGA
65 TGTGAGCGA
* ** * * *
2779 GAAGAGAAAGAGAGGAAAGAGAAGGAGGCACGTGAACTAGAAGA-AAGTGAGAA
1 GAAGAGAAAGAGAAGAAATTGAAGGAAGCTCGTGAACGAGAAGAGAA-TGAGAA
2832 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:2732 original size:30 final size:30
Alignment explanation
Indices: 2697--2787 Score: 128
Period size: 30 Copynumber: 3.0 Consensus size: 30
2687 ATGATAAGAG
2697 ATTGAAGGAAGCTCGTGAACGAGAAGAGAA
1 ATTGAAGGAAGCTCGTGAACGAGAAGAGAA
*
2727 ATTGAAGGAAGCTTGTGAACGAGAAGAGAA
1 ATTGAAGGAAGCTCGTGAACGAGAAGAGAA
** * * *
2757 AGAGGAGGAGGCACGTGAACGAGAAGAGAA
1 ATTGAAGGAAGCTCGTGAACGAGAAGAGAA
2787 A
1 A
2788 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.