Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga10g00919.N2
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, 624
Length: 1041
ACGTcount: A:0.21, C:0.08, G:0.45, T:0.26
Found at i:300 original size:24 final size:24
Alignment explanation
Indices: 273--319 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
263 CGGCGCAGGT
*
273 GGTGGTGGTGGTCTTGGAGGTGGC
1 GGTGGTGGCGGTCTTGGAGGTGGC
297 GGTGGTGGCGGTCTTGGAGGTGG
1 GGTGGTGGCGGTCTTGGAGGTGG
320 AAAAGGTGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.04, C:0.09, G:0.60, T:0.28
Consensus pattern (24 bp):
GGTGGTGGCGGTCTTGGAGGTGGC
Found at i:327 original size:24 final size:24
Alignment explanation
Indices: 276--328 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
266 CGCAGGTGGT
* ****
276 GGTGGTGGTCTTGGAGGTGGCGGT
1 GGTGGCGGTCTTGGAGGTGGAAAA
300 GGTGGCGGTCTTGGAGGTGGAAAA
1 GGTGGCGGTCTTGGAGGTGGAAAA
324 GGTGG
1 GGTGG
329 AGGGATAGGA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.11, C:0.08, G:0.57, T:0.25
Consensus pattern (24 bp):
GGTGGCGGTCTTGGAGGTGGAAAA
Found at i:361 original size:36 final size:36
Alignment explanation
Indices: 315--561 Score: 224
Period size: 36 Copynumber: 6.7 Consensus size: 36
305 CGGTCTTGGA
*
315 GGTGGAAAAGGTGGAGGGATAGGAGGTGGAGCTGGT
1 GGTGGAAAAGGTGGAGGCATAGGAGGTGGAGCTGGT
351 GGTGGAAAAGGTGGAGGCATAGGAGGTGGAGCTGGT
1 GGTGGAAAAGGTGGAGGCATAGGAGGTGGAGCTGGT
**** *
387 GGTGGTGCTGGTGGAGGTATAGGAGGTGGAGCTGGT
1 GGTGGAAAAGGTGGAGGCATAGGAGGTGGAGCTGGT
* * **
423 GGTGGAAAAGGTGGAGGCATAGGAGCAGGTGGTGGTGCC
1 GGTGGAAAAGGTGGAGGCATA-G-G-AGGTGGAGCTGGT
**** * * * * * *** *
462 GGTGGTGGCGCTGGAGGCGGTGCTGGTGTTGGTTTTGGA
1 GGTGGAAAAGGTGGAGGC-AT--AGGAGGTGGAGCTGGT
*
501 GGTGGAAAAGGTGGAGGGATAGGAGGTGGAGCTGGT
1 GGTGGAAAAGGTGGAGGCATAGGAGGTGGAGCTGGT
537 GGTGGAAAAGGTGGAGGCATAGGAG
1 GGTGGAAAAGGTGGAGGCATAGGAG
562 CAGGTGGTGG
Statistics
Matches: 162, Mismatches: 43, Indels: 12
0.75 0.20 0.06
Matches are distributed among these distances:
36 115 0.71
37 1 0.01
38 2 0.01
39 41 0.25
40 2 0.01
41 1 0.01
ACGTcount: A:0.21, C:0.06, G:0.54, T:0.19
Consensus pattern (36 bp):
GGTGGAAAAGGTGGAGGCATAGGAGGTGGAGCTGGT
Found at i:505 original size:114 final size:114
Alignment explanation
Indices: 396--751 Score: 460
Period size: 114 Copynumber: 3.3 Consensus size: 114
386 TGGTGGTGCT
*
396 GGTGGAGGTATAGGAGGTGGAGCTGGTGGTGGAAAAGGTGGAGGCATAGGAGCAGGTGGTGGTGC
1 GGTGGAGGGATAGGAGGTGGAGCTGGTGGTGGAAAAGGTGGAGGCATAGGAGCAGGTGGTGGTGC
* ** * *
461 CGGTGGTGGCGCTGGAGGCGGTGCTGGTGTTGGTTTTGGAGGTGGAAAA
66 CGGTGGTAGAACTGGAGGCAGTGCTGGTGGTGGTTTTGGAGGTGGAAAA
510 GGTGGAGGGATAGGAGGTGGAGCTGGTGGTGGAAAAGGTGGAGGCATAGGAGCAGGTGGTGGTGC
1 GGTGGAGGGATAGGAGGTGGAGCTGGTGGTGGAAAAGGTGGAGGCATAGGAGCAGGTGGTGGTGC
575 CGGTGGTAGAACTGGAGGCAGTGCTGGTGGTGGTTTTGGAGGTGGAAAA
66 CGGTGGTAGAACTGGAGGCAGTGCTGGTGGTGGTTTTGGAGGTGGAAAA
**
624 GGTGGAGGGATAGGAGGT-G-G-T-GT--TGG---AGGTGGAGG--T-GGAGTTGGTGGTGGT--
1 GGTGGAGGGATAGGAGGTGGAGCTGGTGGTGGAAAAGGTGGAGGCATAGGAGCAGGTGGTGGTGC
* * ** *
675 -GGTGG-CG--TTGGAGGGGGTGCTGGTGGTGGCTTTGGAGGTGGAAAA
66 CGGTGGTAGAACTGGAGGCAGTGCTGGTGGTGGTTTTGGAGGTGGAAAA
*
720 GGTGGAGGGATAGGAGGTGGAGCTGGAGGTGG
1 GGTGGAGGGATAGGAGGTGGAGCTGGTGGTGG
752 TGCTGGTGGT
Statistics
Matches: 222, Mismatches: 14, Indels: 24
0.85 0.05 0.09
Matches are distributed among these distances:
96 52 0.23
97 1 0.00
98 2 0.01
99 6 0.03
100 1 0.00
102 16 0.07
103 1 0.00
105 9 0.04
108 3 0.01
110 2 0.01
111 1 0.00
112 1 0.00
113 1 0.00
114 126 0.57
ACGTcount: A:0.18, C:0.06, G:0.55, T:0.22
Consensus pattern (114 bp):
GGTGGAGGGATAGGAGGTGGAGCTGGTGGTGGAAAAGGTGGAGGCATAGGAGCAGGTGGTGGTGC
CGGTGGTAGAACTGGAGGCAGTGCTGGTGGTGGTTTTGGAGGTGGAAAA
Found at i:640 original size:48 final size:48
Alignment explanation
Indices: 588--751 Score: 141
Period size: 48 Copynumber: 3.4 Consensus size: 48
578 TGGTAGAACT
* *
588 GGAGGCAGTGCTGGTGGTGGTTTTGGAGGTGGAAAAGGTGGAGGGATA
1 GGAGGCGGTGCTGGTGGTGGATTTGGAGGTGGAAAAGGTGGAGGGATA
* * * ** * **** * *
636 GGAGGTGGTGTTGGAGGTGGAGGTGGAGTTGGTGGTGGTGGTGGCG-TT
1 GGAGGCGGTGCTGGTGGTGGATTTGGAGGTGGAAAAGGTGGAGG-GATA
* *
684 GGAGGGGGTGCTGGTGGTGGCTTTGGAGGTGGAAAAGGTGGAGGGATA
1 GGAGGCGGTGCTGGTGGTGGATTTGGAGGTGGAAAAGGTGGAGGGATA
* * *
732 GGAGGTGGAGCTGGAGGTGG
1 GGAGGCGGTGCTGGTGGTGG
752 TGCTGGTGGT
Statistics
Matches: 84, Mismatches: 30, Indels: 4
0.71 0.25 0.03
Matches are distributed among these distances:
47 1 0.01
48 82 0.98
49 1 0.01
ACGTcount: A:0.16, C:0.04, G:0.57, T:0.23
Consensus pattern (48 bp):
GGAGGCGGTGCTGGTGGTGGATTTGGAGGTGGAAAAGGTGGAGGGATA
Found at i:643 original size:36 final size:36
Alignment explanation
Indices: 311--656 Score: 208
Period size: 36 Copynumber: 9.3 Consensus size: 36
301 GTGGCGGTCT
* *
311 TGGAGGTGGAAAAGGTGGAGGGATAGGAGGTGGAGC
1 TGGAGGTGGAAAAGGTGGAGGCATAGGAGGTGGTGC
* *
347 TGGTGGTGGAAAAGGTGGAGGCATAGGAGGTGGAGC
1 TGGAGGTGGAAAAGGTGGAGGCATAGGAGGTGGTGC
* **** * *
383 TGGTGGTGGTGCTGGTGGAGGTATAGGAGGTGGAGC
1 TGGAGGTGGAAAAGGTGGAGGCATAGGAGGTGGTGC
* *
419 TGGTGGTGGAAAAGGTGGAGGCATAGGAGCAGGTGGTGG
1 TGGAGGTGGAAAAGGTGGAGGCATA-G-G-AGGTGGTGC
** **** * * * * * **
458 TGCCGGTGGTGGCGCTGGAGGCGGTGCTGGTGTTGGTTT
1 TGGAGGTGGAAAAGGTGGAGGC-AT--AGGAGGTGGTGC
* *
497 TGGAGGTGGAAAAGGTGGAGGGATAGGAGGTGGAGC
1 TGGAGGTGGAAAAGGTGGAGGCATAGGAGGTGGTGC
* *
533 TGGTGGTGGAAAAGGTGGAGGCATAGGAGCAGGTGGTGG
1 TGGAGGTGGAAAAGGTGGAGGCATA-G-G-AGGTGGTGC
** * * * * **
572 TGCCGGTGGTAGAA-CTGGAGGCAGTGCTGGTGGTGGTTT
1 TGGAGGTGG-AAAAGGTGGAGGCA-T--AGGAGGTGGTGC
* *
611 TGGAGGTGGAAAAGGTGGAGGGATAGGAGGTGGTGT
1 TGGAGGTGGAAAAGGTGGAGGCATAGGAGGTGGTGC
647 TGGAGGTGGA
1 TGGAGGTGGA
657 GGTGGAGTTG
Statistics
Matches: 234, Mismatches: 62, Indels: 28
0.72 0.19 0.09
Matches are distributed among these distances:
36 133 0.57
37 2 0.01
38 7 0.03
39 83 0.35
40 7 0.03
41 2 0.01
ACGTcount: A:0.20, C:0.06, G:0.53, T:0.21
Consensus pattern (36 bp):
TGGAGGTGGAAAAGGTGGAGGCATAGGAGGTGGTGC
Found at i:653 original size:12 final size:12
Alignment explanation
Indices: 636--799 Score: 80
Period size: 12 Copynumber: 13.7 Consensus size: 12
626 TGGAGGGATA
636 GGAGGTGGTGTT
1 GGAGGTGGTGTT
* *
648 GGAGGTGGAGGT
1 GGAGGTGGTGTT
* *
660 GGAGTTGGTGGT
1 GGAGGTGGTGTT
* *
672 GGTGGTGGCGTT
1 GGAGGTGGTGTT
* *
684 GGAGGGGGTGCT
1 GGAGGTGGTGTT
*
696 GGTGGTGGCT-TT
1 GGAGGTGG-TGTT
****
708 GGAGGTGGAAAA
1 GGAGGTGGTGTT
* * *
720 GGTGGAGG-GATA
1 GGAGGTGGTG-TT
* *
732 GGAGGTGGAGCT
1 GGAGGTGGTGTT
*
744 GGAGGTGGTGCT
1 GGAGGTGGTGTT
*
756 GGTGGTGGTGTT
1 GGAGGTGGTGTT
*
768 GGAGGTGGTGCT
1 GGAGGTGGTGTT
* *
780 GGCGGTGGTTTT
1 GGAGGTGGTGTT
*
792 GGCGGTGG
1 GGAGGTGG
800 AAAAGGCGGA
Statistics
Matches: 113, Mismatches: 35, Indels: 8
0.72 0.22 0.05
Matches are distributed among these distances:
12 111 0.98
13 2 0.02
ACGTcount: A:0.10, C:0.05, G:0.59, T:0.26
Consensus pattern (12 bp):
GGAGGTGGTGTT
Found at i:657 original size:18 final size:18
Alignment explanation
Indices: 636--688 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
626 TGGAGGGATA
*
636 GGAGGTGGTGTTGGAGGT
1 GGAGGTGGAGTTGGAGGT
*
654 GGAGGTGGAGTTGGTGGT
1 GGAGGTGGAGTTGGAGGT
* *
672 GGTGGTGGCGTTGGAGG
1 GGAGGTGGAGTTGGAGG
689 GGGTGCTGGT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.09, C:0.02, G:0.62, T:0.26
Consensus pattern (18 bp):
GGAGGTGGAGTTGGAGGT
Found at i:713 original size:96 final size:93
Alignment explanation
Indices: 595--881 Score: 322
Period size: 96 Copynumber: 3.1 Consensus size: 93
585 ACTGGAGGCA
595 GTGCTGGTGGTGGTTTTGGAGGTGGAAAAGGTGGAGGGATAGGAGGTGGTGTTGGAGGTGGAGGT
1 GTGCTGGTGGTGGTTTTGGAGGTGGAAAAGGTGGAGGGATAGGAGGTGG-GTTGGAGGTGGAGGT
*
660 GGAGTTGGTGGTGGTGGTGGCGTTGGAGGGG
65 GG-GTTGGTGGTGGTGGT-GCGTTGGAGGTG
* *
691 GTGCTGGTGGTGGCTTTGGAGGTGGAAAAGGTGGAGGGATAGGA----GG-TGGAGCTGGAGGT-
1 GTGCTGGTGGTGGTTTTGGAGGTGGAAAAGGTGGAGGGATAGGAGGTGGGTTGGAGGTGGAGGTG
*
750 GG-TGCTGGTGGTGGT--GTTGGAGGTG
66 GGTTGGTGGTGGTGGTGCGTTGGAGGTG
* * * * *
775 GTGCTGGCGGTGGTTTTGGCGGTGGAAAAGGCGGAGGTATAGGAGGTGGAGTTGGCGGTGGTGGA
1 GTGCTGGTGGTGGTTTTGGAGGTGGAAAAGGTGGAGGGATAGGAGGTGG-GTT---GGAGGTGGA
* * *
840 GGAGGTGTTGGTGGTGGCGGTAGCTTTGGAGGTG
62 GGTGG-GTTGGTGGTGGTGGT-GCGTTGGAGGTG
874 GTGCTGGT
1 GTGCTGGT
882 AGAGGAATTG
Statistics
Matches: 160, Mismatches: 16, Indels: 27
0.79 0.08 0.13
Matches are distributed among these distances:
84 48 0.30
87 12 0.08
88 2 0.01
89 2 0.01
90 13 0.08
91 1 0.01
92 1 0.01
93 9 0.06
94 1 0.01
95 1 0.01
96 54 0.34
99 16 0.10
ACGTcount: A:0.13, C:0.05, G:0.56, T:0.26
Consensus pattern (93 bp):
GTGCTGGTGGTGGTTTTGGAGGTGGAAAAGGTGGAGGGATAGGAGGTGGGTTGGAGGTGGAGGTG
GGTTGGTGGTGGTGGTGCGTTGGAGGTG
Found at i:747 original size:84 final size:84
Alignment explanation
Indices: 648--837 Score: 272
Period size: 84 Copynumber: 2.3 Consensus size: 84
638 AGGTGGTGTT
* * * *
648 GGAGGTGGAGGTGGAGTTGGTGGTGGTGGTGGCGTTGGAGGGGGTGCTGGTGGTGGCTTTGGAGG
1 GGAGGTGGAGCTGGAGGTGGTGCTGGTGGTGGCGTTGGAGGGGGTGCTGGCGGTGGCTTTGGAGG
*
713 TGGAAAAGGTGGAGGGATA
66 TGGAAAAGGCGGAGGGATA
* * * *
732 GGAGGTGGAGCTGGAGGTGGTGCTGGTGGTGGTGTTGGAGGTGGTGCTGGCGGTGGTTTTGGCGG
1 GGAGGTGGAGCTGGAGGTGGTGCTGGTGGTGGCGTTGGAGGGGGTGCTGGCGGTGGCTTTGGAGG
*
797 TGGAAAAGGCGGAGGTATA
66 TGGAAAAGGCGGAGGGATA
* *
816 GGAGGTGGAGTTGGCGGTGGTG
1 GGAGGTGGAGCTGGAGGTGGTG
838 GAGGAGGTGT
Statistics
Matches: 94, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
84 94 1.00
ACGTcount: A:0.13, C:0.05, G:0.57, T:0.24
Consensus pattern (84 bp):
GGAGGTGGAGCTGGAGGTGGTGCTGGTGGTGGCGTTGGAGGGGGTGCTGGCGGTGGCTTTGGAGG
TGGAAAAGGCGGAGGGATA
Found at i:849 original size:21 final size:21
Alignment explanation
Indices: 816--856 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
806 CGGAGGTATA
*
816 GGAGGTGGAGTTGGCGGTGGT
1 GGAGGAGGAGTTGGCGGTGGT
* *
837 GGAGGAGGTGTTGGTGGTGG
1 GGAGGAGGAGTTGGCGGTGG
857 CGGTAGCTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.02, G:0.63, T:0.24
Consensus pattern (21 bp):
GGAGGAGGAGTTGGCGGTGGT
Done.