Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga12g01473.M1
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: 4615
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.32
Found at i:1373 original size:31 final size:30
Alignment explanation
Indices: 1328--1433 Score: 123
Period size: 29 Copynumber: 3.6 Consensus size: 30
1318 GACCTAAGTA
*
1328 TAAATAT-AGAAAAG-TTTGTGGCATAAATTG
1 TAAATATGCGAAAAGTTTTGTGGCAT-AA-TG
1358 TAAATATGCGAAAAGTTTTGTGGCATAA-G
1 TAAATATGCGAAAAGTTTTGTGGCATAATG
*
1387 TAAATATGCGAAAAGTTTTGTGTG-ATAAGTA
1 TAAATATGCGAAAAGTTTTGTG-GCATAA-TG
1418 TAAATATG-GAAAAGTT
1 TAAATATGCGAAAAGTT
1434 GAAGTGAAAG
Statistics
Matches: 69, Mismatches: 2, Indels: 10
0.85 0.02 0.12
Matches are distributed among these distances:
29 27 0.39
30 16 0.23
31 16 0.23
32 10 0.14
ACGTcount: A:0.42, C:0.04, G:0.22, T:0.33
Consensus pattern (30 bp):
TAAATATGCGAAAAGTTTTGTGGCATAATG
Found at i:3075 original size:46 final size:46
Alignment explanation
Indices: 3022--3290 Score: 300
Period size: 46 Copynumber: 5.8 Consensus size: 46
3012 TATTTGGGCA
3022 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
*** * *
3068 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA--
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAATG
*
3115 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
** * *
3161 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGATATGTAACTAG-GCA--
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAATG
*
3208 TCCGATCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
*
3254 -CCTGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCC-GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
3291 GCAGGTTACA
Statistics
Matches: 186, Mismatches: 22, Indels: 30
0.78 0.09 0.13
Matches are distributed among these distances:
43 2 0.01
44 6 0.03
45 4 0.02
46 99 0.53
47 65 0.35
48 2 0.01
49 6 0.03
50 2 0.01
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:3137 original size:47 final size:47
Alignment explanation
Indices: 3018--3236 Score: 229
Period size: 47 Copynumber: 4.7 Consensus size: 47
3008 AGGATATTTG
** *
3018 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGATATGTAACTA
* *
3061 GCGAATGTCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTA
1 G-GCA--TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGATATGTAACTA
* ** *
3111 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGATATGTAACTA
*
3154 GCGAATGTCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGATATGTAACTA
1 G-GCA--TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGATATGTAACTA
*
3204 GGCATCCGATCTCGTTGAGTTGAGTCCGAGTTC
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTC
3237 ACTTATGGAT
Statistics
Matches: 144, Mismatches: 18, Indels: 24
0.77 0.10 0.13
Matches are distributed among these distances:
43 2 0.01
44 5 0.03
45 1 0.01
46 61 0.42
47 65 0.45
48 2 0.01
49 6 0.04
50 2 0.01
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (47 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGATATGTAACTA
Found at i:3177 original size:93 final size:93
Alignment explanation
Indices: 3018--3282 Score: 478
Period size: 93 Copynumber: 2.8 Consensus size: 93
3008 AGGATATTTG
3018 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
3083 TTGAGTCCGAGTTCGAGAGATGTAACTA
66 TTGAGTCCGAGTTCGAGAGATGTAACTA
*
3111 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
*
3176 TTGAGTCCGAGTTCGAGATATGTAACTA
66 TTGAGTCCGAGTTCGAGAGATGTAACTA
* *
3204 GGCATCCGATCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG-CCTGAGCTCGTTGA
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCC-GAACTCGTTGA
3268 GTTGAGTCCGAGTTC
65 GTTGAGTCCGAGTTC
3283 ACTTATGGGC
Statistics
Matches: 167, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
92 2 0.01
93 165 0.99
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
TTGAGTCCGAGTTCGAGAGATGTAACTA
Done.