Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga12g01473.M2
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: 4699
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.32
Found at i:1457 original size:31 final size:30
Alignment explanation
Indices: 1412--1517 Score: 123
Period size: 29 Copynumber: 3.6 Consensus size: 30
1402 GACCTAAGTA
*
1412 TAAATAT-AGAAAAG-TTTGTGGCATAAATTG
1 TAAATATGCGAAAAGTTTTGTGGCAT-AA-TG
1442 TAAATATGCGAAAAGTTTTGTGGCATAA-G
1 TAAATATGCGAAAAGTTTTGTGGCATAATG
*
1471 TAAATATGCGAAAAGTTTTGTGTG-ATAAGTA
1 TAAATATGCGAAAAGTTTTGTG-GCATAA-TG
1502 TAAATATG-GAAAAGTT
1 TAAATATGCGAAAAGTT
1518 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:3159 original size:46 final size:46
Alignment explanation
Indices: 3106--3374 Score: 300
Period size: 46 Copynumber: 5.8 Consensus size: 46
3096 TATTTGGGCA
3106 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
*** * *
3152 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA--
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAATG
*
3199 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
** * *
3245 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGATATGTAACTAG-GCA--
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAATG
*
3292 TCCGATCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
*
3338 -CCTGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCC-GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
3375 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:3221 original size:47 final size:47
Alignment explanation
Indices: 3102--3320 Score: 229
Period size: 47 Copynumber: 4.7 Consensus size: 47
3092 AGGATATTTG
** *
3102 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGATATGTAACTA
* *
3145 GCGAATGTCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTA
1 G-GCA--TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGATATGTAACTA
* ** *
3195 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGATATGTAACTA
*
3238 GCGAATGTCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGATATGTAACTA
1 G-GCA--TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGATATGTAACTA
*
3288 GGCATCCGATCTCGTTGAGTTGAGTCCGAGTTC
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTC
3321 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:3261 original size:93 final size:93
Alignment explanation
Indices: 3102--3366 Score: 478
Period size: 93 Copynumber: 2.8 Consensus size: 93
3092 AGGATATTTG
3102 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
3167 TTGAGTCCGAGTTCGAGAGATGTAACTA
66 TTGAGTCCGAGTTCGAGAGATGTAACTA
*
3195 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
*
3260 TTGAGTCCGAGTTCGAGATATGTAACTA
66 TTGAGTCCGAGTTCGAGAGATGTAACTA
* *
3288 GGCATCCGATCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG-CCTGAGCTCGTTGA
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCC-GAACTCGTTGA
3352 GTTGAGTCCGAGTTC
65 GTTGAGTCCGAGTTC
3367 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.