Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga10g01422.F7
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: 4050
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.26
Found at i:59 original size:2 final size:2
Alignment explanation
Indices: 52--95 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
42 CCCACTCCTC
* *
52 CT CT CT CT AT CT CT CT GT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
94 CT
1 CT
96 TTCATTTTTC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.02, C:0.45, G:0.02, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1945 original size:33 final size:33
Alignment explanation
Indices: 1907--2231 Score: 217
Period size: 33 Copynumber: 9.8 Consensus size: 33
1897 ACCAACCCGC
* * *
1907 GCAGCCAAGTGCGAATCCATATGGCCAGCTTGC
1 GCAGCCAAGTGCTAATCCATATGGCCAGCATGA
* * ** *
1940 TCAGCCCAGTGCTAATCCATATGGCCAAAATGG
1 GCAGCCAAGTGCTAATCCATATGGCCAGCATGA
* * *
1973 GCAACCAAGTGCTAATCCCTATGGCCAGCCTGA
1 GCAGCCAAGTGCTAATCCATATGGCCAGCATGA
** *
2006 GCAGCCCAA-TGCTAATCCATATGGCCAAAATGG
1 GCAG-CCAAGTGCTAATCCATATGGCCAGCATGA
* * * *
2039 GCAACCAAGTGCTAATCCCTATGGCCAGCCTGT
1 GCAGCCAAGTGCTAATCCATATGGCCAGCATGA
* * * ** *
2072 GCAGCCCAGTACTAACCCATATGGCCAAAATGG
1 GCAGCCAAGTGCTAATCCATATGGCCAGCATGA
* * *
2105 GCA-CTCAAGTGCTAATCCCTATGGCCAGCCTGT
1 GCAGC-CAAGTGCTAATCCATATGGCCAGCATGA
* * ** ** * *
2138 GCAGCCCAGTGCTAACCCATACAGCCAAAACGG
1 GCAGCCAAGTGCTAATCCATATGGCCAGCATGA
* * *
2171 GCAGCCAAGTGCTAATCTC-TATGGCCTGCCTGC
1 GCAGCCAAGTGCTAATC-CATATGGCCAGCATGA
* * *
2204 GCCA-CCCAGTGCAAACCCATATGGCCAG
1 G-CAGCCAAGTGCTAATCCATATGGCCAG
2232 TCAAGTGCTA
Statistics
Matches: 217, Mismatches: 68, Indels: 14
0.73 0.23 0.05
Matches are distributed among these distances:
32 6 0.03
33 203 0.94
34 8 0.04
ACGTcount: A:0.27, C:0.32, G:0.22, T:0.18
Consensus pattern (33 bp):
GCAGCCAAGTGCTAATCCATATGGCCAGCATGA
Found at i:1996 original size:66 final size:65
Alignment explanation
Indices: 1911--2230 Score: 419
Period size: 66 Copynumber: 4.8 Consensus size: 65
1901 ACCCGCGCAG
* * * *
1911 CCAAGTGCGAATCCATATGGCCAGCTTGCTCAGCCCAGTGCTAATCCATATGGCCAAAATGGGCA
1 CCAAGTGCTAATCCCTATGGCCAGCCTG-TCAGCCCAGTGCTAACCCATATGGCCAAAATGGGCA
1976 A
65 A
* * *
1977 CCAAGTGCTAATCCCTATGGCCAGCCTGAGCAGCCCAATGCTAATCCATATGGCCAAAATGGGCA
1 CCAAGTGCTAATCCCTATGGCCAGCCTG-TCAGCCCAGTGCTAACCCATATGGCCAAAATGGGCA
2042 A
65 A
*
2043 CCAAGTGCTAATCCCTATGGCCAGCCTGTGCAGCCCAGTACTAACCCATATGGCCAAAATGGGC-
1 CCAAGTGCTAATCCCTATGGCCAGCCTGT-CAGCCCAGTGCTAACCCATATGGCCAAAATGGGCA
2107 A
65 A
** *
2108 CTCAAGTGCTAATCCCTATGGCCAGCCTGTGCAGCCCAGTGCTAACCCATACAGCCAAAACGGGC
1 C-CAAGTGCTAATCCCTATGGCCAGCCTGT-CAGCCCAGTGCTAACCCATATGGCCAAAATGGGC
*
2173 AG
64 AA
* * * *
2175 CCAAGTGCTAATCTCTATGGCCTGCCTGCGCCA-CCCAGTGCAAACCCATATGGCCA
1 CCAAGTGCTAATCCCTATGGCCAGCCT--GTCAGCCCAGTGCTAACCCATATGGCCA
2231 GTCAAGTGCT
Statistics
Matches: 228, Mismatches: 21, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
65 2 0.01
66 222 0.97
67 3 0.01
68 1 0.00
ACGTcount: A:0.28, C:0.33, G:0.22, T:0.18
Consensus pattern (65 bp):
CCAAGTGCTAATCCCTATGGCCAGCCTGTCAGCCCAGTGCTAACCCATATGGCCAAAATGGGCAA
Found at i:2297 original size:33 final size:33
Alignment explanation
Indices: 2237--2344 Score: 117
Period size: 33 Copynumber: 3.3 Consensus size: 33
2227 GCCAGTCAAG
* * * * *
2237 TGCTAATCCCTATGGCCAGCCAACACAACCAAA
1 TGCTAATCCGTATAGTCAACCAGCACAACCAAA
* * * * *
2270 TGCTGATCCTTATGGTCAATCTGCACAACCAAA
1 TGCTAATCCGTATAGTCAACCAGCACAACCAAA
*
2303 TGCTAATCCGTATAGTCAACCAGCACAAGCAAA
1 TGCTAATCCGTATAGTCAACCAGCACAACCAAA
2336 TGCTAATCC
1 TGCTAATCC
2345 ATACAGCCAA
Statistics
Matches: 62, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 62 1.00
ACGTcount: A:0.34, C:0.31, G:0.14, T:0.21
Consensus pattern (33 bp):
TGCTAATCCGTATAGTCAACCAGCACAACCAAA
Found at i:2356 original size:33 final size:33
Alignment explanation
Indices: 2290--2512 Score: 207
Period size: 33 Copynumber: 6.8 Consensus size: 33
2280 TATGGTCAAT
* * * *
2290 CTGCACAACCAAATGCTAATCCGTATAGTCAAC
1 CTGCACAGCCAAATGCTAATCCATACAGCCAAC
*
2323 CAGCACAAG-CAAATGCTAATCCATACAGCCAAC
1 CTGCAC-AGCCAAATGCTAATCCATACAGCCAAC
* ** * *
2356 CTGTACAGGTACATGCTAATCCATA-TGACCAAC
1 CTGCACAGCCAAATGCTAATCCATACAG-CCAAC
* * *
2389 CTGCTCAGCCAAGTGCTAATCCATACAACCAAC
1 CTGCACAGCCAAATGCTAATCCATACAGCCAAC
* * *
2422 CTGCTCAGCCGAATGCTAATCCATACAGCCAGC
1 CTGCACAGCCAAATGCTAATCCATACAGCCAAC
* * **
2455 CTACACAGCCTAATGCTAATCCATATGGCCAAC
1 CTGCACAGCCAAATGCTAATCCATACAGCCAAC
** *
2488 CTGTTCAGCCAAGTGCTAATCCATA
1 CTGCACAGCCAAATGCTAATCCATA
2513 TGCCCAACCC
Statistics
Matches: 153, Mismatches: 33, Indels: 8
0.79 0.17 0.04
Matches are distributed among these distances:
32 3 0.02
33 149 0.97
34 1 0.01
ACGTcount: A:0.34, C:0.32, G:0.14, T:0.20
Consensus pattern (33 bp):
CTGCACAGCCAAATGCTAATCCATACAGCCAAC
Found at i:2521 original size:99 final size:99
Alignment explanation
Indices: 2334--2512 Score: 288
Period size: 99 Copynumber: 1.8 Consensus size: 99
2324 AGCACAAGCA
** *
2334 AATGCTAATCCATACAGCCAACCTGTACAGGTACATGCTAATCCATATGACCAACCTGCTCAGCC
1 AATGCTAATCCATACAGCCAACCTACACAGCTACATGCTAATCCATATGACCAACCTGCTCAGCC
2399 AAGTGCTAATCCATACAACCAACCTGCTCAGCCG
66 AAGTGCTAATCCATACAACCAACCTGCTCAGCCG
* * *
2433 AATGCTAATCCATACAGCCAGCCTACACAGCCTA-ATGCTAATCCATATGGCCAACCTGTTCAGC
1 AATGCTAATCCATACAGCCAACCTACACAG-CTACATGCTAATCCATATGACCAACCTGCTCAGC
2497 CAAGTGCTAATCCATA
65 CAAGTGCTAATCCATA
2513 TGCCCAACCC
Statistics
Matches: 73, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
99 71 0.97
100 2 0.03
ACGTcount: A:0.32, C:0.32, G:0.14, T:0.21
Consensus pattern (99 bp):
AATGCTAATCCATACAGCCAACCTACACAGCTACATGCTAATCCATATGACCAACCTGCTCAGCC
AAGTGCTAATCCATACAACCAACCTGCTCAGCCG
Found at i:3269 original size:18 final size:17
Alignment explanation
Indices: 3248--3539 Score: 93
Period size: 18 Copynumber: 17.8 Consensus size: 17
3238 TGGGGATGAA
3248 CATGGGCATGAACCCAGG
1 CATGGGCATGAA-CCAGG
* *
3266 CATGGGGATGAA-CA-A
1 CATGGGCATGAACCAGG
3281 CATGGGCATGAATCCAGG
1 CATGGGCATGAA-CCAGG
* * *
3299 CATGGGGATG-AGCA-A
1 CATGGGCATGAACCAGG
* *
3314 TATGGGCATAAATCCAGG
1 CATGGGCATGAA-CCAGG
* * *
3332 CATGGGGATG-AGCA-A
1 CATGGGCATGAACCAGG
*
3347 TATGGGCATGAATCCAGG
1 CATGGGCATGAA-CCAGG
* * *
3365 CATGGGGATG-AGCA-A
1 CATGGGCATGAACCAGG
*
3380 TATGGGCATGAATCCAGG
1 CATGGGCATGAA-CCAGG
* ** *
3398 CATGGGGATG-AGTA-A
1 CATGGGCATGAACCAGG
* **
3413 TATGGGCATGAATAAAGG
1 CATGGGCATGAA-CCAGG
*
3431 CATGGGGATG-A--A--
1 CATGGGCATGAACCAGG
3443 CATGGGCATGAATCCAGG
1 CATGGGCATGAA-CCAGG
* *
3461 CATGGGGATGAA-CA-A
1 CATGGGCATGAACCAGG
3476 CATGGGCATGAATCCAGG
1 CATGGGCATGAA-CCAGG
*
3494 CATGGAG-ATGAA-CA-A
1 CATGG-GCATGAACCAGG
* *
3509 TATGGGCATGAGCGCAGG
1 CATGGGCATGAAC-CAGG
*
3527 CATGGGGATGAAC
1 CATGGGCATGAAC
3540 ATGGGAATGG
Statistics
Matches: 192, Mismatches: 53, Indels: 58
0.63 0.17 0.19
Matches are distributed among these distances:
12 9 0.05
13 1 0.01
14 2 0.01
15 61 0.32
16 18 0.09
17 18 0.09
18 82 0.43
19 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.35, T:0.17
Consensus pattern (17 bp):
CATGGGCATGAACCAGG
Found at i:3288 original size:33 final size:33
Alignment explanation
Indices: 3237--3540 Score: 433
Period size: 33 Copynumber: 9.4 Consensus size: 33
3227 GGGCATGGGA
*
3237 ATGGGGATGAAC---ATGGGCATGAACCCAGGC
1 ATGGGGATGAACAATATGGGCATGAATCCAGGC
*
3267 ATGGGGATGAACAACATGGGCATGAATCCAGGC
1 ATGGGGATGAACAATATGGGCATGAATCCAGGC
* *
3300 ATGGGGATGAGCAATATGGGCATAAATCCAGGC
1 ATGGGGATGAACAATATGGGCATGAATCCAGGC
*
3333 ATGGGGATGAGCAATATGGGCATGAATCCAGGC
1 ATGGGGATGAACAATATGGGCATGAATCCAGGC
*
3366 ATGGGGATGAGCAATATGGGCATGAATCCAGGC
1 ATGGGGATGAACAATATGGGCATGAATCCAGGC
** **
3399 ATGGGGATGAGTAATATGGGCATGAATAAAGGC
1 ATGGGGATGAACAATATGGGCATGAATCCAGGC
3432 ATGGGGATGAAC---ATGGGCATGAATCCAGGC
1 ATGGGGATGAACAATATGGGCATGAATCCAGGC
*
3462 ATGGGGATGAACAACATGGGCATGAATCCAGGC
1 ATGGGGATGAACAATATGGGCATGAATCCAGGC
* *
3495 ATGGAGATGAACAATATGGGCATG-AGCGCAGGC
1 ATGGGGATGAACAATATGGGCATGAATC-CAGGC
3528 ATGGGGATGAACA
1 ATGGGGATGAACA
3541 TGGGAATGGG
Statistics
Matches: 251, Mismatches: 16, Indels: 11
0.90 0.06 0.04
Matches are distributed among these distances:
30 40 0.16
32 2 0.01
33 209 0.83
ACGTcount: A:0.33, C:0.15, G:0.36, T:0.17
Consensus pattern (33 bp):
ATGGGGATGAACAATATGGGCATGAATCCAGGC
Done.