Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga10g01197.N1
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: 21805
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.33
Found at i:3309 original size:47 final size:47
Alignment explanation
Indices: 3231--3435 Score: 311
Period size: 47 Copynumber: 4.4 Consensus size: 47
3221 CCCTTCGGGA
* * * * *
3231 CTTATCACATTTATACACTTTTACATCCATCACATTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
*
3278 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
*
3325 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
* * *
3372 CTTATCACACATATGCACTTTCACATTCATCACATGGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
*
3419 TTTATCACATATATACA
1 CTTATCACATATATACA
3436 TATCACACAT
Statistics
Matches: 143, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 143 1.00
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
Found at i:3485 original size:48 final size:48
Alignment explanation
Indices: 3409--3592 Score: 323
Period size: 48 Copynumber: 3.8 Consensus size: 48
3399 CATCACATGG
* *
3409 GCCATTAGGCTTTATCACATATATACATATCACACATATATTTCACATTA
1 GCCATTCGGCTTTA-C-CACATATACATATCACACATATATTTCACATTA
3459 GCCATTCGGCTTTACCACATATACATATCACACATATATTTCACATTA
1 GCCATTCGGCTTTACCACATATACATATCACACATATATTTCACATTA
*
3507 GCCATTCGGCTTTACCACATATACATATCACACATATATTTCACATCA
1 GCCATTCGGCTTTACCACATATACATATCACACATATATTTCACATTA
3555 GCCATTCGGCTTTACCACATATACATATCACACATATA
1 GCCATTCGGCTTTACCACATATACATATCACACATATA
3593 CTTATTTATC
Statistics
Matches: 131, Mismatches: 3, Indels: 2
0.96 0.02 0.01
Matches are distributed among these distances:
48 117 0.89
49 1 0.01
50 13 0.10
ACGTcount: A:0.34, C:0.27, G:0.07, T:0.33
Consensus pattern (48 bp):
GCCATTCGGCTTTACCACATATACATATCACACATATATTTCACATTA
Found at i:3490 original size:94 final size:97
Alignment explanation
Indices: 3260--3586 Score: 340
Period size: 94 Copynumber: 3.4 Consensus size: 97
3250 TTTACATCCA
* * * *
3260 TCACATTGGCCACTCGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 TCACATTAGCCATTCGGCCTTATCACACATATACACTATCACATTCATCACATCGGCCATTAGGC
* *
3325 CTTATCACATATATACACT-T-TCACAT-TCA--
66 TTTATCACATATATACA-TATCACACATAT-ATT
* * * *
3354 TCACATTGGCCATTCGGCCTTATCACACATATGCACTTTCACATTCATCACATGGGCCATTAGGC
1 TCACATTAGCCATTCGGCCTTATCACACATATACACTATCACATTCATCACATCGGCCATTAGGC
3419 TTTATCACATATATACATATCACACATATATT
66 TTTATCACATATATACATATCACACATATATT
* **
3451 TCACATTAGCCATTCGGCTTTA-C-CACATATACA-TATCACACATAT-ATTTCACATTAGCCAT
1 TCACATTAGCCATTCGGCCTTATCACACATATACACTAT--CACAT-TCA--TCACATCGGCCAT
* *
3512 TCGGCTTTA-C-CACATATACATATCACACATATATT
61 TAGGCTTTATCACATATATACATATCACACATATATT
* *
3547 TCACATCAGCCATTCGGCTTTA-C-CACATATACA-TATCACA
1 TCACATTAGCCATTCGGCCTTATCACACATATACACTATCACA
3587 CATATACTTA
Statistics
Matches: 208, Mismatches: 15, Indels: 20
0.86 0.06 0.08
Matches are distributed among these distances:
93 1 0.00
94 84 0.40
95 15 0.07
96 67 0.32
97 22 0.11
98 19 0.09
ACGTcount: A:0.31, C:0.29, G:0.08, T:0.32
Consensus pattern (97 bp):
TCACATTAGCCATTCGGCCTTATCACACATATACACTATCACATTCATCACATCGGCCATTAGGC
TTTATCACATATATACATATCACACATATATT
Found at i:3490 original size:141 final size:141
Alignment explanation
Indices: 3231--3490 Score: 296
Period size: 141 Copynumber: 1.8 Consensus size: 141
3221 CCCTTCGGGA
** * * *
3231 CTTATCACATTTATACACTTTTACATCCATCACATTGGCCACTCGGCCTTATCACATATATACAC
1 CTTATCACACATATACACTTTCACATCCATCACATGGGCCACTAGGCCTTATCACATATATACAC
* * * *
3296 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATT
66 TTACACATTCATCACATCAGCCATTAGGCCTTATCACACATATACACTATCACATTCATCACATT
3361 GGCCATTCGGC
131 GGCCATTCGGC
* * * *
3372 CTTATCACACATATGCACTTTCACATTCATCACATGGGCCATTAGGCTTTATCACATATATACA-
1 CTTATCACACATATACACTTTCACATCCATCACATGGGCCACTAGGCCTTATCACATATATACAC
* * *
3436 TATCACACATAT-ATTTCACATTAGCCATTCGGCTTTA-C-CACATATACA-TATCACA
66 T-T-ACACAT-TCA--TCACATCAGCCATTAGGCCTTATCACACATATACACTATCACA
3491 CATATATTTC
Statistics
Matches: 98, Mismatches: 16, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
140 1 0.01
141 62 0.63
142 15 0.15
143 2 0.02
144 18 0.18
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.33
Consensus pattern (141 bp):
CTTATCACACATATACACTTTCACATCCATCACATGGGCCACTAGGCCTTATCACATATATACAC
TTACACATTCATCACATCAGCCATTAGGCCTTATCACACATATACACTATCACATTCATCACATT
GGCCATTCGGC
Found at i:10324 original size:28 final size:28
Alignment explanation
Indices: 10284--10367 Score: 159
Period size: 28 Copynumber: 3.0 Consensus size: 28
10274 ACCATAGGCC
10284 CATGTGTGACATATAGTCGTATGGCTAA
1 CATGTGTGACATATAGTCGTATGGCTAA
10312 CATGTGTGACATATAGTCGTATGGCTAA
1 CATGTGTGACATATAGTCGTATGGCTAA
*
10340 CATGTGTGACATATAGTCGTGTGGCTAA
1 CATGTGTGACATATAGTCGTATGGCTAA
10368 GCCATGTGGC
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 55 1.00
ACGTcount: A:0.27, C:0.14, G:0.26, T:0.32
Consensus pattern (28 bp):
CATGTGTGACATATAGTCGTATGGCTAA
Done.