Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga05g01684.F1
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, 668
Length: 1114
ACGTcount: A:0.26, C:0.32, G:0.16, T:0.25
Found at i:231 original size:18 final size:18
Alignment explanation
Indices: 188--254 Score: 55
Period size: 18 Copynumber: 3.5 Consensus size: 18
178 GTCCCGCCTA
188 CTCACCCACCAACCCACCACC
1 CTCA-CCACC-ACCC-CCACC
* *
209 ATCACCACCACCCTCACC
1 CTCACCACCACCCCCACC
*
227 CTCACC-CTCACCCCCATC
1 CTCACCAC-CACCCCCACC
245 CTCATCCACC
1 CTCA-CCACC
255 CACTAAGCCC
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
17 1 0.03
18 21 0.55
19 7 0.18
20 6 0.16
21 3 0.08
ACGTcount: A:0.24, C:0.64, G:0.00, T:0.12
Consensus pattern (18 bp):
CTCACCACCACCCCCACC
Found at i:247 original size:12 final size:12
Alignment explanation
Indices: 199--248 Score: 55
Period size: 12 Copynumber: 4.1 Consensus size: 12
189 TCACCCACCA
*
199 ACCCACCACCATC
1 ACCC-CCACCCTC
*
212 ACCACCACCCTC
1 ACCCCCACCCTC
*
224 ACCCTCACCCTC
1 ACCCCCACCCTC
*
236 ACCCCCATCCTC
1 ACCCCCACCCTC
248 A
1 A
249 TCCACCCACT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
12 28 0.90
13 3 0.10
ACGTcount: A:0.24, C:0.64, G:0.00, T:0.12
Consensus pattern (12 bp):
ACCCCCACCCTC
Found at i:310 original size:24 final size:24
Alignment explanation
Indices: 283--381 Score: 117
Period size: 24 Copynumber: 4.1 Consensus size: 24
273 CACTCCTCCT
* * *
283 CCAGTTCATCCACCACCCAAGGCG
1 CCAGTTCAACCACCACCCAAGCCA
* *
307 CCAGTGCAACCACCAACCAAGCCA
1 CCAGTTCAACCACCACCCAAGCCA
*
331 CCAGTTCACCCACCACCCAAGCCA
1 CCAGTTCAACCACCACCCAAGCCA
* * *
355 CCAGTTCAACCTCCAACTAAGCCA
1 CCAGTTCAACCACCACCCAAGCCA
379 CCA
1 CCA
382 ACCAAACCTC
Statistics
Matches: 63, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 63 1.00
ACGTcount: A:0.31, C:0.47, G:0.11, T:0.10
Consensus pattern (24 bp):
CCAGTTCAACCACCACCCAAGCCA
Found at i:335 original size:48 final size:48
Alignment explanation
Indices: 283--381 Score: 144
Period size: 48 Copynumber: 2.1 Consensus size: 48
273 CACTCCTCCT
* * *
283 CCAGTTCATCCACCACCCAAGGCGCCAGTGCAACCACCAACCAAGCCA
1 CCAGTTCACCCACCACCCAAGCCACCAGTGCAACCACCAACCAAGCCA
* * *
331 CCAGTTCACCCACCACCCAAGCCACCAGTTCAACCTCCAACTAAGCCA
1 CCAGTTCACCCACCACCCAAGCCACCAGTGCAACCACCAACCAAGCCA
379 CCA
1 CCA
382 ACCAAACCTC
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.31, C:0.47, G:0.11, T:0.10
Consensus pattern (48 bp):
CCAGTTCACCCACCACCCAAGCCACCAGTGCAACCACCAACCAAGCCA
Found at i:380 original size:36 final size:36
Alignment explanation
Indices: 340--419 Score: 97
Period size: 36 Copynumber: 2.2 Consensus size: 36
330 ACCAGTTCAC
* * ** *
340 CCACCACCCAAGCCACCAGTTCAACCTCCAACTAAG
1 CCACCAACCAAACCACCAACTCAACCCCCAACTAAG
* *
376 CCACCAACCAAACCTCCAACTCAACCCCCGACTAAG
1 CCACCAACCAAACCACCAACTCAACCCCCAACTAAG
412 CCACCAAC
1 CCACCAAC
420 TCAGCCCCCG
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.35, C:0.50, G:0.06, T:0.09
Consensus pattern (36 bp):
CCACCAACCAAACCACCAACTCAACCCCCAACTAAG
Found at i:385 original size:60 final size:60
Alignment explanation
Indices: 316--479 Score: 179
Period size: 60 Copynumber: 2.7 Consensus size: 60
306 GCCAGTGCAA
** ** *
316 CCACCAACCAAGCCACCAGTTC-ACCCACC-ACCCAAGCCACCAGTTCAACCTCCAACTAAG
1 CCACCAACCAAGCCACCAACTCAACCC-CCGA-CCAAGCCACCAACTCAACCCCCAACTAAG
* * * * *
376 CCACCAACCAAACCTCCAACTCAACCCCCGACTAAGCCACCAACTCAGCCCCCGACTAAG
1 CCACCAACCAAGCCACCAACTCAACCCCCGACCAAGCCACCAACTCAACCCCCAACTAAG
* * *
436 CCACCAACCAAGCCTCCAACTCAGCCCCCGACGAAGCCACCAAC
1 CCACCAACCAAGCCACCAACTCAACCCCCGACCAAGCCACCAAC
480 ACACCCACCA
Statistics
Matches: 89, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
60 84 0.94
61 5 0.06
ACGTcount: A:0.33, C:0.50, G:0.09, T:0.08
Consensus pattern (60 bp):
CCACCAACCAAGCCACCAACTCAACCCCCGACCAAGCCACCAACTCAACCCCCAACTAAG
Found at i:449 original size:24 final size:25
Alignment explanation
Indices: 391--449 Score: 97
Period size: 24 Copynumber: 2.5 Consensus size: 25
381 AACCAAACCT
391 CCAACTCAA-CCCCCGACTAAGCCA
1 CCAACTCAAGCCCCCGACTAAGCCA
415 CCAACTC-AGCCCCCGACTAAGCCA
1 CCAACTCAAGCCCCCGACTAAGCCA
439 CCAAC-CAAGCC
1 CCAACTCAAGCC
450 TCCAACTCAG
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
23 2 0.06
24 31 0.94
ACGTcount: A:0.32, C:0.51, G:0.10, T:0.07
Consensus pattern (25 bp):
CCAACTCAAGCCCCCGACTAAGCCA
Found at i:449 original size:36 final size:36
Alignment explanation
Indices: 409--479 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
399 ACCCCCGACT
*
409 AAGCCACCAACTCAGCCCCCGACTAAGCCACCAACC
1 AAGCCACCAACTCAGCCCCCGACGAAGCCACCAACC
*
445 AAGCCTCCAACTCAGCCCCCGACGAAGCCACCAAC
1 AAGCCACCAACTCAGCCCCCGACGAAGCCACCAAC
480 ACACCCACCA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.32, C:0.49, G:0.13, T:0.06
Consensus pattern (36 bp):
AAGCCACCAACTCAGCCCCCGACGAAGCCACCAACC
Found at i:461 original size:24 final size:24
Alignment explanation
Indices: 316--489 Score: 93
Period size: 24 Copynumber: 7.2 Consensus size: 24
306 GCCAGTGCAA
** *
316 CCACCAACCAAGCCACCAGTTCAC
1 CCACCAACCAAGCCACCAACTCAG
* ** *
340 CCACCACCCAAGCCACCAGTTCAA
1 CCACCAACCAAGCCACCAACTCAG
* * *
364 CCTCCAACTAAGCCACCAAC-CAAA
1 CCACCAACCAAGCCACCAACTC-AG
* * * *
388 CCTCCAACTCAA-CCCCCGACTAAG
1 CCACCAAC-CAAGCCACCAACTCAG
* * *
412 CCACCAACTC-AGCCCCCGACTAAG
1 CCACCAAC-CAAGCCACCAACTCAG
*
436 CCACCAACCAAGCCTCCAACTCAG
1 CCACCAACCAAGCCACCAACTCAG
* * * * *
460 CCCCCGACGAAGCCACCAACACAC
1 CCACCAACCAAGCCACCAACTCAG
484 CCACCA
1 CCACCA
490 TCTCATCCTC
Statistics
Matches: 121, Mismatches: 24, Indels: 10
0.78 0.15 0.06
Matches are distributed among these distances:
23 3 0.02
24 116 0.96
25 2 0.02
ACGTcount: A:0.33, C:0.51, G:0.09, T:0.07
Consensus pattern (24 bp):
CCACCAACCAAGCCACCAACTCAG
Done.