Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga04g00126.P3
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: 8147
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Found at i:2089 original size:41 final size:41
Alignment explanation
Indices: 2029--2357 Score: 410
Period size: 41 Copynumber: 8.0 Consensus size: 41
2019 TGTAAAACAT
** * * * *
2029 AGAGCAATAGTTGCGTTTTTGTTAACACGCCGCTAAAAAT-
1 AGAGCAATAGCGGCGCTTTTGGTAAAACGCCGCTAAAAGTC
* * * *
2069 AGAGTAATAGCGGCGTTTTTTGTTAAAACGTCGCTAAAAGTC
1 AGAGCAATAGCGGCG-CTTTTGGTAAAACGCCGCTAAAAGTC
*
2111 GGAGCAATAGCGGCGCTTTTGGTAAAACGCCGCTAAAAGTC
1 AGAGCAATAGCGGCGCTTTTGGTAAAACGCCGCTAAAAGTC
* * ** *
2152 GGAGCAATAGCGGCACTTCAGATAAAACGCCGCTAAAAGT-
1 AGAGCAATAGCGGCGCTTTTGGTAAAACGCCGCTAAAAGTC
* *
2192 AGGAGCAATAGCGGCGCTTTTGGTAAAATGCCACTAAAAGTC
1 A-GAGCAATAGCGGCGCTTTTGGTAAAACGCCGCTAAAAGTC
*
2234 GGAGCAATAGCGGCGCTTTTGGTAAAACGCCGCTAAAAGTC
1 AGAGCAATAGCGGCGCTTTTGGTAAAACGCCGCTAAAAGTC
* *
2275 AGAGCAATAGCGGCGTTTTTGGTAAAACGCCACTAAAAGTC
1 AGAGCAATAGCGGCGCTTTTGGTAAAACGCCGCTAAAAGTC
** *
2316 AGAGCAATAGCGGCGCTTTTAATAAAACGCCACTAAAAGTC
1 AGAGCAATAGCGGCGCTTTTGGTAAAACGCCGCTAAAAGTC
2357 A
1 A
2358 TATAACCCCT
Statistics
Matches: 254, Mismatches: 31, Indels: 7
0.87 0.11 0.02
Matches are distributed among these distances:
40 12 0.05
41 229 0.90
42 13 0.05
ACGTcount: A:0.33, C:0.20, G:0.25, T:0.22
Consensus pattern (41 bp):
AGAGCAATAGCGGCGCTTTTGGTAAAACGCCGCTAAAAGTC
Found at i:2450 original size:16 final size:17
Alignment explanation
Indices: 2424--2457 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
2414 CTAAAATACT
2424 AAACCCTTAAACCCTAA
1 AAACCCTTAAACCCTAA
2441 AAACCC-TAAACCCTAA
1 AAACCCTTAAACCCTAA
2457 A
1 A
2458 CTATAACTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.50, C:0.35, G:0.00, T:0.15
Consensus pattern (17 bp):
AAACCCTTAAACCCTAA
Found at i:2471 original size:53 final size:54
Alignment explanation
Indices: 2369--2482 Score: 131
Period size: 53 Copynumber: 2.1 Consensus size: 54
2359 ATAACCCCTA
* * * *
2369 AAACCCTTAAACCCTAAAAAAATCATGAACACTAATCTATAACCCCTAAAATACT
1 AAACCCTTAAACCCT-AAAAAACCATAAACACTAAACTATAACCCCTAAAACACT
* * ** *
2424 AAACCCTTAAACCCT-AAAAACCCTAAACCCTAAACTATAACTTCTAAAACCCT
1 AAACCCTTAAACCCTAAAAAACCATAAACACTAAACTATAACCCCTAAAACACT
2477 AAACCC
1 AAACCC
2483 CAAAAAACAT
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
53 35 0.70
55 15 0.30
ACGTcount: A:0.47, C:0.32, G:0.01, T:0.20
Consensus pattern (54 bp):
AAACCCTTAAACCCTAAAAAACCATAAACACTAAACTATAACCCCTAAAACACT
Found at i:3249 original size:7 final size:7
Alignment explanation
Indices: 3239--3318 Score: 74
Period size: 7 Copynumber: 11.3 Consensus size: 7
3229 CATTAAATCG
3239 AAATAAA
1 AAATAAA
3246 AAAT--A
1 AAATAAA
*
3251 AACTCAAA
1 AAAT-AAA
3259 AAATAAA
1 AAATAAA
*
3266 AATTAAA
1 AAATAAA
3273 AAATAAAA
1 AAAT-AAA
*
3281 AAATTAA
1 AAATAAA
* *
3288 AATTTAA
1 AAATAAA
3295 AAATAAA
1 AAATAAA
3302 AAATTAAA
1 AAA-TAAA
3310 AAATAAA
1 AAATAAA
3317 AA
1 AA
3319 CTTAAAAATT
Statistics
Matches: 60, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
5 4 0.07
7 38 0.63
8 18 0.30
ACGTcount: A:0.78, C:0.03, G:0.00, T:0.20
Consensus pattern (7 bp):
AAATAAA
Found at i:3259 original size:13 final size:13
Alignment explanation
Indices: 3239--3280 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
3229 CATTAAATCG
3239 AAAT-AAAAAATA
1 AAATCAAAAAATA
*
3251 AACTCAAAAAATAA
1 AAATCAAAAAAT-A
*
3265 AAATTAAAAAATA
1 AAATCAAAAAATA
3278 AAA
1 AAA
3281 AAATTAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
12 3 0.12
13 11 0.44
14 11 0.44
ACGTcount: A:0.79, C:0.05, G:0.00, T:0.17
Consensus pattern (13 bp):
AAATCAAAAAATA
Found at i:3273 original size:14 final size:15
Alignment explanation
Indices: 3256--3326 Score: 83
Period size: 15 Copynumber: 4.9 Consensus size: 15
3246 AAATAAACTC
*
3256 AAAAAA-TAAAAATT
1 AAAAAATTAAAAAAT
*
3270 AAAAAATAAAAAAAT
1 AAAAAATTAAAAAAT
* *
3285 -TAAAATTTAAAAAT
1 AAAAAATTAAAAAAT
3299 AAAAAATTAAAAAAT
1 AAAAAATTAAAAAAT
*
3314 AAAAACTTAAAAA
1 AAAAAATTAAAAA
3327 TTTAATATTT
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
14 17 0.36
15 30 0.64
ACGTcount: A:0.77, C:0.01, G:0.00, T:0.21
Consensus pattern (15 bp):
AAAAAATTAAAAAAT
Found at i:3274 original size:8 final size:8
Alignment explanation
Indices: 3263--3331 Score: 74
Period size: 8 Copynumber: 9.1 Consensus size: 8
3253 CTCAAAAAAT
3263 AAAAATTA
1 AAAAATTA
*
3271 AAAAATAA
1 AAAAATTA
3279 AAAAATT-
1 AAAAATTA
*
3286 -AAAATTT
1 AAAAATTA
3293 AAAAA-TA
1 AAAAATTA
3300 AAAAATTA
1 AAAAATTA
3308 AAAAA-TA
1 AAAAATTA
*
3315 AAAACTTA
1 AAAAATTA
*
3323 AAAATTTA
1 AAAAATTA
3331 A
1 A
3332 TATTTAATAT
Statistics
Matches: 52, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
6 6 0.12
7 12 0.23
8 34 0.65
ACGTcount: A:0.74, C:0.01, G:0.00, T:0.25
Consensus pattern (8 bp):
AAAAATTA
Found at i:3297 original size:37 final size:38
Alignment explanation
Indices: 3256--3331 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 38
3246 AAATAAACTC
3256 AAAAAAT-AAAAATTAAAAAATAAAAAAATT-AAAATTT
1 AAAAAATAAAAAATTAAAAAAT-AAAAAATTAAAAATTT
*
3293 -AAAAATAAAAAATTAAAAAATAAAAACTTAAAAATTT
1 AAAAAATAAAAAATTAAAAAATAAAAAATTAAAAATTT
3330 AA
1 AA
3332 TATTTAATAT
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
36 13 0.37
37 21 0.60
38 1 0.03
ACGTcount: A:0.75, C:0.01, G:0.00, T:0.24
Consensus pattern (38 bp):
AAAAAATAAAAAATTAAAAAATAAAAAATTAAAAATTT
Found at i:3327 original size:14 final size:14
Alignment explanation
Indices: 3239--3327 Score: 76
Period size: 14 Copynumber: 6.3 Consensus size: 14
3229 CATTAAATCG
3239 AAATAAAAAA-T-A
1 AAATAAAAAATTAA
*
3251 AACTCAAAAAA-TAA
1 AAAT-AAAAAATTAA
*
3265 AAATTAAAAAATAAAA
1 AAA-TAAAAAAT-TAA
* *
3281 AAATTAAAATTTAA
1 AAATAAAAAATTAA
3295 AAATAAAAAATTAAA
1 AAATAAAAAATT-AA
*
3310 AAATAAAAACTTAA
1 AAATAAAAAATTAA
3324 AAAT
1 AAAT
3328 TTAATATTTA
Statistics
Matches: 62, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
12 3 0.05
13 7 0.11
14 27 0.44
15 20 0.32
16 5 0.08
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.21
Consensus pattern (14 bp):
AAATAAAAAATTAA
Found at i:3423 original size:18 final size:16
Alignment explanation
Indices: 3402--3439 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 16
3392 TTCAAAAGAG
3402 AAAAATAAAAAATATGTT
1 AAAAATAAAAAA-AT-TT
3420 AAAAATAAAAAAATTT
1 AAAAATAAAAAAATTT
3436 AAAA
1 AAAA
3440 TTAATCAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 6 0.30
17 2 0.10
18 12 0.60
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (16 bp):
AAAAATAAAAAAATTT
Found at i:3424 original size:26 final size:25
Alignment explanation
Indices: 3377--3433 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
3367 TTCAATATTC
* * *
3377 AAAATTAAAAAAAATTTCAAAAGAG
1 AAAAATAAAAAAAATTTAAAAAGAA
* *
3402 AAAAATAAAAAATATGTTAAAAATAA
1 AAAAATAAAAAAAAT-TTAAAAAGAA
3428 AAAAAT
1 AAAAAT
3434 TTAAAATTAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
25 13 0.50
26 13 0.50
ACGTcount: A:0.72, C:0.02, G:0.05, T:0.21
Consensus pattern (25 bp):
AAAAATAAAAAAAATTTAAAAAGAA
Done.