Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga13g01882.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, 582
Length: 971
ACGTcount: A:0.46, C:0.13, G:0.25, T:0.16
Found at i:151 original size:6 final size:6
Alignment explanation
Indices: 140--221 Score: 69
Period size: 6 Copynumber: 13.2 Consensus size: 6
130 AAGGGAGACG
* *
140 AAGAGA AAGAGA AAGAGA AAGA-A AAGAAA AAGA-A GAAGAAGA AAGACA
1 AAGAGA AAGAGA AAGAGA AAGAGA AAGAGA AAGAGA -AAG-AGA AAGAGA
* *
188 AAGATGGGA AAGAGA AAGAGA AAAAGA AAAAGA A
1 AAGA---GA AAGAGA AAGAGA AAGAGA AAGAGA A
222 GAAAAAGGAT
Statistics
Matches: 66, Mismatches: 3, Indels: 14
0.80 0.04 0.17
Matches are distributed among these distances:
5 6 0.09
6 50 0.76
7 4 0.06
8 1 0.02
9 5 0.08
ACGTcount: A:0.70, C:0.01, G:0.28, T:0.01
Consensus pattern (6 bp):
AAGAGA
Found at i:165 original size:48 final size:48
Alignment explanation
Indices: 52--165 Score: 149
Period size: 48 Copynumber: 2.4 Consensus size: 48
42 CAAAGAAGAG
* * *
52 GAGAAGGAGAAGGAGAAGGATAAAGAGGTTAAGGAAAAAGAAGAGAAG
1 GAGAAGGAGAAAGAAAAGGATAAAGAGGTTAAGGAAAAAGAAGAGAAA
* * *
100 GAGAAGGA-AAAGAAAAAGGATAAAGAGGTTAAGGGAGACGAAGAGAAA
1 GAGAAGGAGAAAG-AAAAGGATAAAGAGGTTAAGGAAAAAGAAGAGAAA
*
148 GAGAAAGAGAAAGAAAAG
1 GAGAAGGAGAAAGAAAAG
166 AAAAAGAAGA
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
47 3 0.05
48 50 0.88
49 4 0.07
ACGTcount: A:0.57, C:0.01, G:0.37, T:0.05
Consensus pattern (48 bp):
GAGAAGGAGAAAGAAAAGGATAAAGAGGTTAAGGAAAAAGAAGAGAAA
Found at i:336 original size:9 final size:9
Alignment explanation
Indices: 322--347 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
312 TTCTTCTTCC
322 TCATCGTCG
1 TCATCGTCG
331 TCATCGTCG
1 TCATCGTCG
340 TCATCGTC
1 TCATCGTC
348 ATCTTCTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.12, C:0.35, G:0.19, T:0.35
Consensus pattern (9 bp):
TCATCGTCG
Found at i:364 original size:24 final size:24
Alignment explanation
Indices: 337--389 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
327 GTCGTCATCG
* *
337 TCGTCATCGTCATCTTCTTCTTCC
1 TCGTCATCATCATCATCTTCTTCC
* *
361 TCGTCATCATCTTCATCTTCTTCG
1 TCGTCATCATCATCATCTTCTTCC
385 TCGTC
1 TCGTC
390 TTCTGACTCG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.09, C:0.36, G:0.09, T:0.45
Consensus pattern (24 bp):
TCGTCATCATCATCATCTTCTTCC
Found at i:372 original size:21 final size:21
Alignment explanation
Indices: 346--386 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
336 GTCGTCATCG
*
346 TCATCTTCTTCTTCCTCGTCA
1 TCATCTTCATCTTCCTCGTCA
*
367 TCATCTTCATCTTCTTCGTC
1 TCATCTTCATCTTCCTCGTC
387 GTCTTCTGAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.10, C:0.37, G:0.05, T:0.49
Consensus pattern (21 bp):
TCATCTTCATCTTCCTCGTCA
Found at i:420 original size:6 final size:6
Alignment explanation
Indices: 409--443 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
399 GGATTCAGAT
409 AAGAAA AAG-AA AAGAAA AGAGAAA AAGAAA AAGAA
1 AAGAAA AAGAAA AAGAAA A-AGAAA AAGAAA AAGAA
444 GCAAGAGAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
5 5 0.19
6 16 0.59
7 6 0.22
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (6 bp):
AAGAAA
Found at i:498 original size:24 final size:24
Alignment explanation
Indices: 471--526 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
461 ATAAAGAGCT
*
471 GAAAGAAGATGA-ACACAAAGAGAA
1 GAAAGAAGACGAGACA-AAAGAGAA
*
495 GAAAGATGACGAGACAAAAGAGAA
1 GAAAGAAGACGAGACAAAAGAGAA
519 -AAAGAAGA
1 GAAAGAAGA
527 AAAAGAAGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 7 0.25
24 18 0.64
25 3 0.11
ACGTcount: A:0.62, C:0.07, G:0.27, T:0.04
Consensus pattern (24 bp):
GAAAGAAGACGAGACAAAAGAGAA
Done.