Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga05g03436.P1
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: 13290
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:2852 original size:30 final size:31
Alignment explanation
Indices: 2802--2862 Score: 115
Period size: 30 Copynumber: 2.0 Consensus size: 31
2792 GGTATGTGTA
2802 AGTTTAGGAGAGGAAAAAAAATATTTCTCTG
1 AGTTTAGGAGAGGAAAAAAAATATTTCTCTG
2833 AGTTTAGGAGAGG-AAAAAAATATTTCTCTG
1 AGTTTAGGAGAGGAAAAAAAATATTTCTCTG
2863 TATTGAATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 17 0.57
31 13 0.43
ACGTcount: A:0.41, C:0.07, G:0.23, T:0.30
Consensus pattern (31 bp):
AGTTTAGGAGAGGAAAAAAAATATTTCTCTG
Found at i:4274 original size:84 final size:85
Alignment explanation
Indices: 4125--4343 Score: 379
Period size: 84 Copynumber: 2.6 Consensus size: 85
4115 GAACCACACT
* * * *
4125 GTTTAGGAAAGCATTCTTTACA-CTTAACTACTGGAGAGACCAATCCAAGTGATAGGTCCATATA
1 GTTTAGGAAAGCATTCTTTACATC-CAAATGCTGGAGAGGCCAATCCAAGTGATAGGTCCATATA
4189 AACTTCCTCTAGTAGATTGTA
65 AACTTCCTCTAGTAGATTGTA
4210 GTTTAGG-AAGCATTCTTTACATCCAAATGCTGGAGAGGCCAATCCAAGTGATAGGTCCATATAA
1 GTTTAGGAAAGCATTCTTTACATCCAAATGCTGGAGAGGCCAATCCAAGTGATAGGTCCATATAA
4274 ACTTCCTCTAGTAGATTGTA
66 ACTTCCTCTAGTAGATTGTA
4294 GTTTAGGAAAGCATTCTTTACATCCAAATGCTGGAGAGGCCAATCCAAGT
1 GTTTAGGAAAGCATTCTTTACATCCAAATGCTGGAGAGGCCAATCCAAGT
4344 AAGCTGTAAT
Statistics
Matches: 128, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
84 78 0.61
85 50 0.39
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (85 bp):
GTTTAGGAAAGCATTCTTTACATCCAAATGCTGGAGAGGCCAATCCAAGTGATAGGTCCATATAA
ACTTCCTCTAGTAGATTGTA
Found at i:4587 original size:42 final size:42
Alignment explanation
Indices: 4528--4616 Score: 151
Period size: 42 Copynumber: 2.1 Consensus size: 42
4518 TCCTAATTGG
* *
4528 GAAAATAGTTCCCTTATTCTAATAAACTACTAAAATATAAAA
1 GAAAATAATTCCCTTATTCTAATAAACTACTAAAAGATAAAA
4570 GAAAATAATTCCCTTATTCTAATAAACTACTAAAAGATAAAA
1 GAAAATAATTCCCTTATTCTAATAAACTACTAAAAGATAAAA
*
4612 TAAAA
1 GAAAA
4617 ATACTCCTAG
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.53, C:0.13, G:0.04, T:0.29
Consensus pattern (42 bp):
GAAAATAATTCCCTTATTCTAATAAACTACTAAAAGATAAAA
Found at i:4663 original size:19 final size:18
Alignment explanation
Indices: 4641--4680 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
4631 TGAATAAAAC
4641 TTATCTACCTAA-ATAAGAT
1 TTATCTACC-AATATAA-AT
4660 TTATCTACCAATATAAAT
1 TTATCTACCAATATAAAT
4678 TTA
1 TTA
4681 AAATATATAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.42, C:0.15, G:0.03, T:0.40
Consensus pattern (18 bp):
TTATCTACCAATATAAAT
Found at i:8524 original size:42 final size:42
Alignment explanation
Indices: 8477--8565 Score: 151
Period size: 42 Copynumber: 2.1 Consensus size: 42
8467 TCCTAATTTG
*
8477 GAAAATAGTTCACTTATTCTAATAAACTACTAAAATATAAAA
1 GAAAATAGTTCACTTATTCTAATAAACTACTAAAAGATAAAA
*
8519 GAAAATAGTTCCCTTATTCTAATAAACTACTAAAAGATAAAA
1 GAAAATAGTTCACTTATTCTAATAAACTACTAAAAGATAAAA
*
8561 TAAAA
1 GAAAA
8566 ATATTCCTAG
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.53, C:0.12, G:0.06, T:0.29
Consensus pattern (42 bp):
GAAAATAGTTCACTTATTCTAATAAACTACTAAAAGATAAAA
Found at i:8586 original size:43 final size:42
Alignment explanation
Indices: 8478--8587 Score: 98
Period size: 42 Copynumber: 2.6 Consensus size: 42
8468 CCTAATTTGG
* * * * * *
8478 AAAATAGTTCACTTATTCTAATAAACTACTAAAATATAAAAG
1 AAAATAGTTCCCTGAATATAATAAACTACTAAAAGATAAAAA
* * *
8520 AAAATAGTTCCCTTATTCTAATAAACTACTAAAAGATAAAATA
1 AAAATAGTTCCCTGAATATAATAAACTACTAAAAGATAAAA-A
8563 AAAATA-TT-CCTAGAATATGAATAAA
1 AAAATAGTTCCCT-GAATAT-AATAAA
8588 ACTTATCTAC
Statistics
Matches: 59, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
41 3 0.05
42 44 0.75
43 12 0.20
ACGTcount: A:0.53, C:0.12, G:0.05, T:0.30
Consensus pattern (42 bp):
AAAATAGTTCCCTGAATATAATAAACTACTAAAAGATAAAAA
Found at i:8612 original size:19 final size:18
Alignment explanation
Indices: 8590--8629 Score: 71
Period size: 19 Copynumber: 2.2 Consensus size: 18
8580 TGAATAAAAC
8590 TTATCTACCTAAATAAGAT
1 TTATCTACCTAAATAA-AT
8609 TTATCTACCTAAATAAAT
1 TTATCTACCTAAATAAAT
8627 TTA
1 TTA
8630 AAATATATAC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.42, C:0.15, G:0.03, T:0.40
Consensus pattern (18 bp):
TTATCTACCTAAATAAAT
Done.