Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga01g00120.M4
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: 8570
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.33
Found at i:2886 original size:78 final size:78
Alignment explanation
Indices: 2797--3031 Score: 380
Period size: 78 Copynumber: 3.0 Consensus size: 78
2787 GTCAGGCAGA
* **
2797 GCCAACTAGTGTGACTCAGAAAACCAATTTAACTCGTCCTAATGAAGCTACTGAGTCAGAGGGAC
1 GCCAACTAGTGTGACTCAGAAAACAAATTCGACTCGTCCTAATGAAGCTACTGAGTCAGAGGGAC
2862 CGGCTTTCTGGAC
66 CGGCTTTCTGGAC
*
2875 GCCAACTAGTGTGACTCAGAAAACAAATTCGACTCGTCCTAATGAAGCTATTGAGTCAGAGGGAC
1 GCCAACTAGTGTGACTCAGAAAACAAATTCGACTCGTCCTAATGAAGCTACTGAGTCAGAGGGAC
2940 CGGCTTTCTGGAC
66 CGGCTTTCTGGAC
* * * * *
2953 ACCAACTAGTGTGACTCAGAAAACAAATTCGGCTCGTCCTAATCAAGCTACTGAGTCGGAAGGAC
1 GCCAACTAGTGTGACTCAGAAAACAAATTCGACTCGTCCTAATGAAGCTACTGAGTCAGAGGGAC
*
3018 CAGCTTTCTGGAC
66 CGGCTTTCTGGAC
3031 G
1 G
3032 GCATGTCCGT
Statistics
Matches: 145, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
78 145 1.00
ACGTcount: A:0.30, C:0.24, G:0.23, T:0.23
Consensus pattern (78 bp):
GCCAACTAGTGTGACTCAGAAAACAAATTCGACTCGTCCTAATGAAGCTACTGAGTCAGAGGGAC
CGGCTTTCTGGAC
Found at i:4137 original size:192 final size:189
Alignment explanation
Indices: 3810--4185 Score: 515
Period size: 192 Copynumber: 2.0 Consensus size: 189
3800 AGTTTTTTGG
*
3810 AATTAAAAGATGTTAGGATTATTATTGTATAGCAAGGGTTTTACTTCAGGTTTTATTTTCACTGA
1 AATTAAAAGATGTTAGGATTATTATTGTATAGCAAGGGTTTTACTTCAGGTTTTATATTCACTGA
* * * *
3875 TATTCTGTCAATTTTGGGCTGGTATTGCAATTTGACTTGCCATTTTTGCTTGCATTGTGGTTTTA
66 TATTCTGTCAATTTCGAGCTGGTATTGCAATTTGAATTGCCACTTTTGCTTGCATTGTGGTTTTA
* **
3940 TTATTTGGGGTTGTGCCGTAGTTTAATTTCCATACCATAGTAAAAAGCTTCTTTATTGTAGC
131 TTATTT--AGTCATGCCGTAGTTTAATTTCCATACCATAGT-AAAAGCTTCTTTATTGTAGC
*
4002 AATTAAAAAGATGTT-GG-TTATTGTTGTATAGCAAGGGTTTTACTTCAGGTTTTTATATTCACT
1 AATT-AAAAGATGTTAGGATTATTATTGTATAGCAAGGGTTTTACTTCAGG-TTTTATATTCACT
* * * * *
4065 GATATTCTGTCTATTTCGATCTGGTATTGCATTTTGAATTGCTACTTTTGCTTG-TTTCGTGGTT
64 GATATTCTGTCAATTTCGAGCTGGTATTGCAATTTGAATTGCCACTTTTGCTTGCATT-GTGGTT
* ** *
4129 TTATTATTTAGTCATGCCGTAGTTTATTTTCCATTTCATAGTAGAAGCTTCTTTATT
128 TTATTATTTAGTCATGCCGTAGTTTAATTTCCATACCATAGTAAAAGCTTCTTTATT
4186 ATATATAATC
Statistics
Matches: 163, Mismatches: 18, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
189 14 0.09
190 27 0.17
191 33 0.20
192 79 0.48
193 10 0.06
ACGTcount: A:0.23, C:0.12, G:0.19, T:0.47
Consensus pattern (189 bp):
AATTAAAAGATGTTAGGATTATTATTGTATAGCAAGGGTTTTACTTCAGGTTTTATATTCACTGA
TATTCTGTCAATTTCGAGCTGGTATTGCAATTTGAATTGCCACTTTTGCTTGCATTGTGGTTTTA
TTATTTAGTCATGCCGTAGTTTAATTTCCATACCATAGTAAAAGCTTCTTTATTGTAGC
Found at i:5626 original size:31 final size:31
Alignment explanation
Indices: 5591--5662 Score: 92
Period size: 31 Copynumber: 2.3 Consensus size: 31
5581 TGCAAAATTT
* *
5591 TTATTGAGTTTTTTGAAAGTTTTCA-TTTAAA
1 TTATTGAGTTATTTGAAAGTTAT-ATTTTAAA
* *
5622 TTATTGAATTATTTGAAAGTTATATTTTAAG
1 TTATTGAGTTATTTGAAAGTTATATTTTAAA
5653 TTATTGAGTT
1 TTATTGAGTT
5663 GTTAAGTTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
30 1 0.03
31 34 0.97
ACGTcount: A:0.31, C:0.01, G:0.14, T:0.54
Consensus pattern (31 bp):
TTATTGAGTTATTTGAAAGTTATATTTTAAA
Found at i:6052 original size:41 final size:41
Alignment explanation
Indices: 6006--6131 Score: 185
Period size: 35 Copynumber: 3.2 Consensus size: 41
5996 ACTAAATCAT
*
6006 AATATCTCATATAATACACTTAGATTTGTATGCTTCTGATA
1 AATATCTCATATAATACACTTAGATTTGTATGCTTGTGATA
6047 AATATCTC-----ATA-ACTTAGATTTGTATGCTTGTGATA
1 AATATCTCATATAATACACTTAGATTTGTATGCTTGTGATA
*
6082 AATATCTCATATAATACACTTATATTTGTATGCTTGT-ATA
1 AATATCTCATATAATACACTTAGATTTGTATGCTTGTGATA
6122 AATATCTCAT
1 AATATCTCAT
6132 TTAGTAAGAA
Statistics
Matches: 77, Mismatches: 2, Indels: 13
0.84 0.02 0.14
Matches are distributed among these distances:
35 31 0.40
36 3 0.04
40 16 0.21
41 27 0.35
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.43
Consensus pattern (41 bp):
AATATCTCATATAATACACTTAGATTTGTATGCTTGTGATA
Done.