Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga05g03608.M2
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: 6514
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Found at i:3305 original size:162 final size:164
Alignment explanation
Indices: 3045--3351 Score: 356
Period size: 162 Copynumber: 1.9 Consensus size: 164
3035 GAGAGATGCA
*
3045 ATAATTTGAAATATATCTTCCCAATGTCAGTTGATAATAGCCTTATGCAATTACATACTTTGAAG
1 ATAATTTGAAATATATCTTCCCAATGTCAGTTGATAATAGCCTTAGGCAATTACATACTTTGAAG
* * * * *
3110 ATAAAGAGTTGCAGGAGCTTAGAAGGCATAATCCAATACTCACAAGTCCCATACATAAG-C-CTC
66 ATAAAGAGTTGCAGCAGATTAGAAGACATAATCCAAGACCCACAAGTCCCATACATAAGTCACTC
*
3173 CAAAGTTTAAGGGAAATAGAAGTTGAAAATTGCG
131 CAAAGTCTAAGGGAAATAGAAGTTGAAAATTGCG
* * * * * *
3207 ATAATTT-AAAGTATCTCTTTCCATTGTCGGTTGCA-AATAGCCTT-GGCCAATTGCATATTTTG
1 ATAATTTGAAA-TATATCTTCCCAATGTCAGTTG-ATAATAGCCTTAGG-CAATTACATACTTTG
* * * ** *
3269 AAGATAAAGAGTTGCTCGCA-ATTGGAAGATATAATCCAAGACCCACAAGTGGCATACATATGTC
63 AAGATAAAGAGTTGC-AGCAGATTAGAAGACATAATCCAAGACCCACAAGTCCCATACATAAGTC
3333 TACTCCAAAGTCTAAGGGA
127 -ACTCCAAAGTCTAAGGGA
3352 GGTTTCGTTG
Statistics
Matches: 119, Mismatches: 19, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
161 4 0.03
162 95 0.80
163 4 0.03
165 16 0.13
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.29
Consensus pattern (164 bp):
ATAATTTGAAATATATCTTCCCAATGTCAGTTGATAATAGCCTTAGGCAATTACATACTTTGAAG
ATAAAGAGTTGCAGCAGATTAGAAGACATAATCCAAGACCCACAAGTCCCATACATAAGTCACTC
CAAAGTCTAAGGGAAATAGAAGTTGAAAATTGCG
Found at i:3987 original size:162 final size:162
Alignment explanation
Indices: 3707--4377 Score: 1036
Period size: 162 Copynumber: 4.1 Consensus size: 162
3697 TGCGCCCAAT
* * *
3707 TTGCAAACTTTGAACATAGAGAGGTGCTTTGGAATGGAAGAAATAATCCAAGACTCACAAGTATC
1 TTGCAAACTCTGAAGATAGAGAGGTGCTTTGGAATGGAAGAAATAATCCAACACTCACAAGTATC
* * * * *
3772 AACGATAAGCTTTCAATGTCTAAGGGAAGTACAAGTCACAGAGTGCAATAAATTGAAATTTCTCT
66 AACCATAAACTTCCAATGCCTAAGGGAAGTACAAGTCACAGAATGCAATAAATTGAAATTTCTCT
3837 TCCCAATGTGTGTTGCTAATAGTCTTGGGAAA
131 TCCCAATGTGTGTTGCTAATAGTCTTGGGAAA
*
3869 TTGCAAACTCTAAAGATAGAGAGGTGCTTTGGAATGGAAGAAATAATCCAACACTCACAAGTATC
1 TTGCAAACTCTGAAGATAGAGAGGTGCTTTGGAATGGAAGAAATAATCCAACACTCACAAGTATC
* * * * * * * *
3934 AACCGTAAGCTTTCAATGCCTTAGGAAAGTACAAGTCAAAGAATGCTATAAATTGATATTTCTCT
66 AACCATAAACTTCCAATGCCTAAGGGAAGTACAAGTCACAGAATGCAATAAATTGAAATTTCTCT
3999 TCCCAATGTGTGTTGCTAATAGTCTTGGGAAA
131 TCCCAATGTGTGTTGCTAATAGTCTTGGGAAA
*
4031 TTGCAAACTCTAAAGATAGAGAGGTGCTTTGGAATGGAAGAAATAATCCAACACTCACAAGTATC
1 TTGCAAACTCTGAAGATAGAGAGGTGCTTTGGAATGGAAGAAATAATCCAACACTCACAAGTATC
* * * ** *
4096 AACCACAAACTTCCAATGCCTTACGGAAGTACAAGTCATTGAATGCAATAATTTGAAATTTCTCT
66 AACCATAAACTTCCAATGCCTAAGGGAAGTACAAGTCACAGAATGCAATAAATTGAAATTTCTCT
4161 TCCCAATGTGTGTTGCTAATAGTCTTGGGAAA
131 TCCCAATGTGTGTTGCTAATAGTCTTGGGAAA
* * *
4193 TTGCAAACTCTGAAGATAGAGTGGTGCTTTAGAATTGAAGAAATAATCCAACACTCACAAGTATC
1 TTGCAAACTCTGAAGATAGAGAGGTGCTTTGGAATGGAAGAAATAATCCAACACTCACAAGTATC
* * * *
4258 AACCATAAAATTCCAATGCCTAAGGGAAGTACAAGTCACGGAATGCAATAATTTGAAATATCTCT
66 AACCATAAACTTCCAATGCCTAAGGGAAGTACAAGTCACAGAATGCAATAAATTGAAATTTCTCT
* *
4323 TCCCAATGTGTGTTGCTAATAGTCTTGAGCAA
131 TCCCAATGTGTGTTGCTAATAGTCTTGGGAAA
*
4355 TTGCAAATTCTGAAGATAGAGAG
1 TTGCAAACTCTGAAGATAGAGAG
4378 CTGTTCCCAA
Statistics
Matches: 470, Mismatches: 39, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
162 470 1.00
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.28
Consensus pattern (162 bp):
TTGCAAACTCTGAAGATAGAGAGGTGCTTTGGAATGGAAGAAATAATCCAACACTCACAAGTATC
AACCATAAACTTCCAATGCCTAAGGGAAGTACAAGTCACAGAATGCAATAAATTGAAATTTCTCT
TCCCAATGTGTGTTGCTAATAGTCTTGGGAAA
Found at i:5479 original size:24 final size:24
Alignment explanation
Indices: 5447--5537 Score: 101
Period size: 24 Copynumber: 3.5 Consensus size: 24
5437 GACCAAAGAG
5447 GAAGATGAAAGTGATTTTGAATAT
1 GAAGATGAAAGTGATTTTGAATAT
5471 GAAGATGAAAGTGATGAAGTGACTTTGAATAT
1 GAAGATGAAA--G-TG-A-T---TTTGAATAT
5503 GAAGATGAAAGTGATTTTGAATAT
1 GAAGATGAAAGTGATTTTGAATAT
*
5527 GAAGGTGAAAG
1 GAAGATGAAAG
5538 CACAGGCAAG
Statistics
Matches: 58, Mismatches: 1, Indels: 16
0.77 0.01 0.21
Matches are distributed among these distances:
24 29 0.50
26 1 0.02
27 3 0.05
28 2 0.03
29 3 0.05
30 1 0.02
32 19 0.33
ACGTcount: A:0.42, C:0.01, G:0.29, T:0.29
Consensus pattern (24 bp):
GAAGATGAAAGTGATTTTGAATAT
Found at i:5492 original size:32 final size:33
Alignment explanation
Indices: 5450--5517 Score: 120
Period size: 32 Copynumber: 2.1 Consensus size: 33
5440 CAAAGAGGAA
*
5450 GATGAAAGTGATTTTGAATATGAAGATGAAAGT
1 GATGAAAGTGACTTTGAATATGAAGATGAAAGT
5483 GATG-AAGTGACTTTGAATATGAAGATGAAAGT
1 GATGAAAGTGACTTTGAATATGAAGATGAAAGT
5515 GAT
1 GAT
5518 TTTGAATATG
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 30 0.88
33 4 0.12
ACGTcount: A:0.41, C:0.01, G:0.28, T:0.29
Consensus pattern (33 bp):
GATGAAAGTGACTTTGAATATGAAGATGAAAGT
Found at i:5668 original size:24 final size:24
Alignment explanation
Indices: 5636--5692 Score: 114
Period size: 24 Copynumber: 2.4 Consensus size: 24
5626 GACCAAAGAG
5636 GAAGATGAAAGTGATTTTGAATAT
1 GAAGATGAAAGTGATTTTGAATAT
5660 GAAGATGAAAGTGATTTTGAATAT
1 GAAGATGAAAGTGATTTTGAATAT
5684 GAAGATGAA
1 GAAGATGAA
5693 CAGGCAAGCC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.44, C:0.00, G:0.26, T:0.30
Consensus pattern (24 bp):
GAAGATGAAAGTGATTTTGAATAT
Done.