Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga02g00079.F6
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: 4537
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Found at i:1719 original size:280 final size:282
Alignment explanation
Indices: 912--1772 Score: 739
Period size: 280 Copynumber: 3.0 Consensus size: 282
902 GGAATGTTGC
* * * * * * *
912 TTGAAAATGAAACCTAGCTTGTGCTAAAGCTGCATGTAAATTTAAACTGGAGACTGGAACAAAAA
1 TTGAAAATGAAACCTAACTTGTACCAAAGCTCCATGTAAATTTACACTGGAGAATGGAACAAAGA
* * * * * *
977 ATCATGCAAGTTATATAAT-GGGA-ATCATTTAACAGATTATGAAGCTTATATCTTCAATGAGT-
66 ATCATGCAACTTATATAATAGGAATATCATTTAA-TGATCATGAAGCTTACATCTTC--TGACTG
* * *** * * * *
1039 TTTTTATTCATTAGTAACAGTGAAAGAGTCCCTCTTTCACTTCGATTTGTTCTTGCTGCACATTG
128 TCTTT-TT-ATTAGCAACAGTGAAAGAGGGACACTCTAACTTCAATTTGTTCTTGCTGCACATTG
* * ** ** ** **
1104 GTTCTAGGCCTGCTTGTGTTCTTTCACTACAGTTTAGCTTCTTCCT-TTGTATT-AGCTAGAAT-
191 GTTCTAGGCCTGCTTGTGTTCTTTCACTACTGGTTAGCTTCTTTGTATTGGCTTCCCCT-GTGTG
* ** * * *
1166 CT-AGTGGAA-TTGCATTTTGCCCATGGTGAAATGTT
255 CTCA-T-AAACTAACACTTTG-TC-T--TGTAA---T
* * *
1201 GCTTGAACATGAAACCTAACTTGTACCAAAGCTGCATGTAAATTTACTCTGGAGAATGGAACAAA
1 --TTGAAAATGAAACCTAACTTGTACCAAAGCTCCATGTAAATTTACACTGGAGAATGGAACAAA
*
1266 GAATCATGCAAGTTATATAATAGGAAATATCATTTAATGGATCATGAAGCTTACATCTTCTGACT
64 GAATCATGCAACTTATATAATAGG-AATATCATTTAAT-GATCATGAAGCTTACATCTTCTGACT
* * * *
1331 TTCTTTTTAATTAGTAACATTGAAAGAGGGACACTTTAACTTCAATTTGTTCTTGCTGCACATTG
127 GTCTTTTT-ATTAGCAACAGTGAAAGAGGGACACTCTAACTTCAATTTGTTCTTGCTGCACATTG
* *
1396 GTTCTAGGTCTGCTTGTGTTCTTTCACTAGTGGTTAGCTTCTTTGTATTGGCTTCCCCTGTGTGC
191 GTTCTAGGCCTGCTTGTGTTCTTTCACTACTGGTTAGCTTCTTTGTATTGGCTTCCCCTGTGTGC
1461 TCATAAACTAACAC-TTGCTCTTGTAAT
256 TCATAAACTAACACTTTG-TCTTGTAAT
* * * * *
1488 TTGAAAATGAAACCTAGCTTGTACTAAAGCTCCATGTTAATTTGCACTGGAGAATTGAACAAAGA
1 TTGAAAATGAAACCTAACTTGTACCAAAGCTCCATGTAAATTTACACTGGAGAATGGAACAAAGA
*
1553 ATCATGCAACTTATATAAT-GG-A-ATCATTTAAT-ATACTGTGAAGCTTACATCTT-TGA-TGA
66 ATCATGCAACTTATATAATAGGAATATCATTTAATGAT-C-ATGAAGCTTACATCTTCTGACT--
* * * ** *
1612 GTGTATTTT-TTAGCAACAGTGAAGGAGGGACAAC-CTCACTTGTATTTGTTCTTGTTGCACATT
127 GTCT-TTTTATTAGCAACAGTGAAAGAGGGAC-ACTCTAACTTCAATTTGTTCTTGCTGCACATT
* ** ** * *
1675 TGTTCTCTGCCTGCTTGTGTTCTTTTGCTACTGTTTAGCTTCTTTGTATTGGCTTCCCCTTTGTG
190 GGTTCTAGGCCTGCTTGTGTTCTTTCACTACTGGTTAGCTTCTTTGTATTGGCTTCCCCTGTGTG
* *
1740 GTCATAAACTGACACTTTGTCTTGTAAT
255 CTCATAAACTAACACTTTGTCTTGTAAT
1768 TTGAA
1 TTGAA
1773 GATTAAGAGA
Statistics
Matches: 482, Mismatches: 71, Indels: 45
0.81 0.12 0.08
Matches are distributed among these distances:
279 3 0.01
280 130 0.27
281 32 0.07
282 5 0.01
284 2 0.00
285 75 0.16
287 1 0.00
290 4 0.01
291 76 0.16
292 98 0.20
293 19 0.04
294 36 0.07
295 1 0.00
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.38
Consensus pattern (282 bp):
TTGAAAATGAAACCTAACTTGTACCAAAGCTCCATGTAAATTTACACTGGAGAATGGAACAAAGA
ATCATGCAACTTATATAATAGGAATATCATTTAATGATCATGAAGCTTACATCTTCTGACTGTCT
TTTTATTAGCAACAGTGAAAGAGGGACACTCTAACTTCAATTTGTTCTTGCTGCACATTGGTTCT
AGGCCTGCTTGTGTTCTTTCACTACTGGTTAGCTTCTTTGTATTGGCTTCCCCTGTGTGCTCATA
AACTAACACTTTGTCTTGTAAT
Found at i:1841 original size:21 final size:22
Alignment explanation
Indices: 1798--1860 Score: 71
Period size: 21 Copynumber: 3.0 Consensus size: 22
1788 AGAGAAGGCC
*
1798 AAGAAGGA-AAGGAAGAAAGAA
1 AAGAAGGAGAAGAAAGAAAGAA
1819 AAGAAGGAGAAGAAAG--AGAA
1 AAGAAGGAGAAGAAAGAAAGAA
1839 AA-AACGGGAGAAGAAAGAAAGA
1 AAGAA--GGAGAAGAAAGAAAGA
1861 GATAAGTCTC
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
19 2 0.06
20 6 0.17
21 19 0.53
22 6 0.17
23 3 0.08
ACGTcount: A:0.65, C:0.02, G:0.33, T:0.00
Consensus pattern (22 bp):
AAGAAGGAGAAGAAAGAAAGAA
Done.