Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga03g02046.R1
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: 3681
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29
Found at i:1471 original size:144 final size:144
Alignment explanation
Indices: 1202--1487 Score: 448
Period size: 144 Copynumber: 2.0 Consensus size: 144
1192 TTCTTGATAC
* * *
1202 AGAAAAGGCTGCGCTTCCACTTGAAGTTTCTGCTATTGAAAGTGAAATTACAACTGAATTAGCTC
1 AGAAAAGGCTGCGCCTCCACTGGAAGTTTCTGCTATTGAAAGTGAAACTACAACTGAATTAGCTC
* * * *
1267 CTTCAGAGTCCAGTTCCAAAAGTGAAGTTCCCCACAGTGTTAAGTTGGAAGAGGATGAAAATGCT
66 CTTCAGAGTCCAGTTCCAAAAGTAAAGTTCCCCACAGTGTTAAGTTGGAAAAGGAAGAAAATACT
1332 GGTGCTGAGGAAAA
131 GGTGCTGAGGAAAA
* * *
1346 AGAAAAGGCTTCTCCTCCACTGGAAGCTTT-TGCTATTGAAAGTGAAACTACAACTGCATTAGCT
1 AGAAAAGGCTGCGCCTCCACTGGAAG-TTTCTGCTATTGAAAGTGAAACTACAACTGAATTAGCT
* *
1410 CCTTCAGAGTCCAGTTCCAAAAGTAAAGTTCCCCAGAGTGTTCAGTTGGAAAAGGAAGAAAATAC
65 CCTTCAGAGTCCAGTTCCAAAAGTAAAGTTCCCCACAGTGTTAAGTTGGAAAAGGAAGAAAATAC
1475 TGGTGCTGAGGAA
130 TGGTGCTGAGGAA
1488 GAAGGTGAGG
Statistics
Matches: 129, Mismatches: 12, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
144 126 0.98
145 3 0.02
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.25
Consensus pattern (144 bp):
AGAAAAGGCTGCGCCTCCACTGGAAGTTTCTGCTATTGAAAGTGAAACTACAACTGAATTAGCTC
CTTCAGAGTCCAGTTCCAAAAGTAAAGTTCCCCACAGTGTTAAGTTGGAAAAGGAAGAAAATACT
GGTGCTGAGGAAAA
Found at i:1647 original size:360 final size:360
Alignment explanation
Indices: 986--1707 Score: 1018
Period size: 360 Copynumber: 2.0 Consensus size: 360
976 CTCCTGATAT
* * * * *
986 AGAAAAGGTTTCTCCCCCACTGGGAGCTTCTGATATTGGAAGTGAAATTACAACTGAATCGGCTC
1 AGAAAAGGCTTCTCCCCCACTGGAAGCTTCTGATATTGAAAGTGAAACTACAACTGAATCAGCTC
** *** * *
1051 CTTCAGAGTCTGGTTTGGAAAGTGAAGTTCCCCACAGTGTTAAGTTGGAAGAAGAAGAAAACGCT
66 CTTCAGAGTCCAGTTCCAAAAGTAAAGTTCCCCACAGTGTTAAGTTGGAAGAAGAAGAAAACACT
** *
1116 GGTGCTGAGGAAAATGGTGAGGGGTTTGGTAAAATTGAGTGTACTATTTTGAATACAGAGTCTAA
131 GGTGCTGAGGAAAATGGTGAGGGAATTGGTAAAATTGAGTGTACAATTTTGAATACAGAGTCTAA
* * * * *
1181 GATGGCTTTAGTTCTTGATACAGAAAAGGCTGCGCTTCCACTTGAAGTTTCTGCTATTGAAAGTG
196 GATAGCTTTAGTTCTTGATACAGAAAAGGCTGCGCCTCCACTGGAAGCTTCTGCCATTGAAAGTG
* *
1246 AAATTACAACTGAATTAGCTCCTTCAGAGTCCAGTTCCAAAAGTGAAGTTCCCCACAGTGTTAAG
261 AAATTACAACTGAATCAGCTCCTTCAGAGTCCAGTTCCAAAAGTGAAGATCCCCACAGTGTTAAG
* ** *
1311 TTGGAAGAGGATGAAAATGCTGGTGCTGAGGAAAA
326 TTGGAAGAGGAAGAAAACACTAGTGCTGAGGAAAA
* * * * *
1346 AGAAAAGGCTTCTCCTCCACTGGAAGCTTTTGCTATTGAAAGTGAAACTACAACTGCATTAGCTC
1 AGAAAAGGCTTCTCCCCCACTGGAAGCTTCTGATATTGAAAGTGAAACTACAACTGAATCAGCTC
* * *
1411 CTTCAGAGTCCAGTTCCAAAAGTAAAGTTCCCCAGAGTGTTCAGTTGGAA-AAGGAAGAAAATAC
66 CTTCAGAGTCCAGTTCCAAAAGTAAAGTTCCCCACAGTGTTAAGTTGGAAGAA-GAAGAAAACAC
* *
1475 TGGTGCTGAGGAAGAA-GGTGAGGGAATTGGTAAAATTGAGTTTACAATTTTGAATACGGAGTCT
130 TGGTGCTGAGGAA-AATGGTGAGGGAATTGGTAAAATTGAGTGTACAATTTTGAATACAGAGTCT
* *
1539 AAGATAGCTTTAGTTAC-TGATACAGAAAAGGCTTCTCCTCCACTGGAAGCTTCTGCCATTGAAA
194 AAGATAGCTTTAGTT-CTTGATACAGAAAAGGCTGCGCCTCCACTGGAAGCTTCTGCCATTGAAA
* * *
1603 GTGAAATTACAACTGAATCAGCTCCTTTAGAGTCCGGTTCCAAAAGTGAAGATCCCCAGAGTGTT
258 GTGAAATTACAACTGAATCAGCTCCTTCAGAGTCCAGTTCCAAAAGTGAAGATCCCCACAGTGTT
*
1668 AAGTTGGAAGAGGAAGAAGACACTAGTGCTGAGGAAAA
323 AAGTTGGAAGAGGAAGAAAACACTAGTGCTGAGGAAAA
1706 AG
1 AG
1708 GTGAAAGAAT
Statistics
Matches: 317, Mismatches: 42, Indels: 6
0.87 0.12 0.02
Matches are distributed among these distances:
359 2 0.01
360 312 0.98
361 3 0.01
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.26
Consensus pattern (360 bp):
AGAAAAGGCTTCTCCCCCACTGGAAGCTTCTGATATTGAAAGTGAAACTACAACTGAATCAGCTC
CTTCAGAGTCCAGTTCCAAAAGTAAAGTTCCCCACAGTGTTAAGTTGGAAGAAGAAGAAAACACT
GGTGCTGAGGAAAATGGTGAGGGAATTGGTAAAATTGAGTGTACAATTTTGAATACAGAGTCTAA
GATAGCTTTAGTTCTTGATACAGAAAAGGCTGCGCCTCCACTGGAAGCTTCTGCCATTGAAAGTG
AAATTACAACTGAATCAGCTCCTTCAGAGTCCAGTTCCAAAAGTGAAGATCCCCACAGTGTTAAG
TTGGAAGAGGAAGAAAACACTAGTGCTGAGGAAAA
Found at i:1720 original size:216 final size:216
Alignment explanation
Indices: 1346--1945 Score: 781
Period size: 216 Copynumber: 2.8 Consensus size: 216
1336 CTGAGGAAAA
* *
1346 AGAAAAGGCTTCTCCTCCACTGGAAGCTTTTGCTATTGAAAGTGAAACTACAACTGCATTAGCTC
1 AGAAAAGGCTTCTCCTCCACTGGAAGCTTCTGCTATTGAAAGTGAAACTACAACTGAATTAGCTC
* * * *
1411 CTTCAGAGTCCAGTTCCAAAAGTAAAGTTCCCCAGAGTGTTCAGTTGGAAAAGGAAGAAAATACT
66 CTTTAGAGTCCAGTTCCAAAAGTGAAGTTCCCCAGAGTGTTAAGTTGGAAGAGGAAGAAAATACT
* * * * *
1476 GGTGCTGAGGAAGAAGGTGAGGGAATTGGTAAAATTGAGTTTACAATTTTGAATACGGAGTCTAA
131 GGTGCTGAGGAAAAAGGTGAGAGAATTGGTAAAATTGAGTGTACAACTTCGAATACGGAGTCTAA
1541 GATAGCTTTAGTTACTGATAC
196 GATAGCTTTAGTTACTGATAC
* * *
1562 AGAAAAGGCTTCTCCTCCACTGGAAGCTTCTGCCATTGAAAGTGAAATTACAACTGAATCAGCTC
1 AGAAAAGGCTTCTCCTCCACTGGAAGCTTCTGCTATTGAAAGTGAAACTACAACTGAATTAGCTC
* * * *
1627 CTTTAGAGTCCGGTTCCAAAAGTGAAGATCCCCAGAGTGTTAAGTTGGAAGAGGAAGAAGACACT
66 CTTTAGAGTCCAGTTCCAAAAGTGAAGTTCCCCAGAGTGTTAAGTTGGAAGAGGAAGAAAATACT
* * * * *
1692 AGTGCTGAGGAAAAAGGTGAAAGAATTGGTAAATTTGAGTGTACTACTTCGAATATGGAGTCTAA
131 GGTGCTGAGGAAAAAGGTGAGAGAATTGGTAAAATTGAGTGTACAACTTCGAATACGGAGTCTAA
* * **
1757 GATGGCTTTAGTTCCTGATTT
196 GATAGCTTTAGTTACTGATAC
* * * * * *
1778 AGAAAAGGCTTCTCCTCCATTGGAAGCTCCTGCTAGTGGAAGTGAAACTAGAACTGAATTAGCTT
1 AGAAAAGGCTTCTCCTCCACTGGAAGCTTCTGCTATTGAAAGTGAAACTACAACTGAATTAGCTC
* * * * * *
1843 CTTTAGAG-CTTAGTTCCAAAAGCGAAGTTTCTCACAGTGTTAA-TCTGGAGGAGGAAGAAAATA
66 CTTTAGAGTC-CAGTTCCAAAAGTGAAGTTCCCCAGAGTGTTAAGT-TGGAAGAGGAAGAAAATA
* * * *
1906 GTGGTGCCGGGGAAAATGGTGAGAGAATTGGTAAAATTGA
129 CTGGTGCTGAGGAAAAAGGTGAGAGAATTGGTAAAATTGA
1946 AAGTATTACT
Statistics
Matches: 329, Mismatches: 53, Indels: 4
0.85 0.14 0.01
Matches are distributed among these distances:
215 2 0.01
216 327 0.99
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.27
Consensus pattern (216 bp):
AGAAAAGGCTTCTCCTCCACTGGAAGCTTCTGCTATTGAAAGTGAAACTACAACTGAATTAGCTC
CTTTAGAGTCCAGTTCCAAAAGTGAAGTTCCCCAGAGTGTTAAGTTGGAAGAGGAAGAAAATACT
GGTGCTGAGGAAAAAGGTGAGAGAATTGGTAAAATTGAGTGTACAACTTCGAATACGGAGTCTAA
GATAGCTTTAGTTACTGATAC
Done.