Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga09g02364.F2
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, 964
Length: 1607
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.22
Found at i:584 original size:117 final size:119
Alignment explanation
Indices: 292--1085 Score: 1062
Period size: 117 Copynumber: 6.7 Consensus size: 119
282 GGAAGAGAAT
* * * * * * *
292 GTCGAGGAAGAAAGTCCGTTTGCCGGTGAGAAACCACCTAGTGACGAAGGAGATAAGCCCCCAGA
1 GTCGAGGAAGAGAGTCCATTCGCCGGCGAGAAACCACCTAGTGACGAAGGAGACAATCCTCCAGA
* * *
357 AAGATTACTAAAAGAAATTGAGGTTATCGGTGAGAAACGAAAACTACAAGCAGAT
66 AAGATTACTAAAAGACATTGAGGTCATCGGTGAGAAACGAAAACTACAA-CAGAC
*
412 GTCGAGGAAGAGAGTCCATTCGCCGGCGAGAAACCGCCTAGTGACGAAGGAGACAATCCTCCAGA
1 GTCGAGGAAGAGAGTCCATTCGCCGGCGAGAAACCACCTAGTGACGAAGGAGACAATCCTCCAGA
* *
477 AAGATTACTAAAAGACATCGAGGTCATCGGTGAGAAACGAAAACTAC-A-AGAT
66 AAGATTACTAAAAGACATTGAGGTCATCGGTGAGAAACGAAAACTACAACAGAC
* *
529 GTTGAGGAAGAAAGTCCATTCGCCGGCGAGAAACCACCTAGTGACGAAGGAGACAATCCTCCAGA
1 GTCGAGGAAGAGAGTCCATTCGCCGGCGAGAAACCACCTAGTGACGAAGGAGACAATCCTCCAGA
*
594 AAGATTACTAAAAGACATTGAGGTCATCGGTAAGAAACGAAAACTAC-A-AGAC
66 AAGATTACTAAAAGACATTGAGGTCATCGGTGAGAAACGAAAACTACAACAGAC
* * *
646 GTTGAGGAAGAGAGCCCATTTGCCGGCGAGAAACCACCTAGTGACGAAGGAGACAATCCTCCAGA
1 GTCGAGGAAGAGAGTCCATTCGCCGGCGAGAAACCACCTAGTGACGAAGGAGACAATCCTCCAGA
* * ***
711 AAGATTACTAAAAGACATTGAGGTCGTCGGTGAAAAACGGTTACTACAAGCAGAC
66 AAGATTACTAAAAGACATTGAGGTCATCGGTGAGAAACGAAAACTACAA-CAGAC
* *
766 GTCGAGGAAGAAAGTCCATTCGCCGGCGAGAAACCACCTAGTGACGAAGGAGATAATTCC-CCAG
1 GTCGAGGAAGAGAGTCCATTCGCCGGCGAGAAACCACCTAGTGACGAAGGAGACAA-TCCTCCAG
* * * * **
830 AAAGATTATTAAAAGACATTGAGCTCATCCGTGAGGAACGATTACTAC-A-AGAC
65 AAAGATTACTAAAAGACATTGAGGTCATCGGTGAGAAACGAAAACTACAACAGAC
* * *
883 GTTGAGGAAGAGAGTCCATTCGCCGGCGAGAAACCACCTAGTGACGAAGGAGATAGTCCTCCAGA
1 GTCGAGGAAGAGAGTCCATTCGCCGGCGAGAAACCACCTAGTGACGAAGGAGACAATCCTCCAGA
** * * **
948 AAGATTACTAGCAGGCATTGGGGTCATCGGTGAGAAACGATTACTACAAGCAGAC
66 AAGATTACTAAAAGACATTGAGGTCATCGGTGAGAAACGAAAACTACAA-CAGAC
* * *
1003 GTCGAGGAAGAGAGTCCATTCGCCGGTGAGAAACCACCTAGTGACGACGAAGGAAACAATCCACC
1 GTCGAGGAAGAGAGTCCATTCGCCGGCGAGAAACCACCTAGT---GACGAAGGAGACAATCCTCC
* *
1068 AGCAAGATTACTAGAAGA
63 AGAAAGATTACTAAAAGA
1086 AGAAGACGAC
Statistics
Matches: 605, Mismatches: 58, Indels: 19
0.89 0.09 0.03
Matches are distributed among these distances:
116 3 0.00
117 319 0.53
118 2 0.00
119 2 0.00
120 245 0.40
121 3 0.00
123 31 0.05
ACGTcount: A:0.37, C:0.21, G:0.26, T:0.16
Consensus pattern (119 bp):
GTCGAGGAAGAGAGTCCATTCGCCGGCGAGAAACCACCTAGTGACGAAGGAGACAATCCTCCAGA
AAGATTACTAAAAGACATTGAGGTCATCGGTGAGAAACGAAAACTACAACAGAC
Found at i:775 original size:237 final size:236
Alignment explanation
Indices: 292--1085 Score: 1128
Period size: 237 Copynumber: 3.3 Consensus size: 236
282 GGAAGAGAAT
* * * * *
292 GTCGAGGAAGAAAGTCCGTTTGCCGGTGAGAAACCACCTAGTGACGAAGGAGATAAGCCCCCAGA
1 GTCGAGGAAGAAAGTCCATTCGCCGGCGAGAAACCACCTAGTGACGAAGGAGACAA-TCCCCAGA
* *
357 AAGATTACTAAAAGAAATTGAGGTTATCGGTGAGAAACGAAAACTACAAG-CAGATGTCGAGGAA
65 AAGATTACTAAAAGACATTGAGGTCATCGGTGAGAAACGAAAACTACAAGAC-G-T-T-GAGGAA
*
421 GAGAGTCCATTCGCCGGCGAGAAACCGCCTAGTGACGAAGGAGACAATCCTCCAGAAAGATTACT
126 GAGAGTCCATTCGCCGGCGAGAAACCACCTAGTGACGAAGGAGACAATCCTCCAGAAAGATTACT
* ** *
486 AAAAGACATCGAGGTCATCGGTGAGAAACGAAAACTAC-A--AGAT
191 AAAAGACATTGAGGTCATCGGTGAGAAACGATTACTACAAGCAGAC
*
529 GTTGAGGAAGAAAGTCCATTCGCCGGCGAGAAACCACCTAGTGACGAAGGAGACAATCCTCCAGA
1 GTCGAGGAAGAAAGTCCATTCGCCGGCGAGAAACCACCTAGTGACGAAGGAGACAATCC-CCAGA
*
594 AAGATTACTAAAAGACATTGAGGTCATCGGTAAGAAACGAAAACTACAAGACGTTGAGGAAGAGA
65 AAGATTACTAAAAGACATTGAGGTCATCGGTGAGAAACGAAAACTACAAGACGTTGAGGAAGAGA
* *
659 GCCCATTTGCCGGCGAGAAACCACCTAGTGACGAAGGAGACAATCCTCCAGAAAGATTACTAAAA
130 GTCCATTCGCCGGCGAGAAACCACCTAGTGACGAAGGAGACAATCCTCCAGAAAGATTACTAAAA
* * *
724 GACATTGAGGTCGTCGGTGAAAAACGGTTACTACAAGCAGAC
195 GACATTGAGGTCATCGGTGAGAAACGATTACTACAAGCAGAC
*
766 GTCGAGGAAGAAAGTCCATTCGCCGGCGAGAAACCACCTAGTGACGAAGGAGATAATTCCCCAGA
1 GTCGAGGAAGAAAGTCCATTCGCCGGCGAGAAACCACCTAGTGACGAAGGAGACAA-TCCCCAGA
* * * * **
831 AAGATTATTAAAAGACATTGAGCTCATCCGTGAGGAACGATTACTACAAGACGTTGAGGAAGAGA
65 AAGATTACTAAAAGACATTGAGGTCATCGGTGAGAAACGAAAACTACAAGACGTTGAGGAAGAGA
* * **
896 GTCCATTCGCCGGCGAGAAACCACCTAGTGACGAAGGAGATAGTCCTCCAGAAAGATTACTAGCA
130 GTCCATTCGCCGGCGAGAAACCACCTAGTGACGAAGGAGACAATCCTCCAGAAAGATTACTAAAA
* *
961 GGCATTGGGGTCATCGGTGAGAAACGATTACTACAAGCAGAC
195 GACATTGAGGTCATCGGTGAGAAACGATTACTACAAGCAGAC
* * *
1003 GTCGAGGAAGAGAGTCCATTCGCCGGTGAGAAACCACCTAGTGACGACGAAGGAAACAATCCACC
1 GTCGAGGAAGAAAGTCCATTCGCCGGCGAGAAACCACCTAGT---GACGAAGGAGACAATCC-CC
* *
1068 AGCAAGATTACTAGAAGA
62 AGAAAGATTACTAAAAGA
1086 AGAAGACGAC
Statistics
Matches: 501, Mismatches: 46, Indels: 17
0.89 0.08 0.03
Matches are distributed among these distances:
234 100 0.20
235 2 0.00
236 3 0.01
237 360 0.72
238 4 0.01
239 3 0.01
240 29 0.06
ACGTcount: A:0.37, C:0.21, G:0.26, T:0.16
Consensus pattern (236 bp):
GTCGAGGAAGAAAGTCCATTCGCCGGCGAGAAACCACCTAGTGACGAAGGAGACAATCCCCAGAA
AGATTACTAAAAGACATTGAGGTCATCGGTGAGAAACGAAAACTACAAGACGTTGAGGAAGAGAG
TCCATTCGCCGGCGAGAAACCACCTAGTGACGAAGGAGACAATCCTCCAGAAAGATTACTAAAAG
ACATTGAGGTCATCGGTGAGAAACGATTACTACAAGCAGAC
Found at i:945 original size:354 final size:356
Alignment explanation
Indices: 292--1086 Score: 1146
Period size: 354 Copynumber: 2.2 Consensus size: 356
282 GGAAGAGAAT
* * * * *
292 GTCGAGGAAGAAAGTCCGTTTGCCGGTGAGAAACCACCTAGTGACGAAGGAGATAAGCCCCCAGA
1 GTCGAGGAAGAGAGTCCATTTGCCGGTGAGAAACCACCTAGTGACGAAGGAGACAATCCACCAGA
* * *
357 AAGATTACTAAAAGAAATTGAGGTTATCGGTGAGAAACGAAAACTACAAGCAGATGTCGAGGAAG
66 AAGATTACTAAAAGAAATTGAGGTCATCGGTGAAAAACGAAAACTACAAGCAGACGTCGAGGAAG
* *
422 AGAGTCCATTCGCCGGCGAGAAACCGCCTAGTGACGAAGGAGACAATCCTCCAGAAAGATTACTA
131 AAAGTCCATTCGCCGGCGAGAAACCACCTAGTGACGAAGGAGACAATCCTCCAGAAAGATTACTA
* * *
487 AAAGACATCGAGGTCATCGGTGAGAAACGAAAACTACAAGATGTTGAGGAAGAAAGTCCATTCGC
196 AAAGACATCGAGCTCATCCGTGAGAAACGAAAACTACAAGACGTTGAGGAAGAAAGTCCATTCGC
552 CGGCGAGAAACCACCTAGTGACGAAGGAGACAATCCTCCAGAAAGATTACTAAAAGACATTGAGG
261 CGGCGAGAAACCACCTAGTGACGAAGGAGACAATCCTCCAGAAAGATTACTAAAAGACATTGAGG
617 TCATCGGTAAGAAACGAAAACTAC-A-AGAC
326 TCATCGGTAAGAAACGAAAACTACAACAGAC
* * * *
646 GTTGAGGAAGAGAGCCCATTTGCCGGCGAGAAACCACCTAGTGACGAAGGAGACAATCCTCCAGA
1 GTCGAGGAAGAGAGTCCATTTGCCGGTGAGAAACCACCTAGTGACGAAGGAGACAATCCACCAGA
* * ***
711 AAGATTACTAAAAGACATTGAGGTCGTCGGTGAAAAACGGTTACTACAAGCAGACGTCGAGGAAG
66 AAGATTACTAAAAGAAATTGAGGTCATCGGTGAAAAACGAAAACTACAAGCAGACGTCGAGGAAG
* *
776 AAAGTCCATTCGCCGGCGAGAAACCACCTAGTGACGAAGGAGATAATTCC-CCAGAAAGATTATT
131 AAAGTCCATTCGCCGGCGAGAAACCACCTAGTGACGAAGGAGACAA-TCCTCCAGAAAGATTACT
* * ** *
840 AAAAGACATTGAGCTCATCCGTGAGGAACGATTACTACAAGACGTTGAGGAAGAGAGTCCATTCG
195 AAAAGACATCGAGCTCATCCGTGAGAAACGAAAACTACAAGACGTTGAGGAAGAAAGTCCATTCG
* * ** * *
905 CCGGCGAGAAACCACCTAGTGACGAAGGAGATAGTCCTCCAGAAAGATTACTAGCAGGCATTGGG
260 CCGGCGAGAAACCACCTAGTGACGAAGGAGACAATCCTCCAGAAAGATTACTAAAAGACATTGAG
* **
970 GTCATCGGTGAGAAACGATTACTACAAGCAGAC
325 GTCATCGGTAAGAAACGAAAACTACAA-CAGAC
* *
1003 GTCGAGGAAGAGAGTCCATTCGCCGGTGAGAAACCACCTAGTGACGACGAAGGAAACAATCCACC
1 GTCGAGGAAGAGAGTCCATTTGCCGGTGAGAAACCACCTAGT---GACGAAGGAGACAATCCACC
* *
1068 AGCAAGATTACTAGAAGAA
63 AGAAAGATTACTAAAAGAA
1087 GAAGACGACG
Statistics
Matches: 388, Mismatches: 46, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
354 308 0.79
355 4 0.01
357 42 0.11
360 34 0.09
ACGTcount: A:0.37, C:0.21, G:0.26, T:0.16
Consensus pattern (356 bp):
GTCGAGGAAGAGAGTCCATTTGCCGGTGAGAAACCACCTAGTGACGAAGGAGACAATCCACCAGA
AAGATTACTAAAAGAAATTGAGGTCATCGGTGAAAAACGAAAACTACAAGCAGACGTCGAGGAAG
AAAGTCCATTCGCCGGCGAGAAACCACCTAGTGACGAAGGAGACAATCCTCCAGAAAGATTACTA
AAAGACATCGAGCTCATCCGTGAGAAACGAAAACTACAAGACGTTGAGGAAGAAAGTCCATTCGC
CGGCGAGAAACCACCTAGTGACGAAGGAGACAATCCTCCAGAAAGATTACTAAAAGACATTGAGG
TCATCGGTAAGAAACGAAAACTACAACAGAC
Done.