Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Cotton_A_24753
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, 790
Length: 1317
ACGTcount: A:0.35, C:0.20, G:0.25, T:0.20
Found at i:569 original size:117 final size:119
Alignment explanation
Indices: 277--1070 Score: 1062
Period size: 117 Copynumber: 6.7 Consensus size: 119
267 GGAAGAGAAT
* * * * * * *
277 GTCGAGGAAGAAAGTCCGTTTGCCGGTGAGAAACCACCTAGTGACGAAGGAGATAAGCCCCCAGA
1 GTCGAGGAAGAGAGTCCATTCGCCGGCGAGAAACCACCTAGTGACGAAGGAGACAATCCTCCAGA
* * *
342 AAGATTACTAAAAGAAATTGAGGTTATCGGTGAGAAACGAAAACTACAAGCAGAT
66 AAGATTACTAAAAGACATTGAGGTCATCGGTGAGAAACGAAAACTACAA-CAGAC
*
397 GTCGAGGAAGAGAGTCCATTCGCCGGCGAGAAACCGCCTAGTGACGAAGGAGACAATCCTCCAGA
1 GTCGAGGAAGAGAGTCCATTCGCCGGCGAGAAACCACCTAGTGACGAAGGAGACAATCCTCCAGA
* *
462 AAGATTACTAAAAGACATCGAGGTCATCGGTGAGAAACGAAAACTAC-A-AGAT
66 AAGATTACTAAAAGACATTGAGGTCATCGGTGAGAAACGAAAACTACAACAGAC
* *
514 GTTGAGGAAGAAAGTCCATTCGCCGGCGAGAAACCACCTAGTGACGAAGGAGACAATCCTCCAGA
1 GTCGAGGAAGAGAGTCCATTCGCCGGCGAGAAACCACCTAGTGACGAAGGAGACAATCCTCCAGA
*
579 AAGATTACTAAAAGACATTGAGGTCATCGGTAAGAAACGAAAACTAC-A-AGAC
66 AAGATTACTAAAAGACATTGAGGTCATCGGTGAGAAACGAAAACTACAACAGAC
* * *
631 GTTGAGGAAGAGAGCCCATTTGCCGGCGAGAAACCACCTAGTGACGAAGGAGACAATCCTCCAGA
1 GTCGAGGAAGAGAGTCCATTCGCCGGCGAGAAACCACCTAGTGACGAAGGAGACAATCCTCCAGA
* * ***
696 AAGATTACTAAAAGACATTGAGGTCGTCGGTGAAAAACGGTTACTACAAGCAGAC
66 AAGATTACTAAAAGACATTGAGGTCATCGGTGAGAAACGAAAACTACAA-CAGAC
* *
751 GTCGAGGAAGAAAGTCCATTCGCCGGCGAGAAACCACCTAGTGACGAAGGAGATAATTCC-CCAG
1 GTCGAGGAAGAGAGTCCATTCGCCGGCGAGAAACCACCTAGTGACGAAGGAGACAA-TCCTCCAG
* * * * **
815 AAAGATTATTAAAAGACATTGAGCTCATCCGTGAGGAACGATTACTAC-A-AGAC
65 AAAGATTACTAAAAGACATTGAGGTCATCGGTGAGAAACGAAAACTACAACAGAC
* * *
868 GTTGAGGAAGAGAGTCCATTCGCCGGCGAGAAACCACCTAGTGACGAAGGAGATAGTCCTCCAGA
1 GTCGAGGAAGAGAGTCCATTCGCCGGCGAGAAACCACCTAGTGACGAAGGAGACAATCCTCCAGA
** * * **
933 AAGATTACTAGCAGGCATTGGGGTCATCGGTGAGAAACGATTACTACAAGCAGAC
66 AAGATTACTAAAAGACATTGAGGTCATCGGTGAGAAACGAAAACTACAA-CAGAC
* * *
988 GTCGAGGAAGAGAGTCCATTCGCCGGTGAGAAACCACCTAGTGACGACGAAGGAAACAATCCACC
1 GTCGAGGAAGAGAGTCCATTCGCCGGCGAGAAACCACCTAGT---GACGAAGGAGACAATCCTCC
* *
1053 AGCAAGATTACTAGAAGA
63 AGAAAGATTACTAAAAGA
1071 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:760 original size:237 final size:236
Alignment explanation
Indices: 277--1070 Score: 1128
Period size: 237 Copynumber: 3.3 Consensus size: 236
267 GGAAGAGAAT
* * * * *
277 GTCGAGGAAGAAAGTCCGTTTGCCGGTGAGAAACCACCTAGTGACGAAGGAGATAAGCCCCCAGA
1 GTCGAGGAAGAAAGTCCATTCGCCGGCGAGAAACCACCTAGTGACGAAGGAGACAA-TCCCCAGA
* *
342 AAGATTACTAAAAGAAATTGAGGTTATCGGTGAGAAACGAAAACTACAAG-CAGATGTCGAGGAA
65 AAGATTACTAAAAGACATTGAGGTCATCGGTGAGAAACGAAAACTACAAGAC-G-T-T-GAGGAA
*
406 GAGAGTCCATTCGCCGGCGAGAAACCGCCTAGTGACGAAGGAGACAATCCTCCAGAAAGATTACT
126 GAGAGTCCATTCGCCGGCGAGAAACCACCTAGTGACGAAGGAGACAATCCTCCAGAAAGATTACT
* ** *
471 AAAAGACATCGAGGTCATCGGTGAGAAACGAAAACTAC-A--AGAT
191 AAAAGACATTGAGGTCATCGGTGAGAAACGATTACTACAAGCAGAC
*
514 GTTGAGGAAGAAAGTCCATTCGCCGGCGAGAAACCACCTAGTGACGAAGGAGACAATCCTCCAGA
1 GTCGAGGAAGAAAGTCCATTCGCCGGCGAGAAACCACCTAGTGACGAAGGAGACAATCC-CCAGA
*
579 AAGATTACTAAAAGACATTGAGGTCATCGGTAAGAAACGAAAACTACAAGACGTTGAGGAAGAGA
65 AAGATTACTAAAAGACATTGAGGTCATCGGTGAGAAACGAAAACTACAAGACGTTGAGGAAGAGA
* *
644 GCCCATTTGCCGGCGAGAAACCACCTAGTGACGAAGGAGACAATCCTCCAGAAAGATTACTAAAA
130 GTCCATTCGCCGGCGAGAAACCACCTAGTGACGAAGGAGACAATCCTCCAGAAAGATTACTAAAA
* * *
709 GACATTGAGGTCGTCGGTGAAAAACGGTTACTACAAGCAGAC
195 GACATTGAGGTCATCGGTGAGAAACGATTACTACAAGCAGAC
*
751 GTCGAGGAAGAAAGTCCATTCGCCGGCGAGAAACCACCTAGTGACGAAGGAGATAATTCCCCAGA
1 GTCGAGGAAGAAAGTCCATTCGCCGGCGAGAAACCACCTAGTGACGAAGGAGACAA-TCCCCAGA
* * * * **
816 AAGATTATTAAAAGACATTGAGCTCATCCGTGAGGAACGATTACTACAAGACGTTGAGGAAGAGA
65 AAGATTACTAAAAGACATTGAGGTCATCGGTGAGAAACGAAAACTACAAGACGTTGAGGAAGAGA
* * **
881 GTCCATTCGCCGGCGAGAAACCACCTAGTGACGAAGGAGATAGTCCTCCAGAAAGATTACTAGCA
130 GTCCATTCGCCGGCGAGAAACCACCTAGTGACGAAGGAGACAATCCTCCAGAAAGATTACTAAAA
* *
946 GGCATTGGGGTCATCGGTGAGAAACGATTACTACAAGCAGAC
195 GACATTGAGGTCATCGGTGAGAAACGATTACTACAAGCAGAC
* * *
988 GTCGAGGAAGAGAGTCCATTCGCCGGTGAGAAACCACCTAGTGACGACGAAGGAAACAATCCACC
1 GTCGAGGAAGAAAGTCCATTCGCCGGCGAGAAACCACCTAGT---GACGAAGGAGACAATCC-CC
* *
1053 AGCAAGATTACTAGAAGA
62 AGAAAGATTACTAAAAGA
1071 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:930 original size:354 final size:356
Alignment explanation
Indices: 277--1071 Score: 1146
Period size: 354 Copynumber: 2.2 Consensus size: 356
267 GGAAGAGAAT
* * * * *
277 GTCGAGGAAGAAAGTCCGTTTGCCGGTGAGAAACCACCTAGTGACGAAGGAGATAAGCCCCCAGA
1 GTCGAGGAAGAGAGTCCATTTGCCGGTGAGAAACCACCTAGTGACGAAGGAGACAATCCACCAGA
* * *
342 AAGATTACTAAAAGAAATTGAGGTTATCGGTGAGAAACGAAAACTACAAGCAGATGTCGAGGAAG
66 AAGATTACTAAAAGAAATTGAGGTCATCGGTGAAAAACGAAAACTACAAGCAGACGTCGAGGAAG
* *
407 AGAGTCCATTCGCCGGCGAGAAACCGCCTAGTGACGAAGGAGACAATCCTCCAGAAAGATTACTA
131 AAAGTCCATTCGCCGGCGAGAAACCACCTAGTGACGAAGGAGACAATCCTCCAGAAAGATTACTA
* * *
472 AAAGACATCGAGGTCATCGGTGAGAAACGAAAACTACAAGATGTTGAGGAAGAAAGTCCATTCGC
196 AAAGACATCGAGCTCATCCGTGAGAAACGAAAACTACAAGACGTTGAGGAAGAAAGTCCATTCGC
537 CGGCGAGAAACCACCTAGTGACGAAGGAGACAATCCTCCAGAAAGATTACTAAAAGACATTGAGG
261 CGGCGAGAAACCACCTAGTGACGAAGGAGACAATCCTCCAGAAAGATTACTAAAAGACATTGAGG
602 TCATCGGTAAGAAACGAAAACTAC-A-AGAC
326 TCATCGGTAAGAAACGAAAACTACAACAGAC
* * * *
631 GTTGAGGAAGAGAGCCCATTTGCCGGCGAGAAACCACCTAGTGACGAAGGAGACAATCCTCCAGA
1 GTCGAGGAAGAGAGTCCATTTGCCGGTGAGAAACCACCTAGTGACGAAGGAGACAATCCACCAGA
* * ***
696 AAGATTACTAAAAGACATTGAGGTCGTCGGTGAAAAACGGTTACTACAAGCAGACGTCGAGGAAG
66 AAGATTACTAAAAGAAATTGAGGTCATCGGTGAAAAACGAAAACTACAAGCAGACGTCGAGGAAG
* *
761 AAAGTCCATTCGCCGGCGAGAAACCACCTAGTGACGAAGGAGATAATTCC-CCAGAAAGATTATT
131 AAAGTCCATTCGCCGGCGAGAAACCACCTAGTGACGAAGGAGACAA-TCCTCCAGAAAGATTACT
* * ** *
825 AAAAGACATTGAGCTCATCCGTGAGGAACGATTACTACAAGACGTTGAGGAAGAGAGTCCATTCG
195 AAAAGACATCGAGCTCATCCGTGAGAAACGAAAACTACAAGACGTTGAGGAAGAAAGTCCATTCG
* * ** * *
890 CCGGCGAGAAACCACCTAGTGACGAAGGAGATAGTCCTCCAGAAAGATTACTAGCAGGCATTGGG
260 CCGGCGAGAAACCACCTAGTGACGAAGGAGACAATCCTCCAGAAAGATTACTAAAAGACATTGAG
* **
955 GTCATCGGTGAGAAACGATTACTACAAGCAGAC
325 GTCATCGGTAAGAAACGAAAACTACAA-CAGAC
* *
988 GTCGAGGAAGAGAGTCCATTCGCCGGTGAGAAACCACCTAGTGACGACGAAGGAAACAATCCACC
1 GTCGAGGAAGAGAGTCCATTTGCCGGTGAGAAACCACCTAGT---GACGAAGGAGACAATCCACC
* *
1053 AGCAAGATTACTAGAAGAA
63 AGAAAGATTACTAAAAGAA
1072 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.