Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga10g00741.F1
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, 612
Length: 1020
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Found at i:525 original size:131 final size:131
Alignment explanation
Indices: 356--659 Score: 482
Period size: 131 Copynumber: 2.3 Consensus size: 131
346 AGACAAAGCC
* * * * *
356 GGTGGCTGAAATCTGCTCCATAGCCGATACATGGAGATAAGATTTGTAATTTTCAGTTTGCTTCC
1 GGTGGCTAAAATCTGCTCCATAGCCGATACATGGAGATAAGATCTGTAATTTTCAATCTACTTCC
* * *
421 TGCAACTTAAGGAAGATAAGACTTGTATCTTCAACCTGCTCTTTGTAACCTCAGAGAGATAAGGC
66 TGCAACTTAAGAAAGATAAGACTTGTATCTTCAACCTGCTCTCTGCAACCTCAGAGAGATAAGGC
486 T
131 T
*
487 GGTGGCTAAAATCTGCTCCATAGCCAATACATGGAGATAAGATCTGTAATTTTCAATCTACTTCC
1 GGTGGCTAAAATCTGCTCCATAGCCGATACATGGAGATAAGATCTGTAATTTTCAATCTACTTCC
* * *
552 TGCAACTTCAGAAAGATAAGACTTGTATCTTTAACCTGCTCTCTGCAACTTCAGAGAGATAAGGC
66 TGCAACTTAAGAAAGATAAGACTTGTATCTTCAACCTGCTCTCTGCAACCTCAGAGAGATAAGGC
617 T
131 T
* *
618 GGTGGCTAAAATCTGCTCTATAGCCGATACATGGAGACAAGA
1 GGTGGCTAAAATCTGCTCCATAGCCGATACATGGAGATAAGA
660 CTTGCCATCT
Statistics
Matches: 158, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
131 158 1.00
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.29
Consensus pattern (131 bp):
GGTGGCTAAAATCTGCTCCATAGCCGATACATGGAGATAAGATCTGTAATTTTCAATCTACTTCC
TGCAACTTAAGAAAGATAAGACTTGTATCTTCAACCTGCTCTCTGCAACCTCAGAGAGATAAGGC
T
Found at i:634 original size:43 final size:43
Alignment explanation
Indices: 551--636 Score: 100
Period size: 43 Copynumber: 2.0 Consensus size: 43
541 AATCTACTTC
* * **
551 CTGCAACTTCAGAAAGATAAGACTTGTATCTTTAACCTGCTCT
1 CTGCAACTTCAGAAAGATAAGACTGGTAGCTAAAACCTGCTCT
* * * *
594 CTGCAACTTCAGAGAGATAAGGCTGGTGGCTAAAATCTGCTCT
1 CTGCAACTTCAGAAAGATAAGACTGGTAGCTAAAACCTGCTCT
637 ATAGCCGATA
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
43 35 1.00
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (43 bp):
CTGCAACTTCAGAAAGATAAGACTGGTAGCTAAAACCTGCTCT
Found at i:776 original size:44 final size:44
Alignment explanation
Indices: 728--834 Score: 119
Period size: 44 Copynumber: 2.4 Consensus size: 44
718 GTCTGCTTCT
* *
728 TGCAACTTCAAGAAGATAAGACTTG-CATATTGAGCCTACTCCAC
1 TGCAACTTCAAGAAGATAAGACTTGTCA-ATTCAACCTACTCCAC
* * * *
772 TGCAACTT-TAGAGAGATAAGGCTTGTCACTTCAACCTGCTCCAC
1 TGCAACTTCAAGA-AGATAAGACTTGTCAATTCAACCTACTCCAC
*
816 TGCAACTTCAGGAAGATAA
1 TGCAACTTCAAGAAGATAA
835 TGTTGGTGGC
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
43 3 0.06
44 45 0.87
45 4 0.08
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (44 bp):
TGCAACTTCAAGAAGATAAGACTTGTCAATTCAACCTACTCCAC
Found at i:870 original size:176 final size:172
Alignment explanation
Indices: 420--880 Score: 385
Period size: 176 Copynumber: 2.6 Consensus size: 172
410 AGTTTGCTTC
* ** * *
420 CTGCAACTTAAG-GAAGATAAGACTTGTATCTTCAACCTGCTCTTTGTAACCTCA-GAGAGATAA
1 CTGCAACTTAAGAG-AGATAAGGCTTGTA-CTTCAACCTGCTCCATGCAACTTCAGGA-AGATAA
* **
483 GGCTGGTGGCTAAAATCTGCTCCATAGCCAATACATGGAGATAAGATCTGTAATTTTCAATCTAC
63 -GTTGGTGGCTAAAATCTGCTCCATAGCTGATACATGGAGATAAGATCTGTAATTTTCAATCTAC
* * * * *
548 TTCCTGCAACTTCAGAAAGATAAGACTTGTATCTTTAACCTGCTCT
127 TTCCTGCAACTTCAGAAAGATAAGACTTGCATATTGAACCTACTCA
* * * ** * * * * *
594 CTGCAACTTCAGAGAGATAAGGCTGGTGGCTAAAATCTGCTCTATAGCCGA-TACATGG-AGACA
1 CTGCAACTTAAGAGAGATAAGGCTTGT-ACTTCAACCTGCTCCAT-G-CAACTTCA-GGAAGATA
**** *** ** *
657 AGACTTGCCATCTTCGATCTGCTTTATAG-TCGATACATGGAGATAAGATCTGTAATTTTCAGTC
62 AG--TTGGTGGCTAAAATCTGCTCCATAGCT-GATACATGGAGATAAGATCTGTAATTTTCAATC
* * *
721 TGCTTCTTGCAACTTCA-AGAAGATAAGACTTGCATATTGAGCCTACTCCA
124 TACTTCCTGCAACTTCAGA-AAGATAAGACTTGCATATTGAACCTACT-CA
*
771 CTGCAACTTTAGAGAGATAAGGCTTGTCACTTCAACCTGCTCCACTGCAACTTCAGGAAGATAAT
1 CTGCAACTTAAGAGAGATAAGGCTTGT-ACTTCAACCTGCTCCA-TGCAACTTCAGGAAGATAA-
* *
836 GTTGGTGGCTAAAATCTTCTCCATAGCTGATACATGAAGATAAGA
63 GTTGGTGGCTAAAATCTGCTCCATAGCTGATACATGGAGATAAGA
881 CTCACCATCT
Statistics
Matches: 215, Mismatches: 56, Indels: 30
0.71 0.19 0.10
Matches are distributed among these distances:
174 35 0.16
175 10 0.05
176 120 0.56
177 48 0.22
178 2 0.01
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (172 bp):
CTGCAACTTAAGAGAGATAAGGCTTGTACTTCAACCTGCTCCATGCAACTTCAGGAAGATAAGTT
GGTGGCTAAAATCTGCTCCATAGCTGATACATGGAGATAAGATCTGTAATTTTCAATCTACTTCC
TGCAACTTCAGAAAGATAAGACTTGCATATTGAACCTACTCA
Found at i:891 original size:221 final size:219
Alignment explanation
Indices: 551--1014 Score: 644
Period size: 221 Copynumber: 2.1 Consensus size: 219
541 AATCTACTTC
* * * * *
551 CTGCAACTTCAGAAAGATAAGACTTGTATCTTTAACCTGCTCTCTGCAACTTCAGAGAGATAAGG
1 CTGCAACTTTAGAGAGATAAGGCTTGTATCTTCAACCTGCTCACTGCAACTTCAGAGAGATAAGG
* * ** *
616 CTGGTGGCTAAAATCTGCTCTATAGCCGATACATGGAGACAAGACTTGCCATCTTCGATCTGCTT
66 CTGGTGGCTAAAATCTGCTCCATAGCCGATACATGAAGACAAGACTCACCATCTTCGATCTGCTC
* *
681 TATAGTCGATACATGGAGATAAGATCTGTAATTTTCAGTCTGCTTCTTGCAACTTCAAGAAGATA
131 CATAGTCGATACATGGAGATAAGATCTGTAATTTTCAGTCTGCTTCCTGCAACTTCAAGAAGATA
*
746 AGACTTGCATATTGAGCCTACTCCA
196 AGACTTGCATATTGAACCT-CTCCA
771 CTGCAACTTTAGAGAGATAAGGCTTGTCA-CTTCAACCTGCTCCACTGCAACTTCAG-GAAGATA
1 CTGCAACTTTAGAGAGATAAGGCTTGT-ATCTTCAACCTGCT-CACTGCAACTTCAGAG-AGATA
* * * * *
834 ATGTTGGTGGCTAAAATCTTCTCCATAGCTGATACATGAAGATAAGACTCACCATCTTCGATCTG
63 AGGCTGGTGGCTAAAATCTGCTCCATAGCCGATACATGAAGACAAGACTCACCATCTTCGATCTG
* *
899 CTCCATATTCGATACATGGAGATAAGATCTGTAATTTTTAGTCTGCTTCCTGCAACTTCAAGAAG
128 CTCCATAGTCGATACATGGAGATAAGATCTGTAATTTTCAGTCTGCTTCCTGCAACTTCAAGAAG
* * * * *
964 ATAAGACTTGTATATTTAACCTGTTCT
193 ATAAGACTTGCATATTGAACCTCTCCA
*
991 CTACAACTTTAGAGAGATAAGGCT
1 CTGCAACTTTAGAGAGATAAGGCT
1015 GGTGGC
Statistics
Matches: 215, Mismatches: 26, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
220 61 0.28
221 154 0.72
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (219 bp):
CTGCAACTTTAGAGAGATAAGGCTTGTATCTTCAACCTGCTCACTGCAACTTCAGAGAGATAAGG
CTGGTGGCTAAAATCTGCTCCATAGCCGATACATGAAGACAAGACTCACCATCTTCGATCTGCTC
CATAGTCGATACATGGAGATAAGATCTGTAATTTTCAGTCTGCTTCCTGCAACTTCAAGAAGATA
AGACTTGCATATTGAACCTCTCCA
Done.