Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga01g01219.F3
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, 701
Length: 1169
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Found at i:916 original size:456 final size:456
Alignment explanation
Indices: 58--935 Score: 1103
Period size: 456 Copynumber: 1.9 Consensus size: 456
48 CTCTGACAAG
* * *
58 ATGCAAATCTTTGTTAAAACCCTCACTGGCAAGACCATCACCCTCGAGGTGGAGAGTTCAGACAC
1 ATGCAAATCTTTGTCAAAACCCTCACTGGAAAGACAATCACCCTCGAGGTGGAGAGTTCAGACAC
* * * * * * * * * *
123 CATTGATAATGTGAAGGCTAAGATCCAAGATAAGGAAGGGATCCCACCGGATCAGCAGAGGCTTA
66 CATTGATAATGTGAAAGCCAAGATCCAAGACAAAGAAGGAATCCCACCAGACCAACAGAAGATTA
* * ** *
188 TCTTTGCTGGCAAACAACTTGAGGATGGCCGCACGCTAGCCGACTACAACATTCAGAAAGAATCC
131 TCTTTGCTGGAAAACAACTTGAAGATGGAAGCACGCTAGCCGACTACAACATCCAGAAAGAATCC
* * * *
253 ACCCTTCACTTGGTTCTTCGACTTCGTGGCGGCATGCAAATCTTTGTCAAGACTCTCACTGGAAA
196 ACCCTCCACTTGGTTCTCCGACTTCGTGGCGGCATGCAAATCTTTGTAAAGACTCTCACCGGAAA
* * *
318 GACAATTACCTTGGAGGTTGAAAGCTCTGACACAATAGATAATGTAAAGGCAAAGATCCAAGACA
261 GACAATCACCTTGGAGGTTGAAAGCTCCGACACAATAGACAATGTAAAGGCAAAGATCCAAGACA
* * * * *
383 AGGAAGGGATCCCACCAGATCAGCAGAGGCTTATCTTTGCTGGAAAGCAGCTTGAAGATGGTCGC
326 AGGAAGGGATCCCACCAGACCAGCAAAGGCTCATATTTGCTGGAAAGCAACTTGAAGATGGTCGC
*
448 ACCTTAGCTGATTACAATATCCAAAAAGAGTCCACCCTCCACCTAGTACTTCGTCTTCGAGGTGG
391 ACATTAGCTGATTACAATATCCAAAAAGAGTCCACCCTCCACCTAGTACTTCGTCTTCGAGGTGG
513 C
456 C
* * * * * *
514 ATGCAAATCTTTGTCAAAACTCTCACTGGAAAGACAATTACCTTGGAGGTGGAGAGTTCGGATAC
1 ATGCAAATCTTTGTCAAAACCCTCACTGGAAAGACAATCACCCTCGAGGTGGAGAGTTCAGACAC
* *
579 CATTGATAATGTGAAAGCCAAGATTCAGGACAAAGAAGGAATCCCACCAGACCAACA-AAGATTG
66 CATTGATAATGTGAAAGCCAAGATCCAAGACAAAGAAGGAATCCCACCAGACCAACAGAAGATT-
* * * * * * * * *
643 ATTTTTGCTGGAAAACAACTTGAAGATGGAAGGACTCTTGCCGATTATAATATCCAGAAGGAGTC
130 ATCTTTGCTGGAAAACAACTTGAAGATGGAAGCACGCTAGCCGACTACAACATCCAGAAAGAATC
* * * * * * * *
708 TACTCTCCATTTGGTTCTCCGCCTTCGTGGTGGTATGCAGATCTTTGTAAAGACTCTTACCGGAA
195 CACCCTCCACTTGGTTCTCCGACTTCGTGGCGGCATGCAAATCTTTGTAAAGACTCTCACCGGAA
* * * * * * *
773 AGACCATCACTTTGGAGGTTGAAAGTTCCGATACCATTGACAATGTGAAGGCAAAGATCCAAGAC
260 AGACAATCACCTTGGAGGTTGAAAGCTCCGACACAATAGACAATGTAAAGGCAAAGATCCAAGAC
* *
838 AAGGAGGGGATCCCACCAGACCAGCAAAGGCTCATATTTGCTGGCAAGCAACTTGAAGATGG-CA
325 AAGGAAGGGATCCCACCAGACCAGCAAAGGCTCATATTTGCTGGAAAGCAACTTGAAGATGGTC-
* * * *
902 GGACATTGGCTGATTATAATATCCAAAAGGAGTC
389 GCACATTAGCTGATTACAATATCCAAAAAGAGTC
936 TACTCTGCAT
Statistics
Matches: 351, Mismatches: 69, Indels: 4
0.83 0.16 0.01
Matches are distributed among these distances:
455 5 0.01
456 346 0.99
ACGTcount: A:0.32, C:0.22, G:0.23, T:0.23
Consensus pattern (456 bp):
ATGCAAATCTTTGTCAAAACCCTCACTGGAAAGACAATCACCCTCGAGGTGGAGAGTTCAGACAC
CATTGATAATGTGAAAGCCAAGATCCAAGACAAAGAAGGAATCCCACCAGACCAACAGAAGATTA
TCTTTGCTGGAAAACAACTTGAAGATGGAAGCACGCTAGCCGACTACAACATCCAGAAAGAATCC
ACCCTCCACTTGGTTCTCCGACTTCGTGGCGGCATGCAAATCTTTGTAAAGACTCTCACCGGAAA
GACAATCACCTTGGAGGTTGAAAGCTCCGACACAATAGACAATGTAAAGGCAAAGATCCAAGACA
AGGAAGGGATCCCACCAGACCAGCAAAGGCTCATATTTGCTGGAAAGCAACTTGAAGATGGTCGC
ACATTAGCTGATTACAATATCCAAAAAGAGTCCACCCTCCACCTAGTACTTCGTCTTCGAGGTGG
C
Found at i:936 original size:228 final size:227
Alignment explanation
Indices: 58--968 Score: 907
Period size: 228 Copynumber: 4.0 Consensus size: 227
48 CTCTGACAAG
* * * * * *
58 ATGCAAATCTTTGTTAAA-ACCCTCACTGGCAAGACCATCACCCTCGAGGTGGAGAGTTCAGACA
1 ATGCAAATCTTTG-TAAAGACTCTCACTGGAAAGACAATCACCTTGGAGGTGGAAAGTTCAGACA
* * * * *
122 CCATTGATAATGTGAAGGCTAAGATCCAAGATAAGGAAGGGATCCCACCGGATCAGCAGAGGCTT
65 CCATTGATAATGTGAAGGCAAAGATCCAAGACAAGGAAGGGATCCCACCAGACCAGCAAAGGCTT
* * * * * * * *
187 ATCTTTGCTGGCAAACAACTTGAGGATGGCCGCACGCTAGCCGACTACAACATTCAGAAA-GAAT
130 ATCTTTGCTGGAAAACAACTTGAAGATGGCAGCAC-TTAGCCGATTACAATATCCA-AAAGGAGT
* * *
251 CCACCCTTCACTTGGTTCTTCGACTTCGTGGCGGC
193 CCACCCTCCACTTGGTTCTTCGCCTTCGTGGTGGC
* * * * *
286 ATGCAAATCTTTGTCAAGACTCTCACTGGAAAGACAATTACCTTGGAGGTTGAAAGCTCTGACAC
1 ATGCAAATCTTTGTAAAGACTCTCACTGGAAAGACAATCACCTTGGAGGTGGAAAGTTCAGACAC
* * * * *
351 AATAGATAATGTAAAGGCAAAGATCCAAGACAAGGAAGGGATCCCACCAGATCAGCAGAGGCTTA
66 CATTGATAATGTGAAGGCAAAGATCCAAGACAAGGAAGGGATCCCACCAGACCAGCAAAGGCTTA
* * * *
416 TCTTTGCTGGAAAGCAGCTTGAAGATGGTC-GCACCTTAGCTGATTACAATATCCAAAAAGAGTC
131 TCTTTGCTGGAAAACAACTTGAAGATGG-CAGCA-CTTAGCCGATTACAATATCCAAAAGGAGTC
* * * * *
480 CACCCTCCACCTAGTACTTCGTCTTCGAGGTGGC
194 CACCCTCCACTTGGTTCTTCGCCTTCGTGGTGGC
* * * *
514 ATGCAAATCTTTGTCAAA-ACTCTCACTGGAAAGACAATTACCTTGGAGGTGGAGAGTTCGGATA
1 ATGCAAATCTTTGT-AAAGACTCTCACTGGAAAGACAATCACCTTGGAGGTGGAAAGTTCAGACA
* * * * * * * *
578 CCATTGATAATGTGAAAGCCAAGATTCAGGACAAAGAAGGAATCCCACCAGACCAACAAA-GATT
65 CCATTGATAATGTGAAGGCAAAGATCCAAGACAAGGAAGGGATCCCACCAGACCAGCAAAGGCTT
* * * * * *
642 GATTTTTGCTGGAAAACAACTTGAAGATGGAAGGACTCTTGCCGATTATAATATCCAGAAGGAGT
130 -ATCTTTGCTGGAAAACAACTTGAAGATGGCAGCACT-TAGCCGATTACAATATCCAAAAGGAGT
* * * * *
707 CTACTCTCCATTTGGTTCTCCGCCTTCGTGGTGGT
193 CCACCCTCCACTTGGTTCTTCGCCTTCGTGGTGGC
* * * * * * * *
742 ATGCAGATCTTTGTAAAGACTCTTACCGGAAAGACCATCACTTTGGAGGTTGAAAGTTCCGATAC
1 ATGCAAATCTTTGTAAAGACTCTCACTGGAAAGACAATCACCTTGGAGGTGGAAAGTTCAGACAC
* * *
807 CATTGACAATGTGAAGGCAAAGATCCAAGACAAGGAGGGGATCCCACCAGACCAGCAAAGGCTCA
66 CATTGATAATGTGAAGGCAAAGATCCAAGACAAGGAAGGGATCCCACCAGACCAGCAAAGGCTTA
* * * * * * * *
872 TATTTGCTGGCAAGCAACTTGAAGATGGCAGGACATTGGCTGATTATAATATCCAAAAGGAGTCT
131 TCTTTGCTGGAAAACAACTTGAAGATGGCAGCAC-TTAGCCGATTACAATATCCAAAAGGAGTCC
* * * *
937 ACTCTGCATCTT-GTCCTTCGCCTTCGCGGTGG
195 ACCCTCCA-CTTGGTTCTTCGCCTTCGTGGTGG
969 TTTCTAAGTA
Statistics
Matches: 566, Mismatches: 105, Indels: 24
0.81 0.15 0.03
Matches are distributed among these distances:
227 14 0.02
228 543 0.96
229 9 0.02
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.24
Consensus pattern (227 bp):
ATGCAAATCTTTGTAAAGACTCTCACTGGAAAGACAATCACCTTGGAGGTGGAAAGTTCAGACAC
CATTGATAATGTGAAGGCAAAGATCCAAGACAAGGAAGGGATCCCACCAGACCAGCAAAGGCTTA
TCTTTGCTGGAAAACAACTTGAAGATGGCAGCACTTAGCCGATTACAATATCCAAAAGGAGTCCA
CCCTCCACTTGGTTCTTCGCCTTCGTGGTGGC
Done.