Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga01g01219.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, 838
Length: 1397
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Found at i:484 original size:228 final size:228
Alignment explanation
Indices: 58--1163 Score: 1107
Period size: 228 Copynumber: 4.9 Consensus size: 228
48 CTCTGACAAG
* * * * * * * * *
58 ATGCAAATCTTTGTTAAAACCCTCACTGGCAAGACCATCACCCTCGAGGTGGAGAGTTCAGACAC
1 ATGCAAATCTTTGTCAAGACTCTCACTGGAAAGACAATCACCTTGGAGGTTGAAAGTTCAGACAC
* * * * * *
123 CATTGATAATGTGAAGGCTAAGATCCAAGATAAGGAAGGGATCCCACCGGATCAGCAGAGGCTTA
66 CATTGATAATGTAAAGGCAAAGATCCAAGACAAGGAAGGGATCCCACCAGACCAGCAAAGGCTTA
* * * * * * *
188 TCTTTGCTGGCAAA-CAACTTGAGGATGGCCGCACGC-TAGCCGACTACAACATTCAGAAA-GAA
131 TCTTTGCTGG-AAAGCAACTTGAAGATGGTCGGAC-CTTAGCCGATTACAATATCCA-AAAGGAG
* *
250 TCCACCCTTCACTTGGTTCTTCGACTTCGTGGCGGC
193 TCCACCCTCCACTTGGTTCTTCGACTTCGTGGTGGC
* * *
286 ATGCAAATCTTTGTCAAGACTCTCACTGGAAAGACAATTACCTTGGAGGTTGAAAGCTCTGACAC
1 ATGCAAATCTTTGTCAAGACTCTCACTGGAAAGACAATCACCTTGGAGGTTGAAAGTTCAGACAC
* * * *
351 AATAGATAATGTAAAGGCAAAGATCCAAGACAAGGAAGGGATCCCACCAGATCAGCAGAGGCTTA
66 CATTGATAATGTAAAGGCAAAGATCCAAGACAAGGAAGGGATCCCACCAGACCAGCAAAGGCTTA
* * * *
416 TCTTTGCTGGAAAGCAGCTTGAAGATGGTCGCACCTTAGCTGATTACAATATCCAAAAAGAGTCC
131 TCTTTGCTGGAAAGCAACTTGAAGATGGTCGGACCTTAGCCGATTACAATATCCAAAAGGAGTCC
* * * * *
481 ACCCTCCACCTAGTACTTCGTCTTCGAGGTGGC
196 ACCCTCCACTTGGTTCTTCGACTTCGTGGTGGC
* * * * * *
514 ATGCAAATCTTTGTCAAAACTCTCACTGGAAAGACAATTACCTTGGAGGTGGAGAGTTCGGATAC
1 ATGCAAATCTTTGTCAAGACTCTCACTGGAAAGACAATCACCTTGGAGGTTGAAAGTTCAGACAC
* * * * * * *
579 CATTGATAATGTGAAA-GCCAAGATTCAGGACAAAGAAGGAATCCCACCAGACCAACAAA-GATT
66 CATTGATAATGT-AAAGGCAAAGATCCAAGACAAGGAAGGGATCCCACCAGACCAGCAAAGGCTT
* * ** * *
642 GATTTTTGCTGGAAAACAACTTGAAGATGGAAGGACTCTT-GCCGATTATAATATCCAGAAGGAG
130 -ATCTTTGCTGGAAAGCAACTTGAAGATGGTCGGAC-CTTAGCCGATTACAATATCCAAAAGGAG
* * * * * *
706 TCTACTCTCCATTTGGTTCTCCGCCTTCGTGGTGGT
193 TCCACCCTCCACTTGGTTCTTCGACTTCGTGGTGGC
* * * * * * * *
742 ATGCAGATCTTTGTAAAGACTCTTACCGGAAAGACCATCACTTTGGAGGTTGAAAGTTCCGATAC
1 ATGCAAATCTTTGTCAAGACTCTCACTGGAAAGACAATCACCTTGGAGGTTGAAAGTTCAGACAC
* * * *
807 CATTGACAATGTGAAGGCAAAGATCCAAGACAAGG-AGGGTATCCCCCCAGACCAGCAAAGGCTC
66 CATTGATAATGTAAAGGCAAAGATCCAAGACAAGGAAGGG-ATCCCACCAGACCAGCAAAGGCTT
* * * * * * *
871 ATCTTTGCTGGCAAGCAGCTCGAAGATGGTAGGACATTGGCCGACTACAATATCCAAAAGGAGTC
130 ATCTTTGCTGGAAAGCAACTTGAAGATGGTCGGACCTTAGCCGATTACAATATCCAAAAGGAGTC
* * * * * *
936 TACCCTTCACTTGGTGT-TGCGGCTGCGTGGTGGG
195 CACCCTCCACTTGGT-TCTTCGACTTCGTGGTGGC
* * * * *
970 ATGCAGATCTTTGTTAAGACTCTTACTGGAAAGACTATCA-CTCTAGAGGTTGAAAGTTCAGACA
1 ATGCAAATCTTTGTCAAGACTCTCACTGGAAAGACAATCACCT-TGGAGGTTGAAAGTTCAGACA
* * * *
1034 CCATTGACAATGTTAAGGCAAAGATTCAAGACAAGGAAGGGATCCCACCAGACCAGCAAAGGCTC
65 CCATTGATAATGTAAAGGCAAAGATCCAAGACAAGGAAGGGATCCCACCAGACCAGCAAAGGCTT
* * * * * *
1099 ATATTTGCTGGCAAGCAACTTGAAGATGG-CAGGACATTGGCTGATTATAATATCCAAAAGGAGT
130 ATCTTTGCTGGAAAGCAACTTGAAGATGGTC-GGACCTTAGCCGATTACAATATCCAAAAGGAGT
1163 C
194 C
1164 TACTCTGCAT
Statistics
Matches: 738, Mismatches: 126, Indels: 28
0.83 0.14 0.03
Matches are distributed among these distances:
227 18 0.02
228 707 0.96
229 13 0.02
ACGTcount: A:0.31, C:0.22, G:0.23, T:0.23
Consensus pattern (228 bp):
ATGCAAATCTTTGTCAAGACTCTCACTGGAAAGACAATCACCTTGGAGGTTGAAAGTTCAGACAC
CATTGATAATGTAAAGGCAAAGATCCAAGACAAGGAAGGGATCCCACCAGACCAGCAAAGGCTTA
TCTTTGCTGGAAAGCAACTTGAAGATGGTCGGACCTTAGCCGATTACAATATCCAAAAGGAGTCC
ACCCTCCACTTGGTTCTTCGACTTCGTGGTGGC
Found at i:922 original size:456 final size:455
Alignment explanation
Indices: 58--1197 Score: 1282
Period size: 456 Copynumber: 2.5 Consensus size: 455
48 CTCTGACAAG
* * * * *
58 ATGCAAATCTTTGTTAAAACCCTCACTGGCAAGACCATCACCCTCGAGGTGGAGAGTTCAGACAC
1 ATGCAAATCTTTGTTAAAACTCTCACTGGAAAGACAATCACCTTAGAGGTGGAGAGTTCAGACAC
* * * * * * *
123 CATTGATAATGTGAAGGCTAAGATCCAAGATAAGGAAGGGATCCCACCGGATCAGCAGAGGCTTA
66 CATTGATAATGTGAAGGCAAAGATTCAAGACAAGGAAGGGATCCCACCAGACCAGCA-AAGATTA
* * * * * * * * * * * *
188 TCTTTGCTGGCAAACAACTTGAGGATGGCCGCACGCTAGCCGACTACAACATTCAGAAAGAATCC
130 TATTTGCTGGCAAACAACTTGAAGATGGCAGGACTCTAGCCGATTATAATATCCAGAAGGAGTCT
* * * * * * * *
253 ACCCTTCACTTGGTTCTTCGACTTCGTGGCGGCATGCAAATCTTTGTCAAGACTCTCACTGGAAA
195 ACTCTCCATTTGGTTCTTCGCCTTCGTGGTGGTATGCAAATCTTTGTAAAGACTCTCACCGGAAA
* * *
318 GACAATTACCTTGGAGGTTGAAAGCTCTGACACAATAGATAATGTAAAGGCAAAGATCCAAGACA
260 GACAATCACCTTGGAGGTTGAAAGCTCCGACACAATAGACAATGTAAAGGCAAAGATCCAAGACA
* * * * *
383 AGGAAGGGATCCCACCAGATCAGCAGAGGCTTATCTTTGCTGGAAAGCAGCTTGAAGATGGTCGC
325 AGGAAGGGATCCCACCAGACCAGCAAAGGCTCATCTTTGCTGGAAAGCAGCTCGAAGATGGTAGC
* * * * *
448 ACCTTAGCTGATTACAATATCCAAAAAGAGTCCACCCTCCACCTAGTACTT-CGTCTTCGAGGTG
390 ACATTAGCCGACTACAATATCCAAAAAGAGTCCACCCTCCACCTAGT-CTTGCGGCTGCGAGGTG
512 GC
454 GC
* * * * *
514 ATGCAAATCTTTGTCAAAACTCTCACTGGAAAGACAATTACCTTGGAGGTGGAGAGTTCGGATAC
1 ATGCAAATCTTTGTTAAAACTCTCACTGGAAAGACAATCACCTTAGAGGTGGAGAGTTCAGACAC
* * * * * *
579 CATTGATAATGTGAAAGCCAAGATTCAGGACAAAGAAGGAATCCCACCAGACCAACAAAGATTGA
66 CATTGATAATGTGAAGGCAAAGATTCAAGACAAGGAAGGGATCCCACCAGACCAGCAAAGATT-A
* * * *
644 TTTTTGCTGGAAAACAACTTGAAGATGGAAGGACTCTTGCCGATTATAATATCCAGAAGGAGTCT
130 TATTTGCTGGCAAACAACTTGAAGATGGCAGGACTCTAGCCGATTATAATATCCAGAAGGAGTCT
* * *
709 ACTCTCCATTTGGTTCTCCGCCTTCGTGGTGGTATGCAGATCTTTGTAAAGACTCTTACCGGAAA
195 ACTCTCCATTTGGTTCTTCGCCTTCGTGGTGGTATGCAAATCTTTGTAAAGACTCTCACCGGAAA
* * * * * * *
774 GACCATCACTTTGGAGGTTGAAAGTTCCGATACCATTGACAATGTGAAGGCAAAGATCCAAGACA
260 GACAATCACCTTGGAGGTTGAAAGCTCCGACACAATAGACAATGTAAAGGCAAAGATCCAAGACA
* *
839 AGG-AGGGTATCCCCCCAGACCAGCAAAGGCTCATCTTTGCTGGCAAGCAGCTCGAAGATGGTAG
325 AGGAAGGG-ATCCCACCAGACCAGCAAAGGCTCATCTTTGCTGGAAAGCAGCTCGAAGATGGTAG
* * * * * * * * *
903 GACATTGGCCGACTACAATATCCAAAAGGAGTCTACCCTTCACTTGGTGTTGCGGCTGCGTGGTG
389 CACATTAGCCGACTACAATATCCAAAAAGAGTCCACCCTCCACCTAGTCTTGCGGCTGCGAGGTG
*
968 GG
454 GC
* * * * * *
970 ATGCAGATCTTTGTTAAGACTCTTACTGGAAAGACTATCA-CTCTAGAGGTTGAAAGTTCAGACA
1 ATGCAAATCTTTGTTAAAACTCTCACTGGAAAGACAATCACCT-TAGAGGTGGAGAGTTCAGACA
* * * *
1034 CCATTGACAATGTTAAGGCAAAGATTCAAGACAAGGAAGGGATCCCACCAGACCAGCAAAGGCTC
65 CCATTGATAATGTGAAGGCAAAGATTCAAGACAAGGAAGGGATCCCACCAGACCAGCAAA-GATT
* * * *
1099 ATATTTGCTGGCAAGCAACTTGAAGATGGCAGGACAT-TGGCTGATTATAATATCCAAAAGGAGT
129 ATATTTGCTGGCAAACAACTTGAAGATGGCAGGAC-TCTAGCCGATTATAATATCCAGAAGGAGT
* * *
1163 CTACTCTGCATCTT-GTCCTTCGCCTTCGCGGTGGT
193 CTACTCTCCAT-TTGGTTCTTCGCCTTCGTGGTGGT
1198 TTCTAAGTAA
Statistics
Matches: 566, Mismatches: 111, Indels: 14
0.82 0.16 0.02
Matches are distributed among these distances:
455 12 0.02
456 549 0.97
457 5 0.01
ACGTcount: A:0.31, C:0.22, G:0.23, T:0.24
Consensus pattern (455 bp):
ATGCAAATCTTTGTTAAAACTCTCACTGGAAAGACAATCACCTTAGAGGTGGAGAGTTCAGACAC
CATTGATAATGTGAAGGCAAAGATTCAAGACAAGGAAGGGATCCCACCAGACCAGCAAAGATTAT
ATTTGCTGGCAAACAACTTGAAGATGGCAGGACTCTAGCCGATTATAATATCCAGAAGGAGTCTA
CTCTCCATTTGGTTCTTCGCCTTCGTGGTGGTATGCAAATCTTTGTAAAGACTCTCACCGGAAAG
ACAATCACCTTGGAGGTTGAAAGCTCCGACACAATAGACAATGTAAAGGCAAAGATCCAAGACAA
GGAAGGGATCCCACCAGACCAGCAAAGGCTCATCTTTGCTGGAAAGCAGCTCGAAGATGGTAGCA
CATTAGCCGACTACAATATCCAAAAAGAGTCCACCCTCCACCTAGTCTTGCGGCTGCGAGGTGGC
Done.