Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga04g00763.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, 945
Length: 1576
ACGTcount: A:0.29, C:0.26, G:0.22, T:0.23
Found at i:1291 original size:228 final size:228
Alignment explanation
Indices: 60--1180 Score: 1749
Period size: 228 Copynumber: 4.9 Consensus size: 228
50 CTCTCAAAAG
* * * *
60 ATGCAGATCTTCGTCAAAACCCTT-ACCGGCAAGACCATCACCCTCGAGGTTGAGAGTTCTGACA
1 ATGCAGATCTTCGTCAAAA-CCTTAACCGGCAAGACCATCACCCTCGAAGTCGAGAGCTCCGACA
124 CCATCGATAATGTAAAGTCTAAAATTCAAGACAAGGAAGGCATCCCACCAGACCAGCAGCGTCTC
65 CCATCGATAATGTAAAGTCTAAAATTCAAGACAAGGAAGGCATCCCACCAGACCAGCAGCGTCTC
* * *
189 ATCTTCGCCGGCAAACAGCTCGAGGACGGCCGTACCTTGGCCGATTACAACATTCAGAAGGAATC
130 ATCTTCGCCGGCAAACAGCTCGAAGATGGCCGTACCTTGGCCGATTACAACATCCAGAAGGAATC
254 CACCCTCCACCTTGTCCTCCGTCTTCGTGGGGGT
195 CACCCTCCACCTTGTCCTCCGTCTTCGTGGGGGT
288 ATGCAGATCTTCGTCAAAACCTTAACCGGCAAGACCATCACCCTCGAAGTCGAGAGCTCCGACAC
1 ATGCAGATCTTCGTCAAAACCTTAACCGGCAAGACCATCACCCTCGAAGTCGAGAGCTCCGACAC
* *
353 CATCGATAATGTGAAGTCTAAAATCCAAGACAAGGAAGGCATCCCACCAGACCAGCAGCGTCTCA
66 CATCGATAATGTAAAGTCTAAAATTCAAGACAAGGAAGGCATCCCACCAGACCAGCAGCGTCTCA
*
418 TCTTCGCCGGAAAACAGCTCGAAGATGGCCGTACCTTGGCCGATTACAACATCCAGAAGGAATCC
131 TCTTCGCCGGCAAACAGCTCGAAGATGGCCGTACCTTGGCCGATTACAACATCCAGAAGGAATCC
*
483 ACCCTCCACCTTGTCCTACGTCTTCGTGGGGGT
196 ACCCTCCACCTTGTCCTCCGTCTTCGTGGGGGT
*
516 ATGCAGATCTTCGTCAAAACCTTAACCGGCAAGACCATCACCCTCGAAGTCGAGAGCTCTGACAC
1 ATGCAGATCTTCGTCAAAACCTTAACCGGCAAGACCATCACCCTCGAAGTCGAGAGCTCCGACAC
581 CATCGATAATGTAAAGTCTAAAATTCAAGACAAGGAAGGCATCCCACCAGACCAGCAGCGTCTCA
66 CATCGATAATGTAAAGTCTAAAATTCAAGACAAGGAAGGCATCCCACCAGACCAGCAGCGTCTCA
*
646 TCTTCGCCGGCAAACAGCTCGAAGACGGCCGTACCTTGGCCGATTACAACATCCAGAAGGAATCC
131 TCTTCGCCGGCAAACAGCTCGAAGATGGCCGTACCTTGGCCGATTACAACATCCAGAAGGAATCC
711 ACCCTCCACCTTGTCCTCCGTCTTCGTGGGGGT
196 ACCCTCCACCTTGTCCTCCGTCTTCGTGGGGGT
*
744 ATGCAGATCTTCGTCAAAACCTTAACCGGTAAGACCATCACCCTCGAAGTCGAGAGCTCCGACAC
1 ATGCAGATCTTCGTCAAAACCTTAACCGGCAAGACCATCACCCTCGAAGTCGAGAGCTCCGACAC
* * *
809 CATCGACAATGTCAAGTCTAAAATCCAAGACAAGGAAGGCATCCCACCAGACCAGCAGCGTCTCA
66 CATCGATAATGTAAAGTCTAAAATTCAAGACAAGGAAGGCATCCCACCAGACCAGCAGCGTCTCA
* *
874 TCTTCGCCGGCAAACAGCTCGAAGATGGCCGTACCTTGGCCGATTATAATATCCAGAAGGAATCC
131 TCTTCGCCGGCAAACAGCTCGAAGATGGCCGTACCTTGGCCGATTACAACATCCAGAAGGAATCC
* * *
939 ACCCTCCACCTCGTCCTCCGTCTTCGCGGGGGC
196 ACCCTCCACCTTGTCCTCCGTCTTCGTGGGGGT
* * * * * * * * *
972 ATGCAGATCTTCGTGAAAACCTTGACTGGCAAGACCATCACCTTAGAGGTGGAGAGTTCGGACAC
1 ATGCAGATCTTCGTCAAAACCTTAACCGGCAAGACCATCACCCTCGAAGTCGAGAGCTCCGACAC
* * * * * * * * *
1037 CATCGACAATGTAAAGGCGAAGATTCAAGACAAGGAAGGGATCCCACCAGACCAACAACGTTTGA
66 CATCGATAATGTAAAGTCTAAAATTCAAGACAAGGAAGGCATCCCACCAGACCAGCAGCGTCTCA
* * * * * * ** * * * *
1102 TCTTTGCAGGGAAGCAGCTTGAGGATGGGAGGACCTTGGCTGATTATAACATCCAGAAGGAATCG
131 TCTTCGCCGGCAAACAGCTCGAAGATGGCCGTACCTTGGCCGATTACAACATCCAGAAGGAATCC
*
1167 ACCCTTCACCTTGT
196 ACCCTCCACCTTGT
1181 TTTGAGGCTT
Statistics
Matches: 830, Mismatches: 62, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
227 4 0.00
228 826 1.00
ACGTcount: A:0.29, C:0.30, G:0.22, T:0.20
Consensus pattern (228 bp):
ATGCAGATCTTCGTCAAAACCTTAACCGGCAAGACCATCACCCTCGAAGTCGAGAGCTCCGACAC
CATCGATAATGTAAAGTCTAAAATTCAAGACAAGGAAGGCATCCCACCAGACCAGCAGCGTCTCA
TCTTCGCCGGCAAACAGCTCGAAGATGGCCGTACCTTGGCCGATTACAACATCCAGAAGGAATCC
ACCCTCCACCTTGTCCTCCGTCTTCGTGGGGGT
Found at i:1299 original size:228 final size:228
Alignment explanation
Indices: 60--1411 Score: 961
Period size: 228 Copynumber: 5.9 Consensus size: 228
50 CTCTCAAAAG
* * * * * ** * * * *
60 ATGCAGATCTTCGTCAAAACCCTT-ACCGGCAAGACCATCACCCTCGAGGTTGAGAGTTCTGACA
1 ATGCAGATCTTCGTGAAAA-CATTGACTGGCAAAACAATCACATTAGAGGTGGAAAGTTCGGACA
* * * * * *
124 CCATCGATAATGTAAAGTCTAAAATTCAAGACAAGGAAGGCATCCCACCAGACCAGCAGCGTCTC
65 CAATCGACAATGTAAAGGCGAAGATTCAAGACAAGGAAGGCATCCCACCAGACCAGCAACGTCTC
* * * * ** * * * *
189 ATCTTCGCCGGCAAA-CAGCTCGAGGACGGCCGTACCTTGGCCGATTACAACATTCAGAAGGAAT
130 ATCTTTGCAGG-AAAGCAGCTTGAGGATGGGAGGACCTTGGCTGATTATAACATCCAGAAGGAAT
* * * * * * *
253 CCACCCTCCACCTTGTCCTCCGTCTTCGTGGGGGT
194 CCACCCTTCACCTTGTTCTCAGGCTTCGCGGAGGC
* * * * * * ** * * * * * *
288 ATGCAGATCTTCGTCAAAACCTTAACCGGCAAGACCATCACCCTCGAAGTCGAGAGCTCCGACAC
1 ATGCAGATCTTCGTGAAAACATTGACTGGCAAAACAATCACATTAGAGGTGGAAAGTTCGGACAC
* * * * * * * *
353 CATCGATAATGTGAAGTCTAAAATCCAAGACAAGGAAGGCATCCCACCAGACCAGCAGCGTCTCA
66 AATCGACAATGTAAAGGCGAAGATTCAAGACAAGGAAGGCATCCCACCAGACCAGCAACGTCTCA
* * * * * ** * * *
418 TCTTCGCCGGAAAACAGCTCGAAGATGGCCGTACCTTGGCCGATTACAACATCCAGAAGGAATCC
131 TCTTTGCAGGAAAGCAGCTTGAGGATGGGAGGACCTTGGCTGATTATAACATCCAGAAGGAATCC
* * * * * *
483 ACCCTCCACCTTGTCCT-ACGTCTTCGTGGGGGT
196 ACCCTTCACCTTGTTCTCA-GGCTTCGCGGAGGC
* * * * * * ** * * * * * *
516 ATGCAGATCTTCGTCAAAACCTTAACCGGCAAGACCATCACCCTCGAAGTCGAGAGCTCTGACAC
1 ATGCAGATCTTCGTGAAAACATTGACTGGCAAAACAATCACATTAGAGGTGGAAAGTTCGGACAC
* * * * * *
581 CATCGATAATGTAAAGTCTAAAATTCAAGACAAGGAAGGCATCCCACCAGACCAGCAGCGTCTCA
66 AATCGACAATGTAAAGGCGAAGATTCAAGACAAGGAAGGCATCCCACCAGACCAGCAACGTCTCA
* * * * * ** * * *
646 TCTTCGCCGGCAAA-CAGCTCGAAGACGGCCGTACCTTGGCCGATTACAACATCCAGAAGGAATC
131 TCTTTGCAGG-AAAGCAGCTTGAGGATGGGAGGACCTTGGCTGATTATAACATCCAGAAGGAATC
* * * * * * *
710 CACCCTCCACCTTGTCCTCCGTCTTCGTGGGGGT
195 CACCCTTCACCTTGTTCTCAGGCTTCGCGGAGGC
* * * * * * * ** * * * * * *
744 ATGCAGATCTTCGTCAAAACCTTAACCGGTAAGACCATCACCCTCGAAGTCGAGAGCTCCGACAC
1 ATGCAGATCTTCGTGAAAACATTGACTGGCAAAACAATCACATTAGAGGTGGAAAGTTCGGACAC
* * * * * * *
809 CATCGACAATGTCAAGTCTAAAATCCAAGACAAGGAAGGCATCCCACCAGACCAGCAGCGTCTCA
66 AATCGACAATGTAAAGGCGAAGATTCAAGACAAGGAAGGCATCCCACCAGACCAGCAACGTCTCA
* * * * ** * * *
874 TCTTCGCCGGCAAA-CAGCTCGAAGATGGCCGTACCTTGGCCGATTATAATATCCAGAAGGAATC
131 TCTTTGCAGG-AAAGCAGCTTGAGGATGGGAGGACCTTGGCTGATTATAACATCCAGAAGGAATC
* * * * * *
938 CACCCTCCACCTCGTCCTCCGTCTTCGCGGGGGC
195 CACCCTTCACCTTGTTCTCAGGCTTCGCGGAGGC
* * * * *
972 ATGCAGATCTTCGTGAAAACCTTGACTGGCAAGACCATCACCTTAGAGGTGGAGAGTTCGGACAC
1 ATGCAGATCTTCGTGAAAACATTGACTGGCAAAACAATCACATTAGAGGTGGAAAGTTCGGACAC
* * * * *
1037 CATCGACAATGTAAAGGCGAAGATTCAAGACAAGGAAGGGATCCCACCAGACCAACAACGTTTGA
66 AATCGACAATGTAAAGGCGAAGATTCAAGACAAGGAAGGCATCCCACCAGACCAGCAACGTCTCA
* *
1102 TCTTTGCAGGGAAGCAGCTTGAGGATGGGAGGACCTTGGCTGATTATAACATCCAGAAGGAATCG
131 TCTTTGCAGGAAAGCAGCTTGAGGATGGGAGGACCTTGGCTGATTATAACATCCAGAAGGAATCC
* * *
1167 ACCCTTCACCTTGTTTTGAGGCTTCGTGGAGGC
196 ACCCTTCACCTTGTTCTCAGGCTTCGCGGAGGC
* * * * * *
1200 ATGCAGATTTTCGTTAAGACATTGACTGGGAAAACAATCACATTGGAGGTGGAAAGTTCGGATAC
1 ATGCAGATCTTCGTGAAAACATTGACTGGCAAAACAATCACATTAGAGGTGGAAAGTTCGGACAC
* * * * * * * * *
1265 AATTGATAATGTGAAGGCGAAGATTCAGGACAAGGAAGGTATCCCTCCAGATCAGCAAAGGCTCA
66 AATCGACAATGTAAAGGCGAAGATTCAAGACAAGGAAGGCATCCCACCAGACCAGCAACGTCTCA
* * * * * * *
1330 TCTTTGCTGGAAAGCA-ATTGGAGGATGGGAGGACTTTAGCTGATTATAACATTCAGAAAGAGTC
131 TCTTTGCAGGAAAGCAGCTT-GAGGATGGGAGGACCTTGGCTGATTATAACATCCAGAAGGAATC
1394 CACCCTTCACCTTGTTCT
195 CACCCTTCACCTTGTTCT
1412 TCGTCTCCGT
Statistics
Matches: 1017, Mismatches: 100, Indels: 14
0.90 0.09 0.01
Matches are distributed among these distances:
227 11 0.01
228 1003 0.99
229 3 0.00
ACGTcount: A:0.29, C:0.28, G:0.23, T:0.21
Consensus pattern (228 bp):
ATGCAGATCTTCGTGAAAACATTGACTGGCAAAACAATCACATTAGAGGTGGAAAGTTCGGACAC
AATCGACAATGTAAAGGCGAAGATTCAAGACAAGGAAGGCATCCCACCAGACCAGCAACGTCTCA
TCTTTGCAGGAAAGCAGCTTGAGGATGGGAGGACCTTGGCTGATTATAACATCCAGAAGGAATCC
ACCCTTCACCTTGTTCTCAGGCTTCGCGGAGGC
Found at i:1398 original size:684 final size:684
Alignment explanation
Indices: 60--1423 Score: 1726
Period size: 684 Copynumber: 2.0 Consensus size: 684
50 CTCTCAAAAG
* * * *
60 ATGCAGATCTTCGTCAAAACCCTTACCGGCAAGACCATCACCCTCGAGGTTGAGAGTTCTGACAC
1 ATGCAGATCTTCGTCAAAACCCTTACCGGCAAGACCATCACCCTCGAAGTCGAGAGCTCCGACAC
* *
125 CATCGATAATGTAAAGTCTAAAATTCAAGACAAGGAAGGCATCCCACCAGACCAGCAGCGTCTCA
66 CATCGACAATGTAAAGTCTAAAATCCAAGACAAGGAAGGCATCCCACCAGACCAGCAGCGTCTCA
* *
190 TCTTCGCCGGCAAACAGCTCGAGGACGGCCGTACCTTGGCCGATTACAACATTCAGAAGGAATCC
131 TCTTCGCCGGCAAACAGCTCGAAGACGGCCGTACCTTGGCCGATTACAACATCCAGAAGGAATCC
* * *
255 ACCCTCCACCTTGTCCTCCGTCTTCGTGGGGGTATGCAGATCTTCGTCAAAACCTTAACCGGCAA
196 ACCCTCCACCTCGTCCTCCGTCTTCGCGGGGGCATGCAGATCTTCGTCAAAACCTTAACCGGCAA
* * * * *
320 GACCATCACCCTCGAAGTCGAGAGCTCCGACACCATCGATAATGTGAAGTCTAAAATCCAAGACA
261 GACCATCACCCTAGAAGTCGAGAGCTCCGACACCATCGACAATGTAAAGGCGAAAATCCAAGACA
* * * * *
385 AGGAAGGCATCCCACCAGACCAGCAGCGTCTCATCTTCGCCGGAAAACAGCTCGAAGATGGCCGT
326 AGGAAGGCATCCCACCAGACCAACAACGTCTCATCTTCGCAGGAAAACAGCTCGAAGATGGCAGG
* *
450 ACCTTGGCCGATTACAACATCCAGAAGGAATCCACCCTCCACCTTGTCCTACGTCTTCGTGGGGG
391 ACCTTGGCCGATTACAACATCCAGAAGGAATCCACCCTCCACCTTGTCCTACGGCTTCGTGGAGG
* * * * * * *
515 TATGCAGATCTTCGTCAAAACCTTAACCGGCAAGACCATCACCCTCGAAGTCGAGAGCTCTGACA
456 CATGCAGATCTTCGTCAAAACATTAACCGGCAAAACAATCACACTCGAAGTCGAAAGCTCGGACA
* * * ** *
580 CCATCGATAATGTAAAGTCTAAAATTCAAGACAAGGAAGGCATCCCACCAGACCAGCAGCGTCTC
521 CAATCGATAATGTAAAGGCGAAAATTCAAGACAAGGAAGGCATCCCACCAGACCAGCAAAGGCTC
* * * * *
645 ATCTTCGCCGGCAAACAGCTCGAAGACGGCCGTACCTTGGCCGATTACAACATCCAGAAGGAATC
586 ATCTTCGCCGGCAAACAACTCGAAGACGGCAGGACCTTAGCCGATTACAACATCCAGAAAGAATC
*
710 CACCCTCCACCTTGTCCTCCGTCTTCGTGGGGGT
651 CACCCTCCACCTTGTCCTCCGTCTCCGTGGGGGT
*
744 ATGCAGATCTTCGTCAAAA-CCTTAACCGGTAAGACCATCACCCTCGAAGTCGAGAGCTCCGACA
1 ATGCAGATCTTCGTCAAAACCCTT-ACCGGCAAGACCATCACCCTCGAAGTCGAGAGCTCCGACA
*
808 CCATCGACAATGTCAAGTCTAAAATCCAAGACAAGGAAGGCATCCCACCAGACCAGCAGCGTCTC
65 CCATCGACAATGTAAAGTCTAAAATCCAAGACAAGGAAGGCATCCCACCAGACCAGCAGCGTCTC
* * *
873 ATCTTCGCCGGCAAACAGCTCGAAGATGGCCGTACCTTGGCCGATTATAATATCCAGAAGGAATC
130 ATCTTCGCCGGCAAACAGCTCGAAGACGGCCGTACCTTGGCCGATTACAACATCCAGAAGGAATC
* * *
938 CACCCTCCACCTCGTCCTCCGTCTTCGCGGGGGCATGCAGATCTTCGTGAAAACCTTGACTGGCA
195 CACCCTCCACCTCGTCCTCCGTCTTCGCGGGGGCATGCAGATCTTCGTCAAAACCTTAACCGGCA
* * * * * * *
1003 AGACCATCACCTTAGAGGTGGAGAGTTCGGACACCATCGACAATGTAAAGGCGAAGATTCAAGAC
260 AGACCATCACCCTAGAAGTCGAGAGCTCCGACACCATCGACAATGTAAAGGCGAAAATCCAAGAC
* * * * * * * * *
1068 AAGGAAGGGATCCCACCAGACCAACAACGTTTGATCTTTGCAGGGAAGCAGCTTGAGGATGGGAG
325 AAGGAAGGCATCCCACCAGACCAACAACGTCTCATCTTCGCAGGAAAACAGCTCGAAGATGGCAG
* * * * **
1133 GACCTTGGCTGATTATAACATCCAGAAGGAATCGACCCTTCACCTTGTTTTGA-GGCTTCGTGGA
390 GACCTTGGCCGATTACAACATCCAGAAGGAATCCACCCTCCACCTTGTCCT-ACGGCTTCGTGGA
* * * * * * * * * * *
1197 GGCATGCAGATTTTCGTTAAGACATTGACTGGGAAAACAATCACATTGGAGGTGGAAAGTTCGGA
454 GGCATGCAGATCTTCGTCAAAACATTAACCGGCAAAACAATCACACTCGAAGTCGAAAGCTCGGA
* * * * * * * *
1262 TACAATTGATAATGTGAAGGCGAAGATTCAGGACAAGGAAGGTATCCCTCCAGATCAGCAAAGGC
519 CACAATCGATAATGTAAAGGCGAAAATTCAAGACAAGGAAGGCATCCCACCAGACCAGCAAAGGC
* * * * * * * * * * *
1327 TCATCTTTGCTGG-AAAGCAATTGGAGGATGGGAGGACTTTAGCTGATTATAACATTCAGAAAGA
584 TCATCTTCGCCGGCAAA-CAACTCGAAGACGGCAGGACCTTAGCCGATTACAACATCCAGAAAGA
* * * *
1391 GTCCACCCTTCACCTTGTTCTTCGTCTCCGTGG
648 ATCCACCCTCCACCTTGTCCTCCGTCTCCGTGG
1424 TGGGCAGTGA
Statistics
Matches: 571, Mismatches: 106, Indels: 6
0.84 0.16 0.01
Matches are distributed among these distances:
683 7 0.01
684 563 0.99
685 1 0.00
ACGTcount: A:0.29, C:0.28, G:0.23, T:0.21
Consensus pattern (684 bp):
ATGCAGATCTTCGTCAAAACCCTTACCGGCAAGACCATCACCCTCGAAGTCGAGAGCTCCGACAC
CATCGACAATGTAAAGTCTAAAATCCAAGACAAGGAAGGCATCCCACCAGACCAGCAGCGTCTCA
TCTTCGCCGGCAAACAGCTCGAAGACGGCCGTACCTTGGCCGATTACAACATCCAGAAGGAATCC
ACCCTCCACCTCGTCCTCCGTCTTCGCGGGGGCATGCAGATCTTCGTCAAAACCTTAACCGGCAA
GACCATCACCCTAGAAGTCGAGAGCTCCGACACCATCGACAATGTAAAGGCGAAAATCCAAGACA
AGGAAGGCATCCCACCAGACCAACAACGTCTCATCTTCGCAGGAAAACAGCTCGAAGATGGCAGG
ACCTTGGCCGATTACAACATCCAGAAGGAATCCACCCTCCACCTTGTCCTACGGCTTCGTGGAGG
CATGCAGATCTTCGTCAAAACATTAACCGGCAAAACAATCACACTCGAAGTCGAAAGCTCGGACA
CAATCGATAATGTAAAGGCGAAAATTCAAGACAAGGAAGGCATCCCACCAGACCAGCAAAGGCTC
ATCTTCGCCGGCAAACAACTCGAAGACGGCAGGACCTTAGCCGATTACAACATCCAGAAAGAATC
CACCCTCCACCTTGTCCTCCGTCTCCGTGGGGGT
Done.