Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga05g03834.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, 991
Length: 1653
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.25
Found at i:1139 original size:455 final size:454
Alignment explanation
Indices: 190--1369 Score: 1330
Period size: 455 Copynumber: 2.6 Consensus size: 454
180 CAAAGAAGGC
* * * ** * *
190 ATTCCTCCAGACCAACAGAGGCTT-ATTTTTGCCGGAAAACAACTCGAGGATGGCCGAACTCTTG
1 ATTCCTCCAGACCAGCAGAGG-TTGATTTTTGCCGGAAAGCAGCTCGAGGATGGGAGGACGCTTG
* * * * * * * * *
254 CCGACTACAACATCCAAAAGGAGTCCACCCTCCACCTAGTCCTTCGTCTAAGGGGTGGCATGCAG
65 CGGACTATAACATCCAAAAGGAGTCCACCCTGCACTTGGTCCTGCGACTAAGAGGTGGAATGCAG
* * * * * * * *
319 ATATTTGTGAAAACCCTT-ACGGGCAAGACCATCACCCTCGAGGTGGAAAGTTCTGATACGATTG
130 ATATTTGTGAAAA-CCTTGACTGGAAAAACCATCACCCTGGAGGTGGAGAGCTCAGACACGATTG
* * *
383 ATAATGTCAAGGCCAAGATCCAAGACAAGGAAGGGATCCCTCCAGACCAACAGAGGCTT-ATCTT
194 ATAATGTGAAGACCAAGATCCAAGACAAGG-AGGGAT-CCTCCAGACCAGCAGAGG-TTGATCTT
* * * * *
447 TGCAGGTAAA-CAACTTGAAGATGGCCGAACCCTCGCTGATTACAACATCCAGAAAGAGTCTACC
256 TGCTGG-AAAGCAACTCGAAGATGGCAGAACCCTCGCGGATTACAACATCCAGAAAGAGTCAACC
* * * * *
511 CTCCACCTTGTCCTTCGTCTTCGGGGTGGGATGCAGATATTTGTAAAAACCCTCACCGGAAAAAC
320 CTCCACCTTGTCCTGCGCCTTCGAGGAGGGATGCAGATATTCGTAAAAACCCTCACCGGAAAAAC
* ** * * * * * *
576 CATCACTTTGGAGGTGGAGAGTTCTGATACCATTGATAATGTTAAGGCGAAGATTCAGGACAAGG
385 CATAACACTGGAGGTCGAGAGCTCGGACACCATTGACAATGTTAAAGCGAAGATTCAGGACAAGG
*
641 AGGGT
450 AGGGA
* *
646 ATTCCACCAGATCAGCAGAGGTTGATTTTTGCCGGAAAGCAGCTCGAGGATGGGAGGACGCTTGC
1 ATTCCTCCAGACCAGCAGAGGTTGATTTTTGCCGGAAAGCAGCTCGAGGATGGGAGGACGCTTGC
* * * ** *
711 GGATTATAACATCCAAAAGGAGTCAACCCTGCACTTGGTGCTGCGACTGCGTGGTGGAATGCAGA
66 GGACTATAACATCCAAAAGGAGTCCACCCTGCACTTGGTCCTGCGACTAAGAGGTGGAATGCAGA
* * * * ** *
776 TTTTTGTGAAAACTTTGACTGGAAAAACTATTACATTGGAGGTGGAGAGCTCAGACACAATTGAT
131 TATTTGTGAAAACCTTGACTGGAAAAACCATCACCCTGGAGGTGGAGAGCTCAGACACGATTGAT
* * * *
841 AACGTGAAGACCAAGATCCAAGACAAGGAGGGTATCCACCTGACCAGCAGAGGTTGATTTTTGCT
196 AATGTGAAGACCAAGATCCAAGACAAGGAGGG-ATCCTCCAGACCAGCAGAGGTTGATCTTTGCT
* * * * * * *
906 GGAAAGCAACTCGAGGATGGGAGGACTCTTGCGGATTATAACATCCA-AAAGGAGTCAACCCTGC
260 GGAAAGCAACTCGAAGATGGCAGAACCCTCGCGGATTACAACATCCAGAAA-GAGTCAACCCTCC
* * * * * * *
970 A-CTTGGTTCTGCGCCTTCGAGGAGGGATGCAGATATTCGTTAAGACCCTGACTGGTAAAACCGT
324 ACCTT-GTCCTGCGCCTTCGAGGAGGGATGCAGATATTCGTAAAAACCCTCACCGGAAAAACCAT
1034 AACACTGGAGGTCGAGAGCTCGGACACCATTGACAATGTTAAAGCGAAGATTCAGGACAAGGAGG
388 AACACTGGAGGTCGAGAGCTCGGACACCATTGACAATGTTAAAGCGAAGATTCAGGACAAGGAGG
1099 GA
453 GA
*
1101 ATTCCTCCAGACCAGCAGAGGTTGATTTTTGCCGGAAAGCAGCTTGAGGATGGGAGGACGCTTGC
1 ATTCCTCCAGACCAGCAGAGGTTGATTTTTGCCGGAAAGCAGCTCGAGGATGGGAGGACGCTTGC
* * ** * * *
1166 GGACTATAACATCCAAAAGGAATCCACCCTGCATTTGGTTTTGCGCCTTAGAGGAGGAATGCAGA
66 GGACTATAACATCCAAAAGGAGTCCACCCTGCACTTGGTCCTGCGACTAAGAGGTGGAATGCAGA
* * * * *
1231 TATTCGTGAAGACCTTGACTGGGAAAACCATCACCCTGGAGGTGGAGAGCTCGGACACGATTGAC
131 TATTTGTGAAAACCTTGACTGGAAAAACCATCACCCTGGAGGTGGAGAGCTCAGACACGATTGAT
* * * *
1296 AATGTGAA-ATCTAAGATTCAGGACAAGGAGGGGATTCCTCCGGACCAGCAGAGGTTGATCTTTG
196 AATGTGAAGA-CCAAGATCCAAGACAAGGA-GGGA-TCCTCCAGACCAGCAGAGGTTGATCTTTG
1360 CTGGAAAGCA
258 CTGGAAAGCA
1370 GTTGGAGGAT
Statistics
Matches: 602, Mismatches: 112, Indels: 20
0.82 0.15 0.03
Matches are distributed among these distances:
454 12 0.02
455 374 0.62
456 216 0.36
ACGTcount: A:0.30, C:0.22, G:0.27, T:0.22
Consensus pattern (454 bp):
ATTCCTCCAGACCAGCAGAGGTTGATTTTTGCCGGAAAGCAGCTCGAGGATGGGAGGACGCTTGC
GGACTATAACATCCAAAAGGAGTCCACCCTGCACTTGGTCCTGCGACTAAGAGGTGGAATGCAGA
TATTTGTGAAAACCTTGACTGGAAAAACCATCACCCTGGAGGTGGAGAGCTCAGACACGATTGAT
AATGTGAAGACCAAGATCCAAGACAAGGAGGGATCCTCCAGACCAGCAGAGGTTGATCTTTGCTG
GAAAGCAACTCGAAGATGGCAGAACCCTCGCGGATTACAACATCCAGAAAGAGTCAACCCTCCAC
CTTGTCCTGCGCCTTCGAGGAGGGATGCAGATATTCGTAAAAACCCTCACCGGAAAAACCATAAC
ACTGGAGGTCGAGAGCTCGGACACCATTGACAATGTTAAAGCGAAGATTCAGGACAAGGAGGGA
Found at i:1213 original size:228 final size:228
Alignment explanation
Indices: 85--1381 Score: 1116
Period size: 228 Copynumber: 5.7 Consensus size: 228
75 CTCCCAGAAG
* * * * * * * * *
85 ATGCAGATCTTTGTGAAAACCCTTACTGGTAAAACCATCACCCTTGAGGTGGAAAGCTCCGATAC
1 ATGCAGATATTCGTGAAAACCCTGACTGGAAAAACCATCACACTGGAGGTGGAGAGCTCGGACAC
* * * * * * * * * * * * *
150 TATTGATAATGTCAAGGCCAAAATCCAAGACAAAGAAGGCATTCCTCCAGACCAACAGAGGCTT-
66 CATTGACAATGTTAAAGCGAAGATTCAGGACAAGGAGGGTATTCCACCAGACCAGCAGAGG-TTG
* * ** * * * * *
214 ATTTTTGCCGGAAAACAACTCGAGGATGGCCGAACTCTTGCCGACTACAACATCCAAAAGGAGTC
130 ATTTTTGCCGGAAAGCAGCTCGAGGATGGGAGGACGCTTGCGGATTATAACATCCAAAAGGAGTC
* * * * * * * ** * * *
279 CACCCTCCACCTAGTCCTTCGTCTAAGGGGTGGC
195 AACCCTGCACTTGGTTCTGCGCCTTCGAGGAGGA
* * * * * * * * * * *
313 ATGCAGATATTTGTGAAAACCCTTACGGGCAAGACCATCACCCTCGAGGTGGAAAGTTCTGATAC
1 ATGCAGATATTCGTGAAAACCCTGACTGGAAAAACCATCACACTGGAGGTGGAGAGCTCGGACAC
* * * * * * * * * *
378 GATTGATAATGTCAAGGCCAAGATCCAAGACAAGGAAGGG-ATCCCTCCAGACCAACAGAGGCTT
66 CATTGACAATGTTAAAGCGAAGATTCAGGACAAGG-AGGGTATTCCACCAGACCAGCAGAGG-TT
* * * * * ** * * * * *
442 -ATCTTTGCAGGTAAA-CAACTTGAAGATGGCCGAACCCTCGCTGATTACAACATCCAGAAA-GA
129 GATTTTTGCCGG-AAAGCAGCTCGAGGATGGGAGGACGCTTGCGGATTATAACATCCA-AAAGGA
* * * * * * * *
504 GTCTACCCTCCACCTT-GTCCTTCGTCTTCGGGGTGGG
192 GTCAACCCTGCA-CTTGGTTCTGCGCCTTCGAGGAGGA
* * * * ** * * *
541 ATGCAGATATTTGTAAAAACCCTCACCGGAAAAACCATCACTTTGGAGGTGGAGAGTTCTGATAC
1 ATGCAGATATTCGTGAAAACCCTGACTGGAAAAACCATCACACTGGAGGTGGAGAGCTCGGACAC
* * *
606 CATTGATAATGTTAAGGCGAAGATTCAGGACAAGGAGGGTATTCCACCAGATCAGCAGAGGTTGA
66 CATTGACAATGTTAAAGCGAAGATTCAGGACAAGGAGGGTATTCCACCAGACCAGCAGAGGTTGA
671 TTTTTGCCGGAAAGCAGCTCGAGGATGGGAGGACGCTTGCGGATTATAACATCCAAAAGGAGTCA
131 TTTTTGCCGGAAAGCAGCTCGAGGATGGGAGGACGCTTGCGGATTATAACATCCAAAAGGAGTCA
* * * * *
736 ACCCTGCACTTGGTGCTGCGACTGCGTGGTGGA
196 ACCCTGCACTTGGTTCTGCGCCTTCGAGGAGGA
* * ** * * * *
769 ATGCAGATTTTTGTGAAAACTTTGACTGGAAAAACTATTACATTGGAGGTGGAGAGCTCAGACAC
1 ATGCAGATATTCGTGAAAACCCTGACTGGAAAAACCATCACACTGGAGGTGGAGAGCTCGGACAC
* * * * * * * *
834 AATTGATAACG-TGAAGACCAAGATCCAAGACAAGGAGGGTA-TCCACCTGACCAGCAGAGGTTG
66 CATTGACAATGTTAAAG-CGAAGATTCAGGACAAGGAGGGTATTCCACCAGACCAGCAGAGGTTG
* * *
897 ATTTTTGCTGGAAAGCAACTCGAGGATGGGAGGACTCTTGCGGATTATAACATCCAAAAGGAGTC
130 ATTTTTGCCGGAAAGCAGCTCGAGGATGGGAGGACGCTTGCGGATTATAACATCCAAAAGGAGTC
*
962 AACCCTGCACTTGGTTCTGCGCCTTCGAGGAGGG
195 AACCCTGCACTTGGTTCTGCGCCTTCGAGGAGGA
* * * * * *
996 ATGCAGATATTCGTTAAGACCCTGACTGGTAAAACCGTAACACTGGAGGTCGAGAGCTCGGACAC
1 ATGCAGATATTCGTGAAAACCCTGACTGGAAAAACCATCACACTGGAGGTGGAGAGCTCGGACAC
* *
1061 CATTGACAATGTTAAAGCGAAGATTCAGGACAAGGAGGGAATTCCTCCAGACCAGCAGAGGTTGA
66 CATTGACAATGTTAAAGCGAAGATTCAGGACAAGGAGGGTATTCCACCAGACCAGCAGAGGTTGA
* * * *
1126 TTTTTGCCGGAAAGCAGCTTGAGGATGGGAGGACGCTTGCGGACTATAACATCCAAAAGGAATCC
131 TTTTTGCCGGAAAGCAGCTCGAGGATGGGAGGACGCTTGCGGATTATAACATCCAAAAGGAGTCA
* * *
1191 ACCCTGCATTTGGTTTTGCGCCTTAGAGGAGGA
196 ACCCTGCACTTGGTTCTGCGCCTTCGAGGAGGA
* * * *
1224 ATGCAGATATTCGTGAAGACCTTGACTGGGAAAACCATCACCCTGGAGGTGGAGAGCTCGGACAC
1 ATGCAGATATTCGTGAAAACCCTGACTGGAAAAACCATCACACTGGAGGTGGAGAGCTCGGACAC
* * * * * * *
1289 GATTGACAATGTGAAATCTAAGATTCAGGACAAGGAGGGGATTCCTCCGGACCAGCAGAGGTTGA
66 CATTGACAATGTTAAAGCGAAGATTCAGGACAAGGAGGGTATTCCACCAGACCAGCAGAGGTTGA
* * * *
1354 TCTTTGCTGGAAAGCAGTTGGAGGATGG
131 TTTTTGCCGGAAAGCAGCTCGAGGATGG
1382 TCGAACTTTA
Statistics
Matches: 913, Mismatches: 144, Indels: 24
0.84 0.13 0.02
Matches are distributed among these distances:
227 208 0.23
228 694 0.76
229 11 0.01
ACGTcount: A:0.30, C:0.22, G:0.26, T:0.22
Consensus pattern (228 bp):
ATGCAGATATTCGTGAAAACCCTGACTGGAAAAACCATCACACTGGAGGTGGAGAGCTCGGACAC
CATTGACAATGTTAAAGCGAAGATTCAGGACAAGGAGGGTATTCCACCAGACCAGCAGAGGTTGA
TTTTTGCCGGAAAGCAGCTCGAGGATGGGAGGACGCTTGCGGATTATAACATCCAAAAGGAGTCA
ACCCTGCACTTGGTTCTGCGCCTTCGAGGAGGA
Done.