Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold580
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, 1000
Length: 2186
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.37
Found at i:897 original size:468 final size:473
Alignment explanation
Indices: 1--2185 Score: 3533
Period size: 468 Copynumber: 4.6 Consensus size: 473
1 ATTAGGATACATGACA-TGAT-CTTTGGGGGCACAAGAAAATGTTTTCTTTCCGCCGTTTTTGAT
1 ATTAGGATACATGACATTGATGCTTTGGGGGCACAAGAAAATGTTTTCTTTCCGCCGTTTTTGAT
64 AGAGGTAAAGTTTTATCTCTTAAGTAAGAC-AACATGAATTGTCA-GCTAATCCCCATTCTTTTC
66 AGAGGTAAAG-TTTATCTCTTAAGTAAGACAAACATGAATTGTCATGCTAATCCCCATTCTTTTC
*
127 ATGATTAGGCACCATAAACTTTGTCTTCTCATAAGGATACACTATATTGATGCTTTGGTATCGTA
130 ATGATTAGGCACCATAAACTTTGTCTTCTCATAAGGATACACTATATTGATGCTTTGGTTTCGTA
192 AGAAAGGCTTTCTTGCCACCATTTTTGTAAAGTCTAAGTTCGTGCCTCAAATGAGA-AAACGAGG
195 AGAAAGGCTTTCTTGCCACCATTTTTGTAAAGTCTAAGTTCGTGCCTCAAATGAGACAAACGAGG
256 ATTCTAGTAATGAACTTCATTCA-TTTGTGATTAGGCACTATAAGCACATTCTCTTCATTAGGAT
260 ATTCTAGTAATGAACTTCATTCATTTTGTGATTAGGCACTATAAGCACATTCTCTTCATTAGGAT
320 AAA-GATA-TGATTGTTTTCTTT-TGTTGAAATCTTTTCTTTGCACT-GTTTTCCTTAATATCAA
325 AAACGATATTGATTGTTTTCTTTCTGTTGAAATCTTTTCTTTGCACTAG-TTTCCTTAATATCAA
* ** *
381 AATTCTTCGCTTAAATATGACAAGCATCAATTCTTATAAAAGTCTCCACTTTTTTTTACATTAAG
389 AATTCTTCCCTTAAATATGACAAGCATCAATTC-TATAAAAGTCTCCACTTTTTTCGACATTAGG
*
446 AAGCAAAAGCATATTCCCTTC
453 AAGCAAAAGCATATTCCTTTC
* *
467 ATTAGGATACACGACATTGATGCTTTGGGGGCACAAGAAAATGTTTTCTTTCCGCCGTTCTTGAT
1 ATTAGGATACATGACATTGATGCTTTGGGGGCACAAGAAAATGTTTTCTTTCCGCCGTTTTTGAT
532 AGAGGTAAAGTTTATCTCTTAAGTAAGACAAACATGAATTGTCATGCTAATCCCCATTCTTTTCA
66 AGAGGTAAAGTTTATCTCTTAAGTAAGACAAACATGAATTGTCATGCTAATCCCCATTCTTTTCA
597 TGATTAGGCACCATAAACTTTGTCTTCTCATAAGGATACACTATATTGATGC-TTGGTTTCGTAA
131 TGATTAGGCACCATAAACTTTGTCTTCTCATAAGGATACACTATATTGATGCTTTGGTTTCGTAA
*
661 GAAAGGCTTTCTTGCCACCATTTTTTGTAAAGTCTAAGTTCGTGCCTCAAATGAGACAAACAAGG
196 GAAAGGCTTTCTTGCCACCA-TTTTTGTAAAGTCTAAGTTCGTGCCTCAAATGAGACAAACGAGG
*
726 ATTCTAGTAATGAACTGCATTCATTTTGTGATTAGGCACTATAAGCACATTCTCTTCATTAGGAT
260 ATTCTAGTAATGAACTTCATTCATTTTGTGATTAGGCACTATAAGCACATTCTCTTCATTAGGAT
*
791 AAACGATATTGATTGTTTTCTTTCCGTTG-AATCTTTTCTTTGCACT-GTTTCCTT-ATATCAAA
325 AAACGATATTGATTGTTTTCTTTCTGTTGAAATCTTTTCTTTGCACTAGTTTCCTTAATATCAAA
853 ATTCTTCCCTTAAATATGAC-AGCATCAATTC-ATAAAAGTCTCCACTTTTTTCGACATTAGGAA
390 ATTCTTCCCTTAAATATGACAAGCATCAATTCTATAAAAGTCTCCACTTTTTTCGACATTAGGAA
*
916 GCAAAAGCTTATTCCTTTC
455 GCAAAAGCATATTCCTTTC
* * * * *
935 AGTGGGATACACGACATTGATGCTTTGGGGGCACAAGAAAATGTTTTCTTTCTGCCGTTCTTGAT
1 ATTAGGATACATGACATTGATGCTTTGGGGGCACAAGAAAATGTTTTCTTTCCGCCGTTTTTGAT
* * * *
1000 GGATGTAAAGTTTATCCCTTAAGGAAGACAAACATGAATTGTCATGCTAATCCCCATTCTTTTCA
66 AGAGGTAAAGTTTATCTCTTAAGTAAGACAAACATGAATTGTCATGCTAATCCCCATTCTTTTCA
*
1065 TTCGTTTAATGATAGGCACCATAAACTTTGTCTTCTCATAAAGATACACTATATTGATGC-TTGG
131 -T-G----AT--TAGGCACCATAAACTTTGTCTTCTCATAAGGATACACTATATTGATGCTTTGG
1129 TTTCGTAAGAAAGGCTTTCTTGCCACCATTTTTGTAAAGTCTAAGTTCGTGCCTCAAATGAGACA
188 TTTCGTAAGAAAGGCTTTCTTGCCACCATTTTTGTAAAGTCTAAGTTCGTGCCTCAAATGAGACA
*
1194 AATGAGGATTCTAGTAATGAACTTCATTCA-TTTGTGATTAGGCACTA-AAG--CATTCTCTTCA
253 AACGAGGATTCTAGTAATGAACTTCATTCATTTTGTGATTAGGCACTATAAGCACATTCTCTTCA
* *
1255 TTAGGATAAACGATATTTATTGTTTTCTTTTCTGTTGAAATCTTTTCTTTGCACTATTTTCCTTA
318 TTAGGATAAACGATATTGATTGTTTTC-TTTCTGTTGAAATCTTTTCTTTGCACTAGTTTCCTTA
*
1320 ATATCAAATTTCTT-CCTTAAATATGACAAGCATCAATTCT-TATAAA-TCTCCACTTTTTTCGA
382 ATATCAAAATTCTTCCCTTAAATATGACAAGCATCAATTCTATA-AAAGTCTCCACTTTTTTCGA
1382 CATTAGGAAGCAAAAGCATATTCCTTTC
446 CATTAGGAAGCAAAAGCATATTCCTTTC
*
1410 ATTAGGATACATGACATTGATGCTTTGGGGGCACAAGAAAATGTTTTCTTTCCGCCATTTTTGAT
1 ATTAGGATACATGACATTGATGCTTTGGGGGCACAAGAAAATGTTTTCTTTCCGCCGTTTTTGAT
1475 AGAGGTAAAGTTTAT-TCTTAAGTAAGACAAACATGAATTGTCATGCTAATCCCCATTCTTTTCA
66 AGAGGTAAAGTTTATCTCTTAAGTAAGACAAACATGAATTGTCATGCTAATCCCCATTCTTTTCA
* *
1539 TGATTAGGCACCATAAACTTTGTCTTCTCATAAGGATACAATATATTAATGCTTTGGTTTCGTAA
131 TGATTAGGCACCATAAACTTTGTCTTCTCATAAGGATACACTATATTGATGCTTTGGTTTCGTAA
* * *
1604 GAAAGGCCTTCTTGCCACTAATTTTTGTAAAGTCTAAGTTCGTGCCTCAAATGAGACAAATGAGG
196 GAAAGGCTTTCTTGCCAC-CATTTTTGTAAAGTCTAAGTTCGTGCCTCAAATGAGACAAACGAGG
* *
1669 ATTCTAGTAATGATCTTCATTCATTTTGTGATTAGGCACTATAAACACATTCTCTTCATTAGGAT
260 ATTCTAGTAATGAACTTCATTCATTTTGTGATTAGGCACTATAAGCACATTCTCTTCATTAGGAT
* * *
1734 AAACGATATTTATTGTTTTTTTTCTGTTGAAATC-TTTCTTTGCACTATTTTCCTTAATATCAAA
325 AAACGATATTGATTGTTTTCTTTCTGTTGAAATCTTTTCTTTGCACTAGTTTCCTTAATATCAAA
* *
1798 ATTCTTCCCTTAAATATGACAAGCATCAATTCTTATAAAAGTCTCCATTTTTTTCGAGATTAGGA
390 ATTCTTCCCTTAAATATGACAAGCATCAATTC-TATAAAAGTCTCCACTTTTTTCGACATTAGGA
*
1863 AGCAAAACCATATTCCTTTC
454 AGCAAAAGCATATTCCTTTC
* * *** * *
1883 ATTAGGATACATGGCATTGATGCTTTGGTGTTGCAAGAAAATGTGTTCTTTCCACCGTTTTTGAT
1 ATTAGGATACATGACATTGATGCTTTGGGGGCACAAGAAAATGTTTTCTTTCCGCCGTTTTTGAT
** * * *
1948 AGAAATAAAGTTTGTCTCTTAAATAAGACAAACAAGAATTGTCATGCTAATCCCCATTCTTTTCA
66 AGAGGTAAAGTTTATCTCTTAAGTAAGACAAACATGAATTGTCATGCTAATCCCCATTCTTTTCA
* *
2013 TGATTCGGCACCGTAAACTTTGTCTTCTCATAAGGATACACTATATTGATGCTTTGGTTTCGTAA
131 TGATTAGGCACCATAAACTTTGTCTTCTCATAAGGATACACTATATTGATGCTTTGGTTTCGTAA
2078 GAAAGGCTTTCTTGCCACCAATTTTTGTAAAGTCTAAGTTC-TGCCTCAAATGAGACAAACGAGG
196 GAAAGGCTTTCTTGCCACC-ATTTTTGTAAAGTCTAAGTTCGTGCCTCAAATGAGACAAACGAGG
*
2142 ATTCTAGTAATGATCTTCATTCATTTTGTGATTAGGCACTATAA
260 ATTCTAGTAATGAACTTCATTCATTTTGTGATTAGGCACTATAA
2186 A
Statistics
Matches: 1612, Mismatches: 70, Indels: 67
0.92 0.04 0.04
Matches are distributed among these distances:
466 60 0.04
467 52 0.03
468 335 0.21
469 125 0.08
470 78 0.05
471 147 0.09
472 61 0.04
473 231 0.14
474 236 0.15
475 205 0.13
476 82 0.05
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.37
Consensus pattern (473 bp):
ATTAGGATACATGACATTGATGCTTTGGGGGCACAAGAAAATGTTTTCTTTCCGCCGTTTTTGAT
AGAGGTAAAGTTTATCTCTTAAGTAAGACAAACATGAATTGTCATGCTAATCCCCATTCTTTTCA
TGATTAGGCACCATAAACTTTGTCTTCTCATAAGGATACACTATATTGATGCTTTGGTTTCGTAA
GAAAGGCTTTCTTGCCACCATTTTTGTAAAGTCTAAGTTCGTGCCTCAAATGAGACAAACGAGGA
TTCTAGTAATGAACTTCATTCATTTTGTGATTAGGCACTATAAGCACATTCTCTTCATTAGGATA
AACGATATTGATTGTTTTCTTTCTGTTGAAATCTTTTCTTTGCACTAGTTTCCTTAATATCAAAA
TTCTTCCCTTAAATATGACAAGCATCAATTCTATAAAAGTCTCCACTTTTTTCGACATTAGGAAG
CAAAAGCATATTCCTTTC
Done.