Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold238
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: 1453955
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Warning! 499 characters in sequence are not A, C, G, or T
File 9 of 9
Found at i:1447530 original size:42 final size:42
Alignment explanation
Indices: 1447469--1447587 Score: 193
Period size: 42 Copynumber: 2.8 Consensus size: 42
1447459 TAGCCCTCAA
* *
1447469 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
*
1447511 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
* *
1447553 AGAGATAATAGAGAGAGGAGGGATGACAGGAGGAG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAG
1447588 GAGAGAAGAA
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.43, C:0.03, G:0.46, T:0.08
Consensus pattern (42 bp):
AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
Found at i:1452772 original size:370 final size:368
Alignment explanation
Indices: 1452079--1452818 Score: 1085
Period size: 371 Copynumber: 2.0 Consensus size: 368
1452069 TGCTACCAAT
*
1452079 TGATGACAACCATGAACCAAGGTTGCCTAAATAATGATCTGAGATGAATTTTAATAATAAACAGA
1 TGATGACAACCATGAACCAAGGTTGCCTAAATAATGATCTGAGATGAATTTTAACAATAAACAGA
* * *
1452144 ATTTTGATGCCAGAACAGAGATTGAAGAAGCAGAAAAAAATAACAAAAGGGACATAGATTAGAGA
66 ATTATGATGCAAGAACAGAAATTGAAGAAGCAGAAAAAAATAACAAAAGGGA-ATAGATTAGAGA
* *
1452209 TGGAAGGATGGCACACAATCACAAGATTGATAAGCCAAAAGGAATGATCGCCCAAGAGTCTTGGC
130 TGGAAGGAGGGCACACAATCACAAGATTGATAAGCCAAAAGGAATGATCGCCCAAAAGTCTTGGC
1452274 CTCTTGATAAGATCCAGAAAAATATGGCTCACTCAAGAAACCTAAGAATCACACTCTACACAAAA
195 CTCTTGATAAGATCCAGAAAAATATGGCTCACTCAAGAAACCTAAGAATCACACTCTACACAAAA
1452339 TGTGTTTTAATCTGCAAATATCAATGTCTGCCCCTCCAAATCTGTTTACAAGAGCTATATATGCC
260 TGTGTTTT-ATCTGCAAATATCAATGTCTGCCCCTCCAAATCTGTTTACAAGAGCTATATATG-C
*
1452404 CTCCATAAGCCATCAGTTAACAC-AACCCTAAGGGGCTTATTATGCTAA
323 CT-CATAAGCCA--AGATAACACAAACCCTAAGGGGCTTATTATGCTAA
*
1452452 TGATGTACAACCATGAACCAAGGTTGCCTAAATAATGATCTTGAGATG-GTTTTAAACAATAAAC
1 TGATG-ACAACCATGAACCAAGGTTGCCTAAATAATGATC-TGAGATGAATTTT-AACAATAAAC
* *
1452516 AGAATTATGATGCAAGAATAGAAATTG-A-AAGACAGAGAAAAAATAACAAAATGG-ATAGATTA
63 AGAATTATGATGCAAGAACAGAAATTGAAGAAG-CAGA-AAAAAATAACAAAAGGGAATAGATTA
*
1452578 GAGAT-G-AGGAGGGCGC-CACATCACAAGATTGATAAGCCAAAAGGAATGATCGCCACACAAAG
126 GAGATGGAAGGAGGGCACACA-ATCACAAGATTGATAAGCCAAAAGGAATGATCGCC-CA-AAAG
* *
1452640 TCTTGGCCTTTTGATAAGATCCAGAAAAAT-TGGCTCACTCAAG-AACCTAAGAATCACTCTC-A
188 TCTTGGCCTCTTGATAAGATCCAGAAAAATATGGCTCACTCAAGAAACCTAAGAATCACACTCTA
*
1452702 CACAAAATGTTGTTTCT-TCTGCAAATATGAATGTCT-CCCCTCCCAAATCTG-TTACAAGAGCT
253 CACAAAATG-TGTTT-TATCTGCAAATATCAATGTCTGCCCCT-CCAAATCTGTTTACAAGAGC-
*
1452764 TATATATGCCTCATAAGTCAAGATAACACAAACCCTAAGGGGCTTATTATGCTAA
314 TATATATGCCTCATAAGCCAAGATAACACAAACCCTAAGGGGCTTATTATGCTAA
1452819 CAAGCCCAAC
Statistics
Matches: 339, Mismatches: 15, Indels: 32
0.88 0.04 0.08
Matches are distributed among these distances:
366 8 0.02
367 25 0.07
368 8 0.02
369 18 0.05
370 47 0.14
371 65 0.19
372 17 0.05
373 53 0.16
374 43 0.13
375 55 0.16
ACGTcount: A:0.40, C:0.19, G:0.18, T:0.24
Consensus pattern (368 bp):
TGATGACAACCATGAACCAAGGTTGCCTAAATAATGATCTGAGATGAATTTTAACAATAAACAGA
ATTATGATGCAAGAACAGAAATTGAAGAAGCAGAAAAAAATAACAAAAGGGAATAGATTAGAGAT
GGAAGGAGGGCACACAATCACAAGATTGATAAGCCAAAAGGAATGATCGCCCAAAAGTCTTGGCC
TCTTGATAAGATCCAGAAAAATATGGCTCACTCAAGAAACCTAAGAATCACACTCTACACAAAAT
GTGTTTTATCTGCAAATATCAATGTCTGCCCCTCCAAATCTGTTTACAAGAGCTATATATGCCTC
ATAAGCCAAGATAACACAAACCCTAAGGGGCTTATTATGCTAA
Done.