Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_1096 ID=scaffold_1096-JGI_221_v2.0
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, 600
Length: 1001
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.31
Found at i:114 original size:44 final size:44
Alignment explanation
Indices: 64--932 Score: 177
Period size: 44 Copynumber: 19.8 Consensus size: 44
54 AAGATTCACC
*
64 ATCTTCGATCTGCTCCACTACTGAGTAGGGTGACAGAATCTGCA
1 ATCTTCGATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCA
* * * * *
108 ATCTTCGACCTACTCCACTACTGCTTAGGGTGATAGGA-CT--A
1 ATCTTCGATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCA
** * * * * * * * *
149 ATGGCTTAAATCTGCTTCTCCACTGTATT-GGGAAGATAAGATTC-ACC
1 AT--CTTCGATCTGCTCCACTACTG-ATTAGGG-TGA-CAGAATCTGCA
*
196 ATCTTCGATCTGCTCCACTACTGATTAGGGTGACAGAATCTGTA
1 ATCTTCGATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCA
* * * * * *
240 ATCTTCAACCTACTCCACTACTGCTTAGGGTGATA-AAACT--A
1 ATCTTCGATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCA
* * * * * * *
281 ATGGCTTAGATTTGCTTCTCCACTA-T-ATT-GGGAAGATAAGATTC-ACC
1 AT--CTTCGA--T-CTGCTCCACTACTGATTAGGG-TGA-CAGAATCTGCA
* * * *
328 ATGTTCGATCTACTCCACTACTGCTTAGGGTGACAGAATTTGCA
1 ATCTTCGATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCA
* * * * * *
372 ATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGA-CT--A
1 ATCTTCGATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCA
* ** * * * ** * * *
413 ATGGGTTAAATCTGCTTCTCCACTGTATTAGGAAGATA-ATAT-TAACC
1 AT--CTTCGATCTGCTCCACTACTG-ATTAGGGTGACAGA-ATCT-GCA
* * *
460 ATCTTTGATCTGCTCCACCACTGATTAGGGTGACAAAATCTGCA
1 ATCTTCGATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCA
* * * * ** * *
504 TTCTTCAACCTACTCCACTACTCCTTAGGGTGATAGGA-CT--A
1 ATCTTCGATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCA
* ** * * * * * * * *
545 ATGGTTTAAATCTGCTTCTCCACTGTATT-GGG-AAGATAATATTCA
1 AT--CTTCGATCTGCTCCACTACTG-ATTAGGGTGACAGAATCTGCA
*
590 CCATCTTCGATCTGCTCCACTACTGATTAGGGTGACAGAATCTACA
1 --ATCTTCGATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCA
* * * * * *
636 ATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGA-CT--A
1 ATCTTCGATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCA
** ** * * *
677 ATGGCTTAAATCTGCTTCTCCACTA-T-ATTAGGAAGATA-AGAT-TAACC
1 AT--CTTCGATCTG---CTCCACTACTGATTAGGGTGACAGA-ATCT-GCA
* * *
724 ATCTTTGATCTGCTCCACTACTGATTTGGGTGACAGAATCTACA
1 ATCTTCGATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCA
* ** * * * * * *
768 ATATTTAACCTACTCGACTACTGCTTAGGGTGATAGGA-CT--A
1 ATCTTCGATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCA
** * * * * * * * *
809 ATGGCTTAAATCTGCTTCTCCACTGTATT-GGGAAGATAAGATTC-ACC
1 AT--CTTCGATCTGCTCCACTACTG-ATTAGGG-TGA-CAGAATCTGCA
*
856 ATCTTCGATCTGCTCCACAACTGATTAGGGTGACAGAATCTGCA
1 ATCTTCGATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCA
* * *
900 ATCTTCGACCTACTCCACTACTGCTTAGGGTGA
1 ATCTTCGATCTGCTCCACTACTGATTAGGGTGA
933 TAGGACTAAT
Statistics
Matches: 578, Mismatches: 179, Indels: 136
0.65 0.20 0.15
Matches are distributed among these distances:
41 17 0.03
42 21 0.04
43 108 0.19
44 291 0.50
45 99 0.17
46 30 0.05
47 12 0.02
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.31
Consensus pattern (44 bp):
ATCTTCGATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCA
Found at i:243 original size:132 final size:132
Alignment explanation
Indices: 1--1001 Score: 1669
Period size: 132 Copynumber: 7.6 Consensus size: 132
*
1 TAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTAGGAAGATAAGATTCACCAT
1 TAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCAT
* *
66 CTTCGATCTGCTCCACTACTGAGTAGGGTGACAGAATCTGCAATCTTCGACCTACTCCACTACTG
66 CTTCGATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTG
131 CT
131 CT
133 TAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCAT
1 TAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCAT
*
198 CTTCGATCTGCTCCACTACTGATTAGGGTGACAGAATCTGTAATCTTCAACCTACTCCACTACTG
66 CTTCGATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTG
263 CT
131 CT
** * * *
265 TAGGGTGATAAAACTAATGGCTTAGATTTGCTTCTCCACTATATTGGGAAGATAAGATTCACCAT
1 TAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCAT
* * * *
330 GTTCGATCTACTCCACTACTGCTTAGGGTGACAGAATTTGCAATCTTCAACCTACTCCACTACTG
66 CTTCGATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTG
395 CT
131 CT
* * * *
397 TAGGGTGATAGGACTAATGGGTTAAATCTGCTTCTCCACTGTATTAGGAAGATAATATTAACCAT
1 TAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCAT
* * * * *
462 CTTTGATCTGCTCCACCACTGATTAGGGTGACAAAATCTGCATTCTTCAACCTACTCCACTACTC
66 CTTCGATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTG
527 CT
131 CT
* *
529 TAGGGTGATAGGACTAATGGTTTAAATCTGCTTCTCCACTGTATTGGGAAGATAATATTCACCAT
1 TAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCAT
*
594 CTTCGATCTGCTCCACTACTGATTAGGGTGACAGAATCTACAATCTTCAACCTACTCCACTACTG
66 CTTCGATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTG
659 CT
131 CT
* * *
661 TAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTATATTAGGAAGATAAGATTAACCAT
1 TAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCAT
* * * * * *
726 CTTTGATCTGCTCCACTACTGATTTGGGTGACAGAATCTACAATATTTAACCTACTCGACTACTG
66 CTTCGATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTG
791 CT
131 CT
793 TAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCAT
1 TAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCAT
* *
858 CTTCGATCTGCTCCACAACTGATTAGGGTGACAGAATCTGCAATCTTCGACCTACTCCACTACTG
66 CTTCGATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTG
923 CT
131 CT
*
925 TAGGGTGATAGGACTAATGGTTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCAT
1 TAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCAT
990 CTTCGATCTGCT
66 CTTCGATCTGCT
Statistics
Matches: 806, Mismatches: 63, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
132 806 1.00
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.31
Consensus pattern (132 bp):
TAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCAT
CTTCGATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTG
CT
Done.