Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399923.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3154.0, whole genome shotgun sequence
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: 5483
ACGTcount: A:0.36, C:0.10, G:0.12, T:0.33
Warning! 458 characters in sequence are not A, C, G, or T
Found at i:1056 original size:513 final size:515
Alignment explanation
Indices: 1--4129 Score: 2582
Period size: 513 Copynumber: 8.0 Consensus size: 515
* * * * *
1 TGAGATAATAAAACCATTTAAAGTGGGTAAT-AAGACTTTTGAAGGAATGGGTGACTATAAAT-A
1 TGAGATTATAAAACCATTTAAAGCGAGCAATAAAG-CTTTTGAAGGAAT-GGAGACTATAAATGA
* * * * * * * * *
64 GACTTTTATTGCCCATAAATGCCTTTTTCTTCATGTTTCTCGATGTAAACATTCAA-TCATAATT
64 -ACTTTTCTAGCCAATGAATGCCTTTTTCTTCAAGTTTCTCAAGGTAGACATTCAAGT-ATAATC
* * * *
128 TATTTTAA-TAAAAAA-AATAAAAAAACTTGAACTTAAAATTAATTTTGAGAGTATAAAACCATT
127 TATTTTAACCAAAAAAGAA-AAAAAAA-TTGAACTTAAAATCAATTATGAGATTATAAAACCATT
* ********** * * * *
191 TAAAGTGAGTANNNNNNNNNNTGAAGGAA-TGGGTGATTATAAATAGACTTTTCTTGCCAATGAA
190 TAAAGCGAGTAATAAGGCTTTTGAAGGAATTGAGAGACTATAAATAGACTTTTCTTGCCAATAAA
** * * ** * * * * ***
255 TG-CCTTTCCTTCATGTTCCTC-GGGAAGACATTCCATTATAATCT-TTTGAAATAAAAAATGTA
255 TGTTTTTTTCTTCATGTTTCTCAAAGTAGACATTCAATTATAGTCTGTTT-TAGCCAAAAATGTA
* ********** * * *
317 AAAA-AATTCAACTTAAANNNNNNNNNNAGATTGTAAAA-CTATTTAAAGTGA-CTAAT-AGGTG
319 AAAACAATTGAACTTAAAATCAATTATGAGATTATAAAATC-ATTTAAAGCGAGC-AATAAGG-C
* * *
378 TTTTGAAGGAATG-GTTGACTATAAATAG-ACTTTTCTT-CTCAACGAATAGC--TTTTCTTACA
381 TTTTAAAGGAATGAG-AGACTATAAATAGAACTTTT-TTAC-CAATGAAT-GCTTTTTTCTT-CA
* * * * *** * * * *
438 CGTTT-TCCAAGGTAAACATTCAATCATGGGCTATTTCAAT-AAAAATTGTAAAAACAAATTCAA
441 TGTTTCT-TAAGGTAGACATTCAATTATATTCTGTTTTAATCAAAAA-TAT-AAAA-AAATTAAA
501 CTTAAAATCAATTA
502 CTTAAAATCAATTA
* *
515 TGAGATTAT-AAACCATTTTAAGCGAGTAATAAAGCTTTTGAAGGAATGGACGACTATAAATGAA
1 TGAGATTATAAAACCATTTAAAGCGAGCAATAAAGCTTTTGAAGGAATGGA-GACTATAAATGAA
* * * * *
579 TTTTTCTAGCCAATGAATGCCTTTTTCTTCATGTTTCTCAAAGTAGACTTTCAACTATAATCTAT
65 CTTTTCTAGCCAATGAATGCCTTTTTCTTCAAGTTTCTCAAGGTAGACATTCAAGTATAATCTAT
** * * * * *
644 TTTATGCAAAAAAGAAAAAAAAATTAAACTTCAAACCAATTTTGGGATTATAAAACCATTTAAAG
130 TTTAACCAAAAAAGAAAAAAAAATTGAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAG
* * * * * * *
709 TGAGTAATAAGGCTTTTGAAGGAATTGA-TGATTAT-AATAAACTTTTCTTACCAATGAATGCAT
195 CGAGTAATAAGGCTTTTGAAGGAATTGAGAGACTATAAATAGACTTTTCTTGCCAATAAATG-TT
* * * * * * * *
772 TTTTT-TTCGTGTTCCTCAAGGCAAAAATTCAATTATTGTCTCTTTTAGCCAAAAATGTAAAAA-
259 TTTTTCTTCATGTTTCTCAAAGTAGACATTCAATTATAGTCTGTTTTAGCCAAAAATGTAAAAAC
* * *
835 AATTTAACTTAAAATCAATTATAAGATTAGAAAATCATTTAAAGCGAGCAATAAGGCTTTTAAAG
324 AATTGAACTTAAAATCAATTATGAGATTATAAAATCATTTAAAGCGAGCAATAAGGCTTTTAAAG
*
900 GAATGAGAGACTATAAATAGATA-TTTTTTACCAATGAATACTTTTTTCTTCATGTTTCTTAAGG
389 GAATGAGAGACTATAAATAGA-ACTTTTTTACCAATGAATGCTTTTTTCTTCATGTTTCTTAAGG
* * *
964 TAGACATTCAATTATATTCTGTTTTAATCAAAAATATGAAAATATTAAACTTAACATCAATTA
453 TAGACATTCAATTATATTCTGTTTTAATCAAAAATATAAAAAAATTAAACTTAAAATCAATTA
* * * * * *
1027 TGAGATTATAAAACTATTTAAAACGAGTAATAATGTTTTTGAAGGAATAAGAGACTATAAATGAA
1 TGAGATTATAAAACCATTTAAAGCGAGCAATAAAGCTTTTGAAGGAAT-GGAGACTATAAATGAA
* ** *******
1092 CTTTTCTTAG-CAATGAATGCCTTTTTCTTCAAATTTCTTGAGGTAGACATTC-AGTNNNNNNNN
65 CTTTTC-TAGCCAATGAATGCCTTTTTCTTCAAGTTTCTCAAGGTAGACATTCAAGT-ATAATCT
** * * *
1155 NNTTTAACCAAAAATGTAAAAAAAAGTTGAACTTAAAATCAATTATGAGATTATAAAATCATTTA
128 ATTTTAACCAAAAAAG-AAAAAAAAATTGAACTTAAAATCAATTATGAGATTATAAAACCATTTA
* * * * *
1220 AAGCAAGTACTAAGGCTTTTGAAGGAATAGA-AGACTATAAATGGACTTTTCTTGTCAATAAATG
192 AAGCGAGTAATAAGGCTTTTGAAGGAATTGAGAGACTATAAATAGACTTTTCTTGCCAATAAATG
* *
1284 TTTTTTTCTTCCA--TTTCTCAAAGTAGACATTCAATTATAGTCTGTTTTA-ACTAAAATGTAAA
257 TTTTTTTCTT-CATGTTTCTCAAAGTAGACATTCAATTATAGTCTGTTTTAGCCAAAAATGTAAA
* * * **
1346 AACAATTGAACTTGAAATCAATTATGAGATTATAAAATCATTTAAAGCAAGTAATAAAAC-TTTA
321 AACAATTGAACTTAAAATCAATTATGAGATTATAAAATCATTTAAAGCGAGCAATAAGGCTTTTA
*
1410 AAGGAATAAGAGACTATAAATA-AACTTTTCTTGA-CAATGAATGCTTTTTTCTTCATGTTTCTT
386 AAGGAATGAGAGACTATAAATAGAACTTTT-TT-ACCAATGAATGCTTTTTTCTTCATGTTTCTT
* * * * *
1473 AAGGTAGACGTTCAGTTATAGTCTGTTTTAA-CAAAAAATATAAAAAAAATAACCTTAAAATCAA
449 AAGGTAGACATTCAATTATATTCTGTTTTAATC-AAAAATATAAAAAAATTAAACTTAAAATCAA
*
1537 TTT
513 TTA
* * * * * * * * *
1540 TGAGAGTATGAAACCATTTAAAGCAAGCAATAAGGCTTTTGAAAGAATGGGTGATTATAAAAGGA
1 TGAGATTATAAAACCATTTAAAGCGAGCAATAAAGCTTTTGAAGGAAT-GGAGACTATAAATGAA
* * * * * *
1605 TTTTTCTTGCCAATGAATGCCATTTTCTTCAAGTTTCTTAAGGTAGACATTCAATTATAACCTAT
65 CTTTTCTAGCCAATGAATGCCTTTTTCTTCAAGTTTCTCAAGGTAGACATTCAAGTATAATCTAT
* * * * * * *
1670 TTTAACCAAAAATGTAAAAAAACTTGAACTTAAAATCAATTTTGAGGTTATAAAACTATTTCAAG
130 TTTAACCAAAAAAGAAAAAAAAATTGAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAG
* * **
1735 CGAGTAATATGGCTTTTGAAGGAA-TGAGAGACTATAAATAGACTTTTCTTGTCAATAAATACTT
195 CGAGTAATAAGGCTTTTGAAGGAATTGAGAGACTATAAATAGACTTTTCTTGCCAATAAATGTTT
* ********** * *
1799 TTTTCTTTATGTTTCTNNNNNNNNNNATTCAATTATAGTTTGTTTTAAG-GAAAAATGTAAAAAA
260 TTTTCTTCATGTTTCTCAAAGTAGACATTCAATTATAGTCTGTTTT-AGCCAAAAATGT-AAAAA
* * * * * * * * *
1863 GAATTGAACATAAAATCATTTTTTAGATAATAAAA-CTATTTAAAGTGGGTAATAAGGCTTCTT-
323 CAATTGAACTTAAAATCAATTATGAGATTATAAAATC-ATTTAAAGCGAGCAATAAGGCTT-TTA
* * * * * * *
1926 AATGAATGGGTGACTATTAATA-AACTTTTTTTGCC-ATCGAATGCTTTTTTCTTCAAGTTTCTC
386 AAGGAATGAGAGACTATAAATAGAAC-TTTTTTACCAAT-GAATGCTTTTTTCTTCATGTTTCTT
** * * *
1989 AATATAGACATTCAATTAT-TATCTGTTTTAATCAAAAATATAAAAAAACTTGAACCTAAAATTA
449 AAGGTAGACATTCAATTATAT-TCTGTTTTAATCAAAAATATAAAAAAA-TTAAACTTAAAATCA
2053 ATTA
512 ATTA
* * * * * * *
2057 TAAGATTATAAAACTATTTATAGCGAGCAATAAAGCTTTTAAAGAAATGAAAGACTATAAATGGA
1 TGAGATTATAAAACCATTTAAAGCGAGCAATAAAGCTTTTGAAGGAATG-GAGACTATAAATGAA
* * * * ** *
2122 CTTTTCTTGCCCATGAATG-C-TTTT-TTCAAGTTTCTCGATGTAGACATTCAAGTATTGTGTAT
65 CTTTTCTAGCCAATGAATGCCTTTTTCTTCAAGTTTCTCAAGGTAGACATTCAAGTATAATCTAT
* * * * **
2184 TTTAACC-AAAAATACAAAAACATTTAACTTAAAATCAATTATGAGATTATAAAAATATTTAAAG
130 TTTAACCAAAAAAGAAAAAAAAATTGAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAG
* * * * * *
2248 CGAGCAATATGACTTTTGAA-AAAATGAGAGACTATAAATAGACTTTTCTTGCCAATGAATGTTT
195 CGAGTAATAAGGCTTTTGAAGGAATTGAGAGACTATAAATAGACTTTTCTTGCCAATAAATGTTT
* ** * * * * *
2312 TTTTCTTCAAGTTTCTTGATGTAGACATTCAATTATTA-TCTATTTTAACTAAAAATATAAAAA-
260 TTTTCTTCATGTTTCTCAAAGTAGACATTCAATTA-TAGTCTGTTTTAGCCAAAAATGTAAAAAC
* ********** *
2375 AATTTAACNNNNNNNNNNTTATGAGATTATAAAATCATTTAAAGCGAGCAATAAGGCTTTTGAAG
324 AATTGAACTTAAAATCAATTATGAGATTATAAAATCATTTAAAGCGAGCAATAAGGCTTTTAAAG
* * * * **
2440 AAAT-AGGAGACTATAAAT-GAACTTCTCTTGCCAATGAATGCTTTTCTCTTCATGTTTCTGGAG
389 GAATGA-GAGACTATAAATAGAACTT-TTTTACCAATGAATGCTTTTTTCTTCATGTTTCTTAAG
* * * * * *
2503 GTAGATATTCAATTATAGTT-TGTTCTAATAAAAAATTTAAAAAAAATTGAACTTAAAATTAATT
452 GTAGACATTCAATTATA-TTCTGTTTTAATCAAAAATAT-AAAAAAATTAAACTTAAAATCAATT
2567 A
515 A
*********** *
2568 TGAGATTATAAAACCATTTAAAGTNNNNNNNNNNGCTTTTGAAGGAATAAGAGACTATAAATGAA
1 TGAGATTATAAAACCATTTAAAGCGAGCAATAAAGCTTTTGAAGGAAT-GGAGACTATAAATGAA
* * * * * * *
2633 CTTTTCTTGACAATGAATGCCTTTTTCTTCACGTTTTTTAAGGTAGACATTC-AGTTATAGTCTG
65 CTTTTCTAGCCAATGAATGCCTTTTTCTTCAAGTTTCTCAAGGTAGACATTCAAG-TATAATCTA
* * ******************************
2697 TTTTAACTAAAAATGTAAAAAAAAATTGAANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTTAA
129 TTTTAACCAAAAAAG-AAAAAAAAATTGAACTTAAAATCAATTATGAGATTATAAAACCATTTAA
* * * * ** *
2762 AGCGAGTAGTAAGGCTTTTGAAGGAATTGA-AGACTATAAATGGACTTTTTTTGCAAATGGATGC
193 AGCGAGTAATAAGGCTTTTGAAGGAATTGAGAGACTATAAATAGACTTTTCTTGCCAATAAATGT
* * * * * ***
2826 TTTTTTCATCCA--TTTCTTAAAGCAGACAATCAATTATAGTCAGTTTTA-ATGAAAATGTAAAA
258 TTTTTTC-TTCATGTTTCTCAAAGTAGACATTCAATTATAGTCTGTTTTAGCCAAAAATGTAAAA
* * ********** * *
2888 AAAATTGAACTTGAAATCAATTATGAGNNNNNNNNNNCATTTAAAGCAAGTAATAAGGCTTTTAA
322 ACAATTGAACTTAAAATCAATTATGAGATTATAAAATCATTTAAAGCGAGCAATAAGGCTTTTAA
* * *
2953 AGGAATAAGAGACTATAAATA-AACTTTTCTTGA-TAATGAATGCTTTTTTCTTCACGTTTC-TA
387 AGGAATGAGAGACTATAAATAGAACTTTT-TT-ACCAATGAATGCTTTTTTCTTCATGTTTCTTA
* * * * * * * *
3015 ATGGTAGACATTTAGTTTTATTCTATTTTAA-CTAAAAATGTAAAAAAAATTGAAGTTAAAATTA
450 A-GGTAGACATTCAATTATATTCTGTTTTAATC-AAAAATAT-AAAAAAATTAAACTTAAAATCA
*
3079 ATTT
512 ATTA
* * * ********** * **
3083 TGAGAGTATAAAACTATTTAAAGCAAGCANNNNNNNNNNTGAAGGAATGGGTGACTATAAAAAAA
1 TGAGATTATAAAACCATTTAAAGCGAGCAATAAAGCTTTTGAAGGAAT-GGAGACTATAAATGAA
* * * * * ** * *
3148 TTTTTCTTGTCAATGAATGTCATTTTCTTCAAGTTTCTTGAGGTAGACATTCAATTATAA-CTTG
65 CTTTTCTAGCCAATGAATGCCTTTTTCTTCAAGTTTCTCAAGGTAGACATTCAAGTATAATC-TA
* * * * * *
3212 TTTTAACCAAAAATGTAAAAAAACTTGAACTTAAAATAAAATT-TGAGGTTATAAAATCATTTAA
129 TTTTAACCAAAAAAGAAAAAAAAATTGAACTTAAAAT-CAATTATGAGATTATAAAACCATTTAA
********** * ** * *
3276 AGCGAGTAATAAGGCTTTTGAAGG-NNNNNNNNNNTATAAATGGACTTTTCTTATCAATGAATGC
193 AGCGAGTAATAAGGCTTTTGAAGGAATTGAGAGACTATAAATAGACTTTTCTTGCCAATAAATGT
* * * *
3340 TTTTTTCTTTATATTT-TTAGAGGTAGACATTCAATTATAGTCTGTTTTAAG-CAAAAATGTAAA
258 TTTTTTCTTCATGTTTCTCA-AAGTAGACATTCAATTATAGTCTGTTTT-AGCCAAAAATGT-AA
* * * * * * * *
3403 AAAGAATTGAACATAAAATCATTTTTGAGATAATAAAA-CTATTTAAAGTGGGTAATAAGGCTTT
320 AAACAATTGAACTTAAAATCAATTATGAGATTATAAAATC-ATTTAAAGCGAGCAATAAGGCTTT
* * * * * * *
3467 TGAAGGAATGTGTGACTATTAATA-AACTTTTCTTACCAATGAATGCCTTTTTCTTCAAGATTCT
384 TAAAGGAATGAGAGACTATAAATAGAACTTTT-TTACCAATGAATGCTTTTTTCTTCATGTTTCT
** ** * * * * * * *
3531 CGACATAAACATTCAATTATAATCTATTTTAACCAAAAATGTAAAAAAACTTGAACTTAAAATTA
448 TAAGGTAGACATTCAATTATATTCTGTTTTAATCAAAAATATAAAAAAA-TTAAACTTAAAATCA
3596 ATTA
512 ATTA
* ** * * * *
3600 TAAGATTATAAAATTATTTATAGCGAGCAATAAAGCTTTTGAAGAAATGGAAGACTCTAAATGGA
1 TGAGATTATAAAACCATTTAAAGCGAGCAATAAAGCTTTTGAAGGAATGG-AGACTATAAATGAA
* * * * * ** *
3665 CTTTTCTAGCCCATGAATG-C-GTTT-TTCAAGTTTTTCAACGTAGACATTCAATTATTGTCTGT
65 CTTTTCTAGCCAATGAATGCCTTTTTCTTCAAGTTTCTCAAGGTAGACATTCAAGTATAATCTAT
* * * *********
3727 TTTAA-CAAAAAATG-CATAAAAATTTAACTTAAAATCAATTANNNNNNNNNNAAAA-CATTTAA
130 TTTAACCAAAAAA-GAAAAAAAAATTGAACTTAAAATCAATTA-TGAGATTATAAAACCATTTAA
* * * * * * * *
3789 AGCGAGCAATAAAGCTTTTCAA-GAAATGGGAGACTATAAATAGACTTTTCTTGCAAATGAATAT
193 AGCGAGTAATAAGGCTTTTGAAGGAATTGAGAGACTATAAATAGACTTTTCTTGCCAATAAATGT
* * ** * * * *** **
3853 TTTTTTCTTTAAGTTTCTTGATGTAGACATTCAATTATTGTTTGTTTTAATAAAAAATACAAAAA
258 TTTTTTCTTCATGTTTCTCAAAGTAGACATTCAATTATAGTCTGTTTTAGCCAAAAATGTAAAAA
* * * * *
3918 -AATTCAACTTAAAATCAAGTATGAGATTATAAAATGATTTAAAGCGAGCAATTAGGCTTTTGAA
323 CAATTGAACTTAAAATCAATTATGAGATTATAAAATCATTTAAAGCGAGCAATAAGGCTTTTAAA
* * * * * * **
3982 GAAATGAGAGACCATAAAT-GGACTTTTCTTGCCAATGAATGCTTTTCTCTTCATATTTCTGGAG
388 GGAATGAGAGACTATAAATAGAACTTTT-TTACCAATGAATGCTTTTTTCTTCATGTTTCTTAAG
* * * * * * *
4046 GTAGACATTCAATTATAATCTATTCTAATAAAAAATTTTAAAAAATTAAACTTAAAATTAATTA
452 GTAGACATTCAATTATATTCTGTTTTAATCAAAAATATAAAAAAATTAAACTTAAAATCAATTA
4110 TGAGATTATAAAACCATTTA
1 TGAGATTATAAAACCATTTA
4130 NNNNNNNNNN
Statistics
Matches: 2808, Mismatches: 699, Indels: 220
0.75 0.19 0.06
Matches are distributed among these distances:
510 39 0.01
511 339 0.12
512 199 0.07
513 788 0.28
514 543 0.19
515 419 0.15
516 183 0.07
517 296 0.11
518 2 0.00
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.35
Consensus pattern (515 bp):
TGAGATTATAAAACCATTTAAAGCGAGCAATAAAGCTTTTGAAGGAATGGAGACTATAAATGAAC
TTTTCTAGCCAATGAATGCCTTTTTCTTCAAGTTTCTCAAGGTAGACATTCAAGTATAATCTATT
TTAACCAAAAAAGAAAAAAAAATTGAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGC
GAGTAATAAGGCTTTTGAAGGAATTGAGAGACTATAAATAGACTTTTCTTGCCAATAAATGTTTT
TTTCTTCATGTTTCTCAAAGTAGACATTCAATTATAGTCTGTTTTAGCCAAAAATGTAAAAACAA
TTGAACTTAAAATCAATTATGAGATTATAAAATCATTTAAAGCGAGCAATAAGGCTTTTAAAGGA
ATGAGAGACTATAAATAGAACTTTTTTACCAATGAATGCTTTTTTCTTCATGTTTCTTAAGGTAG
ACATTCAATTATATTCTGTTTTAATCAAAAATATAAAAAAATTAAACTTAAAATCAATTA
Found at i:1805 original size:172 final size:171
Alignment explanation
Indices: 1--4267 Score: 2813
Period size: 172 Copynumber: 24.9 Consensus size: 171
* * * * * * *
1 TGAGATAATAAAACCATTTAAAGTGGGTAATAAGACTTTTGAAGGAATGGGTGACTATAAATAGA
1 TGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATAGA
* * * * * ** * * * * * *
66 CTTTTATTGCCCATAAATGCCTTTTTCTTCATGTTTCTCGATGTAAACATTCAATCATAATTTAT
66 CTTTTCTTGCCAATGAATGCTTTTTTCTTCAAGTTTCTTAAGGTAGACATTCAATTATAGTCTGT
** ** * *
131 TTTAATAAAAAAAATAAAAAAACTTGAACTTAAAATTAATTT
131 TTTAACCAAAAATGTAAAAAAA-TTGAACTTAAAATCAATTA
* * * ********** * * *
173 TGAGAGTATAAAACCATTTAAAGTGAGTANNNNNNNNNNTGAAGGAATGGGTGATTATAAATAGA
1 TGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATAGA
* * * * ** * * *
238 CTTTTCTTGCCAATGAATGC-CTTTCCTTCATG-TTCCTCGGGAAGACATTCCATTATAATCT-T
66 CTTTTCTTGCCAATGAATGCTTTTTTCTTCAAGTTTCTTAAGGTAGACATTCAATTATAGTCTGT
* ** * ********
300 TTGAAATAAAAAATGTAAAAAAATTCAACTTAAANNNNNNNN
131 TT-TAACCAAAAATGTAAAAAAATTGAACTTAAAATCAATTA
** * * * * *
342 NNAGATTGTAAAACTATTTAAAGTGACTAAT-AGGTGTTTTGAAGGAATG-GTTGACTATAAATA
1 TGAGATTATAAAACTATTTAAAGCGAGTAATAAGG-CTTTTGAAGGAATGAG-AGACTATAAATA
* * * * * *
405 GACTTTTCTT-CTCAACGAATAGC--TTTTCTTACACGTTT-TCCAAGGTAAACATTCAATCATG
64 GACTTTTCTTGC-CAATGAAT-GCTTTTTTCTT-CAAGTTTCT-TAAGGTAGACATTCAATTATA
* * * * *
466 GGCTATTTCAA-TAAAAATTGTAAAAACAAATTCAACTTAAAATCAATTA
125 GTCTGTTTTAACCAAAAA-TGT-AAAA-AAATTGAACTTAAAATCAATTA
* * *
515 TGAGATTAT-AAACCATTTTAAGCGAGTAATAAAGCTTTTGAAGGAATG-GACGACTATAAAT-G
1 TGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGA-GACTATAAATAG
* * * * * * * * *
577 AATTTTTCTAGCCAATGAATGCCTTTTTCTTCATGTTTCTCAAAGTAGACTTTCAACTATAATCT
65 -ACTTTTCTTGCCAATGAATGCTTTTTTCTTCAAGTTTCTTAAGGTAGACATTCAATTATAGTCT
* ** * * * * * *
642 ATTTTATGCAAAAAAGAAAAAAAAATTAAACTTCAAACCAATTT
129 GTTTTAACCAAAAATG-TAAAAAAATTGAACTTAAAATCAATTA
* * * * * *
686 TGGGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATTGA-TGATTAT-AATAA
1 TGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAA-TGAGAGACTATAAATAG
* ** * * * * * *
749 ACTTTTCTTACCAATGAATGCATTTTTT-TTCGTGTTCCTCAAGGCAAAAATTCAATTATTGTCT
65 ACTTTTCTTGCCAATGAATGC-TTTTTTCTTCAAGTTTCTTAAGGTAGACATTCAATTATAGTCT
* * *
813 CTTTTAGCCAAAAATGTAAAAAAATTTAACTTAAAATCAATTA
129 GTTTTAACCAAAAATGTAAAAAAATTGAACTTAAAATCAATTA
* * * *
856 TAAGATTAGAAAA-TCATTTAAAGCGAGCAATAAGGCTTTTAAAGGAATGAGAGACTATAAATAG
1 TGAGATTATAAAACT-ATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATAG
* * * * *
920 A-TATTTTTTACCAATGAATACTTTTTTCTTCATGTTTCTTAAGGTAGACATTCAATTATATTCT
65 ACT-TTTCTTGCCAATGAATGCTTTTTTCTTCAAGTTTCTTAAGGTAGACATTCAATTATAGTCT
* * * * * *
984 GTTTTAATCAAAAATATGAAAATATTAAACTTAACATCAATTA
129 GTTTTAACCAAAAATGTAAAAAAATTGAACTTAAAATCAATTA
* * * *
1027 TGAGATTATAAAACTATTTAAAACGAGTAATAATGTTTTTGAAGGAATAAGAGACTATAAAT-GA
1 TGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATAG-
* * * * ********
1091 ACTTTTCTTAG-CAATGAATGCCTTTTTCTTCAAATTTCTTGAGGTAGACATTCAGTNNNNNNNN
65 ACTTTTCTT-GCCAATGAATGCTTTTTTCTTCAAGTTTCTTAAGGTAGACATTCAATTATAGTCT
**
1155 NNTTTAACCAAAAATGTAAAAAAAAGTTGAACTTAAAATCAATTA
129 GTTTTAACCAAAAATGT-AAAAAAA-TTGAACTTAAAATCAATTA
* * *
1200 TGAGATTATAAAA-TCATTTAAAGCAAGTACTAAGGCTTTTGAAGGAAT-AGAAGACTATAAATG
1 TGAGATTATAAAACT-ATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAG-AGACTATAAATA
* * * * * *
1263 GACTTTTCTTGTCAATAAATGTTTTTTTCTTCCA-TTTCTCAAAGTAGACATTCAATTATAGTCT
64 GACTTTTCTTGCCAATGAATGCTTTTTTCTTCAAGTTTCTTAAGGTAGACATTCAATTATAGTCT
* *
1327 GTTTTAA-CTAAAATGTAAAAACAATTGAACTTGAAATCAATTA
129 GTTTTAACCAAAAATGTAAAAA-AATTGAACTTAAAATCAATTA
* ** * * *
1370 TGAGATTATAAAA-TCATTTAAAGCAAGTAATAAAAC-TTTAAAGGAATAAGAGACTATAAATAA
1 TGAGATTATAAAACT-ATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATAG
* * * *
1433 ACTTTTCTTGACAATGAATGCTTTTTTCTTCATGTTTCTTAAGGTAGACGTTCAGTTATAGTCTG
65 ACTTTTCTTGCCAATGAATGCTTTTTTCTTCAAGTTTCTTAAGGTAGACATTCAATTATAGTCTG
* * * *
1498 TTTTAACAAAAAATATAAAAAAAAT-AACCTTAAAATCAATTT
130 TTTTAACCAAAAATGTAAAAAAATTGAA-CTTAAAATCAATTA
* * * * * * * * *
1540 TGAGAGTATGAAACCATTTAAAGCAAGCAATAAGGCTTTTGAAAGAATGGGTGATTATAAA-AGG
1 TGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATA-G
* ** ** *
1604 ATTTTTCTTGCCAATGAATGCCATTTTCTTCAAGTTTCTTAAGGTAGACATTCAATTATAACCTA
65 ACTTTTCTTGCCAATGAATGCTTTTTTCTTCAAGTTTCTTAAGGTAGACATTCAATTATAGTCTG
*
1669 TTTTAACCAAAAATGTAAAAAAACTTGAACTTAAAATCAATTT
130 TTTTAACCAAAAATGTAAAAAAA-TTGAACTTAAAATCAATTA
* * *
1712 TGAGGTTATAAAACTATTTCAAGCGAGTAATATGGCTTTTGAAGGAATGAGAGACTATAAATAGA
1 TGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATAGA
* * * * * ********** *
1777 CTTTTCTTGTCAATAAATACTTTTTTCTTTATGTTTCTNNNNNNNNNNATTCAATTATAGTTTGT
66 CTTTTCTTGCCAATGAATGCTTTTTTCTTCAAGTTTCTTAAGGTAGACATTCAATTATAGTCTGT
** * * *
1842 TTTAAGGAAAAATGTAAAAAAGAATTGAACATAAAATCATTTT
131 TTTAACCAAAAATGT-AAAAA-AATTGAACTTAAAATCAATTA
* * * * * * * * *
1885 TTAGATAATAAAACTATTTAAAGTGGGTAATAAGGCTTCTT-AATGAATGGGTGACTATTAATAA
1 TGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTT-TTGAAGGAATGAGAGACTATAAATAG
* * **
1949 ACTTTTTTTGCC-ATCGAATGCTTTTTTCTTCAAGTTTCTCAATATAGACATTCAATTATTA-TC
65 ACTTTTCTTGCCAAT-GAATGCTTTTTTCTTCAAGTTTCTTAAGGTAGACATTCAATTA-TAGTC
* * * *
2012 TGTTTTAATCAAAAATATAAAAAAACTTGAACCTAAAATTAATTA
128 TGTTTTAACCAAAAATGTAAAAAAA-TTGAACTTAAAATCAATTA
* * * * * * * *
2057 TAAGATTATAAAACTATTTATAGCGAGCAATAAAGCTTTTAAAGAAATGAAAGACTATAAATGGA
1 TGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATAGA
* ** * * * * *
2122 CTTTTCTTGCCCATGAATGC--TTTT-TTCAAGTTTCTCGATGTAGACATTCAAGTATTGTGTAT
66 CTTTTCTTGCCAATGAATGCTTTTTTCTTCAAGTTTCTTAAGGTAGACATTCAATTATAGTCTGT
** * *
2184 TTTAACCAAAAATACAAAAACATTTAACTTAAAATCAATTA
131 TTTAACCAAAAATGTAAAAAAATTGAACTTAAAATCAATTA
* * * * **
2225 TGAGATTATAAAAATATTTAAAGCGAGCAATATGACTTTTGAAAAAATGAGAGACTATAAATAGA
1 TGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATAGA
* * * *
2290 CTTTTCTTGCCAATGAATGTTTTTTTCTTCAAGTTTCTTGATGTAGACATTCAATTATTA-TCTA
66 CTTTTCTTGCCAATGAATGCTTTTTTCTTCAAGTTTCTTAAGGTAGACATTCAATTA-TAGTCTG
* * * **********
2354 TTTTAACTAAAAATATAAAAAAATTTAACNNNNNNNNNNTTA
130 TTTTAACCAAAAATGTAAAAAAATTGAACTTAAAATCAATTA
* *
2396 TGAGATTATAAAA-TCATTTAAAGCGAGCAATAAGGCTTTTGAAGAAAT-AGGAGACTATAAAT-
1 TGAGATTATAAAACT-ATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGA-GAGACTATAAATA
* * * ** * *
2458 GAACTTCTCTTGCCAATGAATGCTTTTCTCTTCATGTTTCTGGAGGTAGATATTCAATTATAGTT
64 G-ACTTTTCTTGCCAATGAATGCTTTTTTCTTCAAGTTTCTTAAGGTAGACATTCAATTATAGTC
* ** * *
2523 TGTTCTAATAAAAAATTTAAAAAAAATTGAACTTAAAATTAATTA
128 TGTTTTAACCAAAAATGT-AAAAAAATTGAACTTAAAATCAATTA
* *********** *
2568 TGAGATTATAAAACCATTTAAAGTNNNNNNNNNNGCTTTTGAAGGAATAAGAGACTATAAAT-GA
1 TGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATAG-
* * * * *
2632 ACTTTTCTTGACAATGAATGCCTTTTTCTTCACGTTTTTTAAGGTAGACATTCAGTTATAGTCTG
65 ACTTTTCTTGCCAATGAATGCTTTTTTCTTCAAGTTTCTTAAGGTAGACATTCAATTATAGTCTG
* **************
2697 TTTTAACTAAAAATGTAAAAAAAAATTGAANNNNNNNNNNNNNN
130 TTTTAACCAAAAATGT--AAAAAAATTGAACTTAAAATCAATTA
**************** * *
2741 NNNNNNNNNNNNNNNNTTTAAAGCGAGTAGTAAGGCTTTTGAAGGAATTGA-AGACTATAAATGG
1 TGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAA-TGAGAGACTATAAATAG
* * * * * * * * *
2805 ACTTTTTTTGCAAATGGATGCTTTTTTCATCCA-TTTCTTAAAGCAGACAATCAATTATAGTCAG
65 ACTTTTCTTGCCAATGAATGCTTTTTTCTTCAAGTTTCTTAAGGTAGACATTCAATTATAGTCTG
** *
2869 TTTTAA-TGAAAATGTAAAAAAAATTGAACTTGAAATCAATTA
130 TTTTAACCAAAAATGT-AAAAAAATTGAACTTAAAATCAATTA
********* * * * *
2911 TGAGNNNNNNNNNNC-ATTTAAAGCAAGTAATAAGGCTTTTAAAGGAATAAGAGACTATAAATAA
1 TGAG-ATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATAG
** * * * * *
2975 ACTTTTCTTGATAATGAATGCTTTTTTCTTCACGTTTC-TAATGGTAGACATTTAGTTTTATTCT
65 ACTTTTCTTGCCAATGAATGCTTTTTTCTTCAAGTTTCTTAA-GGTAGACATTCAATTATAGTCT
* * * * *
3039 ATTTTAACTAAAAATGTAAAAAAAATTGAAGTTAAAATTAATTT
129 GTTTTAACCAAAAATGT-AAAAAAATTGAACTTAAAATCAATTA
* * * ********** * * * *
3083 TGAGAGTATAAAACTATTTAAAGCAAGCANNNNNNNNNNTGAAGGAATGGGTGACTATAAAAAAA
1 TGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATAGA
* * * * *
3148 TTTTTCTTGTCAATGAATG-TCATTTTCTTCAAGTTTCTTGAGGTAGACATTCAATTATA-ACTT
66 CTTTTCTTGCCAATGAATGCT-TTTTTCTTCAAGTTTCTTAAGGTAGACATTCAATTATAGTC-T
*
3211 GTTTTAACCAAAAATGTAAAAAAACTTGAACTTAAAATAAAATT-
129 GTTTTAACCAAAAATGTAAAAAAA-TTGAACTTAAAAT-CAATTA
* ********** *
3255 TGAGGTTATAAAA-TCATTTAAAGCGAGTAATAAGGCTTTTGAAGGNNNNNNNNNNTATAAATGG
1 TGAGATTATAAAACT-ATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATAG
** *
3319 ACTTTTCTTATCAATGAATGCTTTTTTCTTTATA-TTT-TTAGAGGTAGACATTCAATTATAGTC
65 ACTTTTCTTGCCAATGAATGCTTTTTTCTTCA-AGTTTCTTA-AGGTAGACATTCAATTATAGTC
* * * *
3382 TGTTTTAAGCAAAAATGTAAAAAAGAATTGAACATAAAATCATTTT
128 TGTTTTAACCAAAAATGT-AAAAA-AATTGAACTTAAAATCAATTA
* * * * * * *
3428 TGAGATAATAAAACTATTTAAAGTGGGTAATAAGGCTTTTGAAGGAATGTGTGACTATTAATAAA
1 TGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATAGA
* * * ** ** * * *
3493 CTTTTCTTACCAATGAATGCCTTTTTCTTCAAGATTCTCGACATAAACATTCAATTATAATCTAT
66 CTTTTCTTGCCAATGAATGCTTTTTTCTTCAAGTTTCTTAAGGTAGACATTCAATTATAGTCTGT
*
3558 TTTAACCAAAAATGTAAAAAAACTTGAACTTAAAATTAATTA
131 TTTAACCAAAAATGTAAAAAAA-TTGAACTTAAAATCAATTA
* * * * * * * *
3600 TAAGATTATAAAATTATTTATAGCGAGCAATAAAGCTTTTGAAGAAATG-GAAGACTCTAAATGG
1 TGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAG-AGACTATAAATAG
* * * * *
3664 ACTTTTCTAGCCCATGAATGC--GTTT-TTCAAGTTT-TTCAACGTAGACATTCAATTATTGTCT
65 ACTTTTCTTGCCAATGAATGCTTTTTTCTTCAAGTTTCTT-AAGGTAGACATTCAATTATAGTCT
* * * *
3725 GTTTTAACAAAAAATGCATAAAAATTTAACTTAAAATCAATTA
129 GTTTTAACCAAAAATGTAAAAAAATTGAACTTAAAATCAATTA
********* * * * * *
3768 NNNNNNNNNNAAAAC-ATTTAAAGCGAGCAATAAAGCTTTTCAAGAAATGGGAGACTATAAATAG
1 -TGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATAG
* ** * * * * *
3832 ACTTTTCTTGCAAATGAATATTTTTTTCTTTAAGTTTCTTGATGTAGACATTCAATTATTGTTTG
65 ACTTTTCTTGCCAATGAATGCTTTTTTCTTCAAGTTTCTTAAGGTAGACATTCAATTATAGTCTG
** ** * *
3897 TTTTAATAAAAAATACAAAAAAATTCAACTTAAAATCAAGTA
130 TTTTAACCAAAAATGTAAAAAAATTGAACTTAAAATCAATTA
* * * * *
3939 TGAGATTATAAAA-TGATTTAAAGCGAGCAATTAGGCTTTTGAAGAAATGAGAGACCATAAATGG
1 TGAGATTATAAAACT-ATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATAG
* ** *
4003 ACTTTTCTTGCCAATGAATGCTTTTCTCTTCATA-TTTCTGGAGGTAGACATTCAATTATAATCT
65 ACTTTTCTTGCCAATGAATGCTTTTTTCTTCA-AGTTTCTTAAGGTAGACATTCAATTATAGTCT
* * ** * * * *
4067 ATTCTAATAAAAAATTTTAAAAAATTAAACTTAAAATTAATTA
129 GTTTTAACCAAAAATGTAAAAAAATTGAACTTAAAATCAATTA
* ********** *
4110 TGAGATTATAAAACCATTTANNNNNNNNNNTAAGGCTTTTGAAGGAATGAGAGACTATAAATAAA
1 TGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATAGA
* * *
4175 CTTTTCTT-CACAATGAATGTCTTTTTCTTTTTCTTCACA-TTTTTTGAGGTAGACATTCAGTTA
66 CTTTTCTTGC-CAATGAATG-C----T-TTTTTCTTCA-AGTTTCTTAAGGTAGACATTCAATTA
*
4238 TAGTCTGTTTTAACTAAAAATGTAAAAAAA
123 TAGTCTGTTTTAACCAAAAATGTAAAAAAA
4268 AATTGAANNN
Statistics
Matches: 3184, Mismatches: 794, Indels: 229
0.76 0.19 0.05
Matches are distributed among these distances:
168 169 0.05
169 237 0.07
170 361 0.11
171 932 0.29
172 945 0.30
173 471 0.15
174 14 0.00
176 1 0.00
177 54 0.02
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.35
Consensus pattern (171 bp):
TGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATAGA
CTTTTCTTGCCAATGAATGCTTTTTTCTTCAAGTTTCTTAAGGTAGACATTCAATTATAGTCTGT
TTTAACCAAAAATGTAAAAAAATTGAACTTAAAATCAATTA
Found at i:2027 original size:345 final size:339
Alignment explanation
Indices: 1--4268 Score: 1738
Period size: 342 Copynumber: 12.4 Consensus size: 339
* * * * * * *
1 TGAGATAATAAAACCATTTAAAGTGGGTAAT-AAGACTTTTGAAGGAATGGGTGACTATAAATAG
1 TGAGATTATAAAACTATTT-AAGCGAGTAATAAAG-CTTTTAAAGGAATGAGAGACTATAAATAG
* * * * * ** * * * * * *
65 ACTTTTATTGCCCATAAATGCCTTTTTCTTCATGTTTCTCGATGTAAACATTCAATCATAATTTA
64 ACTTTTCTTGACAATGAATGCTTTTTTCTTCATGTTTCTTAAGGTAGACATTCAATTATAGTCTG
* * * * *
130 TTTTAATAAAAAAAATAAAAAAACTTGAA-CTTAAAATTAATTTTGAGAGTATAAAACCATTTAA
129 TTTTAACAAAAAATATAAAAAAA-AT-AACCATAAAATCAATTTTGAGAGTATAAAACCATTTAA
** * ********** * * *
194 AGTGAGTANNNNNNNNNNTGAAGGAATGGGTGATTATAAATAGACTTTTCTTGCCAATGAATGC-
192 AGCAAGCAATAAGGCTTTTGAAAGAATGGGTGACTATAAA-AGATTTTTCTTGCCAATGAATGCT
* * * * ** * * * *
258 CTTTCCTTCATGTTCCTCGGGA-AGACATTCCATTATAATCT-TTTGAAATAAAAAATGTAAAAA
256 TTTTTCTTCAAGTTTCTC-AAATAGACATTCAATTATTATCTGTTT-TAA-CAAAAATGTAAAAA
* ********
321 AA-TTCAACTTAAANNNNNNNN
318 AACTTGAACTTAAAATCAATTA
** * * * * * * *
342 NNAGATTGTAAAACTATTTAAAGTGACTAAT-AGGTGTTTTGAAGGAATG-GTTGACTATAAATA
1 TGAGATTATAAAACTATTT-AAGCGAGTAATAAAG-CTTTTAAAGGAATGAG-AGACTATAAATA
** * * * * * *
405 GACTTTTCTTCTCAACGAATAGC--TTTTCTTACACGTTT-TCCAAGGTAAACATTCAATCATGG
63 GACTTTTCTTGACAATGAAT-GCTTTTTTCTT-CATGTTTCT-TAAGGTAGACATTCAATTATAG
* * * * * * * * *
467 GCTATTTCAATAAAAATTGTAAAAACAAATTCAA-CTTAAAATCAATTATGAGATTAT-AAACCA
125 TCTGTTTTAACAAAAAATATAAAAA-AAA-T-AACCATAAAATCAATTTTGAGAGTATAAAACCA
* * * * * ** * *
530 TTTTAAGCGAGTAATAAAGCTTTTGAAGGAATGGACGACTATAAATGAATTTTTCTAGCCAATGA
187 TTTAAAGCAAGCAATAAGGCTTTTGAAAGAATGGGTGACTATAAAAG-ATTTTTCTTGCCAATGA
* * * * * * * * *
595 ATGCCTTTTTCTTCATGTTTCTCAAAGTAGACTTTCAACTATAATCTATTTTATGCAAAAAAGAA
251 ATGCTTTTTTCTTCAAGTTTCTCAAA-TAGACATTCAATTATTATCTGTTTTA-ACAAAAATGTA
* * * * *
660 AAAAAAATTAAACTTCAAACCAATTT
314 AAAAAACTTGAACTTAAAATCAATTA
* * * * * * * *
686 TGGGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATTGA-TGATTAT-AATAA
1 TGAGATTATAAAACTATTT-AAGCGAGTAATAAAGCTTTTAAAGGAA-TGAGAGACTATAAATAG
* * * * * * *
749 ACTTTTCTT-ACCAATGAATGCATTTTTT-TTCGTGTTCCTCAAGGCAAAAATTCAATTATTGTC
64 ACTTTTCTTGA-CAATGAATGC-TTTTTTCTTCATGTTTCTTAAGGTAGACATTCAATTATAGTC
* * * * * * * * * * *
812 TCTTTTAGCCAAAAATGTAAAAAAATTTAA-CTTAAAATCAATTATAAGATTAGAAAATCATTTA
127 TGTTTTAACAAAAAATATAAAAAAA-ATAACCATAAAATCAATTTTGAGAGTATAAAACCATTTA
* * * *
876 AAGCGAGCAATAAGGCTTTT-AAAGGAATGAGAGACTATAAATAGATATTTT-TTACCAATGAAT
191 AAGCAAGCAATAAGGCTTTTGAAA-GAATGGGTGACTATAAA-AGAT-TTTTCTTGCCAATGAAT
* * * * * *
939 ACTTTTTTCTTCATGTTTCTTAAGGTAGACATTCAATTA-TATTCTGTTTTAATCAAAAATATGA
253 GCTTTTTTCTTCAAGTTTCTCAA-ATAGACATTCAATTATTA-TCTGTTTTAA-CAAAAATGTAA
* * *
1003 AAATA-TTAAACTTAACATCAATTA
315 AAAAACTTGAACTTAAAATCAATTA
* * * * *
1027 TGAGATTATAAAACTATTTAAAACGAGTAATAATGTTTTTGAAGGAATAAGAGACTATAAAT-GA
1 TGAGATTATAAAACTATTT-AAGCGAGTAATAAAGCTTTTAAAGGAATGAGAGACTATAAATAG-
* ** * * ********
1091 ACTTTTCTT-AGCAATGAATGCCTTTTTCTTCAAATTTCTTGAGGTAGACATTCAGTNNNNNNNN
64 ACTTTTCTTGA-CAATGAATGCTTTTTTCTTCATGTTTCTTAAGGTAGACATTCAATTATAGTCT
** * * * * * *
1155 NNTTTAACCAAAAATGTAAAAAAAAGTTGAA-CTTAAAATCAATTATGAGATTATAAAATCATTT
128 GTTTTAACAAAAAATATAAAAAAAA--T-AACCATAAAATCAATTTTGAGAGTATAAAACCATTT
* * * * ** * * * *
1219 AAAGCAAGTACTAAGGCTTTTGAAGGAATAGAAGACTATAAATGGACTTTTCTTGTCAATAAATG
190 AAAGCAAGCAATAAGGCTTTTGAAAGAATGGGTGACTATAAA-AGATTTTTCTTGCCAATGAATG
* * *
1284 TTTTTTTCTTCCA-TTTCTCAAAGTAGACATTCAATTA-TAGTCTGTTTTAACTAAAATGTAAAA
254 CTTTTTTCTTCAAGTTTCTCAAA-TAGACATTCAATTATTA-TCTGTTTTAACAAAAATGTAAAA
*
1347 ACAA-TTGAACTTGAAATCAATTA
317 A-AACTTGAACTTAAAATCAATTA
* * * *
1370 TGAGATTATAAAA-TCATTTAAAGCAAGTAATAAAAC-TTTAAAGGAATAAGAGACTATAAATAA
1 TGAGATTATAAAACT-ATTT-AAGCGAGTAATAAAGCTTTTAAAGGAATGAGAGACTATAAATAG
* *
1433 ACTTTTCTTGACAATGAATGCTTTTTTCTTCATGTTTCTTAAGGTAGACGTTCAGTTATAGTCTG
64 ACTTTTCTTGACAATGAATGCTTTTTTCTTCATGTTTCTTAAGGTAGACATTCAATTATAGTCTG
* *
1498 TTTTAACAAAAAATATAAAAAAAATAACCTTAAAATCAATTTTGAGAGTATGAAACCATTTAAAG
129 TTTTAACAAAAAATATAAAAAAAATAACCATAAAATCAATTTTGAGAGTATAAAACCATTTAAAG
* **
1563 CAAGCAATAAGGCTTTTGAAAGAATGGGTGATTATAAAAGGATTTTTCTTGCCAATGAATGCCAT
194 CAAGCAATAAGGCTTTTGAAAGAATGGGTGACTATAAAA-GATTTTTCTTGCCAATGAATGCTTT
* * * * *
1628 TTTCTTCAAGTTTCTTAAGGTAGACATTCAATTATAACCTATTTTAACCAAAAATGTAAAAAAAC
258 TTTCTTCAAGTTTCTCAA-ATAGACATTCAATTATTATCTGTTTTAA-CAAAAATGTAAAAAAAC
*
1693 TTGAACTTAAAATCAATTT
321 TTGAACTTAAAATCAATTA
* ** *
1712 TGAGGTTATAAAACTATTTCAAGCGAGTAATATGGCTTTTGAAGGAATGAGAGACTATAAATAGA
1 TGAGATTATAAAACTATTT-AAGCGAGTAATAAAGCTTTTAAAGGAATGAGAGACTATAAATAGA
* * * * ********** *
1777 CTTTTCTTGTCAATAAATACTTTTTTCTTTATGTTTCTNNNNNNNNNNATTCAATTATAGTTTGT
65 CTTTTCTTGACAATGAATGCTTTTTTCTTCATGTTTCTTAAGGTAGACATTCAATTATAGTCTGT
** * * * *
1842 TTTAAGGAAAAATGTAAAAAAGAATTGAA-CATAAAATCATTTTTTAGA-TAATAAAACTATTTA
130 TTTAACAAAAAATATAAAAAA-AA-T-AACCATAAAATCAATTTTGAGAGT-ATAAAACCATTTA
*** * *
1905 AAGTGGGTAATAAGGCTTCTT-AATGAATGGGTGACTATTAATAA-ACTTTTT-TTGCC-ATCGA
191 AAGCAAGCAATAAGGCTT-TTGAAAGAATGGGTGACTA-TAA-AAGA-TTTTTCTTGCCAAT-GA
*
1966 ATGCTTTTTTCTTCAAGTTTCTCAATATAGACATTCAATTATTATCTGTTTTAATCAAAAATATA
251 ATGCTTTTTTCTTCAAGTTTCTCAA-ATAGACATTCAATTATTATCTGTTTTAA-CAAAAATGTA
* *
2031 AAAAAACTTGAACCTAAAATTAATTA
314 AAAAAACTTGAACTTAAAATCAATTA
* * * * *
2057 TAAGATTATAAAACTATTTATAGCGAGCAATAAAGCTTTTAAAGAAATGAAAGACTATAAATGGA
1 TGAGATTATAAAACTATTTA-AGCGAGTAATAAAGCTTTTAAAGGAATGAGAGACTATAAATAGA
* * * ** * * * * *
2122 CTTTTCTTGCCCATGAATGC--TTTT-TTCAAGTTTCTCGATGTAGACATTCAAGTATTGTGTAT
65 CTTTTCTTGACAATGAATGCTTTTTTCTTCATGTTTCTTAAGGTAGACATTCAATTATAGTCTGT
* * ** * * * **
2184 TTTAACCAAAAATACAAAAACATTTAA-CTTAAAATCAATTATGAGATTATAAAAATATTTAAAG
130 TTTAACAAAAAATATAAAAA-AAATAACCATAAAATCAATTTTGAGAGTATAAAACCATTTAAAG
* * * * * * * *
2248 CGAGCAATATGACTTTTGAAAAAATGAGAGACTATAAATAGACTTTTCTTGCCAATGAATGTTTT
194 CAAGCAATAAGGCTTTTGAAAGAATGGGTGACTATAAA-AGATTTTTCTTGCCAATGAATGCTTT
* ** * *
2313 TTTCTTCAAGTTTCTTGATGTAGACATTCAATTATTATCTATTTTAACTAAAAATATAAAAAAA-
258 TTTCTTCAAGTTTC-TCAAATAGACATTCAATTATTATCTGTTTTAAC-AAAAATGTAAAAAAAC
* **********
2377 TTTAACNNNNNNNNNNTTA
321 TTGAACTTAAAATCAATTA
* * * *
2396 TGAGATTATAAAA-TCATTTAAAGCGAGCAATAAGGCTTTTGAAGAAAT-AGGAGACTATAAAT-
1 TGAGATTATAAAACT-ATTT-AAGCGAGTAATAAAGCTTTTAAAGGAATGA-GAGACTATAAATA
* * * ** * *
2458 GAACTTCTCTTGCCAATGAATGCTTTTCTCTTCATGTTTCTGGAGGTAGATATTCAATTATAGTT
63 G-ACTTTTCTTGACAATGAATGCTTTTTTCTTCATGTTTCTTAAGGTAGACATTCAATTATAGTC
* * * * * * *
2523 TGTTCTAATAAAAAATTTAAAAAAAATTGAA-CTTAAAATTAATTATGAGATTATAAAACCATTT
127 TGTTTTAACAAAAAATATAAAAAAAA-T-AACCATAAAATCAATTTTGAGAGTATAAAACCATTT
*********** * ** * * * *
2587 AAAGTNNNNNNNNNNGCTTTTGAAGGAATAAGAGACTATAAATGAACTTTTCTTGACAATGAATG
190 AAAGCAAGCAATAAGGCTTTTGAAAGAATGGGTGACTATAAAAG-ATTTTTCTTGCCAATGAATG
* * * * * *
2652 CCTTTTTCTTCACGTTTTTTAAGGTAGACATTCAGTTA-TAGTCTGTTTTAACTAAAAATGTAAA
254 CTTTTTTCTTCAAGTTTCTCAA-ATAGACATTCAATTATTA-TCTGTTTTAAC-AAAAATGT-AA
* **************
2716 AAAAAATTGAANNNNNNNNNNNNNN
315 AAAAACTTGAACTTAAAATCAATTA
**************** * * * *
2741 NNNNNNNNNNNNNNNNTTTAAAGCGAGTAGTAAGGCTTTTGAAGGAATTGA-AGACTATAAATGG
1 TGAGATTATAAAACTATTT-AAGCGAGTAATAAAGCTTTTAAAGGAA-TGAGAGACTATAAATAG
* * * * * *
2805 ACTTTTTTTG-CAAATGGATGCTTTTTTCATCCA--TTTCTTAAAGCAGACAATCAATTATAGTC
64 ACTTTTCTTGAC-AATGAATGCTTTTTTC-TTCATGTTTCTTAAGGTAGACATTCAATTATAGTC
* ** * * * * **********
2867 AGTTTTAA-TGAAAATGTAAAAAAAATTGAA-CTTGAAATCAATTATGAGNNNNNNNNNNCATTT
127 TGTTTTAACAAAAAATATAAAAAAAA-T-AACCATAAAATCAATTTTGAGAGTATAAAACCATTT
* ** * * * **
2930 AAAGCAAGTAATAAGGCTTTT-AAAGGAATAAGAGACTATAAATAAACTTTTCTTGATAATGAAT
190 AAAGCAAGCAATAAGGCTTTTGAAA-GAATGGGTGACTATAAA-AGATTTTTCTTGCCAATGAAT
* * * * *
2994 GCTTTTTTCTTCACGTTTCT-AATGGTAGACATTTAGTT-TTATTCTATTTTAACTAAAAATGTA
253 GCTTTTTTCTTCAAGTTTCTCAA--ATAGACATTCAATTATTA-TCTGTTTTAAC-AAAAATGTA
* * * *
3057 AAAAAAATTGAAGTTAAAATTAATTT
314 AAAAAACTTGAACTTAAAATCAATTA
* * * ********** * * * * *
3083 TGAGAGTATAAAACTATTTAAAGCAAGCANNNNNNNNNNTGAAGGAATGGGTGACTATAAAAAAA
1 TGAGATTATAAAACTATTT-AAGCGAGTAATAAAGCTTTTAAAGGAATGAGAGACTATAAATAGA
* * * * * *
3148 TTTTTCTTGTCAATGAATG-TCATTTTCTTCAAGTTTCTTGAGGTAGACATTCAATTATA-ACTT
65 CTTTTCTTGACAATGAATGCT-TTTTTCTTCATGTTTCTTAAGGTAGACATTCAATTATAGTC-T
* * * * * * *
3211 GTTTTAACCAAAAATGTAAAAAAACTTGAA-CTTAAAATAAAATTTGAG-GTTATAAAATCATTT
128 GTTTTAACAAAAAATATAAAAAAA-AT-AACCATAAAATCAATTTTGAGAG-TATAAAACCATTT
* * * ********** * * **
3274 AAAGCGAGTAATAAGGCTTTTGAAGGNNNNNNNNNNTATAAATGGACTTTTCTTATCAATGAATG
190 AAAGCAAGCAATAAGGCTTTTGAAAGAATGGGTGACTATAAA-AGATTTTTCTTGCCAATGAATG
* * *
3339 CTTTTTTCTTTATA-TTT-TTAGAGGTAGACATTCAATTA-TAGTCTGTTTTAAGCAAAAATGTA
254 CTTTTTTCTTCA-AGTTTCTCA-A-ATAGACATTCAATTATTA-TCTGTTTTAA-CAAAAATGTA
* * * *
3401 AAAAAGAATTGAACATAAAATCATTTT
314 AAAAA-ACTTGAACTTAAAATCAATTA
* * * * * * * * *
3428 TGAGATAATAAAACTATTTAAAGTGGGTAATAAGGCTTTTGAAGGAATGTGTGACTATTAATAAA
1 TGAGATTATAAAACTATTT-AAGCGAGTAATAAAGCTTTTAAAGGAATGAGAGACTATAAATAGA
* * * ** ** * * *
3493 CTTTTCTT-ACCAATGAATGCCTTTTTCTTCAAGATTCTCGACATAAACATTCAATTATAATCTA
65 CTTTTCTTGA-CAATGAATGCTTTTTTCTTCATGTTTCTTAAGGTAGACATTCAATTATAGTCTG
* * * * * * * * ** *
3557 TTTTAACCAAAAATGTAAAAAAACTTGAA-CTTAAAATTAATTATAAGATTATAAAATTATTTAT
129 TTTTAACAAAAAATATAAAAAAA-AT-AACCATAAAATCAATTTTGAGAGTATAAAACCATTTAA
* * ** * * * * *
3621 AGCGAGCAATAAAGCTTTTG-AAGAAATGGAAGACTCTAAATGGACTTTTCTAGCCCATGAATGC
192 AGCAAGCAATAAGGCTTTTGAAAG-AATGGGTGACTATAAA-AGATTTTTCTTGCCAATGAATGC
* * * * * *
3685 --GTTT-TTCAAGTTTTTCAACGTAGACATTCAATTATTGTCTGTTTTAACAAAAAATGCATAAA
255 TTTTTTCTTCAAGTTTCTCAA-ATAGACATTCAATTATTATCTGTTTTAAC-AAAAATGTAAAAA
*
3747 AA-TTTAACTTAAAATCAATTA
318 AACTTGAACTTAAAATCAATTA
********* * * * *
3768 NNNNNNNNNNAAAAC-ATTTAAAGCGAGCAATAAAGCTTTTCAAGAAATGGGAGACTATAAATAG
1 -TGAGATTATAAAACTATTT-AAGCGAGTAATAAAGCTTTTAAAGGAATGAGAGACTATAAATAG
** * * * * * *
3832 ACTTTTCTTG-CAAATGAATATTTTTTTCTTTAAGTTTCTTGATGTAGACATTCAATTATTGTTT
64 ACTTTTCTTGAC-AATGAATGCTTTTTTCTTCATGTTTCTTAAGGTAGACATTCAATTATAGTCT
* * * * * * * **
3896 GTTTTAATAAAAAATACAAAAAAATTCAA-CTTAAAATCAAGTATGAGATTATAAAATGATTTAA
128 GTTTTAACAAAAAATATAAAAAAAAT-AACCATAAAATCAATTTTGAGAGTATAAAACCATTTAA
* * * * * * *
3960 AGCGAGCAATTAGGCTTTTG-AAGAAATGAGAGACCATAAATGGACTTTTCTTGCCAATGAATGC
192 AGCAAGCAATAAGGCTTTTGAAAG-AATGGGTGACTATAAA-AGATTTTTCTTGCCAATGAATGC
* * ** * * * * * *
4024 TTTTCTCTTCATA-TTTCTGGAGGTAGACATTCAATTATAATCTATTCTAATAAAAAATTTTAAA
255 TTTTTTCTTCA-AGTTTCT-CAAATAGACATTCAATTATTATCTGTTTTAA-CAAAAATGTAAAA
* *
4088 AAA-TTAAACTTAAAATTAATTA
317 AAACTTGAACTTAAAATCAATTA
* ********* * * *
4110 TGAGATTATAAAACCATTTANNNNNNNNNNTAAGGCTTTTGAAGGAATGAGAGACTATAAATAAA
1 TGAGATTATAAAACTATTTA-AGCGAGTAATAAAGCTTTTAAAGGAATGAGAGACTATAAATAGA
* ** * * *
4175 CTTTTCTTCACAATGAATGTCTTTTTCTTTTTCTTCACATTTTTTGAGGTAGACATTCAGTTATA
65 CTTTTCTTGACAATGAATG-C----T-TTTTTCTTCATGTTTCTTAAGGTAGACATTCAATTATA
* *
4240 GTCTGTTTTAACTAAAAATGTAAAAAAAA
124 GTCTGTTTTAACAAAAAATATAAAAAAAA
4269 ATTGAANNNN
Statistics
Matches: 3032, Mismatches: 757, Indels: 269
0.75 0.19 0.07
Matches are distributed among these distances:
338 4 0.00
339 183 0.06
340 350 0.12
341 319 0.11
342 685 0.23
343 579 0.19
344 323 0.11
345 513 0.17
346 18 0.01
347 4 0.00
348 54 0.02
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.35
Consensus pattern (339 bp):
TGAGATTATAAAACTATTTAAGCGAGTAATAAAGCTTTTAAAGGAATGAGAGACTATAAATAGAC
TTTTCTTGACAATGAATGCTTTTTTCTTCATGTTTCTTAAGGTAGACATTCAATTATAGTCTGTT
TTAACAAAAAATATAAAAAAAATAACCATAAAATCAATTTTGAGAGTATAAAACCATTTAAAGCA
AGCAATAAGGCTTTTGAAAGAATGGGTGACTATAAAAGATTTTTCTTGCCAATGAATGCTTTTTT
CTTCAAGTTTCTCAAATAGACATTCAATTATTATCTGTTTTAACAAAAATGTAAAAAAACTTGAA
CTTAAAATCAATTA
Found at i:2693 original size:856 final size:857
Alignment explanation
Indices: 487--4129 Score: 2116
Period size: 856 Copynumber: 4.3 Consensus size: 857
477 TAAAAATTGT
* * * * * *
487 AAAAACAAATTCAACTTAAAATCAATTATGAGATTAT-AAACCATTTTAAGCGAGTAATAAAGCT
1 AAAAAC-AATTGAACTTAAAATCAATTATGAGATTATAAAATCATTTAAAGCAAGCAATAAAAC-
* * * * * * * * *
551 TTTGAAGGAAT-GGACGACTATAAATGAATTTTTCTAGCCAATGAATGCCTTTTTCTTCATGTTT
64 TTTAAAGAAATAAGA-GACTATAAATAAACTTTTCTTGACAATGAATGCTTTTTTCTTCAAGTTT
* * * * * * * * *
615 CTCAAAGTAGACTTTCAACTATAATCTATTTTATGCAAAAAAGA-AAAAAAAATTAAACTTCAAA
128 CTTAAGGTAGACATTCAATTATAGTCTATTTTA-ACAAAAAATATAAAAAAAA-TAACCTTAAAA
* * * * ** * * * *
679 CCAATTTTGGGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAAT-TGATGATTA
191 TCAATTATGAGAGTATAAAACCATTTAAAGCAAGCAATAAGGCTTTTGAAAGAATAGGA-GACTA
* * * * ** * * * * *
743 TAATA-AACTTTTCTTACCAATGAATG-CATTTTTTTTCGTGTTCCTCAAGGCAAAAATTCAATT
255 TAAAAGAACTTCTCTTGCCAATGAATGCCA-TTTTCTTCAAGTTTCTGAAGGTAGACATTCAATT
*** * * * * * * * *
806 ATTGTCTCTTTTAGCCAAAAATGT-AAAAAAATTTAACTTAAAATCAATTATAAGATTAGAAAAT
319 ATAACCTATTCTAACAAAAAATGTAAAAAAAATTGAACTTAAAATCAATTATGAGATTATAAAAC
* * * * *
870 CATTTAAAGCGAGCAATAAGGCTTTTAAAGGAATGAGAGACTATAAATAGA-TATTT-TTTACCA
384 CATTTAAAGCGAGTAATATGGCTTTTGAAGGAATAAGAGACTATAAATAGACT-TTTCTTGA-CA
* * * *
933 ATGAATACTTTTTTCTTCATGTTTCTTAAGGTAGACATTCAATTATATTCTGTTTTAATC-AAAA
447 ATAAATACCTTTTTCTTCACGTTTCTTAAGGTAGACATTCAATTATAGTCTGTTTTAA-CGAAAA
** * * * * * * * * ** *
997 A--TATGAAAATATTAAACTTAACATCAATTATGAGATTATAAAACTATTTAAAACGAGTAATAA
511 ATGTAAAAAAAAATTGAACATAAAATCATTTTTTAGATAATAAAACTATTTAAAGTGGGTAATAA
* * * ** * * * * * *
1060 TG-TTTTTGAAGGAATAAGAGACTATAAATGAACTTTTCTTAGCAAT-GAATGCCTTTTTCTTCA
576 GGCTTCTT-AATGAATGGGTGACTATTAATAAACTTTT-TTTGCCATCGAATGCTTTTTTCTTCA
* ** ** * ********** * * *
1123 AATTTCTTGAGGTAGACATTCAGTNNNNNNNNNNTTTAACCAAAAATGTAAAAAAAAGTTGAACT
639 AGTTTCTCAATATAGACATTCAATTATTATCTGTTTTAACCAAAAATATAAAAAAAACTTGAACC
* * * * * *
1188 TAAAATCAATTATGAGATTATAAAATCATTTAAAGCAAGTACTAAGGCTTTTGAAGGAATAGAAG
704 TAAAATCAATTATAAGATTATAAAATCATTTAAAGCAAGCAATAAAGCTTTTAAAGAAATAGAAG
* * *
1253 ACTATAAATGGACTTTTCTTGTCAATAAATGTTTTTTTCTTCCATTTCTCAAAGTAGACATTCAA
769 ACTATAAATGGACTTTTCTTGCCAATAAATG-TCTTTTCTTCAATTTCTCAAAGTAGACATTCAA
* * * **
1318 TTATAGTCTGTTTTAACTAAAATGT
833 GTATAGTCTATTTTAACAAAAATAC
* *
1343 AAAAACAATTGAACTTGAAATCAATTATGAGATTATAAAATCATTTAAAGCAAGTAATAAAACTT
1 AAAAACAATTGAACTTAAAATCAATTATGAGATTATAAAATCATTTAAAGCAAGCAATAAAACTT
* *
1408 TAAAGGAATAAGAGACTATAAATAAACTTTTCTTGACAATGAATGCTTTTTTCTTCATGTTTCTT
66 TAAAGAAATAAGAGACTATAAATAAACTTTTCTTGACAATGAATGCTTTTTTCTTCAAGTTTCTT
* * *
1473 AAGGTAGACGTTCAGTTATAGTCTGTTTTAACAAAAAATATAAAAAAAATAACCTTAAAATCAAT
131 AAGGTAGACATTCAATTATAGTCTATTTTAACAAAAAATATAAAAAAAATAACCTTAAAATCAAT
* * * * *
1538 TTTGAGAGTATGAAACCATTTAAAGCAAGCAATAAGGCTTTTGAAAGAATGGGTGATTATAAAAG
196 TATGAGAGTATAAAACCATTTAAAGCAAGCAATAAGGCTTTTGAAAGAATAGGAGACTATAAAAG
* * * *
1603 GATTTTTCTTGCCAATGAATGCCATTTTCTTCAAGTTTCTTAAGGTAGACATTCAATTATAACCT
261 AACTTCTCTTGCCAATGAATGCCATTTTCTTCAAGTTTCTGAAGGTAGACATTCAATTATAACCT
* * * * * * *
1668 ATTTTAACCAAAAATGTAAAAAAACTTGAACTTAAAATCAATTTTGAGGTTATAAAACTATTTCA
326 ATTCTAACAAAAAATGTAAAAAAAATTGAACTTAAAATCAATTATGAGATTATAAAACCATTTAA
* * *
1733 AGCGAGTAATATGGCTTTTGAAGGAATGAGAGACTATAAATAGACTTTTCTTGTCAATAAATACT
391 AGCGAGTAATATGGCTTTTGAAGGAATAAGAGACTATAAATAGACTTTTCTTGACAATAAATACC
* * ********** * *
1798 TTTTTCTTTATGTTTCTNNNNNNNNNNATTCAATTATAGTTTGTTTTAAGGAAAAATGTAAAAAA
456 TTTTTCTTCACGTTTCTTAAGGTAGACATTCAATTATAGTCTGTTTTAACGAAAAATGTAAAAAA
*
1863 GAATTGAACATAAAATCATTTTTTAGATAATAAAACTATTTAAAGTGGGTAATAAGGCTTCTTAA
521 AAATTGAACATAAAATCATTTTTTAGATAATAAAACTATTTAAAGTGGGTAATAAGGCTTCTTAA
1928 TGAATGGGTGACTATTAATAAACTTTTTTTGCCATCGAATGCTTTTTTCTTCAAGTTTCTCAATA
586 TGAATGGGTGACTATTAATAAACTTTTTTTGCCATCGAATGCTTTTTTCTTCAAGTTTCTCAATA
* *
1993 TAGACATTCAATTATTATCTGTTTTAATCAAAAATAT-AAAAAAACTTGAACCTAAAATTAATTA
651 TAGACATTCAATTATTATCTGTTTTAACCAAAAATATAAAAAAAACTTGAACCTAAAATCAATTA
* *
2057 TAAGATTATAAAA-CTATTTATAGCGAGCAATAAAGCTTTTAAAGAAAT-GAAAGACTATAAATG
716 TAAGATTATAAAATC-ATTTAAAGCAAGCAATAAAGCTTTTAAAGAAATAG-AAGACTATAAATG
* * * * * *
2120 GACTTTTCTTGCCCATGAATG-CTTTT-TTCAAGTTTCTCGATGTAGACATTCAAGTATTGTGTA
779 GACTTTTCTTGCCAATAAATGTCTTTTCTTCAA-TTTCTCAAAGTAGACATTCAAGTATAGTCTA
2183 TTTTAACCAAAAATAC
843 TTTTAA-CAAAAATAC
* * **
2199 AAAAAC-ATTTAACTTAAAATCAATTATGAGATTATAAAAAT-ATTTAAAGCGAGCAATATGACT
1 AAAAACAATTGAACTTAAAATCAATTATGAGATTAT-AAAATCATTTAAAGCAAGCAATAAAAC-
* * * *
2262 TTTGAAA-AAATGAGAGACTATAAATAGACTTTTCTTGCCAATGAATGTTTTTTTCTTCAAGTTT
64 TTT-AAAGAAATAAGAGACTATAAATAAACTTTTCTTGACAATGAATGCTTTTTTCTTCAAGTTT
* * * * ******
2326 CTTGATGTAGACATTCAATTATTA-TCTATTTTAACTAAAAATATAAAAAAATTTAA-CNNNNNN
128 CTTAAGGTAGACATTCAATTA-TAGTCTATTTTAACAAAAAATATAAAAAAA-ATAACCTTAAAA
**** * * *
2389 NNNNTTATGAGATTATAAAATCATTTAAAGCGAGCAATAAGGCTTTTG-AAGAAATAGGAGACTA
191 TCAATTATGAGAGTATAAAACCATTTAAAGCAAGCAATAAGGCTTTTGAAAG-AATAGGAGACTA
* * * * *
2453 TAAATGAACTTCTCTTGCCAATGAATG-CTTTTCTCTTCATGTTTCTGGAGGTAGATATTCAATT
255 TAAAAGAACTTCTCTTGCCAATGAATGCCATTT-TCTTCAAGTTTCTGAAGGTAGACATTCAATT
*** * * * *
2517 ATAGTTTGTTCTAATAAAAAATTTAAAAAAAATTGAACTTAAAATTAATTATGAGATTATAAAAC
319 ATAACCTATTCTAACAAAAAATGTAAAAAAAATTGAACTTAAAATCAATTATGAGATTATAAAAC
***********
2582 CATTTAAAGTNNNNNNNNNNGCTTTTGAAGGAATAAGAGACTATAAAT-GAACTTTTCTTGACAA
384 CATTTAAAGCGAGTAATATGGCTTTTGAAGGAATAAGAGACTATAAATAG-ACTTTTCTTGACAA
* * * * *
2646 TGAATGCCTTTTTCTTCACGTTTTTTAAGGTAGACATTCAGTTATAGTCTGTTTTAACTAAAAAT
448 TAAATACCTTTTTCTTCACGTTTCTTAAGGTAGACATTCAATTATAGTCTGTTTTAACGAAAAAT
****************************** * * *
2711 GTAAAAAAAAATTGAANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTTAAAGCGAGTAGTAAGG
513 GTAAAAAAAAATTGAACATAAAATCATTTTTTAGATAATAAAACTATTTAAAGTGGGTAATAAGG
* * ** * ** * * * *
2776 CTT-TTGAAGGAATTGAAGACTATAAATGGACTTTTTTTGCAAAT-GGATGCTTTTTTCATCCA-
578 CTTCTT-AATGAATGGGTGACTATTAATAAACTTTTTTTGC-CATCGAATGCTTTTTTCTTCAAG
* * * * ** * *
2838 TTTCTTAA-AGCAGACAATCAATTA-TAGTCAGTTTTAA-TGAAAATGTAAAAAAAA-TTGAACT
641 TTTCTCAATA-TAGACATTCAATTATTA-TCTGTTTTAACCAAAAATATAAAAAAAACTTGAACC
* * ********** * * *
2899 TGAAATCAATTATGAGNNNNNNNNNNCATTTAAAGCAAGTAATAAGGCTTTTAAAGGAATA-AGA
704 TAAAATCAATTATAAGATTATAAAATCATTTAAAGCAAGCAATAAAGCTTTTAAAGAAATAGA-A
** ** * * * *
2963 GACTATAAATAAACTTTTCTTGATAATGAATGCTTTTTTCTTCACGTTTCT-AATGGTAGACATT
768 GACTATAAATGGACTTTTCTTGCCAATAAATG-TCTTTTCTTCA-ATTTCTCAA-AGTAGACATT
* * * **
3027 -TAGTTTTATTCTATTTTAACTAAAAATGT
830 CAAG-TATAGTCTATTTTAAC-AAAAATAC
* * * * * *******
3056 AAAAAAAATTGAAGTTAAAATTAATTTTGAGAGTATAAAA-CTATTTAAAGCAAGCANNNNNNNN
1 AAAAACAATTGAACTTAAAATCAATTATGAGATTATAAAATC-ATTTAAAGCAAGCA-ATAAAAC
** * * ** * * * * *
3120 NNTGAAGGAATGGGTGACTATAAAAAAATTTTTCTTGTCAATGAATG-TCATTTTCTTCAAGTTT
64 TTTAAAGAAATAAGAGACTATAAATAAACTTTTCTTGACAATGAATGCT-TTTTTCTTCAAGTTT
* * * * * *
3184 CTTGAGGTAGACATTCAATTATA-ACTTGTTTTAACCAAAAATGTAAAAAAACTTGAA-CTTAAA
128 CTTAAGGTAGACATTCAATTATAGTC-TATTTTAACAAAAAATATAAAAAAA-AT-AACCTTAAA
* * * * * **********
3247 ATAAAATT-TGAG-GTTATAAAATCATTTAAAGCGAGTAATAAGGCTTTTGAAGGNNNNNNNNNN
190 AT-CAATTATGAGAG-TATAAAACCATTTAAAGCAAGCAATAAGGCTTTTGAAAGAATAGGAGAC
* * * ** ** * *
3310 TATAAATGGACTTTTCTTATCAATGAATGCTTTTTTCTTTATA-TTT-TTAGAGGTAGACATTCA
253 TATAAAAGAACTTCTCTTGCCAATGAATGCCATTTTCTTCA-AGTTTCTGA-AGGTAGACATTCA
** * * * * * *
3373 ATTATAGTCTGTTTTAAGC-AAAAATGTAAAAAAGAATTGAACATAAAATCATTTTTGAGATAAT
316 ATTATAACCTATTCTAA-CAAAAAATGTAAAAAA-AATTGAACTTAAAATCAATTATGAGATTAT
* * * * ** * * *
3437 AAAACTATTTAAAGTGGGTAATAAGGCTTTTGAAGGAATGTGTGACTATTAATAAACTTTTCTT-
379 AAAACCATTTAAAGCGAGTAATATGGCTTTTGAAGGAATAAGAGACTATAAATAGACTTTTCTTG
* * * * ** ** * * * *
3501 ACCAATGAATGCCTTTTTCTTCAAGATTCTCGACATAAACATTCAATTATAATCTATTTTAACCA
444 A-CAATAAATACCTTTTTCTTCACGTTTCTTAAGGTAGACATTCAATTATAGTCTGTTTTAACGA
* * * * * * * * * * * *
3566 AAAATGT-AAAAAAACTTGAACTTAAAATTAATTATAAGATTATAAAATTATTTATAGCGAGCAA
508 AAAATGTAAAAAAAAATTGAACATAAAATCATTTTTTAGATAATAAAACTATTTAAAGTGGGTAA
* ** * * ** * * *
3630 TAAAGCTT-TTGAA-GAAATGGAAGACTCTAAATGGACTTTTCTAGCCCAT-GAATGC--GTTT-
573 TAAGGCTTCTT-AATG-AATGGGTGACTATTAATAAACTTTTTTTG-CCATCGAATGCTTTTTTC
* ** * * *
3689 TTCAAGTTTTTCAACGTAGACATTCAATTATTGTCTGTTTTAA-CAAAAA-ATGCATAAAAA-TT
635 TTCAAGTTTCTCAATATAGACATTCAATTATTATCTGTTTTAACCAAAAATAT-AAAAAAAACTT
* * ********* * *
3751 TAACTTAAAATCAATTANNNNNNNNNNAAAA-CATTTAAAGCGAGCAATAAAGCTTTTCAAGAAA
699 GAACCTAAAATCAATTA-TAAGATTATAAAATCATTTAAAGCAAGCAATAAAGCTTTTAAAGAAA
* * * * * * ** *
3815 TGGGAGACTATAAATAGACTTTTCTTGCAAATGAATAT-TTTTTTCTTTAAGTTTCTTGATGTAG
763 TAGAAGACTATAAATGGACTTTTCTTGCCAAT-AA-ATGTCTTTTCTTCAA-TTTCTCAAAGTAG
* * * * *
3879 ACATTCAATTATTGTTTGTTTTAATAAAAAATAC
825 ACATTCAAGTATAGTCTATTTTAA-CAAAAATAC
* * * * * **
3913 AAAAA-AATTCAACTTAAAATCAAGTATGAGATTATAAAATGATTTAAAGCGAGCAATTAGGCTT
1 AAAAACAATTGAACTTAAAATCAATTATGAGATTATAAAATCATTTAAAGCAAGCAATAAAAC-T
* * * ** * *
3977 TTGAAGAAATGAGAGACCATAAATGGACTTTTCTTGCCAATGAATGCTTTTCTCTTCATA-TTTC
65 TTAAAGAAATAAGAGACTATAAATAAACTTTTCTTGACAATGAATGCTTTTTTCTTCA-AGTTTC
** * * * * * * * *
4041 TGGAGGTAGACATTCAATTATAATCTATTCTAATAAAAAATTTTAAAAAATTAAACTTAAAATTA
129 TTAAGGTAGACATTCAATTATAGTCTATTTTAACAAAAAATATAAAAAAAATAACCTTAAAATCA
*
4106 ATTATGAGATTATAAAACCATTTA
194 ATTATGAGAGTATAAAACCATTTA
4130 NNNNNNNNNN
Statistics
Matches: 2148, Mismatches: 558, Indels: 163
0.75 0.19 0.06
Matches are distributed among these distances:
853 1 0.00
854 167 0.08
855 332 0.15
856 741 0.34
857 321 0.15
858 259 0.12
859 188 0.09
860 139 0.06
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.35
Consensus pattern (857 bp):
AAAAACAATTGAACTTAAAATCAATTATGAGATTATAAAATCATTTAAAGCAAGCAATAAAACTT
TAAAGAAATAAGAGACTATAAATAAACTTTTCTTGACAATGAATGCTTTTTTCTTCAAGTTTCTT
AAGGTAGACATTCAATTATAGTCTATTTTAACAAAAAATATAAAAAAAATAACCTTAAAATCAAT
TATGAGAGTATAAAACCATTTAAAGCAAGCAATAAGGCTTTTGAAAGAATAGGAGACTATAAAAG
AACTTCTCTTGCCAATGAATGCCATTTTCTTCAAGTTTCTGAAGGTAGACATTCAATTATAACCT
ATTCTAACAAAAAATGTAAAAAAAATTGAACTTAAAATCAATTATGAGATTATAAAACCATTTAA
AGCGAGTAATATGGCTTTTGAAGGAATAAGAGACTATAAATAGACTTTTCTTGACAATAAATACC
TTTTTCTTCACGTTTCTTAAGGTAGACATTCAATTATAGTCTGTTTTAACGAAAAATGTAAAAAA
AAATTGAACATAAAATCATTTTTTAGATAATAAAACTATTTAAAGTGGGTAATAAGGCTTCTTAA
TGAATGGGTGACTATTAATAAACTTTTTTTGCCATCGAATGCTTTTTTCTTCAAGTTTCTCAATA
TAGACATTCAATTATTATCTGTTTTAACCAAAAATATAAAAAAAACTTGAACCTAAAATCAATTA
TAAGATTATAAAATCATTTAAAGCAAGCAATAAAGCTTTTAAAGAAATAGAAGACTATAAATGGA
CTTTTCTTGCCAATAAATGTCTTTTCTTCAATTTCTCAAAGTAGACATTCAAGTATAGTCTATTT
TAACAAAAATAC
Found at i:3804 original size:168 final size:159
Alignment explanation
Indices: 3615--3935 Score: 349
Period size: 168 Copynumber: 1.9 Consensus size: 159
3605 TTATAAAATT
* * * * **
3615 ATTTATAGCGAGCAATAAAGCTTTTGAAGAAATGGAAGACTCTAAATGGACTTTTCTAGCCCATG
1 ATTTAAAGCGAGCAATAAAGCTTTTCAAGAAATGGAAGACTATAAATAGACTTTTCTAGCAAATG
* *
3680 AATGCGTTTTTC-AAGTTT-TTCAACGTAGACATTCAATTATTGTCTGTTTTAACAAAAAATGCA
66 AATACGTTTTTCTAAGTTTCTT-AACGTAGACATTCAATTATTGTCTGTTTTAACAAAAAATACA
* *
3743 TAAAAATTTAACTTAAAATCAATTANNNNNNNNNNAAAAC
130 AAAAAATTCAACTTAAAATCAATTA----------AAAAC
* *
3783 ATTTAAAGCGAGCAATAAAGCTTTTCAAGAAATGGGAGACTATAAATAGACTTTTCTTGCAAATG
1 ATTTAAAGCGAGCAATAAAGCTTTTCAAGAAATGGAAGACTATAAATAGACTTTTCTAGCAAATG
** * * * *
3848 AATATTTTTTTCTTTAAGTTTCTTGATGTAGACATTCAATTATTGTTTGTTTTAATAAAAAATAC
66 AATACGTTTTTC--TAAGTTTCTTAACGTAGACATTCAATTATTGTCTGTTTTAACAAAAAATAC
3913 AAAAAAATTCAACTTAAAATCAA
129 AAAAAAATTCAACTTAAAATCAA
3936 GTATGAGATT
Statistics
Matches: 131, Mismatches: 18, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
168 66 0.50
171 63 0.48
172 2 0.02
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.34
Consensus pattern (159 bp):
ATTTAAAGCGAGCAATAAAGCTTTTCAAGAAATGGAAGACTATAAATAGACTTTTCTAGCAAATG
AATACGTTTTTCTAAGTTTCTTAACGTAGACATTCAATTATTGTCTGTTTTAACAAAAAATACAA
AAAAATTCAACTTAAAATCAATTAAAAAC
Done.