Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402544.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5617.0, 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: 3788
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Warning! 45 characters in sequence are not A, C, G, or T
Found at i:472 original size:171 final size:169
Alignment explanation
Indices: 1--3036 Score: 2575
Period size: 171 Copynumber: 17.8 Consensus size: 169
* * * *
1 ATGAGATTATAAAATCATTTAAAGCGAGTAAAAAGGCTTTCGAAGGTATAGGTGGCTATAAATGA
1 ATGAGATTATAAAACCATTTAAAG-GAGTAATAAGGCTTTCGAAGGTATAGGTGACTATAAATGG
* * * * * * *
66 ACTTTTCTTGTCAATAAATATA-TTTTTCTCCACGTTGCTTGAGATCGACATTCAATTATAATCT
65 ACTTTTCTTGCCAATGAATA-ACTTTTTCTTCACGTTTCTCGAGGTAGACATTCAATTATAATCT
* * * **
130 ATTTTAATAAAAAATATTAAAAAATTTAACTTTAAAATCAAGA
129 GTTTTAATAAAAAATA-TAAAAAATTCAAC-TTCAAATCAATT
* * * * *
173 ATGAGAATATTAAAA-CATTTAAAGCAGGTAATAAGGCTTTCGAAAGTAT-GAGCGAGTATAAAT
1 ATGAGATTA-TAAAACCATTTAAAGGA-GTAATAAGGCTTTCGAAGGTATAG-GTGACTATAAAT
* ** * * * * *
236 AGACTTGTT-TTGTGAATGAAAAACTTTTTCTTTACATTTCTTGACGTAGACATTCAATTATAAT
63 GGACTT-TTCTTGCCAATGAATAACTTTTTCTTCACGTTTCTCGAGGTAGACATTCAATTATAAT
* ** * * * *
300 CTGCTTTAATAAAAAAGGTGAAAACTCCAACTTCAAATCATTT
127 CTGTTTTAATAAAAAATATAAAAAATTCAACTTCAAATCAATT
* * * *
343 ATGAGATTATAAAACCATTTAAAGTGAATAATAGGGCTTTCGAATGTATATGTGACTATAAATGG
1 ATGAGATTATAAAACCATTTAAAG-GAGTAATAAGGCTTTCGAAGGTATAGGTGACTATAAATGG
* * * * *
408 ACTTTTTTTTGCCAATGAATAACTTTTTCTTTATGTTTCCCGAGGTAGACATTCAATCATAATCT
65 AC-TTTTCTTGCCAATGAATAACTTTTTCTTCACGTTTCTCGAGGTAGACATTCAATTATAATCT
* * * * *
473 GTTTTAACAAAAAATGTAAAAACTTCAATTTTAAATCAATT
129 GTTTTAATAAAAAATATAAAAAATTCAACTTCAAATCAATT
* * * * * **
514 ATGAGATTATAAAACCATTTAAAGCGAGTTATAGGGCTTCCGAATGTATAAGTGACTATAAATTA
1 ATGAGATTATAAAACCATTTAAAG-GAGTAATAAGGCTTTCGAAGGTATAGGTGACTATAAATGG
* * * * * *
579 ACTTTTTGTTGCCAATAAATAACTTTTTCTTTACGTTTC-CTGAGATAGGCATTCAATTATAATT
65 AC-TTTTCTTGCCAATGAATAACTTTTTCTTCACGTTTCTC-GAGGTAGACATTCAATTATAATC
* *
643 TATTTTAATAAAAAA-AGTAAAAACTT-AACTTCAAATCAATT
128 TGTTTTAATAAAAAATA-TAAAAAATTCAACTTCAAATCAATT
* * * * * *
684 ATGAGATTATAAAACCATTTAAAATGAGTAGTAGGGATTACGAATGTATAGGTGACTATAAATGG
1 ATGAGATTATAAAACCATTT-AAAGGAGTAATAAGGCTTTCGAAGGTATAGGTGACTATAAATGG
* * * * *
749 ACTTTTTTTGCCAATGAATAACTTTTTCTTTATGTTTCCCGAGGTAGACATTCAATTATATTCTG
65 ACTTTTCTTGCCAATGAATAACTTTTTCTTCACGTTTCTCGAGGTAGACATTCAATTATAATCTG
* * *
814 TTTTAATAAAAAATATAAAAACTTTAACTTCAAATGAATT
130 TTTTAATAAAAAATATAAAAAATTCAACTTCAAATCAATT
* * * *
854 ATGAGATTATAAAGCCATTTAAAGGGAGTAATAAGGCTTTTGAAGATATAGGTAACTATAAATGG
1 ATGAGATTATAAAACCATTTAAA-GGAGTAATAAGGCTTTCGAAGGTATAGGTGACTATAAATGG
* * * ** * * *
919 ACTTTTTTTGCCAATGAAT-ATTTTTTTTTGCATTTTTCTCAAGGTAAACATTCAGTTATAATCT
65 ACTTTTCTTGCCAATGAATAACTTTTTCTT-CACGTTTCTCGAGGTAGACATTCAATTATAATCT
* *
983 ATTTTAATAAAAAATATAAAAAAAATTCAA-TATAAAATCAAGTT
129 GTTTTAATAAAAAATAT--AAAAAATTCAACT-TCAAATCAA-TT
* * * * * * * * * *
1027 -TGATATTTTAAAAACAATTAAAGCAAGTAATAAGACATTT-GAAGGCATGGGTGAGTATACATG
1 ATGAGATTATAAAACCATTTAAAG-GAGTAATAAGGC-TTTCGAAGGTATAGGTGACTATAAATG
* ** * *** * * *
1090 GA-GTTTCTCACTAATGAATGGTTTTTTCTTCATGTTTCTCGAGGTAGACATTTAATTATAATGT
64 GACTTTTCTTGCCAATGAATAACTTTTTCTTCACGTTTCTCGAGGTAGACATTCAATTATAATCT
* ** *
1154 ATTTTAACCAAAAATGATAAAAAATTCAACTT-AAAGTCAAGT
129 GTTTTAATAAAAAAT-ATAAAAAATTCAACTTCAAA-TCAATT
* * ** * * * *
1196 ATAAGATTATTAGCCCATTTAAAGTGAGTAATAAGGCTTTTGAAAGCATAGGTGACTATATATGG
1 ATGAGATTATAAAACCATTTAAAG-GAGTAATAAGGCTTTCGAAGGTATAGGTGACTATAAATGG
* * *
1261 ACTTTTTGTTGCCAATGAATAACTTTTTCTTTACGTTTC-CTGAGGTAGACATTCGATTATAATC
65 AC-TTTTCTTGCCAATGAATAACTTTTTCTTCACGTTTCTC-GAGGTAGACATTCAATTATAATC
** * *
1325 TGTTTTAATAAAACCTGTAAAAAACATCAACTTCAAATCAATT
128 TGTTTTAATAAAAAATATAAAAAA-TTCAACTTCAAATCAATT
* *
1368 ATGAGATTATAAAACCATTTAAAGCGAGTAATAAGACTTTCGAAGGTATAGGTGATTATAAATGG
1 ATGAGATTATAAAACCATTTAAAG-GAGTAATAAGGCTTTCGAAGGTATAGGTGACTATAAATGG
* * *
1433 ACTTTTCTTACCAATGAATATA-ATTTTCTAT-ACGATTCTCGAGGTAGACATTCAATTATAATC
65 ACTTTTCTTGCCAATGAATA-ACTTTTTCT-TCACGTTTCTCGAGGTAGACATTCAATTATAATC
* * * *
1496 TGTTTTAACAAAAAATGTAAAAAAAAATCAACTCTAAAATCAATT
128 TGTTTTAATAAAAAA--TATAAAAAATTCAACT-TCAAATCAATT
* ** * * * * * * * *
1541 ATGAGAATATAAAAATAATTACAGCAAGTAATAAGGCTTTCGAAGGCAT-GAGCGAGTAGAAATT
1 ATGAGATTATAAAACCATTTAAAG-GAGTAATAAGGCTTTCGAAGGTATAG-GTGACTATAAATG
* * ** * * *
1605 GACTTTTCTCGGCAATGAATGGCTTTTTCTTCACATTTCTCAAGGTAGACATTCAAATATAATCT
64 GACTTTTCTTGCCAATGAATAACTTTTTCTTCACGTTTCTCGAGGTAGACATTCAATTATAATCT
* * *** *
1670 ATTTTGACCGAAAATGA-AAAAAA---AACTT-AAAGTCAGTT
129 GTTTTAATAAAAAAT-ATAAAAAATTCAACTTCAAA-TCAATT
* * * * * *
1708 ATGAGATTATAAAACCATTTAAAGCAAGTAATAAAGCTTTTGAAGATATAGGTAACTATAAATAG
1 ATGAGATTATAAAACCATTTAAAG-GAGTAATAAGGCTTTCGAAGGTATAGGTGACTATAAATGG
* * * ** * * * *
1773 ACTTTTCCTGCCAGTGAATAACTTTTTCTTCACGTTTTTTAAGGTAAATATTTAATTATTATCTG
65 ACTTTTCTTGCCAATGAATAACTTTTTCTTCACGTTTCTCGAGGTAGACATTCAATTATAATCTG
1838 TTTTAATAAAAAATATAAAAAATTCAACTTCAAATCAATT
130 TTTTAATAAAAAATATAAAAAATTCAACTTCAAATCAATT
* * * * * *
1878 ATGAGATTATAAAACCATTTAAAGCAAGTAATAAGGATTTCGAAGGCATACGTGACAATAAATAG
1 ATGAGATTATAAAACCATTTAAAG-GAGTAATAAGGCTTTCGAAGGTATAGGTGACTATAAATGG
* * * ** * * *
1943 AGTTTTCTTGCCAAAGGATATA-TTTTTCCCCACGTTTCTCAAGGTAGACTTTTAATTATAATCT
65 ACTTTTCTTGCCAATGAATA-ACTTTTTCTTCACGTTTCTCGAGGTAGACATTCAATTATAATCT
* * * **
2007 GTTTTAATAAAAAAATATAAACAAATTCAAATTAAAATTAAGA
129 GTTTTAAT-AAAAAATATAAA-AAATTCAACTTCAAATCAATT
* * * * * * * *
2050 ATGAGATTATAAAAACAATTAAAGTAAGTAATATGGCTTTTGAAAGCAT-GAGTGAGTATAAATG
1 ATGAGATTATAAAACCATTTAAAG-GAGTAATAAGGCTTTCGAAGGTATAG-GTGACTATAAATG
** * * *
2114 GACTTTTCTCACCAATGAATGACTTTTTCTTTACGTTTCTC-ATGGTAGATATTCAATTATAATC
64 GACTTTTCTTGCCAATGAATAACTTTTTCTTCACGTTTCTCGA-GGTAGACATTCAATTATAATC
* * ** * * * *
2178 TATTTTGACCAAAAATGAAAAAAAGAAT-AACTTGAAGTCAATT
128 TGTTTTAATAAAAAAT-ATAAAAA-ATTCAACTTCAAATCAATT
* * * * * * *
2221 ATGAGATTATAAAGCCATTT-AAGCGAGTAGTAAGGATTTTGAAGGCATATGTGAATATAAATGG
1 ATGAGATTATAAAACCATTTAAAG-GAGTAATAAGGCTTTCGAAGGTATAGGTGACTATAAATGG
* ** * * **
2285 ACTTTTCCTGTAAATGAATAACTTTTTCTTCACGTTTCTCAAGGTAAACATTCAATTATAATCCA
65 ACTTTTCTTGCCAATGAATAACTTTTTCTTCACGTTTCTCGAGGTAGACATTCAATTATAATCTG
* * *
2350 TTTTGATAGAAAATGTAAAAAAATTCAA-TCTCAAATCAATT
130 TTTTAATAAAAAATAT-AAAAAATTCAACT-TCAAATCAATT
* * * *
2391 ATGAGATTATAAAATCATTTAAAGCGGGTAATAAGGCTTTTGAAGGTATAAGTGACTATAAATGG
1 ATGAGATTATAAAACCATTTAAAG-GAGTAATAAGGCTTTCGAAGGTATAGGTGACTATAAATGG
* * ** * *
2456 ACTTTTCTTACTAATGAATATTTTTTTCTTCACGTTTC-CTGAGGTAGACGTTTAATTATAATCT
65 ACTTTTCTTGCCAATGAATAACTTTTTCTTCACGTTTCTC-GAGGTAGACATTCAATTATAATCT
* * * *
2520 TTTTTAAT-AAAAATATAAAAAATTCAACTTAAAATCGACT
129 GTTTTAATAAAAAATATAAAAAATTCAACTTCAAATCAATT
* * * * * *
2560 ATGAGATTATAAAAACAATTAAAGCAAGTAATAAGGCTTTCAAAGGCAT-GGCTGAGTATAAATG
1 ATGAGATTATAAAACCATTTAAAG-GAGTAATAAGGCTTTCGAAGGTATAGG-TGACTATAAATG
* ** * * **
2624 AACTTTTCTCACCAATGAATAGCTTTTTCTTCATGTTTCTAAAGGTAGACATTCAATTATAATCT
64 GACTTTTCTTGCCAATGAATAACTTTTTCTTCACGTTTCTCGAGGTAGACATTCAATTATAATCT
* * *
2689 GTTTTGACT-AAAAATGAAAAAAAGAAT-AACTT-AAAGTCAATT
129 GTTTT-AATAAAAAAT-ATAAAAA-ATTCAACTTCAAA-TCAATT
* * * * *
2731 ATGAGATTATGAAATCATCTAAAGCGAGTAATAAGGCTTTTGAAGGTATAGGTGACTATAAATAG
1 ATGAGATTATAAAACCATTTAAAG-GAGTAATAAGGCTTTCGAAGGTATAGGTGACTATAAATGG
* * * *
2796 ACTTTT-TTGTTCCAAAGAATATCTTTTTCTTCACGTTT-TCTATGGTAGACATGCAATTATAAT
65 ACTTTTCTTG--CCAATGAATAACTTTTTCTTCACGTTTCTCGA-GGTAGACATTCAATTATAAT
* * * *
2859 ATGTTTTAAT-AAAAGTGTAAAAATATTCAACTGCAAATCAATT
127 CTGTTTTAATAAAAAATATAAAAA-ATTCAACTTCAAATCAATT
* * * * *
2902 ATGAGATTATAAAACCATTTAAAGCTAGTAATAAGGCTTTTGAAGGCATAGGTGAGTATAAGTGG
1 ATGAGATTATAAAACCATTTAAAG-GAGTAATAAGGCTTTCGAAGGTATAGGTGACTATAAATGG
*** ** * * *
2967 ACTTTTCCCACCAATGAATGGCTTTTTCTTCA-GTTTCTTGGGGTAGACATTCAATTATAATATG
65 ACTTTTCTTGCCAATGAATAACTTTTTCTTCACGTTTCTCGAGGTAGACATTCAATTATAATCTG
3031 TTTTAA
130 TTTTAA
3037 CCAAAAATGA
Statistics
Matches: 2331, Mismatches: 451, Indels: 167
0.79 0.15 0.06
Matches are distributed among these distances:
166 4 0.00
167 121 0.05
168 6 0.00
169 263 0.11
170 623 0.27
171 669 0.29
172 501 0.21
173 144 0.06
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (169 bp):
ATGAGATTATAAAACCATTTAAAGGAGTAATAAGGCTTTCGAAGGTATAGGTGACTATAAATGGA
CTTTTCTTGCCAATGAATAACTTTTTCTTCACGTTTCTCGAGGTAGACATTCAATTATAATCTGT
TTTAATAAAAAATATAAAAAATTCAACTTCAAATCAATT
Found at i:1741 original size:682 final size:678
Alignment explanation
Indices: 1--3294 Score: 2782
Period size: 682 Copynumber: 4.9 Consensus size: 678
* * * *
1 ATGAGATTATAAAATCATTTAAAGCGAGTAAAAAGGCTTTCGAAGGTATAGGTGGCTATAAATGA
1 ATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGTATAGGTGACTATAAATGG
** * ** * * * *
66 ACTTTTCTTGTCAATAAATATATTTTTCTCCACGTTGCTTGAGATCGACATTCAATTATAATCTA
66 ACTTTTCTTACCAATGAATATATTTTTCTTTACGTT-CTCGAGGTAGACATTCAATTATAATCTG
* * * * ** *
131 TTTTAATAAAAAATAT-TAAAAAATTTAACTTTAAAATCAAGAATGAGAATATTAAAA-CATTTA
130 TTTTAACAAAAAATGTAAAAAAAATTCAAC-TTAAAATCAATTATGAGATTA-TAAAACCATTTA
* * * * * * ** *
194 AAGCAGGTAATAAGGCTTTCGAAAGTATGAGCGAGTATAAATAGACTTGTT-TTGTGAATGAAAA
193 AAGCAAGTAATAAGGCTTTTGAAGGCAT-AGCGAGTATAAATGGACTT-TTCTCGCCAATGAATA
* ** * **
258 ACTTTTTCTTTACATTTCTTGACGTAGACATTCAATTATAATCTGCTTTAATAAAAAAGGTGAAA
256 ACTTTTTCTTCACATTTCTCAAGGTAGACATTCAATTATAATCTATTTTAATAAAAAA--TGAAA
*** * * * * *
323 ACTCCAA-CTTCAAATCATTTATGAGATTATAAAACCATTTAAAGTGAA-TAATAGGGCTTTCGA
319 A-AAAAATCTT-AAATCAGTTATGAGATTATAAAACCATTTAAAG-CAAGTAATAAGACTTTTGA
* * * ** * * * *
386 ATGTATATGTGACTATAAATGGACTTTTTTTTGCCAATGAATAACTTTTTCTTTATGTTTCCCGA
381 AGGTATAGGTGACTATAAATGGAC-TTTTCTCACTAATGAATAACTTTTTCTTCACGTTTCTCGA
* * * * *
451 GGTAGACATTCAATCATAATCTGTTTTAACAAAAAATGTAAAAACTTCAATTTTAAATCAATTAT
445 GGTAGACATTTAATTATAATCTGTTTTAACAAAAAATATAAAAAATTCAA-CTTAAATCAATTAT
* * * * * * * *
516 GAGATTATAAAACCATTTAAAGCGAGTTATAGGGCTTCCGAATGTATAAGTGACTATAAATTAAC
509 GAGATTATAAAACCATTTAAAGCAAGTAATAAGGCTTTCGAAAGCATAGGTGACTATAAATGAAC
* * * * * * * *
581 TTTTTGTTGCCAATAAATAACTTTTTCTTTACGTTTCCT-GAGATAGGCATTCAATTATAATTTA
574 TTTTTCTTGCCAATGAATAACTTTTTCTTCACGTTT-CTAAAGGTAGACATTCAATTATAATCTG
* *
645 TTTTAATAAAAAAAGT-AAAAAC-TTAACTTCAAATCAATT
638 TTTTAATAAAAAATGTAAAAAACATCAACTTCAAATCAATT
** * * * * *
684 ATGAGATTATAAAACCATTTAAAATGAGTAGTAGGGATTACGAATGTATAGGTGACTATAAATGG
1 ATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGTATAGGTGACTATAAATGG
* * * * *
749 ACTTTTTTTGCCAATGAATA-ACTTTTTCTTTATGTTTCCCGAGGTAGACATTCAATTATATTCT
66 ACTTTTCTTACCAATGAATATA-TTTTTCTTTACG-TTCTCGAGGTAGACATTCAATTATAATCT
* * * * * * *
813 GTTTTAATAAAAAA--TATAAAAACTTTAACTTCAAATGAATTATGAGATTATAAAGCCATTTAA
129 GTTTTAACAAAAAATGTAAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAA
** ** * * *
876 AGGGAGTAATAAGGCTTTTGAAGATATAG-GTAACTATAAATGGACTTTTTTTGCCAATGAAT-A
194 AGCAAGTAATAAGGCTTTTGAAGGCATAGCG--AGTATAAATGGACTTTTCTCGCCAATGAATAA
* * ** * *
939 TTTTTTTTTGCATTTTTCTCAAGGTAAACATTCAGTTATAATCTATTTTAATAAAAAAT-ATAAA
257 CTTTTTCTT-CACATTTCTCAAGGTAGACATTCAATTATAATCTATTTTAATAAAAAATGA-AAA
* * * * *
1003 AAAAATTCAATATAAAATCAAGTT-TGATATTTTAAAAACAATTAAAGCAAGTAATAAGACATTT
320 AAAAA-TC--T-T-AAATC-AGTTATGAGATTATAAAACCATTTAAAGCAAGTAATAAGACTTTT
* * * * * *** *
1067 GAAGGCATGGGTGAGTATACATGGA-GTTTCTCACTAATGAATGGTTTTTTCTTCATGTTTCTCG
379 GAAGGTATAGGTGACTATAAATGGACTTTTCTCACTAATGAATAACTTTTTCTTCACGTTTCTCG
* * * *
1131 AGGTAGACATTTAATTATAATGTATTTTAACCAAAAATGATAAAAAATTCAACTTAAAGTCAAGT
444 AGGTAGACATTTAATTATAATCTGTTTTAACAAAAAAT-ATAAAAAATTCAACTTAAA-TCAATT
* * ** ** * * *
1196 ATAAGATTATTAGCCCATTTAAAGTGAGTAATAAGGCTTTTGAAAGCATAGGTGACTATATATGG
507 ATGAGATTATAAAACCATTTAAAGCAAGTAATAAGGCTTTCGAAAGCATAGGTGACTATAAATGA
* * * *
1261 ACTTTTTGTTGCCAATGAATAACTTTTTCTTTACGTTTCCT-GAGGTAGACATTCGATTATAATC
572 ACTTTTTCTTGCCAATGAATAACTTTTTCTTCACGTTT-CTAAAGGTAGACATTCAATTATAATC
**
1325 TGTTTTAATAAAACCTGTAAAAAACATCAACTTCAAATCAATT
636 TGTTTTAATAAAAAATGTAAAAAACATCAACTTCAAATCAATT
* *
1368 ATGAGATTATAAAACCATTTAAAGCGAGTAATAAGACTTTCGAAGGTATAGGTGATTATAAATGG
1 ATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGTATAGGTGACTATAAATGG
* *
1433 ACTTTTCTTACCAATGAATATAATTTTCTATACGATTCTCGAGGTAGACATTCAATTATAATCTG
66 ACTTTTCTTACCAATGAATATATTTTTCTTTACG-TTCTCGAGGTAGACATTCAATTATAATCTG
* * ** * *
1498 TTTTAACAAAAAATGTAAAAAAAAATCAACTCTAAAATCAATTATGAGAATATAAAAATAATTAC
130 TTTTAACAAAAAATGTAAAAAAAATTCAACT-TAAAATCAATTATGAGATTATAAAACCATTTAA
* * * * **
1563 AGCAAGTAATAAGGCTTTCGAAGGCATGAGCGAGTAGAAATTGACTTTTCTCGGCAATGAATGGC
194 AGCAAGTAATAAGGCTTTTGAAGGCAT-AGCGAGTATAAATGGACTTTTCTCGCCAATGAATAAC
* * ***
1628 TTTTTCTTCACATTTCTCAAGGTAGACATTCAAATATAATCTATTTTGACCGAAAATGAAAAAAA
258 TTTTTCTTCACATTTCTCAAGGTAGACATTCAATTATAATCTATTTTAATAAAAAATGAAAAAAA
*
1693 AA-CTTAAAGTCAGTTATGAGATTATAAAACCATTTAAAGCAAGTAATAA-AGCTTTTGAAGATA
323 AATCTTAAA-TCAGTTATGAGATTATAAAACCATTTAAAGCAAGTAATAAGA-CTTTTGAAGGTA
* * * * **
1756 TAGGTAACTATAAATAGACTTTTCCTGC-C-AGTGAATAACTTTTTCTTCACGTTTTTTAAGGTA
386 TAGGTGACTATAAATGGACTTTT-CT-CACTAATGAATAACTTTTTCTTCACGTTTCTCGAGGTA
* * * *
1819 AATATTTAATTATTATCTGTTTTAATAAAAAATATAAAAAATTCAACTTCAAATCAATTATGAGA
449 GACATTTAATTATAATCTGTTTTAACAAAAAATATAAAAAATTCAACTT-AAATCAATTATGAGA
* * * * *
1884 TTATAAAACCATTTAAAGCAAGTAATAAGGATTTCGAAGGCATACGTGACAATAAAT-AGA-GTT
513 TTATAAAACCATTTAAAGCAAGTAATAAGGCTTTCGAAAGCATAGGTGACTATAAATGA-ACTTT
* * ** * * *
1947 TTCTTGCCAAAGGATATA-TTTTTCCCCACGTTTCTCAAGGTAGACTTTTAATTATAATCTGTTT
577 TTCTTGCCAATGAATA-ACTTTTTCTTCACGTTTCTAAAGGTAGACATTCAATTATAATCTGTTT
* * * * * **
2011 TAATAAAAAAATATAAACAAA-TTCAAATTAAAATTAAGA
641 TAAT-AAAAAATGTAAA-AAACATCAACTTCAAATCAATT
* * ** * * * * *
2050 ATGAGATTATAAAAACAATTAAAGTAAGTAATATGGCTTTTGAAAGCAT-GAGTGAGTATAAATG
1 ATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGTATAG-GTGACTATAAATG
* * *
2114 GACTTTTCTCACCAATGAATGA-CTTTTTCTTTACGTTTCTC-ATGGTAGATATTCAATTATAAT
65 GACTTTTCTTACCAATGAAT-ATATTTTTCTTTACG-TTCTCGA-GGTAGACATTCAATTATAAT
* * * * * * *
2177 CTATTTTGACCAAAAATG-AAAAAAAGAAT-AACTTGAAGTCAATTATGAGATTATAAAGCCATT
127 CTGTTTTAACAAAAAATGTAAAAAAA-ATTCAACTTAAAATCAATTATGAGATTATAAAACCATT
* * * * * **
2240 T-AAGCGAGTAGTAAGGATTTTGAAGGCATATGTGAATATAAATGGACTTTTC-CTGTAAATGAA
191 TAAAGCAAGTAATAAGGCTTTTGAAGGCATA-GCGAGTATAAATGGACTTTTCTC-GCCAATGAA
* * * * *
2303 TAACTTTTTCTTCACGTTTCTCAAGGTAAACATTCAATTATAATCCATTTTGATAGAAAATGTAA
254 TAACTTTTTCTTCACATTTCTCAAGGTAGACATTCAATTATAATCTATTTTAATAAAAAATG-AA
* * * ** *
2368 AAAAATTCAATCTCAAATCAATTATGAGATTATAAAATCATTTAAAGCGGGTAATAAGGCTTTTG
318 AAAAA---AATCTTAAATCAGTTATGAGATTATAAAACCATTTAAAGCAAGTAATAAGACTTTTG
* * **
2433 AAGGTATAAGTGACTATAAATGGACTTTTCTTACTAATGAATATTTTTTTCTTCACGTTTC-CTG
380 AAGGTATAGGTGACTATAAATGGACTTTTCTCACTAATGAATAACTTTTTCTTCACGTTTCTC-G
* * * * *
2497 AGGTAGACGTTTAATTATAATCTTTTTTAA-TAAAAATATAAAAAATTCAACTTAAAATCGACTA
444 AGGTAGACATTTAATTATAATCTGTTTTAACAAAAAATATAAAAAATTCAACTT-AAATCAATTA
* * *
2561 TGAGATTATAAAAACAATTAAAGCAAGTAATAAGGCTTTC-AAAGGCAT-GGCTGAGTATAAATG
508 TGAGATTATAAAACCATTTAAAGCAAGTAATAAGGCTTTCGAAA-GCATAGG-TGACTATAAATG
** * *
2624 AAC-TTTTCTCACCAATGAATAGCTTTTTCTTCATGTTTCTAAAGGTAGACATTCAATTATAATC
571 AACTTTTTCTTGCCAATGAATAACTTTTTCTTCACGTTTCTAAAGGTAGACATTCAATTATAATC
* * *
2688 TGTTTTGACT-AAAAATGAAAAAAAGAAT-AACTT-AAAGTCAATT
636 TGTTTT-AATAAAAAATGTAAAAAA-CATCAACTTCAAA-TCAATT
* * * * *
2731 ATGAGATTATGAAATCATCTAAAGCGAGTAATAAGGCTTTTGAAGGTATAGGTGACTATAAATAG
1 ATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGTATAGGTGACTATAAATGG
* * * * * * * * *
2796 ACTTTTTTGTTCCAAAGAATATCTTTTTCTTCACGTTTTCTATGGTAGACATGCAATTATAATAT
66 ACTTTTCT-TACCAATGAATATATTTTTCTTTACGTTCTCGA-GGTAGACATTCAATTATAATCT
* * * **
2861 GTTTTAA-TAAAAGTGT-AAAAATATTCAACTGCAAATCAATTATGAGATTATAAAACCATTTAA
129 GTTTTAACAAAAAATGTAAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAA
* * * * * **
2924 AGCTAGTAATAAGGCTTTTGAAGGCATAGGTGAGTATAAGTGGACTTTTCCCACCAATGAATGGC
194 AGCAAGTAATAAGGCTTTTGAAGGCATA-GCGAGTATAAATGGACTTTTCTCGCCAATGAATAAC
* *** * * **
2989 TTTTTCTTCA-GTTTCTTGGGGTAGACATTCAATTATAATATGTTTTAACCAAAAATGAAAAAAA
258 TTTTTCTTCACATTTCTCAAGGTAGACATTCAATTATAATCTATTTTAATAAAAAATGAAAAAAA
* * *
3053 AA--TT---TC-------A-A--CTAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGTATA
323 AATCTTAAATCAGTTATGAGATTATAAAACCATTTAAAGCAAGTAATAAGACTTTTGAAGGTATA
** * * * * *
3103 GACGACTATAAATGGACTTTTCTTACCAATGAATATCTTTTTCTTCATGTTTGC-CTAGGTAGAC
388 GGTGACTATAAATGGACTTTTCTCACTAATGAATAACTTTTTCTTCACGTTT-CTCGAGGTAGAC
* * * * ********* * *
3167 ATTCAGTTATAATCTATTTTAATAAAANNNNNNNNNNAATTCAACATAAAATCAAATATGAGATT
452 ATTTAATTATAATCTGTTTTAACAAAA-AATATAAAAAATTCAAC-TTAAATCAATTATGAGATT
** * * * * *
3232 ATAAAAATAATTAAAGCAAGTAATAAAGCTTTCGAAAGGATAGGTGAGTATAAATGGACTTTT
515 ATAAAACCATTTAAAGCAAGTAATAAGGCTTTCGAAAGCATAGGTGACTATAAATGAACTTTT
3295 CTCACTAATG
Statistics
Matches: 2119, Mismatches: 413, Indels: 176
0.78 0.15 0.06
Matches are distributed among these distances:
662 111 0.05
663 5 0.00
664 72 0.03
665 10 0.00
672 2 0.00
675 1 0.00
677 2 0.00
678 5 0.00
679 106 0.05
680 65 0.03
681 409 0.19
682 677 0.32
683 357 0.17
684 152 0.07
685 3 0.00
686 12 0.01
687 119 0.06
688 10 0.00
689 1 0.00
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (678 bp):
ATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGTATAGGTGACTATAAATGG
ACTTTTCTTACCAATGAATATATTTTTCTTTACGTTCTCGAGGTAGACATTCAATTATAATCTGT
TTTAACAAAAAATGTAAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAG
CAAGTAATAAGGCTTTTGAAGGCATAGCGAGTATAAATGGACTTTTCTCGCCAATGAATAACTTT
TTCTTCACATTTCTCAAGGTAGACATTCAATTATAATCTATTTTAATAAAAAATGAAAAAAAAAT
CTTAAATCAGTTATGAGATTATAAAACCATTTAAAGCAAGTAATAAGACTTTTGAAGGTATAGGT
GACTATAAATGGACTTTTCTCACTAATGAATAACTTTTTCTTCACGTTTCTCGAGGTAGACATTT
AATTATAATCTGTTTTAACAAAAAATATAAAAAATTCAACTTAAATCAATTATGAGATTATAAAA
CCATTTAAAGCAAGTAATAAGGCTTTCGAAAGCATAGGTGACTATAAATGAACTTTTTCTTGCCA
ATGAATAACTTTTTCTTCACGTTTCTAAAGGTAGACATTCAATTATAATCTGTTTTAATAAAAAA
TGTAAAAAACATCAACTTCAAATCAATT
Found at i:1839 original size:340 final size:338
Alignment explanation
Indices: 1--3788 Score: 2560
Period size: 342 Copynumber: 11.2 Consensus size: 338
* * * * *
1 ATGAGATTATAAAATCATTTAAAGCGAGTAAAAAGGCTTTCGAAGGTATAGGTGGCTATAAATGA
1 ATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGTATAGGTGACTATAAATGG
** * * * * * *
66 ACTTTTCTTGTCAATAAATATA-TTTTTCTCCACGTTGCTTGAGATCGACATTCAATTATAATCT
66 ACTTTTCTTACCAATGAATA-ACTTTTTCTTCACGTTTCTTAAGGTAGACATTCAATTATAATCT
* * * * ** *
130 ATTTTAATAAAAAATAT-TAAAAAATTTAACTTTAAAATCAAGAATGAGAATATTAAAA-CATTT
130 GTTTTAA-AAAAAATGTAAAAAAAATTCAAC-TTAAAATCAATTATGAGATTA-TAAAACCATTT
* * * * * * **
193 AAAGCAGGTAATAAGGCTTTCGAAAGTATGA-GCGAGTATAAATAGACTTGTT-TTGTGAATGAA
192 AAAGCAAGTAATAAGGCTTTCGAAGGCAT-ACGTGAGTATAAATGGACTT-TTCTCGCCAATGAA
* * * * ** * * * *
256 AAACTTTTTCTTTACATTTCTTGACGTAGACATTCAATTATAATCTGCTTTAATAAAAAAGGTGA
255 TAGCTTTTTCTTCACGTTTCTCAAGGTAGACATTCAATTATAATCTGTTTTGACAAAAAA--TGA
**** *
321 AAACTCCAACTTCAAATCATTT
318 AAAAAATAACTT-AAATCAATT
* * * * * *
343 ATGAGATTATAAAACCATTTAAAGTGAATAATAGGGCTTTCGAATGTATATGTGACTATAAATGG
1 ATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGTATAGGTGACTATAAATGG
* * * * *** *
408 ACTTTTTTTTGCCAATGAATAACTTTTTCTTTATGTTTCCCGAGGTAGACATTCAATCATAATCT
66 AC-TTTTCTTACCAATGAATAACTTTTTCTTCACGTTTCTTAAGGTAGACATTCAATTATAATCT
* * *
473 GTTTTAACAAAAAATGT--AAAAACTTCAATTTTAAATCAATTATGAGATTATAAAACCATTTAA
130 GTTTTAA-AAAAAATGTAAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAA
* * * * * * * * ** * * * *
536 AGCGAGTTATAGGGCTTCCGAATGTATAAGTGACTATAAATTAACTTTTTGTTGCCAATAAATAA
194 AGCAAGTAATAAGGCTTTCGAAGGCATACGTGAGTATAAATGGAC-TTTTCTCGCCAATGAATAG
* * * * * * * * *
601 CTTTTTCTTTACGTTTC-CTGAGATAGGCATTCAATTATAATTTATTTTAATAAAAAAAGTAAAA
258 CTTTTTCTTCACGTTTCTC-AAGGTAGACATTCAATTATAATCTGTTTTGACAAAAAATG-AAAA
**
665 ACTTAACTTCAAATCAATT
321 AAATAACTT-AAATCAATT
** * * * ** *
684 ATGAGATTATAAAACCATTTAAAATGAGTAGTAGGGATTACGAATGTATAGGTGACTATAAATGG
1 ATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGTATAGGTGACTATAAATGG
* * * * *** *
749 ACTTTTTTTGCCAATGAATAACTTTTTCTTTATGTTTCCCGAGGTAGACATTCAATTATATTCTG
66 ACTTTTCTTACCAATGAATAACTTTTTCTTCACGTTTCTTAAGGTAGACATTCAATTATAATCTG
* * * * * *
814 TTTTAATAAAAAA--TATAAAAACTTTAACTTCAAATGAATTATGAGATTATAAAGCCATTTAAA
131 TTTTAA-AAAAAATGTAAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAA
** * ** * * * * * *
877 GGGAGTAATAAGGCTTTTGAAGATATAGGTAACTATAAATGGACTTTTTTTGCCAATGAATA-TT
195 GCAAGTAATAAGGCTTTCGAAGGCATACGTGAGTATAAATGGACTTTTCTCGCCAATGAATAGCT
* ** * * * * * *
941 TTTTTTTGCATTTTTCTCAAGGTAAACATTCAGTTATAATCTATTTTAATAAAAAATATAAAAAA
260 TTTTCTT-CACGTTTCTCAAGGTAGACATTCAATTATAATCTGTTTTGA-CAAAAA-ATGAAAAA
1006 AATTCAA-TATAAAATCAAGTT
322 AA-T-AACT-T-AAATCAA-TT
* * * * * * * * * * *
1027 -TGATATTTTAAAAACAATTAAAGCAAGTAATAAGACATTTGAAGGCATGGGTGAGTATACATGG
1 ATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGTATAGGTGACTATAAATGG
* * * *** * ** * * *
1091 A-GTTTCTCACTAATGAATGGTTTTTTCTTCATGTTTCTCGAGGTAGACATTTAATTATAATGTA
66 ACTTTTCTTACCAATGAATAACTTTTTCTTCACGTTTCTTAAGGTAGACATTCAATTATAATCTG
* * * * * * **
1155 TTTTAACCAAAAATG-ATAAAAAATTCAACTTAAAGTCAAGTATAAGATTATTAGCCCATTTAAA
131 TTTTAA-AAAAAATGTAAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAA
** * * * * * * * *
1219 GTGAGTAATAAGGCTTTTGAAAGCATAGGTGACTATATATGGACTTTTTGTTGCCAATGAATAAC
195 GCAAGTAATAAGGCTTTCGAAGGCATACGTGAGTATAAATGGAC-TTTTCTCGCCAATGAATAGC
* * * * * **
1284 TTTTTCTTTACGTTTC-CTGAGGTAGACATTCGATTATAATCTGTTTTAATAAAACCTGTAAAAA
259 TTTTTCTTCACGTTTCTC-AAGGTAGACATTCAATTATAATCTGTTTTGACAAAAAATG-AAAAA
1348 ACATCAACTTCAAATCAATT
322 A-AT-AACTT-AAATCAATT
* * *
1368 ATGAGATTATAAAACCATTTAAAGCGAGTAATAAGACTTTCGAAGGTATAGGTGATTATAAATGG
1 ATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGTATAGGTGACTATAAATGG
* * **
1433 ACTTTTCTTACCAATGAATATA-ATTTTCTAT-ACGATTCTCGAGGTAGACATTCAATTATAATC
66 ACTTTTCTTACCAATGAATA-ACTTTTTCT-TCACGTTTCTTAAGGTAGACATTCAATTATAATC
* * ** *
1496 TGTTTTAACAAAAAATGTAAAAAAAAATCAACTCTAAAATCAATTATGAGAATATAAAAATAATT
129 TGTTTTAA-AAAAAATGTAAAAAAAATTCAACT-TAAAATCAATTATGAGATTATAAAACCATTT
* * * * *
1561 ACAGCAAGTAATAAGGCTTTCGAAGGCATGA-GCGAGTAGAAATTGACTTTTCTCGGCAATGAAT
192 AAAGCAAGTAATAAGGCTTTCGAAGGCAT-ACGTGAGTATAAATGGACTTTTCTCGCCAATGAAT
* * * * **
1625 GGCTTTTTCTTCACATTTCTCAAGGTAGACATTCAAATATAATCTATTTTGACCGAAAATGAAAA
256 AGCTTTTTCTTCACGTTTCTCAAGGTAGACATTCAATTATAATCTGTTTTGACAAAAAATGAAAA
*
1690 AAA-AACTTAAAGTCAGTT
321 AAATAACTTAAA-TCAATT
* * * * *
1708 ATGAGATTATAAAACCATTTAAAGCAAGTAATAAAGCTTTTGAAGATATAGGTAACTATAAATAG
1 ATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGTATAGGTGACTATAAATGG
* * * * * * * *
1773 ACTTTTCCTGCCAGTGAATAACTTTTTCTTCACGTTTTTTAAGGTAAATATTTAATTATTATCTG
66 ACTTTTCTTACCAATGAATAACTTTTTCTTCACGTTTCTTAAGGTAGACATTCAATTATAATCTG
* *
1838 TTTTAATAAAAAA--TATAAAAAATTCAACTTCAAATCAATTATGAGATTATAAAACCATTTAAA
131 TTTTAA-AAAAAATGTAAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAA
* ** * * * * * **
1901 GCAAGTAATAAGGATTTCGAAGGCATACGTGACAATAAATAGAGTTTTCTTGCCAAAGGATATAT
195 GCAAGTAATAAGGCTTTCGAAGGCATACGTGAGTATAAATGGACTTTTCTCGCCAATGAATAGCT
** * * * *
1966 TTTTCCCCACGTTTCTCAAGGTAGACTTTTAATTATAATCTGTTTTAATAAAAAAAT-ATAAACA
260 TTTTCTTCACGTTTCTCAAGGTAGACATTCAATTATAATCTGTTTTGA-CAAAAAATGA-AAA-A
* * **
2030 AATTCAAATTAAAATTAAGA
322 AA-T-AACTT-AAATCAATT
* * ** * * * *
2050 ATGAGATTATAAAAACAATTAAAGTAAGTAATATGGCTTTTGAAAGCAT-GAGTGAGTATAAATG
1 ATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGTATAG-GTGACTATAAATG
* * * * * *
2114 GACTTTTCTCACCAATGAATGACTTTTTCTTTACGTTTCTCATGGTAGATATTCAATTATAATCT
65 GACTTTTCTTACCAATGAATAACTTTTTCTTCACGTTTCTTAAGGTAGACATTCAATTATAATCT
* ** * * * *
2179 ATTTTGACCAAAAATG-AAAAAAAGAAT-AACTTGAAGTCAATTATGAGATTATAAAGCCATTT-
130 GTTTT-AAAAAAAATGTAAAAAAA-ATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTA
* * * * * * **
2241 AAGCGAGTAGTAAGGATTTTGAAGGCATATGTGAATATAAATGGACTTTTC-CTGTAAATGAATA
193 AAGCAAGTAATAAGGCTTTCGAAGGCATACGTGAGTATAAATGGACTTTTCTC-GCCAATGAATA
* * ** * *
2305 ACTTTTTCTTCACGTTTCTCAAGGTAAACATTCAATTATAATCCATTTTGATAGAAAATGTAAAA
257 GCTTTTTCTTCACGTTTCTCAAGGTAGACATTCAATTATAATCTGTTTTGACAAAAAATG-AAAA
*
2370 AAATTCAATCTCAAATCAATT
321 AAA-T-AA-CTTAAATCAATT
* * *
2391 ATGAGATTATAAAATCATTTAAAGCGGGTAATAAGGCTTTTGAAGGTATAAGTGACTATAAATGG
1 ATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGTATAGGTGACTATAAATGG
* ** * * * * *
2456 ACTTTTCTTACTAATGAATATTTTTTTCTTCACGTTTCCTGAGGTAGACGTTTAATTATAATCTT
66 ACTTTTCTTACCAATGAATAACTTTTTCTTCACGTTTCTTAAGGTAGACATTCAATTATAATCTG
* * * * * *
2521 TTTTAATAAAAA--TATAAAAAATTCAACTTAAAATCGACTATGAGATTATAAAAACAATTAAAG
131 TTTTAAAAAAAATGTAAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAG
* * * *
2584 CAAGTAATAAGGCTTTCAAAGGCAT-GGCTGAGTATAAATGAACTTTTCTCACCAATGAATAGCT
196 CAAGTAATAAGGCTTTCGAAGGCATACG-TGAGTATAAATGGACTTTTCTCGCCAATGAATAGCT
* * *
2648 TTTTCTTCATGTTTCTAAAGGTAGACATTCAATTATAATCTGTTTTGACTAAAAATGAAAAAAAG
260 TTTTCTTCACGTTTCTCAAGGTAGACATTCAATTATAATCTGTTTTGACAAAAAATG--AAAAA-
2713 AATAACTTAAAGTCAATT
322 AATAACTTAAA-TCAATT
* * * *
2731 ATGAGATTATGAAATCATCTAAAGCGAGTAATAAGGCTTTTGAAGGTATAGGTGACTATAAATAG
1 ATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGTATAGGTGACTATAAATGG
* * * * * * *
2796 ACTTTTTTGTTCCAAAGAATATCTTTTTCTTCACGTTT-TCTATGGTAGACATGCAATTATAATA
66 ACTTTTCT-TACCAATGAATAACTTTTTCTTCACGTTTCT-TAAGGTAGACATTCAATTATAATC
* * * **
2860 TGTTTTAATAAAAGTGT-AAAAATATTCAACTGCAAATCAATTATGAGATTATAAAACCATTTAA
129 TGTTTTAAAAAAAATGTAAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAA
* * * * * * *
2924 AGCTAGTAATAAGGCTTTTGAAGGCATAGGTGAGTATAAGTGGACTTTTCCCACCAATGAATGGC
194 AGCAAGTAATAAGGCTTTCGAAGGCATACGTGAGTATAAATGGACTTTTCTCGCCAATGAATAGC
*** * * *
2989 TTTTTCTTCA-GTTTCTTGGGGTAGACATTCAATTATAATATGTTTTAACCAAAAATGAAAAAAA
259 TTTTTCTTCACGTTTCTCAAGGTAGACATTCAATTATAATCTGTTTTGACAAAAAATGAAAAAAA
3053 -AA-TT---TC----
324 TAACTTAAATCAATT
* **
3059 ---A-A--CTAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGTATAGACGACTATAAATGG
1 ATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGTATAGGTGACTATAAATGG
* * * *
3118 ACTTTTCTTACCAATGAATATCTTTTTCTTCATGTTTGCCT-AGGTAGACATTCAGTTATAATCT
66 ACTTTTCTTACCAATGAATAACTTTTTCTTCACGTTT-CTTAAGGTAGACATTCAATTATAATCT
* * ********** * * ** *
3182 ATTTTAATAAAANNNNNNNNNNAATTCAACATAAAATCAAATATGAGATTATAAAAATAATTAAA
130 GTTTTAAAAAAAATGTAAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAA
* * * * ****
3247 GCAAGTAATAAAGCTTTCGAAAGG-ATAGGTGAGTATAAATGGACTTTTCTCACTAATGAANNNN
195 GCAAGTAATAAGGCTTTCG-AAGGCATACGTGAGTATAAATGGACTTTTCTCGCCAATGAATAGC
****** * * * * * **
3311 NNNNNNTAT-ATGTTTCTCGAGGTAGACATTTAATTATAACCTGTTTTAACTGAAAATGAAAAAA
259 TTTTTCT-TCACGTTTCTCAAGGTAGACATTCAATTATAATCTGTTTTGACAAAAAATG-AAAAA
3375 AATTCAACTTAAAGTCAATT
322 AA-T-AACTTAAA-TCAATT
* ************************
3395 ATGAGATTATAAAATCATTTAANNNNNNNNNNNNNNNNNNNNNNNNNTATA----A--AT-AA--
1 ATGAGATTATAAAACCATTTAA-AGCGAGTAATAAGGCTTTTGAAGGTATAGGTGACTATAAATG
* * * * *
3451 -ACTCTT-TTAGCCAATGAATAATTTTTTCTTCACGTCTC-TAGAGGTGGACATTCAATTACAAT
65 GACTTTTCTTA-CCAATGAATAACTTTTTCTTCACGTTTCTTA-AGGTAGACATTCAATTATAAT
* * ** * * * **
3513 CTATTTGAATAAAAAATGT-AAACCAATTCCACTTTAATTCAATTATGAGATTATAAAATTATTT
128 CTGTTTTAA-AAAAAATGTAAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTT
* * * * * ** * * **
3577 TAAGTAAGTAACAAGGCTTTTGAAGGTATGGGTAACTATAAATGGACTTTTCTTACCAATGAAT-
192 AAAGCAAGTAATAAGGCTTTCGAAGGCATACGTGAGTATAAATGGACTTTTCTCGCCAATGAATA
* * * ** **
3641 GACTTTTTCTTCATGTTTCTCGAGGTAGACATTTAATTATGTTCTGTTTCAACAAAAAATGAAAA
257 G-CTTTTTCTTCACGTTTCTCAAGGTAGACATTCAATTATAATCTGTTTTGACAAAAAATG-AAA
*
3706 ACAAATTCAACTTAAAGTGAATT
320 A-AAA-T-AACTTAAA-TCAATT
** * *
3729 ATGAGATTATAAAATTATTTAAAGTGAGTAATAAGGCTTTTGAAGGCATAGGTGACTATA
1 ATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGTATAGGTGACTATA
Statistics
Matches: 2726, Mismatches: 611, Indels: 220
0.77 0.17 0.06
Matches are distributed among these distances:
321 56 0.02
322 144 0.05
323 45 0.02
324 8 0.00
325 1 0.00
327 2 0.00
328 2 0.00
331 1 0.00
332 13 0.00
333 187 0.07
334 45 0.02
336 5 0.00
337 123 0.05
338 34 0.01
339 103 0.04
340 476 0.17
341 437 0.16
342 671 0.25
343 233 0.09
344 82 0.03
345 57 0.02
346 1 0.00
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (338 bp):
ATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGTATAGGTGACTATAAATGG
ACTTTTCTTACCAATGAATAACTTTTTCTTCACGTTTCTTAAGGTAGACATTCAATTATAATCTG
TTTTAAAAAAAATGTAAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAG
CAAGTAATAAGGCTTTCGAAGGCATACGTGAGTATAAATGGACTTTTCTCGCCAATGAATAGCTT
TTTCTTCACGTTTCTCAAGGTAGACATTCAATTATAATCTGTTTTGACAAAAAATGAAAAAAATA
ACTTAAATCAATT
Found at i:3700 original size:171 final size:172
Alignment explanation
Indices: 3461--3788 Score: 424
Period size: 172 Copynumber: 1.9 Consensus size: 172
3451 ACTCTTTTAG
* * * *
3461 CCAATGAATAATTTTTTCTTCACGTCTCTAGAGGTGGACATTCAATTACAATCTATTTGAATAAA
1 CCAATGAATAACTTTTTCTTCACGTCTCTAGAGGTAGACATTCAATTACAATCTATTTCAACAAA
* * * * * *
3526 AAATG-TAAACCAATTCCACTTTAATTCAATTATGAGATTATAAAATTATTTTAAGTAAGTAACA
66 AAATGAAAAACAAATTCAACTTAAAGTCAATTATGAGATTATAAAATTATTTAAAGTAAGTAACA
* *
3590 AGGCTTTTGAAGGTATGGGTAACTATAAATGGACTTTTCTTA
131 AGGCTTTTGAAGGCATAGGTAACTATAAATGGACTTTTCTTA
* * * * * *** *
3632 CCAATGAATGACTTTTTCTTCATGTTTCTCGAGGTAGACATTTAATTATGTTCTGTTTCAACAAA
1 CCAATGAATAACTTTTTCTTCACGTCTCTAGAGGTAGACATTCAATTACAATCTATTTCAACAAA
* * *
3697 AAATGAAAAACAAATTCAACTTAAAGTGAATTATGAGATTATAAAATTATTTAAAGTGAGTAATA
66 AAATGAAAAACAAATTCAACTTAAAGTCAATTATGAGATTATAAAATTATTTAAAGTAAGTAACA
*
3762 AGGCTTTTGAAGGCATAGGTGACTATA
131 AGGCTTTTGAAGGCATAGGTAACTATA
Statistics
Matches: 131, Mismatches: 25, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
171 57 0.44
172 74 0.56
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.36
Consensus pattern (172 bp):
CCAATGAATAACTTTTTCTTCACGTCTCTAGAGGTAGACATTCAATTACAATCTATTTCAACAAA
AAATGAAAAACAAATTCAACTTAAAGTCAATTATGAGATTATAAAATTATTTAAAGTAAGTAACA
AGGCTTTTGAAGGCATAGGTAACTATAAATGGACTTTTCTTA
Done.