Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399377.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2642.0, 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: 2856
ACGTcount: A:0.28, C:0.10, G:0.10, T:0.27
Warning! 711 characters in sequence are not A, C, G, or T
Found at i:498 original size:170 final size:171
Alignment explanation
Indices: 372--2008 Score: 919
Period size: 171 Copynumber: 9.6 Consensus size: 171
362 NNNNNNNNNN
* * *
372 TAAATATCTTTTTCTTCACA-TTT-CTCAAGGCAAACATTCAATTATTATCTATTCTAAC-CAAA
1 TAAATACCTTTTTCTTCA-AGTTTCCT-AAGCCAAACATTCAATTATTATCTATTCTAACTAAAA
* * *
434 ATGTAAAAATATTCAACCTACAATCAATTATGAGATTATGAAACCATTTAAAG-TGAGTAATAAG
64 ACGTAAAAAAATTCAACCTAAAATCAATTATGAGATTATGAAACCATTTAAAGCT-AGTAATAAG
*
498 GCTTTTAAAAGAATGGGTTACTATAAAAGGACTTTTCTTGTCAA
128 GCTTTTAAAAGAATGGGTGACTATAAAAGGACTTTTCTTGTCAA
*
542 TAAATACCTTTTTCTTCAAGTTTCCTAAGCCAAACATTCAATTATTATCTGTTCTAACTAAAAAC
1 TAAATACCTTTTTCTTCAAGTTTCCTAAGCCAAACATTCAATTATTATCTATTCTAACTAAAAAC
********** * *
607 GTAAAAAAATTCAACCTAAAATCNNNNNNNNNNTTATAAAACCATTGAAAG-TGAGTAATAAGGC
66 GTAAAAAAATTCAACCTAAAATCAATTATGAGATTATGAAACCATTTAAAGCT-AGTAATAAGGC
* * * *
671 TTTTAAAGGAAAGGCTGACTATAAATGGACTTTTCTTGTCAA
130 TTTTAAAAGAATGGGTGACTATAAAAGGACTTTTCTTGTCAA
* * * * *
713 TAAATGCCTTTTTCTTCATA-TTT-CTCAAGCTAGACATTCAATTATAATCTATTTTAA-TAAAA
1 TAAATACCTTTTTCTTCA-AGTTTCCT-AAGCCAAACATTCAATTATTATCTATTCTAACT-AAA
* * * * * * * * **
775 AATGTAAAACAATTTGAACTTAAAATCACTTTTGAAATTATAAAATGATTTAAAG-TGAGTAATA
63 AACGTAAAA-AAATTCAACCTAAAATCAATTATGAGATTATGAAACCATTTAAAGCT-AGTAATA
* * ** *
839 AGGCTTTTAAAGGAATGGGTTACTATAAATTGACTTTTCTTGCCAA
126 AGGCTTTTAAAAGAATGGGTGACTATAAAAGGACTTTTCTTGTCAA
** * ** * * * * * * *
885 TGCATACCTTTTTCTTCATGTTTTCC-AAGGTAGATATTCAATCATAATTTGTTCTAACCAAAAA
1 TAAATACCTTTTTCTTCAAG-TTTCCTAAGCCAAACATTCAATTATTATCTATTCTAACTAAAAA
* * * ** *
949 TGTCAAAAAGTTCAATATAAAATCAATTATGAGATTATAAAACCATTTAAAG-TGAGTAATAAGG
65 CGTAAAAAAATTCAACCTAAAATCAATTATGAGATTATGAAACCATTTAAAGCT-AGTAATAAGG
* ** *
1013 CTTTTAAAGGAATGGGCAACTATAAATA-GACTTTTCTTGCCAA
129 CTTTTAAAAGAATGGGTGACTATAAA-AGGACTTTTCTTGTCAA
* * * * ** * * * * * * *
1056 TGAATGCCTTTTTCTTCACA-TTT-GTCGAGGTAGACATTCAATTATAATATGTTTTAACCAATA
1 TAAATACCTTTTTCTTCA-AGTTTCCT-AAGCCAAACATTCAATTATTATCTATTCTAACTAAAA
* ** * * * * *
1119 ACGTACAAAGAATTCAAATTTAAATCAATTTTGAGATTATAAAACCATTCAAAG-TGAGTAATCA
64 ACGTA-AAAAAATTCAACCTAAAATCAATTATGAGATTATGAAACCATTTAAAGCT-AGTAATAA
* * * * *
1183 GGCTTTTGAAGGAATGGGTGATTATAAATGGACTTTTCTTGCCAA
127 GGCTTTTAAAAGAATGGGTGACTATAAAAGGACTTTTCTTGTCAA
* * * * * * * * ** * * * *
1228 TGAATTCCCTTTTATACATGTTTCTTGAGGTAGACATT-ATATTA-TAGCCTGGTT-TAACCAAA
1 TAAATACCTTTTTCTTCAAGTTTCCTAAGCCAAACATTCA-ATTATTA-TCT-ATTCTAACTAAA
* ** * * *
1290 AACGTACAAAGAATTCAAATTCAAATCAATTTTGAGATTATAAAACCATTTAAAG-TGAGTAATA
63 AACGTA-AAAAAATTCAACCTAAAATCAATTATGAGATTATGAAACCATTTAAAGCT-AGTAATA
* * * * * *
1354 AGGCTTTTAAATGAATGAGTGACCATGCATA-GACTTTTCTTGTCAG
126 AGGCTTTTAAAAGAATGGGTGACTAT-AAAAGGACTTTTCTTGTCAA
* * * * * * * * *
1400 TAAATGCCTTTTTCTTCATGTTTCTCCT--GCTAGACAATCAATTATAATCTGTTTTAATTAAAA
1 TAAATACCTTTTTCTTCAAG-TT-TCCTAAGCCAAACATTCAATTATTATCTATTCTAACTAAAA
* * * * * * * *
1463 ATGTAAAAAAATTTGAACTTAGAATGAATTTTGAGATTATAAAACTATTTAAAG-TGAGT-ATAA
64 ACGTAAAAAAA-TTCAACCTAAAATCAATTATGAGATTATGAAACCATTTAAAGCT-AGTAATAA
* ** * * *
1526 GGGCTTTTAAAGGAATAAGTGACTATAAATGGACTTTTGTTGCCAA
127 -GGCTTTTAAAAGAATGGGTGACTATAAAAGGACTTTTCTTGTCAA
* * * * * ** * * * *
1572 TGAATGCCTTTTTGTTTAGGTTTCAC-AAGGTAGACATTCAATTATAATCTGTTCTAACCAAAAA
1 TAAATACCTTTTTCTTCAAGTTTC-CTAAGCCAAACATTCAATTATTATCTATTCTAACTAAAAA
* * * * *
1636 GGTCAAAAAATTCAACCTAAAATCAATTGTGAGGTTATAAAACCATTTAAAG-TGAGTAATAAGG
65 CGTAAAAAAATTCAACCTAAAATCAATTATGAGATTATGAAACCATTTAAAGCT-AGTAATAAGG
* * * * *
1700 CTTTTGAAAGAATGGTTGACTATAAACGGAGTTTTCTTGCCAA
129 CTTTTAAAAGAATGGGTGACTATAAAAGGACTTTTCTTGTCAA
* * ** * *
1743 TGAATGCCTTTTTCTTCACA-TTT-CTCAAGGTAGACATTCAATTA-TAGTCTATT-TAAGTAAA
1 TAAATACCTTTTTCTTCA-AGTTTCCT-AAGCCAAACATTCAATTATTA-TCTATTCTAACTAAA
* * * ** * * * *
1804 AAAGTGCAAAGAATTCAAATTTAAATCAATTTTGAGATTATAAAACCATTTAAA-TTGAGTAATA
63 AACGT-AAAAAAATTCAACCTAAAATCAATTATGAGATTATGAAACCATTTAAAGCT-AGTAATA
* * * * * * * *
1868 AGGCTCTTAAAGGAGTAGGTAACTATAAATGGGCATTTTC-TGCCAA
126 AGGCTTTTAAAAGAATGGGTGACTATAAAAGGAC-TTTTCTTGTCAA
* * * ** * * * * * *
1914 TAAATGCCTTTTTCTTCACGTTT-CTCGAGGTAGAGATTCAATTATAATCTGTTCTAGCAAAAAA
1 TAAATACCTTTTTCTTCAAGTTTCCT-AAGCCAAACATTCAATTATTATCTATTCTAACTAAAAA
** * *
1978 TATAGAAAAATTCAACCTAAAATGAATTATG
65 CGTAAAAAAATTCAACCTAAAATCAATTATG
2009 GCATTACAAA
Statistics
Matches: 1200, Mismatches: 222, Indels: 89
0.79 0.15 0.06
Matches are distributed among these distances:
169 2 0.00
170 69 0.06
171 569 0.47
172 544 0.45
173 12 0.01
174 4 0.00
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.35
Consensus pattern (171 bp):
TAAATACCTTTTTCTTCAAGTTTCCTAAGCCAAACATTCAATTATTATCTATTCTAACTAAAAAC
GTAAAAAAATTCAACCTAAAATCAATTATGAGATTATGAAACCATTTAAAGCTAGTAATAAGGCT
TTTAAAAGAATGGGTGACTATAAAAGGACTTTTCTTGTCAA
Found at i:674 original size:171 final size:171
Alignment explanation
Indices: 1--2024 Score: 1609
Period size: 172 Copynumber: 11.8 Consensus size: 171
* * * * * * * *
1 TGACTATAAATAGACTTTTCTTACCAATGAATACTTTTTTCTTCATGTTTCTTAAAGTAGAAATT
1 TGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTCAAGTTTCCTAAGGTAGACATT
* *** * * *
66 CAATTCTTGCCTGTTTTAACCAAAAATGTAAAAACAATTAAACTTAAAATCAATTATG-GCATTA
66 CAATTATAATCTGTTCTAACCAAAAATGTAAAAA-AATTCAACTTAAAATCAATTTTGAG-ATTA
* * * *************
130 CAAAATCATTTAAAGCGAGTAATAAGGCTTNNNNNNNNNNNNN
129 TAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAAGGAATGGG
* * * * * *
173 NGACTATAAATAGACTTTTCTTGCCAATGAATG-CTTTTCTCTTCATGTTTCTTAAAGCAGACAT
1 TGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTT-TCTTCAAGTTTCCTAAGGTAGACAT
* * * * ***********
237 TCAATTCT-AGCATGTTTTAATCAAAAATGTAAAAACAATTCAACTTNNNNNNNNNNATG-GCAT
65 TCAATTATAATC-TGTTCTAACCAAAAATGTAAAAA-AATTCAACTTAAAATCAATTTTGAG-AT
* * ** *
300 TACAAAACCATTTAAAGCT-AGTAATAAGGTTTTTGTAGGTATGGG
127 TATAAAACCATTTAAAG-TGAGTAATAAGGCTTTTAAAGGAATGGG
********** * ** * *
345 TGACTATAAATGGACTTNNNNNNNNNNTAAATATCTTTTTCTTCACA-TTT-CTCAAGGCAAACA
1 TGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTCA-AGTTTCCT-AAGGTAGACA
* * * * * *
408 TTCAATTATTATCTATTCTAACC-AAAATGTAAAAATATTCAACCTACAATCAATTATGAGATTA
64 TTCAATTATAATCTGTTCTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTTTGAGATTA
* *
472 TGAAACCATTTAAAGTGAGTAATAAGGCTTTTAAAAGAATGGG
129 TAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAAGGAATGGG
* * * * * ** *
515 TTACTATAAAAGGACTTTTCTTGTCAATAAATACCTTTTTCTTCAAGTTTCCTAAGCCAAACATT
1 TGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTCAAGTTTCCTAAGGTAGACATT
* * * * **********
580 CAATTATTATCTGTTCTAACTAAAAACGTAAAAAAATTCAACCTAAAATCNNNNNNNNNNTTATA
66 CAATTATAATCTGTTCTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTTTGAGATTATA
* * *
645 AAACCATTGAAAGTGAGTAATAAGGCTTTTAAAGGAAAGGC
131 AAACCATTTAAAGTGAGTAATAAGGCTTTTAAAGGAATGGG
* * *
686 TGACTATAAATGGACTTTTCTTGTCAATAAATGCCTTTTTCTTCATA-TTT-CTCAAGCTAGACA
1 TGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTCA-AGTTTCCT-AAGGTAGACA
* * ** * * * *
749 TTCAATTATAATCTATTTTAATAAAAAATGTAAAACAATTTGAACTTAAAATCACTTTTGAAATT
64 TTCAATTATAATCTGTTCTAACCAAAAATGTAAAA-AAATTCAACTTAAAATCAATTTTGAGATT
**
814 ATAAAATGATTTAAAGTGAGTAATAAGGCTTTTAAAGGAATGGG
128 ATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAAGGAATGGG
* * * * * *
858 TTACTATAAATTGACTTTTCTTGCCAATGCATACCTTTTTCTTCATGTTTTCC-AAGGTAGATAT
1 TGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTCAAG-TTTCCTAAGGTAGACAT
* * * * *
922 TCAATCATAATTTGTTCTAACCAAAAATGTCAAAAAGTTCAA-TATAAAATCAATTATGAGATTA
65 TCAATTATAATCTGTTCTAACCAAAAATGTAAAAAAATTCAACT-TAAAATCAATTTTGAGATTA
986 TAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAAGGAATGGG
129 TAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAAGGAATGGG
** * * *
1029 CAACTATAAATAGACTTTTCTTGCCAATGAATGCCTTTTTCTTCACA-TTT-GTCGAGGTAGACA
1 TGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTCA-AGTTTCCT-AAGGTAGACA
* * * * * * *
1092 TTCAATTATAATATGTTTTAACCAATAACGTACAAAGAATTCAAATTTAAATCAATTTTGAGATT
64 TTCAATTATAATCTGTTCTAACCAAAAATGTA-AAAAAATTCAACTTAAAATCAATTTTGAGATT
* * *
1157 ATAAAACCATTCAAAGTGAGTAATCAGGCTTTTGAAGGAATGGG
128 ATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAAGGAATGGG
* * * * * * * *
1201 TGATTATAAATGGACTTTTCTTGCCAATGAATTCCCTTTTATACATGTTTCTTGAGGTAGACATT
1 TGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTCAAGTTTCCTAAGGTAGACATT
** * * * *
1266 -ATATTATAGCCTGGTT-TAACCAAAAACGTACAAAGAATTCAAATTCAAATCAATTTTGAGATT
66 CA-ATTATAATCT-GTTCTAACCAAAAATGTA-AAAAAATTCAACTTAAAATCAATTTTGAGATT
* *
1329 ATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAATGAATGAG
128 ATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAAGGAATGGG
* ** * * * * * *
1373 TGACCATGCATAGACTTTTCTTGTCAGTAAATGCCTTTTTCTTCATGTTTCTCCT--GCTAGACA
1 TGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTCAAG-TT-TCCTAAGGTAGACA
* * ** * * *
1436 ATCAATTATAATCTGTTTTAATTAAAAATGTAAAAAAATTTGAACTTAGAATGAATTTTGAGATT
64 TTCAATTATAATCTGTTCTAACCAAAAATGTAAAAAAA-TTCAACTTAAAATCAATTTTGAGATT
* **
1501 ATAAAACTATTTAAAGTGAGT-ATAAGGGCTTTTAAAGGAATAAG
128 ATAAAACCATTTAAAGTGAGTAATAA-GGCTTTTAAAGGAATGGG
* * * *
1545 TGACTATAAATGGACTTTTGTTGCCAATGAATGCCTTTTTGTTTAGGTTTCAC-AAGGTAGACAT
1 TGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTCAAGTTTC-CTAAGGTAGACAT
* * * * *
1609 TCAATTATAATCTGTTCTAACCAAAAAGGTCAAAAAATTCAACCTAAAATCAATTGTGAGGTTAT
65 TCAATTATAATCTGTTCTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTTTGAGATTAT
*
1674 AAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAA-GAATGGT
130 AAAACCATTTAAAGTGAGTAATAAGGCTTTT-AAAGGAATGGG
* *
1716 TGACTATAAACGGAGTTTTCTTGCCAATGAATGCCTTTTTCTTCACA-TTT-CTCAAGGTAGACA
1 TGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTCA-AGTTTCCT-AAGGTAGACA
* * ** * * * * *
1779 TTCAATTATAGTCTATT-TAAGTAAAAAAGTGCAAAGAATTCAAATTTAAATCAATTTTGAGATT
64 TTCAATTATAATCTGTTCTAACCAAAAATGT-AAAAAAATTCAACTTAAAATCAATTTTGAGATT
* * * *
1843 ATAAAACCATTTAAATTGAGTAATAAGGCTCTTAAAGGAGTAGG
128 ATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAAGGAATGGG
* * * * * *
1887 TAACTATAAATGGGCATTTTC-TGCCAATAAATGCCTTTTTCTTCACGTTT-CTCGAGGTAGAGA
1 TGACTATAAATGGAC-TTTTCTTGCCAATGAATGCCTTTTTCTTCAAGTTTCCT-AAGGTAGACA
* * * * * * *
1950 TTCAATTATAATCTGTTCTAGCAAAAAATATAGAAAAATTCAACCTAAAATGAATTATG-GCATT
64 TTCAATTATAATCTGTTCTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTTTGAG-ATT
*
2014 ACAAAACCATT
128 ATAAAACCATT
2025 NNNNNNNNNN
Statistics
Matches: 1495, Mismatches: 309, Indels: 97
0.79 0.16 0.05
Matches are distributed among these distances:
169 3 0.00
170 136 0.09
171 600 0.40
172 734 0.49
173 18 0.01
174 4 0.00
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.34
Consensus pattern (171 bp):
TGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTCAAGTTTCCTAAGGTAGACATT
CAATTATAATCTGTTCTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTTTGAGATTATA
AAACCATTTAAAGTGAGTAATAAGGCTTTTAAAGGAATGGG
Found at i:940 original size:343 final size:343
Alignment explanation
Indices: 379--2024 Score: 1762
Period size: 343 Copynumber: 4.8 Consensus size: 343
369 NNNTAAATAT
* * * **
379 CTTTTTCTTCACATTTCTCAAGGC-AAACATTCAATTATTATCTATTCTAA-CCAAAATGT-AAA
1 CTTTTTCTTCACATTTCTCAA-GCTAGACATTCAATTATAATCTATTTTAATAAAAAATGTAAAA
* * * *
441 -AATATTCAACCTACAATCAATTATGAGATTATGAAACCATTTAAAGTGAGTAATAAGGCTTTTA
65 GAAT-TTCAACTTAAAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTA
* * * * * *
505 AAAGAATGGGTTACTATAAAAGGACTTTTCTTGTCAATAAATACCTTTTTCTTCAAGTTTC-CTA
129 AAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATACCTTTTTCTTCATGTTTCTC-A
** * * * ****
569 AGCCAAACATTCAATTATTATCTGTTCTAACTAAAAACGTAAAAAAATTCAACCTAAAATCNNNN
193 AGGTAGACATTCAATTATAATCTGTTCTAACCAAAAACGTAAAAAAATTCAACCTAAAATCAATT
****** * * *
634 NNNNNNTTATAAAACCATTGAAAGTGAGTAATAAGGCTTTTAAAGGAAAGGCTGACTATAAATGG
258 ATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAAGGAATGGCTGACTATAAATAG
*
699 ACTTTTCTTGTCAATAAATGC
323 ACTTTTCTTGCCAATAAATGC
* *
720 CTTTTTCTTCATATTTCTCAAGCTAGACATTCAATTATAATCTATTTTAATAAAAAATGTAAAAC
1 CTTTTTCTTCACATTTCTCAAGCTAGACATTCAATTATAATCTATTTTAATAAAAAATGTAAAAG
* * * **
785 AATTTGAACTTAAAATCACTTTTGAAATTATAAAATGATTTAAAGTGAGTAATAAGGCTTTTAAA
66 AATTTCAACTTAAAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAA
* * *
850 GGAATGGGTTACTATAAATTGACTTTTCTTGCCAATGCATACCTTTTTCTTCATGTTT-TCCAAG
131 GGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATACCTTTTTCTTCATGTTTCT-CAAG
* * * * * * **
914 GTAGATATTCAATCATAATTTGTTCTAACCAAAAATGTCAAAAAGTTCAATATAAAATCAATTAT
195 GTAGACATTCAATTATAATCTGTTCTAACCAAAAACGTAAAAAAATTCAACCTAAAATCAATTAT
*
979 GAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAAGGAATGGGC-AACTATAAATAGA
260 GAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAAGGAAT-GGCTGACTATAAATAGA
*
1043 CTTTTCTTGCCAATGAATGC
324 CTTTTCTTGCCAATAAATGC
* * * * * ** * *
1063 CTTTTTCTTCACATTTGTCGAGGTAGACATTCAATTATAATATGTTTTAACCAATAACGTACAAA
1 CTTTTTCTTCACATTTCTCAAGCTAGACATTCAATTATAATCTATTTTAATAAAAAATGTA-AAA
* * * * *
1128 GAA-TTCAAATTTAAATCAATTTTGAGATTATAAAACCATTCAAAGTGAGTAATCAGGCTTTTGA
65 GAATTTCAACTTAAAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAA
* * * * * **
1192 AGGAATGGGTGATTATAAATGGACTTTTCTTGCCAATGAATTCCCTTTTATACATGTTTCTTGAG
130 AGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATACCTTTTTCTTCATGTTTCTCAAG
** * ** *
1257 GTAGACATT-ATATTATAGCCTGGTT-TAACCAAAAACGTACAAAGAATTCAAATTCAAATCAAT
195 GTAGACATTCA-ATTATAATCT-GTTCTAACCAAAAACGTA-AAAAAATTCAACCTAAAATCAAT
* * * **
1320 TTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAATGAATGAG-TGACCATGCAT
257 TATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAAGGAATG-GCTGACTATAAAT
* *
1384 AGACTTTTCTTGTCAGTAAATGC
321 AGACTTTTCTTGCCAATAAATGC
** ** * * * *
1407 CTTTTTCTTCATGTTTCTCCTGCTAGACAATCAATTATAATCTGTTTTAATTAAAAATGTAAAAA
1 CTTTTTCTTCACATTTCTCAAGCTAGACATTCAATTATAATCTATTTTAATAAAAAATGTAAAAG
* * * *
1472 AATTTGAACTTAGAATGAATTTTGAGATTATAAAACTATTTAAAGTGAGT-ATAAGGGCTTTTAA
66 AATTTCAACTTAAAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAA-GGCTTTTAA
** * * * * * *
1536 AGGAATAAGTGACTATAAATGGACTTTTGTTGCCAATGAATGCCTTTTTGTTTAGGTTTCACAAG
130 AGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATACCTTTTTCTTCATGTTTCTCAAG
* * *
1601 GTAGACATTCAATTATAATCTGTTCTAACCAAAAAGGTCAAAAAATTCAACCTAAAATCAATTGT
195 GTAGACATTCAATTATAATCTGTTCTAACCAAAAACGTAAAAAAATTCAACCTAAAATCAATTAT
* * **
1666 GAGGTTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAA-GAATGGTTGACTATAAACGGA
260 GAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTT-AAAGGAATGGCTGACTATAAATAGA
* *
1730 GTTTTCTTGCCAATGAATGC
324 CTTTTCTTGCCAATAAATGC
* * *
1750 CTTTTTCTTCACATTTCTCAAGGTAGACATTCAATTATAGTCTA-TTTAAGTAAAAAA-GTGCAA
1 CTTTTTCTTCACATTTCTCAAGCTAGACATTCAATTATAATCTATTTTAA-TAAAAAATGT-AAA
* * * *
1813 AGAA-TTCAAATTTAAATCAATTTTGAGATTATAAAACCATTTAAATTGAGTAATAAGGCTCTTA
64 AGAATTTCAACTTAAAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTA
* * * * * * * *
1877 AAGGAGTAGGTAACTATAAATGGGCATTTTC-TGCCAATAAATGCCTTTTTCTTCACGTTTCTCG
129 AAGGAATGGGTGACTATAAATGGAC-TTTTCTTGCCAATGAATACCTTTTTCTTCATGTTTCTCA
* * * ** * *
1941 AGGTAGAGATTCAATTATAATCTGTTCTAGCAAAAAATATAGAAAAATTCAACCTAAAATGAATT
193 AGGTAGACATTCAATTATAATCTGTTCTAACCAAAAACGTAAAAAAATTCAACCTAAAATCAATT
*
2006 ATG-GCATTACAAAACCATT
258 ATGAG-ATTATAAAACCATT
2025 NNNNNNNNNN
Statistics
Matches: 1082, Mismatches: 198, Indels: 49
0.81 0.15 0.04
Matches are distributed among these distances:
340 2 0.00
341 44 0.04
342 182 0.17
343 563 0.52
344 290 0.27
345 1 0.00
ACGTcount: A:0.38, C:0.14, G:0.13, T:0.35
Consensus pattern (343 bp):
CTTTTTCTTCACATTTCTCAAGCTAGACATTCAATTATAATCTATTTTAATAAAAAATGTAAAAG
AATTTCAACTTAAAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAA
GGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATACCTTTTTCTTCATGTTTCTCAAGG
TAGACATTCAATTATAATCTGTTCTAACCAAAAACGTAAAAAAATTCAACCTAAAATCAATTATG
AGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAAGGAATGGCTGACTATAAATAGACT
TTTCTTGCCAATAAATGC
Found at i:1457 original size:687 final size:686
Alignment explanation
Indices: 379--1947 Score: 1883
Period size: 687 Copynumber: 2.3 Consensus size: 686
369 NNNTAAATAT
* * * * *
379 CTTTTTCTTCACATTTCTCAAGGCAAACATTCAATTATTATCTATTCTAACC-AAAATGTA-AAA
1 CTTTTTCTTCACATTTCTCAAGGTAGACATTCAATTATAATATATT-TAACCAAAAAAGTACAAA
** * * * *
442 -ATATTC-AACCTACAATCAATTATGAGATTATGAAACCATTTAAAGTGAGTAATAAGGCTTTTA
65 GA-ATTCAAATTTA-AATCAATTTTGAGATTATAAAACCATTCAAAGTGAGTAATAAGGCTCTTA
* * * * * * * * * *
505 AAAGAATGGGTTACTATAAAAGGAC-TTTTCTTGTCAATAAATACCTTTTTCTTCAAGTTTC-CT
128 AAGGAATAGGTAACTATAAATGGACATTTTC-TGCCAATAAATGCCCTTTTATACACGTTTCTC-
* ** * * * * ** *
568 AAGCCAAACATTCA-ATTATTA-TCT-GTTCTAACTAAAAACGTA-AAAAAATTCAACCTAAAAT
191 GAGGTAGACATT-ATATTA-TAGCCTGGTT-TAACCAAAAACGTACAAAGAATTCAAATTCAAAT
********** *
629 CNNNNNNNNNNTTATAAAACCATTGAAAGTGAGTAATAAGGCTTTTAAAGGAAAGGCTGACTATA
253 CAATTTTGAGATTATAAAACCATTGAAAGTGAGTAATAAGGCTTTTAAAGGAAAGGCTGACCATA
* *
694 AATGGACTTTTCTTGTCAATAAATGCCTTTTTCTTCATATTTCTCAAGCTAGACATTCAATTATA
318 AATAGACTTTTCTTGTCAATAAATGCCTTTTTCTTCATATTTCTCAAGCTAGACAATCAATTATA
* *
759 ATCTATTTTAATAAAAAATGTAAAACAATTTGAACTTAAAATCACTTTTGAAATTATAAAA-TGA
383 ATCTATTTTAATAAAAAATGTAAAAAAATTTGAACTTAAAATCAATTTTGAAATTATAAAACT-A
** * *
823 TTTAAAGTGAGTAATAA-GGCTTTTAAAGGAATGGGTTACTATAAATTGACTTTTCTTGCCAATG
447 TTTAAAGTGAGT-ATAAGGGCTTTTAAAGGAATAAGTGACTATAAATGGACTTTTCTTGCCAATG
* * * * *
887 CATACCTTTTTCTTCATGTTTTC-CAAGGTAGATATTCAATCATAATTTGTTCTAACCAAAAATG
511 AATACCTTTTTCTTCA-GGTTTCACAAGGTAGACATTCAATCATAATCTGTTCTAACCAAAAAGG
* *
951 TCAAAAAGTTCAATATAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTT
575 TCAAAAAATTCAACATAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTT
*
1016 TT-AAAGGAATGGGCAACTATAAATAGACTTTTCTTGCCAATGAATGC
640 TTGAAA-GAATGGGCAACTATAAACAGACTTTTCTTGCCAATGAATGC
* * * * *
1063 CTTTTTCTTCACATTTGTCGAGGTAGACATTCAATTATAATATGTTTTAACCAATAACGTACAAA
1 CTTTTTCTTCACATTTCTCAAGGTAGACATTCAATTATAATAT-ATTTAACCAAAAAAGTACAAA
* * *
1128 GAATTCAAATTTAAATCAATTTTGAGATTATAAAACCATTCAAAGTGAGTAATCAGGCTTTTGAA
65 GAATTCAAATTTAAATCAATTTTGAGATTATAAAACCATTCAAAGTGAGTAATAAGGCTCTTAAA
* * * * * * *
1193 GGAATGGGTGATTATAAATGGAC-TTTTCTTGCCAATGAATTCCCTTTTATACATGTTTCTTGAG
130 GGAATAGGTAACTATAAATGGACATTTTC-TGCCAATAAATGCCCTTTTATACACGTTTCTCGAG
1257 GTAGACATTATATTATAGCCTGGTTTAACCAAAAACGTACAAAGAATTCAAATTCAAATCAATTT
194 GTAGACATTATATTATAGCCTGGTTTAACCAAAAACGTACAAAGAATTCAAATTCAAATCAATTT
* * * **
1322 TGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAATGAATGAG-TGACCATGCATAG
259 TGAGATTATAAAACCATTGAAAGTGAGTAATAAGGCTTTTAAAGGAAAG-GCTGACCATAAATAG
* * ** *
1386 ACTTTTCTTGTCAGTAAATGCCTTTTTCTTCATGTTTCTCCTGCTAGACAATCAATTATAATCTG
323 ACTTTTCTTGTCAATAAATGCCTTTTTCTTCATATTTCTCAAGCTAGACAATCAATTATAATCTA
* * * *
1451 TTTTAATTAAAAATGTAAAAAAATTTGAACTTAGAATGAATTTTGAGATTATAAAACTATTTAAA
388 TTTTAATAAAAAATGTAAAAAAATTTGAACTTAAAATCAATTTTGAAATTATAAAACTATTTAAA
* *
1516 GTGAGTATAAGGGCTTTTAAAGGAATAAGTGACTATAAATGGACTTTTGTTGCCAATGAATGCCT
453 GTGAGTATAAGGGCTTTTAAAGGAATAAGTGACTATAAATGGACTTTTCTTGCCAATGAATACCT
* * *
1581 TTTTGTTTAGGTTTCACAAGGTAGACATTCAATTATAATCTGTTCTAACCAAAAAGGTCAAAAAA
518 TTTTCTTCAGGTTTCACAAGGTAGACATTCAATCATAATCTGTTCTAACCAAAAAGGTCAAAAAA
* * *
1646 TTCAACCTAAAATCAATTGTGAGGTTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAAGA
583 TTCAACATAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAAGA
*** * *
1711 ATGGTTGACTATAAACGGAGTTTTCTTGCCAATGAATGC
648 ATGGGCAACTATAAACAGACTTTTCTTGCCAATGAATGC
* * ** *
1750 CTTTTTCTTCACATTTCTCAAGGTAGACATTCAATTATAGTCTATTTAAGTAAAAAAGTGCAAAG
1 CTTTTTCTTCACATTTCTCAAGGTAGACATTCAATTATAATATATTTAACCAAAAAAGTACAAAG
* *
1815 AATTCAAATTTAAATCAATTTTGAGATTATAAAACCATTTAAATTGAGTAATAAGGCTCTTAAAG
66 AATTCAAATTTAAATCAATTTTGAGATTATAAAACCATTCAAAGTGAGTAATAAGGCTCTTAAAG
* * * * *
1880 GAGTAGGTAACTATAAATGGGCATTTTCTGCCAATAAATGCCTTTTTCTTCACGTTTCTCGAGGT
131 GAATAGGTAACTATAAATGGACATTTTCTGCCAATAAATGCCCTTTTATACACGTTTCTCGAGGT
1945 AGA
196 AGA
1948 GATTCAATTA
Statistics
Matches: 750, Mismatches: 119, Indels: 30
0.83 0.13 0.03
Matches are distributed among these distances:
684 42 0.06
685 11 0.01
686 264 0.35
687 428 0.57
688 5 0.01
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Consensus pattern (686 bp):
CTTTTTCTTCACATTTCTCAAGGTAGACATTCAATTATAATATATTTAACCAAAAAAGTACAAAG
AATTCAAATTTAAATCAATTTTGAGATTATAAAACCATTCAAAGTGAGTAATAAGGCTCTTAAAG
GAATAGGTAACTATAAATGGACATTTTCTGCCAATAAATGCCCTTTTATACACGTTTCTCGAGGT
AGACATTATATTATAGCCTGGTTTAACCAAAAACGTACAAAGAATTCAAATTCAAATCAATTTTG
AGATTATAAAACCATTGAAAGTGAGTAATAAGGCTTTTAAAGGAAAGGCTGACCATAAATAGACT
TTTCTTGTCAATAAATGCCTTTTTCTTCATATTTCTCAAGCTAGACAATCAATTATAATCTATTT
TAATAAAAAATGTAAAAAAATTTGAACTTAAAATCAATTTTGAAATTATAAAACTATTTAAAGTG
AGTATAAGGGCTTTTAAAGGAATAAGTGACTATAAATGGACTTTTCTTGCCAATGAATACCTTTT
TCTTCAGGTTTCACAAGGTAGACATTCAATCATAATCTGTTCTAACCAAAAAGGTCAAAAAATTC
AACATAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAAGAATG
GGCAACTATAAACAGACTTTTCTTGCCAATGAATGC
Done.