Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399761.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3003.0, 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: 7105
ACGTcount: A:0.29, C:0.09, G:0.10, T:0.28
Warning! 1731 characters in sequence are not A, C, G, or T
Found at i:608 original size:172 final size:169
Alignment explanation
Indices: 2--1212 Score: 795
Period size: 171 Copynumber: 7.1 Consensus size: 169
1 C
*
2 TATAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTTATGTTTCCTGAGGTAGACATTCAAT
1 TATAAATGGACTTTTCTTGCCAATGGATATCTTTTT-TTCATGTTTCCTGAGGTAGACATTCAAT
* * * ********
67 AATTATCAGTTTTAATGAAACACATAAAAAAATTTAATTTAAAATCAATTATGAGANNNNNNNNN
65 AATTATCA-TTTTAATGAAACACGTAAAAAAATTAAACTTAAAATCAATTATGAGA-TTATAAAA
***************** * * * *
132 NNNNNNNNNNNNNNNNNAAAG-CTTTTAAAGGCATGAGTGAC
128 ATATTTAAAGCGAGTAAAAAGCCTTTTGAAGGCGTGGGTGAA
* *
173 TATAAATGGACTTTTCTTGCCAATGGAT-T-TTTTTTTCATGTTTCTTGAGGTTGACATTCAATA
1 TATAAATGGACTTTTCTTGCCAATGGATATCTTTTTTTCATGTTTCCTGAGGTAGACATTCAATA
* * * * *
236 ATCATCAATTTTAATGAAACACGTCAAAAAATTTAATTTAAAATTAATTATGAGATTATAAAAAT
66 ATTATC-ATTTTAATGAAACACGTAAAAAAATTAAACTTAAAATCAATTATGAGATTATAAAAAT
* * * * * * *
301 ATTTGAAGTGAGTAATAAGGCTTTTGAAAGCGCGGGTGAT
130 ATTTAAAGCGAGTAAAAAGCCTTTTGAAGGCGTGGGTGAA
* * * * *
341 TATAAATGGACTTTTCTTGTCACTGGATATCTTTTTGTTCGTATTTACC-AAGGTAGACATTCAA
1 TATAAATGGACTTTTCTTGCCAATGGATATCTTTTT-TTCATGTTT-CCTGAGGTAGACATTCAA
* * * * * * * * ******
405 TTATTAATTATTTCAATCAAAAATGTAAAAAAATTAAACTTAAAATCCATTGTGAGATTNNNNNN
64 TAATT-ATCATTTTAATGAAACACGTAAAAAAATTAAACTTAAAATCAATTATGAGATTATAAAA
****
470 NNNNTTAAAGCGAGTAAAAAGCCTTTTTGAAGGCGTGGGTGAA
128 ATATTTAAAGCGAGTAAAAAGCC-TTTTGAAGGCGTGGGTGAA
*
513 TATAAATGGACTTTTCTTGCCAATAGATATCTTTTTCTTCATGTTTCCTGAGGTAGACATTC-AT
1 TATAAATGGACTTTTCTTGCCAATGGATATCTTTTT-TTCATGTTTCCTGAGGTAGACATTCAAT
* * *
577 AAATTATCAGTTTTAATGAAACACAT-AAAAAATTCAA-TTAAAAATTAATTATGAGATTATAAA
65 -AATTATCA-TTTTAATGAAACACGTAAAAAAATTAAACTT-AAAATCAATTATGAGATTATAAA
********** * * * *
640 AATATTTAAAGNNNNNNNNNNGGCTTTTGAAGACATGGGTGAC
127 AATATTTAAAGCGAGTAAAAAGCCTTTTGAAGGCGTGGGTGAA
* * * *
683 TATAAATGGACTTTTCTTGCTACTGGATATCTTTTTCTTCATGTTTCCCGAGGTAGATATTCAAT
1 TATAAATGGACTTTTCTTGCCAATGGATATCTTTTT-TTCATGTTTCCTGAGGTAGACATTCAAT
* * ** * * * ** *
748 TATTATTTATTTTAACAAAAAATGTAAAAACATTCGACTTAAAATCAATTATGAAATTATAAAAA
65 AATTA-TCATTTTAATGAAACACGTAAAAAAATTAAACTTAAAATCAATTATGAGATTATAAAAA
** *
813 TATTTAAAGCGAGTAAAAAGCCTTTTGAAGATGTGGGTGAC
129 TATTTAAAGCGAGTAAAAAGCCTTTTGAAGGCGTGGGTGAA
* * * * * * *
854 TATAAATAGACTTTTCCTACCAATGAATATCTTTTTCTTCCTGTTTCAC-GAGGCAAACATTCAA
1 TATAAATGGACTTTTCTTGCCAATGGATATCTTTTT-TTCATGTTTC-CTGAGGTAGACATTCAA
* ** * * * * * * *
918 TTATTATCTATTTTAACCAAAAATGTAAAGAAATTCAACTTAAAATCTATTATGACATTATAAAT
64 TAATTATC-ATTTTAATGAAACACGTAAAAAAATTAAACTTAAAATCAATTATGAGATTATAAAA
* * * * * * * * * *
983 GTATTTCAAGCTAGTAATAAGGCTTTCGAAGTCATAGGTGAT
128 ATATTTAAAGCGAGTAAAAAGCCTTTTGAAGGCGTGGGTGAA
* * * *
1025 TATAAATGGAC-TTTCTTGCCAATGGATATCTTTTTCTTCATATTTCCCGAGGTTGACATTCCAT
1 TATAAATGGACTTTTCTTGCCAATGGATATCTTTTT-TTCATGTTTCCTGAGGTAGACATTCAAT
* * * * * ** * * * *
1089 TATAATCTGTTTTAATAAAAAATATAAAAAAATTCAACTTTAAGTCAATTATGAGATTATAAAAC
65 AATTATC-ATTTTAATGAAACACGTAAAAAAATTAAACTTAAAATCAATTATGAGATTATAAAAA
* * * * * *
1154 CATTTAAAGCGAGTAATAA-TCTATTTGAAGGCTTAGGTGAC
129 TATTTAAAGCGAGTAAAAAGCCT-TTTGAAGGCGTGGGTGAA
1195 TATAAATGGACTTTTCTT
1 TATAAATGGACTTTTCTT
1213 NNNNNNNNNN
Statistics
Matches: 813, Mismatches: 206, Indels: 42
0.77 0.19 0.04
Matches are distributed among these distances:
167 3 0.00
168 115 0.14
169 10 0.01
170 233 0.29
171 364 0.45
172 88 0.11
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.36
Consensus pattern (169 bp):
TATAAATGGACTTTTCTTGCCAATGGATATCTTTTTTTCATGTTTCCTGAGGTAGACATTCAATA
ATTATCATTTTAATGAAACACGTAAAAAAATTAAACTTAAAATCAATTATGAGATTATAAAAATA
TTTAAAGCGAGTAAAAAGCCTTTTGAAGGCGTGGGTGAA
Found at i:698 original size:342 final size:341
Alignment explanation
Indices: 149--1399 Score: 1052
Period size: 341 Copynumber: 3.7 Consensus size: 341
139 NNNNNNNNNN
* * *
149 AAAG-CTTTTAAAGGCATGAGTGACTATAAATGGACTTTTCTTGCCAATGGAT-T-TTTTT-TTC
1 AAAGCCTTTTGAAGGCGTGGGTGACTATAAATGGACTTTTCTTGCCAAT-GATATCTTTTTCTTC
* * * * *
210 ATGTTTCTTGAGGTTGACATTCAATAATCATCAATTTTAATGAAACACGTCAAAAAATTTAATTT
65 ATGTTTCCTGAGGTAGACATTCAATAATCATCAATTTTAATGAAACACATCAAAAAATTCAATTA
* *
275 AAAATTAATTATGAGATTATAAAAATATTTGAAGTGAGTAATAAGGCTTTTGAAAGCGCGGGTGA
130 AAAATTAATTATGAGATTATAAAAATATTTAAAGTGAGTAATAAGGCTTTTGAAAGCACGGGTGA
* * *
340 TTATAAATGGACTTTTCTTG-TCACTGGATATCTTTTTGTTCGTATTTACCAAGGTAGACATTCA
195 CTATAAATGGACTTTTCTTGCT-ACTGGATATCTTTTTCTTCATATTTACCAAGGTAGACATTCA
* * * ****
404 ATTATTAATTATTTCAATC-AAAAATGTAAAAAAATTAAACTTAAAATCCATTGTGAGATTNNNN
259 ATTATTAATTATTTCAA-CAAAAAATGTAAAAAAATTAAACTTAAAATCAATTATGAAATTATAA
******
468 NNNNNNTTAAAGCGAGTAA
323 AAATATTTAAAGCGAGTAA
*
487 AAAGCCTTTTTGAAGGCGTGGGTGAATATAAATGGACTTTTCTTGCCAATAGATATCTTTTTCTT
1 AAAGCC-TTTTGAAGGCGTGGGTGACTATAAATGGACTTTTCTTGCCAAT-GATATCTTTTTCTT
* *
552 CATGTTTCCTGAGGTAGACATTC-ATAAATTATCAGTTTTAATGAAACACAT-AAAAAATTCAAT
64 CATGTTTCCTGAGGTAGACATTCAAT-AATCATCAATTTTAATGAAACACATCAAAAAATTCAAT
********** *
615 TAAAAATTAATTATGAGATTATAAAAATATTTAAAGNNNNNNNNNNGGCTTTTG-AAGACATGGG
128 TAAAAATTAATTATGAGATTATAAAAATATTTAAAGTGAGTAATAAGGCTTTTGAAAG-CACGGG
* * * *
679 TGACTATAAATGGACTTTTCTTGCTACTGGATATCTTTTTCTTCATGTTTCCCGAGGTAGATATT
192 TGACTATAAATGGACTTTTCTTGCTACTGGATATCTTTTTCTTCATATTTACCAAGGTAGACATT
* * * **
744 CAATTATTATTTATTTTAACAAAAAATGTAAAAACATTCGACTTAAAATCAATTATGAAATTATA
257 CAATTATTAATTATTTCAACAAAAAATGTAAAAAAATTAAACTTAAAATCAATTATGAAATTATA
809 AAAATATTTAAAGCGAGTAA
322 AAAATATTTAAAGCGAGTAA
** * * *
829 AAAGCCTTTTGAAGATGTGGGTGACTATAAATAGACTTTTCCTACCAATGAATATCTTTTTCTTC
1 AAAGCCTTTTGAAGGCGTGGGTGACTATAAATGGACTTTTCTTGCCAATG-ATATCTTTTTCTTC
* * * * * * ** *
894 CTGTTTCAC-GAGGCAAACATTCAATTATTATCTATTTTAACCAAA-A-ATGTAAAGAAATTCAA
65 ATGTTTC-CTGAGGTAGACATTCAATAATCATCAATTTTAATGAAACACAT-CAAA-AAATTCAA
* ** * *
956 CTT-AAAATCT-ATTATGACATTATAAATGTATTTCAAGCT-AGTAATAAGGCTTTCG-AAGTCA
127 -TTAAAAAT-TAATTATGAGATTATAAAAATATTTAAAG-TGAGTAATAAGGCTTTTGAAAG-CA
** * * * * * *
1017 TAGGTGATTATAAATGGAC-TTTCTTGCCAATGGATATCTTTTTCTTCATATTTCCCGAGGTTGA
188 CGGGTGACTATAAATGGACTTTTCTTGCTACTGGATATCTTTTTCTTCATATTTACCAAGGTAGA
* * * * * * * * *
1081 CATTCCATTA-TAATCTGTTTTAATAAAAAATATAAAAAAATTCAACTTTAAGTCAATTATGAGA
253 CATTCAATTATTAAT-TATTTCAACAAAAAATGTAAAAAAATTAAACTTAAAATCAATTATGAAA
**
1145 TTATAAAACCATTTAAAGCGAGTAA
317 TTATAAAAATATTTAAAGCGAGTAA
* * * * *********
1170 TAA-TCTATTTGAAGGCTTAGGTGACTATAAATGGACTTTTCTTNNNNNNNNNNATCTTTTTCTT
1 AAAGCCT-TTTGAAGGCGTGGGTGACTATAAATGGACTTTTCTT-GCCAATGATATCTTTTTCTT
* * * * * * * * *****
1234 CATGTTTCTTGAGATAAACATTCAACT-ATAATCTATTTTAATAAAAAATAT-AAAAAANNNNNN
64 CATGTTTCCTGAGGTAGACATTCAA-TAATCATCAATTTTAATGAAACACATCAAAAAA-TTCAA
**** * * * * *
1297 NNNNAAATAAATTATAAGATTATAAAATTATTTAAA-TCGAGTAATAAGACTTTTGAAAGCATGG
127 TTAAAAATTAATTATGAGATTATAAAAATATTTAAAGT-GAGTAATAAGGCTTTTGAAAGCACGG
*
1361 GTGACTATAAATGGACTTTTCTTGCTAATGGATATCTTT
191 GTGACTATAAATGGACTTTTCTTGCTACTGGATATCTTT
1400 NNNNNNNNNN
Statistics
Matches: 740, Mismatches: 141, Indels: 60
0.79 0.15 0.06
Matches are distributed among these distances:
338 4 0.01
339 4 0.01
340 52 0.07
341 344 0.46
342 285 0.39
343 51 0.07
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.36
Consensus pattern (341 bp):
AAAGCCTTTTGAAGGCGTGGGTGACTATAAATGGACTTTTCTTGCCAATGATATCTTTTTCTTCA
TGTTTCCTGAGGTAGACATTCAATAATCATCAATTTTAATGAAACACATCAAAAAATTCAATTAA
AAATTAATTATGAGATTATAAAAATATTTAAAGTGAGTAATAAGGCTTTTGAAAGCACGGGTGAC
TATAAATGGACTTTTCTTGCTACTGGATATCTTTTTCTTCATATTTACCAAGGTAGACATTCAAT
TATTAATTATTTCAACAAAAAATGTAAAAAAATTAAACTTAAAATCAATTATGAAATTATAAAAA
TATTTAAAGCGAGTAA
Found at i:714 original size:170 final size:161
Alignment explanation
Indices: 494--1162 Score: 415
Period size: 170 Copynumber: 4.0 Consensus size: 161
484 TAAAAAGCCT
* *
494 TTTTGAAGGCGTGGGTGAATATAAATGGACTTTTCTTGCCAATAGATATCTTTTTCTTCATGTTT
1 TTTTGAAGACATGGGTGAATATAAATGGACTTTTCTTGCCAATAGATATCTTTTTCTTCATGTTT
* ** *
559 CCTGAGGTAGACATTC-ATAAATTA-TCAGTTTTAATGAAACACATAAAAA-ATTC-AATTAAAA
66 CCCGAGGTAGACATTCAAT-AATTATTCA-TTTTAACAAAAAACATAAAAACATTCGAATT-AAA
* *
620 ATTAATTATGAGATTATAAAAATATTTAAAGNNNNNNNNNNGGC
128 ATCAATTATGAAATTATAAAAATATTTAAAG----------GGC
* * * *
664 TTTTGAAGACATGGGTGACTATAAATGGACTTTTCTTGCTACTGGATATCTTTTTCTTCATGTTT
1 TTTTGAAGACATGGGTGAATATAAATGGACTTTTCTTGCCAATAGATATCTTTTTCTTCATGTTT
* * * ** *
729 CCCGAGGTAGATATTCAATTATTATTTATTTTAACAAAAAATGTAAAAACATTCGACTTAAAATC
66 CCCGAGGTAGACATTCAATAATTATTCATTTTAACAAAAAACATAAAAACATTCGAATTAAAATC
794 AATTATGAAATTATAAAAATATTTAAAGCGAGTAAAAAGCC
131 AATTATGAAATTATAAAAATATTTAAA--G-G------G-C
** * * * * *
835 TTTTGAAGATGTGGGTGACTATAAATAGACTTTTCCTACCAAT-GAATATCTTTTTCTTCCTGTT
1 TTTTGAAGACATGGGTGAATATAAATGGACTTTTCTTGCCAATAG-ATATCTTTTTCTTCATGTT
* * * * * **
899 TCACGAGGCAAACATTCAATTATTA-TCTATTTTAACCAAAAATGTAAAGAA-ATTC-AACTTAA
65 TCCCGAGGTAGACATTCAATAATTATTC-ATTTTAACAAAAAACATAAA-AACATTCGAA-TTAA
* * **
961 AATCTATTATGACATTATAAATGTATTTCAAGCTAGTAATAAGGC
127 AATCAATTATGAAATTATAAAAATATTT-AA---AG------GGC
* * * * * *
1006 TTTCGAAGTCATAGGTGATTATAAATGGAC-TTTCTTGCCAATGGATATCTTTTTCTTCATATTT
1 TTTTGAAGACATGGGTGAATATAAATGGACTTTTCTTGCCAATAGATATCTTTTTCTTCATGTTT
* * * * * * * * * *
1070 CCCGAGGTTGACATTCCATTA-TAATCTGTTTTAATAAAAAATATAAAAAAATTC-AACTTTAAG
66 CCCGAGGTAGACATTCAATAATTATTC-ATTTTAACAAAAAACATAAAAACATTCGAA-TTAAAA
* **
1133 TCAATTATGAGATTATAAAACCATTTAAAG
129 TCAATTATGAAATTATAAAAATATTTAAAG
1163 CGAGTAATAA
Statistics
Matches: 405, Mismatches: 65, Indels: 62
0.76 0.12 0.12
Matches are distributed among these distances:
164 1 0.00
166 2 0.00
169 6 0.01
170 192 0.47
171 191 0.47
172 8 0.02
173 2 0.00
175 1 0.00
178 2 0.00
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.37
Consensus pattern (161 bp):
TTTTGAAGACATGGGTGAATATAAATGGACTTTTCTTGCCAATAGATATCTTTTTCTTCATGTTT
CCCGAGGTAGACATTCAATAATTATTCATTTTAACAAAAAACATAAAAACATTCGAATTAAAATC
AATTATGAAATTATAAAAATATTTAAAGGGC
Found at i:1171 original size:170 final size:171
Alignment explanation
Indices: 152--1399 Score: 1040
Period size: 171 Copynumber: 7.3 Consensus size: 171
142 NNNNNNNAAA
* * *
152 GCTTTTAAAGGCATGAGTGACTATAAATGGACTTTTCTTGCCAATGGAT-T-TTTTT-TTCATGT
1 GCTTTTGAAGGCGTGGGTGACTATAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCATGT
** * * * * * * * * * *
214 TTCTTGAGGTTGACATTCAATAATCATCAATTTTAATGAAACACGTCAAAAAATTTAATTTAAAA
66 TTCCCGAGGTAGACATTCAATTATTATCTATTTTAATAAAAAATGTAAAAAAATTCAACTTAAAA
* * *
279 TTAATTATGAGATTATAAAAATATTTGAAGTGAGTAATAAG
131 TCAATTATGAGATTATAAAAATATTTAAAGCGAGTAATAAG
* * * * * * * *
320 GCTTTTGAAAGCGCGGGTGATTATAAATGGACTTTTCTTGTCACTGGATATCTTTTTGTTCGTAT
1 GCTTTTGAAGGCGTGGGTGACTATAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCATGT
* * * * *
385 TTACCAAGGTAGACATTCAATTATTAAT-TATTTCAATCAAAAATGTAAAAAAATTAAACTTAAA
66 TTCCCGAGGTAGACATTCAATTATT-ATCTATTTTAATAAAAAATGTAAAAAAATTCAACTTAAA
* * ********** *
449 ATCCATTGTGAGATTNNNNNNNNNNTTAAAGCGAGTAAAAAG
130 ATCAATTATGAGATTATAAAAATATTTAAAGCGAGTAATAAG
* * *
491 CCTTTTTGAAGGCGTGGGTGAATATAAATGGACTTTTCTTGCCAATAGATATCTTTTTCTTCATG
1 GC-TTTTGAAGGCGTGGGTGACTATAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCATG
* * * * **
556 TTTCCTGAGGTAGACATTC-ATAAATTATC-AGTTTTAATGAAACACAT-AAAAAATTCAA-TTA
65 TTTCCCGAGGTAGACATTCAAT-TATTATCTA-TTTTAATAAAAAATGTAAAAAAATTCAACTT-
* **********
617 AAAATTAATTATGAGATTATAAAAATATTTAAAGNNNNNNNNNNG
127 AAAATCAATTATGAGATTATAAAAATATTTAAAGCGAGTAATAAG
* * * *
662 GCTTTTGAAGACATGGGTGACTATAAATGGACTTTTCTTGCTACTGGATATCTTTTTCTTCATGT
1 GCTTTTGAAGGCGTGGGTGACTATAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCATGT
* * * * *
727 TTCCCGAGGTAGATATTCAATTATTATTTATTTTAACAAAAAATGTAAAAACATTCGACTTAAAA
66 TTCCCGAGGTAGACATTCAATTATTATCTATTTTAATAAAAAATGTAAAAAAATTCAACTTAAAA
* *
792 TCAATTATGAAATTATAAAAATATTTAAAGCGAGTAAAAAG
131 TCAATTATGAGATTATAAAAATATTTAAAGCGAGTAATAAG
* ** * * * * *
833 CCTTTTGAAGATGTGGGTGACTATAAATAGACTTTTCCTACCAATGAATATCTTTTTCTTCCTGT
1 GCTTTTGAAGGCGTGGGTGACTATAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCATGT
* * * ** *
898 TTCACGAGGCAAACATTCAATTATTATCTATTTTAACCAAAAATGTAAAGAAATTCAACTTAAAA
66 TTCCCGAGGTAGACATTCAATTATTATCTATTTTAATAAAAAATGTAAAAAAATTCAACTTAAAA
* * ** * *
963 TCTATTATGACATTATAAATGTATTTCAAGCTAGTAATAAG
131 TCAATTATGAGATTATAAAAATATTTAAAGCGAGTAATAAG
* * * * * *
1004 GCTTTCGAAGTCATAGGTGATTATAAATGGAC-TTTCTTGCCAATGGATATCTTTTTCTTCATAT
1 GCTTTTGAAGGCGTGGGTGACTATAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCATGT
* * * * * * *
1068 TTCCCGAGGTTGACATTCCATTATAATCTGTTTTAATAAAAAATATAAAAAAATTCAACTTTAAG
66 TTCCCGAGGTAGACATTCAATTATTATCTATTTTAATAAAAAATGTAAAAAAATTCAACTTAAAA
**
1133 TCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAA-
131 TCAATTATGAGATTATAAAAATATTTAAAGCGAGTAATAAG
* * * **********
1173 TCTATTTGAAGGCTTAGGTGACTATAAATGGACTTTTCTTNNNNNNNNNNATCTTTTTCTTCATG
1 GCT-TTTGAAGGCGTGGGTGACTATAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCATG
** * * * * * **********
1238 TTTCTTGAGATAAACATTCAACTATAATCTATTTTAATAAAAAATATAAAAAANNNNNNNNNNAA
65 TTTCCCGAGGTAGACATTCAATTATTATCTATTTTAATAAAAAATGTAAAAAAATTCAACTTAAA
* * * *
1303 ATAAATTATAAGATTATAAAATTATTTAAATCGAGTAATAAG
130 ATCAATTATGAGATTATAAAAATATTTAAAGCGAGTAATAAG
* * * *
1345 ACTTTTGAAAGCATGGGTGACTATAAATGGACTTTTCTTGCTAATGGATATCTTT
1 GCTTTTGAAGGCGTGGGTGACTATAAATGGACTTTTCTTGCCAATGGATATCTTT
1400 NNNNNNNNNN
Statistics
Matches: 837, Mismatches: 227, Indels: 29
0.77 0.21 0.03
Matches are distributed among these distances:
168 41 0.05
169 3 0.00
170 233 0.28
171 471 0.56
172 89 0.11
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.36
Consensus pattern (171 bp):
GCTTTTGAAGGCGTGGGTGACTATAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCATGT
TTCCCGAGGTAGACATTCAATTATTATCTATTTTAATAAAAAATGTAAAAAAATTCAACTTAAAA
TCAATTATGAGATTATAAAAATATTTAAAGCGAGTAATAAG
Found at i:2416 original size:171 final size:171
Alignment explanation
Indices: 2061--4082 Score: 1123
Period size: 171 Copynumber: 11.8 Consensus size: 171
2051 NNNNNNNNNN
* * * * * *
2061 AAATGGACTTTTCTTGTCAATGGATATCTTTTTCTTCATG-TTTCTCGAGGTAGATATTCAATAA
1 AAATAGACTTTTCTTGCCAATGAATATCTTTTTCTTCATGTTTTC-CAAGGTAGACATTCAATTA
* * * ** * * * ********** *
2125 TAATGTGTTTTAATAAAAAAATATAGAACAATTCAACTTAAAATCAATTANNNNNNNNNNAAAAT
65 TTATCTATTTTAA-ACGAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAAAC
* * * *
2190 ATTTAATGCGAGTAATAAGACTTTCGAAGGCATGGGTGATTAT
129 ATTTAAAGCGAGTAATAAGGCTTTCGAAGGTATGGGTGACTAT
* * * * *
2233 AAATACACTTTTCTTGTCAATGGATGTCTTTTTCTTCATGTTTTCCAAGTTAGACATTCAATTAT
1 AAATAGACTTTTCTTGCCAATGAATATCTTTTTCTTCATGTTTTCCAAGGTAGACATTCAATTAT
*
2298 TATTTATTTTAAACGAAAATGTAAAAAAATTCAAC-TACAAATCAATTATGAGATTATAAAAACA
66 TATCTATTTTAAACGAAAATGTAAAAAAATTCAACTTA-AAATCAATTATGAGATTATAAAAACA
** * *
2362 TTTACAA-TTAGTAATAAGGCTTTCGAAGGTAAGGGTGAGTAT
130 TTTA-AAGCGAGTAATAAGGCTTTCGAAGGTATGGGTGACTAT
* * * * *
2404 AGATAGACTTTTCCTACCAATGAATATCTTTTTCTTTCCAT-TTCT-CGAGGTAGACATTCAATT
1 AAATAGACTTTTCTTGCCAATGAATATCTTTTTC-TT-CATGTTTTCCAAGGTAGACATTCAATT
* ********** * * * *
2467 ATAATCTANNNNNNNNNNAAATATAAAAATATTTAACTTAAAATCAATTAT-AAATTATAAAAAC
64 ATTATCTATTTTAAACGAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAAAC
* * *
2531 ATTTAAAGCGAGTAATAAGACTTTTGAAGGCATGGGTGACTAT
129 ATTTAAAGCGAGTAATAAGGCTTTCGAAGGTATGGGTGACTAT
* ********************* * * * *
2574 AAATGGACTTNNNNNNNNNNNNNNNNNNNNNTTCTTCAT-ATTTCCTGAGGCAGACATTCAATAA
1 AAATAGACTTTTCTTGCCAATGAATATCTTTTTCTTCATGTTTTCC-AAGGTAGACATTCAATTA
* * * * * * *
2638 TTATTTGTTTT-AATGAAACACGTAAAAAAATTCAA-TTCAAAATGAATTATGAGATTATTAATA
65 TTATCTATTTTAAACGAAA-ATGTAAAAAAATTCAACTT-AAAATCAATTATGAGATTATAAAAA
* * *
2701 CATTTAAAGGGAGTAATAAGGCTTTTGAAGGCATGGGTGACTAT
128 CATTTAAAGCGAGTAATAAGGCTTTCGAAGGTATGGGTGACTAT
* * ** * *
2745 AAATAGACTTTACTTGCCACT-AGATATCTTTTTCTTCCCG-TTTCTCGATGTAGACATTCAATT
1 AAATAGACTTTTCTTGCCAATGA-ATATCTTTTTCTTCATGTTTTC-CAAGGTAGACATTCAATT
* * * * ** * *
2808 ATTGTTTATTTTAACCAAAAATGT-AAAAAATTTGACTTAAAATCAATTATTAGATTATAAAAAT
64 ATTATCTATTTTAAACGAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAAAC
* * * * * *
2872 ATTTAAAGCAAGTAAAAAGCCTTTTGAAGGCATGGATGACTAT
129 ATTTAAAGCGAGTAATAAGGCTTTCGAAGGTATGGGTGACTAT
* * * * *
2915 GAATATACTTTTCTTGCCAATCAATATCTTTTTCTTCCTGTTTTCCTAGGTAGACATTCAATTAT
1 AAATAGACTTTTCTTGCCAATGAATATCTTTTTCTTCATGTTTTCCAAGGTAGACATTCAATTAT
* * ********** * *
2980 TATCTATTTTAACCAAAAATGTANNNNNNNNNNACTTAAAATCCATTATGAGATTATAAAAATAT
66 TATCTATTTTAAACGAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAAACAT
* * * * * *
3045 TTAAAGCTAATAAAAAGGCTTTTGAAGGTGTGGGCGACTAT
131 TTAAAGCGAGTAATAAGGCTTTCGAAGGTATGGGTGACTAT
* * *
3086 AAATAGACTTTTGTTGCCGATGAATATCTTTTTCTTCAT-ATTTCCAAAGGTAGACATTCAATTA
1 AAATAGACTTTTCTTGCCAATGAATATCTTTTTCTTCATGTTTTCC-AAGGTAGACATTCAATTA
* * * * *
3150 TAATCTATTTTAGTAA--AAAATATAAAAAAATTCAACTTAAAAT-AGAATATCAGATTATAAAG
65 TTATCTATTTTA--AACGAAAATGTAAAAAAATTCAACTTAAAATCA-ATTATGAGATTATAAAA
* * **
3212 CCATTTAAAGTGAGTAATAAGGCTTTCGAA-GTCATGGGTGACTNN
127 ACATTTAAAGCGAGTAATAAGGCTTTCGAAGGT-ATGGGTGACTAT
******** * * * * * *
3257 NNNNNNNNTTTTCTTGCCAATGGATATCTTTTTCTTCACGTTTCCCGAGTTAGATATTCAATTAT
1 AAATAGACTTTTCTTGCCAATGAATATCTTTTTCTTCATGTTTTCCAAGGTAGACATTCAATTAT
* * * ***
3322 TATTTATTTT-AACCAAAATGTAAAAAAATTCAACTTAAAATCAATTATAAGATTATAAAAATNN
66 TATCTATTTTAAACGAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAAACAT
******** *
3386 NNNNNNNNAGTAATAAGGCTTTCGAAGGTATGAGTGACTAT
131 TTAAAGCGAGTAATAAGGCTTTCGAAGGTATGGGTGACTAT
* * * ** * *
3427 AGATAGACTTTTCTTGTCAATAAATATCTTTTTCTTCCCG-TTTCTCAAGGTAAACAATCAATTA
1 AAATAGACTTTTCTTGCCAATGAATATCTTTTTCTTCATGTTTTC-CAAGGTAGACATTCAATTA
* * * * * *
3491 TAATCTGTTTTAATA--AAAGATATAAAAAAATTCAACTTGAAATCAAGTATAAGATTATAAAAA
65 TTATCTATTTTAA-ACGAAA-ATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAAA
* * * * *
3554 TATTTAAAGCGAGTAATAAGGC-TACTAAAGTCATGGGTAACTAT
128 CATTTAAAGCGAGTAATAAGGCTTTCGAAGGT-ATGGGTGACTAT
* * * * * * *
3598 AAATGGACTTTTCTTGGCAATCAATATCCTTTTCTTCATG-TTTCCTGAGGCA-AGCATTCAATA
1 AAATAGACTTTTCTTGCCAATGAATATCTTTTTCTTCATGTTTTCC-AAGGTAGA-CATTCAATT
* ** * * * *
3661 ATTATCTATTTT-AATGAAACACATAAAAAATTTTAATTTAAAATCAATTATGAGATTGTAAAAA
64 ATTATCTATTTTAAACGAAA-ATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAAA
* * **********
3725 CATTTAAGGCGAGTAATAAGGCTTTTGAAGNNNNNNNNNNCTAT
128 CATTTAAAGCGAGTAATAAGGCTTTCGAAGGTATGGGTGACTAT
* * * ** ** *
3769 AAATAGACTTTTCTTACCACT-AGATATCTTTTTATTCA-CATTTCTTGAGGCAGACATTCAATT
1 AAATAGACTTTTCTTGCCAATGA-ATATCTTTTTCTTCATGTTTTC-CAAGGTAGACATTCAATT
* * ** * *
3832 ATTATTTATTTT-AACCAAAAGTGTAAAAAAATTTGACTTTAAATAAATTATGAGATTATAAAAA
64 ATTATCTATTTTAAACGAAAA-TGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAAA
* * * * * **********
3896 TATTTAAAGCAAGTAAAAAGTCTTTTGAAGGNNNNNNNNNNTAT
128 CATTTAAAGCGAGTAATAAGGCTTTCGAAGGTATGGGTGACTAT
** * * *** * * *
3940 AAATAGACTTTTCTTATCAATGAATATATTTTTCTTCCTGTTTTTTGATGTAAATATTCAATTAT
1 AAATAGACTTTTCTTGCCAATGAATATCTTTTTCTTCATGTTTTCCAAGGTAGACATTCAATTAT
* * * * * * *
4005 TATCTGTTTT-AACTAAAAATATAAAATAATTGAACTTAAAATCCATTATGAGATTATAAAAATA
66 TATCTATTTTAAAC-GAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAAACA
*
4069 TTTAAAGCTAGTAA
130 TTTAAAGCGAGTAA
4083 AAANNNNNNN
Statistics
Matches: 1414, Mismatches: 388, Indels: 97
0.74 0.20 0.05
Matches are distributed among these distances:
168 7 0.00
169 13 0.01
170 378 0.27
171 916 0.65
172 92 0.07
173 8 0.01
ACGTcount: A:0.37, C:0.11, G:0.12, T:0.35
Consensus pattern (171 bp):
AAATAGACTTTTCTTGCCAATGAATATCTTTTTCTTCATGTTTTCCAAGGTAGACATTCAATTAT
TATCTATTTTAAACGAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAAACAT
TTAAAGCGAGTAATAAGGCTTTCGAAGGTATGGGTGACTAT
Found at i:2972 original size:341 final size:340
Alignment explanation
Indices: 2061--4075 Score: 1383
Period size: 341 Copynumber: 5.9 Consensus size: 340
2051 NNNNNNNNNN
* * * *** * *
2061 AAATGGACTTTTCTTGTCAATGGATATCTTTTTCTTCATGTTTCTCGAGGTAGATATTCAATAAT
1 AAATAGACTTTTCTTGCCAATAGATATCTTTTTCTTCCCATTTCTCGAGGTAGACATTCAATTAT
* * ** * * * **********
2126 AATGTGTTTTAATAAAAAAATATAGAACAATTCAACTTAAAATCAATTANNNNNNNNNNAAAATA
66 AATCTATTTTAA-CCAAAAATATAAAAAAATTTAACTTAAAATCAATTATTAGATTATAAAAATA
* * * * * **
2191 TTTAATGCGAGTAATAAGACTTTCGAAGGCATGGGTGATTATAAATACACTTTTCTTGTCAATGG
130 TTTAAAGCGAGTAATAAGACTTTTGAAGGCATGGGTGACTATAAATAGACTTTTCTTGCCAATCA
* * *
2256 ATGTCTTTTTCTTCATGTTTTCCAAGTTAGACATTCAATTATTATTTATTTTAAACGAAAATGTA
195 ATATCTTTTTCTTCATGTTTTCCTAGGTAGACATTCAATTATTATTTATTTT-AACGAAAATGTA
* **
2321 AAAAAATTCAACTACAAATCAATTATGAGATTATAAAAACATTTACAA-TTAGTAATAAGGCTTT
259 AAAAAATTCAATTA-AAATCAATTATGAGATTATAAAAACATTTA-AAGGGAGTAATAAGGCTTT
* * *
2385 CGAAGGTAAGGGTGAGTAT
322 TGAAGGTATGGGTGACTAT
* * * *
2404 AGATAGACTTTTCCTACCAAT-GAATATCTTTTTCTTTCCATTTCTCGAGGTAGACATTCAATTA
1 AAATAGACTTTTCTTGCCAATAG-ATATCTTTTTCTTCCCATTTCTCGAGGTAGACATTCAATTA
********** * * *
2468 TAATCTANNNNNNNNNNAAATATAAAAATATTTAACTTAAAATCAATTA-TAAATTATAAAAACA
65 TAATCTATTTTAACCAAAAATATAAAAAAATTTAACTTAAAATCAATTATTAGATTATAAAAATA
* *************
2532 TTTAAAGCGAGTAATAAGACTTTTGAAGGCATGGGTGACTATAAATGGACTTNNNNNNNNNNNNN
130 TTTAAAGCGAGTAATAAGACTTTTGAAGGCATGGGTGACTATAAATAGACTTTTCTTGCCAATCA
******** * * * * * *
2597 NNNNNNNNTTCTTCAT-ATTTCCTGAGGCAGACATTCAATAATTATTTGTTTTAATGAAACACGT
195 ATATCTTTTTCTTCATGTTTTCCT-AGGTAGACATTCAATTATTATTTATTTTAACGAAA-ATGT
* * *
2661 AAAAAAATTCAATTCAAAATGAATTATGAGATTATTAATACATTTAAAGGGAGTAATAAGGCTTT
258 AAAAAAATTCAATT-AAAATCAATTATGAGATTATAAAAACATTTAAAGGGAGTAATAAGGCTTT
*
2726 TGAAGGCATGGGTGACTAT
322 TGAAGGTATGGGTGACTAT
* * * *
2745 AAATAGACTTTACTTGCCACTAGATATCTTTTTCTTCCCGTTTCTCGATGTAGACATTCAATTAT
1 AAATAGACTTTTCTTGCCAATAGATATCTTTTTCTTCCCATTTCTCGAGGTAGACATTCAATTAT
** * * *
2810 TGTTTATTTTAACCAAAAATGT-AAAAAATTTGACTTAAAATCAATTATTAGATTATAAAAATAT
66 AATCTATTTTAACCAAAAATATAAAAAAATTTAACTTAAAATCAATTATTAGATTATAAAAATAT
* * * * * *
2874 TTAAAGCAAGTAAAAAGCCTTTTGAAGGCATGGATGACTATGAATATACTTTTCTTGCCAATCAA
131 TTAAAGCGAGTAATAAGACTTTTGAAGGCATGGGTGACTATAAATAGACTTTTCTTGCCAATCAA
* * *
2939 TATCTTTTTCTTCCTGTTTTCCTAGGTAGACATTCAATTATTATCTATTTTAACCAAAAATGTAN
196 TATCTTTTTCTTCATGTTTTCCTAGGTAGACATTCAATTATTATTTATTTTAA-CGAAAATGTA-
********* * * * ** * *
3004 NNNNNNNNNACTTAAAATCCATTATGAGATTATAAAAATATTTAAAGCTAATAAAAAGGCTTTTG
259 AAAAAATTCAATTAAAATCAATTATGAGATTATAAAAACATTTAAAGGGAGTAATAAGGCTTTTG
* *
3069 AAGGTGTGGGCGACTAT
324 AAGGTATGGGTGACTAT
* * ** *
3086 AAATAGACTTTTGTTGCCGAT-GAATATCTTTTTCTTCATATTTC-CAAAGGTAGACATTCAATT
1 AAATAGACTTTTCTTGCCAATAG-ATATCTTTTTCTTCCCATTTCTC-GAGGTAGACATTCAATT
*** * * * **
3149 ATAATCTATTTTAGTAAAAAATATAAAAAAATTCAACTTAAAAT-AGAATATCAGATTATAAAGC
64 ATAATCTATTTTAACCAAAAATATAAAAAAATTTAACTTAAAATCA-ATTATTAGATTATAAAAA
* * * * * **********
3213 CATTTAAAGTGAGTAATAAGGCTTTCGAAGTCATGGGTGACTNNNNNNNNNNTTTTCTTGCCAAT
128 TATTTAAAGCGAGTAATAAGACTTTTGAAGGCATGGGTGACTATAAATAGACTTTTCTTGCCAAT
** * * * * * *
3278 GGATATCTTTTTCTTCACGTTTCCCGAGTTAGATATTCAATTATTATTTATTTTAACCAAAATGT
193 CAATATCTTTTTCTTCATGTTTTCCTAGGTAGACATTCAATTATTATTTATTTTAACGAAAATGT
* ***********
3343 AAAAAAATTCAACTTAAAATCAATTATAAGATTATAAAAATNNNNNNNNNNAGTAATAAGGCTTT
258 AAAAAAATTCAA-TTAAAATCAATTATGAGATTATAAAAACATTTAAAGGGAGTAATAAGGCTTT
* *
3408 CGAAGGTATGAGTGACTAT
322 TGAAGGTATGGGTGACTAT
* * * * * * *
3427 AGATAGACTTTTCTTGTCAATAAATATCTTTTTCTTCCCGTTTCTCAAGGTAAACAATCAATTAT
1 AAATAGACTTTTCTTGCCAATAGATATCTTTTTCTTCCCATTTCTCGAGGTAGACATTCAATTAT
* * * * * *
3492 AATCTGTTTTAA-TAAAAGATATAAAAAAATTCAACTTGAAATCAAGTATAAGATTATAAAAATA
66 AATCTATTTTAACCAAAA-ATATAAAAAAATTTAACTTAAAATCAATTATTAGATTATAAAAATA
* ** * * * * *
3556 TTTAAAGCGAGTAATAAGGCTACTAAAGTCATGGGTAACTATAAATGGACTTTTCTTGGCAATCA
130 TTTAAAGCGAGTAATAAGACTTTTGAAGGCATGGGTGACTATAAATAGACTTTTCTTGCCAATCA
* * * * * **
3621 ATATCCTTTTCTTCATG-TTTCCTGAGGCA-AGCATTCAATAATTATCTATTTTAATGAAACACA
195 ATATCTTTTTCTTCATGTTTTCCT-AGGTAGA-CATTCAATTATTATTTATTTTAACGAAA-ATG
* * *
3684 TAAAAAATTTTAATTTAAAATCAATTATGAGATTGTAAAAACATTT-AAGGCGAGTAATAAGGCT
257 TAAAAAAATTCAA-TTAAAATCAATTATGAGATTATAAAAACATTTAAAGG-GAGTAATAAGGCT
**********
3748 TTTGAAGNNNNNNNNNNCTAT
320 TTTGAAGGTATGGGTGACTAT
* * * * * *
3769 AAATAGACTTTTCTTACCACTAGATATCTTTTTATTCACATTTCTTGAGGCAGACATTCAATTAT
1 AAATAGACTTTTCTTGCCAATAGATATCTTTTTCTTCCCATTTCTCGAGGTAGACATTCAATTAT
* * * * * * * *
3834 TATTTATTTTAACCAAAAGTGTAAAAAAATTTGACTTTAAATAAATTATGAGATTATAAAAATAT
66 AATCTATTTTAACCAAAAATATAAAAAAATTTAACTTAAAATCAATTATTAGATTATAAAAATAT
* * * ********** ** *
3899 TTAAAGCAAGTAAAAAGTCTTTTGAAGGNNNNNNNNNNTATAAATAGACTTTTCTTATCAATGAA
131 TTAAAGCGAGTAATAAGACTTTTGAAGGCATGGGTGACTATAAATAGACTTTTCTTGCCAATCAA
* * * * * * * * * *
3964 TATATTTTTCTTCCTGTTTT-TTGATGTAAATATTCAATTATTATCTGTTTTAACTAAAAATATA
196 TATCTTTTTCTTCATGTTTTCCT-AGGTAGACATTCAATTATTATTTATTTTAAC-GAAAATGTA
* * * *
4028 AAATAATTGAACTTAAAATCCATTATGAGATTATAAAAATATTTAAAG
259 AAAAAATTCAA-TTAAAATCAATTATGAGATTATAAAAACATTTAAAG
4076 CTAGTAAAAA
Statistics
Matches: 1258, Mismatches: 386, Indels: 56
0.74 0.23 0.03
Matches are distributed among these distances:
340 48 0.04
341 688 0.55
342 452 0.36
343 70 0.06
ACGTcount: A:0.37, C:0.11, G:0.12, T:0.35
Consensus pattern (340 bp):
AAATAGACTTTTCTTGCCAATAGATATCTTTTTCTTCCCATTTCTCGAGGTAGACATTCAATTAT
AATCTATTTTAACCAAAAATATAAAAAAATTTAACTTAAAATCAATTATTAGATTATAAAAATAT
TTAAAGCGAGTAATAAGACTTTTGAAGGCATGGGTGACTATAAATAGACTTTTCTTGCCAATCAA
TATCTTTTTCTTCATGTTTTCCTAGGTAGACATTCAATTATTATTTATTTTAACGAAAATGTAAA
AAAATTCAATTAAAATCAATTATGAGATTATAAAAACATTTAAAGGGAGTAATAAGGCTTTTGAA
GGTATGGGTGACTAT
Found at i:3038 original size:512 final size:511
Alignment explanation
Indices: 2185--4085 Score: 1447
Period size: 512 Copynumber: 3.7 Consensus size: 511
2175 NNNNNNNNNN
* * * * * * * *
2185 AAAATATTTAATGCGAGTAATAAGACTTTCGAAGGCATGGGTGATTATAAATACACTTTTCTTGT
1 AAAACATTTAAAGGGAGTAATAAGGCTTTTGAAGGCATGGGTGACTATAAATAGACTTTTCTTGC
* * * * * * *
2250 CAATGGATGTCTTTTTCTTCATGTTT-TCCAAGTTAGACATTCAATTATTATTTATTTTAAACGA
66 CACTAGATATCTTTTTCTTCACGTTTCT-CGAG-TAGACATTCAATTATTATTTATTTTAACCAA
** * * ** *
2314 AAATGTAAAAAAATTCAAC-TACAAATCAATTATGAGATTATAAAAACATTTACAA-TTAGTAAT
129 AAATGTAAAAAAATTTGACTTA-AAATCAATTATAAGATTATAAAAATATTTA-AAGCAAGTAAA
* * * * * * * * * *
2377 AAGGCTTTCGAAGGTAAGGGTGAGTATAGATAGACTTTTCCTACCAATGAATATCTTTTTCTTTC
192 AAGCCTTTTGAAGGCATGAGTGACTATAGATAGACTTTTCTTGCCAATAAATATCTTTTTCTTCC
* * * * ********* * *
2442 CATTTCTCGAGGTAGACATTCAATTATAATCTANNNNNNNNNNAA-ATATAAAAATATTTAACTT
257 CGTTTCTCAAGGTAAACAATCAATTATAATCTA-TTTTAACAAAAGATATAAAAAAATTCAACTT
* * * * * ** * **
2506 AAAATCAATTATAA-ATTATAAAAACATTTAAAGCGAGTAATAAGACTTTTGAAGGCATGGGTGA
321 AAAATCAAGTATAAGATTATAAAAATATTTAAAGCGAATAAAAAGGCTACTAAAGGCATGGGCAA
* *********************
2570 CTATAAATGGACTTNNNNNNNNNNNNNNNNNNNNNTTCTTCATATTTCCTGAGGCAGACATTCAA
386 CTATAAATAGACTTTTCTTGCCAATCAATATCCTTTTCTTCATATTTCCTGAGGCAGACATTCAA
* * * *
2635 TAATTATTTGTTTTAATGAAACACGTAAAAAAATTCAATTCAAAATGAATTATGAGATTATT
451 TAATTATCTATTTTAATGAAACACATAAAAAAATTCAATT-AAAATGAATTATGAGATTATA
* *
2697 AATACATTTAAAGGGAGTAATAAGGCTTTTGAAGGCATGGGTGACTATAAATAGACTTTACTTGC
1 AAAACATTTAAAGGGAGTAATAAGGCTTTTGAAGGCATGGGTGACTATAAATAGACTTTTCTTGC
* *
2762 CACTAGATATCTTTTTCTTCCCGTTTCTCGATGTAGACATTCAATTATTGTTTATTTTAACCAAA
66 CACTAGATATCTTTTTCTTCACGTTTCTCGA-GTAGACATTCAATTATTATTTATTTTAACCAAA
*
2827 AATGT-AAAAAATTTGACTTAAAATCAATTATTAGATTATAAAAATATTTAAAGCAAGTAAAAAG
130 AATGTAAAAAAATTTGACTTAAAATCAATTATAAGATTATAAAAATATTTAAAGCAAGTAAAAAG
* * *
2891 CCTTTTGAAGGCATG-GATGACTAT-GAATATACTTTTCTTGCCAATCAATATCTTTTTCTTCCT
195 CCTTTTGAAGGCATGAG-TGACTATAG-ATAGACTTTTCTTGCCAATAAATATCTTTTTCTTCCC
* * * * * **********
2954 GTTT-TCCTAGGTAGACATTCAATTATTATCTATTTTAACCAAAA-ATGTANNNNNNNNNNACTT
258 GTTTCT-CAAGGTAAACAATCAATTATAATCTATTTTAA-CAAAAGATATAAAAAAATTCAACTT
* * * * ** * ** *
3017 AAAATCCATTATGAGATTATAAAAATATTTAAAGCTAATAAAAAGGCTTTTGAAGGTGTGGGCGA
321 AAAATCAAGTATAAGATTATAAAAATATTTAAAGCGAATAAAAAGGCTACTAAAGGCATGGGCAA
* * * * ** *
3082 CTATAAATAGACTTTTGTTGCCGATGAATATCTTTTTCTTCATATTTCCAAAGGTAGACATTCAA
386 CTATAAATAGACTTTTCTTGCCAATCAATATCCTTTTCTTCATATTTCCTGAGGCAGACATTCAA
* * * * * * *
3147 TTATAATCTATTTTAGTAAAAAATATAAAAAAATTCAACTTAAAATAGAA-TATCAGATTATA
451 TAATTATCTATTTTAATGAAACACATAAAAAAATTCAA-TTAAAAT-GAATTATGAGATTATA
** * * * **********
3209 AAGCCATTTAAAGTGAGTAATAAGGCTTTCGAAGTCATGGGTGACTNNNNNNNNNNTTTTCTTGC
1 AAAACATTTAAAGGGAGTAATAAGGCTTTTGAAGGCATGGGTGACTATAAATAGACTTTTCTTGC
* * * *
3274 CAATGGATATCTTTTTCTTCACGTTTCCCGAGTTAGATATTCAATTATTATTTATTTTAACC-AA
66 CACTAGATATCTTTTTCTTCACGTTTCTCGAG-TAGACATTCAATTATTATTTATTTTAACCAAA
** ********** *
3338 AATGTAAAAAAATTCAACTTAAAATCAATTATAAGATTATAAAAATNNNNNNNNNNAGTAATAAG
130 AATGTAAAAAAATTTGACTTAAAATCAATTATAAGATTATAAAAATATTTAAAGCAAGTAAAAAG
* * * *
3403 GCTTTCGAAGGTATGAGTGACTATAGATAGACTTTTCTTGTCAATAAATATCTTTTTCTTCCCGT
195 CCTTTTGAAGGCATGAGTGACTATAGATAGACTTTTCTTGCCAATAAATATCTTTTTCTTCCCGT
* * *
3468 TTCTCAAGGTAAACAATCAATTATAATCTGTTTTAATAAAAGATATAAAAAAATTCAACTTGAAA
260 TTCTCAAGGTAAACAATCAATTATAATCTATTTTAACAAAAGATATAAAAAAATTCAACTTAAAA
* * * *
3533 TCAAGTATAAGATTATAAAAATATTTAAAGCGAGTAATAAGGCTACTAAAGTCATGGGTAACTAT
325 TCAAGTATAAGATTATAAAAATATTTAAAGCGAATAAAAAGGCTACTAAAGGCATGGGCAACTAT
* * *
3598 AAATGGACTTTTCTTGGCAATCAATATCCTTTTCTTCATGTTTCCTGAGGCA-AGCATTCAATAA
390 AAATAGACTTTTCTTGCCAATCAATATCCTTTTCTTCATATTTCCTGAGGCAGA-CATTCAATAA
* * * *
3662 TTATCTATTTTAATGAAACACATAAAAAATTTTAATTTAAAATCAATTATGAGATTGTA
454 TTATCTATTTTAATGAAACACATAAAAAAATTCAA-TTAAAATGAATTATGAGATTATA
********** *
3721 AAAACATTT-AAGGCGAGTAATAAGGCTTTTGAAGNNNNNNNNNNCTATAAATAGACTTTTCTTA
1 AAAACATTTAAAGG-GAGTAATAAGGCTTTTGAAGGCATGGGTGACTATAAATAGACTTTTCTTG
* * * *
3785 CCACTAGATATCTTTTTATTCACATTTCTTGAGGCAGACATTCAATTATTATTTATTTTAACCAA
65 CCACTAGATATCTTTTTCTTCACGTTTCTCGA-GTAGACATTCAATTATTATTTATTTTAACCAA
* * * *
3850 AAGTGTAAAAAAATTTGACTTTAAATAAATTATGAGATTATAAAAATATTTAAAGCAAGTAAAAA
129 AAATGTAAAAAAATTTGACTTAAAATCAATTATAAGATTATAAAAATATTTAAAGCAAGTAAAAA
* ********** * ** * * *
3915 GTCTTTTGAAGGNNNNNNNNNNTATAAATAGACTTTTCTTATCAATGAATATATTTTTCTTCCTG
194 GCCTTTTGAAGGCATGAGTGACTATAGATAGACTTTTCTTGCCAATAAATATCTTTTTCTTCCCG
* ** * * * * * * *
3980 TTTTTTGATGTAAATATTCAATTATTATCTGTTTTAACTAAAA-ATATAAAATAATTGAACTTAA
259 TTTCTCAAGGTAAACAATCAATTATAATCTATTTTAAC-AAAAGATATAAAAAAATTCAACTTAA
* * * * *
4044 AATCCATTATGAGATTATAAAAATATTTAAAGCTAGTAAAAA
323 AATCAAGTATAAGATTATAAAAATATTTAAAGCGAATAAAAA
4086 NNNNNNNNNN
Statistics
Matches: 1080, Mismatches: 286, Indels: 45
0.77 0.20 0.03
Matches are distributed among these distances:
510 5 0.00
511 161 0.15
512 717 0.66
513 193 0.18
514 4 0.00
ACGTcount: A:0.37, C:0.11, G:0.12, T:0.35
Consensus pattern (511 bp):
AAAACATTTAAAGGGAGTAATAAGGCTTTTGAAGGCATGGGTGACTATAAATAGACTTTTCTTGC
CACTAGATATCTTTTTCTTCACGTTTCTCGAGTAGACATTCAATTATTATTTATTTTAACCAAAA
ATGTAAAAAAATTTGACTTAAAATCAATTATAAGATTATAAAAATATTTAAAGCAAGTAAAAAGC
CTTTTGAAGGCATGAGTGACTATAGATAGACTTTTCTTGCCAATAAATATCTTTTTCTTCCCGTT
TCTCAAGGTAAACAATCAATTATAATCTATTTTAACAAAAGATATAAAAAAATTCAACTTAAAAT
CAAGTATAAGATTATAAAAATATTTAAAGCGAATAAAAAGGCTACTAAAGGCATGGGCAACTATA
AATAGACTTTTCTTGCCAATCAATATCCTTTTCTTCATATTTCCTGAGGCAGACATTCAATAATT
ATCTATTTTAATGAAACACATAAAAAAATTCAATTAAAATGAATTATGAGATTATA
Found at i:4837 original size:170 final size:171
Alignment explanation
Indices: 4345--4884 Score: 543
Period size: 171 Copynumber: 3.2 Consensus size: 171
4335 NNNNNNNNNN
* * *
4345 AAGGCTTTCGAAGGCATGGGTGACTATAAATGAACTTTTCTTACCAATGGATAT-TTTTATTTTC
1 AAGGCTTTCGAAGGCATGGGTGACTATAAATGGACTTTTCTTGCCAATGGATATCTTTT-TCTTC
* * * * *
4409 AAGTTTCTCAAGGCAGACA-TACAATTATAATCTGTTTAAATAGAAAATACT-AAAAAATTTAAT
65 ACGTTTCTCAAGGTAGACATTA-AATTATAATTTGTTTTAATAAAAAATA-TAAAAAAATTTAAT
* * *
4472 TTAGAATTAATTATAAGATTACAAAAATATTTAAAGCGAGTAAT
128 TTAAAATCAATTATAAGATTATAAAAATATTTAAAGCGAGTAAT
* * * * * * * *
4516 AAAGTTTTTGAAGGCATGGGTGAATATAAATAGACTTTTCGTGCCAATGGATACCTTTTTCTTTA
1 AAGGCTTTCGAAGGCATGGGTGACTATAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCA
* * * ** * ********** *
4581 CGTTTCTCAAGTTAGACATTAAATTATTATTTATTTTAACCAAAAATAGANNNNNNNNNNACTTA
66 CGTTTCTCAAGGTAGACATTAAATTATAATTTGTTTTAATAAAAAATATAAAAAAATTTAATTTA
* * **
4646 AAATCAATTATGAGATTATAAAAGTATTTAAAATGAGTAAT
131 AAATCAATTATAAGATTATAAAAATATTTAAAGCGAGTAAT
* *
4687 AAGGCTTTCGAAGGTATGGGTGACTATAGAA-GGACTTTTCTTGCCAAT-GATATCTTTTTCCTC
1 AAGGCTTTCGAAGGCATGGGTGACTATA-AATGGACTTTTCTTGCCAATGGATATCTTTTTCTTC
* * * * *
4750 CCGTTTCTCGAGGTAGAAATTTAATTATAATTTGTTTTCATAAAAAATATAAAAAAATTTAATTT
65 ACGTTTCTCAAGGTAGACATTAAATTATAATTTGTTTTAATAAAAAATATAAAAAAATTTAATTT
* *
4815 AAAATCAATTATAAGGTTATAAAAATATTTAAAGCAAGTAAT
130 AAAATCAATTATAAGATTATAAAAATATTTAAAGCGAGTAAT
* *
4857 AAGGCTTT-TAAGGCATGAGTGACTATAA
1 AAGGCTTTCGAAGGCATGGGTGACTATAA
4885 NNNNNNNNNN
Statistics
Matches: 284, Mismatches: 81, Indels: 11
0.76 0.22 0.03
Matches are distributed among these distances:
168 1 0.00
169 16 0.06
170 99 0.35
171 160 0.56
172 8 0.03
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.36
Consensus pattern (171 bp):
AAGGCTTTCGAAGGCATGGGTGACTATAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCA
CGTTTCTCAAGGTAGACATTAAATTATAATTTGTTTTAATAAAAAATATAAAAAAATTTAATTTA
AAATCAATTATAAGATTATAAAAATATTTAAAGCGAGTAAT
Found at i:6010 original size:171 final size:169
Alignment explanation
Indices: 5717--6646 Score: 839
Period size: 171 Copynumber: 5.4 Consensus size: 169
5707 NNNNNNNNNN
* * * *** *
5717 ATTATGAGATTATAAAAACATTTCAAGCGAGTAATAAGGCTTTTAAAGGCATGGTTGACTATAAA
1 ATTATGAGATTATAAAAATATTTAAAGCGAGTAATAAGGCTTTTGAAGATGTGGGTGACTATAAA
* * * * *
5782 TGGACTTTTCTT-ACAACTGGATATCTCTTTCTTTATGTTTTCTAAGGTAGACATTCAATTATTA
66 TAGACTTTTCTTGCCAA-TGAATATCT-TTTCTTCATG-TTTCTGAGGTAGACATTCAATTATTA
* * *** * *
5846 TTTATTTTAACTAAAAATGTAGAAACTTTTGAA-TTAAAATTA
128 TCTATTTTAACTAAAAATATA-AAAAAATTCAACTTAAAATCA
* * * * *
5888 ATTATGAAATTATAAAAATATTTAAAGCGAGTAAGAAGCCTTTTGAAGATGTAGGTGACAATAAA
1 ATTATGAGATTATAAAAATATTTAAAGCGAGTAATAAGGCTTTTGAAGATGTGGGTGACTATAAA
** *
5953 TAGACTTTTCTTGCCAATGAATATCTTTTCCTTCCCGTTTCATGAGGCAGACATTCAATTATTAT
66 TAGACTTTTCTTGCCAATGAATATCTTTT-CTTCATGTTTC-TGAGGTAGACATTCAATTATTAT
* * * * *
6018 CTATTATATCCAAAAATTTAAAAAAATTCAACTTAAAATCC
129 CTATTTTAACTAAAAATATAAAAAAATTCAACTTAAAATCA
* * * ** * *
6059 GTTATGAGATTATAAAAACATTTCAAGTTAGTAAAAAGGCTTTTGAAGGTGTGGGTGACTATAAA
1 ATTATGAGATTATAAAAATATTTAAAGCGAGTAATAAGGCTTTTGAAGATGTGGGTGACTATAAA
* * * * * * *
6124 TAAATTTTTCTTACCAATGAATATCTTTTTTTTCATGTTTCCCGAGGTAGATC-TTTAATTATAA
66 TAGACTTTTCTTGCCAATGAATATC-TTTTCTTCATGTTT-CTGAGGTAGA-CATTCAATTATTA
*
6188 TCTATTTTAA-TAAAAAATATAAAAAAATTCAACTTAAAATTA
128 TCTATTTTAACT-AAAAATATAAAAAAATTCAACTTAAAATCA
* * ** * * * * *
6230 AGTATGAGATTACAAAGCTATTTAAAGCGAGAAATAAGGCATTCGAAGATATGGGTGACTGTAAA
1 ATTATGAGATTATAAAAATATTTAAAGCGAGTAATAAGGCTTTTGAAGATGTGGGTGACTATAAA
* * * * *
6295 TAGACTTTTCTTGCAAATGCATATCTTTTTCTTCATATTTCTCGAGGTAGATATAT-AATTATAA
66 TAGACTTTTCTTGCCAATGAATATC-TTTTCTTCATGTTTCT-GAGGTAGACAT-TCAATTATTA
* * * * *
6359 TCTGTTTTAA-TAAAAAATATAAACAAATTTAATTTAAAATCG
128 TCTATTTTAACT-AAAAATATAAAAAAATTCAACTTAAAATCA
* * ** * * *
6401 ATTATAAGATTATAAGAATATTTAAAATGAGTAATAAGGCTTTTGAAGGTATGGGTGAATATAAA
1 ATTATGAGATTATAAAAATATTTAAAGCGAGTAATAAGGCTTTTGAAGATGTGGGTGACTATAAA
* * * * *
6466 TAAACTTTTCTTGCCAATGGATATCTCTTTCTTCACGTTTTCTAAGTTAGACATTCAATTATTA-
66 TAGACTTTTCTTGCCAATGAATATCT-TTTCTTCATG-TTTCTGAGGTAGACATTCAATTATTAT
*
6530 CTTATTTTAACTAAAAATATAAAAAAATTCAACTTAAATTCA
129 C-TATTTTAACTAAAAATATAAAAAAATTCAACTTAAAATCA
* * * ** ** *** *
6572 ATTATAAGATTATAAAAACATATAAAATGAGTAATAAGGCTTTCAAAGGCATGGGTGACTATAGA
1 ATTATGAGATTATAAAAATATTTAAAGCGAGTAATAAGGCTTTTGAAGATGTGGGTGACTATAAA
*
6637 TGGACTTTTC
66 TAGACTTTTC
6647 AATTATGAGA
Statistics
Matches: 615, Mismatches: 128, Indels: 32
0.79 0.17 0.04
Matches are distributed among these distances:
170 18 0.03
171 581 0.94
172 16 0.03
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (169 bp):
ATTATGAGATTATAAAAATATTTAAAGCGAGTAATAAGGCTTTTGAAGATGTGGGTGACTATAAA
TAGACTTTTCTTGCCAATGAATATCTTTTCTTCATGTTTCTGAGGTAGACATTCAATTATTATCT
ATTTTAACTAAAAATATAAAAAAATTCAACTTAAAATCA
Found at i:6610 original size:342 final size:342
Alignment explanation
Indices: 5717--6646 Score: 1011
Period size: 342 Copynumber: 2.7 Consensus size: 342
5707 NNNNNNNNNN
* * * *
5717 ATTATGAGATTATAAAAACATTTCAAGCGAGTAATAAGGCTTTTAAAGGCATGGTTGACTATAAA
1 ATTATGAGATTATAAAAACATTTCAAGTGAGTAATAAGGCTTTTGAAGGTATGGGTGACTATAAA
** * * *
5782 TGGACTTTTCTTACAACTGGATATCTCTTTCTTTATGTTTTCTAAGGTAGACATTCAATTATTAT
66 TAAACTTTTCTTCCAA-TGGATATCTCTTTCTTCATGTTTTCTAAGGTAGACATTCAATTATTAA
* *** * *
5847 TTATTTTAACTAAAAATGTAGAAACTTTTGAA-TTAAAATTAATTATGAA-ATTATAAAAATATT
130 TTATTTTAACTAAAAATATA-AAAAAATTCAACTTAAAATTAATTAT-AAGATTATAAAAACATT
* * * * * * *
5910 TAAAGCGAGTAAGAAGCCTTTTGAAGATGTAGGTGACAATAAATAGACTTTTCTTGCCAATGAAT
193 TAAAGCGAGTAATAAGGCTTTCGAAGATATGGGTGACTATAAATAGACTTTTCTTGCAAATGAAT
* * * * *
5975 ATCTTTTCCTTCCCGTTTCATGAGGCAGACATTCAATTATTATCTATTATATCCAAAAATTTAAA
258 ATCTTTTCCTTCACATTTCATGAGGCAGACATTCAATTATAATCTATTATATCAAAAAATATAAA
6040 AAAATTCAACTTAAAATCCG
323 AAAATTCAACTTAAAATCCG
* * *
6060 -TTATGAGATTATAAAAACATTTCAAGTTAGTAAAAAGGCTTTTGAAGGTGTGGGTGACTATAAA
1 ATTATGAGATTATAAAAACATTTCAAGTGAGTAATAAGGCTTTTGAAGGTATGGGTGACTATAAA
* * * * * ** *
6124 TAAATTTTTCTTACCAATGAATATCTTTTTTTTCATGTTTCCCGAGGTAGATC-TTTAATTA-TA
66 TAAACTTTTCTT-CCAATGGATATCTCTTTCTTCATGTTTTCTAAGGTAGA-CATTCAATTATTA
* * * *
6187 ATCTATTTTAA-TAAAAAATATAAAAAAATTCAACTTAAAATTAAGTATGAGATTA-CAAAGCTA
129 AT-TATTTTAACT-AAAAATATAAAAAAATTCAACTTAAAATTAATTATAAGATTATAAAAAC-A
* * * *
6250 TTTAAAGCGAGAAATAAGGCATTCGAAGATATGGGTGACTGTAAATAGACTTTTCTTGCAAATGC
191 TTTAAAGCGAGTAATAAGGCTTTCGAAGATATGGGTGACTATAAATAGACTTTTCTTGCAAATGA
* * * * * *
6315 ATATCTTTTTCTTCATATTTC-TCGAGGTAGATATAT-AATTATAATCTGTTTTAAT-AAAAAAT
256 ATATCTTTTCCTTCACATTTCAT-GAGGCAGACAT-TCAATTATAATCTATTAT-ATCAAAAAAT
* * *
6377 ATAAACAAATTTAATTTAAAAT-CG
318 ATAAAAAAATTCAACTTAAAATCCG
* * * * * *
6401 ATTATAAGATTATAAGAATATTTAAAATGAGTAATAAGGCTTTTGAAGGTATGGGTGAATATAAA
1 ATTATGAGATTATAAAAACATTTCAAGTGAGTAATAAGGCTTTTGAAGGTATGGGTGACTATAAA
* * *
6466 TAAACTTTTCTTGCCAATGGATATCTCTTTCTTCACGTTTTCTAAGTTAGACATTCAATTATTAC
66 TAAACTTTTCTT-CCAATGGATATCTCTTTCTTCATGTTTTCTAAGGTAGACATTCAATTATTAA
*
6531 TTATTTTAACTAAAAATATAAAAAAATTCAACTT-AAATTCAATTATAAGATTATAAAAACATAT
130 TTATTTTAACTAAAAATATAAAAAAATTCAACTTAAAATT-AATTATAAGATTATAAAAACATTT
** * ** * *
6595 AAAATGAGTAATAAGGCTTTCAAAGGCATGGGTGACTATAGATGGACTTTTC
194 AAAGCGAGTAATAAGGCTTTCGAAGATATGGGTGACTATAAATAGACTTTTC
6647 AATTATGAGA
Statistics
Matches: 480, Mismatches: 91, Indels: 33
0.79 0.15 0.05
Matches are distributed among these distances:
341 24 0.05
342 441 0.92
343 15 0.03
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (342 bp):
ATTATGAGATTATAAAAACATTTCAAGTGAGTAATAAGGCTTTTGAAGGTATGGGTGACTATAAA
TAAACTTTTCTTCCAATGGATATCTCTTTCTTCATGTTTTCTAAGGTAGACATTCAATTATTAAT
TATTTTAACTAAAAATATAAAAAAATTCAACTTAAAATTAATTATAAGATTATAAAAACATTTAA
AGCGAGTAATAAGGCTTTCGAAGATATGGGTGACTATAAATAGACTTTTCTTGCAAATGAATATC
TTTTCCTTCACATTTCATGAGGCAGACATTCAATTATAATCTATTATATCAAAAAATATAAAAAA
ATTCAACTTAAAATCCG
Done.