Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400984.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4145.0, 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: 7189
ACGTcount: A:0.27, C:0.08, G:0.10, T:0.25
Warning! 2055 characters in sequence are not A, C, G, or T
Found at i:453 original size:171 final size:169
Alignment explanation
Indices: 4--1404 Score: 849
Period size: 171 Copynumber: 8.2 Consensus size: 169
1 CCA
* * * * *
4 AAAATATAAAAAATTTCAAC-TAAAATCAATTTTAAGATTATAAAA-TCATTTGAAA-TGAGTAA
1 AAAATCTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACT-ATTT-AAAGCGAGTAA
* * ** * * *
66 TAAGGCTTTTGAAGGAATGGGTGACTATAAATGGGCTTTTGTTGCCAATGAATGTCTTATTCTTC
64 TAAGGCTTTTAAAAGAATGGGACACTATAAATGGACTTTTCTTGCCAATGAATGTCTTTTTCTTC
** ** * * **
131 ACATTTCTTGAGATAGACATTCAATTATAAT-ATGCGTTAACC
129 ATGTTTCTAAAG-TAAACATTCAATTATAGTCA-GTTTTAACC
* * * * ********** * *
173 AATAATGTAAAAAAAATTAAACCTAAAATCAATTTTGANNNNNNNNNNCCATTTAAAGTGAGTAA
1 AA-AATCT-AAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGCGAGTAA
* * * ** * *
238 TAAGGCTTTT-GAAGAAATTGGAAACTAGGAATGGACTCTTCTTGCCAATGAATGCCTTTTTCTT
64 TAAGGCTTTTAAAAG-AATGGGACACTATAAATGGACTTTTCTTGCCAATGAATGTCTTTTTCTT
*
302 TATGTTTCCTAAAGTAAACATTCAATTATAGTCAGTTTTAACC
128 CATGTTT-CTAAAGTAAACATTCAATTATAGTCAGTTTTAACC
* **********
345 AATAATCTAAAAAAAATCAACTTAAAATCAATTATGANNNNNNNNNNCTATTTAAAGCGAGTAAT
1 AA-AATCTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGCGAGTAAT
* * * *
410 AATGCTTTTAAAAGAATGGGTCACTATAAATGGACTTTTCTTGCCAATGAATGTGTTTTTCTTTA
65 AAGGCTTTTAAAAGAATGGGACACTATAAATGGACTTTTCTTGCCAATGAATGTCTTTTTCTTCA
* * ********** *
475 CGTTTCTCAAGGTNNNNNNNNNNTTATAGTCTGTTTTAACC
130 TGTTTCT-AAAGTAAACATTCAATTATAGTCAGTTTTAACC
* * * * ** * **
516 AAAATTGTGAAAGAATTTAACTTAAAATCAATTATGAGACCATAAAACAATTTAAAGTAAGTAAT
1 AAAA-TCTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGCGAGTAAT
** * ** * * *
581 CGGGCTTTTAAAGGAATGGGTGACTACAAATGGATTTTTCTTTG-CAATGAATGGT-TTTTTCTA
65 AAGGCTTTTAAAAGAATGGGACACTATAAATGGACTTTTC-TTGCCAATGAAT-GTCTTTTTCTT
* * * * *
644 CATGTTTCCCAAGGCAAACATTCAATTATATTCTGTTTTAACC
128 CATGTTT-CTAAAGTAAACATTCAATTATAGTCAGTTTTAACC
* * * *
687 AAAA-CTATAAAAAATTTCAAC-TAAAATCAATTTTAAGATTATAAAA-TCATTTAAAACAAGTA
1 AAAATCTA-AAAAAA-TTCAACTTAAAATCAATTATGAGATTATAAAACT-ATTTAAAGCGAGTA
* * * * * *
749 ACAAGGCTTTTGAAAGAAT-GGACGACTATAAATGGGCTTTTGTTGTCAATAAATGTCTTTTTCT
63 ATAAGGCTTTTAAAAGAATGGGAC-ACTATAAATGGACTTTTCTTGCCAATGAATGTCTTTTTCT
** * ** * * * *
813 TCACATATCTTGAGATAGACATTCAATTAAAAT-ATGTGTTAACC
127 TCATGTTTCTAAAG-TAAACATTCAATTATAGTCA-GTTTTAACC
* * * * * * * *
857 AATAATGTAAAAAAAATTGAACCTAAAATCAATTTTTAGATTGTAAAACCATTTAAAGTGAGTAA
1 AA-AATCT-AAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGCGAGTAA
* * * * * *
922 TAAGGCTTTT-GAAGAAATAGGAAACTATGAACGGACTTTTCTGGCCAATGAATG-CTTTTTTCT
64 TAAGGCTTTTAAAAG-AATGGGACACTATAAATGGACTTTTCTTGCCAATGAATGTC-TTTTTCT
* * * *
985 TTATGTTTATCAAGGTAAACATTCTATTATAGT-ATGTTTTAACC
127 TCATGTTTCT-AAAGTAAACATTCAATTATAGTCA-GTTTTAACC
*
1029 AATAATCTAAAAAAATTCAACTTAAAATCAATTATAAGATTATAAAACTATTTAAAGCGAGTAAT
1 AA-AATCTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGCGAGTAAT
* * * * *
1094 AATGCTTTTAAAGGAA-GAGGTCACTATAAATGGACTTTTCTTGCCAATGAATGTGTGTTTCTTC
65 AAGGCTTTTAAAAGAATG-GGACACTATAAATGGACTTTTCTTGCCAATGAATGTCTTTTTCTTC
* * * * *
1158 ATGTTTATCCAAGTAGACATTCAATTATAGTCTGTGTTAACC
129 ATGTTTCT-AAAGTAAACATTCAATTATAGTCAGTTTTAACC
* * ** * * *
1200 AAAAT-TGCGAAAGAATTCAACTTAAAATCAATTATGAGACCATAAAACAATTTAAAGTGAGTAG
1 AAAATCT--AAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGCGAGTAA
* * * ** * * * * * *
1264 TAGGGCTTTTAAAGGAATAGGTGAGTACAAATGGATTTTTCTTTCCAATGAATGGTTTTTTTC-A
64 TAAGGCTTTTAAAAGAATGGGACACTATAAATGGACTTTTCTTGCCAATGAAT-GTCTTTTTCTT
* ** * * * *
1328 CAAGTTTCCCAAGGAAAGCATTGAATTATAGTCTGTTTTAACTA
128 CATGTTTCTAAAGTAAA-CATTCAATTATAGTCAGTTTTAAC-C
* *
1372 AAAATGTAAAAAATTTCAACTTAAAATCAATTA
1 AAAATCTAAAAAAATTCAACTTAAAATCAATTA
1405 NNNNNNNNNN
Statistics
Matches: 959, Mismatches: 231, Indels: 82
0.75 0.18 0.06
Matches are distributed among these distances:
169 13 0.01
170 125 0.13
171 558 0.58
172 252 0.26
173 11 0.01
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.34
Consensus pattern (169 bp):
AAAATCTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGCGAGTAATA
AGGCTTTTAAAAGAATGGGACACTATAAATGGACTTTTCTTGCCAATGAATGTCTTTTTCTTCAT
GTTTCTAAAGTAAACATTCAATTATAGTCAGTTTTAACC
Found at i:665 original size:342 final size:341
Alignment explanation
Indices: 60--1404 Score: 1143
Period size: 342 Copynumber: 3.9 Consensus size: 341
50 CATTTGAAAT
* * * * * * * *
60 GAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGGCTTTTGTTGCCAATGAATGTCTTA
1 GAGTAATAATGCTTTTAAAAGAATGGGTCACTATAAATGGACTTTTCTTGCCAATGAATGTGTTT
* ** * * * * * *
125 TTCTTCACATTTCTTGAGATAGACATTCAATTATAATATGCGTTAACCAATAA-TGTAAAAAAAA
66 TTCTTCACGTTTCTCAAGGTAGACATTCAATTATAGTCTGTGTTAACCAA-AATTGT-GAAAGAA
* * * ********** * * * *
189 TTAAACCTAAAATCAATTTTGANNNNNNNNNNCCATTTAAAGTGAGTAATAAGGCTTTTGAAGAA
129 TTCAACTTAAAATCAATTATGAGACCATAAAACAATTTAAAGTGAGTAATAGGGCTTTTAAAGGA
* ** ** * * * ** * *
254 ATTGGAAACTAGGAATGGACTCTTC-TTGCCAATGAATGCCTTTTTCTTTATGTTTCCTAAAGTA
194 ATAGGTGACTACAAATGGATTTTTCTTTG-CAATGAATGCTTTTTTCTACATGTTTCCCAAGGTA
*
318 AACATTCAATTATAGTCAGTTTTAACCAATAATCTAAAAAAAATCAACTTAAAATCAATTATGAN
258 AACATTCAATTATAGTCAGTTTTAACCAATAATCTAAAAAAATTCAACTTAAAATCAATTATGA-
*********
383 NNNNNNNNNCTATTTAAAGC
322 ATAAAAAAACTATTTAAAGC
403 GAGTAATAATGCTTTTAAAAGAATGGGTCACTATAAATGGACTTTTCTTGCCAATGAATGTGTTT
1 GAGTAATAATGCTTTTAAAAGAATGGGTCACTATAAATGGACTTTTCTTGCCAATGAATGTGTTT
* ********** *
468 TTCTTTACGTTTCTCAAGGTNNNNNNNNNNTTATAGTCTGTTTTAACCAAAATTGTGAAAGAATT
66 TTCTTCACGTTTCTCAAGGTAGACATTCAATTATAGTCTGTGTTAACCAAAATTGTGAAAGAATT
* * *
533 TAACTTAAAATCAATTATGAGACCATAAAACAATTTAAAGTAAGTAATCGGGCTTTTAAAGGAAT
131 CAACTTAAAATCAATTATGAGACCATAAAACAATTTAAAGTGAGTAATAGGGCTTTTAAAGGAAT
* * *
598 GGGTGACTACAAATGGATTTTTCTTTGCAATGAATGGTTTTTTCTACATGTTTCCCAAGGCAAAC
196 AGGTGACTACAAATGGATTTTTCTTTGCAATGAATGCTTTTTTCTACATGTTTCCCAAGGTAAAC
* * * *
663 ATTCAATTATATTCTGTTTTAACCAA-AA-CTATAAAAAATTTCAAC-TAAAATCAATTTTAAGA
261 ATTCAATTATAGTCAGTTTTAACCAATAATCTA-AAAAAA-TTCAACTTAAAATCAATTATGA-A
* * *
725 TTATAAAA-TCATTTAAAAC
323 TAAAAAAACT-ATTTAAAGC
* * * * * * * * * *
744 AAGTAACAAGGCTTTTGAAAGAAT-GGACGACTATAAATGGGCTTTTGTTGTCAATAAATGTCTT
1 GAGTAATAATGCTTTTAAAAGAATGGGTC-ACTATAAATGGACTTTTCTTGCCAATGAATGTGTT
* * ** * * * * * *
808 TTTCTTCACATATCTTGAGATAGACATTCAATTAAAATATGTGTTAACCAATAA-TGTAAAAAAA
65 TTTCTTCACGTTTCTCAAGGTAGACATTCAATTATAGTCTGTGTTAACCAA-AATTGT-GAAAGA
* * * * *** * * * *
872 ATTGAACCTAAAATCAATTTTTAGATTGTAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGA
128 ATTCAACTTAAAATCAATTATGAGACCATAAAACAATTTAAAGTGAGTAATAGGGCTTTTAAAGG
** ** * * * ** **
937 AATAGGAAACTATGAACGGACTTTTC-TGGCCAATGAATGCTTTTTTCTTTATGTTTATCAAGGT
193 AATAGGTGACTACAAATGGATTTTTCTTTG-CAATGAATGCTTTTTTCTACATGTTTCCCAAGGT
* *
1001 AAACATTCTATTATAGT-ATGTTTTAACCAATAATCTAAAAAAATTCAACTTAAAATCAATTATA
257 AAACATTCAATTATAGTCA-GTTTTAACCAATAATCTAAAAAAATTCAACTTAAAATCAATTATG
* *
1065 AGATTATAAAACTATTTAAAGC
321 A-ATAAAAAAACTATTTAAAGC
* *
1087 GAGTAATAATGCTTTTAAAGGAA-GAGGTCACTATAAATGGACTTTTCTTGCCAATGAATGTGTG
1 GAGTAATAATGCTTTTAAAAGAATG-GGTCACTATAAATGGACTTTTCTTGCCAATGAATGTGTT
* * *
1151 TTTCTTCATGTTTATCCAA-GTAGACATTCAATTATAGTCTGTGTTAACCAAAATTGCGAAAGAA
65 TTTCTTCACGTTTCT-CAAGGTAGACATTCAATTATAGTCTGTGTTAACCAAAATTGTGAAAGAA
*
1215 TTCAACTTAAAATCAATTATGAGACCATAAAACAATTTAAAGTGAGTAGTAGGGCTTTTAAAGGA
129 TTCAACTTAAAATCAATTATGAGACCATAAAACAATTTAAAGTGAGTAATAGGGCTTTTAAAGGA
* * * *
1280 ATAGGTGAGTACAAATGGATTTTTCTTTCCAATGAATGGTTTTTT-TCACAAGTTTCCCAAGG-A
194 ATAGGTGACTACAAATGGATTTTTCTTTGCAATGAATGCTTTTTTCT-ACATGTTTCCCAAGGTA
* * * * * *
1343 AAGCATTGAATTATAGTCTGTTTTAACTAAAAATGTAAAAAATTTCAACTTAAAATCAATTA
258 AA-CATTCAATTATAGTCAGTTTTAACCAATAATCTAAAAAAATTCAACTTAAAATCAATTA
1405 NNNNNNNNNN
Statistics
Matches: 779, Mismatches: 201, Indels: 45
0.76 0.20 0.04
Matches are distributed among these distances:
340 7 0.01
341 119 0.15
342 422 0.54
343 223 0.29
344 8 0.01
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.34
Consensus pattern (341 bp):
GAGTAATAATGCTTTTAAAAGAATGGGTCACTATAAATGGACTTTTCTTGCCAATGAATGTGTTT
TTCTTCACGTTTCTCAAGGTAGACATTCAATTATAGTCTGTGTTAACCAAAATTGTGAAAGAATT
CAACTTAAAATCAATTATGAGACCATAAAACAATTTAAAGTGAGTAATAGGGCTTTTAAAGGAAT
AGGTGACTACAAATGGATTTTTCTTTGCAATGAATGCTTTTTTCTACATGTTTCCCAAGGTAAAC
ATTCAATTATAGTCAGTTTTAACCAATAATCTAAAAAAATTCAACTTAAAATCAATTATGAATAA
AAAAACTATTTAAAGC
Found at i:1315 original size:684 final size:684
Alignment explanation
Indices: 1--1403 Score: 2017
Period size: 684 Copynumber: 2.0 Consensus size: 684
* **
1 CCAAAAATATAAAAAATTTCAACTAAAATCAATTTTAAGATTATAAAATCATTTGAAATGAGTAA
1 CCAAAAATATAAAAAATTTCAACTAAAATCAATTTTAAGATTATAAAATCATTTAAAACAAGTAA
* * ** *
66 TAAGGCTTTTGAAGGAATGGGTGACTATAAATGGGCTTTTGTTGCCAATGAATGTCTTATTCTTC
66 CAAGGCTTTTGAAAGAATGGACGACTATAAATGGGCTTTTGTTGCCAATAAATGTCTTATTCTTC
* *
131 ACATTTCTTGAGATAGACATTCAATTATAATATGCGTTAACCAATAATGTAAAAAAAATTAAACC
131 ACATATCTTGAGATAGACATTCAATTAAAATATGCGTTAACCAATAATGTAAAAAAAATTAAACC
********** *
196 TAAAATCAATTTTGANNNNNNNNNNCCATTTAAAGTGAGTAATAAGGCTTTTGAAGAAATTGGAA
196 TAAAATCAATTTTGAGATTGTAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGAAATAGGAA
* *
261 ACTAGGAATGGACTCTTCTTGCCAATGAATGCCTTTTTCTTTATGTTTCCTAAAGTAAACATTCA
261 ACTAGGAACGGACTCTTCTGGCCAATGAATGCCTTTTTCTTTATGTTTCCTAAAGTAAACATTCA
* *********
326 ATTATAGTCAGTTTTAACCAATAATCTAAAAAAAATCAACTTAAAATCAATTATGANNNNNNNNN
326 ATTATAGTCAGTTTTAACCAATAATCTAAAAAAAATCAACTTAAAATCAATTATAAGATTATAAA
*
391 NCTATTTAAAGCGAGTAATAATGCTTTTAAAAGAATGGGTCACTATAAATGGACTTTTCTTGCCA
391 ACTATTTAAAGCGAGTAATAATGCTTTTAAAAGAATGGGTCACTATAAATGGACTTTTCTTGCCA
* * * ********** *
456 ATGAATGTGTTTTTCTTTACGTTTCTCAAGGTNNNNNNNNNNTTATAGTCTGTTTTAACCAAAAT
456 ATGAATGTGTGTTTCTTCACGTTTATCAAGGTAGACATTCAATTATAGTCTGTGTTAACCAAAAT
* * *
521 TGTGAAAGAATTTAACTTAAAATCAATTATGAGACCATAAAACAATTTAAAGTAAGTAATCGGGC
521 TGCGAAAGAATTCAACTTAAAATCAATTATGAGACCATAAAACAATTTAAAGTAAGTAATAGGGC
* * *
586 TTTTAAAGGAATGGGTGACTACAAATGGATTTTTCTTTGCAATGAATGG-TTTTTTCTACATGTT
586 TTTTAAAGGAATAGGTGACTACAAATGGATTTTTCTTTCCAATGAATGGTTTTTTTC-ACAAGTT
*
650 TCCCAAGGCAAA-CATTCAATTATATTCTGTTTTAA
650 TCCCAAGG-AAAGCATTCAATTATAGTCTGTTTTAA
*
685 CCAAAACTATAAAAAATTTCAACTAAAATCAATTTTAAGATTATAAAATCATTTAAAACAAGTAA
1 CCAAAAATATAAAAAATTTCAACTAAAATCAATTTTAAGATTATAAAATCATTTAAAACAAGTAA
* *
750 CAAGGCTTTTGAAAGAATGGACGACTATAAATGGGCTTTTGTTGTCAATAAATGTCTTTTTCTTC
66 CAAGGCTTTTGAAAGAATGGACGACTATAAATGGGCTTTTGTTGCCAATAAATGTCTTATTCTTC
* *
815 ACATATCTTGAGATAGACATTCAATTAAAATATGTGTTAACCAATAATGTAAAAAAAATTGAACC
131 ACATATCTTGAGATAGACATTCAATTAAAATATGCGTTAACCAATAATGTAAAAAAAATTAAACC
*
880 TAAAATCAATTTTTAGATTGTAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGAAATAGGAA
196 TAAAATCAATTTTGAGATTGTAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGAAATAGGAA
* * * * *
945 ACTATGAACGGACTTTTCTGGCCAATGAATGCTTTTTTCTTTATGTTT-ATCAAGGTAAACATTC
261 ACTAGGAACGGACTCTTCTGGCCAATGAATGCCTTTTTCTTTATGTTTCCT-AAAGTAAACATTC
* *
1009 TATTATAGT-ATGTTTTAACCAATAATCTAAAAAAATTCAACTTAAAATCAATTATAAGATTATA
325 AATTATAGTCA-GTTTTAACCAATAATCTAAAAAAAATCAACTTAAAATCAATTATAAGATTATA
*
1073 AAACTATTTAAAGCGAGTAATAATGCTTTTAAAGGAA-GAGGTCACTATAAATGGACTTTTCTTG
389 AAACTATTTAAAGCGAGTAATAATGCTTTTAAAAGAATG-GGTCACTATAAATGGACTTTTCTTG
*
1137 CCAATGAATGTGTGTTTCTTCATGTTTATCCAA-GTAGACATTCAATTATAGTCTGTGTTAACCA
453 CCAATGAATGTGTGTTTCTTCACGTTTAT-CAAGGTAGACATTCAATTATAGTCTGTGTTAACCA
* *
1201 AAATTGCGAAAGAATTCAACTTAAAATCAATTATGAGACCATAAAACAATTTAAAGTGAGTAGTA
517 AAATTGCGAAAGAATTCAACTTAAAATCAATTATGAGACCATAAAACAATTTAAAGTAAGTAATA
*
1266 GGGCTTTTAAAGGAATAGGTGAGTACAAATGGATTTTTCTTTCCAATGAATGGTTTTTTTCACAA
582 GGGCTTTTAAAGGAATAGGTGACTACAAATGGATTTTTCTTTCCAATGAATGGTTTTTTTCACAA
*
1331 GTTTCCCAAGGAAAGCATTGAATTATAGTCTGTTTTAA
647 GTTTCCCAAGGAAAGCATTCAATTATAGTCTGTTTTAA
* *
1369 CTAAAAATGTAAAAAATTTCAACTTAAAATCAATT
1 CCAAAAATATAAAAAATTTCAAC-TAAAATCAATT
1404 ANNNNNNNNN
Statistics
Matches: 635, Mismatches: 77, Indels: 13
0.88 0.11 0.02
Matches are distributed among these distances:
683 6 0.01
684 608 0.96
685 21 0.03
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.34
Consensus pattern (684 bp):
CCAAAAATATAAAAAATTTCAACTAAAATCAATTTTAAGATTATAAAATCATTTAAAACAAGTAA
CAAGGCTTTTGAAAGAATGGACGACTATAAATGGGCTTTTGTTGCCAATAAATGTCTTATTCTTC
ACATATCTTGAGATAGACATTCAATTAAAATATGCGTTAACCAATAATGTAAAAAAAATTAAACC
TAAAATCAATTTTGAGATTGTAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGAAATAGGAA
ACTAGGAACGGACTCTTCTGGCCAATGAATGCCTTTTTCTTTATGTTTCCTAAAGTAAACATTCA
ATTATAGTCAGTTTTAACCAATAATCTAAAAAAAATCAACTTAAAATCAATTATAAGATTATAAA
ACTATTTAAAGCGAGTAATAATGCTTTTAAAAGAATGGGTCACTATAAATGGACTTTTCTTGCCA
ATGAATGTGTGTTTCTTCACGTTTATCAAGGTAGACATTCAATTATAGTCTGTGTTAACCAAAAT
TGCGAAAGAATTCAACTTAAAATCAATTATGAGACCATAAAACAATTTAAAGTAAGTAATAGGGC
TTTTAAAGGAATAGGTGACTACAAATGGATTTTTCTTTCCAATGAATGGTTTTTTTCACAAGTTT
CCCAAGGAAAGCATTCAATTATAGTCTGTTTTAA
Found at i:3758 original size:171 final size:171
Alignment explanation
Indices: 3371--4498 Score: 808
Period size: 171 Copynumber: 6.6 Consensus size: 171
3361 NNNNATGGGT
* * * * * * ***** * *
3371 GACTATAAATGGATTTTTGTTGCCAATGAATGTCGTTTTCTTCACATTGCTTGGCCTAGACATTC
1 GACTATAAATGAACTTTTCTTGCCAATGAATATCTTTTTCTTCACATTTCTCAAAGTAGATATTT
* * * * ** * * *
3436 AATTATAATATTTTTTTAACTAATAATGTAAAAAAGATTGGACCTAAAATAAATTTTGAGATTAT
66 AATTATAGT-TTGTTTTAACCAAAAATGTAAAAAA-ATTCAACTTAAAATCAATTATGAGATTAT
* * * *
3501 AAAAACCATTTAAAGCGAGTGATAAGGCTTTTGAACGAATAGGA
129 -AAAACCATTGAAAGCGAGTAATAAGACTTTTGAAGGAATAGGA
* * * * * **
3545 GACTATAAATGGACTTGTCTTTCAAATGAAT-GCTTGTTTCTTCATGTTTCTCAAAGTAGATATT
1 GACTATAAATGAACTTTTCTTGCCAATGAATATCTT-TTTCTTCACATTTCTCAAAGTAGATATT
3609 TAATTATAGTTTGTTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATA
65 TAATTATAGTTTGTTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATA
* * *
3674 AAACCATTGAAAGCGAGTAATAAGACTTTTGATGGAATGGGT
130 AAACCATTGAAAGCGAGTAATAAGACTTTTGAAGGAATAGGA
* * * * * *
3716 GATTATAAATGAACTTTTCTTGCCAATTAATACCTTTTTCTTCACATTTCTCGAGGTAGATATTC
1 GACTATAAATGAACTTTTCTTGCCAATGAATATCTTTTTCTTCACATTTCTCAAAGTAGATATTT
* * * *
3781 AATTCTAGTCTGTTTTAACTAAAAATGTGAAAAAATTCAACTTAAAATCAATTATGAGATTATAA
66 AATTATAGTTTGTTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAA
* * * *
3846 AACCA-TGTAAAGCAAGTAGTAAAACTTTTGAAGGAATAGGT
131 AACCATTG-AAAGCGAGTAATAAGACTTTTGAAGGAATAGGA
* * * * * * * *
3887 GACTATAAATGGACATTTGTTGCCAATGATTGTCTTTTCCTTCACATTTCT-TAAGCTAGACATT
1 GACTATAAATGAACTTTTCTTGCCAATGAATATCTTTTTCTTCACATTTCTCAAAG-TAGATATT
* * ** * * * * * *
3951 TAATTATAATATGTTTTAACCACTAATATAAAAAACAATTGAACCTAAAATAAATTTTAAGATTA
65 TAATTATAGTTTGTTTTAACCAAAAATGT-AAAAA-AATTCAACTTAAAATCAATTATGAGATTA
* ** * *
4016 TAAAACCATTTAAAATGAGTAATAAGGCTTTTGAAGAAATAGGA
128 TAAAACCATTGAAAGCGAGTAATAAGACTTTTGAAGGAATAGGA
* * * * * *
4060 GACTACAAATGGATTCTTTT-TTG-CAGA-AAATATCTTTTTGTTCACGTTTCTCAAGGTAGA-A
1 GACTATAAAT-GA-ACTTTTCTTGCCA-ATGAATATCTTTTTCTTCACATTTCTCAAAGTAGATA
* ** **
4121 GTTTAATTATAGTTGGTTTTAACCAAAAATGTAAGCAAATTCAACTTAAAATCAATTATGAGACC
63 -TTTAATTATAGTTTGTTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATT
** * ** * ** * * * * *
4186 ATAAAATAATTTAAATTGAATGGTAGGGCTTTTAAAGAAATGGGA
127 ATAAAACCATTGAAAGCGAGTAATAAGACTTTTGAAGGAATAGGA
** * * ** * * ** *
4231 GACTCCAAATGGATTTTTCTTTACAATGAATGGT-TTTTTCTACACATTT-TCCATGGTA-AGCA
1 GACTATAAATGAACTTTTCTTGCCAATGAAT-ATCTTTTTCTTCACATTTCT-CAAAGTAGA-TA
* * * * * * *
4293 TTCAATTATAGTCTGTTTTAACC-AAAATATAAAAAATTTCAAC-TAAAATCAATTTTAACATTA
63 TTTAATTATAGTTTGTTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTA
* * * * *
4356 TAAAATCATTTAAAACAAGTAATAAGACTTTTGAAAGAAT-GGA
128 TAAAACCATTGAAAGCGAGTAATAAGACTTTTGAAGGAATAGGA
** * * * ** *
4399 CGACTATAAATGGGCTTTTGTTGCCAATGAATGTCTTTTTCTTCATATTTCT-TGAGATAGACAT
1 -GACTATAAATGAACTTTTCTTGCCAATGAATATCTTTTTCTTCACATTTCTCAAAG-TAGATAT
* * * * *
4463 TCAATTATAATATGTGTTAACCAATAATGTAAAAAA
64 TTAATTATAGTTTGTTTTAACCAAAAATGTAAAAAA
4499 TATTGAANNN
Statistics
Matches: 752, Mismatches: 177, Indels: 54
0.77 0.18 0.05
Matches are distributed among these distances:
168 6 0.01
169 108 0.14
170 39 0.05
171 358 0.48
172 37 0.05
173 139 0.18
174 61 0.08
175 4 0.01
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (171 bp):
GACTATAAATGAACTTTTCTTGCCAATGAATATCTTTTTCTTCACATTTCTCAAAGTAGATATTT
AATTATAGTTTGTTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAA
AACCATTGAAAGCGAGTAATAAGACTTTTGAAGGAATAGGA
Found at i:4166 original size:344 final size:343
Alignment explanation
Indices: 3480--4499 Score: 846
Period size: 344 Copynumber: 3.0 Consensus size: 343
3470 AGATTGGACC
* * * * **
3480 TAAAATAAATTTTGAGATTATAAAAACCATTTAAAGCGAGTGATAAGGCTTTTGAACGAATAGGA
1 TAAAATCAATTATGAGATTATAAAAACCATGTAAAGCAAGTGATAAAACTTTTGAACGAATAGGA
* * ** *
3545 GACTATAAATGGACTTGTCTTTCAAATGAATGCTTGTTTCTTCATGTTTCTCAAAGTAGATATTT
66 GACTATAAATGGACTTGTCTTGCAAATGAATGCTTGTTCCTTCACATTTCTCAAAGTAGACATTT
* * * * * *
3610 AATTATAGTTTGTTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAA
131 AATTATAATATGTTTTAACCAAAAATATAAAAAAATTCAACCTAAAATAAATTATAAGATTATAA
* * * * * * *
3675 AACCATTGAAAGCGAGTAATAAGACTTTTGATGGAATGGGTGATTATAAATGAACTTTTCTTGCC
196 AACCATTGAAAACGAGTAATAAGACTTTTGAAGAAATAGGAGACTACAAATGAACTTTTCTTGCC
* * * *
3740 AATTAATACCTTTTTCTTCACATTTCTCGAGGTAGATATTCAATTCTAGTCTGTTTTAACTAAAA
261 AATAAATACCTTTTTCTTCACATTTCTCAAGGTAGATATTCAATTATAGTCTGTTTTAACCAAAA
3805 ATGTGAAAAAATTCAACT
326 ATGTGAAAAAATTCAACT
*
3823 TAAAATCAATTATGAGATTAT-AAAACCATGTAAAGCAAGT-AGTAAAACTTTTGAAGGAATAGG
1 TAAAATCAATTATGAGATTATAAAAACCATGTAAAGCAAGTGA-TAAAACTTTTGAACGAATAGG
* * * * *
3886 TGACTATAAATGGACATT-TGTTGCCAATGATTGTCTT-TTCCTTCACATTTCT-TAAGCTAGAC
65 AGACTATAAATGGAC-TTGTCTTGCAAATGAATG-CTTGTTCCTTCACATTTCTCAAAG-TAGAC
** * *
3948 ATTTAATTATAATATGTTTTAACCACTAATATAAAAAACAATTGAACCTAAAATAAATTTTAAGA
127 ATTTAATTATAATATGTTTTAACCAAAAATAT-AAAAA-AATTCAACCTAAAATAAATTATAAGA
* * * *
4013 TTATAAAACCATTTAAAATGAGTAATAAGGCTTTTGAAGAAATAGGAGACTACAAATGGATTCTT
190 TTATAAAACCATTGAAAACGAGTAATAAGACTTTTGAAGAAATAGGAGACTACAAAT-GA-ACTT
* * * *
4078 TT-TTG-CAGA-AAATATCTTTTTGTTCACGTTTCTCAAGGTAGA-AGTTTAATTATAGT-TGGT
253 TTCTTGCCA-ATAAATACCTTTTTCTTCACATTTCTCAAGGTAGATA-TTCAATTATAGTCT-GT
*
4138 TTTAACCAAAAATGT-AAGCAAATTCAACT
315 TTTAACCAAAAATGTGAA-AAAATTCAACT
** * * *** *
4167 TAAAATCAATTATGAGACCATAAAATA--ATTTAAATTG-AA-TGGTAGGGCTTTT-AAAGAAAT
1 TAAAATCAATTATGAGATTATAAAA-ACCATGTAAA--GCAAGTGATAAAACTTTTGAACG-AAT
* ** * * * * * * * **
4227 GGGAGACTCCAAATGGATTTTTCTT-TACAATGAATGGTTTTTTCTACACATTT-TCCATGGTA-
62 AGGAGACTATAAATGGACTTGTCTTGCA-AATGAATGCTTGTTCCTTCACATTTCT-CAAAGTAG
* * * * * * *
4289 AGCATTCAATTATAGTCTGTTTTAACC-AAAATATAAAAAATTTCAA-CTAAAATCAATTTTAAC
125 A-CATTTAATTATAATATGTTTTAACCAAAAATATAAAAAAATTCAACCTAAAATAAATTATAAG
* * * * **
4352 ATTATAAAATCATTTAAAACAAGTAATAAGACTTTTGAA-AGAAT-GGACGACTATAAATGGGCT
189 ATTATAAAACCATTGAAAACGAGTAATAAGACTTTTGAAGA-AATAGGA-GACTACAAATGAACT
* * ** * ** * * * * *
4415 TTTGTTGCCAATGAATGTCTTTTTCTTCATATTTCTTGAGATAGACATTCAATTATAATATGTGT
252 TTTCTTGCCAATAAATACCTTTTTCTTCACATTTCTCAAGGTAGATATTCAATTATAGTCTGTTT
*
4480 TAACCAATAATGT-AAAAAAT
317 TAACCAAAAATGTGAAAAAAT
4500 ATTGAANNNN
Statistics
Matches: 547, Mismatches: 99, Indels: 66
0.77 0.14 0.09
Matches are distributed among these distances:
338 5 0.01
339 13 0.02
340 116 0.21
341 11 0.02
342 108 0.20
343 47 0.09
344 228 0.42
345 12 0.02
346 7 0.01
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.36
Consensus pattern (343 bp):
TAAAATCAATTATGAGATTATAAAAACCATGTAAAGCAAGTGATAAAACTTTTGAACGAATAGGA
GACTATAAATGGACTTGTCTTGCAAATGAATGCTTGTTCCTTCACATTTCTCAAAGTAGACATTT
AATTATAATATGTTTTAACCAAAAATATAAAAAAATTCAACCTAAAATAAATTATAAGATTATAA
AACCATTGAAAACGAGTAATAAGACTTTTGAAGAAATAGGAGACTACAAATGAACTTTTCTTGCC
AATAAATACCTTTTTCTTCACATTTCTCAAGGTAGATATTCAATTATAGTCTGTTTTAACCAAAA
ATGTGAAAAAATTCAACT
Found at i:6104 original size:172 final size:171
Alignment explanation
Indices: 5722--6107 Score: 389
Period size: 171 Copynumber: 2.3 Consensus size: 171
5712 NNNNNNNNNG
* * * * *
5722 AGTAATAAGGCTTTTGATA-GAATGGGTGATTATAAATGAACTTTTCTTGCCAATTAATACCTTT
1 AGTAATAAGGCTTTTGA-AGGAATAGGAGACTATAAATGGACTTTTCTTGCCAATGAATACCTTT
* * ** * *
5786 TTCTTCACGTTTCTAGAGGTAGATATTCAATTATAGTCTGTTTTAACTAAAAAAGTGAAAAAATT
65 TTCTTCACATTGCTAGACCTAGACATTCAATTATAATCTGTTTTAACTAAAAAAGTGAAAAAATT
* *
5851 CAACTTAAAATAAATTATGAGATTATAAAACCATGCAAAGTA
130 CAACCTAAAATAAATTATGAGATTATAAAACCATGCAAAGGA
********** * * **
5893 AGTAATAAGGCTTTTGAAGGAATNNNNNNNNNNAAATGGACTTTTGTTGCCAATGATTGTCTTTT
1 AGTAATAAGGCTTTTGAAGGAATAGGAGACTATAAATGGACTTTTCTTGCCAATGAATACCTTTT
* * * * *
5958 TCTTCACATTGCTTGACCTAGACATTCAATTATAATTTTTTTTAACTAATAAAGTAGAAAAGATT
66 TCTTCACATTGCTAGACCTAGACATTCAATTATAATCTGTTTTAACTAAAAAAGT-GAAAAAATT
** * **
6023 GGACCTAAAATAAATTTTGAGATTATAAAACCATTTAAAGCGA
130 CAACCTAAAATAAATTATGAGATTATAAAACCATGCAAAG-GA
*
6066 A-TGATAAGGCTTTTGAAGGAATAGGAGACTATAAATGGACTT
1 AGTAATAAGGCTTTTGAAGGAATAGGAGACTATAAATGGACTT
6108 NNNNNNNNNN
Statistics
Matches: 167, Mismatches: 45, Indels: 5
0.77 0.21 0.02
Matches are distributed among these distances:
170 1 0.01
171 92 0.55
172 72 0.43
173 2 0.01
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.34
Consensus pattern (171 bp):
AGTAATAAGGCTTTTGAAGGAATAGGAGACTATAAATGGACTTTTCTTGCCAATGAATACCTTTT
TCTTCACATTGCTAGACCTAGACATTCAATTATAATCTGTTTTAACTAAAAAAGTGAAAAAATTC
AACCTAAAATAAATTATGAGATTATAAAACCATGCAAAGGA
Done.