Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397509.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1106.0, 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: 11141
ACGTcount: A:0.30, C:0.09, G:0.11, T:0.28
Warning! 2432 characters in sequence are not A, C, G, or T
Found at i:595 original size:174 final size:171
Alignment explanation
Indices: 296--670 Score: 420
Period size: 174 Copynumber: 2.2 Consensus size: 171
286 NNNNNNNNNN
* * *
296 TAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATAGGCGACTATAAATAGGCTTTTTTT
1 TAAAACCATTTAAAGAGAGTAATAAGGCTTTTGAAAGAATAGGCGACTATAAATAGACTTTTCTT
* * *
361 GCTAATGAATATATTTTTCTCCACATTTCTCGAGATAAGCATTCAATTATAGCTTGTTTTAACTA
66 GCTAATGAATACATTTTTCTCCACATTTATCGAGAGAAGCATTCAATTATAGCTTGTTTTAA-TA
** * * *
426 AAAA-TTTAAAAAAATAATTGACCATAAATTCAATTTTGAGATAA
130 AAAAGTGCAAAAAAAT--TTAACC-TAAAATCAATTATGAGATAA
* * * * *
470 TAAAATCATTTAAAGTGAGTAATAAAGCTTTT-AAAGAA-ATGGTTGACTATAAGTAGACTTTTC
1 TAAAACCATTTAAAGAGAGTAATAAGGCTTTTGAAAGAATA-GG-CGACTATAAATAGACTTTTC
* * **
533 TTG-TCAATGAATGCATTTTTCTTCATGTTTATCGAG-GAAGACATTCAATTATAG-TCTGTTTT
64 TTGCT-AATGAATACATTTTTCTCCACATTTATCGAGAGAAG-CATTCAATTATAGCT-TGTTTT
* *
595 AATAAAAAGTGCAAAAACATTTAACCTAAAATCAATTATGAGATTA
126 AATAAAAAGTGCAAAAAAATTTAACCTAAAATCAATTATGAGATAA
*
641 TAAAACCATTTAAAGAGAATAATAAGGCTT
1 TAAAACCATTTAAAGAGAGTAATAAGGCTT
671 NNNNNNNNNN
Statistics
Matches: 170, Mismatches: 25, Indels: 15
0.81 0.12 0.07
Matches are distributed among these distances:
171 43 0.25
172 6 0.04
173 19 0.11
174 102 0.60
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.35
Consensus pattern (171 bp):
TAAAACCATTTAAAGAGAGTAATAAGGCTTTTGAAAGAATAGGCGACTATAAATAGACTTTTCTT
GCTAATGAATACATTTTTCTCCACATTTATCGAGAGAAGCATTCAATTATAGCTTGTTTTAATAA
AAAGTGCAAAAAAATTTAACCTAAAATCAATTATGAGATAA
Found at i:1586 original size:170 final size:170
Alignment explanation
Indices: 811--2855 Score: 1363
Period size: 171 Copynumber: 11.9 Consensus size: 170
801 NNNNNNNNNN
** *
811 TAAAATCAATTATGTGATTATAAAATCATTTAAAGCGAGTAATAAGGCTTTTGACA-GAATGGGT
1 TAAAATCAATTATCAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGA-AGGAATGGGT
* * * * ** * *
875 AACTATAAATAGACTTTTCTTGCCAATGAATG-CATTTTCTTTCACATTTCTCAATGTA-AAACT
65 GACTATAAATGGACTTTTCTTACCAATGAATGCCTTTTTC-TTCATGTTTCTCAAGGTAGACA-T
* * * * *
938 ATCAATTATAGTCTGTTTTAATCAAAAATATAAAAACAAATTGACCA
128 -TCAATTATAATCTGTTTTAACCAAAAATGT-AAAA-AAATT-AACT
* * * * * * *********
985 TAGAATCAATTTTGAGATAATAAAATCATTTAAAACGAGTAATAAGGCTTTTGAAGNNNNNNNNN
1 TAAAATCAATTATCAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTG
* * ** * *
1050 NCTATAAATAGACTTTTCTTACCAATGAATGTATTTTTGTTCATGTTTCTCAAGGAAGACATTCA
66 ACTATAAATGGACTTTTCTTACCAATGAATGCCTTTTTCTTCATGTTTCTCAAGGTAGACATTCA
* * * * * *
1115 ATTATAGTCTGTCTTAA-CAAAAGTGTAAAATATTTAATT
131 ATTATAATCTGTTTTAACCAAAAATGTAAAAAAATTAACT
* * * * * * ***
1154 TAAAACCAATTATGAGATTATAAAACTACTTAAAGAGAGTAGTAAGGCTTTTGAAGGAATGGCAA
1 TAAAATCAATTATCAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTG
* * * * * * * *
1219 ATTATAAATGGACTTTTCTT-CTCAATTAATGGCTTTTACTACATGTTTCACAAGGCA-AGTATT
66 ACTATAAATGGACTTTTCTTAC-CAATGAATGCCTTTTTCTTCATGTTTCTCAAGGTAGA-CATT
* * ** *****
1282 CAATTATAGTATGTTTTAATGAAAAATGTAAAAAAATNNNNNN
129 CAATTATAATCTGTTTTAACCAAAAATGTAAAAAAAT-TAACT
**** ** * * * *
1325 NNNNATCAATTATGTGATTATAAAACTATTTAAAGCGAATAATAAGGCTTTTTAAAAGAATGGGT
1 TAAAATCAATTATCAGATTATAAAACCATTTAAAGCGAGTAATAAGGC-TTTTGAAGGAATGGGT
* * * * * * *
1390 GACTATGAGTGGACTTTTATTGCCAATGAATACCTTTTTCTTCATGTTGCTCAAGGTAGACATTT
65 GACTATAAATGGACTTTTCTTACCAATGAATGCCTTTTTCTTCATGTTTCTCAAGGTAGACATTC
* * **
1455 AATTATAATCTGTTTTAACCAAAAATCTAGAAAAATTAGTT
130 AATTATAATCTGTTTTAACCAAAAATGTAAAAAAATTAACT
* * * * * ** *
1496 TAAAATCAATTATCAGTTTGTAAAACCATTTAAAGCAAGTAATAAGACTTTCGAAGGTTTGCGTG
1 TAAAATCAATTATCAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTG
* * * * * ** *
1561 ACTATAAGTGGACTTTCCCTGCCAATGAATGCCTTTTTTTTCACATTTCTCAAGGTAGACATTTA
66 ACTATAAATGGACTTTTCTTACCAATGAATGCCTTTTTCTTCATGTTTCTCAAGGTAGACATTCA
* * * * **
1626 ATTA-AGTCTATCTTAACCAAAAACGTAAAAAAACTCGACT
131 ATTATAATCTGTTTTAACCAAAAATGTAAAAAAA-TTAACT
* * * *
1666 TAAAATCAATTATGAGACTGTAAAACCATTTAAAGCGAG-AATTAAGTCTTTTGAAGGAATGGGT
1 TAAAATCAATTATCAGATTATAAAACCATTTAAAGCGAGTAA-TAAGGCTTTTGAAGGAATGGGT
* * * * * * * *
1730 GACTATAAATGGATTTTTCTTACCAATAAATGCTTTTTCTCTTCATGCTTATCCAGGTTGACAGT
65 GACTATAAATGGACTTTTCTTACCAATGAATGCCTTTT-TCTTCATGTTTCTCAAGGTAGACATT
*
1795 CAATTATAATCTG-TTTAAGCCAAAAATGTAAAAAAATCAACT
129 CAATTATAATCTGTTTTAA-CCAAAAATGTAAAAAAATTAACT
* * * ** **********
1837 TAAAATCAATTATAAAATTATAAAACTATTTAAATAGNNNNNNNNNNCTTTTGAAGGAATGGGTG
1 TAAAATCAATTATCAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTG
* * * * * **
1902 ACTATAAATGGACTTTTCTTGCTAGTGAATGTCTTTTTCTTCATATTTCTTGAGGTAGACATTCA
66 ACTATAAATGGACTTTTCTTACCAATGAATGCCTTTTTCTTCATGTTTCTCAAGGTAGACATTCA
* * * * **
1967 ATT-TAGTCTGTTTTAAACAAAATTGTAAAAAACTTCGGCT
131 ATTATAATCTGTTTTAACCAAAAATGTAAAAAAATT-AACT
* * * * * * *
2007 GAAAATCAATTATGAGATTGTAAAACTATTTAAAGCGAGTAGTAAGGCTTTTGAGGGAATGTGTG
1 TAAAATCAATTATCAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTG
* **
2072 ACTATAAATGGACTTTTCTTACCAATGAATGCTTTTTTTCTTCATGTTTCTCAAGAAAGACATTC
66 ACTATAAATGGACTTTTCTTACCAATGAATGC-CTTTTTCTTCATGTTTCTCAAGGTAGACATTC
* * * * *
2137 AATTACAATTTGTTTGAGCCAAAAATGTAAAACAATTTAACT
130 AATTATAATCTGTTTTAACCAAAAATGTAAAA-AAATTAACT
* * *
2179 TAAAATCAATTATGC-GATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGTAATAGGT
1 TAAAATCAATTAT-CAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGT
* * * * ** * *
2243 GACTATAAATAGACTTTTCTTACCAATGAATGCTTTTTTGCTTTATGTCTCTTGAGGTAAACATC
65 GACTATAAATGGACTTTTCTTACCAATGAATGCCTTTTT-CTTCATGTTTCTCAAGGTAGACATT
* *
2308 CAATTATAATTTG-TTTAAGCCAAAAATATAAAAAAATCTAACT
129 CAATTATAATCTGTTTTAA-CCAAAAATGTAAAAAAAT-TAACT
* * * *
2351 T-AAATCAATTA-CGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCCTTTGAAGGAATAGTT
1 TAAAATCAATTATC-AGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGT
* ** ** ** **
2414 GACTATAAATAGG-CTTTTATGGCCAATGAATGAATTTTTCTTCATACTTCTTGA-GTAAGACAT
65 GACTATAAAT-GGACTTTTCTTACCAATGAATGCCTTTTTCTTCATGTTTCTCAAGGT-AGACAT
* * * * * * *
2477 TCAAATATAGTCAGTTTTAACTAAAAATATCAAAAACAATTGACCA
128 TCAATTATAATCTGTTTTAACCAAAAATGT-AAAAA-AATT-AACT
* * * ********* * * * *
2523 TAAAATCAATTTTGAGATAATANNNNNNNNNNAAA-TGAGTAATAAGGCTTTTGAAGCAATAGTT
1 TAAAATCAATTATCAGATTATA-AAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGT
* * * * * *
2587 GACTATAAATAGACTTTTCTCACCAATGAATGCATTTTTGTTCATGTTTCTAAAGGAAGACATTC
65 GACTATAAATGGACTTTTCTTACCAATGAATGCCTTTTTCTTCATGTTTCTCAAGGTAGACATTC
* * * * *
2652 AATTATAGTCTGTCTTAA-CAAAAGGTGTAAAAATATTCAATT
130 AATTATAATCTGTTTTAACCAAAA-ATGTAAAAAAATT-AACT
* *********** * **
2694 TAAAATCAATTATGAGATTATAAAANNNNNNNNNNAGAGTAGTAAGGCTTTTGAAGGAATGGCAG
1 TAAAATCAATTATCAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTG
* * * * * * * * *
2759 ACTATAAATGGACTTTTTTTTCTCAATTAATGACTTTTACTACACGTTTCTCAAGGAAGGCATTC
66 ACTATAAATGGACTTTTCTTAC-CAATGAATGCCTTTTTCTTCATGTTTCTCAAGGTAGACATTC
* * ** *
2824 AATTATAGTATGTTTTAATGAAAAATATAAAA
130 AATTATAATCTGTTTTAACCAAAAATGTAAAA
2856 NNNNNNNNNN
Statistics
Matches: 1459, Mismatches: 370, Indels: 86
0.76 0.19 0.04
Matches are distributed among these distances:
168 2 0.00
169 160 0.11
170 318 0.22
171 394 0.27
172 342 0.23
173 140 0.10
174 97 0.07
175 6 0.00
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.34
Consensus pattern (170 bp):
TAAAATCAATTATCAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTG
ACTATAAATGGACTTTTCTTACCAATGAATGCCTTTTTCTTCATGTTTCTCAAGGTAGACATTCA
ATTATAATCTGTTTTAACCAAAAATGTAAAAAAATTAACT
Found at i:1699 original size:341 final size:335
Alignment explanation
Indices: 811--2504 Score: 1059
Period size: 341 Copynumber: 5.0 Consensus size: 335
801 NNNNNNNNNN
** * * * ** * *
811 TAAAATCAATTATGTGATTATAAAATCATTTAAAGCGAGTAATAAGGCTTTTGACAGAATGGGTA
1 TAAAATCAATTATCAGATTATAAAACCATTTAAAG-AAGTAATAAGACTTTTGA-AGGTTTGGTG
* * * *
876 ACTATAAATAGACTTTTCTTGCCAATGAATGCATTTTCTTTCACATTTCTCAATGTA-AAACTAT
64 ACTATAAATGGACTTTTCTTGCCAATGAATGC-TTTTTTTTCACATTTCTCAAGGTAGACA-T-T
* * * ** * * *
940 CAATTATAGTCTGTTTTAATCAAAAATATAAAAACAAATT-GACCAT-AGAATCAATTTTGAGAT
126 CAATTA-AGTCTATCTTAAACAAAAACGT-AAAA-AACTTCGA-C-TGAAAATCAATTATGAGAT
** * * ********** *
1003 AATAAAA-TCATTTAAAACGAGTAATAAGGCTTTTGAAGNNNNNNNNNNCTATAAATAGACTTTT
186 TGTAAAACT-ATTTAAAGCGAATAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTT
* * * *
1067 CTTACCAATGAATG-TATTTTTGTTCATGTTTCTCAAGGAAGACATTCAATTATAGTCTGTCTTA
250 CTTACCAATGAATGCT-TTTTTCTTCATG-TTCTCAAGGTAGACATTCAATTATAATCTGTTTTA
* * *
1131 A-CAAAAGTGTAAAATATTTAATT
313 ACCAAAAATGTAAAA-AATTAACT
* * * * * * ** **
1154 TAAAACCAATTATGAGATTATAAAACTACTTAAAGAGAGTAGTAAGGCTTTTGAAGGAATGGCAA
1 TAAAATCAATTATCAGATTATAAAACCATTTAAAGA-AGTAATAAGACTTTTGAAGGTTTGG-TG
* * ** * ** * * *
1219 ATTATAAATGGACTTTTCTT-CTCAATTAATGGCTTTTACTACATGTTTCACAAGGCA-AGTATT
64 ACTATAAATGGACTTTTCTTGC-CAATGAAT-GCTTTTTTTTCACATTTCTCAAGGTAGA-CATT
* * * ** * * ********** * *
1282 CAATTATAGTATGTTTTAATGAAAAATGTAAAAAAATNNNNNNNNNNATCAATTATGTGATTATA
126 CAATTA-AGTCTATCTTAAACAAAAACGTAAAAAACTTCGACTGAAAATCAATTATGAGATTGTA
* * * * * *
1347 AAACTATTTAAAGCGAATAATAAGGCTTTTTAAAAGAATGGGTGACTATGAGTGGACTTTTATTG
190 AAACTATTTAAAGCGAATAATAAGGC-TTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTA
* * *
1412 CCAATGAATACCTTTTTCTTCATGTTGCTCAAGGTAGACATTTAATTATAATCTGTTTTAACCAA
254 CCAATGAATGCTTTTTTCTTCATGTT-CTCAAGGTAGACATTCAATTATAATCTGTTTTAACCAA
* **
1477 AAATCTAGAAAAATTAGTT
318 AAATGTA-AAAAATTAACT
* * *
1496 TAAAATCAATTATCAGTTTGTAAAACCATTTAAAGCAAGTAATAAGACTTTCGAAGGTTTGCGTG
1 TAAAATCAATTATCAGATTATAAAACCATTTAAAG-AAGTAATAAGACTTTTGAAGGTTTG-GTG
* * * *
1561 ACTATAAGTGGACTTTCCCTGCCAATGAATGCCTTTTTTTTCACATTTCTCAAGGTAGACATTTA
64 ACTATAAATGGACTTTTCTTGCCAATGAATG-CTTTTTTTTCACATTTCTCAAGGTAGACATTCA
* * *
1626 ATTAAGTCTATCTTAACCAAAAACGTAAAAAAAC-TCGACTTAAAATCAATTATGAGACTGTAAA
128 ATTAAGTCTATCTTAAACAAAAACGT-AAAAAACTTCGACTGAAAATCAATTATGAGATTGTAAA
* * * *
1690 ACCATTTAAAGCGAGA-ATTAAGTCTTTTGAAGGAATGGGTGACTATAAATGGATTTTTCTTACC
192 ACTATTTAAAGCGA-ATAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTACC
* * * * *
1754 AATAAATGCTTTTTCTCTTCATGCTTATCCAGGTTGACAGTCAATTATAATCTG-TTTAAGCCAA
256 AATGAATGCTTTTT-TCTTCATG-TTCTCAAGGTAGACATTCAATTATAATCTGTTTTAA-CCAA
*
1818 AAATGTAAAAAAATCAACT
318 AAATGT-AAAAAATTAACT
* * * * ******** * *
1837 TAAAATCAATTATAAAATTATAAAACTATTTAAA-TAGNNNNNNNNNNCTTTTGAAGGAATGGGT
1 TAAAATCAATTATCAGATTATAAAACCATTTAAAGAAG--TAATAAGACTTTTGAAGG-TTTGGT
* * * * **
1901 GACTATAAATGGACTTTTCTTGCTAGTGAATGTCTTTTTCTTCATATTTCTTGAGGTAGACATTC
63 GACTATAAATGGACTTTTCTTGCCAATGAATG-CTTTTTTTTCACATTTCTCAAGGTAGACATTC
* * * ** *
1966 AATTTAGTCTGTTTTAAACAAAATTGTAAAAAACTTCGGCTGAAAATCAATTATGAGATTGTAAA
127 AATTAAGTCTATCTTAAACAAAAACGTAAAAAACTTCGACTGAAAATCAATTATGAGATTGTAAA
* * * *
2031 ACTATTTAAAGCGAGTAGTAAGGCTTTTGAGGGAATGTGTGACTATAAATGGACTTTTCTTACCA
192 ACTATTTAAAGCGAATAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTACCA
** * * * *
2096 ATGAATGCTTTTTTTCTTCATGTTTCTCAAGAAAGACATTCAATTACAATTTGTTTGAGCCAAAA
257 ATGAATGC-TTTTTTCTTCATG-TTCTCAAGGTAGACATTCAATTATAATCTGTTTTAACCAAAA
2161 ATGTAAAACAATTTAACT
320 ATGTAAAA-AA-TTAACT
* * *
2179 TAAAATCAATTATGC-GATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAA-GTAATAGG
1 TAAAATCAATTAT-CAGATTATAAAACCATTTAAAG-AAGTAATAAGACTTTTGAAGGT--TTGG
* * * ** * ** *
2242 TGACTATAAATAGACTTTTCTTACCAATGAATGCTTTTTTGCTTTATGTCTCTTGAGGTAAACAT
62 TGACTATAAATGGACTTTTCTTGCCAATGAATGCTTTTTT--TTCACATTTCTCAAGGTAGACAT
* * * * * ** * * * *
2307 CCAATTATAATTTGT-TTAAGCCAAAAATATAAAAAA-ATCTAACT-TAAATCAATTACGAGATT
125 TCAATTA-AGTCTATCTTAA-ACAAAAACGTAAAAAACTTC-GACTGAAAATCAATTATGAGATT
* * * * * * * *
2369 ATAAAACCATTTAAAGTGAGTAATAAGGCCTTTGAAGGAATAGTTGACTATAAATAGG-CTTTTA
187 GTAAAACTATTTAAAGCGAATAATAAGGCTTTTGAAGGAATGGGTGACTATAAAT-GGACTTTTC
** ** * ** * * *
2433 TGGCCAATGAATGAATTTTTCTTCATACTTCTTGA-GTAAGACATTCAAATATAGTCAGTTTTAA
251 TTACCAATGAATGCTTTTTTCTTCAT-GTTCTCAAGGT-AGACATTCAATTATAATCTGTTTTAA
*
2497 CTAAAAAT
314 CCAAAAAT
2505 ATCAAAAACA
Statistics
Matches: 1050, Mismatches: 255, Indels: 93
0.75 0.18 0.07
Matches are distributed among these distances:
339 2 0.00
340 103 0.10
341 432 0.41
342 281 0.27
343 205 0.20
344 27 0.03
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.35
Consensus pattern (335 bp):
TAAAATCAATTATCAGATTATAAAACCATTTAAAGAAGTAATAAGACTTTTGAAGGTTTGGTGAC
TATAAATGGACTTTTCTTGCCAATGAATGCTTTTTTTTCACATTTCTCAAGGTAGACATTCAATT
AAGTCTATCTTAAACAAAAACGTAAAAAACTTCGACTGAAAATCAATTATGAGATTGTAAAACTA
TTTAAAGCGAATAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTACCAATGA
ATGCTTTTTTCTTCATGTTCTCAAGGTAGACATTCAATTATAATCTGTTTTAACCAAAAATGTAA
AAAATTAACT
Found at i:3254 original size:170 final size:171
Alignment explanation
Indices: 2951--3478 Score: 537
Period size: 170 Copynumber: 3.1 Consensus size: 171
2941 NNNNNNNNNN
* * * * * * ** *
2951 TTTCTCGAGGTAGACATTCAATTATAATCTATTTTAACCAAAAATCTAAAAAAAAATTGGCTTAA
1 TTTCTTGAGGTAGACATTCAATTATAATCTGTCTAAACCAAAAAACT-AAAATAACCTAGCTTAA
* * * ** * **
3016 AATCAATTATCA-ATTTGTAAAACCATTTAAAGCAAGTAATAAGGCTTTCGAAGGCTTACGTGAC
65 AATCAATTATCAGA-TTGTAAAACCATTTAAAGTAAGTAATAAGACTTTTGAAGGAATGCGAAAC
*
3080 TATAAATGGACTTTCCCTGCTAATGAATGTCTTTTTTTTCACA
129 TATAAATGGACTTTTCCTGCTAATGAATGTCTTTTTTTTCACA
* * * * * * *
3123 TTTCTCGAGGTAGACATTCAATTA-AGTCTGTCTAAACTAAAAAAGTTAAA-AACCTCGACTTGA
1 TTTCTTGAGGTAGACATTCAATTATAATCTGTCTAAACCAAAAAACTAAAATAACCTAG-CTTAA
* * * * *
3186 AATCAATTATGAGATTGTACAACCATTTAAAGTGAGTAATGAGGCTTTTGAAGGAATG-GAAAAC
65 AATCAATTATCAGATTGTAAAACCATTTAAAGTAAGTAATAAGACTTTTGAAGGAATGCG-AAAC
* * * * * *
3250 TATAAATGAACTTTTCTTGCCAATGAATGCCTTTTTCTTCA-T
129 TATAAATGGACTTTTCCTGCTAATGAATGTCTTTTTTTTCACA
* * * * * **
3292 TTTTTTGAGGTAAACATTCAATTATAATCTGTTTTAACCAAAAATCTAAAATAATTTAGCTTAAA
1 TTTCTTGAGGTAGACATTCAATTATAATCTGTCTAAACCAAAAAACTAAAATAACCTAGCTTAAA
* * ** **
3357 ATCAATTATCAGTTTGTAAAATCATTTAAAGTAAGTAATAAGACTTTTGAAGGCTTGCGTGACTA
66 ATCAATTATCAGATTGTAAAACCATTTAAAGTAAGTAATAAGACTTTTGAAGGAATGCGAAACTA
3422 TAAATGGACTTTTCCTGCTAATGAATGTC-TTTTTTTCACA
131 TAAATGGACTTTTCCTGCTAATGAATGTCTTTTTTTTCACA
3462 TTTCTTGAGGTAGACAT
1 TTTCTTGAGGTAGACAT
3479 NNNNNNNNNN
Statistics
Matches: 286, Mismatches: 63, Indels: 16
0.78 0.17 0.04
Matches are distributed among these distances:
169 34 0.12
170 207 0.72
171 21 0.07
172 24 0.08
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (171 bp):
TTTCTTGAGGTAGACATTCAATTATAATCTGTCTAAACCAAAAAACTAAAATAACCTAGCTTAAA
ATCAATTATCAGATTGTAAAACCATTTAAAGTAAGTAATAAGACTTTTGAAGGAATGCGAAACTA
TAAATGGACTTTTCCTGCTAATGAATGTCTTTTTTTTCACA
Found at i:5498 original size:169 final size:169
Alignment explanation
Indices: 4989--5765 Score: 673
Period size: 169 Copynumber: 4.6 Consensus size: 169
4979 NNNNNNNNNN
* * * * *
4989 TTCTTGCCAATGAATGCATTTTTCTTCACGTTTCTCAAAGTAGACATTCAATTAGTCTTTTTTAA
1 TTCTTGCCAATGAATACATTTTTCTTCATGTTTCTCGAGGTAGACATTCAATTAGTCTGTTTTAA
* * * * * *
5054 CCCAAAATGTAAAAAAAGTTGAACAT-AAATCAATTTTGACATAAT-AAAGTATTTAAAAAGAGT
66 CCAAAAATGT-AAAAAAGTTCAACATAAAATCAATTATGAGATAATAAAACTATTTAAAGAGAGT
* *
5117 AATAAGGCTTTT-AATGGAATGTG-TGGCTATAAATGGACTT
130 AATAAGGCTTTTGAA-GGAATG-GATGACTATAAATAGACTT
* * * * * * *
5157 TTCTTACTAATGAATATAATTGTCTTCATGTTTCTCGAGGTAGACATTCAATTATAATCAG-TTT
1 TTCTTGCCAATGAATACATTTTTCTTCATGTTTCTCGAGGTAGACATTCAA-T-TAGTCTGTTTT
* * * * * ******
5221 AAGCTAAAAATATAAAAAA-TTCAGCTTAAAATCAATTATGAGATTATAAAACTATTTANNNNNN
64 AA-CCAAAAATGTAAAAAAGTTCAACATAAAATCAATTATGAGATAATAAAACTATTTAAAGAGA
**** * * *
5285 NNNNTAAGGCTTTTGAAGGAATGGGTAACTATAAATTGACTT
128 GTAATAAGGCTTTTGAAGGAATGGATGACTATAAATAGACTT
* *
5327 TTCTTGCCAATGAATACGTTTTTCTTC-TCGTTTCTAGAGGTAGACATTCAATTAGTCTGTTTTA
1 TTCTTGCCAATGAATACATTTTTCTTCAT-GTTTCTCGAGGTAGACATTCAATTAGTCTGTTTTA
* * * *
5391 ACTAAAAATGTAAAAAAGTTAAACATAAAATCAATTTTGACG-TAATAAAAGCT-TTTTAAGAGA
65 ACCAAAAATGTAAAAAAGTTCAACATAAAATCAATTATGA-GATAATAAAA-CTATTTAAAGAGA
* * * *
5454 GTAATAAGGCATTTGAAGGAATGCATGATTATAAATAAACTT
128 GTAATAAGGCTTTTGAAGGAATGGATGACTATAAATAGACTT
* * * * *
5496 TTCTTGCCAGTGAATGCCTTTTTCTTCATG-TTCTCGAGGTAGACATTCTATTTAGTGTGTTTTA
1 TTCTTGCCAATGAATACATTTTTCTTCATGTTTCTCGAGGTAGACATTC-AATTAGTCTGTTTTA
* * * * ** *
5560 A-AAAAAATGT-AAAAACTTCGACGTAAAATCAATTATGAGATTGTAAAACTATTTAAAGCGAGT
65 ACCAAAAATGTAAAAAAGTTCAACATAAAATCAATTATGAGATAATAAAACTATTTAAAGAGAGT
* *
5623 AGTCAA-GCTTTTGAAGAAATGGATGACTATAAATAGACTT
130 AAT-AAGGCTTTTGAAGGAATGGATGACTATAAATAGACTT
* * ** * *
5663 TTCTTACCAACGAATGATTTTTTTCTTCATGTTTCTCGACGTAGACATTCAATTATAATCTG-TT
1 TTCTTGCCAATGAAT-ACATTTTTCTTCATGTTTCTCGAGGTAGACATTCAA-T-TAGTCTGTTT
* * *
5727 TAAGCCAAAAATGTACAAAAAATTTAACTTAAAATCAAT
63 TAA-CCAAAAATGTA-AAAAAGTTCAACATAAAATCAAT
5766 NNNNNNNNNN
Statistics
Matches: 479, Mismatches: 105, Indels: 45
0.76 0.17 0.07
Matches are distributed among these distances:
166 3 0.01
167 82 0.17
168 107 0.22
169 157 0.33
170 101 0.21
171 10 0.02
173 19 0.04
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.36
Consensus pattern (169 bp):
TTCTTGCCAATGAATACATTTTTCTTCATGTTTCTCGAGGTAGACATTCAATTAGTCTGTTTTAA
CCAAAAATGTAAAAAAGTTCAACATAAAATCAATTATGAGATAATAAAACTATTTAAAGAGAGTA
ATAAGGCTTTTGAAGGAATGGATGACTATAAATAGACTT
Found at i:6129 original size:170 final size:168
Alignment explanation
Indices: 5853--6338 Score: 519
Period size: 170 Copynumber: 2.9 Consensus size: 168
5843 NNNNTTGAAG
* * *
5853 GAATGAAAAACTATAAATGGACTTTTCTTTCAAATAAATGAATTTTTCTACACGTTTCTCAAGGC
1 GAATGGAAAACTATAAATGGACTTTTC-TTCAAATAAATGAATTTTTCTACACTTTTCTCAAAGC
* * * * * * * **********
5918 AAGCATTCAATTATAGTATATTTTAATAAAAAATATAAAAAATTTAACTTAAAATNNNNNNNNNN
65 AGGCATTCAATTATTGTCTGTTTTAA-CAAAAATGTAAAAAATTCAACTTAAAATCAATTATCAA
*
5983 ATTATGAAACCATTTAAAGCGAGTAATAAGGCTTTGGAAA
129 ATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTGGAAA
* * * * *
6023 GAATAGG-AGACTATAAATAGACTTTTCTTCAAAATAAATTAATTTTTTTACACTTTTCCCAAAG
1 GAAT-GGAAAACTATAAATGGACTTTTCTTC-AAATAAATGAATTTTTCTACACTTTTCTCAAAG
* *
6087 CAGGCAATCAATTATTGTCTGTTTTAACAAAACACGTAAAAAATTCAACTTAAAATCAATTATCA
64 CAGGCATTCAATTATTGTCTGTTTTAACAAAA-ATGTAAAAAATTCAACTTAAAATCAATTATCA
* * *
6152 AATTATAAAACCCTTTAAAGCGAGTAATAAGGCTTTTGAAG
128 AATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTGGAAA
* * *
6193 GAATGGAAAACTATAAATGGACATTTCTTCTAAATAAATGAGTTTTTCTACA-TGTTTCTC-GAG
1 GAATGGAAAACTATAAATGGACTTTTCTTC-AAATAAATGAATTTTTCTACACT-TTTCTCAAAG
* * * *
6256 CCAGCCATTCAATTATTGTCTGTCTTAACGAAAAATGTAAAAAATTCAACTTGAAATCAATTATG
64 -CAGGCATTCAATTATTGTCTGTTTTAAC-AAAAATGTAAAAAATTCAACTTAAAATCAATTATC
*
6321 AGATTATAAAACCATTTA
127 AAATTATAAAACCATTTA
6339 NNNNNNNNNN
Statistics
Matches: 261, Mismatches: 48, Indels: 14
0.81 0.15 0.04
Matches are distributed among these distances:
169 12 0.05
170 244 0.93
171 5 0.02
ACGTcount: A:0.41, C:0.13, G:0.11, T:0.33
Consensus pattern (168 bp):
GAATGGAAAACTATAAATGGACTTTTCTTCAAATAAATGAATTTTTCTACACTTTTCTCAAAGCA
GGCATTCAATTATTGTCTGTTTTAACAAAAATGTAAAAAATTCAACTTAAAATCAATTATCAAAT
TATAAAACCATTTAAAGCGAGTAATAAGGCTTTGGAAA
Found at i:9015 original size:174 final size:160
Alignment explanation
Indices: 8812--9144 Score: 289
Period size: 172 Copynumber: 2.0 Consensus size: 160
8802 AAAGCCATTT
* *
8812 AAAGCGAGTAATAAGGCTTTTAGAAGAATGAGAGACTATAAAT-GAACTTTTCTTTGCCAATGAA
1 AAAGCGAGTAATAAGGCTTTGAGAAGAATGAGAGACTATAAATAG-ACTTTTC-TTGCAAATGAA
* * * * * * *
8876 TGCTTTTTTTTTTCATGTTTTTCAA-AGCAGACATTTAATTATAGTTTGTTTTAACCATAAATAT
64 TAC-TTTTTTCTACACGTTTCTCAAGA-CAGACATTCAATTATAGTTTGTCTTAACCA-AAA-AT
*
8940 -TAAAAA-AACTGAAAATAAAATTAATTTTGAGATA
125 GTAAAAATAACTGAAAATAAAATCAATTTTGAGATA
* *
8974 NNNNNNNNNNNNAAAGTGAGTAATAAGGCTATTGA-AAGAATGAGAGACTATAAATAGATTTTTC
1 ------------AAAGCGAGTAATAAGGCT-TTGAGAAGAATGAGAGACTATAAATAGACTTTTC
* * * * *
9038 TTGTAAATGAATACTTTTTTCTACACGTTTCTCGAGATAGAGATTCAATTATAGTTTGTCTTAAT
53 TTGCAAATGAATACTTTTTTCTACACGTTTCTCAAGACAGACATTCAATTATAGTTTGTCTTAAC
* *
9103 CAAAAATGTAAAAATAATTGAACATAAAATCAATTTTGAGAT
118 CAAAAATGTAAAAATAACTGAAAATAAAATCAATTTTGAGAT
9145 CATAAAATCA
Statistics
Matches: 135, Mismatches: 19, Indels: 12
0.81 0.11 0.07
Matches are distributed among these distances:
170 2 0.01
171 9 0.07
172 65 0.48
173 12 0.09
174 43 0.32
175 4 0.03
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.35
Consensus pattern (160 bp):
AAAGCGAGTAATAAGGCTTTGAGAAGAATGAGAGACTATAAATAGACTTTTCTTGCAAATGAATA
CTTTTTTCTACACGTTTCTCAAGACAGACATTCAATTATAGTTTGTCTTAACCAAAAATGTAAAA
ATAACTGAAAATAAAATCAATTTTGAGATA
Found at i:9367 original size:172 final size:172
Alignment explanation
Indices: 8993--9382 Score: 397
Period size: 172 Copynumber: 2.3 Consensus size: 172
8983 NNNAAAGTGA
* * * * * *
8993 GTAATAAGGCTATTGAAAGAATGAGAGACTATAAATAGATTTTTCTTGTAAATGAATACTTTTTT
1 GTAATAAGGCTATTGAAGGAATGAGTGACTATAAATGGACTTCTCTTATAAATGAATACTTTTTT
* *
9058 CTACACGTTTCTCGAGATAGAGATTCAATTATAGTTTGTCTTAATCAAAAATGTAAAAATAATTG
66 CTACACGTTTCTCGAGATAAAGATTCAATTATAGTTTATCTTAATCAAAAATGTAAAAATAATTG
9123 AACATAAAATCAATTTTGAGATCATAAAATCATTTAAAATGG
131 AACATAAAATCAATTTTGAGATCATAAAATCATTTAAAATGG
********** * * *
9165 GTAATANNNNNNNNNNAGGAATGTGTGACTATAAATGGACTTCTCTTATAACTGAATGCTTTTTT
1 GTAATAAGGCTATTGAAGGAATGAGTGACTATAAATGGACTTCTCTTATAAATGAATACTTTTTT
* * * * *
9230 CTTCATGTTT-TCTGAGGTAAATATTCAATTATAGTTTATCTTAA-CTAAAAATTTAAAAATAAT
66 CTACACGTTTCTC-GAGATAAAGATTCAATTATAGTTTATCTTAATC-AAAAATGTAAAAATAAT
**********
9293 TGAACATAAAATCAATTTTGAGANNNNNNNNNNATTTAAAATGG
129 TGAACATAAAATCAATTTTGAGATCATAAAATCATTTAAAATGG
* * *
9337 GTAATAAGGCTTTTGAAGGAATAAGTGACTATAAATGAACTTCTCT
1 GTAATAAGGCTATTGAAGGAATGAGTGACTATAAATGGACTTCTCT
9383 AGCAAAAGAA
Statistics
Matches: 167, Mismatches: 49, Indels: 4
0.76 0.22 0.02
Matches are distributed among these distances:
171 3 0.02
172 164 0.98
ACGTcount: A:0.37, C:0.09, G:0.14, T:0.35
Consensus pattern (172 bp):
GTAATAAGGCTATTGAAGGAATGAGTGACTATAAATGGACTTCTCTTATAAATGAATACTTTTTT
CTACACGTTTCTCGAGATAAAGATTCAATTATAGTTTATCTTAATCAAAAATGTAAAAATAATTG
AACATAAAATCAATTTTGAGATCATAAAATCATTTAAAATGG
Found at i:9709 original size:170 final size:160
Alignment explanation
Indices: 9507--9837 Score: 294
Period size: 170 Copynumber: 2.0 Consensus size: 160
9497 ATTTAAAGCG
* * * * * *
9507 AGTAATAAGGCATTTTAAGTAATAGGAGACTATAAAT-G-TTGGTTTCCTCCAAATAAATGGGTT
1 AGTAATAAGGCATTTTAAGGAATAGAAGACTATAAATAGACT--TTTCCTACAAACAAATGGATT
* * * * *
9570 TTTCTAGACGTTTCCTAAGGCAACCATTTAAGTATAGTATGTGTTAATAAAAAATAC-AAAATAT
64 TTTCCAGACATTTCCTAAGGCAACCATTCAAGTATAGTATGTGTTAATAAAAAAT-CTAAAAAAG
9634 TCAACTTAAAATCAATTATGAGATTATAAAACC
128 TCAACTTAAAATCAATTATGAGATTATAAAACC
*
9667 NNNNNNNNNNAGTAATAAGGC-TTTTGAAGGAAT-GTAAGACTATAAATAGACTTTTCTTACAAA
1 ----------AGTAATAAGGCATTTT-AAGGAATAG-AAGACTATAAATAGACTTTTCCTACAAA
* * * ** * * * *
9730 CAAATGGATTTTTCCATACATTTTCTGAGGCAGGCATTCAATTATAGTTTTTTTTAATAAAAAAT
54 CAAATGGATTTTTCCAGACATTTCCTAAGGCAACCATTCAAGTATAGTATGTGTTAATAAAAAAT
*
9795 CTAAAAAAGTCAACTTAAAATCAATTATGAGATTATAAGACC
119 CTAAAAAAGTCAACTTAAAATCAATTATGAGATTATAAAACC
9837 A
1 A
9838 TTTAAAGCGA
Statistics
Matches: 134, Mismatches: 22, Indels: 20
0.76 0.12 0.11
Matches are distributed among these distances:
160 1 0.01
169 6 0.04
170 125 0.93
171 1 0.01
172 1 0.01
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.33
Consensus pattern (160 bp):
AGTAATAAGGCATTTTAAGGAATAGAAGACTATAAATAGACTTTTCCTACAAACAAATGGATTTT
TCCAGACATTTCCTAAGGCAACCATTCAAGTATAGTATGTGTTAATAAAAAATCTAAAAAAGTCA
ACTTAAAATCAATTATGAGATTATAAAACC
Done.