Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398893.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2175.0, 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: 9423
ACGTcount: A:0.28, C:0.10, G:0.10, T:0.27
Warning! 2354 characters in sequence are not A, C, G, or T
Found at i:618 original size:170 final size:161
Alignment explanation
Indices: 343--669 Score: 347
Period size: 170 Copynumber: 2.0 Consensus size: 161
333 TTTAAATGGT
* * * * * *
343 TTTATAATCTTATAATTGATTTTACGCTGAATATTTTTACATTTTTAGTTAAAACAGATTATAAT
1 TTTATAATCTCATAAATAATTTTAAGCTGAATATTCTTACATTTTTAGTTAAAACAGAGTATAAT
* * * * * *
408 TGAATGTGTACCTCGAGAAATATGAAGAGAAAGGCATTCATTATCAAGAAAAGTCCATTTATAGT
66 TGAATGTGTACCTCGAGAAACATGAAGAAAAAGCCATTCATTAACAAAAAAAATCCATTTATAGT
*
473 CACC-AATCTTTCAAAAGCCTTATTACTCGC
131 CACCTAATCCTTCAAAAGCCTTATTACTCGC
* *
503 TTTANNNNNNNNNNTAATCTCATAAATAATTTTAAGTTGAATGTTCTTACATTTTTCA-TTAAAA
1 TTTA----------TAATCTCATAAATAATTTTAAGCTGAATATTCTTACATTTTT-AGTTAAAA
* *
567 TAGAGTATAATTGAATGTGTACCTC-ATGAAACAT-ATAGAAAAAGCCATTCATTAAGAAAAAAA
55 CAGAGTATAATTGAATGTGTACCTCGA-GAAACATGA-AGAAAAAGCCATTCATTAACAAAAAAA
*
630 ATCCATTTATAGTCACCTATTCCTTCAAAAGCCTTATTAC
118 ATCCATTTATAGTCACCTAATCCTTCAAAAGCCTTATTAC
670 AAGCTTTAAA
Statistics
Matches: 135, Mismatches: 18, Indels: 17
0.79 0.11 0.10
Matches are distributed among these distances:
160 4 0.03
169 2 0.01
170 108 0.80
171 21 0.16
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.35
Consensus pattern (161 bp):
TTTATAATCTCATAAATAATTTTAAGCTGAATATTCTTACATTTTTAGTTAAAACAGAGTATAAT
TGAATGTGTACCTCGAGAAACATGAAGAAAAAGCCATTCATTAACAAAAAAAATCCATTTATAGT
CACCTAATCCTTCAAAAGCCTTATTACTCGC
Found at i:4619 original size:170 final size:170
Alignment explanation
Indices: 3803--5104 Score: 854
Period size: 171 Copynumber: 7.6 Consensus size: 170
3793 NNNNNNNNNN
* * * * * **
3803 AAGGCTTTTGAAGGAATGGGTAACTATAAATGGACTTTTCTTCTCAATGAATGGATTTTCCTACA
1 AAGGCTTTTGAAGGAAT-GGTGACTATAAATAGACCTTTCTTATCAATGAATGGCTTTTTTTACA
* * ** * * * *
3868 TGTTTTTCTAAGAAAG-CATTTAATTATAGTCTGTTGTAATGCAAAAA-GTAAAAAAATTCAACT
65 CGTTTCTC-AAGGTAGACACTTAATTATAGTCTGTTTTAATG-AAAAATATAAAAAAATTTAACT
* * * * *
3931 GAAAATCAATTATGAGATTATGAAATCGTTTAAAGTGAGTAAT
128 TAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAAT
* ********* * * ** * * *
3974 AAAGCTTTTGAAGGAATGGNNNNNNNNNNATGGACTTTTCTTGCCAATGAAT-ACCTTTTTCATC
1 AAGGCTTTTGAAGGAATGG-TGACTATAAATAGACCTTTCTTATCAATGAATGGCTTTTTTTA-C
* * * * * * * *
4038 ATGTTTCTCGAGGTAAACA-TTCATTTATAGACTGTTTTAATAAAAAATGTGAAAAGAAATTCAA
64 ACGTTTCTCAAGGTAGACACTT-AATTATAGTCTGTTTTAATGAAAAATAT-AAAA-AAATTTAA
* ********** * *
4102 CTTAAAATTAATTATGAGATNNNNNNNNNNTTTAAAGTGACTAAT
126 CTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAAT
* * * * * *
4147 AAGGCTTTTGAAGAAATAGGTGAGTATAAATAGA-TTTTTTTTTCTAATGAATGGCTTTTTTTAA
1 AAGGCTTTTGAAGGAAT-GGTGACTATAAATAGACCTTTCTTATC-AATGAATGGCTTTTTTTAC
* * * * * *
4211 ACGTTTACT-AAGGTAGGCATTTAATTATAGTCTGGTGTAAAGTAAAATATAAAAAAAATTTAAC
64 ACGTTT-CTCAAGGTAGACACTTAATTATAGTCTGTTTTAATGAAAAATAT-AAAAAAATTTAAC
* * * * *
4275 TTAAAATCAATTATCATATTATAAAACTATTTAAAACAAGTAAT
127 TTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAAT
* * **
4319 AAGGGTTTTGAAGGAATGGATGACTATAAATAGACTTTTCTTA-CTAATGAAT-GCTTTTTTTTT
1 AAGGCTTTTGAAGGAATGG-TGACTATAAATAGACCTTTCTTATC-AATGAATGGCTTTTTTTAC
* * * * * * *
4382 TCGTTTCTCGAGGTA-A-ACTTTCATTTATAGTCTATTTTCA-GCAAAAATGTAAAAAACATTCA
64 ACGTTTCTCAAGGTAGACAC-TT-AATTATAGTCTGTTTTAATG-AAAAATATAAAAAA-ATTTA
* * *
4444 ACTTAAAA-CTAATTCTG-GTATTATAAAACCATTTAAAGGGAATAAT
125 ACTTAAAATC-AATTATGAG-ATTATAAAACCATTTAAAGCGAGTAAT
* *
4490 AAGAC-TTTGAAGGAATAGGTGACTATAAATAGACCTTTCTTATCAATGAATGGGTTTTTTTACA
1 AAGGCTTTTGAAGGAAT-GGTGACTATAAATAGACCTTTCTTATCAATGAATGGCTTTTTTTACA
* *
4554 CGTTTCTCAAGGTAGATACTTAATTATAGTCTGTTTTAATGATAAATATAAAAAAATTTAACTTA
65 CGTTTCTCAAGGTAGACACTTAATTATAGTCTGTTTTAATGAAAAATATAAAAAAATTTAACTTA
********** *
4619 AAATCAATTATGAGANNNNNNNNNNATTTAAAACGAGTAAT
130 AAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAAT
* * * *
4660 AAGGCTTTTGAAGGAATGGGTGGC-ATAACTGGA-CTTTCTTTTCTCAATGAATGGCTTTTTCTT
1 AAGGCTTTTGAAGGAAT-GGTGACTATAAATAGACCTTTC--TTATCAATGAATGGCTTTTT-TT
* * * * *
4723 -CACATTTCTCAAGGCA-AGCA-TTCAATTATAGTCTGTTTTACTAAAAAATATAAAAAAATTCA
62 ACACGTTTCTCAAGGTAGA-CACTT-AATTATAGTCTGTTTTAATGAAAAATATAAAAAAATTTA
* *
4785 ACTT-AAATCAATTATGAGATGATAAAACCATTTAAAGTGAGTAAT
125 ACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAAT
* * ** * * *
4830 AAGGCTTTTGAATGG-ATGAGTGACTATAAATGGACTTTTCTTGCCAATGAATAGCTTTCTCTAC
1 AAGGCTTTTGAA-GGAATG-GTGACTATAAATAGACCTTTCTTATCAATGAATGGCTTTTTTTAC
* * * * * * ** *
4894 ATGTTTCTCAAGGAAGGCACTCAATTATAGTCTGTTCTAATGAAGAATGCAAAAATATTTAACTT
64 ACGTTTCTCAAGGTAGACACTTAATTATAGTCTGTTTTAATGAAAAATATAAAAAAATTTAACTT
* *
4959 AAAATAAATTATGAGATTGTAAAACCATTTAAAGCGAGTAAT
129 AAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAAT
* * ** *
5001 AAGGCTATTGAAGGAATGGATGACTATAAATGGACCTTT-TT-TGCAAATGAATCCCTTGTTCTT
1 AAGGCTTTTGAAGGAATGG-TGACTATAAATAGACCTTTCTTAT-C-AATGAATGGCTT-TTTTT
* * *
5064 -CAAGTTTCTCGAGGTAGACA-TTCAATTATAGTCTCTTTTAA
62 ACACGTTTCTCAAGGTAGACACTT-AATTATAGTCTGTTTTAA
5105 CCAAAAATGT
Statistics
Matches: 871, Mismatches: 211, Indels: 98
0.74 0.18 0.08
Matches are distributed among these distances:
169 8 0.01
170 234 0.27
171 411 0.47
172 95 0.11
173 110 0.13
174 13 0.01
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.35
Consensus pattern (170 bp):
AAGGCTTTTGAAGGAATGGTGACTATAAATAGACCTTTCTTATCAATGAATGGCTTTTTTTACAC
GTTTCTCAAGGTAGACACTTAATTATAGTCTGTTTTAATGAAAAATATAAAAAAATTTAACTTAA
AATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAAT
Found at i:4855 original size:341 final size:340
Alignment explanation
Indices: 3803--5121 Score: 986
Period size: 341 Copynumber: 3.9 Consensus size: 340
3793 NNNNNNNNNN
* * * * * **
3803 AAGGCTTTTGAAGGAATGGGTAACTATAAATGGACTTTTCTTCTCAATGAATGGATTTTCCTACA
1 AAGGCTTTTGAAGG-ATAGGTGACTATAAATAGACTTTTCTTATCAATGAATGGCTTTTTTTACA
* * * * * * *
3868 TGTTTTTCTAA-GAAAGCATTTAATTATAGTCTGTTGTAATGCA-AAA-AGTAAAAAAATTCAAC
65 CGTTTCTC-AAGGTAGGCACTTAATTATAGTCTGTTCTAATG-ATAAATA-TAAAAAAATTTAAC
* * * *** * *
3930 TGAAAATCAATTATGAGATTATGAAA-TCGTTTAAAGTGAGTAATAAAGCTTTTGAAGGAATGGN
127 TTAAAATCAATTATGAGATTATAAAACT-ATTTAAAACAAGTAATAAGGCTTTTGAAGGAATGGA
********* * * * * * ** * *
3994 NNNNNNNNNATGGACTTTTCTTGCCAATGAATACCTTTTTCATCATGTTTCTCGAGGTAAACATT
191 TGACTATAAATAGACTTTTCTTACTAATGAAT-GCTTTTTCTTCACATTTCTCAAGGCAAACATT
* * * * * * *
4059 CATTTATAGACTGTTTTAATAAAAAATGTGAAAAGAA-ATTCAACTTAAAATTAATTATGAG-AT
255 CAATTATAGTCTATTTTCA-CAAAAATAT-AAAA-AACATTCAACTTAAAACTAATTATG-GTAT
********** *
4122 NNNNNNNNNNTTTAAAGTGACTAAT
316 GATAAAACCATTTAAAGTGAATAAT
* * * * *
4147 AAGGCTTTTGAAGAAATAGGTGAGTATAAATAGA-TTTTTTTTTCTAATGAATGGCTTTTTTTAA
1 AAGGCTTTTGAAG-GATAGGTGACTATAAATAGACTTTTCTTATC-AATGAATGGCTTTTTTTAC
* * * *
4211 ACGTTTACT-AAGGTAGGCATTTAATTATAGTCTGGTGTAAAG-TAAAATATAAAAAAAATTTAA
64 ACGTTT-CTCAAGGTAGGCACTTAATTATAGTCTGTTCTAATGAT-AAATAT-AAAAAAATTTAA
* * *
4274 CTTAAAATCAATTATCATATTATAAAACTATTTAAAACAAGTAATAAGGGTTTTGAAGGAATGGA
126 CTTAAAATCAATTATGAGATTATAAAACTATTTAAAACAAGTAATAAGGCTTTTGAAGGAATGGA
* ** * * * *
4339 TGACTATAAATAGACTTTTCTTACTAATGAATGCTTTTTTTTTTCGTTTCTCGAGGTAAACTTTC
191 TGACTATAAATAGACTTTTCTTACTAATGAATGCTTTTTCTTCACATTTCTCAAGGCAAACATTC
* * * *
4404 ATTTATAGTCTATTTTCAGCAAAAATGTAAAAAACATTCAACTTAAAACTAATTCTGGTATTATA
256 AATTATAGTCTATTTTCA-CAAAAATATAAAAAACATTCAACTTAAAACTAATTATGGTATGATA
*
4469 AAACCATTTAAAGGGAATAAT
320 AAACCATTTAAAGTGAATAAT
* * *
4490 AAGAC-TTTGAAGGAATAGGTGACTATAAATAGACCTTTCTTATCAATGAATGGGTTTTTTTACA
1 AAGGCTTTTGAAGG-ATAGGTGACTATAAATAGACTTTTCTTATCAATGAATGGCTTTTTTTACA
** *
4554 CGTTTCTCAAGGTAGATACTTAATTATAGTCTGTTTTAATGATAAATATAAAAAAATTTAACTTA
65 CGTTTCTCAAGGTAGGCACTTAATTATAGTCTGTTCTAATGATAAATATAAAAAAATTTAACTTA
********** * * *
4619 AAATCAATTATGAGANNNNNNNNNNATTTAAAACGAGTAATAAGGCTTTTGAAGGAATGGGTGGC
130 AAATCAATTATGAGATTATAAAACTATTTAAAACAAGTAATAAGGCTTTTGAAGGAATGGATGAC
* * * *
4684 -ATAACTGGAC-TTTCTTTTCTCAATGAATGGCTTTTTCTTCACATTTCTCAAGGCAAGCATTCA
195 TATAAATAGACTTTTC-TTACT-AATGAAT-GCTTTTTCTTCACATTTCTCAAGGCAAACATTCA
* *
4747 ATTATAGTCTGTTTT-ACTAAAAAATATAAAAAA-ATTCAACTTAAATC-AATTATGAG-ATGAT
257 ATTATAGTCTATTTTCAC--AAAAATATAAAAAACATTCAACTTAAAACTAATTATG-GTATGAT
*
4808 AAAACCATTTAAAGTGAGTAAT
319 AAAACCATTTAAAGTGAATAAT
* ** * * *
4830 AAGGCTTTTGAATGGAT-GAGTGACTATAAATGGACTTTTCTTGCCAATGAATAGCTTTCTCTAC
1 AAGGCTTTTGAA-GGATAG-GTGACTATAAATAGACTTTTCTTATCAATGAATGGCTTTTTTTAC
* * * ** *
4894 ATGTTTCTCAAGGAAGGCACTCAATTATAGTCTGTTCTAATGA-AGAATGCAAAAATATTTAACT
64 ACGTTTCTCAAGGTAGGCACTTAATTATAGTCTGTTCTAATGATA-AATATAAAAAAATTTAACT
* * * * * *
4958 TAAAATAAATTATGAGATTGTAAAACCATTTAAAGCGAGTAATAAGGCTATTGAAGGAATGGATG
128 TAAAATCAATTATGAGATTATAAAACTATTTAAAACAAGTAATAAGGCTTTTGAAGGAATGGATG
* * * * * * * *
5023 ACTATAAATGGACCTTTT-TTGCAAATGAATCCCTTGTTCTTCA-AGTTTCTCGAGGTAGACATT
193 ACTATAAATAGA-CTTTTCTTACTAATGAAT-GCTTTTTCTTCACA-TTTCTCAAGGCAAACATT
* * * *
5086 CAATTATAGTCTCTTTTAACCAAAAATGTTAAAAAC
255 CAATTATAGTCTATTTTCA-CAAAAATATAAAAAAC
5122 TATTTAAAGC
Statistics
Matches: 781, Mismatches: 162, Indels: 66
0.77 0.16 0.07
Matches are distributed among these distances:
339 4 0.01
340 50 0.06
341 298 0.38
342 150 0.19
343 63 0.08
344 130 0.17
345 85 0.11
346 1 0.00
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.35
Consensus pattern (340 bp):
AAGGCTTTTGAAGGATAGGTGACTATAAATAGACTTTTCTTATCAATGAATGGCTTTTTTTACAC
GTTTCTCAAGGTAGGCACTTAATTATAGTCTGTTCTAATGATAAATATAAAAAAATTTAACTTAA
AATCAATTATGAGATTATAAAACTATTTAAAACAAGTAATAAGGCTTTTGAAGGAATGGATGACT
ATAAATAGACTTTTCTTACTAATGAATGCTTTTTCTTCACATTTCTCAAGGCAAACATTCAATTA
TAGTCTATTTTCACAAAAATATAAAAAACATTCAACTTAAAACTAATTATGGTATGATAAAACCA
TTTAAAGTGAATAAT
Found at i:5250 original size:137 final size:137
Alignment explanation
Indices: 4979--5257 Score: 386
Period size: 138 Copynumber: 2.0 Consensus size: 137
4969 ATGAGATTGT
* *
4979 AAAACCATTTAAAGCGAGTAATAAGGCTATTGAAGGAATGGATGACTATAAATGGACCTTTTTTG
1 AAAACCATTTAAAGCGAGCAATAAGGCTATTGAAGGAATGGATGACTATAAATAGACCTTTTTTG
*
5044 CAAATGAATCCCTTGTTCTTCAAGTTTCTCGAGGTAGACATTCAATTATAGTCTCTTTTAACCAA
66 CAAATGAATCCATTGTTCTTCAAGTTTCTCGAGGTAGACATTCAATTATAGTCTCTTTTAACCAA
5109 AAATGTTA
131 AAATG-TA
* * * *
5117 AAAACTATTTAAAGCTAGCAATAAGGCTTTTGATGGAATGTG-TGACTATAAATAGA-CTTTTCT
1 AAAACCATTTAAAGCGAGCAATAAGGCTATTGAAGGAATG-GATGACTATAAATAGACCTTTT-T
* * * * *
5180 TGCTAATGAATCCATT-TTTTTCATA-TTTTTTGAGGTAGACATTCAATTATAGTCTGTTTTAAC
64 TGCAAATGAATCCATTGTTCTTCA-AGTTTCTCGAGGTAGACATTCAATTATAGTCTCTTTTAAC
5243 CAAAAATGTA
128 CAAAAATGTA
5253 AAAAC
1 AAAAC
5258 AAATTTANNN
Statistics
Matches: 126, Mismatches: 12, Indels: 8
0.86 0.08 0.05
Matches are distributed among these distances:
136 7 0.06
137 54 0.43
138 64 0.51
139 1 0.01
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36
Consensus pattern (137 bp):
AAAACCATTTAAAGCGAGCAATAAGGCTATTGAAGGAATGGATGACTATAAATAGACCTTTTTTG
CAAATGAATCCATTGTTCTTCAAGTTTCTCGAGGTAGACATTCAATTATAGTCTCTTTTAACCAA
AAATGTA
Found at i:5950 original size:172 final size:170
Alignment explanation
Indices: 5117--6281 Score: 670
Period size: 171 Copynumber: 6.8 Consensus size: 170
5107 AAAAATGTTA
* * * * *
5117 AAAACTATTTAAAGCTAGCAATAAGGCTTTTGATGGAATGTGTGACTATAAATAGACTTTTCTTG
1 AAAACTATTTAAAGCGAGTAATAAGGTTTTTGAAGGAATG-GTGACTATAAATAGACTTTTCTTA
* * ** * ** * * **
5182 CTAATGAAT-CCATTTTT-TTCATATTTTTTGAGGTAGACATTCAATTATAGTCTGTTTTAACCA
65 CCAATGAATGGC-TTTTTCTTCACGTTTCTCAAGGCAGACATTCAATTATAGCCTGTTTTAATGA
* **********
5245 AAAATGTAAAAACAAATTTANNNNNNNNNNAATTATGAGATTAT
129 AAAATGT-AAAA-AAATTCAACTTAAAATCAATTATGAGATTAT
* * * * *
5289 AAAACCA-TTAGAAGCGAGTAATAAGGCTTTTGAAGGAATAAGTGAGTATAAATGGACTTTTCTT
1 AAAACTATTTA-AAGCGAGTAATAAGGTTTTTGAAGGAAT-GGTGACTATAAATAGACTTTTCTT
********** * * * *
5353 NNNNNNNNNNGACTTTTT-TTACACATTTC-CTAAGGCAGACATTCAATTATAGTCTGCTTT-AT
64 ACCAATGAATGGCTTTTTCTT-CACGTTTCTC-AAGGCAGACATTCAATTATAGCCTGTTTTAAT
* * *
5415 GGAAAAATGTAAAAAAAATTTAACTTAAAATCAATTATAACATTAT
127 -GAAAAATGT-AAAAAAATTCAACTTAAAATCAATTATGAGATTAT
* * **********
5461 AAAACTATTTCAAGTGAGTAATAAGGTTTTTGAAGGAATGGATGNNNNNNNNNNGACTTTTCTTA
1 AAAACTATTTAAAGCGAGTAATAAGGTTTTTGAAGGAATGG-TGACTATAAATAGACTTTTCTTA
* * * * * * * **
5526 CTAATGAAT-ACTTTTTTCTTCACGTTTCTCGAGGTAGACTTTCATTTAT-TCTCTGTTTTAACC
65 CCAATGAATGGC-TTTTTCTTCACGTTTCTCAAGGCAGACATTCAATTATAGC-CTGTTTTAATG
* *
5589 AAAAATGTAAAAAAATTCAACTTAGAA-CTAATTCTG-GTATTAT
128 AAAAATGTAAAAAAATTCAACTTAAAATC-AATTATGAG-ATTAT
* * * * * * *
5632 AAAACTATTTAAAGGGAATAGTAAAG-CTTTGAAGGAATGGGTGACTATAAATGGACCTTTCTTA
1 AAAACTATTTAAAGCGAGTAATAAGGTTTTTGAAGGAAT-GGTGACTATAAATAGACTTTTCTTA
* * ** * * * * * *
5696 CCAATGAATGGGTTTTTCTACACGTTTCTGGGAGGTAAATATTTAATTATAGCCTATTTCAAT-A
65 CCAATGAATGGCTTTTTCTTCACGTTTCT-CAAGGCAGACATTCAATTATAGCCTGTTTTAATGA
*
5760 ATAAATGTAAAAAAATTCAACTGAAAATCAATTATGAGATTAT
129 A-AAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTAT
* *
5803 AAAATTATTTAAAGCGACTAATAAGGTTTTTGAAGGAATGAGTGACTATAAATAGAC-TTTCTTT
1 AAAACTATTTAAAGCGAGTAATAAGGTTTTTGAAGGAATG-GTGACTATAAATAGACTTTTC-TT
* * * *
5867 TCTCAATGAACGGCTTTTTCTTCACATTTCTCAAGGCAGACATTCAATTATAGCCTGTTTTACTG
64 AC-CAATGAATGGCTTTTTCTTCACGTTTCTCAAGGCAGACATTCAATTATAGCCTGTTTTAATG
* **********
5932 AAAAATGTTAAAAAATTCAACTTAAAATCAATTCNNNNNNNNN
128 AAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTAT
* * *
5975 NAAACCATTTAAAGCGAGTAATAAGGCTTTTGAATGG-ATGTGTGACTATAAA-AGGACTTTTCT
1 AAAACTATTTAAAGCGAGTAATAAGGTTTTTGAA-GGAATG-GTGACTATAAATA-GACTTTTCT
* * * * * *
6038 TGCCAATGAATAGCTTTTTCTACATGTTTCTCAAGGGAGGCATTCAATTATAGCCTGTTTTAATG
63 TACCAATGAATGGCTTTTTCTTCACGTTTCTCAAGGCAGACATTCAATTATAGCCTGTTTTAATG
* ** * ********
6103 AAGAATACAAAAAAATTTAACTTAAAATCAATTATNNNNNNNN
128 AAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTAT
** * * * * * * *
6146 NNAACCATTTAAAGTGAGTAATAAGGCTATTGATGGAATAGGTGACTATAAATGGACTTTTTTTA
1 AAAACTATTTAAAGCGAGTAATAAGGTTTTTGAAGGAAT-GGTGACTATAAATAGACTTTTCTTA
* ** * * * * **
6211 CTAATGAATCTCTTGTTT-TTCAAGTTTCTCGAGGTAGACATTCAATTATAGTCTGTTTTAACAA
65 CCAATGAATGGCTT-TTTCTTCACGTTTCTCAAGGCAGACATTCAATTATAGCCTGTTTTAATGA
6275 AAAATGT
129 AAAATGT
6282 TNNNNNNNNN
Statistics
Matches: 771, Mismatches: 188, Indels: 69
0.75 0.18 0.07
Matches are distributed among these distances:
170 52 0.07
171 333 0.43
172 302 0.39
173 84 0.11
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.35
Consensus pattern (170 bp):
AAAACTATTTAAAGCGAGTAATAAGGTTTTTGAAGGAATGGTGACTATAAATAGACTTTTCTTAC
CAATGAATGGCTTTTTCTTCACGTTTCTCAAGGCAGACATTCAATTATAGCCTGTTTTAATGAAA
AATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTAT
Found at i:8967 original size:170 final size:169
Alignment explanation
Indices: 8546--8996 Score: 540
Period size: 170 Copynumber: 2.7 Consensus size: 169
8536 NNNNNNNNNC
* * * *
8546 TTTTTCTTCACATTTCTCAAGGTAGGCATTCAATTATAATCTGTTTTAACTAAAAATGTAAAA-A
1 TTTTTCTTCACTTTTCTAAAGGTAGACATTCAATTATAGTCTG-TTTAACTAAAAATGTAAAACA
* * * *
8610 TATTCAGCTTAAAATCAATTATAAGATTCTAAAACTATTTAAAGCGAGTAATAAGACTTTTAAAG
65 -ATTCAACTTAAAATCAATTATAAGATTATAAAACCATTTAAAGCGAGCAATAAGACTTTTAAAG
* *
8675 GAAAGAGAGAATATAATAGACTTCTCTTACTAATGAATGCA
129 GAAAGAGAGAATATAATAGACTTCTCTTACCAATGAATGAA
* * *
8716 TTTTTCTTCA-TATTTC-ACAATGTAGACCA-TCAATTATAGTCTATTTTAAC-CAAAATGTAAA
1 TTTTTCTTCACT-TTTCTA-AAGGTAGA-CATTCAATTATAGTCT-GTTTAACTAAAAATGTAAA
* * *
8777 AGC-ATTCAACTTAAAATCAATTATGAGATTATAAAGCCATTTAAAGCGAGCAATAAGCCTTTTA
62 A-CAATTCAACTTAAAATCAATTATAAGATTATAAAACCATTTAAAGCGAGCAATAAGACTTTTA
* * * * *
8841 AAGGAATG-GTTGACTATAAATGGACTTTTCTTACCAATGAAT-AA
126 AAGGAAAGAG-AGAATAT-AATAGACTTCTCTTACCAATGAATGAA
* *
8885 TTTTTTCTTCACTTTTCTAAAGGTAGACATTCAATTATTGTCTGTTTAACTAAAAATATAAAACA
1 -TTTTTCTTCACTTTTCTAAAGGTAGACATTCAATTATAGTCTGTTTAACTAAAAATGTAAAACA
*
8950 ATTAAACTTAAAATCAATTATAAGATTATAAAACCATTTAAAGCGAG
65 ATTCAACTTAAAATCAATTATAAGATTATAAAACCATTTAAAGCGAG
8997 NNNNNNNNNN
Statistics
Matches: 238, Mismatches: 29, Indels: 28
0.81 0.10 0.09
Matches are distributed among these distances:
168 1 0.00
169 87 0.37
170 146 0.61
171 4 0.02
ACGTcount: A:0.41, C:0.13, G:0.11, T:0.35
Consensus pattern (169 bp):
TTTTTCTTCACTTTTCTAAAGGTAGACATTCAATTATAGTCTGTTTAACTAAAAATGTAAAACAA
TTCAACTTAAAATCAATTATAAGATTATAAAACCATTTAAAGCGAGCAATAAGACTTTTAAAGGA
AAGAGAGAATATAATAGACTTCTCTTACCAATGAATGAA
Done.