Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399921.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3152.1, 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: 4931
ACGTcount: A:0.29, C:0.09, G:0.10, T:0.27
Warning! 1254 characters in sequence are not A, C, G, or T
Found at i:317 original size:170 final size:167
Alignment explanation
Indices: 1--704 Score: 546
Period size: 170 Copynumber: 4.1 Consensus size: 167
* ** **
1 ATTCAACTTAAAATCAATTATGAGAGTATAAAACCATTTAAAGCAAGTAATGGGGCTTTTGAAGG
1 ATTCAACTTAAAATCAATT-TGAGATTAT-AAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGG
* * * ** *
66 AATGAGAG-ACTAAAAATGGA-TATTTCTTTCAAATAAATGGGTTTTTCTAT-ACGTTTC-CTGA
64 AATG-G-GTACTACAAATGAACT-TTTC-TTCCAATAAATGCTTTTTTCT-TCACATTTCTC-GA
** ** * * *
127 GGCAGGCATTTAGTTATAGTCTGTTTTAACAAAAAATATAAAAAA
123 GATACACATTCAATTATAGTCTATTTTAACAAAAAATATAAAAAA
* * * *
172 ATTTAACTTAAAATCAATTTGATATTATAAATTCATTTAAAGTGGGTAATAAGGCTTTTGAAGGA
1 ATTCAACTTAAAATCAATTTGAGATTATAAA-CCATTTAAAGTGAGTAATAAGGCTTTTGAAGGA
* * * *
237 ATGGGCTACTATAAATGAACTTTTCTTGCCTATAAATGCTTTTTTCTTCACATTTCTTGAGCTAC
65 ATGGG-TACTACAAATGAACTTTTCTT-CCAATAAATGCTTTTTTCTTCACATTTCTCGAGATAC
* ** *
302 ACATTCAATTATAGTCTCTTTTAATGAAAAATATAAAACA
128 ACATTCAATTATAGTCTATTTTAACAAAAAATATAAAAAA
********* * * *
342 ATTCAACTTAAAATCAATTANNNNNNNNNNAAACCATTTAAAGCGAGTAATAAGCCTTTTGAAGA
1 ATTCAACTTAAAATCAATT--TGAGATTATAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGG
* * * ** * * *
407 AATGAGAG-ACTACAAATGGATTTTTCTTTCAAATAAATG-GATTTTCTACACGTTTCTCGAGGT
64 AATG-G-GTACTACAAATGAACTTTTC-TTCCAATAAATGCTTTTTTCTTCACATTTCTCGAGAT
* * *
470 AGATATTCAATTATAGTCTATTTTAGCAAAAAATAT-AAAAA
126 ACACATTCAATTATAGTCTATTTTAACAAAAAATATAAAAAA
* * *
511 A-TCAATTTAAAATCAATTTTGAGATTATAAAACCCTTGAAAGTGAGTAATAAGGCTTTTGAAGG
1 ATTCAACTTAAAATCAA-TTTGAGATTAT-AAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGG
* * * *
575 AATAGGTGACTACAAATAGACCCTTTT-TTCCAATGAATGCTTTTTTCTTCA-AGTTTCTCAAGA
64 AATGGGT-ACTACAAAT-GA-ACTTTTCTTCCAATAAATGCTTTTTTCTTCACA-TTTCTCGAGA
* * * *
638 TACACATTGAATTGTAGTCTATTTTAATAAAAAATATAAAACA
125 TACACATTCAATTATAGTCTATTTTAACAAAAAATATAAAAAA
*
681 ATTCGACTTAAAATCAATTATGAG
1 ATTCAACTTAAAATCAATT-TGAG
705 GTTANNNNNN
Statistics
Matches: 414, Mismatches: 96, Indels: 46
0.74 0.17 0.08
Matches are distributed among these distances:
166 1 0.00
167 1 0.00
168 67 0.16
169 62 0.15
170 186 0.45
171 90 0.22
172 6 0.01
173 1 0.00
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.35
Consensus pattern (167 bp):
ATTCAACTTAAAATCAATTTGAGATTATAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAA
TGGGTACTACAAATGAACTTTTCTTCCAATAAATGCTTTTTTCTTCACATTTCTCGAGATACACA
TTCAATTATAGTCTATTTTAACAAAAAATATAAAAAA
Found at i:679 original size:339 final size:331
Alignment explanation
Indices: 29--847 Score: 825
Period size: 339 Copynumber: 2.4 Consensus size: 331
19 TATGAGAGTA
** * *
29 TAAAACCATTTAAAGCAAGTAATGGGGCTTTTGAAGGAATGAGAGACTAAAAATGGATATTTCTT
1 TAAAACCATTTAAAGCAAGTAATAAGCCTTTTGAAGAAATGAGAGACTAAAAATGGATATTTCTT
* * * * * *
94 TCAAATAAATGGGTTTTTCTATACGTTTCCTGAGGCAGGCATTTAGTTATAGTCTGTTTTAACAA
66 TCAAATAAATGGGATTTTCTACACGTTTCCTGAGGCAGACATTCAATTATAGTCTATTTTAACAA
* * ** * *
159 AAAATATAAAAAAATTTAACTTAAAATCAATTTGATATTATAAATTCATTTAAAGTGGGTAATAA
131 AAAATATAAAAAAATTCAACTTAAAATCAATTTGAGATTATAAAACCATTGAAAGTGAGTAATAA
* * *
224 GGCTTTTGAAGGAATGGGCTACTATAAATGAACTTTTCTTGCCTATAAATGCTTTTTTCTTCACA
196 GGCTTTTGAAGGAATAGGCTACTACAAATGAACTTTTCTTGCCAATAAATGCTTTTTTCTTCACA
** * * *
289 TTTCTTGAGCTACACATTCAATTATAGTCTCTTTTAATGAAAAATATAAAACAATTCAACTTAAA
261 TTTCTCAAGATACACATTCAATTATAGTCTATTTTAATAAAAAATATAAAACAATTCAACTTAAA
354 ATCAAT
326 ATCAAT
* *
360 TANNNNNNNNNNAAACCATTTAAAGCGAGTAATAAGCCTTTTGAAGAAATGAGAGACTACAAATG
1 TA----------AAACCATTTAAAGCAAGTAATAAGCCTTTTGAAGAAATGAGAGACTAAAAATG
* * *
425 GATTTTTCTTTCAAATAAAT-GGATTTTCTACACGTTT-CTCGAGGTAGATATTCAATTATAGTC
56 GATATTTCTTTCAAATAAATGGGATTTTCTACACGTTTCCT-GAGGCAGACATTCAATTATAGTC
* * *
488 TATTTTAGCAAAAAATAT-AAAAAA-TCAATTTAAAATCAATTTTGAGATTATAAAACCCTTGAA
120 TATTTTAACAAAAAATATAAAAAAATTCAACTTAAAATCAA-TTTGAGATTATAAAACCATTGAA
* *
551 AGTGAGTAATAAGGCTTTTGAAGGAATAGG-TGACTACAAATAGACCCTTTT-TT-CCAATGAAT
184 AGTGAGTAATAAGGCTTTTGAAGGAATAGGCT-ACTACAAAT-GA-ACTTTTCTTGCCAATAAAT
* *
613 GCTTTTTTCTTCA-AGTTTCTCAAGATACACATTGAATTGTAGTCTATTTTAATAAAAAATATAA
246 GCTTTTTTCTTCACA-TTTCTCAAGATACACATTCAATTATAGTCTATTTTAATAAAAAATATAA
*
677 AACAATTCGACTTAAAATCAAT
310 AACAATTCAACTTAAAATCAAT
** ** * * *
699 TATGA-GGTTANNNNNNNNNNTAAAGCAAGTAATAAGCCTTTT-AGAGGAATGGGAGACTATAAA
1 TAAAACCATT-----------TAAAGCAAGTAATAAGCCTTTTGA-AGAAATGAGAGACTAAAAA
** * * *
762 TAAATTTTTCTTCCAAATAAAT-GGATTTTTCTACACGTTTCCTGAGGCA-AGTATTCAATTATA
54 TGGATATTTCTTTCAAATAAATGGGA-TTTTCTACACGTTTCCTGAGGCAGA-CATTCAATTATA
* *
825 GTCTGTTTTAATAAAAAATATAA
117 GTCTATTTTAACAAAAAATATAA
848 NNNNNNNNNN
Statistics
Matches: 404, Mismatches: 52, Indels: 54
0.79 0.10 0.11
Matches are distributed among these distances:
328 2 0.00
329 1 0.00
331 2 0.00
338 16 0.04
339 207 0.51
340 102 0.25
341 74 0.18
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.34
Consensus pattern (331 bp):
TAAAACCATTTAAAGCAAGTAATAAGCCTTTTGAAGAAATGAGAGACTAAAAATGGATATTTCTT
TCAAATAAATGGGATTTTCTACACGTTTCCTGAGGCAGACATTCAATTATAGTCTATTTTAACAA
AAAATATAAAAAAATTCAACTTAAAATCAATTTGAGATTATAAAACCATTGAAAGTGAGTAATAA
GGCTTTTGAAGGAATAGGCTACTACAAATGAACTTTTCTTGCCAATAAATGCTTTTTTCTTCACA
TTTCTCAAGATACACATTCAATTATAGTCTATTTTAATAAAAAATATAAAACAATTCAACTTAAA
ATCAAT
Found at i:2142 original size:171 final size:167
Alignment explanation
Indices: 1807--3176 Score: 1005
Period size: 171 Copynumber: 8.0 Consensus size: 167
1797 NNNNNNNNNN
** * * * * *
1807 AACCATTTAAAGCAAGTAATAAGGCTTTTGAAGGAATGAGAGACTAAAAATAGATTTTTCTT-CC
1 AACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCC
* *** ** * * * * * * * **
1871 AAATAAATGGGATTTTCTACACTTTTTTTGAGGCAGATATTCAATTATAGTTTGTTTTAACAAAA
66 -AATGAATGCTTTTTTCTTTAC-ATTTTT-AAGTACACATTCAATTATAGTCTATTTTAA-TGAA
* *
1936 AATATAAAAAAATTCAACTTAAAATCAACTATGAGATTATAA
127 AATGT-AAAAAATTCAACTTAAAATCAATTATGAGATTATAA
* * * * * * *
1978 AACCATTTATAGTGGGTAATAAGACTTTCGAATGAATGGGCGACTATAAATGGACTTTTCTTGTC
1 AACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCC
*
2043 AATGAATGCTTTTTTCTTTACATTTTTAGAGATGCACATTCAATTATAGTCTATTTTAATGAAAT
66 AATGAATGCTTTTTTCTTTACATTTTTA-AG-TACACATTCAATTATAGTCTATTTTAATGAAA-
* ** ** *
2108 ATGTAAAACGATTCTGCCAAAAATCACTTATGAGATTATAA
128 ATGTAAAA-AATTCAACTTAAAATCAATTATGAGATTATAA
* ** ** *
2149 AACTATTTAAAGCAAGTAATAAGGCTTTTGAACAAATGGGTGACTATAAATGGATTTTTCTT-CC
1 AACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCC
* ** * * ** * *
2213 AAAGAAATGGGTTTTTCTATACGGTTTTCGAG-GCAAGCATTCAATTATAGAT-TGTTTTTAA--
66 AATG-AATGCTTTTTTCTTTAC-ATTTTTAAGTAC-A-CATTCAATTATAG-TCT-ATTTTAATG
* * * *
2274 AAAAAGTAAAAAAATCAACTTAAAGTCAATTTTGAGATTATAA
125 AAAATGTAAAAAATTCAACTTAAAATCAATTATGAGATTATAA
* * * * * * *
2317 AATCATTTAAAGTGAGTAAGAAGGCTTTCGAAGGAATGAGTAACTATAAGTGGACTTTTCTTGTC
1 AACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCC
* *
2382 AATGAATGTTTTTTTC-TT-CATGTTTCTCAAGATACACATTCAATTATAGTCTGTTTTAATGAG
66 AATGAATGCTTTTTTCTTTACAT-TTT-T-AAG-TACACATTCAATTATAGTCTATTTTAATGA-
* *
2445 AAATGTAAAAAATTCAAGTTTAAATCAATTATGAGATTATAA
126 AAATGTAAAAAATTCAACTTAAAATCAATTATGAGATTATAA
** * ** * * *
2487 AACCATTTAAAACGAGTAATAAGGCTTTTGAAGAAATGGGACACTAAAAATAGATTTTTCTT-CC
1 AACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCC
** ** * *
2551 AAAAAAAATGAGTTTTTC--TACATGTTTTCCGAG-GCAGGCATTCAATTATAGTCTATTTTAAC
66 --AATGAATGCTTTTTTCTTTACAT-TTTT--AAGTACA--CATTCAATTATAGTCTATTTT-A-
** * * *
2613 AAAAAAATATAAAAAATTCAACTTAAAATTAATTTTGAGATTATAA
122 ATGAAAATGTAAAAAATTCAACTTAAAATCAATTATGAGATTATAA
* * * *
2659 AACCATTTAAAGTGAGTGATAAGGCTTTTGATGGAATGGGTGACTATAAATAGACTTTTCTAGCC
1 AACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCC
* * * * *
2724 AATGAATGCTTTTTTCTTCACGTTTCTCAAGGTACGCTTTCAATTATAGTCTATTTTAATGAAAA
66 AATGAATGCTTTTTTCTTTACATTT-TTAA-GTACACATTCAATTATAGTCTATTTTAATG-AAA
* * * *
2789 ATGCAAAACAATTCTACTTAAAAGCAATTATGATATTATAA
128 ATGTAAAA-AATTCAACTTAAAATCAATTATGAGATTATAA
* * * * *
2830 AACCATTTAAAGCGAGTAATAAGGATTTCGAAGGAAT-GGTAGATTTTAAATGGA-TTTTCTT-C
1 AACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGT-GACTATAAATGGACTTTTCTTGC
* * * ** * * * *
2892 CAACTAAATAG-GTTTTTATACACGTTTATCAAGT-CAGGCATTCAATTACAGTCTGTTTTAATG
65 CAA-TGAAT-GCTTTTTTCTTTACATTT-TTAAGTACA--CATTCAATTATAGTCTATTTTAATG
* * * *
2955 AAAAGTATAAAAAAAATTCAACTTAAAATTAATTTTGAGAATATAA
125 AAAA-TGT--AAAAAATTCAACTTAAAATCAATTATGAGATTATAA
** * * *
3001 AATAATTTAATGTGAGTAATAAGGCTTTTGAAGGAATGAGG-GACGATAAATGGACTTTTCTTGT
1 AACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATG-GGTGACTATAAATGGACTTTTCTTGC
* * * * *
3065 CAATGAATGGTTTTTT-TTTTCATGTTTCTCAAGATACACATTCAATTATGGTCTGTCTTAATGA
65 CAATGAATGCTTTTTTCTTTACAT-TTT-T-AAG-TACACATTCAATTATAGTCTATTTTAATGA
*
3129 GAAATGTAAAACAATTCTACTTAAAATCAATTATGAGATTATAA
126 -AAATGTAAAA-AATTCAACTTAAAATCAATTATGAGATTATAA
3173 AACC
1 AACC
3177 NNNNNNNNNN
Statistics
Matches: 936, Mismatches: 206, Indels: 113
0.75 0.16 0.09
Matches are distributed among these distances:
165 1 0.00
166 4 0.00
167 8 0.01
168 100 0.11
169 30 0.03
170 172 0.18
171 416 0.44
172 157 0.17
173 42 0.04
174 4 0.00
175 2 0.00
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (167 bp):
AACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCC
AATGAATGCTTTTTTCTTTACATTTTTAAGTACACATTCAATTATAGTCTATTTTAATGAAAATG
TAAAAAATTCAACTTAAAATCAATTATGAGATTATAA
Found at i:2729 original size:342 final size:342
Alignment explanation
Indices: 1807--3176 Score: 1663
Period size: 342 Copynumber: 4.0 Consensus size: 342
1797 NNNNNNNNNN
* *
1807 AACCATTTAAAGCAAGTAATAAGGCTTTTGAAGGAATGAGAGACTAAAAATAGATTTTTCTTCCA
1 AACCATTTAAAGCAAGTAATAAGGCTTTTGAAGAAATGGGAGACTAAAAATAGATTTTTCTTCCA
* * * * ** *
1872 AATAAATGGGATTTTCTACACTTTTTTTGAGGCAGATATTCAATTATAGTTTGTTTTAAC-AAAA
66 AATAAATGAGTTTTTCTACACTGTTTTCGAGGCAGGCATTCAATTATAGTCTGTTTTAACAAAAA
* * * *
1936 AATATAAAAAAATTCAACTTAAAATCAACTATGAGATTATAAAACCATTTATAGTGGGTAATAAG
131 AATAT-AAAAAATTCAACTTAAAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAAG
* * *
2001 ACTTTCGAATGAATGGGCGACTATAAATGGACTTTTCTTGTCAATGAATGCTTTTTTCTTTACAT
195 GCTTTCGAAGGAATGGGTGACTATAAATGGACTTTTCTTGTCAATGAATGCTTTTTTC-TT-CAT
* * * **
2066 -TTT-T-AGAGATGCACATTCAATTATAGTCTATTTTAATGA-AATATGTAAAACGATTCTGCCA
258 GTTTCTCA-AGATACACATTCAATTATAGTCTATTTTAATGAGAA-ATGTAAAACAATTCTACTT
*
2127 AAAATCACTTATGAGATTATAA
321 AAAATCAATTATGAGATTATAA
* * * * *
2149 AACTATTTAAAGCAAGTAATAAGGCTTTTGAACAAATGGGTGACTATAAATGGATTTTTCTTCCA
1 AACCATTTAAAGCAAGTAATAAGGCTTTTGAAGAAATGGGAGACTAAAAATAGATTTTTCTTCCA
* * * * * *
2214 AAGAAATGGGTTTTTCTATACGGTTTTCGAGGCAAGCATTCAATTATAGAT-TGTTTTTA-AAAA
66 AATAAATGAGTTTTTCTACACTGTTTTCGAGGCAGGCATTCAATTATAG-TCTGTTTTAACAAAA
* * * *
2277 AAGTA-AAAAAA-TCAACTTAAAGTCAATTTTGAGATTATAAAATCATTTAAAGTGAGTAAGAAG
130 AAATATAAAAAATTCAACTTAAAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAAG
* * * *
2340 GCTTTCGAAGGAATGAGTAACTATAAGTGGACTTTTCTTGTCAATGAATGTTTTTTTCTTCATGT
195 GCTTTCGAAGGAATGGGTGACTATAAATGGACTTTTCTTGTCAATGAATGCTTTTTTCTTCATGT
* * * *
2405 TTCTCAAGATACACATTCAATTATAGTCTGTTTTAATGAGAAATGTAAAA-AATTCAAGTTTAAA
260 TTCTCAAGATACACATTCAATTATAGTCTATTTTAATGAGAAATGTAAAACAATTCTACTTAAAA
2469 TCAATTATGAGATTATAA
325 TCAATTATGAGATTATAA
* * *
2487 AACCATTTAAAACGAGTAATAAGGCTTTTGAAGAAATGGGACACTAAAAATAGATTTTTCTTCCA
1 AACCATTTAAAGCAAGTAATAAGGCTTTTGAAGAAATGGGAGACTAAAAATAGATTTTTCTTCC-
* *
2552 AAAAAAATGAGTTTTTCTACA-TGTTTTCCGAGGCAGGCATTCAATTATAGTCTATTTTAACAAA
65 AAATAAATGAGTTTTTCTACACTGTTTT-CGAGGCAGGCATTCAATTATAGTCTGTTTTAACAAA
* *
2616 AAAATATAAAAAATTCAACTTAAAATTAATTTTGAGATTATAAAACCATTTAAAGTGAGTGATAA
129 AAAATATAAAAAATTCAACTTAAAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAA
* * * * * *
2681 GGCTTTTGATGGAATGGGTGACTATAAATAGACTTTTCTAGCCAATGAATGCTTTTTTCTTCACG
194 GGCTTTCGAAGGAATGGGTGACTATAAATGGACTTTTCTTGTCAATGAATGCTTTTTTCTTCATG
* * * * *
2746 TTTCTCAAGGTACGCTTTCAATTATAGTCTATTTTAATGAAAAATGCAAAACAATTCTACTTAAA
259 TTTCTCAAGATACACATTCAATTATAGTCTATTTTAATGAGAAATGTAAAACAATTCTACTTAAA
* *
2811 AGCAATTATGATATTATAA
324 ATCAATTATGAGATTATAA
* * * * * * ** *
2830 AACCATTTAAAGCGAGTAATAAGGATTTCGAAGGAATGGTAGATTTTAAATGGA-TTTTCTTCCA
1 AACCATTTAAAGCAAGTAATAAGGCTTTTGAAGAAATGGGAGACTAAAAATAGATTTTTCTTCCA
* * * * * *
2894 ACTAAAT-AGGTTTTTATACAC-GTTTATCAAGTCAGGCATTCAATTACAGTCTGTTTTAATGAA
66 AATAAATGA-GTTTTTCTACACTGTTT-TCGAGGCAGGCATTCAATTATAGTCTGTTTTAA-CAA
** * * * ** *
2957 AAGTATAAAAAAAATTCAACTTAAAATTAATTTTGAGAATATAAAATAATTTAATGTGAGTAATA
128 AAAAATATAAAAAATTCAACTTAAAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGTAATA
* * * *
3022 AGGCTTTTGAAGGAATGAGG-GACGATAAATGGACTTTTCTTGTCAATGAATGGTTTTTTTTTTC
193 AGGCTTTCGAAGGAATG-GGTGACTATAAATGGACTTTTCTTGTCAATGAAT-GCTTTTTTCTTC
* * *
3086 ATGTTTCTCAAGATACACATTCAATTATGGTCTGTCTTAATGAGAAATGTAAAACAATTCTACTT
256 ATGTTTCTCAAGATACACATTCAATTATAGTCTATTTTAATGAGAAATGTAAAACAATTCTACTT
3151 AAAATCAATTATGAGATTATAA
321 AAAATCAATTATGAGATTATAA
3173 AACC
1 AACC
3177 NNNNNNNNNN
Statistics
Matches: 881, Mismatches: 128, Indels: 37
0.84 0.12 0.04
Matches are distributed among these distances:
337 3 0.00
338 91 0.10
339 181 0.21
340 18 0.02
341 54 0.06
342 370 0.42
343 164 0.19
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (342 bp):
AACCATTTAAAGCAAGTAATAAGGCTTTTGAAGAAATGGGAGACTAAAAATAGATTTTTCTTCCA
AATAAATGAGTTTTTCTACACTGTTTTCGAGGCAGGCATTCAATTATAGTCTGTTTTAACAAAAA
AATATAAAAAATTCAACTTAAAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGG
CTTTCGAAGGAATGGGTGACTATAAATGGACTTTTCTTGTCAATGAATGCTTTTTTCTTCATGTT
TCTCAAGATACACATTCAATTATAGTCTATTTTAATGAGAAATGTAAAACAATTCTACTTAAAAT
CAATTATGAGATTATAA
Found at i:3994 original size:169 final size:168
Alignment explanation
Indices: 3705--4561 Score: 681
Period size: 169 Copynumber: 5.1 Consensus size: 168
3695 NNNNNNNNTA
* * * *
3705 TGAGATTATAAAACCATTTAAAACGAGTAATAAGGCTTTTGAAGGAATGGGAAACTA-AAAAGGA
1 TGAGATTAT-AAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATGG-
* * * * * **
3769 ATTCTTCTTTCAAATAAATGGGTTCTTT-TACATGTTTCCTGAGGCA-AGTATTCAATTATTCTC
64 ATTTTTCTTTCCAATAAAT--GTTTTTTCTTCATGTTTCCTGAGGCACA-CATTCAATTATAGTC
*
3832 TGTTTTAACAAAAAATGTAAAAAATTCAGA-TTAAAATGAATTT
126 TGTTTTAACAAAAAATGTAAAAAATTCA-ACTTAAAATCAATTT
** *
3875 TGAGATTATAAACCATTTAAATTGAGTAATAAGGCTTTTGAAGGGATGAGAGACTATAAATGG-T
1 TGAGATTATAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATGGAT
* * * * *
3939 TTGTTCTTTCCGATAAATGCTTTTTTCTTTATGTTTCTTGAGGTACACATTCAATTATAGTTTGT
66 TT-TTCTTTCCAATAAATG-TTTTTTCTTCATGTTTCCTGAGGCACACATTCAATTATAGTCTGT
* ** * * * *
4004 ATTAATGAAAAATGTAAACCACTTCTACTTAAAATCAATTA
129 TTTAACAAAAAATGTAAA-AAATTCAACTTAAAATCAATTT
* **********
4045 TGAGATTATACAACCATTTAAAGCGTGTAATAAGGCTTTTNNNNNNNNNNGAGACTATAAATGGA
1 TGAGATTATA-AACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATGGA
* * * *
4110 TTTTTC-TTCCAAAGAAATGTGTTTTTCTACACGTTTCCTAAGGCA-AGCATTCAATTATAGTCT
65 TTTTTCTTTCC-AATAAATGT-TTTTTCTTCATGTTTCCTGAGGCACA-CATTCAATTATAGTCT
* *
4173 GTTTTAACAAAAAATATAACAAATTCAACTTAAAATCAA-TT
127 GTTTTAACAAAAAATGTAAAAAATTCAACTTAAAATCAATTT
* * ********** *
4214 TCAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTNNNNNNNNNNAGTGACTATAAATGGA
1 TGAGATTAT-AAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATGGA
* * * * * * ** *
4279 CTTTTCTTGCCAATGAATGTTTTTTTCTTCACGTCTCTTGAGATACACATTCAATTATAGT-TTT
65 TTTTTCTTTCCAATAAATG-TTTTTTCTTCATGTTTCCTGAGGCACACATTCAATTATAGTCTGT
** * *
4343 TTTAATGACAAATGTAAAACAATTCAACTTAAAATCAATTA
129 TTTAACAAAAAATGTAAAA-AATTCAACTTAAAATCAATTT
********* **
4384 TGAGATTATANNNNNNNNNNAAGCGAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATACA
1 TGAGATTATA-AACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATGGA
* * ** * * *
4449 TTTTTCTTTCAAATAAATGAGTTTTTCTTCATGTTTCCCAAGGCACGCATT-AATTATTGGCTGT
65 TTTTTCTTTCCAATAAATG-TTTTTTCTTCATGTTTCCTGAGGCACACATTCAATTATAGTCTGT
*
4513 TTTAACAAAAAATATAAAAAATTCAACTTAAAATCAATTT
129 TTTAACAAAAAATGTAAAAAATTCAACTTAAAATCAATTT
4553 TGAGATTAT
1 TGAGATTAT
4562 GAAANNNNNN
Statistics
Matches: 541, Mismatches: 126, Indels: 41
0.76 0.18 0.06
Matches are distributed among these distances:
167 1 0.00
168 23 0.04
169 255 0.47
170 162 0.30
171 97 0.18
172 3 0.01
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.35
Consensus pattern (168 bp):
TGAGATTATAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATGGAT
TTTTCTTTCCAATAAATGTTTTTTCTTCATGTTTCCTGAGGCACACATTCAATTATAGTCTGTTT
TAACAAAAAATGTAAAAAATTCAACTTAAAATCAATTT
Found at i:4561 original size:339 final size:339
Alignment explanation
Indices: 3703--4561 Score: 965
Period size: 340 Copynumber: 2.5 Consensus size: 339
3693 NNNNNNNNNN
* * * * * *
3703 TATGAGATTATAAAACCATTTAAAACGAGTAATAAGGCTTTTGAAGGAATGGGAAACTAAAAAGG
1 TATGAGATTATACAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAA-T
* * * * *
3768 AATTCTTCTTTCAAATAAATGGGTTCTTT-TACATGTTTCCTGAGGCAAGTATTCAATTATTCTC
65 AATTTTTCTTTCAAATAAATGAGTT-TTTCTACATGTTTCCTAAGGCAAGCATTCAATTATTGTC
* *
3832 TGTTTTAACAAAAAATGTAAAAAATTCAGA-TTAAAATGAATTTTGAGATTATAAACCATTTAAA
129 TGTTTTAACAAAAAATATAAAAAATTCA-ACTTAAAATCAATTTTGAGATTATAAACCATTTAAA
* * * *
3896 TTGAGTAATAAGGCTTTTGAAGGGATGAGAGACTATAAATGGTTTGTTCTTTCCGATAAATGCTT
193 GTGAGTAATAAGGCTTTTGAAGGGATGAGAGACTATAAATGGCTTGTTCTTGCCAATAAATGCTT
* * * * * *
3961 TTTTCTTTATGTTTCTTGAGGTACACATTCAATTATAGTTTGTATTAATGAAAAATGTAAACCAC
258 TTTTCTTCACGTCTCTTGAGATACACATTCAATTATAGTTTGTATTAATGAAAAATGTAAAACAA
*
4026 TTCTACTTAAAATCAAT
323 TTCAACTTAAAATCAAT
* **********
4043 TATGAGATTATACAACCATTTAAAGCGTGTAATAAGGCTTTTNNNNNNNNNNGAGACTATAAATG
1 TATGAGATTATACAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAAT-
* * * * * *
4108 GATTTTTCTTCCAAAGAAATGTGTTTTTCTACACGTTTCCTAAGGCAAGCATTCAATTATAGTCT
65 AATTTTTCTTTCAAATAAATGAGTTTTTCTACATGTTTCCTAAGGCAAGCATTCAATTATTGTCT
* *
4173 GTTTTAACAAAAAATATAACAAATTCAACTTAAAATCAA-TTTCAGATTATAAAACCATTTAAAG
130 GTTTTAACAAAAAATATAAAAAATTCAACTTAAAATCAATTTTGAGATTAT-AAACCATTTAAAG
********** * * *
4237 TGAGTAATAAGGCTTTNNNNNNNNNNAGTGACTATAAATGGACTT-TTCTTGCCAATGAATGTTT
194 TGAGTAATAAGGCTTTTGAAGGGATGAGAGACTATAAATGG-CTTGTTCTTGCCAATAAATGCTT
* *
4301 TTTTCTTCACGTCTCTTGAGATACACATTCAATTATAGTTT-TTTTAATGACAAATGTAAAACAA
258 TTTTCTTCACGTCTCTTGAGATACACATTCAATTATAGTTTGTATTAATGAAAAATGTAAAACAA
4365 TTCAACTTAAAATCAAT
323 TTCAACTTAAAATCAAT
**********
4382 TATGAGATTATANNNNNNNNNNAAGCGAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATA
1 TATGAGATTATACAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATA
* * * *
4447 CATTTTTCTTTCAAATAAATGAGTTTTTCTTCATGTTTCCCAAGGCACGCATT-AATTATTGGCT
66 -ATTTTTCTTTCAAATAAATGAGTTTTTCTACATGTTTCCTAAGGCAAGCATTCAATTATTGTCT
4511 GTTTTAACAAAAAATATAAAAAATTCAACTTAAAATCAATTTTGAGATTAT
130 GTTTTAACAAAAAATATAAAAAATTCAACTTAAAATCAATTTTGAGATTAT
4562 GAAANNNNNN
Statistics
Matches: 423, Mismatches: 89, Indels: 15
0.80 0.17 0.03
Matches are distributed among these distances:
338 47 0.11
339 147 0.35
340 227 0.54
341 2 0.00
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.35
Consensus pattern (339 bp):
TATGAGATTATACAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATA
ATTTTTCTTTCAAATAAATGAGTTTTTCTACATGTTTCCTAAGGCAAGCATTCAATTATTGTCTG
TTTTAACAAAAAATATAAAAAATTCAACTTAAAATCAATTTTGAGATTATAAACCATTTAAAGTG
AGTAATAAGGCTTTTGAAGGGATGAGAGACTATAAATGGCTTGTTCTTGCCAATAAATGCTTTTT
TCTTCACGTCTCTTGAGATACACATTCAATTATAGTTTGTATTAATGAAAAATGTAAAACAATTC
AACTTAAAATCAAT
Done.