Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399117.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2394.0, 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: 16043
ACGTcount: A:0.32, C:0.10, G:0.11, T:0.31
Warning! 2537 characters in sequence are not A, C, G, or T
Found at i:816 original size:171 final size:170
Alignment explanation
Indices: 257--824 Score: 436
Period size: 171 Copynumber: 3.3 Consensus size: 170
247 NNNNNNNNNN
** * * **
257 AACCATTTAAAGCGAGTAATAAGGCCTTTGAAGGAATGGGTGACTATAACTGGACTTTTTATACC
1 AACCATTTAAAGCGACAAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCCTACC
* * * *
322 AATGAATGCCTTTTTCTT-AATGTTTCTCAAGGTAAACATTCAAT--TAATGTCTA-TTTTAACA
66 AATGAATACCTTTTTCTTCACT-TTTATCAAGGTAAACATTAAATGATAA--T-TAGTTTTAACA
* ********** *
383 AAAAATGTAAAAATAA-TCAANNNNNNNNNNATTATGAGATTGTAA
127 AAAAA--TAAAAAAAATTCAACATAAAATCAATTATGAGATTATAA
* * * *
428 AACCATTTAAAGCGAGTAAA-AAGGGTTTTAAAGGAATTGGTGACTATAAATGGACTTTTCCTAC
1 AACCATTTAAAGCGA-CAAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCCTAC
* * * * * * * *
492 CAATGAATCCCTTTTTCTTCACTTTTCTCTAGTTAGACATTCAATTATAGTTAGTTTTAACAAAA
65 CAATGAATACCTTTTTCTTCACTTTTATCAAGGTAAACATTAAATGATAATTAGTTTTAACAAAA
** *
557 AATGTAAAAAATTCAACGTAAAATCAATTATGAGATTAT-A
130 AATAAAAAAAATTCAACATAAAATCAATTATGAGATTATAA
* ** ********** * ***
597 AACCATTTAAAGAGAGTAATAAGGCTTTTGAANNNNNNNNNNACTATAAATGGACTTTTCTTGTT
1 AACCATTTAAAGCGACAAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCCTACC
* * *
662 AGTGAATACTTTTTTCTTTA-TATTTATCAAGGTAAACATTAAATGATAATCT-GTTTTAACTAA
66 AATGAATACCTTTTTCTTCACT-TTTATCAAGGTAAACATTAAATGATAAT-TAGTTTTAAC-AA
* *
725 GAATATAAAAAAAATTGAACATAAAATCAATT-TGAGATTATAA
128 -AAAATAAAAAAAATTCAACATAAAATCAATTATGAGATTATAA
768 AACCATTTAAAGCGACAAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTT
1 AACCATTTAAAGCGACAAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTT
825 NNNNNNNNNN
Statistics
Matches: 308, Mismatches: 77, Indels: 24
0.75 0.19 0.06
Matches are distributed among these distances:
168 3 0.01
169 95 0.31
170 30 0.10
171 174 0.56
172 4 0.01
173 2 0.01
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.33
Consensus pattern (170 bp):
AACCATTTAAAGCGACAAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCCTACC
AATGAATACCTTTTTCTTCACTTTTATCAAGGTAAACATTAAATGATAATTAGTTTTAACAAAAA
ATAAAAAAAATTCAACATAAAATCAATTATGAGATTATAA
Found at i:1503 original size:171 final size:166
Alignment explanation
Indices: 991--1507 Score: 446
Period size: 171 Copynumber: 3.0 Consensus size: 166
981 NNNNNNNNNN
991 CAATTATGAGATTAT-AAAACTATTTAAAGCGTGTAATAAGCATTTTGAAAGAATAGGTGACTAT
1 CAATTATGAGATTATAAAAAC-ATTTAAAGCGTGTAATAAGC-TTTTGAAAGAATAGGTGACTAT
* * * * * ** *
1055 AAA-CAGACTTTCCTTACCAGTGAATTCCTTTTGCTTCACGTTTCTCAAGGTAAACATTCAATTA
64 AAATGA-ACTTT-TTTACCAATGAAAT-CTTTTTCTTCACGTTTCTTGAGGTAGACATTCAATTA
** * * * *
1119 TAACCTGTTTCAGGA-AAAATATAAAGAAATTGAACTTAAATT
126 TAGTCTGTTTTA--ACAAAATATAAAAAAATTCAACTTAAAAT
* * * * * * *
1161 CAATTTTGGGATTATAAAAGCATTTAAAGCGAGTAATAAGGCTTTCGAAAAAATTGGTGACTATA
1 CAATTATGAGATTATAAAAACATTTAAAGCGTGTAATAA-GCTTTTGAAAGAATAGGTGACTATA
* * ** * * *
1226 AATGGTATTTTTTTGTCAATGAATACCTTTTTCTTCATGTTTCTTGAGATAGACATTCAATTATA
65 AAT-GAACTTTTTTACCAATGAA-ATCTTTTTCTTCACGTTTCTTGAGGTAGACATTCAATTATA
******** *
1291 GTCTGTTTTAACAANNNNNNNNNNACAATTCAACTTAAAAT
128 GTCTGTTTTAACAA--AATATAAAAAAATTCAACTTAAAAT
* * * * *
1332 CAATTATGAGATTATAAAAACATTTAAAACGTGCAATAATGCTTTTGAAGGAATGGGTGACAATA
1 CAATTATGAGATTATAAAAACATTTAAAGCGTGTAATAA-GCTTTTGAAAGAATAGGTGACTATA
* *
1397 AATGAACTATTTTTACCAATGATAATCTTTTTCTTTACGTTTCTTGAGGTAGACATTCAATGATA
65 AATGAACT-TTTTTACCAATGA-AATCTTTTTCTTCACGTTTCTTGAGGTAGACATTCAATTATA
* *
1462 GTCTGTTTTAACTTAAAATATAAAAAAATTTAACCTAAAAT
128 GTCTGTTTTAAC--AAAATATAAAAAAATTCAACTTAAAAT
1503 CAATT
1 CAATT
1508 NNNNNNNNNN
Statistics
Matches: 266, Mismatches: 69, Indels: 23
0.74 0.19 0.06
Matches are distributed among these distances:
168 1 0.00
169 2 0.01
170 103 0.39
171 157 0.59
172 1 0.00
173 2 0.01
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.35
Consensus pattern (166 bp):
CAATTATGAGATTATAAAAACATTTAAAGCGTGTAATAAGCTTTTGAAAGAATAGGTGACTATAA
ATGAACTTTTTTACCAATGAAATCTTTTTCTTCACGTTTCTTGAGGTAGACATTCAATTATAGTC
TGTTTTAACAAAATATAAAAAAATTCAACTTAAAAT
Found at i:2531 original size:170 final size:170
Alignment explanation
Indices: 2227--3424 Score: 689
Period size: 170 Copynumber: 7.0 Consensus size: 170
2217 NNNNNNNNNN
* * * ** * *
2227 AAATGGACTTTTCTTGCCAATGAATGCTTTTTTCTTCATGTTTCTTGAGCTAGACAATCAATTAT
1 AAATGGACTTTTCTTGTCAATGAATACCTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTAT
* * * * **********
2292 AGTCTA-TTTTCAA-GAAAAATGTAAAAAAATTCAACTTAAAATTAATTTTGAGNNNNNNNNNNC
66 AGT-AAGTTTT-AACCAAAAATGTAAAAAAA-TCAACTTAAAATCAATTATGAGATTATAAAACC
*
2355 ATTTAAAGCGAGTAATAAGG-TCTTTGAAGGAATGGGTGACTAT
128 ATTTAAAGCGAGTAATAAGGCT-TTTGAAGGAATGAGTGACTAT
* * *
2398 AAATGGAC-TCTCTTGTCAATGAATACCTTTTTCTTCATGTTTCTCGATGTAGACATTCAATTAT
1 AAATGGACTTTTCTTGTCAATGAATACCTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTAT
* * * * *
2462 TGTAAGTTTTAACAAAAAATATAAAAATAATCAACTTAAAATCAATTATGAGATTGTAAAACTAT
66 AGTAAGTTTTAACCAAAAATGTAAAAA-AATCAACTTAAAATCAATTATGAGATTATAAAACCAT
**********
2527 TTAAAGCNNNNNNNNNNGCTTTTGAAGGAATGAGTGACTAT
130 TTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTGACTAT
* * * ** * *
2568 AAATGGACTTTTCTTGTCAATGAATTCCTTTTTCTTCACGTTTTTTGAGTTAGATATTCAATTAT
1 AAATGGACTTTTCTTGTCAATGAATACCTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTAT
* * **********
2633 AGTTAGTTTTAACCAAAAATGTAAAAAATTCAACTTAAAATCAATTANNNNNNNNNNAAACCATT
66 AGTAAGTTTTAACCAAAAATGTAAAAAAATCAACTTAAAATCAATTATGAGATTATAAAACCATT
* ** * * *
2698 TAAAGTGAGTAATAAAACTTTCGAAAGAATGGGTGACTAT
131 TAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTGACTAT
* * * * * * * * *
2738 AAATAGACTTTTCTTGCCAGTGAATACCATTTTCTTTATGTTTCTCAAGGTAAATATTGAATAAT
1 AAATGGACTTTTCTTGTCAATGAATACCTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTAT
* * * * *
2803 AATACGTTTTAACCAAAAATGTAAAAACAAATTGAACATAAAATCAATTTTGAGATTATAAAACC
66 AGTAAGTTTTAACCAAAAATGT-AAAA-AAA-TCAACTTAAAATCAATTATGAGATTATAAAACC
* * *
2868 ATTTAAAGCGAGAAACAAGGCTTTTGAAGGAATGAGTGACTAG
128 ATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTGACTAT
** *
2911 AAATGGACTATTT-TTACCAATGAATGA-TTTTTTCTTCATGTTTC-CTAAGGTAGACATTCAAT
1 AAATGGACT-TTTCTTGTCAATGAAT-ACCTTTTTCTTCATGTTTCTC-AAGGTAGACATTCAAT
** ******************************
2973 TATAGTCTGTTTTANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCAATTATGAGATTATAAAAC
63 TATAGTAAGTTTTA-ACCAAAAATGTAAAAAAATCAACTTAAAATCAATTATGAGATTATAAAAC
* * * *
3038 CATTTAAAGCAAGAAATAAGGCTTTTGAAGGAATTG-GTGATTTT
127 CATTTAAAGCGAGTAATAAGGCTTTTGAAGGAA-TGAGTGACTAT
* * * *
3082 AAAT-GACTTTTCTTGTCAATAAATGCCTTTTTCTTCAAGTTT-TCTAAGGTAAACATTCAATTA
1 AAATGGACTTTTCTTGTCAATGAATACCTTTTTCTTCATGTTTCTC-AAGGTAGACATTCAATTA
* * * * ** * *
3145 TAATCTA-TTTTGACTAAAACCGTAAAAAAAAATTGAA-TATAAAATCAATTTTGAGATTATAAA
65 TAGT-AAGTTTTAACCAAAAATGT--AAAAAAA-TCAACT-TAAAATCAATTATGAGATTATAAA
* * *
3208 ACCATTTAAAGCGAGAAATAATGCTTTTGAAGGAATGGGTGACTAT
125 ACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTGACTAT
* * * * *
3254 AAATAGACTTTT-TTTTACCAATGAATGA-CTTTTTCTTCACGTTTCTCAAAGTTA-ACATCCAA
1 AAATGGACTTTTCTTGT--CAATGAAT-ACCTTTTTCTTCATGTTTCTC-AAGGTAGACATTCAA
* ** * * * * * * *
3316 TTATAATCTGTTTTAACTAAAAATGTAAAAAAAATTAAAATGAAAATCAATTTTTACATTATAAA
62 TTATAGTAAGTTTTAACCAAAAATGT-AAAAAAA-TCAACTTAAAATCAATTATGAGATTATAAA
* *
3381 ACTATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGAGTGACT
125 ACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTGACT
3425 NNNNNNNNNN
Statistics
Matches: 768, Mismatches: 230, Indels: 56
0.73 0.22 0.05
Matches are distributed among these distances:
169 6 0.01
170 298 0.39
171 147 0.19
172 68 0.09
173 188 0.24
174 54 0.07
175 7 0.01
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.34
Consensus pattern (170 bp):
AAATGGACTTTTCTTGTCAATGAATACCTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTAT
AGTAAGTTTTAACCAAAAATGTAAAAAAATCAACTTAAAATCAATTATGAGATTATAAAACCATT
TAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTGACTAT
Found at i:2935 original size:343 final size:330
Alignment explanation
Indices: 2227--2986 Score: 666
Period size: 341 Copynumber: 2.2 Consensus size: 330
2217 NNNNNNNNNN
* * * * * *
2227 AAATGGACTTTTCTTGCCAATGAATG-CTTTTTTCTTCATGTTTCTTGAGCTAGACAATCAATTA
1 AAATGGACTTTTCTTACCAATGAATGAC-TTTTTCTTCACGTTTCCTAAGGTAGACATTCAATTA
* * * ****
2291 TAGTCTATTTTCAA-GAAAAATGTAAAAAAATTCAACTTAAAATTAATTTTGAGNNNNNNNNNNC
65 TAGTCTGTTTT-AACCAAAAATGT-AAAAAATTCAACTTAAAATCAA--TT-A-------AAACC
** * * *
2355 ATTTAAAGCGAGTAATAAGGTCTTTGAAGGAATGGGTGACTATAAATGGACTCTCTTGTCAATGA
118 ATTTAAAGCGAGTAATAAGAACTTTGAAAGAATGGGTGACTATAAATAGACTCTCTTGCCAATGA
* * * * * **
2420 ATACCTTTTTCTTCATGTTTCTCGATGTAGACATTCAATTATTGTAAGTTTTAACAAAAAATATA
183 ATACCATTTTCTTCATGTTTCTCAAGGTAAACATTCAATAATAATAAGTTTTAACAAAAAATATA
* * * * **********
2485 AAAATAATCAACTTAAAATCAATTATGAGATTGTAAAACTATTTAAAGCNNNNNNNNNNGCTTTT
248 AAAAAAATCAACATAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGAAACAAGGCTTTT
*
2550 GAAGGAATGAGTGACTAT
313 GAAGGAATGAGTGACTAG
** ** ** * * *
2568 AAATGGACTTTTCTTGTCAATGAATTCCTTTTTCTTCACGTTTTTTGAGTTAGATATTCAATTAT
1 AAATGGACTTTTCTTACCAATGAATGACTTTTTCTTCACGTTTCCTAAGGTAGACATTCAATTAT
2633 AGT-TAGTTTTAACCAAAAATGTAAAAAATTCAACTTAAAATCAATTANNNNNNNNNNAAACCAT
66 AGTCT-GTTTTAACCAAAAATGTAAAAAATTCAACTTAAAATCAATTA----------AAACCAT
* * *
2697 TTAAAGTGAGTAATAA-AACTTTCGAAAGAATGGGTGACTATAAATAGACTTTTCTTGCCAGTGA
120 TTAAAGCGAGTAATAAGAACTTT-GAAAGAATGGGTGACTATAAATAGAC-TCTCTTGCCAATGA
* * * * * *
2761 ATACCATTTTCTTTATGTTTCTCAAGGTAAATATTGAATAATAATACGTTTTAACCAAAAATGTA
183 ATACCATTTTCTTCATGTTTCTCAAGGTAAACATTCAATAATAATAAGTTTTAACAAAAAATATA
* *
2826 AAAACAAATTGAACATAAAATCAATTTTGAGATTATAAAACCATTTAAAGCGAGAAACAAGGCTT
248 AAAA-AAA-TCAACATAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGAAACAAGGCTT
2891 TTGAAGGAATGAGTGACTAG
311 TTGAAGGAATGAGTGACTAG
* *
2911 AAATGGACTATTT-TTACCAATGAATGATTTTTTCTTCATGTTTCCTAAGGTAGACATTCAATTA
1 AAATGGACT-TTTCTTACCAATGAATGACTTTTTCTTCACGTTTCCTAAGGTAGACATTCAATTA
2975 TAGTCTGTTTTA
65 TAGTCTGTTTTA
2987 NNNNNNNNNN
Statistics
Matches: 343, Mismatches: 64, Indels: 22
0.80 0.15 0.05
Matches are distributed among these distances:
337 1 0.00
338 2 0.01
339 4 0.01
340 72 0.21
341 138 0.40
342 3 0.01
343 119 0.35
344 4 0.01
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.35
Consensus pattern (330 bp):
AAATGGACTTTTCTTACCAATGAATGACTTTTTCTTCACGTTTCCTAAGGTAGACATTCAATTAT
AGTCTGTTTTAACCAAAAATGTAAAAAATTCAACTTAAAATCAATTAAAACCATTTAAAGCGAGT
AATAAGAACTTTGAAAGAATGGGTGACTATAAATAGACTCTCTTGCCAATGAATACCATTTTCTT
CATGTTTCTCAAGGTAAACATTCAATAATAATAAGTTTTAACAAAAAATATAAAAAAAATCAACA
TAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGAAACAAGGCTTTTGAAGGAATGAGTG
ACTAG
Found at i:3133 original size:343 final size:314
Alignment explanation
Indices: 2690--3330 Score: 448
Period size: 343 Copynumber: 1.9 Consensus size: 314
2680 NNNNNNNNNN
** *
2690 AAACCATTTAAAGTGAGTAATAAAACTTTCGAAAGAATGGGTGACTATAAATAGACTTTTCTTGC
1 AAACCATTTAAAGCAAGAAATAAAACTTTCGAAAGAATGGGTGACTATAAATAGACTTTTCTTGC
* * * * * * *
2755 CAGTGAATACCATTTTCTTTATGTTTCTCAAGGTAAATATTGAATAATAATAC-GTTTTAACCAA
66 CAATAAATACCATTTTCTTCAAGTTTCTCAAGGTAAACATTCAATAATAAT-CTATTTTAACCAA
* *
2819 AAATGTAAAAACAAATTGAACATAAAATCAATTTTGAGATTATAAAACCATTTAAAGCGAGAAAC
130 AAACGTAAAAAAAAATTGAACATAAAATCAATTTTGAGATTATAAAACCATTTAAAGCGAGAAAC
* *
2884 AAGGCTTTTGAAGGAATGAGTGACTAGAAATGGAC-TATTTTTACCAATGAATGATTTTTTCTTC
195 AAGGCTTTTGAAGGAATGAGTGACTAGAAATAGACTTATTTTTACCAATGAATGACTTTTTCTTC
* * * * *
2948 ATGTTTC-CTAAGGTAGACATTCAATTATAGTCTGTTTTANNNNNNNNNNNNNNNNNNNNNNNNN
260 ACGTTTCTCAAAGGTA-ACATCCAATTATAATCTGTTTTA------------------------C
******* *
3012 NNNNNNCA-ATTATG
300 AATTATGAGATTATA
* ** ** ** * * * * *
3026 AGATTATAAAACCATTTAAAGCAAGAAATAAGGCTTTTGAAGGAATTGGTGATTTTAAAT-GACT
1 AAACCAT-TTA-------AAGCAAGAAATAAAACTTTCGAAAGAATGGGTGACTATAAATAGACT
* * * *
3090 TTTCTTGTCAATAAATGCCTTTTTCTTCAAGTTT-TCTAAGGTAAACATTCAATTATAATCTATT
58 TTTCTTGCCAATAAATACCATTTTCTTCAAGTTTCTC-AAGGTAAACATTCAATAATAATCTATT
* * * *
3154 TTGACTAAAACCGTAAAAAAAAATTGAATATAAAATCAATTTTGAGATTATAAAACCATTTAAAG
122 TTAACCAAAAACGTAAAAAAAAATTGAACATAAAATCAATTTTGAGATTATAAAACCATTTAAAG
* * * * *
3219 CGAGAAATAATGCTTTTGAAGGAATGGGTGACTATAAATAGACTTTTTTTTACCAATGAATGACT
187 CGAGAAACAAGGCTTTTGAAGGAATGAGTGACTAGAAATAGACTTATTTTTACCAATGAATGACT
*
3284 TTTTCTTCACGTTTCTCAAAGTTAACATCCAATTATAATCTGTTTTA
252 TTTTCTTCACGTTTCTCAAAGGTAACATCCAATTATAATCTGTTTTA
3331 ACTAAAAATG
Statistics
Matches: 249, Mismatches: 44, Indels: 16
0.81 0.14 0.05
Matches are distributed among these distances:
336 4 0.02
337 1 0.00
342 3 0.01
343 149 0.60
344 86 0.35
345 6 0.02
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.34
Consensus pattern (314 bp):
AAACCATTTAAAGCAAGAAATAAAACTTTCGAAAGAATGGGTGACTATAAATAGACTTTTCTTGC
CAATAAATACCATTTTCTTCAAGTTTCTCAAGGTAAACATTCAATAATAATCTATTTTAACCAAA
AACGTAAAAAAAAATTGAACATAAAATCAATTTTGAGATTATAAAACCATTTAAAGCGAGAAACA
AGGCTTTTGAAGGAATGAGTGACTAGAAATAGACTTATTTTTACCAATGAATGACTTTTTCTTCA
CGTTTCTCAAAGGTAACATCCAATTATAATCTGTTTTACAATTATGAGATTATA
Found at i:3227 original size:172 final size:172
Alignment explanation
Indices: 3018--3424 Score: 525
Period size: 173 Copynumber: 2.4 Consensus size: 172
3008 NNNNNNNNNN
* * * * *
3018 CAATTATGAGATTATAAAACCATTTAAAGCAAGAAATAAGGCTTTTGAAGGAATTGGTGATTTTA
1 CAATTTTGAGATTATAAAACCATTTAAAGCGAGAAATAAGGCTTTTGAAGGAATGGGTGACTATA
* * *
3083 AAT-GACTTTTCTTGT-CAATAAATGCCTTTTTCTTCAAGTTT-TCTAAGGTAAACATTCAATTA
66 AATAGACTTTT-TTGTACAATAAATGACTTTTTCTTCAAGTTTCTC-AAAGTAAACATCCAATTA
* * *
3145 TAATCTATTTTGACTAAAACCGTAAAAAAAAATTGAATAT-AAAAT
129 TAATCTATTTTAACTAAAAACGT-AAAAAAAATT-AAAATGAAAAT
*
3190 CAATTTTGAGATTATAAAACCATTTAAAGCGAGAAATAATGCTTTTGAAGGAATGGGTGACTATA
1 CAATTTTGAGATTATAAAACCATTTAAAGCGAGAAATAAGGCTTTTGAAGGAATGGGTGACTATA
* * * *
3255 AATAGACTTTTTTTTACCAATGAATGACTTTTTCTTCACGTTTCTCAAAGTTAACATCCAATTAT
66 AATAGACTTTTTTGTA-CAATAAATGACTTTTTCTTCAAGTTTCTCAAAGTAAACATCCAATTAT
* *
3320 AATCTGTTTTAACTAAAAATGTAAAAAAAATTAAAATGAAAAT
130 AATCTATTTTAACTAAAAACGTAAAAAAAATTAAAATGAAAAT
* * * * * *
3363 CAATTTTTACATTATAAAACTATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGAGTGACT
1 CAATTTTGAGATTATAAAACCATTTAAAGCGAGAAATAAGGCTTTTGAAGGAATGGGTGACT
3425 NNNNNNNNNN
Statistics
Matches: 205, Mismatches: 25, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
172 69 0.34
173 77 0.38
174 57 0.28
175 2 0.01
ACGTcount: A:0.41, C:0.11, G:0.13, T:0.36
Consensus pattern (172 bp):
CAATTTTGAGATTATAAAACCATTTAAAGCGAGAAATAAGGCTTTTGAAGGAATGGGTGACTATA
AATAGACTTTTTTGTACAATAAATGACTTTTTCTTCAAGTTTCTCAAAGTAAACATCCAATTATA
ATCTATTTTAACTAAAAACGTAAAAAAAATTAAAATGAAAAT
Found at i:3965 original size:171 final size:169
Alignment explanation
Indices: 3518--5300 Score: 1252
Period size: 171 Copynumber: 10.4 Consensus size: 169
3508 NNNNNNNNNN
* * * * * * *
3518 TTTAAAGCAAGTAACAAGGTTTTTGAAGGAATGAGAGACTATAAATAGACCTTTCTT-CTGAATA
1 TTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATGGACTTTTCTTGC-CAATG
* * * * ** *
3582 AATGTGTTTTTCTACACGTTTCT-AAGGTAGGCATTCAATTATGGT-TGGTTTTAATGAAAAATC
65 AATG-CTTTTTCTTCACGTTTCTCAA-GTAGACATTCAATTATAGTCT-GTTTTAACAAAAAATG
* * *
3645 TAAGA-AATTCAACTTAAAATCAATTATGAGATTATAAAGCTA
127 TAAAACAATTCAACTTAAAATCAATTATGAGATTATAAAACCA
* * * * *
3687 CTTAAAGCGAGTAATAAGGCTTTTAAAAGAATGAGAGACTATAAATGTACTTTTCTTGCAAATGA
1 TTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATGGACTTTTCTTGCCAATGA
* * * * * * *
3752 ATGGTTTTTGCTACATGTTTCCCAAAGTATACATTTAATTATAGTCTGTTTTAACTAAAAATGTA
66 ATGCTTTTT-CTTCACGTTTCTC-AAGTAGACATTCAATTATAGTCTGTTTTAACAAAAAATGTA
**********
3817 AAACAATNNNNNNNNNNATCAATTATGAGATTATAAAACCA
129 AAACAATTCAACTTAAAATCAATTATGAGATTATAAAACCA
* ** *
3858 TATAAAGCGAGTAATAAAACTTTTGAAGGAACGAGAGACTATAAATGGACTTTTCTTGCCAATGA
1 TTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATGGACTTTTCTTGCCAATGA
** *
3923 ATGCTTCTTTCTTCACGTTTCTTGAGCTAGACATTCAATTATAGTCTATTTTAA-AGAAAAATGT
66 ATGCTT-TTTCTTCACGTTTCTCAAG-TAGACATTCAATTATAGTCTGTTTTAACA-AAAAATGT
* **********
3987 AAAATAATTCAACTTAANNNNNNNNNNGAGATTATAAAACCA
128 AAAACAATTCAACTTAAAATCAATTATGAGATTATAAAACCA
* * * * * *
4029 TTTAGAGCGGGTAATAAGG-TCTTTGAAAGAATGGGTGACTATAAATGGAC-TTTCTTCCCAATG
1 TTTAAAGCGAGTAATAAGGCT-TTTGAAGGAATGAGAGACTATAAATGGACTTTTCTTGCCAATG
* * * *
4092 AATGCCCTTTTCTTCACATTTCTCGATGTAGACATTCAATTATTGTCTGTTTTAACAAAAAATGT
65 AATG-CTTTTTCTTCACGTTTCTC-AAGTAGACATTCAATTATAGTCTGTTTTAACAAAAAATGT
* * * *
4157 AAAA-ATAATCGACTTAAAATCAATTATGAGATTGTAAAACTA
128 AAAACA-ATTCAACTTAAAATCAATTATGAGATTATAAAACCA
* * * * *
4199 TTTAAAGCGAGCAATAAGACTTTTGAACGAATGAGTGACTATAAATGGACTGTTT-TTACCAATG
1 TTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATGGACT-TTTCTTGCCAATG
* * * * *
4263 AATGCCTTTTTCTTCATGTTTCTCGAGATCGACATTCAATTATAGTCTG-TTTACACCAAAACTG
65 AATG-CTTTTTCTTCACGTTTCTCAAG-TAGACATTCAATTATAGTCTGTTTTA-ACAAAAAATG
* * * * **
4327 TAGAACAATTCAAATTAAAATCAATTGTGAGATTATAAATCTG
127 TAAAACAATTCAACTTAAAATCAATTATGAGATTATAAAACCA
* * **********
4370 TTTAAAGTGAATAATAAGGCTTTTGAAGGAATGAGAGACTATAAANNNNNNNNNNTTGCCAATGA
1 TTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATGGACTTTTCTTGCCAATGA
* * * *
4435 ATGCTTTTTTCTTTACGTTTCTCAAGGTAAACATTTAATTATAGTCTGTTTTAGCAAAAAATGTA
66 ATGC-TTTTTCTTCACGTTTCTCAA-GTAGACATTCAATTATAGTCTGTTTTAACAAAAAATGTA
* * * * *
4500 AAAGAAATTGAACATAAAATCAATTTTGAGATTATAAAATCA
129 AAA-CAATTCAACTTAAAATCAATTATGAGATTATAAAACCA
* * * * * *
4542 TTTAAAGCGAGAAACAAGGCTTTTGAAGGAATGGGTGACTAGAAATGGACATTTTTTTG-CAATG
1 TTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATGGAC-TTTTCTTGCCAATG
* * * *
4606 AATGATTTTTTCTTCATGTTTC-CTAAGATAGACATTCAATTATAGTCTGTTTTAATAAAAATTG
65 AATG-CTTTTTCTTCACGTTTCTC-AAG-TAGACATTCAATTATAGTCTGTTTTAACAAAAAATG
* **********
4670 TAAAAGAATTCAACTTAAAATCANNNNNNNNNNTATAAAACCA
127 TAAAACAATTCAACTTAAAATCAATTATGAGATTATAAAACCA
* * * * * * * *
4713 TTTAAAGCAAGAAATAAGACTTTTGAAGGAGTTG-GTGATTTTAAAT-GACTTTTCTTGTCAATG
1 TTTAAAGCGAGTAATAAGGCTTTTGAAGGA-ATGAGAGACTATAAATGGACTTTTCTTGCCAATG
* * * * * *
4776 AATGCCTTTTTCTTCAAGTTTC-CTAACGTAAACATTCAATTATAATCTATTTTGAGC-AAAACT
65 AATG-CTTTTTCTTCACGTTTCTC-AA-GTAGACATTCAATTATAGTCTGTTTT-AACAAAAAAT
* * * *
4839 ATAAAAAAATTGAA-TATAAAATCAATTTTGAGATTATAAAACCA
126 GTAAAACAATTCAACT-TAAAATCAATTATGAGATTATAAAACCA
** * * * * * *
4883 TTTAAAGCGA-TAAATAATACTTTCGAAAGAATGGGTGACTATAAATGGACTTTTTTTACCAATG
1 TTTAAAGCGAGT-AATAAGGCTTTTGAAGGAATGAGAGACTATAAATGGACTTTTCTTGCCAATG
* * * ***
4947 AATGATTTTTTCTTCGCGTTTC-CTAAGGTAGACATTCAATTACAGTCTGTTTTAA-TTTAAATG
65 AATG-CTTTTTCTTCACGTTTCTC-AA-GTAGACATTCAATTATAGTCTGTTTTAACAAAAAATG
* * * * * *
5010 TAACAA-AGTTCACCCTAAAATTAATTATGAGATTGTAAAACTA
127 TAA-AACAATTCAACTTAAAATCAATTATGAGATTATAAAACCA
* * * * * *
5053 TTTAAAGCGAGTAATAAGGCTTTTGAAAGAAT-ACGTGACTGTTAATGGACTTTTTTTGTCAATG
1 TTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGA-GAGACTATAAATGGACTTTTCTTGCCAATG
* * * * ** *****
5117 AATGTCTTTGTCTTCATGTTTCTAAAGGTAGACATTCAATTATACTCTGTTTTAATGAAANNNNN
65 AATG-CTTTTTCTTCACGTTTCTCAA-GTAGACATTCAATTATAGTCTGTTTTAACAAAAAATGT
***** * * *
5182 NNNNNAATTCAACTTAAAATCAATTATGACATTCTAAAACTA
128 AAAACAATTCAACTTAAAATCAATTATGAGATTATAAAACCA
* * ** * * * **
5224 TTTATAGCGGGTAATAAGGCTTTTGAAGGAATTTGTGATTTTAAATGGACTTTTCTTATCAATGA
1 TTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATGGACTTTTCTTGCCAATGA
5289 ATGCCTTTTTCT
66 ATG-CTTTTTCT
5301 NNNNNNNNNN
Statistics
Matches: 1260, Mismatches: 308, Indels: 90
0.76 0.19 0.05
Matches are distributed among these distances:
168 6 0.00
169 76 0.06
170 428 0.34
171 605 0.48
172 142 0.11
173 3 0.00
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.35
Consensus pattern (169 bp):
TTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATGGACTTTTCTTGCCAATGA
ATGCTTTTTCTTCACGTTTCTCAAGTAGACATTCAATTATAGTCTGTTTTAACAAAAAATGTAAA
ACAATTCAACTTAAAATCAATTATGAGATTATAAAACCA
Found at i:4181 original size:341 final size:338
Alignment explanation
Indices: 3518--5170 Score: 1293
Period size: 341 Copynumber: 4.8 Consensus size: 338
3508 NNNNNNNNNN
* * ** * * * * * *
3518 TTTAAAGCAAGTAACAAGGTTTTTGAAGGAATGAGAGACTATAAATAGACCTTTCTT-CTGAATA
1 TTTAAAGCGAGTAATAAGACTTTTGAAGGAATGAGTGACTATAAATGGACTTTTTTTAC-CAATG
* * * * *
3582 AATG-TGTTTTTCTACACGTTT-CTAAGGTAGGCATTCAATTATGGT-TGGTTTTAATGAAAAAT
65 AATGAT-TTTTTCTTCACGTTTCCTAAGATAGACATTCAATTATAGTCT-GTTTTAA-AAAAAAT
* * * * * *
3644 CTAAGA-AATTCAACTTAAAATCAATTATGAGATTATAAAGCTACTTAAAGCGAGTAATAAGGCT
127 GTAAAACAATTCAACTTAAAATCAATTGTGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCT
* * * * * * * **
3708 TTTAAAAGAATGAGAGACTATAAATGTACTTTTCTTGCAAATGAATG-GTTTTTGCTACATGTTT
192 TTTGAAGGAATGGGTGACTATAAATG-AC-TTTCTTGCCAATGAATGCCTTTTT-CTTCACATTT
* * * * * * * *********
3772 CCCAAAGTATACATTTAATTATAGTCTGTTTTAACTAAAAATGTAAAACAATNNNNNNNNNNATC
254 CTCAACGTAAACATTCAATTATAGTCTGTTTTAGCAAAAAATGTAAAAAAAT-TGACTTAAAATC
3837 AATTATGAGATTATAAAACCA
318 AATTATGAGATTATAAAACCA
* * * * * *
3858 TATAAAGCGAGTAATAAAACTTTTGAAGGAACGAGAGACTATAAATGGACTTTTCTTGCCAATGA
1 TTTAAAGCGAGTAATAAGACTTTTGAAGGAATGAGTGACTATAAATGGACTTTTTTTACCAATGA
* * * * * *
3923 ATGCTTCTTTCTTCACGTTTCTTGAGCTAGACATTCAATTATAGTCTATTTTAAAGAAAAATGTA
66 ATGATTTTTTCTTCACGTTTCCTAAGATAGACATTCAATTATAGTCTGTTTTAAA-AAAAATGTA
* ********** * *
3988 AAATAATTCAACTTAANNNNNNNNNNGAGATTATAAAACCATTTAGAGCGGGTAATAAGG-TCTT
130 AAACAATTCAACTTAAAATCAATTGTGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCT-TT
* * * *
4052 TGAAAGAATGGGTGACTATAAATGGACTTTCTTCCCAATGAATGCCCTTTTCTTCACATTTCTCG
194 TGAAGGAATGGGTGACTATAAAT-GACTTTCTTGCCAATGAATGCCTTTTTCTTCACATTTCTCA
* * * * *
4117 ATGTAGACATTCAATTATTGTCTGTTTTAACAAAAAATGTAAAAATAATCGACTTAAAATCAATT
258 ACGTAAACATTCAATTATAGTCTGTTTTAGCAAAAAATGTAAAAA-AATTGACTTAAAATCAATT
* *
4182 ATGAGATTGTAAAACTA
322 ATGAGATTATAAAACCA
* * *
4199 TTTAAAGCGAGCAATAAGACTTTTGAACGAATGAGTGACTATAAATGGACTGTTTTTACCAATGA
1 TTTAAAGCGAGTAATAAGACTTTTGAAGGAATGAGTGACTATAAATGGACTTTTTTTACCAATGA
** * * * * *
4264 ATGCCTTTTTCTTCATGTTT-CTCGAGATCGACATTCAATTATAGTCTG-TTTACACCAAAACTG
66 ATGATTTTTTCTTCACGTTTCCT-AAGATAGACATTCAATTATAGTCTGTTTTA-A-AAAAAATG
* * * ** * *
4327 TAGAACAATTCAAATTAAAATCAATTGTGAGATTATAAATCTGTTTAAAGTGAATAATAAGGCTT
128 TAAAACAATTCAACTTAAAATCAATTGTGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTT
* * ******** * * *
4392 TTGAAGGAATGAGAGACTATAAANNNNNNNNNNTTGCCAATGAATGCTTTTTTCTTTACGTTTCT
193 TTGAAGGAATGGGTGACTATAAA--TGACTTTCTTGCCAATGAATGCCTTTTTCTTCACATTTCT
* * *
4457 CAAGGTAAACATTTAATTATAGTCTGTTTTAGCAAAAAATGTAAAAGAAATTGAACATAAAATCA
256 CAACGTAAACATTCAATTATAGTCTGTTTTAGCAAAAAATGTAAAA-AAATTG-ACTTAAAATCA
* *
4522 ATTTTGAGATTATAAAATCA
319 ATTATGAGATTATAAAACCA
* * * * * *
4542 TTTAAAGCGAGAAACAAGGCTTTTGAAGGAATGGGTGACTAGAAATGGACATTTTTTT-GCAATG
1 TTTAAAGCGAGTAATAAGACTTTTGAAGGAATGAGTGACTATAAATGGAC-TTTTTTTACCAATG
* *
4606 AATGATTTTTTCTTCATGTTTCCTAAGATAGACATTCAATTATAGTCTGTTTTAATAAAAATTGT
65 AATGATTTTTTCTTCACGTTTCCTAAGATAGACATTCAATTATAGTCTGTTTTAA-AAAAAATGT
* ********** * * *
4671 AAAAGAATTCAACTTAAAATCANNNNNNNNNNTATAAAACCATTTAAAGCAAGAAATAAGACTTT
129 AAAACAATTCAACTTAAAATCAATTGTGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTT
* * * * *
4736 TGAAGGAGTTGGTGATTTTAAATGACTTTTCTTGTCAATGAATGCCTTTTTCTTCA-AGTTTC-C
194 TGAAGGAATGGGTGACTATAAATGAC-TTTCTTGCCAATGAATGCCTTTTTCTTCACA-TTTCTC
* * * * *
4799 TAACGTAAACATTCAATTATAATCTATTTTGAGC-AAAACTATAAAAAAATTGAATATAAAATCA
257 -AACGTAAACATTCAATTATAGTCTGTTTT-AGCAAAAAATGTAAAAAAATTGACT-TAAAATCA
*
4863 ATTTTGAGATTATAAAACCA
319 ATTATGAGATTATAAAACCA
* * * *
4883 TTTAAAGCGA-TAAATAATACTTTCGAAAGAATGGGTGACTATAAATGGACTTTTTTTACCAATG
1 TTTAAAGCGAGT-AATAAGACTTTTGAAGGAATGAGTGACTATAAATGGACTTTTTTTACCAATG
* * * ***
4947 AATGATTTTTTCTTCGCGTTTCCTAAGGTAGACATTCAATTACAGTCTGTTTTAATTTAAATGTA
65 AATGATTTTTTCTTCACGTTTCCTAAGATAGACATTCAATTATAGTCTGTTTTAAAAAAAATGTA
* * * * * * *
5012 ACAA-AGTTCACCCTAAAATTAATTATGAGATTGTAAAACTATTTAAAGCGAGTAATAAGGCTTT
130 A-AACAATTCAACTTAAAATCAATTGTGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTT
* ** * * * * * * ** *
5076 TGAAAGAATACGTGACTGTTAATGGACTTTTTTTGTCAATGAATGTCTTTGTCTTCATGTTTCTA
194 TGAAGGAATGGGTGACTATAAAT-GAC-TTTCTTGCCAATGAATGCCTTTTTCTTCACATTTCTC
* * *
5141 AAGGTAGACATTCAATTATACTCTGTTTTA
257 AACGTAAACATTCAATTATAGTCTGTTTTA
5171 ATGAAANNNN
Statistics
Matches: 1035, Mismatches: 246, Indels: 64
0.77 0.18 0.05
Matches are distributed among these distances:
340 146 0.14
341 481 0.46
342 206 0.20
343 190 0.18
344 12 0.01
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.35
Consensus pattern (338 bp):
TTTAAAGCGAGTAATAAGACTTTTGAAGGAATGAGTGACTATAAATGGACTTTTTTTACCAATGA
ATGATTTTTTCTTCACGTTTCCTAAGATAGACATTCAATTATAGTCTGTTTTAAAAAAAATGTAA
AACAATTCAACTTAAAATCAATTGTGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTG
AAGGAATGGGTGACTATAAATGACTTTCTTGCCAATGAATGCCTTTTTCTTCACATTTCTCAACG
TAAACATTCAATTATAGTCTGTTTTAGCAAAAAATGTAAAAAAATTGACTTAAAATCAATTATGA
GATTATAAAACCA
Found at i:6769 original size:171 final size:170
Alignment explanation
Indices: 6114--7777 Score: 858
Period size: 171 Copynumber: 9.7 Consensus size: 170
6104 NNNNNNNNNN
** * ** * * * *
6114 AATGAATGCCTTTTTCTTCATGTTTCTCAAGATCGACATTCAATTATAG-TCAGTTTTCACCAAA
1 AATGAATATCTTTTTCTTCACGTTTCTTGAGGTAGACATTCAATTATAGTTTA-TTTTAACCAAA
** * * * * * * *
6178 AATGTTGAACAATTCAAATTAAAATGAATTATGAGATTATAAATCTATTTAAAGTGAATAATAAG
65 AATGTAAAAAAACTCAACTTAAAATCAATTATGAGATTAGAAAACTATTTAAAGTGAGTAATAAG
* * ** * *
6243 GCTTTTGAAGGAATGAGAGACTATAAATATACTTTTCTTACC
130 GCTTTTGAAGGAAAGGGA-ACTATAAATGGACTTTTTTTGCC
* * ** *
6285 AATTAATA-CTATTTTCTTTACGTTTCTCAAGGTCA-ACATGT-AATTATAGTCTT-TTTTAGCA
1 AATGAATATCT-TTTTCTTCACGTTTCTTGAGGT-AGACAT-TCAATTATAGT-TTATTTTAAC-
* * * * * * *
6346 AAAAAATATAAAAATAA-TTAACTTAAAATTAATTATGAGATTATAAAACCATTGAAAGTGAGTA
61 CAAAAATGTAAAAA-AACTCAACTTAAAATCAATTATGAGATTAGAAAACTATTTAAAGTGAGTA
* * * * *
6410 ATAAGCCTTTTGAAAGAATGGGTAACTATAAATGGACTTTTCTTGCT
125 ATAAGGCTTTTGAAGGAAAGGG-AACTATAAATGGACTTTTTTTGCC
* ** ********** ** * * * * *
6457 AGTGAATGCCTTTNNNNNNNNNNTTCTCAAGGTAAACATTCAATTATAATCTGTTTTAA-AAAAA
1 AATGAATATCTTTTTCTTCACGTTTCTTGAGGTAGACATTCAATTATAGTTTATTTTAACCAAAA
* * * * * * * *
6521 TATATATAAAGAAATTAAACTTAAAATAAATTTTGGGATTATG-AAGCCATTTAAAGTGAGTAAT
66 -ATGTA-AAA-AAACTCAACTTAAAATCAATTATGAGATTA-GAAAACTATTTAAAGTGAGTAAT
*
6585 AAGGCTTTTGAAGGAAAGGGCAACTATAAATAGACTTTTTTTGCC
127 AAGGCTTTTGAAGGAAAGGG-AACTATAAATGGACTTTTTTTGCC
* * *
6630 AATGAATATCTTTTTCTTCACGTTTCTTAAGGTAGAGATTCAATTATAGTTTGTTTTAACCAAAA
1 AATGAATATCTTTTTCTTCACGTTTCTTGAGGTAGACATTCAATTATAGTTTATTTTAACCAAAA
**********
6695 ATGTAAAAAAACTCAACTTAAAATCAATTATGAGATTNNNNNNNNNNTTAAAGTGAGTAATAAGG
66 ATGTAAAAAAACTCAACTTAAAATCAATTATGAGATTAGAAAACTATTTAAAGTGAGTAATAAGG
6760 CTTTTGAAGGAATAGGTGAA-TATAAATGGAC-TTTTTTGCC
131 CTTTTGAAGGAA-AGG-GAACTATAAATGGACTTTTTTTGCC
** * * * * * * * *
6800 AATGAATGCCTTTTTTTTTATGTTTCTCGAGATAGACATTCAATTATGGCTTATTTTACCCAAAA
1 AATGAATATCTTTTTCTTCACGTTTCTTGAGGTAGACATTCAATTATAGTTTATTTTAACCAAAA
* * * *
6865 ATGTAAAACAATTGAACTTAAAATCAATTATGATATTAGAAAACTATTTAAAGTGAGTAATAAGG
66 ATGTAAAAAAACTCAACTTAAAATCAATTATGAGATTAGAAAACTATTTAAAGTGAGTAATAAGG
* * * * *
6930 CTTATGAAGGAATGGGTGACTACAAATGGACTTTTTTTGTC
131 CTTTTGAAGGAAAGGG-AACTATAAATGGACTTTTTTTGCC
* *
6971 AATGAATATCTTTTTCTTCACATTTCTTGAGGTAGACATTCAATTATCA-TCTATTTTAACCAAA
1 AATGAATATCTTTTTCTTCACGTTTCTTGAGGTAGACATTCAATTAT-AGTTTATTTTAACCAAA
* * * ********** * **
7035 AATGTAAAAATATTTANNNNNNNNNNAATTATGAGATTAGAAAATTATTTAAAGCAAGTAATAAG
65 AATGTAAAAAAACTCAACTTAAAATCAATTATGAGATTAGAAAACTATTTAAAGTGAGTAATAAG
* * *
7100 GC-TTTGAAGGAATAGGTG-ATTTTAAATGGACTTTTTTTACC
130 GCTTTTGAAGGAA-AGG-GAACTATAAATGGACTTTTTTTGCC
* * * * * * * *
7141 AATAAATACCTTTTT-TTCACGTTTCTCGAGGTAGATAATT-AATTATTGTCTGTTTTAA-TAAA
1 AATGAATATCTTTTTCTTCACGTTTCTTGAGGTAGA-CATTCAATTATAGTTTATTTTAACCAAA
* * * * *
7203 AATTTAAAAATAA-TCAATTTAAAATCAATTATGAGATTATAAAGCCT-TTTAGAA-CGAGTAAT
65 AATGTAAAAA-AACTCAACTTAAAATCAATTATGAGATTAGAAA-ACTATTTA-AAGTGAGTAAT
* * * *
7265 AAGCCTTTTGAA-GAAATGGATAACTATAAATGAACTTTTCTTGCC
127 AAGGCTTTTGAAGGAAA-GG-GAACTATAAATGGACTTTTTTTGCC
* ** * ** ** * * * * *****
7310 AGTGAATGCCTTTTTCTTCACATTTCTCAAGACAAACATTCAATTATAATCTGTTTTAACNNNNN
1 AATGAATATCTTTTTCTTCACGTTTCTTGAGGTAGACATTCAATTATAGTTTATTTTAACCAAAA
***** * * * * * * * *
7375 NNNNNAAGAAATTGAAATTAAAATCAATT-TTAGGATTATG-AAACCATTCAAAGTGACTAATAA
66 ATGTAAAAAAACTCAACTTAAAATCAATTATGA-GATTA-GAAAACTATTTAAAGTGAGTAATAA
* * * * *
7438 GGCTTTTGAAGGAATGGGCGACTATAAATAGATTTTTTTTGCA
129 GGCTTTTGAAGGAAAGGG-AACTATAAATGGACTTTTTTTGCC
* * ** * * * * * ***
7481 AATAAATA-CATTTTTCTTCACATTTCTCAATGTAGAGATTCAATTATAATCTGTTTTAACCNNN
1 AATGAATATC-TTTTTCTTCACGTTTCTTGAGGTAGACATTCAATTATAGTTTATTTTAACCAAA
******* * * * * * * *
7545 NNNNNNNAACAATTCAACTTAAAATCAATTTTGTGATTATAAAACTGTTTAAA-TGGAGTGATAA
65 AATGTAAAAAAACTCAACTTAAAATCAATTATGAGATTAGAAAACTATTTAAAGT-GAGTAATAA
* * * * * * *
7609 GGGTGTTGAAGGAATTGGCAACTATGAATAGACTTTTTTT-CTA
129 GGCTTTTGAAGGAA-AGGGAACTATAAATGGACTTTTTTTGC-C
* * ** * * * *
7652 AATGAATACCTTTTTCTTCATGTTTCTCAAGGTAGAAATTTAATTATAGTCTATTTTGACCAAAA
1 AATGAATATCTTTTTCTTCACGTTTCTTGAGGTAGACATTCAATTATAGTTTATTTTAACCAAAA
* * * * * *
7717 TTGTAATACAATTCAACTTAAAATTAATTATGAGATTATAAAACTATTTAAAGTGAGTAAT
66 ATGTAAAAAAACTCAACTTAAAATCAATTATGAGATTAGAAAACTATTTAAAGTGAGTAAT
7778 NNNNNNNNNN
Statistics
Matches: 1153, Mismatches: 287, Indels: 106
0.75 0.19 0.07
Matches are distributed among these distances:
167 1 0.00
168 51 0.04
169 79 0.07
170 224 0.19
171 517 0.45
172 145 0.13
173 132 0.11
174 4 0.00
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.36
Consensus pattern (170 bp):
AATGAATATCTTTTTCTTCACGTTTCTTGAGGTAGACATTCAATTATAGTTTATTTTAACCAAAA
ATGTAAAAAAACTCAACTTAAAATCAATTATGAGATTAGAAAACTATTTAAAGTGAGTAATAAGG
CTTTTGAAGGAAAGGGAACTATAAATGGACTTTTTTTGCC
Found at i:7369 original size:339 final size:331
Alignment explanation
Indices: 6750--7369 Score: 680
Period size: 339 Copynumber: 1.8 Consensus size: 331
6740 NNTTAAAGTG
* * *
6750 AGTAATAAGGCTTTTGAAGGAATAGGTGAATATAAATGGACTTTTTTGCCAATGAATGCCTTTTT
1 AGTAATAAGGCTTTTGAAGGAATAGGTGAATATAAATGGACTTTTTTACCAATAAATACCTTTTT
* * * * * *
6815 TTTTATGTTTCTCGAGATAGACATTCAATTATGGCTTATTTTACCCAAAAATGTAAAACAATTGA
66 TTTCACGTTTCTCGAGATAGAAATTCAATTATGGCTTATTTTACACAAAAATGTAAAACAAATCA
* * * *
6880 ACTTAAAATCAATTATGATATTAGAAAACTATTTAAAGTGAGTAATAAGGCTTATGAAGGAATGG
131 ACTTAAAATCAATTATGAGATTAGAAAACTATTTAAAGCGAGTAATAAGCCTTATGAAGAAATGG
* * * * * * ** ** *
6945 GTGACTACAAATGGACTTTTTTTGTCAATGAATATCTTTTTCTTCACATTTCTTGAGGTAGACAT
196 ATAACTACAAATGAACTTTTCTTGCCAATGAATACCTTTTTCTTCACATTTCTCAAGACAAACAT
*
7010 TCAATTATCATCTATTTTAACCAAAAATGTAAAAATATTTANNNNNNNNNNAATTATGAGATTAG
261 TCAATTATAATCTATTTTAACCAAAAATGTAAAAATATTTA----------AATTATGAGATTAG
7075 AAAATTATTTAAAGCA
316 AAAATTATTTAAAGCA
* *
7091 AGTAATAAGGC-TTTGAAGGAATAGGTGATTTTAAATGGACTTTTTTTACCAATAAATACC-TTT
1 AGTAATAAGGCTTTTGAAGGAATAGGTGAATATAAATGGAC-TTTTTTACCAATAAATACCTTTT
* * * * *
7154 TTTTCACGTTTCTCGAGGTAGATAATT-AATTATTG-TCTGTTTTA-ATAAAAATTTAAAA-ATA
65 TTTTCACGTTTCTCGAGATAGA-AATTCAATTATGGCT-TATTTTACACAAAAATGTAAAACA-A
* * * *
7215 ATCAATTTAAAATCAATTATGAGATTATAAAGCCT-TTTAGAA-CGAGTAATAAGCCTTTTGAAG
127 ATCAACTTAAAATCAATTATGAGATTAGAAA-ACTATTTA-AAGCGAGTAATAAGCCTTATGAAG
* * *
7278 AAATGGATAACTATAAATGAACTTTTCTTGCCAGTGAATGCCTTTTTCTTCACATTTCTCAAGAC
190 AAATGGATAACTACAAATGAACTTTTCTTGCCAATGAATACCTTTTTCTTCACATTTCTCAAGAC
*
7343 AAACATTCAATTATAATCTGTTTTAAC
255 AAACATTCAATTATAATCTATTTTAAC
7370 NNNNNNNNNN
Statistics
Matches: 233, Mismatches: 40, Indels: 14
0.81 0.14 0.05
Matches are distributed among these distances:
338 1 0.00
339 136 0.58
340 66 0.28
341 30 0.13
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.37
Consensus pattern (331 bp):
AGTAATAAGGCTTTTGAAGGAATAGGTGAATATAAATGGACTTTTTTACCAATAAATACCTTTTT
TTTCACGTTTCTCGAGATAGAAATTCAATTATGGCTTATTTTACACAAAAATGTAAAACAAATCA
ACTTAAAATCAATTATGAGATTAGAAAACTATTTAAAGCGAGTAATAAGCCTTATGAAGAAATGG
ATAACTACAAATGAACTTTTCTTGCCAATGAATACCTTTTTCTTCACATTTCTCAAGACAAACAT
TCAATTATAATCTATTTTAACCAAAAATGTAAAAATATTTAAATTATGAGATTAGAAAATTATTT
AAAGCA
Found at i:8673 original size:169 final size:169
Alignment explanation
Indices: 8256--8698 Score: 473
Period size: 169 Copynumber: 2.6 Consensus size: 169
8246 GTAAAAATTC
* * ** *
8256 AAAATATATAAAGAAATTGAACTTAAAATCAATTTTGAGATTATAAAACCGTTCAAAGTGAGTAA
1 AAAATATAT-AA-AAATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGTGAGTAA
* * * * ** *
8321 TAAGGCTTTTGAAGAAATATGTGACTATAAAT-ATAGTTTTTTTGTCAATGAATACCTTTTTCTT
64 TAAGGCTTTTGAAGGAATAGGTGACTATAAATGA-A-CTTATTTACCAATGAATACATTTTTCTT
* *
8385 CATGTTTCTTATCGTAGACATTCAATTATAGTCTGTTTTAACCA
127 CA-GTTTCTCAACGTAGACATTCAATTATAGTCTGTTTTAACCA
* * * *
8429 AATATGTA-AAACAATTCAACTTAAAATTAATTAT-ACGATTATAAAACTATTTAAAG-CATGTA
1 AAAATATATAAA-AATTCAACTTAAAATCAATTATGA-GATTATAAAACTATTTAAAGTGA-GTA
* * * * * * *
8491 AAAATGTTTTTGAAGGAATGGGTGACTATAAATGGACTTATTTACCAATGAATATATTTTTTTTA
63 ATAAGGCTTTTGAAGGAATAGGTGACTATAAATGAACTTATTTACCAATGAATACATTTTTCTT-
* * *
8556 CA-TTTCTCAAGGTAGATATTCAATTATAGTCTGTTTTAACTA
127 CAGTTTCTCAACGTAGACATTCAATTATAGTCTGTTTTAACCA
** * *
8598 AAAATATATAAAAATTTTACTTAAAATCAATTATGAGATTATAAAACTATTTAGAGTGAGTAATG
1 AAAATATATAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGTGAGTAATA
*
8663 AGGCTTTTGAAAGAATAGGTGACTATAAATGAACTT
66 AGGCTTTTGAAGGAATAGGTGACTATAAATGAACTT
8699 TTCTTGCCAA
Statistics
Matches: 220, Mismatches: 42, Indels: 20
0.78 0.15 0.07
Matches are distributed among these distances:
169 114 0.52
170 29 0.13
171 71 0.32
173 6 0.03
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.38
Consensus pattern (169 bp):
AAAATATATAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGTGAGTAATA
AGGCTTTTGAAGGAATAGGTGACTATAAATGAACTTATTTACCAATGAATACATTTTTCTTCAGT
TTCTCAACGTAGACATTCAATTATAGTCTGTTTTAACCA
Found at i:10321 original size:171 final size:169
Alignment explanation
Indices: 9676--10485 Score: 653
Period size: 171 Copynumber: 4.8 Consensus size: 169
9666 NNNNNNNNNN
* * * *
9676 GATTTTAAGTTGAATTCTTTTATATTTTTGGTTAAAACAGATTATAATTGAATGTCTATCTTGAG
1 GATTTTAAGTTAAATTTTTTTAAATTTTTGGTTAAAACAGATTATAATTGAATGTCTA-CTCGAG
* * * * *
9741 AAACGTAAAG-AAAAGGCATTCATTAGCAAAAAAAAAT-CATTTATAGCCACCCATTCCTTCAAA
65 AAACATGAAGAAAAAGGCATTCATTGGC-AAAAAAAGTCCATTTATAGTCACCCATTCCTTCAAA
* * **********
9804 AGCCTTATTGCTCACTTTAAATNNNNNNNNNNTCTCATAATT
129 AGCCTTATTACTC-GTTTAAATGGTTTTATAATCTCATAATT
* * * * *
9846 GATTTTAAGTTAAACTTTTTTACA-TTTTGGTT-AAACAGACTATAATTAAATGTCGACTCTGAG
1 GATTTTAAGTTAAATTTTTTTAAATTTTTGGTTAAAACAGATTATAATTGAATGTCTACTC-GAG
* ** * *
9909 AAACCTGAAGAAAAAATCATTCATTCGTAAAAAAAGTCCATTTATAGTCACCCATTCCTTCAAAA
65 AAACATGAAGAAAAAGGCATTCATTGGCAAAAAAAGTCCATTTATAGTCACCCATTCCTTCAAAA
* ********* *
9974 GCCTTATTGCTNNNNNNNNNNGGTTTTATAATCTCAAAATT
130 GCCTTATTACT-CGTTTAAATGGTTTTATAATCTCATAATT
* * * * * * * *
10015 GATTTTATGTTCAATTTTTTTTATATTTTTGATTAAAACAGATTATAATTCAATATTTACTTTGA
1 GATTTTAAGTT-AAATTTTTTTAAATTTTTGGTTAAAACAGATTATAATTGAATGTCTAC-TCGA
* ********** * *** **
10080 GAAACTTGAAGAAAAAGGCNNNNNNNNNNAAGAAAAGTCCATTTATAGTCACTTTTTTATTCAAA
64 GAAACATGAAGAAAAAGGCATTCATTGGCAAAAAAAGTCCATTTATAGTCACCCATTCCTTCAAA
* *
10145 AGCCTTATTACTCGTTATAGATGGTTTTATAAGCTCATAATT
129 AGCCTTATTACTCGTT-TAAATGGTTTTATAATCTCATAATT
*
10187 GATTTTAAGTTAAATTTTTTTAAATTTTTTGTTAAAACAGATTATAATTGAATGTCTATCTCGAG
1 GATTTTAAGTTAAATTTTTTTAAATTTTTGGTTAAAACAGATTATAATTGAATGTCTA-CTCGAG
* * * * *
10252 AAACATAAAGAAATAGGCATTCATTGGCAAAAAAAGTCTATTTATAGTCATCCATTCCTTCATAA
65 AAACATGAAGAAAAAGGCATTCATTGGCAAAAAAAGTCCATTTATAGTCACCCATTCCTTCAAAA
*
10317 GCCTTATTACTCGCTTTAAATGGTCTTATAATCTCATAATT
130 GCCTTATTACTCG-TTTAAATGGTTTTATAATCTCATAATT
* * * * * * *
10358 GATTTTAGGTTGAATTTATTT-AATTTTTAGTTAGAACAGATTATAATTGAATGTTTAC-CTTAG
1 GATTTTAAGTTAAATTTTTTTAAATTTTTGGTTAAAACAGATTATAATTGAATGTCTACTC-GAG
* * ** * *
10421 AAAACATGTATAAAAAACCATTGATTGAG-AAAAAAAGTCTATTTATAGTCACCCATTCCTTCAA
65 -AAACATGAAGAAAAAGGCATTCATTG-GCAAAAAAAGTCCATTTATAGTCACCCATTCCTTCAA
10485 A
128 A
10486 NNNNNNNNNN
Statistics
Matches: 498, Mismatches: 128, Indels: 28
0.76 0.20 0.04
Matches are distributed among these distances:
167 2 0.00
168 41 0.08
169 80 0.16
170 116 0.23
171 148 0.30
172 110 0.22
173 1 0.00
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.37
Consensus pattern (169 bp):
GATTTTAAGTTAAATTTTTTTAAATTTTTGGTTAAAACAGATTATAATTGAATGTCTACTCGAGA
AACATGAAGAAAAAGGCATTCATTGGCAAAAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAG
CCTTATTACTCGTTTAAATGGTTTTATAATCTCATAATT
Found at i:11279 original size:170 final size:170
Alignment explanation
Indices: 10611--11300 Score: 543
Period size: 171 Copynumber: 4.0 Consensus size: 170
10601 NNNNNNNNNN
*
10611 TATAATCTCATAATTGATTTTAAGTTGAATTGTTTTACATTTTTTGTAAAAACAGACTATAATTG
1 TATAATCTCATAATTGATTTTAAGTTGAATT-TTTTACATTTTTTGTTAAAACAGACTATAATTG
* * * * **
10676 AATGTGTACCTCAAGAAACGTGAAGAAAAAGGCATTTC-TTGATAAAAAAAA-TTTATTTATAGT
65 AATGTCTACCTCGAGAAACTTGAAGAAAAAGGCA-TTCATTGACAAAAAAAAGTCCATTTATAGT
** * **
10739 CACCCATTATTTTAAGAGCCTTATTACTCTTTTTAAATAGTTT
129 CACCCATTCCTTCAA-AGCCTTATTACTCGCTTTAAATAGTTT
********* **
10782 T-TAAATCTCATAATTGATTTTAAGTTGANNNNNNNNNNATTTTTCATTAAAACAGA-TAATAAT
1 TAT-AATCTCATAATTGATTTTAAGTTGA-ATTTTTTACATTTTTTGTTAAAACAGACT-ATAAT
* * * * ** * *
10845 TGAATGTGTACCTTGAGAAA-TGTGAAGAAAAAGGTATTTATTG-GTAGAAAAAGTCCATTTAGA
63 TGAATGTCTACCTCGAGAAACT-TGAAGAAAAAGGCATTCATTGACAAAAAAAAGTCCATTTATA
* * * * * *
10908 GTTACTCATTCCATCAAAAGTCTTATTACTCACTTTAAATGGTTT
127 GTCACCCATTCCTTC-AAAGCCTTATTACTCGCTTTAAATAGTTT
********** * *
10953 TATAATCTCNNNNNNNNNNTTAAGTTAAATGTTTTTACATTTTTTGTTAAAACAGACTATAAGTG
1 TATAATCTCATAATTGATTTTAAGTTGAAT-TTTTTACATTTTTTGTTAAAACAGACTATAATTG
* * * * *
11018 AATGTCTACCTCGAGAAACAT-AAAAAAAAAGTATTCATTGAC-AAGAAAAGTCCATTTATAGTC
65 AATGTCTACCTCGAGAAACTTGAAGAAAAAGGCATTCATTGACAAAAAAAAGTCCATTTATAGTC
* * ********* * *
11081 TCTCATTNNNNNNNNNNCCTTCTTACTCGCTTTAAATGGTTT
130 ACCCATT-CCTTCAAAGCCTTATTACTCGCTTTAAATAGTTT
* * *
11123 TATAATCTCATAATTGATTTTTAGTTGAA-TTTTTATATTTTTGGTTAAAACAGACTATAATTGA
1 TATAATCTCATAATTGATTTTAAGTTGAATTTTTTACATTTTTTGTTAAAACAGACTATAATTGA
* * * * *
11187 ATGTCAACCTTGAGAAACTTGAAGAAAAAGGCATTCATTGGCAAAAAAAAGTCTATTTACAGTCA
66 ATGTCTACCTCGAGAAACTTGAAGAAAAAGGCATTCATTGACAAAAAAAAGTCCATTTATAGTCA
11252 CCCATTCCTTCAGAAGCCTTATTACTCGCTTTAAATAGTTT
131 CCCATTCCTTCA-AAGCCTTATTACTCGCTTTAAATAGTTT
11293 TATAATCT
1 TATAATCT
11301 NNNNNNNNNN
Statistics
Matches: 385, Mismatches: 118, Indels: 33
0.72 0.22 0.06
Matches are distributed among these distances:
168 49 0.13
169 17 0.04
170 142 0.37
171 173 0.45
172 4 0.01
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.37
Consensus pattern (170 bp):
TATAATCTCATAATTGATTTTAAGTTGAATTTTTTACATTTTTTGTTAAAACAGACTATAATTGA
ATGTCTACCTCGAGAAACTTGAAGAAAAAGGCATTCATTGACAAAAAAAAGTCCATTTATAGTCA
CCCATTCCTTCAAAGCCTTATTACTCGCTTTAAATAGTTT
Found at i:11732 original size:159 final size:160
Alignment explanation
Indices: 11425--11743 Score: 423
Period size: 161 Copynumber: 2.0 Consensus size: 160
11415 TGAAAGAATA
* *
11425 GGTGACTATAAATGAACTTTTCTTGCCAATAAATACCTTTTTCTTCATGTTTTCGAAGGTAGACA
1 GGTGACTATAAATGAACTTTTCTTGCAAATAAATACCTTTATCTTCATGTTTTCGAAGGTAGACA
* *
11490 TTCAATTATGATCTGTTCTAATAAAACATGTGAAAAAATTCAACCTAAAATCAATTTTGAGATTA
66 TTCAATTATGATCTGTTCTAACAAAACATGT-AAAAAATTCAACCTAAAATCAATTATGAGATTA
* *
11555 TAAAACCATTTAATGCGAGTAATAAGGCTTG
130 TAAAACCACTTAAAGCGAGTAATAAGGCTTG
* * * * * *
11586 GGTGACTATAAATGGACTTTTTTTGCAAATGAATGCCTTTATCTTCATGTTTCTC-AAGGTTGAT
1 GGTGACTATAAATGAACTTTTCTTGCAAATAAATACCTTTATCTTCATGTTT-TCGAAGGTAGAC
* *
11650 ATTCAATTAT-AGTCTGTTTTAACCAAAA-ATGT-AAAAATTTAA-CTAAAAATCAATTATGAGA
65 ATTCAATTATGA-TCTGTTCTAA-CAAAACATGTAAAAAATTCAACCT-AAAATCAATTATGAGA
*
11711 TTATAAAACTACTTAAAGCGAGTAATAAGGCTT
127 TTATAAAACCACTTAAAGCGAGTAATAAGGCTT
11744 NNNNNNNNNN
Statistics
Matches: 139, Mismatches: 15, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
158 2 0.01
159 54 0.39
160 1 0.01
161 76 0.55
162 6 0.04
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.36
Consensus pattern (160 bp):
GGTGACTATAAATGAACTTTTCTTGCAAATAAATACCTTTATCTTCATGTTTTCGAAGGTAGACA
TTCAATTATGATCTGTTCTAACAAAACATGTAAAAAATTCAACCTAAAATCAATTATGAGATTAT
AAAACCACTTAAAGCGAGTAATAAGGCTTG
Found at i:14372 original size:171 final size:169
Alignment explanation
Indices: 13260--16043 Score: 1477
Period size: 171 Copynumber: 16.3 Consensus size: 169
13250 NNNNNNNNNN
* * * *
13260 AAAAAATTTAACTTAAAATCAATTATGATATTATACAACTATTTAAAGCGAGTAATAAGGCTTTC
1 AAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTT
* * * * **
13325 GAAGGAAT-AGGTGACAATGAATGAACTTTTCTTGCTAAAGAATGCCTTTTTCTTCATATTT-TC
66 GAAGGAATGA-GTGACTATAAATGAACTTTT-TTGCCAATGAATGCCTTTTTCTTCACGTTTCT-
** * * * **
13388 AAAGGCAGACATTCAATTATAATCTGTTCTAACCAAAAATGT
128 TGAGGTAGACATTCAATTATAGTCTGTTTTAATAAAAAATGT
********* * *
13430 AAAANNNNNNNNNNTAAAATCAATTATAAGATTATAAAACTATTTAAAGCGAGTAATAAAGCTTT
1 AAAA-AATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTT
* * * ** *
13495 TCAAGGAATGAGTGACTATAAATGGACTTTTTGTGACAATGAATGATTTTTTTCTTCACATTTCT
65 TGAAGGAATGAGTGACTATAAATGAACTTTTT-TGCCAATGAATG-CCTTTTTCTTCACGTTTCT
** * ************
13560 CAAGGTA-AGCATTTAATTATAGTCTG-TTNNNNNNNNNNNNT
128 TGAGGTAGA-CATTCAATTATAGTCTGTTTTAATAAAAAATGT
* * * * *
13601 AAAAAAGTTCAACTTAAAATTAATTATGAGATTATAAAACCATTTAAAGCGAGCAATCATGCTTT
1 AAAAAA-TTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTT
* * *********
13666 TGAAGGAAT-AGGTGAATATAAATG-GCTTTTTTTTGCCAATGAATGCCTTTTTCTNNNNNNNNN
65 TGAAGGAATGA-GTGACTATAAATGAAC--TTTTTTGCCAATGAATGCCTTTTTCTTCACGTTTC
*** * *
13729 NCAAAGTAGACATTCAATTATAGTTTGTTTTAA-ACAAAAATGT
127 TTGAGGTAGACATTCAATTATAGTCTGTTTTAATA-AAAAATGT
* **********
13772 AAAATAATTCAACATAAAATCAATTANNNNNNNNNNAAA-TCATTTAAAGCGAGTAATAAGGCTT
1 AAAA-AATTCAACTTAAAATCAATTATGAGATTATAAAACT-ATTTAAAGCGAGTAATAAGGCTT
* * * *
13836 CTGAAAGAATGAGAGACTATAAA-CAGACTTTTCTTGCCAATGAATGCCTTTTTCTT-ATCGTTT
64 TTGAAGGAATGAGTGACTATAAATGA-ACTTTT-TTGCCAATGAATGCCTTTTTCTTCA-CGTTT
* * **
13899 TTTGAGGTAGACATTCAATCATAGTCTGTTTTAACCAAAAATGT
126 CTTGAGGTAGACATTCAATTATAGTCTGTTTTAATAAAAAATGT
********** * *
13943 AAAAAAATTTNNNNNNNNNNT-AATTATGAGATAATAAAACTATTTAAAGTGAGTAATAAGGCTT
1 -AAAAAA-TTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTT
* * * * ** *
14007 TTGAAGGAAT-ATGTGATTTTCAATGGACTTTTCTTATCAATGAATGCCTTTTTCTTCACCTTTC
64 TTGAAGGAATGA-GTGACTATAAATGAACTTTT-TTGCCAATGAATGCCTTTTTCTTCACGTTTC
* * * *
14071 TTGAGGTAGACATTCAATTATAATTTGTTTTGATGAAAAATGT
127 TTGAGGTAGACATTCAATTATAGTCTGTTTTAATAAAAAATGT
* * * * **********
14114 AAAAACAAATTGAACTTAAAATCAATTTTGGGATTATAAAACCATTNNNNNNNNNNAATAAGGCT
1 --AAA-AAATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCT
* *
14179 TTTGAAGGAATGGGTGACTATAAATGAACTTGTTTTGCCAATGAATGCCTTTTTCTTCATGTTTC
63 TTTGAAGGAATGAGTGACTATAAATGAACTT-TTTTGCCAATGAATGCCTTTTTCTTCACGTTTC
* * * *
14244 TTGAGATAGACGTTCAATTATAGTCTGTTTTGATAAAAAATAT
127 TTGAGGTAGACATTCAATTATAGTCTGTTTTAATAAAAAATGT
* *
14287 AAGAAAATTCAACTAAAAATCAAATATGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTT
1 AA-AAAATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTT
* * * * * ** * **
14352 TGGAGGAATGCGTGACTATAAGTGGACTTTTTTACCAATGAATATCTTTGTCTTCATATTTCTTG
65 TGAAGGAATGAGTGACTATAAATGAACTTTTTTGCCAATGAATGCCTTTTTCTTCACGTTTCTTG
* * * ********
14417 AGGTAGACATTCAATTATAATCTGTTCTAACANNNNNNNNN
130 AGGTAGACATTCAATTATAGTCTGTTTTAATA-AAAAATGT
* * * * * * *
14458 NAAAAATTCAACCTAAAATCAATTATGAGATTAAAAAATTATTTAAAGTGAATAAGAAGG-TTTG
1 AAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTT-
* * * *
14522 TGAAGGAATGAGTGACTATAAAT-AGACTTTTTTTGTCAATGATTGCCTTTTTCGTCATGTTTCT
65 TGAAGGAATGAGTGACTATAAATGA-AC-TTTTTTGCCAATGAATGCCTTTTTCTTCACGTTTCT
* * * *
14586 CGATGCT-GACATTCAATTATAGTCTATTTTAACAAAAAATGT
128 TGA-GGTAGACATTCAATTATAGTCTGTTTTAATAAAAAATGT
* ********** * *
14628 AAAAAATTTAACTTAAAATCAATTATGAGATTANNNNNNNNNNTAAAGTGAGTAATAAGACTTTT
1 AAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTT
* * * **
14693 GAAGGAATGGGTGACTATAAATGAACTTTTTTGGTCAATGAATGCCTTTTTCTTCACGTGTCTCA
66 GAAGGAATGAGTGACTATAAATGAACTTTTTT-GCCAATGAATGCCTTTTTCTTCACGTTTCTTG
* * * *
14758 AGGTAAACACTT-AATTATTGTCTGTTTTAATGAAAAATAT
130 AGGTAGACA-TTCAATTATAGTCTGTTTTAATAAAAAATGT
********** * *
14798 AAAAATATTCAACTTAAANNNNNNNNNNAGATTATAAAA-TCATTTAAAGCAAATAATAAGGCTT
1 AAAAA-ATTCAACTTAAAATCAATTATGAGATTATAAAACT-ATTTAAAGCGAGTAATAAGGCTT
* * * * *
14862 TTGAAAGAATGAGTCACTATAAAT-AGACTTTTTTTTCTCAATAAATACCTTTTTCTTCACGTTT
64 TTGAAGGAATGAGTGACTATAAATGA-AC-TTTTTTGC-CAATGAATGCCTTTTTCTTCACGTTT
* * *
14926 CTTGAGGTAGACATTCAATTAGAGTCTGTTTTATCTAAAAATAT-A
126 CTTGAGGTAGACATTCAATTATAGTCTGTTTTA-ATAAAAA-ATGT
*************** *
14971 AAAAAATTCAACTTAAAATCAATTATGAGATNNNNNNNNNNNNNNNAGTGAGTAATAAGGCTTTT
1 AAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTT
* * * * *
15036 GAAGGAATGAGTGACTATAAATGGACTTTTTTTACGAATGAATG-ATTTTTCTTCACATTT-TTC
66 GAAGGAATGAGTGACTATAAATGAAC-TTTTTTGCCAATGAATGCCTTTTTCTTCACGTTTCTT-
* * * * ** *
15099 AAGGTAAACATTGAATTATAGTCTATTTTAACCAAAAATAT
129 GAGGTAGACATTCAATTATAGTCTGTTTTAATAAAAAATGT
* * * ********** *
15140 AAAAAATTTAACGTAAAGTCAATTATGAGATTATAAANNNNNNNNNNGCGAGTAATAAGGCTTTG
1 AAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTT
* * * * * ** * * ** *
15205 GAAGGAATG-GTTTACTATTAATGGA-TTTTTCTTCTCAATCAATGGGTTTCTCTACATATTCCT
66 GAAGGAATGAG-TGACTATAAATGAACTTTTT-TGC-CAATGAATGCCTTTTTCTTCACGTTTCT
* * * *
15268 TGAGGCACG-CATTTAATTA-AGTCTCTTTTAATAAAAATTGT
128 TGAGGTA-GACATTCAATTATAGTCTGTTTTAATAAAAAATGT
* * * * * *
15309 AAAAATATTTAACTTAAAATCGATTATGAGATTGTAAAACCATTTCAAGCTAGTAATAAGGCTTT
1 AAAAA-ATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTT
* * ** * *
15374 TGAAGGAAT-ACGTGACTACAAATGGACTTTTCTTGTTAATGAATGCCCTTTTCTTCACATTTCT
65 TGAAGGAATGA-GTGACTATAAATGAACTTTT-TTGCCAATGAATGCCTTTTTCTTCACGTTTCT
** * *
15438 AAAGGTTA-ACATTCAATTATAATATGTTTTAACT-AAAAATGT
128 TGAGG-TAGACATTCAATTATAGTCTGTTTTAA-TAAAAAATGT
* * * * * **********
15480 AAACAAAATGAACTTAAAATCAATTTTGAGATTTTAAAACCATTTANNNNNNNNNNTAAGGCTTT
1 AAA-AAATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTT
* * * * *
15545 TGAAAGAATG-GATGACTATAAATGGACTGTTTTTGTCAATGAGTGCCTTTTTCTTCACATTTCT
65 TGAAGGAATGAG-TGACTATAAATGAACT-TTTTTGCCAATGAATGCCTTTTTCTTCACGTTTCT
* * * *
15609 TGAGGTAAACATTCAATTATAGTATGTTGTAACAAAAAATGT
128 TGAGGTAGACATTCAATTATAGTCTGTTTTAATAAAAAATGT
********** * * * *
15651 AAAATAATTCAACTTAAANNNNNNNNNNAGATTATAAATCCATTTAAAGCAAGTAATAAGGCTTG
1 AAAA-AATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTT
* * *
15716 TGAAGGAATAAGTGACTATAAATTAACTTTTCTTGCCAATAAATGCCTTTTTC-T----TTTCAT
65 TGAAGGAATGAGTGACTATAAATGAACTTTT-TTGCCAATGAATGCCTTTTTCTTCACGTTTC-T
* * * * **
15776 TTA--AAAACATTCAATTATAGTCTATTTTTGTAAAAAATGT
128 TGAGGTAGACATTCAATTATAGTCTGTTTTAATAAAAAATGT
* * ** * * *
15816 AAAAAAATTCAACTTAAAATCAATGATAAGATTATAAAACTATTTAAAGTAAGAAATAAAGTTTT
1 -AAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTT
* * ******** * * *
15881 TGAAAGAAT-ATGTGA-TTTNNNNNNNNNNTTTCTTGTCAATGAATGCCTTTTTCCTCACGTTTC
65 TGAAGGAATGA-GTGACTAT--AAATGAACTTTTTTGCCAATGAATGCCTTTTTCTTCACGTTTC
*** ** * * *
15944 GCAATATAGACATTCACTTATAGTCTGTTTTGATAAAAAATAT
127 TTGAGGTAGACATTCAATTATAGTCTGTTTTAATAAAAAATGT
* *
15987 AATACAATTTAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGCGAGTAAT
1 AA-AAAATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGCGAGTAAT
Statistics
Matches: 1952, Mismatches: 570, Indels: 183
0.72 0.21 0.07
Matches are distributed among these distances:
164 3 0.00
165 104 0.05
166 12 0.01
167 8 0.00
168 5 0.00
169 121 0.06
170 468 0.24
171 909 0.47
172 187 0.10
173 131 0.07
174 4 0.00
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.35
Consensus pattern (169 bp):
AAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTT
GAAGGAATGAGTGACTATAAATGAACTTTTTTGCCAATGAATGCCTTTTTCTTCACGTTTCTTGA
GGTAGACATTCAATTATAGTCTGTTTTAATAAAAAATGT
Found at i:15046 original size:172 final size:154
Alignment explanation
Indices: 14851--15170 Score: 293
Period size: 170 Copynumber: 2.0 Consensus size: 154
14841 TTAAAGCAAA
*
14851 TAATAAGGCTTTTGAAAGAATGAGTCACTATAAATAGACTTTTTTTTCTCAATAAAT-ACCTTTT
1 TAATAAGGCTTTTGAAAGAATGAGTCACTATAAATAGACTTTTTTTAC-CAATAAATGA--TTTT
* * * * * *
14915 TCTTCACGTTTCTT-GAGGTAGACATTCAATTAGAGTCTGTTTTATCTAAAAATATAAAAAAATT
63 TCTTCACATTT-TTCAAGGTAAACATTCAATTAGAGTCTATTTTAACCAAAAATAT-AAAAAATT
*
14979 CAACTTAAAATCAATTATGAGATNNNNNNNNNNNNNNNAGTGAG
126 CAACGTAAAATCAATTATGAGAT---------------AGTGAG
* * * * *
15023 TAATAAGGCTTTTGAAGGAATGAGTGACTATAAATGGACTTTTTTTACGAATGAATGATTTTTCT
1 TAATAAGGCTTTTGAAAGAATGAGTCACTATAAATAGACTTTTTTTACCAATAAATGATTTTTCT
* * *
15088 TCACATTTTTCAAGGTAAACATTGAATTATAGTCTATTTTAACCAAAAATATAAAAAATTTAACG
66 TCACATTTTTCAAGGTAAACATTCAATTAGAGTCTATTTTAACCAAAAATATAAAAAATTCAACG
*
15153 TAAAGTCAATTATGAGAT
131 TAAAATCAATTATGAGAT
15171 TATAAANNNN
Statistics
Matches: 129, Mismatches: 17, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
169 30 0.23
170 48 0.37
171 6 0.05
172 45 0.35
ACGTcount: A:0.37, C:0.10, G:0.13, T:0.36
Consensus pattern (154 bp):
TAATAAGGCTTTTGAAAGAATGAGTCACTATAAATAGACTTTTTTTACCAATAAATGATTTTTCT
TCACATTTTTCAAGGTAAACATTCAATTAGAGTCTATTTTAACCAAAAATATAAAAAATTCAACG
TAAAATCAATTATGAGATAGTGAG
Done.