Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018403206.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_875.0, 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: 28975
ACGTcount: A:0.28, C:0.09, G:0.09, T:0.28
Warning! 7678 characters in sequence are not A, C, G, or T
Found at i:606 original size:171 final size:167
Alignment explanation
Indices: 1--1135 Score: 906
Period size: 171 Copynumber: 6.6 Consensus size: 167
* * *
1 ATCTGTTTTAATAAAAAGTATAAAAAAATTCAACTTAAAATCAATTATGAGGTTATAAAATTATT
1 ATCTATTTTAA-AAAAA-TAT-AAAAAATTCAACTAAAAATCAATTATGAGGTTATAAAATCATT
* * * ** * * *
66 TAAAGTGGGTAATAAAGCTTCCGTAGGCATGGGTGACTATAAATGGACTTTTCTTCCCAATAGAT
63 TAAAGCGAGTAATAAGGCTTTTGAAGGCAT-GGTGACTATAAATGGACTTTTCTTACCAATGGAT
* * * * *
131 GTATTTTTCTTCACGTTTCTTGAA-GTAGATATTCAATTAAA
127 ATCTTTTTCTTCACGTTTC-TGAAGGTAAACATTCAATTATA
* ********* ** *
172 ATCTGTTTTAATAAAAAATATAAANNNNNNNNNNTTCAAATCAATTATAAGGTTATAAAATCATT
1 ATCTATTTT-A-AAAAAATATAAA-AAATTCAACTAAAAATCAATTATGAGGTTATAAAATCATT
* * * *
237 TAAAGC-AGGTAATAAGGCTTTTGAAAGTATGGGTAACTATAAATGGACTTTTCTTACCAATAGA
63 TAAAGCGA-GTAATAAGGCTTTTGAAGGCAT-GGTGACTATAAATGGACTTTTCTTACCAATGGA
* * *
301 TATCTTATTCTTCACGTTTCTTGAA-GTAAATATTCAATGATA
126 TATCTTTTTCTTCACGTTTC-TGAAGGTAAACATTCAATTATA
*
343 ATCTGTTTTAATAAAAAAATATAAAAAAGTTCAACTAAAAATCAATTATGAGGTTATAAAATCAT
1 ATCT-ATTT--TAAAAAAATATAAAAAA-TTCAACTAAAAATCAATTATGAGGTTATAAAATCAT
* * * * **
408 ATAAAGCGAGTAATAAAGCTTTTGAAGGCATGGTTGACTATAAATCGACTTTTTTTGTCAATGGA
62 TTAAAGCGAGTAATAAGGCTTTTGAAGGCATGG-TGACTATAAATGGACTTTTCTTACCAATGGA
* *
473 TATCTTTTTCTTCACGTTT-TCCAAGGTAAACATTCAATTATT
126 TATCTTTTTCTTCACGTTTCT-GAAGGTAAACATTCAATTATA
* * * *
515 ATCTATTTTAACCAAAAATATATAAAAATTCAAGTAAAAATTAATTATGAGATTCTAAACA-CAT
1 ATCTATTTTAA--AAAAATATA-AAAAATTCAACTAAAAATCAATTATGAGGTTATAAA-ATCAT
* *
579 TTTAGGC-ACGTAATAAGGCTTTTGAAGGCATCGGTGACTATAAATGGACTTTTCTTACCAATGG
62 TTAAAGCGA-GTAATAAGGCTTTTGAAGGCAT-GGTGACTATAAATGGACTTTTCTTACCAATGG
* * * * *
643 ATATCTATTTCTTCATGTTTCTTG-GGGCAGACATTCAATTATA
125 ATATCTTTTTCTTCACGTTTC-TGAAGGTAAACATTCAATTATA
* * *
686 ATC-AGTTTTTTAAAAAATATGAAAAAATTCAACTTAAAATCAATTATGAGGTAATAAAATCATT
1 ATCTA--TTTTAAAAAAATAT-AAAAAATTCAACTAAAAATCAATTATGAGGTTATAAAATCATT
********** * *
750 TAAAGCGAGTAATAAGGCTNNNNNNNNNNTTGGTGACTATAAATGGACTTTTTTTGCCAATGGAT
63 TAAAGCGAGTAATAAGGCT-TTTGAAGGCATGGTGACTATAAATGGACTTTTCTTACCAATGGAT
*
815 ATCTTTTTCTTCACGTTTCTGAAGGTAGACATTCAATTATA
127 ATCTTTTTCTTCACGTTTCTGAAGGTAAACATTCAATTATA
* *
856 ATCTATTTTAATAAAAAATATAAGAAAATTCAACTTAAAATCAATTATGATGTTATAAAATCATT
1 ATCTATTTT-A-AAAAAATATAA-AAAATTCAACTAAAAATCAATTATGAGGTTATAAAATCATT
*************** **
921 TAAAGCGAGTAATAANNNNNNNNNNNNNNNNGGTGACTATAAATGGACTTTTCTTGTCAATGGAT
63 TAAAGCGAGTAATAA-GGCTTTTGAAGGCATGGTGACTATAAATGGACTTTTCTTACCAATGGAT
* * * * *
986 ATCTTTTTGTTCATGTTTCTTGAA-ATAGACACTCAATTATA
127 ATCTTTTTCTTCACGTTTC-TGAAGGTAAACATTCAATTATA
* * * * *
1027 ATCTGTTTTAATAAAAAATATAAAAAAATTTAACTCAAAGTCAATTATGAGATTATAAAAAT-AT
1 ATCTATTTT-A-AAAAAATAT-AAAAAATTCAACTAAAAATCAATTATGAGGTTAT-AAAATCAT
* * *
1091 TTAAAGCAAGTAAT-AGTGCTTTTGAAGGCGTGAGTAACTATAAAT
62 TTAAAGCGAGTAATAAG-GCTTTTGAAGGCATG-GTGACTATAAAT
1136 AAAAAATGCA
Statistics
Matches: 788, Mismatches: 139, Indels: 74
0.79 0.14 0.07
Matches are distributed among these distances:
169 10 0.01
170 136 0.17
171 479 0.61
172 158 0.20
173 4 0.01
174 1 0.00
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.35
Consensus pattern (167 bp):
ATCTATTTTAAAAAAATATAAAAAATTCAACTAAAAATCAATTATGAGGTTATAAAATCATTTAA
AGCGAGTAATAAGGCTTTTGAAGGCATGGTGACTATAAATGGACTTTTCTTACCAATGGATATCT
TTTTCTTCACGTTTCTGAAGGTAAACATTCAATTATA
Found at i:831 original size:341 final size:342
Alignment explanation
Indices: 5--905 Score: 931
Period size: 343 Copynumber: 2.6 Consensus size: 342
1 ATCT
* * * * * *
5 GTTTTA-ATAAAAAGTATAAAAAAATTCAACTTAAAATCAATTATGAGGTTATAAAATTATTTAA
1 GTTTTATA-AAAAAATATAAAAAAGTTCAACTAAAAATCAATTATGAGGTAATAAAATCATATAA
* * ** * * * * * * * *
69 AGTGGGTAATAAAGCTTCCGTAGGCATGGGTGACTATAAATGGACTTTTCTTCCCAATAGATGTA
65 AGCGAGTAATAAAGCTTTTGAAGGCATGGTTGACTATAAATCGACTTTTTTTGCCAATGGATATC
* * * * * *
134 TTTTTCTTCACGTTTCTTGAA-GTAGATATTCAATTAAAATCTGTTTTAATAAAAAATATAA-AN
130 TTTTTCTTCACGTTTC-TCAAGGTAAACATTCAATTATAATCTATTTTAACAAAAAATATAAGA-
********* ** * * * * * *
197 NNNNNNNNNTTCAAATCAATTATAAGGTTATAAA-ATCATTTAAAGCAGGTAATAAGGCTTTTGA
193 AAATTCAACTAAAAATCAATTATGAGATTCTAAACA-CATTTTAGGCACGTAATAAGGCTTTTGA
* *
261 AAGTATGGGTAACTATAAATGGACTTTTCTTACCAATAGATATCTTATTCTTCACGTTTCTTGAA
257 AAGCATCGGTAACTATAAATGGACTTTTCTTACCAATAGATATCTTATTCTTCACGTTTCTTGAA
* * *
326 GTAAATATTCAATGATAATCT
322 GCAAACATTCAATGATAATCA
*
347 GTTTTAATAAAAAAATATAAAAAAGTTCAACTAAAAATCAATTATGAGGTTATAAAATCATATAA
1 GTTTT-ATAAAAAAATATAAAAAAGTTCAACTAAAAATCAATTATGAGGTAATAAAATCATATAA
*
412 AGCGAGTAATAAAGCTTTTGAAGGCATGGTTGACTATAAATCGACTTTTTTTGTCAATGGATATC
65 AGCGAGTAATAAAGCTTTTGAAGGCATGGTTGACTATAAATCGACTTTTTTTGCCAATGGATATC
* *
477 TTTTTCTTCACGTTT-TCCAAGGTAAACATTCAATTATTATCTATTTTAACCAAAAATATATA-A
130 TTTTTCTTCACGTTTCT-CAAGGTAAACATTCAATTATAATCTATTTTAACAAAAAATATA-AGA
* *
540 AAATTCAAGTAAAAATTAATTATGAGATTCTAAACACATTTTAGGCACGTAATAAGGCTTTTGAA
193 AAATTCAACTAAAAATCAATTATGAGATTCTAAACACATTTTAGGCACGTAATAAGGCTTTTGAA
* * * * **
605 GGCATCGGTGACTATAAATGGACTTTTCTTACCAATGGATATC-TATTTCTTCATGTTTCTTGGG
258 AGCATCGGTAACTATAAATGGACTTTTCTTACCAATAGATATCTTA-TTCTTCACGTTTCTTGAA
* *
669 GCAGACATTCAATTATAATCA
322 GCAAACATTCAATGATAATCA
* * *
690 GTTTT-TTAAAAAATATGAAAAAA-TTCAACTTAAAATCAATTATGAGGTAATAAAATCATTTAA
1 GTTTTATAAAAAAATAT-AAAAAAGTTCAACTAAAAATCAATTATGAGGTAATAAAATCATATAA
* ********** *
753 AGCGAGTAATAAGGCTNNNNNNNNNNTTGG-TGACTATAAATGGACTTTTTTTGCCAATGGATAT
65 AGCGAGTAATAAAGCT-TTTGAAGGCATGGTTGACTATAAATCGACTTTTTTTGCCAATGGATAT
* * *
817 CTTTTTCTTCACGTTTCTGAAGGTAGACATTCAATTATAATCTATTTTAATAAAAAATATAAGAA
129 CTTTTTCTTCACGTTTCTCAAGGTAAACATTCAATTATAATCTATTTTAACAAAAAATATAAGAA
*
882 AATTCAACTTAAAATCAATTATGA
194 AATTCAACTAAAAATCAATTATGA
906 TGTTATAAAA
Statistics
Matches: 466, Mismatches: 82, Indels: 23
0.82 0.14 0.04
Matches are distributed among these distances:
340 1 0.00
341 172 0.37
342 19 0.04
343 270 0.58
344 4 0.01
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.36
Consensus pattern (342 bp):
GTTTTATAAAAAAATATAAAAAAGTTCAACTAAAAATCAATTATGAGGTAATAAAATCATATAAA
GCGAGTAATAAAGCTTTTGAAGGCATGGTTGACTATAAATCGACTTTTTTTGCCAATGGATATCT
TTTTCTTCACGTTTCTCAAGGTAAACATTCAATTATAATCTATTTTAACAAAAAATATAAGAAAA
TTCAACTAAAAATCAATTATGAGATTCTAAACACATTTTAGGCACGTAATAAGGCTTTTGAAAGC
ATCGGTAACTATAAATGGACTTTTCTTACCAATAGATATCTTATTCTTCACGTTTCTTGAAGCAA
ACATTCAATGATAATCA
Found at i:935 original size:341 final size:338
Alignment explanation
Indices: 1--1105 Score: 1090
Period size: 341 Copynumber: 3.2 Consensus size: 338
* * *
1 ATCTGTTTTAATAAAAAGTATAAAAAAATTCAACTTAAAATCAATTATGAGGTTATAAAATTATT
1 ATCTGTTTTATTAAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGGTTATAAAATCATT
* * * * * * * *
66 TAAAGTGGGTAATAAAGCTTCCGTAGGCATGGGTGACTATAAATGGACTTTTCTTCCCAATAGAT
66 TAAAGCGAGTAATAAAGC-TCCGGAAGCATTGGTGACTATAAATGGACTTTTTTTGCCAATGGAT
* * * * *
131 GTATTTTTCTTCACGTTTCTTGAA-GTAGATATTCAATTAAAATCTGTTTTAATAAAAAATATAA
130 ATCTTTTTCTTCACGTTTC-TGAAGGTAGACATTCAATTATAATCTATTTTAATAAAAAATATAA
********* * * *
195 ANNNNNNNNNNTTCAAATCAATTATAAGGTTATAAAATCATTTAAAGCAGGTAATAAGGCTTTTG
194 A-AAATTCAACTTAAAATCAATTATGA-GTTATAAAATCATTTAAAGCACGTAATAAGGCTTTTG
* * * * *
260 AAAGTATGGGTAACTATAAATGGACTTTTCTTACCAATAGATATCTTATTCTTCACGTTTCTTGA
257 AAAGCATCGGTGACTATAAATGGACTTTTCTTACCAATGGATATCTT-TTCTTCATGTTTCTTGA
* * *
325 AGTAAATATTCAATGATA
321 AGTAGACATTCAATTATA
* * *
343 ATCTGTTTTAATAAAAAAATATAAAAAAGTTCAACTAAAAATCAATTATGAGGTTATAAAATCAT
1 ATCTGTTTT-ATTAAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGGTTATAAAATCAT
* *** * *
408 ATAAAGCGAGTAATAAAGCTTTTGAAGGCA-TGGTTGACTATAAATCGACTTTTTTTGTCAATGG
65 TTAAAGCGAGTAATAAAGCTCCGGAA-GCATTGG-TGACTATAAATGGACTTTTTTTGCCAATGG
* * * **
472 ATATCTTTTTCTTCACGTTT-TCCAAGGTAAACATTCAATTATTATCTATTTTAACCAAAAATAT
128 ATATCTTTTTCTTCACGTTTCT-GAAGGTAGACATTCAATTATAATCTATTTTAATAAAAAATAT
* * * * * *
536 ATAAAAATTCAAGTAAAAATTAATTATGAGATTCTAAACA-CATTTTAGGCACGTAATAAGGCTT
192 A-AAAAATTCAACTTAAAATCAATTATGAG-TTATAAA-ATCATTTAAAGCACGTAATAAGGCTT
*
600 TTGAAGGCATCGGTGACTATAAATGGACTTTTCTTACCAATGGATATCTATTTCTTCATGTTTCT
254 TTGAAAGCATCGGTGACTATAAATGGACTTTTCTTACCAATGGATATCT-TTTCTTCATGTTTCT
** *
665 TGGGGCAGACATTCAATTATA
318 TGAAGTAGACATTCAATTATA
* * *
686 ATCAGTTTT-TTAAAAAATATGAAAAAATTCAACTTAAAATCAATTATGAGGTAATAAAATCATT
1 ATCTGTTTTATTAAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGGTTATAAAATCATT
* *********
750 TAAAGCGAGTAATAAGGCTNNNNNNNNNNTTGGTGACTATAAATGGACTTTTTTTGCCAATGGAT
66 TAAAGCGAGTAATAAAGCT-CCGGAAGCATTGGTGACTATAAATGGACTTTTTTTGCCAATGGAT
815 ATCTTTTTCTTCACGTTTCTGAAGGTAGACATTCAATTATAATCTATTTTAATAAAAAATATAAG
130 ATCTTTTTCTTCACGTTTCTGAAGGTAGACATTCAATTATAATCTATTTTAATAAAAAATATAA-
********
880 AAAATTCAACTTAAAATCAATTATGATGTTATAAAATCATTTAAAGCGA-GTAATAANNNNNNNN
194 AAAATTCAACTTAAAATCAATTATGA-GTTATAAAATCATTTAAAGC-ACGTAATAAGGCTTTTG
******** ** *
944 NNNNNNNNGGTGACTATAAATGGACTTTTCTTGTCAATGGATATCTTTTTGTTCATGTTTCTTGA
257 AAAGCATCGGTGACTATAAATGGACTTTTCTTACCAATGGATATC-TTTTCTTCATGTTTCTTGA
* *
1009 AATAGACACTCAATTATA
321 AGTAGACATTCAATTATA
* * * * *
1027 ATCTGTTTTAATAAAAAATATAAAAAAATTTAACTCAAAGTCAATTATGAGATTATAAAAAT-AT
1 ATCTGTTTTATTAAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGGTTAT-AAAATCAT
*
1091 TTAAAGCAAGTAATA
65 TTAAAGCGAGTAATA
1106 GTGCTTTTGA
Statistics
Matches: 622, Mismatches: 122, Indels: 38
0.80 0.16 0.05
Matches are distributed among these distances:
340 2 0.00
341 271 0.44
342 78 0.13
343 267 0.43
344 4 0.01
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.35
Consensus pattern (338 bp):
ATCTGTTTTATTAAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGGTTATAAAATCATT
TAAAGCGAGTAATAAAGCTCCGGAAGCATTGGTGACTATAAATGGACTTTTTTTGCCAATGGATA
TCTTTTTCTTCACGTTTCTGAAGGTAGACATTCAATTATAATCTATTTTAATAAAAAATATAAAA
AATTCAACTTAAAATCAATTATGAGTTATAAAATCATTTAAAGCACGTAATAAGGCTTTTGAAAG
CATCGGTGACTATAAATGGACTTTTCTTACCAATGGATATCTTTTCTTCATGTTTCTTGAAGTAG
ACATTCAATTATA
Found at i:2131 original size:170 final size:171
Alignment explanation
Indices: 1575--3339 Score: 1481
Period size: 170 Copynumber: 10.4 Consensus size: 171
1565 NNNNNNNNNN
* * * *
1575 ACATTCAATTATAATCTGTTTTATTAAAAAATAT-AAAAAATTTAACTTAAAATAAATTATGAGA
1 ACATTCAATTATAATCTGTTTTAATAAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGG
* * * * * * *
1639 TTATAAAATTATTTAAAGCGAGTAATAAGTCTTTTGAAAGAATGGATGACTATAAATAGACTTTT
66 TTATAAAATCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGGACTTTT
* * * * **
1704 CTTGCCAATGAATAACTTTTTCTTCACGTTTCTTGAGGTAG
131 CTTGTCAATGGATATCTTTTTCTTCATGTTTCTCAAGGTAG
* * * * ** * * * **
1745 ACATTCAATTATATTCTGTTTTAATAATAAATAGAAAAATATTTTACTCAAAGTCAATTACGACA
1 ACATTCAATTATAATCTGTTTTAATAAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGG
* * * * * *
1810 TTATAAAAAT-ATTTAAAGCGAGTAATAAGGCTTTTGAAAGCGTGGGTAACTATAAGTAGG-CTA
66 TTAT-AAAATCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAAT-GGACTT
* * * **********
1873 TTCTTGCCAACGAATATCTTTTTCTTCNNNNNNNNNNAGGTAG
129 TTCTTGTCAATGGATATCTTTTTCTTCATGTTTCTCAAGGTAG
* * * * * * **
1916 ACATTCAATTATAATATGTTTTTA-AAAAAATGTAAAAAAATTTAACTTAAAATTAATTATTAAA
1 ACATTCAATTATAATCTGTTTTAATAAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGG
* * * * * *
1980 TTATTAAATCATTTAACGCGACTAATAAGGCCTTCGAAGGTATGGGTGACTATATATGGACTTTT
66 TTATAAAATCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGGACTTTT
* * * *
2045 -TTGTCAATGGATATCTATATCTTCACGTTTCTCAAGGTAA
131 CTTGTCAATGGATATCTTTTTCTTCATGTTTCTCAAGGTAG
* * * * * * *
2085 ATAATAAATTATAATCTATTTTAATAAAAAATATAAAAAAATTTAACTAAAAATCAATTATGAAG
1 ACATTCAATTATAATCTGTTTTAATAAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGG
* * * * * *
2150 TTAAAAAATCATTTAAAGCGAGTAATTAGGCTTTTGAAGGAATGAGTGAGTATAAATGGACTTTT
66 TTATAAAATCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGGACTTTT
* * * **
2215 TTTATCAATGGATATC-TTTTCTTCATGTTTATTGAGGTAG
131 CTTGTCAATGGATATCTTTTTCTTCATGTTTCTCAAGGTAG
** * *
2255 ACATTCAATTATAATCTGTTTTGTTAAAAAATATAAAAAAATTTAACTTAAAATCAATGATGAGG
1 ACATTCAATTATAATCTGTTTTAATAAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGG
* * * * * * **
2320 TTATAAAATCATTTGAAGTGAGTAATAAGTCTTTCGAAGGAATGGATGACTAAAAATAAACTTTT
66 TTATAAAATCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGGACTTTT
* * * *
2385 CTTGCCAATGTATATCTTTTTTTTCATGTTTCTCGAGGTAG
131 CTTGTCAATGGATATCTTTTTCTTCATGTTTCTCAAGGTAG
****************** * * *
2426 ACATTCAATTATAATCTGTTTTAANNNNNNNNNNNNNNNNNNTCTACTTAAAGTCAATTATGAGA
1 ACATTCAATTATAATCTGTTTTAATAAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGG
* * ** * ** * *
2491 TTATAAAAACATTTAAAGCGAGTAATAAGACTTTTAAAGGCGTGGGCAACTATAAATAGACTATT
66 TTATAAAATCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGGACTTTT
* * * * * *
2556 CTTG-CTAACGAATATCTTTTTCTTTATATTTTTGAAGGTAG
131 CTTGTC-AATGGATATCTTTTTCTTCATGTTTCTCAAGGTAG
* ********** **
2597 ACATTCAATTATAATATG-NNNNNNNNNNAATATAAAAAAATTCAACTTAAAATTGATTATGAGG
1 ACATTCAATTATAATCTGTTTTAATAAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGG
* * * *
2661 TTATAAAATCATTTAAAGCGAGTAATAAGGATTTCGAAAGTATGGGTGACTATAAAAGGACTTTT
66 TTATAAAATCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGGACTTTT
* * *
2726 CTTCTTAATGGATATCTTTTTCTTCATATTTCTCAAGGTAG
131 CTTGTCAATGGATATCTTTTTCTTCATGTTTCTCAAGGTAG
* * * * **
2767 ACATTTAATTATAATTTGTTTTAATAGAAAATATAAAAAAATTCAAGTTAAGGTCAATTATGAGG
1 ACATTCAATTATAATCTGTTTTAATAAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGG
* * * * * *** * *
2832 TTATAAAATTATTTAATGTGAGTAATGAGGACTTT-GAAAGCACAAGTGACTA-CAATAGACTTT
66 TTATAAAATCATTTAAAGCGAGTAATAAGG-CTTTCGAAGGCATGGGTGACTATAAATGGACTTT
* * * * *
2895 TCTTGCCAATGGGTATCTTTTTCTTCACGTTTTTCAAAGTAG
130 TCTTGTCAATGGATATCTTTTTCTTCATGTTTCTCAAGGTAG
* * * *
2937 ACACTCAATTTTAATCTATTTTAATAAAAAATATAAAAAAATTAAACTTAAAATCAATTATGAGG
1 ACATTCAATTATAATCTGTTTTAATAAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGG
* * * *
3002 TTATGAAACCATTTAACA-CGAGTAATAACGCTTTCGAAGCCATGGGT-A-TATAAATGGACTTT
66 TTATAAAATCATTTAA-AGCGAGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGGACTTT
* * * * *
3064 TCTTGCCAATAGATATCTTTTTTTTCATGTTTCACAAGGCAG
130 TCTTGTCAATGGATATCTTTTTCTTCATGTTTCTCAAGGTAG
* * * *
3106 ACATTTAATTATAGA-CTGTTTTAATAAAAAATATATAAAAATTCAACTTAAAATTAATTATAAG
1 ACATTCAATTATA-ATCTGTTTTAATAAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAG
* * * ** *
3170 ATTATAAAATAATCTAAAGCGAGTAATAAGAATTTCGAAGGCATGGGTGACTA-ACAATGGATTT
65 GTTATAAAATCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGACTATA-AATGGACTT
* * * * *
3234 TTCTTATCAATAGATATCATTTTCTTCATGTTTCTCAAGATAA
129 TTCTTGTCAATGGATATCTTTTTCTTCATGTTTCTCAAGGTAG
* * * * *
3277 ATATTCAATTATATTCTATTTTAATAAAAAATATAAAAAAATTCAAATTAAAATTAATTATGA
1 ACATTCAATTATAATCTGTTTTAATAAAAAATATAAAAAAATTCAACTTAAAATCAATTATGA
3340 AGTTNNNNNN
Statistics
Matches: 1250, Mismatches: 324, Indels: 41
0.77 0.20 0.03
Matches are distributed among these distances:
168 3 0.00
169 187 0.15
170 585 0.47
171 466 0.37
172 9 0.01
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.36
Consensus pattern (171 bp):
ACATTCAATTATAATCTGTTTTAATAAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGG
TTATAAAATCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGGACTTTT
CTTGTCAATGGATATCTTTTTCTTCATGTTTCTCAAGGTAG
Found at i:2573 original size:341 final size:338
Alignment explanation
Indices: 1575--3199 Score: 1196
Period size: 341 Copynumber: 4.8 Consensus size: 338
1565 NNNNNNNNNN
* *
1575 ACATTCAATTATAATCTGTTTTATTAAAAAATAT-AAAAAATTTAACTTAAAATAAATTATGAGA
1 ACATTCAATTATAATATGTTTT-TTAAAAAATATAAAAAAATTTAACTTAAAATTAATTATGAGA
* * * *
1639 TTATAAAATTATTTAAAGCGAGTAATAAGTCTTTTGAAAGAATGGATGACTATAAATAGACTTTT
65 TTATAAAATCATTTAAAGCGAGTAATAAGGCTTTCGAAAGAATGGATGACTAAAAATAGACTTTT
* * ** *
1704 CTTGCCAATGAATAACTTTTTCTTCACGTTTCTTGAGGTAGACATTCAATTATATTCTGTTTTAA
130 CTTGCCAATGGATATCTTTTTCTTCACGTTTCTCAAGGTAGACATTCAATTATAATCTGTTTTAA
* * * * * * * *
1769 TAATAAATAGAAAAATATTTTACTCAAAGTCAATTACGACATTATAAAAATATTTAAAGCGAGTA
195 -AAAAAAAAAAAAAAAAATTTACTAAAAGTCAATTATGA-ATTATAAAAACATTTAAAGCGAGTA
* * *
1834 ATAAGGCTTTTGAAA-GCGTGGGTAACTATAAGTAGGCTATTCTTGCCAACGAATATCTTTTTCT
258 ATAAGGCTTTT-AAAGGCGTGGGTAACTATAAATAGACTATTCTTGCTAACGAATATCTTTTTCT
*********
1898 TCNNNNNNNNNNAGGTAG
322 TC-ATATTTTTGAGGTAG
* * * *
1916 ACATTCAATTATAATATGTTTTTAAAAAAATGTAAAAAAATTTAACTTAAAATTAATTATTAAAT
1 ACATTCAATTATAATATGTTTTTTAAAAAATATAAAAAAATTTAACTTAAAATTAATTATGAGAT
* * * * * * * * * *
1981 TATTAAATCATTTAACGCGACTAATAAGGCCTTCGAAGGTATGGGTGACTATATATGGACTTTT-
66 TATAAAATCATTTAAAGCGAGTAATAAGGCTTTCGAAAGAATGGATGACTAAAAATAGACTTTTC
* * * * * * * * *
2045 TTGTCAATGGATATCTATATCTTCACGTTTCTCAAGGTAAATAATAAATTATAATCTATTTTAAT
131 TTGCCAATGGATATCTTTTTCTTCACGTTTCTCAAGGTAGACATTCAATTATAATCTGTTTTAAA
* * *
2110 AAAAAATATAAAAAAATTTAACTAAAAATCAATTATGAAGTTA-AAAAATCATTTAAAGCGAGTA
196 AAAAAAAAAAAAAAAATTT-ACTAAAAGTCAATTATGAA-TTATAAAAA-CATTTAAAGCGAGTA
* * ** * * * * * ** * *
2174 ATTAGGCTTTTGAAGGAATGAGTGAGTATAAATGGACT-TTTTTTATCAATGGATATC-TTTTCT
258 ATAAGGCTTTTAAAGGCGTGGGTAACTATAAATAGACTATTCTTGCT-AACGAATATCTTTTTCT
*
2237 TCATGTTTATTGAGGTAG
322 TCATATTT-TTGAGGTAG
* * * *
2255 ACATTCAATTATAATCTGTTTTGTTAAAAAATATAAAAAAATTTAACTTAAAATCAATGATGAGG
1 ACATTCAATTATAATATGTTTT-TTAAAAAATATAAAAAAATTTAACTTAAAATTAATTATGAGA
* * * * *
2320 TTATAAAATCATTTGAAGTGAGTAATAAGTCTTTCGAAGGAATGGATGACTAAAAATAAACTTTT
65 TTATAAAATCATTTAAAGCGAGTAATAAGGCTTTCGAAAGAATGGATGACTAAAAATAGACTTTT
* * * *
2385 CTTGCCAATGTATATCTTTTTTTTCATGTTTCTCGAGGTAGACATTCAATTATAATCTGTTTTAA
130 CTTGCCAATGGATATCTTTTTCTTCACGTTTCTCAAGGTAGACATTCAATTATAATCTGTTTTAA
***************** * *
2450 NNNNNNNNNNNNNNNNNNTCTACTTAAAGTCAATTATGAGATTATAAAAACATTTAAAGCGAGTA
195 -AAAAAAAAAAAAAAAAATTTACTAAAAGTCAATTATGA-ATTATAAAAACATTTAAAGCGAGTA
* *
2515 ATAAGACTTTTAAAGGCGTGGGCAACTATAAATAGACTATTCTTGCTAACGAATATCTTTTTCTT
258 ATAAGGCTTTTAAAGGCGTGGGTAACTATAAATAGACTATTCTTGCTAACGAATATCTTTTTCTT
*
2580 TATATTTTTGAAGGTAG
323 CATATTTTTG-AGGTAG
********** * * *
2597 ACATTCAATTATAATATGNNNNNNNNNNAATATAAAAAAATTCAACTTAAAATTGATTATGAGGT
1 ACATTCAATTATAATATGTTTTTTAAAAAATATAAAAAAATTTAACTTAAAATTAATTATGAGAT
* * * *
2662 TATAAAATCATTTAAAGCGAGTAATAAGGATTTCGAAAGTATGGGTGACTATAAAA-GGACTTTT
66 TATAAAATCATTTAAAGCGAGTAATAAGGCTTTCGAAAGAATGGATGACTA-AAAATAGACTTTT
* ** * *
2726 CTT-CTTAATGGATATCTTTTTCTTCATATTTCTCAAGGTAGACATTTAATTATAATTTGTTTTA
130 CTTGC-CAATGGATATCTTTTTCTTCACGTTTCTCAAGGTAGACATTCAATTATAATCTGTTTTA
* * * * * * * * * ** * *
2790 ATAGAAAATATAAAAAAATTCAAGTTAAGGTCAATTATGAGGTTATAAAATTATTTAATGTGAGT
194 AAAAAAAAAAAAAAAAAATT-TACTAAAAGTCAATTATGA-ATTATAAAAACATTTAAAGCGAGT
* * **** * * * * * **
2855 AATGAGGACTTTGAAA-GCACAAGTGACTA-CAATAGACTTTTCTTGCCAATGGGTATCTTTTTC
257 AATAAGG-CTTTTAAAGGCGTGGGTAACTATAAATAGACTATTCTTGCTAACGAATATCTTTTTC
** * *
2918 TTCACGTTTTTCAAAGTAG
321 TTCATATTTTT-GAGGTAG
* * * * * * * *
2937 ACACTCAATTTTAATCTATTTTAATAAAAAATATAAAAAAATTAAACTTAAAATCAATTATGAGG
1 ACATTCAATTATAATATGTTTT-TTAAAAAATATAAAAAAATTTAACTTAAAATTAATTATGAGA
* * * * * * *
3002 TTATGAAACCATTTAACA-CGAGTAATAACGCTTTCG-AAGCCATGGGT-A-TATAAATGGACTT
65 TTATAAAATCATTTAA-AGCGAGTAATAAGGCTTTCGAAAG-AATGGATGACTAAAAATAGACTT
* * * * * *
3063 TTCTTGCCAATAGATATCTTTTTTTTCATGTTTCACAAGGCAGACATTTAATTATAGA-CTGTTT
128 TTCTTGCCAATGGATATCTTTTTCTTCACGTTTCTCAAGGTAGACATTCAATTATA-ATCTGTTT
* * * * * * * *
3127 TAATAAAAAATATATAAAAATTCAACTTAAAA-TTAATTATAAGATTATAAAATA-ATCTAAAGC
192 TAAAAAAAAAAAAAAAAAAATT-TAC-TAAAAGTCAATTATGA-ATTATAAAA-ACATTTAAAGC
3190 GAGTAATAAG
253 GAGTAATAAG
3200 AATTTCGAAG
Statistics
Matches: 998, Mismatches: 258, Indels: 58
0.76 0.20 0.04
Matches are distributed among these distances:
338 3 0.00
339 175 0.18
340 278 0.28
341 482 0.48
342 60 0.06
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.36
Consensus pattern (338 bp):
ACATTCAATTATAATATGTTTTTTAAAAAATATAAAAAAATTTAACTTAAAATTAATTATGAGAT
TATAAAATCATTTAAAGCGAGTAATAAGGCTTTCGAAAGAATGGATGACTAAAAATAGACTTTTC
TTGCCAATGGATATCTTTTTCTTCACGTTTCTCAAGGTAGACATTCAATTATAATCTGTTTTAAA
AAAAAAAAAAAAAAAATTTACTAAAAGTCAATTATGAATTATAAAAACATTTAAAGCGAGTAATA
AGGCTTTTAAAGGCGTGGGTAACTATAAATAGACTATTCTTGCTAACGAATATCTTTTTCTTCAT
ATTTTTGAGGTAG
Found at i:4035 original size:171 final size:171
Alignment explanation
Indices: 3608--4507 Score: 540
Period size: 171 Copynumber: 5.3 Consensus size: 171
3598 NNNNNNNNNN
* * * * * * *
3608 TAAGGCTTTCGAAAGCATGGGTGAGTATAAATGGAATTTTCTTACCAATAGATATCTTCTTCTTC
1 TAAGGCTTTCGAACGCATGGGTGACTATAAATGGACTTCTCTTACCAATGGATATCTTTTTCTTT
* * ** * **********
3673 ATG-TTTCTCGAGACAGACATTCAATTATAATCTGTTTTAATAANNNNNNNNNNAAAATTCAACT
66 ACGTTTTTTAAAG-CAGACATTCAATTATAATCTATTTTAATAAAACATATCAAAAAATTCAACT
* * *
3737 TAAAATCAATTATGAGGTTTTAAAATTATTTAAAGTGAGTAA
130 TAAAATCAATTATAAGGTTATAAAACTATTTAAAGTGAGTAA
* * * * * * *
3779 TAAGGGTTTCGAAGGCATGGGTGACTATAAATGGAGTTTTCTTGCCAATGGATATCTTTTTGTTN
1 TAAGGCTTTCGAACGCATGGGTGACTATAAATGGACTTCTCTTACCAATGGATATCTTTTTCTTT
********* * * * *
3844 NNNNNNNNNAAGGTAGACATTCAATTATAATCTATTTTAA-AAATATATAT-ATAAAAATTTAAC
66 ACGTTTTTTAAAGCAGACATTCAATTATAATCTATTTTAATAAA-ACATATCA-AAAAATTCAAC
*
3907 TTAAAATCAATTATAAGGTTATAAGAA-TATTTAAGGTGAGTAA
129 TTAAAATCAATTATAAGGTTATAA-AACTATTTAAAGTGAGTAA
* *
3950 TAAAGCTTTCGAACGCATGGGTGACTATAAATGGACTTCTCTTACCAATGGGTATCTTTTTCTTT
1 TAAGGCTTTCGAACGCATGGGTGACTATAAATGGACTTCTCTTACCAATGGATATCTTTTTCTTT
* * **
4015 ACGTTTTTTAAAGCAGACATTCAATTATAATCTATTTTAATAAAACATGTCAAAAAGTTCAACCA
66 ACGTTTTTTAAAGCAGACATTCAATTATAATCTATTTTAATAAAACATATCAAAAAATTCAACTT
* * *
4080 AAAACCAATTATAAGATTAAAAAACTATTTAAAGTGAGTAA
131 AAAATCAATTATAAGGTTATAAAACTATTTAAAGTGAGTAA
* ********** * * *
4121 TAAGGCTTTCGAAGGNNNNNNNNNNTATAAATAGACTTTTCTTGCCAATGGATATCTTTTTCTTT
1 TAAGGCTTTCGAACGCATGGGTGACTATAAATGGACTTCTCTTACCAATGGATATCTTTTTCTTT
* * ** * * * * * ** * * *
4186 ATGGTTCCTGAGGTAGACATTCAATTATTATCTGTTTTACCCAAAA-ATGTAAAAAAATTCAATT
66 ACGTTTTTTAAAGCAGACATTCAATTATAATCTATTTTA-ATAAAACATATCAAAAAATTCAACT
* * * * **
4250 TAAAATCATTTATGAGATTATGAAACTATTTAAAACGAGTAA
130 TAAAATCAATTATAAGGTTATAAAACTATTTAAAGTGAGTAA
* * * * * * * **
4292 TAAGGGTTTTGGAACACATGGGTAACTATAAGTAGACTTCTCTT-CCAAATGAATGGCTTTTTCT
1 TAA-GGCTTTCGAACGCATGGGTGACTATAAATGGACTTCTCTTACC-AATGGATATCTTTTTCT
* * ** * * *** * * *
4356 TCAGGTTTCCCT-AGGCAAACATTTGGTTATTAT-TTTTTTGAATTAAAA-ATATAAAAAAATTC
64 TTACGTTT-TTTAAAGCAGACATTCAATTATAATCTATTTT-AA-TAAAACATATCAAAAAATTC
* * * * * * *
4418 AGCTTGAAATCAATTATGAGATTAGAAAAATATTTAAAGCGAGTAA
126 AACTTAAAATCAATTATAAGGTTATAAAACTATTTAAAGTGAGTAA
* * ** * *
4464 TAAGGCTTTCAAACTCATCAGTGACTACAAATGGACTTTTCTTA
1 TAAGGCTTTCGAACGCATGGGTGACTATAAATGGACTTCTCTTA
4508 TCAANNNNNN
Statistics
Matches: 561, Mismatches: 154, Indels: 27
0.76 0.21 0.04
Matches are distributed among these distances:
170 4 0.01
171 425 0.76
172 129 0.23
173 3 0.01
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.35
Consensus pattern (171 bp):
TAAGGCTTTCGAACGCATGGGTGACTATAAATGGACTTCTCTTACCAATGGATATCTTTTTCTTT
ACGTTTTTTAAAGCAGACATTCAATTATAATCTATTTTAATAAAACATATCAAAAAATTCAACTT
AAAATCAATTATAAGGTTATAAAACTATTTAAAGTGAGTAA
Found at i:4597 original size:22 final size:21
Alignment explanation
Indices: 4572--4640 Score: 52
Period size: 22 Copynumber: 3.2 Consensus size: 21
4562 ATTTTAACCA
4572 AAAATGTAAAAAAATTTAACTT
1 AAAAT-TAAAAAAATTTAACTT
* * *
4594 AAAATCAACTAAGATTTAA--T
1 AAAATTAA-AAAAATTTAACTT
*
4614 AAAAATATAAAAAATTTCAACTT
1 AAAATTA-AAAAAATTT-AACTT
4637 AAAA
1 AAAA
4641 CTAATTATGA
Statistics
Matches: 35, Mismatches: 7, Indels: 9
0.69 0.14 0.18
Matches are distributed among these distances:
20 12 0.34
21 5 0.14
22 13 0.37
23 5 0.14
ACGTcount: A:0.61, C:0.07, G:0.03, T:0.29
Consensus pattern (21 bp):
AAAATTAAAAAAATTTAACTT
Found at i:7126 original size:171 final size:169
Alignment explanation
Indices: 6814--7292 Score: 491
Period size: 171 Copynumber: 2.8 Consensus size: 169
6804 NNNNNNNNNN
* * * * **
6814 GCCTTAAATGTTTTTATAATCTCATAGTTGATTTTAAG-TTAAATTGCTTTACATTTTTAGTTAA
1 GCCTTAAATATTTTTACAATCTCGTAATTGATTTTAAGCTT--ATTTTTTTACATTTTTAGTTAA
* * * *
6878 AACAAATAATAATTGAATGTTTGCCTTGAGAAA-TGTAAACAAAAA-CATATTCATGGGCATGAA
64 AACAAATAATAATTGAATGTTTGCC-TGGGAAACT-TAAAGAAAAAGC-TATTCATTGGCAAGAA
* ** ** ** *
6941 AAGCCCATTTGTAGTCACTGATGTCTTTGAAAGCCTTATTTC-T
126 AAGTCCATTTGTAGTCACCCATAACTTCAAAAGCCTTATTACGT
* *
6984 CGCTTTAAATATTTTTACAATCTCGTAATTGATTTTAAGCTCTATTTTTTTACATTTTTAATTAA
1 -GCCTTAAATATTTTTACAATCTCGTAATTGATTTTAAGCT-TATTTTTTTACATTTTTAGTTAA
* * *
7049 AACAAATAATAACTGAATGTTTGCCTAGGGAAACTTAAAGAAAAAGCCATTCATTAGCAAGAAAA
64 AACAAATAATAATTGAATGTTTGCCT-GGGAAACTTAAAGAAAAAGCTATTCATTGGCAAGAAAA
7114 GTCCATTTGTAGTCACCCATAACTTCAAAAGCCTTATTACGT
128 GTCCATTTGTAGTCACCCATAACTTCAAAAGCCTTATTACGT
* * * **
7156 GCCTAAAATATTTTTAGAATCTCGTACTTGATTTTAA-CTTGAATTTTCATACATTTTTAGTTAA
1 GCCTTAAATATTTTTACAATCTCGTAATTGATTTTAAGCTT--ATTTTTTTACATTTTTAGTTAA
* * * ** * * * *
7220 AATAGATAATAATTAAATGTCTACCCTGGGAAACATGAAGAAAAAGATATCCATTGGCAAGAAAA
64 AACAAATAATAATTGAATGT-TTGCCTGGGAAACTTAAAGAAAAAGCTATTCATTGGCAAGAAAA
7285 GTCCATTT
128 GTCCATTT
7293 ATANNNNNNN
Statistics
Matches: 257, Mismatches: 42, Indels: 18
0.81 0.13 0.06
Matches are distributed among these distances:
169 1 0.00
170 3 0.01
171 244 0.95
172 8 0.03
173 1 0.00
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.37
Consensus pattern (169 bp):
GCCTTAAATATTTTTACAATCTCGTAATTGATTTTAAGCTTATTTTTTTACATTTTTAGTTAAAA
CAAATAATAATTGAATGTTTGCCTGGGAAACTTAAAGAAAAAGCTATTCATTGGCAAGAAAAGTC
CATTTGTAGTCACCCATAACTTCAAAAGCCTTATTACGT
Found at i:7858 original size:171 final size:172
Alignment explanation
Indices: 7427--8426 Score: 507
Period size: 171 Copynumber: 5.8 Consensus size: 172
7417 NNNNNNNNNN
* * ** * *
7427 GAAGAAAAAAATATCCATTGATAAGAAAAGTCCATTTATAGTCACTCATGCCTTCAAAAGCCTTC
1 GAAGAAAAAGATATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATGCCTTCAAAAGCCTTA
* * * * *
7492 TTACTCGCTTTAATTTATTTTATAATCTCATAGTAGATTTTAAGTTGAATCTTTTTACATTTTTT
66 TTACTCGCTTTAAATAATTTTATAATCTCATAATAGACTTTAAGTAGAATCTTTTTACATTTTTT
* * *
7557 TATTAAAATAGATTATAATTGAATGTCTACCTCAGGAAACAT
131 TATTAAAACAGATTAAAATTGAATGCCTACCTCAGGAAACAT
* * * ** *
7599 GAATAATAAGATATTCATTGGCAAGAATAGTCCATTTATAGTCACCCACACCTTCAAAAGCCTTN
1 GAAGAAAAAGATATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATGCCTTCAAAAGCCTTA
********* * * * *
7664 NNNNNNNNNTTAAATATTTTTATAATCTTATAATTGACTTTAAGTAGAAT-TTCTTTTCA-TTTT
66 TTACTCGCTTTAAATAATTTTATAATCTCATAATAGACTTTAAGTAGAATCTT-TTTACATTTTT
* * *
7727 TTATTGAAACAGATTAAAATTGAATGCCTTCTTC-GAGAAACAT
130 TTATTAAAACAGATTAAAATTGAATGCCTACCTCAG-GAAACAT
* * * * * *
7770 GAAGAAAAAGATATTTATTGGCAAGAAAAGTCTACTTATTGTCACCCATGTCTTCAAAACCCTTA
1 GAAGAAAAAGATATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATGCCTTCAAAAGCCTTA
** ********* * * * *
7835 TTACTCGCTTTAAATGGTTTTATANNNNNNNNNNTA-ATTTTAAGTTGAATTTTTTTACA-TTTA
66 TTACTCGCTTTAAATAATTTTATA-ATCTCATAATAGACTTTAAGTAGAATCTTTTTACATTTTT
*** ** ** * *
7898 TGGGTAAAACAGA-TAATAATTGAATGTTTGTCTC-GACAAACGT
130 TTATTAAAACAGATTAA-AATTGAATGCCTACCTCAG-GAAACAT
* ** * * **
7941 AAAGAAAAAGCCATTCATTGGCAAGAAAAGTCCATTTATAGTCTCCCATGCATTTGAAAGCCTTA
1 GAAGAAAAAGATATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATGCCTTCAAAAGCCTTA
* *********** * * * * *
8006 TTACTCGGTTTAAATGNNNNNNNNNNCTTATAATTGATTTTAAGTTGAAT-TGTTTTA-AATTTT
66 TTACTCGCTTTAAATAATTTTATAATCTCATAATAGACTTTAAGTAGAATCT-TTTTACATTTTT
** * * * **
8069 TTATTAAAACAGATTGTAATTGAATGTCTATCTCAAGAAATGT
130 TTATTAAAACAGATTAAAATTGAATGCCTACCTCAGGAAACAT
* * * * * *
8112 GAACAAAAAGCTATCCATTGGCAAGAAAAGTTCATTTATAGTCAGCCATGCCTTCGAAAGCCTTA
1 GAAGAAAAAGATATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATGCCTTCAAAAGCCTTA
*********** ** * * * *
8177 TTACTCANNNNNNNNNNTTTTATAGCCTCATAATTGATTTTAAGTAGAATATTTTTACA-TTTTC
66 TTACTCGCTTTAAATAATTTTATAATCTCATAATAGACTTTAAGTAGAATCTTTTTACATTTTTT
* * * ** *
8241 TCTTAAAACAAATTATAATTGAATATCTAGCTC-GAGAAACAT
131 TATTAAAACAGATTAAAATTGAATGCCTACCTCAG-GAAACAT
* * * ** **********
8283 GATGAAAAGGATATCCATTGAAAAGAAAAGTCCATTTATAGTCACCCNNNNNNNNNNAAGCCTTA
1 GAAGAAAAAGATATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATGCCTTCAAAAGCCTTA
* * * * *
8348 TTACTCGCTTTAAATAATTTTATAACCTTATAATTGA-TTTGAAGTTA-AATTTTTTTATA-TTT
66 TTACTCGCTTTAAATAATTTTATAATCTCATAATAGACTTT-AAG-TAGAATCTTTTTACATTTT
8410 TTTATTAAAACAGATTA
129 TTTATTAAAACAGATTA
8427 NNNNNNNNNN
Statistics
Matches: 614, Mismatches: 199, Indels: 31
0.73 0.24 0.04
Matches are distributed among these distances:
170 12 0.02
171 502 0.82
172 100 0.16
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.36
Consensus pattern (172 bp):
GAAGAAAAAGATATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATGCCTTCAAAAGCCTTA
TTACTCGCTTTAAATAATTTTATAATCTCATAATAGACTTTAAGTAGAATCTTTTTACATTTTTT
TATTAAAACAGATTAAAATTGAATGCCTACCTCAGGAAACAT
Found at i:9455 original size:172 final size:171
Alignment explanation
Indices: 9271--9639 Score: 429
Period size: 172 Copynumber: 2.1 Consensus size: 171
9261 NNNNNNNNNN
* * **
9271 GCCTTATTACTCACTTTAAATAATTTTT-TAATCTCATAATTGGTTTTTGGTTGAACGTTTTGAC
1 GCCTTATTACTCACTTTAAAT-ATTTTTATAACCTCATAATTGATTTTAAGTTGAA--TTTTGAC
* * * *
9335 ATGT-T-TTATTACAATAGATTATAATTGAATGTCTGCTTTAAAAAAAGTAAAAAAAAAACATAT
63 ATATATATTATTAAAACAGATTATAATTGAATGTCTGCCTTAAAAAAAGT-AAAAAAAAACATAT
* * ** *
9398 CCATTGGTAAGAGAAGTCCATTCATAGTCACCCATGCGTTCGAAA
127 CCATTGGCAAGAAAACACCATTCATAGTCACCCATGCCTTCGAAA
* * * * *
9443 GCTTTATTACTCACCTTAAATATTTTTATAACCTTATAATTGATTTTAAGTTGAATTTTTATATA
1 GCCTTATTACTCACTTTAAATATTTTTATAACCTCATAATTGATTTTAAGTTGAATTTTGACATA
* * * * * * *
9508 TATATTTTTAAAACAGATTATAATTGAATGTCTGCCTTGAGAAACGTGAACAAAAAGATATCCAT
66 TATATTATTAAAACAGATTATAATTGAATGTCTGCCTTAAAAAAAGTAAAAAAAAACATATCCAT
**
9573 TGGCAAGAAAACACCATTTGTAGTCACCCATGCCTTCGAAA
131 TGGCAAGAAAACACCATTCATAGTCACCCATGCCTTCGAAA
9614 GCCTTATTACTCACTTTAAATGATTT
1 GCCTTATTACTCACTTTAAAT-ATTT
9640 NNNNNNNNNN
Statistics
Matches: 164, Mismatches: 29, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
170 8 0.05
171 75 0.46
172 81 0.49
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (171 bp):
GCCTTATTACTCACTTTAAATATTTTTATAACCTCATAATTGATTTTAAGTTGAATTTTGACATA
TATATTATTAAAACAGATTATAATTGAATGTCTGCCTTAAAAAAAGTAAAAAAAAACATATCCAT
TGGCAAGAAAACACCATTCATAGTCACCCATGCCTTCGAAA
Found at i:14935 original size:171 final size:170
Alignment explanation
Indices: 14216--14946 Score: 407
Period size: 170 Copynumber: 4.3 Consensus size: 170
14206 NNNNNNNNNN
* * * * * *
14216 ATAACCTCATAATTGATTTTAAGTTATATTTTTTTTACATTTTT--TTAAAAACATATTATAATT
1 ATAATCTCATAATTGATTTTAAGTGA-A-ATTTTTTATATTTTTCATT-AAAACAGATAATAATT
* *** * * * * * **
14279 AAATGTCTGTTTTAAGAAATATGAAAAAAAAGATATCCATTAGCACAAAAAGTTAATTTATAGTC
63 GAATGTCTACCTTAACAAACATGAAGAAAAAGACATCCATTAGCAAAAAAAGTCCATTTATAGTC
* * * * ** *
14344 ACCCACGTCTTCAAAAGCCTTATTAG-TCGGTTTAAATATTTTT
128 ACCAATGCCTTCGAAAGCCTTATTAGCTC-AATTAAATAATTTT
* * * * * ** *
14387 ATAATCTTATAATTGACTTTAAGTAGAATTTTTTTACATTTTTTATTAAAGTAGATTATAATTGA
1 ATAATCTCATAATTGATTTTAAGT-GAAATTTTTTATATTTTTCATTAAAACAGATAATAATTGA
* ** *** * * * * * * * *
14452 AT-ACTTGTCTT-GGGAACGTGAAGAAAAAGATATTCTTTGGCAAGAAAAGTCTAGTTATAGTCA
65 ATGTC-TACCTTAACAAACATGAAGAAAAAGACATCCATTAGCAAAAAAAGTCCATTTATAGTCA
* ************* *
14515 CCAATGCCTTCAAAAGCNNNNNNNNNNGTTTTAAATGATTTT
129 CCAATGCCTTCGAAAGCCTTATTAGCTCAATTAAATAATTTT
* * *** *
14557 ATAATCTCATAAATGATTTTAAGTGGAATTTTTTATATTTTTGGGTGAAACAGATAATAATTGAA
1 ATAATCTCATAATTGATTTTAAGTGAAATTTTTTATATTTTTCATTAAAACAGATAATAATTGAA
* * * * * * * *
14622 TGTTTATCTTGACAAACGTGAAGAAAAAGCCATTCATTGGCAACAAAAGTCCATTTATAGTCACC
66 TGTCTACCTTAACAAACATGAAGAAAAAGACATCCATTAGCAAAAAAAGTCCATTTATAGTCACC
* ** * * *
14687 AATGCCTTCGAAAGCTTTATTATTTGATTTAAATTATTTT
131 AATGCCTTCGAAAGCCTTATTAGCTCAATTAAATAATTTT
* ********* * *
14727 ATAACCTCATAATTGATTTTANNNNNNNNNNTTTTATATTTTTCATTAAAACAGTTTATAATTGA
1 ATAATCTCATAATTGATTTTA-AGTGAAATTTTTTATATTTTTCATTAAAACAGATAATAATTGA
* * *
14792 ATGTCTACCTTAAGAAACATGAAGAAAATA-ATATCCATTAGCAAAAAAAGTCCATTTGTAGTCA
65 ATGTCTACCTTAACAAACATGAAGAAAA-AGACATCCATTAGCAAAAAAAGTCCATTTATAGTCA
* *
14856 GCC-ATGCCTTTGAAGGCCTTATT-GCTCACATTAAATAATTTT
129 -CCAATGCCTTCGAAAGCCTTATTAGCTCA-ATTAAATAATTTT
* *
14898 ATAATCTCATAATTGATTTTAAGTTAAATGTTTTTATATTTTTTATTAA
1 ATAATCTCATAATTGATTTTAAGTGAAAT-TTTTTATATTTTTCATTAA
14947 NNNNNNNNNN
Statistics
Matches: 424, Mismatches: 124, Indels: 24
0.74 0.22 0.04
Matches are distributed among these distances:
169 37 0.09
170 194 0.46
171 187 0.44
172 6 0.01
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.39
Consensus pattern (170 bp):
ATAATCTCATAATTGATTTTAAGTGAAATTTTTTATATTTTTCATTAAAACAGATAATAATTGAA
TGTCTACCTTAACAAACATGAAGAAAAAGACATCCATTAGCAAAAAAAGTCCATTTATAGTCACC
AATGCCTTCGAAAGCCTTATTAGCTCAATTAAATAATTTT
Found at i:16172 original size:170 final size:170
Alignment explanation
Indices: 15885--17554 Score: 777
Period size: 171 Copynumber: 9.8 Consensus size: 170
15875 NNNNNNNNNG
* * * *
15885 TAGACATTCAATTATAATCTGTTTTAATAAAAAATATAAAAAAATTCAACTTACAATCAATTATA
1 TAGACATTCAATTATAATCTGTTTCAACAAAAAATATAAAAAAATTCAACTTAAAATCAATTATG
* * *
15950 AGGTTATAAAATCATTTAAATCAAGTAATAAAGCTTTCGAAG-CATGGGTGACTATAAATGGACT
66 AGATTATAAAATCATTTAAAACAAGTAATAAAGCTTTCGAAGACATGGGTGACTATAAATAGACT
** *
16014 TTTGTTGTCAATGAATGGCTTTTTCTTCACATTTGTCAAGA
131 TTTGTTG-CAATGAATATCTTTTTCTTCACATTTCTCAAGA
* * * * * * * *
16055 AAAACATTCAATTATTATCTGTTTCACCCAAAAATGT-AAAAAATTCTACTTAAAATCATTTATG
1 TAGACATTCAATTATAATCTGTTTCAACAAAAAATATAAAAAAATTCAACTTAAAATCAATTATG
* * * * * *
16119 AGATTATGAAATCATTTAAAACGAGTAATAAGGCTTTTGAAGACATTGGTGACTATAACTAGACT
66 AGATTATAAAATCATTTAAAACAAGTAATAAAGCTTTCGAAGACATGGGTGACTATAAATAGACT
* *
16184 TTT-TCTGCCAAAGAATATCTTTTTCTTCACGTTTCTCAAGA
131 TTTGT-TG-CAATGAATATCTTTTTCTTCACATTTCTCAAGA
* * * **********
16225 TAGGCATTCAATTATAATCTGTTTCAATAAAAAATATAAAAAAATTCTACTTAAANNNNNNNNNN
1 TAGACATTCAATTATAATCTGTTTCAACAAAAAATATAAAAAAATTCAACTTAAAATCAATTATG
* * * * * * *
16290 AGATTATAAAAAT-ATTTGAAGCGACTAATAAAGCTTTTGAAGACGTGGGTGACTATAAATTGAC
66 AGATTAT-AAAATCATTTAAAACAAGTAATAAAGCTTTCGAAGACATGGGTGACTATAAATAGAC
* * * * *
16354 TTTTCG-TGCTAATGGATATCTTTTTTTTCACTTTTCTCGAGG
130 TTTT-GTTGC-AATGAATATCTTTTTCTTCACATTTCTCAAGA
* *
16396 TAGACATTCAATTATAATCTGTTTTAACAAAAAATATTAAAAAA-TCAACTTAAAATCAATTATG
1 TAGACATTCAATTATAATCTGTTTCAACAAAAAATATAAAAAAATTCAACTTAAAATCAATTATG
* ** ***********
16460 ATG-TTATAAAATCATTTAAAACAAGTAATAAGGCTTTCGAAGGTATGGGTNNNNNNNNNNGGAC
66 A-GATTATAAAATCATTTAAAACAAGTAATAAAGCTTTCGAAGACATGGGTGACTATAAATAGAC
* ** *
16524 TTTTCTTGCCAAT-AGATATCATTTTT-TTCATGTTTC-CTAAGG
130 TTTTGTTG-CAATGA-ATATC-TTTTTCTTCACATTTCTC-AAGA
* * * ** * * * * *
16566 TAGATATTCCATTATTATCAATTTTAGCCAACAATGTAAAAAAATTCAACTTAAAAT-AATTATG
1 TAGACATTCAATTATAATCTGTTTCAACAAAAAATATAAAAAAATTCAACTTAAAATCAATTATG
* * * * * * * *
16630 AGATTATAAAAAT-ATTTAAAACGAA-TAATAAGGTTTTTGAATG-CGTTGGCGACAATAAATGG
66 AGATTAT-AAAATCATTTAAAAC-AAGTAATAAAGCTTTCGAA-GACATGGGTGACTATAAATAG
* * * * * * * *
16692 TCTATTCTTGCCAATGTATATATTTTTCCTT-ACGTTTC-CTGAGG
128 ACTTTTGTTG-CAATGAATATCTTTTT-CTTCACATTTCTC-AAGA
* * * * ** ** *
16736 TAGATATTCAATTATTATCTGTTTTAACTAAAAAGGTAAAAACGTTCAACTTAAAATCCATTATG
1 TAGACATTCAATTATAATCTGTTTCAACAAAAAATATAAAAAAATTCAACTTAAAATCAATTATG
* * * ** * * *
16801 AGATTATAAAAAGC-TTTAAAGCAAATAA-AAAGGCTTTTAAAGGCGTCGGTGACTATAAAT-GA
66 AGATTAT-AAAATCATTTAAAACAAGTAATAAA-GCTTTCGAAGACATGGGTGACTATAAATAG-
* * * * * *
16863 ACTTTTCTTATCAATAAATATCTTTTTTTTCACGTTTCT-AGAGG
128 ACTTTTGTT-GCAATGAATATCTTTTTCTTCACATTTCTCA-AGA
* * * * * * **********
16907 TAAACATTGAATTATAATGTATTTTAATAAAAAATATAANNNNNNNNNNCTTAAAATCAATTATG
1 TAGACATTCAATTATAATCTGTTTCAACAAAAAATATAAAAAAATTCAACTTAAAATCAATTATG
* * * * * * *
16972 AGATTATGAAATCGTTTAACACGAGTAATAAGGCTTTCGAAGGCATGGGT--CTATAAATGGACT
66 AGATTATAAAATCATTTAAAACAAGTAATAAAGCTTTCGAAGACATGGGTGACTATAAATAGACT
* * ** * *
17035 TTTCTTATCAAT-AGATATCTTTTTCTTCATGTTTCACAAGG
131 TTTGTT-GCAATGA-ATATCTTTTTCTTCACATTTCTCAAGA
* * * * * * * * *
17076 CAAACATTTAATTATAAACTATTTTAATAAAAAATATATAAAAATTCAATTTAAAATCAATTATG
1 TAGACATTCAATTATAATCTGTTTCAACAAAAAATATAAAAAAATTCAACTTAAAATCAATTATG
* * * * * * * * *
17141 AAATTATAAAATCATCTAAAGCGAGTAATAAGGATTCCGAAGGCATGGGTGACTATAAATGGACN
66 AGATTATAAAATCATTTAAAACAAGTAATAAAGCTTTCGAAGACATGGGTGACTATAAATAGAC-
********* * **
17206 NNNNNNNNNAAT-AGATATCATTTTCTTCATGTTTCAT-AAGA
130 TTTTGTTGCAATGA-ATATCTTTTTCTTCACATTTC-TCAAGA
* * * ********** *
17247 TAGACATTCAATTATATTCTGTTTTAATAAAAAATATAAAAANNNNNNNNNNAAAATAAATTATG
1 TAGACATTCAATTATAATCTGTTTCAACAAAAAATATAAAAAAATTCAACTTAAAATCAATTATG
* * *** * * * * *
17312 AGGTTATAAAATCTTTTAAAGTGAGTAATAAGGCTTCCGACGGCATGGGCGACTATAAAT-GTAC
66 AGATTATAAAATCATTTAAAACAAGTAATAAAGCTTTCGAAGACATGGGTGACTATAAATAG-AC
* * * * ** ******
17376 TTTTCTTACTAATGGATATCTTTTTCTTTATGTTTCNNNNNN
130 TTTTGTTGC-AATGAATATCTTTTTCTTCACATTTCTCAAGA
**** * * * * * *
17418 NNNNCATTCAATTATAATCTATTTTAATAAACAATAT-AAAAAATTTAACCTAAAATCAATTATG
1 TAGACATTCAATTATAATCTGTTTCAACAAAAAATATAAAAAAATTCAACTTAAAATCAATTATG
* * *** * *
17482 AGGTTATCAAATCATTTAAAGTTAGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAAT-GAAC
66 AGATTATAAAATCATTTAAAACAAGTAATAAAGCTTTCGAAGACATGGGTGACTATAAATAG-AC
*
17546 TTTTCTTGC
130 TTTTGTTGC
17555 TAATNNNNNN
Statistics
Matches: 1157, Mismatches: 298, Indels: 90
0.75 0.19 0.06
Matches are distributed among these distances:
168 1 0.00
169 208 0.18
170 427 0.37
171 515 0.45
172 6 0.01
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.35
Consensus pattern (170 bp):
TAGACATTCAATTATAATCTGTTTCAACAAAAAATATAAAAAAATTCAACTTAAAATCAATTATG
AGATTATAAAATCATTTAAAACAAGTAATAAAGCTTTCGAAGACATGGGTGACTATAAATAGACT
TTTGTTGCAATGAATATCTTTTTCTTCACATTTCTCAAGA
Found at i:16347 original size:171 final size:170
Alignment explanation
Indices: 15885--17200 Score: 650
Period size: 170 Copynumber: 7.7 Consensus size: 170
15875 NNNNNNNNNG
* * * * * *
15885 TAGACATTCAATTATAATCTGTTTTAATAAAAAATATAAAAAAATTCAACTTACAATCAATTATA
1 TAGACATTCAATTATAATCTGTTTCAACAAAAAATAT-AAAAAATTCTACTTAAAATCATTTATG
* * * * * *
15950 AGGTTATAAAATCATTTAAATCAAGTAATAAAGCTTTCGAAG-CATGGGTGACTATAAATGGACT
65 AGATTATAAAATCATTTAAAACGACTAATAAAGCTTTTGAAGACATGGGTGACTATAAATAGACT
* ** *
16014 TTTGT-TGTCAATGAATGGCTTTTTCTTCACATTTGTCAAGA
130 TTT-TCTGCCAATGAATATCTTTTTCTTCACATTTCTCAAGA
* * * * * *
16055 AAAACATTCAATTATTATCTGTTTCACCCAAAAATGTAAAAAATTCTACTTAAAATCATTTATGA
1 TAGACATTCAATTATAATCTGTTTCAACAAAAAATATAAAAAATTCTACTTAAAATCATTTATGA
* * * * *
16120 GATTATGAAATCATTTAAAACGAGTAATAAGGCTTTTGAAGACATTGGTGACTATAACTAGACTT
66 GATTATAAAATCATTTAAAACGACTAATAAAGCTTTTGAAGACATGGGTGACTATAAATAGACTT
* *
16185 TTTCTGCCAAAGAATATCTTTTTCTTCACGTTTCTCAAGA
131 TTTCTGCCAATGAATATCTTTTTCTTCACATTTCTCAAGA
* * **********
16225 TAGGCATTCAATTATAATCTGTTTCAATAAAAAATATAAAAAAATTCTACTTAAANNNNNNNNNN
1 TAGACATTCAATTATAATCTGTTTCAACAAAAAATAT-AAAAAATTCTACTTAAAATCATTTATG
* * * *
16290 AGATTATAAAAAT-ATTTGAAGCGACTAATAAAGCTTTTGAAGACGTGGGTGACTATAAATTGAC
65 AGATTAT-AAAATCATTTAAAACGACTAATAAAGCTTTTGAAGACATGGGTGACTATAAATAGAC
* * * * * *
16354 -TTTTCGTGCTAATGGATATCTTTTTTTTCACTTTTCTCGAGG
129 TTTTTC-TGCCAATGAATATCTTTTTCTTCACATTTCTCAAGA
* * *
16396 TAGACATTCAATTATAATCTGTTTTAACAAAAAATATTAAAAAA-TCAACTTAAAATCAATTATG
1 TAGACATTCAATTATAATCTGTTTCAACAAAAAATA-TAAAAAATTCTACTTAAAATCATTTATG
* * * * ** ***********
16460 ATG-TTATAAAATCATTTAAAACAAGTAATAAGGCTTTCGAAGGTATGGGTNNNNNNNNNNGGAC
65 A-GATTATAAAATCATTTAAAACGACTAATAAAGCTTTTGAAGACATGGGTGACTATAAATAGAC
** *
16524 -TTTTCTTGCCAAT-AGATATCATTTTT-TTCATGTTTC-CTAAGG
129 TTTTTC-TGCCAATGA-ATATC-TTTTTCTTCACATTTCTC-AAGA
* * * ** * * * * * * *
16566 TAGATATTCCATTATTATCAATTTTAGCCAACAATGTAAAAAAATTCAACTTAAAAT-AATTATG
1 TAGACATTCAATTATAATCTGTTTCAACAAAAAATAT-AAAAAATTCTACTTAAAATCATTTATG
* * * * * * * * *
16630 AGATTATAAAAAT-ATTTAAAACGAATAATAAGGTTTTTGAATG-CGTTGGCGACAATAAATGGT
65 AGATTAT-AAAATCATTTAAAACGACTAATAAAGCTTTTGAA-GACATGGGTGACTATAAATAGA
* * * * * *
16693 C-TATTCTTGCCAATGTATATATTTTTCCTT-ACGTTTC-CTGAGG
128 CTTTTTC-TGCCAATGAATATCTTTTT-CTTCACATTTCTC-AAGA
* * * * ** * *
16736 TAGATATTCAATTATTATCTGTTTTAACTAAAAAGGTAAAAACGTTCAACTTAAAATCCA-TTAT
1 TAGACATTCAATTATAATCTGTTTCAACAAAAAATATAAAAA-ATTCTACTTAAAAT-CATTTAT
* * * * * * * *
16800 GAGATTATAAAAAGC-TTTAAAGCAAATAA-AAAGGCTTTTAAAGGCGTCGGTGACTATAAAT-G
64 GAGATTAT-AAAATCATTTAAAACGACTAATAAA-GCTTTTGAAGACATGGGTGACTATAAATAG
** * * * *
16862 AAC-TTTTCTTATCAATAAATATCTTTTTTTTCACGTTTCT-AGAGG
127 -ACTTTTTC-TGCCAATGAATATCTTTTTCTTCACATTTCTCA-AGA
* * * * * * ********* *
16907 TAAACATTGAATTATAATGTATTTTAATAAAAAATATAANNNNNNNNNNCTTAAAATCAATTATG
1 TAGACATTCAATTATAATCTGTTTCAACAAAAAATATAA-AAAATTCTACTTAAAATCATTTATG
* * * * * * * *
16972 AGATTATGAAATCGTTTAACACGAGTAATAAGGCTTTCGAAGGCATGGGT--CTATAAATGGAC-
65 AGATTATAAAATCATTTAAAACGACTAATAAAGCTTTTGAAGACATGGGTGACTATAAATAGACT
** ** * *
17034 TTTTCTTATCAAT-AGATATCTTTTTCTTCATGTTTCACAAGG
130 TTTTC-TGCCAATGA-ATATCTTTTTCTTCACATTTCTCAAGA
* * * * * * * * * *
17076 CAAACATTTAATTATAAACTATTTTAATAAAAAATATATAAAAATTCAATTTAAAATCAATTATG
1 TAGACATTCAATTATAATCTGTTTCAACAAAAAATATA-AAAAATTCTACTTAAAATCATTTATG
* * * * * * ** *
17141 AAATTATAAAATCATCTAAAGCGAGTAATAAGGATTCCGAAGGCATGGGTGACTATAAAT
65 AGATTATAAAATCATTTAAAACGACTAATAAAGCTTTTGAAGACATGGGTGACTATAAAT
17201 GGACNNNNNN
Statistics
Matches: 892, Mismatches: 215, Indels: 77
0.75 0.18 0.07
Matches are distributed among these distances:
168 1 0.00
169 214 0.24
170 347 0.39
171 322 0.36
172 8 0.01
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.35
Consensus pattern (170 bp):
TAGACATTCAATTATAATCTGTTTCAACAAAAAATATAAAAAATTCTACTTAAAATCATTTATGA
GATTATAAAATCATTTAAAACGACTAATAAAGCTTTTGAAGACATGGGTGACTATAAATAGACTT
TTTCTGCCAATGAATATCTTTTTCTTCACATTTCTCAAGA
Found at i:17194 original size:340 final size:334
Alignment explanation
Indices: 15888--17552 Score: 723
Period size: 340 Copynumber: 4.9 Consensus size: 334
15878 NNNNNNGTAG
* * * * *
15888 ACATTCAATTATAATCTGTTTTAATAAAAAATATAAAAAAATTCAACTTACAATCAATTATAAGG
1 ACATTCAATTATAATCTATTTTAATAAAAAATAT----AAA---AACTTAAAATAAATTATGAGA
* * * * * *
15953 TTATAAAATCATTTAAATCAAGTAATAAAGCTTTCGAA-GCATGGGTGACTATAAATGGACTTTT
59 TTATAAAATCGTTTAAAGCGAGTAATAAGGCTTCCGAAGGCATGGGCGACTATAAATGGACTTTT
* * ** ** ** * * *
16017 GTT-GTCAAT-GA-ATGGCTTTTTCTTCACATTTGTCAAGAAAAACATTCAATTATTATCTGTTT
124 CTTACT-AATAGATAT--CTTTTTCTTCATGTTTCACAAGGCAAACATTCAATTATAAACTATTT
* *** * * * * * * * *
16079 CACCCAAAAATGTAAAAAATTCTACTTAAAATCATTTATGAGATTATGAAATCATTTAAAACGAG
186 TAATAAAAAATATAAAAAATTCAACCTAAAATCAATTATGAAATTATAAAATCATCTAAAGCGAG
* ** * * * ** *
16144 TAATAAGGCTTTTGAAGACATTGGTGACTATAACT-AGACTTTT-TCTGCCAA-AGAATATCTTT
251 TAATAAGGATTCCGAAGGCATGGGTGACTATAAATGA-ACTTTTCT-TATCAATA-AATATCATT
*
16206 TTCTTCACGTTTC-TCAAGATAG
313 TTCTTCACGTTTCAT-AAGATAA
* * * * * ** *****
16228 GCATTCAATTATAATCTGTTTCAATAAAAAATATAAAAAAATTCTACTTAAANNNNNNNNNNAGA
1 ACATTCAATTATAATCTATTTTAATAAAAAATAT-AAAAACTT-AAAATAAA-----TTATGAGA
* * * * ** * * * *
16293 TTATAAAAAT-ATTTGAAGCGACTAATAAAGCTTTTGAAGACGTGGGTGACTATAAATTGACTTT
59 TTAT-AAAATCGTTTAAAGCGAGTAATAAGGCTTCCGAAGGCATGGGCGACTATAAATGGACTTT
* * * * * * * * * *
16357 TCGTGCTAATGGATATCTTTTTTTTCACT-TTTCTCGAGGTAGACATTCAATTATAATCTGTTTT
123 TCTTACTAATAGATATCTTTTTCTTCA-TGTTTCACAAGGCAAACATTCAATTATAAACTATTTT
* * ** * * *
16421 AACAAAAAATATTAAAAAA-TCAACTTAAAATCAATTATGATGTTATAAAATCATTTAAAACAAG
187 AATAAAAAATA-TAAAAAATTCAACCTAAAATCAATTATGAAATTATAAAATCATCTAAAGCGAG
* * * ********** * ** * *
16485 TAATAAGGCTTTCGAAGGTATGGGTNNNNNNNNNNGGACTTTTCTTGCCAATAGATATCATTTTT
251 TAATAAGGATTCCGAAGGCATGGGTGACTATAAATGAACTTTTCTTATCAATAAATATCATTTTC
* * * *
16550 TTCATGTTTCCTAAGGTAG
316 TTCACGTTTCATAAGATAA
* * * * ** *
16569 ATATTCCATTATTATCAATTTTAGCCAACAATGTAA-AAAAATTCAACTTAAAAT-AATTATGAG
1 ACATTCAATTATAATCTATTTTA-ATAA-AA---AATATAAA---AACTTAAAATAAATTATGAG
* * * * ** * * * * * *
16632 ATTATAAAAAT-ATTTAAAACGAATAATAAGGTTTTTGAATGCGTTGGCGACAATAAATGGTCTA
58 ATTAT-AAAATCGTTTAAAGCGAGTAATAAGGCTTCCGAAGGCATGGGCGACTATAAATGGACTT
* * * * * * * * * * *
16696 TTCTTGCCAAT-GTATATATTTTTCCTT-ACGTTTC-CTGAGGTAGATATTCAATTATTATCTGT
122 TTCTTACTAATAG-ATATCTTTTT-CTTCATGTTTCAC-AAGGCAAACATTCAATTATAAACTAT
* ** * * * * *
16758 TTTAACTAAAAAGGTA-AAAACGTTCAACTTAAAATCCATTATGAGATTATAAAAAGC-TTTAAA
184 TTTAA-TAAAAA-ATATAAAAAATTCAACCTAAAATCAATTATGAAATTAT-AAAATCATCTAAA
* * * * *** * * *
16821 GCAAATAAAAAGGCTTTTAAAGGCGTCGGTGACTATAAATGAACTTTTCTTATCAATAAATATCT
246 GCGAGTAATAAGGATTCCGAAGGCATGGGTGACTATAAATGAACTTTTCTTATCAATAAATATCA
* *
16886 TTTTTTTCACGTTTC-TAGAGGTAA
311 TTTTCTTCACGTTTCATA-AGATAA
* * *** *
16910 ACATTGAATTATAATGTATTTTAATAAAAAATATAANNNNNNNNNNCTTAAAATCAATTATGAGA
1 ACATTCAATTATAATCTATTTTAATAAAAAATATAA-------AAACTTAAAATAAATTATGAGA
* * *
16975 TTATGAAATCGTTTAACA-CGAGTAATAAGGCTTTCGAAGGCAT-GG-GTCTATAAATGGACTTT
59 TTATAAAATCGTTTAA-AGCGAGTAATAAGGCTTCCGAAGGCATGGGCGACTATAAATGGACTTT
*
17037 TCTTA-TCAATAGATATCTTTTTCTTCATGTTTCACAAGGCAAACATTTAATTATAAACTATTTT
123 TCTTACT-AATAGATATCTTTTTCTTCATGTTTCACAAGGCAAACATTCAATTATAAACTATTTT
**
17101 AATAAAAAATATATAAAAATTCAATTTAAAATCAATTATGAAATTATAAAATCATCTAAAGCGAG
187 AATAAAAAATATA-AAAAATTCAACCTAAAATCAATTATGAAATTATAAAATCATCTAAAGCGAG
* ********** *
17166 TAATAAGGATTCCGAAGGCATGGGTGACTATAAATGGACNNNNNNNNNNAATAGATATCATTTTC
251 TAATAAGGATTCCGAAGGCATGGGTGACTATAAATGAACTTTTCTTATCAATAAATATCATTTTC
* *
17231 TTCATGTTTCATAAGATAG
316 TTCACGTTTCATAAGATAA
* * *** *
17250 ACATTCAATTATATTCTGTTTTAATAAAAAATATAAAAANNNNNNNNNNAAAATAAATTATGAGG
1 ACATTCAATTATAATCTATTTTAATAAAAAATATAAAAA-------CTTAAAATAAATTATGAGA
* * * *
17315 TTATAAAATCTTTTAAAGTGAGTAATAAGGCTTCCGACGGCATGGGCGACTATAAATGTACTTTT
59 TTATAAAATCGTTTAAAGCGAGTAATAAGGCTTCCGAAGGCATGGGCGACTATAAATGGACTTTT
* * ********** *
17380 CTTACTAATGGATATCTTTTTCTTTATGTTTCNNNNNNNNNNCATTCAATTATAATCTATTTTAA
124 CTTACTAATAGATATCTTTTTCTTCATGTTTCACAAGGCAAACATTCAATTATAAACTATTTTAA
* * ** * * **
17445 TAAACAATATAAAAAATTTAACCTAAAATCAATTATGAGGTTATCAAATCATTTAAAGTTAGTAA
189 TAAAAAATATAAAAAATTCAACCTAAAATCAATTATGAAATTATAAAATCATCTAAAGCGAGTAA
* *
17510 TAAGGCTTTCGAAGGCATGGGTGACTATAAATGAACTTTTCTT
254 TAAGGATTCCGAAGGCATGGGTGACTATAAATGAACTTTTCTT
17553 GCTAATNNNN
Statistics
Matches: 1004, Mismatches: 257, Indels: 127
0.72 0.19 0.09
Matches are distributed among these distances:
334 4 0.00
335 3 0.00
336 2 0.00
337 7 0.01
338 2 0.00
339 20 0.02
340 407 0.41
341 403 0.40
342 136 0.14
343 6 0.01
344 3 0.00
345 3 0.00
346 4 0.00
347 4 0.00
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.35
Consensus pattern (334 bp):
ACATTCAATTATAATCTATTTTAATAAAAAATATAAAAACTTAAAATAAATTATGAGATTATAAA
ATCGTTTAAAGCGAGTAATAAGGCTTCCGAAGGCATGGGCGACTATAAATGGACTTTTCTTACTA
ATAGATATCTTTTTCTTCATGTTTCACAAGGCAAACATTCAATTATAAACTATTTTAATAAAAAA
TATAAAAAATTCAACCTAAAATCAATTATGAAATTATAAAATCATCTAAAGCGAGTAATAAGGAT
TCCGAAGGCATGGGTGACTATAAATGAACTTTTCTTATCAATAAATATCATTTTCTTCACGTTTC
ATAAGATAA
Found at i:21301 original size:9 final size:10
Alignment explanation
Indices: 21285--21311 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
21275 TTTAAGTTGA
21285 ATTTTTTTAC
1 ATTTTTTTAC
21295 ATTTTTTTAC
1 ATTTTTTTAC
21305 ATTTTTT
1 ATTTTTT
21312 GTTAAAACAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.19, C:0.07, G:0.00, T:0.74
Consensus pattern (10 bp):
ATTTTTTTAC
Found at i:23573 original size:172 final size:171
Alignment explanation
Indices: 23269--23663 Score: 408
Period size: 172 Copynumber: 2.3 Consensus size: 171
23259 NNNNNNNNNN
* * * * *
23269 ATTATAATTGAATGTCTACCTTAAGAAACATGAAGAAAAAGATATTCATTGGTATGAATACTCTA
1 ATTAAAATTGAATGCCTACCTTAAGAAACATGAAGAAAAAGATATACATTGGAAGGAATACTCTA
* * ** * *
23334 TTTATTGTCAGTCACTCCTTCAAAAGCCTTATTACATGTTTTAAATGTTTTTATAATCTCATAAT
66 TTTATAGTCAGTCACTCCTTCAAAAGCCTTATTACACGCCTAAAATGTTTTTAGAATCTCATAAT
* * *
23399 TGACTTTAA-GTAGAGTTTTTTTACATGTTTT-ATTAAAATCAG
131 TGACTTTAACCTA-AATTTTTATACAT-TTTTGATTAAAA-CAG
* * * * * *
23441 ATTAAAATTGAATGCCTTCTTTTAGAAACGTGAAGAAAAAGCTATACATTGGCAAGGAA-AGTCT
1 ATTAAAATTGAATGCCTACCTTAAGAAACATGAAGAAAAAGATATACATTGG-AAGGAATACTCT
* *
23505 ATTTATAGTCA-TC-CATGCCTTCAAAAGCCTTATTACGCGCCTAAAATGTTTTTAGAATCTCGT
65 ATTTATAGTCAGTCAC-T-CCTTCAAAAGCCTTATTACACGCCTAAAATGTTTTTAGAATCTCAT
* *
23568 AATTGATTTTAACCTAAATTTTTATACATTTTTGGTTAAAACAG
128 AATTGACTTTAACCTAAATTTTTATACATTTTTGATTAAAACAG
* * * * *
23612 A-TAATAATTGAATGTCTACCCTT-GGAAATAAGAAGAAAAAGATATCCATTGG
1 ATTAA-AATTGAATGCCTA-CCTTAAGAAACATGAAGAAAAAGATATACATTGG
23664 CAAGAAAAGT
Statistics
Matches: 183, Mismatches: 33, Indels: 15
0.79 0.14 0.06
Matches are distributed among these distances:
170 4 0.02
171 45 0.25
172 128 0.70
173 6 0.03
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.37
Consensus pattern (171 bp):
ATTAAAATTGAATGCCTACCTTAAGAAACATGAAGAAAAAGATATACATTGGAAGGAATACTCTA
TTTATAGTCAGTCACTCCTTCAAAAGCCTTATTACACGCCTAAAATGTTTTTAGAATCTCATAAT
TGACTTTAACCTAAATTTTTATACATTTTTGATTAAAACAG
Found at i:23706 original size:171 final size:162
Alignment explanation
Indices: 23517--23845 Score: 315
Period size: 172 Copynumber: 2.0 Consensus size: 162
23507 TTATAGTCAT
** * *
23517 CCATGCCTTCAAAAGCCTTATTACGCGCCTAAAATGTTTTTAGAA-TCTCGTAATTGATTTTAAC
1 CCATGCCTTCAAAAGCCTTATTACGCGCCTAAAATAATTTTAGAACT-TCATAATTGATTTAAAC
* * *
23581 CTAAA-TTTTTATACATTTTTGGTT-AAAACAGATAATAATTGAATGTCTACCCTTG-GAAATAA
65 CTAAATTTTTTATACATTTTTGATTAAAAAAAG-TAATAATTGAATGTCTA-CCTCGAGAAATAA
*
23643 GAAGAAAAAGATATCCATTGGCAAGAAAAGTNNNNNNNNNNTCAC
128 GAAGAAAAAGATATCCATTGACAAGAAAAGT----------TCAC
* * * * * * **
23688 CCATGTCTTCGAAAGCCTTATTACTCGCTTTAAATAATTTTATAACTTCATAATTGATTTAAAGT
1 CCATGCCTTCAAAAGCCTTATTACGCGCCTAAAATAATTTTAGAACTTCATAATTGATTTAAACC
* * * * *
23753 TAAATTTTTTTTACATTTTTTATTAAAAAAAGTTATAATTGAATGTTTACCTCGAGAAATATGAA
66 TAAATTTTTTATACATTTTTGATTAAAAAAAGTAATAATTGAATGTCTACCTCGAGAAATAAGAA
*
23818 GAAAAAGATATCCATTGATAAGAAAAGT
131 GAAAAAGATATCCATTGACAAGAAAAGT
23846 CCANNNNNNN
Statistics
Matches: 132, Mismatches: 22, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
171 59 0.45
172 67 0.51
173 6 0.05
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.35
Consensus pattern (162 bp):
CCATGCCTTCAAAAGCCTTATTACGCGCCTAAAATAATTTTAGAACTTCATAATTGATTTAAACC
TAAATTTTTTATACATTTTTGATTAAAAAAAGTAATAATTGAATGTCTACCTCGAGAAATAAGAA
GAAAAAGATATCCATTGACAAGAAAAGTTCAC
Found at i:24344 original size:171 final size:170
Alignment explanation
Indices: 24101--24891 Score: 536
Period size: 171 Copynumber: 4.6 Consensus size: 170
24091 CTACCTTGGG
* * * *
24101 AAACATGAAGAAAAAGATATTCGTTGGCAAGAATAGTCCATTTATAGTCACCCA-CGCCTTCGAA
1 AAACATGAAGAAAAAGATATTCATTGGCAAGAAAAGTCTATTTATAGTCACCCATC-CCTTTGAA
* * * *
24165 AGCCTTATTACTCGCTTAAAATAGTTTTATAATCTTATAATTGACTTTAAGTAGAATTTTTTTAC
65 AGCCTTATTACTCGCTTTAAATAGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTAC
* *
24230 ATTTTTTATTAGAACAGATTAAAATTGAATGCCTTTTTCAAA
130 ATTTTTTATTAAAACATATTAAAATTGAATG-CTTTTTCAAA
* **
24272 AAACATGAAGAAAAAGATATTCATTGGTAAGAAAAGTCTACGTATAGTCACCCATCCCTTTGAAA
1 AAACATGAAGAAAAAGATATTCATTGGCAAGAAAAGTCTATTTATAGTCACCCATCCCTTTGAAA
* * **********
24337 CCCTTATTACTCGCTTTAAATGGTTTTATANNNNNNNNNNTGATTTTAAGTTGAATTTTTTTACA
66 GCCTTATTACTCGCTTTAAATAGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACA
* ** *** * * *
24402 TTTATGT-GCAAAACATA-TAATAATCTTCTTG-TTTGTCTGAC
131 TTT-TTTATTAAAACATATTAA-AAT-TGAATGCTTTTTC-AAA
* ** * * * * * *
24443 AAACATGAAGAAAAAGCTATTCATTGATAAGAAAAGTCAATTTAAAATCCCCCATGCATTTGAAA
1 AAACATGAAGAAAAAGATATTCATTGGCAAGAAAAGTCTATTTATAGTCACCCATCCCTTTGAAA
* * * * *
24508 GCCTTATTACCCGGTTTAAATCA-TTTTATAATCTCATAATTGATTTTAAGTTGAATTGTTCTAT
66 GCCTTATTACTCGCTTTAAAT-AGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTAC
* ** *
24572 ATTTTTTATTAAAACATATTATAATTGAATGTCTGCCTT-AAG
130 ATTTTTTATTAAAACATATTAAAATTGAATG-CT-TTTTCAAA
** ** *
24614 AAATGTGAAGAAAAAGATATTCATTGGCAAGAAAAGTCTATTTATAGTCATTCAT-GCTTTCGAA
1 AAACATGAAGAAAAAGATATTCATTGGCAAGAAAAGTCTATTTATAGTCACCCATCCCTTT-GAA
********** * *
24678 AGCCTTATTACTCGCTTNNNNNNNNNNTATAACCTCATAATTGATTTTAAG-TGAAATTGTTTTA
65 AGCCTTATTACTCGCTTTAAATAGTTTTATAATCTCATAATTGATTTTAAGTTG-AATTTTTTTA
* * * ********** *** *
24742 TATTTTTTATTAAAAAAGANNNNNNNNNNATGTCTACCTCAAG
129 CATTTTTTATTAAAACATATTAAAATTGAATG-CTTTTTCAAA
* * * ** * ** * *
24785 AAACGTGAAGAGAAAGATATCCATTGATAAGAAAAGTCCATTTATAGTCACTTATGCCTTCGAAA
1 AAACATGAAGAAAAAGATATTCATTGGCAAGAAAAGTCTATTTATAGTCACCCATCCCTTTGAAA
* *
24850 GCCTTATTACTCACTCTAAATAGTTTTATAATCTCATAATTG
66 GCCTTATTACTCGCTTTAAATAGTTTTATAATCTCATAATTG
24892 NNNNNNNNNN
Statistics
Matches: 469, Mismatches: 135, Indels: 32
0.74 0.21 0.05
Matches are distributed among these distances:
170 20 0.04
171 436 0.93
172 12 0.03
173 1 0.00
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.36
Consensus pattern (170 bp):
AAACATGAAGAAAAAGATATTCATTGGCAAGAAAAGTCTATTTATAGTCACCCATCCCTTTGAAA
GCCTTATTACTCGCTTTAAATAGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACA
TTTTTTATTAAAACATATTAAAATTGAATGCTTTTTCAAA
Done.