Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402062.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_516.0, 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: 13762
ACGTcount: A:0.31, C:0.09, G:0.11, T:0.29
Warning! 2779 characters in sequence are not A, C, G, or T
Found at i:385 original size:172 final size:172
Alignment explanation
Indices: 144--527 Score: 431
Period size: 172 Copynumber: 2.2 Consensus size: 172
134 GGTGACCATG
* * * *
144 GACTTTTCTTTCTAATGAGTGTC-TTTTTCTTCA-AGTTTCTAGACGTAGACATTCAATTATAAT
1 GACTTTTCTTGCTAATGAATGTCTTTTTTCTTTACA-TTTCTAGAAGTAGACATTCAATTATAAT
* ** * *
207 CTGTTTTATCAAAAAATGTCAAAAA-ACTTGAACT-TAAAATCTATTTTGAGATTATAAAACTAT
65 CTGTTTTAACAAAAAATGT-AAAAAGA-TTG-ACTATAAAATAAATTTTGAGATAATAAAACCAT
* * * * ** *
270 TTAAGACGAGTAATAAGTCTTTTGAAGGAATGGGAGACTATAAATA
127 TTAAAACGAGTAATAAGGCTTCTAAAGGAATGAAAAACTATAAATA
* * *
316 GACTTTTCTTGCTAATGAAT-TCTTTTTTCTTTACATTTTTTGAAGTAGATATTCAATTATAATC
1 GACTTTTCTTGCTAATGAATGTCTTTTTTCTTTACATTTCTAGAAGTAGACATTCAATTATAATC
* *
380 TGTTTTAACCAAAAATGTAAAAAGTATTGAGTATAAAATAAATTTTGAGATAATAAAACCATTTA
66 TGTTTTAACAAAAAATGTAAAAAG-ATTGACTATAAAATAAATTTTGAGATAATAAAACCATTTA
* * *
445 AAATGGGTAATAGGGCTTCTAAAGGAATGAAAAACTATAAATA
130 AAACGAGTAATAAGGCTTCTAAAGGAATGAAAAACTATAAATA
* *
488 GACTTTTCCTG-TCAATGAATGT-TTTTTTCTTTGCATTTCT
1 GACTTTTCTTGCT-AATGAATGTCTTTTTTCTTTACATTTCT
528 CAACGTAAAN
Statistics
Matches: 178, Mismatches: 27, Indels: 14
0.81 0.12 0.06
Matches are distributed among these distances:
171 10 0.06
172 165 0.93
173 3 0.02
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.40
Consensus pattern (172 bp):
GACTTTTCTTGCTAATGAATGTCTTTTTTCTTTACATTTCTAGAAGTAGACATTCAATTATAATC
TGTTTTAACAAAAAATGTAAAAAGATTGACTATAAAATAAATTTTGAGATAATAAAACCATTTAA
AACGAGTAATAAGGCTTCTAAAGGAATGAAAAACTATAAATA
Found at i:1572 original size:170 final size:170
Alignment explanation
Indices: 1026--2980 Score: 1135
Period size: 170 Copynumber: 11.5 Consensus size: 170
1016 NNNNNNNNNA
* * *
1026 GAGTAATAAGGCTTTTGAAGGAAT-AGGTGACTATAAATTAACTTTTCATGCCAATGAATACTTT
1 GAGTAATAAGGCTTTTGAAGGAATGA-GAGACTATAAATGAACTTTTCTTGCCAATGAATAC-TT
* * * * *
1090 TTTTTTTCACGTTT-TTCAA-AGTAAACACTCAACTATAATCTGTTTTAA-ATAAAAAGTAAAAA
64 TTTTCTTCACGTTTCTT-AAGA-TAAACATTCAATTATAGTCTGTTTTAACAAAAAAAGTAAAAA
* * *
1152 AATTGAACTTAAAA-CTAATTTTGAGATTATAAAATCGTTTAAAGT
127 AATTGAACTTAAAATC-AATTATGAGATTATAAAA-CATTTAAAAT
*
1197 GAGTAATAAGGCTTTTGAAGGAATGA-ATGACTAT-AATGGACTTTTCTTGCCAATGAATACTTT
1 GAGTAATAAGGCTTTTGAAGGAATGAGA-GACTATAAATGAACTTTTCTTGCCAATGAATACTTT
********** * * * * * * *
1260 NNNNNNNNNNTTTCTCAAGTTAGACATTCAATTATTA-TTTGTTTTAATC-GAAAATGTGAAAAA
65 TTTCTTCACGTTTCTTAAGATAAACATTCAATTA-TAGTCTGTTTTAA-CAAAAAAAGTAAAAAA
***
1323 ATTGAACTTAAAATCAATTATGAGATTATAAAACTATTTAANNN
128 ATTGAACTTAAAATCAATTATGAGATTATAAAAC-ATTTAAAAT
***************************** * *
1367 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNACTATAAATAAACTTTTCTTGGCAATGAATACTTTT
1 GAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATGAACTTTTCTTGCCAATGAATACTTTT
* * * *
1432 TTCTTCACATTTCTTAAGATAAACAGTCAATTATAGTCTGTTTTGACAAAAAAAGT-AAACAATT
66 TTCTTCACGTTTCTTAAGATAAACATTCAATTATAGTCTGTTTTAACAAAAAAAGTAAAAAAATT
* * *
1496 AAACTTAAAATCAATTATAAGATTATAAAATCATTTAAAAC
131 GAACTTAAAATCAATTATGAGATTATAAAA-CATTTAAAAT
* * * * *
1537 GGGTAATTAGGCTTTTGAAGGAATGGGAGACTATAAATGGTTTTTACTTTTCATGCCAATGAATA
1 GAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAAT-G----AACTTTTCTTGCCAATGAATA
* * * * * * **
1602 CCTTTTTCTTTACATTT-TTCAA-AGTAAACATTCAACTATAATATGTTTTAAGTAAAAAAGTAA
61 CTTTTTTCTTCACGTTTCTT-AAGA-TAAACATTCAATTATAGTCTGTTTTAACAAAAAAAGTAA
* * * *
1665 AAAAATTGAACTTAAAACCAATTTTGAGATTACAAAACATTTAAAGT
124 AAAAATTGAACTTAAAATCAATTATGAGATTATAAAACATTTAAAAT
* * * *
1712 GAGTAACAAGGCTTTTGAAGGAATGA-ATGACTAT-AATGGACTTTTCTTGCCAACGAATGC--T
1 GAGTAATAAGGCTTTTGAAGGAATGAGA-GACTATAAATGAACTTTTCTTGCCAATGAATACTTT
* * ** * *
1773 TTT-TTCATGTTTCTTAAGTTAGAA-ATTCAATTATTA-TCTGTTTTAACTGAAAATGTGAAAAA
65 TTTCTTCACGTTTCTTAAGATA-AACATTCAATTA-TAGTCTGTTTTAACAAAAAAAGTAAAAAA
*
1835 ATTGAACTT-AAATCAATTATGAGATTATAAAACTATATAAAAT
128 ATTGAACTTAAAATCAATTATGAGATTATAAAAC-ATTTAAAAT
* * **********
1878 GACTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATAAANNNNNNNNNNCAATGAATACTTTT
1 GAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATGAACTTTTCTTGCCAATGAATACTTTT
* * * * * *
1943 TTCTTCACATTTCTTAAGGTAGAGAGTCAATTATAGTATGTTTTAAC-AAAAAA-TATAAAAAAT
66 TTCTTCACGTTTCTTAAGATAAACATTCAATTATAGTCTGTTTTAACAAAAAAAGTA-AAAAAAT
* * *
2006 TAAACGTAAAATCAATTATGAGAATATAAAACCATTTAAAAT
130 TGAACTTAAAATCAATTATGAGATTATAAAA-CATTTAAAAT
* * * * * **
2048 GAGCAGTTAGGCTTTTGAAAGAATGAGAGACTATAAATGAACTTTTCCTGAAAATGAATA-TTTT
1 GAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATGAACTTTTCTTGCCAATGAATACTTTT
* * *** * * * * * *
2112 TTTTTCATGTTTCCCGAGACAAGCAATCAATCATAGTCTATTTTAATAAAAAATA-TAAAAAAAT
66 TTCTTCACGTTTCTTAAGATAAACATTCAATTATAGTCTGTTTTAACAAAAAA-AGTAAAAAAAT
* * * *
2176 TGAACTTAAAATCAATGATGAGATTATTAAACTATTTATAAC
130 TGAACTTAAAATCAATTATGAGATTATAAAAC-ATTTAAAAT
* *
2218 GAGTAATAAGGCTTTTG--GGAAATGGGAGACTATAAATGAACTTTGCTTGCCAATGAATACTTT
1 GAGTAATAAGGCTTTTGAAGG-AATGAGAGACTATAAATGAACTTTTCTTGCCAATGAATACTTT
* ************ * * *
2281 TTTCTTCATGTTNNNNNNNNNNGGCATTCAGTTTTAGTCTGTTTTAACAAAAAATGTAACAAAAA
65 TTTCTTCACGTTTCTTAAGATAAACATTCAATTATAGTCTGTTTTAACAAAAAAAGTAA-AAAAA
*
2346 TTGAACTTAAAATTAATTATGAGATTATAAAACCATTTAAAGA-
129 TTGAACTTAAAATCAATTATGAGATTATAAAA-CATTTAAA-AT
* * * * **
2389 GAGTAATAGGGTTTTTAAAGGAATGAGAGACCATAAATGAACTTTTCTTGATAATGAATACTTTT
1 GAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATGAACTTTTCTTGCCAATGAATACTTTT
** * * * * * * ** *
2454 CCCTTCACGCTTCTTAAGGTAGATATTCAGTTATAGTTTGTTTTAACCAAAAAGTGTAAAAAAAA
66 TTCTTCACGTTTCTTAAGATAAACATTCAATTATAGTCTGTTTTAA-CAAAAAAAGTAAAAAAAT
* * * *
2519 TGAACATAAAATCAATTTTGAGATAATAAAATCATTTAAAAA
130 TGAACTTAAAATCAATTATGAGATTATAAAA-CATTTAAAAT
* ********** * *
2561 GGGTAATAAGGCTTTTGAAGGAATGNNNNNNNNNNAATGGACTTTTCTTAG-CAATGAA-AGCCT
1 GAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATGAACTTTTCTT-GCCAATGAATA-CTT
* * * * * * *
2624 TTTTCTTCATGTTTCTCAATG-TAGAGATTCAATTATAAT-TGTTTAAACCAAAAAAGTAAAAAC
64 TTTTCTTCACGTTTCTTAA-GATAAACATTCAATTATAGTCTGTTTTAACAAAAAAAGT-AAAA-
* ********* *
2687 AAATTGAACTTAAAATCAATTTTGAGATTATNNNNNNNNNNAAAGT
126 AAATTGAACTTAAAATCAATTATGAGATTAT-AAAACATTTAAAAT
* * * *
2733 GAGCAATAAGGCTTTTGAAGGAATG-GATGACTATAAAT-AGAC-TTTCTTGCTAATGAATGC-C
1 GAGTAATAAGGCTTTTGAAGGAATGAGA-GACTATAAATGA-ACTTTTCTTGCCAATGAATACTT
* ** * * *
2794 TTTTCTTCAAC-TTTCTCAACCTAGACATTCAATTATTA-TCTGTTTTAGCAAAAAATGTAAAAA
64 TTTTCTTC-ACGTTTCTTAAGATAAACATTCAATTA-TAGTCTGTTTTAACAAAAAAAGTAAAAA
* * * * *
2857 AATTTAACTAAAAATTAATTATGAGATTATAAAAAATTTTAAA-
127 AATTGAACTTAAAATCAATTATGAGATTATAAAACATTTAAAAT
* * * * *
2900 GCCAGCAATAAGACTTTTGAAGAAAT-AGGAGACTATAAATGGAGTTTTCTTGCCAATGAATACT
1 G--AGTAATAAGGCTTTTGAAGGAATGA-GAGACTATAAATGAACTTTTCTTGCCAATGAATACT
*
2964 TTTTTCTTCATGTTTCT
63 TTTTTCTTCACGTTTCT
2981 CAANNNNNNN
Statistics
Matches: 1333, Mismatches: 378, Indels: 146
0.72 0.20 0.08
Matches are distributed among these distances:
165 21 0.02
166 85 0.06
167 24 0.02
168 4 0.00
169 199 0.15
170 398 0.30
171 206 0.15
172 240 0.18
173 16 0.01
174 7 0.01
175 101 0.08
176 32 0.02
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.34
Consensus pattern (170 bp):
GAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATGAACTTTTCTTGCCAATGAATACTTTT
TTCTTCACGTTTCTTAAGATAAACATTCAATTATAGTCTGTTTTAACAAAAAAAGTAAAAAAATT
GAACTTAAAATCAATTATGAGATTATAAAACATTTAAAAT
Found at i:1935 original size:511 final size:511
Alignment explanation
Indices: 1026--2973 Score: 1285
Period size: 511 Copynumber: 3.8 Consensus size: 511
1016 NNNNNNNNNA
* * * *
1026 GAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAAA--TTAACTTTTCATGCCAATGAATACTT
1 GAGTAATTAGGCTTTTGAAGGAATGGGAGACTATAAATGTTAACTTTTCATGCCAATGAATACCT
* * *
1089 TTTTTTTTCACGTTTTTCAAAGTAAACACTCAACTATAATCTGTTTTAAATAAAAAGTAAAAAAA
66 TTTTCTTTCACATTTTTCAAAGTAAACACTCAACTATAATATGTTTTAAATAAAAAGTAAAAAAA
* * * *
1154 TTGAACTTAAAACTAATTTTGAGATTATAAAATCGTTTAAAGTGAGTAATAAGGCTTTTGAAGGA
131 TTGAACTTAAAACCAATTTTGAGATTACAAAATCATTTAAAGTGAGTAACAAGGCTTTTGAAGGA
* ********
1219 ATGAATGACTATAATGGACTTTTCTTGCCAATGAATACTTTNNNNNNNNNNTTTCTCAAGTTAGA
196 ATGAATGACTATAATGGACTTTTCTTGCCAACGAATACTTT--ATTTCATGTTTCTCAAGTTAGA
* *
1284 CATTCAATTATTATTTGTTTTAATCGAAAATGTGAAAAAATTGAACTTAAAATCAATTATGAGAT
259 AATTCAATTATTATCTGTTTTAATCGAAAATGTGAAAAAATTGAACTTAAAATCAATTATGAGAT
* ********************************
1349 TATAAAACTATTTAANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNACTATAAATAAACTTTTC
324 TATAAAACTATATAAAATGACTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATAAACTTTTC
* *
1414 TTGGCAATGAATACTTTTTTCTTCACATTTCTTAAGATAAACAGTCAATTATAGTCTGTTTTGAC
389 TTGGCAATGAATACTTTTTTCTTCACATTTCTTAAGATAAACAGTCAATTATAGTATGTTTTAAC
* * * *
1479 AAAAAA-AGTAAACAATTAAACTTAAAATCAATTATAAGATTATAAAATCATTTAAAAC
454 AAAAAATA-TAAAAAATTAAACGTAAAATCAATTATAAGAATATAAAACCATTTAAAAC
* *
1537 GGGTAATTAGGCTTTTGAAGGAATGGGAGACTATAAATGGTTTTTACTTTTCATGCCAATGAATA
1 GAGTAATTAGGCTTTTGAAGGAATGGGAGACTATAAAT-G--TTAACTTTTCATGCCAATGAATA
* *
1602 CCTTTTTCTTT-ACATTTTTCAAAGTAAACATTCAACTATAATATGTTTTAAGTAAAAAAGTAAA
63 CCTTTTTCTTTCACATTTTTCAAAGTAAACACTCAACTATAATATGTTTTAAAT-AAAAAGTAAA
1666 AAAATTGAACTTAAAACCAATTTTGAGATTACAAAA-CATTTAAAGTGAGTAACAAGGCTTTTGA
127 AAAATTGAACTTAAAACCAATTTTGAGATTACAAAATCATTTAAAGTGAGTAACAAGGCTTTTGA
* *
1730 AGGAATGAATGACTATAATGGACTTTTCTTGCCAACGAATGCTTT-TTTCATGTTTCTTAAGTTA
192 AGGAATGAATGACTATAATGGACTTTTCTTGCCAACGAATACTTTATTTCATGTTTCTCAAGTTA
1794 GAAATTCAATTATTATCTGTTTTAA-CTGAAAATGTGAAAAAATTGAACTT-AAATCAATTATGA
257 GAAATTCAATTATTATCTGTTTTAATC-GAAAATGTGAAAAAATTGAACTTAAAATCAATTATGA
***
1857 GATTATAAAACTATATAAAATGACTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATAAANNN
321 GATTATAAAACTATATAAAATGACTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATAAACTT
******* * * *
1922 NNNNNNNCAATGAATACTTTTTTCTTCACATTTCTTAAGGTAGAGAGTCAATTATAGTATGTTTT
386 TTCTTGGCAATGAATACTTTTTTCTTCACATTTCTTAAGATAAACAGTCAATTATAGTATGTTTT
* *
1987 AACAAAAAATATAAAAAATTAAACGTAAAATCAATTATGAGAATATAAAACCATTTAAAAT
451 AACAAAAAATATAAAAAATTAAACGTAAAATCAATTATAAGAATATAAAACCATTTAAAAC
* * * * * **
2048 GAGCAGTTAGGCTTTTGAAAGAATGAGAGACTATAAATG--AACTTTTCCTGAAAATGAATA--T
1 GAGTAATTAGGCTTTTGAAGGAATGGGAGACTATAAATGTTAACTTTTCATGCCAATGAATACCT
* * ** * * * * *
2109 TTTT-TTT-TCATGTTTCCCGAG-ACAAGCAATCAA-TCATAGTCTATTTT-AATAAAAAATATA
66 TTTTCTTTCACAT-TTTTCAAAGTA-AA-CACTCAACT-ATAATATGTTTTAAAT-AAAAA-GTA
* ** ** * *
2169 AAAAAATTGAACTTAAAATCAATGATGAGATTATTAAA-CTATTTATAA-CGAGTAATAAGGCTT
125 AAAAAATTGAACTTAAAACCAATTTTGAGATTACAAAATC-ATTTA-AAGTGAGTAACAAGGCTT
* * * * * *
2232 TTG--GGAAATGGGA-GACTATAAATGAACTTTGCTTGCCAATGAATACTTTTTTCTTCATGTTN
188 TTGAAGG-AAT-GAATGACTAT-AATGGACTTTTCTTGCCAACGAATAC-TTTAT-TTCATGTTT
********* ** * * *
2294 NNNNNNNNNGGCATTCAGTT-TTAGTCTGTTTTAA-CAAAAAATGTAACAAAAATTGAACTTAAA
248 CTCAAGTTAGAAATTCAATTATTA-TCTGTTTTAATC-GAAAATGTGA-AAAAATTGAACTTAAA
* * * * * * * *
2357 ATTAATTATGAGATTATAAAACCATTTAAAGA-GAGTAATAGGGTTTTTAAAGGAATGAGAGACC
310 ATCAATTATGAGATTATAAAACTATATAAA-ATGACTAATAAGGCTTTTGAAGGAATGAGAGACT
* ** ** ** * * * * *
2421 ATAAATGAACTTTTCTTGATAATGAATACTTTTCCCTTCACGCTTCTTAAGGTAGATATTCAGTT
374 ATAAATAAACTTTTCTTGGCAATGAATACTTTTTTCTTCACATTTCTTAAGATAAACAGTCAATT
* * * * * * * *
2486 ATAGTTTGTTTTAACCAAAAAGTGTAAAAAAAATGAACATAAAATCAATTTTGAG-ATAATAAAA
439 ATAGTATGTTTTAA-CAAAAAATAT-AAAAAATTAAACGTAAAATCAATTATAAGAAT-ATAAAA
* *
2550 TCATTTAAAAA
501 CCATTTAAAAC
* * ********** * *
2561 GGGTAATAAGGCTTTTGAAGGAATGNNNNNNNNNNAATG--GACTTTTCTTAG-CAATGAA-AGC
1 GAGTAATTAGGCTTTTGAAGGAATGGGAGACTATAAATGTTAACTTTTCAT-GCCAATGAATA-C
** * * * * * * *
2622 CTTTTTC-TTCATGTTTCTCAATGTAGAGATTCAATTATAAT-TG-TTTAAACCAAAAAAGTAAA
64 CTTTTTCTTTCACATTTTTCAAAGTAAACACTCAACTATAATATGTTTTAAA--TAAAAAGT-AA
* *********** * *
2684 AACAAATTGAACTTAAAATCAATTTTGAGATTATNNNNNNNNNNAAAGTGAGCAATAAGGCTTTT
126 AA-AAATTGAACTTAAAACCAATTTTGAGATTACAAAATCATTTAAAGTGAGTAACAAGGCTTTT
* * * * * **
2749 GAAGGAATGGATGACTATAAATAGAC-TTTCTTGCTAATGAATGCCTTT-TCTTCAACTTTCTCA
190 GAAGGAATGAATGACTAT-AATGGACTTTTCTTGCCAACGAAT-ACTTTAT-TTCATGTTTCTCA
** * * * * * * *
2812 ACCTAGACATTCAATTATTATCTGTTTT-AGCAAAAAATGTAAAAAAATTTAACTAAAAATTAAT
252 AGTTAGAAATTCAATTATTATCTGTTTTAATC-GAAAATGTGAAAAAATTGAACTTAAAATCAAT
* * * * *
2876 TATGAGATTATAAAA-AATTTTAAA-GCCAGC-AATAAGACTTTTGAAGAAAT-AGGAGACTATA
316 TATGAGATTATAAAACTATATAAAATG--A-CTAATAAGGCTTTTGAAGGAATGA-GAGACTATA
** * *
2937 AATGGAGTTTTCTTGCCAATGAATACTTTTTTCTTCA
377 AATAAACTTTTCTTGGCAATGAATACTTTTTTCTTCA
2974 TGTTTCTCAA
Statistics
Matches: 1138, Mismatches: 246, Indels: 104
0.76 0.17 0.07
Matches are distributed among these distances:
503 7 0.01
504 24 0.02
505 60 0.05
506 62 0.05
507 5 0.00
508 4 0.00
509 35 0.03
510 14 0.01
511 332 0.29
512 80 0.07
513 173 0.15
514 58 0.05
515 189 0.17
516 93 0.08
517 2 0.00
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.34
Consensus pattern (511 bp):
GAGTAATTAGGCTTTTGAAGGAATGGGAGACTATAAATGTTAACTTTTCATGCCAATGAATACCT
TTTTCTTTCACATTTTTCAAAGTAAACACTCAACTATAATATGTTTTAAATAAAAAGTAAAAAAA
TTGAACTTAAAACCAATTTTGAGATTACAAAATCATTTAAAGTGAGTAACAAGGCTTTTGAAGGA
ATGAATGACTATAATGGACTTTTCTTGCCAACGAATACTTTATTTCATGTTTCTCAAGTTAGAAA
TTCAATTATTATCTGTTTTAATCGAAAATGTGAAAAAATTGAACTTAAAATCAATTATGAGATTA
TAAAACTATATAAAATGACTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATAAACTTTTCTT
GGCAATGAATACTTTTTTCTTCACATTTCTTAAGATAAACAGTCAATTATAGTATGTTTTAACAA
AAAATATAAAAAATTAAACGTAAAATCAATTATAAGAATATAAAACCATTTAAAAC
Found at i:3911 original size:170 final size:168
Alignment explanation
Indices: 3677--4232 Score: 528
Period size: 171 Copynumber: 3.3 Consensus size: 168
3667 GGAATAGGTG
* * * * * *
3677 ACTATAAATGGACTTTTCATGCCAATGAATGCCTTTTTCTTCACGTTTTTTAAAGTAAACATTCA
1 ACTATAAATGAACTTTTCTTGCCAATGAATGCTTTTTTCTTCACG-TTTATCAAGTAGACATTCA
* *
3742 ACTATAATCTGTTTTAAACAAAAAAG-CAAAAAAGTTGAACTTAAAACTAATTTTGAGATTATAA
65 A-TATAGTCTGTTTTAAACAAAAAAGTGAAAAAA-TTGAACTTAAAA-TAATTTTGAGATTATAA
**********
3806 AACCNNNNNNNNNNAGTAATAAGGCTTTTGAAGGAATGA-ATA
127 AACCATTTAAAATTAGTAATAAGGCTTTTGAAGGAATGAGA-A
* * *
3848 ACTAT-AATGCACTTTTCTTGCCAATGAATGCTTTTTTCTTCATGTTTATCGAGTTAGACATTCA
1 ACTATAAATGAACTTTTCTTGCCAATGAATGCTTTTTTCTTCACGTTTATCAAG-TAGACATTCA
* * * * * * *
3912 ATTTTGTCTGTTTTAATCGAAAATGTGAAAAAATTGAACTTAAAATCAATTATGAAATTATAAAA
65 ATATAGTCTGTTTTAAACAAAAAAGTGAAAAAATTGAACTTAAAAT-AATTTTGAGATTATAAAA
* ** *
3977 CTATTTAAAATTAGTAATAAGGCTTTTGAAGGGTTGAGAG
129 CCATTTAAAATTAGTAATAAGGCTTTTGAAGGAATGAGAA
* * * * * *
4017 ACTATAAATAAACTTTTCTTGGCAATGAATTCTTTTTTCTTCACATTTCTCAAGGTAGACAGTCA
1 ACTATAAATGAACTTTTCTTGCCAATGAATGCTTTTTTCTTCACGTTTATCAA-GTAGACATTCA
* *
4082 ATTATAGTCTGTTTT-AACAAAAAATGTGAAAAAATTAAACTTAAAATCATTTATGAGATTATAA
65 A-TATAGTCTGTTTTAAACAAAAAA-GTGAAAAAATTGAACTTAAAATAATTT-TGAGATTATAA
* ** * * *
4146 AAGCATTTAAAACGAGTAATTAGGCTTTTGAAGAAATG-GCAG
127 AACCATTTAAAATTAGTAATAAGGCTTTTGAAGGAATGAG-AA
* **
4188 ACTATAAATGAACTTTTTTTGGAAATGAATGCTTTTTTCTTCACG
1 ACTATAAATGAACTTTTCTTGCCAATGAATGCTTTTTTCTTCACG
4233 ATTTTTGATG
Statistics
Matches: 313, Mismatches: 62, Indels: 20
0.79 0.16 0.05
Matches are distributed among these distances:
168 1 0.00
169 81 0.26
170 111 0.35
171 120 0.38
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.36
Consensus pattern (168 bp):
ACTATAAATGAACTTTTCTTGCCAATGAATGCTTTTTTCTTCACGTTTATCAAGTAGACATTCAA
TATAGTCTGTTTTAAACAAAAAAGTGAAAAAATTGAACTTAAAATAATTTTGAGATTATAAAACC
ATTTAAAATTAGTAATAAGGCTTTTGAAGGAATGAGAA
Found at i:4128 original size:171 final size:170
Alignment explanation
Indices: 3820--4236 Score: 529
Period size: 171 Copynumber: 2.4 Consensus size: 170
3810 NNNNNNNNNN
* * *
3820 AGTAATAAGGCTTTTGAAGGAATGA-ATAACTAT-AATGCACTTTTCTTGCCAATGAATGCTTTT
1 AGTAATAAGGCTTTTGAAGGAATGAGA-GACTATAAATGAACTTTTCTTGGCAATGAATGCTTTT
** * * * * * *
3883 TTCTTCATGTTTATCGAGTTAGACATTCAATTTTGTCTGTTTTAATCGAAAATGTGAAAAAATTG
65 TTCTTCACATTTATCAAGGTAGACAGTCAATTTAGTCTGTTTTAATCAAAAATGTGAAAAAATTA
**
3948 AACTTAAAATCAATTATGAAATTATAAAA-CTATTTAAAATT
130 AACTTAAAATCAATTATGAAATTATAAAAGC-ATTTAAAACG
** * *
3989 AGTAATAAGGCTTTTGAAGGGTTGAGAGACTATAAATAAACTTTTCTTGGCAATGAATTCTTTTT
1 AGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATGAACTTTTCTTGGCAATGAATGCTTTTT
*
4054 TCTTCACATTTCTCAAGGTAGACAGTCAATTATAGTCTGTTTTAA-CAAAAAATGTGAAAAAATT
66 TCTTCACATTTATCAAGGTAGACAGTCAATT-TAGTCTGTTTTAATC-AAAAATGTGAAAAAATT
* *
4118 AAACTTAAAATCATTTATGAGATTATAAAAGCATTTAAAACG
129 AAACTTAAAATCAATTATGAAATTATAAAAGCATTTAAAACG
* * * *
4160 AGTAATTAGGCTTTTGAAGAAATG-GCAGACTATAAATGAACTTTTTTTGGAAATGAATGCTTTT
1 AGTAATAAGGCTTTTGAAGGAATGAG-AGACTATAAATGAACTTTTCTTGGCAATGAATGCTTTT
4224 TTCTTCACGATTT
65 TTCTTCAC-ATTT
4237 TTGATGTAAG
Statistics
Matches: 213, Mismatches: 28, Indels: 11
0.85 0.11 0.04
Matches are distributed among these distances:
169 28 0.13
170 55 0.26
171 125 0.59
172 5 0.02
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.38
Consensus pattern (170 bp):
AGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATGAACTTTTCTTGGCAATGAATGCTTTTT
TCTTCACATTTATCAAGGTAGACAGTCAATTTAGTCTGTTTTAATCAAAAATGTGAAAAAATTAA
ACTTAAAATCAATTATGAAATTATAAAAGCATTTAAAACG
Found at i:5817 original size:169 final size:171
Alignment explanation
Indices: 5459--5844 Score: 481
Period size: 169 Copynumber: 2.3 Consensus size: 171
5449 NNNNNNNNNN
* * *
5459 AAAAATTGAATTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAAAAAGACTTTTG
1 AAAAATTGAATATAAAATCAATTTTGAGA-TATAAAACTATTTAAAGCGAGTAAAAAGACTTTTG
* ** **
5524 CAGGAATGAGAGACTATAAATAAACTTTTCTTGGAAATGAATGCTTTTCTTTTCATGTTTCTTAA
65 AAGGAATGAGAGACTATAAATAAACTTTTCTTCCAAATGAATGCTTTTCTTTTCACATTTCTTAA
* * *
5589 GGTAGACATTCAATTATAATATGTTTGAACCGAAAATGTAAA
130 GGTAGACATTCAATTATAATACGTTTGAAACAAAAATGTAAA
* * * * * **
5631 AAAAATTGAAGATAAAATCAATTTTGAGATACTAAAACTATTTAAGGTGGGTAATAAGGTTTTTG
1 AAAAATTGAATATAAAATCAATTTTGAGATA-TAAAACTATTTAAAGCGAGTAAAAAGACTTTTG
** * * *
5696 AAGGAATGAGAGACTATAAATGGAC-TTTCTTCCCAATGAATG-TTTT-TTTTCACATTTTTTGA
65 AAGGAATGAGAGACTATAAATAAACTTTTCTTCCAAATGAATGCTTTTCTTTTCACATTTCTTAA
* * * *
5758 GGTAGACATTCAATTATAGTCCGTTTTAAATAAAAATGTAAA
130 GGTAGACATTCAATTATAATACGTTTGAAACAAAAATGTAAA
5800 AAAAATTGAATATAAAATCAATTTTGAGATAATAAAACTATTTAA
1 AAAAATTGAATATAAAATCAATTTTGAGAT-ATAAAACTATTTAA
5845 NNNNNNNNNN
Statistics
Matches: 184, Mismatches: 28, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
169 89 0.48
170 5 0.03
171 16 0.09
172 74 0.40
ACGTcount: A:0.42, C:0.09, G:0.15, T:0.35
Consensus pattern (171 bp):
AAAAATTGAATATAAAATCAATTTTGAGATATAAAACTATTTAAAGCGAGTAAAAAGACTTTTGA
AGGAATGAGAGACTATAAATAAACTTTTCTTCCAAATGAATGCTTTTCTTTTCACATTTCTTAAG
GTAGACATTCAATTATAATACGTTTGAAACAAAAATGTAAA
Found at i:7849 original size:171 final size:170
Alignment explanation
Indices: 5943--8746 Score: 1879
Period size: 171 Copynumber: 16.4 Consensus size: 170
5933 NNNNNNNNNN
* *
5943 TCTTCATGTTTC-TAGAGGTAGACATTCAATTATAGTATGTTTTAATCAAAAATAG-AAAAAAAT
1 TCTTCATGTTTCTTA-AGGTAGACATTCAATTATAGTCTGTTTTAAACAAAAAT-GTAAAAAAAT
* * ** *
6006 TGAACTTAAAATCAATGATGAGATTATTAAACTATTTAAAACGAGTAATAAGGCTTTTG-GGGAA
64 TGAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGTGAGTAATAAGGCTTTTGAAGGAA
* * * **
6070 TTG-GAGACTATAAATGAAC-TTACTTGCAAATGAATATTTTTT
129 -TGAGAGACTATAAATGGACTTTTCTTGCCAATGAAT-GCTTTT
* * * * * * * * *
6112 TCTTCATGTATCTTGAGGTAGGCATTCAGTTTTAGTCTATTTTCACCAAAAATATAAAAAAAATT
1 TCTTCATGTTTCTTAAGGTAGACATTCAATTATAGTCTGTTTTAAACAAAAATGT-AAAAAAATT
********** *
6177 GAACTTAAAATCAATTATGAGATTANNNNNNNNNNTAAAGTGAGTAATAAGGCTTTTAAAGGAAT
65 GAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGTGAGTAATAAGGCTTTTGAAGGAAT
* * *
6242 GAGAGATTATAAATGAACTTTTCTTTG-TAATGAATGCTTTTT
130 GAGAGACTATAAATGGACTTTTC-TTGCCAATGAATGC-TTTT
* * * * * * *
6284 TCTTCATGCTTCTTAATGCAGAGATTCAGTTATAGTCTGTTTTAATCAAAAATATAAAAAAAATT
1 TCTTCATGTTTCTTAAGGTAGACATTCAATTATAGTCTGTTTTAAACAAAAATGT-AAAAAAATT
********** * * *
6349 GAACATNNNNNNNNNNT-TGAGATAATAAAACCATTTAAAGTTG-GTAATAAGGCTTTTGATGGA
65 GAAC-TTAAAATCAATTATGAGATTATAAAACTATTTAAAG-TGAGTAATAAGGCTTTTGAAGGA
* * *
6412 ATG-GATGACTATAAATAGACTTTTCTTGACAATGAAAGCCTTTT
128 ATGAGA-GACTATAAATGGACTTTTCTTGCCAATGAATG-CTTTT
** * * * * * *
6456 TCTTCATGTTTCTCGACGCAAACATTCAATTATAATCTG-TTTAAGCCAAAAAAGTAAAAAAAAT
1 TCTTCATGTTTCTTAAGGTAGACATTCAATTATAGTCTGTTTTAA-ACAAAAATGT-AAAAAAAT
* * * * * *
6520 TAAAGTTAAAATCAATTTTGAGATTATAAAA-TCATTTAAAGCGAGCAATAAAGCTTTTGAAGGA
64 TGAACTTAAAATCAATTATGAGATTATAAAACT-ATTTAAAGTGAGTAATAAGGCTTTTGAAGGA
* * * *
6584 AT-AGGTGACTAGAAATGGACTTTTCTTGCCAATAAATGCCTTT
128 ATGA-GAGACTATAAATGGACTTTTCTTGCCAATGAATGCTTTT
* * ** * * * ** * *
6627 TCTTCAAGTTTCTCACCGTAGACATTCAATTAT-GGCTGTTTTAACCATAAATACAAGAAAATTC
1 TCTTCATGTTTCTTAAGGTAGACATTCAATTATAGTCTGTTTTAAACAAAAATGTAAAAAAATTG
* * * * * * *
6691 AACTGAAAATTAATTATGAGATTATAAAAAC-ATTTAAAGCGAGCAAAAAGGATTTTGAAGAAAT
66 AACTTAAAATCAATTATGAGATTAT-AAAACTATTTAAAGTGAGTAATAAGGCTTTTGAAGGAAT
*
6755 GAGAGACTATAAATGGAGTTTTCTTGCCAATGAATGCTTTT
130 GAGAGACTATAAATGGACTTTTCTTGCCAATGAATGCTTTT
* *
6796 TACTTCATGTTT-TTCAAGGTAGACATTCAATTATAGTCCGTTTT-AACTAAAAATTTAAAAAAA
1 T-CTTCATGTTTCTT-AAGGTAGACATTCAATTATAGTCTGTTTTAAAC-AAAAATGTAAAAAAA
********** ** * *
6859 TTGAACTTAAAANNNNNNNNNNGATTATAAAACTATTTAAAGCAAGTAATAAAG-TTTTGGAAGA
63 TTGAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGTGAGTAATAAGGCTTTT-GAAGG
* ** * *
6923 AATGAGAGGCTATAAATAAACTTTTCTTGGCAGTGAATGCTTTT
127 AATGAGAGACTATAAATGGACTTTTCTTGCCAATGAATGCTTTT
* * * * *
6967 TTTTCACGTTTCTCAAGGTAAACATTCAATTATAGTCTGTTTTGATAAGAAAAATGT-AAAAAAT
1 TCTTCATGTTTCTTAAGGTAGACATTCAATTATAGTCTGTTTT-A-AACAAAAATGTAAAAAAAT
********** * * * * *
7031 TGAACTTAAAATCAATNNNNNNNNNNT-AAAGTCATTTAAAGCGAGTAAAAAAGTTTTTGAAGGA
64 TGAACTTAAAATCAATTATGAGATTATAAAACT-ATTTAAAGTGAGTAATAAGGCTTTTGAAGGA
* * * * *
7095 ATGAGAGA-TAATAAATGAACTTTTTTTGGCAAATGAAAGTTTTTT
128 ATGAGAGACT-ATAAATGGACTTTTCTT-GCCAATGAATG-CTTTT
* * * * * ** *
7140 TCTTCATATTTCTTAAAGTAGACATTCAATTATCA-TTTGTTTGAACCAAAAATAAAAAAAAAAT
1 TCTTCATGTTTCTTAAGGTAGACATTCAATTAT-AGTCTGTTTTAAACAAAAATGTAAAAAAATT
* * * *
7204 -CACATAAAATCAATTTTGAGATAATAAAACTATTTAAAGT-AGGTAATAAGGCTTTTGAAGGAA
65 GAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGTGA-GTAATAAGGCTTTTGAAGGAA
* * *
7267 TGAGAGTCTACAAATGGAC-TTTGTTGCCAATGAATGCTTTTT
129 TGAGAGACTATAAATGGACTTTTCTTGCCAATGAATGC-TTTT
* ** * *
7309 TGTTCATGTTTCTCGAGGTAGACATTCAATTATAGTCTGTTTT-AACAAAAACTATATAAGAAAT
1 TCTTCATGTTTCTTAAGGTAGACATTCAATTATAGTCTGTTTTAAACAAAAA-TGTA-AAAAAAT
*********** * *
7373 TGAACTTAAAATCAATTATGANNNNNNNNNNTTATTTAAAGTGAGTAATAAGACTTTTGAAAGAA
64 TGAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGTGAGTAATAAGGCTTTTGAAGGAA
* * * *
7438 TGAGAGACTCTATATAGAC-TTTCTTGCCAAGGAATGCTTTTT
129 TGAGAGACTATAAATGGACTTTTCTTGCCAATGAATGC-TTTT
** * *
7480 TCTTCACATTTCTTAAGATAGACATTTAATTATAGTCTGTTTTAAACAAAAATGTAAAAAAAAAT
1 TCTTCATGTTTCTTAAGGTAGACATTCAATTATAGTCTGTTTTAAACAAAAATGT--AAAAAAAT
* * * * **********
7545 TGAA-TATAAAATTAATTTTGAGATGATAAAACTATTTAAAGTGGGTAANNNNNNNNNNGAAGGA
64 TGAACT-TAAAATCAATTATGAGATTATAAAACTATTTAAAGTGAGTAATAAGGCTTTTGAAGGA
* * ** * *
7609 ATGGGTGACTATAAAATGG-CTTTTCTTTTCAACGAATTTCTTTT
128 ATGAGAGACTAT-AAATGGACTTTTCTTGCCAATGAA-TGCTTTT
* * * * * * * **
7653 TCTTCAAGTTTTTTGATGTAAACATTCAATTGTAATCTGTTTTATTCAAAAATGTAAAAAAAGTT
1 TCTTCATGTTTCTTAAGGTAGACATTCAATTATAGTCTGTTTTAAACAAAAATGTAAAAAAA-TT
* * * * *
7718 GAACTTAAATTCAATTTTGAGAGTATAAAACTATTTAAAGTGAGTAATAAGGTTTTTGAAAGAAT
65 GAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGTGAGTAATAAGGCTTTTGAAGGAAT
* * *
7783 TAGTGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTT
130 GAGAGACTATAAATGGACTTTTCTTGCCAATGAATGCTTTT
* * * *
7824 TCTTCACGTTTCTTAAGGTAAACATTCAATTACAGT-T-TTTTGTAACGAAAAATGTAAAAAAAT
1 TCTTCATGTTTCTTAAGGTAGACATTCAATTATAGTCTGTTTT-AAAC-AAAAATGTAAAAAAAT
* ********** * * *
7887 TCANNNNNNNNNNAATTATGAGATTATAAAACTAATTAAAATGAGTAAT-AGGACTTTTGATGGA
64 TGAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGTGAGTAATAAGG-CTTTTGAAGGA
* * *
7951 ATGA-ATGACTATAAATGAACTTTT-TTTCTCAATAAATAGCTTTT
128 ATGAGA-GACTATAAATGGACTTTTCTTGC-CAATGAAT-GCTTTT
* * * * *
7995 T-TTACACGTTTCTTTAGGCA-AGCATTCAATCATAGTCTATTTTAATA-AAAAATGTAAAAAAA
1 TCTT-CATGTTTCTTAAGGTAGA-CATTCAATTATAGTCTGTTTTAA-ACAAAAATGTAAAAAAA
* * ********** * * *
8057 TTCAATTTAAAATCAATTNNNNNNNNNNAAAACCATTTAAAGCGAGTAATAAGACTTTTGAAGGA
63 TTGAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGTGAGTAATAAGGCTTTTGAAGGA
* * *
8122 ATGAGCA-ACTATAAATGGACTTTCCGTGCCAGTGAATGCTTTTT
128 ATGAG-AGACTATAAATGGACTTTTCTTGCCAATGAATGC-TTTT
* * * * * * * * *
8166 TCTTCACGTTTCTCAAAGTAGACATTCAACTATAATATGTTTTAAGCAAAAAAGCAAAAAAATTG
1 TCTTCATGTTTCTTAAGGTAGACATTCAATTATAGTCTGTTTTAAACAAAAATGTAAAAAAATTG
* ********** *
8231 AACTTAAAA-CTAATTTTGAGATTATNNNNNNNNNNAAAGTGAGTAATAAGGCTTTTCAAGGAAT
66 AACTTAAAATC-AATTATGAGATTATAAAACTATTTAAAGTGAGTAATAAGGCTTTTGAAGGAAT
*
8295 G-GATGACTAT-AATGGACTTTTCTTGCCAATGAATGATTGTT
130 GAGA-GACTATAAATGGACTTTTCTTGCCAATGAATGCTT-TT
* * * * * *
8336 T-TTCATGTTTC-TAGAGATAGACGTTCAATTATAGTTTGTTTTAACCGAAAATGTGAAAAAATT
1 TCTTCATGTTTCTTA-AGGTAGACATTCAATTATAGTCTGTTTTAAACAAAAATGTAAAAAAATT
* * * *
8399 GGACTTAAAATCAATTATGAGATTATAAAACTATTTAAAATGAGTAATAAGGGTTTTGAACGAAT
65 GAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGTGAGTAATAAGGCTTTTGAAGGAAT
* *
8464 GAGAGACTATAAATGAACTTTTCTTGGCAATGAATGCTTTT
130 GAGAGACTATAAATGGACTTTTCTTGCCAATGAATGCTTTT
* * * * * * *
8505 TCCTTCATATTTGTCAAGGTAGACATTCAATTATAGTATATTTT-AACTAAAAATATGAAAAAAT
1 T-CTTCATGTTTCTTAAGGTAGACATTCAATTATAGTCTGTTTTAAAC-AAAAATGTAAAAAAAT
* * * ** *
8569 TAAACTTAAAATTAATTATGAGATTATAAAA-TCATTTAAAATGAGTAATAAGATTTTTGAAAGA
64 TGAACTTAAAATCAATTATGAGATTATAAAACT-ATTTAAAGTGAGTAATAAGGCTTTTGAAGGA
* *
8633 AT--GAG-C-ATAAATGAACTTTTCTTGGCAATGAATGCTTTTT
128 ATGAGAGACTATAAATGGACTTTTCTTGCCAATGAATGC-TTTT
** * * *
8673 TCTTCATGTTTCTGGAGGTGGACATTCAGTTATAGTCTGTTTTAACCAAAAATGTAAAAACAAAT
1 TCTTCATGTTTCTTAAGGTAGACATTCAATTATAGTCTGTTTTAAACAAAAATGT-AAAA-AAAT
8738 TGAACTTAA
64 TGAACTTAA
8747 TGTTGGCTCC
Statistics
Matches: 2026, Mismatches: 514, Indels: 190
0.74 0.19 0.07
Matches are distributed among these distances:
167 70 0.03
168 20 0.01
169 318 0.16
170 294 0.15
171 780 0.38
172 422 0.21
173 119 0.06
174 3 0.00
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.34
Consensus pattern (170 bp):
TCTTCATGTTTCTTAAGGTAGACATTCAATTATAGTCTGTTTTAAACAAAAATGTAAAAAAATTG
AACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATG
AGAGACTATAAATGGACTTTTCTTGCCAATGAATGCTTTT
Found at i:9980 original size:172 final size:170
Alignment explanation
Indices: 9365--10121 Score: 603
Period size: 172 Copynumber: 4.4 Consensus size: 170
9355 NNNNNNNNNN
* * * * * *
9365 GCCTTATTACCCACTTTAAATAGTTTTATTATCTCAAAATTGATTTTATA-TTCATTTTTTTTGT
1 GCCTTTTTACTCACTTTAAATAGTTTTATAATCTCATAATTGATTTTA-AGTTCA-ATTTTTTGC
* * * * * * * *
9429 ACATTTTTGTTTAAAACAAACTATAATAGAATGTCTACCTAGAGAACCGTAAAGAAAAAAGCATT
64 ATATTTTGGTTT-AAACAGACTATAATTGAATGTCTACCTTGAAAAACATAAAGAAAAAAGCATT
* * * * *
9494 CCTTGGCAAGAAAGTCCATATATAGTCTCTCATTCTTTTAAAA
128 CATTGCCAAGAAAGTCCATTTATAGTCTCTCATTCCTTCAAAA
* * * ********** *
9537 GCCTTATCACTCACTTTAAATGGNNNNNNNNNNTCATAATTGATTTTAAGTTCAATATTTTTTAC
1 GCCTTTTTACTCACTTTAAATAGTTTTATAATCTCATAATTGATTTTAAGTTC-A-ATTTTTTGC
* * * * *
9602 A-GTTTTAGTTAAAATAGACTATAATTGAATGTCTACCTTGAAAAACATGAAA-AAAAAAGTATT
64 ATATTTTGGTTTAAACAGACTATAATTGAATGTCTACCTTGAAAAACAT-AAAGAAAAAAGCATT
* * * * *
9665 TATTAG-CAAGAAAGTCCTTTTGTAGTCTCTCATTTCTTCCAAA
128 CATT-GCCAAGAAAGTCCATTTATAGTCTCTCATTCCTTCAAAA
* * * * * * **
9708 GCCTTTTTACCCACTGTCAATAGTTTTATTATCTCAAAATTGATTTTATGTTCAATTTTTTTTTA
1 GCCTTTTTACTCACTTTAAATAGTTTTATAATCTCATAATTGATTTTAAGTTCAA-TTTTTTGCA
* * * * * * *
9773 CATTTTCGATTCAAACAGACGATAATTGAATGTCTACCTTGAGAAATATAAAGAAAAAAACATTC
65 TATTTT-GGTTTAAACAGACTATAATTGAATGTCTACCTTGAAAAACATAAAGAAAAAAGCATTC
* *
9838 ATTGCCAGGAAAAGTTCATTTATAGTCTCTCATTCCTTCAAAA
129 ATTGCCAAG-AAAGTCCATTTATAGTCTCTCATTCCTTCAAAA
* * * *
9881 GCCTTTTTACTCGCTTTAAATGGCTTTATAATCTCATAATTGATTTTAAGTTCAAGTTTTTGCAT
1 GCCTTTTTACTCACTTTAAATAGTTTTATAATCTCATAATTGATTTTAAGTTCAATTTTTTGCAT
* * *
9946 ATATTTGGTTTAAACAGACTGTAATTGAATGTCTACCTTAAAAAACATGAAGAAAAAAGCATTCA
66 AT-TTTGGTTTAAACAGACTATAATTGAATGTCTACCTTGAAAAACATAAAGAAAAAAGCATTCA
******** * *
10011 TTGCNNNNNNNNNNT-TATTTATAGGCTCTCATTCCTTCAAAA
130 TTGC--CAAGAAAGTCCATTTATAGTCTCTCATTCCTTCAAAA
**
10053 G-CTTTATTACTCGTTTTAAA-ATGTTTTATAATCTCATAATTGATTTTAAGTTCAATTTTTT-C
1 GCCTTT-TTACTCACTTTAAATA-GTTTTATAATCTCATAATTGATTTTAAGTTCAATTTTTTGC
*
10115 AAATTTT
64 ATATTTT
10122 TGATTAAANN
Statistics
Matches: 459, Mismatches: 111, Indels: 32
0.76 0.18 0.05
Matches are distributed among these distances:
169 1 0.00
170 11 0.02
171 124 0.27
172 236 0.51
173 87 0.19
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.39
Consensus pattern (170 bp):
GCCTTTTTACTCACTTTAAATAGTTTTATAATCTCATAATTGATTTTAAGTTCAATTTTTTGCAT
ATTTTGGTTTAAACAGACTATAATTGAATGTCTACCTTGAAAAACATAAAGAAAAAAGCATTCAT
TGCCAAGAAAGTCCATTTATAGTCTCTCATTCCTTCAAAA
Found at i:10004 original size:344 final size:343
Alignment explanation
Indices: 9365--10004 Score: 827
Period size: 344 Copynumber: 1.9 Consensus size: 343
9355 NNNNNNNNNN
*
9365 GCCTTATTACCCACTTTAAATAGTTTTATTATCTCAAAATTGATTTTATATTCATTTTTTTTGTA
1 GCCTTATTACCCACTGTAAATAGTTTTATTATCTCAAAATTGATTTTATATTCATTTTTTTTGTA
* * * * * *
9430 CATTTTTGTTTAAAACAAACTATAATAGAATGTCTACCTAGAGAACCGTAAAGAAAAAAGCATTC
66 CATTTTCGATTAAAACAAACGATAATAGAATGTCTACCTAGAGAAACATAAAGAAAAAAACATTC
* * * *
9495 CTTGGCAAGAAAGTCCATATATAGTCTCTCATTCTTTTAAAAGCCTTATCACTCACTTTAAATGG
131 ATTGCCAAGAAAGTCCATATATAGTCTCTCATTCCTTCAAAAGCCTTATCACTCACTTTAAATGG
********** * * *
9560 NNNNNNNNNNTCATAATTGATTTTAAGTTCAATATTTTTTACAGTTTTAGTTAAAATAGACTATA
196 CTTTATAATCTCATAATTGATTTTAAGTTCAATAGTTTTTACAATTTTAGTTAAAACAGACTATA
*
9625 ATTGAATGTCTACCTTGAAAAACATGAAAAAAAAAGTATTTATTAGCAAGAAAGTCCTTTTGTAG
261 ATTGAATGTCTACCTTAAAAAACATGAAAAAAAAAGTATTTATTAGCAAGAAAGTCCTTTTGTAG
9690 TCTCTCATTTCTTCCAAA
326 TCTCTCATTTCTTCCAAA
* * *
9708 GCCTTTTTACCCACTGTCAATAGTTTTATTATCTCAAAATTGATTTTATGTTCAATTTTTTTT-T
1 GCCTTATTACCCACTGTAAATAGTTTTATTATCTCAAAATTGATTTTATATTC-ATTTTTTTTGT
* * * * *
9772 ACATTTTCGATTCAAACAGACGATAATTGAATGTCTACCTTGAGAAATATAAAGAAAAAAACATT
65 ACATTTTCGATTAAAACAAACGATAATAGAATGTCTACCTAGAGAAACATAAAGAAAAAAACATT
* * * * * *
9837 CATTGCCAGGAAAAGTTCATTTATAGTCTCTCATTCCTTCAAAAGCCTTTTTACTCGCTTTAAAT
130 CATTGCCAAG-AAAGTCCATATATAGTCTCTCATTCCTTCAAAAGCCTTATCACTCACTTTAAAT
* * *
9902 GGCTTTATAATCTCATAATTGATTTTAAGTTC-A-AGTTTTTGCATATATTTGGTTTAAACAGAC
194 GGCTTTATAATCTCATAATTGATTTTAAGTTCAATAGTTTTTACA-AT-TTTAGTTAAAACAGAC
* *
9965 TGTAATTGAATGTCTACCTTAAAAAACATGAAGAAAAAAG
257 TATAATTGAATGTCTACCTTAAAAAACATGAAAAAAAAAG
10005 CATTCATTGC
Statistics
Matches: 249, Mismatches: 44, Indels: 7
0.83 0.15 0.02
Matches are distributed among these distances:
342 8 0.03
343 113 0.45
344 128 0.51
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.38
Consensus pattern (343 bp):
GCCTTATTACCCACTGTAAATAGTTTTATTATCTCAAAATTGATTTTATATTCATTTTTTTTGTA
CATTTTCGATTAAAACAAACGATAATAGAATGTCTACCTAGAGAAACATAAAGAAAAAAACATTC
ATTGCCAAGAAAGTCCATATATAGTCTCTCATTCCTTCAAAAGCCTTATCACTCACTTTAAATGG
CTTTATAATCTCATAATTGATTTTAAGTTCAATAGTTTTTACAATTTTAGTTAAAACAGACTATA
ATTGAATGTCTACCTTAAAAAACATGAAAAAAAAAGTATTTATTAGCAAGAAAGTCCTTTTGTAG
TCTCTCATTTCTTCCAAA
Found at i:10969 original size:172 final size:172
Alignment explanation
Indices: 10661--11231 Score: 738
Period size: 172 Copynumber: 3.3 Consensus size: 172
10651 NTATCTCAAA
* * * *
10661 ATTGATTTTATGTTCAATTTTTTTTATATTTTTAGTTAAAACAGACTATAACTGAAT-CTCTACC
1 ATTGATTTTAAGTTCAATTTTTTTTATATTTTTGGTTAAAACAGACTAAAACTGAATGC-CTACA
* ** * * *** * * *
10725 TTAAGA-AGTGTGAAGAAAAAAGCATTCATTATAAAGAAAAGTTCATTTATAGTCTCTAATTCCT
65 TCAAGATA-CATGAAGAAAAAAGTATCCATTGGCATGTAAAGTTCATTTATAGTCTCTCATTCCT
** * * **
10789 TTAAAAGCCTTATTACTAGTTTTGAATAGTTTTATAATCTCAGA
129 CCAAAAGCCTTATTACTTGTTTTAAATAGTTTTATAATCTCATC
* * * *
10833 ATTAATTTTAAGTTTAATTTTTTTTATATTTTTGGTTAAAATAGACTAAAACTGAATGCCTACCT
1 ATTGATTTTAAGTTCAATTTTTTTTATATTTTTGGTTAAAACAGACTAAAACTGAATGCCTACAT
*********
10898 CAAGATACATGAAGAAAAAAGTANNNNNNNNNNA-GTAAAGTTCATTTATAGTCTCTCATTCCTC
66 CAAGATACATGAAGAAAAAAGTA-TCCATTGGCATGTAAAGTTCATTTATAGTCTCTCATTCCTC
10962 CAAAAGCCTTATTACTTGTTTTAAATAGTTTTATAATCTCATC
130 CAAAAGCCTTATTACTTGTTTTAAATAGTTTTATAATCTCATC
11005 ATTGATTTTAAGTTCAATTTTTTTTATATTTTTGGTTAAAACAGACTAAAACTGAATGCCTACAT
1 ATTGATTTTAAGTTCAATTTTTTTTATATTTTTGGTTAAAACAGACTAAAACTGAATGCCTACAT
*
11070 CAAGATACATGAAGAAAAAAGTATCCATTGGCATGTAAAGTTCATTTATAGTCTCTCGTTCCTCC
66 CAAGATACATGAAGAAAAAAGTATCCATTGGCATGTAAAGTTCATTTATAGTCTCTCATTCCTCC
11135 AAAAGCCTTATTACTTGTTTTAAATAGTTTTATAATCTCATC
131 AAAAGCCTTATTACTTGTTTTAAATAGTTTTATAATCTCATC
* **
11177 A-TGATTTTAAGTTCAA-TTTTTTCATATTTTTAATTAAAACAGACTAAAACTGAAT
1 ATTGATTTTAAGTTCAATTTTTTTTATATTTTTGGTTAAAACAGACTAAAACTGAAT
11232 NNNNNNNNNN
Statistics
Matches: 351, Mismatches: 44, Indels: 10
0.87 0.11 0.02
Matches are distributed among these distances:
170 36 0.10
171 16 0.05
172 296 0.84
173 3 0.01
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.40
Consensus pattern (172 bp):
ATTGATTTTAAGTTCAATTTTTTTTATATTTTTGGTTAAAACAGACTAAAACTGAATGCCTACAT
CAAGATACATGAAGAAAAAAGTATCCATTGGCATGTAAAGTTCATTTATAGTCTCTCATTCCTCC
AAAAGCCTTATTACTTGTTTTAAATAGTTTTATAATCTCATC
Found at i:13655 original size:172 final size:172
Alignment explanation
Indices: 13305--13759 Score: 556
Period size: 172 Copynumber: 2.6 Consensus size: 172
13295 GCAATGAATG
* **
13305 CTTTTTTCTTCATGTTTTTCAAGGTAGACATTCAATTATAGTCTGTTTAAACCAAAAATATGCAA
1 CTTTTTTCTTCATGTTTTTCAAGGTAGACATTCAATTATAGTCTGTTTAAACTAAAAATATAAAA
* * * * **
13370 AAATTTGAACTTAAAATTAATTATGAGATTATAAAGCCATTTAAAGCGAGTAGAAAGGCTTTTGA
66 AAAATTGAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAAAAAGGCTTCGGA
* * * * **
13435 AGGAATGAGAGACTATAAATGAACTTTTCCTGACAATGAATG
131 AGAAATAAGAGACTACAAATGAACTTTTCCTGACAATAAAAA
* * * * *
13477 CTTTTTTCTTCATATTTCTCAAGGTAGACATTCAATTATCGTCTGTTTAAATTAAAAATGTTAAA
1 CTTTTTTCTTCATGTTTTTCAAGGTAGACATTCAATTATAGTCTGTTTAAACTAAAAAT-ATAAA
* * * * * * *
13542 AAAAATTGAACATAAAAACAATTTTGAGATAATAAAACTA-TTAGAAGTGGGTAAAAAGGCTTCG
65 AAAAATTGAACTTAAAATCAATTATGAGATTATAAAACCATTTA-AAGCGAGTAAAAAGGCTTCG
* * *
13606 GAAGAAATAAGAGACTACAAATGGAC-TTTCTTGCCAATAAAAA
129 GAAGAAATAAGAGACTACAAATGAACTTTTCCTGACAATAAAAA
* * *
13649 CTTTTTTCTTCATGTTTTTC-AGAGTAGACATTCAATTATAGTCTTTTTTAACTAAAACTATAAA
1 CTTTTTTCTTCATGTTTTTCAAG-GTAGACATTCAATTATAGTCTGTTTAAACTAAAAATATAAA
*
13713 AAATATTGAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAG
65 AAAAATTGAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAG
13760 TGA
Statistics
Matches: 235, Mismatches: 44, Indels: 9
0.82 0.15 0.03
Matches are distributed among these distances:
171 43 0.18
172 121 0.51
173 71 0.30
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (172 bp):
CTTTTTTCTTCATGTTTTTCAAGGTAGACATTCAATTATAGTCTGTTTAAACTAAAAATATAAAA
AAAATTGAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAAAAAGGCTTCGGA
AGAAATAAGAGACTACAAATGAACTTTTCCTGACAATAAAAA
Done.