Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008362.1 Hibiscus syriacus cultivar Beakdansim tig00111101_pilon, 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: 636979
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
File 2 of 3
Found at i:269431 original size:27 final size:29
Alignment explanation
Indices: 269401--269462 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
269391 AAGTATGCAG
269401 AAATAAGTA-TAAATATAAAAGATA-AAT
1 AAATAAGTATTAAATATAAAAGATATAAT
* * *
269428 AAATAAATTATTATATATAGAAGATATAAT
1 AAAT-AAGTATTAAATATAAAAGATATAAT
269458 AAATA
1 AAATA
269463 TTATATCTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
27 4 0.14
28 4 0.14
29 14 0.48
30 7 0.24
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (29 bp):
AAATAAGTATTAAATATAAAAGATATAAT
Found at i:269960 original size:20 final size:20
Alignment explanation
Indices: 269924--269961 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
269914 ATCCTATTCC
**
269924 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
269944 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
269962 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:271676 original size:41 final size:41
Alignment explanation
Indices: 271615--271696 Score: 137
Period size: 41 Copynumber: 2.0 Consensus size: 41
271605 TCTGTCCTCC
* *
271615 ATTGGAGCACCATGGCTAGCCTCCGCTCTGCTGCAGTTATG
1 ATTGGAGCACCATGGATAGCCTCCGCTCCGCTGCAGTTATG
*
271656 ATTGGAGCACCATGGATAGCCTCCTCTCCGCTGCAGTTATG
1 ATTGGAGCACCATGGATAGCCTCCGCTCCGCTGCAGTTATG
271697 TCCGATCAGA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.18, C:0.29, G:0.26, T:0.27
Consensus pattern (41 bp):
ATTGGAGCACCATGGATAGCCTCCGCTCCGCTGCAGTTATG
Found at i:281822 original size:25 final size:25
Alignment explanation
Indices: 281788--281841 Score: 99
Period size: 25 Copynumber: 2.2 Consensus size: 25
281778 TATTTTATAT
*
281788 TTTTATATTAATTATATATATAATA
1 TTTTATATTAATTATATATAAAATA
281813 TTTTATATTAATTATATATAAAATA
1 TTTTATATTAATTATATATAAAATA
281838 TTTT
1 TTTT
281842 CGGGTTCGGG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (25 bp):
TTTTATATTAATTATATATAAAATA
Found at i:281864 original size:20 final size:20
Alignment explanation
Indices: 281834--281871 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
281824 TTATATATAA
281834 AATATTTTCGGGTTCGGGTAT
1 AATATTTTCGGG-TCGGGTAT
281855 AATA-TTTCGGGTCGGGT
1 AATATTTTCGGGTCGGGT
281872 TCGGGGACGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 6 0.35
20 7 0.41
21 4 0.24
ACGTcount: A:0.18, C:0.11, G:0.32, T:0.39
Consensus pattern (20 bp):
AATATTTTCGGGTCGGGTAT
Found at i:292040 original size:28 final size:28
Alignment explanation
Indices: 291989--292042 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
291979 GTTTTGTTTT
* **
291989 TCAATTGAGTTTCCTTGCCCATGCTACA
1 TCAATTGAATTTCCTTGCAAATGCTACA
292017 TCAATTGAATTTCCTTGCAAATGCTA
1 TCAATTGAATTTCCTTGCAAATGCTA
292043 GATTTCCTCT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.26, C:0.24, G:0.13, T:0.37
Consensus pattern (28 bp):
TCAATTGAATTTCCTTGCAAATGCTACA
Found at i:300609 original size:22 final size:22
Alignment explanation
Indices: 300584--300642 Score: 100
Period size: 22 Copynumber: 2.7 Consensus size: 22
300574 TACGGTGTTT
* *
300584 ATGTCTCAAGGGAGACGAGTTC
1 ATGTATCAAGAGAGACGAGTTC
300606 ATGTATCAAGAGAGACGAGTTC
1 ATGTATCAAGAGAGACGAGTTC
300628 ATGTATCAAGAGAGA
1 ATGTATCAAGAGAGA
300643 TGAGATTTAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.36, C:0.14, G:0.29, T:0.22
Consensus pattern (22 bp):
ATGTATCAAGAGAGACGAGTTC
Found at i:302726 original size:24 final size:24
Alignment explanation
Indices: 302699--302752 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
302689 TTTAAGAATT
302699 AACGAATTTATAAAATTTCAAGGG
1 AACGAATTTATAAAATTTCAAGGG
302723 AACGAATTTATAAAATTTCAAGGG
1 AACGAATTTATAAAATTTCAAGGG
*
302747 GACGAA
1 AACGAA
302753 AATAAATTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.46, C:0.09, G:0.19, T:0.26
Consensus pattern (24 bp):
AACGAATTTATAAAATTTCAAGGG
Found at i:304887 original size:2 final size:2
Alignment explanation
Indices: 304880--304914 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
304870 TTAGATCTTT
304880 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
304915 TAATAATCTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:307135 original size:2 final size:2
Alignment explanation
Indices: 307128--307153 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
307118 TATCTAGCGT
307128 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
307154 GTTTTTTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:310546 original size:18 final size:17
Alignment explanation
Indices: 310523--310557 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
310513 TAGATTTTGG
*
310523 TTTTAATATTATATATTA
1 TTTTAAAATTAT-TATTA
310541 TTTTAAAATTATTATTA
1 TTTTAAAATTATTATTA
310558 AATCAATCGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TTTTAAAATTATTATTA
Found at i:311145 original size:31 final size:30
Alignment explanation
Indices: 311110--311196 Score: 104
Period size: 31 Copynumber: 2.8 Consensus size: 30
311100 TCAATAAAGT
*
311110 TTAAAAAATTATAAAATAGTTATTAAATTTA
1 TTAAAATATTATAAAATA-TTATTAAATTTA
*
311141 TTAAAATATTATAAAATTATTAATAAATTTA
1 TTAAAATATTATAAAA-TATTATTAAATTTA
*
311172 TCT-AAATACTATAAAATAATTATTA
1 T-TAAAATATTATAAAAT-ATTATTA
311197 TATTATCGAA
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
30 1 0.02
31 45 0.92
32 3 0.06
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.43
Consensus pattern (30 bp):
TTAAAATATTATAAAATATTATTAAATTTA
Found at i:311155 original size:19 final size:21
Alignment explanation
Indices: 311114--311163 Score: 70
Period size: 19 Copynumber: 2.5 Consensus size: 21
311104 TAAAGTTTAA
311114 AAAATTA-TAAAATAGTTATT
1 AAAATTATTAAAATAGTTATT
*
311134 AAATTTATTAAAATA-TTA-T
1 AAAATTATTAAAATAGTTATT
311153 AAAATTATTAA
1 AAAATTATTAA
311164 TAAATTTATC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 11 0.41
20 9 0.33
21 7 0.26
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (21 bp):
AAAATTATTAAAATAGTTATT
Found at i:311172 original size:20 final size:19
Alignment explanation
Indices: 311109--311172 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
311099 GTCAATAAAG
*
311109 TTTAAAAAATTA-TAAAATA
1 TTTATAAAATTATTAAAA-A
* *
311128 GTTATTAAATTTATT-AAAA
1 TTTA-TAAAATTATTAAAAA
311147 TATTATAAAATTATTAATAAA
1 T-TTATAAAATTATTAA-AAA
311168 TTTAT
1 TTTAT
311173 CTAAATACTA
Statistics
Matches: 35, Mismatches: 5, Indels: 9
0.71 0.10 0.18
Matches are distributed among these distances:
19 13 0.37
20 17 0.49
21 5 0.14
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (19 bp):
TTTATAAAATTATTAAAAA
Found at i:312333 original size:31 final size:29
Alignment explanation
Indices: 312285--312343 Score: 73
Period size: 31 Copynumber: 2.0 Consensus size: 29
312275 ATAGGTAAAT
**
312285 TTATATTTAGTGTCTAAACTATTACTTTTA
1 TTATATTTAGTACCTAAACT-TTACTTTTA
*
312315 TTATATTTTAGTACCTAAACTTTATTTTT
1 TTATA-TTTAGTACCTAAACTTTACTTTT
312344 GTCAAAATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 12 0.48
31 13 0.52
ACGTcount: A:0.29, C:0.10, G:0.05, T:0.56
Consensus pattern (29 bp):
TTATATTTAGTACCTAAACTTTACTTTTA
Found at i:314444 original size:52 final size:53
Alignment explanation
Indices: 314351--314454 Score: 167
Period size: 53 Copynumber: 2.0 Consensus size: 53
314341 TAGTCATCTA
314351 ACTATTCATATGTTCCAAACTCGTCATTTTTTTGTTAAAAAATTAATGGTCAG
1 ACTATTCATATGTTCCAAACTCGTCATTTTTTTGTTAAAAAATTAATGGTCAG
* *
314404 ACTATTCATATGTTCCAAACTCGTCCTTTTTTAT-TT-AAAAATTGATGGTCA
1 ACTATTCATATGTTCCAAACTCGTCATTTTTT-TGTTAAAAAATTAATGGTCA
314455 TATGAACTGG
Statistics
Matches: 48, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
52 14 0.29
53 33 0.69
54 1 0.02
ACGTcount: A:0.31, C:0.16, G:0.11, T:0.42
Consensus pattern (53 bp):
ACTATTCATATGTTCCAAACTCGTCATTTTTTTGTTAAAAAATTAATGGTCAG
Found at i:315119 original size:186 final size:185
Alignment explanation
Indices: 314881--315260 Score: 643
Period size: 186 Copynumber: 2.0 Consensus size: 185
314871 TAAAAAAATA
*
314881 AATATTTTACAATTCAAAAAAAAGTTTATAATTAATTTAAATAATATATAATTATAAAATAAAAA
1 AATATTTTACAATTCAAAAAAAAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAA
* *
314946 TTTTATATAAATTTTTTAATTAATTAATATTGGTTTAGGTTTAAAAGTTATTGGATCTTAAATTA
66 TTTTATATAAAATTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAATTA
* * * *
315011 TTAATTAGGTTTTAAATGGTTTGGGCTGAGCTCATATGTTATATATAATATATTT
131 TTAATTAGATTTTAAATGGTTTGAGCTGAACCCATATGTTATATATAATATATTT
** * *
315066 AATATTTTTTAATTCAGAAAAATAGTTTACATTTAATTTAAATAATATATAATTATAAAATAAAA
1 AATATTTTACAATTCA-AAAAAAAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAA
315131 ATTTTATATAAAATTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAATT
65 ATTTTATATAAAATTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAATT
315196 ATTAATTAGATTTTAAATGGTTTGAGCTGAACCCATATGTTATATATAATATATTT
130 ATTAATTAGATTTTAAATGGTTTGAGCTGAACCCATATGTTATATATAATATATTT
*
315252 AAAATTTTA
1 AATATTTTA
315261 TTTCGATTAA
Statistics
Matches: 181, Mismatches: 13, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
185 14 0.08
186 167 0.92
ACGTcount: A:0.42, C:0.03, G:0.09, T:0.46
Consensus pattern (185 bp):
AATATTTTACAATTCAAAAAAAAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAA
TTTTATATAAAATTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAATTA
TTAATTAGATTTTAAATGGTTTGAGCTGAACCCATATGTTATATATAATATATTT
Found at i:316457 original size:75 final size:75
Alignment explanation
Indices: 316334--316485 Score: 286
Period size: 75 Copynumber: 2.0 Consensus size: 75
316324 GAATGGTTAA
*
316334 AATATAAAATGGTTTCTAAATTATTTTATTTTAATACATATCTTTAATATTTTTTAGTAAAGAGG
1 AATATAAAATGGTTTCTAAATTATTTTATTTTAATACATATCTTTAATATTTTTGAGTAAAGAGG
*
316399 CCCAGTAACT
66 CCCAATAACT
316409 AATATAAAATGGTTTCTAAATTATTTTATTTTAATACATATCTTTAATATTTTTGAGTAAAGAGG
1 AATATAAAATGGTTTCTAAATTATTTTATTTTAATACATATCTTTAATATTTTTGAGTAAAGAGG
316474 CCCAATAACT
66 CCCAATAACT
316484 AA
1 AA
316486 CACCCTCTCG
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
75 75 1.00
ACGTcount: A:0.39, C:0.09, G:0.09, T:0.43
Consensus pattern (75 bp):
AATATAAAATGGTTTCTAAATTATTTTATTTTAATACATATCTTTAATATTTTTGAGTAAAGAGG
CCCAATAACT
Found at i:328318 original size:43 final size:44
Alignment explanation
Indices: 328288--328560 Score: 195
Period size: 43 Copynumber: 6.3 Consensus size: 44
328278 GGGTTTAAAC
* **
328288 TATAAAAGTAAAAAGT-ATGATTGAAAAAATTAGGGACCCCAAT
1 TATAAAAGTAAAAAGTGATGATTGAAAAAATTAGGGGCATCAAT
* * *
328331 TATAAAGGTAAAAAGTGAT-ATTAAAAAAAATAGGGGCATCAAT
1 TATAAAAGTAAAAAGTGATGATTGAAAAAATTAGGGGCATCAAT
* * * *
328374 TTTAAAGGTAAAAAGTGA-GATTGAAAAAAATGAGGGGCATAAAT
1 TATAAAAGTAAAAAGTGATGATTG-AAAAAATTAGGGGCATCAAT
** * * *
328418 TATATGAGTAAAAAAT-AGGATTAAAAAAATTAGGGGTC-TCAAT
1 TATAAAAGTAAAAAGTGATGATTGAAAAAATTAGGGG-CATCAAT
** * * *
328461 TAT-AAAGATAAAAAGTGAT-ATTGAAAAAAAACATGAGC-TTAAT
1 TATAAAAG-TAAAAAGTGATGATTG-AAAAAATTAGGGGCATCAAT
* * ** * **
328504 TATAAAGGTACACGGTGA-GATTGAAAAACTTAGGATCATCAAT
1 TATAAAAGTAAAAAGTGATGATTGAAAAAATTAGGGGCATCAAT
*
328547 TATAAATGTAAAAA
1 TATAAAAGTAAAAA
328561 AAAATGGGAT
Statistics
Matches: 176, Mismatches: 43, Indels: 22
0.73 0.18 0.09
Matches are distributed among these distances:
42 11 0.06
43 117 0.66
44 48 0.27
ACGTcount: A:0.51, C:0.06, G:0.18, T:0.25
Consensus pattern (44 bp):
TATAAAAGTAAAAAGTGATGATTGAAAAAATTAGGGGCATCAAT
Found at i:328445 original size:130 final size:130
Alignment explanation
Indices: 328294--328531 Score: 325
Period size: 130 Copynumber: 1.8 Consensus size: 130
328284 AAACTATAAA
* * * *
328294 AGTAAAAAGTATGATTGAAAAAATTAGGGACCCCAATTATAAAGGTAAAAAGTGATATT-AAAAA
1 AGTAAAAAATAGGATTAAAAAAATTAGGGACCCCAATTATAAAGATAAAAAGTGATATTGAAAAA
* * *
328358 AAATAGGGGCATCAATTTTAAAGGTAAAAAGTGAGATTGAAAAAAATGAGGGGCATAAATTATAT
66 AAACAGGAGC-TCAATTATAAAGGTAAAAAGTGAGATTGAAAAAAATGAGGGGCATAAATTATAT
328423 G
130 G
** *
328424 AGTAAAAAATAGGATTAAAAAAATTAGGGGTCTCAATTATAAAGATAAAAAGTGATATTGAAAAA
1 AGTAAAAAATAGGATTAAAAAAATTAGGGACCCCAATTATAAAGATAAAAAGTGATATTGAAAAA
* * * **
328489 AAACATGAGCTTAATTATAAAGGTACACGGTGAGATTGAAAAA
66 AAACAGGAGCTCAATTATAAAGGTAAAAAGTGAGATTGAAAAA
328532 CTTAGGATCA
Statistics
Matches: 92, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
130 80 0.87
131 12 0.13
ACGTcount: A:0.51, C:0.05, G:0.20, T:0.24
Consensus pattern (130 bp):
AGTAAAAAATAGGATTAAAAAAATTAGGGACCCCAATTATAAAGATAAAAAGTGATATTGAAAAA
AAACAGGAGCTCAATTATAAAGGTAAAAAGTGAGATTGAAAAAAATGAGGGGCATAAATTATATG
Found at i:328561 original size:130 final size:129
Alignment explanation
Indices: 328283--328610 Score: 311
Period size: 130 Copynumber: 2.5 Consensus size: 129
328273 ATTAGGGGTT
* * * * * *
328283 TAAACTATAAAAGTAAAAAGTATGATTGAAAAAATTA-GGGACCCCAATTATAAAGGTAAAAAGT
1 TAAATTAT-AAAGTAAAAAATAGGATTAAAAAAATTAGGGGA-CTCAATTATAAAGATAAAAAGT
* * * *
328347 GATATTAAAAAAAATAGGGGCATCAATTTTAAAGGTAAAAAGTGAGATTGAAAAAAATGAGGGGC
64 GATATTAAAAAAAACAGGAGCATCAATTATAAAGGTAAAAAGTGAGATTGAAAAAAATGAGGAGC
328412 A
129 A
* *
328413 TAAATTATATGAGTAAAAAATAGGATTAAAAAAATTAGGGGTCTCAATTATAAAGATAAAAAGTG
1 TAAATTATA-AAGTAAAAAATAGGATTAAAAAAATTAGGGGACTCAATTATAAAGATAAAAAGTG
* * * ** * * *
328478 ATATTGAAAAAAAACATGAGC-TTAATTATAAAGGTACACGGTGAGATTG-AAAAACTTAGGATC
65 ATATT-AAAAAAAACAGGAGCATCAATTATAAAGGTAAAAAGTGAGATTGAAAAAAATGAGGAGC
328541 A
129 A
* * * * * *
328542 TCAATTATAAATGTAAAAAAAAATGGGATTGAAAAAAAATTAAGAGACTCCATTATAATGATAAA
1 TAAATTATAAA-GT---AAAAAATAGGATT--AAAAAAATTAGGGGACTCAATTATAAAGATAAA
328607 AAGT
60 AAGT
328611 AGGATTACAA
Statistics
Matches: 161, Mismatches: 28, Indels: 14
0.79 0.14 0.07
Matches are distributed among these distances:
128 1 0.01
129 22 0.14
130 79 0.49
131 15 0.09
132 12 0.07
134 32 0.20
ACGTcount: A:0.52, C:0.06, G:0.18, T:0.25
Consensus pattern (129 bp):
TAAATTATAAAGTAAAAAATAGGATTAAAAAAATTAGGGGACTCAATTATAAAGATAAAAAGTGA
TATTAAAAAAAACAGGAGCATCAATTATAAAGGTAAAAAGTGAGATTGAAAAAAATGAGGAGCA
Found at i:329470 original size:16 final size:17
Alignment explanation
Indices: 329426--329470 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
329416 TTATGAAGTG
329426 AAAA-AATATATTATTGT
1 AAAATAATAT-TTATTGT
*
329443 AAAAT-ATGTTTATT-T
1 AAAATAATATTTATTGT
329458 AAAATAATATTTA
1 AAAATAATATTTA
329471 ACTTTGAGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
15 6 0.25
16 11 0.46
17 7 0.29
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.44
Consensus pattern (17 bp):
AAAATAATATTTATTGT
Found at i:334682 original size:17 final size:16
Alignment explanation
Indices: 334656--334687 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
334646 TTGCCTGCTG
334656 GCCGCTGCCGCCGCCC
1 GCCGCTGCCGCCGCCC
334672 GCCGTCTGCCGCCGCC
1 GCCG-CTGCCGCCGCC
334688 GTCAGCCGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.00, C:0.59, G:0.31, T:0.09
Consensus pattern (16 bp):
GCCGCTGCCGCCGCCC
Found at i:334687 original size:20 final size:20
Alignment explanation
Indices: 334657--334704 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
334647 TGCCTGCTGG
* *
334657 CCGCTGCCGCCGCCCGCCGT
1 CCGCCGCCGCCGCCAGCCGT
* *
334677 CTGCCGCCGCCGTCAGCCGT
1 CCGCCGCCGCCGCCAGCCGT
334697 CCGCCGCC
1 CCGCCGCC
334705 ACACTCTGAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.02, C:0.58, G:0.29, T:0.10
Consensus pattern (20 bp):
CCGCCGCCGCCGCCAGCCGT
Found at i:337068 original size:18 final size:17
Alignment explanation
Indices: 337045--337090 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 17
337035 TGTAGGAAAT
337045 AGACTGTAGAAAGAAAAC
1 AGACTGTAG-AAGAAAAC
*
337063 AGACTGTATTGTAGAAAAC
1 AGACTGTA--GAAGAAAAC
337082 AGACTGTAG
1 AGACTGTAG
337091 GAAACATACA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 1 0.04
18 8 0.32
19 15 0.60
20 1 0.04
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.20
Consensus pattern (17 bp):
AGACTGTAGAAGAAAAC
Found at i:351045 original size:2 final size:2
Alignment explanation
Indices: 351028--351070 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
351018 CGAATAGTAC
* *
351028 TA TA CA TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
351070 T
1 T
351071 TATTCTTTGA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:362509 original size:18 final size:18
Alignment explanation
Indices: 362486--362521 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
362476 TTTGTTTGAG
362486 TTAAAA-TTTAATTAGGTC
1 TTAAAAGTTTAA-TAGGTC
362504 TTAAAAGTTTAATAGGTC
1 TTAAAAGTTTAATAGGTC
362522 CAGTAATAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.39, C:0.06, G:0.14, T:0.42
Consensus pattern (18 bp):
TTAAAAGTTTAATAGGTC
Found at i:365055 original size:30 final size:30
Alignment explanation
Indices: 365019--365075 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
365009 AATCATCCCT
365019 CAACCAAGAGAAGCCGACATCTCCATCAAC
1 CAACCAAGAGAAGCCGACATCTCCATCAAC
* *
365049 CAACCAAGAGATGCCGACATCTTCATC
1 CAACCAAGAGAAGCCGACATCTCCATC
365076 CACACGTATC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.37, C:0.35, G:0.14, T:0.14
Consensus pattern (30 bp):
CAACCAAGAGAAGCCGACATCTCCATCAAC
Found at i:365421 original size:23 final size:24
Alignment explanation
Indices: 365385--365429 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
365375 TGGGTTTGTG
365385 TTAAAGCTTAAATCAAACTCAAAT
1 TTAAAGCTTAAATCAAACTCAAAT
*
365409 TTAAA-CTTAAATCGAACTCAA
1 TTAAAGCTTAAATCAAACTCAA
365430 GTTCAATCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.49, C:0.18, G:0.04, T:0.29
Consensus pattern (24 bp):
TTAAAGCTTAAATCAAACTCAAAT
Found at i:377075 original size:22 final size:22
Alignment explanation
Indices: 377050--377098 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
377040 ATATATTTAT
377050 TAATATTTATAATAATATAATA
1 TAATATTTATAATAATATAATA
* *
377072 TAATATTTTTAATATTATAATA
1 TAATATTTATAATAATATAATA
*
377094 AAATA
1 TAATA
377099 ATCAATTATA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
TAATATTTATAATAATATAATA
Found at i:377113 original size:23 final size:23
Alignment explanation
Indices: 377083--377136 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 23
377073 AATATTTTTA
377083 ATATTATAATAAAATAATCA-ATT
1 ATATTATAATAAAATAA-CATATT
* *
377106 ATATTATAATAATATAAGATATT
1 ATATTATAATAAAATAACATATT
377129 ATATTATA
1 ATATTATA
377137 TTATATTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 1 0.04
23 27 0.96
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (23 bp):
ATATTATAATAAAATAACATATT
Found at i:377127 original size:18 final size:18
Alignment explanation
Indices: 377050--377171 Score: 76
Period size: 18 Copynumber: 6.9 Consensus size: 18
377040 ATATATTTAT
377050 TAATAT-TTATAATAATA
1 TAATATATTATAATAATA
* **
377067 TAATATAATATTTTTAATA
1 TAATATATTA-TAATAATA
* *
377086 T--TATAATAAAATAATCA
1 TAATATATTATAATAAT-A
*
377103 -ATTATATTATAATAATA
1 TAATATATTATAATAATA
* *
377120 TAAGATATTAT-ATTATA
1 TAATATATTATAATAATA
* *
377137 TTATATTTTAATAAT-ATA
1 TAATATATT-ATAATAATA
377155 TAATATATTATTAATAA
1 TAATATATTA-TAATAA
377172 AATTTATATT
Statistics
Matches: 79, Mismatches: 16, Indels: 18
0.70 0.14 0.16
Matches are distributed among these distances:
16 4 0.05
17 27 0.34
18 38 0.48
19 10 0.13
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.48
Consensus pattern (18 bp):
TAATATATTATAATAATA
Found at i:379195 original size:17 final size:16
Alignment explanation
Indices: 379171--379215 Score: 63
Period size: 17 Copynumber: 2.7 Consensus size: 16
379161 TAGGGATTTT
379171 GATTTTTTTAAAAATA
1 GATTTTTTTAAAAATA
379187 GATTATTTTTAAAAATA
1 GATT-TTTTTAAAAATA
*
379204 AATGTTTTTTAA
1 GAT-TTTTTTAA
379216 TTTTTTTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 4 0.15
17 21 0.81
18 1 0.04
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (16 bp):
GATTTTTTTAAAAATA
Found at i:379789 original size:3 final size:3
Alignment explanation
Indices: 379781--379805 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
379771 AGTATTTATT
379781 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
379806 TTAAAGCGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:388186 original size:2 final size:2
Alignment explanation
Indices: 388179--388207 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
388169 GCCTTGTAAT
388179 TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
388208 AATAGGGCAG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:390479 original size:13 final size:13
Alignment explanation
Indices: 390461--390486 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
390451 AAGGCTCTAC
390461 TCATACGGATTTT
1 TCATACGGATTTT
390474 TCATACGGATTTT
1 TCATACGGATTTT
390487 GAATTAAACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.15, G:0.15, T:0.46
Consensus pattern (13 bp):
TCATACGGATTTT
Found at i:397867 original size:2 final size:2
Alignment explanation
Indices: 397860--397884 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
397850 ATCCTGTCTG
397860 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
397885 TAAAGTATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:406133 original size:13 final size:13
Alignment explanation
Indices: 406115--406139 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
406105 TTTGATTCAT
406115 TAAATTTTAATTA
1 TAAATTTTAATTA
406128 TAAATTTTAATT
1 TAAATTTTAATT
406140 TATATATTAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TAAATTTTAATTA
Found at i:407300 original size:163 final size:162
Alignment explanation
Indices: 407023--407318 Score: 398
Period size: 163 Copynumber: 1.8 Consensus size: 162
407013 AGTTAAAATG
*
407023 TGGTTGAAACTAATTACATATTTGGACAAACTAGTGATAGAATTGGAAGATTTAAAAGTACGGGA
1 TGGTTGAAACTAATTACATATTTGGACAAACTAGTGATAGAATTGGAAGATTCAAAAGTACGGGA
* * * *
407088 CCAATTTAGAACGTAGTTCATAATTTGGAGATAAAATTAGAATGTTCAAAAGTTTAAGAACCAAT
66 CAAATTCAGAACGTAGGTCATAATTTGGAGATAAAATTAGAACGTTCAAAAGTTTAAGAACCAAT
407153 TTATACTGAGAGTCATAGTTTATGTTAAGTTA
131 TTATACTGAGAGTCATAGTTTATGTTAAGTTA
** * **
407185 TGGTTGAAACTAATTACATATTTGGACGAATTTGGTGAT-GAAATTGGAAGATTCAAAAGTTTGG
1 TGGTTGAAACTAATTACATATTTGGAC-AAACTAGTGATAG-AATTGGAAGATTCAAAAGTACGG
* * ** * * *
407249 GATAAATTCA-TATTTATGGTCATAGTTTGGAGATGAAATTGGAACGTTCAAAAGTTTAAGAACC
64 GACAAATTCAGAACGTA-GGTCATAATTTGGAGATAAAATTAGAACGTTCAAAAGTTTAAGAACC
407313 AATTTA
128 AATTTA
407319 GTTCAAAAGT
Statistics
Matches: 114, Mismatches: 17, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
162 31 0.27
163 83 0.73
ACGTcount: A:0.38, C:0.08, G:0.20, T:0.33
Consensus pattern (162 bp):
TGGTTGAAACTAATTACATATTTGGACAAACTAGTGATAGAATTGGAAGATTCAAAAGTACGGGA
CAAATTCAGAACGTAGGTCATAATTTGGAGATAAAATTAGAACGTTCAAAAGTTTAAGAACCAAT
TTATACTGAGAGTCATAGTTTATGTTAAGTTA
Found at i:407322 original size:25 final size:25
Alignment explanation
Indices: 407294--407344 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
407284 AAATTGGAAC
407294 GTTCAAAAGTTTAAGAACCAATTTA
1 GTTCAAAAGTTTAAGAACCAATTTA
407319 GTTCAAAAGTTTAAGAACCAATTTA
1 GTTCAAAAGTTTAAGAACCAATTTA
407344 G
1 G
407345 AATGAGAATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.31
Consensus pattern (25 bp):
GTTCAAAAGTTTAAGAACCAATTTA
Found at i:414787 original size:26 final size:26
Alignment explanation
Indices: 414727--414790 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 26
414717 AAATATATTG
414727 AATTTCAT--AACATTCGTATAGTTT
1 AATTTCATAAAACATTCGTATAGTTT
* * *
414751 -TTTTAATTAAAACATTTGTATAGTTT
1 AATTTCA-TAAAACATTCGTATAGTTT
414777 AATTTCATAAAACA
1 AATTTCATAAAACA
414791 ACATAAAATT
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
23 4 0.13
24 1 0.03
26 22 0.71
27 4 0.13
ACGTcount: A:0.39, C:0.09, G:0.06, T:0.45
Consensus pattern (26 bp):
AATTTCATAAAACATTCGTATAGTTT
Found at i:414860 original size:12 final size:13
Alignment explanation
Indices: 414843--414882 Score: 55
Period size: 14 Copynumber: 3.1 Consensus size: 13
414833 TTAAAATTCA
414843 ATTATT-AATAAT
1 ATTATTAAATAAT
414855 ATTATTAGAATAAT
1 ATTATTA-AATAAT
*
414869 ATTATAAAATAAT
1 ATTATTAAATAAT
414882 A
1 A
414883 AATTTAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
12 6 0.24
13 7 0.28
14 12 0.48
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (13 bp):
ATTATTAAATAAT
Found at i:416836 original size:30 final size:30
Alignment explanation
Indices: 416802--416868 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 30
416792 TTATCCTGTC
416802 ATTTTTAATTAATCAAATAATTATTTTATA
1 ATTTTTAATTAATCAAATAATTATTTTATA
* * *
416832 ATTTTTTATTAATTAAATGATTATTTTATA
1 ATTTTTAATTAATCAAATAATTATTTTATA
*
416862 TTTTTTA
1 ATTTTTA
416869 TAAAAATATT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.60
Consensus pattern (30 bp):
ATTTTTAATTAATCAAATAATTATTTTATA
Found at i:416909 original size:27 final size:27
Alignment explanation
Indices: 416872--416935 Score: 119
Period size: 27 Copynumber: 2.4 Consensus size: 27
416862 TTTTTTATAA
416872 AAATATTTTAGAATCTAATGACTATCT
1 AAATATTTTAGAATCTAATGACTATCT
416899 AAATATTTTAGAATCTAATGACTATCT
1 AAATATTTTAGAATCTAATGACTATCT
*
416926 AAATAATTTA
1 AAATATTTTA
416936 TCCTTTATTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.44, C:0.09, G:0.06, T:0.41
Consensus pattern (27 bp):
AAATATTTTAGAATCTAATGACTATCT
Found at i:420639 original size:15 final size:15
Alignment explanation
Indices: 420619--420652 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
420609 AGGCAATGGC
420619 ATATAT-TAATAT-T
1 ATATATATAATATGT
420632 ATATATATAATATGT
1 ATATATATAATATGT
420647 ATATAT
1 ATATAT
420653 GCATGCATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 6 0.32
14 6 0.32
15 7 0.37
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (15 bp):
ATATATATAATATGT
Found at i:424646 original size:71 final size:70
Alignment explanation
Indices: 424531--424671 Score: 273
Period size: 71 Copynumber: 2.0 Consensus size: 70
424521 GTAGTAGATT
424531 TGCTTTTATCCAAATCTCTGCATAGTCAGAATCGACATACCTATTTATTAGTAAGTTTGATCCTC
1 TGCTTTTATCCAAATCTCTGCATAGTCAGAATCGACATACCTATTTATTAGTAAGTTTGATCCTC
424596 CGTAA
66 CGTAA
424601 TGCTTTTATCCAAATCTCCTGCATAGTCAGAATCGACATACCTATTTATTAGTAAGTTTGATCCT
1 TGCTTTTATCCAAATCT-CTGCATAGTCAGAATCGACATACCTATTTATTAGTAAGTTTGATCCT
424666 CCGTAA
65 CCGTAA
424672 CATAATGCAA
Statistics
Matches: 70, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
70 17 0.24
71 53 0.76
ACGTcount: A:0.28, C:0.22, G:0.13, T:0.37
Consensus pattern (70 bp):
TGCTTTTATCCAAATCTCTGCATAGTCAGAATCGACATACCTATTTATTAGTAAGTTTGATCCTC
CGTAA
Found at i:439667 original size:21 final size:22
Alignment explanation
Indices: 439643--439684 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
439633 AAAAGTAATA
*
439643 TAATA-TAATGTAATTTTATAT
1 TAATATTAATATAATTTTATAT
*
439664 TAATATTAATATATTTTTATA
1 TAATATTAATATAATTTTATA
439685 ATCAAATTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (22 bp):
TAATATTAATATAATTTTATAT
Found at i:456737 original size:11 final size:11
Alignment explanation
Indices: 456721--456750 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
456711 AATGATTTCC
456721 GTGAAATTATA
1 GTGAAATTATA
456732 GTGAAATTATA
1 GTGAAATTATA
*
456743 GTAAAATT
1 GTGAAATT
456751 TATAATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.17, T:0.37
Consensus pattern (11 bp):
GTGAAATTATA
Found at i:456790 original size:8 final size:8
Alignment explanation
Indices: 456774--456806 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
456764 TAACTAATAA
*
456774 TATTTATT
1 TATTAATT
456782 TATTAATT
1 TATTAATT
456790 TATTAATT
1 TATTAATT
456798 TATTAATT
1 TATTAATT
456806 T
1 T
456807 GGATCATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (8 bp):
TATTAATT
Found at i:458899 original size:35 final size:34
Alignment explanation
Indices: 458835--458953 Score: 134
Period size: 35 Copynumber: 3.5 Consensus size: 34
458825 AGCCGGGGGT
* *
458835 GGTTCAGATTGTTTAGCTTTGTTCTGAGCTGCTGGC
1 GGTTGAGATTGTTTAG-GTTGTTCTGAGCTGC-GGC
*
458871 GGTTGAGATTGTTTAGGTTGTTCTGAGCTGCCGGA
1 GGTTGAGATTGTTTAGGTTGTTCTGAGCTG-CGGC
* * *
458906 GGTCGAGCTTGTTGAGGTTGTTCTGAGC--CGGC
1 GGTTGAGATTGTTTAGGTTGTTCTGAGCTGCGGC
*
458938 GGTTGAGCTTGTTTAG
1 GGTTGAGATTGTTTAG
458954 CTTTTCCCAA
Statistics
Matches: 73, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
32 17 0.23
35 40 0.55
36 16 0.22
ACGTcount: A:0.12, C:0.14, G:0.36, T:0.38
Consensus pattern (34 bp):
GGTTGAGATTGTTTAGGTTGTTCTGAGCTGCGGC
Found at i:460061 original size:3 final size:3
Alignment explanation
Indices: 460053--460113 Score: 122
Period size: 3 Copynumber: 20.3 Consensus size: 3
460043 TTAAATATGG
460053 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
460101 AAT AAT AAT AAT A
1 AAT AAT AAT AAT A
460114 GAAGACATGT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:463642 original size:31 final size:30
Alignment explanation
Indices: 463603--463694 Score: 82
Period size: 31 Copynumber: 3.0 Consensus size: 30
463593 ATAGTCGAGG
463603 GTTACCTATGTCTTTCAAGACATATGGATA
1 GTTACCTATGTCTTTCAAGACATATGGATA
* ** *
463633 GTTTACCTATGCCCTTT-GGGACATATGGACA
1 G-TTACCTATG-TCTTTCAAGACATATGGATA
*
463664 GTTACATATGT-TCTTCGAA-ACATATGGATA
1 GTTACCTATGTCT-TTC-AAGACATATGGATA
463694 G
1 G
463695 GTCATTCGGG
Statistics
Matches: 48, Mismatches: 9, Indels: 10
0.72 0.13 0.15
Matches are distributed among these distances:
28 1 0.02
29 2 0.04
30 20 0.42
31 21 0.44
32 4 0.08
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (30 bp):
GTTACCTATGTCTTTCAAGACATATGGATA
Found at i:472269 original size:2 final size:2
Alignment explanation
Indices: 472262--472291 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
472252 ATTTTAATAA
*
472262 AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
472292 TGATATGATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:476847 original size:22 final size:22
Alignment explanation
Indices: 476790--476848 Score: 75
Period size: 21 Copynumber: 2.7 Consensus size: 22
476780 ACACGATTCT
476790 GACTATCGCATTGCGATTTTCC
1 GACTATCGCATTGCGATTTTCC
* * *
476812 AAAT-TCGCGTTGCGATTTTCC
1 GACTATCGCATTGCGATTTTCC
*
476833 GACTATCGCAATGCGA
1 GACTATCGCATTGCGA
476849 ATATGTAAAT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
21 18 0.62
22 11 0.38
ACGTcount: A:0.22, C:0.25, G:0.20, T:0.32
Consensus pattern (22 bp):
GACTATCGCATTGCGATTTTCC
Found at i:476880 original size:20 final size:20
Alignment explanation
Indices: 476857--476970 Score: 156
Period size: 20 Copynumber: 5.7 Consensus size: 20
476847 GAATATGTAA
* * *
476857 ATCGCAATGCGAGTATGACT
1 ATCGCAACGCGATTCTGACT
476877 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
476897 ATCGCAACGAGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
476917 GTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
* *
476937 GTCGCAACGCGATGCTGACT
1 ATCGCAACGCGATTCTGACT
*
476957 ATCGCAATGCGATT
1 ATCGCAACGCGATT
476971 TTCAAAGCGC
Statistics
Matches: 84, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 84 1.00
ACGTcount: A:0.25, C:0.26, G:0.24, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:477170 original size:22 final size:22
Alignment explanation
Indices: 477145--477187 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
477135 GGCGACATCC
477145 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
*
477167 GTCCCCATCTCCGGCGAAATC
1 GTCCCCATCTCCGACGAAATC
477188 CGTCTATCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.23, C:0.42, G:0.16, T:0.19
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:479379 original size:18 final size:18
Alignment explanation
Indices: 479356--479405 Score: 91
Period size: 18 Copynumber: 2.8 Consensus size: 18
479346 TTTACTAGTA
479356 ATTTCACTTAGATTAACC
1 ATTTCACTTAGATTAACC
*
479374 ATTTCACTTAGATTAACT
1 ATTTCACTTAGATTAACC
479392 ATTTCACTTAGATT
1 ATTTCACTTAGATT
479406 GCTTAGTAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.32, C:0.18, G:0.06, T:0.44
Consensus pattern (18 bp):
ATTTCACTTAGATTAACC
Found at i:481607 original size:14 final size:14
Alignment explanation
Indices: 481573--481634 Score: 52
Period size: 14 Copynumber: 4.3 Consensus size: 14
481563 TTTCTTGTTT
*
481573 AATTGATTTATAAA
1 AATTGATTTGTAAA
*
481587 AACTGATTTGTAAA
1 AATTGATTTGTAAA
* *
481601 AGTTGATTTGTTTAA
1 AATTGATTTG-TAAA
* *
481616 TATTGATGTGTAAA
1 AATTGATTTGTAAA
481630 TAATT
1 -AATT
481635 CTTATTTGTG
Statistics
Matches: 36, Mismatches: 10, Indels: 3
0.73 0.20 0.06
Matches are distributed among these distances:
14 23 0.64
15 13 0.36
ACGTcount: A:0.39, C:0.02, G:0.15, T:0.45
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:481783 original size:20 final size:20
Alignment explanation
Indices: 481733--481786 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
481723 AGGTACACTT
* **
481733 TCGCAACGCTAAACTCAAAA
1 TCGCAACGCGAAAGACAAAA
**
481753 TCGCATTGCGAAAGACAAAA
1 TCGCAACGCGAAAGACAAAA
481773 TCGCAACGCGAAAG
1 TCGCAACGCGAAAG
481787 TCAATTCGCG
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.43, C:0.26, G:0.19, T:0.13
Consensus pattern (20 bp):
TCGCAACGCGAAAGACAAAA
Found at i:481916 original size:94 final size:94
Alignment explanation
Indices: 481789--481971 Score: 242
Period size: 94 Copynumber: 1.9 Consensus size: 94
481779 CGCGAAAGTC
* * **
481789 AATTCGCGTTGCGATAGTCTAATACATTTTGCGATTTTCT-CGTTGCGATAGTCAAATACCCATT
1 AATTCGCGTTGCGATAGACAAATACACATTGCGATTTT-TGCGTTGCGATAGTCAAATACCCATT
481853 GCGATAATCAAATTCGCGTTGCGATACTCA
65 GCGATAATCAAATTCGCGTTGCGATACTCA
* * * * ***
481883 AATTCGCGTTGCGATAGACAAATTCGCATTGCGATTTTTGCGTTGCGATAGTCATATTCGTGTTG
1 AATTCGCGTTGCGATAGACAAATACACATTGCGATTTTTGCGTTGCGATAGTCAAATACCCATTG
*
481948 CGATAGTCAAATTCGCGTTGCGAT
66 CGATAATCAAATTCGCGTTGCGAT
481972 TTTTGAGTTG
Statistics
Matches: 76, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
93 1 0.01
94 75 0.99
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.34
Consensus pattern (94 bp):
AATTCGCGTTGCGATAGACAAATACACATTGCGATTTTTGCGTTGCGATAGTCAAATACCCATTG
CGATAATCAAATTCGCGTTGCGATACTCA
Found at i:482006 original size:20 final size:20
Alignment explanation
Indices: 481829--482013 Score: 160
Period size: 20 Copynumber: 9.8 Consensus size: 20
481819 GCGATTTTCT
* *
481829 CGTTGCGATAGTCAAATACC
1 CGTTGCGATAGTCAAATTCG
* *
481849 CATTGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
481869 CGTTGCGATACTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
481889 CGTTGCGATAGACAAATTCG
1 CGTTGCGATAGTCAAATTCG
* *
481909 CATTGCGAT--T----TTTG
1 CGTTGCGATAGTCAAATTCG
*
481923 CGTTGCGATAGTCATATTCG
1 CGTTGCGATAGTCAAATTCG
*
481943 TGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
481963 CGTTGCGAT--T----TTTG
1 CGTTGCGATAGTCAAATTCG
* *
481977 AGTTGTGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
481997 CGTTGCGATATTCAAAT
1 CGTTGCGATAGTCAAAT
482014 GAATGTGTAA
Statistics
Matches: 130, Mismatches: 23, Indels: 24
0.73 0.13 0.14
Matches are distributed among these distances:
14 21 0.16
16 2 0.02
18 1 0.01
20 106 0.82
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.34
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:482012 original size:54 final size:54
Alignment explanation
Indices: 481870--482013 Score: 216
Period size: 54 Copynumber: 2.7 Consensus size: 54
481860 TCAAATTCGC
* * *
481870 GTTGCGATACTCAAATTCGCGTTGCGATAGACAAATTCGCATTGCGATTTTTGC
1 GTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCATTGCGATTTTTGA
* * *
481924 GTTGCGATAGTCATATTCGTGTTGCGATAGTCAAATTCGCGTTGCGATTTTTGA
1 GTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCATTGCGATTTTTGA
* *
481978 GTTGTGATAGTCAAATTCGCGTTGCGATATTCAAAT
1 GTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAAT
482014 GAATGTGTAA
Statistics
Matches: 80, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 80 1.00
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.36
Consensus pattern (54 bp):
GTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCATTGCGATTTTTGA
Found at i:482236 original size:140 final size:140
Alignment explanation
Indices: 481984--482253 Score: 513
Period size: 140 Copynumber: 1.9 Consensus size: 140
481974 TTGAGTTGTG
* *
481984 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCA
1 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTAAACAGATCA
*
482049 TAGCAATGTTCAAACTCAAGTTACTAATACATGTCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
482114 AATACGCATA
131 AATACGCATA
482124 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTAAACAGATCA
1 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTAAACAGATCA
482189 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
482254 TACAACGTTT
Statistics
Matches: 127, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
140 127 1.00
ACGTcount: A:0.42, C:0.15, G:0.14, T:0.29
Consensus pattern (140 bp):
ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTAAACAGATCA
TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
AATACGCATA
Found at i:482336 original size:18 final size:18
Alignment explanation
Indices: 482313--482347 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
482303 AAGCCGGTTG
482313 TGATTGAGATTTTGATTT
1 TGATTGAGATTTTGATTT
*
482331 TGATTGCGATTTTGATT
1 TGATTGAGATTTTGATT
482348 GCATTTTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.03, G:0.23, T:0.54
Consensus pattern (18 bp):
TGATTGAGATTTTGATTT
Found at i:482355 original size:12 final size:12
Alignment explanation
Indices: 482326--482354 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
482316 TTGAGATTTT
482326 GATTTTGATTGC
1 GATTTTGATTGC
482338 GATTTTGATTGC
1 GATTTTGATTGC
482350 -ATTTT
1 GATTTT
482355 TCTTGACACC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.17, C:0.07, G:0.21, T:0.55
Consensus pattern (12 bp):
GATTTTGATTGC
Found at i:484403 original size:14 final size:14
Alignment explanation
Indices: 484384--484419 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
484374 TCCCGTGACA
484384 TTTTCTTCGGGGAC
1 TTTTCTTCGGGGAC
*
484398 TTTTCTTCGGGGAT
1 TTTTCTTCGGGGAC
484412 TTTTCTTC
1 TTTTCTTC
484420 TTCAGGGTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.06, C:0.19, G:0.22, T:0.53
Consensus pattern (14 bp):
TTTTCTTCGGGGAC
Found at i:484631 original size:24 final size:24
Alignment explanation
Indices: 484597--484650 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
484587 CTGAAACATT
484597 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
484621 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
484645 ATCAAA
1 ATCAAA
484651 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:485516 original size:20 final size:20
Alignment explanation
Indices: 485473--485543 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
485463 AAATTCAGTG
* * *
485473 TTGCGACAGTCAGAATCGCG
1 TTGCGATAGTCATAATCGCA
*
485493 TTGCGATAGTCATAATCGTA
1 TTGCGATAGTCATAATCGCA
* *
485513 TTGCGAT-TTACATATTCGCA
1 TTGCGATAGT-CATAATCGCA
485533 TTGCGATAGTC
1 TTGCGATAGTC
485544 GAAAAATCGC
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
19 1 0.02
20 39 0.95
21 1 0.02
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (20 bp):
TTGCGATAGTCATAATCGCA
Found at i:486200 original size:2 final size:2
Alignment explanation
Indices: 486195--486230 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
486185 ACAGAAAGCC
486195 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
486231 GAATTTTAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:491839 original size:27 final size:27
Alignment explanation
Indices: 491801--491865 Score: 112
Period size: 27 Copynumber: 2.4 Consensus size: 27
491791 CAAAACAGTG
*
491801 TTGAATGATTCAACACAGAAATATATT
1 TTGAATGATTCAACACAGAAATACATT
491828 TTGAATGATTCAACACAGAAATACATT
1 TTGAATGATTCAACACAGAAATACATT
*
491855 CTGAATGATTC
1 TTGAATGATTC
491866 GAAGCCATTA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.42, C:0.14, G:0.12, T:0.32
Consensus pattern (27 bp):
TTGAATGATTCAACACAGAAATACATT
Found at i:493417 original size:31 final size:31
Alignment explanation
Indices: 493380--493455 Score: 98
Period size: 31 Copynumber: 2.5 Consensus size: 31
493370 GATAAGATAG
* * *
493380 ATGATCACATATTAATTAAATAAAAATGAAT
1 ATGATCACATATTAATAAAATAAAAATAAAA
* *
493411 GTGATCACATTTTAATAAAATAAAAATAAAA
1 ATGATCACATATTAATAAAATAAAAATAAAA
*
493442 ATGATCAAATATTA
1 ATGATCACATATTA
493456 TATTTTTTAA
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.55, C:0.07, G:0.07, T:0.32
Consensus pattern (31 bp):
ATGATCACATATTAATAAAATAAAAATAAAA
Found at i:497098 original size:60 final size:60
Alignment explanation
Indices: 497016--497139 Score: 214
Period size: 60 Copynumber: 2.1 Consensus size: 60
497006 GAAACTGTCA
**
497016 CTAATGAAAGAAGCAATCAACATAATAAAGTTGTTGCAGCCGAGGGCTTTGAAAT-GCCTT
1 CTAATGAAAGAAGCAATCAACATAATAAAGTTACTGCAGCCGAGGGCTTTG-AATGGCCTT
497076 CTAATGAAAGAAGCAATCAACATAATAAAGTTACTGCAGCCGAGGGCTTTGAATGGCCTT
1 CTAATGAAAGAAGCAATCAACATAATAAAGTTACTGCAGCCGAGGGCTTTGAATGGCCTT
497136 CTAA
1 CTAA
497140 CTTGGAGTAT
Statistics
Matches: 61, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
59 3 0.05
60 58 0.95
ACGTcount: A:0.37, C:0.18, G:0.21, T:0.24
Consensus pattern (60 bp):
CTAATGAAAGAAGCAATCAACATAATAAAGTTACTGCAGCCGAGGGCTTTGAATGGCCTT
Found at i:508965 original size:15 final size:15
Alignment explanation
Indices: 508894--508965 Score: 71
Period size: 15 Copynumber: 4.9 Consensus size: 15
508884 ATAGCTAAAG
508894 AATAAAATATAT-AT
1 AATAAAATATATAAT
*
508908 -ATATATATATATAAT
1 AATA-AAATATATAAT
* *
508923 AATCAAATATAGAAT
1 AATAAAATATATAAT
508938 AATAAAATA-ATAAGT
1 AATAAAATATATAA-T
508953 AA-AAAATATATAA
1 AATAAAATATATAA
508966 AAAATGTACA
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
13 3 0.06
14 16 0.34
15 26 0.55
16 2 0.04
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.32
Consensus pattern (15 bp):
AATAAAATATATAAT
Found at i:509003 original size:28 final size:28
Alignment explanation
Indices: 508938--509013 Score: 72
Period size: 27 Copynumber: 2.8 Consensus size: 28
508928 AATATAGAAT
508938 AATAAAATA-ATAAGTAAAAA-ATATATA
1 AATAAAATACATAAG-AAAAATATATATA
*
508965 AA-AAATGTACATAAGAAAAATATA-ATA
1 AATAAA-ATACATAAGAAAAATATATATA
*
508992 CAATAAAATACATGA-AAAAATA
1 -AATAAAATACATAAGAAAAATA
509014 GCTAAATATA
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
26 3 0.07
27 19 0.46
28 16 0.39
29 3 0.07
ACGTcount: A:0.68, C:0.04, G:0.05, T:0.22
Consensus pattern (28 bp):
AATAAAATACATAAGAAAAATATATATA
Found at i:509142 original size:27 final size:25
Alignment explanation
Indices: 509112--509178 Score: 71
Period size: 27 Copynumber: 2.5 Consensus size: 25
509102 AAAATATAAT
509112 TAAATAATAATAATGATAGATATAGTA
1 TAAATAATAATAAT-ATAGATATA-TA
* *
509139 TAAAAAATAATAAATATATATATATA
1 TAAATAATAAT-AATATAGATATATA
*
509165 TATATATATAATAA
1 TAAATA-ATAATAA
509179 AATGAAAGTA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
26 8 0.24
27 23 0.68
28 3 0.09
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (25 bp):
TAAATAATAATAATATAGATATATA
Found at i:509222 original size:28 final size:28
Alignment explanation
Indices: 509127--509272 Score: 74
Period size: 32 Copynumber: 5.0 Consensus size: 28
509117 AATAATAATG
509127 ATAGATATAGTATA-AAAAAT-A-ATAAA
1 ATAGATATA-TATATAAAAATAAGATAAA
* *
509153 TATATATATATATATATATATAATAAAATGAAA
1 -ATAGATATATATATA-A-A-AATAAGAT-AAA
*
509186 GTATG-TATATATATACAAAATAAGATAAA
1 ATA-GATATATATATA-AAAATAAGATAAA
509215 ATA-ATATAATAATTATAAAAAATAA-ATAGAA
1 ATAGATAT-AT-A-TAT-AAAAATAAGATA-AA
* *
509246 ATAGATA-AAATATAAAAA-AAGGTAAA
1 ATAGATATATATATAAAAATAAGATAAA
509272 A
1 A
509273 ATAAGCATAA
Statistics
Matches: 95, Mismatches: 8, Indels: 33
0.70 0.06 0.24
Matches are distributed among these distances:
26 9 0.09
27 16 0.17
28 7 0.07
29 9 0.09
30 15 0.16
31 17 0.18
32 19 0.20
33 3 0.03
ACGTcount: A:0.63, C:0.01, G:0.07, T:0.29
Consensus pattern (28 bp):
ATAGATATATATATAAAAATAAGATAAA
Found at i:509239 original size:31 final size:28
Alignment explanation
Indices: 509196--509264 Score: 77
Period size: 31 Copynumber: 2.4 Consensus size: 28
509186 GTATGTATAT
* *
509196 ATATACAAAATAAGATA-AAATAATATAATA
1 ATATAAAAAATAA-ATAGAAAT-AGATAA-A
509226 ATTATAAAAAATAAATAGAAATAGATAAA
1 A-TATAAAAAATAAATAGAAATAGATAAA
509255 ATATAAAAAA
1 ATATAAAAAA
509265 AGGTAAAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
28 9 0.26
29 2 0.06
30 9 0.26
31 15 0.43
ACGTcount: A:0.70, C:0.01, G:0.04, T:0.25
Consensus pattern (28 bp):
ATATAAAAAATAAATAGAAATAGATAAA
Found at i:510322 original size:2 final size:2
Alignment explanation
Indices: 510309--510344 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
510299 ATAAACATAA
*
510309 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
510345 AAAAATGTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:510324 original size:12 final size:12
Alignment explanation
Indices: 510299--510337 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
510289 ATACGTTTAA
* *
510299 ATAAACATAAAT
1 ATAAATATATAT
510311 ATAAATATATAT
1 ATAAATATATAT
*
510323 ATATATATATAT
1 ATAAATATATAT
510335 ATA
1 ATA
510338 TATTATAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (12 bp):
ATAAATATATAT
Found at i:517090 original size:178 final size:178
Alignment explanation
Indices: 516792--517147 Score: 671
Period size: 178 Copynumber: 2.0 Consensus size: 178
516782 AAATATTTTG
516792 AAAACTAAAAACAAAACCCAAAACGAAACATTTTGATGAGGTTGTTAAACAATAAAATTAAAAAA
1 AAAACTAAAAACAAAACCCAAAACGAAACATTTTGATGAGGTTGTTAAACAATAAAATTAAAAAA
516857 TTTAAATTTTAAAAGTTGAATAACACAAAAGATAATTTACAGAAATAAAAGCATATTTGATTTAA
66 TTTAAATTTTAAAAGTTGAATAACACAAAAGATAATTTACAGAAATAAAAGCATATTTGATTTAA
516922 TTCCA-TTCGAGAGCCATGATAGTATAAAGAGAAAATCGTCTCAGTGA
131 TTCCATTTCGAGAGCCATGATAGTATAAAGAGAAAATCGTCTCAGTGA
516969 AAAACTAAAAACAAAACCC-AAACGAAACATTTTGATGAGGTTGTTAAACAATTAAAATTAAAAA
1 AAAACTAAAAACAAAACCCAAAACGAAACATTTTGATGAGGTTGTTAAACAA-TAAAATT-AAAA
517033 AATTTAAATTTTAAAAGTTGAATAACACAAAAGATAATTTACAGAAATAAAAGCATATTTGATTT
64 AATTTAAATTTTAAAAGTTGAATAACACAAAAGATAATTTACAGAAATAAAAGCATATTTGATTT
*
517098 AATTCCATTTGGAGAGCCATGATAGTATAAAGAGAAAATCGTCTCAGTGA
129 AATTCCATTTCGAGAGCCATGATAGTATAAAGAGAAAATCGTCTCAGTGA
517148 CCAAAAATAG
Statistics
Matches: 175, Mismatches: 1, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
176 32 0.18
177 26 0.15
178 76 0.43
179 41 0.23
ACGTcount: A:0.49, C:0.11, G:0.13, T:0.27
Consensus pattern (178 bp):
AAAACTAAAAACAAAACCCAAAACGAAACATTTTGATGAGGTTGTTAAACAATAAAATTAAAAAA
TTTAAATTTTAAAAGTTGAATAACACAAAAGATAATTTACAGAAATAAAAGCATATTTGATTTAA
TTCCATTTCGAGAGCCATGATAGTATAAAGAGAAAATCGTCTCAGTGA
Found at i:517362 original size:20 final size:21
Alignment explanation
Indices: 517337--517388 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
517327 TTTTCCCAAT
517337 TCGCAATGCGAATAAGT-AAA
1 TCGCAATGCGAATAAGTAAAA
* **
517357 TCGCAACGCGAATTGGTAAAA
1 TCGCAATGCGAATAAGTAAAA
517378 TCGCAATGCGA
1 TCGCAATGCGA
517389 TACTGACTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 14 0.52
21 13 0.48
ACGTcount: A:0.38, C:0.19, G:0.23, T:0.19
Consensus pattern (21 bp):
TCGCAATGCGAATAAGTAAAA
Found at i:517401 original size:41 final size:41
Alignment explanation
Indices: 517374--517511 Score: 136
Period size: 41 Copynumber: 3.4 Consensus size: 41
517364 GCGAATTGGT
*
517374 AAAATCGCAATGCGATACTGACTATCGCAACGCGATAATAC
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * *
517415 AAAATCGCAACGCGATGCTGACTTTCGCAACGCGATACTGAC
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGATAAT-AC
** * * * *
517457 --TTTCGCAATGCGATTCTGACTTTCGCAACGAGATAATAC
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * *
517496 AGAATTGCAATGCGAT
1 AAAATCGCAACGCGAT
517512 TTTCAAAGTT
Statistics
Matches: 81, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
39 2 0.02
40 31 0.38
41 46 0.57
42 2 0.02
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.23
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:517402 original size:20 final size:20
Alignment explanation
Indices: 517377--517491 Score: 115
Period size: 20 Copynumber: 5.7 Consensus size: 20
517367 AATTGGTAAA
*
517377 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
517397 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
517418 ATCGCAACGCGATGCTGACT
1 ATCGCAACGCGATACTGACT
*
517438 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
517458 TTCGCAATGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
* *
517478 TTCGCAACGAGATA
1 ATCGCAACGCGATA
517492 ATACAGAATT
Statistics
Matches: 79, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.03
20 61 0.77
21 14 0.18
22 2 0.03
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:518243 original size:24 final size:24
Alignment explanation
Indices: 518216--518269 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
518206 GTATTCAAAA
*
518216 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
518240 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
518264 TTTGAT
1 TTTGAT
518270 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:518461 original size:12 final size:12
Alignment explanation
Indices: 518444--518468 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
518434 ATATAATCCT
518444 GAAGAAGAAAAA
1 GAAGAAGAAAAA
518456 GAAGAAGAAAAA
1 GAAGAAGAAAAA
518468 G
1 G
518469 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:520789 original size:33 final size:33
Alignment explanation
Indices: 520747--520873 Score: 202
Period size: 33 Copynumber: 3.8 Consensus size: 33
520737 GGAAATTACT
*
520747 ATCGCAATGCGAAATGAAAATCACAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
520780 ATCGCAATGCGAAATGAAAATCGCAACGCGA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
520812 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
520846 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
520874 CGAATTTAAT
Statistics
Matches: 86, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
32 1 0.01
33 84 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:520803 original size:19 final size:19
Alignment explanation
Indices: 520747--520877 Score: 94
Period size: 19 Copynumber: 7.7 Consensus size: 19
520737 GGAAATTACT
520747 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
520766 ATCACAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
520780 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
520799 ATCGCAACGCG-AAT----
1 ATCGCAATGCGAAATGAAA
*
520813 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
520832 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
520846 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
520865 ATCGCAACGCGAA
1 ATCGCAATGCGAA
520878 TTTAATTTCG
Statistics
Matches: 84, Mismatches: 13, Indels: 30
0.66 0.10 0.24
Matches are distributed among these distances:
14 27 0.32
15 5 0.06
16 4 0.05
17 4 0.05
18 5 0.06
19 39 0.46
ACGTcount: A:0.44, C:0.20, G:0.23, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:520830 original size:66 final size:66
Alignment explanation
Indices: 520748--520880 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
520738 GAAATTACTA
520748 TCGCAATGCGAAATGAAAATCACAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCACAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
520813 T
66 T
* *
520814 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCACAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
520879 T
66 T
520880 T
1 T
520881 AATTTCGCGT
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.42, C:0.20, G:0.23, T:0.16
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCACAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:520945 original size:33 final size:34
Alignment explanation
Indices: 520882--520963 Score: 130
Period size: 33 Copynumber: 2.4 Consensus size: 34
520872 CGCGAATTTA
*
520882 ATTTCGCGTTGCGATTCTCCTCGTTGCGATTTTC
1 ATTTCGCGTTGCGATTCTCCTCGTTACGATTTTC
520916 ATTTCGCGTTGCGATTCT-CTCGTTACGATTTTC
1 ATTTCGCGTTGCGATTCTCCTCGTTACGATTTTC
* *
520949 ATTTCACATTGCGAT
1 ATTTCGCGTTGCGAT
520964 AGTACTTTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
33 27 0.60
34 18 0.40
ACGTcount: A:0.13, C:0.24, G:0.18, T:0.44
Consensus pattern (34 bp):
ATTTCGCGTTGCGATTCTCCTCGTTACGATTTTC
Found at i:521087 original size:14 final size:14
Alignment explanation
Indices: 521068--521103 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
521058 CATCAATTAA
*
521068 ACAAATCAACTTTT
1 ACAAATCAACCTTT
521082 ACAAATC-ACCTTT
1 ACAAATCAACCTTT
521095 ACAAATCAA
1 ACAAATCAA
521104 TTAAACAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.47, C:0.25, G:0.00, T:0.28
Consensus pattern (14 bp):
ACAAATCAACCTTT
Found at i:522011 original size:171 final size:170
Alignment explanation
Indices: 521727--522069 Score: 677
Period size: 171 Copynumber: 2.0 Consensus size: 170
521717 GCTATGGAAA
521727 ATGAAACGACCAGGATTGTTACCCCAAAACAGGCCAAACCAGGGCTACAGAACTCAAGAAGGACT
1 ATGAAACGACCAGGATTGTTACCCCAAAACAGGCCAAACCAGGGCTACAGAACTCAAGAAGGACT
521792 CGAACTGAAGAGTTTCAAGCCGGGTCTCCACTGGTTTTGCTTAGATCAATCGAGTTTATTGAAAA
66 CGAACTGAAGAGTTTCAAGCCGGGTCTCCACTGGTTTTGCTTAGATCAATCGAGTTTATTGAAAA
521857 TTAGTCTCTCATGGTCTCTCTTCTTCGTGCTTGCCGTCGG
131 TTAGTCTCTCATGGTCTCTCTTCTTCGTGCTTGCCGTCGG
521897 ATGAAACGACCAGGATTTGTTACCCCAAAACAGGCCAAACCAGGGCTACAGAACTCAAGAAGGAC
1 ATGAAACGACCAGGA-TTGTTACCCCAAAACAGGCCAAACCAGGGCTACAGAACTCAAGAAGGAC
521962 TCGAACTGAAGAGTTTCAAGCCGGGTCTCCACTGGTTTTGCTTAGATCAATCGAGTTTATTGAAA
65 TCGAACTGAAGAGTTTCAAGCCGGGTCTCCACTGGTTTTGCTTAGATCAATCGAGTTTATTGAAA
522027 ATTAGTCTCTCATGGTCTCTCTTCTTCGTGCTTGCCGTCGG
130 ATTAGTCTCTCATGGTCTCTCTTCTTCGTGCTTGCCGTCGG
522068 AT
1 AT
522070 TCCTATCATT
Statistics
Matches: 172, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
170 15 0.09
171 157 0.91
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.27
Consensus pattern (170 bp):
ATGAAACGACCAGGATTGTTACCCCAAAACAGGCCAAACCAGGGCTACAGAACTCAAGAAGGACT
CGAACTGAAGAGTTTCAAGCCGGGTCTCCACTGGTTTTGCTTAGATCAATCGAGTTTATTGAAAA
TTAGTCTCTCATGGTCTCTCTTCTTCGTGCTTGCCGTCGG
Found at i:522856 original size:92 final size:87
Alignment explanation
Indices: 522735--522915 Score: 240
Period size: 88 Copynumber: 2.0 Consensus size: 87
522725 ATTTCAAACT
* *
522735 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
1 TTCAACC-AAAGACAAAACAAAGAAAAATACTAACTTCACAGTGTT----AATAAACAGTTTAGC
522800 AGAATTGGCAGCAACCGAATAA-ATTTAC
61 AGAATTGGCAGCAA-CGAA-AATATTTAC
* *
522828 TTCAACC-AAGATAAAACAAAAGAAAAATACTAACTTCACAGTGTTAATAAACAGTTTAGCAGTA
1 TTCAACCAAAGACAAAAC-AAAGAAAAATACTAACTTCACAGTGTTAATAAACAGTTTAGCAGAA
522892 TTGGCAGCAACGAAAATATTTAC
65 TTGGCAGCAACGAAAATATTTAC
522915 T
1 T
522916 AAGCAATCTA
Statistics
Matches: 82, Mismatches: 4, Indels: 10
0.85 0.04 0.10
Matches are distributed among these distances:
86 2 0.02
87 11 0.13
88 27 0.33
91 9 0.11
92 26 0.32
93 7 0.09
ACGTcount: A:0.47, C:0.18, G:0.13, T:0.23
Consensus pattern (87 bp):
TTCAACCAAAGACAAAACAAAGAAAAATACTAACTTCACAGTGTTAATAAACAGTTTAGCAGAAT
TGGCAGCAACGAAAATATTTAC
Found at i:524652 original size:19 final size:19
Alignment explanation
Indices: 524588--524686 Score: 126
Period size: 19 Copynumber: 5.1 Consensus size: 19
524578 TCTTTTGGTT
*
524588 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
524607 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
524627 GGAAATGACTATCGCAACGC
1 -GAAATGAAAATCGCAACGC
*
524647 GAAATGAAAATCGCATCGC
1 GAAATGAAAATCGCAACGC
*
524666 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
524685 GA
1 GA
524687 TTTTGGTTTC
Statistics
Matches: 69, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
19 37 0.54
20 30 0.43
21 2 0.03
ACGTcount: A:0.43, C:0.19, G:0.23, T:0.14
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:524704 original size:19 final size:19
Alignment explanation
Indices: 524682--524729 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
524672 AAAATCGCAA
*
524682 TGCGATTTTGGTTT-CGCGT
1 TGCGATTTT-ATTTCCGCGT
*
524701 TGCGATAGTTATTTCCGCGT
1 TGCGAT-TTTATTTCCGCGT
524721 TGCGATTTT
1 TGCGATTTT
524730 CATTCACGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.10, C:0.17, G:0.27, T:0.46
Consensus pattern (19 bp):
TGCGATTTTATTTCCGCGT
Found at i:525311 original size:20 final size:20
Alignment explanation
Indices: 525286--525339 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
525276 GATTTTGTAT
525286 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
525306 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
525326 TATCGCATTGCGAT
1 TATCGCATTGCGAT
525340 TTTCCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:525723 original size:33 final size:33
Alignment explanation
Indices: 525681--525747 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
525671 ATCACAGCCG
525681 TTAATCTCCCGAAACCACACCCTTATCATAATC
1 TTAATCTCCCGAAACCACACCCTTATCATAATC
525714 TTAATCTCCCGAAACCACACCCTTATCATAATC
1 TTAATCTCCCGAAACCACACCCTTATCATAATC
525747 T
1 T
525748 CACTGGCATC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.33, C:0.36, G:0.03, T:0.28
Consensus pattern (33 bp):
TTAATCTCCCGAAACCACACCCTTATCATAATC
Found at i:533804 original size:21 final size:21
Alignment explanation
Indices: 533775--533827 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 21
533765 ATAATAGCTA
* *
533775 ACATGATATCTTACTTTAATT
1 ACATAATATCTTACATTAATT
533796 ACATAATATCTTACATTAATT
1 ACATAATATCTTACATTAATT
533817 ACTATATATAT
1 AC-ATA-ATAT
533828 ATATATATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 21 0.75
22 3 0.11
23 4 0.14
ACGTcount: A:0.40, C:0.13, G:0.02, T:0.45
Consensus pattern (21 bp):
ACATAATATCTTACATTAATT
Found at i:533826 original size:2 final size:2
Alignment explanation
Indices: 533819--533861 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
533809 CATTAATTAC
*
533819 TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
533861 T
1 T
533862 CAACCTTTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:534087 original size:30 final size:30
Alignment explanation
Indices: 534043--534118 Score: 91
Period size: 30 Copynumber: 2.5 Consensus size: 30
534033 TGTTTGTGTT
* *
534043 TGTTTGTTTGTTTATTTTTGTAAG-TGTTCA
1 TGTTCGTTTATTTATTTTTG-AAGTTGTTCA
*
534073 TGTTCGTTTATTTATTTTTGAAGTTGTTCG
1 TGTTCGTTTATTTATTTTTGAAGTTGTTCA
* *
534103 TGTTCATTTTTTTATT
1 TGTTCGTTTATTTATT
534119 GTTCGCGAAC
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
29 3 0.08
30 37 0.93
ACGTcount: A:0.13, C:0.05, G:0.17, T:0.64
Consensus pattern (30 bp):
TGTTCGTTTATTTATTTTTGAAGTTGTTCA
Found at i:536079 original size:21 final size:21
Alignment explanation
Indices: 536037--536080 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
536027 TATTGTATAA
* *
536037 TGATGGTGGTGGCGGTAGTGG
1 TGATGGTGGTGACGGGAGTGG
536058 TGATGGTGGTGACGAGGA-TGG
1 TGATGGTGGTGACG-GGAGTGG
536079 TG
1 TG
536081 GATCATCGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 18 0.90
22 2 0.10
ACGTcount: A:0.14, C:0.05, G:0.55, T:0.27
Consensus pattern (21 bp):
TGATGGTGGTGACGGGAGTGG
Found at i:543243 original size:18 final size:17
Alignment explanation
Indices: 543222--543278 Score: 57
Period size: 18 Copynumber: 3.4 Consensus size: 17
543212 CATATTTTAA
543222 AATAAATCAATCTATACT
1 AATAAATCAAT-TATACT
* *
543240 AATAAAT-TATT-TA-A
1 AATAAATCAATTATACT
543254 AATAAATCAATTCATACT
1 AATAAATCAATT-ATACT
543272 AATAAAT
1 AATAAAT
543279 TATTTAAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
14 7 0.23
15 5 0.16
16 1 0.03
17 4 0.13
18 14 0.45
ACGTcount: A:0.54, C:0.11, G:0.00, T:0.35
Consensus pattern (17 bp):
AATAAATCAATTATACT
Found at i:543246 original size:22 final size:21
Alignment explanation
Indices: 543194--543246 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 21
543184 TTCATACAAC
543194 TATAAT-AATAAATCAATCCA
1 TATAATAAATAAATCAATCCA
** *
543214 TATTTTAAAATAAATCAATCTA
1 TATAAT-AAATAAATCAATCCA
543236 TACTAATAAAT
1 TA-TAATAAAT
543247 TATTTAAAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
20 4 0.16
22 19 0.76
23 2 0.08
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.36
Consensus pattern (21 bp):
TATAATAAATAAATCAATCCA
Found at i:543253 original size:32 final size:32
Alignment explanation
Indices: 543217--543378 Score: 186
Period size: 32 Copynumber: 5.4 Consensus size: 32
543207 CAATCCATAT
543217 TTTAAAATAAATCAATCTATACTAATAAATTA
1 TTTAAAATAAATCAATCTATACTAATAAATTA
543249 TTTAAAATAAATCAAT-TCATACTAATAAATTA
1 TTTAAAATAAATCAATCT-ATACTAATAAATTA
*
543281 TTTAAAATAAATTAATC----C--AT--A-T-
1 TTTAAAATAAATCAATCTATACTAATAAATTA
*
543303 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCTATACTAATAAATTA
*
543335 TTTAAAATAAATCAAT-TCATATTAATAAATTA
1 TTTAAAATAAATCAATCT-ATACTAATAAATTA
*
543367 TTAAAAATAAAT
1 TTTAAAATAAAT
543379 TATTTTAAAA
Statistics
Matches: 112, Mismatches: 5, Indels: 26
0.78 0.03 0.18
Matches are distributed among these distances:
22 16 0.14
23 1 0.01
24 1 0.01
26 3 0.03
28 3 0.03
30 1 0.01
31 2 0.02
32 85 0.76
ACGTcount: A:0.54, C:0.09, G:0.00, T:0.38
Consensus pattern (32 bp):
TTTAAAATAAATCAATCTATACTAATAAATTA
Found at i:543259 original size:14 final size:14
Alignment explanation
Indices: 543240--543294 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
543230 AATCTATACT
543240 AATAAATTATTTAA
1 AATAAATTATTTAA
* *
543254 AATAAATCAATTCATACT
1 AATAAAT-TATT--TA-A
543272 AATAAATTATTTAA
1 AATAAATTATTTAA
543286 AATAAATTA
1 AATAAATTA
543295 ATCCATATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
14 16 0.48
15 5 0.15
17 5 0.15
18 7 0.21
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (14 bp):
AATAAATTATTTAA
Found at i:543296 original size:22 final size:22
Alignment explanation
Indices: 543271--543314 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
543261 CAATTCATAC
543271 TAATAAAT-TATTTAAAATAAAT
1 TAATAAATAT-TTTAAAATAAAT
**
543293 TAATCCATATTTTAAAATAAAT
1 TAATAAATATTTTAAAATAAAT
543315 CAATCCATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 18 0.95
23 1 0.05
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.41
Consensus pattern (22 bp):
TAATAAATATTTTAAAATAAAT
Found at i:543307 original size:54 final size:54
Alignment explanation
Indices: 543249--543357 Score: 191
Period size: 54 Copynumber: 2.0 Consensus size: 54
543239 TAATAAATTA
* *
543249 TTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATTAATCCATAT
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAT
*
543303 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATTCATAT
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAT
543357 T
1 T
543358 AATAAATTAT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.39
Consensus pattern (54 bp):
TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAT
Found at i:543319 original size:22 final size:22
Alignment explanation
Indices: 543281--543323 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
543271 TAATAAATTA
*
543281 TTTAAAATAAATTAATCCATAT
1 TTTAAAATAAATCAATCCATAT
543303 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
543324 CTAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:543325 original size:86 final size:85
Alignment explanation
Indices: 543157--543380 Score: 343
Period size: 86 Copynumber: 2.7 Consensus size: 85
543147 TTCAGTTTTA
* *
543157 ACTAATAAATTATTTAAAATAAATCAATTCATAC-AACT--A-TA--ATAATAAATCAATCCATA
1 ACTAATAAATTATTTAAAATAAATCAATTCATACTAA-TAAATTATTAAAATAAATTAATCCATA
*
543216 TTTTAAAATAAATCAATCTAT
65 TTTTAAAATAAATCAATCCAT
543237 ACTAATAAATTATTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATTAATCCATA
1 ACTAATAAATTATTTAAAATAAATCAATTCATACTAATAAATTA-TTAAAATAAATTAATCCATA
543302 TTTTAAAATAAATCAATCCAT
65 TTTTAAAATAAATCAATCCAT
*
543323 ACTAATAAATTATTTAAAATAAATCAATTCATATTAATAAATTATTAAAAATAAATTA
1 ACTAATAAATTATTTAAAATAAATCAATTCATACTAATAAATTATT-AAAATAAATTA
543381 TTTTAAAATA
Statistics
Matches: 132, Mismatches: 4, Indels: 10
0.90 0.03 0.07
Matches are distributed among these distances:
80 35 0.27
81 2 0.02
82 1 0.01
83 2 0.02
85 2 0.02
86 90 0.68
ACGTcount: A:0.54, C:0.10, G:0.00, T:0.37
Consensus pattern (85 bp):
ACTAATAAATTATTTAAAATAAATCAATTCATACTAATAAATTATTAAAATAAATTAATCCATAT
TTTAAAATAAATCAATCCAT
Found at i:543332 original size:22 final size:22
Alignment explanation
Indices: 543283--543331 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
543273 ATAAATTATT
* **
543283 TAAAATAAATTAATCCATATTT
1 TAAAATAAATCAATCCATATAA
543305 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
543328 TAAA
1 TAAA
543332 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:543345 original size:14 final size:14
Alignment explanation
Indices: 543326--543393 Score: 64
Period size: 14 Copynumber: 4.5 Consensus size: 14
543316 AATCCATACT
543326 AATAAATTATTTAA
1 AATAAATTATTTAA
* *
543340 AATAAATCAATTCATATT
1 AATAAAT-TATT--TA-A
*
543358 AATAAATTATTAAA
1 AATAAATTATTTAA
543372 AATAAATTATTTTAA
1 AATAAATTA-TTTAA
543387 AATAAAT
1 AATAAAT
543394 AACCTTATTA
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
14 16 0.37
15 15 0.35
17 5 0.12
18 7 0.16
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (14 bp):
AATAAATTATTTAA
Found at i:546724 original size:14 final size:14
Alignment explanation
Indices: 546705--546735 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
546695 AATAAATTTG
*
546705 ACTCGACTTAAATA
1 ACTCGAATTAAATA
546719 ACTCGAATTAAATA
1 ACTCGAATTAAATA
546733 ACT
1 ACT
546736 GTAAAAGAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.45, C:0.19, G:0.06, T:0.29
Consensus pattern (14 bp):
ACTCGAATTAAATA
Found at i:547191 original size:20 final size:20
Alignment explanation
Indices: 547166--547217 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
547156 ACTGTAGACT
*
547166 ATCGCAACGCGAACTGGAAA
1 ATCGCAACGCGAAATGGAAA
547186 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
547206 ATCGCAACGCGA
1 ATCGCAACGCGA
547218 TTTTCAACTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.40, C:0.25, G:0.25, T:0.10
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:547232 original size:21 final size:21
Alignment explanation
Indices: 547206--547259 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
547196 GAAATGGAAA
547206 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
*
547227 ATCGCAACACGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
547248 ATCGCAACGCGA
1 ATCGCAACGCGA
547260 AATGCAACGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.31, C:0.30, G:0.15, T:0.24
Consensus pattern (21 bp):
ATCGCAACGCGATTTTCAACT
Found at i:547267 original size:21 final size:21
Alignment explanation
Indices: 547163--547267 Score: 88
Period size: 21 Copynumber: 5.1 Consensus size: 21
547153 ACAACTGTAG
* *
547163 ACTATCGCAACGCGAACTGGA
1 ACTATCGCAACGCGAAATGCA
* *
547184 A-AATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGAAATGCA
* ** *
547204 A-AATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGCA
* ** *
547224 ACTATCGCAACACGATTTTCA
1 ACTATCGCAACGCGAAATGCA
547245 ACTATCGCAACGCGAAATGCA
1 ACTATCGCAACGCGAAATGCA
547266 AC
1 AC
547268 GCGAATTTAT
Statistics
Matches: 71, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
20 34 0.48
21 37 0.52
ACGTcount: A:0.37, C:0.27, G:0.18, T:0.18
Consensus pattern (21 bp):
ACTATCGCAACGCGAAATGCA
Found at i:552397 original size:2 final size:2
Alignment explanation
Indices: 552392--552432 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
552382 ATTTTTTCAA
* *
552392 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
552433 AAAGATAAGT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (2 bp):
AT
Found at i:554472 original size:35 final size:37
Alignment explanation
Indices: 554400--554495 Score: 106
Period size: 35 Copynumber: 2.6 Consensus size: 37
554390 ATGCTTTTTT
* * * * * * *
554400 AAAACTATATATTATACATGTTTTTAAAAACGTTTTA
1 AAAATTATATATAATATATATTTTCAGAAACGGTTTA
554437 AAAATT-T-TATAATATATATTTTCAGAAACGGTTTA
1 AAAATTATATATAATATATATTTTCAGAAACGGTTTA
*
554472 AAAATTATATATTATATATATTTT
1 AAAATTATATATAATATATATTTT
554496 TAAAATGTTT
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
35 28 0.57
36 2 0.04
37 19 0.39
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (37 bp):
AAAATTATATATAATATATATTTTCAGAAACGGTTTA
Found at i:554519 original size:38 final size:36
Alignment explanation
Indices: 554395--554723 Score: 211
Period size: 37 Copynumber: 8.8 Consensus size: 36
554385 CCAAAATGCT
* * * *
554395 TTTTTAAAACTATATATTATACATGTTTTTAAAAACG
1 TTTTAAAAACTATATATTATATATATTTTT-AAAATG
* * * *
554432 TTTTAAAAA-T-TTTATAATATATATTTTCAGAAACG
1 TTTTAAAAACTATATATTATATATATTTTTA-AAATG
* *
554467 GTTTAAAAATTATATATTATATATATTTTTAAAATG
1 TTTTAAAAACTATATATTATATATATTTTTAAAATG
* * * * **
554503 TTTTTCAAAAATTATATAATATTTAAATGTTTTTAAAAAA
1 -TTTT-AAAAACTATAT-AT-TATATATATTTTTAAAATG
** * *
554543 AATTCAAAACAATATATTATATA-ATTTTTCAAAAATG
1 TTTTAAAAACTATATATTATATATATTTTT--AAAATG
554580 ATTTTAAAAACTATATATTATATATATTTTTTCTAAAATG
1 -TTTTAAAAACTATATATTATATATA--TTTT-TAAAATG
** *
554620 TTTTAAAAACTATATA--ATATATAGTTTCAACAAATA
1 TTTTAAAAACTATATATTATATATA-TTTTTA-AAATG
* * *
554656 TTTTTAAAACTATATATTATATACATTTTCAAAATG
1 TTTTAAAAACTATATATTATATATATTTTTAAAATG
*
554692 TTTTCAAAAATTATGTATATTATA-AGTATTTT
1 TTTT-AAAAACTA--TATATTATATA-TATTTT
554724 CAAAGACCGT
Statistics
Matches: 228, Mismatches: 43, Indels: 40
0.73 0.14 0.13
Matches are distributed among these distances:
34 1 0.00
35 32 0.14
36 40 0.18
37 50 0.22
38 45 0.20
39 35 0.15
40 20 0.09
41 4 0.02
42 1 0.00
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.46
Consensus pattern (36 bp):
TTTTAAAAACTATATATTATATATATTTTTAAAATG
Found at i:554546 original size:31 final size:31
Alignment explanation
Indices: 554482--554542 Score: 90
Period size: 29 Copynumber: 2.0 Consensus size: 31
554472 AAAATTATAT
* *
554482 ATTATATATATTTTTAAAATGTTTTTCAAAA
1 ATTATATATATATTTAAAATGTTTTTAAAAA
554513 ATTATATA-ATATTT-AAATGTTTTTAAAAA
1 ATTATATATATATTTAAAATGTTTTTAAAAA
554542 A
1 A
554543 AATTCAAAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 15 0.54
30 5 0.18
31 8 0.29
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (31 bp):
ATTATATATATATTTAAAATGTTTTTAAAAA
Found at i:555508 original size:33 final size:33
Alignment explanation
Indices: 555466--555531 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
555456 GCGGAGTCGA
555466 ACTCGAAGGTCTTTTGGTCACAGATAACCCTTC
1 ACTCGAAGGTCTTTTGGTCACAGATAACCCTTC
555499 ACTCGAAGGTCTTTTGGTCACAGATAACCCTTC
1 ACTCGAAGGTCTTTTGGTCACAGATAACCCTTC
555532 TAGCCTTGAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.24, C:0.27, G:0.18, T:0.30
Consensus pattern (33 bp):
ACTCGAAGGTCTTTTGGTCACAGATAACCCTTC
Found at i:555720 original size:84 final size:84
Alignment explanation
Indices: 555499--555884 Score: 473
Period size: 81 Copynumber: 4.7 Consensus size: 84
555489 ATAACCCTTC
555499 ACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCC
1 ACTCGAAGGTCTTTTGGT-ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCC
*
555564 TCGAAGCTGAGTGTAATCGA
65 TCGAAGCTGAGCGTAATCGA
** * * * * * *
555584 ACTCGGGGGTC-TTTGG--CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG-CCT
1 ACTCGAAGGTCTTTTGGTACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCT
* * *
555645 TGGAGCTGAGCGTAGTCGA
66 CGAAGCTGAGCGTAATCGA
555664 ACTCGAAGGTCTTTTGGTTACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCC
1 ACTCGAAGGTCTTTTGG-TACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCC
*
555729 TCGAAGCTGAGTGTAATCGA
65 TCGAAGCTGAGCGTAATCGA
** * * * * * *
555749 ACTCGGGGGTC-TTTGG--CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG-CCT
1 ACTCGAAGGTCTTTTGGTACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCT
* * *
555810 TGGAGCTGAGCGTAGTCGA
66 CGAAGCTGAGCGTAATCGA
555829 ACTCGAAGGTCTTTTGGTTACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAAT
1 ACTCGAAGGTCTTTTGG-TACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAAT
555885 AGTTTGTTTA
Statistics
Matches: 248, Mismatches: 44, Indels: 19
0.80 0.14 0.06
Matches are distributed among these distances:
80 54 0.22
81 82 0.33
84 76 0.31
85 36 0.15
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.30
Consensus pattern (84 bp):
ACTCGAAGGTCTTTTGGTACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCT
CGAAGCTGAGCGTAATCGA
Done.