Multiple sequence alignment - TraesCS2B01G469500

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS2B01G469500 chr2B 100.000 3194 0 0 1 3194 665857191 665860384 0.000000e+00 5899.0
1 TraesCS2B01G469500 chr2D 92.300 2000 91 26 335 2295 557683376 557685351 0.000000e+00 2782.0
2 TraesCS2B01G469500 chr2D 84.921 630 60 25 2495 3105 557685547 557686160 3.520000e-169 604.0
3 TraesCS2B01G469500 chr2D 95.133 226 11 0 1 226 557683063 557683288 1.090000e-94 357.0
4 TraesCS2B01G469500 chr2D 86.722 241 24 2 1 241 557666401 557666633 8.790000e-66 261.0
5 TraesCS2B01G469500 chr2D 88.000 75 2 1 3107 3181 557688470 557688537 7.340000e-12 82.4
6 TraesCS2B01G469500 chr2A 91.176 1904 108 20 389 2262 698091986 698093859 0.000000e+00 2531.0
7 TraesCS2B01G469500 chr2A 92.771 249 14 1 1 245 698091671 698091919 1.090000e-94 357.0
8 TraesCS2B01G469500 chr2A 87.879 297 22 7 2898 3181 698099883 698100178 1.420000e-88 337.0
9 TraesCS2B01G469500 chr2A 81.743 241 32 7 1 241 698083554 698083782 1.170000e-44 191.0
10 TraesCS2B01G469500 chr6D 84.122 655 84 11 1028 1672 354369085 354369729 1.630000e-172 616.0
11 TraesCS2B01G469500 chr6A 83.792 654 88 9 1028 1672 487771312 487770668 3.520000e-169 604.0
12 TraesCS2B01G469500 chr4D 95.556 45 2 0 245 289 497247555 497247599 4.420000e-09 73.1
13 TraesCS2B01G469500 chr4A 93.617 47 3 0 244 290 141572432 141572386 1.590000e-08 71.3
14 TraesCS2B01G469500 chr4A 90.385 52 3 1 240 289 17854612 17854663 2.060000e-07 67.6
15 TraesCS2B01G469500 chr7D 93.478 46 3 0 244 289 591222195 591222240 5.720000e-08 69.4
16 TraesCS2B01G469500 chr7B 93.478 46 3 0 244 289 635699559 635699604 5.720000e-08 69.4
17 TraesCS2B01G469500 chr3A 93.617 47 2 1 249 294 456381680 456381726 5.720000e-08 69.4
18 TraesCS2B01G469500 chr7A 91.667 48 4 0 243 290 56727791 56727744 2.060000e-07 67.6
19 TraesCS2B01G469500 chr1D 90.385 52 3 2 239 290 80001395 80001444 2.060000e-07 67.6
20 TraesCS2B01G469500 chr1D 91.837 49 3 1 242 289 418301154 418301202 2.060000e-07 67.6


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2B01G469500 chr2B 665857191 665860384 3193 False 5899.00 5899 100.0000 1 3194 1 chr2B.!!$F1 3193
1 TraesCS2B01G469500 chr2D 557683063 557688537 5474 False 956.35 2782 90.0885 1 3181 4 chr2D.!!$F2 3180
2 TraesCS2B01G469500 chr2A 698091671 698093859 2188 False 1444.00 2531 91.9735 1 2262 2 chr2A.!!$F3 2261
3 TraesCS2B01G469500 chr6D 354369085 354369729 644 False 616.00 616 84.1220 1028 1672 1 chr6D.!!$F1 644
4 TraesCS2B01G469500 chr6A 487770668 487771312 644 True 604.00 604 83.7920 1028 1672 1 chr6A.!!$R1 644

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
951 1025 0.037790 GTCTCTGTTTCTCGCCTGCT 60.038 55.0 0.0 0.0 0.0 4.24 F
990 1067 0.469144 GGTGCTAGGAGGAGGAGGAG 60.469 65.0 0.0 0.0 0.0 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1815 1903 0.033991 CCTCCTCTGTTCCCTCTCGA 60.034 60.0 0.0 0.0 0.0 4.04 R
2383 2530 0.244178 GAGTGGTGGAGGAGACGAAC 59.756 60.0 0.0 0.0 0.0 3.95 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 52 0.387929 GCCATCATCGTCTCCCGTTA 59.612 55.000 0.00 0.00 37.94 3.18
169 174 0.323178 AGCTCTGAATGCCACCCTTG 60.323 55.000 0.00 0.00 0.00 3.61
186 191 5.358160 CACCCTTGATAAATCTCTTTGGTCC 59.642 44.000 0.00 0.00 0.00 4.46
213 218 6.070596 TCAGATCACTTTGGAATTAGAGCAGA 60.071 38.462 0.00 0.00 0.00 4.26
230 235 3.561725 AGCAGACTTTAGCTTTCACACAC 59.438 43.478 0.00 0.00 38.01 3.82
236 241 6.096846 AGACTTTAGCTTTCACACACCAAATT 59.903 34.615 0.00 0.00 0.00 1.82
238 250 7.777095 ACTTTAGCTTTCACACACCAAATTAA 58.223 30.769 0.00 0.00 0.00 1.40
245 257 8.558700 GCTTTCACACACCAAATTAATGAAAAT 58.441 29.630 0.00 0.00 35.00 1.82
255 267 9.990868 ACCAAATTAATGAAAATACTACTCCCT 57.009 29.630 0.00 0.00 0.00 4.20
261 273 7.741554 AATGAAAATACTACTCCCTCACTCT 57.258 36.000 0.00 0.00 0.00 3.24
262 274 6.777213 TGAAAATACTACTCCCTCACTCTC 57.223 41.667 0.00 0.00 0.00 3.20
263 275 6.253758 TGAAAATACTACTCCCTCACTCTCA 58.746 40.000 0.00 0.00 0.00 3.27
264 276 6.897966 TGAAAATACTACTCCCTCACTCTCAT 59.102 38.462 0.00 0.00 0.00 2.90
265 277 8.059461 TGAAAATACTACTCCCTCACTCTCATA 58.941 37.037 0.00 0.00 0.00 2.15
266 278 8.840200 AAAATACTACTCCCTCACTCTCATAA 57.160 34.615 0.00 0.00 0.00 1.90
267 279 9.440761 AAAATACTACTCCCTCACTCTCATAAT 57.559 33.333 0.00 0.00 0.00 1.28
272 284 9.747898 ACTACTCCCTCACTCTCATAATATAAG 57.252 37.037 0.00 0.00 0.00 1.73
273 285 9.967451 CTACTCCCTCACTCTCATAATATAAGA 57.033 37.037 0.00 0.00 0.00 2.10
274 286 8.877864 ACTCCCTCACTCTCATAATATAAGAG 57.122 38.462 0.00 0.00 41.84 2.85
275 287 7.396055 ACTCCCTCACTCTCATAATATAAGAGC 59.604 40.741 0.37 0.00 40.15 4.09
276 288 6.375736 TCCCTCACTCTCATAATATAAGAGCG 59.624 42.308 0.37 0.00 40.15 5.03
277 289 6.151985 CCCTCACTCTCATAATATAAGAGCGT 59.848 42.308 0.37 0.00 40.15 5.07
278 290 7.309499 CCCTCACTCTCATAATATAAGAGCGTT 60.309 40.741 0.37 0.00 40.15 4.84
279 291 8.085296 CCTCACTCTCATAATATAAGAGCGTTT 58.915 37.037 0.37 0.00 40.15 3.60
280 292 9.469807 CTCACTCTCATAATATAAGAGCGTTTT 57.530 33.333 0.37 0.00 40.15 2.43
281 293 9.817809 TCACTCTCATAATATAAGAGCGTTTTT 57.182 29.630 0.37 0.00 40.15 1.94
303 315 8.441312 TTTTTACACTATGAAACCGAGAAAGT 57.559 30.769 0.00 0.00 0.00 2.66
332 375 7.730364 TTGAAAACTACTCTTGTGAGATTCC 57.270 36.000 0.00 0.00 42.73 3.01
339 382 4.256920 ACTCTTGTGAGATTCCATTTCCG 58.743 43.478 0.00 0.00 42.73 4.30
342 385 5.800296 TCTTGTGAGATTCCATTTCCGTTA 58.200 37.500 0.00 0.00 0.00 3.18
361 405 6.373216 TCCGTTATTTTTGGGAACTATCAGTG 59.627 38.462 0.00 0.00 0.00 3.66
370 414 3.879892 GGGAACTATCAGTGGAAGATTGC 59.120 47.826 0.00 0.00 0.00 3.56
415 465 8.928733 GCAAATTATCATGTTCATGTTTTCTGT 58.071 29.630 11.73 0.00 0.00 3.41
426 476 8.724229 TGTTCATGTTTTCTGTTCATCATCTAG 58.276 33.333 0.00 0.00 0.00 2.43
459 513 4.635765 ACAATCATATTTCCAGTGGACACG 59.364 41.667 12.69 0.00 36.20 4.49
513 567 3.978571 GAGGAAAGGGACGGCAGCC 62.979 68.421 0.00 0.00 0.00 4.85
539 593 0.758734 GGGCAGGGCAAAGAAAAAGT 59.241 50.000 0.00 0.00 0.00 2.66
604 659 0.185901 AGATGCCAACAACCACCAGT 59.814 50.000 0.00 0.00 0.00 4.00
605 660 0.598065 GATGCCAACAACCACCAGTC 59.402 55.000 0.00 0.00 0.00 3.51
606 661 0.827507 ATGCCAACAACCACCAGTCC 60.828 55.000 0.00 0.00 0.00 3.85
607 662 1.454847 GCCAACAACCACCAGTCCA 60.455 57.895 0.00 0.00 0.00 4.02
608 663 1.455383 GCCAACAACCACCAGTCCAG 61.455 60.000 0.00 0.00 0.00 3.86
618 673 1.122019 ACCAGTCCAGTCCAGTCCAC 61.122 60.000 0.00 0.00 0.00 4.02
715 773 1.315690 CCAGCGCCATCATCTGATTT 58.684 50.000 2.29 0.00 31.21 2.17
769 827 2.486548 CCACTTCCCAACCTCGAGAAAA 60.487 50.000 15.71 0.00 0.00 2.29
807 865 1.300542 GCCTACGCAGATGCTCCTC 60.301 63.158 2.95 0.00 39.32 3.71
816 874 1.068921 GATGCTCCTCCGCCTTCTC 59.931 63.158 0.00 0.00 0.00 2.87
856 914 1.556911 GATTTGGCCCAGAGAGACTCA 59.443 52.381 0.00 0.00 32.06 3.41
881 939 1.285078 TCCTCTGCTAGTACCTGAGCA 59.715 52.381 12.61 12.61 46.24 4.26
887 945 1.853963 CTAGTACCTGAGCACCCAGT 58.146 55.000 0.00 0.00 32.43 4.00
895 953 3.343788 GAGCACCCAGTCGTCTCGG 62.344 68.421 0.00 0.00 0.00 4.63
896 954 3.371063 GCACCCAGTCGTCTCGGA 61.371 66.667 0.00 0.00 0.00 4.55
897 955 2.567049 CACCCAGTCGTCTCGGAC 59.433 66.667 0.00 0.00 37.19 4.79
945 1019 3.906998 ACACATCTGTCTCTGTTTCTCG 58.093 45.455 0.00 0.00 0.00 4.04
951 1025 0.037790 GTCTCTGTTTCTCGCCTGCT 60.038 55.000 0.00 0.00 0.00 4.24
989 1066 1.221909 TGGTGCTAGGAGGAGGAGGA 61.222 60.000 0.00 0.00 0.00 3.71
990 1067 0.469144 GGTGCTAGGAGGAGGAGGAG 60.469 65.000 0.00 0.00 0.00 3.69
999 1076 3.773154 GAGGAGGAGGGGGAGGCT 61.773 72.222 0.00 0.00 0.00 4.58
1083 1162 3.791586 GACTGCTCCCAGGGGCTC 61.792 72.222 10.51 0.00 43.53 4.70
1218 1306 3.945434 GCCATCATCGGCGTGCTG 61.945 66.667 6.85 6.57 43.52 4.41
1510 1598 4.116328 TCTGCCTCGGCGAGTTCG 62.116 66.667 32.41 19.86 45.51 3.95
1626 1714 2.741985 TGCCGCTCCAACATCACG 60.742 61.111 0.00 0.00 0.00 4.35
1743 1831 2.034305 GGATGAATTGGAGAGCATGTGC 59.966 50.000 0.00 0.00 42.49 4.57
1811 1899 1.215423 TGATGATCAGGAGACGGAGGA 59.785 52.381 0.09 0.00 38.16 3.71
1815 1903 0.333312 ATCAGGAGACGGAGGACAGT 59.667 55.000 0.00 0.00 38.16 3.55
1825 1913 0.323542 GGAGGACAGTCGAGAGGGAA 60.324 60.000 0.00 0.00 0.00 3.97
1863 1957 0.179048 CCAATGGCACGGCTGAGATA 60.179 55.000 0.00 0.00 0.00 1.98
2166 2260 2.741122 GAGTCGTCGTCGATTCAGAT 57.259 50.000 19.22 0.00 46.81 2.90
2184 2278 0.469917 ATAATCCAGTGCGAGGTGGG 59.530 55.000 0.00 0.00 34.27 4.61
2237 2350 0.099436 GTTTCTGCGCATGATGGGAC 59.901 55.000 12.24 5.43 31.21 4.46
2242 2355 3.424300 CGCATGATGGGACGCAAT 58.576 55.556 3.03 0.00 31.21 3.56
2259 2372 4.067192 CGCAATTGAGGACCATATCATCA 58.933 43.478 10.34 0.00 46.17 3.07
2260 2373 4.698780 CGCAATTGAGGACCATATCATCAT 59.301 41.667 10.34 0.00 46.98 2.45
2261 2374 5.876460 CGCAATTGAGGACCATATCATCATA 59.124 40.000 10.34 0.00 46.98 2.15
2262 2375 6.183360 CGCAATTGAGGACCATATCATCATAC 60.183 42.308 10.34 0.00 46.98 2.39
2263 2376 6.656270 GCAATTGAGGACCATATCATCATACA 59.344 38.462 10.34 0.00 46.98 2.29
2295 2408 0.805614 AGATGTCGTCGTCCTGTGAG 59.194 55.000 0.00 0.00 0.00 3.51
2314 2458 3.389329 TGAGATGCTTGGGTAAGATCTCC 59.611 47.826 17.11 0.00 41.16 3.71
2316 2460 3.390639 AGATGCTTGGGTAAGATCTCCTG 59.609 47.826 0.00 0.00 35.92 3.86
2322 2466 3.994317 TGGGTAAGATCTCCTGTGATGA 58.006 45.455 0.00 0.00 0.00 2.92
2331 2475 5.539574 AGATCTCCTGTGATGATAGTTCAGG 59.460 44.000 0.00 0.00 44.69 3.86
2337 2481 1.069204 TGATGATAGTTCAGGAGGCGC 59.931 52.381 0.00 0.00 34.73 6.53
2344 2488 1.687146 TTCAGGAGGCGCTGGATCT 60.687 57.895 7.64 0.00 0.00 2.75
2350 2494 1.432270 GAGGCGCTGGATCTTTTCGG 61.432 60.000 7.64 0.00 0.00 4.30
2401 2548 1.186267 GGTTCGTCTCCTCCACCACT 61.186 60.000 0.00 0.00 0.00 4.00
2402 2549 0.244178 GTTCGTCTCCTCCACCACTC 59.756 60.000 0.00 0.00 0.00 3.51
2403 2550 0.178973 TTCGTCTCCTCCACCACTCA 60.179 55.000 0.00 0.00 0.00 3.41
2404 2551 0.609406 TCGTCTCCTCCACCACTCAG 60.609 60.000 0.00 0.00 0.00 3.35
2405 2552 0.896019 CGTCTCCTCCACCACTCAGT 60.896 60.000 0.00 0.00 0.00 3.41
2406 2553 0.892063 GTCTCCTCCACCACTCAGTC 59.108 60.000 0.00 0.00 0.00 3.51
2407 2554 0.251832 TCTCCTCCACCACTCAGTCC 60.252 60.000 0.00 0.00 0.00 3.85
2408 2555 0.542938 CTCCTCCACCACTCAGTCCA 60.543 60.000 0.00 0.00 0.00 4.02
2409 2556 0.117140 TCCTCCACCACTCAGTCCAT 59.883 55.000 0.00 0.00 0.00 3.41
2411 2558 1.339438 CCTCCACCACTCAGTCCATTG 60.339 57.143 0.00 0.00 0.00 2.82
2413 2560 2.567169 CTCCACCACTCAGTCCATTGTA 59.433 50.000 0.00 0.00 0.00 2.41
2434 2581 2.653726 TCAGTGGACATGTTTTGCTGT 58.346 42.857 0.00 0.00 0.00 4.40
2435 2582 3.023119 TCAGTGGACATGTTTTGCTGTT 58.977 40.909 0.00 0.00 0.00 3.16
2445 2592 4.811555 TGTTTTGCTGTTAGTGCAGTAG 57.188 40.909 0.72 0.00 41.71 2.57
2446 2593 4.196193 TGTTTTGCTGTTAGTGCAGTAGT 58.804 39.130 0.72 0.00 41.71 2.73
2447 2594 5.361427 TGTTTTGCTGTTAGTGCAGTAGTA 58.639 37.500 0.72 0.00 41.71 1.82
2459 2606 2.897326 TGCAGTAGTAACAGGCTCAAGA 59.103 45.455 0.00 0.00 0.00 3.02
2460 2607 3.515502 TGCAGTAGTAACAGGCTCAAGAT 59.484 43.478 0.00 0.00 0.00 2.40
2461 2608 4.020218 TGCAGTAGTAACAGGCTCAAGATT 60.020 41.667 0.00 0.00 0.00 2.40
2462 2609 4.938226 GCAGTAGTAACAGGCTCAAGATTT 59.062 41.667 0.00 0.00 0.00 2.17
2463 2610 5.064071 GCAGTAGTAACAGGCTCAAGATTTC 59.936 44.000 0.00 0.00 0.00 2.17
2464 2611 5.582665 CAGTAGTAACAGGCTCAAGATTTCC 59.417 44.000 0.00 0.00 0.00 3.13
2465 2612 3.956744 AGTAACAGGCTCAAGATTTCCC 58.043 45.455 0.00 0.00 0.00 3.97
2466 2613 2.222227 AACAGGCTCAAGATTTCCCC 57.778 50.000 0.00 0.00 0.00 4.81
2467 2614 0.332972 ACAGGCTCAAGATTTCCCCC 59.667 55.000 0.00 0.00 0.00 5.40
2485 2632 3.567478 CCCCCTCGAATGATCTTTTCT 57.433 47.619 0.00 0.00 0.00 2.52
2486 2633 3.891049 CCCCCTCGAATGATCTTTTCTT 58.109 45.455 0.00 0.00 0.00 2.52
2487 2634 4.273318 CCCCCTCGAATGATCTTTTCTTT 58.727 43.478 0.00 0.00 0.00 2.52
2488 2635 4.336713 CCCCCTCGAATGATCTTTTCTTTC 59.663 45.833 0.00 0.00 35.94 2.62
2489 2636 4.943705 CCCCTCGAATGATCTTTTCTTTCA 59.056 41.667 0.00 0.00 38.03 2.69
2490 2637 5.163713 CCCCTCGAATGATCTTTTCTTTCAC 60.164 44.000 0.00 0.00 38.03 3.18
2491 2638 5.645497 CCCTCGAATGATCTTTTCTTTCACT 59.355 40.000 0.00 0.00 38.03 3.41
2492 2639 6.402983 CCCTCGAATGATCTTTTCTTTCACTG 60.403 42.308 0.00 0.00 38.03 3.66
2493 2640 5.931532 TCGAATGATCTTTTCTTTCACTGC 58.068 37.500 0.00 0.00 38.03 4.40
2509 2656 5.378292 TCACTGCTTTTGTGTGTGTTTAA 57.622 34.783 0.00 0.00 36.83 1.52
2510 2657 5.157781 TCACTGCTTTTGTGTGTGTTTAAC 58.842 37.500 0.00 0.00 36.83 2.01
2512 2659 4.219725 ACTGCTTTTGTGTGTGTTTAACCT 59.780 37.500 0.00 0.00 0.00 3.50
2515 2662 5.406780 TGCTTTTGTGTGTGTTTAACCTTTG 59.593 36.000 0.00 0.00 0.00 2.77
2516 2663 5.670094 GCTTTTGTGTGTGTTTAACCTTTGC 60.670 40.000 0.00 0.00 0.00 3.68
2517 2664 4.521130 TTGTGTGTGTTTAACCTTTGCA 57.479 36.364 0.00 0.00 0.00 4.08
2523 2670 7.063544 TGTGTGTGTTTAACCTTTGCAAATTAC 59.936 33.333 13.23 2.29 0.00 1.89
2537 2684 4.517453 TGCAAATTACCTGTAAAGCGAGTT 59.483 37.500 0.00 0.00 0.00 3.01
2549 2696 3.813529 AAGCGAGTTTGAAATCCGAAG 57.186 42.857 6.19 0.00 0.00 3.79
2568 2715 5.975410 GAAGGATCGAATGTAGGACTTTG 57.025 43.478 0.00 0.00 0.00 2.77
2570 2717 5.422214 AGGATCGAATGTAGGACTTTGTT 57.578 39.130 0.00 0.00 0.00 2.83
2571 2718 6.540438 AGGATCGAATGTAGGACTTTGTTA 57.460 37.500 0.00 0.00 0.00 2.41
2573 2720 6.986817 AGGATCGAATGTAGGACTTTGTTATG 59.013 38.462 0.00 0.00 0.00 1.90
2574 2721 6.984474 GGATCGAATGTAGGACTTTGTTATGA 59.016 38.462 0.00 0.00 0.00 2.15
2575 2722 7.494625 GGATCGAATGTAGGACTTTGTTATGAA 59.505 37.037 0.00 0.00 0.00 2.57
2576 2723 7.827819 TCGAATGTAGGACTTTGTTATGAAG 57.172 36.000 0.00 0.00 0.00 3.02
2577 2724 6.816640 TCGAATGTAGGACTTTGTTATGAAGG 59.183 38.462 0.00 0.00 0.00 3.46
2579 2726 7.119262 CGAATGTAGGACTTTGTTATGAAGGTT 59.881 37.037 0.00 0.00 0.00 3.50
2580 2727 7.923414 ATGTAGGACTTTGTTATGAAGGTTC 57.077 36.000 0.00 0.00 0.00 3.62
2583 2730 5.617252 AGGACTTTGTTATGAAGGTTCGAA 58.383 37.500 0.00 0.00 0.00 3.71
2586 2733 6.647895 GGACTTTGTTATGAAGGTTCGAACTA 59.352 38.462 26.32 9.01 30.99 2.24
2593 2741 7.876068 TGTTATGAAGGTTCGAACTAGAATTGT 59.124 33.333 26.32 9.09 32.25 2.71
2606 2754 7.063426 CGAACTAGAATTGTTCTCTTGCATACA 59.937 37.037 0.00 0.00 40.95 2.29
2607 2755 7.840342 ACTAGAATTGTTCTCTTGCATACAG 57.160 36.000 0.00 0.00 41.14 2.74
2608 2756 7.615403 ACTAGAATTGTTCTCTTGCATACAGA 58.385 34.615 0.00 0.00 41.14 3.41
2609 2757 6.981762 AGAATTGTTCTCTTGCATACAGAG 57.018 37.500 7.47 7.47 34.07 3.35
2610 2758 5.353678 AGAATTGTTCTCTTGCATACAGAGC 59.646 40.000 8.75 3.60 34.07 4.09
2611 2759 3.683365 TGTTCTCTTGCATACAGAGCA 57.317 42.857 8.75 5.91 40.85 4.26
2612 2760 3.329386 TGTTCTCTTGCATACAGAGCAC 58.671 45.455 8.75 8.91 42.54 4.40
2613 2761 3.244181 TGTTCTCTTGCATACAGAGCACA 60.244 43.478 13.25 13.25 42.54 4.57
2614 2762 2.964740 TCTCTTGCATACAGAGCACAC 58.035 47.619 8.75 0.00 42.54 3.82
2615 2763 2.005451 CTCTTGCATACAGAGCACACC 58.995 52.381 1.06 0.00 42.54 4.16
2616 2764 1.625315 TCTTGCATACAGAGCACACCT 59.375 47.619 0.00 0.00 42.54 4.00
2617 2765 1.736126 CTTGCATACAGAGCACACCTG 59.264 52.381 0.00 0.00 42.54 4.00
2627 2775 2.706636 GCACACCTGTTGAGCTCAA 58.293 52.632 25.16 25.16 38.67 3.02
2630 2778 2.606308 GCACACCTGTTGAGCTCAAATG 60.606 50.000 29.99 24.53 38.67 2.32
2642 2809 7.012327 TGTTGAGCTCAAATGCATTATAGTACC 59.988 37.037 29.99 12.36 37.63 3.34
2690 2858 9.319143 AGAGATAAGTATATTTGCAGTGTGTTC 57.681 33.333 0.00 0.00 0.00 3.18
2717 2885 1.915614 GACGCTTGCTGTGGTCCATG 61.916 60.000 0.00 0.00 0.00 3.66
2719 2887 1.028330 CGCTTGCTGTGGTCCATGAT 61.028 55.000 0.00 0.00 0.00 2.45
2720 2888 0.454600 GCTTGCTGTGGTCCATGATG 59.545 55.000 0.00 0.00 0.00 3.07
2722 2890 2.439409 CTTGCTGTGGTCCATGATGAA 58.561 47.619 0.00 0.00 0.00 2.57
2723 2891 2.812836 TGCTGTGGTCCATGATGAAT 57.187 45.000 0.00 0.00 0.00 2.57
2724 2892 3.090210 TGCTGTGGTCCATGATGAATT 57.910 42.857 0.00 0.00 0.00 2.17
2727 2895 3.004106 GCTGTGGTCCATGATGAATTAGC 59.996 47.826 0.00 0.00 0.00 3.09
2741 2911 6.498303 TGATGAATTAGCTAGCCTGATCCTAA 59.502 38.462 12.13 1.74 0.00 2.69
2744 2914 5.736951 ATTAGCTAGCCTGATCCTAACAG 57.263 43.478 12.13 0.00 35.43 3.16
2767 2937 1.167781 TGTAGACCGACAGTGCACGA 61.168 55.000 12.01 0.00 0.00 4.35
2779 2949 4.957971 ACAGTGCACGATTTTTCTATTCG 58.042 39.130 12.01 0.00 38.76 3.34
2785 2955 5.289917 TGCACGATTTTTCTATTCGATTCGA 59.710 36.000 4.29 4.29 36.73 3.71
2794 2964 2.476873 ATTCGATTCGACGGAGACTG 57.523 50.000 8.55 0.00 34.89 3.51
2795 2965 1.445871 TTCGATTCGACGGAGACTGA 58.554 50.000 8.55 0.00 34.89 3.41
2811 2981 3.008330 GACTGATGATGAGTTGCTTGCT 58.992 45.455 0.00 0.00 0.00 3.91
2846 3016 4.407296 GGTCAGATCTGGGTTTGAGATAGT 59.593 45.833 22.42 0.00 29.97 2.12
2847 3017 5.598830 GGTCAGATCTGGGTTTGAGATAGTA 59.401 44.000 22.42 0.00 29.97 1.82
2848 3018 6.239176 GGTCAGATCTGGGTTTGAGATAGTAG 60.239 46.154 22.42 0.00 29.97 2.57
2849 3019 6.322712 GTCAGATCTGGGTTTGAGATAGTAGT 59.677 42.308 22.42 0.00 29.97 2.73
2914 3084 3.727726 CAGGAAAAGGAATGGCGTTTTT 58.272 40.909 0.00 0.00 42.68 1.94
2922 3092 3.818773 AGGAATGGCGTTTTTATATCGGG 59.181 43.478 0.00 0.00 0.00 5.14
2928 3098 1.862201 CGTTTTTATATCGGGCAGCGA 59.138 47.619 0.00 0.00 0.00 4.93
2973 3143 1.660167 GGGGTTACGGACAATAGTGC 58.340 55.000 0.00 0.00 0.00 4.40
3014 3184 2.248086 AATCCCGTCCGTGGTTAGGC 62.248 60.000 0.00 0.00 0.00 3.93
3015 3185 4.462280 CCCGTCCGTGGTTAGGCC 62.462 72.222 0.00 0.00 37.90 5.19
3016 3186 3.387947 CCGTCCGTGGTTAGGCCT 61.388 66.667 11.78 11.78 38.35 5.19
3017 3187 2.660802 CGTCCGTGGTTAGGCCTT 59.339 61.111 12.58 0.00 38.35 4.35
3018 3188 1.004200 CGTCCGTGGTTAGGCCTTT 60.004 57.895 12.58 0.00 38.35 3.11
3019 3189 1.296056 CGTCCGTGGTTAGGCCTTTG 61.296 60.000 12.58 0.00 38.35 2.77
3030 3200 3.700109 GCCTTTGCCTTTCCCCTC 58.300 61.111 0.00 0.00 0.00 4.30
3039 3209 1.002533 CTTTCCCCTCCCCTCCGTA 59.997 63.158 0.00 0.00 0.00 4.02
3048 3218 2.181021 CCCTCCGTAGCACGTGTC 59.819 66.667 18.38 9.62 40.58 3.67
3072 3242 1.405526 GGCGTTCCAGATCTGTGCTTA 60.406 52.381 21.11 0.00 0.00 3.09
3073 3243 2.555199 GCGTTCCAGATCTGTGCTTAT 58.445 47.619 21.11 0.00 0.00 1.73
3083 3253 4.460382 AGATCTGTGCTTATGGTTTGGTTG 59.540 41.667 0.00 0.00 0.00 3.77
3087 3257 5.414454 TCTGTGCTTATGGTTTGGTTGATAC 59.586 40.000 0.00 0.00 0.00 2.24
3105 3275 4.515191 TGATACGGCAGAGGCAAATAATTC 59.485 41.667 0.00 0.00 43.71 2.17
3108 3278 2.542411 CGGCAGAGGCAAATAATTCAGC 60.542 50.000 0.00 0.00 43.71 4.26
3123 5601 2.044123 TCAGCACTCTATCTGCGAGA 57.956 50.000 0.00 0.00 39.79 4.04
3183 5661 2.510768 CGGGAGGTTGCAGATACTAC 57.489 55.000 0.00 0.00 0.00 2.73
3184 5662 1.754803 CGGGAGGTTGCAGATACTACA 59.245 52.381 0.00 0.00 0.00 2.74
3185 5663 2.223829 CGGGAGGTTGCAGATACTACAG 60.224 54.545 0.00 0.00 0.00 2.74
3186 5664 2.766828 GGGAGGTTGCAGATACTACAGT 59.233 50.000 0.00 0.00 0.00 3.55
3187 5665 3.958798 GGGAGGTTGCAGATACTACAGTA 59.041 47.826 0.00 0.00 34.67 2.74
3188 5666 4.589374 GGGAGGTTGCAGATACTACAGTAT 59.411 45.833 1.48 1.48 43.38 2.12
3189 5667 5.070580 GGGAGGTTGCAGATACTACAGTATT 59.929 44.000 3.49 0.00 40.99 1.89
3190 5668 6.267014 GGGAGGTTGCAGATACTACAGTATTA 59.733 42.308 3.49 0.00 40.99 0.98
3191 5669 7.038941 GGGAGGTTGCAGATACTACAGTATTAT 60.039 40.741 3.49 0.00 40.99 1.28
3192 5670 9.021807 GGAGGTTGCAGATACTACAGTATTATA 57.978 37.037 3.49 0.00 40.99 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
136 141 3.657634 TCAGAGCTTTGCTAACTGTCAG 58.342 45.455 0.00 0.00 39.88 3.51
169 174 5.661458 TCTGACGGACCAAAGAGATTTATC 58.339 41.667 0.00 0.00 0.00 1.75
186 191 5.006165 GCTCTAATTCCAAAGTGATCTGACG 59.994 44.000 0.00 0.00 0.00 4.35
213 218 5.852282 ATTTGGTGTGTGAAAGCTAAAGT 57.148 34.783 0.00 0.00 0.00 2.66
236 241 8.840200 AGAGTGAGGGAGTAGTATTTTCATTA 57.160 34.615 0.00 0.00 0.00 1.90
238 250 6.897966 TGAGAGTGAGGGAGTAGTATTTTCAT 59.102 38.462 0.00 0.00 0.00 2.57
246 258 9.747898 CTTATATTATGAGAGTGAGGGAGTAGT 57.252 37.037 0.00 0.00 0.00 2.73
247 259 9.967451 TCTTATATTATGAGAGTGAGGGAGTAG 57.033 37.037 0.00 0.00 0.00 2.57
248 260 9.967451 CTCTTATATTATGAGAGTGAGGGAGTA 57.033 37.037 14.40 0.00 37.99 2.59
249 261 7.396055 GCTCTTATATTATGAGAGTGAGGGAGT 59.604 40.741 20.50 0.00 42.95 3.85
250 262 7.771183 GCTCTTATATTATGAGAGTGAGGGAG 58.229 42.308 20.50 1.81 42.95 4.30
251 263 7.710676 GCTCTTATATTATGAGAGTGAGGGA 57.289 40.000 20.50 0.00 42.95 4.20
278 290 8.441312 ACTTTCTCGGTTTCATAGTGTAAAAA 57.559 30.769 0.00 0.00 0.00 1.94
279 291 9.715121 ATACTTTCTCGGTTTCATAGTGTAAAA 57.285 29.630 0.00 0.00 0.00 1.52
283 295 9.886132 AAATATACTTTCTCGGTTTCATAGTGT 57.114 29.630 0.00 0.00 0.00 3.55
289 301 9.887406 GTTTTCAAATATACTTTCTCGGTTTCA 57.113 29.630 0.00 0.00 0.00 2.69
293 305 9.939802 AGTAGTTTTCAAATATACTTTCTCGGT 57.060 29.630 0.00 0.00 0.00 4.69
316 328 5.046591 ACGGAAATGGAATCTCACAAGAGTA 60.047 40.000 0.00 0.00 42.66 2.59
317 329 4.256920 CGGAAATGGAATCTCACAAGAGT 58.743 43.478 0.00 0.00 42.66 3.24
330 373 5.540719 AGTTCCCAAAAATAACGGAAATGGA 59.459 36.000 0.00 0.00 36.19 3.41
331 374 5.789521 AGTTCCCAAAAATAACGGAAATGG 58.210 37.500 0.00 0.00 36.19 3.16
332 375 8.247562 TGATAGTTCCCAAAAATAACGGAAATG 58.752 33.333 0.00 0.00 36.19 2.32
339 382 7.696992 TCCACTGATAGTTCCCAAAAATAAC 57.303 36.000 0.00 0.00 0.00 1.89
342 385 6.552008 TCTTCCACTGATAGTTCCCAAAAAT 58.448 36.000 0.00 0.00 0.00 1.82
361 405 1.883021 CCCACCAACGCAATCTTCC 59.117 57.895 0.00 0.00 0.00 3.46
370 414 1.377202 ATAGTGCAGCCCACCAACG 60.377 57.895 0.00 0.00 45.83 4.10
431 481 8.713971 TGTCCACTGGAAATATGATTGTACTAT 58.286 33.333 0.00 0.00 31.38 2.12
432 482 7.985184 GTGTCCACTGGAAATATGATTGTACTA 59.015 37.037 0.00 0.00 31.38 1.82
433 483 6.823689 GTGTCCACTGGAAATATGATTGTACT 59.176 38.462 0.00 0.00 31.38 2.73
434 484 6.238103 CGTGTCCACTGGAAATATGATTGTAC 60.238 42.308 0.00 0.00 31.38 2.90
435 485 5.815222 CGTGTCCACTGGAAATATGATTGTA 59.185 40.000 0.00 0.00 31.38 2.41
446 496 0.391597 GGAGAACGTGTCCACTGGAA 59.608 55.000 11.52 0.00 31.38 3.53
450 504 0.822532 ACGAGGAGAACGTGTCCACT 60.823 55.000 17.30 5.95 42.37 4.00
539 593 0.036952 CGCAGCTCCTCTTTCCTTCA 60.037 55.000 0.00 0.00 0.00 3.02
604 659 0.832135 GTGGAGTGGACTGGACTGGA 60.832 60.000 0.00 0.00 0.00 3.86
605 660 1.674057 GTGGAGTGGACTGGACTGG 59.326 63.158 0.00 0.00 0.00 4.00
606 661 1.121407 TGGTGGAGTGGACTGGACTG 61.121 60.000 0.00 0.00 0.00 3.51
607 662 0.178891 ATGGTGGAGTGGACTGGACT 60.179 55.000 0.00 0.00 0.00 3.85
608 663 0.250513 GATGGTGGAGTGGACTGGAC 59.749 60.000 0.00 0.00 0.00 4.02
618 673 2.608752 GCAAAGCAAAGTGATGGTGGAG 60.609 50.000 0.00 0.00 0.00 3.86
738 796 3.165071 GTTGGGAAGTGGGAAATGTGAT 58.835 45.455 0.00 0.00 0.00 3.06
769 827 1.718757 GCTCGATCCATGGCGCTTTT 61.719 55.000 6.96 0.00 0.00 2.27
828 886 3.028850 CTCTGGGCCAAATCATTGTGAT 58.971 45.455 8.04 0.00 39.09 3.06
856 914 3.719479 TCAGGTACTAGCAGAGGATCTCT 59.281 47.826 0.00 0.00 40.94 3.10
881 939 2.435219 AGTCCGAGACGACTGGGT 59.565 61.111 14.75 0.00 41.60 4.51
887 945 0.035036 ACTCACTCAGTCCGAGACGA 59.965 55.000 0.00 0.00 45.45 4.20
895 953 2.030363 CACCTCACTCACTCACTCAGTC 60.030 54.545 0.00 0.00 30.26 3.51
896 954 1.959985 CACCTCACTCACTCACTCAGT 59.040 52.381 0.00 0.00 34.67 3.41
897 955 1.271934 CCACCTCACTCACTCACTCAG 59.728 57.143 0.00 0.00 0.00 3.35
898 956 1.332195 CCACCTCACTCACTCACTCA 58.668 55.000 0.00 0.00 0.00 3.41
935 993 0.106708 AACAGCAGGCGAGAAACAGA 59.893 50.000 0.00 0.00 0.00 3.41
937 995 1.785041 GCAACAGCAGGCGAGAAACA 61.785 55.000 0.00 0.00 0.00 2.83
951 1025 0.749649 AAATCTTGGCAACCGCAACA 59.250 45.000 0.00 0.00 41.24 3.33
989 1066 4.499116 ACGCCATAGCCTCCCCCT 62.499 66.667 0.00 0.00 34.57 4.79
990 1067 3.942439 GACGCCATAGCCTCCCCC 61.942 72.222 0.00 0.00 34.57 5.40
1510 1598 3.519930 GAGGCTCTCCCCGTCGTC 61.520 72.222 7.40 0.00 0.00 4.20
1551 1639 2.591429 CACTGCTGGTGGAACGCA 60.591 61.111 0.00 0.00 43.02 5.24
1578 1666 1.301716 GGAGTGCGACTTGAGCCAA 60.302 57.895 0.00 0.00 0.00 4.52
1714 1802 5.071370 GCTCTCCAATTCATCCATCTCAAT 58.929 41.667 0.00 0.00 0.00 2.57
1743 1831 3.407657 GCATCCTGCTGCTCTTCG 58.592 61.111 0.00 0.00 40.96 3.79
1811 1899 1.540267 CTCTGTTCCCTCTCGACTGT 58.460 55.000 0.00 0.00 0.00 3.55
1815 1903 0.033991 CCTCCTCTGTTCCCTCTCGA 60.034 60.000 0.00 0.00 0.00 4.04
1825 1913 0.398381 GCATCCTCCTCCTCCTCTGT 60.398 60.000 0.00 0.00 0.00 3.41
1863 1957 0.603975 GTGGCACGCCTTCTTCTCTT 60.604 55.000 9.92 0.00 36.94 2.85
2166 2260 1.904771 CCCACCTCGCACTGGATTA 59.095 57.895 0.00 0.00 0.00 1.75
2184 2278 1.517257 CCAGGATCGTCACGACTGC 60.517 63.158 0.00 0.00 39.18 4.40
2237 2350 4.067192 TGATGATATGGTCCTCAATTGCG 58.933 43.478 0.00 0.00 29.90 4.85
2240 2353 7.982252 ACTGTATGATGATATGGTCCTCAATT 58.018 34.615 0.00 0.00 35.52 2.32
2242 2355 7.730332 AGTACTGTATGATGATATGGTCCTCAA 59.270 37.037 0.00 0.00 35.52 3.02
2259 2372 8.453238 ACGACATCTCTGAATTAGTACTGTAT 57.547 34.615 5.39 0.00 0.00 2.29
2260 2373 7.254353 CGACGACATCTCTGAATTAGTACTGTA 60.254 40.741 5.39 0.00 0.00 2.74
2261 2374 6.457122 CGACGACATCTCTGAATTAGTACTGT 60.457 42.308 5.39 0.00 0.00 3.55
2262 2375 5.904630 CGACGACATCTCTGAATTAGTACTG 59.095 44.000 5.39 0.00 0.00 2.74
2263 2376 5.585445 ACGACGACATCTCTGAATTAGTACT 59.415 40.000 0.00 0.00 0.00 2.73
2295 2408 3.135530 ACAGGAGATCTTACCCAAGCATC 59.864 47.826 0.00 0.00 0.00 3.91
2314 2458 3.726607 GCCTCCTGAACTATCATCACAG 58.273 50.000 0.00 0.00 34.37 3.66
2316 2460 2.748605 CGCCTCCTGAACTATCATCAC 58.251 52.381 0.00 0.00 34.37 3.06
2322 2466 0.687757 TCCAGCGCCTCCTGAACTAT 60.688 55.000 2.29 0.00 34.77 2.12
2331 2475 1.432270 CCGAAAAGATCCAGCGCCTC 61.432 60.000 2.29 0.00 0.00 4.70
2332 2476 1.450312 CCGAAAAGATCCAGCGCCT 60.450 57.895 2.29 0.00 0.00 5.52
2367 2511 4.889995 AGACGAACCTATGTCATCAGATGA 59.110 41.667 9.21 9.21 37.58 2.92
2370 2517 3.632604 GGAGACGAACCTATGTCATCAGA 59.367 47.826 0.00 0.00 37.58 3.27
2373 2520 3.004944 GGAGGAGACGAACCTATGTCATC 59.995 52.174 0.00 0.00 37.93 2.92
2383 2530 0.244178 GAGTGGTGGAGGAGACGAAC 59.756 60.000 0.00 0.00 0.00 3.95
2405 2552 4.842531 ACATGTCCACTGATACAATGGA 57.157 40.909 0.00 0.00 40.27 3.41
2406 2553 5.902613 AAACATGTCCACTGATACAATGG 57.097 39.130 0.00 0.00 34.58 3.16
2407 2554 5.574055 GCAAAACATGTCCACTGATACAATG 59.426 40.000 0.00 0.00 0.00 2.82
2408 2555 5.477984 AGCAAAACATGTCCACTGATACAAT 59.522 36.000 0.00 0.00 0.00 2.71
2409 2556 4.826733 AGCAAAACATGTCCACTGATACAA 59.173 37.500 0.00 0.00 0.00 2.41
2411 2558 4.216257 ACAGCAAAACATGTCCACTGATAC 59.784 41.667 19.13 0.00 0.00 2.24
2413 2560 3.225104 ACAGCAAAACATGTCCACTGAT 58.775 40.909 19.13 3.97 0.00 2.90
2434 2581 3.830178 TGAGCCTGTTACTACTGCACTAA 59.170 43.478 0.00 0.00 0.00 2.24
2435 2582 3.427573 TGAGCCTGTTACTACTGCACTA 58.572 45.455 0.00 0.00 0.00 2.74
2445 2592 3.017442 GGGGAAATCTTGAGCCTGTTAC 58.983 50.000 0.00 0.00 0.00 2.50
2446 2593 2.025321 GGGGGAAATCTTGAGCCTGTTA 60.025 50.000 0.00 0.00 0.00 2.41
2447 2594 1.272704 GGGGGAAATCTTGAGCCTGTT 60.273 52.381 0.00 0.00 0.00 3.16
2465 2612 3.567478 AGAAAAGATCATTCGAGGGGG 57.433 47.619 0.00 0.00 32.04 5.40
2466 2613 4.943705 TGAAAGAAAAGATCATTCGAGGGG 59.056 41.667 0.00 0.00 38.33 4.79
2467 2614 5.645497 AGTGAAAGAAAAGATCATTCGAGGG 59.355 40.000 0.00 0.00 38.33 4.30
2468 2615 6.541086 CAGTGAAAGAAAAGATCATTCGAGG 58.459 40.000 0.00 0.00 38.33 4.63
2469 2616 6.020372 GCAGTGAAAGAAAAGATCATTCGAG 58.980 40.000 0.00 0.00 38.33 4.04
2470 2617 5.702670 AGCAGTGAAAGAAAAGATCATTCGA 59.297 36.000 0.00 0.00 38.33 3.71
2471 2618 5.936054 AGCAGTGAAAGAAAAGATCATTCG 58.064 37.500 0.00 0.00 38.33 3.34
2472 2619 8.485591 CAAAAGCAGTGAAAGAAAAGATCATTC 58.514 33.333 0.00 0.00 36.52 2.67
2473 2620 7.983484 ACAAAAGCAGTGAAAGAAAAGATCATT 59.017 29.630 0.00 0.00 0.00 2.57
2474 2621 7.437267 CACAAAAGCAGTGAAAGAAAAGATCAT 59.563 33.333 0.00 0.00 39.30 2.45
2475 2622 6.753279 CACAAAAGCAGTGAAAGAAAAGATCA 59.247 34.615 0.00 0.00 39.30 2.92
2476 2623 6.753744 ACACAAAAGCAGTGAAAGAAAAGATC 59.246 34.615 0.00 0.00 40.16 2.75
2477 2624 6.532657 CACACAAAAGCAGTGAAAGAAAAGAT 59.467 34.615 0.00 0.00 40.16 2.40
2478 2625 5.863397 CACACAAAAGCAGTGAAAGAAAAGA 59.137 36.000 0.00 0.00 40.16 2.52
2479 2626 5.634859 ACACACAAAAGCAGTGAAAGAAAAG 59.365 36.000 0.00 0.00 40.16 2.27
2480 2627 5.404968 CACACACAAAAGCAGTGAAAGAAAA 59.595 36.000 0.00 0.00 40.16 2.29
2481 2628 4.922692 CACACACAAAAGCAGTGAAAGAAA 59.077 37.500 0.00 0.00 40.16 2.52
2482 2629 4.022416 ACACACACAAAAGCAGTGAAAGAA 60.022 37.500 0.00 0.00 40.16 2.52
2483 2630 3.505680 ACACACACAAAAGCAGTGAAAGA 59.494 39.130 0.00 0.00 40.16 2.52
2484 2631 3.836949 ACACACACAAAAGCAGTGAAAG 58.163 40.909 0.00 0.00 40.16 2.62
2485 2632 3.932545 ACACACACAAAAGCAGTGAAA 57.067 38.095 0.00 0.00 40.16 2.69
2486 2633 3.932545 AACACACACAAAAGCAGTGAA 57.067 38.095 0.00 0.00 40.16 3.18
2487 2634 3.932545 AAACACACACAAAAGCAGTGA 57.067 38.095 0.00 0.00 40.16 3.41
2488 2635 4.326009 GGTTAAACACACACAAAAGCAGTG 59.674 41.667 0.00 0.00 42.56 3.66
2489 2636 4.219725 AGGTTAAACACACACAAAAGCAGT 59.780 37.500 0.00 0.00 0.00 4.40
2490 2637 4.743493 AGGTTAAACACACACAAAAGCAG 58.257 39.130 0.00 0.00 0.00 4.24
2491 2638 4.792521 AGGTTAAACACACACAAAAGCA 57.207 36.364 0.00 0.00 0.00 3.91
2492 2639 5.670094 GCAAAGGTTAAACACACACAAAAGC 60.670 40.000 0.00 0.00 0.00 3.51
2493 2640 5.406780 TGCAAAGGTTAAACACACACAAAAG 59.593 36.000 0.00 0.00 0.00 2.27
2509 2656 5.538118 GCTTTACAGGTAATTTGCAAAGGT 58.462 37.500 18.19 10.41 32.19 3.50
2510 2657 4.621034 CGCTTTACAGGTAATTTGCAAAGG 59.379 41.667 18.19 5.31 32.19 3.11
2512 2659 5.009210 ACTCGCTTTACAGGTAATTTGCAAA 59.991 36.000 15.44 15.44 0.00 3.68
2515 2662 4.680171 ACTCGCTTTACAGGTAATTTGC 57.320 40.909 0.00 0.00 0.00 3.68
2516 2663 6.664515 TCAAACTCGCTTTACAGGTAATTTG 58.335 36.000 7.09 7.09 0.00 2.32
2517 2664 6.870971 TCAAACTCGCTTTACAGGTAATTT 57.129 33.333 0.00 0.00 0.00 1.82
2523 2670 4.669197 CGGATTTCAAACTCGCTTTACAGG 60.669 45.833 0.00 0.00 0.00 4.00
2537 2684 4.513442 ACATTCGATCCTTCGGATTTCAA 58.487 39.130 0.00 0.00 40.81 2.69
2549 2696 6.984474 TCATAACAAAGTCCTACATTCGATCC 59.016 38.462 0.00 0.00 0.00 3.36
2554 2701 7.923414 ACCTTCATAACAAAGTCCTACATTC 57.077 36.000 0.00 0.00 0.00 2.67
2560 2707 5.223449 TCGAACCTTCATAACAAAGTCCT 57.777 39.130 0.00 0.00 0.00 3.85
2563 2710 7.439381 TCTAGTTCGAACCTTCATAACAAAGT 58.561 34.615 24.22 3.55 0.00 2.66
2564 2711 7.884816 TCTAGTTCGAACCTTCATAACAAAG 57.115 36.000 24.22 0.39 0.00 2.77
2565 2712 8.842358 ATTCTAGTTCGAACCTTCATAACAAA 57.158 30.769 24.22 5.64 0.00 2.83
2566 2713 8.717821 CAATTCTAGTTCGAACCTTCATAACAA 58.282 33.333 24.22 6.40 0.00 2.83
2567 2714 7.876068 ACAATTCTAGTTCGAACCTTCATAACA 59.124 33.333 24.22 0.28 0.00 2.41
2568 2715 8.252964 ACAATTCTAGTTCGAACCTTCATAAC 57.747 34.615 24.22 0.00 0.00 1.89
2570 2717 8.475331 GAACAATTCTAGTTCGAACCTTCATA 57.525 34.615 24.22 9.13 36.40 2.15
2571 2718 7.365840 GAACAATTCTAGTTCGAACCTTCAT 57.634 36.000 24.22 8.40 36.40 2.57
2583 2730 7.615403 TCTGTATGCAAGAGAACAATTCTAGT 58.385 34.615 0.00 0.00 40.87 2.57
2586 2733 5.353678 GCTCTGTATGCAAGAGAACAATTCT 59.646 40.000 16.44 0.00 44.21 2.40
2593 2741 3.329386 GTGTGCTCTGTATGCAAGAGAA 58.671 45.455 16.44 4.37 42.41 2.87
2606 2754 4.787871 GCTCAACAGGTGTGCTCT 57.212 55.556 5.20 0.00 42.32 4.09
2609 2757 1.024271 TTTGAGCTCAACAGGTGTGC 58.976 50.000 28.46 4.20 45.26 4.57
2610 2758 2.606308 GCATTTGAGCTCAACAGGTGTG 60.606 50.000 28.46 18.79 35.28 3.82
2611 2759 1.610522 GCATTTGAGCTCAACAGGTGT 59.389 47.619 28.46 8.05 35.28 4.16
2612 2760 1.610038 TGCATTTGAGCTCAACAGGTG 59.390 47.619 28.46 22.46 35.28 4.00
2613 2761 1.985473 TGCATTTGAGCTCAACAGGT 58.015 45.000 28.46 12.17 35.28 4.00
2614 2762 3.587797 AATGCATTTGAGCTCAACAGG 57.412 42.857 28.46 20.06 35.28 4.00
2615 2763 7.024340 ACTATAATGCATTTGAGCTCAACAG 57.976 36.000 28.46 22.68 35.28 3.16
2616 2764 7.012327 GGTACTATAATGCATTTGAGCTCAACA 59.988 37.037 28.46 22.34 35.28 3.33
2617 2765 7.355778 GGTACTATAATGCATTTGAGCTCAAC 58.644 38.462 28.46 17.48 35.28 3.18
2627 2775 6.599437 GCGAATTTCGGTACTATAATGCATT 58.401 36.000 17.56 17.56 40.84 3.56
2630 2778 4.433805 CCGCGAATTTCGGTACTATAATGC 60.434 45.833 19.53 0.00 40.84 3.56
2642 2809 2.514013 CCCGTCTCCGCGAATTTCG 61.514 63.158 8.23 14.33 43.89 3.46
2658 2825 4.870991 GCAAATATACTTATCTCTCGGCCC 59.129 45.833 0.00 0.00 0.00 5.80
2717 2885 5.419239 AGGATCAGGCTAGCTAATTCATC 57.581 43.478 15.72 7.69 0.00 2.92
2719 2887 5.602561 TGTTAGGATCAGGCTAGCTAATTCA 59.397 40.000 15.72 0.00 0.00 2.57
2720 2888 6.015010 TCTGTTAGGATCAGGCTAGCTAATTC 60.015 42.308 15.72 7.15 34.15 2.17
2722 2890 5.398236 TCTGTTAGGATCAGGCTAGCTAAT 58.602 41.667 15.72 5.72 34.15 1.73
2723 2891 4.804597 TCTGTTAGGATCAGGCTAGCTAA 58.195 43.478 15.72 0.21 34.15 3.09
2724 2892 4.141135 ACTCTGTTAGGATCAGGCTAGCTA 60.141 45.833 15.72 0.73 34.15 3.32
2727 2895 4.404073 ACAACTCTGTTAGGATCAGGCTAG 59.596 45.833 0.00 0.00 34.15 3.42
2741 2911 2.293677 CACTGTCGGTCTACAACTCTGT 59.706 50.000 0.00 0.00 39.75 3.41
2744 2914 1.000607 TGCACTGTCGGTCTACAACTC 60.001 52.381 0.00 0.00 0.00 3.01
2767 2937 6.198591 GTCTCCGTCGAATCGAATAGAAAAAT 59.801 38.462 7.01 0.00 37.72 1.82
2779 2949 3.003793 TCATCATCAGTCTCCGTCGAATC 59.996 47.826 0.00 0.00 0.00 2.52
2785 2955 2.417924 GCAACTCATCATCAGTCTCCGT 60.418 50.000 0.00 0.00 0.00 4.69
2794 2964 2.190325 GCAGCAAGCAACTCATCATC 57.810 50.000 0.00 0.00 44.79 2.92
2811 2981 1.830587 ATCTGACCAAGAGCCGTGCA 61.831 55.000 0.00 0.00 38.67 4.57
2846 3016 3.628008 TCAGGTTCCGCTTCATCTACTA 58.372 45.455 0.00 0.00 0.00 1.82
2847 3017 2.457598 TCAGGTTCCGCTTCATCTACT 58.542 47.619 0.00 0.00 0.00 2.57
2848 3018 2.961526 TCAGGTTCCGCTTCATCTAC 57.038 50.000 0.00 0.00 0.00 2.59
2849 3019 3.181465 GGAATCAGGTTCCGCTTCATCTA 60.181 47.826 0.00 0.00 46.53 1.98
2874 3044 0.530431 GCAAAGTGCAAAGTGGGTGG 60.530 55.000 0.00 0.00 44.26 4.61
2885 3055 2.888834 TTCCTTTTCCTGCAAAGTGC 57.111 45.000 0.00 0.00 45.29 4.40
2896 3066 6.416750 CCGATATAAAAACGCCATTCCTTTTC 59.583 38.462 0.00 0.00 0.00 2.29
2922 3092 1.578206 GGAACAAAGGGAGTCGCTGC 61.578 60.000 10.92 0.00 0.00 5.25
2928 3098 2.979678 TCAGCTTAGGAACAAAGGGAGT 59.020 45.455 0.00 0.00 0.00 3.85
2973 3143 1.576421 GCTGCAGAAACTTCCACGG 59.424 57.895 20.43 0.00 0.00 4.94
3014 3184 1.305297 GGGAGGGGAAAGGCAAAGG 60.305 63.158 0.00 0.00 0.00 3.11
3015 3185 1.305297 GGGGAGGGGAAAGGCAAAG 60.305 63.158 0.00 0.00 0.00 2.77
3016 3186 1.782608 AGGGGAGGGGAAAGGCAAA 60.783 57.895 0.00 0.00 0.00 3.68
3017 3187 2.121042 AGGGGAGGGGAAAGGCAA 60.121 61.111 0.00 0.00 0.00 4.52
3018 3188 2.614013 GAGGGGAGGGGAAAGGCA 60.614 66.667 0.00 0.00 0.00 4.75
3019 3189 3.421386 GGAGGGGAGGGGAAAGGC 61.421 72.222 0.00 0.00 0.00 4.35
3021 3191 1.002533 TACGGAGGGGAGGGGAAAG 59.997 63.158 0.00 0.00 0.00 2.62
3024 3194 4.153330 GCTACGGAGGGGAGGGGA 62.153 72.222 0.00 0.00 0.00 4.81
3025 3195 4.475444 TGCTACGGAGGGGAGGGG 62.475 72.222 0.00 0.00 0.00 4.79
3026 3196 3.155167 GTGCTACGGAGGGGAGGG 61.155 72.222 0.00 0.00 0.00 4.30
3027 3197 3.528370 CGTGCTACGGAGGGGAGG 61.528 72.222 0.00 0.00 38.08 4.30
3039 3209 3.151958 AACGCCAGAGACACGTGCT 62.152 57.895 17.22 13.89 40.44 4.40
3072 3242 2.091541 CTGCCGTATCAACCAAACCAT 58.908 47.619 0.00 0.00 0.00 3.55
3073 3243 1.072489 TCTGCCGTATCAACCAAACCA 59.928 47.619 0.00 0.00 0.00 3.67
3083 3253 4.515191 TGAATTATTTGCCTCTGCCGTATC 59.485 41.667 0.00 0.00 36.33 2.24
3087 3257 2.542411 GCTGAATTATTTGCCTCTGCCG 60.542 50.000 0.00 0.00 36.33 5.69
3105 3275 2.607526 CCATCTCGCAGATAGAGTGCTG 60.608 54.545 0.00 0.00 38.88 4.41
3108 3278 3.724508 AACCATCTCGCAGATAGAGTG 57.275 47.619 0.00 0.00 32.12 3.51
3123 5601 3.582208 AGAGCAGAACAGAGAGAAACCAT 59.418 43.478 0.00 0.00 0.00 3.55


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.