Multiple sequence alignment - TraesCS2D01G438000

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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 TraesCS2D01G438000 chr2D 100.000 4212 0 0 1 4212 547765957 547761746 0.000000e+00 7779.0
1 TraesCS2D01G438000 chr2D 94.768 669 20 6 3533 4195 547696257 547695598 0.000000e+00 1027.0
2 TraesCS2D01G438000 chr2D 85.152 330 40 6 2039 2365 547763723 547763400 3.140000e-86 329.0
3 TraesCS2D01G438000 chr2D 85.152 330 40 6 2235 2558 547763919 547763593 3.140000e-86 329.0
4 TraesCS2D01G438000 chr2D 92.558 215 12 1 3242 3452 547696728 547696514 5.290000e-79 305.0
5 TraesCS2D01G438000 chr2D 93.985 133 8 0 2860 2992 74863079 74862947 7.140000e-48 202.0
6 TraesCS2D01G438000 chr2D 85.227 88 13 0 1415 1502 62034272 62034185 1.610000e-14 91.6
7 TraesCS2D01G438000 chr2A 92.992 2497 103 25 767 3207 691180830 691183310 0.000000e+00 3576.0
8 TraesCS2D01G438000 chr2A 86.998 623 47 14 3593 4210 691183926 691184519 0.000000e+00 671.0
9 TraesCS2D01G438000 chr2A 92.623 366 21 1 3830 4195 691215453 691215812 4.830000e-144 521.0
10 TraesCS2D01G438000 chr2A 88.146 329 31 6 1 324 691178964 691179289 6.610000e-103 385.0
11 TraesCS2D01G438000 chr2A 86.402 353 17 4 3206 3530 691183349 691183698 1.440000e-94 357.0
12 TraesCS2D01G438000 chr2A 85.758 330 40 5 2235 2558 691182112 691182440 4.030000e-90 342.0
13 TraesCS2D01G438000 chr2A 84.709 327 43 5 2039 2362 691182308 691182630 1.890000e-83 320.0
14 TraesCS2D01G438000 chr2A 84.091 88 14 0 1415 1502 62371527 62371440 7.500000e-13 86.1
15 TraesCS2D01G438000 chr2B 91.599 1107 51 16 2137 3207 654358466 654357366 0.000000e+00 1491.0
16 TraesCS2D01G438000 chr2B 90.803 685 37 11 3536 4210 654356818 654356150 0.000000e+00 893.0
17 TraesCS2D01G438000 chr2B 86.486 777 48 25 818 1572 654360941 654360200 0.000000e+00 800.0
18 TraesCS2D01G438000 chr2B 89.711 554 30 13 3649 4195 654325436 654324903 0.000000e+00 682.0
19 TraesCS2D01G438000 chr2B 88.737 293 17 5 3242 3530 654352953 654352673 1.120000e-90 344.0
20 TraesCS2D01G438000 chr2B 84.337 332 42 8 2039 2365 654358370 654358044 2.440000e-82 316.0
21 TraesCS2D01G438000 chr2B 90.749 227 17 4 2333 2558 654358461 654358238 2.460000e-77 300.0
22 TraesCS2D01G438000 chr2B 86.777 242 23 5 3211 3452 654357322 654357090 1.160000e-65 261.0
23 TraesCS2D01G438000 chr2B 91.667 168 10 3 2838 3005 113613373 113613210 3.280000e-56 230.0
24 TraesCS2D01G438000 chr2B 94.406 143 7 1 1892 2034 654359607 654359466 7.090000e-53 219.0
25 TraesCS2D01G438000 chr2B 94.872 78 4 0 3533 3610 654352449 654352372 5.720000e-24 122.0
26 TraesCS2D01G438000 chr2B 73.458 373 72 24 2201 2558 654358044 654358404 9.570000e-22 115.0
27 TraesCS2D01G438000 chr6B 85.393 89 13 0 1415 1503 553748582 553748670 4.480000e-15 93.5
28 TraesCS2D01G438000 chr3B 88.312 77 9 0 1426 1502 80351400 80351476 4.480000e-15 93.5
29 TraesCS2D01G438000 chr3B 85.393 89 13 0 1415 1503 350050280 350050368 4.480000e-15 93.5
30 TraesCS2D01G438000 chr3B 83.146 89 15 0 1415 1503 773211947 773212035 9.710000e-12 82.4
31 TraesCS2D01G438000 chr3A 85.393 89 13 0 1415 1503 691208721 691208809 4.480000e-15 93.5


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 TraesCS2D01G438000 chr2D 547761746 547765957 4211 True 2812.333333 7779 90.101333 1 4212 3 chr2D.!!$R4 4211
1 TraesCS2D01G438000 chr2D 547695598 547696728 1130 True 666.000000 1027 93.663000 3242 4195 2 chr2D.!!$R3 953
2 TraesCS2D01G438000 chr2A 691178964 691184519 5555 False 941.833333 3576 87.500833 1 4210 6 chr2A.!!$F2 4209
3 TraesCS2D01G438000 chr2B 654324903 654325436 533 True 682.000000 682 89.711000 3649 4195 1 chr2B.!!$R2 546
4 TraesCS2D01G438000 chr2B 654352372 654360941 8569 True 527.333333 1491 89.862889 818 4210 9 chr2B.!!$R3 3392

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
400 423 0.041312 GCATATGCTAACCAACCGCG 60.041 55.0 20.64 0.0 38.21 6.46 F
403 426 0.246910 TATGCTAACCAACCGCGACA 59.753 50.0 8.23 0.0 0.00 4.35 F
810 2015 0.248498 CGCGGAGAAGCAGACGAATA 60.248 55.0 0.00 0.0 36.85 1.75 F
1167 2389 0.916809 TCCCCTCGAAATTTCTCCCC 59.083 55.0 15.92 0.0 0.00 4.81 F
2262 4678 1.150827 TCGAGCTCTGTTTCGACGTA 58.849 50.0 12.85 0.0 40.55 3.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1658 3147 0.596082 GCCGTACAAGCACAACCATT 59.404 50.000 0.13 0.00 0.00 3.16 R
1808 3297 1.065998 GGTTGTGATACTACCGCCCAA 60.066 52.381 0.00 0.00 34.57 4.12 R
2034 3553 1.208614 GCTCGCTGTCAGCCAAAAG 59.791 57.895 19.14 11.96 38.18 2.27 R
2309 4727 1.389555 AGCTGACACGATCCGTATCA 58.610 50.000 0.57 0.57 41.00 2.15 R
3391 5888 0.179234 TGCCTCCAGTGTTCGAAACA 59.821 50.000 0.00 0.00 39.52 2.83 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
30 31 4.039245 CGCTCCAAATCTCCATCCTACTTA 59.961 45.833 0.00 0.00 0.00 2.24
36 37 6.933521 CCAAATCTCCATCCTACTTATGTGAG 59.066 42.308 0.00 0.00 0.00 3.51
45 46 7.256475 CCATCCTACTTATGTGAGCCTAATCTT 60.256 40.741 0.00 0.00 0.00 2.40
48 49 5.365021 ACTTATGTGAGCCTAATCTTGCT 57.635 39.130 0.00 0.00 41.42 3.91
85 86 5.048782 GGACATGTAAGAAACAATGAGCACA 60.049 40.000 0.00 0.00 42.70 4.57
86 87 6.389830 ACATGTAAGAAACAATGAGCACAA 57.610 33.333 0.00 0.00 42.70 3.33
88 89 7.086376 ACATGTAAGAAACAATGAGCACAATC 58.914 34.615 0.00 0.00 42.70 2.67
89 90 6.882610 TGTAAGAAACAATGAGCACAATCT 57.117 33.333 0.00 0.00 34.29 2.40
107 108 8.749499 GCACAATCTTTGAAATATATTGCTCAC 58.251 33.333 5.03 0.00 32.10 3.51
124 125 6.716934 TGCTCACCCTTCTCTATTAGTTAG 57.283 41.667 0.00 0.00 0.00 2.34
127 128 6.495526 GCTCACCCTTCTCTATTAGTTAGGAT 59.504 42.308 0.00 0.00 32.89 3.24
130 131 9.280456 TCACCCTTCTCTATTAGTTAGGATTTT 57.720 33.333 0.00 0.00 32.89 1.82
147 148 7.552050 AGGATTTTTGGTGAATCATTTGGTA 57.448 32.000 0.00 0.00 35.66 3.25
153 154 9.650539 TTTTTGGTGAATCATTTGGTATATGTG 57.349 29.630 0.00 0.00 0.00 3.21
154 155 8.586879 TTTGGTGAATCATTTGGTATATGTGA 57.413 30.769 0.00 0.00 0.00 3.58
155 156 8.586879 TTGGTGAATCATTTGGTATATGTGAA 57.413 30.769 0.00 0.00 0.00 3.18
156 157 8.765488 TGGTGAATCATTTGGTATATGTGAAT 57.235 30.769 0.00 0.00 0.00 2.57
194 197 3.250040 CGGAACCAAATGTCTCGAGTTTT 59.750 43.478 13.13 8.42 0.00 2.43
204 207 7.406031 AATGTCTCGAGTTTTAGATCCAGTA 57.594 36.000 13.13 0.00 0.00 2.74
207 210 7.088905 TGTCTCGAGTTTTAGATCCAGTAAAC 58.911 38.462 13.13 0.00 0.00 2.01
209 212 7.273815 GTCTCGAGTTTTAGATCCAGTAAACAG 59.726 40.741 13.13 0.00 33.94 3.16
212 215 7.813148 TCGAGTTTTAGATCCAGTAAACAGAAG 59.187 37.037 0.00 0.00 33.94 2.85
222 225 7.900782 TCCAGTAAACAGAAGCACTATTAAC 57.099 36.000 0.00 0.00 0.00 2.01
252 258 4.018870 TGCAACCTATATTGAACCCACTCA 60.019 41.667 0.00 0.00 0.00 3.41
257 263 7.079451 ACCTATATTGAACCCACTCATAAGG 57.921 40.000 0.00 0.00 0.00 2.69
261 267 1.553248 TGAACCCACTCATAAGGACCG 59.447 52.381 0.00 0.00 0.00 4.79
274 280 0.394625 AGGACCGGAGCAGACTAGAC 60.395 60.000 9.46 0.00 0.00 2.59
278 284 0.453793 CCGGAGCAGACTAGACACAG 59.546 60.000 0.00 0.00 0.00 3.66
282 288 2.163412 GGAGCAGACTAGACACAGAGTG 59.837 54.545 0.00 0.00 39.75 3.51
311 317 8.960591 AGTGTTGAAATATCTTATTCACCCTTG 58.039 33.333 0.00 0.00 35.42 3.61
326 332 8.831715 ATTCACCCTTGTTCATTAATTTTCAC 57.168 30.769 0.00 0.00 0.00 3.18
333 356 6.154203 TGTTCATTAATTTTCACTGGTGCA 57.846 33.333 0.00 0.00 0.00 4.57
350 373 7.651304 CACTGGTGCATGAAGTAAATACAAAAA 59.349 33.333 0.00 0.00 0.00 1.94
371 394 3.788672 GGGTTGATAGCCCTGTGAG 57.211 57.895 0.00 0.00 42.81 3.51
372 395 0.181350 GGGTTGATAGCCCTGTGAGG 59.819 60.000 0.00 0.00 42.81 3.86
373 396 0.912486 GGTTGATAGCCCTGTGAGGT 59.088 55.000 0.00 0.00 31.93 3.85
374 397 1.407437 GGTTGATAGCCCTGTGAGGTG 60.407 57.143 0.00 0.00 31.93 4.00
375 398 0.911769 TTGATAGCCCTGTGAGGTGG 59.088 55.000 0.00 0.00 31.93 4.61
376 399 0.042581 TGATAGCCCTGTGAGGTGGA 59.957 55.000 0.00 0.00 31.93 4.02
377 400 0.755686 GATAGCCCTGTGAGGTGGAG 59.244 60.000 0.00 0.00 31.93 3.86
378 401 0.692419 ATAGCCCTGTGAGGTGGAGG 60.692 60.000 0.00 0.00 31.93 4.30
379 402 1.811025 TAGCCCTGTGAGGTGGAGGA 61.811 60.000 0.00 0.00 31.93 3.71
380 403 1.997874 GCCCTGTGAGGTGGAGGAT 60.998 63.158 0.00 0.00 31.93 3.24
381 404 1.910722 CCCTGTGAGGTGGAGGATG 59.089 63.158 0.00 0.00 31.93 3.51
382 405 1.222936 CCTGTGAGGTGGAGGATGC 59.777 63.158 0.00 0.00 0.00 3.91
383 406 1.556373 CCTGTGAGGTGGAGGATGCA 61.556 60.000 0.00 0.00 0.00 3.96
384 407 0.545171 CTGTGAGGTGGAGGATGCAT 59.455 55.000 0.00 0.00 39.99 3.96
385 408 1.764723 CTGTGAGGTGGAGGATGCATA 59.235 52.381 0.00 0.00 39.99 3.14
386 409 2.371179 CTGTGAGGTGGAGGATGCATAT 59.629 50.000 0.00 0.00 39.99 1.78
387 410 2.105306 TGTGAGGTGGAGGATGCATATG 59.895 50.000 0.00 0.00 39.99 1.78
388 411 1.072806 TGAGGTGGAGGATGCATATGC 59.927 52.381 21.09 21.09 39.99 3.14
389 412 1.350351 GAGGTGGAGGATGCATATGCT 59.650 52.381 27.13 13.57 39.99 3.79
390 413 2.568956 GAGGTGGAGGATGCATATGCTA 59.431 50.000 27.13 14.66 39.99 3.49
391 414 2.981784 AGGTGGAGGATGCATATGCTAA 59.018 45.455 27.13 9.73 39.99 3.09
392 415 3.077359 GGTGGAGGATGCATATGCTAAC 58.923 50.000 27.13 16.56 39.99 2.34
393 416 3.077359 GTGGAGGATGCATATGCTAACC 58.923 50.000 27.13 23.90 39.99 2.85
394 417 2.710471 TGGAGGATGCATATGCTAACCA 59.290 45.455 27.13 22.75 42.66 3.67
395 418 3.138098 TGGAGGATGCATATGCTAACCAA 59.862 43.478 27.13 7.43 42.66 3.67
396 419 3.503748 GGAGGATGCATATGCTAACCAAC 59.496 47.826 27.13 20.65 42.66 3.77
397 420 3.490348 AGGATGCATATGCTAACCAACC 58.510 45.455 27.13 14.84 42.66 3.77
398 421 2.226437 GGATGCATATGCTAACCAACCG 59.774 50.000 27.13 0.00 42.66 4.44
399 422 1.021202 TGCATATGCTAACCAACCGC 58.979 50.000 27.13 0.00 42.66 5.68
400 423 0.041312 GCATATGCTAACCAACCGCG 60.041 55.000 20.64 0.00 38.21 6.46
401 424 1.577468 CATATGCTAACCAACCGCGA 58.423 50.000 8.23 0.00 0.00 5.87
402 425 1.260561 CATATGCTAACCAACCGCGAC 59.739 52.381 8.23 0.00 0.00 5.19
403 426 0.246910 TATGCTAACCAACCGCGACA 59.753 50.000 8.23 0.00 0.00 4.35
404 427 0.392461 ATGCTAACCAACCGCGACAT 60.392 50.000 8.23 0.00 0.00 3.06
405 428 1.295357 TGCTAACCAACCGCGACATG 61.295 55.000 8.23 2.83 0.00 3.21
406 429 1.423845 CTAACCAACCGCGACATGC 59.576 57.895 8.23 0.00 41.47 4.06
407 430 1.977594 CTAACCAACCGCGACATGCC 61.978 60.000 8.23 0.00 42.08 4.40
411 434 4.424711 AACCGCGACATGCCCCAT 62.425 61.111 8.23 0.00 42.08 4.00
416 439 2.903855 CGACATGCCCCATGCCTC 60.904 66.667 5.19 0.00 44.80 4.70
417 440 2.520260 GACATGCCCCATGCCTCC 60.520 66.667 5.19 0.00 44.80 4.30
424 447 2.446848 CCCCATGCCTCCGAGACAT 61.447 63.158 0.00 0.00 0.00 3.06
429 452 4.760757 GCCTCCGAGACATAAGGC 57.239 61.111 0.00 0.00 46.76 4.35
438 461 3.947834 CCGAGACATAAGGCAAAAAGGAT 59.052 43.478 0.00 0.00 0.00 3.24
445 468 7.615365 AGACATAAGGCAAAAAGGATATTGACA 59.385 33.333 0.00 0.00 37.01 3.58
451 474 5.067023 GGCAAAAAGGATATTGACAGGAGAG 59.933 44.000 0.00 0.00 34.61 3.20
455 478 4.286813 AGGATATTGACAGGAGAGGGAA 57.713 45.455 0.00 0.00 0.00 3.97
457 480 4.657969 AGGATATTGACAGGAGAGGGAAAG 59.342 45.833 0.00 0.00 0.00 2.62
458 481 4.656112 GGATATTGACAGGAGAGGGAAAGA 59.344 45.833 0.00 0.00 0.00 2.52
470 493 5.536538 GGAGAGGGAAAGAAAAGAAACATGT 59.463 40.000 0.00 0.00 0.00 3.21
472 495 7.230712 GGAGAGGGAAAGAAAAGAAACATGTTA 59.769 37.037 12.39 0.00 0.00 2.41
475 498 7.726216 AGGGAAAGAAAAGAAACATGTTAAGG 58.274 34.615 12.39 0.00 0.00 2.69
476 499 7.563556 AGGGAAAGAAAAGAAACATGTTAAGGA 59.436 33.333 12.39 0.00 0.00 3.36
477 500 8.201464 GGGAAAGAAAAGAAACATGTTAAGGAA 58.799 33.333 12.39 0.00 0.00 3.36
478 501 9.764363 GGAAAGAAAAGAAACATGTTAAGGAAT 57.236 29.630 12.39 0.00 0.00 3.01
482 505 9.807921 AGAAAAGAAACATGTTAAGGAATAGGA 57.192 29.630 12.39 0.00 0.00 2.94
489 569 9.838339 AAACATGTTAAGGAATAGGATGTCTAG 57.162 33.333 12.39 0.00 0.00 2.43
504 584 8.738645 AGGATGTCTAGACAATTAATTTGGAC 57.261 34.615 28.43 3.26 45.41 4.02
505 585 7.495934 AGGATGTCTAGACAATTAATTTGGACG 59.504 37.037 28.43 0.00 45.41 4.79
507 587 6.703319 TGTCTAGACAATTAATTTGGACGGA 58.297 36.000 23.24 0.00 39.80 4.69
508 588 6.816640 TGTCTAGACAATTAATTTGGACGGAG 59.183 38.462 23.24 0.00 39.80 4.63
511 591 4.018779 AGACAATTAATTTGGACGGAGGGA 60.019 41.667 0.00 0.00 39.80 4.20
512 592 4.270008 ACAATTAATTTGGACGGAGGGAG 58.730 43.478 0.00 0.00 39.80 4.30
513 593 4.263771 ACAATTAATTTGGACGGAGGGAGT 60.264 41.667 0.00 0.00 39.80 3.85
514 594 5.045432 ACAATTAATTTGGACGGAGGGAGTA 60.045 40.000 0.00 0.00 39.80 2.59
519 599 3.622166 TTGGACGGAGGGAGTATTTTC 57.378 47.619 0.00 0.00 0.00 2.29
522 602 4.355549 TGGACGGAGGGAGTATTTTCTAA 58.644 43.478 0.00 0.00 0.00 2.10
532 612 9.678941 GAGGGAGTATTTTCTAAAACAAAGTTG 57.321 33.333 0.00 0.00 0.00 3.16
574 654 9.906660 TGTAATGAAAAATACACAAATCTGTCC 57.093 29.630 0.00 0.00 31.64 4.02
620 700 8.586570 TGTCATTTTGTCAACCAATACATTTC 57.413 30.769 0.00 0.00 31.81 2.17
622 702 9.039870 GTCATTTTGTCAACCAATACATTTCAA 57.960 29.630 0.00 0.00 31.81 2.69
627 707 7.418840 TGTCAACCAATACATTTCAAATTGC 57.581 32.000 0.00 0.00 30.81 3.56
628 708 6.988580 TGTCAACCAATACATTTCAAATTGCA 59.011 30.769 0.00 0.00 30.81 4.08
629 709 7.496920 TGTCAACCAATACATTTCAAATTGCAA 59.503 29.630 0.00 0.00 30.81 4.08
631 711 9.064706 TCAACCAATACATTTCAAATTGCAAAT 57.935 25.926 1.71 0.00 30.81 2.32
642 722 9.768662 ATTTCAAATTGCAAATATACTCCATCC 57.231 29.630 1.71 0.00 0.00 3.51
643 723 6.969366 TCAAATTGCAAATATACTCCATCCG 58.031 36.000 1.71 0.00 0.00 4.18
645 725 6.959639 AATTGCAAATATACTCCATCCGTT 57.040 33.333 1.71 0.00 0.00 4.44
646 726 6.959639 ATTGCAAATATACTCCATCCGTTT 57.040 33.333 1.71 0.00 0.00 3.60
647 727 6.371809 TTGCAAATATACTCCATCCGTTTC 57.628 37.500 0.00 0.00 0.00 2.78
648 728 5.432645 TGCAAATATACTCCATCCGTTTCA 58.567 37.500 0.00 0.00 0.00 2.69
650 730 6.545666 TGCAAATATACTCCATCCGTTTCATT 59.454 34.615 0.00 0.00 0.00 2.57
651 731 7.068103 TGCAAATATACTCCATCCGTTTCATTT 59.932 33.333 0.00 0.00 0.00 2.32
652 732 7.591426 GCAAATATACTCCATCCGTTTCATTTC 59.409 37.037 0.00 0.00 0.00 2.17
653 733 8.840321 CAAATATACTCCATCCGTTTCATTTCT 58.160 33.333 0.00 0.00 0.00 2.52
654 734 8.608844 AATATACTCCATCCGTTTCATTTCTC 57.391 34.615 0.00 0.00 0.00 2.87
655 735 3.610911 ACTCCATCCGTTTCATTTCTCC 58.389 45.455 0.00 0.00 0.00 3.71
656 736 2.609459 CTCCATCCGTTTCATTTCTCCG 59.391 50.000 0.00 0.00 0.00 4.63
657 737 2.235155 TCCATCCGTTTCATTTCTCCGA 59.765 45.455 0.00 0.00 0.00 4.55
658 738 2.351726 CCATCCGTTTCATTTCTCCGAC 59.648 50.000 0.00 0.00 0.00 4.79
659 739 1.705256 TCCGTTTCATTTCTCCGACG 58.295 50.000 0.00 0.00 0.00 5.12
660 740 0.719465 CCGTTTCATTTCTCCGACGG 59.281 55.000 7.84 7.84 43.12 4.79
661 741 0.719465 CGTTTCATTTCTCCGACGGG 59.281 55.000 15.25 4.97 0.00 5.28
662 742 1.804601 GTTTCATTTCTCCGACGGGT 58.195 50.000 15.25 0.00 33.83 5.28
663 743 2.671914 CGTTTCATTTCTCCGACGGGTA 60.672 50.000 15.25 0.00 33.83 3.69
664 744 3.528532 GTTTCATTTCTCCGACGGGTAT 58.471 45.455 15.25 0.00 33.83 2.73
665 745 3.899052 TTCATTTCTCCGACGGGTATT 57.101 42.857 15.25 0.00 33.83 1.89
666 746 3.899052 TCATTTCTCCGACGGGTATTT 57.101 42.857 15.25 0.00 33.83 1.40
667 747 4.210724 TCATTTCTCCGACGGGTATTTT 57.789 40.909 15.25 0.00 33.83 1.82
668 748 4.581868 TCATTTCTCCGACGGGTATTTTT 58.418 39.130 15.25 0.00 33.83 1.94
669 749 4.393680 TCATTTCTCCGACGGGTATTTTTG 59.606 41.667 15.25 4.16 33.83 2.44
670 750 2.389962 TCTCCGACGGGTATTTTTGG 57.610 50.000 15.25 0.00 33.83 3.28
671 751 1.901159 TCTCCGACGGGTATTTTTGGA 59.099 47.619 15.25 0.00 33.83 3.53
672 752 2.004733 CTCCGACGGGTATTTTTGGAC 58.995 52.381 15.25 0.00 33.83 4.02
673 753 1.347050 TCCGACGGGTATTTTTGGACA 59.653 47.619 15.25 0.00 33.83 4.02
674 754 2.152830 CCGACGGGTATTTTTGGACAA 58.847 47.619 5.81 0.00 0.00 3.18
675 755 2.553172 CCGACGGGTATTTTTGGACAAA 59.447 45.455 5.81 0.00 0.00 2.83
676 756 3.365565 CCGACGGGTATTTTTGGACAAAG 60.366 47.826 5.81 0.00 0.00 2.77
677 757 3.365565 CGACGGGTATTTTTGGACAAAGG 60.366 47.826 0.00 0.00 0.00 3.11
678 758 2.894765 ACGGGTATTTTTGGACAAAGGG 59.105 45.455 0.00 0.00 0.00 3.95
679 759 3.158676 CGGGTATTTTTGGACAAAGGGA 58.841 45.455 0.00 0.00 0.00 4.20
680 760 3.192633 CGGGTATTTTTGGACAAAGGGAG 59.807 47.826 0.00 0.00 0.00 4.30
681 761 4.157246 GGGTATTTTTGGACAAAGGGAGT 58.843 43.478 0.00 0.00 0.00 3.85
682 762 5.326900 GGGTATTTTTGGACAAAGGGAGTA 58.673 41.667 0.00 0.00 0.00 2.59
683 763 5.184479 GGGTATTTTTGGACAAAGGGAGTAC 59.816 44.000 0.00 0.00 0.00 2.73
684 764 6.008331 GGTATTTTTGGACAAAGGGAGTACT 58.992 40.000 0.00 0.00 0.00 2.73
685 765 6.150641 GGTATTTTTGGACAAAGGGAGTACTC 59.849 42.308 14.87 14.87 0.00 2.59
734 814 9.787532 ATTGTTAATCACCAATCTATGAAAACG 57.212 29.630 0.00 0.00 31.96 3.60
740 820 8.731275 ATCACCAATCTATGAAAACGTAATGA 57.269 30.769 0.00 0.00 0.00 2.57
743 823 7.692291 CACCAATCTATGAAAACGTAATGACAC 59.308 37.037 0.00 0.00 0.00 3.67
744 824 7.606456 ACCAATCTATGAAAACGTAATGACACT 59.394 33.333 0.00 0.00 0.00 3.55
745 825 8.116753 CCAATCTATGAAAACGTAATGACACTC 58.883 37.037 0.00 0.00 0.00 3.51
746 826 8.873830 CAATCTATGAAAACGTAATGACACTCT 58.126 33.333 0.00 0.00 0.00 3.24
748 828 8.462143 TCTATGAAAACGTAATGACACTCTTC 57.538 34.615 0.00 0.00 0.00 2.87
750 830 4.753107 TGAAAACGTAATGACACTCTTCCC 59.247 41.667 0.00 0.00 0.00 3.97
753 833 1.278238 GTAATGACACTCTTCCCGCG 58.722 55.000 0.00 0.00 0.00 6.46
755 835 1.541310 AATGACACTCTTCCCGCGGA 61.541 55.000 30.73 10.38 0.00 5.54
756 836 1.541310 ATGACACTCTTCCCGCGGAA 61.541 55.000 30.73 17.86 39.66 4.30
806 2011 1.978712 TAGACGCGGAGAAGCAGACG 61.979 60.000 12.47 0.00 36.85 4.18
807 2012 3.324099 GACGCGGAGAAGCAGACGA 62.324 63.158 12.47 0.00 36.85 4.20
809 2014 1.517257 CGCGGAGAAGCAGACGAAT 60.517 57.895 0.00 0.00 36.85 3.34
810 2015 0.248498 CGCGGAGAAGCAGACGAATA 60.248 55.000 0.00 0.00 36.85 1.75
811 2016 1.600663 CGCGGAGAAGCAGACGAATAT 60.601 52.381 0.00 0.00 36.85 1.28
818 2023 6.402118 CGGAGAAGCAGACGAATATTTTTGAA 60.402 38.462 0.00 0.00 0.00 2.69
822 2027 8.567948 AGAAGCAGACGAATATTTTTGAAAGAA 58.432 29.630 0.00 0.00 0.00 2.52
954 2173 1.684386 CCAAACCAGCAAACAGGCCA 61.684 55.000 5.01 0.00 0.00 5.36
993 2212 2.681344 GCCGACGAAACTCCCAAATTAT 59.319 45.455 0.00 0.00 0.00 1.28
1167 2389 0.916809 TCCCCTCGAAATTTCTCCCC 59.083 55.000 15.92 0.00 0.00 4.81
1174 2396 4.273318 CTCGAAATTTCTCCCCTGGATTT 58.727 43.478 15.92 0.00 0.00 2.17
1211 2434 4.449068 CGGATCTGGATATTTCGAGTTTGG 59.551 45.833 0.00 0.00 0.00 3.28
1215 2438 6.049955 TCTGGATATTTCGAGTTTGGTTCT 57.950 37.500 0.00 0.00 0.00 3.01
1216 2439 6.106673 TCTGGATATTTCGAGTTTGGTTCTC 58.893 40.000 0.00 0.00 0.00 2.87
1218 2441 5.045869 TGGATATTTCGAGTTTGGTTCTCCT 60.046 40.000 0.00 0.00 34.23 3.69
1219 2442 6.155565 TGGATATTTCGAGTTTGGTTCTCCTA 59.844 38.462 0.00 0.00 34.23 2.94
1222 2445 9.760077 GATATTTCGAGTTTGGTTCTCCTAATA 57.240 33.333 0.00 0.00 31.90 0.98
1266 2489 2.280524 CCCGCGGCGATTATTCCA 60.281 61.111 25.92 0.00 0.00 3.53
1272 2495 2.477189 CGCGGCGATTATTCCAAGTTTT 60.477 45.455 19.16 0.00 0.00 2.43
1299 2522 4.666149 GCATCTGATTTGATCTCGCGATTC 60.666 45.833 10.36 10.88 0.00 2.52
1303 2526 3.553105 TGATTTGATCTCGCGATTCTGTG 59.447 43.478 10.36 0.00 0.00 3.66
1311 2536 5.432885 TCTCGCGATTCTGTGTCAATATA 57.567 39.130 10.36 0.00 0.00 0.86
1312 2537 6.013842 TCTCGCGATTCTGTGTCAATATAT 57.986 37.500 10.36 0.00 0.00 0.86
1313 2538 6.447162 TCTCGCGATTCTGTGTCAATATATT 58.553 36.000 10.36 0.00 0.00 1.28
1314 2539 6.923508 TCTCGCGATTCTGTGTCAATATATTT 59.076 34.615 10.36 0.00 0.00 1.40
1402 2635 1.423845 CATCGTTCTTTTCCGGCGG 59.576 57.895 22.51 22.51 0.00 6.13
1584 3073 6.672266 TTGAGATTGGTAGTTTCAGTCTCT 57.328 37.500 14.46 0.00 43.72 3.10
1603 3092 4.451096 TCTCTTTTGTGTGAGAATTACCGC 59.549 41.667 0.00 0.00 36.52 5.68
1644 3133 6.491745 TCATGACCAATTTGCCTTTGTTACTA 59.508 34.615 0.00 0.00 0.00 1.82
1645 3134 6.716934 TGACCAATTTGCCTTTGTTACTAA 57.283 33.333 0.00 0.00 0.00 2.24
1646 3135 7.113658 TGACCAATTTGCCTTTGTTACTAAA 57.886 32.000 0.00 0.00 0.00 1.85
1647 3136 7.556844 TGACCAATTTGCCTTTGTTACTAAAA 58.443 30.769 0.00 0.00 0.00 1.52
1648 3137 8.207545 TGACCAATTTGCCTTTGTTACTAAAAT 58.792 29.630 0.00 0.00 0.00 1.82
1658 3147 9.699703 GCCTTTGTTACTAAAATAATTTGGTGA 57.300 29.630 2.76 0.00 40.08 4.02
1676 3165 1.876799 TGAATGGTTGTGCTTGTACGG 59.123 47.619 0.00 0.00 0.00 4.02
1717 3206 6.487299 AGTTAGGTGGCCTCTTATTTCTAG 57.513 41.667 3.32 0.00 34.61 2.43
1746 3235 5.468409 GCTAAGGCTAAAAGAGGATCATGTC 59.532 44.000 0.00 0.00 34.24 3.06
1808 3297 6.175471 TCTCTGTCATTTGTGCATCAGTATT 58.825 36.000 0.00 0.00 0.00 1.89
1813 3302 3.591196 TTTGTGCATCAGTATTTGGGC 57.409 42.857 0.00 0.00 0.00 5.36
1842 3331 8.408043 AGTATCACAACCAATTTCATCTGAAA 57.592 30.769 7.74 7.74 46.60 2.69
1869 3358 5.470368 TGGTGTTTGTTTCAAAATTCGACA 58.530 33.333 0.00 0.00 0.00 4.35
1918 3437 5.163509 TGTTGCTGCCAAGTATTTTGTGTTA 60.164 36.000 0.00 0.00 0.00 2.41
2017 3536 5.308014 GTGATCACATATGTATGGGCTTCA 58.692 41.667 21.07 1.91 37.03 3.02
2034 3553 5.695363 GGGCTTCACGTTATATAGGAGTTTC 59.305 44.000 0.00 0.00 0.00 2.78
2064 3585 3.243892 GCGAGCTCTGCTTCGACG 61.244 66.667 19.01 2.74 39.88 5.12
2225 4641 5.045213 TGTTAGGATGACCATAAGCAAAGGA 60.045 40.000 0.00 0.00 38.94 3.36
2245 4661 1.452110 TCAATTGGTGGCTGACATCG 58.548 50.000 5.42 0.00 30.79 3.84
2262 4678 1.150827 TCGAGCTCTGTTTCGACGTA 58.849 50.000 12.85 0.00 40.55 3.57
2555 4975 2.698855 TGCTTCTGGATCAGCCTAAC 57.301 50.000 0.00 0.00 37.63 2.34
2561 4981 5.435291 CTTCTGGATCAGCCTAACATCTTT 58.565 41.667 0.00 0.00 37.63 2.52
2570 4990 6.649155 TCAGCCTAACATCTTTAGTATTGCA 58.351 36.000 0.00 0.00 0.00 4.08
2592 5012 1.278413 GTGACTTTCCCTAGGACCCAC 59.722 57.143 11.48 5.73 0.00 4.61
2594 5014 0.178912 ACTTTCCCTAGGACCCACGT 60.179 55.000 11.48 0.00 0.00 4.49
2596 5016 2.181975 CTTTCCCTAGGACCCACGTTA 58.818 52.381 11.48 0.00 0.00 3.18
2597 5017 1.856629 TTCCCTAGGACCCACGTTAG 58.143 55.000 11.48 0.00 0.00 2.34
2598 5018 0.706433 TCCCTAGGACCCACGTTAGT 59.294 55.000 11.48 0.00 0.00 2.24
2599 5019 1.922447 TCCCTAGGACCCACGTTAGTA 59.078 52.381 11.48 0.00 0.00 1.82
2616 5037 5.576774 CGTTAGTAGATGATGTTTGTCTGCA 59.423 40.000 0.00 0.00 0.00 4.41
2617 5038 6.237675 CGTTAGTAGATGATGTTTGTCTGCAG 60.238 42.308 7.63 7.63 0.00 4.41
2639 5060 6.093633 GCAGGTTGTAATTAGGTTTGACTAGG 59.906 42.308 0.00 0.00 0.00 3.02
2640 5061 7.166167 CAGGTTGTAATTAGGTTTGACTAGGT 58.834 38.462 0.00 0.00 0.00 3.08
2643 5064 8.509690 GGTTGTAATTAGGTTTGACTAGGTTTC 58.490 37.037 0.00 0.00 0.00 2.78
2711 5159 4.021544 GGCTAGATTCCAGAGGACTGTATG 60.022 50.000 0.00 0.00 42.05 2.39
3207 5660 3.003480 GTTGCACTGGATTACCTGAGAC 58.997 50.000 0.00 0.00 38.29 3.36
3237 5730 3.818961 TCTTTCTCTGCGAAATTGCTG 57.181 42.857 0.00 0.00 40.62 4.41
3271 5764 6.096141 TGAAAGGCAGTTTTGTGTCTAATGAA 59.904 34.615 0.00 0.00 30.14 2.57
3287 5780 9.627123 TGTCTAATGAAGGGACCAAATTTATAG 57.373 33.333 0.00 0.00 0.00 1.31
3320 5813 4.082787 CCAACACCAAATAAGCACCTACTG 60.083 45.833 0.00 0.00 0.00 2.74
3436 5933 5.396484 CAGAACTTAATGTGGTTGCATCAG 58.604 41.667 0.00 0.00 0.00 2.90
3489 6010 5.507817 GCACATTGAACAATCCAACAGAGAA 60.508 40.000 0.00 0.00 0.00 2.87
3490 6011 6.506147 CACATTGAACAATCCAACAGAGAAA 58.494 36.000 0.00 0.00 0.00 2.52
3491 6012 7.149973 CACATTGAACAATCCAACAGAGAAAT 58.850 34.615 0.00 0.00 0.00 2.17
3492 6013 8.298854 CACATTGAACAATCCAACAGAGAAATA 58.701 33.333 0.00 0.00 0.00 1.40
3575 6321 3.840666 AGCTAGGACAATCAAGTTCCTCA 59.159 43.478 0.00 0.00 32.43 3.86
3583 6329 2.260844 TCAAGTTCCTCAAGCACCAG 57.739 50.000 0.00 0.00 0.00 4.00
3685 6432 4.378459 CCCTTTCGAATTCGGACTTTTGAG 60.378 45.833 26.47 11.63 40.29 3.02
3808 6586 9.485206 GAAGCGGAAAGTATAAAATGGATAGTA 57.515 33.333 0.00 0.00 0.00 1.82
3810 6588 8.648693 AGCGGAAAGTATAAAATGGATAGTACT 58.351 33.333 0.00 0.00 0.00 2.73
3811 6589 8.709646 GCGGAAAGTATAAAATGGATAGTACTG 58.290 37.037 5.39 0.00 0.00 2.74
3812 6590 8.709646 CGGAAAGTATAAAATGGATAGTACTGC 58.290 37.037 5.39 0.00 0.00 4.40
3813 6591 9.555727 GGAAAGTATAAAATGGATAGTACTGCA 57.444 33.333 5.39 0.00 0.00 4.41
4072 6856 3.070018 CGATGATTATCACCTTCCCTGC 58.930 50.000 0.00 0.00 32.67 4.85
4073 6857 3.416156 GATGATTATCACCTTCCCTGCC 58.584 50.000 0.00 0.00 33.38 4.85
4074 6858 1.494721 TGATTATCACCTTCCCTGCCC 59.505 52.381 0.00 0.00 0.00 5.36
4075 6859 0.853530 ATTATCACCTTCCCTGCCCC 59.146 55.000 0.00 0.00 0.00 5.80
4076 6860 0.253630 TTATCACCTTCCCTGCCCCT 60.254 55.000 0.00 0.00 0.00 4.79
4077 6861 0.988145 TATCACCTTCCCTGCCCCTG 60.988 60.000 0.00 0.00 0.00 4.45
4189 6973 6.575162 ATCCCACAAGTCAAAAACTATCAC 57.425 37.500 0.00 0.00 37.17 3.06
4197 6981 9.262358 ACAAGTCAAAAACTATCACTAAGAGAC 57.738 33.333 0.00 0.00 37.17 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 5.012561 GGCTCACATAAGTAGGATGGAGATT 59.987 44.000 0.00 0.00 0.00 2.40
30 31 5.587844 CACTAAAGCAAGATTAGGCTCACAT 59.412 40.000 0.00 0.00 40.01 3.21
36 37 3.282885 AGGCACTAAAGCAAGATTAGGC 58.717 45.455 0.00 0.00 36.02 3.93
45 46 2.536066 TGTCCTCTAGGCACTAAAGCA 58.464 47.619 0.00 0.00 42.17 3.91
48 49 5.955959 TCTTACATGTCCTCTAGGCACTAAA 59.044 40.000 0.00 0.00 42.17 1.85
85 86 8.773033 AGGGTGAGCAATATATTTCAAAGATT 57.227 30.769 0.00 0.00 0.00 2.40
86 87 8.773033 AAGGGTGAGCAATATATTTCAAAGAT 57.227 30.769 0.00 0.00 0.00 2.40
88 89 8.230472 AGAAGGGTGAGCAATATATTTCAAAG 57.770 34.615 0.00 0.00 0.00 2.77
89 90 8.055181 AGAGAAGGGTGAGCAATATATTTCAAA 58.945 33.333 0.00 0.00 0.00 2.69
107 108 9.343539 CCAAAAATCCTAACTAATAGAGAAGGG 57.656 37.037 0.00 0.00 34.47 3.95
127 128 9.650539 CACATATACCAAATGATTCACCAAAAA 57.349 29.630 0.00 0.00 0.00 1.94
130 131 8.586879 TTCACATATACCAAATGATTCACCAA 57.413 30.769 0.00 0.00 0.00 3.67
173 176 4.830826 AAAACTCGAGACATTTGGTTCC 57.169 40.909 21.68 0.00 0.00 3.62
194 197 7.661536 ATAGTGCTTCTGTTTACTGGATCTA 57.338 36.000 0.00 0.00 0.00 1.98
222 225 7.122055 TGGGTTCAATATAGGTTGCACTTTTAG 59.878 37.037 0.00 0.00 0.00 1.85
241 247 1.553248 CGGTCCTTATGAGTGGGTTCA 59.447 52.381 0.00 0.00 0.00 3.18
252 258 2.175069 TCTAGTCTGCTCCGGTCCTTAT 59.825 50.000 0.00 0.00 0.00 1.73
257 263 0.452585 GTGTCTAGTCTGCTCCGGTC 59.547 60.000 0.00 0.00 0.00 4.79
261 267 2.163412 CACTCTGTGTCTAGTCTGCTCC 59.837 54.545 0.00 0.00 0.00 4.70
282 288 8.398665 GGGTGAATAAGATATTTCAACACTCAC 58.601 37.037 5.50 0.00 40.54 3.51
288 294 9.788960 GAACAAGGGTGAATAAGATATTTCAAC 57.211 33.333 0.00 0.00 38.54 3.18
311 317 6.867816 TCATGCACCAGTGAAAATTAATGAAC 59.132 34.615 0.99 0.00 0.00 3.18
319 325 6.403866 TTTACTTCATGCACCAGTGAAAAT 57.596 33.333 0.99 0.00 34.26 1.82
324 330 5.878332 TGTATTTACTTCATGCACCAGTG 57.122 39.130 0.00 0.00 0.00 3.66
325 331 6.892658 TTTGTATTTACTTCATGCACCAGT 57.107 33.333 0.00 0.00 0.00 4.00
326 332 8.081633 TCTTTTTGTATTTACTTCATGCACCAG 58.918 33.333 0.00 0.00 0.00 4.00
333 356 9.362151 TCAACCCTCTTTTTGTATTTACTTCAT 57.638 29.630 0.00 0.00 0.00 2.57
361 384 2.483329 ATCCTCCACCTCACAGGGCT 62.483 60.000 0.00 0.00 40.58 5.19
366 389 1.878211 TATGCATCCTCCACCTCACA 58.122 50.000 0.19 0.00 0.00 3.58
367 390 2.775890 CATATGCATCCTCCACCTCAC 58.224 52.381 0.19 0.00 0.00 3.51
369 392 1.350351 AGCATATGCATCCTCCACCTC 59.650 52.381 28.62 0.00 45.16 3.85
370 393 1.442773 AGCATATGCATCCTCCACCT 58.557 50.000 28.62 1.58 45.16 4.00
371 394 3.077359 GTTAGCATATGCATCCTCCACC 58.923 50.000 28.62 3.18 45.16 4.61
372 395 3.077359 GGTTAGCATATGCATCCTCCAC 58.923 50.000 28.62 13.21 45.16 4.02
373 396 2.710471 TGGTTAGCATATGCATCCTCCA 59.290 45.455 28.62 22.75 45.16 3.86
374 397 3.423539 TGGTTAGCATATGCATCCTCC 57.576 47.619 28.62 20.80 45.16 4.30
375 398 3.503748 GGTTGGTTAGCATATGCATCCTC 59.496 47.826 28.62 19.92 45.16 3.71
376 399 3.490348 GGTTGGTTAGCATATGCATCCT 58.510 45.455 28.62 11.23 45.16 3.24
377 400 2.226437 CGGTTGGTTAGCATATGCATCC 59.774 50.000 28.62 24.16 45.16 3.51
378 401 2.350772 GCGGTTGGTTAGCATATGCATC 60.351 50.000 28.62 17.10 45.16 3.91
379 402 1.608590 GCGGTTGGTTAGCATATGCAT 59.391 47.619 28.62 16.04 45.16 3.96
380 403 1.021202 GCGGTTGGTTAGCATATGCA 58.979 50.000 28.62 12.53 45.16 3.96
381 404 0.041312 CGCGGTTGGTTAGCATATGC 60.041 55.000 20.36 20.36 42.49 3.14
382 405 1.260561 GTCGCGGTTGGTTAGCATATG 59.739 52.381 6.13 0.00 0.00 1.78
383 406 1.134640 TGTCGCGGTTGGTTAGCATAT 60.135 47.619 6.13 0.00 0.00 1.78
384 407 0.246910 TGTCGCGGTTGGTTAGCATA 59.753 50.000 6.13 0.00 0.00 3.14
385 408 0.392461 ATGTCGCGGTTGGTTAGCAT 60.392 50.000 6.13 0.00 0.00 3.79
386 409 1.004320 ATGTCGCGGTTGGTTAGCA 60.004 52.632 6.13 0.00 0.00 3.49
387 410 1.423845 CATGTCGCGGTTGGTTAGC 59.576 57.895 6.13 0.00 0.00 3.09
388 411 1.423845 GCATGTCGCGGTTGGTTAG 59.576 57.895 6.13 0.00 0.00 2.34
389 412 2.036006 GGCATGTCGCGGTTGGTTA 61.036 57.895 6.13 0.00 43.84 2.85
390 413 3.361977 GGCATGTCGCGGTTGGTT 61.362 61.111 6.13 0.00 43.84 3.67
394 417 4.424711 ATGGGGCATGTCGCGGTT 62.425 61.111 6.13 0.00 43.84 4.44
400 423 2.520260 GGAGGCATGGGGCATGTC 60.520 66.667 0.00 0.00 45.61 3.06
405 428 4.554036 GTCTCGGAGGCATGGGGC 62.554 72.222 4.40 0.00 43.74 5.80
406 429 1.121407 TATGTCTCGGAGGCATGGGG 61.121 60.000 30.04 0.00 41.30 4.96
407 430 0.758734 TTATGTCTCGGAGGCATGGG 59.241 55.000 30.04 0.00 41.30 4.00
408 431 1.270518 CCTTATGTCTCGGAGGCATGG 60.271 57.143 30.04 21.22 41.30 3.66
409 432 2.160822 CCTTATGTCTCGGAGGCATG 57.839 55.000 30.04 16.87 41.30 4.06
412 435 4.760757 GCCTTATGTCTCGGAGGC 57.239 61.111 1.83 1.83 46.81 4.70
413 436 2.691409 TTTGCCTTATGTCTCGGAGG 57.309 50.000 4.96 0.00 0.00 4.30
414 437 3.375299 CCTTTTTGCCTTATGTCTCGGAG 59.625 47.826 0.00 0.00 0.00 4.63
415 438 3.008594 TCCTTTTTGCCTTATGTCTCGGA 59.991 43.478 0.00 0.00 0.00 4.55
416 439 3.343617 TCCTTTTTGCCTTATGTCTCGG 58.656 45.455 0.00 0.00 0.00 4.63
417 440 6.867662 ATATCCTTTTTGCCTTATGTCTCG 57.132 37.500 0.00 0.00 0.00 4.04
421 444 7.147846 CCTGTCAATATCCTTTTTGCCTTATGT 60.148 37.037 0.00 0.00 0.00 2.29
424 447 6.489603 TCCTGTCAATATCCTTTTTGCCTTA 58.510 36.000 0.00 0.00 0.00 2.69
429 452 5.591877 CCCTCTCCTGTCAATATCCTTTTTG 59.408 44.000 0.00 0.00 0.00 2.44
430 453 5.492524 TCCCTCTCCTGTCAATATCCTTTTT 59.507 40.000 0.00 0.00 0.00 1.94
438 461 6.272324 TCTTTTCTTTCCCTCTCCTGTCAATA 59.728 38.462 0.00 0.00 0.00 1.90
445 468 5.388599 TGTTTCTTTTCTTTCCCTCTCCT 57.611 39.130 0.00 0.00 0.00 3.69
451 474 7.722363 TCCTTAACATGTTTCTTTTCTTTCCC 58.278 34.615 17.78 0.00 0.00 3.97
478 501 9.832445 GTCCAAATTAATTGTCTAGACATCCTA 57.168 33.333 25.68 11.77 41.52 2.94
480 503 7.254795 CCGTCCAAATTAATTGTCTAGACATCC 60.255 40.741 25.68 0.00 41.52 3.51
481 504 7.494625 TCCGTCCAAATTAATTGTCTAGACATC 59.505 37.037 25.68 0.00 41.52 3.06
482 505 7.335627 TCCGTCCAAATTAATTGTCTAGACAT 58.664 34.615 25.68 14.67 41.52 3.06
484 507 6.258068 CCTCCGTCCAAATTAATTGTCTAGAC 59.742 42.308 16.32 16.32 37.32 2.59
489 569 4.266714 TCCCTCCGTCCAAATTAATTGTC 58.733 43.478 0.39 0.00 37.32 3.18
499 579 3.178865 AGAAAATACTCCCTCCGTCCAA 58.821 45.455 0.00 0.00 0.00 3.53
504 584 7.174426 ACTTTGTTTTAGAAAATACTCCCTCCG 59.826 37.037 0.00 0.00 0.00 4.63
505 585 8.405418 ACTTTGTTTTAGAAAATACTCCCTCC 57.595 34.615 0.00 0.00 0.00 4.30
507 587 9.416284 TCAACTTTGTTTTAGAAAATACTCCCT 57.584 29.630 0.00 0.00 0.00 4.20
590 670 7.984050 TGTATTGGTTGACAAAATGACATGTTT 59.016 29.630 0.00 0.00 43.46 2.83
593 673 8.537049 AATGTATTGGTTGACAAAATGACATG 57.463 30.769 0.00 0.00 43.46 3.21
594 674 9.206870 GAAATGTATTGGTTGACAAAATGACAT 57.793 29.630 0.00 0.00 43.46 3.06
597 677 9.605275 TTTGAAATGTATTGGTTGACAAAATGA 57.395 25.926 0.00 0.00 43.46 2.57
601 681 8.341173 GCAATTTGAAATGTATTGGTTGACAAA 58.659 29.630 0.00 0.00 43.46 2.83
620 700 6.738114 ACGGATGGAGTATATTTGCAATTTG 58.262 36.000 0.00 0.00 0.00 2.32
622 702 6.959639 AACGGATGGAGTATATTTGCAATT 57.040 33.333 0.00 0.00 0.00 2.32
625 705 5.432645 TGAAACGGATGGAGTATATTTGCA 58.567 37.500 0.00 0.00 0.00 4.08
626 706 6.560253 ATGAAACGGATGGAGTATATTTGC 57.440 37.500 0.00 0.00 0.00 3.68
627 707 8.840321 AGAAATGAAACGGATGGAGTATATTTG 58.160 33.333 0.00 0.00 0.00 2.32
628 708 8.980481 AGAAATGAAACGGATGGAGTATATTT 57.020 30.769 0.00 0.00 0.00 1.40
629 709 7.661847 GGAGAAATGAAACGGATGGAGTATATT 59.338 37.037 0.00 0.00 0.00 1.28
631 711 6.522054 GGAGAAATGAAACGGATGGAGTATA 58.478 40.000 0.00 0.00 0.00 1.47
635 715 2.609459 CGGAGAAATGAAACGGATGGAG 59.391 50.000 0.00 0.00 0.00 3.86
636 716 2.235155 TCGGAGAAATGAAACGGATGGA 59.765 45.455 0.00 0.00 0.00 3.41
637 717 2.351726 GTCGGAGAAATGAAACGGATGG 59.648 50.000 0.00 0.00 39.69 3.51
638 718 2.029244 CGTCGGAGAAATGAAACGGATG 59.971 50.000 0.00 0.00 39.69 3.51
640 720 1.705256 CGTCGGAGAAATGAAACGGA 58.295 50.000 0.00 0.00 39.69 4.69
641 721 0.719465 CCGTCGGAGAAATGAAACGG 59.281 55.000 4.91 0.00 42.97 4.44
642 722 0.719465 CCCGTCGGAGAAATGAAACG 59.281 55.000 14.39 0.00 39.69 3.60
643 723 1.804601 ACCCGTCGGAGAAATGAAAC 58.195 50.000 14.39 0.00 39.69 2.78
645 725 3.899052 AATACCCGTCGGAGAAATGAA 57.101 42.857 14.39 0.00 39.69 2.57
646 726 3.899052 AAATACCCGTCGGAGAAATGA 57.101 42.857 14.39 0.00 39.69 2.57
647 727 4.438200 CCAAAAATACCCGTCGGAGAAATG 60.438 45.833 14.39 2.87 39.69 2.32
648 728 3.692593 CCAAAAATACCCGTCGGAGAAAT 59.307 43.478 14.39 0.00 39.69 2.17
650 730 2.302445 TCCAAAAATACCCGTCGGAGAA 59.698 45.455 14.39 0.00 39.69 2.87
651 731 1.901159 TCCAAAAATACCCGTCGGAGA 59.099 47.619 14.39 0.00 0.00 3.71
652 732 2.004733 GTCCAAAAATACCCGTCGGAG 58.995 52.381 14.39 5.47 0.00 4.63
653 733 1.347050 TGTCCAAAAATACCCGTCGGA 59.653 47.619 14.39 0.00 0.00 4.55
654 734 1.810959 TGTCCAAAAATACCCGTCGG 58.189 50.000 3.60 3.60 0.00 4.79
655 735 3.365565 CCTTTGTCCAAAAATACCCGTCG 60.366 47.826 0.00 0.00 0.00 5.12
656 736 3.057104 CCCTTTGTCCAAAAATACCCGTC 60.057 47.826 0.00 0.00 0.00 4.79
657 737 2.894765 CCCTTTGTCCAAAAATACCCGT 59.105 45.455 0.00 0.00 0.00 5.28
658 738 3.158676 TCCCTTTGTCCAAAAATACCCG 58.841 45.455 0.00 0.00 0.00 5.28
659 739 4.157246 ACTCCCTTTGTCCAAAAATACCC 58.843 43.478 0.00 0.00 0.00 3.69
660 740 6.008331 AGTACTCCCTTTGTCCAAAAATACC 58.992 40.000 0.00 0.00 0.00 2.73
661 741 6.150641 GGAGTACTCCCTTTGTCCAAAAATAC 59.849 42.308 28.87 0.00 43.94 1.89
662 742 6.243148 GGAGTACTCCCTTTGTCCAAAAATA 58.757 40.000 28.87 0.00 43.94 1.40
663 743 5.077564 GGAGTACTCCCTTTGTCCAAAAAT 58.922 41.667 28.87 0.00 43.94 1.82
664 744 4.466827 GGAGTACTCCCTTTGTCCAAAAA 58.533 43.478 28.87 0.00 43.94 1.94
665 745 4.094830 GGAGTACTCCCTTTGTCCAAAA 57.905 45.455 28.87 0.00 43.94 2.44
666 746 3.782656 GGAGTACTCCCTTTGTCCAAA 57.217 47.619 28.87 0.00 43.94 3.28
719 799 7.974675 AGTGTCATTACGTTTTCATAGATTGG 58.025 34.615 0.00 0.00 0.00 3.16
734 814 1.278238 CGCGGGAAGAGTGTCATTAC 58.722 55.000 0.00 0.00 0.00 1.89
738 818 2.204461 TTCCGCGGGAAGAGTGTCA 61.204 57.895 27.83 0.00 36.71 3.58
739 819 2.654877 TTCCGCGGGAAGAGTGTC 59.345 61.111 27.83 0.00 36.71 3.67
759 839 4.024641 GGTTCCGAGTGTCATTACGTTTTT 60.025 41.667 0.00 0.00 0.00 1.94
760 840 3.495753 GGTTCCGAGTGTCATTACGTTTT 59.504 43.478 0.00 0.00 0.00 2.43
761 841 3.062042 GGTTCCGAGTGTCATTACGTTT 58.938 45.455 0.00 0.00 0.00 3.60
762 842 2.036217 TGGTTCCGAGTGTCATTACGTT 59.964 45.455 0.00 0.00 0.00 3.99
764 844 2.357327 TGGTTCCGAGTGTCATTACG 57.643 50.000 0.00 0.00 0.00 3.18
765 845 5.622770 AAATTGGTTCCGAGTGTCATTAC 57.377 39.130 0.00 0.00 0.00 1.89
766 846 6.592607 GTCTAAATTGGTTCCGAGTGTCATTA 59.407 38.462 0.00 0.00 0.00 1.90
767 847 5.411669 GTCTAAATTGGTTCCGAGTGTCATT 59.588 40.000 0.00 0.00 0.00 2.57
768 848 4.935808 GTCTAAATTGGTTCCGAGTGTCAT 59.064 41.667 0.00 0.00 0.00 3.06
770 850 3.367025 CGTCTAAATTGGTTCCGAGTGTC 59.633 47.826 0.00 0.00 0.00 3.67
771 851 3.323243 CGTCTAAATTGGTTCCGAGTGT 58.677 45.455 0.00 0.00 0.00 3.55
772 852 2.093783 GCGTCTAAATTGGTTCCGAGTG 59.906 50.000 0.00 0.00 0.00 3.51
774 854 1.323534 CGCGTCTAAATTGGTTCCGAG 59.676 52.381 0.00 0.00 0.00 4.63
775 855 1.352114 CGCGTCTAAATTGGTTCCGA 58.648 50.000 0.00 0.00 0.00 4.55
822 2027 3.653164 AGAAAGGGTGGTCCATGTTTTT 58.347 40.909 0.00 0.00 38.24 1.94
828 2033 0.328258 CGGAAGAAAGGGTGGTCCAT 59.672 55.000 0.00 0.00 38.24 3.41
830 2035 0.109913 AACGGAAGAAAGGGTGGTCC 59.890 55.000 0.00 0.00 0.00 4.46
831 2036 1.235724 CAACGGAAGAAAGGGTGGTC 58.764 55.000 0.00 0.00 0.00 4.02
954 2173 4.160626 GTCGGCCTCTGCTTTATATAGGAT 59.839 45.833 0.00 0.00 37.74 3.24
993 2212 4.856509 TCTCCCTCTCTGTTTTCTCGATA 58.143 43.478 0.00 0.00 0.00 2.92
1167 2389 0.894835 CCCGGGGAAAACAAATCCAG 59.105 55.000 14.71 0.00 38.80 3.86
1211 2434 5.585390 TCGAAACATCGGTATTAGGAGAAC 58.415 41.667 0.00 0.00 0.00 3.01
1215 2438 5.909477 ACAATCGAAACATCGGTATTAGGA 58.091 37.500 0.00 0.00 0.00 2.94
1216 2439 5.107989 CGACAATCGAAACATCGGTATTAGG 60.108 44.000 0.00 0.00 43.74 2.69
1218 2441 4.741185 CCGACAATCGAAACATCGGTATTA 59.259 41.667 17.70 0.00 45.73 0.98
1219 2442 3.554324 CCGACAATCGAAACATCGGTATT 59.446 43.478 17.70 0.00 45.73 1.89
1222 2445 1.355971 CCGACAATCGAAACATCGGT 58.644 50.000 17.70 0.00 45.73 4.69
1266 2489 5.957842 TCAAATCAGATGCGGTAAAACTT 57.042 34.783 0.00 0.00 0.00 2.66
1272 2495 3.642705 CGAGATCAAATCAGATGCGGTA 58.357 45.455 0.00 0.00 0.00 4.02
1299 2522 6.194463 CCAGCGAACAAATATATTGACACAG 58.806 40.000 0.00 0.00 0.00 3.66
1303 2526 5.237344 AGAGCCAGCGAACAAATATATTGAC 59.763 40.000 0.00 0.00 0.00 3.18
1311 2536 1.373570 GCTAGAGCCAGCGAACAAAT 58.626 50.000 0.00 0.00 34.31 2.32
1312 2537 2.840974 GCTAGAGCCAGCGAACAAA 58.159 52.632 0.00 0.00 34.31 2.83
1313 2538 4.598257 GCTAGAGCCAGCGAACAA 57.402 55.556 0.00 0.00 34.31 2.83
1584 3073 3.482436 AGGCGGTAATTCTCACACAAAA 58.518 40.909 0.00 0.00 0.00 2.44
1603 3092 7.812690 TGGTCATGATGAAAATCAAGATAGG 57.187 36.000 0.00 0.00 32.03 2.57
1644 3133 6.997476 AGCACAACCATTCACCAAATTATTTT 59.003 30.769 0.00 0.00 0.00 1.82
1645 3134 6.532826 AGCACAACCATTCACCAAATTATTT 58.467 32.000 0.00 0.00 0.00 1.40
1646 3135 6.112927 AGCACAACCATTCACCAAATTATT 57.887 33.333 0.00 0.00 0.00 1.40
1647 3136 5.743636 AGCACAACCATTCACCAAATTAT 57.256 34.783 0.00 0.00 0.00 1.28
1648 3137 5.163364 ACAAGCACAACCATTCACCAAATTA 60.163 36.000 0.00 0.00 0.00 1.40
1658 3147 0.596082 GCCGTACAAGCACAACCATT 59.404 50.000 0.13 0.00 0.00 3.16
1676 3165 8.440833 CACCTAACTTAAGTATACAGTTTGTGC 58.559 37.037 8.92 0.00 32.88 4.57
1717 3206 5.959618 TCCTCTTTTAGCCTTAGCAAAAC 57.040 39.130 0.00 0.00 43.56 2.43
1808 3297 1.065998 GGTTGTGATACTACCGCCCAA 60.066 52.381 0.00 0.00 34.57 4.12
1813 3302 6.538742 AGATGAAATTGGTTGTGATACTACCG 59.461 38.462 7.79 0.00 45.08 4.02
1842 3331 7.960195 GTCGAATTTTGAAACAAACACCATTTT 59.040 29.630 0.00 0.00 0.00 1.82
1869 3358 4.033009 GGGAATCACATGGGGAAAGAATT 58.967 43.478 0.00 0.00 0.00 2.17
1918 3437 3.500343 GGCAAGATGGGGCTACAAATAT 58.500 45.455 0.00 0.00 0.00 1.28
2017 3536 7.280205 CAGCCAAAAGAAACTCCTATATAACGT 59.720 37.037 0.00 0.00 0.00 3.99
2034 3553 1.208614 GCTCGCTGTCAGCCAAAAG 59.791 57.895 19.14 11.96 38.18 2.27
2193 4609 5.543507 ATGGTCATCCTAACATGAGAGAC 57.456 43.478 0.00 0.00 33.29 3.36
2194 4610 6.239430 GCTTATGGTCATCCTAACATGAGAGA 60.239 42.308 0.00 0.00 33.29 3.10
2225 4641 2.019249 CGATGTCAGCCACCAATTGAT 58.981 47.619 7.12 0.00 0.00 2.57
2245 4661 2.097791 AGGATACGTCGAAACAGAGCTC 59.902 50.000 5.27 5.27 46.39 4.09
2262 4678 7.940137 CCTACTCTAGTTGTGACAGTATAGGAT 59.060 40.741 0.00 0.00 0.00 3.24
2309 4727 1.389555 AGCTGACACGATCCGTATCA 58.610 50.000 0.57 0.57 41.00 2.15
2555 4975 7.965107 GGAAAGTCACTTGCAATACTAAAGATG 59.035 37.037 0.00 0.00 0.00 2.90
2561 4981 5.499004 AGGGAAAGTCACTTGCAATACTA 57.501 39.130 0.00 0.00 0.00 1.82
2570 4990 2.267192 GGGTCCTAGGGAAAGTCACTT 58.733 52.381 9.46 0.00 29.55 3.16
2592 5012 5.576774 TGCAGACAAACATCATCTACTAACG 59.423 40.000 0.00 0.00 0.00 3.18
2594 5014 6.108687 CCTGCAGACAAACATCATCTACTAA 58.891 40.000 17.39 0.00 0.00 2.24
2596 5016 4.019860 ACCTGCAGACAAACATCATCTACT 60.020 41.667 17.39 0.00 0.00 2.57
2597 5017 4.256920 ACCTGCAGACAAACATCATCTAC 58.743 43.478 17.39 0.00 0.00 2.59
2598 5018 4.558226 ACCTGCAGACAAACATCATCTA 57.442 40.909 17.39 0.00 0.00 1.98
2599 5019 3.430042 ACCTGCAGACAAACATCATCT 57.570 42.857 17.39 0.00 0.00 2.90
2616 5037 7.325725 ACCTAGTCAAACCTAATTACAACCT 57.674 36.000 0.00 0.00 0.00 3.50
2617 5038 7.991084 AACCTAGTCAAACCTAATTACAACC 57.009 36.000 0.00 0.00 0.00 3.77
2639 5060 7.011482 CAGTGTCTATATAGTTGCAAGGGAAAC 59.989 40.741 9.58 0.00 32.20 2.78
2640 5061 7.047891 CAGTGTCTATATAGTTGCAAGGGAAA 58.952 38.462 9.58 0.00 0.00 3.13
2643 5064 5.163301 ACCAGTGTCTATATAGTTGCAAGGG 60.163 44.000 9.58 12.51 0.00 3.95
2672 5115 7.442666 GGAATCTAGCCCATGTAGAGTTTTAAG 59.557 40.741 0.00 0.00 30.04 1.85
2711 5159 6.506464 GCATTGTGCAAATCAGATTCATAC 57.494 37.500 0.00 0.00 44.26 2.39
3013 5465 5.675970 TCGTTTCGCAATAAAGAAGACTTG 58.324 37.500 0.00 0.00 36.39 3.16
3207 5660 1.462670 GCAGAGAAAGAAAGAGGCACG 59.537 52.381 0.00 0.00 0.00 5.34
3237 5730 3.863142 AACTGCCTTTCATTGCTCATC 57.137 42.857 0.00 0.00 0.00 2.92
3271 5764 5.736616 ACTCTTCCCTATAAATTTGGTCCCT 59.263 40.000 0.00 0.00 0.00 4.20
3287 5780 2.943036 TTGGTGTTGGTACTCTTCCC 57.057 50.000 0.00 0.00 0.00 3.97
3391 5888 0.179234 TGCCTCCAGTGTTCGAAACA 59.821 50.000 0.00 0.00 39.52 2.83
3436 5933 2.540973 GCAACTCCGGTTTTCAGTTGAC 60.541 50.000 27.98 18.36 46.74 3.18
3489 6010 7.232118 AGCCAACAACTCTGCTTTTATTATT 57.768 32.000 0.00 0.00 0.00 1.40
3490 6011 6.840780 AGCCAACAACTCTGCTTTTATTAT 57.159 33.333 0.00 0.00 0.00 1.28
3491 6012 7.393234 ACATAGCCAACAACTCTGCTTTTATTA 59.607 33.333 0.00 0.00 35.34 0.98
3492 6013 6.209391 ACATAGCCAACAACTCTGCTTTTATT 59.791 34.615 0.00 0.00 35.34 1.40
3499 6020 3.561725 GGATACATAGCCAACAACTCTGC 59.438 47.826 0.00 0.00 0.00 4.26
3530 6051 1.616628 ACCCTTTGGATCTCGGCCT 60.617 57.895 0.00 0.00 34.81 5.19
3575 6321 2.566833 TCAATGCTACACTGGTGCTT 57.433 45.000 0.17 0.00 0.00 3.91
3583 6329 8.741101 TTTCAACAACAATATCAATGCTACAC 57.259 30.769 0.00 0.00 0.00 2.90
3666 6413 4.373527 TCACTCAAAAGTCCGAATTCGAA 58.626 39.130 28.76 5.90 35.85 3.71
3808 6586 9.911788 CCTTTTCCCTCATATATATATTGCAGT 57.088 33.333 2.28 0.00 0.00 4.40
3810 6588 9.905713 GTCCTTTTCCCTCATATATATATTGCA 57.094 33.333 2.28 0.00 0.00 4.08
3818 6596 8.776119 CATGGATAGTCCTTTTCCCTCATATAT 58.224 37.037 0.00 0.00 37.46 0.86
3819 6597 7.182749 CCATGGATAGTCCTTTTCCCTCATATA 59.817 40.741 5.56 0.00 37.46 0.86


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

AutoCloner maintained by Alex Coulton.