Multiple sequence alignment - TraesCS5D01G366300

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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 TraesCS5D01G366300 chr5D 100.000 4220 0 0 1 4220 443248104 443252323 0.000000e+00 7793
1 TraesCS5D01G366300 chr5D 91.860 86 5 2 1 85 26674792 26674876 7.410000e-23 119
2 TraesCS5D01G366300 chr5B 92.484 3486 157 54 569 4001 539458043 539461476 0.000000e+00 4889
3 TraesCS5D01G366300 chr5B 95.122 82 3 1 3362 3443 201387430 201387350 1.230000e-25 128
4 TraesCS5D01G366300 chr5A 90.565 3699 182 73 585 4220 559505284 559508878 0.000000e+00 4743
5 TraesCS5D01G366300 chr5A 89.189 185 18 2 1 184 451928701 451928884 3.280000e-56 230
6 TraesCS5D01G366300 chrUn 92.326 417 28 3 1 416 22791071 22791484 1.310000e-164 590
7 TraesCS5D01G366300 chr1D 89.209 417 28 5 1 416 442783092 442782692 4.870000e-139 505
8 TraesCS5D01G366300 chr2D 87.311 331 31 7 88 416 599804191 599803870 6.670000e-98 368
9 TraesCS5D01G366300 chr2D 89.474 95 8 2 1 94 599804329 599804236 7.410000e-23 119
10 TraesCS5D01G366300 chr1A 86.322 329 34 6 90 416 556819831 556819512 8.680000e-92 348
11 TraesCS5D01G366300 chr1A 86.322 329 34 6 90 416 556834257 556834576 8.680000e-92 348
12 TraesCS5D01G366300 chr1A 85.542 332 36 7 90 418 553065500 553065822 1.880000e-88 337
13 TraesCS5D01G366300 chr1A 85.106 329 37 7 90 416 555944010 555943692 4.070000e-85 326
14 TraesCS5D01G366300 chr1A 83.430 344 31 13 91 416 14809420 14809755 3.190000e-76 296
15 TraesCS5D01G366300 chr1A 91.860 86 5 2 1 85 553063233 553063317 7.410000e-23 119
16 TraesCS5D01G366300 chr1A 89.474 95 8 2 1 94 555946275 555946182 7.410000e-23 119
17 TraesCS5D01G366300 chr1A 89.474 95 8 2 1 94 556822102 556822009 7.410000e-23 119
18 TraesCS5D01G366300 chr1A 90.698 86 6 2 1 85 556831987 556832071 3.450000e-21 113
19 TraesCS5D01G366300 chr7A 86.061 330 35 6 90 417 589764702 589764382 1.120000e-90 344
20 TraesCS5D01G366300 chr2B 95.294 85 3 1 3359 3443 720521379 720521462 2.650000e-27 134
21 TraesCS5D01G366300 chr3D 91.860 86 5 2 1 85 104032978 104033062 7.410000e-23 119


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 TraesCS5D01G366300 chr5D 443248104 443252323 4219 False 7793.0 7793 100.000 1 4220 1 chr5D.!!$F2 4219
1 TraesCS5D01G366300 chr5B 539458043 539461476 3433 False 4889.0 4889 92.484 569 4001 1 chr5B.!!$F1 3432
2 TraesCS5D01G366300 chr5A 559505284 559508878 3594 False 4743.0 4743 90.565 585 4220 1 chr5A.!!$F2 3635
3 TraesCS5D01G366300 chr1A 556819512 556822102 2590 True 233.5 348 87.898 1 416 2 chr1A.!!$R2 415
4 TraesCS5D01G366300 chr1A 556831987 556834576 2589 False 230.5 348 88.510 1 416 2 chr1A.!!$F3 415
5 TraesCS5D01G366300 chr1A 553063233 553065822 2589 False 228.0 337 88.701 1 418 2 chr1A.!!$F2 417
6 TraesCS5D01G366300 chr1A 555943692 555946275 2583 True 222.5 326 87.290 1 416 2 chr1A.!!$R1 415

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
579 2765 0.039708 GTCAAACAAGAGCAGCAGGC 60.040 55.0 0.0 0.0 45.3 4.85 F
1326 3530 0.027586 CGCCCGTGGAATCGAATTTC 59.972 55.0 0.0 0.0 0.0 2.17 F
1659 3874 0.035881 CTCAACTCTGCCAAGCCTCA 59.964 55.0 0.0 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1536 3750 0.974010 CTGCAACCGTACCTCCCCTA 60.974 60.0 0.00 0.00 0.00 3.53 R
2816 5056 0.106469 CCTCCTCATCCTCGTCCTCA 60.106 60.0 0.00 0.00 0.00 3.86 R
3537 5830 0.320946 CCCTGCCCAGCAAATTTGTG 60.321 55.0 19.03 14.71 38.41 3.33 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
85 86 3.724478 TGGAGAGGTACATGACAGGAAT 58.276 45.455 0.00 0.00 0.00 3.01
87 88 4.536090 TGGAGAGGTACATGACAGGAATTT 59.464 41.667 0.00 0.00 0.00 1.82
119 2303 5.825679 ACACAAAACATCTTAGTAGCAACCA 59.174 36.000 0.00 0.00 0.00 3.67
129 2313 6.296026 TCTTAGTAGCAACCAGTTTTGACAT 58.704 36.000 0.00 0.00 0.00 3.06
130 2314 4.836125 AGTAGCAACCAGTTTTGACATG 57.164 40.909 0.00 0.00 0.00 3.21
147 2331 7.606858 TTGACATGAATTTTTGTTTTGCAGA 57.393 28.000 0.00 0.00 0.00 4.26
148 2332 7.606858 TGACATGAATTTTTGTTTTGCAGAA 57.393 28.000 0.00 0.00 0.00 3.02
151 2335 7.987649 ACATGAATTTTTGTTTTGCAGAACAT 58.012 26.923 21.97 8.14 39.12 2.71
163 2347 7.229306 TGTTTTGCAGAACATAATGAAGTCTCT 59.771 33.333 18.10 0.00 34.77 3.10
164 2348 6.732531 TTGCAGAACATAATGAAGTCTCTG 57.267 37.500 0.00 0.00 33.54 3.35
167 2351 6.369890 TGCAGAACATAATGAAGTCTCTGTTC 59.630 38.462 5.35 5.35 41.58 3.18
169 2353 7.065563 GCAGAACATAATGAAGTCTCTGTTCAT 59.934 37.037 13.70 0.00 44.77 2.57
171 2355 9.593134 AGAACATAATGAAGTCTCTGTTCATAC 57.407 33.333 13.70 0.00 42.58 2.39
179 2363 9.646427 ATGAAGTCTCTGTTCATACTTAGAAAC 57.354 33.333 0.00 0.00 41.79 2.78
189 2373 5.927030 TCATACTTAGAAACGCAAGCTTTG 58.073 37.500 0.00 0.00 45.62 2.77
235 2419 6.166279 ACTATCATGGTGTGTAGTTCACTTG 58.834 40.000 1.38 0.00 46.27 3.16
236 2420 3.738982 TCATGGTGTGTAGTTCACTTGG 58.261 45.455 1.38 0.00 46.27 3.61
238 2422 1.235724 GGTGTGTAGTTCACTTGGCC 58.764 55.000 0.00 0.00 46.27 5.36
239 2423 1.476110 GGTGTGTAGTTCACTTGGCCA 60.476 52.381 0.00 0.00 46.27 5.36
240 2424 2.294074 GTGTGTAGTTCACTTGGCCAA 58.706 47.619 19.25 19.25 46.27 4.52
241 2425 2.884639 GTGTGTAGTTCACTTGGCCAAT 59.115 45.455 20.85 5.30 46.27 3.16
254 2438 7.488322 TCACTTGGCCAATATAAATAAAGTGC 58.512 34.615 20.85 0.00 41.76 4.40
272 2456 5.931441 AGTGCATTGTCAGTTTTAGAGTC 57.069 39.130 0.00 0.00 0.00 3.36
290 2474 9.618890 TTTAGAGTCCAAATTAAGATCATCAGG 57.381 33.333 0.00 0.00 0.00 3.86
291 2475 7.443302 AGAGTCCAAATTAAGATCATCAGGA 57.557 36.000 0.00 0.00 0.00 3.86
373 2559 4.413641 AGTAAACAAGGGCCCCTTATTT 57.586 40.909 21.83 21.83 42.67 1.40
378 2564 2.111792 ACAAGGGCCCCTTATTTCTGTT 59.888 45.455 21.43 0.00 42.67 3.16
435 2621 4.018796 GACGACGACGACGAACTC 57.981 61.111 25.15 9.57 42.66 3.01
436 2622 1.508746 GACGACGACGACGAACTCC 60.509 63.158 25.15 6.03 42.66 3.85
437 2623 1.895280 GACGACGACGACGAACTCCT 61.895 60.000 25.15 2.32 42.66 3.69
438 2624 1.206072 CGACGACGACGAACTCCTT 59.794 57.895 15.32 0.00 42.66 3.36
439 2625 0.385223 CGACGACGACGAACTCCTTT 60.385 55.000 15.32 0.00 42.66 3.11
440 2626 1.325647 GACGACGACGAACTCCTTTC 58.674 55.000 15.32 0.00 42.66 2.62
441 2627 0.950116 ACGACGACGAACTCCTTTCT 59.050 50.000 15.32 0.00 42.66 2.52
442 2628 1.336125 ACGACGACGAACTCCTTTCTT 59.664 47.619 15.32 0.00 42.66 2.52
443 2629 1.977412 CGACGACGAACTCCTTTCTTC 59.023 52.381 0.00 0.00 42.66 2.87
444 2630 2.603892 CGACGACGAACTCCTTTCTTCA 60.604 50.000 0.00 0.00 42.66 3.02
445 2631 3.576648 GACGACGAACTCCTTTCTTCAT 58.423 45.455 0.00 0.00 33.05 2.57
446 2632 3.576648 ACGACGAACTCCTTTCTTCATC 58.423 45.455 0.00 0.00 33.05 2.92
447 2633 2.924290 CGACGAACTCCTTTCTTCATCC 59.076 50.000 0.00 0.00 33.05 3.51
448 2634 3.367498 CGACGAACTCCTTTCTTCATCCT 60.367 47.826 0.00 0.00 33.05 3.24
449 2635 4.177783 GACGAACTCCTTTCTTCATCCTC 58.822 47.826 0.00 0.00 33.57 3.71
450 2636 3.182967 CGAACTCCTTTCTTCATCCTCG 58.817 50.000 0.00 0.00 31.20 4.63
451 2637 3.119459 CGAACTCCTTTCTTCATCCTCGA 60.119 47.826 0.00 0.00 31.20 4.04
452 2638 4.429108 GAACTCCTTTCTTCATCCTCGAG 58.571 47.826 5.13 5.13 0.00 4.04
453 2639 3.436243 ACTCCTTTCTTCATCCTCGAGT 58.564 45.455 12.31 0.00 0.00 4.18
454 2640 4.601084 ACTCCTTTCTTCATCCTCGAGTA 58.399 43.478 12.31 0.00 0.00 2.59
455 2641 4.642885 ACTCCTTTCTTCATCCTCGAGTAG 59.357 45.833 12.31 0.48 0.00 2.57
456 2642 4.856509 TCCTTTCTTCATCCTCGAGTAGA 58.143 43.478 12.31 2.45 0.00 2.59
457 2643 5.262009 TCCTTTCTTCATCCTCGAGTAGAA 58.738 41.667 12.31 10.87 0.00 2.10
458 2644 5.715279 TCCTTTCTTCATCCTCGAGTAGAAA 59.285 40.000 12.31 14.90 32.52 2.52
459 2645 6.381420 TCCTTTCTTCATCCTCGAGTAGAAAT 59.619 38.462 12.31 0.00 32.91 2.17
460 2646 6.478344 CCTTTCTTCATCCTCGAGTAGAAATG 59.522 42.308 12.31 10.49 32.91 2.32
461 2647 6.531503 TTCTTCATCCTCGAGTAGAAATGT 57.468 37.500 12.31 0.00 0.00 2.71
462 2648 5.895928 TCTTCATCCTCGAGTAGAAATGTG 58.104 41.667 12.31 0.00 0.00 3.21
463 2649 4.655762 TCATCCTCGAGTAGAAATGTGG 57.344 45.455 12.31 0.00 0.00 4.17
464 2650 4.278310 TCATCCTCGAGTAGAAATGTGGA 58.722 43.478 12.31 0.00 0.00 4.02
465 2651 4.098044 TCATCCTCGAGTAGAAATGTGGAC 59.902 45.833 12.31 0.00 0.00 4.02
466 2652 2.422479 TCCTCGAGTAGAAATGTGGACG 59.578 50.000 12.31 0.00 0.00 4.79
467 2653 2.479730 CCTCGAGTAGAAATGTGGACGG 60.480 54.545 12.31 0.00 0.00 4.79
468 2654 1.475280 TCGAGTAGAAATGTGGACGGG 59.525 52.381 0.00 0.00 0.00 5.28
469 2655 1.203994 CGAGTAGAAATGTGGACGGGT 59.796 52.381 0.00 0.00 0.00 5.28
470 2656 2.618053 GAGTAGAAATGTGGACGGGTG 58.382 52.381 0.00 0.00 0.00 4.61
471 2657 2.232941 GAGTAGAAATGTGGACGGGTGA 59.767 50.000 0.00 0.00 0.00 4.02
472 2658 2.838202 AGTAGAAATGTGGACGGGTGAT 59.162 45.455 0.00 0.00 0.00 3.06
473 2659 2.879103 AGAAATGTGGACGGGTGATT 57.121 45.000 0.00 0.00 0.00 2.57
474 2660 3.154827 AGAAATGTGGACGGGTGATTT 57.845 42.857 0.00 0.00 0.00 2.17
475 2661 3.496331 AGAAATGTGGACGGGTGATTTT 58.504 40.909 0.00 0.00 0.00 1.82
476 2662 3.895041 AGAAATGTGGACGGGTGATTTTT 59.105 39.130 0.00 0.00 0.00 1.94
477 2663 5.074115 AGAAATGTGGACGGGTGATTTTTA 58.926 37.500 0.00 0.00 0.00 1.52
478 2664 5.714806 AGAAATGTGGACGGGTGATTTTTAT 59.285 36.000 0.00 0.00 0.00 1.40
479 2665 5.993748 AATGTGGACGGGTGATTTTTATT 57.006 34.783 0.00 0.00 0.00 1.40
480 2666 5.993748 ATGTGGACGGGTGATTTTTATTT 57.006 34.783 0.00 0.00 0.00 1.40
481 2667 5.793030 TGTGGACGGGTGATTTTTATTTT 57.207 34.783 0.00 0.00 0.00 1.82
482 2668 6.896021 TGTGGACGGGTGATTTTTATTTTA 57.104 33.333 0.00 0.00 0.00 1.52
483 2669 7.469537 TGTGGACGGGTGATTTTTATTTTAT 57.530 32.000 0.00 0.00 0.00 1.40
484 2670 7.897864 TGTGGACGGGTGATTTTTATTTTATT 58.102 30.769 0.00 0.00 0.00 1.40
485 2671 8.368668 TGTGGACGGGTGATTTTTATTTTATTT 58.631 29.630 0.00 0.00 0.00 1.40
486 2672 9.210329 GTGGACGGGTGATTTTTATTTTATTTT 57.790 29.630 0.00 0.00 0.00 1.82
487 2673 9.209175 TGGACGGGTGATTTTTATTTTATTTTG 57.791 29.630 0.00 0.00 0.00 2.44
488 2674 8.661257 GGACGGGTGATTTTTATTTTATTTTGG 58.339 33.333 0.00 0.00 0.00 3.28
489 2675 9.425577 GACGGGTGATTTTTATTTTATTTTGGA 57.574 29.630 0.00 0.00 0.00 3.53
490 2676 9.210329 ACGGGTGATTTTTATTTTATTTTGGAC 57.790 29.630 0.00 0.00 0.00 4.02
491 2677 9.209175 CGGGTGATTTTTATTTTATTTTGGACA 57.791 29.630 0.00 0.00 0.00 4.02
504 2690 8.970859 TTTATTTTGGACAATGAAATGTTGGT 57.029 26.923 0.00 0.00 32.57 3.67
505 2691 6.864360 ATTTTGGACAATGAAATGTTGGTG 57.136 33.333 0.00 0.00 32.57 4.17
506 2692 4.333913 TTGGACAATGAAATGTTGGTGG 57.666 40.909 0.00 0.00 32.57 4.61
507 2693 2.632028 TGGACAATGAAATGTTGGTGGG 59.368 45.455 0.00 0.00 32.57 4.61
508 2694 2.632512 GGACAATGAAATGTTGGTGGGT 59.367 45.455 0.00 0.00 32.57 4.51
509 2695 3.554752 GGACAATGAAATGTTGGTGGGTG 60.555 47.826 0.00 0.00 32.57 4.61
510 2696 3.303938 ACAATGAAATGTTGGTGGGTGA 58.696 40.909 0.00 0.00 0.00 4.02
511 2697 3.903090 ACAATGAAATGTTGGTGGGTGAT 59.097 39.130 0.00 0.00 0.00 3.06
512 2698 4.247258 CAATGAAATGTTGGTGGGTGATG 58.753 43.478 0.00 0.00 0.00 3.07
513 2699 3.235750 TGAAATGTTGGTGGGTGATGA 57.764 42.857 0.00 0.00 0.00 2.92
514 2700 3.777087 TGAAATGTTGGTGGGTGATGAT 58.223 40.909 0.00 0.00 0.00 2.45
515 2701 3.510753 TGAAATGTTGGTGGGTGATGATG 59.489 43.478 0.00 0.00 0.00 3.07
516 2702 1.477553 ATGTTGGTGGGTGATGATGC 58.522 50.000 0.00 0.00 0.00 3.91
517 2703 0.959867 TGTTGGTGGGTGATGATGCG 60.960 55.000 0.00 0.00 0.00 4.73
518 2704 2.045708 TTGGTGGGTGATGATGCGC 61.046 57.895 0.00 0.00 0.00 6.09
519 2705 2.124570 GGTGGGTGATGATGCGCT 60.125 61.111 9.73 0.00 0.00 5.92
520 2706 2.182842 GGTGGGTGATGATGCGCTC 61.183 63.158 9.73 4.27 0.00 5.03
521 2707 1.153289 GTGGGTGATGATGCGCTCT 60.153 57.895 9.73 0.00 0.00 4.09
522 2708 0.745845 GTGGGTGATGATGCGCTCTT 60.746 55.000 9.73 1.79 0.00 2.85
523 2709 0.745486 TGGGTGATGATGCGCTCTTG 60.745 55.000 9.73 0.00 0.00 3.02
524 2710 0.462581 GGGTGATGATGCGCTCTTGA 60.463 55.000 9.73 0.00 0.00 3.02
525 2711 1.590932 GGTGATGATGCGCTCTTGAT 58.409 50.000 9.73 0.00 0.00 2.57
526 2712 1.530293 GGTGATGATGCGCTCTTGATC 59.470 52.381 9.73 2.95 0.00 2.92
527 2713 1.530293 GTGATGATGCGCTCTTGATCC 59.470 52.381 9.73 0.00 0.00 3.36
528 2714 1.415289 TGATGATGCGCTCTTGATCCT 59.585 47.619 9.73 0.00 0.00 3.24
529 2715 2.067766 GATGATGCGCTCTTGATCCTC 58.932 52.381 9.73 1.47 0.00 3.71
530 2716 0.826062 TGATGCGCTCTTGATCCTCA 59.174 50.000 9.73 0.00 0.00 3.86
531 2717 1.415289 TGATGCGCTCTTGATCCTCAT 59.585 47.619 9.73 0.00 0.00 2.90
532 2718 1.799403 GATGCGCTCTTGATCCTCATG 59.201 52.381 9.73 0.00 0.00 3.07
533 2719 0.812811 TGCGCTCTTGATCCTCATGC 60.813 55.000 9.73 0.00 0.00 4.06
534 2720 0.532417 GCGCTCTTGATCCTCATGCT 60.532 55.000 0.00 0.00 0.00 3.79
535 2721 1.218763 CGCTCTTGATCCTCATGCTG 58.781 55.000 0.00 0.00 0.00 4.41
536 2722 0.945813 GCTCTTGATCCTCATGCTGC 59.054 55.000 0.00 0.00 0.00 5.25
537 2723 1.475392 GCTCTTGATCCTCATGCTGCT 60.475 52.381 0.00 0.00 0.00 4.24
538 2724 2.920524 CTCTTGATCCTCATGCTGCTT 58.079 47.619 0.00 0.00 0.00 3.91
539 2725 2.873472 CTCTTGATCCTCATGCTGCTTC 59.127 50.000 0.00 0.00 0.00 3.86
540 2726 2.504585 TCTTGATCCTCATGCTGCTTCT 59.495 45.455 0.00 0.00 0.00 2.85
541 2727 2.327200 TGATCCTCATGCTGCTTCTG 57.673 50.000 0.00 0.00 0.00 3.02
542 2728 0.945813 GATCCTCATGCTGCTTCTGC 59.054 55.000 0.00 0.00 40.20 4.26
543 2729 0.547075 ATCCTCATGCTGCTTCTGCT 59.453 50.000 0.00 0.00 40.48 4.24
544 2730 0.107800 TCCTCATGCTGCTTCTGCTC 60.108 55.000 0.00 0.00 40.48 4.26
545 2731 0.107606 CCTCATGCTGCTTCTGCTCT 60.108 55.000 0.00 0.00 40.48 4.09
546 2732 1.679336 CCTCATGCTGCTTCTGCTCTT 60.679 52.381 0.00 0.00 40.48 2.85
547 2733 1.398739 CTCATGCTGCTTCTGCTCTTG 59.601 52.381 0.00 0.00 40.48 3.02
548 2734 1.002773 TCATGCTGCTTCTGCTCTTGA 59.997 47.619 0.00 0.00 40.48 3.02
549 2735 1.810755 CATGCTGCTTCTGCTCTTGAA 59.189 47.619 0.00 0.00 40.48 2.69
550 2736 1.233019 TGCTGCTTCTGCTCTTGAAC 58.767 50.000 0.00 0.00 40.48 3.18
551 2737 1.233019 GCTGCTTCTGCTCTTGAACA 58.767 50.000 0.00 0.00 40.48 3.18
552 2738 1.811359 GCTGCTTCTGCTCTTGAACAT 59.189 47.619 0.00 0.00 40.48 2.71
553 2739 2.414293 GCTGCTTCTGCTCTTGAACATG 60.414 50.000 0.00 0.00 40.48 3.21
554 2740 3.072211 CTGCTTCTGCTCTTGAACATGA 58.928 45.455 0.00 0.00 40.48 3.07
555 2741 3.072211 TGCTTCTGCTCTTGAACATGAG 58.928 45.455 0.00 11.62 40.48 2.90
563 2749 3.922910 CTCTTGAACATGAGCTGAGTCA 58.077 45.455 0.00 0.00 0.00 3.41
564 2750 4.313282 CTCTTGAACATGAGCTGAGTCAA 58.687 43.478 0.00 0.00 33.98 3.18
565 2751 4.707105 TCTTGAACATGAGCTGAGTCAAA 58.293 39.130 0.00 0.00 34.39 2.69
566 2752 4.512944 TCTTGAACATGAGCTGAGTCAAAC 59.487 41.667 0.00 0.00 34.39 2.93
567 2753 3.807553 TGAACATGAGCTGAGTCAAACA 58.192 40.909 0.00 0.00 0.00 2.83
568 2754 4.198530 TGAACATGAGCTGAGTCAAACAA 58.801 39.130 0.00 0.00 0.00 2.83
569 2755 4.274214 TGAACATGAGCTGAGTCAAACAAG 59.726 41.667 0.00 0.00 0.00 3.16
570 2756 4.077300 ACATGAGCTGAGTCAAACAAGA 57.923 40.909 0.00 0.00 0.00 3.02
571 2757 4.063689 ACATGAGCTGAGTCAAACAAGAG 58.936 43.478 0.00 0.00 0.00 2.85
572 2758 2.487934 TGAGCTGAGTCAAACAAGAGC 58.512 47.619 0.00 0.00 0.00 4.09
573 2759 2.158914 TGAGCTGAGTCAAACAAGAGCA 60.159 45.455 0.00 0.00 0.00 4.26
574 2760 2.479656 GAGCTGAGTCAAACAAGAGCAG 59.520 50.000 0.00 0.00 0.00 4.24
575 2761 1.069364 GCTGAGTCAAACAAGAGCAGC 60.069 52.381 0.00 0.00 38.84 5.25
576 2762 2.216046 CTGAGTCAAACAAGAGCAGCA 58.784 47.619 0.00 0.00 0.00 4.41
577 2763 2.216046 TGAGTCAAACAAGAGCAGCAG 58.784 47.619 0.00 0.00 0.00 4.24
578 2764 1.534595 GAGTCAAACAAGAGCAGCAGG 59.465 52.381 0.00 0.00 0.00 4.85
579 2765 0.039708 GTCAAACAAGAGCAGCAGGC 60.040 55.000 0.00 0.00 45.30 4.85
649 2835 2.592308 GATGGGAGCCAGTGGACC 59.408 66.667 15.20 15.02 36.75 4.46
871 3068 3.518068 CCGCCCAAGAAATCCGGC 61.518 66.667 0.00 0.00 38.07 6.13
873 3070 4.193334 GCCCAAGAAATCCGGCGC 62.193 66.667 0.00 0.00 0.00 6.53
874 3071 2.749839 CCCAAGAAATCCGGCGCA 60.750 61.111 10.83 0.00 0.00 6.09
1003 3201 3.846430 CTAGGGTTCCGGGTCCGC 61.846 72.222 0.00 0.00 38.24 5.54
1255 3459 1.463674 CGCTGCCTCCCTTGTTATTT 58.536 50.000 0.00 0.00 0.00 1.40
1310 3514 3.195698 GACCGTGATTCCAGCGCC 61.196 66.667 2.29 0.00 0.00 6.53
1311 3515 4.778143 ACCGTGATTCCAGCGCCC 62.778 66.667 2.29 0.00 0.00 6.13
1319 3523 3.969250 TTCCAGCGCCCGTGGAATC 62.969 63.158 21.84 0.00 46.96 2.52
1326 3530 0.027586 CGCCCGTGGAATCGAATTTC 59.972 55.000 0.00 0.00 0.00 2.17
1328 3532 2.017113 GCCCGTGGAATCGAATTTCCT 61.017 52.381 16.70 0.00 44.63 3.36
1363 3568 1.140804 GCAAGGTGTGGTTTGCGTT 59.859 52.632 0.00 0.00 40.09 4.84
1395 3600 2.830370 CCAAGGAATCCGGCTGGC 60.830 66.667 6.73 0.00 34.14 4.85
1416 3621 1.237458 GGCCCCTAGATCTGGAGGT 59.763 63.158 7.81 0.00 0.00 3.85
1423 3628 2.564947 CCTAGATCTGGAGGTGTATGCC 59.435 54.545 7.81 0.00 0.00 4.40
1506 3711 2.251371 GCGGTTGGTTTCTGCGAC 59.749 61.111 0.00 0.00 0.00 5.19
1536 3750 2.634815 CAGATCTAGGTGGCTGCATT 57.365 50.000 0.50 0.00 0.00 3.56
1571 3785 1.074775 CAGGTGCAAACCTAGGCCA 59.925 57.895 9.30 0.00 38.22 5.36
1587 3801 0.958091 GCCAGTACATTGTGCCAACA 59.042 50.000 0.00 0.00 0.00 3.33
1637 3852 1.747355 GGCAGGTGTTGATGATTCCAG 59.253 52.381 0.00 0.00 0.00 3.86
1656 3871 2.338785 GCCTCAACTCTGCCAAGCC 61.339 63.158 0.00 0.00 0.00 4.35
1657 3872 1.377994 CCTCAACTCTGCCAAGCCT 59.622 57.895 0.00 0.00 0.00 4.58
1658 3873 0.676151 CCTCAACTCTGCCAAGCCTC 60.676 60.000 0.00 0.00 0.00 4.70
1659 3874 0.035881 CTCAACTCTGCCAAGCCTCA 59.964 55.000 0.00 0.00 0.00 3.86
1660 3875 0.473755 TCAACTCTGCCAAGCCTCAA 59.526 50.000 0.00 0.00 0.00 3.02
1661 3876 0.879765 CAACTCTGCCAAGCCTCAAG 59.120 55.000 0.00 0.00 0.00 3.02
1662 3877 0.767375 AACTCTGCCAAGCCTCAAGA 59.233 50.000 0.00 0.00 0.00 3.02
1663 3878 0.767375 ACTCTGCCAAGCCTCAAGAA 59.233 50.000 0.00 0.00 0.00 2.52
1679 3894 8.103305 AGCCTCAAGAAGAAGATTGTTATTGTA 58.897 33.333 8.93 0.00 35.14 2.41
1763 3978 2.369633 TGTCCCATCATGGAGCGCT 61.370 57.895 11.27 11.27 40.96 5.92
1866 4083 3.692690 TGTGAATAAGGTTTAGGTGGGC 58.307 45.455 0.00 0.00 0.00 5.36
1928 4145 4.147322 GTCGCGTGTGATTGGCCG 62.147 66.667 5.77 0.00 0.00 6.13
1981 4200 5.453567 AGGTTCTCAGTTATGTTTTTGGC 57.546 39.130 0.00 0.00 0.00 4.52
2056 4275 0.537653 AGCTCTTACGGAAGCCCTTC 59.462 55.000 1.22 0.00 38.80 3.46
2069 4288 7.847096 ACGGAAGCCCTTCAATTAATTTAATT 58.153 30.769 8.30 8.30 41.20 1.40
2295 4532 6.261826 GCTTACTGATCATGGTTGAATAAGCT 59.738 38.462 13.66 0.00 34.96 3.74
2418 4655 2.164422 GGAAGCTGTAAACAATGGAGCC 59.836 50.000 0.00 0.00 0.00 4.70
2484 4721 7.559335 TCATTACCCTATTCTGCATATGACT 57.441 36.000 6.97 0.00 0.00 3.41
2533 4770 1.755959 TGACTGGTTTGTGCAATGCTT 59.244 42.857 6.82 0.00 0.00 3.91
2534 4771 2.168106 TGACTGGTTTGTGCAATGCTTT 59.832 40.909 6.82 0.00 0.00 3.51
2567 4804 3.063180 GCAGAATCAAATCCGAGACTGTG 59.937 47.826 0.00 0.00 0.00 3.66
2603 4840 1.804372 GCAGGGTCTGATGACGATGAC 60.804 57.143 0.00 0.00 43.79 3.06
2669 4906 1.998444 ATGATGCCGATGCTGGGGAA 61.998 55.000 0.00 0.00 38.71 3.97
2678 4915 1.556911 GATGCTGGGGAAGACTTCTCA 59.443 52.381 16.88 12.86 0.00 3.27
2708 4945 1.352404 CGAGGACGATGACGAGGAC 59.648 63.158 0.00 0.00 42.66 3.85
2711 4948 1.062206 GGACGATGACGAGGACGAC 59.938 63.158 0.00 0.00 42.66 4.34
2726 4963 2.893398 GACGACCCTGAGGCGAAT 59.107 61.111 5.52 0.00 36.54 3.34
2774 5014 3.006217 ACGATGATGATGGTGATGACGAT 59.994 43.478 0.00 0.00 0.00 3.73
2807 5047 0.103208 AAGATGGCGAGGATGACGAC 59.897 55.000 0.00 0.00 39.41 4.34
2816 5056 2.095516 CGAGGATGACGACGATGATGAT 60.096 50.000 0.00 0.00 0.00 2.45
2918 5158 4.569162 TCAGTGTTTCAGTCCGTTAGTTTG 59.431 41.667 0.00 0.00 0.00 2.93
3160 5400 4.450053 CTTTGAATGGCTTTTGGGTTCAA 58.550 39.130 0.00 0.00 37.11 2.69
3161 5401 3.467374 TGAATGGCTTTTGGGTTCAAC 57.533 42.857 0.00 0.00 31.78 3.18
3162 5402 3.037549 TGAATGGCTTTTGGGTTCAACT 58.962 40.909 0.00 0.00 31.78 3.16
3177 5417 6.496565 TGGGTTCAACTTGTATGAAATCCAAT 59.503 34.615 8.95 0.00 38.40 3.16
3204 5444 8.846943 TCTTTATGCTTCTTGTGAGTGAATAA 57.153 30.769 0.00 0.00 0.00 1.40
3244 5485 6.127535 ACTGCTATCTGAATGTTTGGATTTGG 60.128 38.462 0.00 0.00 0.00 3.28
3277 5519 2.475685 GGAAAAGGCGCGTCAATCTAAC 60.476 50.000 15.58 0.00 0.00 2.34
3304 5546 3.126001 ACCGAAGAAGCATTTGAGACA 57.874 42.857 0.00 0.00 0.00 3.41
3306 5548 4.074970 ACCGAAGAAGCATTTGAGACATT 58.925 39.130 0.00 0.00 0.00 2.71
3307 5549 4.154918 ACCGAAGAAGCATTTGAGACATTC 59.845 41.667 0.00 0.00 0.00 2.67
3308 5550 4.437930 CCGAAGAAGCATTTGAGACATTCC 60.438 45.833 0.00 0.00 0.00 3.01
3309 5551 4.656041 GAAGAAGCATTTGAGACATTCCG 58.344 43.478 0.00 0.00 0.00 4.30
3310 5552 3.679389 AGAAGCATTTGAGACATTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
3311 5553 4.074970 AGAAGCATTTGAGACATTCCGTT 58.925 39.130 0.00 0.00 0.00 4.44
3312 5554 4.154918 AGAAGCATTTGAGACATTCCGTTC 59.845 41.667 0.00 0.00 0.00 3.95
3313 5555 3.679389 AGCATTTGAGACATTCCGTTCT 58.321 40.909 0.00 0.00 0.00 3.01
3315 5557 3.484229 GCATTTGAGACATTCCGTTCTCG 60.484 47.826 0.00 0.00 32.32 4.04
3316 5558 1.710013 TTGAGACATTCCGTTCTCGC 58.290 50.000 0.00 0.00 35.54 5.03
3317 5559 0.456142 TGAGACATTCCGTTCTCGCG 60.456 55.000 0.00 0.00 35.54 5.87
3318 5560 0.179171 GAGACATTCCGTTCTCGCGA 60.179 55.000 9.26 9.26 35.54 5.87
3320 5562 0.847035 GACATTCCGTTCTCGCGATC 59.153 55.000 10.36 2.38 35.54 3.69
3399 5679 3.681593 TCCATTCCAAAATTGTGCCAG 57.318 42.857 0.00 0.00 0.00 4.85
3405 5685 5.798125 TTCCAAAATTGTGCCAGAACATA 57.202 34.783 0.00 0.00 0.00 2.29
3417 5702 6.091577 TGTGCCAGAACATAACTAAACATACG 59.908 38.462 0.00 0.00 0.00 3.06
3443 5736 2.354821 CCGCAGAAAAGGCCTATACAAC 59.645 50.000 5.16 0.00 0.00 3.32
3536 5829 3.324930 CCAGTGCCCAGGAGCTCA 61.325 66.667 17.19 0.00 0.00 4.26
3537 5830 2.046507 CAGTGCCCAGGAGCTCAC 60.047 66.667 17.19 4.33 0.00 3.51
3538 5831 2.527624 AGTGCCCAGGAGCTCACA 60.528 61.111 17.19 2.28 32.25 3.58
3593 5888 2.755103 ACGGATTTTCCTTCTGAATGGC 59.245 45.455 0.00 0.00 33.30 4.40
3617 5912 6.681865 GCCCTTTGACTACTGATTACTCTCTC 60.682 46.154 0.00 0.00 0.00 3.20
3628 5923 7.107542 ACTGATTACTCTCTCTTAACGACTCT 58.892 38.462 0.00 0.00 0.00 3.24
3945 6240 2.159254 GCAAAGGCAGTGAGTCAACAAA 60.159 45.455 0.00 0.00 40.72 2.83
3966 6261 6.828785 ACAAATACCAATAGAAGAAATCGCCT 59.171 34.615 0.00 0.00 0.00 5.52
4013 6322 5.163591 CCCCTTTCCACCGTTTGAATTATAC 60.164 44.000 0.00 0.00 0.00 1.47
4015 6324 6.404293 CCCTTTCCACCGTTTGAATTATACAG 60.404 42.308 0.00 0.00 0.00 2.74
4016 6325 6.373216 CCTTTCCACCGTTTGAATTATACAGA 59.627 38.462 0.00 0.00 0.00 3.41
4018 6327 6.045072 TCCACCGTTTGAATTATACAGACT 57.955 37.500 0.00 0.00 0.00 3.24
4019 6328 6.103997 TCCACCGTTTGAATTATACAGACTC 58.896 40.000 0.00 0.00 0.00 3.36
4020 6329 5.005394 CCACCGTTTGAATTATACAGACTCG 59.995 44.000 0.00 0.00 0.00 4.18
4021 6330 5.575606 CACCGTTTGAATTATACAGACTCGT 59.424 40.000 0.00 0.00 0.00 4.18
4022 6331 6.090358 CACCGTTTGAATTATACAGACTCGTT 59.910 38.462 0.00 0.00 0.00 3.85
4173 6482 6.646267 TGTCCAGGGTTTGATATAGTAACAC 58.354 40.000 0.00 0.00 0.00 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 9.859427 CATTGCTCAACTTTCTGGAATAATAAA 57.141 29.630 0.00 0.00 0.00 1.40
49 50 3.439476 CCTCTCCATTGCTCAACTTTCTG 59.561 47.826 0.00 0.00 0.00 3.02
85 86 8.908903 ACTAAGATGTTTTGTGTTACCATCAAA 58.091 29.630 0.00 0.00 35.50 2.69
87 88 9.214957 CTACTAAGATGTTTTGTGTTACCATCA 57.785 33.333 0.00 0.00 35.50 3.07
103 2287 6.204688 TGTCAAAACTGGTTGCTACTAAGATG 59.795 38.462 8.09 5.23 0.00 2.90
108 2292 5.616270 TCATGTCAAAACTGGTTGCTACTA 58.384 37.500 0.00 0.00 0.00 1.82
119 2303 8.295288 TGCAAAACAAAAATTCATGTCAAAACT 58.705 25.926 0.00 0.00 0.00 2.66
129 2313 9.932699 CATTATGTTCTGCAAAACAAAAATTCA 57.067 25.926 10.11 0.00 42.10 2.57
147 2331 9.950496 AAGTATGAACAGAGACTTCATTATGTT 57.050 29.630 0.00 0.00 38.86 2.71
163 2347 4.994852 AGCTTGCGTTTCTAAGTATGAACA 59.005 37.500 0.00 0.00 0.00 3.18
164 2348 5.532025 AGCTTGCGTTTCTAAGTATGAAC 57.468 39.130 0.00 0.00 0.00 3.18
167 2351 5.088739 CCAAAGCTTGCGTTTCTAAGTATG 58.911 41.667 0.00 0.00 0.00 2.39
169 2353 4.131596 ACCAAAGCTTGCGTTTCTAAGTA 58.868 39.130 0.00 0.00 0.00 2.24
171 2355 3.555518 GACCAAAGCTTGCGTTTCTAAG 58.444 45.455 0.00 0.00 0.00 2.18
179 2363 1.136336 GTAGTTCGACCAAAGCTTGCG 60.136 52.381 0.00 2.16 0.00 4.85
189 2373 7.772332 AGTAATGAAATGATGTAGTTCGACC 57.228 36.000 0.00 0.00 36.20 4.79
235 2419 7.925483 TGACAATGCACTTTATTTATATTGGCC 59.075 33.333 0.00 0.00 32.52 5.36
236 2420 8.870160 TGACAATGCACTTTATTTATATTGGC 57.130 30.769 0.00 0.00 33.75 4.52
250 2434 4.757149 GGACTCTAAAACTGACAATGCACT 59.243 41.667 0.00 0.00 0.00 4.40
251 2435 4.515191 TGGACTCTAAAACTGACAATGCAC 59.485 41.667 0.00 0.00 0.00 4.57
267 2451 7.443302 TCCTGATGATCTTAATTTGGACTCT 57.557 36.000 0.00 0.00 0.00 3.24
272 2456 8.577048 AGCATATCCTGATGATCTTAATTTGG 57.423 34.615 0.00 0.00 34.76 3.28
302 2486 9.515226 TTCAAAAGCAAAGTAATATCCAGTAGT 57.485 29.630 0.00 0.00 0.00 2.73
345 2529 4.140876 AGGGGCCCTTGTTTACTTAAAAGA 60.141 41.667 22.67 0.00 0.00 2.52
350 2534 5.539669 AATAAGGGGCCCTTGTTTACTTA 57.460 39.130 41.71 23.47 41.08 2.24
351 2535 4.413641 AATAAGGGGCCCTTGTTTACTT 57.586 40.909 41.71 21.05 41.08 2.24
394 2580 1.991230 GGCCGGCCCATAGATACAT 59.009 57.895 36.64 0.00 0.00 2.29
417 2603 1.852351 GAGTTCGTCGTCGTCGTCG 60.852 63.158 14.18 14.18 46.06 5.12
418 2604 1.508746 GGAGTTCGTCGTCGTCGTC 60.509 63.158 11.41 6.72 38.33 4.20
419 2605 1.502163 AAGGAGTTCGTCGTCGTCGT 61.502 55.000 11.41 0.00 38.33 4.34
420 2606 0.385223 AAAGGAGTTCGTCGTCGTCG 60.385 55.000 5.50 5.50 38.33 5.12
421 2607 1.069364 AGAAAGGAGTTCGTCGTCGTC 60.069 52.381 1.33 0.00 41.52 4.20
422 2608 0.950116 AGAAAGGAGTTCGTCGTCGT 59.050 50.000 1.33 0.00 41.52 4.34
423 2609 1.977412 GAAGAAAGGAGTTCGTCGTCG 59.023 52.381 0.00 0.00 41.52 5.12
424 2610 3.009301 TGAAGAAAGGAGTTCGTCGTC 57.991 47.619 0.00 0.00 44.86 4.20
425 2611 3.576648 GATGAAGAAAGGAGTTCGTCGT 58.423 45.455 0.00 0.00 44.86 4.34
426 2612 2.924290 GGATGAAGAAAGGAGTTCGTCG 59.076 50.000 0.00 0.00 44.86 5.12
427 2613 4.177783 GAGGATGAAGAAAGGAGTTCGTC 58.822 47.826 0.00 0.00 42.96 4.20
428 2614 3.367498 CGAGGATGAAGAAAGGAGTTCGT 60.367 47.826 0.00 0.00 41.52 3.85
429 2615 3.119459 TCGAGGATGAAGAAAGGAGTTCG 60.119 47.826 0.00 0.00 41.52 3.95
430 2616 4.081917 ACTCGAGGATGAAGAAAGGAGTTC 60.082 45.833 18.41 0.00 36.38 3.01
431 2617 3.835395 ACTCGAGGATGAAGAAAGGAGTT 59.165 43.478 18.41 0.00 29.85 3.01
432 2618 3.436243 ACTCGAGGATGAAGAAAGGAGT 58.564 45.455 18.41 0.00 0.00 3.85
433 2619 4.884744 TCTACTCGAGGATGAAGAAAGGAG 59.115 45.833 18.41 0.00 0.00 3.69
434 2620 4.856509 TCTACTCGAGGATGAAGAAAGGA 58.143 43.478 18.41 0.00 0.00 3.36
435 2621 5.584253 TTCTACTCGAGGATGAAGAAAGG 57.416 43.478 18.41 0.00 0.00 3.11
436 2622 7.009999 CACATTTCTACTCGAGGATGAAGAAAG 59.990 40.741 18.41 15.83 36.66 2.62
437 2623 6.813649 CACATTTCTACTCGAGGATGAAGAAA 59.186 38.462 18.41 20.04 37.36 2.52
438 2624 6.333416 CACATTTCTACTCGAGGATGAAGAA 58.667 40.000 18.41 13.47 0.00 2.52
439 2625 5.163509 CCACATTTCTACTCGAGGATGAAGA 60.164 44.000 18.41 8.31 0.00 2.87
440 2626 5.046529 CCACATTTCTACTCGAGGATGAAG 58.953 45.833 18.41 9.08 0.00 3.02
441 2627 4.709886 TCCACATTTCTACTCGAGGATGAA 59.290 41.667 18.41 14.11 0.00 2.57
442 2628 4.098044 GTCCACATTTCTACTCGAGGATGA 59.902 45.833 18.41 8.70 0.00 2.92
443 2629 4.363999 GTCCACATTTCTACTCGAGGATG 58.636 47.826 18.41 13.82 0.00 3.51
444 2630 3.066900 CGTCCACATTTCTACTCGAGGAT 59.933 47.826 18.41 0.00 0.00 3.24
445 2631 2.422479 CGTCCACATTTCTACTCGAGGA 59.578 50.000 18.41 7.44 0.00 3.71
446 2632 2.479730 CCGTCCACATTTCTACTCGAGG 60.480 54.545 18.41 0.00 0.00 4.63
447 2633 2.479730 CCCGTCCACATTTCTACTCGAG 60.480 54.545 11.84 11.84 0.00 4.04
448 2634 1.475280 CCCGTCCACATTTCTACTCGA 59.525 52.381 0.00 0.00 0.00 4.04
449 2635 1.203994 ACCCGTCCACATTTCTACTCG 59.796 52.381 0.00 0.00 0.00 4.18
450 2636 2.232941 TCACCCGTCCACATTTCTACTC 59.767 50.000 0.00 0.00 0.00 2.59
451 2637 2.253610 TCACCCGTCCACATTTCTACT 58.746 47.619 0.00 0.00 0.00 2.57
452 2638 2.754946 TCACCCGTCCACATTTCTAC 57.245 50.000 0.00 0.00 0.00 2.59
453 2639 3.992943 AATCACCCGTCCACATTTCTA 57.007 42.857 0.00 0.00 0.00 2.10
454 2640 2.879103 AATCACCCGTCCACATTTCT 57.121 45.000 0.00 0.00 0.00 2.52
455 2641 3.934457 AAAATCACCCGTCCACATTTC 57.066 42.857 0.00 0.00 0.00 2.17
456 2642 5.993748 ATAAAAATCACCCGTCCACATTT 57.006 34.783 0.00 0.00 0.00 2.32
457 2643 5.993748 AATAAAAATCACCCGTCCACATT 57.006 34.783 0.00 0.00 0.00 2.71
458 2644 5.993748 AAATAAAAATCACCCGTCCACAT 57.006 34.783 0.00 0.00 0.00 3.21
459 2645 5.793030 AAAATAAAAATCACCCGTCCACA 57.207 34.783 0.00 0.00 0.00 4.17
460 2646 8.766000 AAATAAAATAAAAATCACCCGTCCAC 57.234 30.769 0.00 0.00 0.00 4.02
461 2647 9.209175 CAAAATAAAATAAAAATCACCCGTCCA 57.791 29.630 0.00 0.00 0.00 4.02
462 2648 8.661257 CCAAAATAAAATAAAAATCACCCGTCC 58.339 33.333 0.00 0.00 0.00 4.79
463 2649 9.425577 TCCAAAATAAAATAAAAATCACCCGTC 57.574 29.630 0.00 0.00 0.00 4.79
464 2650 9.210329 GTCCAAAATAAAATAAAAATCACCCGT 57.790 29.630 0.00 0.00 0.00 5.28
465 2651 9.209175 TGTCCAAAATAAAATAAAAATCACCCG 57.791 29.630 0.00 0.00 0.00 5.28
478 2664 9.401058 ACCAACATTTCATTGTCCAAAATAAAA 57.599 25.926 0.00 0.00 0.00 1.52
479 2665 8.834465 CACCAACATTTCATTGTCCAAAATAAA 58.166 29.630 0.00 0.00 0.00 1.40
480 2666 7.443575 CCACCAACATTTCATTGTCCAAAATAA 59.556 33.333 0.00 0.00 0.00 1.40
481 2667 6.933521 CCACCAACATTTCATTGTCCAAAATA 59.066 34.615 0.00 0.00 0.00 1.40
482 2668 5.764192 CCACCAACATTTCATTGTCCAAAAT 59.236 36.000 0.00 0.00 0.00 1.82
483 2669 5.121811 CCACCAACATTTCATTGTCCAAAA 58.878 37.500 0.00 0.00 0.00 2.44
484 2670 4.444022 CCCACCAACATTTCATTGTCCAAA 60.444 41.667 0.00 0.00 0.00 3.28
485 2671 3.070734 CCCACCAACATTTCATTGTCCAA 59.929 43.478 0.00 0.00 0.00 3.53
486 2672 2.632028 CCCACCAACATTTCATTGTCCA 59.368 45.455 0.00 0.00 0.00 4.02
487 2673 2.632512 ACCCACCAACATTTCATTGTCC 59.367 45.455 0.00 0.00 0.00 4.02
488 2674 3.320541 TCACCCACCAACATTTCATTGTC 59.679 43.478 0.00 0.00 0.00 3.18
489 2675 3.303938 TCACCCACCAACATTTCATTGT 58.696 40.909 0.00 0.00 0.00 2.71
490 2676 4.021280 TCATCACCCACCAACATTTCATTG 60.021 41.667 0.00 0.00 0.00 2.82
491 2677 4.158786 TCATCACCCACCAACATTTCATT 58.841 39.130 0.00 0.00 0.00 2.57
492 2678 3.777087 TCATCACCCACCAACATTTCAT 58.223 40.909 0.00 0.00 0.00 2.57
493 2679 3.235750 TCATCACCCACCAACATTTCA 57.764 42.857 0.00 0.00 0.00 2.69
494 2680 3.676873 GCATCATCACCCACCAACATTTC 60.677 47.826 0.00 0.00 0.00 2.17
495 2681 2.234414 GCATCATCACCCACCAACATTT 59.766 45.455 0.00 0.00 0.00 2.32
496 2682 1.826720 GCATCATCACCCACCAACATT 59.173 47.619 0.00 0.00 0.00 2.71
497 2683 1.477553 GCATCATCACCCACCAACAT 58.522 50.000 0.00 0.00 0.00 2.71
498 2684 0.959867 CGCATCATCACCCACCAACA 60.960 55.000 0.00 0.00 0.00 3.33
499 2685 1.802636 CGCATCATCACCCACCAAC 59.197 57.895 0.00 0.00 0.00 3.77
500 2686 2.045708 GCGCATCATCACCCACCAA 61.046 57.895 0.30 0.00 0.00 3.67
501 2687 2.438254 GCGCATCATCACCCACCA 60.438 61.111 0.30 0.00 0.00 4.17
502 2688 2.124570 AGCGCATCATCACCCACC 60.125 61.111 11.47 0.00 0.00 4.61
503 2689 0.745845 AAGAGCGCATCATCACCCAC 60.746 55.000 11.47 0.00 0.00 4.61
504 2690 0.745486 CAAGAGCGCATCATCACCCA 60.745 55.000 11.47 0.00 0.00 4.51
505 2691 0.462581 TCAAGAGCGCATCATCACCC 60.463 55.000 11.47 0.00 0.00 4.61
506 2692 1.530293 GATCAAGAGCGCATCATCACC 59.470 52.381 11.47 0.00 0.00 4.02
507 2693 1.530293 GGATCAAGAGCGCATCATCAC 59.470 52.381 11.47 0.00 0.00 3.06
508 2694 1.415289 AGGATCAAGAGCGCATCATCA 59.585 47.619 11.47 0.00 0.00 3.07
509 2695 2.067766 GAGGATCAAGAGCGCATCATC 58.932 52.381 11.47 6.89 33.17 2.92
510 2696 1.415289 TGAGGATCAAGAGCGCATCAT 59.585 47.619 11.47 0.00 45.97 2.45
511 2697 0.826062 TGAGGATCAAGAGCGCATCA 59.174 50.000 11.47 0.00 45.97 3.07
512 2698 3.675086 TGAGGATCAAGAGCGCATC 57.325 52.632 11.47 2.63 45.97 3.91
520 2706 5.088010 GCAGAAGCAGCATGAGGATCAAG 62.088 52.174 0.00 0.00 45.72 3.02
521 2707 3.262777 GCAGAAGCAGCATGAGGATCAA 61.263 50.000 0.00 0.00 45.72 2.57
522 2708 1.746171 GCAGAAGCAGCATGAGGATCA 60.746 52.381 0.00 0.00 46.38 2.92
523 2709 0.945813 GCAGAAGCAGCATGAGGATC 59.054 55.000 0.00 0.00 39.69 3.36
524 2710 0.547075 AGCAGAAGCAGCATGAGGAT 59.453 50.000 0.00 0.00 45.49 3.24
525 2711 0.107800 GAGCAGAAGCAGCATGAGGA 60.108 55.000 0.00 0.00 45.49 3.71
526 2712 0.107606 AGAGCAGAAGCAGCATGAGG 60.108 55.000 0.00 0.00 45.49 3.86
527 2713 1.398739 CAAGAGCAGAAGCAGCATGAG 59.601 52.381 0.00 0.00 45.49 2.90
528 2714 1.002773 TCAAGAGCAGAAGCAGCATGA 59.997 47.619 0.00 0.00 45.49 3.07
529 2715 1.450025 TCAAGAGCAGAAGCAGCATG 58.550 50.000 0.00 0.00 45.49 4.06
530 2716 1.811359 GTTCAAGAGCAGAAGCAGCAT 59.189 47.619 0.00 0.00 45.49 3.79
531 2717 1.233019 GTTCAAGAGCAGAAGCAGCA 58.767 50.000 0.00 0.00 45.49 4.41
532 2718 1.233019 TGTTCAAGAGCAGAAGCAGC 58.767 50.000 0.00 0.00 45.49 5.25
533 2719 3.072211 TCATGTTCAAGAGCAGAAGCAG 58.928 45.455 0.00 0.00 45.49 4.24
534 2720 3.072211 CTCATGTTCAAGAGCAGAAGCA 58.928 45.455 0.00 0.00 45.49 3.91
535 2721 3.743567 CTCATGTTCAAGAGCAGAAGC 57.256 47.619 0.00 0.00 42.56 3.86
542 2728 3.922910 TGACTCAGCTCATGTTCAAGAG 58.077 45.455 0.00 1.36 35.01 2.85
543 2729 4.341366 TTGACTCAGCTCATGTTCAAGA 57.659 40.909 0.00 0.00 32.09 3.02
544 2730 4.274214 TGTTTGACTCAGCTCATGTTCAAG 59.726 41.667 0.00 0.00 35.13 3.02
545 2731 4.198530 TGTTTGACTCAGCTCATGTTCAA 58.801 39.130 0.00 0.00 33.18 2.69
546 2732 3.807553 TGTTTGACTCAGCTCATGTTCA 58.192 40.909 0.00 0.00 0.00 3.18
547 2733 4.512944 TCTTGTTTGACTCAGCTCATGTTC 59.487 41.667 0.00 0.00 0.00 3.18
548 2734 4.454678 TCTTGTTTGACTCAGCTCATGTT 58.545 39.130 0.00 0.00 0.00 2.71
549 2735 4.063689 CTCTTGTTTGACTCAGCTCATGT 58.936 43.478 0.00 0.00 0.00 3.21
550 2736 3.120269 GCTCTTGTTTGACTCAGCTCATG 60.120 47.826 0.00 0.00 0.00 3.07
551 2737 3.072944 GCTCTTGTTTGACTCAGCTCAT 58.927 45.455 0.00 0.00 0.00 2.90
552 2738 2.158914 TGCTCTTGTTTGACTCAGCTCA 60.159 45.455 0.00 0.00 0.00 4.26
553 2739 2.479656 CTGCTCTTGTTTGACTCAGCTC 59.520 50.000 0.00 0.00 0.00 4.09
554 2740 2.492012 CTGCTCTTGTTTGACTCAGCT 58.508 47.619 0.00 0.00 0.00 4.24
555 2741 1.069364 GCTGCTCTTGTTTGACTCAGC 60.069 52.381 0.00 0.00 38.62 4.26
556 2742 2.216046 TGCTGCTCTTGTTTGACTCAG 58.784 47.619 0.00 0.00 0.00 3.35
557 2743 2.216046 CTGCTGCTCTTGTTTGACTCA 58.784 47.619 0.00 0.00 0.00 3.41
558 2744 1.534595 CCTGCTGCTCTTGTTTGACTC 59.465 52.381 0.00 0.00 0.00 3.36
559 2745 1.602311 CCTGCTGCTCTTGTTTGACT 58.398 50.000 0.00 0.00 0.00 3.41
560 2746 0.039708 GCCTGCTGCTCTTGTTTGAC 60.040 55.000 0.00 0.00 36.87 3.18
561 2747 0.466007 TGCCTGCTGCTCTTGTTTGA 60.466 50.000 0.00 0.00 42.00 2.69
562 2748 0.386476 TTGCCTGCTGCTCTTGTTTG 59.614 50.000 0.00 0.00 42.00 2.93
563 2749 0.386838 GTTGCCTGCTGCTCTTGTTT 59.613 50.000 0.00 0.00 42.00 2.83
564 2750 0.752743 TGTTGCCTGCTGCTCTTGTT 60.753 50.000 0.00 0.00 42.00 2.83
565 2751 0.752743 TTGTTGCCTGCTGCTCTTGT 60.753 50.000 0.00 0.00 42.00 3.16
566 2752 0.318445 GTTGTTGCCTGCTGCTCTTG 60.318 55.000 0.00 0.00 42.00 3.02
567 2753 0.466922 AGTTGTTGCCTGCTGCTCTT 60.467 50.000 0.00 0.00 42.00 2.85
568 2754 0.888285 GAGTTGTTGCCTGCTGCTCT 60.888 55.000 0.00 0.00 42.00 4.09
569 2755 1.578423 GAGTTGTTGCCTGCTGCTC 59.422 57.895 0.00 0.00 42.00 4.26
570 2756 1.900498 GGAGTTGTTGCCTGCTGCT 60.900 57.895 0.00 0.00 42.00 4.24
571 2757 2.647297 GGAGTTGTTGCCTGCTGC 59.353 61.111 0.00 0.00 41.77 5.25
572 2758 3.359002 GGGAGTTGTTGCCTGCTG 58.641 61.111 0.00 0.00 33.76 4.41
577 2763 2.203480 TGCCAGGGAGTTGTTGCC 60.203 61.111 0.00 0.00 37.61 4.52
578 2764 0.610232 ATCTGCCAGGGAGTTGTTGC 60.610 55.000 8.03 0.00 0.00 4.17
579 2765 1.171308 CATCTGCCAGGGAGTTGTTG 58.829 55.000 8.03 0.00 0.00 3.33
580 2766 0.038744 CCATCTGCCAGGGAGTTGTT 59.961 55.000 15.83 0.00 0.00 2.83
581 2767 1.687612 CCATCTGCCAGGGAGTTGT 59.312 57.895 15.83 0.00 0.00 3.32
626 2812 2.203126 CTGGCTCCCATCGGCTTC 60.203 66.667 0.00 0.00 30.82 3.86
726 2916 0.323629 TCCTAGGGTTTTGGTGCGAG 59.676 55.000 9.46 0.00 0.00 5.03
770 2965 3.375443 TAGGCTCGGGTGGAGGGAG 62.375 68.421 0.00 0.00 43.36 4.30
771 2966 3.352748 TAGGCTCGGGTGGAGGGA 61.353 66.667 0.00 0.00 43.36 4.20
782 2978 1.990060 TGGACTGTGGGCTAGGCTC 60.990 63.158 16.80 10.25 0.00 4.70
985 3183 3.152400 CGGACCCGGAACCCTAGG 61.152 72.222 0.73 0.06 35.56 3.02
1200 3398 2.254508 ACAAGGCGGAGGTAGTAAGTT 58.745 47.619 0.00 0.00 0.00 2.66
1202 3400 4.667519 ATAACAAGGCGGAGGTAGTAAG 57.332 45.455 0.00 0.00 0.00 2.34
1255 3459 2.931325 AGCAACTCGTAACAACAAACGA 59.069 40.909 0.00 0.00 45.17 3.85
1317 3521 5.391629 GCCTAACGAACAAAGGAAATTCGAT 60.392 40.000 12.10 3.42 46.28 3.59
1348 3553 1.101049 CAGGAACGCAAACCACACCT 61.101 55.000 0.00 0.00 0.00 4.00
1395 3600 1.055040 CTCCAGATCTAGGGGCCAAG 58.945 60.000 4.39 1.64 0.00 3.61
1416 3621 2.912771 CATTACGGTCAAGGGCATACA 58.087 47.619 0.00 0.00 0.00 2.29
1423 3628 1.940613 GCCTAAGCATTACGGTCAAGG 59.059 52.381 0.00 0.00 39.53 3.61
1451 3656 1.270839 TGTTTAGCAGGACACAGAGGC 60.271 52.381 0.00 0.00 0.00 4.70
1524 3738 1.619363 TCCCCTAATGCAGCCACCT 60.619 57.895 0.00 0.00 0.00 4.00
1536 3750 0.974010 CTGCAACCGTACCTCCCCTA 60.974 60.000 0.00 0.00 0.00 3.53
1587 3801 6.071784 TGCAATGCAGACAGATATTTTTCTGT 60.072 34.615 2.72 6.80 45.48 3.41
1588 3802 6.327154 TGCAATGCAGACAGATATTTTTCTG 58.673 36.000 2.72 5.29 40.42 3.02
1602 3817 1.000646 TGCCCTGATGCAATGCAGA 60.001 52.632 14.98 1.54 43.65 4.26
1656 3871 8.887717 CCCTACAATAACAATCTTCTTCTTGAG 58.112 37.037 0.00 0.00 0.00 3.02
1657 3872 8.383175 ACCCTACAATAACAATCTTCTTCTTGA 58.617 33.333 0.00 0.00 0.00 3.02
1658 3873 8.567285 ACCCTACAATAACAATCTTCTTCTTG 57.433 34.615 0.00 0.00 0.00 3.02
1659 3874 9.588096 AAACCCTACAATAACAATCTTCTTCTT 57.412 29.630 0.00 0.00 0.00 2.52
1660 3875 9.588096 AAAACCCTACAATAACAATCTTCTTCT 57.412 29.630 0.00 0.00 0.00 2.85
1661 3876 9.626045 CAAAACCCTACAATAACAATCTTCTTC 57.374 33.333 0.00 0.00 0.00 2.87
1662 3877 8.088365 GCAAAACCCTACAATAACAATCTTCTT 58.912 33.333 0.00 0.00 0.00 2.52
1663 3878 7.309805 GGCAAAACCCTACAATAACAATCTTCT 60.310 37.037 0.00 0.00 0.00 2.85
1679 3894 2.863809 CTCTACAACTGGCAAAACCCT 58.136 47.619 0.00 0.00 37.83 4.34
2009 4228 4.545610 CCAACAGCAAACGTAATCACAAT 58.454 39.130 0.00 0.00 0.00 2.71
2077 4296 4.935205 TCATTCAACAGCCACAGTACATAC 59.065 41.667 0.00 0.00 0.00 2.39
2094 4313 2.670905 CCGCAAATACGACACTCATTCA 59.329 45.455 0.00 0.00 34.06 2.57
2154 4373 6.995686 GGATTTTCAATAAAACCAGTTTGGGT 59.004 34.615 0.00 0.00 40.89 4.51
2484 4721 6.714810 ACAGAAAACTATACATTGCAGTGGAA 59.285 34.615 14.25 0.00 0.00 3.53
2533 4770 5.480642 TTTGATTCTGCCAAATTGCCTAA 57.519 34.783 0.00 0.00 0.00 2.69
2534 4771 5.395546 GGATTTGATTCTGCCAAATTGCCTA 60.396 40.000 0.00 0.00 42.35 3.93
2567 4804 1.093159 CTGCATCCTTGTTCTCAGGC 58.907 55.000 0.00 0.00 0.00 4.85
2603 4840 3.632855 TCCTCATCTTCATCATCGTCG 57.367 47.619 0.00 0.00 0.00 5.12
2669 4906 2.301583 GCCTTCTTCACCTGAGAAGTCT 59.698 50.000 11.58 0.00 44.18 3.24
2678 4915 1.878656 CGTCCTCGCCTTCTTCACCT 61.879 60.000 0.00 0.00 0.00 4.00
2708 4945 3.064987 ATTCGCCTCAGGGTCGTCG 62.065 63.158 0.00 0.00 35.06 5.12
2711 4948 2.202932 CCATTCGCCTCAGGGTCG 60.203 66.667 0.00 0.00 34.90 4.79
2774 5014 3.483421 GCCATCTTCACCATCATCATCA 58.517 45.455 0.00 0.00 0.00 3.07
2807 5047 1.882623 TCCTCGTCCTCATCATCATCG 59.117 52.381 0.00 0.00 0.00 3.84
2816 5056 0.106469 CCTCCTCATCCTCGTCCTCA 60.106 60.000 0.00 0.00 0.00 3.86
2918 5158 5.840715 TCAATCATCATCTAGACAGCAGAC 58.159 41.667 0.00 0.00 0.00 3.51
3177 5417 7.566760 TTCACTCACAAGAAGCATAAAGAAA 57.433 32.000 0.00 0.00 0.00 2.52
3204 5444 7.069208 TCAGATAGCAGTCATACAAACTCTGAT 59.931 37.037 0.00 0.00 0.00 2.90
3244 5485 2.683362 CGCCTTTTCCTTCCAGGTTATC 59.317 50.000 0.00 0.00 36.53 1.75
3265 5506 3.060895 CGGTTCTTCTGTTAGATTGACGC 59.939 47.826 0.00 0.00 0.00 5.19
3277 5519 4.214119 TCAAATGCTTCTTCGGTTCTTCTG 59.786 41.667 0.00 0.00 0.00 3.02
3312 5554 1.916651 CTGAAACACTGAGATCGCGAG 59.083 52.381 16.66 2.26 0.00 5.03
3313 5555 1.402852 CCTGAAACACTGAGATCGCGA 60.403 52.381 13.09 13.09 0.00 5.87
3315 5557 2.370281 TCCTGAAACACTGAGATCGC 57.630 50.000 0.00 0.00 0.00 4.58
3316 5558 3.193263 CCATCCTGAAACACTGAGATCG 58.807 50.000 0.00 0.00 0.00 3.69
3317 5559 3.198635 TCCCATCCTGAAACACTGAGATC 59.801 47.826 0.00 0.00 0.00 2.75
3318 5560 3.054802 GTCCCATCCTGAAACACTGAGAT 60.055 47.826 0.00 0.00 0.00 2.75
3320 5562 2.038952 TGTCCCATCCTGAAACACTGAG 59.961 50.000 0.00 0.00 0.00 3.35
3345 5625 1.203287 GTTTTCCATTGCTGGGAGCTC 59.797 52.381 4.71 4.71 42.97 4.09
3399 5679 6.245724 GGTGCACGTATGTTTAGTTATGTTC 58.754 40.000 11.45 0.00 0.00 3.18
3405 5685 1.461897 GCGGTGCACGTATGTTTAGTT 59.538 47.619 11.45 0.00 46.52 2.24
3417 5702 2.050077 GCCTTTTCTGCGGTGCAC 60.050 61.111 8.80 8.80 33.79 4.57
3443 5736 7.988028 TCCATATACGGTAGAGATCTCTGTATG 59.012 40.741 31.46 23.95 40.71 2.39
3536 5829 0.393820 CCTGCCCAGCAAATTTGTGT 59.606 50.000 19.03 4.82 38.41 3.72
3537 5830 0.320946 CCCTGCCCAGCAAATTTGTG 60.321 55.000 19.03 14.71 38.41 3.33
3538 5831 0.763986 ACCCTGCCCAGCAAATTTGT 60.764 50.000 19.03 3.98 38.41 2.83
3593 5888 6.605594 AGAGAGAGTAATCAGTAGTCAAAGGG 59.394 42.308 0.00 0.00 34.93 3.95
3617 5912 3.589988 AGTTGGCATCAGAGTCGTTAAG 58.410 45.455 0.00 0.00 0.00 1.85
3628 5923 3.896888 AGGATTTCAACAAGTTGGCATCA 59.103 39.130 12.54 0.00 40.78 3.07
3945 6240 7.881775 AAAAGGCGATTTCTTCTATTGGTAT 57.118 32.000 0.00 0.00 0.00 2.73
3966 6261 4.470334 AGCAGAGTTGGCAAAAGAAAAA 57.530 36.364 0.00 0.00 0.00 1.94
4013 6322 3.119316 AGTGCCAATCTCTAACGAGTCTG 60.119 47.826 0.00 0.00 38.45 3.51
4015 6324 3.119459 TCAGTGCCAATCTCTAACGAGTC 60.119 47.826 0.00 0.00 38.45 3.36
4016 6325 2.826128 TCAGTGCCAATCTCTAACGAGT 59.174 45.455 0.00 0.00 38.45 4.18
4018 6327 3.953712 TTCAGTGCCAATCTCTAACGA 57.046 42.857 0.00 0.00 0.00 3.85
4019 6328 3.997021 AGTTTCAGTGCCAATCTCTAACG 59.003 43.478 0.00 0.00 0.00 3.18
4020 6329 5.351740 GGTAGTTTCAGTGCCAATCTCTAAC 59.648 44.000 0.00 0.00 0.00 2.34
4021 6330 5.012664 TGGTAGTTTCAGTGCCAATCTCTAA 59.987 40.000 0.00 0.00 30.07 2.10
4022 6331 4.530553 TGGTAGTTTCAGTGCCAATCTCTA 59.469 41.667 0.00 0.00 30.07 2.43
4186 6495 3.356290 CCCCTTTGTTTGGACCAGATAG 58.644 50.000 0.00 0.00 0.00 2.08
4189 6498 0.187361 CCCCCTTTGTTTGGACCAGA 59.813 55.000 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.