Multiple sequence alignment - TraesCS4B01G135100

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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 TraesCS4B01G135100 chr4B 100.000 3492 0 0 1 3492 176269077 176265586 0.000000e+00 6449
1 TraesCS4B01G135100 chr4A 96.266 1687 50 7 833 2508 460905150 460903466 0.000000e+00 2754
2 TraesCS4B01G135100 chr4A 95.874 824 21 3 2669 3492 460903467 460902657 0.000000e+00 1321
3 TraesCS4B01G135100 chr4A 90.229 829 67 6 1 821 460906431 460905609 0.000000e+00 1070
4 TraesCS4B01G135100 chr4A 94.350 177 9 1 2502 2678 713022189 713022014 1.600000e-68 270
5 TraesCS4B01G135100 chr4D 95.026 1568 43 15 952 2508 115932148 115933691 0.000000e+00 2431
6 TraesCS4B01G135100 chr4D 97.451 824 17 2 2669 3492 115933690 115934509 0.000000e+00 1402
7 TraesCS4B01G135100 chr4D 89.676 833 76 5 1 826 115929526 115930355 0.000000e+00 1053
8 TraesCS4B01G135100 chr6B 96.450 169 6 0 2502 2670 29400051 29399883 2.650000e-71 279
9 TraesCS4B01G135100 chr6B 92.778 180 12 1 2491 2670 703686140 703685962 3.460000e-65 259
10 TraesCS4B01G135100 chr7D 95.833 168 7 0 2503 2670 99776868 99776701 4.440000e-69 272
11 TraesCS4B01G135100 chr7D 94.767 172 9 0 2496 2667 485741494 485741665 5.750000e-68 268
12 TraesCS4B01G135100 chr5D 96.364 165 6 0 2507 2671 198477388 198477552 4.440000e-69 272
13 TraesCS4B01G135100 chr1D 94.286 175 10 0 2496 2670 315471097 315470923 5.750000e-68 268
14 TraesCS4B01G135100 chr2B 93.820 178 10 1 2502 2678 243786509 243786686 2.070000e-67 267
15 TraesCS4B01G135100 chr5B 93.296 179 10 2 2502 2679 64265978 64265801 2.670000e-66 263


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 TraesCS4B01G135100 chr4B 176265586 176269077 3491 True 6449.000000 6449 100.000 1 3492 1 chr4B.!!$R1 3491
1 TraesCS4B01G135100 chr4A 460902657 460906431 3774 True 1715.000000 2754 94.123 1 3492 3 chr4A.!!$R2 3491
2 TraesCS4B01G135100 chr4D 115929526 115934509 4983 False 1628.666667 2431 94.051 1 3492 3 chr4D.!!$F1 3491

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
746 755 0.169009 TCACTGTGAGCTCGACATCG 59.831 55.0 16.08 11.58 41.45 3.84 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2653 4470 0.043637 ACCTATTCCCTCCGTTCCCA 59.956 55.0 0.0 0.0 0.0 4.37 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
19 20 2.153401 CAACCAGACCCCCAGACCA 61.153 63.158 0.00 0.00 0.00 4.02
50 51 3.763057 TCTTATATAGCCAGGCTGACGA 58.237 45.455 25.59 3.72 40.10 4.20
65 66 1.770061 TGACGAACACCCCTTAAACCT 59.230 47.619 0.00 0.00 0.00 3.50
103 104 4.572571 TTGGAGCCGCCCAAACGT 62.573 61.111 9.99 0.00 42.75 3.99
190 191 8.307483 GGATCAAATCCTAGTGATTCTCGATTA 58.693 37.037 6.84 0.00 42.97 1.75
206 207 6.936279 TCTCGATTAACTCCATTTTCAGTCT 58.064 36.000 0.00 0.00 0.00 3.24
210 211 3.515602 AACTCCATTTTCAGTCTGCCT 57.484 42.857 0.00 0.00 0.00 4.75
235 237 0.616679 CCCAACCTAACCTCTCCGGA 60.617 60.000 2.93 2.93 36.31 5.14
239 241 2.236395 CAACCTAACCTCTCCGGACATT 59.764 50.000 0.00 0.00 36.31 2.71
259 261 3.610040 TTCCGACATGACTAGCAACAT 57.390 42.857 0.00 0.00 0.00 2.71
314 316 1.953686 GAGCTAGACTCCTGCTCGAAT 59.046 52.381 0.00 0.00 42.70 3.34
339 341 1.360852 AGGGGACATCTGTCAGTCTCT 59.639 52.381 12.10 0.00 46.47 3.10
394 396 4.660938 GCCGGAGCCACCCTTGTT 62.661 66.667 5.05 0.00 34.64 2.83
445 447 3.084039 CCACTCAGGCAAAAATCTAGCA 58.916 45.455 0.00 0.00 0.00 3.49
486 488 2.879070 CTCGCGCCACATGAGCATC 61.879 63.158 0.00 0.00 0.00 3.91
489 491 1.816679 GCGCCACATGAGCATCTCA 60.817 57.895 0.00 0.00 44.99 3.27
519 521 1.078497 GCCCACATGACACCGATGA 60.078 57.895 0.00 0.00 0.00 2.92
593 595 0.872021 GACGATGGAGATGCGTGTCC 60.872 60.000 15.17 15.17 38.51 4.02
596 598 0.460284 GATGGAGATGCGTGTCCGTT 60.460 55.000 17.39 7.60 40.62 4.44
638 640 4.129380 CTCGATGAAGGCATTGGTGAATA 58.871 43.478 0.00 0.00 36.68 1.75
687 689 2.069273 CAATCTTCAACTTCGGCTCGT 58.931 47.619 0.00 0.00 0.00 4.18
715 717 1.203313 AGGTTACCAGAGAAGAGGGCA 60.203 52.381 3.51 0.00 0.00 5.36
746 755 0.169009 TCACTGTGAGCTCGACATCG 59.831 55.000 16.08 11.58 41.45 3.84
750 759 1.398739 CTGTGAGCTCGACATCGTACT 59.601 52.381 16.08 0.07 40.80 2.73
821 830 0.179040 GTCTTCGTGGTTTGGGGTGA 60.179 55.000 0.00 0.00 0.00 4.02
826 835 1.147600 GTGGTTTGGGGTGACGAGT 59.852 57.895 0.00 0.00 0.00 4.18
828 837 1.052124 TGGTTTGGGGTGACGAGTCT 61.052 55.000 4.78 0.00 0.00 3.24
829 838 0.971386 GGTTTGGGGTGACGAGTCTA 59.029 55.000 4.78 0.00 0.00 2.59
830 839 1.067071 GGTTTGGGGTGACGAGTCTAG 60.067 57.143 4.78 0.00 0.00 2.43
836 2629 2.440409 GGGTGACGAGTCTAGGTAACA 58.560 52.381 4.78 0.00 41.41 2.41
884 2680 6.701340 AGATGGGTCTGCTTTTAAAATTTCC 58.299 36.000 0.09 1.13 32.13 3.13
894 2690 6.058833 GCTTTTAAAATTTCCACTTTCCCCA 58.941 36.000 0.09 0.00 0.00 4.96
1155 2951 0.108329 CGCCGGTAACTTCTCCACAT 60.108 55.000 1.90 0.00 0.00 3.21
1211 3007 3.085533 CAATCGACATTACCCCCAAACA 58.914 45.455 0.00 0.00 0.00 2.83
1215 3011 3.009695 TCGACATTACCCCCAAACAGATT 59.990 43.478 0.00 0.00 0.00 2.40
1216 3012 4.225492 TCGACATTACCCCCAAACAGATTA 59.775 41.667 0.00 0.00 0.00 1.75
1219 3015 5.646215 ACATTACCCCCAAACAGATTAACA 58.354 37.500 0.00 0.00 0.00 2.41
1621 3418 2.516930 GGGGATCCGTCCGTCGTA 60.517 66.667 5.45 0.00 46.09 3.43
1760 3557 2.202864 GCGAGAAGAGAGCCCAGC 60.203 66.667 0.00 0.00 0.00 4.85
1804 3601 3.734597 GCGCATTTGGTTAGCAATGATCA 60.735 43.478 0.30 0.00 32.91 2.92
1826 3635 4.154918 CACCCTCTCTTGTTTGCATTCTAC 59.845 45.833 0.00 0.00 0.00 2.59
1842 3651 2.343101 TCTACTTTCGGCGAACCATTG 58.657 47.619 23.64 11.37 34.57 2.82
1911 3720 8.844244 ACATGAAGATAAAATGGCTATCTGTTC 58.156 33.333 0.00 0.00 36.46 3.18
1929 3738 5.530543 TCTGTTCTGTGCATGATTTACAACA 59.469 36.000 0.00 0.00 0.00 3.33
2007 3816 2.031157 CGTTGCCGAAAACTGGAAAGAT 60.031 45.455 0.00 0.00 35.63 2.40
2141 3950 5.239306 TGTGAGCTGGTTTCTTTCTTACATG 59.761 40.000 0.00 0.00 0.00 3.21
2367 4178 4.660789 AGCAACTCTTTTCACAGCAAAT 57.339 36.364 0.00 0.00 0.00 2.32
2379 4190 3.441496 ACAGCAAATTCAGTGTTGTGG 57.559 42.857 0.00 0.00 38.76 4.17
2401 4212 7.227116 TGTGGAGTGTACACTTTGGTTTATAAC 59.773 37.037 28.49 11.51 42.66 1.89
2497 4314 5.984926 TCAAATGACAATTCTTTTCCTGTGC 59.015 36.000 0.00 0.00 28.95 4.57
2506 4323 5.401531 TTCTTTTCCTGTGCGTACTATCT 57.598 39.130 4.97 0.00 0.00 1.98
2507 4324 6.519679 TTCTTTTCCTGTGCGTACTATCTA 57.480 37.500 4.97 0.00 0.00 1.98
2508 4325 5.888105 TCTTTTCCTGTGCGTACTATCTAC 58.112 41.667 4.97 0.00 0.00 2.59
2509 4326 5.651139 TCTTTTCCTGTGCGTACTATCTACT 59.349 40.000 4.97 0.00 0.00 2.57
2510 4327 5.496133 TTTCCTGTGCGTACTATCTACTC 57.504 43.478 4.97 0.00 0.00 2.59
2511 4328 3.474600 TCCTGTGCGTACTATCTACTCC 58.525 50.000 4.97 0.00 0.00 3.85
2512 4329 2.553172 CCTGTGCGTACTATCTACTCCC 59.447 54.545 4.97 0.00 0.00 4.30
2513 4330 3.478509 CTGTGCGTACTATCTACTCCCT 58.521 50.000 4.97 0.00 0.00 4.20
2514 4331 3.474600 TGTGCGTACTATCTACTCCCTC 58.525 50.000 4.97 0.00 0.00 4.30
2515 4332 2.813172 GTGCGTACTATCTACTCCCTCC 59.187 54.545 0.00 0.00 0.00 4.30
2516 4333 2.075338 GCGTACTATCTACTCCCTCCG 58.925 57.143 0.00 0.00 0.00 4.63
2517 4334 2.549778 GCGTACTATCTACTCCCTCCGT 60.550 54.545 0.00 0.00 0.00 4.69
2518 4335 3.737850 CGTACTATCTACTCCCTCCGTT 58.262 50.000 0.00 0.00 0.00 4.44
2519 4336 3.745458 CGTACTATCTACTCCCTCCGTTC 59.255 52.174 0.00 0.00 0.00 3.95
2520 4337 3.226682 ACTATCTACTCCCTCCGTTCC 57.773 52.381 0.00 0.00 0.00 3.62
2521 4338 2.158490 ACTATCTACTCCCTCCGTTCCC 60.158 54.545 0.00 0.00 0.00 3.97
2522 4339 0.635009 ATCTACTCCCTCCGTTCCCA 59.365 55.000 0.00 0.00 0.00 4.37
2523 4340 0.410663 TCTACTCCCTCCGTTCCCAA 59.589 55.000 0.00 0.00 0.00 4.12
2524 4341 1.203212 TCTACTCCCTCCGTTCCCAAA 60.203 52.381 0.00 0.00 0.00 3.28
2525 4342 1.838077 CTACTCCCTCCGTTCCCAAAT 59.162 52.381 0.00 0.00 0.00 2.32
2526 4343 1.961133 ACTCCCTCCGTTCCCAAATA 58.039 50.000 0.00 0.00 0.00 1.40
2527 4344 2.488836 ACTCCCTCCGTTCCCAAATAT 58.511 47.619 0.00 0.00 0.00 1.28
2528 4345 2.850568 ACTCCCTCCGTTCCCAAATATT 59.149 45.455 0.00 0.00 0.00 1.28
2529 4346 3.268595 ACTCCCTCCGTTCCCAAATATTT 59.731 43.478 0.00 0.00 0.00 1.40
2530 4347 3.626930 TCCCTCCGTTCCCAAATATTTG 58.373 45.455 19.40 19.40 37.90 2.32
2531 4348 3.010808 TCCCTCCGTTCCCAAATATTTGT 59.989 43.478 23.24 0.00 36.45 2.83
2532 4349 3.380320 CCCTCCGTTCCCAAATATTTGTC 59.620 47.826 23.24 11.68 36.45 3.18
2533 4350 4.270008 CCTCCGTTCCCAAATATTTGTCT 58.730 43.478 23.24 0.00 36.45 3.41
2534 4351 4.705023 CCTCCGTTCCCAAATATTTGTCTT 59.295 41.667 23.24 0.00 36.45 3.01
2535 4352 5.185056 CCTCCGTTCCCAAATATTTGTCTTT 59.815 40.000 23.24 0.00 36.45 2.52
2536 4353 6.262193 TCCGTTCCCAAATATTTGTCTTTC 57.738 37.500 23.24 10.84 36.45 2.62
2537 4354 6.007703 TCCGTTCCCAAATATTTGTCTTTCT 58.992 36.000 23.24 0.00 36.45 2.52
2538 4355 7.169591 TCCGTTCCCAAATATTTGTCTTTCTA 58.830 34.615 23.24 5.03 36.45 2.10
2539 4356 7.335924 TCCGTTCCCAAATATTTGTCTTTCTAG 59.664 37.037 23.24 8.23 36.45 2.43
2540 4357 7.415206 CCGTTCCCAAATATTTGTCTTTCTAGG 60.415 40.741 23.24 15.51 36.45 3.02
2541 4358 7.258441 GTTCCCAAATATTTGTCTTTCTAGGC 58.742 38.462 23.24 3.57 36.45 3.93
2542 4359 6.489603 TCCCAAATATTTGTCTTTCTAGGCA 58.510 36.000 23.24 5.94 36.45 4.75
2543 4360 7.125391 TCCCAAATATTTGTCTTTCTAGGCAT 58.875 34.615 23.24 0.00 35.56 4.40
2544 4361 7.619302 TCCCAAATATTTGTCTTTCTAGGCATT 59.381 33.333 23.24 0.00 35.56 3.56
2545 4362 8.260114 CCCAAATATTTGTCTTTCTAGGCATTT 58.740 33.333 23.24 0.00 35.56 2.32
2546 4363 9.305925 CCAAATATTTGTCTTTCTAGGCATTTC 57.694 33.333 23.24 0.00 35.56 2.17
2547 4364 9.859427 CAAATATTTGTCTTTCTAGGCATTTCA 57.141 29.630 18.32 0.00 35.56 2.69
2551 4368 8.767478 ATTTGTCTTTCTAGGCATTTCAAATG 57.233 30.769 5.68 5.68 35.56 2.32
2552 4369 6.271488 TGTCTTTCTAGGCATTTCAAATGG 57.729 37.500 12.14 0.00 29.10 3.16
2553 4370 6.009589 TGTCTTTCTAGGCATTTCAAATGGA 58.990 36.000 12.14 0.00 29.10 3.41
2554 4371 6.071952 TGTCTTTCTAGGCATTTCAAATGGAC 60.072 38.462 12.14 8.23 29.10 4.02
2555 4372 6.009589 TCTTTCTAGGCATTTCAAATGGACA 58.990 36.000 12.14 0.00 0.00 4.02
2556 4373 5.643379 TTCTAGGCATTTCAAATGGACAC 57.357 39.130 12.14 0.00 0.00 3.67
2557 4374 4.661222 TCTAGGCATTTCAAATGGACACA 58.339 39.130 12.14 0.00 0.00 3.72
2558 4375 5.076182 TCTAGGCATTTCAAATGGACACAA 58.924 37.500 12.14 0.00 0.00 3.33
2559 4376 3.993920 AGGCATTTCAAATGGACACAAC 58.006 40.909 12.14 0.00 0.00 3.32
2560 4377 3.387374 AGGCATTTCAAATGGACACAACA 59.613 39.130 12.14 0.00 0.00 3.33
2561 4378 4.040706 AGGCATTTCAAATGGACACAACAT 59.959 37.500 12.14 0.00 0.00 2.71
2562 4379 5.245751 AGGCATTTCAAATGGACACAACATA 59.754 36.000 12.14 0.00 0.00 2.29
2563 4380 5.348451 GGCATTTCAAATGGACACAACATAC 59.652 40.000 12.14 0.00 0.00 2.39
2564 4381 5.060816 GCATTTCAAATGGACACAACATACG 59.939 40.000 12.14 0.00 0.00 3.06
2565 4382 4.757799 TTCAAATGGACACAACATACGG 57.242 40.909 0.00 0.00 0.00 4.02
2566 4383 4.009370 TCAAATGGACACAACATACGGA 57.991 40.909 0.00 0.00 0.00 4.69
2567 4384 4.584874 TCAAATGGACACAACATACGGAT 58.415 39.130 0.00 0.00 0.00 4.18
2568 4385 4.394610 TCAAATGGACACAACATACGGATG 59.605 41.667 5.94 5.94 39.16 3.51
2570 4387 4.746535 ATGGACACAACATACGGATGTA 57.253 40.909 15.10 0.00 45.93 2.29
2571 4388 4.746535 TGGACACAACATACGGATGTAT 57.253 40.909 15.10 2.23 45.93 2.29
2608 4425 9.677567 TTTAAAGTGTAGATTCACTCATTTTGC 57.322 29.630 0.00 0.00 46.25 3.68
2609 4426 7.516198 AAAGTGTAGATTCACTCATTTTGCT 57.484 32.000 0.00 0.00 46.25 3.91
2610 4427 7.516198 AAGTGTAGATTCACTCATTTTGCTT 57.484 32.000 0.00 0.00 46.25 3.91
2611 4428 7.138692 AGTGTAGATTCACTCATTTTGCTTC 57.861 36.000 0.00 0.00 44.07 3.86
2612 4429 6.017933 GTGTAGATTCACTCATTTTGCTTCG 58.982 40.000 0.00 0.00 35.68 3.79
2613 4430 5.700832 TGTAGATTCACTCATTTTGCTTCGT 59.299 36.000 0.00 0.00 0.00 3.85
2614 4431 6.871492 TGTAGATTCACTCATTTTGCTTCGTA 59.129 34.615 0.00 0.00 0.00 3.43
2615 4432 6.992063 AGATTCACTCATTTTGCTTCGTAT 57.008 33.333 0.00 0.00 0.00 3.06
2616 4433 6.779117 AGATTCACTCATTTTGCTTCGTATG 58.221 36.000 0.00 0.00 0.00 2.39
2617 4434 5.940192 TTCACTCATTTTGCTTCGTATGT 57.060 34.783 0.00 0.00 0.00 2.29
2618 4435 7.549134 AGATTCACTCATTTTGCTTCGTATGTA 59.451 33.333 0.00 0.00 0.00 2.29
2619 4436 6.647212 TCACTCATTTTGCTTCGTATGTAG 57.353 37.500 0.00 0.00 0.00 2.74
2620 4437 6.163476 TCACTCATTTTGCTTCGTATGTAGT 58.837 36.000 0.00 0.00 0.00 2.73
2621 4438 6.310467 TCACTCATTTTGCTTCGTATGTAGTC 59.690 38.462 0.00 0.00 0.00 2.59
2622 4439 6.090763 CACTCATTTTGCTTCGTATGTAGTCA 59.909 38.462 0.00 0.00 0.00 3.41
2623 4440 6.090898 ACTCATTTTGCTTCGTATGTAGTCAC 59.909 38.462 0.00 0.00 0.00 3.67
2624 4441 6.163476 TCATTTTGCTTCGTATGTAGTCACT 58.837 36.000 0.00 0.00 0.00 3.41
2625 4442 6.649141 TCATTTTGCTTCGTATGTAGTCACTT 59.351 34.615 0.00 0.00 0.00 3.16
2626 4443 5.839262 TTTGCTTCGTATGTAGTCACTTG 57.161 39.130 0.00 0.00 0.00 3.16
2627 4444 4.776795 TGCTTCGTATGTAGTCACTTGA 57.223 40.909 0.00 0.00 0.00 3.02
2628 4445 5.324784 TGCTTCGTATGTAGTCACTTGAT 57.675 39.130 0.00 0.00 0.00 2.57
2629 4446 5.102313 TGCTTCGTATGTAGTCACTTGATG 58.898 41.667 0.00 0.00 0.00 3.07
2630 4447 5.105917 TGCTTCGTATGTAGTCACTTGATGA 60.106 40.000 0.00 0.00 33.79 2.92
2631 4448 5.805486 GCTTCGTATGTAGTCACTTGATGAA 59.195 40.000 0.00 0.00 39.72 2.57
2632 4449 6.310467 GCTTCGTATGTAGTCACTTGATGAAA 59.690 38.462 0.00 0.00 39.72 2.69
2633 4450 7.010552 GCTTCGTATGTAGTCACTTGATGAAAT 59.989 37.037 0.00 0.00 39.72 2.17
2634 4451 7.987268 TCGTATGTAGTCACTTGATGAAATC 57.013 36.000 0.00 0.00 45.83 2.17
2635 4452 7.772166 TCGTATGTAGTCACTTGATGAAATCT 58.228 34.615 0.00 0.00 45.81 2.40
2636 4453 8.251026 TCGTATGTAGTCACTTGATGAAATCTT 58.749 33.333 0.00 0.00 45.81 2.40
2637 4454 8.873830 CGTATGTAGTCACTTGATGAAATCTTT 58.126 33.333 0.00 0.00 45.81 2.52
2641 4458 9.996554 TGTAGTCACTTGATGAAATCTTTAGAA 57.003 29.630 0.00 0.00 45.81 2.10
2644 4461 9.784531 AGTCACTTGATGAAATCTTTAGAAAGA 57.215 29.630 7.15 7.15 45.81 2.52
2645 4462 9.818796 GTCACTTGATGAAATCTTTAGAAAGAC 57.181 33.333 6.85 0.00 45.81 3.01
2646 4463 9.559732 TCACTTGATGAAATCTTTAGAAAGACA 57.440 29.630 6.85 2.17 45.81 3.41
2660 4477 9.341899 CTTTAGAAAGACAAATATTTGGGAACG 57.658 33.333 27.43 6.31 42.34 3.95
2661 4478 6.267496 AGAAAGACAAATATTTGGGAACGG 57.733 37.500 27.43 5.66 42.34 4.44
2662 4479 6.007703 AGAAAGACAAATATTTGGGAACGGA 58.992 36.000 27.43 0.00 42.34 4.69
2663 4480 5.897377 AAGACAAATATTTGGGAACGGAG 57.103 39.130 27.43 4.34 42.34 4.63
2664 4481 4.270008 AGACAAATATTTGGGAACGGAGG 58.730 43.478 27.43 3.68 42.34 4.30
2665 4482 3.361786 ACAAATATTTGGGAACGGAGGG 58.638 45.455 27.43 3.22 42.34 4.30
2666 4483 3.010808 ACAAATATTTGGGAACGGAGGGA 59.989 43.478 27.43 0.00 42.34 4.20
2667 4484 4.020543 CAAATATTTGGGAACGGAGGGAA 58.979 43.478 18.72 0.00 34.59 3.97
2832 4649 2.238898 AGATTACCCCTTTGTTCCCTCG 59.761 50.000 0.00 0.00 0.00 4.63
2954 4771 7.070447 TGTCAGATAGCTCACCTATTCAATTCT 59.930 37.037 0.00 0.00 36.88 2.40
3344 5161 1.667724 CTTAGCTCTCCACAATTGCCG 59.332 52.381 5.05 0.00 0.00 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 51 5.594199 ATGAACTAGGTTTAAGGGGTGTT 57.406 39.130 0.00 0.00 0.00 3.32
65 66 5.589855 CCAAATCTGTGGCACATATGAACTA 59.410 40.000 22.35 0.00 44.52 2.24
103 104 1.913262 AGGTCCGACATGGCAGACA 60.913 57.895 16.72 0.00 37.80 3.41
131 132 1.908619 GGAAGGGGATTTTGTGGCATT 59.091 47.619 0.00 0.00 0.00 3.56
190 191 3.515602 AGGCAGACTGAAAATGGAGTT 57.484 42.857 6.65 0.00 0.00 3.01
206 207 1.431195 TTAGGTTGGGGAGCAAGGCA 61.431 55.000 0.00 0.00 0.00 4.75
210 211 0.696501 GAGGTTAGGTTGGGGAGCAA 59.303 55.000 0.00 0.00 0.00 3.91
235 237 3.610040 TGCTAGTCATGTCGGAAATGT 57.390 42.857 7.99 0.00 0.00 2.71
239 241 3.610040 ATGTTGCTAGTCATGTCGGAA 57.390 42.857 0.00 0.00 0.00 4.30
270 272 4.022242 CCAGTCGATGTATCCGGATTAGTT 60.022 45.833 24.71 5.38 0.00 2.24
273 275 2.823747 CCCAGTCGATGTATCCGGATTA 59.176 50.000 24.71 12.97 0.00 1.75
275 277 1.203013 TCCCAGTCGATGTATCCGGAT 60.203 52.381 22.95 22.95 0.00 4.18
307 309 0.537188 TGTCCCCTTCTCATTCGAGC 59.463 55.000 0.00 0.00 39.30 5.03
314 316 2.182827 CTGACAGATGTCCCCTTCTCA 58.817 52.381 10.34 0.00 44.15 3.27
339 341 3.574952 CCAGGACTGGTGGACCAA 58.425 61.111 10.22 0.00 46.97 3.67
361 363 1.890894 GGCGACAGAGCTGGAGTAA 59.109 57.895 0.00 0.00 37.29 2.24
441 443 1.202758 CCATAATTGACGCCCCTGCTA 60.203 52.381 0.00 0.00 34.43 3.49
445 447 1.525995 CGCCATAATTGACGCCCCT 60.526 57.895 0.00 0.00 0.00 4.79
508 510 2.428530 CAGGATCTCTTCATCGGTGTCA 59.571 50.000 0.00 0.00 0.00 3.58
593 595 1.129809 GCGTGACGTGGATCAAACG 59.870 57.895 16.09 16.09 46.32 3.60
596 598 1.075979 CATCGCGTGACGTGGATCAA 61.076 55.000 18.98 0.00 44.19 2.57
746 755 4.384846 CCACTACATGACACGTTTGAGTAC 59.615 45.833 0.00 0.00 0.00 2.73
750 759 2.139917 GCCACTACATGACACGTTTGA 58.860 47.619 0.00 0.00 0.00 2.69
932 2728 4.158394 CGGGTCATTCATTTGAAATGGAGT 59.842 41.667 17.01 2.09 37.61 3.85
1022 2818 1.392534 GGGGGAAGAGGACAGGAGA 59.607 63.158 0.00 0.00 0.00 3.71
1155 2951 2.110578 TGGATCAAGAAGCGATCTGGA 58.889 47.619 2.59 2.59 42.43 3.86
1211 3007 4.383118 CGAGGTGGAATCTGGTGTTAATCT 60.383 45.833 0.00 0.00 0.00 2.40
1215 3011 1.553248 CCGAGGTGGAATCTGGTGTTA 59.447 52.381 0.00 0.00 42.00 2.41
1216 3012 0.324943 CCGAGGTGGAATCTGGTGTT 59.675 55.000 0.00 0.00 42.00 3.32
1219 3015 1.553704 GTTACCGAGGTGGAATCTGGT 59.446 52.381 4.80 0.00 42.00 4.00
1357 3154 2.752640 TAGGCGACGCAGCTGGTA 60.753 61.111 23.09 0.00 37.29 3.25
1414 3211 1.225704 GGTCTTGCCCAGGATCCAG 59.774 63.158 15.82 5.70 0.00 3.86
1586 3383 2.677875 GGGAGGCAGGTGCTTTGG 60.678 66.667 1.26 0.00 41.70 3.28
1621 3418 1.572085 GCAGCTCACACGTGCAATCT 61.572 55.000 17.22 5.29 37.16 2.40
1804 3601 3.515602 AGAATGCAAACAAGAGAGGGT 57.484 42.857 0.00 0.00 0.00 4.34
1826 3635 1.511887 CGCAATGGTTCGCCGAAAG 60.512 57.895 0.00 0.00 41.18 2.62
1842 3651 8.510132 AATACAACAAAATTACCAAACTACGC 57.490 30.769 0.00 0.00 0.00 4.42
1873 3682 7.667043 TTTATCTTCATGTGGTGTCACTTAC 57.333 36.000 2.35 3.70 43.94 2.34
1874 3683 8.729756 CATTTTATCTTCATGTGGTGTCACTTA 58.270 33.333 2.35 0.00 43.94 2.24
1911 3720 6.151004 TGATGTTGTTGTAAATCATGCACAG 58.849 36.000 0.00 0.00 0.00 3.66
1929 3738 4.330250 CACTTCTTCCATGACCTGATGTT 58.670 43.478 0.00 0.00 0.00 2.71
1992 3801 4.488126 TTCAGCATCTTTCCAGTTTTCG 57.512 40.909 0.00 0.00 0.00 3.46
2007 3816 1.428448 CTCGGATGACGTTTTCAGCA 58.572 50.000 0.00 0.00 42.92 4.41
2106 3915 7.398024 AGAAACCAGCTCACAGTTAATTATCT 58.602 34.615 0.00 0.00 0.00 1.98
2115 3924 3.567478 AGAAAGAAACCAGCTCACAGT 57.433 42.857 0.00 0.00 0.00 3.55
2141 3950 9.738832 GTTCTAACCTCACAGAAGAAGTATATC 57.261 37.037 0.00 0.00 31.62 1.63
2212 4023 9.123902 TGACATGTGGAGGAATATTTCAAATAG 57.876 33.333 1.15 0.00 0.00 1.73
2305 4116 6.355928 CACACATACATTGAACAAACACGTAC 59.644 38.462 0.00 0.00 0.00 3.67
2367 4178 3.527533 GTGTACACTCCACAACACTGAA 58.472 45.455 18.92 0.00 39.27 3.02
2379 4190 6.646240 TCCGTTATAAACCAAAGTGTACACTC 59.354 38.462 28.04 10.43 41.58 3.51
2401 4212 5.932303 TGAGGATAAGTTCAAGTTTCTTCCG 59.068 40.000 0.00 0.00 0.00 4.30
2497 4314 3.399440 ACGGAGGGAGTAGATAGTACG 57.601 52.381 0.00 0.00 0.00 3.67
2506 4323 1.961133 ATTTGGGAACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
2507 4324 1.961133 TATTTGGGAACGGAGGGAGT 58.039 50.000 0.00 0.00 0.00 3.85
2508 4325 3.577805 AATATTTGGGAACGGAGGGAG 57.422 47.619 0.00 0.00 0.00 4.30
2509 4326 3.010808 ACAAATATTTGGGAACGGAGGGA 59.989 43.478 27.43 0.00 42.34 4.20
2510 4327 3.361786 ACAAATATTTGGGAACGGAGGG 58.638 45.455 27.43 3.22 42.34 4.30
2511 4328 4.270008 AGACAAATATTTGGGAACGGAGG 58.730 43.478 27.43 3.68 42.34 4.30
2512 4329 5.897377 AAGACAAATATTTGGGAACGGAG 57.103 39.130 27.43 4.34 42.34 4.63
2513 4330 6.007703 AGAAAGACAAATATTTGGGAACGGA 58.992 36.000 27.43 0.00 42.34 4.69
2514 4331 6.267496 AGAAAGACAAATATTTGGGAACGG 57.733 37.500 27.43 5.66 42.34 4.44
2515 4332 7.472543 CCTAGAAAGACAAATATTTGGGAACG 58.527 38.462 27.43 6.31 42.34 3.95
2516 4333 7.093945 TGCCTAGAAAGACAAATATTTGGGAAC 60.094 37.037 27.43 16.80 42.34 3.62
2517 4334 6.951198 TGCCTAGAAAGACAAATATTTGGGAA 59.049 34.615 27.43 11.57 42.34 3.97
2518 4335 6.489603 TGCCTAGAAAGACAAATATTTGGGA 58.510 36.000 27.43 8.88 42.34 4.37
2519 4336 6.773976 TGCCTAGAAAGACAAATATTTGGG 57.226 37.500 27.43 18.18 42.34 4.12
2520 4337 9.305925 GAAATGCCTAGAAAGACAAATATTTGG 57.694 33.333 27.43 12.85 42.34 3.28
2521 4338 9.859427 TGAAATGCCTAGAAAGACAAATATTTG 57.141 29.630 23.60 23.60 43.62 2.32
2525 4342 9.859427 CATTTGAAATGCCTAGAAAGACAAATA 57.141 29.630 4.82 0.00 34.96 1.40
2526 4343 7.820872 CCATTTGAAATGCCTAGAAAGACAAAT 59.179 33.333 12.26 0.00 36.38 2.32
2527 4344 7.015098 TCCATTTGAAATGCCTAGAAAGACAAA 59.985 33.333 12.26 0.00 0.00 2.83
2528 4345 6.493115 TCCATTTGAAATGCCTAGAAAGACAA 59.507 34.615 12.26 0.00 0.00 3.18
2529 4346 6.009589 TCCATTTGAAATGCCTAGAAAGACA 58.990 36.000 12.26 0.00 0.00 3.41
2530 4347 6.071952 TGTCCATTTGAAATGCCTAGAAAGAC 60.072 38.462 12.26 11.27 0.00 3.01
2531 4348 6.009589 TGTCCATTTGAAATGCCTAGAAAGA 58.990 36.000 12.26 0.00 0.00 2.52
2532 4349 6.095377 GTGTCCATTTGAAATGCCTAGAAAG 58.905 40.000 12.26 0.00 0.00 2.62
2533 4350 5.538053 TGTGTCCATTTGAAATGCCTAGAAA 59.462 36.000 12.26 0.00 0.00 2.52
2534 4351 5.076182 TGTGTCCATTTGAAATGCCTAGAA 58.924 37.500 12.26 0.00 0.00 2.10
2535 4352 4.661222 TGTGTCCATTTGAAATGCCTAGA 58.339 39.130 12.26 1.83 0.00 2.43
2536 4353 5.163513 GTTGTGTCCATTTGAAATGCCTAG 58.836 41.667 12.26 0.00 0.00 3.02
2537 4354 4.586421 TGTTGTGTCCATTTGAAATGCCTA 59.414 37.500 12.26 0.00 0.00 3.93
2538 4355 3.387374 TGTTGTGTCCATTTGAAATGCCT 59.613 39.130 12.26 0.00 0.00 4.75
2539 4356 3.726607 TGTTGTGTCCATTTGAAATGCC 58.273 40.909 12.26 5.75 0.00 4.40
2540 4357 5.060816 CGTATGTTGTGTCCATTTGAAATGC 59.939 40.000 12.26 0.87 0.00 3.56
2541 4358 5.572511 CCGTATGTTGTGTCCATTTGAAATG 59.427 40.000 10.84 10.84 0.00 2.32
2542 4359 5.475220 TCCGTATGTTGTGTCCATTTGAAAT 59.525 36.000 0.00 0.00 0.00 2.17
2543 4360 4.822350 TCCGTATGTTGTGTCCATTTGAAA 59.178 37.500 0.00 0.00 0.00 2.69
2544 4361 4.390264 TCCGTATGTTGTGTCCATTTGAA 58.610 39.130 0.00 0.00 0.00 2.69
2545 4362 4.009370 TCCGTATGTTGTGTCCATTTGA 57.991 40.909 0.00 0.00 0.00 2.69
2546 4363 4.155826 ACATCCGTATGTTGTGTCCATTTG 59.844 41.667 0.00 0.00 44.07 2.32
2547 4364 4.331968 ACATCCGTATGTTGTGTCCATTT 58.668 39.130 0.00 0.00 44.07 2.32
2548 4365 3.950397 ACATCCGTATGTTGTGTCCATT 58.050 40.909 0.00 0.00 44.07 3.16
2549 4366 3.627395 ACATCCGTATGTTGTGTCCAT 57.373 42.857 0.00 0.00 44.07 3.41
2550 4367 4.438148 CATACATCCGTATGTTGTGTCCA 58.562 43.478 0.00 0.00 46.70 4.02
2588 4405 6.017933 CGAAGCAAAATGAGTGAATCTACAC 58.982 40.000 0.00 0.00 40.60 2.90
2589 4406 5.700832 ACGAAGCAAAATGAGTGAATCTACA 59.299 36.000 0.00 0.00 0.00 2.74
2590 4407 6.170675 ACGAAGCAAAATGAGTGAATCTAC 57.829 37.500 0.00 0.00 0.00 2.59
2591 4408 7.549134 ACATACGAAGCAAAATGAGTGAATCTA 59.451 33.333 0.00 0.00 0.00 1.98
2592 4409 6.372659 ACATACGAAGCAAAATGAGTGAATCT 59.627 34.615 0.00 0.00 0.00 2.40
2593 4410 6.546395 ACATACGAAGCAAAATGAGTGAATC 58.454 36.000 0.00 0.00 0.00 2.52
2594 4411 6.500684 ACATACGAAGCAAAATGAGTGAAT 57.499 33.333 0.00 0.00 0.00 2.57
2595 4412 5.940192 ACATACGAAGCAAAATGAGTGAA 57.060 34.783 0.00 0.00 0.00 3.18
2596 4413 6.163476 ACTACATACGAAGCAAAATGAGTGA 58.837 36.000 0.00 0.00 0.00 3.41
2597 4414 6.090763 TGACTACATACGAAGCAAAATGAGTG 59.909 38.462 0.00 0.00 0.00 3.51
2598 4415 6.090898 GTGACTACATACGAAGCAAAATGAGT 59.909 38.462 0.00 0.00 0.00 3.41
2599 4416 6.311445 AGTGACTACATACGAAGCAAAATGAG 59.689 38.462 0.00 0.00 0.00 2.90
2600 4417 6.163476 AGTGACTACATACGAAGCAAAATGA 58.837 36.000 0.00 0.00 0.00 2.57
2601 4418 6.408858 AGTGACTACATACGAAGCAAAATG 57.591 37.500 0.00 0.00 0.00 2.32
2602 4419 6.649141 TCAAGTGACTACATACGAAGCAAAAT 59.351 34.615 0.00 0.00 0.00 1.82
2603 4420 5.986741 TCAAGTGACTACATACGAAGCAAAA 59.013 36.000 0.00 0.00 0.00 2.44
2604 4421 5.534407 TCAAGTGACTACATACGAAGCAAA 58.466 37.500 0.00 0.00 0.00 3.68
2605 4422 5.128992 TCAAGTGACTACATACGAAGCAA 57.871 39.130 0.00 0.00 0.00 3.91
2606 4423 4.776795 TCAAGTGACTACATACGAAGCA 57.223 40.909 0.00 0.00 0.00 3.91
2607 4424 5.340803 TCATCAAGTGACTACATACGAAGC 58.659 41.667 0.00 0.00 0.00 3.86
2608 4425 7.812309 TTTCATCAAGTGACTACATACGAAG 57.188 36.000 0.00 0.00 36.32 3.79
2609 4426 8.251026 AGATTTCATCAAGTGACTACATACGAA 58.749 33.333 0.00 0.00 36.32 3.85
2610 4427 7.772166 AGATTTCATCAAGTGACTACATACGA 58.228 34.615 0.00 0.00 36.32 3.43
2611 4428 7.993821 AGATTTCATCAAGTGACTACATACG 57.006 36.000 0.00 0.00 36.32 3.06
2615 4432 9.996554 TTCTAAAGATTTCATCAAGTGACTACA 57.003 29.630 0.00 0.00 36.32 2.74
2618 4435 9.784531 TCTTTCTAAAGATTTCATCAAGTGACT 57.215 29.630 1.00 0.00 39.95 3.41
2619 4436 9.818796 GTCTTTCTAAAGATTTCATCAAGTGAC 57.181 33.333 8.31 0.00 45.83 3.67
2620 4437 9.559732 TGTCTTTCTAAAGATTTCATCAAGTGA 57.440 29.630 8.31 0.00 45.83 3.41
2634 4451 9.341899 CGTTCCCAAATATTTGTCTTTCTAAAG 57.658 33.333 23.24 7.00 36.45 1.85
2635 4452 8.301002 CCGTTCCCAAATATTTGTCTTTCTAAA 58.699 33.333 23.24 6.21 36.45 1.85
2636 4453 7.666388 TCCGTTCCCAAATATTTGTCTTTCTAA 59.334 33.333 23.24 7.04 36.45 2.10
2637 4454 7.169591 TCCGTTCCCAAATATTTGTCTTTCTA 58.830 34.615 23.24 5.03 36.45 2.10
2638 4455 6.007703 TCCGTTCCCAAATATTTGTCTTTCT 58.992 36.000 23.24 0.00 36.45 2.52
2639 4456 6.262193 TCCGTTCCCAAATATTTGTCTTTC 57.738 37.500 23.24 10.84 36.45 2.62
2640 4457 5.185056 CCTCCGTTCCCAAATATTTGTCTTT 59.815 40.000 23.24 0.00 36.45 2.52
2641 4458 4.705023 CCTCCGTTCCCAAATATTTGTCTT 59.295 41.667 23.24 0.00 36.45 3.01
2642 4459 4.270008 CCTCCGTTCCCAAATATTTGTCT 58.730 43.478 23.24 0.00 36.45 3.41
2643 4460 3.380320 CCCTCCGTTCCCAAATATTTGTC 59.620 47.826 23.24 11.68 36.45 3.18
2644 4461 3.010808 TCCCTCCGTTCCCAAATATTTGT 59.989 43.478 23.24 0.00 36.45 2.83
2645 4462 3.626930 TCCCTCCGTTCCCAAATATTTG 58.373 45.455 19.40 19.40 37.90 2.32
2646 4463 4.325084 TTCCCTCCGTTCCCAAATATTT 57.675 40.909 0.00 0.00 0.00 1.40
2647 4464 4.536295 ATTCCCTCCGTTCCCAAATATT 57.464 40.909 0.00 0.00 0.00 1.28
2648 4465 4.042934 CCTATTCCCTCCGTTCCCAAATAT 59.957 45.833 0.00 0.00 0.00 1.28
2649 4466 3.393278 CCTATTCCCTCCGTTCCCAAATA 59.607 47.826 0.00 0.00 0.00 1.40
2650 4467 2.174854 CCTATTCCCTCCGTTCCCAAAT 59.825 50.000 0.00 0.00 0.00 2.32
2651 4468 1.562475 CCTATTCCCTCCGTTCCCAAA 59.438 52.381 0.00 0.00 0.00 3.28
2652 4469 1.209621 CCTATTCCCTCCGTTCCCAA 58.790 55.000 0.00 0.00 0.00 4.12
2653 4470 0.043637 ACCTATTCCCTCCGTTCCCA 59.956 55.000 0.00 0.00 0.00 4.37
2654 4471 1.690893 GTACCTATTCCCTCCGTTCCC 59.309 57.143 0.00 0.00 0.00 3.97
2655 4472 2.675583 AGTACCTATTCCCTCCGTTCC 58.324 52.381 0.00 0.00 0.00 3.62
2656 4473 3.255395 GCTAGTACCTATTCCCTCCGTTC 59.745 52.174 0.00 0.00 0.00 3.95
2657 4474 3.229293 GCTAGTACCTATTCCCTCCGTT 58.771 50.000 0.00 0.00 0.00 4.44
2658 4475 2.490535 GGCTAGTACCTATTCCCTCCGT 60.491 54.545 0.00 0.00 0.00 4.69
2659 4476 2.169330 GGCTAGTACCTATTCCCTCCG 58.831 57.143 0.00 0.00 0.00 4.63
2660 4477 3.166679 CAGGCTAGTACCTATTCCCTCC 58.833 54.545 0.00 0.00 38.26 4.30
2661 4478 2.563620 GCAGGCTAGTACCTATTCCCTC 59.436 54.545 0.00 0.00 38.26 4.30
2662 4479 2.180308 AGCAGGCTAGTACCTATTCCCT 59.820 50.000 0.00 0.00 38.26 4.20
2663 4480 2.610873 AGCAGGCTAGTACCTATTCCC 58.389 52.381 0.00 0.00 38.26 3.97
2664 4481 3.641906 TCAAGCAGGCTAGTACCTATTCC 59.358 47.826 0.00 0.00 38.26 3.01
2665 4482 4.939052 TCAAGCAGGCTAGTACCTATTC 57.061 45.455 0.00 0.00 38.26 1.75
2666 4483 4.141688 GGTTCAAGCAGGCTAGTACCTATT 60.142 45.833 0.00 0.00 38.26 1.73
2667 4484 3.388350 GGTTCAAGCAGGCTAGTACCTAT 59.612 47.826 0.00 0.00 38.26 2.57
2920 4737 5.188555 AGGTGAGCTATCTGACAGAATTTCA 59.811 40.000 9.70 8.45 0.00 2.69
2921 4738 5.669477 AGGTGAGCTATCTGACAGAATTTC 58.331 41.667 9.70 6.04 0.00 2.17
2954 4771 6.061441 CCATGCACCACTACCAAAATATCTA 58.939 40.000 0.00 0.00 0.00 1.98
3038 4855 7.556275 GGACACCCAGAGTTCATTATTGAAATA 59.444 37.037 1.74 0.00 43.29 1.40
3307 5124 1.191535 AAGCATTGCAGCACATCCAT 58.808 45.000 11.91 0.00 36.85 3.41


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

AutoCloner maintained by Alex Coulton.