Multiple sequence alignment - TraesCS2B01G071200

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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 TraesCS2B01G071200 chr2B 100.000 4145 0 0 1 4145 37711435 37707291 0.000000e+00 7655.0
1 TraesCS2B01G071200 chr2B 96.995 1298 35 1 2852 4145 37731360 37730063 0.000000e+00 2178.0
2 TraesCS2B01G071200 chr2B 95.243 1072 51 0 1780 2851 37550513 37549442 0.000000e+00 1698.0
3 TraesCS2B01G071200 chr2B 94.963 1072 54 0 1780 2851 38337377 38336306 0.000000e+00 1681.0
4 TraesCS2B01G071200 chr2B 90.927 1025 75 12 729 1742 37552269 37551252 0.000000e+00 1362.0
5 TraesCS2B01G071200 chr2B 89.116 1075 73 9 729 1770 38339101 38338038 0.000000e+00 1297.0
6 TraesCS2B01G071200 chr2B 90.311 547 40 8 849 1384 38018395 38017851 0.000000e+00 704.0
7 TraesCS2B01G071200 chr2B 93.243 370 18 4 1 366 37552963 37552597 4.710000e-149 538.0
8 TraesCS2B01G071200 chr2B 90.845 284 22 1 451 730 38339423 38339140 1.090000e-100 377.0
9 TraesCS2B01G071200 chr2B 95.833 216 9 0 1381 1596 38017750 38017535 2.370000e-92 350.0
10 TraesCS2B01G071200 chr2B 86.364 286 19 13 455 734 38018785 38018514 1.130000e-75 294.0
11 TraesCS2B01G071200 chr2B 96.689 151 5 0 1592 1742 38013338 38013188 6.880000e-63 252.0
12 TraesCS2B01G071200 chr2B 90.741 54 5 0 165 218 38090897 38090844 5.750000e-09 73.1
13 TraesCS2B01G071200 chr5B 97.377 1296 28 3 2852 4145 679208082 679209373 0.000000e+00 2200.0
14 TraesCS2B01G071200 chr5B 96.991 1296 37 2 2852 4145 540516817 540518112 0.000000e+00 2176.0
15 TraesCS2B01G071200 chr5B 96.373 1296 45 2 2852 4145 668619246 668617951 0.000000e+00 2132.0
16 TraesCS2B01G071200 chr3B 97.160 1303 35 2 2845 4145 770051350 770052652 0.000000e+00 2200.0
17 TraesCS2B01G071200 chr7B 96.911 1295 39 1 2852 4145 730348214 730349508 0.000000e+00 2169.0
18 TraesCS2B01G071200 chr7B 96.764 1298 41 1 2849 4145 713740298 713739001 0.000000e+00 2163.0
19 TraesCS2B01G071200 chr7B 96.302 1298 41 4 2852 4145 579648403 579649697 0.000000e+00 2124.0
20 TraesCS2B01G071200 chr7B 95.789 95 3 1 367 461 569932933 569932840 7.180000e-33 152.0
21 TraesCS2B01G071200 chr7B 89.189 111 11 1 343 452 750040551 750040661 2.010000e-28 137.0
22 TraesCS2B01G071200 chr6B 95.785 1305 47 3 2848 4145 133617166 133618469 0.000000e+00 2098.0
23 TraesCS2B01G071200 chr6B 96.667 90 3 0 364 453 252247779 252247868 2.580000e-32 150.0
24 TraesCS2B01G071200 chr2D 95.149 1072 52 0 1780 2851 22917997 22919068 0.000000e+00 1692.0
25 TraesCS2B01G071200 chr2D 94.157 890 47 3 896 1784 22915986 22916871 0.000000e+00 1351.0
26 TraesCS2B01G071200 chr2D 94.293 368 17 4 1 368 22914958 22915321 1.010000e-155 560.0
27 TraesCS2B01G071200 chrUn 94.302 702 40 0 1780 2481 322040096 322039395 0.000000e+00 1075.0
28 TraesCS2B01G071200 chrUn 94.302 702 40 0 1780 2481 322043365 322042664 0.000000e+00 1075.0
29 TraesCS2B01G071200 chrUn 94.302 702 40 0 1780 2481 366001915 366001214 0.000000e+00 1075.0
30 TraesCS2B01G071200 chrUn 91.024 635 46 9 729 1358 463653343 463652715 0.000000e+00 846.0
31 TraesCS2B01G071200 chrUn 96.748 369 12 0 2483 2851 364592379 364592011 2.120000e-172 616.0
32 TraesCS2B01G071200 chrUn 96.748 369 12 0 2483 2851 469505500 469505868 2.120000e-172 616.0
33 TraesCS2B01G071200 chrUn 91.325 415 30 4 1363 1772 322042563 322042150 2.800000e-156 562.0
34 TraesCS2B01G071200 chrUn 91.325 415 30 4 1363 1772 322045832 322045419 2.800000e-156 562.0
35 TraesCS2B01G071200 chrUn 93.784 370 16 4 1 366 474150450 474150084 2.180000e-152 549.0
36 TraesCS2B01G071200 chr2A 89.617 366 35 3 1 366 24485420 24485782 2.920000e-126 462.0
37 TraesCS2B01G071200 chr7A 96.667 90 3 0 363 452 238816406 238816495 2.580000e-32 150.0
38 TraesCS2B01G071200 chr4D 96.667 90 3 0 364 453 116822002 116821913 2.580000e-32 150.0
39 TraesCS2B01G071200 chr4A 93.939 99 6 0 364 462 615436794 615436892 2.580000e-32 150.0
40 TraesCS2B01G071200 chr4A 93.878 98 4 2 360 456 4152064 4151968 3.340000e-31 147.0
41 TraesCS2B01G071200 chr4A 93.878 98 5 1 364 460 728648004 728648101 3.340000e-31 147.0
42 TraesCS2B01G071200 chr3A 94.681 94 5 0 359 452 81463464 81463371 3.340000e-31 147.0


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 TraesCS2B01G071200 chr2B 37707291 37711435 4144 True 7655.000000 7655 100.000000 1 4145 1 chr2B.!!$R1 4144
1 TraesCS2B01G071200 chr2B 37730063 37731360 1297 True 2178.000000 2178 96.995000 2852 4145 1 chr2B.!!$R2 1293
2 TraesCS2B01G071200 chr2B 37549442 37552963 3521 True 1199.333333 1698 93.137667 1 2851 3 chr2B.!!$R5 2850
3 TraesCS2B01G071200 chr2B 38336306 38339423 3117 True 1118.333333 1681 91.641333 451 2851 3 chr2B.!!$R7 2400
4 TraesCS2B01G071200 chr2B 38017535 38018785 1250 True 449.333333 704 90.836000 455 1596 3 chr2B.!!$R6 1141
5 TraesCS2B01G071200 chr5B 679208082 679209373 1291 False 2200.000000 2200 97.377000 2852 4145 1 chr5B.!!$F2 1293
6 TraesCS2B01G071200 chr5B 540516817 540518112 1295 False 2176.000000 2176 96.991000 2852 4145 1 chr5B.!!$F1 1293
7 TraesCS2B01G071200 chr5B 668617951 668619246 1295 True 2132.000000 2132 96.373000 2852 4145 1 chr5B.!!$R1 1293
8 TraesCS2B01G071200 chr3B 770051350 770052652 1302 False 2200.000000 2200 97.160000 2845 4145 1 chr3B.!!$F1 1300
9 TraesCS2B01G071200 chr7B 730348214 730349508 1294 False 2169.000000 2169 96.911000 2852 4145 1 chr7B.!!$F2 1293
10 TraesCS2B01G071200 chr7B 713739001 713740298 1297 True 2163.000000 2163 96.764000 2849 4145 1 chr7B.!!$R2 1296
11 TraesCS2B01G071200 chr7B 579648403 579649697 1294 False 2124.000000 2124 96.302000 2852 4145 1 chr7B.!!$F1 1293
12 TraesCS2B01G071200 chr6B 133617166 133618469 1303 False 2098.000000 2098 95.785000 2848 4145 1 chr6B.!!$F1 1297
13 TraesCS2B01G071200 chr2D 22914958 22919068 4110 False 1201.000000 1692 94.533000 1 2851 3 chr2D.!!$F1 2850
14 TraesCS2B01G071200 chrUn 366001214 366001915 701 True 1075.000000 1075 94.302000 1780 2481 1 chrUn.!!$R2 701
15 TraesCS2B01G071200 chrUn 463652715 463653343 628 True 846.000000 846 91.024000 729 1358 1 chrUn.!!$R3 629
16 TraesCS2B01G071200 chrUn 322039395 322045832 6437 True 818.500000 1075 92.813500 1363 2481 4 chrUn.!!$R5 1118

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
347 352 0.268869 AGGAGGAGGCCATGACCATA 59.731 55.0 5.01 0.00 0.0 2.74 F
1566 1948 0.540923 AGCAGATCAGAGGGCAGTTC 59.459 55.0 0.00 0.00 0.0 3.01 F
2372 5813 1.668826 AGGCCTTGTCCATGGAAGTA 58.331 50.0 18.20 2.96 0.0 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1930 5371 0.545171 AGCTACATGATGCAGCCACT 59.455 50.00 13.75 0.0 37.47 4.00 R
2639 6256 0.036952 CTGACGTGGGACAAGCTCAT 60.037 55.00 0.00 0.0 44.16 2.90 R
3686 7321 5.750352 TTTAACCTCTCGACAATAGGGTT 57.250 39.13 0.00 0.0 39.81 4.11 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
24 25 4.048241 TGTGAGTTGTGACACGATTGTA 57.952 40.909 0.00 0.00 39.52 2.41
57 58 6.653020 TGCATTTCACTCTACTTGGTATCAT 58.347 36.000 0.00 0.00 0.00 2.45
87 88 1.889829 ACTGACACTCTTCTCCTTCCG 59.110 52.381 0.00 0.00 0.00 4.30
89 90 0.456995 GACACTCTTCTCCTTCCGCG 60.457 60.000 0.00 0.00 0.00 6.46
173 174 6.390504 TGGGATATCCTACTGTGTCCTTAAT 58.609 40.000 21.18 0.00 36.20 1.40
174 175 6.270000 TGGGATATCCTACTGTGTCCTTAATG 59.730 42.308 21.18 0.00 36.20 1.90
247 248 3.746045 ACACGAAGTACTTCCACACAT 57.254 42.857 26.12 6.80 41.61 3.21
347 352 0.268869 AGGAGGAGGCCATGACCATA 59.731 55.000 5.01 0.00 0.00 2.74
368 373 4.538746 AAGAGAGGTGGCAACTAACTAC 57.461 45.455 4.28 0.00 37.61 2.73
370 375 3.764972 AGAGAGGTGGCAACTAACTACTC 59.235 47.826 4.28 7.63 37.61 2.59
371 376 2.832733 AGAGGTGGCAACTAACTACTCC 59.167 50.000 4.28 0.00 37.61 3.85
372 377 1.907255 AGGTGGCAACTAACTACTCCC 59.093 52.381 1.40 0.00 37.61 4.30
373 378 1.907255 GGTGGCAACTAACTACTCCCT 59.093 52.381 0.00 0.00 37.61 4.20
374 379 2.093606 GGTGGCAACTAACTACTCCCTC 60.094 54.545 0.00 0.00 37.61 4.30
375 380 2.093606 GTGGCAACTAACTACTCCCTCC 60.094 54.545 0.00 0.00 37.61 4.30
376 381 1.136500 GGCAACTAACTACTCCCTCCG 59.864 57.143 0.00 0.00 0.00 4.63
377 382 1.823610 GCAACTAACTACTCCCTCCGT 59.176 52.381 0.00 0.00 0.00 4.69
378 383 2.233186 GCAACTAACTACTCCCTCCGTT 59.767 50.000 0.00 0.00 0.00 4.44
379 384 3.675502 GCAACTAACTACTCCCTCCGTTC 60.676 52.174 0.00 0.00 0.00 3.95
380 385 2.732763 ACTAACTACTCCCTCCGTTCC 58.267 52.381 0.00 0.00 0.00 3.62
381 386 2.042162 ACTAACTACTCCCTCCGTTCCA 59.958 50.000 0.00 0.00 0.00 3.53
382 387 2.019807 AACTACTCCCTCCGTTCCAA 57.980 50.000 0.00 0.00 0.00 3.53
383 388 2.019807 ACTACTCCCTCCGTTCCAAA 57.980 50.000 0.00 0.00 0.00 3.28
384 389 2.332117 ACTACTCCCTCCGTTCCAAAA 58.668 47.619 0.00 0.00 0.00 2.44
385 390 2.910977 ACTACTCCCTCCGTTCCAAAAT 59.089 45.455 0.00 0.00 0.00 1.82
386 391 4.098894 ACTACTCCCTCCGTTCCAAAATA 58.901 43.478 0.00 0.00 0.00 1.40
387 392 4.533311 ACTACTCCCTCCGTTCCAAAATAA 59.467 41.667 0.00 0.00 0.00 1.40
388 393 4.376225 ACTCCCTCCGTTCCAAAATAAA 57.624 40.909 0.00 0.00 0.00 1.40
389 394 4.930696 ACTCCCTCCGTTCCAAAATAAAT 58.069 39.130 0.00 0.00 0.00 1.40
390 395 4.705023 ACTCCCTCCGTTCCAAAATAAATG 59.295 41.667 0.00 0.00 0.00 2.32
391 396 4.924625 TCCCTCCGTTCCAAAATAAATGA 58.075 39.130 0.00 0.00 0.00 2.57
392 397 5.515106 TCCCTCCGTTCCAAAATAAATGAT 58.485 37.500 0.00 0.00 0.00 2.45
393 398 5.592688 TCCCTCCGTTCCAAAATAAATGATC 59.407 40.000 0.00 0.00 0.00 2.92
394 399 5.221244 CCCTCCGTTCCAAAATAAATGATCC 60.221 44.000 0.00 0.00 0.00 3.36
395 400 5.359576 CCTCCGTTCCAAAATAAATGATCCA 59.640 40.000 0.00 0.00 0.00 3.41
396 401 6.127479 CCTCCGTTCCAAAATAAATGATCCAA 60.127 38.462 0.00 0.00 0.00 3.53
397 402 6.626302 TCCGTTCCAAAATAAATGATCCAAC 58.374 36.000 0.00 0.00 0.00 3.77
398 403 6.435904 TCCGTTCCAAAATAAATGATCCAACT 59.564 34.615 0.00 0.00 0.00 3.16
399 404 7.039363 TCCGTTCCAAAATAAATGATCCAACTT 60.039 33.333 0.00 0.00 0.00 2.66
400 405 7.602265 CCGTTCCAAAATAAATGATCCAACTTT 59.398 33.333 0.00 0.00 0.00 2.66
401 406 8.434661 CGTTCCAAAATAAATGATCCAACTTTG 58.565 33.333 0.00 0.00 0.00 2.77
402 407 9.271828 GTTCCAAAATAAATGATCCAACTTTGT 57.728 29.630 0.00 0.00 0.00 2.83
404 409 9.921637 TCCAAAATAAATGATCCAACTTTGTAC 57.078 29.630 0.00 0.00 0.00 2.90
405 410 9.927668 CCAAAATAAATGATCCAACTTTGTACT 57.072 29.630 0.00 0.00 0.00 2.73
428 433 7.567458 ACTAAAGTTAGTACAAAGTTGGGTCA 58.433 34.615 1.81 0.00 41.92 4.02
429 434 8.215736 ACTAAAGTTAGTACAAAGTTGGGTCAT 58.784 33.333 1.81 0.00 41.92 3.06
430 435 7.506328 AAAGTTAGTACAAAGTTGGGTCATC 57.494 36.000 0.00 0.00 0.00 2.92
431 436 6.435292 AGTTAGTACAAAGTTGGGTCATCT 57.565 37.500 0.00 0.00 0.00 2.90
432 437 7.549147 AGTTAGTACAAAGTTGGGTCATCTA 57.451 36.000 0.00 0.00 0.00 1.98
433 438 8.147244 AGTTAGTACAAAGTTGGGTCATCTAT 57.853 34.615 0.00 0.00 0.00 1.98
434 439 8.603304 AGTTAGTACAAAGTTGGGTCATCTATT 58.397 33.333 0.00 0.00 0.00 1.73
435 440 9.227777 GTTAGTACAAAGTTGGGTCATCTATTT 57.772 33.333 0.00 0.00 0.00 1.40
436 441 9.802039 TTAGTACAAAGTTGGGTCATCTATTTT 57.198 29.630 0.00 0.00 0.00 1.82
437 442 8.110860 AGTACAAAGTTGGGTCATCTATTTTG 57.889 34.615 0.00 0.00 0.00 2.44
438 443 7.942341 AGTACAAAGTTGGGTCATCTATTTTGA 59.058 33.333 0.00 0.00 0.00 2.69
439 444 7.595819 ACAAAGTTGGGTCATCTATTTTGAA 57.404 32.000 0.00 0.00 0.00 2.69
440 445 8.017418 ACAAAGTTGGGTCATCTATTTTGAAA 57.983 30.769 0.00 0.00 0.00 2.69
441 446 7.926018 ACAAAGTTGGGTCATCTATTTTGAAAC 59.074 33.333 0.00 0.00 0.00 2.78
442 447 6.254281 AGTTGGGTCATCTATTTTGAAACG 57.746 37.500 0.00 0.00 0.00 3.60
443 448 5.183140 AGTTGGGTCATCTATTTTGAAACGG 59.817 40.000 0.00 0.00 0.00 4.44
444 449 4.912586 TGGGTCATCTATTTTGAAACGGA 58.087 39.130 0.00 0.00 0.00 4.69
445 450 4.941263 TGGGTCATCTATTTTGAAACGGAG 59.059 41.667 0.00 0.00 0.00 4.63
446 451 4.335594 GGGTCATCTATTTTGAAACGGAGG 59.664 45.833 0.00 0.00 0.00 4.30
447 452 4.335594 GGTCATCTATTTTGAAACGGAGGG 59.664 45.833 0.00 0.00 0.00 4.30
448 453 5.183228 GTCATCTATTTTGAAACGGAGGGA 58.817 41.667 0.00 0.00 0.00 4.20
449 454 5.294552 GTCATCTATTTTGAAACGGAGGGAG 59.705 44.000 0.00 0.00 0.00 4.30
450 455 4.903045 TCTATTTTGAAACGGAGGGAGT 57.097 40.909 0.00 0.00 0.00 3.85
451 456 6.155565 TCATCTATTTTGAAACGGAGGGAGTA 59.844 38.462 0.00 0.00 0.00 2.59
452 457 6.363167 TCTATTTTGAAACGGAGGGAGTAA 57.637 37.500 0.00 0.00 0.00 2.24
453 458 6.168389 TCTATTTTGAAACGGAGGGAGTAAC 58.832 40.000 0.00 0.00 0.00 2.50
479 484 6.002062 ACAAGCCTTTCTCATTAAGAAACG 57.998 37.500 0.00 0.00 46.64 3.60
512 526 8.371699 ACCATTTAGCAAGCACCTATTTTTAAA 58.628 29.630 0.00 0.00 0.00 1.52
524 538 8.188799 GCACCTATTTTTAAATTGAGGGACTAC 58.811 37.037 12.12 0.00 41.55 2.73
592 612 1.156736 GATTTGTCGTCACCACCTGG 58.843 55.000 0.00 0.00 42.17 4.45
603 625 1.685820 CCACCTGGTTTCCTCTCCC 59.314 63.158 0.00 0.00 0.00 4.30
618 640 1.992557 TCTCCCTGGTTTGGCTTGTAT 59.007 47.619 0.00 0.00 0.00 2.29
635 657 5.491982 CTTGTATTCCAAGCTGGTCTAACT 58.508 41.667 0.00 0.00 43.84 2.24
638 660 1.919240 TCCAAGCTGGTCTAACTCGA 58.081 50.000 0.00 0.00 39.03 4.04
657 679 7.763172 ACTCGAGTGATTAGTCAATTGATTC 57.237 36.000 19.30 7.43 40.83 2.52
687 709 3.408634 ACAGTTTACCAAATCCACGGAG 58.591 45.455 0.00 0.00 0.00 4.63
707 729 1.715585 CTAATTGACCAGGCACGCG 59.284 57.895 3.53 3.53 0.00 6.01
754 837 4.982295 GGGTCAGTTGCTTGTCAAAATTAC 59.018 41.667 0.00 0.00 36.26 1.89
863 995 2.159184 TCGTCAAGCCATCATCTCTCAC 60.159 50.000 0.00 0.00 0.00 3.51
868 1001 3.823281 AGCCATCATCTCTCACTCAAG 57.177 47.619 0.00 0.00 0.00 3.02
916 1180 4.176404 ATGGAGGTCATGGCAGGT 57.824 55.556 0.00 0.00 34.22 4.00
1035 1304 2.516460 CTGGAGAGCATGCAGGCC 60.516 66.667 21.42 17.17 43.30 5.19
1491 1873 2.154462 GATGGTCAACTGAAGGTGGTG 58.846 52.381 0.00 0.00 0.00 4.17
1500 1882 2.154462 CTGAAGGTGGTGTCCATTGTC 58.846 52.381 0.00 0.00 35.28 3.18
1530 1912 2.571757 CTGGGCAAGACGACGCTA 59.428 61.111 0.00 0.00 0.00 4.26
1566 1948 0.540923 AGCAGATCAGAGGGCAGTTC 59.459 55.000 0.00 0.00 0.00 3.01
1680 2062 1.747355 GAGGTTGAAGCATGGGATGTG 59.253 52.381 0.00 0.00 0.00 3.21
1803 5244 8.770438 TTTGTTTTTGATTCTAATATGGTGCC 57.230 30.769 0.00 0.00 0.00 5.01
1809 5250 6.449635 TGATTCTAATATGGTGCCACAAAC 57.550 37.500 0.00 0.00 0.00 2.93
1864 5305 2.098117 GGACGAATCAGCTTGGAATTGG 59.902 50.000 0.00 0.00 0.00 3.16
1877 5318 5.591877 GCTTGGAATTGGATCAAGACTGTAT 59.408 40.000 6.49 0.00 39.97 2.29
1924 5365 6.128661 GCAGAGTAATCACAACAACACGAATA 60.129 38.462 0.00 0.00 0.00 1.75
1929 5370 2.223144 TCACAACAACACGAATAGCTGC 59.777 45.455 0.00 0.00 0.00 5.25
1930 5371 2.032117 CACAACAACACGAATAGCTGCA 60.032 45.455 1.02 0.00 0.00 4.41
1933 5374 1.800586 ACAACACGAATAGCTGCAGTG 59.199 47.619 16.64 7.02 38.63 3.66
2056 5497 3.937706 GTGAAGATGGTTCTCATGTGGAG 59.062 47.826 0.00 0.00 45.49 3.86
2236 5677 4.769688 TGGAGAACATGCGTCAGATATTT 58.230 39.130 0.00 0.00 0.00 1.40
2372 5813 1.668826 AGGCCTTGTCCATGGAAGTA 58.331 50.000 18.20 2.96 0.00 2.24
2569 6186 4.946478 AGATAGCCATCAACCTAGTGAC 57.054 45.455 0.00 0.00 33.21 3.67
2605 6222 8.783833 AGATACATCGATTATCCATCCAAAAG 57.216 34.615 16.97 0.00 0.00 2.27
2627 6244 5.717119 AGAATCAAGAAAATCACACCATGC 58.283 37.500 0.00 0.00 0.00 4.06
2639 6256 3.008923 TCACACCATGCCACTTTCTATGA 59.991 43.478 0.00 0.00 0.00 2.15
2656 6273 0.037326 TGATGAGCTTGTCCCACGTC 60.037 55.000 0.00 0.00 0.00 4.34
2700 6317 1.543358 TGCTACAAAATTGATGCCGCA 59.457 42.857 0.00 0.00 32.40 5.69
2777 6394 8.663167 ACTTGGAGAATCATCATATTGATGGTA 58.337 33.333 15.44 0.55 46.72 3.25
3023 6648 1.934459 TTTTGGTCCCGGTTGGTGGA 61.934 55.000 0.00 0.00 34.77 4.02
3042 6667 0.179012 AACGAACCGGGACCAATGTT 60.179 50.000 6.32 0.00 0.00 2.71
3103 6728 1.971695 GAACCGGGACCAAAGGCTG 60.972 63.158 6.32 0.00 0.00 4.85
3107 6732 4.299796 GGGACCAAAGGCTGCCCA 62.300 66.667 16.57 0.00 38.68 5.36
3122 6747 0.182775 GCCCATTAGTCCCGGTTCAT 59.817 55.000 0.00 0.00 0.00 2.57
3128 6753 1.906105 TAGTCCCGGTTCATGCCACC 61.906 60.000 0.00 4.21 0.00 4.61
3686 7321 2.362717 GTTGAACCGGAAATTCCAACCA 59.637 45.455 9.46 1.43 35.91 3.67
3969 9510 8.095512 CGCATTGAAATGTTTTACATAGTTTCG 58.904 33.333 5.02 0.00 37.97 3.46
4060 9601 9.559958 GTACTTTGGTTTTAATGTGATGATGAG 57.440 33.333 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 6.476378 AGTAGAGTGAAATGCATAAACCACT 58.524 36.000 17.44 17.44 37.55 4.00
57 58 6.600032 GGAGAAGAGTGTCAGTATTAGTCTGA 59.400 42.308 0.00 0.00 39.25 3.27
69 70 0.603569 GCGGAAGGAGAAGAGTGTCA 59.396 55.000 0.00 0.00 0.00 3.58
87 88 0.460722 GGTAGGAAGGAGAGAACCGC 59.539 60.000 0.00 0.00 34.73 5.68
89 90 2.140839 TCGGTAGGAAGGAGAGAACC 57.859 55.000 0.00 0.00 0.00 3.62
131 132 2.417719 CCAATTGATAGAGGTAGCGGC 58.582 52.381 7.12 0.00 0.00 6.53
173 174 4.994852 GTGTTGTCTGCTTCCAGTATAACA 59.005 41.667 0.00 0.00 40.09 2.41
174 175 4.994852 TGTGTTGTCTGCTTCCAGTATAAC 59.005 41.667 0.00 0.00 40.09 1.89
247 248 2.920912 GTCTGTCCGACCCCACCA 60.921 66.667 0.00 0.00 36.62 4.17
272 273 8.301002 AGCCTCTTAAGACGATTCATAACTATC 58.699 37.037 0.00 0.00 0.00 2.08
273 274 8.184304 AGCCTCTTAAGACGATTCATAACTAT 57.816 34.615 0.00 0.00 0.00 2.12
274 275 7.584122 AGCCTCTTAAGACGATTCATAACTA 57.416 36.000 0.00 0.00 0.00 2.24
347 352 4.161102 AGTAGTTAGTTGCCACCTCTCTT 58.839 43.478 0.00 0.00 0.00 2.85
368 373 4.947388 TCATTTATTTTGGAACGGAGGGAG 59.053 41.667 0.00 0.00 0.00 4.30
370 375 5.221244 GGATCATTTATTTTGGAACGGAGGG 60.221 44.000 0.00 0.00 0.00 4.30
371 376 5.359576 TGGATCATTTATTTTGGAACGGAGG 59.640 40.000 0.00 0.00 0.00 4.30
372 377 6.449635 TGGATCATTTATTTTGGAACGGAG 57.550 37.500 0.00 0.00 0.00 4.63
373 378 6.435904 AGTTGGATCATTTATTTTGGAACGGA 59.564 34.615 0.00 0.00 0.00 4.69
374 379 6.630071 AGTTGGATCATTTATTTTGGAACGG 58.370 36.000 0.00 0.00 0.00 4.44
375 380 8.434661 CAAAGTTGGATCATTTATTTTGGAACG 58.565 33.333 0.00 0.00 0.00 3.95
376 381 9.271828 ACAAAGTTGGATCATTTATTTTGGAAC 57.728 29.630 0.00 0.00 0.00 3.62
378 383 9.921637 GTACAAAGTTGGATCATTTATTTTGGA 57.078 29.630 0.00 0.00 0.00 3.53
379 384 9.927668 AGTACAAAGTTGGATCATTTATTTTGG 57.072 29.630 0.00 0.00 0.00 3.28
402 407 8.703743 TGACCCAACTTTGTACTAACTTTAGTA 58.296 33.333 4.98 4.98 43.36 1.82
403 408 7.567458 TGACCCAACTTTGTACTAACTTTAGT 58.433 34.615 6.85 6.85 45.39 2.24
404 409 8.617290 ATGACCCAACTTTGTACTAACTTTAG 57.383 34.615 0.00 0.00 36.82 1.85
405 410 8.434392 AGATGACCCAACTTTGTACTAACTTTA 58.566 33.333 0.00 0.00 0.00 1.85
406 411 7.287810 AGATGACCCAACTTTGTACTAACTTT 58.712 34.615 0.00 0.00 0.00 2.66
407 412 6.838382 AGATGACCCAACTTTGTACTAACTT 58.162 36.000 0.00 0.00 0.00 2.66
408 413 6.435292 AGATGACCCAACTTTGTACTAACT 57.565 37.500 0.00 0.00 0.00 2.24
409 414 8.788325 AATAGATGACCCAACTTTGTACTAAC 57.212 34.615 0.00 0.00 0.00 2.34
410 415 9.802039 AAAATAGATGACCCAACTTTGTACTAA 57.198 29.630 0.00 0.00 0.00 2.24
411 416 9.226606 CAAAATAGATGACCCAACTTTGTACTA 57.773 33.333 0.00 0.00 0.00 1.82
412 417 7.942341 TCAAAATAGATGACCCAACTTTGTACT 59.058 33.333 0.00 0.00 0.00 2.73
413 418 8.106247 TCAAAATAGATGACCCAACTTTGTAC 57.894 34.615 0.00 0.00 0.00 2.90
414 419 8.698973 TTCAAAATAGATGACCCAACTTTGTA 57.301 30.769 0.00 0.00 0.00 2.41
415 420 7.595819 TTCAAAATAGATGACCCAACTTTGT 57.404 32.000 0.00 0.00 0.00 2.83
416 421 7.114811 CGTTTCAAAATAGATGACCCAACTTTG 59.885 37.037 0.00 0.00 0.00 2.77
417 422 7.145323 CGTTTCAAAATAGATGACCCAACTTT 58.855 34.615 0.00 0.00 0.00 2.66
418 423 6.294508 CCGTTTCAAAATAGATGACCCAACTT 60.295 38.462 0.00 0.00 0.00 2.66
419 424 5.183140 CCGTTTCAAAATAGATGACCCAACT 59.817 40.000 0.00 0.00 0.00 3.16
420 425 5.182380 TCCGTTTCAAAATAGATGACCCAAC 59.818 40.000 0.00 0.00 0.00 3.77
421 426 5.317808 TCCGTTTCAAAATAGATGACCCAA 58.682 37.500 0.00 0.00 0.00 4.12
422 427 4.912586 TCCGTTTCAAAATAGATGACCCA 58.087 39.130 0.00 0.00 0.00 4.51
423 428 4.335594 CCTCCGTTTCAAAATAGATGACCC 59.664 45.833 0.00 0.00 0.00 4.46
424 429 4.335594 CCCTCCGTTTCAAAATAGATGACC 59.664 45.833 0.00 0.00 0.00 4.02
425 430 5.183228 TCCCTCCGTTTCAAAATAGATGAC 58.817 41.667 0.00 0.00 0.00 3.06
426 431 5.045869 ACTCCCTCCGTTTCAAAATAGATGA 60.046 40.000 0.00 0.00 0.00 2.92
427 432 5.186198 ACTCCCTCCGTTTCAAAATAGATG 58.814 41.667 0.00 0.00 0.00 2.90
428 433 5.437191 ACTCCCTCCGTTTCAAAATAGAT 57.563 39.130 0.00 0.00 0.00 1.98
429 434 4.903045 ACTCCCTCCGTTTCAAAATAGA 57.097 40.909 0.00 0.00 0.00 1.98
430 435 6.171213 AGTTACTCCCTCCGTTTCAAAATAG 58.829 40.000 0.00 0.00 0.00 1.73
431 436 6.117975 AGTTACTCCCTCCGTTTCAAAATA 57.882 37.500 0.00 0.00 0.00 1.40
432 437 4.981812 AGTTACTCCCTCCGTTTCAAAAT 58.018 39.130 0.00 0.00 0.00 1.82
433 438 4.426736 AGTTACTCCCTCCGTTTCAAAA 57.573 40.909 0.00 0.00 0.00 2.44
434 439 4.426736 AAGTTACTCCCTCCGTTTCAAA 57.573 40.909 0.00 0.00 0.00 2.69
435 440 4.344679 TGTAAGTTACTCCCTCCGTTTCAA 59.655 41.667 14.00 0.00 0.00 2.69
436 441 3.896888 TGTAAGTTACTCCCTCCGTTTCA 59.103 43.478 14.00 0.00 0.00 2.69
437 442 4.525912 TGTAAGTTACTCCCTCCGTTTC 57.474 45.455 14.00 0.00 0.00 2.78
438 443 4.801914 GCTTGTAAGTTACTCCCTCCGTTT 60.802 45.833 14.00 0.00 0.00 3.60
439 444 3.306571 GCTTGTAAGTTACTCCCTCCGTT 60.307 47.826 14.00 0.00 0.00 4.44
440 445 2.233186 GCTTGTAAGTTACTCCCTCCGT 59.767 50.000 14.00 0.00 0.00 4.69
441 446 2.418334 GGCTTGTAAGTTACTCCCTCCG 60.418 54.545 14.00 0.00 0.00 4.63
442 447 2.838813 AGGCTTGTAAGTTACTCCCTCC 59.161 50.000 14.00 8.02 0.00 4.30
443 448 4.554960 AAGGCTTGTAAGTTACTCCCTC 57.445 45.455 14.00 1.34 0.00 4.30
444 449 4.597940 AGAAAGGCTTGTAAGTTACTCCCT 59.402 41.667 14.00 12.54 0.00 4.20
445 450 4.907809 AGAAAGGCTTGTAAGTTACTCCC 58.092 43.478 14.00 10.74 0.00 4.30
446 451 5.548406 TGAGAAAGGCTTGTAAGTTACTCC 58.452 41.667 14.00 11.63 0.00 3.85
447 452 7.674471 AATGAGAAAGGCTTGTAAGTTACTC 57.326 36.000 14.00 1.91 0.00 2.59
448 453 9.220767 CTTAATGAGAAAGGCTTGTAAGTTACT 57.779 33.333 14.00 0.00 0.00 2.24
449 454 9.216117 TCTTAATGAGAAAGGCTTGTAAGTTAC 57.784 33.333 0.00 6.06 0.00 2.50
450 455 9.787435 TTCTTAATGAGAAAGGCTTGTAAGTTA 57.213 29.630 0.00 0.00 41.34 2.24
451 456 8.691661 TTCTTAATGAGAAAGGCTTGTAAGTT 57.308 30.769 0.00 0.00 41.34 2.66
452 457 8.691661 TTTCTTAATGAGAAAGGCTTGTAAGT 57.308 30.769 0.00 0.00 46.69 2.24
479 484 4.226761 GTGCTTGCTAAATGGTTGTACAC 58.773 43.478 0.00 0.00 0.00 2.90
512 526 2.167900 GGTAGTTGCGTAGTCCCTCAAT 59.832 50.000 0.00 0.00 0.00 2.57
524 538 4.705337 AGAAGAAGACTAGGTAGTTGCG 57.295 45.455 0.00 0.00 36.50 4.85
592 612 1.911057 CCAAACCAGGGAGAGGAAAC 58.089 55.000 0.00 0.00 0.00 2.78
618 640 2.231478 CTCGAGTTAGACCAGCTTGGAA 59.769 50.000 3.62 0.00 40.96 3.53
635 657 5.748630 CCGAATCAATTGACTAATCACTCGA 59.251 40.000 11.07 0.00 33.38 4.04
638 660 6.094048 CCAACCGAATCAATTGACTAATCACT 59.906 38.462 11.07 0.00 33.38 3.41
657 679 1.970092 TGGTAAACTGTTCCCAACCG 58.030 50.000 8.86 0.00 0.00 4.44
687 709 1.993369 GCGTGCCTGGTCAATTAGCC 61.993 60.000 0.00 0.00 0.00 3.93
754 837 4.956085 TGTATACACGATGGAGAAATGGG 58.044 43.478 0.08 0.00 0.00 4.00
863 995 5.792741 AGAAGTGTTTCTCTGGATCTTGAG 58.207 41.667 8.53 8.53 39.46 3.02
1035 1304 2.249692 GGATACTCTCTCGAGGGCG 58.750 63.158 13.56 6.68 41.71 6.13
1259 1534 3.247056 TTGACGCGGCCCTTGATGA 62.247 57.895 10.82 0.00 0.00 2.92
1359 1637 2.046023 CCATGCAAGCGAGGGTCA 60.046 61.111 0.00 0.00 0.00 4.02
1491 1873 2.438434 CCAGCCCCGACAATGGAC 60.438 66.667 0.00 0.00 34.60 4.02
1530 1912 1.081641 CTGGTACACGACGTTCGCT 60.082 57.895 0.00 0.00 45.12 4.93
1566 1948 1.225745 GACAAAGGCGTCGCAATCG 60.226 57.895 20.50 6.97 0.00 3.34
1680 2062 5.241506 TCTGATTTTGTCAATGAGTTCCACC 59.758 40.000 0.00 0.00 36.14 4.61
1786 5227 6.186957 AGTTTGTGGCACCATATTAGAATCA 58.813 36.000 16.26 0.00 0.00 2.57
1787 5228 6.318648 TGAGTTTGTGGCACCATATTAGAATC 59.681 38.462 16.26 0.00 0.00 2.52
1788 5229 6.095440 GTGAGTTTGTGGCACCATATTAGAAT 59.905 38.462 16.26 0.00 0.00 2.40
1864 5305 8.988064 TGTTCTCAACTAATACAGTCTTGATC 57.012 34.615 0.00 0.00 36.04 2.92
1929 5370 0.661552 GCTACATGATGCAGCCACTG 59.338 55.000 6.37 0.00 30.64 3.66
1930 5371 0.545171 AGCTACATGATGCAGCCACT 59.455 50.000 13.75 0.00 37.47 4.00
1933 5374 1.872313 GAAGAGCTACATGATGCAGCC 59.128 52.381 13.75 6.10 37.47 4.85
1945 5386 2.336945 TACCGTCGATGGAAGAGCTA 57.663 50.000 30.28 7.98 0.00 3.32
2056 5497 8.659925 TGATTTTCTCAGATATTTCTCTCAGC 57.340 34.615 0.00 0.00 0.00 4.26
2324 5765 4.123497 TCCATCTTCGTACCAAGTGATG 57.877 45.455 0.00 0.00 0.00 3.07
2372 5813 8.390921 CCCCACTTTATATAAGGTATCCACATT 58.609 37.037 9.67 0.00 32.50 2.71
2605 6222 4.866486 GGCATGGTGTGATTTTCTTGATTC 59.134 41.667 0.00 0.00 0.00 2.52
2627 6244 4.574013 GGACAAGCTCATCATAGAAAGTGG 59.426 45.833 0.00 0.00 0.00 4.00
2639 6256 0.036952 CTGACGTGGGACAAGCTCAT 60.037 55.000 0.00 0.00 44.16 2.90
2656 6273 8.719648 GCACTAGGAAAGATGATAAATGATCTG 58.280 37.037 0.00 0.00 31.04 2.90
2700 6317 7.572724 CTCGCAGAACTTGAAATCTTGAAAGAT 60.573 37.037 0.00 0.00 41.73 2.40
3023 6648 0.179012 AACATTGGTCCCGGTTCGTT 60.179 50.000 0.00 0.00 0.00 3.85
3042 6667 3.650950 GTGGGCCAGGAGCAAGGA 61.651 66.667 6.40 0.00 46.50 3.36
3062 6687 0.538516 CCACCAACCGGGACAAATGA 60.539 55.000 6.32 0.00 41.15 2.57
3103 6728 0.182775 ATGAACCGGGACTAATGGGC 59.817 55.000 6.32 0.00 0.00 5.36
3107 6732 0.916086 TGGCATGAACCGGGACTAAT 59.084 50.000 6.32 0.00 0.00 1.73
3128 6753 2.418060 GGCAATTAATTGGTCCCGGTTG 60.418 50.000 25.61 2.50 38.21 3.77
3686 7321 5.750352 TTTAACCTCTCGACAATAGGGTT 57.250 39.130 0.00 0.00 39.81 4.11
3758 7394 6.149616 ACTCCAATATCATCTTCTCCTCCTT 58.850 40.000 0.00 0.00 0.00 3.36
3999 9540 7.615403 TCTCATCTAACAACATAAAGCTCTGT 58.385 34.615 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.