Multiple sequence alignment - TraesCS6D01G037500

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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 TraesCS6D01G037500 chr6D 100.000 3025 0 0 1 3025 15552657 15549633 0.000000e+00 5587
1 TraesCS6D01G037500 chr6D 90.816 1557 103 18 1493 3024 15586383 15584842 0.000000e+00 2047
2 TraesCS6D01G037500 chr6D 93.158 570 36 2 1490 2059 15640509 15641075 0.000000e+00 833
3 TraesCS6D01G037500 chr6D 89.648 483 39 7 1 477 15600312 15599835 3.340000e-169 604
4 TraesCS6D01G037500 chr6D 88.155 515 36 9 953 1467 15639951 15640440 9.340000e-165 590
5 TraesCS6D01G037500 chr6D 91.932 409 16 9 473 876 15599929 15599533 9.470000e-155 556
6 TraesCS6D01G037500 chr6D 90.000 340 23 5 864 1195 15589836 15589500 2.150000e-116 429
7 TraesCS6D01G037500 chr6D 88.095 336 25 3 569 893 15639599 15639930 4.730000e-103 385
8 TraesCS6D01G037500 chrUn 89.609 1636 99 36 1013 2606 319198050 319196444 0.000000e+00 2013
9 TraesCS6D01G037500 chrUn 91.087 1178 77 11 1677 2837 348953558 348954724 0.000000e+00 1568
10 TraesCS6D01G037500 chrUn 91.605 941 57 9 1677 2606 459176789 459177718 0.000000e+00 1280
11 TraesCS6D01G037500 chrUn 89.730 964 64 18 1161 2123 76408988 76409917 0.000000e+00 1199
12 TraesCS6D01G037500 chrUn 92.893 591 32 5 809 1396 441169748 441169165 0.000000e+00 850
13 TraesCS6D01G037500 chrUn 87.840 699 58 12 2335 3025 76413671 76414350 0.000000e+00 795
14 TraesCS6D01G037500 chrUn 91.981 424 24 4 743 1159 76417691 76417271 1.210000e-163 586
15 TraesCS6D01G037500 chrUn 91.981 424 24 4 743 1159 311042688 311042268 1.210000e-163 586
16 TraesCS6D01G037500 chrUn 87.315 473 34 15 1013 1477 347746851 347746397 4.470000e-143 518
17 TraesCS6D01G037500 chrUn 91.282 195 17 0 2831 3025 404648240 404648434 1.790000e-67 267
18 TraesCS6D01G037500 chrUn 92.568 148 11 0 2690 2837 322192708 322192561 2.360000e-51 213
19 TraesCS6D01G037500 chrUn 92.568 148 11 0 2690 2837 425808720 425808573 2.360000e-51 213
20 TraesCS6D01G037500 chrUn 93.519 108 6 1 2151 2257 76413454 76413561 3.120000e-35 159
21 TraesCS6D01G037500 chr6B 90.058 1388 98 16 1394 2759 27485855 27484486 0.000000e+00 1762
22 TraesCS6D01G037500 chr6B 89.409 1388 108 16 1394 2759 27532445 27531075 0.000000e+00 1712
23 TraesCS6D01G037500 chr6B 89.345 1389 108 17 1394 2759 27419655 27418284 0.000000e+00 1709
24 TraesCS6D01G037500 chr6B 89.170 1385 110 16 1397 2759 27455720 27454354 0.000000e+00 1690
25 TraesCS6D01G037500 chr6B 91.604 929 53 13 474 1396 27486814 27485905 0.000000e+00 1260
26 TraesCS6D01G037500 chr6B 91.604 929 53 13 474 1396 27533404 27532495 0.000000e+00 1260
27 TraesCS6D01G037500 chr6B 91.955 895 50 11 505 1396 27420580 27419705 0.000000e+00 1234
28 TraesCS6D01G037500 chr6B 91.844 895 51 11 505 1396 27456648 27455773 0.000000e+00 1229
29 TraesCS6D01G037500 chr6A 86.642 1078 59 42 470 1480 16337043 16338102 0.000000e+00 1114
30 TraesCS6D01G037500 chr6A 91.238 719 42 10 1490 2204 16338168 16338869 0.000000e+00 959
31 TraesCS6D01G037500 chr6A 89.648 483 37 9 1 477 16336665 16337140 1.200000e-168 603
32 TraesCS6D01G037500 chr6A 89.664 387 28 4 2461 2837 16287984 16287600 1.630000e-132 483
33 TraesCS6D01G037500 chr6A 91.282 195 17 0 2831 3025 16286333 16286139 1.790000e-67 267
34 TraesCS6D01G037500 chr1B 80.903 864 87 39 592 1417 405674160 405673337 7.170000e-171 610


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 TraesCS6D01G037500 chr6D 15549633 15552657 3024 True 5587.000000 5587 100.000000 1 3025 1 chr6D.!!$R1 3024
1 TraesCS6D01G037500 chr6D 15584842 15589836 4994 True 1238.000000 2047 90.408000 864 3024 2 chr6D.!!$R2 2160
2 TraesCS6D01G037500 chr6D 15639599 15641075 1476 False 602.666667 833 89.802667 569 2059 3 chr6D.!!$F1 1490
3 TraesCS6D01G037500 chr6D 15599533 15600312 779 True 580.000000 604 90.790000 1 876 2 chr6D.!!$R3 875
4 TraesCS6D01G037500 chrUn 319196444 319198050 1606 True 2013.000000 2013 89.609000 1013 2606 1 chrUn.!!$R3 1593
5 TraesCS6D01G037500 chrUn 348953558 348954724 1166 False 1568.000000 1568 91.087000 1677 2837 1 chrUn.!!$F1 1160
6 TraesCS6D01G037500 chrUn 459176789 459177718 929 False 1280.000000 1280 91.605000 1677 2606 1 chrUn.!!$F3 929
7 TraesCS6D01G037500 chrUn 441169165 441169748 583 True 850.000000 850 92.893000 809 1396 1 chrUn.!!$R7 587
8 TraesCS6D01G037500 chrUn 76408988 76414350 5362 False 717.666667 1199 90.363000 1161 3025 3 chrUn.!!$F4 1864
9 TraesCS6D01G037500 chr6B 27484486 27486814 2328 True 1511.000000 1762 90.831000 474 2759 2 chr6B.!!$R3 2285
10 TraesCS6D01G037500 chr6B 27531075 27533404 2329 True 1486.000000 1712 90.506500 474 2759 2 chr6B.!!$R4 2285
11 TraesCS6D01G037500 chr6B 27418284 27420580 2296 True 1471.500000 1709 90.650000 505 2759 2 chr6B.!!$R1 2254
12 TraesCS6D01G037500 chr6B 27454354 27456648 2294 True 1459.500000 1690 90.507000 505 2759 2 chr6B.!!$R2 2254
13 TraesCS6D01G037500 chr6A 16336665 16338869 2204 False 892.000000 1114 89.176000 1 2204 3 chr6A.!!$F1 2203
14 TraesCS6D01G037500 chr6A 16286139 16287984 1845 True 375.000000 483 90.473000 2461 3025 2 chr6A.!!$R1 564
15 TraesCS6D01G037500 chr1B 405673337 405674160 823 True 610.000000 610 80.903000 592 1417 1 chr1B.!!$R1 825

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
897 923 0.178964 GGCCTGCCTATAAATGCCCA 60.179 55.0 0.0 0.0 32.74 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2389 8981 0.033642 GCTCTAATCCACGGGGTAGC 59.966 60.0 2.12 2.65 34.93 3.58 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
66 67 3.661936 GCGTCTTTTCATCGAACTGTGTC 60.662 47.826 0.00 0.00 0.00 3.67
69 70 3.981416 TCTTTTCATCGAACTGTGTCTCG 59.019 43.478 0.00 0.00 36.39 4.04
70 71 3.364889 TTTCATCGAACTGTGTCTCGT 57.635 42.857 0.00 0.00 36.46 4.18
172 179 4.495911 TTTGTCTAATGTTTGCGATGCA 57.504 36.364 0.00 0.00 36.47 3.96
176 183 2.422832 TCTAATGTTTGCGATGCATGCA 59.577 40.909 25.04 25.04 38.76 3.96
186 193 0.939419 GATGCATGCATCGCACACTA 59.061 50.000 37.33 7.21 43.04 2.74
212 219 3.502920 CTCCAAGAGTGTGTGATACGTC 58.497 50.000 0.00 0.00 0.00 4.34
220 227 4.801891 AGTGTGTGATACGTCGTTTGTAT 58.198 39.130 1.78 0.00 35.30 2.29
227 234 4.386350 TGATACGTCGTTTGTATGTTGGTG 59.614 41.667 1.78 0.00 32.84 4.17
253 260 2.096762 CGATGGTGCTTACATGCATACG 60.097 50.000 0.00 0.00 45.23 3.06
260 267 1.930503 CTTACATGCATACGCGTTGGA 59.069 47.619 20.78 17.21 42.97 3.53
261 268 2.232756 TACATGCATACGCGTTGGAT 57.767 45.000 20.78 18.73 42.97 3.41
289 297 3.748048 GCACATTCTGCAGTAGTGAGAAA 59.252 43.478 27.51 10.41 46.29 2.52
326 334 3.911868 ACATGCATGCACGTACAAAATT 58.088 36.364 25.37 0.00 0.00 1.82
393 401 9.871238 AAGGACTATAATTGGTTATACATAGCG 57.129 33.333 0.00 0.00 32.84 4.26
394 402 8.475639 AGGACTATAATTGGTTATACATAGCGG 58.524 37.037 0.00 0.00 32.84 5.52
395 403 8.472413 GGACTATAATTGGTTATACATAGCGGA 58.528 37.037 0.00 0.00 32.84 5.54
398 406 9.477484 CTATAATTGGTTATACATAGCGGATCC 57.523 37.037 0.00 0.00 32.84 3.36
399 407 5.755409 ATTGGTTATACATAGCGGATCCA 57.245 39.130 13.41 0.00 0.00 3.41
400 408 5.755409 TTGGTTATACATAGCGGATCCAT 57.245 39.130 13.41 1.69 0.00 3.41
401 409 6.860790 TTGGTTATACATAGCGGATCCATA 57.139 37.500 13.41 4.23 0.00 2.74
402 410 7.432148 TTGGTTATACATAGCGGATCCATAT 57.568 36.000 13.41 6.61 0.00 1.78
403 411 7.432148 TGGTTATACATAGCGGATCCATATT 57.568 36.000 13.41 3.89 0.00 1.28
404 412 7.857456 TGGTTATACATAGCGGATCCATATTT 58.143 34.615 13.41 5.33 0.00 1.40
405 413 7.985184 TGGTTATACATAGCGGATCCATATTTC 59.015 37.037 13.41 0.00 0.00 2.17
406 414 7.985184 GGTTATACATAGCGGATCCATATTTCA 59.015 37.037 13.41 0.00 0.00 2.69
407 415 9.547753 GTTATACATAGCGGATCCATATTTCAT 57.452 33.333 13.41 5.15 0.00 2.57
408 416 9.764363 TTATACATAGCGGATCCATATTTCATC 57.236 33.333 13.41 0.00 0.00 2.92
409 417 6.053632 ACATAGCGGATCCATATTTCATCA 57.946 37.500 13.41 0.00 0.00 3.07
410 418 6.656902 ACATAGCGGATCCATATTTCATCAT 58.343 36.000 13.41 0.00 0.00 2.45
411 419 7.795047 ACATAGCGGATCCATATTTCATCATA 58.205 34.615 13.41 0.00 0.00 2.15
412 420 7.712639 ACATAGCGGATCCATATTTCATCATAC 59.287 37.037 13.41 0.00 0.00 2.39
413 421 6.305272 AGCGGATCCATATTTCATCATACT 57.695 37.500 13.41 0.00 0.00 2.12
414 422 6.344500 AGCGGATCCATATTTCATCATACTC 58.656 40.000 13.41 0.00 0.00 2.59
415 423 6.070596 AGCGGATCCATATTTCATCATACTCA 60.071 38.462 13.41 0.00 0.00 3.41
416 424 6.595326 GCGGATCCATATTTCATCATACTCAA 59.405 38.462 13.41 0.00 0.00 3.02
417 425 7.119699 GCGGATCCATATTTCATCATACTCAAA 59.880 37.037 13.41 0.00 0.00 2.69
418 426 9.002600 CGGATCCATATTTCATCATACTCAAAA 57.997 33.333 13.41 0.00 0.00 2.44
427 435 6.748333 TCATCATACTCAAAAGAAAGCTGG 57.252 37.500 0.00 0.00 0.00 4.85
428 436 6.475504 TCATCATACTCAAAAGAAAGCTGGA 58.524 36.000 0.00 0.00 0.00 3.86
429 437 6.372659 TCATCATACTCAAAAGAAAGCTGGAC 59.627 38.462 0.00 0.00 0.00 4.02
430 438 5.620206 TCATACTCAAAAGAAAGCTGGACA 58.380 37.500 0.00 0.00 0.00 4.02
431 439 6.240894 TCATACTCAAAAGAAAGCTGGACAT 58.759 36.000 0.00 0.00 0.00 3.06
432 440 4.843220 ACTCAAAAGAAAGCTGGACATG 57.157 40.909 0.00 0.00 0.00 3.21
433 441 4.464008 ACTCAAAAGAAAGCTGGACATGA 58.536 39.130 0.00 0.00 0.00 3.07
434 442 5.075493 ACTCAAAAGAAAGCTGGACATGAT 58.925 37.500 0.00 0.00 0.00 2.45
435 443 5.537674 ACTCAAAAGAAAGCTGGACATGATT 59.462 36.000 0.00 0.00 0.00 2.57
436 444 6.716628 ACTCAAAAGAAAGCTGGACATGATTA 59.283 34.615 0.00 0.00 0.00 1.75
437 445 7.094463 ACTCAAAAGAAAGCTGGACATGATTAG 60.094 37.037 0.00 0.00 0.00 1.73
438 446 5.573337 AAAGAAAGCTGGACATGATTAGC 57.427 39.130 0.00 5.72 36.45 3.09
439 447 4.226427 AGAAAGCTGGACATGATTAGCA 57.774 40.909 17.35 0.00 38.59 3.49
440 448 4.197750 AGAAAGCTGGACATGATTAGCAG 58.802 43.478 17.35 0.00 38.59 4.24
441 449 3.920231 AAGCTGGACATGATTAGCAGA 57.080 42.857 17.35 0.00 38.59 4.26
442 450 3.920231 AGCTGGACATGATTAGCAGAA 57.080 42.857 17.35 0.00 38.59 3.02
443 451 3.539604 AGCTGGACATGATTAGCAGAAC 58.460 45.455 17.35 0.00 38.59 3.01
444 452 3.199508 AGCTGGACATGATTAGCAGAACT 59.800 43.478 17.35 0.07 38.59 3.01
445 453 4.406972 AGCTGGACATGATTAGCAGAACTA 59.593 41.667 17.35 0.00 38.59 2.24
446 454 5.071519 AGCTGGACATGATTAGCAGAACTAT 59.928 40.000 17.35 0.00 38.59 2.12
447 455 6.268617 AGCTGGACATGATTAGCAGAACTATA 59.731 38.462 17.35 0.00 38.59 1.31
448 456 6.589523 GCTGGACATGATTAGCAGAACTATAG 59.410 42.308 0.00 0.00 36.24 1.31
449 457 6.459066 TGGACATGATTAGCAGAACTATAGC 58.541 40.000 0.00 0.00 0.00 2.97
450 458 6.041979 TGGACATGATTAGCAGAACTATAGCA 59.958 38.462 0.00 0.00 0.00 3.49
451 459 6.367422 GGACATGATTAGCAGAACTATAGCAC 59.633 42.308 0.00 0.00 0.00 4.40
452 460 6.820335 ACATGATTAGCAGAACTATAGCACA 58.180 36.000 0.00 0.00 0.00 4.57
453 461 6.927936 ACATGATTAGCAGAACTATAGCACAG 59.072 38.462 0.00 0.00 0.00 3.66
454 462 6.715347 TGATTAGCAGAACTATAGCACAGA 57.285 37.500 0.00 0.00 0.00 3.41
455 463 6.507900 TGATTAGCAGAACTATAGCACAGAC 58.492 40.000 0.00 0.00 0.00 3.51
456 464 6.322456 TGATTAGCAGAACTATAGCACAGACT 59.678 38.462 0.00 0.00 0.00 3.24
457 465 6.531503 TTAGCAGAACTATAGCACAGACTT 57.468 37.500 0.00 0.00 0.00 3.01
458 466 5.413309 AGCAGAACTATAGCACAGACTTT 57.587 39.130 0.00 0.00 0.00 2.66
459 467 5.799213 AGCAGAACTATAGCACAGACTTTT 58.201 37.500 0.00 0.00 0.00 2.27
460 468 6.234177 AGCAGAACTATAGCACAGACTTTTT 58.766 36.000 0.00 0.00 0.00 1.94
461 469 6.148480 AGCAGAACTATAGCACAGACTTTTTG 59.852 38.462 0.00 0.00 0.00 2.44
462 470 6.310197 CAGAACTATAGCACAGACTTTTTGC 58.690 40.000 0.00 0.00 36.45 3.68
463 471 5.997746 AGAACTATAGCACAGACTTTTTGCA 59.002 36.000 0.00 0.00 38.81 4.08
464 472 6.486657 AGAACTATAGCACAGACTTTTTGCAA 59.513 34.615 0.00 0.00 38.81 4.08
465 473 6.633500 ACTATAGCACAGACTTTTTGCAAA 57.367 33.333 8.05 8.05 38.81 3.68
466 474 6.438763 ACTATAGCACAGACTTTTTGCAAAC 58.561 36.000 12.39 0.00 38.81 2.93
467 475 3.591196 AGCACAGACTTTTTGCAAACA 57.409 38.095 12.39 4.32 38.81 2.83
468 476 4.127566 AGCACAGACTTTTTGCAAACAT 57.872 36.364 12.39 0.00 38.81 2.71
469 477 4.506758 AGCACAGACTTTTTGCAAACATT 58.493 34.783 12.39 0.00 38.81 2.71
470 478 4.937015 AGCACAGACTTTTTGCAAACATTT 59.063 33.333 12.39 0.00 38.81 2.32
471 479 5.412286 AGCACAGACTTTTTGCAAACATTTT 59.588 32.000 12.39 0.00 38.81 1.82
484 492 8.430801 TTGCAAACATTTTAATATACATGGCC 57.569 30.769 0.00 0.00 0.00 5.36
511 522 7.048629 TCCACATTTCATACAAAAGAAAGCA 57.951 32.000 0.00 0.00 37.19 3.91
528 539 5.996513 AGAAAGCAGGACATGATTAGCATAG 59.003 40.000 0.00 0.00 36.22 2.23
584 595 8.618702 AATATCTGAAATGGCTAGAATCAGTG 57.381 34.615 0.00 0.00 38.83 3.66
739 765 1.653114 GTATTGTACGCGCGTAAACCA 59.347 47.619 40.68 31.04 31.86 3.67
759 785 1.972660 GCCGGTGCCTGTATTCCTCT 61.973 60.000 1.90 0.00 0.00 3.69
897 923 0.178964 GGCCTGCCTATAAATGCCCA 60.179 55.000 0.00 0.00 32.74 5.36
958 985 7.817418 ACACAAACAAACAGGAATAGTACAT 57.183 32.000 0.00 0.00 0.00 2.29
1028 1097 2.104967 CATCTCCACCAATGCCATTGT 58.895 47.619 15.83 2.15 38.59 2.71
1076 1151 3.095278 CGTCACGTCCGTCCGTTG 61.095 66.667 0.00 0.00 39.45 4.10
1155 1230 3.702048 GCCACCTGGTACGGAGCA 61.702 66.667 7.36 0.00 36.31 4.26
1236 1324 5.038683 CGCACATTTTCATGCATCAACTAT 58.961 37.500 0.00 0.00 42.17 2.12
1473 4428 2.029918 GTCAAACTCAAACCTCCCATGC 60.030 50.000 0.00 0.00 0.00 4.06
1474 4429 1.962807 CAAACTCAAACCTCCCATGCA 59.037 47.619 0.00 0.00 0.00 3.96
1475 4430 2.564062 CAAACTCAAACCTCCCATGCAT 59.436 45.455 0.00 0.00 0.00 3.96
1476 4431 1.843368 ACTCAAACCTCCCATGCATG 58.157 50.000 20.19 20.19 0.00 4.06
1508 4519 2.271800 GTCCTTCAGATTCGATGCGTT 58.728 47.619 0.00 0.00 0.00 4.84
1697 4713 3.241530 TTCAGGAGGGTGCGCTGT 61.242 61.111 9.73 0.00 0.00 4.40
2040 5056 8.989131 AGTTCTACTGATTTTGGCTTACCTATA 58.011 33.333 0.00 0.00 36.63 1.31
2044 5060 9.654663 CTACTGATTTTGGCTTACCTATATACC 57.345 37.037 0.00 0.00 36.63 2.73
2054 5073 5.393243 GCTTACCTATATACCTGCTTCTCCG 60.393 48.000 0.00 0.00 0.00 4.63
2101 5120 3.779183 TGCTCCTGGATTTCTCTTCTCAT 59.221 43.478 0.00 0.00 0.00 2.90
2147 8688 5.935789 TGTAAGTGATAAGGCCTTGTACAAC 59.064 40.000 28.77 21.33 0.00 3.32
2166 8707 2.504367 ACGCAATGCAAGGTCTTTAGT 58.496 42.857 5.91 0.00 0.00 2.24
2267 8816 4.827284 AGACACCACTGTTATCCAAAAAGG 59.173 41.667 0.00 0.00 39.47 3.11
2382 8973 1.312371 GCATGTTGCCGGGCTCTTTA 61.312 55.000 21.46 2.58 37.42 1.85
2383 8974 1.173043 CATGTTGCCGGGCTCTTTAA 58.827 50.000 21.46 2.18 0.00 1.52
2385 8976 1.917872 TGTTGCCGGGCTCTTTAATT 58.082 45.000 21.46 0.00 0.00 1.40
2389 8981 0.938008 GCCGGGCTCTTTAATTCTCG 59.062 55.000 12.87 0.00 0.00 4.04
2413 9005 1.141881 CCGTGGATTAGAGCTGCGT 59.858 57.895 0.00 0.00 0.00 5.24
2444 9036 6.636044 CGAGTAATATGTCGGTTTTCTACCTC 59.364 42.308 0.00 0.00 45.40 3.85
2446 9038 8.757982 AGTAATATGTCGGTTTTCTACCTCTA 57.242 34.615 0.00 0.00 45.40 2.43
2452 9044 7.001099 TGTCGGTTTTCTACCTCTATTTCTT 57.999 36.000 0.00 0.00 45.40 2.52
2621 9240 4.222124 ACACCAGGATATCACCAAACTC 57.778 45.455 4.83 0.00 0.00 3.01
2866 10768 3.840831 GCAGGACACATGCTACTCA 57.159 52.632 0.00 0.00 40.59 3.41
2871 10773 3.102972 AGGACACATGCTACTCAGACAT 58.897 45.455 0.00 0.00 0.00 3.06
2872 10774 3.118847 AGGACACATGCTACTCAGACATG 60.119 47.826 0.00 0.00 45.28 3.21
2878 10780 7.278135 ACACATGCTACTCAGACATGAATTAT 58.722 34.615 0.00 0.00 43.04 1.28
2887 10789 7.089538 ACTCAGACATGAATTATATCAGAGCG 58.910 38.462 0.00 0.00 34.23 5.03
2899 10801 0.241213 TCAGAGCGACAAAGACCGAG 59.759 55.000 0.00 0.00 0.00 4.63
2948 10850 0.811281 GGCGCAAAAGCTATGTCCTT 59.189 50.000 10.83 0.00 37.29 3.36
2957 10859 2.307768 AGCTATGTCCTTAGCAGCGTA 58.692 47.619 12.88 0.00 45.72 4.42
2980 10882 1.271840 TTCTATGAGGGCACGGGCTT 61.272 55.000 10.74 0.00 40.87 4.35
3007 10909 2.281761 CCACCCACACACCTCTGC 60.282 66.667 0.00 0.00 0.00 4.26
3019 10921 0.549469 ACCTCTGCCATCATGCATGA 59.451 50.000 30.47 30.47 41.16 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 3.650409 GCGATCCTCGACAAGATGT 57.350 52.632 0.00 0.00 43.74 3.06
69 70 0.522495 GTGCAAACCGTGTGTGTCAC 60.522 55.000 0.00 0.00 43.03 3.67
70 71 1.649390 GGTGCAAACCGTGTGTGTCA 61.649 55.000 0.00 0.00 0.00 3.58
154 160 2.785477 GCATGCATCGCAAACATTAGAC 59.215 45.455 14.21 0.00 43.62 2.59
172 179 0.583438 GCGAATAGTGTGCGATGCAT 59.417 50.000 0.00 0.00 41.91 3.96
176 183 0.459899 TGGAGCGAATAGTGTGCGAT 59.540 50.000 0.00 0.00 0.00 4.58
186 193 1.344438 TCACACACTCTTGGAGCGAAT 59.656 47.619 0.00 0.00 32.04 3.34
212 219 2.349060 CGTCACCACCAACATACAAACG 60.349 50.000 0.00 0.00 0.00 3.60
220 227 0.533978 CACCATCGTCACCACCAACA 60.534 55.000 0.00 0.00 0.00 3.33
227 234 1.665679 CATGTAAGCACCATCGTCACC 59.334 52.381 0.00 0.00 0.00 4.02
253 260 1.597742 ATGTGCTATGGATCCAACGC 58.402 50.000 20.67 22.91 0.00 4.84
280 288 6.244552 AGCTCCATCATTGATTTCTCACTA 57.755 37.500 0.00 0.00 0.00 2.74
286 294 5.919141 GCATGTAAGCTCCATCATTGATTTC 59.081 40.000 0.00 0.00 0.00 2.17
289 297 4.466827 TGCATGTAAGCTCCATCATTGAT 58.533 39.130 0.00 0.00 34.99 2.57
326 334 5.404466 AAATTTTGATTCTTGATCGGCCA 57.596 34.783 2.24 0.00 37.60 5.36
367 375 9.871238 CGCTATGTATAACCAATTATAGTCCTT 57.129 33.333 0.00 0.00 34.57 3.36
381 389 8.942338 TGAAATATGGATCCGCTATGTATAAC 57.058 34.615 7.39 0.00 0.00 1.89
382 390 9.764363 GATGAAATATGGATCCGCTATGTATAA 57.236 33.333 7.39 0.00 0.00 0.98
383 391 8.923270 TGATGAAATATGGATCCGCTATGTATA 58.077 33.333 7.39 0.00 0.00 1.47
384 392 7.795047 TGATGAAATATGGATCCGCTATGTAT 58.205 34.615 7.39 0.00 0.00 2.29
385 393 7.181569 TGATGAAATATGGATCCGCTATGTA 57.818 36.000 7.39 0.00 0.00 2.29
386 394 6.053632 TGATGAAATATGGATCCGCTATGT 57.946 37.500 7.39 1.87 0.00 2.29
387 395 7.930325 AGTATGATGAAATATGGATCCGCTATG 59.070 37.037 7.39 0.00 0.00 2.23
388 396 8.027524 AGTATGATGAAATATGGATCCGCTAT 57.972 34.615 7.39 4.06 0.00 2.97
389 397 7.124147 TGAGTATGATGAAATATGGATCCGCTA 59.876 37.037 7.39 1.53 0.00 4.26
390 398 6.070596 TGAGTATGATGAAATATGGATCCGCT 60.071 38.462 7.39 0.00 0.00 5.52
391 399 6.108687 TGAGTATGATGAAATATGGATCCGC 58.891 40.000 7.39 0.00 0.00 5.54
392 400 8.552083 TTTGAGTATGATGAAATATGGATCCG 57.448 34.615 7.39 0.00 0.00 4.18
401 409 8.248945 CCAGCTTTCTTTTGAGTATGATGAAAT 58.751 33.333 0.00 0.00 0.00 2.17
402 410 7.448161 TCCAGCTTTCTTTTGAGTATGATGAAA 59.552 33.333 0.00 0.00 0.00 2.69
403 411 6.942005 TCCAGCTTTCTTTTGAGTATGATGAA 59.058 34.615 0.00 0.00 0.00 2.57
404 412 6.372659 GTCCAGCTTTCTTTTGAGTATGATGA 59.627 38.462 0.00 0.00 0.00 2.92
405 413 6.149973 TGTCCAGCTTTCTTTTGAGTATGATG 59.850 38.462 0.00 0.00 0.00 3.07
406 414 6.240894 TGTCCAGCTTTCTTTTGAGTATGAT 58.759 36.000 0.00 0.00 0.00 2.45
407 415 5.620206 TGTCCAGCTTTCTTTTGAGTATGA 58.380 37.500 0.00 0.00 0.00 2.15
408 416 5.947228 TGTCCAGCTTTCTTTTGAGTATG 57.053 39.130 0.00 0.00 0.00 2.39
409 417 6.240894 TCATGTCCAGCTTTCTTTTGAGTAT 58.759 36.000 0.00 0.00 0.00 2.12
410 418 5.620206 TCATGTCCAGCTTTCTTTTGAGTA 58.380 37.500 0.00 0.00 0.00 2.59
411 419 4.464008 TCATGTCCAGCTTTCTTTTGAGT 58.536 39.130 0.00 0.00 0.00 3.41
412 420 5.640189 ATCATGTCCAGCTTTCTTTTGAG 57.360 39.130 0.00 0.00 0.00 3.02
413 421 6.349611 GCTAATCATGTCCAGCTTTCTTTTGA 60.350 38.462 7.60 0.00 0.00 2.69
414 422 5.803967 GCTAATCATGTCCAGCTTTCTTTTG 59.196 40.000 7.60 0.00 0.00 2.44
415 423 5.477984 TGCTAATCATGTCCAGCTTTCTTTT 59.522 36.000 13.55 0.00 35.05 2.27
416 424 5.012239 TGCTAATCATGTCCAGCTTTCTTT 58.988 37.500 13.55 0.00 35.05 2.52
417 425 4.592942 TGCTAATCATGTCCAGCTTTCTT 58.407 39.130 13.55 0.00 35.05 2.52
418 426 4.080695 TCTGCTAATCATGTCCAGCTTTCT 60.081 41.667 13.55 0.00 35.05 2.52
419 427 4.194640 TCTGCTAATCATGTCCAGCTTTC 58.805 43.478 13.55 0.00 35.05 2.62
420 428 4.226427 TCTGCTAATCATGTCCAGCTTT 57.774 40.909 13.55 0.00 35.05 3.51
421 429 3.920231 TCTGCTAATCATGTCCAGCTT 57.080 42.857 13.55 0.00 35.05 3.74
422 430 3.199508 AGTTCTGCTAATCATGTCCAGCT 59.800 43.478 13.55 0.00 35.05 4.24
423 431 3.539604 AGTTCTGCTAATCATGTCCAGC 58.460 45.455 7.83 7.83 34.56 4.85
424 432 6.589523 GCTATAGTTCTGCTAATCATGTCCAG 59.410 42.308 0.84 0.00 32.72 3.86
425 433 6.041979 TGCTATAGTTCTGCTAATCATGTCCA 59.958 38.462 0.84 0.00 32.72 4.02
426 434 6.367422 GTGCTATAGTTCTGCTAATCATGTCC 59.633 42.308 0.84 0.00 32.72 4.02
427 435 6.925718 TGTGCTATAGTTCTGCTAATCATGTC 59.074 38.462 0.84 0.00 32.72 3.06
428 436 6.820335 TGTGCTATAGTTCTGCTAATCATGT 58.180 36.000 0.84 0.00 32.72 3.21
429 437 7.116090 GTCTGTGCTATAGTTCTGCTAATCATG 59.884 40.741 0.84 0.00 32.72 3.07
430 438 7.015098 AGTCTGTGCTATAGTTCTGCTAATCAT 59.985 37.037 0.84 0.00 32.72 2.45
431 439 6.322456 AGTCTGTGCTATAGTTCTGCTAATCA 59.678 38.462 0.84 0.00 32.72 2.57
432 440 6.744112 AGTCTGTGCTATAGTTCTGCTAATC 58.256 40.000 0.84 0.00 32.72 1.75
433 441 6.723298 AGTCTGTGCTATAGTTCTGCTAAT 57.277 37.500 0.84 0.00 32.72 1.73
434 442 6.531503 AAGTCTGTGCTATAGTTCTGCTAA 57.468 37.500 0.84 0.00 32.72 3.09
435 443 6.531503 AAAGTCTGTGCTATAGTTCTGCTA 57.468 37.500 0.84 0.00 0.00 3.49
436 444 5.413309 AAAGTCTGTGCTATAGTTCTGCT 57.587 39.130 0.84 0.06 0.00 4.24
437 445 6.310197 CAAAAAGTCTGTGCTATAGTTCTGC 58.690 40.000 0.84 0.00 0.00 4.26
438 446 6.073058 TGCAAAAAGTCTGTGCTATAGTTCTG 60.073 38.462 0.84 0.16 39.09 3.02
439 447 5.997746 TGCAAAAAGTCTGTGCTATAGTTCT 59.002 36.000 0.84 0.00 39.09 3.01
440 448 6.241207 TGCAAAAAGTCTGTGCTATAGTTC 57.759 37.500 0.84 0.00 39.09 3.01
441 449 6.633500 TTGCAAAAAGTCTGTGCTATAGTT 57.367 33.333 0.00 0.00 39.09 2.24
442 450 6.039270 TGTTTGCAAAAAGTCTGTGCTATAGT 59.961 34.615 14.67 0.00 39.09 2.12
443 451 6.437928 TGTTTGCAAAAAGTCTGTGCTATAG 58.562 36.000 14.67 0.00 39.09 1.31
444 452 6.384258 TGTTTGCAAAAAGTCTGTGCTATA 57.616 33.333 14.67 0.00 39.09 1.31
445 453 5.261209 TGTTTGCAAAAAGTCTGTGCTAT 57.739 34.783 14.67 0.00 39.09 2.97
446 454 4.710423 TGTTTGCAAAAAGTCTGTGCTA 57.290 36.364 14.67 0.00 39.09 3.49
447 455 3.591196 TGTTTGCAAAAAGTCTGTGCT 57.409 38.095 14.67 0.00 39.09 4.40
448 456 4.863152 AATGTTTGCAAAAAGTCTGTGC 57.137 36.364 14.67 0.00 38.78 4.57
458 466 8.887717 GGCCATGTATATTAAAATGTTTGCAAA 58.112 29.630 8.05 8.05 0.00 3.68
459 467 7.223582 CGGCCATGTATATTAAAATGTTTGCAA 59.776 33.333 2.24 0.00 0.00 4.08
460 468 6.699204 CGGCCATGTATATTAAAATGTTTGCA 59.301 34.615 2.24 0.00 0.00 4.08
461 469 6.920758 TCGGCCATGTATATTAAAATGTTTGC 59.079 34.615 2.24 0.00 0.00 3.68
462 470 9.128107 GATCGGCCATGTATATTAAAATGTTTG 57.872 33.333 2.24 0.00 0.00 2.93
463 471 8.303876 GGATCGGCCATGTATATTAAAATGTTT 58.696 33.333 2.24 0.00 36.34 2.83
464 472 7.450014 TGGATCGGCCATGTATATTAAAATGTT 59.550 33.333 2.24 0.00 43.33 2.71
465 473 6.945435 TGGATCGGCCATGTATATTAAAATGT 59.055 34.615 2.24 0.00 43.33 2.71
466 474 7.389803 TGGATCGGCCATGTATATTAAAATG 57.610 36.000 2.24 0.00 43.33 2.32
481 489 2.571212 TGTATGAAATGTGGATCGGCC 58.429 47.619 0.00 0.00 37.10 6.13
484 492 7.008628 GCTTTCTTTTGTATGAAATGTGGATCG 59.991 37.037 0.00 0.00 32.65 3.69
491 499 7.147312 TGTCCTGCTTTCTTTTGTATGAAATG 58.853 34.615 0.00 0.00 32.65 2.32
511 522 7.969690 ACTATAGCTATGCTAATCATGTCCT 57.030 36.000 16.77 0.00 44.62 3.85
528 539 7.117812 TGTTTGCAAGAAAGTCTGTACTATAGC 59.882 37.037 0.00 0.00 33.75 2.97
564 575 3.314635 GGCACTGATTCTAGCCATTTCAG 59.685 47.826 0.00 0.00 46.26 3.02
583 594 2.469826 CGCACGTTATATCTTCAGGCA 58.530 47.619 0.00 0.00 0.00 4.75
584 595 1.792949 CCGCACGTTATATCTTCAGGC 59.207 52.381 0.00 0.00 0.00 4.85
706 721 6.563196 GCGCGTACAATACAATCACATATTGA 60.563 38.462 8.43 0.00 39.96 2.57
739 765 1.972660 GAGGAATACAGGCACCGGCT 61.973 60.000 0.00 0.00 40.87 5.52
759 785 2.391926 TGGCTACGGAGGGAATCATA 57.608 50.000 0.00 0.00 0.00 2.15
897 923 1.224592 GGACGGGATGACATTGCCT 59.775 57.895 0.00 0.00 0.00 4.75
958 985 7.567622 ACCTTCTTGCTAACCTTGTAGGATATA 59.432 37.037 0.00 0.00 37.67 0.86
976 1033 4.188247 TGGTCGACTATGAACCTTCTTG 57.812 45.455 16.46 0.00 0.00 3.02
1076 1151 2.356553 TGTCGTAGTTGGCCGCAC 60.357 61.111 0.00 0.00 0.00 5.34
1236 1324 5.819379 AGCACTATTACTAGCACTACGTACA 59.181 40.000 0.00 0.00 0.00 2.90
1295 1408 3.872771 GGTACTGGTTCACGTTCTTGAAA 59.127 43.478 0.00 0.00 37.24 2.69
1473 4428 3.622612 TGAAGGACGAATACATGCACATG 59.377 43.478 9.06 9.06 44.15 3.21
1474 4429 3.872696 TGAAGGACGAATACATGCACAT 58.127 40.909 0.00 0.00 0.00 3.21
1475 4430 3.056179 TCTGAAGGACGAATACATGCACA 60.056 43.478 0.00 0.00 0.00 4.57
1476 4431 3.521560 TCTGAAGGACGAATACATGCAC 58.478 45.455 0.00 0.00 0.00 4.57
1508 4519 2.909965 GAAGGGTTGTTGGCGGCA 60.910 61.111 7.97 7.97 0.00 5.69
1697 4713 0.254747 CCTTCATGCCCGGGAAGTTA 59.745 55.000 29.31 0.00 39.04 2.24
1963 4979 1.144057 CAGTAGGCCGGGATGACAC 59.856 63.158 2.18 0.00 0.00 3.67
2040 5056 1.982660 TCGATCGGAGAAGCAGGTAT 58.017 50.000 16.41 0.00 43.58 2.73
2044 5060 3.084686 CGATCGATCGGAGAAGCAG 57.915 57.895 34.54 8.20 45.93 4.24
2066 5085 2.419159 CCAGGAGCATCAACTCAATCGA 60.419 50.000 0.00 0.00 38.50 3.59
2071 5090 3.265221 AGAAATCCAGGAGCATCAACTCA 59.735 43.478 0.00 0.00 38.50 3.41
2101 5120 5.703592 ACAATGAACAATAGGTAGCGTTTGA 59.296 36.000 14.22 0.00 0.00 2.69
2147 8688 2.483877 TCACTAAAGACCTTGCATTGCG 59.516 45.455 3.84 0.00 0.00 4.85
2166 8707 7.769970 CCGGTACCTTTTTACAAATATACCTCA 59.230 37.037 10.90 0.00 33.66 3.86
2187 8728 7.147915 ACACCGATACTTAAGAAATTACCGGTA 60.148 37.037 11.16 11.16 43.63 4.02
2223 8765 7.544566 GTGTCTAAGTAAGCTTATGTGCTACAA 59.455 37.037 9.88 0.00 43.24 2.41
2267 8816 2.022195 GGTTTTCCTTAAGCCCCGATC 58.978 52.381 0.00 0.00 36.94 3.69
2382 8973 0.974010 TCCACGGGGTAGCGAGAATT 60.974 55.000 2.12 0.00 34.93 2.17
2383 8974 0.759436 ATCCACGGGGTAGCGAGAAT 60.759 55.000 2.12 0.00 34.93 2.40
2385 8976 0.106569 TAATCCACGGGGTAGCGAGA 60.107 55.000 2.12 0.00 34.93 4.04
2389 8981 0.033642 GCTCTAATCCACGGGGTAGC 59.966 60.000 2.12 2.65 34.93 3.58
2594 9213 4.878968 TGGTGATATCCTGGTGTTCTAGA 58.121 43.478 0.00 0.00 0.00 2.43
2692 9317 6.887545 ACATACACCCGAATGAATAGGAAAAA 59.112 34.615 0.00 0.00 0.00 1.94
2809 9438 2.494059 TGACCTGCTAACTGCTTTGTC 58.506 47.619 0.00 0.00 43.37 3.18
2866 10768 6.986250 TGTCGCTCTGATATAATTCATGTCT 58.014 36.000 0.00 0.00 0.00 3.41
2871 10773 6.701841 GGTCTTTGTCGCTCTGATATAATTCA 59.298 38.462 0.00 0.00 0.00 2.57
2872 10774 6.129062 CGGTCTTTGTCGCTCTGATATAATTC 60.129 42.308 0.00 0.00 0.00 2.17
2878 10780 2.089201 TCGGTCTTTGTCGCTCTGATA 58.911 47.619 0.00 0.00 0.00 2.15
2887 10789 1.149148 GTGCCTTCTCGGTCTTTGTC 58.851 55.000 0.00 0.00 34.25 3.18
2899 10801 1.648467 GCCCTTGTCATCGTGCCTTC 61.648 60.000 0.00 0.00 0.00 3.46
2948 10850 4.262036 CCCTCATAGAAACATACGCTGCTA 60.262 45.833 0.00 0.00 0.00 3.49
2957 10859 1.134098 CCCGTGCCCTCATAGAAACAT 60.134 52.381 0.00 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.