Multiple sequence alignment - TraesCS4A01G090200

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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 TraesCS4A01G090200 chr4A 100.000 7463 0 0 1 7463 96434812 96427350 0.000000e+00 13782
1 TraesCS4A01G090200 chr4A 93.730 5439 260 33 1505 6911 96488074 96482685 0.000000e+00 8080
2 TraesCS4A01G090200 chr4A 94.218 588 28 3 453 1035 96519405 96518819 0.000000e+00 893
3 TraesCS4A01G090200 chr4A 90.135 446 25 15 1033 1478 96495224 96494798 5.060000e-156 562
4 TraesCS4A01G090200 chr4A 92.268 388 28 2 1 387 96520062 96519676 3.940000e-152 549
5 TraesCS4A01G090200 chr4A 94.667 75 3 1 384 457 96519714 96519640 1.700000e-21 115
6 TraesCS4A01G090200 chr3B 94.140 5290 206 34 1427 6635 784490399 784485133 0.000000e+00 7956
7 TraesCS4A01G090200 chr3B 94.115 5285 212 33 1427 6635 784556615 784551354 0.000000e+00 7945
8 TraesCS4A01G090200 chr3B 92.445 1006 43 20 387 1389 784557586 784556611 0.000000e+00 1406
9 TraesCS4A01G090200 chr3B 91.956 1007 47 20 387 1389 784491371 784490395 0.000000e+00 1380
10 TraesCS4A01G090200 chr3B 90.464 388 26 8 1 387 784491713 784491336 1.120000e-137 501
11 TraesCS4A01G090200 chr3B 90.206 388 26 9 1 387 784557927 784557551 5.200000e-136 496
12 TraesCS4A01G090200 chr5D 96.554 4440 130 18 1714 6134 285457363 285461798 0.000000e+00 7330
13 TraesCS4A01G090200 chr5D 91.608 1430 59 28 378 1797 285455948 285457326 0.000000e+00 1919
14 TraesCS4A01G090200 chr5D 95.336 729 32 2 6185 6911 285461813 285462541 0.000000e+00 1157
15 TraesCS4A01G090200 chr5D 92.652 558 37 3 6909 7463 269969786 269970342 0.000000e+00 800
16 TraesCS4A01G090200 chr5D 92.446 556 38 4 6909 7463 1002209 1001657 0.000000e+00 791
17 TraesCS4A01G090200 chr5D 94.087 389 20 3 1 387 285455605 285455992 8.340000e-164 588
18 TraesCS4A01G090200 chr7D 92.973 555 35 3 6909 7460 473688950 473688397 0.000000e+00 806
19 TraesCS4A01G090200 chr7D 92.626 556 40 1 6909 7463 240864183 240863628 0.000000e+00 798
20 TraesCS4A01G090200 chr1D 92.832 558 36 3 6908 7462 102072077 102072633 0.000000e+00 806
21 TraesCS4A01G090200 chr6D 92.639 557 39 2 6909 7463 126909040 126908484 0.000000e+00 800
22 TraesCS4A01G090200 chr6D 92.599 554 40 1 6911 7463 383788002 383787449 0.000000e+00 795
23 TraesCS4A01G090200 chr2D 92.199 564 38 5 6902 7463 416538462 416539021 0.000000e+00 793
24 TraesCS4A01G090200 chr3D 92.280 557 41 2 6909 7463 202180846 202180290 0.000000e+00 789


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 TraesCS4A01G090200 chr4A 96427350 96434812 7462 True 13782.000000 13782 100.000000 1 7463 1 chr4A.!!$R1 7462
1 TraesCS4A01G090200 chr4A 96482685 96488074 5389 True 8080.000000 8080 93.730000 1505 6911 1 chr4A.!!$R2 5406
2 TraesCS4A01G090200 chr4A 96518819 96520062 1243 True 519.000000 893 93.717667 1 1035 3 chr4A.!!$R4 1034
3 TraesCS4A01G090200 chr3B 784551354 784557927 6573 True 3282.333333 7945 92.255333 1 6635 3 chr3B.!!$R2 6634
4 TraesCS4A01G090200 chr3B 784485133 784491713 6580 True 3279.000000 7956 92.186667 1 6635 3 chr3B.!!$R1 6634
5 TraesCS4A01G090200 chr5D 285455605 285462541 6936 False 2748.500000 7330 94.396250 1 6911 4 chr5D.!!$F2 6910
6 TraesCS4A01G090200 chr5D 269969786 269970342 556 False 800.000000 800 92.652000 6909 7463 1 chr5D.!!$F1 554
7 TraesCS4A01G090200 chr5D 1001657 1002209 552 True 791.000000 791 92.446000 6909 7463 1 chr5D.!!$R1 554
8 TraesCS4A01G090200 chr7D 473688397 473688950 553 True 806.000000 806 92.973000 6909 7460 1 chr7D.!!$R2 551
9 TraesCS4A01G090200 chr7D 240863628 240864183 555 True 798.000000 798 92.626000 6909 7463 1 chr7D.!!$R1 554
10 TraesCS4A01G090200 chr1D 102072077 102072633 556 False 806.000000 806 92.832000 6908 7462 1 chr1D.!!$F1 554
11 TraesCS4A01G090200 chr6D 126908484 126909040 556 True 800.000000 800 92.639000 6909 7463 1 chr6D.!!$R1 554
12 TraesCS4A01G090200 chr6D 383787449 383788002 553 True 795.000000 795 92.599000 6911 7463 1 chr6D.!!$R2 552
13 TraesCS4A01G090200 chr2D 416538462 416539021 559 False 793.000000 793 92.199000 6902 7463 1 chr2D.!!$F1 561
14 TraesCS4A01G090200 chr3D 202180290 202180846 556 True 789.000000 789 92.280000 6909 7463 1 chr3D.!!$R1 554

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
379 381 0.243907 TCGGTTCTGAGCAGCTACAC 59.756 55.000 0.0 0.0 0.00 2.90 F
381 383 0.610687 GGTTCTGAGCAGCTACACCT 59.389 55.000 0.0 0.0 0.00 4.00 F
385 387 1.186200 CTGAGCAGCTACACCTACCA 58.814 55.000 0.0 0.0 0.00 3.25 F
386 388 1.759445 CTGAGCAGCTACACCTACCAT 59.241 52.381 0.0 0.0 0.00 3.55 F
2146 2557 1.841277 ACAACGACCCCCATAATGCTA 59.159 47.619 0.0 0.0 0.00 3.49 F
2876 3317 1.894466 CCAGATCCATTTGTTGTGGCA 59.106 47.619 0.0 0.0 36.66 4.92 F
3339 3790 0.391597 GTTGGTTCAGGTCAGGTCGA 59.608 55.000 0.0 0.0 0.00 4.20 F
3402 3863 0.678048 AGCAGATTTCTCGGGTTGGC 60.678 55.000 0.0 0.0 0.00 4.52 F
4546 5008 0.251742 TGGGCTTGTGGGATTGAAGG 60.252 55.000 0.0 0.0 0.00 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1494 1752 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.0 0.00 3.72 R
1551 1809 1.242076 AATGCGGCATCAATAGCTCC 58.758 50.000 16.98 0.0 0.00 4.70 R
2053 2464 3.307691 CCATGAGAACTCCCAACAGCTAA 60.308 47.826 0.00 0.0 0.00 3.09 R
2783 3224 4.576053 TGATGATTCAAAAGCATACCTCGG 59.424 41.667 0.00 0.0 37.69 4.63 R
3204 3652 0.179073 CTGACATGACCCGTCCATCC 60.179 60.000 0.00 0.0 32.15 3.51 R
4037 4498 1.151668 CGGTGGCAAGAAGTCAAGAG 58.848 55.000 0.00 0.0 30.62 2.85 R
4546 5008 2.537560 CGCCATGGTTGATCGGCTC 61.538 63.158 14.67 0.0 42.59 4.70 R
4679 5142 3.119919 CGTGTACTCACTCTTCCAGGTAC 60.120 52.174 0.00 0.0 41.89 3.34 R
6890 7380 0.693622 TAGTCCATGAAACGGGGCAA 59.306 50.000 0.00 0.0 0.00 4.52 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
70 71 5.607477 ACAACTCAAGGAATGTAGAACGAA 58.393 37.500 0.00 0.00 0.00 3.85
71 72 5.465724 ACAACTCAAGGAATGTAGAACGAAC 59.534 40.000 0.00 0.00 0.00 3.95
77 78 3.008049 AGGAATGTAGAACGAACTTGCCT 59.992 43.478 0.00 0.00 0.00 4.75
132 133 4.078980 ACTCCCTCCGTCCCTAAATAACTA 60.079 45.833 0.00 0.00 0.00 2.24
134 135 5.470501 TCCCTCCGTCCCTAAATAACTATT 58.529 41.667 0.00 0.00 0.00 1.73
140 141 8.866970 TCCGTCCCTAAATAACTATTGTTTTT 57.133 30.769 0.00 2.54 37.59 1.94
285 287 0.951558 GTCGGTCAAACTTGTGGCAT 59.048 50.000 0.00 0.00 0.00 4.40
298 300 0.887933 GTGGCATGGAAACCAACGAT 59.112 50.000 0.00 0.00 37.79 3.73
324 326 0.759346 CATTTAGGGACGGAGGGAGG 59.241 60.000 0.00 0.00 0.00 4.30
329 331 1.689582 GGGACGGAGGGAGGACAAT 60.690 63.158 0.00 0.00 0.00 2.71
363 365 3.724374 TCAGCTCCCGTAAAATTATCGG 58.276 45.455 8.33 8.33 43.30 4.18
364 366 3.133362 TCAGCTCCCGTAAAATTATCGGT 59.867 43.478 12.51 0.00 42.30 4.69
365 367 3.875134 CAGCTCCCGTAAAATTATCGGTT 59.125 43.478 12.51 0.00 42.30 4.44
366 368 4.025145 CAGCTCCCGTAAAATTATCGGTTC 60.025 45.833 12.51 4.34 42.30 3.62
367 369 4.124970 GCTCCCGTAAAATTATCGGTTCT 58.875 43.478 12.51 0.00 42.30 3.01
368 370 4.025145 GCTCCCGTAAAATTATCGGTTCTG 60.025 45.833 12.51 1.51 42.30 3.02
369 371 5.341872 TCCCGTAAAATTATCGGTTCTGA 57.658 39.130 12.51 3.29 42.30 3.27
370 372 5.353938 TCCCGTAAAATTATCGGTTCTGAG 58.646 41.667 12.51 0.72 42.30 3.35
371 373 4.025145 CCCGTAAAATTATCGGTTCTGAGC 60.025 45.833 12.51 0.00 42.30 4.26
372 374 4.569162 CCGTAAAATTATCGGTTCTGAGCA 59.431 41.667 7.44 0.00 39.51 4.26
373 375 5.276868 CCGTAAAATTATCGGTTCTGAGCAG 60.277 44.000 7.44 0.00 39.51 4.24
374 376 4.622701 AAAATTATCGGTTCTGAGCAGC 57.377 40.909 0.00 0.00 0.00 5.25
375 377 3.550437 AATTATCGGTTCTGAGCAGCT 57.450 42.857 0.00 0.00 0.00 4.24
376 378 4.672587 AATTATCGGTTCTGAGCAGCTA 57.327 40.909 0.00 0.00 0.00 3.32
377 379 3.438297 TTATCGGTTCTGAGCAGCTAC 57.562 47.619 0.00 0.00 0.00 3.58
378 380 1.186200 ATCGGTTCTGAGCAGCTACA 58.814 50.000 0.00 0.00 0.00 2.74
379 381 0.243907 TCGGTTCTGAGCAGCTACAC 59.756 55.000 0.00 0.00 0.00 2.90
380 382 0.737715 CGGTTCTGAGCAGCTACACC 60.738 60.000 0.00 0.00 0.00 4.16
381 383 0.610687 GGTTCTGAGCAGCTACACCT 59.389 55.000 0.00 0.00 0.00 4.00
382 384 1.825474 GGTTCTGAGCAGCTACACCTA 59.175 52.381 0.00 0.00 0.00 3.08
383 385 2.417515 GGTTCTGAGCAGCTACACCTAC 60.418 54.545 0.00 0.00 0.00 3.18
384 386 1.475403 TCTGAGCAGCTACACCTACC 58.525 55.000 0.00 0.00 0.00 3.18
385 387 1.186200 CTGAGCAGCTACACCTACCA 58.814 55.000 0.00 0.00 0.00 3.25
386 388 1.759445 CTGAGCAGCTACACCTACCAT 59.241 52.381 0.00 0.00 0.00 3.55
387 389 2.959030 CTGAGCAGCTACACCTACCATA 59.041 50.000 0.00 0.00 0.00 2.74
388 390 3.371034 TGAGCAGCTACACCTACCATAA 58.629 45.455 0.00 0.00 0.00 1.90
389 391 3.772572 TGAGCAGCTACACCTACCATAAA 59.227 43.478 0.00 0.00 0.00 1.40
390 392 4.224147 TGAGCAGCTACACCTACCATAAAA 59.776 41.667 0.00 0.00 0.00 1.52
391 393 5.104527 TGAGCAGCTACACCTACCATAAAAT 60.105 40.000 0.00 0.00 0.00 1.82
392 394 5.755849 AGCAGCTACACCTACCATAAAATT 58.244 37.500 0.00 0.00 0.00 1.82
393 395 6.895782 AGCAGCTACACCTACCATAAAATTA 58.104 36.000 0.00 0.00 0.00 1.40
394 396 7.518188 AGCAGCTACACCTACCATAAAATTAT 58.482 34.615 0.00 0.00 0.00 1.28
395 397 7.661847 AGCAGCTACACCTACCATAAAATTATC 59.338 37.037 0.00 0.00 0.00 1.75
396 398 7.444183 GCAGCTACACCTACCATAAAATTATCA 59.556 37.037 0.00 0.00 0.00 2.15
428 430 5.473931 CAGCTACACCTACACATCATATCC 58.526 45.833 0.00 0.00 0.00 2.59
482 727 3.824151 CAAATCAATCATGCACGTGTCA 58.176 40.909 18.38 15.67 0.00 3.58
621 866 4.631377 TGCAAATCACGAGACCTTTCTATG 59.369 41.667 0.00 0.00 29.47 2.23
649 894 8.421784 AGCCTAATTAATTCGTCATTAGAGACA 58.578 33.333 3.39 0.00 38.43 3.41
805 1054 2.081462 TCGAAGTCACTGTAGCGATGA 58.919 47.619 0.00 0.00 0.00 2.92
863 1114 7.125659 TCAGAACATACTGAGAATGGGTTGATA 59.874 37.037 0.00 0.00 41.21 2.15
2050 2461 4.320870 GACCCTCCTCGAAAAATACAACA 58.679 43.478 0.00 0.00 0.00 3.33
2053 2464 4.700213 CCCTCCTCGAAAAATACAACATGT 59.300 41.667 0.00 0.00 0.00 3.21
2146 2557 1.841277 ACAACGACCCCCATAATGCTA 59.159 47.619 0.00 0.00 0.00 3.49
2226 2637 9.915629 CAGGATGAGGTACTTAATTATACACTC 57.084 37.037 0.00 0.00 41.55 3.51
2427 2844 9.603921 AATTTGCATCCCTATTATTTTGTTCAG 57.396 29.630 0.00 0.00 0.00 3.02
2726 3147 4.494350 AAGAGCTAATGTGTGCTTGTTG 57.506 40.909 0.00 0.00 39.91 3.33
2792 3233 4.342862 ACAGATGGAAATCCGAGGTATG 57.657 45.455 0.00 0.00 39.43 2.39
2807 3248 5.066375 CCGAGGTATGCTTTTGAATCATCAA 59.934 40.000 0.00 0.00 43.70 2.57
2876 3317 1.894466 CCAGATCCATTTGTTGTGGCA 59.106 47.619 0.00 0.00 36.66 4.92
3138 3586 4.318949 CGGGTCGGGTTCGGGTTT 62.319 66.667 0.00 0.00 36.95 3.27
3178 3626 6.486993 GGGTTAGTTTGGCCTTCTAGAATATG 59.513 42.308 5.44 0.00 0.00 1.78
3204 3652 3.562732 GAGTTGGGTCGGGTTGGGG 62.563 68.421 0.00 0.00 0.00 4.96
3218 3666 2.772622 GGGGGATGGACGGGTCAT 60.773 66.667 0.75 0.00 0.00 3.06
3318 3769 2.040412 GGGTCAGTTTTGGATCTGGTCT 59.960 50.000 0.00 0.00 33.13 3.85
3338 3789 0.602905 GGTTGGTTCAGGTCAGGTCG 60.603 60.000 0.00 0.00 0.00 4.79
3339 3790 0.391597 GTTGGTTCAGGTCAGGTCGA 59.608 55.000 0.00 0.00 0.00 4.20
3371 3827 2.089201 GGAAAATGTCGGGTCGGATTT 58.911 47.619 0.00 0.00 0.00 2.17
3372 3828 3.272581 GGAAAATGTCGGGTCGGATTTA 58.727 45.455 0.00 0.00 0.00 1.40
3373 3829 3.690628 GGAAAATGTCGGGTCGGATTTAA 59.309 43.478 0.00 0.00 0.00 1.52
3374 3830 4.201881 GGAAAATGTCGGGTCGGATTTAAG 60.202 45.833 0.00 0.00 0.00 1.85
3375 3831 3.622166 AATGTCGGGTCGGATTTAAGT 57.378 42.857 0.00 0.00 0.00 2.24
3402 3863 0.678048 AGCAGATTTCTCGGGTTGGC 60.678 55.000 0.00 0.00 0.00 4.52
3486 3947 6.395629 CAGATTGAAATCACAGCTCCAAAAT 58.604 36.000 5.86 0.00 37.89 1.82
3488 3949 8.195436 CAGATTGAAATCACAGCTCCAAAATAT 58.805 33.333 5.86 0.00 37.89 1.28
3527 3988 5.186198 CCCCTCAAATCGTTCAAGTTCTAT 58.814 41.667 0.00 0.00 0.00 1.98
3542 4003 6.096141 TCAAGTTCTATGCCACAAAAGAACAA 59.904 34.615 19.68 8.83 46.57 2.83
3568 4029 7.928706 ACCTACGAATTCTGATGGAATAAAGAG 59.071 37.037 3.52 0.00 43.17 2.85
3622 4083 8.515414 GTGGTGAGTAATGCTTAAGATTTTCTT 58.485 33.333 6.67 0.00 40.35 2.52
3844 4305 7.824779 AGGACTTATGTTGATGGAAAACTAGTC 59.175 37.037 0.00 0.00 34.33 2.59
4082 4543 7.080353 ACCGATAAAGCTGTTATTTACCAAC 57.920 36.000 0.00 0.00 0.00 3.77
4157 4618 9.971922 ATTTTGTTTTAATCTCAGGAAGAACAG 57.028 29.630 0.00 0.00 37.61 3.16
4162 4623 1.661463 TCTCAGGAAGAACAGCCCAT 58.339 50.000 0.00 0.00 0.00 4.00
4286 4747 1.374343 CCATGAGAGCTGCAATGCGT 61.374 55.000 1.02 0.00 38.13 5.24
4453 4915 9.599866 TGTACAGTTTACCTGATATTCTGATTG 57.400 33.333 0.00 0.00 44.49 2.67
4546 5008 0.251742 TGGGCTTGTGGGATTGAAGG 60.252 55.000 0.00 0.00 0.00 3.46
4575 5037 3.055021 TCAACCATGGCGTACCTTATTCA 60.055 43.478 13.04 0.00 36.63 2.57
4679 5142 1.202405 GCTGCAAATAATTCCCCACCG 60.202 52.381 0.00 0.00 0.00 4.94
4727 5190 4.524802 ATGTTTGGCATCCATTCCTCTA 57.475 40.909 0.00 0.00 31.53 2.43
4728 5191 3.620488 TGTTTGGCATCCATTCCTCTAC 58.380 45.455 0.00 0.00 31.53 2.59
4729 5192 3.266772 TGTTTGGCATCCATTCCTCTACT 59.733 43.478 0.00 0.00 31.53 2.57
4910 5377 3.728076 ACTCGACACAAACAGCTAGAA 57.272 42.857 0.00 0.00 0.00 2.10
5094 5562 1.064825 TTGGTCTCAAGGGGGAAGAC 58.935 55.000 0.00 0.00 0.00 3.01
5483 5951 8.850454 TTTAGTTTTCAAGAATTCCGAAACTG 57.150 30.769 22.79 7.28 0.00 3.16
5499 5967 7.215789 TCCGAAACTGTTATTGTACTAACCAA 58.784 34.615 0.00 0.00 31.83 3.67
5575 6043 4.615513 ACCTTAGCACCACTCTCTAATCT 58.384 43.478 0.00 0.00 0.00 2.40
5688 6157 8.601476 GTTAAATAAAGAGGATTACCGTGTCTG 58.399 37.037 0.00 0.00 41.83 3.51
5697 6166 2.851263 TACCGTGTCTGATGCCTTTT 57.149 45.000 0.00 0.00 0.00 2.27
5707 6176 7.588854 CGTGTCTGATGCCTTTTATAATGATTG 59.411 37.037 0.00 0.00 0.00 2.67
5862 6331 4.401022 AGTGACAAGGATGCAATTGAAGA 58.599 39.130 10.34 0.00 0.00 2.87
6172 6644 2.917933 ACGATGTGACCATTATGGGTG 58.082 47.619 16.35 0.00 43.37 4.61
6183 6655 3.381272 CCATTATGGGTGCTTTACTGGTG 59.619 47.826 2.72 0.00 32.67 4.17
6187 6675 1.347707 TGGGTGCTTTACTGGTGAGAG 59.652 52.381 0.00 0.00 0.00 3.20
6206 6694 7.657761 GGTGAGAGAAAAGAAGTAGTCAAATGA 59.342 37.037 0.00 0.00 0.00 2.57
6223 6711 9.965902 AGTCAAATGAGGAAGTACTAATTTGAT 57.034 29.630 16.11 6.12 42.61 2.57
6414 6902 4.396166 CACTACCCTGAAATTACTGCCAAG 59.604 45.833 0.00 0.00 0.00 3.61
6478 6966 8.237267 CAGACTACTAGTGCAAAAATAAAAGGG 58.763 37.037 5.39 0.00 0.00 3.95
6481 6969 4.591072 ACTAGTGCAAAAATAAAAGGGCCA 59.409 37.500 6.18 0.00 0.00 5.36
6484 6973 4.071423 GTGCAAAAATAAAAGGGCCATGT 58.929 39.130 6.18 0.00 0.00 3.21
6505 6994 6.063640 TGTCATATGTACTGCATGCAATTC 57.936 37.500 22.88 10.61 38.47 2.17
6507 6996 4.815846 TCATATGTACTGCATGCAATTCGT 59.184 37.500 22.88 17.84 38.47 3.85
6625 7115 6.474427 GGATTCATTATTGCATGACACAAGTG 59.526 38.462 0.00 0.00 32.68 3.16
6648 7138 9.855021 AGTGGTATGCTTATTTGTTTACATTTC 57.145 29.630 0.00 0.00 0.00 2.17
6717 7207 6.557633 GGGAAATAAGTAGGAGGAGACCATAA 59.442 42.308 0.00 0.00 0.00 1.90
6723 7213 7.989947 AAGTAGGAGGAGACCATAAAACATA 57.010 36.000 0.00 0.00 0.00 2.29
6790 7280 6.542574 TTGGTTTTGGTTACAGTGTATACG 57.457 37.500 3.28 0.00 0.00 3.06
6835 7325 9.822185 AATTAAAGAAATATTGGGCTTGATCAC 57.178 29.630 0.00 0.00 0.00 3.06
6886 7376 0.825425 TCCAGTCGCAATTTTGGCCA 60.825 50.000 0.00 0.00 0.00 5.36
6890 7380 2.807392 CAGTCGCAATTTTGGCCAATTT 59.193 40.909 21.26 13.54 0.00 1.82
6892 7382 3.250521 AGTCGCAATTTTGGCCAATTTTG 59.749 39.130 25.63 25.63 0.00 2.44
7007 7497 6.801862 GCTTTACTCAATTTTGTGTATTCGCT 59.198 34.615 6.17 0.00 37.11 4.93
7036 7526 1.201921 GCATCTAAAACCAGCGTCGTG 60.202 52.381 0.00 0.00 0.00 4.35
7094 7584 2.119391 TGGGCCCCCAAACATGTC 59.881 61.111 22.27 0.00 44.12 3.06
7130 7620 1.073284 GGCCCAAAGTCCAGAACTGTA 59.927 52.381 0.00 0.00 38.58 2.74
7300 7792 3.372660 GGGTACCGTTTGCAAAATTGA 57.627 42.857 14.67 0.00 40.86 2.57
7320 7812 7.698163 ATTGACATAGTTTCCTTCCTATCCT 57.302 36.000 0.00 0.00 0.00 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 52 5.389935 GCAAGTTCGTTCTACATTCCTTGAG 60.390 44.000 0.00 0.00 31.94 3.02
54 55 3.751698 GGCAAGTTCGTTCTACATTCCTT 59.248 43.478 0.00 0.00 0.00 3.36
70 71 3.087031 CAGATGATTTGACCAGGCAAGT 58.913 45.455 0.00 0.00 0.00 3.16
71 72 3.087031 ACAGATGATTTGACCAGGCAAG 58.913 45.455 0.00 0.00 0.00 4.01
77 78 7.148035 CCATTGTTGATACAGATGATTTGACCA 60.148 37.037 0.00 0.00 35.28 4.02
132 133 5.848406 TGTTTATCGGGAAGCAAAAACAAT 58.152 33.333 0.00 0.00 34.80 2.71
134 135 4.920640 TGTTTATCGGGAAGCAAAAACA 57.079 36.364 0.00 0.00 35.21 2.83
140 141 4.023536 GTCAAAGTTGTTTATCGGGAAGCA 60.024 41.667 0.00 0.00 0.00 3.91
254 256 5.794894 AGTTTGACCGACATTTGTATCTCT 58.205 37.500 0.00 0.00 0.00 3.10
285 287 3.949132 TGATGATCATCGTTGGTTTCCA 58.051 40.909 26.52 6.74 40.63 3.53
298 300 3.324846 CCTCCGTCCCTAAATGATGATCA 59.675 47.826 0.00 0.00 0.00 2.92
324 326 5.605534 AGCTGATACAGTGATACCATTGTC 58.394 41.667 0.00 0.00 41.48 3.18
329 331 2.965831 GGGAGCTGATACAGTGATACCA 59.034 50.000 0.00 0.00 33.43 3.25
363 365 2.417515 GGTAGGTGTAGCTGCTCAGAAC 60.418 54.545 4.91 0.00 0.00 3.01
364 366 1.825474 GGTAGGTGTAGCTGCTCAGAA 59.175 52.381 4.91 0.00 0.00 3.02
365 367 1.272480 TGGTAGGTGTAGCTGCTCAGA 60.272 52.381 4.91 0.00 0.00 3.27
366 368 1.186200 TGGTAGGTGTAGCTGCTCAG 58.814 55.000 4.91 0.00 0.00 3.35
367 369 1.866015 ATGGTAGGTGTAGCTGCTCA 58.134 50.000 4.91 1.15 0.00 4.26
368 370 4.402056 TTTATGGTAGGTGTAGCTGCTC 57.598 45.455 4.91 0.00 0.00 4.26
369 371 4.837093 TTTTATGGTAGGTGTAGCTGCT 57.163 40.909 7.57 7.57 0.00 4.24
370 372 7.444183 TGATAATTTTATGGTAGGTGTAGCTGC 59.556 37.037 0.00 0.00 0.00 5.25
371 373 8.902540 TGATAATTTTATGGTAGGTGTAGCTG 57.097 34.615 0.00 0.00 0.00 4.24
372 374 8.714906 ACTGATAATTTTATGGTAGGTGTAGCT 58.285 33.333 0.00 0.00 0.00 3.32
373 375 8.904099 ACTGATAATTTTATGGTAGGTGTAGC 57.096 34.615 0.00 0.00 0.00 3.58
376 378 9.396022 CAGAACTGATAATTTTATGGTAGGTGT 57.604 33.333 0.00 0.00 0.00 4.16
377 379 9.613428 TCAGAACTGATAATTTTATGGTAGGTG 57.387 33.333 0.00 0.00 34.14 4.00
378 380 9.838339 CTCAGAACTGATAATTTTATGGTAGGT 57.162 33.333 4.96 0.00 39.13 3.08
379 381 8.778358 GCTCAGAACTGATAATTTTATGGTAGG 58.222 37.037 4.96 0.00 39.13 3.18
380 382 9.330063 TGCTCAGAACTGATAATTTTATGGTAG 57.670 33.333 4.96 0.00 39.13 3.18
381 383 9.330063 CTGCTCAGAACTGATAATTTTATGGTA 57.670 33.333 4.96 0.00 39.13 3.25
382 384 7.201767 GCTGCTCAGAACTGATAATTTTATGGT 60.202 37.037 4.96 0.00 39.13 3.55
383 385 7.013083 AGCTGCTCAGAACTGATAATTTTATGG 59.987 37.037 4.96 0.00 39.13 2.74
384 386 7.928103 AGCTGCTCAGAACTGATAATTTTATG 58.072 34.615 4.96 0.00 39.13 1.90
385 387 9.050601 GTAGCTGCTCAGAACTGATAATTTTAT 57.949 33.333 4.91 0.00 39.13 1.40
386 388 8.040727 TGTAGCTGCTCAGAACTGATAATTTTA 58.959 33.333 4.91 0.00 39.13 1.52
387 389 6.881065 TGTAGCTGCTCAGAACTGATAATTTT 59.119 34.615 4.91 0.00 39.13 1.82
388 390 6.314896 GTGTAGCTGCTCAGAACTGATAATTT 59.685 38.462 4.91 0.00 39.13 1.82
389 391 5.814705 GTGTAGCTGCTCAGAACTGATAATT 59.185 40.000 4.91 0.00 39.13 1.40
390 392 5.355596 GTGTAGCTGCTCAGAACTGATAAT 58.644 41.667 4.91 0.00 39.13 1.28
391 393 4.382040 GGTGTAGCTGCTCAGAACTGATAA 60.382 45.833 4.91 0.00 39.13 1.75
392 394 3.131223 GGTGTAGCTGCTCAGAACTGATA 59.869 47.826 4.91 0.00 39.13 2.15
393 395 2.093764 GGTGTAGCTGCTCAGAACTGAT 60.094 50.000 4.91 0.00 39.13 2.90
394 396 1.273606 GGTGTAGCTGCTCAGAACTGA 59.726 52.381 4.91 4.45 38.06 3.41
395 397 1.274728 AGGTGTAGCTGCTCAGAACTG 59.725 52.381 4.91 0.00 0.00 3.16
396 398 1.638529 AGGTGTAGCTGCTCAGAACT 58.361 50.000 4.91 0.00 0.00 3.01
446 452 9.605275 ATGATTGATTTGCTGCGTACTATATAT 57.395 29.630 0.00 0.00 0.00 0.86
482 727 4.081406 TGCAATCTAAACACAGCCTCAAT 58.919 39.130 0.00 0.00 0.00 2.57
530 775 5.984725 TCCTAAATAGCATCCGAAAAGTGA 58.015 37.500 0.00 0.00 0.00 3.41
621 866 9.477484 TCTCTAATGACGAATTAATTAGGCTTC 57.523 33.333 14.33 3.75 35.51 3.86
649 894 4.714632 ACAATGTGGTGCTACAGTAAACT 58.285 39.130 0.00 0.00 33.44 2.66
696 941 3.731274 GCTTTTGCGAGACCTTTCTAG 57.269 47.619 0.00 0.00 34.86 2.43
1479 1737 3.541916 CACACACACTTTTAGTTGCGTTG 59.458 43.478 0.00 0.00 0.00 4.10
1481 1739 2.745281 ACACACACACTTTTAGTTGCGT 59.255 40.909 0.00 0.00 0.00 5.24
1483 1741 3.851403 CACACACACACACTTTTAGTTGC 59.149 43.478 0.00 0.00 0.00 4.17
1485 1743 4.517453 ACACACACACACACACTTTTAGTT 59.483 37.500 0.00 0.00 0.00 2.24
1486 1744 4.069304 ACACACACACACACACTTTTAGT 58.931 39.130 0.00 0.00 0.00 2.24
1488 1746 3.815962 ACACACACACACACACACTTTTA 59.184 39.130 0.00 0.00 0.00 1.52
1490 1748 2.031245 CACACACACACACACACACTTT 60.031 45.455 0.00 0.00 0.00 2.66
1491 1749 1.535028 CACACACACACACACACACTT 59.465 47.619 0.00 0.00 0.00 3.16
1492 1750 1.155889 CACACACACACACACACACT 58.844 50.000 0.00 0.00 0.00 3.55
1494 1752 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1496 1754 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1551 1809 1.242076 AATGCGGCATCAATAGCTCC 58.758 50.000 16.98 0.00 0.00 4.70
1654 1945 6.338214 TGGTGCATCAAACTTAATTTAGCA 57.662 33.333 0.00 0.00 32.53 3.49
2050 2461 3.327757 TGAGAACTCCCAACAGCTAACAT 59.672 43.478 0.00 0.00 0.00 2.71
2053 2464 3.307691 CCATGAGAACTCCCAACAGCTAA 60.308 47.826 0.00 0.00 0.00 3.09
2783 3224 4.576053 TGATGATTCAAAAGCATACCTCGG 59.424 41.667 0.00 0.00 37.69 4.63
2828 3269 8.382030 TCATCAACTGCATCGATAAATAACAT 57.618 30.769 0.00 0.00 0.00 2.71
2876 3317 2.106511 TCTCCTGGCTAACAGCTTTGTT 59.893 45.455 0.00 0.00 46.14 2.83
3138 3586 3.717913 ACTAACCCAACAAGTCTAACCCA 59.282 43.478 0.00 0.00 0.00 4.51
3178 3626 2.260743 GACCCAACTCGACCCGAC 59.739 66.667 0.00 0.00 0.00 4.79
3204 3652 0.179073 CTGACATGACCCGTCCATCC 60.179 60.000 0.00 0.00 32.15 3.51
3218 3666 8.408043 AAGTTGATATTGAAATTGGTCTGACA 57.592 30.769 10.38 0.00 0.00 3.58
3257 3705 5.424252 AGCATCCAATCCAACTCAAATCAAT 59.576 36.000 0.00 0.00 0.00 2.57
3318 3769 0.472471 GACCTGACCTGAACCAACCA 59.528 55.000 0.00 0.00 0.00 3.67
3338 3789 6.073819 CCCGACATTTTCCAAAAAGTCAAATC 60.074 38.462 16.32 0.00 43.16 2.17
3339 3790 5.757808 CCCGACATTTTCCAAAAAGTCAAAT 59.242 36.000 16.32 0.00 43.16 2.32
3371 3827 3.690139 AGAAATCTGCTCGACTCGACTTA 59.310 43.478 0.00 0.00 0.00 2.24
3372 3828 2.490115 AGAAATCTGCTCGACTCGACTT 59.510 45.455 0.00 0.00 0.00 3.01
3373 3829 2.088423 AGAAATCTGCTCGACTCGACT 58.912 47.619 0.00 0.00 0.00 4.18
3374 3830 2.446282 GAGAAATCTGCTCGACTCGAC 58.554 52.381 0.00 0.00 0.00 4.20
3375 3831 2.834574 GAGAAATCTGCTCGACTCGA 57.165 50.000 0.29 0.29 0.00 4.04
3527 3988 2.356382 CGTAGGTTGTTCTTTTGTGGCA 59.644 45.455 0.00 0.00 0.00 4.92
3542 4003 7.792032 TCTTTATTCCATCAGAATTCGTAGGT 58.208 34.615 0.00 0.00 42.86 3.08
3568 4029 2.414138 GTGCGGACATTGTAGTAACCAC 59.586 50.000 0.63 0.00 0.00 4.16
3844 4305 4.927978 AAGAAGACCGTCATCTCCTATG 57.072 45.455 6.74 0.00 0.00 2.23
3847 4308 3.866449 GCAAAAGAAGACCGTCATCTCCT 60.866 47.826 6.74 0.00 0.00 3.69
4036 4497 1.541233 CGGTGGCAAGAAGTCAAGAGT 60.541 52.381 0.00 0.00 30.62 3.24
4037 4498 1.151668 CGGTGGCAAGAAGTCAAGAG 58.848 55.000 0.00 0.00 30.62 2.85
4157 4618 4.630644 TTCTTCATCTGATAGGATGGGC 57.369 45.455 4.91 0.00 42.22 5.36
4162 4623 9.480861 ACCGATATAATTCTTCATCTGATAGGA 57.519 33.333 0.00 0.00 0.00 2.94
4286 4747 9.812347 AGATAAATATATCCTCACCAATTTGCA 57.188 29.630 0.00 0.00 39.02 4.08
4346 4808 4.955811 AAGTAATACCATCATCAGCGGA 57.044 40.909 0.00 0.00 0.00 5.54
4350 4812 8.400947 CACTTGGAAAAGTAATACCATCATCAG 58.599 37.037 0.00 0.00 32.31 2.90
4453 4915 7.093509 ACCCAATAATCCATACCTTCACAAAAC 60.094 37.037 0.00 0.00 0.00 2.43
4546 5008 2.537560 CGCCATGGTTGATCGGCTC 61.538 63.158 14.67 0.00 42.59 4.70
4575 5037 5.930135 ACACTGGTAAACTCTTCAGTCAAT 58.070 37.500 0.00 0.00 38.27 2.57
4679 5142 3.119919 CGTGTACTCACTCTTCCAGGTAC 60.120 52.174 0.00 0.00 41.89 3.34
4701 5164 6.041296 AGAGGAATGGATGCCAAACATAAATC 59.959 38.462 0.00 0.00 39.84 2.17
4867 5333 5.545063 TCAGTGTCTAATGTCAGGTTCAA 57.455 39.130 0.00 0.00 0.00 2.69
5094 5562 6.773976 TCAAACCCTATTTTTGATAGCTGG 57.226 37.500 0.00 0.00 37.91 4.85
5460 5928 7.562454 ACAGTTTCGGAATTCTTGAAAACTA 57.438 32.000 20.40 4.41 33.78 2.24
5462 5930 8.797266 ATAACAGTTTCGGAATTCTTGAAAAC 57.203 30.769 20.40 16.57 33.78 2.43
5681 6150 6.603237 TCATTATAAAAGGCATCAGACACG 57.397 37.500 0.00 0.00 0.00 4.49
5688 6157 7.428020 TCAGTGCAATCATTATAAAAGGCATC 58.572 34.615 0.00 0.00 32.16 3.91
5862 6331 9.833917 CATCATCTCCATATATTGCTCTTATGT 57.166 33.333 0.00 0.00 0.00 2.29
6077 6549 7.814587 GTGAAAATTAGCTTAAGCCACATTCTT 59.185 33.333 23.71 14.12 43.38 2.52
6172 6644 5.760743 ACTTCTTTTCTCTCACCAGTAAAGC 59.239 40.000 0.00 0.00 0.00 3.51
6183 6655 8.091449 TCCTCATTTGACTACTTCTTTTCTCTC 58.909 37.037 0.00 0.00 0.00 3.20
6187 6675 8.384607 ACTTCCTCATTTGACTACTTCTTTTC 57.615 34.615 0.00 0.00 0.00 2.29
6478 6966 3.365666 GCATGCAGTACATATGACATGGC 60.366 47.826 14.21 6.92 36.64 4.40
6481 6969 6.567132 CGAATTGCATGCAGTACATATGACAT 60.567 38.462 21.50 3.79 36.64 3.06
6484 6973 4.815846 ACGAATTGCATGCAGTACATATGA 59.184 37.500 21.50 2.55 36.64 2.15
6505 6994 9.355215 ACAACTAATACTTCATAGAACTTGACG 57.645 33.333 0.00 0.00 0.00 4.35
6684 7174 5.513267 CCTCCTACTTATTTCCCAGCCATAC 60.513 48.000 0.00 0.00 0.00 2.39
6723 7213 9.745018 TGTAATCAAAGAGAAGATTGAAGGAAT 57.255 29.630 0.00 0.00 38.88 3.01
6871 7361 3.553532 CAAAATTGGCCAAAATTGCGAC 58.446 40.909 24.71 0.00 30.21 5.19
6886 7376 1.974236 TCCATGAAACGGGGCAAAATT 59.026 42.857 0.00 0.00 0.00 1.82
6890 7380 0.693622 TAGTCCATGAAACGGGGCAA 59.306 50.000 0.00 0.00 0.00 4.52
6892 7382 2.922740 TATAGTCCATGAAACGGGGC 57.077 50.000 0.00 0.00 0.00 5.80
6930 7420 6.037500 CGACAATTCCTAATCAGCAATCAGAA 59.962 38.462 0.00 0.00 0.00 3.02
6942 7432 6.978343 TGAAATCGAACGACAATTCCTAAT 57.022 33.333 0.00 0.00 0.00 1.73
6950 7440 6.617741 GCTGTTAGAATGAAATCGAACGACAA 60.618 38.462 0.00 0.00 37.64 3.18
7036 7526 5.276067 GCTTTTCATATTGCAAGCAATCGAC 60.276 40.000 22.19 6.62 44.50 4.20
7152 7642 7.669722 CACATACATTATGGGGGTTTAGCTAAT 59.330 37.037 7.08 0.00 40.47 1.73
7154 7644 6.539173 CACATACATTATGGGGGTTTAGCTA 58.461 40.000 0.00 0.00 40.47 3.32
7287 7778 7.713764 AGGAAACTATGTCAATTTTGCAAAC 57.286 32.000 12.39 0.70 40.61 2.93
7300 7792 6.903534 TCTGAAGGATAGGAAGGAAACTATGT 59.096 38.462 0.00 0.00 42.68 2.29
7349 7841 0.682209 ATGGTGTGCTTGCCATCCTC 60.682 55.000 0.00 0.00 41.24 3.71


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

AutoCloner maintained by Alex Coulton.