Multiple sequence alignment - TraesCS3D01G108000

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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 TraesCS3D01G108000 chr3D 100.000 8011 0 0 1 8011 61576675 61568665 0.000000e+00 14794.0
1 TraesCS3D01G108000 chr3D 100.000 74 0 0 5428 5501 61571174 61571101 3.900000e-28 137.0
2 TraesCS3D01G108000 chr3D 100.000 74 0 0 5502 5575 61571248 61571175 3.900000e-28 137.0
3 TraesCS3D01G108000 chr3A 97.106 5495 107 15 14 5501 69654101 69648652 0.000000e+00 9219.0
4 TraesCS3D01G108000 chr3A 95.826 1773 45 8 5639 7384 69648367 69646597 0.000000e+00 2837.0
5 TraesCS3D01G108000 chr3A 94.636 522 17 4 7499 8011 69642914 69642395 0.000000e+00 798.0
6 TraesCS3D01G108000 chr3A 97.717 219 2 1 5582 5800 69648581 69648366 2.730000e-99 374.0
7 TraesCS3D01G108000 chr3A 100.000 59 0 0 5526 5584 69648701 69648643 8.500000e-20 110.0
8 TraesCS3D01G108000 chr3B 96.840 5507 125 14 5 5501 97745392 97739925 0.000000e+00 9160.0
9 TraesCS3D01G108000 chr3B 96.429 1876 44 9 5526 7401 97739974 97738122 0.000000e+00 3072.0
10 TraesCS3D01G108000 chr3B 93.169 527 12 8 7492 8011 97737843 97737334 0.000000e+00 752.0
11 TraesCS3D01G108000 chr1D 87.500 80 6 1 6063 6138 458142836 458142915 1.110000e-13 89.8
12 TraesCS3D01G108000 chr1D 87.500 80 6 1 6066 6141 458142932 458142853 1.110000e-13 89.8
13 TraesCS3D01G108000 chr4A 93.103 58 3 1 6054 6110 120379632 120379689 5.150000e-12 84.2
14 TraesCS3D01G108000 chr4A 79.208 101 11 5 6063 6155 698043102 698043004 2.410000e-05 62.1
15 TraesCS3D01G108000 chr2D 86.076 79 6 2 6065 6139 7074394 7074471 6.660000e-11 80.5
16 TraesCS3D01G108000 chr5A 86.957 69 7 2 6041 6109 42569301 42569367 8.620000e-10 76.8
17 TraesCS3D01G108000 chr7D 84.000 75 9 2 6063 6135 560996289 560996216 1.440000e-07 69.4


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 TraesCS3D01G108000 chr3D 61568665 61576675 8010 True 14794.0 14794 100.000000 1 8011 1 chr3D.!!$R1 8010
1 TraesCS3D01G108000 chr3A 69642395 69654101 11706 True 2667.6 9219 97.057000 14 8011 5 chr3A.!!$R1 7997
2 TraesCS3D01G108000 chr3B 97737334 97745392 8058 True 4328.0 9160 95.479333 5 8011 3 chr3B.!!$R1 8006

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
183 185 0.179163 CTTCGGCCGCTTGGATTTTC 60.179 55.000 23.51 0.00 33.02 2.29 F
349 354 0.883370 GTTCCCTCGGTTGCGTTTCT 60.883 55.000 0.00 0.00 0.00 2.52 F
1021 1030 0.961753 GGGTCCAGCAAAAGGTTCTG 59.038 55.000 0.00 0.00 0.00 3.02 F
1291 1300 5.193728 AGAGGAAGAGGTCAGACTTAGATCT 59.806 44.000 0.00 0.00 0.00 2.75 F
2751 2762 5.009310 GTGTACCAGTTTTACTTCCTTTGGG 59.991 44.000 0.00 0.00 0.00 4.12 F
3308 3319 0.322456 TCCGAACCAAAGAGCCATGG 60.322 55.000 7.63 7.63 42.60 3.66 F
3715 3727 0.988063 GGAAGGGCTTTCTCCTGTCT 59.012 55.000 9.35 0.00 36.03 3.41 F
3960 3972 1.066573 TCTTCTGTGGCAGCTTCTAGC 60.067 52.381 0.00 0.00 42.84 3.42 F
5494 5508 1.134965 GCGACAGCCTTCAGTAGATGT 60.135 52.381 0.00 0.00 37.42 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1300 1309 0.381089 GTGCATCAGCTCATCCTTGC 59.619 55.000 0.00 0.00 42.74 4.01 R
1676 1685 1.985473 AACATCACTGCAGGCTGAAA 58.015 45.000 20.86 4.23 0.00 2.69 R
1883 1892 5.630680 CAGCAGTTCAAATATCCAACACAAC 59.369 40.000 0.00 0.00 0.00 3.32 R
2779 2790 7.552330 GGAGAGCTTCCATCATTATTTATCTCC 59.448 40.741 9.31 0.00 46.01 3.71 R
4234 4246 3.914426 ACTGCCATTAGACTAACTGGG 57.086 47.619 17.91 12.39 0.00 4.45 R
5044 5058 0.954452 CAACTGAAAAAGGCCGAGCT 59.046 50.000 0.00 0.00 0.00 4.09 R
5548 5562 1.134965 ACATCTACTGAAGGCTGTCGC 60.135 52.381 0.00 0.00 0.00 5.19 R
5550 5564 2.234908 ACCACATCTACTGAAGGCTGTC 59.765 50.000 0.00 0.00 0.00 3.51 R
7264 7521 0.110295 TGCAAGCCAAGCAGACCTAA 59.890 50.000 0.00 0.00 37.02 2.69 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
72 73 1.802337 GAGGTTTGTGGGGGCGTTTC 61.802 60.000 0.00 0.00 0.00 2.78
120 122 3.641159 GAATTTTGCGGCCCCGTGG 62.641 63.158 8.66 0.00 42.09 4.94
183 185 0.179163 CTTCGGCCGCTTGGATTTTC 60.179 55.000 23.51 0.00 33.02 2.29
210 212 1.128692 CAGTTCCCGTCGAAGATTTGC 59.871 52.381 0.00 0.00 40.67 3.68
349 354 0.883370 GTTCCCTCGGTTGCGTTTCT 60.883 55.000 0.00 0.00 0.00 2.52
508 517 3.058155 TGCGGATCTTATCTAACTCGCTC 60.058 47.826 0.00 0.00 42.01 5.03
738 747 4.744795 TGGCTAGGAGATTCAAAGTCTC 57.255 45.455 0.00 0.00 41.05 3.36
1021 1030 0.961753 GGGTCCAGCAAAAGGTTCTG 59.038 55.000 0.00 0.00 0.00 3.02
1151 1160 9.987272 TTGATGATAGATTCATTTACGATGACT 57.013 29.630 0.00 0.00 45.29 3.41
1197 1206 6.833933 ACCACATTTCCCCATTCTTAAGATAC 59.166 38.462 5.89 0.00 0.00 2.24
1291 1300 5.193728 AGAGGAAGAGGTCAGACTTAGATCT 59.806 44.000 0.00 0.00 0.00 2.75
1883 1892 9.474920 TGCTTTGGTAAGATTTTGATGTTTTAG 57.525 29.630 0.00 0.00 32.92 1.85
1949 1958 9.185680 GGTTATGTGAAATCCCTGTACTTTATT 57.814 33.333 0.00 0.00 0.00 1.40
2751 2762 5.009310 GTGTACCAGTTTTACTTCCTTTGGG 59.991 44.000 0.00 0.00 0.00 4.12
2779 2790 5.824904 ATGCTACAAACAAGGCTAATGAG 57.175 39.130 0.00 0.00 0.00 2.90
3152 3163 5.182380 TGTGTCATGTGAGTCGTGAATACTA 59.818 40.000 0.00 0.00 42.74 1.82
3194 3205 7.259882 TGAAATGATGCATAAAATGGTCTGAC 58.740 34.615 0.00 0.00 0.00 3.51
3297 3308 3.767673 ACTCTAGCTTATTGTCCGAACCA 59.232 43.478 0.00 0.00 0.00 3.67
3298 3309 4.222145 ACTCTAGCTTATTGTCCGAACCAA 59.778 41.667 0.00 0.00 0.00 3.67
3308 3319 0.322456 TCCGAACCAAAGAGCCATGG 60.322 55.000 7.63 7.63 42.60 3.66
3493 3505 5.136828 TCAGAGGAGATGATGGTCTTAGAC 58.863 45.833 3.36 3.36 0.00 2.59
3575 3587 1.202348 CAGGTTCGCCAAATTTCTCCC 59.798 52.381 0.00 0.00 40.60 4.30
3715 3727 0.988063 GGAAGGGCTTTCTCCTGTCT 59.012 55.000 9.35 0.00 36.03 3.41
3761 3773 1.818642 AGTGATTCCAGTGCTTCAGC 58.181 50.000 0.00 0.00 42.50 4.26
3871 3883 6.620429 TCCAAATTTTAGAAGGTCCCTTTCT 58.380 36.000 0.00 0.20 36.26 2.52
3960 3972 1.066573 TCTTCTGTGGCAGCTTCTAGC 60.067 52.381 0.00 0.00 42.84 3.42
4198 4210 6.650427 ATTCCTTTGAAGTGGACCTTAAAC 57.350 37.500 0.00 0.00 33.05 2.01
4469 4483 6.460123 CCGATGGAAATTGACCCTCAAATAAG 60.460 42.308 7.55 0.00 40.12 1.73
4514 4528 8.369218 AGAAAATCCAAAGTACAATGCAAAAG 57.631 30.769 0.00 0.00 0.00 2.27
4563 4577 7.415877 GGTGCCGATAATTTACAGGTACATTTT 60.416 37.037 16.31 0.00 38.95 1.82
4873 4887 7.319646 TGTAGCATTGTTTCTTTGTCTGTTTT 58.680 30.769 0.00 0.00 0.00 2.43
5044 5058 4.287552 GGGATTCTCTACCAACAGACCTA 58.712 47.826 0.00 0.00 0.00 3.08
5353 5367 8.611051 AAGGAAGAATAAGCTTTCCTAGTCTA 57.389 34.615 15.43 0.00 30.47 2.59
5428 5442 4.423625 AGGACTATGACCATGTTAAGCC 57.576 45.455 0.00 0.00 0.00 4.35
5429 5443 4.040755 AGGACTATGACCATGTTAAGCCT 58.959 43.478 0.00 0.00 0.00 4.58
5430 5444 5.216622 AGGACTATGACCATGTTAAGCCTA 58.783 41.667 0.00 0.00 0.00 3.93
5431 5445 5.305644 AGGACTATGACCATGTTAAGCCTAG 59.694 44.000 0.00 0.00 0.00 3.02
5432 5446 5.070580 GGACTATGACCATGTTAAGCCTAGT 59.929 44.000 0.00 0.00 0.00 2.57
5433 5447 6.163135 ACTATGACCATGTTAAGCCTAGTC 57.837 41.667 0.00 0.00 0.00 2.59
5434 5448 5.900123 ACTATGACCATGTTAAGCCTAGTCT 59.100 40.000 0.00 0.00 0.00 3.24
5435 5449 4.471904 TGACCATGTTAAGCCTAGTCTG 57.528 45.455 0.00 0.00 0.00 3.51
5436 5450 3.838317 TGACCATGTTAAGCCTAGTCTGT 59.162 43.478 0.00 0.00 0.00 3.41
5437 5451 5.020795 TGACCATGTTAAGCCTAGTCTGTA 58.979 41.667 0.00 0.00 0.00 2.74
5438 5452 5.482526 TGACCATGTTAAGCCTAGTCTGTAA 59.517 40.000 0.00 0.00 0.00 2.41
5439 5453 6.014070 TGACCATGTTAAGCCTAGTCTGTAAA 60.014 38.462 0.00 0.00 0.00 2.01
5440 5454 6.171213 ACCATGTTAAGCCTAGTCTGTAAAC 58.829 40.000 0.00 0.00 0.00 2.01
5441 5455 6.170506 CCATGTTAAGCCTAGTCTGTAAACA 58.829 40.000 0.00 0.81 0.00 2.83
5442 5456 6.823689 CCATGTTAAGCCTAGTCTGTAAACAT 59.176 38.462 4.47 4.47 36.91 2.71
5443 5457 7.201644 CCATGTTAAGCCTAGTCTGTAAACATG 60.202 40.741 19.73 19.73 46.25 3.21
5444 5458 6.999950 TGTTAAGCCTAGTCTGTAAACATGA 58.000 36.000 0.00 0.00 0.00 3.07
5445 5459 7.620880 TGTTAAGCCTAGTCTGTAAACATGAT 58.379 34.615 0.00 0.00 0.00 2.45
5446 5460 8.100791 TGTTAAGCCTAGTCTGTAAACATGATT 58.899 33.333 0.00 0.00 0.00 2.57
5447 5461 9.595823 GTTAAGCCTAGTCTGTAAACATGATTA 57.404 33.333 0.00 0.00 0.00 1.75
5448 5462 9.817809 TTAAGCCTAGTCTGTAAACATGATTAG 57.182 33.333 0.00 0.00 0.00 1.73
5449 5463 6.284459 AGCCTAGTCTGTAAACATGATTAGC 58.716 40.000 0.00 0.00 0.00 3.09
5450 5464 5.467063 GCCTAGTCTGTAAACATGATTAGCC 59.533 44.000 0.00 0.00 0.00 3.93
5493 5507 1.565305 GCGACAGCCTTCAGTAGATG 58.435 55.000 0.00 0.00 37.42 2.90
5494 5508 1.134965 GCGACAGCCTTCAGTAGATGT 60.135 52.381 0.00 0.00 37.42 3.06
5495 5509 2.534298 CGACAGCCTTCAGTAGATGTG 58.466 52.381 0.00 0.00 0.00 3.21
5496 5510 2.736719 CGACAGCCTTCAGTAGATGTGG 60.737 54.545 0.00 0.00 0.00 4.17
5497 5511 2.234908 GACAGCCTTCAGTAGATGTGGT 59.765 50.000 0.00 0.00 0.00 4.16
5498 5512 2.639839 ACAGCCTTCAGTAGATGTGGTT 59.360 45.455 0.00 0.00 0.00 3.67
5499 5513 3.073062 ACAGCCTTCAGTAGATGTGGTTT 59.927 43.478 0.00 0.00 0.00 3.27
5500 5514 4.074970 CAGCCTTCAGTAGATGTGGTTTT 58.925 43.478 0.00 0.00 0.00 2.43
5501 5515 4.154918 CAGCCTTCAGTAGATGTGGTTTTC 59.845 45.833 0.00 0.00 0.00 2.29
5502 5516 3.440522 GCCTTCAGTAGATGTGGTTTTCC 59.559 47.826 0.00 0.00 41.14 3.13
5503 5517 4.807643 GCCTTCAGTAGATGTGGTTTTCCT 60.808 45.833 0.00 0.00 41.38 3.36
5504 5518 5.570844 GCCTTCAGTAGATGTGGTTTTCCTA 60.571 44.000 0.00 0.00 41.38 2.94
5505 5519 6.109359 CCTTCAGTAGATGTGGTTTTCCTAG 58.891 44.000 0.00 0.00 41.38 3.02
5506 5520 6.295916 CCTTCAGTAGATGTGGTTTTCCTAGT 60.296 42.308 0.00 0.00 41.38 2.57
5507 5521 6.282199 TCAGTAGATGTGGTTTTCCTAGTC 57.718 41.667 0.00 0.00 41.38 2.59
5508 5522 6.017192 TCAGTAGATGTGGTTTTCCTAGTCT 58.983 40.000 0.00 0.00 41.38 3.24
5509 5523 6.071334 TCAGTAGATGTGGTTTTCCTAGTCTG 60.071 42.308 0.00 0.00 41.38 3.51
5510 5524 5.780793 AGTAGATGTGGTTTTCCTAGTCTGT 59.219 40.000 0.00 0.00 41.38 3.41
5511 5525 6.952358 AGTAGATGTGGTTTTCCTAGTCTGTA 59.048 38.462 0.00 0.00 41.38 2.74
5512 5526 6.681729 AGATGTGGTTTTCCTAGTCTGTAA 57.318 37.500 0.00 0.00 41.38 2.41
5513 5527 7.074653 AGATGTGGTTTTCCTAGTCTGTAAA 57.925 36.000 0.00 0.00 41.38 2.01
5514 5528 6.935208 AGATGTGGTTTTCCTAGTCTGTAAAC 59.065 38.462 0.00 0.00 41.38 2.01
5515 5529 5.991861 TGTGGTTTTCCTAGTCTGTAAACA 58.008 37.500 0.00 0.00 41.38 2.83
5516 5530 6.597562 TGTGGTTTTCCTAGTCTGTAAACAT 58.402 36.000 0.00 0.00 41.38 2.71
5517 5531 6.485313 TGTGGTTTTCCTAGTCTGTAAACATG 59.515 38.462 0.00 0.00 41.38 3.21
5518 5532 6.708949 GTGGTTTTCCTAGTCTGTAAACATGA 59.291 38.462 0.00 0.00 41.38 3.07
5519 5533 7.390718 GTGGTTTTCCTAGTCTGTAAACATGAT 59.609 37.037 0.00 0.00 41.38 2.45
5520 5534 7.942341 TGGTTTTCCTAGTCTGTAAACATGATT 59.058 33.333 0.00 0.00 41.38 2.57
5521 5535 9.444600 GGTTTTCCTAGTCTGTAAACATGATTA 57.555 33.333 0.00 0.00 36.94 1.75
5523 5537 8.718102 TTTCCTAGTCTGTAAACATGATTAGC 57.282 34.615 0.00 0.00 0.00 3.09
5524 5538 6.817184 TCCTAGTCTGTAAACATGATTAGCC 58.183 40.000 0.00 0.00 0.00 3.93
5525 5539 6.611642 TCCTAGTCTGTAAACATGATTAGCCT 59.388 38.462 0.00 0.00 0.00 4.58
5526 5540 7.125811 TCCTAGTCTGTAAACATGATTAGCCTT 59.874 37.037 0.00 0.00 0.00 4.35
5527 5541 7.439655 CCTAGTCTGTAAACATGATTAGCCTTC 59.560 40.741 0.00 0.00 0.00 3.46
5528 5542 6.116126 AGTCTGTAAACATGATTAGCCTTCC 58.884 40.000 0.00 0.00 0.00 3.46
5529 5543 5.880332 GTCTGTAAACATGATTAGCCTTCCA 59.120 40.000 0.00 0.00 0.00 3.53
5530 5544 6.543831 GTCTGTAAACATGATTAGCCTTCCAT 59.456 38.462 0.00 0.00 0.00 3.41
5531 5545 7.067494 GTCTGTAAACATGATTAGCCTTCCATT 59.933 37.037 0.00 0.00 0.00 3.16
5532 5546 7.067372 TCTGTAAACATGATTAGCCTTCCATTG 59.933 37.037 0.00 0.00 0.00 2.82
5533 5547 6.889177 TGTAAACATGATTAGCCTTCCATTGA 59.111 34.615 0.00 0.00 0.00 2.57
5534 5548 6.855763 AAACATGATTAGCCTTCCATTGAA 57.144 33.333 0.00 0.00 0.00 2.69
5535 5549 6.855763 AACATGATTAGCCTTCCATTGAAA 57.144 33.333 0.00 0.00 0.00 2.69
5536 5550 6.855763 ACATGATTAGCCTTCCATTGAAAA 57.144 33.333 0.00 0.00 0.00 2.29
5537 5551 6.870769 ACATGATTAGCCTTCCATTGAAAAG 58.129 36.000 0.00 0.00 0.00 2.27
5538 5552 6.438425 ACATGATTAGCCTTCCATTGAAAAGT 59.562 34.615 0.00 0.00 0.00 2.66
5539 5553 7.615365 ACATGATTAGCCTTCCATTGAAAAGTA 59.385 33.333 0.00 0.00 0.00 2.24
5540 5554 7.391148 TGATTAGCCTTCCATTGAAAAGTAC 57.609 36.000 0.00 0.00 0.00 2.73
5541 5555 7.175104 TGATTAGCCTTCCATTGAAAAGTACT 58.825 34.615 0.00 0.00 0.00 2.73
5542 5556 8.325787 TGATTAGCCTTCCATTGAAAAGTACTA 58.674 33.333 0.00 0.00 0.00 1.82
5543 5557 9.174166 GATTAGCCTTCCATTGAAAAGTACTAA 57.826 33.333 0.00 0.00 0.00 2.24
5544 5558 9.700831 ATTAGCCTTCCATTGAAAAGTACTAAT 57.299 29.630 0.00 12.43 31.67 1.73
5545 5559 9.528489 TTAGCCTTCCATTGAAAAGTACTAATT 57.472 29.630 0.00 0.00 0.00 1.40
5546 5560 8.422577 AGCCTTCCATTGAAAAGTACTAATTT 57.577 30.769 0.00 0.00 0.00 1.82
5547 5561 8.306761 AGCCTTCCATTGAAAAGTACTAATTTG 58.693 33.333 0.00 0.00 0.00 2.32
5548 5562 7.545615 GCCTTCCATTGAAAAGTACTAATTTGG 59.454 37.037 0.00 0.45 0.00 3.28
5549 5563 7.545615 CCTTCCATTGAAAAGTACTAATTTGGC 59.454 37.037 0.00 0.00 0.00 4.52
5550 5564 6.616947 TCCATTGAAAAGTACTAATTTGGCG 58.383 36.000 0.00 0.00 0.00 5.69
5551 5565 6.431543 TCCATTGAAAAGTACTAATTTGGCGA 59.568 34.615 0.00 0.00 0.00 5.54
5552 5566 6.526674 CCATTGAAAAGTACTAATTTGGCGAC 59.473 38.462 0.00 0.00 0.00 5.19
5553 5567 6.621316 TTGAAAAGTACTAATTTGGCGACA 57.379 33.333 0.00 0.00 39.83 4.35
5554 5568 6.236017 TGAAAAGTACTAATTTGGCGACAG 57.764 37.500 0.00 0.00 44.54 3.51
5555 5569 4.680171 AAAGTACTAATTTGGCGACAGC 57.320 40.909 0.00 0.00 44.54 4.40
5617 5695 4.283363 TGTAATTTGGCATGCAACCATT 57.717 36.364 21.36 11.58 36.96 3.16
5688 5926 4.655963 AGCACATGTACTTCCTTGATGTT 58.344 39.130 0.00 0.00 0.00 2.71
6080 6318 6.733509 AGCTAATATATACTCCTTCCGTCCT 58.266 40.000 0.00 0.00 0.00 3.85
6190 6428 4.263462 ACATCAAATACTGCTTGGTCCTCA 60.263 41.667 0.00 0.00 0.00 3.86
6523 6761 1.346068 AGTCCTTCTGGCAACTCTCAC 59.654 52.381 0.00 0.00 37.61 3.51
6579 6818 7.905604 TCAACTCAATATGTCGTTGATTTCT 57.094 32.000 8.88 0.00 40.33 2.52
6944 7183 3.000041 CGAGATAGAGAGCTACATCGCT 59.000 50.000 0.00 0.00 44.33 4.93
6947 7186 4.141287 AGATAGAGAGCTACATCGCTGTT 58.859 43.478 0.00 0.00 41.08 3.16
6968 7207 2.695666 TGTCAAGAGCCAGATACTAGCC 59.304 50.000 0.00 0.00 0.00 3.93
7081 7338 0.035439 TCAAAAGGCCCTCGGTGATC 60.035 55.000 0.00 0.00 0.00 2.92
7090 7347 1.050988 CCTCGGTGATCCTGGGTGAT 61.051 60.000 0.00 0.00 0.00 3.06
7092 7349 0.830648 TCGGTGATCCTGGGTGATTC 59.169 55.000 0.00 0.00 0.00 2.52
7152 7409 1.675801 CTCAACTCTCTGCCCTGCA 59.324 57.895 0.00 0.00 36.92 4.41
7325 7583 6.879400 ACTCACAGGAACAATAAGAGATACC 58.121 40.000 0.00 0.00 0.00 2.73
7403 7667 8.885722 TGTTATAACGGTTTTGCTAAATCCTAG 58.114 33.333 10.92 0.00 0.00 3.02
7408 7672 3.064958 GGTTTTGCTAAATCCTAGTCCGC 59.935 47.826 0.00 0.00 0.00 5.54
7410 7674 2.890808 TGCTAAATCCTAGTCCGCTG 57.109 50.000 0.00 0.00 0.00 5.18
7411 7675 2.108168 TGCTAAATCCTAGTCCGCTGT 58.892 47.619 0.00 0.00 0.00 4.40
7413 7677 2.362717 GCTAAATCCTAGTCCGCTGTCT 59.637 50.000 0.00 0.00 0.00 3.41
7414 7678 3.551250 GCTAAATCCTAGTCCGCTGTCTC 60.551 52.174 0.00 0.00 0.00 3.36
7415 7679 1.025812 AATCCTAGTCCGCTGTCTCG 58.974 55.000 0.00 0.00 0.00 4.04
7416 7680 0.180642 ATCCTAGTCCGCTGTCTCGA 59.819 55.000 0.00 0.00 0.00 4.04
7421 7685 1.135731 GTCCGCTGTCTCGACTGAG 59.864 63.158 7.95 4.74 43.99 3.35
7436 8031 5.053811 TCGACTGAGAATTTGTTGCACTAA 58.946 37.500 0.00 0.00 0.00 2.24
7487 8133 9.793259 AATTACATAAGAAAACTCAAGGACTCA 57.207 29.630 0.00 0.00 0.00 3.41
7488 8134 8.603242 TTACATAAGAAAACTCAAGGACTCAC 57.397 34.615 0.00 0.00 0.00 3.51
7490 8136 6.708054 ACATAAGAAAACTCAAGGACTCACTG 59.292 38.462 0.00 0.00 0.00 3.66
7556 11415 5.016831 TCTCTGTCTGCCTAATTCACTGTA 58.983 41.667 0.00 0.00 0.00 2.74
7557 11416 5.658634 TCTCTGTCTGCCTAATTCACTGTAT 59.341 40.000 0.00 0.00 0.00 2.29
7598 11457 3.906720 TTCCCTGTGCCTATTACACTC 57.093 47.619 0.00 0.00 38.86 3.51
7616 11479 9.614792 ATTACACTCACTACTATCCAAAAATCC 57.385 33.333 0.00 0.00 0.00 3.01
7885 11755 3.604582 CAGGAACCTCTTGATGAACTCC 58.395 50.000 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 1.067060 CGAGCGAGAGAGAGAGAGAGA 59.933 57.143 0.00 0.00 0.00 3.10
9 10 0.529773 GAGCGAGCGAGAGAGAGAGA 60.530 60.000 0.00 0.00 0.00 3.10
13 14 3.568743 GCGAGCGAGCGAGAGAGA 61.569 66.667 1.41 0.00 0.00 3.10
15 16 3.568743 GAGCGAGCGAGCGAGAGA 61.569 66.667 1.41 0.00 43.00 3.10
16 17 4.605967 GGAGCGAGCGAGCGAGAG 62.606 72.222 1.41 0.00 43.00 3.20
72 73 2.295472 CTTCTCCGAGAGCAGCCCAG 62.295 65.000 0.00 0.00 0.00 4.45
120 122 2.484264 AGACCATCTAAAACGTGCAAGC 59.516 45.455 0.00 0.00 0.00 4.01
163 165 0.608035 AAAATCCAAGCGGCCGAAGA 60.608 50.000 33.48 19.15 0.00 2.87
183 185 1.171308 TCGACGGGAACTGGTTCTAG 58.829 55.000 12.34 9.35 40.47 2.43
210 212 4.112341 GCAGGCAAGCCTCGCAAG 62.112 66.667 22.12 9.86 46.28 4.01
337 342 1.061131 CAGATAGCAGAAACGCAACCG 59.939 52.381 0.00 0.00 41.14 4.44
437 446 3.186409 TGGAAACGAAGAAGAGAATTGCG 59.814 43.478 0.00 0.00 0.00 4.85
508 517 4.919754 GCTGTCCAAAGCAATGTAAGAAAG 59.080 41.667 0.00 0.00 43.01 2.62
572 581 6.046593 ACTGAATTGTCTGACGAACTGTAAA 58.953 36.000 1.10 0.00 0.00 2.01
585 594 1.347707 TCCGCCAGAACTGAATTGTCT 59.652 47.619 3.19 0.00 0.00 3.41
738 747 4.978083 AGCTTTAATCAGGCAATCACAG 57.022 40.909 0.00 0.00 0.00 3.66
927 936 3.118956 AGCAACCTCAGTATGCAGTAGTC 60.119 47.826 0.00 0.00 42.45 2.59
1021 1030 3.071874 TGTGATCTTGTGGATTGTCCC 57.928 47.619 0.00 0.00 35.03 4.46
1151 1160 3.058016 GTGTACTCGTGCTACAACTACCA 60.058 47.826 0.00 0.00 0.00 3.25
1291 1300 0.907486 CTCATCCTTGCTCCAGTGGA 59.093 55.000 12.40 12.40 0.00 4.02
1300 1309 0.381089 GTGCATCAGCTCATCCTTGC 59.619 55.000 0.00 0.00 42.74 4.01
1361 1370 8.043429 AGAGATGGAAATATGAGATCCAAACT 57.957 34.615 0.00 1.56 45.75 2.66
1675 1684 2.211250 ACATCACTGCAGGCTGAAAT 57.789 45.000 20.86 0.00 0.00 2.17
1676 1685 1.985473 AACATCACTGCAGGCTGAAA 58.015 45.000 20.86 4.23 0.00 2.69
1763 1772 5.041287 TCTACAACAAGAAACGTCAGTCTG 58.959 41.667 0.00 0.00 0.00 3.51
1883 1892 5.630680 CAGCAGTTCAAATATCCAACACAAC 59.369 40.000 0.00 0.00 0.00 3.32
1949 1958 6.381420 TGTTATGGAACCAACCAAAAAGAGAA 59.619 34.615 0.00 0.00 43.47 2.87
2779 2790 7.552330 GGAGAGCTTCCATCATTATTTATCTCC 59.448 40.741 9.31 0.00 46.01 3.71
3194 3205 9.265901 CTCCATCTCCAAATAAGTACACATAAG 57.734 37.037 0.00 0.00 0.00 1.73
3308 3319 1.880819 CTGTGTTTCCATGGCCAGCC 61.881 60.000 13.05 0.38 0.00 4.85
3317 3328 3.153919 GCCCATTTAGACTGTGTTTCCA 58.846 45.455 0.00 0.00 0.00 3.53
3493 3505 0.673985 TCACCAGACTCTCCAACACG 59.326 55.000 0.00 0.00 0.00 4.49
3715 3727 8.317891 TCTTGCTTCGTTTGTTTAGATTGATA 57.682 30.769 0.00 0.00 0.00 2.15
3871 3883 8.902540 ATGTTTTGTTACTTCTGTATGAGTCA 57.097 30.769 0.00 0.00 0.00 3.41
3960 3972 4.512944 ACAGCATGAAGACAAGTACAACTG 59.487 41.667 0.00 0.00 39.69 3.16
4198 4210 9.834628 AAAAGAACACATATATGTTTACGGTTG 57.165 29.630 15.85 5.05 42.89 3.77
4234 4246 3.914426 ACTGCCATTAGACTAACTGGG 57.086 47.619 17.91 12.39 0.00 4.45
4469 4483 6.560253 TTCTTTTGCTCTTCCTTGACATAC 57.440 37.500 0.00 0.00 0.00 2.39
5044 5058 0.954452 CAACTGAAAAAGGCCGAGCT 59.046 50.000 0.00 0.00 0.00 4.09
5353 5367 7.069826 CCACATTGGAAGGGTAATCATGTTTAT 59.930 37.037 0.00 0.00 40.96 1.40
5428 5442 7.439655 GGAAGGCTAATCATGTTTACAGACTAG 59.560 40.741 0.00 0.00 0.00 2.57
5429 5443 7.093068 TGGAAGGCTAATCATGTTTACAGACTA 60.093 37.037 0.00 0.00 0.00 2.59
5430 5444 6.116126 GGAAGGCTAATCATGTTTACAGACT 58.884 40.000 0.00 0.00 0.00 3.24
5431 5445 5.880332 TGGAAGGCTAATCATGTTTACAGAC 59.120 40.000 0.00 0.00 0.00 3.51
5432 5446 6.061022 TGGAAGGCTAATCATGTTTACAGA 57.939 37.500 0.00 0.00 0.00 3.41
5433 5447 6.949352 ATGGAAGGCTAATCATGTTTACAG 57.051 37.500 0.00 0.00 0.00 2.74
5434 5448 6.889177 TCAATGGAAGGCTAATCATGTTTACA 59.111 34.615 0.00 0.00 0.00 2.41
5435 5449 7.333528 TCAATGGAAGGCTAATCATGTTTAC 57.666 36.000 0.00 0.00 0.00 2.01
5436 5450 7.953005 TTCAATGGAAGGCTAATCATGTTTA 57.047 32.000 0.00 0.00 0.00 2.01
5437 5451 6.855763 TTCAATGGAAGGCTAATCATGTTT 57.144 33.333 0.00 0.00 0.00 2.83
5438 5452 6.855763 TTTCAATGGAAGGCTAATCATGTT 57.144 33.333 0.00 0.00 33.82 2.71
5439 5453 6.438425 ACTTTTCAATGGAAGGCTAATCATGT 59.562 34.615 0.00 0.00 33.82 3.21
5440 5454 6.870769 ACTTTTCAATGGAAGGCTAATCATG 58.129 36.000 0.00 0.00 33.82 3.07
5441 5455 7.836183 AGTACTTTTCAATGGAAGGCTAATCAT 59.164 33.333 0.00 0.00 33.82 2.45
5442 5456 7.175104 AGTACTTTTCAATGGAAGGCTAATCA 58.825 34.615 0.00 0.00 33.82 2.57
5443 5457 7.631717 AGTACTTTTCAATGGAAGGCTAATC 57.368 36.000 0.00 0.00 33.82 1.75
5444 5458 9.700831 ATTAGTACTTTTCAATGGAAGGCTAAT 57.299 29.630 0.00 14.77 34.37 1.73
5445 5459 9.528489 AATTAGTACTTTTCAATGGAAGGCTAA 57.472 29.630 0.00 12.94 33.82 3.09
5446 5460 9.528489 AAATTAGTACTTTTCAATGGAAGGCTA 57.472 29.630 0.00 2.87 33.82 3.93
5447 5461 8.306761 CAAATTAGTACTTTTCAATGGAAGGCT 58.693 33.333 0.00 0.00 33.82 4.58
5448 5462 7.545615 CCAAATTAGTACTTTTCAATGGAAGGC 59.454 37.037 0.00 0.00 33.82 4.35
5449 5463 7.545615 GCCAAATTAGTACTTTTCAATGGAAGG 59.454 37.037 0.00 0.00 33.82 3.46
5450 5464 7.273381 CGCCAAATTAGTACTTTTCAATGGAAG 59.727 37.037 0.00 0.00 33.82 3.46
5491 5505 6.597562 TGTTTACAGACTAGGAAAACCACAT 58.402 36.000 0.00 0.00 30.75 3.21
5492 5506 5.991861 TGTTTACAGACTAGGAAAACCACA 58.008 37.500 0.00 0.00 30.75 4.17
5493 5507 6.708949 TCATGTTTACAGACTAGGAAAACCAC 59.291 38.462 0.00 0.00 30.75 4.16
5494 5508 6.833041 TCATGTTTACAGACTAGGAAAACCA 58.167 36.000 0.00 0.00 30.75 3.67
5495 5509 7.923414 ATCATGTTTACAGACTAGGAAAACC 57.077 36.000 0.00 0.00 30.75 3.27
5497 5511 9.162764 GCTAATCATGTTTACAGACTAGGAAAA 57.837 33.333 0.00 0.00 0.00 2.29
5498 5512 7.769044 GGCTAATCATGTTTACAGACTAGGAAA 59.231 37.037 0.00 0.00 0.00 3.13
5499 5513 7.125811 AGGCTAATCATGTTTACAGACTAGGAA 59.874 37.037 0.00 0.00 0.00 3.36
5500 5514 6.611642 AGGCTAATCATGTTTACAGACTAGGA 59.388 38.462 0.00 0.00 0.00 2.94
5501 5515 6.821388 AGGCTAATCATGTTTACAGACTAGG 58.179 40.000 0.00 0.00 0.00 3.02
5502 5516 7.439655 GGAAGGCTAATCATGTTTACAGACTAG 59.560 40.741 0.00 0.00 0.00 2.57
5503 5517 7.093068 TGGAAGGCTAATCATGTTTACAGACTA 60.093 37.037 0.00 0.00 0.00 2.59
5504 5518 6.116126 GGAAGGCTAATCATGTTTACAGACT 58.884 40.000 0.00 0.00 0.00 3.24
5505 5519 5.880332 TGGAAGGCTAATCATGTTTACAGAC 59.120 40.000 0.00 0.00 0.00 3.51
5506 5520 6.061022 TGGAAGGCTAATCATGTTTACAGA 57.939 37.500 0.00 0.00 0.00 3.41
5507 5521 6.949352 ATGGAAGGCTAATCATGTTTACAG 57.051 37.500 0.00 0.00 0.00 2.74
5508 5522 6.889177 TCAATGGAAGGCTAATCATGTTTACA 59.111 34.615 0.00 0.00 0.00 2.41
5509 5523 7.333528 TCAATGGAAGGCTAATCATGTTTAC 57.666 36.000 0.00 0.00 0.00 2.01
5510 5524 7.953005 TTCAATGGAAGGCTAATCATGTTTA 57.047 32.000 0.00 0.00 0.00 2.01
5511 5525 6.855763 TTCAATGGAAGGCTAATCATGTTT 57.144 33.333 0.00 0.00 0.00 2.83
5512 5526 6.855763 TTTCAATGGAAGGCTAATCATGTT 57.144 33.333 0.00 0.00 33.82 2.71
5513 5527 6.438425 ACTTTTCAATGGAAGGCTAATCATGT 59.562 34.615 0.00 0.00 33.82 3.21
5514 5528 6.870769 ACTTTTCAATGGAAGGCTAATCATG 58.129 36.000 0.00 0.00 33.82 3.07
5515 5529 7.836183 AGTACTTTTCAATGGAAGGCTAATCAT 59.164 33.333 0.00 0.00 33.82 2.45
5516 5530 7.175104 AGTACTTTTCAATGGAAGGCTAATCA 58.825 34.615 0.00 0.00 33.82 2.57
5517 5531 7.631717 AGTACTTTTCAATGGAAGGCTAATC 57.368 36.000 0.00 0.00 33.82 1.75
5518 5532 9.700831 ATTAGTACTTTTCAATGGAAGGCTAAT 57.299 29.630 0.00 14.77 34.37 1.73
5519 5533 9.528489 AATTAGTACTTTTCAATGGAAGGCTAA 57.472 29.630 0.00 12.94 33.82 3.09
5520 5534 9.528489 AAATTAGTACTTTTCAATGGAAGGCTA 57.472 29.630 0.00 2.87 33.82 3.93
5521 5535 8.306761 CAAATTAGTACTTTTCAATGGAAGGCT 58.693 33.333 0.00 0.00 33.82 4.58
5522 5536 7.545615 CCAAATTAGTACTTTTCAATGGAAGGC 59.454 37.037 0.00 0.00 33.82 4.35
5523 5537 7.545615 GCCAAATTAGTACTTTTCAATGGAAGG 59.454 37.037 0.00 0.00 33.82 3.46
5524 5538 7.273381 CGCCAAATTAGTACTTTTCAATGGAAG 59.727 37.037 0.00 0.00 33.82 3.46
5525 5539 7.040340 TCGCCAAATTAGTACTTTTCAATGGAA 60.040 33.333 0.00 0.00 0.00 3.53
5526 5540 6.431543 TCGCCAAATTAGTACTTTTCAATGGA 59.568 34.615 0.00 0.00 0.00 3.41
5527 5541 6.526674 GTCGCCAAATTAGTACTTTTCAATGG 59.473 38.462 0.00 4.35 0.00 3.16
5528 5542 7.081349 TGTCGCCAAATTAGTACTTTTCAATG 58.919 34.615 0.00 0.00 0.00 2.82
5529 5543 7.209471 TGTCGCCAAATTAGTACTTTTCAAT 57.791 32.000 0.00 0.00 0.00 2.57
5530 5544 6.621316 TGTCGCCAAATTAGTACTTTTCAA 57.379 33.333 0.00 0.00 0.00 2.69
5531 5545 5.334569 GCTGTCGCCAAATTAGTACTTTTCA 60.335 40.000 0.00 0.00 0.00 2.69
5532 5546 5.086727 GCTGTCGCCAAATTAGTACTTTTC 58.913 41.667 0.00 0.00 0.00 2.29
5533 5547 5.043189 GCTGTCGCCAAATTAGTACTTTT 57.957 39.130 0.00 0.00 0.00 2.27
5534 5548 4.680171 GCTGTCGCCAAATTAGTACTTT 57.320 40.909 0.00 0.00 0.00 2.66
5548 5562 1.134965 ACATCTACTGAAGGCTGTCGC 60.135 52.381 0.00 0.00 0.00 5.19
5549 5563 2.534298 CACATCTACTGAAGGCTGTCG 58.466 52.381 0.00 0.00 0.00 4.35
5550 5564 2.234908 ACCACATCTACTGAAGGCTGTC 59.765 50.000 0.00 0.00 0.00 3.51
5551 5565 2.260822 ACCACATCTACTGAAGGCTGT 58.739 47.619 0.00 0.00 0.00 4.40
5552 5566 3.340814 AACCACATCTACTGAAGGCTG 57.659 47.619 0.00 0.00 0.00 4.85
5553 5567 4.373156 AAAACCACATCTACTGAAGGCT 57.627 40.909 0.00 0.00 0.00 4.58
5554 5568 6.759497 ATTAAAACCACATCTACTGAAGGC 57.241 37.500 0.00 0.00 0.00 4.35
5555 5569 8.786826 TGTATTAAAACCACATCTACTGAAGG 57.213 34.615 0.00 0.00 0.00 3.46
5558 5572 9.826574 GGTATGTATTAAAACCACATCTACTGA 57.173 33.333 0.00 0.00 34.78 3.41
5559 5573 9.607988 TGGTATGTATTAAAACCACATCTACTG 57.392 33.333 0.00 0.00 37.09 2.74
5688 5926 5.868454 TCACCTTGAGATTCTTGAATGACA 58.132 37.500 0.09 0.00 0.00 3.58
6523 6761 2.449031 TACCGTGGCTGCACAGAAGG 62.449 60.000 0.50 4.24 0.00 3.46
6569 6807 3.492313 GCCTAAGCAACAGAAATCAACG 58.508 45.455 0.00 0.00 39.53 4.10
6944 7183 4.382040 GCTAGTATCTGGCTCTTGACAACA 60.382 45.833 0.00 0.00 35.09 3.33
6947 7186 2.695666 GGCTAGTATCTGGCTCTTGACA 59.304 50.000 5.23 0.00 38.07 3.58
7028 7267 1.837499 CGGAGGGACCCTGGGTATC 60.837 68.421 20.90 16.55 35.25 2.24
7081 7338 2.840651 AGTCTTGGTAGAATCACCCAGG 59.159 50.000 4.19 0.40 37.84 4.45
7090 7347 2.547218 GCCGTCACAAGTCTTGGTAGAA 60.547 50.000 16.85 0.00 34.12 2.10
7092 7349 1.270094 TGCCGTCACAAGTCTTGGTAG 60.270 52.381 16.85 6.58 34.12 3.18
7152 7409 4.272018 CGCTGCATTTCTAAGCTAATGTCT 59.728 41.667 8.37 0.00 34.88 3.41
7264 7521 0.110295 TGCAAGCCAAGCAGACCTAA 59.890 50.000 0.00 0.00 37.02 2.69
7360 7624 1.821216 ACAAAATTCAGCCGTCCGAT 58.179 45.000 0.00 0.00 0.00 4.18
7403 7667 1.135731 CTCAGTCGAGACAGCGGAC 59.864 63.158 5.99 0.00 42.34 4.79
7408 7672 8.667295 GTGCAACAAATTCTCAGTCGAGACAG 62.667 46.154 5.99 0.00 42.20 3.51
7410 7674 4.609336 GTGCAACAAATTCTCAGTCGAGAC 60.609 45.833 0.00 0.00 42.20 3.36
7411 7675 3.494626 GTGCAACAAATTCTCAGTCGAGA 59.505 43.478 0.00 0.00 41.29 4.04
7413 7677 3.466836 AGTGCAACAAATTCTCAGTCGA 58.533 40.909 0.00 0.00 41.43 4.20
7414 7678 3.885484 AGTGCAACAAATTCTCAGTCG 57.115 42.857 0.00 0.00 41.43 4.18
7436 8031 5.127682 TCAGTACACATACACTGAGATGCAT 59.872 40.000 0.00 0.00 44.70 3.96
7487 8133 0.843984 AGTGTTTGGGTAGGCACAGT 59.156 50.000 0.00 0.00 34.59 3.55
7488 8134 1.202758 TGAGTGTTTGGGTAGGCACAG 60.203 52.381 0.00 0.00 34.59 3.66
7490 8136 1.880027 CTTGAGTGTTTGGGTAGGCAC 59.120 52.381 0.00 0.00 0.00 5.01
7598 11457 6.375455 AGTTGCAGGATTTTTGGATAGTAGTG 59.625 38.462 0.00 0.00 0.00 2.74
7631 11494 9.443283 GAATAGAAACATGAATGACAGCATTAC 57.557 33.333 0.00 0.00 44.47 1.89


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

AutoCloner maintained by Alex Coulton.