Multiple sequence alignment - TraesCS6A01G203700

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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 TraesCS6A01G203700 chr6A 100.000 8349 0 0 1 8349 349528664 349520316 0.000000e+00 15418.0
1 TraesCS6A01G203700 chr6A 96.215 502 16 3 2165 2666 349597615 349597117 0.000000e+00 819.0
2 TraesCS6A01G203700 chr6A 100.000 240 0 0 8645 8884 349520020 349519781 2.280000e-120 444.0
3 TraesCS6A01G203700 chr6D 97.939 6163 80 12 744 6892 249439599 249445728 0.000000e+00 10634.0
4 TraesCS6A01G203700 chr6D 96.112 1466 44 8 6890 8344 249445907 249447370 0.000000e+00 2379.0
5 TraesCS6A01G203700 chr6D 91.068 515 40 6 187 698 68049744 68050255 0.000000e+00 691.0
6 TraesCS6A01G203700 chr6D 96.512 172 6 0 1 172 124896464 124896635 1.460000e-72 285.0
7 TraesCS6A01G203700 chr6D 95.349 172 8 0 1 172 379067141 379066970 3.160000e-69 274.0
8 TraesCS6A01G203700 chr6D 100.000 28 0 0 701 728 249439575 249439602 1.600000e-02 52.8
9 TraesCS6A01G203700 chr6B 97.457 6057 112 18 2200 8240 337218714 337224744 0.000000e+00 10294.0
10 TraesCS6A01G203700 chr6B 98.261 1150 15 3 1004 2150 337217569 337218716 0.000000e+00 2008.0
11 TraesCS6A01G203700 chr6B 96.347 219 6 1 701 917 337216996 337217214 8.480000e-95 359.0
12 TraesCS6A01G203700 chr6B 91.379 116 9 1 8202 8317 337224748 337224862 3.320000e-34 158.0
13 TraesCS6A01G203700 chr6B 86.022 93 6 2 8694 8779 337225172 337225264 9.500000e-15 93.5
14 TraesCS6A01G203700 chrUn 92.205 526 41 0 172 697 111930626 111931151 0.000000e+00 745.0
15 TraesCS6A01G203700 chrUn 97.674 172 4 0 1 172 111930330 111930501 6.740000e-76 296.0
16 TraesCS6A01G203700 chr4D 90.769 520 42 6 187 703 504224747 504225263 0.000000e+00 689.0
17 TraesCS6A01G203700 chr1D 89.922 516 48 4 187 699 340541485 340541999 0.000000e+00 662.0
18 TraesCS6A01G203700 chr2A 89.564 527 43 6 172 696 649499837 649500353 0.000000e+00 658.0
19 TraesCS6A01G203700 chr2A 95.930 172 7 0 1 172 602693524 602693695 6.790000e-71 279.0
20 TraesCS6A01G203700 chr2A 95.349 172 8 0 1 172 88320337 88320508 3.160000e-69 274.0
21 TraesCS6A01G203700 chr2D 89.168 517 46 7 187 699 355407398 355406888 3.500000e-178 636.0
22 TraesCS6A01G203700 chr2D 95.349 172 8 0 1 172 355407708 355407537 3.160000e-69 274.0
23 TraesCS6A01G203700 chr7D 89.084 513 50 6 187 696 88344039 88344548 4.530000e-177 632.0
24 TraesCS6A01G203700 chr7D 88.953 516 52 5 187 698 161273227 161273741 4.530000e-177 632.0
25 TraesCS6A01G203700 chr7D 94.767 172 9 0 1 172 88343729 88343900 1.470000e-67 268.0
26 TraesCS6A01G203700 chr7D 94.767 172 9 0 1 172 161272911 161273082 1.470000e-67 268.0
27 TraesCS6A01G203700 chr1A 88.447 528 55 4 172 699 540460342 540459821 4.530000e-177 632.0
28 TraesCS6A01G203700 chr1A 86.567 134 17 1 6190 6323 547341809 547341677 7.190000e-31 147.0
29 TraesCS6A01G203700 chr3D 95.349 172 8 0 1 172 19872541 19872370 3.160000e-69 274.0


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 TraesCS6A01G203700 chr6A 349519781 349528664 8883 True 7931.000000 15418 100.0000 1 8884 2 chr6A.!!$R2 8883
1 TraesCS6A01G203700 chr6D 249439575 249447370 7795 False 4355.266667 10634 98.0170 701 8344 3 chr6D.!!$F3 7643
2 TraesCS6A01G203700 chr6D 68049744 68050255 511 False 691.000000 691 91.0680 187 698 1 chr6D.!!$F1 511
3 TraesCS6A01G203700 chr6B 337216996 337225264 8268 False 2582.500000 10294 93.8932 701 8779 5 chr6B.!!$F1 8078
4 TraesCS6A01G203700 chrUn 111930330 111931151 821 False 520.500000 745 94.9395 1 697 2 chrUn.!!$F1 696
5 TraesCS6A01G203700 chr4D 504224747 504225263 516 False 689.000000 689 90.7690 187 703 1 chr4D.!!$F1 516
6 TraesCS6A01G203700 chr1D 340541485 340541999 514 False 662.000000 662 89.9220 187 699 1 chr1D.!!$F1 512
7 TraesCS6A01G203700 chr2A 649499837 649500353 516 False 658.000000 658 89.5640 172 696 1 chr2A.!!$F3 524
8 TraesCS6A01G203700 chr2D 355406888 355407708 820 True 455.000000 636 92.2585 1 699 2 chr2D.!!$R1 698
9 TraesCS6A01G203700 chr7D 88343729 88344548 819 False 450.000000 632 91.9255 1 696 2 chr7D.!!$F1 695
10 TraesCS6A01G203700 chr7D 161272911 161273741 830 False 450.000000 632 91.8600 1 698 2 chr7D.!!$F2 697
11 TraesCS6A01G203700 chr1A 540459821 540460342 521 True 632.000000 632 88.4470 172 699 1 chr1A.!!$R1 527

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
97 98 0.746659 GATTCCGGGGAATGCAAAGG 59.253 55.000 17.29 0.0 43.98 3.11 F
613 768 1.227973 GGGATGCGGGTTCTGATCC 60.228 63.158 0.00 0.0 34.67 3.36 F
1522 1958 0.945743 TCAGTGTGTGCGATCAGTGC 60.946 55.000 0.00 0.0 35.66 4.40 F
2600 3036 0.310543 TGGATGCTGTTCGTTTGTGC 59.689 50.000 0.00 0.0 0.00 4.57 F
3830 4268 2.361104 GCCAGGTTCATCGGGCAA 60.361 61.111 0.00 0.0 45.70 4.52 F
5087 5526 2.045536 GTCCAGGCAGGGAAGCTG 60.046 66.667 0.00 0.0 39.05 4.24 F
6544 6992 2.827800 TCTCAGGTCTGACAGCTTTG 57.172 50.000 10.38 0.4 35.46 2.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1176 1609 1.291877 CGTTGAGCCCGAACTTCCTG 61.292 60.000 0.00 0.00 0.00 3.86 R
2190 2626 4.036027 ACTTGCAAGAAACTGACTGACATG 59.964 41.667 32.50 0.97 0.00 3.21 R
2653 3089 1.948834 TGCAGGTAATTCATCGGCATG 59.051 47.619 0.00 0.00 0.00 4.06 R
3997 4435 4.125703 CCTAGAACATCATCAGTTGAGGC 58.874 47.826 0.00 0.00 39.78 4.70 R
5757 6196 2.025037 CCTTCCCATCATCCCAAAGTCA 60.025 50.000 0.00 0.00 0.00 3.41 R
6556 7004 1.338973 GGCATCATGTTACAGCCATGG 59.661 52.381 7.63 7.63 44.59 3.66 R
8304 8986 0.036858 GACTCCACAGCCCTTCACTC 60.037 60.000 0.00 0.00 0.00 3.51 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
36 37 2.901249 CGGTGGATACGTTGGATTCTT 58.099 47.619 0.00 0.00 42.51 2.52
69 70 2.768253 TGCATCAACATCTCGTTCCT 57.232 45.000 0.00 0.00 34.86 3.36
97 98 0.746659 GATTCCGGGGAATGCAAAGG 59.253 55.000 17.29 0.00 43.98 3.11
220 361 2.944409 AAACGCACTAACCGGTGGCA 62.944 55.000 8.52 0.00 37.65 4.92
396 547 2.749839 CCCGCAGATTTGGCCGAA 60.750 61.111 8.18 8.18 0.00 4.30
494 648 1.295423 GTCCCGCCAACTGCTTCTA 59.705 57.895 0.00 0.00 38.05 2.10
500 654 1.394917 CGCCAACTGCTTCTATGTGAC 59.605 52.381 0.00 0.00 38.05 3.67
567 721 2.648454 GTTGGGATTTTGCCGCGT 59.352 55.556 4.92 0.00 0.00 6.01
613 768 1.227973 GGGATGCGGGTTCTGATCC 60.228 63.158 0.00 0.00 34.67 3.36
626 782 1.351017 TCTGATCCGGCAGGTTTTTCT 59.649 47.619 8.95 0.00 39.05 2.52
699 857 3.445805 GGTCTGCTAGAGTTGCTCTAAGT 59.554 47.826 7.22 0.00 41.74 2.24
732 890 3.518590 ACGGACGCGAGATAAGATTTTT 58.481 40.909 15.93 0.00 0.00 1.94
1176 1609 2.007547 GCGTTTACTGAGGAGGAAGCC 61.008 57.143 0.00 0.00 0.00 4.35
1522 1958 0.945743 TCAGTGTGTGCGATCAGTGC 60.946 55.000 0.00 0.00 35.66 4.40
1649 2085 3.187700 GTGTAATGCAAGGAGTAGGTCG 58.812 50.000 0.00 0.00 0.00 4.79
1937 2373 4.039124 GCTTCCTCATTCTGGGTTGAAAAA 59.961 41.667 0.00 0.00 0.00 1.94
2115 2551 6.199393 AGAACTTAATCACGCAAACAGAAAC 58.801 36.000 0.00 0.00 0.00 2.78
2166 2602 3.335579 CACAAAGCTTAGGTACCTGGAC 58.664 50.000 25.33 12.77 0.00 4.02
2190 2626 7.760437 ACTTCTATCTTTTCGTACTCCACTAC 58.240 38.462 0.00 0.00 0.00 2.73
2310 2746 2.280797 TCAACCACGTGCAGCCTC 60.281 61.111 10.91 0.00 0.00 4.70
2312 2748 2.281070 AACCACGTGCAGCCTCAG 60.281 61.111 10.91 0.00 0.00 3.35
2441 2877 7.900782 TGAAGTGTAATCCAACTACTTTAGC 57.099 36.000 0.00 0.00 32.23 3.09
2600 3036 0.310543 TGGATGCTGTTCGTTTGTGC 59.689 50.000 0.00 0.00 0.00 4.57
3006 3442 4.504858 AGGGCTTGTTTCATTACTCGTAG 58.495 43.478 0.00 0.00 0.00 3.51
3007 3443 3.063588 GGGCTTGTTTCATTACTCGTAGC 59.936 47.826 0.00 0.00 0.00 3.58
3030 3466 7.875971 AGCGAAAAGTCTGTGAATCTTAAAAT 58.124 30.769 0.00 0.00 0.00 1.82
3050 3486 5.864418 AATAAGTATTCAGTACTCCCGCA 57.136 39.130 0.00 0.00 42.83 5.69
3209 3647 6.205464 CCCTATCTGCATATGAAACATCGTTT 59.795 38.462 6.97 0.00 0.00 3.60
3308 3746 4.922103 GTCGTTGAAATCTTACCGTCTCTT 59.078 41.667 0.00 0.00 0.00 2.85
3508 3946 5.583061 TCTTGTCAGTTAAAAACTTCTCGCA 59.417 36.000 0.00 0.00 40.46 5.10
3830 4268 2.361104 GCCAGGTTCATCGGGCAA 60.361 61.111 0.00 0.00 45.70 4.52
3997 4435 6.748333 TCTTTTCAAACCATCAGCTGATAG 57.252 37.500 28.27 23.44 32.63 2.08
4174 4612 5.125578 TGTTACTATCTCACGCTTGTCAGAT 59.874 40.000 0.94 0.94 0.00 2.90
4175 4613 4.727507 ACTATCTCACGCTTGTCAGATT 57.272 40.909 0.57 0.00 0.00 2.40
4225 4663 7.948278 ATATAACAGACTATCGGAAGCAAAC 57.052 36.000 0.00 0.00 0.00 2.93
4306 4744 5.073437 AGGTAGAGTTCTCTAGGCATCAT 57.927 43.478 9.47 0.00 0.00 2.45
4387 4825 6.294176 GGCTTACATCTTGATGTTGACTTTGT 60.294 38.462 19.49 0.00 36.08 2.83
4699 5138 3.094572 CAGGTTCCTTCCATGCAGAAAT 58.905 45.455 0.00 0.00 0.00 2.17
5067 5506 6.055231 TGTAGTTGTTTCAATTGGACTTCG 57.945 37.500 5.42 0.00 0.00 3.79
5068 5507 4.568152 AGTTGTTTCAATTGGACTTCGG 57.432 40.909 5.42 0.00 0.00 4.30
5069 5508 3.951680 AGTTGTTTCAATTGGACTTCGGT 59.048 39.130 5.42 0.00 0.00 4.69
5070 5509 3.980646 TGTTTCAATTGGACTTCGGTG 57.019 42.857 5.42 0.00 0.00 4.94
5071 5510 3.283751 TGTTTCAATTGGACTTCGGTGT 58.716 40.909 5.42 0.00 0.00 4.16
5072 5511 3.314080 TGTTTCAATTGGACTTCGGTGTC 59.686 43.478 5.42 1.05 36.31 3.67
5087 5526 2.045536 GTCCAGGCAGGGAAGCTG 60.046 66.667 0.00 0.00 39.05 4.24
5336 5775 3.181507 GCAATGTCTTCTGCGCTCAAATA 60.182 43.478 9.73 0.00 0.00 1.40
5338 5777 5.393124 CAATGTCTTCTGCGCTCAAATAAA 58.607 37.500 9.73 0.00 0.00 1.40
5560 5999 4.235079 TGGGTGCAGCTCTATTTATGTT 57.765 40.909 16.65 0.00 0.00 2.71
5757 6196 3.941629 TGGTGGGAGGCTTATCTTCTAT 58.058 45.455 0.00 0.00 0.00 1.98
5969 6408 5.070446 CCTGCAGACAATAATGTAGACCCTA 59.930 44.000 17.39 0.00 40.74 3.53
6186 6634 3.952628 AACGCCGCTTAGCCTCACC 62.953 63.158 0.00 0.00 0.00 4.02
6205 6653 4.565166 TCACCGCGTTCTGTTTATCTATTG 59.435 41.667 4.92 0.00 0.00 1.90
6544 6992 2.827800 TCTCAGGTCTGACAGCTTTG 57.172 50.000 10.38 0.40 35.46 2.77
6556 7004 3.748048 TGACAGCTTTGCATGTAGAGAAC 59.252 43.478 5.49 0.00 0.00 3.01
6602 7050 3.490419 GCTTCATGGCTCCTTATGCTTTG 60.490 47.826 0.00 0.00 0.00 2.77
7042 7671 6.038356 CAGAGTTGAAAAACTTGCACAGATT 58.962 36.000 0.00 0.00 32.22 2.40
7075 7704 6.509418 TTGGTATCTACAATGTTCTTTGGC 57.491 37.500 0.00 0.00 0.00 4.52
7188 7817 4.718940 TCGTGTCAGAGCATTAGAATCA 57.281 40.909 0.00 0.00 0.00 2.57
7431 8060 5.678483 CCGCTCGATTCATTTATTTGAACTG 59.322 40.000 0.00 0.00 38.37 3.16
7534 8163 2.108250 GGCCATGAACACCCCTATATGT 59.892 50.000 0.00 0.00 0.00 2.29
7599 8228 6.183360 GCTAATACCATCCTCTGTTGTGAAAC 60.183 42.308 0.00 0.00 37.35 2.78
7607 8236 0.378257 CTGTTGTGAAACGCTGCTGT 59.622 50.000 0.00 0.00 42.39 4.40
7891 8520 1.227943 GCACTGCCTGAGTTCACCA 60.228 57.895 0.00 0.00 29.75 4.17
7911 8540 1.774110 ATCGACCAGTGAGAGCTGAT 58.226 50.000 0.00 0.00 38.70 2.90
8145 8774 4.565022 TCACTTTCTGTCGCATACATCAA 58.435 39.130 0.00 0.00 37.50 2.57
8157 8788 4.686091 CGCATACATCAATTCATAGACGGT 59.314 41.667 0.00 0.00 0.00 4.83
8174 8805 1.724582 GGTTGGTGTGTGCCTGTGTC 61.725 60.000 0.00 0.00 0.00 3.67
8189 8826 1.301087 TGTCGACCCGATTTGCGTT 60.301 52.632 14.12 0.00 38.42 4.84
8205 8887 4.325304 TTCACACGGACGCGCGTA 62.325 61.111 37.91 16.34 0.00 4.42
8237 8919 4.643387 GCCTCAGGCCCGTGTGTT 62.643 66.667 3.37 0.00 44.06 3.32
8279 8961 4.580167 GCTGGTCCTGATAAATGTTATGCA 59.420 41.667 0.00 0.00 0.00 3.96
8282 8964 4.574828 GGTCCTGATAAATGTTATGCACGT 59.425 41.667 0.00 0.00 0.00 4.49
8309 8991 2.435410 CGCATGCCAGCTGAGTGA 60.435 61.111 17.39 0.00 0.00 3.41
8311 8993 1.801332 GCATGCCAGCTGAGTGAAG 59.199 57.895 17.39 0.00 0.00 3.02
8317 8999 1.374190 CAGCTGAGTGAAGGGCTGT 59.626 57.895 8.42 0.00 44.69 4.40
8344 9288 2.811431 CCACGTGTCTTTTCTAATGGCA 59.189 45.455 15.65 0.00 0.00 4.92
8345 9289 3.252215 CCACGTGTCTTTTCTAATGGCAA 59.748 43.478 15.65 0.00 0.00 4.52
8346 9290 4.261405 CCACGTGTCTTTTCTAATGGCAAA 60.261 41.667 15.65 0.00 0.00 3.68
8347 9291 5.277825 CACGTGTCTTTTCTAATGGCAAAA 58.722 37.500 7.58 0.00 0.00 2.44
8348 9292 5.399301 CACGTGTCTTTTCTAATGGCAAAAG 59.601 40.000 7.58 0.00 39.84 2.27
8684 9628 1.511464 GTCCACGTCTAGTCACGCG 60.511 63.158 3.53 3.53 43.93 6.01
8685 9629 1.962822 TCCACGTCTAGTCACGCGT 60.963 57.895 5.58 5.58 43.93 6.01
8686 9630 3.737182 CACGTCTAGTCACGCGTG 58.263 61.111 32.76 32.76 46.28 5.34
8687 9631 2.559840 ACGTCTAGTCACGCGTGG 59.440 61.111 36.41 21.65 43.93 4.94
8688 9632 2.874780 CGTCTAGTCACGCGTGGC 60.875 66.667 35.18 35.18 31.96 5.01
8689 9633 2.506438 GTCTAGTCACGCGTGGCC 60.506 66.667 37.67 27.07 35.39 5.36
8690 9634 3.755628 TCTAGTCACGCGTGGCCC 61.756 66.667 37.67 24.68 35.39 5.80
8691 9635 3.760035 CTAGTCACGCGTGGCCCT 61.760 66.667 37.67 29.30 35.39 5.19
8692 9636 3.296709 CTAGTCACGCGTGGCCCTT 62.297 63.158 37.67 23.43 35.39 3.95
8693 9637 3.291101 TAGTCACGCGTGGCCCTTC 62.291 63.158 37.67 20.00 35.39 3.46
8736 9680 1.299648 CCATGGGTGGCTTCTTCGA 59.700 57.895 2.85 0.00 39.01 3.71
8749 9700 1.056660 TCTTCGACAAGGGAAAGCCT 58.943 50.000 0.00 0.00 0.00 4.58
8755 9706 4.366684 AAGGGAAAGCCTGGGCCG 62.367 66.667 8.11 0.00 43.17 6.13
8781 9732 3.725819 CACGGTCGTGCCAAGAAA 58.274 55.556 10.59 0.00 39.39 2.52
8782 9733 1.569493 CACGGTCGTGCCAAGAAAG 59.431 57.895 10.59 0.00 39.39 2.62
8783 9734 1.597027 ACGGTCGTGCCAAGAAAGG 60.597 57.895 0.00 0.00 36.97 3.11
8784 9735 1.301401 CGGTCGTGCCAAGAAAGGA 60.301 57.895 0.00 0.00 36.97 3.36
8785 9736 1.291877 CGGTCGTGCCAAGAAAGGAG 61.292 60.000 0.00 0.00 36.97 3.69
8786 9737 0.955919 GGTCGTGCCAAGAAAGGAGG 60.956 60.000 0.00 0.00 37.17 4.30
8787 9738 0.955919 GTCGTGCCAAGAAAGGAGGG 60.956 60.000 0.00 0.00 0.00 4.30
8788 9739 2.335712 CGTGCCAAGAAAGGAGGGC 61.336 63.158 0.00 0.00 46.58 5.19
8789 9740 1.075659 GTGCCAAGAAAGGAGGGCT 59.924 57.895 0.00 0.00 46.53 5.19
8790 9741 0.962855 GTGCCAAGAAAGGAGGGCTC 60.963 60.000 0.00 0.00 46.53 4.70
8791 9742 1.380302 GCCAAGAAAGGAGGGCTCA 59.620 57.895 0.00 0.00 43.09 4.26
8792 9743 0.962855 GCCAAGAAAGGAGGGCTCAC 60.963 60.000 0.00 0.00 43.09 3.51
8793 9744 0.322906 CCAAGAAAGGAGGGCTCACC 60.323 60.000 0.00 0.00 40.67 4.02
8794 9745 0.674895 CAAGAAAGGAGGGCTCACCG 60.675 60.000 0.00 0.00 46.96 4.94
8795 9746 1.842381 AAGAAAGGAGGGCTCACCGG 61.842 60.000 0.00 0.00 46.96 5.28
8796 9747 3.978571 GAAAGGAGGGCTCACCGGC 62.979 68.421 0.00 0.00 46.96 6.13
8805 9756 4.394712 CTCACCGGCCACAGGACC 62.395 72.222 0.00 0.00 0.00 4.46
8810 9761 3.697747 CGGCCACAGGACCGGTTA 61.698 66.667 9.42 0.00 45.74 2.85
8811 9762 2.995547 GGCCACAGGACCGGTTAT 59.004 61.111 9.42 0.00 0.00 1.89
8812 9763 1.678598 CGGCCACAGGACCGGTTATA 61.679 60.000 9.42 0.00 45.74 0.98
8813 9764 0.179065 GGCCACAGGACCGGTTATAC 60.179 60.000 9.42 0.00 0.00 1.47
8814 9765 0.538118 GCCACAGGACCGGTTATACA 59.462 55.000 9.42 0.00 0.00 2.29
8815 9766 1.140252 GCCACAGGACCGGTTATACAT 59.860 52.381 9.42 0.00 0.00 2.29
8816 9767 2.420967 GCCACAGGACCGGTTATACATT 60.421 50.000 9.42 0.00 0.00 2.71
8817 9768 3.881220 CCACAGGACCGGTTATACATTT 58.119 45.455 9.42 0.00 0.00 2.32
8818 9769 3.875134 CCACAGGACCGGTTATACATTTC 59.125 47.826 9.42 0.00 0.00 2.17
8819 9770 3.875134 CACAGGACCGGTTATACATTTCC 59.125 47.826 9.42 0.87 0.00 3.13
8820 9771 3.128349 CAGGACCGGTTATACATTTCCG 58.872 50.000 9.42 0.00 42.22 4.30
8821 9772 2.767960 AGGACCGGTTATACATTTCCGT 59.232 45.455 9.42 0.00 41.17 4.69
8822 9773 2.867975 GGACCGGTTATACATTTCCGTG 59.132 50.000 9.42 0.00 41.17 4.94
8823 9774 2.282407 ACCGGTTATACATTTCCGTGC 58.718 47.619 0.00 0.00 41.17 5.34
8824 9775 2.281517 CCGGTTATACATTTCCGTGCA 58.718 47.619 0.00 0.00 41.17 4.57
8825 9776 2.031191 CCGGTTATACATTTCCGTGCAC 59.969 50.000 6.82 6.82 41.17 4.57
8826 9777 2.031191 CGGTTATACATTTCCGTGCACC 59.969 50.000 12.15 0.00 38.45 5.01
8827 9778 2.031191 GGTTATACATTTCCGTGCACCG 59.969 50.000 12.15 4.82 0.00 4.94
8855 9806 3.803082 CACTGCCGTGGCCGAATG 61.803 66.667 8.69 0.00 41.09 2.67
8856 9807 4.329545 ACTGCCGTGGCCGAATGT 62.330 61.111 8.69 0.00 41.09 2.71
8857 9808 3.499737 CTGCCGTGGCCGAATGTC 61.500 66.667 8.69 0.00 41.09 3.06
8858 9809 4.321966 TGCCGTGGCCGAATGTCA 62.322 61.111 8.69 0.00 41.09 3.58
8859 9810 3.053291 GCCGTGGCCGAATGTCAA 61.053 61.111 0.00 0.00 35.63 3.18
8860 9811 2.867472 CCGTGGCCGAATGTCAAC 59.133 61.111 0.00 0.00 35.63 3.18
8861 9812 2.686816 CCGTGGCCGAATGTCAACC 61.687 63.158 0.00 0.00 35.63 3.77
8862 9813 1.671054 CGTGGCCGAATGTCAACCT 60.671 57.895 0.00 0.00 35.63 3.50
8863 9814 1.635663 CGTGGCCGAATGTCAACCTC 61.636 60.000 0.00 0.00 35.63 3.85
8864 9815 1.002624 TGGCCGAATGTCAACCTCC 60.003 57.895 0.00 0.00 0.00 4.30
8865 9816 1.749258 GGCCGAATGTCAACCTCCC 60.749 63.158 0.00 0.00 0.00 4.30
8866 9817 2.106683 GCCGAATGTCAACCTCCCG 61.107 63.158 0.00 0.00 0.00 5.14
8867 9818 2.106683 CCGAATGTCAACCTCCCGC 61.107 63.158 0.00 0.00 0.00 6.13
8868 9819 1.375396 CGAATGTCAACCTCCCGCA 60.375 57.895 0.00 0.00 0.00 5.69
8869 9820 1.635663 CGAATGTCAACCTCCCGCAC 61.636 60.000 0.00 0.00 0.00 5.34
8870 9821 0.605319 GAATGTCAACCTCCCGCACA 60.605 55.000 0.00 0.00 0.00 4.57
8871 9822 0.179004 AATGTCAACCTCCCGCACAA 60.179 50.000 0.00 0.00 0.00 3.33
8872 9823 0.038166 ATGTCAACCTCCCGCACAAT 59.962 50.000 0.00 0.00 0.00 2.71
8873 9824 0.179004 TGTCAACCTCCCGCACAATT 60.179 50.000 0.00 0.00 0.00 2.32
8874 9825 0.240945 GTCAACCTCCCGCACAATTG 59.759 55.000 3.24 3.24 0.00 2.32
8875 9826 0.893270 TCAACCTCCCGCACAATTGG 60.893 55.000 10.83 0.00 0.00 3.16
8876 9827 2.275380 AACCTCCCGCACAATTGGC 61.275 57.895 10.83 9.40 0.00 4.52
8877 9828 2.676121 CCTCCCGCACAATTGGCA 60.676 61.111 10.83 0.00 0.00 4.92
8878 9829 2.053865 CCTCCCGCACAATTGGCAT 61.054 57.895 10.83 0.00 0.00 4.40
8879 9830 1.434696 CTCCCGCACAATTGGCATC 59.565 57.895 10.83 0.00 0.00 3.91
8880 9831 1.001020 TCCCGCACAATTGGCATCT 60.001 52.632 10.83 0.00 0.00 2.90
8881 9832 1.031571 TCCCGCACAATTGGCATCTC 61.032 55.000 10.83 0.00 0.00 2.75
8882 9833 1.063006 CCGCACAATTGGCATCTCG 59.937 57.895 10.83 3.74 0.00 4.04
8883 9834 1.368345 CCGCACAATTGGCATCTCGA 61.368 55.000 10.83 0.00 0.00 4.04
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 3.934457 TGATGCAAGACTACTTCACGA 57.066 42.857 0.00 0.00 33.70 4.35
69 70 2.076207 TCCCCGGAATCGTCATCTTA 57.924 50.000 0.73 0.00 33.95 2.10
156 157 4.521256 GGTTTAGTTTGGTCATGGCACTTA 59.479 41.667 0.00 0.00 0.00 2.24
248 390 3.766691 GTCGTGCCCGCCTCCTAA 61.767 66.667 0.00 0.00 0.00 2.69
302 444 2.187493 CGGATCCGGCGAGAAGAGA 61.187 63.158 26.95 0.00 35.56 3.10
418 571 4.394712 CCGACCGCCCTTGCTTCT 62.395 66.667 0.00 0.00 34.43 2.85
552 706 3.059386 GGACGCGGCAAAATCCCA 61.059 61.111 17.00 0.00 0.00 4.37
578 733 2.744709 CGTCCCGGTCCGCAAAAT 60.745 61.111 5.50 0.00 0.00 1.82
605 760 2.159382 GAAAAACCTGCCGGATCAGAA 58.841 47.619 5.05 0.00 36.19 3.02
626 782 1.680651 CAAAATGCGGGTAGGGGCA 60.681 57.895 0.00 0.00 44.29 5.36
699 857 1.727880 CGCGTCCGTCCAATTTTAAGA 59.272 47.619 0.00 0.00 0.00 2.10
745 905 7.008357 CACGTGGAAAGTTTCTTTCTTTCTTTC 59.992 37.037 15.05 0.00 45.56 2.62
881 1041 2.741055 GGAAGGGCCAGAGGAGAGC 61.741 68.421 6.18 0.00 36.34 4.09
1159 1592 1.909302 CCTGGCTTCCTCCTCAGTAAA 59.091 52.381 0.00 0.00 0.00 2.01
1176 1609 1.291877 CGTTGAGCCCGAACTTCCTG 61.292 60.000 0.00 0.00 0.00 3.86
1584 2020 6.728200 TGAAGTCTTTAGTCAAAGCAACATG 58.272 36.000 0.00 0.00 40.89 3.21
1649 2085 8.677300 TCATTCCAGCTAGAACAAAATATGAAC 58.323 33.333 0.00 0.00 0.00 3.18
1937 2373 5.171339 ACAGACACCTGCAAGATTTAGAT 57.829 39.130 0.00 0.00 44.16 1.98
2115 2551 7.992180 AAACCTTTAATATAGTACCGTGTCG 57.008 36.000 0.00 0.00 0.00 4.35
2166 2602 7.759465 TGTAGTGGAGTACGAAAAGATAGAAG 58.241 38.462 0.00 0.00 0.00 2.85
2190 2626 4.036027 ACTTGCAAGAAACTGACTGACATG 59.964 41.667 32.50 0.97 0.00 3.21
2271 2707 5.300539 TGACAAGTAAAGCCTAAATGTGCAA 59.699 36.000 0.00 0.00 0.00 4.08
2272 2708 4.824537 TGACAAGTAAAGCCTAAATGTGCA 59.175 37.500 0.00 0.00 0.00 4.57
2441 2877 6.515272 AAGGCACCTTTTATGACATGTAAG 57.485 37.500 0.00 0.00 31.29 2.34
2600 3036 8.935741 ACTAAGAATATGTAGGGAACTTTAGGG 58.064 37.037 0.00 0.00 43.67 3.53
2653 3089 1.948834 TGCAGGTAATTCATCGGCATG 59.051 47.619 0.00 0.00 0.00 4.06
3006 3442 9.607285 TTATTTTAAGATTCACAGACTTTTCGC 57.393 29.630 0.00 0.00 0.00 4.70
3030 3466 5.664294 TTTGCGGGAGTACTGAATACTTA 57.336 39.130 0.00 0.00 44.64 2.24
3288 3726 6.541111 AACAAGAGACGGTAAGATTTCAAC 57.459 37.500 0.00 0.00 0.00 3.18
3308 3746 2.322081 GCCGGCGCTAACAGAAACA 61.322 57.895 12.58 0.00 0.00 2.83
3458 3896 6.183360 ACGACTATTTTACTACGCTGATCTGT 60.183 38.462 1.27 0.00 0.00 3.41
3508 3946 9.178758 CTGCTAGTTACCAAAAATCTAGGAAAT 57.821 33.333 0.00 0.00 31.09 2.17
3997 4435 4.125703 CCTAGAACATCATCAGTTGAGGC 58.874 47.826 0.00 0.00 39.78 4.70
4306 4744 4.436242 TTGACACCAAAACGCTGTTTTA 57.564 36.364 15.54 1.69 0.00 1.52
4699 5138 6.054941 TGTTGCTTGAGAGTCTATTCACAAA 58.945 36.000 0.00 0.00 29.43 2.83
5067 5506 2.352805 CTTCCCTGCCTGGACACC 59.647 66.667 0.00 0.00 38.35 4.16
5068 5507 2.360475 GCTTCCCTGCCTGGACAC 60.360 66.667 0.00 0.00 38.35 3.67
5069 5508 2.530151 AGCTTCCCTGCCTGGACA 60.530 61.111 0.00 0.00 38.35 4.02
5070 5509 2.045536 CAGCTTCCCTGCCTGGAC 60.046 66.667 0.00 0.00 38.35 4.02
5087 5526 2.362077 TCTCAAACTGCAAAAGGGAAGC 59.638 45.455 0.00 0.00 0.00 3.86
5389 5828 6.583427 TGATTCATTTGAATGCATTATAGCGC 59.417 34.615 12.97 0.00 44.14 5.92
5757 6196 2.025037 CCTTCCCATCATCCCAAAGTCA 60.025 50.000 0.00 0.00 0.00 3.41
5969 6408 6.263842 ACACATGATGTTCTGTCAAACTTCAT 59.736 34.615 0.00 15.55 46.54 2.57
6186 6634 7.326305 AGCTATACAATAGATAAACAGAACGCG 59.674 37.037 3.53 3.53 0.00 6.01
6205 6653 4.677832 GCTAGACGCTCTTCAAAGCTATAC 59.322 45.833 0.00 0.00 40.23 1.47
6544 6992 1.945394 CAGCCATGGTTCTCTACATGC 59.055 52.381 14.67 0.00 42.31 4.06
6556 7004 1.338973 GGCATCATGTTACAGCCATGG 59.661 52.381 7.63 7.63 44.59 3.66
6751 7199 2.775911 TCAGAGAAGGCCATGTCAAG 57.224 50.000 5.01 0.00 0.00 3.02
6982 7611 4.507710 ACACATTGTAGAATGCACGAGAT 58.492 39.130 12.27 0.00 42.54 2.75
7042 7671 7.045416 ACATTGTAGATACCAAACGCTCAATA 58.955 34.615 0.00 0.00 0.00 1.90
7075 7704 2.094752 CCAGCAAACCACGGAAAATAGG 60.095 50.000 0.00 0.00 0.00 2.57
7188 7817 5.278022 GGCAACTCTTTGAAACGATCTTTCT 60.278 40.000 14.59 0.00 34.24 2.52
7281 7910 4.021719 CAGCCCTAAATTCCCATAGCAATG 60.022 45.833 0.00 0.00 0.00 2.82
7431 8060 3.441572 CCATGATCAAGGACACAAGTTCC 59.558 47.826 11.68 0.00 0.00 3.62
7465 8094 3.610242 CGACAGTCAGATGAAAGTACAGC 59.390 47.826 0.41 0.00 0.00 4.40
7534 8163 2.167075 ACAGAGCACGACATCATGATCA 59.833 45.455 4.86 0.00 33.63 2.92
7607 8236 2.146724 CCACTCCCTGGGTGACACA 61.147 63.158 21.06 0.00 36.18 3.72
7630 8259 1.435577 CGAGGTTTACCAAACTCCCG 58.564 55.000 1.13 0.00 41.14 5.14
7633 8262 2.998670 GGTAGCGAGGTTTACCAAACTC 59.001 50.000 1.13 0.00 41.14 3.01
7891 8520 1.550327 TCAGCTCTCACTGGTCGATT 58.450 50.000 0.00 0.00 38.26 3.34
7911 8540 7.972832 ACGTATTACACTGAAATCTTTTGGA 57.027 32.000 0.00 0.00 0.00 3.53
8083 8712 8.764524 GCTGTGCTATACTGCTTATATTTACT 57.235 34.615 0.00 0.00 46.92 2.24
8145 8774 3.334691 CACACACCAACCGTCTATGAAT 58.665 45.455 0.00 0.00 0.00 2.57
8157 8788 1.817520 CGACACAGGCACACACCAA 60.818 57.895 0.00 0.00 0.00 3.67
8174 8805 1.131826 GTGAACGCAAATCGGGTCG 59.868 57.895 0.00 0.00 40.50 4.79
8205 8887 1.954362 GAGGCTGACACCGAGCAGAT 61.954 60.000 0.00 0.00 38.27 2.90
8253 8935 4.574674 AACATTTATCAGGACCAGCAGA 57.425 40.909 0.00 0.00 0.00 4.26
8255 8937 4.580167 GCATAACATTTATCAGGACCAGCA 59.420 41.667 0.00 0.00 0.00 4.41
8303 8985 0.764369 ACTCCACAGCCCTTCACTCA 60.764 55.000 0.00 0.00 0.00 3.41
8304 8986 0.036858 GACTCCACAGCCCTTCACTC 60.037 60.000 0.00 0.00 0.00 3.51
8317 8999 1.760613 AGAAAAGACACGTGGACTCCA 59.239 47.619 21.57 0.00 0.00 3.86
8644 9588 1.423921 GGAGTGGGGAAAAGAAGTGGA 59.576 52.381 0.00 0.00 0.00 4.02
8645 9589 1.547901 GGGAGTGGGGAAAAGAAGTGG 60.548 57.143 0.00 0.00 0.00 4.00
8646 9590 1.882352 CGGGAGTGGGGAAAAGAAGTG 60.882 57.143 0.00 0.00 0.00 3.16
8647 9591 0.400594 CGGGAGTGGGGAAAAGAAGT 59.599 55.000 0.00 0.00 0.00 3.01
8648 9592 0.400594 ACGGGAGTGGGGAAAAGAAG 59.599 55.000 0.00 0.00 44.82 2.85
8649 9593 2.547171 ACGGGAGTGGGGAAAAGAA 58.453 52.632 0.00 0.00 44.82 2.52
8650 9594 4.324521 ACGGGAGTGGGGAAAAGA 57.675 55.556 0.00 0.00 44.82 2.52
8690 9634 3.726517 CAGTGTTGGCCGGCGAAG 61.727 66.667 25.25 9.00 0.00 3.79
8691 9635 4.243008 TCAGTGTTGGCCGGCGAA 62.243 61.111 20.90 20.90 0.00 4.70
8692 9636 4.980805 GTCAGTGTTGGCCGGCGA 62.981 66.667 22.54 15.52 0.00 5.54
8701 9645 0.830444 TGGCGACTAGGGTCAGTGTT 60.830 55.000 0.00 0.00 42.21 3.32
8736 9680 2.118294 GCCCAGGCTTTCCCTTGT 59.882 61.111 0.08 0.00 43.06 3.16
8771 9722 0.962855 GAGCCCTCCTTTCTTGGCAC 60.963 60.000 1.86 0.00 46.45 5.01
8779 9730 4.035102 GCCGGTGAGCCCTCCTTT 62.035 66.667 1.90 0.00 0.00 3.11
8788 9739 4.394712 GGTCCTGTGGCCGGTGAG 62.395 72.222 1.90 0.00 0.00 3.51
8793 9744 1.678598 TATAACCGGTCCTGTGGCCG 61.679 60.000 8.04 0.00 46.80 6.13
8794 9745 0.179065 GTATAACCGGTCCTGTGGCC 60.179 60.000 8.04 0.00 0.00 5.36
8795 9746 0.538118 TGTATAACCGGTCCTGTGGC 59.462 55.000 8.04 0.00 0.00 5.01
8796 9747 3.553828 AATGTATAACCGGTCCTGTGG 57.446 47.619 8.04 0.00 0.00 4.17
8797 9748 3.875134 GGAAATGTATAACCGGTCCTGTG 59.125 47.826 8.04 0.00 0.00 3.66
8798 9749 3.431207 CGGAAATGTATAACCGGTCCTGT 60.431 47.826 8.04 0.00 41.41 4.00
8799 9750 3.128349 CGGAAATGTATAACCGGTCCTG 58.872 50.000 8.04 0.00 41.41 3.86
8800 9751 3.464111 CGGAAATGTATAACCGGTCCT 57.536 47.619 8.04 0.00 41.41 3.85
8806 9757 2.031191 CGGTGCACGGAAATGTATAACC 59.969 50.000 18.87 0.00 39.42 2.85
8807 9758 3.313274 CGGTGCACGGAAATGTATAAC 57.687 47.619 18.87 0.00 39.42 1.89
8839 9790 4.329545 ACATTCGGCCACGGCAGT 62.330 61.111 10.83 0.00 44.11 4.40
8840 9791 3.499737 GACATTCGGCCACGGCAG 61.500 66.667 10.83 6.08 44.11 4.85
8841 9792 3.834013 TTGACATTCGGCCACGGCA 62.834 57.895 10.83 0.00 44.11 5.69
8842 9793 3.053291 TTGACATTCGGCCACGGC 61.053 61.111 2.24 0.00 41.39 5.68
8843 9794 2.686816 GGTTGACATTCGGCCACGG 61.687 63.158 2.24 0.00 41.39 4.94
8844 9795 1.635663 GAGGTTGACATTCGGCCACG 61.636 60.000 2.24 0.00 42.74 4.94
8845 9796 1.305930 GGAGGTTGACATTCGGCCAC 61.306 60.000 2.24 0.00 0.00 5.01
8846 9797 1.002624 GGAGGTTGACATTCGGCCA 60.003 57.895 2.24 0.00 0.00 5.36
8847 9798 1.749258 GGGAGGTTGACATTCGGCC 60.749 63.158 0.00 0.00 0.00 6.13
8848 9799 2.106683 CGGGAGGTTGACATTCGGC 61.107 63.158 0.00 0.00 0.00 5.54
8849 9800 2.106683 GCGGGAGGTTGACATTCGG 61.107 63.158 0.00 0.00 0.00 4.30
8850 9801 1.375396 TGCGGGAGGTTGACATTCG 60.375 57.895 0.00 0.00 0.00 3.34
8851 9802 0.605319 TGTGCGGGAGGTTGACATTC 60.605 55.000 0.00 0.00 0.00 2.67
8852 9803 0.179004 TTGTGCGGGAGGTTGACATT 60.179 50.000 0.00 0.00 0.00 2.71
8853 9804 0.038166 ATTGTGCGGGAGGTTGACAT 59.962 50.000 0.00 0.00 0.00 3.06
8854 9805 0.179004 AATTGTGCGGGAGGTTGACA 60.179 50.000 0.00 0.00 0.00 3.58
8855 9806 0.240945 CAATTGTGCGGGAGGTTGAC 59.759 55.000 0.00 0.00 0.00 3.18
8856 9807 0.893270 CCAATTGTGCGGGAGGTTGA 60.893 55.000 4.43 0.00 0.00 3.18
8857 9808 1.586028 CCAATTGTGCGGGAGGTTG 59.414 57.895 4.43 0.00 0.00 3.77
8858 9809 2.275380 GCCAATTGTGCGGGAGGTT 61.275 57.895 4.43 0.00 0.00 3.50
8859 9810 2.676471 GCCAATTGTGCGGGAGGT 60.676 61.111 4.43 0.00 0.00 3.85
8860 9811 2.008268 GATGCCAATTGTGCGGGAGG 62.008 60.000 4.43 0.00 0.00 4.30
8861 9812 1.033746 AGATGCCAATTGTGCGGGAG 61.034 55.000 4.43 0.00 0.00 4.30
8862 9813 1.001020 AGATGCCAATTGTGCGGGA 60.001 52.632 4.43 0.00 0.00 5.14
8863 9814 1.434696 GAGATGCCAATTGTGCGGG 59.565 57.895 4.43 0.00 0.00 6.13
8864 9815 1.063006 CGAGATGCCAATTGTGCGG 59.937 57.895 4.43 0.00 0.00 5.69
8865 9816 2.089017 TCGAGATGCCAATTGTGCG 58.911 52.632 4.43 0.00 0.00 5.34


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

AutoCloner maintained by Alex Coulton.