Multiple sequence alignment - TraesCS6B01G334100

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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 TraesCS6B01G334100 chr6B 100.000 2951 0 0 1 2951 586077004 586074054 0.000000e+00 5450.0
1 TraesCS6B01G334100 chr6A 90.728 1402 87 17 818 2194 538540674 538542057 0.000000e+00 1829.0
2 TraesCS6B01G334100 chr6A 85.734 708 72 15 2230 2922 538543354 538544047 0.000000e+00 721.0
3 TraesCS6B01G334100 chr6A 88.423 596 34 16 1 579 12374947 12374370 0.000000e+00 686.0
4 TraesCS6B01G334100 chr6A 100.000 32 0 0 2193 2224 538542141 538542172 3.180000e-05 60.2
5 TraesCS6B01G334100 chr6D 90.383 1435 73 26 818 2209 392586062 392587474 0.000000e+00 1825.0
6 TraesCS6B01G334100 chr6D 89.043 575 39 10 26 582 266373490 266372922 0.000000e+00 691.0
7 TraesCS6B01G334100 chr6D 92.276 246 16 1 578 823 392583105 392583347 2.180000e-91 346.0
8 TraesCS6B01G334100 chr6D 92.442 172 5 4 819 983 392584033 392584203 3.800000e-59 239.0
9 TraesCS6B01G334100 chr6D 87.379 206 20 5 2344 2545 392614200 392614403 6.360000e-57 231.0
10 TraesCS6B01G334100 chr6D 90.909 99 3 4 987 1083 392584361 392584455 8.580000e-26 128.0
11 TraesCS6B01G334100 chr6D 85.075 134 7 10 2626 2749 392614821 392614951 1.110000e-24 124.0
12 TraesCS6B01G334100 chr3D 91.608 572 29 6 9 580 474817279 474816727 0.000000e+00 773.0
13 TraesCS6B01G334100 chr1B 89.297 626 34 16 2 599 43957828 43958448 0.000000e+00 754.0
14 TraesCS6B01G334100 chr1B 89.752 605 39 9 1 585 685084110 685083509 0.000000e+00 752.0
15 TraesCS6B01G334100 chr1B 89.683 126 10 3 2257 2379 520095412 520095287 1.090000e-34 158.0
16 TraesCS6B01G334100 chr5A 89.073 604 42 9 1 582 338848558 338847957 0.000000e+00 728.0
17 TraesCS6B01G334100 chr5A 83.833 600 68 21 1 582 659503281 659502693 7.190000e-151 544.0
18 TraesCS6B01G334100 chr5A 91.016 256 17 5 330 583 29625490 29625239 1.010000e-89 340.0
19 TraesCS6B01G334100 chr5A 88.085 235 17 9 349 582 7504269 7504493 4.850000e-68 268.0
20 TraesCS6B01G334100 chr4A 86.522 601 48 19 4 585 83740794 83741380 5.370000e-177 630.0
21 TraesCS6B01G334100 chr5D 86.555 595 51 10 1 579 80188461 80187880 1.930000e-176 628.0
22 TraesCS6B01G334100 chr5D 81.062 433 57 10 166 581 564766691 564767115 3.670000e-84 322.0
23 TraesCS6B01G334100 chr5B 86.509 593 49 14 1 579 522024786 522025361 8.980000e-175 623.0
24 TraesCS6B01G334100 chr5B 88.172 93 9 2 2443 2534 328373949 328373858 3.110000e-20 110.0
25 TraesCS6B01G334100 chr3A 80.872 596 82 20 3 579 723649125 723649707 9.710000e-120 440.0
26 TraesCS6B01G334100 chr7D 77.386 765 106 41 945 1682 542885900 542886624 2.760000e-105 392.0
27 TraesCS6B01G334100 chr7D 77.479 706 88 43 1007 1682 542825918 542826582 1.010000e-94 357.0
28 TraesCS6B01G334100 chr2A 88.379 327 34 2 1 327 25086944 25087266 9.920000e-105 390.0
29 TraesCS6B01G334100 chr7B 78.049 656 80 31 1056 1682 586240663 586241283 3.620000e-94 355.0
30 TraesCS6B01G334100 chr7B 77.353 680 87 39 1034 1682 586116438 586117081 1.010000e-89 340.0
31 TraesCS6B01G334100 chr7B 75.679 773 109 46 945 1682 585944423 585945151 2.210000e-81 313.0
32 TraesCS6B01G334100 chr7B 75.613 775 106 48 945 1682 586067193 586067921 1.030000e-79 307.0
33 TraesCS6B01G334100 chr7B 79.085 306 42 14 945 1231 585991672 585991974 1.080000e-44 191.0
34 TraesCS6B01G334100 chr7B 90.551 127 9 3 2256 2379 516296129 516296003 6.540000e-37 165.0
35 TraesCS6B01G334100 chr7A 76.425 772 98 48 945 1682 624887220 624887941 1.010000e-89 340.0
36 TraesCS6B01G334100 chr7A 75.581 688 97 43 1034 1682 624957671 624958326 1.040000e-69 274.0
37 TraesCS6B01G334100 chr7A 79.558 362 48 15 1343 1682 624840983 624841340 4.920000e-58 235.0
38 TraesCS6B01G334100 chr4B 81.429 140 23 2 2397 2534 34729958 34729820 8.650000e-21 111.0
39 TraesCS6B01G334100 chr1D 79.042 167 26 7 2387 2546 145941512 145941676 4.020000e-19 106.0
40 TraesCS6B01G334100 chr1D 90.000 80 8 0 2444 2523 465721943 465721864 1.450000e-18 104.0
41 TraesCS6B01G334100 chr2D 80.000 155 20 11 2396 2546 274849605 274849752 1.450000e-18 104.0
42 TraesCS6B01G334100 chr1A 78.750 160 26 6 2392 2546 143819047 143819203 1.870000e-17 100.0
43 TraesCS6B01G334100 chrUn 86.022 93 12 1 2443 2534 17162801 17162893 6.730000e-17 99.0
44 TraesCS6B01G334100 chr2B 89.130 46 3 2 2562 2607 557224795 557224838 4.110000e-04 56.5


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 TraesCS6B01G334100 chr6B 586074054 586077004 2950 True 5450.000000 5450 100.0000 1 2951 1 chr6B.!!$R1 2950
1 TraesCS6B01G334100 chr6A 538540674 538544047 3373 False 870.066667 1829 92.1540 818 2922 3 chr6A.!!$F1 2104
2 TraesCS6B01G334100 chr6A 12374370 12374947 577 True 686.000000 686 88.4230 1 579 1 chr6A.!!$R1 578
3 TraesCS6B01G334100 chr6D 266372922 266373490 568 True 691.000000 691 89.0430 26 582 1 chr6D.!!$R1 556
4 TraesCS6B01G334100 chr6D 392583105 392587474 4369 False 634.500000 1825 91.5025 578 2209 4 chr6D.!!$F1 1631
5 TraesCS6B01G334100 chr3D 474816727 474817279 552 True 773.000000 773 91.6080 9 580 1 chr3D.!!$R1 571
6 TraesCS6B01G334100 chr1B 43957828 43958448 620 False 754.000000 754 89.2970 2 599 1 chr1B.!!$F1 597
7 TraesCS6B01G334100 chr1B 685083509 685084110 601 True 752.000000 752 89.7520 1 585 1 chr1B.!!$R2 584
8 TraesCS6B01G334100 chr5A 338847957 338848558 601 True 728.000000 728 89.0730 1 582 1 chr5A.!!$R2 581
9 TraesCS6B01G334100 chr5A 659502693 659503281 588 True 544.000000 544 83.8330 1 582 1 chr5A.!!$R3 581
10 TraesCS6B01G334100 chr4A 83740794 83741380 586 False 630.000000 630 86.5220 4 585 1 chr4A.!!$F1 581
11 TraesCS6B01G334100 chr5D 80187880 80188461 581 True 628.000000 628 86.5550 1 579 1 chr5D.!!$R1 578
12 TraesCS6B01G334100 chr5B 522024786 522025361 575 False 623.000000 623 86.5090 1 579 1 chr5B.!!$F1 578
13 TraesCS6B01G334100 chr3A 723649125 723649707 582 False 440.000000 440 80.8720 3 579 1 chr3A.!!$F1 576
14 TraesCS6B01G334100 chr7D 542885900 542886624 724 False 392.000000 392 77.3860 945 1682 1 chr7D.!!$F2 737
15 TraesCS6B01G334100 chr7D 542825918 542826582 664 False 357.000000 357 77.4790 1007 1682 1 chr7D.!!$F1 675
16 TraesCS6B01G334100 chr7B 586240663 586241283 620 False 355.000000 355 78.0490 1056 1682 1 chr7B.!!$F5 626
17 TraesCS6B01G334100 chr7B 586116438 586117081 643 False 340.000000 340 77.3530 1034 1682 1 chr7B.!!$F4 648
18 TraesCS6B01G334100 chr7B 585944423 585945151 728 False 313.000000 313 75.6790 945 1682 1 chr7B.!!$F1 737
19 TraesCS6B01G334100 chr7B 586067193 586067921 728 False 307.000000 307 75.6130 945 1682 1 chr7B.!!$F3 737
20 TraesCS6B01G334100 chr7A 624887220 624887941 721 False 340.000000 340 76.4250 945 1682 1 chr7A.!!$F2 737
21 TraesCS6B01G334100 chr7A 624957671 624958326 655 False 274.000000 274 75.5810 1034 1682 1 chr7A.!!$F3 648

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
771 811 0.172803 ACTATCCGTGTCGCAAGGAC 59.827 55.0 14.38 0.0 43.94 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2650 6754 0.395312 TGTTCCACTCCCTCCGTTTC 59.605 55.0 0.0 0.0 0.0 2.78 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
106 108 3.068691 CGGTCTTGAGCTCCGGGA 61.069 66.667 12.15 3.75 40.49 5.14
234 243 5.833131 TCAAGGTGAAAACCTAGAATTTGCT 59.167 36.000 0.00 0.00 39.65 3.91
288 297 0.177604 AGCATCGCTTCCTTCCTGAG 59.822 55.000 0.00 0.00 33.89 3.35
327 336 1.148310 GTCGATGTCCTTGTGGTGTG 58.852 55.000 0.00 0.00 34.23 3.82
333 359 4.635765 CGATGTCCTTGTGGTGTGAATATT 59.364 41.667 0.00 0.00 34.23 1.28
491 530 1.004628 TGTTGGCTGTGTGCATCCTAT 59.995 47.619 0.00 0.00 45.15 2.57
598 638 0.609131 AAAGACCAATCCACCTGGCG 60.609 55.000 0.00 0.00 37.48 5.69
646 686 1.271926 ACCACCACAGCCTACCAAATC 60.272 52.381 0.00 0.00 0.00 2.17
652 692 0.918983 CAGCCTACCAAATCCTCCCA 59.081 55.000 0.00 0.00 0.00 4.37
675 715 2.123425 CTACTCGCCCCTAGCCCA 60.123 66.667 0.00 0.00 38.78 5.36
743 783 1.556911 CAGCCTGTACCCATCTTCTGT 59.443 52.381 0.00 0.00 0.00 3.41
746 786 2.159028 GCCTGTACCCATCTTCTGTCTC 60.159 54.545 0.00 0.00 0.00 3.36
755 795 2.873094 TCTTCTGTCTCCGTCCACTA 57.127 50.000 0.00 0.00 0.00 2.74
771 811 0.172803 ACTATCCGTGTCGCAAGGAC 59.827 55.000 14.38 0.00 43.94 3.85
975 1710 4.877823 CGATGTTGCCTATATATGCATGGT 59.122 41.667 10.16 0.04 37.33 3.55
977 1712 4.252878 TGTTGCCTATATATGCATGGTCG 58.747 43.478 10.16 0.00 37.33 4.79
1038 3808 0.250727 GGCACTGAACCACCAGCTAA 60.251 55.000 0.00 0.00 37.68 3.09
1146 3922 3.134442 CCCTCCTCATTCTCTTCCTTCTG 59.866 52.174 0.00 0.00 0.00 3.02
1173 3949 2.596851 GGTGCCTGCCTTCCTCAGA 61.597 63.158 0.00 0.00 33.54 3.27
1304 4080 4.680237 CCGGCACCTGTCTTCGCA 62.680 66.667 0.00 0.00 0.00 5.10
1336 4112 1.474478 CTGTCACGCCTGTCAGTATCT 59.526 52.381 0.00 0.00 31.16 1.98
1337 4113 1.893137 TGTCACGCCTGTCAGTATCTT 59.107 47.619 0.00 0.00 0.00 2.40
1340 4116 1.066858 CACGCCTGTCAGTATCTTGGT 60.067 52.381 0.00 0.00 0.00 3.67
1348 4124 3.322541 TGTCAGTATCTTGGTTTCACCGA 59.677 43.478 0.00 0.00 42.58 4.69
1364 4146 0.471617 CCGATTCAGAGGGCTGGATT 59.528 55.000 0.00 0.00 40.53 3.01
1403 4191 2.874694 CGGCGGTTGCAGATGATCG 61.875 63.158 0.00 0.00 45.35 3.69
1409 4203 2.463620 TTGCAGATGATCGTGCGGC 61.464 57.895 9.26 0.00 42.96 6.53
1411 4205 2.249535 GCAGATGATCGTGCGGCAT 61.250 57.895 5.72 0.00 0.00 4.40
1554 4352 3.106552 CGAGTCAGCGGAGAGGAG 58.893 66.667 0.00 0.00 0.00 3.69
1555 4353 2.804856 GAGTCAGCGGAGAGGAGC 59.195 66.667 0.00 0.00 0.00 4.70
1688 4510 0.380378 CAGAGGCAGTAGCTCTCGAC 59.620 60.000 0.00 0.00 40.66 4.20
1691 4513 2.485582 GCAGTAGCTCTCGACGCA 59.514 61.111 0.00 0.00 37.91 5.24
1699 4533 1.560860 GCTCTCGACGCAAGCTTTGT 61.561 55.000 12.33 0.00 45.62 2.83
1711 4545 4.686972 GCAAGCTTTGTCTTTCCTTTTCT 58.313 39.130 0.00 0.00 0.00 2.52
1713 4547 6.273071 GCAAGCTTTGTCTTTCCTTTTCTTA 58.727 36.000 0.00 0.00 0.00 2.10
1717 4552 9.967346 AAGCTTTGTCTTTCCTTTTCTTATTAC 57.033 29.630 0.00 0.00 0.00 1.89
1722 4557 9.734984 TTGTCTTTCCTTTTCTTATTACTAGGG 57.265 33.333 0.00 0.00 0.00 3.53
1723 4558 8.887393 TGTCTTTCCTTTTCTTATTACTAGGGT 58.113 33.333 0.00 0.00 0.00 4.34
1725 4560 9.108111 TCTTTCCTTTTCTTATTACTAGGGTGA 57.892 33.333 0.00 0.00 0.00 4.02
1833 4670 0.179089 ACATGAGGTGAGCGAGATGC 60.179 55.000 0.00 0.00 46.98 3.91
1851 4688 1.874872 TGCGCCTGTAGTTTTGGTAAC 59.125 47.619 4.18 0.00 0.00 2.50
1893 4730 7.335422 CCACTTTAGCAGTTCAACTCTATCATT 59.665 37.037 0.00 0.00 30.92 2.57
1981 4822 7.166167 ACTTTGTTTATTTCTACAGGACCGAT 58.834 34.615 0.00 0.00 0.00 4.18
1988 4829 4.996788 TTCTACAGGACCGATAACTTCC 57.003 45.455 0.00 0.00 0.00 3.46
2021 4862 2.303890 TCATGTTGAGGTGCTGAGATGT 59.696 45.455 0.00 0.00 0.00 3.06
2102 4943 6.403636 GGAGCAACATGTAAATAGGACAACAG 60.404 42.308 0.00 0.00 0.00 3.16
2141 4982 9.436957 TGAGAGGAGAAATATTGTTTAGTGAAC 57.563 33.333 0.00 0.00 38.78 3.18
2170 5011 4.915704 TCTACAAAAGTTCCTGCAAAACG 58.084 39.130 6.10 0.00 0.00 3.60
2182 5023 3.315191 CCTGCAAAACGAAAGAGGAGAAA 59.685 43.478 0.00 0.00 0.00 2.52
2224 5150 6.815641 GTGAAATCTGCATTAAGTCTCTCTCA 59.184 38.462 0.00 0.00 0.00 3.27
2226 5152 5.929058 ATCTGCATTAAGTCTCTCTCACA 57.071 39.130 0.00 0.00 0.00 3.58
2228 5154 5.658468 TCTGCATTAAGTCTCTCTCACATG 58.342 41.667 0.00 0.00 0.00 3.21
2234 6336 4.782019 AAGTCTCTCTCACATGTCTCAC 57.218 45.455 0.00 0.00 0.00 3.51
2254 6356 2.745281 ACCGTTGTGAACATAAATCCCG 59.255 45.455 0.00 0.00 0.00 5.14
2262 6364 4.698304 GTGAACATAAATCCCGGTCTCAAA 59.302 41.667 0.00 0.00 0.00 2.69
2299 6401 2.223340 GCAATATCCTGTTGTGGAAGCG 60.223 50.000 0.00 0.00 39.85 4.68
2300 6402 3.009723 CAATATCCTGTTGTGGAAGCGT 58.990 45.455 0.00 0.00 39.85 5.07
2308 6410 1.461127 GTTGTGGAAGCGTCATCTGAC 59.539 52.381 1.14 0.07 41.47 3.51
2327 6429 2.505819 GACAATCCCAAGCTTCCTCCTA 59.494 50.000 0.00 0.00 0.00 2.94
2340 6442 4.327680 CTTCCTCCTAAACTCAAAGTGGG 58.672 47.826 0.00 0.00 0.00 4.61
2342 6444 2.437413 CTCCTAAACTCAAAGTGGGCC 58.563 52.381 0.00 0.00 0.00 5.80
2345 6447 2.437413 CTAAACTCAAAGTGGGCCCTC 58.563 52.381 25.70 20.95 0.00 4.30
2349 6451 1.351350 ACTCAAAGTGGGCCCTCTTAC 59.649 52.381 33.70 19.64 0.00 2.34
2366 6468 7.565680 CCCTCTTACATATAACAGTCCAAACT 58.434 38.462 0.00 0.00 35.60 2.66
2395 6497 5.172205 AGCTGAATCTACTTTCTTCGTTCC 58.828 41.667 0.00 0.00 0.00 3.62
2422 6524 8.702163 AAATGTTTGAAGTTCTAGGTTTTGTG 57.298 30.769 4.17 0.00 0.00 3.33
2423 6525 6.202516 TGTTTGAAGTTCTAGGTTTTGTGG 57.797 37.500 4.17 0.00 0.00 4.17
2429 6531 7.114095 TGAAGTTCTAGGTTTTGTGGTAAGTT 58.886 34.615 4.17 0.00 0.00 2.66
2431 6533 8.672823 AAGTTCTAGGTTTTGTGGTAAGTTAG 57.327 34.615 0.00 0.00 0.00 2.34
2434 6536 9.112725 GTTCTAGGTTTTGTGGTAAGTTAGAAA 57.887 33.333 0.00 0.00 0.00 2.52
2503 6605 8.353423 ACAACACCAAATTAGCTTCATTAGAT 57.647 30.769 0.00 0.00 0.00 1.98
2506 6608 8.579850 ACACCAAATTAGCTTCATTAGATTCA 57.420 30.769 0.00 0.00 0.00 2.57
2631 6735 3.132289 AGAAGTTCGTCTCAGGACAAACA 59.868 43.478 0.00 0.00 40.64 2.83
2633 6737 4.866508 AGTTCGTCTCAGGACAAACATA 57.133 40.909 3.41 0.00 40.64 2.29
2634 6738 4.810790 AGTTCGTCTCAGGACAAACATAG 58.189 43.478 3.41 0.00 40.64 2.23
2659 6763 9.908152 AGAACTTTAAATATTTTGAAACGGAGG 57.092 29.630 5.91 0.00 0.00 4.30
2664 6768 5.897377 AATATTTTGAAACGGAGGGAGTG 57.103 39.130 0.00 0.00 0.00 3.51
2665 6769 1.975660 TTTTGAAACGGAGGGAGTGG 58.024 50.000 0.00 0.00 0.00 4.00
2689 6793 8.537016 TGGAACACATGTAAACTAGTAAGCTAT 58.463 33.333 0.00 0.00 0.00 2.97
2692 6796 9.587772 AACACATGTAAACTAGTAAGCTATCTG 57.412 33.333 0.00 0.00 0.00 2.90
2693 6797 8.967918 ACACATGTAAACTAGTAAGCTATCTGA 58.032 33.333 0.00 0.00 0.00 3.27
2694 6798 9.457110 CACATGTAAACTAGTAAGCTATCTGAG 57.543 37.037 0.00 0.00 0.00 3.35
2695 6799 8.634444 ACATGTAAACTAGTAAGCTATCTGAGG 58.366 37.037 0.00 0.00 0.00 3.86
2707 6820 6.814954 AGCTATCTGAGGGTCAAAGATAAA 57.185 37.500 0.00 0.00 33.63 1.40
2759 6872 0.533491 ACATGCAAATGCCAAGCGAT 59.467 45.000 2.46 0.00 41.18 4.58
2760 6873 1.750206 ACATGCAAATGCCAAGCGATA 59.250 42.857 2.46 0.00 41.18 2.92
2761 6874 2.363038 ACATGCAAATGCCAAGCGATAT 59.637 40.909 2.46 0.00 41.18 1.63
2762 6875 3.569277 ACATGCAAATGCCAAGCGATATA 59.431 39.130 2.46 0.00 41.18 0.86
2763 6876 4.219070 ACATGCAAATGCCAAGCGATATAT 59.781 37.500 2.46 0.00 41.18 0.86
2764 6877 5.415389 ACATGCAAATGCCAAGCGATATATA 59.585 36.000 2.46 0.00 41.18 0.86
2765 6878 5.550232 TGCAAATGCCAAGCGATATATAG 57.450 39.130 2.46 0.00 41.18 1.31
2770 6883 1.200483 CCAAGCGATATATAGCGGCG 58.800 55.000 20.84 0.51 38.61 6.46
2773 6886 3.116300 CAAGCGATATATAGCGGCGAAT 58.884 45.455 20.84 5.64 38.61 3.34
2775 6888 2.619177 AGCGATATATAGCGGCGAATCT 59.381 45.455 20.84 6.36 38.61 2.40
2785 6898 1.003866 GCGGCGAATCTTATTCCACAC 60.004 52.381 12.98 0.00 0.00 3.82
2787 6900 1.003866 GGCGAATCTTATTCCACACGC 60.004 52.381 0.00 0.00 43.19 5.34
2823 6936 2.168326 GGAACCAAAATTGCACCCTG 57.832 50.000 0.00 0.00 0.00 4.45
2824 6937 1.511850 GAACCAAAATTGCACCCTGC 58.488 50.000 0.00 0.00 45.29 4.85
2837 6950 0.255890 ACCCTGCATCTGCGGTAATT 59.744 50.000 9.97 0.00 45.66 1.40
2838 6951 0.664761 CCCTGCATCTGCGGTAATTG 59.335 55.000 9.97 0.00 45.66 2.32
2842 6955 2.032981 CATCTGCGGTAATTGGCCC 58.967 57.895 0.00 0.00 0.00 5.80
2848 6961 2.123468 GGTAATTGGCCCGCCCAT 60.123 61.111 0.00 0.00 44.89 4.00
2849 6962 2.200337 GGTAATTGGCCCGCCCATC 61.200 63.158 0.00 0.00 44.89 3.51
2889 7002 5.022282 CTTCACATTTGTTTTGGGAAGGT 57.978 39.130 7.61 0.00 46.31 3.50
2890 7003 5.427378 CTTCACATTTGTTTTGGGAAGGTT 58.573 37.500 7.61 0.00 46.31 3.50
2891 7004 5.017294 TCACATTTGTTTTGGGAAGGTTC 57.983 39.130 0.00 0.00 0.00 3.62
2892 7005 4.714308 TCACATTTGTTTTGGGAAGGTTCT 59.286 37.500 0.00 0.00 0.00 3.01
2893 7006 5.894393 TCACATTTGTTTTGGGAAGGTTCTA 59.106 36.000 0.00 0.00 0.00 2.10
2896 7011 6.265422 ACATTTGTTTTGGGAAGGTTCTAGAG 59.735 38.462 0.00 0.00 0.00 2.43
2909 7024 5.026790 AGGTTCTAGAGCCTTACATGAACT 58.973 41.667 21.58 0.00 39.07 3.01
2911 7026 5.337652 GGTTCTAGAGCCTTACATGAACTGT 60.338 44.000 17.80 0.00 42.13 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 4.385310 GCCACCACTTTTCCACTATCCTAT 60.385 45.833 0.00 0.00 0.00 2.57
28 29 0.818040 GTCGCCACCACTTTTCCACT 60.818 55.000 0.00 0.00 0.00 4.00
106 108 4.993705 TGGTTCTGACCTAGGTTTTCAT 57.006 40.909 17.53 0.00 46.66 2.57
234 243 0.466555 CCGGAACCAACCACCAAAGA 60.467 55.000 0.00 0.00 0.00 2.52
288 297 2.290641 ACATTCTTCAACAGCAACGTCC 59.709 45.455 0.00 0.00 0.00 4.79
290 299 2.032894 CGACATTCTTCAACAGCAACGT 60.033 45.455 0.00 0.00 0.00 3.99
327 336 7.692291 CGACAACCTACAACAATGACAATATTC 59.308 37.037 0.00 0.00 0.00 1.75
333 359 4.061357 TCGACAACCTACAACAATGACA 57.939 40.909 0.00 0.00 0.00 3.58
457 496 1.666700 GCCAACACTAACGAACACACA 59.333 47.619 0.00 0.00 0.00 3.72
464 503 1.577468 CACACAGCCAACACTAACGA 58.423 50.000 0.00 0.00 0.00 3.85
491 530 1.278985 CACACCCAACCTCTGCATAGA 59.721 52.381 0.00 0.00 0.00 1.98
598 638 1.128692 GCGTCTGTAATCTGCAACACC 59.871 52.381 0.00 0.00 0.00 4.16
646 686 1.433879 CGAGTAGTTCGCTGGGAGG 59.566 63.158 0.00 0.00 43.22 4.30
675 715 2.282958 TCGCCGAAGTGGAGAGGT 60.283 61.111 0.00 0.00 42.18 3.85
678 718 2.261671 GCTTCGCCGAAGTGGAGA 59.738 61.111 25.97 0.00 45.74 3.71
679 719 3.181967 CGCTTCGCCGAAGTGGAG 61.182 66.667 27.91 13.97 43.76 3.86
702 742 3.076785 TGGGAAGCTAAAAGGGAATTGGA 59.923 43.478 0.00 0.00 0.00 3.53
731 771 1.187087 GACGGAGACAGAAGATGGGT 58.813 55.000 0.00 0.00 0.00 4.51
732 772 0.461961 GGACGGAGACAGAAGATGGG 59.538 60.000 0.00 0.00 0.00 4.00
743 783 2.789842 CACGGATAGTGGACGGAGA 58.210 57.895 0.00 0.00 46.77 3.71
755 795 2.264794 GGTCCTTGCGACACGGAT 59.735 61.111 7.99 0.00 43.95 4.18
771 811 4.891727 CCTCGCCATCGGTTCCGG 62.892 72.222 11.37 0.00 36.13 5.14
885 1615 7.569639 TCACGTAGAGAAACATATCTTAGCT 57.430 36.000 0.00 0.00 0.00 3.32
1038 3808 1.134946 GCTTTGCCGACTTGCCAATAT 59.865 47.619 0.00 0.00 0.00 1.28
1252 4028 1.153349 GGTCGGAAGAGGTCATGGC 60.153 63.158 0.00 0.00 43.49 4.40
1295 4071 0.315251 CTGACCAGTCTGCGAAGACA 59.685 55.000 25.49 3.33 41.02 3.41
1304 4080 1.810606 CGTGACAGCCTGACCAGTCT 61.811 60.000 0.00 0.00 32.41 3.24
1340 4116 0.984230 AGCCCTCTGAATCGGTGAAA 59.016 50.000 0.00 0.00 0.00 2.69
1348 4124 2.708325 GGACTAATCCAGCCCTCTGAAT 59.292 50.000 0.00 0.00 45.47 2.57
1364 4146 1.191535 CTGGTCGTTGGGATGGACTA 58.808 55.000 0.00 0.00 0.00 2.59
1409 4203 1.542492 ACTTGCTCCAAAGGCAGATG 58.458 50.000 0.00 0.00 40.90 2.90
1411 4205 2.158682 TGTTACTTGCTCCAAAGGCAGA 60.159 45.455 0.00 0.00 40.90 4.26
1554 4352 1.435408 GCTTCTCTTCGGATGCCTGC 61.435 60.000 0.00 0.00 32.49 4.85
1555 4353 0.107993 TGCTTCTCTTCGGATGCCTG 60.108 55.000 0.00 0.00 36.12 4.85
1688 4510 2.781945 AAGGAAAGACAAAGCTTGCG 57.218 45.000 0.00 0.00 0.00 4.85
1691 4513 9.967346 GTAATAAGAAAAGGAAAGACAAAGCTT 57.033 29.630 0.00 0.00 0.00 3.74
1699 4533 9.108111 TCACCCTAGTAATAAGAAAAGGAAAGA 57.892 33.333 0.00 0.00 0.00 2.52
1717 4552 9.179909 CCTATCAAGTACAGTATATCACCCTAG 57.820 40.741 0.00 0.00 0.00 3.02
1720 4555 6.210784 TGCCTATCAAGTACAGTATATCACCC 59.789 42.308 0.00 0.00 0.00 4.61
1721 4556 7.091443 GTGCCTATCAAGTACAGTATATCACC 58.909 42.308 0.00 0.00 0.00 4.02
1722 4557 6.802348 CGTGCCTATCAAGTACAGTATATCAC 59.198 42.308 0.00 1.23 0.00 3.06
1723 4558 6.569801 GCGTGCCTATCAAGTACAGTATATCA 60.570 42.308 0.00 0.00 0.00 2.15
1725 4560 5.477291 AGCGTGCCTATCAAGTACAGTATAT 59.523 40.000 0.00 0.00 0.00 0.86
1727 4562 3.637229 AGCGTGCCTATCAAGTACAGTAT 59.363 43.478 0.00 0.00 0.00 2.12
1728 4563 3.021695 AGCGTGCCTATCAAGTACAGTA 58.978 45.455 0.00 0.00 0.00 2.74
1729 4564 1.825474 AGCGTGCCTATCAAGTACAGT 59.175 47.619 0.00 0.00 0.00 3.55
1730 4565 2.586258 AGCGTGCCTATCAAGTACAG 57.414 50.000 0.00 0.00 0.00 2.74
1731 4566 2.734175 CGAAGCGTGCCTATCAAGTACA 60.734 50.000 0.00 0.00 0.00 2.90
1732 4567 1.852895 CGAAGCGTGCCTATCAAGTAC 59.147 52.381 0.00 0.00 0.00 2.73
1763 4598 3.402628 AGCAACGGACAAACAGATACT 57.597 42.857 0.00 0.00 0.00 2.12
1764 4599 4.243270 AGTAGCAACGGACAAACAGATAC 58.757 43.478 0.00 0.00 0.00 2.24
1769 4604 4.062677 AGTTAGTAGCAACGGACAAACA 57.937 40.909 0.00 0.00 33.50 2.83
1833 4670 3.562557 ACTTGTTACCAAAACTACAGGCG 59.437 43.478 0.00 0.00 0.00 5.52
1851 4688 7.121168 TGCTAAAGTGGATTTCCTCAATACTTG 59.879 37.037 0.00 0.00 36.82 3.16
1855 4692 6.721318 ACTGCTAAAGTGGATTTCCTCAATA 58.279 36.000 0.00 0.00 37.88 1.90
1867 4704 6.166279 TGATAGAGTTGAACTGCTAAAGTGG 58.834 40.000 0.90 0.00 39.81 4.00
1893 4730 5.541101 TGTAACCTGGAAGCTGAACTACTTA 59.459 40.000 0.00 0.00 0.00 2.24
1981 4822 4.365514 TGATGGCTGAACAAGGAAGTTA 57.634 40.909 0.00 0.00 0.00 2.24
1988 4829 3.119602 CCTCAACATGATGGCTGAACAAG 60.120 47.826 0.00 0.00 0.00 3.16
2021 4862 8.521170 ACTTATAGCAGATTGTACTGACACTA 57.479 34.615 0.00 0.00 39.94 2.74
2102 4943 6.723298 TTCTCCTCTCATCTTTGATACTCC 57.277 41.667 0.00 0.00 0.00 3.85
2141 4982 5.296780 TGCAGGAACTTTTGTAGAACTTCTG 59.703 40.000 1.17 0.00 34.60 3.02
2170 5011 3.679389 TGACATGCCTTTCTCCTCTTTC 58.321 45.455 0.00 0.00 0.00 2.62
2234 6336 2.096819 CCGGGATTTATGTTCACAACGG 59.903 50.000 0.00 0.00 0.00 4.44
2254 6356 2.715046 TGATGTGCCTCATTTGAGACC 58.285 47.619 9.15 1.00 44.74 3.85
2262 6364 5.651139 GGATATTGCTTATGATGTGCCTCAT 59.349 40.000 0.00 0.00 39.22 2.90
2299 6401 2.996631 AGCTTGGGATTGTCAGATGAC 58.003 47.619 6.01 6.01 44.97 3.06
2300 6402 3.614092 GAAGCTTGGGATTGTCAGATGA 58.386 45.455 2.10 0.00 0.00 2.92
2308 6410 3.652057 TTAGGAGGAAGCTTGGGATTG 57.348 47.619 2.10 0.00 0.00 2.67
2327 6429 0.853530 AGAGGGCCCACTTTGAGTTT 59.146 50.000 27.56 0.00 0.00 2.66
2340 6442 5.546621 TGGACTGTTATATGTAAGAGGGC 57.453 43.478 10.49 3.14 35.95 5.19
2342 6444 8.425577 CAGTTTGGACTGTTATATGTAAGAGG 57.574 38.462 10.49 0.00 46.57 3.69
2395 6497 9.150348 ACAAAACCTAGAACTTCAAACATTTTG 57.850 29.630 0.00 0.00 38.58 2.44
2469 6571 9.515226 AAGCTAATTTGGTGTTGTAGAGATTTA 57.485 29.630 0.00 0.00 0.00 1.40
2470 6572 8.409358 AAGCTAATTTGGTGTTGTAGAGATTT 57.591 30.769 0.00 0.00 0.00 2.17
2474 6576 6.801539 TGAAGCTAATTTGGTGTTGTAGAG 57.198 37.500 0.00 0.00 0.00 2.43
2476 6578 8.946085 TCTAATGAAGCTAATTTGGTGTTGTAG 58.054 33.333 0.29 0.00 0.00 2.74
2616 6720 4.810790 AGTTCTATGTTTGTCCTGAGACG 58.189 43.478 0.00 0.00 46.74 4.18
2617 6721 8.603242 TTAAAGTTCTATGTTTGTCCTGAGAC 57.397 34.615 0.00 0.00 43.83 3.36
2618 6722 9.793259 ATTTAAAGTTCTATGTTTGTCCTGAGA 57.207 29.630 0.00 0.00 0.00 3.27
2633 6737 9.908152 CCTCCGTTTCAAAATATTTAAAGTTCT 57.092 29.630 0.01 0.00 0.00 3.01
2634 6738 9.135843 CCCTCCGTTTCAAAATATTTAAAGTTC 57.864 33.333 0.01 0.00 0.00 3.01
2650 6754 0.395312 TGTTCCACTCCCTCCGTTTC 59.605 55.000 0.00 0.00 0.00 2.78
2659 6763 5.548406 ACTAGTTTACATGTGTTCCACTCC 58.452 41.667 9.11 0.00 35.11 3.85
2664 6768 8.943909 ATAGCTTACTAGTTTACATGTGTTCC 57.056 34.615 9.11 0.00 0.00 3.62
2665 6769 9.804758 AGATAGCTTACTAGTTTACATGTGTTC 57.195 33.333 9.11 0.00 0.00 3.18
2680 6784 5.273208 TCTTTGACCCTCAGATAGCTTACT 58.727 41.667 0.00 0.00 0.00 2.24
2685 6789 6.823689 TGTTTTATCTTTGACCCTCAGATAGC 59.176 38.462 0.00 0.00 0.00 2.97
2689 6793 7.461749 AGATTGTTTTATCTTTGACCCTCAGA 58.538 34.615 0.00 0.00 30.76 3.27
2692 6796 9.841880 GTTTAGATTGTTTTATCTTTGACCCTC 57.158 33.333 0.00 0.00 36.34 4.30
2693 6797 9.362151 TGTTTAGATTGTTTTATCTTTGACCCT 57.638 29.630 0.00 0.00 36.34 4.34
2759 6872 6.127563 TGTGGAATAAGATTCGCCGCTATATA 60.128 38.462 0.00 0.00 0.00 0.86
2760 6873 5.109903 GTGGAATAAGATTCGCCGCTATAT 58.890 41.667 0.00 0.00 0.00 0.86
2761 6874 4.021807 TGTGGAATAAGATTCGCCGCTATA 60.022 41.667 0.00 0.00 0.00 1.31
2762 6875 3.244078 TGTGGAATAAGATTCGCCGCTAT 60.244 43.478 0.00 0.00 0.00 2.97
2763 6876 2.101750 TGTGGAATAAGATTCGCCGCTA 59.898 45.455 0.00 0.00 0.00 4.26
2764 6877 1.134521 TGTGGAATAAGATTCGCCGCT 60.135 47.619 0.00 0.00 0.00 5.52
2765 6878 1.003866 GTGTGGAATAAGATTCGCCGC 60.004 52.381 0.00 0.00 0.00 6.53
2770 6883 3.187700 ACTCGCGTGTGGAATAAGATTC 58.812 45.455 13.75 0.00 0.00 2.52
2773 6886 1.542472 TGACTCGCGTGTGGAATAAGA 59.458 47.619 19.71 0.00 0.00 2.10
2775 6888 1.403647 CCTGACTCGCGTGTGGAATAA 60.404 52.381 19.71 0.00 0.00 1.40
2785 6898 2.439701 TACCCCTCCTGACTCGCG 60.440 66.667 0.00 0.00 0.00 5.87
2787 6900 1.455959 CCCTACCCCTCCTGACTCG 60.456 68.421 0.00 0.00 0.00 4.18
2823 6936 1.360192 GGCCAATTACCGCAGATGC 59.640 57.895 0.00 0.00 37.78 3.91
2824 6937 1.785041 CGGGCCAATTACCGCAGATG 61.785 60.000 4.39 0.00 43.96 2.90
2825 6938 1.525995 CGGGCCAATTACCGCAGAT 60.526 57.895 4.39 0.00 43.96 2.90
2837 6950 0.032615 AAAAATAGATGGGCGGGCCA 60.033 50.000 26.51 26.51 37.98 5.36
2838 6951 2.820845 AAAAATAGATGGGCGGGCC 58.179 52.632 14.65 14.65 0.00 5.80
2859 6972 8.160765 TCCCAAAACAAATGTGAAGATAGAGTA 58.839 33.333 0.00 0.00 0.00 2.59
2860 6973 7.004086 TCCCAAAACAAATGTGAAGATAGAGT 58.996 34.615 0.00 0.00 0.00 3.24
2871 6984 6.133356 TCTAGAACCTTCCCAAAACAAATGT 58.867 36.000 0.00 0.00 0.00 2.71
2889 7002 6.360370 AACAGTTCATGTAAGGCTCTAGAA 57.640 37.500 0.00 0.00 43.00 2.10
2890 7003 6.360370 AAACAGTTCATGTAAGGCTCTAGA 57.640 37.500 0.00 0.00 43.00 2.43
2891 7004 7.440523 AAAAACAGTTCATGTAAGGCTCTAG 57.559 36.000 0.00 0.00 43.00 2.43


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

AutoCloner maintained by Alex Coulton.