Multiple sequence alignment - TraesCS5B01G324700

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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 TraesCS5B01G324700 chr5B 100.000 3692 0 0 1 3692 508776182 508779873 0.000000e+00 6818
1 TraesCS5B01G324700 chr5B 85.590 576 39 20 1053 1590 548796621 548796052 6.920000e-157 564
2 TraesCS5B01G324700 chr5B 80.825 485 35 29 1053 1485 544198468 544197990 9.890000e-86 327
3 TraesCS5B01G324700 chr5B 93.373 166 10 1 1647 1811 548796056 548795891 1.020000e-60 244
4 TraesCS5B01G324700 chr5D 89.465 1927 106 27 1291 3186 422007650 422009510 0.000000e+00 2344
5 TraesCS5B01G324700 chr5D 89.514 1297 94 17 1 1272 422006310 422007589 0.000000e+00 1604
6 TraesCS5B01G324700 chr5D 91.927 384 23 5 3315 3692 422010370 422010751 7.020000e-147 531
7 TraesCS5B01G324700 chr5D 90.909 99 6 2 3184 3279 422010183 422010281 2.990000e-26 130
8 TraesCS5B01G324700 chr5A 90.873 1271 56 30 1921 3186 535567010 535568225 0.000000e+00 1650
9 TraesCS5B01G324700 chr5A 91.256 812 58 7 472 1272 535565392 535566201 0.000000e+00 1094
10 TraesCS5B01G324700 chr5A 85.410 658 48 17 1287 1920 535566266 535566899 1.120000e-179 640
11 TraesCS5B01G324700 chr5A 92.683 369 23 2 112 480 535564560 535564924 2.520000e-146 529
12 TraesCS5B01G324700 chr6B 84.264 591 34 29 1053 1590 532709474 532708890 4.230000e-144 521
13 TraesCS5B01G324700 chr6B 82.852 589 38 26 1058 1591 720341906 720341326 1.550000e-128 470
14 TraesCS5B01G324700 chr6B 83.087 473 47 16 2139 2589 46921272 46920811 2.070000e-107 399
15 TraesCS5B01G324700 chr6B 81.237 485 34 28 1053 1485 99587513 99587992 4.570000e-89 339
16 TraesCS5B01G324700 chr6B 85.659 258 22 9 1053 1295 711836646 711836903 1.320000e-64 257
17 TraesCS5B01G324700 chr6B 93.939 165 10 0 1647 1811 532708894 532708730 2.200000e-62 250
18 TraesCS5B01G324700 chr4A 83.821 581 35 28 1059 1586 713842021 713841447 7.120000e-137 497
19 TraesCS5B01G324700 chr4A 93.333 165 11 0 1647 1811 713841447 713841283 1.020000e-60 244
20 TraesCS5B01G324700 chr6A 83.418 591 39 26 1053 1590 573618194 573617610 9.210000e-136 494
21 TraesCS5B01G324700 chr6A 83.051 590 42 28 1053 1590 157000932 157001515 1.990000e-132 483
22 TraesCS5B01G324700 chr6A 93.939 165 9 1 1647 1811 573617614 573617451 7.920000e-62 248
23 TraesCS5B01G324700 chr4B 83.080 591 41 31 1053 1590 668389402 668389986 1.990000e-132 483
24 TraesCS5B01G324700 chr4B 92.857 168 12 0 1644 1811 603737558 603737725 1.020000e-60 244
25 TraesCS5B01G324700 chr4B 92.857 168 12 0 1644 1811 668389979 668390146 1.020000e-60 244
26 TraesCS5B01G324700 chr7B 82.653 588 42 27 1053 1586 312503105 312503686 2.010000e-127 466
27 TraesCS5B01G324700 chr7B 82.572 591 32 29 1053 1590 744983977 744984549 4.350000e-124 455
28 TraesCS5B01G324700 chr3A 82.624 587 43 29 1053 1586 688812656 688813236 7.220000e-127 464
29 TraesCS5B01G324700 chr3B 80.825 485 36 30 1053 1485 795400093 795400572 9.890000e-86 327
30 TraesCS5B01G324700 chr3B 93.865 163 10 0 1647 1809 41468441 41468279 2.850000e-61 246
31 TraesCS5B01G324700 chr1A 84.906 265 22 11 1053 1301 76840363 76840101 6.120000e-63 252


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 TraesCS5B01G324700 chr5B 508776182 508779873 3691 False 6818.00 6818 100.00000 1 3692 1 chr5B.!!$F1 3691
1 TraesCS5B01G324700 chr5B 548795891 548796621 730 True 404.00 564 89.48150 1053 1811 2 chr5B.!!$R2 758
2 TraesCS5B01G324700 chr5D 422006310 422010751 4441 False 1152.25 2344 90.45375 1 3692 4 chr5D.!!$F1 3691
3 TraesCS5B01G324700 chr5A 535564560 535568225 3665 False 978.25 1650 90.05550 112 3186 4 chr5A.!!$F1 3074
4 TraesCS5B01G324700 chr6B 720341326 720341906 580 True 470.00 470 82.85200 1058 1591 1 chr6B.!!$R2 533
5 TraesCS5B01G324700 chr6B 532708730 532709474 744 True 385.50 521 89.10150 1053 1811 2 chr6B.!!$R3 758
6 TraesCS5B01G324700 chr4A 713841283 713842021 738 True 370.50 497 88.57700 1059 1811 2 chr4A.!!$R1 752
7 TraesCS5B01G324700 chr6A 157000932 157001515 583 False 483.00 483 83.05100 1053 1590 1 chr6A.!!$F1 537
8 TraesCS5B01G324700 chr6A 573617451 573618194 743 True 371.00 494 88.67850 1053 1811 2 chr6A.!!$R1 758
9 TraesCS5B01G324700 chr4B 668389402 668390146 744 False 363.50 483 87.96850 1053 1811 2 chr4B.!!$F2 758
10 TraesCS5B01G324700 chr7B 312503105 312503686 581 False 466.00 466 82.65300 1053 1586 1 chr7B.!!$F1 533
11 TraesCS5B01G324700 chr7B 744983977 744984549 572 False 455.00 455 82.57200 1053 1590 1 chr7B.!!$F2 537
12 TraesCS5B01G324700 chr3A 688812656 688813236 580 False 464.00 464 82.62400 1053 1586 1 chr3A.!!$F1 533

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
906 1409 0.953471 TGTTTGGGCCACGATTCGAG 60.953 55.0 13.95 4.61 0.0 4.04 F
1272 1794 0.180878 TTCGCATGCCTGGATCATCA 59.819 50.0 13.15 0.00 0.0 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2340 3082 0.634465 ACAAACCTTTCCACCAGGGT 59.366 50.000 0.00 0.0 35.46 4.34 R
2693 3435 1.679944 CCACAGTGGTGCCCTTGATAG 60.680 57.143 11.99 0.0 43.88 2.08 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
22 23 2.747446 AGGTTTGATTATTGCGCGAGTT 59.253 40.909 12.10 0.00 0.00 3.01
26 27 6.259167 AGGTTTGATTATTGCGCGAGTTAATA 59.741 34.615 12.10 5.87 0.00 0.98
31 32 3.961477 ATTGCGCGAGTTAATAATGCA 57.039 38.095 12.10 0.00 0.00 3.96
35 36 2.601979 GCGCGAGTTAATAATGCATGCA 60.602 45.455 25.04 25.04 0.00 3.96
36 37 3.813800 CGCGAGTTAATAATGCATGCAT 58.186 40.909 27.46 27.46 38.46 3.96
37 38 4.668941 GCGCGAGTTAATAATGCATGCATA 60.669 41.667 32.36 20.21 35.31 3.14
38 39 5.017612 CGCGAGTTAATAATGCATGCATAG 58.982 41.667 32.36 11.17 35.31 2.23
60 61 1.066918 CGTACCGGTGCATAGGACC 59.933 63.158 23.00 0.00 0.00 4.46
219 220 1.271127 TGTCCCCGAATCTGATGGCA 61.271 55.000 0.00 0.00 0.00 4.92
230 231 2.821366 GATGGCACGGCTGACCAG 60.821 66.667 15.54 0.00 36.78 4.00
348 355 3.341848 CCGTACGGCTCGCTATCT 58.658 61.111 23.44 0.00 0.00 1.98
351 358 1.426423 CGTACGGCTCGCTATCTAGA 58.574 55.000 7.57 0.00 0.00 2.43
398 405 3.369756 GTGTCGTCGATCAGGCATAAAAA 59.630 43.478 0.00 0.00 0.00 1.94
415 422 6.291479 GCATAAAAACTCGTCTACATACGGTC 60.291 42.308 0.00 0.00 43.05 4.79
416 423 3.772060 AAACTCGTCTACATACGGTCC 57.228 47.619 0.00 0.00 43.05 4.46
432 439 1.204792 GTCCGCGTGTGCAAAAATTT 58.795 45.000 4.92 0.00 42.97 1.82
514 997 3.458163 CCGCCTTGACCTCGGCTA 61.458 66.667 0.00 0.00 44.11 3.93
621 1104 1.002134 CTTCCACCGGTCCAAGCAT 60.002 57.895 2.59 0.00 0.00 3.79
624 1107 2.819595 CACCGGTCCAAGCATCCG 60.820 66.667 2.59 0.00 43.30 4.18
642 1125 2.202623 GCGATTCGTGGCGTCTCT 60.203 61.111 8.03 0.00 0.00 3.10
696 1179 1.201965 GCAGTAACACGATCTTGCAGC 60.202 52.381 0.00 0.00 0.00 5.25
849 1352 1.268899 GGAGGGGACACGTCGTATATG 59.731 57.143 0.00 0.00 34.85 1.78
877 1380 4.883585 GGACATGTATGTATGGGCCATATG 59.116 45.833 27.97 22.76 41.95 1.78
898 1401 1.227527 GCCTGTTTGTTTGGGCCAC 60.228 57.895 5.23 0.00 38.77 5.01
906 1409 0.953471 TGTTTGGGCCACGATTCGAG 60.953 55.000 13.95 4.61 0.00 4.04
945 1448 1.000955 TCTCAAAGGGAAGAGTGTCGC 59.999 52.381 0.00 0.00 33.63 5.19
958 1464 3.114065 GAGTGTCGCGAACCCTAATAAG 58.886 50.000 12.06 0.00 0.00 1.73
967 1473 3.982058 CGAACCCTAATAAGCGATCTGTC 59.018 47.826 0.00 0.00 0.00 3.51
991 1497 4.489771 AAATCCGCCGCCAGGGAG 62.490 66.667 0.00 0.00 38.47 4.30
1116 1622 4.475135 GCGCCAGTCCCTTCCTCC 62.475 72.222 0.00 0.00 0.00 4.30
1130 1639 2.123077 CTCCTCCTCCGCCTCCAT 60.123 66.667 0.00 0.00 0.00 3.41
1231 1740 4.096003 GCGAGGTAAGCCCCTGCA 62.096 66.667 0.00 0.00 41.13 4.41
1272 1794 0.180878 TTCGCATGCCTGGATCATCA 59.819 50.000 13.15 0.00 0.00 3.07
1279 1801 1.224075 GCCTGGATCATCACATGACG 58.776 55.000 0.00 0.00 43.01 4.35
1284 1873 2.101415 TGGATCATCACATGACGAGACC 59.899 50.000 0.00 0.00 43.01 3.85
1288 1877 0.683179 ATCACATGACGAGACCCCGA 60.683 55.000 0.00 0.00 0.00 5.14
1334 1934 1.003928 TGATTCAGATGGCAGTGCACT 59.996 47.619 15.25 15.25 0.00 4.40
1430 2033 1.800586 CAGCTGCGTACATCAAACAGT 59.199 47.619 0.00 0.00 0.00 3.55
1431 2034 2.993220 CAGCTGCGTACATCAAACAGTA 59.007 45.455 0.00 0.00 0.00 2.74
1432 2035 3.431912 CAGCTGCGTACATCAAACAGTAA 59.568 43.478 0.00 0.00 0.00 2.24
1433 2036 4.062293 AGCTGCGTACATCAAACAGTAAA 58.938 39.130 0.00 0.00 0.00 2.01
1564 2167 4.498345 GCTAATTCTCAGTCGACCGAGATT 60.498 45.833 27.49 21.81 38.06 2.40
1571 2174 3.254903 TCAGTCGACCGAGATTTTCTTGA 59.745 43.478 13.01 1.58 29.08 3.02
1591 2194 9.658799 TTCTTGAGTCTAGATTGATTTTTCGAT 57.341 29.630 5.09 0.00 0.00 3.59
1592 2195 9.091784 TCTTGAGTCTAGATTGATTTTTCGATG 57.908 33.333 0.00 0.00 0.00 3.84
1593 2196 8.777865 TTGAGTCTAGATTGATTTTTCGATGT 57.222 30.769 0.00 0.00 0.00 3.06
1618 2221 9.480053 GTATCTCTACATATATAGACGGACCTC 57.520 40.741 0.00 0.00 0.00 3.85
1673 2290 5.106673 GGGAAGACGAGGAATGTTTACTTTG 60.107 44.000 0.00 0.00 0.00 2.77
1850 2478 9.965824 CCTTTTGTATCATTACTCTTTTGTGTT 57.034 29.630 0.00 0.00 0.00 3.32
1860 2488 5.116069 ACTCTTTTGTGTTGTCGTTTTGT 57.884 34.783 0.00 0.00 0.00 2.83
1861 2489 5.525199 ACTCTTTTGTGTTGTCGTTTTGTT 58.475 33.333 0.00 0.00 0.00 2.83
1948 2686 4.127566 AGATTAAATTGCATGTGGGTGC 57.872 40.909 0.00 0.00 45.25 5.01
1997 2735 2.961062 AGCATTTGAAGTGCACCTTTCT 59.039 40.909 14.63 0.00 44.87 2.52
2012 2750 4.399303 CACCTTTCTGTTTTCACCTTGAGT 59.601 41.667 0.00 0.00 0.00 3.41
2013 2751 5.016831 ACCTTTCTGTTTTCACCTTGAGTT 58.983 37.500 0.00 0.00 0.00 3.01
2034 2772 8.370940 TGAGTTCTTACTGTCAGAATTCATTCT 58.629 33.333 19.64 7.56 40.28 2.40
2038 2776 9.730705 TTCTTACTGTCAGAATTCATTCTTGAT 57.269 29.630 6.91 0.00 44.28 2.57
2039 2777 9.159364 TCTTACTGTCAGAATTCATTCTTGATG 57.841 33.333 6.91 2.93 44.28 3.07
2058 2796 7.815840 TTGATGTGACAAGAGTAAATTGGAA 57.184 32.000 0.00 0.00 31.76 3.53
2078 2816 5.104360 TGGAATTAGCTGGAGCAAATCTACT 60.104 40.000 0.00 0.00 45.16 2.57
2086 2824 2.223433 GGAGCAAATCTACTGTGCATGC 60.223 50.000 11.82 11.82 40.83 4.06
2104 2842 4.747108 GCATGCTGGTTAGTAGTATGACAG 59.253 45.833 11.37 0.00 39.63 3.51
2105 2843 5.451937 GCATGCTGGTTAGTAGTATGACAGA 60.452 44.000 11.37 0.00 39.63 3.41
2127 2865 8.817100 ACAGATGTATATGTTGTGTATTTCGTG 58.183 33.333 0.00 0.00 0.00 4.35
2141 2879 6.364165 GTGTATTTCGTGTACAAGTAGAAGCA 59.636 38.462 8.68 5.55 34.15 3.91
2162 2900 4.826183 GCATTGCTTCCTAAAGATCTCCAT 59.174 41.667 0.16 0.00 34.14 3.41
2250 2992 6.542821 ACTGTGAACAATGGATCTTTTCCTA 58.457 36.000 0.00 0.00 45.68 2.94
2255 2997 7.595130 GTGAACAATGGATCTTTTCCTACAAAC 59.405 37.037 0.00 0.00 45.68 2.93
2268 3010 2.811431 CCTACAAACGGAATGAACAGCA 59.189 45.455 0.00 0.00 0.00 4.41
2340 3082 1.850377 CAACACGAAAATGCAAGCCA 58.150 45.000 0.00 0.00 0.00 4.75
2486 3228 4.201705 GCAAAAATGTAATGCACCATTCCG 60.202 41.667 8.13 3.08 39.81 4.30
2534 3276 6.808704 GGTCTCCTTGAAAATACAGATTTTGC 59.191 38.462 0.56 0.00 43.76 3.68
2587 3329 1.610038 CAGCATCCTTGTCTGTTGCAA 59.390 47.619 0.00 0.00 35.79 4.08
2627 3369 2.567497 CTGGGCTTGGTGGCACAAG 61.567 63.158 20.82 19.75 45.50 3.16
2693 3435 2.109126 GCAACTCAGGGCGATGACC 61.109 63.158 0.00 0.00 0.00 4.02
2700 3442 1.688735 TCAGGGCGATGACCTATCAAG 59.311 52.381 0.00 0.00 40.42 3.02
2722 3464 2.281070 CCACTGTGGTCAGCGCTT 60.281 61.111 18.76 0.00 44.77 4.68
2811 3553 3.679389 AGGCTTGTGTTCTCCTGTTATG 58.321 45.455 0.00 0.00 0.00 1.90
2839 3582 0.472044 TGTTGCTACAGTTGGCTCCA 59.528 50.000 0.00 0.00 0.00 3.86
2862 3609 6.875195 CCATGGCAAGAAAAATAGTGAACAAT 59.125 34.615 0.00 0.00 0.00 2.71
2889 3636 0.532573 TAGAAGAAGACTGCGGCTGG 59.467 55.000 11.64 2.14 0.00 4.85
2932 3679 1.554392 CATTCTGAAGTCTCGCGAGG 58.446 55.000 33.98 17.89 0.00 4.63
2998 3745 3.090952 TGGCCGTTTCTGTTGATTTTG 57.909 42.857 0.00 0.00 0.00 2.44
2999 3746 2.690497 TGGCCGTTTCTGTTGATTTTGA 59.310 40.909 0.00 0.00 0.00 2.69
3033 3780 1.055338 GCGACACAAGATGCAAAAGC 58.945 50.000 0.00 0.00 0.00 3.51
3046 3793 6.694447 AGATGCAAAAGCTGTACATCAAATT 58.306 32.000 17.72 0.09 39.64 1.82
3060 3807 8.278639 TGTACATCAAATTCATAAGGGGTGTAT 58.721 33.333 0.00 0.00 0.00 2.29
3143 3890 2.842394 ATCACGCCCAGCTGAAGTCG 62.842 60.000 17.39 14.43 0.00 4.18
3153 3900 3.070018 CAGCTGAAGTCGATGAAAACCT 58.930 45.455 8.42 0.00 0.00 3.50
3190 4612 5.111293 CCCATCTGGTTGTTTTATCAATGC 58.889 41.667 0.00 0.00 0.00 3.56
3198 4620 6.700960 TGGTTGTTTTATCAATGCTGTTCAAG 59.299 34.615 0.00 0.00 0.00 3.02
3224 4646 4.764823 TGGCACTAAACCACTAAAAGATGG 59.235 41.667 0.00 0.00 42.13 3.51
3265 4687 2.806244 GCCTTCGTCTGCTTAAAACAGA 59.194 45.455 4.19 4.19 41.78 3.41
3274 4696 6.791887 TCTGCTTAAAACAGACATCAGAAG 57.208 37.500 4.19 0.00 39.21 2.85
3298 4735 4.561105 CTCTTCACCAACAGTTCTCCTAC 58.439 47.826 0.00 0.00 0.00 3.18
3299 4736 3.323979 TCTTCACCAACAGTTCTCCTACC 59.676 47.826 0.00 0.00 0.00 3.18
3300 4737 1.616865 TCACCAACAGTTCTCCTACCG 59.383 52.381 0.00 0.00 0.00 4.02
3301 4738 1.343465 CACCAACAGTTCTCCTACCGT 59.657 52.381 0.00 0.00 0.00 4.83
3302 4739 1.617357 ACCAACAGTTCTCCTACCGTC 59.383 52.381 0.00 0.00 0.00 4.79
3303 4740 1.067071 CCAACAGTTCTCCTACCGTCC 60.067 57.143 0.00 0.00 0.00 4.79
3304 4741 1.893801 CAACAGTTCTCCTACCGTCCT 59.106 52.381 0.00 0.00 0.00 3.85
3305 4742 3.087031 CAACAGTTCTCCTACCGTCCTA 58.913 50.000 0.00 0.00 0.00 2.94
3306 4743 2.720915 ACAGTTCTCCTACCGTCCTAC 58.279 52.381 0.00 0.00 0.00 3.18
3317 4754 1.752498 ACCGTCCTACGCATGTCATAA 59.248 47.619 0.00 0.00 40.91 1.90
3319 4756 2.794910 CCGTCCTACGCATGTCATAAAG 59.205 50.000 0.00 0.00 40.91 1.85
3357 4843 9.539825 AAGTTGTTAGATCACATAGTCATCATC 57.460 33.333 0.00 0.00 0.00 2.92
3411 4899 6.711277 ACTGTTTATTCAGCTATCTCAACCA 58.289 36.000 0.00 0.00 38.84 3.67
3438 4926 3.283751 CAAAGGGCCAACGAATATACCA 58.716 45.455 6.18 0.00 0.00 3.25
3467 4956 4.846779 TGTGATACAAAAAGGACCAAGC 57.153 40.909 0.00 0.00 0.00 4.01
3482 4971 7.872113 AGGACCAAGCTATTTTGATTCTTAG 57.128 36.000 0.00 0.00 0.00 2.18
3485 4974 8.184848 GGACCAAGCTATTTTGATTCTTAGAAC 58.815 37.037 0.00 0.00 0.00 3.01
3486 4975 8.635765 ACCAAGCTATTTTGATTCTTAGAACA 57.364 30.769 0.00 0.00 0.00 3.18
3487 4976 8.734386 ACCAAGCTATTTTGATTCTTAGAACAG 58.266 33.333 0.00 0.00 0.00 3.16
3488 4977 8.950210 CCAAGCTATTTTGATTCTTAGAACAGA 58.050 33.333 0.00 0.00 0.00 3.41
3489 4978 9.985318 CAAGCTATTTTGATTCTTAGAACAGAG 57.015 33.333 0.00 0.00 0.00 3.35
3491 4980 7.281999 AGCTATTTTGATTCTTAGAACAGAGGC 59.718 37.037 0.00 0.00 0.00 4.70
3498 4988 2.299013 TCTTAGAACAGAGGCGCAAAGA 59.701 45.455 10.83 0.81 0.00 2.52
3522 5012 6.114187 TCGATCCATTTGGTATTCTAGCAT 57.886 37.500 0.00 0.00 35.91 3.79
3533 5023 7.136822 TGGTATTCTAGCATGTAGACCAAAT 57.863 36.000 0.00 0.00 0.00 2.32
3545 5035 9.109393 GCATGTAGACCAAATGATAAAAGAGTA 57.891 33.333 0.00 0.00 0.00 2.59
3559 5049 8.922676 TGATAAAAGAGTACAGAAAATCGTCAC 58.077 33.333 0.00 0.00 0.00 3.67
3593 5085 1.896465 AGAAGCAGAACTTAGCGAGGT 59.104 47.619 0.00 0.00 39.29 3.85
3598 5090 2.686915 GCAGAACTTAGCGAGGTAGGTA 59.313 50.000 0.00 0.00 0.00 3.08
3619 5111 3.558931 TGTCCAAGAAACAAGCTCTCA 57.441 42.857 0.00 0.00 0.00 3.27
3630 5122 1.002888 CAAGCTCTCACTCCATGGTGT 59.997 52.381 13.73 13.73 38.28 4.16
3636 5128 2.432146 TCTCACTCCATGGTGTAGCATC 59.568 50.000 18.69 0.00 38.28 3.91
3663 5155 1.251527 ACCCTGAGCTGACGACGAAT 61.252 55.000 0.00 0.00 0.00 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 7.886191 TTATTAACTCGCGCAATAATCAAAC 57.114 32.000 8.75 0.00 0.00 2.93
8 9 5.996219 TGCATTATTAACTCGCGCAATAAT 58.004 33.333 8.75 12.07 35.99 1.28
14 15 1.971962 GCATGCATTATTAACTCGCGC 59.028 47.619 14.21 0.00 0.00 6.86
214 215 4.415150 CCTGGTCAGCCGTGCCAT 62.415 66.667 0.00 0.00 37.67 4.40
258 259 2.106938 GTCGCCGATGATCAGCCA 59.893 61.111 5.18 0.00 0.00 4.75
293 300 0.109643 CGACATGTTCGTCCGGTACA 60.110 55.000 0.00 2.50 43.24 2.90
348 355 4.713553 TGGATGAAAACTTGCAGTGTCTA 58.286 39.130 0.00 0.00 0.00 2.59
351 358 3.890756 TGATGGATGAAAACTTGCAGTGT 59.109 39.130 0.00 0.00 0.00 3.55
374 381 1.934220 ATGCCTGATCGACGACACGT 61.934 55.000 0.00 0.00 45.10 4.49
398 405 1.293924 CGGACCGTATGTAGACGAGT 58.706 55.000 5.48 0.00 45.82 4.18
415 422 4.854291 TCTAATAAATTTTTGCACACGCGG 59.146 37.500 12.47 1.27 42.97 6.46
416 423 5.983790 TCTAATAAATTTTTGCACACGCG 57.016 34.783 3.53 3.53 42.97 6.01
470 477 3.176924 AGGAACTCAAGGTCAGCTCTA 57.823 47.619 0.00 0.00 0.00 2.43
597 1080 0.395312 TGGACCGGTGGAAGAAAGAC 59.605 55.000 14.63 0.00 0.00 3.01
624 1107 3.255379 GAGACGCCACGAATCGCC 61.255 66.667 1.15 0.00 0.00 5.54
632 1115 2.179517 CCGAGACAGAGACGCCAC 59.820 66.667 0.00 0.00 0.00 5.01
642 1125 1.080093 GTCGACAATGGCCGAGACA 60.080 57.895 11.55 0.00 35.31 3.41
696 1179 1.882198 CAACAATAACCGCTGCTTCG 58.118 50.000 0.00 0.00 0.00 3.79
752 1235 1.672854 ATCGATCGCCGTCCTCCAAA 61.673 55.000 11.09 0.00 39.75 3.28
757 1240 3.661131 CGGATCGATCGCCGTCCT 61.661 66.667 21.50 0.00 42.49 3.85
849 1352 3.476552 CCCATACATACATGTCCACCAC 58.523 50.000 0.00 0.00 41.97 4.16
851 1354 2.504367 GCCCATACATACATGTCCACC 58.496 52.381 0.00 0.00 41.97 4.61
852 1355 2.158682 TGGCCCATACATACATGTCCAC 60.159 50.000 0.00 0.00 41.97 4.02
877 1380 1.367471 GCCCAAACAAACAGGCCTC 59.633 57.895 0.00 0.00 39.60 4.70
898 1401 2.202566 GGGCCTAAAGAACTCGAATCG 58.797 52.381 0.84 0.00 0.00 3.34
945 1448 3.978687 ACAGATCGCTTATTAGGGTTCG 58.021 45.455 0.00 0.00 37.83 3.95
991 1497 1.465689 CGGAATGTCCATTGTTCGTGC 60.466 52.381 0.00 0.00 35.91 5.34
1039 1545 3.072468 CGCCGGGGAGTAGTCCAA 61.072 66.667 14.46 0.00 46.07 3.53
1116 1622 2.519541 TCGATGGAGGCGGAGGAG 60.520 66.667 0.00 0.00 0.00 3.69
1231 1740 4.689612 ACAGACACAGATTACCAGTTGT 57.310 40.909 0.00 0.00 0.00 3.32
1272 1794 0.175760 CAATCGGGGTCTCGTCATGT 59.824 55.000 0.00 0.00 0.00 3.21
1279 1801 4.141914 ACAGATCTAAACAATCGGGGTCTC 60.142 45.833 0.00 0.00 0.00 3.36
1284 1873 5.671493 ACCTTACAGATCTAAACAATCGGG 58.329 41.667 0.00 0.00 0.00 5.14
1288 1877 6.979238 GCGTCTACCTTACAGATCTAAACAAT 59.021 38.462 0.00 0.00 0.00 2.71
1334 1934 2.100584 ACAAAAGACGCAAATGCTTCCA 59.899 40.909 8.11 0.00 39.79 3.53
1347 1948 2.735823 CCAGCTGCAAGAACAAAAGAC 58.264 47.619 8.66 0.00 34.07 3.01
1430 2033 2.368548 TCAGGAGCTTGTCTGCACTTTA 59.631 45.455 7.52 0.00 35.33 1.85
1431 2034 1.141657 TCAGGAGCTTGTCTGCACTTT 59.858 47.619 7.52 0.00 35.33 2.66
1432 2035 0.761187 TCAGGAGCTTGTCTGCACTT 59.239 50.000 7.52 0.00 35.33 3.16
1433 2036 0.034616 GTCAGGAGCTTGTCTGCACT 59.965 55.000 7.52 0.00 35.33 4.40
1471 2074 3.547746 TGTTATGGAAACCCCGAATAGC 58.452 45.455 0.00 0.00 37.93 2.97
1564 2167 9.489084 TCGAAAAATCAATCTAGACTCAAGAAA 57.511 29.630 0.00 0.00 0.00 2.52
1591 2194 8.990203 AGGTCCGTCTATATATGTAGAGATACA 58.010 37.037 9.28 0.00 31.39 2.29
1592 2195 9.480053 GAGGTCCGTCTATATATGTAGAGATAC 57.520 40.741 9.28 7.63 31.39 2.24
1593 2196 8.358895 CGAGGTCCGTCTATATATGTAGAGATA 58.641 40.741 9.28 0.00 31.39 1.98
1595 2198 6.571605 CGAGGTCCGTCTATATATGTAGAGA 58.428 44.000 9.28 2.56 31.66 3.10
1596 2199 6.831727 CGAGGTCCGTCTATATATGTAGAG 57.168 45.833 9.28 4.74 31.66 2.43
1618 2221 5.005299 GGAAGAACAACAAAATTGGTCAACG 59.995 40.000 7.40 0.00 38.54 4.10
1736 2354 2.447244 AGTGGTTTCTGCTCTCTTCG 57.553 50.000 0.00 0.00 0.00 3.79
1816 2438 6.913170 AGTAATGATACAAAAGGTGCACTTG 58.087 36.000 17.98 15.64 35.47 3.16
1861 2489 8.855110 TGATTATTAGCACTTTCTCCACAAAAA 58.145 29.630 0.00 0.00 0.00 1.94
1997 2735 6.177610 ACAGTAAGAACTCAAGGTGAAAACA 58.822 36.000 0.00 0.00 31.97 2.83
2012 2750 9.730705 ATCAAGAATGAATTCTGACAGTAAGAA 57.269 29.630 2.51 2.51 45.83 2.52
2013 2751 9.159364 CATCAAGAATGAATTCTGACAGTAAGA 57.841 33.333 7.05 0.00 45.83 2.10
2034 2772 7.815840 TTCCAATTTACTCTTGTCACATCAA 57.184 32.000 0.00 0.00 0.00 2.57
2038 2776 7.665559 AGCTAATTCCAATTTACTCTTGTCACA 59.334 33.333 0.00 0.00 0.00 3.58
2039 2777 7.965107 CAGCTAATTCCAATTTACTCTTGTCAC 59.035 37.037 0.00 0.00 0.00 3.67
2058 2796 5.121811 CACAGTAGATTTGCTCCAGCTAAT 58.878 41.667 7.81 7.81 46.11 1.73
2078 2816 4.161377 TCATACTACTAACCAGCATGCACA 59.839 41.667 21.98 0.00 31.97 4.57
2105 2843 9.589111 TGTACACGAAATACACAACATATACAT 57.411 29.630 0.00 0.00 0.00 2.29
2124 2862 3.679980 AGCAATGCTTCTACTTGTACACG 59.320 43.478 0.00 0.00 33.89 4.49
2141 2879 5.832060 CCAATGGAGATCTTTAGGAAGCAAT 59.168 40.000 0.00 0.00 32.75 3.56
2185 2927 7.068962 ACATCATGCAATTAGGAATGATGAACA 59.931 33.333 23.97 0.00 44.67 3.18
2250 2992 2.571212 TCTGCTGTTCATTCCGTTTGT 58.429 42.857 0.00 0.00 0.00 2.83
2255 2997 2.086869 ACCAATCTGCTGTTCATTCCG 58.913 47.619 0.00 0.00 0.00 4.30
2268 3010 4.622220 GCCTGCAAAATGATGAACCAATCT 60.622 41.667 0.00 0.00 0.00 2.40
2340 3082 0.634465 ACAAACCTTTCCACCAGGGT 59.366 50.000 0.00 0.00 35.46 4.34
2534 3276 2.124403 GCCCAGCATCCCAGACAG 60.124 66.667 0.00 0.00 0.00 3.51
2627 3369 3.142174 AGCAAGTCACTTCCTTTGTAGC 58.858 45.455 0.00 0.00 0.00 3.58
2662 3404 3.341823 CTGAGTTGCTATTGCCTTCAGT 58.658 45.455 12.85 0.00 36.28 3.41
2693 3435 1.679944 CCACAGTGGTGCCCTTGATAG 60.680 57.143 11.99 0.00 43.88 2.08
2722 3464 5.305902 TCCAAATAATATGTGCGGTCTCCTA 59.694 40.000 0.00 0.00 0.00 2.94
2775 3517 5.049828 CACAAGCCTCGACAATGTCATATA 58.950 41.667 14.24 0.00 32.09 0.86
2776 3518 3.873361 CACAAGCCTCGACAATGTCATAT 59.127 43.478 14.24 0.00 32.09 1.78
2781 3523 1.873591 GAACACAAGCCTCGACAATGT 59.126 47.619 0.00 0.00 0.00 2.71
2839 3582 9.995003 TTAATTGTTCACTATTTTTCTTGCCAT 57.005 25.926 0.00 0.00 0.00 4.40
2862 3609 5.523916 GCCGCAGTCTTCTTCTATCAATTAA 59.476 40.000 0.00 0.00 0.00 1.40
2889 3636 1.680207 GCCATTCAATCTCAAGCCTCC 59.320 52.381 0.00 0.00 0.00 4.30
2998 3745 2.768492 CGCCTTTGCCCAGCATCTC 61.768 63.158 0.00 0.00 38.76 2.75
2999 3746 2.753043 CGCCTTTGCCCAGCATCT 60.753 61.111 0.00 0.00 38.76 2.90
3033 3780 6.603201 ACACCCCTTATGAATTTGATGTACAG 59.397 38.462 0.33 0.00 0.00 2.74
3046 3793 4.471747 TGCTACACAATACACCCCTTATGA 59.528 41.667 0.00 0.00 0.00 2.15
3060 3807 3.181490 CCGATACTGCTACTGCTACACAA 60.181 47.826 0.00 0.00 40.48 3.33
3190 4612 3.568538 GTTTAGTGCCATGCTTGAACAG 58.431 45.455 0.22 0.00 0.00 3.16
3198 4620 4.217550 TCTTTTAGTGGTTTAGTGCCATGC 59.782 41.667 0.00 0.00 38.40 4.06
3203 4625 4.157840 CCCCATCTTTTAGTGGTTTAGTGC 59.842 45.833 0.00 0.00 33.55 4.40
3265 4687 1.980765 TGGTGAAGAGGCTTCTGATGT 59.019 47.619 0.00 0.00 32.79 3.06
3271 4693 2.262423 ACTGTTGGTGAAGAGGCTTC 57.738 50.000 0.00 0.00 0.00 3.86
3273 4695 1.771255 AGAACTGTTGGTGAAGAGGCT 59.229 47.619 0.00 0.00 0.00 4.58
3274 4696 2.147150 GAGAACTGTTGGTGAAGAGGC 58.853 52.381 0.00 0.00 0.00 4.70
3298 4735 2.502213 TTATGACATGCGTAGGACGG 57.498 50.000 0.00 0.00 42.82 4.79
3299 4736 3.242944 CACTTTATGACATGCGTAGGACG 59.757 47.826 0.00 0.00 45.88 4.79
3300 4737 3.001330 GCACTTTATGACATGCGTAGGAC 59.999 47.826 0.00 0.00 0.00 3.85
3301 4738 3.194861 GCACTTTATGACATGCGTAGGA 58.805 45.455 0.00 0.00 0.00 2.94
3302 4739 2.935849 TGCACTTTATGACATGCGTAGG 59.064 45.455 0.00 0.00 41.07 3.18
3303 4740 4.801147 ATGCACTTTATGACATGCGTAG 57.199 40.909 0.00 0.00 41.07 3.51
3304 4741 4.394610 ACAATGCACTTTATGACATGCGTA 59.605 37.500 0.00 0.00 41.07 4.42
3305 4742 3.191162 ACAATGCACTTTATGACATGCGT 59.809 39.130 0.00 0.00 41.07 5.24
3306 4743 3.761657 ACAATGCACTTTATGACATGCG 58.238 40.909 0.00 0.00 41.07 4.73
3317 4754 7.744087 TCTAACAACTTCATACAATGCACTT 57.256 32.000 0.00 0.00 0.00 3.16
3319 4756 7.693951 GTGATCTAACAACTTCATACAATGCAC 59.306 37.037 0.00 0.00 0.00 4.57
3357 4843 4.634443 TCTTGAAGAGATGCATGTCATGTG 59.366 41.667 24.25 10.95 35.05 3.21
3452 4941 6.478512 TCAAAATAGCTTGGTCCTTTTTGT 57.521 33.333 0.00 0.00 36.17 2.83
3459 4948 7.865706 TCTAAGAATCAAAATAGCTTGGTCC 57.134 36.000 0.00 0.00 0.00 4.46
3460 4949 8.730680 TGTTCTAAGAATCAAAATAGCTTGGTC 58.269 33.333 0.00 0.00 0.00 4.02
3462 4951 8.950210 TCTGTTCTAAGAATCAAAATAGCTTGG 58.050 33.333 0.00 0.00 0.00 3.61
3463 4952 9.985318 CTCTGTTCTAAGAATCAAAATAGCTTG 57.015 33.333 0.00 0.00 0.00 4.01
3467 4956 7.625553 CGCCTCTGTTCTAAGAATCAAAATAG 58.374 38.462 0.00 0.00 0.00 1.73
3482 4971 0.371645 CGATCTTTGCGCCTCTGTTC 59.628 55.000 4.18 0.00 0.00 3.18
3485 4974 0.857935 GATCGATCTTTGCGCCTCTG 59.142 55.000 18.29 0.00 0.00 3.35
3486 4975 0.249657 GGATCGATCTTTGCGCCTCT 60.250 55.000 23.96 0.00 0.00 3.69
3487 4976 0.530650 TGGATCGATCTTTGCGCCTC 60.531 55.000 23.96 5.56 0.00 4.70
3488 4977 0.107456 ATGGATCGATCTTTGCGCCT 59.893 50.000 23.96 0.00 0.00 5.52
3489 4978 0.947244 AATGGATCGATCTTTGCGCC 59.053 50.000 23.96 7.69 0.00 6.53
3491 4980 2.355756 ACCAAATGGATCGATCTTTGCG 59.644 45.455 24.32 20.52 38.94 4.85
3498 4988 6.114187 TGCTAGAATACCAAATGGATCGAT 57.886 37.500 6.42 0.00 38.94 3.59
3522 5012 9.653287 CTGTACTCTTTTATCATTTGGTCTACA 57.347 33.333 0.00 0.00 0.00 2.74
3533 5023 8.922676 GTGACGATTTTCTGTACTCTTTTATCA 58.077 33.333 0.00 0.00 0.00 2.15
3545 5035 8.455682 TCAAAGTTTTTAGTGACGATTTTCTGT 58.544 29.630 0.00 0.00 0.00 3.41
3559 5049 8.917415 AGTTCTGCTTCTTTCAAAGTTTTTAG 57.083 30.769 0.00 0.00 0.00 1.85
3593 5085 5.248477 AGAGCTTGTTTCTTGGACATACCTA 59.752 40.000 0.00 0.00 39.86 3.08
3598 5090 3.817647 GTGAGAGCTTGTTTCTTGGACAT 59.182 43.478 0.00 0.00 0.00 3.06
3619 5111 0.465705 CCGATGCTACACCATGGAGT 59.534 55.000 21.47 20.17 28.73 3.85
3663 5155 1.343142 TGAGTTGTTCTCGGCTGCTAA 59.657 47.619 0.00 0.00 45.46 3.09


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

AutoCloner maintained by Alex Coulton.