Multiple sequence alignment - TraesCS6D01G161700

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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 TraesCS6D01G161700 chr6D 100.000 7028 0 0 1 7028 140081734 140088761 0.000000e+00 12979.0
1 TraesCS6D01G161700 chr6D 91.461 527 35 9 6511 7028 116854652 116854127 0.000000e+00 715.0
2 TraesCS6D01G161700 chr6D 92.222 90 3 4 5127 5213 1551880 1551792 2.660000e-24 124.0
3 TraesCS6D01G161700 chr6D 93.878 49 3 0 2897 2945 56935178 56935226 2.720000e-09 75.0
4 TraesCS6D01G161700 chr6D 79.612 103 9 11 2831 2929 372948617 372948711 5.890000e-06 63.9
5 TraesCS6D01G161700 chr6B 95.614 4811 159 28 1 4787 240037360 240042142 0.000000e+00 7668.0
6 TraesCS6D01G161700 chr6B 94.673 1483 50 11 4786 6264 240042171 240043628 0.000000e+00 2274.0
7 TraesCS6D01G161700 chr6B 96.154 78 2 1 6413 6490 240043835 240043911 7.400000e-25 126.0
8 TraesCS6D01G161700 chr6A 95.649 3631 101 21 810 4428 183379455 183375870 0.000000e+00 5777.0
9 TraesCS6D01G161700 chr6A 93.824 1020 40 8 5386 6400 183369497 183368496 0.000000e+00 1513.0
10 TraesCS6D01G161700 chr6A 91.115 529 41 4 6506 7028 78006848 78006320 0.000000e+00 712.0
11 TraesCS6D01G161700 chr6A 87.679 560 59 5 277 828 183383035 183382478 1.650000e-180 643.0
12 TraesCS6D01G161700 chr6A 98.780 246 3 0 4417 4662 183370855 183370610 8.370000e-119 438.0
13 TraesCS6D01G161700 chr6A 91.270 252 21 1 27 278 183383367 183383117 6.750000e-90 342.0
14 TraesCS6D01G161700 chr6A 98.507 134 2 0 4654 4787 183369668 183369535 3.280000e-58 237.0
15 TraesCS6D01G161700 chr6A 94.444 90 5 0 6401 6490 183368433 183368344 9.510000e-29 139.0
16 TraesCS6D01G161700 chr6A 100.000 31 0 0 1 31 183533174 183533144 2.740000e-04 58.4
17 TraesCS6D01G161700 chr1A 91.802 1659 110 15 1858 3502 13912118 13913764 0.000000e+00 2287.0
18 TraesCS6D01G161700 chr1A 93.777 1141 54 8 3558 4697 13913765 13914889 0.000000e+00 1698.0
19 TraesCS6D01G161700 chr1A 91.254 949 55 9 5464 6399 13915514 13916447 0.000000e+00 1267.0
20 TraesCS6D01G161700 chr1A 94.307 404 21 2 3529 3931 13898785 13899187 1.000000e-172 617.0
21 TraesCS6D01G161700 chr1A 87.695 512 28 17 1040 1548 13903689 13904168 1.320000e-156 564.0
22 TraesCS6D01G161700 chr1A 91.247 377 30 2 4786 5159 13914989 13915365 1.750000e-140 510.0
23 TraesCS6D01G161700 chr1A 87.050 278 28 1 1 278 13902467 13902736 2.460000e-79 307.0
24 TraesCS6D01G161700 chr1A 86.742 264 17 1 1597 1860 13904450 13904695 1.930000e-70 278.0
25 TraesCS6D01G161700 chr1A 94.194 155 9 0 5203 5357 13915365 13915519 3.280000e-58 237.0
26 TraesCS6D01G161700 chr1A 84.536 97 12 3 2833 2926 539874232 539874136 7.510000e-15 93.5
27 TraesCS6D01G161700 chr5D 91.825 526 38 4 6507 7028 370461514 370460990 0.000000e+00 728.0
28 TraesCS6D01G161700 chr5D 91.699 518 37 4 6512 7028 242974203 242974715 0.000000e+00 713.0
29 TraesCS6D01G161700 chr5D 82.609 184 21 6 2822 3002 406358005 406357830 1.220000e-32 152.0
30 TraesCS6D01G161700 chr3D 91.939 521 34 7 6516 7028 531258992 531259512 0.000000e+00 723.0
31 TraesCS6D01G161700 chr3D 91.304 529 39 6 6506 7028 89805858 89806385 0.000000e+00 715.0
32 TraesCS6D01G161700 chr3D 90.722 97 8 1 2865 2961 47653625 47653530 2.060000e-25 128.0
33 TraesCS6D01G161700 chr3D 82.000 150 20 7 2806 2951 563049543 563049689 3.440000e-23 121.0
34 TraesCS6D01G161700 chr3D 91.209 91 5 3 5127 5214 609945054 609944964 3.440000e-23 121.0
35 TraesCS6D01G161700 chr2D 91.731 520 39 4 6511 7028 376325039 376325556 0.000000e+00 719.0
36 TraesCS6D01G161700 chr2D 94.186 86 3 2 5127 5210 534925546 534925461 5.720000e-26 130.0
37 TraesCS6D01G161700 chr2D 95.181 83 2 2 5127 5207 643235827 643235909 5.720000e-26 130.0
38 TraesCS6D01G161700 chr1D 92.054 516 32 7 6515 7028 78119155 78118647 0.000000e+00 717.0
39 TraesCS6D01G161700 chr2A 91.205 523 42 4 6509 7028 655847102 655847623 0.000000e+00 708.0
40 TraesCS6D01G161700 chr7A 79.960 499 89 9 277 771 693808879 693809370 2.410000e-94 357.0
41 TraesCS6D01G161700 chr3B 88.462 130 12 3 2828 2955 74891945 74892073 3.390000e-33 154.0
42 TraesCS6D01G161700 chr3B 94.118 85 3 2 5127 5209 372246378 372246294 2.060000e-25 128.0
43 TraesCS6D01G161700 chr3B 93.023 86 6 0 5128 5213 246157532 246157447 7.400000e-25 126.0
44 TraesCS6D01G161700 chr5B 82.209 163 19 7 2861 3023 487252707 487252555 1.590000e-26 132.0
45 TraesCS6D01G161700 chr5B 92.105 38 2 1 4448 4484 655029307 655029270 1.300000e-02 52.8
46 TraesCS6D01G161700 chr1B 96.250 80 3 0 5128 5207 580632877 580632956 1.590000e-26 132.0
47 TraesCS6D01G161700 chr4A 96.250 80 2 1 5127 5206 703339202 703339124 5.720000e-26 130.0
48 TraesCS6D01G161700 chr4A 86.585 82 9 2 2840 2919 40869204 40869123 9.710000e-14 89.8
49 TraesCS6D01G161700 chr5A 91.304 92 5 2 5127 5216 3296080 3296170 9.570000e-24 122.0
50 TraesCS6D01G161700 chr7D 80.916 131 18 7 2806 2931 76629921 76630049 5.800000e-16 97.1
51 TraesCS6D01G161700 chr7D 79.231 130 15 10 2823 2945 571003636 571003760 5.840000e-11 80.5
52 TraesCS6D01G161700 chr7D 79.279 111 19 4 2825 2931 76569951 76570061 2.720000e-09 75.0
53 TraesCS6D01G161700 chr7B 81.746 126 14 7 2825 2942 23412001 23412125 5.800000e-16 97.1
54 TraesCS6D01G161700 chr4B 100.000 30 0 0 2922 2951 635043240 635043269 1.000000e-03 56.5
55 TraesCS6D01G161700 chrUn 92.105 38 2 1 4448 4484 309639049 309639012 1.300000e-02 52.8
56 TraesCS6D01G161700 chrUn 92.105 38 2 1 4448 4484 320342874 320342837 1.300000e-02 52.8
57 TraesCS6D01G161700 chrUn 92.105 38 2 1 4448 4484 381254585 381254622 1.300000e-02 52.8
58 TraesCS6D01G161700 chrUn 92.105 38 2 1 4448 4484 397859841 397859804 1.300000e-02 52.8


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 TraesCS6D01G161700 chr6D 140081734 140088761 7027 False 12979.00 12979 100.000000 1 7028 1 chr6D.!!$F2 7027
1 TraesCS6D01G161700 chr6D 116854127 116854652 525 True 715.00 715 91.461000 6511 7028 1 chr6D.!!$R2 517
2 TraesCS6D01G161700 chr6B 240037360 240043911 6551 False 3356.00 7668 95.480333 1 6490 3 chr6B.!!$F1 6489
3 TraesCS6D01G161700 chr6A 183375870 183383367 7497 True 2254.00 5777 91.532667 27 4428 3 chr6A.!!$R4 4401
4 TraesCS6D01G161700 chr6A 78006320 78006848 528 True 712.00 712 91.115000 6506 7028 1 chr6A.!!$R1 522
5 TraesCS6D01G161700 chr6A 183368344 183370855 2511 True 581.75 1513 96.388750 4417 6490 4 chr6A.!!$R3 2073
6 TraesCS6D01G161700 chr1A 13912118 13916447 4329 False 1199.80 2287 92.454800 1858 6399 5 chr1A.!!$F2 4541
7 TraesCS6D01G161700 chr1A 13898785 13904695 5910 False 441.50 617 88.948500 1 3931 4 chr1A.!!$F1 3930
8 TraesCS6D01G161700 chr5D 370460990 370461514 524 True 728.00 728 91.825000 6507 7028 1 chr5D.!!$R1 521
9 TraesCS6D01G161700 chr5D 242974203 242974715 512 False 713.00 713 91.699000 6512 7028 1 chr5D.!!$F1 516
10 TraesCS6D01G161700 chr3D 531258992 531259512 520 False 723.00 723 91.939000 6516 7028 1 chr3D.!!$F2 512
11 TraesCS6D01G161700 chr3D 89805858 89806385 527 False 715.00 715 91.304000 6506 7028 1 chr3D.!!$F1 522
12 TraesCS6D01G161700 chr2D 376325039 376325556 517 False 719.00 719 91.731000 6511 7028 1 chr2D.!!$F1 517
13 TraesCS6D01G161700 chr1D 78118647 78119155 508 True 717.00 717 92.054000 6515 7028 1 chr1D.!!$R1 513
14 TraesCS6D01G161700 chr2A 655847102 655847623 521 False 708.00 708 91.205000 6509 7028 1 chr2A.!!$F1 519

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
699 4466 0.890542 TGAGATGCTTGTGTGGGTGC 60.891 55.000 0.00 0.0 0.00 5.01 F
765 4549 1.040646 CTATGACGGCAGGGCTTAGA 58.959 55.000 0.00 0.0 0.00 2.10 F
1176 8144 2.027192 TCCGATGTTAGCTTCTTTGGCT 60.027 45.455 0.00 0.0 43.02 4.75 F
2631 9905 0.607217 TGAGTCTCGGGTCGTTAGCA 60.607 55.000 0.00 0.0 0.00 3.49 F
3014 10299 2.159114 AGACTTTTTGCGTGCATGGTTT 60.159 40.909 8.27 0.0 0.00 3.27 F
4899 13176 3.325870 TGGTTCACGTAATCTCAAGCAG 58.674 45.455 0.00 0.0 0.00 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1702 8930 0.909133 TGCCTAGGAGATGCACACCA 60.909 55.000 14.75 0.0 0.00 4.17 R
1705 8933 1.117994 CTCTGCCTAGGAGATGCACA 58.882 55.000 14.75 0.0 33.03 4.57 R
2817 10094 0.179032 ATTCCCACAGCAACACACGA 60.179 50.000 0.00 0.0 0.00 4.35 R
3489 10780 1.378882 GATCAATCAGCCCAAGCGCA 61.379 55.000 11.47 0.0 46.67 6.09 R
4957 13234 1.145738 AGAACTGTTGCAGGAATGGGT 59.854 47.619 0.00 0.0 35.51 4.51 R
6614 15090 0.302288 CGAAAGCGGACACAAAACGA 59.698 50.000 0.00 0.0 0.00 3.85 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
206 3890 3.719924 ACAAACAACCACATGCAGATTG 58.280 40.909 0.00 0.00 0.00 2.67
210 3894 1.542472 CAACCACATGCAGATTGCTCA 59.458 47.619 2.48 0.00 45.31 4.26
361 4128 1.152333 AAAGGGAAGTTGGGGTGGC 60.152 57.895 0.00 0.00 0.00 5.01
425 4192 1.003233 GTTGGCGGAAGAAGGAGCT 60.003 57.895 0.00 0.00 0.00 4.09
428 4195 2.267324 GCGGAAGAAGGAGCTGCT 59.733 61.111 0.00 0.00 0.00 4.24
502 4269 1.663379 CCGCGTGAGGTAGACCATGA 61.663 60.000 4.92 0.00 38.89 3.07
518 4285 4.751060 ACCATGACGAGCGAGTATTTTTA 58.249 39.130 0.00 0.00 0.00 1.52
588 4355 2.035832 CGAAAAGGCACCCATGTTTTCT 59.964 45.455 12.42 0.00 36.95 2.52
635 4402 1.358725 GCGAGCTAACGAACATGGCA 61.359 55.000 0.00 0.00 35.09 4.92
680 4447 6.952358 TGTAGACTCCTTAACTAGTCCAACAT 59.048 38.462 0.00 0.00 42.56 2.71
687 4454 5.525378 CCTTAACTAGTCCAACATGAGATGC 59.475 44.000 0.00 0.00 0.00 3.91
688 4455 4.833478 AACTAGTCCAACATGAGATGCT 57.167 40.909 0.00 0.00 0.00 3.79
690 4457 4.511527 ACTAGTCCAACATGAGATGCTTG 58.488 43.478 0.00 0.00 0.00 4.01
695 4462 2.094906 CCAACATGAGATGCTTGTGTGG 60.095 50.000 0.00 0.00 35.32 4.17
696 4463 1.830279 ACATGAGATGCTTGTGTGGG 58.170 50.000 0.00 0.00 34.00 4.61
699 4466 0.890542 TGAGATGCTTGTGTGGGTGC 60.891 55.000 0.00 0.00 0.00 5.01
700 4467 1.589716 GAGATGCTTGTGTGGGTGCC 61.590 60.000 0.00 0.00 0.00 5.01
765 4549 1.040646 CTATGACGGCAGGGCTTAGA 58.959 55.000 0.00 0.00 0.00 2.10
779 4563 2.370189 GGCTTAGAGCACCCTACATGAT 59.630 50.000 0.00 0.00 44.75 2.45
792 4576 8.629158 GCACCCTACATGATAATTGTTTAATGA 58.371 33.333 0.00 0.00 0.00 2.57
837 7667 7.790782 AAATAGAAATCCTTTGGCCAGTTTA 57.209 32.000 5.11 0.00 0.00 2.01
894 7724 2.782922 ACATCCACCATATACACCCCA 58.217 47.619 0.00 0.00 0.00 4.96
1096 8064 2.727392 CCGCATCCCGTTCCAGGTA 61.727 63.158 0.00 0.00 34.38 3.08
1166 8134 2.096013 GGTTTTGCTCTCCGATGTTAGC 59.904 50.000 0.00 0.00 35.51 3.09
1176 8144 2.027192 TCCGATGTTAGCTTCTTTGGCT 60.027 45.455 0.00 0.00 43.02 4.75
1227 8195 2.035674 GTGTTCGTCGATTAGTCATGCG 60.036 50.000 0.00 0.00 0.00 4.73
1397 8366 6.812998 TGCTATTCTTGTAGGGTGTGTATAC 58.187 40.000 0.00 0.00 0.00 1.47
1447 8418 8.682936 AGATTGATATGGTTGAGGTAATGAAC 57.317 34.615 0.00 0.00 0.00 3.18
1512 8488 2.245159 TTGGCTCATAGAATCCTGCG 57.755 50.000 0.00 0.00 0.00 5.18
1682 8910 4.699735 TCACCGATGCAAACTATTGTGAAT 59.300 37.500 0.00 0.00 38.85 2.57
1705 8933 3.072476 CCTGTAGCCAGCAGTGGT 58.928 61.111 0.00 0.00 46.96 4.16
1765 9011 1.227205 CGGCTCACATCTCTCAGGC 60.227 63.158 0.00 0.00 0.00 4.85
1850 9096 3.099438 CGGAAGCGACGCTAGAGA 58.901 61.111 24.77 0.00 38.25 3.10
1851 9097 1.428219 CGGAAGCGACGCTAGAGAA 59.572 57.895 24.77 0.00 38.25 2.87
1867 9113 2.812591 AGAGAAACTGCAATGCTGACAG 59.187 45.455 18.78 3.89 34.67 3.51
2109 9381 8.459394 ACCATTCCATTCCATAATATTCCTTCT 58.541 33.333 0.00 0.00 0.00 2.85
2135 9407 5.008712 CCAAACAAACTCTAGAACTGTTCCC 59.991 44.000 16.48 0.00 30.16 3.97
2217 9489 5.071250 ACCAAACGCACCCATAGAGAATATA 59.929 40.000 0.00 0.00 0.00 0.86
2234 9506 6.435164 AGAATATAGTTGGGGATTTGCTTGT 58.565 36.000 0.00 0.00 0.00 3.16
2395 9667 7.396906 TCCCTTTCCCTTTCCGTATTATATT 57.603 36.000 0.00 0.00 0.00 1.28
2467 9741 9.174166 ACATTGTAATCTTTAACCTGGTATCAC 57.826 33.333 0.00 0.00 0.00 3.06
2468 9742 9.173021 CATTGTAATCTTTAACCTGGTATCACA 57.827 33.333 0.00 0.00 0.00 3.58
2469 9743 9.747898 ATTGTAATCTTTAACCTGGTATCACAA 57.252 29.630 0.00 0.00 0.00 3.33
2470 9744 8.786826 TGTAATCTTTAACCTGGTATCACAAG 57.213 34.615 0.00 0.00 0.00 3.16
2471 9745 8.380099 TGTAATCTTTAACCTGGTATCACAAGT 58.620 33.333 0.00 0.00 0.00 3.16
2472 9746 9.880157 GTAATCTTTAACCTGGTATCACAAGTA 57.120 33.333 0.00 0.00 0.00 2.24
2514 9788 8.545472 ACTACAACATGAGGCTATTTAACCTAA 58.455 33.333 0.00 0.00 36.05 2.69
2545 9819 4.826733 TGTGTTAAGTGTGCCAGAATGAAT 59.173 37.500 0.00 0.00 39.69 2.57
2631 9905 0.607217 TGAGTCTCGGGTCGTTAGCA 60.607 55.000 0.00 0.00 0.00 3.49
2721 9998 7.012894 TGGTGTTTATTTCAAGTTCGAGTCAAT 59.987 33.333 0.00 0.00 0.00 2.57
2738 10015 2.219903 TCAATGCCGTAATATTGTCGCG 59.780 45.455 0.00 0.00 36.09 5.87
2817 10094 6.352516 CATTTTCAGTTGCTAGAGGATACCT 58.647 40.000 0.00 0.00 36.03 3.08
3014 10299 2.159114 AGACTTTTTGCGTGCATGGTTT 60.159 40.909 8.27 0.00 0.00 3.27
3615 10907 5.070981 TCACATCCTAATTCATGTCTCCTCC 59.929 44.000 0.00 0.00 30.48 4.30
3691 10983 7.139392 GTGTGTTTATCACTTTTCCCTCTTTC 58.861 38.462 0.00 0.00 46.27 2.62
3747 11041 7.502561 GGTATAAAGATATTGCCACAAGAACCT 59.497 37.037 0.00 0.00 0.00 3.50
3890 11184 4.384940 AGCTCTTTTTGTCCTCTTCTGAC 58.615 43.478 0.00 0.00 0.00 3.51
3907 11201 7.060421 TCTTCTGACTTTCTGGGTTTTGTAAT 58.940 34.615 0.00 0.00 0.00 1.89
4147 11441 4.574828 TCTTTTATTCTATTCAGGGCGTGC 59.425 41.667 1.51 0.00 0.00 5.34
4447 11742 7.640597 ATTTAGAATTAGTAGCGGGCTTTTT 57.359 32.000 0.00 0.00 0.00 1.94
4899 13176 3.325870 TGGTTCACGTAATCTCAAGCAG 58.674 45.455 0.00 0.00 0.00 4.24
4957 13234 3.088532 ACAATAGCTTCCGGATTGCAAA 58.911 40.909 25.27 16.16 34.55 3.68
5123 13401 3.631145 TCTTTTGCATCAGTGTCTTGC 57.369 42.857 8.03 8.03 36.91 4.01
5131 13411 0.681733 TCAGTGTCTTGCAGTCCCTC 59.318 55.000 0.00 0.00 0.00 4.30
5236 13516 2.752354 TGTGGGAATATTTGTTGGCTCG 59.248 45.455 0.00 0.00 0.00 5.03
5381 13661 6.434340 ACATAATTGTCCCTCAGAAAAAGGTC 59.566 38.462 0.00 0.00 31.51 3.85
5410 13690 5.756347 TGTGGGATATCGTCCTTAATTTTCG 59.244 40.000 0.00 0.00 46.91 3.46
5512 13792 9.851686 ATAAAGTGTCTAATTAGCCATCATCAA 57.148 29.630 7.67 0.00 0.00 2.57
5749 14032 7.865706 AGTGTGCTAATTACTTAGGGAAATG 57.134 36.000 2.42 0.00 35.79 2.32
5810 14093 4.517285 TGTCCAAGACCAGCTGAAATATC 58.483 43.478 17.39 4.59 0.00 1.63
5826 14109 8.165428 GCTGAAATATCATCTAAATGTACTCGC 58.835 37.037 0.00 0.00 34.37 5.03
5827 14110 8.534333 TGAAATATCATCTAAATGTACTCGCC 57.466 34.615 0.00 0.00 34.32 5.54
5829 14112 6.859112 ATATCATCTAAATGTACTCGCCCT 57.141 37.500 0.00 0.00 34.32 5.19
5830 14113 5.552870 ATCATCTAAATGTACTCGCCCTT 57.447 39.130 0.00 0.00 34.32 3.95
5832 14115 5.116180 TCATCTAAATGTACTCGCCCTTTG 58.884 41.667 0.00 0.00 34.32 2.77
5833 14116 3.267483 TCTAAATGTACTCGCCCTTTGC 58.733 45.455 0.00 0.00 0.00 3.68
5834 14117 1.173913 AAATGTACTCGCCCTTTGCC 58.826 50.000 0.00 0.00 36.24 4.52
5835 14118 0.037590 AATGTACTCGCCCTTTGCCA 59.962 50.000 0.00 0.00 36.24 4.92
5836 14119 0.676782 ATGTACTCGCCCTTTGCCAC 60.677 55.000 0.00 0.00 36.24 5.01
5837 14120 1.302192 GTACTCGCCCTTTGCCACA 60.302 57.895 0.00 0.00 36.24 4.17
5838 14121 0.887387 GTACTCGCCCTTTGCCACAA 60.887 55.000 0.00 0.00 36.24 3.33
5839 14122 0.179015 TACTCGCCCTTTGCCACAAA 60.179 50.000 0.00 0.00 36.24 2.83
5840 14123 1.040339 ACTCGCCCTTTGCCACAAAA 61.040 50.000 0.00 0.00 36.24 2.44
5841 14124 0.318120 CTCGCCCTTTGCCACAAAAT 59.682 50.000 0.00 0.00 36.24 1.82
5876 14159 7.177890 TGGTACAATTGGATCGAGTAATTCGG 61.178 42.308 10.83 0.00 42.91 4.30
5893 14176 3.587797 TCGGTCGTTCTTCTAGCAATT 57.412 42.857 0.00 0.00 0.00 2.32
5968 14262 5.670485 TGAGCTTCTTAATTTATCGGCAGA 58.330 37.500 0.00 0.00 0.00 4.26
5972 14266 8.000780 AGCTTCTTAATTTATCGGCAGATTTT 57.999 30.769 4.22 0.16 38.26 1.82
6000 14294 1.074951 GGTGGTGGAAGTGAAGGGG 59.925 63.158 0.00 0.00 0.00 4.79
6044 14338 7.894708 TGTGTATGACATGTTTTTGGATCATT 58.105 30.769 0.00 0.00 0.00 2.57
6087 14381 2.002586 CGTTGACTAAGGCATCCACTG 58.997 52.381 0.00 0.00 0.00 3.66
6192 14486 5.724328 TGGATCTCTGTGATGTAACTTGTC 58.276 41.667 0.00 0.00 35.14 3.18
6277 14686 6.610830 TGGTTCAAGCAATATTACCCATCATT 59.389 34.615 0.00 0.00 0.00 2.57
6299 14708 2.796593 GCCGTAAACAAGTCACGTTACT 59.203 45.455 0.00 0.00 33.93 2.24
6308 14717 0.032952 GTCACGTTACTGGACCAGCA 59.967 55.000 21.95 5.73 34.37 4.41
6387 14796 2.357154 CGAGGGATTTGGGGATGAACTT 60.357 50.000 0.00 0.00 0.00 2.66
6390 14799 3.273084 AGGGATTTGGGGATGAACTTGAT 59.727 43.478 0.00 0.00 0.00 2.57
6411 14882 4.274794 TCTAGGGTTCTTGTATAGCCCA 57.725 45.455 0.00 0.00 41.67 5.36
6420 14891 4.929479 TCTTGTATAGCCCAACAATGGTT 58.071 39.130 0.00 0.00 46.01 3.67
6495 14966 3.895025 CAGCCGTTGGATGGTCTG 58.105 61.111 0.00 0.00 35.19 3.51
6496 14967 1.003355 CAGCCGTTGGATGGTCTGT 60.003 57.895 0.00 0.00 35.19 3.41
6497 14968 1.021390 CAGCCGTTGGATGGTCTGTC 61.021 60.000 0.00 0.00 35.19 3.51
6498 14969 1.745489 GCCGTTGGATGGTCTGTCC 60.745 63.158 0.00 0.00 36.26 4.02
6499 14970 1.447838 CCGTTGGATGGTCTGTCCG 60.448 63.158 0.00 0.00 38.64 4.79
6500 14971 1.292223 CGTTGGATGGTCTGTCCGT 59.708 57.895 0.00 0.00 38.64 4.69
6501 14972 0.320421 CGTTGGATGGTCTGTCCGTT 60.320 55.000 0.00 0.00 38.64 4.44
6502 14973 1.067425 CGTTGGATGGTCTGTCCGTTA 60.067 52.381 0.00 0.00 38.64 3.18
6503 14974 2.610976 CGTTGGATGGTCTGTCCGTTAA 60.611 50.000 0.00 0.00 38.64 2.01
6504 14975 2.740447 GTTGGATGGTCTGTCCGTTAAC 59.260 50.000 0.00 0.00 38.64 2.01
6505 14976 2.253610 TGGATGGTCTGTCCGTTAACT 58.746 47.619 3.71 0.00 38.64 2.24
6506 14977 2.028476 TGGATGGTCTGTCCGTTAACTG 60.028 50.000 3.71 0.00 38.64 3.16
6507 14978 2.232941 GGATGGTCTGTCCGTTAACTGA 59.767 50.000 3.71 0.00 39.52 3.41
6508 14979 3.118738 GGATGGTCTGTCCGTTAACTGAT 60.119 47.826 3.71 0.00 39.52 2.90
6509 14980 3.587797 TGGTCTGTCCGTTAACTGATC 57.412 47.619 3.71 0.00 39.52 2.92
6510 14981 2.232941 TGGTCTGTCCGTTAACTGATCC 59.767 50.000 3.71 5.57 39.52 3.36
6511 14982 2.496470 GGTCTGTCCGTTAACTGATCCT 59.504 50.000 3.71 0.00 31.06 3.24
6512 14983 3.698040 GGTCTGTCCGTTAACTGATCCTA 59.302 47.826 3.71 0.00 31.06 2.94
6513 14984 4.159135 GGTCTGTCCGTTAACTGATCCTAA 59.841 45.833 3.71 0.00 31.06 2.69
6554 15030 1.929860 TATCCTGTCCGGTCCCGTCT 61.930 60.000 0.00 0.00 37.81 4.18
6614 15090 2.159156 GGGAAGCAAACGGACTTTTGTT 60.159 45.455 3.71 0.00 38.51 2.83
6856 15342 3.362797 AGTTCGGACGCGAGCTCA 61.363 61.111 15.93 0.00 0.00 4.26
6871 15357 4.285790 TCACCCAGCCCCTTCCCT 62.286 66.667 0.00 0.00 0.00 4.20
6942 15428 2.510906 CGGATTTGGGGCGGATCT 59.489 61.111 0.00 0.00 0.00 2.75
6946 15432 0.395724 GATTTGGGGCGGATCTGGTT 60.396 55.000 3.14 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
110 3794 9.360093 CTCGTATTCTTGTTCAACTCTTCTATT 57.640 33.333 0.00 0.00 0.00 1.73
206 3890 2.368439 TGGCCAACATCATTACTGAGC 58.632 47.619 0.61 0.00 34.12 4.26
361 4128 0.788391 GGTTCAACGGTTGCTCTACG 59.212 55.000 15.89 0.00 0.00 3.51
415 4182 0.767375 TTGGTCAGCAGCTCCTTCTT 59.233 50.000 0.00 0.00 0.00 2.52
443 4210 2.292267 CCAAGAACGGCAGAGCAATAT 58.708 47.619 0.00 0.00 0.00 1.28
502 4269 4.171754 GGACTGTAAAAATACTCGCTCGT 58.828 43.478 0.00 0.00 0.00 4.18
588 4355 1.621317 TCCACATTGACGGCTGACTTA 59.379 47.619 0.00 0.00 0.00 2.24
635 4402 3.151022 GCCGCCTCCTGCTACTCT 61.151 66.667 0.00 0.00 38.05 3.24
680 4447 0.890542 GCACCCACACAAGCATCTCA 60.891 55.000 0.00 0.00 0.00 3.27
687 4454 1.152777 TTCCTGGCACCCACACAAG 60.153 57.895 0.00 0.00 0.00 3.16
688 4455 1.152777 CTTCCTGGCACCCACACAA 60.153 57.895 0.00 0.00 0.00 3.33
690 4457 0.328258 ATACTTCCTGGCACCCACAC 59.672 55.000 0.00 0.00 0.00 3.82
695 4462 3.877508 GACATAACATACTTCCTGGCACC 59.122 47.826 0.00 0.00 0.00 5.01
696 4463 3.555956 CGACATAACATACTTCCTGGCAC 59.444 47.826 0.00 0.00 0.00 5.01
699 4466 4.508124 GCTTCGACATAACATACTTCCTGG 59.492 45.833 0.00 0.00 0.00 4.45
700 4467 5.109210 TGCTTCGACATAACATACTTCCTG 58.891 41.667 0.00 0.00 0.00 3.86
765 4549 8.632679 CATTAAACAATTATCATGTAGGGTGCT 58.367 33.333 0.00 0.00 0.00 4.40
837 7667 7.148306 GGTGTGTATACGGTTGATCAGAAAAAT 60.148 37.037 0.00 0.00 0.00 1.82
894 7724 2.094545 CCTGCCTTGCTCGCTAATTTTT 60.095 45.455 0.00 0.00 0.00 1.94
1166 8134 1.074752 GCGAGAGACAGCCAAAGAAG 58.925 55.000 0.00 0.00 0.00 2.85
1176 8144 2.039818 ATCTTAGTCCGCGAGAGACA 57.960 50.000 8.23 0.00 36.68 3.41
1272 8240 4.074970 CACATGAACCATAATCCTAGGCC 58.925 47.826 2.96 0.00 0.00 5.19
1447 8418 5.326200 AGAACGGTTCCACTACATTCTAG 57.674 43.478 16.84 0.00 0.00 2.43
1497 8473 3.068732 TCCACTTCGCAGGATTCTATGAG 59.931 47.826 0.00 0.00 0.00 2.90
1512 8488 3.821033 AGCACATGGTTAAGTTCCACTTC 59.179 43.478 0.00 0.00 39.51 3.01
1700 8928 1.198713 CCTAGGAGATGCACACCACT 58.801 55.000 1.05 0.00 0.00 4.00
1702 8930 0.909133 TGCCTAGGAGATGCACACCA 60.909 55.000 14.75 0.00 0.00 4.17
1705 8933 1.117994 CTCTGCCTAGGAGATGCACA 58.882 55.000 14.75 0.00 33.03 4.57
1748 8994 1.227205 CGCCTGAGAGATGTGAGCC 60.227 63.158 0.00 0.00 0.00 4.70
1850 9096 1.985473 TCCTGTCAGCATTGCAGTTT 58.015 45.000 11.91 0.00 31.03 2.66
1851 9097 1.985473 TTCCTGTCAGCATTGCAGTT 58.015 45.000 11.91 0.00 31.03 3.16
1867 9113 9.406828 GTAAACAAGATAAATCCAACAGTTTCC 57.593 33.333 0.00 0.00 0.00 3.13
1982 9236 5.485620 ACCTCTAGCACATGCATGTATATG 58.514 41.667 30.92 19.68 45.16 1.78
2109 9381 6.764560 GGAACAGTTCTAGAGTTTGTTTGGTA 59.235 38.462 13.13 0.00 32.58 3.25
2217 9489 1.341080 CCACAAGCAAATCCCCAACT 58.659 50.000 0.00 0.00 0.00 3.16
2395 9667 1.596934 CTACAGAGAGCGGGGCAAA 59.403 57.895 0.00 0.00 0.00 3.68
2493 9767 7.630082 TGAGTTAGGTTAAATAGCCTCATGTT 58.370 34.615 0.00 0.00 38.01 2.71
2514 9788 3.403038 GCACACTTAACACAGGATGAGT 58.597 45.455 0.00 0.00 43.33 3.41
2545 9819 2.756400 CAGCTGTACCCTGGCCAA 59.244 61.111 7.01 0.00 0.00 4.52
2631 9905 2.158559 TCTGCATGCAAATGGTAACGT 58.841 42.857 22.88 0.00 42.51 3.99
2721 9998 1.202203 GACGCGACAATATTACGGCA 58.798 50.000 15.93 0.00 0.00 5.69
2738 10015 7.608308 ATTCATCTTACAAAGAGAAGCAGAC 57.392 36.000 0.00 0.00 41.61 3.51
2795 10072 5.978814 GAGGTATCCTCTAGCAACTGAAAA 58.021 41.667 8.38 0.00 46.41 2.29
2817 10094 0.179032 ATTCCCACAGCAACACACGA 60.179 50.000 0.00 0.00 0.00 4.35
3004 10289 1.334960 CCTCAACGTGAAACCATGCAC 60.335 52.381 0.00 0.00 0.00 4.57
3014 10299 2.847234 AGGCCCACCTCAACGTGA 60.847 61.111 0.00 0.00 46.34 4.35
3032 10317 2.235016 AGCAACTACGCATGGGAAAAA 58.765 42.857 17.76 0.00 0.00 1.94
3441 10729 7.667219 ACTGTCTTTGTCACCAAGATTTCATAT 59.333 33.333 0.00 0.00 0.00 1.78
3489 10780 1.378882 GATCAATCAGCCCAAGCGCA 61.379 55.000 11.47 0.00 46.67 6.09
3691 10983 8.644318 ACTAGAAAATATAACACAAGTAGGCG 57.356 34.615 0.00 0.00 0.00 5.52
3747 11041 5.009631 CACTTCCAATACCCTGAAATCACA 58.990 41.667 0.00 0.00 0.00 3.58
3890 11184 8.550376 CAAACATGAATTACAAAACCCAGAAAG 58.450 33.333 0.00 0.00 0.00 2.62
3931 11225 7.861629 TCTGTTCTTGGGACATATCAATTAGT 58.138 34.615 0.00 0.00 39.30 2.24
4043 11337 6.049149 GCTAACATGAAAGGATGCTACTACA 58.951 40.000 0.00 0.00 0.00 2.74
4147 11441 5.381174 TGGAGAATTGATTTGCAGAACAG 57.619 39.130 0.00 0.00 0.00 3.16
4807 13084 4.160329 CCTAATGCTCCTATAGGTGTCCA 58.840 47.826 18.51 10.51 36.34 4.02
4885 13162 9.900710 ATAGATACTTAACTGCTTGAGATTACG 57.099 33.333 0.00 0.00 0.00 3.18
4925 13202 6.371548 TCCGGAAGCTATTGTTATCATTATGC 59.628 38.462 0.00 0.00 0.00 3.14
4957 13234 1.145738 AGAACTGTTGCAGGAATGGGT 59.854 47.619 0.00 0.00 35.51 4.51
5067 13344 7.884816 ATGATGTTTTTCAAAGCATTCAGAG 57.115 32.000 3.48 0.00 39.47 3.35
5175 13455 9.765795 CCCTCTGTAAAGAAATATAAGATCGTT 57.234 33.333 0.00 0.00 0.00 3.85
5176 13456 9.144298 TCCCTCTGTAAAGAAATATAAGATCGT 57.856 33.333 0.00 0.00 0.00 3.73
5177 13457 9.632807 CTCCCTCTGTAAAGAAATATAAGATCG 57.367 37.037 0.00 0.00 0.00 3.69
5193 13473 9.090103 CCACATATAAAAGATACTCCCTCTGTA 57.910 37.037 0.00 0.00 0.00 2.74
5216 13496 3.013921 TCGAGCCAACAAATATTCCCAC 58.986 45.455 0.00 0.00 0.00 4.61
5236 13516 7.454260 ACTGAAATTCCTGTCCATTAACTTC 57.546 36.000 0.00 0.00 0.00 3.01
5381 13661 2.135664 GGACGATATCCCACAAGACG 57.864 55.000 0.00 0.00 42.46 4.18
5410 13690 0.961019 TGGTTTGATGCAGCAAGGAC 59.039 50.000 17.90 13.78 0.00 3.85
5624 13904 7.068593 TCCAAATATGTTTAAAGCAGATGGGAG 59.931 37.037 11.01 0.00 0.00 4.30
5810 14093 4.260784 GCAAAGGGCGAGTACATTTAGATG 60.261 45.833 0.00 0.00 39.25 2.90
5826 14109 2.906691 TGTGATTTTGTGGCAAAGGG 57.093 45.000 0.00 0.00 0.00 3.95
5827 14110 5.528320 AGATTTTGTGATTTTGTGGCAAAGG 59.472 36.000 0.00 0.00 31.87 3.11
5829 14112 5.296283 CCAGATTTTGTGATTTTGTGGCAAA 59.704 36.000 0.00 0.00 0.00 3.68
5830 14113 4.815308 CCAGATTTTGTGATTTTGTGGCAA 59.185 37.500 0.00 0.00 0.00 4.52
5832 14115 4.379652 ACCAGATTTTGTGATTTTGTGGC 58.620 39.130 0.00 0.00 0.00 5.01
5833 14116 6.511416 TGTACCAGATTTTGTGATTTTGTGG 58.489 36.000 0.00 0.00 0.00 4.17
5834 14117 8.592105 ATTGTACCAGATTTTGTGATTTTGTG 57.408 30.769 0.00 0.00 0.00 3.33
5835 14118 9.044150 CAATTGTACCAGATTTTGTGATTTTGT 57.956 29.630 0.00 0.00 0.00 2.83
5836 14119 8.497554 CCAATTGTACCAGATTTTGTGATTTTG 58.502 33.333 4.43 0.00 0.00 2.44
5837 14120 8.428063 TCCAATTGTACCAGATTTTGTGATTTT 58.572 29.630 4.43 0.00 0.00 1.82
5838 14121 7.961351 TCCAATTGTACCAGATTTTGTGATTT 58.039 30.769 4.43 0.00 0.00 2.17
5839 14122 7.537596 TCCAATTGTACCAGATTTTGTGATT 57.462 32.000 4.43 0.00 0.00 2.57
5840 14123 7.415541 CGATCCAATTGTACCAGATTTTGTGAT 60.416 37.037 4.43 0.00 0.00 3.06
5841 14124 6.128035 CGATCCAATTGTACCAGATTTTGTGA 60.128 38.462 4.43 0.00 0.00 3.58
5968 14262 3.008594 TCCACCACCATAGACGACAAAAT 59.991 43.478 0.00 0.00 0.00 1.82
5972 14266 1.548719 CTTCCACCACCATAGACGACA 59.451 52.381 0.00 0.00 0.00 4.35
6000 14294 2.793946 CGCCACATAACCAGCAGC 59.206 61.111 0.00 0.00 0.00 5.25
6044 14338 2.877097 TTCCAACAAGCATCCTAGCA 57.123 45.000 0.00 0.00 36.85 3.49
6087 14381 3.244579 GCTAATCACGGAAACATACGGAC 59.755 47.826 0.00 0.00 0.00 4.79
6277 14686 1.654317 AACGTGACTTGTTTACGGCA 58.346 45.000 13.12 0.00 41.74 5.69
6299 14708 2.741092 GAGGTCGTTGCTGGTCCA 59.259 61.111 0.00 0.00 0.00 4.02
6387 14796 4.838986 GGGCTATACAAGAACCCTAGATCA 59.161 45.833 0.00 0.00 37.59 2.92
6390 14799 4.274794 TGGGCTATACAAGAACCCTAGA 57.725 45.455 0.00 0.00 41.44 2.43
6411 14882 6.998074 TCTACTGTTCATCTTCAACCATTGTT 59.002 34.615 0.00 0.00 34.14 2.83
6420 14891 5.920840 CGTCACTTTCTACTGTTCATCTTCA 59.079 40.000 0.00 0.00 0.00 3.02
6490 14961 2.496470 AGGATCAGTTAACGGACAGACC 59.504 50.000 10.74 11.41 0.00 3.85
6491 14962 3.870633 AGGATCAGTTAACGGACAGAC 57.129 47.619 10.74 2.31 0.00 3.51
6492 14963 4.142227 GCTTAGGATCAGTTAACGGACAGA 60.142 45.833 10.74 0.97 0.00 3.41
6493 14964 4.113354 GCTTAGGATCAGTTAACGGACAG 58.887 47.826 10.74 4.06 0.00 3.51
6494 14965 3.118884 GGCTTAGGATCAGTTAACGGACA 60.119 47.826 10.74 0.00 0.00 4.02
6495 14966 3.118884 TGGCTTAGGATCAGTTAACGGAC 60.119 47.826 10.74 5.40 0.00 4.79
6496 14967 3.101437 TGGCTTAGGATCAGTTAACGGA 58.899 45.455 10.92 10.92 0.00 4.69
6497 14968 3.536956 TGGCTTAGGATCAGTTAACGG 57.463 47.619 0.00 0.00 0.00 4.44
6498 14969 4.504858 AGTTGGCTTAGGATCAGTTAACG 58.495 43.478 0.00 0.00 0.00 3.18
6499 14970 4.876679 GGAGTTGGCTTAGGATCAGTTAAC 59.123 45.833 0.00 0.00 0.00 2.01
6500 14971 4.534500 TGGAGTTGGCTTAGGATCAGTTAA 59.466 41.667 0.00 0.00 0.00 2.01
6501 14972 4.081087 GTGGAGTTGGCTTAGGATCAGTTA 60.081 45.833 0.00 0.00 0.00 2.24
6502 14973 2.912956 TGGAGTTGGCTTAGGATCAGTT 59.087 45.455 0.00 0.00 0.00 3.16
6503 14974 2.237392 GTGGAGTTGGCTTAGGATCAGT 59.763 50.000 0.00 0.00 0.00 3.41
6504 14975 2.420687 GGTGGAGTTGGCTTAGGATCAG 60.421 54.545 0.00 0.00 0.00 2.90
6505 14976 1.559682 GGTGGAGTTGGCTTAGGATCA 59.440 52.381 0.00 0.00 0.00 2.92
6506 14977 1.473434 CGGTGGAGTTGGCTTAGGATC 60.473 57.143 0.00 0.00 0.00 3.36
6507 14978 0.541863 CGGTGGAGTTGGCTTAGGAT 59.458 55.000 0.00 0.00 0.00 3.24
6508 14979 1.980052 CGGTGGAGTTGGCTTAGGA 59.020 57.895 0.00 0.00 0.00 2.94
6509 14980 1.745489 GCGGTGGAGTTGGCTTAGG 60.745 63.158 0.00 0.00 0.00 2.69
6510 14981 2.100631 CGCGGTGGAGTTGGCTTAG 61.101 63.158 0.00 0.00 0.00 2.18
6511 14982 2.047655 CGCGGTGGAGTTGGCTTA 60.048 61.111 0.00 0.00 0.00 3.09
6532 15005 1.232216 GGGACCGGACAGGATAGGA 59.768 63.158 9.46 0.00 45.00 2.94
6554 15030 2.431954 TGTCCGTTTTACCCCAAACA 57.568 45.000 0.00 0.00 36.58 2.83
6593 15069 1.407618 ACAAAAGTCCGTTTGCTTCCC 59.592 47.619 5.75 0.00 41.33 3.97
6596 15072 2.162809 ACGAACAAAAGTCCGTTTGCTT 59.837 40.909 5.75 1.15 41.33 3.91
6614 15090 0.302288 CGAAAGCGGACACAAAACGA 59.698 50.000 0.00 0.00 0.00 3.85
6659 15135 1.104577 GTCCGTTTCACCCCAAAGCA 61.105 55.000 0.00 0.00 0.00 3.91
6695 15172 2.049063 GGACAAGCGCAGACGACT 60.049 61.111 11.47 0.00 43.93 4.18
6736 15213 1.303806 GAAAAAGGCCCGCCCTGTA 60.304 57.895 0.00 0.00 45.62 2.74
6789 15268 0.321671 CAGCGAGGGAAAGAGTGGAA 59.678 55.000 0.00 0.00 0.00 3.53
6856 15342 2.941583 GAAGGGAAGGGGCTGGGT 60.942 66.667 0.00 0.00 0.00 4.51
6942 15428 1.301716 GCGAGCTCAAGACCAACCA 60.302 57.895 15.40 0.00 0.00 3.67
6946 15432 4.069232 CGGGCGAGCTCAAGACCA 62.069 66.667 15.40 0.00 34.45 4.02


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

AutoCloner maintained by Alex Coulton.