Multiple sequence alignment - TraesCS6B01G157000

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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 TraesCS6B01G157000 chr6B 100.000 4220 0 0 1 4220 159400959 159405178 0.000000e+00 7793.0
1 TraesCS6B01G157000 chr6B 93.504 2771 177 2 1057 3824 158149854 158147084 0.000000e+00 4117.0
2 TraesCS6B01G157000 chr6B 85.268 2179 294 16 1063 3230 158103940 158101778 0.000000e+00 2220.0
3 TraesCS6B01G157000 chr6B 90.489 368 31 2 426 789 158151216 158150849 2.280000e-132 483.0
4 TraesCS6B01G157000 chr6B 98.773 163 2 0 3815 3977 643217258 643217420 1.480000e-74 291.0
5 TraesCS6B01G157000 chr6B 91.220 205 13 5 859 1063 158150839 158150640 1.490000e-69 274.0
6 TraesCS6B01G157000 chr6D 95.770 3333 116 13 496 3822 83540000 83543313 0.000000e+00 5350.0
7 TraesCS6B01G157000 chr6D 93.277 2737 165 2 1057 3793 83124785 83122068 0.000000e+00 4017.0
8 TraesCS6B01G157000 chr6D 86.311 2177 275 13 1063 3230 83057981 83055819 0.000000e+00 2348.0
9 TraesCS6B01G157000 chr6D 85.849 2120 284 14 1114 3227 83046865 83044756 0.000000e+00 2239.0
10 TraesCS6B01G157000 chr6D 93.730 925 47 6 496 1419 83827352 83828266 0.000000e+00 1376.0
11 TraesCS6B01G157000 chr6D 90.210 429 37 4 409 832 83126185 83125757 4.770000e-154 555.0
12 TraesCS6B01G157000 chr6D 92.881 295 14 2 3537 3824 83104994 83104700 5.040000e-114 422.0
13 TraesCS6B01G157000 chr6D 90.030 331 26 4 170 499 83539713 83540037 5.040000e-114 422.0
14 TraesCS6B01G157000 chr6D 87.571 354 21 5 1 352 83820764 83821096 5.120000e-104 388.0
15 TraesCS6B01G157000 chr6D 93.496 246 13 2 3977 4220 83104560 83104316 3.100000e-96 363.0
16 TraesCS6B01G157000 chr6D 89.573 211 17 3 3618 3824 84028491 84028700 3.240000e-66 263.0
17 TraesCS6B01G157000 chr6D 88.293 205 16 6 859 1063 83125758 83125562 5.450000e-59 239.0
18 TraesCS6B01G157000 chr6D 92.105 152 12 0 348 499 83827238 83827389 9.190000e-52 215.0
19 TraesCS6B01G157000 chr6D 93.103 116 5 2 1 113 83539580 83539695 2.610000e-37 167.0
20 TraesCS6B01G157000 chr6D 100.000 29 0 0 366 394 382609891 382609919 2.000000e-03 54.7
21 TraesCS6B01G157000 chr6A 96.058 2968 97 7 859 3824 100802795 100805744 0.000000e+00 4815.0
22 TraesCS6B01G157000 chr6A 96.318 2580 85 9 859 3433 100760726 100763300 0.000000e+00 4229.0
23 TraesCS6B01G157000 chr6A 92.605 2772 172 16 1057 3824 100185143 100182401 0.000000e+00 3952.0
24 TraesCS6B01G157000 chr6A 85.256 2184 290 21 1063 3230 100087936 100085769 0.000000e+00 2220.0
25 TraesCS6B01G157000 chr6A 90.855 842 64 8 1 832 100759889 100760727 0.000000e+00 1116.0
26 TraesCS6B01G157000 chr6A 96.148 675 23 2 2762 3433 100809263 100809937 0.000000e+00 1099.0
27 TraesCS6B01G157000 chr6A 89.311 842 65 12 1 832 100801970 100802796 0.000000e+00 1033.0
28 TraesCS6B01G157000 chr6A 86.343 659 57 17 409 1063 100186501 100185872 0.000000e+00 688.0
29 TraesCS6B01G157000 chr6A 96.114 386 15 0 3439 3824 100763260 100763645 7.700000e-177 630.0
30 TraesCS6B01G157000 chr6A 96.114 386 15 0 3439 3824 100809897 100810282 7.700000e-177 630.0
31 TraesCS6B01G157000 chr6A 97.166 247 5 2 3975 4220 100808417 100808662 2.350000e-112 416.0
32 TraesCS6B01G157000 chr6A 98.298 235 3 1 3987 4220 100810415 100810649 1.090000e-110 411.0
33 TraesCS6B01G157000 chr6A 97.458 236 4 2 3987 4220 100763778 100764013 6.570000e-108 401.0
34 TraesCS6B01G157000 chr4B 99.375 160 1 0 3818 3977 429720099 429720258 1.480000e-74 291.0
35 TraesCS6B01G157000 chr4B 98.193 166 1 2 3822 3987 321360564 321360401 5.340000e-74 289.0
36 TraesCS6B01G157000 chr4B 97.633 169 2 2 3813 3980 673191025 673191192 5.340000e-74 289.0
37 TraesCS6B01G157000 chr2B 99.379 161 0 1 3817 3977 67298302 67298143 1.480000e-74 291.0
38 TraesCS6B01G157000 chr7A 98.182 165 2 1 3814 3977 15838121 15837957 1.920000e-73 287.0
39 TraesCS6B01G157000 chr5B 97.619 168 3 1 3810 3977 21402531 21402697 1.920000e-73 287.0
40 TraesCS6B01G157000 chr3A 97.605 167 4 0 3811 3977 471496393 471496559 1.920000e-73 287.0
41 TraesCS6B01G157000 chr3A 96.970 33 0 1 363 394 685813826 685813858 2.000000e-03 54.7
42 TraesCS6B01G157000 chr2A 97.093 172 2 2 3809 3977 660841350 660841521 1.920000e-73 287.0
43 TraesCS6B01G157000 chr3D 97.059 34 0 1 364 396 5672716 5672749 5.890000e-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 TraesCS6B01G157000 chr6B 159400959 159405178 4219 False 7793.000000 7793 100.000000 1 4220 1 chr6B.!!$F1 4219
1 TraesCS6B01G157000 chr6B 158101778 158103940 2162 True 2220.000000 2220 85.268000 1063 3230 1 chr6B.!!$R1 2167
2 TraesCS6B01G157000 chr6B 158147084 158151216 4132 True 1624.666667 4117 91.737667 426 3824 3 chr6B.!!$R2 3398
3 TraesCS6B01G157000 chr6D 83055819 83057981 2162 True 2348.000000 2348 86.311000 1063 3230 1 chr6D.!!$R2 2167
4 TraesCS6B01G157000 chr6D 83044756 83046865 2109 True 2239.000000 2239 85.849000 1114 3227 1 chr6D.!!$R1 2113
5 TraesCS6B01G157000 chr6D 83539580 83543313 3733 False 1979.666667 5350 92.967667 1 3822 3 chr6D.!!$F4 3821
6 TraesCS6B01G157000 chr6D 83122068 83126185 4117 True 1603.666667 4017 90.593333 409 3793 3 chr6D.!!$R4 3384
7 TraesCS6B01G157000 chr6D 83827238 83828266 1028 False 795.500000 1376 92.917500 348 1419 2 chr6D.!!$F5 1071
8 TraesCS6B01G157000 chr6D 83104316 83104994 678 True 392.500000 422 93.188500 3537 4220 2 chr6D.!!$R3 683
9 TraesCS6B01G157000 chr6A 100182401 100186501 4100 True 2320.000000 3952 89.474000 409 3824 2 chr6A.!!$R2 3415
10 TraesCS6B01G157000 chr6A 100085769 100087936 2167 True 2220.000000 2220 85.256000 1063 3230 1 chr6A.!!$R1 2167
11 TraesCS6B01G157000 chr6A 100759889 100764013 4124 False 1594.000000 4229 95.186250 1 4220 4 chr6A.!!$F1 4219
12 TraesCS6B01G157000 chr6A 100801970 100810649 8679 False 1400.666667 4815 95.515833 1 4220 6 chr6A.!!$F2 4219

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
717 814 0.391661 AGCCACCTGTACAATGAGCG 60.392 55.0 8.1 0.0 0.00 5.03 F
718 815 0.673644 GCCACCTGTACAATGAGCGT 60.674 55.0 8.1 0.0 0.00 5.07 F
803 902 0.886490 CAACTGCCAGTGAGACACCC 60.886 60.0 0.0 0.0 34.49 4.61 F
1165 2131 0.957888 GCTGCTGGTCTCTTTGGTCC 60.958 60.0 0.0 0.0 0.00 4.46 F
2679 3646 0.037447 AGGTCTTCTTTGAGCTGCCC 59.963 55.0 0.0 0.0 42.36 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1864 2831 0.106335 ATGCCATCGAGAGCTCCTTG 59.894 55.000 10.93 3.00 0.00 3.61 R
1890 2857 1.416401 ACGGTGACCAGATTTGTGAGT 59.584 47.619 1.11 0.00 0.00 3.41 R
1909 2876 1.672881 CTCATTCCCGCCAAGATCAAC 59.327 52.381 0.00 0.00 0.00 3.18 R
2863 3830 0.671781 AGCATCTGCAGGTTCGTGAC 60.672 55.000 15.13 2.98 45.16 3.67 R
3873 9428 0.605589 CAAAGTGGTCGGACCCTTCC 60.606 60.000 23.81 9.51 37.50 3.46 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
33 34 1.244816 GCCCACAGGTTAAAGGTCAC 58.755 55.000 0.00 0.00 34.57 3.67
82 86 5.538849 TTTTGGGTCCATAAACCAAGAAC 57.461 39.130 0.00 0.00 44.32 3.01
127 131 5.928264 CCCACAAGATTTGCTTTTCTTTAGG 59.072 40.000 0.00 0.00 33.60 2.69
128 132 6.462909 CCCACAAGATTTGCTTTTCTTTAGGT 60.463 38.462 0.00 0.00 33.60 3.08
167 177 2.478831 TGTTTCCGGAAAATGCTTTGC 58.521 42.857 30.49 15.91 31.33 3.68
172 186 1.799994 CCGGAAAATGCTTTGCCTTTG 59.200 47.619 0.00 0.00 29.47 2.77
245 260 7.338449 GCCTCTTTGTCTAACCCACAATATTTA 59.662 37.037 0.00 0.00 33.76 1.40
256 271 6.790319 ACCCACAATATTTAAACCTCAGTCT 58.210 36.000 0.00 0.00 0.00 3.24
288 303 8.841300 GCTTAATTGCTAAAGGCTTACTCTTAT 58.159 33.333 0.00 0.00 42.39 1.73
330 345 3.206964 TGCAACCGTGTCAAAGACAATA 58.793 40.909 0.82 0.00 44.49 1.90
333 348 4.083537 GCAACCGTGTCAAAGACAATATGA 60.084 41.667 0.82 0.00 44.49 2.15
335 350 5.801350 ACCGTGTCAAAGACAATATGATG 57.199 39.130 0.82 0.00 44.49 3.07
360 375 1.004560 CAGACACATGCCCGTCAGT 60.005 57.895 11.71 0.00 34.48 3.41
377 392 2.169769 TCAGTTGACGGTTTGAGAGGTT 59.830 45.455 0.00 0.00 0.00 3.50
378 393 2.943033 CAGTTGACGGTTTGAGAGGTTT 59.057 45.455 0.00 0.00 0.00 3.27
413 428 1.953559 AAGCGTTCACAGACACATGT 58.046 45.000 0.00 0.00 0.00 3.21
420 435 3.767902 TCACAGACACATGTCCATCAA 57.232 42.857 8.41 0.00 45.85 2.57
471 523 1.040646 GTGACTCTGTGAGGTGGACA 58.959 55.000 0.00 0.00 33.35 4.02
499 585 9.474920 TTTGTACAAAGCAATAAGAATTTGAGG 57.525 29.630 17.01 0.00 36.41 3.86
500 586 8.177119 TGTACAAAGCAATAAGAATTTGAGGT 57.823 30.769 0.00 0.00 36.41 3.85
501 587 8.081633 TGTACAAAGCAATAAGAATTTGAGGTG 58.918 33.333 0.00 0.00 36.41 4.00
502 588 6.458210 ACAAAGCAATAAGAATTTGAGGTGG 58.542 36.000 3.73 0.00 36.41 4.61
503 589 5.665916 AAGCAATAAGAATTTGAGGTGGG 57.334 39.130 0.00 0.00 0.00 4.61
504 590 4.677182 AGCAATAAGAATTTGAGGTGGGT 58.323 39.130 0.00 0.00 0.00 4.51
505 591 5.086621 AGCAATAAGAATTTGAGGTGGGTT 58.913 37.500 0.00 0.00 0.00 4.11
506 592 5.543790 AGCAATAAGAATTTGAGGTGGGTTT 59.456 36.000 0.00 0.00 0.00 3.27
507 593 6.043127 AGCAATAAGAATTTGAGGTGGGTTTT 59.957 34.615 0.00 0.00 0.00 2.43
508 594 6.710295 GCAATAAGAATTTGAGGTGGGTTTTT 59.290 34.615 0.00 0.00 0.00 1.94
539 625 3.491267 GCAATAAGAATTCGAGACCTCCG 59.509 47.826 0.00 0.00 0.00 4.63
561 648 2.796031 CAAAGTCGTAAAGTGGTACGCA 59.204 45.455 0.01 0.00 45.12 5.24
715 812 6.112734 TGTTATTAGCCACCTGTACAATGAG 58.887 40.000 8.10 1.24 0.00 2.90
717 814 0.391661 AGCCACCTGTACAATGAGCG 60.392 55.000 8.10 0.00 0.00 5.03
718 815 0.673644 GCCACCTGTACAATGAGCGT 60.674 55.000 8.10 0.00 0.00 5.07
736 833 3.130633 GCGTTGACATATATGCACTCCA 58.869 45.455 12.79 1.20 0.00 3.86
789 888 7.224753 ACACGAAATATTATAGCCACTCAACTG 59.775 37.037 0.00 0.00 0.00 3.16
803 902 0.886490 CAACTGCCAGTGAGACACCC 60.886 60.000 0.00 0.00 34.49 4.61
918 1057 8.995220 CATCAAGATGACATCACCAAAAATTTT 58.005 29.630 17.57 0.00 41.20 1.82
919 1058 8.592105 TCAAGATGACATCACCAAAAATTTTC 57.408 30.769 17.57 0.00 0.00 2.29
920 1059 8.202811 TCAAGATGACATCACCAAAAATTTTCA 58.797 29.630 17.57 0.00 0.00 2.69
1143 2109 1.003580 CCTTCACTTGGCTTGGCTCTA 59.996 52.381 0.00 0.00 0.00 2.43
1165 2131 0.957888 GCTGCTGGTCTCTTTGGTCC 60.958 60.000 0.00 0.00 0.00 4.46
1236 2202 3.474570 GCCGGGCTCTCACAGGAT 61.475 66.667 12.87 0.00 0.00 3.24
1250 2216 4.467084 GGATGGCGGCCTCACGAA 62.467 66.667 21.46 0.00 35.47 3.85
1335 2301 1.069227 GTCACTGATGTTTCGTTGGCC 60.069 52.381 0.00 0.00 0.00 5.36
1409 2375 2.282180 GCGCCTCAACCTTTCCCA 60.282 61.111 0.00 0.00 0.00 4.37
1413 2379 1.614317 CGCCTCAACCTTTCCCAGAAT 60.614 52.381 0.00 0.00 0.00 2.40
1441 2407 2.564721 GGTGGCTTGCCACTGGAAC 61.565 63.158 34.40 19.49 40.24 3.62
1675 2641 5.122239 CAGATACCAACTACACCATGTGTTG 59.878 44.000 5.06 6.25 45.08 3.33
1864 2831 7.881751 ACCTCTCTTTACCTAACAATTGGTTAC 59.118 37.037 10.83 0.00 40.96 2.50
1890 2857 1.660167 CTCTCGATGGCATCAGCAAA 58.340 50.000 25.88 6.58 44.61 3.68
1909 2876 2.169832 ACTCACAAATCTGGTCACCG 57.830 50.000 0.00 0.00 0.00 4.94
2056 3023 7.168972 GCAACTGCACAAATCTTGTAACAATTA 59.831 33.333 0.00 0.00 43.23 1.40
2266 3233 0.915364 AGGCAATCTGAAGTCCCTCC 59.085 55.000 0.00 0.00 0.00 4.30
2514 3481 2.158914 GGGGATGCTATTTTTGCAAGGG 60.159 50.000 0.00 0.00 44.01 3.95
2679 3646 0.037447 AGGTCTTCTTTGAGCTGCCC 59.963 55.000 0.00 0.00 42.36 5.36
3031 3999 4.178540 CACGTTTCCGGATTCTAGCTTTA 58.821 43.478 4.15 0.00 38.78 1.85
3232 8776 2.666272 TGGCTGAAACCATGTAACCA 57.334 45.000 0.00 0.00 33.75 3.67
3241 8785 6.249192 TGAAACCATGTAACCATTATCACCA 58.751 36.000 0.00 0.00 0.00 4.17
3343 8887 0.823356 GGGAAAGCACACAAGAGGCA 60.823 55.000 0.00 0.00 0.00 4.75
3608 9154 0.668535 GACCAACTTTGTGTCCCTGC 59.331 55.000 0.00 0.00 0.00 4.85
3693 9246 1.203994 CCCAAAAGCATCCTCTTGCAG 59.796 52.381 0.00 0.00 45.23 4.41
3701 9254 2.489329 GCATCCTCTTGCAGTGCTAAAA 59.511 45.455 17.60 1.05 42.31 1.52
3772 9327 7.984422 ATCATGTACTGTTTCATGTCAGAAA 57.016 32.000 18.13 0.00 41.22 2.52
3824 9379 3.587923 GCATGGTGCATAAGAAAGCAAA 58.412 40.909 0.00 0.00 44.26 3.68
3825 9380 3.995705 GCATGGTGCATAAGAAAGCAAAA 59.004 39.130 0.00 0.00 44.26 2.44
3849 9404 4.413928 GGCAACCTGGTGCATGTA 57.586 55.556 18.44 0.00 46.81 2.29
3852 9407 0.962356 GCAACCTGGTGCATGTAGCT 60.962 55.000 14.15 0.00 44.29 3.32
3853 9408 1.089920 CAACCTGGTGCATGTAGCTC 58.910 55.000 14.15 0.00 45.94 4.09
3859 9414 1.450312 GTGCATGTAGCTCCCGCTT 60.450 57.895 0.00 0.00 46.47 4.68
3860 9415 1.450134 TGCATGTAGCTCCCGCTTG 60.450 57.895 0.00 0.00 46.47 4.01
3861 9416 2.828128 GCATGTAGCTCCCGCTTGC 61.828 63.158 0.00 0.00 46.47 4.01
3862 9417 2.202932 ATGTAGCTCCCGCTTGCG 60.203 61.111 8.14 8.14 46.47 4.85
3877 9432 4.785453 GCGCAGGGTCCAGGGAAG 62.785 72.222 0.30 0.00 0.00 3.46
3878 9433 4.101448 CGCAGGGTCCAGGGAAGG 62.101 72.222 0.00 0.00 0.00 3.46
3879 9434 3.732849 GCAGGGTCCAGGGAAGGG 61.733 72.222 0.00 0.00 0.00 3.95
3880 9435 2.204151 CAGGGTCCAGGGAAGGGT 60.204 66.667 0.00 0.00 0.00 4.34
3882 9437 3.015753 GGGTCCAGGGAAGGGTCC 61.016 72.222 0.00 0.00 44.10 4.46
3885 9440 2.284405 TCCAGGGAAGGGTCCGAC 60.284 66.667 0.00 0.00 46.04 4.79
3886 9441 3.400054 CCAGGGAAGGGTCCGACC 61.400 72.222 9.30 9.30 46.04 4.79
3887 9442 2.606519 CAGGGAAGGGTCCGACCA 60.607 66.667 19.43 0.00 46.04 4.02
3888 9443 2.606826 AGGGAAGGGTCCGACCAC 60.607 66.667 19.43 8.70 46.04 4.16
3889 9444 2.606826 GGGAAGGGTCCGACCACT 60.607 66.667 19.43 10.80 46.04 4.00
3890 9445 2.222013 GGGAAGGGTCCGACCACTT 61.222 63.158 19.43 17.88 46.04 3.16
3891 9446 1.759236 GGAAGGGTCCGACCACTTT 59.241 57.895 19.43 9.96 41.02 2.66
3892 9447 0.605589 GGAAGGGTCCGACCACTTTG 60.606 60.000 19.43 0.00 41.02 2.77
3908 9463 4.360563 CACTTTGGGTCTATAGTACGCAG 58.639 47.826 16.00 11.29 40.36 5.18
3909 9464 3.181478 ACTTTGGGTCTATAGTACGCAGC 60.181 47.826 16.00 2.07 40.36 5.25
3910 9465 1.325355 TGGGTCTATAGTACGCAGCC 58.675 55.000 13.98 8.23 35.18 4.85
3911 9466 1.133575 TGGGTCTATAGTACGCAGCCT 60.134 52.381 13.98 0.00 35.18 4.58
3913 9468 2.364647 GGGTCTATAGTACGCAGCCTTT 59.635 50.000 0.00 0.00 0.00 3.11
3914 9469 3.552478 GGGTCTATAGTACGCAGCCTTTC 60.552 52.174 0.00 0.00 0.00 2.62
3915 9470 3.552478 GGTCTATAGTACGCAGCCTTTCC 60.552 52.174 0.00 0.00 0.00 3.13
3919 9474 0.535797 AGTACGCAGCCTTTCCCTAC 59.464 55.000 0.00 0.00 0.00 3.18
3920 9475 0.248289 GTACGCAGCCTTTCCCTACA 59.752 55.000 0.00 0.00 0.00 2.74
3921 9476 1.134491 GTACGCAGCCTTTCCCTACAT 60.134 52.381 0.00 0.00 0.00 2.29
3922 9477 0.328258 ACGCAGCCTTTCCCTACATT 59.672 50.000 0.00 0.00 0.00 2.71
3924 9479 1.401905 CGCAGCCTTTCCCTACATTTC 59.598 52.381 0.00 0.00 0.00 2.17
3925 9480 2.728007 GCAGCCTTTCCCTACATTTCT 58.272 47.619 0.00 0.00 0.00 2.52
3926 9481 2.424956 GCAGCCTTTCCCTACATTTCTG 59.575 50.000 0.00 0.00 0.00 3.02
3930 9485 5.355350 CAGCCTTTCCCTACATTTCTGTAAG 59.645 44.000 0.00 0.00 37.41 2.34
3943 9498 3.685139 TCTGTAAGAGGCTGTTTCCAG 57.315 47.619 0.90 9.48 38.67 3.86
3944 9499 2.303022 TCTGTAAGAGGCTGTTTCCAGG 59.697 50.000 17.71 5.83 38.67 4.45
3946 9501 2.038557 TGTAAGAGGCTGTTTCCAGGAC 59.961 50.000 0.90 0.00 39.22 3.85
3948 9503 1.439543 AGAGGCTGTTTCCAGGACTT 58.560 50.000 0.00 0.00 39.22 3.01
3949 9504 1.072965 AGAGGCTGTTTCCAGGACTTG 59.927 52.381 0.00 0.00 39.22 3.16
3950 9505 1.072331 GAGGCTGTTTCCAGGACTTGA 59.928 52.381 0.00 0.00 39.22 3.02
3951 9506 1.494721 AGGCTGTTTCCAGGACTTGAA 59.505 47.619 0.00 0.00 39.22 2.69
3952 9507 1.609072 GGCTGTTTCCAGGACTTGAAC 59.391 52.381 0.00 0.00 39.22 3.18
3953 9508 1.609072 GCTGTTTCCAGGACTTGAACC 59.391 52.381 0.00 0.00 39.22 3.62
3956 9511 2.176798 TGTTTCCAGGACTTGAACCCAT 59.823 45.455 0.00 0.00 0.00 4.00
3957 9512 2.558359 GTTTCCAGGACTTGAACCCATG 59.442 50.000 0.00 0.00 0.00 3.66
3958 9513 1.741028 TCCAGGACTTGAACCCATGA 58.259 50.000 0.00 0.00 0.00 3.07
3959 9514 1.351017 TCCAGGACTTGAACCCATGAC 59.649 52.381 0.00 0.00 0.00 3.06
3960 9515 1.614317 CCAGGACTTGAACCCATGACC 60.614 57.143 0.00 0.00 34.29 4.02
3961 9516 1.352352 CAGGACTTGAACCCATGACCT 59.648 52.381 0.00 0.00 40.96 3.85
3962 9517 1.630878 AGGACTTGAACCCATGACCTC 59.369 52.381 0.00 0.00 37.82 3.85
3964 9519 2.025887 GGACTTGAACCCATGACCTCAT 60.026 50.000 0.00 0.00 36.96 2.90
4186 9744 9.297037 TGTCAGCTATCTATGCACTTAATACTA 57.703 33.333 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 8.196771 AGGTTAATGCATGGTTAAATACATGTG 58.803 33.333 9.11 0.00 44.74 3.21
127 131 3.389329 ACATGGTCTCCCTCATACATCAC 59.611 47.826 0.00 0.00 0.00 3.06
128 132 3.657610 ACATGGTCTCCCTCATACATCA 58.342 45.455 0.00 0.00 0.00 3.07
150 160 1.337118 AGGCAAAGCATTTTCCGGAA 58.663 45.000 14.35 14.35 46.38 4.30
151 161 1.337118 AAGGCAAAGCATTTTCCGGA 58.663 45.000 0.00 0.00 46.38 5.14
155 165 4.500117 GCAAAACAAAGGCAAAGCATTTTC 59.500 37.500 0.00 0.00 39.52 2.29
167 177 1.365999 GGTCCCCGCAAAACAAAGG 59.634 57.895 0.00 0.00 0.00 3.11
172 186 1.676635 GGTAGGGTCCCCGCAAAAC 60.677 63.158 3.51 0.00 41.95 2.43
200 215 4.633547 GGGTTCCCGCTCCCTATA 57.366 61.111 0.00 0.00 40.48 1.31
219 234 2.561478 TGTGGGTTAGACAAAGAGGC 57.439 50.000 0.00 0.00 0.00 4.70
245 260 2.355010 AGCAGCAAAGACTGAGGTTT 57.645 45.000 0.00 0.00 40.25 3.27
256 271 4.244862 GCCTTTAGCAATTAAGCAGCAAA 58.755 39.130 0.00 0.00 42.97 3.68
288 303 5.594725 TGCAAAGTATAGTGGTTCCAACAAA 59.405 36.000 0.00 0.00 0.00 2.83
360 375 2.294074 CCAAACCTCTCAAACCGTCAA 58.706 47.619 0.00 0.00 0.00 3.18
413 428 4.956700 AGGAGAAGATCGTAAGTTGATGGA 59.043 41.667 0.00 0.00 39.48 3.41
420 435 4.773149 ACTTGGAAGGAGAAGATCGTAAGT 59.227 41.667 0.00 0.00 39.48 2.24
505 591 9.737427 TCGAATTCTTATTGCTTTGTACAAAAA 57.263 25.926 20.89 13.98 0.00 1.94
506 592 9.393249 CTCGAATTCTTATTGCTTTGTACAAAA 57.607 29.630 20.89 7.98 0.00 2.44
507 593 8.779303 TCTCGAATTCTTATTGCTTTGTACAAA 58.221 29.630 19.53 19.53 0.00 2.83
508 594 8.227791 GTCTCGAATTCTTATTGCTTTGTACAA 58.772 33.333 3.59 3.59 0.00 2.41
509 595 7.148474 GGTCTCGAATTCTTATTGCTTTGTACA 60.148 37.037 3.52 0.00 0.00 2.90
510 596 7.064728 AGGTCTCGAATTCTTATTGCTTTGTAC 59.935 37.037 3.52 0.00 0.00 2.90
511 597 7.103641 AGGTCTCGAATTCTTATTGCTTTGTA 58.896 34.615 3.52 0.00 0.00 2.41
512 598 5.940470 AGGTCTCGAATTCTTATTGCTTTGT 59.060 36.000 3.52 0.00 0.00 2.83
513 599 6.428385 AGGTCTCGAATTCTTATTGCTTTG 57.572 37.500 3.52 0.00 0.00 2.77
514 600 5.586643 GGAGGTCTCGAATTCTTATTGCTTT 59.413 40.000 3.52 0.00 0.00 3.51
515 601 5.119694 GGAGGTCTCGAATTCTTATTGCTT 58.880 41.667 3.52 0.00 0.00 3.91
516 602 4.698575 GGAGGTCTCGAATTCTTATTGCT 58.301 43.478 3.52 0.00 0.00 3.91
517 603 3.491267 CGGAGGTCTCGAATTCTTATTGC 59.509 47.826 3.52 0.00 0.00 3.56
518 604 3.491267 GCGGAGGTCTCGAATTCTTATTG 59.509 47.826 3.52 0.00 0.00 1.90
519 605 3.132289 TGCGGAGGTCTCGAATTCTTATT 59.868 43.478 3.52 0.00 0.00 1.40
520 606 2.693591 TGCGGAGGTCTCGAATTCTTAT 59.306 45.455 3.52 0.00 0.00 1.73
521 607 2.097036 TGCGGAGGTCTCGAATTCTTA 58.903 47.619 3.52 0.00 0.00 2.10
522 608 0.895530 TGCGGAGGTCTCGAATTCTT 59.104 50.000 3.52 0.00 0.00 2.52
523 609 0.895530 TTGCGGAGGTCTCGAATTCT 59.104 50.000 3.52 0.00 0.00 2.40
524 610 1.661112 CTTTGCGGAGGTCTCGAATTC 59.339 52.381 0.00 0.00 0.00 2.17
525 611 1.002087 ACTTTGCGGAGGTCTCGAATT 59.998 47.619 0.00 0.00 0.00 2.17
526 612 0.608640 ACTTTGCGGAGGTCTCGAAT 59.391 50.000 0.00 0.00 0.00 3.34
527 613 0.038526 GACTTTGCGGAGGTCTCGAA 60.039 55.000 5.22 0.00 0.00 3.71
528 614 1.585006 GACTTTGCGGAGGTCTCGA 59.415 57.895 5.22 0.00 0.00 4.04
539 625 2.410646 GCGTACCACTTTACGACTTTGC 60.411 50.000 6.85 0.00 46.37 3.68
686 783 5.583061 TGTACAGGTGGCTAATAACATTTCG 59.417 40.000 0.00 0.00 0.00 3.46
715 812 3.130633 TGGAGTGCATATATGTCAACGC 58.869 45.455 14.14 11.17 0.00 4.84
717 814 7.263100 TCAATTGGAGTGCATATATGTCAAC 57.737 36.000 14.14 10.08 0.00 3.18
718 815 7.878547 TTCAATTGGAGTGCATATATGTCAA 57.121 32.000 14.14 10.81 0.00 3.18
789 888 1.215647 CTACGGGTGTCTCACTGGC 59.784 63.158 0.06 0.00 34.40 4.85
803 902 4.378030 GTGTTAAGTCGAGTGTTGACTACG 59.622 45.833 0.00 0.00 45.62 3.51
883 1022 4.508551 TGTCATCTTGATGCCACCTAAT 57.491 40.909 5.78 0.00 0.00 1.73
898 1037 8.610896 TGTTTGAAAATTTTTGGTGATGTCATC 58.389 29.630 4.63 5.83 0.00 2.92
977 1119 8.197439 GCATGCTAAACTACCATTTCCTAAATT 58.803 33.333 11.37 0.00 0.00 1.82
1143 2109 0.250640 CCAAAGAGACCAGCAGCACT 60.251 55.000 0.00 0.00 0.00 4.40
1165 2131 4.154347 GCAGGAGCTGGTCGGAGG 62.154 72.222 0.00 0.00 37.91 4.30
1230 2196 4.101448 GTGAGGCCGCCATCCTGT 62.101 66.667 13.15 0.00 33.24 4.00
1236 2202 4.373116 GACTTCGTGAGGCCGCCA 62.373 66.667 13.15 0.00 0.00 5.69
1303 2269 5.606348 ACATCAGTGACCTTCCTATCTTC 57.394 43.478 0.00 0.00 0.00 2.87
1409 2375 1.202976 AGCCACCAGACAGCAAATTCT 60.203 47.619 0.00 0.00 0.00 2.40
1413 2379 1.737355 GCAAGCCACCAGACAGCAAA 61.737 55.000 0.00 0.00 0.00 3.68
1441 2407 2.812591 GGATGCTGCTGGATGACATTAG 59.187 50.000 1.45 0.00 0.00 1.73
1675 2641 4.120331 AGCAAAAGATGGCGCGCC 62.120 61.111 42.35 42.35 34.54 6.53
1707 2673 2.618709 GTTCCCACTGAGTTGGTTGAAG 59.381 50.000 2.37 0.00 34.44 3.02
1864 2831 0.106335 ATGCCATCGAGAGCTCCTTG 59.894 55.000 10.93 3.00 0.00 3.61
1890 2857 1.416401 ACGGTGACCAGATTTGTGAGT 59.584 47.619 1.11 0.00 0.00 3.41
1909 2876 1.672881 CTCATTCCCGCCAAGATCAAC 59.327 52.381 0.00 0.00 0.00 3.18
2056 3023 4.503123 GCTAAATTGGTTTGCCTTGAGGTT 60.503 41.667 0.00 0.00 37.57 3.50
2134 3101 4.270008 CCGGTGAAGTTATTGGAAAGGAT 58.730 43.478 0.00 0.00 0.00 3.24
2136 3103 2.163613 GCCGGTGAAGTTATTGGAAAGG 59.836 50.000 1.90 0.00 0.00 3.11
2514 3481 5.048507 GGTATCGGTCCAGTTAGTTGATTC 58.951 45.833 0.00 0.00 0.00 2.52
2679 3646 5.231991 CAGAAATTGGTTCTTGTTCCAAACG 59.768 40.000 0.82 0.00 44.64 3.60
2863 3830 0.671781 AGCATCTGCAGGTTCGTGAC 60.672 55.000 15.13 2.98 45.16 3.67
3031 3999 2.495669 CACACAGTTTTGGGTTTCCACT 59.504 45.455 0.00 0.00 37.83 4.00
3278 8822 8.486210 ACTGCAGAGTCAAATGTCCTTATATTA 58.514 33.333 23.35 0.00 0.00 0.98
3309 8853 6.323739 TGTGCTTTCCCTGTAGATTTTCTTTT 59.676 34.615 0.00 0.00 0.00 2.27
3701 9254 9.745880 CACGGTGTCTGTATCTAACTTATTTAT 57.254 33.333 0.00 0.00 0.00 1.40
3772 9327 8.223330 AGCTCATGGGAGAATCAGTAAAAATAT 58.777 33.333 0.00 0.00 44.26 1.28
3827 9382 0.763986 ATGCACCAGGTTGCCCTTTT 60.764 50.000 10.46 0.00 42.25 2.27
3828 9383 1.152269 ATGCACCAGGTTGCCCTTT 60.152 52.632 10.46 0.00 42.25 3.11
3829 9384 1.909781 CATGCACCAGGTTGCCCTT 60.910 57.895 10.46 0.00 42.25 3.95
3831 9386 1.304052 TACATGCACCAGGTTGCCC 60.304 57.895 10.46 0.00 42.25 5.36
3832 9387 1.937546 GCTACATGCACCAGGTTGCC 61.938 60.000 10.46 0.00 39.88 4.52
3833 9388 0.962356 AGCTACATGCACCAGGTTGC 60.962 55.000 8.03 8.03 44.17 4.17
3834 9389 1.089920 GAGCTACATGCACCAGGTTG 58.910 55.000 0.00 0.00 45.94 3.77
3860 9415 4.785453 CTTCCCTGGACCCTGCGC 62.785 72.222 0.00 0.00 0.00 6.09
3861 9416 4.101448 CCTTCCCTGGACCCTGCG 62.101 72.222 0.00 0.00 0.00 5.18
3862 9417 3.732849 CCCTTCCCTGGACCCTGC 61.733 72.222 0.00 0.00 0.00 4.85
3863 9418 2.204151 ACCCTTCCCTGGACCCTG 60.204 66.667 0.00 0.00 0.00 4.45
3866 9421 3.400054 CGGACCCTTCCCTGGACC 61.400 72.222 0.00 0.00 38.99 4.46
3867 9422 2.284405 TCGGACCCTTCCCTGGAC 60.284 66.667 0.00 0.00 38.99 4.02
3868 9423 2.284405 GTCGGACCCTTCCCTGGA 60.284 66.667 0.00 0.00 38.99 3.86
3869 9424 3.400054 GGTCGGACCCTTCCCTGG 61.400 72.222 16.55 0.00 38.99 4.45
3870 9425 2.606519 TGGTCGGACCCTTCCCTG 60.607 66.667 23.81 0.00 38.99 4.45
3871 9426 2.606826 GTGGTCGGACCCTTCCCT 60.607 66.667 23.81 0.00 38.99 4.20
3872 9427 1.775934 AAAGTGGTCGGACCCTTCCC 61.776 60.000 23.81 7.17 38.99 3.97
3873 9428 0.605589 CAAAGTGGTCGGACCCTTCC 60.606 60.000 23.81 9.51 37.50 3.46
3875 9430 1.454539 CCAAAGTGGTCGGACCCTT 59.545 57.895 23.81 21.08 37.50 3.95
3876 9431 2.526046 CCCAAAGTGGTCGGACCCT 61.526 63.158 23.81 16.82 37.50 4.34
3877 9432 2.033602 CCCAAAGTGGTCGGACCC 59.966 66.667 23.81 14.91 37.50 4.46
3878 9433 1.302271 GACCCAAAGTGGTCGGACC 60.302 63.158 20.36 20.36 44.98 4.46
3879 9434 4.373771 GACCCAAAGTGGTCGGAC 57.626 61.111 0.00 0.00 44.98 4.79
3885 9440 3.131577 TGCGTACTATAGACCCAAAGTGG 59.868 47.826 6.78 0.00 37.25 4.00
3886 9441 4.360563 CTGCGTACTATAGACCCAAAGTG 58.639 47.826 6.78 0.00 0.00 3.16
3887 9442 3.181478 GCTGCGTACTATAGACCCAAAGT 60.181 47.826 6.78 0.00 0.00 2.66
3888 9443 3.381949 GCTGCGTACTATAGACCCAAAG 58.618 50.000 6.78 0.00 0.00 2.77
3889 9444 2.101917 GGCTGCGTACTATAGACCCAAA 59.898 50.000 6.78 0.00 0.00 3.28
3890 9445 1.684983 GGCTGCGTACTATAGACCCAA 59.315 52.381 6.78 0.00 0.00 4.12
3891 9446 1.133575 AGGCTGCGTACTATAGACCCA 60.134 52.381 6.78 0.00 0.00 4.51
3892 9447 1.618487 AGGCTGCGTACTATAGACCC 58.382 55.000 6.78 0.00 0.00 4.46
3896 9451 2.628657 AGGGAAAGGCTGCGTACTATAG 59.371 50.000 0.00 0.00 0.00 1.31
3897 9452 2.674420 AGGGAAAGGCTGCGTACTATA 58.326 47.619 0.00 0.00 0.00 1.31
3899 9454 1.753073 GTAGGGAAAGGCTGCGTACTA 59.247 52.381 0.00 0.00 34.81 1.82
3902 9457 1.200519 ATGTAGGGAAAGGCTGCGTA 58.799 50.000 0.00 0.00 0.00 4.42
3904 9459 1.401905 GAAATGTAGGGAAAGGCTGCG 59.598 52.381 0.00 0.00 0.00 5.18
3908 9463 5.497474 TCTTACAGAAATGTAGGGAAAGGC 58.503 41.667 0.00 0.00 0.00 4.35
3909 9464 6.116126 CCTCTTACAGAAATGTAGGGAAAGG 58.884 44.000 0.00 0.00 0.00 3.11
3910 9465 5.586643 GCCTCTTACAGAAATGTAGGGAAAG 59.413 44.000 0.00 0.00 0.00 2.62
3911 9466 5.250774 AGCCTCTTACAGAAATGTAGGGAAA 59.749 40.000 0.00 0.00 0.00 3.13
3913 9468 4.162320 CAGCCTCTTACAGAAATGTAGGGA 59.838 45.833 0.00 0.00 0.00 4.20
3914 9469 4.080863 ACAGCCTCTTACAGAAATGTAGGG 60.081 45.833 0.00 0.66 0.00 3.53
3915 9470 5.091261 ACAGCCTCTTACAGAAATGTAGG 57.909 43.478 0.00 0.00 0.00 3.18
3919 9474 4.761739 TGGAAACAGCCTCTTACAGAAATG 59.238 41.667 0.00 0.00 35.01 2.32
3920 9475 4.985538 TGGAAACAGCCTCTTACAGAAAT 58.014 39.130 0.00 0.00 35.01 2.17
3921 9476 4.431416 TGGAAACAGCCTCTTACAGAAA 57.569 40.909 0.00 0.00 35.01 2.52
3935 9490 1.566703 TGGGTTCAAGTCCTGGAAACA 59.433 47.619 0.00 0.00 32.36 2.83
3936 9491 2.358322 TGGGTTCAAGTCCTGGAAAC 57.642 50.000 0.00 0.00 0.00 2.78
3937 9492 2.445145 TCATGGGTTCAAGTCCTGGAAA 59.555 45.455 0.00 0.00 0.00 3.13
3938 9493 2.061848 TCATGGGTTCAAGTCCTGGAA 58.938 47.619 0.00 0.00 0.00 3.53
3940 9495 1.614317 GGTCATGGGTTCAAGTCCTGG 60.614 57.143 0.00 0.00 0.00 4.45
3941 9496 1.352352 AGGTCATGGGTTCAAGTCCTG 59.648 52.381 0.00 0.00 0.00 3.86
3943 9498 1.351017 TGAGGTCATGGGTTCAAGTCC 59.649 52.381 0.00 0.00 0.00 3.85
3944 9499 2.859165 TGAGGTCATGGGTTCAAGTC 57.141 50.000 0.00 0.00 0.00 3.01
3959 9514 2.092753 ACTATGCCTTGTGACCATGAGG 60.093 50.000 0.00 0.00 42.21 3.86
3960 9515 3.272574 ACTATGCCTTGTGACCATGAG 57.727 47.619 0.00 0.00 0.00 2.90
3961 9516 5.511373 GCTATACTATGCCTTGTGACCATGA 60.511 44.000 0.00 0.00 0.00 3.07
3962 9517 4.692625 GCTATACTATGCCTTGTGACCATG 59.307 45.833 0.00 0.00 0.00 3.66
3964 9519 3.709141 TGCTATACTATGCCTTGTGACCA 59.291 43.478 0.00 0.00 0.00 4.02
3965 9520 4.310769 CTGCTATACTATGCCTTGTGACC 58.689 47.826 0.00 0.00 0.00 4.02
3966 9521 4.310769 CCTGCTATACTATGCCTTGTGAC 58.689 47.826 0.00 0.00 0.00 3.67
3967 9522 3.324846 CCCTGCTATACTATGCCTTGTGA 59.675 47.826 0.00 0.00 0.00 3.58
3968 9523 3.557898 CCCCTGCTATACTATGCCTTGTG 60.558 52.174 0.00 0.00 0.00 3.33
3969 9524 2.639839 CCCCTGCTATACTATGCCTTGT 59.360 50.000 0.00 0.00 0.00 3.16
3970 9525 2.906389 TCCCCTGCTATACTATGCCTTG 59.094 50.000 0.00 0.00 0.00 3.61
3971 9526 3.275848 TCCCCTGCTATACTATGCCTT 57.724 47.619 0.00 0.00 0.00 4.35
3972 9527 3.177228 CTTCCCCTGCTATACTATGCCT 58.823 50.000 0.00 0.00 0.00 4.75
3973 9528 2.237392 CCTTCCCCTGCTATACTATGCC 59.763 54.545 0.00 0.00 0.00 4.40
3974 9529 2.907042 ACCTTCCCCTGCTATACTATGC 59.093 50.000 0.00 0.00 0.00 3.14
3975 9530 7.973048 TTATACCTTCCCCTGCTATACTATG 57.027 40.000 0.00 0.00 0.00 2.23
4060 9616 7.051000 AGAATAAGCACCTTCCTATGTTTCTC 58.949 38.462 0.00 0.00 0.00 2.87


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

AutoCloner maintained by Alex Coulton.