Multiple sequence alignment - TraesCS3B01G330000

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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 TraesCS3B01G330000 chr3B 100.000 2926 0 0 1 2926 533455444 533452519 0.000000e+00 5404.0
1 TraesCS3B01G330000 chr3D 93.634 2152 71 34 700 2803 407748332 407746199 0.000000e+00 3155.0
2 TraesCS3B01G330000 chr3D 93.491 507 17 6 76 573 407749121 407748622 0.000000e+00 739.0
3 TraesCS3B01G330000 chr3A 92.164 1391 47 32 738 2081 544190666 544192041 0.000000e+00 1908.0
4 TraesCS3B01G330000 chr3A 86.041 788 50 26 2075 2809 544193307 544194087 0.000000e+00 791.0
5 TraesCS3B01G330000 chr3A 88.986 572 29 15 69 625 544190043 544190595 0.000000e+00 676.0
6 TraesCS3B01G330000 chr3A 97.143 35 1 0 19 53 544190009 544190043 3.150000e-05 60.2
7 TraesCS3B01G330000 chr4A 99.145 117 1 0 2810 2926 658405422 658405538 8.220000e-51 211.0
8 TraesCS3B01G330000 chr1B 97.521 121 3 0 2806 2926 2112902 2112782 1.060000e-49 207.0
9 TraesCS3B01G330000 chr1B 96.639 119 4 0 2808 2926 492305035 492304917 6.400000e-47 198.0
10 TraesCS3B01G330000 chr7B 97.436 117 3 0 2810 2926 488783383 488783499 1.780000e-47 200.0
11 TraesCS3B01G330000 chr7B 97.436 117 3 0 2810 2926 677059090 677059206 1.780000e-47 200.0
12 TraesCS3B01G330000 chr7B 96.639 119 4 0 2808 2926 117799342 117799224 6.400000e-47 198.0
13 TraesCS3B01G330000 chr4B 96.667 120 4 0 2807 2926 623405907 623406026 1.780000e-47 200.0
14 TraesCS3B01G330000 chr2B 97.436 117 3 0 2810 2926 298558840 298558956 1.780000e-47 200.0
15 TraesCS3B01G330000 chr5D 94.444 126 7 0 2801 2926 103650407 103650282 8.270000e-46 195.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3B01G330000 chr3B 533452519 533455444 2925 True 5404.0 5404 100.0000 1 2926 1 chr3B.!!$R1 2925
1 TraesCS3B01G330000 chr3D 407746199 407749121 2922 True 1947.0 3155 93.5625 76 2803 2 chr3D.!!$R1 2727
2 TraesCS3B01G330000 chr3A 544190009 544194087 4078 False 858.8 1908 91.0835 19 2809 4 chr3A.!!$F1 2790

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
474 493 0.106819 ATGAGCCCATGAGAACCAGC 60.107 55.0 0.0 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2274 3830 0.030101 CTCTCGCTTCCATCTCCGAC 59.97 60.0 0.0 0.0 0.0 4.79 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
53 54 1.948611 GCGGCATTTGTCAACCCTCTA 60.949 52.381 0.00 0.00 0.00 2.43
54 55 2.009774 CGGCATTTGTCAACCCTCTAG 58.990 52.381 0.00 0.00 0.00 2.43
55 56 2.615493 CGGCATTTGTCAACCCTCTAGT 60.615 50.000 0.00 0.00 0.00 2.57
56 57 3.421844 GGCATTTGTCAACCCTCTAGTT 58.578 45.455 0.00 0.00 0.00 2.24
57 58 3.826729 GGCATTTGTCAACCCTCTAGTTT 59.173 43.478 0.00 0.00 0.00 2.66
58 59 4.280929 GGCATTTGTCAACCCTCTAGTTTT 59.719 41.667 0.00 0.00 0.00 2.43
59 60 5.222631 GCATTTGTCAACCCTCTAGTTTTG 58.777 41.667 0.00 0.00 0.00 2.44
60 61 5.221244 GCATTTGTCAACCCTCTAGTTTTGT 60.221 40.000 0.00 0.00 0.00 2.83
61 62 6.016610 GCATTTGTCAACCCTCTAGTTTTGTA 60.017 38.462 0.00 0.00 0.00 2.41
62 63 7.584987 CATTTGTCAACCCTCTAGTTTTGTAG 58.415 38.462 0.00 0.00 0.00 2.74
63 64 6.488769 TTGTCAACCCTCTAGTTTTGTAGA 57.511 37.500 0.00 0.00 0.00 2.59
64 65 6.488769 TGTCAACCCTCTAGTTTTGTAGAA 57.511 37.500 0.00 0.00 0.00 2.10
65 66 7.074653 TGTCAACCCTCTAGTTTTGTAGAAT 57.925 36.000 0.00 0.00 0.00 2.40
66 67 6.934645 TGTCAACCCTCTAGTTTTGTAGAATG 59.065 38.462 0.00 0.00 0.00 2.67
67 68 7.159372 GTCAACCCTCTAGTTTTGTAGAATGA 58.841 38.462 0.00 0.00 0.00 2.57
68 69 7.824779 GTCAACCCTCTAGTTTTGTAGAATGAT 59.175 37.037 0.00 0.00 0.00 2.45
91 92 9.743057 TGATGGTGTATAAAAAGAAAACTGTTG 57.257 29.630 0.00 0.00 0.00 3.33
96 97 7.911727 GTGTATAAAAAGAAAACTGTTGGACGT 59.088 33.333 0.00 0.00 0.00 4.34
329 331 2.528818 CCCAGCCCTCAAGTCACCA 61.529 63.158 0.00 0.00 0.00 4.17
334 336 1.445942 CCCTCAAGTCACCACACGT 59.554 57.895 0.00 0.00 0.00 4.49
335 337 0.677288 CCCTCAAGTCACCACACGTA 59.323 55.000 0.00 0.00 0.00 3.57
336 338 1.604693 CCCTCAAGTCACCACACGTAC 60.605 57.143 0.00 0.00 0.00 3.67
378 384 5.337554 CAGATTGAAATCACCGTACTACGA 58.662 41.667 10.27 0.00 39.87 3.43
387 393 2.096335 CACCGTACTACGATGCTACACA 59.904 50.000 10.27 0.00 46.05 3.72
388 394 2.353889 ACCGTACTACGATGCTACACAG 59.646 50.000 10.27 0.00 46.05 3.66
397 403 4.735132 GCTACACAGGCGCACCGA 62.735 66.667 10.83 0.00 42.76 4.69
398 404 2.809601 CTACACAGGCGCACCGAC 60.810 66.667 10.83 0.00 42.76 4.79
408 416 2.125106 GCACCGACTGGATGGACC 60.125 66.667 0.00 0.00 39.21 4.46
442 455 2.185608 GAGCGCCTTCCACTCTCC 59.814 66.667 2.29 0.00 0.00 3.71
443 456 2.284258 AGCGCCTTCCACTCTCCT 60.284 61.111 2.29 0.00 0.00 3.69
444 457 2.185608 GCGCCTTCCACTCTCCTC 59.814 66.667 0.00 0.00 0.00 3.71
469 488 1.478105 GGCATGATGAGCCCATGAGAA 60.478 52.381 0.00 0.00 46.50 2.87
470 489 1.607628 GCATGATGAGCCCATGAGAAC 59.392 52.381 0.00 0.00 42.89 3.01
471 490 2.228059 CATGATGAGCCCATGAGAACC 58.772 52.381 0.00 0.00 42.89 3.62
472 491 1.288188 TGATGAGCCCATGAGAACCA 58.712 50.000 0.00 0.00 32.09 3.67
473 492 1.211212 TGATGAGCCCATGAGAACCAG 59.789 52.381 0.00 0.00 32.09 4.00
474 493 0.106819 ATGAGCCCATGAGAACCAGC 60.107 55.000 0.00 0.00 0.00 4.85
476 495 2.202236 GAGCCCATGAGAACCAGCCA 62.202 60.000 0.00 0.00 0.00 4.75
477 496 1.751927 GCCCATGAGAACCAGCCAG 60.752 63.158 0.00 0.00 0.00 4.85
478 497 1.751927 CCCATGAGAACCAGCCAGC 60.752 63.158 0.00 0.00 0.00 4.85
479 498 1.751927 CCATGAGAACCAGCCAGCC 60.752 63.158 0.00 0.00 0.00 4.85
480 499 1.751927 CATGAGAACCAGCCAGCCC 60.752 63.158 0.00 0.00 0.00 5.19
481 500 2.988839 ATGAGAACCAGCCAGCCCC 61.989 63.158 0.00 0.00 0.00 5.80
482 501 4.432741 GAGAACCAGCCAGCCCCC 62.433 72.222 0.00 0.00 0.00 5.40
625 660 4.333926 ACGCTCAATCCTAATTCTTCTTGC 59.666 41.667 0.00 0.00 0.00 4.01
626 661 4.574013 CGCTCAATCCTAATTCTTCTTGCT 59.426 41.667 0.00 0.00 0.00 3.91
627 662 5.503683 CGCTCAATCCTAATTCTTCTTGCTG 60.504 44.000 0.00 0.00 0.00 4.41
629 664 5.255687 TCAATCCTAATTCTTCTTGCTGCA 58.744 37.500 0.00 0.00 0.00 4.41
630 665 5.124457 TCAATCCTAATTCTTCTTGCTGCAC 59.876 40.000 0.00 0.00 0.00 4.57
631 666 4.019792 TCCTAATTCTTCTTGCTGCACA 57.980 40.909 0.00 0.00 0.00 4.57
632 667 4.592942 TCCTAATTCTTCTTGCTGCACAT 58.407 39.130 0.00 0.00 0.00 3.21
633 668 4.637534 TCCTAATTCTTCTTGCTGCACATC 59.362 41.667 0.00 0.00 0.00 3.06
634 669 3.482722 AATTCTTCTTGCTGCACATCG 57.517 42.857 0.00 0.00 0.00 3.84
635 670 2.168326 TTCTTCTTGCTGCACATCGA 57.832 45.000 0.00 0.00 0.00 3.59
636 671 1.432514 TCTTCTTGCTGCACATCGAC 58.567 50.000 0.00 0.00 0.00 4.20
637 672 0.445436 CTTCTTGCTGCACATCGACC 59.555 55.000 0.00 0.00 0.00 4.79
638 673 0.955428 TTCTTGCTGCACATCGACCC 60.955 55.000 0.00 0.00 0.00 4.46
639 674 2.359850 TTGCTGCACATCGACCCC 60.360 61.111 0.00 0.00 0.00 4.95
640 675 3.918253 TTGCTGCACATCGACCCCC 62.918 63.158 0.00 0.00 0.00 5.40
670 705 5.106038 TGCTCATTCACTCTGCAAATTAAGG 60.106 40.000 0.00 0.00 0.00 2.69
696 898 2.029623 AGTGAGTCGTAGTTGTGTGGT 58.970 47.619 0.00 0.00 0.00 4.16
805 1023 0.175531 GTTGCCCCATACACCATTGC 59.824 55.000 0.00 0.00 0.00 3.56
849 1067 2.765689 AGTATCCCTACAGCAGAGCT 57.234 50.000 0.00 0.00 40.77 4.09
852 1070 1.743321 ATCCCTACAGCAGAGCTCGC 61.743 60.000 18.76 18.76 36.40 5.03
876 1094 1.996070 GATCCTGCCAAGGTACCCCC 61.996 65.000 8.74 0.00 44.82 5.40
918 1136 1.674322 CGCACCAAAAGGACCCGAT 60.674 57.895 0.00 0.00 0.00 4.18
935 1153 2.379972 CGATACCAGGTGAGGTTCTCT 58.620 52.381 0.76 0.00 43.08 3.10
1009 1231 0.759060 TAGCTGGCCGCCTTATGAGA 60.759 55.000 11.61 0.00 40.39 3.27
1133 1367 0.944311 CGGTCGGTTCAGTTGAGTGG 60.944 60.000 0.00 0.00 0.00 4.00
1135 1369 1.070786 TCGGTTCAGTTGAGTGGGC 59.929 57.895 0.00 0.00 0.00 5.36
1246 1484 2.026879 GAGATCAGCGAGCCCGTC 59.973 66.667 0.00 0.00 38.24 4.79
1778 2039 9.468532 CTTCTTTTCATTTCTTCCTTTCGATTT 57.531 29.630 0.00 0.00 0.00 2.17
1796 2057 9.774413 TTTCGATTTTCTAGTTTACTTCCTCTT 57.226 29.630 0.00 0.00 0.00 2.85
1839 2102 3.851969 CGCTTCGGCCTCTTTTATTTTTC 59.148 43.478 0.00 0.00 37.76 2.29
1860 2123 3.792736 CATCTTTCCCCGGCCCGA 61.793 66.667 3.71 0.00 0.00 5.14
1921 2184 2.893424 ACAGGGTGAATGATGCCTTTT 58.107 42.857 0.00 0.00 0.00 2.27
1922 2185 2.564062 ACAGGGTGAATGATGCCTTTTG 59.436 45.455 0.00 0.00 0.00 2.44
1923 2186 2.564062 CAGGGTGAATGATGCCTTTTGT 59.436 45.455 0.00 0.00 0.00 2.83
1924 2187 2.564062 AGGGTGAATGATGCCTTTTGTG 59.436 45.455 0.00 0.00 0.00 3.33
1926 2189 3.006752 GGGTGAATGATGCCTTTTGTGAA 59.993 43.478 0.00 0.00 0.00 3.18
1927 2190 4.240096 GGTGAATGATGCCTTTTGTGAAG 58.760 43.478 0.00 0.00 0.00 3.02
1957 2220 8.112099 AGATACAATTTTTGCTAGTACGTACG 57.888 34.615 19.49 15.01 0.00 3.67
1992 2260 8.644318 TCTCTTTACGATTTCCTAATTACAGC 57.356 34.615 0.00 0.00 0.00 4.40
2135 3683 0.458543 TGCTCGCACTTGCTACTAGC 60.459 55.000 0.61 0.61 42.82 3.42
2192 3748 0.253160 TACTCCTCCAAGTGGGCCAT 60.253 55.000 10.70 0.00 36.21 4.40
2198 3754 2.301346 CTCCAAGTGGGCCATTGATAC 58.699 52.381 22.32 5.96 36.21 2.24
2207 3763 1.447317 GCCATTGATACTGGTGCGGG 61.447 60.000 0.00 0.00 36.10 6.13
2218 3774 1.950909 CTGGTGCGGGTTTGTAAAGAA 59.049 47.619 0.00 0.00 0.00 2.52
2274 3830 0.941542 TTTCACTCGCCCTTTTGTCG 59.058 50.000 0.00 0.00 0.00 4.35
2351 3910 4.276183 AGCATGCATCTTGTTCTGATCATC 59.724 41.667 21.98 0.00 0.00 2.92
2644 4227 9.351570 CTTGCTTTTCCTTTAATGATTTCTCTC 57.648 33.333 0.00 0.00 0.00 3.20
2650 4233 9.454859 TTTCCTTTAATGATTTCTCTCTTCTCC 57.545 33.333 0.00 0.00 0.00 3.71
2668 4257 2.101917 CTCCGTATGGGTTATGGTTCGT 59.898 50.000 0.00 0.00 38.07 3.85
2745 4345 2.350388 GGCACGTACAATGTGTTCCTTG 60.350 50.000 0.00 0.00 37.43 3.61
2777 4377 1.144057 CCTTCCATCGAACGGGAGG 59.856 63.158 15.42 15.42 34.02 4.30
2809 4415 2.455163 CCTCCCTCCCTCCCTTATCTAA 59.545 54.545 0.00 0.00 0.00 2.10
2810 4416 3.503227 CCTCCCTCCCTCCCTTATCTAAG 60.503 56.522 0.00 0.00 0.00 2.18
2823 4429 5.788450 CCTTATCTAAGGCTGGTCATAGTG 58.212 45.833 3.14 0.00 45.56 2.74
2824 4430 5.279708 CCTTATCTAAGGCTGGTCATAGTGG 60.280 48.000 3.14 0.00 45.56 4.00
2825 4431 3.398318 TCTAAGGCTGGTCATAGTGGA 57.602 47.619 0.00 0.00 0.00 4.02
2826 4432 3.719871 TCTAAGGCTGGTCATAGTGGAA 58.280 45.455 0.00 0.00 0.00 3.53
2827 4433 3.706594 TCTAAGGCTGGTCATAGTGGAAG 59.293 47.826 0.00 0.00 0.00 3.46
2828 4434 1.958288 AGGCTGGTCATAGTGGAAGT 58.042 50.000 0.00 0.00 0.00 3.01
2829 4435 3.116096 AGGCTGGTCATAGTGGAAGTA 57.884 47.619 0.00 0.00 0.00 2.24
2830 4436 3.450904 AGGCTGGTCATAGTGGAAGTAA 58.549 45.455 0.00 0.00 0.00 2.24
2831 4437 3.197983 AGGCTGGTCATAGTGGAAGTAAC 59.802 47.826 0.00 0.00 0.00 2.50
2832 4438 3.197983 GGCTGGTCATAGTGGAAGTAACT 59.802 47.826 0.00 0.00 0.00 2.24
2833 4439 4.323562 GGCTGGTCATAGTGGAAGTAACTT 60.324 45.833 0.00 0.00 0.00 2.66
2834 4440 5.105064 GGCTGGTCATAGTGGAAGTAACTTA 60.105 44.000 0.00 0.00 0.00 2.24
2835 4441 6.043411 GCTGGTCATAGTGGAAGTAACTTAG 58.957 44.000 0.00 0.00 0.00 2.18
2836 4442 5.974108 TGGTCATAGTGGAAGTAACTTAGC 58.026 41.667 0.00 0.00 0.00 3.09
2837 4443 5.720041 TGGTCATAGTGGAAGTAACTTAGCT 59.280 40.000 0.00 0.00 0.00 3.32
2838 4444 6.893554 TGGTCATAGTGGAAGTAACTTAGCTA 59.106 38.462 0.00 0.00 0.00 3.32
2839 4445 7.068348 TGGTCATAGTGGAAGTAACTTAGCTAG 59.932 40.741 0.00 0.00 0.00 3.42
2840 4446 7.068470 GGTCATAGTGGAAGTAACTTAGCTAGT 59.932 40.741 0.00 0.00 39.32 2.57
2841 4447 9.118300 GTCATAGTGGAAGTAACTTAGCTAGTA 57.882 37.037 0.00 0.00 35.54 1.82
2842 4448 9.690913 TCATAGTGGAAGTAACTTAGCTAGTAA 57.309 33.333 0.00 0.00 35.54 2.24
2843 4449 9.733219 CATAGTGGAAGTAACTTAGCTAGTAAC 57.267 37.037 0.00 0.00 35.54 2.50
2844 4450 7.771927 AGTGGAAGTAACTTAGCTAGTAACA 57.228 36.000 0.00 0.00 35.54 2.41
2845 4451 8.363761 AGTGGAAGTAACTTAGCTAGTAACAT 57.636 34.615 0.00 0.00 35.54 2.71
2846 4452 9.471702 AGTGGAAGTAACTTAGCTAGTAACATA 57.528 33.333 0.00 0.00 35.54 2.29
2847 4453 9.733219 GTGGAAGTAACTTAGCTAGTAACATAG 57.267 37.037 0.00 0.00 35.54 2.23
2856 4462 4.103697 GCTAGTAACATAGCGCTTTTCG 57.896 45.455 18.68 4.15 38.90 3.46
2857 4463 3.795101 GCTAGTAACATAGCGCTTTTCGA 59.205 43.478 18.68 0.00 38.90 3.71
2858 4464 4.085517 GCTAGTAACATAGCGCTTTTCGAG 60.086 45.833 18.68 8.88 38.90 4.04
2859 4465 4.106029 AGTAACATAGCGCTTTTCGAGA 57.894 40.909 18.68 0.00 41.67 4.04
2860 4466 4.491676 AGTAACATAGCGCTTTTCGAGAA 58.508 39.130 18.68 0.00 41.67 2.87
2861 4467 4.927425 AGTAACATAGCGCTTTTCGAGAAA 59.073 37.500 18.68 0.00 41.67 2.52
2862 4468 4.742438 AACATAGCGCTTTTCGAGAAAA 57.258 36.364 18.68 10.17 41.67 2.29
2863 4469 4.946784 ACATAGCGCTTTTCGAGAAAAT 57.053 36.364 18.68 0.00 39.29 1.82
2864 4470 6.417191 AACATAGCGCTTTTCGAGAAAATA 57.583 33.333 18.68 0.00 39.29 1.40
2865 4471 5.796813 ACATAGCGCTTTTCGAGAAAATAC 58.203 37.500 18.68 6.47 39.29 1.89
2866 4472 5.581085 ACATAGCGCTTTTCGAGAAAATACT 59.419 36.000 18.68 10.67 39.29 2.12
2867 4473 4.327854 AGCGCTTTTCGAGAAAATACTG 57.672 40.909 2.64 2.13 39.29 2.74
2868 4474 2.840752 GCGCTTTTCGAGAAAATACTGC 59.159 45.455 10.90 9.84 39.29 4.40
2869 4475 3.424962 GCGCTTTTCGAGAAAATACTGCT 60.425 43.478 10.90 0.00 39.29 4.24
2870 4476 4.712763 CGCTTTTCGAGAAAATACTGCTT 58.287 39.130 10.90 0.00 39.29 3.91
2871 4477 5.670341 GCGCTTTTCGAGAAAATACTGCTTA 60.670 40.000 10.90 0.00 39.29 3.09
2872 4478 6.478588 CGCTTTTCGAGAAAATACTGCTTAT 58.521 36.000 10.90 0.00 39.29 1.73
2873 4479 6.409185 CGCTTTTCGAGAAAATACTGCTTATG 59.591 38.462 10.90 0.00 39.29 1.90
2874 4480 7.244192 GCTTTTCGAGAAAATACTGCTTATGT 58.756 34.615 10.90 0.00 39.29 2.29
2875 4481 7.217070 GCTTTTCGAGAAAATACTGCTTATGTG 59.783 37.037 10.90 0.00 39.29 3.21
2876 4482 6.662414 TTCGAGAAAATACTGCTTATGTGG 57.338 37.500 0.00 0.00 0.00 4.17
2877 4483 4.570772 TCGAGAAAATACTGCTTATGTGGC 59.429 41.667 0.00 0.00 0.00 5.01
2878 4484 4.332543 CGAGAAAATACTGCTTATGTGGCA 59.667 41.667 0.00 0.00 38.10 4.92
2879 4485 5.163764 CGAGAAAATACTGCTTATGTGGCAA 60.164 40.000 0.00 0.00 39.30 4.52
2880 4486 6.199937 AGAAAATACTGCTTATGTGGCAAG 57.800 37.500 0.00 0.00 39.30 4.01
2881 4487 5.711976 AGAAAATACTGCTTATGTGGCAAGT 59.288 36.000 0.00 0.00 39.30 3.16
2882 4488 6.884295 AGAAAATACTGCTTATGTGGCAAGTA 59.116 34.615 0.00 0.00 39.30 2.24
2883 4489 7.393234 AGAAAATACTGCTTATGTGGCAAGTAA 59.607 33.333 0.00 0.00 39.30 2.24
2884 4490 7.645058 AAATACTGCTTATGTGGCAAGTAAT 57.355 32.000 0.00 0.00 39.30 1.89
2885 4491 7.645058 AATACTGCTTATGTGGCAAGTAATT 57.355 32.000 0.00 0.00 39.30 1.40
2886 4492 8.746052 AATACTGCTTATGTGGCAAGTAATTA 57.254 30.769 0.00 0.00 39.30 1.40
2887 4493 8.746052 ATACTGCTTATGTGGCAAGTAATTAA 57.254 30.769 0.00 0.00 39.30 1.40
2888 4494 7.645058 ACTGCTTATGTGGCAAGTAATTAAT 57.355 32.000 0.00 0.00 39.30 1.40
2889 4495 7.483307 ACTGCTTATGTGGCAAGTAATTAATG 58.517 34.615 0.00 0.00 39.30 1.90
2890 4496 7.339212 ACTGCTTATGTGGCAAGTAATTAATGA 59.661 33.333 0.00 0.00 39.30 2.57
2891 4497 7.706159 TGCTTATGTGGCAAGTAATTAATGAG 58.294 34.615 0.00 0.00 36.71 2.90
2892 4498 7.555914 TGCTTATGTGGCAAGTAATTAATGAGA 59.444 33.333 0.00 0.00 36.71 3.27
2893 4499 8.072567 GCTTATGTGGCAAGTAATTAATGAGAG 58.927 37.037 0.00 0.00 0.00 3.20
2894 4500 6.949352 ATGTGGCAAGTAATTAATGAGAGG 57.051 37.500 0.00 0.00 0.00 3.69
2895 4501 5.815581 TGTGGCAAGTAATTAATGAGAGGT 58.184 37.500 0.00 0.00 0.00 3.85
2896 4502 5.647658 TGTGGCAAGTAATTAATGAGAGGTG 59.352 40.000 0.00 0.00 0.00 4.00
2897 4503 5.066505 GTGGCAAGTAATTAATGAGAGGTGG 59.933 44.000 0.00 0.00 0.00 4.61
2898 4504 5.193679 GGCAAGTAATTAATGAGAGGTGGT 58.806 41.667 4.19 0.00 0.00 4.16
2899 4505 6.069905 TGGCAAGTAATTAATGAGAGGTGGTA 60.070 38.462 4.19 0.00 0.00 3.25
2900 4506 6.826741 GGCAAGTAATTAATGAGAGGTGGTAA 59.173 38.462 4.19 0.00 0.00 2.85
2901 4507 7.201705 GGCAAGTAATTAATGAGAGGTGGTAAC 60.202 40.741 4.19 0.00 0.00 2.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.263842 GCATTGTATTTCCATGGATGAGAAGA 59.736 38.462 17.06 0.57 0.00 2.87
1 2 6.040054 TGCATTGTATTTCCATGGATGAGAAG 59.960 38.462 17.06 3.40 0.00 2.85
2 3 5.892686 TGCATTGTATTTCCATGGATGAGAA 59.107 36.000 17.06 7.21 0.00 2.87
3 4 5.300034 GTGCATTGTATTTCCATGGATGAGA 59.700 40.000 17.06 1.73 0.00 3.27
4 5 5.068067 TGTGCATTGTATTTCCATGGATGAG 59.932 40.000 17.06 1.46 0.00 2.90
5 6 4.954826 TGTGCATTGTATTTCCATGGATGA 59.045 37.500 17.06 8.10 0.00 2.92
6 7 5.265350 TGTGCATTGTATTTCCATGGATG 57.735 39.130 17.06 10.14 0.00 3.51
7 8 5.599242 TGATGTGCATTGTATTTCCATGGAT 59.401 36.000 17.06 3.82 0.00 3.41
8 9 4.954826 TGATGTGCATTGTATTTCCATGGA 59.045 37.500 11.44 11.44 0.00 3.41
9 10 5.265350 TGATGTGCATTGTATTTCCATGG 57.735 39.130 4.97 4.97 0.00 3.66
10 11 6.763303 CATGATGTGCATTGTATTTCCATG 57.237 37.500 0.00 0.00 34.15 3.66
65 66 9.743057 CAACAGTTTTCTTTTTATACACCATCA 57.257 29.630 0.00 0.00 0.00 3.07
66 67 9.191995 CCAACAGTTTTCTTTTTATACACCATC 57.808 33.333 0.00 0.00 0.00 3.51
67 68 8.919145 TCCAACAGTTTTCTTTTTATACACCAT 58.081 29.630 0.00 0.00 0.00 3.55
68 69 8.192110 GTCCAACAGTTTTCTTTTTATACACCA 58.808 33.333 0.00 0.00 0.00 4.17
91 92 1.142778 GCTCTCGCTTGATCACGTCC 61.143 60.000 0.00 0.00 0.00 4.79
293 295 3.214123 CCTGCATGGACCGCATGG 61.214 66.667 0.00 0.00 39.02 3.66
323 325 3.109230 CGTAGTAGTACGTGTGGTGAC 57.891 52.381 19.78 0.00 45.84 3.67
334 336 3.256383 TGCAAAGAAGGCACGTAGTAGTA 59.744 43.478 0.00 0.00 41.61 1.82
335 337 2.036733 TGCAAAGAAGGCACGTAGTAGT 59.963 45.455 0.00 0.00 41.61 2.73
336 338 2.668457 CTGCAAAGAAGGCACGTAGTAG 59.332 50.000 0.00 0.00 41.61 2.57
378 384 2.436646 GGTGCGCCTGTGTAGCAT 60.437 61.111 9.68 0.00 43.17 3.79
387 393 4.457496 CATCCAGTCGGTGCGCCT 62.457 66.667 15.69 0.00 0.00 5.52
408 416 3.605486 GCGCTCTGTAAAAATTCAGCTTG 59.395 43.478 0.00 0.00 0.00 4.01
442 455 1.574925 GCTCATCATGCCATGCGAG 59.425 57.895 15.61 15.61 34.57 5.03
443 456 3.740513 GCTCATCATGCCATGCGA 58.259 55.556 0.00 0.00 0.00 5.10
477 496 0.333652 TTTGGTTAAGGCTAGGGGGC 59.666 55.000 0.00 0.00 41.20 5.80
478 497 1.639108 ACTTTGGTTAAGGCTAGGGGG 59.361 52.381 0.00 0.00 38.23 5.40
479 498 3.264964 TGTACTTTGGTTAAGGCTAGGGG 59.735 47.826 0.00 0.00 38.23 4.79
480 499 4.259356 GTGTACTTTGGTTAAGGCTAGGG 58.741 47.826 0.00 0.00 38.23 3.53
481 500 3.930848 CGTGTACTTTGGTTAAGGCTAGG 59.069 47.826 0.00 0.00 38.23 3.02
482 501 4.813027 TCGTGTACTTTGGTTAAGGCTAG 58.187 43.478 0.00 0.00 38.23 3.42
483 502 4.870123 TCGTGTACTTTGGTTAAGGCTA 57.130 40.909 0.00 0.00 38.23 3.93
573 608 8.161699 TCTACTCATTTTAGCCTTTCGTTTTT 57.838 30.769 0.00 0.00 0.00 1.94
574 609 7.660208 TCTCTACTCATTTTAGCCTTTCGTTTT 59.340 33.333 0.00 0.00 0.00 2.43
575 610 7.117956 GTCTCTACTCATTTTAGCCTTTCGTTT 59.882 37.037 0.00 0.00 0.00 3.60
576 611 6.590677 GTCTCTACTCATTTTAGCCTTTCGTT 59.409 38.462 0.00 0.00 0.00 3.85
577 612 6.100668 GTCTCTACTCATTTTAGCCTTTCGT 58.899 40.000 0.00 0.00 0.00 3.85
578 613 6.035112 GTGTCTCTACTCATTTTAGCCTTTCG 59.965 42.308 0.00 0.00 0.00 3.46
579 614 6.035112 CGTGTCTCTACTCATTTTAGCCTTTC 59.965 42.308 0.00 0.00 0.00 2.62
580 615 5.869888 CGTGTCTCTACTCATTTTAGCCTTT 59.130 40.000 0.00 0.00 0.00 3.11
581 616 5.411781 CGTGTCTCTACTCATTTTAGCCTT 58.588 41.667 0.00 0.00 0.00 4.35
582 617 4.678309 GCGTGTCTCTACTCATTTTAGCCT 60.678 45.833 0.00 0.00 0.00 4.58
583 618 3.552294 GCGTGTCTCTACTCATTTTAGCC 59.448 47.826 0.00 0.00 0.00 3.93
644 679 4.634184 ATTTGCAGAGTGAATGAGCATC 57.366 40.909 0.00 0.00 34.87 3.91
645 680 6.405508 CCTTAATTTGCAGAGTGAATGAGCAT 60.406 38.462 0.00 0.00 34.87 3.79
646 681 5.106038 CCTTAATTTGCAGAGTGAATGAGCA 60.106 40.000 0.00 0.00 0.00 4.26
647 682 5.338365 CCTTAATTTGCAGAGTGAATGAGC 58.662 41.667 0.00 0.00 0.00 4.26
648 683 5.106038 TGCCTTAATTTGCAGAGTGAATGAG 60.106 40.000 0.00 0.00 32.77 2.90
649 684 4.766373 TGCCTTAATTTGCAGAGTGAATGA 59.234 37.500 0.00 0.00 32.77 2.57
650 685 5.063180 TGCCTTAATTTGCAGAGTGAATG 57.937 39.130 0.00 0.00 32.77 2.67
675 710 2.034305 ACCACACAACTACGACTCACTC 59.966 50.000 0.00 0.00 0.00 3.51
689 891 2.734591 GCTCCTGACGACCACACA 59.265 61.111 0.00 0.00 0.00 3.72
696 898 2.360726 TACTGCCGCTCCTGACGA 60.361 61.111 0.00 0.00 0.00 4.20
805 1023 9.600646 CTATATAGACGACTCTGTATTTGTGTG 57.399 37.037 3.44 0.00 33.90 3.82
852 1070 0.988145 TACCTTGGCAGGATCCTGGG 60.988 60.000 36.92 30.65 44.19 4.45
876 1094 7.411588 GCGGGTATGTTCGAGCTTTTTATATAG 60.412 40.741 0.00 0.00 0.00 1.31
918 1136 1.273098 GGGAGAGAACCTCACCTGGTA 60.273 57.143 0.00 0.00 43.76 3.25
1049 1274 2.838225 CGCTATCCCTGTCCCCGT 60.838 66.667 0.00 0.00 0.00 5.28
1056 1281 0.465705 TTGCTCTTCCGCTATCCCTG 59.534 55.000 0.00 0.00 0.00 4.45
1116 1350 1.228657 GCCCACTCAACTGAACCGAC 61.229 60.000 0.00 0.00 0.00 4.79
1133 1367 1.227674 GGATGGTCTCCATGACGCC 60.228 63.158 5.98 0.00 45.26 5.68
1135 1369 1.068083 CCGGATGGTCTCCATGACG 59.932 63.158 5.98 9.93 45.26 4.35
1527 1777 3.726517 CTGGAGCGTTGTTGCCGG 61.727 66.667 0.00 0.00 34.65 6.13
1796 2057 3.347216 GCAAGCAGAGGGAATTAACAGA 58.653 45.455 0.00 0.00 0.00 3.41
1860 2123 2.103373 TGATGCTCGCTCTAAAGGAGT 58.897 47.619 0.00 0.00 43.62 3.85
1896 2159 3.266772 AGGCATCATTCACCCTGTAAAGA 59.733 43.478 0.00 0.00 0.00 2.52
1921 2184 9.598517 AGCAAAAATTGTATCTTTTTCTTCACA 57.401 25.926 0.00 0.00 34.46 3.58
1957 2220 7.011857 AGGAAATCGTAAAGAGAAAGATGCATC 59.988 37.037 19.37 19.37 0.00 3.91
1992 2260 3.149899 CTGCTTAGTCCCACAGCTG 57.850 57.895 13.48 13.48 34.42 4.24
2085 3633 0.256177 CAGGAGAAAAGGTAGGGGGC 59.744 60.000 0.00 0.00 0.00 5.80
2192 3748 1.202830 ACAAACCCGCACCAGTATCAA 60.203 47.619 0.00 0.00 0.00 2.57
2198 3754 1.600023 TCTTTACAAACCCGCACCAG 58.400 50.000 0.00 0.00 0.00 4.00
2218 3774 3.063997 CGCTGCACGGAATTCTAAGATTT 59.936 43.478 5.23 0.00 38.44 2.17
2274 3830 0.030101 CTCTCGCTTCCATCTCCGAC 59.970 60.000 0.00 0.00 0.00 4.79
2351 3910 2.802247 TCAGAACTTTCGTGCACTCATG 59.198 45.455 16.19 5.93 0.00 3.07
2420 3979 1.221909 TCTCTGCTAGTGGAGGGGGA 61.222 60.000 12.01 0.00 32.53 4.81
2605 4186 1.198759 AAGCAAGGCCCTCCTAACGA 61.199 55.000 0.00 0.00 43.40 3.85
2644 4227 4.377897 GAACCATAACCCATACGGAGAAG 58.622 47.826 0.00 0.00 34.64 2.85
2650 4233 2.031191 GCAACGAACCATAACCCATACG 59.969 50.000 0.00 0.00 0.00 3.06
2745 4345 2.541466 TGGAAGGAGAGAAAGGAGGAC 58.459 52.381 0.00 0.00 0.00 3.85
2777 4377 2.285743 AGGGAGGGAGTGGCCTTC 60.286 66.667 3.32 1.15 41.86 3.46
2809 4415 1.958288 ACTTCCACTATGACCAGCCT 58.042 50.000 0.00 0.00 0.00 4.58
2810 4416 3.197983 AGTTACTTCCACTATGACCAGCC 59.802 47.826 0.00 0.00 0.00 4.85
2811 4417 4.473477 AGTTACTTCCACTATGACCAGC 57.527 45.455 0.00 0.00 0.00 4.85
2812 4418 6.043411 GCTAAGTTACTTCCACTATGACCAG 58.957 44.000 0.00 0.00 0.00 4.00
2813 4419 5.720041 AGCTAAGTTACTTCCACTATGACCA 59.280 40.000 0.00 0.00 0.00 4.02
2814 4420 6.223351 AGCTAAGTTACTTCCACTATGACC 57.777 41.667 0.00 0.00 0.00 4.02
2815 4421 7.998580 ACTAGCTAAGTTACTTCCACTATGAC 58.001 38.462 0.00 0.00 33.35 3.06
2816 4422 9.690913 TTACTAGCTAAGTTACTTCCACTATGA 57.309 33.333 0.00 0.00 39.80 2.15
2817 4423 9.733219 GTTACTAGCTAAGTTACTTCCACTATG 57.267 37.037 0.00 0.57 39.80 2.23
2818 4424 9.471702 TGTTACTAGCTAAGTTACTTCCACTAT 57.528 33.333 0.00 0.00 38.33 2.12
2819 4425 8.868522 TGTTACTAGCTAAGTTACTTCCACTA 57.131 34.615 0.00 1.62 38.33 2.74
2820 4426 7.771927 TGTTACTAGCTAAGTTACTTCCACT 57.228 36.000 0.00 0.43 38.33 4.00
2821 4427 9.733219 CTATGTTACTAGCTAAGTTACTTCCAC 57.267 37.037 0.00 0.00 38.33 4.02
2822 4428 8.411683 GCTATGTTACTAGCTAAGTTACTTCCA 58.588 37.037 0.00 0.00 40.79 3.53
2823 4429 7.590689 CGCTATGTTACTAGCTAAGTTACTTCC 59.409 40.741 0.00 0.00 41.61 3.46
2824 4430 7.113264 GCGCTATGTTACTAGCTAAGTTACTTC 59.887 40.741 0.00 0.00 41.61 3.01
2825 4431 6.916932 GCGCTATGTTACTAGCTAAGTTACTT 59.083 38.462 0.00 2.32 41.61 2.24
2826 4432 6.262720 AGCGCTATGTTACTAGCTAAGTTACT 59.737 38.462 8.99 0.00 41.61 2.24
2827 4433 6.437094 AGCGCTATGTTACTAGCTAAGTTAC 58.563 40.000 8.99 0.79 41.61 2.50
2828 4434 6.630444 AGCGCTATGTTACTAGCTAAGTTA 57.370 37.500 8.99 0.00 41.61 2.24
2829 4435 5.517322 AGCGCTATGTTACTAGCTAAGTT 57.483 39.130 8.99 0.00 41.61 2.66
2830 4436 5.517322 AAGCGCTATGTTACTAGCTAAGT 57.483 39.130 12.05 0.00 41.61 2.24
2831 4437 6.345093 CGAAAAGCGCTATGTTACTAGCTAAG 60.345 42.308 12.05 0.00 41.61 2.18
2832 4438 5.457799 CGAAAAGCGCTATGTTACTAGCTAA 59.542 40.000 12.05 0.00 41.61 3.09
2833 4439 4.974275 CGAAAAGCGCTATGTTACTAGCTA 59.026 41.667 12.05 0.00 41.61 3.32
2834 4440 3.797256 CGAAAAGCGCTATGTTACTAGCT 59.203 43.478 12.05 0.00 41.61 3.32
2835 4441 3.795101 TCGAAAAGCGCTATGTTACTAGC 59.205 43.478 12.05 4.52 40.61 3.42
2836 4442 5.271625 TCTCGAAAAGCGCTATGTTACTAG 58.728 41.667 12.05 1.28 40.61 2.57
2837 4443 5.239359 TCTCGAAAAGCGCTATGTTACTA 57.761 39.130 12.05 0.00 40.61 1.82
2838 4444 4.106029 TCTCGAAAAGCGCTATGTTACT 57.894 40.909 12.05 0.00 40.61 2.24
2839 4445 4.835199 TTCTCGAAAAGCGCTATGTTAC 57.165 40.909 12.05 0.00 40.61 2.50
2840 4446 5.849357 TTTTCTCGAAAAGCGCTATGTTA 57.151 34.783 12.05 0.00 40.61 2.41
2841 4447 4.742438 TTTTCTCGAAAAGCGCTATGTT 57.258 36.364 12.05 5.31 40.61 2.71
2842 4448 4.946784 ATTTTCTCGAAAAGCGCTATGT 57.053 36.364 12.05 0.00 42.72 2.29
2843 4449 5.898606 CAGTATTTTCTCGAAAAGCGCTATG 59.101 40.000 12.05 0.24 42.72 2.23
2844 4450 5.502544 GCAGTATTTTCTCGAAAAGCGCTAT 60.503 40.000 12.05 1.76 42.72 2.97
2845 4451 4.201685 GCAGTATTTTCTCGAAAAGCGCTA 60.202 41.667 12.05 0.00 42.72 4.26
2846 4452 3.424962 GCAGTATTTTCTCGAAAAGCGCT 60.425 43.478 2.64 2.64 42.72 5.92
2847 4453 2.840752 GCAGTATTTTCTCGAAAAGCGC 59.159 45.455 0.00 0.00 42.72 5.92
2848 4454 4.327854 AGCAGTATTTTCTCGAAAAGCG 57.672 40.909 10.21 0.00 42.72 4.68
2849 4455 7.217070 CACATAAGCAGTATTTTCTCGAAAAGC 59.783 37.037 10.21 8.02 42.72 3.51
2850 4456 7.693951 CCACATAAGCAGTATTTTCTCGAAAAG 59.306 37.037 10.21 0.00 42.72 2.27
2851 4457 7.526608 CCACATAAGCAGTATTTTCTCGAAAA 58.473 34.615 7.22 7.22 43.48 2.29
2852 4458 6.403200 GCCACATAAGCAGTATTTTCTCGAAA 60.403 38.462 0.00 0.00 0.00 3.46
2853 4459 5.064707 GCCACATAAGCAGTATTTTCTCGAA 59.935 40.000 0.00 0.00 0.00 3.71
2854 4460 4.570772 GCCACATAAGCAGTATTTTCTCGA 59.429 41.667 0.00 0.00 0.00 4.04
2855 4461 4.332543 TGCCACATAAGCAGTATTTTCTCG 59.667 41.667 0.00 0.00 34.69 4.04
2856 4462 5.818136 TGCCACATAAGCAGTATTTTCTC 57.182 39.130 0.00 0.00 34.69 2.87
2857 4463 5.711976 ACTTGCCACATAAGCAGTATTTTCT 59.288 36.000 0.00 0.00 42.17 2.52
2858 4464 5.954335 ACTTGCCACATAAGCAGTATTTTC 58.046 37.500 0.00 0.00 42.17 2.29
2859 4465 5.982890 ACTTGCCACATAAGCAGTATTTT 57.017 34.783 0.00 0.00 42.17 1.82
2860 4466 7.645058 ATTACTTGCCACATAAGCAGTATTT 57.355 32.000 0.00 0.00 42.17 1.40
2861 4467 7.645058 AATTACTTGCCACATAAGCAGTATT 57.355 32.000 0.00 0.00 42.17 1.89
2862 4468 8.746052 TTAATTACTTGCCACATAAGCAGTAT 57.254 30.769 0.00 0.00 42.17 2.12
2863 4469 8.620416 CATTAATTACTTGCCACATAAGCAGTA 58.380 33.333 0.00 0.00 42.17 2.74
2864 4470 7.339212 TCATTAATTACTTGCCACATAAGCAGT 59.661 33.333 0.00 0.00 42.17 4.40
2865 4471 7.706159 TCATTAATTACTTGCCACATAAGCAG 58.294 34.615 0.00 0.00 42.17 4.24
2866 4472 7.555914 TCTCATTAATTACTTGCCACATAAGCA 59.444 33.333 0.00 0.00 38.81 3.91
2867 4473 7.930217 TCTCATTAATTACTTGCCACATAAGC 58.070 34.615 0.00 0.00 0.00 3.09
2868 4474 8.562892 CCTCTCATTAATTACTTGCCACATAAG 58.437 37.037 0.00 0.00 0.00 1.73
2869 4475 8.052748 ACCTCTCATTAATTACTTGCCACATAA 58.947 33.333 0.00 0.00 0.00 1.90
2870 4476 7.498900 CACCTCTCATTAATTACTTGCCACATA 59.501 37.037 0.00 0.00 0.00 2.29
2871 4477 6.319658 CACCTCTCATTAATTACTTGCCACAT 59.680 38.462 0.00 0.00 0.00 3.21
2872 4478 5.647658 CACCTCTCATTAATTACTTGCCACA 59.352 40.000 0.00 0.00 0.00 4.17
2873 4479 5.066505 CCACCTCTCATTAATTACTTGCCAC 59.933 44.000 0.00 0.00 0.00 5.01
2874 4480 5.192927 CCACCTCTCATTAATTACTTGCCA 58.807 41.667 0.00 0.00 0.00 4.92
2875 4481 5.193679 ACCACCTCTCATTAATTACTTGCC 58.806 41.667 0.00 0.00 0.00 4.52
2876 4482 7.335924 TGTTACCACCTCTCATTAATTACTTGC 59.664 37.037 0.00 0.00 0.00 4.01
2877 4483 8.786826 TGTTACCACCTCTCATTAATTACTTG 57.213 34.615 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.