Multiple sequence alignment - TraesCS3B01G293000

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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 TraesCS3B01G293000 chr3B 100.000 3489 0 0 1 3489 471802255 471798767 0.000000e+00 6444.0
1 TraesCS3B01G293000 chr3B 81.229 293 35 13 1300 1589 37970916 37971191 5.860000e-53 219.0
2 TraesCS3B01G293000 chr3B 79.293 198 24 9 2737 2918 119401367 119401563 4.730000e-24 122.0
3 TraesCS3B01G293000 chr3D 89.535 2647 107 49 112 2685 362071546 362068997 0.000000e+00 3197.0
4 TraesCS3B01G293000 chr3D 81.656 785 115 19 2719 3485 68885162 68885935 2.960000e-175 625.0
5 TraesCS3B01G293000 chr3D 87.863 379 27 7 2282 2656 362042925 362042562 8.950000e-116 427.0
6 TraesCS3B01G293000 chr3D 93.956 182 10 1 1825 2006 538374007 538374187 1.230000e-69 274.0
7 TraesCS3B01G293000 chr3D 84.342 281 27 4 1982 2256 362043192 362042923 3.450000e-65 259.0
8 TraesCS3B01G293000 chr3D 100.000 31 0 0 2654 2684 362042551 362042521 1.350000e-04 58.4
9 TraesCS3B01G293000 chr3A 90.202 2133 94 34 585 2685 482185137 482183088 0.000000e+00 2675.0
10 TraesCS3B01G293000 chr3A 84.349 607 36 27 1 586 482187222 482186654 1.100000e-149 540.0
11 TraesCS3B01G293000 chr3A 83.103 290 46 3 1686 1972 30997355 30997644 9.610000e-66 261.0
12 TraesCS3B01G293000 chr7B 86.173 810 89 12 2695 3485 488365736 488364931 0.000000e+00 854.0
13 TraesCS3B01G293000 chr7B 84.363 793 97 16 2717 3485 558322675 558321886 0.000000e+00 752.0
14 TraesCS3B01G293000 chr1B 86.101 813 90 13 2692 3485 646181891 646182699 0.000000e+00 854.0
15 TraesCS3B01G293000 chr1B 86.443 745 75 11 2756 3485 120063238 120063971 0.000000e+00 793.0
16 TraesCS3B01G293000 chr1B 84.777 808 102 10 2695 3485 10950796 10949993 0.000000e+00 791.0
17 TraesCS3B01G293000 chr1B 84.645 788 104 15 2709 3489 67545243 67544466 0.000000e+00 769.0
18 TraesCS3B01G293000 chr1B 85.694 713 77 16 1295 1984 625082781 625083491 0.000000e+00 728.0
19 TraesCS3B01G293000 chr1B 85.075 737 78 23 1277 1986 625145396 625146127 0.000000e+00 723.0
20 TraesCS3B01G293000 chr1B 83.924 734 78 30 1277 1979 624971001 624971725 0.000000e+00 665.0
21 TraesCS3B01G293000 chr7D 85.785 809 93 14 2695 3485 4750525 4749721 0.000000e+00 837.0
22 TraesCS3B01G293000 chr5B 85.732 813 86 14 2695 3485 544395684 544394880 0.000000e+00 832.0
23 TraesCS3B01G293000 chr2B 84.994 813 101 10 2692 3487 388585899 388586707 0.000000e+00 806.0
24 TraesCS3B01G293000 chr2B 84.920 809 87 13 2704 3485 525557874 525557074 0.000000e+00 785.0
25 TraesCS3B01G293000 chr2B 84.615 793 78 15 2717 3487 653622012 653622782 0.000000e+00 749.0
26 TraesCS3B01G293000 chr4B 86.409 699 53 24 1999 2684 89359159 89359828 0.000000e+00 726.0
27 TraesCS3B01G293000 chr4B 88.669 556 51 8 1456 2006 89357989 89358537 0.000000e+00 667.0
28 TraesCS3B01G293000 chr1D 82.080 904 101 40 1101 1984 454458406 454457544 0.000000e+00 715.0
29 TraesCS3B01G293000 chr1D 85.278 720 70 27 1295 1984 454812949 454813662 0.000000e+00 710.0
30 TraesCS3B01G293000 chr1D 84.636 729 86 19 1277 1984 454493643 454492920 0.000000e+00 702.0
31 TraesCS3B01G293000 chr1A 84.986 726 82 19 1277 1979 548733538 548734259 0.000000e+00 712.0
32 TraesCS3B01G293000 chr1A 84.831 712 85 16 1295 1984 548772602 548773312 0.000000e+00 695.0
33 TraesCS3B01G293000 chr2A 89.655 551 50 5 1456 2006 751920223 751920766 0.000000e+00 695.0
34 TraesCS3B01G293000 chr2A 82.561 453 38 18 1999 2441 751942877 751943298 9.210000e-96 361.0
35 TraesCS3B01G293000 chr2A 90.270 185 12 3 2500 2684 751943330 751943508 1.620000e-58 237.0
36 TraesCS3B01G293000 chr2D 81.369 789 112 16 2717 3487 180537817 180538588 8.280000e-171 610.0
37 TraesCS3B01G293000 chr6A 89.868 454 38 7 1456 1909 17776491 17776936 8.400000e-161 577.0
38 TraesCS3B01G293000 chr6A 82.836 134 18 4 2036 2165 17776931 17777063 7.910000e-22 115.0
39 TraesCS3B01G293000 chr7A 79.623 795 118 26 2719 3485 55819861 55819083 6.630000e-147 531.0
40 TraesCS3B01G293000 chr5D 87.445 454 29 13 2237 2684 48052499 48052068 6.730000e-137 497.0
41 TraesCS3B01G293000 chr5D 93.956 182 10 1 1825 2006 457997831 457998011 1.230000e-69 274.0
42 TraesCS3B01G293000 chr4D 92.857 182 11 2 1825 2006 33242069 33241890 2.670000e-66 263.0
43 TraesCS3B01G293000 chr4D 81.308 107 20 0 2718 2824 479386355 479386461 1.730000e-13 87.9
44 TraesCS3B01G293000 chrUn 82.069 290 49 3 1692 1978 270382314 270382025 9.670000e-61 244.0
45 TraesCS3B01G293000 chr4A 80.368 163 17 7 2765 2912 698433724 698433562 3.680000e-20 110.0


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 TraesCS3B01G293000 chr3B 471798767 471802255 3488 True 6444.000000 6444 100.0000 1 3489 1 chr3B.!!$R1 3488
1 TraesCS3B01G293000 chr3D 362068997 362071546 2549 True 3197.000000 3197 89.5350 112 2685 1 chr3D.!!$R1 2573
2 TraesCS3B01G293000 chr3D 68885162 68885935 773 False 625.000000 625 81.6560 2719 3485 1 chr3D.!!$F1 766
3 TraesCS3B01G293000 chr3D 362042521 362043192 671 True 248.133333 427 90.7350 1982 2684 3 chr3D.!!$R2 702
4 TraesCS3B01G293000 chr3A 482183088 482187222 4134 True 1607.500000 2675 87.2755 1 2685 2 chr3A.!!$R1 2684
5 TraesCS3B01G293000 chr7B 488364931 488365736 805 True 854.000000 854 86.1730 2695 3485 1 chr7B.!!$R1 790
6 TraesCS3B01G293000 chr7B 558321886 558322675 789 True 752.000000 752 84.3630 2717 3485 1 chr7B.!!$R2 768
7 TraesCS3B01G293000 chr1B 646181891 646182699 808 False 854.000000 854 86.1010 2692 3485 1 chr1B.!!$F5 793
8 TraesCS3B01G293000 chr1B 120063238 120063971 733 False 793.000000 793 86.4430 2756 3485 1 chr1B.!!$F1 729
9 TraesCS3B01G293000 chr1B 10949993 10950796 803 True 791.000000 791 84.7770 2695 3485 1 chr1B.!!$R1 790
10 TraesCS3B01G293000 chr1B 67544466 67545243 777 True 769.000000 769 84.6450 2709 3489 1 chr1B.!!$R2 780
11 TraesCS3B01G293000 chr1B 625082781 625083491 710 False 728.000000 728 85.6940 1295 1984 1 chr1B.!!$F3 689
12 TraesCS3B01G293000 chr1B 625145396 625146127 731 False 723.000000 723 85.0750 1277 1986 1 chr1B.!!$F4 709
13 TraesCS3B01G293000 chr1B 624971001 624971725 724 False 665.000000 665 83.9240 1277 1979 1 chr1B.!!$F2 702
14 TraesCS3B01G293000 chr7D 4749721 4750525 804 True 837.000000 837 85.7850 2695 3485 1 chr7D.!!$R1 790
15 TraesCS3B01G293000 chr5B 544394880 544395684 804 True 832.000000 832 85.7320 2695 3485 1 chr5B.!!$R1 790
16 TraesCS3B01G293000 chr2B 388585899 388586707 808 False 806.000000 806 84.9940 2692 3487 1 chr2B.!!$F1 795
17 TraesCS3B01G293000 chr2B 525557074 525557874 800 True 785.000000 785 84.9200 2704 3485 1 chr2B.!!$R1 781
18 TraesCS3B01G293000 chr2B 653622012 653622782 770 False 749.000000 749 84.6150 2717 3487 1 chr2B.!!$F2 770
19 TraesCS3B01G293000 chr4B 89357989 89359828 1839 False 696.500000 726 87.5390 1456 2684 2 chr4B.!!$F1 1228
20 TraesCS3B01G293000 chr1D 454457544 454458406 862 True 715.000000 715 82.0800 1101 1984 1 chr1D.!!$R1 883
21 TraesCS3B01G293000 chr1D 454812949 454813662 713 False 710.000000 710 85.2780 1295 1984 1 chr1D.!!$F1 689
22 TraesCS3B01G293000 chr1D 454492920 454493643 723 True 702.000000 702 84.6360 1277 1984 1 chr1D.!!$R2 707
23 TraesCS3B01G293000 chr1A 548733538 548734259 721 False 712.000000 712 84.9860 1277 1979 1 chr1A.!!$F1 702
24 TraesCS3B01G293000 chr1A 548772602 548773312 710 False 695.000000 695 84.8310 1295 1984 1 chr1A.!!$F2 689
25 TraesCS3B01G293000 chr2A 751920223 751920766 543 False 695.000000 695 89.6550 1456 2006 1 chr2A.!!$F1 550
26 TraesCS3B01G293000 chr2A 751942877 751943508 631 False 299.000000 361 86.4155 1999 2684 2 chr2A.!!$F2 685
27 TraesCS3B01G293000 chr2D 180537817 180538588 771 False 610.000000 610 81.3690 2717 3487 1 chr2D.!!$F1 770
28 TraesCS3B01G293000 chr6A 17776491 17777063 572 False 346.000000 577 86.3520 1456 2165 2 chr6A.!!$F1 709
29 TraesCS3B01G293000 chr7A 55819083 55819861 778 True 531.000000 531 79.6230 2719 3485 1 chr7A.!!$R1 766

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
397 449 0.037590 AAGCCCAATCCACTTGCGTA 59.962 50.0 0.00 0.00 33.2 4.42 F
536 590 0.105593 CTAGCCGGCACACATCATCT 59.894 55.0 31.54 5.89 0.0 2.90 F
665 2263 0.180171 CTGACTGACCCACACCAACA 59.820 55.0 0.00 0.00 0.0 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1729 3404 2.037136 CAGCCTGTTCAGCTTCCCG 61.037 63.158 0.00 0.00 38.95 5.14 R
2056 4372 2.920912 GACTGGTCCACGGGGTCA 60.921 66.667 2.12 2.57 34.93 4.02 R
2648 5024 1.016130 CACATCACGTCTCAGGGTGC 61.016 60.000 0.00 0.00 34.20 5.01 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
28 29 1.817099 CTTGGAGGCAGCGGCTTAG 60.817 63.158 9.17 0.00 38.98 2.18
31 32 1.068250 GGAGGCAGCGGCTTAGTAG 59.932 63.158 9.17 0.00 38.98 2.57
32 33 1.677637 GGAGGCAGCGGCTTAGTAGT 61.678 60.000 9.17 0.00 38.98 2.73
33 34 1.030457 GAGGCAGCGGCTTAGTAGTA 58.970 55.000 9.17 0.00 38.98 1.82
34 35 1.407979 GAGGCAGCGGCTTAGTAGTAA 59.592 52.381 9.17 0.00 38.98 2.24
35 36 1.136500 AGGCAGCGGCTTAGTAGTAAC 59.864 52.381 9.17 0.00 40.87 2.50
36 37 1.568606 GCAGCGGCTTAGTAGTAACC 58.431 55.000 0.00 0.00 36.96 2.85
44 45 3.243805 GGCTTAGTAGTAACCTGGCTAGC 60.244 52.174 6.04 6.04 0.00 3.42
51 52 4.100279 AGTAACCTGGCTAGCTGTTTTT 57.900 40.909 15.72 4.69 0.00 1.94
52 53 3.821033 AGTAACCTGGCTAGCTGTTTTTG 59.179 43.478 15.72 0.00 0.00 2.44
53 54 2.364972 ACCTGGCTAGCTGTTTTTGT 57.635 45.000 15.72 0.00 0.00 2.83
54 55 2.230660 ACCTGGCTAGCTGTTTTTGTC 58.769 47.619 15.72 0.00 0.00 3.18
55 56 2.158608 ACCTGGCTAGCTGTTTTTGTCT 60.159 45.455 15.72 0.00 0.00 3.41
56 57 3.072476 ACCTGGCTAGCTGTTTTTGTCTA 59.928 43.478 15.72 0.00 0.00 2.59
57 58 4.263506 ACCTGGCTAGCTGTTTTTGTCTAT 60.264 41.667 15.72 0.00 0.00 1.98
58 59 4.095483 CCTGGCTAGCTGTTTTTGTCTATG 59.905 45.833 15.72 0.00 0.00 2.23
78 79 9.817809 GTCTATGATGATTAAACCAACAGAGTA 57.182 33.333 10.55 0.82 30.83 2.59
79 80 9.817809 TCTATGATGATTAAACCAACAGAGTAC 57.182 33.333 10.55 0.00 30.83 2.73
80 81 7.865706 ATGATGATTAAACCAACAGAGTACC 57.134 36.000 0.00 0.00 0.00 3.34
81 82 5.872617 TGATGATTAAACCAACAGAGTACCG 59.127 40.000 0.00 0.00 0.00 4.02
82 83 4.571919 TGATTAAACCAACAGAGTACCGG 58.428 43.478 0.00 0.00 0.00 5.28
83 84 4.040706 TGATTAAACCAACAGAGTACCGGT 59.959 41.667 13.98 13.98 0.00 5.28
84 85 2.249844 AAACCAACAGAGTACCGGTG 57.750 50.000 19.93 1.54 0.00 4.94
85 86 1.125633 AACCAACAGAGTACCGGTGT 58.874 50.000 19.93 3.63 0.00 4.16
99 100 4.708726 ACCGGTGTAGTGTGTTATCTAC 57.291 45.455 6.12 0.00 37.58 2.59
100 101 4.338879 ACCGGTGTAGTGTGTTATCTACT 58.661 43.478 6.12 0.00 37.83 2.57
101 102 4.397417 ACCGGTGTAGTGTGTTATCTACTC 59.603 45.833 6.12 0.00 37.83 2.59
102 103 4.201990 CCGGTGTAGTGTGTTATCTACTCC 60.202 50.000 0.00 11.15 42.46 3.85
103 104 4.201990 CGGTGTAGTGTGTTATCTACTCCC 60.202 50.000 13.87 8.58 42.70 4.30
104 105 4.954826 GGTGTAGTGTGTTATCTACTCCCT 59.045 45.833 10.45 0.00 41.23 4.20
105 106 5.163540 GGTGTAGTGTGTTATCTACTCCCTG 60.164 48.000 10.45 0.00 41.23 4.45
106 107 4.954202 TGTAGTGTGTTATCTACTCCCTGG 59.046 45.833 0.00 0.00 37.83 4.45
107 108 2.766828 AGTGTGTTATCTACTCCCTGGC 59.233 50.000 0.00 0.00 0.00 4.85
108 109 1.754803 TGTGTTATCTACTCCCTGGCG 59.245 52.381 0.00 0.00 0.00 5.69
109 110 2.029623 GTGTTATCTACTCCCTGGCGA 58.970 52.381 0.00 0.00 0.00 5.54
110 111 2.034812 GTGTTATCTACTCCCTGGCGAG 59.965 54.545 9.73 9.73 35.88 5.03
132 133 3.209410 CAAGTGCTGGACTTTTCTGTCT 58.791 45.455 12.11 0.00 42.70 3.41
180 181 2.354510 CGTATGGACGGACAAATGCATT 59.645 45.455 5.99 5.99 45.63 3.56
181 182 2.945447 ATGGACGGACAAATGCATTG 57.055 45.000 13.82 9.78 44.95 2.82
182 183 0.243365 TGGACGGACAAATGCATTGC 59.757 50.000 13.82 0.46 43.13 3.56
183 184 0.243365 GGACGGACAAATGCATTGCA 59.757 50.000 13.82 14.72 43.13 4.08
193 194 3.910817 TGCATTGCATGGGTGTTTC 57.089 47.368 7.38 0.00 31.71 2.78
194 195 1.340088 TGCATTGCATGGGTGTTTCT 58.660 45.000 7.38 0.00 31.71 2.52
195 196 1.001068 TGCATTGCATGGGTGTTTCTG 59.999 47.619 7.38 0.00 31.71 3.02
196 197 1.673626 GCATTGCATGGGTGTTTCTGG 60.674 52.381 3.15 0.00 0.00 3.86
197 198 0.609662 ATTGCATGGGTGTTTCTGGC 59.390 50.000 0.00 0.00 0.00 4.85
262 272 3.392947 TCCTGTGGATGGTGAAGTTGTAA 59.607 43.478 0.00 0.00 0.00 2.41
269 279 4.764823 GGATGGTGAAGTTGTAAATGACCA 59.235 41.667 0.00 0.00 36.48 4.02
320 336 1.410517 CCTCGCTAGTCCATGTCACAT 59.589 52.381 0.00 0.00 0.00 3.21
397 449 0.037590 AAGCCCAATCCACTTGCGTA 59.962 50.000 0.00 0.00 33.20 4.42
536 590 0.105593 CTAGCCGGCACACATCATCT 59.894 55.000 31.54 5.89 0.00 2.90
548 602 3.884693 ACACATCATCTGCAACAAGAACA 59.115 39.130 0.00 0.00 0.00 3.18
609 2181 4.460731 TCCATCTACCTTCATCATCTAGCG 59.539 45.833 0.00 0.00 0.00 4.26
627 2199 2.499289 AGCGATAGATAGATGGCCCTTG 59.501 50.000 0.00 0.00 39.76 3.61
629 2201 3.430098 GCGATAGATAGATGGCCCTTGAG 60.430 52.174 0.00 0.00 39.76 3.02
633 2228 0.394565 ATAGATGGCCCTTGAGCGAC 59.605 55.000 0.00 0.00 0.00 5.19
635 2230 4.473520 ATGGCCCTTGAGCGACCG 62.474 66.667 0.00 0.00 0.00 4.79
664 2262 1.166531 GCTGACTGACCCACACCAAC 61.167 60.000 0.00 0.00 0.00 3.77
665 2263 0.180171 CTGACTGACCCACACCAACA 59.820 55.000 0.00 0.00 0.00 3.33
707 2305 3.607310 CGCTCTGACCACGTATCTATGTC 60.607 52.174 0.00 0.00 0.00 3.06
708 2306 3.566322 GCTCTGACCACGTATCTATGTCT 59.434 47.826 0.00 0.00 0.00 3.41
709 2307 4.319911 GCTCTGACCACGTATCTATGTCTC 60.320 50.000 0.00 0.00 0.00 3.36
710 2308 3.808174 TCTGACCACGTATCTATGTCTCG 59.192 47.826 0.00 0.00 0.00 4.04
711 2309 3.800531 TGACCACGTATCTATGTCTCGA 58.199 45.455 0.00 0.00 0.00 4.04
712 2310 4.386711 TGACCACGTATCTATGTCTCGAT 58.613 43.478 0.00 0.00 0.00 3.59
713 2311 4.451435 TGACCACGTATCTATGTCTCGATC 59.549 45.833 0.00 0.00 0.00 3.69
714 2312 3.752222 ACCACGTATCTATGTCTCGATCC 59.248 47.826 0.00 0.00 0.00 3.36
715 2313 3.751698 CCACGTATCTATGTCTCGATCCA 59.248 47.826 0.00 0.00 0.00 3.41
716 2314 4.142795 CCACGTATCTATGTCTCGATCCAG 60.143 50.000 0.00 0.00 0.00 3.86
717 2315 3.437395 ACGTATCTATGTCTCGATCCAGC 59.563 47.826 0.00 0.00 0.00 4.85
791 2393 4.909696 TTATATGGTTTGCATTCACCGG 57.090 40.909 0.00 0.00 35.60 5.28
797 2399 0.316841 TTTGCATTCACCGGAAAGCC 59.683 50.000 9.46 0.00 44.81 4.35
889 2491 0.896940 GAGCATGGTATGGGCATGGG 60.897 60.000 0.00 0.00 0.00 4.00
890 2492 1.909781 GCATGGTATGGGCATGGGG 60.910 63.158 0.00 0.00 0.00 4.96
891 2493 1.852707 CATGGTATGGGCATGGGGA 59.147 57.895 0.00 0.00 0.00 4.81
892 2494 0.251474 CATGGTATGGGCATGGGGAG 60.251 60.000 0.00 0.00 0.00 4.30
893 2495 0.403304 ATGGTATGGGCATGGGGAGA 60.403 55.000 0.00 0.00 0.00 3.71
894 2496 1.061905 TGGTATGGGCATGGGGAGAG 61.062 60.000 0.00 0.00 0.00 3.20
935 2537 1.078708 CATACACGACACCCACCCC 60.079 63.158 0.00 0.00 0.00 4.95
936 2538 1.536907 ATACACGACACCCACCCCA 60.537 57.895 0.00 0.00 0.00 4.96
937 2539 1.833787 ATACACGACACCCACCCCAC 61.834 60.000 0.00 0.00 0.00 4.61
938 2540 4.636435 CACGACACCCACCCCACC 62.636 72.222 0.00 0.00 0.00 4.61
2122 4441 2.649034 GGCGTCGACCTTCTGACA 59.351 61.111 10.58 0.00 34.78 3.58
2340 4688 6.350103 AGCTTAGCTTAATTAGTCCCTTGTC 58.650 40.000 0.00 0.00 33.89 3.18
2403 4759 5.709164 GCATGCCCTGATGTAAATCTTATCT 59.291 40.000 6.36 0.00 0.00 1.98
2405 4761 7.255730 GCATGCCCTGATGTAAATCTTATCTTT 60.256 37.037 6.36 0.00 0.00 2.52
2408 4764 6.073003 GCCCTGATGTAAATCTTATCTTTCCG 60.073 42.308 0.00 0.00 0.00 4.30
2481 4856 0.658244 CAACCGACGACGACGAAGAA 60.658 55.000 20.63 0.00 42.66 2.52
2482 4857 0.385223 AACCGACGACGACGAAGAAG 60.385 55.000 20.63 6.36 42.66 2.85
2483 4858 1.224069 ACCGACGACGACGAAGAAGA 61.224 55.000 20.63 0.00 42.66 2.87
2484 4859 0.110509 CCGACGACGACGAAGAAGAA 60.111 55.000 20.63 0.00 42.66 2.52
2631 5006 5.291293 TCTTGCGCCTTTTTATACACTTC 57.709 39.130 4.18 0.00 0.00 3.01
2633 5008 6.167685 TCTTGCGCCTTTTTATACACTTCTA 58.832 36.000 4.18 0.00 0.00 2.10
2636 5011 5.114081 GCGCCTTTTTATACACTTCTAGGA 58.886 41.667 0.00 0.00 0.00 2.94
2685 5074 6.368791 GTGATGTGATTGTTGTGTAGCTAAGA 59.631 38.462 0.00 0.00 0.00 2.10
2686 5075 6.591448 TGATGTGATTGTTGTGTAGCTAAGAG 59.409 38.462 0.00 0.00 0.00 2.85
2687 5076 4.690748 TGTGATTGTTGTGTAGCTAAGAGC 59.309 41.667 0.00 0.00 42.84 4.09
2688 5077 4.690748 GTGATTGTTGTGTAGCTAAGAGCA 59.309 41.667 0.00 0.00 45.56 4.26
2689 5078 5.352569 GTGATTGTTGTGTAGCTAAGAGCAT 59.647 40.000 0.00 0.00 45.56 3.79
2690 5079 5.582269 TGATTGTTGTGTAGCTAAGAGCATC 59.418 40.000 0.00 0.00 45.56 3.91
2693 5082 1.409064 TGTGTAGCTAAGAGCATCCGG 59.591 52.381 0.00 0.00 45.56 5.14
2699 5088 2.388890 CTAAGAGCATCCGGCCCCAG 62.389 65.000 0.00 0.00 46.50 4.45
2746 5137 1.586154 CTGGCATCGAAAAACGCCCT 61.586 55.000 9.70 0.00 44.22 5.19
2753 5144 0.444651 CGAAAAACGCCCTAATCGCA 59.555 50.000 0.00 0.00 34.51 5.10
2754 5145 1.063469 CGAAAAACGCCCTAATCGCAT 59.937 47.619 0.00 0.00 34.51 4.73
2844 5260 2.351276 GGAGCTCCGGCAAAGGAA 59.649 61.111 19.06 0.00 40.25 3.36
2848 5264 0.673985 AGCTCCGGCAAAGGAAAAAC 59.326 50.000 0.00 0.00 40.25 2.43
2853 5269 1.335233 CCGGCAAAGGAAAAACGTACC 60.335 52.381 0.00 0.00 0.00 3.34
2909 5342 1.829222 GTCCAGATTTACCTCCGACCA 59.171 52.381 0.00 0.00 0.00 4.02
2971 5414 2.358125 CGTCGTCCATTGCCCACA 60.358 61.111 0.00 0.00 0.00 4.17
2974 5417 0.889186 GTCGTCCATTGCCCACAACT 60.889 55.000 0.00 0.00 38.99 3.16
3053 5501 1.778027 CGTCGTCCGGGCAACTTTTT 61.778 55.000 6.96 0.00 0.00 1.94
3083 5532 4.132441 CGCGTAGGGCCCGTACAA 62.132 66.667 18.44 0.00 38.94 2.41
3135 5584 3.561120 TTCGGTGATTTGCCCGGCT 62.561 57.895 11.61 0.00 44.32 5.52
3162 5616 1.285078 TGGACTCGGAAGATGAGGAGA 59.715 52.381 0.00 0.00 40.84 3.71
3225 5679 0.757512 GGAGCAGGAGCATCTCATGA 59.242 55.000 11.99 0.00 43.80 3.07
3324 5779 0.320374 AAAGAACCGGCATCGTCTGA 59.680 50.000 0.00 0.00 33.95 3.27
3408 5863 2.892334 CGGCGCCGTTATTGGATGG 61.892 63.158 39.71 8.03 34.35 3.51
3424 5879 0.541764 ATGGGCCGAAAGCTTTTCCA 60.542 50.000 14.05 17.51 43.05 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 1.261938 TACTAAGCCGCTGCCTCCAA 61.262 55.000 0.00 0.00 38.69 3.53
28 29 3.889520 AACAGCTAGCCAGGTTACTAC 57.110 47.619 12.13 0.00 0.00 2.73
31 32 3.568430 ACAAAAACAGCTAGCCAGGTTAC 59.432 43.478 12.13 0.00 0.00 2.50
32 33 3.818773 GACAAAAACAGCTAGCCAGGTTA 59.181 43.478 12.13 0.00 0.00 2.85
33 34 2.623416 GACAAAAACAGCTAGCCAGGTT 59.377 45.455 12.13 11.01 0.00 3.50
34 35 2.158608 AGACAAAAACAGCTAGCCAGGT 60.159 45.455 12.13 4.66 0.00 4.00
35 36 2.508526 AGACAAAAACAGCTAGCCAGG 58.491 47.619 12.13 3.94 0.00 4.45
36 37 4.937620 TCATAGACAAAAACAGCTAGCCAG 59.062 41.667 12.13 7.21 0.00 4.85
51 52 8.321353 ACTCTGTTGGTTTAATCATCATAGACA 58.679 33.333 8.14 0.00 0.00 3.41
52 53 8.723942 ACTCTGTTGGTTTAATCATCATAGAC 57.276 34.615 8.14 0.00 0.00 2.59
53 54 9.817809 GTACTCTGTTGGTTTAATCATCATAGA 57.182 33.333 8.14 0.00 0.00 1.98
54 55 9.046296 GGTACTCTGTTGGTTTAATCATCATAG 57.954 37.037 0.00 1.70 0.00 2.23
55 56 7.709182 CGGTACTCTGTTGGTTTAATCATCATA 59.291 37.037 0.00 0.00 0.00 2.15
56 57 6.538742 CGGTACTCTGTTGGTTTAATCATCAT 59.461 38.462 0.00 0.00 0.00 2.45
57 58 5.872617 CGGTACTCTGTTGGTTTAATCATCA 59.127 40.000 0.00 0.00 0.00 3.07
58 59 5.293569 CCGGTACTCTGTTGGTTTAATCATC 59.706 44.000 0.00 0.00 0.00 2.92
67 68 1.891150 CTACACCGGTACTCTGTTGGT 59.109 52.381 6.87 0.00 0.00 3.67
73 74 2.283145 ACACACTACACCGGTACTCT 57.717 50.000 6.87 0.00 0.00 3.24
78 79 4.338879 AGTAGATAACACACTACACCGGT 58.661 43.478 0.00 0.00 40.68 5.28
79 80 4.201990 GGAGTAGATAACACACTACACCGG 60.202 50.000 0.00 0.00 39.24 5.28
80 81 4.201990 GGGAGTAGATAACACACTACACCG 60.202 50.000 0.00 0.00 44.87 4.94
81 82 4.954826 AGGGAGTAGATAACACACTACACC 59.045 45.833 0.00 0.00 43.97 4.16
82 83 5.163540 CCAGGGAGTAGATAACACACTACAC 60.164 48.000 0.00 0.00 40.68 2.90
83 84 4.954202 CCAGGGAGTAGATAACACACTACA 59.046 45.833 0.00 0.00 40.68 2.74
84 85 4.202131 GCCAGGGAGTAGATAACACACTAC 60.202 50.000 0.00 0.00 39.15 2.73
85 86 3.958798 GCCAGGGAGTAGATAACACACTA 59.041 47.826 0.00 0.00 29.70 2.74
99 100 2.435586 CACTTGCTCGCCAGGGAG 60.436 66.667 7.33 7.33 37.11 4.30
100 101 4.704833 GCACTTGCTCGCCAGGGA 62.705 66.667 0.00 0.00 38.21 4.20
109 110 6.741431 AGACAGAAAAGTCCAGCACTTGCT 62.741 45.833 0.00 0.00 45.32 3.91
110 111 1.678101 ACAGAAAAGTCCAGCACTTGC 59.322 47.619 0.00 0.00 45.32 4.01
132 133 0.673985 GACATGATCCGGATCGACCA 59.326 55.000 33.49 20.72 40.63 4.02
180 181 0.403655 TAGCCAGAAACACCCATGCA 59.596 50.000 0.00 0.00 0.00 3.96
181 182 1.098050 CTAGCCAGAAACACCCATGC 58.902 55.000 0.00 0.00 0.00 4.06
182 183 2.496899 ACTAGCCAGAAACACCCATG 57.503 50.000 0.00 0.00 0.00 3.66
183 184 3.074538 AGAAACTAGCCAGAAACACCCAT 59.925 43.478 0.00 0.00 0.00 4.00
184 185 2.441750 AGAAACTAGCCAGAAACACCCA 59.558 45.455 0.00 0.00 0.00 4.51
185 186 3.141767 AGAAACTAGCCAGAAACACCC 57.858 47.619 0.00 0.00 0.00 4.61
186 187 3.883489 ACAAGAAACTAGCCAGAAACACC 59.117 43.478 0.00 0.00 0.00 4.16
187 188 5.500645 AACAAGAAACTAGCCAGAAACAC 57.499 39.130 0.00 0.00 0.00 3.32
188 189 5.417580 ACAAACAAGAAACTAGCCAGAAACA 59.582 36.000 0.00 0.00 0.00 2.83
189 190 5.891451 ACAAACAAGAAACTAGCCAGAAAC 58.109 37.500 0.00 0.00 0.00 2.78
190 191 6.038936 GGTACAAACAAGAAACTAGCCAGAAA 59.961 38.462 0.00 0.00 0.00 2.52
191 192 5.529800 GGTACAAACAAGAAACTAGCCAGAA 59.470 40.000 0.00 0.00 0.00 3.02
192 193 5.061179 GGTACAAACAAGAAACTAGCCAGA 58.939 41.667 0.00 0.00 0.00 3.86
193 194 4.084013 CGGTACAAACAAGAAACTAGCCAG 60.084 45.833 0.00 0.00 0.00 4.85
194 195 3.810941 CGGTACAAACAAGAAACTAGCCA 59.189 43.478 0.00 0.00 0.00 4.75
195 196 3.811497 ACGGTACAAACAAGAAACTAGCC 59.189 43.478 0.00 0.00 0.00 3.93
196 197 5.413969 AACGGTACAAACAAGAAACTAGC 57.586 39.130 0.00 0.00 0.00 3.42
197 198 5.049886 GGGAACGGTACAAACAAGAAACTAG 60.050 44.000 0.00 0.00 0.00 2.57
234 242 5.640147 ACTTCACCATCCACAGGAAAATTA 58.360 37.500 0.00 0.00 34.34 1.40
262 272 2.424842 TTTGGAGGCGGCTGGTCATT 62.425 55.000 19.63 0.00 0.00 2.57
269 279 1.179174 GGAAGTTTTTGGAGGCGGCT 61.179 55.000 13.09 13.09 0.00 5.52
320 336 2.515757 TGTGCTGGCTTGTCGCAA 60.516 55.556 0.00 0.00 41.67 4.85
397 449 2.560542 TGTGGCGGAATTAATGTTGCTT 59.439 40.909 0.00 0.00 0.00 3.91
405 457 2.865079 TGAGGTTTGTGGCGGAATTAA 58.135 42.857 0.00 0.00 0.00 1.40
526 580 3.884693 TGTTCTTGTTGCAGATGATGTGT 59.115 39.130 0.00 0.00 0.00 3.72
536 590 5.336150 TGGAAAAGATTGTTCTTGTTGCA 57.664 34.783 0.00 0.00 41.42 4.08
548 602 4.837093 TGGTCTACGGATGGAAAAGATT 57.163 40.909 0.00 0.00 0.00 2.40
609 2181 3.430098 CGCTCAAGGGCCATCTATCTATC 60.430 52.174 6.18 0.00 0.00 2.08
620 2192 4.388499 TTCGGTCGCTCAAGGGCC 62.388 66.667 0.00 0.00 0.00 5.80
627 2199 1.519455 CTCATGGGTTCGGTCGCTC 60.519 63.158 0.00 0.00 0.00 5.03
629 2201 3.195698 GCTCATGGGTTCGGTCGC 61.196 66.667 0.00 0.00 0.00 5.19
633 2228 0.742281 CAGTCAGCTCATGGGTTCGG 60.742 60.000 0.00 0.00 0.00 4.30
635 2230 1.677217 GGTCAGTCAGCTCATGGGTTC 60.677 57.143 0.00 0.00 0.00 3.62
707 2305 2.420890 GGCTGAGGCTGGATCGAG 59.579 66.667 0.00 0.00 38.73 4.04
708 2306 3.157252 GGGCTGAGGCTGGATCGA 61.157 66.667 5.84 0.00 38.73 3.59
709 2307 3.473647 TGGGCTGAGGCTGGATCG 61.474 66.667 5.84 0.00 38.73 3.69
710 2308 2.191641 GTGGGCTGAGGCTGGATC 59.808 66.667 5.84 0.00 38.73 3.36
711 2309 3.790437 CGTGGGCTGAGGCTGGAT 61.790 66.667 5.84 0.00 38.73 3.41
808 2410 5.428253 TCTGCTGTTTTTAGGCTCGAATAT 58.572 37.500 0.00 0.00 0.00 1.28
810 2412 3.674997 TCTGCTGTTTTTAGGCTCGAAT 58.325 40.909 0.00 0.00 0.00 3.34
811 2413 3.120321 TCTGCTGTTTTTAGGCTCGAA 57.880 42.857 0.00 0.00 0.00 3.71
812 2414 2.806244 GTTCTGCTGTTTTTAGGCTCGA 59.194 45.455 0.00 0.00 0.00 4.04
813 2415 2.548057 TGTTCTGCTGTTTTTAGGCTCG 59.452 45.455 0.00 0.00 0.00 5.03
814 2416 4.568152 TTGTTCTGCTGTTTTTAGGCTC 57.432 40.909 0.00 0.00 0.00 4.70
815 2417 5.337578 TTTTGTTCTGCTGTTTTTAGGCT 57.662 34.783 0.00 0.00 0.00 4.58
816 2418 6.699642 TGTATTTTGTTCTGCTGTTTTTAGGC 59.300 34.615 0.00 0.00 0.00 3.93
817 2419 7.382218 CCTGTATTTTGTTCTGCTGTTTTTAGG 59.618 37.037 0.00 0.00 0.00 2.69
818 2420 7.920682 ACCTGTATTTTGTTCTGCTGTTTTTAG 59.079 33.333 0.00 0.00 0.00 1.85
858 2460 4.393155 ATGCTCCGCGTGGCTCAA 62.393 61.111 11.05 0.00 34.14 3.02
889 2491 1.511768 GTACGGTGCCACTCTCTCC 59.488 63.158 0.00 0.00 0.00 3.71
890 2492 1.248785 TGGTACGGTGCCACTCTCTC 61.249 60.000 14.29 0.00 0.00 3.20
891 2493 1.228769 TGGTACGGTGCCACTCTCT 60.229 57.895 14.29 0.00 0.00 3.10
892 2494 3.373226 TGGTACGGTGCCACTCTC 58.627 61.111 14.29 0.00 0.00 3.20
935 2537 4.864334 GATCCCAGCGGCAGGGTG 62.864 72.222 27.23 5.88 46.82 4.61
938 2540 3.764160 GAAGGATCCCAGCGGCAGG 62.764 68.421 8.55 4.14 0.00 4.85
939 2541 2.203126 GAAGGATCCCAGCGGCAG 60.203 66.667 8.55 0.00 0.00 4.85
1729 3404 2.037136 CAGCCTGTTCAGCTTCCCG 61.037 63.158 0.00 0.00 38.95 5.14
2056 4372 2.920912 GACTGGTCCACGGGGTCA 60.921 66.667 2.12 2.57 34.93 4.02
2077 4396 3.560251 ACGGCCTTCTGCACAGGT 61.560 61.111 0.00 0.00 43.89 4.00
2340 4688 8.964420 ATAAACAAACAAAGTTGATGATACCG 57.036 30.769 0.00 0.00 32.59 4.02
2403 4759 9.893634 TCCTCAATTAGTATACATTTTCGGAAA 57.106 29.630 5.50 0.00 0.00 3.13
2405 4761 9.542462 CTTCCTCAATTAGTATACATTTTCGGA 57.458 33.333 5.50 0.18 0.00 4.55
2408 4764 8.568794 GGGCTTCCTCAATTAGTATACATTTTC 58.431 37.037 5.50 0.00 0.00 2.29
2631 5006 5.755375 CAGGGTGCGCATATAAATATCCTAG 59.245 44.000 15.91 0.00 0.00 3.02
2633 5008 4.225042 TCAGGGTGCGCATATAAATATCCT 59.775 41.667 15.91 0.00 0.00 3.24
2636 5011 5.178797 GTCTCAGGGTGCGCATATAAATAT 58.821 41.667 15.91 0.00 0.00 1.28
2648 5024 1.016130 CACATCACGTCTCAGGGTGC 61.016 60.000 0.00 0.00 34.20 5.01
2699 5088 1.187567 AAACACTTGGGAGGGCATGC 61.188 55.000 9.90 9.90 0.00 4.06
2702 5091 3.625314 AAAAACACTTGGGAGGGCA 57.375 47.368 0.00 0.00 0.00 5.36
2746 5137 2.683968 GGCGTATTGAGGATGCGATTA 58.316 47.619 0.81 0.00 45.26 1.75
2753 5144 2.767505 GGAATTCGGCGTATTGAGGAT 58.232 47.619 16.50 0.00 0.00 3.24
2754 5145 1.537348 CGGAATTCGGCGTATTGAGGA 60.537 52.381 16.50 0.00 34.75 3.71
2829 5245 0.673985 GTTTTTCCTTTGCCGGAGCT 59.326 50.000 5.05 0.00 40.80 4.09
2839 5255 1.612676 GCCCAGGTACGTTTTTCCTT 58.387 50.000 0.00 0.00 0.00 3.36
2841 5257 0.537828 TGGCCCAGGTACGTTTTTCC 60.538 55.000 0.00 0.00 0.00 3.13
2844 5260 0.820482 GTGTGGCCCAGGTACGTTTT 60.820 55.000 0.00 0.00 0.00 2.43
2848 5264 2.047274 CAGTGTGGCCCAGGTACG 60.047 66.667 0.00 0.00 0.00 3.67
2971 5414 4.202264 CGGGAAATGGTCTATCTAGCAGTT 60.202 45.833 0.00 0.00 37.81 3.16
2974 5417 2.037251 GCGGGAAATGGTCTATCTAGCA 59.963 50.000 0.00 0.00 0.00 3.49
3036 5484 1.500512 CGAAAAAGTTGCCCGGACGA 61.501 55.000 0.73 0.00 0.00 4.20
3077 5526 2.552268 CAAACCCGCCGTTGTACG 59.448 61.111 0.00 0.00 42.11 3.67
3135 5584 2.682136 TTCCGAGTCCATGGCCGA 60.682 61.111 18.30 3.07 0.00 5.54
3140 5594 2.034878 TCCTCATCTTCCGAGTCCATG 58.965 52.381 0.00 0.00 0.00 3.66
3259 5713 3.494336 CTTGCCGCGGCTTCTCAG 61.494 66.667 45.79 29.30 42.51 3.35
3293 5747 1.001378 CGGTTCTTTGCTTTCACCCAG 60.001 52.381 0.00 0.00 0.00 4.45
3324 5779 2.503356 AGTAGAGCATGCAGTAGCCTTT 59.497 45.455 21.98 0.00 41.13 3.11
3408 5863 0.039165 CTGTGGAAAAGCTTTCGGCC 60.039 55.000 13.10 14.39 43.05 6.13
3424 5879 3.282021 CGGATGGAATTCACAATCCTGT 58.718 45.455 22.02 0.96 36.64 4.00


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

AutoCloner maintained by Alex Coulton.