Multiple sequence alignment - TraesCS5D01G500800

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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 TraesCS5D01G500800 chr5D 100.000 5686 0 0 1 5686 529214471 529220156 0.000000e+00 10501
1 TraesCS5D01G500800 chr5D 86.227 1031 107 26 2017 3029 416413231 416414244 0.000000e+00 1085
2 TraesCS5D01G500800 chr5D 84.654 997 80 35 3874 4852 416414867 416415808 0.000000e+00 926
3 TraesCS5D01G500800 chr5D 78.740 508 58 25 993 1456 416412416 416412917 1.550000e-75 294
4 TraesCS5D01G500800 chr5D 94.048 168 10 0 3694 3861 377988000 377988167 7.310000e-64 255
5 TraesCS5D01G500800 chr5B 90.733 2320 118 36 3394 5686 667674883 667677132 0.000000e+00 3003
6 TraesCS5D01G500800 chr5B 97.483 1629 36 2 1835 3463 667673263 667674886 0.000000e+00 2776
7 TraesCS5D01G500800 chr5B 92.234 1867 91 23 1 1845 667671254 667673088 0.000000e+00 2595
8 TraesCS5D01G500800 chr5B 86.117 1030 107 26 2017 3029 503214242 503215252 0.000000e+00 1077
9 TraesCS5D01G500800 chr5B 84.686 986 87 32 3874 4841 503215871 503216810 0.000000e+00 926
10 TraesCS5D01G500800 chr5B 76.434 488 58 33 999 1448 503213457 503213925 1.610000e-50 211
11 TraesCS5D01G500800 chr5B 86.131 137 15 3 5435 5571 503217109 503217241 1.650000e-30 145
12 TraesCS5D01G500800 chr5A 89.807 883 67 15 3977 4851 657381028 657381895 0.000000e+00 1110
13 TraesCS5D01G500800 chr5A 86.320 1038 103 14 2007 3037 657379476 657380481 0.000000e+00 1094
14 TraesCS5D01G500800 chr5A 85.256 997 83 30 3874 4852 529086022 529086972 0.000000e+00 968
15 TraesCS5D01G500800 chr5A 86.962 767 79 13 2188 2946 529084956 529085709 0.000000e+00 843
16 TraesCS5D01G500800 chr5A 81.900 663 85 18 5030 5686 657382045 657382678 1.400000e-145 527
17 TraesCS5D01G500800 chr5A 81.836 523 31 21 776 1265 657378455 657378946 1.160000e-101 381
18 TraesCS5D01G500800 chr5A 86.620 284 20 11 3430 3695 657380658 657380941 1.200000e-76 298
19 TraesCS5D01G500800 chr5A 77.576 495 58 35 999 1455 529084200 529084679 3.400000e-62 250
20 TraesCS5D01G500800 chr4D 96.386 166 6 0 3692 3857 34661523 34661688 2.020000e-69 274
21 TraesCS5D01G500800 chr4A 96.914 162 5 0 3696 3857 137966979 137967140 7.260000e-69 272
22 TraesCS5D01G500800 chr4A 96.914 162 5 0 3696 3857 137972830 137972669 7.260000e-69 272
23 TraesCS5D01G500800 chr4A 92.982 114 5 2 3067 3177 599587737 599587624 4.560000e-36 163
24 TraesCS5D01G500800 chr4A 90.833 120 7 3 3067 3183 309514989 309515107 2.120000e-34 158
25 TraesCS5D01G500800 chr6B 95.238 168 8 0 3690 3857 226361512 226361679 3.380000e-67 267
26 TraesCS5D01G500800 chr2B 92.473 186 13 1 3696 3880 608226725 608226910 1.210000e-66 265
27 TraesCS5D01G500800 chr7D 95.181 166 8 0 3692 3857 454079412 454079247 4.370000e-66 263
28 TraesCS5D01G500800 chr7D 90.833 120 7 3 3067 3183 88647411 88647529 2.120000e-34 158
29 TraesCS5D01G500800 chr3D 93.750 176 8 3 3685 3857 87926175 87926000 1.570000e-65 261
30 TraesCS5D01G500800 chr1D 93.860 114 5 1 3067 3178 397089072 397088959 2.720000e-38 171
31 TraesCS5D01G500800 chr7A 93.043 115 5 2 3067 3178 439137854 439137740 1.270000e-36 165
32 TraesCS5D01G500800 chr2D 93.043 115 5 2 3067 3178 440358775 440358889 1.270000e-36 165
33 TraesCS5D01G500800 chr3B 92.982 114 5 2 3067 3177 810706825 810706712 4.560000e-36 163
34 TraesCS5D01G500800 chrUn 92.174 115 6 2 3067 3178 216518744 216518630 5.900000e-35 159


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 TraesCS5D01G500800 chr5D 529214471 529220156 5685 False 10501.000000 10501 100.000000 1 5686 1 chr5D.!!$F2 5685
1 TraesCS5D01G500800 chr5D 416412416 416415808 3392 False 768.333333 1085 83.207000 993 4852 3 chr5D.!!$F3 3859
2 TraesCS5D01G500800 chr5B 667671254 667677132 5878 False 2791.333333 3003 93.483333 1 5686 3 chr5B.!!$F2 5685
3 TraesCS5D01G500800 chr5B 503213457 503217241 3784 False 589.750000 1077 83.342000 999 5571 4 chr5B.!!$F1 4572
4 TraesCS5D01G500800 chr5A 529084200 529086972 2772 False 687.000000 968 83.264667 999 4852 3 chr5A.!!$F1 3853
5 TraesCS5D01G500800 chr5A 657378455 657382678 4223 False 682.000000 1110 85.296600 776 5686 5 chr5A.!!$F2 4910

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
752 764 0.109319 GCGTGGCCCACATAGTTTTG 60.109 55.000 15.45 0.0 33.40 2.44 F
754 766 0.965439 GTGGCCCACATAGTTTTGCA 59.035 50.000 9.55 0.0 34.08 4.08 F
755 767 1.342819 GTGGCCCACATAGTTTTGCAA 59.657 47.619 9.55 0.0 34.08 4.08 F
2553 2904 0.973632 TGCGAGCTAGACCAAGGAAA 59.026 50.000 0.00 0.0 0.00 3.13 F
3316 3733 0.766674 TACAGGACCAGGGTGCAGTT 60.767 55.000 12.80 0.0 37.39 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1554 1658 3.121030 CGGCCTGCGAACCTCAAG 61.121 66.667 0.00 0.00 0.00 3.02 R
2340 2689 3.319122 GGGCTTCCATCATCCACAATAAC 59.681 47.826 0.00 0.00 0.00 1.89 R
2599 2950 7.811653 TCATTAACACGAACATCAAGCATAAA 58.188 30.769 0.00 0.00 0.00 1.40 R
3445 3929 1.939934 ACACAAGAACACGTGTCCATG 59.060 47.619 23.61 21.19 42.61 3.66 R
4986 5544 0.393132 GTTCCTCCCAAGGTAGCAGC 60.393 60.000 0.00 0.00 43.82 5.25 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
21 22 2.867109 AGAACCATCACTGAACCAGG 57.133 50.000 0.00 0.00 35.51 4.45
74 75 9.553064 TTCTTTTGCTTTTCCTTTTTATATGCA 57.447 25.926 0.00 0.00 0.00 3.96
146 147 5.722021 AAGTTTTTGAATATCCGGCAACT 57.278 34.783 0.00 0.00 0.00 3.16
243 244 4.734398 AACATTCTTTGCACCAGTGAAA 57.266 36.364 0.99 0.00 0.00 2.69
244 245 4.942761 ACATTCTTTGCACCAGTGAAAT 57.057 36.364 0.99 0.00 0.00 2.17
300 311 8.614469 TGGAAACAAATTTGAGAACAGTTTTT 57.386 26.923 24.64 10.68 37.44 1.94
301 312 8.502387 TGGAAACAAATTTGAGAACAGTTTTTG 58.498 29.630 24.64 4.88 37.44 2.44
305 316 8.702163 ACAAATTTGAGAACAGTTTTTGGTAG 57.298 30.769 24.64 0.00 31.57 3.18
324 335 7.397892 TGGTAGTTCATGAACACTTTTCAAA 57.602 32.000 33.92 11.49 43.47 2.69
428 439 8.608317 CAAACGTTTTTGGATTTAATGAACCTT 58.392 29.630 11.66 0.00 38.82 3.50
620 632 9.701355 AACGCTTTTTGAAATTATGAACTTTTG 57.299 25.926 0.00 0.00 0.00 2.44
643 655 5.748630 TGTTCTGGAATTCGATATTCGTGAG 59.251 40.000 0.00 8.76 41.35 3.51
644 656 4.299155 TCTGGAATTCGATATTCGTGAGC 58.701 43.478 0.00 0.00 41.35 4.26
718 730 5.047802 ACCATTGGATCTTTTGCAAGTACTG 60.048 40.000 10.37 0.00 39.20 2.74
729 741 2.772287 GCAAGTACTGCCTCTTCTTGT 58.228 47.619 0.00 0.00 46.13 3.16
733 745 1.461127 GTACTGCCTCTTCTTGTTGCG 59.539 52.381 0.00 0.00 0.00 4.85
734 746 1.208614 CTGCCTCTTCTTGTTGCGC 59.791 57.895 0.00 0.00 0.00 6.09
736 748 2.607892 GCCTCTTCTTGTTGCGCGT 61.608 57.895 8.43 0.00 0.00 6.01
749 761 2.435938 CGCGTGGCCCACATAGTT 60.436 61.111 15.45 0.00 33.40 2.24
750 762 2.038269 CGCGTGGCCCACATAGTTT 61.038 57.895 15.45 0.00 33.40 2.66
752 764 0.109319 GCGTGGCCCACATAGTTTTG 60.109 55.000 15.45 0.00 33.40 2.44
754 766 0.965439 GTGGCCCACATAGTTTTGCA 59.035 50.000 9.55 0.00 34.08 4.08
755 767 1.342819 GTGGCCCACATAGTTTTGCAA 59.657 47.619 9.55 0.00 34.08 4.08
756 768 1.617850 TGGCCCACATAGTTTTGCAAG 59.382 47.619 0.00 0.00 0.00 4.01
757 769 1.618343 GGCCCACATAGTTTTGCAAGT 59.382 47.619 0.00 0.00 0.00 3.16
759 771 3.366985 GGCCCACATAGTTTTGCAAGTAC 60.367 47.826 0.00 2.32 0.00 2.73
761 773 4.698304 GCCCACATAGTTTTGCAAGTACTA 59.302 41.667 19.54 19.54 0.00 1.82
762 774 5.391629 GCCCACATAGTTTTGCAAGTACTAC 60.392 44.000 19.61 7.36 0.00 2.73
763 775 5.123344 CCCACATAGTTTTGCAAGTACTACC 59.877 44.000 19.61 0.00 0.00 3.18
764 776 5.938125 CCACATAGTTTTGCAAGTACTACCT 59.062 40.000 19.61 7.84 0.00 3.08
765 777 6.430000 CCACATAGTTTTGCAAGTACTACCTT 59.570 38.462 19.61 7.31 0.00 3.50
766 778 7.040686 CCACATAGTTTTGCAAGTACTACCTTT 60.041 37.037 19.61 7.05 0.00 3.11
767 779 8.349983 CACATAGTTTTGCAAGTACTACCTTTT 58.650 33.333 19.61 6.78 0.00 2.27
769 781 9.180678 CATAGTTTTGCAAGTACTACCTTTTTG 57.819 33.333 19.61 12.31 0.00 2.44
770 782 6.569780 AGTTTTGCAAGTACTACCTTTTTGG 58.430 36.000 12.91 0.00 42.93 3.28
771 783 4.577834 TTGCAAGTACTACCTTTTTGGC 57.422 40.909 0.00 0.00 40.22 4.52
773 785 3.316868 TGCAAGTACTACCTTTTTGGCAC 59.683 43.478 0.00 0.00 40.22 5.01
775 787 4.022329 GCAAGTACTACCTTTTTGGCACAT 60.022 41.667 0.00 0.00 39.30 3.21
776 788 5.182380 GCAAGTACTACCTTTTTGGCACATA 59.818 40.000 0.00 0.00 39.30 2.29
823 839 3.691342 CCCGACTTGACTGCCCGA 61.691 66.667 0.00 0.00 0.00 5.14
1020 1047 2.770475 GAGAAGGGAGGGGAGGCC 60.770 72.222 0.00 0.00 0.00 5.19
1319 1405 3.647921 ATGGCTCTGGGGCTCTCCA 62.648 63.158 1.76 0.00 41.48 3.86
1365 1458 4.189231 CTGTATAAGACCCCTTTGGAACG 58.811 47.826 0.00 0.00 38.00 3.95
1554 1658 6.958255 ACTGAAAATTTTGTTGCTAATTGCC 58.042 32.000 8.47 0.00 42.00 4.52
1571 1675 3.121030 CTTGAGGTTCGCAGGCCG 61.121 66.667 0.00 0.00 38.61 6.13
1709 1814 5.446073 GCTCATTGTCGCTTTTTAGAGGTAC 60.446 44.000 0.00 0.00 0.00 3.34
1897 2190 7.332182 GGAAGTTAGTCAGAGTTATCCAAAGTG 59.668 40.741 0.00 0.00 0.00 3.16
1909 2202 6.215636 AGTTATCCAAAGTGTATCTGGTCCTT 59.784 38.462 0.00 0.00 0.00 3.36
2005 2348 6.875076 TGGTTAGCTCTGAATAACTTCCTAC 58.125 40.000 0.00 0.00 33.36 3.18
2265 2610 6.377780 TGATGTTGGTGTATTTCAAATCACG 58.622 36.000 0.00 0.00 0.00 4.35
2340 2689 1.064060 GGGATGCCAAGTTCGAAATCG 59.936 52.381 0.00 0.00 41.45 3.34
2553 2904 0.973632 TGCGAGCTAGACCAAGGAAA 59.026 50.000 0.00 0.00 0.00 3.13
2559 2910 3.108376 AGCTAGACCAAGGAAACTAGGG 58.892 50.000 0.00 0.00 42.68 3.53
2588 2939 2.507471 AGCTTAGCTGCCCATTTCTACT 59.493 45.455 5.70 0.00 37.57 2.57
2599 2950 6.194235 TGCCCATTTCTACTTATGGTGATTT 58.806 36.000 0.00 0.00 39.75 2.17
2704 3055 5.403897 AGTTCGTTGTTATAATGGATGCG 57.596 39.130 0.00 0.00 0.00 4.73
3128 3529 2.210644 CCCTGGGGGTCTTAATTACCA 58.789 52.381 4.27 0.00 38.25 3.25
3137 3538 4.575236 GGGTCTTAATTACCAGTGCTTAGC 59.425 45.833 0.00 0.00 38.87 3.09
3138 3539 5.429130 GGTCTTAATTACCAGTGCTTAGCT 58.571 41.667 5.60 0.00 36.96 3.32
3139 3540 5.880887 GGTCTTAATTACCAGTGCTTAGCTT 59.119 40.000 5.60 0.00 36.96 3.74
3140 3541 6.374613 GGTCTTAATTACCAGTGCTTAGCTTT 59.625 38.462 5.60 0.00 36.96 3.51
3316 3733 0.766674 TACAGGACCAGGGTGCAGTT 60.767 55.000 12.80 0.00 37.39 3.16
3355 3772 3.055963 CCAACCCAATTGCTCTGCATAAA 60.056 43.478 0.00 0.00 38.76 1.40
3445 3929 2.846827 TCCCTTCTTTCTTGGATCCTCC 59.153 50.000 14.23 0.00 36.96 4.30
3520 4005 3.245016 TGTGGCAGTGAGGAGAAATTGAT 60.245 43.478 0.00 0.00 0.00 2.57
3654 4173 1.379443 CTGGCATGGGCACTGACAT 60.379 57.895 0.00 0.00 43.71 3.06
3704 4223 4.423625 AGTGCACATTTATACTCCCTCC 57.576 45.455 21.04 0.00 0.00 4.30
3716 4235 7.530426 TTATACTCCCTCCGTTCCTAAATAC 57.470 40.000 0.00 0.00 0.00 1.89
3800 4319 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
3810 4329 5.105310 ACTCATTTTGCTCCGTATGTAGTCT 60.105 40.000 0.00 0.00 0.00 3.24
3835 4354 7.596494 TGCATTGGAATCTCTAAAAAGACTTG 58.404 34.615 0.00 0.00 0.00 3.16
3947 4466 1.795768 TAGCCAGTTTGCTCTTGTCG 58.204 50.000 0.00 0.00 41.68 4.35
4304 4840 2.094906 TGGATCGTTTAGGTGTGTCTCG 60.095 50.000 0.00 0.00 0.00 4.04
4495 5034 2.972625 TCACATTGAAGAGGTAAGCCG 58.027 47.619 0.00 0.00 40.50 5.52
4523 5062 3.742369 CACTCACCCATTTTCATTTGTGC 59.258 43.478 0.00 0.00 0.00 4.57
4598 5140 2.027561 CCAGGTCCCAATCACTTTCGTA 60.028 50.000 0.00 0.00 0.00 3.43
4723 5267 7.066307 TGTATGCATGACTGTTATAGGACAT 57.934 36.000 10.16 0.00 0.00 3.06
4862 5412 9.926751 CTTATATGAATTGTGTCATGTGACTTC 57.073 33.333 13.71 9.48 44.99 3.01
4863 5413 9.671279 TTATATGAATTGTGTCATGTGACTTCT 57.329 29.630 13.71 3.65 44.99 2.85
4865 5415 6.785488 TGAATTGTGTCATGTGACTTCTAC 57.215 37.500 13.71 4.88 44.99 2.59
4866 5416 5.700832 TGAATTGTGTCATGTGACTTCTACC 59.299 40.000 13.71 1.79 44.99 3.18
4867 5417 4.955811 TTGTGTCATGTGACTTCTACCT 57.044 40.909 13.71 0.00 44.99 3.08
4868 5418 4.521130 TGTGTCATGTGACTTCTACCTC 57.479 45.455 13.71 0.00 44.99 3.85
4885 5435 3.947868 ACCTCATGTATCATGGCATAGC 58.052 45.455 0.00 0.00 0.00 2.97
4886 5436 3.586174 ACCTCATGTATCATGGCATAGCT 59.414 43.478 0.00 0.00 0.00 3.32
4889 5439 4.572909 TCATGTATCATGGCATAGCTGTC 58.427 43.478 0.00 0.00 0.00 3.51
4890 5440 4.040706 TCATGTATCATGGCATAGCTGTCA 59.959 41.667 0.00 0.00 42.19 3.58
4891 5441 3.999046 TGTATCATGGCATAGCTGTCAG 58.001 45.455 0.00 0.00 41.07 3.51
4892 5442 1.893544 ATCATGGCATAGCTGTCAGC 58.106 50.000 17.48 17.48 41.07 4.26
4893 5443 0.179037 TCATGGCATAGCTGTCAGCC 60.179 55.000 21.32 7.16 43.77 4.85
4895 5445 2.501128 GGCATAGCTGTCAGCCGA 59.499 61.111 21.32 10.29 43.77 5.54
4896 5446 1.884926 GGCATAGCTGTCAGCCGAC 60.885 63.158 21.32 8.85 43.77 4.79
4897 5447 2.233654 GCATAGCTGTCAGCCGACG 61.234 63.158 21.32 8.78 45.80 5.12
4898 5448 2.105128 ATAGCTGTCAGCCGACGC 59.895 61.111 21.32 8.30 45.80 5.19
4899 5449 2.710902 ATAGCTGTCAGCCGACGCA 61.711 57.895 21.32 0.61 45.80 5.24
4942 5492 0.104304 GCCGGCTTAGCTGCTTACTA 59.896 55.000 22.15 0.00 32.89 1.82
4946 5496 3.053455 CGGCTTAGCTGCTTACTATGTC 58.947 50.000 7.79 0.00 0.00 3.06
4947 5497 3.490933 CGGCTTAGCTGCTTACTATGTCA 60.491 47.826 7.79 0.00 0.00 3.58
4959 5509 9.750125 CTGCTTACTATGTCATTACATGAGTTA 57.250 33.333 0.00 0.00 45.99 2.24
4986 5544 5.871524 CGTATCCATGGGATTACTGATTCAG 59.128 44.000 13.02 12.17 39.79 3.02
4999 5558 1.065199 TGATTCAGCTGCTACCTTGGG 60.065 52.381 9.47 0.00 0.00 4.12
5000 5559 1.210478 GATTCAGCTGCTACCTTGGGA 59.790 52.381 9.47 0.00 0.00 4.37
5014 5573 3.974642 ACCTTGGGAGGAACTATATGACC 59.025 47.826 0.00 0.00 46.74 4.02
5036 5644 6.231211 ACCGTATATTGATGAACATTCCTCC 58.769 40.000 0.00 0.00 0.00 4.30
5038 5646 6.936900 CCGTATATTGATGAACATTCCTCCTT 59.063 38.462 0.00 0.00 0.00 3.36
5050 5658 8.548025 TGAACATTCCTCCTTAAGTTATCATGA 58.452 33.333 0.00 0.00 0.00 3.07
5067 5675 8.636213 GTTATCATGAAAGTGAAATGGATGGAT 58.364 33.333 0.00 0.00 0.00 3.41
5176 5790 6.461509 GGGAAAAGATTCACAGAACACACATT 60.462 38.462 0.00 0.00 38.90 2.71
5207 5821 2.437281 CCATCTCAGAGCACCCTTATGT 59.563 50.000 0.00 0.00 0.00 2.29
5212 5826 5.023452 TCTCAGAGCACCCTTATGTTTAGA 58.977 41.667 0.00 0.00 0.00 2.10
5325 5940 6.953520 TGGAAATCAGTCCCAGAAAACATAAT 59.046 34.615 0.00 0.00 36.80 1.28
5339 5954 6.429692 AGAAAACATAATCACGAATGACCACA 59.570 34.615 0.00 0.00 37.79 4.17
5352 5967 5.395682 AATGACCACACATCATCAAAAGG 57.604 39.130 0.00 0.00 35.72 3.11
5384 5999 4.360951 TGTAGGTCCTTTTGGTTGGTAG 57.639 45.455 0.00 0.00 41.38 3.18
5439 6057 6.234177 TCAATCTTCACTCTTCTCCTTTTCC 58.766 40.000 0.00 0.00 0.00 3.13
5461 6079 4.631813 CCTTTTCTAGCTTCTGTAACGCAT 59.368 41.667 0.00 0.00 0.00 4.73
5496 6114 9.066892 AGTTAGAATGCATTTCAGAACAAGTTA 57.933 29.630 14.33 0.00 36.02 2.24
5529 6147 3.984508 ACATGCAGCAAATATCAGAGC 57.015 42.857 0.00 0.00 0.00 4.09
5564 6182 8.616076 ACTTAGAAATTCTGAGAAACACAAGTG 58.384 33.333 19.66 0.00 34.16 3.16
5567 6185 2.708216 TCTGAGAAACACAAGTGGCA 57.292 45.000 5.08 0.00 34.19 4.92
5571 6189 0.106519 AGAAACACAAGTGGCAGCCT 60.107 50.000 14.15 0.00 34.19 4.58
5575 6193 0.178981 ACACAAGTGGCAGCCTCATT 60.179 50.000 14.15 1.51 34.19 2.57
5612 6230 6.741992 TGTACCAAAAAGCATACAGATGAG 57.258 37.500 0.00 0.00 34.73 2.90
5623 6241 6.878317 AGCATACAGATGAGTAAGTTAAGCA 58.122 36.000 0.00 0.00 34.73 3.91
5638 6256 4.216257 AGTTAAGCACACAACTATTGCCTG 59.784 41.667 0.00 0.00 36.91 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 8.338986 AGCAAAAGAAAGAACAAAAACGAAAAA 58.661 25.926 0.00 0.00 0.00 1.94
32 33 7.856556 AGCAAAAGAAAGAACAAAAACGAAAA 58.143 26.923 0.00 0.00 0.00 2.29
33 34 7.414814 AGCAAAAGAAAGAACAAAAACGAAA 57.585 28.000 0.00 0.00 0.00 3.46
34 35 7.414814 AAGCAAAAGAAAGAACAAAAACGAA 57.585 28.000 0.00 0.00 0.00 3.85
35 36 7.414814 AAAGCAAAAGAAAGAACAAAAACGA 57.585 28.000 0.00 0.00 0.00 3.85
36 37 7.268235 GGAAAAGCAAAAGAAAGAACAAAAACG 59.732 33.333 0.00 0.00 0.00 3.60
37 38 8.289618 AGGAAAAGCAAAAGAAAGAACAAAAAC 58.710 29.630 0.00 0.00 0.00 2.43
165 166 5.703730 AATGGTTCCCGGAGTAAGAAATA 57.296 39.130 0.73 0.00 0.00 1.40
211 212 9.171877 TGGTGCAAAGAATGTTAAGAAAAATTT 57.828 25.926 0.00 0.00 0.00 1.82
214 215 7.277539 CACTGGTGCAAAGAATGTTAAGAAAAA 59.722 33.333 4.72 0.00 0.00 1.94
218 219 5.129634 TCACTGGTGCAAAGAATGTTAAGA 58.870 37.500 4.72 0.00 0.00 2.10
219 220 5.437289 TCACTGGTGCAAAGAATGTTAAG 57.563 39.130 4.72 0.00 0.00 1.85
276 278 7.962373 CCAAAAACTGTTCTCAAATTTGTTTCC 59.038 33.333 17.47 6.02 0.00 3.13
278 280 8.389779 ACCAAAAACTGTTCTCAAATTTGTTT 57.610 26.923 17.47 6.48 0.00 2.83
281 283 8.702163 ACTACCAAAAACTGTTCTCAAATTTG 57.298 30.769 12.15 12.15 0.00 2.32
300 311 7.397892 TTTGAAAAGTGTTCATGAACTACCA 57.602 32.000 32.57 20.22 41.67 3.25
301 312 8.871686 AATTTGAAAAGTGTTCATGAACTACC 57.128 30.769 32.57 21.97 41.67 3.18
404 415 8.725405 AAAGGTTCATTAAATCCAAAAACGTT 57.275 26.923 0.00 0.00 0.00 3.99
433 444 6.289834 TCCAATCAAAACATGTTTGCAGATT 58.710 32.000 23.93 24.99 37.39 2.40
435 446 5.273674 TCCAATCAAAACATGTTTGCAGA 57.726 34.783 23.93 20.44 37.39 4.26
436 447 4.449743 CCTCCAATCAAAACATGTTTGCAG 59.550 41.667 23.93 16.33 37.39 4.41
437 448 4.100653 TCCTCCAATCAAAACATGTTTGCA 59.899 37.500 23.93 13.83 37.39 4.08
438 449 4.630111 TCCTCCAATCAAAACATGTTTGC 58.370 39.130 23.93 0.00 37.39 3.68
471 483 8.870160 TCGAATTCAAAAATGTTCTTGAACAT 57.130 26.923 19.61 19.61 42.62 2.71
530 542 9.902196 TCACGAATTTTTAAAAACTAGGGATTC 57.098 29.630 15.35 11.78 0.00 2.52
620 632 5.332656 GCTCACGAATATCGAATTCCAGAAC 60.333 44.000 6.78 5.35 43.74 3.01
625 637 4.051922 ACTGCTCACGAATATCGAATTCC 58.948 43.478 6.78 2.76 43.74 3.01
643 655 7.928908 TGTTATTTTTCACATTGAGAACTGC 57.071 32.000 0.00 0.00 0.00 4.40
673 685 8.846943 ATGGTTCTTGTTTTTCTTCTTTGTTT 57.153 26.923 0.00 0.00 0.00 2.83
679 691 6.790232 TCCAATGGTTCTTGTTTTTCTTCT 57.210 33.333 0.00 0.00 0.00 2.85
718 730 2.174349 CGCGCAACAAGAAGAGGC 59.826 61.111 8.75 0.00 0.00 4.70
733 745 0.109319 CAAAACTATGTGGGCCACGC 60.109 55.000 30.14 9.82 37.14 5.34
734 746 0.109319 GCAAAACTATGTGGGCCACG 60.109 55.000 30.14 19.07 37.14 4.94
736 748 1.617850 CTTGCAAAACTATGTGGGCCA 59.382 47.619 0.00 0.00 0.00 5.36
747 759 5.233476 GCCAAAAAGGTAGTACTTGCAAAAC 59.767 40.000 0.00 1.75 40.61 2.43
748 760 5.105310 TGCCAAAAAGGTAGTACTTGCAAAA 60.105 36.000 0.00 0.00 40.61 2.44
749 761 4.402793 TGCCAAAAAGGTAGTACTTGCAAA 59.597 37.500 0.00 0.00 40.61 3.68
750 762 3.954904 TGCCAAAAAGGTAGTACTTGCAA 59.045 39.130 0.00 0.00 40.61 4.08
752 764 3.316868 TGTGCCAAAAAGGTAGTACTTGC 59.683 43.478 0.00 0.00 40.61 4.01
754 766 6.540083 ACTATGTGCCAAAAAGGTAGTACTT 58.460 36.000 0.00 0.00 40.61 2.24
755 767 6.123045 ACTATGTGCCAAAAAGGTAGTACT 57.877 37.500 0.00 0.00 40.61 2.73
756 768 6.812879 AACTATGTGCCAAAAAGGTAGTAC 57.187 37.500 0.00 0.00 40.61 2.73
757 769 7.653647 CAAAACTATGTGCCAAAAAGGTAGTA 58.346 34.615 0.00 0.00 40.61 1.82
759 771 5.405269 GCAAAACTATGTGCCAAAAAGGTAG 59.595 40.000 0.00 0.00 40.61 3.18
761 773 4.126437 GCAAAACTATGTGCCAAAAAGGT 58.874 39.130 0.00 0.00 40.61 3.50
762 774 3.184178 CGCAAAACTATGTGCCAAAAAGG 59.816 43.478 0.00 0.00 37.47 3.11
763 775 4.373532 CGCAAAACTATGTGCCAAAAAG 57.626 40.909 0.00 0.00 37.47 2.27
771 783 2.596575 CGTATCGGCGCAAAACTATGTG 60.597 50.000 10.83 0.00 0.00 3.21
773 785 2.279250 CGTATCGGCGCAAAACTATG 57.721 50.000 10.83 0.00 0.00 2.23
802 818 2.035442 GGCAGTCAAGTCGGGCTTC 61.035 63.158 0.00 0.00 34.69 3.86
823 839 3.370231 GCCGGCCGGTGTCAAAAT 61.370 61.111 42.53 0.00 37.65 1.82
1030 1057 2.279517 GATGCTGTACTCCGGCCG 60.280 66.667 21.04 21.04 45.48 6.13
1365 1458 4.531332 GCCTGAATCGAATGCAATAGTTC 58.469 43.478 0.00 0.00 0.00 3.01
1554 1658 3.121030 CGGCCTGCGAACCTCAAG 61.121 66.667 0.00 0.00 0.00 3.02
1571 1675 5.416013 AGCTACTGAATTTTCTGCTTAACCC 59.584 40.000 0.00 0.00 0.00 4.11
1879 2172 6.758886 CCAGATACACTTTGGATAACTCTGAC 59.241 42.308 0.00 0.00 33.76 3.51
1897 2190 4.265073 AGCACATTGAAAGGACCAGATAC 58.735 43.478 0.00 0.00 0.00 2.24
1909 2202 3.888323 TGAAACCAGCTAAGCACATTGAA 59.112 39.130 0.00 0.00 0.00 2.69
2046 2389 6.238049 CGCTTGTAAGATTCAGAGAAATCTGG 60.238 42.308 5.48 0.00 43.53 3.86
2265 2610 8.244113 AGTTAAGTAAATAAATGCAACAGCCTC 58.756 33.333 0.00 0.00 0.00 4.70
2340 2689 3.319122 GGGCTTCCATCATCCACAATAAC 59.681 47.826 0.00 0.00 0.00 1.89
2588 2939 9.585099 GAACATCAAGCATAAAAATCACCATAA 57.415 29.630 0.00 0.00 0.00 1.90
2599 2950 7.811653 TCATTAACACGAACATCAAGCATAAA 58.188 30.769 0.00 0.00 0.00 1.40
2704 3055 9.941325 AAGAAACATACATGATGAGATAGATCC 57.059 33.333 0.00 0.00 39.06 3.36
2885 3240 4.780815 ACTAATCCAATCATTCTTGCCGA 58.219 39.130 0.00 0.00 0.00 5.54
3109 3510 2.850568 ACTGGTAATTAAGACCCCCAGG 59.149 50.000 17.31 4.84 42.95 4.45
3110 3511 3.886123 CACTGGTAATTAAGACCCCCAG 58.114 50.000 13.37 13.37 43.98 4.45
3128 3529 3.575687 AGGCAAATTGAAAGCTAAGCACT 59.424 39.130 0.00 0.00 0.00 4.40
3137 3538 4.524316 TGATGGTCAGGCAAATTGAAAG 57.476 40.909 0.00 0.00 0.00 2.62
3138 3539 4.952071 TTGATGGTCAGGCAAATTGAAA 57.048 36.364 0.00 0.00 0.00 2.69
3139 3540 4.952071 TTTGATGGTCAGGCAAATTGAA 57.048 36.364 0.00 0.00 0.00 2.69
3140 3541 5.486735 AATTTGATGGTCAGGCAAATTGA 57.513 34.783 18.07 0.00 45.33 2.57
3175 3576 2.065899 TTTTTGGTCTGTGGAGTGGG 57.934 50.000 0.00 0.00 0.00 4.61
3316 3733 0.709397 TGGAGGGATCCCAATTTGCA 59.291 50.000 32.69 19.88 38.92 4.08
3323 3740 0.554865 ATTGGGTTGGAGGGATCCCA 60.555 55.000 32.69 9.66 46.77 4.37
3355 3772 2.046285 GTGGCGCTACCCTTGCATT 61.046 57.895 13.67 0.00 37.83 3.56
3445 3929 1.939934 ACACAAGAACACGTGTCCATG 59.060 47.619 23.61 21.19 42.61 3.66
3453 3937 2.542766 ACAAAGCACACAAGAACACG 57.457 45.000 0.00 0.00 0.00 4.49
3520 4005 1.956629 GCAGCTGTAAGACCGGCCTA 61.957 60.000 16.64 0.00 34.07 3.93
3654 4173 3.433306 ACAAAGCATACAGTAGGGCAA 57.567 42.857 9.12 0.00 0.00 4.52
3778 4297 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
3779 4298 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
3780 4299 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
3781 4300 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
3782 4301 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
3783 4302 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
3784 4303 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
3785 4304 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
3786 4305 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
3787 4306 5.233050 CAGACTACATACGGAGCAAAATGAG 59.767 44.000 0.00 0.00 0.00 2.90
3788 4307 5.109210 CAGACTACATACGGAGCAAAATGA 58.891 41.667 0.00 0.00 0.00 2.57
3800 4319 6.520272 AGAGATTCCAATGCAGACTACATAC 58.480 40.000 0.00 0.00 0.00 2.39
3810 4329 7.231317 ACAAGTCTTTTTAGAGATTCCAATGCA 59.769 33.333 0.00 0.00 0.00 3.96
3835 4354 5.859205 TTACTCCCTCCGTTCCTAAATAC 57.141 43.478 0.00 0.00 0.00 1.89
3842 4361 8.687292 AATTTATATTTTACTCCCTCCGTTCC 57.313 34.615 0.00 0.00 0.00 3.62
3947 4466 3.432186 GCCAAAATTCCATTTCTAGGCCC 60.432 47.826 0.00 0.00 38.01 5.80
3978 4497 6.986817 ACACTCAACAAGGTACATATCTATGC 59.013 38.462 0.00 0.00 37.19 3.14
4038 4561 6.382859 TGGATAGTCAGCTATACCAAACTTCA 59.617 38.462 0.00 0.00 37.66 3.02
4334 4871 6.254281 AGCGTCAAATAACAGTAAGCATTT 57.746 33.333 0.00 0.00 0.00 2.32
4338 4875 4.320953 GCAAAGCGTCAAATAACAGTAAGC 59.679 41.667 0.00 0.00 0.00 3.09
4339 4876 4.851558 GGCAAAGCGTCAAATAACAGTAAG 59.148 41.667 0.00 0.00 0.00 2.34
4495 5034 2.034053 TGAAAATGGGTGAGTGCGAAAC 59.966 45.455 0.00 0.00 0.00 2.78
4523 5062 5.182760 GCCAAGAGATTATAATCCAGCCTTG 59.817 44.000 23.50 23.50 36.04 3.61
4598 5140 2.104170 GAGATTCCGAAGACCCTGTCT 58.896 52.381 0.00 0.00 45.64 3.41
4776 5326 4.304110 TGTAGGTCTGAAAACGTTAGCAG 58.696 43.478 18.93 18.93 0.00 4.24
4862 5412 5.105023 AGCTATGCCATGATACATGAGGTAG 60.105 44.000 12.46 10.99 34.92 3.18
4863 5413 4.779489 AGCTATGCCATGATACATGAGGTA 59.221 41.667 12.46 0.00 36.16 3.08
4864 5414 3.586174 AGCTATGCCATGATACATGAGGT 59.414 43.478 12.46 5.48 0.00 3.85
4865 5415 3.939592 CAGCTATGCCATGATACATGAGG 59.060 47.826 12.46 0.00 0.00 3.86
4866 5416 4.576879 ACAGCTATGCCATGATACATGAG 58.423 43.478 12.46 4.15 0.00 2.90
4867 5417 4.040706 TGACAGCTATGCCATGATACATGA 59.959 41.667 12.46 0.00 0.00 3.07
4868 5418 4.320870 TGACAGCTATGCCATGATACATG 58.679 43.478 0.00 4.94 0.00 3.21
4894 5444 2.665185 AACAAGACGGCCTGCGTC 60.665 61.111 0.00 3.13 36.71 5.19
4895 5445 2.972505 CAACAAGACGGCCTGCGT 60.973 61.111 0.00 0.00 0.00 5.24
4896 5446 4.389576 GCAACAAGACGGCCTGCG 62.390 66.667 0.00 0.00 0.00 5.18
4897 5447 4.389576 CGCAACAAGACGGCCTGC 62.390 66.667 0.00 0.02 0.00 4.85
4898 5448 4.389576 GCGCAACAAGACGGCCTG 62.390 66.667 0.30 0.00 0.00 4.85
4904 5454 0.657368 CAGTTTCGGCGCAACAAGAC 60.657 55.000 23.23 1.71 0.00 3.01
4908 5458 3.959975 GGCAGTTTCGGCGCAACA 61.960 61.111 23.23 0.00 0.00 3.33
4916 5466 1.741770 AGCTAAGCCGGCAGTTTCG 60.742 57.895 31.54 11.68 0.00 3.46
4946 5496 8.659491 CCATGGATACGATTAACTCATGTAATG 58.341 37.037 5.56 0.00 44.17 1.90
4947 5497 7.824289 CCCATGGATACGATTAACTCATGTAAT 59.176 37.037 15.22 0.00 42.51 1.89
4959 5509 6.627087 ATCAGTAATCCCATGGATACGATT 57.373 37.500 15.22 15.43 42.27 3.34
4963 5513 5.645497 GCTGAATCAGTAATCCCATGGATAC 59.355 44.000 15.22 13.15 36.19 2.24
4986 5544 0.393132 GTTCCTCCCAAGGTAGCAGC 60.393 60.000 0.00 0.00 43.82 5.25
4999 5558 9.737427 CATCAATATACGGTCATATAGTTCCTC 57.263 37.037 0.00 0.00 0.00 3.71
5000 5559 9.475620 TCATCAATATACGGTCATATAGTTCCT 57.524 33.333 0.00 0.00 0.00 3.36
5014 5573 7.969536 AAGGAGGAATGTTCATCAATATACG 57.030 36.000 9.29 0.00 39.58 3.06
5050 5658 3.196254 GTGCCATCCATCCATTTCACTTT 59.804 43.478 0.00 0.00 0.00 2.66
5067 5675 5.565509 TCCTGTCTTATTGTTTATGTGCCA 58.434 37.500 0.00 0.00 0.00 4.92
5081 5689 4.415881 TGCTCTTGTGTTTCCTGTCTTA 57.584 40.909 0.00 0.00 0.00 2.10
5176 5790 5.451798 GGTGCTCTGAGATGGAAAACAAAAA 60.452 40.000 9.28 0.00 0.00 1.94
5207 5821 7.603963 TTACATATTTCTGCGTTGCTCTAAA 57.396 32.000 0.00 0.00 0.00 1.85
5212 5826 6.582295 CAGTTTTTACATATTTCTGCGTTGCT 59.418 34.615 0.00 0.00 0.00 3.91
5325 5940 2.829741 TGATGTGTGGTCATTCGTGA 57.170 45.000 0.00 0.00 0.00 4.35
5339 5954 7.232127 ACAAGAAATCTCACCTTTTGATGATGT 59.768 33.333 0.00 0.00 32.17 3.06
5352 5967 6.072452 CCAAAAGGACCTACAAGAAATCTCAC 60.072 42.308 0.00 0.00 0.00 3.51
5399 6017 2.509561 GAGAAGGAAGGACGGCGC 60.510 66.667 6.90 0.00 0.00 6.53
5400 6018 0.108138 ATTGAGAAGGAAGGACGGCG 60.108 55.000 4.80 4.80 0.00 6.46
5439 6057 5.220491 GGATGCGTTACAGAAGCTAGAAAAG 60.220 44.000 0.00 0.00 0.00 2.27
5461 6079 7.950512 TGAAATGCATTCTAACTTCTTTTGGA 58.049 30.769 13.38 0.00 38.92 3.53
5529 6147 5.675970 TCAGAATTTCTAAGTCGTTTTGCG 58.324 37.500 0.00 0.00 43.01 4.85
5564 6182 3.084786 AGACAAAACTAATGAGGCTGCC 58.915 45.455 11.65 11.65 0.00 4.85
5567 6185 9.765795 GTACATATAGACAAAACTAATGAGGCT 57.234 33.333 0.00 0.00 0.00 4.58
5599 6217 6.758886 GTGCTTAACTTACTCATCTGTATGCT 59.241 38.462 0.00 0.00 32.76 3.79
5612 6230 6.072673 AGGCAATAGTTGTGTGCTTAACTTAC 60.073 38.462 0.00 0.00 38.11 2.34
5623 6241 3.056607 GGAATTGCAGGCAATAGTTGTGT 60.057 43.478 18.85 2.61 44.86 3.72
5638 6256 4.261114 GCAGCTTCAGATAAGAGGAATTGC 60.261 45.833 0.00 0.00 0.00 3.56


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

AutoCloner maintained by Alex Coulton.