Multiple sequence alignment - TraesCS1B01G336500

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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 TraesCS1B01G336500 chr1B 100.000 2860 0 0 1 2860 563496688 563499547 0.000000e+00 5282.0
1 TraesCS1B01G336500 chr1B 95.954 1928 73 3 142 2066 646717142 646719067 0.000000e+00 3123.0
2 TraesCS1B01G336500 chr1B 92.846 657 43 4 2068 2723 646769287 646769940 0.000000e+00 950.0
3 TraesCS1B01G336500 chr1B 95.833 144 5 1 1 143 646716944 646717087 6.160000e-57 231.0
4 TraesCS1B01G336500 chr4D 94.054 2590 140 10 142 2726 157628840 157631420 0.000000e+00 3917.0
5 TraesCS1B01G336500 chr4D 94.444 144 7 1 1 143 157628642 157628785 1.330000e-53 220.0
6 TraesCS1B01G336500 chr7B 87.792 2613 236 33 147 2726 707241495 707244057 0.000000e+00 2981.0
7 TraesCS1B01G336500 chr7B 87.524 2052 191 23 705 2727 64339547 64337532 0.000000e+00 2311.0
8 TraesCS1B01G336500 chr4B 91.422 2180 135 24 577 2726 366674847 366672690 0.000000e+00 2942.0
9 TraesCS1B01G336500 chr3B 88.325 2304 202 25 454 2726 9351095 9348828 0.000000e+00 2702.0
10 TraesCS1B01G336500 chr3B 94.958 119 5 1 26 143 809693697 809693579 4.870000e-43 185.0
11 TraesCS1B01G336500 chr3B 94.643 56 2 1 142 196 809693525 809693470 5.080000e-13 86.1
12 TraesCS1B01G336500 chr5A 87.932 1939 174 23 815 2727 17083451 17085355 0.000000e+00 2230.0
13 TraesCS1B01G336500 chr5A 90.556 593 39 7 142 718 17082840 17083431 0.000000e+00 769.0
14 TraesCS1B01G336500 chr5A 95.798 119 4 1 26 143 17082668 17082786 1.050000e-44 191.0
15 TraesCS1B01G336500 chr7A 87.255 1938 187 19 815 2726 372242950 372241047 0.000000e+00 2156.0
16 TraesCS1B01G336500 chr7A 91.980 586 37 5 142 718 372243554 372242970 0.000000e+00 813.0
17 TraesCS1B01G336500 chr7A 94.958 119 5 1 26 143 372243726 372243608 4.870000e-43 185.0
18 TraesCS1B01G336500 chr6D 87.152 1938 182 21 815 2726 315864955 315863059 0.000000e+00 2137.0
19 TraesCS1B01G336500 chr6D 92.321 586 35 5 142 718 315865559 315864975 0.000000e+00 824.0
20 TraesCS1B01G336500 chr6D 94.118 119 6 1 26 143 315865731 315865613 2.260000e-41 180.0
21 TraesCS1B01G336500 chr3A 88.125 1760 151 18 815 2548 160390699 160392426 0.000000e+00 2039.0
22 TraesCS1B01G336500 chr3A 86.951 1525 146 22 1205 2700 160368049 160369549 0.000000e+00 1664.0
23 TraesCS1B01G336500 chr3A 90.956 586 43 5 142 718 160390095 160390679 0.000000e+00 780.0
24 TraesCS1B01G336500 chr3A 95.798 119 4 1 26 143 160389923 160390041 1.050000e-44 191.0
25 TraesCS1B01G336500 chr1A 91.248 1474 121 7 1256 2726 139175167 139176635 0.000000e+00 2001.0
26 TraesCS1B01G336500 chr1A 93.711 1113 65 3 231 1339 139173952 139175063 0.000000e+00 1663.0
27 TraesCS1B01G336500 chr1A 93.750 144 8 1 1 143 139173722 139173865 6.210000e-52 215.0
28 TraesCS1B01G336500 chr1A 86.538 104 9 1 2727 2825 514033792 514033895 3.010000e-20 110.0
29 TraesCS1B01G336500 chr3D 84.522 1234 117 35 1519 2726 555289884 555291069 0.000000e+00 1153.0
30 TraesCS1B01G336500 chr3D 90.988 688 45 5 815 1497 555287123 555287798 0.000000e+00 911.0
31 TraesCS1B01G336500 chr3D 92.491 586 34 5 142 718 555286519 555287103 0.000000e+00 830.0
32 TraesCS1B01G336500 chr3D 94.958 119 5 1 26 143 555286347 555286465 4.870000e-43 185.0
33 TraesCS1B01G336500 chr1D 87.431 724 83 6 2005 2726 22074580 22073863 0.000000e+00 826.0
34 TraesCS1B01G336500 chr1D 77.817 852 102 37 1273 2088 33771083 33771883 2.020000e-121 446.0


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 TraesCS1B01G336500 chr1B 563496688 563499547 2859 False 5282.000000 5282 100.000000 1 2860 1 chr1B.!!$F1 2859
1 TraesCS1B01G336500 chr1B 646716944 646719067 2123 False 1677.000000 3123 95.893500 1 2066 2 chr1B.!!$F3 2065
2 TraesCS1B01G336500 chr1B 646769287 646769940 653 False 950.000000 950 92.846000 2068 2723 1 chr1B.!!$F2 655
3 TraesCS1B01G336500 chr4D 157628642 157631420 2778 False 2068.500000 3917 94.249000 1 2726 2 chr4D.!!$F1 2725
4 TraesCS1B01G336500 chr7B 707241495 707244057 2562 False 2981.000000 2981 87.792000 147 2726 1 chr7B.!!$F1 2579
5 TraesCS1B01G336500 chr7B 64337532 64339547 2015 True 2311.000000 2311 87.524000 705 2727 1 chr7B.!!$R1 2022
6 TraesCS1B01G336500 chr4B 366672690 366674847 2157 True 2942.000000 2942 91.422000 577 2726 1 chr4B.!!$R1 2149
7 TraesCS1B01G336500 chr3B 9348828 9351095 2267 True 2702.000000 2702 88.325000 454 2726 1 chr3B.!!$R1 2272
8 TraesCS1B01G336500 chr5A 17082668 17085355 2687 False 1063.333333 2230 91.428667 26 2727 3 chr5A.!!$F1 2701
9 TraesCS1B01G336500 chr7A 372241047 372243726 2679 True 1051.333333 2156 91.397667 26 2726 3 chr7A.!!$R1 2700
10 TraesCS1B01G336500 chr6D 315863059 315865731 2672 True 1047.000000 2137 91.197000 26 2726 3 chr6D.!!$R1 2700
11 TraesCS1B01G336500 chr3A 160368049 160369549 1500 False 1664.000000 1664 86.951000 1205 2700 1 chr3A.!!$F1 1495
12 TraesCS1B01G336500 chr3A 160389923 160392426 2503 False 1003.333333 2039 91.626333 26 2548 3 chr3A.!!$F2 2522
13 TraesCS1B01G336500 chr1A 139173722 139176635 2913 False 1293.000000 2001 92.903000 1 2726 3 chr1A.!!$F2 2725
14 TraesCS1B01G336500 chr3D 555286347 555291069 4722 False 769.750000 1153 90.739750 26 2726 4 chr3D.!!$F1 2700
15 TraesCS1B01G336500 chr1D 22073863 22074580 717 True 826.000000 826 87.431000 2005 2726 1 chr1D.!!$R1 721
16 TraesCS1B01G336500 chr1D 33771083 33771883 800 False 446.000000 446 77.817000 1273 2088 1 chr1D.!!$F1 815

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
582 654 1.699634 ACCCTGTGCACTGTGATAACT 59.3 47.619 19.41 0.0 0.0 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1907 4260 0.178953 AGGCAGGTTCCAGCACATTT 60.179 50.0 8.38 0.0 0.0 2.32 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
67 69 3.191669 TCAGTACAAACACAACACTCCG 58.808 45.455 0.00 0.00 0.00 4.63
491 563 3.638860 ACCAAATCACTGATCCATGCAT 58.361 40.909 0.00 0.00 0.00 3.96
582 654 1.699634 ACCCTGTGCACTGTGATAACT 59.300 47.619 19.41 0.00 0.00 2.24
635 709 7.913297 TGCAAACTGTTTATGTGAAAGTAACTC 59.087 33.333 5.31 0.00 0.00 3.01
642 716 7.438757 TGTTTATGTGAAAGTAACTCGCAACTA 59.561 33.333 0.00 0.00 36.91 2.24
791 868 6.097839 AGTGTTTTGGGCTCGAACTATATCTA 59.902 38.462 4.54 0.00 0.00 1.98
897 974 3.391665 CTCCCTTGCCTACAGCCCG 62.392 68.421 0.00 0.00 42.71 6.13
972 1050 9.476928 AGTAGAGTTCAATATTGGTACTGTACT 57.523 33.333 30.03 30.03 40.70 2.73
1034 1116 6.549364 TGTTGTTTTCAGGGAGACAAATACAT 59.451 34.615 0.00 0.00 34.20 2.29
1289 1404 7.835822 TGTGCTATAATACTTGCCACATTTTT 58.164 30.769 0.00 0.00 0.00 1.94
1426 1707 5.693961 TCTGTACATGGAAATGTGGCATAT 58.306 37.500 0.00 0.00 36.08 1.78
1503 2453 3.429410 GCATGGCTAGGTTGAAATGGAAC 60.429 47.826 0.00 0.00 0.00 3.62
1626 3973 0.537143 GCATGTGAGGGTCCAACACA 60.537 55.000 18.20 18.20 46.04 3.72
1651 3998 0.589223 GAGAGATCCAGTCGTAGCGG 59.411 60.000 0.00 0.00 0.00 5.52
1672 4019 0.034059 CGTGAGGCAGAACAGGAAGT 59.966 55.000 0.00 0.00 0.00 3.01
1779 4129 3.480470 CAAGAAGAAGCAAGGACCAAGA 58.520 45.455 0.00 0.00 0.00 3.02
1974 4335 1.815003 ACTGCTTATGAAGTTGCTGGC 59.185 47.619 0.00 0.00 0.00 4.85
2255 4698 4.148079 TGACAAACAGCATAATGGACCAA 58.852 39.130 0.00 0.00 0.00 3.67
2440 4891 2.812836 TGCCACATCAGATCCACATT 57.187 45.000 0.00 0.00 0.00 2.71
2552 5003 0.527817 CCGCATCAGTAACGGTCCTC 60.528 60.000 0.00 0.00 42.01 3.71
2577 5028 2.541556 GTCCTAAATCTGTGACGGCTC 58.458 52.381 0.00 0.00 0.00 4.70
2590 5041 1.511887 CGGCTCGGCATTTTTGTCG 60.512 57.895 0.00 0.00 38.38 4.35
2615 5066 5.621104 CGGCTTGTGCTGTTGGAAAATTATA 60.621 40.000 0.00 0.00 40.53 0.98
2633 5084 9.982291 AAAATTATAACGTGTGATACATGACAC 57.018 29.630 0.00 2.15 40.75 3.67
2647 5098 7.393234 TGATACATGACACATCTCATATCCGTA 59.607 37.037 0.00 0.00 29.28 4.02
2700 5152 3.006003 TGCTGTGACGGTTTGTATCTGTA 59.994 43.478 0.00 0.00 0.00 2.74
2727 5179 3.609103 AAGCAAGTTTCTTGTAGTGCG 57.391 42.857 10.49 0.00 37.09 5.34
2728 5180 2.833794 AGCAAGTTTCTTGTAGTGCGA 58.166 42.857 10.49 0.00 37.09 5.10
2729 5181 3.202906 AGCAAGTTTCTTGTAGTGCGAA 58.797 40.909 10.49 0.00 37.09 4.70
2730 5182 3.248602 AGCAAGTTTCTTGTAGTGCGAAG 59.751 43.478 10.49 0.00 37.09 3.79
2731 5183 3.002348 GCAAGTTTCTTGTAGTGCGAAGT 59.998 43.478 10.49 0.00 0.00 3.01
2732 5184 4.210537 GCAAGTTTCTTGTAGTGCGAAGTA 59.789 41.667 10.49 0.00 0.00 2.24
2733 5185 5.277154 GCAAGTTTCTTGTAGTGCGAAGTAA 60.277 40.000 10.49 0.00 0.00 2.24
2734 5186 6.711579 CAAGTTTCTTGTAGTGCGAAGTAAA 58.288 36.000 0.00 0.00 0.00 2.01
2735 5187 6.283161 AGTTTCTTGTAGTGCGAAGTAAAC 57.717 37.500 0.00 0.00 0.00 2.01
2736 5188 6.047231 AGTTTCTTGTAGTGCGAAGTAAACT 58.953 36.000 0.00 0.00 31.73 2.66
2737 5189 6.537660 AGTTTCTTGTAGTGCGAAGTAAACTT 59.462 34.615 0.00 0.00 39.23 2.66
2738 5190 7.707893 AGTTTCTTGTAGTGCGAAGTAAACTTA 59.292 33.333 0.00 0.00 36.11 2.24
2739 5191 7.633361 TTCTTGTAGTGCGAAGTAAACTTAG 57.367 36.000 0.00 0.00 36.11 2.18
2745 5197 3.643121 GCGAAGTAAACTTAGCTCTGC 57.357 47.619 17.40 3.38 46.49 4.26
2746 5198 2.993899 GCGAAGTAAACTTAGCTCTGCA 59.006 45.455 17.40 0.00 46.49 4.41
2747 5199 3.061429 GCGAAGTAAACTTAGCTCTGCAG 59.939 47.826 17.40 7.63 46.49 4.41
2748 5200 4.486090 CGAAGTAAACTTAGCTCTGCAGA 58.514 43.478 17.19 17.19 36.11 4.26
2749 5201 4.324936 CGAAGTAAACTTAGCTCTGCAGAC 59.675 45.833 13.74 10.17 36.11 3.51
2750 5202 4.195225 AGTAAACTTAGCTCTGCAGACC 57.805 45.455 13.74 6.62 0.00 3.85
2751 5203 2.086054 AAACTTAGCTCTGCAGACCG 57.914 50.000 13.74 5.34 0.00 4.79
2752 5204 0.390472 AACTTAGCTCTGCAGACCGC 60.390 55.000 13.74 16.16 42.89 5.68
2753 5205 1.520342 CTTAGCTCTGCAGACCGCC 60.520 63.158 20.84 7.41 41.33 6.13
2754 5206 2.914777 CTTAGCTCTGCAGACCGCCC 62.915 65.000 20.84 5.21 41.33 6.13
2755 5207 3.965026 TAGCTCTGCAGACCGCCCT 62.965 63.158 20.84 9.05 41.33 5.19
2756 5208 4.400961 GCTCTGCAGACCGCCCTT 62.401 66.667 13.74 0.00 41.33 3.95
2757 5209 2.348998 CTCTGCAGACCGCCCTTT 59.651 61.111 13.74 0.00 41.33 3.11
2758 5210 1.302832 CTCTGCAGACCGCCCTTTT 60.303 57.895 13.74 0.00 41.33 2.27
2759 5211 0.890996 CTCTGCAGACCGCCCTTTTT 60.891 55.000 13.74 0.00 41.33 1.94
2779 5231 5.398603 TTTTTGAAAGAAGTGTGCAGGAA 57.601 34.783 0.00 0.00 0.00 3.36
2780 5232 4.370364 TTTGAAAGAAGTGTGCAGGAAC 57.630 40.909 0.00 0.00 0.00 3.62
2781 5233 2.297701 TGAAAGAAGTGTGCAGGAACC 58.702 47.619 0.00 0.00 0.00 3.62
2782 5234 1.609072 GAAAGAAGTGTGCAGGAACCC 59.391 52.381 0.00 0.00 0.00 4.11
2783 5235 0.178990 AAGAAGTGTGCAGGAACCCC 60.179 55.000 0.00 0.00 0.00 4.95
2784 5236 1.150536 GAAGTGTGCAGGAACCCCA 59.849 57.895 0.00 0.00 33.88 4.96
2785 5237 0.251341 GAAGTGTGCAGGAACCCCAT 60.251 55.000 0.00 0.00 33.88 4.00
2786 5238 0.251341 AAGTGTGCAGGAACCCCATC 60.251 55.000 0.00 0.00 33.88 3.51
2787 5239 1.074775 GTGTGCAGGAACCCCATCA 59.925 57.895 0.00 0.00 33.88 3.07
2788 5240 0.962356 GTGTGCAGGAACCCCATCAG 60.962 60.000 0.00 0.00 33.88 2.90
2789 5241 1.379044 GTGCAGGAACCCCATCAGG 60.379 63.158 0.00 0.00 33.88 3.86
2790 5242 2.440980 GCAGGAACCCCATCAGGC 60.441 66.667 0.00 0.00 33.88 4.85
2791 5243 2.276740 CAGGAACCCCATCAGGCC 59.723 66.667 0.00 0.00 33.88 5.19
2792 5244 3.023735 AGGAACCCCATCAGGCCC 61.024 66.667 0.00 0.00 33.88 5.80
2793 5245 4.143301 GGAACCCCATCAGGCCCC 62.143 72.222 0.00 0.00 0.00 5.80
2794 5246 3.346734 GAACCCCATCAGGCCCCA 61.347 66.667 0.00 0.00 0.00 4.96
2795 5247 2.868566 AACCCCATCAGGCCCCAA 60.869 61.111 0.00 0.00 0.00 4.12
2796 5248 3.238197 AACCCCATCAGGCCCCAAC 62.238 63.158 0.00 0.00 0.00 3.77
2797 5249 4.820744 CCCCATCAGGCCCCAACG 62.821 72.222 0.00 0.00 0.00 4.10
2798 5250 3.727258 CCCATCAGGCCCCAACGA 61.727 66.667 0.00 0.00 0.00 3.85
2799 5251 2.597340 CCATCAGGCCCCAACGAT 59.403 61.111 0.00 0.00 0.00 3.73
2800 5252 1.076777 CCATCAGGCCCCAACGATT 60.077 57.895 0.00 0.00 0.00 3.34
2801 5253 0.684153 CCATCAGGCCCCAACGATTT 60.684 55.000 0.00 0.00 0.00 2.17
2802 5254 0.740737 CATCAGGCCCCAACGATTTC 59.259 55.000 0.00 0.00 0.00 2.17
2803 5255 0.331278 ATCAGGCCCCAACGATTTCA 59.669 50.000 0.00 0.00 0.00 2.69
2804 5256 0.331278 TCAGGCCCCAACGATTTCAT 59.669 50.000 0.00 0.00 0.00 2.57
2805 5257 1.562008 TCAGGCCCCAACGATTTCATA 59.438 47.619 0.00 0.00 0.00 2.15
2806 5258 1.949525 CAGGCCCCAACGATTTCATAG 59.050 52.381 0.00 0.00 0.00 2.23
2807 5259 1.133792 AGGCCCCAACGATTTCATAGG 60.134 52.381 0.00 0.00 0.00 2.57
2808 5260 1.133915 GGCCCCAACGATTTCATAGGA 60.134 52.381 0.00 0.00 0.00 2.94
2809 5261 2.650322 GCCCCAACGATTTCATAGGAA 58.350 47.619 0.00 0.00 0.00 3.36
2810 5262 3.020984 GCCCCAACGATTTCATAGGAAA 58.979 45.455 4.85 4.85 46.36 3.13
2811 5263 3.181490 GCCCCAACGATTTCATAGGAAAC 60.181 47.826 4.42 0.00 45.22 2.78
2812 5264 4.013728 CCCCAACGATTTCATAGGAAACA 58.986 43.478 4.42 0.00 45.22 2.83
2813 5265 4.644685 CCCCAACGATTTCATAGGAAACAT 59.355 41.667 4.42 0.00 45.22 2.71
2814 5266 5.127031 CCCCAACGATTTCATAGGAAACATT 59.873 40.000 4.42 0.00 45.22 2.71
2815 5267 6.350949 CCCCAACGATTTCATAGGAAACATTT 60.351 38.462 4.42 0.00 45.22 2.32
2816 5268 6.531240 CCCAACGATTTCATAGGAAACATTTG 59.469 38.462 4.42 8.11 45.22 2.32
2817 5269 7.312154 CCAACGATTTCATAGGAAACATTTGA 58.688 34.615 4.42 0.00 45.22 2.69
2818 5270 7.975616 CCAACGATTTCATAGGAAACATTTGAT 59.024 33.333 4.42 0.00 45.22 2.57
2827 5279 9.573166 TCATAGGAAACATTTGATATAGGGTTG 57.427 33.333 0.00 0.00 0.00 3.77
2828 5280 9.354673 CATAGGAAACATTTGATATAGGGTTGT 57.645 33.333 0.00 0.00 0.00 3.32
2829 5281 9.936329 ATAGGAAACATTTGATATAGGGTTGTT 57.064 29.630 0.00 0.00 0.00 2.83
2830 5282 8.066612 AGGAAACATTTGATATAGGGTTGTTG 57.933 34.615 0.00 0.00 0.00 3.33
2831 5283 7.673926 AGGAAACATTTGATATAGGGTTGTTGT 59.326 33.333 0.00 0.00 0.00 3.32
2832 5284 7.973944 GGAAACATTTGATATAGGGTTGTTGTC 59.026 37.037 0.00 0.00 0.00 3.18
2833 5285 8.415950 AAACATTTGATATAGGGTTGTTGTCA 57.584 30.769 0.00 0.00 0.00 3.58
2834 5286 7.391148 ACATTTGATATAGGGTTGTTGTCAC 57.609 36.000 0.00 0.00 0.00 3.67
2835 5287 6.377146 ACATTTGATATAGGGTTGTTGTCACC 59.623 38.462 0.00 0.00 0.00 4.02
2836 5288 5.772393 TTGATATAGGGTTGTTGTCACCT 57.228 39.130 0.00 0.00 37.13 4.00
2837 5289 5.353394 TGATATAGGGTTGTTGTCACCTC 57.647 43.478 0.00 0.00 34.59 3.85
2838 5290 4.163458 TGATATAGGGTTGTTGTCACCTCC 59.837 45.833 0.00 0.00 34.59 4.30
2839 5291 2.112279 TAGGGTTGTTGTCACCTCCT 57.888 50.000 0.00 0.00 34.59 3.69
2840 5292 0.765510 AGGGTTGTTGTCACCTCCTC 59.234 55.000 0.00 0.00 0.00 3.71
2841 5293 0.250770 GGGTTGTTGTCACCTCCTCC 60.251 60.000 0.00 0.00 0.00 4.30
2842 5294 0.765510 GGTTGTTGTCACCTCCTCCT 59.234 55.000 0.00 0.00 0.00 3.69
2843 5295 1.270893 GGTTGTTGTCACCTCCTCCTC 60.271 57.143 0.00 0.00 0.00 3.71
2844 5296 1.416401 GTTGTTGTCACCTCCTCCTCA 59.584 52.381 0.00 0.00 0.00 3.86
2845 5297 1.342074 TGTTGTCACCTCCTCCTCAG 58.658 55.000 0.00 0.00 0.00 3.35
2846 5298 1.343069 GTTGTCACCTCCTCCTCAGT 58.657 55.000 0.00 0.00 0.00 3.41
2847 5299 2.158370 TGTTGTCACCTCCTCCTCAGTA 60.158 50.000 0.00 0.00 0.00 2.74
2848 5300 3.100671 GTTGTCACCTCCTCCTCAGTAT 58.899 50.000 0.00 0.00 0.00 2.12
2849 5301 4.264217 TGTTGTCACCTCCTCCTCAGTATA 60.264 45.833 0.00 0.00 0.00 1.47
2850 5302 4.816048 TGTCACCTCCTCCTCAGTATAT 57.184 45.455 0.00 0.00 0.00 0.86
2851 5303 4.474394 TGTCACCTCCTCCTCAGTATATG 58.526 47.826 0.00 0.00 0.00 1.78
2852 5304 3.257127 GTCACCTCCTCCTCAGTATATGC 59.743 52.174 0.00 0.00 0.00 3.14
2853 5305 2.564947 CACCTCCTCCTCAGTATATGCC 59.435 54.545 0.00 0.00 0.00 4.40
2854 5306 2.180086 ACCTCCTCCTCAGTATATGCCA 59.820 50.000 0.00 0.00 0.00 4.92
2855 5307 3.181402 ACCTCCTCCTCAGTATATGCCAT 60.181 47.826 0.00 0.00 0.00 4.40
2856 5308 3.197333 CCTCCTCCTCAGTATATGCCATG 59.803 52.174 0.00 0.00 0.00 3.66
2857 5309 3.837146 CTCCTCCTCAGTATATGCCATGT 59.163 47.826 0.00 0.00 0.00 3.21
2858 5310 3.834813 TCCTCCTCAGTATATGCCATGTC 59.165 47.826 0.00 0.00 0.00 3.06
2859 5311 3.580022 CCTCCTCAGTATATGCCATGTCA 59.420 47.826 0.00 0.00 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 54 2.319136 TGTAGCGGAGTGTTGTGTTT 57.681 45.000 0.00 0.00 0.00 2.83
67 69 6.557110 GCTACTAGCTAATACAGGATGTAGC 58.443 44.000 15.76 15.76 46.58 3.58
582 654 6.358178 TCCAGACACATGTTTAACTTACCAA 58.642 36.000 0.00 0.00 0.00 3.67
754 831 4.736464 GCCCAAAACACTGAACCTTAACAG 60.736 45.833 0.00 0.00 39.65 3.16
791 868 0.906756 TAGCAGGAGCAGCAGAGGTT 60.907 55.000 0.00 0.00 45.49 3.50
972 1050 7.319646 AGCTAACATTTGTGAAGAAACAACAA 58.680 30.769 0.00 0.00 39.70 2.83
1034 1116 2.972713 AGTGCAGTAGGTTCTTTCTCCA 59.027 45.455 0.00 0.00 0.00 3.86
1289 1404 8.685838 AAATAGCAAGTACTTTACACAAGGAA 57.314 30.769 5.07 0.00 0.00 3.36
1503 2453 1.547820 TGTAGGCTGAGAAGCACTCTG 59.452 52.381 0.00 11.28 45.13 3.35
1626 3973 2.037901 ACGACTGGATCTCTCATGCAT 58.962 47.619 0.00 0.00 0.00 3.96
1672 4019 1.130054 AGCTGTTCCCCTCTTCTGCA 61.130 55.000 0.00 0.00 0.00 4.41
1779 4129 5.300539 GCTTTTTCCTGTTCTCCTCTTCTTT 59.699 40.000 0.00 0.00 0.00 2.52
1840 4191 5.163468 TGAGCTCATCTTGGAGTAATCTGAC 60.163 44.000 13.74 0.00 37.24 3.51
1907 4260 0.178953 AGGCAGGTTCCAGCACATTT 60.179 50.000 8.38 0.00 0.00 2.32
2159 4592 6.280643 TCACAATGAAGAACTTCTCTTTCGA 58.719 36.000 14.31 0.00 44.82 3.71
2255 4698 8.719645 ACTTCTATCTGATAGCCTATTTCTGT 57.280 34.615 17.89 5.22 32.85 3.41
2440 4891 1.941975 CTGATGTATTGCGTGGCATCA 59.058 47.619 11.46 11.46 43.44 3.07
2488 4939 1.304134 GGCCCAGGTTTCGGTGATT 60.304 57.895 0.00 0.00 0.00 2.57
2536 4987 1.134788 GGTGGAGGACCGTTACTGATG 60.135 57.143 0.00 0.00 39.42 3.07
2552 5003 2.618053 GTCACAGATTTAGGACGGTGG 58.382 52.381 0.00 0.00 34.19 4.61
2560 5011 1.560923 CCGAGCCGTCACAGATTTAG 58.439 55.000 0.00 0.00 0.00 1.85
2577 5028 3.171911 GCCGCGACAAAAATGCCG 61.172 61.111 8.23 0.00 0.00 5.69
2585 5036 3.648982 CAGCACAAGCCGCGACAA 61.649 61.111 8.23 0.00 43.56 3.18
2590 5041 2.348605 TTTCCAACAGCACAAGCCGC 62.349 55.000 0.00 0.00 43.56 6.53
2615 5066 4.820897 AGATGTGTCATGTATCACACGTT 58.179 39.130 17.65 6.76 45.03 3.99
2633 5084 5.473039 TGCATCTGTTACGGATATGAGATG 58.527 41.667 6.34 4.54 39.77 2.90
2647 5098 0.957395 CGTCAGGCCTTGCATCTGTT 60.957 55.000 0.00 0.00 0.00 3.16
2700 5152 7.520614 GCACTACAAGAAACTTGCTTATCTGTT 60.521 37.037 10.78 0.00 0.00 3.16
2727 5179 4.627900 GGTCTGCAGAGCTAAGTTTACTTC 59.372 45.833 33.19 10.24 39.31 3.01
2728 5180 4.570930 GGTCTGCAGAGCTAAGTTTACTT 58.429 43.478 33.19 0.29 39.31 2.24
2729 5181 3.367498 CGGTCTGCAGAGCTAAGTTTACT 60.367 47.826 35.49 0.00 40.17 2.24
2730 5182 2.924290 CGGTCTGCAGAGCTAAGTTTAC 59.076 50.000 35.49 14.11 40.17 2.01
2731 5183 2.674177 GCGGTCTGCAGAGCTAAGTTTA 60.674 50.000 35.49 2.29 45.45 2.01
2732 5184 1.941668 GCGGTCTGCAGAGCTAAGTTT 60.942 52.381 35.49 0.00 45.45 2.66
2733 5185 0.390472 GCGGTCTGCAGAGCTAAGTT 60.390 55.000 35.49 0.00 45.45 2.66
2734 5186 1.216710 GCGGTCTGCAGAGCTAAGT 59.783 57.895 35.49 0.00 45.45 2.24
2735 5187 4.100981 GCGGTCTGCAGAGCTAAG 57.899 61.111 35.49 24.36 45.45 2.18
2757 5209 5.167845 GTTCCTGCACACTTCTTTCAAAAA 58.832 37.500 0.00 0.00 0.00 1.94
2758 5210 4.381505 GGTTCCTGCACACTTCTTTCAAAA 60.382 41.667 0.00 0.00 0.00 2.44
2759 5211 3.130340 GGTTCCTGCACACTTCTTTCAAA 59.870 43.478 0.00 0.00 0.00 2.69
2760 5212 2.687935 GGTTCCTGCACACTTCTTTCAA 59.312 45.455 0.00 0.00 0.00 2.69
2761 5213 2.297701 GGTTCCTGCACACTTCTTTCA 58.702 47.619 0.00 0.00 0.00 2.69
2762 5214 1.609072 GGGTTCCTGCACACTTCTTTC 59.391 52.381 0.00 0.00 0.00 2.62
2763 5215 1.692411 GGGTTCCTGCACACTTCTTT 58.308 50.000 0.00 0.00 0.00 2.52
2764 5216 0.178990 GGGGTTCCTGCACACTTCTT 60.179 55.000 0.00 0.00 0.00 2.52
2765 5217 1.352622 TGGGGTTCCTGCACACTTCT 61.353 55.000 0.00 0.00 0.00 2.85
2766 5218 0.251341 ATGGGGTTCCTGCACACTTC 60.251 55.000 0.00 0.00 0.00 3.01
2767 5219 0.251341 GATGGGGTTCCTGCACACTT 60.251 55.000 0.00 0.00 0.00 3.16
2768 5220 1.380302 GATGGGGTTCCTGCACACT 59.620 57.895 0.00 0.00 0.00 3.55
2769 5221 0.962356 CTGATGGGGTTCCTGCACAC 60.962 60.000 0.00 0.00 0.00 3.82
2770 5222 1.379916 CTGATGGGGTTCCTGCACA 59.620 57.895 0.00 0.00 0.00 4.57
2771 5223 1.379044 CCTGATGGGGTTCCTGCAC 60.379 63.158 0.00 0.00 0.00 4.57
2772 5224 3.089838 CCTGATGGGGTTCCTGCA 58.910 61.111 0.00 0.00 0.00 4.41
2773 5225 2.440980 GCCTGATGGGGTTCCTGC 60.441 66.667 0.00 0.00 35.12 4.85
2774 5226 2.276740 GGCCTGATGGGGTTCCTG 59.723 66.667 0.00 0.00 35.12 3.86
2775 5227 3.023735 GGGCCTGATGGGGTTCCT 61.024 66.667 0.84 0.00 35.12 3.36
2776 5228 4.143301 GGGGCCTGATGGGGTTCC 62.143 72.222 0.84 0.00 35.12 3.62
2777 5229 2.929964 TTGGGGCCTGATGGGGTTC 61.930 63.158 0.84 0.00 35.12 3.62
2778 5230 2.868566 TTGGGGCCTGATGGGGTT 60.869 61.111 0.84 0.00 35.12 4.11
2779 5231 3.672503 GTTGGGGCCTGATGGGGT 61.673 66.667 0.84 0.00 35.12 4.95
2780 5232 4.820744 CGTTGGGGCCTGATGGGG 62.821 72.222 0.84 0.00 35.12 4.96
2781 5233 2.572333 AATCGTTGGGGCCTGATGGG 62.572 60.000 0.84 0.00 38.36 4.00
2782 5234 0.684153 AAATCGTTGGGGCCTGATGG 60.684 55.000 0.84 0.00 0.00 3.51
2783 5235 0.740737 GAAATCGTTGGGGCCTGATG 59.259 55.000 0.84 0.00 0.00 3.07
2784 5236 0.331278 TGAAATCGTTGGGGCCTGAT 59.669 50.000 0.84 0.00 0.00 2.90
2785 5237 0.331278 ATGAAATCGTTGGGGCCTGA 59.669 50.000 0.84 0.00 0.00 3.86
2786 5238 1.949525 CTATGAAATCGTTGGGGCCTG 59.050 52.381 0.84 0.00 0.00 4.85
2787 5239 1.133792 CCTATGAAATCGTTGGGGCCT 60.134 52.381 0.84 0.00 0.00 5.19
2788 5240 1.133915 TCCTATGAAATCGTTGGGGCC 60.134 52.381 0.00 0.00 0.00 5.80
2789 5241 2.341846 TCCTATGAAATCGTTGGGGC 57.658 50.000 3.78 0.00 0.00 5.80
2790 5242 4.013728 TGTTTCCTATGAAATCGTTGGGG 58.986 43.478 3.78 0.00 42.20 4.96
2791 5243 5.835113 ATGTTTCCTATGAAATCGTTGGG 57.165 39.130 3.78 0.00 42.20 4.12
2792 5244 7.312154 TCAAATGTTTCCTATGAAATCGTTGG 58.688 34.615 0.00 0.00 42.20 3.77
2793 5245 8.915871 ATCAAATGTTTCCTATGAAATCGTTG 57.084 30.769 0.00 2.78 42.20 4.10
2801 5253 9.573166 CAACCCTATATCAAATGTTTCCTATGA 57.427 33.333 0.00 0.00 0.00 2.15
2802 5254 9.354673 ACAACCCTATATCAAATGTTTCCTATG 57.645 33.333 0.00 0.00 0.00 2.23
2803 5255 9.936329 AACAACCCTATATCAAATGTTTCCTAT 57.064 29.630 0.00 0.00 0.00 2.57
2804 5256 9.184523 CAACAACCCTATATCAAATGTTTCCTA 57.815 33.333 0.00 0.00 0.00 2.94
2805 5257 7.673926 ACAACAACCCTATATCAAATGTTTCCT 59.326 33.333 0.00 0.00 0.00 3.36
2806 5258 7.836842 ACAACAACCCTATATCAAATGTTTCC 58.163 34.615 0.00 0.00 0.00 3.13
2807 5259 8.519526 TGACAACAACCCTATATCAAATGTTTC 58.480 33.333 0.00 0.00 0.00 2.78
2808 5260 8.303876 GTGACAACAACCCTATATCAAATGTTT 58.696 33.333 0.00 0.00 0.00 2.83
2809 5261 7.093945 GGTGACAACAACCCTATATCAAATGTT 60.094 37.037 0.00 0.00 0.00 2.71
2810 5262 6.377146 GGTGACAACAACCCTATATCAAATGT 59.623 38.462 0.00 0.00 0.00 2.71
2811 5263 6.603201 AGGTGACAACAACCCTATATCAAATG 59.397 38.462 0.00 0.00 33.63 2.32
2812 5264 6.731467 AGGTGACAACAACCCTATATCAAAT 58.269 36.000 0.00 0.00 33.63 2.32
2813 5265 6.134535 AGGTGACAACAACCCTATATCAAA 57.865 37.500 0.00 0.00 33.63 2.69
2814 5266 5.338871 GGAGGTGACAACAACCCTATATCAA 60.339 44.000 0.00 0.00 33.63 2.57
2815 5267 4.163458 GGAGGTGACAACAACCCTATATCA 59.837 45.833 0.00 0.00 33.63 2.15
2816 5268 4.409247 AGGAGGTGACAACAACCCTATATC 59.591 45.833 0.00 0.00 34.36 1.63
2817 5269 4.371681 AGGAGGTGACAACAACCCTATAT 58.628 43.478 0.00 0.00 34.36 0.86
2818 5270 3.773119 GAGGAGGTGACAACAACCCTATA 59.227 47.826 0.00 0.00 35.57 1.31
2819 5271 2.572104 GAGGAGGTGACAACAACCCTAT 59.428 50.000 0.00 0.00 35.57 2.57
2820 5272 1.975680 GAGGAGGTGACAACAACCCTA 59.024 52.381 0.00 0.00 35.57 3.53
2821 5273 0.765510 GAGGAGGTGACAACAACCCT 59.234 55.000 0.00 0.00 37.20 4.34
2822 5274 0.250770 GGAGGAGGTGACAACAACCC 60.251 60.000 0.00 0.00 33.63 4.11
2823 5275 0.765510 AGGAGGAGGTGACAACAACC 59.234 55.000 0.00 0.00 33.63 3.77
2824 5276 1.416401 TGAGGAGGAGGTGACAACAAC 59.584 52.381 0.00 0.00 0.00 3.32
2825 5277 1.694150 CTGAGGAGGAGGTGACAACAA 59.306 52.381 0.00 0.00 0.00 2.83
2826 5278 1.342074 CTGAGGAGGAGGTGACAACA 58.658 55.000 0.00 0.00 0.00 3.33
2827 5279 1.343069 ACTGAGGAGGAGGTGACAAC 58.657 55.000 0.00 0.00 0.00 3.32
2828 5280 2.992847 TACTGAGGAGGAGGTGACAA 57.007 50.000 0.00 0.00 0.00 3.18
2829 5281 4.474394 CATATACTGAGGAGGAGGTGACA 58.526 47.826 0.00 0.00 0.00 3.58
2830 5282 3.257127 GCATATACTGAGGAGGAGGTGAC 59.743 52.174 0.00 0.00 0.00 3.67
2831 5283 3.501349 GCATATACTGAGGAGGAGGTGA 58.499 50.000 0.00 0.00 0.00 4.02
2832 5284 2.564947 GGCATATACTGAGGAGGAGGTG 59.435 54.545 0.00 0.00 0.00 4.00
2833 5285 2.180086 TGGCATATACTGAGGAGGAGGT 59.820 50.000 0.00 0.00 0.00 3.85
2834 5286 2.894731 TGGCATATACTGAGGAGGAGG 58.105 52.381 0.00 0.00 0.00 4.30
2835 5287 3.837146 ACATGGCATATACTGAGGAGGAG 59.163 47.826 0.00 0.00 0.00 3.69
2836 5288 3.834813 GACATGGCATATACTGAGGAGGA 59.165 47.826 0.00 0.00 0.00 3.71
2837 5289 3.580022 TGACATGGCATATACTGAGGAGG 59.420 47.826 0.00 0.00 0.00 4.30
2838 5290 4.879197 TGACATGGCATATACTGAGGAG 57.121 45.455 0.00 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.