Multiple sequence alignment - TraesCS6B01G245600

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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 TraesCS6B01G245600 chr6B 100.000 3209 0 0 1 3209 438384861 438388069 0.000000e+00 5927
1 TraesCS6B01G245600 chr6B 82.422 256 36 7 579 831 540604153 540603904 6.970000e-52 215
2 TraesCS6B01G245600 chr6B 81.641 256 37 6 579 831 560180567 560180815 1.510000e-48 204
3 TraesCS6B01G245600 chr6D 93.232 1980 76 23 854 2815 276455696 276457635 0.000000e+00 2861
4 TraesCS6B01G245600 chr6A 93.693 1871 58 22 837 2694 399723198 399721375 0.000000e+00 2747
5 TraesCS6B01G245600 chr6A 89.929 844 67 15 1 831 399724083 399723245 0.000000e+00 1072
6 TraesCS6B01G245600 chr6A 89.170 277 24 3 2930 3205 399721177 399720906 1.100000e-89 340
7 TraesCS6B01G245600 chr6A 80.000 335 53 9 503 831 71663349 71663675 5.350000e-58 235
8 TraesCS6B01G245600 chr6A 90.566 106 7 2 2691 2796 399721295 399721193 1.550000e-28 137
9 TraesCS6B01G245600 chr3B 85.829 995 91 25 953 1933 766632361 766631403 0.000000e+00 1011
10 TraesCS6B01G245600 chr3B 81.360 1191 150 36 916 2059 769055217 769056382 0.000000e+00 904
11 TraesCS6B01G245600 chr3B 81.758 899 93 33 1001 1865 768903788 768904649 0.000000e+00 686
12 TraesCS6B01G245600 chr3B 80.255 785 106 35 7 777 169333965 169333216 2.180000e-151 545
13 TraesCS6B01G245600 chr3B 82.396 676 68 20 1260 1906 768928763 768929416 2.820000e-150 542
14 TraesCS6B01G245600 chr3B 81.642 670 82 20 119 777 801186882 801187521 4.750000e-143 518
15 TraesCS6B01G245600 chr3A 84.774 1018 98 26 933 1933 711218957 711217980 0.000000e+00 968
16 TraesCS6B01G245600 chr3A 83.268 1022 113 30 929 1933 711204083 711203103 0.000000e+00 887
17 TraesCS6B01G245600 chr3A 87.365 554 48 8 1049 1592 712571253 712571794 1.640000e-172 616
18 TraesCS6B01G245600 chr3A 83.425 543 55 20 1384 1906 712571792 712572319 3.750000e-129 472
19 TraesCS6B01G245600 chr3A 74.178 426 47 32 1976 2353 711217868 711217458 5.620000e-23 119
20 TraesCS6B01G245600 chr3D 85.000 1000 91 33 957 1933 575726973 575726010 0.000000e+00 961
21 TraesCS6B01G245600 chr3D 85.155 869 93 21 1049 1906 577254843 577255686 0.000000e+00 857
22 TraesCS6B01G245600 chr3D 92.331 326 19 1 1264 1583 577263861 577264186 2.920000e-125 459
23 TraesCS6B01G245600 chr3D 81.922 437 52 19 1 424 495181399 495180977 8.520000e-91 344
24 TraesCS6B01G245600 chr3D 78.516 512 83 20 1 500 580329277 580329773 8.640000e-81 311
25 TraesCS6B01G245600 chr3D 76.033 242 38 8 917 1143 577263627 577263863 1.220000e-19 108
26 TraesCS6B01G245600 chr7D 84.829 468 52 14 1 458 490439775 490439317 1.360000e-123 453
27 TraesCS6B01G245600 chr5D 84.110 472 51 15 1 457 449947278 449947740 4.920000e-118 435
28 TraesCS6B01G245600 chr5D 87.861 346 34 6 1049 1390 91405500 91405841 1.790000e-107 399
29 TraesCS6B01G245600 chr5D 82.405 449 64 13 338 777 524330195 524330637 8.400000e-101 377
30 TraesCS6B01G245600 chr5A 88.150 346 33 6 1049 1390 85164085 85164426 3.850000e-109 405
31 TraesCS6B01G245600 chr5A 90.541 222 14 4 1388 1608 85164670 85164885 1.460000e-73 287
32 TraesCS6B01G245600 chr5B 87.283 346 36 6 1049 1390 96764290 96764631 3.880000e-104 388
33 TraesCS6B01G245600 chr5B 82.596 339 43 5 498 831 54463377 54463704 5.240000e-73 285
34 TraesCS6B01G245600 chr5B 82.188 320 49 6 518 831 322558488 322558171 5.280000e-68 268
35 TraesCS6B01G245600 chr1A 80.980 510 72 16 1 500 531655221 531655715 6.500000e-102 381
36 TraesCS6B01G245600 chr2D 80.855 491 53 25 1 480 64725871 64726331 6.590000e-92 348
37 TraesCS6B01G245600 chr2D 82.597 385 47 14 126 499 636126856 636127231 3.990000e-84 322
38 TraesCS6B01G245600 chr2D 78.058 515 84 22 1 500 624794757 624795257 6.730000e-77 298
39 TraesCS6B01G245600 chr2D 83.082 331 48 6 505 829 55317940 55317612 8.710000e-76 294
40 TraesCS6B01G245600 chr2D 80.997 321 52 6 504 818 572258750 572258433 2.470000e-61 246
41 TraesCS6B01G245600 chr4A 81.674 442 58 17 71 499 467154509 467154078 2.370000e-91 346
42 TraesCS6B01G245600 chr1B 77.448 337 67 6 1054 1390 406037568 406037241 3.270000e-45 193
43 TraesCS6B01G245600 chr2B 77.812 329 57 13 506 831 16879613 16879928 4.230000e-44 189


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 TraesCS6B01G245600 chr6B 438384861 438388069 3208 False 5927.0 5927 100.0000 1 3209 1 chr6B.!!$F1 3208
1 TraesCS6B01G245600 chr6D 276455696 276457635 1939 False 2861.0 2861 93.2320 854 2815 1 chr6D.!!$F1 1961
2 TraesCS6B01G245600 chr6A 399720906 399724083 3177 True 1074.0 2747 90.8395 1 3205 4 chr6A.!!$R1 3204
3 TraesCS6B01G245600 chr3B 766631403 766632361 958 True 1011.0 1011 85.8290 953 1933 1 chr3B.!!$R2 980
4 TraesCS6B01G245600 chr3B 769055217 769056382 1165 False 904.0 904 81.3600 916 2059 1 chr3B.!!$F3 1143
5 TraesCS6B01G245600 chr3B 768903788 768904649 861 False 686.0 686 81.7580 1001 1865 1 chr3B.!!$F1 864
6 TraesCS6B01G245600 chr3B 169333216 169333965 749 True 545.0 545 80.2550 7 777 1 chr3B.!!$R1 770
7 TraesCS6B01G245600 chr3B 768928763 768929416 653 False 542.0 542 82.3960 1260 1906 1 chr3B.!!$F2 646
8 TraesCS6B01G245600 chr3B 801186882 801187521 639 False 518.0 518 81.6420 119 777 1 chr3B.!!$F4 658
9 TraesCS6B01G245600 chr3A 711203103 711204083 980 True 887.0 887 83.2680 929 1933 1 chr3A.!!$R1 1004
10 TraesCS6B01G245600 chr3A 712571253 712572319 1066 False 544.0 616 85.3950 1049 1906 2 chr3A.!!$F1 857
11 TraesCS6B01G245600 chr3A 711217458 711218957 1499 True 543.5 968 79.4760 933 2353 2 chr3A.!!$R2 1420
12 TraesCS6B01G245600 chr3D 575726010 575726973 963 True 961.0 961 85.0000 957 1933 1 chr3D.!!$R2 976
13 TraesCS6B01G245600 chr3D 577254843 577255686 843 False 857.0 857 85.1550 1049 1906 1 chr3D.!!$F1 857
14 TraesCS6B01G245600 chr3D 577263627 577264186 559 False 283.5 459 84.1820 917 1583 2 chr3D.!!$F3 666
15 TraesCS6B01G245600 chr5A 85164085 85164885 800 False 346.0 405 89.3455 1049 1608 2 chr5A.!!$F1 559
16 TraesCS6B01G245600 chr2D 624794757 624795257 500 False 298.0 298 78.0580 1 500 1 chr2D.!!$F2 499

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
486 550 0.319469 TCTCTCGTTGCAATGCACGA 60.319 50.0 23.35 23.35 38.71 4.35 F
1036 1187 0.179000 GATGCCTTCCACGGATGAGT 59.821 55.0 0.65 0.00 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2072 2855 0.250166 AACCACCAGAGTACGGCAAC 60.250 55.000 0.00 0.0 0.0 4.17 R
2566 3391 1.270550 ACTTTCAGCTGGGCATTTTCG 59.729 47.619 15.13 0.0 0.0 3.46 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
84 85 8.726650 TTGATTCATAGAATGTTCGTTGTTTG 57.273 30.769 0.00 0.00 0.00 2.93
157 160 6.813649 TCGTGAATTTCAAAATTTGTTCCACA 59.186 30.769 5.56 0.65 38.64 4.17
325 349 8.984482 TGTTTTATGAATTTGAAAAATGTGCG 57.016 26.923 0.00 0.00 0.00 5.34
334 358 5.886715 TTGAAAAATGTGCGTGATTTCAG 57.113 34.783 0.00 0.00 40.07 3.02
336 360 5.771469 TGAAAAATGTGCGTGATTTCAGAT 58.229 33.333 0.00 0.00 35.67 2.90
353 396 9.907576 GATTTCAGATATGTTCACGAGTTTTAG 57.092 33.333 0.00 0.00 0.00 1.85
450 510 4.561123 GCAAAATGTGGTCATGTCCATTGA 60.561 41.667 20.32 8.37 39.81 2.57
486 550 0.319469 TCTCTCGTTGCAATGCACGA 60.319 50.000 23.35 23.35 38.71 4.35
589 656 9.784680 CTAGAATTGTTCATGGATTCAAGAAAG 57.215 33.333 0.00 0.00 33.22 2.62
597 664 9.528018 GTTCATGGATTCAAGAAAGTTGTTTAA 57.472 29.630 0.00 0.00 33.22 1.52
831 904 4.325972 TCTCAGTGATGCAGCAAAATGTA 58.674 39.130 6.05 0.00 0.00 2.29
835 949 3.125829 AGTGATGCAGCAAAATGTAGACG 59.874 43.478 6.05 0.00 0.00 4.18
840 954 2.843077 CAGCAAAATGTAGACGCACAG 58.157 47.619 0.00 0.00 0.00 3.66
848 962 2.214216 TAGACGCACAGGCCCTTGT 61.214 57.895 0.00 0.00 36.38 3.16
849 963 0.901114 TAGACGCACAGGCCCTTGTA 60.901 55.000 0.00 0.00 36.38 2.41
946 1068 1.198637 ACGTAGTAGCACACGAAGACC 59.801 52.381 0.62 0.00 41.94 3.85
997 1129 2.286294 CAGCTAGCTTGGCACGATTAAG 59.714 50.000 16.46 0.00 0.00 1.85
1036 1187 0.179000 GATGCCTTCCACGGATGAGT 59.821 55.000 0.65 0.00 0.00 3.41
1075 1233 1.248785 GGACGAGGGAGCTGTACACA 61.249 60.000 0.00 0.00 0.00 3.72
1658 2313 2.293677 CACTCTACCGTCACTGTCAAGT 59.706 50.000 0.00 0.00 36.98 3.16
2014 2780 2.498726 GCGAGGAGGCAGAAGAGG 59.501 66.667 0.00 0.00 0.00 3.69
2071 2854 1.359459 CCCGCTTTCGCTGGTTACTC 61.359 60.000 0.00 0.00 35.96 2.59
2072 2855 1.683790 CCGCTTTCGCTGGTTACTCG 61.684 60.000 0.00 0.00 0.00 4.18
2161 2959 4.319177 TCAAGTGCTAAGCTTCTTCTTCC 58.681 43.478 0.00 0.00 0.00 3.46
2180 2978 6.882656 TCTTCCTCTACCAGATCAAATCAAG 58.117 40.000 0.00 0.00 0.00 3.02
2197 2995 2.969950 TCAAGAGGAGGAAAAGGACGAA 59.030 45.455 0.00 0.00 0.00 3.85
2242 3048 0.117140 TGGAGAAAGGAGGAGCCAGA 59.883 55.000 0.00 0.00 40.02 3.86
2458 3282 6.065976 TCATAGAGGCATCTTTTTCTTGGA 57.934 37.500 6.05 0.00 36.96 3.53
2486 3311 2.554806 CGGAGTCGTAGCAATGTACA 57.445 50.000 0.00 0.00 0.00 2.90
2487 3312 3.079960 CGGAGTCGTAGCAATGTACAT 57.920 47.619 1.41 1.41 0.00 2.29
2488 3313 4.219143 CGGAGTCGTAGCAATGTACATA 57.781 45.455 9.21 0.00 0.00 2.29
2492 3317 5.793952 GGAGTCGTAGCAATGTACATATACG 59.206 44.000 26.46 26.46 37.83 3.06
2530 3355 1.532868 GCAATCAGTGACGAGCTTGTT 59.467 47.619 8.34 0.00 0.00 2.83
2532 3357 3.548818 GCAATCAGTGACGAGCTTGTTTT 60.549 43.478 8.34 0.00 0.00 2.43
2533 3358 4.319477 GCAATCAGTGACGAGCTTGTTTTA 60.319 41.667 8.34 0.00 0.00 1.52
2536 3361 6.560253 ATCAGTGACGAGCTTGTTTTATTT 57.440 33.333 8.34 0.00 0.00 1.40
2542 3367 7.012044 AGTGACGAGCTTGTTTTATTTTGTACT 59.988 33.333 8.34 0.00 0.00 2.73
2566 3391 5.121142 TGCGAAAATACCAAACTAGTGCTAC 59.879 40.000 0.00 0.00 0.00 3.58
2593 3418 1.878953 CCCAGCTGAAAGTTACGTGT 58.121 50.000 17.39 0.00 35.30 4.49
2756 3664 7.970384 TCGAAAGATACAATGTTGGATGTAAC 58.030 34.615 0.00 0.00 35.79 2.50
2758 3666 7.404671 AAAGATACAATGTTGGATGTAACCC 57.595 36.000 0.00 0.00 35.79 4.11
2773 3681 3.904965 TGTAACCCATAGTCAGTTCACCA 59.095 43.478 0.00 0.00 0.00 4.17
2809 3718 6.395629 ACATGTAACTTAGTTGTACTCGCAT 58.604 36.000 8.00 0.00 0.00 4.73
2815 3724 9.167239 GTAACTTAGTTGTACTCGCATATAGTG 57.833 37.037 8.00 0.00 0.00 2.74
2816 3725 6.736123 ACTTAGTTGTACTCGCATATAGTGG 58.264 40.000 0.00 0.00 0.00 4.00
2817 3726 3.978687 AGTTGTACTCGCATATAGTGGC 58.021 45.455 0.00 0.00 0.00 5.01
2836 3745 3.675467 GCGGTGCCAAGATTTAACTAG 57.325 47.619 0.00 0.00 0.00 2.57
2837 3746 2.354821 GCGGTGCCAAGATTTAACTAGG 59.645 50.000 0.00 0.00 0.00 3.02
2838 3747 3.869065 CGGTGCCAAGATTTAACTAGGA 58.131 45.455 0.00 0.00 0.00 2.94
2839 3748 3.621715 CGGTGCCAAGATTTAACTAGGAC 59.378 47.826 0.00 0.00 0.00 3.85
2840 3749 3.945921 GGTGCCAAGATTTAACTAGGACC 59.054 47.826 0.00 0.00 31.67 4.46
2841 3750 4.566907 GGTGCCAAGATTTAACTAGGACCA 60.567 45.833 0.00 0.00 36.00 4.02
2842 3751 5.007682 GTGCCAAGATTTAACTAGGACCAA 58.992 41.667 0.00 0.00 0.00 3.67
2843 3752 5.123979 GTGCCAAGATTTAACTAGGACCAAG 59.876 44.000 0.00 0.00 0.00 3.61
2844 3753 5.013704 TGCCAAGATTTAACTAGGACCAAGA 59.986 40.000 0.00 0.00 0.00 3.02
2845 3754 6.122964 GCCAAGATTTAACTAGGACCAAGAT 58.877 40.000 0.00 0.00 0.00 2.40
2846 3755 6.603599 GCCAAGATTTAACTAGGACCAAGATT 59.396 38.462 0.00 0.00 0.00 2.40
2847 3756 7.122799 GCCAAGATTTAACTAGGACCAAGATTT 59.877 37.037 0.00 0.00 0.00 2.17
2848 3757 9.681062 CCAAGATTTAACTAGGACCAAGATTTA 57.319 33.333 0.00 0.00 0.00 1.40
2854 3763 8.842358 TTAACTAGGACCAAGATTTAACAGTG 57.158 34.615 0.00 0.00 0.00 3.66
2855 3764 6.435292 ACTAGGACCAAGATTTAACAGTGT 57.565 37.500 0.00 0.00 0.00 3.55
2856 3765 6.465084 ACTAGGACCAAGATTTAACAGTGTC 58.535 40.000 0.00 0.00 0.00 3.67
2857 3766 4.652822 AGGACCAAGATTTAACAGTGTCC 58.347 43.478 0.00 0.00 41.00 4.02
2858 3767 4.351111 AGGACCAAGATTTAACAGTGTCCT 59.649 41.667 0.00 0.00 44.83 3.85
2859 3768 5.801380 GGACCAAGATTTAACAGTGTCCTA 58.199 41.667 0.00 0.00 38.36 2.94
2860 3769 5.642491 GGACCAAGATTTAACAGTGTCCTAC 59.358 44.000 0.00 0.00 38.36 3.18
2861 3770 5.557866 ACCAAGATTTAACAGTGTCCTACC 58.442 41.667 0.00 0.00 0.00 3.18
2862 3771 5.309806 ACCAAGATTTAACAGTGTCCTACCT 59.690 40.000 0.00 0.00 0.00 3.08
2863 3772 6.499350 ACCAAGATTTAACAGTGTCCTACCTA 59.501 38.462 0.00 0.00 0.00 3.08
2864 3773 6.817140 CCAAGATTTAACAGTGTCCTACCTAC 59.183 42.308 0.00 0.00 0.00 3.18
2865 3774 7.310485 CCAAGATTTAACAGTGTCCTACCTACT 60.310 40.741 0.00 0.00 0.00 2.57
2866 3775 8.746530 CAAGATTTAACAGTGTCCTACCTACTA 58.253 37.037 0.00 0.00 0.00 1.82
2867 3776 8.291191 AGATTTAACAGTGTCCTACCTACTAC 57.709 38.462 0.00 0.00 0.00 2.73
2868 3777 7.892241 AGATTTAACAGTGTCCTACCTACTACA 59.108 37.037 0.00 0.00 0.00 2.74
2869 3778 7.458409 TTTAACAGTGTCCTACCTACTACAG 57.542 40.000 0.00 0.00 0.00 2.74
2870 3779 4.654389 ACAGTGTCCTACCTACTACAGT 57.346 45.455 0.00 0.00 0.00 3.55
2871 3780 4.995536 ACAGTGTCCTACCTACTACAGTT 58.004 43.478 0.00 0.00 0.00 3.16
2872 3781 6.131972 ACAGTGTCCTACCTACTACAGTTA 57.868 41.667 0.00 0.00 0.00 2.24
2873 3782 6.546484 ACAGTGTCCTACCTACTACAGTTAA 58.454 40.000 0.00 0.00 0.00 2.01
2874 3783 6.432472 ACAGTGTCCTACCTACTACAGTTAAC 59.568 42.308 0.00 0.00 0.00 2.01
2875 3784 6.432162 CAGTGTCCTACCTACTACAGTTAACA 59.568 42.308 8.61 0.00 0.00 2.41
2876 3785 7.006509 AGTGTCCTACCTACTACAGTTAACAA 58.993 38.462 8.61 0.00 0.00 2.83
2877 3786 7.506938 AGTGTCCTACCTACTACAGTTAACAAA 59.493 37.037 8.61 0.00 0.00 2.83
2878 3787 7.811713 GTGTCCTACCTACTACAGTTAACAAAG 59.188 40.741 8.61 4.50 0.00 2.77
2879 3788 7.725397 TGTCCTACCTACTACAGTTAACAAAGA 59.275 37.037 8.61 0.00 0.00 2.52
2880 3789 8.242739 GTCCTACCTACTACAGTTAACAAAGAG 58.757 40.741 8.61 2.15 0.00 2.85
2881 3790 8.166061 TCCTACCTACTACAGTTAACAAAGAGA 58.834 37.037 8.61 0.00 0.00 3.10
2882 3791 8.968969 CCTACCTACTACAGTTAACAAAGAGAT 58.031 37.037 8.61 0.00 0.00 2.75
2889 3798 9.000486 ACTACAGTTAACAAAGAGATTTTAGGC 58.000 33.333 8.61 0.00 0.00 3.93
2890 3799 7.215719 ACAGTTAACAAAGAGATTTTAGGCC 57.784 36.000 8.61 0.00 0.00 5.19
2891 3800 6.775629 ACAGTTAACAAAGAGATTTTAGGCCA 59.224 34.615 5.01 0.00 0.00 5.36
2892 3801 7.084486 CAGTTAACAAAGAGATTTTAGGCCAC 58.916 38.462 5.01 0.00 0.00 5.01
2893 3802 4.766404 AACAAAGAGATTTTAGGCCACG 57.234 40.909 5.01 0.00 0.00 4.94
2894 3803 2.488153 ACAAAGAGATTTTAGGCCACGC 59.512 45.455 5.01 0.00 0.00 5.34
2935 3844 2.565841 GCCTAGGGCTTGAGTGTAATG 58.434 52.381 11.72 0.00 46.69 1.90
2938 3847 4.040461 GCCTAGGGCTTGAGTGTAATGATA 59.960 45.833 11.72 0.00 46.69 2.15
3039 3948 7.610305 TCTTTGTGGTATTAATCCTTGAAGGTC 59.390 37.037 11.60 0.00 36.53 3.85
3053 3962 7.153985 TCCTTGAAGGTCAAATGCAATAAAAG 58.846 34.615 11.60 0.00 35.73 2.27
3078 3987 2.426522 CGAAAGCCCTTGAATCACTCA 58.573 47.619 0.00 0.00 0.00 3.41
3080 3989 3.064545 CGAAAGCCCTTGAATCACTCATC 59.935 47.826 0.00 0.00 32.78 2.92
3085 3994 3.129988 GCCCTTGAATCACTCATCCAAAG 59.870 47.826 0.00 0.00 32.78 2.77
3088 3997 5.494724 CCTTGAATCACTCATCCAAAGAGA 58.505 41.667 0.00 0.00 36.91 3.10
3105 4014 6.253746 CAAAGAGATGAAAAGTCATAAGCGG 58.746 40.000 0.00 0.00 44.83 5.52
3107 4016 2.945668 AGATGAAAAGTCATAAGCGGCC 59.054 45.455 0.00 0.00 44.83 6.13
3108 4017 2.192664 TGAAAAGTCATAAGCGGCCA 57.807 45.000 2.24 0.00 0.00 5.36
3109 4018 2.509569 TGAAAAGTCATAAGCGGCCAA 58.490 42.857 2.24 0.00 0.00 4.52
3110 4019 2.487762 TGAAAAGTCATAAGCGGCCAAG 59.512 45.455 2.24 0.00 0.00 3.61
3111 4020 0.811281 AAAGTCATAAGCGGCCAAGC 59.189 50.000 2.24 0.00 37.41 4.01
3112 4021 1.032114 AAGTCATAAGCGGCCAAGCC 61.032 55.000 2.24 0.00 46.75 4.35
3134 4043 3.560636 ACGTATTTGAGGAAGATGGGG 57.439 47.619 0.00 0.00 0.00 4.96
3137 4046 3.388024 CGTATTTGAGGAAGATGGGGAGA 59.612 47.826 0.00 0.00 0.00 3.71
3143 4052 2.174424 GAGGAAGATGGGGAGAGCAAAT 59.826 50.000 0.00 0.00 0.00 2.32
3147 4057 4.384940 GAAGATGGGGAGAGCAAATAGTC 58.615 47.826 0.00 0.00 0.00 2.59
3148 4058 3.387962 AGATGGGGAGAGCAAATAGTCA 58.612 45.455 0.00 0.00 0.00 3.41
3151 4061 3.686016 TGGGGAGAGCAAATAGTCAAAC 58.314 45.455 0.00 0.00 0.00 2.93
3161 4071 6.006449 AGCAAATAGTCAAACCACAAGATCT 58.994 36.000 0.00 0.00 0.00 2.75
3163 4073 6.803807 GCAAATAGTCAAACCACAAGATCTTC 59.196 38.462 4.57 0.00 0.00 2.87
3175 4085 3.195610 ACAAGATCTTCGCCATAGTGTCA 59.804 43.478 4.57 0.00 0.00 3.58
3197 4107 9.349713 TGTCAAGGTAAGATTTCAACAAATAGT 57.650 29.630 0.00 0.00 31.94 2.12
3205 4115 8.871686 AAGATTTCAACAAATAGTCAAACCAC 57.128 30.769 0.00 0.00 31.94 4.16
3206 4116 8.006298 AGATTTCAACAAATAGTCAAACCACA 57.994 30.769 0.00 0.00 31.94 4.17
3207 4117 8.474025 AGATTTCAACAAATAGTCAAACCACAA 58.526 29.630 0.00 0.00 31.94 3.33
3208 4118 9.092876 GATTTCAACAAATAGTCAAACCACAAA 57.907 29.630 0.00 0.00 31.94 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
182 185 9.098355 TGAATAGACAAACATTTCTAGAATCGG 57.902 33.333 5.89 1.71 0.00 4.18
301 324 8.881231 CACGCACATTTTTCAAATTCATAAAAC 58.119 29.630 0.00 0.00 0.00 2.43
302 325 8.820933 TCACGCACATTTTTCAAATTCATAAAA 58.179 25.926 0.00 0.00 0.00 1.52
314 338 7.485913 ACATATCTGAAATCACGCACATTTTTC 59.514 33.333 0.00 0.00 0.00 2.29
325 349 6.893958 ACTCGTGAACATATCTGAAATCAC 57.106 37.500 0.00 0.00 34.12 3.06
336 360 9.872757 GAACATTTTCTAAAACTCGTGAACATA 57.127 29.630 0.00 0.00 0.00 2.29
466 530 0.512518 CGTGCATTGCAACGAGAGAA 59.487 50.000 21.17 0.00 41.47 2.87
480 544 0.955428 CTAGCAAAAGGGCTCGTGCA 60.955 55.000 12.07 0.00 44.54 4.57
569 636 7.111247 ACAACTTTCTTGAATCCATGAACAA 57.889 32.000 0.00 0.00 36.55 2.83
688 757 9.605275 TTCAAATCCATGAACACAATTACAAAA 57.395 25.926 0.00 0.00 34.50 2.44
831 904 2.214216 TACAAGGGCCTGTGCGTCT 61.214 57.895 6.92 0.00 38.85 4.18
835 949 0.613777 ACTAGTACAAGGGCCTGTGC 59.386 55.000 6.92 11.35 32.62 4.57
840 954 5.349061 TTTTAGCTACTAGTACAAGGGCC 57.651 43.478 0.00 0.00 0.00 5.80
946 1068 2.105328 TGACGTCCGGTGTGTGTG 59.895 61.111 14.12 0.00 0.00 3.82
1028 1177 1.264749 TGACCCCTTCCACTCATCCG 61.265 60.000 0.00 0.00 0.00 4.18
1036 1187 1.003118 CAGTTCGATTGACCCCTTCCA 59.997 52.381 0.00 0.00 0.00 3.53
1075 1233 4.008933 GACTGGCAGCCCGACACT 62.009 66.667 15.89 0.00 0.00 3.55
1658 2313 0.250510 TGTGGCCGACATTGCAGTTA 60.251 50.000 0.00 0.00 0.00 2.24
2002 2768 2.185608 GTCGCCCTCTTCTGCCTC 59.814 66.667 0.00 0.00 0.00 4.70
2072 2855 0.250166 AACCACCAGAGTACGGCAAC 60.250 55.000 0.00 0.00 0.00 4.17
2161 2959 6.462768 CCTCCTCTTGATTTGATCTGGTAGAG 60.463 46.154 0.00 0.00 0.00 2.43
2180 2978 1.900486 TCCTTCGTCCTTTTCCTCCTC 59.100 52.381 0.00 0.00 0.00 3.71
2197 2995 3.813443 CCATCTCCGTTCATTCATTCCT 58.187 45.455 0.00 0.00 0.00 3.36
2426 3250 4.580868 AGATGCCTCTATGATCTGCAATG 58.419 43.478 0.00 0.00 35.30 2.82
2482 3307 4.181578 GGATCATGTGGCCGTATATGTAC 58.818 47.826 0.00 0.00 0.00 2.90
2483 3308 3.119280 CGGATCATGTGGCCGTATATGTA 60.119 47.826 13.03 0.00 40.17 2.29
2484 3309 2.353704 CGGATCATGTGGCCGTATATGT 60.354 50.000 13.03 0.00 40.17 2.29
2485 3310 2.270923 CGGATCATGTGGCCGTATATG 58.729 52.381 13.03 0.00 40.17 1.78
2486 3311 2.672961 CGGATCATGTGGCCGTATAT 57.327 50.000 13.03 0.00 40.17 0.86
2492 3317 1.718757 GCAAGACGGATCATGTGGCC 61.719 60.000 0.00 0.00 0.00 5.36
2530 3355 9.745880 TTTGGTATTTTCGCAGTACAAAATAAA 57.254 25.926 9.28 2.81 36.61 1.40
2532 3357 8.569641 AGTTTGGTATTTTCGCAGTACAAAATA 58.430 29.630 0.00 0.43 34.68 1.40
2533 3358 7.430441 AGTTTGGTATTTTCGCAGTACAAAAT 58.570 30.769 0.00 1.41 36.43 1.82
2536 3361 6.707161 ACTAGTTTGGTATTTTCGCAGTACAA 59.293 34.615 0.00 0.00 0.00 2.41
2542 3367 4.069304 AGCACTAGTTTGGTATTTTCGCA 58.931 39.130 0.00 0.00 0.00 5.10
2566 3391 1.270550 ACTTTCAGCTGGGCATTTTCG 59.729 47.619 15.13 0.00 0.00 3.46
2593 3418 3.068064 TGATCCTCTGCCGACGCA 61.068 61.111 0.00 0.00 44.78 5.24
2629 3454 6.238456 CGGTATCTTGTACGTAACCACTATCA 60.238 42.308 11.38 0.00 0.00 2.15
2724 3632 7.390440 TCCAACATTGTATCTTTCGATGTTCTT 59.610 33.333 8.11 0.00 43.67 2.52
2756 3664 4.848357 AGAAATGGTGAACTGACTATGGG 58.152 43.478 0.00 0.00 0.00 4.00
2796 3704 3.978687 GCCACTATATGCGAGTACAACT 58.021 45.455 0.00 0.00 0.00 3.16
2816 3725 2.354821 CCTAGTTAAATCTTGGCACCGC 59.645 50.000 0.00 0.00 0.00 5.68
2817 3726 3.621715 GTCCTAGTTAAATCTTGGCACCG 59.378 47.826 0.00 0.00 32.08 4.94
2818 3727 3.945921 GGTCCTAGTTAAATCTTGGCACC 59.054 47.826 0.00 0.00 32.08 5.01
2819 3728 4.585879 TGGTCCTAGTTAAATCTTGGCAC 58.414 43.478 0.00 0.00 32.08 5.01
2820 3729 4.919774 TGGTCCTAGTTAAATCTTGGCA 57.080 40.909 0.00 0.00 32.08 4.92
2821 3730 5.497474 TCTTGGTCCTAGTTAAATCTTGGC 58.503 41.667 0.00 0.00 32.08 4.52
2822 3731 8.581253 AAATCTTGGTCCTAGTTAAATCTTGG 57.419 34.615 0.00 0.00 0.00 3.61
2828 3737 9.280174 CACTGTTAAATCTTGGTCCTAGTTAAA 57.720 33.333 0.00 0.00 0.00 1.52
2829 3738 8.434392 ACACTGTTAAATCTTGGTCCTAGTTAA 58.566 33.333 0.00 0.00 0.00 2.01
2830 3739 7.970102 ACACTGTTAAATCTTGGTCCTAGTTA 58.030 34.615 0.00 0.00 0.00 2.24
2831 3740 6.838382 ACACTGTTAAATCTTGGTCCTAGTT 58.162 36.000 0.00 0.00 0.00 2.24
2832 3741 6.435292 ACACTGTTAAATCTTGGTCCTAGT 57.565 37.500 0.00 0.00 0.00 2.57
2833 3742 5.875359 GGACACTGTTAAATCTTGGTCCTAG 59.125 44.000 0.00 0.00 40.23 3.02
2834 3743 5.801380 GGACACTGTTAAATCTTGGTCCTA 58.199 41.667 0.00 0.00 40.23 2.94
2835 3744 4.351111 AGGACACTGTTAAATCTTGGTCCT 59.649 41.667 0.00 0.00 46.63 3.85
2836 3745 4.652822 AGGACACTGTTAAATCTTGGTCC 58.347 43.478 0.00 0.00 42.94 4.46
2837 3746 5.642491 GGTAGGACACTGTTAAATCTTGGTC 59.358 44.000 0.00 0.00 0.00 4.02
2838 3747 5.309806 AGGTAGGACACTGTTAAATCTTGGT 59.690 40.000 0.00 0.00 0.00 3.67
2839 3748 5.805728 AGGTAGGACACTGTTAAATCTTGG 58.194 41.667 0.00 0.00 0.00 3.61
2840 3749 7.612677 AGTAGGTAGGACACTGTTAAATCTTG 58.387 38.462 0.00 0.00 0.00 3.02
2841 3750 7.793948 AGTAGGTAGGACACTGTTAAATCTT 57.206 36.000 0.00 0.00 0.00 2.40
2842 3751 7.892241 TGTAGTAGGTAGGACACTGTTAAATCT 59.108 37.037 0.00 0.00 0.00 2.40
2843 3752 8.059798 TGTAGTAGGTAGGACACTGTTAAATC 57.940 38.462 0.00 0.00 0.00 2.17
2844 3753 7.673082 ACTGTAGTAGGTAGGACACTGTTAAAT 59.327 37.037 0.00 0.00 0.00 1.40
2845 3754 7.006509 ACTGTAGTAGGTAGGACACTGTTAAA 58.993 38.462 0.00 0.00 0.00 1.52
2846 3755 6.546484 ACTGTAGTAGGTAGGACACTGTTAA 58.454 40.000 0.00 0.00 0.00 2.01
2847 3756 6.131972 ACTGTAGTAGGTAGGACACTGTTA 57.868 41.667 0.00 0.00 0.00 2.41
2848 3757 4.995536 ACTGTAGTAGGTAGGACACTGTT 58.004 43.478 0.00 0.00 0.00 3.16
2849 3758 4.654389 ACTGTAGTAGGTAGGACACTGT 57.346 45.455 0.00 0.00 0.00 3.55
2850 3759 6.432162 TGTTAACTGTAGTAGGTAGGACACTG 59.568 42.308 7.22 0.00 28.34 3.66
2851 3760 6.546484 TGTTAACTGTAGTAGGTAGGACACT 58.454 40.000 7.22 0.00 28.34 3.55
2852 3761 6.824305 TGTTAACTGTAGTAGGTAGGACAC 57.176 41.667 7.22 0.00 28.34 3.67
2853 3762 7.725397 TCTTTGTTAACTGTAGTAGGTAGGACA 59.275 37.037 7.22 0.00 28.34 4.02
2854 3763 8.115490 TCTTTGTTAACTGTAGTAGGTAGGAC 57.885 38.462 7.22 0.00 28.34 3.85
2855 3764 8.166061 TCTCTTTGTTAACTGTAGTAGGTAGGA 58.834 37.037 7.22 0.00 28.34 2.94
2856 3765 8.345724 TCTCTTTGTTAACTGTAGTAGGTAGG 57.654 38.462 7.22 0.00 28.34 3.18
2863 3772 9.000486 GCCTAAAATCTCTTTGTTAACTGTAGT 58.000 33.333 7.22 0.00 0.00 2.73
2864 3773 8.451748 GGCCTAAAATCTCTTTGTTAACTGTAG 58.548 37.037 7.22 1.93 0.00 2.74
2865 3774 7.940137 TGGCCTAAAATCTCTTTGTTAACTGTA 59.060 33.333 3.32 0.00 0.00 2.74
2866 3775 6.775629 TGGCCTAAAATCTCTTTGTTAACTGT 59.224 34.615 3.32 0.00 0.00 3.55
2867 3776 7.084486 GTGGCCTAAAATCTCTTTGTTAACTG 58.916 38.462 3.32 0.00 0.00 3.16
2868 3777 6.072673 CGTGGCCTAAAATCTCTTTGTTAACT 60.073 38.462 3.32 0.00 0.00 2.24
2869 3778 6.084277 CGTGGCCTAAAATCTCTTTGTTAAC 58.916 40.000 3.32 0.00 0.00 2.01
2870 3779 5.335348 GCGTGGCCTAAAATCTCTTTGTTAA 60.335 40.000 3.32 0.00 0.00 2.01
2871 3780 4.155280 GCGTGGCCTAAAATCTCTTTGTTA 59.845 41.667 3.32 0.00 0.00 2.41
2872 3781 3.057526 GCGTGGCCTAAAATCTCTTTGTT 60.058 43.478 3.32 0.00 0.00 2.83
2873 3782 2.488153 GCGTGGCCTAAAATCTCTTTGT 59.512 45.455 3.32 0.00 0.00 2.83
2874 3783 2.159379 GGCGTGGCCTAAAATCTCTTTG 60.159 50.000 3.32 0.00 46.69 2.77
2875 3784 2.092323 GGCGTGGCCTAAAATCTCTTT 58.908 47.619 3.32 0.00 46.69 2.52
2876 3785 1.751437 GGCGTGGCCTAAAATCTCTT 58.249 50.000 3.32 0.00 46.69 2.85
2877 3786 3.478540 GGCGTGGCCTAAAATCTCT 57.521 52.632 3.32 0.00 46.69 3.10
2903 3812 4.906792 CTAGGCAGGCCGAGCTGC 62.907 72.222 20.27 13.91 45.04 5.25
2904 3813 4.232878 CCTAGGCAGGCCGAGCTG 62.233 72.222 20.27 4.29 41.95 4.24
2916 3825 4.696479 ATCATTACACTCAAGCCCTAGG 57.304 45.455 0.06 0.06 0.00 3.02
2917 3826 6.014242 TCCATATCATTACACTCAAGCCCTAG 60.014 42.308 0.00 0.00 0.00 3.02
2918 3827 5.843969 TCCATATCATTACACTCAAGCCCTA 59.156 40.000 0.00 0.00 0.00 3.53
2919 3828 4.660303 TCCATATCATTACACTCAAGCCCT 59.340 41.667 0.00 0.00 0.00 5.19
2920 3829 4.973168 TCCATATCATTACACTCAAGCCC 58.027 43.478 0.00 0.00 0.00 5.19
2921 3830 7.161404 TGTATCCATATCATTACACTCAAGCC 58.839 38.462 0.00 0.00 0.00 4.35
2922 3831 8.607441 TTGTATCCATATCATTACACTCAAGC 57.393 34.615 0.00 0.00 0.00 4.01
3004 3913 7.496263 GGATTAATACCACAAAGAAGAGGTCTC 59.504 40.741 0.00 0.00 34.56 3.36
3009 3918 8.792830 TCAAGGATTAATACCACAAAGAAGAG 57.207 34.615 0.00 0.00 0.00 2.85
3039 3948 6.791775 GCTTTCGGAAACTTTTATTGCATTTG 59.208 34.615 0.00 0.00 0.00 2.32
3053 3962 2.556622 TGATTCAAGGGCTTTCGGAAAC 59.443 45.455 0.00 0.00 0.00 2.78
3078 3987 7.201679 CGCTTATGACTTTTCATCTCTTTGGAT 60.202 37.037 0.00 0.00 41.87 3.41
3080 3989 6.253746 CGCTTATGACTTTTCATCTCTTTGG 58.746 40.000 0.00 0.00 41.87 3.28
3085 3994 3.002759 GGCCGCTTATGACTTTTCATCTC 59.997 47.826 0.00 0.00 41.87 2.75
3088 3997 2.722094 TGGCCGCTTATGACTTTTCAT 58.278 42.857 0.00 0.00 45.04 2.57
3105 4014 1.135402 CCTCAAATACGTTGGCTTGGC 60.135 52.381 0.00 0.00 37.85 4.52
3107 4016 3.751175 TCTTCCTCAAATACGTTGGCTTG 59.249 43.478 0.00 0.00 37.85 4.01
3108 4017 4.015872 TCTTCCTCAAATACGTTGGCTT 57.984 40.909 0.00 0.00 37.85 4.35
3109 4018 3.695830 TCTTCCTCAAATACGTTGGCT 57.304 42.857 0.00 0.00 37.85 4.75
3110 4019 3.065371 CCATCTTCCTCAAATACGTTGGC 59.935 47.826 0.00 0.00 37.85 4.52
3111 4020 3.627577 CCCATCTTCCTCAAATACGTTGG 59.372 47.826 0.00 0.00 37.85 3.77
3112 4021 3.627577 CCCCATCTTCCTCAAATACGTTG 59.372 47.826 0.00 0.00 38.71 4.10
3134 4043 5.470098 TCTTGTGGTTTGACTATTTGCTCTC 59.530 40.000 0.00 0.00 0.00 3.20
3137 4046 6.006449 AGATCTTGTGGTTTGACTATTTGCT 58.994 36.000 0.00 0.00 0.00 3.91
3143 4052 3.994392 GCGAAGATCTTGTGGTTTGACTA 59.006 43.478 14.00 0.00 0.00 2.59
3147 4057 1.879380 TGGCGAAGATCTTGTGGTTTG 59.121 47.619 14.00 0.00 0.00 2.93
3148 4058 2.270352 TGGCGAAGATCTTGTGGTTT 57.730 45.000 14.00 0.00 0.00 3.27
3151 4061 2.868583 CACTATGGCGAAGATCTTGTGG 59.131 50.000 14.00 3.05 0.00 4.17
3161 4071 3.512329 TCTTACCTTGACACTATGGCGAA 59.488 43.478 0.00 0.00 0.00 4.70
3163 4073 3.520290 TCTTACCTTGACACTATGGCG 57.480 47.619 0.00 0.00 0.00 5.69


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

AutoCloner maintained by Alex Coulton.