Multiple sequence alignment - TraesCS6B01G025900

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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 TraesCS6B01G025900 chr6B 100.000 3155 0 0 1 3155 15752000 15748846 0.000000e+00 5827.0
1 TraesCS6B01G025900 chr6B 78.870 1221 236 22 953 2161 15234900 15233690 0.000000e+00 806.0
2 TraesCS6B01G025900 chr6B 78.925 1172 231 12 997 2157 15744079 15742913 0.000000e+00 782.0
3 TraesCS6B01G025900 chr6B 79.043 1150 223 12 1072 2211 14550131 14548990 0.000000e+00 773.0
4 TraesCS6B01G025900 chr6B 78.947 1178 208 28 997 2161 65175116 65173966 0.000000e+00 765.0
5 TraesCS6B01G025900 chr6B 79.091 1100 198 22 1069 2152 14333508 14334591 0.000000e+00 728.0
6 TraesCS6B01G025900 chr6B 85.298 687 54 23 1 665 716768485 716769146 0.000000e+00 665.0
7 TraesCS6B01G025900 chr6B 77.323 807 161 17 1412 2208 52573770 52572976 1.030000e-124 457.0
8 TraesCS6B01G025900 chr6B 79.905 423 81 4 1754 2174 15298768 15298348 1.100000e-79 307.0
9 TraesCS6B01G025900 chr6B 81.778 225 29 8 2933 3155 15114207 15113993 8.990000e-41 178.0
10 TraesCS6B01G025900 chr6B 87.324 71 4 2 2701 2766 52566470 52566400 3.370000e-10 76.8
11 TraesCS6B01G025900 chr6B 89.831 59 1 2 2701 2754 16430833 16430891 1.570000e-08 71.3
12 TraesCS6B01G025900 chr6B 89.796 49 3 2 627 675 525060527 525060573 9.450000e-06 62.1
13 TraesCS6B01G025900 chr6A 93.692 1617 69 6 812 2426 9335855 9337440 0.000000e+00 2390.0
14 TraesCS6B01G025900 chr6A 80.825 1163 202 18 1022 2174 9364627 9365778 0.000000e+00 893.0
15 TraesCS6B01G025900 chr6A 79.494 1107 199 21 1069 2161 7991367 7992459 0.000000e+00 761.0
16 TraesCS6B01G025900 chr6A 89.286 588 30 12 2498 3076 9337484 9338047 0.000000e+00 706.0
17 TraesCS6B01G025900 chr6D 93.638 1399 68 9 847 2239 8659965 8658582 0.000000e+00 2071.0
18 TraesCS6B01G025900 chr6D 84.226 691 81 14 1 668 346840094 346839409 0.000000e+00 647.0
19 TraesCS6B01G025900 chr6D 95.640 367 13 1 2792 3155 8658356 8657990 1.260000e-163 586.0
20 TraesCS6B01G025900 chr6D 75.210 1428 252 43 1412 2768 8802445 8803841 1.630000e-162 582.0
21 TraesCS6B01G025900 chr6D 88.095 168 20 0 2498 2665 8817121 8817288 1.920000e-47 200.0
22 TraesCS6B01G025900 chr6D 79.720 286 46 8 2875 3155 7680787 7681065 2.480000e-46 196.0
23 TraesCS6B01G025900 chr6D 83.173 208 28 6 2951 3155 8251335 8251538 1.930000e-42 183.0
24 TraesCS6B01G025900 chr6D 84.568 162 21 2 2797 2958 33898473 33898630 1.170000e-34 158.0
25 TraesCS6B01G025900 chr6D 87.500 72 4 2 2700 2766 8395331 8395260 9.380000e-11 78.7
26 TraesCS6B01G025900 chr6D 87.324 71 4 2 2701 2766 8901387 8901457 3.370000e-10 76.8
27 TraesCS6B01G025900 chr6D 94.872 39 2 0 2815 2853 8970890 8970928 9.450000e-06 62.1
28 TraesCS6B01G025900 chr6D 85.965 57 6 2 691 746 429354547 429354492 3.400000e-05 60.2
29 TraesCS6B01G025900 chr1B 87.805 697 58 7 1 672 362879035 362879729 0.000000e+00 791.0
30 TraesCS6B01G025900 chr1B 78.648 1213 230 22 968 2162 27678153 27676952 0.000000e+00 778.0
31 TraesCS6B01G025900 chr1B 80.000 100 10 5 689 780 512638896 512638993 7.300000e-07 65.8
32 TraesCS6B01G025900 chr5B 78.541 1179 234 17 994 2161 556628245 556627075 0.000000e+00 758.0
33 TraesCS6B01G025900 chr5D 85.694 692 74 11 1 671 520507206 520506519 0.000000e+00 706.0
34 TraesCS6B01G025900 chr5D 84.270 356 43 8 2804 3155 499860904 499860558 5.040000e-88 335.0
35 TraesCS6B01G025900 chr5D 93.333 45 3 0 702 746 205455862 205455906 2.030000e-07 67.6
36 TraesCS6B01G025900 chr3D 85.244 698 74 16 1 675 606140866 606140175 0.000000e+00 691.0
37 TraesCS6B01G025900 chr3D 93.053 475 26 3 204 671 596062213 596061739 0.000000e+00 688.0
38 TraesCS6B01G025900 chr3A 86.265 648 65 10 10 635 434121559 434120914 0.000000e+00 682.0
39 TraesCS6B01G025900 chr3A 89.474 57 5 1 691 746 393104223 393104279 1.570000e-08 71.3
40 TraesCS6B01G025900 chr2D 84.682 692 81 13 1 671 112310668 112309981 0.000000e+00 667.0
41 TraesCS6B01G025900 chr2D 87.931 58 6 1 690 746 560153886 560153943 2.030000e-07 67.6
42 TraesCS6B01G025900 chr4A 86.589 604 60 9 1 584 531304840 531304238 0.000000e+00 647.0
43 TraesCS6B01G025900 chr1A 84.077 672 80 14 1 650 405547108 405547774 9.610000e-175 623.0
44 TraesCS6B01G025900 chr1A 82.997 694 91 16 2 672 461258386 461257697 1.250000e-168 603.0
45 TraesCS6B01G025900 chr7D 84.281 598 70 11 1 577 605083600 605083006 2.120000e-156 562.0
46 TraesCS6B01G025900 chr5A 82.609 345 44 8 2819 3155 624201546 624201210 1.110000e-74 291.0
47 TraesCS6B01G025900 chr1D 81.761 159 21 4 3002 3155 416354446 416354291 3.300000e-25 126.0
48 TraesCS6B01G025900 chr3B 95.238 42 1 1 625 665 492103461 492103502 7.300000e-07 65.8
49 TraesCS6B01G025900 chr3B 92.500 40 2 1 627 665 662767780 662767819 4.400000e-04 56.5


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 TraesCS6B01G025900 chr6B 15748846 15752000 3154 True 5827.0 5827 100.000 1 3155 1 chr6B.!!$R6 3154
1 TraesCS6B01G025900 chr6B 15233690 15234900 1210 True 806.0 806 78.870 953 2161 1 chr6B.!!$R3 1208
2 TraesCS6B01G025900 chr6B 15742913 15744079 1166 True 782.0 782 78.925 997 2157 1 chr6B.!!$R5 1160
3 TraesCS6B01G025900 chr6B 14548990 14550131 1141 True 773.0 773 79.043 1072 2211 1 chr6B.!!$R1 1139
4 TraesCS6B01G025900 chr6B 65173966 65175116 1150 True 765.0 765 78.947 997 2161 1 chr6B.!!$R9 1164
5 TraesCS6B01G025900 chr6B 14333508 14334591 1083 False 728.0 728 79.091 1069 2152 1 chr6B.!!$F1 1083
6 TraesCS6B01G025900 chr6B 716768485 716769146 661 False 665.0 665 85.298 1 665 1 chr6B.!!$F4 664
7 TraesCS6B01G025900 chr6B 52572976 52573770 794 True 457.0 457 77.323 1412 2208 1 chr6B.!!$R8 796
8 TraesCS6B01G025900 chr6A 9335855 9338047 2192 False 1548.0 2390 91.489 812 3076 2 chr6A.!!$F3 2264
9 TraesCS6B01G025900 chr6A 9364627 9365778 1151 False 893.0 893 80.825 1022 2174 1 chr6A.!!$F2 1152
10 TraesCS6B01G025900 chr6A 7991367 7992459 1092 False 761.0 761 79.494 1069 2161 1 chr6A.!!$F1 1092
11 TraesCS6B01G025900 chr6D 8657990 8659965 1975 True 1328.5 2071 94.639 847 3155 2 chr6D.!!$R4 2308
12 TraesCS6B01G025900 chr6D 346839409 346840094 685 True 647.0 647 84.226 1 668 1 chr6D.!!$R2 667
13 TraesCS6B01G025900 chr6D 8802445 8803841 1396 False 582.0 582 75.210 1412 2768 1 chr6D.!!$F3 1356
14 TraesCS6B01G025900 chr1B 362879035 362879729 694 False 791.0 791 87.805 1 672 1 chr1B.!!$F1 671
15 TraesCS6B01G025900 chr1B 27676952 27678153 1201 True 778.0 778 78.648 968 2162 1 chr1B.!!$R1 1194
16 TraesCS6B01G025900 chr5B 556627075 556628245 1170 True 758.0 758 78.541 994 2161 1 chr5B.!!$R1 1167
17 TraesCS6B01G025900 chr5D 520506519 520507206 687 True 706.0 706 85.694 1 671 1 chr5D.!!$R2 670
18 TraesCS6B01G025900 chr3D 606140175 606140866 691 True 691.0 691 85.244 1 675 1 chr3D.!!$R2 674
19 TraesCS6B01G025900 chr3A 434120914 434121559 645 True 682.0 682 86.265 10 635 1 chr3A.!!$R1 625
20 TraesCS6B01G025900 chr2D 112309981 112310668 687 True 667.0 667 84.682 1 671 1 chr2D.!!$R1 670
21 TraesCS6B01G025900 chr4A 531304238 531304840 602 True 647.0 647 86.589 1 584 1 chr4A.!!$R1 583
22 TraesCS6B01G025900 chr1A 405547108 405547774 666 False 623.0 623 84.077 1 650 1 chr1A.!!$F1 649
23 TraesCS6B01G025900 chr1A 461257697 461258386 689 True 603.0 603 82.997 2 672 1 chr1A.!!$R1 670
24 TraesCS6B01G025900 chr7D 605083006 605083600 594 True 562.0 562 84.281 1 577 1 chr7D.!!$R1 576

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
448 483 0.585029 GCGCGCGAGAAAATCTTCTG 60.585 55.000 37.18 0.0 42.19 3.02 F
710 765 1.286248 ACTTCCCCGCTCCTAAATGT 58.714 50.000 0.00 0.0 0.00 2.71 F
1568 1665 1.374758 CGTTCCTGAGGGAGTGCAC 60.375 63.158 9.40 9.4 43.29 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1442 1536 0.753867 GAAGAGGGCCAGGTAGTAGC 59.246 60.000 6.18 0.0 0.00 3.58 R
2091 2188 1.207390 CTGCATAGTCTTCAGCGAGC 58.793 55.000 0.00 0.0 0.00 5.03 R
2688 2852 1.931841 CTGCATCCTCAACAGTGATCG 59.068 52.381 0.00 0.0 31.85 3.69 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
46 48 4.336433 CCTTCTTGTCTTTTCTGTGCAGAA 59.664 41.667 10.26 10.26 44.94 3.02
193 196 6.739112 AGTTCATAAAAAGAAACCTGTGCTC 58.261 36.000 0.00 0.00 0.00 4.26
202 205 2.949177 AACCTGTGCTCAACATGGTA 57.051 45.000 0.00 0.00 38.55 3.25
415 431 1.630369 CCTGGAAGTGAGATGTGGGAA 59.370 52.381 0.00 0.00 0.00 3.97
448 483 0.585029 GCGCGCGAGAAAATCTTCTG 60.585 55.000 37.18 0.00 42.19 3.02
510 555 4.154942 ACCTAGTTTCCGTTTCCTACTCA 58.845 43.478 0.00 0.00 0.00 3.41
539 585 3.184683 CTTCTGCTCTCGTGCGCC 61.185 66.667 4.18 0.00 35.36 6.53
578 627 6.014584 TCCTAGTGTGTTGCTTTATTCTCTGA 60.015 38.462 0.00 0.00 0.00 3.27
585 634 6.094048 GTGTTGCTTTATTCTCTGATTAGGCA 59.906 38.462 0.00 0.00 0.00 4.75
589 638 6.830324 TGCTTTATTCTCTGATTAGGCACATT 59.170 34.615 0.00 0.00 0.00 2.71
590 639 7.137426 GCTTTATTCTCTGATTAGGCACATTG 58.863 38.462 0.00 0.00 0.00 2.82
665 720 4.019792 GGCAACCCCTTTCATTCAAAAT 57.980 40.909 0.00 0.00 0.00 1.82
668 723 6.179756 GGCAACCCCTTTCATTCAAAATAAT 58.820 36.000 0.00 0.00 0.00 1.28
671 726 9.394767 GCAACCCCTTTCATTCAAAATAATAAT 57.605 29.630 0.00 0.00 0.00 1.28
701 756 8.661752 ATTTTACTATATACTACTTCCCCGCT 57.338 34.615 0.00 0.00 0.00 5.52
702 757 7.693969 TTTACTATATACTACTTCCCCGCTC 57.306 40.000 0.00 0.00 0.00 5.03
703 758 4.598022 ACTATATACTACTTCCCCGCTCC 58.402 47.826 0.00 0.00 0.00 4.70
704 759 3.829728 ATATACTACTTCCCCGCTCCT 57.170 47.619 0.00 0.00 0.00 3.69
705 760 4.942363 ATATACTACTTCCCCGCTCCTA 57.058 45.455 0.00 0.00 0.00 2.94
706 761 3.607490 ATACTACTTCCCCGCTCCTAA 57.393 47.619 0.00 0.00 0.00 2.69
707 762 2.242882 ACTACTTCCCCGCTCCTAAA 57.757 50.000 0.00 0.00 0.00 1.85
708 763 2.760581 ACTACTTCCCCGCTCCTAAAT 58.239 47.619 0.00 0.00 0.00 1.40
709 764 2.434702 ACTACTTCCCCGCTCCTAAATG 59.565 50.000 0.00 0.00 0.00 2.32
710 765 1.286248 ACTTCCCCGCTCCTAAATGT 58.714 50.000 0.00 0.00 0.00 2.71
711 766 2.474112 ACTTCCCCGCTCCTAAATGTA 58.526 47.619 0.00 0.00 0.00 2.29
712 767 2.841881 ACTTCCCCGCTCCTAAATGTAA 59.158 45.455 0.00 0.00 0.00 2.41
713 768 3.118371 ACTTCCCCGCTCCTAAATGTAAG 60.118 47.826 0.00 0.00 0.00 2.34
714 769 2.474112 TCCCCGCTCCTAAATGTAAGT 58.526 47.619 0.00 0.00 0.00 2.24
715 770 2.169769 TCCCCGCTCCTAAATGTAAGTG 59.830 50.000 0.00 0.00 0.00 3.16
716 771 2.093128 CCCCGCTCCTAAATGTAAGTGT 60.093 50.000 0.00 0.00 0.00 3.55
717 772 3.195661 CCCGCTCCTAAATGTAAGTGTC 58.804 50.000 0.00 0.00 0.00 3.67
718 773 3.118738 CCCGCTCCTAAATGTAAGTGTCT 60.119 47.826 0.00 0.00 0.00 3.41
719 774 4.504858 CCGCTCCTAAATGTAAGTGTCTT 58.495 43.478 0.00 0.00 0.00 3.01
720 775 4.935808 CCGCTCCTAAATGTAAGTGTCTTT 59.064 41.667 0.00 0.00 0.00 2.52
721 776 6.103997 CCGCTCCTAAATGTAAGTGTCTTTA 58.896 40.000 0.00 0.00 0.00 1.85
722 777 6.255887 CCGCTCCTAAATGTAAGTGTCTTTAG 59.744 42.308 0.00 0.00 33.16 1.85
723 778 7.033791 CGCTCCTAAATGTAAGTGTCTTTAGA 58.966 38.462 0.00 0.00 34.56 2.10
724 779 7.221067 CGCTCCTAAATGTAAGTGTCTTTAGAG 59.779 40.741 0.00 0.00 34.56 2.43
725 780 8.251721 GCTCCTAAATGTAAGTGTCTTTAGAGA 58.748 37.037 0.00 0.00 34.56 3.10
751 806 9.703892 ATTTCAATAGAGACTACATACATGAGC 57.296 33.333 0.00 0.00 0.00 4.26
752 807 6.903419 TCAATAGAGACTACATACATGAGCG 58.097 40.000 0.00 0.00 0.00 5.03
753 808 6.710744 TCAATAGAGACTACATACATGAGCGA 59.289 38.462 0.00 0.00 0.00 4.93
754 809 7.228706 TCAATAGAGACTACATACATGAGCGAA 59.771 37.037 0.00 0.00 0.00 4.70
755 810 7.695480 ATAGAGACTACATACATGAGCGAAT 57.305 36.000 0.00 0.00 0.00 3.34
756 811 6.007936 AGAGACTACATACATGAGCGAATC 57.992 41.667 0.00 0.00 0.00 2.52
757 812 5.767665 AGAGACTACATACATGAGCGAATCT 59.232 40.000 0.00 0.00 0.00 2.40
758 813 6.937465 AGAGACTACATACATGAGCGAATCTA 59.063 38.462 0.00 0.00 0.00 1.98
759 814 7.609918 AGAGACTACATACATGAGCGAATCTAT 59.390 37.037 0.00 0.00 0.00 1.98
760 815 8.794335 AGACTACATACATGAGCGAATCTATA 57.206 34.615 0.00 0.00 0.00 1.31
761 816 9.402320 AGACTACATACATGAGCGAATCTATAT 57.598 33.333 0.00 0.00 0.00 0.86
810 865 5.529581 AAACTTGTGTTTAGGAATGGTGG 57.470 39.130 0.00 0.00 43.76 4.61
913 970 1.807165 CACGCAGGTCATCTCCACG 60.807 63.158 0.00 0.00 36.10 4.94
916 977 1.520342 GCAGGTCATCTCCACGAGC 60.520 63.158 0.00 0.00 0.00 5.03
941 1002 4.681978 GCTCGCACCACCGTTCCT 62.682 66.667 0.00 0.00 0.00 3.36
1125 1219 3.864686 CCAAGCATCGGGTTCGCG 61.865 66.667 0.00 0.00 36.13 5.87
1442 1536 2.242572 CCATCATCGACAGGCTGCG 61.243 63.158 15.89 18.58 0.00 5.18
1568 1665 1.374758 CGTTCCTGAGGGAGTGCAC 60.375 63.158 9.40 9.40 43.29 4.57
2384 2510 5.423886 TGGTATGCTCGTTATGTCATTCAA 58.576 37.500 0.00 0.00 0.00 2.69
2428 2555 5.059833 GCTATTAACTTGTCCCTCCTCATG 58.940 45.833 0.00 0.00 0.00 3.07
2430 2557 4.993705 TTAACTTGTCCCTCCTCATGTT 57.006 40.909 0.00 0.00 36.45 2.71
2431 2558 3.884037 AACTTGTCCCTCCTCATGTTT 57.116 42.857 0.00 0.00 31.25 2.83
2522 2686 6.938030 TCTTTACGTTCTGAAATAACCATGGT 59.062 34.615 13.00 13.00 0.00 3.55
2529 2693 8.079809 CGTTCTGAAATAACCATGGTAGTTTTT 58.920 33.333 20.12 14.84 0.00 1.94
2557 2721 8.627208 TGCAATCCTTAATCTATCTTTCCATC 57.373 34.615 0.00 0.00 0.00 3.51
2629 2793 9.631257 ACTTTCCTTTGGATGAAAATTTTGAAT 57.369 25.926 8.47 1.75 30.65 2.57
2661 2825 4.036971 CCGCGGGAAACATTTATGGATTTA 59.963 41.667 20.10 0.00 0.00 1.40
2672 2836 7.899973 ACATTTATGGATTTATTGATGGCCTC 58.100 34.615 3.32 0.00 0.00 4.70
2677 2841 3.575687 GGATTTATTGATGGCCTCTTGGG 59.424 47.826 3.32 0.00 38.36 4.12
2927 3106 3.492313 GCTAGTGGCATTTTTCTTGACG 58.508 45.455 0.00 0.00 41.35 4.35
2928 3107 3.670627 GCTAGTGGCATTTTTCTTGACGG 60.671 47.826 0.00 0.00 41.35 4.79
2929 3108 2.306847 AGTGGCATTTTTCTTGACGGT 58.693 42.857 0.00 0.00 0.00 4.83
2930 3109 2.293399 AGTGGCATTTTTCTTGACGGTC 59.707 45.455 0.00 0.00 0.00 4.79
2931 3110 2.293399 GTGGCATTTTTCTTGACGGTCT 59.707 45.455 9.88 0.00 0.00 3.85
2932 3111 3.500680 GTGGCATTTTTCTTGACGGTCTA 59.499 43.478 9.88 0.43 0.00 2.59
2933 3112 3.500680 TGGCATTTTTCTTGACGGTCTAC 59.499 43.478 9.88 0.00 0.00 2.59
2934 3113 3.751698 GGCATTTTTCTTGACGGTCTACT 59.248 43.478 9.88 0.00 0.00 2.57
2935 3114 4.215613 GGCATTTTTCTTGACGGTCTACTT 59.784 41.667 9.88 0.00 0.00 2.24
2936 3115 5.147162 GCATTTTTCTTGACGGTCTACTTG 58.853 41.667 9.88 0.00 0.00 3.16
2937 3116 5.277828 GCATTTTTCTTGACGGTCTACTTGT 60.278 40.000 9.88 0.00 0.00 3.16
2938 3117 6.073440 GCATTTTTCTTGACGGTCTACTTGTA 60.073 38.462 9.88 0.00 0.00 2.41
2939 3118 7.360946 GCATTTTTCTTGACGGTCTACTTGTAT 60.361 37.037 9.88 0.00 0.00 2.29
2940 3119 9.146984 CATTTTTCTTGACGGTCTACTTGTATA 57.853 33.333 9.88 0.00 0.00 1.47
2941 3120 9.886132 ATTTTTCTTGACGGTCTACTTGTATAT 57.114 29.630 9.88 0.00 0.00 0.86
2942 3121 8.922058 TTTTCTTGACGGTCTACTTGTATATC 57.078 34.615 9.88 0.00 0.00 1.63
2943 3122 7.634671 TTCTTGACGGTCTACTTGTATATCA 57.365 36.000 9.88 0.00 0.00 2.15
2944 3123 7.024340 TCTTGACGGTCTACTTGTATATCAC 57.976 40.000 9.88 0.00 0.00 3.06
2945 3124 6.827251 TCTTGACGGTCTACTTGTATATCACT 59.173 38.462 9.88 0.00 0.00 3.41
2946 3125 7.989170 TCTTGACGGTCTACTTGTATATCACTA 59.011 37.037 9.88 0.00 0.00 2.74
2947 3126 8.687292 TTGACGGTCTACTTGTATATCACTAT 57.313 34.615 9.88 0.00 0.00 2.12
2948 3127 8.095937 TGACGGTCTACTTGTATATCACTATG 57.904 38.462 9.88 0.00 0.00 2.23
2949 3128 7.718314 TGACGGTCTACTTGTATATCACTATGT 59.282 37.037 9.88 0.00 0.00 2.29
3116 3321 8.310122 ACCATGTTAATTCAGCCATATCTTTT 57.690 30.769 0.00 0.00 0.00 2.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 48 7.474398 CATCAAATGATGTACAGATTCGAGT 57.526 36.000 13.95 0.00 45.10 4.18
193 196 4.276678 CCACAAGCTCCATATACCATGTTG 59.723 45.833 0.00 0.00 0.00 3.33
202 205 5.211973 TCTTAGTCTCCACAAGCTCCATAT 58.788 41.667 0.00 0.00 0.00 1.78
415 431 2.439156 GCGCCTTTCATGCTCCCT 60.439 61.111 0.00 0.00 0.00 4.20
448 483 3.103742 AGATCAGAAGGAGAGGGAACAC 58.896 50.000 0.00 0.00 0.00 3.32
510 555 3.238597 AGAGCAGAAGTTCTCTCCAACT 58.761 45.455 19.93 6.70 38.30 3.16
534 579 0.611062 AGACTACACTACCTGGCGCA 60.611 55.000 10.83 0.00 0.00 6.09
539 585 4.636648 CACACTAGGAGACTACACTACCTG 59.363 50.000 0.00 0.00 43.67 4.00
578 627 3.053395 ACCAGATCCACAATGTGCCTAAT 60.053 43.478 8.05 0.00 31.34 1.73
585 634 3.149196 GTCACAACCAGATCCACAATGT 58.851 45.455 0.00 0.00 0.00 2.71
589 638 1.543208 GCAGTCACAACCAGATCCACA 60.543 52.381 0.00 0.00 0.00 4.17
590 639 1.160137 GCAGTCACAACCAGATCCAC 58.840 55.000 0.00 0.00 0.00 4.02
675 730 9.759473 AGCGGGGAAGTAGTATATAGTAAAATA 57.241 33.333 0.00 0.00 0.00 1.40
676 731 8.661752 AGCGGGGAAGTAGTATATAGTAAAAT 57.338 34.615 0.00 0.00 0.00 1.82
677 732 7.177392 GGAGCGGGGAAGTAGTATATAGTAAAA 59.823 40.741 0.00 0.00 0.00 1.52
678 733 6.660949 GGAGCGGGGAAGTAGTATATAGTAAA 59.339 42.308 0.00 0.00 0.00 2.01
679 734 6.012157 AGGAGCGGGGAAGTAGTATATAGTAA 60.012 42.308 0.00 0.00 0.00 2.24
680 735 5.490357 AGGAGCGGGGAAGTAGTATATAGTA 59.510 44.000 0.00 0.00 0.00 1.82
681 736 4.291777 AGGAGCGGGGAAGTAGTATATAGT 59.708 45.833 0.00 0.00 0.00 2.12
682 737 4.857679 AGGAGCGGGGAAGTAGTATATAG 58.142 47.826 0.00 0.00 0.00 1.31
683 738 4.942363 AGGAGCGGGGAAGTAGTATATA 57.058 45.455 0.00 0.00 0.00 0.86
684 739 3.829728 AGGAGCGGGGAAGTAGTATAT 57.170 47.619 0.00 0.00 0.00 0.86
685 740 4.729552 TTAGGAGCGGGGAAGTAGTATA 57.270 45.455 0.00 0.00 0.00 1.47
686 741 3.607490 TTAGGAGCGGGGAAGTAGTAT 57.393 47.619 0.00 0.00 0.00 2.12
687 742 3.386932 TTTAGGAGCGGGGAAGTAGTA 57.613 47.619 0.00 0.00 0.00 1.82
688 743 2.242882 TTTAGGAGCGGGGAAGTAGT 57.757 50.000 0.00 0.00 0.00 2.73
689 744 2.434702 ACATTTAGGAGCGGGGAAGTAG 59.565 50.000 0.00 0.00 0.00 2.57
690 745 2.474112 ACATTTAGGAGCGGGGAAGTA 58.526 47.619 0.00 0.00 0.00 2.24
691 746 1.286248 ACATTTAGGAGCGGGGAAGT 58.714 50.000 0.00 0.00 0.00 3.01
692 747 3.118371 ACTTACATTTAGGAGCGGGGAAG 60.118 47.826 0.00 0.00 0.00 3.46
693 748 2.841881 ACTTACATTTAGGAGCGGGGAA 59.158 45.455 0.00 0.00 0.00 3.97
694 749 2.169769 CACTTACATTTAGGAGCGGGGA 59.830 50.000 0.00 0.00 0.00 4.81
695 750 2.093128 ACACTTACATTTAGGAGCGGGG 60.093 50.000 0.00 0.00 0.00 5.73
696 751 3.118738 AGACACTTACATTTAGGAGCGGG 60.119 47.826 0.00 0.00 0.00 6.13
697 752 4.124851 AGACACTTACATTTAGGAGCGG 57.875 45.455 0.00 0.00 0.00 5.52
698 753 7.033791 TCTAAAGACACTTACATTTAGGAGCG 58.966 38.462 0.00 0.00 36.39 5.03
699 754 8.251721 TCTCTAAAGACACTTACATTTAGGAGC 58.748 37.037 0.00 0.00 36.39 4.70
725 780 9.703892 GCTCATGTATGTAGTCTCTATTGAAAT 57.296 33.333 0.00 0.00 0.00 2.17
726 781 7.862873 CGCTCATGTATGTAGTCTCTATTGAAA 59.137 37.037 0.00 0.00 0.00 2.69
727 782 7.228706 TCGCTCATGTATGTAGTCTCTATTGAA 59.771 37.037 0.00 0.00 0.00 2.69
728 783 6.710744 TCGCTCATGTATGTAGTCTCTATTGA 59.289 38.462 0.00 0.00 0.00 2.57
729 784 6.903419 TCGCTCATGTATGTAGTCTCTATTG 58.097 40.000 0.00 0.00 0.00 1.90
730 785 7.511959 TTCGCTCATGTATGTAGTCTCTATT 57.488 36.000 0.00 0.00 0.00 1.73
731 786 7.609918 AGATTCGCTCATGTATGTAGTCTCTAT 59.390 37.037 0.00 0.00 0.00 1.98
732 787 6.937465 AGATTCGCTCATGTATGTAGTCTCTA 59.063 38.462 0.00 0.00 0.00 2.43
733 788 5.767665 AGATTCGCTCATGTATGTAGTCTCT 59.232 40.000 0.00 0.00 0.00 3.10
734 789 6.007936 AGATTCGCTCATGTATGTAGTCTC 57.992 41.667 0.00 0.00 0.00 3.36
735 790 7.695480 ATAGATTCGCTCATGTATGTAGTCT 57.305 36.000 0.00 0.00 0.00 3.24
786 841 6.070481 ACCACCATTCCTAAACACAAGTTTTT 60.070 34.615 0.00 0.00 45.32 1.94
787 842 5.423931 ACCACCATTCCTAAACACAAGTTTT 59.576 36.000 0.00 0.00 45.32 2.43
789 844 4.542697 ACCACCATTCCTAAACACAAGTT 58.457 39.130 0.00 0.00 40.40 2.66
790 845 4.178956 ACCACCATTCCTAAACACAAGT 57.821 40.909 0.00 0.00 0.00 3.16
791 846 8.519799 AATATACCACCATTCCTAAACACAAG 57.480 34.615 0.00 0.00 0.00 3.16
792 847 8.887264 AAATATACCACCATTCCTAAACACAA 57.113 30.769 0.00 0.00 0.00 3.33
793 848 8.887264 AAAATATACCACCATTCCTAAACACA 57.113 30.769 0.00 0.00 0.00 3.72
794 849 9.797556 GAAAAATATACCACCATTCCTAAACAC 57.202 33.333 0.00 0.00 0.00 3.32
795 850 9.762381 AGAAAAATATACCACCATTCCTAAACA 57.238 29.630 0.00 0.00 0.00 2.83
841 896 6.283694 TCAATCTCATGTTGACTGCCTATAC 58.716 40.000 0.00 0.00 31.07 1.47
916 977 2.125552 TGGTGCGAGCGAGAATGG 60.126 61.111 0.00 0.00 0.00 3.16
941 1002 3.311110 GGCGGCGAGGGGATATGA 61.311 66.667 12.98 0.00 0.00 2.15
1442 1536 0.753867 GAAGAGGGCCAGGTAGTAGC 59.246 60.000 6.18 0.00 0.00 3.58
1568 1665 3.187227 GGCAATATCACAAGCACCTATCG 59.813 47.826 0.00 0.00 0.00 2.92
1683 1780 4.528674 CAGAACATCCTGGAGCCG 57.471 61.111 1.52 0.00 0.00 5.52
1834 1931 2.360852 CAGCAGGCCCTTGGACAG 60.361 66.667 0.00 0.00 29.21 3.51
1844 1941 1.744741 GACTTCCTCTGCAGCAGGC 60.745 63.158 22.62 9.07 45.13 4.85
2091 2188 1.207390 CTGCATAGTCTTCAGCGAGC 58.793 55.000 0.00 0.00 0.00 5.03
2301 2400 2.159627 GCACCACCAAATGAGAACGTAG 59.840 50.000 0.00 0.00 0.00 3.51
2384 2510 3.129988 GCAGTGCAATGCTTTCTTCCTAT 59.870 43.478 30.37 0.00 43.07 2.57
2451 2587 3.649502 TGTAGGATGCCATGATCTCACAT 59.350 43.478 0.00 0.00 0.00 3.21
2515 2679 6.440328 AGGATTGCATTAAAAACTACCATGGT 59.560 34.615 23.55 23.55 0.00 3.55
2653 2817 4.836736 CCAAGAGGCCATCAATAAATCCAT 59.163 41.667 5.01 0.00 0.00 3.41
2677 2841 3.479370 GTGATCGGCACACTCTGC 58.521 61.111 4.75 0.00 46.91 4.26
2688 2852 1.931841 CTGCATCCTCAACAGTGATCG 59.068 52.381 0.00 0.00 31.85 3.69
2942 3121 9.669353 GGCATTTGAAATATCTGTTACATAGTG 57.331 33.333 0.00 0.00 0.00 2.74
2943 3122 8.850156 GGGCATTTGAAATATCTGTTACATAGT 58.150 33.333 0.00 0.00 0.00 2.12
2944 3123 9.071276 AGGGCATTTGAAATATCTGTTACATAG 57.929 33.333 0.00 0.00 0.00 2.23
2945 3124 8.849168 CAGGGCATTTGAAATATCTGTTACATA 58.151 33.333 0.00 0.00 0.00 2.29
2946 3125 7.201938 CCAGGGCATTTGAAATATCTGTTACAT 60.202 37.037 10.90 0.00 0.00 2.29
2947 3126 6.096705 CCAGGGCATTTGAAATATCTGTTACA 59.903 38.462 10.90 0.00 0.00 2.41
2948 3127 6.096846 ACCAGGGCATTTGAAATATCTGTTAC 59.903 38.462 10.90 0.00 0.00 2.50
2949 3128 6.194235 ACCAGGGCATTTGAAATATCTGTTA 58.806 36.000 10.90 0.00 0.00 2.41
3084 3289 8.938801 ATGGCTGAATTAACATGGTAATGATA 57.061 30.769 16.65 5.74 37.24 2.15
3093 3298 9.403110 GCTAAAAGATATGGCTGAATTAACATG 57.597 33.333 0.00 0.00 0.00 3.21


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

AutoCloner maintained by Alex Coulton.