Multiple sequence alignment - TraesCS6A01G412400

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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 TraesCS6A01G412400 chr6A 100.000 3183 0 0 1 3183 614099510 614096328 0.000000e+00 5879.0
1 TraesCS6A01G412400 chr6A 82.445 769 121 10 1119 1876 614131129 614130364 0.000000e+00 660.0
2 TraesCS6A01G412400 chr6A 74.688 561 112 24 27 568 614128203 614127654 4.130000e-54 222.0
3 TraesCS6A01G412400 chr6D 97.738 1459 23 7 942 2390 468017216 468015758 0.000000e+00 2503.0
4 TraesCS6A01G412400 chr6D 79.152 849 119 26 2384 3182 262293772 262292932 4.670000e-148 534.0
5 TraesCS6A01G412400 chrUn 88.807 1349 119 19 1054 2390 79652538 79651210 0.000000e+00 1626.0
6 TraesCS6A01G412400 chrUn 85.570 1483 166 29 934 2390 79583413 79584873 0.000000e+00 1509.0
7 TraesCS6A01G412400 chrUn 85.570 1483 166 29 934 2390 268073346 268074806 0.000000e+00 1509.0
8 TraesCS6A01G412400 chrUn 90.665 782 60 8 4 778 79491903 79491128 0.000000e+00 1027.0
9 TraesCS6A01G412400 chrUn 96.520 546 19 0 1 546 79683989 79684534 0.000000e+00 904.0
10 TraesCS6A01G412400 chrUn 100.000 415 0 0 1305 1719 477256423 477256009 0.000000e+00 767.0
11 TraesCS6A01G412400 chrUn 81.953 809 122 18 1107 1895 79497383 79496579 0.000000e+00 664.0
12 TraesCS6A01G412400 chrUn 96.070 229 7 2 553 780 79686200 79686427 3.880000e-99 372.0
13 TraesCS6A01G412400 chrUn 80.134 448 71 8 4 448 79649957 79649525 5.120000e-83 318.0
14 TraesCS6A01G412400 chrUn 90.196 51 5 0 29 79 79694266 79694316 2.050000e-07 67.6
15 TraesCS6A01G412400 chrUn 90.196 51 5 0 29 79 79771157 79771207 2.050000e-07 67.6
16 TraesCS6A01G412400 chrUn 90.196 51 5 0 29 79 299936905 299936955 2.050000e-07 67.6
17 TraesCS6A01G412400 chrUn 90.196 51 5 0 29 79 324932288 324932238 2.050000e-07 67.6
18 TraesCS6A01G412400 chrUn 90.196 51 5 0 29 79 354795750 354795700 2.050000e-07 67.6
19 TraesCS6A01G412400 chr7A 94.378 747 33 3 2384 3122 538763185 538762440 0.000000e+00 1138.0
20 TraesCS6A01G412400 chr7A 93.850 748 37 3 2384 3123 721944440 721943694 0.000000e+00 1118.0
21 TraesCS6A01G412400 chr7A 94.262 732 35 1 2391 3115 24539727 24540458 0.000000e+00 1112.0
22 TraesCS6A01G412400 chr7A 93.236 754 41 5 2384 3128 236439364 236440116 0.000000e+00 1101.0
23 TraesCS6A01G412400 chr7A 93.449 748 40 3 2384 3123 672285549 672286295 0.000000e+00 1101.0
24 TraesCS6A01G412400 chr7A 84.777 762 86 13 2388 3123 46954108 46954865 0.000000e+00 737.0
25 TraesCS6A01G412400 chr7A 82.827 757 97 16 2390 3128 687896469 687895728 0.000000e+00 647.0
26 TraesCS6A01G412400 chr5A 94.459 740 33 2 2391 3123 658548947 658549685 0.000000e+00 1133.0
27 TraesCS6A01G412400 chr5A 93.717 748 37 4 2384 3123 563069237 563069982 0.000000e+00 1112.0
28 TraesCS6A01G412400 chr5A 93.449 748 40 3 2384 3123 446418258 446417512 0.000000e+00 1101.0
29 TraesCS6A01G412400 chr5A 92.598 743 43 7 2390 3123 524932092 524931353 0.000000e+00 1057.0
30 TraesCS6A01G412400 chr5A 92.027 740 52 1 2391 3123 661674719 661675458 0.000000e+00 1033.0
31 TraesCS6A01G412400 chr5A 90.968 775 35 9 2382 3122 563063599 563064372 0.000000e+00 1011.0
32 TraesCS6A01G412400 chr5A 84.543 744 93 7 2391 3123 439537085 439537817 0.000000e+00 717.0
33 TraesCS6A01G412400 chr3A 93.717 748 38 3 2384 3123 63054391 63053645 0.000000e+00 1112.0
34 TraesCS6A01G412400 chr2A 93.458 749 36 5 2384 3123 705844999 705845743 0.000000e+00 1099.0
35 TraesCS6A01G412400 chr2A 90.731 766 44 12 2384 3123 5133041 5132277 0.000000e+00 996.0
36 TraesCS6A01G412400 chr2A 78.598 271 39 11 2865 3121 716185237 716184972 9.140000e-36 161.0
37 TraesCS6A01G412400 chr6B 84.068 885 121 14 983 1855 714197787 714196911 0.000000e+00 835.0
38 TraesCS6A01G412400 chr6B 86.181 673 87 2 1165 1831 714195943 714195271 0.000000e+00 723.0
39 TraesCS6A01G412400 chr6B 75.676 518 91 23 1339 1831 714049024 714049531 3.190000e-55 226.0
40 TraesCS6A01G412400 chr6B 91.489 47 3 1 1942 1987 378287098 378287144 2.650000e-06 63.9
41 TraesCS6A01G412400 chr6B 82.667 75 8 4 1914 1986 70745724 70745795 9.530000e-06 62.1
42 TraesCS6A01G412400 chr1D 85.390 794 94 5 2391 3163 63916609 63915817 0.000000e+00 804.0
43 TraesCS6A01G412400 chr1D 92.053 151 8 1 781 931 468553385 468553531 3.220000e-50 209.0
44 TraesCS6A01G412400 chr1D 96.364 55 2 0 3128 3182 448435289 448435235 1.220000e-14 91.6
45 TraesCS6A01G412400 chr1D 94.545 55 3 0 3128 3182 50951478 50951424 5.660000e-13 86.1
46 TraesCS6A01G412400 chr4A 85.847 756 75 19 2384 3123 6440917 6440178 0.000000e+00 774.0
47 TraesCS6A01G412400 chr7B 93.373 166 7 1 778 943 745290899 745291060 3.170000e-60 243.0
48 TraesCS6A01G412400 chr7B 94.545 55 3 0 3128 3182 31806755 31806701 5.660000e-13 86.1
49 TraesCS6A01G412400 chr7D 92.899 169 6 3 777 945 30773232 30773394 1.140000e-59 241.0
50 TraesCS6A01G412400 chr7D 91.667 168 14 0 778 945 30811932 30812099 1.910000e-57 233.0
51 TraesCS6A01G412400 chr7D 91.250 80 3 1 866 945 30810582 30810657 4.340000e-19 106.0
52 TraesCS6A01G412400 chr3B 92.857 168 8 1 781 948 800173667 800173504 1.140000e-59 241.0
53 TraesCS6A01G412400 chr4D 92.353 170 8 2 780 949 506630841 506630677 1.480000e-58 237.0
54 TraesCS6A01G412400 chr4D 90.533 169 10 3 781 949 506623143 506622981 5.350000e-53 219.0
55 TraesCS6A01G412400 chr2B 73.668 319 68 13 48 354 46831560 46831246 3.360000e-20 110.0
56 TraesCS6A01G412400 chr5B 96.364 55 2 0 3128 3182 531615548 531615494 1.220000e-14 91.6
57 TraesCS6A01G412400 chr1B 94.545 55 3 0 3128 3182 394199130 394199184 5.660000e-13 86.1
58 TraesCS6A01G412400 chr1B 94.545 55 3 0 3128 3182 394283806 394283860 5.660000e-13 86.1
59 TraesCS6A01G412400 chr3D 89.394 66 6 1 3118 3182 475137412 475137477 7.320000e-12 82.4
60 TraesCS6A01G412400 chr3D 85.075 67 10 0 1915 1981 254362307 254362241 5.700000e-08 69.4
61 TraesCS6A01G412400 chr3D 82.432 74 9 3 1916 1986 172897164 172897236 9.530000e-06 62.1
62 TraesCS6A01G412400 chr5D 88.060 67 5 2 1915 1981 443922965 443923028 3.400000e-10 76.8


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 TraesCS6A01G412400 chr6A 614096328 614099510 3182 True 5879 5879 100.0000 1 3183 1 chr6A.!!$R1 3182
1 TraesCS6A01G412400 chr6A 614127654 614131129 3475 True 441 660 78.5665 27 1876 2 chr6A.!!$R2 1849
2 TraesCS6A01G412400 chr6D 468015758 468017216 1458 True 2503 2503 97.7380 942 2390 1 chr6D.!!$R2 1448
3 TraesCS6A01G412400 chr6D 262292932 262293772 840 True 534 534 79.1520 2384 3182 1 chr6D.!!$R1 798
4 TraesCS6A01G412400 chrUn 79583413 79584873 1460 False 1509 1509 85.5700 934 2390 1 chrUn.!!$F1 1456
5 TraesCS6A01G412400 chrUn 268073346 268074806 1460 False 1509 1509 85.5700 934 2390 1 chrUn.!!$F4 1456
6 TraesCS6A01G412400 chrUn 79491128 79491903 775 True 1027 1027 90.6650 4 778 1 chrUn.!!$R1 774
7 TraesCS6A01G412400 chrUn 79649525 79652538 3013 True 972 1626 84.4705 4 2390 2 chrUn.!!$R6 2386
8 TraesCS6A01G412400 chrUn 79496579 79497383 804 True 664 664 81.9530 1107 1895 1 chrUn.!!$R2 788
9 TraesCS6A01G412400 chrUn 79683989 79686427 2438 False 638 904 96.2950 1 780 2 chrUn.!!$F6 779
10 TraesCS6A01G412400 chr7A 538762440 538763185 745 True 1138 1138 94.3780 2384 3122 1 chr7A.!!$R1 738
11 TraesCS6A01G412400 chr7A 721943694 721944440 746 True 1118 1118 93.8500 2384 3123 1 chr7A.!!$R3 739
12 TraesCS6A01G412400 chr7A 24539727 24540458 731 False 1112 1112 94.2620 2391 3115 1 chr7A.!!$F1 724
13 TraesCS6A01G412400 chr7A 236439364 236440116 752 False 1101 1101 93.2360 2384 3128 1 chr7A.!!$F3 744
14 TraesCS6A01G412400 chr7A 672285549 672286295 746 False 1101 1101 93.4490 2384 3123 1 chr7A.!!$F4 739
15 TraesCS6A01G412400 chr7A 46954108 46954865 757 False 737 737 84.7770 2388 3123 1 chr7A.!!$F2 735
16 TraesCS6A01G412400 chr7A 687895728 687896469 741 True 647 647 82.8270 2390 3128 1 chr7A.!!$R2 738
17 TraesCS6A01G412400 chr5A 658548947 658549685 738 False 1133 1133 94.4590 2391 3123 1 chr5A.!!$F4 732
18 TraesCS6A01G412400 chr5A 563069237 563069982 745 False 1112 1112 93.7170 2384 3123 1 chr5A.!!$F3 739
19 TraesCS6A01G412400 chr5A 446417512 446418258 746 True 1101 1101 93.4490 2384 3123 1 chr5A.!!$R1 739
20 TraesCS6A01G412400 chr5A 524931353 524932092 739 True 1057 1057 92.5980 2390 3123 1 chr5A.!!$R2 733
21 TraesCS6A01G412400 chr5A 661674719 661675458 739 False 1033 1033 92.0270 2391 3123 1 chr5A.!!$F5 732
22 TraesCS6A01G412400 chr5A 563063599 563064372 773 False 1011 1011 90.9680 2382 3122 1 chr5A.!!$F2 740
23 TraesCS6A01G412400 chr5A 439537085 439537817 732 False 717 717 84.5430 2391 3123 1 chr5A.!!$F1 732
24 TraesCS6A01G412400 chr3A 63053645 63054391 746 True 1112 1112 93.7170 2384 3123 1 chr3A.!!$R1 739
25 TraesCS6A01G412400 chr2A 705844999 705845743 744 False 1099 1099 93.4580 2384 3123 1 chr2A.!!$F1 739
26 TraesCS6A01G412400 chr2A 5132277 5133041 764 True 996 996 90.7310 2384 3123 1 chr2A.!!$R1 739
27 TraesCS6A01G412400 chr6B 714195271 714197787 2516 True 779 835 85.1245 983 1855 2 chr6B.!!$R1 872
28 TraesCS6A01G412400 chr6B 714049024 714049531 507 False 226 226 75.6760 1339 1831 1 chr6B.!!$F3 492
29 TraesCS6A01G412400 chr1D 63915817 63916609 792 True 804 804 85.3900 2391 3163 1 chr1D.!!$R2 772
30 TraesCS6A01G412400 chr4A 6440178 6440917 739 True 774 774 85.8470 2384 3123 1 chr4A.!!$R1 739

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
882 2549 0.107263 TGCATGTATGTGTGGCCGAT 60.107 50.0 0.0 0.0 0.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2798 6244 0.111639 AAGGTTTTTGGGGAGCGCTA 59.888 50.0 11.5 0.0 0.0 4.26 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
66 67 3.819245 TGCCTTTGCACTTGGTACT 57.181 47.368 0.00 0.00 44.23 2.73
152 153 6.837312 TCATATTGGTGTATTACTCTTGGGG 58.163 40.000 0.00 0.00 0.00 4.96
166 167 1.753073 CTTGGGGAATGACAATCAGCC 59.247 52.381 0.00 0.00 0.00 4.85
274 275 6.575267 GTGGTCCTTATCCTTTCTTCTCTAC 58.425 44.000 0.00 0.00 0.00 2.59
460 467 3.300388 TGGAGACTTCGGATCTGCTATT 58.700 45.455 0.00 0.00 35.68 1.73
467 474 7.767261 AGACTTCGGATCTGCTATTATCATAC 58.233 38.462 0.00 0.00 0.00 2.39
547 554 7.040478 CCTTTCATTGTCCAAGAGTTAATGTGA 60.040 37.037 0.00 0.00 32.22 3.58
550 557 8.408043 TCATTGTCCAAGAGTTAATGTGATTT 57.592 30.769 0.00 0.00 32.22 2.17
596 2263 8.637986 TGAAGTATTTTCCTGCAACTACATTTT 58.362 29.630 0.00 0.00 0.00 1.82
720 2387 2.024080 TCTTCCTTTGGGCTGGCATATT 60.024 45.455 2.88 0.00 0.00 1.28
754 2421 3.058016 CCGTCAATCACATTCAGCAGTTT 60.058 43.478 0.00 0.00 0.00 2.66
765 2432 6.017605 CACATTCAGCAGTTTTACACTCTCTT 60.018 38.462 0.00 0.00 30.92 2.85
780 2447 1.552337 TCTCTTGAGCGCTTCTGGATT 59.448 47.619 13.26 0.00 0.00 3.01
781 2448 1.664659 CTCTTGAGCGCTTCTGGATTG 59.335 52.381 13.26 0.00 0.00 2.67
782 2449 1.002430 TCTTGAGCGCTTCTGGATTGT 59.998 47.619 13.26 0.00 0.00 2.71
783 2450 1.808945 CTTGAGCGCTTCTGGATTGTT 59.191 47.619 13.26 0.00 0.00 2.83
784 2451 2.760634 TGAGCGCTTCTGGATTGTTA 57.239 45.000 13.26 0.00 0.00 2.41
785 2452 2.621338 TGAGCGCTTCTGGATTGTTAG 58.379 47.619 13.26 0.00 0.00 2.34
786 2453 1.936547 GAGCGCTTCTGGATTGTTAGG 59.063 52.381 13.26 0.00 0.00 2.69
787 2454 1.555075 AGCGCTTCTGGATTGTTAGGA 59.445 47.619 2.64 0.00 0.00 2.94
788 2455 2.027192 AGCGCTTCTGGATTGTTAGGAA 60.027 45.455 2.64 0.00 0.00 3.36
789 2456 2.945668 GCGCTTCTGGATTGTTAGGAAT 59.054 45.455 0.00 0.00 0.00 3.01
790 2457 4.127171 GCGCTTCTGGATTGTTAGGAATA 58.873 43.478 0.00 0.00 0.00 1.75
791 2458 4.574828 GCGCTTCTGGATTGTTAGGAATAA 59.425 41.667 0.00 0.00 0.00 1.40
792 2459 5.277538 GCGCTTCTGGATTGTTAGGAATAAG 60.278 44.000 0.00 0.00 0.00 1.73
793 2460 5.277538 CGCTTCTGGATTGTTAGGAATAAGC 60.278 44.000 0.00 0.00 33.92 3.09
794 2461 5.009110 GCTTCTGGATTGTTAGGAATAAGCC 59.991 44.000 0.00 0.00 38.38 4.35
795 2462 4.703897 TCTGGATTGTTAGGAATAAGCCG 58.296 43.478 0.00 0.00 40.44 5.52
796 2463 4.163458 TCTGGATTGTTAGGAATAAGCCGT 59.837 41.667 0.00 0.00 40.44 5.68
797 2464 4.196193 TGGATTGTTAGGAATAAGCCGTG 58.804 43.478 0.00 0.00 40.44 4.94
798 2465 3.564225 GGATTGTTAGGAATAAGCCGTGG 59.436 47.826 0.00 0.00 28.54 4.94
799 2466 2.032680 TGTTAGGAATAAGCCGTGGC 57.967 50.000 1.67 1.67 42.33 5.01
845 2512 4.873129 CGGACGCATCGGGACCAG 62.873 72.222 0.00 0.00 0.00 4.00
870 2537 2.584064 CAGGCTCGGGTGCATGTA 59.416 61.111 0.00 0.00 39.52 2.29
871 2538 1.146930 CAGGCTCGGGTGCATGTAT 59.853 57.895 0.00 0.00 39.52 2.29
872 2539 1.146930 AGGCTCGGGTGCATGTATG 59.853 57.895 0.00 0.00 34.04 2.39
873 2540 1.153168 GGCTCGGGTGCATGTATGT 60.153 57.895 0.00 0.00 34.04 2.29
874 2541 1.439353 GGCTCGGGTGCATGTATGTG 61.439 60.000 0.00 0.00 34.04 3.21
875 2542 0.744414 GCTCGGGTGCATGTATGTGT 60.744 55.000 0.00 0.00 0.00 3.72
876 2543 1.009078 CTCGGGTGCATGTATGTGTG 58.991 55.000 0.00 0.00 0.00 3.82
877 2544 0.392327 TCGGGTGCATGTATGTGTGG 60.392 55.000 0.00 0.00 0.00 4.17
878 2545 1.809207 GGGTGCATGTATGTGTGGC 59.191 57.895 0.00 0.00 0.00 5.01
879 2546 1.666209 GGGTGCATGTATGTGTGGCC 61.666 60.000 0.00 0.00 0.00 5.36
880 2547 1.429021 GTGCATGTATGTGTGGCCG 59.571 57.895 0.00 0.00 0.00 6.13
881 2548 1.024046 GTGCATGTATGTGTGGCCGA 61.024 55.000 0.00 0.00 0.00 5.54
882 2549 0.107263 TGCATGTATGTGTGGCCGAT 60.107 50.000 0.00 0.00 0.00 4.18
883 2550 0.588252 GCATGTATGTGTGGCCGATC 59.412 55.000 0.00 0.00 0.00 3.69
884 2551 1.952193 CATGTATGTGTGGCCGATCA 58.048 50.000 0.00 0.00 0.00 2.92
885 2552 2.287769 CATGTATGTGTGGCCGATCAA 58.712 47.619 0.00 0.00 0.00 2.57
886 2553 2.022764 TGTATGTGTGGCCGATCAAG 57.977 50.000 0.00 0.00 0.00 3.02
887 2554 1.299541 GTATGTGTGGCCGATCAAGG 58.700 55.000 0.00 0.00 0.00 3.61
888 2555 0.180171 TATGTGTGGCCGATCAAGGG 59.820 55.000 0.00 0.00 0.00 3.95
889 2556 1.561769 ATGTGTGGCCGATCAAGGGA 61.562 55.000 0.00 0.00 0.00 4.20
890 2557 1.450312 GTGTGGCCGATCAAGGGAG 60.450 63.158 0.00 0.00 0.00 4.30
891 2558 1.918293 TGTGGCCGATCAAGGGAGT 60.918 57.895 0.00 0.00 0.00 3.85
892 2559 1.450312 GTGGCCGATCAAGGGAGTG 60.450 63.158 0.00 0.00 0.00 3.51
893 2560 1.918293 TGGCCGATCAAGGGAGTGT 60.918 57.895 0.00 0.00 0.00 3.55
894 2561 1.450312 GGCCGATCAAGGGAGTGTG 60.450 63.158 0.00 0.00 0.00 3.82
895 2562 2.109126 GCCGATCAAGGGAGTGTGC 61.109 63.158 0.00 0.00 0.00 4.57
896 2563 1.811266 CCGATCAAGGGAGTGTGCG 60.811 63.158 0.00 0.00 0.00 5.34
897 2564 1.079819 CGATCAAGGGAGTGTGCGT 60.080 57.895 0.00 0.00 0.00 5.24
898 2565 1.354337 CGATCAAGGGAGTGTGCGTG 61.354 60.000 0.00 0.00 0.00 5.34
899 2566 1.639298 GATCAAGGGAGTGTGCGTGC 61.639 60.000 0.00 0.00 0.00 5.34
900 2567 3.716006 CAAGGGAGTGTGCGTGCG 61.716 66.667 0.00 0.00 0.00 5.34
901 2568 4.235762 AAGGGAGTGTGCGTGCGT 62.236 61.111 0.00 0.00 0.00 5.24
902 2569 4.969196 AGGGAGTGTGCGTGCGTG 62.969 66.667 0.00 0.00 0.00 5.34
906 2573 4.934942 AGTGTGCGTGCGTGCGTA 62.935 61.111 3.11 0.00 37.81 4.42
907 2574 4.409588 GTGTGCGTGCGTGCGTAG 62.410 66.667 3.11 0.00 37.81 3.51
910 2577 4.953868 TGCGTGCGTGCGTAGGTT 62.954 61.111 4.59 0.00 37.81 3.50
911 2578 3.708734 GCGTGCGTGCGTAGGTTT 61.709 61.111 4.59 0.00 0.00 3.27
912 2579 2.170036 CGTGCGTGCGTAGGTTTG 59.830 61.111 0.00 0.00 0.00 2.93
913 2580 2.127383 GTGCGTGCGTAGGTTTGC 60.127 61.111 0.00 0.00 0.00 3.68
914 2581 2.280524 TGCGTGCGTAGGTTTGCT 60.281 55.556 0.00 0.00 0.00 3.91
915 2582 2.173382 GCGTGCGTAGGTTTGCTG 59.827 61.111 0.00 0.00 0.00 4.41
916 2583 2.860293 CGTGCGTAGGTTTGCTGG 59.140 61.111 0.00 0.00 0.00 4.85
917 2584 2.561373 GTGCGTAGGTTTGCTGGC 59.439 61.111 0.00 0.00 0.00 4.85
918 2585 3.047280 TGCGTAGGTTTGCTGGCG 61.047 61.111 0.00 0.00 0.00 5.69
919 2586 2.740826 GCGTAGGTTTGCTGGCGA 60.741 61.111 0.00 0.00 0.00 5.54
920 2587 2.106683 GCGTAGGTTTGCTGGCGAT 61.107 57.895 0.00 0.00 0.00 4.58
921 2588 1.715585 CGTAGGTTTGCTGGCGATG 59.284 57.895 0.00 0.00 0.00 3.84
922 2589 1.705337 CGTAGGTTTGCTGGCGATGG 61.705 60.000 0.00 0.00 0.00 3.51
923 2590 0.392461 GTAGGTTTGCTGGCGATGGA 60.392 55.000 0.00 0.00 0.00 3.41
924 2591 0.107703 TAGGTTTGCTGGCGATGGAG 60.108 55.000 0.00 0.00 0.00 3.86
925 2592 2.486966 GTTTGCTGGCGATGGAGC 59.513 61.111 0.00 0.00 35.65 4.70
933 2600 4.292178 GCGATGGAGCCGGAGAGG 62.292 72.222 5.05 0.00 44.97 3.69
934 2601 2.835431 CGATGGAGCCGGAGAGGT 60.835 66.667 5.05 0.00 43.70 3.85
935 2602 2.818132 GATGGAGCCGGAGAGGTG 59.182 66.667 5.05 0.00 43.70 4.00
936 2603 1.758514 GATGGAGCCGGAGAGGTGA 60.759 63.158 5.05 0.00 43.70 4.02
937 2604 2.022240 GATGGAGCCGGAGAGGTGAC 62.022 65.000 5.05 0.00 43.70 3.67
938 2605 3.462678 GGAGCCGGAGAGGTGACC 61.463 72.222 5.05 0.00 43.70 4.02
943 2610 4.477975 CGGAGAGGTGACCGCGTC 62.478 72.222 4.92 3.35 42.55 5.19
944 2611 4.477975 GGAGAGGTGACCGCGTCG 62.478 72.222 4.92 0.00 34.95 5.12
945 2612 3.735029 GAGAGGTGACCGCGTCGT 61.735 66.667 4.92 0.00 34.95 4.34
955 2622 4.498520 CGCGTCGTCCCTGCTCAT 62.499 66.667 0.00 0.00 0.00 2.90
981 2648 2.693864 CCCACCCCTCTGCATCCT 60.694 66.667 0.00 0.00 0.00 3.24
1015 2688 6.005583 TCGTCGTTCTACATATACCCATTC 57.994 41.667 0.00 0.00 0.00 2.67
1028 2701 0.896940 CCCATTCACAGGCACAGCTT 60.897 55.000 0.00 0.00 0.00 3.74
1031 2704 0.111061 ATTCACAGGCACAGCTTGGA 59.889 50.000 6.09 0.00 40.00 3.53
1033 2723 1.526686 CACAGGCACAGCTTGGACA 60.527 57.895 6.09 0.00 40.00 4.02
1052 2742 2.628657 ACACACACTCCTCTACTTCACC 59.371 50.000 0.00 0.00 0.00 4.02
2313 4561 4.395959 TCACCCATACTGAATCGGTTAC 57.604 45.455 0.00 0.00 24.13 2.50
2396 4644 1.734465 GCGACTCTTTGATCTGTTGGG 59.266 52.381 0.00 0.00 0.00 4.12
2481 4839 1.665679 CCGCGATAAAGCAAGTCATGT 59.334 47.619 8.23 0.00 36.85 3.21
2501 4866 5.728351 TGTAACTTGACGGAGAAAAAGTG 57.272 39.130 0.00 0.00 33.30 3.16
2798 6244 1.519455 GAAGCCAGTAGTCGCGCAT 60.519 57.895 8.75 0.00 0.00 4.73
2940 6795 1.759445 CTCAGAGATGGAACCGATGGT 59.241 52.381 0.00 0.00 37.65 3.55
2951 6808 0.326618 ACCGATGGTGAGGGAAGGAT 60.327 55.000 0.00 0.00 32.98 3.24
2960 6817 3.536570 GTGAGGGAAGGATTAGTTCTGC 58.463 50.000 0.00 0.00 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
66 67 7.391554 GGAGCAATTGGAGCTAACATCATATAA 59.608 37.037 7.72 0.00 43.58 0.98
152 153 4.882671 ACAATACGGCTGATTGTCATTC 57.117 40.909 14.05 0.00 42.51 2.67
166 167 3.990469 AGTGCAGTGAAGAGAACAATACG 59.010 43.478 0.00 0.00 0.00 3.06
274 275 3.429410 GCCAACTTAAAGGCCAGCAATAG 60.429 47.826 5.01 0.00 45.18 1.73
467 474 8.818141 TCACTACAGTTCTCAAGAAACATAAG 57.182 34.615 0.00 0.00 35.58 1.73
489 496 5.779806 AGAAATACACGCACACTATTCAC 57.220 39.130 0.00 0.00 0.00 3.18
550 557 8.445275 ACTTCAATCATTGTGTACACTGTTAA 57.555 30.769 25.60 12.66 0.00 2.01
561 2227 7.092079 TGCAGGAAAATACTTCAATCATTGTG 58.908 34.615 0.00 0.00 0.00 3.33
596 2263 9.935682 GAGTCATAAATATCATCTTCGCAAAAA 57.064 29.630 0.00 0.00 0.00 1.94
765 2432 2.621338 CTAACAATCCAGAAGCGCTCA 58.379 47.619 12.06 0.00 0.00 4.26
780 2447 1.741055 CGCCACGGCTTATTCCTAACA 60.741 52.381 6.48 0.00 39.32 2.41
781 2448 0.935196 CGCCACGGCTTATTCCTAAC 59.065 55.000 6.48 0.00 39.32 2.34
782 2449 0.179067 CCGCCACGGCTTATTCCTAA 60.179 55.000 6.48 0.00 41.17 2.69
783 2450 1.444250 CCGCCACGGCTTATTCCTA 59.556 57.895 6.48 0.00 41.17 2.94
784 2451 2.189521 CCGCCACGGCTTATTCCT 59.810 61.111 6.48 0.00 41.17 3.36
785 2452 2.900337 CCCGCCACGGCTTATTCC 60.900 66.667 6.48 0.00 46.86 3.01
786 2453 3.583086 GCCCGCCACGGCTTATTC 61.583 66.667 6.48 0.00 46.86 1.75
828 2495 4.873129 CTGGTCCCGATGCGTCCG 62.873 72.222 0.00 0.00 0.00 4.79
852 2519 2.947938 ATACATGCACCCGAGCCTGC 62.948 60.000 0.00 0.00 34.08 4.85
853 2520 1.146930 ATACATGCACCCGAGCCTG 59.853 57.895 0.00 0.00 36.40 4.85
854 2521 1.146930 CATACATGCACCCGAGCCT 59.853 57.895 0.00 0.00 0.00 4.58
855 2522 1.153168 ACATACATGCACCCGAGCC 60.153 57.895 0.00 0.00 0.00 4.70
856 2523 0.744414 ACACATACATGCACCCGAGC 60.744 55.000 0.00 0.00 0.00 5.03
857 2524 1.009078 CACACATACATGCACCCGAG 58.991 55.000 0.00 0.00 0.00 4.63
858 2525 0.392327 CCACACATACATGCACCCGA 60.392 55.000 0.00 0.00 0.00 5.14
859 2526 1.992233 GCCACACATACATGCACCCG 61.992 60.000 0.00 0.00 0.00 5.28
860 2527 1.666209 GGCCACACATACATGCACCC 61.666 60.000 0.00 0.00 0.00 4.61
861 2528 1.809207 GGCCACACATACATGCACC 59.191 57.895 0.00 0.00 0.00 5.01
862 2529 1.024046 TCGGCCACACATACATGCAC 61.024 55.000 2.24 0.00 0.00 4.57
863 2530 0.107263 ATCGGCCACACATACATGCA 60.107 50.000 2.24 0.00 0.00 3.96
864 2531 0.588252 GATCGGCCACACATACATGC 59.412 55.000 2.24 0.00 0.00 4.06
865 2532 1.952193 TGATCGGCCACACATACATG 58.048 50.000 2.24 0.00 0.00 3.21
866 2533 2.564771 CTTGATCGGCCACACATACAT 58.435 47.619 2.24 0.00 0.00 2.29
867 2534 1.406751 CCTTGATCGGCCACACATACA 60.407 52.381 2.24 0.00 0.00 2.29
868 2535 1.299541 CCTTGATCGGCCACACATAC 58.700 55.000 2.24 0.00 0.00 2.39
869 2536 0.180171 CCCTTGATCGGCCACACATA 59.820 55.000 2.24 0.00 0.00 2.29
870 2537 1.077501 CCCTTGATCGGCCACACAT 60.078 57.895 2.24 0.00 0.00 3.21
871 2538 2.184020 CTCCCTTGATCGGCCACACA 62.184 60.000 2.24 0.00 0.00 3.72
872 2539 1.450312 CTCCCTTGATCGGCCACAC 60.450 63.158 2.24 0.00 0.00 3.82
873 2540 1.918293 ACTCCCTTGATCGGCCACA 60.918 57.895 2.24 0.00 0.00 4.17
874 2541 1.450312 CACTCCCTTGATCGGCCAC 60.450 63.158 2.24 0.00 0.00 5.01
875 2542 1.918293 ACACTCCCTTGATCGGCCA 60.918 57.895 2.24 0.00 0.00 5.36
876 2543 1.450312 CACACTCCCTTGATCGGCC 60.450 63.158 0.00 0.00 0.00 6.13
877 2544 2.109126 GCACACTCCCTTGATCGGC 61.109 63.158 0.00 0.00 0.00 5.54
878 2545 1.811266 CGCACACTCCCTTGATCGG 60.811 63.158 0.00 0.00 0.00 4.18
879 2546 1.079819 ACGCACACTCCCTTGATCG 60.080 57.895 0.00 0.00 0.00 3.69
880 2547 1.639298 GCACGCACACTCCCTTGATC 61.639 60.000 0.00 0.00 0.00 2.92
881 2548 1.672356 GCACGCACACTCCCTTGAT 60.672 57.895 0.00 0.00 0.00 2.57
882 2549 2.280797 GCACGCACACTCCCTTGA 60.281 61.111 0.00 0.00 0.00 3.02
883 2550 3.716006 CGCACGCACACTCCCTTG 61.716 66.667 0.00 0.00 0.00 3.61
884 2551 4.235762 ACGCACGCACACTCCCTT 62.236 61.111 0.00 0.00 0.00 3.95
885 2552 4.969196 CACGCACGCACACTCCCT 62.969 66.667 0.00 0.00 0.00 4.20
889 2556 4.934942 TACGCACGCACGCACACT 62.935 61.111 0.00 0.00 36.19 3.55
890 2557 4.409588 CTACGCACGCACGCACAC 62.410 66.667 0.00 0.00 36.19 3.82
893 2560 4.953868 AACCTACGCACGCACGCA 62.954 61.111 0.00 0.00 36.19 5.24
894 2561 3.708734 AAACCTACGCACGCACGC 61.709 61.111 0.00 0.00 36.19 5.34
895 2562 2.170036 CAAACCTACGCACGCACG 59.830 61.111 0.00 0.00 39.50 5.34
896 2563 2.127383 GCAAACCTACGCACGCAC 60.127 61.111 0.00 0.00 0.00 5.34
897 2564 2.280524 AGCAAACCTACGCACGCA 60.281 55.556 0.00 0.00 0.00 5.24
898 2565 2.173382 CAGCAAACCTACGCACGC 59.827 61.111 0.00 0.00 0.00 5.34
899 2566 2.860293 CCAGCAAACCTACGCACG 59.140 61.111 0.00 0.00 0.00 5.34
900 2567 2.561373 GCCAGCAAACCTACGCAC 59.439 61.111 0.00 0.00 0.00 5.34
901 2568 2.796483 ATCGCCAGCAAACCTACGCA 62.796 55.000 0.00 0.00 0.00 5.24
902 2569 2.106683 ATCGCCAGCAAACCTACGC 61.107 57.895 0.00 0.00 0.00 4.42
903 2570 1.705337 CCATCGCCAGCAAACCTACG 61.705 60.000 0.00 0.00 0.00 3.51
904 2571 0.392461 TCCATCGCCAGCAAACCTAC 60.392 55.000 0.00 0.00 0.00 3.18
905 2572 0.107703 CTCCATCGCCAGCAAACCTA 60.108 55.000 0.00 0.00 0.00 3.08
906 2573 1.377725 CTCCATCGCCAGCAAACCT 60.378 57.895 0.00 0.00 0.00 3.50
907 2574 3.056313 GCTCCATCGCCAGCAAACC 62.056 63.158 0.00 0.00 35.56 3.27
908 2575 2.486966 GCTCCATCGCCAGCAAAC 59.513 61.111 0.00 0.00 35.56 2.93
915 2582 4.292178 CTCTCCGGCTCCATCGCC 62.292 72.222 0.00 0.00 46.68 5.54
916 2583 4.292178 CCTCTCCGGCTCCATCGC 62.292 72.222 0.00 0.00 0.00 4.58
917 2584 2.835431 ACCTCTCCGGCTCCATCG 60.835 66.667 0.00 0.00 35.61 3.84
918 2585 1.758514 TCACCTCTCCGGCTCCATC 60.759 63.158 0.00 0.00 35.61 3.51
919 2586 2.060980 GTCACCTCTCCGGCTCCAT 61.061 63.158 0.00 0.00 35.61 3.41
920 2587 2.680352 GTCACCTCTCCGGCTCCA 60.680 66.667 0.00 0.00 35.61 3.86
921 2588 3.462678 GGTCACCTCTCCGGCTCC 61.463 72.222 0.00 0.00 35.61 4.70
922 2589 3.827898 CGGTCACCTCTCCGGCTC 61.828 72.222 0.00 0.00 42.61 4.70
927 2594 4.477975 CGACGCGGTCACCTCTCC 62.478 72.222 12.47 0.00 32.09 3.71
928 2595 3.664223 GACGACGCGGTCACCTCTC 62.664 68.421 12.47 0.00 36.91 3.20
929 2596 3.735029 GACGACGCGGTCACCTCT 61.735 66.667 12.47 0.00 36.91 3.69
930 2597 4.773117 GGACGACGCGGTCACCTC 62.773 72.222 12.47 0.00 38.70 3.85
938 2605 4.498520 ATGAGCAGGGACGACGCG 62.499 66.667 3.53 3.53 0.00 6.01
939 2606 2.583593 GATGAGCAGGGACGACGC 60.584 66.667 0.00 0.00 0.00 5.19
940 2607 1.064946 GAGATGAGCAGGGACGACG 59.935 63.158 0.00 0.00 0.00 5.12
941 2608 0.179124 GTGAGATGAGCAGGGACGAC 60.179 60.000 0.00 0.00 0.00 4.34
942 2609 1.323271 GGTGAGATGAGCAGGGACGA 61.323 60.000 0.00 0.00 0.00 4.20
943 2610 1.142748 GGTGAGATGAGCAGGGACG 59.857 63.158 0.00 0.00 0.00 4.79
944 2611 1.267574 TGGGTGAGATGAGCAGGGAC 61.268 60.000 0.00 0.00 0.00 4.46
945 2612 1.080907 TGGGTGAGATGAGCAGGGA 59.919 57.895 0.00 0.00 0.00 4.20
955 2622 3.864983 GAGGGGTGGGTGGGTGAGA 62.865 68.421 0.00 0.00 0.00 3.27
981 2648 0.859232 GAACGACGAGAGCAAGCAAA 59.141 50.000 0.00 0.00 0.00 3.68
1015 2688 1.526686 TGTCCAAGCTGTGCCTGTG 60.527 57.895 0.00 0.00 0.00 3.66
1028 2701 2.677542 AGTAGAGGAGTGTGTGTCCA 57.322 50.000 0.00 0.00 36.43 4.02
1031 2704 2.628657 GGTGAAGTAGAGGAGTGTGTGT 59.371 50.000 0.00 0.00 0.00 3.72
1033 2723 2.628657 GTGGTGAAGTAGAGGAGTGTGT 59.371 50.000 0.00 0.00 0.00 3.72
1052 2742 3.695556 TGGACTGCAAATGTATGGATGTG 59.304 43.478 0.00 0.00 0.00 3.21
1719 3447 3.885297 CCATTTTCCAGTAAGATGGCGAT 59.115 43.478 0.00 0.00 41.49 4.58
2113 3907 3.143728 GTTACGTCCCCACAAAAGATGT 58.856 45.455 0.00 0.00 45.34 3.06
2313 4561 6.370442 TGTTCTCCAAGTTTTGTATGGTATCG 59.630 38.462 0.00 0.00 35.66 2.92
2481 4839 7.095355 GCTATTCACTTTTTCTCCGTCAAGTTA 60.095 37.037 0.00 0.00 0.00 2.24
2501 4866 9.159364 TCAAGTTCATATATGCAGATGCTATTC 57.841 33.333 7.92 0.00 42.66 1.75
2571 5195 4.081420 CCTGCATGTGTTAGGTTCTACTCT 60.081 45.833 0.00 0.00 0.00 3.24
2798 6244 0.111639 AAGGTTTTTGGGGAGCGCTA 59.888 50.000 11.50 0.00 0.00 4.26
2940 6795 3.198635 CAGCAGAACTAATCCTTCCCTCA 59.801 47.826 0.00 0.00 0.00 3.86
2951 6808 2.095008 CAGAGAGACGCAGCAGAACTAA 60.095 50.000 0.00 0.00 0.00 2.24
2960 6817 1.379176 TCCTCCCAGAGAGACGCAG 60.379 63.158 0.00 0.00 46.50 5.18
3018 6919 0.754472 TCTTCGTTTCACCTCCCGTT 59.246 50.000 0.00 0.00 0.00 4.44
3066 7014 3.056328 GAACGGTGCAGCCCTTCC 61.056 66.667 10.90 0.00 0.00 3.46


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

AutoCloner maintained by Alex Coulton.