Multiple sequence alignment - TraesCS7A01G211500

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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 TraesCS7A01G211500 chr7A 100.000 2122 0 0 1 2122 174275246 174273125 0.000000e+00 3919.0
1 TraesCS7A01G211500 chr7A 100.000 292 0 0 2508 2799 174272739 174272448 8.820000e-150 540.0
2 TraesCS7A01G211500 chr7D 94.531 1536 59 14 592 2121 171373198 171371682 0.000000e+00 2348.0
3 TraesCS7A01G211500 chr7D 92.479 585 13 10 1 575 171373744 171373181 0.000000e+00 808.0
4 TraesCS7A01G211500 chr7D 88.166 169 17 3 2634 2799 164485023 164484855 6.120000e-47 198.0
5 TraesCS7A01G211500 chr7D 91.304 69 6 0 2532 2600 171371303 171371235 8.250000e-16 95.3
6 TraesCS7A01G211500 chr7B 91.827 1248 62 15 592 1826 137881184 137879964 0.000000e+00 1703.0
7 TraesCS7A01G211500 chr7B 93.276 580 16 4 1 575 137881728 137881167 0.000000e+00 833.0
8 TraesCS7A01G211500 chr7B 91.065 291 19 5 1832 2121 137879786 137879502 1.220000e-103 387.0
9 TraesCS7A01G211500 chr4D 88.953 172 15 3 2630 2799 123953057 123952888 2.830000e-50 209.0
10 TraesCS7A01G211500 chr6D 89.697 165 14 3 2636 2799 58220194 58220032 1.020000e-49 207.0
11 TraesCS7A01G211500 chr3D 88.953 172 14 5 2629 2799 21372672 21372839 1.020000e-49 207.0
12 TraesCS7A01G211500 chr2D 88.889 171 15 4 2631 2799 38262272 38262104 1.020000e-49 207.0
13 TraesCS7A01G211500 chr2D 89.697 165 14 3 2637 2799 90367880 90368043 1.020000e-49 207.0
14 TraesCS7A01G211500 chr5D 88.166 169 18 2 2633 2799 463084576 463084744 1.700000e-47 200.0
15 TraesCS7A01G211500 chr3A 88.166 169 17 3 2633 2799 57366833 57366666 6.120000e-47 198.0
16 TraesCS7A01G211500 chr1B 87.861 173 15 6 2631 2799 442065102 442065272 6.120000e-47 198.0


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 TraesCS7A01G211500 chr7A 174272448 174275246 2798 True 2229.500000 3919 100.000000 1 2799 2 chr7A.!!$R1 2798
1 TraesCS7A01G211500 chr7D 171371235 171373744 2509 True 1083.766667 2348 92.771333 1 2600 3 chr7D.!!$R2 2599
2 TraesCS7A01G211500 chr7B 137879502 137881728 2226 True 974.333333 1703 92.056000 1 2121 3 chr7B.!!$R1 2120


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
190 191 0.251354 ATCTCTGCTTGCACGGATGT 59.749 50.0 0.0 0.0 0.0 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1885 2105 1.183549 GAACTCGCAACCTCTCCCTA 58.816 55.0 0.0 0.0 0.0 3.53 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
29 30 0.389948 GTGACCCTAGTGGCAACTCG 60.390 60.000 0.00 0.00 37.88 4.18
98 99 7.976135 AACAGATATGAAAGGAGCATATGAC 57.024 36.000 6.97 0.00 38.64 3.06
147 148 6.560003 TTATCTCCTCACAGCTATTTGGAA 57.440 37.500 0.00 0.00 0.00 3.53
186 187 2.789917 GCATCTCTGCTTGCACGG 59.210 61.111 0.00 0.00 45.32 4.94
187 188 1.742880 GCATCTCTGCTTGCACGGA 60.743 57.895 0.00 0.00 45.32 4.69
188 189 1.094073 GCATCTCTGCTTGCACGGAT 61.094 55.000 0.00 0.00 45.32 4.18
189 190 0.656259 CATCTCTGCTTGCACGGATG 59.344 55.000 14.05 14.05 0.00 3.51
190 191 0.251354 ATCTCTGCTTGCACGGATGT 59.749 50.000 0.00 0.00 0.00 3.06
191 192 0.894835 TCTCTGCTTGCACGGATGTA 59.105 50.000 0.00 0.00 0.00 2.29
275 276 0.843984 AACCACCAACTACAGTGCCT 59.156 50.000 0.00 0.00 32.48 4.75
276 277 0.396811 ACCACCAACTACAGTGCCTC 59.603 55.000 0.00 0.00 32.48 4.70
277 278 0.321653 CCACCAACTACAGTGCCTCC 60.322 60.000 0.00 0.00 32.48 4.30
278 279 0.687354 CACCAACTACAGTGCCTCCT 59.313 55.000 0.00 0.00 0.00 3.69
420 435 1.077265 ACCTCCCCACAATGCCAAG 59.923 57.895 0.00 0.00 0.00 3.61
430 445 1.337074 ACAATGCCAAGTTGCCAATCG 60.337 47.619 0.00 0.00 0.00 3.34
459 474 1.271934 CACCCCATCATGAAACGCAAA 59.728 47.619 0.00 0.00 0.00 3.68
460 475 1.545582 ACCCCATCATGAAACGCAAAG 59.454 47.619 0.00 0.00 0.00 2.77
464 479 3.119388 CCCATCATGAAACGCAAAGACAT 60.119 43.478 0.00 0.00 0.00 3.06
487 502 6.947644 TGAAGGACATGTAAATGGATGATG 57.052 37.500 0.00 0.00 0.00 3.07
488 503 5.829391 TGAAGGACATGTAAATGGATGATGG 59.171 40.000 0.00 0.00 0.00 3.51
489 504 5.651612 AGGACATGTAAATGGATGATGGA 57.348 39.130 0.00 0.00 0.00 3.41
490 505 6.210172 AGGACATGTAAATGGATGATGGAT 57.790 37.500 0.00 0.00 0.00 3.41
491 506 6.243900 AGGACATGTAAATGGATGATGGATC 58.756 40.000 0.00 0.00 0.00 3.36
492 507 5.122869 GGACATGTAAATGGATGATGGATCG 59.877 44.000 0.00 0.00 30.87 3.69
493 508 4.456911 ACATGTAAATGGATGATGGATCGC 59.543 41.667 0.00 0.00 30.87 4.58
494 509 4.356405 TGTAAATGGATGATGGATCGCT 57.644 40.909 0.00 0.00 30.87 4.93
495 510 4.717877 TGTAAATGGATGATGGATCGCTT 58.282 39.130 0.00 0.00 30.87 4.68
496 511 4.756642 TGTAAATGGATGATGGATCGCTTC 59.243 41.667 0.00 0.00 30.87 3.86
497 512 3.497103 AATGGATGATGGATCGCTTCA 57.503 42.857 3.42 3.42 30.87 3.02
498 513 2.538512 TGGATGATGGATCGCTTCAG 57.461 50.000 6.15 0.00 30.87 3.02
499 514 1.155042 GGATGATGGATCGCTTCAGC 58.845 55.000 6.73 6.73 37.78 4.26
566 596 0.962356 CGCTGGCTGGAAATGGTTCT 60.962 55.000 0.00 0.00 33.92 3.01
575 605 4.202151 GCTGGAAATGGTTCTTCACTGTTT 60.202 41.667 0.00 0.00 33.92 2.83
576 606 5.682212 GCTGGAAATGGTTCTTCACTGTTTT 60.682 40.000 0.00 0.00 33.92 2.43
577 607 6.293004 TGGAAATGGTTCTTCACTGTTTTT 57.707 33.333 0.00 0.00 33.92 1.94
601 631 3.712091 TTTGCGGGTTAAATTGTTCGT 57.288 38.095 0.00 0.00 0.00 3.85
602 632 2.973419 TGCGGGTTAAATTGTTCGTC 57.027 45.000 0.00 0.00 0.00 4.20
603 633 2.219458 TGCGGGTTAAATTGTTCGTCA 58.781 42.857 0.00 0.00 0.00 4.35
604 634 2.031857 TGCGGGTTAAATTGTTCGTCAC 60.032 45.455 0.00 0.00 0.00 3.67
605 635 2.224784 GCGGGTTAAATTGTTCGTCACT 59.775 45.455 0.00 0.00 0.00 3.41
606 636 3.805823 CGGGTTAAATTGTTCGTCACTG 58.194 45.455 0.00 0.00 0.00 3.66
607 637 3.249080 CGGGTTAAATTGTTCGTCACTGT 59.751 43.478 0.00 0.00 0.00 3.55
608 638 4.260866 CGGGTTAAATTGTTCGTCACTGTT 60.261 41.667 0.00 0.00 0.00 3.16
609 639 5.584442 GGGTTAAATTGTTCGTCACTGTTT 58.416 37.500 0.00 0.00 0.00 2.83
655 692 4.767255 CAGTCGCCCACCTCTGCC 62.767 72.222 0.00 0.00 0.00 4.85
1075 1118 9.619316 CTATACTCCATTATTTCTCTGTTCTCG 57.381 37.037 0.00 0.00 0.00 4.04
1077 1120 4.442706 TCCATTATTTCTCTGTTCTCGCC 58.557 43.478 0.00 0.00 0.00 5.54
1193 1236 1.298264 TGCAAACGCAGCGTCTTTG 60.298 52.632 23.22 22.84 39.99 2.77
1248 1291 1.351076 TCATCTCCTGTTCCAGTGCA 58.649 50.000 0.00 0.00 0.00 4.57
1251 1294 1.071987 CTCCTGTTCCAGTGCAGCA 59.928 57.895 0.00 0.00 0.00 4.41
1253 1296 1.228063 CCTGTTCCAGTGCAGCAGT 60.228 57.895 0.00 0.00 0.00 4.40
1582 1625 4.593864 GATGAGGGACGAGCGGGC 62.594 72.222 0.00 0.00 0.00 6.13
1764 1809 2.488153 GCAAATGGCTTCCTTCGTAGTT 59.512 45.455 0.00 0.00 40.25 2.24
1767 1813 5.528870 CAAATGGCTTCCTTCGTAGTTTTT 58.471 37.500 0.00 0.00 0.00 1.94
1809 1856 2.163818 TCTGTTCGCCGAATCTTTGT 57.836 45.000 1.55 0.00 0.00 2.83
1822 1869 4.201685 CGAATCTTTGTTCCATGTACCGAC 60.202 45.833 0.00 0.00 0.00 4.79
1826 1873 6.045072 TCTTTGTTCCATGTACCGACTAAT 57.955 37.500 0.00 0.00 0.00 1.73
1827 1874 7.172868 TCTTTGTTCCATGTACCGACTAATA 57.827 36.000 0.00 0.00 0.00 0.98
1830 2049 8.795842 TTTGTTCCATGTACCGACTAATATTT 57.204 30.769 0.00 0.00 0.00 1.40
1899 2119 3.081804 ACAAAAATAGGGAGAGGTTGCG 58.918 45.455 0.00 0.00 0.00 4.85
1929 2149 6.311723 CGACCACCACATATTTCAAACTAAC 58.688 40.000 0.00 0.00 0.00 2.34
1930 2150 6.072948 CGACCACCACATATTTCAAACTAACA 60.073 38.462 0.00 0.00 0.00 2.41
1931 2151 7.361713 CGACCACCACATATTTCAAACTAACAT 60.362 37.037 0.00 0.00 0.00 2.71
1932 2152 7.601856 ACCACCACATATTTCAAACTAACATG 58.398 34.615 0.00 0.00 0.00 3.21
1935 2155 9.554724 CACCACATATTTCAAACTAACATGTAC 57.445 33.333 0.00 0.00 0.00 2.90
1948 2168 6.040878 ACTAACATGTACGTAGGAGCATTTC 58.959 40.000 0.00 0.00 0.00 2.17
1990 2210 7.275560 GGCGAAGTTGATACATAAAGCAAAAAT 59.724 33.333 0.00 0.00 0.00 1.82
2107 2328 4.842574 TGCAGTTGTCTATATTGCCTCAA 58.157 39.130 0.00 0.00 33.98 3.02
2121 2342 4.944962 TGCCTCAAAATTGTCGTATCAG 57.055 40.909 0.00 0.00 0.00 2.90
2524 2745 4.830765 TGCACTATGCCGCCGTCC 62.831 66.667 0.00 0.00 44.23 4.79
2525 2746 4.830765 GCACTATGCCGCCGTCCA 62.831 66.667 0.00 0.00 37.42 4.02
2526 2747 2.108976 CACTATGCCGCCGTCCAT 59.891 61.111 0.00 0.00 0.00 3.41
2527 2748 2.108976 ACTATGCCGCCGTCCATG 59.891 61.111 0.00 0.00 0.00 3.66
2528 2749 2.108976 CTATGCCGCCGTCCATGT 59.891 61.111 0.00 0.00 0.00 3.21
2529 2750 1.523711 CTATGCCGCCGTCCATGTT 60.524 57.895 0.00 0.00 0.00 2.71
2530 2751 1.775039 CTATGCCGCCGTCCATGTTG 61.775 60.000 0.00 0.00 0.00 3.33
2539 2760 2.232696 GCCGTCCATGTTGGGTAAAATT 59.767 45.455 0.00 0.00 38.32 1.82
2542 2763 4.262249 CCGTCCATGTTGGGTAAAATTGTT 60.262 41.667 0.00 0.00 38.32 2.83
2545 2766 6.750039 CGTCCATGTTGGGTAAAATTGTTATC 59.250 38.462 0.00 0.00 38.32 1.75
2546 2767 6.750039 GTCCATGTTGGGTAAAATTGTTATCG 59.250 38.462 0.00 0.00 38.32 2.92
2589 2810 4.785301 ACATGCCAGCATCTATAGTTGTT 58.215 39.130 1.19 3.89 33.90 2.83
2597 2818 3.561725 GCATCTATAGTTGTTGGTGCTCC 59.438 47.826 11.53 0.00 0.00 4.70
2600 2821 3.838317 TCTATAGTTGTTGGTGCTCCACT 59.162 43.478 7.09 3.97 44.22 4.00
2601 2822 2.543777 TAGTTGTTGGTGCTCCACTC 57.456 50.000 7.09 4.71 44.22 3.51
2602 2823 0.546122 AGTTGTTGGTGCTCCACTCA 59.454 50.000 7.09 7.34 44.22 3.41
2603 2824 1.143684 AGTTGTTGGTGCTCCACTCAT 59.856 47.619 7.09 0.00 44.22 2.90
2604 2825 1.267806 GTTGTTGGTGCTCCACTCATG 59.732 52.381 7.09 0.00 44.22 3.07
2619 2840 6.364568 CCACTCATGGTAGAATGGATATGA 57.635 41.667 0.00 0.00 41.64 2.15
2620 2841 6.772605 CCACTCATGGTAGAATGGATATGAA 58.227 40.000 0.00 0.00 41.64 2.57
2621 2842 7.400439 CCACTCATGGTAGAATGGATATGAAT 58.600 38.462 0.00 0.00 41.64 2.57
2622 2843 7.336176 CCACTCATGGTAGAATGGATATGAATG 59.664 40.741 0.00 0.00 41.64 2.67
2623 2844 7.336176 CACTCATGGTAGAATGGATATGAATGG 59.664 40.741 0.00 0.00 0.00 3.16
2624 2845 7.017950 ACTCATGGTAGAATGGATATGAATGGT 59.982 37.037 0.00 0.00 0.00 3.55
2625 2846 7.170277 TCATGGTAGAATGGATATGAATGGTG 58.830 38.462 0.00 0.00 0.00 4.17
2626 2847 5.316167 TGGTAGAATGGATATGAATGGTGC 58.684 41.667 0.00 0.00 0.00 5.01
2627 2848 4.702131 GGTAGAATGGATATGAATGGTGCC 59.298 45.833 0.00 0.00 0.00 5.01
2628 2849 4.458256 AGAATGGATATGAATGGTGCCA 57.542 40.909 0.00 0.00 0.00 4.92
2629 2850 4.806892 AGAATGGATATGAATGGTGCCAA 58.193 39.130 0.00 0.00 0.00 4.52
2630 2851 5.399991 AGAATGGATATGAATGGTGCCAAT 58.600 37.500 0.00 0.00 0.00 3.16
2631 2852 5.245301 AGAATGGATATGAATGGTGCCAATG 59.755 40.000 0.00 0.00 0.00 2.82
2632 2853 2.629137 TGGATATGAATGGTGCCAATGC 59.371 45.455 0.00 0.00 38.26 3.56
2633 2854 2.895404 GGATATGAATGGTGCCAATGCT 59.105 45.455 0.00 0.00 38.71 3.79
2634 2855 3.322828 GGATATGAATGGTGCCAATGCTT 59.677 43.478 0.00 0.00 38.71 3.91
2635 2856 4.523943 GGATATGAATGGTGCCAATGCTTA 59.476 41.667 0.00 0.00 38.71 3.09
2636 2857 5.336213 GGATATGAATGGTGCCAATGCTTAG 60.336 44.000 0.00 0.00 38.71 2.18
2637 2858 3.084536 TGAATGGTGCCAATGCTTAGA 57.915 42.857 0.00 0.00 38.71 2.10
2638 2859 3.018856 TGAATGGTGCCAATGCTTAGAG 58.981 45.455 0.00 0.00 38.71 2.43
2639 2860 1.396653 ATGGTGCCAATGCTTAGAGC 58.603 50.000 0.00 0.00 42.82 4.09
2681 2902 2.117423 CCCCCAGGGCGACTTTTT 59.883 61.111 0.00 0.00 35.35 1.94
2695 2916 4.105727 TTTTTCGTGTCGACGCCA 57.894 50.000 22.62 8.06 45.68 5.69
2696 2917 2.381109 TTTTTCGTGTCGACGCCAA 58.619 47.368 22.62 14.24 45.68 4.52
2697 2918 0.725686 TTTTTCGTGTCGACGCCAAA 59.274 45.000 22.62 19.34 45.68 3.28
2698 2919 0.725686 TTTTCGTGTCGACGCCAAAA 59.274 45.000 24.41 24.41 45.68 2.44
2699 2920 0.725686 TTTCGTGTCGACGCCAAAAA 59.274 45.000 22.62 16.67 45.68 1.94
2715 2936 3.340789 AAAAACCCTCAGTCGCGC 58.659 55.556 0.00 0.00 0.00 6.86
2716 2937 2.258726 AAAAACCCTCAGTCGCGCC 61.259 57.895 0.00 0.00 0.00 6.53
2717 2938 4.699522 AAACCCTCAGTCGCGCCC 62.700 66.667 0.00 0.00 0.00 6.13
2720 2941 3.458163 CCCTCAGTCGCGCCCTTA 61.458 66.667 0.00 0.00 0.00 2.69
2721 2942 2.577059 CCTCAGTCGCGCCCTTAA 59.423 61.111 0.00 0.00 0.00 1.85
2722 2943 1.519455 CCTCAGTCGCGCCCTTAAG 60.519 63.158 0.00 0.00 0.00 1.85
2723 2944 1.511305 CTCAGTCGCGCCCTTAAGA 59.489 57.895 0.00 0.00 0.00 2.10
2724 2945 0.802607 CTCAGTCGCGCCCTTAAGAC 60.803 60.000 0.00 1.68 0.00 3.01
2725 2946 2.158959 CAGTCGCGCCCTTAAGACG 61.159 63.158 0.00 8.70 38.53 4.18
2729 2950 4.807039 GCGCCCTTAAGACGCCGA 62.807 66.667 23.99 0.00 46.63 5.54
2730 2951 2.125832 CGCCCTTAAGACGCCGAA 60.126 61.111 3.36 0.00 0.00 4.30
2731 2952 1.738830 CGCCCTTAAGACGCCGAAA 60.739 57.895 3.36 0.00 0.00 3.46
2732 2953 1.087771 CGCCCTTAAGACGCCGAAAT 61.088 55.000 3.36 0.00 0.00 2.17
2733 2954 0.656259 GCCCTTAAGACGCCGAAATC 59.344 55.000 3.36 0.00 0.00 2.17
2734 2955 1.296727 CCCTTAAGACGCCGAAATCC 58.703 55.000 3.36 0.00 0.00 3.01
2735 2956 0.928229 CCTTAAGACGCCGAAATCCG 59.072 55.000 3.36 0.00 38.18 4.18
2736 2957 0.300789 CTTAAGACGCCGAAATCCGC 59.699 55.000 0.00 0.00 36.84 5.54
2737 2958 1.085501 TTAAGACGCCGAAATCCGCC 61.086 55.000 0.00 0.00 36.84 6.13
2755 2976 2.951458 GGCTCGGACCGTTTTTGG 59.049 61.111 14.79 0.15 0.00 3.28
2756 2977 2.622962 GGCTCGGACCGTTTTTGGG 61.623 63.158 14.79 0.00 0.00 4.12
2757 2978 2.951458 CTCGGACCGTTTTTGGGC 59.049 61.111 14.79 0.00 35.71 5.36
2761 2982 3.676605 GACCGTTTTTGGGCCCGG 61.677 66.667 19.37 16.04 45.72 5.73
2764 2985 2.673687 CGTTTTTGGGCCCGGCTA 60.674 61.111 19.37 0.00 0.00 3.93
2765 2986 2.049767 CGTTTTTGGGCCCGGCTAT 61.050 57.895 19.37 0.00 0.00 2.97
2766 2987 1.813859 GTTTTTGGGCCCGGCTATC 59.186 57.895 19.37 1.81 0.00 2.08
2767 2988 1.380650 TTTTTGGGCCCGGCTATCC 60.381 57.895 19.37 2.51 0.00 2.59
2768 2989 2.864770 TTTTTGGGCCCGGCTATCCC 62.865 60.000 19.37 11.11 40.47 3.85
2773 2994 3.942439 GCCCGGCTATCCCAGGAC 61.942 72.222 0.71 0.00 31.45 3.85
2774 2995 3.616721 CCCGGCTATCCCAGGACG 61.617 72.222 0.00 0.00 31.45 4.79
2775 2996 2.520982 CCGGCTATCCCAGGACGA 60.521 66.667 0.00 0.00 31.45 4.20
2776 2997 2.131709 CCGGCTATCCCAGGACGAA 61.132 63.158 0.00 0.00 31.45 3.85
2777 2998 1.067582 CGGCTATCCCAGGACGAAC 59.932 63.158 0.00 0.00 0.00 3.95
2778 2999 1.446366 GGCTATCCCAGGACGAACC 59.554 63.158 0.00 0.00 39.35 3.62
2779 3000 1.335132 GGCTATCCCAGGACGAACCA 61.335 60.000 0.00 0.00 42.04 3.67
2780 3001 0.105039 GCTATCCCAGGACGAACCAG 59.895 60.000 0.00 0.00 42.04 4.00
2781 3002 0.753262 CTATCCCAGGACGAACCAGG 59.247 60.000 7.57 7.57 43.84 4.45
2784 3005 3.636231 CCAGGACGAACCAGGGCA 61.636 66.667 0.00 0.00 41.01 5.36
2785 3006 2.358737 CAGGACGAACCAGGGCAC 60.359 66.667 0.00 0.00 42.04 5.01
2786 3007 2.526873 AGGACGAACCAGGGCACT 60.527 61.111 0.00 0.00 42.04 4.40
2787 3008 2.358737 GGACGAACCAGGGCACTG 60.359 66.667 9.70 9.70 44.51 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
186 187 6.827641 TGTTTGCGTAAAGAGAATGTACATC 58.172 36.000 9.23 3.13 0.00 3.06
187 188 6.795098 TGTTTGCGTAAAGAGAATGTACAT 57.205 33.333 1.41 1.41 0.00 2.29
188 189 6.606234 TTGTTTGCGTAAAGAGAATGTACA 57.394 33.333 0.00 0.00 0.00 2.90
189 190 9.769093 ATAATTGTTTGCGTAAAGAGAATGTAC 57.231 29.630 0.00 0.00 0.00 2.90
420 435 1.266718 TGCTTCAGAACGATTGGCAAC 59.733 47.619 0.00 0.00 0.00 4.17
430 445 1.747355 CATGATGGGGTGCTTCAGAAC 59.253 52.381 0.00 0.00 0.00 3.01
464 479 5.829391 CCATCATCCATTTACATGTCCTTCA 59.171 40.000 0.00 0.00 0.00 3.02
492 507 3.290619 GTCGATCGACGCTGAAGC 58.709 61.111 30.46 7.41 42.26 3.86
579 609 4.430908 ACGAACAATTTAACCCGCAAAAA 58.569 34.783 0.00 0.00 0.00 1.94
580 610 4.043037 ACGAACAATTTAACCCGCAAAA 57.957 36.364 0.00 0.00 0.00 2.44
581 611 3.066342 TGACGAACAATTTAACCCGCAAA 59.934 39.130 0.00 0.00 0.00 3.68
582 612 2.617308 TGACGAACAATTTAACCCGCAA 59.383 40.909 0.00 0.00 0.00 4.85
583 613 2.031857 GTGACGAACAATTTAACCCGCA 60.032 45.455 0.00 0.00 0.00 5.69
584 614 2.224784 AGTGACGAACAATTTAACCCGC 59.775 45.455 0.00 0.00 0.00 6.13
585 615 3.249080 ACAGTGACGAACAATTTAACCCG 59.751 43.478 0.00 0.00 0.00 5.28
586 616 4.823790 ACAGTGACGAACAATTTAACCC 57.176 40.909 0.00 0.00 0.00 4.11
587 617 5.051973 GCAAACAGTGACGAACAATTTAACC 60.052 40.000 0.00 0.00 0.00 2.85
588 618 5.051973 GGCAAACAGTGACGAACAATTTAAC 60.052 40.000 0.00 0.00 0.00 2.01
589 619 5.038033 GGCAAACAGTGACGAACAATTTAA 58.962 37.500 0.00 0.00 0.00 1.52
590 620 4.096532 TGGCAAACAGTGACGAACAATTTA 59.903 37.500 0.00 0.00 38.59 1.40
591 621 3.119316 TGGCAAACAGTGACGAACAATTT 60.119 39.130 0.00 0.00 38.59 1.82
592 622 2.425312 TGGCAAACAGTGACGAACAATT 59.575 40.909 0.00 0.00 38.59 2.32
593 623 2.020720 TGGCAAACAGTGACGAACAAT 58.979 42.857 0.00 0.00 38.59 2.71
594 624 1.454201 TGGCAAACAGTGACGAACAA 58.546 45.000 0.00 0.00 38.59 2.83
595 625 1.131504 GTTGGCAAACAGTGACGAACA 59.868 47.619 0.00 0.00 38.59 3.18
596 626 1.533129 GGTTGGCAAACAGTGACGAAC 60.533 52.381 11.10 0.00 38.59 3.95
597 627 0.736053 GGTTGGCAAACAGTGACGAA 59.264 50.000 11.10 0.00 38.59 3.85
598 628 0.107410 AGGTTGGCAAACAGTGACGA 60.107 50.000 18.93 0.00 38.59 4.20
599 629 0.307760 GAGGTTGGCAAACAGTGACG 59.692 55.000 18.93 0.00 38.59 4.35
600 630 0.668535 GGAGGTTGGCAAACAGTGAC 59.331 55.000 18.93 3.24 38.10 3.67
601 631 0.817634 CGGAGGTTGGCAAACAGTGA 60.818 55.000 18.93 0.00 38.10 3.41
602 632 0.817634 TCGGAGGTTGGCAAACAGTG 60.818 55.000 18.93 6.18 38.10 3.66
603 633 0.535102 CTCGGAGGTTGGCAAACAGT 60.535 55.000 18.93 0.00 38.10 3.55
604 634 1.856265 GCTCGGAGGTTGGCAAACAG 61.856 60.000 18.93 7.02 38.10 3.16
605 635 1.896660 GCTCGGAGGTTGGCAAACA 60.897 57.895 18.93 0.00 38.10 2.83
606 636 0.321298 TAGCTCGGAGGTTGGCAAAC 60.321 55.000 15.66 7.31 35.40 2.93
607 637 0.036388 CTAGCTCGGAGGTTGGCAAA 60.036 55.000 15.66 0.00 0.00 3.68
608 638 0.902984 TCTAGCTCGGAGGTTGGCAA 60.903 55.000 15.66 0.00 0.00 4.52
609 639 1.304962 TCTAGCTCGGAGGTTGGCA 60.305 57.895 15.66 0.00 0.00 4.92
1077 1120 1.435515 GTAGCTGAGCCAGAGGACG 59.564 63.158 0.00 0.00 32.44 4.79
1251 1294 3.629398 GGCAATTGCATTAGACTGCTACT 59.371 43.478 30.32 0.00 42.75 2.57
1253 1296 2.951642 GGGCAATTGCATTAGACTGCTA 59.048 45.455 30.32 0.00 42.75 3.49
1268 1311 3.426117 CTCGTCGGCGTAGGGCAAT 62.426 63.158 10.18 0.00 46.16 3.56
1582 1625 4.527583 GCCTCCTCTGCAGCTCCG 62.528 72.222 9.47 0.00 0.00 4.63
1775 1821 7.118680 TCGGCGAACAGAAAGAAATTATTAAGT 59.881 33.333 7.35 0.00 0.00 2.24
1877 2096 3.127030 CGCAACCTCTCCCTATTTTTGTC 59.873 47.826 0.00 0.00 0.00 3.18
1885 2105 1.183549 GAACTCGCAACCTCTCCCTA 58.816 55.000 0.00 0.00 0.00 3.53
1899 2119 2.981859 ATATGTGGTGGTCGGAACTC 57.018 50.000 0.00 0.00 0.00 3.01
1948 2168 1.586154 CGCCACCAAAGCCACTTAGG 61.586 60.000 0.00 0.00 41.84 2.69
2064 2285 7.093814 ACTGCATAACATGTTGTGTATGGATTT 60.094 33.333 28.90 11.25 41.14 2.17
2098 2319 5.883661 CTGATACGACAATTTTGAGGCAAT 58.116 37.500 0.00 0.00 0.00 3.56
2099 2320 5.295431 CTGATACGACAATTTTGAGGCAA 57.705 39.130 0.00 0.00 0.00 4.52
2508 2729 4.830765 TGGACGGCGGCATAGTGC 62.831 66.667 17.61 4.82 44.08 4.40
2509 2730 2.108976 ATGGACGGCGGCATAGTG 59.891 61.111 17.61 0.00 0.00 2.74
2510 2731 2.108976 CATGGACGGCGGCATAGT 59.891 61.111 17.61 0.00 0.00 2.12
2511 2732 1.523711 AACATGGACGGCGGCATAG 60.524 57.895 17.61 5.39 0.00 2.23
2512 2733 1.817520 CAACATGGACGGCGGCATA 60.818 57.895 17.61 2.35 0.00 3.14
2513 2734 3.133464 CAACATGGACGGCGGCAT 61.133 61.111 17.61 2.98 0.00 4.40
2516 2737 2.806503 TTACCCAACATGGACGGCGG 62.807 60.000 13.24 0.00 40.96 6.13
2517 2738 0.956410 TTTACCCAACATGGACGGCG 60.956 55.000 4.80 4.80 40.96 6.46
2518 2739 1.249407 TTTTACCCAACATGGACGGC 58.751 50.000 0.00 0.00 40.96 5.68
2519 2740 3.257127 ACAATTTTACCCAACATGGACGG 59.743 43.478 0.00 0.00 40.96 4.79
2520 2741 4.513198 ACAATTTTACCCAACATGGACG 57.487 40.909 0.00 0.00 40.96 4.79
2521 2742 6.750039 CGATAACAATTTTACCCAACATGGAC 59.250 38.462 0.00 0.00 40.96 4.02
2522 2743 6.127591 CCGATAACAATTTTACCCAACATGGA 60.128 38.462 0.00 0.00 40.96 3.41
2523 2744 6.039616 CCGATAACAATTTTACCCAACATGG 58.960 40.000 0.00 0.00 37.25 3.66
2524 2745 6.626302 ACCGATAACAATTTTACCCAACATG 58.374 36.000 0.00 0.00 0.00 3.21
2525 2746 6.661805 AGACCGATAACAATTTTACCCAACAT 59.338 34.615 0.00 0.00 0.00 2.71
2526 2747 6.005198 AGACCGATAACAATTTTACCCAACA 58.995 36.000 0.00 0.00 0.00 3.33
2527 2748 6.403964 GGAGACCGATAACAATTTTACCCAAC 60.404 42.308 0.00 0.00 0.00 3.77
2528 2749 5.648960 GGAGACCGATAACAATTTTACCCAA 59.351 40.000 0.00 0.00 0.00 4.12
2529 2750 5.045432 AGGAGACCGATAACAATTTTACCCA 60.045 40.000 0.00 0.00 0.00 4.51
2530 2751 5.434408 AGGAGACCGATAACAATTTTACCC 58.566 41.667 0.00 0.00 0.00 3.69
2539 2760 3.698040 GGTTGAGTAGGAGACCGATAACA 59.302 47.826 0.00 0.00 0.00 2.41
2542 2763 3.552875 CAGGTTGAGTAGGAGACCGATA 58.447 50.000 0.00 0.00 37.26 2.92
2545 2766 0.173708 GCAGGTTGAGTAGGAGACCG 59.826 60.000 0.00 0.00 37.26 4.79
2546 2767 1.267121 TGCAGGTTGAGTAGGAGACC 58.733 55.000 0.00 0.00 0.00 3.85
2597 2818 7.336176 CCATTCATATCCATTCTACCATGAGTG 59.664 40.741 0.00 0.00 32.84 3.51
2600 2821 7.170277 CACCATTCATATCCATTCTACCATGA 58.830 38.462 0.00 0.00 0.00 3.07
2601 2822 6.127814 GCACCATTCATATCCATTCTACCATG 60.128 42.308 0.00 0.00 0.00 3.66
2602 2823 5.948162 GCACCATTCATATCCATTCTACCAT 59.052 40.000 0.00 0.00 0.00 3.55
2603 2824 5.316167 GCACCATTCATATCCATTCTACCA 58.684 41.667 0.00 0.00 0.00 3.25
2604 2825 4.702131 GGCACCATTCATATCCATTCTACC 59.298 45.833 0.00 0.00 0.00 3.18
2605 2826 5.316167 TGGCACCATTCATATCCATTCTAC 58.684 41.667 0.00 0.00 0.00 2.59
2606 2827 5.581350 TGGCACCATTCATATCCATTCTA 57.419 39.130 0.00 0.00 0.00 2.10
2607 2828 4.458256 TGGCACCATTCATATCCATTCT 57.542 40.909 0.00 0.00 0.00 2.40
2608 2829 5.475719 CATTGGCACCATTCATATCCATTC 58.524 41.667 0.00 0.00 0.00 2.67
2609 2830 4.262721 GCATTGGCACCATTCATATCCATT 60.263 41.667 0.00 0.00 40.72 3.16
2610 2831 3.259876 GCATTGGCACCATTCATATCCAT 59.740 43.478 0.00 0.00 40.72 3.41
2611 2832 2.629137 GCATTGGCACCATTCATATCCA 59.371 45.455 0.00 0.00 40.72 3.41
2612 2833 2.895404 AGCATTGGCACCATTCATATCC 59.105 45.455 0.00 0.00 44.61 2.59
2613 2834 4.595762 AAGCATTGGCACCATTCATATC 57.404 40.909 0.00 0.00 44.61 1.63
2614 2835 5.387788 TCTAAGCATTGGCACCATTCATAT 58.612 37.500 0.00 0.00 44.61 1.78
2615 2836 4.790937 TCTAAGCATTGGCACCATTCATA 58.209 39.130 0.00 0.00 44.61 2.15
2616 2837 3.634504 TCTAAGCATTGGCACCATTCAT 58.365 40.909 0.00 0.00 44.61 2.57
2617 2838 3.018856 CTCTAAGCATTGGCACCATTCA 58.981 45.455 0.00 0.00 44.61 2.57
2618 2839 2.223665 GCTCTAAGCATTGGCACCATTC 60.224 50.000 0.00 0.00 44.61 2.67
2619 2840 1.753073 GCTCTAAGCATTGGCACCATT 59.247 47.619 0.00 0.00 44.61 3.16
2620 2841 1.396653 GCTCTAAGCATTGGCACCAT 58.603 50.000 0.00 0.00 44.61 3.55
2621 2842 2.872408 GCTCTAAGCATTGGCACCA 58.128 52.632 0.00 0.00 44.61 4.17
2631 2852 0.599728 CGGCTGGAGATGCTCTAAGC 60.600 60.000 11.59 11.59 42.82 3.09
2632 2853 0.599728 GCGGCTGGAGATGCTCTAAG 60.600 60.000 0.00 0.00 0.00 2.18
2633 2854 1.443407 GCGGCTGGAGATGCTCTAA 59.557 57.895 0.00 0.00 0.00 2.10
2634 2855 2.849964 CGCGGCTGGAGATGCTCTA 61.850 63.158 0.00 0.00 0.00 2.43
2635 2856 4.218578 CGCGGCTGGAGATGCTCT 62.219 66.667 0.00 0.00 0.00 4.09
2698 2919 2.258726 GGCGCGACTGAGGGTTTTT 61.259 57.895 12.10 0.00 0.00 1.94
2699 2920 2.668550 GGCGCGACTGAGGGTTTT 60.669 61.111 12.10 0.00 0.00 2.43
2700 2921 4.699522 GGGCGCGACTGAGGGTTT 62.700 66.667 13.91 0.00 0.00 3.27
2703 2924 2.907897 CTTAAGGGCGCGACTGAGGG 62.908 65.000 13.91 0.00 0.00 4.30
2704 2925 1.519455 CTTAAGGGCGCGACTGAGG 60.519 63.158 13.91 0.00 0.00 3.86
2705 2926 0.802607 GTCTTAAGGGCGCGACTGAG 60.803 60.000 13.91 9.86 0.00 3.35
2706 2927 1.214589 GTCTTAAGGGCGCGACTGA 59.785 57.895 13.91 0.00 0.00 3.41
2707 2928 2.158959 CGTCTTAAGGGCGCGACTG 61.159 63.158 13.91 0.00 0.00 3.51
2708 2929 2.181021 CGTCTTAAGGGCGCGACT 59.819 61.111 13.91 4.58 0.00 4.18
2709 2930 3.551915 GCGTCTTAAGGGCGCGAC 61.552 66.667 22.26 6.99 41.70 5.19
2714 2935 0.656259 GATTTCGGCGTCTTAAGGGC 59.344 55.000 6.85 6.75 0.00 5.19
2715 2936 1.296727 GGATTTCGGCGTCTTAAGGG 58.703 55.000 6.85 0.00 0.00 3.95
2716 2937 0.928229 CGGATTTCGGCGTCTTAAGG 59.072 55.000 6.85 0.00 34.75 2.69
2717 2938 0.300789 GCGGATTTCGGCGTCTTAAG 59.699 55.000 6.85 0.00 39.69 1.85
2718 2939 2.375981 GCGGATTTCGGCGTCTTAA 58.624 52.632 6.85 0.00 39.69 1.85
2719 2940 4.097828 GCGGATTTCGGCGTCTTA 57.902 55.556 6.85 0.00 39.69 2.10
2738 2959 2.622962 CCCAAAAACGGTCCGAGCC 61.623 63.158 20.51 0.00 0.00 4.70
2739 2960 2.951458 CCCAAAAACGGTCCGAGC 59.049 61.111 20.51 0.00 0.00 5.03
2740 2961 2.622962 GGCCCAAAAACGGTCCGAG 61.623 63.158 20.51 1.98 0.00 4.63
2741 2962 2.595172 GGCCCAAAAACGGTCCGA 60.595 61.111 20.51 0.00 0.00 4.55
2742 2963 3.676605 GGGCCCAAAAACGGTCCG 61.677 66.667 19.95 10.48 34.85 4.79
2743 2964 3.676605 CGGGCCCAAAAACGGTCC 61.677 66.667 24.92 0.00 42.19 4.46
2744 2965 3.676605 CCGGGCCCAAAAACGGTC 61.677 66.667 24.92 0.00 41.34 4.79
2747 2968 2.000215 GATAGCCGGGCCCAAAAACG 62.000 60.000 24.92 6.17 0.00 3.60
2748 2969 1.672854 GGATAGCCGGGCCCAAAAAC 61.673 60.000 24.92 7.96 0.00 2.43
2749 2970 1.380650 GGATAGCCGGGCCCAAAAA 60.381 57.895 24.92 4.16 0.00 1.94
2750 2971 2.277404 GGATAGCCGGGCCCAAAA 59.723 61.111 24.92 3.72 0.00 2.44
2751 2972 3.816090 GGGATAGCCGGGCCCAAA 61.816 66.667 24.92 3.30 41.64 3.28
2756 2977 3.942439 GTCCTGGGATAGCCGGGC 61.942 72.222 12.11 12.11 33.83 6.13
2757 2978 3.616721 CGTCCTGGGATAGCCGGG 61.617 72.222 2.18 0.00 33.83 5.73
2758 2979 2.131709 TTCGTCCTGGGATAGCCGG 61.132 63.158 0.00 0.00 33.83 6.13
2759 2980 1.067582 GTTCGTCCTGGGATAGCCG 59.932 63.158 0.00 0.00 33.83 5.52
2760 2981 1.335132 TGGTTCGTCCTGGGATAGCC 61.335 60.000 0.00 0.00 37.07 3.93
2761 2982 0.105039 CTGGTTCGTCCTGGGATAGC 59.895 60.000 0.00 0.00 37.07 2.97
2768 2989 2.358737 GTGCCCTGGTTCGTCCTG 60.359 66.667 0.00 1.40 37.07 3.86
2769 2990 2.526873 AGTGCCCTGGTTCGTCCT 60.527 61.111 0.00 0.00 37.07 3.85
2770 2991 2.358737 CAGTGCCCTGGTTCGTCC 60.359 66.667 0.00 0.00 34.90 4.79



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

AutoCloner maintained by Alex Coulton.