Multiple sequence alignment - TraesCS7D01G414000

Loading Multiple Alignment...

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 TraesCS7D01G414000 chr7D 100.000 3019 0 0 1 3019 532370892 532367874 0.000000e+00 5576
1 TraesCS7D01G414000 chr7D 88.650 652 38 18 2382 3018 532264106 532263476 0.000000e+00 761
2 TraesCS7D01G414000 chr7A 93.498 2184 85 17 889 3019 612599232 612597053 0.000000e+00 3193
3 TraesCS7D01G414000 chr7A 88.190 652 43 16 2382 3018 612585334 612584702 0.000000e+00 747
4 TraesCS7D01G414000 chr7A 87.762 621 35 12 176 795 612599836 612599256 0.000000e+00 688
5 TraesCS7D01G414000 chr7A 93.103 290 19 1 1563 1852 612585946 612585658 1.000000e-114 424
6 TraesCS7D01G414000 chr7A 96.154 182 6 1 1 181 612604156 612603975 2.280000e-76 296
7 TraesCS7D01G414000 chr7A 88.679 212 16 2 2019 2222 612585662 612585451 5.000000e-63 252
8 TraesCS7D01G414000 chr7B 93.063 1355 52 18 889 2222 572652039 572650706 0.000000e+00 1943
9 TraesCS7D01G414000 chr7B 92.273 660 41 5 2364 3018 572650693 572650039 0.000000e+00 928
10 TraesCS7D01G414000 chr7B 89.088 669 45 11 1563 2222 572639999 572639350 0.000000e+00 806
11 TraesCS7D01G414000 chr7B 87.322 702 48 18 2333 3016 572639273 572638595 0.000000e+00 765
12 TraesCS7D01G414000 chr7B 92.208 385 24 3 14 392 572652706 572652322 9.520000e-150 540
13 TraesCS7D01G414000 chr7B 89.418 189 14 1 14 196 572654622 572654434 1.810000e-57 233
14 TraesCS7D01G414000 chr7B 85.246 244 15 4 552 795 572652285 572652063 6.510000e-57 231
15 TraesCS7D01G414000 chr2A 82.545 275 40 6 1043 1315 135203522 135203790 5.030000e-58 235
16 TraesCS7D01G414000 chr2D 81.818 275 42 6 1043 1315 128406569 128406837 1.090000e-54 224
17 TraesCS7D01G414000 chr2B 81.203 266 42 6 1052 1315 182004849 182004590 1.100000e-49 207


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 TraesCS7D01G414000 chr7D 532367874 532370892 3018 True 5576.000000 5576 100.000000 1 3019 1 chr7D.!!$R2 3018
1 TraesCS7D01G414000 chr7D 532263476 532264106 630 True 761.000000 761 88.650000 2382 3018 1 chr7D.!!$R1 636
2 TraesCS7D01G414000 chr7A 612597053 612599836 2783 True 1940.500000 3193 90.630000 176 3019 2 chr7A.!!$R3 2843
3 TraesCS7D01G414000 chr7A 612584702 612585946 1244 True 474.333333 747 89.990667 1563 3018 3 chr7A.!!$R2 1455
4 TraesCS7D01G414000 chr7B 572638595 572639999 1404 True 785.500000 806 88.205000 1563 3016 2 chr7B.!!$R1 1453
5 TraesCS7D01G414000 chr7B 572650039 572654622 4583 True 775.000000 1943 90.441600 14 3018 5 chr7B.!!$R2 3004

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
375 2299 0.035056 GCTGCATTACTCTGGGTGGT 60.035 55.0 0.0 0.0 0.00 4.16 F
857 2802 0.035915 TAGTTACATGCCGCAGCCAA 60.036 50.0 0.0 0.0 38.69 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1379 3326 1.129624 TCGCATTTCAACACGTATGGC 59.870 47.619 0.00 0.0 0.0 4.40 R
2361 4364 1.198637 GGTGTGACTGAAAGCTGCATC 59.801 52.381 1.02 0.0 37.6 3.91 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
19 20 2.923035 CACCCACCCACTCGGTCT 60.923 66.667 0.00 0.00 43.58 3.85
38 39 3.003897 GTCTATCTAGTCCAACTGCTCCG 59.996 52.174 0.00 0.00 0.00 4.63
83 2000 2.352457 CGTCTCCGAATCGCCTCG 60.352 66.667 0.00 0.00 38.58 4.63
132 2049 0.448990 TCGACCATACTCCGTTCGTG 59.551 55.000 0.00 0.00 0.00 4.35
142 2059 1.268899 CTCCGTTCGTGAGGTACAACT 59.731 52.381 0.00 0.00 0.00 3.16
154 2071 2.386113 AGGTACAACTAGTTCCTCCCCT 59.614 50.000 4.77 4.28 43.82 4.79
167 2084 0.036010 CTCCCCTAGTGCCACTTGTG 60.036 60.000 1.02 0.00 0.00 3.33
261 2184 1.721133 CGCGGTTCGTCAACTTTGC 60.721 57.895 0.00 0.00 32.50 3.68
340 2264 3.935203 CACACTCTGACTGAAGTTTGTGT 59.065 43.478 0.00 0.00 37.82 3.72
345 2269 2.540101 CTGACTGAAGTTTGTGTCGTCC 59.460 50.000 0.00 0.00 32.64 4.79
375 2299 0.035056 GCTGCATTACTCTGGGTGGT 60.035 55.000 0.00 0.00 0.00 4.16
392 2316 3.564225 GGTGGTAGTTTGTTGAACAGAGG 59.436 47.826 0.00 0.00 40.84 3.69
394 2318 3.456644 TGGTAGTTTGTTGAACAGAGGGA 59.543 43.478 0.00 0.00 40.84 4.20
395 2319 4.065789 GGTAGTTTGTTGAACAGAGGGAG 58.934 47.826 0.00 0.00 40.84 4.30
397 2321 3.545703 AGTTTGTTGAACAGAGGGAGTG 58.454 45.455 0.00 0.00 40.84 3.51
398 2322 2.618709 GTTTGTTGAACAGAGGGAGTGG 59.381 50.000 0.00 0.00 38.18 4.00
399 2323 1.507140 TGTTGAACAGAGGGAGTGGT 58.493 50.000 0.00 0.00 0.00 4.16
400 2324 2.684943 TGTTGAACAGAGGGAGTGGTA 58.315 47.619 0.00 0.00 0.00 3.25
401 2325 2.632996 TGTTGAACAGAGGGAGTGGTAG 59.367 50.000 0.00 0.00 0.00 3.18
402 2326 2.633481 GTTGAACAGAGGGAGTGGTAGT 59.367 50.000 0.00 0.00 0.00 2.73
403 2327 2.248248 TGAACAGAGGGAGTGGTAGTG 58.752 52.381 0.00 0.00 0.00 2.74
404 2328 2.249139 GAACAGAGGGAGTGGTAGTGT 58.751 52.381 0.00 0.00 0.00 3.55
417 2341 8.741841 GGGAGTGGTAGTGTAATATAAGATCTC 58.258 40.741 0.00 0.00 0.00 2.75
448 2372 5.215252 TCACTTAGTTTTCAGAGGGAGTG 57.785 43.478 0.00 0.00 35.73 3.51
459 2383 4.023980 TCAGAGGGAGTGGTAGTGTAATG 58.976 47.826 0.00 0.00 0.00 1.90
460 2384 3.133003 CAGAGGGAGTGGTAGTGTAATGG 59.867 52.174 0.00 0.00 0.00 3.16
478 2402 5.633830 AATGGAGTACAAGCTTTCATGTG 57.366 39.130 0.00 0.00 0.00 3.21
531 2455 2.032071 GCGTAGGCAGTGGTGGTT 59.968 61.111 1.75 0.00 39.62 3.67
532 2456 1.599797 GCGTAGGCAGTGGTGGTTT 60.600 57.895 1.75 0.00 39.62 3.27
533 2457 1.170290 GCGTAGGCAGTGGTGGTTTT 61.170 55.000 1.75 0.00 39.62 2.43
534 2458 1.314730 CGTAGGCAGTGGTGGTTTTT 58.685 50.000 0.00 0.00 0.00 1.94
535 2459 1.001815 CGTAGGCAGTGGTGGTTTTTG 60.002 52.381 0.00 0.00 0.00 2.44
536 2460 2.303175 GTAGGCAGTGGTGGTTTTTGA 58.697 47.619 0.00 0.00 0.00 2.69
537 2461 1.111277 AGGCAGTGGTGGTTTTTGAC 58.889 50.000 0.00 0.00 0.00 3.18
538 2462 1.111277 GGCAGTGGTGGTTTTTGACT 58.889 50.000 0.00 0.00 0.00 3.41
550 2474 6.869388 GGTGGTTTTTGACTTTTTGTGTAGAA 59.131 34.615 0.00 0.00 0.00 2.10
608 2532 0.109412 GCTGCTGAACTGATGTTGGC 60.109 55.000 0.00 0.00 36.39 4.52
615 2539 0.179004 AACTGATGTTGGCCGTTGGA 60.179 50.000 0.00 0.00 34.71 3.53
617 2541 1.586154 CTGATGTTGGCCGTTGGACC 61.586 60.000 0.00 0.00 0.00 4.46
644 2568 2.919772 TGGAGTATCAGGACAGTCCA 57.080 50.000 22.31 1.78 41.07 4.02
672 2596 4.361451 CAAATCTTGCACGATTTAGCCT 57.639 40.909 25.42 6.12 40.59 4.58
675 2599 1.089920 CTTGCACGATTTAGCCTGCT 58.910 50.000 0.00 0.00 0.00 4.24
676 2600 1.470098 CTTGCACGATTTAGCCTGCTT 59.530 47.619 0.00 0.00 0.00 3.91
677 2601 1.086696 TGCACGATTTAGCCTGCTTC 58.913 50.000 0.00 0.00 0.00 3.86
678 2602 0.378610 GCACGATTTAGCCTGCTTCC 59.621 55.000 0.00 0.00 0.00 3.46
679 2603 1.737838 CACGATTTAGCCTGCTTCCA 58.262 50.000 0.00 0.00 0.00 3.53
680 2604 2.292267 CACGATTTAGCCTGCTTCCAT 58.708 47.619 0.00 0.00 0.00 3.41
681 2605 2.684881 CACGATTTAGCCTGCTTCCATT 59.315 45.455 0.00 0.00 0.00 3.16
682 2606 3.129287 CACGATTTAGCCTGCTTCCATTT 59.871 43.478 0.00 0.00 0.00 2.32
683 2607 4.335315 CACGATTTAGCCTGCTTCCATTTA 59.665 41.667 0.00 0.00 0.00 1.40
684 2608 4.576463 ACGATTTAGCCTGCTTCCATTTAG 59.424 41.667 0.00 0.00 0.00 1.85
685 2609 4.576463 CGATTTAGCCTGCTTCCATTTAGT 59.424 41.667 0.00 0.00 0.00 2.24
686 2610 5.758296 CGATTTAGCCTGCTTCCATTTAGTA 59.242 40.000 0.00 0.00 0.00 1.82
687 2611 6.073548 CGATTTAGCCTGCTTCCATTTAGTAG 60.074 42.308 0.00 0.00 0.00 2.57
688 2612 3.567478 AGCCTGCTTCCATTTAGTAGG 57.433 47.619 0.00 0.00 45.21 3.18
689 2613 3.115390 AGCCTGCTTCCATTTAGTAGGA 58.885 45.455 10.60 0.00 45.24 2.94
690 2614 3.523564 AGCCTGCTTCCATTTAGTAGGAA 59.476 43.478 10.60 0.00 45.24 3.36
695 2619 3.553828 TTCCATTTAGTAGGAAGCCCG 57.446 47.619 0.00 0.00 38.91 6.13
722 2667 4.235360 CGTACCCTTGTGTAGTTTCTGAG 58.765 47.826 0.00 0.00 0.00 3.35
724 2669 5.048504 CGTACCCTTGTGTAGTTTCTGAGTA 60.049 44.000 0.00 0.00 0.00 2.59
781 2726 3.567585 AGCTGCAGACCTTCTTTTCTTTC 59.432 43.478 20.43 0.00 0.00 2.62
792 2737 6.378280 ACCTTCTTTTCTTTCTCTTGCTTTGA 59.622 34.615 0.00 0.00 0.00 2.69
795 2740 5.652014 TCTTTTCTTTCTCTTGCTTTGACCA 59.348 36.000 0.00 0.00 0.00 4.02
797 2742 6.469782 TTTCTTTCTCTTGCTTTGACCATT 57.530 33.333 0.00 0.00 0.00 3.16
799 2744 6.469782 TCTTTCTCTTGCTTTGACCATTTT 57.530 33.333 0.00 0.00 0.00 1.82
800 2745 6.507023 TCTTTCTCTTGCTTTGACCATTTTC 58.493 36.000 0.00 0.00 0.00 2.29
801 2746 4.853924 TCTCTTGCTTTGACCATTTTCC 57.146 40.909 0.00 0.00 0.00 3.13
802 2747 4.473444 TCTCTTGCTTTGACCATTTTCCT 58.527 39.130 0.00 0.00 0.00 3.36
803 2748 4.895297 TCTCTTGCTTTGACCATTTTCCTT 59.105 37.500 0.00 0.00 0.00 3.36
804 2749 5.363580 TCTCTTGCTTTGACCATTTTCCTTT 59.636 36.000 0.00 0.00 0.00 3.11
806 2751 5.363580 TCTTGCTTTGACCATTTTCCTTTCT 59.636 36.000 0.00 0.00 0.00 2.52
807 2752 4.947645 TGCTTTGACCATTTTCCTTTCTG 58.052 39.130 0.00 0.00 0.00 3.02
809 2754 4.309933 CTTTGACCATTTTCCTTTCTGGC 58.690 43.478 0.00 0.00 35.26 4.85
812 2757 4.671831 TGACCATTTTCCTTTCTGGCATA 58.328 39.130 0.00 0.00 35.26 3.14
813 2758 4.706476 TGACCATTTTCCTTTCTGGCATAG 59.294 41.667 0.00 0.00 35.26 2.23
816 2761 5.960202 ACCATTTTCCTTTCTGGCATAGATT 59.040 36.000 0.00 0.00 34.80 2.40
817 2762 7.125391 ACCATTTTCCTTTCTGGCATAGATTA 58.875 34.615 0.00 0.00 34.80 1.75
818 2763 7.786464 ACCATTTTCCTTTCTGGCATAGATTAT 59.214 33.333 0.00 0.00 34.80 1.28
819 2764 8.302438 CCATTTTCCTTTCTGGCATAGATTATC 58.698 37.037 0.00 0.00 34.80 1.75
820 2765 8.853126 CATTTTCCTTTCTGGCATAGATTATCA 58.147 33.333 0.00 0.00 34.80 2.15
821 2766 9.597681 ATTTTCCTTTCTGGCATAGATTATCAT 57.402 29.630 0.00 0.00 34.80 2.45
822 2767 7.991084 TTCCTTTCTGGCATAGATTATCATG 57.009 36.000 0.00 0.00 34.80 3.07
823 2768 6.479006 TCCTTTCTGGCATAGATTATCATGG 58.521 40.000 0.00 0.00 34.80 3.66
824 2769 6.044754 TCCTTTCTGGCATAGATTATCATGGT 59.955 38.462 0.00 0.00 34.80 3.55
825 2770 6.373774 CCTTTCTGGCATAGATTATCATGGTC 59.626 42.308 0.00 0.00 34.80 4.02
826 2771 6.438186 TTCTGGCATAGATTATCATGGTCA 57.562 37.500 0.00 0.00 34.80 4.02
827 2772 5.798132 TCTGGCATAGATTATCATGGTCAC 58.202 41.667 0.00 0.00 0.00 3.67
828 2773 4.910195 TGGCATAGATTATCATGGTCACC 58.090 43.478 0.00 0.00 0.00 4.02
829 2774 4.350520 TGGCATAGATTATCATGGTCACCA 59.649 41.667 0.00 0.00 38.19 4.17
830 2775 5.163109 TGGCATAGATTATCATGGTCACCAA 60.163 40.000 0.00 0.00 36.95 3.67
831 2776 5.769662 GGCATAGATTATCATGGTCACCAAA 59.230 40.000 0.00 0.00 36.95 3.28
832 2777 6.265196 GGCATAGATTATCATGGTCACCAAAA 59.735 38.462 0.00 0.00 36.95 2.44
833 2778 7.039504 GGCATAGATTATCATGGTCACCAAAAT 60.040 37.037 0.00 0.00 36.95 1.82
834 2779 8.362639 GCATAGATTATCATGGTCACCAAAATT 58.637 33.333 0.00 0.00 36.95 1.82
835 2780 9.687210 CATAGATTATCATGGTCACCAAAATTG 57.313 33.333 0.00 0.00 36.95 2.32
851 2796 4.568152 AAATTGGATAGTTACATGCCGC 57.432 40.909 0.00 0.00 0.00 6.53
852 2797 2.700722 TTGGATAGTTACATGCCGCA 57.299 45.000 0.00 0.00 0.00 5.69
853 2798 2.238942 TGGATAGTTACATGCCGCAG 57.761 50.000 0.00 0.00 0.00 5.18
854 2799 0.868406 GGATAGTTACATGCCGCAGC 59.132 55.000 0.00 0.00 40.48 5.25
855 2800 0.868406 GATAGTTACATGCCGCAGCC 59.132 55.000 0.00 0.00 38.69 4.85
856 2801 0.180171 ATAGTTACATGCCGCAGCCA 59.820 50.000 0.00 0.00 38.69 4.75
857 2802 0.035915 TAGTTACATGCCGCAGCCAA 60.036 50.000 0.00 0.00 38.69 4.52
858 2803 1.137404 GTTACATGCCGCAGCCAAG 59.863 57.895 0.00 0.00 38.69 3.61
859 2804 1.002746 TTACATGCCGCAGCCAAGA 60.003 52.632 0.00 0.00 38.69 3.02
860 2805 0.607762 TTACATGCCGCAGCCAAGAA 60.608 50.000 0.00 0.00 38.69 2.52
861 2806 1.026182 TACATGCCGCAGCCAAGAAG 61.026 55.000 0.00 0.00 38.69 2.85
862 2807 2.042259 CATGCCGCAGCCAAGAAGA 61.042 57.895 0.00 0.00 38.69 2.87
863 2808 1.077212 ATGCCGCAGCCAAGAAGAT 60.077 52.632 0.00 0.00 38.69 2.40
864 2809 0.181114 ATGCCGCAGCCAAGAAGATA 59.819 50.000 0.00 0.00 38.69 1.98
865 2810 0.181114 TGCCGCAGCCAAGAAGATAT 59.819 50.000 0.00 0.00 38.69 1.63
866 2811 0.871057 GCCGCAGCCAAGAAGATATC 59.129 55.000 0.00 0.00 0.00 1.63
867 2812 1.811558 GCCGCAGCCAAGAAGATATCA 60.812 52.381 5.32 0.00 0.00 2.15
868 2813 2.564771 CCGCAGCCAAGAAGATATCAA 58.435 47.619 5.32 0.00 0.00 2.57
869 2814 2.945008 CCGCAGCCAAGAAGATATCAAA 59.055 45.455 5.32 0.00 0.00 2.69
870 2815 3.378112 CCGCAGCCAAGAAGATATCAAAA 59.622 43.478 5.32 0.00 0.00 2.44
871 2816 4.037208 CCGCAGCCAAGAAGATATCAAAAT 59.963 41.667 5.32 0.00 0.00 1.82
872 2817 5.450965 CCGCAGCCAAGAAGATATCAAAATT 60.451 40.000 5.32 0.00 0.00 1.82
873 2818 5.457799 CGCAGCCAAGAAGATATCAAAATTG 59.542 40.000 5.32 4.54 0.00 2.32
874 2819 5.751990 GCAGCCAAGAAGATATCAAAATTGG 59.248 40.000 17.83 17.83 38.95 3.16
875 2820 6.406177 GCAGCCAAGAAGATATCAAAATTGGA 60.406 38.462 22.81 0.00 38.35 3.53
876 2821 7.686127 GCAGCCAAGAAGATATCAAAATTGGAT 60.686 37.037 22.81 17.54 38.35 3.41
877 2822 8.853126 CAGCCAAGAAGATATCAAAATTGGATA 58.147 33.333 22.81 0.00 38.35 2.59
878 2823 9.075678 AGCCAAGAAGATATCAAAATTGGATAG 57.924 33.333 22.81 6.47 38.35 2.08
879 2824 8.854117 GCCAAGAAGATATCAAAATTGGATAGT 58.146 33.333 22.81 0.00 38.35 2.12
887 2832 9.846248 GATATCAAAATTGGATAGTTACATGCC 57.154 33.333 0.00 0.00 31.27 4.40
904 2849 3.641437 TGCCTTTGGTTCTGAATTTCG 57.359 42.857 0.00 0.00 0.00 3.46
1320 3267 5.934625 AGCGGTATTGTATGATCTTTCCATC 59.065 40.000 0.00 0.00 0.00 3.51
1326 3273 5.201713 TGTATGATCTTTCCATCTCGGTC 57.798 43.478 0.00 0.00 35.57 4.79
1397 3344 1.472480 AGGCCATACGTGTTGAAATGC 59.528 47.619 5.01 0.00 0.00 3.56
1407 3354 1.750206 TGTTGAAATGCGATCCATGGG 59.250 47.619 13.02 0.00 33.49 4.00
1556 3511 3.440522 GCAGTAGAATTCTTCCCAACACC 59.559 47.826 14.36 0.00 0.00 4.16
1603 3558 4.036852 GTGGTTGCTCAATTAAGGGCTATC 59.963 45.833 0.00 0.00 0.00 2.08
1869 3824 6.424812 TGAATGATGTGCTTAGATACATTCCG 59.575 38.462 0.00 0.00 40.35 4.30
1937 3893 2.433970 AGAGTTGCTCCTTCCATAGCTC 59.566 50.000 0.00 0.00 39.53 4.09
2119 4084 2.003301 GCAGTGCACTACTAGCTTTCC 58.997 52.381 21.20 0.00 37.60 3.13
2124 4091 4.642885 AGTGCACTACTAGCTTTCCTAGAG 59.357 45.833 20.16 0.00 45.30 2.43
2175 4150 1.405391 GCTTTTGCAACAACTGGGTGT 60.405 47.619 0.00 0.00 46.58 4.16
2207 4182 2.223340 CCATTTGCGGATGTCTTAGCAC 60.223 50.000 0.00 0.00 39.51 4.40
2219 4194 6.642950 GGATGTCTTAGCACTGTACATACATC 59.357 42.308 0.00 0.00 39.79 3.06
2222 4197 7.203218 TGTCTTAGCACTGTACATACATCATC 58.797 38.462 0.00 0.00 35.36 2.92
2223 4198 7.068716 TGTCTTAGCACTGTACATACATCATCT 59.931 37.037 0.00 0.00 35.36 2.90
2224 4199 8.568794 GTCTTAGCACTGTACATACATCATCTA 58.431 37.037 0.00 0.00 35.36 1.98
2226 4201 9.920133 CTTAGCACTGTACATACATCATCTATT 57.080 33.333 0.00 0.00 35.36 1.73
2361 4364 3.836949 ACACAAAATTTGAGGCTATGCG 58.163 40.909 13.19 0.00 0.00 4.73
2402 4415 3.435890 CCCACTGTTTCTGTTTCCCCTTA 60.436 47.826 0.00 0.00 0.00 2.69
2410 4423 4.153673 TCTGTTTCCCCTTACGACAAAA 57.846 40.909 0.00 0.00 0.00 2.44
2594 4611 3.181445 ACAGTTAGATGTTGACCAAGCCA 60.181 43.478 0.00 0.00 0.00 4.75
2612 4637 2.355513 GCCAGTTCATGACACTCCATCT 60.356 50.000 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 2.158652 TGGACTAGATAGACCGAGTGGG 60.159 54.545 0.00 0.00 40.33 4.61
9 10 3.210232 TGGACTAGATAGACCGAGTGG 57.790 52.381 0.00 0.00 40.33 4.00
10 11 4.035792 CAGTTGGACTAGATAGACCGAGTG 59.964 50.000 14.85 14.85 42.37 3.51
11 12 4.200874 CAGTTGGACTAGATAGACCGAGT 58.799 47.826 0.00 2.86 40.33 4.18
12 13 3.003897 GCAGTTGGACTAGATAGACCGAG 59.996 52.174 0.00 0.00 40.33 4.63
67 1984 1.783031 TAGCGAGGCGATTCGGAGAC 61.783 60.000 8.34 0.00 40.79 3.36
119 2036 2.715046 TGTACCTCACGAACGGAGTAT 58.285 47.619 0.00 0.00 45.00 2.12
132 2049 2.765135 GGGGAGGAACTAGTTGTACCTC 59.235 54.545 24.18 24.18 41.55 3.85
142 2059 0.714180 TGGCACTAGGGGAGGAACTA 59.286 55.000 0.00 0.00 41.55 2.24
151 2068 0.674895 GAGCACAAGTGGCACTAGGG 60.675 60.000 22.37 15.65 0.00 3.53
154 2071 0.321671 GAGGAGCACAAGTGGCACTA 59.678 55.000 22.37 0.00 0.00 2.74
167 2084 1.398692 AAGAGGAGACATCGAGGAGC 58.601 55.000 3.06 0.00 0.00 4.70
253 2176 0.318107 CCACGAAGCCTGCAAAGTTG 60.318 55.000 0.00 0.00 0.00 3.16
261 2184 1.746615 CATGGACCCACGAAGCCTG 60.747 63.158 0.00 0.00 0.00 4.85
310 2234 0.109342 AGTCAGAGTGTGCCCAAAGG 59.891 55.000 0.00 0.00 0.00 3.11
340 2264 1.153978 AGCGCGAATTTACGGACGA 60.154 52.632 12.10 0.00 0.00 4.20
345 2269 2.026990 GTAATGCAGCGCGAATTTACG 58.973 47.619 12.10 0.00 0.00 3.18
375 2299 4.444306 CCACTCCCTCTGTTCAACAAACTA 60.444 45.833 0.00 0.00 38.76 2.24
392 2316 8.452534 CGAGATCTTATATTACACTACCACTCC 58.547 40.741 0.00 0.00 0.00 3.85
394 2318 8.921353 ACGAGATCTTATATTACACTACCACT 57.079 34.615 0.00 0.00 0.00 4.00
417 2341 7.911205 CCTCTGAAAACTAAGTGATCTACTACG 59.089 40.741 0.00 0.00 39.18 3.51
448 2372 5.340439 AGCTTGTACTCCATTACACTACC 57.660 43.478 0.00 0.00 31.53 3.18
459 2383 2.162408 GCCACATGAAAGCTTGTACTCC 59.838 50.000 0.00 0.00 31.87 3.85
460 2384 2.159653 CGCCACATGAAAGCTTGTACTC 60.160 50.000 0.00 0.00 31.87 2.59
529 2453 8.850452 CAGAGTTCTACACAAAAAGTCAAAAAC 58.150 33.333 0.00 0.00 0.00 2.43
530 2454 8.788806 TCAGAGTTCTACACAAAAAGTCAAAAA 58.211 29.630 0.00 0.00 0.00 1.94
531 2455 8.330466 TCAGAGTTCTACACAAAAAGTCAAAA 57.670 30.769 0.00 0.00 0.00 2.44
532 2456 7.915293 TCAGAGTTCTACACAAAAAGTCAAA 57.085 32.000 0.00 0.00 0.00 2.69
533 2457 7.768582 TGATCAGAGTTCTACACAAAAAGTCAA 59.231 33.333 0.00 0.00 0.00 3.18
534 2458 7.272244 TGATCAGAGTTCTACACAAAAAGTCA 58.728 34.615 0.00 0.00 0.00 3.41
535 2459 7.715265 TGATCAGAGTTCTACACAAAAAGTC 57.285 36.000 0.00 0.00 0.00 3.01
536 2460 8.682936 AATGATCAGAGTTCTACACAAAAAGT 57.317 30.769 0.09 0.00 0.00 2.66
550 2474 6.014413 CCATCCAGACAGATAATGATCAGAGT 60.014 42.308 0.09 0.00 34.17 3.24
615 2539 2.764572 CCTGATACTCCAAAGTACCGGT 59.235 50.000 13.98 13.98 40.74 5.28
617 2541 3.446161 TGTCCTGATACTCCAAAGTACCG 59.554 47.826 0.00 0.00 40.74 4.02
675 2599 2.841881 ACGGGCTTCCTACTAAATGGAA 59.158 45.455 0.00 0.00 39.73 3.53
676 2600 2.169769 CACGGGCTTCCTACTAAATGGA 59.830 50.000 0.00 0.00 0.00 3.41
677 2601 2.561569 CACGGGCTTCCTACTAAATGG 58.438 52.381 0.00 0.00 0.00 3.16
678 2602 1.940613 GCACGGGCTTCCTACTAAATG 59.059 52.381 0.00 0.00 36.96 2.32
679 2603 1.134189 GGCACGGGCTTCCTACTAAAT 60.134 52.381 10.74 0.00 40.87 1.40
680 2604 0.251073 GGCACGGGCTTCCTACTAAA 59.749 55.000 10.74 0.00 40.87 1.85
681 2605 1.619807 GGGCACGGGCTTCCTACTAA 61.620 60.000 10.74 0.00 40.87 2.24
682 2606 2.062177 GGGCACGGGCTTCCTACTA 61.062 63.158 10.74 0.00 40.87 1.82
683 2607 3.400054 GGGCACGGGCTTCCTACT 61.400 66.667 10.74 0.00 40.87 2.57
684 2608 4.832608 CGGGCACGGGCTTCCTAC 62.833 72.222 10.74 0.00 40.87 3.18
685 2609 3.961225 TACGGGCACGGGCTTCCTA 62.961 63.158 15.46 0.00 46.48 2.94
692 2616 4.770874 CAAGGGTACGGGCACGGG 62.771 72.222 15.46 0.00 46.48 5.28
693 2617 4.011517 ACAAGGGTACGGGCACGG 62.012 66.667 15.46 0.00 46.48 4.94
695 2619 0.390735 CTACACAAGGGTACGGGCAC 60.391 60.000 0.00 0.00 0.00 5.01
722 2667 4.254492 GACTGAAAGACTCCCACCAATAC 58.746 47.826 0.00 0.00 37.43 1.89
724 2669 2.289694 CGACTGAAAGACTCCCACCAAT 60.290 50.000 0.00 0.00 37.43 3.16
781 2726 4.861102 AGGAAAATGGTCAAAGCAAGAG 57.139 40.909 0.00 0.00 0.00 2.85
792 2737 4.934356 TCTATGCCAGAAAGGAAAATGGT 58.066 39.130 0.00 0.00 41.22 3.55
795 2740 9.597681 ATGATAATCTATGCCAGAAAGGAAAAT 57.402 29.630 0.00 0.00 41.22 1.82
797 2742 7.449395 CCATGATAATCTATGCCAGAAAGGAAA 59.551 37.037 0.00 0.00 41.22 3.13
799 2744 6.044754 ACCATGATAATCTATGCCAGAAAGGA 59.955 38.462 0.00 0.00 41.22 3.36
800 2745 6.243900 ACCATGATAATCTATGCCAGAAAGG 58.756 40.000 0.00 0.00 36.67 3.11
801 2746 6.938596 TGACCATGATAATCTATGCCAGAAAG 59.061 38.462 0.00 0.00 36.67 2.62
802 2747 6.712095 GTGACCATGATAATCTATGCCAGAAA 59.288 38.462 0.00 0.00 36.67 2.52
803 2748 6.233434 GTGACCATGATAATCTATGCCAGAA 58.767 40.000 0.00 0.00 36.67 3.02
804 2749 5.280164 GGTGACCATGATAATCTATGCCAGA 60.280 44.000 0.00 0.00 37.79 3.86
806 2751 4.350520 TGGTGACCATGATAATCTATGCCA 59.649 41.667 0.00 0.00 0.00 4.92
807 2752 4.910195 TGGTGACCATGATAATCTATGCC 58.090 43.478 0.00 0.00 0.00 4.40
809 2754 9.687210 CAATTTTGGTGACCATGATAATCTATG 57.313 33.333 4.56 0.00 31.53 2.23
812 2757 7.116075 CCAATTTTGGTGACCATGATAATCT 57.884 36.000 4.56 0.00 43.43 2.40
828 2773 4.739716 GCGGCATGTAACTATCCAATTTTG 59.260 41.667 0.00 0.00 0.00 2.44
829 2774 4.400884 TGCGGCATGTAACTATCCAATTTT 59.599 37.500 0.00 0.00 0.00 1.82
830 2775 3.951037 TGCGGCATGTAACTATCCAATTT 59.049 39.130 0.00 0.00 0.00 1.82
831 2776 3.550820 TGCGGCATGTAACTATCCAATT 58.449 40.909 0.00 0.00 0.00 2.32
832 2777 3.141398 CTGCGGCATGTAACTATCCAAT 58.859 45.455 1.75 0.00 0.00 3.16
833 2778 2.560504 CTGCGGCATGTAACTATCCAA 58.439 47.619 1.75 0.00 0.00 3.53
834 2779 1.810031 GCTGCGGCATGTAACTATCCA 60.810 52.381 14.08 0.00 38.54 3.41
835 2780 0.868406 GCTGCGGCATGTAACTATCC 59.132 55.000 14.08 0.00 38.54 2.59
836 2781 0.868406 GGCTGCGGCATGTAACTATC 59.132 55.000 21.31 0.00 40.87 2.08
837 2782 0.180171 TGGCTGCGGCATGTAACTAT 59.820 50.000 21.31 0.00 40.87 2.12
838 2783 0.035915 TTGGCTGCGGCATGTAACTA 60.036 50.000 21.31 0.00 38.08 2.24
839 2784 1.303236 TTGGCTGCGGCATGTAACT 60.303 52.632 21.31 0.00 38.08 2.24
840 2785 1.137404 CTTGGCTGCGGCATGTAAC 59.863 57.895 21.31 0.39 38.08 2.50
841 2786 0.607762 TTCTTGGCTGCGGCATGTAA 60.608 50.000 21.31 7.65 38.08 2.41
842 2787 1.002746 TTCTTGGCTGCGGCATGTA 60.003 52.632 21.31 6.54 38.08 2.29
843 2788 2.282391 TTCTTGGCTGCGGCATGT 60.282 55.556 21.31 0.00 38.08 3.21
844 2789 1.381928 ATCTTCTTGGCTGCGGCATG 61.382 55.000 21.31 14.48 38.08 4.06
845 2790 0.181114 TATCTTCTTGGCTGCGGCAT 59.819 50.000 21.31 4.58 38.08 4.40
846 2791 0.181114 ATATCTTCTTGGCTGCGGCA 59.819 50.000 21.31 10.39 40.87 5.69
847 2792 0.871057 GATATCTTCTTGGCTGCGGC 59.129 55.000 9.72 9.72 37.82 6.53
848 2793 2.245159 TGATATCTTCTTGGCTGCGG 57.755 50.000 3.98 0.00 0.00 5.69
849 2794 4.621068 TTTTGATATCTTCTTGGCTGCG 57.379 40.909 3.98 0.00 0.00 5.18
850 2795 5.751990 CCAATTTTGATATCTTCTTGGCTGC 59.248 40.000 3.98 0.00 0.00 5.25
851 2796 7.104043 TCCAATTTTGATATCTTCTTGGCTG 57.896 36.000 15.91 2.02 33.36 4.85
852 2797 7.909485 ATCCAATTTTGATATCTTCTTGGCT 57.091 32.000 15.91 8.60 33.36 4.75
853 2798 8.854117 ACTATCCAATTTTGATATCTTCTTGGC 58.146 33.333 15.91 0.00 33.36 4.52
861 2806 9.846248 GGCATGTAACTATCCAATTTTGATATC 57.154 33.333 0.00 0.00 0.00 1.63
862 2807 9.592196 AGGCATGTAACTATCCAATTTTGATAT 57.408 29.630 0.00 0.00 0.00 1.63
863 2808 8.995027 AGGCATGTAACTATCCAATTTTGATA 57.005 30.769 0.00 0.00 0.00 2.15
864 2809 7.902920 AGGCATGTAACTATCCAATTTTGAT 57.097 32.000 0.00 0.00 0.00 2.57
865 2810 7.716799 AAGGCATGTAACTATCCAATTTTGA 57.283 32.000 0.00 0.00 0.00 2.69
866 2811 7.278424 CCAAAGGCATGTAACTATCCAATTTTG 59.722 37.037 0.00 0.00 0.00 2.44
867 2812 7.038373 ACCAAAGGCATGTAACTATCCAATTTT 60.038 33.333 0.00 0.00 0.00 1.82
868 2813 6.440328 ACCAAAGGCATGTAACTATCCAATTT 59.560 34.615 0.00 0.00 0.00 1.82
869 2814 5.957774 ACCAAAGGCATGTAACTATCCAATT 59.042 36.000 0.00 0.00 0.00 2.32
870 2815 5.518865 ACCAAAGGCATGTAACTATCCAAT 58.481 37.500 0.00 0.00 0.00 3.16
871 2816 4.929479 ACCAAAGGCATGTAACTATCCAA 58.071 39.130 0.00 0.00 0.00 3.53
872 2817 4.584638 ACCAAAGGCATGTAACTATCCA 57.415 40.909 0.00 0.00 0.00 3.41
873 2818 5.066505 CAGAACCAAAGGCATGTAACTATCC 59.933 44.000 0.00 0.00 0.00 2.59
874 2819 5.880332 TCAGAACCAAAGGCATGTAACTATC 59.120 40.000 0.00 0.00 0.00 2.08
875 2820 5.815581 TCAGAACCAAAGGCATGTAACTAT 58.184 37.500 0.00 0.00 0.00 2.12
876 2821 5.235850 TCAGAACCAAAGGCATGTAACTA 57.764 39.130 0.00 0.00 0.00 2.24
877 2822 4.098914 TCAGAACCAAAGGCATGTAACT 57.901 40.909 0.00 0.00 0.00 2.24
878 2823 4.846779 TTCAGAACCAAAGGCATGTAAC 57.153 40.909 0.00 0.00 0.00 2.50
879 2824 6.418057 AAATTCAGAACCAAAGGCATGTAA 57.582 33.333 0.00 0.00 0.00 2.41
880 2825 5.335583 CGAAATTCAGAACCAAAGGCATGTA 60.336 40.000 0.00 0.00 0.00 2.29
881 2826 4.559300 CGAAATTCAGAACCAAAGGCATGT 60.559 41.667 0.00 0.00 0.00 3.21
882 2827 3.922240 CGAAATTCAGAACCAAAGGCATG 59.078 43.478 0.00 0.00 0.00 4.06
883 2828 3.826157 TCGAAATTCAGAACCAAAGGCAT 59.174 39.130 0.00 0.00 0.00 4.40
884 2829 3.218453 TCGAAATTCAGAACCAAAGGCA 58.782 40.909 0.00 0.00 0.00 4.75
885 2830 3.915437 TCGAAATTCAGAACCAAAGGC 57.085 42.857 0.00 0.00 0.00 4.35
886 2831 5.181690 TGTTCGAAATTCAGAACCAAAGG 57.818 39.130 19.64 0.00 44.30 3.11
887 2832 7.698836 AAATGTTCGAAATTCAGAACCAAAG 57.301 32.000 19.64 0.00 44.30 2.77
904 2849 4.692228 TGTTGCCAGAAAGGAAAATGTTC 58.308 39.130 0.00 0.00 36.38 3.18
1122 3067 4.220382 TGCATTTCCAATCTGTAACCAAGG 59.780 41.667 0.00 0.00 0.00 3.61
1123 3068 5.389859 TGCATTTCCAATCTGTAACCAAG 57.610 39.130 0.00 0.00 0.00 3.61
1127 3074 5.063817 GGCAAATGCATTTCCAATCTGTAAC 59.936 40.000 21.70 2.11 44.36 2.50
1320 3267 4.600012 AAATGCTCAATTTACGACCGAG 57.400 40.909 0.00 0.00 36.69 4.63
1326 3273 8.540492 CCACTACTACTAAATGCTCAATTTACG 58.460 37.037 0.00 0.00 39.29 3.18
1379 3326 1.129624 TCGCATTTCAACACGTATGGC 59.870 47.619 0.00 0.00 0.00 4.40
1397 3344 1.432514 CTAACGATGCCCATGGATCG 58.567 55.000 26.12 26.12 45.58 3.69
1407 3354 3.303395 GCACATCCTTTAGCTAACGATGC 60.303 47.826 27.54 19.34 0.00 3.91
1480 3435 7.867403 ACAAAATGATGTTGTATCACAAGGTTC 59.133 33.333 0.00 0.00 39.00 3.62
1556 3511 9.227490 CACGTATTAGACAAATAAGAGAGACAG 57.773 37.037 0.00 0.00 34.66 3.51
1603 3558 4.862574 TCGATTAGAACCAATCAAGTGACG 59.137 41.667 0.00 0.00 35.09 4.35
1869 3824 8.919777 ATTAATATTAGTTACCTGGCTCAACC 57.080 34.615 0.00 0.00 39.84 3.77
1984 3940 7.770897 AGAAATAATCTATCAACGGAAGCACTT 59.229 33.333 0.00 0.00 36.32 3.16
2119 4084 9.853555 CTATAGATGGATAAACTTGCACTCTAG 57.146 37.037 0.00 0.00 0.00 2.43
2152 4127 2.289945 ACCCAGTTGTTGCAAAAGCAAA 60.290 40.909 0.00 0.00 0.00 3.68
2168 4143 2.374184 TGGTCAACTTTTCACACCCAG 58.626 47.619 0.00 0.00 0.00 4.45
2175 4150 2.690497 TCCGCAAATGGTCAACTTTTCA 59.310 40.909 0.00 0.00 0.00 2.69
2186 4161 2.016318 TGCTAAGACATCCGCAAATGG 58.984 47.619 0.90 0.00 0.00 3.16
2207 4182 9.723447 GTCCGATAATAGATGATGTATGTACAG 57.277 37.037 0.33 0.00 39.92 2.74
2219 4194 8.353684 AGTTGTCTACTTGTCCGATAATAGATG 58.646 37.037 0.00 0.00 31.29 2.90
2222 4197 7.704271 TCAGTTGTCTACTTGTCCGATAATAG 58.296 38.462 0.00 0.00 33.85 1.73
2223 4198 7.634671 TCAGTTGTCTACTTGTCCGATAATA 57.365 36.000 0.00 0.00 33.85 0.98
2224 4199 6.525578 TCAGTTGTCTACTTGTCCGATAAT 57.474 37.500 0.00 0.00 33.85 1.28
2226 4201 5.970317 TTCAGTTGTCTACTTGTCCGATA 57.030 39.130 0.00 0.00 33.85 2.92
2263 4260 7.989170 ACATGCACATATAGTCTTTTGAGATGA 59.011 33.333 0.00 0.00 0.00 2.92
2299 4296 7.796054 TGTTTCCCAGAATAAAAATTTGTCCA 58.204 30.769 0.00 0.00 0.00 4.02
2300 4297 8.310406 CTGTTTCCCAGAATAAAAATTTGTCC 57.690 34.615 0.00 0.00 44.49 4.02
2361 4364 1.198637 GGTGTGACTGAAAGCTGCATC 59.801 52.381 1.02 0.00 37.60 3.91
2402 4415 4.554723 CGGAAAGAGAAGCAATTTTGTCGT 60.555 41.667 0.00 0.00 0.00 4.34
2410 4423 4.821805 TGTTTCTTCGGAAAGAGAAGCAAT 59.178 37.500 5.36 0.00 43.56 3.56
2594 4611 2.570752 AGCAGATGGAGTGTCATGAACT 59.429 45.455 0.00 3.51 0.00 3.01
2835 4865 3.223435 GACGCACAACACGCCTGTC 62.223 63.158 0.00 0.00 0.00 3.51
2891 4921 3.598715 AAGCGGTCGACGTGGTCA 61.599 61.111 9.92 0.00 46.52 4.02


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

AutoCloner maintained by Alex Coulton.