Multiple sequence alignment - TraesCS1A01G293400

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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 TraesCS1A01G293400 chr1A 100.000 3303 0 0 1 3303 488618059 488621361 0.000000e+00 6100.0
1 TraesCS1A01G293400 chr1A 97.230 1372 33 3 1932 3303 590673218 590671852 0.000000e+00 2318.0
2 TraesCS1A01G293400 chr1A 84.321 759 102 10 1945 2700 525030546 525031290 0.000000e+00 726.0
3 TraesCS1A01G293400 chr1A 93.708 445 27 1 2859 3303 525039884 525040327 0.000000e+00 665.0
4 TraesCS1A01G293400 chr1A 88.053 226 27 0 2214 2439 525030862 525031087 5.430000e-68 268.0
5 TraesCS1A01G293400 chr1A 95.364 151 6 1 1931 2080 590649464 590649614 4.260000e-59 239.0
6 TraesCS1A01G293400 chr1A 92.617 149 11 0 1932 2080 525044135 525043987 7.180000e-52 215.0
7 TraesCS1A01G293400 chr7A 96.725 1374 43 1 1930 3303 92425570 92424199 0.000000e+00 2287.0
8 TraesCS1A01G293400 chr7A 93.056 144 9 1 1938 2080 92420343 92420486 3.340000e-50 209.0
9 TraesCS1A01G293400 chr7A 83.562 219 34 2 2281 2498 92425278 92425061 1.550000e-48 204.0
10 TraesCS1A01G293400 chr5A 93.596 1140 56 3 1932 3055 41393257 41392119 0.000000e+00 1685.0
11 TraesCS1A01G293400 chr5A 93.591 1139 56 3 1933 3055 41391096 41389959 0.000000e+00 1683.0
12 TraesCS1A01G293400 chr5A 95.669 254 11 0 3050 3303 41389760 41389507 3.070000e-110 409.0
13 TraesCS1A01G293400 chr5A 95.669 254 11 0 3050 3303 41391920 41391667 3.070000e-110 409.0
14 TraesCS1A01G293400 chr1B 90.370 1298 61 28 670 1937 525910290 525909027 0.000000e+00 1646.0
15 TraesCS1A01G293400 chr3A 93.846 845 44 2 1925 2769 26151726 26152562 0.000000e+00 1266.0
16 TraesCS1A01G293400 chr3A 83.282 969 104 26 2339 3303 732973939 732974853 0.000000e+00 839.0
17 TraesCS1A01G293400 chr3A 91.515 165 6 5 2751 2908 26153673 26153836 1.540000e-53 220.0
18 TraesCS1A01G293400 chr3A 82.192 219 37 2 2281 2498 26152022 26152239 1.560000e-43 187.0
19 TraesCS1A01G293400 chr3A 88.679 53 6 0 510 562 728069518 728069570 7.650000e-07 65.8
20 TraesCS1A01G293400 chr6A 95.213 564 24 3 1 562 457317472 457318034 0.000000e+00 889.0
21 TraesCS1A01G293400 chr6A 90.018 571 37 7 1 552 512826015 512826584 0.000000e+00 721.0
22 TraesCS1A01G293400 chr6A 92.354 497 33 5 1 495 596601713 596602206 0.000000e+00 702.0
23 TraesCS1A01G293400 chr6A 95.148 371 14 3 1 371 50405497 50405863 1.710000e-162 582.0
24 TraesCS1A01G293400 chr6A 94.609 371 15 3 1 371 50462097 50462462 1.330000e-158 569.0
25 TraesCS1A01G293400 chr6A 85.492 193 10 10 369 561 50407693 50407867 5.630000e-43 185.0
26 TraesCS1A01G293400 chr6A 84.974 193 11 10 369 561 50464285 50464459 2.620000e-41 180.0
27 TraesCS1A01G293400 chr2D 92.322 534 31 5 1 532 545768057 545767532 0.000000e+00 750.0
28 TraesCS1A01G293400 chr2D 93.785 354 15 5 1 352 79536880 79536532 2.920000e-145 525.0
29 TraesCS1A01G293400 chr5D 93.750 496 24 6 1 495 454270079 454269590 0.000000e+00 737.0
30 TraesCS1A01G293400 chr5D 82.463 536 62 18 2785 3303 228504841 228504321 1.090000e-119 440.0
31 TraesCS1A01G293400 chr7D 92.944 496 28 6 1 494 558893574 558893084 0.000000e+00 715.0
32 TraesCS1A01G293400 chr6B 81.766 872 119 26 2348 3198 351227954 351228806 0.000000e+00 693.0
33 TraesCS1A01G293400 chr6B 85.921 277 33 4 3033 3303 351228584 351228860 1.160000e-74 291.0
34 TraesCS1A01G293400 chr6B 89.899 198 19 1 2233 2429 351227955 351228152 1.520000e-63 254.0
35 TraesCS1A01G293400 chr6B 84.211 247 37 2 2290 2535 351227954 351228199 4.260000e-59 239.0
36 TraesCS1A01G293400 chr4B 86.921 604 67 5 2583 3177 562691297 562691897 0.000000e+00 667.0
37 TraesCS1A01G293400 chr4B 90.244 246 22 2 1931 2174 562686457 562686702 1.480000e-83 320.0
38 TraesCS1A01G293400 chr4B 81.267 363 54 11 1581 1934 53863705 53863348 6.980000e-72 281.0
39 TraesCS1A01G293400 chr4B 89.140 221 18 4 3089 3303 562691701 562691921 1.510000e-68 270.0
40 TraesCS1A01G293400 chr4B 95.425 153 7 0 339 491 5973276 5973428 9.160000e-61 244.0
41 TraesCS1A01G293400 chr4B 86.624 157 15 2 989 1139 53864284 53864128 5.670000e-38 169.0
42 TraesCS1A01G293400 chr4A 89.414 444 40 5 985 1422 565430202 565430644 1.340000e-153 553.0
43 TraesCS1A01G293400 chr4D 89.245 437 44 1 989 1422 36843795 36843359 8.060000e-151 544.0
44 TraesCS1A01G293400 chr4D 82.073 357 59 5 1581 1934 36843199 36842845 1.930000e-77 300.0
45 TraesCS1A01G293400 chr2A 81.733 427 58 16 2889 3303 88731760 88732178 4.080000e-89 339.0
46 TraesCS1A01G293400 chr2A 93.333 210 13 1 1931 2139 4908151 4908360 3.200000e-80 309.0


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 TraesCS1A01G293400 chr1A 488618059 488621361 3302 False 6100.000000 6100 100.000000 1 3303 1 chr1A.!!$F1 3302
1 TraesCS1A01G293400 chr1A 590671852 590673218 1366 True 2318.000000 2318 97.230000 1932 3303 1 chr1A.!!$R2 1371
2 TraesCS1A01G293400 chr1A 525030546 525031290 744 False 497.000000 726 86.187000 1945 2700 2 chr1A.!!$F4 755
3 TraesCS1A01G293400 chr7A 92424199 92425570 1371 True 1245.500000 2287 90.143500 1930 3303 2 chr7A.!!$R1 1373
4 TraesCS1A01G293400 chr5A 41389507 41393257 3750 True 1046.500000 1685 94.631250 1932 3303 4 chr5A.!!$R1 1371
5 TraesCS1A01G293400 chr1B 525909027 525910290 1263 True 1646.000000 1646 90.370000 670 1937 1 chr1B.!!$R1 1267
6 TraesCS1A01G293400 chr3A 732973939 732974853 914 False 839.000000 839 83.282000 2339 3303 1 chr3A.!!$F2 964
7 TraesCS1A01G293400 chr3A 26151726 26153836 2110 False 557.666667 1266 89.184333 1925 2908 3 chr3A.!!$F3 983
8 TraesCS1A01G293400 chr6A 457317472 457318034 562 False 889.000000 889 95.213000 1 562 1 chr6A.!!$F1 561
9 TraesCS1A01G293400 chr6A 512826015 512826584 569 False 721.000000 721 90.018000 1 552 1 chr6A.!!$F2 551
10 TraesCS1A01G293400 chr6A 50405497 50407867 2370 False 383.500000 582 90.320000 1 561 2 chr6A.!!$F4 560
11 TraesCS1A01G293400 chr6A 50462097 50464459 2362 False 374.500000 569 89.791500 1 561 2 chr6A.!!$F5 560
12 TraesCS1A01G293400 chr2D 545767532 545768057 525 True 750.000000 750 92.322000 1 532 1 chr2D.!!$R2 531
13 TraesCS1A01G293400 chr5D 228504321 228504841 520 True 440.000000 440 82.463000 2785 3303 1 chr5D.!!$R1 518
14 TraesCS1A01G293400 chr6B 351227954 351228860 906 False 369.250000 693 85.449250 2233 3303 4 chr6B.!!$F1 1070
15 TraesCS1A01G293400 chr4B 562691297 562691921 624 False 468.500000 667 88.030500 2583 3303 2 chr4B.!!$F3 720
16 TraesCS1A01G293400 chr4B 53863348 53864284 936 True 225.000000 281 83.945500 989 1934 2 chr4B.!!$R1 945
17 TraesCS1A01G293400 chr4D 36842845 36843795 950 True 422.000000 544 85.659000 989 1934 2 chr4D.!!$R1 945

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
666 2532 0.030909 TGGCCCGTCCCCTCTTATTA 60.031 55.0 0.0 0.0 0.0 0.98 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2432 6772 1.228245 GGCTGCAACCTCAGGAACA 60.228 57.895 0.0 0.0 34.74 3.18 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
135 140 1.573108 TGGGACAGATGAAGGGAGAC 58.427 55.000 0.00 0.00 0.00 3.36
217 222 4.868734 GGTGTCCGTTAAGTCTTCCTATTG 59.131 45.833 0.00 0.00 0.00 1.90
227 232 4.282496 AGTCTTCCTATTGTCCACGATCT 58.718 43.478 0.00 0.00 0.00 2.75
255 284 3.904136 ACAAGCAACGATCCTCAAAAG 57.096 42.857 0.00 0.00 0.00 2.27
262 294 7.214467 AGCAACGATCCTCAAAAGAAAAATA 57.786 32.000 0.00 0.00 0.00 1.40
302 334 3.578282 GGCAAGAAAAATGGAAGAAGGGA 59.422 43.478 0.00 0.00 0.00 4.20
317 349 1.227615 GGGACCAACGAACCAACGA 60.228 57.895 0.00 0.00 37.03 3.85
401 2267 1.609555 GGACAGAGACTTGAGACACGT 59.390 52.381 0.00 0.00 0.00 4.49
594 2460 9.668497 AGGACTACATTAAAGTGTTCCTATTTC 57.332 33.333 11.39 0.00 37.50 2.17
595 2461 8.601476 GGACTACATTAAAGTGTTCCTATTTCG 58.399 37.037 0.00 0.00 33.62 3.46
596 2462 9.148104 GACTACATTAAAGTGTTCCTATTTCGT 57.852 33.333 0.00 0.00 33.62 3.85
607 2473 9.584008 AGTGTTCCTATTTCGTATAGGATAAGA 57.416 33.333 21.49 10.23 46.70 2.10
608 2474 9.623350 GTGTTCCTATTTCGTATAGGATAAGAC 57.377 37.037 21.49 17.90 46.70 3.01
609 2475 8.800332 TGTTCCTATTTCGTATAGGATAAGACC 58.200 37.037 21.49 11.23 46.70 3.85
610 2476 9.022884 GTTCCTATTTCGTATAGGATAAGACCT 57.977 37.037 21.49 0.00 46.70 3.85
611 2477 8.577048 TCCTATTTCGTATAGGATAAGACCTG 57.423 38.462 18.76 0.00 43.71 4.00
612 2478 7.614583 TCCTATTTCGTATAGGATAAGACCTGG 59.385 40.741 18.76 0.00 43.71 4.45
613 2479 7.396623 CCTATTTCGTATAGGATAAGACCTGGT 59.603 40.741 16.49 0.00 42.90 4.00
614 2480 6.401047 TTTCGTATAGGATAAGACCTGGTG 57.599 41.667 2.82 0.00 40.81 4.17
615 2481 5.057843 TCGTATAGGATAAGACCTGGTGT 57.942 43.478 2.82 0.00 40.81 4.16
616 2482 5.068636 TCGTATAGGATAAGACCTGGTGTC 58.931 45.833 2.82 0.00 44.82 3.67
617 2483 4.217983 CGTATAGGATAAGACCTGGTGTCC 59.782 50.000 2.82 6.56 45.68 4.02
618 2484 1.486211 AGGATAAGACCTGGTGTCCG 58.514 55.000 2.82 0.00 45.68 4.79
619 2485 1.006758 AGGATAAGACCTGGTGTCCGA 59.993 52.381 2.82 0.00 45.68 4.55
620 2486 1.136500 GGATAAGACCTGGTGTCCGAC 59.864 57.143 2.82 0.00 45.68 4.79
621 2487 1.822990 GATAAGACCTGGTGTCCGACA 59.177 52.381 2.82 0.00 45.68 4.35
637 2503 2.972505 CACGGTGTGTGTCAGCCC 60.973 66.667 0.00 0.00 43.88 5.19
638 2504 4.250305 ACGGTGTGTGTCAGCCCC 62.250 66.667 0.00 0.00 40.98 5.80
639 2505 4.248842 CGGTGTGTGTCAGCCCCA 62.249 66.667 0.00 0.00 40.98 4.96
640 2506 2.281761 GGTGTGTGTCAGCCCCAG 60.282 66.667 0.00 0.00 38.46 4.45
641 2507 2.980233 GTGTGTGTCAGCCCCAGC 60.980 66.667 0.00 0.00 40.32 4.85
642 2508 4.269523 TGTGTGTCAGCCCCAGCC 62.270 66.667 0.00 0.00 41.25 4.85
663 2529 2.686106 GTGGCCCGTCCCCTCTTA 60.686 66.667 0.00 0.00 0.00 2.10
664 2530 2.070650 GTGGCCCGTCCCCTCTTAT 61.071 63.158 0.00 0.00 0.00 1.73
665 2531 1.307517 TGGCCCGTCCCCTCTTATT 60.308 57.895 0.00 0.00 0.00 1.40
666 2532 0.030909 TGGCCCGTCCCCTCTTATTA 60.031 55.000 0.00 0.00 0.00 0.98
667 2533 1.134228 GGCCCGTCCCCTCTTATTAA 58.866 55.000 0.00 0.00 0.00 1.40
668 2534 1.491754 GGCCCGTCCCCTCTTATTAAA 59.508 52.381 0.00 0.00 0.00 1.52
700 2566 2.041686 GTCTCTCCGGCTCTCACGT 61.042 63.158 0.00 0.00 0.00 4.49
720 2586 3.305064 CGTCCAAACCCATTGTTTACTGG 60.305 47.826 0.00 0.00 45.35 4.00
726 2592 1.529226 CCATTGTTTACTGGCGTCCA 58.471 50.000 0.00 0.00 0.00 4.02
727 2593 1.199097 CCATTGTTTACTGGCGTCCAC 59.801 52.381 0.00 0.00 0.00 4.02
728 2594 1.876799 CATTGTTTACTGGCGTCCACA 59.123 47.619 0.00 0.00 0.00 4.17
729 2595 2.039818 TTGTTTACTGGCGTCCACAA 57.960 45.000 0.00 0.00 0.00 3.33
731 2597 2.577700 TGTTTACTGGCGTCCACAAAT 58.422 42.857 0.00 0.00 0.00 2.32
760 2627 1.142748 CTCTTCGGCAGGTGCTAGG 59.857 63.158 1.26 0.00 41.70 3.02
761 2628 2.512515 CTTCGGCAGGTGCTAGGC 60.513 66.667 1.26 0.00 41.70 3.93
814 2696 2.663196 CTCCAAGGTGTCCCGTCC 59.337 66.667 0.00 0.00 35.12 4.79
816 2698 4.029809 CCAAGGTGTCCCGTCCCC 62.030 72.222 0.00 0.00 35.12 4.81
817 2699 4.029809 CAAGGTGTCCCGTCCCCC 62.030 72.222 0.00 0.00 35.12 5.40
818 2700 4.265507 AAGGTGTCCCGTCCCCCT 62.266 66.667 0.00 0.00 35.12 4.79
819 2701 4.716977 AGGTGTCCCGTCCCCCTC 62.717 72.222 0.00 0.00 35.12 4.30
833 2715 1.269831 CCCCCTCGCGATTTCTTCTAG 60.270 57.143 10.36 0.00 0.00 2.43
835 2717 2.621998 CCCCTCGCGATTTCTTCTAGTA 59.378 50.000 10.36 0.00 0.00 1.82
836 2718 3.256136 CCCCTCGCGATTTCTTCTAGTAT 59.744 47.826 10.36 0.00 0.00 2.12
837 2719 4.477780 CCCTCGCGATTTCTTCTAGTATC 58.522 47.826 10.36 0.00 0.00 2.24
839 2721 5.150683 CCTCGCGATTTCTTCTAGTATCTG 58.849 45.833 10.36 0.00 0.00 2.90
840 2722 5.109662 TCGCGATTTCTTCTAGTATCTGG 57.890 43.478 3.71 0.00 0.00 3.86
865 2756 4.273257 GCCCTAGCTCCTCGCGAC 62.273 72.222 3.71 0.00 45.59 5.19
870 2761 0.524392 CTAGCTCCTCGCGACTGTTG 60.524 60.000 3.71 0.00 45.59 3.33
871 2762 1.241990 TAGCTCCTCGCGACTGTTGT 61.242 55.000 3.71 0.00 45.59 3.32
872 2763 1.664965 GCTCCTCGCGACTGTTGTT 60.665 57.895 3.71 0.00 0.00 2.83
873 2764 1.891060 GCTCCTCGCGACTGTTGTTG 61.891 60.000 3.71 0.00 0.00 3.33
874 2765 1.284982 CTCCTCGCGACTGTTGTTGG 61.285 60.000 3.71 1.82 0.00 3.77
875 2766 1.594293 CCTCGCGACTGTTGTTGGT 60.594 57.895 3.71 0.00 0.00 3.67
876 2767 0.319211 CCTCGCGACTGTTGTTGGTA 60.319 55.000 3.71 0.00 0.00 3.25
877 2768 1.671850 CCTCGCGACTGTTGTTGGTAT 60.672 52.381 3.71 0.00 0.00 2.73
878 2769 2.066262 CTCGCGACTGTTGTTGGTATT 58.934 47.619 3.71 0.00 0.00 1.89
881 2772 2.315901 GCGACTGTTGTTGGTATTTGC 58.684 47.619 0.00 0.00 0.00 3.68
886 2777 3.243501 ACTGTTGTTGGTATTTGCTGCTG 60.244 43.478 0.00 0.00 0.00 4.41
899 2790 1.001048 TGCTGCTGTTGCTGAACAATC 60.001 47.619 0.00 0.00 41.62 2.67
902 2793 1.946081 TGCTGTTGCTGAACAATCGAA 59.054 42.857 0.00 0.00 41.62 3.71
908 2799 4.024472 TGTTGCTGAACAATCGAATCGAAA 60.024 37.500 10.12 0.00 41.27 3.46
909 2800 4.944962 TGCTGAACAATCGAATCGAAAT 57.055 36.364 10.12 0.00 39.99 2.17
910 2801 5.295431 TGCTGAACAATCGAATCGAAATT 57.705 34.783 10.12 4.23 39.99 1.82
911 2802 5.088068 TGCTGAACAATCGAATCGAAATTG 58.912 37.500 10.12 13.12 39.99 2.32
913 2804 5.794945 GCTGAACAATCGAATCGAAATTGAA 59.205 36.000 21.22 8.82 39.99 2.69
914 2805 6.470235 GCTGAACAATCGAATCGAAATTGAAT 59.530 34.615 21.22 11.82 39.99 2.57
915 2806 7.639850 GCTGAACAATCGAATCGAAATTGAATA 59.360 33.333 21.22 8.80 39.99 1.75
916 2807 8.820628 TGAACAATCGAATCGAAATTGAATAC 57.179 30.769 21.22 11.52 39.99 1.89
948 2839 1.269448 GATCTCTCTGCGTCCAGATCC 59.731 57.143 4.84 0.00 46.44 3.36
959 2850 3.181475 GCGTCCAGATCCATCTCAGTTTA 60.181 47.826 0.00 0.00 34.22 2.01
960 2851 4.363999 CGTCCAGATCCATCTCAGTTTAC 58.636 47.826 0.00 0.00 34.22 2.01
962 2853 4.162320 GTCCAGATCCATCTCAGTTTACCA 59.838 45.833 0.00 0.00 34.22 3.25
963 2854 4.162320 TCCAGATCCATCTCAGTTTACCAC 59.838 45.833 0.00 0.00 34.22 4.16
964 2855 4.163078 CCAGATCCATCTCAGTTTACCACT 59.837 45.833 0.00 0.00 34.22 4.00
965 2856 5.338708 CCAGATCCATCTCAGTTTACCACTT 60.339 44.000 0.00 0.00 34.22 3.16
966 2857 5.814705 CAGATCCATCTCAGTTTACCACTTC 59.185 44.000 0.00 0.00 34.22 3.01
968 2859 4.168101 TCCATCTCAGTTTACCACTTCCT 58.832 43.478 0.00 0.00 30.92 3.36
969 2860 4.597507 TCCATCTCAGTTTACCACTTCCTT 59.402 41.667 0.00 0.00 30.92 3.36
970 2861 4.697352 CCATCTCAGTTTACCACTTCCTTG 59.303 45.833 0.00 0.00 30.92 3.61
971 2862 3.740115 TCTCAGTTTACCACTTCCTTGC 58.260 45.455 0.00 0.00 30.92 4.01
972 2863 3.135712 TCTCAGTTTACCACTTCCTTGCA 59.864 43.478 0.00 0.00 30.92 4.08
973 2864 4.074970 CTCAGTTTACCACTTCCTTGCAT 58.925 43.478 0.00 0.00 30.92 3.96
974 2865 4.469657 TCAGTTTACCACTTCCTTGCATT 58.530 39.130 0.00 0.00 30.92 3.56
975 2866 5.626142 TCAGTTTACCACTTCCTTGCATTA 58.374 37.500 0.00 0.00 30.92 1.90
976 2867 5.472137 TCAGTTTACCACTTCCTTGCATTAC 59.528 40.000 0.00 0.00 30.92 1.89
977 2868 5.473504 CAGTTTACCACTTCCTTGCATTACT 59.526 40.000 0.00 0.00 30.92 2.24
978 2869 6.016276 CAGTTTACCACTTCCTTGCATTACTT 60.016 38.462 0.00 0.00 30.92 2.24
979 2870 5.957842 TTACCACTTCCTTGCATTACTTG 57.042 39.130 0.00 0.00 0.00 3.16
980 2871 3.832527 ACCACTTCCTTGCATTACTTGT 58.167 40.909 0.00 0.00 0.00 3.16
981 2872 3.569701 ACCACTTCCTTGCATTACTTGTG 59.430 43.478 0.00 0.00 0.00 3.33
982 2873 3.057315 CCACTTCCTTGCATTACTTGTGG 60.057 47.826 9.68 9.68 36.85 4.17
983 2874 3.569701 CACTTCCTTGCATTACTTGTGGT 59.430 43.478 0.00 0.00 0.00 4.16
984 2875 4.759693 CACTTCCTTGCATTACTTGTGGTA 59.240 41.667 0.00 0.00 0.00 3.25
985 2876 5.240623 CACTTCCTTGCATTACTTGTGGTAA 59.759 40.000 0.00 0.00 43.49 2.85
989 2880 4.142902 CCTTGCATTACTTGTGGTAAGTCG 60.143 45.833 0.00 0.00 42.74 4.18
1074 2965 7.355778 GTGTAAAAGAGTCTCAGGTTTTCATG 58.644 38.462 1.94 0.00 0.00 3.07
1086 2977 1.266718 GTTTTCATGAGCACGCTCCAA 59.733 47.619 16.12 4.14 42.09 3.53
1092 2983 0.894835 TGAGCACGCTCCAACATCTA 59.105 50.000 16.12 0.00 42.09 1.98
1108 2999 1.952635 CTATTAACGGCGGCGACCC 60.953 63.158 38.93 1.24 0.00 4.46
1176 3076 2.798689 CGCTGGCTACTCACGCTA 59.201 61.111 0.00 0.00 0.00 4.26
1422 3322 1.599797 CGAAAAGCCACGGGGTTCT 60.600 57.895 5.12 0.00 43.04 3.01
1426 3326 0.609131 AAAGCCACGGGGTTCTCATG 60.609 55.000 5.12 0.00 43.04 3.07
1427 3327 3.134127 GCCACGGGGTTCTCATGC 61.134 66.667 5.12 0.00 36.17 4.06
1452 3352 2.966050 GTCCTGCTGAAAGACGAAGAT 58.034 47.619 0.00 0.00 34.07 2.40
1458 3358 3.990469 TGCTGAAAGACGAAGATGAACTC 59.010 43.478 0.00 0.00 34.07 3.01
1496 3415 0.321653 GGAGAAACAGTGCCATCGGT 60.322 55.000 0.00 0.00 0.00 4.69
1504 3423 0.104304 AGTGCCATCGGTATTCGTCC 59.896 55.000 0.00 0.00 40.32 4.79
1701 3930 3.482809 CTCGACACGGAGCGACTA 58.517 61.111 0.00 0.00 32.51 2.59
1950 4182 4.774503 GCGAGGCTTGCCTGCTCT 62.775 66.667 19.84 0.00 0.00 4.09
2080 4328 5.630680 GTCGGTCGTGTCTCTTAATTAAACA 59.369 40.000 0.00 0.00 0.00 2.83
2218 4513 4.344865 GCGGGAGGGTTTGCTCCA 62.345 66.667 0.00 0.00 41.34 3.86
2231 4526 1.890979 GCTCCATGCTCGTCCCATG 60.891 63.158 0.00 5.96 39.74 3.66
2423 6763 2.763881 GCTTCGCTCGTTGTCGAC 59.236 61.111 9.11 9.11 41.35 4.20
2529 6986 1.654220 CTTCGTGGCCCTGTTTGTG 59.346 57.895 0.00 0.00 0.00 3.33
2660 7119 5.940470 ACCGCTGTTCTTCTAATTTCTGAAT 59.060 36.000 0.00 0.00 0.00 2.57
2700 7159 0.459237 GTGAGGTCGGTGAGATGCAG 60.459 60.000 0.00 0.00 0.00 4.41
2738 7197 2.427095 ACAAGAACTGTGCTTTTGGTCC 59.573 45.455 0.00 0.00 36.69 4.46
2852 8446 8.817100 CACTTAATTAAGTAGTGCATTCGATCA 58.183 33.333 26.38 0.00 44.19 2.92
2985 8592 6.376864 TGTTGGAAGAAGACTTGATTTTGACA 59.623 34.615 0.00 0.00 36.39 3.58
3023 8630 0.038021 TGGCTGCAGTGGAGCATTTA 59.962 50.000 33.67 16.47 44.68 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
135 140 5.416952 ACTCATTCTCTATTTGGGCACTTTG 59.583 40.000 0.00 0.00 0.00 2.77
217 222 5.810587 TGCTTGTATTTTCTAGATCGTGGAC 59.189 40.000 0.00 0.00 0.00 4.02
227 232 6.403049 TGAGGATCGTTGCTTGTATTTTCTA 58.597 36.000 0.00 0.00 38.61 2.10
255 284 4.497507 GCCTGCTATCGTGGGTTATTTTTC 60.498 45.833 0.00 0.00 0.00 2.29
262 294 1.221840 CAGCCTGCTATCGTGGGTT 59.778 57.895 0.00 0.00 0.00 4.11
302 334 1.802365 GCTTATCGTTGGTTCGTTGGT 59.198 47.619 0.00 0.00 0.00 3.67
317 349 2.100631 GTCACGTGCAGCCGCTTAT 61.101 57.895 11.67 0.00 39.64 1.73
401 2267 6.183360 CCGTTAATCGTTTTGTTTATCTCGGA 60.183 38.462 0.00 0.00 37.94 4.55
568 2434 9.668497 GAAATAGGAACACTTTAATGTAGTCCT 57.332 33.333 20.23 20.23 36.75 3.85
569 2435 8.601476 CGAAATAGGAACACTTTAATGTAGTCC 58.399 37.037 11.76 11.76 30.75 3.85
570 2436 9.148104 ACGAAATAGGAACACTTTAATGTAGTC 57.852 33.333 0.00 0.00 30.75 2.59
587 2453 7.396623 ACCAGGTCTTATCCTATACGAAATAGG 59.603 40.741 17.36 17.36 41.90 2.57
588 2454 8.244802 CACCAGGTCTTATCCTATACGAAATAG 58.755 40.741 0.00 0.00 35.87 1.73
589 2455 7.727186 ACACCAGGTCTTATCCTATACGAAATA 59.273 37.037 0.00 0.00 35.87 1.40
590 2456 6.553852 ACACCAGGTCTTATCCTATACGAAAT 59.446 38.462 0.00 0.00 35.87 2.17
591 2457 5.895534 ACACCAGGTCTTATCCTATACGAAA 59.104 40.000 0.00 0.00 35.87 3.46
592 2458 5.452255 ACACCAGGTCTTATCCTATACGAA 58.548 41.667 0.00 0.00 35.87 3.85
593 2459 5.057843 ACACCAGGTCTTATCCTATACGA 57.942 43.478 0.00 0.00 35.87 3.43
594 2460 4.217983 GGACACCAGGTCTTATCCTATACG 59.782 50.000 0.00 0.00 46.16 3.06
595 2461 4.217983 CGGACACCAGGTCTTATCCTATAC 59.782 50.000 0.00 0.00 46.16 1.47
596 2462 4.105217 TCGGACACCAGGTCTTATCCTATA 59.895 45.833 0.00 0.00 46.16 1.31
597 2463 3.117246 TCGGACACCAGGTCTTATCCTAT 60.117 47.826 0.00 0.00 46.16 2.57
598 2464 2.242965 TCGGACACCAGGTCTTATCCTA 59.757 50.000 0.00 0.00 46.16 2.94
599 2465 1.006758 TCGGACACCAGGTCTTATCCT 59.993 52.381 0.00 0.00 46.16 3.24
600 2466 1.136500 GTCGGACACCAGGTCTTATCC 59.864 57.143 2.62 0.00 46.16 2.59
601 2467 1.822990 TGTCGGACACCAGGTCTTATC 59.177 52.381 6.76 0.00 46.16 1.75
602 2468 1.549170 GTGTCGGACACCAGGTCTTAT 59.451 52.381 26.86 0.00 46.16 1.73
603 2469 0.963962 GTGTCGGACACCAGGTCTTA 59.036 55.000 26.86 0.00 46.16 2.10
604 2470 1.746517 GTGTCGGACACCAGGTCTT 59.253 57.895 26.86 0.00 46.16 3.01
605 2471 2.561956 CGTGTCGGACACCAGGTCT 61.562 63.158 29.76 0.00 45.93 3.85
606 2472 2.049433 CGTGTCGGACACCAGGTC 60.049 66.667 29.76 9.47 45.93 3.85
621 2487 4.250305 GGGGCTGACACACACCGT 62.250 66.667 0.00 0.00 0.00 4.83
622 2488 4.248842 TGGGGCTGACACACACCG 62.249 66.667 0.00 0.00 0.00 4.94
623 2489 2.281761 CTGGGGCTGACACACACC 60.282 66.667 0.00 0.00 0.00 4.16
624 2490 2.980233 GCTGGGGCTGACACACAC 60.980 66.667 0.00 0.00 35.22 3.82
625 2491 4.269523 GGCTGGGGCTGACACACA 62.270 66.667 0.00 0.00 38.73 3.72
646 2512 1.632965 AATAAGAGGGGACGGGCCAC 61.633 60.000 4.39 0.00 41.99 5.01
647 2513 0.030909 TAATAAGAGGGGACGGGCCA 60.031 55.000 4.39 0.00 38.95 5.36
648 2514 1.134228 TTAATAAGAGGGGACGGGCC 58.866 55.000 0.00 0.00 0.00 5.80
649 2515 2.847441 CTTTAATAAGAGGGGACGGGC 58.153 52.381 0.00 0.00 32.92 6.13
650 2516 2.486727 GGCTTTAATAAGAGGGGACGGG 60.487 54.545 0.00 0.00 32.92 5.28
651 2517 2.486727 GGGCTTTAATAAGAGGGGACGG 60.487 54.545 0.00 0.00 32.92 4.79
652 2518 2.805657 CGGGCTTTAATAAGAGGGGACG 60.806 54.545 0.00 0.00 32.92 4.79
653 2519 2.847441 CGGGCTTTAATAAGAGGGGAC 58.153 52.381 0.00 0.00 32.92 4.46
654 2520 1.142262 GCGGGCTTTAATAAGAGGGGA 59.858 52.381 0.00 0.00 32.92 4.81
655 2521 1.605753 GCGGGCTTTAATAAGAGGGG 58.394 55.000 0.00 0.00 32.92 4.79
656 2522 1.605753 GGCGGGCTTTAATAAGAGGG 58.394 55.000 0.00 0.00 32.92 4.30
657 2523 1.605753 GGGCGGGCTTTAATAAGAGG 58.394 55.000 0.26 0.00 32.92 3.69
658 2524 1.143073 AGGGGCGGGCTTTAATAAGAG 59.857 52.381 0.26 0.00 32.92 2.85
659 2525 1.218844 AGGGGCGGGCTTTAATAAGA 58.781 50.000 0.26 0.00 32.92 2.10
660 2526 2.067365 AAGGGGCGGGCTTTAATAAG 57.933 50.000 0.26 0.00 34.36 1.73
661 2527 2.498078 CAAAAGGGGCGGGCTTTAATAA 59.502 45.455 0.26 0.00 0.00 1.40
662 2528 2.104170 CAAAAGGGGCGGGCTTTAATA 58.896 47.619 0.26 0.00 0.00 0.98
663 2529 0.901827 CAAAAGGGGCGGGCTTTAAT 59.098 50.000 0.26 0.00 0.00 1.40
664 2530 0.470268 ACAAAAGGGGCGGGCTTTAA 60.470 50.000 0.26 0.00 0.00 1.52
665 2531 0.896479 GACAAAAGGGGCGGGCTTTA 60.896 55.000 0.26 0.00 0.00 1.85
666 2532 2.123033 ACAAAAGGGGCGGGCTTT 60.123 55.556 0.26 0.00 0.00 3.51
667 2533 2.600470 GACAAAAGGGGCGGGCTT 60.600 61.111 0.26 0.00 0.00 4.35
668 2534 3.569200 GAGACAAAAGGGGCGGGCT 62.569 63.158 0.26 0.00 0.00 5.19
726 2592 5.585047 GCCGAAGAGAACCACTATTATTTGT 59.415 40.000 0.00 0.00 29.65 2.83
727 2593 5.584649 TGCCGAAGAGAACCACTATTATTTG 59.415 40.000 0.00 0.00 29.65 2.32
728 2594 5.741011 TGCCGAAGAGAACCACTATTATTT 58.259 37.500 0.00 0.00 29.65 1.40
729 2595 5.353394 TGCCGAAGAGAACCACTATTATT 57.647 39.130 0.00 0.00 29.65 1.40
731 2597 3.132289 CCTGCCGAAGAGAACCACTATTA 59.868 47.826 0.00 0.00 29.65 0.98
739 2606 0.246635 TAGCACCTGCCGAAGAGAAC 59.753 55.000 0.00 0.00 43.38 3.01
778 2660 1.450531 GGCGGATCAGGATTGCCTTG 61.451 60.000 15.27 0.00 43.90 3.61
787 2669 2.370445 ACCTTGGAGGCGGATCAGG 61.370 63.158 0.00 0.00 39.63 3.86
791 2673 2.670148 GGACACCTTGGAGGCGGAT 61.670 63.158 0.00 0.00 39.63 4.18
814 2696 1.409427 ACTAGAAGAAATCGCGAGGGG 59.591 52.381 16.66 0.00 0.00 4.79
816 2698 5.150683 CAGATACTAGAAGAAATCGCGAGG 58.849 45.833 16.66 0.00 0.00 4.63
817 2699 5.150683 CCAGATACTAGAAGAAATCGCGAG 58.849 45.833 16.66 0.00 0.00 5.03
818 2700 4.579340 ACCAGATACTAGAAGAAATCGCGA 59.421 41.667 13.09 13.09 0.00 5.87
819 2701 4.861210 ACCAGATACTAGAAGAAATCGCG 58.139 43.478 0.00 0.00 0.00 5.87
820 2702 6.864165 CCTTACCAGATACTAGAAGAAATCGC 59.136 42.308 0.00 0.00 0.00 4.58
821 2703 8.167605 TCCTTACCAGATACTAGAAGAAATCG 57.832 38.462 0.00 0.00 0.00 3.34
833 2715 3.007074 GCTAGGGCTTCCTTACCAGATAC 59.993 52.174 0.00 0.00 41.96 2.24
835 2717 2.050918 GCTAGGGCTTCCTTACCAGAT 58.949 52.381 0.00 0.00 41.96 2.90
836 2718 1.497161 GCTAGGGCTTCCTTACCAGA 58.503 55.000 0.00 0.00 41.96 3.86
858 2749 1.710013 ATACCAACAACAGTCGCGAG 58.290 50.000 10.24 0.00 0.00 5.03
865 2756 3.243501 ACAGCAGCAAATACCAACAACAG 60.244 43.478 0.00 0.00 0.00 3.16
870 2761 2.061028 GCAACAGCAGCAAATACCAAC 58.939 47.619 0.00 0.00 0.00 3.77
871 2762 1.962807 AGCAACAGCAGCAAATACCAA 59.037 42.857 0.00 0.00 0.00 3.67
872 2763 1.270274 CAGCAACAGCAGCAAATACCA 59.730 47.619 0.00 0.00 0.00 3.25
873 2764 1.541147 TCAGCAACAGCAGCAAATACC 59.459 47.619 0.00 0.00 0.00 2.73
874 2765 2.982470 GTTCAGCAACAGCAGCAAATAC 59.018 45.455 0.00 0.00 32.14 1.89
875 2766 2.622470 TGTTCAGCAACAGCAGCAAATA 59.378 40.909 0.00 0.00 37.61 1.40
876 2767 1.409790 TGTTCAGCAACAGCAGCAAAT 59.590 42.857 0.00 0.00 37.61 2.32
877 2768 0.816373 TGTTCAGCAACAGCAGCAAA 59.184 45.000 0.00 0.00 37.61 3.68
878 2769 0.816373 TTGTTCAGCAACAGCAGCAA 59.184 45.000 0.00 0.00 43.54 3.91
881 2772 1.532437 TCGATTGTTCAGCAACAGCAG 59.468 47.619 0.00 0.00 43.54 4.24
886 2777 3.722555 TCGATTCGATTGTTCAGCAAC 57.277 42.857 4.29 0.00 40.28 4.17
899 2790 6.692392 TCTGTTCGTATTCAATTTCGATTCG 58.308 36.000 0.00 0.00 32.54 3.34
902 2793 8.196802 TGATTCTGTTCGTATTCAATTTCGAT 57.803 30.769 0.00 0.00 32.54 3.59
908 2799 8.420222 AGAGATCTGATTCTGTTCGTATTCAAT 58.580 33.333 0.00 0.00 0.00 2.57
909 2800 7.776107 AGAGATCTGATTCTGTTCGTATTCAA 58.224 34.615 0.00 0.00 0.00 2.69
910 2801 7.284261 AGAGAGATCTGATTCTGTTCGTATTCA 59.716 37.037 0.00 0.00 0.00 2.57
911 2802 7.591057 CAGAGAGATCTGATTCTGTTCGTATTC 59.409 40.741 0.00 0.00 39.99 1.75
913 2804 6.514870 GCAGAGAGATCTGATTCTGTTCGTAT 60.515 42.308 20.86 0.00 39.99 3.06
914 2805 5.220951 GCAGAGAGATCTGATTCTGTTCGTA 60.221 44.000 20.86 0.00 39.99 3.43
915 2806 4.439974 GCAGAGAGATCTGATTCTGTTCGT 60.440 45.833 20.86 0.00 39.99 3.85
916 2807 4.043750 GCAGAGAGATCTGATTCTGTTCG 58.956 47.826 20.86 5.40 39.99 3.95
937 2828 0.749649 ACTGAGATGGATCTGGACGC 59.250 55.000 0.00 0.00 37.25 5.19
948 2839 4.154918 GCAAGGAAGTGGTAAACTGAGATG 59.845 45.833 0.00 0.00 39.81 2.90
959 2850 3.569701 CACAAGTAATGCAAGGAAGTGGT 59.430 43.478 0.00 0.00 0.00 4.16
960 2851 3.057315 CCACAAGTAATGCAAGGAAGTGG 60.057 47.826 11.46 11.46 38.15 4.00
962 2853 3.832527 ACCACAAGTAATGCAAGGAAGT 58.167 40.909 0.00 0.00 0.00 3.01
963 2854 5.473504 ACTTACCACAAGTAATGCAAGGAAG 59.526 40.000 0.00 0.00 40.18 3.46
964 2855 5.381757 ACTTACCACAAGTAATGCAAGGAA 58.618 37.500 0.00 0.00 40.18 3.36
965 2856 4.980573 ACTTACCACAAGTAATGCAAGGA 58.019 39.130 0.00 0.00 40.18 3.36
966 2857 4.142902 CGACTTACCACAAGTAATGCAAGG 60.143 45.833 0.00 0.00 40.18 3.61
968 2859 4.633175 TCGACTTACCACAAGTAATGCAA 58.367 39.130 0.00 0.00 40.18 4.08
969 2860 4.021807 TCTCGACTTACCACAAGTAATGCA 60.022 41.667 0.00 0.00 40.18 3.96
970 2861 4.491676 TCTCGACTTACCACAAGTAATGC 58.508 43.478 0.00 0.00 40.18 3.56
971 2862 5.749109 GGATCTCGACTTACCACAAGTAATG 59.251 44.000 0.00 0.00 40.18 1.90
972 2863 5.421056 TGGATCTCGACTTACCACAAGTAAT 59.579 40.000 0.00 0.00 40.18 1.89
973 2864 4.768448 TGGATCTCGACTTACCACAAGTAA 59.232 41.667 0.00 0.00 38.65 2.24
974 2865 4.338012 TGGATCTCGACTTACCACAAGTA 58.662 43.478 0.00 0.00 0.00 2.24
975 2866 3.162666 TGGATCTCGACTTACCACAAGT 58.837 45.455 0.00 0.00 0.00 3.16
976 2867 3.868757 TGGATCTCGACTTACCACAAG 57.131 47.619 0.00 0.00 0.00 3.16
977 2868 3.132289 GGATGGATCTCGACTTACCACAA 59.868 47.826 0.00 0.00 33.38 3.33
978 2869 2.693591 GGATGGATCTCGACTTACCACA 59.306 50.000 0.00 0.00 33.38 4.17
979 2870 2.693591 TGGATGGATCTCGACTTACCAC 59.306 50.000 0.00 0.00 33.38 4.16
980 2871 3.026707 TGGATGGATCTCGACTTACCA 57.973 47.619 0.00 0.00 35.09 3.25
981 2872 3.919216 CATGGATGGATCTCGACTTACC 58.081 50.000 0.00 0.00 0.00 2.85
1074 2965 2.231215 ATAGATGTTGGAGCGTGCTC 57.769 50.000 13.40 13.40 42.04 4.26
1086 2977 0.386476 TCGCCGCCGTTAATAGATGT 59.614 50.000 0.00 0.00 35.54 3.06
1092 2983 4.085204 TGGGTCGCCGCCGTTAAT 62.085 61.111 0.00 0.00 35.54 1.40
1108 2999 2.567049 GTCAGGGTCGTCGGTCTG 59.433 66.667 0.00 0.00 0.00 3.51
1128 3025 2.671177 CCAGCACCTCGTCTTTGCG 61.671 63.158 0.00 0.00 41.33 4.85
1131 3031 2.032681 GCCCAGCACCTCGTCTTT 59.967 61.111 0.00 0.00 0.00 2.52
1176 3076 2.429236 CGCAGCGAAGTCGTGTCT 60.429 61.111 9.98 0.00 42.22 3.41
1257 3157 1.529244 GCACTTGCAGTTCTGGGGT 60.529 57.895 0.00 0.00 41.59 4.95
1407 3307 0.609131 CATGAGAACCCCGTGGCTTT 60.609 55.000 0.00 0.00 33.59 3.51
1422 3322 3.381983 AGCAGGACGACGGCATGA 61.382 61.111 21.29 0.00 43.19 3.07
1426 3326 2.357034 TTTCAGCAGGACGACGGC 60.357 61.111 0.00 0.00 40.88 5.68
1427 3327 1.009389 GTCTTTCAGCAGGACGACGG 61.009 60.000 0.00 0.00 0.00 4.79
1452 3352 2.805353 GAGAAGCGCGCGAGTTCA 60.805 61.111 37.18 0.00 0.00 3.18
1496 3415 4.039973 AGTTGTGTTTCTCCAGGACGAATA 59.960 41.667 0.00 0.00 0.00 1.75
1504 3423 2.874701 CTGTCCAGTTGTGTTTCTCCAG 59.125 50.000 0.00 0.00 0.00 3.86
1701 3930 3.805307 CAGCTCCGCTCGACTCGT 61.805 66.667 0.00 0.00 36.40 4.18
1950 4182 1.375853 CGGATGGGAGCATTTTCGCA 61.376 55.000 0.00 0.00 43.05 5.10
2061 4293 6.751157 TCCTGTGTTTAATTAAGAGACACGA 58.249 36.000 19.40 12.52 42.53 4.35
2080 4328 1.600916 GCGGCTGGTCTTTTCCTGT 60.601 57.895 0.00 0.00 0.00 4.00
2218 4513 4.552365 CCGCCATGGGACGAGCAT 62.552 66.667 15.13 0.00 0.00 3.79
2432 6772 1.228245 GGCTGCAACCTCAGGAACA 60.228 57.895 0.00 0.00 34.74 3.18
2660 7119 7.094975 CCTCACACGGACAAAAATAGTATTTGA 60.095 37.037 8.88 0.00 39.56 2.69
2666 7125 4.062991 GACCTCACACGGACAAAAATAGT 58.937 43.478 0.00 0.00 0.00 2.12
2852 8446 1.140312 ATGGGGAGTCCGTGCATATT 58.860 50.000 2.26 0.00 38.76 1.28
3023 8630 4.508551 TGATGATAAGACACCCAGCATT 57.491 40.909 0.00 0.00 0.00 3.56


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

AutoCloner maintained by Alex Coulton.