Multiple sequence alignment - TraesCS7A01G302700

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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 TraesCS7A01G302700 chr7A 100.000 3821 0 0 1 3821 424552225 424548405 0.000000e+00 7057.0
1 TraesCS7A01G302700 chr7A 85.593 472 62 4 377 846 545478436 545478903 1.230000e-134 490.0
2 TraesCS7A01G302700 chr7A 87.436 390 41 8 1 386 545478018 545478403 3.500000e-120 442.0
3 TraesCS7A01G302700 chr7A 97.436 39 1 0 3479 3517 257125983 257126021 2.460000e-07 67.6
4 TraesCS7A01G302700 chr7D 95.151 2557 90 10 894 3435 376949489 376946952 0.000000e+00 4004.0
5 TraesCS7A01G302700 chr7D 87.179 156 20 0 3054 3209 588735636 588735481 1.090000e-40 178.0
6 TraesCS7A01G302700 chr7D 92.308 104 8 0 3205 3308 588735168 588735065 8.550000e-32 148.0
7 TraesCS7A01G302700 chr7B 94.039 2634 104 12 924 3517 372039454 372036834 0.000000e+00 3945.0
8 TraesCS7A01G302700 chr7B 96.269 134 3 2 3690 3821 372036653 372036520 6.430000e-53 219.0
9 TraesCS7A01G302700 chr7B 91.489 47 2 2 3472 3517 164277257 164277212 3.190000e-06 63.9
10 TraesCS7A01G302700 chr4A 94.330 388 16 4 1 386 217133777 217134160 1.180000e-164 590.0
11 TraesCS7A01G302700 chr4A 87.339 466 54 3 383 846 650838952 650838490 2.610000e-146 529.0
12 TraesCS7A01G302700 chr4A 97.727 44 1 0 3474 3517 686974708 686974665 4.090000e-10 76.8
13 TraesCS7A01G302700 chr4A 91.304 46 4 0 3472 3517 116182518 116182563 3.190000e-06 63.9
14 TraesCS7A01G302700 chr4A 94.872 39 2 0 2672 2710 435613045 435613007 1.150000e-05 62.1
15 TraesCS7A01G302700 chr5B 88.723 470 41 9 383 846 617252592 617252129 7.170000e-157 564.0
16 TraesCS7A01G302700 chr5B 88.627 466 46 6 383 846 579518467 579518007 9.270000e-156 560.0
17 TraesCS7A01G302700 chr5B 92.784 388 26 2 1 386 617253020 617252633 9.270000e-156 560.0
18 TraesCS7A01G302700 chr5B 91.495 388 28 5 1 385 579518895 579518510 2.610000e-146 529.0
19 TraesCS7A01G302700 chr5B 84.848 66 10 0 3361 3426 374439251 374439186 2.460000e-07 67.6
20 TraesCS7A01G302700 chr5B 91.489 47 2 2 3472 3517 133234687 133234642 3.190000e-06 63.9
21 TraesCS7A01G302700 chr5B 93.023 43 3 0 3652 3694 618474565 618474607 3.190000e-06 63.9
22 TraesCS7A01G302700 chr5B 92.857 42 3 0 3651 3692 40979543 40979584 1.150000e-05 62.1
23 TraesCS7A01G302700 chr2B 92.784 388 26 2 1 386 737452181 737452568 9.270000e-156 560.0
24 TraesCS7A01G302700 chr2B 88.470 477 37 13 377 846 737452603 737453068 9.270000e-156 560.0
25 TraesCS7A01G302700 chr2B 92.765 387 23 4 4 386 325837267 325836882 4.310000e-154 555.0
26 TraesCS7A01G302700 chr2B 87.789 475 37 10 383 846 325836841 325836377 1.560000e-148 536.0
27 TraesCS7A01G302700 chr2B 75.319 235 38 15 603 831 769481332 769481552 1.130000e-15 95.3
28 TraesCS7A01G302700 chr5D 90.255 431 34 6 419 846 234841110 234841535 1.200000e-154 556.0
29 TraesCS7A01G302700 chr5D 89.583 48 5 0 3645 3692 43299756 43299803 1.150000e-05 62.1
30 TraesCS7A01G302700 chr3D 81.702 705 84 15 2647 3332 524731969 524732647 2.600000e-151 545.0
31 TraesCS7A01G302700 chr3D 95.745 47 2 0 3358 3404 523563878 523563924 4.090000e-10 76.8
32 TraesCS7A01G302700 chr1B 91.774 389 28 4 1 386 38917822 38918209 4.340000e-149 538.0
33 TraesCS7A01G302700 chr1B 95.349 43 2 0 3475 3517 481708440 481708482 6.850000e-08 69.4
34 TraesCS7A01G302700 chr1B 93.023 43 3 0 3475 3517 462971526 462971568 3.190000e-06 63.9
35 TraesCS7A01G302700 chr3B 91.538 390 29 3 1 386 126368770 126369159 5.620000e-148 534.0
36 TraesCS7A01G302700 chr5A 86.910 466 55 4 383 846 51457914 51457453 5.660000e-143 518.0
37 TraesCS7A01G302700 chr5A 92.857 42 3 0 3651 3692 33119865 33119906 1.150000e-05 62.1
38 TraesCS7A01G302700 chr6B 90.769 390 30 5 1 385 667178223 667177835 2.040000e-142 516.0
39 TraesCS7A01G302700 chr6B 74.502 251 48 11 603 844 52113076 52113319 1.130000e-15 95.3
40 TraesCS7A01G302700 chr6B 97.561 41 1 0 3360 3400 162615740 162615700 1.900000e-08 71.3
41 TraesCS7A01G302700 chr6B 91.111 45 4 0 3473 3517 140760754 140760710 1.150000e-05 62.1
42 TraesCS7A01G302700 chr4B 81.184 473 74 8 384 847 118229114 118229580 2.170000e-97 366.0
43 TraesCS7A01G302700 chr2A 88.406 69 8 0 3351 3419 13425703 13425771 2.450000e-12 84.2
44 TraesCS7A01G302700 chr2A 97.674 43 1 0 3361 3403 34480073 34480031 1.470000e-09 75.0
45 TraesCS7A01G302700 chr2A 93.333 45 2 1 3474 3517 7730934 7730890 8.860000e-07 65.8
46 TraesCS7A01G302700 chr6D 90.323 62 4 2 3358 3419 465579542 465579601 3.160000e-11 80.5
47 TraesCS7A01G302700 chr3A 95.122 41 2 0 3652 3692 698275101 698275141 8.860000e-07 65.8
48 TraesCS7A01G302700 chr6A 91.304 46 4 0 3446 3491 147150892 147150847 3.190000e-06 63.9
49 TraesCS7A01G302700 chr6A 92.500 40 3 0 3653 3692 51755366 51755405 1.480000e-04 58.4
50 TraesCS7A01G302700 chr2D 93.023 43 3 0 3652 3694 180173350 180173392 3.190000e-06 63.9
51 TraesCS7A01G302700 chr1A 95.000 40 2 0 3653 3692 15915204 15915165 3.190000e-06 63.9
52 TraesCS7A01G302700 chr1D 100.000 33 0 0 3652 3684 7777226 7777194 1.150000e-05 62.1


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 TraesCS7A01G302700 chr7A 424548405 424552225 3820 True 7057.0 7057 100.0000 1 3821 1 chr7A.!!$R1 3820
1 TraesCS7A01G302700 chr7A 545478018 545478903 885 False 466.0 490 86.5145 1 846 2 chr7A.!!$F2 845
2 TraesCS7A01G302700 chr7D 376946952 376949489 2537 True 4004.0 4004 95.1510 894 3435 1 chr7D.!!$R1 2541
3 TraesCS7A01G302700 chr7B 372036520 372039454 2934 True 2082.0 3945 95.1540 924 3821 2 chr7B.!!$R2 2897
4 TraesCS7A01G302700 chr5B 617252129 617253020 891 True 562.0 564 90.7535 1 846 2 chr5B.!!$R4 845
5 TraesCS7A01G302700 chr5B 579518007 579518895 888 True 544.5 560 90.0610 1 846 2 chr5B.!!$R3 845
6 TraesCS7A01G302700 chr2B 737452181 737453068 887 False 560.0 560 90.6270 1 846 2 chr2B.!!$F2 845
7 TraesCS7A01G302700 chr2B 325836377 325837267 890 True 545.5 555 90.2770 4 846 2 chr2B.!!$R1 842
8 TraesCS7A01G302700 chr3D 524731969 524732647 678 False 545.0 545 81.7020 2647 3332 1 chr3D.!!$F2 685

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
730 798 0.036765 GACACGCTACATGGGTTGGA 60.037 55.0 0.00 0.0 39.99 3.53 F
849 917 0.040067 CTGCGCAGGACAAGTTTTCC 60.040 55.0 29.88 0.0 0.00 3.13 F
938 1006 0.114168 AGAGAGCAGAGAGGGTGTGT 59.886 55.0 0.00 0.0 0.00 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1683 1751 0.250124 ACTCGTTTGGCCGAACATCA 60.250 50.000 30.90 15.70 36.24 3.07 R
2520 2588 0.465097 CCATTGCCTTCATCCGCTCT 60.465 55.000 0.00 0.00 0.00 4.09 R
2881 2979 2.164827 TCCAATGCATCACATGTCTTGC 59.835 45.455 18.37 18.37 39.60 4.01 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
125 128 7.492344 CGCCATATATATACATCAACTGAGCAA 59.508 37.037 0.00 0.00 0.00 3.91
127 130 8.824781 CCATATATATACATCAACTGAGCAAGC 58.175 37.037 0.00 0.00 0.00 4.01
141 144 2.935201 GAGCAAGCTTGAGAGGTACATG 59.065 50.000 30.39 0.00 32.23 3.21
495 547 3.129638 GCCGGTGCTCCAAAATTACATTA 59.870 43.478 1.90 0.00 33.53 1.90
566 618 2.595655 GTATGGCCTGGTGGACCC 59.404 66.667 3.32 0.00 42.00 4.46
588 641 2.096268 CCTATGCGTGCAACATAATCCG 60.096 50.000 10.86 0.00 35.74 4.18
664 732 4.358841 CATGTCCGGGCCACCCAA 62.359 66.667 2.12 0.00 45.83 4.12
680 748 1.674057 CAACGACTTCCCTGCTCCT 59.326 57.895 0.00 0.00 0.00 3.69
718 786 1.148273 ACCACCACATTGACACGCT 59.852 52.632 0.00 0.00 0.00 5.07
726 794 1.003118 ACATTGACACGCTACATGGGT 59.997 47.619 0.00 0.00 42.91 4.51
729 797 0.321210 TGACACGCTACATGGGTTGG 60.321 55.000 0.00 0.00 39.99 3.77
730 798 0.036765 GACACGCTACATGGGTTGGA 60.037 55.000 0.00 0.00 39.99 3.53
731 799 0.321298 ACACGCTACATGGGTTGGAC 60.321 55.000 0.00 0.00 39.99 4.02
754 822 4.962498 CGACGTACGTCTGGATACAAATGT 60.962 45.833 37.11 5.25 42.54 2.71
772 840 8.518430 ACAAATGTAGGCATCATATTTACACA 57.482 30.769 0.00 0.00 33.50 3.72
774 842 8.623903 CAAATGTAGGCATCATATTTACACAGT 58.376 33.333 0.00 0.00 33.50 3.55
776 844 6.288294 TGTAGGCATCATATTTACACAGTCC 58.712 40.000 0.00 0.00 0.00 3.85
809 877 8.500753 TCGAGCACCTATTTTATGTATTTTGT 57.499 30.769 0.00 0.00 0.00 2.83
846 914 0.463654 TGACTGCGCAGGACAAGTTT 60.464 50.000 38.27 17.33 0.00 2.66
847 915 0.663153 GACTGCGCAGGACAAGTTTT 59.337 50.000 38.27 16.56 0.00 2.43
848 916 0.663153 ACTGCGCAGGACAAGTTTTC 59.337 50.000 38.27 0.00 0.00 2.29
849 917 0.040067 CTGCGCAGGACAAGTTTTCC 60.040 55.000 29.88 0.00 0.00 3.13
850 918 0.749818 TGCGCAGGACAAGTTTTCCA 60.750 50.000 5.66 0.00 35.33 3.53
851 919 0.383949 GCGCAGGACAAGTTTTCCAA 59.616 50.000 10.65 0.00 35.33 3.53
852 920 1.864029 GCGCAGGACAAGTTTTCCAAC 60.864 52.381 10.65 1.15 35.33 3.77
853 921 1.403679 CGCAGGACAAGTTTTCCAACA 59.596 47.619 10.65 0.00 35.33 3.33
854 922 2.034558 CGCAGGACAAGTTTTCCAACAT 59.965 45.455 10.65 0.00 35.33 2.71
855 923 3.252215 CGCAGGACAAGTTTTCCAACATA 59.748 43.478 10.65 0.00 35.33 2.29
856 924 4.082787 CGCAGGACAAGTTTTCCAACATAT 60.083 41.667 10.65 0.00 35.33 1.78
857 925 5.564651 CGCAGGACAAGTTTTCCAACATATT 60.565 40.000 10.65 0.00 35.33 1.28
858 926 6.223120 GCAGGACAAGTTTTCCAACATATTT 58.777 36.000 10.65 0.00 35.33 1.40
859 927 7.375053 GCAGGACAAGTTTTCCAACATATTTA 58.625 34.615 10.65 0.00 35.33 1.40
860 928 7.870445 GCAGGACAAGTTTTCCAACATATTTAA 59.130 33.333 10.65 0.00 35.33 1.52
861 929 9.191995 CAGGACAAGTTTTCCAACATATTTAAC 57.808 33.333 10.65 0.00 35.33 2.01
862 930 9.143155 AGGACAAGTTTTCCAACATATTTAACT 57.857 29.630 10.65 0.00 35.33 2.24
863 931 9.758651 GGACAAGTTTTCCAACATATTTAACTT 57.241 29.630 3.04 0.00 35.43 2.66
917 985 4.495690 TTTTTCCAACAAAAGGGAAGGG 57.504 40.909 0.00 0.00 43.59 3.95
922 990 2.893489 CCAACAAAAGGGAAGGGAAGAG 59.107 50.000 0.00 0.00 0.00 2.85
927 995 1.284313 AAGGGAAGGGAAGAGAGCAG 58.716 55.000 0.00 0.00 0.00 4.24
938 1006 0.114168 AGAGAGCAGAGAGGGTGTGT 59.886 55.000 0.00 0.00 0.00 3.72
944 1012 1.261480 CAGAGAGGGTGTGTACAGCT 58.739 55.000 13.17 0.95 43.37 4.24
950 1018 1.374252 GGTGTGTACAGCTCCCACG 60.374 63.158 0.00 0.00 40.88 4.94
963 1031 2.681778 CCACGCTCCCACTCTCCT 60.682 66.667 0.00 0.00 0.00 3.69
964 1032 2.286523 CCACGCTCCCACTCTCCTT 61.287 63.158 0.00 0.00 0.00 3.36
965 1033 1.079543 CACGCTCCCACTCTCCTTG 60.080 63.158 0.00 0.00 0.00 3.61
987 1055 2.763215 GTTCCCCATGCCTGTCCA 59.237 61.111 0.00 0.00 0.00 4.02
1029 1097 1.285023 CCGACTTCGTCTCGGTGTT 59.715 57.895 9.19 0.00 44.82 3.32
1596 1664 1.671379 GCCGGTGAGGAACTTGGTC 60.671 63.158 1.90 0.00 41.55 4.02
1639 1707 3.366883 GGGCTATGTCAAAAATTCACGCA 60.367 43.478 0.00 0.00 0.00 5.24
1655 1723 0.659427 CGCACGGATGATGCTTTGAT 59.341 50.000 0.00 0.00 41.10 2.57
1815 1883 3.576982 TGAGTCGGAGAATAACTGTTGGT 59.423 43.478 2.69 0.00 39.69 3.67
2101 2169 2.176045 TGCAGGAAATCTACGGAGTCA 58.824 47.619 0.00 0.00 43.93 3.41
2151 2219 1.260538 TGGATCTTCTGTGCCGAGCT 61.261 55.000 0.00 0.00 0.00 4.09
2217 2285 0.543749 AGCCACATCCTTCTGCCTAC 59.456 55.000 0.00 0.00 0.00 3.18
2247 2315 6.106673 TCTATTGGCTGCTTGTAGAGTTTAC 58.893 40.000 0.00 0.00 0.00 2.01
2299 2367 3.181440 TGGAAAGCTGATCCAACAGAACT 60.181 43.478 16.96 0.00 43.84 3.01
2306 2374 4.129380 CTGATCCAACAGAACTCACACAA 58.871 43.478 0.00 0.00 39.94 3.33
2364 2432 1.377725 AGCAAATCAGTGGGCCGAG 60.378 57.895 0.00 0.00 0.00 4.63
2446 2514 2.041081 TGGGTTGAGATAAAGGGTGTGG 59.959 50.000 0.00 0.00 0.00 4.17
2475 2543 9.106070 CATGAGTTCAGATCAAATGACAGATTA 57.894 33.333 0.00 0.00 0.00 1.75
2512 2580 6.430925 TCGTTTGATTCATGAAAGATTGGACT 59.569 34.615 13.09 0.00 0.00 3.85
2520 2588 4.177537 TGAAAGATTGGACTGGTTGGAA 57.822 40.909 0.00 0.00 0.00 3.53
2546 2614 2.036346 GGATGAAGGCAATGGGTTATGC 59.964 50.000 0.00 0.00 41.82 3.14
2583 2651 4.712122 TGTACTGCATGATGTAGACGAA 57.288 40.909 17.41 0.00 34.09 3.85
2810 2878 1.616091 GGGCATTGTTCATGTGGGGG 61.616 60.000 0.00 0.00 34.98 5.40
2827 2895 2.374170 GGGGGTTACTGGTGAAGAAAGA 59.626 50.000 0.00 0.00 0.00 2.52
2882 2980 6.166982 ACAGTAGTTGATCCTTAACAAGAGC 58.833 40.000 0.00 0.00 0.00 4.09
2883 2981 6.166279 CAGTAGTTGATCCTTAACAAGAGCA 58.834 40.000 0.00 0.00 0.00 4.26
2884 2982 6.650807 CAGTAGTTGATCCTTAACAAGAGCAA 59.349 38.462 0.00 0.00 0.00 3.91
2885 2983 6.876257 AGTAGTTGATCCTTAACAAGAGCAAG 59.124 38.462 0.00 0.00 0.00 4.01
2886 2984 5.869579 AGTTGATCCTTAACAAGAGCAAGA 58.130 37.500 0.00 0.00 0.00 3.02
2887 2985 5.703130 AGTTGATCCTTAACAAGAGCAAGAC 59.297 40.000 0.00 0.00 0.00 3.01
2888 2986 5.227569 TGATCCTTAACAAGAGCAAGACA 57.772 39.130 0.00 0.00 0.00 3.41
2889 2987 5.809001 TGATCCTTAACAAGAGCAAGACAT 58.191 37.500 0.00 0.00 0.00 3.06
2890 2988 5.645067 TGATCCTTAACAAGAGCAAGACATG 59.355 40.000 0.00 0.00 0.00 3.21
2891 2989 4.973168 TCCTTAACAAGAGCAAGACATGT 58.027 39.130 0.00 0.00 0.00 3.21
2892 2990 4.756642 TCCTTAACAAGAGCAAGACATGTG 59.243 41.667 1.15 0.00 0.00 3.21
2893 2991 4.756642 CCTTAACAAGAGCAAGACATGTGA 59.243 41.667 1.15 0.00 0.00 3.58
2894 2992 5.413833 CCTTAACAAGAGCAAGACATGTGAT 59.586 40.000 1.15 0.00 0.00 3.06
3005 3117 2.489073 CCCTGTGAGGTTAGGCAAAACT 60.489 50.000 3.26 0.00 38.04 2.66
3007 3119 3.636764 CCTGTGAGGTTAGGCAAAACTTT 59.363 43.478 3.26 0.00 34.34 2.66
3009 3121 5.048713 CCTGTGAGGTTAGGCAAAACTTTAG 60.049 44.000 3.26 0.00 34.34 1.85
3019 3131 6.025749 AGGCAAAACTTTAGAACCTATTGC 57.974 37.500 0.00 0.00 40.73 3.56
3031 3143 0.447801 CCTATTGCGGCACTTGACAC 59.552 55.000 0.05 0.00 0.00 3.67
3035 3147 0.746204 TTGCGGCACTTGACACAGAA 60.746 50.000 0.05 0.00 0.00 3.02
3181 3293 1.134818 CCCAGCACTATTCGTACTGCA 60.135 52.381 5.46 0.00 35.97 4.41
3235 3347 1.406539 CAGTTTGCACTTGTCAGCCTT 59.593 47.619 0.00 0.00 0.00 4.35
3275 3387 1.066787 GGACCAGTTAGAGGAGCACAC 60.067 57.143 0.00 0.00 0.00 3.82
3278 3390 1.402984 CCAGTTAGAGGAGCACACGAC 60.403 57.143 0.00 0.00 0.00 4.34
3312 3424 8.788813 GTTTATGTTGTAGATCTTGATTTTGCG 58.211 33.333 0.00 0.00 0.00 4.85
3354 3468 4.637534 TGAGAGTCTTAAAATGCAGATGCC 59.362 41.667 1.72 0.00 41.18 4.40
3382 3496 3.016736 GGCGAATCCAGGAAGAAAATGA 58.983 45.455 0.00 0.00 34.01 2.57
3465 3602 4.725790 AGCTCAAACTTCCCAATATTGC 57.274 40.909 10.11 0.00 0.00 3.56
3469 3606 5.358160 GCTCAAACTTCCCAATATTGCTACT 59.642 40.000 10.11 0.00 0.00 2.57
3484 3621 4.202245 TGCTACTGGAAACATGTACTCC 57.798 45.455 16.61 16.61 41.51 3.85
3509 3646 2.684001 TCCGGAATTACTTGTCGCAT 57.316 45.000 0.00 0.00 0.00 4.73
3517 3654 6.199393 GGAATTACTTGTCGCATAAATGGAC 58.801 40.000 5.24 5.24 0.00 4.02
3518 3655 5.751243 ATTACTTGTCGCATAAATGGACC 57.249 39.130 8.27 0.00 31.35 4.46
3519 3656 3.066291 ACTTGTCGCATAAATGGACCA 57.934 42.857 0.00 0.00 31.35 4.02
3520 3657 3.620488 ACTTGTCGCATAAATGGACCAT 58.380 40.909 0.00 0.00 31.35 3.55
3522 3659 4.462483 ACTTGTCGCATAAATGGACCATTT 59.538 37.500 30.29 30.29 44.74 2.32
3523 3660 4.368874 TGTCGCATAAATGGACCATTTG 57.631 40.909 33.49 23.31 42.91 2.32
3526 3663 3.631686 TCGCATAAATGGACCATTTGAGG 59.368 43.478 33.49 24.35 42.91 3.86
3527 3664 3.243501 CGCATAAATGGACCATTTGAGGG 60.244 47.826 33.49 27.79 42.91 4.30
3528 3665 3.960102 GCATAAATGGACCATTTGAGGGA 59.040 43.478 33.49 18.99 42.91 4.20
3529 3666 4.038402 GCATAAATGGACCATTTGAGGGAG 59.962 45.833 33.49 19.97 42.91 4.30
3530 3667 3.833559 AAATGGACCATTTGAGGGAGT 57.166 42.857 27.95 4.90 41.70 3.85
3531 3668 4.946160 AAATGGACCATTTGAGGGAGTA 57.054 40.909 27.95 0.00 41.70 2.59
3532 3669 4.510167 AATGGACCATTTGAGGGAGTAG 57.490 45.455 14.28 0.00 28.76 2.57
3534 3671 4.069312 TGGACCATTTGAGGGAGTAGTA 57.931 45.455 0.00 0.00 0.00 1.82
3535 3672 4.631234 TGGACCATTTGAGGGAGTAGTAT 58.369 43.478 0.00 0.00 0.00 2.12
3536 3673 5.036916 TGGACCATTTGAGGGAGTAGTATT 58.963 41.667 0.00 0.00 0.00 1.89
3538 3675 6.674861 TGGACCATTTGAGGGAGTAGTATTTA 59.325 38.462 0.00 0.00 0.00 1.40
3539 3676 6.990939 GGACCATTTGAGGGAGTAGTATTTAC 59.009 42.308 0.00 0.00 0.00 2.01
3541 3678 7.565680 ACCATTTGAGGGAGTAGTATTTACTG 58.434 38.462 0.45 0.00 37.10 2.74
3542 3679 7.402071 ACCATTTGAGGGAGTAGTATTTACTGA 59.598 37.037 0.45 0.00 37.10 3.41
3543 3680 8.432805 CCATTTGAGGGAGTAGTATTTACTGAT 58.567 37.037 0.45 0.00 37.10 2.90
3593 3730 7.727331 CAAAACTTGGATCATTTAAGCCAAA 57.273 32.000 0.00 0.00 39.67 3.28
3594 3731 8.326680 CAAAACTTGGATCATTTAAGCCAAAT 57.673 30.769 0.00 0.00 39.67 2.32
3595 3732 9.434420 CAAAACTTGGATCATTTAAGCCAAATA 57.566 29.630 0.00 0.00 39.67 1.40
3596 3733 9.657419 AAAACTTGGATCATTTAAGCCAAATAG 57.343 29.630 0.00 0.00 39.67 1.73
3597 3734 6.809869 ACTTGGATCATTTAAGCCAAATAGC 58.190 36.000 0.00 0.00 39.67 2.97
3607 3744 9.807649 CATTTAAGCCAAATAGCCATTATATCC 57.192 33.333 0.00 0.00 34.99 2.59
3609 3746 4.526970 AGCCAAATAGCCATTATATCCCG 58.473 43.478 0.00 0.00 0.00 5.14
3615 3752 6.831664 AATAGCCATTATATCCCGATCCTT 57.168 37.500 0.00 0.00 0.00 3.36
3618 3755 4.163078 AGCCATTATATCCCGATCCTTCTG 59.837 45.833 0.00 0.00 0.00 3.02
3635 3772 5.505173 CTTCTGTCCAAAGAAGCTCAAAA 57.495 39.130 1.31 0.00 44.88 2.44
3639 3776 6.877236 TCTGTCCAAAGAAGCTCAAAATTTT 58.123 32.000 0.00 0.00 0.00 1.82
3641 3778 6.048509 TGTCCAAAGAAGCTCAAAATTTTCC 58.951 36.000 0.00 0.00 0.00 3.13
3650 3787 8.302438 AGAAGCTCAAAATTTTCCAGATTAGTG 58.698 33.333 0.00 0.00 0.00 2.74
3651 3788 7.530426 AGCTCAAAATTTTCCAGATTAGTGT 57.470 32.000 0.00 0.00 0.00 3.55
3652 3789 8.635765 AGCTCAAAATTTTCCAGATTAGTGTA 57.364 30.769 0.00 0.00 0.00 2.90
3654 3791 8.515414 GCTCAAAATTTTCCAGATTAGTGTAGT 58.485 33.333 0.00 0.00 0.00 2.73
3655 3792 9.831737 CTCAAAATTTTCCAGATTAGTGTAGTG 57.168 33.333 0.00 0.00 0.00 2.74
3656 3793 9.567776 TCAAAATTTTCCAGATTAGTGTAGTGA 57.432 29.630 0.00 0.00 0.00 3.41
3659 3796 9.965902 AAATTTTCCAGATTAGTGTAGTGATCT 57.034 29.630 0.00 0.00 0.00 2.75
3663 3800 9.871238 TTTCCAGATTAGTGTAGTGATCTAAAC 57.129 33.333 0.00 0.00 35.28 2.01
3664 3801 8.589701 TCCAGATTAGTGTAGTGATCTAAACA 57.410 34.615 0.00 0.00 36.97 2.83
3665 3802 8.467598 TCCAGATTAGTGTAGTGATCTAAACAC 58.532 37.037 13.69 13.69 36.97 3.32
3668 3805 9.244292 AGATTAGTGTAGTGATCTAAACACTCA 57.756 33.333 22.33 15.97 45.58 3.41
3688 3825 7.985184 ACACTCATATATTTCTTTACAGCGGAA 59.015 33.333 0.00 0.00 0.00 4.30
3787 3972 5.923733 AGACAACCAATAGAGATCGAACT 57.076 39.130 0.00 0.00 0.00 3.01
3798 3983 2.279937 GATCGAACTGGTGAACGCGC 62.280 60.000 5.73 0.00 0.00 6.86
3813 3998 1.635663 CGCGCTAAGAAACTGGTGGG 61.636 60.000 5.56 0.00 0.00 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
85 88 0.826256 ATGGCGCTCGTATGGGTCTA 60.826 55.000 7.64 0.00 0.00 2.59
125 128 1.279496 TGCCATGTACCTCTCAAGCT 58.721 50.000 0.00 0.00 0.00 3.74
127 130 2.290260 TGGTTGCCATGTACCTCTCAAG 60.290 50.000 9.47 0.00 35.41 3.02
141 144 3.402110 CCAAAATTCCTCTTTGGTTGCC 58.598 45.455 6.23 0.00 45.21 4.52
252 256 3.243877 GTCACTTAGAGCACATGCATACG 59.756 47.826 6.64 0.00 45.16 3.06
429 481 8.846211 TCGAAGGTCAAAGAAACAGATTTTTAT 58.154 29.630 0.00 0.00 0.00 1.40
463 515 1.795170 GAGCACCGGCACATTGTGTT 61.795 55.000 17.64 0.00 44.61 3.32
464 516 2.203337 AGCACCGGCACATTGTGT 60.203 55.556 17.64 0.00 44.61 3.72
531 583 6.040616 GGCCATACCGTGCTTAGTAGATATAT 59.959 42.308 0.00 0.00 0.00 0.86
548 600 2.595655 GGTCCACCAGGCCATACC 59.404 66.667 5.01 0.00 39.61 2.73
566 618 2.226437 GGATTATGTTGCACGCATAGGG 59.774 50.000 9.31 0.00 31.44 3.53
588 641 6.209788 TCACATAGGAAACCCCACAAATTTAC 59.790 38.462 0.00 0.00 37.41 2.01
664 732 1.324005 GCTAGGAGCAGGGAAGTCGT 61.324 60.000 0.00 0.00 41.89 4.34
680 748 1.374947 GCCCAACTGTCAGTGGCTA 59.625 57.895 21.57 0.00 35.20 3.93
718 786 1.202114 GTACGTCGTCCAACCCATGTA 59.798 52.381 0.00 0.00 0.00 2.29
749 817 8.752005 ACTGTGTAAATATGATGCCTACATTT 57.248 30.769 0.00 0.00 36.35 2.32
754 822 5.303333 TCGGACTGTGTAAATATGATGCCTA 59.697 40.000 0.00 0.00 0.00 3.93
768 836 3.267900 CGAACTTGTCGGACTGTGT 57.732 52.632 9.88 2.91 46.45 3.72
809 877 5.699458 GCAGTCAGTTTAGTGCCTAAAGTTA 59.301 40.000 10.55 3.61 37.45 2.24
896 964 4.104831 TCCCTTCCCTTTTGTTGGAAAAA 58.895 39.130 0.00 0.00 40.02 1.94
897 965 3.725634 TCCCTTCCCTTTTGTTGGAAAA 58.274 40.909 0.00 0.00 40.02 2.29
898 966 3.406512 TCCCTTCCCTTTTGTTGGAAA 57.593 42.857 0.00 0.00 40.02 3.13
899 967 3.052490 TCTTCCCTTCCCTTTTGTTGGAA 60.052 43.478 0.00 0.00 38.30 3.53
900 968 2.516277 TCTTCCCTTCCCTTTTGTTGGA 59.484 45.455 0.00 0.00 0.00 3.53
901 969 2.893489 CTCTTCCCTTCCCTTTTGTTGG 59.107 50.000 0.00 0.00 0.00 3.77
917 985 1.204467 CACACCCTCTCTGCTCTCTTC 59.796 57.143 0.00 0.00 0.00 2.87
922 990 1.203523 CTGTACACACCCTCTCTGCTC 59.796 57.143 0.00 0.00 0.00 4.26
927 995 0.533032 GGAGCTGTACACACCCTCTC 59.467 60.000 0.00 0.00 0.00 3.20
944 1012 2.680352 GAGAGTGGGAGCGTGGGA 60.680 66.667 0.00 0.00 0.00 4.37
950 1018 1.216710 CGACAAGGAGAGTGGGAGC 59.783 63.158 0.00 0.00 0.00 4.70
987 1055 0.107993 CGATCATCTGTGTGGCACCT 60.108 55.000 16.26 0.00 32.73 4.00
993 1061 2.528743 GCGCCCGATCATCTGTGTG 61.529 63.158 0.00 0.00 0.00 3.82
1617 1685 3.179048 GCGTGAATTTTTGACATAGCCC 58.821 45.455 0.00 0.00 0.00 5.19
1639 1707 2.019249 CACCATCAAAGCATCATCCGT 58.981 47.619 0.00 0.00 0.00 4.69
1655 1723 3.056821 CCTGACTATCGTCTTGAACACCA 60.057 47.826 0.00 0.00 40.86 4.17
1683 1751 0.250124 ACTCGTTTGGCCGAACATCA 60.250 50.000 30.90 15.70 36.24 3.07
1914 1982 3.817084 GCTGTGCATAGCCTGAAATCATA 59.183 43.478 23.66 0.00 37.73 2.15
2052 2120 7.323656 GTCTCAAAACACTGTATTCCAAAATCG 59.676 37.037 0.00 0.00 0.00 3.34
2151 2219 2.099592 CACAGCTCTTTCAAGCAAACCA 59.900 45.455 0.00 0.00 45.00 3.67
2217 2285 0.745845 AAGCAGCCAATAGAGTGCCG 60.746 55.000 0.00 0.00 36.54 5.69
2247 2315 3.629398 ACTCAGCAAACTCCAAGTTCTTG 59.371 43.478 5.66 5.66 37.47 3.02
2306 2374 2.106332 GTACATAGGCGCCTGCGT 59.894 61.111 38.98 32.95 44.10 5.24
2349 2417 1.201429 AGACCTCGGCCCACTGATTT 61.201 55.000 0.00 0.00 0.00 2.17
2446 2514 7.118825 TCTGTCATTTGATCTGAACTCATGAAC 59.881 37.037 0.00 0.00 0.00 3.18
2475 2543 2.839486 TCAAACGAAGCTGAGGATGT 57.161 45.000 0.00 0.00 0.00 3.06
2512 2580 0.690192 TTCATCCGCTCTTCCAACCA 59.310 50.000 0.00 0.00 0.00 3.67
2520 2588 0.465097 CCATTGCCTTCATCCGCTCT 60.465 55.000 0.00 0.00 0.00 4.09
2546 2614 5.645067 TGCAGTACAAAATCAAGATCTGGAG 59.355 40.000 5.89 0.00 0.00 3.86
2583 2651 3.710209 AGCATCTGCACCTTAAGACTT 57.290 42.857 3.36 0.00 45.16 3.01
2881 2979 2.164827 TCCAATGCATCACATGTCTTGC 59.835 45.455 18.37 18.37 39.60 4.01
2882 2980 4.338400 AGATCCAATGCATCACATGTCTTG 59.662 41.667 0.00 0.00 39.60 3.02
2883 2981 4.338400 CAGATCCAATGCATCACATGTCTT 59.662 41.667 0.00 0.00 39.60 3.01
2884 2982 3.883489 CAGATCCAATGCATCACATGTCT 59.117 43.478 0.00 0.00 39.60 3.41
2885 2983 3.630769 ACAGATCCAATGCATCACATGTC 59.369 43.478 0.00 0.00 39.60 3.06
2886 2984 3.380320 CACAGATCCAATGCATCACATGT 59.620 43.478 0.00 0.00 39.60 3.21
2887 2985 3.630312 TCACAGATCCAATGCATCACATG 59.370 43.478 0.00 0.00 39.60 3.21
2888 2986 3.893521 TCACAGATCCAATGCATCACAT 58.106 40.909 0.00 0.00 42.30 3.21
2889 2987 3.353370 TCACAGATCCAATGCATCACA 57.647 42.857 0.00 0.00 0.00 3.58
2890 2988 3.693085 ACTTCACAGATCCAATGCATCAC 59.307 43.478 0.00 0.00 0.00 3.06
2891 2989 3.959293 ACTTCACAGATCCAATGCATCA 58.041 40.909 0.00 0.00 0.00 3.07
2892 2990 5.121811 ACTACTTCACAGATCCAATGCATC 58.878 41.667 0.00 0.00 0.00 3.91
2893 2991 5.108187 ACTACTTCACAGATCCAATGCAT 57.892 39.130 0.00 0.00 0.00 3.96
2894 2992 4.020307 TGACTACTTCACAGATCCAATGCA 60.020 41.667 0.00 0.00 0.00 3.96
3005 3117 3.343941 AGTGCCGCAATAGGTTCTAAA 57.656 42.857 0.00 0.00 0.00 1.85
3007 3119 2.235155 TCAAGTGCCGCAATAGGTTCTA 59.765 45.455 0.00 0.00 0.00 2.10
3009 3121 1.130561 GTCAAGTGCCGCAATAGGTTC 59.869 52.381 0.00 0.00 0.00 3.62
3019 3131 2.033299 ACAATTTCTGTGTCAAGTGCCG 59.967 45.455 0.00 0.00 36.69 5.69
3031 3143 5.231702 TGCCACATCAATCAACAATTTCTG 58.768 37.500 0.00 0.00 0.00 3.02
3035 3147 5.046878 ACTCATGCCACATCAATCAACAATT 60.047 36.000 0.00 0.00 0.00 2.32
3181 3293 6.014242 TCTGAACTCATGAATCAACTACTGGT 60.014 38.462 10.96 0.00 0.00 4.00
3235 3347 6.267242 TGGTCCAATCTTTCATGAATCAAACA 59.733 34.615 9.40 0.00 0.00 2.83
3275 3387 2.095466 ACAACATAAACCATTGCCGTCG 60.095 45.455 0.00 0.00 0.00 5.12
3278 3390 4.955925 TCTACAACATAAACCATTGCCG 57.044 40.909 0.00 0.00 0.00 5.69
3312 3424 3.671716 TCATCCATCTACATCATGCAGC 58.328 45.455 0.00 0.00 0.00 5.25
3382 3496 3.883489 GTGTTAACTTTGAGCTCACCCTT 59.117 43.478 18.03 9.85 0.00 3.95
3431 3545 8.789762 GGGAAGTTTGAGCTTATTTACACTTTA 58.210 33.333 0.00 0.00 0.00 1.85
3435 3549 6.569179 TGGGAAGTTTGAGCTTATTTACAC 57.431 37.500 0.00 0.00 0.00 2.90
3455 3592 5.360714 ACATGTTTCCAGTAGCAATATTGGG 59.639 40.000 17.02 9.14 0.00 4.12
3464 3601 3.197983 AGGGAGTACATGTTTCCAGTAGC 59.802 47.826 23.03 10.78 32.50 3.58
3465 3602 4.141914 GGAGGGAGTACATGTTTCCAGTAG 60.142 50.000 23.03 0.00 32.50 2.57
3469 3606 2.626785 TGGAGGGAGTACATGTTTCCA 58.373 47.619 23.03 15.27 32.50 3.53
3509 3646 4.946160 ACTCCCTCAAATGGTCCATTTA 57.054 40.909 26.01 14.93 41.40 1.40
3517 3654 7.792032 TCAGTAAATACTACTCCCTCAAATGG 58.208 38.462 0.00 0.00 34.13 3.16
3518 3655 9.838339 AATCAGTAAATACTACTCCCTCAAATG 57.162 33.333 0.00 0.00 34.13 2.32
3568 3705 7.391275 ATTTGGCTTAAATGATCCAAGTTTTGG 59.609 33.333 1.36 1.36 43.46 3.28
3569 3706 7.727331 TTTGGCTTAAATGATCCAAGTTTTG 57.273 32.000 0.00 0.00 39.46 2.44
3570 3707 9.657419 CTATTTGGCTTAAATGATCCAAGTTTT 57.343 29.630 8.94 0.00 39.29 2.43
3571 3708 7.765819 GCTATTTGGCTTAAATGATCCAAGTTT 59.234 33.333 8.94 0.00 39.29 2.66
3572 3709 7.267857 GCTATTTGGCTTAAATGATCCAAGTT 58.732 34.615 8.94 0.00 39.29 2.66
3573 3710 6.183360 GGCTATTTGGCTTAAATGATCCAAGT 60.183 38.462 8.94 0.00 39.29 3.16
3574 3711 6.183360 TGGCTATTTGGCTTAAATGATCCAAG 60.183 38.462 8.94 0.00 39.29 3.61
3575 3712 5.660417 TGGCTATTTGGCTTAAATGATCCAA 59.340 36.000 8.94 0.00 39.29 3.53
3576 3713 5.207354 TGGCTATTTGGCTTAAATGATCCA 58.793 37.500 8.94 9.47 39.29 3.41
3577 3714 5.789643 TGGCTATTTGGCTTAAATGATCC 57.210 39.130 8.94 7.73 39.29 3.36
3581 3718 9.807649 GGATATAATGGCTATTTGGCTTAAATG 57.192 33.333 0.00 2.75 39.29 2.32
3582 3719 8.981659 GGGATATAATGGCTATTTGGCTTAAAT 58.018 33.333 0.00 5.16 41.68 1.40
3583 3720 7.122055 CGGGATATAATGGCTATTTGGCTTAAA 59.878 37.037 0.00 0.00 42.34 1.52
3584 3721 6.601613 CGGGATATAATGGCTATTTGGCTTAA 59.398 38.462 0.00 0.00 42.34 1.85
3585 3722 6.069905 TCGGGATATAATGGCTATTTGGCTTA 60.070 38.462 0.00 0.00 42.34 3.09
3586 3723 4.949856 CGGGATATAATGGCTATTTGGCTT 59.050 41.667 0.00 0.00 42.34 4.35
3587 3724 4.227300 TCGGGATATAATGGCTATTTGGCT 59.773 41.667 0.00 0.00 42.34 4.75
3588 3725 4.523083 TCGGGATATAATGGCTATTTGGC 58.477 43.478 0.00 0.00 42.18 4.52
3589 3726 5.765182 GGATCGGGATATAATGGCTATTTGG 59.235 44.000 0.00 0.00 0.00 3.28
3590 3727 6.595682 AGGATCGGGATATAATGGCTATTTG 58.404 40.000 0.00 0.00 0.00 2.32
3591 3728 6.831664 AGGATCGGGATATAATGGCTATTT 57.168 37.500 0.00 0.00 0.00 1.40
3592 3729 6.617371 AGAAGGATCGGGATATAATGGCTATT 59.383 38.462 0.00 0.00 0.00 1.73
3593 3730 6.042552 CAGAAGGATCGGGATATAATGGCTAT 59.957 42.308 0.00 0.00 0.00 2.97
3594 3731 5.363868 CAGAAGGATCGGGATATAATGGCTA 59.636 44.000 0.00 0.00 0.00 3.93
3595 3732 4.163078 CAGAAGGATCGGGATATAATGGCT 59.837 45.833 0.00 0.00 0.00 4.75
3596 3733 4.080863 ACAGAAGGATCGGGATATAATGGC 60.081 45.833 0.00 0.00 0.00 4.40
3597 3734 5.395768 GGACAGAAGGATCGGGATATAATGG 60.396 48.000 0.00 0.00 0.00 3.16
3607 3744 3.265791 CTTCTTTGGACAGAAGGATCGG 58.734 50.000 2.96 0.00 44.29 4.18
3609 3746 3.938334 GAGCTTCTTTGGACAGAAGGATC 59.062 47.826 11.47 0.00 46.95 3.36
3615 3752 6.469782 AAATTTTGAGCTTCTTTGGACAGA 57.530 33.333 0.00 0.00 0.00 3.41
3618 3755 6.048509 TGGAAAATTTTGAGCTTCTTTGGAC 58.951 36.000 8.47 0.00 0.00 4.02
3639 3776 8.467598 GTGTTTAGATCACTACACTAATCTGGA 58.532 37.037 13.68 0.00 32.46 3.86
3641 3778 9.509855 GAGTGTTTAGATCACTACACTAATCTG 57.490 37.037 19.98 0.00 44.68 2.90
3660 3797 8.612619 CCGCTGTAAAGAAATATATGAGTGTTT 58.387 33.333 0.00 0.00 0.00 2.83
3661 3798 7.985184 TCCGCTGTAAAGAAATATATGAGTGTT 59.015 33.333 0.00 0.00 0.00 3.32
3662 3799 7.497595 TCCGCTGTAAAGAAATATATGAGTGT 58.502 34.615 0.00 0.00 0.00 3.55
3663 3800 7.946655 TCCGCTGTAAAGAAATATATGAGTG 57.053 36.000 0.00 0.00 0.00 3.51
3664 3801 8.204836 ACTTCCGCTGTAAAGAAATATATGAGT 58.795 33.333 0.00 0.00 0.00 3.41
3665 3802 8.594881 ACTTCCGCTGTAAAGAAATATATGAG 57.405 34.615 0.00 0.00 0.00 2.90
3666 3803 9.692749 CTACTTCCGCTGTAAAGAAATATATGA 57.307 33.333 0.00 0.00 0.00 2.15
3671 3808 9.880157 AAATACTACTTCCGCTGTAAAGAAATA 57.120 29.630 0.00 0.00 0.00 1.40
3674 3811 9.880157 AATAAATACTACTTCCGCTGTAAAGAA 57.120 29.630 0.00 0.00 0.00 2.52
3675 3812 9.309516 CAATAAATACTACTTCCGCTGTAAAGA 57.690 33.333 0.00 0.00 0.00 2.52
3677 3814 8.259411 TCCAATAAATACTACTTCCGCTGTAAA 58.741 33.333 0.00 0.00 0.00 2.01
3678 3815 7.784037 TCCAATAAATACTACTTCCGCTGTAA 58.216 34.615 0.00 0.00 0.00 2.41
3679 3816 7.350744 TCCAATAAATACTACTTCCGCTGTA 57.649 36.000 0.00 0.00 0.00 2.74
3681 3818 7.226720 ACAATCCAATAAATACTACTTCCGCTG 59.773 37.037 0.00 0.00 0.00 5.18
3683 3820 7.492352 ACAATCCAATAAATACTACTTCCGC 57.508 36.000 0.00 0.00 0.00 5.54
3787 3972 0.863144 GTTTCTTAGCGCGTTCACCA 59.137 50.000 8.43 0.00 0.00 4.17


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

AutoCloner maintained by Alex Coulton.