Multiple sequence alignment - TraesCS3A01G110700

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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 TraesCS3A01G110700 chr3A 100.000 2747 0 0 1 2747 77707465 77710211 0.000000e+00 5073
1 TraesCS3A01G110700 chr3A 99.648 1990 7 0 1 1990 77593911 77595900 0.000000e+00 3637
2 TraesCS3A01G110700 chr3A 93.377 1389 44 14 630 1990 77548000 77549368 0.000000e+00 2012
3 TraesCS3A01G110700 chr3A 88.372 387 25 5 1992 2366 77595948 77596326 5.400000e-122 448
4 TraesCS3A01G110700 chr3A 86.923 390 26 11 1991 2366 77549416 77549794 5.470000e-112 414
5 TraesCS3A01G110700 chr3D 91.137 1399 73 13 630 1987 66552979 66554367 0.000000e+00 1849
6 TraesCS3A01G110700 chr3D 88.031 1529 124 33 763 2247 66561416 66562929 0.000000e+00 1755
7 TraesCS3A01G110700 chr3D 87.524 529 28 9 16 522 593291171 593290659 6.600000e-161 577
8 TraesCS3A01G110700 chr3D 89.791 382 30 6 1991 2366 66554418 66554796 5.320000e-132 481
9 TraesCS3A01G110700 chr3D 87.760 384 33 11 2365 2741 104393582 104393958 1.170000e-118 436
10 TraesCS3A01G110700 chr3D 96.250 160 5 1 609 768 66557693 66557851 7.550000e-66 261
11 TraesCS3A01G110700 chr3B 89.962 1315 85 16 630 1912 110735573 110736872 0.000000e+00 1653
12 TraesCS3A01G110700 chr3B 89.558 1063 59 10 609 1658 110741389 110742412 0.000000e+00 1301
13 TraesCS3A01G110700 chr3B 86.788 386 34 8 1993 2366 110738114 110738494 5.470000e-112 414
14 TraesCS3A01G110700 chr3B 78.534 573 68 32 1717 2247 110742413 110742972 2.640000e-85 326
15 TraesCS3A01G110700 chr4A 87.179 741 62 21 1037 1745 697432888 697433627 0.000000e+00 811
16 TraesCS3A01G110700 chr4A 86.803 735 64 20 1043 1745 697439333 697440066 0.000000e+00 789
17 TraesCS3A01G110700 chr4A 85.971 613 47 20 16 609 320492234 320491642 1.080000e-173 619
18 TraesCS3A01G110700 chr7D 90.397 604 42 9 16 609 104606032 104605435 0.000000e+00 780
19 TraesCS3A01G110700 chr7D 86.066 732 72 21 1044 1745 31101997 31101266 0.000000e+00 760
20 TraesCS3A01G110700 chr7D 88.960 625 36 8 16 609 576204498 576203876 0.000000e+00 741
21 TraesCS3A01G110700 chr7D 81.499 854 97 38 869 1679 31070934 31070099 0.000000e+00 645
22 TraesCS3A01G110700 chr7D 84.921 630 35 21 16 602 587445768 587446380 1.420000e-162 582
23 TraesCS3A01G110700 chr7D 84.628 631 33 21 16 602 460082150 460081540 1.100000e-158 569
24 TraesCS3A01G110700 chr7D 90.977 399 36 0 1347 1745 31055803 31055405 3.110000e-149 538
25 TraesCS3A01G110700 chr7D 88.946 389 31 9 2365 2747 134434668 134434286 1.150000e-128 470
26 TraesCS3A01G110700 chr7D 88.918 388 30 9 2365 2747 571725666 571725287 1.490000e-127 466
27 TraesCS3A01G110700 chr7D 92.941 85 6 0 1661 1745 31063506 31063422 1.030000e-24 124
28 TraesCS3A01G110700 chr7A 85.849 742 72 19 1037 1745 31511965 31511224 0.000000e+00 758
29 TraesCS3A01G110700 chr7A 87.814 558 45 8 16 550 717475968 717475411 1.390000e-177 632
30 TraesCS3A01G110700 chr2D 87.774 638 32 13 16 609 498283940 498283305 0.000000e+00 704
31 TraesCS3A01G110700 chr2D 85.474 654 32 22 16 608 638285405 638286056 8.350000e-175 623
32 TraesCS3A01G110700 chr2D 90.026 391 29 7 2365 2747 636073171 636073559 5.280000e-137 497
33 TraesCS3A01G110700 chr6A 87.844 617 49 8 17 608 613706071 613705456 0.000000e+00 701
34 TraesCS3A01G110700 chr6A 86.371 631 42 10 17 603 9496534 9495904 0.000000e+00 649
35 TraesCS3A01G110700 chr6A 85.737 638 45 19 17 608 14692092 14692729 1.390000e-177 632
36 TraesCS3A01G110700 chr6D 87.344 640 36 10 16 610 435883928 435883289 0.000000e+00 691
37 TraesCS3A01G110700 chr6D 83.254 633 42 30 16 612 30186090 30186694 8.720000e-145 523
38 TraesCS3A01G110700 chr6D 87.824 386 36 7 2367 2747 462288190 462288569 2.510000e-120 442
39 TraesCS3A01G110700 chr5A 86.499 637 42 10 17 609 698083744 698083108 0.000000e+00 660
40 TraesCS3A01G110700 chr5A 87.565 386 35 9 2365 2747 435701738 435702113 4.200000e-118 435
41 TraesCS3A01G110700 chr1D 85.344 655 33 12 16 608 236041849 236041196 1.080000e-173 619
42 TraesCS3A01G110700 chr1D 84.786 631 34 23 16 602 303062222 303062834 6.600000e-161 577
43 TraesCS3A01G110700 chrUn 85.038 655 32 18 16 608 137755614 137756264 8.410000e-170 606
44 TraesCS3A01G110700 chrUn 84.494 632 33 23 16 602 24613496 24614107 5.140000e-157 564
45 TraesCS3A01G110700 chrUn 84.202 633 34 23 16 602 24583212 24583824 3.090000e-154 555
46 TraesCS3A01G110700 chrUn 92.188 128 8 1 1778 1903 378540026 378540153 2.170000e-41 180
47 TraesCS3A01G110700 chrUn 92.188 128 8 1 1778 1903 378540992 378541119 2.170000e-41 180
48 TraesCS3A01G110700 chrUn 92.188 128 8 1 1778 1903 378541822 378541949 2.170000e-41 180
49 TraesCS3A01G110700 chrUn 92.188 128 8 1 1778 1903 378542788 378542915 2.170000e-41 180
50 TraesCS3A01G110700 chrUn 91.406 128 9 1 1778 1903 378540509 378540636 1.010000e-39 174
51 TraesCS3A01G110700 chrUn 91.406 128 9 1 1778 1903 378542305 378542432 1.010000e-39 174
52 TraesCS3A01G110700 chrUn 91.406 128 9 1 1778 1903 431546651 431546778 1.010000e-39 174
53 TraesCS3A01G110700 chrUn 91.406 128 9 1 1778 1903 443782976 443782849 1.010000e-39 174
54 TraesCS3A01G110700 chrUn 91.406 128 9 1 1778 1903 443783459 443783332 1.010000e-39 174
55 TraesCS3A01G110700 chr5D 84.748 636 36 19 16 609 437166127 437165511 5.100000e-162 580
56 TraesCS3A01G110700 chr5D 89.203 389 32 6 2365 2747 558062795 558062411 6.880000e-131 477
57 TraesCS3A01G110700 chr5D 86.737 377 39 4 19 386 496573372 496572998 2.550000e-110 409
58 TraesCS3A01G110700 chr5D 83.766 154 18 5 1037 1184 37207160 37207008 3.690000e-29 139
59 TraesCS3A01G110700 chr2A 89.231 390 32 8 2363 2747 768685154 768684770 1.910000e-131 479
60 TraesCS3A01G110700 chr4D 88.010 392 29 15 2365 2747 16929589 16929207 5.400000e-122 448
61 TraesCS3A01G110700 chr2B 93.750 128 6 1 1778 1903 49887407 49887534 1.000000e-44 191
62 TraesCS3A01G110700 chr2B 92.969 128 7 1 1778 1903 49890789 49890916 4.670000e-43 185
63 TraesCS3A01G110700 chr2B 92.188 128 8 1 1778 1903 49893204 49893331 2.170000e-41 180
64 TraesCS3A01G110700 chr2B 89.437 142 13 1 1778 1917 49888374 49888515 7.820000e-41 178
65 TraesCS3A01G110700 chr2B 89.437 142 13 1 1778 1917 49894652 49894793 7.820000e-41 178


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 TraesCS3A01G110700 chr3A 77707465 77710211 2746 False 5073.0 5073 100.00000 1 2747 1 chr3A.!!$F1 2746
1 TraesCS3A01G110700 chr3A 77593911 77596326 2415 False 2042.5 3637 94.01000 1 2366 2 chr3A.!!$F3 2365
2 TraesCS3A01G110700 chr3A 77548000 77549794 1794 False 1213.0 2012 90.15000 630 2366 2 chr3A.!!$F2 1736
3 TraesCS3A01G110700 chr3D 66552979 66562929 9950 False 1086.5 1849 91.30225 609 2366 4 chr3D.!!$F2 1757
4 TraesCS3A01G110700 chr3D 593290659 593291171 512 True 577.0 577 87.52400 16 522 1 chr3D.!!$R1 506
5 TraesCS3A01G110700 chr3B 110735573 110742972 7399 False 923.5 1653 86.21050 609 2366 4 chr3B.!!$F1 1757
6 TraesCS3A01G110700 chr4A 697432888 697433627 739 False 811.0 811 87.17900 1037 1745 1 chr4A.!!$F1 708
7 TraesCS3A01G110700 chr4A 697439333 697440066 733 False 789.0 789 86.80300 1043 1745 1 chr4A.!!$F2 702
8 TraesCS3A01G110700 chr4A 320491642 320492234 592 True 619.0 619 85.97100 16 609 1 chr4A.!!$R1 593
9 TraesCS3A01G110700 chr7D 104605435 104606032 597 True 780.0 780 90.39700 16 609 1 chr7D.!!$R5 593
10 TraesCS3A01G110700 chr7D 31101266 31101997 731 True 760.0 760 86.06600 1044 1745 1 chr7D.!!$R4 701
11 TraesCS3A01G110700 chr7D 576203876 576204498 622 True 741.0 741 88.96000 16 609 1 chr7D.!!$R9 593
12 TraesCS3A01G110700 chr7D 31070099 31070934 835 True 645.0 645 81.49900 869 1679 1 chr7D.!!$R3 810
13 TraesCS3A01G110700 chr7D 587445768 587446380 612 False 582.0 582 84.92100 16 602 1 chr7D.!!$F1 586
14 TraesCS3A01G110700 chr7D 460081540 460082150 610 True 569.0 569 84.62800 16 602 1 chr7D.!!$R7 586
15 TraesCS3A01G110700 chr7A 31511224 31511965 741 True 758.0 758 85.84900 1037 1745 1 chr7A.!!$R1 708
16 TraesCS3A01G110700 chr7A 717475411 717475968 557 True 632.0 632 87.81400 16 550 1 chr7A.!!$R2 534
17 TraesCS3A01G110700 chr2D 498283305 498283940 635 True 704.0 704 87.77400 16 609 1 chr2D.!!$R1 593
18 TraesCS3A01G110700 chr2D 638285405 638286056 651 False 623.0 623 85.47400 16 608 1 chr2D.!!$F2 592
19 TraesCS3A01G110700 chr6A 613705456 613706071 615 True 701.0 701 87.84400 17 608 1 chr6A.!!$R2 591
20 TraesCS3A01G110700 chr6A 9495904 9496534 630 True 649.0 649 86.37100 17 603 1 chr6A.!!$R1 586
21 TraesCS3A01G110700 chr6A 14692092 14692729 637 False 632.0 632 85.73700 17 608 1 chr6A.!!$F1 591
22 TraesCS3A01G110700 chr6D 435883289 435883928 639 True 691.0 691 87.34400 16 610 1 chr6D.!!$R1 594
23 TraesCS3A01G110700 chr6D 30186090 30186694 604 False 523.0 523 83.25400 16 612 1 chr6D.!!$F1 596
24 TraesCS3A01G110700 chr5A 698083108 698083744 636 True 660.0 660 86.49900 17 609 1 chr5A.!!$R1 592
25 TraesCS3A01G110700 chr1D 236041196 236041849 653 True 619.0 619 85.34400 16 608 1 chr1D.!!$R1 592
26 TraesCS3A01G110700 chr1D 303062222 303062834 612 False 577.0 577 84.78600 16 602 1 chr1D.!!$F1 586
27 TraesCS3A01G110700 chrUn 137755614 137756264 650 False 606.0 606 85.03800 16 608 1 chrUn.!!$F3 592
28 TraesCS3A01G110700 chrUn 24613496 24614107 611 False 564.0 564 84.49400 16 602 1 chrUn.!!$F2 586
29 TraesCS3A01G110700 chrUn 24583212 24583824 612 False 555.0 555 84.20200 16 602 1 chrUn.!!$F1 586
30 TraesCS3A01G110700 chr5D 437165511 437166127 616 True 580.0 580 84.74800 16 609 1 chr5D.!!$R2 593


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
565 716 3.492102 ATATGACGGGGGTCAAGAATG 57.508 47.619 0.58 0.0 36.88 2.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2528 3951 0.031043 CCGGGGAAAACCAAAACGTC 59.969 55.0 0.0 0.0 42.91 4.34 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
565 716 3.492102 ATATGACGGGGGTCAAGAATG 57.508 47.619 0.58 0.00 36.88 2.67
2030 3442 3.265791 GGCGATCCATATGAGTCATTCC 58.734 50.000 11.68 0.00 0.00 3.01
2068 3480 3.779759 CACTTTCCTCTTCTCTCCATCG 58.220 50.000 0.00 0.00 0.00 3.84
2094 3506 7.833284 ATAATCGAAACTCGTGTACTAATCG 57.167 36.000 0.00 0.00 41.35 3.34
2119 3531 3.131709 TCTTTGCTTCCCTCTTGTCTG 57.868 47.619 0.00 0.00 0.00 3.51
2141 3553 5.373222 TGGCAAAACTATAGTGTGTTGACT 58.627 37.500 21.66 0.00 42.25 3.41
2163 3575 6.634805 ACTTATCACGTGATCAAGTTCTCAT 58.365 36.000 33.11 14.42 36.05 2.90
2165 3577 8.251026 ACTTATCACGTGATCAAGTTCTCATAA 58.749 33.333 33.11 16.30 36.05 1.90
2171 3583 5.008019 CGTGATCAAGTTCTCATAAATGGGG 59.992 44.000 0.00 0.00 0.00 4.96
2178 3590 2.338809 TCTCATAAATGGGGAGCGGAT 58.661 47.619 0.00 0.00 0.00 4.18
2207 3619 0.317160 TGCTCTTCGCGAAGGAGAAA 59.683 50.000 39.79 24.03 43.27 2.52
2211 3623 1.611977 TCTTCGCGAAGGAGAAAGTGA 59.388 47.619 39.79 20.62 38.88 3.41
2234 3646 4.927782 TGTGGCGGCAGCGAGTTT 62.928 61.111 13.91 0.00 46.35 2.66
2242 3654 1.132640 GCAGCGAGTTTGGCTTACG 59.867 57.895 0.00 0.00 39.08 3.18
2366 3789 6.659242 AGGAAGTAATACTTTTCACATGTGGG 59.341 38.462 25.16 14.78 38.80 4.61
2368 3791 7.148239 GGAAGTAATACTTTTCACATGTGGGAG 60.148 40.741 25.16 20.32 38.80 4.30
2369 3792 5.648092 AGTAATACTTTTCACATGTGGGAGC 59.352 40.000 25.16 7.86 0.00 4.70
2370 3793 2.363306 ACTTTTCACATGTGGGAGCA 57.637 45.000 25.16 2.82 0.00 4.26
2372 3795 2.362077 ACTTTTCACATGTGGGAGCAAC 59.638 45.455 25.16 0.00 0.00 4.17
2373 3796 2.363306 TTTCACATGTGGGAGCAACT 57.637 45.000 25.16 0.00 0.00 3.16
2375 3798 2.768253 TCACATGTGGGAGCAACTAG 57.232 50.000 25.16 0.00 0.00 2.57
2376 3799 1.977854 TCACATGTGGGAGCAACTAGT 59.022 47.619 25.16 0.00 0.00 2.57
2377 3800 2.371841 TCACATGTGGGAGCAACTAGTT 59.628 45.455 25.16 1.12 0.00 2.24
2379 3802 4.041075 TCACATGTGGGAGCAACTAGTTAA 59.959 41.667 25.16 0.00 0.00 2.01
2380 3803 4.154195 CACATGTGGGAGCAACTAGTTAAC 59.846 45.833 18.51 3.72 0.00 2.01
2381 3804 3.034721 TGTGGGAGCAACTAGTTAACG 57.965 47.619 8.04 0.00 0.00 3.18
2383 3806 3.251571 GTGGGAGCAACTAGTTAACGAG 58.748 50.000 13.50 13.50 0.00 4.18
2385 3808 1.918609 GGAGCAACTAGTTAACGAGCG 59.081 52.381 14.82 8.20 0.00 5.03
2388 3811 1.320852 GCAACTAGTTAACGAGCGCTC 59.679 52.381 27.64 27.64 0.00 5.03
2389 3812 1.918609 CAACTAGTTAACGAGCGCTCC 59.081 52.381 30.66 16.60 0.00 4.70
2392 3815 2.230750 ACTAGTTAACGAGCGCTCCTTT 59.769 45.455 30.66 24.45 0.00 3.11
2393 3816 1.429463 AGTTAACGAGCGCTCCTTTG 58.571 50.000 30.66 19.09 0.00 2.77
2394 3817 0.442699 GTTAACGAGCGCTCCTTTGG 59.557 55.000 30.66 18.71 0.00 3.28
2395 3818 0.672401 TTAACGAGCGCTCCTTTGGG 60.672 55.000 30.66 17.99 0.00 4.12
2396 3819 1.537814 TAACGAGCGCTCCTTTGGGA 61.538 55.000 30.66 8.40 39.70 4.37
2406 3829 2.335712 CCTTTGGGAGCCTCGCAAC 61.336 63.158 22.16 0.00 46.71 4.17
2407 3830 2.668212 TTTGGGAGCCTCGCAACG 60.668 61.111 22.16 0.00 46.71 4.10
2408 3831 3.171828 TTTGGGAGCCTCGCAACGA 62.172 57.895 22.16 7.67 46.71 3.85
2410 3833 2.586357 GGGAGCCTCGCAACGATC 60.586 66.667 3.57 0.00 34.61 3.69
2411 3834 2.184322 GGAGCCTCGCAACGATCA 59.816 61.111 0.00 0.00 34.61 2.92
2412 3835 1.880340 GGAGCCTCGCAACGATCAG 60.880 63.158 0.00 0.00 34.61 2.90
2413 3836 2.510238 AGCCTCGCAACGATCAGC 60.510 61.111 0.00 0.00 34.61 4.26
2423 3846 3.084579 CGATCAGCGTCACTTGGC 58.915 61.111 0.00 0.00 34.64 4.52
2431 3854 3.482783 GTCACTTGGCGCGCTCTC 61.483 66.667 32.29 15.45 0.00 3.20
2432 3855 3.989787 TCACTTGGCGCGCTCTCA 61.990 61.111 32.29 18.24 0.00 3.27
2433 3856 3.485431 CACTTGGCGCGCTCTCAG 61.485 66.667 32.29 21.96 0.00 3.35
2434 3857 3.996124 ACTTGGCGCGCTCTCAGT 61.996 61.111 32.29 22.60 0.00 3.41
2435 3858 3.184683 CTTGGCGCGCTCTCAGTC 61.185 66.667 32.29 12.98 0.00 3.51
2436 3859 3.921767 CTTGGCGCGCTCTCAGTCA 62.922 63.158 32.29 15.77 0.00 3.41
2437 3860 3.300934 TTGGCGCGCTCTCAGTCAT 62.301 57.895 32.29 0.00 0.00 3.06
2439 3862 2.520904 GGCGCGCTCTCAGTCATTC 61.521 63.158 32.29 5.31 0.00 2.67
2440 3863 2.854214 GCGCGCTCTCAGTCATTCG 61.854 63.158 26.67 0.00 0.00 3.34
2441 3864 2.854214 CGCGCTCTCAGTCATTCGC 61.854 63.158 5.56 0.00 39.26 4.70
2442 3865 2.520904 GCGCTCTCAGTCATTCGCC 61.521 63.158 0.00 0.00 37.02 5.54
2444 3867 1.416813 CGCTCTCAGTCATTCGCCAC 61.417 60.000 0.00 0.00 0.00 5.01
2445 3868 1.416813 GCTCTCAGTCATTCGCCACG 61.417 60.000 0.00 0.00 0.00 4.94
2446 3869 0.109086 CTCTCAGTCATTCGCCACGT 60.109 55.000 0.00 0.00 0.00 4.49
2447 3870 0.388520 TCTCAGTCATTCGCCACGTG 60.389 55.000 9.08 9.08 0.00 4.49
2448 3871 0.667487 CTCAGTCATTCGCCACGTGT 60.667 55.000 15.65 0.00 0.00 4.49
2449 3872 0.666274 TCAGTCATTCGCCACGTGTC 60.666 55.000 15.65 0.00 0.00 3.67
2450 3873 1.733041 AGTCATTCGCCACGTGTCG 60.733 57.895 13.61 13.61 0.00 4.35
2451 3874 3.109547 TCATTCGCCACGTGTCGC 61.110 61.111 15.09 10.47 0.00 5.19
2468 3891 2.657237 CGTTCTGGACGCTCCCTT 59.343 61.111 0.00 0.00 45.86 3.95
2469 3892 1.446272 CGTTCTGGACGCTCCCTTC 60.446 63.158 0.00 0.00 45.86 3.46
2470 3893 1.446272 GTTCTGGACGCTCCCTTCG 60.446 63.158 2.23 0.00 35.03 3.79
2471 3894 2.646175 TTCTGGACGCTCCCTTCGG 61.646 63.158 2.23 0.00 35.03 4.30
2472 3895 3.068691 CTGGACGCTCCCTTCGGA 61.069 66.667 2.23 0.00 35.03 4.55
2473 3896 2.363795 TGGACGCTCCCTTCGGAT 60.364 61.111 2.23 0.00 37.60 4.18
2474 3897 1.961180 CTGGACGCTCCCTTCGGATT 61.961 60.000 2.23 0.00 37.60 3.01
2475 3898 1.221021 GGACGCTCCCTTCGGATTT 59.779 57.895 0.00 0.00 37.60 2.17
2476 3899 0.392595 GGACGCTCCCTTCGGATTTT 60.393 55.000 0.00 0.00 37.60 1.82
2477 3900 0.727398 GACGCTCCCTTCGGATTTTG 59.273 55.000 0.00 0.00 37.60 2.44
2478 3901 0.036306 ACGCTCCCTTCGGATTTTGT 59.964 50.000 0.00 0.00 37.60 2.83
2479 3902 1.165270 CGCTCCCTTCGGATTTTGTT 58.835 50.000 0.00 0.00 37.60 2.83
2480 3903 1.539827 CGCTCCCTTCGGATTTTGTTT 59.460 47.619 0.00 0.00 37.60 2.83
2481 3904 2.030274 CGCTCCCTTCGGATTTTGTTTT 60.030 45.455 0.00 0.00 37.60 2.43
2482 3905 3.552068 CGCTCCCTTCGGATTTTGTTTTT 60.552 43.478 0.00 0.00 37.60 1.94
2505 3928 4.894798 TTATTTTTCCGCACGCATTTTC 57.105 36.364 0.00 0.00 0.00 2.29
2507 3930 0.661780 TTTTCCGCACGCATTTTCGG 60.662 50.000 0.00 0.00 42.96 4.30
2508 3931 3.602924 TTCCGCACGCATTTTCGGC 62.603 57.895 0.00 0.00 41.49 5.54
2512 3935 1.274798 CGCACGCATTTTCGGCTTTT 61.275 50.000 0.00 0.00 0.00 2.27
2513 3936 0.858583 GCACGCATTTTCGGCTTTTT 59.141 45.000 0.00 0.00 0.00 1.94
2516 3939 3.060205 GCACGCATTTTCGGCTTTTTAAA 60.060 39.130 0.00 0.00 0.00 1.52
2517 3940 4.441825 CACGCATTTTCGGCTTTTTAAAC 58.558 39.130 0.00 0.00 0.00 2.01
2518 3941 3.180782 ACGCATTTTCGGCTTTTTAAACG 59.819 39.130 0.00 0.00 0.00 3.60
2519 3942 3.421184 CGCATTTTCGGCTTTTTAAACGG 60.421 43.478 0.00 0.00 0.00 4.44
2520 3943 3.120820 GCATTTTCGGCTTTTTAAACGGG 60.121 43.478 0.00 0.00 0.00 5.28
2545 3968 1.023502 TCGACGTTTTGGTTTTCCCC 58.976 50.000 0.00 0.00 39.73 4.81
2546 3969 0.317186 CGACGTTTTGGTTTTCCCCG 60.317 55.000 0.00 0.00 39.73 5.73
2547 3970 0.031043 GACGTTTTGGTTTTCCCCGG 59.969 55.000 0.00 0.00 39.73 5.73
2549 3972 0.031043 CGTTTTGGTTTTCCCCGGTC 59.969 55.000 0.00 0.00 39.73 4.79
2550 3973 1.405872 GTTTTGGTTTTCCCCGGTCT 58.594 50.000 0.00 0.00 39.73 3.85
2552 3975 1.694844 TTTGGTTTTCCCCGGTCTTC 58.305 50.000 0.00 0.00 39.73 2.87
2553 3976 0.178984 TTGGTTTTCCCCGGTCTTCC 60.179 55.000 0.00 0.00 39.73 3.46
2557 3980 2.617276 GGTTTTCCCCGGTCTTCCTTAG 60.617 54.545 0.00 0.00 0.00 2.18
2558 3981 0.616891 TTTCCCCGGTCTTCCTTAGC 59.383 55.000 0.00 0.00 0.00 3.09
2560 3983 0.686769 TCCCCGGTCTTCCTTAGCTC 60.687 60.000 0.00 0.00 0.00 4.09
2563 6265 1.137282 CCCGGTCTTCCTTAGCTCTTC 59.863 57.143 0.00 0.00 0.00 2.87
2564 6266 1.202313 CCGGTCTTCCTTAGCTCTTCG 60.202 57.143 0.00 0.00 0.00 3.79
2571 6273 6.817140 GGTCTTCCTTAGCTCTTCGATAAAAA 59.183 38.462 0.00 0.00 0.00 1.94
2621 6323 7.754801 AAAAACGCGTTTTCTTTTCTTTTTC 57.245 28.000 40.39 0.00 41.45 2.29
2622 6324 6.699895 AAACGCGTTTTCTTTTCTTTTTCT 57.300 29.167 30.36 3.49 0.00 2.52
2623 6325 6.699895 AACGCGTTTTCTTTTCTTTTTCTT 57.300 29.167 20.79 0.00 0.00 2.52
2624 6326 6.699895 ACGCGTTTTCTTTTCTTTTTCTTT 57.300 29.167 5.58 0.00 0.00 2.52
2625 6327 7.112528 ACGCGTTTTCTTTTCTTTTTCTTTT 57.887 28.000 5.58 0.00 0.00 2.27
2626 6328 7.007117 ACGCGTTTTCTTTTCTTTTTCTTTTG 58.993 30.769 5.58 0.00 0.00 2.44
2627 6329 6.023333 CGCGTTTTCTTTTCTTTTTCTTTTGC 60.023 34.615 0.00 0.00 0.00 3.68
2628 6330 6.023333 GCGTTTTCTTTTCTTTTTCTTTTGCG 60.023 34.615 0.00 0.00 0.00 4.85
2630 6332 7.738176 CGTTTTCTTTTCTTTTTCTTTTGCGAA 59.262 29.630 0.00 0.00 0.00 4.70
2631 6333 9.376171 GTTTTCTTTTCTTTTTCTTTTGCGAAA 57.624 25.926 0.00 0.00 0.00 3.46
2632 6334 9.592720 TTTTCTTTTCTTTTTCTTTTGCGAAAG 57.407 25.926 18.91 18.91 42.92 2.62
2633 6335 7.883229 TCTTTTCTTTTTCTTTTGCGAAAGT 57.117 28.000 22.94 0.00 42.32 2.66
2634 6336 7.949186 TCTTTTCTTTTTCTTTTGCGAAAGTC 58.051 30.769 22.94 0.00 42.32 3.01
2636 6338 6.626199 TTCTTTTTCTTTTGCGAAAGTCAC 57.374 33.333 22.94 0.00 42.32 3.67
2637 6339 5.704888 TCTTTTTCTTTTGCGAAAGTCACA 58.295 33.333 22.94 4.12 42.32 3.58
2638 6340 5.799936 TCTTTTTCTTTTGCGAAAGTCACAG 59.200 36.000 22.94 15.57 42.32 3.66
2641 6343 4.695217 TCTTTTGCGAAAGTCACAGTTT 57.305 36.364 22.94 0.00 42.32 2.66
2642 6344 5.054390 TCTTTTGCGAAAGTCACAGTTTT 57.946 34.783 22.94 0.00 42.32 2.43
2675 6377 2.230892 CACGGTTGTGCTTTAGCGA 58.769 52.632 10.18 0.00 45.83 4.93
2676 6378 0.163788 CACGGTTGTGCTTTAGCGAG 59.836 55.000 10.18 0.56 45.83 5.03
2679 6381 1.797025 GGTTGTGCTTTAGCGAGAGT 58.203 50.000 0.00 0.00 45.83 3.24
2681 6383 2.404215 GTTGTGCTTTAGCGAGAGTCA 58.596 47.619 0.00 0.00 45.83 3.41
2682 6384 2.065993 TGTGCTTTAGCGAGAGTCAC 57.934 50.000 0.00 5.49 45.83 3.67
2683 6385 0.985549 GTGCTTTAGCGAGAGTCACG 59.014 55.000 5.53 5.53 45.83 4.35
2684 6386 0.109272 TGCTTTAGCGAGAGTCACGG 60.109 55.000 11.95 0.00 45.83 4.94
2686 6388 0.802607 CTTTAGCGAGAGTCACGGCC 60.803 60.000 11.95 0.00 0.00 6.13
2746 11015 3.854286 TTTTTCTTTCGCGAGAGTCAC 57.146 42.857 24.05 0.00 43.69 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
565 716 4.645136 CCCCTAACTCAATTTTCTAAGGGC 59.355 45.833 0.00 0.00 40.99 5.19
1981 3346 5.450818 TCTTTGCTCAGGGGTATATTGTT 57.549 39.130 0.00 0.00 0.00 2.83
1994 3406 1.686355 TCGCCCTTTTTCTTTGCTCA 58.314 45.000 0.00 0.00 0.00 4.26
2030 3442 1.002624 TGCCCGGCAAGTAAAGGAG 60.003 57.895 10.50 0.00 34.76 3.69
2068 3480 8.408202 CGATTAGTACACGAGTTTCGATTATTC 58.592 37.037 5.38 0.00 43.74 1.75
2094 3506 1.902938 AGAGGGAAGCAAAGAAGCAC 58.097 50.000 0.00 0.00 36.85 4.40
2119 3531 5.941948 AGTCAACACACTATAGTTTTGCC 57.058 39.130 1.56 0.00 0.00 4.52
2141 3553 8.996024 TTTATGAGAACTTGATCACGTGATAA 57.004 30.769 30.04 21.40 34.37 1.75
2163 3575 2.930950 CAGAAATCCGCTCCCCATTTA 58.069 47.619 0.00 0.00 0.00 1.40
2165 3577 0.753111 GCAGAAATCCGCTCCCCATT 60.753 55.000 0.00 0.00 0.00 3.16
2171 3583 0.248784 GCATTGGCAGAAATCCGCTC 60.249 55.000 0.00 0.00 40.72 5.03
2207 3619 4.082523 CCGCCACATCCCGTCACT 62.083 66.667 0.00 0.00 0.00 3.41
2366 3789 1.320852 GCGCTCGTTAACTAGTTGCTC 59.679 52.381 18.56 3.86 0.00 4.26
2368 3791 1.320852 GAGCGCTCGTTAACTAGTTGC 59.679 52.381 23.61 11.18 0.00 4.17
2369 3792 1.918609 GGAGCGCTCGTTAACTAGTTG 59.081 52.381 29.81 1.62 0.00 3.16
2370 3793 1.817447 AGGAGCGCTCGTTAACTAGTT 59.183 47.619 29.81 13.68 0.00 2.24
2372 3795 2.563471 AAGGAGCGCTCGTTAACTAG 57.437 50.000 36.34 3.24 36.12 2.57
2373 3796 2.602878 CAAAGGAGCGCTCGTTAACTA 58.397 47.619 36.98 0.00 36.77 2.24
2375 3798 0.442699 CCAAAGGAGCGCTCGTTAAC 59.557 55.000 36.98 21.50 36.77 2.01
2376 3799 0.672401 CCCAAAGGAGCGCTCGTTAA 60.672 55.000 36.98 0.00 36.77 2.01
2377 3800 1.079405 CCCAAAGGAGCGCTCGTTA 60.079 57.895 36.98 0.00 36.77 3.18
2379 3802 3.311110 TCCCAAAGGAGCGCTCGT 61.311 61.111 29.81 27.91 37.19 4.18
2388 3811 2.034066 TTGCGAGGCTCCCAAAGG 59.966 61.111 11.99 0.00 0.00 3.11
2389 3812 2.680913 CGTTGCGAGGCTCCCAAAG 61.681 63.158 15.69 13.85 0.00 2.77
2392 3815 3.371097 GATCGTTGCGAGGCTCCCA 62.371 63.158 9.32 2.72 39.91 4.37
2393 3816 2.586357 GATCGTTGCGAGGCTCCC 60.586 66.667 9.32 0.00 39.91 4.30
2394 3817 1.880340 CTGATCGTTGCGAGGCTCC 60.880 63.158 9.32 2.37 39.91 4.70
2395 3818 2.520904 GCTGATCGTTGCGAGGCTC 61.521 63.158 3.87 3.87 39.91 4.70
2396 3819 2.510238 GCTGATCGTTGCGAGGCT 60.510 61.111 0.00 0.00 39.91 4.58
2406 3829 2.792290 CGCCAAGTGACGCTGATCG 61.792 63.158 0.00 0.00 45.38 3.69
2407 3830 3.084579 CGCCAAGTGACGCTGATC 58.915 61.111 0.00 0.00 0.00 2.92
2415 3838 3.921767 CTGAGAGCGCGCCAAGTGA 62.922 63.158 30.33 6.19 0.00 3.41
2416 3839 3.485431 CTGAGAGCGCGCCAAGTG 61.485 66.667 30.33 12.20 0.00 3.16
2417 3840 3.923563 GACTGAGAGCGCGCCAAGT 62.924 63.158 30.33 24.68 0.00 3.16
2418 3841 3.184683 GACTGAGAGCGCGCCAAG 61.185 66.667 30.33 21.57 0.00 3.61
2419 3842 2.786539 AATGACTGAGAGCGCGCCAA 62.787 55.000 30.33 10.12 0.00 4.52
2420 3843 3.300934 AATGACTGAGAGCGCGCCA 62.301 57.895 30.33 18.19 0.00 5.69
2421 3844 2.510238 AATGACTGAGAGCGCGCC 60.510 61.111 30.33 19.60 0.00 6.53
2422 3845 2.854214 CGAATGACTGAGAGCGCGC 61.854 63.158 26.66 26.66 0.00 6.86
2423 3846 2.854214 GCGAATGACTGAGAGCGCG 61.854 63.158 0.00 0.00 35.02 6.86
2424 3847 2.520904 GGCGAATGACTGAGAGCGC 61.521 63.158 0.00 0.00 43.27 5.92
2425 3848 1.153765 TGGCGAATGACTGAGAGCG 60.154 57.895 0.00 0.00 0.00 5.03
2426 3849 1.416813 CGTGGCGAATGACTGAGAGC 61.417 60.000 0.00 0.00 0.00 4.09
2427 3850 0.109086 ACGTGGCGAATGACTGAGAG 60.109 55.000 0.00 0.00 0.00 3.20
2428 3851 0.388520 CACGTGGCGAATGACTGAGA 60.389 55.000 7.95 0.00 0.00 3.27
2430 3853 0.666274 GACACGTGGCGAATGACTGA 60.666 55.000 21.57 0.00 0.00 3.41
2431 3854 1.781555 GACACGTGGCGAATGACTG 59.218 57.895 21.57 0.00 0.00 3.51
2432 3855 4.261888 GACACGTGGCGAATGACT 57.738 55.556 21.57 0.00 0.00 3.41
2444 3867 3.458579 CGTCCAGAACGCGACACG 61.459 66.667 15.93 8.88 45.76 4.49
2452 3875 1.446272 CGAAGGGAGCGTCCAGAAC 60.446 63.158 6.41 0.00 38.64 3.01
2481 3904 5.659048 AAATGCGTGCGGAAAAATAAAAA 57.341 30.435 0.00 0.00 0.00 1.94
2482 3905 5.610552 CGAAAATGCGTGCGGAAAAATAAAA 60.611 36.000 0.00 0.00 0.00 1.52
2483 3906 4.143514 CGAAAATGCGTGCGGAAAAATAAA 60.144 37.500 0.00 0.00 0.00 1.40
2484 3907 3.362237 CGAAAATGCGTGCGGAAAAATAA 59.638 39.130 0.00 0.00 0.00 1.40
2485 3908 2.911723 CGAAAATGCGTGCGGAAAAATA 59.088 40.909 0.00 0.00 0.00 1.40
2486 3909 1.718711 CGAAAATGCGTGCGGAAAAAT 59.281 42.857 0.00 0.00 0.00 1.82
2487 3910 1.124462 CGAAAATGCGTGCGGAAAAA 58.876 45.000 0.00 0.00 0.00 1.94
2488 3911 0.661780 CCGAAAATGCGTGCGGAAAA 60.662 50.000 8.91 0.00 46.29 2.29
2489 3912 1.081774 CCGAAAATGCGTGCGGAAA 60.082 52.632 8.91 0.00 46.29 3.13
2491 3914 4.096558 GCCGAAAATGCGTGCGGA 62.097 61.111 16.50 0.00 46.29 5.54
2498 3921 3.120820 CCCGTTTAAAAAGCCGAAAATGC 60.121 43.478 0.00 0.00 0.00 3.56
2502 3925 3.797451 AACCCGTTTAAAAAGCCGAAA 57.203 38.095 0.00 0.00 0.00 3.46
2526 3949 1.023502 GGGGAAAACCAAAACGTCGA 58.976 50.000 0.00 0.00 42.91 4.20
2527 3950 0.317186 CGGGGAAAACCAAAACGTCG 60.317 55.000 0.00 0.00 42.91 5.12
2528 3951 0.031043 CCGGGGAAAACCAAAACGTC 59.969 55.000 0.00 0.00 42.91 4.34
2530 3953 0.031043 GACCGGGGAAAACCAAAACG 59.969 55.000 6.32 0.00 42.91 3.60
2531 3954 1.405872 AGACCGGGGAAAACCAAAAC 58.594 50.000 6.32 0.00 42.91 2.43
2533 3956 1.694844 GAAGACCGGGGAAAACCAAA 58.305 50.000 6.32 0.00 42.91 3.28
2534 3957 0.178984 GGAAGACCGGGGAAAACCAA 60.179 55.000 6.32 0.00 42.91 3.67
2536 3959 0.111832 AAGGAAGACCGGGGAAAACC 59.888 55.000 6.32 1.16 41.83 3.27
2537 3960 2.708051 CTAAGGAAGACCGGGGAAAAC 58.292 52.381 6.32 0.00 41.83 2.43
2538 3961 1.003928 GCTAAGGAAGACCGGGGAAAA 59.996 52.381 6.32 0.00 41.83 2.29
2539 3962 0.616891 GCTAAGGAAGACCGGGGAAA 59.383 55.000 6.32 0.00 41.83 3.13
2541 3964 0.686769 GAGCTAAGGAAGACCGGGGA 60.687 60.000 6.32 0.00 41.83 4.81
2542 3965 0.688087 AGAGCTAAGGAAGACCGGGG 60.688 60.000 6.32 0.00 41.83 5.73
2543 3966 1.137282 GAAGAGCTAAGGAAGACCGGG 59.863 57.143 6.32 0.00 41.83 5.73
2545 3968 1.743958 TCGAAGAGCTAAGGAAGACCG 59.256 52.381 0.00 0.00 41.83 4.79
2546 3969 5.517322 TTATCGAAGAGCTAAGGAAGACC 57.483 43.478 0.00 0.00 43.63 3.85
2547 3970 7.829378 TTTTTATCGAAGAGCTAAGGAAGAC 57.171 36.000 0.00 0.00 43.63 3.01
2602 6304 6.023333 GCAAAAGAAAAAGAAAAGAAAACGCG 60.023 34.615 3.53 3.53 0.00 6.01
2603 6305 6.023333 CGCAAAAGAAAAAGAAAAGAAAACGC 60.023 34.615 0.00 0.00 0.00 4.84
2604 6306 7.224024 TCGCAAAAGAAAAAGAAAAGAAAACG 58.776 30.769 0.00 0.00 0.00 3.60
2605 6307 8.927315 TTCGCAAAAGAAAAAGAAAAGAAAAC 57.073 26.923 0.00 0.00 0.00 2.43
2606 6308 9.592720 CTTTCGCAAAAGAAAAAGAAAAGAAAA 57.407 25.926 0.00 0.00 43.90 2.29
2607 6309 8.769891 ACTTTCGCAAAAGAAAAAGAAAAGAAA 58.230 25.926 3.65 0.00 43.90 2.52
2608 6310 8.305441 ACTTTCGCAAAAGAAAAAGAAAAGAA 57.695 26.923 3.65 0.00 43.90 2.52
2609 6311 7.596995 TGACTTTCGCAAAAGAAAAAGAAAAGA 59.403 29.630 3.65 0.00 43.90 2.52
2611 6313 7.169982 TGTGACTTTCGCAAAAGAAAAAGAAAA 59.830 29.630 3.65 0.00 43.90 2.29
2613 6315 6.153067 TGTGACTTTCGCAAAAGAAAAAGAA 58.847 32.000 3.65 0.00 43.90 2.52
2614 6316 5.704888 TGTGACTTTCGCAAAAGAAAAAGA 58.295 33.333 3.65 0.00 43.90 2.52
2615 6317 5.572896 ACTGTGACTTTCGCAAAAGAAAAAG 59.427 36.000 3.65 0.00 43.90 2.27
2616 6318 5.465935 ACTGTGACTTTCGCAAAAGAAAAA 58.534 33.333 3.65 0.00 43.90 1.94
2617 6319 5.054390 ACTGTGACTTTCGCAAAAGAAAA 57.946 34.783 3.65 0.00 43.90 2.29
2618 6320 4.695217 ACTGTGACTTTCGCAAAAGAAA 57.305 36.364 3.65 0.00 43.90 2.52
2619 6321 4.695217 AACTGTGACTTTCGCAAAAGAA 57.305 36.364 3.65 0.00 43.90 2.52
2620 6322 4.695217 AAACTGTGACTTTCGCAAAAGA 57.305 36.364 3.65 0.00 43.90 2.52
2621 6323 5.761818 AAAAACTGTGACTTTCGCAAAAG 57.238 34.783 0.00 0.00 46.11 2.27
2649 6351 3.414700 CACAACCGTGCCTCTCGC 61.415 66.667 0.00 0.00 36.06 5.03
2657 6359 0.163788 CTCGCTAAAGCACAACCGTG 59.836 55.000 2.44 0.00 46.56 4.94
2658 6360 0.032952 TCTCGCTAAAGCACAACCGT 59.967 50.000 2.44 0.00 42.21 4.83
2659 6361 0.716108 CTCTCGCTAAAGCACAACCG 59.284 55.000 2.44 0.00 42.21 4.44
2660 6362 1.727335 GACTCTCGCTAAAGCACAACC 59.273 52.381 2.44 0.00 42.21 3.77
2661 6363 2.155924 GTGACTCTCGCTAAAGCACAAC 59.844 50.000 2.44 0.00 42.21 3.32
2663 6365 1.666023 CGTGACTCTCGCTAAAGCACA 60.666 52.381 2.44 0.00 42.21 4.57
2664 6366 0.985549 CGTGACTCTCGCTAAAGCAC 59.014 55.000 2.44 0.00 42.21 4.40
2665 6367 0.109272 CCGTGACTCTCGCTAAAGCA 60.109 55.000 2.44 0.00 42.21 3.91
2666 6368 1.414527 GCCGTGACTCTCGCTAAAGC 61.415 60.000 0.00 0.00 37.78 3.51
2667 6369 0.802607 GGCCGTGACTCTCGCTAAAG 60.803 60.000 0.00 0.00 0.00 1.85
2668 6370 1.214589 GGCCGTGACTCTCGCTAAA 59.785 57.895 0.00 0.00 0.00 1.85
2669 6371 2.882876 GGCCGTGACTCTCGCTAA 59.117 61.111 0.00 0.00 0.00 3.09
2670 6372 3.506096 CGGCCGTGACTCTCGCTA 61.506 66.667 19.50 0.00 0.00 4.26



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

AutoCloner maintained by Alex Coulton.