Multiple sequence alignment - TraesCS3A01G133500

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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 TraesCS3A01G133500 chr3A 100.000 3471 0 0 1 3471 110683455 110679985 0.000000e+00 6410.0
1 TraesCS3A01G133500 chr3A 95.846 1661 52 4 1811 3471 377489000 377487357 0.000000e+00 2669.0
2 TraesCS3A01G133500 chr3A 83.173 416 41 8 408 820 645409594 645409983 1.530000e-93 353.0
3 TraesCS3A01G133500 chr3A 92.958 71 5 0 1272 1342 164372765 164372695 1.700000e-18 104.0
4 TraesCS3A01G133500 chr2A 96.599 2646 75 8 829 3471 377597491 377594858 0.000000e+00 4373.0
5 TraesCS3A01G133500 chr2A 91.265 664 50 6 829 1489 403876840 403876182 0.000000e+00 898.0
6 TraesCS3A01G133500 chr2A 93.016 315 19 1 1175 1489 401918261 401917950 1.140000e-124 457.0
7 TraesCS3A01G133500 chr2A 93.016 315 19 1 1175 1489 403876153 403875842 1.140000e-124 457.0
8 TraesCS3A01G133500 chr2A 100.000 30 0 0 1460 1489 401918319 401918290 4.840000e-04 56.5
9 TraesCS3A01G133500 chr5D 96.451 2649 69 9 829 3471 235910390 235907761 0.000000e+00 4348.0
10 TraesCS3A01G133500 chr4B 94.490 2668 103 16 829 3471 175640240 175637592 0.000000e+00 4072.0
11 TraesCS3A01G133500 chr4B 91.601 1012 64 14 1486 2480 248831322 248832329 0.000000e+00 1378.0
12 TraesCS3A01G133500 chr4B 96.184 760 19 5 2712 3471 422772912 422772163 0.000000e+00 1234.0
13 TraesCS3A01G133500 chr4B 96.000 500 18 1 2200 2699 422773453 422772956 0.000000e+00 811.0
14 TraesCS3A01G133500 chr1A 93.849 1902 87 11 1486 3377 254959205 254957324 0.000000e+00 2837.0
15 TraesCS3A01G133500 chr2B 91.831 1016 59 14 1486 2483 169701666 169700657 0.000000e+00 1395.0
16 TraesCS3A01G133500 chr2B 90.398 854 77 5 2525 3377 339206187 339205338 0.000000e+00 1118.0
17 TraesCS3A01G133500 chr2B 90.164 854 79 5 2525 3377 331503578 331502729 0.000000e+00 1107.0
18 TraesCS3A01G133500 chr2B 92.368 642 44 3 829 1465 331216870 331217511 0.000000e+00 909.0
19 TraesCS3A01G133500 chr2B 89.278 485 39 6 1 482 174323422 174322948 2.310000e-166 595.0
20 TraesCS3A01G133500 chr2B 83.333 210 34 1 615 823 512918022 512918231 3.540000e-45 193.0
21 TraesCS3A01G133500 chr5B 91.321 1014 68 14 1486 2483 294279233 294280242 0.000000e+00 1367.0
22 TraesCS3A01G133500 chr5B 97.973 148 3 0 1 148 298164087 298163940 1.240000e-64 257.0
23 TraesCS3A01G133500 chr7D 95.923 834 31 3 1 831 301863511 301864344 0.000000e+00 1349.0
24 TraesCS3A01G133500 chr7B 94.817 791 37 4 44 831 74394436 74395225 0.000000e+00 1230.0
25 TraesCS3A01G133500 chr7B 90.103 485 36 6 1 482 325752918 325752443 1.370000e-173 619.0
26 TraesCS3A01G133500 chr7B 95.200 250 10 2 1 249 74391443 74391691 9.030000e-106 394.0
27 TraesCS3A01G133500 chr7B 97.973 148 3 0 1 148 215520985 215520838 1.240000e-64 257.0
28 TraesCS3A01G133500 chr7B 96.622 148 5 0 1 148 283702064 283702211 2.680000e-61 246.0
29 TraesCS3A01G133500 chr7B 97.887 142 3 0 1 142 392311959 392312100 2.680000e-61 246.0
30 TraesCS3A01G133500 chr7B 82.938 211 33 3 615 823 586368952 586369161 1.640000e-43 187.0
31 TraesCS3A01G133500 chr7B 88.732 71 4 2 1420 1489 355610031 355609964 2.220000e-12 84.2
32 TraesCS3A01G133500 chr3B 90.749 854 73 6 2525 3377 326265866 326265018 0.000000e+00 1134.0
33 TraesCS3A01G133500 chr3B 95.462 595 16 7 2877 3471 678841798 678841215 0.000000e+00 939.0
34 TraesCS3A01G133500 chr3B 84.399 782 72 19 1486 2267 39599960 39600691 0.000000e+00 723.0
35 TraesCS3A01G133500 chr3B 96.429 112 4 0 3360 3471 608373140 608373251 5.920000e-43 185.0
36 TraesCS3A01G133500 chr3B 96.774 62 1 1 1486 1547 611895230 611895290 6.130000e-18 102.0
37 TraesCS3A01G133500 chr4A 93.359 768 36 8 63 823 361463387 361464146 0.000000e+00 1122.0
38 TraesCS3A01G133500 chr4A 98.649 148 2 0 1 148 181373802 181373655 2.660000e-66 263.0
39 TraesCS3A01G133500 chr1B 94.453 667 29 4 829 1489 425357082 425356418 0.000000e+00 1020.0
40 TraesCS3A01G133500 chr1B 95.800 500 19 1 2200 2699 368095495 368095992 0.000000e+00 806.0
41 TraesCS3A01G133500 chr1B 95.400 500 21 1 2200 2699 499392320 499391823 0.000000e+00 795.0
42 TraesCS3A01G133500 chr1B 83.173 416 41 8 408 820 533962323 533961934 1.530000e-93 353.0
43 TraesCS3A01G133500 chr6B 84.527 782 71 19 1486 2267 422991193 422991924 0.000000e+00 728.0
44 TraesCS3A01G133500 chr6B 90.309 485 35 6 1 482 297412181 297412656 2.940000e-175 625.0
45 TraesCS3A01G133500 chr6B 89.485 485 38 6 1 482 375613250 375612776 4.960000e-168 601.0
46 TraesCS3A01G133500 chr4D 82.921 404 42 15 402 803 417164233 417164611 4.290000e-89 339.0
47 TraesCS3A01G133500 chr6A 81.170 393 46 11 431 820 291415643 291416010 1.220000e-74 291.0


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 TraesCS3A01G133500 chr3A 110679985 110683455 3470 True 6410.0 6410 100.0000 1 3471 1 chr3A.!!$R1 3470
1 TraesCS3A01G133500 chr3A 377487357 377489000 1643 True 2669.0 2669 95.8460 1811 3471 1 chr3A.!!$R3 1660
2 TraesCS3A01G133500 chr2A 377594858 377597491 2633 True 4373.0 4373 96.5990 829 3471 1 chr2A.!!$R1 2642
3 TraesCS3A01G133500 chr2A 403875842 403876840 998 True 677.5 898 92.1405 829 1489 2 chr2A.!!$R3 660
4 TraesCS3A01G133500 chr5D 235907761 235910390 2629 True 4348.0 4348 96.4510 829 3471 1 chr5D.!!$R1 2642
5 TraesCS3A01G133500 chr4B 175637592 175640240 2648 True 4072.0 4072 94.4900 829 3471 1 chr4B.!!$R1 2642
6 TraesCS3A01G133500 chr4B 248831322 248832329 1007 False 1378.0 1378 91.6010 1486 2480 1 chr4B.!!$F1 994
7 TraesCS3A01G133500 chr4B 422772163 422773453 1290 True 1022.5 1234 96.0920 2200 3471 2 chr4B.!!$R2 1271
8 TraesCS3A01G133500 chr1A 254957324 254959205 1881 True 2837.0 2837 93.8490 1486 3377 1 chr1A.!!$R1 1891
9 TraesCS3A01G133500 chr2B 169700657 169701666 1009 True 1395.0 1395 91.8310 1486 2483 1 chr2B.!!$R1 997
10 TraesCS3A01G133500 chr2B 339205338 339206187 849 True 1118.0 1118 90.3980 2525 3377 1 chr2B.!!$R4 852
11 TraesCS3A01G133500 chr2B 331502729 331503578 849 True 1107.0 1107 90.1640 2525 3377 1 chr2B.!!$R3 852
12 TraesCS3A01G133500 chr2B 331216870 331217511 641 False 909.0 909 92.3680 829 1465 1 chr2B.!!$F1 636
13 TraesCS3A01G133500 chr5B 294279233 294280242 1009 False 1367.0 1367 91.3210 1486 2483 1 chr5B.!!$F1 997
14 TraesCS3A01G133500 chr7D 301863511 301864344 833 False 1349.0 1349 95.9230 1 831 1 chr7D.!!$F1 830
15 TraesCS3A01G133500 chr7B 74391443 74395225 3782 False 812.0 1230 95.0085 1 831 2 chr7B.!!$F4 830
16 TraesCS3A01G133500 chr3B 326265018 326265866 848 True 1134.0 1134 90.7490 2525 3377 1 chr3B.!!$R1 852
17 TraesCS3A01G133500 chr3B 678841215 678841798 583 True 939.0 939 95.4620 2877 3471 1 chr3B.!!$R2 594
18 TraesCS3A01G133500 chr3B 39599960 39600691 731 False 723.0 723 84.3990 1486 2267 1 chr3B.!!$F1 781
19 TraesCS3A01G133500 chr4A 361463387 361464146 759 False 1122.0 1122 93.3590 63 823 1 chr4A.!!$F1 760
20 TraesCS3A01G133500 chr1B 425356418 425357082 664 True 1020.0 1020 94.4530 829 1489 1 chr1B.!!$R1 660
21 TraesCS3A01G133500 chr6B 422991193 422991924 731 False 728.0 728 84.5270 1486 2267 1 chr6B.!!$F2 781

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
922 3880 0.890542 GGATGTGCCTTGCTGTGTCA 60.891 55.0 0.00 0.0 0.00 3.58 F
1031 3992 0.105246 TTGTTGGGGTGGAGCCAAAT 60.105 50.0 0.00 0.0 39.65 2.32 F
1621 4992 0.384669 AGCGCTACTGGATAACCGTC 59.615 55.0 8.99 0.0 39.42 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2053 5544 1.075525 CCACCCTCGTATCCCCTCA 60.076 63.158 0.00 0.00 0.00 3.86 R
2363 5859 2.444388 AGAAATGGCATATGCAGAGGGA 59.556 45.455 28.07 5.73 44.36 4.20 R
3201 6816 1.805943 CATGACACGACAATGGCTTCA 59.194 47.619 0.00 0.00 0.00 3.02 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
92 3043 7.563724 TCCTGATGATCTTGATATCCAATCA 57.436 36.000 11.80 11.80 33.68 2.57
149 3100 8.492415 TTGGCTAGGAATCTATATGTACAGTT 57.508 34.615 0.33 0.00 0.00 3.16
261 3213 6.612247 TGTAGTAATTATTTGGCACATCCG 57.388 37.500 0.00 0.00 39.30 4.18
284 3236 2.846193 ACTCAACCAGTTTATGCGTGT 58.154 42.857 0.00 0.00 26.56 4.49
320 3272 7.494298 GTGTATTTGGTTCCAAAGTGAACAAAT 59.506 33.333 19.48 0.00 45.12 2.32
500 3458 6.403866 TGCTATTTATTGTGGCCCTTAATG 57.596 37.500 0.00 0.00 0.00 1.90
563 3521 9.823647 CTCAACTATATATCCATGGATGTTACC 57.176 37.037 33.41 0.00 36.17 2.85
716 3674 4.894784 TCCTCATTGACAACAAGTACTCC 58.105 43.478 0.00 0.00 39.46 3.85
717 3675 3.679980 CCTCATTGACAACAAGTACTCCG 59.320 47.826 0.00 0.00 39.46 4.63
718 3676 4.556233 CTCATTGACAACAAGTACTCCGA 58.444 43.478 0.00 0.00 39.46 4.55
719 3677 5.147330 TCATTGACAACAAGTACTCCGAT 57.853 39.130 0.00 0.00 39.46 4.18
720 3678 6.275494 TCATTGACAACAAGTACTCCGATA 57.725 37.500 0.00 0.00 39.46 2.92
721 3679 6.693466 TCATTGACAACAAGTACTCCGATAA 58.307 36.000 0.00 0.00 39.46 1.75
722 3680 6.588756 TCATTGACAACAAGTACTCCGATAAC 59.411 38.462 0.00 0.00 39.46 1.89
723 3681 5.456548 TGACAACAAGTACTCCGATAACA 57.543 39.130 0.00 0.00 0.00 2.41
724 3682 5.845103 TGACAACAAGTACTCCGATAACAA 58.155 37.500 0.00 0.00 0.00 2.83
725 3683 6.460781 TGACAACAAGTACTCCGATAACAAT 58.539 36.000 0.00 0.00 0.00 2.71
726 3684 6.932400 TGACAACAAGTACTCCGATAACAATT 59.068 34.615 0.00 0.00 0.00 2.32
727 3685 7.442969 TGACAACAAGTACTCCGATAACAATTT 59.557 33.333 0.00 0.00 0.00 1.82
728 3686 8.836268 ACAACAAGTACTCCGATAACAATTTA 57.164 30.769 0.00 0.00 0.00 1.40
729 3687 9.444600 ACAACAAGTACTCCGATAACAATTTAT 57.555 29.630 0.00 0.00 0.00 1.40
766 3724 7.715265 AATTTCACAAGTATACAGATAGCCG 57.285 36.000 5.50 0.00 0.00 5.52
767 3725 6.459670 TTTCACAAGTATACAGATAGCCGA 57.540 37.500 5.50 0.00 0.00 5.54
768 3726 5.434352 TCACAAGTATACAGATAGCCGAC 57.566 43.478 5.50 0.00 0.00 4.79
769 3727 4.885325 TCACAAGTATACAGATAGCCGACA 59.115 41.667 5.50 0.00 0.00 4.35
770 3728 5.358725 TCACAAGTATACAGATAGCCGACAA 59.641 40.000 5.50 0.00 0.00 3.18
771 3729 5.687730 CACAAGTATACAGATAGCCGACAAG 59.312 44.000 5.50 0.00 0.00 3.16
772 3730 5.221263 ACAAGTATACAGATAGCCGACAAGG 60.221 44.000 5.50 0.00 44.97 3.61
781 3739 2.180017 CCGACAAGGCAGCAATGC 59.820 61.111 0.00 0.00 0.00 3.56
782 3740 2.338015 CCGACAAGGCAGCAATGCT 61.338 57.895 0.00 0.00 40.77 3.79
783 3741 1.026182 CCGACAAGGCAGCAATGCTA 61.026 55.000 7.70 0.00 36.40 3.49
784 3742 1.019673 CGACAAGGCAGCAATGCTAT 58.980 50.000 7.70 0.00 36.40 2.97
785 3743 1.402968 CGACAAGGCAGCAATGCTATT 59.597 47.619 7.70 0.13 36.40 1.73
786 3744 2.793585 CGACAAGGCAGCAATGCTATTG 60.794 50.000 19.04 19.04 36.40 1.90
787 3745 2.165030 GACAAGGCAGCAATGCTATTGT 59.835 45.455 23.52 23.52 42.58 2.71
788 3746 2.564062 ACAAGGCAGCAATGCTATTGTT 59.436 40.909 20.01 6.26 39.62 2.83
789 3747 3.184541 CAAGGCAGCAATGCTATTGTTC 58.815 45.455 7.70 0.00 36.40 3.18
790 3748 2.449464 AGGCAGCAATGCTATTGTTCA 58.551 42.857 7.70 0.00 36.40 3.18
791 3749 2.827322 AGGCAGCAATGCTATTGTTCAA 59.173 40.909 7.70 0.00 36.40 2.69
792 3750 3.258872 AGGCAGCAATGCTATTGTTCAAA 59.741 39.130 7.70 0.00 36.40 2.69
793 3751 4.081309 AGGCAGCAATGCTATTGTTCAAAT 60.081 37.500 7.70 0.00 36.40 2.32
794 3752 4.033587 GGCAGCAATGCTATTGTTCAAATG 59.966 41.667 7.70 0.00 36.40 2.32
795 3753 4.628333 GCAGCAATGCTATTGTTCAAATGT 59.372 37.500 7.70 0.00 36.40 2.71
796 3754 5.806502 GCAGCAATGCTATTGTTCAAATGTA 59.193 36.000 7.70 0.00 36.40 2.29
797 3755 6.020121 GCAGCAATGCTATTGTTCAAATGTAG 60.020 38.462 7.70 0.00 36.40 2.74
798 3756 7.031372 CAGCAATGCTATTGTTCAAATGTAGT 58.969 34.615 7.70 0.00 36.40 2.73
799 3757 7.543172 CAGCAATGCTATTGTTCAAATGTAGTT 59.457 33.333 7.70 0.00 36.40 2.24
800 3758 7.543172 AGCAATGCTATTGTTCAAATGTAGTTG 59.457 33.333 5.69 0.00 36.99 3.16
801 3759 7.541783 GCAATGCTATTGTTCAAATGTAGTTGA 59.458 33.333 0.00 0.00 35.72 3.18
802 3760 9.069078 CAATGCTATTGTTCAAATGTAGTTGAG 57.931 33.333 0.00 0.00 38.69 3.02
803 3761 7.744087 TGCTATTGTTCAAATGTAGTTGAGT 57.256 32.000 0.00 0.00 38.69 3.41
804 3762 8.165239 TGCTATTGTTCAAATGTAGTTGAGTT 57.835 30.769 0.00 0.00 38.69 3.01
805 3763 8.075574 TGCTATTGTTCAAATGTAGTTGAGTTG 58.924 33.333 0.00 0.00 38.69 3.16
806 3764 8.289618 GCTATTGTTCAAATGTAGTTGAGTTGA 58.710 33.333 0.00 0.00 38.69 3.18
807 3765 9.817365 CTATTGTTCAAATGTAGTTGAGTTGAG 57.183 33.333 0.00 0.00 38.69 3.02
808 3766 6.060028 TGTTCAAATGTAGTTGAGTTGAGC 57.940 37.500 0.00 0.00 38.69 4.26
809 3767 5.822519 TGTTCAAATGTAGTTGAGTTGAGCT 59.177 36.000 0.00 0.00 38.69 4.09
810 3768 6.318648 TGTTCAAATGTAGTTGAGTTGAGCTT 59.681 34.615 0.00 0.00 38.69 3.74
811 3769 6.942532 TCAAATGTAGTTGAGTTGAGCTTT 57.057 33.333 0.00 0.00 32.56 3.51
812 3770 8.342634 GTTCAAATGTAGTTGAGTTGAGCTTTA 58.657 33.333 0.00 0.00 38.69 1.85
813 3771 8.087982 TCAAATGTAGTTGAGTTGAGCTTTAG 57.912 34.615 0.00 0.00 32.56 1.85
814 3772 7.173218 TCAAATGTAGTTGAGTTGAGCTTTAGG 59.827 37.037 0.00 0.00 32.56 2.69
815 3773 5.546621 TGTAGTTGAGTTGAGCTTTAGGT 57.453 39.130 0.00 0.00 0.00 3.08
816 3774 5.297547 TGTAGTTGAGTTGAGCTTTAGGTG 58.702 41.667 0.00 0.00 0.00 4.00
817 3775 4.423625 AGTTGAGTTGAGCTTTAGGTGT 57.576 40.909 0.00 0.00 0.00 4.16
818 3776 4.781934 AGTTGAGTTGAGCTTTAGGTGTT 58.218 39.130 0.00 0.00 0.00 3.32
819 3777 5.193679 AGTTGAGTTGAGCTTTAGGTGTTT 58.806 37.500 0.00 0.00 0.00 2.83
820 3778 5.297029 AGTTGAGTTGAGCTTTAGGTGTTTC 59.703 40.000 0.00 0.00 0.00 2.78
821 3779 4.776349 TGAGTTGAGCTTTAGGTGTTTCA 58.224 39.130 0.00 0.00 0.00 2.69
822 3780 4.816385 TGAGTTGAGCTTTAGGTGTTTCAG 59.184 41.667 0.00 0.00 0.00 3.02
823 3781 4.781934 AGTTGAGCTTTAGGTGTTTCAGT 58.218 39.130 0.00 0.00 0.00 3.41
824 3782 5.925509 AGTTGAGCTTTAGGTGTTTCAGTA 58.074 37.500 0.00 0.00 0.00 2.74
825 3783 6.354130 AGTTGAGCTTTAGGTGTTTCAGTAA 58.646 36.000 0.00 0.00 0.00 2.24
826 3784 6.260271 AGTTGAGCTTTAGGTGTTTCAGTAAC 59.740 38.462 0.00 0.00 37.26 2.50
827 3785 5.676552 TGAGCTTTAGGTGTTTCAGTAACA 58.323 37.500 0.00 0.00 44.31 2.41
873 3831 5.163602 TGTTTGTTTCGGTTTCTTATGCTGT 60.164 36.000 0.00 0.00 0.00 4.40
922 3880 0.890542 GGATGTGCCTTGCTGTGTCA 60.891 55.000 0.00 0.00 0.00 3.58
935 3893 2.756760 GCTGTGTCATTTGTGATCCCAT 59.243 45.455 0.00 0.00 0.00 4.00
953 3913 2.557452 CCATTTTTAGACCCTGGTGGCT 60.557 50.000 0.00 0.00 37.83 4.75
1031 3992 0.105246 TTGTTGGGGTGGAGCCAAAT 60.105 50.000 0.00 0.00 39.65 2.32
1057 4018 4.489771 CCCTGCCGCCAGTTAGGG 62.490 72.222 0.00 0.00 43.56 3.53
1104 4065 1.227380 GGCACTGTCCGCCTATGAG 60.227 63.158 2.12 0.00 46.56 2.90
1139 4100 7.124573 TGCAAGCTATAGAATTCTTACAGGA 57.875 36.000 14.36 0.00 0.00 3.86
1289 4263 5.226396 CAAAATTTTGCCGATCCTGTGTAA 58.774 37.500 17.48 0.00 0.00 2.41
1293 4267 2.851263 TGCCGATCCTGTGTAAGTTT 57.149 45.000 0.00 0.00 0.00 2.66
1296 4270 2.161609 GCCGATCCTGTGTAAGTTTTGG 59.838 50.000 0.00 0.00 0.00 3.28
1540 4854 7.415765 CCCCGTGTTTTATATGTAAGCAATCAA 60.416 37.037 0.00 0.00 0.00 2.57
1542 4856 7.431084 CCGTGTTTTATATGTAAGCAATCAACC 59.569 37.037 0.00 0.00 0.00 3.77
1621 4992 0.384669 AGCGCTACTGGATAACCGTC 59.615 55.000 8.99 0.00 39.42 4.79
2121 5612 2.060980 GCGGAGTGGGAGAGGTGAT 61.061 63.158 0.00 0.00 0.00 3.06
2373 5869 3.326006 CAGTATGTATGGTCCCTCTGCAT 59.674 47.826 0.00 0.00 0.00 3.96
2387 5883 3.887110 CCTCTGCATATGCCATTTCTTCA 59.113 43.478 24.54 1.84 41.18 3.02
2675 6171 1.681486 TAATGTCAGGCGCCGATGGA 61.681 55.000 23.20 14.82 0.00 3.41
3084 6680 8.361169 TCATATCATATTTGTCGTGGGATCTA 57.639 34.615 0.00 0.00 0.00 1.98
3391 7025 6.533819 TGAAGTTGTATAAACCACGTTCTG 57.466 37.500 0.00 0.00 0.00 3.02
3392 7026 6.050432 TGAAGTTGTATAAACCACGTTCTGT 58.950 36.000 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
142 3093 8.094548 TCATAGCCCATTCATACATAACTGTAC 58.905 37.037 0.00 0.00 40.57 2.90
149 3100 9.812347 AAAAGAATCATAGCCCATTCATACATA 57.188 29.630 0.00 0.00 32.28 2.29
261 3213 4.212636 ACACGCATAAACTGGTTGAGTTAC 59.787 41.667 0.00 0.00 44.68 2.50
284 3236 7.825331 TGGAACCAAATACACACTAAATCAA 57.175 32.000 0.00 0.00 0.00 2.57
465 3423 9.701098 CCACAATAAATAGCAAAAGCATATCAT 57.299 29.630 0.00 0.00 0.00 2.45
500 3458 1.618837 TGGGTTCACAGCAGAGTAGTC 59.381 52.381 0.00 0.00 0.00 2.59
740 3698 9.424319 CGGCTATCTGTATACTTGTGAAATTAT 57.576 33.333 4.17 0.00 0.00 1.28
741 3699 8.635328 TCGGCTATCTGTATACTTGTGAAATTA 58.365 33.333 4.17 0.00 0.00 1.40
742 3700 7.438459 GTCGGCTATCTGTATACTTGTGAAATT 59.562 37.037 4.17 0.00 0.00 1.82
743 3701 6.924060 GTCGGCTATCTGTATACTTGTGAAAT 59.076 38.462 4.17 0.00 0.00 2.17
744 3702 6.127563 TGTCGGCTATCTGTATACTTGTGAAA 60.128 38.462 4.17 0.00 0.00 2.69
745 3703 5.358725 TGTCGGCTATCTGTATACTTGTGAA 59.641 40.000 4.17 0.00 0.00 3.18
746 3704 4.885325 TGTCGGCTATCTGTATACTTGTGA 59.115 41.667 4.17 0.00 0.00 3.58
747 3705 5.183014 TGTCGGCTATCTGTATACTTGTG 57.817 43.478 4.17 0.00 0.00 3.33
748 3706 5.221263 CCTTGTCGGCTATCTGTATACTTGT 60.221 44.000 4.17 0.00 0.00 3.16
749 3707 5.223382 CCTTGTCGGCTATCTGTATACTTG 58.777 45.833 4.17 0.00 0.00 3.16
750 3708 5.455056 CCTTGTCGGCTATCTGTATACTT 57.545 43.478 4.17 0.00 0.00 2.24
764 3722 2.180017 GCATTGCTGCCTTGTCGG 59.820 61.111 0.16 0.00 42.88 4.79
773 3731 7.031372 ACTACATTTGAACAATAGCATTGCTG 58.969 34.615 21.31 8.07 40.10 4.41
774 3732 7.161773 ACTACATTTGAACAATAGCATTGCT 57.838 32.000 16.63 16.63 43.41 3.91
775 3733 7.541783 TCAACTACATTTGAACAATAGCATTGC 59.458 33.333 0.00 0.00 32.42 3.56
776 3734 8.969121 TCAACTACATTTGAACAATAGCATTG 57.031 30.769 7.16 7.16 32.42 2.82
777 3735 8.796475 ACTCAACTACATTTGAACAATAGCATT 58.204 29.630 0.00 0.00 35.07 3.56
778 3736 8.340618 ACTCAACTACATTTGAACAATAGCAT 57.659 30.769 0.00 0.00 35.07 3.79
779 3737 7.744087 ACTCAACTACATTTGAACAATAGCA 57.256 32.000 0.00 0.00 35.07 3.49
780 3738 8.289618 TCAACTCAACTACATTTGAACAATAGC 58.710 33.333 0.00 0.00 35.07 2.97
781 3739 9.817365 CTCAACTCAACTACATTTGAACAATAG 57.183 33.333 0.00 0.00 35.07 1.73
782 3740 8.289618 GCTCAACTCAACTACATTTGAACAATA 58.710 33.333 0.00 0.00 35.07 1.90
783 3741 7.013655 AGCTCAACTCAACTACATTTGAACAAT 59.986 33.333 0.00 0.00 35.07 2.71
784 3742 6.318648 AGCTCAACTCAACTACATTTGAACAA 59.681 34.615 0.00 0.00 35.07 2.83
785 3743 5.822519 AGCTCAACTCAACTACATTTGAACA 59.177 36.000 0.00 0.00 35.07 3.18
786 3744 6.305693 AGCTCAACTCAACTACATTTGAAC 57.694 37.500 0.00 0.00 35.07 3.18
787 3745 6.942532 AAGCTCAACTCAACTACATTTGAA 57.057 33.333 0.00 0.00 35.07 2.69
788 3746 6.942532 AAAGCTCAACTCAACTACATTTGA 57.057 33.333 0.00 0.00 34.30 2.69
789 3747 7.041098 ACCTAAAGCTCAACTCAACTACATTTG 60.041 37.037 0.00 0.00 0.00 2.32
790 3748 6.998673 ACCTAAAGCTCAACTCAACTACATTT 59.001 34.615 0.00 0.00 0.00 2.32
791 3749 6.428159 CACCTAAAGCTCAACTCAACTACATT 59.572 38.462 0.00 0.00 0.00 2.71
792 3750 5.934625 CACCTAAAGCTCAACTCAACTACAT 59.065 40.000 0.00 0.00 0.00 2.29
793 3751 5.163343 ACACCTAAAGCTCAACTCAACTACA 60.163 40.000 0.00 0.00 0.00 2.74
794 3752 5.298347 ACACCTAAAGCTCAACTCAACTAC 58.702 41.667 0.00 0.00 0.00 2.73
795 3753 5.546621 ACACCTAAAGCTCAACTCAACTA 57.453 39.130 0.00 0.00 0.00 2.24
796 3754 4.423625 ACACCTAAAGCTCAACTCAACT 57.576 40.909 0.00 0.00 0.00 3.16
797 3755 5.065988 TGAAACACCTAAAGCTCAACTCAAC 59.934 40.000 0.00 0.00 0.00 3.18
798 3756 5.189928 TGAAACACCTAAAGCTCAACTCAA 58.810 37.500 0.00 0.00 0.00 3.02
799 3757 4.776349 TGAAACACCTAAAGCTCAACTCA 58.224 39.130 0.00 0.00 0.00 3.41
800 3758 4.816925 ACTGAAACACCTAAAGCTCAACTC 59.183 41.667 0.00 0.00 0.00 3.01
801 3759 4.781934 ACTGAAACACCTAAAGCTCAACT 58.218 39.130 0.00 0.00 0.00 3.16
802 3760 6.037830 TGTTACTGAAACACCTAAAGCTCAAC 59.962 38.462 0.00 0.00 43.22 3.18
803 3761 6.116806 TGTTACTGAAACACCTAAAGCTCAA 58.883 36.000 0.00 0.00 43.22 3.02
804 3762 5.676552 TGTTACTGAAACACCTAAAGCTCA 58.323 37.500 0.00 0.00 43.22 4.26
805 3763 5.758784 ACTGTTACTGAAACACCTAAAGCTC 59.241 40.000 0.00 0.00 43.22 4.09
806 3764 5.527582 CACTGTTACTGAAACACCTAAAGCT 59.472 40.000 0.00 0.00 43.22 3.74
807 3765 5.296035 ACACTGTTACTGAAACACCTAAAGC 59.704 40.000 0.00 0.00 43.22 3.51
808 3766 6.920569 ACACTGTTACTGAAACACCTAAAG 57.079 37.500 0.00 0.00 43.22 1.85
809 3767 6.403855 GCAACACTGTTACTGAAACACCTAAA 60.404 38.462 0.00 0.00 43.22 1.85
810 3768 5.065474 GCAACACTGTTACTGAAACACCTAA 59.935 40.000 0.00 0.00 43.22 2.69
811 3769 4.573201 GCAACACTGTTACTGAAACACCTA 59.427 41.667 0.00 0.00 43.22 3.08
812 3770 3.377172 GCAACACTGTTACTGAAACACCT 59.623 43.478 0.00 0.00 43.22 4.00
813 3771 3.691498 GCAACACTGTTACTGAAACACC 58.309 45.455 0.00 0.00 43.22 4.16
814 3772 3.181514 ACGCAACACTGTTACTGAAACAC 60.182 43.478 0.00 0.00 43.22 3.32
815 3773 3.004171 ACGCAACACTGTTACTGAAACA 58.996 40.909 0.00 0.00 45.90 2.83
816 3774 3.350912 CACGCAACACTGTTACTGAAAC 58.649 45.455 0.00 0.00 38.67 2.78
817 3775 2.223157 GCACGCAACACTGTTACTGAAA 60.223 45.455 0.00 0.00 0.00 2.69
818 3776 1.329292 GCACGCAACACTGTTACTGAA 59.671 47.619 0.00 0.00 0.00 3.02
819 3777 0.934496 GCACGCAACACTGTTACTGA 59.066 50.000 0.00 0.00 0.00 3.41
820 3778 0.383002 CGCACGCAACACTGTTACTG 60.383 55.000 0.00 0.00 0.00 2.74
821 3779 0.808453 ACGCACGCAACACTGTTACT 60.808 50.000 0.00 0.00 0.00 2.24
822 3780 0.653323 CACGCACGCAACACTGTTAC 60.653 55.000 0.00 0.00 0.00 2.50
823 3781 1.639000 CACGCACGCAACACTGTTA 59.361 52.632 0.00 0.00 0.00 2.41
824 3782 2.403186 CACGCACGCAACACTGTT 59.597 55.556 0.00 0.00 0.00 3.16
825 3783 4.236416 GCACGCACGCAACACTGT 62.236 61.111 0.00 0.00 0.00 3.55
826 3784 2.918163 AAAGCACGCACGCAACACTG 62.918 55.000 0.00 0.00 0.00 3.66
827 3785 1.433053 TAAAGCACGCACGCAACACT 61.433 50.000 0.00 0.00 0.00 3.55
922 3880 6.155049 CAGGGTCTAAAAATGGGATCACAAAT 59.845 38.462 0.00 0.00 0.00 2.32
953 3913 0.383949 GAGCGGGCAAACAAAACTGA 59.616 50.000 0.00 0.00 0.00 3.41
1031 3992 3.695606 GCGGCAGGGAGACACTGA 61.696 66.667 5.14 0.00 38.20 3.41
1052 4013 1.440618 TGCCCAGAAGAACACCCTAA 58.559 50.000 0.00 0.00 0.00 2.69
1057 4018 0.954452 CCAGTTGCCCAGAAGAACAC 59.046 55.000 0.00 0.00 0.00 3.32
1126 4087 8.879759 TGATTTACATCGTTCCTGTAAGAATTC 58.120 33.333 0.00 0.00 39.51 2.17
1139 4100 5.627499 ACAGCAACATGATTTACATCGTT 57.373 34.783 0.00 0.00 37.07 3.85
1296 4270 2.855660 ACACGTTTAACTGGGCAAAC 57.144 45.000 0.00 0.00 0.00 2.93
1553 4867 3.959975 TCGGGCAAAGCAACACGC 61.960 61.111 0.00 0.00 42.91 5.34
1675 5047 5.567138 AACTTGCAGGATTATGTGCTAAC 57.433 39.130 1.40 0.00 40.54 2.34
1820 5193 9.699410 ATTATCTCTGTGGGATTGACAAAAATA 57.301 29.630 0.00 0.00 0.00 1.40
2053 5544 1.075525 CCACCCTCGTATCCCCTCA 60.076 63.158 0.00 0.00 0.00 3.86
2363 5859 2.444388 AGAAATGGCATATGCAGAGGGA 59.556 45.455 28.07 5.73 44.36 4.20
2373 5869 8.796475 GCCTCTTAAATATGAAGAAATGGCATA 58.204 33.333 16.73 0.00 39.67 3.14
2387 5883 5.394562 AAGCTTGAGGGCCTCTTAAATAT 57.605 39.130 32.28 11.37 0.00 1.28
2498 5994 7.659799 TGCTAGAAGCTGACAAAAGTATTACAA 59.340 33.333 0.00 0.00 42.97 2.41
2872 6401 6.549433 AATGCCTGGTCATCAATATTTTGT 57.451 33.333 0.00 0.00 34.32 2.83
3084 6680 6.530019 CCAGGAAAATATGGTAAAGCAGTT 57.470 37.500 0.00 0.00 0.00 3.16
3201 6816 1.805943 CATGACACGACAATGGCTTCA 59.194 47.619 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.