Multiple sequence alignment - TraesCS3A01G469000

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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 TraesCS3A01G469000 chr3A 100.000 3586 0 0 1 3586 701850063 701853648 0.000000e+00 6623.0
1 TraesCS3A01G469000 chr3A 99.192 2600 10 2 997 3586 700562646 700565244 0.000000e+00 4674.0
2 TraesCS3A01G469000 chr3D 96.578 789 24 2 2801 3586 567227704 567226916 0.000000e+00 1304.0
3 TraesCS3A01G469000 chr3D 85.391 883 95 17 1794 2648 567233146 567232270 0.000000e+00 885.0
4 TraesCS3A01G469000 chr3D 94.737 494 20 4 994 1487 569522758 569523245 0.000000e+00 763.0
5 TraesCS3A01G469000 chr3D 91.501 553 24 4 941 1476 567233868 567233322 0.000000e+00 739.0
6 TraesCS3A01G469000 chr3D 87.162 592 75 1 2055 2645 569523706 569524297 0.000000e+00 671.0
7 TraesCS3A01G469000 chr3D 78.759 838 125 26 1979 2802 569526744 569527542 2.470000e-141 512.0
8 TraesCS3A01G469000 chr3D 91.034 290 14 2 1529 1817 569523261 569523539 7.270000e-102 381.0
9 TraesCS3A01G469000 chr3D 91.005 189 16 1 1543 1731 567233332 567233145 1.650000e-63 254.0
10 TraesCS3A01G469000 chr3D 79.891 368 50 8 2804 3163 567218112 567217761 7.690000e-62 248.0
11 TraesCS3A01G469000 chr3D 90.000 60 6 0 878 937 567233950 567233891 1.070000e-10 78.7
12 TraesCS3A01G469000 chr3D 97.222 36 1 0 3124 3159 564320636 564320601 1.080000e-05 62.1
13 TraesCS3A01G469000 chr3B 91.381 789 59 6 1987 2768 754969484 754970270 0.000000e+00 1072.0
14 TraesCS3A01G469000 chr3B 86.519 675 83 5 1 671 756200115 756199445 0.000000e+00 736.0
15 TraesCS3A01G469000 chr3B 93.145 496 11 2 2764 3258 754970334 754970807 0.000000e+00 706.0
16 TraesCS3A01G469000 chr3B 88.246 570 48 12 839 1402 754967565 754968121 0.000000e+00 664.0
17 TraesCS3A01G469000 chr3B 92.747 455 27 4 957 1405 756196739 756196285 0.000000e+00 652.0
18 TraesCS3A01G469000 chr3B 96.296 270 7 1 3317 3586 754970806 754971072 1.180000e-119 440.0
19 TraesCS3A01G469000 chr3B 97.222 36 1 0 3124 3159 752111179 752111144 1.080000e-05 62.1
20 TraesCS3A01G469000 chrUn 87.867 750 31 16 791 1487 255061768 255061026 0.000000e+00 826.0
21 TraesCS3A01G469000 chrUn 87.867 750 31 16 791 1487 269238774 269238032 0.000000e+00 826.0
22 TraesCS3A01G469000 chrUn 86.702 752 80 11 2029 2772 255058047 255057308 0.000000e+00 817.0
23 TraesCS3A01G469000 chrUn 86.702 752 80 11 2029 2772 269235053 269234314 0.000000e+00 817.0
24 TraesCS3A01G469000 chrUn 100.000 422 0 0 2045 2466 476761470 476761891 0.000000e+00 780.0
25 TraesCS3A01G469000 chrUn 87.747 506 59 3 2145 2648 255060341 255059837 3.990000e-164 588.0
26 TraesCS3A01G469000 chrUn 87.747 506 59 3 2145 2648 269237347 269236843 3.990000e-164 588.0
27 TraesCS3A01G469000 chrUn 89.325 459 41 4 120 574 255062308 255061854 1.440000e-158 569.0
28 TraesCS3A01G469000 chrUn 89.325 459 41 4 120 574 269239314 269238860 1.440000e-158 569.0
29 TraesCS3A01G469000 chrUn 77.812 640 73 25 1529 2156 255061009 255060427 7.420000e-87 331.0
30 TraesCS3A01G469000 chrUn 81.176 85 15 1 609 692 255061855 255061771 2.310000e-07 67.6
31 TraesCS3A01G469000 chrUn 81.176 85 15 1 609 692 269238861 269238777 2.310000e-07 67.6
32 TraesCS3A01G469000 chr6A 80.030 671 78 34 1529 2183 192715388 192716018 2.540000e-121 446.0
33 TraesCS3A01G469000 chr6D 79.819 664 91 27 1529 2183 211956500 211957129 9.140000e-121 444.0
34 TraesCS3A01G469000 chr7A 79.809 629 72 30 1571 2183 142485214 142484625 1.200000e-109 407.0
35 TraesCS3A01G469000 chr1D 79.857 561 68 31 1633 2183 166604773 166605298 5.660000e-98 368.0
36 TraesCS3A01G469000 chr1D 88.393 112 13 0 1529 1640 166597395 166597506 6.250000e-28 135.0
37 TraesCS3A01G469000 chr1D 78.505 107 15 5 4 109 293337192 293337093 2.990000e-06 63.9
38 TraesCS3A01G469000 chr1D 100.000 29 0 0 1459 1487 166597346 166597374 2.000000e-03 54.7
39 TraesCS3A01G469000 chr7D 88.462 208 21 2 1529 1735 10598112 10598317 7.690000e-62 248.0
40 TraesCS3A01G469000 chr5D 90.741 162 15 0 1529 1690 60728937 60728776 2.170000e-52 217.0
41 TraesCS3A01G469000 chr2A 87.143 140 18 0 1529 1668 208156041 208156180 3.710000e-35 159.0


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 TraesCS3A01G469000 chr3A 701850063 701853648 3585 False 6623.000 6623 100.000000 1 3586 1 chr3A.!!$F2 3585
1 TraesCS3A01G469000 chr3A 700562646 700565244 2598 False 4674.000 4674 99.192000 997 3586 1 chr3A.!!$F1 2589
2 TraesCS3A01G469000 chr3D 567226916 567227704 788 True 1304.000 1304 96.578000 2801 3586 1 chr3D.!!$R3 785
3 TraesCS3A01G469000 chr3D 569522758 569527542 4784 False 581.750 763 87.923000 994 2802 4 chr3D.!!$F1 1808
4 TraesCS3A01G469000 chr3D 567232270 567233950 1680 True 489.175 885 89.474250 878 2648 4 chr3D.!!$R4 1770
5 TraesCS3A01G469000 chr3B 754967565 754971072 3507 False 720.500 1072 92.267000 839 3586 4 chr3B.!!$F1 2747
6 TraesCS3A01G469000 chr3B 756196285 756200115 3830 True 694.000 736 89.633000 1 1405 2 chr3B.!!$R2 1404
7 TraesCS3A01G469000 chrUn 269234314 269239314 5000 True 573.520 826 86.563400 120 2772 5 chrUn.!!$R2 2652
8 TraesCS3A01G469000 chrUn 255057308 255062308 5000 True 533.100 826 85.104833 120 2772 6 chrUn.!!$R1 2652
9 TraesCS3A01G469000 chr6A 192715388 192716018 630 False 446.000 446 80.030000 1529 2183 1 chr6A.!!$F1 654
10 TraesCS3A01G469000 chr6D 211956500 211957129 629 False 444.000 444 79.819000 1529 2183 1 chr6D.!!$F1 654
11 TraesCS3A01G469000 chr7A 142484625 142485214 589 True 407.000 407 79.809000 1571 2183 1 chr7A.!!$R1 612
12 TraesCS3A01G469000 chr1D 166604773 166605298 525 False 368.000 368 79.857000 1633 2183 1 chr1D.!!$F1 550

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
28 29 0.037232 GGACAACGTGGAGAGGGAAG 60.037 60.0 0.0 0.0 0.00 3.46 F
505 511 0.179040 GACGGGTGGGTCAAACAGAA 60.179 55.0 0.0 0.0 36.91 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1609 4643 2.905415 TGACCCCAAATGAGCTGAAT 57.095 45.000 0.00 0.0 0.0 2.57 R
2932 12148 6.429385 ACTTCTTGATCAATCTCCAGTTTCAC 59.571 38.462 8.96 0.0 0.0 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
19 20 0.939577 CACGAGTGAGGACAACGTGG 60.940 60.000 0.00 0.00 45.33 4.94
21 22 0.387367 CGAGTGAGGACAACGTGGAG 60.387 60.000 0.00 0.00 0.00 3.86
25 26 1.185618 TGAGGACAACGTGGAGAGGG 61.186 60.000 0.00 0.00 0.00 4.30
28 29 0.037232 GGACAACGTGGAGAGGGAAG 60.037 60.000 0.00 0.00 0.00 3.46
41 42 3.166679 AGAGGGAAGACTAGTGTTGGTC 58.833 50.000 10.44 4.03 35.22 4.02
44 45 2.633481 GGGAAGACTAGTGTTGGTCTGT 59.367 50.000 10.44 0.00 43.50 3.41
49 50 1.692519 ACTAGTGTTGGTCTGTGGGAC 59.307 52.381 0.00 0.00 43.79 4.46
62 63 2.619177 CTGTGGGACAGTCTAGATACCG 59.381 54.545 0.00 0.00 41.80 4.02
95 96 2.863346 CGAGAACCGGTGGTGGTGA 61.863 63.158 8.52 0.00 42.89 4.02
112 113 2.354821 GGTGACCGAGGCATTACATTTC 59.645 50.000 0.00 0.00 0.00 2.17
114 115 3.006940 TGACCGAGGCATTACATTTCAC 58.993 45.455 0.00 0.00 0.00 3.18
157 158 6.089954 CGTATGTGATGAATGACTATTGCGAT 59.910 38.462 0.00 0.00 0.00 4.58
177 178 4.697352 CGATGACATTGAGGAGGAAGTTTT 59.303 41.667 0.00 0.00 0.00 2.43
216 217 3.165875 ACGTCTTCATTCCCTCTTCTGA 58.834 45.455 0.00 0.00 0.00 3.27
240 241 4.660303 TGGCATGAAGGATATAAGGTGAGT 59.340 41.667 0.00 0.00 0.00 3.41
244 245 3.958147 TGAAGGATATAAGGTGAGTCGCA 59.042 43.478 5.95 0.00 0.00 5.10
245 246 4.038042 TGAAGGATATAAGGTGAGTCGCAG 59.962 45.833 5.95 0.00 0.00 5.18
246 247 3.567397 AGGATATAAGGTGAGTCGCAGT 58.433 45.455 5.95 0.00 0.00 4.40
247 248 3.961408 AGGATATAAGGTGAGTCGCAGTT 59.039 43.478 5.95 1.07 0.00 3.16
248 249 5.138276 AGGATATAAGGTGAGTCGCAGTTA 58.862 41.667 5.95 3.35 0.00 2.24
266 267 3.071167 AGTTAGCAAACTCGAAGGACCTT 59.929 43.478 6.40 6.40 42.42 3.50
267 268 1.884235 AGCAAACTCGAAGGACCTTG 58.116 50.000 12.68 4.42 0.00 3.61
307 311 8.517878 CCTTTCATGATTTTTCTGCTTCTAAGA 58.482 33.333 0.00 0.00 0.00 2.10
316 320 8.911247 TTTTTCTGCTTCTAAGAACAACTTTC 57.089 30.769 0.00 0.00 39.72 2.62
317 321 7.865706 TTTCTGCTTCTAAGAACAACTTTCT 57.134 32.000 0.00 0.00 39.72 2.52
341 345 7.660208 TCTTAGATAACAAACCCTCAAGTTCAC 59.340 37.037 0.00 0.00 0.00 3.18
383 389 7.310052 GCCCCTCAATAACTTTGAGAGATTTTT 60.310 37.037 15.12 0.00 46.57 1.94
398 404 6.368805 AGAGATTTTTGGTCCTTCAAGTCTT 58.631 36.000 0.00 0.00 0.00 3.01
410 416 7.664318 GGTCCTTCAAGTCTTAAACTGGATAAA 59.336 37.037 0.00 0.00 37.79 1.40
505 511 0.179040 GACGGGTGGGTCAAACAGAA 60.179 55.000 0.00 0.00 36.91 3.02
527 533 2.879026 GTTTGTTTTCTTCCTCCTCGCT 59.121 45.455 0.00 0.00 0.00 4.93
528 534 2.930826 TGTTTTCTTCCTCCTCGCTT 57.069 45.000 0.00 0.00 0.00 4.68
530 536 2.104111 TGTTTTCTTCCTCCTCGCTTCA 59.896 45.455 0.00 0.00 0.00 3.02
545 551 2.097825 GCTTCAATCCATGGCAACTCT 58.902 47.619 6.96 0.00 37.61 3.24
549 555 3.972133 TCAATCCATGGCAACTCTGAAT 58.028 40.909 6.96 0.00 37.61 2.57
554 560 4.661222 TCCATGGCAACTCTGAATGTTTA 58.339 39.130 6.96 0.00 37.61 2.01
557 563 5.396484 CATGGCAACTCTGAATGTTTACAG 58.604 41.667 0.00 0.00 35.72 2.74
571 577 4.378774 TGTTTACAGCGGCAAGTTTAGTA 58.621 39.130 1.45 0.00 0.00 1.82
583 589 5.519206 GGCAAGTTTAGTAACACGAGGATAG 59.481 44.000 0.00 0.00 36.70 2.08
591 597 6.276832 AGTAACACGAGGATAGCAACTTTA 57.723 37.500 0.00 0.00 0.00 1.85
614 620 4.439305 TTGCTAAGCATGGCAACTTTAG 57.561 40.909 8.74 10.12 46.53 1.85
633 640 7.485810 ACTTTAGTGCTTCGGTTTATTTTTGT 58.514 30.769 0.00 0.00 0.00 2.83
634 641 7.434013 ACTTTAGTGCTTCGGTTTATTTTTGTG 59.566 33.333 0.00 0.00 0.00 3.33
636 643 6.084326 AGTGCTTCGGTTTATTTTTGTGAT 57.916 33.333 0.00 0.00 0.00 3.06
640 647 8.921670 GTGCTTCGGTTTATTTTTGTGATAAAT 58.078 29.630 0.00 0.00 33.13 1.40
641 648 8.920665 TGCTTCGGTTTATTTTTGTGATAAATG 58.079 29.630 0.00 0.00 33.13 2.32
642 649 7.897800 GCTTCGGTTTATTTTTGTGATAAATGC 59.102 33.333 0.00 0.00 33.13 3.56
676 683 5.798125 TTGAAAATTGCCATCCTTGTGTA 57.202 34.783 0.00 0.00 0.00 2.90
680 687 6.491745 TGAAAATTGCCATCCTTGTGTAACTA 59.508 34.615 0.00 0.00 38.04 2.24
687 694 6.266558 TGCCATCCTTGTGTAACTAAAATTGT 59.733 34.615 0.00 0.00 38.04 2.71
692 699 7.802738 TCCTTGTGTAACTAAAATTGTCATCG 58.197 34.615 0.00 0.00 38.04 3.84
693 700 7.658167 TCCTTGTGTAACTAAAATTGTCATCGA 59.342 33.333 0.00 0.00 38.04 3.59
694 701 8.286800 CCTTGTGTAACTAAAATTGTCATCGAA 58.713 33.333 0.00 0.00 38.04 3.71
695 702 9.825972 CTTGTGTAACTAAAATTGTCATCGAAT 57.174 29.630 0.00 0.00 38.04 3.34
696 703 9.820229 TTGTGTAACTAAAATTGTCATCGAATC 57.180 29.630 0.00 0.00 38.04 2.52
697 704 8.994170 TGTGTAACTAAAATTGTCATCGAATCA 58.006 29.630 0.00 0.00 38.04 2.57
698 705 9.820229 GTGTAACTAAAATTGTCATCGAATCAA 57.180 29.630 0.00 0.00 0.00 2.57
708 715 7.789341 TTGTCATCGAATCAAAAATTTACCG 57.211 32.000 0.00 0.00 0.00 4.02
709 716 6.904498 TGTCATCGAATCAAAAATTTACCGT 58.096 32.000 0.00 0.00 0.00 4.83
710 717 6.799441 TGTCATCGAATCAAAAATTTACCGTG 59.201 34.615 0.00 0.00 0.00 4.94
711 718 6.799925 GTCATCGAATCAAAAATTTACCGTGT 59.200 34.615 0.00 0.00 0.00 4.49
712 719 6.799441 TCATCGAATCAAAAATTTACCGTGTG 59.201 34.615 0.00 0.00 0.00 3.82
713 720 6.062434 TCGAATCAAAAATTTACCGTGTGT 57.938 33.333 0.00 0.00 0.00 3.72
714 721 6.137415 TCGAATCAAAAATTTACCGTGTGTC 58.863 36.000 0.00 0.00 0.00 3.67
715 722 5.910166 CGAATCAAAAATTTACCGTGTGTCA 59.090 36.000 0.00 0.00 0.00 3.58
716 723 6.580791 CGAATCAAAAATTTACCGTGTGTCAT 59.419 34.615 0.00 0.00 0.00 3.06
717 724 7.114247 CGAATCAAAAATTTACCGTGTGTCATT 59.886 33.333 0.00 0.00 0.00 2.57
718 725 9.400638 GAATCAAAAATTTACCGTGTGTCATTA 57.599 29.630 0.00 0.00 0.00 1.90
719 726 8.964420 ATCAAAAATTTACCGTGTGTCATTAG 57.036 30.769 0.00 0.00 0.00 1.73
720 727 8.155821 TCAAAAATTTACCGTGTGTCATTAGA 57.844 30.769 0.00 0.00 0.00 2.10
721 728 8.622157 TCAAAAATTTACCGTGTGTCATTAGAA 58.378 29.630 0.00 0.00 0.00 2.10
722 729 9.239002 CAAAAATTTACCGTGTGTCATTAGAAA 57.761 29.630 0.00 0.00 0.00 2.52
723 730 9.974980 AAAAATTTACCGTGTGTCATTAGAAAT 57.025 25.926 0.00 0.00 0.00 2.17
724 731 9.974980 AAAATTTACCGTGTGTCATTAGAAATT 57.025 25.926 0.00 0.00 0.00 1.82
725 732 8.964420 AATTTACCGTGTGTCATTAGAAATTG 57.036 30.769 0.00 0.00 0.00 2.32
726 733 4.419522 ACCGTGTGTCATTAGAAATTGC 57.580 40.909 0.00 0.00 0.00 3.56
727 734 3.190535 ACCGTGTGTCATTAGAAATTGCC 59.809 43.478 0.00 0.00 0.00 4.52
728 735 3.190327 CCGTGTGTCATTAGAAATTGCCA 59.810 43.478 0.00 0.00 0.00 4.92
729 736 4.142403 CCGTGTGTCATTAGAAATTGCCAT 60.142 41.667 0.00 0.00 0.00 4.40
730 737 5.030295 CGTGTGTCATTAGAAATTGCCATC 58.970 41.667 0.00 0.00 0.00 3.51
731 738 5.343249 GTGTGTCATTAGAAATTGCCATCC 58.657 41.667 0.00 0.00 0.00 3.51
732 739 5.126061 GTGTGTCATTAGAAATTGCCATCCT 59.874 40.000 0.00 0.00 0.00 3.24
733 740 5.716228 TGTGTCATTAGAAATTGCCATCCTT 59.284 36.000 0.00 0.00 0.00 3.36
734 741 6.038356 GTGTCATTAGAAATTGCCATCCTTG 58.962 40.000 0.00 0.00 0.00 3.61
735 742 5.716228 TGTCATTAGAAATTGCCATCCTTGT 59.284 36.000 0.00 0.00 0.00 3.16
740 747 5.841957 AGAAATTGCCATCCTTGTATGAC 57.158 39.130 0.00 0.00 0.00 3.06
743 750 2.715749 TGCCATCCTTGTATGACTGG 57.284 50.000 0.00 0.00 0.00 4.00
746 753 3.202818 TGCCATCCTTGTATGACTGGAAT 59.797 43.478 0.00 0.00 31.87 3.01
765 772 4.392754 GGAATTGCCATGGAAAAACATCAC 59.607 41.667 18.40 0.00 36.34 3.06
766 773 4.620589 ATTGCCATGGAAAAACATCACA 57.379 36.364 18.40 0.00 0.00 3.58
768 775 2.964464 TGCCATGGAAAAACATCACAGT 59.036 40.909 18.40 0.00 0.00 3.55
770 777 3.005684 GCCATGGAAAAACATCACAGTCA 59.994 43.478 18.40 0.00 0.00 3.41
771 778 4.501229 GCCATGGAAAAACATCACAGTCAA 60.501 41.667 18.40 0.00 0.00 3.18
775 782 7.424803 CATGGAAAAACATCACAGTCAAAGTA 58.575 34.615 0.00 0.00 0.00 2.24
779 786 5.751243 AAACATCACAGTCAAAGTACCAC 57.249 39.130 0.00 0.00 0.00 4.16
786 793 0.865769 GTCAAAGTACCACGCACCTG 59.134 55.000 0.00 0.00 0.00 4.00
789 796 0.466543 AAAGTACCACGCACCTGACA 59.533 50.000 0.00 0.00 0.00 3.58
829 836 6.721571 TGAGTTTACTAATTTCAAGCCGAG 57.278 37.500 0.00 0.00 0.00 4.63
842 852 3.513912 TCAAGCCGAGTAAGATTTCCTCA 59.486 43.478 0.00 0.00 0.00 3.86
848 858 4.563184 CCGAGTAAGATTTCCTCAAAGTCG 59.437 45.833 0.00 0.00 35.30 4.18
851 861 5.172205 AGTAAGATTTCCTCAAAGTCGAGC 58.828 41.667 0.00 0.00 0.00 5.03
855 865 0.671796 TTCCTCAAAGTCGAGCGTCA 59.328 50.000 0.00 0.00 0.00 4.35
861 871 2.475111 TCAAAGTCGAGCGTCAATTCAC 59.525 45.455 0.00 0.00 0.00 3.18
886 2595 9.389755 ACAAAATGCAACTTTAGGTAAAAACAT 57.610 25.926 0.00 0.00 0.00 2.71
933 3419 3.452786 CTCGGCTCGCTTCCTCCA 61.453 66.667 0.00 0.00 0.00 3.86
939 3427 0.318275 GCTCGCTTCCTCCATCTACG 60.318 60.000 0.00 0.00 0.00 3.51
980 3493 2.287547 CGCATAACCAAATCAATCCCCG 60.288 50.000 0.00 0.00 0.00 5.73
1498 4532 7.255625 GCTAATTTCCAATCCTAGGGTTGATTC 60.256 40.741 32.52 11.92 0.00 2.52
1513 4547 5.163663 GGGTTGATTCGATCAGCACAAAATA 60.164 40.000 11.55 0.00 42.63 1.40
3087 12327 3.261643 TGTGTATGCTCACATCCTCTGTT 59.738 43.478 6.01 0.00 42.36 3.16
3088 12328 4.256920 GTGTATGCTCACATCCTCTGTTT 58.743 43.478 0.00 0.00 37.74 2.83
3089 12329 4.697352 GTGTATGCTCACATCCTCTGTTTT 59.303 41.667 0.00 0.00 37.74 2.43
3090 12330 4.937620 TGTATGCTCACATCCTCTGTTTTC 59.062 41.667 0.00 0.00 37.74 2.29
3091 12331 3.777106 TGCTCACATCCTCTGTTTTCT 57.223 42.857 0.00 0.00 35.29 2.52
3092 12332 3.668447 TGCTCACATCCTCTGTTTTCTC 58.332 45.455 0.00 0.00 35.29 2.87
3093 12333 3.071457 TGCTCACATCCTCTGTTTTCTCA 59.929 43.478 0.00 0.00 35.29 3.27
3094 12334 4.260170 GCTCACATCCTCTGTTTTCTCAT 58.740 43.478 0.00 0.00 35.29 2.90
3095 12335 4.094590 GCTCACATCCTCTGTTTTCTCATG 59.905 45.833 0.00 0.00 35.29 3.07
3096 12336 5.485620 CTCACATCCTCTGTTTTCTCATGA 58.514 41.667 0.00 0.00 35.29 3.07
3097 12337 5.240891 TCACATCCTCTGTTTTCTCATGAC 58.759 41.667 0.00 0.00 35.29 3.06
3098 12338 4.394300 CACATCCTCTGTTTTCTCATGACC 59.606 45.833 0.00 0.00 35.29 4.02
3099 12339 4.288105 ACATCCTCTGTTTTCTCATGACCT 59.712 41.667 0.00 0.00 32.90 3.85
3100 12340 5.485353 ACATCCTCTGTTTTCTCATGACCTA 59.515 40.000 0.00 0.00 32.90 3.08
3101 12341 6.157645 ACATCCTCTGTTTTCTCATGACCTAT 59.842 38.462 0.00 0.00 32.90 2.57
3102 12342 5.982356 TCCTCTGTTTTCTCATGACCTATG 58.018 41.667 0.00 0.00 38.17 2.23
3103 12343 5.104776 TCCTCTGTTTTCTCATGACCTATGG 60.105 44.000 0.00 0.00 37.39 2.74
3104 12344 4.517285 TCTGTTTTCTCATGACCTATGGC 58.483 43.478 0.00 0.00 37.39 4.40
3105 12345 3.620488 TGTTTTCTCATGACCTATGGCC 58.380 45.455 0.00 0.00 37.39 5.36
3106 12346 3.266772 TGTTTTCTCATGACCTATGGCCT 59.733 43.478 3.32 0.00 37.39 5.19
3107 12347 3.845781 TTTCTCATGACCTATGGCCTC 57.154 47.619 3.32 0.00 37.39 4.70
3108 12348 2.783379 TCTCATGACCTATGGCCTCT 57.217 50.000 3.32 0.00 37.39 3.69
3382 12624 2.472695 TGGCACTAGTGACATTCCAC 57.527 50.000 27.87 5.83 45.07 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 0.038159 CCTCTCCACGTTGTCCTCAC 60.038 60.000 0.00 0.00 0.00 3.51
9 10 0.037232 CTTCCCTCTCCACGTTGTCC 60.037 60.000 0.00 0.00 0.00 4.02
15 16 1.746220 CACTAGTCTTCCCTCTCCACG 59.254 57.143 0.00 0.00 0.00 4.94
19 20 3.166679 ACCAACACTAGTCTTCCCTCTC 58.833 50.000 0.00 0.00 0.00 3.20
21 22 3.056465 CAGACCAACACTAGTCTTCCCTC 60.056 52.174 0.00 0.00 41.38 4.30
25 26 3.555168 CCCACAGACCAACACTAGTCTTC 60.555 52.174 0.00 0.00 41.38 2.87
28 29 1.968493 TCCCACAGACCAACACTAGTC 59.032 52.381 0.00 0.00 0.00 2.59
44 45 1.688772 GCGGTATCTAGACTGTCCCA 58.311 55.000 3.76 0.00 0.00 4.37
49 50 0.315568 GCCTGGCGGTATCTAGACTG 59.684 60.000 1.35 0.00 0.00 3.51
85 86 4.699522 GCCTCGGTCACCACCACC 62.700 72.222 0.00 0.00 44.02 4.61
89 90 0.036765 TGTAATGCCTCGGTCACCAC 60.037 55.000 0.00 0.00 0.00 4.16
90 91 0.908910 ATGTAATGCCTCGGTCACCA 59.091 50.000 0.00 0.00 0.00 4.17
91 92 2.038387 AATGTAATGCCTCGGTCACC 57.962 50.000 0.00 0.00 0.00 4.02
92 93 3.006940 TGAAATGTAATGCCTCGGTCAC 58.993 45.455 0.00 0.00 0.00 3.67
95 96 3.350219 AGTGAAATGTAATGCCTCGGT 57.650 42.857 0.00 0.00 0.00 4.69
126 127 6.954487 AGTCATTCATCACATACGGTAGTA 57.046 37.500 0.00 0.00 37.24 1.82
157 158 5.308825 GAGAAAACTTCCTCCTCAATGTCA 58.691 41.667 0.00 0.00 0.00 3.58
177 178 5.877491 AGACGTAGGACATATATGTGGAGA 58.123 41.667 22.93 2.99 41.95 3.71
216 217 5.311649 ACTCACCTTATATCCTTCATGCCAT 59.688 40.000 0.00 0.00 0.00 4.40
240 241 2.058798 CTTCGAGTTTGCTAACTGCGA 58.941 47.619 18.34 20.26 44.51 5.10
245 246 3.041508 AGGTCCTTCGAGTTTGCTAAC 57.958 47.619 2.56 2.56 34.36 2.34
246 247 3.181458 ACAAGGTCCTTCGAGTTTGCTAA 60.181 43.478 0.00 0.00 0.00 3.09
247 248 2.367567 ACAAGGTCCTTCGAGTTTGCTA 59.632 45.455 0.00 0.00 0.00 3.49
248 249 1.141053 ACAAGGTCCTTCGAGTTTGCT 59.859 47.619 0.00 0.00 0.00 3.91
307 311 8.762481 AGGGTTTGTTATCTAAGAAAGTTGTT 57.238 30.769 0.00 0.00 30.47 2.83
316 320 7.360101 CGTGAACTTGAGGGTTTGTTATCTAAG 60.360 40.741 0.00 0.00 0.00 2.18
317 321 6.425721 CGTGAACTTGAGGGTTTGTTATCTAA 59.574 38.462 0.00 0.00 0.00 2.10
326 330 6.894339 ATATTTTCGTGAACTTGAGGGTTT 57.106 33.333 0.00 0.00 0.00 3.27
341 345 4.582656 TGAGGGGCCAAATGTATATTTTCG 59.417 41.667 4.39 0.00 34.34 3.46
383 389 4.410883 TCCAGTTTAAGACTTGAAGGACCA 59.589 41.667 0.00 0.00 36.10 4.02
448 454 4.759183 GGAAGAGAGAAAATCACTTGCACT 59.241 41.667 0.00 0.00 43.33 4.40
505 511 2.879026 GCGAGGAGGAAGAAAACAAACT 59.121 45.455 0.00 0.00 0.00 2.66
527 533 3.438216 TCAGAGTTGCCATGGATTGAA 57.562 42.857 18.40 0.00 0.00 2.69
528 534 3.438216 TTCAGAGTTGCCATGGATTGA 57.562 42.857 18.40 6.08 0.00 2.57
530 536 3.705051 ACATTCAGAGTTGCCATGGATT 58.295 40.909 18.40 0.00 0.00 3.01
545 551 2.226330 ACTTGCCGCTGTAAACATTCA 58.774 42.857 0.00 0.00 0.00 2.57
549 555 3.207778 ACTAAACTTGCCGCTGTAAACA 58.792 40.909 0.00 0.00 0.00 2.83
554 560 2.546789 GTGTTACTAAACTTGCCGCTGT 59.453 45.455 0.00 0.00 36.51 4.40
557 563 1.794116 TCGTGTTACTAAACTTGCCGC 59.206 47.619 0.00 0.00 36.51 6.53
571 577 5.148651 ACTAAAGTTGCTATCCTCGTGTT 57.851 39.130 0.00 0.00 0.00 3.32
600 606 2.599659 GAAGCACTAAAGTTGCCATGC 58.400 47.619 0.00 0.00 0.00 4.06
605 611 3.349488 AAACCGAAGCACTAAAGTTGC 57.651 42.857 0.00 0.00 0.00 4.17
613 619 5.508200 TCACAAAAATAAACCGAAGCACT 57.492 34.783 0.00 0.00 0.00 4.40
614 620 7.861176 TTATCACAAAAATAAACCGAAGCAC 57.139 32.000 0.00 0.00 0.00 4.40
633 640 2.772287 TGACACACGGTGCATTTATCA 58.228 42.857 8.30 0.70 36.98 2.15
634 641 4.097714 CAATGACACACGGTGCATTTATC 58.902 43.478 8.30 0.00 37.79 1.75
636 643 3.142174 TCAATGACACACGGTGCATTTA 58.858 40.909 8.30 0.00 37.79 1.40
640 647 1.383523 TTTCAATGACACACGGTGCA 58.616 45.000 8.30 0.00 36.98 4.57
641 648 2.483583 TTTTCAATGACACACGGTGC 57.516 45.000 8.30 0.00 36.98 5.01
642 649 3.182173 GCAATTTTCAATGACACACGGTG 59.818 43.478 6.58 6.58 39.75 4.94
687 694 6.799441 CACACGGTAAATTTTTGATTCGATGA 59.201 34.615 0.00 0.00 0.00 2.92
692 699 7.867445 ATGACACACGGTAAATTTTTGATTC 57.133 32.000 0.00 0.00 0.00 2.52
693 700 9.405587 CTAATGACACACGGTAAATTTTTGATT 57.594 29.630 0.00 0.00 0.00 2.57
694 701 8.788806 TCTAATGACACACGGTAAATTTTTGAT 58.211 29.630 0.00 0.00 0.00 2.57
695 702 8.155821 TCTAATGACACACGGTAAATTTTTGA 57.844 30.769 0.00 0.00 0.00 2.69
696 703 8.789881 TTCTAATGACACACGGTAAATTTTTG 57.210 30.769 0.00 0.00 0.00 2.44
697 704 9.974980 ATTTCTAATGACACACGGTAAATTTTT 57.025 25.926 0.00 0.00 0.00 1.94
698 705 9.974980 AATTTCTAATGACACACGGTAAATTTT 57.025 25.926 0.00 0.00 0.00 1.82
699 706 9.405587 CAATTTCTAATGACACACGGTAAATTT 57.594 29.630 0.00 0.00 0.00 1.82
700 707 7.540745 GCAATTTCTAATGACACACGGTAAATT 59.459 33.333 0.00 0.00 0.00 1.82
701 708 7.027161 GCAATTTCTAATGACACACGGTAAAT 58.973 34.615 0.00 0.00 0.00 1.40
702 709 6.375377 GCAATTTCTAATGACACACGGTAAA 58.625 36.000 0.00 0.00 0.00 2.01
703 710 5.106475 GGCAATTTCTAATGACACACGGTAA 60.106 40.000 0.00 0.00 0.00 2.85
704 711 4.393680 GGCAATTTCTAATGACACACGGTA 59.606 41.667 0.00 0.00 0.00 4.02
705 712 3.190535 GGCAATTTCTAATGACACACGGT 59.809 43.478 0.00 0.00 0.00 4.83
706 713 3.190327 TGGCAATTTCTAATGACACACGG 59.810 43.478 0.00 0.00 27.07 4.94
707 714 4.418013 TGGCAATTTCTAATGACACACG 57.582 40.909 0.00 0.00 27.07 4.49
708 715 5.126061 AGGATGGCAATTTCTAATGACACAC 59.874 40.000 0.00 0.00 37.40 3.82
709 716 5.263599 AGGATGGCAATTTCTAATGACACA 58.736 37.500 0.00 0.00 37.40 3.72
710 717 5.841957 AGGATGGCAATTTCTAATGACAC 57.158 39.130 0.00 0.00 37.40 3.67
711 718 5.716228 ACAAGGATGGCAATTTCTAATGACA 59.284 36.000 0.00 0.00 39.30 3.58
712 719 6.212888 ACAAGGATGGCAATTTCTAATGAC 57.787 37.500 0.00 0.00 0.00 3.06
713 720 7.779326 TCATACAAGGATGGCAATTTCTAATGA 59.221 33.333 0.00 0.00 0.00 2.57
714 721 7.864379 GTCATACAAGGATGGCAATTTCTAATG 59.136 37.037 0.00 0.00 31.46 1.90
715 722 7.781693 AGTCATACAAGGATGGCAATTTCTAAT 59.218 33.333 0.00 0.00 33.68 1.73
716 723 7.067372 CAGTCATACAAGGATGGCAATTTCTAA 59.933 37.037 0.00 0.00 33.68 2.10
717 724 6.543465 CAGTCATACAAGGATGGCAATTTCTA 59.457 38.462 0.00 0.00 33.68 2.10
718 725 5.359009 CAGTCATACAAGGATGGCAATTTCT 59.641 40.000 0.00 0.00 33.68 2.52
719 726 5.450965 CCAGTCATACAAGGATGGCAATTTC 60.451 44.000 0.00 0.00 33.68 2.17
720 727 4.403432 CCAGTCATACAAGGATGGCAATTT 59.597 41.667 0.00 0.00 33.68 1.82
721 728 3.956199 CCAGTCATACAAGGATGGCAATT 59.044 43.478 0.00 0.00 33.68 2.32
722 729 3.202818 TCCAGTCATACAAGGATGGCAAT 59.797 43.478 0.00 0.00 33.68 3.56
723 730 2.575735 TCCAGTCATACAAGGATGGCAA 59.424 45.455 0.00 0.00 33.68 4.52
724 731 2.195727 TCCAGTCATACAAGGATGGCA 58.804 47.619 0.00 0.00 33.68 4.92
725 732 3.281727 TTCCAGTCATACAAGGATGGC 57.718 47.619 0.00 0.00 0.00 4.40
726 733 4.037208 GCAATTCCAGTCATACAAGGATGG 59.963 45.833 0.00 0.00 0.00 3.51
727 734 4.037208 GGCAATTCCAGTCATACAAGGATG 59.963 45.833 0.00 0.00 34.01 3.51
728 735 4.210331 GGCAATTCCAGTCATACAAGGAT 58.790 43.478 0.00 0.00 34.01 3.24
729 736 3.010027 TGGCAATTCCAGTCATACAAGGA 59.990 43.478 0.00 0.00 40.72 3.36
730 737 3.355378 TGGCAATTCCAGTCATACAAGG 58.645 45.455 0.00 0.00 40.72 3.61
743 750 4.996122 TGTGATGTTTTTCCATGGCAATTC 59.004 37.500 6.96 0.00 0.00 2.17
746 753 3.387374 ACTGTGATGTTTTTCCATGGCAA 59.613 39.130 6.96 0.00 0.00 4.52
753 760 6.183360 TGGTACTTTGACTGTGATGTTTTTCC 60.183 38.462 0.00 0.00 0.00 3.13
754 761 6.691388 GTGGTACTTTGACTGTGATGTTTTTC 59.309 38.462 0.00 0.00 0.00 2.29
761 768 2.224185 TGCGTGGTACTTTGACTGTGAT 60.224 45.455 0.00 0.00 0.00 3.06
765 772 0.865769 GGTGCGTGGTACTTTGACTG 59.134 55.000 0.00 0.00 0.00 3.51
766 773 0.756903 AGGTGCGTGGTACTTTGACT 59.243 50.000 0.00 0.00 0.00 3.41
768 775 0.753867 TCAGGTGCGTGGTACTTTGA 59.246 50.000 0.00 0.00 0.00 2.69
770 777 0.466543 TGTCAGGTGCGTGGTACTTT 59.533 50.000 0.00 0.00 0.00 2.66
771 778 0.685097 ATGTCAGGTGCGTGGTACTT 59.315 50.000 0.00 0.00 0.00 2.24
775 782 0.613260 ACATATGTCAGGTGCGTGGT 59.387 50.000 1.41 0.00 0.00 4.16
820 827 3.513912 TGAGGAAATCTTACTCGGCTTGA 59.486 43.478 0.00 0.00 34.03 3.02
829 836 4.031878 CGCTCGACTTTGAGGAAATCTTAC 59.968 45.833 0.00 0.00 36.47 2.34
842 852 2.479837 TGTGAATTGACGCTCGACTTT 58.520 42.857 0.00 0.00 0.00 2.66
848 858 3.307674 TGCATTTTGTGAATTGACGCTC 58.692 40.909 0.00 0.00 0.00 5.03
851 861 5.640218 AAGTTGCATTTTGTGAATTGACG 57.360 34.783 0.00 0.00 0.00 4.35
855 865 9.606631 TTTACCTAAAGTTGCATTTTGTGAATT 57.393 25.926 6.90 0.00 0.00 2.17
886 2595 7.836685 TGGATATTTCAGTTTGGCCACTTATTA 59.163 33.333 3.88 0.00 0.00 0.98
1609 4643 2.905415 TGACCCCAAATGAGCTGAAT 57.095 45.000 0.00 0.00 0.00 2.57
2932 12148 6.429385 ACTTCTTGATCAATCTCCAGTTTCAC 59.571 38.462 8.96 0.00 0.00 3.18
3087 12327 3.387962 AGAGGCCATAGGTCATGAGAAA 58.612 45.455 5.01 0.00 36.69 2.52
3088 12328 2.968574 GAGAGGCCATAGGTCATGAGAA 59.031 50.000 5.01 0.00 36.69 2.87
3089 12329 2.178764 AGAGAGGCCATAGGTCATGAGA 59.821 50.000 5.01 0.00 36.69 3.27
3090 12330 2.607499 AGAGAGGCCATAGGTCATGAG 58.393 52.381 5.01 0.00 36.69 2.90
3091 12331 2.783379 AGAGAGGCCATAGGTCATGA 57.217 50.000 5.01 0.00 36.69 3.07
3092 12332 4.081198 GGAATAGAGAGGCCATAGGTCATG 60.081 50.000 5.01 0.00 0.00 3.07
3093 12333 4.100373 GGAATAGAGAGGCCATAGGTCAT 58.900 47.826 5.01 0.00 0.00 3.06
3094 12334 3.142977 AGGAATAGAGAGGCCATAGGTCA 59.857 47.826 5.01 0.00 0.00 4.02
3095 12335 3.767131 GAGGAATAGAGAGGCCATAGGTC 59.233 52.174 5.01 0.00 0.00 3.85
3096 12336 3.142977 TGAGGAATAGAGAGGCCATAGGT 59.857 47.826 5.01 0.00 0.00 3.08
3097 12337 3.784178 TGAGGAATAGAGAGGCCATAGG 58.216 50.000 5.01 0.00 0.00 2.57
3098 12338 4.837860 AGTTGAGGAATAGAGAGGCCATAG 59.162 45.833 5.01 0.00 0.00 2.23
3099 12339 4.590647 CAGTTGAGGAATAGAGAGGCCATA 59.409 45.833 5.01 0.00 0.00 2.74
3100 12340 3.390639 CAGTTGAGGAATAGAGAGGCCAT 59.609 47.826 5.01 0.00 0.00 4.40
3101 12341 2.768527 CAGTTGAGGAATAGAGAGGCCA 59.231 50.000 5.01 0.00 0.00 5.36
3102 12342 3.034635 TCAGTTGAGGAATAGAGAGGCC 58.965 50.000 0.00 0.00 0.00 5.19
3103 12343 3.957497 TCTCAGTTGAGGAATAGAGAGGC 59.043 47.826 9.13 0.00 42.30 4.70
3104 12344 6.775142 TGTATCTCAGTTGAGGAATAGAGAGG 59.225 42.308 9.13 0.00 42.30 3.69
3105 12345 7.815840 TGTATCTCAGTTGAGGAATAGAGAG 57.184 40.000 9.13 0.00 42.30 3.20
3106 12346 7.782168 ACATGTATCTCAGTTGAGGAATAGAGA 59.218 37.037 9.13 0.00 42.30 3.10
3107 12347 7.866898 CACATGTATCTCAGTTGAGGAATAGAG 59.133 40.741 9.13 0.00 42.30 2.43
3108 12348 7.343057 ACACATGTATCTCAGTTGAGGAATAGA 59.657 37.037 9.13 0.86 42.30 1.98
3382 12624 5.182760 GGCCCTGATAATTGAATTCAGCTAG 59.817 44.000 8.41 3.36 36.41 3.42


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

AutoCloner maintained by Alex Coulton.