Multiple sequence alignment - TraesCS4A01G116900

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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 TraesCS4A01G116900 chr4A 100.000 2981 0 0 1 2981 141573165 141570185 0.000000e+00 5505.0
1 TraesCS4A01G116900 chr4A 92.308 78 6 0 735 812 440964819 440964896 8.730000e-21 111.0
2 TraesCS4A01G116900 chr4B 95.655 1335 47 7 874 2200 408180097 408181428 0.000000e+00 2134.0
3 TraesCS4A01G116900 chr4B 80.564 674 101 20 2314 2981 408189382 408190031 2.670000e-135 492.0
4 TraesCS4A01G116900 chr4B 89.180 305 27 6 6 308 552581280 552580980 2.810000e-100 375.0
5 TraesCS4A01G116900 chr4B 96.000 75 3 0 811 885 408178732 408178806 4.040000e-24 122.0
6 TraesCS4A01G116900 chr4B 88.000 75 6 3 395 468 552580852 552580780 5.290000e-13 86.1
7 TraesCS4A01G116900 chr4D 96.737 1226 32 4 811 2034 328541255 328542474 0.000000e+00 2036.0
8 TraesCS4A01G116900 chr4D 86.570 618 48 23 1 603 442434035 442434632 0.000000e+00 649.0
9 TraesCS4A01G116900 chr4D 94.048 168 8 1 2034 2199 328542814 328542981 1.370000e-63 254.0
10 TraesCS4A01G116900 chr4D 92.405 79 5 1 734 812 252227697 252227620 8.730000e-21 111.0
11 TraesCS4A01G116900 chr7A 79.739 765 114 28 2204 2938 164820322 164821075 1.580000e-142 516.0
12 TraesCS4A01G116900 chr7A 74.375 800 134 51 2203 2947 671496747 671495964 2.930000e-70 276.0
13 TraesCS4A01G116900 chr7A 80.515 272 32 18 168 428 464229787 464230048 3.920000e-44 189.0
14 TraesCS4A01G116900 chr7A 93.671 79 5 0 734 812 56727790 56727712 5.220000e-23 119.0
15 TraesCS4A01G116900 chr1A 78.796 764 106 33 2203 2947 308211219 308211945 2.090000e-126 462.0
16 TraesCS4A01G116900 chr1A 88.064 377 31 10 1 366 548225467 548225094 4.560000e-118 435.0
17 TraesCS4A01G116900 chr1A 82.377 488 70 15 2468 2947 27352065 27352544 7.690000e-111 411.0
18 TraesCS4A01G116900 chr1A 87.435 191 22 2 2231 2419 7081774 7081584 5.000000e-53 219.0
19 TraesCS4A01G116900 chr1A 83.333 228 29 6 2203 2421 7064986 7064759 5.040000e-48 202.0
20 TraesCS4A01G116900 chr2D 84.388 474 53 17 2468 2934 472480214 472480673 2.110000e-121 446.0
21 TraesCS4A01G116900 chr2D 77.168 692 101 29 2203 2864 512838481 512839145 1.700000e-92 350.0
22 TraesCS4A01G116900 chr2D 87.879 198 22 2 2224 2419 55317569 55317766 6.430000e-57 231.0
23 TraesCS4A01G116900 chr2A 77.586 812 132 39 2190 2980 25129936 25129154 2.110000e-121 446.0
24 TraesCS4A01G116900 chr6B 81.073 634 53 28 1 596 52026175 52025571 7.580000e-121 444.0
25 TraesCS4A01G116900 chr6B 87.356 348 33 10 1 346 150216517 150216855 3.600000e-104 388.0
26 TraesCS4A01G116900 chr7D 83.656 465 61 14 2489 2946 548906912 548906456 9.880000e-115 424.0
27 TraesCS4A01G116900 chr7D 81.404 527 74 18 2469 2981 29310062 29310578 2.770000e-110 409.0
28 TraesCS4A01G116900 chr5D 82.077 491 76 11 2468 2950 51022550 51022064 2.770000e-110 409.0
29 TraesCS4A01G116900 chr5D 91.139 79 7 0 734 812 294640230 294640308 1.130000e-19 108.0
30 TraesCS4A01G116900 chr5D 91.139 79 6 1 734 812 104972927 104973004 4.060000e-19 106.0
31 TraesCS4A01G116900 chr1D 77.056 754 106 38 2202 2921 475528778 475529498 3.630000e-99 372.0
32 TraesCS4A01G116900 chr1D 93.333 75 5 0 738 812 80001402 80001476 8.730000e-21 111.0
33 TraesCS4A01G116900 chr1D 92.105 76 6 0 739 814 139162835 139162910 1.130000e-19 108.0
34 TraesCS4A01G116900 chr1D 89.286 84 8 1 731 814 421923326 421923244 1.460000e-18 104.0
35 TraesCS4A01G116900 chr3A 84.000 225 29 7 2202 2421 595757565 595757787 3.010000e-50 209.0
36 TraesCS4A01G116900 chrUn 82.960 223 33 5 2201 2419 35648587 35648366 2.340000e-46 196.0
37 TraesCS4A01G116900 chr2B 81.590 239 37 5 2183 2419 372084869 372085102 1.090000e-44 191.0
38 TraesCS4A01G116900 chr3D 93.333 75 5 0 738 812 55092868 55092794 8.730000e-21 111.0
39 TraesCS4A01G116900 chr6D 97.222 36 1 0 9 44 13174714 13174679 8.920000e-06 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 TraesCS4A01G116900 chr4A 141570185 141573165 2980 True 5505.00 5505 100.0000 1 2981 1 chr4A.!!$R1 2980
1 TraesCS4A01G116900 chr4B 408178732 408181428 2696 False 1128.00 2134 95.8275 811 2200 2 chr4B.!!$F2 1389
2 TraesCS4A01G116900 chr4B 408189382 408190031 649 False 492.00 492 80.5640 2314 2981 1 chr4B.!!$F1 667
3 TraesCS4A01G116900 chr4B 552580780 552581280 500 True 230.55 375 88.5900 6 468 2 chr4B.!!$R1 462
4 TraesCS4A01G116900 chr4D 328541255 328542981 1726 False 1145.00 2036 95.3925 811 2199 2 chr4D.!!$F2 1388
5 TraesCS4A01G116900 chr4D 442434035 442434632 597 False 649.00 649 86.5700 1 603 1 chr4D.!!$F1 602
6 TraesCS4A01G116900 chr7A 164820322 164821075 753 False 516.00 516 79.7390 2204 2938 1 chr7A.!!$F1 734
7 TraesCS4A01G116900 chr7A 671495964 671496747 783 True 276.00 276 74.3750 2203 2947 1 chr7A.!!$R2 744
8 TraesCS4A01G116900 chr1A 308211219 308211945 726 False 462.00 462 78.7960 2203 2947 1 chr1A.!!$F2 744
9 TraesCS4A01G116900 chr2D 512838481 512839145 664 False 350.00 350 77.1680 2203 2864 1 chr2D.!!$F3 661
10 TraesCS4A01G116900 chr2A 25129154 25129936 782 True 446.00 446 77.5860 2190 2980 1 chr2A.!!$R1 790
11 TraesCS4A01G116900 chr6B 52025571 52026175 604 True 444.00 444 81.0730 1 596 1 chr6B.!!$R1 595
12 TraesCS4A01G116900 chr7D 29310062 29310578 516 False 409.00 409 81.4040 2469 2981 1 chr7D.!!$F1 512
13 TraesCS4A01G116900 chr1D 475528778 475529498 720 False 372.00 372 77.0560 2202 2921 1 chr1D.!!$F3 719

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
658 755 0.179062 CTGGCCCATGTAGCTCACTC 60.179 60.0 0.0 0.0 0.0 3.51 F
695 792 0.179234 TCCTGTGCGTTCCTTTGACA 59.821 50.0 0.0 0.0 0.0 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1604 3010 1.201647 CCACGATGTACCTTGTCTCGT 59.798 52.381 0.0 0.0 42.75 4.18 R
2212 3961 1.546589 CCATTGCAACACATGGGCCT 61.547 55.000 0.0 0.0 0.00 5.19 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
50 51 7.345422 TGATGTGAACAAATTTGGAAAGAGA 57.655 32.000 21.74 0.97 0.00 3.10
59 60 8.877808 ACAAATTTGGAAAGAGAGAACATTTC 57.122 30.769 21.74 0.00 33.20 2.17
74 75 9.317936 AGAGAACATTTCTTGAATTTTTGAACC 57.682 29.630 0.00 0.00 40.87 3.62
493 585 6.531503 AGAATTCTCGACAGATGGTCTTTA 57.468 37.500 0.88 0.00 44.68 1.85
497 589 7.979444 ATTCTCGACAGATGGTCTTTAAAAA 57.021 32.000 0.00 0.00 44.68 1.94
598 695 7.275560 CAGAAAAGCGGAAAAAGAAGAAAAGAA 59.724 33.333 0.00 0.00 0.00 2.52
619 716 4.813296 AAAAAGACCAAGAAGTAGCACG 57.187 40.909 0.00 0.00 0.00 5.34
620 717 2.457366 AAGACCAAGAAGTAGCACGG 57.543 50.000 0.00 0.00 0.00 4.94
621 718 1.339097 AGACCAAGAAGTAGCACGGT 58.661 50.000 0.00 0.00 0.00 4.83
622 719 2.522185 AGACCAAGAAGTAGCACGGTA 58.478 47.619 0.00 0.00 0.00 4.02
623 720 2.895404 AGACCAAGAAGTAGCACGGTAA 59.105 45.455 0.00 0.00 0.00 2.85
624 721 3.514309 AGACCAAGAAGTAGCACGGTAAT 59.486 43.478 0.00 0.00 0.00 1.89
625 722 3.858247 ACCAAGAAGTAGCACGGTAATC 58.142 45.455 0.00 0.00 0.00 1.75
626 723 3.195661 CCAAGAAGTAGCACGGTAATCC 58.804 50.000 0.00 0.00 0.00 3.01
627 724 3.369052 CCAAGAAGTAGCACGGTAATCCA 60.369 47.826 0.00 0.00 0.00 3.41
628 725 4.442706 CAAGAAGTAGCACGGTAATCCAT 58.557 43.478 0.00 0.00 0.00 3.41
629 726 4.323553 AGAAGTAGCACGGTAATCCATC 57.676 45.455 0.00 0.00 0.00 3.51
630 727 3.704566 AGAAGTAGCACGGTAATCCATCA 59.295 43.478 0.00 0.00 0.00 3.07
631 728 3.735237 AGTAGCACGGTAATCCATCAG 57.265 47.619 0.00 0.00 0.00 2.90
632 729 3.031736 AGTAGCACGGTAATCCATCAGT 58.968 45.455 0.00 0.00 0.00 3.41
633 730 4.212716 AGTAGCACGGTAATCCATCAGTA 58.787 43.478 0.00 0.00 0.00 2.74
634 731 3.735237 AGCACGGTAATCCATCAGTAG 57.265 47.619 0.00 0.00 0.00 2.57
635 732 3.031736 AGCACGGTAATCCATCAGTAGT 58.968 45.455 0.00 0.00 0.00 2.73
636 733 3.123804 GCACGGTAATCCATCAGTAGTG 58.876 50.000 0.00 0.00 0.00 2.74
637 734 3.717707 CACGGTAATCCATCAGTAGTGG 58.282 50.000 0.00 0.00 38.11 4.00
638 735 2.698797 ACGGTAATCCATCAGTAGTGGG 59.301 50.000 0.00 0.00 37.34 4.61
639 736 2.548067 CGGTAATCCATCAGTAGTGGGC 60.548 54.545 0.00 0.00 37.34 5.36
640 737 2.706190 GGTAATCCATCAGTAGTGGGCT 59.294 50.000 0.00 0.00 37.34 5.19
641 738 3.495100 GGTAATCCATCAGTAGTGGGCTG 60.495 52.174 0.00 0.00 37.34 4.85
642 739 1.135094 ATCCATCAGTAGTGGGCTGG 58.865 55.000 0.00 3.42 37.34 4.85
643 740 1.153086 CCATCAGTAGTGGGCTGGC 60.153 63.158 0.00 0.00 34.89 4.85
644 741 1.153086 CATCAGTAGTGGGCTGGCC 60.153 63.158 14.23 14.23 34.89 5.36
654 751 2.203266 GGCTGGCCCATGTAGCTC 60.203 66.667 11.44 0.00 37.58 4.09
655 752 2.591753 GCTGGCCCATGTAGCTCA 59.408 61.111 0.00 0.00 34.70 4.26
656 753 1.821332 GCTGGCCCATGTAGCTCAC 60.821 63.158 0.00 0.00 34.70 3.51
657 754 1.910722 CTGGCCCATGTAGCTCACT 59.089 57.895 0.00 0.00 0.00 3.41
658 755 0.179062 CTGGCCCATGTAGCTCACTC 60.179 60.000 0.00 0.00 0.00 3.51
659 756 1.227380 GGCCCATGTAGCTCACTCG 60.227 63.158 0.00 0.00 0.00 4.18
660 757 1.884926 GCCCATGTAGCTCACTCGC 60.885 63.158 0.00 0.00 0.00 5.03
661 758 1.819229 CCCATGTAGCTCACTCGCT 59.181 57.895 0.00 0.00 43.83 4.93
662 759 0.249238 CCCATGTAGCTCACTCGCTC 60.249 60.000 0.00 0.00 41.30 5.03
663 760 0.593518 CCATGTAGCTCACTCGCTCG 60.594 60.000 0.00 0.00 41.30 5.03
664 761 0.593518 CATGTAGCTCACTCGCTCGG 60.594 60.000 0.00 0.00 41.30 4.63
665 762 1.032657 ATGTAGCTCACTCGCTCGGT 61.033 55.000 0.00 0.00 41.30 4.69
666 763 1.062845 GTAGCTCACTCGCTCGGTC 59.937 63.158 0.00 0.00 41.30 4.79
667 764 2.461945 TAGCTCACTCGCTCGGTCG 61.462 63.158 0.00 0.00 41.30 4.79
669 766 3.805307 CTCACTCGCTCGGTCGCT 61.805 66.667 0.00 0.00 0.00 4.93
670 767 3.726631 CTCACTCGCTCGGTCGCTC 62.727 68.421 0.00 0.00 0.00 5.03
671 768 4.838486 CACTCGCTCGGTCGCTCC 62.838 72.222 0.00 0.00 0.00 4.70
673 770 4.544689 CTCGCTCGGTCGCTCCTG 62.545 72.222 0.00 0.00 0.00 3.86
675 772 4.421479 CGCTCGGTCGCTCCTGTT 62.421 66.667 0.00 0.00 0.00 3.16
676 773 2.048127 GCTCGGTCGCTCCTGTTT 60.048 61.111 0.00 0.00 0.00 2.83
677 774 2.095252 GCTCGGTCGCTCCTGTTTC 61.095 63.158 0.00 0.00 0.00 2.78
678 775 1.446272 CTCGGTCGCTCCTGTTTCC 60.446 63.158 0.00 0.00 0.00 3.13
679 776 1.878656 CTCGGTCGCTCCTGTTTCCT 61.879 60.000 0.00 0.00 0.00 3.36
680 777 1.738099 CGGTCGCTCCTGTTTCCTG 60.738 63.158 0.00 0.00 0.00 3.86
681 778 1.371558 GGTCGCTCCTGTTTCCTGT 59.628 57.895 0.00 0.00 0.00 4.00
682 779 0.951040 GGTCGCTCCTGTTTCCTGTG 60.951 60.000 0.00 0.00 0.00 3.66
683 780 1.301716 TCGCTCCTGTTTCCTGTGC 60.302 57.895 0.00 0.00 0.00 4.57
684 781 2.671177 CGCTCCTGTTTCCTGTGCG 61.671 63.158 0.00 0.00 36.19 5.34
685 782 1.598130 GCTCCTGTTTCCTGTGCGT 60.598 57.895 0.00 0.00 0.00 5.24
686 783 1.166531 GCTCCTGTTTCCTGTGCGTT 61.167 55.000 0.00 0.00 0.00 4.84
687 784 0.868406 CTCCTGTTTCCTGTGCGTTC 59.132 55.000 0.00 0.00 0.00 3.95
688 785 0.534203 TCCTGTTTCCTGTGCGTTCC 60.534 55.000 0.00 0.00 0.00 3.62
689 786 0.535102 CCTGTTTCCTGTGCGTTCCT 60.535 55.000 0.00 0.00 0.00 3.36
690 787 1.308998 CTGTTTCCTGTGCGTTCCTT 58.691 50.000 0.00 0.00 0.00 3.36
691 788 1.676006 CTGTTTCCTGTGCGTTCCTTT 59.324 47.619 0.00 0.00 0.00 3.11
692 789 1.403679 TGTTTCCTGTGCGTTCCTTTG 59.596 47.619 0.00 0.00 0.00 2.77
693 790 1.673920 GTTTCCTGTGCGTTCCTTTGA 59.326 47.619 0.00 0.00 0.00 2.69
694 791 1.305201 TTCCTGTGCGTTCCTTTGAC 58.695 50.000 0.00 0.00 0.00 3.18
695 792 0.179234 TCCTGTGCGTTCCTTTGACA 59.821 50.000 0.00 0.00 0.00 3.58
696 793 1.021202 CCTGTGCGTTCCTTTGACAA 58.979 50.000 0.00 0.00 0.00 3.18
697 794 1.608590 CCTGTGCGTTCCTTTGACAAT 59.391 47.619 0.00 0.00 0.00 2.71
698 795 2.034558 CCTGTGCGTTCCTTTGACAATT 59.965 45.455 0.00 0.00 0.00 2.32
699 796 3.490761 CCTGTGCGTTCCTTTGACAATTT 60.491 43.478 0.00 0.00 0.00 1.82
700 797 3.443037 TGTGCGTTCCTTTGACAATTTG 58.557 40.909 0.00 0.00 0.00 2.32
701 798 2.218530 GTGCGTTCCTTTGACAATTTGC 59.781 45.455 0.00 0.00 0.00 3.68
702 799 1.792367 GCGTTCCTTTGACAATTTGCC 59.208 47.619 0.00 0.00 0.00 4.52
703 800 2.050691 CGTTCCTTTGACAATTTGCCG 58.949 47.619 0.00 0.00 0.00 5.69
704 801 1.792367 GTTCCTTTGACAATTTGCCGC 59.208 47.619 0.00 0.00 0.00 6.53
705 802 1.035923 TCCTTTGACAATTTGCCGCA 58.964 45.000 0.00 0.00 0.00 5.69
706 803 1.410517 TCCTTTGACAATTTGCCGCAA 59.589 42.857 0.38 0.38 0.00 4.85
707 804 2.036992 TCCTTTGACAATTTGCCGCAAT 59.963 40.909 6.64 0.00 0.00 3.56
708 805 2.807392 CCTTTGACAATTTGCCGCAATT 59.193 40.909 6.64 0.06 0.00 2.32
709 806 3.993081 CCTTTGACAATTTGCCGCAATTA 59.007 39.130 6.64 0.00 0.00 1.40
710 807 4.091800 CCTTTGACAATTTGCCGCAATTAG 59.908 41.667 6.64 2.36 0.00 1.73
711 808 2.605030 TGACAATTTGCCGCAATTAGC 58.395 42.857 6.64 0.00 40.87 3.09
729 826 8.182227 GCAATTAGCGTTAAATAGGATATTCCC 58.818 37.037 0.00 0.00 37.19 3.97
730 827 9.449719 CAATTAGCGTTAAATAGGATATTCCCT 57.550 33.333 0.00 0.00 37.19 4.20
733 830 7.549147 AGCGTTAAATAGGATATTCCCTACA 57.451 36.000 0.00 0.00 41.25 2.74
734 831 7.970102 AGCGTTAAATAGGATATTCCCTACAA 58.030 34.615 0.00 0.00 41.25 2.41
735 832 8.603304 AGCGTTAAATAGGATATTCCCTACAAT 58.397 33.333 0.00 0.00 41.25 2.71
736 833 8.665685 GCGTTAAATAGGATATTCCCTACAATG 58.334 37.037 0.00 0.00 41.25 2.82
737 834 8.665685 CGTTAAATAGGATATTCCCTACAATGC 58.334 37.037 0.00 0.00 41.25 3.56
738 835 9.740710 GTTAAATAGGATATTCCCTACAATGCT 57.259 33.333 0.00 0.00 41.25 3.79
741 838 8.686739 AATAGGATATTCCCTACAATGCTACT 57.313 34.615 0.00 0.00 41.25 2.57
742 839 6.613153 AGGATATTCCCTACAATGCTACTC 57.387 41.667 0.00 0.00 37.19 2.59
743 840 5.485708 AGGATATTCCCTACAATGCTACTCC 59.514 44.000 0.00 0.00 37.19 3.85
744 841 5.338463 GGATATTCCCTACAATGCTACTCCC 60.338 48.000 0.00 0.00 0.00 4.30
745 842 2.868964 TCCCTACAATGCTACTCCCT 57.131 50.000 0.00 0.00 0.00 4.20
746 843 2.679082 TCCCTACAATGCTACTCCCTC 58.321 52.381 0.00 0.00 0.00 4.30
747 844 2.023404 TCCCTACAATGCTACTCCCTCA 60.023 50.000 0.00 0.00 0.00 3.86
748 845 2.366916 CCCTACAATGCTACTCCCTCAG 59.633 54.545 0.00 0.00 0.00 3.35
749 846 3.034635 CCTACAATGCTACTCCCTCAGT 58.965 50.000 0.00 0.00 39.41 3.41
750 847 3.068873 CCTACAATGCTACTCCCTCAGTC 59.931 52.174 0.00 0.00 36.43 3.51
751 848 1.834263 ACAATGCTACTCCCTCAGTCC 59.166 52.381 0.00 0.00 36.43 3.85
752 849 1.139853 CAATGCTACTCCCTCAGTCCC 59.860 57.143 0.00 0.00 36.43 4.46
753 850 0.339859 ATGCTACTCCCTCAGTCCCA 59.660 55.000 0.00 0.00 36.43 4.37
754 851 0.339859 TGCTACTCCCTCAGTCCCAT 59.660 55.000 0.00 0.00 36.43 4.00
755 852 1.573857 TGCTACTCCCTCAGTCCCATA 59.426 52.381 0.00 0.00 36.43 2.74
756 853 2.023404 TGCTACTCCCTCAGTCCCATAA 60.023 50.000 0.00 0.00 36.43 1.90
757 854 3.243724 GCTACTCCCTCAGTCCCATAAT 58.756 50.000 0.00 0.00 36.43 1.28
758 855 4.140782 TGCTACTCCCTCAGTCCCATAATA 60.141 45.833 0.00 0.00 36.43 0.98
759 856 5.026790 GCTACTCCCTCAGTCCCATAATAT 58.973 45.833 0.00 0.00 36.43 1.28
760 857 6.195700 GCTACTCCCTCAGTCCCATAATATA 58.804 44.000 0.00 0.00 36.43 0.86
761 858 6.668283 GCTACTCCCTCAGTCCCATAATATAA 59.332 42.308 0.00 0.00 36.43 0.98
762 859 7.147811 GCTACTCCCTCAGTCCCATAATATAAG 60.148 44.444 0.00 0.00 36.43 1.73
763 860 6.875469 ACTCCCTCAGTCCCATAATATAAGA 58.125 40.000 0.00 0.00 0.00 2.10
764 861 6.957020 ACTCCCTCAGTCCCATAATATAAGAG 59.043 42.308 0.00 0.00 0.00 2.85
765 862 5.721960 TCCCTCAGTCCCATAATATAAGAGC 59.278 44.000 0.00 0.00 0.00 4.09
766 863 5.394663 CCCTCAGTCCCATAATATAAGAGCG 60.395 48.000 0.00 0.00 0.00 5.03
767 864 5.186021 CCTCAGTCCCATAATATAAGAGCGT 59.814 44.000 0.00 0.00 0.00 5.07
768 865 6.295349 CCTCAGTCCCATAATATAAGAGCGTT 60.295 42.308 0.00 0.00 0.00 4.84
769 866 7.062749 TCAGTCCCATAATATAAGAGCGTTT 57.937 36.000 0.00 0.00 0.00 3.60
770 867 7.506114 TCAGTCCCATAATATAAGAGCGTTTT 58.494 34.615 0.00 0.00 0.00 2.43
771 868 7.990886 TCAGTCCCATAATATAAGAGCGTTTTT 59.009 33.333 0.00 0.00 0.00 1.94
960 2366 0.969149 TTCTGTCGACACCTGCTGAT 59.031 50.000 15.76 0.00 0.00 2.90
1022 2428 2.095969 TGCACAGCGTTACATTGCTTAC 60.096 45.455 0.00 0.00 40.03 2.34
1225 2631 3.385384 CCGCACTCTCCAGCCTCA 61.385 66.667 0.00 0.00 0.00 3.86
1836 3242 3.181483 GGTTCATGATGACCAAATGGCTC 60.181 47.826 11.09 0.00 39.32 4.70
1873 3279 2.199236 CGGTTAACTCTATTCCGGCAC 58.801 52.381 5.42 0.00 37.92 5.01
2001 3407 4.467795 TGAGGTGTGGTTGGAATTTGAAAA 59.532 37.500 0.00 0.00 0.00 2.29
2006 3413 5.296531 GTGTGGTTGGAATTTGAAAAATGCT 59.703 36.000 0.00 0.00 0.00 3.79
2007 3414 6.481644 GTGTGGTTGGAATTTGAAAAATGCTA 59.518 34.615 0.00 0.00 0.00 3.49
2008 3415 6.705381 TGTGGTTGGAATTTGAAAAATGCTAG 59.295 34.615 0.00 0.00 0.00 3.42
2262 4016 6.692849 ATCATAATCTCTAGTGGCCATGAA 57.307 37.500 9.72 0.00 0.00 2.57
2287 4041 3.829886 TTTTGTTGCATCACCGAGATC 57.170 42.857 0.00 0.00 33.72 2.75
2433 4266 8.412608 TCGAACATTTTAATCTGTTTGCAAAA 57.587 26.923 14.67 0.00 36.91 2.44
2515 4382 9.632638 TTTTGGAAATCAATGGACCAAATTTTA 57.367 25.926 0.00 0.00 45.62 1.52
2518 4385 9.804977 TGGAAATCAATGGACCAAATTTTAAAT 57.195 25.926 0.00 0.00 0.00 1.40
2694 4605 6.886307 TGAATTGGCGAAATTTTGTTCAATC 58.114 32.000 19.77 15.68 38.64 2.67
2717 4629 9.853555 AATCTCATTAACATTGTTTAATTCGCA 57.146 25.926 7.45 0.00 30.65 5.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 51 9.447157 TTGGTTCAAAAATTCAAGAAATGTTCT 57.553 25.926 0.00 0.00 43.15 3.01
316 379 7.912056 TGTTCACAAATTCCAAAAATGTTCA 57.088 28.000 0.00 0.00 0.00 3.18
317 380 9.786105 AATTGTTCACAAATTCCAAAAATGTTC 57.214 25.926 0.00 0.00 39.55 3.18
556 653 7.063426 CCGCTTTTCTGTTTCTTTTTCTTCTTT 59.937 33.333 0.00 0.00 0.00 2.52
562 659 6.641176 TTTCCGCTTTTCTGTTTCTTTTTC 57.359 33.333 0.00 0.00 0.00 2.29
574 671 7.520119 TTCTTTTCTTCTTTTTCCGCTTTTC 57.480 32.000 0.00 0.00 0.00 2.29
598 695 3.564225 CCGTGCTACTTCTTGGTCTTTTT 59.436 43.478 0.00 0.00 0.00 1.94
603 700 3.308438 TTACCGTGCTACTTCTTGGTC 57.692 47.619 0.00 0.00 0.00 4.02
604 701 3.369157 GGATTACCGTGCTACTTCTTGGT 60.369 47.826 0.00 0.00 0.00 3.67
605 702 3.195661 GGATTACCGTGCTACTTCTTGG 58.804 50.000 0.00 0.00 0.00 3.61
606 703 3.857052 TGGATTACCGTGCTACTTCTTG 58.143 45.455 0.00 0.00 39.42 3.02
607 704 4.161565 TGATGGATTACCGTGCTACTTCTT 59.838 41.667 0.00 0.00 39.42 2.52
608 705 3.704566 TGATGGATTACCGTGCTACTTCT 59.295 43.478 0.00 0.00 39.42 2.85
609 706 4.051922 CTGATGGATTACCGTGCTACTTC 58.948 47.826 0.00 0.00 39.42 3.01
610 707 3.451178 ACTGATGGATTACCGTGCTACTT 59.549 43.478 0.00 0.00 39.42 2.24
611 708 3.031736 ACTGATGGATTACCGTGCTACT 58.968 45.455 0.00 0.00 39.42 2.57
612 709 3.454371 ACTGATGGATTACCGTGCTAC 57.546 47.619 0.00 0.00 39.42 3.58
613 710 4.037565 CACTACTGATGGATTACCGTGCTA 59.962 45.833 0.00 0.00 39.42 3.49
614 711 3.031736 ACTACTGATGGATTACCGTGCT 58.968 45.455 0.00 0.00 39.42 4.40
615 712 3.123804 CACTACTGATGGATTACCGTGC 58.876 50.000 0.00 0.00 39.42 5.34
616 713 3.492656 CCCACTACTGATGGATTACCGTG 60.493 52.174 0.00 0.00 39.87 4.94
617 714 2.698797 CCCACTACTGATGGATTACCGT 59.301 50.000 0.00 0.00 39.87 4.83
618 715 2.548067 GCCCACTACTGATGGATTACCG 60.548 54.545 0.00 0.00 39.87 4.02
619 716 2.706190 AGCCCACTACTGATGGATTACC 59.294 50.000 0.00 0.00 39.87 2.85
620 717 3.495100 CCAGCCCACTACTGATGGATTAC 60.495 52.174 0.00 0.00 39.87 1.89
621 718 2.705658 CCAGCCCACTACTGATGGATTA 59.294 50.000 0.00 0.00 39.87 1.75
622 719 1.492176 CCAGCCCACTACTGATGGATT 59.508 52.381 0.00 0.00 39.87 3.01
623 720 1.135094 CCAGCCCACTACTGATGGAT 58.865 55.000 0.00 0.00 39.87 3.41
624 721 1.626356 GCCAGCCCACTACTGATGGA 61.626 60.000 0.00 0.00 39.87 3.41
625 722 1.153086 GCCAGCCCACTACTGATGG 60.153 63.158 0.00 0.00 37.32 3.51
626 723 1.153086 GGCCAGCCCACTACTGATG 60.153 63.158 0.00 0.00 37.32 3.07
627 724 3.324713 GGCCAGCCCACTACTGAT 58.675 61.111 0.00 0.00 37.32 2.90
637 734 2.203266 GAGCTACATGGGCCAGCC 60.203 66.667 13.78 0.00 35.88 4.85
638 735 1.821332 GTGAGCTACATGGGCCAGC 60.821 63.158 13.78 10.20 35.49 4.85
639 736 0.179062 GAGTGAGCTACATGGGCCAG 60.179 60.000 13.78 6.92 0.00 4.85
640 737 1.907739 GAGTGAGCTACATGGGCCA 59.092 57.895 9.61 9.61 0.00 5.36
641 738 1.227380 CGAGTGAGCTACATGGGCC 60.227 63.158 0.00 0.00 0.00 5.80
642 739 1.884926 GCGAGTGAGCTACATGGGC 60.885 63.158 0.00 0.72 0.00 5.36
643 740 4.427394 GCGAGTGAGCTACATGGG 57.573 61.111 0.00 0.00 0.00 4.00
652 749 3.726631 GAGCGACCGAGCGAGTGAG 62.727 68.421 1.05 0.00 43.00 3.51
653 750 3.800863 GAGCGACCGAGCGAGTGA 61.801 66.667 1.05 0.00 43.00 3.41
654 751 4.838486 GGAGCGACCGAGCGAGTG 62.838 72.222 1.05 0.00 43.00 3.51
656 753 4.544689 CAGGAGCGACCGAGCGAG 62.545 72.222 1.05 0.00 44.74 5.03
658 755 3.916392 AAACAGGAGCGACCGAGCG 62.916 63.158 0.00 0.00 44.74 5.03
659 756 2.048127 AAACAGGAGCGACCGAGC 60.048 61.111 0.00 0.00 44.74 5.03
660 757 1.446272 GGAAACAGGAGCGACCGAG 60.446 63.158 0.00 0.00 44.74 4.63
661 758 1.906824 AGGAAACAGGAGCGACCGA 60.907 57.895 0.00 0.00 44.74 4.69
662 759 1.738099 CAGGAAACAGGAGCGACCG 60.738 63.158 0.00 0.00 44.74 4.79
663 760 0.951040 CACAGGAAACAGGAGCGACC 60.951 60.000 0.00 0.00 39.35 4.79
664 761 1.569479 GCACAGGAAACAGGAGCGAC 61.569 60.000 0.00 0.00 0.00 5.19
665 762 1.301716 GCACAGGAAACAGGAGCGA 60.302 57.895 0.00 0.00 0.00 4.93
666 763 2.671177 CGCACAGGAAACAGGAGCG 61.671 63.158 0.00 0.00 39.52 5.03
667 764 1.166531 AACGCACAGGAAACAGGAGC 61.167 55.000 0.00 0.00 0.00 4.70
668 765 0.868406 GAACGCACAGGAAACAGGAG 59.132 55.000 0.00 0.00 0.00 3.69
669 766 0.534203 GGAACGCACAGGAAACAGGA 60.534 55.000 0.00 0.00 0.00 3.86
670 767 0.535102 AGGAACGCACAGGAAACAGG 60.535 55.000 0.00 0.00 0.00 4.00
671 768 1.308998 AAGGAACGCACAGGAAACAG 58.691 50.000 0.00 0.00 0.00 3.16
672 769 1.403679 CAAAGGAACGCACAGGAAACA 59.596 47.619 0.00 0.00 0.00 2.83
673 770 1.673920 TCAAAGGAACGCACAGGAAAC 59.326 47.619 0.00 0.00 0.00 2.78
674 771 1.673920 GTCAAAGGAACGCACAGGAAA 59.326 47.619 0.00 0.00 0.00 3.13
675 772 1.305201 GTCAAAGGAACGCACAGGAA 58.695 50.000 0.00 0.00 0.00 3.36
676 773 0.179234 TGTCAAAGGAACGCACAGGA 59.821 50.000 0.00 0.00 0.00 3.86
677 774 1.021202 TTGTCAAAGGAACGCACAGG 58.979 50.000 0.00 0.00 0.00 4.00
678 775 3.354089 AATTGTCAAAGGAACGCACAG 57.646 42.857 0.00 0.00 0.00 3.66
679 776 3.443037 CAAATTGTCAAAGGAACGCACA 58.557 40.909 0.00 0.00 0.00 4.57
680 777 2.218530 GCAAATTGTCAAAGGAACGCAC 59.781 45.455 0.00 0.00 0.00 5.34
681 778 2.468831 GCAAATTGTCAAAGGAACGCA 58.531 42.857 0.00 0.00 0.00 5.24
682 779 1.792367 GGCAAATTGTCAAAGGAACGC 59.208 47.619 0.00 0.00 0.00 4.84
683 780 2.050691 CGGCAAATTGTCAAAGGAACG 58.949 47.619 0.00 0.00 0.00 3.95
684 781 1.792367 GCGGCAAATTGTCAAAGGAAC 59.208 47.619 0.00 0.00 0.00 3.62
685 782 1.410517 TGCGGCAAATTGTCAAAGGAA 59.589 42.857 0.00 0.00 0.00 3.36
686 783 1.035923 TGCGGCAAATTGTCAAAGGA 58.964 45.000 0.00 0.00 0.00 3.36
687 784 1.863267 TTGCGGCAAATTGTCAAAGG 58.137 45.000 13.93 0.00 0.00 3.11
688 785 4.434593 GCTAATTGCGGCAAATTGTCAAAG 60.435 41.667 20.48 5.61 32.16 2.77
689 786 3.431572 GCTAATTGCGGCAAATTGTCAAA 59.568 39.130 20.48 0.00 32.16 2.69
690 787 2.992543 GCTAATTGCGGCAAATTGTCAA 59.007 40.909 20.48 0.00 32.16 3.18
691 788 2.605030 GCTAATTGCGGCAAATTGTCA 58.395 42.857 20.48 0.00 32.16 3.58
703 800 8.182227 GGGAATATCCTATTTAACGCTAATTGC 58.818 37.037 0.00 0.00 36.57 3.56
704 801 9.449719 AGGGAATATCCTATTTAACGCTAATTG 57.550 33.333 0.00 0.00 36.57 2.32
707 804 9.092338 TGTAGGGAATATCCTATTTAACGCTAA 57.908 33.333 0.00 0.00 41.03 3.09
708 805 8.654485 TGTAGGGAATATCCTATTTAACGCTA 57.346 34.615 0.00 0.00 41.03 4.26
709 806 7.549147 TGTAGGGAATATCCTATTTAACGCT 57.451 36.000 0.00 0.00 41.03 5.07
710 807 8.665685 CATTGTAGGGAATATCCTATTTAACGC 58.334 37.037 0.00 0.00 41.03 4.84
711 808 8.665685 GCATTGTAGGGAATATCCTATTTAACG 58.334 37.037 0.00 0.00 41.03 3.18
712 809 9.740710 AGCATTGTAGGGAATATCCTATTTAAC 57.259 33.333 0.00 0.00 41.03 2.01
715 812 9.117223 AGTAGCATTGTAGGGAATATCCTATTT 57.883 33.333 0.00 0.00 41.03 1.40
716 813 8.686739 AGTAGCATTGTAGGGAATATCCTATT 57.313 34.615 0.00 0.00 41.03 1.73
717 814 7.345914 GGAGTAGCATTGTAGGGAATATCCTAT 59.654 40.741 0.00 0.00 41.03 2.57
718 815 6.668283 GGAGTAGCATTGTAGGGAATATCCTA 59.332 42.308 0.00 0.00 38.30 2.94
719 816 5.485708 GGAGTAGCATTGTAGGGAATATCCT 59.514 44.000 0.00 0.00 40.79 3.24
720 817 5.338463 GGGAGTAGCATTGTAGGGAATATCC 60.338 48.000 0.00 0.00 35.23 2.59
721 818 5.485708 AGGGAGTAGCATTGTAGGGAATATC 59.514 44.000 0.00 0.00 0.00 1.63
722 819 5.415961 AGGGAGTAGCATTGTAGGGAATAT 58.584 41.667 0.00 0.00 0.00 1.28
723 820 4.827789 AGGGAGTAGCATTGTAGGGAATA 58.172 43.478 0.00 0.00 0.00 1.75
724 821 3.648545 GAGGGAGTAGCATTGTAGGGAAT 59.351 47.826 0.00 0.00 0.00 3.01
725 822 3.039011 GAGGGAGTAGCATTGTAGGGAA 58.961 50.000 0.00 0.00 0.00 3.97
726 823 2.023404 TGAGGGAGTAGCATTGTAGGGA 60.023 50.000 0.00 0.00 0.00 4.20
727 824 2.366916 CTGAGGGAGTAGCATTGTAGGG 59.633 54.545 0.00 0.00 0.00 3.53
728 825 3.034635 ACTGAGGGAGTAGCATTGTAGG 58.965 50.000 0.00 0.00 30.86 3.18
729 826 3.068873 GGACTGAGGGAGTAGCATTGTAG 59.931 52.174 0.00 0.00 33.83 2.74
730 827 3.031736 GGACTGAGGGAGTAGCATTGTA 58.968 50.000 0.00 0.00 33.83 2.41
731 828 1.834263 GGACTGAGGGAGTAGCATTGT 59.166 52.381 0.00 0.00 33.83 2.71
732 829 1.139853 GGGACTGAGGGAGTAGCATTG 59.860 57.143 0.00 0.00 33.83 2.82
733 830 1.273838 TGGGACTGAGGGAGTAGCATT 60.274 52.381 0.00 0.00 33.83 3.56
734 831 0.339859 TGGGACTGAGGGAGTAGCAT 59.660 55.000 0.00 0.00 33.83 3.79
735 832 0.339859 ATGGGACTGAGGGAGTAGCA 59.660 55.000 0.00 0.00 33.83 3.49
736 833 2.383442 TATGGGACTGAGGGAGTAGC 57.617 55.000 0.00 0.00 33.83 3.58
737 834 8.116669 TCTTATATTATGGGACTGAGGGAGTAG 58.883 40.741 0.00 0.00 33.83 2.57
738 835 8.008104 TCTTATATTATGGGACTGAGGGAGTA 57.992 38.462 0.00 0.00 33.83 2.59
739 836 6.875469 TCTTATATTATGGGACTGAGGGAGT 58.125 40.000 0.00 0.00 37.76 3.85
740 837 6.127196 GCTCTTATATTATGGGACTGAGGGAG 60.127 46.154 0.00 0.00 0.00 4.30
741 838 5.721960 GCTCTTATATTATGGGACTGAGGGA 59.278 44.000 0.00 0.00 0.00 4.20
742 839 5.394663 CGCTCTTATATTATGGGACTGAGGG 60.395 48.000 0.00 0.00 0.00 4.30
743 840 5.186021 ACGCTCTTATATTATGGGACTGAGG 59.814 44.000 0.00 0.00 0.00 3.86
744 841 6.274157 ACGCTCTTATATTATGGGACTGAG 57.726 41.667 0.00 0.00 0.00 3.35
745 842 6.665992 AACGCTCTTATATTATGGGACTGA 57.334 37.500 0.00 0.00 0.00 3.41
746 843 7.730364 AAAACGCTCTTATATTATGGGACTG 57.270 36.000 0.00 0.00 0.00 3.51
806 903 9.862371 GATAGTCATTGATAAACGTCATCCTAT 57.138 33.333 7.44 6.60 0.00 2.57
807 904 8.856103 TGATAGTCATTGATAAACGTCATCCTA 58.144 33.333 7.44 3.01 0.00 2.94
808 905 7.726216 TGATAGTCATTGATAAACGTCATCCT 58.274 34.615 7.44 1.27 0.00 3.24
809 906 7.946655 TGATAGTCATTGATAAACGTCATCC 57.053 36.000 7.44 0.00 0.00 3.51
875 972 5.221087 CGTCCAACTATCTAAGAGGGACTTC 60.221 48.000 0.00 0.00 43.59 3.01
960 2366 2.614481 GCGGTGGAGTGGTCAAGAAATA 60.614 50.000 0.00 0.00 0.00 1.40
1022 2428 4.033932 TGGTAATGATCTGCGATTTCGTTG 59.966 41.667 1.55 0.00 42.22 4.10
1225 2631 3.315749 GTCTCGAGGAGGTAATCGTTGAT 59.684 47.826 13.56 0.00 39.86 2.57
1377 2783 1.004918 GTCAGCACTGCTACCGGTT 60.005 57.895 15.04 0.00 36.40 4.44
1440 2846 1.528824 CCGCAGATCATCCAACCCT 59.471 57.895 0.00 0.00 0.00 4.34
1604 3010 1.201647 CCACGATGTACCTTGTCTCGT 59.798 52.381 0.00 0.00 42.75 4.18
1674 3080 4.373116 GCCGTCCGAACTGCCTCA 62.373 66.667 0.00 0.00 30.10 3.86
1836 3242 4.832608 GTCCGCTTGTAGGGCCCG 62.833 72.222 18.44 1.87 0.00 6.13
1873 3279 1.594293 CTAATGCCGTACCCGCTGG 60.594 63.158 0.00 0.00 37.80 4.85
2001 3407 7.921786 TCTGCAAACTTTACATACTAGCATT 57.078 32.000 0.00 0.00 0.00 3.56
2106 3855 9.148104 AGTGACCTAACAAATTAATACTCGTTC 57.852 33.333 0.00 0.00 0.00 3.95
2200 3949 5.144832 ACACATGGGCCTTTTTACTAGTTT 58.855 37.500 4.53 0.00 0.00 2.66
2207 3956 2.042464 TGCAACACATGGGCCTTTTTA 58.958 42.857 4.53 0.00 0.00 1.52
2212 3961 1.546589 CCATTGCAACACATGGGCCT 61.547 55.000 0.00 0.00 0.00 5.19
2262 4016 4.699735 TCTCGGTGATGCAACAAAATATGT 59.300 37.500 0.00 0.00 46.82 2.29
2287 4041 7.854557 TTCATGAAATTGAGAGTGATAGTGG 57.145 36.000 5.45 0.00 0.00 4.00
2368 4164 7.591057 TGTTCACGAATCTGAAAAATGTTCATC 59.409 33.333 0.00 0.00 31.90 2.92
2383 4179 9.829637 GAAAATTTGTAAAAGTGTTCACGAATC 57.170 29.630 0.00 0.00 0.00 2.52
2462 4306 2.862512 TCGCCGATTCAAGAAAAATGC 58.137 42.857 0.00 0.00 0.00 3.56
2571 4443 8.809159 TCATAAAATGTTCGCTGATTCAAAAA 57.191 26.923 0.00 0.00 0.00 1.94
2572 4444 8.809159 TTCATAAAATGTTCGCTGATTCAAAA 57.191 26.923 0.00 0.00 0.00 2.44
2694 4605 9.726034 GTTTGCGAATTAAACAATGTTAATGAG 57.274 29.630 0.00 0.68 37.82 2.90


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

AutoCloner maintained by Alex Coulton.