Multiple sequence alignment - TraesCS2A01G211500

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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 TraesCS2A01G211500 chr2A 100.000 2804 0 0 1 2804 195772547 195775350 0.000000e+00 5179.0
1 TraesCS2A01G211500 chr2A 100.000 35 0 0 1948 1982 618978377 618978411 6.480000e-07 65.8
2 TraesCS2A01G211500 chr2A 100.000 32 0 0 1948 1979 751613853 751613884 3.020000e-05 60.2
3 TraesCS2A01G211500 chr4D 91.795 1231 75 16 824 2040 15243713 15244931 0.000000e+00 1690.0
4 TraesCS2A01G211500 chr4D 93.135 437 18 7 1 427 342884597 342885031 5.100000e-177 630.0
5 TraesCS2A01G211500 chr4D 92.328 378 25 4 2043 2418 15245185 15245560 4.110000e-148 534.0
6 TraesCS2A01G211500 chr4D 88.934 244 24 3 583 823 307281331 307281574 5.870000e-77 298.0
7 TraesCS2A01G211500 chr4D 87.500 248 26 5 582 825 8196528 8196282 5.910000e-72 281.0
8 TraesCS2A01G211500 chr4D 94.175 103 5 1 480 581 15243609 15243711 3.740000e-34 156.0
9 TraesCS2A01G211500 chr4A 95.098 918 24 3 912 1826 585646886 585647785 0.000000e+00 1426.0
10 TraesCS2A01G211500 chr4A 97.365 683 7 3 1829 2509 585654995 585655668 0.000000e+00 1151.0
11 TraesCS2A01G211500 chr4A 97.770 583 13 0 1 583 585617662 585618244 0.000000e+00 1005.0
12 TraesCS2A01G211500 chr4A 98.990 297 3 0 2506 2802 585656377 585656673 1.480000e-147 532.0
13 TraesCS2A01G211500 chr4A 90.769 195 12 3 824 1012 585546037 585546231 3.580000e-64 255.0
14 TraesCS2A01G211500 chr4A 96.970 99 3 0 824 922 585618244 585618342 1.730000e-37 167.0
15 TraesCS2A01G211500 chr4A 100.000 33 0 0 1948 1980 694846473 694846505 8.390000e-06 62.1
16 TraesCS2A01G211500 chr4B 89.210 899 58 21 1388 2260 25571127 25572012 0.000000e+00 1086.0
17 TraesCS2A01G211500 chr4B 93.662 568 36 0 824 1391 25559098 25559665 0.000000e+00 850.0
18 TraesCS2A01G211500 chr4B 93.960 298 14 2 2506 2803 25499328 25499035 5.510000e-122 448.0
19 TraesCS2A01G211500 chr4B 93.220 118 8 0 466 583 25558981 25559098 1.030000e-39 174.0
20 TraesCS2A01G211500 chr4B 97.059 34 1 0 436 469 25558973 25559006 1.080000e-04 58.4
21 TraesCS2A01G211500 chr3D 93.905 443 16 6 1 433 101685796 101685355 0.000000e+00 658.0
22 TraesCS2A01G211500 chr3D 100.000 32 0 0 1948 1979 615202847 615202878 3.020000e-05 60.2
23 TraesCS2A01G211500 chr5D 93.379 438 18 6 1 427 193125046 193125483 3.050000e-179 638.0
24 TraesCS2A01G211500 chr5D 93.364 437 16 8 1 426 442185440 442185874 3.940000e-178 634.0
25 TraesCS2A01G211500 chr5D 89.370 254 22 4 578 826 350228903 350229156 5.830000e-82 315.0
26 TraesCS2A01G211500 chr1D 93.379 438 17 7 1 427 387955931 387956367 3.050000e-179 638.0
27 TraesCS2A01G211500 chr1D 91.796 451 24 8 1 441 298580007 298580454 1.430000e-172 616.0
28 TraesCS2A01G211500 chr7D 93.166 439 18 7 1 427 97944697 97945135 3.940000e-178 634.0
29 TraesCS2A01G211500 chr7A 93.103 435 20 5 1 427 523058631 523059063 1.830000e-176 628.0
30 TraesCS2A01G211500 chr3A 96.016 251 9 1 576 825 702494729 702494979 9.350000e-110 407.0
31 TraesCS2A01G211500 chr3A 88.259 247 26 2 582 825 36337587 36337341 2.730000e-75 292.0
32 TraesCS2A01G211500 chr3A 100.000 33 0 0 1948 1980 128131966 128131998 8.390000e-06 62.1
33 TraesCS2A01G211500 chr3B 87.405 262 29 3 568 825 507885857 507886118 5.870000e-77 298.0
34 TraesCS2A01G211500 chr3B 87.805 246 27 2 583 825 68254232 68254477 4.570000e-73 285.0
35 TraesCS2A01G211500 chr3B 100.000 32 0 0 1948 1979 420875945 420875914 3.020000e-05 60.2
36 TraesCS2A01G211500 chr1B 87.755 245 28 2 582 825 240502265 240502508 4.570000e-73 285.0
37 TraesCS2A01G211500 chr1A 86.719 256 27 7 575 825 552263078 552262825 7.650000e-71 278.0
38 TraesCS2A01G211500 chr6D 94.872 39 2 0 1948 1986 445412978 445413016 8.390000e-06 62.1
39 TraesCS2A01G211500 chr6A 100.000 33 0 0 1948 1980 23878296 23878328 8.390000e-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 TraesCS2A01G211500 chr2A 195772547 195775350 2803 False 5179.000000 5179 100.0000 1 2804 1 chr2A.!!$F1 2803
1 TraesCS2A01G211500 chr4D 15243609 15245560 1951 False 793.333333 1690 92.7660 480 2418 3 chr4D.!!$F3 1938
2 TraesCS2A01G211500 chr4A 585646886 585647785 899 False 1426.000000 1426 95.0980 912 1826 1 chr4A.!!$F2 914
3 TraesCS2A01G211500 chr4A 585654995 585656673 1678 False 841.500000 1151 98.1775 1829 2802 2 chr4A.!!$F5 973
4 TraesCS2A01G211500 chr4A 585617662 585618342 680 False 586.000000 1005 97.3700 1 922 2 chr4A.!!$F4 921
5 TraesCS2A01G211500 chr4B 25571127 25572012 885 False 1086.000000 1086 89.2100 1388 2260 1 chr4B.!!$F1 872
6 TraesCS2A01G211500 chr4B 25558973 25559665 692 False 360.800000 850 94.6470 436 1391 3 chr4B.!!$F2 955

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
746 748 0.171903 GCTCGCCATTGAAGCAATGT 59.828 50.0 16.29 0.0 46.69 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2419 2736 0.958876 CACGGCCAGTTTACCCCTTC 60.959 60.0 2.24 0.0 0.0 3.46 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
267 268 6.912203 TGTTCAGATTTCTTTCGTTGTGTA 57.088 33.333 0.00 0.00 0.00 2.90
289 290 3.606687 AGAGGGTGACGCGAAAATAAAT 58.393 40.909 15.93 0.00 0.00 1.40
413 414 0.528470 GCGAGACTACCAACTGCTCT 59.472 55.000 0.00 0.00 0.00 4.09
499 500 8.122472 TGTGTAGATATGGTATGGACTATGTG 57.878 38.462 0.00 0.00 0.00 3.21
560 562 0.178301 TGTCACCAAAGGCACGTACA 59.822 50.000 0.00 0.00 0.00 2.90
582 584 3.225104 CACCCCTGGCGTACTATAACTA 58.775 50.000 0.00 0.00 0.00 2.24
583 585 3.005155 CACCCCTGGCGTACTATAACTAC 59.995 52.174 0.00 0.00 0.00 2.73
584 586 3.117360 ACCCCTGGCGTACTATAACTACT 60.117 47.826 0.00 0.00 0.00 2.57
585 587 4.104738 ACCCCTGGCGTACTATAACTACTA 59.895 45.833 0.00 0.00 0.00 1.82
586 588 4.699257 CCCCTGGCGTACTATAACTACTAG 59.301 50.000 0.00 0.00 0.00 2.57
587 589 5.312079 CCCTGGCGTACTATAACTACTAGT 58.688 45.833 0.00 0.00 34.01 2.57
588 590 6.467677 CCCTGGCGTACTATAACTACTAGTA 58.532 44.000 1.89 1.89 31.96 1.82
589 591 6.936900 CCCTGGCGTACTATAACTACTAGTAA 59.063 42.308 3.76 0.00 34.39 2.24
590 592 7.445402 CCCTGGCGTACTATAACTACTAGTAAA 59.555 40.741 3.76 0.00 34.39 2.01
591 593 8.840321 CCTGGCGTACTATAACTACTAGTAAAA 58.160 37.037 3.76 0.00 34.39 1.52
594 596 9.159470 GGCGTACTATAACTACTAGTAAAAACG 57.841 37.037 3.76 6.86 34.39 3.60
595 597 8.674145 GCGTACTATAACTACTAGTAAAAACGC 58.326 37.037 16.20 16.20 41.86 4.84
596 598 9.702726 CGTACTATAACTACTAGTAAAAACGCA 57.297 33.333 3.76 0.00 34.39 5.24
598 600 8.606727 ACTATAACTACTAGTAAAAACGCACG 57.393 34.615 3.76 0.00 0.00 5.34
599 601 8.237267 ACTATAACTACTAGTAAAAACGCACGT 58.763 33.333 3.76 0.00 0.00 4.49
600 602 5.565723 AACTACTAGTAAAAACGCACGTG 57.434 39.130 12.28 12.28 0.00 4.49
601 603 2.936050 ACTAGTAAAAACGCACGTGC 57.064 45.000 30.42 30.42 37.78 5.34
602 604 2.203401 ACTAGTAAAAACGCACGTGCA 58.797 42.857 37.03 16.48 42.21 4.57
603 605 2.608546 ACTAGTAAAAACGCACGTGCAA 59.391 40.909 37.03 14.01 42.21 4.08
604 606 1.817609 AGTAAAAACGCACGTGCAAC 58.182 45.000 37.03 23.21 42.21 4.17
605 607 1.130749 AGTAAAAACGCACGTGCAACA 59.869 42.857 37.03 14.74 42.21 3.33
606 608 1.250749 GTAAAAACGCACGTGCAACAC 59.749 47.619 37.03 21.42 42.21 3.32
607 609 0.387367 AAAAACGCACGTGCAACACA 60.387 45.000 37.03 0.00 42.21 3.72
608 610 1.068287 AAAACGCACGTGCAACACAC 61.068 50.000 37.03 9.13 46.45 3.82
620 622 5.783298 GTGCAACACACGTTAACATTTAG 57.217 39.130 6.39 0.00 40.07 1.85
621 623 4.673311 GTGCAACACACGTTAACATTTAGG 59.327 41.667 6.39 0.00 40.07 2.69
622 624 3.666797 GCAACACACGTTAACATTTAGGC 59.333 43.478 6.39 0.00 32.75 3.93
623 625 4.790123 GCAACACACGTTAACATTTAGGCA 60.790 41.667 6.39 0.00 32.75 4.75
624 626 5.274718 CAACACACGTTAACATTTAGGCAA 58.725 37.500 6.39 0.00 32.75 4.52
625 627 5.699097 ACACACGTTAACATTTAGGCAAT 57.301 34.783 6.39 0.00 0.00 3.56
626 628 6.804770 ACACACGTTAACATTTAGGCAATA 57.195 33.333 6.39 0.00 0.00 1.90
627 629 7.385778 ACACACGTTAACATTTAGGCAATAT 57.614 32.000 6.39 0.00 0.00 1.28
628 630 8.495361 ACACACGTTAACATTTAGGCAATATA 57.505 30.769 6.39 0.00 0.00 0.86
629 631 9.116067 ACACACGTTAACATTTAGGCAATATAT 57.884 29.630 6.39 0.00 0.00 0.86
630 632 9.944663 CACACGTTAACATTTAGGCAATATATT 57.055 29.630 6.39 0.00 0.00 1.28
655 657 9.656040 TTAATTGCATGTGAAATTAGAAATGCT 57.344 25.926 11.29 0.00 40.74 3.79
657 659 9.826574 AATTGCATGTGAAATTAGAAATGCTAT 57.173 25.926 11.29 7.64 40.74 2.97
658 660 8.861033 TTGCATGTGAAATTAGAAATGCTATC 57.139 30.769 11.29 0.00 40.74 2.08
659 661 7.998580 TGCATGTGAAATTAGAAATGCTATCA 58.001 30.769 11.29 0.00 40.74 2.15
660 662 8.635328 TGCATGTGAAATTAGAAATGCTATCAT 58.365 29.630 11.29 0.00 40.74 2.45
661 663 9.472361 GCATGTGAAATTAGAAATGCTATCATT 57.528 29.630 0.00 0.00 44.32 2.57
675 677 7.928307 ATGCTATCATTTGTGTTAACTCTGT 57.072 32.000 7.22 0.00 0.00 3.41
676 678 7.132694 TGCTATCATTTGTGTTAACTCTGTG 57.867 36.000 7.22 4.58 0.00 3.66
677 679 6.934083 TGCTATCATTTGTGTTAACTCTGTGA 59.066 34.615 7.22 9.24 0.00 3.58
678 680 7.607607 TGCTATCATTTGTGTTAACTCTGTGAT 59.392 33.333 7.22 14.53 0.00 3.06
679 681 8.454106 GCTATCATTTGTGTTAACTCTGTGATT 58.546 33.333 18.61 9.96 0.00 2.57
682 684 8.902540 TCATTTGTGTTAACTCTGTGATTAGT 57.097 30.769 7.22 0.00 0.00 2.24
683 685 8.773645 TCATTTGTGTTAACTCTGTGATTAGTG 58.226 33.333 7.22 0.00 0.00 2.74
684 686 6.539649 TTGTGTTAACTCTGTGATTAGTGC 57.460 37.500 7.22 0.00 0.00 4.40
685 687 5.606505 TGTGTTAACTCTGTGATTAGTGCA 58.393 37.500 7.22 0.00 0.00 4.57
686 688 6.052360 TGTGTTAACTCTGTGATTAGTGCAA 58.948 36.000 7.22 0.00 0.00 4.08
687 689 6.710295 TGTGTTAACTCTGTGATTAGTGCAAT 59.290 34.615 7.22 0.00 0.00 3.56
688 690 7.875554 TGTGTTAACTCTGTGATTAGTGCAATA 59.124 33.333 7.22 0.00 0.00 1.90
689 691 8.883731 GTGTTAACTCTGTGATTAGTGCAATAT 58.116 33.333 7.22 0.00 0.00 1.28
690 692 9.448438 TGTTAACTCTGTGATTAGTGCAATATT 57.552 29.630 7.22 0.00 0.00 1.28
693 695 7.325660 ACTCTGTGATTAGTGCAATATTTGG 57.674 36.000 0.00 0.00 0.00 3.28
694 696 6.886459 ACTCTGTGATTAGTGCAATATTTGGT 59.114 34.615 0.00 0.00 0.00 3.67
695 697 8.046708 ACTCTGTGATTAGTGCAATATTTGGTA 58.953 33.333 0.00 0.00 0.00 3.25
696 698 8.978874 TCTGTGATTAGTGCAATATTTGGTAT 57.021 30.769 0.00 0.00 0.00 2.73
697 699 8.839343 TCTGTGATTAGTGCAATATTTGGTATG 58.161 33.333 0.00 0.00 0.00 2.39
698 700 8.744568 TGTGATTAGTGCAATATTTGGTATGA 57.255 30.769 0.00 0.00 0.00 2.15
699 701 9.353431 TGTGATTAGTGCAATATTTGGTATGAT 57.647 29.630 0.00 0.00 0.00 2.45
721 723 9.865321 ATGATAGTAACTACATGTTAAACACGT 57.135 29.630 2.30 0.00 42.12 4.49
726 728 9.185192 AGTAACTACATGTTAAACACGTAGAAC 57.815 33.333 15.25 12.32 44.85 3.01
727 729 6.680055 ACTACATGTTAAACACGTAGAACG 57.320 37.500 15.25 0.00 44.85 3.95
728 730 5.117592 ACTACATGTTAAACACGTAGAACGC 59.882 40.000 15.25 0.00 44.85 4.84
729 731 5.344128 CTACATGTTAAACACGTAGAACGCT 59.656 40.000 2.30 0.00 44.85 5.07
730 732 6.452090 CTACATGTTAAACACGTAGAACGCTC 60.452 42.308 2.30 0.00 44.85 5.03
731 733 9.464167 CTACATGTTAAACACGTAGAACGCTCG 62.464 44.444 2.30 0.00 44.85 5.03
736 738 4.088421 CGTAGAACGCTCGCCATT 57.912 55.556 0.00 0.00 33.65 3.16
737 739 1.631072 CGTAGAACGCTCGCCATTG 59.369 57.895 0.00 0.00 33.65 2.82
738 740 0.800683 CGTAGAACGCTCGCCATTGA 60.801 55.000 0.00 0.00 33.65 2.57
739 741 1.355971 GTAGAACGCTCGCCATTGAA 58.644 50.000 0.00 0.00 0.00 2.69
740 742 1.324736 GTAGAACGCTCGCCATTGAAG 59.675 52.381 0.00 0.00 0.00 3.02
741 743 1.226128 GAACGCTCGCCATTGAAGC 60.226 57.895 0.00 0.00 0.00 3.86
742 744 1.911293 GAACGCTCGCCATTGAAGCA 61.911 55.000 0.00 0.00 0.00 3.91
743 745 1.514678 AACGCTCGCCATTGAAGCAA 61.515 50.000 0.00 0.00 0.00 3.91
744 746 1.308069 ACGCTCGCCATTGAAGCAAT 61.308 50.000 0.00 0.00 34.04 3.56
746 748 0.171903 GCTCGCCATTGAAGCAATGT 59.828 50.000 16.29 0.00 46.69 2.71
747 749 1.401552 GCTCGCCATTGAAGCAATGTA 59.598 47.619 16.29 4.06 46.69 2.29
748 750 2.540361 GCTCGCCATTGAAGCAATGTAG 60.540 50.000 16.29 12.08 46.69 2.74
749 751 2.016318 TCGCCATTGAAGCAATGTAGG 58.984 47.619 16.29 5.36 46.69 3.18
750 752 1.745087 CGCCATTGAAGCAATGTAGGT 59.255 47.619 16.29 0.00 46.69 3.08
751 753 2.223340 CGCCATTGAAGCAATGTAGGTC 60.223 50.000 16.29 3.01 46.69 3.85
752 754 2.223340 GCCATTGAAGCAATGTAGGTCG 60.223 50.000 16.29 4.20 46.69 4.79
753 755 3.009723 CCATTGAAGCAATGTAGGTCGT 58.990 45.455 16.29 0.00 46.69 4.34
754 756 3.440173 CCATTGAAGCAATGTAGGTCGTT 59.560 43.478 16.29 0.00 46.69 3.85
755 757 4.406069 CATTGAAGCAATGTAGGTCGTTG 58.594 43.478 11.04 0.00 44.12 4.10
756 758 2.422597 TGAAGCAATGTAGGTCGTTGG 58.577 47.619 0.00 0.00 41.74 3.77
757 759 2.037902 TGAAGCAATGTAGGTCGTTGGA 59.962 45.455 0.00 0.00 41.74 3.53
758 760 3.270877 GAAGCAATGTAGGTCGTTGGAT 58.729 45.455 0.00 0.00 41.74 3.41
759 761 3.350219 AGCAATGTAGGTCGTTGGATT 57.650 42.857 0.00 0.00 41.74 3.01
760 762 3.009723 AGCAATGTAGGTCGTTGGATTG 58.990 45.455 0.00 0.00 41.74 2.67
761 763 3.006940 GCAATGTAGGTCGTTGGATTGA 58.993 45.455 0.00 0.00 41.74 2.57
762 764 3.181510 GCAATGTAGGTCGTTGGATTGAC 60.182 47.826 0.00 0.00 41.74 3.18
763 765 4.253685 CAATGTAGGTCGTTGGATTGACT 58.746 43.478 0.00 0.00 38.85 3.41
764 766 4.553330 ATGTAGGTCGTTGGATTGACTT 57.447 40.909 0.00 0.00 35.45 3.01
765 767 5.670792 ATGTAGGTCGTTGGATTGACTTA 57.329 39.130 0.00 0.00 35.45 2.24
766 768 5.068234 TGTAGGTCGTTGGATTGACTTAG 57.932 43.478 0.00 0.00 35.45 2.18
767 769 4.525487 TGTAGGTCGTTGGATTGACTTAGT 59.475 41.667 0.00 0.00 35.45 2.24
768 770 4.618920 AGGTCGTTGGATTGACTTAGTT 57.381 40.909 0.00 0.00 35.45 2.24
769 771 4.969484 AGGTCGTTGGATTGACTTAGTTT 58.031 39.130 0.00 0.00 35.45 2.66
770 772 4.755123 AGGTCGTTGGATTGACTTAGTTTG 59.245 41.667 0.00 0.00 35.45 2.93
771 773 4.753107 GGTCGTTGGATTGACTTAGTTTGA 59.247 41.667 0.00 0.00 35.45 2.69
772 774 5.411669 GGTCGTTGGATTGACTTAGTTTGAT 59.588 40.000 0.00 0.00 35.45 2.57
773 775 6.307155 GTCGTTGGATTGACTTAGTTTGATG 58.693 40.000 0.00 0.00 32.37 3.07
774 776 5.411361 TCGTTGGATTGACTTAGTTTGATGG 59.589 40.000 0.00 0.00 0.00 3.51
775 777 5.402398 GTTGGATTGACTTAGTTTGATGGC 58.598 41.667 0.00 0.00 0.00 4.40
776 778 4.016444 TGGATTGACTTAGTTTGATGGCC 58.984 43.478 0.00 0.00 0.00 5.36
777 779 4.016444 GGATTGACTTAGTTTGATGGCCA 58.984 43.478 8.56 8.56 0.00 5.36
778 780 4.462483 GGATTGACTTAGTTTGATGGCCAA 59.538 41.667 10.96 0.00 0.00 4.52
779 781 5.393461 GGATTGACTTAGTTTGATGGCCAAG 60.393 44.000 10.96 1.50 35.94 3.61
780 782 4.365514 TGACTTAGTTTGATGGCCAAGA 57.634 40.909 10.96 0.00 35.94 3.02
781 783 4.922206 TGACTTAGTTTGATGGCCAAGAT 58.078 39.130 10.96 0.00 35.94 2.40
782 784 4.943705 TGACTTAGTTTGATGGCCAAGATC 59.056 41.667 10.96 3.00 35.94 2.75
783 785 4.922206 ACTTAGTTTGATGGCCAAGATCA 58.078 39.130 10.96 6.45 35.94 2.92
784 786 4.946157 ACTTAGTTTGATGGCCAAGATCAG 59.054 41.667 10.96 0.98 35.94 2.90
785 787 3.446442 AGTTTGATGGCCAAGATCAGT 57.554 42.857 10.96 0.00 35.94 3.41
786 788 3.771216 AGTTTGATGGCCAAGATCAGTT 58.229 40.909 10.96 0.00 35.94 3.16
787 789 3.508793 AGTTTGATGGCCAAGATCAGTTG 59.491 43.478 10.96 0.00 35.94 3.16
801 803 3.063510 TCAGTTGGATCTGCCTCTTTG 57.936 47.619 0.00 0.00 37.63 2.77
802 804 2.639347 TCAGTTGGATCTGCCTCTTTGA 59.361 45.455 0.00 0.00 37.63 2.69
803 805 3.008330 CAGTTGGATCTGCCTCTTTGAG 58.992 50.000 0.00 0.00 37.63 3.02
804 806 2.641815 AGTTGGATCTGCCTCTTTGAGT 59.358 45.455 0.00 0.00 37.63 3.41
805 807 3.073650 AGTTGGATCTGCCTCTTTGAGTT 59.926 43.478 0.00 0.00 37.63 3.01
806 808 3.795688 TGGATCTGCCTCTTTGAGTTT 57.204 42.857 0.00 0.00 37.63 2.66
807 809 4.104383 TGGATCTGCCTCTTTGAGTTTT 57.896 40.909 0.00 0.00 37.63 2.43
808 810 4.473444 TGGATCTGCCTCTTTGAGTTTTT 58.527 39.130 0.00 0.00 37.63 1.94
1023 1025 0.546122 AAGCCATCGCCAAGTCCATA 59.454 50.000 0.00 0.00 34.57 2.74
1110 1112 2.126071 CGCGTCACCTCCATCGTT 60.126 61.111 0.00 0.00 0.00 3.85
1198 1200 0.318441 CCTCGACCTCAGCTTCAACA 59.682 55.000 0.00 0.00 0.00 3.33
1385 1387 1.456287 GGGACCTTGTCACCTGCTT 59.544 57.895 0.00 0.00 33.68 3.91
1407 1409 2.492090 CTACGCAGCTTCTCCGCT 59.508 61.111 0.00 0.00 41.90 5.52
1436 1438 3.069729 GCCTCCGTATATGACAACTTCCT 59.930 47.826 0.00 0.00 0.00 3.36
1515 1532 2.610859 AGGATGTCTGGGGCCGTT 60.611 61.111 0.00 0.00 0.00 4.44
1602 1619 1.696097 ATAAGATCACCGGCCGCCTT 61.696 55.000 22.85 17.94 0.00 4.35
1702 1722 1.148273 AAGCTTGTCAACCTCCGCA 59.852 52.632 0.00 0.00 0.00 5.69
1728 1748 2.738643 CGATGCATCCTACAACGACCTT 60.739 50.000 20.87 0.00 35.59 3.50
1732 1752 3.007074 TGCATCCTACAACGACCTTTGTA 59.993 43.478 0.00 0.00 40.29 2.41
1990 2053 3.553511 CAGAAGGAGTATGTGATTGCGTC 59.446 47.826 0.00 0.00 0.00 5.19
2418 2735 0.391263 GTCTGCACGGAAGGGGTAAG 60.391 60.000 0.00 0.00 32.68 2.34
2419 2736 1.078426 CTGCACGGAAGGGGTAAGG 60.078 63.158 0.00 0.00 32.68 2.69
2420 2737 1.536907 TGCACGGAAGGGGTAAGGA 60.537 57.895 0.00 0.00 32.68 3.36
2421 2738 1.128809 TGCACGGAAGGGGTAAGGAA 61.129 55.000 0.00 0.00 32.68 3.36
2422 2739 0.392595 GCACGGAAGGGGTAAGGAAG 60.393 60.000 0.00 0.00 32.68 3.46
2423 2740 0.252197 CACGGAAGGGGTAAGGAAGG 59.748 60.000 0.00 0.00 0.00 3.46
2802 3831 0.530650 AGGCAGATGCGTTGTATCGG 60.531 55.000 0.00 0.00 43.26 4.18
2803 3832 0.810031 GGCAGATGCGTTGTATCGGT 60.810 55.000 0.00 0.00 43.26 4.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
243 244 6.377327 ACACAACGAAAGAAATCTGAACAT 57.623 33.333 0.00 0.00 0.00 2.71
267 268 2.754946 TATTTTCGCGTCACCCTCTT 57.245 45.000 5.77 0.00 0.00 2.85
289 290 1.689233 CCCTCCCCCACTTCATCGA 60.689 63.158 0.00 0.00 0.00 3.59
387 388 2.891580 AGTTGGTAGTCTCGCTTTCAGA 59.108 45.455 0.00 0.00 0.00 3.27
499 500 5.467063 GGATCACGGAAATTCTATCAACTCC 59.533 44.000 0.00 0.00 0.00 3.85
582 584 2.203401 TGCACGTGCGTTTTTACTAGT 58.797 42.857 33.22 0.00 45.83 2.57
583 585 2.934107 TGCACGTGCGTTTTTACTAG 57.066 45.000 33.22 0.00 45.83 2.57
584 586 2.350804 TGTTGCACGTGCGTTTTTACTA 59.649 40.909 33.22 11.66 45.83 1.82
585 587 1.130749 TGTTGCACGTGCGTTTTTACT 59.869 42.857 33.22 0.00 45.83 2.24
586 588 1.250749 GTGTTGCACGTGCGTTTTTAC 59.749 47.619 33.22 22.34 45.83 2.01
587 589 1.135774 TGTGTTGCACGTGCGTTTTTA 60.136 42.857 33.22 14.00 45.83 1.52
588 590 0.387367 TGTGTTGCACGTGCGTTTTT 60.387 45.000 33.22 0.00 45.83 1.94
589 591 1.068287 GTGTGTTGCACGTGCGTTTT 61.068 50.000 33.22 0.00 45.83 2.43
590 592 1.513160 GTGTGTTGCACGTGCGTTT 60.513 52.632 33.22 0.00 45.83 3.60
591 593 2.099446 GTGTGTTGCACGTGCGTT 59.901 55.556 33.22 0.00 45.83 4.84
598 600 4.673311 CCTAAATGTTAACGTGTGTTGCAC 59.327 41.667 0.00 0.00 44.36 4.57
599 601 4.790123 GCCTAAATGTTAACGTGTGTTGCA 60.790 41.667 0.00 0.00 39.12 4.08
600 602 3.666797 GCCTAAATGTTAACGTGTGTTGC 59.333 43.478 0.00 0.00 39.12 4.17
601 603 4.849883 TGCCTAAATGTTAACGTGTGTTG 58.150 39.130 0.00 0.00 39.12 3.33
602 604 5.502153 TTGCCTAAATGTTAACGTGTGTT 57.498 34.783 0.00 0.00 42.19 3.32
603 605 5.699097 ATTGCCTAAATGTTAACGTGTGT 57.301 34.783 0.00 0.00 0.00 3.72
604 606 9.944663 AATATATTGCCTAAATGTTAACGTGTG 57.055 29.630 0.00 0.00 0.00 3.82
629 631 9.656040 AGCATTTCTAATTTCACATGCAATTAA 57.344 25.926 12.30 0.00 39.62 1.40
631 633 9.826574 ATAGCATTTCTAATTTCACATGCAATT 57.173 25.926 12.30 0.00 39.62 2.32
632 634 9.472361 GATAGCATTTCTAATTTCACATGCAAT 57.528 29.630 12.30 0.00 39.62 3.56
633 635 8.468399 TGATAGCATTTCTAATTTCACATGCAA 58.532 29.630 12.30 0.00 39.62 4.08
634 636 7.998580 TGATAGCATTTCTAATTTCACATGCA 58.001 30.769 12.30 0.00 39.62 3.96
635 637 9.472361 AATGATAGCATTTCTAATTTCACATGC 57.528 29.630 0.00 0.00 41.87 4.06
650 652 8.239314 CACAGAGTTAACACAAATGATAGCATT 58.761 33.333 8.61 0.00 46.35 3.56
651 653 7.607607 TCACAGAGTTAACACAAATGATAGCAT 59.392 33.333 8.61 0.00 35.92 3.79
652 654 6.934083 TCACAGAGTTAACACAAATGATAGCA 59.066 34.615 8.61 0.00 0.00 3.49
653 655 7.364522 TCACAGAGTTAACACAAATGATAGC 57.635 36.000 8.61 0.00 0.00 2.97
656 658 9.507329 ACTAATCACAGAGTTAACACAAATGAT 57.493 29.630 8.61 9.10 0.00 2.45
657 659 8.773645 CACTAATCACAGAGTTAACACAAATGA 58.226 33.333 8.61 7.26 0.00 2.57
658 660 7.535258 GCACTAATCACAGAGTTAACACAAATG 59.465 37.037 8.61 2.08 0.00 2.32
659 661 7.228507 TGCACTAATCACAGAGTTAACACAAAT 59.771 33.333 8.61 0.00 0.00 2.32
660 662 6.540551 TGCACTAATCACAGAGTTAACACAAA 59.459 34.615 8.61 0.00 0.00 2.83
661 663 6.052360 TGCACTAATCACAGAGTTAACACAA 58.948 36.000 8.61 0.00 0.00 3.33
662 664 5.606505 TGCACTAATCACAGAGTTAACACA 58.393 37.500 8.61 0.00 0.00 3.72
663 665 6.539649 TTGCACTAATCACAGAGTTAACAC 57.460 37.500 8.61 0.95 0.00 3.32
664 666 9.448438 AATATTGCACTAATCACAGAGTTAACA 57.552 29.630 8.61 0.00 0.00 2.41
667 669 8.892723 CCAAATATTGCACTAATCACAGAGTTA 58.107 33.333 0.00 0.00 0.00 2.24
668 670 7.394359 ACCAAATATTGCACTAATCACAGAGTT 59.606 33.333 0.00 0.00 0.00 3.01
669 671 6.886459 ACCAAATATTGCACTAATCACAGAGT 59.114 34.615 0.00 0.00 0.00 3.24
670 672 7.325660 ACCAAATATTGCACTAATCACAGAG 57.674 36.000 0.00 0.00 0.00 3.35
671 673 8.839343 CATACCAAATATTGCACTAATCACAGA 58.161 33.333 0.00 0.00 0.00 3.41
672 674 8.839343 TCATACCAAATATTGCACTAATCACAG 58.161 33.333 0.00 0.00 0.00 3.66
673 675 8.744568 TCATACCAAATATTGCACTAATCACA 57.255 30.769 0.00 0.00 0.00 3.58
695 697 9.865321 ACGTGTTTAACATGTAGTTACTATCAT 57.135 29.630 19.85 0.00 45.70 2.45
706 708 5.221880 AGCGTTCTACGTGTTTAACATGTA 58.778 37.500 23.45 23.45 45.70 2.29
708 710 4.625135 GAGCGTTCTACGTGTTTAACATG 58.375 43.478 14.93 14.93 44.73 3.21
709 711 3.362831 CGAGCGTTCTACGTGTTTAACAT 59.637 43.478 0.00 0.00 44.73 2.71
710 712 2.720578 CGAGCGTTCTACGTGTTTAACA 59.279 45.455 0.00 0.00 44.73 2.41
711 713 2.469661 GCGAGCGTTCTACGTGTTTAAC 60.470 50.000 0.00 0.00 44.73 2.01
712 714 1.715519 GCGAGCGTTCTACGTGTTTAA 59.284 47.619 0.00 0.00 44.73 1.52
713 715 1.330306 GCGAGCGTTCTACGTGTTTA 58.670 50.000 0.00 0.00 44.73 2.01
714 716 1.280206 GGCGAGCGTTCTACGTGTTT 61.280 55.000 0.00 0.00 44.73 2.83
715 717 1.731969 GGCGAGCGTTCTACGTGTT 60.732 57.895 0.00 0.00 44.73 3.32
716 718 2.126580 GGCGAGCGTTCTACGTGT 60.127 61.111 0.00 0.00 44.73 4.49
717 719 1.076533 AATGGCGAGCGTTCTACGTG 61.077 55.000 0.00 0.00 44.73 4.49
718 720 1.076533 CAATGGCGAGCGTTCTACGT 61.077 55.000 0.00 0.00 44.73 3.57
719 721 0.800683 TCAATGGCGAGCGTTCTACG 60.801 55.000 0.00 0.00 45.88 3.51
720 722 1.324736 CTTCAATGGCGAGCGTTCTAC 59.675 52.381 0.00 0.00 0.00 2.59
721 723 1.640428 CTTCAATGGCGAGCGTTCTA 58.360 50.000 0.00 0.00 0.00 2.10
722 724 1.639298 GCTTCAATGGCGAGCGTTCT 61.639 55.000 0.00 0.00 0.00 3.01
723 725 1.226128 GCTTCAATGGCGAGCGTTC 60.226 57.895 0.00 0.00 0.00 3.95
724 726 1.514678 TTGCTTCAATGGCGAGCGTT 61.515 50.000 0.00 0.00 39.23 4.84
725 727 1.308069 ATTGCTTCAATGGCGAGCGT 61.308 50.000 0.00 0.00 39.23 5.07
726 728 0.864377 CATTGCTTCAATGGCGAGCG 60.864 55.000 10.74 0.00 45.03 5.03
727 729 2.953669 CATTGCTTCAATGGCGAGC 58.046 52.632 10.74 0.00 45.03 5.03
734 736 3.440173 CCAACGACCTACATTGCTTCAAT 59.560 43.478 0.00 0.00 34.04 2.57
735 737 2.811431 CCAACGACCTACATTGCTTCAA 59.189 45.455 0.00 0.00 0.00 2.69
736 738 2.037902 TCCAACGACCTACATTGCTTCA 59.962 45.455 0.00 0.00 0.00 3.02
737 739 2.695359 TCCAACGACCTACATTGCTTC 58.305 47.619 0.00 0.00 0.00 3.86
738 740 2.851263 TCCAACGACCTACATTGCTT 57.149 45.000 0.00 0.00 0.00 3.91
739 741 3.009723 CAATCCAACGACCTACATTGCT 58.990 45.455 0.00 0.00 0.00 3.91
740 742 3.006940 TCAATCCAACGACCTACATTGC 58.993 45.455 0.00 0.00 0.00 3.56
741 743 4.253685 AGTCAATCCAACGACCTACATTG 58.746 43.478 0.00 0.00 32.33 2.82
742 744 4.553330 AGTCAATCCAACGACCTACATT 57.447 40.909 0.00 0.00 32.33 2.71
743 745 4.553330 AAGTCAATCCAACGACCTACAT 57.447 40.909 0.00 0.00 32.33 2.29
744 746 4.525487 ACTAAGTCAATCCAACGACCTACA 59.475 41.667 0.00 0.00 32.33 2.74
745 747 5.069501 ACTAAGTCAATCCAACGACCTAC 57.930 43.478 0.00 0.00 32.33 3.18
746 748 5.733620 AACTAAGTCAATCCAACGACCTA 57.266 39.130 0.00 0.00 32.33 3.08
747 749 4.618920 AACTAAGTCAATCCAACGACCT 57.381 40.909 0.00 0.00 32.33 3.85
748 750 4.753107 TCAAACTAAGTCAATCCAACGACC 59.247 41.667 0.00 0.00 32.33 4.79
749 751 5.917541 TCAAACTAAGTCAATCCAACGAC 57.082 39.130 0.00 0.00 0.00 4.34
750 752 5.411361 CCATCAAACTAAGTCAATCCAACGA 59.589 40.000 0.00 0.00 0.00 3.85
751 753 5.631026 CCATCAAACTAAGTCAATCCAACG 58.369 41.667 0.00 0.00 0.00 4.10
752 754 5.402398 GCCATCAAACTAAGTCAATCCAAC 58.598 41.667 0.00 0.00 0.00 3.77
753 755 4.462483 GGCCATCAAACTAAGTCAATCCAA 59.538 41.667 0.00 0.00 0.00 3.53
754 756 4.016444 GGCCATCAAACTAAGTCAATCCA 58.984 43.478 0.00 0.00 0.00 3.41
755 757 4.016444 TGGCCATCAAACTAAGTCAATCC 58.984 43.478 0.00 0.00 0.00 3.01
756 758 5.415701 TCTTGGCCATCAAACTAAGTCAATC 59.584 40.000 6.09 0.00 34.56 2.67
757 759 5.324409 TCTTGGCCATCAAACTAAGTCAAT 58.676 37.500 6.09 0.00 34.56 2.57
758 760 4.724399 TCTTGGCCATCAAACTAAGTCAA 58.276 39.130 6.09 0.00 34.56 3.18
759 761 4.365514 TCTTGGCCATCAAACTAAGTCA 57.634 40.909 6.09 0.00 34.56 3.41
760 762 4.943705 TGATCTTGGCCATCAAACTAAGTC 59.056 41.667 6.09 0.00 34.56 3.01
761 763 4.922206 TGATCTTGGCCATCAAACTAAGT 58.078 39.130 6.09 0.00 34.56 2.24
762 764 4.946157 ACTGATCTTGGCCATCAAACTAAG 59.054 41.667 6.09 0.00 34.56 2.18
763 765 4.922206 ACTGATCTTGGCCATCAAACTAA 58.078 39.130 6.09 0.00 34.56 2.24
764 766 4.574674 ACTGATCTTGGCCATCAAACTA 57.425 40.909 6.09 0.00 34.56 2.24
765 767 3.446442 ACTGATCTTGGCCATCAAACT 57.554 42.857 6.09 0.00 34.56 2.66
766 768 3.367703 CCAACTGATCTTGGCCATCAAAC 60.368 47.826 6.09 0.00 34.50 2.93
767 769 2.827322 CCAACTGATCTTGGCCATCAAA 59.173 45.455 6.09 0.00 34.50 2.69
768 770 2.041485 TCCAACTGATCTTGGCCATCAA 59.959 45.455 6.09 0.00 40.66 2.57
769 771 1.634973 TCCAACTGATCTTGGCCATCA 59.365 47.619 6.09 6.84 40.66 3.07
770 772 2.425143 TCCAACTGATCTTGGCCATC 57.575 50.000 6.09 0.91 40.66 3.51
771 773 2.941480 GATCCAACTGATCTTGGCCAT 58.059 47.619 6.09 0.00 45.46 4.40
772 774 2.425143 GATCCAACTGATCTTGGCCA 57.575 50.000 0.00 0.00 45.46 5.36
779 781 8.752188 ACTCAAAGAGGCAGATCCAACTGATC 62.752 46.154 0.00 0.00 41.02 2.92
780 782 3.265221 TCAAAGAGGCAGATCCAACTGAT 59.735 43.478 0.00 0.00 39.94 2.90
781 783 2.639347 TCAAAGAGGCAGATCCAACTGA 59.361 45.455 0.00 0.00 39.94 3.41
782 784 3.008330 CTCAAAGAGGCAGATCCAACTG 58.992 50.000 0.00 0.00 40.43 3.16
783 785 2.641815 ACTCAAAGAGGCAGATCCAACT 59.358 45.455 0.00 0.00 37.29 3.16
784 786 3.064900 ACTCAAAGAGGCAGATCCAAC 57.935 47.619 0.00 0.00 37.29 3.77
785 787 3.795688 AACTCAAAGAGGCAGATCCAA 57.204 42.857 0.00 0.00 37.29 3.53
786 788 3.795688 AAACTCAAAGAGGCAGATCCA 57.204 42.857 0.00 0.00 37.29 3.41
806 808 9.073475 GGTGTGCCATCTATACCAATATAAAAA 57.927 33.333 0.00 0.00 34.09 1.94
807 809 8.444783 AGGTGTGCCATCTATACCAATATAAAA 58.555 33.333 0.00 0.00 37.19 1.52
808 810 7.984475 AGGTGTGCCATCTATACCAATATAAA 58.016 34.615 0.00 0.00 37.19 1.40
809 811 7.568128 AGGTGTGCCATCTATACCAATATAA 57.432 36.000 0.00 0.00 37.19 0.98
810 812 6.127451 CGAGGTGTGCCATCTATACCAATATA 60.127 42.308 0.00 0.00 37.19 0.86
811 813 5.337571 CGAGGTGTGCCATCTATACCAATAT 60.338 44.000 0.00 0.00 37.19 1.28
812 814 4.021456 CGAGGTGTGCCATCTATACCAATA 60.021 45.833 0.00 0.00 37.19 1.90
813 815 3.244215 CGAGGTGTGCCATCTATACCAAT 60.244 47.826 0.00 0.00 37.19 3.16
814 816 2.102420 CGAGGTGTGCCATCTATACCAA 59.898 50.000 0.00 0.00 37.19 3.67
815 817 1.686587 CGAGGTGTGCCATCTATACCA 59.313 52.381 0.00 0.00 37.19 3.25
816 818 1.687123 ACGAGGTGTGCCATCTATACC 59.313 52.381 0.00 0.00 37.19 2.73
817 819 2.743938 CACGAGGTGTGCCATCTATAC 58.256 52.381 0.00 0.00 42.70 1.47
1225 1227 4.357947 GTGCTGGTGAGGCGTCGA 62.358 66.667 0.00 0.00 0.00 4.20
1323 1325 0.785708 CGTTGTTGTCGAGCGCAATC 60.786 55.000 11.47 0.00 0.00 2.67
1326 1328 2.278923 TCGTTGTTGTCGAGCGCA 60.279 55.556 11.47 0.00 33.38 6.09
1407 1409 3.380954 TGTCATATACGGAGGCGTTGTTA 59.619 43.478 0.00 0.00 0.00 2.41
1436 1438 1.065358 GACGTCGCCGAAGAAATTGA 58.935 50.000 7.12 0.00 37.88 2.57
1471 1488 4.019983 GAGGGACAGCCTCTCGAA 57.980 61.111 0.00 0.00 0.00 3.71
1602 1619 1.052617 TGTCGGGGATGAACAAGTCA 58.947 50.000 0.00 0.00 41.67 3.41
1702 1722 3.068165 TCGTTGTAGGATGCATCGAAGAT 59.932 43.478 20.15 6.44 46.79 2.40
1728 1748 1.541670 GCGAACTTGGGGTGTCTACAA 60.542 52.381 0.00 0.00 0.00 2.41
1732 1752 2.430367 GGCGAACTTGGGGTGTCT 59.570 61.111 0.00 0.00 0.00 3.41
1990 2053 1.616865 TGAGGACCAGACAAACTACCG 59.383 52.381 0.00 0.00 0.00 4.02
2050 2364 3.876210 ACGATACGAAACGAAATGACG 57.124 42.857 0.00 0.00 39.31 4.35
2418 2735 1.378119 CGGCCAGTTTACCCCTTCC 60.378 63.158 2.24 0.00 0.00 3.46
2419 2736 0.958876 CACGGCCAGTTTACCCCTTC 60.959 60.000 2.24 0.00 0.00 3.46
2420 2737 1.074248 CACGGCCAGTTTACCCCTT 59.926 57.895 2.24 0.00 0.00 3.95
2421 2738 2.754375 CACGGCCAGTTTACCCCT 59.246 61.111 2.24 0.00 0.00 4.79
2422 2739 3.060000 GCACGGCCAGTTTACCCC 61.060 66.667 2.24 0.00 0.00 4.95
2493 2810 6.915300 TCAATTTGATTAAACAGGTTGTGTCG 59.085 34.615 0.00 0.00 39.03 4.35
2547 3576 2.841215 TGCTACCAAAAGTGCGTAGTT 58.159 42.857 0.00 0.00 34.00 2.24
2552 3581 5.236263 TGTGATATATGCTACCAAAAGTGCG 59.764 40.000 0.00 0.00 0.00 5.34


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

AutoCloner maintained by Alex Coulton.