Multiple sequence alignment - TraesCS5D01G121800

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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 TraesCS5D01G121800 chr5D 100.000 2421 0 0 1 2421 175640922 175638502 0.000000e+00 4471.0
1 TraesCS5D01G121800 chr5D 94.512 656 36 0 1 656 251661223 251660568 0.000000e+00 1013.0
2 TraesCS5D01G121800 chr5D 88.347 841 70 14 1011 1833 72369490 72370320 0.000000e+00 985.0
3 TraesCS5D01G121800 chr5D 95.263 570 26 1 1 570 83262888 83263456 0.000000e+00 902.0
4 TraesCS5D01G121800 chr5D 95.833 48 1 1 817 863 101454714 101454761 2.580000e-10 76.8
5 TraesCS5D01G121800 chr5D 93.750 48 2 1 817 863 311906654 311906701 1.200000e-08 71.3
6 TraesCS5D01G121800 chr5D 95.556 45 1 1 817 860 513911005 513911049 1.200000e-08 71.3
7 TraesCS5D01G121800 chr1B 93.408 1426 75 3 1015 2421 39622064 39620639 0.000000e+00 2095.0
8 TraesCS5D01G121800 chr7A 94.732 1063 53 2 866 1926 310601857 310600796 0.000000e+00 1650.0
9 TraesCS5D01G121800 chr7A 93.789 483 28 1 1924 2406 310598061 310597581 0.000000e+00 725.0
10 TraesCS5D01G121800 chr3B 93.229 960 53 4 1462 2421 64568973 64569920 0.000000e+00 1402.0
11 TraesCS5D01G121800 chr3B 92.422 607 43 2 861 1465 64558259 64558864 0.000000e+00 863.0
12 TraesCS5D01G121800 chr3D 93.103 638 44 0 19 656 153750966 153750329 0.000000e+00 935.0
13 TraesCS5D01G121800 chr3D 95.088 570 28 0 1 570 401223313 401223882 0.000000e+00 898.0
14 TraesCS5D01G121800 chr3D 94.737 570 30 0 1 570 485813919 485814488 0.000000e+00 887.0
15 TraesCS5D01G121800 chr3D 96.610 177 4 2 655 831 346313530 346313704 2.350000e-75 292.0
16 TraesCS5D01G121800 chr3D 95.628 183 4 4 643 822 402850809 402850628 8.470000e-75 291.0
17 TraesCS5D01G121800 chr3D 79.255 376 60 10 894 1269 8955988 8955631 1.860000e-61 246.0
18 TraesCS5D01G121800 chr7D 94.912 570 29 0 1 570 129995069 129994500 0.000000e+00 893.0
19 TraesCS5D01G121800 chr7D 96.591 176 4 2 649 824 604569373 604569200 8.470000e-75 291.0
20 TraesCS5D01G121800 chr4D 94.921 571 27 2 1 570 90284944 90284375 0.000000e+00 893.0
21 TraesCS5D01G121800 chr4D 94.561 570 31 0 1 570 325742264 325741695 0.000000e+00 881.0
22 TraesCS5D01G121800 chr4D 95.135 185 8 1 655 839 113186984 113187167 8.470000e-75 291.0
23 TraesCS5D01G121800 chr4D 95.531 179 8 0 649 827 95133671 95133849 1.100000e-73 287.0
24 TraesCS5D01G121800 chr4D 95.028 181 9 0 476 656 307065206 307065386 3.940000e-73 285.0
25 TraesCS5D01G121800 chr2D 94.912 570 29 0 1 570 499279958 499280527 0.000000e+00 893.0
26 TraesCS5D01G121800 chr2D 98.256 172 3 0 647 818 5107939 5108110 3.910000e-78 302.0
27 TraesCS5D01G121800 chr2D 98.235 170 2 1 655 824 641099361 641099193 1.820000e-76 296.0
28 TraesCS5D01G121800 chr2D 96.571 175 6 0 646 820 75834215 75834389 8.470000e-75 291.0
29 TraesCS5D01G121800 chr2D 94.253 87 5 0 570 656 29743447 29743533 1.510000e-27 134.0
30 TraesCS5D01G121800 chr2D 93.750 48 2 1 817 863 406696570 406696617 1.200000e-08 71.3
31 TraesCS5D01G121800 chr4A 84.740 865 93 18 995 1833 707825713 707826564 0.000000e+00 830.0
32 TraesCS5D01G121800 chr5B 92.241 232 18 0 2018 2249 46147949 46147718 1.790000e-86 329.0
33 TraesCS5D01G121800 chr5B 92.763 152 9 2 2271 2421 46127817 46127667 4.050000e-53 219.0
34 TraesCS5D01G121800 chr5B 94.253 87 4 1 570 656 340302998 340302913 5.430000e-27 132.0
35 TraesCS5D01G121800 chr1D 96.045 177 7 0 643 819 115018770 115018594 3.050000e-74 289.0
36 TraesCS5D01G121800 chr2B 81.667 180 26 1 2061 2240 634221318 634221490 2.510000e-30 143.0
37 TraesCS5D01G121800 chr2B 90.099 101 7 3 556 656 430765852 430765949 7.030000e-26 128.0
38 TraesCS5D01G121800 chr5A 94.318 88 5 0 569 656 677489848 677489761 4.200000e-28 135.0
39 TraesCS5D01G121800 chr6D 89.899 99 8 1 560 656 38212460 38212558 2.530000e-25 126.0
40 TraesCS5D01G121800 chr6D 93.750 48 2 1 817 863 406112485 406112438 1.200000e-08 71.3
41 TraesCS5D01G121800 chr3A 87.037 108 11 3 550 656 606609203 606609308 4.230000e-23 119.0
42 TraesCS5D01G121800 chr3A 95.833 48 1 1 817 863 699567063 699567110 2.580000e-10 76.8
43 TraesCS5D01G121800 chr7B 96.154 52 1 1 813 863 467252395 467252446 1.540000e-12 84.2
44 TraesCS5D01G121800 chr4B 95.833 48 1 1 817 863 133609481 133609528 2.580000e-10 76.8
45 TraesCS5D01G121800 chr1A 95.652 46 1 1 819 863 558280247 558280202 3.340000e-09 73.1


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 TraesCS5D01G121800 chr5D 175638502 175640922 2420 True 4471.0 4471 100.0000 1 2421 1 chr5D.!!$R1 2420
1 TraesCS5D01G121800 chr5D 251660568 251661223 655 True 1013.0 1013 94.5120 1 656 1 chr5D.!!$R2 655
2 TraesCS5D01G121800 chr5D 72369490 72370320 830 False 985.0 985 88.3470 1011 1833 1 chr5D.!!$F1 822
3 TraesCS5D01G121800 chr5D 83262888 83263456 568 False 902.0 902 95.2630 1 570 1 chr5D.!!$F2 569
4 TraesCS5D01G121800 chr1B 39620639 39622064 1425 True 2095.0 2095 93.4080 1015 2421 1 chr1B.!!$R1 1406
5 TraesCS5D01G121800 chr7A 310597581 310601857 4276 True 1187.5 1650 94.2605 866 2406 2 chr7A.!!$R1 1540
6 TraesCS5D01G121800 chr3B 64568973 64569920 947 False 1402.0 1402 93.2290 1462 2421 1 chr3B.!!$F2 959
7 TraesCS5D01G121800 chr3B 64558259 64558864 605 False 863.0 863 92.4220 861 1465 1 chr3B.!!$F1 604
8 TraesCS5D01G121800 chr3D 153750329 153750966 637 True 935.0 935 93.1030 19 656 1 chr3D.!!$R2 637
9 TraesCS5D01G121800 chr3D 401223313 401223882 569 False 898.0 898 95.0880 1 570 1 chr3D.!!$F2 569
10 TraesCS5D01G121800 chr3D 485813919 485814488 569 False 887.0 887 94.7370 1 570 1 chr3D.!!$F3 569
11 TraesCS5D01G121800 chr7D 129994500 129995069 569 True 893.0 893 94.9120 1 570 1 chr7D.!!$R1 569
12 TraesCS5D01G121800 chr4D 90284375 90284944 569 True 893.0 893 94.9210 1 570 1 chr4D.!!$R1 569
13 TraesCS5D01G121800 chr4D 325741695 325742264 569 True 881.0 881 94.5610 1 570 1 chr4D.!!$R2 569
14 TraesCS5D01G121800 chr2D 499279958 499280527 569 False 893.0 893 94.9120 1 570 1 chr2D.!!$F5 569
15 TraesCS5D01G121800 chr4A 707825713 707826564 851 False 830.0 830 84.7400 995 1833 1 chr4A.!!$F1 838

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
874 875 0.099436 CACGCTAAGCCCTCATTTGC 59.901 55.0 0.0 0.0 0.0 3.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1939 4703 3.065233 CGTAATGGCATGTAACTGCACAT 59.935 43.478 0.0 0.0 44.12 3.21 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
42 43 8.819974 CATTTTGTTAGCTAAATATTTGGCCAG 58.180 33.333 27.10 11.21 44.55 4.85
95 96 3.557228 ACTAGGACGGAGGTAGTAGTG 57.443 52.381 0.00 0.00 0.00 2.74
254 255 8.805175 GTCTTTTAGTAGTACTTCCTCCTTTCT 58.195 37.037 8.40 0.00 0.00 2.52
273 274 8.109634 TCCTTTCTAGTTTATGGCTCAATTTCT 58.890 33.333 0.00 0.00 0.00 2.52
407 408 7.287466 TCAATTTCAAAATCTCTCCAACCAAGA 59.713 33.333 0.00 0.00 0.00 3.02
411 412 6.418101 TCAAAATCTCTCCAACCAAGATAGG 58.582 40.000 0.00 0.00 0.00 2.57
445 446 7.033185 GGTGGAATTAATTTCGTAGTTTGCAT 58.967 34.615 1.43 0.00 34.98 3.96
532 533 6.435591 TGCATGTATGACCACTAAATTTCCAA 59.564 34.615 0.00 0.00 0.00 3.53
664 665 9.367444 GATATTATTTACATGTTACTCCCTCCG 57.633 37.037 2.30 0.00 0.00 4.63
665 666 6.549433 TTATTTACATGTTACTCCCTCCGT 57.451 37.500 2.30 0.00 0.00 4.69
666 667 4.895668 TTTACATGTTACTCCCTCCGTT 57.104 40.909 2.30 0.00 0.00 4.44
667 668 4.460948 TTACATGTTACTCCCTCCGTTC 57.539 45.455 2.30 0.00 0.00 3.95
668 669 1.553704 ACATGTTACTCCCTCCGTTCC 59.446 52.381 0.00 0.00 0.00 3.62
669 670 1.831736 CATGTTACTCCCTCCGTTCCT 59.168 52.381 0.00 0.00 0.00 3.36
670 671 2.905415 TGTTACTCCCTCCGTTCCTA 57.095 50.000 0.00 0.00 0.00 2.94
671 672 3.173953 TGTTACTCCCTCCGTTCCTAA 57.826 47.619 0.00 0.00 0.00 2.69
672 673 3.509442 TGTTACTCCCTCCGTTCCTAAA 58.491 45.455 0.00 0.00 0.00 1.85
673 674 4.098894 TGTTACTCCCTCCGTTCCTAAAT 58.901 43.478 0.00 0.00 0.00 1.40
674 675 5.271598 TGTTACTCCCTCCGTTCCTAAATA 58.728 41.667 0.00 0.00 0.00 1.40
675 676 5.127682 TGTTACTCCCTCCGTTCCTAAATAC 59.872 44.000 0.00 0.00 0.00 1.89
676 677 3.991683 ACTCCCTCCGTTCCTAAATACT 58.008 45.455 0.00 0.00 0.00 2.12
677 678 4.359996 ACTCCCTCCGTTCCTAAATACTT 58.640 43.478 0.00 0.00 0.00 2.24
678 679 4.161754 ACTCCCTCCGTTCCTAAATACTTG 59.838 45.833 0.00 0.00 0.00 3.16
679 680 4.098894 TCCCTCCGTTCCTAAATACTTGT 58.901 43.478 0.00 0.00 0.00 3.16
680 681 4.161001 TCCCTCCGTTCCTAAATACTTGTC 59.839 45.833 0.00 0.00 0.00 3.18
681 682 4.161754 CCCTCCGTTCCTAAATACTTGTCT 59.838 45.833 0.00 0.00 0.00 3.41
682 683 5.338137 CCCTCCGTTCCTAAATACTTGTCTT 60.338 44.000 0.00 0.00 0.00 3.01
683 684 6.171213 CCTCCGTTCCTAAATACTTGTCTTT 58.829 40.000 0.00 0.00 0.00 2.52
684 685 6.313164 CCTCCGTTCCTAAATACTTGTCTTTC 59.687 42.308 0.00 0.00 0.00 2.62
685 686 7.001099 TCCGTTCCTAAATACTTGTCTTTCT 57.999 36.000 0.00 0.00 0.00 2.52
686 687 8.125978 TCCGTTCCTAAATACTTGTCTTTCTA 57.874 34.615 0.00 0.00 0.00 2.10
687 688 8.248945 TCCGTTCCTAAATACTTGTCTTTCTAG 58.751 37.037 0.00 0.00 0.00 2.43
688 689 7.491696 CCGTTCCTAAATACTTGTCTTTCTAGG 59.508 40.741 0.00 0.00 0.00 3.02
689 690 7.010275 CGTTCCTAAATACTTGTCTTTCTAGGC 59.990 40.741 0.00 0.00 0.00 3.93
690 691 7.490657 TCCTAAATACTTGTCTTTCTAGGCA 57.509 36.000 0.00 0.00 33.22 4.75
691 692 8.090788 TCCTAAATACTTGTCTTTCTAGGCAT 57.909 34.615 0.00 0.00 35.56 4.40
692 693 8.548877 TCCTAAATACTTGTCTTTCTAGGCATT 58.451 33.333 0.00 0.00 35.56 3.56
693 694 9.178758 CCTAAATACTTGTCTTTCTAGGCATTT 57.821 33.333 0.00 0.00 35.56 2.32
695 696 8.635765 AAATACTTGTCTTTCTAGGCATTTCA 57.364 30.769 0.00 0.00 35.56 2.69
696 697 8.635765 AATACTTGTCTTTCTAGGCATTTCAA 57.364 30.769 0.00 0.00 35.56 2.69
697 698 6.319141 ACTTGTCTTTCTAGGCATTTCAAC 57.681 37.500 0.00 0.00 35.56 3.18
698 699 5.827797 ACTTGTCTTTCTAGGCATTTCAACA 59.172 36.000 0.00 0.00 35.56 3.33
699 700 6.321181 ACTTGTCTTTCTAGGCATTTCAACAA 59.679 34.615 0.00 0.00 35.56 2.83
700 701 6.317789 TGTCTTTCTAGGCATTTCAACAAG 57.682 37.500 0.00 0.00 29.10 3.16
701 702 5.827797 TGTCTTTCTAGGCATTTCAACAAGT 59.172 36.000 0.00 0.00 29.10 3.16
702 703 6.145535 GTCTTTCTAGGCATTTCAACAAGTG 58.854 40.000 0.00 0.00 0.00 3.16
703 704 6.017109 GTCTTTCTAGGCATTTCAACAAGTGA 60.017 38.462 0.00 0.00 0.00 3.41
704 705 5.689383 TTCTAGGCATTTCAACAAGTGAC 57.311 39.130 0.00 0.00 35.39 3.67
705 706 4.973168 TCTAGGCATTTCAACAAGTGACT 58.027 39.130 0.00 0.00 40.60 3.41
706 707 6.109156 TCTAGGCATTTCAACAAGTGACTA 57.891 37.500 0.00 0.00 38.51 2.59
707 708 5.932303 TCTAGGCATTTCAACAAGTGACTAC 59.068 40.000 0.00 0.00 38.51 2.73
708 709 4.460263 AGGCATTTCAACAAGTGACTACA 58.540 39.130 0.00 0.00 35.84 2.74
709 710 5.072741 AGGCATTTCAACAAGTGACTACAT 58.927 37.500 0.00 0.00 35.84 2.29
710 711 6.237901 AGGCATTTCAACAAGTGACTACATA 58.762 36.000 0.00 0.00 35.84 2.29
711 712 6.149474 AGGCATTTCAACAAGTGACTACATAC 59.851 38.462 0.00 0.00 35.84 2.39
712 713 6.015504 GCATTTCAACAAGTGACTACATACG 58.984 40.000 0.00 0.00 35.39 3.06
713 714 6.534059 CATTTCAACAAGTGACTACATACGG 58.466 40.000 0.00 0.00 35.39 4.02
714 715 5.456548 TTCAACAAGTGACTACATACGGA 57.543 39.130 0.00 0.00 35.39 4.69
715 716 5.055642 TCAACAAGTGACTACATACGGAG 57.944 43.478 0.00 0.00 0.00 4.63
716 717 5.010314 TTCAACAAGTGACTACATACGGAGT 59.990 40.000 0.00 0.00 39.84 3.85
717 718 6.207221 TTCAACAAGTGACTACATACGGAGTA 59.793 38.462 0.00 0.00 41.66 2.59
718 719 7.255555 TTCAACAAGTGACTACATACGGAGTAA 60.256 37.037 0.00 0.00 41.03 2.24
734 735 6.931838 ACGGAGTAAAATGAGTGAATCTACA 58.068 36.000 0.00 0.00 41.94 2.74
735 736 6.812160 ACGGAGTAAAATGAGTGAATCTACAC 59.188 38.462 0.00 0.00 41.94 2.90
776 777 8.763049 CATACATCCGTATGTGATAGTCATTT 57.237 34.615 3.56 0.00 46.70 2.32
777 778 8.650714 CATACATCCGTATGTGATAGTCATTTG 58.349 37.037 3.56 0.00 46.70 2.32
778 779 6.816136 ACATCCGTATGTGATAGTCATTTGA 58.184 36.000 0.00 0.00 44.79 2.69
779 780 7.272244 ACATCCGTATGTGATAGTCATTTGAA 58.728 34.615 0.00 0.00 44.79 2.69
780 781 7.768582 ACATCCGTATGTGATAGTCATTTGAAA 59.231 33.333 0.00 0.00 44.79 2.69
781 782 8.777413 CATCCGTATGTGATAGTCATTTGAAAT 58.223 33.333 0.00 0.00 0.00 2.17
782 783 8.141835 TCCGTATGTGATAGTCATTTGAAATG 57.858 34.615 11.54 11.54 0.00 2.32
783 784 6.852853 CCGTATGTGATAGTCATTTGAAATGC 59.147 38.462 12.86 8.33 0.00 3.56
784 785 6.852853 CGTATGTGATAGTCATTTGAAATGCC 59.147 38.462 12.86 1.61 0.00 4.40
785 786 7.254898 CGTATGTGATAGTCATTTGAAATGCCT 60.255 37.037 12.86 9.73 0.00 4.75
786 787 9.056005 GTATGTGATAGTCATTTGAAATGCCTA 57.944 33.333 10.59 10.59 0.00 3.93
787 788 7.936496 TGTGATAGTCATTTGAAATGCCTAA 57.064 32.000 11.99 0.00 0.00 2.69
788 789 8.347004 TGTGATAGTCATTTGAAATGCCTAAA 57.653 30.769 11.99 2.57 0.00 1.85
789 790 8.801299 TGTGATAGTCATTTGAAATGCCTAAAA 58.199 29.630 11.99 2.26 0.00 1.52
790 791 9.638239 GTGATAGTCATTTGAAATGCCTAAAAA 57.362 29.630 11.99 0.11 0.00 1.94
813 814 6.812879 AAACAAGTATTTAGAAACGGAGGG 57.187 37.500 0.00 0.00 0.00 4.30
814 815 5.750352 ACAAGTATTTAGAAACGGAGGGA 57.250 39.130 0.00 0.00 0.00 4.20
815 816 5.731591 ACAAGTATTTAGAAACGGAGGGAG 58.268 41.667 0.00 0.00 0.00 4.30
816 817 5.247792 ACAAGTATTTAGAAACGGAGGGAGT 59.752 40.000 0.00 0.00 0.00 3.85
817 818 6.438425 ACAAGTATTTAGAAACGGAGGGAGTA 59.562 38.462 0.00 0.00 0.00 2.59
818 819 7.125356 ACAAGTATTTAGAAACGGAGGGAGTAT 59.875 37.037 0.00 0.00 0.00 2.12
819 820 7.672122 AGTATTTAGAAACGGAGGGAGTATT 57.328 36.000 0.00 0.00 0.00 1.89
820 821 8.773033 AGTATTTAGAAACGGAGGGAGTATTA 57.227 34.615 0.00 0.00 0.00 0.98
821 822 9.377238 AGTATTTAGAAACGGAGGGAGTATTAT 57.623 33.333 0.00 0.00 0.00 1.28
822 823 9.420551 GTATTTAGAAACGGAGGGAGTATTATG 57.579 37.037 0.00 0.00 0.00 1.90
823 824 7.427989 TTTAGAAACGGAGGGAGTATTATGT 57.572 36.000 0.00 0.00 0.00 2.29
824 825 8.537728 TTTAGAAACGGAGGGAGTATTATGTA 57.462 34.615 0.00 0.00 0.00 2.29
825 826 8.716674 TTAGAAACGGAGGGAGTATTATGTAT 57.283 34.615 0.00 0.00 0.00 2.29
826 827 7.613551 AGAAACGGAGGGAGTATTATGTATT 57.386 36.000 0.00 0.00 0.00 1.89
827 828 8.716674 AGAAACGGAGGGAGTATTATGTATTA 57.283 34.615 0.00 0.00 0.00 0.98
828 829 9.151177 AGAAACGGAGGGAGTATTATGTATTAA 57.849 33.333 0.00 0.00 0.00 1.40
829 830 9.768662 GAAACGGAGGGAGTATTATGTATTAAA 57.231 33.333 0.00 0.00 0.00 1.52
831 832 9.551734 AACGGAGGGAGTATTATGTATTAAAAC 57.448 33.333 0.00 0.00 0.00 2.43
832 833 8.931568 ACGGAGGGAGTATTATGTATTAAAACT 58.068 33.333 0.00 0.00 0.00 2.66
858 859 6.932901 ATTTGACATGAAATTAACTGCACG 57.067 33.333 0.00 0.00 0.00 5.34
859 860 3.820689 TGACATGAAATTAACTGCACGC 58.179 40.909 0.00 0.00 0.00 5.34
864 865 4.078363 TGAAATTAACTGCACGCTAAGC 57.922 40.909 0.00 0.00 0.00 3.09
874 875 0.099436 CACGCTAAGCCCTCATTTGC 59.901 55.000 0.00 0.00 0.00 3.68
878 879 1.821136 GCTAAGCCCTCATTTGCTTGT 59.179 47.619 6.98 0.00 46.66 3.16
889 890 0.608035 TTTGCTTGTCGTGGATCCCC 60.608 55.000 9.90 0.00 0.00 4.81
908 909 2.757077 GGGGATCCCGGCCTTATG 59.243 66.667 24.90 0.00 36.85 1.90
940 942 4.003788 CCACGGGCCGAGTTGACT 62.004 66.667 35.78 4.66 0.00 3.41
1001 1003 2.626467 GGACCCCTGCCCTTTCCAT 61.626 63.158 0.00 0.00 0.00 3.41
1037 1039 2.702478 AGCGATTCCCTGATCTCATCAA 59.298 45.455 0.00 0.00 39.11 2.57
1101 1103 4.379243 CCGAGCTTGTGCCTCCGT 62.379 66.667 0.00 0.00 40.80 4.69
1102 1104 2.357517 CGAGCTTGTGCCTCCGTT 60.358 61.111 0.00 0.00 40.80 4.44
1271 1281 1.081892 CCTCAGACGAACAGCAATGG 58.918 55.000 0.00 0.00 0.00 3.16
1289 1299 2.187163 GCTAGCGGTCACCTTCCC 59.813 66.667 0.00 0.00 0.00 3.97
1432 1457 7.334421 TCATTTTACAGCTAATCAGACTTGGAC 59.666 37.037 0.00 0.00 0.00 4.02
1456 1481 5.658190 CCTCTCCCACCATTGTCAAATTAAT 59.342 40.000 0.00 0.00 0.00 1.40
1566 1592 8.097038 GTGAGGTCTGATGCTATATTTTGGATA 58.903 37.037 0.00 0.00 0.00 2.59
1644 1670 4.943705 CCTAATGTGTGGCAGTTTGTCTAT 59.056 41.667 0.00 0.00 0.00 1.98
1674 1700 9.224267 AGTTAGATTATTGGCTGCATACATTAG 57.776 33.333 0.50 0.00 0.00 1.73
1719 1745 2.104451 TGTGGCAAATGCAGTGGATTTT 59.896 40.909 18.83 3.47 44.36 1.82
1939 4703 4.398988 CCATGGCATACTTTTTAGACAGCA 59.601 41.667 0.00 0.00 0.00 4.41
1960 4724 4.637483 ATGTGCAGTTACATGCCATTAC 57.363 40.909 0.00 0.00 45.91 1.89
2011 4775 9.030452 ACACTCTTCTTGTATCTATGGATATCC 57.970 37.037 15.39 15.39 36.88 2.59
2059 4825 3.128415 CACACATGACAAAGGACACAACA 59.872 43.478 0.00 0.00 0.00 3.33
2060 4826 3.128589 ACACATGACAAAGGACACAACAC 59.871 43.478 0.00 0.00 0.00 3.32
2071 4837 6.723298 AAGGACACAACACCAAATAAATCA 57.277 33.333 0.00 0.00 0.00 2.57
2116 4882 9.429359 CACTGACTCATGTCTTAGACTTTATTT 57.571 33.333 13.86 0.00 43.29 1.40
2170 4936 4.806330 ACATAAGGTGTGTAGACAGTTCG 58.194 43.478 0.00 0.00 40.28 3.95
2235 5001 6.843069 ATTTATTTTGCGCCATTATTGACC 57.157 33.333 4.18 0.00 0.00 4.02
2236 5002 5.590530 TTATTTTGCGCCATTATTGACCT 57.409 34.783 4.18 0.00 0.00 3.85
2259 5042 7.016268 ACCTGAGTTTTATCTGAACCTGAGTTA 59.984 37.037 0.00 0.00 35.94 2.24
2300 5083 3.146847 AGATCCACGAACCTTTGTTTCC 58.853 45.455 0.00 0.00 33.97 3.13
2301 5084 2.421751 TCCACGAACCTTTGTTTCCA 57.578 45.000 0.00 0.00 33.97 3.53
2320 5103 5.241403 TCCAAACTCTGCCTATTCTTTCA 57.759 39.130 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 4.226761 CCTTTGTAGTTCGTGCCAAATTC 58.773 43.478 0.00 0.00 0.00 2.17
139 140 5.246307 AGTAAAATTTTCTCCTCGTCCTGG 58.754 41.667 6.72 0.00 0.00 4.45
244 245 5.030147 TGAGCCATAAACTAGAAAGGAGGA 58.970 41.667 0.00 0.00 0.00 3.71
254 255 7.669722 ACTCCAAAGAAATTGAGCCATAAACTA 59.330 33.333 0.00 0.00 41.85 2.24
299 300 5.358160 GGACTCCAAGAAAATTGATGTAGGG 59.642 44.000 0.00 0.00 0.00 3.53
306 307 3.146066 CCACGGACTCCAAGAAAATTGA 58.854 45.455 0.00 0.00 0.00 2.57
313 314 2.099652 CTGCACCACGGACTCCAAGA 62.100 60.000 0.00 0.00 0.00 3.02
407 408 0.907704 TTCCACCACTCACCGCCTAT 60.908 55.000 0.00 0.00 0.00 2.57
411 412 1.816074 TTAATTCCACCACTCACCGC 58.184 50.000 0.00 0.00 0.00 5.68
445 446 8.766000 TGAGAAAAACGAGCATACATTACTTA 57.234 30.769 0.00 0.00 0.00 2.24
513 514 8.934023 AAGTTCTTGGAAATTTAGTGGTCATA 57.066 30.769 0.00 0.00 0.00 2.15
532 533 4.910195 TCACCAATGCATGTAGAAGTTCT 58.090 39.130 10.87 10.87 0.00 3.01
648 649 1.553704 GGAACGGAGGGAGTAACATGT 59.446 52.381 0.00 0.00 0.00 3.21
656 657 4.161754 ACAAGTATTTAGGAACGGAGGGAG 59.838 45.833 0.00 0.00 0.00 4.30
657 658 4.098894 ACAAGTATTTAGGAACGGAGGGA 58.901 43.478 0.00 0.00 0.00 4.20
658 659 4.161754 AGACAAGTATTTAGGAACGGAGGG 59.838 45.833 0.00 0.00 0.00 4.30
659 660 5.340439 AGACAAGTATTTAGGAACGGAGG 57.660 43.478 0.00 0.00 0.00 4.30
660 661 7.097834 AGAAAGACAAGTATTTAGGAACGGAG 58.902 38.462 0.00 0.00 0.00 4.63
661 662 7.001099 AGAAAGACAAGTATTTAGGAACGGA 57.999 36.000 0.00 0.00 0.00 4.69
662 663 7.491696 CCTAGAAAGACAAGTATTTAGGAACGG 59.508 40.741 4.01 0.00 26.70 4.44
663 664 7.010275 GCCTAGAAAGACAAGTATTTAGGAACG 59.990 40.741 11.40 0.00 26.70 3.95
664 665 7.822822 TGCCTAGAAAGACAAGTATTTAGGAAC 59.177 37.037 11.40 0.00 26.70 3.62
665 666 7.913789 TGCCTAGAAAGACAAGTATTTAGGAA 58.086 34.615 11.40 1.02 26.70 3.36
666 667 7.490657 TGCCTAGAAAGACAAGTATTTAGGA 57.509 36.000 11.40 0.00 26.70 2.94
667 668 8.738645 AATGCCTAGAAAGACAAGTATTTAGG 57.261 34.615 5.26 5.26 0.00 2.69
669 670 9.733556 TGAAATGCCTAGAAAGACAAGTATTTA 57.266 29.630 0.00 0.00 0.00 1.40
670 671 8.635765 TGAAATGCCTAGAAAGACAAGTATTT 57.364 30.769 0.00 0.00 0.00 1.40
671 672 8.515414 GTTGAAATGCCTAGAAAGACAAGTATT 58.485 33.333 0.00 0.00 0.00 1.89
672 673 7.665559 TGTTGAAATGCCTAGAAAGACAAGTAT 59.334 33.333 0.00 0.00 0.00 2.12
673 674 6.995686 TGTTGAAATGCCTAGAAAGACAAGTA 59.004 34.615 0.00 0.00 0.00 2.24
674 675 5.827797 TGTTGAAATGCCTAGAAAGACAAGT 59.172 36.000 0.00 0.00 0.00 3.16
675 676 6.317789 TGTTGAAATGCCTAGAAAGACAAG 57.682 37.500 0.00 0.00 0.00 3.16
676 677 6.321181 ACTTGTTGAAATGCCTAGAAAGACAA 59.679 34.615 0.00 0.00 0.00 3.18
677 678 5.827797 ACTTGTTGAAATGCCTAGAAAGACA 59.172 36.000 0.00 0.00 0.00 3.41
678 679 6.017109 TCACTTGTTGAAATGCCTAGAAAGAC 60.017 38.462 0.00 0.00 0.00 3.01
679 680 6.017109 GTCACTTGTTGAAATGCCTAGAAAGA 60.017 38.462 0.00 0.00 35.39 2.52
680 681 6.016777 AGTCACTTGTTGAAATGCCTAGAAAG 60.017 38.462 0.00 0.00 35.39 2.62
681 682 5.827797 AGTCACTTGTTGAAATGCCTAGAAA 59.172 36.000 0.00 0.00 35.39 2.52
682 683 5.376625 AGTCACTTGTTGAAATGCCTAGAA 58.623 37.500 0.00 0.00 35.39 2.10
683 684 4.973168 AGTCACTTGTTGAAATGCCTAGA 58.027 39.130 0.00 0.00 35.39 2.43
684 685 5.700832 TGTAGTCACTTGTTGAAATGCCTAG 59.299 40.000 0.00 0.00 35.39 3.02
685 686 5.616270 TGTAGTCACTTGTTGAAATGCCTA 58.384 37.500 0.00 0.00 35.39 3.93
686 687 4.460263 TGTAGTCACTTGTTGAAATGCCT 58.540 39.130 0.00 0.00 35.39 4.75
687 688 4.829064 TGTAGTCACTTGTTGAAATGCC 57.171 40.909 0.00 0.00 35.39 4.40
688 689 6.015504 CGTATGTAGTCACTTGTTGAAATGC 58.984 40.000 0.00 0.00 35.39 3.56
689 690 6.367695 TCCGTATGTAGTCACTTGTTGAAATG 59.632 38.462 0.00 0.00 35.39 2.32
690 691 6.460781 TCCGTATGTAGTCACTTGTTGAAAT 58.539 36.000 0.00 0.00 35.39 2.17
691 692 5.845103 TCCGTATGTAGTCACTTGTTGAAA 58.155 37.500 0.00 0.00 35.39 2.69
692 693 5.010314 ACTCCGTATGTAGTCACTTGTTGAA 59.990 40.000 0.00 0.00 35.39 2.69
693 694 4.521639 ACTCCGTATGTAGTCACTTGTTGA 59.478 41.667 0.00 0.00 0.00 3.18
694 695 4.806330 ACTCCGTATGTAGTCACTTGTTG 58.194 43.478 0.00 0.00 0.00 3.33
695 696 6.579666 TTACTCCGTATGTAGTCACTTGTT 57.420 37.500 0.00 0.00 0.00 2.83
696 697 6.579666 TTTACTCCGTATGTAGTCACTTGT 57.420 37.500 0.00 0.00 0.00 3.16
697 698 7.758076 TCATTTTACTCCGTATGTAGTCACTTG 59.242 37.037 0.00 0.00 0.00 3.16
698 699 7.833786 TCATTTTACTCCGTATGTAGTCACTT 58.166 34.615 0.00 0.00 0.00 3.16
699 700 7.122353 ACTCATTTTACTCCGTATGTAGTCACT 59.878 37.037 0.00 0.00 0.00 3.41
700 701 7.220300 CACTCATTTTACTCCGTATGTAGTCAC 59.780 40.741 0.00 0.00 0.00 3.67
701 702 7.121611 TCACTCATTTTACTCCGTATGTAGTCA 59.878 37.037 0.00 0.00 0.00 3.41
702 703 7.478322 TCACTCATTTTACTCCGTATGTAGTC 58.522 38.462 0.00 0.00 0.00 2.59
703 704 7.400599 TCACTCATTTTACTCCGTATGTAGT 57.599 36.000 0.00 0.00 0.00 2.73
704 705 8.873215 ATTCACTCATTTTACTCCGTATGTAG 57.127 34.615 0.00 0.00 0.00 2.74
705 706 8.692710 AGATTCACTCATTTTACTCCGTATGTA 58.307 33.333 0.00 0.00 0.00 2.29
706 707 7.556844 AGATTCACTCATTTTACTCCGTATGT 58.443 34.615 0.00 0.00 0.00 2.29
707 708 8.969267 GTAGATTCACTCATTTTACTCCGTATG 58.031 37.037 0.00 0.00 0.00 2.39
708 709 8.692710 TGTAGATTCACTCATTTTACTCCGTAT 58.307 33.333 0.00 0.00 0.00 3.06
709 710 7.972277 GTGTAGATTCACTCATTTTACTCCGTA 59.028 37.037 0.00 0.00 35.68 4.02
710 711 6.812160 GTGTAGATTCACTCATTTTACTCCGT 59.188 38.462 0.00 0.00 35.68 4.69
711 712 7.036220 AGTGTAGATTCACTCATTTTACTCCG 58.964 38.462 0.00 0.00 44.07 4.63
752 753 8.585018 TCAAATGACTATCACATACGGATGTAT 58.415 33.333 14.23 10.02 44.82 2.29
753 754 7.947282 TCAAATGACTATCACATACGGATGTA 58.053 34.615 14.23 2.61 44.82 2.29
755 756 7.713764 TTCAAATGACTATCACATACGGATG 57.286 36.000 5.94 5.94 39.16 3.51
756 757 8.777413 CATTTCAAATGACTATCACATACGGAT 58.223 33.333 3.82 0.00 0.00 4.18
757 758 7.254761 GCATTTCAAATGACTATCACATACGGA 60.255 37.037 14.65 0.00 0.00 4.69
758 759 6.852853 GCATTTCAAATGACTATCACATACGG 59.147 38.462 14.65 0.00 0.00 4.02
759 760 6.852853 GGCATTTCAAATGACTATCACATACG 59.147 38.462 14.65 0.00 0.00 3.06
760 761 7.934457 AGGCATTTCAAATGACTATCACATAC 58.066 34.615 17.52 0.00 35.20 2.39
761 762 9.625747 TTAGGCATTTCAAATGACTATCACATA 57.374 29.630 23.80 7.51 39.21 2.29
762 763 8.523915 TTAGGCATTTCAAATGACTATCACAT 57.476 30.769 23.80 1.95 39.21 3.21
763 764 7.936496 TTAGGCATTTCAAATGACTATCACA 57.064 32.000 23.80 8.54 39.21 3.58
764 765 9.638239 TTTTTAGGCATTTCAAATGACTATCAC 57.362 29.630 23.80 0.32 39.21 3.06
788 789 7.503230 TCCCTCCGTTTCTAAATACTTGTTTTT 59.497 33.333 0.00 0.00 0.00 1.94
789 790 6.999871 TCCCTCCGTTTCTAAATACTTGTTTT 59.000 34.615 0.00 0.00 0.00 2.43
790 791 6.536447 TCCCTCCGTTTCTAAATACTTGTTT 58.464 36.000 0.00 0.00 0.00 2.83
791 792 6.117975 TCCCTCCGTTTCTAAATACTTGTT 57.882 37.500 0.00 0.00 0.00 2.83
792 793 5.247792 ACTCCCTCCGTTTCTAAATACTTGT 59.752 40.000 0.00 0.00 0.00 3.16
793 794 5.731591 ACTCCCTCCGTTTCTAAATACTTG 58.268 41.667 0.00 0.00 0.00 3.16
794 795 7.672122 ATACTCCCTCCGTTTCTAAATACTT 57.328 36.000 0.00 0.00 0.00 2.24
795 796 7.672122 AATACTCCCTCCGTTTCTAAATACT 57.328 36.000 0.00 0.00 0.00 2.12
796 797 9.420551 CATAATACTCCCTCCGTTTCTAAATAC 57.579 37.037 0.00 0.00 0.00 1.89
797 798 9.151177 ACATAATACTCCCTCCGTTTCTAAATA 57.849 33.333 0.00 0.00 0.00 1.40
798 799 8.030913 ACATAATACTCCCTCCGTTTCTAAAT 57.969 34.615 0.00 0.00 0.00 1.40
799 800 7.427989 ACATAATACTCCCTCCGTTTCTAAA 57.572 36.000 0.00 0.00 0.00 1.85
800 801 8.716674 ATACATAATACTCCCTCCGTTTCTAA 57.283 34.615 0.00 0.00 0.00 2.10
801 802 8.716674 AATACATAATACTCCCTCCGTTTCTA 57.283 34.615 0.00 0.00 0.00 2.10
802 803 7.613551 AATACATAATACTCCCTCCGTTTCT 57.386 36.000 0.00 0.00 0.00 2.52
803 804 9.768662 TTTAATACATAATACTCCCTCCGTTTC 57.231 33.333 0.00 0.00 0.00 2.78
805 806 9.551734 GTTTTAATACATAATACTCCCTCCGTT 57.448 33.333 0.00 0.00 0.00 4.44
806 807 8.931568 AGTTTTAATACATAATACTCCCTCCGT 58.068 33.333 0.00 0.00 32.39 4.69
832 833 9.715123 CGTGCAGTTAATTTCATGTCAAATATA 57.285 29.630 0.00 0.00 0.00 0.86
833 834 7.220683 GCGTGCAGTTAATTTCATGTCAAATAT 59.779 33.333 0.00 0.00 0.00 1.28
834 835 6.526325 GCGTGCAGTTAATTTCATGTCAAATA 59.474 34.615 0.00 0.00 0.00 1.40
835 836 5.345741 GCGTGCAGTTAATTTCATGTCAAAT 59.654 36.000 0.00 0.00 0.00 2.32
836 837 4.679197 GCGTGCAGTTAATTTCATGTCAAA 59.321 37.500 0.00 0.00 0.00 2.69
837 838 4.023279 AGCGTGCAGTTAATTTCATGTCAA 60.023 37.500 0.00 0.00 0.00 3.18
838 839 3.501828 AGCGTGCAGTTAATTTCATGTCA 59.498 39.130 0.00 0.00 0.00 3.58
839 840 4.083581 AGCGTGCAGTTAATTTCATGTC 57.916 40.909 0.00 0.00 0.00 3.06
840 841 5.621197 TTAGCGTGCAGTTAATTTCATGT 57.379 34.783 0.00 0.00 0.00 3.21
841 842 4.496895 GCTTAGCGTGCAGTTAATTTCATG 59.503 41.667 0.00 0.00 0.00 3.07
842 843 4.438744 GGCTTAGCGTGCAGTTAATTTCAT 60.439 41.667 0.00 0.00 0.00 2.57
843 844 3.119990 GGCTTAGCGTGCAGTTAATTTCA 60.120 43.478 0.00 0.00 0.00 2.69
844 845 3.426323 GGCTTAGCGTGCAGTTAATTTC 58.574 45.455 0.00 0.00 0.00 2.17
845 846 2.163613 GGGCTTAGCGTGCAGTTAATTT 59.836 45.455 0.00 0.00 0.00 1.82
846 847 1.743394 GGGCTTAGCGTGCAGTTAATT 59.257 47.619 0.00 0.00 0.00 1.40
847 848 1.065418 AGGGCTTAGCGTGCAGTTAAT 60.065 47.619 0.00 0.00 0.00 1.40
848 849 0.323629 AGGGCTTAGCGTGCAGTTAA 59.676 50.000 0.00 0.00 0.00 2.01
849 850 0.108329 GAGGGCTTAGCGTGCAGTTA 60.108 55.000 0.00 0.00 0.00 2.24
850 851 1.376037 GAGGGCTTAGCGTGCAGTT 60.376 57.895 0.00 0.00 0.00 3.16
851 852 1.903877 ATGAGGGCTTAGCGTGCAGT 61.904 55.000 0.00 0.00 0.00 4.40
852 853 0.745845 AATGAGGGCTTAGCGTGCAG 60.746 55.000 0.00 0.00 0.00 4.41
853 854 0.322456 AAATGAGGGCTTAGCGTGCA 60.322 50.000 0.00 0.00 0.00 4.57
854 855 0.099436 CAAATGAGGGCTTAGCGTGC 59.901 55.000 0.00 0.00 0.00 5.34
855 856 0.099436 GCAAATGAGGGCTTAGCGTG 59.901 55.000 0.00 0.00 0.00 5.34
856 857 0.035056 AGCAAATGAGGGCTTAGCGT 60.035 50.000 0.00 0.00 36.92 5.07
857 858 2.785868 AGCAAATGAGGGCTTAGCG 58.214 52.632 0.00 0.00 36.92 4.26
864 865 0.523072 CCACGACAAGCAAATGAGGG 59.477 55.000 0.00 0.00 0.00 4.30
874 875 2.186903 CCGGGGATCCACGACAAG 59.813 66.667 37.71 17.14 0.00 3.16
908 909 3.661648 TGGCTTCTTCCCCCAGGC 61.662 66.667 0.00 0.00 0.00 4.85
1037 1039 4.153957 AGGATTTCCTGCCCGACT 57.846 55.556 0.00 0.00 46.55 4.18
1077 1079 1.078143 GCACAAGCTCGGGAGGATT 60.078 57.895 0.00 0.00 37.91 3.01
1155 1157 0.106521 GGATCTTGGCAGGAGAGAGC 59.893 60.000 5.31 0.00 0.00 4.09
1206 1216 1.542492 TCTCGCCGGAAGTAGAAACT 58.458 50.000 5.05 0.00 37.65 2.66
1271 1281 2.187163 GGAAGGTGACCGCTAGCC 59.813 66.667 9.66 0.00 0.00 3.93
1432 1457 2.584835 TTTGACAATGGTGGGAGAGG 57.415 50.000 0.00 0.00 0.00 3.69
1456 1481 1.980765 AGGAAGAGATTGTGCTCACCA 59.019 47.619 0.00 0.00 37.37 4.17
1566 1592 7.282901 CCAAACAAGAAAAATGGTCCTTGAAAT 59.717 33.333 0.00 0.00 39.28 2.17
1644 1670 7.555914 TGTATGCAGCCAATAATCTAACTTCAA 59.444 33.333 0.00 0.00 0.00 2.69
1674 1700 8.031277 ACATTCTTCAGAATTGCACCTAAATTC 58.969 33.333 0.00 0.62 42.41 2.17
1719 1745 6.711277 AGACTCACCAGTAATTTAATGCAGA 58.289 36.000 0.00 0.00 30.63 4.26
1727 1753 6.357367 AGTTCACAAGACTCACCAGTAATTT 58.643 36.000 0.00 0.00 30.63 1.82
1939 4703 3.065233 CGTAATGGCATGTAACTGCACAT 59.935 43.478 0.00 0.00 44.12 3.21
1960 4724 3.249320 AGCTATGCAAAGTGTATGATGCG 59.751 43.478 0.00 0.00 41.61 4.73
2011 4775 9.552114 GAAACAAACTTGACATCAATAGATCAG 57.448 33.333 0.00 0.00 35.02 2.90
2071 4837 9.911788 AGTCAGTGGTATTGATGAATATTTCTT 57.088 29.630 0.00 0.00 0.00 2.52
2116 4882 3.253188 CGCAGAAATTTCCTCCTTGAACA 59.747 43.478 14.61 0.00 0.00 3.18
2120 4886 3.181493 CCATCGCAGAAATTTCCTCCTTG 60.181 47.826 14.61 7.23 43.58 3.61
2170 4936 9.974750 GTAGTGCAGAACAAGAAAATATAAGAC 57.025 33.333 0.00 0.00 0.00 3.01
2259 5042 7.290948 TGGATCTACAAACAGTCAGATGGATAT 59.709 37.037 0.00 0.00 0.00 1.63
2300 5083 6.309737 GCAAATGAAAGAATAGGCAGAGTTTG 59.690 38.462 0.00 0.00 0.00 2.93
2301 5084 6.015180 TGCAAATGAAAGAATAGGCAGAGTTT 60.015 34.615 0.00 0.00 0.00 2.66


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

AutoCloner maintained by Alex Coulton.