Multiple sequence alignment - TraesCS4B01G315700

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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 TraesCS4B01G315700 chr4B 100.000 2809 0 0 1 2809 605280658 605277850 0.000000e+00 5188.0
1 TraesCS4B01G315700 chr4B 75.216 928 91 60 1197 2041 605273432 605272561 7.560000e-81 311.0
2 TraesCS4B01G315700 chr4D 94.328 2045 84 14 774 2809 478674428 478672407 0.000000e+00 3105.0
3 TraesCS4B01G315700 chr4D 94.951 515 21 3 2 511 478675202 478674688 0.000000e+00 802.0
4 TraesCS4B01G315700 chr4D 75.725 931 83 54 1195 2041 478668294 478667423 4.480000e-88 335.0
5 TraesCS4B01G315700 chr4A 90.854 1826 94 31 771 2545 685309650 685307847 0.000000e+00 2379.0
6 TraesCS4B01G315700 chr4A 91.991 462 30 3 3 457 685310179 685309718 2.360000e-180 641.0
7 TraesCS4B01G315700 chr4A 79.111 675 52 37 1195 1827 685302029 685301402 1.580000e-102 383.0
8 TraesCS4B01G315700 chr4A 90.036 281 23 4 2532 2809 685306882 685306604 2.660000e-95 359.0
9 TraesCS4B01G315700 chr1A 92.857 98 7 0 1205 1302 158493627 158493530 2.920000e-30 143.0
10 TraesCS4B01G315700 chr1D 91.837 98 8 0 1205 1302 131412501 131412404 1.360000e-28 137.0
11 TraesCS4B01G315700 chr7D 90.164 61 3 3 656 713 263515643 263515583 3.000000e-10 76.8
12 TraesCS4B01G315700 chr3D 97.727 44 1 0 664 707 288297319 288297362 3.000000e-10 76.8
13 TraesCS4B01G315700 chr6D 93.478 46 2 1 668 712 447056255 447056300 1.810000e-07 67.6
14 TraesCS4B01G315700 chr2B 91.667 48 3 1 667 713 386593658 386593611 6.490000e-07 65.8
15 TraesCS4B01G315700 chr2B 93.182 44 2 1 668 710 306923516 306923559 2.340000e-06 63.9
16 TraesCS4B01G315700 chr7A 91.489 47 3 1 668 713 1900100 1900146 2.340000e-06 63.9
17 TraesCS4B01G315700 chr5A 91.304 46 3 1 668 712 633269786 633269741 8.400000e-06 62.1
18 TraesCS4B01G315700 chr5D 97.059 34 0 1 740 773 419532373 419532341 3.910000e-04 56.5
19 TraesCS4B01G315700 chr3B 100.000 28 0 0 680 707 670022805 670022832 5.000000e-03 52.8


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 TraesCS4B01G315700 chr4B 605277850 605280658 2808 True 5188.000000 5188 100.000000 1 2809 1 chr4B.!!$R2 2808
1 TraesCS4B01G315700 chr4B 605272561 605273432 871 True 311.000000 311 75.216000 1197 2041 1 chr4B.!!$R1 844
2 TraesCS4B01G315700 chr4D 478672407 478675202 2795 True 1953.500000 3105 94.639500 2 2809 2 chr4D.!!$R2 2807
3 TraesCS4B01G315700 chr4D 478667423 478668294 871 True 335.000000 335 75.725000 1195 2041 1 chr4D.!!$R1 846
4 TraesCS4B01G315700 chr4A 685306604 685310179 3575 True 1126.333333 2379 90.960333 3 2809 3 chr4A.!!$R2 2806
5 TraesCS4B01G315700 chr4A 685301402 685302029 627 True 383.000000 383 79.111000 1195 1827 1 chr4A.!!$R1 632

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
979 1122 0.107459 GCCAATCTCAGTCCCTGTCC 60.107 60.0 0.0 0.0 32.61 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2727 3966 0.747255 GCTCCGCTGATTACTCTGGA 59.253 55.0 0.0 0.0 0.0 3.86 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
200 203 8.706322 ACTTTCCAGTCACCTGTTTATAAAAT 57.294 30.769 0.00 0.00 36.95 1.82
256 259 3.695830 ACGCAGGGAGACAAAATAAGA 57.304 42.857 0.00 0.00 0.00 2.10
258 261 2.678336 CGCAGGGAGACAAAATAAGACC 59.322 50.000 0.00 0.00 0.00 3.85
406 413 6.054941 ACTTTGGAAATTAAGCAAGGGTTTG 58.945 36.000 0.00 0.00 37.36 2.93
436 443 9.669353 GTGATAGTGCAATTAATTTCATCGATT 57.331 29.630 3.83 0.00 0.00 3.34
453 462 2.269520 ATTCTACGCATGCAGGGCCA 62.270 55.000 19.57 0.00 0.00 5.36
465 474 0.465097 CAGGGCCAGCTCAATGGTAG 60.465 60.000 6.18 0.00 42.75 3.18
467 476 0.749454 GGGCCAGCTCAATGGTAGTG 60.749 60.000 4.39 0.00 42.75 2.74
468 477 1.379642 GGCCAGCTCAATGGTAGTGC 61.380 60.000 0.00 0.00 42.75 4.40
495 508 0.166814 GCAACACCAGAAGCGCTAAG 59.833 55.000 12.05 3.08 0.00 2.18
511 524 2.213499 CTAAGCATAACCGGAGCAAGG 58.787 52.381 9.46 0.00 0.00 3.61
513 526 0.839946 AGCATAACCGGAGCAAGGAT 59.160 50.000 9.46 0.00 0.00 3.24
514 527 0.947244 GCATAACCGGAGCAAGGATG 59.053 55.000 9.46 1.58 0.00 3.51
515 528 1.475034 GCATAACCGGAGCAAGGATGA 60.475 52.381 9.46 0.00 0.00 2.92
517 530 3.557054 GCATAACCGGAGCAAGGATGATA 60.557 47.826 9.46 0.00 0.00 2.15
518 531 2.918712 AACCGGAGCAAGGATGATAG 57.081 50.000 9.46 0.00 0.00 2.08
520 533 1.414181 ACCGGAGCAAGGATGATAGTG 59.586 52.381 9.46 0.00 0.00 2.74
522 535 2.628178 CCGGAGCAAGGATGATAGTGTA 59.372 50.000 0.00 0.00 0.00 2.90
523 536 3.069586 CCGGAGCAAGGATGATAGTGTAA 59.930 47.826 0.00 0.00 0.00 2.41
526 539 5.428253 GGAGCAAGGATGATAGTGTAAACA 58.572 41.667 0.00 0.00 0.00 2.83
528 541 6.299805 AGCAAGGATGATAGTGTAAACAGA 57.700 37.500 0.00 0.00 0.00 3.41
529 542 6.344500 AGCAAGGATGATAGTGTAAACAGAG 58.656 40.000 0.00 0.00 0.00 3.35
530 543 5.007136 GCAAGGATGATAGTGTAAACAGAGC 59.993 44.000 0.00 0.00 0.00 4.09
533 546 6.344500 AGGATGATAGTGTAAACAGAGCAAG 58.656 40.000 0.00 0.00 0.00 4.01
534 547 5.007136 GGATGATAGTGTAAACAGAGCAAGC 59.993 44.000 0.00 0.00 0.00 4.01
535 548 4.893608 TGATAGTGTAAACAGAGCAAGCA 58.106 39.130 0.00 0.00 0.00 3.91
536 549 5.304778 TGATAGTGTAAACAGAGCAAGCAA 58.695 37.500 0.00 0.00 0.00 3.91
537 550 3.971032 AGTGTAAACAGAGCAAGCAAC 57.029 42.857 0.00 0.00 0.00 4.17
538 551 3.278574 AGTGTAAACAGAGCAAGCAACA 58.721 40.909 0.00 0.00 0.00 3.33
539 552 3.885297 AGTGTAAACAGAGCAAGCAACAT 59.115 39.130 0.00 0.00 0.00 2.71
540 553 5.063204 AGTGTAAACAGAGCAAGCAACATA 58.937 37.500 0.00 0.00 0.00 2.29
541 554 5.530915 AGTGTAAACAGAGCAAGCAACATAA 59.469 36.000 0.00 0.00 0.00 1.90
542 555 5.625311 GTGTAAACAGAGCAAGCAACATAAC 59.375 40.000 0.00 0.00 0.00 1.89
543 556 5.530915 TGTAAACAGAGCAAGCAACATAACT 59.469 36.000 0.00 0.00 0.00 2.24
544 557 4.494350 AACAGAGCAAGCAACATAACTG 57.506 40.909 0.00 0.00 0.00 3.16
545 558 2.816087 ACAGAGCAAGCAACATAACTGG 59.184 45.455 0.00 0.00 0.00 4.00
546 559 3.076621 CAGAGCAAGCAACATAACTGGA 58.923 45.455 0.00 0.00 0.00 3.86
565 696 4.998788 TGGAGTAAGAATCGATCAGTGTG 58.001 43.478 0.00 0.00 0.00 3.82
577 708 0.391528 TCAGTGTGGTGATGATGCCG 60.392 55.000 0.00 0.00 0.00 5.69
645 782 3.243535 CGAAGCAGCTCTGTATCCATGTA 60.244 47.826 0.00 0.00 0.00 2.29
646 783 3.742433 AGCAGCTCTGTATCCATGTAC 57.258 47.619 0.00 0.00 0.00 2.90
647 784 3.303938 AGCAGCTCTGTATCCATGTACT 58.696 45.455 0.00 0.00 0.00 2.73
648 785 3.320541 AGCAGCTCTGTATCCATGTACTC 59.679 47.826 0.00 0.00 0.00 2.59
649 786 3.553922 GCAGCTCTGTATCCATGTACTCC 60.554 52.174 0.00 0.00 0.00 3.85
650 787 3.006323 CAGCTCTGTATCCATGTACTCCC 59.994 52.174 0.00 0.00 0.00 4.30
651 788 3.116939 AGCTCTGTATCCATGTACTCCCT 60.117 47.826 0.00 0.00 0.00 4.20
652 789 3.257127 GCTCTGTATCCATGTACTCCCTC 59.743 52.174 0.00 0.00 0.00 4.30
653 790 3.829601 CTCTGTATCCATGTACTCCCTCC 59.170 52.174 0.00 0.00 0.00 4.30
654 791 2.558795 CTGTATCCATGTACTCCCTCCG 59.441 54.545 0.00 0.00 0.00 4.63
655 792 2.091499 TGTATCCATGTACTCCCTCCGT 60.091 50.000 0.00 0.00 0.00 4.69
656 793 1.705873 ATCCATGTACTCCCTCCGTC 58.294 55.000 0.00 0.00 0.00 4.79
657 794 0.333652 TCCATGTACTCCCTCCGTCA 59.666 55.000 0.00 0.00 0.00 4.35
658 795 0.460311 CCATGTACTCCCTCCGTCAC 59.540 60.000 0.00 0.00 0.00 3.67
659 796 1.182667 CATGTACTCCCTCCGTCACA 58.817 55.000 0.00 0.00 0.00 3.58
660 797 1.548719 CATGTACTCCCTCCGTCACAA 59.451 52.381 0.00 0.00 0.00 3.33
661 798 1.707106 TGTACTCCCTCCGTCACAAA 58.293 50.000 0.00 0.00 0.00 2.83
662 799 2.253610 TGTACTCCCTCCGTCACAAAT 58.746 47.619 0.00 0.00 0.00 2.32
663 800 3.433343 TGTACTCCCTCCGTCACAAATA 58.567 45.455 0.00 0.00 0.00 1.40
664 801 3.833650 TGTACTCCCTCCGTCACAAATAA 59.166 43.478 0.00 0.00 0.00 1.40
665 802 3.611766 ACTCCCTCCGTCACAAATAAG 57.388 47.619 0.00 0.00 0.00 1.73
666 803 2.904434 ACTCCCTCCGTCACAAATAAGT 59.096 45.455 0.00 0.00 0.00 2.24
667 804 3.326880 ACTCCCTCCGTCACAAATAAGTT 59.673 43.478 0.00 0.00 0.00 2.66
668 805 4.529377 ACTCCCTCCGTCACAAATAAGTTA 59.471 41.667 0.00 0.00 0.00 2.24
669 806 4.824289 TCCCTCCGTCACAAATAAGTTAC 58.176 43.478 0.00 0.00 0.00 2.50
670 807 4.529377 TCCCTCCGTCACAAATAAGTTACT 59.471 41.667 0.00 0.00 0.00 2.24
671 808 4.868734 CCCTCCGTCACAAATAAGTTACTC 59.131 45.833 0.00 0.00 0.00 2.59
672 809 4.868734 CCTCCGTCACAAATAAGTTACTCC 59.131 45.833 0.00 0.00 0.00 3.85
673 810 4.824289 TCCGTCACAAATAAGTTACTCCC 58.176 43.478 0.00 0.00 0.00 4.30
674 811 4.529377 TCCGTCACAAATAAGTTACTCCCT 59.471 41.667 0.00 0.00 0.00 4.20
675 812 4.868734 CCGTCACAAATAAGTTACTCCCTC 59.131 45.833 0.00 0.00 0.00 4.30
676 813 5.337330 CCGTCACAAATAAGTTACTCCCTCT 60.337 44.000 0.00 0.00 0.00 3.69
677 814 5.577164 CGTCACAAATAAGTTACTCCCTCTG 59.423 44.000 0.00 0.00 0.00 3.35
678 815 6.465084 GTCACAAATAAGTTACTCCCTCTGT 58.535 40.000 0.00 0.00 0.00 3.41
679 816 6.590677 GTCACAAATAAGTTACTCCCTCTGTC 59.409 42.308 0.00 0.00 0.00 3.51
680 817 5.875359 CACAAATAAGTTACTCCCTCTGTCC 59.125 44.000 0.00 0.00 0.00 4.02
681 818 5.045797 ACAAATAAGTTACTCCCTCTGTCCC 60.046 44.000 0.00 0.00 0.00 4.46
682 819 4.628661 ATAAGTTACTCCCTCTGTCCCT 57.371 45.455 0.00 0.00 0.00 4.20
683 820 5.745988 ATAAGTTACTCCCTCTGTCCCTA 57.254 43.478 0.00 0.00 0.00 3.53
684 821 4.415224 AAGTTACTCCCTCTGTCCCTAA 57.585 45.455 0.00 0.00 0.00 2.69
685 822 4.628661 AGTTACTCCCTCTGTCCCTAAT 57.371 45.455 0.00 0.00 0.00 1.73
686 823 5.745988 AGTTACTCCCTCTGTCCCTAATA 57.254 43.478 0.00 0.00 0.00 0.98
687 824 6.296435 AGTTACTCCCTCTGTCCCTAATAT 57.704 41.667 0.00 0.00 0.00 1.28
688 825 7.417811 AGTTACTCCCTCTGTCCCTAATATA 57.582 40.000 0.00 0.00 0.00 0.86
689 826 7.834046 AGTTACTCCCTCTGTCCCTAATATAA 58.166 38.462 0.00 0.00 0.00 0.98
690 827 8.294690 AGTTACTCCCTCTGTCCCTAATATAAA 58.705 37.037 0.00 0.00 0.00 1.40
691 828 8.931568 GTTACTCCCTCTGTCCCTAATATAAAA 58.068 37.037 0.00 0.00 0.00 1.52
692 829 9.510062 TTACTCCCTCTGTCCCTAATATAAAAA 57.490 33.333 0.00 0.00 0.00 1.94
693 830 7.803131 ACTCCCTCTGTCCCTAATATAAAAAC 58.197 38.462 0.00 0.00 0.00 2.43
694 831 6.823497 TCCCTCTGTCCCTAATATAAAAACG 58.177 40.000 0.00 0.00 0.00 3.60
695 832 6.384886 TCCCTCTGTCCCTAATATAAAAACGT 59.615 38.462 0.00 0.00 0.00 3.99
696 833 7.052248 CCCTCTGTCCCTAATATAAAAACGTT 58.948 38.462 0.00 0.00 0.00 3.99
697 834 7.555195 CCCTCTGTCCCTAATATAAAAACGTTT 59.445 37.037 7.96 7.96 0.00 3.60
698 835 8.953313 CCTCTGTCCCTAATATAAAAACGTTTT 58.047 33.333 20.26 20.26 0.00 2.43
702 839 9.896263 TGTCCCTAATATAAAAACGTTTTTGAC 57.104 29.630 36.92 30.87 40.33 3.18
703 840 9.896263 GTCCCTAATATAAAAACGTTTTTGACA 57.104 29.630 36.92 25.32 40.33 3.58
704 841 9.896263 TCCCTAATATAAAAACGTTTTTGACAC 57.104 29.630 36.92 0.00 40.33 3.67
705 842 9.902196 CCCTAATATAAAAACGTTTTTGACACT 57.098 29.630 36.92 23.38 40.33 3.55
715 852 8.530269 AAACGTTTTTGACACTATACTAGAGG 57.470 34.615 7.96 0.00 0.00 3.69
716 853 6.628185 ACGTTTTTGACACTATACTAGAGGG 58.372 40.000 0.00 0.00 0.00 4.30
717 854 6.435277 ACGTTTTTGACACTATACTAGAGGGA 59.565 38.462 0.00 0.00 0.00 4.20
718 855 6.973474 CGTTTTTGACACTATACTAGAGGGAG 59.027 42.308 0.00 0.00 0.00 4.30
719 856 6.466885 TTTTGACACTATACTAGAGGGAGC 57.533 41.667 0.00 0.00 0.00 4.70
720 857 4.790718 TGACACTATACTAGAGGGAGCA 57.209 45.455 0.00 0.00 0.00 4.26
721 858 4.720046 TGACACTATACTAGAGGGAGCAG 58.280 47.826 0.00 0.00 0.00 4.24
722 859 4.166337 TGACACTATACTAGAGGGAGCAGT 59.834 45.833 0.00 0.00 0.00 4.40
723 860 5.368816 TGACACTATACTAGAGGGAGCAGTA 59.631 44.000 0.00 0.00 0.00 2.74
724 861 6.044520 TGACACTATACTAGAGGGAGCAGTAT 59.955 42.308 0.00 0.00 38.63 2.12
725 862 7.237055 TGACACTATACTAGAGGGAGCAGTATA 59.763 40.741 0.00 0.00 36.92 1.47
726 863 7.986704 ACACTATACTAGAGGGAGCAGTATAA 58.013 38.462 0.00 0.00 37.32 0.98
727 864 8.446394 ACACTATACTAGAGGGAGCAGTATAAA 58.554 37.037 0.00 0.00 37.32 1.40
728 865 9.298250 CACTATACTAGAGGGAGCAGTATAAAA 57.702 37.037 0.00 0.00 37.32 1.52
732 869 7.439108 ACTAGAGGGAGCAGTATAAAATTGT 57.561 36.000 0.00 0.00 0.00 2.71
733 870 8.548880 ACTAGAGGGAGCAGTATAAAATTGTA 57.451 34.615 0.00 0.00 0.00 2.41
734 871 8.643324 ACTAGAGGGAGCAGTATAAAATTGTAG 58.357 37.037 0.00 0.00 0.00 2.74
735 872 7.439108 AGAGGGAGCAGTATAAAATTGTAGT 57.561 36.000 0.00 0.00 0.00 2.73
736 873 8.548880 AGAGGGAGCAGTATAAAATTGTAGTA 57.451 34.615 0.00 0.00 0.00 1.82
737 874 8.422566 AGAGGGAGCAGTATAAAATTGTAGTAC 58.577 37.037 0.00 0.00 0.00 2.73
738 875 8.320338 AGGGAGCAGTATAAAATTGTAGTACT 57.680 34.615 0.00 0.00 0.00 2.73
739 876 9.430399 AGGGAGCAGTATAAAATTGTAGTACTA 57.570 33.333 0.00 0.00 0.00 1.82
760 897 9.620660 GTACTAAGTTGACACATTTATTTTGGG 57.379 33.333 0.00 0.00 0.00 4.12
761 898 8.472007 ACTAAGTTGACACATTTATTTTGGGA 57.528 30.769 0.00 0.00 0.00 4.37
762 899 8.357402 ACTAAGTTGACACATTTATTTTGGGAC 58.643 33.333 0.00 0.00 0.00 4.46
763 900 5.768317 AGTTGACACATTTATTTTGGGACG 58.232 37.500 0.00 0.00 0.00 4.79
764 901 4.775058 TGACACATTTATTTTGGGACGG 57.225 40.909 0.00 0.00 0.00 4.79
765 902 4.399219 TGACACATTTATTTTGGGACGGA 58.601 39.130 0.00 0.00 0.00 4.69
766 903 4.457603 TGACACATTTATTTTGGGACGGAG 59.542 41.667 0.00 0.00 0.00 4.63
842 979 4.878439 TCCGTATTGCACACCATATCTAC 58.122 43.478 0.00 0.00 0.00 2.59
843 980 4.342665 TCCGTATTGCACACCATATCTACA 59.657 41.667 0.00 0.00 0.00 2.74
979 1122 0.107459 GCCAATCTCAGTCCCTGTCC 60.107 60.000 0.00 0.00 32.61 4.02
1328 1475 4.719369 ACGACGTCAGCTTCCCGC 62.719 66.667 17.16 0.00 39.57 6.13
1388 1538 1.593787 CACGTCCCTGATGAGCAGT 59.406 57.895 0.00 0.00 43.33 4.40
1418 1568 0.173935 CCATGTTGTACTACGGCCGA 59.826 55.000 35.90 14.96 0.00 5.54
1620 1797 2.726351 CCGGAGAGGAAGCTGGACC 61.726 68.421 0.00 0.00 45.00 4.46
1698 1889 0.829990 TGGTGCAACTCAGACACAGA 59.170 50.000 2.04 0.00 36.00 3.41
1740 1960 1.542108 GCATGGGCTTCCTAGCTAGTG 60.542 57.143 19.31 10.88 46.90 2.74
1771 1997 9.677567 TTCAGTTCTTTTGTTGCTTAATATCAC 57.322 29.630 0.00 0.00 0.00 3.06
1922 2165 7.755582 TCGCATAATTCGGAGAACATATATG 57.244 36.000 11.29 11.29 45.90 1.78
1946 2191 5.535030 GGGAAGAACAAAAGTGTAGGATTGT 59.465 40.000 0.00 0.00 36.80 2.71
1985 2230 8.733458 TGTCTTCTTGAATTTTACATGATCCAG 58.267 33.333 0.00 0.00 0.00 3.86
2051 2307 3.746492 AGGATAAACGCAGTGACAAAGAC 59.254 43.478 0.00 0.00 45.00 3.01
2056 2312 4.370364 AACGCAGTGACAAAGACATTTT 57.630 36.364 0.00 0.00 45.00 1.82
2284 2540 7.978099 AATTTGCTAATGGAAGGTAGGAAAT 57.022 32.000 4.84 4.84 45.03 2.17
2375 2631 9.692749 ATGAAATTGCATCATTTGATAGATCAC 57.307 29.630 1.10 0.00 33.84 3.06
2379 2635 4.517832 TGCATCATTTGATAGATCACAGGC 59.482 41.667 0.00 0.00 36.36 4.85
2401 2657 8.730680 CAGGCATTAAGTTTAGTTTATGACACT 58.269 33.333 5.29 0.00 0.00 3.55
2437 2693 1.433121 ATCCTCCTCAATGAGCCTCC 58.567 55.000 4.40 0.00 0.00 4.30
2470 2726 4.350368 TTCTCCATAGTTGAGTTGTGCA 57.650 40.909 0.00 0.00 0.00 4.57
2583 3817 1.699054 TTGCTCATCCCCTCATCCCG 61.699 60.000 0.00 0.00 0.00 5.14
2617 3852 3.449377 TCCTGTCATTCAATACACCGCTA 59.551 43.478 0.00 0.00 0.00 4.26
2620 3855 3.615056 TGTCATTCAATACACCGCTAACG 59.385 43.478 0.00 0.00 39.67 3.18
2651 3886 2.563179 TGCTCCTAGTCTGTCAAGAACC 59.437 50.000 0.00 0.00 33.05 3.62
2658 3893 2.896685 AGTCTGTCAAGAACCTCTCCAG 59.103 50.000 0.00 0.00 33.05 3.86
2659 3894 2.028567 GTCTGTCAAGAACCTCTCCAGG 60.029 54.545 0.00 0.00 46.87 4.45
2660 3895 2.158310 TCTGTCAAGAACCTCTCCAGGA 60.158 50.000 0.00 0.00 43.65 3.86
2661 3896 2.836981 CTGTCAAGAACCTCTCCAGGAT 59.163 50.000 0.00 0.00 43.65 3.24
2662 3897 2.834549 TGTCAAGAACCTCTCCAGGATC 59.165 50.000 0.00 0.00 43.65 3.36
2663 3898 2.103373 TCAAGAACCTCTCCAGGATCG 58.897 52.381 0.00 0.00 44.68 3.69
2679 3918 5.011125 CCAGGATCGATATGTGGTACTTCTT 59.989 44.000 0.00 0.00 0.00 2.52
2717 3956 5.109662 GAGCATCCATGAGACATGATTTG 57.890 43.478 12.46 8.15 0.00 2.32
2741 3980 4.132336 TCATTGCATCCAGAGTAATCAGC 58.868 43.478 0.00 0.00 0.00 4.26
2761 4000 3.461946 CGGAGCAACTGTTGAAAGATC 57.538 47.619 23.81 11.75 0.00 2.75
2805 4044 0.398318 GCCACTCCATATCCAGGGTC 59.602 60.000 0.00 0.00 0.00 4.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.910746 AATCTTACGATATGCATGACGC 57.089 40.909 21.10 4.18 42.89 5.19
11 12 6.051074 TCATGCATGACTGAAATCTTACGAT 58.949 36.000 25.42 0.00 0.00 3.73
193 196 7.499563 TCGCCTGCAAGTGGTAAATATTTTATA 59.500 33.333 5.91 0.00 0.00 0.98
200 203 2.772077 TCGCCTGCAAGTGGTAAATA 57.228 45.000 0.00 0.00 0.00 1.40
202 205 1.904287 AATCGCCTGCAAGTGGTAAA 58.096 45.000 0.00 0.00 0.00 2.01
406 413 8.915871 ATGAAATTAATTGCACTATCACACAC 57.084 30.769 11.20 0.00 0.00 3.82
436 443 3.390183 CTGGCCCTGCATGCGTAGA 62.390 63.158 14.09 0.00 0.00 2.59
453 462 3.452264 TGTCATAGCACTACCATTGAGCT 59.548 43.478 0.00 0.00 39.22 4.09
468 477 2.417933 GCTTCTGGTGTTGCTGTCATAG 59.582 50.000 0.00 0.00 0.00 2.23
495 508 0.947244 CATCCTTGCTCCGGTTATGC 59.053 55.000 0.00 2.82 0.00 3.14
502 515 2.898729 ACACTATCATCCTTGCTCCG 57.101 50.000 0.00 0.00 0.00 4.63
511 524 5.582269 TGCTTGCTCTGTTTACACTATCATC 59.418 40.000 0.00 0.00 0.00 2.92
513 526 4.893608 TGCTTGCTCTGTTTACACTATCA 58.106 39.130 0.00 0.00 0.00 2.15
514 527 5.179368 TGTTGCTTGCTCTGTTTACACTATC 59.821 40.000 0.00 0.00 0.00 2.08
515 528 5.063204 TGTTGCTTGCTCTGTTTACACTAT 58.937 37.500 0.00 0.00 0.00 2.12
517 530 3.278574 TGTTGCTTGCTCTGTTTACACT 58.721 40.909 0.00 0.00 0.00 3.55
518 531 3.691049 TGTTGCTTGCTCTGTTTACAC 57.309 42.857 0.00 0.00 0.00 2.90
520 533 5.853282 CAGTTATGTTGCTTGCTCTGTTTAC 59.147 40.000 0.00 0.00 0.00 2.01
522 535 4.261741 CCAGTTATGTTGCTTGCTCTGTTT 60.262 41.667 0.00 0.00 0.00 2.83
523 536 3.254166 CCAGTTATGTTGCTTGCTCTGTT 59.746 43.478 0.00 0.00 0.00 3.16
526 539 3.244700 ACTCCAGTTATGTTGCTTGCTCT 60.245 43.478 0.00 0.00 0.00 4.09
528 541 3.146104 ACTCCAGTTATGTTGCTTGCT 57.854 42.857 0.00 0.00 0.00 3.91
529 542 4.695455 TCTTACTCCAGTTATGTTGCTTGC 59.305 41.667 0.00 0.00 0.00 4.01
530 543 6.801539 TTCTTACTCCAGTTATGTTGCTTG 57.198 37.500 0.00 0.00 0.00 4.01
533 546 5.810587 TCGATTCTTACTCCAGTTATGTTGC 59.189 40.000 0.00 0.00 0.00 4.17
534 547 7.706607 TGATCGATTCTTACTCCAGTTATGTTG 59.293 37.037 0.00 0.00 0.00 3.33
535 548 7.782049 TGATCGATTCTTACTCCAGTTATGTT 58.218 34.615 0.00 0.00 0.00 2.71
536 549 7.068839 ACTGATCGATTCTTACTCCAGTTATGT 59.931 37.037 0.00 0.00 30.42 2.29
537 550 7.380870 CACTGATCGATTCTTACTCCAGTTATG 59.619 40.741 8.83 0.00 32.06 1.90
538 551 7.068839 ACACTGATCGATTCTTACTCCAGTTAT 59.931 37.037 8.83 0.34 32.06 1.89
539 552 6.377429 ACACTGATCGATTCTTACTCCAGTTA 59.623 38.462 8.83 0.00 32.06 2.24
540 553 5.186021 ACACTGATCGATTCTTACTCCAGTT 59.814 40.000 8.83 1.11 32.06 3.16
541 554 4.707448 ACACTGATCGATTCTTACTCCAGT 59.293 41.667 0.00 2.70 34.38 4.00
542 555 5.039984 CACACTGATCGATTCTTACTCCAG 58.960 45.833 0.00 2.01 0.00 3.86
543 556 4.142160 CCACACTGATCGATTCTTACTCCA 60.142 45.833 0.00 0.00 0.00 3.86
544 557 4.142138 ACCACACTGATCGATTCTTACTCC 60.142 45.833 0.00 0.00 0.00 3.85
545 558 4.800993 CACCACACTGATCGATTCTTACTC 59.199 45.833 0.00 0.00 0.00 2.59
546 559 4.462834 TCACCACACTGATCGATTCTTACT 59.537 41.667 0.00 0.00 0.00 2.24
565 696 4.737855 ATACTATACCGGCATCATCACC 57.262 45.455 0.00 0.00 0.00 4.02
635 772 2.557490 GACGGAGGGAGTACATGGATAC 59.443 54.545 0.00 0.00 0.00 2.24
645 782 2.904434 ACTTATTTGTGACGGAGGGAGT 59.096 45.455 0.00 0.00 0.00 3.85
646 783 3.611766 ACTTATTTGTGACGGAGGGAG 57.388 47.619 0.00 0.00 0.00 4.30
647 784 4.529377 AGTAACTTATTTGTGACGGAGGGA 59.471 41.667 0.00 0.00 0.00 4.20
648 785 4.828829 AGTAACTTATTTGTGACGGAGGG 58.171 43.478 0.00 0.00 0.00 4.30
649 786 4.868734 GGAGTAACTTATTTGTGACGGAGG 59.131 45.833 0.00 0.00 0.00 4.30
650 787 4.868734 GGGAGTAACTTATTTGTGACGGAG 59.131 45.833 0.00 0.00 0.00 4.63
651 788 4.529377 AGGGAGTAACTTATTTGTGACGGA 59.471 41.667 0.00 0.00 0.00 4.69
652 789 4.828829 AGGGAGTAACTTATTTGTGACGG 58.171 43.478 0.00 0.00 0.00 4.79
653 790 5.577164 CAGAGGGAGTAACTTATTTGTGACG 59.423 44.000 0.00 0.00 0.00 4.35
654 791 6.465084 ACAGAGGGAGTAACTTATTTGTGAC 58.535 40.000 0.00 0.00 0.00 3.67
655 792 6.295688 GGACAGAGGGAGTAACTTATTTGTGA 60.296 42.308 0.00 0.00 0.00 3.58
656 793 5.875359 GGACAGAGGGAGTAACTTATTTGTG 59.125 44.000 0.00 0.00 0.00 3.33
657 794 5.045797 GGGACAGAGGGAGTAACTTATTTGT 60.046 44.000 0.00 0.00 0.00 2.83
658 795 5.189934 AGGGACAGAGGGAGTAACTTATTTG 59.810 44.000 0.00 0.00 0.00 2.32
659 796 5.351405 AGGGACAGAGGGAGTAACTTATTT 58.649 41.667 0.00 0.00 0.00 1.40
660 797 4.961585 AGGGACAGAGGGAGTAACTTATT 58.038 43.478 0.00 0.00 0.00 1.40
661 798 4.628661 AGGGACAGAGGGAGTAACTTAT 57.371 45.455 0.00 0.00 0.00 1.73
662 799 5.541258 TTAGGGACAGAGGGAGTAACTTA 57.459 43.478 0.00 0.00 0.00 2.24
663 800 4.415224 TTAGGGACAGAGGGAGTAACTT 57.585 45.455 0.00 0.00 0.00 2.66
664 801 4.628661 ATTAGGGACAGAGGGAGTAACT 57.371 45.455 0.00 0.00 0.00 2.24
665 802 8.488308 TTTATATTAGGGACAGAGGGAGTAAC 57.512 38.462 0.00 0.00 0.00 2.50
666 803 9.510062 TTTTTATATTAGGGACAGAGGGAGTAA 57.490 33.333 0.00 0.00 0.00 2.24
667 804 8.931568 GTTTTTATATTAGGGACAGAGGGAGTA 58.068 37.037 0.00 0.00 0.00 2.59
668 805 7.418712 CGTTTTTATATTAGGGACAGAGGGAGT 60.419 40.741 0.00 0.00 0.00 3.85
669 806 6.929606 CGTTTTTATATTAGGGACAGAGGGAG 59.070 42.308 0.00 0.00 0.00 4.30
670 807 6.384886 ACGTTTTTATATTAGGGACAGAGGGA 59.615 38.462 0.00 0.00 0.00 4.20
671 808 6.589135 ACGTTTTTATATTAGGGACAGAGGG 58.411 40.000 0.00 0.00 0.00 4.30
672 809 8.502105 AAACGTTTTTATATTAGGGACAGAGG 57.498 34.615 7.96 0.00 0.00 3.69
676 813 9.896263 GTCAAAAACGTTTTTATATTAGGGACA 57.104 29.630 32.12 6.51 38.23 4.02
677 814 9.896263 TGTCAAAAACGTTTTTATATTAGGGAC 57.104 29.630 32.12 28.62 38.23 4.46
678 815 9.896263 GTGTCAAAAACGTTTTTATATTAGGGA 57.104 29.630 32.12 21.46 38.23 4.20
679 816 9.902196 AGTGTCAAAAACGTTTTTATATTAGGG 57.098 29.630 32.12 19.85 38.23 3.53
689 826 8.985805 CCTCTAGTATAGTGTCAAAAACGTTTT 58.014 33.333 20.26 20.26 40.38 2.43
690 827 7.601508 CCCTCTAGTATAGTGTCAAAAACGTTT 59.398 37.037 7.96 7.96 40.38 3.60
691 828 7.039504 TCCCTCTAGTATAGTGTCAAAAACGTT 60.040 37.037 0.00 0.00 40.38 3.99
692 829 6.435277 TCCCTCTAGTATAGTGTCAAAAACGT 59.565 38.462 0.00 0.00 40.38 3.99
693 830 6.860080 TCCCTCTAGTATAGTGTCAAAAACG 58.140 40.000 0.00 0.00 40.38 3.60
694 831 6.757478 GCTCCCTCTAGTATAGTGTCAAAAAC 59.243 42.308 0.00 0.00 40.38 2.43
695 832 6.439375 TGCTCCCTCTAGTATAGTGTCAAAAA 59.561 38.462 0.00 0.00 40.38 1.94
696 833 5.955959 TGCTCCCTCTAGTATAGTGTCAAAA 59.044 40.000 0.00 0.00 40.38 2.44
697 834 5.516044 TGCTCCCTCTAGTATAGTGTCAAA 58.484 41.667 0.00 0.00 40.38 2.69
698 835 5.125367 TGCTCCCTCTAGTATAGTGTCAA 57.875 43.478 0.00 0.00 40.38 3.18
699 836 4.166337 ACTGCTCCCTCTAGTATAGTGTCA 59.834 45.833 0.00 0.00 40.38 3.58
700 837 4.721132 ACTGCTCCCTCTAGTATAGTGTC 58.279 47.826 0.00 0.00 40.38 3.67
701 838 4.799715 ACTGCTCCCTCTAGTATAGTGT 57.200 45.455 0.00 0.00 40.38 3.55
702 839 8.865420 TTTATACTGCTCCCTCTAGTATAGTG 57.135 38.462 0.00 0.00 39.61 2.74
706 843 9.160412 ACAATTTTATACTGCTCCCTCTAGTAT 57.840 33.333 0.00 0.00 39.96 2.12
707 844 8.548880 ACAATTTTATACTGCTCCCTCTAGTA 57.451 34.615 0.00 0.00 0.00 1.82
708 845 7.439108 ACAATTTTATACTGCTCCCTCTAGT 57.561 36.000 0.00 0.00 0.00 2.57
709 846 8.643324 ACTACAATTTTATACTGCTCCCTCTAG 58.357 37.037 0.00 0.00 0.00 2.43
710 847 8.548880 ACTACAATTTTATACTGCTCCCTCTA 57.451 34.615 0.00 0.00 0.00 2.43
711 848 7.439108 ACTACAATTTTATACTGCTCCCTCT 57.561 36.000 0.00 0.00 0.00 3.69
712 849 8.422566 AGTACTACAATTTTATACTGCTCCCTC 58.577 37.037 0.00 0.00 0.00 4.30
713 850 8.320338 AGTACTACAATTTTATACTGCTCCCT 57.680 34.615 0.00 0.00 0.00 4.20
734 871 9.620660 CCCAAAATAAATGTGTCAACTTAGTAC 57.379 33.333 0.00 0.00 0.00 2.73
735 872 9.575868 TCCCAAAATAAATGTGTCAACTTAGTA 57.424 29.630 0.00 0.00 0.00 1.82
736 873 8.357402 GTCCCAAAATAAATGTGTCAACTTAGT 58.643 33.333 0.00 0.00 0.00 2.24
737 874 7.537306 CGTCCCAAAATAAATGTGTCAACTTAG 59.463 37.037 0.00 0.00 0.00 2.18
738 875 7.364200 CGTCCCAAAATAAATGTGTCAACTTA 58.636 34.615 0.00 0.00 0.00 2.24
739 876 6.212955 CGTCCCAAAATAAATGTGTCAACTT 58.787 36.000 0.00 0.00 0.00 2.66
740 877 5.278758 CCGTCCCAAAATAAATGTGTCAACT 60.279 40.000 0.00 0.00 0.00 3.16
741 878 4.920927 CCGTCCCAAAATAAATGTGTCAAC 59.079 41.667 0.00 0.00 0.00 3.18
742 879 4.827835 TCCGTCCCAAAATAAATGTGTCAA 59.172 37.500 0.00 0.00 0.00 3.18
743 880 4.399219 TCCGTCCCAAAATAAATGTGTCA 58.601 39.130 0.00 0.00 0.00 3.58
744 881 4.457949 ACTCCGTCCCAAAATAAATGTGTC 59.542 41.667 0.00 0.00 0.00 3.67
745 882 4.403734 ACTCCGTCCCAAAATAAATGTGT 58.596 39.130 0.00 0.00 0.00 3.72
746 883 6.150474 ACTTACTCCGTCCCAAAATAAATGTG 59.850 38.462 0.00 0.00 0.00 3.21
747 884 6.243148 ACTTACTCCGTCCCAAAATAAATGT 58.757 36.000 0.00 0.00 0.00 2.71
748 885 6.753107 ACTTACTCCGTCCCAAAATAAATG 57.247 37.500 0.00 0.00 0.00 2.32
753 890 9.470399 AAAAATATACTTACTCCGTCCCAAAAT 57.530 29.630 0.00 0.00 0.00 1.82
754 891 8.866970 AAAAATATACTTACTCCGTCCCAAAA 57.133 30.769 0.00 0.00 0.00 2.44
783 920 3.592070 GCCTTCGGCCTTTTCTCC 58.408 61.111 0.00 0.00 44.06 3.71
842 979 0.829333 ATGACTCTGCCCTAGCTGTG 59.171 55.000 0.00 0.00 40.80 3.66
843 980 0.829333 CATGACTCTGCCCTAGCTGT 59.171 55.000 0.00 0.00 40.80 4.40
979 1122 3.717294 CAGAACCCGGGGGACAGG 61.717 72.222 27.92 4.98 46.42 4.00
989 1132 4.462834 GGGGCTAATATATTTGCAGAACCC 59.537 45.833 26.03 22.72 39.67 4.11
991 1134 4.156008 CGGGGGCTAATATATTTGCAGAAC 59.844 45.833 26.03 15.74 39.67 3.01
992 1135 4.331968 CGGGGGCTAATATATTTGCAGAA 58.668 43.478 26.03 0.00 39.67 3.02
1202 1349 2.117156 GCACTCGTAGTAGGGCCGA 61.117 63.158 0.00 0.00 40.18 5.54
1328 1475 1.534595 GCCAAGTTGCACTCTGTGTTG 60.535 52.381 0.00 0.00 35.75 3.33
1447 1603 3.075005 GGCTACCAGGGCTCACGA 61.075 66.667 0.00 0.00 0.00 4.35
1698 1889 6.223120 TGCATGTATATAGATGAGTGCGTTT 58.777 36.000 20.92 0.00 34.28 3.60
1740 1960 8.905103 TTAAGCAACAAAAGAACTGAAGTAAC 57.095 30.769 0.00 0.00 0.00 2.50
1771 1997 6.128499 GCAGCAGAAGATGAGAATAGCAATAG 60.128 42.308 0.00 0.00 31.30 1.73
1922 2165 5.535030 ACAATCCTACACTTTTGTTCTTCCC 59.465 40.000 0.00 0.00 37.15 3.97
2051 2307 8.662781 TTGCAGTACTATTAGCTAGGAAAATG 57.337 34.615 0.00 0.00 0.00 2.32
2056 2312 7.597288 TCATTTGCAGTACTATTAGCTAGGA 57.403 36.000 0.00 0.00 0.00 2.94
2284 2540 8.418597 AGAAGTAACTTGTTACACTCTCCATA 57.581 34.615 21.10 0.00 0.00 2.74
2359 2615 8.929260 TTAATGCCTGTGATCTATCAAATGAT 57.071 30.769 1.01 1.01 38.75 2.45
2375 2631 8.730680 AGTGTCATAAACTAAACTTAATGCCTG 58.269 33.333 0.00 0.00 0.00 4.85
2401 2657 4.344104 GAGGATTGAGGTTGGAAATGGAA 58.656 43.478 0.00 0.00 0.00 3.53
2437 2693 3.829601 ACTATGGAGAAAGGGATAGCGAG 59.170 47.826 0.00 0.00 0.00 5.03
2493 2749 5.440234 TTTGCCGCTAACACAAAGATAAA 57.560 34.783 0.00 0.00 0.00 1.40
2496 2752 3.758554 AGATTTGCCGCTAACACAAAGAT 59.241 39.130 0.00 0.00 36.78 2.40
2620 3855 2.124736 TAGGAGCACCGCAATGGC 60.125 61.111 0.00 0.00 43.94 4.40
2651 3886 3.161067 ACCACATATCGATCCTGGAGAG 58.839 50.000 18.28 0.00 0.00 3.20
2658 3893 7.216973 ACTAAGAAGTACCACATATCGATCC 57.783 40.000 0.00 0.00 32.84 3.36
2679 3918 9.778741 CATGGATGCTCCTTTAAGTATTAACTA 57.221 33.333 4.21 0.00 35.78 2.24
2699 3938 4.788679 TGAGCAAATCATGTCTCATGGAT 58.211 39.130 9.39 1.04 37.31 3.41
2717 3956 4.132336 TGATTACTCTGGATGCAATGAGC 58.868 43.478 3.74 0.00 45.96 4.26
2727 3966 0.747255 GCTCCGCTGATTACTCTGGA 59.253 55.000 0.00 0.00 0.00 3.86
2741 3980 3.070018 AGATCTTTCAACAGTTGCTCCG 58.930 45.455 8.58 0.00 0.00 4.63
2755 3994 4.466370 TCACCGTCTTGATGGTAGATCTTT 59.534 41.667 13.49 0.00 36.50 2.52
2761 4000 1.469251 CGGTCACCGTCTTGATGGTAG 60.469 57.143 8.54 8.94 42.73 3.18


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

AutoCloner maintained by Alex Coulton.