Multiple sequence alignment - TraesCS4B01G136800

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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 TraesCS4B01G136800 chr4B 100.000 2767 0 0 1 2767 180554430 180551664 0.000000e+00 5110
1 TraesCS4B01G136800 chr4B 98.486 1915 29 0 853 2767 665272020 665273934 0.000000e+00 3376
2 TraesCS4B01G136800 chr4B 98.876 89 1 0 473 561 560525084 560525172 2.850000e-35 159
3 TraesCS4B01G136800 chr4B 98.876 89 1 0 473 561 640085411 640085499 2.850000e-35 159
4 TraesCS4B01G136800 chr2D 98.016 1915 36 2 853 2767 164267614 164269526 0.000000e+00 3325
5 TraesCS4B01G136800 chr2D 96.919 1915 58 1 853 2767 632246364 632244451 0.000000e+00 3208
6 TraesCS4B01G136800 chr7D 97.125 1913 54 1 855 2767 518101138 518099227 0.000000e+00 3227
7 TraesCS4B01G136800 chr7D 97.471 1621 40 1 1147 2767 426459152 426457533 0.000000e+00 2765
8 TraesCS4B01G136800 chr3D 96.823 1920 55 2 853 2767 363055468 363057386 0.000000e+00 3203
9 TraesCS4B01G136800 chr3D 96.240 1915 61 3 853 2767 605575431 605573528 0.000000e+00 3127
10 TraesCS4B01G136800 chr1B 94.990 1916 95 1 853 2767 534195978 534194063 0.000000e+00 3005
11 TraesCS4B01G136800 chr1B 98.876 89 1 0 473 561 148289514 148289602 2.850000e-35 159
12 TraesCS4B01G136800 chr1B 98.876 89 1 0 473 561 544910807 544910895 2.850000e-35 159
13 TraesCS4B01G136800 chr3A 92.901 1789 119 8 981 2767 527582759 527584541 0.000000e+00 2593
14 TraesCS4B01G136800 chr3A 94.074 135 8 0 853 987 527575878 527576012 3.610000e-49 206
15 TraesCS4B01G136800 chr4D 92.729 839 31 19 2 838 118324283 118323473 0.000000e+00 1184
16 TraesCS4B01G136800 chr4D 94.898 98 5 0 467 564 449455709 449455612 1.330000e-33 154
17 TraesCS4B01G136800 chr4A 98.093 472 6 2 8 477 455277875 455278345 0.000000e+00 819
18 TraesCS4B01G136800 chr4A 94.306 281 9 3 558 838 455278343 455278616 9.160000e-115 424
19 TraesCS4B01G136800 chr4A 98.876 89 1 0 473 561 650352920 650353008 2.850000e-35 159
20 TraesCS4B01G136800 chr5B 98.889 90 1 0 473 562 25131097 25131186 7.930000e-36 161
21 TraesCS4B01G136800 chr7B 95.098 102 3 2 465 566 203031449 203031548 2.850000e-35 159
22 TraesCS4B01G136800 chr5A 96.809 94 3 0 468 561 630026367 630026274 1.030000e-34 158


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 TraesCS4B01G136800 chr4B 180551664 180554430 2766 True 5110.0 5110 100.0000 1 2767 1 chr4B.!!$R1 2766
1 TraesCS4B01G136800 chr4B 665272020 665273934 1914 False 3376.0 3376 98.4860 853 2767 1 chr4B.!!$F3 1914
2 TraesCS4B01G136800 chr2D 164267614 164269526 1912 False 3325.0 3325 98.0160 853 2767 1 chr2D.!!$F1 1914
3 TraesCS4B01G136800 chr2D 632244451 632246364 1913 True 3208.0 3208 96.9190 853 2767 1 chr2D.!!$R1 1914
4 TraesCS4B01G136800 chr7D 518099227 518101138 1911 True 3227.0 3227 97.1250 855 2767 1 chr7D.!!$R2 1912
5 TraesCS4B01G136800 chr7D 426457533 426459152 1619 True 2765.0 2765 97.4710 1147 2767 1 chr7D.!!$R1 1620
6 TraesCS4B01G136800 chr3D 363055468 363057386 1918 False 3203.0 3203 96.8230 853 2767 1 chr3D.!!$F1 1914
7 TraesCS4B01G136800 chr3D 605573528 605575431 1903 True 3127.0 3127 96.2400 853 2767 1 chr3D.!!$R1 1914
8 TraesCS4B01G136800 chr1B 534194063 534195978 1915 True 3005.0 3005 94.9900 853 2767 1 chr1B.!!$R1 1914
9 TraesCS4B01G136800 chr3A 527582759 527584541 1782 False 2593.0 2593 92.9010 981 2767 1 chr3A.!!$F2 1786
10 TraesCS4B01G136800 chr4D 118323473 118324283 810 True 1184.0 1184 92.7290 2 838 1 chr4D.!!$R1 836
11 TraesCS4B01G136800 chr4A 455277875 455278616 741 False 621.5 819 96.1995 8 838 2 chr4A.!!$F2 830

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
720 725 0.17902 CCAGACAGGGCTGTTGTGAA 60.179 55.0 0.79 0.0 45.05 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2310 2357 0.517316 GTGGTCGTTGAAGGTGATGC 59.483 55.0 0.0 0.0 0.0 3.91 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
112 114 3.125829 TCATGATCGTGAAAGCTTTCTGC 59.874 43.478 33.03 24.96 43.29 4.26
295 299 4.651778 TCAGTATGAGTTGTCTTTTGGGG 58.348 43.478 0.00 0.00 42.56 4.96
366 370 3.386932 TTATGCTTCCTGCCCAAGAAT 57.613 42.857 0.00 0.00 42.00 2.40
429 434 5.574055 TGCATAACGACCTACTAGAAAAACG 59.426 40.000 0.00 0.00 0.00 3.60
487 492 2.027469 ACAAAATGGTACTCCCTCCGTC 60.027 50.000 0.00 0.00 0.00 4.79
488 493 2.236395 CAAAATGGTACTCCCTCCGTCT 59.764 50.000 0.00 0.00 0.00 4.18
489 494 1.777941 AATGGTACTCCCTCCGTCTC 58.222 55.000 0.00 0.00 0.00 3.36
490 495 0.629596 ATGGTACTCCCTCCGTCTCA 59.370 55.000 0.00 0.00 0.00 3.27
491 496 0.629596 TGGTACTCCCTCCGTCTCAT 59.370 55.000 0.00 0.00 0.00 2.90
494 499 3.117246 TGGTACTCCCTCCGTCTCATAAT 60.117 47.826 0.00 0.00 0.00 1.28
495 500 3.256136 GGTACTCCCTCCGTCTCATAATG 59.744 52.174 0.00 0.00 0.00 1.90
498 503 4.543689 ACTCCCTCCGTCTCATAATGTAA 58.456 43.478 0.00 0.00 0.00 2.41
499 504 4.585162 ACTCCCTCCGTCTCATAATGTAAG 59.415 45.833 0.00 0.00 0.00 2.34
500 505 4.800023 TCCCTCCGTCTCATAATGTAAGA 58.200 43.478 0.00 0.00 0.00 2.10
534 539 4.690122 ACTACACTAGTGTCAAAAAGCGT 58.310 39.130 31.11 13.23 43.74 5.07
535 540 4.743644 ACTACACTAGTGTCAAAAAGCGTC 59.256 41.667 31.11 0.00 43.74 5.19
543 548 9.865321 ACTAGTGTCAAAAAGCGTCTTATATTA 57.135 29.630 0.00 0.00 0.00 0.98
546 551 8.612619 AGTGTCAAAAAGCGTCTTATATTATGG 58.387 33.333 0.00 0.00 0.00 2.74
547 552 7.855904 GTGTCAAAAAGCGTCTTATATTATGGG 59.144 37.037 0.00 0.00 0.00 4.00
554 559 4.677250 GCGTCTTATATTATGGGACGGAGG 60.677 50.000 22.36 6.98 46.26 4.30
555 560 4.142227 CGTCTTATATTATGGGACGGAGGG 60.142 50.000 17.59 0.46 43.69 4.30
556 561 5.021458 GTCTTATATTATGGGACGGAGGGA 58.979 45.833 0.00 0.00 0.00 4.20
587 592 1.068541 GCCCCAATTCAAAGACGACAC 60.069 52.381 0.00 0.00 0.00 3.67
632 637 7.728847 ATTTGGAAAGAAAAAGTAACCATGC 57.271 32.000 0.00 0.00 0.00 4.06
644 649 1.340088 AACCATGCATGACCAAGCAA 58.660 45.000 28.31 0.00 44.88 3.91
646 651 0.459585 CCATGCATGACCAAGCAAGC 60.460 55.000 28.31 0.00 44.88 4.01
694 699 9.190317 GAGAGTGTATTTCCCCAAAAGAAATAT 57.810 33.333 8.67 0.00 44.05 1.28
695 700 9.190317 AGAGTGTATTTCCCCAAAAGAAATATC 57.810 33.333 8.67 4.17 44.05 1.63
696 701 9.190317 GAGTGTATTTCCCCAAAAGAAATATCT 57.810 33.333 8.67 9.80 44.05 1.98
697 702 9.190317 AGTGTATTTCCCCAAAAGAAATATCTC 57.810 33.333 8.67 5.26 44.05 2.75
698 703 8.966868 GTGTATTTCCCCAAAAGAAATATCTCA 58.033 33.333 8.67 1.77 44.05 3.27
699 704 9.189156 TGTATTTCCCCAAAAGAAATATCTCAG 57.811 33.333 8.67 0.00 44.05 3.35
700 705 7.666063 ATTTCCCCAAAAGAAATATCTCAGG 57.334 36.000 0.00 0.00 41.10 3.86
701 706 4.536765 TCCCCAAAAGAAATATCTCAGGC 58.463 43.478 0.00 0.00 33.77 4.85
702 707 3.638627 CCCCAAAAGAAATATCTCAGGCC 59.361 47.826 0.00 0.00 33.77 5.19
703 708 4.280819 CCCAAAAGAAATATCTCAGGCCA 58.719 43.478 5.01 0.00 33.77 5.36
704 709 4.340381 CCCAAAAGAAATATCTCAGGCCAG 59.660 45.833 5.01 0.00 33.77 4.85
705 710 5.195940 CCAAAAGAAATATCTCAGGCCAGA 58.804 41.667 5.01 0.00 33.77 3.86
706 711 5.067023 CCAAAAGAAATATCTCAGGCCAGAC 59.933 44.000 5.01 0.00 33.77 3.51
707 712 5.441718 AAAGAAATATCTCAGGCCAGACA 57.558 39.130 5.01 0.00 33.77 3.41
708 713 4.686191 AGAAATATCTCAGGCCAGACAG 57.314 45.455 5.01 0.00 0.00 3.51
709 714 3.390639 AGAAATATCTCAGGCCAGACAGG 59.609 47.826 5.01 0.00 41.84 4.00
710 715 1.727062 ATATCTCAGGCCAGACAGGG 58.273 55.000 5.01 0.00 38.09 4.45
718 723 4.069869 CCAGACAGGGCTGTTGTG 57.930 61.111 0.79 0.00 45.05 3.33
719 724 1.451504 CCAGACAGGGCTGTTGTGA 59.548 57.895 0.79 0.00 45.05 3.58
720 725 0.179020 CCAGACAGGGCTGTTGTGAA 60.179 55.000 0.79 0.00 45.05 3.18
721 726 0.947244 CAGACAGGGCTGTTGTGAAC 59.053 55.000 0.00 0.00 45.05 3.18
722 727 0.546122 AGACAGGGCTGTTGTGAACA 59.454 50.000 0.00 0.00 45.05 3.18
742 747 3.938963 ACAGCCAATGTTATCAGTAACCG 59.061 43.478 0.00 0.00 39.96 4.44
743 748 3.938963 CAGCCAATGTTATCAGTAACCGT 59.061 43.478 0.00 0.00 39.55 4.83
744 749 4.394920 CAGCCAATGTTATCAGTAACCGTT 59.605 41.667 0.00 0.00 39.55 4.44
745 750 4.394920 AGCCAATGTTATCAGTAACCGTTG 59.605 41.667 0.00 0.00 39.55 4.10
746 751 4.438200 GCCAATGTTATCAGTAACCGTTGG 60.438 45.833 18.39 18.39 45.96 3.77
747 752 4.698304 CCAATGTTATCAGTAACCGTTGGT 59.302 41.667 16.36 0.00 42.80 3.67
748 753 5.391523 CCAATGTTATCAGTAACCGTTGGTG 60.392 44.000 16.36 0.00 42.80 4.17
749 754 4.603989 TGTTATCAGTAACCGTTGGTGA 57.396 40.909 0.00 0.00 39.55 4.02
750 755 4.958509 TGTTATCAGTAACCGTTGGTGAA 58.041 39.130 0.00 0.00 39.55 3.18
751 756 5.366460 TGTTATCAGTAACCGTTGGTGAAA 58.634 37.500 0.00 0.00 39.55 2.69
752 757 5.467399 TGTTATCAGTAACCGTTGGTGAAAG 59.533 40.000 0.00 0.00 39.55 2.62
753 758 3.547054 TCAGTAACCGTTGGTGAAAGT 57.453 42.857 0.00 0.00 35.34 2.66
754 759 4.669206 TCAGTAACCGTTGGTGAAAGTA 57.331 40.909 0.00 0.00 35.34 2.24
755 760 5.217978 TCAGTAACCGTTGGTGAAAGTAT 57.782 39.130 0.00 0.00 35.34 2.12
756 761 5.613329 TCAGTAACCGTTGGTGAAAGTATT 58.387 37.500 0.00 0.00 35.34 1.89
757 762 5.467399 TCAGTAACCGTTGGTGAAAGTATTG 59.533 40.000 0.00 0.00 35.34 1.90
758 763 5.237779 CAGTAACCGTTGGTGAAAGTATTGT 59.762 40.000 0.00 0.00 35.34 2.71
759 764 4.561735 AACCGTTGGTGAAAGTATTGTG 57.438 40.909 0.00 0.00 35.34 3.33
760 765 2.292292 ACCGTTGGTGAAAGTATTGTGC 59.708 45.455 0.00 0.00 32.98 4.57
761 766 2.552315 CCGTTGGTGAAAGTATTGTGCT 59.448 45.455 0.00 0.00 0.00 4.40
762 767 3.749088 CCGTTGGTGAAAGTATTGTGCTA 59.251 43.478 0.00 0.00 0.00 3.49
763 768 4.394920 CCGTTGGTGAAAGTATTGTGCTAT 59.605 41.667 0.00 0.00 0.00 2.97
764 769 5.583061 CCGTTGGTGAAAGTATTGTGCTATA 59.417 40.000 0.00 0.00 0.00 1.31
765 770 6.456449 CCGTTGGTGAAAGTATTGTGCTATAC 60.456 42.308 0.00 0.00 0.00 1.47
766 771 6.312918 CGTTGGTGAAAGTATTGTGCTATACT 59.687 38.462 1.51 1.51 41.84 2.12
767 772 7.464178 CGTTGGTGAAAGTATTGTGCTATACTC 60.464 40.741 6.73 0.00 39.75 2.59
768 773 6.941857 TGGTGAAAGTATTGTGCTATACTCA 58.058 36.000 6.73 1.12 39.75 3.41
769 774 6.816640 TGGTGAAAGTATTGTGCTATACTCAC 59.183 38.462 12.78 12.78 39.75 3.51
770 775 7.042335 GGTGAAAGTATTGTGCTATACTCACT 58.958 38.462 16.82 5.30 39.75 3.41
771 776 7.010552 GGTGAAAGTATTGTGCTATACTCACTG 59.989 40.741 16.82 0.00 39.75 3.66
772 777 6.535150 TGAAAGTATTGTGCTATACTCACTGC 59.465 38.462 6.73 0.00 39.75 4.40
773 778 5.860941 AGTATTGTGCTATACTCACTGCT 57.139 39.130 1.51 0.00 36.81 4.24
774 779 6.227298 AGTATTGTGCTATACTCACTGCTT 57.773 37.500 1.51 0.00 36.81 3.91
775 780 7.348080 AGTATTGTGCTATACTCACTGCTTA 57.652 36.000 1.51 0.00 36.81 3.09
776 781 7.782049 AGTATTGTGCTATACTCACTGCTTAA 58.218 34.615 1.51 0.00 36.81 1.85
777 782 7.923344 AGTATTGTGCTATACTCACTGCTTAAG 59.077 37.037 0.00 0.00 36.81 1.85
778 783 5.661056 TGTGCTATACTCACTGCTTAAGT 57.339 39.130 4.02 0.00 40.93 2.24
779 784 6.037786 TGTGCTATACTCACTGCTTAAGTT 57.962 37.500 4.02 0.00 36.83 2.66
780 785 6.464222 TGTGCTATACTCACTGCTTAAGTTT 58.536 36.000 4.02 0.00 36.83 2.66
781 786 7.608153 TGTGCTATACTCACTGCTTAAGTTTA 58.392 34.615 4.02 0.00 36.83 2.01
782 787 7.759886 TGTGCTATACTCACTGCTTAAGTTTAG 59.240 37.037 4.02 3.48 36.83 1.85
783 788 6.757010 TGCTATACTCACTGCTTAAGTTTAGC 59.243 38.462 6.92 6.92 44.19 3.09
784 789 6.757010 GCTATACTCACTGCTTAAGTTTAGCA 59.243 38.462 15.26 15.26 43.77 3.49
785 790 7.439655 GCTATACTCACTGCTTAAGTTTAGCAT 59.560 37.037 16.30 4.81 46.63 3.79
786 791 7.778470 ATACTCACTGCTTAAGTTTAGCATC 57.222 36.000 16.30 0.00 46.63 3.91
787 792 5.799213 ACTCACTGCTTAAGTTTAGCATCT 58.201 37.500 16.30 3.14 46.63 2.90
788 793 6.936279 ACTCACTGCTTAAGTTTAGCATCTA 58.064 36.000 16.30 4.89 46.63 1.98
789 794 6.814146 ACTCACTGCTTAAGTTTAGCATCTAC 59.186 38.462 16.30 0.00 46.63 2.59
790 795 6.936279 TCACTGCTTAAGTTTAGCATCTACT 58.064 36.000 16.30 0.00 46.63 2.57
791 796 7.386851 TCACTGCTTAAGTTTAGCATCTACTT 58.613 34.615 16.30 0.00 46.63 2.24
792 797 7.878127 TCACTGCTTAAGTTTAGCATCTACTTT 59.122 33.333 16.30 0.00 46.63 2.66
793 798 8.507249 CACTGCTTAAGTTTAGCATCTACTTTT 58.493 33.333 16.30 0.00 46.63 2.27
794 799 9.720769 ACTGCTTAAGTTTAGCATCTACTTTTA 57.279 29.630 16.30 0.00 46.63 1.52
801 806 9.944376 AAGTTTAGCATCTACTTTTATCACAGA 57.056 29.630 0.00 0.00 0.00 3.41
802 807 9.944376 AGTTTAGCATCTACTTTTATCACAGAA 57.056 29.630 0.00 0.00 0.00 3.02
814 819 8.159344 CTTTTATCACAGAAAAGTTCCAGACT 57.841 34.615 0.00 0.00 38.52 3.24
815 820 7.496529 TTTATCACAGAAAAGTTCCAGACTG 57.503 36.000 0.00 0.00 39.00 3.51
816 821 4.753516 TCACAGAAAAGTTCCAGACTGA 57.246 40.909 3.32 0.00 39.00 3.41
817 822 5.097742 TCACAGAAAAGTTCCAGACTGAA 57.902 39.130 3.32 0.00 39.00 3.02
818 823 5.496556 TCACAGAAAAGTTCCAGACTGAAA 58.503 37.500 3.32 0.00 39.00 2.69
819 824 5.586243 TCACAGAAAAGTTCCAGACTGAAAG 59.414 40.000 3.32 0.00 39.00 2.62
820 825 4.884164 ACAGAAAAGTTCCAGACTGAAAGG 59.116 41.667 3.32 0.00 39.00 3.11
821 826 4.276926 CAGAAAAGTTCCAGACTGAAAGGG 59.723 45.833 3.32 0.00 39.00 3.95
822 827 3.953542 AAAGTTCCAGACTGAAAGGGT 57.046 42.857 3.32 0.00 39.00 4.34
823 828 5.132144 AGAAAAGTTCCAGACTGAAAGGGTA 59.868 40.000 3.32 0.00 39.00 3.69
824 829 5.382664 AAAGTTCCAGACTGAAAGGGTAA 57.617 39.130 3.32 0.00 39.00 2.85
825 830 4.353383 AGTTCCAGACTGAAAGGGTAAC 57.647 45.455 3.32 0.00 39.30 2.50
826 831 3.974642 AGTTCCAGACTGAAAGGGTAACT 59.025 43.478 3.32 0.00 39.30 2.24
827 832 4.412528 AGTTCCAGACTGAAAGGGTAACTT 59.587 41.667 3.32 0.00 37.98 2.66
828 833 4.351874 TCCAGACTGAAAGGGTAACTTG 57.648 45.455 3.32 0.00 39.96 3.16
829 834 2.814336 CCAGACTGAAAGGGTAACTTGC 59.186 50.000 3.32 0.00 39.96 4.01
830 835 3.496870 CCAGACTGAAAGGGTAACTTGCT 60.497 47.826 3.32 0.00 39.96 3.91
831 836 4.137543 CAGACTGAAAGGGTAACTTGCTT 58.862 43.478 0.00 0.00 39.96 3.91
832 837 4.023707 CAGACTGAAAGGGTAACTTGCTTG 60.024 45.833 0.00 0.00 39.96 4.01
833 838 4.134563 GACTGAAAGGGTAACTTGCTTGA 58.865 43.478 0.00 0.00 39.96 3.02
834 839 4.532834 ACTGAAAGGGTAACTTGCTTGAA 58.467 39.130 0.00 0.00 39.96 2.69
835 840 4.953579 ACTGAAAGGGTAACTTGCTTGAAA 59.046 37.500 0.00 0.00 39.96 2.69
836 841 5.067805 ACTGAAAGGGTAACTTGCTTGAAAG 59.932 40.000 0.00 0.00 39.96 2.62
837 842 4.953579 TGAAAGGGTAACTTGCTTGAAAGT 59.046 37.500 0.00 0.00 42.21 2.66
838 843 8.718426 ACTGAAAGGGTAACTTGCTTGAAAGTT 61.718 37.037 11.07 11.07 44.95 2.66
839 844 5.515797 AAGGGTAACTTGCTTGAAAGTTC 57.484 39.130 9.77 3.45 45.10 3.01
840 845 3.889538 AGGGTAACTTGCTTGAAAGTTCC 59.110 43.478 9.77 10.61 45.10 3.62
841 846 3.634910 GGGTAACTTGCTTGAAAGTTCCA 59.365 43.478 9.77 0.00 45.10 3.53
842 847 4.261614 GGGTAACTTGCTTGAAAGTTCCAG 60.262 45.833 9.77 0.00 45.10 3.86
843 848 3.443099 AACTTGCTTGAAAGTTCCAGC 57.557 42.857 9.57 9.57 45.10 4.85
844 849 1.683385 ACTTGCTTGAAAGTTCCAGCC 59.317 47.619 12.96 0.00 43.20 4.85
845 850 1.682854 CTTGCTTGAAAGTTCCAGCCA 59.317 47.619 12.96 3.41 43.20 4.75
846 851 1.999648 TGCTTGAAAGTTCCAGCCAT 58.000 45.000 12.96 0.00 43.20 4.40
847 852 1.614903 TGCTTGAAAGTTCCAGCCATG 59.385 47.619 12.96 0.00 43.20 3.66
1195 1200 0.607489 GGATGTGACTGCTGCAACCT 60.607 55.000 3.02 0.00 0.00 3.50
1368 1373 2.790791 CGATGAGGAGGCCGAGCTT 61.791 63.158 0.00 0.00 0.00 3.74
1705 1746 4.310769 CTCAACCGATCAACTTCTTGAGT 58.689 43.478 0.00 0.00 39.83 3.41
1748 1789 1.189524 CCCGGATAGGCGGTCCATAA 61.190 60.000 0.73 0.00 39.21 1.90
2310 2357 1.814772 TTTTGCAATGCGGAGTGGGG 61.815 55.000 6.49 0.00 0.00 4.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.507233 TGACTTCTGTGGGATGCAAATTC 59.493 43.478 0.00 0.00 0.00 2.17
291 295 8.723365 AGTGTACATATATGAAGAATTTCCCCA 58.277 33.333 19.63 0.00 32.09 4.96
366 370 2.028385 GGGGCTAGAGTTGAAAGACGAA 60.028 50.000 0.00 0.00 0.00 3.85
429 434 6.873997 TCTCTTTTTCCCTTCCTTTTGTTTC 58.126 36.000 0.00 0.00 0.00 2.78
512 517 4.690122 ACGCTTTTTGACACTAGTGTAGT 58.310 39.130 27.98 14.12 45.05 2.73
513 518 4.982916 AGACGCTTTTTGACACTAGTGTAG 59.017 41.667 27.98 20.94 45.05 2.74
514 519 4.940463 AGACGCTTTTTGACACTAGTGTA 58.060 39.130 27.98 11.50 45.05 2.90
516 521 4.795970 AAGACGCTTTTTGACACTAGTG 57.204 40.909 21.44 21.44 0.00 2.74
517 522 8.773404 AATATAAGACGCTTTTTGACACTAGT 57.227 30.769 0.00 0.00 0.00 2.57
520 525 8.612619 CCATAATATAAGACGCTTTTTGACACT 58.387 33.333 0.00 0.00 0.00 3.55
521 526 7.855904 CCCATAATATAAGACGCTTTTTGACAC 59.144 37.037 0.00 0.00 0.00 3.67
522 527 7.771361 TCCCATAATATAAGACGCTTTTTGACA 59.229 33.333 0.00 0.00 0.00 3.58
523 528 8.068380 GTCCCATAATATAAGACGCTTTTTGAC 58.932 37.037 0.00 0.00 0.00 3.18
524 529 7.042321 CGTCCCATAATATAAGACGCTTTTTGA 60.042 37.037 10.06 0.00 43.07 2.69
525 530 7.069569 CGTCCCATAATATAAGACGCTTTTTG 58.930 38.462 10.06 0.00 43.07 2.44
526 531 6.204108 CCGTCCCATAATATAAGACGCTTTTT 59.796 38.462 14.86 0.00 46.66 1.94
527 532 5.699458 CCGTCCCATAATATAAGACGCTTTT 59.301 40.000 14.86 0.00 46.66 2.27
528 533 5.011329 TCCGTCCCATAATATAAGACGCTTT 59.989 40.000 14.86 0.00 46.66 3.51
529 534 4.525487 TCCGTCCCATAATATAAGACGCTT 59.475 41.667 14.86 0.00 46.66 4.68
530 535 4.084287 TCCGTCCCATAATATAAGACGCT 58.916 43.478 14.86 0.00 46.66 5.07
531 536 4.421948 CTCCGTCCCATAATATAAGACGC 58.578 47.826 14.86 0.00 46.66 5.19
533 538 5.021458 TCCCTCCGTCCCATAATATAAGAC 58.979 45.833 0.00 0.00 0.00 3.01
534 539 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
535 540 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
543 548 1.229131 TACTACTCCCTCCGTCCCAT 58.771 55.000 0.00 0.00 0.00 4.00
544 549 1.133575 CATACTACTCCCTCCGTCCCA 60.134 57.143 0.00 0.00 0.00 4.37
545 550 1.144503 TCATACTACTCCCTCCGTCCC 59.855 57.143 0.00 0.00 0.00 4.46
546 551 2.653234 TCATACTACTCCCTCCGTCC 57.347 55.000 0.00 0.00 0.00 4.79
547 552 2.229302 GCATCATACTACTCCCTCCGTC 59.771 54.545 0.00 0.00 0.00 4.79
554 559 4.202461 TGAATTGGGGCATCATACTACTCC 60.202 45.833 0.00 0.00 0.00 3.85
555 560 4.973168 TGAATTGGGGCATCATACTACTC 58.027 43.478 0.00 0.00 0.00 2.59
556 561 5.387113 TTGAATTGGGGCATCATACTACT 57.613 39.130 0.00 0.00 0.00 2.57
631 636 2.159327 AAAAGCTTGCTTGGTCATGC 57.841 45.000 8.73 2.40 37.38 4.06
632 637 3.986277 AGAAAAAGCTTGCTTGGTCATG 58.014 40.909 8.73 0.00 0.00 3.07
671 676 9.190317 GAGATATTTCTTTTGGGGAAATACACT 57.810 33.333 9.93 11.45 43.68 3.55
672 677 8.966868 TGAGATATTTCTTTTGGGGAAATACAC 58.033 33.333 9.93 8.20 43.68 2.90
694 699 3.005539 GCCCTGTCTGGCCTGAGA 61.006 66.667 13.36 11.13 46.11 3.27
701 706 0.179020 TTCACAACAGCCCTGTCTGG 60.179 55.000 0.79 0.00 44.13 3.86
702 707 0.947244 GTTCACAACAGCCCTGTCTG 59.053 55.000 0.79 5.47 44.13 3.51
703 708 0.546122 TGTTCACAACAGCCCTGTCT 59.454 50.000 0.79 0.00 44.13 3.41
704 709 3.094386 TGTTCACAACAGCCCTGTC 57.906 52.632 0.79 0.00 44.13 3.51
712 717 4.582240 TGATAACATTGGCTGTTCACAACA 59.418 37.500 0.00 0.00 44.99 3.33
713 718 5.119931 TGATAACATTGGCTGTTCACAAC 57.880 39.130 0.00 0.00 44.99 3.32
714 719 4.826733 ACTGATAACATTGGCTGTTCACAA 59.173 37.500 0.00 0.00 44.99 3.33
715 720 4.397420 ACTGATAACATTGGCTGTTCACA 58.603 39.130 0.00 0.00 44.99 3.58
716 721 6.314784 GTTACTGATAACATTGGCTGTTCAC 58.685 40.000 0.00 0.00 44.99 3.18
717 722 5.414454 GGTTACTGATAACATTGGCTGTTCA 59.586 40.000 0.00 0.00 44.99 3.18
718 723 5.447279 CGGTTACTGATAACATTGGCTGTTC 60.447 44.000 0.00 0.00 44.99 3.18
720 725 3.938963 CGGTTACTGATAACATTGGCTGT 59.061 43.478 0.08 0.00 42.26 4.40
721 726 3.938963 ACGGTTACTGATAACATTGGCTG 59.061 43.478 0.00 0.00 42.26 4.85
722 727 4.216411 ACGGTTACTGATAACATTGGCT 57.784 40.909 0.00 0.00 42.26 4.75
723 728 4.438200 CCAACGGTTACTGATAACATTGGC 60.438 45.833 14.51 0.00 44.17 4.52
724 729 5.229921 CCAACGGTTACTGATAACATTGG 57.770 43.478 13.62 13.62 44.42 3.16
725 730 5.410132 TCACCAACGGTTACTGATAACATTG 59.590 40.000 0.00 3.88 42.26 2.82
726 731 5.553123 TCACCAACGGTTACTGATAACATT 58.447 37.500 0.00 0.00 42.26 2.71
727 732 5.155278 TCACCAACGGTTACTGATAACAT 57.845 39.130 0.00 0.00 42.26 2.71
728 733 4.603989 TCACCAACGGTTACTGATAACA 57.396 40.909 0.00 0.00 42.26 2.41
729 734 5.467735 ACTTTCACCAACGGTTACTGATAAC 59.532 40.000 0.00 0.00 40.12 1.89
730 735 5.613329 ACTTTCACCAACGGTTACTGATAA 58.387 37.500 0.00 0.00 31.02 1.75
731 736 5.217978 ACTTTCACCAACGGTTACTGATA 57.782 39.130 0.00 0.00 31.02 2.15
732 737 4.081322 ACTTTCACCAACGGTTACTGAT 57.919 40.909 0.00 0.00 31.02 2.90
733 738 3.547054 ACTTTCACCAACGGTTACTGA 57.453 42.857 0.00 0.00 31.02 3.41
734 739 5.237779 ACAATACTTTCACCAACGGTTACTG 59.762 40.000 0.00 0.00 31.02 2.74
735 740 5.237779 CACAATACTTTCACCAACGGTTACT 59.762 40.000 0.00 0.00 31.02 2.24
736 741 5.445845 CACAATACTTTCACCAACGGTTAC 58.554 41.667 0.00 0.00 31.02 2.50
737 742 4.023878 GCACAATACTTTCACCAACGGTTA 60.024 41.667 0.00 0.00 31.02 2.85
738 743 3.243267 GCACAATACTTTCACCAACGGTT 60.243 43.478 0.00 0.00 31.02 4.44
739 744 2.292292 GCACAATACTTTCACCAACGGT 59.708 45.455 0.00 0.00 35.62 4.83
740 745 2.552315 AGCACAATACTTTCACCAACGG 59.448 45.455 0.00 0.00 0.00 4.44
741 746 3.896648 AGCACAATACTTTCACCAACG 57.103 42.857 0.00 0.00 0.00 4.10
742 747 7.333423 TGAGTATAGCACAATACTTTCACCAAC 59.667 37.037 7.55 0.00 41.65 3.77
743 748 7.333423 GTGAGTATAGCACAATACTTTCACCAA 59.667 37.037 7.55 0.00 41.65 3.67
744 749 6.816640 GTGAGTATAGCACAATACTTTCACCA 59.183 38.462 7.55 0.41 41.65 4.17
745 750 7.010552 CAGTGAGTATAGCACAATACTTTCACC 59.989 40.741 15.19 4.20 41.65 4.02
746 751 7.464710 GCAGTGAGTATAGCACAATACTTTCAC 60.465 40.741 0.00 13.00 41.65 3.18
747 752 6.535150 GCAGTGAGTATAGCACAATACTTTCA 59.465 38.462 0.00 1.71 41.65 2.69
748 753 6.758886 AGCAGTGAGTATAGCACAATACTTTC 59.241 38.462 0.00 5.23 41.65 2.62
749 754 6.644347 AGCAGTGAGTATAGCACAATACTTT 58.356 36.000 0.00 0.00 41.65 2.66
750 755 6.227298 AGCAGTGAGTATAGCACAATACTT 57.773 37.500 0.00 0.00 41.65 2.24
751 756 5.860941 AGCAGTGAGTATAGCACAATACT 57.139 39.130 0.00 6.20 43.72 2.12
752 757 7.707035 ACTTAAGCAGTGAGTATAGCACAATAC 59.293 37.037 1.29 0.00 38.70 1.89
753 758 7.782049 ACTTAAGCAGTGAGTATAGCACAATA 58.218 34.615 1.29 0.00 38.70 1.90
754 759 6.644347 ACTTAAGCAGTGAGTATAGCACAAT 58.356 36.000 1.29 0.00 38.70 2.71
755 760 6.037786 ACTTAAGCAGTGAGTATAGCACAA 57.962 37.500 1.29 0.00 38.70 3.33
756 761 5.661056 ACTTAAGCAGTGAGTATAGCACA 57.339 39.130 1.29 0.00 38.70 4.57
757 762 6.969828 AAACTTAAGCAGTGAGTATAGCAC 57.030 37.500 1.29 0.00 35.12 4.40
758 763 6.757010 GCTAAACTTAAGCAGTGAGTATAGCA 59.243 38.462 1.29 0.00 39.83 3.49
759 764 6.757010 TGCTAAACTTAAGCAGTGAGTATAGC 59.243 38.462 1.29 4.68 44.78 2.97
775 780 9.944376 TCTGTGATAAAAGTAGATGCTAAACTT 57.056 29.630 0.00 0.00 35.01 2.66
776 781 9.944376 TTCTGTGATAAAAGTAGATGCTAAACT 57.056 29.630 0.00 0.00 0.00 2.66
789 794 8.072567 CAGTCTGGAACTTTTCTGTGATAAAAG 58.927 37.037 6.73 6.73 45.33 2.27
790 795 7.773224 TCAGTCTGGAACTTTTCTGTGATAAAA 59.227 33.333 0.00 0.00 35.45 1.52
791 796 7.279615 TCAGTCTGGAACTTTTCTGTGATAAA 58.720 34.615 0.00 0.00 35.45 1.40
792 797 6.826668 TCAGTCTGGAACTTTTCTGTGATAA 58.173 36.000 0.00 0.00 35.45 1.75
793 798 6.419484 TCAGTCTGGAACTTTTCTGTGATA 57.581 37.500 0.00 0.00 35.45 2.15
794 799 5.296151 TCAGTCTGGAACTTTTCTGTGAT 57.704 39.130 0.00 0.00 35.45 3.06
795 800 4.753516 TCAGTCTGGAACTTTTCTGTGA 57.246 40.909 0.00 0.00 35.45 3.58
796 801 5.220931 CCTTTCAGTCTGGAACTTTTCTGTG 60.221 44.000 0.00 0.00 35.45 3.66
797 802 4.884164 CCTTTCAGTCTGGAACTTTTCTGT 59.116 41.667 0.00 0.00 35.45 3.41
798 803 4.276926 CCCTTTCAGTCTGGAACTTTTCTG 59.723 45.833 0.00 0.00 35.45 3.02
799 804 4.079730 ACCCTTTCAGTCTGGAACTTTTCT 60.080 41.667 0.00 0.00 35.45 2.52
800 805 4.207955 ACCCTTTCAGTCTGGAACTTTTC 58.792 43.478 0.00 0.00 35.45 2.29
801 806 4.251103 ACCCTTTCAGTCTGGAACTTTT 57.749 40.909 0.00 0.00 35.45 2.27
802 807 3.953542 ACCCTTTCAGTCTGGAACTTT 57.046 42.857 0.00 0.00 35.45 2.66
803 808 4.412528 AGTTACCCTTTCAGTCTGGAACTT 59.587 41.667 0.00 0.00 35.45 2.66
804 809 3.974642 AGTTACCCTTTCAGTCTGGAACT 59.025 43.478 0.00 0.00 39.44 3.01
805 810 4.353383 AGTTACCCTTTCAGTCTGGAAC 57.647 45.455 0.00 0.00 0.00 3.62
806 811 4.714632 CAAGTTACCCTTTCAGTCTGGAA 58.285 43.478 0.00 0.00 0.00 3.53
807 812 3.496160 GCAAGTTACCCTTTCAGTCTGGA 60.496 47.826 0.00 0.00 0.00 3.86
808 813 2.814336 GCAAGTTACCCTTTCAGTCTGG 59.186 50.000 0.00 0.00 0.00 3.86
809 814 3.744660 AGCAAGTTACCCTTTCAGTCTG 58.255 45.455 0.00 0.00 0.00 3.51
810 815 4.137543 CAAGCAAGTTACCCTTTCAGTCT 58.862 43.478 0.00 0.00 0.00 3.24
811 816 4.134563 TCAAGCAAGTTACCCTTTCAGTC 58.865 43.478 0.00 0.00 0.00 3.51
812 817 4.164843 TCAAGCAAGTTACCCTTTCAGT 57.835 40.909 0.00 0.00 0.00 3.41
813 818 5.067805 ACTTTCAAGCAAGTTACCCTTTCAG 59.932 40.000 0.00 0.00 32.81 3.02
814 819 4.953579 ACTTTCAAGCAAGTTACCCTTTCA 59.046 37.500 0.00 0.00 32.81 2.69
815 820 5.515797 ACTTTCAAGCAAGTTACCCTTTC 57.484 39.130 0.00 0.00 32.81 2.62
816 821 5.163447 GGAACTTTCAAGCAAGTTACCCTTT 60.163 40.000 0.30 0.00 45.23 3.11
817 822 4.341235 GGAACTTTCAAGCAAGTTACCCTT 59.659 41.667 0.30 0.00 45.23 3.95
818 823 3.889538 GGAACTTTCAAGCAAGTTACCCT 59.110 43.478 0.30 0.00 45.23 4.34
819 824 3.634910 TGGAACTTTCAAGCAAGTTACCC 59.365 43.478 7.05 3.62 44.27 3.69
820 825 4.860072 CTGGAACTTTCAAGCAAGTTACC 58.140 43.478 7.05 7.59 44.27 2.85
829 834 2.242043 ACCATGGCTGGAACTTTCAAG 58.758 47.619 13.04 0.00 46.37 3.02
830 835 2.380064 ACCATGGCTGGAACTTTCAA 57.620 45.000 13.04 0.00 46.37 2.69
831 836 3.153919 GTTACCATGGCTGGAACTTTCA 58.846 45.455 13.04 0.00 46.37 2.69
832 837 2.492088 GGTTACCATGGCTGGAACTTTC 59.508 50.000 13.04 0.00 46.37 2.62
833 838 2.110011 AGGTTACCATGGCTGGAACTTT 59.890 45.455 13.04 2.14 46.37 2.66
834 839 1.710809 AGGTTACCATGGCTGGAACTT 59.289 47.619 13.04 4.99 46.37 2.66
835 840 1.004745 CAGGTTACCATGGCTGGAACT 59.995 52.381 13.04 0.00 46.37 3.01
836 841 1.271926 ACAGGTTACCATGGCTGGAAC 60.272 52.381 13.04 10.95 46.37 3.62
837 842 1.072266 ACAGGTTACCATGGCTGGAA 58.928 50.000 13.04 0.00 46.37 3.53
838 843 1.072266 AACAGGTTACCATGGCTGGA 58.928 50.000 13.04 0.00 46.37 3.86
840 845 1.812571 GACAACAGGTTACCATGGCTG 59.187 52.381 13.04 13.46 0.00 4.85
841 846 1.271926 GGACAACAGGTTACCATGGCT 60.272 52.381 13.04 1.45 0.00 4.75
842 847 1.173913 GGACAACAGGTTACCATGGC 58.826 55.000 13.04 1.41 0.00 4.40
843 848 2.436417 CTGGACAACAGGTTACCATGG 58.564 52.381 11.19 11.19 43.70 3.66
1195 1200 2.398554 GCTCCGCGAAGGCATCAAA 61.399 57.895 8.23 0.00 40.77 2.69
1368 1373 0.321919 CTTAGGTTGCAGCCTGCTGA 60.322 55.000 30.39 9.10 46.30 4.26
1705 1746 3.335484 AGTTAAGGCCCCTAACATTCCAA 59.665 43.478 21.50 0.00 0.00 3.53
2236 2283 0.976641 TCTCGTTGCTCCAGGTGAAT 59.023 50.000 0.00 0.00 0.00 2.57
2310 2357 0.517316 GTGGTCGTTGAAGGTGATGC 59.483 55.000 0.00 0.00 0.00 3.91
2489 2536 2.591715 GTGTGGCTCGGTGTGCTT 60.592 61.111 0.00 0.00 0.00 3.91


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

AutoCloner maintained by Alex Coulton.