Multiple sequence alignment - TraesCS3B01G372500

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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 TraesCS3B01G372500 chr3B 100.000 3098 0 0 1 3098 585022619 585025716 0.000000e+00 5722
1 TraesCS3B01G372500 chr3B 88.103 891 79 14 2 877 585138188 585139066 0.000000e+00 1033
2 TraesCS3B01G372500 chr3B 85.461 846 78 26 23 840 584984372 584985200 0.000000e+00 839
3 TraesCS3B01G372500 chr1A 97.118 2221 64 0 878 3098 79116294 79114074 0.000000e+00 3747
4 TraesCS3B01G372500 chr7A 96.983 2221 67 0 878 3098 735987065 735989285 0.000000e+00 3731
5 TraesCS3B01G372500 chr7A 95.812 191 8 0 877 1067 735991714 735991904 3.000000e-80 309
6 TraesCS3B01G372500 chr5D 96.725 2229 69 4 870 3098 321692860 321690636 0.000000e+00 3709
7 TraesCS3B01G372500 chr5D 96.758 2221 68 2 878 3098 408228600 408226384 0.000000e+00 3699
8 TraesCS3B01G372500 chr5D 79.307 1068 187 25 2057 3098 478571638 478570579 0.000000e+00 717
9 TraesCS3B01G372500 chr5D 81.377 639 119 0 1304 1942 478572409 478571771 3.540000e-144 521
10 TraesCS3B01G372500 chr1B 96.488 2221 75 2 878 3098 22956030 22953813 0.000000e+00 3666
11 TraesCS3B01G372500 chr3D 96.408 2227 61 7 872 3098 566132742 566134949 0.000000e+00 3651
12 TraesCS3B01G372500 chr3D 91.129 868 65 7 2 859 446109236 446110101 0.000000e+00 1166
13 TraesCS3B01G372500 chr3D 90.279 895 67 8 1 877 446190887 446191779 0.000000e+00 1153
14 TraesCS3B01G372500 chr3D 86.512 860 78 23 23 859 446074752 446075596 0.000000e+00 911
15 TraesCS3B01G372500 chr5A 95.597 2226 81 3 875 3098 632437276 632439486 0.000000e+00 3552
16 TraesCS3B01G372500 chr4B 88.652 1172 126 7 878 2047 473842904 473841738 0.000000e+00 1421
17 TraesCS3B01G372500 chr4B 89.693 815 79 5 2285 3098 473591392 473590582 0.000000e+00 1035
18 TraesCS3B01G372500 chr3A 91.455 866 64 7 2 858 587905442 587906306 0.000000e+00 1181
19 TraesCS3B01G372500 chr3A 90.899 890 64 8 1 877 587965615 587966500 0.000000e+00 1179
20 TraesCS3B01G372500 chr3A 86.914 810 67 25 23 808 587883918 587884712 0.000000e+00 872


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 TraesCS3B01G372500 chr3B 585022619 585025716 3097 False 5722 5722 100.0000 1 3098 1 chr3B.!!$F2 3097
1 TraesCS3B01G372500 chr3B 585138188 585139066 878 False 1033 1033 88.1030 2 877 1 chr3B.!!$F3 875
2 TraesCS3B01G372500 chr3B 584984372 584985200 828 False 839 839 85.4610 23 840 1 chr3B.!!$F1 817
3 TraesCS3B01G372500 chr1A 79114074 79116294 2220 True 3747 3747 97.1180 878 3098 1 chr1A.!!$R1 2220
4 TraesCS3B01G372500 chr7A 735987065 735991904 4839 False 2020 3731 96.3975 877 3098 2 chr7A.!!$F1 2221
5 TraesCS3B01G372500 chr5D 321690636 321692860 2224 True 3709 3709 96.7250 870 3098 1 chr5D.!!$R1 2228
6 TraesCS3B01G372500 chr5D 408226384 408228600 2216 True 3699 3699 96.7580 878 3098 1 chr5D.!!$R2 2220
7 TraesCS3B01G372500 chr5D 478570579 478572409 1830 True 619 717 80.3420 1304 3098 2 chr5D.!!$R3 1794
8 TraesCS3B01G372500 chr1B 22953813 22956030 2217 True 3666 3666 96.4880 878 3098 1 chr1B.!!$R1 2220
9 TraesCS3B01G372500 chr3D 566132742 566134949 2207 False 3651 3651 96.4080 872 3098 1 chr3D.!!$F4 2226
10 TraesCS3B01G372500 chr3D 446109236 446110101 865 False 1166 1166 91.1290 2 859 1 chr3D.!!$F2 857
11 TraesCS3B01G372500 chr3D 446190887 446191779 892 False 1153 1153 90.2790 1 877 1 chr3D.!!$F3 876
12 TraesCS3B01G372500 chr3D 446074752 446075596 844 False 911 911 86.5120 23 859 1 chr3D.!!$F1 836
13 TraesCS3B01G372500 chr5A 632437276 632439486 2210 False 3552 3552 95.5970 875 3098 1 chr5A.!!$F1 2223
14 TraesCS3B01G372500 chr4B 473841738 473842904 1166 True 1421 1421 88.6520 878 2047 1 chr4B.!!$R2 1169
15 TraesCS3B01G372500 chr4B 473590582 473591392 810 True 1035 1035 89.6930 2285 3098 1 chr4B.!!$R1 813
16 TraesCS3B01G372500 chr3A 587905442 587906306 864 False 1181 1181 91.4550 2 858 1 chr3A.!!$F2 856
17 TraesCS3B01G372500 chr3A 587965615 587966500 885 False 1179 1179 90.8990 1 877 1 chr3A.!!$F3 876
18 TraesCS3B01G372500 chr3A 587883918 587884712 794 False 872 872 86.9140 23 808 1 chr3A.!!$F1 785

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
855 888 0.031449 GGAGACGGAGATGCTGTAGC 59.969 60.0 0.00 0.0 35.85 3.58 F
866 899 0.108186 TGCTGTAGCTGATTGGTCGG 60.108 55.0 5.38 0.0 42.66 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2096 2268 0.606401 CGTCCATGGGTTGAACTGCT 60.606 55.0 13.02 0.0 0.00 4.24 R
2281 2462 0.953727 TGCAGCATGTTGGAGTTGTC 59.046 50.0 11.80 0.0 39.31 3.18 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
58 60 0.108424 ACAGATCGGCTTGCTCTCAC 60.108 55.000 0.00 0.00 0.00 3.51
71 73 3.337889 CTCACGCCCACACACACG 61.338 66.667 0.00 0.00 0.00 4.49
78 80 1.736645 CCCACACACACGGATCGAC 60.737 63.158 0.00 0.00 0.00 4.20
122 126 1.075151 TCCAACCCAACCCCAAACC 60.075 57.895 0.00 0.00 0.00 3.27
303 330 4.947147 TGCACCACCAGGCGGAAC 62.947 66.667 0.00 0.00 39.06 3.62
331 358 4.796231 CGACCACCTCCTTCGGCG 62.796 72.222 0.00 0.00 0.00 6.46
402 429 2.682494 GCGTAGGACCCCTCCACA 60.682 66.667 0.00 0.00 39.39 4.17
492 525 0.032952 GCTTGACTGTGTACACGGGA 59.967 55.000 32.69 19.29 41.89 5.14
539 572 4.463879 CCACTGCTCGCCCTGGAG 62.464 72.222 0.00 0.00 37.11 3.86
540 573 4.463879 CACTGCTCGCCCTGGAGG 62.464 72.222 0.00 0.00 34.56 4.30
549 582 4.785453 CCCTGGAGGCTGAACCGC 62.785 72.222 0.00 0.00 46.52 5.68
550 583 3.710722 CCTGGAGGCTGAACCGCT 61.711 66.667 0.00 0.00 46.52 5.52
551 584 2.348998 CTGGAGGCTGAACCGCTT 59.651 61.111 0.00 0.00 46.52 4.68
552 585 2.032528 TGGAGGCTGAACCGCTTG 59.967 61.111 0.00 0.00 46.52 4.01
553 586 3.435186 GGAGGCTGAACCGCTTGC 61.435 66.667 0.00 0.00 46.52 4.01
554 587 3.793144 GAGGCTGAACCGCTTGCG 61.793 66.667 8.14 8.14 46.52 4.85
614 647 4.539881 GACCTCGTCGCCGCTCTC 62.540 72.222 0.00 0.00 0.00 3.20
637 670 4.456253 CGTAGCTGTCGACGCGGT 62.456 66.667 20.83 17.03 34.79 5.68
638 671 2.787249 GTAGCTGTCGACGCGGTA 59.213 61.111 20.83 16.19 0.00 4.02
639 672 1.297451 GTAGCTGTCGACGCGGTAG 60.297 63.158 20.83 10.30 0.00 3.18
640 673 2.466982 TAGCTGTCGACGCGGTAGG 61.467 63.158 20.83 0.00 0.00 3.18
642 675 4.849329 CTGTCGACGCGGTAGGCC 62.849 72.222 12.47 0.00 38.94 5.19
644 677 4.849329 GTCGACGCGGTAGGCCAG 62.849 72.222 12.47 0.00 38.94 4.85
647 680 4.078516 GACGCGGTAGGCCAGGTT 62.079 66.667 12.47 0.00 38.94 3.50
648 681 4.388499 ACGCGGTAGGCCAGGTTG 62.388 66.667 12.47 0.00 38.94 3.77
656 689 4.621087 GGCCAGGTTGCCCTTGGT 62.621 66.667 0.00 0.00 46.11 3.67
657 690 2.438795 GCCAGGTTGCCCTTGGTA 59.561 61.111 3.99 0.00 39.89 3.25
658 691 1.000359 GCCAGGTTGCCCTTGGTAT 60.000 57.895 3.99 0.00 39.89 2.73
659 692 0.614697 GCCAGGTTGCCCTTGGTATT 60.615 55.000 3.99 0.00 39.89 1.89
660 693 1.185315 CCAGGTTGCCCTTGGTATTG 58.815 55.000 0.00 0.00 39.89 1.90
661 694 1.272425 CCAGGTTGCCCTTGGTATTGA 60.272 52.381 0.00 0.00 39.89 2.57
662 695 2.524306 CAGGTTGCCCTTGGTATTGAA 58.476 47.619 0.00 0.00 39.89 2.69
663 696 2.231235 CAGGTTGCCCTTGGTATTGAAC 59.769 50.000 0.00 0.00 39.89 3.18
664 697 2.158385 AGGTTGCCCTTGGTATTGAACA 60.158 45.455 0.00 0.00 38.13 3.18
665 698 2.029380 GGTTGCCCTTGGTATTGAACAC 60.029 50.000 0.00 0.00 0.00 3.32
666 699 1.917872 TGCCCTTGGTATTGAACACC 58.082 50.000 0.00 0.00 36.54 4.16
667 700 0.808755 GCCCTTGGTATTGAACACCG 59.191 55.000 0.00 0.00 39.04 4.94
668 701 1.884928 GCCCTTGGTATTGAACACCGT 60.885 52.381 0.00 0.00 39.04 4.83
669 702 1.810151 CCCTTGGTATTGAACACCGTG 59.190 52.381 0.00 0.00 39.04 4.94
670 703 2.551287 CCCTTGGTATTGAACACCGTGA 60.551 50.000 5.28 0.00 39.04 4.35
671 704 3.142951 CCTTGGTATTGAACACCGTGAA 58.857 45.455 5.28 0.00 39.04 3.18
672 705 3.058501 CCTTGGTATTGAACACCGTGAAC 60.059 47.826 5.28 0.00 39.04 3.18
673 706 2.496111 TGGTATTGAACACCGTGAACC 58.504 47.619 5.28 3.75 39.04 3.62
674 707 1.808343 GGTATTGAACACCGTGAACCC 59.192 52.381 5.28 0.00 0.00 4.11
675 708 1.808343 GTATTGAACACCGTGAACCCC 59.192 52.381 5.28 0.00 0.00 4.95
676 709 0.476771 ATTGAACACCGTGAACCCCT 59.523 50.000 5.28 0.00 0.00 4.79
677 710 0.256464 TTGAACACCGTGAACCCCTT 59.744 50.000 5.28 0.00 0.00 3.95
678 711 0.464735 TGAACACCGTGAACCCCTTG 60.465 55.000 5.28 0.00 0.00 3.61
679 712 1.792118 GAACACCGTGAACCCCTTGC 61.792 60.000 5.28 0.00 0.00 4.01
680 713 2.203280 CACCGTGAACCCCTTGCA 60.203 61.111 0.00 0.00 0.00 4.08
681 714 2.113139 ACCGTGAACCCCTTGCAG 59.887 61.111 0.00 0.00 0.00 4.41
682 715 2.113139 CCGTGAACCCCTTGCAGT 59.887 61.111 0.00 0.00 0.00 4.40
683 716 1.966451 CCGTGAACCCCTTGCAGTC 60.966 63.158 0.00 0.00 0.00 3.51
684 717 2.317609 CGTGAACCCCTTGCAGTCG 61.318 63.158 0.00 0.00 0.00 4.18
685 718 1.070786 GTGAACCCCTTGCAGTCGA 59.929 57.895 0.00 0.00 0.00 4.20
686 719 0.534203 GTGAACCCCTTGCAGTCGAA 60.534 55.000 0.00 0.00 0.00 3.71
687 720 0.534203 TGAACCCCTTGCAGTCGAAC 60.534 55.000 0.00 0.00 0.00 3.95
688 721 0.534203 GAACCCCTTGCAGTCGAACA 60.534 55.000 0.00 0.00 0.00 3.18
689 722 0.535102 AACCCCTTGCAGTCGAACAG 60.535 55.000 0.00 0.00 0.00 3.16
690 723 2.328099 CCCCTTGCAGTCGAACAGC 61.328 63.158 0.00 0.00 0.00 4.40
691 724 1.597854 CCCTTGCAGTCGAACAGCA 60.598 57.895 3.84 3.84 38.88 4.41
692 725 1.572085 CCCTTGCAGTCGAACAGCAG 61.572 60.000 7.58 3.72 41.57 4.24
693 726 1.206072 CTTGCAGTCGAACAGCAGC 59.794 57.895 7.58 0.00 41.57 5.25
694 727 2.490262 CTTGCAGTCGAACAGCAGCG 62.490 60.000 7.58 0.00 41.57 5.18
695 728 2.734723 GCAGTCGAACAGCAGCGA 60.735 61.111 0.00 0.00 30.40 4.93
699 732 3.936653 TCGAACAGCAGCGACTTG 58.063 55.556 0.00 0.00 0.00 3.16
700 733 2.171940 CGAACAGCAGCGACTTGC 59.828 61.111 0.00 0.00 44.41 4.01
711 744 4.012895 GACTTGCGCCACACCGTG 62.013 66.667 4.18 0.00 0.00 4.94
712 745 4.539083 ACTTGCGCCACACCGTGA 62.539 61.111 4.18 0.00 35.23 4.35
713 746 3.716006 CTTGCGCCACACCGTGAG 61.716 66.667 4.18 0.00 35.23 3.51
719 752 4.640855 CCACACCGTGAGCGTCGT 62.641 66.667 5.28 0.00 35.23 4.34
720 753 2.657296 CACACCGTGAGCGTCGTT 60.657 61.111 5.28 0.00 35.23 3.85
721 754 2.657296 ACACCGTGAGCGTCGTTG 60.657 61.111 5.28 0.00 36.15 4.10
722 755 3.403057 CACCGTGAGCGTCGTTGG 61.403 66.667 0.00 0.00 36.15 3.77
735 768 4.410400 GTTGGCCCCTCCGTGGAG 62.410 72.222 9.02 9.02 41.63 3.86
798 831 4.943373 ACCATGTTGGGGTGAACC 57.057 55.556 0.00 0.00 43.37 3.62
799 832 2.250494 ACCATGTTGGGGTGAACCT 58.750 52.632 0.00 0.00 43.37 3.50
800 833 0.560688 ACCATGTTGGGGTGAACCTT 59.439 50.000 0.00 0.00 43.37 3.50
801 834 1.256812 CCATGTTGGGGTGAACCTTC 58.743 55.000 0.00 0.00 40.03 3.46
802 835 0.881118 CATGTTGGGGTGAACCTTCG 59.119 55.000 0.00 0.00 40.03 3.79
803 836 0.893727 ATGTTGGGGTGAACCTTCGC 60.894 55.000 0.00 0.00 40.03 4.70
819 852 4.996976 GCCATGCGGAGTATCGAT 57.003 55.556 2.16 2.16 34.37 3.59
820 853 2.743195 GCCATGCGGAGTATCGATC 58.257 57.895 0.00 0.00 34.37 3.69
821 854 0.038251 GCCATGCGGAGTATCGATCA 60.038 55.000 0.00 0.00 34.37 2.92
822 855 1.605457 GCCATGCGGAGTATCGATCAA 60.605 52.381 0.00 0.00 34.37 2.57
823 856 2.332104 CCATGCGGAGTATCGATCAAG 58.668 52.381 0.00 0.00 34.37 3.02
824 857 2.332104 CATGCGGAGTATCGATCAAGG 58.668 52.381 0.00 0.00 34.37 3.61
825 858 1.399714 TGCGGAGTATCGATCAAGGT 58.600 50.000 0.00 0.00 34.37 3.50
826 859 1.754803 TGCGGAGTATCGATCAAGGTT 59.245 47.619 0.00 0.00 34.37 3.50
827 860 2.128035 GCGGAGTATCGATCAAGGTTG 58.872 52.381 0.00 0.00 34.37 3.77
828 861 2.223735 GCGGAGTATCGATCAAGGTTGA 60.224 50.000 0.00 0.00 37.57 3.18
829 862 3.737047 GCGGAGTATCGATCAAGGTTGAA 60.737 47.826 0.00 0.00 36.94 2.69
830 863 4.045104 CGGAGTATCGATCAAGGTTGAAG 58.955 47.826 0.00 0.00 36.94 3.02
831 864 4.372656 GGAGTATCGATCAAGGTTGAAGG 58.627 47.826 0.00 0.00 36.94 3.46
832 865 4.099573 GGAGTATCGATCAAGGTTGAAGGA 59.900 45.833 0.00 0.00 36.94 3.36
833 866 5.269505 AGTATCGATCAAGGTTGAAGGAG 57.730 43.478 0.00 0.00 41.13 3.69
834 867 2.386661 TCGATCAAGGTTGAAGGAGC 57.613 50.000 0.00 0.00 41.13 4.70
835 868 1.902508 TCGATCAAGGTTGAAGGAGCT 59.097 47.619 0.00 0.00 41.13 4.09
836 869 2.005451 CGATCAAGGTTGAAGGAGCTG 58.995 52.381 0.00 0.00 41.13 4.24
837 870 2.363683 GATCAAGGTTGAAGGAGCTGG 58.636 52.381 0.00 0.00 41.13 4.85
838 871 1.434188 TCAAGGTTGAAGGAGCTGGA 58.566 50.000 0.00 0.00 33.55 3.86
839 872 1.349026 TCAAGGTTGAAGGAGCTGGAG 59.651 52.381 0.00 0.00 33.55 3.86
840 873 1.349026 CAAGGTTGAAGGAGCTGGAGA 59.651 52.381 0.00 0.00 0.00 3.71
841 874 0.980423 AGGTTGAAGGAGCTGGAGAC 59.020 55.000 0.00 0.00 0.00 3.36
842 875 0.390472 GGTTGAAGGAGCTGGAGACG 60.390 60.000 0.00 0.00 0.00 4.18
843 876 0.390472 GTTGAAGGAGCTGGAGACGG 60.390 60.000 0.00 0.00 40.79 4.79
844 877 0.541998 TTGAAGGAGCTGGAGACGGA 60.542 55.000 0.00 0.00 39.98 4.69
845 878 0.967887 TGAAGGAGCTGGAGACGGAG 60.968 60.000 0.00 0.00 39.98 4.63
846 879 0.681564 GAAGGAGCTGGAGACGGAGA 60.682 60.000 0.00 0.00 39.98 3.71
847 880 0.032615 AAGGAGCTGGAGACGGAGAT 60.033 55.000 0.00 0.00 39.98 2.75
848 881 0.754957 AGGAGCTGGAGACGGAGATG 60.755 60.000 0.00 0.00 39.98 2.90
849 882 1.067250 GAGCTGGAGACGGAGATGC 59.933 63.158 0.00 0.00 39.98 3.91
850 883 1.381056 AGCTGGAGACGGAGATGCT 60.381 57.895 0.00 0.00 39.98 3.79
851 884 1.227205 GCTGGAGACGGAGATGCTG 60.227 63.158 0.00 0.00 39.98 4.41
852 885 1.954362 GCTGGAGACGGAGATGCTGT 61.954 60.000 0.00 0.00 39.98 4.40
853 886 1.393603 CTGGAGACGGAGATGCTGTA 58.606 55.000 0.00 0.00 39.98 2.74
854 887 1.336440 CTGGAGACGGAGATGCTGTAG 59.664 57.143 0.00 0.00 39.98 2.74
855 888 0.031449 GGAGACGGAGATGCTGTAGC 59.969 60.000 0.00 0.00 35.85 3.58
856 889 1.028905 GAGACGGAGATGCTGTAGCT 58.971 55.000 5.38 0.00 42.66 3.32
857 890 0.743688 AGACGGAGATGCTGTAGCTG 59.256 55.000 5.38 0.00 42.66 4.24
858 891 0.741326 GACGGAGATGCTGTAGCTGA 59.259 55.000 5.38 0.00 42.66 4.26
859 892 1.339610 GACGGAGATGCTGTAGCTGAT 59.660 52.381 5.38 0.00 42.66 2.90
860 893 1.759445 ACGGAGATGCTGTAGCTGATT 59.241 47.619 5.38 0.00 42.66 2.57
861 894 2.133553 CGGAGATGCTGTAGCTGATTG 58.866 52.381 5.38 0.00 42.66 2.67
862 895 2.492012 GGAGATGCTGTAGCTGATTGG 58.508 52.381 5.38 0.00 42.66 3.16
863 896 2.158842 GGAGATGCTGTAGCTGATTGGT 60.159 50.000 5.38 0.00 42.66 3.67
864 897 3.129871 GAGATGCTGTAGCTGATTGGTC 58.870 50.000 5.38 0.00 42.66 4.02
865 898 1.863454 GATGCTGTAGCTGATTGGTCG 59.137 52.381 5.38 0.00 42.66 4.79
866 899 0.108186 TGCTGTAGCTGATTGGTCGG 60.108 55.000 5.38 0.00 42.66 4.79
867 900 0.811616 GCTGTAGCTGATTGGTCGGG 60.812 60.000 0.00 0.00 38.21 5.14
868 901 0.811616 CTGTAGCTGATTGGTCGGGC 60.812 60.000 0.00 0.00 0.00 6.13
869 902 1.264749 TGTAGCTGATTGGTCGGGCT 61.265 55.000 0.00 0.00 38.75 5.19
870 903 0.811616 GTAGCTGATTGGTCGGGCTG 60.812 60.000 0.00 0.00 36.92 4.85
871 904 1.971505 TAGCTGATTGGTCGGGCTGG 61.972 60.000 0.00 0.00 36.92 4.85
872 905 2.989639 CTGATTGGTCGGGCTGGA 59.010 61.111 0.00 0.00 0.00 3.86
873 906 1.528824 CTGATTGGTCGGGCTGGAT 59.471 57.895 0.00 0.00 0.00 3.41
874 907 0.816825 CTGATTGGTCGGGCTGGATG 60.817 60.000 0.00 0.00 0.00 3.51
875 908 1.271127 TGATTGGTCGGGCTGGATGA 61.271 55.000 0.00 0.00 0.00 2.92
876 909 0.533755 GATTGGTCGGGCTGGATGAG 60.534 60.000 0.00 0.00 0.00 2.90
889 922 5.128919 GGCTGGATGAGTGTTAGATGATTT 58.871 41.667 0.00 0.00 0.00 2.17
930 963 4.059511 TCGACCACGTGTTGTAATTGATT 58.940 39.130 15.65 0.00 40.69 2.57
931 964 4.084276 TCGACCACGTGTTGTAATTGATTG 60.084 41.667 15.65 0.00 40.69 2.67
1030 1065 9.948964 ATATACCAATCAATGAGATCAATCGAA 57.051 29.630 0.00 0.00 35.39 3.71
1377 1413 1.116536 TGACCGCCTCCAACTACACA 61.117 55.000 0.00 0.00 0.00 3.72
1508 1544 1.799121 GCGACGACTACACGGTTCC 60.799 63.158 0.00 0.00 37.61 3.62
1746 1782 0.392863 TGGATGTTGGCCAGACGATG 60.393 55.000 5.11 0.00 0.00 3.84
1845 1882 2.434774 GTGCCCTTCCCCTCGTTT 59.565 61.111 0.00 0.00 0.00 3.60
1848 1885 1.379146 GCCCTTCCCCTCGTTTCTT 59.621 57.895 0.00 0.00 0.00 2.52
2096 2268 4.858433 CGGCCGCGACAATCCGTA 62.858 66.667 14.67 0.00 37.33 4.02
2458 2648 5.026790 ACTCTCTAATACCACCTGCTTCTT 58.973 41.667 0.00 0.00 0.00 2.52
2491 2681 5.832060 ACTATTGGTAACGGTGCTACTCTAT 59.168 40.000 0.00 0.00 42.51 1.98
2612 2802 2.217750 TGTTCGTCAATTCACCACTGG 58.782 47.619 0.00 0.00 0.00 4.00
2739 2929 1.681327 CCAAGCCAGCCATGAAGCT 60.681 57.895 0.00 0.00 46.45 3.74
2971 3168 3.455910 TGATCTTTGGACATCCCCTGTAG 59.544 47.826 0.00 0.00 38.54 2.74
3034 3231 7.227314 TCGATGATCTCACTCAATATTTTTGGG 59.773 37.037 0.00 0.00 0.00 4.12
3035 3232 7.227314 CGATGATCTCACTCAATATTTTTGGGA 59.773 37.037 0.00 0.00 0.00 4.37
3040 3237 8.477419 TCTCACTCAATATTTTTGGGACTTTT 57.523 30.769 0.00 0.00 0.00 2.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 2.291282 TGATGCCCCCAAAATTACGAGT 60.291 45.455 0.00 0.00 0.00 4.18
17 18 2.955660 TCGATGATGCCCCCAAAATTAC 59.044 45.455 0.00 0.00 0.00 1.89
58 60 3.118454 GATCCGTGTGTGTGGGCG 61.118 66.667 0.00 0.00 0.00 6.13
71 73 2.328639 GCGAGAGTCGGTCGATCC 59.671 66.667 6.01 0.00 40.84 3.36
78 80 0.179100 ATTGTGATGGCGAGAGTCGG 60.179 55.000 0.00 0.00 40.84 4.79
158 168 4.503767 TGTTTGTTTGTTACGTCTCGAC 57.496 40.909 0.00 0.00 0.00 4.20
231 258 2.959071 GTGGCGCTCGAGCAGATC 60.959 66.667 34.69 20.60 42.21 2.75
475 508 0.031043 CGTCCCGTGTACACAGTCAA 59.969 55.000 24.98 3.40 0.00 3.18
537 570 3.793144 CGCAAGCGGTTCAGCCTC 61.793 66.667 6.55 0.00 38.01 4.70
609 642 3.213402 AGCTACGCCTCCGAGAGC 61.213 66.667 0.00 0.00 42.81 4.09
610 643 2.054140 GACAGCTACGCCTCCGAGAG 62.054 65.000 0.00 0.00 38.29 3.20
611 644 2.045242 ACAGCTACGCCTCCGAGA 60.045 61.111 0.00 0.00 38.29 4.04
612 645 2.409651 GACAGCTACGCCTCCGAG 59.590 66.667 0.00 0.00 38.29 4.63
613 646 3.506096 CGACAGCTACGCCTCCGA 61.506 66.667 0.00 0.00 38.29 4.55
614 647 3.506096 TCGACAGCTACGCCTCCG 61.506 66.667 7.47 0.00 41.14 4.63
615 648 2.102553 GTCGACAGCTACGCCTCC 59.897 66.667 11.55 0.00 0.00 4.30
616 649 2.277373 CGTCGACAGCTACGCCTC 60.277 66.667 17.16 1.64 31.66 4.70
620 653 2.944662 CTACCGCGTCGACAGCTACG 62.945 65.000 23.08 14.76 41.92 3.51
621 654 1.297451 CTACCGCGTCGACAGCTAC 60.297 63.158 23.08 5.44 0.00 3.58
622 655 2.466982 CCTACCGCGTCGACAGCTA 61.467 63.158 23.08 12.92 0.00 3.32
623 656 3.812019 CCTACCGCGTCGACAGCT 61.812 66.667 23.08 12.57 0.00 4.24
625 658 4.849329 GGCCTACCGCGTCGACAG 62.849 72.222 17.16 8.71 38.94 3.51
627 660 4.849329 CTGGCCTACCGCGTCGAC 62.849 72.222 5.18 5.18 39.70 4.20
630 663 4.078516 AACCTGGCCTACCGCGTC 62.079 66.667 3.32 0.00 39.70 5.19
631 664 4.388499 CAACCTGGCCTACCGCGT 62.388 66.667 3.32 0.00 39.70 6.01
645 678 2.029380 GGTGTTCAATACCAAGGGCAAC 60.029 50.000 0.00 0.00 38.12 4.17
646 679 2.243810 GGTGTTCAATACCAAGGGCAA 58.756 47.619 0.00 0.00 38.12 4.52
647 680 1.884497 CGGTGTTCAATACCAAGGGCA 60.884 52.381 3.96 0.00 38.11 5.36
648 681 0.808755 CGGTGTTCAATACCAAGGGC 59.191 55.000 3.96 0.00 38.11 5.19
649 682 1.810151 CACGGTGTTCAATACCAAGGG 59.190 52.381 3.96 0.00 38.11 3.95
650 683 2.773487 TCACGGTGTTCAATACCAAGG 58.227 47.619 8.17 0.00 38.11 3.61
651 684 3.058501 GGTTCACGGTGTTCAATACCAAG 60.059 47.826 8.17 0.00 38.11 3.61
652 685 2.879646 GGTTCACGGTGTTCAATACCAA 59.120 45.455 8.17 0.00 38.11 3.67
653 686 2.496111 GGTTCACGGTGTTCAATACCA 58.504 47.619 8.17 0.00 38.11 3.25
654 687 1.808343 GGGTTCACGGTGTTCAATACC 59.192 52.381 8.17 0.00 34.81 2.73
655 688 1.808343 GGGGTTCACGGTGTTCAATAC 59.192 52.381 8.17 0.00 0.00 1.89
656 689 1.700739 AGGGGTTCACGGTGTTCAATA 59.299 47.619 8.17 0.00 0.00 1.90
657 690 0.476771 AGGGGTTCACGGTGTTCAAT 59.523 50.000 8.17 0.00 0.00 2.57
658 691 0.256464 AAGGGGTTCACGGTGTTCAA 59.744 50.000 8.17 0.00 0.00 2.69
659 692 0.464735 CAAGGGGTTCACGGTGTTCA 60.465 55.000 8.17 0.00 0.00 3.18
660 693 1.792118 GCAAGGGGTTCACGGTGTTC 61.792 60.000 8.17 2.72 0.00 3.18
661 694 1.826487 GCAAGGGGTTCACGGTGTT 60.826 57.895 8.17 0.00 0.00 3.32
662 695 2.203294 GCAAGGGGTTCACGGTGT 60.203 61.111 8.17 0.00 0.00 4.16
663 696 2.203280 TGCAAGGGGTTCACGGTG 60.203 61.111 0.56 0.56 0.00 4.94
664 697 2.113139 CTGCAAGGGGTTCACGGT 59.887 61.111 0.00 0.00 0.00 4.83
665 698 1.966451 GACTGCAAGGGGTTCACGG 60.966 63.158 0.00 0.00 39.30 4.94
666 699 2.317609 CGACTGCAAGGGGTTCACG 61.318 63.158 0.00 0.00 39.30 4.35
667 700 0.534203 TTCGACTGCAAGGGGTTCAC 60.534 55.000 0.00 0.00 39.30 3.18
668 701 0.534203 GTTCGACTGCAAGGGGTTCA 60.534 55.000 0.00 0.00 39.30 3.18
669 702 0.534203 TGTTCGACTGCAAGGGGTTC 60.534 55.000 0.00 0.00 39.30 3.62
670 703 0.535102 CTGTTCGACTGCAAGGGGTT 60.535 55.000 0.00 0.00 39.30 4.11
671 704 1.071471 CTGTTCGACTGCAAGGGGT 59.929 57.895 0.00 0.00 39.30 4.95
672 705 2.328099 GCTGTTCGACTGCAAGGGG 61.328 63.158 10.40 0.00 41.83 4.79
673 706 3.257933 GCTGTTCGACTGCAAGGG 58.742 61.111 10.40 0.00 41.83 3.95
678 711 2.734723 TCGCTGCTGTTCGACTGC 60.735 61.111 0.00 8.98 42.44 4.40
682 715 2.310233 GCAAGTCGCTGCTGTTCGA 61.310 57.895 0.00 0.00 39.34 3.71
683 716 2.171940 GCAAGTCGCTGCTGTTCG 59.828 61.111 0.00 0.00 39.34 3.95
684 717 2.171940 CGCAAGTCGCTGCTGTTC 59.828 61.111 0.00 0.00 40.33 3.18
695 728 4.539083 TCACGGTGTGGCGCAAGT 62.539 61.111 10.83 3.16 33.87 3.16
696 729 3.716006 CTCACGGTGTGGCGCAAG 61.716 66.667 10.83 2.43 33.87 4.01
702 735 4.640855 ACGACGCTCACGGTGTGG 62.641 66.667 8.17 3.98 46.04 4.17
703 736 2.657296 AACGACGCTCACGGTGTG 60.657 61.111 8.17 6.94 46.04 3.82
704 737 2.657296 CAACGACGCTCACGGTGT 60.657 61.111 8.17 0.00 46.04 4.16
705 738 3.403057 CCAACGACGCTCACGGTG 61.403 66.667 0.56 0.56 46.13 4.94
718 751 4.410400 CTCCACGGAGGGGCCAAC 62.410 72.222 4.39 0.00 38.51 3.77
776 809 4.676951 ACCCCAACATGGTGCCCG 62.677 66.667 4.81 0.00 35.17 6.13
777 810 2.996734 CACCCCAACATGGTGCCC 60.997 66.667 4.81 0.00 46.13 5.36
781 814 0.560688 AAGGTTCACCCCAACATGGT 59.439 50.000 0.00 0.00 35.17 3.55
782 815 1.256812 GAAGGTTCACCCCAACATGG 58.743 55.000 0.00 0.00 37.25 3.66
783 816 0.881118 CGAAGGTTCACCCCAACATG 59.119 55.000 0.00 0.00 36.42 3.21
784 817 0.893727 GCGAAGGTTCACCCCAACAT 60.894 55.000 0.00 0.00 36.42 2.71
785 818 1.527380 GCGAAGGTTCACCCCAACA 60.527 57.895 0.00 0.00 36.42 3.33
786 819 2.265904 GGCGAAGGTTCACCCCAAC 61.266 63.158 0.00 0.00 36.42 3.77
787 820 2.075355 ATGGCGAAGGTTCACCCCAA 62.075 55.000 0.00 0.00 36.42 4.12
788 821 2.534396 ATGGCGAAGGTTCACCCCA 61.534 57.895 0.00 0.00 36.42 4.96
789 822 2.046285 CATGGCGAAGGTTCACCCC 61.046 63.158 0.00 0.00 36.42 4.95
790 823 2.700773 GCATGGCGAAGGTTCACCC 61.701 63.158 0.00 0.00 36.42 4.61
791 824 2.877691 GCATGGCGAAGGTTCACC 59.122 61.111 0.00 0.00 0.00 4.02
802 835 0.038251 TGATCGATACTCCGCATGGC 60.038 55.000 0.00 0.00 34.14 4.40
803 836 2.332104 CTTGATCGATACTCCGCATGG 58.668 52.381 0.00 0.00 0.00 3.66
804 837 2.288457 ACCTTGATCGATACTCCGCATG 60.288 50.000 0.00 0.00 0.00 4.06
805 838 1.964223 ACCTTGATCGATACTCCGCAT 59.036 47.619 0.00 0.00 0.00 4.73
806 839 1.399714 ACCTTGATCGATACTCCGCA 58.600 50.000 0.00 0.00 0.00 5.69
807 840 2.128035 CAACCTTGATCGATACTCCGC 58.872 52.381 0.00 0.00 0.00 5.54
808 841 3.710326 TCAACCTTGATCGATACTCCG 57.290 47.619 0.00 0.00 31.01 4.63
809 842 4.099573 TCCTTCAACCTTGATCGATACTCC 59.900 45.833 0.00 0.00 37.00 3.85
810 843 5.263968 TCCTTCAACCTTGATCGATACTC 57.736 43.478 0.00 0.00 37.00 2.59
811 844 4.442192 GCTCCTTCAACCTTGATCGATACT 60.442 45.833 0.00 0.00 37.00 2.12
812 845 3.804873 GCTCCTTCAACCTTGATCGATAC 59.195 47.826 0.00 0.00 37.00 2.24
813 846 3.706594 AGCTCCTTCAACCTTGATCGATA 59.293 43.478 0.00 0.00 37.00 2.92
814 847 2.503356 AGCTCCTTCAACCTTGATCGAT 59.497 45.455 0.00 0.00 37.00 3.59
815 848 1.902508 AGCTCCTTCAACCTTGATCGA 59.097 47.619 0.00 0.00 37.00 3.59
816 849 2.005451 CAGCTCCTTCAACCTTGATCG 58.995 52.381 0.00 0.00 37.00 3.69
817 850 2.026822 TCCAGCTCCTTCAACCTTGATC 60.027 50.000 0.00 0.00 37.00 2.92
818 851 1.988107 TCCAGCTCCTTCAACCTTGAT 59.012 47.619 0.00 0.00 37.00 2.57
819 852 1.349026 CTCCAGCTCCTTCAACCTTGA 59.651 52.381 0.00 0.00 34.92 3.02
820 853 1.349026 TCTCCAGCTCCTTCAACCTTG 59.651 52.381 0.00 0.00 0.00 3.61
821 854 1.349357 GTCTCCAGCTCCTTCAACCTT 59.651 52.381 0.00 0.00 0.00 3.50
822 855 0.980423 GTCTCCAGCTCCTTCAACCT 59.020 55.000 0.00 0.00 0.00 3.50
823 856 0.390472 CGTCTCCAGCTCCTTCAACC 60.390 60.000 0.00 0.00 0.00 3.77
824 857 0.390472 CCGTCTCCAGCTCCTTCAAC 60.390 60.000 0.00 0.00 0.00 3.18
825 858 0.541998 TCCGTCTCCAGCTCCTTCAA 60.542 55.000 0.00 0.00 0.00 2.69
826 859 0.967887 CTCCGTCTCCAGCTCCTTCA 60.968 60.000 0.00 0.00 0.00 3.02
827 860 0.681564 TCTCCGTCTCCAGCTCCTTC 60.682 60.000 0.00 0.00 0.00 3.46
828 861 0.032615 ATCTCCGTCTCCAGCTCCTT 60.033 55.000 0.00 0.00 0.00 3.36
829 862 0.754957 CATCTCCGTCTCCAGCTCCT 60.755 60.000 0.00 0.00 0.00 3.69
830 863 1.739049 CATCTCCGTCTCCAGCTCC 59.261 63.158 0.00 0.00 0.00 4.70
831 864 1.067250 GCATCTCCGTCTCCAGCTC 59.933 63.158 0.00 0.00 0.00 4.09
832 865 1.381056 AGCATCTCCGTCTCCAGCT 60.381 57.895 0.00 0.00 0.00 4.24
833 866 1.227205 CAGCATCTCCGTCTCCAGC 60.227 63.158 0.00 0.00 0.00 4.85
834 867 1.336440 CTACAGCATCTCCGTCTCCAG 59.664 57.143 0.00 0.00 0.00 3.86
835 868 1.393603 CTACAGCATCTCCGTCTCCA 58.606 55.000 0.00 0.00 0.00 3.86
836 869 0.031449 GCTACAGCATCTCCGTCTCC 59.969 60.000 0.00 0.00 41.59 3.71
837 870 1.028905 AGCTACAGCATCTCCGTCTC 58.971 55.000 3.70 0.00 45.16 3.36
838 871 0.743688 CAGCTACAGCATCTCCGTCT 59.256 55.000 3.70 0.00 45.16 4.18
839 872 0.741326 TCAGCTACAGCATCTCCGTC 59.259 55.000 3.70 0.00 45.16 4.79
840 873 1.407936 ATCAGCTACAGCATCTCCGT 58.592 50.000 3.70 0.00 45.16 4.69
841 874 2.133553 CAATCAGCTACAGCATCTCCG 58.866 52.381 3.70 0.00 45.16 4.63
842 875 2.158842 ACCAATCAGCTACAGCATCTCC 60.159 50.000 3.70 0.00 45.16 3.71
843 876 3.129871 GACCAATCAGCTACAGCATCTC 58.870 50.000 3.70 0.00 45.16 2.75
844 877 2.482664 CGACCAATCAGCTACAGCATCT 60.483 50.000 3.70 0.00 45.16 2.90
845 878 1.863454 CGACCAATCAGCTACAGCATC 59.137 52.381 3.70 0.00 45.16 3.91
846 879 1.473965 CCGACCAATCAGCTACAGCAT 60.474 52.381 3.70 0.00 45.16 3.79
847 880 0.108186 CCGACCAATCAGCTACAGCA 60.108 55.000 3.70 0.00 45.16 4.41
848 881 0.811616 CCCGACCAATCAGCTACAGC 60.812 60.000 0.00 0.00 42.49 4.40
849 882 0.811616 GCCCGACCAATCAGCTACAG 60.812 60.000 0.00 0.00 0.00 2.74
850 883 1.220749 GCCCGACCAATCAGCTACA 59.779 57.895 0.00 0.00 0.00 2.74
851 884 0.811616 CAGCCCGACCAATCAGCTAC 60.812 60.000 0.00 0.00 33.43 3.58
852 885 1.522092 CAGCCCGACCAATCAGCTA 59.478 57.895 0.00 0.00 33.43 3.32
853 886 2.270205 CAGCCCGACCAATCAGCT 59.730 61.111 0.00 0.00 35.08 4.24
854 887 2.615227 ATCCAGCCCGACCAATCAGC 62.615 60.000 0.00 0.00 0.00 4.26
855 888 0.816825 CATCCAGCCCGACCAATCAG 60.817 60.000 0.00 0.00 0.00 2.90
856 889 1.224315 CATCCAGCCCGACCAATCA 59.776 57.895 0.00 0.00 0.00 2.57
857 890 0.533755 CTCATCCAGCCCGACCAATC 60.534 60.000 0.00 0.00 0.00 2.67
858 891 1.274703 ACTCATCCAGCCCGACCAAT 61.275 55.000 0.00 0.00 0.00 3.16
859 892 1.918293 ACTCATCCAGCCCGACCAA 60.918 57.895 0.00 0.00 0.00 3.67
860 893 2.284625 ACTCATCCAGCCCGACCA 60.285 61.111 0.00 0.00 0.00 4.02
861 894 2.185310 AACACTCATCCAGCCCGACC 62.185 60.000 0.00 0.00 0.00 4.79
862 895 0.535335 TAACACTCATCCAGCCCGAC 59.465 55.000 0.00 0.00 0.00 4.79
863 896 0.824109 CTAACACTCATCCAGCCCGA 59.176 55.000 0.00 0.00 0.00 5.14
864 897 0.824109 TCTAACACTCATCCAGCCCG 59.176 55.000 0.00 0.00 0.00 6.13
865 898 2.435805 TCATCTAACACTCATCCAGCCC 59.564 50.000 0.00 0.00 0.00 5.19
866 899 3.827008 TCATCTAACACTCATCCAGCC 57.173 47.619 0.00 0.00 0.00 4.85
867 900 6.690194 AAAATCATCTAACACTCATCCAGC 57.310 37.500 0.00 0.00 0.00 4.85
868 901 9.334947 ACATAAAATCATCTAACACTCATCCAG 57.665 33.333 0.00 0.00 0.00 3.86
873 906 9.778741 GGGATACATAAAATCATCTAACACTCA 57.221 33.333 0.00 0.00 39.74 3.41
874 907 9.220767 GGGGATACATAAAATCATCTAACACTC 57.779 37.037 0.00 0.00 39.74 3.51
875 908 8.723365 TGGGGATACATAAAATCATCTAACACT 58.277 33.333 0.00 0.00 39.74 3.55
876 909 8.918202 TGGGGATACATAAAATCATCTAACAC 57.082 34.615 0.00 0.00 39.74 3.32
889 922 2.300723 CGATCCGGTTGGGGATACATAA 59.699 50.000 0.00 0.00 46.75 1.90
930 963 9.216148 ACCTTATATGGTAACCAACTATACACA 57.784 33.333 8.51 0.00 38.79 3.72
1030 1065 1.318576 GGGCTGTTAAAGTGCACACT 58.681 50.000 21.04 7.82 44.94 3.55
1043 1078 6.109156 TGTAATGTAATATGATCGGGCTGT 57.891 37.500 0.00 0.00 0.00 4.40
1377 1413 2.591715 AACAGCTCGCGCCAGTTT 60.592 55.556 0.00 0.00 32.93 2.66
1508 1544 5.271598 AGATAGAGCCATAGATCCAAGAGG 58.728 45.833 0.00 0.00 0.00 3.69
1550 1586 3.740128 GATCTGGGGCGCATGACGT 62.740 63.158 10.83 0.00 46.11 4.34
1845 1882 3.760035 GCCGAGCGGGTCTGAAGA 61.760 66.667 11.30 0.00 38.44 2.87
2096 2268 0.606401 CGTCCATGGGTTGAACTGCT 60.606 55.000 13.02 0.00 0.00 4.24
2281 2462 0.953727 TGCAGCATGTTGGAGTTGTC 59.046 50.000 11.80 0.00 39.31 3.18
2458 2648 6.334989 CACCGTTACCAATAGTGACAGATTA 58.665 40.000 0.00 0.00 34.70 1.75
2491 2681 7.347222 AGAGTAGGAACCAATATGTGTAATGGA 59.653 37.037 0.00 0.00 34.95 3.41
2612 2802 1.214367 TTCGACGGAACAAGAGTTGC 58.786 50.000 0.00 0.00 42.03 4.17
2739 2929 2.094026 CGAAGGAGATGTGGTGACATGA 60.094 50.000 0.00 0.00 43.22 3.07
2921 3118 4.650754 AGACGCTCAAACGGACTAATAT 57.349 40.909 0.00 0.00 37.37 1.28
2926 3123 0.956633 TGTAGACGCTCAAACGGACT 59.043 50.000 0.00 0.00 37.37 3.85
3016 3213 8.579863 AGAAAAGTCCCAAAAATATTGAGTGAG 58.420 33.333 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.