Multiple sequence alignment - TraesCS3D01G055000

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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 TraesCS3D01G055000 chr3D 100.000 2844 0 0 1 2844 22728390 22725547 0.000000e+00 5252.0
1 TraesCS3D01G055000 chr3D 99.536 647 3 0 1 647 22738160 22737514 0.000000e+00 1179.0
2 TraesCS3D01G055000 chr3D 97.389 651 13 3 1 647 575652884 575652234 0.000000e+00 1105.0
3 TraesCS3D01G055000 chr3D 97.381 649 15 1 1 647 1580900 1580252 0.000000e+00 1103.0
4 TraesCS3D01G055000 chr3D 84.493 690 79 19 2160 2837 23054639 23055312 0.000000e+00 656.0
5 TraesCS3D01G055000 chr3D 84.262 610 63 22 1985 2590 22930184 22930764 5.320000e-157 564.0
6 TraesCS3D01G055000 chr3D 80.533 488 62 20 2160 2643 22384400 22384858 7.540000e-91 344.0
7 TraesCS3D01G055000 chr3D 86.585 246 32 1 974 1219 22929016 22929260 1.300000e-68 270.0
8 TraesCS3D01G055000 chr3D 90.909 198 17 1 2641 2837 22376586 22376783 6.040000e-67 265.0
9 TraesCS3D01G055000 chr3D 83.810 210 21 5 2641 2837 22384889 22385098 1.350000e-43 187.0
10 TraesCS3D01G055000 chr3B 92.984 1967 65 25 939 2842 40163776 40165732 0.000000e+00 2800.0
11 TraesCS3D01G055000 chr3B 83.333 690 86 21 2160 2837 40232037 40232709 6.740000e-171 610.0
12 TraesCS3D01G055000 chr3B 80.624 609 65 22 1985 2590 40193413 40193971 3.390000e-114 422.0
13 TraesCS3D01G055000 chr3B 85.944 249 31 2 971 1219 40192327 40192571 2.170000e-66 263.0
14 TraesCS3D01G055000 chr3B 94.937 158 8 0 754 911 40163358 40163515 6.080000e-62 248.0
15 TraesCS3D01G055000 chr6D 98.148 648 9 2 3 647 397184271 397184918 0.000000e+00 1127.0
16 TraesCS3D01G055000 chrUn 97.682 647 13 2 3 647 141932083 141931437 0.000000e+00 1110.0
17 TraesCS3D01G055000 chr2D 97.531 648 14 2 1 647 165379831 165379185 0.000000e+00 1107.0
18 TraesCS3D01G055000 chr2D 97.385 650 12 3 1 647 560529460 560528813 0.000000e+00 1101.0
19 TraesCS3D01G055000 chr2D 93.182 44 2 1 655 697 371613928 371613971 2.370000e-06 63.9
20 TraesCS3D01G055000 chr2D 93.182 44 1 2 655 698 413612598 413612639 2.370000e-06 63.9
21 TraesCS3D01G055000 chr2D 88.235 51 3 3 655 703 121856077 121856028 1.100000e-04 58.4
22 TraesCS3D01G055000 chr5D 97.523 646 14 2 3 647 480387943 480388587 0.000000e+00 1103.0
23 TraesCS3D01G055000 chr5D 97.385 650 14 2 1 647 518942322 518941673 0.000000e+00 1103.0
24 TraesCS3D01G055000 chr5D 89.796 49 1 3 655 700 356108477 356108524 3.060000e-05 60.2
25 TraesCS3D01G055000 chr3A 85.167 209 29 2 2157 2365 32142783 32142989 2.220000e-51 213.0
26 TraesCS3D01G055000 chr3A 84.804 204 20 5 2641 2844 32143545 32143737 8.040000e-46 195.0
27 TraesCS3D01G055000 chr7A 88.535 157 16 2 2643 2797 17964104 17963948 3.740000e-44 189.0
28 TraesCS3D01G055000 chr7A 89.041 73 4 1 2575 2643 17964209 17964137 1.400000e-13 87.9
29 TraesCS3D01G055000 chr7A 89.041 73 4 1 2575 2643 35743285 35743357 1.400000e-13 87.9
30 TraesCS3D01G055000 chr1A 88.535 157 13 3 2643 2797 526135426 526135273 4.840000e-43 185.0
31 TraesCS3D01G055000 chr1A 86.232 138 14 4 2663 2797 406350949 406351084 8.210000e-31 145.0
32 TraesCS3D01G055000 chr1A 85.612 139 16 4 2663 2797 481249520 481249658 2.950000e-30 143.0
33 TraesCS3D01G055000 chr1A 88.889 72 4 1 2575 2642 526135531 526135460 5.050000e-13 86.1
34 TraesCS3D01G055000 chr2B 88.667 150 15 2 2650 2797 73073036 73072887 6.260000e-42 182.0
35 TraesCS3D01G055000 chr5A 87.342 158 17 3 2643 2797 500029954 500029797 8.100000e-41 178.0
36 TraesCS3D01G055000 chr5A 87.037 54 4 3 655 708 457682759 457682709 1.100000e-04 58.4
37 TraesCS3D01G055000 chr6B 86.076 158 17 5 2643 2797 125200968 125200813 6.300000e-37 165.0
38 TraesCS3D01G055000 chr6A 86.301 73 6 1 2575 2643 44077066 44077138 3.040000e-10 76.8
39 TraesCS3D01G055000 chr1D 93.182 44 0 3 655 698 419714981 419715021 8.510000e-06 62.1
40 TraesCS3D01G055000 chr1D 88.462 52 3 3 655 705 412601004 412601053 3.060000e-05 60.2
41 TraesCS3D01G055000 chr2A 91.111 45 2 1 655 699 235229488 235229530 3.060000e-05 60.2
42 TraesCS3D01G055000 chr7D 100.000 29 0 0 655 683 428760591 428760619 1.000000e-03 54.7


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 TraesCS3D01G055000 chr3D 22725547 22728390 2843 True 5252.0 5252 100.0000 1 2844 1 chr3D.!!$R2 2843
1 TraesCS3D01G055000 chr3D 22737514 22738160 646 True 1179.0 1179 99.5360 1 647 1 chr3D.!!$R3 646
2 TraesCS3D01G055000 chr3D 575652234 575652884 650 True 1105.0 1105 97.3890 1 647 1 chr3D.!!$R4 646
3 TraesCS3D01G055000 chr3D 1580252 1580900 648 True 1103.0 1103 97.3810 1 647 1 chr3D.!!$R1 646
4 TraesCS3D01G055000 chr3D 23054639 23055312 673 False 656.0 656 84.4930 2160 2837 1 chr3D.!!$F2 677
5 TraesCS3D01G055000 chr3D 22929016 22930764 1748 False 417.0 564 85.4235 974 2590 2 chr3D.!!$F4 1616
6 TraesCS3D01G055000 chr3D 22384400 22385098 698 False 265.5 344 82.1715 2160 2837 2 chr3D.!!$F3 677
7 TraesCS3D01G055000 chr3B 40163358 40165732 2374 False 1524.0 2800 93.9605 754 2842 2 chr3B.!!$F2 2088
8 TraesCS3D01G055000 chr3B 40232037 40232709 672 False 610.0 610 83.3330 2160 2837 1 chr3B.!!$F1 677
9 TraesCS3D01G055000 chr3B 40192327 40193971 1644 False 342.5 422 83.2840 971 2590 2 chr3B.!!$F3 1619
10 TraesCS3D01G055000 chr6D 397184271 397184918 647 False 1127.0 1127 98.1480 3 647 1 chr6D.!!$F1 644
11 TraesCS3D01G055000 chrUn 141931437 141932083 646 True 1110.0 1110 97.6820 3 647 1 chrUn.!!$R1 644
12 TraesCS3D01G055000 chr2D 165379185 165379831 646 True 1107.0 1107 97.5310 1 647 1 chr2D.!!$R2 646
13 TraesCS3D01G055000 chr2D 560528813 560529460 647 True 1101.0 1101 97.3850 1 647 1 chr2D.!!$R3 646
14 TraesCS3D01G055000 chr5D 480387943 480388587 644 False 1103.0 1103 97.5230 3 647 1 chr5D.!!$F2 644
15 TraesCS3D01G055000 chr5D 518941673 518942322 649 True 1103.0 1103 97.3850 1 647 1 chr5D.!!$R1 646
16 TraesCS3D01G055000 chr3A 32142783 32143737 954 False 204.0 213 84.9855 2157 2844 2 chr3A.!!$F1 687

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
888 894 0.031585 TCTTTCGACACGTGTCCCTG 59.968 55.0 36.01 24.84 41.86 4.45 F
937 943 0.176910 CCCTCCTTCGCTTCTTCCTC 59.823 60.0 0.00 0.00 0.00 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1813 2269 0.251634 GTGCCTCCTCCTCCTTCTTG 59.748 60.0 0.00 0.0 0.0 3.02 R
2367 2900 0.826715 AGTGCACACAGACACAGAGT 59.173 50.0 21.04 0.0 39.3 3.24 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
32 33 2.939103 GCTTGCGAGTACTTTGGATGAT 59.061 45.455 2.14 0.00 0.00 2.45
117 120 1.393746 TGGAGTCCAGGAGCCAGAT 59.606 57.895 8.12 0.00 0.00 2.90
647 653 5.126699 AGGATCTTTTACTCCTCGACCTA 57.873 43.478 0.00 0.00 37.30 3.08
648 654 5.134661 AGGATCTTTTACTCCTCGACCTAG 58.865 45.833 0.00 0.00 37.30 3.02
649 655 4.278919 GGATCTTTTACTCCTCGACCTAGG 59.721 50.000 7.41 7.41 38.06 3.02
650 656 3.022406 TCTTTTACTCCTCGACCTAGGC 58.978 50.000 9.30 0.36 36.51 3.93
651 657 1.386533 TTTACTCCTCGACCTAGGCG 58.613 55.000 9.30 13.79 36.51 5.52
652 658 0.254178 TTACTCCTCGACCTAGGCGT 59.746 55.000 20.20 7.77 38.18 5.68
653 659 0.179062 TACTCCTCGACCTAGGCGTC 60.179 60.000 20.20 7.29 36.09 5.19
654 660 1.153127 CTCCTCGACCTAGGCGTCT 60.153 63.158 20.20 0.00 36.51 4.18
655 661 0.106335 CTCCTCGACCTAGGCGTCTA 59.894 60.000 20.20 0.00 36.51 2.59
656 662 0.106335 TCCTCGACCTAGGCGTCTAG 59.894 60.000 17.33 17.33 41.95 2.43
657 663 0.179051 CCTCGACCTAGGCGTCTAGT 60.179 60.000 21.96 10.64 40.98 2.57
658 664 0.938713 CTCGACCTAGGCGTCTAGTG 59.061 60.000 21.96 15.45 40.98 2.74
659 665 0.251354 TCGACCTAGGCGTCTAGTGT 59.749 55.000 21.96 18.31 40.98 3.55
660 666 1.482182 TCGACCTAGGCGTCTAGTGTA 59.518 52.381 21.96 4.12 40.98 2.90
661 667 1.596727 CGACCTAGGCGTCTAGTGTAC 59.403 57.143 21.96 9.48 40.98 2.90
662 668 1.596727 GACCTAGGCGTCTAGTGTACG 59.403 57.143 21.96 9.25 40.98 3.67
663 669 0.942962 CCTAGGCGTCTAGTGTACGG 59.057 60.000 21.96 3.33 40.98 4.02
664 670 1.661341 CTAGGCGTCTAGTGTACGGT 58.339 55.000 16.08 0.00 40.64 4.83
665 671 1.596727 CTAGGCGTCTAGTGTACGGTC 59.403 57.143 16.08 0.00 40.64 4.79
666 672 0.321919 AGGCGTCTAGTGTACGGTCA 60.322 55.000 0.00 0.00 40.64 4.02
667 673 0.523072 GGCGTCTAGTGTACGGTCAA 59.477 55.000 4.82 0.00 40.64 3.18
668 674 1.068333 GGCGTCTAGTGTACGGTCAAA 60.068 52.381 4.82 0.00 40.64 2.69
669 675 2.416431 GGCGTCTAGTGTACGGTCAAAT 60.416 50.000 4.82 0.00 40.64 2.32
670 676 2.850647 GCGTCTAGTGTACGGTCAAATC 59.149 50.000 4.82 0.00 40.64 2.17
671 677 3.096461 CGTCTAGTGTACGGTCAAATCG 58.904 50.000 0.00 0.00 36.71 3.34
672 678 3.432782 GTCTAGTGTACGGTCAAATCGG 58.567 50.000 0.00 0.00 0.00 4.18
673 679 2.424601 TCTAGTGTACGGTCAAATCGGG 59.575 50.000 0.00 0.00 0.00 5.14
674 680 0.248289 AGTGTACGGTCAAATCGGGG 59.752 55.000 0.00 0.00 0.00 5.73
675 681 0.741927 GTGTACGGTCAAATCGGGGG 60.742 60.000 0.00 0.00 0.00 5.40
676 682 1.816679 GTACGGTCAAATCGGGGGC 60.817 63.158 0.00 0.00 0.00 5.80
677 683 3.374012 TACGGTCAAATCGGGGGCG 62.374 63.158 0.00 0.00 0.00 6.13
678 684 4.770874 CGGTCAAATCGGGGGCGT 62.771 66.667 0.00 0.00 0.00 5.68
679 685 2.822701 GGTCAAATCGGGGGCGTC 60.823 66.667 0.00 0.00 0.00 5.19
680 686 2.046700 GTCAAATCGGGGGCGTCA 60.047 61.111 0.00 0.00 0.00 4.35
681 687 2.046700 TCAAATCGGGGGCGTCAC 60.047 61.111 0.00 0.00 0.00 3.67
682 688 2.359354 CAAATCGGGGGCGTCACA 60.359 61.111 0.00 0.00 0.00 3.58
683 689 1.748879 CAAATCGGGGGCGTCACAT 60.749 57.895 0.00 0.00 0.00 3.21
684 690 0.462937 CAAATCGGGGGCGTCACATA 60.463 55.000 0.00 0.00 0.00 2.29
685 691 0.179056 AAATCGGGGGCGTCACATAG 60.179 55.000 0.00 0.00 0.00 2.23
686 692 2.040009 AATCGGGGGCGTCACATAGG 62.040 60.000 0.00 0.00 0.00 2.57
687 693 4.910585 CGGGGGCGTCACATAGGC 62.911 72.222 0.00 0.00 38.28 3.93
696 702 3.416119 CGTCACATAGGCGTCTAGAAA 57.584 47.619 1.99 0.00 41.32 2.52
697 703 3.766151 CGTCACATAGGCGTCTAGAAAA 58.234 45.455 1.99 0.00 41.32 2.29
698 704 3.546670 CGTCACATAGGCGTCTAGAAAAC 59.453 47.826 1.99 0.00 41.32 2.43
699 705 4.491676 GTCACATAGGCGTCTAGAAAACA 58.508 43.478 1.99 0.00 0.00 2.83
700 706 4.326548 GTCACATAGGCGTCTAGAAAACAC 59.673 45.833 1.99 0.00 0.00 3.32
701 707 4.021807 TCACATAGGCGTCTAGAAAACACA 60.022 41.667 1.99 0.00 0.00 3.72
702 708 4.688879 CACATAGGCGTCTAGAAAACACAA 59.311 41.667 1.99 0.00 0.00 3.33
703 709 4.689345 ACATAGGCGTCTAGAAAACACAAC 59.311 41.667 1.99 0.00 0.00 3.32
704 710 3.188159 AGGCGTCTAGAAAACACAACA 57.812 42.857 0.00 0.00 0.00 3.33
705 711 3.537580 AGGCGTCTAGAAAACACAACAA 58.462 40.909 0.00 0.00 0.00 2.83
706 712 3.560068 AGGCGTCTAGAAAACACAACAAG 59.440 43.478 0.00 0.00 0.00 3.16
707 713 3.311596 GGCGTCTAGAAAACACAACAAGT 59.688 43.478 0.00 0.00 0.00 3.16
708 714 4.515432 GCGTCTAGAAAACACAACAAGTC 58.485 43.478 0.00 0.00 0.00 3.01
709 715 4.033587 GCGTCTAGAAAACACAACAAGTCA 59.966 41.667 0.00 0.00 0.00 3.41
710 716 5.277345 GCGTCTAGAAAACACAACAAGTCAT 60.277 40.000 0.00 0.00 0.00 3.06
711 717 6.129393 CGTCTAGAAAACACAACAAGTCATG 58.871 40.000 0.00 0.00 0.00 3.07
712 718 5.909610 GTCTAGAAAACACAACAAGTCATGC 59.090 40.000 0.00 0.00 0.00 4.06
713 719 4.045636 AGAAAACACAACAAGTCATGCC 57.954 40.909 0.00 0.00 0.00 4.40
714 720 2.888834 AAACACAACAAGTCATGCCC 57.111 45.000 0.00 0.00 0.00 5.36
715 721 2.071778 AACACAACAAGTCATGCCCT 57.928 45.000 0.00 0.00 0.00 5.19
716 722 1.321474 ACACAACAAGTCATGCCCTG 58.679 50.000 0.00 0.00 0.00 4.45
717 723 1.321474 CACAACAAGTCATGCCCTGT 58.679 50.000 0.00 0.00 0.00 4.00
718 724 1.682854 CACAACAAGTCATGCCCTGTT 59.317 47.619 0.00 0.00 0.00 3.16
719 725 1.682854 ACAACAAGTCATGCCCTGTTG 59.317 47.619 14.91 14.91 41.39 3.33
720 726 1.682854 CAACAAGTCATGCCCTGTTGT 59.317 47.619 9.54 2.13 33.96 3.32
721 727 1.321474 ACAAGTCATGCCCTGTTGTG 58.679 50.000 0.00 0.00 30.25 3.33
722 728 0.599558 CAAGTCATGCCCTGTTGTGG 59.400 55.000 0.00 0.00 0.00 4.17
745 751 2.161831 CACGATGTGGTCAATGCGT 58.838 52.632 0.00 0.00 33.02 5.24
746 752 0.179217 CACGATGTGGTCAATGCGTG 60.179 55.000 0.00 0.00 39.32 5.34
747 753 1.298157 ACGATGTGGTCAATGCGTGG 61.298 55.000 0.00 0.00 32.17 4.94
748 754 1.298157 CGATGTGGTCAATGCGTGGT 61.298 55.000 0.00 0.00 0.00 4.16
749 755 1.732941 GATGTGGTCAATGCGTGGTA 58.267 50.000 0.00 0.00 0.00 3.25
750 756 2.288666 GATGTGGTCAATGCGTGGTAT 58.711 47.619 0.00 0.00 0.00 2.73
751 757 1.447945 TGTGGTCAATGCGTGGTATG 58.552 50.000 0.00 0.00 0.00 2.39
752 758 0.732571 GTGGTCAATGCGTGGTATGG 59.267 55.000 0.00 0.00 0.00 2.74
761 767 2.530701 TGCGTGGTATGGGGAAATTTT 58.469 42.857 0.00 0.00 0.00 1.82
767 773 3.245300 TGGTATGGGGAAATTTTGGACGA 60.245 43.478 0.00 0.00 0.00 4.20
773 779 3.883489 GGGGAAATTTTGGACGATAGGAG 59.117 47.826 0.00 0.00 43.77 3.69
774 780 3.883489 GGGAAATTTTGGACGATAGGAGG 59.117 47.826 0.00 0.00 43.77 4.30
866 872 2.755650 TCCTGCAGAAGAAACTCGAAC 58.244 47.619 17.39 0.00 0.00 3.95
888 894 0.031585 TCTTTCGACACGTGTCCCTG 59.968 55.000 36.01 24.84 41.86 4.45
891 897 1.393487 TTCGACACGTGTCCCTGGAA 61.393 55.000 36.01 29.42 41.86 3.53
911 917 2.462723 ACTCCCACTCCTCTCTAAAGC 58.537 52.381 0.00 0.00 0.00 3.51
912 918 1.407258 CTCCCACTCCTCTCTAAAGCG 59.593 57.143 0.00 0.00 0.00 4.68
913 919 0.179097 CCCACTCCTCTCTAAAGCGC 60.179 60.000 0.00 0.00 0.00 5.92
914 920 0.526524 CCACTCCTCTCTAAAGCGCG 60.527 60.000 0.00 0.00 0.00 6.86
915 921 0.526524 CACTCCTCTCTAAAGCGCGG 60.527 60.000 8.83 0.00 0.00 6.46
916 922 1.590259 CTCCTCTCTAAAGCGCGGC 60.590 63.158 8.83 0.00 0.00 6.53
917 923 2.184322 CCTCTCTAAAGCGCGGCA 59.816 61.111 8.83 0.00 0.00 5.69
918 924 2.167861 CCTCTCTAAAGCGCGGCAC 61.168 63.158 8.83 0.00 0.00 5.01
919 925 2.125673 TCTCTAAAGCGCGGCACC 60.126 61.111 8.83 0.00 0.00 5.01
920 926 3.195698 CTCTAAAGCGCGGCACCC 61.196 66.667 8.83 0.00 0.00 4.61
921 927 3.665675 CTCTAAAGCGCGGCACCCT 62.666 63.158 8.83 0.00 0.00 4.34
922 928 3.195698 CTAAAGCGCGGCACCCTC 61.196 66.667 8.83 0.00 0.00 4.30
923 929 4.770874 TAAAGCGCGGCACCCTCC 62.771 66.667 8.83 0.00 0.00 4.30
930 936 4.394712 CGGCACCCTCCTTCGCTT 62.395 66.667 0.00 0.00 0.00 4.68
931 937 2.436824 GGCACCCTCCTTCGCTTC 60.437 66.667 0.00 0.00 0.00 3.86
932 938 2.665603 GCACCCTCCTTCGCTTCT 59.334 61.111 0.00 0.00 0.00 2.85
933 939 1.003233 GCACCCTCCTTCGCTTCTT 60.003 57.895 0.00 0.00 0.00 2.52
934 940 1.021920 GCACCCTCCTTCGCTTCTTC 61.022 60.000 0.00 0.00 0.00 2.87
935 941 0.391793 CACCCTCCTTCGCTTCTTCC 60.392 60.000 0.00 0.00 0.00 3.46
936 942 0.545548 ACCCTCCTTCGCTTCTTCCT 60.546 55.000 0.00 0.00 0.00 3.36
937 943 0.176910 CCCTCCTTCGCTTCTTCCTC 59.823 60.000 0.00 0.00 0.00 3.71
949 1188 1.303317 CTTCCTCCACAAACCCCCG 60.303 63.158 0.00 0.00 0.00 5.73
951 1190 3.576259 CCTCCACAAACCCCCGGT 61.576 66.667 0.00 0.00 37.65 5.28
952 1191 2.033602 CTCCACAAACCCCCGGTC 59.966 66.667 0.00 0.00 33.12 4.79
953 1192 3.562732 CTCCACAAACCCCCGGTCC 62.563 68.421 0.00 0.00 33.12 4.46
1179 1418 0.762418 TCTCGGACAAGAGCCCAAAA 59.238 50.000 0.00 0.00 38.12 2.44
1230 1469 1.448717 GCAAGGGGAGCTTCTCGTC 60.449 63.158 0.00 0.00 0.00 4.20
1323 1562 3.199946 ACTTCAAATCAGGCCTATCGGAA 59.800 43.478 3.98 5.40 0.00 4.30
1426 1674 6.092748 AGAAGCGTTTTGTTGGCTTATTATG 58.907 36.000 0.00 0.00 46.23 1.90
1427 1675 5.637006 AGCGTTTTGTTGGCTTATTATGA 57.363 34.783 0.00 0.00 31.91 2.15
1428 1676 6.019779 AGCGTTTTGTTGGCTTATTATGAA 57.980 33.333 0.00 0.00 31.91 2.57
1512 1895 0.964358 GGTTGATTCTGCTGCAGGCT 60.964 55.000 27.79 16.02 42.39 4.58
1570 1953 2.228545 TGAGGATCTCAGTGCACTCT 57.771 50.000 18.64 10.04 35.39 3.24
1583 1966 4.800993 CAGTGCACTCTTTACTTATCCTCG 59.199 45.833 18.64 0.00 0.00 4.63
1631 2033 0.984995 GGGCTCTTACCTGTTGGACT 59.015 55.000 0.00 0.00 37.04 3.85
1669 2071 1.748879 GGCGATTGCTACCAAGGCA 60.749 57.895 4.59 0.00 42.25 4.75
1700 2102 1.796017 GGAGGAGAGGGGTAAGGAAG 58.204 60.000 0.00 0.00 0.00 3.46
1744 2146 0.305922 CGGCGGCTCAGAAATTCATC 59.694 55.000 7.61 0.00 0.00 2.92
1811 2267 4.394610 GCTGGAAGAAGAAGAAGGATGAAC 59.605 45.833 0.00 0.00 34.07 3.18
1812 2268 4.911390 TGGAAGAAGAAGAAGGATGAACC 58.089 43.478 0.00 0.00 39.35 3.62
1813 2269 4.263506 TGGAAGAAGAAGAAGGATGAACCC 60.264 45.833 0.00 0.00 40.05 4.11
1817 2282 4.599241 AGAAGAAGAAGGATGAACCCAAGA 59.401 41.667 0.00 0.00 40.05 3.02
1848 2316 0.615850 GCACCCAAGAAGTAGAGGCT 59.384 55.000 0.00 0.00 0.00 4.58
1852 2320 2.979678 ACCCAAGAAGTAGAGGCTCAAA 59.020 45.455 18.26 0.78 0.00 2.69
1899 2367 4.681074 TTTTGTTCATTGAAAGGGGGTC 57.319 40.909 0.00 0.00 0.00 4.46
1900 2368 2.302587 TGTTCATTGAAAGGGGGTCC 57.697 50.000 0.00 0.00 0.00 4.46
1901 2369 1.203125 TGTTCATTGAAAGGGGGTCCC 60.203 52.381 0.00 0.00 45.90 4.46
2069 2579 6.886459 TGATGATGTTTCTTTTAAGGAGGAGG 59.114 38.462 0.00 0.00 0.00 4.30
2147 2666 1.443194 CCAATTGTGCTGCACGCTC 60.443 57.895 25.88 4.66 37.14 5.03
2172 2691 3.000925 CGTCGCATGACCCATTAGTTAAC 59.999 47.826 0.00 0.00 42.37 2.01
2194 2713 4.471386 ACTCTATGTAATGTTCAGGTGCCT 59.529 41.667 0.00 0.00 0.00 4.75
2339 2860 6.398918 GGTTGCTCTACATCTTACTTCTTCA 58.601 40.000 0.00 0.00 0.00 3.02
2365 2898 9.965902 ATCCTCTTTTCACAGACTTGTTATTAT 57.034 29.630 0.00 0.00 34.62 1.28
2366 2899 9.793259 TCCTCTTTTCACAGACTTGTTATTATT 57.207 29.630 0.00 0.00 34.62 1.40
2441 3232 2.829720 TCTAGTGCGGGTTTAGTGACAT 59.170 45.455 0.00 0.00 0.00 3.06
2446 3237 1.737793 GCGGGTTTAGTGACATCTTGG 59.262 52.381 0.00 0.00 0.00 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 2.029290 GGAGAGAAGCAACCGTGAGTAA 60.029 50.000 0.00 0.00 0.00 2.24
525 530 0.251916 CGGCCAAGGAGTGTGGATAA 59.748 55.000 2.24 0.00 38.54 1.75
647 653 0.321919 TGACCGTACACTAGACGCCT 60.322 55.000 0.00 0.00 38.99 5.52
648 654 0.523072 TTGACCGTACACTAGACGCC 59.477 55.000 0.00 0.00 38.99 5.68
649 655 2.336554 TTTGACCGTACACTAGACGC 57.663 50.000 0.00 0.00 38.99 5.19
650 656 3.096461 CGATTTGACCGTACACTAGACG 58.904 50.000 0.00 0.00 40.02 4.18
651 657 3.432782 CCGATTTGACCGTACACTAGAC 58.567 50.000 0.00 0.00 0.00 2.59
652 658 2.424601 CCCGATTTGACCGTACACTAGA 59.575 50.000 0.00 0.00 0.00 2.43
653 659 2.480759 CCCCGATTTGACCGTACACTAG 60.481 54.545 0.00 0.00 0.00 2.57
654 660 1.477700 CCCCGATTTGACCGTACACTA 59.522 52.381 0.00 0.00 0.00 2.74
655 661 0.248289 CCCCGATTTGACCGTACACT 59.752 55.000 0.00 0.00 0.00 3.55
656 662 0.741927 CCCCCGATTTGACCGTACAC 60.742 60.000 0.00 0.00 0.00 2.90
657 663 1.597989 CCCCCGATTTGACCGTACA 59.402 57.895 0.00 0.00 0.00 2.90
658 664 1.816679 GCCCCCGATTTGACCGTAC 60.817 63.158 0.00 0.00 0.00 3.67
659 665 2.585698 GCCCCCGATTTGACCGTA 59.414 61.111 0.00 0.00 0.00 4.02
660 666 4.770874 CGCCCCCGATTTGACCGT 62.771 66.667 0.00 0.00 36.29 4.83
661 667 4.770874 ACGCCCCCGATTTGACCG 62.771 66.667 0.00 0.00 38.29 4.79
662 668 2.822701 GACGCCCCCGATTTGACC 60.823 66.667 0.00 0.00 38.29 4.02
663 669 2.046700 TGACGCCCCCGATTTGAC 60.047 61.111 0.00 0.00 38.29 3.18
664 670 2.046700 GTGACGCCCCCGATTTGA 60.047 61.111 0.00 0.00 38.29 2.69
665 671 0.462937 TATGTGACGCCCCCGATTTG 60.463 55.000 0.00 0.00 38.29 2.32
666 672 0.179056 CTATGTGACGCCCCCGATTT 60.179 55.000 0.00 0.00 38.29 2.17
667 673 1.445942 CTATGTGACGCCCCCGATT 59.554 57.895 0.00 0.00 38.29 3.34
668 674 2.507854 CCTATGTGACGCCCCCGAT 61.508 63.158 0.00 0.00 38.29 4.18
669 675 3.151710 CCTATGTGACGCCCCCGA 61.152 66.667 0.00 0.00 38.29 5.14
670 676 4.910585 GCCTATGTGACGCCCCCG 62.911 72.222 0.00 0.00 41.14 5.73
671 677 4.910585 CGCCTATGTGACGCCCCC 62.911 72.222 0.00 0.00 0.00 5.40
672 678 4.157120 ACGCCTATGTGACGCCCC 62.157 66.667 0.00 0.00 0.00 5.80
673 679 1.731433 TAGACGCCTATGTGACGCCC 61.731 60.000 0.00 0.00 0.00 6.13
674 680 0.317938 CTAGACGCCTATGTGACGCC 60.318 60.000 0.00 0.00 0.00 5.68
675 681 0.661552 TCTAGACGCCTATGTGACGC 59.338 55.000 0.00 0.00 0.00 5.19
676 682 3.416119 TTTCTAGACGCCTATGTGACG 57.584 47.619 0.00 0.00 0.00 4.35
677 683 4.326548 GTGTTTTCTAGACGCCTATGTGAC 59.673 45.833 0.00 0.00 0.00 3.67
678 684 4.021807 TGTGTTTTCTAGACGCCTATGTGA 60.022 41.667 0.00 0.00 0.00 3.58
679 685 4.242475 TGTGTTTTCTAGACGCCTATGTG 58.758 43.478 0.00 0.00 0.00 3.21
680 686 4.530710 TGTGTTTTCTAGACGCCTATGT 57.469 40.909 0.00 0.00 0.00 2.29
681 687 4.688879 TGTTGTGTTTTCTAGACGCCTATG 59.311 41.667 0.00 0.00 0.00 2.23
682 688 4.890088 TGTTGTGTTTTCTAGACGCCTAT 58.110 39.130 0.00 0.00 0.00 2.57
683 689 4.325028 TGTTGTGTTTTCTAGACGCCTA 57.675 40.909 0.00 0.00 0.00 3.93
684 690 3.188159 TGTTGTGTTTTCTAGACGCCT 57.812 42.857 0.00 0.00 0.00 5.52
685 691 3.311596 ACTTGTTGTGTTTTCTAGACGCC 59.688 43.478 0.00 0.00 0.00 5.68
686 692 4.033587 TGACTTGTTGTGTTTTCTAGACGC 59.966 41.667 0.00 0.00 0.00 5.19
687 693 5.712217 TGACTTGTTGTGTTTTCTAGACG 57.288 39.130 0.00 0.00 0.00 4.18
688 694 5.909610 GCATGACTTGTTGTGTTTTCTAGAC 59.090 40.000 0.00 0.00 0.00 2.59
689 695 5.008613 GGCATGACTTGTTGTGTTTTCTAGA 59.991 40.000 0.00 0.00 0.00 2.43
690 696 5.215160 GGCATGACTTGTTGTGTTTTCTAG 58.785 41.667 0.00 0.00 0.00 2.43
691 697 4.037446 GGGCATGACTTGTTGTGTTTTCTA 59.963 41.667 0.00 0.00 0.00 2.10
692 698 3.181476 GGGCATGACTTGTTGTGTTTTCT 60.181 43.478 0.00 0.00 0.00 2.52
693 699 3.123050 GGGCATGACTTGTTGTGTTTTC 58.877 45.455 0.00 0.00 0.00 2.29
694 700 2.765699 AGGGCATGACTTGTTGTGTTTT 59.234 40.909 0.00 0.00 0.00 2.43
695 701 2.101249 CAGGGCATGACTTGTTGTGTTT 59.899 45.455 1.65 0.00 0.00 2.83
696 702 1.682854 CAGGGCATGACTTGTTGTGTT 59.317 47.619 1.65 0.00 0.00 3.32
697 703 1.321474 CAGGGCATGACTTGTTGTGT 58.679 50.000 1.65 0.00 0.00 3.72
698 704 1.321474 ACAGGGCATGACTTGTTGTG 58.679 50.000 11.17 0.00 0.00 3.33
699 705 1.682854 CAACAGGGCATGACTTGTTGT 59.317 47.619 36.16 14.37 33.96 3.32
700 706 1.682854 ACAACAGGGCATGACTTGTTG 59.317 47.619 40.04 40.04 41.39 3.33
701 707 1.682854 CACAACAGGGCATGACTTGTT 59.317 47.619 22.50 22.50 28.46 2.83
702 708 1.321474 CACAACAGGGCATGACTTGT 58.679 50.000 11.17 11.17 30.44 3.16
703 709 0.599558 CCACAACAGGGCATGACTTG 59.400 55.000 9.53 9.53 0.00 3.16
704 710 3.040965 CCACAACAGGGCATGACTT 57.959 52.632 5.99 0.00 0.00 3.01
705 711 4.828409 CCACAACAGGGCATGACT 57.172 55.556 5.99 0.00 0.00 3.41
727 733 0.179217 CACGCATTGACCACATCGTG 60.179 55.000 0.00 0.00 37.80 4.35
728 734 1.298157 CCACGCATTGACCACATCGT 61.298 55.000 0.00 0.00 0.00 3.73
729 735 1.298157 ACCACGCATTGACCACATCG 61.298 55.000 0.00 0.00 0.00 3.84
730 736 1.732941 TACCACGCATTGACCACATC 58.267 50.000 0.00 0.00 0.00 3.06
731 737 2.016318 CATACCACGCATTGACCACAT 58.984 47.619 0.00 0.00 0.00 3.21
732 738 1.447945 CATACCACGCATTGACCACA 58.552 50.000 0.00 0.00 0.00 4.17
733 739 0.732571 CCATACCACGCATTGACCAC 59.267 55.000 0.00 0.00 0.00 4.16
734 740 0.393673 CCCATACCACGCATTGACCA 60.394 55.000 0.00 0.00 0.00 4.02
735 741 1.101049 CCCCATACCACGCATTGACC 61.101 60.000 0.00 0.00 0.00 4.02
736 742 0.107410 TCCCCATACCACGCATTGAC 60.107 55.000 0.00 0.00 0.00 3.18
737 743 0.621082 TTCCCCATACCACGCATTGA 59.379 50.000 0.00 0.00 0.00 2.57
738 744 1.468985 TTTCCCCATACCACGCATTG 58.531 50.000 0.00 0.00 0.00 2.82
739 745 2.452600 ATTTCCCCATACCACGCATT 57.547 45.000 0.00 0.00 0.00 3.56
740 746 2.452600 AATTTCCCCATACCACGCAT 57.547 45.000 0.00 0.00 0.00 4.73
741 747 2.223803 AAATTTCCCCATACCACGCA 57.776 45.000 0.00 0.00 0.00 5.24
742 748 2.418060 CCAAAATTTCCCCATACCACGC 60.418 50.000 0.00 0.00 0.00 5.34
743 749 3.093057 TCCAAAATTTCCCCATACCACG 58.907 45.455 0.00 0.00 0.00 4.94
744 750 3.119280 CGTCCAAAATTTCCCCATACCAC 60.119 47.826 0.00 0.00 0.00 4.16
745 751 3.093057 CGTCCAAAATTTCCCCATACCA 58.907 45.455 0.00 0.00 0.00 3.25
746 752 3.358118 TCGTCCAAAATTTCCCCATACC 58.642 45.455 0.00 0.00 0.00 2.73
747 753 5.240844 CCTATCGTCCAAAATTTCCCCATAC 59.759 44.000 0.00 0.00 0.00 2.39
748 754 5.132985 TCCTATCGTCCAAAATTTCCCCATA 59.867 40.000 0.00 0.00 0.00 2.74
749 755 4.079443 TCCTATCGTCCAAAATTTCCCCAT 60.079 41.667 0.00 0.00 0.00 4.00
750 756 3.267291 TCCTATCGTCCAAAATTTCCCCA 59.733 43.478 0.00 0.00 0.00 4.96
751 757 3.883489 CTCCTATCGTCCAAAATTTCCCC 59.117 47.826 0.00 0.00 0.00 4.81
752 758 3.883489 CCTCCTATCGTCCAAAATTTCCC 59.117 47.826 0.00 0.00 0.00 3.97
761 767 1.850998 TCTTCCTCCTCCTATCGTCCA 59.149 52.381 0.00 0.00 0.00 4.02
767 773 3.643792 CCACGAATTCTTCCTCCTCCTAT 59.356 47.826 3.52 0.00 0.00 2.57
773 779 0.909623 TCCCCACGAATTCTTCCTCC 59.090 55.000 3.52 0.00 0.00 4.30
774 780 1.555533 AGTCCCCACGAATTCTTCCTC 59.444 52.381 3.52 0.00 0.00 3.71
851 857 3.014604 AGACCGTTCGAGTTTCTTCTG 57.985 47.619 0.00 0.00 0.00 3.02
888 894 2.830651 TAGAGAGGAGTGGGAGTTCC 57.169 55.000 0.00 0.00 0.00 3.62
891 897 2.462723 GCTTTAGAGAGGAGTGGGAGT 58.537 52.381 0.00 0.00 0.00 3.85
913 919 4.394712 AAGCGAAGGAGGGTGCCG 62.395 66.667 0.00 0.00 0.00 5.69
914 920 2.436824 GAAGCGAAGGAGGGTGCC 60.437 66.667 0.00 0.00 0.00 5.01
915 921 1.003233 AAGAAGCGAAGGAGGGTGC 60.003 57.895 0.00 0.00 0.00 5.01
916 922 0.391793 GGAAGAAGCGAAGGAGGGTG 60.392 60.000 0.00 0.00 0.00 4.61
917 923 0.545548 AGGAAGAAGCGAAGGAGGGT 60.546 55.000 0.00 0.00 0.00 4.34
918 924 0.176910 GAGGAAGAAGCGAAGGAGGG 59.823 60.000 0.00 0.00 0.00 4.30
919 925 0.176910 GGAGGAAGAAGCGAAGGAGG 59.823 60.000 0.00 0.00 0.00 4.30
920 926 0.898320 TGGAGGAAGAAGCGAAGGAG 59.102 55.000 0.00 0.00 0.00 3.69
921 927 0.608640 GTGGAGGAAGAAGCGAAGGA 59.391 55.000 0.00 0.00 0.00 3.36
922 928 0.321671 TGTGGAGGAAGAAGCGAAGG 59.678 55.000 0.00 0.00 0.00 3.46
923 929 2.169832 TTGTGGAGGAAGAAGCGAAG 57.830 50.000 0.00 0.00 0.00 3.79
924 930 2.218603 GTTTGTGGAGGAAGAAGCGAA 58.781 47.619 0.00 0.00 0.00 4.70
925 931 1.542547 GGTTTGTGGAGGAAGAAGCGA 60.543 52.381 0.00 0.00 0.00 4.93
926 932 0.875059 GGTTTGTGGAGGAAGAAGCG 59.125 55.000 0.00 0.00 0.00 4.68
927 933 1.248486 GGGTTTGTGGAGGAAGAAGC 58.752 55.000 0.00 0.00 0.00 3.86
928 934 1.547901 GGGGGTTTGTGGAGGAAGAAG 60.548 57.143 0.00 0.00 0.00 2.85
929 935 0.481128 GGGGGTTTGTGGAGGAAGAA 59.519 55.000 0.00 0.00 0.00 2.52
930 936 1.774894 CGGGGGTTTGTGGAGGAAGA 61.775 60.000 0.00 0.00 0.00 2.87
931 937 1.303317 CGGGGGTTTGTGGAGGAAG 60.303 63.158 0.00 0.00 0.00 3.46
932 938 2.836187 CCGGGGGTTTGTGGAGGAA 61.836 63.158 0.00 0.00 0.00 3.36
933 939 3.253838 CCGGGGGTTTGTGGAGGA 61.254 66.667 0.00 0.00 0.00 3.71
934 940 3.562732 GACCGGGGGTTTGTGGAGG 62.563 68.421 6.32 0.00 35.25 4.30
935 941 2.033602 GACCGGGGGTTTGTGGAG 59.966 66.667 6.32 0.00 35.25 3.86
936 942 3.572222 GGACCGGGGGTTTGTGGA 61.572 66.667 6.32 0.00 35.25 4.02
937 943 4.671590 GGGACCGGGGGTTTGTGG 62.672 72.222 6.32 0.00 35.25 4.17
949 1188 3.366739 CTACGCAAGACCGGGGACC 62.367 68.421 6.32 0.00 45.25 4.46
951 1190 2.283388 ACTACGCAAGACCGGGGA 60.283 61.111 6.32 0.00 43.62 4.81
952 1191 2.183555 GACTACGCAAGACCGGGG 59.816 66.667 6.32 0.00 43.62 5.73
953 1192 2.202570 CGACTACGCAAGACCGGG 60.203 66.667 6.32 0.00 43.62 5.73
1179 1418 4.681978 GCGCGGTCAAGGTGGTCT 62.682 66.667 8.83 0.00 0.00 3.85
1230 1469 1.740025 GAAATGACCTTGCCTTCCTCG 59.260 52.381 0.00 0.00 0.00 4.63
1323 1562 4.631813 GCAAAAGACGACTACCTGATGATT 59.368 41.667 0.00 0.00 0.00 2.57
1402 1641 4.584327 AATAAGCCAACAAAACGCTTCT 57.416 36.364 0.00 0.00 41.76 2.85
1405 1644 5.637006 TCATAATAAGCCAACAAAACGCT 57.363 34.783 0.00 0.00 0.00 5.07
1440 1691 1.304052 CCAATCAGGCCCAAACGGA 60.304 57.895 0.00 0.00 0.00 4.69
1512 1895 1.134759 CCCAATGATGGCGAAATTGCA 60.135 47.619 0.00 0.00 46.09 4.08
1583 1966 1.338136 ATGAGGATCCCACCGGTGAC 61.338 60.000 36.07 21.34 34.73 3.67
1607 2009 0.698818 AACAGGTAAGAGCCCCCAAG 59.301 55.000 0.00 0.00 0.00 3.61
1631 2033 3.018856 CCTTCATGTGAGGCTTGCATAA 58.981 45.455 5.22 0.00 0.00 1.90
1669 2071 0.984230 TCTCCTCCGCCTTGTCAATT 59.016 50.000 0.00 0.00 0.00 2.32
1700 2102 1.227853 ACTTGTCCGACCTTGCCAC 60.228 57.895 0.00 0.00 0.00 5.01
1744 2146 1.742761 AACTGTTGATGGCCTGATCG 58.257 50.000 3.32 0.00 0.00 3.69
1811 2267 1.631071 GCCTCCTCCTCCTTCTTGGG 61.631 65.000 0.00 0.00 36.20 4.12
1812 2268 0.911525 TGCCTCCTCCTCCTTCTTGG 60.912 60.000 0.00 0.00 37.10 3.61
1813 2269 0.251634 GTGCCTCCTCCTCCTTCTTG 59.748 60.000 0.00 0.00 0.00 3.02
1817 2282 2.285743 GGGTGCCTCCTCCTCCTT 60.286 66.667 0.00 0.00 36.25 3.36
1848 2316 1.789576 GCCCTCCTCCTTGGGTTTGA 61.790 60.000 0.00 0.00 45.06 2.69
1852 2320 2.936032 GTGCCCTCCTCCTTGGGT 60.936 66.667 0.00 0.00 45.06 4.51
1889 2357 3.339738 AATCGCGGGACCCCCTTTC 62.340 63.158 6.13 0.00 42.67 2.62
1908 2376 2.422276 AAAAACTGATTGGCGCAGTC 57.578 45.000 10.83 4.16 45.27 3.51
1949 2435 6.671190 CAACACATTGATAAGTTTGAGAGCA 58.329 36.000 0.00 0.00 38.15 4.26
2172 2691 4.813161 CAGGCACCTGAACATTACATAGAG 59.187 45.833 11.43 0.00 46.30 2.43
2194 2713 1.142060 ACAAGAACCGGGAACACATCA 59.858 47.619 6.32 0.00 0.00 3.07
2339 2860 9.965902 ATAATAACAAGTCTGTGAAAAGAGGAT 57.034 29.630 0.00 0.00 35.37 3.24
2365 2898 2.430694 AGTGCACACAGACACAGAGTAA 59.569 45.455 21.04 0.00 39.30 2.24
2366 2899 2.031870 AGTGCACACAGACACAGAGTA 58.968 47.619 21.04 0.00 39.30 2.59
2367 2900 0.826715 AGTGCACACAGACACAGAGT 59.173 50.000 21.04 0.00 39.30 3.24
2368 2901 1.596260 CAAGTGCACACAGACACAGAG 59.404 52.381 21.04 0.00 39.30 3.35
2369 2902 1.206849 TCAAGTGCACACAGACACAGA 59.793 47.619 21.04 0.14 39.30 3.41
2370 2903 1.655484 TCAAGTGCACACAGACACAG 58.345 50.000 21.04 0.00 39.30 3.66
2371 2904 2.158914 AGATCAAGTGCACACAGACACA 60.159 45.455 21.04 0.00 39.30 3.72
2372 2905 2.487934 AGATCAAGTGCACACAGACAC 58.512 47.619 21.04 10.84 37.05 3.67
2373 2906 2.916702 AGATCAAGTGCACACAGACA 57.083 45.000 21.04 0.00 0.00 3.41
2374 2907 4.058124 TGTAAGATCAAGTGCACACAGAC 58.942 43.478 21.04 7.40 0.00 3.51
2427 3218 3.053831 ACCAAGATGTCACTAAACCCG 57.946 47.619 0.00 0.00 0.00 5.28
2441 3232 3.835395 AGGAAACACAAAACCAACCAAGA 59.165 39.130 0.00 0.00 0.00 3.02
2446 3237 7.708998 TGTTATCTAGGAAACACAAAACCAAC 58.291 34.615 6.69 0.00 30.88 3.77


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

AutoCloner maintained by Alex Coulton.