Multiple sequence alignment - TraesCS2B01G577800

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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 TraesCS2B01G577800 chr2B 100.000 4628 0 0 1 4628 765924915 765920288 0.000000e+00 8547.0
1 TraesCS2B01G577800 chr2B 81.593 766 106 21 1 751 766014274 766013529 6.630000e-168 601.0
2 TraesCS2B01G577800 chr2B 90.517 116 9 2 748 862 418953671 418953557 8.020000e-33 152.0
3 TraesCS2B01G577800 chr2B 90.517 116 9 2 747 860 774087962 774087847 8.020000e-33 152.0
4 TraesCS2B01G577800 chr7D 91.420 3683 238 39 965 4628 534338042 534334419 0.000000e+00 4979.0
5 TraesCS2B01G577800 chr2D 89.931 2016 147 28 2650 4628 624096792 624094796 0.000000e+00 2547.0
6 TraesCS2B01G577800 chr2D 94.481 761 33 4 979 1735 624098639 624097884 0.000000e+00 1164.0
7 TraesCS2B01G577800 chr2D 90.374 748 61 6 1 744 624185236 624184496 0.000000e+00 972.0
8 TraesCS2B01G577800 chr2D 87.958 764 69 12 1 744 624102833 624102073 0.000000e+00 880.0
9 TraesCS2B01G577800 chr2D 89.816 599 50 5 2062 2651 624097470 624096874 0.000000e+00 758.0
10 TraesCS2B01G577800 chr2D 82.353 765 101 16 1 751 624195078 624194334 6.530000e-178 634.0
11 TraesCS2B01G577800 chr2D 85.271 516 54 13 67 572 624140080 624139577 3.190000e-141 512.0
12 TraesCS2B01G577800 chr2D 90.066 151 14 1 592 741 624132992 624132842 1.310000e-45 195.0
13 TraesCS2B01G577800 chr2D 91.071 112 10 0 858 969 624102076 624101965 8.020000e-33 152.0
14 TraesCS2B01G577800 chr2D 81.699 153 14 10 2518 2666 623758049 623758191 1.050000e-21 115.0
15 TraesCS2B01G577800 chr2A 94.022 1656 86 10 2976 4628 755365810 755364165 0.000000e+00 2497.0
16 TraesCS2B01G577800 chr2A 91.460 1007 72 13 1980 2978 755366891 755365891 0.000000e+00 1371.0
17 TraesCS2B01G577800 chr2A 94.588 850 35 7 1008 1856 755367832 755366993 0.000000e+00 1304.0
18 TraesCS2B01G577800 chr2A 85.227 792 89 17 3368 4153 755045619 755046388 0.000000e+00 789.0
19 TraesCS2B01G577800 chr2A 84.641 306 46 1 4146 4451 755047823 755048127 2.090000e-78 303.0
20 TraesCS2B01G577800 chr2A 84.817 191 28 1 517 706 755587038 755586848 1.700000e-44 191.0
21 TraesCS2B01G577800 chr2A 92.727 110 7 1 746 855 619208137 619208029 1.720000e-34 158.0
22 TraesCS2B01G577800 chr2A 96.970 33 1 0 973 1005 755399702 755399670 6.470000e-04 56.5
23 TraesCS2B01G577800 chr4B 89.623 424 33 4 2068 2483 378001367 378001787 3.170000e-146 529.0
24 TraesCS2B01G577800 chr4B 89.151 424 35 4 2068 2483 14570294 14569874 6.860000e-143 518.0
25 TraesCS2B01G577800 chr4B 85.507 276 34 4 2917 3190 378002139 378002410 2.730000e-72 283.0
26 TraesCS2B01G577800 chr4B 84.722 288 36 6 2917 3201 14569522 14569240 9.800000e-72 281.0
27 TraesCS2B01G577800 chr4B 90.517 116 10 1 743 857 186741780 186741665 8.020000e-33 152.0
28 TraesCS2B01G577800 chr6D 85.915 213 25 4 102 313 56853648 56853440 6.030000e-54 222.0
29 TraesCS2B01G577800 chr6D 90.517 116 7 4 738 852 466538116 466538228 2.880000e-32 150.0
30 TraesCS2B01G577800 chr6D 88.043 92 11 0 1795 1886 318960155 318960246 4.900000e-20 110.0
31 TraesCS2B01G577800 chr6A 82.203 236 35 4 85 315 592700115 592699882 3.650000e-46 196.0
32 TraesCS2B01G577800 chr1D 88.608 158 18 0 3044 3201 437804167 437804324 4.730000e-45 193.0
33 TraesCS2B01G577800 chrUn 88.387 155 18 0 3047 3201 256117882 256117728 2.200000e-43 187.0
34 TraesCS2B01G577800 chrUn 87.975 158 19 0 3044 3201 342150559 342150716 2.200000e-43 187.0
35 TraesCS2B01G577800 chrUn 87.975 158 19 0 3044 3201 342153049 342153206 2.200000e-43 187.0
36 TraesCS2B01G577800 chr3A 79.845 258 38 7 68 319 156264806 156265055 4.760000e-40 176.0
37 TraesCS2B01G577800 chr6B 86.395 147 14 6 711 853 336181360 336181216 6.200000e-34 156.0
38 TraesCS2B01G577800 chr5B 91.892 111 8 1 750 859 561916996 561917106 2.230000e-33 154.0
39 TraesCS2B01G577800 chr3B 91.892 111 8 1 750 859 629921371 629921481 2.230000e-33 154.0
40 TraesCS2B01G577800 chr3B 93.939 99 6 0 756 854 5951427 5951329 2.880000e-32 150.0
41 TraesCS2B01G577800 chr3D 80.193 207 29 10 113 313 160475559 160475759 1.340000e-30 145.0
42 TraesCS2B01G577800 chr7A 79.812 213 30 11 113 319 307462653 307462448 4.830000e-30 143.0
43 TraesCS2B01G577800 chr1B 80.296 203 28 10 113 309 313761617 313761421 4.830000e-30 143.0
44 TraesCS2B01G577800 chr4A 79.343 213 32 10 113 319 403748174 403747968 6.240000e-29 139.0


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 TraesCS2B01G577800 chr2B 765920288 765924915 4627 True 8547.0 8547 100.000000 1 4628 1 chr2B.!!$R2 4627
1 TraesCS2B01G577800 chr2B 766013529 766014274 745 True 601.0 601 81.593000 1 751 1 chr2B.!!$R3 750
2 TraesCS2B01G577800 chr7D 534334419 534338042 3623 True 4979.0 4979 91.420000 965 4628 1 chr7D.!!$R1 3663
3 TraesCS2B01G577800 chr2D 624094796 624102833 8037 True 1100.2 2547 90.651400 1 4628 5 chr2D.!!$R5 4627
4 TraesCS2B01G577800 chr2D 624184496 624185236 740 True 972.0 972 90.374000 1 744 1 chr2D.!!$R3 743
5 TraesCS2B01G577800 chr2D 624194334 624195078 744 True 634.0 634 82.353000 1 751 1 chr2D.!!$R4 750
6 TraesCS2B01G577800 chr2D 624139577 624140080 503 True 512.0 512 85.271000 67 572 1 chr2D.!!$R2 505
7 TraesCS2B01G577800 chr2A 755364165 755367832 3667 True 1724.0 2497 93.356667 1008 4628 3 chr2A.!!$R4 3620
8 TraesCS2B01G577800 chr2A 755045619 755048127 2508 False 546.0 789 84.934000 3368 4451 2 chr2A.!!$F1 1083
9 TraesCS2B01G577800 chr4B 378001367 378002410 1043 False 406.0 529 87.565000 2068 3190 2 chr4B.!!$F1 1122
10 TraesCS2B01G577800 chr4B 14569240 14570294 1054 True 399.5 518 86.936500 2068 3201 2 chr4B.!!$R2 1133

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
848 883 0.393267 CTTATTTTGGGACGGCGGGA 60.393 55.000 13.24 0.0 0.0 5.14 F
849 884 0.393267 TTATTTTGGGACGGCGGGAG 60.393 55.000 13.24 0.0 0.0 4.30 F
856 891 0.683412 GGGACGGCGGGAGTATAAAT 59.317 55.000 13.24 0.0 0.0 1.40 F
857 892 1.071228 GGGACGGCGGGAGTATAAATT 59.929 52.381 13.24 0.0 0.0 1.82 F
2134 5684 2.099141 TCTTTTGGATGCTCAGGTCG 57.901 50.000 0.00 0.0 0.0 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2540 6106 2.550606 TGTACATGTTTGACCGCCTTTC 59.449 45.455 2.30 0.0 0.00 2.62 R
2544 6110 5.050363 CACTATATGTACATGTTTGACCGCC 60.050 44.000 18.81 0.0 0.00 6.13 R
2767 6418 6.545298 AGATATGGAAAAGAGAGGCAAACATC 59.455 38.462 0.00 0.0 0.00 3.06 R
2859 6515 5.163447 ACACTGCATAAGCGATAAAGTCCTA 60.163 40.000 0.00 0.0 46.23 2.94 R
3641 7420 0.036765 TTTTCGTGGAGGATCGGTGG 60.037 55.000 0.00 0.0 34.37 4.61 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
53 54 4.458989 GGGCCTATTTGATTCGCATGATTA 59.541 41.667 0.84 0.00 0.00 1.75
64 65 8.382030 TGATTCGCATGATTATAAGAACATGT 57.618 30.769 20.59 0.00 41.14 3.21
95 106 1.415289 TCGAATGGCATGCTCATCTCT 59.585 47.619 18.92 4.74 0.00 3.10
98 109 4.001652 CGAATGGCATGCTCATCTCTATT 58.998 43.478 18.92 4.13 0.00 1.73
180 195 4.697514 TGAGTGCATGCTAGAAATCCTAC 58.302 43.478 20.33 4.24 0.00 3.18
186 201 4.703897 CATGCTAGAAATCCTACGGGAAA 58.296 43.478 0.00 0.00 45.78 3.13
257 274 9.941664 CTATGAATAAACAAGCAACATAGGAAG 57.058 33.333 0.00 0.00 34.96 3.46
302 319 9.707957 TCCTCCAAAATTCCTATAAAAATGCTA 57.292 29.630 0.00 0.00 0.00 3.49
413 430 4.527038 TCCTATATGGTTCGAGATCCAACC 59.473 45.833 10.59 10.59 42.28 3.77
425 442 1.959282 GATCCAACCCCTTCATGATGC 59.041 52.381 0.00 0.00 0.00 3.91
588 616 1.382914 AAGTGGGGCCCTGTATTTCT 58.617 50.000 25.93 6.88 0.00 2.52
590 618 2.789219 AGTGGGGCCCTGTATTTCTAT 58.211 47.619 25.93 0.00 0.00 1.98
598 626 5.598417 GGGCCCTGTATTTCTATCAATGTTT 59.402 40.000 17.04 0.00 0.00 2.83
672 702 0.537188 AGCATCACGTTGGGAGGTAG 59.463 55.000 0.00 0.00 0.00 3.18
683 713 4.014406 GTTGGGAGGTAGGTGTATTTTGG 58.986 47.826 0.00 0.00 0.00 3.28
693 723 9.054580 AGGTAGGTGTATTTTGGTCTAGTATTT 57.945 33.333 0.00 0.00 0.00 1.40
769 804 8.434392 TGTATAATGTATTACTCCCTTTGTCCC 58.566 37.037 0.00 0.00 0.00 4.46
770 805 5.789574 AATGTATTACTCCCTTTGTCCCA 57.210 39.130 0.00 0.00 0.00 4.37
771 806 5.789574 ATGTATTACTCCCTTTGTCCCAA 57.210 39.130 0.00 0.00 0.00 4.12
772 807 5.586155 TGTATTACTCCCTTTGTCCCAAA 57.414 39.130 0.00 0.00 0.00 3.28
773 808 5.954757 TGTATTACTCCCTTTGTCCCAAAA 58.045 37.500 0.00 0.00 0.00 2.44
774 809 6.557568 TGTATTACTCCCTTTGTCCCAAAAT 58.442 36.000 0.00 0.00 0.00 1.82
775 810 7.700846 TGTATTACTCCCTTTGTCCCAAAATA 58.299 34.615 0.00 0.00 0.00 1.40
776 811 8.171400 TGTATTACTCCCTTTGTCCCAAAATAA 58.829 33.333 0.00 0.00 0.00 1.40
777 812 7.718334 ATTACTCCCTTTGTCCCAAAATAAG 57.282 36.000 0.00 0.00 0.00 1.73
778 813 5.074746 ACTCCCTTTGTCCCAAAATAAGT 57.925 39.130 0.00 0.00 0.00 2.24
779 814 4.832823 ACTCCCTTTGTCCCAAAATAAGTG 59.167 41.667 0.00 0.00 0.00 3.16
780 815 4.810345 TCCCTTTGTCCCAAAATAAGTGT 58.190 39.130 0.00 0.00 0.00 3.55
781 816 4.830600 TCCCTTTGTCCCAAAATAAGTGTC 59.169 41.667 0.00 0.00 0.00 3.67
782 817 4.832823 CCCTTTGTCCCAAAATAAGTGTCT 59.167 41.667 0.00 0.00 0.00 3.41
783 818 5.048013 CCCTTTGTCCCAAAATAAGTGTCTC 60.048 44.000 0.00 0.00 0.00 3.36
784 819 5.534654 CCTTTGTCCCAAAATAAGTGTCTCA 59.465 40.000 0.00 0.00 0.00 3.27
785 820 6.040391 CCTTTGTCCCAAAATAAGTGTCTCAA 59.960 38.462 0.00 0.00 0.00 3.02
786 821 6.385649 TTGTCCCAAAATAAGTGTCTCAAC 57.614 37.500 0.00 0.00 0.00 3.18
787 822 5.690865 TGTCCCAAAATAAGTGTCTCAACT 58.309 37.500 0.00 0.00 0.00 3.16
788 823 6.126409 TGTCCCAAAATAAGTGTCTCAACTT 58.874 36.000 0.00 0.00 42.89 2.66
789 824 6.605594 TGTCCCAAAATAAGTGTCTCAACTTT 59.394 34.615 0.00 0.00 40.77 2.66
790 825 6.918022 GTCCCAAAATAAGTGTCTCAACTTTG 59.082 38.462 0.00 0.00 40.77 2.77
791 826 6.605594 TCCCAAAATAAGTGTCTCAACTTTGT 59.394 34.615 0.00 0.00 40.77 2.83
792 827 7.776030 TCCCAAAATAAGTGTCTCAACTTTGTA 59.224 33.333 0.00 0.00 40.77 2.41
793 828 7.860872 CCCAAAATAAGTGTCTCAACTTTGTAC 59.139 37.037 0.00 0.00 40.77 2.90
794 829 8.621286 CCAAAATAAGTGTCTCAACTTTGTACT 58.379 33.333 0.00 0.00 40.77 2.73
797 832 8.535690 AATAAGTGTCTCAACTTTGTACTAGC 57.464 34.615 0.00 0.00 40.77 3.42
798 833 5.793030 AGTGTCTCAACTTTGTACTAGCT 57.207 39.130 0.00 0.00 0.00 3.32
799 834 5.774630 AGTGTCTCAACTTTGTACTAGCTC 58.225 41.667 0.00 0.00 0.00 4.09
800 835 5.536916 AGTGTCTCAACTTTGTACTAGCTCT 59.463 40.000 0.00 0.00 0.00 4.09
801 836 6.715718 AGTGTCTCAACTTTGTACTAGCTCTA 59.284 38.462 0.00 0.00 0.00 2.43
802 837 7.024768 GTGTCTCAACTTTGTACTAGCTCTAG 58.975 42.308 0.00 2.55 39.04 2.43
804 839 7.881751 TGTCTCAACTTTGTACTAGCTCTAGTA 59.118 37.037 11.59 11.59 43.98 1.82
805 840 8.895737 GTCTCAACTTTGTACTAGCTCTAGTAT 58.104 37.037 16.96 1.87 46.57 2.12
840 875 9.856162 ACTAAGTTTAAGACACTTATTTTGGGA 57.144 29.630 0.00 0.00 36.39 4.37
842 877 7.198306 AGTTTAAGACACTTATTTTGGGACG 57.802 36.000 0.00 0.00 0.00 4.79
843 878 6.206048 AGTTTAAGACACTTATTTTGGGACGG 59.794 38.462 0.00 0.00 0.00 4.79
844 879 2.433436 AGACACTTATTTTGGGACGGC 58.567 47.619 0.00 0.00 0.00 5.68
845 880 1.129811 GACACTTATTTTGGGACGGCG 59.870 52.381 4.80 4.80 0.00 6.46
846 881 0.450184 CACTTATTTTGGGACGGCGG 59.550 55.000 13.24 0.00 0.00 6.13
847 882 0.678684 ACTTATTTTGGGACGGCGGG 60.679 55.000 13.24 0.00 0.00 6.13
848 883 0.393267 CTTATTTTGGGACGGCGGGA 60.393 55.000 13.24 0.00 0.00 5.14
849 884 0.393267 TTATTTTGGGACGGCGGGAG 60.393 55.000 13.24 0.00 0.00 4.30
850 885 1.555477 TATTTTGGGACGGCGGGAGT 61.555 55.000 13.24 0.00 0.00 3.85
851 886 1.555477 ATTTTGGGACGGCGGGAGTA 61.555 55.000 13.24 0.00 0.00 2.59
852 887 1.555477 TTTTGGGACGGCGGGAGTAT 61.555 55.000 13.24 0.00 0.00 2.12
853 888 0.687098 TTTGGGACGGCGGGAGTATA 60.687 55.000 13.24 0.00 0.00 1.47
854 889 0.687098 TTGGGACGGCGGGAGTATAA 60.687 55.000 13.24 0.00 0.00 0.98
855 890 0.687098 TGGGACGGCGGGAGTATAAA 60.687 55.000 13.24 0.00 0.00 1.40
856 891 0.683412 GGGACGGCGGGAGTATAAAT 59.317 55.000 13.24 0.00 0.00 1.40
857 892 1.071228 GGGACGGCGGGAGTATAAATT 59.929 52.381 13.24 0.00 0.00 1.82
863 898 6.650390 GGACGGCGGGAGTATAAATTTATAAA 59.350 38.462 17.49 0.00 0.00 1.40
912 947 5.643777 GGTGTGTGTATTCTCAATGTAGCTT 59.356 40.000 0.00 0.00 0.00 3.74
928 963 9.941664 CAATGTAGCTTCCATTATCTAACAAAG 57.058 33.333 10.05 0.00 31.52 2.77
960 995 4.355543 TTGCAAAGTGTGACTTGAAGAC 57.644 40.909 0.00 0.00 38.66 3.01
962 997 3.126858 TGCAAAGTGTGACTTGAAGACAC 59.873 43.478 18.39 18.39 38.66 3.67
1006 4357 6.924612 TGTTTGTGGAGTTTTCATCATGAATG 59.075 34.615 0.00 0.00 36.11 2.67
1082 4440 4.741239 GCACCCCTCTCCCTCCCA 62.741 72.222 0.00 0.00 0.00 4.37
1459 4826 4.019983 CCGAGTACTGGCTCCTGT 57.980 61.111 0.00 3.94 32.11 4.00
1900 5267 7.010552 CCAAGGAAGTGACTTACTATGAAATCG 59.989 40.741 11.06 0.00 39.18 3.34
1911 5278 8.684520 ACTTACTATGAAATCGCACTAGTTAGT 58.315 33.333 0.00 0.00 36.90 2.24
1916 5283 9.731819 CTATGAAATCGCACTAGTTAGTAAGAA 57.268 33.333 0.00 0.00 34.13 2.52
1956 5323 3.085533 AGTCTGTGTGTGCCTAGTAGAG 58.914 50.000 0.00 0.00 0.00 2.43
2054 5604 5.300286 ACTTTTATGCAAGTGAAGTGAAGCT 59.700 36.000 0.00 0.00 35.57 3.74
2134 5684 2.099141 TCTTTTGGATGCTCAGGTCG 57.901 50.000 0.00 0.00 0.00 4.79
2507 6065 7.386299 GCTATCTGGATTACATCTTGTACTTGG 59.614 40.741 0.00 0.00 31.69 3.61
2511 6069 6.346096 TGGATTACATCTTGTACTTGGCTAC 58.654 40.000 0.00 0.00 31.69 3.58
2549 6115 7.502226 TCATCATTAATTTCATAGAAAGGCGGT 59.498 33.333 0.00 0.00 0.00 5.68
2598 6164 5.853572 TTTACTTCTTGACCCTGGGTTAT 57.146 39.130 21.59 2.67 35.25 1.89
2775 6426 9.455847 CTAGCCTTTTCAAATATAGATGTTTGC 57.544 33.333 6.81 0.00 38.34 3.68
2785 6436 9.727627 CAAATATAGATGTTTGCCTCTCTTTTC 57.272 33.333 0.00 0.00 33.32 2.29
2786 6437 8.457238 AATATAGATGTTTGCCTCTCTTTTCC 57.543 34.615 0.00 0.00 0.00 3.13
2794 6447 7.402054 TGTTTGCCTCTCTTTTCCATATCTAA 58.598 34.615 0.00 0.00 0.00 2.10
2889 6551 6.525121 TTATCGCTTATGCAGTGTACATTC 57.475 37.500 0.00 0.00 39.64 2.67
2909 6592 3.345414 TCGTAGAACTCCTGAGGTTCTC 58.655 50.000 7.55 0.00 46.96 2.87
2967 6662 3.314541 AACTAGCACTAGGTTGTTCCG 57.685 47.619 9.41 0.00 36.70 4.30
2971 6666 1.140252 AGCACTAGGTTGTTCCGTTGT 59.860 47.619 0.00 0.00 41.99 3.32
2986 6764 6.370442 TGTTCCGTTGTTTTGTATATCTGAGG 59.630 38.462 0.00 0.00 0.00 3.86
2990 6768 6.542370 CCGTTGTTTTGTATATCTGAGGGAAT 59.458 38.462 0.00 0.00 0.00 3.01
2991 6769 7.254795 CCGTTGTTTTGTATATCTGAGGGAATC 60.255 40.741 0.00 0.00 0.00 2.52
2992 6770 7.279981 CGTTGTTTTGTATATCTGAGGGAATCA 59.720 37.037 0.00 0.00 36.21 2.57
3237 7015 0.598065 GTGACACCCCAAGTTCATGC 59.402 55.000 0.00 0.00 0.00 4.06
3243 7021 1.026718 CCCCAAGTTCATGCCGTCTC 61.027 60.000 0.00 0.00 0.00 3.36
3488 7266 3.441101 ACAGTCACCATAGTAGCAAGGA 58.559 45.455 0.00 0.00 0.00 3.36
3494 7272 3.701542 CACCATAGTAGCAAGGACTCTGA 59.298 47.826 0.00 0.00 0.00 3.27
3502 7280 1.072331 GCAAGGACTCTGACCCAGAAA 59.928 52.381 0.00 0.00 40.18 2.52
3641 7420 3.954904 TGTACCTGACCATCTCTCTTAGC 59.045 47.826 0.00 0.00 0.00 3.09
3668 7447 1.630244 CCTCCACGAAAAGCTCAGCG 61.630 60.000 0.00 0.00 0.00 5.18
3732 7514 3.244735 TGAGCATGTAACAGTAGGCCAAA 60.245 43.478 5.01 0.00 0.00 3.28
3745 7527 0.453390 GGCCAAAGCTTCTTCATCCG 59.547 55.000 0.00 0.00 39.73 4.18
3782 7572 5.397142 GGAATGATTTCCCATATTGCTCC 57.603 43.478 0.00 0.00 44.96 4.70
3833 7625 6.088016 TCACTGAAGAAATTGTCCATTTGG 57.912 37.500 0.00 0.00 35.02 3.28
3989 7791 1.903877 CTGGTGCCAGTACAGGAGGG 61.904 65.000 8.77 0.00 39.10 4.30
4173 9417 1.451028 GCCTGATCCCAGCTGACAC 60.451 63.158 17.39 4.29 39.07 3.67
4261 9510 0.100682 ACGCGTGCGATATTCTGTCT 59.899 50.000 22.32 0.00 42.83 3.41
4263 9512 2.031069 ACGCGTGCGATATTCTGTCTAT 60.031 45.455 22.32 0.00 42.83 1.98
4421 9670 0.598419 GCAAAGCCTGTGAAGCCAAC 60.598 55.000 0.00 0.00 0.00 3.77
4446 9695 2.812591 CAAGCAGATGCAGAAACTCAGT 59.187 45.455 7.68 0.00 45.16 3.41
4451 9700 4.082895 GCAGATGCAGAAACTCAGTGAAAT 60.083 41.667 0.00 0.00 41.59 2.17
4460 9710 7.646314 CAGAAACTCAGTGAAATGAACAGATT 58.354 34.615 0.00 0.00 0.00 2.40
4468 9718 7.714813 TCAGTGAAATGAACAGATTGTCAAGTA 59.285 33.333 0.00 0.00 0.00 2.24
4487 9738 5.888982 AGTATAATGGGGTGTTACAGGAG 57.111 43.478 0.00 0.00 0.00 3.69
4489 9740 1.072266 AATGGGGTGTTACAGGAGCA 58.928 50.000 0.00 0.00 0.00 4.26
4494 9745 2.039348 GGGGTGTTACAGGAGCAGTAAA 59.961 50.000 0.00 0.00 33.64 2.01
4502 9753 3.074412 ACAGGAGCAGTAAACCATTTCG 58.926 45.455 0.00 0.00 0.00 3.46
4529 9780 4.529219 TCGCCGCCGCTCATCATT 62.529 61.111 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 5.551233 CGAATCAAATAGGCCCTGATTCTA 58.449 41.667 27.65 6.91 46.98 2.10
64 65 5.764686 AGCATGCCATTCGAATACTTATTCA 59.235 36.000 15.66 2.05 41.59 2.57
70 71 3.198409 TGAGCATGCCATTCGAATACT 57.802 42.857 15.66 1.83 0.00 2.12
76 87 1.880271 AGAGATGAGCATGCCATTCG 58.120 50.000 15.66 0.00 0.00 3.34
98 109 7.953005 TGCAATCAAACCAAAATCCTATAGA 57.047 32.000 0.00 0.00 0.00 1.98
180 195 6.267496 AGGATTTCTTTGTACAATTTCCCG 57.733 37.500 9.56 0.00 0.00 5.14
222 238 8.579850 TGCTTGTTTATTCATAGGACTGAATT 57.420 30.769 4.79 0.00 41.89 2.17
293 310 6.042437 GGGATCCTTGGATTCATAGCATTTTT 59.958 38.462 12.58 0.00 0.00 1.94
299 316 3.795688 TGGGATCCTTGGATTCATAGC 57.204 47.619 12.58 0.00 0.00 2.97
302 319 3.853207 CCATTGGGATCCTTGGATTCAT 58.147 45.455 18.60 0.00 35.59 2.57
413 430 7.597743 GCTTTTAATATTCAGCATCATGAAGGG 59.402 37.037 0.00 0.00 42.20 3.95
483 504 9.941325 AAAATCAAGTATGTGCCAATTATTTCA 57.059 25.926 0.00 0.00 0.00 2.69
560 588 0.835971 GGGCCCCACTTTTCCACAAT 60.836 55.000 12.23 0.00 0.00 2.71
598 626 5.822519 GGTGGAGACAATTGATAATGTGCTA 59.177 40.000 13.59 0.00 46.06 3.49
610 638 3.814504 AGAACCATGGTGGAGACAATT 57.185 42.857 20.60 0.00 46.06 2.32
618 646 1.984026 GCCCCAAGAACCATGGTGG 60.984 63.158 20.60 15.24 45.02 4.61
672 702 7.827729 AGTCCAAATACTAGACCAAAATACACC 59.172 37.037 0.00 0.00 0.00 4.16
743 778 8.434392 GGGACAAAGGGAGTAATACATTATACA 58.566 37.037 0.00 0.00 0.00 2.29
744 779 8.434392 TGGGACAAAGGGAGTAATACATTATAC 58.566 37.037 0.00 0.00 31.92 1.47
745 780 8.570038 TGGGACAAAGGGAGTAATACATTATA 57.430 34.615 0.00 0.00 31.92 0.98
746 781 7.460214 TGGGACAAAGGGAGTAATACATTAT 57.540 36.000 0.00 0.00 31.92 1.28
747 782 6.894735 TGGGACAAAGGGAGTAATACATTA 57.105 37.500 0.00 0.00 31.92 1.90
748 783 5.789574 TGGGACAAAGGGAGTAATACATT 57.210 39.130 0.00 0.00 31.92 2.71
762 797 7.123547 AAGTTGAGACACTTATTTTGGGACAAA 59.876 33.333 0.00 0.00 38.34 2.83
763 798 6.605594 AAGTTGAGACACTTATTTTGGGACAA 59.394 34.615 0.00 0.00 38.34 3.18
764 799 5.690865 AGTTGAGACACTTATTTTGGGACA 58.309 37.500 0.00 0.00 0.00 4.02
765 800 6.635030 AAGTTGAGACACTTATTTTGGGAC 57.365 37.500 0.00 0.00 35.10 4.46
766 801 6.605594 ACAAAGTTGAGACACTTATTTTGGGA 59.394 34.615 0.00 0.00 35.87 4.37
767 802 6.805713 ACAAAGTTGAGACACTTATTTTGGG 58.194 36.000 0.00 0.00 35.87 4.12
768 803 8.621286 AGTACAAAGTTGAGACACTTATTTTGG 58.379 33.333 0.00 0.00 35.87 3.28
771 806 8.989980 GCTAGTACAAAGTTGAGACACTTATTT 58.010 33.333 0.00 0.00 35.87 1.40
772 807 8.368668 AGCTAGTACAAAGTTGAGACACTTATT 58.631 33.333 0.00 0.00 35.87 1.40
773 808 7.897864 AGCTAGTACAAAGTTGAGACACTTAT 58.102 34.615 0.00 0.00 35.87 1.73
774 809 7.230913 AGAGCTAGTACAAAGTTGAGACACTTA 59.769 37.037 0.00 0.00 35.87 2.24
775 810 6.041069 AGAGCTAGTACAAAGTTGAGACACTT 59.959 38.462 0.00 0.00 38.74 3.16
776 811 5.536916 AGAGCTAGTACAAAGTTGAGACACT 59.463 40.000 0.00 0.00 0.00 3.55
777 812 5.774630 AGAGCTAGTACAAAGTTGAGACAC 58.225 41.667 0.00 0.00 0.00 3.67
778 813 6.715718 ACTAGAGCTAGTACAAAGTTGAGACA 59.284 38.462 8.35 0.00 43.98 3.41
779 814 7.148355 ACTAGAGCTAGTACAAAGTTGAGAC 57.852 40.000 8.35 0.00 43.98 3.36
814 849 9.856162 TCCCAAAATAAGTGTCTTAAACTTAGT 57.144 29.630 4.92 0.14 41.95 2.24
816 851 8.776470 CGTCCCAAAATAAGTGTCTTAAACTTA 58.224 33.333 1.70 1.70 42.63 2.24
817 852 7.255346 CCGTCCCAAAATAAGTGTCTTAAACTT 60.255 37.037 0.00 0.00 40.82 2.66
818 853 6.206048 CCGTCCCAAAATAAGTGTCTTAAACT 59.794 38.462 0.00 0.00 0.00 2.66
819 854 6.376177 CCGTCCCAAAATAAGTGTCTTAAAC 58.624 40.000 0.00 0.00 0.00 2.01
820 855 5.048573 GCCGTCCCAAAATAAGTGTCTTAAA 60.049 40.000 0.00 0.00 0.00 1.52
821 856 4.456566 GCCGTCCCAAAATAAGTGTCTTAA 59.543 41.667 0.00 0.00 0.00 1.85
822 857 4.004982 GCCGTCCCAAAATAAGTGTCTTA 58.995 43.478 0.00 0.00 0.00 2.10
823 858 2.817844 GCCGTCCCAAAATAAGTGTCTT 59.182 45.455 0.00 0.00 0.00 3.01
824 859 2.433436 GCCGTCCCAAAATAAGTGTCT 58.567 47.619 0.00 0.00 0.00 3.41
825 860 1.129811 CGCCGTCCCAAAATAAGTGTC 59.870 52.381 0.00 0.00 0.00 3.67
826 861 1.161843 CGCCGTCCCAAAATAAGTGT 58.838 50.000 0.00 0.00 0.00 3.55
827 862 0.450184 CCGCCGTCCCAAAATAAGTG 59.550 55.000 0.00 0.00 0.00 3.16
828 863 0.678684 CCCGCCGTCCCAAAATAAGT 60.679 55.000 0.00 0.00 0.00 2.24
829 864 0.393267 TCCCGCCGTCCCAAAATAAG 60.393 55.000 0.00 0.00 0.00 1.73
830 865 0.393267 CTCCCGCCGTCCCAAAATAA 60.393 55.000 0.00 0.00 0.00 1.40
831 866 1.222387 CTCCCGCCGTCCCAAAATA 59.778 57.895 0.00 0.00 0.00 1.40
832 867 1.555477 TACTCCCGCCGTCCCAAAAT 61.555 55.000 0.00 0.00 0.00 1.82
833 868 1.555477 ATACTCCCGCCGTCCCAAAA 61.555 55.000 0.00 0.00 0.00 2.44
834 869 0.687098 TATACTCCCGCCGTCCCAAA 60.687 55.000 0.00 0.00 0.00 3.28
835 870 0.687098 TTATACTCCCGCCGTCCCAA 60.687 55.000 0.00 0.00 0.00 4.12
836 871 0.687098 TTTATACTCCCGCCGTCCCA 60.687 55.000 0.00 0.00 0.00 4.37
837 872 0.683412 ATTTATACTCCCGCCGTCCC 59.317 55.000 0.00 0.00 0.00 4.46
838 873 2.538512 AATTTATACTCCCGCCGTCC 57.461 50.000 0.00 0.00 0.00 4.79
839 874 7.656707 TTTATAAATTTATACTCCCGCCGTC 57.343 36.000 15.92 0.00 0.00 4.79
840 875 7.120138 CCATTTATAAATTTATACTCCCGCCGT 59.880 37.037 15.92 0.00 0.00 5.68
841 876 7.334921 TCCATTTATAAATTTATACTCCCGCCG 59.665 37.037 15.92 1.85 0.00 6.46
842 877 8.456471 GTCCATTTATAAATTTATACTCCCGCC 58.544 37.037 15.92 1.35 0.00 6.13
843 878 9.005777 TGTCCATTTATAAATTTATACTCCCGC 57.994 33.333 15.92 7.77 0.00 6.13
872 907 2.606519 CCCCGGGGACAGAGACAA 60.607 66.667 38.41 0.00 37.50 3.18
878 913 4.329545 CACACACCCCGGGGACAG 62.330 72.222 46.68 33.36 38.96 3.51
882 917 1.078001 GAATACACACACCCCGGGG 60.078 63.158 39.18 39.18 42.03 5.73
928 963 6.310224 AGTCACACTTTGCAATTTTGTGTAAC 59.690 34.615 23.97 19.59 39.46 2.50
931 966 4.819769 AGTCACACTTTGCAATTTTGTGT 58.180 34.783 23.97 20.48 41.75 3.72
942 977 4.944962 TGTGTCTTCAAGTCACACTTTG 57.055 40.909 12.77 0.00 38.86 2.77
1001 4352 3.469899 CGAAATTCAGTTCGGCATTCA 57.530 42.857 1.51 0.00 45.21 2.57
1034 4385 0.586319 CGCTTCGCCTGAACTTTTCA 59.414 50.000 0.00 0.00 38.17 2.69
1078 4436 3.807839 CGGCATGGTGGGATGGGA 61.808 66.667 0.00 0.00 0.00 4.37
1536 4903 1.448013 GGCGAAGAAGGGGACGAAG 60.448 63.158 0.00 0.00 0.00 3.79
1588 4955 4.660938 GAAGGCGCCCTTGGTGGT 62.661 66.667 26.15 0.00 44.82 4.16
1749 5116 8.712285 TTACAACTTTACAAGGATAGGATTCG 57.288 34.615 0.00 0.00 0.00 3.34
1817 5184 4.883585 CCAGCTATGCTAACCTTGATTCAA 59.116 41.667 0.00 0.00 36.40 2.69
1900 5267 7.491696 CCACATAGGTTTCTTACTAACTAGTGC 59.508 40.741 0.00 0.00 37.10 4.40
1911 5278 6.000246 TGCATGATCCACATAGGTTTCTTA 58.000 37.500 0.00 0.00 37.46 2.10
1916 5283 4.080129 AGACTTGCATGATCCACATAGGTT 60.080 41.667 6.60 0.00 37.46 3.50
1956 5323 7.793927 ATTTTTCTAACCTATACTGAGCTGC 57.206 36.000 0.00 0.00 0.00 5.25
1993 5543 8.540388 TCTCCTTTACTGAACTGTGCTAATATT 58.460 33.333 0.00 0.00 0.00 1.28
2015 5565 7.816640 TGCATAAAAGTACAATGTTTCTCTCC 58.183 34.615 0.00 0.00 0.00 3.71
2054 5604 7.665690 ACATAAACAATACACCAAATGCTTCA 58.334 30.769 0.00 0.00 0.00 3.02
2134 5684 7.750903 GTCAAAGAATGCCTCAGTATTTAACAC 59.249 37.037 0.00 0.00 0.00 3.32
2466 6024 5.667626 TCCAGATAGCAGATAAACCTTTCCT 59.332 40.000 0.00 0.00 0.00 3.36
2507 6065 4.952262 TGATGAAATGCAAGTGAGTAGC 57.048 40.909 0.00 0.00 0.00 3.58
2511 6069 9.361315 TGAAATTAATGATGAAATGCAAGTGAG 57.639 29.630 0.00 0.00 0.00 3.51
2540 6106 2.550606 TGTACATGTTTGACCGCCTTTC 59.449 45.455 2.30 0.00 0.00 2.62
2544 6110 5.050363 CACTATATGTACATGTTTGACCGCC 60.050 44.000 18.81 0.00 0.00 6.13
2588 6154 6.996282 ACAGATAAAAACGATATAACCCAGGG 59.004 38.462 2.85 2.85 0.00 4.45
2763 6414 6.957631 TGGAAAAGAGAGGCAAACATCTATA 58.042 36.000 0.00 0.00 0.00 1.31
2767 6418 6.545298 AGATATGGAAAAGAGAGGCAAACATC 59.455 38.462 0.00 0.00 0.00 3.06
2858 6514 5.928839 CACTGCATAAGCGATAAAGTCCTAT 59.071 40.000 0.00 0.00 46.23 2.57
2859 6515 5.163447 ACACTGCATAAGCGATAAAGTCCTA 60.163 40.000 0.00 0.00 46.23 2.94
2889 6551 3.127895 CAGAGAACCTCAGGAGTTCTACG 59.872 52.174 0.00 0.00 37.54 3.51
2948 6639 2.245582 ACGGAACAACCTAGTGCTAGT 58.754 47.619 5.62 0.00 36.31 2.57
2967 6662 8.506168 TGATTCCCTCAGATATACAAAACAAC 57.494 34.615 0.00 0.00 0.00 3.32
2986 6764 6.425417 GCTAGGCTGAAGTTAGTTATGATTCC 59.575 42.308 0.00 0.00 0.00 3.01
2990 6768 6.546428 AAGCTAGGCTGAAGTTAGTTATGA 57.454 37.500 0.00 0.00 39.62 2.15
2991 6769 9.413048 GTATAAGCTAGGCTGAAGTTAGTTATG 57.587 37.037 0.00 0.00 39.62 1.90
2992 6770 9.369672 AGTATAAGCTAGGCTGAAGTTAGTTAT 57.630 33.333 0.00 0.00 39.62 1.89
3040 6818 5.695851 AACGGATTGATCAGATAAATGGC 57.304 39.130 0.00 0.00 0.00 4.40
3243 7021 1.331756 AGACTTGCAACAGCGTCAAAG 59.668 47.619 16.22 0.00 0.00 2.77
3641 7420 0.036765 TTTTCGTGGAGGATCGGTGG 60.037 55.000 0.00 0.00 34.37 4.61
3732 7514 2.030805 GTGCAAAACGGATGAAGAAGCT 60.031 45.455 0.00 0.00 0.00 3.74
3782 7572 2.178912 ACCCCGTACAACAACTCATG 57.821 50.000 0.00 0.00 0.00 3.07
3833 7625 5.049818 CGTATCCAGCCTTCTCAATTCATTC 60.050 44.000 0.00 0.00 0.00 2.67
3894 7686 7.775053 ACACCCATGTCTAAACATTTGTTAT 57.225 32.000 0.00 0.00 43.74 1.89
3989 7791 9.585099 TGAATATATGAACAAATGTTTTGAGCC 57.415 29.630 6.96 0.00 38.56 4.70
4173 9417 0.390603 TCGTGGCTTGGTTACATCCG 60.391 55.000 0.00 0.00 0.00 4.18
4252 9501 4.954202 ACTCCCGTTGTCATAGACAGAATA 59.046 41.667 0.00 0.00 43.69 1.75
4261 9510 0.108992 GACGCACTCCCGTTGTCATA 60.109 55.000 0.00 0.00 42.24 2.15
4263 9512 2.028484 GACGCACTCCCGTTGTCA 59.972 61.111 0.00 0.00 42.24 3.58
4421 9670 2.753452 AGTTTCTGCATCTGCTTGGATG 59.247 45.455 3.53 9.42 44.08 3.51
4451 9700 6.828273 CCCCATTATACTTGACAATCTGTTCA 59.172 38.462 0.00 0.00 0.00 3.18
4460 9710 6.375830 TGTAACACCCCATTATACTTGACA 57.624 37.500 0.00 0.00 0.00 3.58
4468 9718 2.849943 TGCTCCTGTAACACCCCATTAT 59.150 45.455 0.00 0.00 0.00 1.28
4529 9780 0.323087 TCGGGATCGTCTCCTTGTCA 60.323 55.000 6.72 0.00 44.28 3.58


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

AutoCloner maintained by Alex Coulton.