Multiple sequence alignment - TraesCS7B01G464100

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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 TraesCS7B01G464100 chr7B 100.000 1629 0 0 699 2327 720888292 720886664 0.000000e+00 3009.0
1 TraesCS7B01G464100 chr7B 98.897 1450 15 1 879 2327 720843850 720842401 0.000000e+00 2588.0
2 TraesCS7B01G464100 chr7B 100.000 418 0 0 1 418 720888990 720888573 0.000000e+00 773.0
3 TraesCS7B01G464100 chr7A 86.202 1464 137 29 902 2327 718354603 718353167 0.000000e+00 1524.0
4 TraesCS7B01G464100 chr7A 87.567 1126 104 16 877 1971 718271364 718270244 0.000000e+00 1271.0
5 TraesCS7B01G464100 chr7A 79.909 662 90 20 920 1546 718997808 718997155 1.640000e-121 446.0
6 TraesCS7B01G464100 chr7A 77.792 788 110 35 920 1654 719037465 719036690 2.140000e-115 425.0
7 TraesCS7B01G464100 chr7A 81.489 470 58 16 1209 1654 719271363 719270899 2.200000e-95 359.0
8 TraesCS7B01G464100 chr7A 81.404 285 44 6 920 1203 719271675 719271399 8.370000e-55 224.0
9 TraesCS7B01G464100 chr7D 86.537 1077 111 13 924 1971 623353130 623354201 0.000000e+00 1155.0
10 TraesCS7B01G464100 chr7D 96.897 419 12 1 1 418 8873529 8873947 0.000000e+00 701.0
11 TraesCS7B01G464100 chr7D 84.071 113 18 0 1094 1206 623027438 623027550 2.440000e-20 110.0
12 TraesCS7B01G464100 chr7D 95.349 43 2 0 1287 1329 623283941 623283983 4.150000e-08 69.4
13 TraesCS7B01G464100 chr7D 95.349 43 2 0 1287 1329 623293940 623293982 4.150000e-08 69.4
14 TraesCS7B01G464100 chr7D 84.286 70 11 0 1260 1329 623390642 623390711 4.150000e-08 69.4
15 TraesCS7B01G464100 chr3B 97.143 420 10 2 1 418 535525603 535526022 0.000000e+00 708.0
16 TraesCS7B01G464100 chr3B 93.989 183 11 0 699 881 27230330 27230148 6.330000e-71 278.0
17 TraesCS7B01G464100 chr3B 94.915 177 8 1 699 875 532670804 532670979 2.280000e-70 276.0
18 TraesCS7B01G464100 chr6B 97.136 419 11 1 1 418 659954033 659954451 0.000000e+00 706.0
19 TraesCS7B01G464100 chr6B 96.897 419 12 1 1 418 560195696 560196114 0.000000e+00 701.0
20 TraesCS7B01G464100 chr6B 94.915 177 9 0 699 875 659954561 659954737 6.330000e-71 278.0
21 TraesCS7B01G464100 chr6B 94.413 179 10 0 699 877 502006204 502006026 2.280000e-70 276.0
22 TraesCS7B01G464100 chr5B 96.897 419 12 1 1 418 585272720 585272302 0.000000e+00 701.0
23 TraesCS7B01G464100 chr5B 95.480 177 8 0 699 875 115644340 115644516 1.360000e-72 283.0
24 TraesCS7B01G464100 chr4B 96.897 419 12 1 1 418 4778865 4778447 0.000000e+00 701.0
25 TraesCS7B01G464100 chr4B 96.897 419 11 2 1 418 67505853 67505436 0.000000e+00 701.0
26 TraesCS7B01G464100 chr3D 96.897 419 12 1 1 418 11571322 11570904 0.000000e+00 701.0
27 TraesCS7B01G464100 chr1B 96.897 419 11 2 1 418 11856019 11856436 0.000000e+00 701.0
28 TraesCS7B01G464100 chr1B 94.413 179 9 1 699 877 638773754 638773931 8.190000e-70 274.0
29 TraesCS7B01G464100 chr2B 94.915 177 9 0 699 875 739985583 739985759 6.330000e-71 278.0
30 TraesCS7B01G464100 chr2B 94.915 177 9 0 699 875 760938728 760938904 6.330000e-71 278.0
31 TraesCS7B01G464100 chr4A 94.413 179 9 1 699 877 689446193 689446016 8.190000e-70 274.0


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 TraesCS7B01G464100 chr7B 720886664 720888990 2326 True 1891.0 3009 100.0000 1 2327 2 chr7B.!!$R2 2326
1 TraesCS7B01G464100 chr7B 720842401 720843850 1449 True 2588.0 2588 98.8970 879 2327 1 chr7B.!!$R1 1448
2 TraesCS7B01G464100 chr7A 718353167 718354603 1436 True 1524.0 1524 86.2020 902 2327 1 chr7A.!!$R2 1425
3 TraesCS7B01G464100 chr7A 718270244 718271364 1120 True 1271.0 1271 87.5670 877 1971 1 chr7A.!!$R1 1094
4 TraesCS7B01G464100 chr7A 718997155 718997808 653 True 446.0 446 79.9090 920 1546 1 chr7A.!!$R3 626
5 TraesCS7B01G464100 chr7A 719036690 719037465 775 True 425.0 425 77.7920 920 1654 1 chr7A.!!$R4 734
6 TraesCS7B01G464100 chr7A 719270899 719271675 776 True 291.5 359 81.4465 920 1654 2 chr7A.!!$R5 734
7 TraesCS7B01G464100 chr7D 623353130 623354201 1071 False 1155.0 1155 86.5370 924 1971 1 chr7D.!!$F5 1047
8 TraesCS7B01G464100 chr6B 659954033 659954737 704 False 492.0 706 96.0255 1 875 2 chr6B.!!$F2 874

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
775 776 0.033781 AAACGGACGGAATTCGGACA 59.966 50.0 18.83 0.0 44.45 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1883 2187 4.489679 AAAGATTCTTTTGAGTGTCGGC 57.51 40.909 5.82 0.0 0.0 5.54 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
268 269 1.068250 CCCTCCTCTTCGCCGATTC 59.932 63.158 0.00 0.00 0.00 2.52
278 279 3.861263 GCCGATTCCGCGTCCAAC 61.861 66.667 4.92 0.00 0.00 3.77
279 280 2.125673 CCGATTCCGCGTCCAACT 60.126 61.111 4.92 0.00 0.00 3.16
280 281 1.740296 CCGATTCCGCGTCCAACTT 60.740 57.895 4.92 0.00 0.00 2.66
281 282 1.419922 CGATTCCGCGTCCAACTTG 59.580 57.895 4.92 0.00 0.00 3.16
282 283 1.794222 GATTCCGCGTCCAACTTGG 59.206 57.895 4.92 0.74 39.43 3.61
283 284 2.253414 GATTCCGCGTCCAACTTGGC 62.253 60.000 4.92 0.00 37.47 4.52
287 288 2.785258 GCGTCCAACTTGGCGATC 59.215 61.111 21.49 7.33 38.63 3.69
288 289 1.741770 GCGTCCAACTTGGCGATCT 60.742 57.895 21.49 0.00 38.63 2.75
289 290 1.696832 GCGTCCAACTTGGCGATCTC 61.697 60.000 21.49 6.55 38.63 2.75
290 291 1.084370 CGTCCAACTTGGCGATCTCC 61.084 60.000 15.48 0.00 38.63 3.71
291 292 0.250513 GTCCAACTTGGCGATCTCCT 59.749 55.000 2.88 0.00 37.47 3.69
292 293 0.537188 TCCAACTTGGCGATCTCCTC 59.463 55.000 2.88 0.00 37.47 3.71
293 294 0.462759 CCAACTTGGCGATCTCCTCC 60.463 60.000 2.88 0.00 0.00 4.30
294 295 0.807667 CAACTTGGCGATCTCCTCCG 60.808 60.000 2.88 0.00 0.00 4.63
295 296 1.961180 AACTTGGCGATCTCCTCCGG 61.961 60.000 2.88 0.00 0.00 5.14
299 300 4.933064 GCGATCTCCTCCGGCGTG 62.933 72.222 6.01 0.00 0.00 5.34
300 301 4.933064 CGATCTCCTCCGGCGTGC 62.933 72.222 6.01 0.00 0.00 5.34
301 302 3.838271 GATCTCCTCCGGCGTGCA 61.838 66.667 6.01 0.00 0.00 4.57
302 303 4.148825 ATCTCCTCCGGCGTGCAC 62.149 66.667 6.82 6.82 0.00 4.57
304 305 4.803426 CTCCTCCGGCGTGCACTC 62.803 72.222 16.19 6.81 0.00 3.51
329 330 3.443925 GGCTTCCTTGGCGCCTTC 61.444 66.667 29.70 8.17 40.62 3.46
330 331 2.360475 GCTTCCTTGGCGCCTTCT 60.360 61.111 29.70 0.00 0.00 2.85
331 332 1.973812 GCTTCCTTGGCGCCTTCTT 60.974 57.895 29.70 0.00 0.00 2.52
332 333 1.927608 GCTTCCTTGGCGCCTTCTTC 61.928 60.000 29.70 6.96 0.00 2.87
333 334 0.322008 CTTCCTTGGCGCCTTCTTCT 60.322 55.000 29.70 0.00 0.00 2.85
334 335 0.110486 TTCCTTGGCGCCTTCTTCTT 59.890 50.000 29.70 0.00 0.00 2.52
335 336 0.321653 TCCTTGGCGCCTTCTTCTTC 60.322 55.000 29.70 0.00 0.00 2.87
336 337 0.606401 CCTTGGCGCCTTCTTCTTCA 60.606 55.000 29.70 0.00 0.00 3.02
337 338 0.519077 CTTGGCGCCTTCTTCTTCAC 59.481 55.000 29.70 0.00 0.00 3.18
338 339 0.889186 TTGGCGCCTTCTTCTTCACC 60.889 55.000 29.70 0.00 0.00 4.02
339 340 1.003233 GGCGCCTTCTTCTTCACCT 60.003 57.895 22.15 0.00 0.00 4.00
340 341 0.606673 GGCGCCTTCTTCTTCACCTT 60.607 55.000 22.15 0.00 0.00 3.50
341 342 1.239347 GCGCCTTCTTCTTCACCTTT 58.761 50.000 0.00 0.00 0.00 3.11
342 343 1.068954 GCGCCTTCTTCTTCACCTTTG 60.069 52.381 0.00 0.00 0.00 2.77
343 344 1.068954 CGCCTTCTTCTTCACCTTTGC 60.069 52.381 0.00 0.00 0.00 3.68
344 345 1.068954 GCCTTCTTCTTCACCTTTGCG 60.069 52.381 0.00 0.00 0.00 4.85
345 346 1.537202 CCTTCTTCTTCACCTTTGCGG 59.463 52.381 0.00 0.00 39.35 5.69
346 347 1.537202 CTTCTTCTTCACCTTTGCGGG 59.463 52.381 0.00 0.00 36.97 6.13
347 348 0.889186 TCTTCTTCACCTTTGCGGGC 60.889 55.000 0.00 0.00 36.97 6.13
348 349 2.187599 CTTCTTCACCTTTGCGGGCG 62.188 60.000 0.00 0.00 36.97 6.13
349 350 3.737172 CTTCACCTTTGCGGGCGG 61.737 66.667 0.00 0.00 36.97 6.13
403 404 3.866582 GCCATGGACGGGGGAGAG 61.867 72.222 18.40 0.00 0.00 3.20
404 405 2.041922 CCATGGACGGGGGAGAGA 60.042 66.667 5.56 0.00 0.00 3.10
405 406 2.136878 CCATGGACGGGGGAGAGAG 61.137 68.421 5.56 0.00 0.00 3.20
406 407 2.136878 CATGGACGGGGGAGAGAGG 61.137 68.421 0.00 0.00 0.00 3.69
407 408 3.396822 ATGGACGGGGGAGAGAGGG 62.397 68.421 0.00 0.00 0.00 4.30
408 409 4.862823 GGACGGGGGAGAGAGGGG 62.863 77.778 0.00 0.00 0.00 4.79
409 410 4.862823 GACGGGGGAGAGAGGGGG 62.863 77.778 0.00 0.00 0.00 5.40
717 718 4.719616 GCGCGCTGTCCGTTTCAC 62.720 66.667 26.67 0.00 39.71 3.18
718 719 4.072088 CGCGCTGTCCGTTTCACC 62.072 66.667 5.56 0.00 39.71 4.02
719 720 3.723348 GCGCTGTCCGTTTCACCC 61.723 66.667 0.00 0.00 39.71 4.61
720 721 3.047877 CGCTGTCCGTTTCACCCC 61.048 66.667 0.00 0.00 0.00 4.95
721 722 2.112297 GCTGTCCGTTTCACCCCA 59.888 61.111 0.00 0.00 0.00 4.96
722 723 1.527380 GCTGTCCGTTTCACCCCAA 60.527 57.895 0.00 0.00 0.00 4.12
723 724 1.104577 GCTGTCCGTTTCACCCCAAA 61.105 55.000 0.00 0.00 0.00 3.28
724 725 0.666374 CTGTCCGTTTCACCCCAAAC 59.334 55.000 0.00 0.00 33.57 2.93
725 726 0.752376 TGTCCGTTTCACCCCAAACC 60.752 55.000 0.00 0.00 33.37 3.27
726 727 1.526455 TCCGTTTCACCCCAAACCG 60.526 57.895 0.00 0.00 33.37 4.44
727 728 1.526455 CCGTTTCACCCCAAACCGA 60.526 57.895 0.00 0.00 33.37 4.69
728 729 1.512156 CCGTTTCACCCCAAACCGAG 61.512 60.000 0.00 0.00 33.37 4.63
729 730 1.658114 GTTTCACCCCAAACCGAGC 59.342 57.895 0.00 0.00 31.10 5.03
730 731 1.894756 TTTCACCCCAAACCGAGCG 60.895 57.895 0.00 0.00 0.00 5.03
733 734 4.572571 ACCCCAAACCGAGCGCAA 62.573 61.111 11.47 0.00 0.00 4.85
734 735 4.038080 CCCCAAACCGAGCGCAAC 62.038 66.667 11.47 1.68 0.00 4.17
735 736 2.978010 CCCAAACCGAGCGCAACT 60.978 61.111 11.47 0.00 0.00 3.16
736 737 2.551912 CCCAAACCGAGCGCAACTT 61.552 57.895 11.47 0.00 0.00 2.66
737 738 1.358759 CCAAACCGAGCGCAACTTT 59.641 52.632 11.47 0.00 0.00 2.66
738 739 0.934436 CCAAACCGAGCGCAACTTTG 60.934 55.000 11.47 11.15 0.00 2.77
739 740 0.934436 CAAACCGAGCGCAACTTTGG 60.934 55.000 11.47 4.35 0.00 3.28
740 741 2.070654 AAACCGAGCGCAACTTTGGG 62.071 55.000 11.47 0.76 43.22 4.12
747 748 4.986708 GCAACTTTGGGCCGGGGA 62.987 66.667 2.18 0.00 0.00 4.81
748 749 2.037208 CAACTTTGGGCCGGGGAT 59.963 61.111 2.18 0.00 0.00 3.85
749 750 2.037208 AACTTTGGGCCGGGGATG 59.963 61.111 2.18 0.00 0.00 3.51
750 751 3.600410 AACTTTGGGCCGGGGATGG 62.600 63.158 2.18 0.00 0.00 3.51
751 752 4.839706 CTTTGGGCCGGGGATGGG 62.840 72.222 2.18 0.00 0.00 4.00
757 758 4.104183 GCCGGGGATGGGTCGAAA 62.104 66.667 2.18 0.00 0.00 3.46
758 759 2.672295 CCGGGGATGGGTCGAAAA 59.328 61.111 0.00 0.00 0.00 2.29
759 760 1.747745 CCGGGGATGGGTCGAAAAC 60.748 63.158 0.00 0.00 0.00 2.43
760 761 2.104253 CGGGGATGGGTCGAAAACG 61.104 63.158 0.00 0.00 0.00 3.60
761 762 1.747745 GGGGATGGGTCGAAAACGG 60.748 63.158 0.00 0.00 0.00 4.44
762 763 1.297364 GGGATGGGTCGAAAACGGA 59.703 57.895 0.00 0.00 0.00 4.69
763 764 1.022982 GGGATGGGTCGAAAACGGAC 61.023 60.000 0.00 0.00 0.00 4.79
764 765 1.356527 GGATGGGTCGAAAACGGACG 61.357 60.000 0.00 0.00 35.24 4.79
765 766 1.356527 GATGGGTCGAAAACGGACGG 61.357 60.000 0.00 0.00 35.24 4.79
766 767 1.818959 ATGGGTCGAAAACGGACGGA 61.819 55.000 0.00 0.00 35.24 4.69
767 768 1.300853 GGGTCGAAAACGGACGGAA 60.301 57.895 0.00 0.00 35.24 4.30
768 769 0.671472 GGGTCGAAAACGGACGGAAT 60.671 55.000 0.00 0.00 35.24 3.01
769 770 1.150827 GGTCGAAAACGGACGGAATT 58.849 50.000 0.00 0.00 35.24 2.17
770 771 1.127397 GGTCGAAAACGGACGGAATTC 59.873 52.381 0.00 0.00 35.24 2.17
771 772 1.062258 TCGAAAACGGACGGAATTCG 58.938 50.000 16.75 16.75 42.97 3.34
772 773 0.094046 CGAAAACGGACGGAATTCGG 59.906 55.000 11.17 11.17 44.45 4.30
773 774 1.431496 GAAAACGGACGGAATTCGGA 58.569 50.000 18.83 0.00 44.45 4.55
774 775 1.127397 GAAAACGGACGGAATTCGGAC 59.873 52.381 18.83 12.63 44.45 4.79
775 776 0.033781 AAACGGACGGAATTCGGACA 59.966 50.000 18.83 0.00 44.45 4.02
776 777 0.248289 AACGGACGGAATTCGGACAT 59.752 50.000 18.83 3.39 44.45 3.06
777 778 0.248289 ACGGACGGAATTCGGACATT 59.752 50.000 18.83 1.91 44.45 2.71
778 779 1.338389 ACGGACGGAATTCGGACATTT 60.338 47.619 18.83 0.00 44.45 2.32
779 780 1.062002 CGGACGGAATTCGGACATTTG 59.938 52.381 18.83 2.05 44.45 2.32
780 781 2.081462 GGACGGAATTCGGACATTTGT 58.919 47.619 18.83 0.00 44.45 2.83
781 782 2.095372 GGACGGAATTCGGACATTTGTC 59.905 50.000 18.83 1.99 44.45 3.18
782 783 3.000727 GACGGAATTCGGACATTTGTCT 58.999 45.455 18.83 0.00 44.20 3.41
790 791 3.542712 CGGACATTTGTCTGTTTGAGG 57.457 47.619 10.73 0.00 44.33 3.86
791 792 2.350772 CGGACATTTGTCTGTTTGAGGC 60.351 50.000 10.73 0.00 44.33 4.70
792 793 2.029918 GGACATTTGTCTGTTTGAGGCC 60.030 50.000 10.32 0.00 44.20 5.19
793 794 1.608590 ACATTTGTCTGTTTGAGGCCG 59.391 47.619 0.00 0.00 0.00 6.13
794 795 0.598065 ATTTGTCTGTTTGAGGCCGC 59.402 50.000 0.00 0.00 0.00 6.53
795 796 1.781025 TTTGTCTGTTTGAGGCCGCG 61.781 55.000 0.00 0.00 0.00 6.46
796 797 4.090057 GTCTGTTTGAGGCCGCGC 62.090 66.667 0.00 0.00 0.00 6.86
813 814 3.365265 CGCTGGGCCGCTTCTTTT 61.365 61.111 16.17 0.00 0.00 2.27
814 815 2.259511 GCTGGGCCGCTTCTTTTG 59.740 61.111 12.15 0.00 0.00 2.44
815 816 2.564721 GCTGGGCCGCTTCTTTTGT 61.565 57.895 12.15 0.00 0.00 2.83
816 817 1.581447 CTGGGCCGCTTCTTTTGTC 59.419 57.895 0.00 0.00 0.00 3.18
817 818 1.866853 CTGGGCCGCTTCTTTTGTCC 61.867 60.000 0.00 0.00 0.00 4.02
818 819 2.636412 GGGCCGCTTCTTTTGTCCC 61.636 63.158 0.00 0.00 0.00 4.46
819 820 1.603739 GGCCGCTTCTTTTGTCCCT 60.604 57.895 0.00 0.00 0.00 4.20
820 821 1.179174 GGCCGCTTCTTTTGTCCCTT 61.179 55.000 0.00 0.00 0.00 3.95
821 822 0.673985 GCCGCTTCTTTTGTCCCTTT 59.326 50.000 0.00 0.00 0.00 3.11
822 823 1.068588 GCCGCTTCTTTTGTCCCTTTT 59.931 47.619 0.00 0.00 0.00 2.27
823 824 2.295070 GCCGCTTCTTTTGTCCCTTTTA 59.705 45.455 0.00 0.00 0.00 1.52
824 825 3.855895 GCCGCTTCTTTTGTCCCTTTTAC 60.856 47.826 0.00 0.00 0.00 2.01
825 826 3.305131 CCGCTTCTTTTGTCCCTTTTACC 60.305 47.826 0.00 0.00 0.00 2.85
826 827 3.305131 CGCTTCTTTTGTCCCTTTTACCC 60.305 47.826 0.00 0.00 0.00 3.69
827 828 3.006537 GCTTCTTTTGTCCCTTTTACCCC 59.993 47.826 0.00 0.00 0.00 4.95
828 829 3.975479 TCTTTTGTCCCTTTTACCCCA 57.025 42.857 0.00 0.00 0.00 4.96
829 830 4.267341 TCTTTTGTCCCTTTTACCCCAA 57.733 40.909 0.00 0.00 0.00 4.12
830 831 4.621769 TCTTTTGTCCCTTTTACCCCAAA 58.378 39.130 0.00 0.00 0.00 3.28
831 832 4.406326 TCTTTTGTCCCTTTTACCCCAAAC 59.594 41.667 0.00 0.00 0.00 2.93
832 833 1.984066 TGTCCCTTTTACCCCAAACG 58.016 50.000 0.00 0.00 0.00 3.60
833 834 1.250328 GTCCCTTTTACCCCAAACGG 58.750 55.000 0.00 0.00 35.72 4.44
834 835 1.147333 TCCCTTTTACCCCAAACGGA 58.853 50.000 0.00 0.00 37.67 4.69
835 836 1.202915 TCCCTTTTACCCCAAACGGAC 60.203 52.381 0.00 0.00 37.67 4.79
836 837 0.876399 CCTTTTACCCCAAACGGACG 59.124 55.000 0.00 0.00 37.67 4.79
837 838 0.876399 CTTTTACCCCAAACGGACGG 59.124 55.000 0.00 0.00 0.00 4.79
838 839 0.536915 TTTTACCCCAAACGGACGGG 60.537 55.000 0.00 0.00 43.05 5.28
850 851 3.782443 GACGGGGGCGGACAGAAT 61.782 66.667 0.00 0.00 0.00 2.40
851 852 2.364579 ACGGGGGCGGACAGAATA 60.365 61.111 0.00 0.00 0.00 1.75
852 853 2.365095 GACGGGGGCGGACAGAATAG 62.365 65.000 0.00 0.00 0.00 1.73
853 854 2.131709 CGGGGGCGGACAGAATAGA 61.132 63.158 0.00 0.00 0.00 1.98
854 855 1.749033 GGGGGCGGACAGAATAGAG 59.251 63.158 0.00 0.00 0.00 2.43
855 856 1.049289 GGGGGCGGACAGAATAGAGT 61.049 60.000 0.00 0.00 0.00 3.24
856 857 0.831307 GGGGCGGACAGAATAGAGTT 59.169 55.000 0.00 0.00 0.00 3.01
857 858 1.473434 GGGGCGGACAGAATAGAGTTG 60.473 57.143 0.00 0.00 0.00 3.16
858 859 1.291132 GGCGGACAGAATAGAGTTGC 58.709 55.000 0.00 0.00 0.00 4.17
859 860 0.924090 GCGGACAGAATAGAGTTGCG 59.076 55.000 0.00 0.00 0.00 4.85
860 861 0.924090 CGGACAGAATAGAGTTGCGC 59.076 55.000 0.00 0.00 0.00 6.09
861 862 0.924090 GGACAGAATAGAGTTGCGCG 59.076 55.000 0.00 0.00 0.00 6.86
862 863 0.924090 GACAGAATAGAGTTGCGCGG 59.076 55.000 8.83 0.00 0.00 6.46
863 864 0.246635 ACAGAATAGAGTTGCGCGGT 59.753 50.000 8.83 0.00 0.00 5.68
864 865 0.647410 CAGAATAGAGTTGCGCGGTG 59.353 55.000 8.83 0.00 0.00 4.94
865 866 0.460284 AGAATAGAGTTGCGCGGTGG 60.460 55.000 8.83 0.00 0.00 4.61
866 867 0.459585 GAATAGAGTTGCGCGGTGGA 60.460 55.000 8.83 0.00 0.00 4.02
867 868 0.460284 AATAGAGTTGCGCGGTGGAG 60.460 55.000 8.83 0.00 0.00 3.86
868 869 1.605058 ATAGAGTTGCGCGGTGGAGT 61.605 55.000 8.83 0.00 0.00 3.85
869 870 1.812686 TAGAGTTGCGCGGTGGAGTT 61.813 55.000 8.83 0.00 0.00 3.01
870 871 2.954753 GAGTTGCGCGGTGGAGTTG 61.955 63.158 8.83 0.00 0.00 3.16
871 872 4.025401 GTTGCGCGGTGGAGTTGG 62.025 66.667 8.83 0.00 0.00 3.77
1681 1979 3.386486 TGCGTCTCAAAATAAGTGTCGT 58.614 40.909 0.00 0.00 0.00 4.34
2068 2384 3.757947 ATTAAACAAGAAGGGGAGGGG 57.242 47.619 0.00 0.00 0.00 4.79
2313 2631 2.944349 CTGGCCTTGTTTGTTTTGCAAT 59.056 40.909 3.32 0.00 36.89 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 3.633094 CTACGCACTGCCAGTCGCT 62.633 63.158 13.92 6.56 38.78 4.93
277 278 3.211288 CGGAGGAGATCGCCAAGT 58.789 61.111 18.44 0.00 34.79 3.16
313 314 1.927608 GAAGAAGGCGCCAAGGAAGC 61.928 60.000 31.54 7.63 0.00 3.86
314 315 0.322008 AGAAGAAGGCGCCAAGGAAG 60.322 55.000 31.54 0.00 0.00 3.46
315 316 0.110486 AAGAAGAAGGCGCCAAGGAA 59.890 50.000 31.54 0.00 0.00 3.36
316 317 0.321653 GAAGAAGAAGGCGCCAAGGA 60.322 55.000 31.54 0.00 0.00 3.36
317 318 0.606401 TGAAGAAGAAGGCGCCAAGG 60.606 55.000 31.54 0.00 0.00 3.61
318 319 0.519077 GTGAAGAAGAAGGCGCCAAG 59.481 55.000 31.54 0.00 0.00 3.61
319 320 0.889186 GGTGAAGAAGAAGGCGCCAA 60.889 55.000 31.54 0.00 0.00 4.52
320 321 1.302511 GGTGAAGAAGAAGGCGCCA 60.303 57.895 31.54 0.00 0.00 5.69
321 322 0.606673 AAGGTGAAGAAGAAGGCGCC 60.607 55.000 21.89 21.89 0.00 6.53
322 323 1.068954 CAAAGGTGAAGAAGAAGGCGC 60.069 52.381 0.00 0.00 0.00 6.53
323 324 1.068954 GCAAAGGTGAAGAAGAAGGCG 60.069 52.381 0.00 0.00 0.00 5.52
324 325 1.068954 CGCAAAGGTGAAGAAGAAGGC 60.069 52.381 0.00 0.00 0.00 4.35
325 326 1.537202 CCGCAAAGGTGAAGAAGAAGG 59.463 52.381 0.00 0.00 34.51 3.46
326 327 1.537202 CCCGCAAAGGTGAAGAAGAAG 59.463 52.381 0.00 0.00 38.74 2.85
327 328 1.604604 CCCGCAAAGGTGAAGAAGAA 58.395 50.000 0.00 0.00 38.74 2.52
328 329 0.889186 GCCCGCAAAGGTGAAGAAGA 60.889 55.000 0.00 0.00 38.74 2.87
329 330 1.581447 GCCCGCAAAGGTGAAGAAG 59.419 57.895 0.00 0.00 38.74 2.85
330 331 2.258013 CGCCCGCAAAGGTGAAGAA 61.258 57.895 0.00 0.00 39.99 2.52
331 332 2.668212 CGCCCGCAAAGGTGAAGA 60.668 61.111 0.00 0.00 39.99 2.87
332 333 3.737172 CCGCCCGCAAAGGTGAAG 61.737 66.667 0.00 0.00 39.99 3.02
386 387 3.866582 CTCTCCCCCGTCCATGGC 61.867 72.222 6.96 0.96 0.00 4.40
387 388 2.041922 TCTCTCCCCCGTCCATGG 60.042 66.667 4.97 4.97 0.00 3.66
388 389 2.136878 CCTCTCTCCCCCGTCCATG 61.137 68.421 0.00 0.00 0.00 3.66
389 390 2.283809 CCTCTCTCCCCCGTCCAT 59.716 66.667 0.00 0.00 0.00 3.41
390 391 4.075793 CCCTCTCTCCCCCGTCCA 62.076 72.222 0.00 0.00 0.00 4.02
391 392 4.862823 CCCCTCTCTCCCCCGTCC 62.863 77.778 0.00 0.00 0.00 4.79
392 393 4.862823 CCCCCTCTCTCCCCCGTC 62.863 77.778 0.00 0.00 0.00 4.79
700 701 4.719616 GTGAAACGGACAGCGCGC 62.720 66.667 26.66 26.66 0.00 6.86
701 702 4.072088 GGTGAAACGGACAGCGCG 62.072 66.667 0.00 0.00 38.12 6.86
702 703 3.723348 GGGTGAAACGGACAGCGC 61.723 66.667 0.00 0.00 38.12 5.92
703 704 3.047877 GGGGTGAAACGGACAGCG 61.048 66.667 0.00 0.00 38.12 5.18
704 705 1.104577 TTTGGGGTGAAACGGACAGC 61.105 55.000 0.00 0.00 38.12 4.40
705 706 0.666374 GTTTGGGGTGAAACGGACAG 59.334 55.000 0.00 0.00 38.12 3.51
706 707 0.752376 GGTTTGGGGTGAAACGGACA 60.752 55.000 0.00 0.00 38.12 4.02
707 708 1.788067 CGGTTTGGGGTGAAACGGAC 61.788 60.000 0.00 0.00 38.01 4.79
708 709 1.526455 CGGTTTGGGGTGAAACGGA 60.526 57.895 0.00 0.00 38.01 4.69
709 710 1.512156 CTCGGTTTGGGGTGAAACGG 61.512 60.000 0.00 0.00 38.12 4.44
710 711 1.946267 CTCGGTTTGGGGTGAAACG 59.054 57.895 0.00 0.00 38.12 3.60
711 712 1.658114 GCTCGGTTTGGGGTGAAAC 59.342 57.895 0.00 0.00 35.45 2.78
712 713 1.894756 CGCTCGGTTTGGGGTGAAA 60.895 57.895 0.00 0.00 0.00 2.69
713 714 2.281208 CGCTCGGTTTGGGGTGAA 60.281 61.111 0.00 0.00 0.00 3.18
716 717 4.572571 TTGCGCTCGGTTTGGGGT 62.573 61.111 9.73 0.00 0.00 4.95
717 718 4.038080 GTTGCGCTCGGTTTGGGG 62.038 66.667 9.73 0.00 0.00 4.96
718 719 2.070654 AAAGTTGCGCTCGGTTTGGG 62.071 55.000 9.73 0.00 0.00 4.12
719 720 0.934436 CAAAGTTGCGCTCGGTTTGG 60.934 55.000 9.73 0.00 0.00 3.28
720 721 0.934436 CCAAAGTTGCGCTCGGTTTG 60.934 55.000 9.73 12.76 0.00 2.93
721 722 1.358759 CCAAAGTTGCGCTCGGTTT 59.641 52.632 9.73 0.00 0.00 3.27
722 723 2.551912 CCCAAAGTTGCGCTCGGTT 61.552 57.895 9.73 0.00 0.00 4.44
723 724 2.978010 CCCAAAGTTGCGCTCGGT 60.978 61.111 9.73 0.00 0.00 4.69
724 725 4.404654 GCCCAAAGTTGCGCTCGG 62.405 66.667 9.73 0.00 0.00 4.63
725 726 4.404654 GGCCCAAAGTTGCGCTCG 62.405 66.667 9.73 0.00 32.76 5.03
726 727 4.404654 CGGCCCAAAGTTGCGCTC 62.405 66.667 9.73 1.40 32.76 5.03
730 731 4.986708 TCCCCGGCCCAAAGTTGC 62.987 66.667 0.00 0.00 0.00 4.17
731 732 2.037208 ATCCCCGGCCCAAAGTTG 59.963 61.111 0.00 0.00 0.00 3.16
732 733 2.037208 CATCCCCGGCCCAAAGTT 59.963 61.111 0.00 0.00 0.00 2.66
733 734 4.060667 CCATCCCCGGCCCAAAGT 62.061 66.667 0.00 0.00 0.00 2.66
734 735 4.839706 CCCATCCCCGGCCCAAAG 62.840 72.222 0.00 0.00 0.00 2.77
740 741 3.631952 TTTTCGACCCATCCCCGGC 62.632 63.158 0.00 0.00 0.00 6.13
741 742 1.747745 GTTTTCGACCCATCCCCGG 60.748 63.158 0.00 0.00 0.00 5.73
742 743 3.899395 GTTTTCGACCCATCCCCG 58.101 61.111 0.00 0.00 0.00 5.73
751 752 4.345465 CCGAATTCCGTCCGTTTTCGAC 62.345 54.545 13.67 0.00 41.09 4.20
752 753 2.260550 CCGAATTCCGTCCGTTTTCGA 61.261 52.381 13.67 0.00 41.09 3.71
753 754 0.094046 CCGAATTCCGTCCGTTTTCG 59.906 55.000 0.00 0.00 39.00 3.46
754 755 1.127397 GTCCGAATTCCGTCCGTTTTC 59.873 52.381 0.00 0.00 36.31 2.29
755 756 1.150827 GTCCGAATTCCGTCCGTTTT 58.849 50.000 0.00 0.00 36.31 2.43
756 757 0.033781 TGTCCGAATTCCGTCCGTTT 59.966 50.000 0.00 0.00 36.31 3.60
757 758 0.248289 ATGTCCGAATTCCGTCCGTT 59.752 50.000 0.00 0.00 36.31 4.44
758 759 0.248289 AATGTCCGAATTCCGTCCGT 59.752 50.000 0.00 0.00 36.31 4.69
759 760 1.062002 CAAATGTCCGAATTCCGTCCG 59.938 52.381 0.00 0.00 36.31 4.79
760 761 2.081462 ACAAATGTCCGAATTCCGTCC 58.919 47.619 0.00 0.00 36.31 4.79
761 762 3.000727 AGACAAATGTCCGAATTCCGTC 58.999 45.455 9.84 0.00 45.85 4.79
762 763 2.742053 CAGACAAATGTCCGAATTCCGT 59.258 45.455 9.84 0.00 45.85 4.69
763 764 2.742053 ACAGACAAATGTCCGAATTCCG 59.258 45.455 9.84 0.00 45.85 4.30
764 765 4.766404 AACAGACAAATGTCCGAATTCC 57.234 40.909 9.84 0.00 45.85 3.01
765 766 5.757886 TCAAACAGACAAATGTCCGAATTC 58.242 37.500 9.84 0.00 45.85 2.17
766 767 5.278463 CCTCAAACAGACAAATGTCCGAATT 60.278 40.000 9.84 0.00 45.85 2.17
767 768 4.216257 CCTCAAACAGACAAATGTCCGAAT 59.784 41.667 9.84 0.00 45.85 3.34
768 769 3.563808 CCTCAAACAGACAAATGTCCGAA 59.436 43.478 9.84 0.00 45.85 4.30
769 770 3.138304 CCTCAAACAGACAAATGTCCGA 58.862 45.455 9.84 0.00 45.85 4.55
770 771 2.350772 GCCTCAAACAGACAAATGTCCG 60.351 50.000 9.84 2.65 45.85 4.79
771 772 2.029918 GGCCTCAAACAGACAAATGTCC 60.030 50.000 9.84 0.00 45.85 4.02
772 773 2.350772 CGGCCTCAAACAGACAAATGTC 60.351 50.000 0.00 5.40 45.08 3.06
773 774 1.608590 CGGCCTCAAACAGACAAATGT 59.391 47.619 0.00 0.00 33.96 2.71
774 775 1.666888 GCGGCCTCAAACAGACAAATG 60.667 52.381 0.00 0.00 0.00 2.32
775 776 0.598065 GCGGCCTCAAACAGACAAAT 59.402 50.000 0.00 0.00 0.00 2.32
776 777 1.781025 CGCGGCCTCAAACAGACAAA 61.781 55.000 0.00 0.00 0.00 2.83
777 778 2.250939 CGCGGCCTCAAACAGACAA 61.251 57.895 0.00 0.00 0.00 3.18
778 779 2.664851 CGCGGCCTCAAACAGACA 60.665 61.111 0.00 0.00 0.00 3.41
779 780 4.090057 GCGCGGCCTCAAACAGAC 62.090 66.667 8.83 0.00 0.00 3.51
796 797 3.365265 AAAAGAAGCGGCCCAGCG 61.365 61.111 0.00 0.00 43.00 5.18
797 798 2.259511 CAAAAGAAGCGGCCCAGC 59.740 61.111 0.00 0.00 37.41 4.85
798 799 1.581447 GACAAAAGAAGCGGCCCAG 59.419 57.895 0.00 0.00 0.00 4.45
799 800 1.901464 GGACAAAAGAAGCGGCCCA 60.901 57.895 0.00 0.00 0.00 5.36
800 801 2.636412 GGGACAAAAGAAGCGGCCC 61.636 63.158 0.00 0.00 0.00 5.80
801 802 1.179174 AAGGGACAAAAGAAGCGGCC 61.179 55.000 0.00 0.00 0.00 6.13
802 803 0.673985 AAAGGGACAAAAGAAGCGGC 59.326 50.000 0.00 0.00 0.00 6.53
803 804 3.305131 GGTAAAAGGGACAAAAGAAGCGG 60.305 47.826 0.00 0.00 0.00 5.52
804 805 3.305131 GGGTAAAAGGGACAAAAGAAGCG 60.305 47.826 0.00 0.00 0.00 4.68
805 806 3.006537 GGGGTAAAAGGGACAAAAGAAGC 59.993 47.826 0.00 0.00 0.00 3.86
806 807 4.219919 TGGGGTAAAAGGGACAAAAGAAG 58.780 43.478 0.00 0.00 0.00 2.85
807 808 4.267341 TGGGGTAAAAGGGACAAAAGAA 57.733 40.909 0.00 0.00 0.00 2.52
808 809 3.975479 TGGGGTAAAAGGGACAAAAGA 57.025 42.857 0.00 0.00 0.00 2.52
809 810 4.699637 GTTTGGGGTAAAAGGGACAAAAG 58.300 43.478 0.00 0.00 30.73 2.27
810 811 3.132467 CGTTTGGGGTAAAAGGGACAAAA 59.868 43.478 0.00 0.00 30.73 2.44
811 812 2.694109 CGTTTGGGGTAAAAGGGACAAA 59.306 45.455 0.00 0.00 0.00 2.83
812 813 2.308690 CGTTTGGGGTAAAAGGGACAA 58.691 47.619 0.00 0.00 0.00 3.18
813 814 1.479021 CCGTTTGGGGTAAAAGGGACA 60.479 52.381 2.96 0.00 44.29 4.02
814 815 1.202915 TCCGTTTGGGGTAAAAGGGAC 60.203 52.381 6.93 0.00 44.84 4.46
815 816 1.147333 TCCGTTTGGGGTAAAAGGGA 58.853 50.000 6.93 6.93 46.53 4.20
816 817 1.250328 GTCCGTTTGGGGTAAAAGGG 58.750 55.000 0.00 2.72 44.83 3.95
817 818 0.876399 CGTCCGTTTGGGGTAAAAGG 59.124 55.000 0.00 0.00 45.73 3.11
818 819 0.876399 CCGTCCGTTTGGGGTAAAAG 59.124 55.000 0.00 0.00 36.01 2.27
819 820 0.536915 CCCGTCCGTTTGGGGTAAAA 60.537 55.000 0.00 0.00 42.05 1.52
820 821 1.072852 CCCGTCCGTTTGGGGTAAA 59.927 57.895 0.00 0.00 42.05 2.01
821 822 2.749016 CCCGTCCGTTTGGGGTAA 59.251 61.111 0.00 0.00 42.05 2.85
833 834 2.365095 CTATTCTGTCCGCCCCCGTC 62.365 65.000 0.00 0.00 0.00 4.79
834 835 2.364579 TATTCTGTCCGCCCCCGT 60.365 61.111 0.00 0.00 0.00 5.28
835 836 2.088674 CTCTATTCTGTCCGCCCCCG 62.089 65.000 0.00 0.00 0.00 5.73
836 837 1.049289 ACTCTATTCTGTCCGCCCCC 61.049 60.000 0.00 0.00 0.00 5.40
837 838 0.831307 AACTCTATTCTGTCCGCCCC 59.169 55.000 0.00 0.00 0.00 5.80
838 839 1.941325 CAACTCTATTCTGTCCGCCC 58.059 55.000 0.00 0.00 0.00 6.13
839 840 1.291132 GCAACTCTATTCTGTCCGCC 58.709 55.000 0.00 0.00 0.00 6.13
840 841 0.924090 CGCAACTCTATTCTGTCCGC 59.076 55.000 0.00 0.00 0.00 5.54
841 842 0.924090 GCGCAACTCTATTCTGTCCG 59.076 55.000 0.30 0.00 0.00 4.79
842 843 0.924090 CGCGCAACTCTATTCTGTCC 59.076 55.000 8.75 0.00 0.00 4.02
843 844 0.924090 CCGCGCAACTCTATTCTGTC 59.076 55.000 8.75 0.00 0.00 3.51
844 845 0.246635 ACCGCGCAACTCTATTCTGT 59.753 50.000 8.75 0.00 0.00 3.41
845 846 0.647410 CACCGCGCAACTCTATTCTG 59.353 55.000 8.75 0.00 0.00 3.02
846 847 0.460284 CCACCGCGCAACTCTATTCT 60.460 55.000 8.75 0.00 0.00 2.40
847 848 0.459585 TCCACCGCGCAACTCTATTC 60.460 55.000 8.75 0.00 0.00 1.75
848 849 0.460284 CTCCACCGCGCAACTCTATT 60.460 55.000 8.75 0.00 0.00 1.73
849 850 1.141881 CTCCACCGCGCAACTCTAT 59.858 57.895 8.75 0.00 0.00 1.98
850 851 1.812686 AACTCCACCGCGCAACTCTA 61.813 55.000 8.75 0.00 0.00 2.43
851 852 3.165160 AACTCCACCGCGCAACTCT 62.165 57.895 8.75 0.00 0.00 3.24
852 853 2.665185 AACTCCACCGCGCAACTC 60.665 61.111 8.75 0.00 0.00 3.01
853 854 2.972505 CAACTCCACCGCGCAACT 60.973 61.111 8.75 0.00 0.00 3.16
854 855 4.025401 CCAACTCCACCGCGCAAC 62.025 66.667 8.75 0.00 0.00 4.17
859 860 4.329545 TGAGGCCAACTCCACCGC 62.330 66.667 5.01 0.00 46.01 5.68
860 861 2.358737 GTGAGGCCAACTCCACCG 60.359 66.667 5.01 0.00 46.01 4.94
861 862 2.034221 GGTGAGGCCAACTCCACC 59.966 66.667 5.01 10.38 46.01 4.61
862 863 2.836154 TGGTGAGGCCAACTCCAC 59.164 61.111 16.17 10.40 45.94 4.02
1574 1871 6.484643 CCCTAAAGTGGACATTCAGACATATG 59.515 42.308 0.00 0.00 0.00 1.78
1883 2187 4.489679 AAAGATTCTTTTGAGTGTCGGC 57.510 40.909 5.82 0.00 0.00 5.54
2068 2384 5.564848 GCCTACATCAACAGAACCCTTTTTC 60.565 44.000 0.00 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.