Multiple sequence alignment - TraesCS5A01G507700

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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 TraesCS5A01G507700 chr5A 100.000 3834 0 0 1 3834 671979784 671975951 0.000000e+00 7081.0
1 TraesCS5A01G507700 chr5A 81.164 1306 157 37 1703 3002 672027960 672026738 0.000000e+00 966.0
2 TraesCS5A01G507700 chr5A 85.544 588 65 9 1028 1611 671990616 671990045 7.090000e-167 597.0
3 TraesCS5A01G507700 chr5A 78.398 986 150 36 1263 2222 671954983 671955931 1.990000e-162 582.0
4 TraesCS5A01G507700 chr5A 80.081 738 98 28 3103 3830 671957211 671957909 1.590000e-138 503.0
5 TraesCS5A01G507700 chr5A 84.524 504 54 13 2511 3011 671988873 671988391 9.640000e-131 477.0
6 TraesCS5A01G507700 chr5A 80.218 642 83 23 3139 3763 671988135 671987521 3.520000e-120 442.0
7 TraesCS5A01G507700 chr5A 100.000 33 0 0 885 917 379236669 379236637 1.150000e-05 62.1
8 TraesCS5A01G507700 chr5A 97.143 35 0 1 885 919 53465044 53465077 1.490000e-04 58.4
9 TraesCS5A01G507700 chr5A 100.000 31 0 0 885 915 583688704 583688734 1.490000e-04 58.4
10 TraesCS5A01G507700 chr4D 92.415 3019 145 29 839 3832 490405460 490402501 0.000000e+00 4229.0
11 TraesCS5A01G507700 chr4D 80.795 1963 278 54 1073 3011 490413392 490411505 0.000000e+00 1445.0
12 TraesCS5A01G507700 chr4D 79.919 737 100 28 3103 3830 490377753 490378450 7.400000e-137 497.0
13 TraesCS5A01G507700 chr4D 79.907 642 85 24 3139 3763 490411253 490410639 7.610000e-117 431.0
14 TraesCS5A01G507700 chr4B 91.844 2918 158 29 946 3832 630015962 630013094 0.000000e+00 3997.0
15 TraesCS5A01G507700 chr4B 80.931 1138 145 36 979 2085 630099923 630098827 0.000000e+00 833.0
16 TraesCS5A01G507700 chr4B 78.806 1340 187 49 1689 2996 630043735 630042461 0.000000e+00 811.0
17 TraesCS5A01G507700 chr4B 82.209 860 105 25 2087 2933 630098742 630097918 0.000000e+00 697.0
18 TraesCS5A01G507700 chr4B 84.437 604 73 11 1019 1621 630044654 630044071 3.320000e-160 575.0
19 TraesCS5A01G507700 chr7D 86.683 826 87 11 2 808 636488240 636489061 0.000000e+00 894.0
20 TraesCS5A01G507700 chr7D 83.231 817 102 22 2 794 95861215 95862020 0.000000e+00 717.0
21 TraesCS5A01G507700 chr3D 83.836 829 99 20 2 800 546200652 546199829 0.000000e+00 756.0
22 TraesCS5A01G507700 chr6D 87.669 665 59 9 2 646 80063313 80062652 0.000000e+00 752.0
23 TraesCS5A01G507700 chr6D 82.156 835 96 25 2 794 148164111 148164934 0.000000e+00 667.0
24 TraesCS5A01G507700 chr7A 83.273 831 103 21 2 800 51667679 51666853 0.000000e+00 732.0
25 TraesCS5A01G507700 chr1D 83.516 819 100 20 2 794 249758584 249759393 0.000000e+00 732.0
26 TraesCS5A01G507700 chr1D 82.403 824 87 27 2 794 331882595 331883391 0.000000e+00 665.0
27 TraesCS5A01G507700 chr1D 100.000 31 0 0 887 917 483523622 483523652 1.490000e-04 58.4
28 TraesCS5A01G507700 chr4A 85.387 698 76 12 2 680 696107198 696106508 0.000000e+00 701.0
29 TraesCS5A01G507700 chr2A 82.557 837 93 34 10 808 333765730 333764909 0.000000e+00 688.0
30 TraesCS5A01G507700 chr5B 80.714 840 101 35 10 808 621566656 621567475 7.090000e-167 597.0
31 TraesCS5A01G507700 chr5B 82.712 671 87 17 963 1629 505779529 505778884 1.550000e-158 569.0
32 TraesCS5A01G507700 chr2D 80.301 731 71 49 117 808 284521441 284522137 5.760000e-133 484.0
33 TraesCS5A01G507700 chr2B 88.136 59 5 2 2746 2804 668033236 668033180 6.870000e-08 69.4
34 TraesCS5A01G507700 chr2B 100.000 31 0 0 885 915 408298656 408298626 1.490000e-04 58.4
35 TraesCS5A01G507700 chr1B 97.222 36 1 0 885 920 223148182 223148217 1.150000e-05 62.1
36 TraesCS5A01G507700 chr3B 100.000 31 0 0 885 915 583085484 583085514 1.490000e-04 58.4
37 TraesCS5A01G507700 chrUn 100.000 30 0 0 887 916 26725234 26725205 5.350000e-04 56.5


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 TraesCS5A01G507700 chr5A 671975951 671979784 3833 True 7081.000000 7081 100.000000 1 3834 1 chr5A.!!$R2 3833
1 TraesCS5A01G507700 chr5A 672026738 672027960 1222 True 966.000000 966 81.164000 1703 3002 1 chr5A.!!$R3 1299
2 TraesCS5A01G507700 chr5A 671954983 671957909 2926 False 542.500000 582 79.239500 1263 3830 2 chr5A.!!$F3 2567
3 TraesCS5A01G507700 chr5A 671987521 671990616 3095 True 505.333333 597 83.428667 1028 3763 3 chr5A.!!$R4 2735
4 TraesCS5A01G507700 chr4D 490402501 490405460 2959 True 4229.000000 4229 92.415000 839 3832 1 chr4D.!!$R1 2993
5 TraesCS5A01G507700 chr4D 490410639 490413392 2753 True 938.000000 1445 80.351000 1073 3763 2 chr4D.!!$R2 2690
6 TraesCS5A01G507700 chr4D 490377753 490378450 697 False 497.000000 497 79.919000 3103 3830 1 chr4D.!!$F1 727
7 TraesCS5A01G507700 chr4B 630013094 630015962 2868 True 3997.000000 3997 91.844000 946 3832 1 chr4B.!!$R1 2886
8 TraesCS5A01G507700 chr4B 630097918 630099923 2005 True 765.000000 833 81.570000 979 2933 2 chr4B.!!$R3 1954
9 TraesCS5A01G507700 chr4B 630042461 630044654 2193 True 693.000000 811 81.621500 1019 2996 2 chr4B.!!$R2 1977
10 TraesCS5A01G507700 chr7D 636488240 636489061 821 False 894.000000 894 86.683000 2 808 1 chr7D.!!$F2 806
11 TraesCS5A01G507700 chr7D 95861215 95862020 805 False 717.000000 717 83.231000 2 794 1 chr7D.!!$F1 792
12 TraesCS5A01G507700 chr3D 546199829 546200652 823 True 756.000000 756 83.836000 2 800 1 chr3D.!!$R1 798
13 TraesCS5A01G507700 chr6D 80062652 80063313 661 True 752.000000 752 87.669000 2 646 1 chr6D.!!$R1 644
14 TraesCS5A01G507700 chr6D 148164111 148164934 823 False 667.000000 667 82.156000 2 794 1 chr6D.!!$F1 792
15 TraesCS5A01G507700 chr7A 51666853 51667679 826 True 732.000000 732 83.273000 2 800 1 chr7A.!!$R1 798
16 TraesCS5A01G507700 chr1D 249758584 249759393 809 False 732.000000 732 83.516000 2 794 1 chr1D.!!$F1 792
17 TraesCS5A01G507700 chr1D 331882595 331883391 796 False 665.000000 665 82.403000 2 794 1 chr1D.!!$F2 792
18 TraesCS5A01G507700 chr4A 696106508 696107198 690 True 701.000000 701 85.387000 2 680 1 chr4A.!!$R1 678
19 TraesCS5A01G507700 chr2A 333764909 333765730 821 True 688.000000 688 82.557000 10 808 1 chr2A.!!$R1 798
20 TraesCS5A01G507700 chr5B 621566656 621567475 819 False 597.000000 597 80.714000 10 808 1 chr5B.!!$F1 798
21 TraesCS5A01G507700 chr5B 505778884 505779529 645 True 569.000000 569 82.712000 963 1629 1 chr5B.!!$R1 666
22 TraesCS5A01G507700 chr2D 284521441 284522137 696 False 484.000000 484 80.301000 117 808 1 chr2D.!!$F1 691

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
809 933 0.039437 CGGGAGATATTGACGTCCGG 60.039 60.0 14.12 0.00 33.27 5.14 F
815 939 0.104304 ATATTGACGTCCGGCAGTCC 59.896 55.0 21.06 8.41 36.61 3.85 F
1898 2403 0.179089 CCCGAGCCAGATTGTCAGAG 60.179 60.0 0.00 0.00 0.00 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1895 2400 0.459489 GCTCTGACAATCTCCGCTCT 59.541 55.0 0.00 0.0 0.00 4.09 R
2272 2887 0.698238 TTAGCACAGTTCCTGCCCAT 59.302 50.0 0.00 0.0 35.01 4.00 R
3434 4563 2.118313 AATAACTAACCCGTGGGCAC 57.882 50.0 4.41 0.0 39.32 5.01 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
74 81 6.355747 TGGTGCACTCATGATAATATTCACA 58.644 36.000 17.98 0.00 0.00 3.58
126 136 9.296400 GTAATGTGCATCACGGTAAATTTAAAT 57.704 29.630 0.00 0.00 37.14 1.40
181 226 7.278424 CACCATTTGGCAAACTTATAGATTTGG 59.722 37.037 16.00 16.17 39.32 3.28
182 227 7.180051 ACCATTTGGCAAACTTATAGATTTGGA 59.820 33.333 21.93 0.00 39.32 3.53
199 244 3.985019 TGGATTTGCCATCAATGCTTT 57.015 38.095 0.00 0.00 43.33 3.51
236 281 9.791820 CCATTGAAAATTTTCTTTCTTTTTGCT 57.208 25.926 26.73 0.00 38.02 3.91
252 297 8.419076 TCTTTTTGCTTCTTGTCAAAATTACC 57.581 30.769 0.00 0.00 40.50 2.85
253 298 8.257306 TCTTTTTGCTTCTTGTCAAAATTACCT 58.743 29.630 0.00 0.00 40.50 3.08
297 345 5.554822 TTAGTTTTATGGTCACGGCAATC 57.445 39.130 0.00 0.00 0.00 2.67
341 389 2.993264 GTTGTGCTGGCCATGGCT 60.993 61.111 34.70 0.00 41.60 4.75
342 390 2.992689 TTGTGCTGGCCATGGCTG 60.993 61.111 34.70 26.82 41.60 4.85
520 598 6.349300 ACTGTGGTAGCCTCAACAATTATAG 58.651 40.000 0.00 0.00 0.00 1.31
593 679 4.081697 CAGTTTTCCAGTTGGGTTGTCTTT 60.082 41.667 0.00 0.00 38.11 2.52
682 801 1.215382 CAGCTGACGTGGGATTCGA 59.785 57.895 8.42 0.00 0.00 3.71
722 844 2.096614 GGAAGATCGCAACGAACGAAAA 60.097 45.455 0.14 0.00 43.71 2.29
774 898 1.868987 TTCGTTCGGATCGCTCACCA 61.869 55.000 3.66 0.00 0.00 4.17
779 903 2.125106 GGATCGCTCACCACCCAC 60.125 66.667 0.00 0.00 0.00 4.61
808 932 0.949397 TCGGGAGATATTGACGTCCG 59.051 55.000 14.12 6.65 37.61 4.79
809 933 0.039437 CGGGAGATATTGACGTCCGG 60.039 60.000 14.12 0.00 33.27 5.14
810 934 0.319641 GGGAGATATTGACGTCCGGC 60.320 60.000 14.12 0.00 0.00 6.13
811 935 0.387929 GGAGATATTGACGTCCGGCA 59.612 55.000 14.12 0.00 0.00 5.69
812 936 1.603172 GGAGATATTGACGTCCGGCAG 60.603 57.143 14.12 0.00 33.06 4.85
813 937 1.067212 GAGATATTGACGTCCGGCAGT 59.933 52.381 14.12 0.00 33.06 4.40
814 938 1.067212 AGATATTGACGTCCGGCAGTC 59.933 52.381 14.12 18.36 33.06 3.51
815 939 0.104304 ATATTGACGTCCGGCAGTCC 59.896 55.000 21.06 8.41 36.61 3.85
816 940 1.952102 TATTGACGTCCGGCAGTCCC 61.952 60.000 21.06 4.38 36.61 4.46
818 942 4.736896 GACGTCCGGCAGTCCCAC 62.737 72.222 15.47 0.00 0.00 4.61
820 944 4.308458 CGTCCGGCAGTCCCACAA 62.308 66.667 0.00 0.00 0.00 3.33
821 945 2.358737 GTCCGGCAGTCCCACAAG 60.359 66.667 0.00 0.00 0.00 3.16
822 946 4.329545 TCCGGCAGTCCCACAAGC 62.330 66.667 0.00 0.00 0.00 4.01
830 954 4.257654 TCCCACAAGCGGCGGAAA 62.258 61.111 9.78 0.00 0.00 3.13
831 955 3.291383 CCCACAAGCGGCGGAAAA 61.291 61.111 9.78 0.00 0.00 2.29
832 956 2.725008 CCACAAGCGGCGGAAAAA 59.275 55.556 9.78 0.00 0.00 1.94
853 977 2.252346 GCCGCTGCAGATGATCTGG 61.252 63.158 22.69 9.17 44.43 3.86
855 979 2.595878 CGCTGCAGATGATCTGGCG 61.596 63.158 24.07 24.07 44.18 5.69
921 1045 2.752829 CGCCCATCAGTCCCCATTTTAT 60.753 50.000 0.00 0.00 0.00 1.40
922 1046 3.497763 CGCCCATCAGTCCCCATTTTATA 60.498 47.826 0.00 0.00 0.00 0.98
923 1047 3.826729 GCCCATCAGTCCCCATTTTATAC 59.173 47.826 0.00 0.00 0.00 1.47
924 1048 4.407365 CCCATCAGTCCCCATTTTATACC 58.593 47.826 0.00 0.00 0.00 2.73
925 1049 4.407365 CCATCAGTCCCCATTTTATACCC 58.593 47.826 0.00 0.00 0.00 3.69
926 1050 4.141041 CCATCAGTCCCCATTTTATACCCA 60.141 45.833 0.00 0.00 0.00 4.51
962 1090 2.486042 GAGTCTCCACTCGACGCC 59.514 66.667 0.00 0.00 39.91 5.68
993 1121 1.080538 ACTCCCGAACCCTAGCCTT 59.919 57.895 0.00 0.00 0.00 4.35
1241 1378 2.881352 CGGCTTCTTCGACGAGGC 60.881 66.667 16.40 16.40 37.71 4.70
1246 1383 1.737363 GCTTCTTCGACGAGGCATTCT 60.737 52.381 19.17 0.00 36.19 2.40
1483 1620 1.228862 TGCAGGAAAAAGGGGAGGC 60.229 57.895 0.00 0.00 0.00 4.70
1605 1764 0.944386 ATTCTGACGGCACACACAAC 59.056 50.000 0.00 0.00 0.00 3.32
1617 1776 1.135024 ACACACAACTTTGCTTGCCTG 60.135 47.619 0.00 0.00 0.00 4.85
1621 1780 3.004734 ACACAACTTTGCTTGCCTGTATC 59.995 43.478 0.00 0.00 0.00 2.24
1623 1782 3.636300 ACAACTTTGCTTGCCTGTATCAA 59.364 39.130 0.00 0.00 0.00 2.57
1817 2322 3.369385 CGGCAGACGTTAATGTAGTAGG 58.631 50.000 0.00 0.00 37.93 3.18
1895 2400 0.690192 TTTCCCGAGCCAGATTGTCA 59.310 50.000 0.00 0.00 0.00 3.58
1896 2401 0.250234 TTCCCGAGCCAGATTGTCAG 59.750 55.000 0.00 0.00 0.00 3.51
1897 2402 0.614697 TCCCGAGCCAGATTGTCAGA 60.615 55.000 0.00 0.00 0.00 3.27
1898 2403 0.179089 CCCGAGCCAGATTGTCAGAG 60.179 60.000 0.00 0.00 0.00 3.35
1899 2404 0.809241 CCGAGCCAGATTGTCAGAGC 60.809 60.000 0.00 0.00 0.00 4.09
1900 2405 1.144565 CGAGCCAGATTGTCAGAGCG 61.145 60.000 0.00 0.00 0.00 5.03
1901 2406 0.809241 GAGCCAGATTGTCAGAGCGG 60.809 60.000 0.00 0.00 0.00 5.52
1902 2407 1.219124 GCCAGATTGTCAGAGCGGA 59.781 57.895 0.00 0.00 0.00 5.54
1903 2408 0.809241 GCCAGATTGTCAGAGCGGAG 60.809 60.000 0.00 0.00 0.00 4.63
1904 2409 0.820226 CCAGATTGTCAGAGCGGAGA 59.180 55.000 0.00 0.00 0.00 3.71
1905 2410 1.411977 CCAGATTGTCAGAGCGGAGAT 59.588 52.381 0.00 0.00 0.00 2.75
1906 2411 2.158986 CCAGATTGTCAGAGCGGAGATT 60.159 50.000 0.00 0.00 0.00 2.40
1907 2412 2.864946 CAGATTGTCAGAGCGGAGATTG 59.135 50.000 0.00 0.00 0.00 2.67
1976 2481 0.603065 GTTGTTGGATGGGAACTGCC 59.397 55.000 0.00 0.00 0.00 4.85
2012 2529 4.641989 GCTAGATGGGCTCTTTTCATTTGA 59.358 41.667 0.00 0.00 35.28 2.69
2023 2540 2.940994 TTCATTTGAACTGACCGGGA 57.059 45.000 6.32 0.00 0.00 5.14
2031 2548 2.143925 GAACTGACCGGGAAGTCAAAG 58.856 52.381 6.32 0.00 45.77 2.77
2131 2731 3.871594 GCTTGAGTCCACGCAGTTTATAT 59.128 43.478 0.00 0.00 41.61 0.86
2162 2762 8.761575 ATTGAACACCAAAGCAATTACATTAG 57.238 30.769 0.00 0.00 38.43 1.73
2163 2763 7.517614 TGAACACCAAAGCAATTACATTAGA 57.482 32.000 0.00 0.00 0.00 2.10
2175 2775 6.260271 GCAATTACATTAGAACCAGGACCTAC 59.740 42.308 0.00 0.00 0.00 3.18
2198 2798 9.627395 CTACTATCCGTACAGAAATTTCTATGG 57.373 37.037 20.07 18.80 35.34 2.74
2217 2817 2.498481 TGGTACAGGTAATCCCTTGTCG 59.502 50.000 0.00 0.00 42.73 4.35
2272 2887 4.265893 TCTAATTATTGGCAACTGGCGAA 58.734 39.130 0.00 0.00 46.16 4.70
2302 3038 7.865706 AGGAACTGTGCTAAAACTATATTGG 57.134 36.000 0.00 0.00 37.18 3.16
2616 3383 8.074613 ACAGCTAAACAGTCCTAACATGTATA 57.925 34.615 0.00 0.00 0.00 1.47
2617 3384 8.537016 ACAGCTAAACAGTCCTAACATGTATAA 58.463 33.333 0.00 0.00 0.00 0.98
2657 3428 3.510388 TGATTGTCTCTCTACCTTGCG 57.490 47.619 0.00 0.00 0.00 4.85
2659 3430 0.966179 TTGTCTCTCTACCTTGCGCA 59.034 50.000 5.66 5.66 0.00 6.09
2866 3652 5.877012 CCCATTAGGTATGCTAATGTGCTAG 59.123 44.000 2.76 0.00 40.97 3.42
2867 3653 6.467677 CCATTAGGTATGCTAATGTGCTAGT 58.532 40.000 2.76 0.00 40.97 2.57
2868 3654 7.310423 CCCATTAGGTATGCTAATGTGCTAGTA 60.310 40.741 2.76 0.00 40.97 1.82
2892 3678 4.219507 TGTTTGTTGAACAAGTGATGTGGT 59.780 37.500 10.91 0.00 44.95 4.16
2996 3786 7.095691 GCTGTAATCATTAGCAGAGATCAGTTC 60.096 40.741 9.79 0.00 37.40 3.01
2998 3788 7.708322 TGTAATCATTAGCAGAGATCAGTTCAC 59.292 37.037 0.00 0.00 0.00 3.18
3003 3793 2.757314 AGCAGAGATCAGTTCACGATGA 59.243 45.455 0.00 0.00 0.00 2.92
3006 3796 3.490155 CAGAGATCAGTTCACGATGATGC 59.510 47.826 0.00 0.00 36.30 3.91
3007 3797 3.384146 AGAGATCAGTTCACGATGATGCT 59.616 43.478 0.00 0.00 36.30 3.79
3008 3798 4.118410 GAGATCAGTTCACGATGATGCTT 58.882 43.478 0.00 0.00 36.30 3.91
3009 3799 4.118410 AGATCAGTTCACGATGATGCTTC 58.882 43.478 0.00 0.00 36.30 3.86
3010 3800 3.599730 TCAGTTCACGATGATGCTTCT 57.400 42.857 0.88 0.00 0.00 2.85
3011 3801 3.256558 TCAGTTCACGATGATGCTTCTG 58.743 45.455 0.88 0.00 0.00 3.02
3012 3802 3.056607 TCAGTTCACGATGATGCTTCTGA 60.057 43.478 0.88 0.00 0.00 3.27
3013 3803 3.869832 CAGTTCACGATGATGCTTCTGAT 59.130 43.478 0.88 0.00 0.00 2.90
3014 3804 4.331992 CAGTTCACGATGATGCTTCTGATT 59.668 41.667 0.88 0.00 0.00 2.57
3015 3805 4.940046 AGTTCACGATGATGCTTCTGATTT 59.060 37.500 0.88 0.00 0.00 2.17
3016 3806 5.413833 AGTTCACGATGATGCTTCTGATTTT 59.586 36.000 0.88 0.00 0.00 1.82
3017 3807 6.595326 AGTTCACGATGATGCTTCTGATTTTA 59.405 34.615 0.88 0.00 0.00 1.52
3018 3808 7.281774 AGTTCACGATGATGCTTCTGATTTTAT 59.718 33.333 0.88 0.00 0.00 1.40
3019 3809 7.558161 TCACGATGATGCTTCTGATTTTATT 57.442 32.000 0.88 0.00 0.00 1.40
3020 3810 7.988737 TCACGATGATGCTTCTGATTTTATTT 58.011 30.769 0.88 0.00 0.00 1.40
3021 3811 8.461222 TCACGATGATGCTTCTGATTTTATTTT 58.539 29.630 0.88 0.00 0.00 1.82
3022 3812 9.720667 CACGATGATGCTTCTGATTTTATTTTA 57.279 29.630 0.88 0.00 0.00 1.52
3199 4314 6.719370 TCATATTTTCCTTGCAACTAACAGGT 59.281 34.615 0.00 0.00 0.00 4.00
3275 4394 9.639563 TGATTTATGGAGGCATCTTATTGTTTA 57.360 29.630 0.00 0.00 0.00 2.01
3324 4443 5.305139 TGTTCGAATTAGTGACATCTCGA 57.695 39.130 0.00 0.00 33.83 4.04
3348 4467 3.627395 TGGTTATTACAGACCTGGCAG 57.373 47.619 7.75 7.75 36.86 4.85
3353 4472 2.163818 TTACAGACCTGGCAGTTTCG 57.836 50.000 14.43 8.30 34.19 3.46
3377 4496 6.144080 CGTTGTATCTAAGCTGCATTAGTACC 59.856 42.308 1.02 1.52 34.87 3.34
3384 4503 2.100916 AGCTGCATTAGTACCGTACTGG 59.899 50.000 19.60 10.81 46.41 4.00
3410 4539 2.121786 TGTTTGCTTCGTAGTGTCGAC 58.878 47.619 9.11 9.11 39.58 4.20
3434 4563 6.757010 ACAACGTAGACTGAAATATGCTTAGG 59.243 38.462 0.00 0.00 0.00 2.69
3497 4626 6.801539 GACTACATGTCAGATGGTTTCAAA 57.198 37.500 0.00 0.00 44.73 2.69
3498 4627 6.560253 ACTACATGTCAGATGGTTTCAAAC 57.440 37.500 0.00 0.00 0.00 2.93
3499 4628 6.299141 ACTACATGTCAGATGGTTTCAAACT 58.701 36.000 0.00 0.00 0.00 2.66
3681 4815 7.816513 TGATGCAGCATGAATACTAGAGAATAC 59.183 37.037 14.22 0.00 31.27 1.89
3717 4851 9.209175 CCATAGTTATGCTATTAAGGAACTGAC 57.791 37.037 0.00 0.00 37.18 3.51
3832 4969 9.627395 GTATGTACCAATCATCATACTAGTGAC 57.373 37.037 5.39 0.00 39.32 3.67
3833 4970 7.898014 TGTACCAATCATCATACTAGTGACT 57.102 36.000 5.39 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 23 2.025605 ACTGCCATGAGACATGGACATT 60.026 45.455 27.90 17.82 41.64 2.71
51 54 6.866010 TGTGAATATTATCATGAGTGCACC 57.134 37.500 14.63 5.76 0.00 5.01
52 55 9.740239 AAAATGTGAATATTATCATGAGTGCAC 57.260 29.630 9.40 9.40 0.00 4.57
80 90 7.124901 ACATTACCCCATGCATTAACATGTTTA 59.875 33.333 17.78 8.27 44.88 2.01
126 136 2.952978 AGTGGTGTAAATTTGCCGTTGA 59.047 40.909 0.00 0.00 0.00 3.18
205 250 9.889128 AAAGAAAGAAAATTTTCAATGGTCAGA 57.111 25.926 28.00 0.00 39.08 3.27
236 281 8.973378 CGCATAAAAAGGTAATTTTGACAAGAA 58.027 29.630 0.00 0.00 40.27 2.52
251 296 1.476085 TGCCATGGTCGCATAAAAAGG 59.524 47.619 14.67 0.00 0.00 3.11
252 297 2.937469 TGCCATGGTCGCATAAAAAG 57.063 45.000 14.67 0.00 0.00 2.27
253 298 3.667497 TTTGCCATGGTCGCATAAAAA 57.333 38.095 14.67 0.00 35.83 1.94
325 373 2.992689 CAGCCATGGCCAGCACAA 60.993 61.111 33.14 0.00 43.17 3.33
331 379 1.892474 GTAAAGAAACAGCCATGGCCA 59.108 47.619 33.14 8.56 43.17 5.36
333 381 1.732405 GCGTAAAGAAACAGCCATGGC 60.732 52.381 30.12 30.12 42.33 4.40
341 389 1.508808 GCCGTGGGCGTAAAGAAACA 61.509 55.000 0.00 0.00 39.62 2.83
342 390 1.208358 GCCGTGGGCGTAAAGAAAC 59.792 57.895 0.00 0.00 39.62 2.78
490 561 3.682592 TGAGGCTACCACAGTACCTAT 57.317 47.619 0.00 0.00 33.07 2.57
520 598 6.035327 GCCACAAAAATCTAGACATCAATTGC 59.965 38.462 0.00 0.00 0.00 3.56
568 652 2.758423 ACAACCCAACTGGAAAACTGAC 59.242 45.455 0.00 0.00 37.39 3.51
682 801 2.597340 CCAGCCCGAACCATCCAT 59.403 61.111 0.00 0.00 0.00 3.41
722 844 0.829182 AGGGAAGTACCACCGAACGT 60.829 55.000 0.00 0.00 41.20 3.99
774 898 4.303993 CGAACGTTCGGGGTGGGT 62.304 66.667 36.53 0.00 46.30 4.51
813 937 3.776347 TTTTCCGCCGCTTGTGGGA 62.776 57.895 2.21 0.00 45.26 4.37
814 938 2.851071 TTTTTCCGCCGCTTGTGGG 61.851 57.895 2.21 0.00 45.26 4.61
815 939 2.725008 TTTTTCCGCCGCTTGTGG 59.275 55.556 0.00 0.00 46.66 4.17
835 959 2.252346 CCAGATCATCTGCAGCGGC 61.252 63.158 9.41 0.31 42.98 6.53
836 960 2.252346 GCCAGATCATCTGCAGCGG 61.252 63.158 9.41 3.20 42.98 5.52
837 961 2.595878 CGCCAGATCATCTGCAGCG 61.596 63.158 19.63 19.63 44.18 5.18
838 962 2.252346 CCGCCAGATCATCTGCAGC 61.252 63.158 9.41 7.44 42.98 5.25
839 963 2.252346 GCCGCCAGATCATCTGCAG 61.252 63.158 9.41 7.63 42.98 4.41
840 964 2.203112 GCCGCCAGATCATCTGCA 60.203 61.111 9.41 0.00 42.98 4.41
841 965 2.976903 GGCCGCCAGATCATCTGC 60.977 66.667 9.41 4.22 42.98 4.26
842 966 2.664185 CGGCCGCCAGATCATCTG 60.664 66.667 14.67 7.79 43.91 2.90
921 1045 2.193301 AAGGGGTAGGGGGTGGGTA 61.193 63.158 0.00 0.00 0.00 3.69
922 1046 3.559172 AAGGGGTAGGGGGTGGGT 61.559 66.667 0.00 0.00 0.00 4.51
923 1047 2.694992 GAAGGGGTAGGGGGTGGG 60.695 72.222 0.00 0.00 0.00 4.61
924 1048 2.126372 TGAAGGGGTAGGGGGTGG 59.874 66.667 0.00 0.00 0.00 4.61
925 1049 1.229853 AGTGAAGGGGTAGGGGGTG 60.230 63.158 0.00 0.00 0.00 4.61
926 1050 1.082392 GAGTGAAGGGGTAGGGGGT 59.918 63.158 0.00 0.00 0.00 4.95
974 1102 1.265454 AAGGCTAGGGTTCGGGAGTG 61.265 60.000 0.00 0.00 0.00 3.51
993 1121 4.802051 GGGCTGCTCATTCCGGCA 62.802 66.667 0.00 0.00 36.31 5.69
1241 1378 0.725686 CCGCTTGTCTCTGCAGAATG 59.274 55.000 18.85 7.29 40.87 2.67
1246 1383 4.704833 GGGCCGCTTGTCTCTGCA 62.705 66.667 0.00 0.00 0.00 4.41
1380 1517 1.153489 GCGCTTCTGGCAGATGAGA 60.153 57.895 29.29 11.59 41.91 3.27
1605 1764 3.488047 CCGATTGATACAGGCAAGCAAAG 60.488 47.826 0.00 0.00 31.54 2.77
1715 2199 3.134442 AGAAACCAGCCAGCAAAATGAAA 59.866 39.130 0.00 0.00 0.00 2.69
1817 2322 1.404315 CGAGAAAGGACCAGTGGTAGC 60.404 57.143 16.72 3.21 35.25 3.58
1895 2400 0.459489 GCTCTGACAATCTCCGCTCT 59.541 55.000 0.00 0.00 0.00 4.09
1896 2401 0.869454 CGCTCTGACAATCTCCGCTC 60.869 60.000 0.00 0.00 0.00 5.03
1897 2402 1.140589 CGCTCTGACAATCTCCGCT 59.859 57.895 0.00 0.00 0.00 5.52
1898 2403 1.880340 CCGCTCTGACAATCTCCGC 60.880 63.158 0.00 0.00 0.00 5.54
1899 2404 0.738975 TACCGCTCTGACAATCTCCG 59.261 55.000 0.00 0.00 0.00 4.63
1900 2405 2.362397 TGATACCGCTCTGACAATCTCC 59.638 50.000 0.00 0.00 0.00 3.71
1901 2406 3.717400 TGATACCGCTCTGACAATCTC 57.283 47.619 0.00 0.00 0.00 2.75
1902 2407 3.006323 GGATGATACCGCTCTGACAATCT 59.994 47.826 0.00 0.00 0.00 2.40
1903 2408 3.243873 TGGATGATACCGCTCTGACAATC 60.244 47.826 0.00 0.00 0.00 2.67
1904 2409 2.700371 TGGATGATACCGCTCTGACAAT 59.300 45.455 0.00 0.00 0.00 2.71
1905 2410 2.107366 TGGATGATACCGCTCTGACAA 58.893 47.619 0.00 0.00 0.00 3.18
1906 2411 1.775385 TGGATGATACCGCTCTGACA 58.225 50.000 0.00 0.00 0.00 3.58
1907 2412 2.890808 TTGGATGATACCGCTCTGAC 57.109 50.000 0.00 0.00 0.00 3.51
1976 2481 3.313526 CCCATCTAGCTGAATGGTTTTCG 59.686 47.826 21.28 7.74 32.48 3.46
2012 2529 1.202770 CCTTTGACTTCCCGGTCAGTT 60.203 52.381 0.00 0.00 45.29 3.16
2023 2540 2.423538 GCATCATAACCGCCTTTGACTT 59.576 45.455 0.00 0.00 0.00 3.01
2031 2548 1.898574 CCCCTGCATCATAACCGCC 60.899 63.158 0.00 0.00 0.00 6.13
2156 2756 5.839606 GGATAGTAGGTCCTGGTTCTAATGT 59.160 44.000 0.00 0.00 32.85 2.71
2161 2761 2.244252 ACGGATAGTAGGTCCTGGTTCT 59.756 50.000 0.00 0.00 33.46 3.01
2162 2762 2.664015 ACGGATAGTAGGTCCTGGTTC 58.336 52.381 0.00 0.00 33.46 3.62
2163 2763 2.842645 ACGGATAGTAGGTCCTGGTT 57.157 50.000 0.00 0.00 33.46 3.67
2175 2775 9.408069 GTACCATAGAAATTTCTGTACGGATAG 57.592 37.037 27.37 9.87 38.19 2.08
2217 2817 2.393271 ATACACCAAGAGCAGACAGC 57.607 50.000 0.00 0.00 46.19 4.40
2272 2887 0.698238 TTAGCACAGTTCCTGCCCAT 59.302 50.000 0.00 0.00 35.01 4.00
2285 3021 6.626302 TGGTTTGCCAATATAGTTTTAGCAC 58.374 36.000 0.00 0.00 42.83 4.40
2301 3037 8.940768 ACACATTACATATAAAATGGTTTGCC 57.059 30.769 11.75 0.00 37.40 4.52
2341 3091 4.672587 TCAAGATACATAGCACTCCACC 57.327 45.455 0.00 0.00 0.00 4.61
2411 3161 7.844493 AGCAATGTTTTCCCATGTATGATAT 57.156 32.000 0.00 0.00 0.00 1.63
2511 3263 9.757227 CAATGTCAAATGGGTAAAGAAACTAAA 57.243 29.630 0.00 0.00 0.00 1.85
2512 3264 7.870445 GCAATGTCAAATGGGTAAAGAAACTAA 59.130 33.333 0.00 0.00 0.00 2.24
2513 3265 7.232534 AGCAATGTCAAATGGGTAAAGAAACTA 59.767 33.333 0.00 0.00 0.00 2.24
2514 3266 6.041979 AGCAATGTCAAATGGGTAAAGAAACT 59.958 34.615 0.00 0.00 0.00 2.66
2519 3271 4.220382 TCCAGCAATGTCAAATGGGTAAAG 59.780 41.667 0.00 0.00 0.00 1.85
2657 3428 4.608948 AACCATATCTACTGCTAGGTGC 57.391 45.455 0.00 0.00 43.25 5.01
2659 3430 7.380423 AATGAAACCATATCTACTGCTAGGT 57.620 36.000 0.00 0.00 0.00 3.08
2866 3652 6.417635 CCACATCACTTGTTCAACAAACATAC 59.582 38.462 4.13 0.00 46.94 2.39
2867 3653 6.096141 ACCACATCACTTGTTCAACAAACATA 59.904 34.615 4.13 0.00 46.94 2.29
2868 3654 5.105392 ACCACATCACTTGTTCAACAAACAT 60.105 36.000 4.13 0.00 46.94 2.71
2971 3761 7.924947 TGAACTGATCTCTGCTAATGATTACAG 59.075 37.037 0.00 7.85 0.00 2.74
2996 3786 8.624701 AAAATAAAATCAGAAGCATCATCGTG 57.375 30.769 0.00 0.00 0.00 4.35
3010 3800 9.784531 TCACTTGCCCAAAATAAAATAAAATCA 57.215 25.926 0.00 0.00 0.00 2.57
3014 3804 9.784531 TCATTCACTTGCCCAAAATAAAATAAA 57.215 25.926 0.00 0.00 0.00 1.40
3015 3805 9.956640 ATCATTCACTTGCCCAAAATAAAATAA 57.043 25.926 0.00 0.00 0.00 1.40
3016 3806 9.381033 CATCATTCACTTGCCCAAAATAAAATA 57.619 29.630 0.00 0.00 0.00 1.40
3017 3807 7.148205 GCATCATTCACTTGCCCAAAATAAAAT 60.148 33.333 0.00 0.00 0.00 1.82
3018 3808 6.149142 GCATCATTCACTTGCCCAAAATAAAA 59.851 34.615 0.00 0.00 0.00 1.52
3019 3809 5.642919 GCATCATTCACTTGCCCAAAATAAA 59.357 36.000 0.00 0.00 0.00 1.40
3020 3810 5.046448 AGCATCATTCACTTGCCCAAAATAA 60.046 36.000 0.00 0.00 37.07 1.40
3021 3811 4.467082 AGCATCATTCACTTGCCCAAAATA 59.533 37.500 0.00 0.00 37.07 1.40
3022 3812 3.262405 AGCATCATTCACTTGCCCAAAAT 59.738 39.130 0.00 0.00 37.07 1.82
3023 3813 2.633967 AGCATCATTCACTTGCCCAAAA 59.366 40.909 0.00 0.00 37.07 2.44
3029 3819 4.634184 ATCAGAAGCATCATTCACTTGC 57.366 40.909 0.00 0.00 36.63 4.01
3199 4314 3.889815 CACAAGCCTGGAATAAGGATGA 58.110 45.455 0.00 0.00 40.02 2.92
3294 4413 4.094887 GTCACTAATTCGAACATGTGGCAT 59.905 41.667 19.19 0.00 31.37 4.40
3324 4443 4.165950 TGCCAGGTCTGTAATAACCATCAT 59.834 41.667 0.00 0.00 38.06 2.45
3348 4467 4.921470 TGCAGCTTAGATACAACGAAAC 57.079 40.909 0.00 0.00 0.00 2.78
3353 4472 6.144080 CGGTACTAATGCAGCTTAGATACAAC 59.856 42.308 12.89 4.40 33.73 3.32
3377 4496 4.201589 CGAAGCAAACAATAGACCAGTACG 60.202 45.833 0.00 0.00 0.00 3.67
3384 4503 5.442909 CGACACTACGAAGCAAACAATAGAC 60.443 44.000 0.00 0.00 35.09 2.59
3386 4505 4.619760 TCGACACTACGAAGCAAACAATAG 59.380 41.667 0.00 0.00 39.34 1.73
3410 4539 6.757010 ACCTAAGCATATTTCAGTCTACGTTG 59.243 38.462 0.00 0.00 0.00 4.10
3434 4563 2.118313 AATAACTAACCCGTGGGCAC 57.882 50.000 4.41 0.00 39.32 5.01
3492 4621 9.814899 ACATGACATAACAATTGAAAGTTTGAA 57.185 25.926 13.59 0.00 0.00 2.69
3493 4622 9.462174 GACATGACATAACAATTGAAAGTTTGA 57.538 29.630 13.59 0.00 0.00 2.69
3494 4623 8.702438 GGACATGACATAACAATTGAAAGTTTG 58.298 33.333 13.59 9.08 0.00 2.93
3495 4624 8.641541 AGGACATGACATAACAATTGAAAGTTT 58.358 29.630 13.59 0.00 0.00 2.66
3496 4625 8.181904 AGGACATGACATAACAATTGAAAGTT 57.818 30.769 13.59 0.00 0.00 2.66
3497 4626 7.765695 AGGACATGACATAACAATTGAAAGT 57.234 32.000 13.59 4.93 0.00 2.66
3498 4627 7.912250 GCTAGGACATGACATAACAATTGAAAG 59.088 37.037 13.59 1.57 0.00 2.62
3499 4628 7.392953 TGCTAGGACATGACATAACAATTGAAA 59.607 33.333 13.59 0.00 0.00 2.69
3652 4786 5.243207 TCTAGTATTCATGCTGCATCATGG 58.757 41.667 25.79 11.30 42.96 3.66
3789 4926 6.127026 GGTACATACCTGGAGAAACTCTTCAT 60.127 42.308 0.00 0.00 43.10 2.57


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

AutoCloner maintained by Alex Coulton.