Multiple sequence alignment - TraesCS7A01G079200

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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 TraesCS7A01G079200 chr7A 100.000 4543 0 0 1 4543 44820840 44825382 0.000000e+00 8390.0
1 TraesCS7A01G079200 chr7A 94.410 2755 122 19 1017 3752 46062028 46059287 0.000000e+00 4205.0
2 TraesCS7A01G079200 chr7A 94.737 2641 114 12 1028 3653 46100609 46097979 0.000000e+00 4084.0
3 TraesCS7A01G079200 chr7A 90.526 2586 185 21 1084 3649 44448267 44445722 0.000000e+00 3363.0
4 TraesCS7A01G079200 chr7A 87.970 2793 240 46 897 3649 45982586 45979850 0.000000e+00 3208.0
5 TraesCS7A01G079200 chr7A 85.936 2581 298 40 1108 3644 45857672 45855113 0.000000e+00 2695.0
6 TraesCS7A01G079200 chr7A 90.727 949 70 9 1 941 46065144 46064206 0.000000e+00 1249.0
7 TraesCS7A01G079200 chr7A 97.009 535 15 1 4010 4543 46059131 46058597 0.000000e+00 898.0
8 TraesCS7A01G079200 chr7A 96.699 515 13 1 4033 4543 46097566 46097052 0.000000e+00 854.0
9 TraesCS7A01G079200 chr7A 88.025 476 22 17 436 898 44770221 44770674 8.650000e-147 531.0
10 TraesCS7A01G079200 chr7A 91.884 345 26 2 391 733 46109228 46108884 8.840000e-132 481.0
11 TraesCS7A01G079200 chr7A 92.334 287 9 9 711 989 46108870 46108589 3.290000e-106 396.0
12 TraesCS7A01G079200 chr7A 83.260 454 23 26 403 843 45983078 45982665 7.180000e-98 368.0
13 TraesCS7A01G079200 chr7A 90.521 211 20 0 111 321 46111324 46111114 3.460000e-71 279.0
14 TraesCS7A01G079200 chr7A 96.324 136 4 1 3652 3786 46097855 46097720 5.920000e-54 222.0
15 TraesCS7A01G079200 chr7A 90.303 165 14 1 3790 3952 689363081 689363245 9.900000e-52 215.0
16 TraesCS7A01G079200 chr7A 90.826 109 8 2 7 114 355548398 355548505 1.320000e-30 145.0
17 TraesCS7A01G079200 chr7A 90.826 109 8 2 7 114 595777753 595777646 1.320000e-30 145.0
18 TraesCS7A01G079200 chr7A 100.000 59 0 0 3950 4008 46059218 46059160 4.810000e-20 110.0
19 TraesCS7A01G079200 chr7A 96.429 56 2 0 3953 4008 46097712 46097657 4.840000e-15 93.5
20 TraesCS7A01G079200 chr7A 91.228 57 5 0 4487 4543 36365794 36365850 1.360000e-10 78.7
21 TraesCS7A01G079200 chr7A 89.474 57 6 0 4487 4543 31695803 31695747 6.300000e-09 73.1
22 TraesCS7A01G079200 chr7A 87.719 57 7 0 4487 4543 736411279 736411223 2.930000e-07 67.6
23 TraesCS7A01G079200 chr4A 87.786 3234 288 41 502 3649 654060275 654057063 0.000000e+00 3685.0
24 TraesCS7A01G079200 chr4A 91.071 2296 176 17 1028 3300 652815051 652817340 0.000000e+00 3077.0
25 TraesCS7A01G079200 chr4A 86.305 2563 291 37 1111 3644 653074415 653076946 0.000000e+00 2734.0
26 TraesCS7A01G079200 chr4A 88.479 1736 147 20 1943 3633 653410942 653412669 0.000000e+00 2049.0
27 TraesCS7A01G079200 chr4A 88.543 899 80 12 1028 1908 653410051 653410944 0.000000e+00 1068.0
28 TraesCS7A01G079200 chr4A 89.831 118 7 5 897 1011 653409965 653410080 3.660000e-31 147.0
29 TraesCS7A01G079200 chr4A 90.826 109 8 2 7 114 500404391 500404498 1.320000e-30 145.0
30 TraesCS7A01G079200 chr4A 88.983 118 8 5 897 1011 652814965 652815080 1.700000e-29 141.0
31 TraesCS7A01G079200 chr4A 94.000 50 3 0 332 381 741185759 741185808 4.870000e-10 76.8
32 TraesCS7A01G079200 chr7D 87.274 2491 271 28 1108 3571 43634550 43632079 0.000000e+00 2802.0
33 TraesCS7A01G079200 chr7D 91.019 1492 121 9 1934 3415 43637647 43636159 0.000000e+00 2001.0
34 TraesCS7A01G079200 chr7D 87.809 566 37 8 898 1457 43660729 43660190 6.410000e-178 634.0
35 TraesCS7A01G079200 chr7D 87.456 566 39 8 898 1457 43682088 43681549 1.390000e-174 623.0
36 TraesCS7A01G079200 chr7D 90.735 313 24 4 466 773 43666586 43666274 3.270000e-111 412.0
37 TraesCS7A01G079200 chr7D 90.096 313 26 4 466 773 43687962 43687650 7.080000e-108 401.0
38 TraesCS7A01G079200 chr7D 88.546 227 23 2 111 337 43667092 43666869 5.790000e-69 272.0
39 TraesCS7A01G079200 chr7D 83.448 290 20 17 504 771 43662540 43662257 1.260000e-60 244.0
40 TraesCS7A01G079200 chr7D 83.448 290 20 17 504 771 43683894 43683611 1.260000e-60 244.0
41 TraesCS7A01G079200 chr7D 92.523 107 7 1 11 116 526532410 526532304 7.870000e-33 152.0
42 TraesCS7A01G079200 chr7D 84.967 153 12 7 624 771 43687629 43687483 1.320000e-30 145.0
43 TraesCS7A01G079200 chr7D 93.750 48 3 0 339 386 443326097 443326144 6.300000e-09 73.1
44 TraesCS7A01G079200 chr3D 92.216 167 13 0 3787 3953 6667273 6667439 2.110000e-58 237.0
45 TraesCS7A01G079200 chr3D 90.741 54 5 0 4487 4540 576381017 576381070 6.300000e-09 73.1
46 TraesCS7A01G079200 chr3D 89.474 57 5 1 4487 4543 538606966 538606911 2.270000e-08 71.3
47 TraesCS7A01G079200 chr5D 91.279 172 14 1 3790 3961 53583077 53583247 2.730000e-57 233.0
48 TraesCS7A01G079200 chr5D 88.202 178 19 2 3776 3952 351556024 351556200 1.280000e-50 211.0
49 TraesCS7A01G079200 chr5D 91.837 49 4 0 333 381 502752414 502752366 8.160000e-08 69.4
50 TraesCS7A01G079200 chr5A 89.714 175 17 1 3780 3953 558675486 558675660 5.920000e-54 222.0
51 TraesCS7A01G079200 chr5A 100.000 29 0 0 353 381 651616517 651616545 2.000000e-03 54.7
52 TraesCS7A01G079200 chr7B 90.000 170 16 1 3790 3959 650609092 650608924 7.650000e-53 219.0
53 TraesCS7A01G079200 chr3B 90.741 162 15 0 3790 3951 527752141 527751980 2.750000e-52 217.0
54 TraesCS7A01G079200 chr4B 89.080 174 16 2 3782 3952 190690792 190690965 3.560000e-51 213.0
55 TraesCS7A01G079200 chr4B 100.000 29 0 0 352 380 134392201 134392173 2.000000e-03 54.7
56 TraesCS7A01G079200 chr2B 89.412 170 17 1 3783 3951 648814040 648814209 3.560000e-51 213.0
57 TraesCS7A01G079200 chr2B 93.636 110 7 0 7 116 482626739 482626630 1.010000e-36 165.0
58 TraesCS7A01G079200 chr6D 90.991 111 8 2 7 116 434404462 434404353 1.020000e-31 148.0
59 TraesCS7A01G079200 chr6D 89.655 58 6 0 4483 4540 7439129 7439186 1.750000e-09 75.0
60 TraesCS7A01G079200 chr2A 90.826 109 8 2 7 114 597933667 597933774 1.320000e-30 145.0
61 TraesCS7A01G079200 chr2D 90.000 110 11 0 7 116 408443500 408443609 4.740000e-30 143.0
62 TraesCS7A01G079200 chr5B 88.889 54 6 0 4487 4540 23404315 23404368 2.930000e-07 67.6
63 TraesCS7A01G079200 chr4D 96.774 31 1 0 1034 1064 24338338 24338308 8.000000e-03 52.8


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 TraesCS7A01G079200 chr7A 44820840 44825382 4542 False 8390.000000 8390 100.000000 1 4543 1 chr7A.!!$F3 4542
1 TraesCS7A01G079200 chr7A 44445722 44448267 2545 True 3363.000000 3363 90.526000 1084 3649 1 chr7A.!!$R2 2565
2 TraesCS7A01G079200 chr7A 45855113 45857672 2559 True 2695.000000 2695 85.936000 1108 3644 1 chr7A.!!$R3 2536
3 TraesCS7A01G079200 chr7A 45979850 45983078 3228 True 1788.000000 3208 85.615000 403 3649 2 chr7A.!!$R6 3246
4 TraesCS7A01G079200 chr7A 46058597 46065144 6547 True 1615.500000 4205 95.536500 1 4543 4 chr7A.!!$R7 4542
5 TraesCS7A01G079200 chr7A 46097052 46100609 3557 True 1313.375000 4084 96.047250 1028 4543 4 chr7A.!!$R8 3515
6 TraesCS7A01G079200 chr7A 46108589 46111324 2735 True 385.333333 481 91.579667 111 989 3 chr7A.!!$R9 878
7 TraesCS7A01G079200 chr4A 654057063 654060275 3212 True 3685.000000 3685 87.786000 502 3649 1 chr4A.!!$R1 3147
8 TraesCS7A01G079200 chr4A 653074415 653076946 2531 False 2734.000000 2734 86.305000 1111 3644 1 chr4A.!!$F2 2533
9 TraesCS7A01G079200 chr4A 652814965 652817340 2375 False 1609.000000 3077 90.027000 897 3300 2 chr4A.!!$F4 2403
10 TraesCS7A01G079200 chr4A 653409965 653412669 2704 False 1088.000000 2049 88.951000 897 3633 3 chr4A.!!$F5 2736
11 TraesCS7A01G079200 chr7D 43632079 43637647 5568 True 2401.500000 2802 89.146500 1108 3571 2 chr7D.!!$R2 2463
12 TraesCS7A01G079200 chr7D 43660190 43667092 6902 True 390.500000 634 87.634500 111 1457 4 chr7D.!!$R3 1346
13 TraesCS7A01G079200 chr7D 43681549 43687962 6413 True 353.250000 623 86.491750 466 1457 4 chr7D.!!$R4 991

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
412 2229 0.392461 GGTATGGCCTTGCGACTTGA 60.392 55.000 3.32 0.00 0.00 3.02 F
1103 10937 1.078848 CTCTGTTCCCCTTGCGAGG 60.079 63.158 13.75 13.75 43.15 4.63 F
2381 12240 0.391228 TTATGGAGCTCGCCGCATTA 59.609 50.000 7.83 0.00 42.61 1.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1487 11336 1.073125 TGTTCCTTTTCGAGGCATCCA 59.927 47.619 0.00 0.0 45.87 3.41 R
3036 12922 1.064611 AGCATCCTCTCAAGCTGCAAT 60.065 47.619 1.02 0.0 35.72 3.56 R
3571 13502 1.073177 GCAACCAAACATGCATGCTC 58.927 50.000 26.53 0.0 42.12 4.26 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
70 71 1.446618 GGTCGTTGTCCGCGGTTAT 60.447 57.895 27.15 0.00 36.19 1.89
126 127 0.911769 TCTGAGTTGCCGGAATGGAT 59.088 50.000 5.05 0.00 42.00 3.41
221 222 1.064825 GTGGGGGAAGAGAAGTTGGA 58.935 55.000 0.00 0.00 0.00 3.53
293 294 1.419387 GGATAGCAGCTCCATCCTTGT 59.581 52.381 14.87 0.00 36.17 3.16
312 313 3.483869 GCCCGGGAGCTGAGGAAT 61.484 66.667 29.31 0.00 0.00 3.01
370 371 1.073474 ATGCAGAGGCCAGGGGATA 60.073 57.895 5.01 0.00 40.13 2.59
412 2229 0.392461 GGTATGGCCTTGCGACTTGA 60.392 55.000 3.32 0.00 0.00 3.02
574 2619 1.534203 GGGAGAGGAGGAATTGGGC 59.466 63.158 0.00 0.00 0.00 5.36
799 6627 3.001939 GTCGTCGCTGAGAAAAAGGAAAA 59.998 43.478 0.00 0.00 0.00 2.29
885 6781 2.292802 GACGCGCGGAAGGAATCAAC 62.293 60.000 35.22 6.21 0.00 3.18
1099 10933 1.676967 CTGGCTCTGTTCCCCTTGC 60.677 63.158 0.00 0.00 0.00 4.01
1103 10937 1.078848 CTCTGTTCCCCTTGCGAGG 60.079 63.158 13.75 13.75 43.15 4.63
1104 10938 1.535444 TCTGTTCCCCTTGCGAGGA 60.535 57.895 22.68 0.00 46.74 3.71
1105 10939 1.376037 CTGTTCCCCTTGCGAGGAC 60.376 63.158 22.68 12.28 46.74 3.85
1106 10940 1.831652 CTGTTCCCCTTGCGAGGACT 61.832 60.000 22.68 0.00 46.74 3.85
1116 10956 3.070987 GCGAGGACTAGGAGGGGGA 62.071 68.421 0.00 0.00 0.00 4.81
1129 10969 2.351276 GGGGATGGTGTCTTGCGT 59.649 61.111 0.00 0.00 0.00 5.24
1135 10975 1.100463 ATGGTGTCTTGCGTGCACAA 61.100 50.000 18.64 3.40 35.05 3.33
1151 10991 4.626081 AACCTCAACTGCCGCGCT 62.626 61.111 5.56 0.00 0.00 5.92
1264 11107 2.683933 GAGAGTTCCGGGCCTCCA 60.684 66.667 15.12 0.00 0.00 3.86
1316 11165 1.828979 GTCTCCTCGACCTTGTCTCT 58.171 55.000 0.00 0.00 36.62 3.10
1346 11195 2.529389 AACACCCTCGCCCTCCTT 60.529 61.111 0.00 0.00 0.00 3.36
1487 11336 3.785887 TGGCCTTCCTCATGGTATACTTT 59.214 43.478 3.32 0.00 34.23 2.66
1526 11378 3.303928 GCCGCCCGCTACCTCTAT 61.304 66.667 0.00 0.00 0.00 1.98
1601 11453 1.743252 GGAGGGTGAAGAAGCGCTG 60.743 63.158 12.58 0.00 0.00 5.18
1614 11466 2.743928 CGCTGCTGGACCCTGAAC 60.744 66.667 0.00 0.00 0.00 3.18
2106 11965 0.901827 TCTAAAGATGCGCCTCCACA 59.098 50.000 4.18 0.00 0.00 4.17
2142 12001 1.003476 TGCATCAAGGCGCTCAAGA 60.003 52.632 7.64 0.56 36.28 3.02
2330 12189 3.210074 ACATACTGGACCCCCTATCTCTT 59.790 47.826 0.00 0.00 0.00 2.85
2381 12240 0.391228 TTATGGAGCTCGCCGCATTA 59.609 50.000 7.83 0.00 42.61 1.90
2796 12673 2.579738 GGAGGAGCTGGTTCCGTC 59.420 66.667 0.00 0.00 42.29 4.79
2856 12739 4.956075 AGCATTTTTGGGTAGGTATCCTTG 59.044 41.667 0.00 0.00 34.61 3.61
2859 12742 1.974028 TTGGGTAGGTATCCTTGGCA 58.026 50.000 0.00 0.00 34.61 4.92
2864 12747 2.907042 GGTAGGTATCCTTGGCAGCTAT 59.093 50.000 0.00 0.00 34.61 2.97
2868 12751 3.580458 AGGTATCCTTGGCAGCTATGTAG 59.420 47.826 0.00 0.00 0.00 2.74
2882 12765 7.380602 GGCAGCTATGTAGATTTGCTTTAATTG 59.619 37.037 0.00 0.00 31.68 2.32
2908 12791 6.374417 TTCATTTGGCCTACTCTCTTACTT 57.626 37.500 3.32 0.00 0.00 2.24
3036 12922 5.050490 GTGAACTTCACTGCTACTTCTGAA 58.950 41.667 13.77 0.00 43.73 3.02
3318 13221 0.670546 CATCCCGCACGATATCACCC 60.671 60.000 3.12 0.00 0.00 4.61
3384 13290 1.186200 CCTCAGTTCGGAGATGGACA 58.814 55.000 1.84 0.00 37.05 4.02
3407 13313 3.879295 TGAAGCTTGTGGAGAAACTCAAG 59.121 43.478 2.10 0.00 39.83 3.02
3484 13411 2.744202 GCTGTGAAGTTGGACCATAGTG 59.256 50.000 0.00 0.00 0.00 2.74
3650 13594 4.039730 TGCTTGCTTGGCCTTGTTAAATAA 59.960 37.500 3.32 0.00 0.00 1.40
3731 13800 3.244387 GCAATGGTTTTTAAGGAAGGCCA 60.244 43.478 5.01 0.00 36.29 5.36
3741 13810 1.142688 AGGAAGGCCAATGGTGAGGT 61.143 55.000 5.01 0.00 36.29 3.85
3767 13866 7.674120 AGTTATGTTTACTAGACGGGTTCTTT 58.326 34.615 0.00 0.00 35.55 2.52
3815 13915 8.672823 ACTCCCTCCGTTTTTAAATATATGTC 57.327 34.615 0.00 0.00 0.00 3.06
3816 13916 8.491958 ACTCCCTCCGTTTTTAAATATATGTCT 58.508 33.333 0.00 0.00 0.00 3.41
3817 13917 9.338622 CTCCCTCCGTTTTTAAATATATGTCTT 57.661 33.333 0.00 0.00 0.00 3.01
3818 13918 9.689501 TCCCTCCGTTTTTAAATATATGTCTTT 57.310 29.630 0.00 0.00 0.00 2.52
3838 13938 9.436957 TGTCTTTTTAGAGATTCCATTACAGAC 57.563 33.333 0.00 0.00 0.00 3.51
3839 13939 9.660180 GTCTTTTTAGAGATTCCATTACAGACT 57.340 33.333 0.00 0.00 0.00 3.24
3846 13946 7.877003 AGAGATTCCATTACAGACTACATACG 58.123 38.462 0.00 0.00 0.00 3.06
3847 13947 6.982852 AGATTCCATTACAGACTACATACGG 58.017 40.000 0.00 0.00 0.00 4.02
3848 13948 6.776116 AGATTCCATTACAGACTACATACGGA 59.224 38.462 0.00 0.00 0.00 4.69
3849 13949 6.971726 TTCCATTACAGACTACATACGGAT 57.028 37.500 0.00 0.00 0.00 4.18
3850 13950 6.327279 TCCATTACAGACTACATACGGATG 57.673 41.667 5.94 5.94 39.16 3.51
3852 13952 6.999871 TCCATTACAGACTACATACGGATGTA 59.000 38.462 19.32 19.32 44.77 2.29
3853 13953 7.668469 TCCATTACAGACTACATACGGATGTAT 59.332 37.037 20.64 11.04 45.42 2.29
3854 13954 8.953313 CCATTACAGACTACATACGGATGTATA 58.047 37.037 20.64 7.39 45.42 1.47
3859 13959 9.381033 ACAGACTACATACGGATGTATATAGAC 57.619 37.037 20.64 11.15 45.42 2.59
3860 13960 9.379791 CAGACTACATACGGATGTATATAGACA 57.620 37.037 20.64 2.07 45.42 3.41
3880 13980 9.696572 ATAGACATACTTAAGAGTGTAGGTTCA 57.303 33.333 10.09 0.00 34.47 3.18
3881 13981 7.828712 AGACATACTTAAGAGTGTAGGTTCAC 58.171 38.462 10.09 0.61 34.47 3.18
3891 13991 4.718961 AGTGTAGGTTCACTCATTTTGCT 58.281 39.130 0.00 0.00 44.07 3.91
3892 13992 4.757149 AGTGTAGGTTCACTCATTTTGCTC 59.243 41.667 0.00 0.00 44.07 4.26
3893 13993 4.757149 GTGTAGGTTCACTCATTTTGCTCT 59.243 41.667 0.00 0.00 35.68 4.09
3894 13994 4.756642 TGTAGGTTCACTCATTTTGCTCTG 59.243 41.667 0.00 0.00 0.00 3.35
3895 13995 3.825328 AGGTTCACTCATTTTGCTCTGT 58.175 40.909 0.00 0.00 0.00 3.41
3896 13996 4.973168 AGGTTCACTCATTTTGCTCTGTA 58.027 39.130 0.00 0.00 0.00 2.74
3897 13997 5.564550 AGGTTCACTCATTTTGCTCTGTAT 58.435 37.500 0.00 0.00 0.00 2.29
3898 13998 5.413833 AGGTTCACTCATTTTGCTCTGTATG 59.586 40.000 0.00 0.00 0.00 2.39
3899 13999 5.182001 GGTTCACTCATTTTGCTCTGTATGT 59.818 40.000 0.00 0.00 0.00 2.29
3900 14000 6.371548 GGTTCACTCATTTTGCTCTGTATGTA 59.628 38.462 0.00 0.00 0.00 2.29
3901 14001 7.413438 GGTTCACTCATTTTGCTCTGTATGTAG 60.413 40.741 0.00 0.00 0.00 2.74
3902 14002 6.701340 TCACTCATTTTGCTCTGTATGTAGT 58.299 36.000 0.00 0.00 0.00 2.73
3903 14003 6.813649 TCACTCATTTTGCTCTGTATGTAGTC 59.186 38.462 0.00 0.00 0.00 2.59
3904 14004 6.036517 CACTCATTTTGCTCTGTATGTAGTCC 59.963 42.308 0.00 0.00 0.00 3.85
3905 14005 6.048732 TCATTTTGCTCTGTATGTAGTCCA 57.951 37.500 0.00 0.00 0.00 4.02
3906 14006 6.653020 TCATTTTGCTCTGTATGTAGTCCAT 58.347 36.000 0.00 0.00 37.58 3.41
3907 14007 6.539826 TCATTTTGCTCTGTATGTAGTCCATG 59.460 38.462 0.00 0.00 34.86 3.66
3908 14008 4.406648 TTGCTCTGTATGTAGTCCATGG 57.593 45.455 4.97 4.97 34.86 3.66
3909 14009 3.374764 TGCTCTGTATGTAGTCCATGGT 58.625 45.455 12.58 0.00 34.86 3.55
3910 14010 4.542697 TGCTCTGTATGTAGTCCATGGTA 58.457 43.478 12.58 0.00 34.86 3.25
3911 14011 4.959839 TGCTCTGTATGTAGTCCATGGTAA 59.040 41.667 12.58 0.00 34.86 2.85
3912 14012 5.423931 TGCTCTGTATGTAGTCCATGGTAAA 59.576 40.000 12.58 0.00 34.86 2.01
3913 14013 6.070481 TGCTCTGTATGTAGTCCATGGTAAAA 60.070 38.462 12.58 0.00 34.86 1.52
3914 14014 6.992715 GCTCTGTATGTAGTCCATGGTAAAAT 59.007 38.462 12.58 1.85 34.86 1.82
3915 14015 7.171678 GCTCTGTATGTAGTCCATGGTAAAATC 59.828 40.741 12.58 0.00 34.86 2.17
3916 14016 8.319057 TCTGTATGTAGTCCATGGTAAAATCT 57.681 34.615 12.58 4.86 34.86 2.40
3917 14017 8.421784 TCTGTATGTAGTCCATGGTAAAATCTC 58.578 37.037 12.58 0.00 34.86 2.75
3918 14018 8.319057 TGTATGTAGTCCATGGTAAAATCTCT 57.681 34.615 12.58 1.94 34.86 3.10
3919 14019 9.429109 TGTATGTAGTCCATGGTAAAATCTCTA 57.571 33.333 12.58 1.07 34.86 2.43
3926 14026 9.232473 AGTCCATGGTAAAATCTCTAAAAAGAC 57.768 33.333 12.58 0.00 0.00 3.01
3927 14027 9.232473 GTCCATGGTAAAATCTCTAAAAAGACT 57.768 33.333 12.58 0.00 0.00 3.24
3928 14028 9.807921 TCCATGGTAAAATCTCTAAAAAGACTT 57.192 29.630 12.58 0.00 0.00 3.01
4008 14108 8.462143 TTCTTAGTTTTCTTGTATGTCTAGCG 57.538 34.615 0.00 0.00 0.00 4.26
4086 14256 6.827251 AGTTGTTCATGCATGAGAGAATACAT 59.173 34.615 27.25 12.12 38.19 2.29
4095 14265 6.649557 TGCATGAGAGAATACATGATCATGAC 59.350 38.462 36.37 23.54 44.22 3.06
4120 14290 3.041508 ACCGGTAGAGCAGAAGTTTTC 57.958 47.619 4.49 0.00 0.00 2.29
4152 14322 0.498095 GTTTCATGCACGTGTTTGCG 59.502 50.000 18.38 1.93 46.20 4.85
4231 14402 3.126831 GAGGTTTATGATGGTCGCTGAG 58.873 50.000 0.00 0.00 0.00 3.35
4282 14453 5.637006 TTTACTGGTGTAATTCATGGTGC 57.363 39.130 0.00 0.00 38.31 5.01
4521 14692 1.566703 TGGGGCATTTTTATCGAGGGA 59.433 47.619 0.00 0.00 0.00 4.20
4524 14695 3.641436 GGGGCATTTTTATCGAGGGAAAT 59.359 43.478 0.00 0.00 0.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 0.178903 TAGGTGGTCTCAACCTGCCT 60.179 55.000 6.12 13.11 46.60 4.75
40 41 4.954118 ACGACCAGGGACCAGGCA 62.954 66.667 0.00 0.00 0.00 4.75
66 67 7.793427 TCGTTAAGCGTGTTACTTTGAAATAAC 59.207 33.333 0.00 0.00 42.13 1.89
70 71 5.519566 TCTCGTTAAGCGTGTTACTTTGAAA 59.480 36.000 0.00 0.00 42.13 2.69
101 102 1.808411 TCCGGCAACTCAGATCAAAC 58.192 50.000 0.00 0.00 0.00 2.93
147 148 2.411765 CTTCCCTTCCGGCCAGTGTT 62.412 60.000 2.24 0.00 0.00 3.32
148 149 2.852075 TTCCCTTCCGGCCAGTGT 60.852 61.111 2.24 0.00 0.00 3.55
187 188 1.918800 CCACCCCCTTTCGACCTCT 60.919 63.158 0.00 0.00 0.00 3.69
312 313 1.783071 TACCCCATACATGAGCGTCA 58.217 50.000 0.00 0.00 0.00 4.35
382 383 4.735369 CAAGGCCATACCCCATACATTTA 58.265 43.478 5.01 0.00 40.58 1.40
412 2229 1.739338 TTCCAACGCCGGCAACAAAT 61.739 50.000 28.98 1.60 0.00 2.32
574 2619 1.959226 CACCGTTGTTGACTCCCCG 60.959 63.158 0.00 0.00 0.00 5.73
605 2651 1.687123 CCTTCATCTCCGGTCGGTAAT 59.313 52.381 9.36 1.88 36.47 1.89
764 2986 2.279918 ACGACTCGCGGCAAAACT 60.280 55.556 6.13 0.00 46.49 2.66
885 6781 2.203771 CCGGTCCTAGGCTAGCTGG 61.204 68.421 16.26 13.40 0.00 4.85
992 8666 1.062880 CTTCTGGAGAGAGACGTACGC 59.937 57.143 16.72 8.42 0.00 4.42
1099 10933 0.540830 CATCCCCCTCCTAGTCCTCG 60.541 65.000 0.00 0.00 0.00 4.63
1103 10937 0.031010 ACACCATCCCCCTCCTAGTC 60.031 60.000 0.00 0.00 0.00 2.59
1104 10938 0.031010 GACACCATCCCCCTCCTAGT 60.031 60.000 0.00 0.00 0.00 2.57
1105 10939 0.266152 AGACACCATCCCCCTCCTAG 59.734 60.000 0.00 0.00 0.00 3.02
1106 10940 0.722676 AAGACACCATCCCCCTCCTA 59.277 55.000 0.00 0.00 0.00 2.94
1116 10956 1.100463 TTGTGCACGCAAGACACCAT 61.100 50.000 13.13 0.00 43.74 3.55
1129 10969 2.186160 CGGCAGTTGAGGTTGTGCA 61.186 57.895 0.00 0.00 37.68 4.57
1165 11008 1.886730 TTCCAGGTCGAGGGGGAGAT 61.887 60.000 0.00 0.00 0.00 2.75
1251 11094 4.754667 GTCGTGGAGGCCCGGAAC 62.755 72.222 0.73 0.00 34.29 3.62
1298 11147 3.244805 TGTTAGAGACAAGGTCGAGGAGA 60.245 47.826 0.00 0.00 37.67 3.71
1309 11158 6.166279 GTGTTGAGGATGATGTTAGAGACAA 58.834 40.000 0.00 0.00 42.62 3.18
1310 11159 5.337571 GGTGTTGAGGATGATGTTAGAGACA 60.338 44.000 0.00 0.00 43.71 3.41
1316 11165 3.118775 CGAGGGTGTTGAGGATGATGTTA 60.119 47.826 0.00 0.00 0.00 2.41
1389 11238 4.640201 CACTTGTCTTTTGGACCTCTTTGA 59.360 41.667 0.00 0.00 43.89 2.69
1487 11336 1.073125 TGTTCCTTTTCGAGGCATCCA 59.927 47.619 0.00 0.00 45.87 3.41
1577 11429 2.633488 GCTTCTTCACCCTCCACATAC 58.367 52.381 0.00 0.00 0.00 2.39
1601 11453 1.335132 TATCGGGTTCAGGGTCCAGC 61.335 60.000 0.00 0.00 0.00 4.85
1614 11466 4.301027 GGCCTGCGTCCTATCGGG 62.301 72.222 0.00 0.00 0.00 5.14
2106 11965 6.175471 TGATGCAGAAGTTGTGAATCATACT 58.825 36.000 17.68 0.00 0.00 2.12
2330 12189 2.523168 TGGACCTGTGTGCGGAGA 60.523 61.111 0.00 0.00 35.21 3.71
2796 12673 2.886523 TCAGCACCTGTTCAATCTTTGG 59.113 45.455 0.00 0.00 32.61 3.28
2856 12739 4.907879 AAAGCAAATCTACATAGCTGCC 57.092 40.909 0.00 0.00 35.42 4.85
2859 12742 7.286316 AGGCAATTAAAGCAAATCTACATAGCT 59.714 33.333 0.00 0.00 37.08 3.32
2864 12747 7.225784 TGAAGGCAATTAAAGCAAATCTACA 57.774 32.000 5.74 0.00 0.00 2.74
2868 12751 7.245604 CCAAATGAAGGCAATTAAAGCAAATC 58.754 34.615 5.74 1.99 0.00 2.17
2908 12791 2.618241 CCTACAACAAGCAAGCAAGTCA 59.382 45.455 0.00 0.00 0.00 3.41
3036 12922 1.064611 AGCATCCTCTCAAGCTGCAAT 60.065 47.619 1.02 0.00 35.72 3.56
3318 13221 2.390599 CGTGGCAGGTTCCGTCATG 61.391 63.158 0.00 0.00 0.00 3.07
3384 13290 4.090761 TGAGTTTCTCCACAAGCTTCAT 57.909 40.909 0.00 0.00 0.00 2.57
3407 13313 1.392853 CACTCTTCAGTGCGCATCTTC 59.607 52.381 15.91 0.00 43.77 2.87
3571 13502 1.073177 GCAACCAAACATGCATGCTC 58.927 50.000 26.53 0.00 42.12 4.26
3650 13594 2.341101 ACGGGCTTCACGACGAGAT 61.341 57.895 0.00 0.00 34.93 2.75
3731 13800 9.263446 TCTAGTAAACATAACTACCTCACCATT 57.737 33.333 0.00 0.00 0.00 3.16
3741 13810 7.944729 AGAACCCGTCTAGTAAACATAACTA 57.055 36.000 0.00 0.00 33.56 2.24
3789 13889 9.768662 GACATATATTTAAAAACGGAGGGAGTA 57.231 33.333 0.00 0.00 0.00 2.59
3790 13890 8.491958 AGACATATATTTAAAAACGGAGGGAGT 58.508 33.333 0.00 0.00 0.00 3.85
3791 13891 8.904099 AGACATATATTTAAAAACGGAGGGAG 57.096 34.615 0.00 0.00 0.00 4.30
3792 13892 9.689501 AAAGACATATATTTAAAAACGGAGGGA 57.310 29.630 0.00 0.00 0.00 4.20
3812 13912 9.436957 GTCTGTAATGGAATCTCTAAAAAGACA 57.563 33.333 0.00 0.00 0.00 3.41
3813 13913 9.660180 AGTCTGTAATGGAATCTCTAAAAAGAC 57.340 33.333 0.00 0.00 0.00 3.01
3820 13920 9.000486 CGTATGTAGTCTGTAATGGAATCTCTA 58.000 37.037 0.00 0.00 0.00 2.43
3821 13921 7.040340 CCGTATGTAGTCTGTAATGGAATCTCT 60.040 40.741 0.00 0.00 0.00 3.10
3822 13922 7.040617 TCCGTATGTAGTCTGTAATGGAATCTC 60.041 40.741 0.00 0.00 0.00 2.75
3823 13923 6.776116 TCCGTATGTAGTCTGTAATGGAATCT 59.224 38.462 0.00 0.00 0.00 2.40
3824 13924 6.978338 TCCGTATGTAGTCTGTAATGGAATC 58.022 40.000 0.00 0.00 0.00 2.52
3825 13925 6.971726 TCCGTATGTAGTCTGTAATGGAAT 57.028 37.500 0.00 0.00 0.00 3.01
3826 13926 6.322969 ACATCCGTATGTAGTCTGTAATGGAA 59.677 38.462 0.00 0.00 44.66 3.53
3827 13927 5.831525 ACATCCGTATGTAGTCTGTAATGGA 59.168 40.000 0.00 0.00 44.66 3.41
3828 13928 6.085555 ACATCCGTATGTAGTCTGTAATGG 57.914 41.667 0.00 0.00 44.66 3.16
3854 13954 9.696572 TGAACCTACACTCTTAAGTATGTCTAT 57.303 33.333 14.83 4.38 33.25 1.98
3855 13955 8.954350 GTGAACCTACACTCTTAAGTATGTCTA 58.046 37.037 14.83 2.41 37.73 2.59
3856 13956 7.670559 AGTGAACCTACACTCTTAAGTATGTCT 59.329 37.037 14.83 5.07 46.36 3.41
3857 13957 7.828712 AGTGAACCTACACTCTTAAGTATGTC 58.171 38.462 14.83 4.85 46.36 3.06
3858 13958 7.778185 AGTGAACCTACACTCTTAAGTATGT 57.222 36.000 15.46 15.46 46.36 2.29
3870 13970 4.757149 AGAGCAAAATGAGTGAACCTACAC 59.243 41.667 0.00 0.00 40.60 2.90
3871 13971 4.756642 CAGAGCAAAATGAGTGAACCTACA 59.243 41.667 0.00 0.00 0.00 2.74
3872 13972 4.757149 ACAGAGCAAAATGAGTGAACCTAC 59.243 41.667 0.00 0.00 0.00 3.18
3873 13973 4.973168 ACAGAGCAAAATGAGTGAACCTA 58.027 39.130 0.00 0.00 0.00 3.08
3874 13974 3.825328 ACAGAGCAAAATGAGTGAACCT 58.175 40.909 0.00 0.00 0.00 3.50
3875 13975 5.182001 ACATACAGAGCAAAATGAGTGAACC 59.818 40.000 0.00 0.00 0.00 3.62
3876 13976 6.246420 ACATACAGAGCAAAATGAGTGAAC 57.754 37.500 0.00 0.00 0.00 3.18
3877 13977 7.161404 ACTACATACAGAGCAAAATGAGTGAA 58.839 34.615 0.00 0.00 0.00 3.18
3878 13978 6.701340 ACTACATACAGAGCAAAATGAGTGA 58.299 36.000 0.00 0.00 0.00 3.41
3879 13979 6.036517 GGACTACATACAGAGCAAAATGAGTG 59.963 42.308 0.00 0.00 0.00 3.51
3880 13980 6.109359 GGACTACATACAGAGCAAAATGAGT 58.891 40.000 0.00 0.00 0.00 3.41
3881 13981 6.108687 TGGACTACATACAGAGCAAAATGAG 58.891 40.000 0.00 0.00 0.00 2.90
3882 13982 6.048732 TGGACTACATACAGAGCAAAATGA 57.951 37.500 0.00 0.00 0.00 2.57
3883 13983 6.238566 CCATGGACTACATACAGAGCAAAATG 60.239 42.308 5.56 0.00 37.84 2.32
3884 13984 5.824624 CCATGGACTACATACAGAGCAAAAT 59.175 40.000 5.56 0.00 37.84 1.82
3885 13985 5.185454 CCATGGACTACATACAGAGCAAAA 58.815 41.667 5.56 0.00 37.84 2.44
3886 13986 4.225042 ACCATGGACTACATACAGAGCAAA 59.775 41.667 21.47 0.00 37.84 3.68
3887 13987 3.774766 ACCATGGACTACATACAGAGCAA 59.225 43.478 21.47 0.00 37.84 3.91
3888 13988 3.374764 ACCATGGACTACATACAGAGCA 58.625 45.455 21.47 0.00 37.84 4.26
3889 13989 5.531122 TTACCATGGACTACATACAGAGC 57.469 43.478 21.47 0.00 37.84 4.09
3890 13990 8.424918 AGATTTTACCATGGACTACATACAGAG 58.575 37.037 21.47 0.00 37.84 3.35
3891 13991 8.319057 AGATTTTACCATGGACTACATACAGA 57.681 34.615 21.47 0.00 37.84 3.41
3892 13992 8.424918 AGAGATTTTACCATGGACTACATACAG 58.575 37.037 21.47 0.00 37.84 2.74
3893 13993 8.319057 AGAGATTTTACCATGGACTACATACA 57.681 34.615 21.47 0.00 37.84 2.29
3900 14000 9.232473 GTCTTTTTAGAGATTTTACCATGGACT 57.768 33.333 21.47 7.34 0.00 3.85
3901 14001 9.232473 AGTCTTTTTAGAGATTTTACCATGGAC 57.768 33.333 21.47 0.00 0.00 4.02
3902 14002 9.807921 AAGTCTTTTTAGAGATTTTACCATGGA 57.192 29.630 21.47 0.00 0.00 3.41
3923 14023 9.453830 ACTCCCTCCATTCTTAAATATAAGTCT 57.546 33.333 0.00 0.00 39.65 3.24
3931 14031 9.547279 AACAAAATACTCCCTCCATTCTTAAAT 57.453 29.630 0.00 0.00 0.00 1.40
3932 14032 8.950007 AACAAAATACTCCCTCCATTCTTAAA 57.050 30.769 0.00 0.00 0.00 1.52
3933 14033 9.457436 GTAACAAAATACTCCCTCCATTCTTAA 57.543 33.333 0.00 0.00 0.00 1.85
3934 14034 8.607713 TGTAACAAAATACTCCCTCCATTCTTA 58.392 33.333 0.00 0.00 0.00 2.10
3935 14035 7.466804 TGTAACAAAATACTCCCTCCATTCTT 58.533 34.615 0.00 0.00 0.00 2.52
3936 14036 7.027874 TGTAACAAAATACTCCCTCCATTCT 57.972 36.000 0.00 0.00 0.00 2.40
3937 14037 7.682021 GCATGTAACAAAATACTCCCTCCATTC 60.682 40.741 0.00 0.00 0.00 2.67
3938 14038 6.096846 GCATGTAACAAAATACTCCCTCCATT 59.903 38.462 0.00 0.00 0.00 3.16
3939 14039 5.594317 GCATGTAACAAAATACTCCCTCCAT 59.406 40.000 0.00 0.00 0.00 3.41
3940 14040 4.947388 GCATGTAACAAAATACTCCCTCCA 59.053 41.667 0.00 0.00 0.00 3.86
3941 14041 4.035208 CGCATGTAACAAAATACTCCCTCC 59.965 45.833 0.00 0.00 0.00 4.30
3942 14042 4.873827 TCGCATGTAACAAAATACTCCCTC 59.126 41.667 0.00 0.00 0.00 4.30
3943 14043 4.839121 TCGCATGTAACAAAATACTCCCT 58.161 39.130 0.00 0.00 0.00 4.20
3944 14044 4.634443 ACTCGCATGTAACAAAATACTCCC 59.366 41.667 0.00 0.00 0.00 4.30
3945 14045 5.581085 AGACTCGCATGTAACAAAATACTCC 59.419 40.000 0.00 0.00 0.00 3.85
3946 14046 6.648725 AGACTCGCATGTAACAAAATACTC 57.351 37.500 0.00 0.00 0.00 2.59
3947 14047 7.435068 AAAGACTCGCATGTAACAAAATACT 57.565 32.000 0.00 0.00 0.00 2.12
3948 14048 9.769093 AATAAAGACTCGCATGTAACAAAATAC 57.231 29.630 0.00 0.00 0.00 1.89
4086 14256 3.767131 TCTACCGGTTTCTGTCATGATCA 59.233 43.478 15.04 0.00 0.00 2.92
4095 14265 2.028930 ACTTCTGCTCTACCGGTTTCTG 60.029 50.000 15.04 1.91 0.00 3.02
4282 14453 9.151471 CATATATAGGTAACGAACTTCCAATGG 57.849 37.037 0.00 0.00 46.39 3.16


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

AutoCloner maintained by Alex Coulton.