Multiple sequence alignment - TraesCS3B01G252500

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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 TraesCS3B01G252500 chr3B 100.000 5807 0 0 1 5807 405779382 405785188 0.000000e+00 10724.0
1 TraesCS3B01G252500 chr3B 99.173 967 6 2 4842 5807 754927488 754926523 0.000000e+00 1740.0
2 TraesCS3B01G252500 chr3D 96.383 2516 79 6 2373 4882 313818677 313816168 0.000000e+00 4132.0
3 TraesCS3B01G252500 chr3D 92.097 949 43 19 665 1592 313820752 313819815 0.000000e+00 1308.0
4 TraesCS3B01G252500 chr3D 88.139 489 38 11 1 482 313821752 313821277 1.090000e-156 564.0
5 TraesCS3B01G252500 chr3D 89.286 224 18 6 467 689 313820975 313820757 5.730000e-70 276.0
6 TraesCS3B01G252500 chr3A 93.787 2543 91 30 678 3156 416312928 416310389 0.000000e+00 3759.0
7 TraesCS3B01G252500 chr3A 96.312 1437 45 3 3419 4849 416307843 416306409 0.000000e+00 2353.0
8 TraesCS3B01G252500 chr3A 88.988 672 52 10 1 665 416313566 416312910 0.000000e+00 811.0
9 TraesCS3B01G252500 chr3A 95.745 282 11 1 3154 3434 416310082 416309801 2.470000e-123 453.0
10 TraesCS3B01G252500 chr3A 89.286 112 9 3 2233 2344 679924278 679924170 2.820000e-28 137.0
11 TraesCS3B01G252500 chr6A 86.183 1766 170 31 2360 4106 586837644 586835934 0.000000e+00 1842.0
12 TraesCS3B01G252500 chr6A 82.552 533 42 20 1722 2222 586838181 586837668 6.960000e-114 422.0
13 TraesCS3B01G252500 chr7A 99.478 958 5 0 4850 5807 124663551 124664508 0.000000e+00 1742.0
14 TraesCS3B01G252500 chr7A 99.172 966 7 1 4843 5807 2015438 2014473 0.000000e+00 1738.0
15 TraesCS3B01G252500 chr7A 92.126 127 7 2 2219 2342 400068824 400068950 5.980000e-40 176.0
16 TraesCS3B01G252500 chr7A 90.909 121 9 1 2222 2340 667232138 667232018 1.670000e-35 161.0
17 TraesCS3B01G252500 chr7B 99.174 968 5 3 4841 5807 220958904 220959869 0.000000e+00 1740.0
18 TraesCS3B01G252500 chr7B 99.068 966 7 2 4842 5807 6168656 6167693 0.000000e+00 1733.0
19 TraesCS3B01G252500 chr7B 86.777 121 10 6 4124 4243 48465500 48465615 4.720000e-26 130.0
20 TraesCS3B01G252500 chr7B 88.571 70 8 0 1345 1414 511463109 511463040 1.040000e-12 86.1
21 TraesCS3B01G252500 chr4A 99.478 958 4 1 4850 5807 658636041 658636997 0.000000e+00 1740.0
22 TraesCS3B01G252500 chr4A 92.126 127 8 2 2219 2344 617850698 617850573 1.660000e-40 178.0
23 TraesCS3B01G252500 chr4A 85.211 142 10 8 4114 4248 543368437 543368300 1.010000e-27 135.0
24 TraesCS3B01G252500 chr2A 99.070 968 8 1 4841 5807 277940339 277941306 0.000000e+00 1736.0
25 TraesCS3B01G252500 chr2A 91.339 127 9 1 2219 2343 88010248 88010122 7.740000e-39 172.0
26 TraesCS3B01G252500 chr1B 99.068 966 8 1 4842 5807 467199199 467198235 0.000000e+00 1733.0
27 TraesCS3B01G252500 chr5B 98.671 978 9 4 4833 5807 32473902 32474878 0.000000e+00 1731.0
28 TraesCS3B01G252500 chr5B 91.603 131 8 2 2217 2344 693677507 693677637 1.660000e-40 178.0
29 TraesCS3B01G252500 chr6D 87.100 938 90 7 2360 3293 438308710 438307800 0.000000e+00 1033.0
30 TraesCS3B01G252500 chr6D 88.060 335 29 2 3499 3822 438305479 438305145 2.540000e-103 387.0
31 TraesCS3B01G252500 chr6D 90.530 264 23 2 3853 4116 438305145 438304884 1.200000e-91 348.0
32 TraesCS3B01G252500 chr6D 84.328 134 13 5 4124 4254 153810665 153810793 2.200000e-24 124.0
33 TraesCS3B01G252500 chr6B 85.926 945 93 21 2360 3296 663709882 663708970 0.000000e+00 972.0
34 TraesCS3B01G252500 chr6B 83.397 524 44 19 1722 2222 663710409 663709906 4.130000e-121 446.0
35 TraesCS3B01G252500 chr6B 91.257 183 16 0 3551 3733 663706416 663706234 3.470000e-62 250.0
36 TraesCS3B01G252500 chr6B 91.765 85 7 0 3722 3806 663698166 663698082 1.020000e-22 119.0
37 TraesCS3B01G252500 chr6B 91.935 62 5 0 2219 2280 713117910 713117971 2.880000e-13 87.9
38 TraesCS3B01G252500 chr5A 93.750 128 6 1 2219 2344 494231046 494231173 2.140000e-44 191.0
39 TraesCS3B01G252500 chr2D 93.798 129 5 2 2219 2344 87754317 87754189 2.140000e-44 191.0
40 TraesCS3B01G252500 chr2D 86.667 135 5 6 4125 4249 133769546 133769415 2.820000e-28 137.0
41 TraesCS3B01G252500 chr1D 92.000 125 8 1 2222 2344 324746968 324747092 2.150000e-39 174.0
42 TraesCS3B01G252500 chr1D 93.258 89 6 0 4016 4104 484391666 484391578 1.310000e-26 132.0
43 TraesCS3B01G252500 chr7D 86.777 121 10 6 4124 4243 94441114 94441229 4.720000e-26 130.0
44 TraesCS3B01G252500 chr7D 82.993 147 15 8 4114 4254 242791483 242791341 2.200000e-24 124.0
45 TraesCS3B01G252500 chr4D 84.507 142 11 8 4114 4248 53759994 53760131 4.720000e-26 130.0


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 TraesCS3B01G252500 chr3B 405779382 405785188 5806 False 10724.000000 10724 100.000000 1 5807 1 chr3B.!!$F1 5806
1 TraesCS3B01G252500 chr3B 754926523 754927488 965 True 1740.000000 1740 99.173000 4842 5807 1 chr3B.!!$R1 965
2 TraesCS3B01G252500 chr3D 313816168 313821752 5584 True 1570.000000 4132 91.476250 1 4882 4 chr3D.!!$R1 4881
3 TraesCS3B01G252500 chr3A 416306409 416313566 7157 True 1844.000000 3759 93.708000 1 4849 4 chr3A.!!$R2 4848
4 TraesCS3B01G252500 chr6A 586835934 586838181 2247 True 1132.000000 1842 84.367500 1722 4106 2 chr6A.!!$R1 2384
5 TraesCS3B01G252500 chr7A 124663551 124664508 957 False 1742.000000 1742 99.478000 4850 5807 1 chr7A.!!$F1 957
6 TraesCS3B01G252500 chr7A 2014473 2015438 965 True 1738.000000 1738 99.172000 4843 5807 1 chr7A.!!$R1 964
7 TraesCS3B01G252500 chr7B 220958904 220959869 965 False 1740.000000 1740 99.174000 4841 5807 1 chr7B.!!$F2 966
8 TraesCS3B01G252500 chr7B 6167693 6168656 963 True 1733.000000 1733 99.068000 4842 5807 1 chr7B.!!$R1 965
9 TraesCS3B01G252500 chr4A 658636041 658636997 956 False 1740.000000 1740 99.478000 4850 5807 1 chr4A.!!$F1 957
10 TraesCS3B01G252500 chr2A 277940339 277941306 967 False 1736.000000 1736 99.070000 4841 5807 1 chr2A.!!$F1 966
11 TraesCS3B01G252500 chr1B 467198235 467199199 964 True 1733.000000 1733 99.068000 4842 5807 1 chr1B.!!$R1 965
12 TraesCS3B01G252500 chr5B 32473902 32474878 976 False 1731.000000 1731 98.671000 4833 5807 1 chr5B.!!$F1 974
13 TraesCS3B01G252500 chr6D 438304884 438308710 3826 True 589.333333 1033 88.563333 2360 4116 3 chr6D.!!$R1 1756
14 TraesCS3B01G252500 chr6B 663706234 663710409 4175 True 556.000000 972 86.860000 1722 3733 3 chr6B.!!$R2 2011

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
734 1124 0.108138 CCTTCGAACCGAATGAGCCT 60.108 55.000 0.00 0.0 44.85 4.58 F
1110 1526 1.003696 AGGCCAGTGAGCTTTAAGACC 59.996 52.381 5.01 0.0 0.00 3.85 F
1490 1915 1.271379 TCACTCGTTATCGCTGGTTGT 59.729 47.619 0.00 0.0 36.96 3.32 F
2246 2925 0.539438 TGCTACCCTTTGGCTGTTGG 60.539 55.000 0.00 0.0 33.59 3.77 F
3294 4506 0.769247 GGGTGGAAACTGGTAGTGGT 59.231 55.000 0.00 0.0 0.00 4.16 F
3984 11629 1.004628 TCATGTATGCACTTGGCCACT 59.995 47.619 3.88 0.0 43.89 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1689 2145 3.055530 GTGATTGTGTCTCCTCATCACCT 60.056 47.826 0.00 0.00 33.04 4.00 R
2146 2816 5.047847 TCGTTTATAGGTGCTTGATAGTGC 58.952 41.667 0.00 0.00 0.00 4.40 R
3453 8775 2.929161 GCCAACCCCGAAATTTAAGCAC 60.929 50.000 0.00 0.00 0.00 4.40 R
3984 11629 5.244851 TGCAAATACTCAAGTAAATTGCCCA 59.755 36.000 25.31 14.64 45.96 5.36 R
4680 12331 1.047002 CCCCCTTCACAAATGCAACA 58.953 50.000 0.00 0.00 0.00 3.33 R
4846 12497 2.709397 ACGGGCCCTTTTGCTAGTATAT 59.291 45.455 22.43 0.00 0.00 0.86 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
78 84 6.722328 AGTTTAAAAATAGAGTAGCTGGGCT 58.278 36.000 0.00 0.00 43.41 5.19
79 85 7.858498 AGTTTAAAAATAGAGTAGCTGGGCTA 58.142 34.615 0.00 0.00 40.44 3.93
84 90 5.693769 AATAGAGTAGCTGGGCTAAAACA 57.306 39.130 0.00 0.00 43.07 2.83
173 179 2.748461 TGCACGAAAAAGGAAGAACG 57.252 45.000 0.00 0.00 0.00 3.95
180 186 4.820173 ACGAAAAAGGAAGAACGAGGATTT 59.180 37.500 0.00 0.00 0.00 2.17
199 205 4.532314 TTTAAACTCGGGTCTCCTCTTC 57.468 45.455 0.00 0.00 0.00 2.87
200 206 0.889306 AAACTCGGGTCTCCTCTTCG 59.111 55.000 0.00 0.00 0.00 3.79
201 207 0.966370 AACTCGGGTCTCCTCTTCGG 60.966 60.000 0.00 0.00 0.00 4.30
202 208 1.077644 CTCGGGTCTCCTCTTCGGA 60.078 63.158 0.00 0.00 40.30 4.55
269 275 0.831711 AAACATTTGGGGCCTCGCTT 60.832 50.000 0.84 0.00 0.00 4.68
312 318 3.435671 CGGCGACTTAGAAGGAAAAACAT 59.564 43.478 0.00 0.00 0.00 2.71
338 348 3.586470 TTCCATTTACCGGTGGCATAT 57.414 42.857 19.93 0.00 35.43 1.78
348 358 1.885887 CGGTGGCATATGGGGTAATTG 59.114 52.381 4.56 0.00 0.00 2.32
359 369 7.255942 GCATATGGGGTAATTGCTGATAACTTT 60.256 37.037 4.56 0.00 0.00 2.66
374 385 7.939588 GCTGATAACTTTAGGGGTAAATCTGAT 59.060 37.037 0.00 0.00 0.00 2.90
394 405 1.569479 GACGGGCAGACAGAAGCAAC 61.569 60.000 0.00 0.00 0.00 4.17
396 407 1.165907 CGGGCAGACAGAAGCAACAA 61.166 55.000 0.00 0.00 0.00 2.83
400 411 1.299541 CAGACAGAAGCAACAACCGT 58.700 50.000 0.00 0.00 0.00 4.83
482 812 9.801873 TTTTAATAATAAAAGTGCCATGCTCTC 57.198 29.630 0.00 0.00 36.36 3.20
574 904 1.134965 CCCAAAAGCAAACCGACAACA 60.135 47.619 0.00 0.00 0.00 3.33
588 918 1.597663 GACAACAGAACCGGTGAACTG 59.402 52.381 25.00 25.00 36.58 3.16
607 938 1.020861 GGCGGTCCGACGGTAAAAAT 61.021 55.000 17.49 0.00 0.00 1.82
615 946 3.055675 TCCGACGGTAAAAATCTGACCAT 60.056 43.478 14.79 0.00 32.39 3.55
650 1040 5.390145 CGATTCGATTACCTGTTCGGTTTTT 60.390 40.000 0.00 0.00 46.37 1.94
651 1041 4.996062 TCGATTACCTGTTCGGTTTTTC 57.004 40.909 0.00 0.00 46.37 2.29
652 1042 4.378774 TCGATTACCTGTTCGGTTTTTCA 58.621 39.130 0.00 0.00 46.37 2.69
653 1043 4.815308 TCGATTACCTGTTCGGTTTTTCAA 59.185 37.500 0.00 0.00 46.37 2.69
654 1044 5.296283 TCGATTACCTGTTCGGTTTTTCAAA 59.704 36.000 0.00 0.00 46.37 2.69
655 1045 5.397240 CGATTACCTGTTCGGTTTTTCAAAC 59.603 40.000 0.00 0.00 46.37 2.93
656 1046 5.900865 TTACCTGTTCGGTTTTTCAAACT 57.099 34.783 0.00 0.00 46.37 2.66
657 1047 4.365899 ACCTGTTCGGTTTTTCAAACTC 57.634 40.909 0.00 0.00 46.37 3.01
658 1048 4.014406 ACCTGTTCGGTTTTTCAAACTCT 58.986 39.130 0.00 0.00 46.37 3.24
659 1049 4.142469 ACCTGTTCGGTTTTTCAAACTCTG 60.142 41.667 0.00 0.00 46.37 3.35
660 1050 3.765026 TGTTCGGTTTTTCAAACTCTGC 58.235 40.909 0.00 0.00 0.00 4.26
661 1051 3.442273 TGTTCGGTTTTTCAAACTCTGCT 59.558 39.130 0.00 0.00 0.00 4.24
662 1052 4.636648 TGTTCGGTTTTTCAAACTCTGCTA 59.363 37.500 0.00 0.00 0.00 3.49
663 1053 4.806342 TCGGTTTTTCAAACTCTGCTAC 57.194 40.909 0.00 0.00 0.00 3.58
664 1054 4.448210 TCGGTTTTTCAAACTCTGCTACT 58.552 39.130 0.00 0.00 0.00 2.57
665 1055 4.879545 TCGGTTTTTCAAACTCTGCTACTT 59.120 37.500 0.00 0.00 0.00 2.24
666 1056 5.355910 TCGGTTTTTCAAACTCTGCTACTTT 59.644 36.000 0.00 0.00 0.00 2.66
667 1057 6.033966 CGGTTTTTCAAACTCTGCTACTTTT 58.966 36.000 0.00 0.00 0.00 2.27
668 1058 6.530181 CGGTTTTTCAAACTCTGCTACTTTTT 59.470 34.615 0.00 0.00 0.00 1.94
734 1124 0.108138 CCTTCGAACCGAATGAGCCT 60.108 55.000 0.00 0.00 44.85 4.58
748 1138 3.608432 GCCTTTAGCTGGGCCTTG 58.392 61.111 4.53 0.00 42.30 3.61
810 1207 2.048222 TCGTCAAAGCCAGCTCGG 60.048 61.111 0.00 0.00 38.11 4.63
848 1245 4.367023 CCGCAGAACCGAACGGGA 62.367 66.667 17.44 0.00 41.95 5.14
911 1308 2.515996 GAATTCACGCCCGGACTCCA 62.516 60.000 0.73 0.00 0.00 3.86
1110 1526 1.003696 AGGCCAGTGAGCTTTAAGACC 59.996 52.381 5.01 0.00 0.00 3.85
1121 1537 2.609916 GCTTTAAGACCAAGAGGATCGC 59.390 50.000 0.00 0.00 42.67 4.58
1174 1590 2.351276 GGGCCACCAAGACGATGT 59.649 61.111 4.39 0.00 36.50 3.06
1198 1621 4.933064 CCTCATCGTCCGCTCGGC 62.933 72.222 2.96 0.00 34.68 5.54
1199 1622 3.893763 CTCATCGTCCGCTCGGCT 61.894 66.667 2.96 0.00 34.68 5.52
1230 1653 3.288381 AGAGAGGTGGGGGAGGCT 61.288 66.667 0.00 0.00 0.00 4.58
1339 1762 2.736347 TGACCCTACTGTTCTCTAGGC 58.264 52.381 0.00 0.00 0.00 3.93
1341 1764 1.361543 ACCCTACTGTTCTCTAGGCCA 59.638 52.381 5.01 0.00 0.00 5.36
1442 1867 2.047830 GGGGTAAGATGGTCACTAGGG 58.952 57.143 0.00 0.00 0.00 3.53
1446 1871 4.226620 GGGTAAGATGGTCACTAGGGAAAA 59.773 45.833 0.00 0.00 0.00 2.29
1447 1872 5.280830 GGGTAAGATGGTCACTAGGGAAAAA 60.281 44.000 0.00 0.00 0.00 1.94
1490 1915 1.271379 TCACTCGTTATCGCTGGTTGT 59.729 47.619 0.00 0.00 36.96 3.32
1504 1958 3.119849 GCTGGTTGTCGCATTTGTAGATT 60.120 43.478 0.00 0.00 0.00 2.40
1505 1959 4.094294 GCTGGTTGTCGCATTTGTAGATTA 59.906 41.667 0.00 0.00 0.00 1.75
1664 2120 2.336945 TTCCTAGTCCGCGTAGATGA 57.663 50.000 4.92 0.00 0.00 2.92
1694 2150 6.822442 TGTCAAGTACATACTTCAAAGGTGA 58.178 36.000 1.18 0.00 44.19 4.02
1867 2330 6.795114 GCTGAAAATTGCAAAAATGTCTCATG 59.205 34.615 1.71 0.00 0.00 3.07
1901 2364 7.338703 ACAGATTCTGTAATTAGTACTCGGTGA 59.661 37.037 17.63 0.00 43.46 4.02
1978 2441 1.400242 GGCGTCAATTGCTTGTGTCTC 60.400 52.381 0.00 0.00 33.87 3.36
2146 2816 1.071542 TGGTGATGTGTGGTACTGTGG 59.928 52.381 0.00 0.00 0.00 4.17
2246 2925 0.539438 TGCTACCCTTTGGCTGTTGG 60.539 55.000 0.00 0.00 33.59 3.77
2324 3216 7.929245 TGACTAAATATATGCTAAACGGCTTGA 59.071 33.333 0.00 0.00 0.00 3.02
2362 3254 6.711277 ACATATCCATATCGGTGCAAAGTAT 58.289 36.000 0.00 0.00 35.57 2.12
2646 3538 4.101790 GGTGGTTCATGTGCCGCG 62.102 66.667 0.00 0.00 36.21 6.46
2750 3642 5.805486 TGATGTTTACTCATGAGCGTTACTC 59.195 40.000 22.83 13.00 46.45 2.59
2757 3649 5.003804 ACTCATGAGCGTTACTCCAAAATT 58.996 37.500 22.83 0.00 45.61 1.82
2777 3673 9.330063 CAAAATTATTCAGTGCATCTAGTAGGA 57.670 33.333 0.00 0.00 0.00 2.94
3131 4034 8.984891 TTTAAATTTGCGATGAATCTCATTGT 57.015 26.923 0.00 0.00 39.82 2.71
3136 4039 2.604914 GCGATGAATCTCATTGTGACGT 59.395 45.455 0.00 0.00 39.82 4.34
3138 4041 4.267690 GCGATGAATCTCATTGTGACGTAA 59.732 41.667 5.90 0.00 39.82 3.18
3242 4454 9.434420 ACATTCACTTTTCTTTGTCAAATGAAA 57.566 25.926 11.71 12.94 37.55 2.69
3294 4506 0.769247 GGGTGGAAACTGGTAGTGGT 59.231 55.000 0.00 0.00 0.00 4.16
3376 4593 5.245751 ACTGAAAATGCATATGGGAAACACA 59.754 36.000 0.00 0.00 0.00 3.72
3453 8775 7.041440 TGTTGGATAATGCATTTATGTCGTAGG 60.041 37.037 18.75 0.00 30.44 3.18
3698 11343 1.550976 AGTGGTAAGCCTGACACTAGC 59.449 52.381 0.00 0.00 41.95 3.42
3916 11561 8.397575 TCATTAACTTGCTGTTGTTTATACCA 57.602 30.769 6.04 0.00 39.55 3.25
3984 11629 1.004628 TCATGTATGCACTTGGCCACT 59.995 47.619 3.88 0.00 43.89 4.00
4122 11767 9.393786 AGGTCAGTATACCATAATACTCCATTT 57.606 33.333 0.00 0.00 40.02 2.32
4183 11830 4.889241 ACGTTTTAGTGTTTGTTCACTCG 58.111 39.130 2.59 3.92 45.79 4.18
4187 11834 6.303733 CGTTTTAGTGTTTGTTCACTCGTTTT 59.696 34.615 2.59 0.00 45.79 2.43
4249 11896 2.781681 AGTATTTGTGAACGGAGGGG 57.218 50.000 0.00 0.00 0.00 4.79
4304 11951 5.508124 TTTATTTTCCATTTCTTTGCGCG 57.492 34.783 0.00 0.00 0.00 6.86
4386 12037 3.681593 TGTGGCAAATAGGGACTTGTAC 58.318 45.455 0.00 0.00 41.75 2.90
4412 12063 5.754543 TCGTACCGACATGTGATGTATTA 57.245 39.130 1.15 0.00 45.03 0.98
4545 12196 3.694734 ACAATTCGTTGACTTGTGCAAG 58.305 40.909 10.09 10.09 43.79 4.01
4680 12331 2.412937 GTGGTTTTGCAGCACGCT 59.587 55.556 0.00 0.00 43.81 5.07
4697 12348 1.787012 GCTGTTGCATTTGTGAAGGG 58.213 50.000 0.00 0.00 39.41 3.95
4707 12358 2.531942 GTGAAGGGGGAGGTGGGT 60.532 66.667 0.00 0.00 0.00 4.51
4740 12391 1.677217 GCCCGAAAGCTGACAGAGATT 60.677 52.381 6.65 0.00 0.00 2.40
4812 12463 1.136085 CACCGTGCCAAATAAGTGACG 60.136 52.381 0.00 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
78 84 5.900425 TCTTTGCACAATCTTGCTGTTTTA 58.100 33.333 0.00 0.00 43.41 1.52
79 85 4.757594 TCTTTGCACAATCTTGCTGTTTT 58.242 34.783 0.00 0.00 43.41 2.43
84 90 2.232941 CCCATCTTTGCACAATCTTGCT 59.767 45.455 0.00 0.00 43.41 3.91
98 104 0.767998 GCCTAGCCTAAGCCCATCTT 59.232 55.000 0.00 0.00 41.25 2.40
173 179 3.451540 AGGAGACCCGAGTTTAAATCCTC 59.548 47.826 0.00 0.00 37.58 3.71
180 186 2.089980 CGAAGAGGAGACCCGAGTTTA 58.910 52.381 0.00 0.00 37.58 2.01
200 206 2.756207 GAGCCTAATATCTCCGGTCTCC 59.244 54.545 0.00 0.00 0.00 3.71
201 207 3.422796 TGAGCCTAATATCTCCGGTCTC 58.577 50.000 0.00 0.00 0.00 3.36
202 208 3.527507 TGAGCCTAATATCTCCGGTCT 57.472 47.619 0.00 0.00 0.00 3.85
203 209 4.382147 GGATTGAGCCTAATATCTCCGGTC 60.382 50.000 0.00 0.00 0.00 4.79
204 210 3.515901 GGATTGAGCCTAATATCTCCGGT 59.484 47.826 0.00 0.00 0.00 5.28
205 211 3.515502 TGGATTGAGCCTAATATCTCCGG 59.484 47.826 0.00 0.00 0.00 5.14
206 212 4.499183 GTGGATTGAGCCTAATATCTCCG 58.501 47.826 0.00 0.00 0.00 4.63
269 275 7.583860 GCCGTTGGCTTTATTGTTTATTTAA 57.416 32.000 0.00 0.00 46.69 1.52
289 295 2.804527 GTTTTTCCTTCTAAGTCGCCGT 59.195 45.455 0.00 0.00 0.00 5.68
320 330 1.885887 CCATATGCCACCGGTAAATGG 59.114 52.381 6.87 12.24 39.16 3.16
323 333 0.183971 CCCCATATGCCACCGGTAAA 59.816 55.000 6.87 0.00 0.00 2.01
338 348 6.126409 CCTAAAGTTATCAGCAATTACCCCA 58.874 40.000 0.00 0.00 0.00 4.96
348 358 7.280356 TCAGATTTACCCCTAAAGTTATCAGC 58.720 38.462 0.00 0.00 0.00 4.26
359 369 2.969950 CCCGTCATCAGATTTACCCCTA 59.030 50.000 0.00 0.00 0.00 3.53
374 385 2.038814 TTGCTTCTGTCTGCCCGTCA 62.039 55.000 0.00 0.00 0.00 4.35
527 857 9.729281 AAATTTTATCACTTCTTCATGGCAATT 57.271 25.926 0.00 0.00 0.00 2.32
574 904 2.030562 CGCCAGTTCACCGGTTCT 59.969 61.111 2.97 0.22 0.00 3.01
588 918 1.020861 ATTTTTACCGTCGGACCGCC 61.021 55.000 20.51 0.00 0.00 6.13
607 938 1.754803 CGGTAAGGCTGTATGGTCAGA 59.245 52.381 0.00 0.00 37.61 3.27
615 946 4.261741 GGTAATCGAATCGGTAAGGCTGTA 60.262 45.833 1.76 0.00 0.00 2.74
748 1138 2.817423 CGCTGCGAAATGAGGCCTC 61.817 63.158 26.78 26.78 0.00 4.70
791 1188 1.664649 CGAGCTGGCTTTGACGACA 60.665 57.895 0.00 0.00 0.00 4.35
848 1245 1.280457 AGAAATCGAGCCCCTGTTCT 58.720 50.000 0.00 0.00 0.00 3.01
1015 1431 2.266055 CTCCTGGTCCTTGACGCC 59.734 66.667 0.00 0.00 32.65 5.68
1110 1526 2.125552 TGCCACGCGATCCTCTTG 60.126 61.111 15.93 0.00 0.00 3.02
1199 1622 0.325671 CTCTCTGGCTCCCCTTACCA 60.326 60.000 0.00 0.00 0.00 3.25
1291 1714 3.683847 GCATGATGTTACCTCTTCCAGCT 60.684 47.826 0.00 0.00 0.00 4.24
1381 1806 1.289231 TGGCCTAGATCCTCTCACTGT 59.711 52.381 3.32 0.00 0.00 3.55
1446 1871 5.944007 ACGAGGAACCAAGCTATGTATTTTT 59.056 36.000 0.00 0.00 0.00 1.94
1447 1872 5.497474 ACGAGGAACCAAGCTATGTATTTT 58.503 37.500 0.00 0.00 0.00 1.82
1527 1981 3.421844 ACTAAACACATGAGGGCTTTCC 58.578 45.455 0.00 0.00 0.00 3.13
1532 1986 3.610911 AGCTAACTAAACACATGAGGGC 58.389 45.455 0.00 0.00 0.00 5.19
1689 2145 3.055530 GTGATTGTGTCTCCTCATCACCT 60.056 47.826 0.00 0.00 33.04 4.00
1694 2150 4.019051 TCAATGGTGATTGTGTCTCCTCAT 60.019 41.667 0.00 0.00 40.43 2.90
1978 2441 8.502387 CAAAAAGGTTCAGTGAGAGAGAAATAG 58.498 37.037 0.00 0.00 0.00 1.73
2146 2816 5.047847 TCGTTTATAGGTGCTTGATAGTGC 58.952 41.667 0.00 0.00 0.00 4.40
2246 2925 9.860898 ATCCATAATTCTAACAAAAGCAAGAAC 57.139 29.630 0.00 0.00 31.20 3.01
2362 3254 9.256228 AGGAATATAATAGAAGACGAATAGGCA 57.744 33.333 0.00 0.00 0.00 4.75
2530 3422 7.004086 TCTCACCATCAAATACTCCAAAAAGT 58.996 34.615 0.00 0.00 0.00 2.66
2646 3538 5.799827 ATAAGTGCTCCTTGAGATACTCC 57.200 43.478 0.00 0.00 34.46 3.85
2750 3642 8.562892 CCTACTAGATGCACTGAATAATTTTGG 58.437 37.037 0.00 0.00 0.00 3.28
2757 3649 8.678199 CGATTATCCTACTAGATGCACTGAATA 58.322 37.037 0.00 0.00 0.00 1.75
3176 4388 6.183360 TGCATTACTGACATGATACGACAAAC 60.183 38.462 0.00 0.00 0.00 2.93
3242 4454 4.801330 TGAAACACGATCTGTCCAGTAT 57.199 40.909 0.00 0.00 30.29 2.12
3294 4506 7.455641 ACAAACACCGGATATTTCACATTAA 57.544 32.000 9.46 0.00 0.00 1.40
3376 4593 7.051000 GGAAACATAGCTCCTATTCAGTCTTT 58.949 38.462 0.00 0.00 0.00 2.52
3453 8775 2.929161 GCCAACCCCGAAATTTAAGCAC 60.929 50.000 0.00 0.00 0.00 4.40
3725 11370 7.870826 AGATATTTCAACAAACACGTGATTGA 58.129 30.769 35.83 26.38 32.92 2.57
3756 11401 7.137426 GCAAAACAAACATTTGGCATTATCAA 58.863 30.769 9.09 0.00 42.34 2.57
3916 11561 6.892658 TTGTGTAATGGTATCTTTGCAGTT 57.107 33.333 0.00 0.00 0.00 3.16
3984 11629 5.244851 TGCAAATACTCAAGTAAATTGCCCA 59.755 36.000 25.31 14.64 45.96 5.36
4183 11830 8.975439 CAATATGGACTACATACGGACTAAAAC 58.025 37.037 0.00 0.00 44.41 2.43
4187 11834 8.467963 TTTCAATATGGACTACATACGGACTA 57.532 34.615 0.00 0.00 44.41 2.59
4249 11896 3.056607 AGCTGTGCATGAAATTTGGTACC 60.057 43.478 4.43 4.43 0.00 3.34
4278 11925 6.249050 GCGCAAAGAAATGGAAAATAAAATGC 59.751 34.615 0.30 0.00 0.00 3.56
4304 11951 4.767928 ACCGGAGATCTATTGGTAGTCATC 59.232 45.833 9.46 0.00 0.00 2.92
4412 12063 3.815401 GGTGCACTAGACATGTCAAGTTT 59.185 43.478 27.02 9.10 0.00 2.66
4545 12196 7.213678 CCTGAAGAGAATAAGAGATGGTAACC 58.786 42.308 0.00 0.00 0.00 2.85
4680 12331 1.047002 CCCCCTTCACAAATGCAACA 58.953 50.000 0.00 0.00 0.00 3.33
4740 12391 3.659092 CTCCCACGCGCAAAAGCA 61.659 61.111 5.73 0.00 36.85 3.91
4761 12412 9.489084 TCTACAACTATGCATGTTATATTGTCC 57.511 33.333 10.16 0.00 31.81 4.02
4844 12495 4.348754 ACGGGCCCTTTTGCTAGTATATAA 59.651 41.667 22.43 0.00 0.00 0.98
4845 12496 3.905591 ACGGGCCCTTTTGCTAGTATATA 59.094 43.478 22.43 0.00 0.00 0.86
4846 12497 2.709397 ACGGGCCCTTTTGCTAGTATAT 59.291 45.455 22.43 0.00 0.00 0.86


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

AutoCloner maintained by Alex Coulton.