Multiple sequence alignment - TraesCS2B01G401200

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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 TraesCS2B01G401200 chr2B 100.000 2648 0 0 1 2648 569484831 569487478 0.000000e+00 4891
1 TraesCS2B01G401200 chr2B 90.341 176 14 3 736 909 569113395 569113221 7.370000e-56 228
2 TraesCS2B01G401200 chr2D 90.382 2017 120 32 44 2017 484833142 484835127 0.000000e+00 2582
3 TraesCS2B01G401200 chr2D 89.989 949 61 16 858 1782 484380815 484381753 0.000000e+00 1195
4 TraesCS2B01G401200 chr2D 88.406 552 31 12 2013 2547 484846525 484847060 3.720000e-178 634
5 TraesCS2B01G401200 chr2D 86.735 98 7 5 2547 2644 484847160 484847251 1.300000e-18 104
6 TraesCS2B01G401200 chr2D 95.238 63 3 0 736 798 484380756 484380818 1.680000e-17 100
7 TraesCS2B01G401200 chr1A 81.971 477 72 7 1 475 507975125 507974661 2.470000e-105 392
8 TraesCS2B01G401200 chr7B 82.030 473 71 7 1 470 465787933 465788394 8.890000e-105 390
9 TraesCS2B01G401200 chr7B 80.804 224 32 5 1 223 508799030 508799243 5.860000e-37 165
10 TraesCS2B01G401200 chr4B 81.917 459 67 8 21 475 434584770 434584324 8.950000e-100 374
11 TraesCS2B01G401200 chr3D 80.802 474 81 6 2 473 477024140 477023675 1.940000e-96 363
12 TraesCS2B01G401200 chr3D 80.705 482 75 13 1 478 438564818 438565285 2.510000e-95 359
13 TraesCS2B01G401200 chr2A 84.334 383 24 15 2188 2547 628701336 628701705 2.520000e-90 342
14 TraesCS2B01G401200 chr3B 79.710 483 77 14 1 473 636266398 636265927 1.960000e-86 329
15 TraesCS2B01G401200 chr3A 79.245 477 83 10 1 476 696398506 696398045 4.250000e-83 318
16 TraesCS2B01G401200 chr3A 79.046 482 82 14 1 478 577556194 577556660 1.980000e-81 313
17 TraesCS2B01G401200 chr7D 79.412 476 69 12 1 474 512737990 512737542 2.560000e-80 309
18 TraesCS2B01G401200 chr6D 78.631 482 74 16 1 475 163147628 163148087 2.580000e-75 292
19 TraesCS2B01G401200 chr5D 82.436 353 44 10 1 349 327645733 327645395 2.580000e-75 292
20 TraesCS2B01G401200 chr6A 83.133 166 27 1 1 165 603787981 603788146 1.640000e-32 150


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 TraesCS2B01G401200 chr2B 569484831 569487478 2647 False 4891.0 4891 100.0000 1 2648 1 chr2B.!!$F1 2647
1 TraesCS2B01G401200 chr2D 484833142 484835127 1985 False 2582.0 2582 90.3820 44 2017 1 chr2D.!!$F1 1973
2 TraesCS2B01G401200 chr2D 484380756 484381753 997 False 647.5 1195 92.6135 736 1782 2 chr2D.!!$F2 1046
3 TraesCS2B01G401200 chr2D 484846525 484847251 726 False 369.0 634 87.5705 2013 2644 2 chr2D.!!$F3 631

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
837 852 0.040425 CCAACGCGAACCTTTTCCAG 60.04 55.0 15.93 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2499 2576 0.037326 TGAGGAATCGACAGCCACAC 60.037 55.0 0.0 0.0 0.0 3.82 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
19 20 2.804697 TTCATCGAACAAGTGTCGGA 57.195 45.000 0.00 0.00 0.00 4.55
20 21 2.060326 TCATCGAACAAGTGTCGGAC 57.940 50.000 0.00 0.00 0.00 4.79
21 22 1.338655 TCATCGAACAAGTGTCGGACA 59.661 47.619 6.76 6.76 0.00 4.02
22 23 2.029380 TCATCGAACAAGTGTCGGACAT 60.029 45.455 14.78 0.00 0.00 3.06
23 24 1.778334 TCGAACAAGTGTCGGACATG 58.222 50.000 14.78 11.82 0.00 3.21
24 25 0.790207 CGAACAAGTGTCGGACATGG 59.210 55.000 14.78 9.28 0.00 3.66
25 26 1.872237 CGAACAAGTGTCGGACATGGT 60.872 52.381 14.78 8.10 0.00 3.55
26 27 2.608506 CGAACAAGTGTCGGACATGGTA 60.609 50.000 14.78 0.00 0.00 3.25
27 28 2.743636 ACAAGTGTCGGACATGGTAG 57.256 50.000 14.78 5.89 0.00 3.18
28 29 1.968493 ACAAGTGTCGGACATGGTAGT 59.032 47.619 14.78 6.49 0.00 2.73
29 30 3.159472 ACAAGTGTCGGACATGGTAGTA 58.841 45.455 14.78 0.00 0.00 1.82
30 31 3.767673 ACAAGTGTCGGACATGGTAGTAT 59.232 43.478 14.78 0.00 0.00 2.12
31 32 4.951715 ACAAGTGTCGGACATGGTAGTATA 59.048 41.667 14.78 0.00 0.00 1.47
32 33 5.067413 ACAAGTGTCGGACATGGTAGTATAG 59.933 44.000 14.78 0.00 0.00 1.31
33 34 3.568853 AGTGTCGGACATGGTAGTATAGC 59.431 47.826 14.78 0.00 40.09 2.97
42 43 3.497103 TGGTAGTATAGCAGTAGCGGA 57.503 47.619 0.00 0.00 45.27 5.54
53 54 1.069258 GTAGCGGATGGTACCTGGC 59.931 63.158 14.36 10.81 42.02 4.85
54 55 1.382009 TAGCGGATGGTACCTGGCA 60.382 57.895 14.36 0.00 0.00 4.92
55 56 0.978667 TAGCGGATGGTACCTGGCAA 60.979 55.000 14.36 0.00 0.00 4.52
65 66 3.691342 CCTGGCAAGACGGTCGGA 61.691 66.667 1.89 0.00 0.00 4.55
84 85 2.747686 GAGAGGGGTTGAACGGCA 59.252 61.111 0.00 0.00 0.00 5.69
97 98 2.224523 TGAACGGCAATGGAGAAGAAGT 60.225 45.455 0.00 0.00 0.00 3.01
137 138 1.606601 CCTGGAGGTGACGGAGACA 60.607 63.158 0.00 0.00 0.00 3.41
154 155 1.227674 CATAGAGTTCCGGCAGGGC 60.228 63.158 2.05 0.00 38.33 5.19
155 156 1.383248 ATAGAGTTCCGGCAGGGCT 60.383 57.895 2.05 1.54 38.33 5.19
156 157 1.690219 ATAGAGTTCCGGCAGGGCTG 61.690 60.000 2.05 0.00 38.33 4.85
166 167 2.933287 CAGGGCTGGGGTGTGGTA 60.933 66.667 0.00 0.00 0.00 3.25
272 273 2.994995 CCGGGAAGGGTTTTGGGC 60.995 66.667 0.00 0.00 35.97 5.36
275 276 2.116556 GGAAGGGTTTTGGGCGGA 59.883 61.111 0.00 0.00 0.00 5.54
301 302 0.167689 GTGTCGGAGTCCTACGTGTC 59.832 60.000 7.77 0.00 38.28 3.67
316 317 4.990288 GTCTGTTGTCCGGACTCC 57.010 61.111 33.39 23.36 44.69 3.85
334 335 3.818787 CGCAAGCTGCCCCATGTC 61.819 66.667 0.00 0.00 41.12 3.06
340 341 1.451028 GCTGCCCCATGTCTGTCTC 60.451 63.158 0.00 0.00 0.00 3.36
346 347 0.324943 CCCATGTCTGTCTCCGGTTT 59.675 55.000 0.00 0.00 0.00 3.27
347 348 1.442769 CCATGTCTGTCTCCGGTTTG 58.557 55.000 0.00 0.00 0.00 2.93
348 349 0.798776 CATGTCTGTCTCCGGTTTGC 59.201 55.000 0.00 0.00 0.00 3.68
351 352 3.423154 CTGTCTCCGGTTTGCGGC 61.423 66.667 0.00 0.00 0.00 6.53
360 361 0.318614 CGGTTTGCGGCAGAAAATGT 60.319 50.000 1.67 0.00 0.00 2.71
361 362 1.864565 GGTTTGCGGCAGAAAATGTT 58.135 45.000 1.67 0.00 0.00 2.71
363 364 2.611751 GGTTTGCGGCAGAAAATGTTTT 59.388 40.909 1.67 0.00 0.00 2.43
364 365 3.064682 GGTTTGCGGCAGAAAATGTTTTT 59.935 39.130 1.67 0.00 0.00 1.94
366 367 2.208431 TGCGGCAGAAAATGTTTTTGG 58.792 42.857 0.00 0.00 0.00 3.28
371 372 2.220824 GCAGAAAATGTTTTTGGACCGC 59.779 45.455 0.00 0.00 0.00 5.68
377 378 4.896829 TTTTTGGACCGCCCCGCA 62.897 61.111 0.00 0.00 0.00 5.69
392 393 0.108615 CCGCAGACCGATTCAAGACT 60.109 55.000 0.00 0.00 40.02 3.24
393 394 0.994995 CGCAGACCGATTCAAGACTG 59.005 55.000 0.00 0.00 40.02 3.51
395 396 1.674221 GCAGACCGATTCAAGACTGCT 60.674 52.381 15.77 0.00 44.51 4.24
403 404 3.686241 CGATTCAAGACTGCTTTGGATGA 59.314 43.478 0.00 0.00 30.14 2.92
404 405 4.436584 CGATTCAAGACTGCTTTGGATGAC 60.437 45.833 0.00 0.00 30.14 3.06
428 440 1.518572 CGGTATGGACAGCGTGGTC 60.519 63.158 0.64 0.64 37.06 4.02
429 441 1.898154 GGTATGGACAGCGTGGTCT 59.102 57.895 8.20 0.00 37.91 3.85
443 455 4.760047 GTCTGGACGCATGCGGGT 62.760 66.667 39.95 23.58 44.69 5.28
452 464 3.361158 CATGCGGGTGGTTTGCGA 61.361 61.111 0.00 0.00 0.00 5.10
453 465 3.055719 ATGCGGGTGGTTTGCGAG 61.056 61.111 0.00 0.00 0.00 5.03
560 574 0.944386 GACGATTGTGTGTGCCAGTT 59.056 50.000 0.00 0.00 0.00 3.16
561 575 1.333619 GACGATTGTGTGTGCCAGTTT 59.666 47.619 0.00 0.00 0.00 2.66
562 576 1.065401 ACGATTGTGTGTGCCAGTTTG 59.935 47.619 0.00 0.00 0.00 2.93
563 577 1.333308 CGATTGTGTGTGCCAGTTTGA 59.667 47.619 0.00 0.00 0.00 2.69
564 578 2.030893 CGATTGTGTGTGCCAGTTTGAT 60.031 45.455 0.00 0.00 0.00 2.57
565 579 3.568538 GATTGTGTGTGCCAGTTTGATC 58.431 45.455 0.00 0.00 0.00 2.92
566 580 2.049888 TGTGTGTGCCAGTTTGATCA 57.950 45.000 0.00 0.00 0.00 2.92
567 581 2.373224 TGTGTGTGCCAGTTTGATCAA 58.627 42.857 3.38 3.38 0.00 2.57
568 582 2.358582 TGTGTGTGCCAGTTTGATCAAG 59.641 45.455 8.41 0.00 0.00 3.02
569 583 2.358898 GTGTGTGCCAGTTTGATCAAGT 59.641 45.455 8.41 0.00 0.00 3.16
575 589 6.801862 GTGTGCCAGTTTGATCAAGTAAATAC 59.198 38.462 8.41 2.96 0.00 1.89
580 594 8.391106 GCCAGTTTGATCAAGTAAATACTGTAG 58.609 37.037 23.99 15.64 36.50 2.74
624 638 9.443323 TGCATATATAATATGTTACGGCAAAGT 57.557 29.630 8.32 0.00 0.00 2.66
638 652 6.870971 ACGGCAAAGTAAAATCTAAAGACA 57.129 33.333 0.00 0.00 0.00 3.41
684 698 5.244626 GTGGAGGTGTGAAGTAACTAGGTTA 59.755 44.000 0.00 0.00 0.00 2.85
686 700 5.337089 GGAGGTGTGAAGTAACTAGGTTACC 60.337 48.000 14.46 0.00 46.50 2.85
766 780 6.346096 TCGATTGATAACCTTCTCCGAAATT 58.654 36.000 0.00 0.00 0.00 1.82
795 809 5.350365 TGCACAACTTAATCATCTTACGGTC 59.650 40.000 0.00 0.00 0.00 4.79
804 818 9.708222 CTTAATCATCTTACGGTCAATTTTGAG 57.292 33.333 0.00 0.00 37.98 3.02
833 848 1.000717 CCAATCCAACGCGAACCTTTT 60.001 47.619 15.93 0.00 0.00 2.27
834 849 2.315901 CAATCCAACGCGAACCTTTTC 58.684 47.619 15.93 0.00 0.00 2.29
837 852 0.040425 CCAACGCGAACCTTTTCCAG 60.040 55.000 15.93 0.00 0.00 3.86
851 866 6.311735 ACCTTTTCCAGCCTAAAAAGACATA 58.688 36.000 13.63 0.00 42.44 2.29
854 869 3.869065 TCCAGCCTAAAAAGACATACCG 58.131 45.455 0.00 0.00 0.00 4.02
855 870 2.354821 CCAGCCTAAAAAGACATACCGC 59.645 50.000 0.00 0.00 0.00 5.68
859 895 3.064958 GCCTAAAAAGACATACCGCTTCC 59.935 47.826 0.00 0.00 0.00 3.46
902 939 1.956629 AACGTGATCGATCCGGGCTT 61.957 55.000 27.98 16.97 40.62 4.35
922 967 6.929606 GGGCTTTCTGGGTTATATATATAGCG 59.070 42.308 9.65 0.00 0.00 4.26
946 991 2.040939 TGTACTTGAGGACGGGAAACA 58.959 47.619 0.00 0.00 0.00 2.83
954 1005 1.313091 GGACGGGAAACAAGGCATCC 61.313 60.000 0.00 0.00 0.00 3.51
970 1023 5.685728 AGGCATCCTTAATTAACTCACTCC 58.314 41.667 0.00 0.00 0.00 3.85
976 1029 4.504858 CTTAATTAACTCACTCCAGCCGT 58.495 43.478 0.00 0.00 0.00 5.68
992 1045 1.272715 CGTGCGCGTGAATACATCC 59.727 57.895 12.43 0.00 0.00 3.51
1102 1161 3.496692 GGTGACTGCCATGGATATGCTAA 60.497 47.826 18.40 0.00 32.79 3.09
1105 1164 3.944015 GACTGCCATGGATATGCTAATCC 59.056 47.826 18.40 10.09 44.96 3.01
1128 1187 5.336531 CCTGGTCTTCGTTCTGTGTATAGTT 60.337 44.000 0.00 0.00 0.00 2.24
1181 1240 4.113815 CGGCTTGGAGGCATCCCA 62.114 66.667 16.13 2.24 46.04 4.37
1197 1256 2.344203 CCAGCGACCGGAGTTCTCT 61.344 63.158 9.46 0.00 0.00 3.10
1260 1319 1.927174 CGGACGTTCAATCTCACCATC 59.073 52.381 0.00 0.00 0.00 3.51
1275 1334 4.133820 TCACCATCGTCATCAACAACTTT 58.866 39.130 0.00 0.00 0.00 2.66
1291 1350 0.902531 CTTTAGGGGCAAGTCCGAGA 59.097 55.000 0.00 0.00 34.94 4.04
1392 1451 1.308998 CCAAGTGCTCCACGAAGTTT 58.691 50.000 0.00 0.00 41.61 2.66
1652 1711 3.470709 CCAGCTTTCTGTTCTGACTTCA 58.529 45.455 0.00 0.00 38.66 3.02
1664 1723 3.809918 CTGACTTCAGAGAAAGCTTGC 57.190 47.619 0.00 0.00 46.59 4.01
1705 1764 7.504403 TGTCTGCATTTTCCTTTTATTTTCCA 58.496 30.769 0.00 0.00 0.00 3.53
1730 1789 7.221259 CAGTTGGTACATAATTCATGCATGTTG 59.779 37.037 25.43 17.21 39.30 3.33
1741 1800 6.572167 TTCATGCATGTTGATGTACAAGAA 57.428 33.333 25.43 5.61 39.30 2.52
1742 1801 6.762702 TCATGCATGTTGATGTACAAGAAT 57.237 33.333 25.43 0.00 39.30 2.40
1785 1844 5.280215 GCTCTGGCCTATATGTACTTGGATT 60.280 44.000 3.32 0.00 0.00 3.01
1795 1854 9.639601 CTATATGTACTTGGATTTAGCGATGAA 57.360 33.333 0.00 0.00 0.00 2.57
1810 1869 2.359900 GATGAACACGCTCCATCCTTT 58.640 47.619 0.00 0.00 32.68 3.11
1821 1880 3.445450 GCTCCATCCTTTTCCTTCCTTTC 59.555 47.826 0.00 0.00 0.00 2.62
1849 1908 1.535462 CATCGCCGTTCAGAACCTTTT 59.465 47.619 7.76 0.00 0.00 2.27
1860 1919 2.031682 CAGAACCTTTTTCGCAGTCAGG 60.032 50.000 0.00 0.00 0.00 3.86
1866 1925 1.021202 TTTTCGCAGTCAGGGTGTTG 58.979 50.000 0.00 0.00 0.00 3.33
1867 1926 1.444119 TTTCGCAGTCAGGGTGTTGC 61.444 55.000 0.00 0.00 0.00 4.17
1868 1927 3.357079 CGCAGTCAGGGTGTTGCC 61.357 66.667 0.00 0.00 33.10 4.52
1869 1928 2.203337 GCAGTCAGGGTGTTGCCA 60.203 61.111 0.00 0.00 39.65 4.92
1870 1929 1.827789 GCAGTCAGGGTGTTGCCAA 60.828 57.895 0.00 0.00 39.65 4.52
1871 1930 1.391157 GCAGTCAGGGTGTTGCCAAA 61.391 55.000 0.00 0.00 39.65 3.28
1872 1931 1.110442 CAGTCAGGGTGTTGCCAAAA 58.890 50.000 0.00 0.00 39.65 2.44
1873 1932 1.067516 CAGTCAGGGTGTTGCCAAAAG 59.932 52.381 0.00 0.00 39.65 2.27
1907 1966 7.413438 GCGATGATAGTTGTTGATGTTTCTCTT 60.413 37.037 0.00 0.00 0.00 2.85
1909 1968 8.853077 ATGATAGTTGTTGATGTTTCTCTTCA 57.147 30.769 0.00 0.00 0.00 3.02
1912 1971 4.276926 AGTTGTTGATGTTTCTCTTCAGGC 59.723 41.667 0.00 0.00 33.00 4.85
1931 1990 1.086696 CGGATGTACACCTTGCCTTG 58.913 55.000 0.00 0.00 0.00 3.61
2009 2069 5.404466 TCCCAATTTTAACATTGCAGAGG 57.596 39.130 8.55 5.27 33.42 3.69
2052 2112 6.876257 GTCAAGTGGCAGAATATATAGGGAAG 59.124 42.308 0.00 0.00 0.00 3.46
2053 2113 6.787458 TCAAGTGGCAGAATATATAGGGAAGA 59.213 38.462 0.00 0.00 0.00 2.87
2056 2116 7.019388 AGTGGCAGAATATATAGGGAAGAAGA 58.981 38.462 0.00 0.00 0.00 2.87
2134 2194 7.525688 TTTAACATCGACTGAGATTTAGCAG 57.474 36.000 0.00 0.00 38.10 4.24
2275 2336 1.982958 GAGGTCAAAGGGGAGGTGTTA 59.017 52.381 0.00 0.00 0.00 2.41
2299 2360 9.542462 TTATTAAGATTAAGTTCGACAGATGGG 57.458 33.333 0.00 0.00 0.00 4.00
2345 2406 7.309560 GGTTAGCCAAGTGTAAATTGTACCAAT 60.310 37.037 0.00 0.00 40.94 3.16
2355 2416 9.139174 GTGTAAATTGTACCAATGAATTCCTTG 57.861 33.333 14.52 14.52 0.00 3.61
2356 2417 9.083422 TGTAAATTGTACCAATGAATTCCTTGA 57.917 29.630 20.98 5.02 0.00 3.02
2388 2449 2.237143 TCTTTGATGGCGGATCTGTCTT 59.763 45.455 7.82 0.13 31.55 3.01
2401 2462 0.520404 CTGTCTTCCATGCAGTGTGC 59.480 55.000 0.00 0.00 45.29 4.57
2423 2500 3.004315 CGCAGAAAACCTTAAGGCTTCAA 59.996 43.478 26.93 0.00 39.32 2.69
2444 2521 4.881157 AATAATCCCTTGCCCAAGTACT 57.119 40.909 7.21 0.00 36.72 2.73
2450 2527 1.408822 CCTTGCCCAAGTACTCCATCC 60.409 57.143 0.00 0.00 36.72 3.51
2463 2540 3.274288 ACTCCATCCGAAATGCTTTCTC 58.726 45.455 6.94 0.00 37.52 2.87
2464 2541 3.273434 CTCCATCCGAAATGCTTTCTCA 58.727 45.455 6.94 0.00 37.52 3.27
2468 2545 4.261072 CCATCCGAAATGCTTTCTCAGATG 60.261 45.833 15.96 15.96 38.13 2.90
2477 2554 3.065655 GCTTTCTCAGATGCGCATCTAT 58.934 45.455 43.30 26.48 45.78 1.98
2478 2555 3.497640 GCTTTCTCAGATGCGCATCTATT 59.502 43.478 43.30 25.78 45.78 1.73
2479 2556 4.687948 GCTTTCTCAGATGCGCATCTATTA 59.312 41.667 43.30 31.15 45.78 0.98
2480 2557 5.163972 GCTTTCTCAGATGCGCATCTATTAG 60.164 44.000 43.30 36.34 45.78 1.73
2481 2558 5.712152 TTCTCAGATGCGCATCTATTAGA 57.288 39.130 43.30 37.53 45.78 2.10
2482 2559 5.911378 TCTCAGATGCGCATCTATTAGAT 57.089 39.130 43.30 23.67 45.78 1.98
2483 2560 7.396540 TTCTCAGATGCGCATCTATTAGATA 57.603 36.000 43.30 29.44 45.78 1.98
2484 2561 7.579761 TCTCAGATGCGCATCTATTAGATAT 57.420 36.000 43.30 22.28 45.78 1.63
2485 2562 8.005192 TCTCAGATGCGCATCTATTAGATATT 57.995 34.615 43.30 21.58 45.78 1.28
2526 2603 3.496130 GCTGTCGATTCCTCACATAATGG 59.504 47.826 0.00 0.00 0.00 3.16
2555 2732 3.719871 TCACTAGTTAGAGGGGATGCAA 58.280 45.455 0.00 0.00 0.00 4.08
2556 2733 3.451178 TCACTAGTTAGAGGGGATGCAAC 59.549 47.826 0.00 0.00 0.00 4.17
2571 2748 3.944871 CAACAGAGGTGGTTGTTGC 57.055 52.632 4.65 0.00 45.09 4.17
2577 2754 1.701847 AGAGGTGGTTGTTGCATCTCT 59.298 47.619 0.00 0.00 0.00 3.10
2582 2759 2.999355 GTGGTTGTTGCATCTCTCTCTC 59.001 50.000 0.00 0.00 0.00 3.20
2583 2760 2.902486 TGGTTGTTGCATCTCTCTCTCT 59.098 45.455 0.00 0.00 0.00 3.10
2584 2761 3.056250 TGGTTGTTGCATCTCTCTCTCTC 60.056 47.826 0.00 0.00 0.00 3.20
2585 2762 3.195396 GGTTGTTGCATCTCTCTCTCTCT 59.805 47.826 0.00 0.00 0.00 3.10
2586 2763 4.423732 GTTGTTGCATCTCTCTCTCTCTC 58.576 47.826 0.00 0.00 0.00 3.20
2587 2764 3.966979 TGTTGCATCTCTCTCTCTCTCT 58.033 45.455 0.00 0.00 0.00 3.10
2588 2765 3.947196 TGTTGCATCTCTCTCTCTCTCTC 59.053 47.826 0.00 0.00 0.00 3.20
2592 2769 3.002656 GCATCTCTCTCTCTCTCTCGTTG 59.997 52.174 0.00 0.00 0.00 4.10
2599 2776 2.876645 CTCTCTCGTTGCCGCGTC 60.877 66.667 4.92 0.00 0.00 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.223852 TGTCCGACACTTGTTCGATGAA 60.224 45.455 0.00 0.00 0.00 2.57
1 2 1.338655 TGTCCGACACTTGTTCGATGA 59.661 47.619 0.00 0.00 0.00 2.92
2 3 1.778334 TGTCCGACACTTGTTCGATG 58.222 50.000 0.00 0.00 0.00 3.84
3 4 2.337583 CATGTCCGACACTTGTTCGAT 58.662 47.619 2.57 0.00 0.00 3.59
4 5 1.604438 CCATGTCCGACACTTGTTCGA 60.604 52.381 2.57 0.00 0.00 3.71
5 6 0.790207 CCATGTCCGACACTTGTTCG 59.210 55.000 2.57 0.00 0.00 3.95
6 7 1.878953 ACCATGTCCGACACTTGTTC 58.121 50.000 2.57 0.00 0.00 3.18
7 8 2.367567 ACTACCATGTCCGACACTTGTT 59.632 45.455 2.57 0.00 0.00 2.83
8 9 1.968493 ACTACCATGTCCGACACTTGT 59.032 47.619 2.57 4.20 0.00 3.16
9 10 2.743636 ACTACCATGTCCGACACTTG 57.256 50.000 2.57 0.00 0.00 3.16
10 11 4.037684 GCTATACTACCATGTCCGACACTT 59.962 45.833 2.57 0.00 0.00 3.16
11 12 3.568853 GCTATACTACCATGTCCGACACT 59.431 47.826 2.57 0.00 0.00 3.55
12 13 3.317149 TGCTATACTACCATGTCCGACAC 59.683 47.826 2.57 0.00 0.00 3.67
13 14 3.558033 TGCTATACTACCATGTCCGACA 58.442 45.455 3.10 3.10 0.00 4.35
14 15 3.568853 ACTGCTATACTACCATGTCCGAC 59.431 47.826 0.00 0.00 0.00 4.79
15 16 3.828921 ACTGCTATACTACCATGTCCGA 58.171 45.455 0.00 0.00 0.00 4.55
16 17 4.379603 GCTACTGCTATACTACCATGTCCG 60.380 50.000 0.00 0.00 36.03 4.79
17 18 4.379603 CGCTACTGCTATACTACCATGTCC 60.380 50.000 0.00 0.00 36.97 4.02
18 19 4.379603 CCGCTACTGCTATACTACCATGTC 60.380 50.000 0.00 0.00 36.97 3.06
19 20 3.506455 CCGCTACTGCTATACTACCATGT 59.494 47.826 0.00 0.00 36.97 3.21
20 21 3.756963 TCCGCTACTGCTATACTACCATG 59.243 47.826 0.00 0.00 36.97 3.66
21 22 4.030314 TCCGCTACTGCTATACTACCAT 57.970 45.455 0.00 0.00 36.97 3.55
22 23 3.497103 TCCGCTACTGCTATACTACCA 57.503 47.619 0.00 0.00 36.97 3.25
23 24 3.128938 CCATCCGCTACTGCTATACTACC 59.871 52.174 0.00 0.00 36.97 3.18
24 25 3.757493 ACCATCCGCTACTGCTATACTAC 59.243 47.826 0.00 0.00 36.97 2.73
25 26 4.030314 ACCATCCGCTACTGCTATACTA 57.970 45.455 0.00 0.00 36.97 1.82
26 27 2.877866 ACCATCCGCTACTGCTATACT 58.122 47.619 0.00 0.00 36.97 2.12
27 28 3.119566 GGTACCATCCGCTACTGCTATAC 60.120 52.174 7.15 0.00 36.97 1.47
28 29 3.087031 GGTACCATCCGCTACTGCTATA 58.913 50.000 7.15 0.00 36.97 1.31
29 30 1.893801 GGTACCATCCGCTACTGCTAT 59.106 52.381 7.15 0.00 36.97 2.97
30 31 1.133575 AGGTACCATCCGCTACTGCTA 60.134 52.381 15.94 0.00 36.97 3.49
31 32 0.397254 AGGTACCATCCGCTACTGCT 60.397 55.000 15.94 0.00 36.97 4.24
32 33 0.249489 CAGGTACCATCCGCTACTGC 60.249 60.000 15.94 0.00 0.00 4.40
33 34 0.389391 CCAGGTACCATCCGCTACTG 59.611 60.000 15.94 0.00 0.00 2.74
34 35 1.400530 GCCAGGTACCATCCGCTACT 61.401 60.000 15.94 0.00 0.00 2.57
35 36 1.069258 GCCAGGTACCATCCGCTAC 59.931 63.158 15.94 0.00 0.00 3.58
36 37 0.978667 TTGCCAGGTACCATCCGCTA 60.979 55.000 15.94 3.75 0.00 4.26
37 38 2.257409 CTTGCCAGGTACCATCCGCT 62.257 60.000 15.94 0.00 0.00 5.52
38 39 1.819632 CTTGCCAGGTACCATCCGC 60.820 63.158 15.94 9.94 0.00 5.54
39 40 0.462047 GTCTTGCCAGGTACCATCCG 60.462 60.000 15.94 0.00 0.00 4.18
40 41 0.462047 CGTCTTGCCAGGTACCATCC 60.462 60.000 15.94 1.53 0.00 3.51
41 42 0.462047 CCGTCTTGCCAGGTACCATC 60.462 60.000 15.94 2.80 0.00 3.51
42 43 1.198759 ACCGTCTTGCCAGGTACCAT 61.199 55.000 15.94 0.00 36.34 3.55
53 54 1.658686 CCTCTCCTCCGACCGTCTTG 61.659 65.000 0.00 0.00 0.00 3.02
54 55 1.378778 CCTCTCCTCCGACCGTCTT 60.379 63.158 0.00 0.00 0.00 3.01
55 56 2.272797 CCTCTCCTCCGACCGTCT 59.727 66.667 0.00 0.00 0.00 4.18
65 66 2.593956 GCCGTTCAACCCCTCTCCT 61.594 63.158 0.00 0.00 0.00 3.69
84 85 1.355720 CCACCCCACTTCTTCTCCATT 59.644 52.381 0.00 0.00 0.00 3.16
137 138 1.383248 AGCCCTGCCGGAACTCTAT 60.383 57.895 5.05 0.00 0.00 1.98
154 155 0.752743 CATGCCATACCACACCCCAG 60.753 60.000 0.00 0.00 0.00 4.45
155 156 1.305959 CATGCCATACCACACCCCA 59.694 57.895 0.00 0.00 0.00 4.96
156 157 1.455587 CCATGCCATACCACACCCC 60.456 63.158 0.00 0.00 0.00 4.95
157 158 2.127232 GCCATGCCATACCACACCC 61.127 63.158 0.00 0.00 0.00 4.61
158 159 2.480610 CGCCATGCCATACCACACC 61.481 63.158 0.00 0.00 0.00 4.16
198 199 2.999355 CCTTCTTTCTCTCTTGCCTTCG 59.001 50.000 0.00 0.00 0.00 3.79
322 323 1.451028 GAGACAGACATGGGGCAGC 60.451 63.158 0.00 0.00 0.00 5.25
323 324 1.222936 GGAGACAGACATGGGGCAG 59.777 63.158 0.00 0.00 0.00 4.85
324 325 2.659063 CGGAGACAGACATGGGGCA 61.659 63.158 0.00 0.00 0.00 5.36
325 326 2.187946 CGGAGACAGACATGGGGC 59.812 66.667 0.00 0.00 0.00 5.80
326 327 1.553690 AACCGGAGACAGACATGGGG 61.554 60.000 9.46 0.00 0.00 4.96
346 347 2.159043 TCCAAAAACATTTTCTGCCGCA 60.159 40.909 0.00 0.00 0.00 5.69
347 348 2.220824 GTCCAAAAACATTTTCTGCCGC 59.779 45.455 0.00 0.00 0.00 6.53
348 349 2.799978 GGTCCAAAAACATTTTCTGCCG 59.200 45.455 0.00 0.00 0.00 5.69
351 352 2.799978 GGCGGTCCAAAAACATTTTCTG 59.200 45.455 0.00 0.00 0.00 3.02
360 361 4.896829 TGCGGGGCGGTCCAAAAA 62.897 61.111 0.00 0.00 37.22 1.94
371 372 1.815421 CTTGAATCGGTCTGCGGGG 60.815 63.158 0.00 0.00 0.00 5.73
377 378 3.070018 CAAAGCAGTCTTGAATCGGTCT 58.930 45.455 0.00 0.00 31.78 3.85
378 379 2.160417 CCAAAGCAGTCTTGAATCGGTC 59.840 50.000 0.00 0.00 31.78 4.79
385 386 3.777106 AGTCATCCAAAGCAGTCTTGA 57.223 42.857 0.00 0.00 31.78 3.02
409 410 2.221906 GACCACGCTGTCCATACCGT 62.222 60.000 0.00 0.00 0.00 4.83
411 412 0.460284 CAGACCACGCTGTCCATACC 60.460 60.000 1.62 0.00 35.83 2.73
414 426 1.913262 TCCAGACCACGCTGTCCAT 60.913 57.895 1.62 0.00 35.83 3.41
424 436 4.758251 CCGCATGCGTCCAGACCA 62.758 66.667 35.55 0.00 37.81 4.02
435 447 3.326889 CTCGCAAACCACCCGCATG 62.327 63.158 0.00 0.00 0.00 4.06
452 464 1.168714 GGGCATCTTCAAAGCGAACT 58.831 50.000 0.00 0.00 0.00 3.01
453 465 1.168714 AGGGCATCTTCAAAGCGAAC 58.831 50.000 0.00 0.00 0.00 3.95
521 533 9.469807 AATCGTCATACAATCTTCATCTAACTC 57.530 33.333 0.00 0.00 0.00 3.01
598 612 9.443323 ACTTTGCCGTAACATATTATATATGCA 57.557 29.630 6.59 0.00 0.00 3.96
633 647 7.174599 GGCAATAAGAGCATGAGAATATGTCTT 59.825 37.037 0.00 0.00 36.41 3.01
638 652 5.410746 CACGGCAATAAGAGCATGAGAATAT 59.589 40.000 0.00 0.00 0.00 1.28
651 665 1.086696 CACACCTCCACGGCAATAAG 58.913 55.000 0.00 0.00 35.61 1.73
684 698 2.140792 CCTATGGCGCAGGGTAGGT 61.141 63.158 10.83 0.00 31.20 3.08
686 700 1.668294 CTCCTATGGCGCAGGGTAG 59.332 63.158 10.83 5.20 33.66 3.18
766 780 8.764287 CGTAAGATGATTAAGTTGTGCATATCA 58.236 33.333 0.00 0.00 43.02 2.15
795 809 5.062558 GGATTGGCAATCGTTCTCAAAATTG 59.937 40.000 28.48 0.00 38.82 2.32
804 818 1.895051 CGTTGGATTGGCAATCGTTC 58.105 50.000 28.48 20.07 38.82 3.95
833 848 3.869065 CGGTATGTCTTTTTAGGCTGGA 58.131 45.455 0.00 0.00 0.00 3.86
834 849 2.354821 GCGGTATGTCTTTTTAGGCTGG 59.645 50.000 0.00 0.00 0.00 4.85
837 852 3.064958 GGAAGCGGTATGTCTTTTTAGGC 59.935 47.826 0.00 0.00 0.00 3.93
851 866 1.837439 TCATGTAGGATTGGAAGCGGT 59.163 47.619 0.00 0.00 0.00 5.68
854 869 3.879892 GGAGTTCATGTAGGATTGGAAGC 59.120 47.826 0.00 0.00 0.00 3.86
855 870 4.878397 GTGGAGTTCATGTAGGATTGGAAG 59.122 45.833 0.00 0.00 0.00 3.46
859 895 3.618594 CGTGTGGAGTTCATGTAGGATTG 59.381 47.826 0.00 0.00 0.00 2.67
922 967 4.460948 TTCCCGTCCTCAAGTACATTAC 57.539 45.455 0.00 0.00 0.00 1.89
932 977 1.072505 GCCTTGTTTCCCGTCCTCA 59.927 57.895 0.00 0.00 0.00 3.86
946 991 6.122964 GGAGTGAGTTAATTAAGGATGCCTT 58.877 40.000 0.00 3.94 46.63 4.35
954 1005 4.330074 CACGGCTGGAGTGAGTTAATTAAG 59.670 45.833 0.00 0.00 41.83 1.85
970 1023 3.185365 TATTCACGCGCACGGCTG 61.185 61.111 5.73 0.00 46.04 4.85
976 1029 0.724549 GTTGGATGTATTCACGCGCA 59.275 50.000 5.73 0.00 0.00 6.09
992 1045 0.387202 TTTTGCGTCCATGGTGGTTG 59.613 50.000 12.58 0.00 39.03 3.77
1102 1161 1.971357 ACACAGAACGAAGACCAGGAT 59.029 47.619 0.00 0.00 0.00 3.24
1105 1164 5.312120 ACTATACACAGAACGAAGACCAG 57.688 43.478 0.00 0.00 0.00 4.00
1181 1240 1.604023 ACAGAGAACTCCGGTCGCT 60.604 57.895 0.00 0.00 0.00 4.93
1197 1256 1.207089 GAGAATCCGTCCATGACCACA 59.793 52.381 0.00 0.00 0.00 4.17
1260 1319 2.161609 GCCCCTAAAGTTGTTGATGACG 59.838 50.000 0.00 0.00 0.00 4.35
1275 1334 0.261991 AGATCTCGGACTTGCCCCTA 59.738 55.000 0.00 0.00 0.00 3.53
1652 1711 1.920610 AAGGCATGCAAGCTTTCTCT 58.079 45.000 21.36 0.21 34.17 3.10
1664 1723 1.342174 AGACAAACTGGCAAAGGCATG 59.658 47.619 0.00 0.00 43.71 4.06
1705 1764 7.122501 TCAACATGCATGAATTATGTACCAACT 59.877 33.333 32.75 1.36 39.08 3.16
1721 1780 7.400599 AGAATTCTTGTACATCAACATGCAT 57.599 32.000 0.88 0.00 32.57 3.96
1741 1800 9.643693 CCAGAGCATATTTTACAAAACAAGAAT 57.356 29.630 0.00 0.00 0.00 2.40
1742 1801 7.598493 GCCAGAGCATATTTTACAAAACAAGAA 59.402 33.333 0.00 0.00 39.53 2.52
1795 1854 0.693049 AGGAAAAGGATGGAGCGTGT 59.307 50.000 0.00 0.00 0.00 4.49
1810 1869 1.780309 TGCCTCAAGGAAAGGAAGGAA 59.220 47.619 0.00 0.00 35.83 3.36
1849 1908 1.891919 GCAACACCCTGACTGCGAA 60.892 57.895 0.00 0.00 0.00 4.70
1907 1966 0.249120 CAAGGTGTACATCCGCCTGA 59.751 55.000 1.47 0.00 44.50 3.86
1912 1971 1.086696 CAAGGCAAGGTGTACATCCG 58.913 55.000 1.47 0.00 0.00 4.18
1931 1990 2.658807 AAAAAGGGTCCACAGAGGTC 57.341 50.000 0.00 0.00 39.02 3.85
1953 2012 4.450976 CATTAGGATTGACACATCGGGAA 58.549 43.478 0.00 0.00 0.00 3.97
1957 2016 3.470709 AGCCATTAGGATTGACACATCG 58.529 45.455 0.00 0.00 36.89 3.84
1984 2044 6.166984 TCTGCAATGTTAAAATTGGGAACA 57.833 33.333 18.08 7.98 37.89 3.18
1989 2049 4.567971 TGCCTCTGCAATGTTAAAATTGG 58.432 39.130 18.08 4.30 46.66 3.16
2009 2069 3.926616 TGACTAAGACTTGCCTAAGTGC 58.073 45.455 0.00 0.00 46.79 4.40
2085 2145 9.956640 AATTTGTGAGATCTTATATGGAGATCC 57.043 33.333 19.39 14.21 46.88 3.36
2106 2166 9.214953 GCTAAATCTCAGTCGATGTTAAATTTG 57.785 33.333 0.00 0.00 0.00 2.32
2114 2174 4.677584 GACTGCTAAATCTCAGTCGATGT 58.322 43.478 6.62 0.00 46.32 3.06
2162 2222 2.168106 TGTTTTGCCATATGCCATCCAC 59.832 45.455 0.00 0.00 40.16 4.02
2247 2307 0.616679 CCCTTTGACCTCCCTCGGTA 60.617 60.000 0.00 0.00 37.42 4.02
2275 2336 6.483640 GCCCATCTGTCGAACTTAATCTTAAT 59.516 38.462 0.00 0.00 0.00 1.40
2296 2357 1.448893 GCATTCGTTCGGTAGCCCA 60.449 57.895 0.00 0.00 0.00 5.36
2297 2358 0.814010 ATGCATTCGTTCGGTAGCCC 60.814 55.000 0.00 0.00 0.00 5.19
2298 2359 1.792949 CTATGCATTCGTTCGGTAGCC 59.207 52.381 3.54 0.00 0.00 3.93
2299 2360 1.792949 CCTATGCATTCGTTCGGTAGC 59.207 52.381 3.54 0.00 0.00 3.58
2363 2424 3.826157 ACAGATCCGCCATCAAAGAAAAA 59.174 39.130 0.00 0.00 33.29 1.94
2368 2429 2.322355 AGACAGATCCGCCATCAAAG 57.678 50.000 0.00 0.00 33.29 2.77
2379 2440 2.676839 CACACTGCATGGAAGACAGATC 59.323 50.000 4.53 0.00 35.38 2.75
2388 2449 3.051479 CTGCGCACACTGCATGGA 61.051 61.111 5.66 0.00 45.36 3.41
2401 2462 2.552315 TGAAGCCTTAAGGTTTTCTGCG 59.448 45.455 26.92 4.52 38.80 5.18
2423 2500 4.386424 GGAGTACTTGGGCAAGGGATTATT 60.386 45.833 0.00 0.00 42.53 1.40
2463 2540 7.169476 CCAGAATATCTAATAGATGCGCATCTG 59.831 40.741 46.91 34.93 46.80 2.90
2468 2545 7.205992 TCATCCAGAATATCTAATAGATGCGC 58.794 38.462 12.73 0.00 35.37 6.09
2477 2554 9.948964 CACACCATAATCATCCAGAATATCTAA 57.051 33.333 0.00 0.00 0.00 2.10
2478 2555 8.542926 CCACACCATAATCATCCAGAATATCTA 58.457 37.037 0.00 0.00 0.00 1.98
2479 2556 7.400439 CCACACCATAATCATCCAGAATATCT 58.600 38.462 0.00 0.00 0.00 1.98
2480 2557 6.094603 GCCACACCATAATCATCCAGAATATC 59.905 42.308 0.00 0.00 0.00 1.63
2481 2558 5.948162 GCCACACCATAATCATCCAGAATAT 59.052 40.000 0.00 0.00 0.00 1.28
2482 2559 5.073554 AGCCACACCATAATCATCCAGAATA 59.926 40.000 0.00 0.00 0.00 1.75
2483 2560 4.141088 AGCCACACCATAATCATCCAGAAT 60.141 41.667 0.00 0.00 0.00 2.40
2484 2561 3.202818 AGCCACACCATAATCATCCAGAA 59.797 43.478 0.00 0.00 0.00 3.02
2485 2562 2.779430 AGCCACACCATAATCATCCAGA 59.221 45.455 0.00 0.00 0.00 3.86
2496 2573 0.392998 GGAATCGACAGCCACACCAT 60.393 55.000 0.00 0.00 0.00 3.55
2499 2576 0.037326 TGAGGAATCGACAGCCACAC 60.037 55.000 0.00 0.00 0.00 3.82
2526 2603 7.613551 TCCCCTCTAACTAGTGATAAAATCC 57.386 40.000 0.00 0.00 0.00 3.01
2555 2732 1.143684 AGATGCAACAACCACCTCTGT 59.856 47.619 0.00 0.00 0.00 3.41
2556 2733 1.808945 GAGATGCAACAACCACCTCTG 59.191 52.381 0.00 0.00 0.00 3.35
2571 2748 3.002656 GCAACGAGAGAGAGAGAGAGATG 59.997 52.174 0.00 0.00 0.00 2.90
2599 2776 3.522731 ACTCGCCTCGCTGCCTAG 61.523 66.667 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.