Multiple sequence alignment - TraesCS2A01G212800

Loading Multiple Alignment...

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 TraesCS2A01G212800 chr2A 100.000 5036 0 0 1 5036 197559888 197564923 0.000000e+00 9300
1 TraesCS2A01G212800 chr2A 95.682 2339 87 7 2709 5036 197333272 197335607 0.000000e+00 3747
2 TraesCS2A01G212800 chr2A 86.334 1822 186 31 2123 3923 166632945 166631166 0.000000e+00 1927
3 TraesCS2A01G212800 chr2A 87.129 1383 109 25 755 2108 166634520 166633178 0.000000e+00 1504
4 TraesCS2A01G212800 chr2A 91.134 970 80 3 4070 5036 166630316 166629350 0.000000e+00 1310
5 TraesCS2A01G212800 chr2A 82.526 1465 171 29 2123 3566 447943255 447944655 0.000000e+00 1208
6 TraesCS2A01G212800 chr2A 95.841 529 21 1 2123 2650 197332750 197333278 0.000000e+00 854
7 TraesCS2A01G212800 chr2A 89.118 340 34 3 2124 2462 398765344 398765007 2.170000e-113 420
8 TraesCS2A01G212800 chr2A 88.824 340 35 3 2124 2462 398506414 398506077 1.010000e-111 414
9 TraesCS2A01G212800 chr2A 88.824 170 18 1 1939 2108 447942904 447943072 1.840000e-49 207
10 TraesCS2A01G212800 chr2A 88.235 170 19 1 1939 2108 398506766 398506598 8.550000e-48 202
11 TraesCS2A01G212800 chr2A 87.647 170 20 1 1939 2108 398765696 398765528 3.980000e-46 196
12 TraesCS2A01G212800 chr2D 97.668 1801 40 1 3236 5036 182572865 182574663 0.000000e+00 3092
13 TraesCS2A01G212800 chr2D 86.082 1825 176 33 2123 3923 156712317 156710547 0.000000e+00 1892
14 TraesCS2A01G212800 chr2D 94.328 1093 38 10 1019 2094 182570521 182571606 0.000000e+00 1653
15 TraesCS2A01G212800 chr2D 87.273 1375 124 14 753 2108 156713868 156712526 0.000000e+00 1522
16 TraesCS2A01G212800 chr2D 92.997 971 60 5 4070 5036 156709688 156708722 0.000000e+00 1410
17 TraesCS2A01G212800 chr2D 93.289 894 60 0 4143 5036 156594604 156593711 0.000000e+00 1319
18 TraesCS2A01G212800 chr2D 91.455 550 19 3 2123 2650 182571837 182572380 0.000000e+00 730
19 TraesCS2A01G212800 chr2D 94.820 444 14 3 2709 3143 182572374 182572817 0.000000e+00 684
20 TraesCS2A01G212800 chr2D 97.248 218 4 1 751 968 182569905 182570120 7.970000e-98 368
21 TraesCS2A01G212800 chr2B 86.012 1823 185 29 2123 3923 214317767 214315993 0.000000e+00 1890
22 TraesCS2A01G212800 chr2B 87.345 1375 117 22 753 2108 214319307 214317971 0.000000e+00 1522
23 TraesCS2A01G212800 chr2B 92.268 970 66 4 4070 5036 214315157 214314194 0.000000e+00 1367
24 TraesCS2A01G212800 chr2B 82.731 498 51 12 773 1267 281487341 281486876 1.300000e-110 411
25 TraesCS2A01G212800 chr2B 82.438 484 50 10 262 713 789010994 789011474 1.700000e-104 390
26 TraesCS2A01G212800 chr2B 81.386 505 57 18 768 1267 673104350 673104822 1.320000e-100 377
27 TraesCS2A01G212800 chr2B 83.268 257 24 4 2 243 789009615 789009867 8.490000e-53 219
28 TraesCS2A01G212800 chr1D 93.036 919 60 3 4119 5036 93102997 93103912 0.000000e+00 1339
29 TraesCS2A01G212800 chr1D 94.194 775 9 6 1 757 208419515 208418759 0.000000e+00 1149
30 TraesCS2A01G212800 chr1A 92.818 919 58 4 4119 5036 90161332 90162243 0.000000e+00 1325
31 TraesCS2A01G212800 chr1A 90.854 164 14 1 1943 2106 512491085 512491247 8.490000e-53 219
32 TraesCS2A01G212800 chr1B 92.492 919 65 3 4119 5036 148414116 148415031 0.000000e+00 1312
33 TraesCS2A01G212800 chr1B 82.463 804 81 24 2 753 427626911 427627706 0.000000e+00 649
34 TraesCS2A01G212800 chr1B 81.583 657 58 17 2 611 338886234 338885594 7.580000e-133 484
35 TraesCS2A01G212800 chr1B 81.431 657 59 17 2 611 339078500 339077860 3.530000e-131 479
36 TraesCS2A01G212800 chr6D 81.759 762 70 22 2 713 336836929 336836187 1.570000e-159 573
37 TraesCS2A01G212800 chr6A 81.555 759 76 20 2 713 555579991 555580732 7.320000e-158 568
38 TraesCS2A01G212800 chr5A 81.447 760 77 20 1 713 601237593 601238335 9.460000e-157 564
39 TraesCS2A01G212800 chr6B 81.316 760 77 19 2 713 42819652 42818910 1.580000e-154 556
40 TraesCS2A01G212800 chr4B 82.087 508 53 14 773 1275 639306252 639306726 2.820000e-107 399
41 TraesCS2A01G212800 chr7A 82.734 417 45 14 2 398 21613292 21613701 3.730000e-91 346
42 TraesCS2A01G212800 chr7B 86.513 304 40 1 965 1267 292238093 292238396 2.910000e-87 333
43 TraesCS2A01G212800 chr7B 85.948 306 38 5 965 1267 271756726 271756423 6.290000e-84 322
44 TraesCS2A01G212800 chr4A 85.621 306 39 5 965 1267 670970275 670969972 2.930000e-82 316
45 TraesCS2A01G212800 chrUn 80.672 357 40 12 2 333 311753657 311754009 3.010000e-62 250
46 TraesCS2A01G212800 chrUn 80.672 357 40 12 2 333 311765276 311765628 3.010000e-62 250
47 TraesCS2A01G212800 chrUn 80.672 357 40 12 2 333 353101312 353101664 3.010000e-62 250


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 TraesCS2A01G212800 chr2A 197559888 197564923 5035 False 9300.000000 9300 100.000000 1 5036 1 chr2A.!!$F1 5035
1 TraesCS2A01G212800 chr2A 197332750 197335607 2857 False 2300.500000 3747 95.761500 2123 5036 2 chr2A.!!$F2 2913
2 TraesCS2A01G212800 chr2A 166629350 166634520 5170 True 1580.333333 1927 88.199000 755 5036 3 chr2A.!!$R1 4281
3 TraesCS2A01G212800 chr2A 447942904 447944655 1751 False 707.500000 1208 85.675000 1939 3566 2 chr2A.!!$F3 1627
4 TraesCS2A01G212800 chr2A 398506077 398506766 689 True 308.000000 414 88.529500 1939 2462 2 chr2A.!!$R2 523
5 TraesCS2A01G212800 chr2A 398765007 398765696 689 True 308.000000 420 88.382500 1939 2462 2 chr2A.!!$R3 523
6 TraesCS2A01G212800 chr2D 156708722 156713868 5146 True 1608.000000 1892 88.784000 753 5036 3 chr2D.!!$R2 4283
7 TraesCS2A01G212800 chr2D 156593711 156594604 893 True 1319.000000 1319 93.289000 4143 5036 1 chr2D.!!$R1 893
8 TraesCS2A01G212800 chr2D 182569905 182574663 4758 False 1305.400000 3092 95.103800 751 5036 5 chr2D.!!$F1 4285
9 TraesCS2A01G212800 chr2B 214314194 214319307 5113 True 1593.000000 1890 88.541667 753 5036 3 chr2B.!!$R2 4283
10 TraesCS2A01G212800 chr2B 789009615 789011474 1859 False 304.500000 390 82.853000 2 713 2 chr2B.!!$F2 711
11 TraesCS2A01G212800 chr1D 93102997 93103912 915 False 1339.000000 1339 93.036000 4119 5036 1 chr1D.!!$F1 917
12 TraesCS2A01G212800 chr1D 208418759 208419515 756 True 1149.000000 1149 94.194000 1 757 1 chr1D.!!$R1 756
13 TraesCS2A01G212800 chr1A 90161332 90162243 911 False 1325.000000 1325 92.818000 4119 5036 1 chr1A.!!$F1 917
14 TraesCS2A01G212800 chr1B 148414116 148415031 915 False 1312.000000 1312 92.492000 4119 5036 1 chr1B.!!$F1 917
15 TraesCS2A01G212800 chr1B 427626911 427627706 795 False 649.000000 649 82.463000 2 753 1 chr1B.!!$F2 751
16 TraesCS2A01G212800 chr1B 338885594 338886234 640 True 484.000000 484 81.583000 2 611 1 chr1B.!!$R1 609
17 TraesCS2A01G212800 chr1B 339077860 339078500 640 True 479.000000 479 81.431000 2 611 1 chr1B.!!$R2 609
18 TraesCS2A01G212800 chr6D 336836187 336836929 742 True 573.000000 573 81.759000 2 713 1 chr6D.!!$R1 711
19 TraesCS2A01G212800 chr6A 555579991 555580732 741 False 568.000000 568 81.555000 2 713 1 chr6A.!!$F1 711
20 TraesCS2A01G212800 chr5A 601237593 601238335 742 False 564.000000 564 81.447000 1 713 1 chr5A.!!$F1 712
21 TraesCS2A01G212800 chr6B 42818910 42819652 742 True 556.000000 556 81.316000 2 713 1 chr6B.!!$R1 711

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
676 1865 0.037232 GTGGACCAAACGAGCTAGCT 60.037 55.0 19.45 19.45 0.00 3.32 F
677 1866 0.246635 TGGACCAAACGAGCTAGCTC 59.753 55.0 31.12 31.12 39.55 4.09 F
709 1898 0.387622 CAAACCTTGCACCGCAGATG 60.388 55.0 0.00 0.00 40.61 2.90 F
710 1899 0.537143 AAACCTTGCACCGCAGATGA 60.537 50.0 0.00 0.00 40.61 2.92 F
722 1911 0.723981 GCAGATGAACGCCTCAAGAC 59.276 55.0 0.00 0.00 37.67 3.01 F
724 1913 0.737715 AGATGAACGCCTCAAGACGC 60.738 55.0 0.00 0.00 37.67 5.19 F
2115 3725 0.981183 TGGATCTTAACCACAGGCGT 59.019 50.0 0.00 0.00 32.03 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2111 3721 2.032030 CCACGAAATCATATTCCACGCC 60.032 50.000 0.00 0.0 0.00 5.68 R
2469 4332 2.227388 CTCGAAAGAAATTGCCTGCACT 59.773 45.455 0.00 0.0 41.32 4.40 R
2684 4547 1.627329 GATCAGGGAGCATGCATCCTA 59.373 52.381 24.99 16.3 37.01 2.94 R
2793 4656 1.536073 CCTCGTCAGCCACCTCTTCA 61.536 60.000 0.00 0.0 0.00 3.02 R
2896 4770 8.920174 TGAAGAGAATTGTCCCTTACGAATATA 58.080 33.333 0.00 0.0 0.00 0.86 R
3070 4950 6.608002 TGTTAAGTTGGGTTTCAGGTTGTAAT 59.392 34.615 0.00 0.0 0.00 1.89 R
4337 6974 0.752658 CTGACTGCCGATCATACCCA 59.247 55.000 0.00 0.0 0.00 4.51 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
293 1451 1.670949 GCAGACCATCTCGCCTCTGA 61.671 60.000 0.00 0.00 33.30 3.27
429 1590 7.167968 CGTGCTACACTACTTTTGTACAAACTA 59.832 37.037 20.43 11.60 31.34 2.24
491 1678 6.356556 TGCTGCCTCTGTGTTTATATACATT 58.643 36.000 0.00 0.00 0.00 2.71
503 1690 9.722056 GTGTTTATATACATTCTTGCTTTCCAG 57.278 33.333 0.00 0.00 0.00 3.86
645 1834 3.692593 TCATGTCCATGAGCAAATGAGTG 59.307 43.478 5.88 0.00 42.42 3.51
646 1835 3.421919 TGTCCATGAGCAAATGAGTGA 57.578 42.857 0.00 0.00 0.00 3.41
647 1836 3.753815 TGTCCATGAGCAAATGAGTGAA 58.246 40.909 0.00 0.00 0.00 3.18
648 1837 4.338012 TGTCCATGAGCAAATGAGTGAAT 58.662 39.130 0.00 0.00 0.00 2.57
649 1838 4.157105 TGTCCATGAGCAAATGAGTGAATG 59.843 41.667 0.00 0.00 0.00 2.67
650 1839 4.157289 GTCCATGAGCAAATGAGTGAATGT 59.843 41.667 0.00 0.00 0.00 2.71
651 1840 4.397103 TCCATGAGCAAATGAGTGAATGTC 59.603 41.667 0.00 0.00 0.00 3.06
652 1841 4.157105 CCATGAGCAAATGAGTGAATGTCA 59.843 41.667 0.00 0.00 0.00 3.58
653 1842 5.163550 CCATGAGCAAATGAGTGAATGTCAT 60.164 40.000 0.00 0.00 36.14 3.06
654 1843 6.038936 CCATGAGCAAATGAGTGAATGTCATA 59.961 38.462 0.00 0.00 33.34 2.15
655 1844 7.415877 CCATGAGCAAATGAGTGAATGTCATAA 60.416 37.037 0.00 0.00 33.34 1.90
656 1845 7.634671 TGAGCAAATGAGTGAATGTCATAAT 57.365 32.000 0.00 0.00 33.34 1.28
657 1846 7.477494 TGAGCAAATGAGTGAATGTCATAATG 58.523 34.615 0.00 0.00 33.34 1.90
658 1847 7.121611 TGAGCAAATGAGTGAATGTCATAATGT 59.878 33.333 0.00 0.00 33.34 2.71
659 1848 7.255569 AGCAAATGAGTGAATGTCATAATGTG 58.744 34.615 0.00 0.00 33.34 3.21
660 1849 6.474427 GCAAATGAGTGAATGTCATAATGTGG 59.526 38.462 0.00 0.00 33.34 4.17
661 1850 7.629008 GCAAATGAGTGAATGTCATAATGTGGA 60.629 37.037 0.00 0.00 33.34 4.02
662 1851 6.932356 ATGAGTGAATGTCATAATGTGGAC 57.068 37.500 0.00 0.00 32.69 4.02
663 1852 5.185454 TGAGTGAATGTCATAATGTGGACC 58.815 41.667 0.00 0.00 33.09 4.46
664 1853 5.178096 AGTGAATGTCATAATGTGGACCA 57.822 39.130 0.00 0.00 33.09 4.02
665 1854 5.569355 AGTGAATGTCATAATGTGGACCAA 58.431 37.500 0.00 0.00 33.09 3.67
666 1855 6.009589 AGTGAATGTCATAATGTGGACCAAA 58.990 36.000 0.00 0.00 33.09 3.28
667 1856 6.071952 AGTGAATGTCATAATGTGGACCAAAC 60.072 38.462 0.00 0.00 33.09 2.93
668 1857 4.963276 ATGTCATAATGTGGACCAAACG 57.037 40.909 0.00 0.00 33.09 3.60
669 1858 4.009370 TGTCATAATGTGGACCAAACGA 57.991 40.909 0.00 0.00 33.09 3.85
670 1859 4.000325 TGTCATAATGTGGACCAAACGAG 59.000 43.478 0.00 0.00 33.09 4.18
671 1860 3.006940 TCATAATGTGGACCAAACGAGC 58.993 45.455 0.00 0.00 0.00 5.03
672 1861 2.851263 TAATGTGGACCAAACGAGCT 57.149 45.000 0.00 0.00 0.00 4.09
673 1862 2.851263 AATGTGGACCAAACGAGCTA 57.149 45.000 0.00 0.00 0.00 3.32
674 1863 2.386661 ATGTGGACCAAACGAGCTAG 57.613 50.000 0.00 0.00 0.00 3.42
675 1864 0.320421 TGTGGACCAAACGAGCTAGC 60.320 55.000 6.62 6.62 0.00 3.42
676 1865 0.037232 GTGGACCAAACGAGCTAGCT 60.037 55.000 19.45 19.45 0.00 3.32
677 1866 0.246635 TGGACCAAACGAGCTAGCTC 59.753 55.000 31.12 31.12 39.55 4.09
678 1867 0.246635 GGACCAAACGAGCTAGCTCA 59.753 55.000 36.92 0.00 42.86 4.26
679 1868 1.337823 GGACCAAACGAGCTAGCTCAA 60.338 52.381 36.92 0.00 42.86 3.02
680 1869 2.622436 GACCAAACGAGCTAGCTCAAT 58.378 47.619 36.92 24.95 42.86 2.57
681 1870 2.349886 GACCAAACGAGCTAGCTCAATG 59.650 50.000 36.92 29.85 42.86 2.82
682 1871 1.667724 CCAAACGAGCTAGCTCAATGG 59.332 52.381 36.92 33.27 42.86 3.16
683 1872 1.667724 CAAACGAGCTAGCTCAATGGG 59.332 52.381 36.92 25.04 42.86 4.00
684 1873 0.462759 AACGAGCTAGCTCAATGGGC 60.463 55.000 36.92 15.19 42.86 5.36
685 1874 1.953138 CGAGCTAGCTCAATGGGCG 60.953 63.158 36.92 22.18 42.86 6.13
686 1875 1.596477 GAGCTAGCTCAATGGGCGG 60.596 63.158 34.70 0.00 42.31 6.13
687 1876 3.282920 GCTAGCTCAATGGGCGGC 61.283 66.667 7.70 9.82 34.52 6.53
688 1877 2.190313 CTAGCTCAATGGGCGGCA 59.810 61.111 12.47 0.00 34.52 5.69
689 1878 1.890979 CTAGCTCAATGGGCGGCAG 60.891 63.158 12.47 0.00 34.52 4.85
707 1896 3.431055 CAAACCTTGCACCGCAGA 58.569 55.556 0.00 0.00 40.61 4.26
708 1897 1.959085 CAAACCTTGCACCGCAGAT 59.041 52.632 0.00 0.00 40.61 2.90
709 1898 0.387622 CAAACCTTGCACCGCAGATG 60.388 55.000 0.00 0.00 40.61 2.90
710 1899 0.537143 AAACCTTGCACCGCAGATGA 60.537 50.000 0.00 0.00 40.61 2.92
711 1900 0.537143 AACCTTGCACCGCAGATGAA 60.537 50.000 0.00 0.00 40.61 2.57
712 1901 1.237285 ACCTTGCACCGCAGATGAAC 61.237 55.000 0.00 0.00 40.61 3.18
713 1902 1.133253 CTTGCACCGCAGATGAACG 59.867 57.895 0.00 0.00 40.61 3.95
714 1903 2.839324 CTTGCACCGCAGATGAACGC 62.839 60.000 0.00 0.00 40.61 4.84
715 1904 4.166011 GCACCGCAGATGAACGCC 62.166 66.667 0.00 0.00 0.00 5.68
716 1905 2.434884 CACCGCAGATGAACGCCT 60.435 61.111 0.00 0.00 0.00 5.52
717 1906 2.125512 ACCGCAGATGAACGCCTC 60.126 61.111 0.00 0.00 0.00 4.70
718 1907 2.125552 CCGCAGATGAACGCCTCA 60.126 61.111 0.00 0.00 38.81 3.86
719 1908 1.741401 CCGCAGATGAACGCCTCAA 60.741 57.895 0.00 0.00 37.67 3.02
720 1909 1.699656 CCGCAGATGAACGCCTCAAG 61.700 60.000 0.00 0.00 37.67 3.02
721 1910 0.737367 CGCAGATGAACGCCTCAAGA 60.737 55.000 0.00 0.00 37.67 3.02
722 1911 0.723981 GCAGATGAACGCCTCAAGAC 59.276 55.000 0.00 0.00 37.67 3.01
723 1912 0.994995 CAGATGAACGCCTCAAGACG 59.005 55.000 0.00 0.00 37.67 4.18
724 1913 0.737715 AGATGAACGCCTCAAGACGC 60.738 55.000 0.00 0.00 37.67 5.19
731 1920 3.490759 CCTCAAGACGCGCGCAAT 61.491 61.111 32.58 19.22 0.00 3.56
732 1921 2.164663 CCTCAAGACGCGCGCAATA 61.165 57.895 32.58 11.12 0.00 1.90
733 1922 1.270968 CTCAAGACGCGCGCAATAG 59.729 57.895 32.58 17.34 0.00 1.73
734 1923 2.350091 CAAGACGCGCGCAATAGC 60.350 61.111 32.58 14.37 37.42 2.97
744 1933 4.552745 GCAATAGCGCGCCCCAAC 62.553 66.667 30.33 11.72 0.00 3.77
745 1934 3.887868 CAATAGCGCGCCCCAACC 61.888 66.667 30.33 0.00 0.00 3.77
940 2129 1.517832 CTGGGAAATCGAGCTCCGT 59.482 57.895 8.47 0.00 39.75 4.69
975 2164 2.835431 CCGGAGTCTCCTCGCCAT 60.835 66.667 17.00 0.00 38.70 4.40
979 2168 1.064946 GAGTCTCCTCGCCATCACG 59.935 63.158 0.00 0.00 0.00 4.35
980 2169 2.583593 GTCTCCTCGCCATCACGC 60.584 66.667 0.00 0.00 0.00 5.34
1160 2707 4.389077 CGACTTAGCGATTCTTGGTTTCTT 59.611 41.667 0.00 0.00 0.00 2.52
1165 2712 3.813166 AGCGATTCTTGGTTTCTTTCGAA 59.187 39.130 0.00 0.00 0.00 3.71
1263 2810 6.368791 CCTGAATCTCGTGTTTCTTGATTACA 59.631 38.462 9.09 0.00 0.00 2.41
1330 2879 2.432444 TCGGGATGTGGAATTTGTGAC 58.568 47.619 0.00 0.00 0.00 3.67
1410 2972 5.533528 GGGCCAATCTGGTTTTATTATACGT 59.466 40.000 4.39 0.00 40.46 3.57
1453 3015 7.544622 TGATTATTACTACGTGCTCTTCTTGT 58.455 34.615 0.00 0.00 0.00 3.16
1472 3040 4.090761 TGTCATCTTGGAATATGGAGGC 57.909 45.455 0.00 0.00 0.00 4.70
1473 3041 3.459227 TGTCATCTTGGAATATGGAGGCA 59.541 43.478 0.00 0.00 0.00 4.75
1474 3042 4.079844 TGTCATCTTGGAATATGGAGGCAA 60.080 41.667 0.00 0.00 0.00 4.52
1475 3043 4.518211 GTCATCTTGGAATATGGAGGCAAG 59.482 45.833 0.00 0.00 0.00 4.01
1476 3044 4.166725 TCATCTTGGAATATGGAGGCAAGT 59.833 41.667 0.00 0.00 0.00 3.16
1477 3045 3.889815 TCTTGGAATATGGAGGCAAGTG 58.110 45.455 0.00 0.00 0.00 3.16
1532 3100 6.692681 CGAATATGTTTAAGATTTGGGTGCTG 59.307 38.462 0.00 0.00 0.00 4.41
1544 3112 1.452108 GGTGCTGGTGCCTGTATCC 60.452 63.158 0.00 0.00 38.71 2.59
1555 3123 5.104151 TGGTGCCTGTATCCATTCATTCTTA 60.104 40.000 0.00 0.00 0.00 2.10
1609 3179 1.339929 GCGTTGGAAAACACTGGGAAT 59.660 47.619 0.00 0.00 0.00 3.01
1730 3301 8.444783 TGGATGGTGTTATAGGCATAGTTAATT 58.555 33.333 0.00 0.00 0.00 1.40
1768 3339 3.378427 GGTTGCTTACCTGGACATGATTC 59.622 47.826 0.00 0.00 44.10 2.52
1833 3404 9.103861 CACCGCCCACAAAATAAATAATTAAAT 57.896 29.630 0.00 0.00 0.00 1.40
2057 3633 5.774690 TCTTAAATCCTGGCTGTGATGTTTT 59.225 36.000 0.00 0.00 0.00 2.43
2059 3635 5.649782 AAATCCTGGCTGTGATGTTTTAG 57.350 39.130 0.00 0.00 0.00 1.85
2109 3719 8.947115 GGCAAGTTATATATGGATCTTAACCAC 58.053 37.037 0.00 0.00 40.36 4.16
2110 3720 9.502091 GCAAGTTATATATGGATCTTAACCACA 57.498 33.333 0.00 0.00 40.36 4.17
2113 3723 8.322091 AGTTATATATGGATCTTAACCACAGGC 58.678 37.037 0.00 0.00 40.36 4.85
2114 3724 2.332063 ATGGATCTTAACCACAGGCG 57.668 50.000 0.00 0.00 40.36 5.52
2115 3725 0.981183 TGGATCTTAACCACAGGCGT 59.019 50.000 0.00 0.00 32.03 5.68
2116 3726 1.338674 TGGATCTTAACCACAGGCGTG 60.339 52.381 4.53 4.53 43.21 5.34
2238 4073 7.628769 TGAGTGTATGAAACATTGCACATAT 57.371 32.000 15.41 0.00 41.10 1.78
2239 4074 8.054152 TGAGTGTATGAAACATTGCACATATT 57.946 30.769 15.41 0.00 41.10 1.28
2240 4075 8.522003 TGAGTGTATGAAACATTGCACATATTT 58.478 29.630 15.41 0.00 41.10 1.40
2241 4076 8.915871 AGTGTATGAAACATTGCACATATTTC 57.084 30.769 15.41 0.00 41.10 2.17
2242 4077 8.742777 AGTGTATGAAACATTGCACATATTTCT 58.257 29.630 15.41 3.31 41.10 2.52
2243 4078 9.013490 GTGTATGAAACATTGCACATATTTCTC 57.987 33.333 11.34 5.77 41.10 2.87
2334 4176 1.492319 TTCCGGAGAACGTGCAAACG 61.492 55.000 3.34 0.00 42.24 3.60
2359 4201 7.008440 AGAAAAGCAGAAGCAAAACAAAATC 57.992 32.000 0.00 0.00 45.49 2.17
2388 4230 3.058914 ACGTTTTAGATCTGTTGCTGCAC 60.059 43.478 5.18 0.00 0.00 4.57
2469 4332 1.144716 CCTCTTATCTGCCTGCGCA 59.855 57.895 10.98 10.98 44.78 6.09
2494 4357 1.177401 GGCAATTTCTTTCGAGGGCT 58.823 50.000 0.00 0.00 0.00 5.19
2651 4514 6.158695 AGGAGCTTCATAATTTCCTACCTTGA 59.841 38.462 0.00 0.00 36.54 3.02
2666 4529 3.767711 ACCTTGAAATTGTCCTTCTCCC 58.232 45.455 0.00 0.00 0.00 4.30
2668 4531 4.601857 ACCTTGAAATTGTCCTTCTCCCTA 59.398 41.667 0.00 0.00 0.00 3.53
2670 4533 6.190587 CCTTGAAATTGTCCTTCTCCCTATT 58.809 40.000 0.00 0.00 0.00 1.73
2679 4542 6.134754 TGTCCTTCTCCCTATTCCTTAGTAC 58.865 44.000 0.00 0.00 0.00 2.73
2684 4547 7.951245 CCTTCTCCCTATTCCTTAGTACACTAT 59.049 40.741 0.00 0.00 0.00 2.12
2695 4558 6.071334 TCCTTAGTACACTATAGGATGCATGC 60.071 42.308 11.82 11.82 34.19 4.06
2793 4656 2.091994 AGAATGCCTCCTTGCAGCTATT 60.092 45.455 0.00 0.00 45.93 1.73
2808 4671 2.093235 AGCTATTGAAGAGGTGGCTGAC 60.093 50.000 0.00 0.00 0.00 3.51
3199 5080 1.538047 TGAAATGCTTCAGACCTGCC 58.462 50.000 0.00 0.00 36.62 4.85
3328 5209 8.173130 CGATTTGTTACCCTAGTTATGTTTGTC 58.827 37.037 0.00 0.00 0.00 3.18
3427 5310 5.596361 TGGAATGGTTACCAAATGCGATATT 59.404 36.000 8.63 0.00 36.95 1.28
3520 5404 5.928839 CAGATTGATCCCCGTATTAACTGAG 59.071 44.000 0.00 0.00 0.00 3.35
3698 5582 8.519799 AAAACACTTCTCAACTTATCCTTCAA 57.480 30.769 0.00 0.00 0.00 2.69
3699 5583 8.519799 AAACACTTCTCAACTTATCCTTCAAA 57.480 30.769 0.00 0.00 0.00 2.69
3719 5604 7.020827 TCAAAGTCATCAACCTATCTTTCCT 57.979 36.000 0.00 0.00 0.00 3.36
4060 6619 1.939934 TGCATGGCGCTACAAGTATTC 59.060 47.619 7.64 0.00 43.06 1.75
4337 6974 1.740296 GCGCATGAACCGGTACAGT 60.740 57.895 8.00 0.00 0.00 3.55
4934 7572 0.256752 AGCAGTATGAAGCCATGGCA 59.743 50.000 37.18 18.81 41.07 4.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
84 88 4.439860 AGGTAGAAATCTCAGTCCCCTTT 58.560 43.478 0.00 0.00 0.00 3.11
200 219 5.398603 TTGCTTCTTCCAAAACTGTTCAA 57.601 34.783 0.00 0.00 0.00 2.69
293 1451 5.709164 AGAGCTTTGCATGTAAGATCAGTTT 59.291 36.000 21.63 6.32 39.76 2.66
429 1590 7.183475 AGCTCAGATCCATTATACACCCATTAT 59.817 37.037 0.00 0.00 0.00 1.28
503 1690 5.713025 ACTTGTGTGTGGATTGATATTTGC 58.287 37.500 0.00 0.00 0.00 3.68
645 1834 5.123186 TCGTTTGGTCCACATTATGACATTC 59.877 40.000 0.00 0.00 33.09 2.67
646 1835 5.007034 TCGTTTGGTCCACATTATGACATT 58.993 37.500 0.00 0.00 33.09 2.71
647 1836 4.584874 TCGTTTGGTCCACATTATGACAT 58.415 39.130 0.00 0.00 33.09 3.06
648 1837 4.000325 CTCGTTTGGTCCACATTATGACA 59.000 43.478 0.00 0.00 33.09 3.58
649 1838 3.181510 GCTCGTTTGGTCCACATTATGAC 60.182 47.826 0.00 0.00 0.00 3.06
650 1839 3.006940 GCTCGTTTGGTCCACATTATGA 58.993 45.455 0.00 0.00 0.00 2.15
651 1840 3.009723 AGCTCGTTTGGTCCACATTATG 58.990 45.455 0.00 0.00 0.00 1.90
652 1841 3.350219 AGCTCGTTTGGTCCACATTAT 57.650 42.857 0.00 0.00 0.00 1.28
653 1842 2.851263 AGCTCGTTTGGTCCACATTA 57.149 45.000 0.00 0.00 0.00 1.90
654 1843 2.699954 CTAGCTCGTTTGGTCCACATT 58.300 47.619 0.00 0.00 0.00 2.71
655 1844 1.676014 GCTAGCTCGTTTGGTCCACAT 60.676 52.381 7.70 0.00 0.00 3.21
656 1845 0.320421 GCTAGCTCGTTTGGTCCACA 60.320 55.000 7.70 0.00 0.00 4.17
657 1846 0.037232 AGCTAGCTCGTTTGGTCCAC 60.037 55.000 12.68 0.00 0.00 4.02
658 1847 0.246635 GAGCTAGCTCGTTTGGTCCA 59.753 55.000 28.04 0.00 33.06 4.02
659 1848 0.246635 TGAGCTAGCTCGTTTGGTCC 59.753 55.000 33.55 12.92 45.48 4.46
660 1849 2.080286 TTGAGCTAGCTCGTTTGGTC 57.920 50.000 33.55 13.81 45.48 4.02
661 1850 2.350522 CATTGAGCTAGCTCGTTTGGT 58.649 47.619 33.55 16.20 45.48 3.67
662 1851 1.667724 CCATTGAGCTAGCTCGTTTGG 59.332 52.381 33.55 31.63 45.48 3.28
663 1852 1.667724 CCCATTGAGCTAGCTCGTTTG 59.332 52.381 33.55 28.15 45.48 2.93
664 1853 2.014068 GCCCATTGAGCTAGCTCGTTT 61.014 52.381 33.55 20.71 45.48 3.60
665 1854 0.462759 GCCCATTGAGCTAGCTCGTT 60.463 55.000 33.55 22.99 45.48 3.85
666 1855 1.144936 GCCCATTGAGCTAGCTCGT 59.855 57.895 33.55 24.13 45.48 4.18
667 1856 1.953138 CGCCCATTGAGCTAGCTCG 60.953 63.158 33.55 22.26 45.48 5.03
668 1857 1.596477 CCGCCCATTGAGCTAGCTC 60.596 63.158 33.47 33.47 43.01 4.09
669 1858 2.507944 CCGCCCATTGAGCTAGCT 59.492 61.111 19.45 19.45 0.00 3.32
670 1859 3.282920 GCCGCCCATTGAGCTAGC 61.283 66.667 6.62 6.62 0.00 3.42
671 1860 1.890979 CTGCCGCCCATTGAGCTAG 60.891 63.158 0.00 0.00 0.00 3.42
672 1861 2.190313 CTGCCGCCCATTGAGCTA 59.810 61.111 0.00 0.00 0.00 3.32
675 1864 2.638354 TTTGCTGCCGCCCATTGAG 61.638 57.895 0.00 0.00 34.43 3.02
676 1865 2.599875 TTTGCTGCCGCCCATTGA 60.600 55.556 0.00 0.00 34.43 2.57
677 1866 2.432972 GTTTGCTGCCGCCCATTG 60.433 61.111 0.00 0.00 34.43 2.82
678 1867 3.694538 GGTTTGCTGCCGCCCATT 61.695 61.111 0.00 0.00 34.43 3.16
679 1868 4.684134 AGGTTTGCTGCCGCCCAT 62.684 61.111 0.00 0.00 34.43 4.00
680 1869 4.912395 AAGGTTTGCTGCCGCCCA 62.912 61.111 0.00 0.00 34.43 5.36
681 1870 4.362476 CAAGGTTTGCTGCCGCCC 62.362 66.667 0.00 0.00 34.43 6.13
690 1879 0.387622 CATCTGCGGTGCAAGGTTTG 60.388 55.000 0.00 0.00 38.41 2.93
691 1880 0.537143 TCATCTGCGGTGCAAGGTTT 60.537 50.000 0.00 0.00 38.41 3.27
692 1881 0.537143 TTCATCTGCGGTGCAAGGTT 60.537 50.000 0.00 0.00 38.41 3.50
693 1882 1.073025 TTCATCTGCGGTGCAAGGT 59.927 52.632 0.00 0.00 38.41 3.50
694 1883 1.503542 GTTCATCTGCGGTGCAAGG 59.496 57.895 0.00 0.00 38.41 3.61
695 1884 1.133253 CGTTCATCTGCGGTGCAAG 59.867 57.895 0.00 0.00 38.41 4.01
696 1885 2.965147 GCGTTCATCTGCGGTGCAA 61.965 57.895 0.00 0.00 38.41 4.08
697 1886 3.422303 GCGTTCATCTGCGGTGCA 61.422 61.111 0.00 0.00 36.92 4.57
698 1887 4.166011 GGCGTTCATCTGCGGTGC 62.166 66.667 0.00 0.00 0.00 5.01
699 1888 2.434884 AGGCGTTCATCTGCGGTG 60.435 61.111 0.00 0.00 0.00 4.94
700 1889 2.125512 GAGGCGTTCATCTGCGGT 60.126 61.111 0.00 0.00 0.00 5.68
701 1890 1.699656 CTTGAGGCGTTCATCTGCGG 61.700 60.000 0.00 0.00 35.27 5.69
702 1891 0.737367 TCTTGAGGCGTTCATCTGCG 60.737 55.000 0.00 0.00 35.27 5.18
703 1892 0.723981 GTCTTGAGGCGTTCATCTGC 59.276 55.000 0.00 0.00 35.27 4.26
704 1893 0.994995 CGTCTTGAGGCGTTCATCTG 59.005 55.000 0.00 0.00 35.27 2.90
705 1894 0.737715 GCGTCTTGAGGCGTTCATCT 60.738 55.000 6.88 0.00 35.27 2.90
706 1895 1.710339 GCGTCTTGAGGCGTTCATC 59.290 57.895 6.88 0.00 35.27 2.92
707 1896 2.094659 CGCGTCTTGAGGCGTTCAT 61.095 57.895 23.70 0.00 46.79 2.57
708 1897 2.733218 CGCGTCTTGAGGCGTTCA 60.733 61.111 23.70 0.00 46.79 3.18
714 1903 2.082437 CTATTGCGCGCGTCTTGAGG 62.082 60.000 32.35 11.84 0.00 3.86
715 1904 1.270968 CTATTGCGCGCGTCTTGAG 59.729 57.895 32.35 17.81 0.00 3.02
716 1905 2.798501 GCTATTGCGCGCGTCTTGA 61.799 57.895 32.35 13.10 0.00 3.02
717 1906 2.350091 GCTATTGCGCGCGTCTTG 60.350 61.111 32.35 18.11 0.00 3.02
727 1916 4.552745 GTTGGGGCGCGCTATTGC 62.553 66.667 32.29 13.86 0.00 3.56
728 1917 3.887868 GGTTGGGGCGCGCTATTG 61.888 66.667 32.29 0.00 0.00 1.90
735 1924 4.043100 AACTAGGGGTTGGGGCGC 62.043 66.667 0.00 0.00 36.70 6.53
742 1931 0.187361 TTGCTTGCCAACTAGGGGTT 59.813 50.000 0.00 0.00 38.93 4.11
743 1932 0.251341 CTTGCTTGCCAACTAGGGGT 60.251 55.000 0.00 0.00 38.09 4.95
744 1933 0.038166 TCTTGCTTGCCAACTAGGGG 59.962 55.000 0.00 0.00 38.09 4.79
745 1934 1.541588 GTTCTTGCTTGCCAACTAGGG 59.458 52.381 0.00 0.00 38.09 3.53
746 1935 1.541588 GGTTCTTGCTTGCCAACTAGG 59.458 52.381 0.00 0.00 41.84 3.02
747 1936 1.197721 CGGTTCTTGCTTGCCAACTAG 59.802 52.381 0.00 0.00 0.00 2.57
748 1937 1.234821 CGGTTCTTGCTTGCCAACTA 58.765 50.000 0.00 0.00 0.00 2.24
749 1938 1.455383 CCGGTTCTTGCTTGCCAACT 61.455 55.000 0.00 0.00 0.00 3.16
869 2058 3.844090 GGCGGAGGAGAGTGAGGC 61.844 72.222 0.00 0.00 0.00 4.70
1008 2197 3.762528 TTCGAAGATTCAGCCCTCGGC 62.763 57.143 0.00 0.00 43.77 5.54
1012 2201 0.107459 GGCTTCGAAGATTCAGCCCT 60.107 55.000 28.95 0.00 36.52 5.19
1014 2203 1.432270 CCGGCTTCGAAGATTCAGCC 61.432 60.000 28.95 20.31 38.91 4.85
1017 2206 0.175760 CCTCCGGCTTCGAAGATTCA 59.824 55.000 28.95 8.11 35.04 2.57
1263 2810 5.506982 GCACAAAGAAGAGCAAAGAATCAGT 60.507 40.000 0.00 0.00 0.00 3.41
1330 2879 2.289072 ACATTCCACACGAACTCTGAGG 60.289 50.000 9.85 0.00 31.79 3.86
1439 3001 3.062763 CAAGATGACAAGAAGAGCACGT 58.937 45.455 0.00 0.00 0.00 4.49
1453 3015 4.166725 ACTTGCCTCCATATTCCAAGATGA 59.833 41.667 5.78 0.00 37.08 2.92
1472 3040 3.797039 TCACAGAGAGGTTGTTCACTTG 58.203 45.455 0.00 0.00 0.00 3.16
1473 3041 4.696479 ATCACAGAGAGGTTGTTCACTT 57.304 40.909 0.00 0.00 0.00 3.16
1474 3042 4.696479 AATCACAGAGAGGTTGTTCACT 57.304 40.909 0.00 0.00 0.00 3.41
1475 3043 5.542779 ACTAATCACAGAGAGGTTGTTCAC 58.457 41.667 0.00 0.00 0.00 3.18
1476 3044 5.304357 TGACTAATCACAGAGAGGTTGTTCA 59.696 40.000 0.00 0.00 0.00 3.18
1477 3045 5.784177 TGACTAATCACAGAGAGGTTGTTC 58.216 41.667 0.00 0.00 0.00 3.18
1544 3112 7.384932 TGCTACCACACGATATAAGAATGAATG 59.615 37.037 0.00 0.00 0.00 2.67
1555 3123 6.036470 CGATGAATATGCTACCACACGATAT 58.964 40.000 0.00 0.00 0.00 1.63
1593 3163 5.255397 AGACATATTCCCAGTGTTTTCCA 57.745 39.130 0.00 0.00 0.00 3.53
1609 3179 5.973899 TGCATGCCTAAAACAAAGACATA 57.026 34.783 16.68 0.00 0.00 2.29
1730 3301 7.665559 GGTAAGCAACCCTGAATAATCATATGA 59.334 37.037 8.10 8.10 43.16 2.15
1768 3339 3.809832 GTGAATGACCAATGATCTACGGG 59.190 47.826 0.00 0.00 0.00 5.28
1833 3404 5.808366 AATCAGAGTAAGTGGTCAGTGAA 57.192 39.130 0.00 0.00 0.00 3.18
1955 3527 2.629137 ACAACTGATGCTGCAAAATCCA 59.371 40.909 6.36 0.00 0.00 3.41
2010 3582 7.001073 AGAATACAAAATAGGGGAATGAGAGC 58.999 38.462 0.00 0.00 0.00 4.09
2059 3635 9.983804 GCCAAACTTATAAGTAATTGTACAGAC 57.016 33.333 18.31 0.00 38.57 3.51
2109 3719 2.872245 ACGAAATCATATTCCACGCCTG 59.128 45.455 0.00 0.00 0.00 4.85
2110 3720 2.872245 CACGAAATCATATTCCACGCCT 59.128 45.455 0.00 0.00 0.00 5.52
2111 3721 2.032030 CCACGAAATCATATTCCACGCC 60.032 50.000 0.00 0.00 0.00 5.68
2112 3722 2.869801 TCCACGAAATCATATTCCACGC 59.130 45.455 0.00 0.00 0.00 5.34
2113 3723 5.673337 ATTCCACGAAATCATATTCCACG 57.327 39.130 0.00 0.00 0.00 4.94
2114 3724 7.023575 GCATATTCCACGAAATCATATTCCAC 58.976 38.462 0.00 0.00 0.00 4.02
2115 3725 6.942005 AGCATATTCCACGAAATCATATTCCA 59.058 34.615 0.00 0.00 0.00 3.53
2116 3726 7.383102 AGCATATTCCACGAAATCATATTCC 57.617 36.000 0.00 0.00 0.00 3.01
2118 3728 8.627208 AGAAGCATATTCCACGAAATCATATT 57.373 30.769 0.00 0.00 0.00 1.28
2120 3730 8.988934 GTAAGAAGCATATTCCACGAAATCATA 58.011 33.333 0.00 0.00 0.00 2.15
2334 4176 6.407475 TTTTGTTTTGCTTCTGCTTTTCTC 57.593 33.333 0.00 0.00 40.48 2.87
2359 4201 5.446473 GCAACAGATCTAAAACGTGATCCAG 60.446 44.000 9.34 6.20 39.72 3.86
2388 4230 7.153985 TCTAAAGCCTGATGGAAATTTTGTTG 58.846 34.615 0.00 0.00 34.57 3.33
2469 4332 2.227388 CTCGAAAGAAATTGCCTGCACT 59.773 45.455 0.00 0.00 41.32 4.40
2494 4357 4.661222 TGTTCAGCACAATAATCAAGGGA 58.339 39.130 0.00 0.00 29.87 4.20
2651 4514 6.408770 AAGGAATAGGGAGAAGGACAATTT 57.591 37.500 0.00 0.00 0.00 1.82
2666 4529 9.244292 TGCATCCTATAGTGTACTAAGGAATAG 57.756 37.037 18.28 14.38 38.26 1.73
2668 4531 8.535335 CATGCATCCTATAGTGTACTAAGGAAT 58.465 37.037 18.28 10.51 38.26 3.01
2670 4533 6.071334 GCATGCATCCTATAGTGTACTAAGGA 60.071 42.308 14.21 17.40 38.66 3.36
2679 4542 2.570752 AGGGAGCATGCATCCTATAGTG 59.429 50.000 24.48 0.00 37.01 2.74
2684 4547 1.627329 GATCAGGGAGCATGCATCCTA 59.373 52.381 24.99 16.30 37.01 2.94
2793 4656 1.536073 CCTCGTCAGCCACCTCTTCA 61.536 60.000 0.00 0.00 0.00 3.02
2896 4770 8.920174 TGAAGAGAATTGTCCCTTACGAATATA 58.080 33.333 0.00 0.00 0.00 0.86
3070 4950 6.608002 TGTTAAGTTGGGTTTCAGGTTGTAAT 59.392 34.615 0.00 0.00 0.00 1.89
3199 5080 2.229675 TGGCTACATCATGAGAAGCG 57.770 50.000 16.21 0.61 0.00 4.68
3427 5310 4.023536 GCCTGAAACAATCCGTGAGTTAAA 60.024 41.667 0.00 0.00 0.00 1.52
3520 5404 8.764287 CAGAAAACCAAACATATCAAAAACCTC 58.236 33.333 0.00 0.00 0.00 3.85
3698 5582 7.020827 TGAAGGAAAGATAGGTTGATGACTT 57.979 36.000 0.00 0.00 0.00 3.01
3699 5583 6.214412 ACTGAAGGAAAGATAGGTTGATGACT 59.786 38.462 0.00 0.00 0.00 3.41
3719 5604 8.306038 CAGAAACATTAATTGGGATGAACTGAA 58.694 33.333 0.00 0.00 0.00 3.02
4324 6961 1.551430 CATACCCACTGTACCGGTTCA 59.449 52.381 15.04 14.25 30.62 3.18
4337 6974 0.752658 CTGACTGCCGATCATACCCA 59.247 55.000 0.00 0.00 0.00 4.51
4448 7085 2.687425 GTTTGCCAAGGTTGCCAAATTT 59.313 40.909 2.54 0.00 0.00 1.82
4934 7572 0.678048 GCTTCAAGGGTGCCGAGATT 60.678 55.000 0.00 0.00 0.00 2.40


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

AutoCloner maintained by Alex Coulton.