Multiple sequence alignment - TraesCS3B01G406100

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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 TraesCS3B01G406100 chr3B 100.000 2465 0 0 1 2465 641665585 641668049 0.000000e+00 4553.0
1 TraesCS3B01G406100 chr3B 100.000 95 0 0 1654 1748 811423162 811423256 2.520000e-40 176.0
2 TraesCS3B01G406100 chr3B 96.491 57 2 0 378 434 829121985 829121929 7.260000e-16 95.3
3 TraesCS3B01G406100 chr3A 88.066 1567 118 33 1 1553 623615320 623616831 0.000000e+00 1794.0
4 TraesCS3B01G406100 chr3A 89.059 457 36 9 2007 2459 623619622 623620068 2.770000e-154 555.0
5 TraesCS3B01G406100 chr3A 89.655 203 20 1 1551 1752 623618922 623619124 8.750000e-65 257.0
6 TraesCS3B01G406100 chr3A 96.907 97 3 0 1653 1749 734018544 734018640 1.960000e-36 163.0
7 TraesCS3B01G406100 chr3D 85.684 1411 116 45 478 1877 480849579 480850914 0.000000e+00 1408.0
8 TraesCS3B01G406100 chr3D 87.643 437 37 12 2037 2459 480858090 480858523 2.200000e-135 492.0
9 TraesCS3B01G406100 chr3D 88.015 267 24 7 2041 2300 480857281 480857546 2.380000e-80 309.0
10 TraesCS3B01G406100 chr3D 87.500 152 17 2 1901 2050 480857879 480858030 9.060000e-40 174.0
11 TraesCS3B01G406100 chr3D 97.849 93 2 0 1656 1748 604377372 604377464 7.050000e-36 161.0
12 TraesCS3B01G406100 chr3D 96.491 57 2 0 378 434 611411044 611410988 7.260000e-16 95.3
13 TraesCS3B01G406100 chr3D 94.118 51 3 0 378 428 26227915 26227865 7.310000e-11 78.7
14 TraesCS3B01G406100 chr2D 81.752 274 44 2 1179 1449 375027185 375027455 8.870000e-55 224.0
15 TraesCS3B01G406100 chr2A 82.353 255 39 2 1166 1417 507376519 507376770 1.480000e-52 217.0
16 TraesCS3B01G406100 chr2B 81.022 274 46 2 1179 1449 445172658 445172928 1.920000e-51 213.0
17 TraesCS3B01G406100 chr2B 95.050 101 4 1 1659 1758 447507584 447507684 9.130000e-35 158.0
18 TraesCS3B01G406100 chrUn 97.895 95 2 0 1654 1748 42164816 42164722 5.450000e-37 165.0
19 TraesCS3B01G406100 chrUn 90.598 117 7 4 1632 1748 42173913 42173801 4.250000e-33 152.0
20 TraesCS3B01G406100 chr1D 100.000 89 0 0 1661 1749 371655220 371655308 5.450000e-37 165.0
21 TraesCS3B01G406100 chr7B 93.151 73 5 0 391 463 724956447 724956375 9.320000e-20 108.0
22 TraesCS3B01G406100 chr7B 83.333 84 13 1 384 466 724348978 724349061 2.630000e-10 76.8
23 TraesCS3B01G406100 chr7A 88.506 87 10 0 377 463 538573025 538572939 3.350000e-19 106.0
24 TraesCS3B01G406100 chr5A 96.078 51 2 0 378 428 290394512 290394462 1.570000e-12 84.2
25 TraesCS3B01G406100 chr1B 92.727 55 4 0 378 432 442949272 442949218 2.030000e-11 80.5


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3B01G406100 chr3B 641665585 641668049 2464 False 4553.000000 4553 100.000000 1 2465 1 chr3B.!!$F1 2464
1 TraesCS3B01G406100 chr3A 623615320 623620068 4748 False 868.666667 1794 88.926667 1 2459 3 chr3A.!!$F2 2458
2 TraesCS3B01G406100 chr3D 480849579 480850914 1335 False 1408.000000 1408 85.684000 478 1877 1 chr3D.!!$F1 1399
3 TraesCS3B01G406100 chr3D 480857281 480858523 1242 False 325.000000 492 87.719333 1901 2459 3 chr3D.!!$F3 558

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
924 935 0.040157 TCTATTAATACCGCGCGCGT 60.04 50.0 45.51 35.15 37.81 6.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1861 3978 0.250513 AGGGATGAGAGTGGTTTCGC 59.749 55.0 0.0 0.0 0.0 4.7 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
244 246 4.720649 TGGACGTGTTTCAAAAATTCCA 57.279 36.364 0.00 0.00 0.00 3.53
250 252 4.739716 CGTGTTTCAAAAATTCCAGTGGAG 59.260 41.667 12.67 0.00 31.21 3.86
267 269 6.320171 CAGTGGAGTTTCTATTTGCATGAAG 58.680 40.000 0.00 0.00 0.00 3.02
269 271 6.888632 AGTGGAGTTTCTATTTGCATGAAGAT 59.111 34.615 0.00 0.00 0.00 2.40
270 272 7.395489 AGTGGAGTTTCTATTTGCATGAAGATT 59.605 33.333 0.00 0.00 0.00 2.40
271 273 8.031277 GTGGAGTTTCTATTTGCATGAAGATTT 58.969 33.333 0.00 0.00 0.00 2.17
272 274 8.587608 TGGAGTTTCTATTTGCATGAAGATTTT 58.412 29.630 0.00 0.00 0.00 1.82
386 390 5.125367 ACCCAAAATACATTACTCCCTCC 57.875 43.478 0.00 0.00 0.00 4.30
389 393 4.814771 CCAAAATACATTACTCCCTCCGAC 59.185 45.833 0.00 0.00 0.00 4.79
439 443 7.570507 GCACAAAGTTGTACTAAATCATCGACA 60.571 37.037 0.00 0.00 39.91 4.35
442 446 9.825972 CAAAGTTGTACTAAATCATCGACAATT 57.174 29.630 0.00 0.00 0.00 2.32
443 447 9.825972 AAAGTTGTACTAAATCATCGACAATTG 57.174 29.630 3.24 3.24 0.00 2.32
476 480 7.732996 TCGGAGGGAGTAATAATTTTTCCTAG 58.267 38.462 0.00 0.00 0.00 3.02
645 649 2.895039 CGAGGCCGCGTTATAATGT 58.105 52.632 21.77 0.00 0.00 2.71
711 715 0.313987 TGTCTACACCTGCACGACAG 59.686 55.000 0.00 0.00 46.77 3.51
712 716 1.009389 GTCTACACCTGCACGACAGC 61.009 60.000 4.92 0.00 45.78 4.40
716 720 3.295273 ACCTGCACGACAGCTCGA 61.295 61.111 1.98 0.00 45.78 4.04
767 775 4.219507 TCTGCTTCTTTCTCTCGATGAAGT 59.780 41.667 0.00 0.00 34.95 3.01
791 799 6.737720 AGGATATGTTCTGATGCTTCTACA 57.262 37.500 0.88 3.76 0.00 2.74
826 834 1.357690 GTGTCGTCACTCGTCACCA 59.642 57.895 5.50 0.00 46.69 4.17
855 866 2.833913 CCCAAGGACACCAGCCACT 61.834 63.158 0.00 0.00 0.00 4.00
856 867 1.488705 CCCAAGGACACCAGCCACTA 61.489 60.000 0.00 0.00 0.00 2.74
885 896 2.124942 GAGGCTGCTACTGGTGCC 60.125 66.667 0.00 0.00 45.21 5.01
896 907 2.359850 TGGTGCCGCTCAACATCC 60.360 61.111 0.00 0.00 37.50 3.51
902 913 3.499737 CGCTCAACATCCCACGCC 61.500 66.667 0.00 0.00 0.00 5.68
905 916 3.605749 CTCAACATCCCACGCCCGT 62.606 63.158 0.00 0.00 0.00 5.28
916 927 2.611224 CCCACGCCCGTCTATTAATACC 60.611 54.545 0.00 0.00 0.00 2.73
917 928 2.322161 CACGCCCGTCTATTAATACCG 58.678 52.381 0.00 0.00 0.00 4.02
918 929 1.336240 ACGCCCGTCTATTAATACCGC 60.336 52.381 0.00 0.00 0.00 5.68
919 930 1.343506 GCCCGTCTATTAATACCGCG 58.656 55.000 0.00 0.00 0.00 6.46
924 935 0.040157 TCTATTAATACCGCGCGCGT 60.040 50.000 45.51 35.15 37.81 6.01
958 969 1.792367 CGTTCTCAAGTTGTGATCGCA 59.208 47.619 19.51 4.45 35.07 5.10
959 970 2.410262 CGTTCTCAAGTTGTGATCGCAC 60.410 50.000 19.51 10.07 45.35 5.34
985 1002 3.244105 TCGCAAGCGAAGTTCTGC 58.756 55.556 15.45 10.47 46.01 4.26
997 1016 4.798387 GCGAAGTTCTGCTTTCTTTTTGAA 59.202 37.500 10.99 0.00 37.59 2.69
999 1018 5.230097 CGAAGTTCTGCTTTCTTTTTGAACC 59.770 40.000 0.56 0.00 37.59 3.62
1056 1075 4.451150 TCCGGCGTCAGGTGCATC 62.451 66.667 6.01 0.00 0.00 3.91
1060 1079 4.451150 GCGTCAGGTGCATCCCGA 62.451 66.667 5.57 0.00 36.75 5.14
1356 1376 2.987547 GTGGACCAGTCGGACGGA 60.988 66.667 20.51 1.82 35.59 4.69
1365 1385 1.063811 GTCGGACGGATCGTTCCTC 59.936 63.158 10.71 7.08 41.37 3.71
1465 1485 1.488393 AGGAAGAGGAGGTGCATTAGC 59.512 52.381 0.00 0.00 42.57 3.09
1469 1489 4.202409 GGAAGAGGAGGTGCATTAGCTTAT 60.202 45.833 0.00 0.00 42.74 1.73
1470 1490 5.012148 GGAAGAGGAGGTGCATTAGCTTATA 59.988 44.000 0.00 0.00 42.74 0.98
1562 3675 5.392811 GCTGTGTAGTGGAGTAGTATCGTTT 60.393 44.000 0.00 0.00 0.00 3.60
1605 3718 5.912360 TGCTCAAAGTGAATAGCATATCG 57.088 39.130 0.00 0.00 39.92 2.92
1625 3738 3.874543 TCGTCAGTTTTGCTAGCTTTTCA 59.125 39.130 17.23 0.00 0.00 2.69
1627 3740 4.437820 CGTCAGTTTTGCTAGCTTTTCAAC 59.562 41.667 17.23 10.85 0.00 3.18
1629 3742 5.804979 GTCAGTTTTGCTAGCTTTTCAACAA 59.195 36.000 17.23 0.00 0.00 2.83
1630 3743 5.804979 TCAGTTTTGCTAGCTTTTCAACAAC 59.195 36.000 17.23 3.96 0.00 3.32
1631 3744 5.807011 CAGTTTTGCTAGCTTTTCAACAACT 59.193 36.000 17.23 6.26 0.00 3.16
1637 3751 5.820423 TGCTAGCTTTTCAACAACTACAAGA 59.180 36.000 17.23 0.00 0.00 3.02
1770 3887 3.826729 GGATGTTTGCCTGGATAATACCC 59.173 47.826 0.00 0.00 0.00 3.69
1774 3891 3.857157 TTGCCTGGATAATACCCTGAC 57.143 47.619 0.00 0.00 0.00 3.51
1781 3898 2.095161 GGATAATACCCTGACGAGCTCG 60.095 54.545 33.45 33.45 46.33 5.03
1789 3906 2.336809 GACGAGCTCGGCTATGGG 59.663 66.667 36.93 10.16 45.57 4.00
1791 3908 2.336809 CGAGCTCGGCTATGGGTC 59.663 66.667 28.40 0.00 39.88 4.46
1792 3909 2.490148 CGAGCTCGGCTATGGGTCA 61.490 63.158 28.40 0.00 39.88 4.02
1793 3910 1.068250 GAGCTCGGCTATGGGTCAC 59.932 63.158 0.00 0.00 39.88 3.67
1794 3911 2.109181 GCTCGGCTATGGGTCACC 59.891 66.667 0.00 0.00 37.24 4.02
1795 3912 2.435693 GCTCGGCTATGGGTCACCT 61.436 63.158 0.00 0.00 37.76 4.00
1797 3914 1.749334 CTCGGCTATGGGTCACCTCC 61.749 65.000 0.00 0.00 37.76 4.30
1798 3915 1.762460 CGGCTATGGGTCACCTCCT 60.762 63.158 0.00 0.00 37.76 3.69
1799 3916 1.832912 GGCTATGGGTCACCTCCTG 59.167 63.158 0.00 0.00 37.76 3.86
1800 3917 1.147153 GCTATGGGTCACCTCCTGC 59.853 63.158 0.00 0.00 37.76 4.85
1801 3918 1.341156 GCTATGGGTCACCTCCTGCT 61.341 60.000 0.00 0.00 37.76 4.24
1802 3919 1.207791 CTATGGGTCACCTCCTGCTT 58.792 55.000 0.00 0.00 37.76 3.91
1803 3920 1.561542 CTATGGGTCACCTCCTGCTTT 59.438 52.381 0.00 0.00 37.76 3.51
1805 3922 1.440618 TGGGTCACCTCCTGCTTTTA 58.559 50.000 0.00 0.00 37.76 1.52
1806 3923 1.992557 TGGGTCACCTCCTGCTTTTAT 59.007 47.619 0.00 0.00 37.76 1.40
1807 3924 2.378547 TGGGTCACCTCCTGCTTTTATT 59.621 45.455 0.00 0.00 37.76 1.40
1808 3925 3.589735 TGGGTCACCTCCTGCTTTTATTA 59.410 43.478 0.00 0.00 37.76 0.98
1809 3926 3.945921 GGGTCACCTCCTGCTTTTATTAC 59.054 47.826 0.00 0.00 0.00 1.89
1810 3927 3.945921 GGTCACCTCCTGCTTTTATTACC 59.054 47.826 0.00 0.00 0.00 2.85
1811 3928 4.324331 GGTCACCTCCTGCTTTTATTACCT 60.324 45.833 0.00 0.00 0.00 3.08
1813 3930 4.783227 TCACCTCCTGCTTTTATTACCTCT 59.217 41.667 0.00 0.00 0.00 3.69
1814 3931 4.878397 CACCTCCTGCTTTTATTACCTCTG 59.122 45.833 0.00 0.00 0.00 3.35
1816 3933 3.531538 TCCTGCTTTTATTACCTCTGCG 58.468 45.455 0.00 0.00 0.00 5.18
1820 3937 2.936498 GCTTTTATTACCTCTGCGCTCA 59.064 45.455 9.73 0.00 0.00 4.26
1821 3938 3.374058 GCTTTTATTACCTCTGCGCTCAA 59.626 43.478 9.73 0.00 0.00 3.02
1823 3940 3.603158 TTATTACCTCTGCGCTCAACA 57.397 42.857 9.73 0.00 0.00 3.33
1826 3943 2.507110 TACCTCTGCGCTCAACAGCC 62.507 60.000 9.73 0.00 43.56 4.85
1827 3944 2.357881 CTCTGCGCTCAACAGCCA 60.358 61.111 9.73 0.00 43.56 4.75
1828 3945 1.962822 CTCTGCGCTCAACAGCCAA 60.963 57.895 9.73 0.00 43.56 4.52
1829 3946 2.180131 CTCTGCGCTCAACAGCCAAC 62.180 60.000 9.73 0.00 43.56 3.77
1830 3947 2.515757 TGCGCTCAACAGCCAACA 60.516 55.556 9.73 0.00 43.56 3.33
1831 3948 2.050985 GCGCTCAACAGCCAACAC 60.051 61.111 0.00 0.00 43.56 3.32
1833 3950 2.024918 CGCTCAACAGCCAACACTT 58.975 52.632 0.00 0.00 43.56 3.16
1834 3951 0.040958 CGCTCAACAGCCAACACTTC 60.041 55.000 0.00 0.00 43.56 3.01
1836 3953 0.954452 CTCAACAGCCAACACTTCCC 59.046 55.000 0.00 0.00 0.00 3.97
1841 3958 1.271597 ACAGCCAACACTTCCCTCATC 60.272 52.381 0.00 0.00 0.00 2.92
1844 3961 2.108952 AGCCAACACTTCCCTCATCTTT 59.891 45.455 0.00 0.00 0.00 2.52
1846 3963 3.321968 GCCAACACTTCCCTCATCTTTTT 59.678 43.478 0.00 0.00 0.00 1.94
1847 3964 4.559502 GCCAACACTTCCCTCATCTTTTTC 60.560 45.833 0.00 0.00 0.00 2.29
1848 3965 4.320494 CCAACACTTCCCTCATCTTTTTCG 60.320 45.833 0.00 0.00 0.00 3.46
1851 3968 4.263506 ACACTTCCCTCATCTTTTTCGGAT 60.264 41.667 0.00 0.00 0.00 4.18
1852 3969 4.333926 CACTTCCCTCATCTTTTTCGGATC 59.666 45.833 0.00 0.00 0.00 3.36
1853 3970 4.019321 ACTTCCCTCATCTTTTTCGGATCA 60.019 41.667 0.00 0.00 0.00 2.92
1854 3971 4.778213 TCCCTCATCTTTTTCGGATCAT 57.222 40.909 0.00 0.00 0.00 2.45
1855 3972 4.454678 TCCCTCATCTTTTTCGGATCATG 58.545 43.478 0.00 0.00 0.00 3.07
1856 3973 4.080356 TCCCTCATCTTTTTCGGATCATGT 60.080 41.667 0.00 0.00 0.00 3.21
1858 3975 4.877823 CCTCATCTTTTTCGGATCATGTCA 59.122 41.667 0.00 0.00 0.00 3.58
1861 3978 5.234972 TCATCTTTTTCGGATCATGTCATCG 59.765 40.000 0.00 0.00 0.00 3.84
1862 3979 3.309682 TCTTTTTCGGATCATGTCATCGC 59.690 43.478 0.00 0.00 0.00 4.58
1863 3980 1.208259 TTTCGGATCATGTCATCGCG 58.792 50.000 0.00 0.00 0.00 5.87
1864 3981 0.383949 TTCGGATCATGTCATCGCGA 59.616 50.000 13.09 13.09 0.00 5.87
1865 3982 0.383949 TCGGATCATGTCATCGCGAA 59.616 50.000 15.24 0.00 0.00 4.70
1866 3983 1.202359 TCGGATCATGTCATCGCGAAA 60.202 47.619 15.24 0.49 0.00 3.46
1867 3984 1.071239 CGGATCATGTCATCGCGAAAC 60.071 52.381 15.24 15.56 0.00 2.78
1869 3986 1.933181 GATCATGTCATCGCGAAACCA 59.067 47.619 15.24 10.34 0.00 3.67
1871 3988 1.078709 CATGTCATCGCGAAACCACT 58.921 50.000 15.24 0.00 0.00 4.00
1872 3989 1.061131 CATGTCATCGCGAAACCACTC 59.939 52.381 15.24 0.30 0.00 3.51
1873 3990 0.317160 TGTCATCGCGAAACCACTCT 59.683 50.000 15.24 0.00 0.00 3.24
1874 3991 0.992802 GTCATCGCGAAACCACTCTC 59.007 55.000 15.24 0.00 0.00 3.20
1877 3994 1.590238 CATCGCGAAACCACTCTCATC 59.410 52.381 15.24 0.00 0.00 2.92
1878 3995 0.108804 TCGCGAAACCACTCTCATCC 60.109 55.000 6.20 0.00 0.00 3.51
1880 3997 0.250513 GCGAAACCACTCTCATCCCT 59.749 55.000 0.00 0.00 0.00 4.20
1881 3998 1.339151 GCGAAACCACTCTCATCCCTT 60.339 52.381 0.00 0.00 0.00 3.95
1882 3999 2.622436 CGAAACCACTCTCATCCCTTC 58.378 52.381 0.00 0.00 0.00 3.46
1883 4000 2.234908 CGAAACCACTCTCATCCCTTCT 59.765 50.000 0.00 0.00 0.00 2.85
1884 4001 3.677424 CGAAACCACTCTCATCCCTTCTC 60.677 52.174 0.00 0.00 0.00 2.87
1886 4003 2.465813 ACCACTCTCATCCCTTCTCAG 58.534 52.381 0.00 0.00 0.00 3.35
1887 4004 1.138661 CCACTCTCATCCCTTCTCAGC 59.861 57.143 0.00 0.00 0.00 4.26
1888 4005 1.829849 CACTCTCATCCCTTCTCAGCA 59.170 52.381 0.00 0.00 0.00 4.41
1890 4007 3.113824 ACTCTCATCCCTTCTCAGCAAT 58.886 45.455 0.00 0.00 0.00 3.56
1891 4008 3.118334 ACTCTCATCCCTTCTCAGCAATG 60.118 47.826 0.00 0.00 0.00 2.82
1892 4009 2.842496 TCTCATCCCTTCTCAGCAATGT 59.158 45.455 0.00 0.00 0.00 2.71
1893 4010 3.118482 TCTCATCCCTTCTCAGCAATGTC 60.118 47.826 0.00 0.00 0.00 3.06
1895 4012 1.361204 TCCCTTCTCAGCAATGTCCA 58.639 50.000 0.00 0.00 0.00 4.02
1896 4013 1.704628 TCCCTTCTCAGCAATGTCCAA 59.295 47.619 0.00 0.00 0.00 3.53
1897 4014 2.108075 TCCCTTCTCAGCAATGTCCAAA 59.892 45.455 0.00 0.00 0.00 3.28
1898 4015 2.892852 CCCTTCTCAGCAATGTCCAAAA 59.107 45.455 0.00 0.00 0.00 2.44
1939 4286 8.918658 CACCATGTTATCTTCAAAACAATCTTG 58.081 33.333 0.00 0.00 38.95 3.02
1950 4297 7.094508 TCAAAACAATCTTGAGCAACAACTA 57.905 32.000 0.00 0.00 34.56 2.24
1954 4302 7.744087 AACAATCTTGAGCAACAACTATGTA 57.256 32.000 0.00 0.00 39.40 2.29
2131 4591 9.173021 TGAAGACAAATATCCAAATCGTATGTT 57.827 29.630 0.00 0.00 0.00 2.71
2189 4650 9.809096 TCAGTAATGATCTCTAGAACATCAAAC 57.191 33.333 14.96 14.93 36.69 2.93
2370 4834 9.836076 GTTAAATTACCCAATGTTCTCTTGTAC 57.164 33.333 0.00 0.00 0.00 2.90
2414 4883 8.954950 TTTGCACCAAAATATTCTCAAAGAAA 57.045 26.923 0.00 0.00 32.42 2.52
2445 4915 4.170468 TCAAAATATCCTCCTTCAGGCC 57.830 45.455 0.00 0.00 43.08 5.19
2447 4917 4.168675 TCAAAATATCCTCCTTCAGGCCAT 59.831 41.667 5.01 0.00 43.08 4.40
2459 4929 1.990060 AGGCCATGTAGCGGTGACT 60.990 57.895 5.01 0.00 0.00 3.41
2460 4930 1.815421 GGCCATGTAGCGGTGACTG 60.815 63.158 0.00 0.00 0.00 3.51
2461 4931 1.218047 GCCATGTAGCGGTGACTGA 59.782 57.895 0.00 0.00 0.00 3.41
2462 4932 0.179073 GCCATGTAGCGGTGACTGAT 60.179 55.000 0.00 0.00 0.00 2.90
2463 4933 1.068588 GCCATGTAGCGGTGACTGATA 59.931 52.381 0.00 0.00 0.00 2.15
2464 4934 2.289072 GCCATGTAGCGGTGACTGATAT 60.289 50.000 0.00 0.00 0.00 1.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
65 67 7.972623 AAATGTGTTTGTGCATTTCAATTTG 57.027 28.000 0.00 0.00 40.10 2.32
183 185 9.206870 AGCGTTCACAAATTTTTGAATCATAAT 57.793 25.926 19.67 4.48 40.55 1.28
184 186 8.586570 AGCGTTCACAAATTTTTGAATCATAA 57.413 26.923 19.67 0.00 40.55 1.90
186 188 7.481275 AAGCGTTCACAAATTTTTGAATCAT 57.519 28.000 19.67 8.42 40.55 2.45
187 189 6.900568 AAGCGTTCACAAATTTTTGAATCA 57.099 29.167 19.67 0.00 40.55 2.57
188 190 9.862585 AAATAAGCGTTCACAAATTTTTGAATC 57.137 25.926 19.67 14.96 40.55 2.52
244 246 6.240894 TCTTCATGCAAATAGAAACTCCACT 58.759 36.000 0.00 0.00 0.00 4.00
359 363 9.197306 GAGGGAGTAATGTATTTTGGGTAAAAT 57.803 33.333 0.00 0.00 45.71 1.82
376 380 3.339713 AATATGGGTCGGAGGGAGTAA 57.660 47.619 0.00 0.00 0.00 2.24
379 383 4.041691 ACAATTAATATGGGTCGGAGGGAG 59.958 45.833 0.00 0.00 0.00 4.30
389 393 7.023575 GCTAAATCAGCGACAATTAATATGGG 58.976 38.462 0.00 0.00 41.37 4.00
432 436 6.183360 CCTCCGATCAATATCAATTGTCGATG 60.183 42.308 12.35 6.01 42.58 3.84
434 438 5.230182 CCTCCGATCAATATCAATTGTCGA 58.770 41.667 12.35 1.93 42.58 4.20
439 443 5.832539 ACTCCCTCCGATCAATATCAATT 57.167 39.130 0.00 0.00 31.93 2.32
442 446 8.609617 ATTATTACTCCCTCCGATCAATATCA 57.390 34.615 0.00 0.00 31.93 2.15
443 447 9.892130 AAATTATTACTCCCTCCGATCAATATC 57.108 33.333 0.00 0.00 0.00 1.63
448 452 6.996282 GGAAAAATTATTACTCCCTCCGATCA 59.004 38.462 0.00 0.00 0.00 2.92
565 569 5.884771 AGTGCTGTTTCTTTTCTTCAGTTC 58.115 37.500 0.00 0.00 0.00 3.01
568 572 6.610741 AGTAGTGCTGTTTCTTTTCTTCAG 57.389 37.500 0.00 0.00 0.00 3.02
569 573 6.823689 AGAAGTAGTGCTGTTTCTTTTCTTCA 59.176 34.615 0.00 0.00 32.75 3.02
609 613 4.530857 CCCACGCGCCCTCCTAAG 62.531 72.222 5.73 0.00 0.00 2.18
645 649 0.680280 GGGACAGAGGAGTGCGTCTA 60.680 60.000 0.00 0.00 37.16 2.59
686 690 1.264288 GTGCAGGTGTAGACAGCAAAC 59.736 52.381 13.85 5.48 46.03 2.93
711 715 2.506438 GCCGTACAGGTGTCGAGC 60.506 66.667 0.00 0.00 43.70 5.03
712 716 1.154016 CAGCCGTACAGGTGTCGAG 60.154 63.158 0.00 0.00 43.70 4.04
767 775 7.839680 TGTAGAAGCATCAGAACATATCCTA 57.160 36.000 0.00 0.00 0.00 2.94
826 834 1.203288 TGTCCTTGGGAAATGGCCATT 60.203 47.619 25.73 25.73 31.38 3.16
872 883 2.510238 GAGCGGCACCAGTAGCAG 60.510 66.667 1.45 0.00 0.00 4.24
885 896 3.499737 GGCGTGGGATGTTGAGCG 61.500 66.667 0.00 0.00 0.00 5.03
896 907 2.680577 GGTATTAATAGACGGGCGTGG 58.319 52.381 0.00 0.00 0.00 4.94
902 913 0.979811 CGCGCGGTATTAATAGACGG 59.020 55.000 24.84 6.60 0.00 4.79
905 916 2.715758 CGCGCGCGGTATTAATAGA 58.284 52.632 43.28 0.00 35.56 1.98
933 944 0.588252 CACAACTTGAGAACGGCAGG 59.412 55.000 0.00 0.00 0.00 4.85
938 949 1.792367 TGCGATCACAACTTGAGAACG 59.208 47.619 12.43 12.43 37.77 3.95
939 950 2.410262 CGTGCGATCACAACTTGAGAAC 60.410 50.000 0.00 0.00 43.28 3.01
958 969 1.136147 CGCTTGCGAGTACTACCGT 59.864 57.895 9.60 0.00 0.00 4.83
959 970 0.179181 TTCGCTTGCGAGTACTACCG 60.179 55.000 17.06 0.00 0.00 4.02
960 971 1.135460 ACTTCGCTTGCGAGTACTACC 60.135 52.381 17.06 0.00 0.00 3.18
961 972 2.259505 ACTTCGCTTGCGAGTACTAC 57.740 50.000 17.06 0.00 0.00 2.73
962 973 2.486982 AGAACTTCGCTTGCGAGTACTA 59.513 45.455 17.06 2.24 0.00 1.82
963 974 1.269998 AGAACTTCGCTTGCGAGTACT 59.730 47.619 17.06 12.29 0.00 2.73
985 1002 5.118286 AGTTGCCATGGTTCAAAAAGAAAG 58.882 37.500 14.67 0.00 38.13 2.62
990 1009 3.181467 CCAGAGTTGCCATGGTTCAAAAA 60.181 43.478 14.67 0.00 0.00 1.94
997 1016 2.036256 GCCCAGAGTTGCCATGGT 59.964 61.111 14.67 0.00 31.85 3.55
999 1018 3.818787 GCGCCCAGAGTTGCCATG 61.819 66.667 0.00 0.00 0.00 3.66
1054 1073 2.746277 GGCAGCAAACGTCGGGAT 60.746 61.111 0.00 0.00 0.00 3.85
1098 1117 4.680537 AGAGAGGCGGTGGGACGT 62.681 66.667 0.00 0.00 35.98 4.34
1113 1133 2.649034 GTCGTGGGTCGCTTCAGA 59.351 61.111 0.00 0.00 39.67 3.27
1170 1190 3.281751 CTTCACCTTGTGCGTCGCG 62.282 63.158 13.38 0.00 32.98 5.87
1208 1228 2.043450 CCTCCAGCTCCGTCTCCT 60.043 66.667 0.00 0.00 0.00 3.69
1465 1485 4.686554 GGCACGATTTGGTCTAGCTATAAG 59.313 45.833 0.00 0.00 0.00 1.73
1469 1489 1.828595 TGGCACGATTTGGTCTAGCTA 59.171 47.619 0.00 0.00 0.00 3.32
1470 1490 0.613260 TGGCACGATTTGGTCTAGCT 59.387 50.000 0.00 0.00 0.00 3.32
1534 1554 1.204941 CTACTCCACTACACAGCACCC 59.795 57.143 0.00 0.00 0.00 4.61
1562 3675 4.707563 CAAACAAATCATACAGCGTTCGA 58.292 39.130 0.00 0.00 0.00 3.71
1605 3718 5.339990 TGTTGAAAAGCTAGCAAAACTGAC 58.660 37.500 18.83 7.69 0.00 3.51
1647 3761 5.938125 GGCCAAACTGTCTTAGTGAAATCTA 59.062 40.000 0.00 0.00 40.26 1.98
1649 3763 4.378459 CGGCCAAACTGTCTTAGTGAAATC 60.378 45.833 2.24 0.00 40.26 2.17
1656 3770 2.069273 CACTCGGCCAAACTGTCTTAG 58.931 52.381 2.24 0.00 0.00 2.18
1657 3771 1.270625 CCACTCGGCCAAACTGTCTTA 60.271 52.381 2.24 0.00 0.00 2.10
1752 3869 3.883489 GTCAGGGTATTATCCAGGCAAAC 59.117 47.826 0.00 0.00 0.00 2.93
1763 3880 1.315690 CCGAGCTCGTCAGGGTATTA 58.684 55.000 32.41 0.00 37.74 0.98
1770 3887 1.007964 CCATAGCCGAGCTCGTCAG 60.008 63.158 32.41 19.51 40.44 3.51
1774 3891 2.336809 GACCCATAGCCGAGCTCG 59.663 66.667 29.06 29.06 40.44 5.03
1781 3898 1.832912 CAGGAGGTGACCCATAGCC 59.167 63.158 0.00 0.00 0.00 3.93
1785 3902 0.779997 AAAAGCAGGAGGTGACCCAT 59.220 50.000 0.00 0.00 0.00 4.00
1787 3904 2.808906 ATAAAAGCAGGAGGTGACCC 57.191 50.000 0.00 0.00 0.00 4.46
1788 3905 3.945921 GGTAATAAAAGCAGGAGGTGACC 59.054 47.826 0.00 0.00 0.00 4.02
1789 3906 4.844884 AGGTAATAAAAGCAGGAGGTGAC 58.155 43.478 0.00 0.00 0.00 3.67
1791 3908 4.878397 CAGAGGTAATAAAAGCAGGAGGTG 59.122 45.833 0.00 0.00 0.00 4.00
1792 3909 4.626529 GCAGAGGTAATAAAAGCAGGAGGT 60.627 45.833 0.00 0.00 0.00 3.85
1793 3910 3.879892 GCAGAGGTAATAAAAGCAGGAGG 59.120 47.826 0.00 0.00 0.00 4.30
1794 3911 3.557595 CGCAGAGGTAATAAAAGCAGGAG 59.442 47.826 0.00 0.00 0.00 3.69
1795 3912 3.531538 CGCAGAGGTAATAAAAGCAGGA 58.468 45.455 0.00 0.00 0.00 3.86
1797 3914 2.939103 AGCGCAGAGGTAATAAAAGCAG 59.061 45.455 11.47 0.00 0.00 4.24
1798 3915 2.936498 GAGCGCAGAGGTAATAAAAGCA 59.064 45.455 11.47 0.00 0.00 3.91
1799 3916 2.936498 TGAGCGCAGAGGTAATAAAAGC 59.064 45.455 11.47 0.00 0.00 3.51
1800 3917 4.391830 TGTTGAGCGCAGAGGTAATAAAAG 59.608 41.667 11.47 0.00 0.00 2.27
1801 3918 4.320023 TGTTGAGCGCAGAGGTAATAAAA 58.680 39.130 11.47 0.00 0.00 1.52
1802 3919 3.932710 CTGTTGAGCGCAGAGGTAATAAA 59.067 43.478 11.47 0.00 36.12 1.40
1803 3920 3.521560 CTGTTGAGCGCAGAGGTAATAA 58.478 45.455 11.47 0.00 36.12 1.40
1805 3922 2.009042 GCTGTTGAGCGCAGAGGTAAT 61.009 52.381 11.47 0.00 34.87 1.89
1806 3923 0.670546 GCTGTTGAGCGCAGAGGTAA 60.671 55.000 11.47 0.00 34.87 2.85
1807 3924 1.079819 GCTGTTGAGCGCAGAGGTA 60.080 57.895 11.47 0.00 34.87 3.08
1808 3925 2.358003 GCTGTTGAGCGCAGAGGT 60.358 61.111 11.47 0.00 34.87 3.85
1816 3933 0.312102 GGAAGTGTTGGCTGTTGAGC 59.688 55.000 0.00 0.00 45.40 4.26
1820 3937 0.550914 TGAGGGAAGTGTTGGCTGTT 59.449 50.000 0.00 0.00 0.00 3.16
1821 3938 0.773644 ATGAGGGAAGTGTTGGCTGT 59.226 50.000 0.00 0.00 0.00 4.40
1823 3940 1.366319 AGATGAGGGAAGTGTTGGCT 58.634 50.000 0.00 0.00 0.00 4.75
1826 3943 4.320494 CCGAAAAAGATGAGGGAAGTGTTG 60.320 45.833 0.00 0.00 0.00 3.33
1827 3944 3.821033 CCGAAAAAGATGAGGGAAGTGTT 59.179 43.478 0.00 0.00 0.00 3.32
1828 3945 3.072476 TCCGAAAAAGATGAGGGAAGTGT 59.928 43.478 0.00 0.00 0.00 3.55
1829 3946 3.674997 TCCGAAAAAGATGAGGGAAGTG 58.325 45.455 0.00 0.00 0.00 3.16
1830 3947 4.019321 TGATCCGAAAAAGATGAGGGAAGT 60.019 41.667 0.00 0.00 0.00 3.01
1831 3948 4.517285 TGATCCGAAAAAGATGAGGGAAG 58.483 43.478 0.00 0.00 0.00 3.46
1833 3950 4.080356 ACATGATCCGAAAAAGATGAGGGA 60.080 41.667 0.00 0.00 0.00 4.20
1834 3951 4.202441 ACATGATCCGAAAAAGATGAGGG 58.798 43.478 0.00 0.00 0.00 4.30
1836 3953 6.563567 CGATGACATGATCCGAAAAAGATGAG 60.564 42.308 0.00 0.00 0.00 2.90
1841 3958 3.611517 GCGATGACATGATCCGAAAAAG 58.388 45.455 0.00 0.00 0.00 2.27
1844 3961 1.202359 TCGCGATGACATGATCCGAAA 60.202 47.619 3.71 0.00 0.00 3.46
1846 3963 0.383949 TTCGCGATGACATGATCCGA 59.616 50.000 10.88 2.15 0.00 4.55
1847 3964 1.071239 GTTTCGCGATGACATGATCCG 60.071 52.381 10.88 0.00 0.00 4.18
1848 3965 1.261619 GGTTTCGCGATGACATGATCC 59.738 52.381 10.88 0.00 0.00 3.36
1851 3968 1.075542 GTGGTTTCGCGATGACATGA 58.924 50.000 10.88 0.00 0.00 3.07
1852 3969 1.061131 GAGTGGTTTCGCGATGACATG 59.939 52.381 10.88 0.00 0.00 3.21
1853 3970 1.066858 AGAGTGGTTTCGCGATGACAT 60.067 47.619 10.88 2.19 0.00 3.06
1854 3971 0.317160 AGAGTGGTTTCGCGATGACA 59.683 50.000 10.88 6.31 0.00 3.58
1855 3972 0.992802 GAGAGTGGTTTCGCGATGAC 59.007 55.000 10.88 12.26 0.00 3.06
1856 3973 0.601057 TGAGAGTGGTTTCGCGATGA 59.399 50.000 10.88 0.00 0.00 2.92
1858 3975 1.471676 GGATGAGAGTGGTTTCGCGAT 60.472 52.381 10.88 0.00 0.00 4.58
1861 3978 0.250513 AGGGATGAGAGTGGTTTCGC 59.749 55.000 0.00 0.00 0.00 4.70
1862 3979 2.234908 AGAAGGGATGAGAGTGGTTTCG 59.765 50.000 0.00 0.00 0.00 3.46
1863 3980 3.261897 TGAGAAGGGATGAGAGTGGTTTC 59.738 47.826 0.00 0.00 0.00 2.78
1864 3981 3.251484 TGAGAAGGGATGAGAGTGGTTT 58.749 45.455 0.00 0.00 0.00 3.27
1865 3982 2.836981 CTGAGAAGGGATGAGAGTGGTT 59.163 50.000 0.00 0.00 0.00 3.67
1866 3983 2.465813 CTGAGAAGGGATGAGAGTGGT 58.534 52.381 0.00 0.00 0.00 4.16
1867 3984 1.138661 GCTGAGAAGGGATGAGAGTGG 59.861 57.143 0.00 0.00 0.00 4.00
1869 3986 2.244486 TGCTGAGAAGGGATGAGAGT 57.756 50.000 0.00 0.00 0.00 3.24
1871 3988 2.842496 ACATTGCTGAGAAGGGATGAGA 59.158 45.455 0.00 0.00 0.00 3.27
1872 3989 3.204526 GACATTGCTGAGAAGGGATGAG 58.795 50.000 0.00 0.00 0.00 2.90
1873 3990 2.092753 GGACATTGCTGAGAAGGGATGA 60.093 50.000 0.00 0.00 0.00 2.92
1874 3991 2.295885 GGACATTGCTGAGAAGGGATG 58.704 52.381 0.00 0.00 0.00 3.51
1877 3994 2.205022 TTGGACATTGCTGAGAAGGG 57.795 50.000 0.00 0.00 0.00 3.95
1878 3995 4.589216 TTTTTGGACATTGCTGAGAAGG 57.411 40.909 0.00 0.00 0.00 3.46
1900 4017 7.844009 AGATAACATGGTGCTTTCATGATTTT 58.156 30.769 16.97 7.38 43.25 1.82
1901 4018 7.414222 AGATAACATGGTGCTTTCATGATTT 57.586 32.000 16.97 7.89 43.25 2.17
1903 4020 6.604396 TGAAGATAACATGGTGCTTTCATGAT 59.396 34.615 16.97 10.35 43.25 2.45
1904 4021 5.945191 TGAAGATAACATGGTGCTTTCATGA 59.055 36.000 16.97 0.00 43.25 3.07
1939 4286 7.367285 TGTTTGGAAATACATAGTTGTTGCTC 58.633 34.615 0.00 0.00 37.28 4.26
1996 4344 6.650427 ACCTTGGGAAATTTGACTAGAAAC 57.350 37.500 0.00 0.00 0.00 2.78
2303 4767 8.976353 TGCAGTACATAATAAATTGGATGGTTT 58.024 29.630 0.00 0.00 0.00 3.27
2370 4834 7.693536 GGTGCAAAGAACATTTTGAAGAAAAAG 59.306 33.333 0.00 0.00 41.00 2.27
2418 4887 8.302438 GCCTGAAGGAGGATATTTTGATTTATG 58.698 37.037 0.00 0.00 46.33 1.90
2419 4888 7.452813 GGCCTGAAGGAGGATATTTTGATTTAT 59.547 37.037 0.00 0.00 46.33 1.40
2420 4889 6.777580 GGCCTGAAGGAGGATATTTTGATTTA 59.222 38.462 0.00 0.00 46.33 1.40
2428 4898 3.059097 ACATGGCCTGAAGGAGGATATT 58.941 45.455 3.32 0.00 46.33 1.28


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

AutoCloner maintained by Alex Coulton.