Multiple sequence alignment - TraesCS2A01G519200

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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 TraesCS2A01G519200 chr2A 100.000 2258 0 0 1 2258 742575097 742577354 0.000000e+00 4170
1 TraesCS2A01G519200 chr2A 86.268 903 97 8 725 1620 752003367 752004249 0.000000e+00 955
2 TraesCS2A01G519200 chr2A 87.436 589 59 8 1672 2258 742693707 742693132 0.000000e+00 664
3 TraesCS2A01G519200 chr6D 90.208 960 57 20 687 1621 293060271 293059324 0.000000e+00 1218
4 TraesCS2A01G519200 chr6D 86.525 282 32 2 573 854 293060460 293060185 2.820000e-79 305
5 TraesCS2A01G519200 chr5D 89.884 949 68 17 682 1620 557175318 557174388 0.000000e+00 1195
6 TraesCS2A01G519200 chr5D 86.667 285 29 6 573 854 313382978 313382700 7.830000e-80 307
7 TraesCS2A01G519200 chr2D 89.572 959 60 22 687 1620 641205427 641204484 0.000000e+00 1181
8 TraesCS2A01G519200 chr2D 96.354 576 18 3 1 573 621419114 621418539 0.000000e+00 944
9 TraesCS2A01G519200 chr2D 85.934 455 49 7 1805 2258 609664556 609664116 2.630000e-129 472
10 TraesCS2A01G519200 chr2D 84.878 410 48 8 1848 2255 609551355 609551752 3.490000e-108 401
11 TraesCS2A01G519200 chr7B 88.562 953 75 18 687 1620 315601409 315600472 0.000000e+00 1125
12 TraesCS2A01G519200 chr7B 85.512 283 34 4 573 854 315290883 315290607 2.840000e-74 289
13 TraesCS2A01G519200 chr7A 86.902 962 88 21 683 1620 699322293 699321346 0.000000e+00 1044
14 TraesCS2A01G519200 chr7A 97.217 575 13 3 1 573 73625974 73625401 0.000000e+00 970
15 TraesCS2A01G519200 chr7A 96.348 575 19 2 1 573 653108265 653108839 0.000000e+00 944
16 TraesCS2A01G519200 chr2B 86.819 918 96 11 711 1620 364337367 364336467 0.000000e+00 1002
17 TraesCS2A01G519200 chr2B 86.857 875 90 14 764 1619 42194150 42195018 0.000000e+00 955
18 TraesCS2A01G519200 chr2B 86.102 921 78 18 725 1620 649656743 649655848 0.000000e+00 946
19 TraesCS2A01G519200 chr2B 86.971 591 63 7 1669 2258 744116483 744115906 0.000000e+00 652
20 TraesCS2A01G519200 chr2B 86.091 417 44 7 1842 2258 744089701 744089299 9.580000e-119 436
21 TraesCS2A01G519200 chr5B 86.952 889 88 8 740 1620 433001756 433000888 0.000000e+00 974
22 TraesCS2A01G519200 chr5B 85.348 976 100 19 674 1620 297111155 297112116 0.000000e+00 970
23 TraesCS2A01G519200 chr5B 86.727 889 90 8 740 1620 351468859 351467991 0.000000e+00 963
24 TraesCS2A01G519200 chr5B 87.737 791 70 11 855 1620 35438901 35439689 0.000000e+00 898
25 TraesCS2A01G519200 chr5B 86.525 282 32 2 573 854 491840460 491840185 2.820000e-79 305
26 TraesCS2A01G519200 chr5B 87.898 157 16 2 573 729 565842292 565842445 4.950000e-42 182
27 TraesCS2A01G519200 chr6A 97.213 574 15 1 1 573 436828667 436828094 0.000000e+00 970
28 TraesCS2A01G519200 chr6A 96.880 577 14 3 1 573 476985201 476985777 0.000000e+00 963
29 TraesCS2A01G519200 chr6A 96.875 576 14 4 1 573 545354159 545354733 0.000000e+00 961
30 TraesCS2A01G519200 chr6A 96.696 575 17 2 1 573 561940409 561939835 0.000000e+00 955
31 TraesCS2A01G519200 chr6A 96.034 580 20 2 1 579 56568983 56568406 0.000000e+00 941
32 TraesCS2A01G519200 chr5A 86.283 904 96 8 725 1620 300955658 300956541 0.000000e+00 957
33 TraesCS2A01G519200 chr3A 96.522 575 16 3 1 573 650955966 650955394 0.000000e+00 948
34 TraesCS2A01G519200 chr3A 84.397 282 29 10 573 854 145558492 145558226 1.720000e-66 263
35 TraesCS2A01G519200 chr4B 79.982 1099 135 39 574 1620 653623664 653624729 0.000000e+00 732
36 TraesCS2A01G519200 chrUn 87.215 571 51 9 711 1274 441532634 441533189 4.090000e-177 630
37 TraesCS2A01G519200 chr1A 91.943 422 34 0 674 1095 432261938 432262359 1.930000e-165 592
38 TraesCS2A01G519200 chr3D 94.540 348 16 2 669 1016 549428220 549428564 3.300000e-148 534
39 TraesCS2A01G519200 chr3D 94.526 274 12 2 571 844 549428083 549428353 9.640000e-114 420


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 TraesCS2A01G519200 chr2A 742575097 742577354 2257 False 4170.0 4170 100.0000 1 2258 1 chr2A.!!$F1 2257
1 TraesCS2A01G519200 chr2A 752003367 752004249 882 False 955.0 955 86.2680 725 1620 1 chr2A.!!$F2 895
2 TraesCS2A01G519200 chr2A 742693132 742693707 575 True 664.0 664 87.4360 1672 2258 1 chr2A.!!$R1 586
3 TraesCS2A01G519200 chr6D 293059324 293060460 1136 True 761.5 1218 88.3665 573 1621 2 chr6D.!!$R1 1048
4 TraesCS2A01G519200 chr5D 557174388 557175318 930 True 1195.0 1195 89.8840 682 1620 1 chr5D.!!$R2 938
5 TraesCS2A01G519200 chr2D 641204484 641205427 943 True 1181.0 1181 89.5720 687 1620 1 chr2D.!!$R3 933
6 TraesCS2A01G519200 chr2D 621418539 621419114 575 True 944.0 944 96.3540 1 573 1 chr2D.!!$R2 572
7 TraesCS2A01G519200 chr7B 315600472 315601409 937 True 1125.0 1125 88.5620 687 1620 1 chr7B.!!$R2 933
8 TraesCS2A01G519200 chr7A 699321346 699322293 947 True 1044.0 1044 86.9020 683 1620 1 chr7A.!!$R2 937
9 TraesCS2A01G519200 chr7A 73625401 73625974 573 True 970.0 970 97.2170 1 573 1 chr7A.!!$R1 572
10 TraesCS2A01G519200 chr7A 653108265 653108839 574 False 944.0 944 96.3480 1 573 1 chr7A.!!$F1 572
11 TraesCS2A01G519200 chr2B 364336467 364337367 900 True 1002.0 1002 86.8190 711 1620 1 chr2B.!!$R1 909
12 TraesCS2A01G519200 chr2B 42194150 42195018 868 False 955.0 955 86.8570 764 1619 1 chr2B.!!$F1 855
13 TraesCS2A01G519200 chr2B 649655848 649656743 895 True 946.0 946 86.1020 725 1620 1 chr2B.!!$R2 895
14 TraesCS2A01G519200 chr2B 744115906 744116483 577 True 652.0 652 86.9710 1669 2258 1 chr2B.!!$R4 589
15 TraesCS2A01G519200 chr5B 433000888 433001756 868 True 974.0 974 86.9520 740 1620 1 chr5B.!!$R2 880
16 TraesCS2A01G519200 chr5B 297111155 297112116 961 False 970.0 970 85.3480 674 1620 1 chr5B.!!$F2 946
17 TraesCS2A01G519200 chr5B 351467991 351468859 868 True 963.0 963 86.7270 740 1620 1 chr5B.!!$R1 880
18 TraesCS2A01G519200 chr5B 35438901 35439689 788 False 898.0 898 87.7370 855 1620 1 chr5B.!!$F1 765
19 TraesCS2A01G519200 chr6A 436828094 436828667 573 True 970.0 970 97.2130 1 573 1 chr6A.!!$R2 572
20 TraesCS2A01G519200 chr6A 476985201 476985777 576 False 963.0 963 96.8800 1 573 1 chr6A.!!$F1 572
21 TraesCS2A01G519200 chr6A 545354159 545354733 574 False 961.0 961 96.8750 1 573 1 chr6A.!!$F2 572
22 TraesCS2A01G519200 chr6A 561939835 561940409 574 True 955.0 955 96.6960 1 573 1 chr6A.!!$R3 572
23 TraesCS2A01G519200 chr6A 56568406 56568983 577 True 941.0 941 96.0340 1 579 1 chr6A.!!$R1 578
24 TraesCS2A01G519200 chr5A 300955658 300956541 883 False 957.0 957 86.2830 725 1620 1 chr5A.!!$F1 895
25 TraesCS2A01G519200 chr3A 650955394 650955966 572 True 948.0 948 96.5220 1 573 1 chr3A.!!$R2 572
26 TraesCS2A01G519200 chr4B 653623664 653624729 1065 False 732.0 732 79.9820 574 1620 1 chr4B.!!$F1 1046
27 TraesCS2A01G519200 chrUn 441532634 441533189 555 False 630.0 630 87.2150 711 1274 1 chrUn.!!$F1 563

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
887 1049 0.321741 TCGGCCTTCGGTTATTTGCA 60.322 50.0 0.0 0.0 39.77 4.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1996 2217 0.31179 ACCATGCTTTGTTCGCACTG 59.688 50.0 0.0 0.0 40.65 3.66 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
23 24 2.834549 GGAGGTGGAGAGAATGAAGTGA 59.165 50.000 0.00 0.00 0.00 3.41
122 123 5.415701 CCTAAATGCGCCATTAGTAATCCAT 59.584 40.000 20.98 0.00 32.43 3.41
397 408 1.019278 ACTATGTTTGGACAGGCGCG 61.019 55.000 0.00 0.00 39.58 6.86
406 417 1.519455 GACAGGCGCGCTAGTCAAT 60.519 57.895 34.47 16.60 0.00 2.57
488 500 0.821517 TGGCGTATCAGTAGGTGGTG 59.178 55.000 0.00 0.00 0.00 4.17
490 502 3.251817 CGTATCAGTAGGTGGTGCG 57.748 57.895 0.00 0.00 39.12 5.34
588 600 4.973168 AGTAGTGGACATGCAAGAAAAGA 58.027 39.130 0.00 0.00 0.00 2.52
594 606 5.812127 GTGGACATGCAAGAAAAGAAAAACT 59.188 36.000 0.00 0.00 0.00 2.66
597 609 6.534793 GGACATGCAAGAAAAGAAAAACTTCA 59.465 34.615 0.00 0.00 37.93 3.02
638 650 3.444388 ACTAGCCGTAGAGGAAAGACAAG 59.556 47.826 0.00 0.00 45.00 3.16
664 676 2.358737 GTGGCTCCGGTGGTGAAG 60.359 66.667 0.00 0.00 0.00 3.02
680 731 1.132849 TGAAGGAGGTGGAAGAGGTGA 60.133 52.381 0.00 0.00 0.00 4.02
690 744 0.678048 GAAGAGGTGATGGTGGTGGC 60.678 60.000 0.00 0.00 0.00 5.01
695 749 1.743995 GTGATGGTGGTGGCCGTAC 60.744 63.158 0.00 0.00 0.00 3.67
707 761 1.574702 GGCCGTACAGGAAGCACAAC 61.575 60.000 7.77 0.00 45.00 3.32
709 763 1.337447 GCCGTACAGGAAGCACAACTA 60.337 52.381 7.77 0.00 45.00 2.24
710 764 2.607187 CCGTACAGGAAGCACAACTAG 58.393 52.381 0.00 0.00 45.00 2.57
729 810 2.221299 TAGAGGTGGTGGTGGTGGC 61.221 63.158 0.00 0.00 0.00 5.01
730 811 2.689573 TAGAGGTGGTGGTGGTGGCT 62.690 60.000 0.00 0.00 0.00 4.75
733 814 2.824880 GGTGGTGGTGGTGGCTGTA 61.825 63.158 0.00 0.00 0.00 2.74
737 818 1.296715 GTGGTGGTGGCTGTAGAGG 59.703 63.158 0.00 0.00 0.00 3.69
760 841 1.800805 CACAAGTGCTAGAGGTGGTG 58.199 55.000 0.00 0.00 0.00 4.17
766 847 0.766674 TGCTAGAGGTGGTGGTGGTT 60.767 55.000 0.00 0.00 0.00 3.67
812 968 0.457337 GGTGATGGTCGTGGTCGTAC 60.457 60.000 0.00 0.00 38.33 3.67
841 1003 0.977395 AAGTGCTAGAGGTGGTGGTC 59.023 55.000 0.00 0.00 0.00 4.02
887 1049 0.321741 TCGGCCTTCGGTTATTTGCA 60.322 50.000 0.00 0.00 39.77 4.08
893 1055 4.278419 GGCCTTCGGTTATTTGCATAATCT 59.722 41.667 0.00 0.00 0.00 2.40
977 1175 8.359060 TGTTTACTTTGTTCATGTATTTTGCC 57.641 30.769 0.00 0.00 0.00 4.52
1067 1266 1.078759 GACATGCCGAAGACGTGGAG 61.079 60.000 0.00 0.00 37.88 3.86
1068 1267 1.079819 CATGCCGAAGACGTGGAGT 60.080 57.895 0.00 0.00 37.88 3.85
1103 1309 1.075601 AAGGAGAAGGATGTGCCCAA 58.924 50.000 0.00 0.00 37.37 4.12
1231 1437 1.666553 CGTGCTCGGCCAACTAACA 60.667 57.895 2.24 0.00 0.00 2.41
1413 1621 1.390463 GACCAACGTCGAGATTGCTTC 59.610 52.381 0.00 0.00 0.00 3.86
1448 1656 0.756294 TTCGAGGAGTCCTTTGCACA 59.244 50.000 14.41 0.00 31.76 4.57
1526 1734 2.264455 AGAGAGGGCACACAAAGAGAT 58.736 47.619 0.00 0.00 0.00 2.75
1527 1735 2.641815 AGAGAGGGCACACAAAGAGATT 59.358 45.455 0.00 0.00 0.00 2.40
1545 1753 5.045724 AGAGATTGAGGCTTGTCAAGAAGAT 60.046 40.000 16.99 2.47 39.78 2.40
1549 1757 4.096681 TGAGGCTTGTCAAGAAGATAGGA 58.903 43.478 16.99 0.00 0.00 2.94
1593 1813 0.043183 TGCCCAAGAGGAGGATGAGA 59.957 55.000 0.00 0.00 38.24 3.27
1625 1845 3.283020 GGGAAAGTGGCCCTAAAGG 57.717 57.895 0.00 0.00 42.56 3.11
1626 1846 0.702316 GGGAAAGTGGCCCTAAAGGA 59.298 55.000 0.00 0.00 42.56 3.36
1627 1847 1.288037 GGGAAAGTGGCCCTAAAGGAT 59.712 52.381 0.00 0.00 42.56 3.24
1628 1848 2.292257 GGGAAAGTGGCCCTAAAGGATT 60.292 50.000 0.00 0.00 42.56 3.01
1629 1849 2.760650 GGAAAGTGGCCCTAAAGGATTG 59.239 50.000 0.00 0.00 38.24 2.67
1630 1850 2.532250 AAGTGGCCCTAAAGGATTGG 57.468 50.000 0.00 0.00 38.24 3.16
1631 1851 1.382914 AGTGGCCCTAAAGGATTGGT 58.617 50.000 0.00 0.00 38.24 3.67
1632 1852 1.285078 AGTGGCCCTAAAGGATTGGTC 59.715 52.381 0.00 0.00 38.24 4.02
1633 1853 0.629058 TGGCCCTAAAGGATTGGTCC 59.371 55.000 0.00 0.00 45.45 4.46
1646 1866 5.304686 GGATTGGTCCATGTTGGTATAGA 57.695 43.478 0.00 0.00 44.42 1.98
1647 1867 5.308825 GGATTGGTCCATGTTGGTATAGAG 58.691 45.833 0.00 0.00 44.42 2.43
1648 1868 5.071788 GGATTGGTCCATGTTGGTATAGAGA 59.928 44.000 0.00 0.00 44.42 3.10
1649 1869 6.409234 GGATTGGTCCATGTTGGTATAGAGAA 60.409 42.308 0.00 0.00 44.42 2.87
1650 1870 5.614324 TGGTCCATGTTGGTATAGAGAAG 57.386 43.478 0.00 0.00 39.03 2.85
1651 1871 5.277250 TGGTCCATGTTGGTATAGAGAAGA 58.723 41.667 0.00 0.00 39.03 2.87
1652 1872 5.363868 TGGTCCATGTTGGTATAGAGAAGAG 59.636 44.000 0.00 0.00 39.03 2.85
1653 1873 5.364157 GGTCCATGTTGGTATAGAGAAGAGT 59.636 44.000 0.00 0.00 39.03 3.24
1654 1874 6.127026 GGTCCATGTTGGTATAGAGAAGAGTT 60.127 42.308 0.00 0.00 39.03 3.01
1655 1875 7.331791 GTCCATGTTGGTATAGAGAAGAGTTT 58.668 38.462 0.00 0.00 39.03 2.66
1656 1876 7.278868 GTCCATGTTGGTATAGAGAAGAGTTTG 59.721 40.741 0.00 0.00 39.03 2.93
1657 1877 6.037610 CCATGTTGGTATAGAGAAGAGTTTGC 59.962 42.308 0.00 0.00 31.35 3.68
1658 1878 6.109156 TGTTGGTATAGAGAAGAGTTTGCA 57.891 37.500 0.00 0.00 0.00 4.08
1659 1879 6.711277 TGTTGGTATAGAGAAGAGTTTGCAT 58.289 36.000 0.00 0.00 0.00 3.96
1660 1880 7.168219 TGTTGGTATAGAGAAGAGTTTGCATT 58.832 34.615 0.00 0.00 0.00 3.56
1661 1881 7.119699 TGTTGGTATAGAGAAGAGTTTGCATTG 59.880 37.037 0.00 0.00 0.00 2.82
1662 1882 6.946340 TGGTATAGAGAAGAGTTTGCATTGA 58.054 36.000 0.00 0.00 0.00 2.57
1663 1883 7.568349 TGGTATAGAGAAGAGTTTGCATTGAT 58.432 34.615 0.00 0.00 0.00 2.57
1664 1884 7.496920 TGGTATAGAGAAGAGTTTGCATTGATG 59.503 37.037 0.00 0.00 0.00 3.07
1695 1915 9.178758 GGTTTGTTATTTGGAGAGAAGACATAT 57.821 33.333 0.00 0.00 0.00 1.78
1803 2024 9.691362 TTTTTGAGGATAGCAAATGAGTTTAAC 57.309 29.630 0.00 0.00 35.41 2.01
1821 2042 9.547753 GAGTTTAACTAATCTATTGGAGATGCA 57.452 33.333 0.00 0.00 44.68 3.96
1866 2087 8.951787 ACAACACTTTGTTATTGTAGTCAGTA 57.048 30.769 0.00 0.00 43.89 2.74
1867 2088 9.555727 ACAACACTTTGTTATTGTAGTCAGTAT 57.444 29.630 0.00 0.00 43.89 2.12
1895 2116 1.544691 GAGGAGGTCGTTAGTCAAGCA 59.455 52.381 0.00 0.00 0.00 3.91
1896 2117 1.272769 AGGAGGTCGTTAGTCAAGCAC 59.727 52.381 0.00 0.00 0.00 4.40
1902 2123 3.529085 GTCGTTAGTCAAGCACGTTTTC 58.471 45.455 0.00 0.00 35.40 2.29
1910 2131 3.848019 GTCAAGCACGTTTTCTATGCATG 59.152 43.478 10.16 0.00 41.97 4.06
1920 2141 1.926561 TCTATGCATGTGTCTGTCGC 58.073 50.000 10.16 0.00 0.00 5.19
1923 2144 4.489795 GCATGTGTCTGTCGCGCG 62.490 66.667 26.76 26.76 0.00 6.86
1980 2201 2.439507 AGGAGGCACAAGAGAAGTTGAA 59.560 45.455 0.00 0.00 0.00 2.69
1983 2204 3.620488 AGGCACAAGAGAAGTTGAAACA 58.380 40.909 0.00 0.00 0.00 2.83
1990 2211 4.519906 AGAGAAGTTGAAACAAGGGGAA 57.480 40.909 0.00 0.00 0.00 3.97
1991 2212 4.464947 AGAGAAGTTGAAACAAGGGGAAG 58.535 43.478 0.00 0.00 0.00 3.46
1992 2213 2.959030 AGAAGTTGAAACAAGGGGAAGC 59.041 45.455 0.00 0.00 0.00 3.86
1993 2214 1.704641 AGTTGAAACAAGGGGAAGCC 58.295 50.000 0.00 0.00 0.00 4.35
1994 2215 1.063266 AGTTGAAACAAGGGGAAGCCA 60.063 47.619 0.00 0.00 0.00 4.75
1995 2216 1.970640 GTTGAAACAAGGGGAAGCCAT 59.029 47.619 0.00 0.00 0.00 4.40
1996 2217 1.923356 TGAAACAAGGGGAAGCCATC 58.077 50.000 0.00 0.00 0.00 3.51
1997 2218 1.146774 TGAAACAAGGGGAAGCCATCA 59.853 47.619 0.00 0.00 0.00 3.07
1998 2219 1.821136 GAAACAAGGGGAAGCCATCAG 59.179 52.381 0.00 0.00 0.00 2.90
1999 2220 0.779997 AACAAGGGGAAGCCATCAGT 59.220 50.000 0.00 0.00 0.00 3.41
2000 2221 0.038744 ACAAGGGGAAGCCATCAGTG 59.961 55.000 0.00 0.00 0.00 3.66
2001 2222 1.000396 AAGGGGAAGCCATCAGTGC 60.000 57.895 0.00 0.00 0.00 4.40
2002 2223 2.825836 GGGGAAGCCATCAGTGCG 60.826 66.667 0.00 0.00 0.00 5.34
2003 2224 2.268920 GGGAAGCCATCAGTGCGA 59.731 61.111 0.00 0.00 0.00 5.10
2004 2225 1.377202 GGGAAGCCATCAGTGCGAA 60.377 57.895 0.00 0.00 0.00 4.70
2005 2226 1.648467 GGGAAGCCATCAGTGCGAAC 61.648 60.000 0.00 0.00 0.00 3.95
2006 2227 0.955428 GGAAGCCATCAGTGCGAACA 60.955 55.000 0.00 0.00 0.00 3.18
2007 2228 0.874390 GAAGCCATCAGTGCGAACAA 59.126 50.000 0.00 0.00 0.00 2.83
2008 2229 1.266718 GAAGCCATCAGTGCGAACAAA 59.733 47.619 0.00 0.00 0.00 2.83
2030 2251 3.117169 AGCATGGTGGCCTTAATGGAATA 60.117 43.478 3.32 0.00 38.35 1.75
2047 2268 6.566079 TGGAATAGTCATGATCCAAGACTT 57.434 37.500 12.42 1.60 38.97 3.01
2097 2318 3.051650 AGGGGAACAAAACTTTAGGGGTT 60.052 43.478 0.00 0.00 0.00 4.11
2115 2336 1.339929 GTTTCAAGGTGGTGCGGATTT 59.660 47.619 0.00 0.00 0.00 2.17
2116 2337 1.698506 TTCAAGGTGGTGCGGATTTT 58.301 45.000 0.00 0.00 0.00 1.82
2117 2338 1.698506 TCAAGGTGGTGCGGATTTTT 58.301 45.000 0.00 0.00 0.00 1.94
2122 2343 1.202475 GGTGGTGCGGATTTTTGTTGT 60.202 47.619 0.00 0.00 0.00 3.32
2125 2346 1.002251 GGTGCGGATTTTTGTTGTCGA 60.002 47.619 0.00 0.00 0.00 4.20
2137 2359 0.108804 GTTGTCGAGAAGGGCATCGA 60.109 55.000 0.00 0.00 45.06 3.59
2143 2365 1.153086 AGAAGGGCATCGATGGTGC 60.153 57.895 26.00 14.07 41.78 5.01
2159 2381 3.707316 TGGTGCAAAATAGGCAAGGTAT 58.293 40.909 0.00 0.00 43.91 2.73
2193 2415 4.321750 CGACACTAACAGTAGGAACACCAT 60.322 45.833 0.00 0.00 0.00 3.55
2208 2430 0.998928 ACCATGACTACAATGGGCCA 59.001 50.000 9.61 9.61 39.68 5.36
2210 2432 2.233271 CCATGACTACAATGGGCCATC 58.767 52.381 21.48 7.63 0.00 3.51
2222 2444 4.052518 GCCATCTGTGCTGGGGGT 62.053 66.667 0.00 0.00 34.16 4.95
2240 2462 1.601914 GGTTTGCGTCAACCAATGGTC 60.602 52.381 4.95 0.00 33.12 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 1.807814 ACCCACACTCACTTTCTCCT 58.192 50.000 0.00 0.00 0.00 3.69
122 123 1.406341 GGAGGTGCGCCATTAGTAACA 60.406 52.381 20.59 0.00 37.19 2.41
529 541 4.836825 AGATGGGATTGATACTAATGGCG 58.163 43.478 0.00 0.00 0.00 5.69
664 676 0.543749 CCATCACCTCTTCCACCTCC 59.456 60.000 0.00 0.00 0.00 4.30
680 731 2.668632 CTGTACGGCCACCACCAT 59.331 61.111 2.24 0.00 0.00 3.55
690 744 2.029290 ACTAGTTGTGCTTCCTGTACGG 60.029 50.000 0.00 0.00 33.83 4.02
695 749 3.511934 ACCTCTACTAGTTGTGCTTCCTG 59.488 47.826 0.00 0.00 0.00 3.86
707 761 1.825474 CACCACCACCACCTCTACTAG 59.175 57.143 0.00 0.00 0.00 2.57
709 763 0.836400 CCACCACCACCACCTCTACT 60.836 60.000 0.00 0.00 0.00 2.57
710 764 1.677552 CCACCACCACCACCTCTAC 59.322 63.158 0.00 0.00 0.00 2.59
719 800 1.192146 TCCTCTACAGCCACCACCAC 61.192 60.000 0.00 0.00 0.00 4.16
721 802 0.250513 CTTCCTCTACAGCCACCACC 59.749 60.000 0.00 0.00 0.00 4.61
723 804 0.835971 TGCTTCCTCTACAGCCACCA 60.836 55.000 0.00 0.00 34.91 4.17
729 810 2.072298 GCACTTGTGCTTCCTCTACAG 58.928 52.381 17.36 0.00 0.00 2.74
730 811 1.694150 AGCACTTGTGCTTCCTCTACA 59.306 47.619 20.95 0.00 43.52 2.74
733 814 2.233431 CTCTAGCACTTGTGCTTCCTCT 59.767 50.000 29.37 10.28 43.52 3.69
737 818 2.072298 CACCTCTAGCACTTGTGCTTC 58.928 52.381 29.37 1.49 43.52 3.86
754 835 0.601841 CTACGACAACCACCACCACC 60.602 60.000 0.00 0.00 0.00 4.61
755 836 0.390124 TCTACGACAACCACCACCAC 59.610 55.000 0.00 0.00 0.00 4.16
756 837 0.677288 CTCTACGACAACCACCACCA 59.323 55.000 0.00 0.00 0.00 4.17
757 838 0.037605 CCTCTACGACAACCACCACC 60.038 60.000 0.00 0.00 0.00 4.61
758 839 0.963962 TCCTCTACGACAACCACCAC 59.036 55.000 0.00 0.00 0.00 4.16
759 840 1.616865 CTTCCTCTACGACAACCACCA 59.383 52.381 0.00 0.00 0.00 4.17
760 841 1.672145 GCTTCCTCTACGACAACCACC 60.672 57.143 0.00 0.00 0.00 4.61
766 847 1.961394 ACTTGTGCTTCCTCTACGACA 59.039 47.619 0.00 0.00 0.00 4.35
795 876 0.524414 CTGTACGACCACGACCATCA 59.476 55.000 0.00 0.00 42.66 3.07
796 877 0.179145 CCTGTACGACCACGACCATC 60.179 60.000 0.00 0.00 42.66 3.51
797 878 0.609957 TCCTGTACGACCACGACCAT 60.610 55.000 0.00 0.00 42.66 3.55
812 968 2.344950 CTCTAGCACTTGTGCTTCCTG 58.655 52.381 29.37 17.96 43.52 3.86
841 1003 2.933495 TCAACCATTCCTCTACGACG 57.067 50.000 0.00 0.00 0.00 5.12
970 1167 6.602803 ACAAGAGGAAAAATTGTTGGCAAAAT 59.397 30.769 0.00 1.68 38.21 1.82
1067 1266 0.890996 CTTGTCCAACCTGGCCTCAC 60.891 60.000 3.32 0.00 37.47 3.51
1068 1267 1.455849 CTTGTCCAACCTGGCCTCA 59.544 57.895 3.32 0.00 37.47 3.86
1231 1437 2.170012 ACCGGTGGTAGGTCATATGT 57.830 50.000 6.12 0.00 37.44 2.29
1361 1569 5.421056 ACATCTTTTGGTACCTCGTGATCTA 59.579 40.000 14.36 0.00 0.00 1.98
1362 1570 4.223032 ACATCTTTTGGTACCTCGTGATCT 59.777 41.667 14.36 0.00 0.00 2.75
1423 1631 0.832135 AAGGACTCCTCGAACAGGCA 60.832 55.000 0.00 0.00 43.08 4.75
1448 1656 3.483869 GCTCCCGCTCCAATCCCT 61.484 66.667 0.00 0.00 0.00 4.20
1526 1734 4.532126 TCCTATCTTCTTGACAAGCCTCAA 59.468 41.667 10.50 0.00 0.00 3.02
1527 1735 4.081420 GTCCTATCTTCTTGACAAGCCTCA 60.081 45.833 10.50 0.00 0.00 3.86
1545 1753 3.486383 CCCTTGCAAGTTTCTTGTCCTA 58.514 45.455 24.35 0.00 0.00 2.94
1549 1757 1.683385 GAGCCCTTGCAAGTTTCTTGT 59.317 47.619 24.35 2.36 41.13 3.16
1577 1786 1.135915 CGTGTCTCATCCTCCTCTTGG 59.864 57.143 0.00 0.00 0.00 3.61
1593 1813 2.093128 ACTTTCCCTTCTTGTCACGTGT 60.093 45.455 16.51 0.00 0.00 4.49
1621 1841 3.258722 ACCAACATGGACCAATCCTTT 57.741 42.857 0.00 0.00 46.43 3.11
1622 1842 2.999185 ACCAACATGGACCAATCCTT 57.001 45.000 0.00 0.00 46.43 3.36
1623 1843 4.975147 TCTATACCAACATGGACCAATCCT 59.025 41.667 0.00 0.00 46.43 3.24
1624 1844 5.071788 TCTCTATACCAACATGGACCAATCC 59.928 44.000 0.00 0.00 46.48 3.01
1625 1845 6.174720 TCTCTATACCAACATGGACCAATC 57.825 41.667 0.00 0.00 40.96 2.67
1626 1846 6.386927 TCTTCTCTATACCAACATGGACCAAT 59.613 38.462 0.00 0.00 40.96 3.16
1627 1847 5.724370 TCTTCTCTATACCAACATGGACCAA 59.276 40.000 0.00 0.00 40.96 3.67
1628 1848 5.277250 TCTTCTCTATACCAACATGGACCA 58.723 41.667 2.85 0.00 40.96 4.02
1629 1849 5.364157 ACTCTTCTCTATACCAACATGGACC 59.636 44.000 2.85 0.00 40.96 4.46
1630 1850 6.472686 ACTCTTCTCTATACCAACATGGAC 57.527 41.667 2.85 0.00 40.96 4.02
1631 1851 7.331026 CAAACTCTTCTCTATACCAACATGGA 58.669 38.462 2.85 0.00 40.96 3.41
1632 1852 6.037610 GCAAACTCTTCTCTATACCAACATGG 59.962 42.308 0.00 0.00 45.02 3.66
1633 1853 6.595326 TGCAAACTCTTCTCTATACCAACATG 59.405 38.462 0.00 0.00 0.00 3.21
1634 1854 6.711277 TGCAAACTCTTCTCTATACCAACAT 58.289 36.000 0.00 0.00 0.00 2.71
1635 1855 6.109156 TGCAAACTCTTCTCTATACCAACA 57.891 37.500 0.00 0.00 0.00 3.33
1636 1856 7.334421 TCAATGCAAACTCTTCTCTATACCAAC 59.666 37.037 0.00 0.00 0.00 3.77
1637 1857 7.394016 TCAATGCAAACTCTTCTCTATACCAA 58.606 34.615 0.00 0.00 0.00 3.67
1638 1858 6.946340 TCAATGCAAACTCTTCTCTATACCA 58.054 36.000 0.00 0.00 0.00 3.25
1639 1859 7.859598 CATCAATGCAAACTCTTCTCTATACC 58.140 38.462 0.00 0.00 0.00 2.73
1658 1878 7.166851 TCCAAATAACAAACCATTGCATCAAT 58.833 30.769 0.00 0.00 40.34 2.57
1659 1879 6.528321 TCCAAATAACAAACCATTGCATCAA 58.472 32.000 0.00 0.00 40.34 2.57
1660 1880 6.014755 TCTCCAAATAACAAACCATTGCATCA 60.015 34.615 0.00 0.00 40.34 3.07
1661 1881 6.397272 TCTCCAAATAACAAACCATTGCATC 58.603 36.000 0.00 0.00 40.34 3.91
1662 1882 6.211184 TCTCTCCAAATAACAAACCATTGCAT 59.789 34.615 0.00 0.00 40.34 3.96
1663 1883 5.538053 TCTCTCCAAATAACAAACCATTGCA 59.462 36.000 0.00 0.00 40.34 4.08
1664 1884 6.024552 TCTCTCCAAATAACAAACCATTGC 57.975 37.500 0.00 0.00 40.34 3.56
1665 1885 7.809806 GTCTTCTCTCCAAATAACAAACCATTG 59.190 37.037 0.00 0.00 42.46 2.82
1666 1886 7.505585 TGTCTTCTCTCCAAATAACAAACCATT 59.494 33.333 0.00 0.00 0.00 3.16
1667 1887 7.004086 TGTCTTCTCTCCAAATAACAAACCAT 58.996 34.615 0.00 0.00 0.00 3.55
1734 1955 4.263462 TGTGCTCCAACAGATGACCTAAAT 60.263 41.667 0.00 0.00 0.00 1.40
1740 1961 4.510038 AAAATGTGCTCCAACAGATGAC 57.490 40.909 0.00 0.00 32.52 3.06
1803 2024 5.180868 GCCAAGTGCATCTCCAATAGATTAG 59.819 44.000 0.00 0.00 42.62 1.73
1814 2035 1.076485 ATGGGGCCAAGTGCATCTC 60.076 57.895 4.39 0.00 43.89 2.75
1821 2042 1.358787 TCAGAAATGATGGGGCCAAGT 59.641 47.619 4.39 0.00 0.00 3.16
1866 2087 5.202004 ACTAACGACCTCCTCATTGTCTAT 58.798 41.667 0.00 0.00 0.00 1.98
1867 2088 4.597004 ACTAACGACCTCCTCATTGTCTA 58.403 43.478 0.00 0.00 0.00 2.59
1877 2098 1.711206 GTGCTTGACTAACGACCTCC 58.289 55.000 0.00 0.00 0.00 4.30
1895 2116 4.065088 ACAGACACATGCATAGAAAACGT 58.935 39.130 0.00 0.00 0.00 3.99
1896 2117 4.641954 GACAGACACATGCATAGAAAACG 58.358 43.478 0.00 0.00 0.00 3.60
1902 2123 0.573987 CGCGACAGACACATGCATAG 59.426 55.000 0.00 0.00 0.00 2.23
1920 2141 3.013276 TCAACTATAATGAGAGGCGCG 57.987 47.619 0.00 0.00 0.00 6.86
1923 2144 8.845413 ATGAAGAATCAACTATAATGAGAGGC 57.155 34.615 0.00 0.00 39.49 4.70
1980 2201 0.779997 ACTGATGGCTTCCCCTTGTT 59.220 50.000 0.00 0.00 0.00 2.83
1983 2204 1.000396 GCACTGATGGCTTCCCCTT 60.000 57.895 0.00 0.00 0.00 3.95
1990 2211 0.877071 CTTTGTTCGCACTGATGGCT 59.123 50.000 0.00 0.00 0.00 4.75
1991 2212 0.730494 GCTTTGTTCGCACTGATGGC 60.730 55.000 0.00 0.00 0.00 4.40
1992 2213 0.592637 TGCTTTGTTCGCACTGATGG 59.407 50.000 0.00 0.00 31.40 3.51
1993 2214 2.247637 CATGCTTTGTTCGCACTGATG 58.752 47.619 0.00 0.00 40.65 3.07
1994 2215 1.200716 CCATGCTTTGTTCGCACTGAT 59.799 47.619 0.00 0.00 40.65 2.90
1995 2216 0.592637 CCATGCTTTGTTCGCACTGA 59.407 50.000 0.00 0.00 40.65 3.41
1996 2217 0.311790 ACCATGCTTTGTTCGCACTG 59.688 50.000 0.00 0.00 40.65 3.66
1997 2218 0.311790 CACCATGCTTTGTTCGCACT 59.688 50.000 0.00 0.00 40.65 4.40
1998 2219 0.664166 CCACCATGCTTTGTTCGCAC 60.664 55.000 0.00 0.00 40.65 5.34
1999 2220 1.659233 CCACCATGCTTTGTTCGCA 59.341 52.632 0.00 0.00 42.25 5.10
2000 2221 1.734117 GCCACCATGCTTTGTTCGC 60.734 57.895 0.00 0.00 0.00 4.70
2001 2222 1.080569 GGCCACCATGCTTTGTTCG 60.081 57.895 0.00 0.00 0.00 3.95
2002 2223 0.681175 AAGGCCACCATGCTTTGTTC 59.319 50.000 5.01 0.00 0.00 3.18
2003 2224 2.008242 TAAGGCCACCATGCTTTGTT 57.992 45.000 5.01 0.00 32.36 2.83
2004 2225 2.008242 TTAAGGCCACCATGCTTTGT 57.992 45.000 5.01 0.00 32.36 2.83
2005 2226 2.419021 CCATTAAGGCCACCATGCTTTG 60.419 50.000 5.01 0.00 32.36 2.77
2006 2227 1.832998 CCATTAAGGCCACCATGCTTT 59.167 47.619 5.01 0.00 34.64 3.51
2007 2228 1.006998 TCCATTAAGGCCACCATGCTT 59.993 47.619 5.01 0.00 37.29 3.91
2008 2229 0.630673 TCCATTAAGGCCACCATGCT 59.369 50.000 5.01 0.00 37.29 3.79
2030 2251 4.288105 ACCTCAAAGTCTTGGATCATGACT 59.712 41.667 0.00 9.66 46.13 3.41
2047 2268 2.567169 CACCCTCACAGACATACCTCAA 59.433 50.000 0.00 0.00 0.00 3.02
2097 2318 1.698506 AAAATCCGCACCACCTTGAA 58.301 45.000 0.00 0.00 0.00 2.69
2115 2336 2.151202 GATGCCCTTCTCGACAACAAA 58.849 47.619 0.00 0.00 0.00 2.83
2116 2337 1.808411 GATGCCCTTCTCGACAACAA 58.192 50.000 0.00 0.00 0.00 2.83
2117 2338 0.389817 CGATGCCCTTCTCGACAACA 60.390 55.000 0.00 0.00 37.05 3.33
2122 2343 1.043116 ACCATCGATGCCCTTCTCGA 61.043 55.000 20.25 0.00 46.71 4.04
2125 2346 1.153086 GCACCATCGATGCCCTTCT 60.153 57.895 20.25 0.00 37.08 2.85
2137 2359 2.539302 ACCTTGCCTATTTTGCACCAT 58.461 42.857 0.00 0.00 38.72 3.55
2168 2390 4.500375 GGTGTTCCTACTGTTAGTGTCGTT 60.500 45.833 0.00 0.00 0.00 3.85
2193 2415 1.915489 ACAGATGGCCCATTGTAGTCA 59.085 47.619 0.00 0.00 0.00 3.41
2208 2430 1.607467 GCAAACCCCCAGCACAGAT 60.607 57.895 0.00 0.00 0.00 2.90
2210 2432 3.673484 CGCAAACCCCCAGCACAG 61.673 66.667 0.00 0.00 0.00 3.66
2222 2444 0.671251 GGACCATTGGTTGACGCAAA 59.329 50.000 10.29 0.00 35.25 3.68


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

AutoCloner maintained by Alex Coulton.