Multiple sequence alignment - TraesCS7A01G468900

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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 TraesCS7A01G468900 chr7A 100.000 2402 0 0 1 2402 664874570 664872169 0.000000e+00 4436.0
1 TraesCS7A01G468900 chr7A 84.218 697 72 19 946 1612 664603168 664603856 0.000000e+00 643.0
2 TraesCS7A01G468900 chr7A 83.866 688 61 15 962 1615 664781112 664780441 5.680000e-171 610.0
3 TraesCS7A01G468900 chr7A 86.943 314 26 7 1606 1913 664700118 664700422 2.960000e-89 339.0
4 TraesCS7A01G468900 chr7A 83.453 139 12 9 4 138 664697686 664697817 4.190000e-23 119.0
5 TraesCS7A01G468900 chr7A 78.571 140 19 7 1785 1918 664614063 664614197 5.500000e-12 82.4
6 TraesCS7A01G468900 chr7D 86.688 1585 131 33 824 2373 575218113 575216574 0.000000e+00 1685.0
7 TraesCS7A01G468900 chr7D 88.113 816 54 13 824 1615 575149650 575148854 0.000000e+00 929.0
8 TraesCS7A01G468900 chr7D 85.523 822 90 13 822 1615 574925455 574924635 0.000000e+00 832.0
9 TraesCS7A01G468900 chr7D 88.427 674 55 10 949 1615 575074321 575073664 0.000000e+00 791.0
10 TraesCS7A01G468900 chr7D 85.106 376 37 8 1609 1973 575073625 575073258 1.360000e-97 366.0
11 TraesCS7A01G468900 chr7D 83.946 299 37 7 1621 1918 574875638 574875926 2.350000e-70 276.0
12 TraesCS7A01G468900 chr7D 82.743 226 24 11 156 381 575220226 575220016 1.130000e-43 187.0
13 TraesCS7A01G468900 chr7D 88.000 150 9 4 13 158 575078031 575077887 4.110000e-38 169.0
14 TraesCS7A01G468900 chr7D 86.620 142 8 5 2242 2373 32786421 32786281 1.920000e-31 147.0
15 TraesCS7A01G468900 chr7D 82.550 149 14 8 13 150 575001539 575001392 1.170000e-23 121.0
16 TraesCS7A01G468900 chr7D 88.764 89 4 5 236 324 575076493 575076411 1.170000e-18 104.0
17 TraesCS7A01G468900 chr7D 79.618 157 19 7 17 160 574872841 574872997 1.520000e-17 100.0
18 TraesCS7A01G468900 chr7B 86.855 814 70 14 824 1611 636433272 636432470 0.000000e+00 876.0
19 TraesCS7A01G468900 chr7B 83.129 978 96 32 685 1612 635300770 635301728 0.000000e+00 828.0
20 TraesCS7A01G468900 chr7B 87.034 671 59 10 970 1615 635749105 635748438 0.000000e+00 732.0
21 TraesCS7A01G468900 chr7B 87.542 594 44 13 886 1456 635170596 635171182 0.000000e+00 660.0
22 TraesCS7A01G468900 chr7B 85.670 321 36 5 1618 1936 635748399 635748087 1.780000e-86 329.0
23 TraesCS7A01G468900 chr7B 83.191 351 38 11 1618 1955 635935438 635935096 3.880000e-78 302.0
24 TraesCS7A01G468900 chr7B 84.354 294 37 4 1621 1913 635301782 635302067 1.820000e-71 279.0
25 TraesCS7A01G468900 chr7B 83.793 290 22 17 1630 1903 636432423 636432143 3.960000e-63 252.0
26 TraesCS7A01G468900 chr7B 86.538 156 13 3 11 158 636014610 636014455 5.310000e-37 165.0
27 TraesCS7A01G468900 chr7B 85.000 120 16 2 1609 1728 635171316 635171433 1.170000e-23 121.0
28 TraesCS7A01G468900 chr7B 80.220 182 11 9 156 318 635750257 635750082 1.950000e-21 113.0
29 TraesCS7A01G468900 chr7B 94.118 68 2 2 2307 2373 187538432 187538498 4.220000e-18 102.0
30 TraesCS7A01G468900 chr7B 90.411 73 4 2 2303 2373 447694528 447694457 2.540000e-15 93.5
31 TraesCS7A01G468900 chr7B 93.182 44 3 0 395 438 635749711 635749668 5.540000e-07 65.8
32 TraesCS7A01G468900 chr1B 81.622 185 22 9 2199 2373 629925129 629925311 2.490000e-30 143.0
33 TraesCS7A01G468900 chr5A 81.379 145 17 4 2238 2373 30026826 30026969 2.520000e-20 110.0
34 TraesCS7A01G468900 chr1D 79.375 160 18 8 2228 2373 453479452 453479294 5.460000e-17 99.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7A01G468900 chr7A 664872169 664874570 2401 True 4436.00 4436 100.00000 1 2402 1 chr7A.!!$R2 2401
1 TraesCS7A01G468900 chr7A 664603168 664603856 688 False 643.00 643 84.21800 946 1612 1 chr7A.!!$F1 666
2 TraesCS7A01G468900 chr7A 664780441 664781112 671 True 610.00 610 83.86600 962 1615 1 chr7A.!!$R1 653
3 TraesCS7A01G468900 chr7A 664697686 664700422 2736 False 229.00 339 85.19800 4 1913 2 chr7A.!!$F3 1909
4 TraesCS7A01G468900 chr7D 575216574 575220226 3652 True 936.00 1685 84.71550 156 2373 2 chr7D.!!$R6 2217
5 TraesCS7A01G468900 chr7D 575148854 575149650 796 True 929.00 929 88.11300 824 1615 1 chr7D.!!$R4 791
6 TraesCS7A01G468900 chr7D 574924635 574925455 820 True 832.00 832 85.52300 822 1615 1 chr7D.!!$R2 793
7 TraesCS7A01G468900 chr7D 575073258 575078031 4773 True 357.50 791 87.57425 13 1973 4 chr7D.!!$R5 1960
8 TraesCS7A01G468900 chr7B 636432143 636433272 1129 True 564.00 876 85.32400 824 1903 2 chr7B.!!$R5 1079
9 TraesCS7A01G468900 chr7B 635300770 635302067 1297 False 553.50 828 83.74150 685 1913 2 chr7B.!!$F3 1228
10 TraesCS7A01G468900 chr7B 635170596 635171433 837 False 390.50 660 86.27100 886 1728 2 chr7B.!!$F2 842
11 TraesCS7A01G468900 chr7B 635748087 635750257 2170 True 309.95 732 86.52650 156 1936 4 chr7B.!!$R4 1780

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
47 48 0.0982 CATTCATGCGTGCTGGTCTG 59.902 55.0 0.0 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1999 5758 0.313043 CTGGCAAGCAGTTGTGAAGG 59.687 55.0 0.0 0.0 35.92 3.46 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
27 28 6.240438 CGGAGGATAGGATAGGAGGATATCAT 60.240 46.154 4.83 0.00 34.42 2.45
31 32 8.755039 AGGATAGGATAGGAGGATATCATCATT 58.245 37.037 18.38 8.88 34.42 2.57
47 48 0.098200 CATTCATGCGTGCTGGTCTG 59.902 55.000 0.00 0.00 0.00 3.51
48 49 1.028330 ATTCATGCGTGCTGGTCTGG 61.028 55.000 0.00 0.00 0.00 3.86
49 50 2.359107 CATGCGTGCTGGTCTGGT 60.359 61.111 0.00 0.00 0.00 4.00
107 113 1.370900 GTACCGGTATAGTGCGCGG 60.371 63.158 19.19 0.00 0.00 6.46
133 142 1.958323 GCCTACGGCCTAGTCTAGC 59.042 63.158 0.00 0.00 44.06 3.42
144 153 3.011119 CCTAGTCTAGCGACACACTTCT 58.989 50.000 0.86 0.00 42.73 2.85
151 160 1.068472 AGCGACACACTTCTCCTAACG 60.068 52.381 0.00 0.00 0.00 3.18
174 231 5.278071 CGTGCTAGTATTTCTAGGGTCTCAG 60.278 48.000 4.44 0.00 44.48 3.35
186 1497 1.270550 GGGTCTCAGCCAATTGTGTTG 59.729 52.381 4.43 4.76 35.40 3.33
234 1589 4.266976 CACGTATAACAAAGTAGAAGGCGG 59.733 45.833 0.00 0.00 0.00 6.13
267 1622 1.270147 ACTGCTACGGGTTGACAAGAC 60.270 52.381 0.00 0.00 0.00 3.01
270 1625 1.798813 GCTACGGGTTGACAAGACAAG 59.201 52.381 0.00 0.00 0.00 3.16
275 1630 2.544267 CGGGTTGACAAGACAAGAGTTC 59.456 50.000 0.00 0.00 0.00 3.01
320 1686 1.064463 CACCTGCTCCTCTCTCTCTCT 60.064 57.143 0.00 0.00 0.00 3.10
324 1690 2.437281 CTGCTCCTCTCTCTCTCTCTCT 59.563 54.545 0.00 0.00 0.00 3.10
325 1691 2.435805 TGCTCCTCTCTCTCTCTCTCTC 59.564 54.545 0.00 0.00 0.00 3.20
334 1700 4.871822 TCTCTCTCTCTCTCTCTCTCTCA 58.128 47.826 0.00 0.00 0.00 3.27
381 1757 3.989167 CACTTGCTTTGTCTCTCTCTCTG 59.011 47.826 0.00 0.00 0.00 3.35
385 1761 3.505680 TGCTTTGTCTCTCTCTCTGTCTC 59.494 47.826 0.00 0.00 0.00 3.36
389 1765 4.206477 TGTCTCTCTCTCTGTCTCTCTG 57.794 50.000 0.00 0.00 0.00 3.35
392 1768 3.119137 TCTCTCTCTCTGTCTCTCTGTCG 60.119 52.174 0.00 0.00 0.00 4.35
397 2354 5.838529 TCTCTCTGTCTCTCTGTCGTATAG 58.161 45.833 0.00 0.00 0.00 1.31
400 2359 5.100344 TCTGTCTCTCTGTCGTATAGGTT 57.900 43.478 0.00 0.00 0.00 3.50
404 2363 3.869832 TCTCTCTGTCGTATAGGTTCACG 59.130 47.826 0.00 0.00 39.48 4.35
441 2455 4.182339 CTCTCACATGGTCACTGAATGAG 58.818 47.826 0.00 0.00 38.28 2.90
537 2569 7.009568 CAATTTCGTTGGAAGGAAGATAGAG 57.990 40.000 0.00 0.00 34.69 2.43
541 2573 3.536570 GTTGGAAGGAAGATAGAGGTGC 58.463 50.000 0.00 0.00 0.00 5.01
542 2574 3.121929 TGGAAGGAAGATAGAGGTGCT 57.878 47.619 0.00 0.00 0.00 4.40
582 2614 1.519455 GGACGATGCCGAGTTGAGG 60.519 63.158 0.00 0.00 39.50 3.86
585 2617 1.218047 CGATGCCGAGTTGAGGGAA 59.782 57.895 0.00 0.00 38.22 3.97
594 2626 1.228552 GTTGAGGGAAGCAAGGCCA 60.229 57.895 5.01 0.00 0.00 5.36
595 2627 0.827507 GTTGAGGGAAGCAAGGCCAA 60.828 55.000 5.01 0.00 0.00 4.52
600 2632 1.285950 GGAAGCAAGGCCAAACGAC 59.714 57.895 5.01 0.00 0.00 4.34
607 2639 3.587933 GGCCAAACGACGCCAACA 61.588 61.111 0.00 0.00 45.01 3.33
657 2700 0.389948 AGCGGCGAGTTAGAAGGTTG 60.390 55.000 12.98 0.00 0.00 3.77
659 2702 1.739371 GCGGCGAGTTAGAAGGTTGAT 60.739 52.381 12.98 0.00 0.00 2.57
661 2704 2.674177 CGGCGAGTTAGAAGGTTGATGT 60.674 50.000 0.00 0.00 0.00 3.06
668 2711 5.238583 AGTTAGAAGGTTGATGTGTGTAGC 58.761 41.667 0.00 0.00 0.00 3.58
669 2712 5.012148 AGTTAGAAGGTTGATGTGTGTAGCT 59.988 40.000 0.00 0.00 0.00 3.32
673 2716 0.179215 GTTGATGTGTGTAGCTGCGC 60.179 55.000 8.58 8.58 0.00 6.09
674 2717 0.320683 TTGATGTGTGTAGCTGCGCT 60.321 50.000 16.48 8.09 43.41 5.92
676 2719 2.301902 GATGTGTGTAGCTGCGCTGC 62.302 60.000 29.38 29.38 40.10 5.25
680 2723 4.312941 TGTAGCTGCGCTGCACCA 62.313 61.111 35.70 27.90 45.44 4.17
681 2724 3.049674 GTAGCTGCGCTGCACCAA 61.050 61.111 35.70 18.25 40.83 3.67
682 2725 2.743538 TAGCTGCGCTGCACCAAG 60.744 61.111 35.70 12.92 40.10 3.61
716 3900 8.504005 ACAGTTTCTTATTCACCAAGTTTATCG 58.496 33.333 0.00 0.00 0.00 2.92
726 3910 5.062934 TCACCAAGTTTATCGCGATTTAGTG 59.937 40.000 28.81 22.07 0.00 2.74
744 4226 2.552599 TGTGAAACACGGCCAGATTA 57.447 45.000 2.24 0.00 45.67 1.75
793 4275 2.352960 CCGAAGCAGACTGGCTAAAATC 59.647 50.000 4.26 0.00 45.07 2.17
794 4276 2.352960 CGAAGCAGACTGGCTAAAATCC 59.647 50.000 4.26 0.00 45.07 3.01
795 4277 3.347216 GAAGCAGACTGGCTAAAATCCA 58.653 45.455 4.26 0.00 45.07 3.41
797 4279 3.973425 AGCAGACTGGCTAAAATCCATT 58.027 40.909 4.26 0.00 43.70 3.16
818 4343 4.981806 TCCGAGAAAAATAATGGCAAGG 57.018 40.909 0.00 0.00 0.00 3.61
819 4344 3.130340 TCCGAGAAAAATAATGGCAAGGC 59.870 43.478 0.00 0.00 0.00 4.35
848 4384 2.744202 CAACTTGCAGCTCTTCCGTTAT 59.256 45.455 0.00 0.00 0.00 1.89
849 4385 2.350522 ACTTGCAGCTCTTCCGTTATG 58.649 47.619 0.00 0.00 0.00 1.90
868 4407 1.563879 TGTATAAGCAGCCACCATGGT 59.436 47.619 13.00 13.00 40.46 3.55
889 4428 1.719780 CGTCTCAGTACAAACGCCTTC 59.280 52.381 0.00 0.00 0.00 3.46
894 4433 2.364324 TCAGTACAAACGCCTTCTGTCT 59.636 45.455 0.00 0.00 0.00 3.41
900 4439 2.447244 AACGCCTTCTGTCTTCTCAG 57.553 50.000 0.00 0.00 36.85 3.35
919 4466 1.880894 CTTAGTGTCGTCCCTCGCA 59.119 57.895 0.00 0.00 39.67 5.10
964 4513 2.987125 GGCCTCCGCTTCCAAGTA 59.013 61.111 0.00 0.00 34.44 2.24
968 4517 0.460311 CCTCCGCTTCCAAGTATCGT 59.540 55.000 0.00 0.00 0.00 3.73
1107 4698 4.214327 GCGAAGGCCTCCTCCTCG 62.214 72.222 17.57 17.57 34.82 4.63
1115 4706 0.747283 GCCTCCTCCTCGTCGTTCTA 60.747 60.000 0.00 0.00 0.00 2.10
1444 5042 3.069318 ACCCTCCTCGTTCGGCTC 61.069 66.667 0.00 0.00 0.00 4.70
1467 5070 1.923356 TGGAGGGCTTGATTGGAAAC 58.077 50.000 0.00 0.00 0.00 2.78
1471 5074 1.428912 AGGGCTTGATTGGAAACTGGA 59.571 47.619 0.00 0.00 0.00 3.86
1492 5095 1.838396 CCTGGCAAAGGCAAAGGGT 60.838 57.895 0.00 0.00 43.71 4.34
1493 5096 1.368579 CTGGCAAAGGCAAAGGGTG 59.631 57.895 0.00 0.00 43.71 4.61
1497 5115 1.286880 CAAAGGCAAAGGGTGAGCG 59.713 57.895 0.00 0.00 0.00 5.03
1526 5149 1.962822 CCAGCTGCTGCGTTCTGAA 60.963 57.895 23.86 0.00 45.42 3.02
1589 5215 1.272554 GGGTTGGTGGAGGGTAGGAG 61.273 65.000 0.00 0.00 0.00 3.69
1598 5224 0.568697 GAGGGTAGGAGGGGGATTCT 59.431 60.000 0.00 0.00 0.00 2.40
1637 5362 9.541143 TTCTTCTTCTTCTTCTTCTTCTTCTTC 57.459 33.333 0.00 0.00 0.00 2.87
1638 5363 8.923270 TCTTCTTCTTCTTCTTCTTCTTCTTCT 58.077 33.333 0.00 0.00 0.00 2.85
1640 5365 9.541143 TTCTTCTTCTTCTTCTTCTTCTTCTTC 57.459 33.333 0.00 0.00 0.00 2.87
1674 5405 5.779241 AGCTCTAGATCTAGCTCTGGTAT 57.221 43.478 22.81 0.00 45.92 2.73
1704 5435 4.020662 TGGAGCTTCTTCTTCCTCTTCTTC 60.021 45.833 0.00 0.00 0.00 2.87
1731 5464 4.338879 AGGGATTTTGAGGTCATGACAAG 58.661 43.478 26.47 0.00 0.00 3.16
1732 5465 4.082125 GGGATTTTGAGGTCATGACAAGT 58.918 43.478 26.47 10.99 0.00 3.16
1781 5521 6.293698 CCTCATGTGAGTGAATGGATGATTA 58.706 40.000 9.03 0.00 40.48 1.75
1838 5583 5.107375 GGTGTAAAATGCAATGCACTTCAAG 60.107 40.000 11.23 0.00 43.04 3.02
1839 5584 5.463061 GTGTAAAATGCAATGCACTTCAAGT 59.537 36.000 11.23 0.00 43.04 3.16
1840 5585 5.691305 TGTAAAATGCAATGCACTTCAAGTC 59.309 36.000 11.23 0.00 43.04 3.01
1841 5586 4.595762 AAATGCAATGCACTTCAAGTCT 57.404 36.364 11.23 0.00 43.04 3.24
1842 5587 4.595762 AATGCAATGCACTTCAAGTCTT 57.404 36.364 11.23 0.00 43.04 3.01
1843 5588 3.631145 TGCAATGCACTTCAAGTCTTC 57.369 42.857 2.72 0.00 31.71 2.87
1844 5589 2.950975 TGCAATGCACTTCAAGTCTTCA 59.049 40.909 2.72 0.00 31.71 3.02
1845 5590 3.380954 TGCAATGCACTTCAAGTCTTCAA 59.619 39.130 2.72 0.00 31.71 2.69
1846 5591 3.732721 GCAATGCACTTCAAGTCTTCAAC 59.267 43.478 0.00 0.00 0.00 3.18
1936 5695 5.494390 ACCAGTTACTAAACTACTTGGGG 57.506 43.478 0.00 0.00 44.28 4.96
1951 5710 0.971959 TGGGGCTGTGGATGCATTTC 60.972 55.000 0.00 0.00 0.00 2.17
1956 5715 3.256558 GGCTGTGGATGCATTTCTTTTC 58.743 45.455 0.00 0.00 0.00 2.29
1970 5729 5.668558 TTTCTTTTCTTGAACGTCTAGGC 57.331 39.130 0.00 0.00 0.00 3.93
1999 5758 2.805099 GCATATACTTCAGAGGCACTGC 59.195 50.000 7.09 0.00 45.38 4.40
2053 5812 0.991146 TGGCCAGGTTCAGAATAGCA 59.009 50.000 0.00 0.00 0.00 3.49
2054 5813 1.354031 TGGCCAGGTTCAGAATAGCAA 59.646 47.619 0.00 0.00 0.00 3.91
2095 5854 4.202020 ACAGATACAGTGCGTGTGTATAGG 60.202 45.833 5.63 4.49 40.47 2.57
2102 5861 3.374058 AGTGCGTGTGTATAGGATTTTGC 59.626 43.478 0.00 0.00 0.00 3.68
2103 5862 3.126171 GTGCGTGTGTATAGGATTTTGCA 59.874 43.478 0.00 0.00 0.00 4.08
2110 5869 7.244192 GTGTGTATAGGATTTTGCAGAACTTC 58.756 38.462 0.00 0.00 0.00 3.01
2131 5890 6.972901 ACTTCTTTTCAAAGCGGAGTAAAAAG 59.027 34.615 0.00 0.00 35.99 2.27
2134 5893 7.540299 TCTTTTCAAAGCGGAGTAAAAAGAAA 58.460 30.769 5.81 0.00 38.85 2.52
2135 5894 8.194769 TCTTTTCAAAGCGGAGTAAAAAGAAAT 58.805 29.630 5.81 0.00 38.85 2.17
2136 5895 7.692908 TTTCAAAGCGGAGTAAAAAGAAATG 57.307 32.000 0.00 0.00 0.00 2.32
2137 5896 6.385649 TCAAAGCGGAGTAAAAAGAAATGT 57.614 33.333 0.00 0.00 0.00 2.71
2139 5898 7.932335 TCAAAGCGGAGTAAAAAGAAATGTAA 58.068 30.769 0.00 0.00 0.00 2.41
2141 5900 7.739498 AAGCGGAGTAAAAAGAAATGTAAGA 57.261 32.000 0.00 0.00 0.00 2.10
2142 5901 7.130303 AGCGGAGTAAAAAGAAATGTAAGAC 57.870 36.000 0.00 0.00 0.00 3.01
2169 5928 2.769663 ACAACCGGACTTGGCATATCTA 59.230 45.455 9.46 0.00 0.00 1.98
2184 5943 1.895020 ATCTACGCCTCAAACGCCCA 61.895 55.000 0.00 0.00 0.00 5.36
2206 5965 2.579787 CGCGTCCGATGACTGGTC 60.580 66.667 0.00 0.00 39.47 4.02
2221 5980 6.275494 TGACTGGTCACGTCTCAAATAATA 57.725 37.500 0.00 0.00 34.14 0.98
2222 5981 6.097356 TGACTGGTCACGTCTCAAATAATAC 58.903 40.000 0.00 0.00 34.14 1.89
2235 5994 8.345565 GTCTCAAATAATACATTCCACATCCAC 58.654 37.037 0.00 0.00 0.00 4.02
2249 6008 5.547276 TCCACATCCACATATGTCATATCCA 59.453 40.000 5.07 0.00 38.01 3.41
2271 6030 7.422512 TCCAGCATCCTATATTCATACTACCT 58.577 38.462 0.00 0.00 0.00 3.08
2279 6038 9.541884 TCCTATATTCATACTACCTATGCAACA 57.458 33.333 0.00 0.00 33.32 3.33
2290 6049 6.986817 ACTACCTATGCAACATGATGAACTAC 59.013 38.462 7.22 0.00 0.00 2.73
2301 6060 4.012319 TGATGAACTACTCTACGCGAAC 57.988 45.455 15.93 0.00 0.00 3.95
2303 6062 1.129251 TGAACTACTCTACGCGAACGG 59.871 52.381 15.93 2.42 46.04 4.44
2348 6107 4.384547 GGACAACGAAATGCACATAAAACC 59.615 41.667 0.00 0.00 0.00 3.27
2349 6108 4.303282 ACAACGAAATGCACATAAAACCC 58.697 39.130 0.00 0.00 0.00 4.11
2351 6110 3.908213 ACGAAATGCACATAAAACCCAC 58.092 40.909 0.00 0.00 0.00 4.61
2353 6112 3.919804 CGAAATGCACATAAAACCCACTG 59.080 43.478 0.00 0.00 0.00 3.66
2373 6132 2.684374 TGCATCATCCAAAAGATCACCG 59.316 45.455 0.00 0.00 30.59 4.94
2374 6133 2.033801 GCATCATCCAAAAGATCACCGG 59.966 50.000 0.00 0.00 30.59 5.28
2375 6134 2.418368 TCATCCAAAAGATCACCGGG 57.582 50.000 6.32 0.00 30.59 5.73
2376 6135 1.912731 TCATCCAAAAGATCACCGGGA 59.087 47.619 6.32 0.00 30.59 5.14
2377 6136 2.307392 TCATCCAAAAGATCACCGGGAA 59.693 45.455 6.32 0.00 30.59 3.97
2378 6137 2.489938 TCCAAAAGATCACCGGGAAG 57.510 50.000 6.32 0.00 0.00 3.46
2379 6138 1.702957 TCCAAAAGATCACCGGGAAGT 59.297 47.619 6.32 0.00 0.00 3.01
2380 6139 2.107552 TCCAAAAGATCACCGGGAAGTT 59.892 45.455 6.32 0.00 0.00 2.66
2381 6140 2.890945 CCAAAAGATCACCGGGAAGTTT 59.109 45.455 6.32 2.12 0.00 2.66
2382 6141 3.320826 CCAAAAGATCACCGGGAAGTTTT 59.679 43.478 6.32 7.87 0.00 2.43
2383 6142 4.202212 CCAAAAGATCACCGGGAAGTTTTT 60.202 41.667 6.32 4.43 0.00 1.94
2384 6143 5.010213 CCAAAAGATCACCGGGAAGTTTTTA 59.990 40.000 6.32 0.00 0.00 1.52
2385 6144 6.461788 CCAAAAGATCACCGGGAAGTTTTTAA 60.462 38.462 6.32 0.00 0.00 1.52
2386 6145 5.700722 AAGATCACCGGGAAGTTTTTAAC 57.299 39.130 6.32 0.00 0.00 2.01
2387 6146 4.981812 AGATCACCGGGAAGTTTTTAACT 58.018 39.130 6.32 0.00 45.46 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.641714 CCTCCTATCCTATCCTCCGGT 59.358 57.143 0.00 0.00 0.00 5.28
1 2 1.923850 TCCTCCTATCCTATCCTCCGG 59.076 57.143 0.00 0.00 0.00 5.14
2 3 3.963476 ATCCTCCTATCCTATCCTCCG 57.037 52.381 0.00 0.00 0.00 4.63
27 28 0.036105 AGACCAGCACGCATGAATGA 60.036 50.000 0.00 0.00 0.00 2.57
31 32 2.046988 CCAGACCAGCACGCATGA 60.047 61.111 0.00 0.00 0.00 3.07
47 48 2.737252 GAGACATTTTCACGTGGAGACC 59.263 50.000 17.00 0.00 0.00 3.85
48 49 2.408704 CGAGACATTTTCACGTGGAGAC 59.591 50.000 17.00 0.00 33.99 3.36
49 50 2.672714 CGAGACATTTTCACGTGGAGA 58.327 47.619 17.00 1.55 33.99 3.71
133 142 2.316792 CACGTTAGGAGAAGTGTGTCG 58.683 52.381 0.00 0.00 0.00 4.35
144 153 5.533903 CCCTAGAAATACTAGCACGTTAGGA 59.466 44.000 3.65 0.00 45.09 2.94
151 160 5.508320 GCTGAGACCCTAGAAATACTAGCAC 60.508 48.000 0.00 0.00 45.09 4.40
186 1497 6.970484 ACAATACTTGGATTTTCACAGTGAC 58.030 36.000 1.52 0.00 34.12 3.67
234 1589 5.067544 ACCCGTAGCAGTAGTATTCTCTTTC 59.932 44.000 0.00 0.00 0.00 2.62
275 1630 2.277969 CAATAGACTGCTGGAGTGCTG 58.722 52.381 6.54 0.00 33.83 4.41
320 1686 6.009589 ACAATTTGACTGAGAGAGAGAGAGA 58.990 40.000 2.79 0.00 0.00 3.10
324 1690 4.520874 ACGACAATTTGACTGAGAGAGAGA 59.479 41.667 2.79 0.00 0.00 3.10
325 1691 4.804108 ACGACAATTTGACTGAGAGAGAG 58.196 43.478 2.79 0.00 0.00 3.20
334 1700 8.301720 TGATTAGTACTGTACGACAATTTGACT 58.698 33.333 11.97 0.00 0.00 3.41
381 1757 4.260294 CGTGAACCTATACGACAGAGAGAC 60.260 50.000 0.00 0.00 42.54 3.36
385 1761 2.355132 AGCGTGAACCTATACGACAGAG 59.645 50.000 0.00 0.00 42.54 3.35
389 1765 1.402968 TGGAGCGTGAACCTATACGAC 59.597 52.381 0.00 0.00 42.54 4.34
392 1768 2.135933 GCATGGAGCGTGAACCTATAC 58.864 52.381 0.00 0.00 0.00 1.47
404 2363 2.203181 GAGCTGGGAGCATGGAGC 60.203 66.667 0.00 0.00 45.56 4.70
466 2480 4.510038 CAATTTACTTGCAGCTGAACCT 57.490 40.909 20.43 0.00 0.00 3.50
541 2573 3.730761 GGACTTGGTGCAGCGCAG 61.731 66.667 11.47 12.05 40.08 5.18
542 2574 3.848301 ATGGACTTGGTGCAGCGCA 62.848 57.895 11.47 0.00 37.30 6.09
577 2609 0.105760 TTTGGCCTTGCTTCCCTCAA 60.106 50.000 3.32 0.00 0.00 3.02
582 2614 1.285950 GTCGTTTGGCCTTGCTTCC 59.714 57.895 3.32 0.00 0.00 3.46
585 2617 3.660111 GCGTCGTTTGGCCTTGCT 61.660 61.111 3.32 0.00 0.00 3.91
621 2653 1.956170 CTGTCGGTTGCAGCTCGTT 60.956 57.895 0.00 0.00 0.00 3.85
640 2683 1.927174 CATCAACCTTCTAACTCGCCG 59.073 52.381 0.00 0.00 0.00 6.46
642 2685 3.123621 CACACATCAACCTTCTAACTCGC 59.876 47.826 0.00 0.00 0.00 5.03
673 2716 1.203052 CTGTAAATGGCCTTGGTGCAG 59.797 52.381 3.32 5.35 0.00 4.41
674 2717 1.255882 CTGTAAATGGCCTTGGTGCA 58.744 50.000 3.32 0.00 0.00 4.57
676 2719 3.573967 AGAAACTGTAAATGGCCTTGGTG 59.426 43.478 3.32 0.00 0.00 4.17
677 2720 3.844640 AGAAACTGTAAATGGCCTTGGT 58.155 40.909 3.32 0.00 0.00 3.67
678 2721 4.871933 AAGAAACTGTAAATGGCCTTGG 57.128 40.909 3.32 0.00 0.00 3.61
679 2722 7.542130 GTGAATAAGAAACTGTAAATGGCCTTG 59.458 37.037 3.32 0.00 0.00 3.61
680 2723 7.309805 GGTGAATAAGAAACTGTAAATGGCCTT 60.310 37.037 3.32 0.00 0.00 4.35
681 2724 6.152831 GGTGAATAAGAAACTGTAAATGGCCT 59.847 38.462 3.32 0.00 0.00 5.19
682 2725 6.071616 TGGTGAATAAGAAACTGTAAATGGCC 60.072 38.462 0.00 0.00 0.00 5.36
683 2726 6.919721 TGGTGAATAAGAAACTGTAAATGGC 58.080 36.000 0.00 0.00 0.00 4.40
716 3900 2.834689 CCGTGTTTCACACTAAATCGC 58.165 47.619 5.53 0.00 46.46 4.58
726 3910 5.554822 TTTATAATCTGGCCGTGTTTCAC 57.445 39.130 0.00 0.00 0.00 3.18
734 4216 2.814336 GCCTCCTTTTATAATCTGGCCG 59.186 50.000 0.00 0.00 33.66 6.13
740 4222 6.264744 GGGGTTACTTGCCTCCTTTTATAATC 59.735 42.308 0.00 0.00 0.00 1.75
744 4226 3.623954 CGGGGTTACTTGCCTCCTTTTAT 60.624 47.826 0.00 0.00 0.00 1.40
793 4275 5.261209 TGCCATTATTTTTCTCGGAATGG 57.739 39.130 7.44 7.44 38.86 3.16
794 4276 5.750067 CCTTGCCATTATTTTTCTCGGAATG 59.250 40.000 0.00 0.00 0.00 2.67
795 4277 5.682212 GCCTTGCCATTATTTTTCTCGGAAT 60.682 40.000 0.00 0.00 0.00 3.01
797 4279 3.130340 GCCTTGCCATTATTTTTCTCGGA 59.870 43.478 0.00 0.00 0.00 4.55
848 4384 1.563879 ACCATGGTGGCTGCTTATACA 59.436 47.619 18.99 0.00 42.67 2.29
849 4385 2.222027 GACCATGGTGGCTGCTTATAC 58.778 52.381 25.52 0.00 42.67 1.47
868 4407 0.956633 AGGCGTTTGTACTGAGACGA 59.043 50.000 12.58 0.00 37.69 4.20
889 4428 3.057876 ACGACACTAAGCTGAGAAGACAG 60.058 47.826 4.63 0.00 40.43 3.51
894 4433 1.544691 GGGACGACACTAAGCTGAGAA 59.455 52.381 4.63 0.00 0.00 2.87
900 4439 1.516603 GCGAGGGACGACACTAAGC 60.517 63.158 0.00 0.00 45.77 3.09
919 4466 2.597510 GGCGGTGGCTGGTTCTTT 60.598 61.111 0.00 0.00 39.81 2.52
964 4513 3.823330 GACGCCGGAGACCACGAT 61.823 66.667 13.83 0.00 0.00 3.73
1412 5009 0.848053 AGGGTGAAACGGGGAAGAAA 59.152 50.000 0.00 0.00 38.12 2.52
1444 5042 1.108776 CCAATCAAGCCCTCCATGTG 58.891 55.000 0.00 0.00 0.00 3.21
1467 5070 2.036256 CCTTTGCCAGGGGTCCAG 59.964 66.667 0.00 0.00 39.39 3.86
1471 5074 1.838396 CTTTGCCTTTGCCAGGGGT 60.838 57.895 1.35 0.00 44.16 4.95
1497 5115 3.207669 CAGCTGGCGATTGGCTCC 61.208 66.667 5.57 0.00 42.94 4.70
1526 5149 0.468585 TCCACGCAGGGGTATATCGT 60.469 55.000 0.00 0.00 38.24 3.73
1589 5215 2.123726 AATGCGGCAGAATCCCCC 60.124 61.111 9.25 0.00 0.00 5.40
1598 5224 2.479566 AGAAGAAGAAGAATGCGGCA 57.520 45.000 4.58 4.58 0.00 5.69
1637 5362 6.935741 TCTAGAGCTAGCTACAAGAAGAAG 57.064 41.667 19.38 5.00 33.32 2.85
1638 5363 7.287061 AGATCTAGAGCTAGCTACAAGAAGAA 58.713 38.462 19.38 0.03 33.32 2.52
1640 5365 8.256611 CTAGATCTAGAGCTAGCTACAAGAAG 57.743 42.308 27.25 10.82 40.05 2.85
1674 5405 3.341823 GAAGAAGAAGCTCCATTGCAGA 58.658 45.455 0.00 0.00 34.99 4.26
1704 5435 4.080356 TCATGACCTCAAAATCCCTACCAG 60.080 45.833 0.00 0.00 0.00 4.00
1731 5464 2.287915 CCTTGCGGCTTACATGATGTAC 59.712 50.000 4.50 0.00 31.69 2.90
1732 5465 2.093181 ACCTTGCGGCTTACATGATGTA 60.093 45.455 0.23 0.23 0.00 2.29
1838 5583 2.663826 AGCTGGAGATCGTTGAAGAC 57.336 50.000 0.00 0.00 0.00 3.01
1839 5584 2.099921 GCTAGCTGGAGATCGTTGAAGA 59.900 50.000 7.70 0.00 0.00 2.87
1840 5585 2.100584 AGCTAGCTGGAGATCGTTGAAG 59.899 50.000 18.57 0.00 0.00 3.02
1841 5586 2.103373 AGCTAGCTGGAGATCGTTGAA 58.897 47.619 18.57 0.00 0.00 2.69
1842 5587 1.769026 AGCTAGCTGGAGATCGTTGA 58.231 50.000 18.57 0.00 0.00 3.18
1843 5588 2.593346 AAGCTAGCTGGAGATCGTTG 57.407 50.000 20.16 0.00 0.00 4.10
1844 5589 4.081642 TGTTAAAGCTAGCTGGAGATCGTT 60.082 41.667 20.16 8.64 0.00 3.85
1845 5590 3.447586 TGTTAAAGCTAGCTGGAGATCGT 59.552 43.478 20.16 0.00 0.00 3.73
1846 5591 4.046938 TGTTAAAGCTAGCTGGAGATCG 57.953 45.455 20.16 0.00 0.00 3.69
1913 5663 5.746952 GCCCCAAGTAGTTTAGTAACTGGTT 60.747 44.000 0.00 0.00 44.22 3.67
1936 5695 4.184079 AGAAAAGAAATGCATCCACAGC 57.816 40.909 0.00 0.00 0.00 4.40
1951 5710 4.511826 ACAAGCCTAGACGTTCAAGAAAAG 59.488 41.667 0.00 0.00 0.00 2.27
1956 5715 3.026630 TCACAAGCCTAGACGTTCAAG 57.973 47.619 0.00 0.00 0.00 3.02
1970 5729 5.178996 GCCTCTGAAGTATATGCATCACAAG 59.821 44.000 0.19 2.88 0.00 3.16
1999 5758 0.313043 CTGGCAAGCAGTTGTGAAGG 59.687 55.000 0.00 0.00 35.92 3.46
2029 5788 4.829492 GCTATTCTGAACCTGGCCATAAAT 59.171 41.667 5.51 1.45 0.00 1.40
2053 5812 6.425210 TCTGTATGGCTCTATATGCAGTTT 57.575 37.500 0.00 0.00 37.96 2.66
2054 5813 6.617782 ATCTGTATGGCTCTATATGCAGTT 57.382 37.500 0.00 0.00 37.96 3.16
2061 5820 5.123979 CGCACTGTATCTGTATGGCTCTATA 59.876 44.000 0.00 0.00 0.00 1.31
2062 5821 4.082517 CGCACTGTATCTGTATGGCTCTAT 60.083 45.833 0.00 0.00 0.00 1.98
2095 5854 7.121911 GCTTTGAAAAGAAGTTCTGCAAAATC 58.878 34.615 20.20 14.60 38.28 2.17
2102 5861 4.035675 ACTCCGCTTTGAAAAGAAGTTCTG 59.964 41.667 6.06 0.00 38.28 3.02
2103 5862 4.200092 ACTCCGCTTTGAAAAGAAGTTCT 58.800 39.130 6.98 0.00 38.28 3.01
2110 5869 7.749539 TTTCTTTTTACTCCGCTTTGAAAAG 57.250 32.000 0.00 0.00 39.03 2.27
2131 5890 5.293569 CCGGTTGTAGATGGTCTTACATTTC 59.706 44.000 0.00 0.00 0.00 2.17
2134 5893 4.028131 TCCGGTTGTAGATGGTCTTACAT 58.972 43.478 0.00 0.00 0.00 2.29
2135 5894 3.194116 GTCCGGTTGTAGATGGTCTTACA 59.806 47.826 0.00 0.00 0.00 2.41
2136 5895 3.446516 AGTCCGGTTGTAGATGGTCTTAC 59.553 47.826 0.00 0.00 0.00 2.34
2137 5896 3.705051 AGTCCGGTTGTAGATGGTCTTA 58.295 45.455 0.00 0.00 0.00 2.10
2139 5898 2.233305 AGTCCGGTTGTAGATGGTCT 57.767 50.000 0.00 0.00 0.00 3.85
2141 5900 1.278127 CCAAGTCCGGTTGTAGATGGT 59.722 52.381 0.00 0.00 0.00 3.55
2142 5901 2.012051 GCCAAGTCCGGTTGTAGATGG 61.012 57.143 0.00 3.16 0.00 3.51
2151 5910 1.340248 CGTAGATATGCCAAGTCCGGT 59.660 52.381 0.00 0.00 0.00 5.28
2197 5956 3.685139 ATTTGAGACGTGACCAGTCAT 57.315 42.857 3.41 0.00 42.18 3.06
2200 5959 6.032956 TGTATTATTTGAGACGTGACCAGT 57.967 37.500 0.00 0.00 0.00 4.00
2206 5965 7.302350 TGTGGAATGTATTATTTGAGACGTG 57.698 36.000 0.00 0.00 0.00 4.49
2221 5980 5.114764 TGACATATGTGGATGTGGAATGT 57.885 39.130 14.43 0.00 40.18 2.71
2222 5981 7.066645 GGATATGACATATGTGGATGTGGAATG 59.933 40.741 14.43 0.00 40.18 2.67
2239 5998 7.738437 TGAATATAGGATGCTGGATATGACA 57.262 36.000 0.00 0.00 0.00 3.58
2240 5999 9.703892 GTATGAATATAGGATGCTGGATATGAC 57.296 37.037 0.00 0.00 0.00 3.06
2249 6008 8.865090 GCATAGGTAGTATGAATATAGGATGCT 58.135 37.037 0.00 0.00 41.17 3.79
2261 6020 7.301868 TCATCATGTTGCATAGGTAGTATGA 57.698 36.000 0.00 0.00 41.17 2.15
2271 6030 6.918022 CGTAGAGTAGTTCATCATGTTGCATA 59.082 38.462 0.00 0.00 0.00 3.14
2278 6037 4.210832 TCGCGTAGAGTAGTTCATCATG 57.789 45.455 5.77 0.00 0.00 3.07
2279 6038 4.599047 GTTCGCGTAGAGTAGTTCATCAT 58.401 43.478 5.77 0.00 0.00 2.45
2290 6049 1.129998 TCTTTCTCCGTTCGCGTAGAG 59.870 52.381 5.77 8.48 36.93 2.43
2301 6060 2.279741 TGATGCCGATTTCTTTCTCCG 58.720 47.619 0.00 0.00 0.00 4.63
2303 6062 4.091424 CGTTTGATGCCGATTTCTTTCTC 58.909 43.478 0.00 0.00 0.00 2.87
2348 6107 3.697542 TGATCTTTTGGATGATGCAGTGG 59.302 43.478 0.00 0.00 34.33 4.00
2349 6108 4.439700 GGTGATCTTTTGGATGATGCAGTG 60.440 45.833 0.00 0.00 34.33 3.66
2351 6110 3.242969 CGGTGATCTTTTGGATGATGCAG 60.243 47.826 0.00 0.00 34.33 4.41
2353 6112 2.033801 CCGGTGATCTTTTGGATGATGC 59.966 50.000 0.00 0.00 34.33 3.91


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

AutoCloner maintained by Alex Coulton.