Multiple sequence alignment - TraesCS7D01G340500

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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 TraesCS7D01G340500 chr7D 100.000 2843 0 0 1 2843 436475481 436478323 0.000000e+00 5251.0
1 TraesCS7D01G340500 chr7D 87.172 725 89 4 1 722 421148118 421147395 0.000000e+00 821.0
2 TraesCS7D01G340500 chr7B 93.678 1123 50 7 703 1804 453112678 453113800 0.000000e+00 1661.0
3 TraesCS7D01G340500 chr7B 90.741 270 21 2 2244 2511 453114968 453115235 9.690000e-95 357.0
4 TraesCS7D01G340500 chr7B 86.166 253 17 4 2597 2842 453117474 453117715 1.010000e-64 257.0
5 TraesCS7D01G340500 chr7B 86.826 167 16 4 1984 2147 453114092 453114255 6.260000e-42 182.0
6 TraesCS7D01G340500 chr7B 94.340 53 3 0 2165 2217 518929528 518929580 6.530000e-12 82.4
7 TraesCS7D01G340500 chr7A 88.296 1162 86 17 740 1861 486180730 486179579 0.000000e+00 1347.0
8 TraesCS7D01G340500 chr7A 87.847 288 23 6 2320 2599 486178979 486178696 7.590000e-86 327.0
9 TraesCS7D01G340500 chr7A 83.333 246 21 8 2597 2842 486178656 486178431 2.870000e-50 209.0
10 TraesCS7D01G340500 chr7A 97.619 42 1 0 2253 2294 486179022 486178981 3.930000e-09 73.1
11 TraesCS7D01G340500 chr5D 90.767 704 56 9 3 703 443352264 443352961 0.000000e+00 931.0
12 TraesCS7D01G340500 chr2D 89.400 717 61 6 1 705 601265778 601265065 0.000000e+00 889.0
13 TraesCS7D01G340500 chr2D 81.579 722 91 21 1 703 116650596 116649898 2.470000e-155 558.0
14 TraesCS7D01G340500 chr2D 97.143 35 1 0 2182 2216 376364947 376364913 3.060000e-05 60.2
15 TraesCS7D01G340500 chr3D 87.758 727 59 10 1 703 63396376 63395656 0.000000e+00 822.0
16 TraesCS7D01G340500 chr1B 87.340 703 79 4 1 703 223767804 223768496 0.000000e+00 797.0
17 TraesCS7D01G340500 chr1B 89.286 56 6 0 2162 2217 482703652 482703707 1.410000e-08 71.3
18 TraesCS7D01G340500 chr3B 86.750 717 77 12 1 709 666806731 666806025 0.000000e+00 782.0
19 TraesCS7D01G340500 chr5B 90.317 568 48 7 1 565 628674540 628673977 0.000000e+00 737.0
20 TraesCS7D01G340500 chr5B 89.789 568 51 7 1 565 625094991 625094428 0.000000e+00 721.0
21 TraesCS7D01G340500 chr5B 88.037 535 52 10 77 605 626833504 626832976 8.650000e-175 623.0
22 TraesCS7D01G340500 chr5B 87.664 535 54 10 77 605 623162457 623161929 1.870000e-171 612.0
23 TraesCS7D01G340500 chr5B 91.228 57 4 1 2160 2216 544408155 544408100 3.040000e-10 76.8
24 TraesCS7D01G340500 chr5B 89.474 57 5 1 2160 2216 622082303 622082248 1.410000e-08 71.3
25 TraesCS7D01G340500 chr6B 91.071 56 5 0 2161 2216 102080242 102080187 3.040000e-10 76.8
26 TraesCS7D01G340500 chr6B 92.593 54 3 1 2160 2213 690342203 690342255 3.040000e-10 76.8
27 TraesCS7D01G340500 chr2B 92.453 53 3 1 2165 2217 784485669 784485720 1.090000e-09 75.0
28 TraesCS7D01G340500 chr1D 92.453 53 3 1 2165 2217 234045482 234045533 1.090000e-09 75.0
29 TraesCS7D01G340500 chr6A 92.157 51 4 0 2170 2220 513334071 513334021 3.930000e-09 73.1
30 TraesCS7D01G340500 chr3A 90.741 54 4 1 2160 2213 646736494 646736546 1.410000e-08 71.3
31 TraesCS7D01G340500 chr6D 95.455 44 1 1 2170 2213 79596760 79596802 5.080000e-08 69.4


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 TraesCS7D01G340500 chr7D 436475481 436478323 2842 False 5251.000 5251 100.00000 1 2843 1 chr7D.!!$F1 2842
1 TraesCS7D01G340500 chr7D 421147395 421148118 723 True 821.000 821 87.17200 1 722 1 chr7D.!!$R1 721
2 TraesCS7D01G340500 chr7B 453112678 453117715 5037 False 614.250 1661 89.35275 703 2842 4 chr7B.!!$F2 2139
3 TraesCS7D01G340500 chr7A 486178431 486180730 2299 True 489.025 1347 89.27375 740 2842 4 chr7A.!!$R1 2102
4 TraesCS7D01G340500 chr5D 443352264 443352961 697 False 931.000 931 90.76700 3 703 1 chr5D.!!$F1 700
5 TraesCS7D01G340500 chr2D 601265065 601265778 713 True 889.000 889 89.40000 1 705 1 chr2D.!!$R3 704
6 TraesCS7D01G340500 chr2D 116649898 116650596 698 True 558.000 558 81.57900 1 703 1 chr2D.!!$R1 702
7 TraesCS7D01G340500 chr3D 63395656 63396376 720 True 822.000 822 87.75800 1 703 1 chr3D.!!$R1 702
8 TraesCS7D01G340500 chr1B 223767804 223768496 692 False 797.000 797 87.34000 1 703 1 chr1B.!!$F1 702
9 TraesCS7D01G340500 chr3B 666806025 666806731 706 True 782.000 782 86.75000 1 709 1 chr3B.!!$R1 708
10 TraesCS7D01G340500 chr5B 628673977 628674540 563 True 737.000 737 90.31700 1 565 1 chr5B.!!$R6 564
11 TraesCS7D01G340500 chr5B 625094428 625094991 563 True 721.000 721 89.78900 1 565 1 chr5B.!!$R4 564
12 TraesCS7D01G340500 chr5B 626832976 626833504 528 True 623.000 623 88.03700 77 605 1 chr5B.!!$R5 528
13 TraesCS7D01G340500 chr5B 623161929 623162457 528 True 612.000 612 87.66400 77 605 1 chr5B.!!$R3 528

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
524 575 0.97401 TTTCGACCCGTATCTGCCCT 60.974 55.0 0.0 0.0 0.0 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2383 3430 0.037232 GCCAACGGTAGAAGCTGACT 60.037 55.0 0.0 0.0 0.0 3.41 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
318 337 2.671963 GGCCCTTGTTCGTCCACC 60.672 66.667 0.00 0.00 0.00 4.61
320 339 1.966451 GCCCTTGTTCGTCCACCTG 60.966 63.158 0.00 0.00 0.00 4.00
461 510 1.813513 CGGCAAGAAATGTGAGGAGT 58.186 50.000 0.00 0.00 0.00 3.85
486 536 2.813908 GGAATTGCGGCGAGACGT 60.814 61.111 12.98 0.00 35.98 4.34
524 575 0.974010 TTTCGACCCGTATCTGCCCT 60.974 55.000 0.00 0.00 0.00 5.19
548 599 5.128171 TGTGAACCCGTAGATATACTGCTTT 59.872 40.000 0.00 0.00 0.00 3.51
553 604 3.323979 CCGTAGATATACTGCTTTGGGGT 59.676 47.826 0.00 0.00 0.00 4.95
574 637 2.936032 GGGAGGGAGTTGTGGGCT 60.936 66.667 0.00 0.00 0.00 5.19
626 689 2.436109 GGGCTCTGTTCTGGCCAA 59.564 61.111 7.01 0.00 46.87 4.52
630 693 1.620323 GGCTCTGTTCTGGCCAAAAAT 59.380 47.619 7.01 0.00 44.69 1.82
655 718 1.440060 CAAGCCCGTATACTCGCCA 59.560 57.895 0.56 0.00 0.00 5.69
665 728 4.438200 CCGTATACTCGCCAAAATTTTGCT 60.438 41.667 22.90 7.73 36.86 3.91
682 745 1.135333 TGCTGGTTCGCGACATATACA 59.865 47.619 9.15 0.00 0.00 2.29
777 840 4.292186 ACAGAGTCAAACATATGCACCT 57.708 40.909 1.58 0.00 0.00 4.00
890 956 9.490379 AATAGACGGAAAAATAATAATCTCGCT 57.510 29.630 0.00 0.00 0.00 4.93
923 998 2.033675 TGACTGAACATTTGTGCTGCAG 59.966 45.455 10.11 10.11 0.00 4.41
968 1045 7.539366 GCTCTAGCTACGAATTAAACAGATAGG 59.461 40.741 0.00 0.00 38.21 2.57
1019 1103 7.348080 TCAGTATGATCTTAGTACCACCAAG 57.652 40.000 0.00 0.00 42.56 3.61
1022 1106 4.471904 TGATCTTAGTACCACCAAGCAG 57.528 45.455 0.00 0.00 0.00 4.24
1034 1118 0.029300 CCAAGCAGGTCACAACAACG 59.971 55.000 0.00 0.00 0.00 4.10
1054 1138 2.013563 GCTTCCAGTGCCGATCATCAA 61.014 52.381 0.00 0.00 0.00 2.57
1059 1143 0.673333 AGTGCCGATCATCAAACGCA 60.673 50.000 0.00 0.00 0.00 5.24
1065 1149 2.652893 GATCATCAAACGCAGCCGCC 62.653 60.000 0.00 0.00 38.22 6.13
1605 1704 3.313874 CCTCCTCAGGCCGACATT 58.686 61.111 0.00 0.00 30.98 2.71
1758 1866 2.965831 TGAGGGTAGGATGTACATGCTC 59.034 50.000 30.31 21.02 40.14 4.26
1790 1902 4.851558 GTCATGGCTGTATTTTTGTTCGAC 59.148 41.667 0.00 0.00 0.00 4.20
1827 1939 8.734386 GTCCATGGTTTCATAGGATTAATGATC 58.266 37.037 12.58 0.00 35.05 2.92
1828 1940 7.607607 TCCATGGTTTCATAGGATTAATGATCG 59.392 37.037 12.58 0.00 33.52 3.69
1829 1941 7.607607 CCATGGTTTCATAGGATTAATGATCGA 59.392 37.037 2.57 0.00 33.52 3.59
1830 1942 9.170734 CATGGTTTCATAGGATTAATGATCGAT 57.829 33.333 0.00 0.00 33.52 3.59
1831 1943 8.777865 TGGTTTCATAGGATTAATGATCGATC 57.222 34.615 18.72 18.72 35.49 3.69
1893 2005 4.860802 TGGATCTCTCTGTCTTCTCTCT 57.139 45.455 0.00 0.00 0.00 3.10
1897 2009 5.163258 GGATCTCTCTGTCTTCTCTCTCTCT 60.163 48.000 0.00 0.00 0.00 3.10
1898 2010 5.344743 TCTCTCTGTCTTCTCTCTCTCTC 57.655 47.826 0.00 0.00 0.00 3.20
1900 2012 6.194967 TCTCTCTGTCTTCTCTCTCTCTCTA 58.805 44.000 0.00 0.00 0.00 2.43
1901 2013 6.096987 TCTCTCTGTCTTCTCTCTCTCTCTAC 59.903 46.154 0.00 0.00 0.00 2.59
1902 2014 5.719563 TCTCTGTCTTCTCTCTCTCTCTACA 59.280 44.000 0.00 0.00 0.00 2.74
1905 2017 6.666113 TCTGTCTTCTCTCTCTCTCTACAGTA 59.334 42.308 0.00 0.00 34.77 2.74
1906 2018 7.344612 TCTGTCTTCTCTCTCTCTCTACAGTAT 59.655 40.741 0.00 0.00 34.77 2.12
1909 2021 9.174166 GTCTTCTCTCTCTCTCTACAGTATTTT 57.826 37.037 0.00 0.00 0.00 1.82
1912 2024 9.961264 TTCTCTCTCTCTCTACAGTATTTTACA 57.039 33.333 0.00 0.00 0.00 2.41
1929 2041 9.921637 GTATTTTACAAATTTCAGGAACATCCA 57.078 29.630 0.00 0.00 39.61 3.41
1932 2044 5.410355 ACAAATTTCAGGAACATCCATGG 57.590 39.130 4.97 4.97 39.61 3.66
1933 2045 5.085920 ACAAATTTCAGGAACATCCATGGA 58.914 37.500 18.88 18.88 39.61 3.41
1934 2046 5.543405 ACAAATTTCAGGAACATCCATGGAA 59.457 36.000 20.67 1.96 39.61 3.53
1936 2048 2.806945 TCAGGAACATCCATGGAACC 57.193 50.000 20.67 18.53 39.61 3.62
1937 2049 1.991813 TCAGGAACATCCATGGAACCA 59.008 47.619 20.67 0.00 39.61 3.67
1938 2050 2.582172 TCAGGAACATCCATGGAACCAT 59.418 45.455 20.67 5.41 39.61 3.55
1939 2051 3.785325 TCAGGAACATCCATGGAACCATA 59.215 43.478 20.67 9.13 39.61 2.74
1940 2052 4.139786 CAGGAACATCCATGGAACCATAG 58.860 47.826 20.67 7.28 39.61 2.23
1941 2053 3.139025 AGGAACATCCATGGAACCATAGG 59.861 47.826 20.67 10.11 39.61 2.57
1942 2054 3.117512 GGAACATCCATGGAACCATAGGT 60.118 47.826 20.67 0.00 36.28 3.08
1943 2055 3.582998 ACATCCATGGAACCATAGGTG 57.417 47.619 20.67 12.30 35.34 4.00
1984 2359 5.275067 ACTAATTTGCACACACCAATGTT 57.725 34.783 0.00 0.00 36.72 2.71
1986 2361 6.112058 ACTAATTTGCACACACCAATGTTTT 58.888 32.000 0.00 0.00 36.72 2.43
1987 2362 7.268586 ACTAATTTGCACACACCAATGTTTTA 58.731 30.769 0.00 0.00 36.72 1.52
1991 2366 6.992063 TTGCACACACCAATGTTTTATTTT 57.008 29.167 0.00 0.00 36.72 1.82
2029 2415 4.918810 AGAAAAACAAGGACGAAGCAAT 57.081 36.364 0.00 0.00 0.00 3.56
2078 2491 4.079558 AGCCACCTCTTTGATGAACCATAT 60.080 41.667 0.00 0.00 0.00 1.78
2095 2508 4.103153 ACCATATGATCTTGATCCAACGGT 59.897 41.667 3.65 6.99 0.00 4.83
2128 2542 1.840635 GCTCCCATCACTAACCTTCCT 59.159 52.381 0.00 0.00 0.00 3.36
2150 2564 7.062322 TCCTATATGCATTTCCACAAGAATGT 58.938 34.615 3.54 0.00 41.61 2.71
2153 2567 2.562298 TGCATTTCCACAAGAATGTCCC 59.438 45.455 0.00 0.00 37.82 4.46
2154 2568 2.562298 GCATTTCCACAAGAATGTCCCA 59.438 45.455 0.00 0.00 37.82 4.37
2155 2569 3.196254 GCATTTCCACAAGAATGTCCCAT 59.804 43.478 0.00 0.00 37.82 4.00
2156 2570 4.402155 GCATTTCCACAAGAATGTCCCATA 59.598 41.667 0.00 0.00 37.82 2.74
2157 2571 5.679638 GCATTTCCACAAGAATGTCCCATAC 60.680 44.000 0.00 0.00 37.82 2.39
2158 2572 4.649267 TTCCACAAGAATGTCCCATACA 57.351 40.909 0.00 0.00 43.86 2.29
2159 2573 3.950397 TCCACAAGAATGTCCCATACAC 58.050 45.455 0.00 0.00 42.09 2.90
2160 2574 2.677836 CCACAAGAATGTCCCATACACG 59.322 50.000 0.00 0.00 42.09 4.49
2164 2578 2.467880 AGAATGTCCCATACACGGTCT 58.532 47.619 0.00 0.00 42.09 3.85
2165 2579 2.838202 AGAATGTCCCATACACGGTCTT 59.162 45.455 0.00 0.00 42.09 3.01
2166 2580 2.981859 ATGTCCCATACACGGTCTTC 57.018 50.000 0.00 0.00 42.09 2.87
2167 2581 0.528924 TGTCCCATACACGGTCTTCG 59.471 55.000 0.00 0.00 45.88 3.79
2177 2591 3.247033 CGGTCTTCGTCCGGTTATC 57.753 57.895 0.00 0.00 43.68 1.75
2178 2592 0.248784 CGGTCTTCGTCCGGTTATCC 60.249 60.000 0.00 0.00 43.68 2.59
2199 2613 9.841295 TTATCCGTTAATTAACTAGGCAATTCT 57.159 29.630 22.57 5.31 34.12 2.40
2210 2624 6.054860 ACTAGGCAATTCTCTTCTGCTTAA 57.945 37.500 0.00 0.00 36.32 1.85
2211 2625 6.657875 ACTAGGCAATTCTCTTCTGCTTAAT 58.342 36.000 0.00 0.00 36.32 1.40
2212 2626 7.115414 ACTAGGCAATTCTCTTCTGCTTAATT 58.885 34.615 0.00 0.00 36.32 1.40
2214 2628 5.948162 AGGCAATTCTCTTCTGCTTAATTGA 59.052 36.000 9.58 0.00 38.99 2.57
2215 2629 6.606395 AGGCAATTCTCTTCTGCTTAATTGAT 59.394 34.615 9.58 0.00 38.99 2.57
2216 2630 6.916932 GGCAATTCTCTTCTGCTTAATTGATC 59.083 38.462 9.58 0.00 38.99 2.92
2217 2631 7.415989 GGCAATTCTCTTCTGCTTAATTGATCA 60.416 37.037 9.58 0.00 38.99 2.92
2218 2632 7.972277 GCAATTCTCTTCTGCTTAATTGATCAA 59.028 33.333 11.26 11.26 38.99 2.57
2222 2636 7.478322 TCTCTTCTGCTTAATTGATCAATTGC 58.522 34.615 33.94 29.44 40.83 3.56
2223 2637 7.121611 TCTCTTCTGCTTAATTGATCAATTGCA 59.878 33.333 33.94 31.53 40.83 4.08
2224 2638 7.778083 TCTTCTGCTTAATTGATCAATTGCAT 58.222 30.769 33.94 17.20 40.83 3.96
2225 2639 7.919091 TCTTCTGCTTAATTGATCAATTGCATC 59.081 33.333 33.94 22.45 40.83 3.91
2226 2640 6.203647 TCTGCTTAATTGATCAATTGCATCG 58.796 36.000 33.94 24.76 40.83 3.84
2227 2641 5.893687 TGCTTAATTGATCAATTGCATCGT 58.106 33.333 33.94 15.61 40.83 3.73
2228 2642 6.331845 TGCTTAATTGATCAATTGCATCGTT 58.668 32.000 33.94 15.59 40.83 3.85
2230 2644 7.009448 TGCTTAATTGATCAATTGCATCGTTTC 59.991 33.333 33.94 16.99 40.83 2.78
2231 2645 7.009448 GCTTAATTGATCAATTGCATCGTTTCA 59.991 33.333 33.94 14.32 40.83 2.69
2233 2647 7.655236 AATTGATCAATTGCATCGTTTCAAA 57.345 28.000 28.57 0.00 39.36 2.69
2236 2650 7.107834 TGATCAATTGCATCGTTTCAAAAAG 57.892 32.000 0.00 0.00 0.00 2.27
2294 3339 4.272100 GCCAGCAGCAAAACCATG 57.728 55.556 0.00 0.00 42.97 3.66
2306 3351 2.627699 CAAAACCATGCCAGTAACAGGT 59.372 45.455 0.00 0.00 0.00 4.00
2313 3358 0.685097 GCCAGTAACAGGTGTGGAGA 59.315 55.000 0.00 0.00 31.04 3.71
2335 3380 3.119990 ACGCACACCAATTAGAATTTCCG 60.120 43.478 0.00 0.00 0.00 4.30
2353 3398 6.721571 TTTCCGTTCAGTCTATTTAGCTTG 57.278 37.500 0.00 0.00 0.00 4.01
2383 3430 1.930133 AGGCATCCACCATGTCCCA 60.930 57.895 0.00 0.00 37.92 4.37
2426 3474 2.157668 CCGACATGAAGGAAAGTTCACG 59.842 50.000 0.00 0.00 39.25 4.35
2477 3525 1.300963 CCTGTCACATCCAGGGGTG 59.699 63.158 0.00 0.00 44.77 4.61
2555 5734 0.029300 TTGACAGCTGTTTTGCGCTC 59.971 50.000 22.65 5.86 38.13 5.03
2564 5743 1.000385 TGTTTTGCGCTCCCAATCAAG 60.000 47.619 9.73 0.00 0.00 3.02
2566 5745 0.881118 TTTGCGCTCCCAATCAAGTC 59.119 50.000 9.73 0.00 0.00 3.01
2569 5748 0.674895 GCGCTCCCAATCAAGTCACT 60.675 55.000 0.00 0.00 0.00 3.41
2650 5891 3.485947 AAATGACACACACACACACAC 57.514 42.857 0.00 0.00 0.00 3.82
2651 5892 2.106477 ATGACACACACACACACACA 57.894 45.000 0.00 0.00 0.00 3.72
2652 5893 1.152510 TGACACACACACACACACAC 58.847 50.000 0.00 0.00 0.00 3.82
2653 5894 1.152510 GACACACACACACACACACA 58.847 50.000 0.00 0.00 0.00 3.72
2654 5895 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2655 5896 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2656 5897 1.136000 CACACACACACACACACACAG 60.136 52.381 0.00 0.00 0.00 3.66
2657 5898 1.270571 ACACACACACACACACACAGA 60.271 47.619 0.00 0.00 0.00 3.41
2658 5899 1.394572 CACACACACACACACACAGAG 59.605 52.381 0.00 0.00 0.00 3.35
2659 5900 0.374758 CACACACACACACACAGAGC 59.625 55.000 0.00 0.00 0.00 4.09
2660 5901 0.036483 ACACACACACACACAGAGCA 60.036 50.000 0.00 0.00 0.00 4.26
2661 5902 0.654160 CACACACACACACAGAGCAG 59.346 55.000 0.00 0.00 0.00 4.24
2662 5903 1.091771 ACACACACACACAGAGCAGC 61.092 55.000 0.00 0.00 0.00 5.25
2663 5904 1.524621 ACACACACACAGAGCAGCC 60.525 57.895 0.00 0.00 0.00 4.85
2664 5905 2.111878 ACACACACAGAGCAGCCC 59.888 61.111 0.00 0.00 0.00 5.19
2665 5906 2.670934 CACACACAGAGCAGCCCC 60.671 66.667 0.00 0.00 0.00 5.80
2666 5907 3.170672 ACACACAGAGCAGCCCCA 61.171 61.111 0.00 0.00 0.00 4.96
2706 5947 1.437986 GAGCCGACGACCTTGCTAT 59.562 57.895 0.00 0.00 33.41 2.97
2707 5948 0.872021 GAGCCGACGACCTTGCTATG 60.872 60.000 0.00 0.00 33.41 2.23
2708 5949 2.526120 GCCGACGACCTTGCTATGC 61.526 63.158 0.00 0.00 0.00 3.14
2709 5950 1.141881 CCGACGACCTTGCTATGCT 59.858 57.895 0.00 0.00 0.00 3.79
2710 5951 0.384309 CCGACGACCTTGCTATGCTA 59.616 55.000 0.00 0.00 0.00 3.49
2732 5973 1.608283 CCAAGGGACCAGAGTCGAAAC 60.608 57.143 0.00 0.00 44.54 2.78
2791 6032 1.732809 GCGGTTGAGAAGAAGCTTACC 59.267 52.381 0.00 0.00 0.00 2.85
2842 6083 0.322816 TCAGCCCTTGCAGAATCACC 60.323 55.000 0.00 0.00 41.13 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 4.223964 GGCCGATTTCGACGCAGC 62.224 66.667 0.67 0.00 43.02 5.25
29 30 3.115892 GTGGCCGATTTCGACGCA 61.116 61.111 0.00 0.00 43.02 5.24
446 491 3.244700 CCACTCCACTCCTCACATTTCTT 60.245 47.826 0.00 0.00 0.00 2.52
461 510 2.354729 CCGCAATTCCCCACTCCA 59.645 61.111 0.00 0.00 0.00 3.86
486 536 2.445845 CCTATCCCCTCGCCACCA 60.446 66.667 0.00 0.00 0.00 4.17
494 544 2.926539 GGTCGAAACCCTATCCCCT 58.073 57.895 0.00 0.00 39.93 4.79
524 575 4.212716 AGCAGTATATCTACGGGTTCACA 58.787 43.478 0.00 0.00 31.05 3.58
560 611 4.335647 CGCAGCCCACAACTCCCT 62.336 66.667 0.00 0.00 0.00 4.20
563 614 0.887387 TTTACCGCAGCCCACAACTC 60.887 55.000 0.00 0.00 0.00 3.01
564 615 0.466555 TTTTACCGCAGCCCACAACT 60.467 50.000 0.00 0.00 0.00 3.16
626 689 1.419381 ACGGGCTTGGTCCAAATTTT 58.581 45.000 5.64 0.00 0.00 1.82
630 693 1.910671 AGTATACGGGCTTGGTCCAAA 59.089 47.619 5.64 0.00 0.00 3.28
638 701 0.538118 TTTGGCGAGTATACGGGCTT 59.462 50.000 19.11 0.00 0.00 4.35
655 718 2.124122 GTCGCGAACCAGCAAAATTTT 58.876 42.857 12.06 0.00 36.85 1.82
665 728 1.067974 CCCTGTATATGTCGCGAACCA 59.932 52.381 12.06 6.02 0.00 3.67
682 745 1.190643 GAGCAACTCTAGCAGACCCT 58.809 55.000 0.00 0.00 0.00 4.34
777 840 0.968405 GGCCTTCCTCATGCACAAAA 59.032 50.000 0.00 0.00 0.00 2.44
890 956 4.118093 TGTTCAGTCAAACGAAGACTCA 57.882 40.909 6.27 1.15 44.11 3.41
923 998 6.658188 AGAGCAGGTATAAATAGGACAGAC 57.342 41.667 0.00 0.00 0.00 3.51
1019 1103 0.317020 GAAGCGTTGTTGTGACCTGC 60.317 55.000 0.00 0.00 0.00 4.85
1022 1106 0.307760 CTGGAAGCGTTGTTGTGACC 59.692 55.000 0.00 0.00 0.00 4.02
1024 1108 1.013596 CACTGGAAGCGTTGTTGTGA 58.986 50.000 0.00 0.00 37.60 3.58
1034 1118 0.462581 TGATGATCGGCACTGGAAGC 60.463 55.000 0.00 0.00 37.60 3.86
1065 1149 0.249657 GAAGTAGCAGATGGAGGGCG 60.250 60.000 0.00 0.00 0.00 6.13
1155 1239 1.538876 CAGGTTCACCCCCTGGAGA 60.539 63.158 0.00 0.00 44.77 3.71
1215 1299 2.404789 CAGGCGGCGCTTATGTTG 59.595 61.111 32.30 15.67 0.00 3.33
1407 1491 4.681025 GCAAGAAAAGATTTGTGCGAATGA 59.319 37.500 0.00 0.00 0.00 2.57
1758 1866 1.830279 ACAGCCATGACCACAAGATG 58.170 50.000 0.00 0.00 0.00 2.90
1827 1939 6.128715 CCCAAGTCATTCAGATTAATCGATCG 60.129 42.308 9.36 9.36 0.00 3.69
1828 1940 6.348050 GCCCAAGTCATTCAGATTAATCGATC 60.348 42.308 9.78 0.00 0.00 3.69
1829 1941 5.471456 GCCCAAGTCATTCAGATTAATCGAT 59.529 40.000 9.78 0.00 0.00 3.59
1830 1942 4.816385 GCCCAAGTCATTCAGATTAATCGA 59.184 41.667 9.78 7.68 0.00 3.59
1831 1943 4.576053 TGCCCAAGTCATTCAGATTAATCG 59.424 41.667 9.78 5.54 0.00 3.34
1905 2017 9.439500 CATGGATGTTCCTGAAATTTGTAAAAT 57.561 29.630 0.00 0.00 37.46 1.82
1906 2018 7.877097 CCATGGATGTTCCTGAAATTTGTAAAA 59.123 33.333 5.56 0.00 37.46 1.52
1909 2021 6.252233 TCCATGGATGTTCCTGAAATTTGTA 58.748 36.000 11.44 0.00 37.46 2.41
1910 2022 5.085920 TCCATGGATGTTCCTGAAATTTGT 58.914 37.500 11.44 0.00 37.46 2.83
1912 2024 5.046376 GGTTCCATGGATGTTCCTGAAATTT 60.046 40.000 17.06 0.00 37.46 1.82
1914 2026 4.026052 GGTTCCATGGATGTTCCTGAAAT 58.974 43.478 17.06 0.00 37.46 2.17
1915 2027 3.181424 TGGTTCCATGGATGTTCCTGAAA 60.181 43.478 17.06 0.00 37.46 2.69
1916 2028 2.378208 TGGTTCCATGGATGTTCCTGAA 59.622 45.455 17.06 0.00 37.46 3.02
1917 2029 1.991813 TGGTTCCATGGATGTTCCTGA 59.008 47.619 17.06 0.00 37.46 3.86
1918 2030 2.512692 TGGTTCCATGGATGTTCCTG 57.487 50.000 17.06 0.00 37.46 3.86
1919 2031 3.139025 CCTATGGTTCCATGGATGTTCCT 59.861 47.826 17.06 8.54 37.46 3.36
1920 2032 3.117512 ACCTATGGTTCCATGGATGTTCC 60.118 47.826 17.06 15.59 31.22 3.62
1922 2034 3.902218 CACCTATGGTTCCATGGATGTT 58.098 45.455 17.06 3.78 31.02 2.71
1923 2035 2.423373 GCACCTATGGTTCCATGGATGT 60.423 50.000 17.06 4.65 31.02 3.06
1924 2036 2.233271 GCACCTATGGTTCCATGGATG 58.767 52.381 17.06 9.35 31.02 3.51
1925 2037 1.145738 GGCACCTATGGTTCCATGGAT 59.854 52.381 17.06 2.53 38.83 3.41
1926 2038 0.550914 GGCACCTATGGTTCCATGGA 59.449 55.000 11.44 11.44 38.83 3.41
1927 2039 0.258484 TGGCACCTATGGTTCCATGG 59.742 55.000 4.97 4.97 43.58 3.66
1928 2040 3.901087 TGGCACCTATGGTTCCATG 57.099 52.632 13.86 1.68 43.58 3.66
1932 2044 3.189568 TGCATGGCACCTATGGTTC 57.810 52.632 0.00 0.00 31.02 3.62
1942 2054 0.177373 TTGCTTTTGTGTGCATGGCA 59.823 45.000 0.00 0.00 39.07 4.92
1943 2055 1.003652 GTTTGCTTTTGTGTGCATGGC 60.004 47.619 0.00 0.00 39.07 4.40
1945 2057 5.910637 ATTAGTTTGCTTTTGTGTGCATG 57.089 34.783 0.00 0.00 39.07 4.06
1946 2058 6.717413 CAAATTAGTTTGCTTTTGTGTGCAT 58.283 32.000 0.00 0.00 38.39 3.96
2003 2378 5.099575 GCTTCGTCCTTGTTTTTCTTTTCA 58.900 37.500 0.00 0.00 0.00 2.69
2004 2379 5.099575 TGCTTCGTCCTTGTTTTTCTTTTC 58.900 37.500 0.00 0.00 0.00 2.29
2037 2423 2.879026 GGCTACTGGCAAAGTAATAGCC 59.121 50.000 12.66 12.66 46.12 3.93
2038 2424 3.541632 TGGCTACTGGCAAAGTAATAGC 58.458 45.455 0.00 4.31 46.03 2.97
2078 2491 4.278310 TCTAGACCGTTGGATCAAGATCA 58.722 43.478 11.78 0.00 39.54 2.92
2095 2508 3.181433 TGATGGGAGCGGTCTAATCTAGA 60.181 47.826 21.89 0.00 0.00 2.43
2128 2542 6.265196 GGGACATTCTTGTGGAAATGCATATA 59.735 38.462 0.00 0.00 37.49 0.86
2160 2574 3.656066 GGATAACCGGACGAAGACC 57.344 57.895 9.46 0.00 39.42 3.85
2171 2585 7.790823 TTGCCTAGTTAATTAACGGATAACC 57.209 36.000 20.33 9.84 40.96 2.85
2172 2586 9.874215 GAATTGCCTAGTTAATTAACGGATAAC 57.126 33.333 20.33 11.85 40.96 1.89
2173 2587 9.841295 AGAATTGCCTAGTTAATTAACGGATAA 57.159 29.630 20.33 15.32 40.96 1.75
2174 2588 9.485206 GAGAATTGCCTAGTTAATTAACGGATA 57.515 33.333 20.33 9.83 40.96 2.59
2175 2589 8.211629 AGAGAATTGCCTAGTTAATTAACGGAT 58.788 33.333 20.33 9.30 40.96 4.18
2176 2590 7.562135 AGAGAATTGCCTAGTTAATTAACGGA 58.438 34.615 20.33 13.40 40.96 4.69
2177 2591 7.787725 AGAGAATTGCCTAGTTAATTAACGG 57.212 36.000 19.92 17.06 40.96 4.44
2178 2592 9.099454 AGAAGAGAATTGCCTAGTTAATTAACG 57.901 33.333 19.92 9.40 40.96 3.18
2180 2594 8.893727 GCAGAAGAGAATTGCCTAGTTAATTAA 58.106 33.333 0.00 0.00 31.79 1.40
2188 2602 7.281774 TCAATTAAGCAGAAGAGAATTGCCTAG 59.718 37.037 0.00 0.00 37.40 3.02
2189 2603 7.112122 TCAATTAAGCAGAAGAGAATTGCCTA 58.888 34.615 0.00 0.00 37.40 3.93
2190 2604 5.948162 TCAATTAAGCAGAAGAGAATTGCCT 59.052 36.000 0.00 0.00 37.40 4.75
2199 2613 7.160547 TGCAATTGATCAATTAAGCAGAAGA 57.839 32.000 28.74 14.90 38.84 2.87
2210 2624 7.655236 TTTTGAAACGATGCAATTGATCAAT 57.345 28.000 15.36 15.36 37.14 2.57
2211 2625 7.437565 TCTTTTTGAAACGATGCAATTGATCAA 59.562 29.630 11.26 11.26 36.24 2.57
2212 2626 6.922407 TCTTTTTGAAACGATGCAATTGATCA 59.078 30.769 10.34 0.00 0.00 2.92
2214 2628 7.712264 TTCTTTTTGAAACGATGCAATTGAT 57.288 28.000 10.34 0.00 0.00 2.57
2215 2629 7.531280 TTTCTTTTTGAAACGATGCAATTGA 57.469 28.000 10.34 0.00 39.50 2.57
2216 2630 8.598509 TTTTTCTTTTTGAAACGATGCAATTG 57.401 26.923 0.00 0.00 43.55 2.32
2240 2654 2.812011 GTTGGCAGTACGGAGACATTTT 59.188 45.455 0.00 0.00 0.00 1.82
2241 2655 2.224426 TGTTGGCAGTACGGAGACATTT 60.224 45.455 0.00 0.00 0.00 2.32
2242 2656 1.346395 TGTTGGCAGTACGGAGACATT 59.654 47.619 0.00 0.00 0.00 2.71
2294 3339 0.685097 TCTCCACACCTGTTACTGGC 59.315 55.000 8.22 0.00 0.00 4.85
2306 3351 0.179032 AATTGGTGTGCGTCTCCACA 60.179 50.000 2.70 0.00 42.99 4.17
2313 3358 3.119990 CGGAAATTCTAATTGGTGTGCGT 60.120 43.478 0.00 0.00 0.00 5.24
2335 3380 5.351740 GGGACACAAGCTAAATAGACTGAAC 59.648 44.000 0.00 0.00 0.00 3.18
2383 3430 0.037232 GCCAACGGTAGAAGCTGACT 60.037 55.000 0.00 0.00 0.00 3.41
2477 3525 4.699522 GGACGGGGTGCCACACTC 62.700 72.222 0.00 0.00 34.40 3.51
2489 3537 0.966920 ACTGTAGACCACAAGGACGG 59.033 55.000 0.00 0.00 36.48 4.79
2555 5734 2.341257 CGTCAGAGTGACTTGATTGGG 58.659 52.381 5.57 0.00 44.85 4.12
2564 5743 2.089349 GGAAGCGCGTCAGAGTGAC 61.089 63.158 24.41 1.75 43.65 3.67
2566 5745 2.811317 GGGAAGCGCGTCAGAGTG 60.811 66.667 24.41 0.00 0.00 3.51
2632 5853 1.737236 GTGTGTGTGTGTGTGTGTCAT 59.263 47.619 0.00 0.00 0.00 3.06
2650 5891 2.670934 GTGGGGCTGCTCTGTGTG 60.671 66.667 0.00 0.00 0.00 3.82
2651 5892 3.958860 GGTGGGGCTGCTCTGTGT 61.959 66.667 0.00 0.00 0.00 3.72
2652 5893 4.729918 GGGTGGGGCTGCTCTGTG 62.730 72.222 0.00 0.00 0.00 3.66
2656 5897 4.748144 CTTGGGGTGGGGCTGCTC 62.748 72.222 0.00 0.00 0.00 4.26
2666 5907 1.357272 TTGGTACACAGCCTTGGGGT 61.357 55.000 0.00 0.00 39.29 4.95
2706 5947 0.909610 CTCTGGTCCCTTGGGTAGCA 60.910 60.000 5.51 7.53 0.00 3.49
2707 5948 0.910088 ACTCTGGTCCCTTGGGTAGC 60.910 60.000 5.51 3.44 0.00 3.58
2708 5949 1.196012 GACTCTGGTCCCTTGGGTAG 58.804 60.000 5.51 3.76 36.53 3.18
2709 5950 0.613853 CGACTCTGGTCCCTTGGGTA 60.614 60.000 5.51 0.00 39.15 3.69
2710 5951 1.913762 CGACTCTGGTCCCTTGGGT 60.914 63.158 5.51 0.00 39.15 4.51
2732 5973 1.714899 CCCTATCTTTGCCGCGTTGG 61.715 60.000 4.92 0.00 42.50 3.77
2791 6032 0.718343 GCAAGTAGCTGCTGAGTTCG 59.282 55.000 13.43 0.00 39.34 3.95


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

AutoCloner maintained by Alex Coulton.