Multiple sequence alignment - TraesCS4A01G306700

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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 TraesCS4A01G306700 chr4A 100.000 2516 0 0 1 2516 601169067 601171582 0.000000e+00 4647.0
1 TraesCS4A01G306700 chr4A 99.494 989 5 0 1 989 601162146 601163134 0.000000e+00 1799.0
2 TraesCS4A01G306700 chr4A 98.483 989 15 0 1 989 607993457 607992469 0.000000e+00 1744.0
3 TraesCS4A01G306700 chr4A 83.777 826 126 8 996 1819 601156564 601157383 0.000000e+00 776.0
4 TraesCS4A01G306700 chr4A 89.963 269 23 4 1838 2105 159363457 159363722 6.660000e-91 344.0
5 TraesCS4A01G306700 chr4A 78.189 541 106 6 989 1517 601178346 601178886 4.010000e-88 335.0
6 TraesCS4A01G306700 chr7B 98.684 988 13 0 1 988 394977120 394978107 0.000000e+00 1753.0
7 TraesCS4A01G306700 chr7B 98.483 989 15 0 1 989 394970239 394971227 0.000000e+00 1744.0
8 TraesCS4A01G306700 chr7B 91.829 257 19 2 1853 2107 579906651 579906395 8.560000e-95 357.0
9 TraesCS4A01G306700 chr7A 98.684 988 13 0 1 988 701505000 701504013 0.000000e+00 1753.0
10 TraesCS4A01G306700 chr6A 98.686 989 11 2 1 989 431227283 431228269 0.000000e+00 1753.0
11 TraesCS4A01G306700 chr6A 98.583 988 12 2 1 988 431234112 431235097 0.000000e+00 1746.0
12 TraesCS4A01G306700 chr6A 92.015 263 19 2 1842 2103 290614251 290613990 3.950000e-98 368.0
13 TraesCS4A01G306700 chr6A 91.635 263 21 1 1842 2103 290705042 290704780 1.840000e-96 363.0
14 TraesCS4A01G306700 chr2B 98.583 988 12 2 1 988 519562485 519563470 0.000000e+00 1746.0
15 TraesCS4A01G306700 chr2B 98.483 989 13 2 1 989 519555774 519556760 0.000000e+00 1742.0
16 TraesCS4A01G306700 chr2B 88.333 60 6 1 2349 2408 100032024 100031966 1.250000e-08 71.3
17 TraesCS4A01G306700 chrUn 95.678 856 36 1 989 1844 60935812 60936666 0.000000e+00 1375.0
18 TraesCS4A01G306700 chrUn 84.532 834 121 6 996 1828 60928837 60929663 0.000000e+00 819.0
19 TraesCS4A01G306700 chrUn 95.021 241 10 2 2101 2341 60936664 60936902 6.570000e-101 377.0
20 TraesCS4A01G306700 chrUn 77.820 532 112 2 989 1517 60943496 60944024 8.680000e-85 324.0
21 TraesCS4A01G306700 chrUn 95.000 120 6 0 2332 2451 60937284 60937403 3.300000e-44 189.0
22 TraesCS4A01G306700 chr4B 84.830 824 121 4 996 1819 5522669 5523488 0.000000e+00 826.0
23 TraesCS4A01G306700 chr4B 78.692 535 108 3 989 1517 5532132 5532666 3.980000e-93 351.0
24 TraesCS4A01G306700 chr5D 79.658 526 104 2 999 1521 412448957 412449482 2.360000e-100 375.0
25 TraesCS4A01G306700 chr5A 79.626 535 100 7 999 1531 524309530 524310057 2.360000e-100 375.0
26 TraesCS4A01G306700 chr5A 78.897 526 108 2 999 1521 524389412 524389937 1.110000e-93 353.0
27 TraesCS4A01G306700 chr3D 90.943 265 22 2 1840 2103 586578933 586579196 3.080000e-94 355.0
28 TraesCS4A01G306700 chr6D 90.602 266 23 2 1839 2103 265185667 265185931 3.980000e-93 351.0
29 TraesCS4A01G306700 chr5B 77.759 598 111 16 1001 1580 496549877 496550470 5.150000e-92 348.0
30 TraesCS4A01G306700 chr5B 78.612 533 100 10 999 1521 496569563 496570091 8.620000e-90 340.0
31 TraesCS4A01G306700 chr7D 90.000 270 24 3 1842 2109 326788305 326788573 1.850000e-91 346.0
32 TraesCS4A01G306700 chr3A 89.706 272 24 4 1839 2109 227910622 227910890 6.660000e-91 344.0
33 TraesCS4A01G306700 chr2D 89.668 271 26 2 1840 2109 204112946 204112677 6.660000e-91 344.0
34 TraesCS4A01G306700 chr1A 83.529 170 27 1 2239 2408 32549227 32549395 9.320000e-35 158.0
35 TraesCS4A01G306700 chr1D 79.878 164 29 3 2238 2401 449973104 449972945 1.580000e-22 117.0
36 TraesCS4A01G306700 chr3B 87.097 62 8 0 2345 2406 804810012 804810073 1.250000e-08 71.3


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 TraesCS4A01G306700 chr4A 601169067 601171582 2515 False 4647 4647 100.000 1 2516 1 chr4A.!!$F4 2515
1 TraesCS4A01G306700 chr4A 601162146 601163134 988 False 1799 1799 99.494 1 989 1 chr4A.!!$F3 988
2 TraesCS4A01G306700 chr4A 607992469 607993457 988 True 1744 1744 98.483 1 989 1 chr4A.!!$R1 988
3 TraesCS4A01G306700 chr4A 601156564 601157383 819 False 776 776 83.777 996 1819 1 chr4A.!!$F2 823
4 TraesCS4A01G306700 chr4A 601178346 601178886 540 False 335 335 78.189 989 1517 1 chr4A.!!$F5 528
5 TraesCS4A01G306700 chr7B 394977120 394978107 987 False 1753 1753 98.684 1 988 1 chr7B.!!$F2 987
6 TraesCS4A01G306700 chr7B 394970239 394971227 988 False 1744 1744 98.483 1 989 1 chr7B.!!$F1 988
7 TraesCS4A01G306700 chr7A 701504013 701505000 987 True 1753 1753 98.684 1 988 1 chr7A.!!$R1 987
8 TraesCS4A01G306700 chr6A 431227283 431228269 986 False 1753 1753 98.686 1 989 1 chr6A.!!$F1 988
9 TraesCS4A01G306700 chr6A 431234112 431235097 985 False 1746 1746 98.583 1 988 1 chr6A.!!$F2 987
10 TraesCS4A01G306700 chr2B 519562485 519563470 985 False 1746 1746 98.583 1 988 1 chr2B.!!$F2 987
11 TraesCS4A01G306700 chr2B 519555774 519556760 986 False 1742 1742 98.483 1 989 1 chr2B.!!$F1 988
12 TraesCS4A01G306700 chrUn 60928837 60929663 826 False 819 819 84.532 996 1828 1 chrUn.!!$F1 832
13 TraesCS4A01G306700 chrUn 60935812 60937403 1591 False 647 1375 95.233 989 2451 3 chrUn.!!$F3 1462
14 TraesCS4A01G306700 chrUn 60943496 60944024 528 False 324 324 77.820 989 1517 1 chrUn.!!$F2 528
15 TraesCS4A01G306700 chr4B 5522669 5523488 819 False 826 826 84.830 996 1819 1 chr4B.!!$F1 823
16 TraesCS4A01G306700 chr4B 5532132 5532666 534 False 351 351 78.692 989 1517 1 chr4B.!!$F2 528
17 TraesCS4A01G306700 chr5D 412448957 412449482 525 False 375 375 79.658 999 1521 1 chr5D.!!$F1 522
18 TraesCS4A01G306700 chr5A 524309530 524310057 527 False 375 375 79.626 999 1531 1 chr5A.!!$F1 532
19 TraesCS4A01G306700 chr5A 524389412 524389937 525 False 353 353 78.897 999 1521 1 chr5A.!!$F2 522
20 TraesCS4A01G306700 chr5B 496549877 496550470 593 False 348 348 77.759 1001 1580 1 chr5B.!!$F1 579
21 TraesCS4A01G306700 chr5B 496569563 496570091 528 False 340 340 78.612 999 1521 1 chr5B.!!$F2 522

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
554 556 3.431411 TGGCCCTATATATAGTGGGGG 57.569 52.381 20.24 15.51 39.99 5.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2173 2196 0.027979 CAGCACCAGTTTGTCACACG 59.972 55.0 0.0 0.0 0.0 4.49 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
554 556 3.431411 TGGCCCTATATATAGTGGGGG 57.569 52.381 20.24 15.51 39.99 5.40
1059 1064 3.685435 GTCACGAACGGGACCCTA 58.315 61.111 17.21 0.00 42.35 3.53
1231 1245 1.668151 GTCCTCAACGGTGCACTCC 60.668 63.158 17.98 0.00 0.00 3.85
1281 1295 2.558795 GCTCTACACACAAGACCTCTCA 59.441 50.000 0.00 0.00 0.00 3.27
1535 1557 5.043903 GTGATACATATGTGCTCTTGTCGT 58.956 41.667 18.81 0.00 0.00 4.34
1547 1569 4.202161 TGCTCTTGTCGTTCTTCTTCTTCT 60.202 41.667 0.00 0.00 0.00 2.85
1607 1630 1.143305 GCTAGCGCATGATAGTGGTG 58.857 55.000 11.47 0.00 36.46 4.17
1673 1696 9.448438 TGACTTGTAATAATATGCTTCTTGTGT 57.552 29.630 0.00 0.00 0.00 3.72
1744 1767 7.436080 GGTGTTAAGAATGTGCCATCAAATATG 59.564 37.037 0.00 0.00 0.00 1.78
1866 1889 9.892130 ATACTCCCTATGTTTCTTTTTAGTCTG 57.108 33.333 0.00 0.00 0.00 3.51
1867 1890 6.655425 ACTCCCTATGTTTCTTTTTAGTCTGC 59.345 38.462 0.00 0.00 0.00 4.26
1868 1891 6.539173 TCCCTATGTTTCTTTTTAGTCTGCA 58.461 36.000 0.00 0.00 0.00 4.41
1869 1892 7.175104 TCCCTATGTTTCTTTTTAGTCTGCAT 58.825 34.615 0.00 0.00 0.00 3.96
1870 1893 8.325787 TCCCTATGTTTCTTTTTAGTCTGCATA 58.674 33.333 0.00 0.00 0.00 3.14
1871 1894 9.125026 CCCTATGTTTCTTTTTAGTCTGCATAT 57.875 33.333 0.00 0.00 0.00 1.78
1876 1899 9.515226 TGTTTCTTTTTAGTCTGCATATAAGGT 57.485 29.630 0.00 0.00 0.00 3.50
1880 1903 8.956426 TCTTTTTAGTCTGCATATAAGGTTTGG 58.044 33.333 0.00 0.00 0.00 3.28
1881 1904 8.644374 TTTTTAGTCTGCATATAAGGTTTGGT 57.356 30.769 0.00 0.00 0.00 3.67
1882 1905 7.859325 TTTAGTCTGCATATAAGGTTTGGTC 57.141 36.000 0.00 0.00 0.00 4.02
1883 1906 5.435686 AGTCTGCATATAAGGTTTGGTCA 57.564 39.130 0.00 0.00 0.00 4.02
1884 1907 5.815581 AGTCTGCATATAAGGTTTGGTCAA 58.184 37.500 0.00 0.00 0.00 3.18
1885 1908 6.245408 AGTCTGCATATAAGGTTTGGTCAAA 58.755 36.000 0.00 0.00 0.00 2.69
1886 1909 6.375455 AGTCTGCATATAAGGTTTGGTCAAAG 59.625 38.462 0.00 0.00 0.00 2.77
1887 1910 6.151144 GTCTGCATATAAGGTTTGGTCAAAGT 59.849 38.462 0.00 0.00 0.00 2.66
1888 1911 6.374333 TCTGCATATAAGGTTTGGTCAAAGTC 59.626 38.462 0.00 0.00 0.00 3.01
1889 1912 6.007076 TGCATATAAGGTTTGGTCAAAGTCA 58.993 36.000 0.00 0.00 0.00 3.41
1890 1913 6.491745 TGCATATAAGGTTTGGTCAAAGTCAA 59.508 34.615 0.00 0.00 0.00 3.18
1891 1914 7.029563 GCATATAAGGTTTGGTCAAAGTCAAG 58.970 38.462 0.00 0.00 0.00 3.02
1892 1915 3.801114 AAGGTTTGGTCAAAGTCAAGC 57.199 42.857 0.00 0.00 0.00 4.01
1893 1916 3.018423 AGGTTTGGTCAAAGTCAAGCT 57.982 42.857 0.00 0.00 0.00 3.74
1894 1917 3.365472 AGGTTTGGTCAAAGTCAAGCTT 58.635 40.909 0.00 0.00 39.52 3.74
1911 1934 6.510746 CAAGCTTTGTAAAGTTTGCCTAAC 57.489 37.500 17.01 0.00 45.55 2.34
2070 2093 9.959749 TTATGTAGTTTGACTTTGACCAAATTC 57.040 29.630 6.06 6.06 35.14 2.17
2071 2094 7.639113 TGTAGTTTGACTTTGACCAAATTCT 57.361 32.000 12.07 0.00 35.14 2.40
2072 2095 8.740123 TGTAGTTTGACTTTGACCAAATTCTA 57.260 30.769 12.07 4.41 35.14 2.10
2073 2096 9.349713 TGTAGTTTGACTTTGACCAAATTCTAT 57.650 29.630 12.07 2.05 35.14 1.98
2076 2099 9.349713 AGTTTGACTTTGACCAAATTCTATACA 57.650 29.630 12.07 0.00 35.14 2.29
2077 2100 9.394477 GTTTGACTTTGACCAAATTCTATACAC 57.606 33.333 12.07 0.81 35.14 2.90
2078 2101 8.684386 TTGACTTTGACCAAATTCTATACACA 57.316 30.769 12.07 0.00 33.02 3.72
2079 2102 8.322906 TGACTTTGACCAAATTCTATACACAG 57.677 34.615 12.07 0.00 33.02 3.66
2080 2103 8.154203 TGACTTTGACCAAATTCTATACACAGA 58.846 33.333 12.07 0.00 33.02 3.41
2081 2104 8.553459 ACTTTGACCAAATTCTATACACAGAG 57.447 34.615 0.00 0.00 0.00 3.35
2082 2105 8.157476 ACTTTGACCAAATTCTATACACAGAGT 58.843 33.333 0.00 0.00 0.00 3.24
2083 2106 9.653287 CTTTGACCAAATTCTATACACAGAGTA 57.347 33.333 0.00 0.00 37.06 2.59
2109 2132 6.840780 AAAAATGGAGGGAGTACATTTGAG 57.159 37.500 0.00 0.00 42.21 3.02
2125 2148 4.764050 TTTGAGTAGTGTTCTGGTTCCA 57.236 40.909 0.00 0.00 0.00 3.53
2173 2196 0.105039 CGAGATGGCCTAACTCCACC 59.895 60.000 3.32 0.00 36.26 4.61
2176 2199 0.462047 GATGGCCTAACTCCACCGTG 60.462 60.000 3.32 0.00 36.26 4.94
2197 2220 1.416030 TGACAAACTGGTGCTGCTCTA 59.584 47.619 0.00 0.00 0.00 2.43
2237 2260 6.037720 TCGTGTTTTGAAGTATTTTCTGCTCA 59.962 34.615 0.00 0.00 0.00 4.26
2255 2278 4.620982 GCTCAAGCAGTTTTAACATGGTT 58.379 39.130 0.00 0.85 41.59 3.67
2283 2306 3.259374 TGCCTCCTCTTAACACAAGAGAG 59.741 47.826 14.15 9.74 44.96 3.20
2341 2364 3.428532 TGAAGTAGTGGGTCTGAGTACC 58.571 50.000 0.00 0.00 38.94 3.34
2342 2365 3.075582 TGAAGTAGTGGGTCTGAGTACCT 59.924 47.826 0.00 0.00 39.65 3.08
2360 2774 7.560626 TGAGTACCTCTTATCTTCTTAACTCCC 59.439 40.741 0.00 0.00 30.96 4.30
2408 2822 7.651704 AGGACCATGTTAAAATTTGTCTTTTCG 59.348 33.333 0.00 0.00 31.15 3.46
2413 2827 6.801575 TGTTAAAATTTGTCTTTTCGGCTCT 58.198 32.000 0.00 0.00 31.15 4.09
2417 2831 2.169832 TTGTCTTTTCGGCTCTCTGG 57.830 50.000 0.00 0.00 0.00 3.86
2428 2842 0.176910 GCTCTCTGGACTAACCTGCC 59.823 60.000 0.00 0.00 39.86 4.85
2451 2865 2.456577 AGGTGTTTTGGAGTTTGCTGT 58.543 42.857 0.00 0.00 0.00 4.40
2452 2866 2.166254 AGGTGTTTTGGAGTTTGCTGTG 59.834 45.455 0.00 0.00 0.00 3.66
2453 2867 2.094234 GGTGTTTTGGAGTTTGCTGTGT 60.094 45.455 0.00 0.00 0.00 3.72
2454 2868 2.923020 GTGTTTTGGAGTTTGCTGTGTG 59.077 45.455 0.00 0.00 0.00 3.82
2455 2869 2.560542 TGTTTTGGAGTTTGCTGTGTGT 59.439 40.909 0.00 0.00 0.00 3.72
2456 2870 2.923020 GTTTTGGAGTTTGCTGTGTGTG 59.077 45.455 0.00 0.00 0.00 3.82
2457 2871 1.832883 TTGGAGTTTGCTGTGTGTGT 58.167 45.000 0.00 0.00 0.00 3.72
2458 2872 1.093972 TGGAGTTTGCTGTGTGTGTG 58.906 50.000 0.00 0.00 0.00 3.82
2459 2873 1.094785 GGAGTTTGCTGTGTGTGTGT 58.905 50.000 0.00 0.00 0.00 3.72
2460 2874 1.202177 GGAGTTTGCTGTGTGTGTGTG 60.202 52.381 0.00 0.00 0.00 3.82
2461 2875 1.468520 GAGTTTGCTGTGTGTGTGTGT 59.531 47.619 0.00 0.00 0.00 3.72
2462 2876 1.199789 AGTTTGCTGTGTGTGTGTGTG 59.800 47.619 0.00 0.00 0.00 3.82
2463 2877 1.068610 GTTTGCTGTGTGTGTGTGTGT 60.069 47.619 0.00 0.00 0.00 3.72
2464 2878 0.520847 TTGCTGTGTGTGTGTGTGTG 59.479 50.000 0.00 0.00 0.00 3.82
2465 2879 0.605050 TGCTGTGTGTGTGTGTGTGT 60.605 50.000 0.00 0.00 0.00 3.72
2466 2880 0.179192 GCTGTGTGTGTGTGTGTGTG 60.179 55.000 0.00 0.00 0.00 3.82
2467 2881 1.155889 CTGTGTGTGTGTGTGTGTGT 58.844 50.000 0.00 0.00 0.00 3.72
2468 2882 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2469 2883 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2470 2884 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2471 2885 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2472 2886 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2473 2887 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2474 2888 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2475 2889 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2476 2890 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2477 2891 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2478 2892 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2479 2893 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2480 2894 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2481 2895 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2482 2896 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2483 2897 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2484 2898 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2485 2899 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2486 2900 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2487 2901 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2488 2902 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2489 2903 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2490 2904 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2491 2905 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2492 2906 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2493 2907 1.152510 GTGTGTGTGTGTGTGTGTGA 58.847 50.000 0.00 0.00 0.00 3.58
2494 2908 1.128507 GTGTGTGTGTGTGTGTGTGAG 59.871 52.381 0.00 0.00 0.00 3.51
2495 2909 1.001406 TGTGTGTGTGTGTGTGTGAGA 59.999 47.619 0.00 0.00 0.00 3.27
2496 2910 1.660607 GTGTGTGTGTGTGTGTGAGAG 59.339 52.381 0.00 0.00 0.00 3.20
2497 2911 1.548269 TGTGTGTGTGTGTGTGAGAGA 59.452 47.619 0.00 0.00 0.00 3.10
2498 2912 2.196749 GTGTGTGTGTGTGTGAGAGAG 58.803 52.381 0.00 0.00 0.00 3.20
2499 2913 2.099405 TGTGTGTGTGTGTGAGAGAGA 58.901 47.619 0.00 0.00 0.00 3.10
2500 2914 2.099756 TGTGTGTGTGTGTGAGAGAGAG 59.900 50.000 0.00 0.00 0.00 3.20
2501 2915 2.359214 GTGTGTGTGTGTGAGAGAGAGA 59.641 50.000 0.00 0.00 0.00 3.10
2502 2916 2.620585 TGTGTGTGTGTGAGAGAGAGAG 59.379 50.000 0.00 0.00 0.00 3.20
2503 2917 2.881513 GTGTGTGTGTGAGAGAGAGAGA 59.118 50.000 0.00 0.00 0.00 3.10
2504 2918 3.058293 GTGTGTGTGTGAGAGAGAGAGAG 60.058 52.174 0.00 0.00 0.00 3.20
2505 2919 3.181450 TGTGTGTGTGAGAGAGAGAGAGA 60.181 47.826 0.00 0.00 0.00 3.10
2506 2920 3.436704 GTGTGTGTGAGAGAGAGAGAGAG 59.563 52.174 0.00 0.00 0.00 3.20
2507 2921 3.326297 TGTGTGTGAGAGAGAGAGAGAGA 59.674 47.826 0.00 0.00 0.00 3.10
2508 2922 3.935203 GTGTGTGAGAGAGAGAGAGAGAG 59.065 52.174 0.00 0.00 0.00 3.20
2509 2923 3.837731 TGTGTGAGAGAGAGAGAGAGAGA 59.162 47.826 0.00 0.00 0.00 3.10
2510 2924 4.081476 TGTGTGAGAGAGAGAGAGAGAGAG 60.081 50.000 0.00 0.00 0.00 3.20
2511 2925 4.160439 GTGTGAGAGAGAGAGAGAGAGAGA 59.840 50.000 0.00 0.00 0.00 3.10
2512 2926 4.403752 TGTGAGAGAGAGAGAGAGAGAGAG 59.596 50.000 0.00 0.00 0.00 3.20
2513 2927 4.646945 GTGAGAGAGAGAGAGAGAGAGAGA 59.353 50.000 0.00 0.00 0.00 3.10
2514 2928 4.892345 TGAGAGAGAGAGAGAGAGAGAGAG 59.108 50.000 0.00 0.00 0.00 3.20
2515 2929 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
554 556 2.238395 AGGTCTGATTGCTCCTCCTTTC 59.762 50.000 0.00 0.00 0.00 2.62
1052 1057 2.808206 CGAGGCCATGGTAGGGTCC 61.808 68.421 14.67 4.52 0.00 4.46
1057 1062 1.622607 TTCCACCGAGGCCATGGTAG 61.623 60.000 17.61 11.51 36.50 3.18
1059 1064 2.933287 TTCCACCGAGGCCATGGT 60.933 61.111 14.67 12.85 39.66 3.55
1393 1407 2.821366 CACGGAGGCAGGCACATC 60.821 66.667 0.00 0.00 0.00 3.06
1420 1434 0.880278 AGCACGACGTTGTCAATGCT 60.880 50.000 15.92 15.92 44.42 3.79
1535 1557 5.622460 GCGATACAGTGGAGAAGAAGAAGAA 60.622 44.000 0.00 0.00 0.00 2.52
1547 1569 2.889617 CGGTGGCGATACAGTGGA 59.110 61.111 0.00 0.00 0.00 4.02
1607 1630 4.202326 ACCTCACAATACCATCGGGATTAC 60.202 45.833 0.00 0.00 38.05 1.89
1673 1696 8.795513 ACATGATCACAATATCAACTCACAAAA 58.204 29.630 0.00 0.00 39.25 2.44
1744 1767 2.919666 ATTGCATAACCGACACAAGC 57.080 45.000 0.00 0.00 0.00 4.01
1844 1867 6.539173 TGCAGACTAAAAAGAAACATAGGGA 58.461 36.000 0.00 0.00 0.00 4.20
1845 1868 6.817765 TGCAGACTAAAAAGAAACATAGGG 57.182 37.500 0.00 0.00 0.00 3.53
1850 1873 9.515226 ACCTTATATGCAGACTAAAAAGAAACA 57.485 29.630 0.00 0.00 0.00 2.83
1854 1877 8.956426 CCAAACCTTATATGCAGACTAAAAAGA 58.044 33.333 0.00 0.00 0.00 2.52
1855 1878 8.739972 ACCAAACCTTATATGCAGACTAAAAAG 58.260 33.333 0.00 0.00 0.00 2.27
1856 1879 8.644374 ACCAAACCTTATATGCAGACTAAAAA 57.356 30.769 0.00 0.00 0.00 1.94
1857 1880 7.885922 TGACCAAACCTTATATGCAGACTAAAA 59.114 33.333 0.00 0.00 0.00 1.52
1858 1881 7.398829 TGACCAAACCTTATATGCAGACTAAA 58.601 34.615 0.00 0.00 0.00 1.85
1859 1882 6.953101 TGACCAAACCTTATATGCAGACTAA 58.047 36.000 0.00 0.00 0.00 2.24
1860 1883 6.553953 TGACCAAACCTTATATGCAGACTA 57.446 37.500 0.00 0.00 0.00 2.59
1861 1884 5.435686 TGACCAAACCTTATATGCAGACT 57.564 39.130 0.00 0.00 0.00 3.24
1862 1885 6.151144 ACTTTGACCAAACCTTATATGCAGAC 59.849 38.462 0.00 0.00 0.00 3.51
1863 1886 6.245408 ACTTTGACCAAACCTTATATGCAGA 58.755 36.000 0.00 0.00 0.00 4.26
1864 1887 6.150976 TGACTTTGACCAAACCTTATATGCAG 59.849 38.462 0.00 0.00 0.00 4.41
1865 1888 6.007076 TGACTTTGACCAAACCTTATATGCA 58.993 36.000 0.00 0.00 0.00 3.96
1866 1889 6.509418 TGACTTTGACCAAACCTTATATGC 57.491 37.500 0.00 0.00 0.00 3.14
1867 1890 7.029563 GCTTGACTTTGACCAAACCTTATATG 58.970 38.462 0.00 0.00 0.00 1.78
1868 1891 6.948309 AGCTTGACTTTGACCAAACCTTATAT 59.052 34.615 0.00 0.00 0.00 0.86
1869 1892 6.303839 AGCTTGACTTTGACCAAACCTTATA 58.696 36.000 0.00 0.00 0.00 0.98
1870 1893 5.140454 AGCTTGACTTTGACCAAACCTTAT 58.860 37.500 0.00 0.00 0.00 1.73
1871 1894 4.532834 AGCTTGACTTTGACCAAACCTTA 58.467 39.130 0.00 0.00 0.00 2.69
1872 1895 3.365472 AGCTTGACTTTGACCAAACCTT 58.635 40.909 0.00 0.00 0.00 3.50
1873 1896 3.018423 AGCTTGACTTTGACCAAACCT 57.982 42.857 0.00 0.00 0.00 3.50
1874 1897 3.801114 AAGCTTGACTTTGACCAAACC 57.199 42.857 0.00 0.00 33.71 3.27
1884 1907 5.109210 GGCAAACTTTACAAAGCTTGACTT 58.891 37.500 17.68 0.00 43.44 3.01
1885 1908 4.682787 GGCAAACTTTACAAAGCTTGACT 58.317 39.130 17.68 0.00 43.44 3.41
1886 1909 4.682787 AGGCAAACTTTACAAAGCTTGAC 58.317 39.130 17.68 15.62 45.82 3.18
1887 1910 6.096282 AGTTAGGCAAACTTTACAAAGCTTGA 59.904 34.615 17.68 0.00 46.61 3.02
1888 1911 6.273071 AGTTAGGCAAACTTTACAAAGCTTG 58.727 36.000 0.00 11.66 46.61 4.01
1889 1912 6.465439 AGTTAGGCAAACTTTACAAAGCTT 57.535 33.333 0.00 0.00 46.61 3.74
2044 2067 9.959749 GAATTTGGTCAAAGTCAAACTACATAA 57.040 29.630 15.95 0.00 42.79 1.90
2045 2068 9.349713 AGAATTTGGTCAAAGTCAAACTACATA 57.650 29.630 20.80 0.00 44.87 2.29
2046 2069 8.237811 AGAATTTGGTCAAAGTCAAACTACAT 57.762 30.769 20.80 1.07 44.87 2.29
2047 2070 7.639113 AGAATTTGGTCAAAGTCAAACTACA 57.361 32.000 20.80 0.00 44.87 2.74
2050 2073 9.349713 TGTATAGAATTTGGTCAAAGTCAAACT 57.650 29.630 20.80 7.35 44.87 2.66
2051 2074 9.394477 GTGTATAGAATTTGGTCAAAGTCAAAC 57.606 33.333 20.80 15.97 44.87 2.93
2052 2075 9.126151 TGTGTATAGAATTTGGTCAAAGTCAAA 57.874 29.630 20.80 11.82 44.87 2.69
2053 2076 8.684386 TGTGTATAGAATTTGGTCAAAGTCAA 57.316 30.769 20.80 7.66 44.87 3.18
2054 2077 8.154203 TCTGTGTATAGAATTTGGTCAAAGTCA 58.846 33.333 20.80 10.70 44.87 3.41
2055 2078 8.547967 TCTGTGTATAGAATTTGGTCAAAGTC 57.452 34.615 13.82 13.82 43.37 3.01
2056 2079 8.157476 ACTCTGTGTATAGAATTTGGTCAAAGT 58.843 33.333 2.55 0.00 33.32 2.66
2057 2080 8.553459 ACTCTGTGTATAGAATTTGGTCAAAG 57.447 34.615 2.55 0.00 33.32 2.77
2086 2109 6.314917 ACTCAAATGTACTCCCTCCATTTTT 58.685 36.000 0.00 0.00 36.84 1.94
2087 2110 5.892348 ACTCAAATGTACTCCCTCCATTTT 58.108 37.500 0.00 0.00 36.84 1.82
2088 2111 5.520748 ACTCAAATGTACTCCCTCCATTT 57.479 39.130 0.00 0.00 38.87 2.32
2089 2112 5.726793 ACTACTCAAATGTACTCCCTCCATT 59.273 40.000 0.00 0.00 0.00 3.16
2090 2113 5.129485 CACTACTCAAATGTACTCCCTCCAT 59.871 44.000 0.00 0.00 0.00 3.41
2091 2114 4.466370 CACTACTCAAATGTACTCCCTCCA 59.534 45.833 0.00 0.00 0.00 3.86
2092 2115 4.466726 ACACTACTCAAATGTACTCCCTCC 59.533 45.833 0.00 0.00 0.00 4.30
2093 2116 5.662674 ACACTACTCAAATGTACTCCCTC 57.337 43.478 0.00 0.00 0.00 4.30
2094 2117 5.780793 AGAACACTACTCAAATGTACTCCCT 59.219 40.000 0.00 0.00 0.00 4.20
2095 2118 5.869888 CAGAACACTACTCAAATGTACTCCC 59.130 44.000 0.00 0.00 0.00 4.30
2096 2119 5.869888 CCAGAACACTACTCAAATGTACTCC 59.130 44.000 0.00 0.00 0.00 3.85
2097 2120 6.456501 ACCAGAACACTACTCAAATGTACTC 58.543 40.000 0.00 0.00 0.00 2.59
2098 2121 6.420913 ACCAGAACACTACTCAAATGTACT 57.579 37.500 0.00 0.00 0.00 2.73
2099 2122 6.147328 GGAACCAGAACACTACTCAAATGTAC 59.853 42.308 0.00 0.00 0.00 2.90
2100 2123 6.183361 TGGAACCAGAACACTACTCAAATGTA 60.183 38.462 0.00 0.00 0.00 2.29
2101 2124 5.063880 GGAACCAGAACACTACTCAAATGT 58.936 41.667 0.00 0.00 0.00 2.71
2102 2125 5.063204 TGGAACCAGAACACTACTCAAATG 58.937 41.667 0.00 0.00 0.00 2.32
2109 2132 8.788325 ATAACTAAATGGAACCAGAACACTAC 57.212 34.615 0.00 0.00 0.00 2.73
2125 2148 9.343539 GGAGTGAGGCTGAAATAATAACTAAAT 57.656 33.333 0.00 0.00 0.00 1.40
2173 2196 0.027979 CAGCACCAGTTTGTCACACG 59.972 55.000 0.00 0.00 0.00 4.49
2176 2199 0.308993 GAGCAGCACCAGTTTGTCAC 59.691 55.000 0.00 0.00 0.00 3.67
2197 2220 1.604023 ACGAGAGGGTTGAGCGTCT 60.604 57.895 5.22 5.22 0.00 4.18
2237 2260 5.140454 AGAGGAACCATGTTAAAACTGCTT 58.860 37.500 0.00 0.00 0.00 3.91
2255 2278 2.567615 GTGTTAAGAGGAGGCAAGAGGA 59.432 50.000 0.00 0.00 0.00 3.71
2314 2337 5.249393 ACTCAGACCCACTACTTCATGAAAT 59.751 40.000 9.88 1.39 0.00 2.17
2317 2340 3.779444 ACTCAGACCCACTACTTCATGA 58.221 45.455 0.00 0.00 0.00 3.07
2318 2341 4.142138 GGTACTCAGACCCACTACTTCATG 60.142 50.000 0.00 0.00 32.88 3.07
2319 2342 4.024670 GGTACTCAGACCCACTACTTCAT 58.975 47.826 0.00 0.00 32.88 2.57
2320 2343 3.075582 AGGTACTCAGACCCACTACTTCA 59.924 47.826 0.00 0.00 40.74 3.02
2321 2344 3.699413 AGGTACTCAGACCCACTACTTC 58.301 50.000 0.00 0.00 40.74 3.01
2341 2364 7.786030 TCACATGGGAGTTAAGAAGATAAGAG 58.214 38.462 0.00 0.00 0.00 2.85
2342 2365 7.733773 TCACATGGGAGTTAAGAAGATAAGA 57.266 36.000 0.00 0.00 0.00 2.10
2360 2774 4.301072 TCTTACCTCCCCTTTTCACATG 57.699 45.455 0.00 0.00 0.00 3.21
2408 2822 0.176910 GCAGGTTAGTCCAGAGAGCC 59.823 60.000 0.00 0.00 39.02 4.70
2413 2827 0.895530 CTTCGGCAGGTTAGTCCAGA 59.104 55.000 0.00 0.00 39.02 3.86
2428 2842 2.099098 AGCAAACTCCAAAACACCTTCG 59.901 45.455 0.00 0.00 0.00 3.79
2451 2865 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2452 2866 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2453 2867 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2454 2868 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2455 2869 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2456 2870 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2457 2871 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2458 2872 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2459 2873 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2460 2874 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2461 2875 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2462 2876 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2463 2877 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2464 2878 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2465 2879 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2466 2880 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2467 2881 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2468 2882 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2469 2883 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2470 2884 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2471 2885 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2472 2886 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2473 2887 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2474 2888 1.128507 CTCACACACACACACACACAC 59.871 52.381 0.00 0.00 0.00 3.82
2475 2889 1.001406 TCTCACACACACACACACACA 59.999 47.619 0.00 0.00 0.00 3.72
2476 2890 1.660607 CTCTCACACACACACACACAC 59.339 52.381 0.00 0.00 0.00 3.82
2477 2891 1.548269 TCTCTCACACACACACACACA 59.452 47.619 0.00 0.00 0.00 3.72
2478 2892 2.159240 TCTCTCTCACACACACACACAC 60.159 50.000 0.00 0.00 0.00 3.82
2479 2893 2.099405 TCTCTCTCACACACACACACA 58.901 47.619 0.00 0.00 0.00 3.72
2480 2894 2.359214 TCTCTCTCTCACACACACACAC 59.641 50.000 0.00 0.00 0.00 3.82
2481 2895 2.620585 CTCTCTCTCTCACACACACACA 59.379 50.000 0.00 0.00 0.00 3.72
2482 2896 2.881513 TCTCTCTCTCTCACACACACAC 59.118 50.000 0.00 0.00 0.00 3.82
2483 2897 3.145286 CTCTCTCTCTCTCACACACACA 58.855 50.000 0.00 0.00 0.00 3.72
2484 2898 3.407698 TCTCTCTCTCTCTCACACACAC 58.592 50.000 0.00 0.00 0.00 3.82
2485 2899 3.326297 TCTCTCTCTCTCTCTCACACACA 59.674 47.826 0.00 0.00 0.00 3.72
2486 2900 3.935203 CTCTCTCTCTCTCTCTCACACAC 59.065 52.174 0.00 0.00 0.00 3.82
2487 2901 3.837731 TCTCTCTCTCTCTCTCTCACACA 59.162 47.826 0.00 0.00 0.00 3.72
2488 2902 4.160439 TCTCTCTCTCTCTCTCTCTCACAC 59.840 50.000 0.00 0.00 0.00 3.82
2489 2903 4.352893 TCTCTCTCTCTCTCTCTCTCACA 58.647 47.826 0.00 0.00 0.00 3.58
2490 2904 4.646945 TCTCTCTCTCTCTCTCTCTCTCAC 59.353 50.000 0.00 0.00 0.00 3.51
2491 2905 4.871822 TCTCTCTCTCTCTCTCTCTCTCA 58.128 47.826 0.00 0.00 0.00 3.27
2492 2906 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2493 2907 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10


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

AutoCloner maintained by Alex Coulton.