Multiple sequence alignment - TraesCS1A01G293000

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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 TraesCS1A01G293000 chr1A 100.000 2567 0 0 1 2567 488218200 488220766 0.000000e+00 4741.0
1 TraesCS1A01G293000 chr1A 99.206 126 1 0 2442 2567 488225574 488225699 7.150000e-56 228.0
2 TraesCS1A01G293000 chr1A 86.207 145 20 0 431 575 488218250 488218394 9.510000e-35 158.0
3 TraesCS1A01G293000 chr1A 86.207 145 20 0 51 195 488218630 488218774 9.510000e-35 158.0
4 TraesCS1A01G293000 chr1A 95.402 87 3 1 2481 2567 293731396 293731481 1.240000e-28 137.0
5 TraesCS1A01G293000 chr1B 88.111 1186 94 28 581 1753 523043022 523041871 0.000000e+00 1365.0
6 TraesCS1A01G293000 chr1B 90.061 825 62 10 933 1745 523144114 523144930 0.000000e+00 1051.0
7 TraesCS1A01G293000 chr1B 87.154 506 33 7 1946 2441 523147120 523147603 1.740000e-151 545.0
8 TraesCS1A01G293000 chr1B 92.887 239 13 4 704 940 523138948 523139184 6.800000e-91 344.0
9 TraesCS1A01G293000 chr1B 84.195 348 41 10 244 583 523043119 523042778 2.460000e-85 326.0
10 TraesCS1A01G293000 chr1B 81.704 399 48 15 87 480 523136941 523137319 2.480000e-80 309.0
11 TraesCS1A01G293000 chr1B 79.195 447 41 21 2018 2440 523012226 523011808 1.960000e-66 263.0
12 TraesCS1A01G293000 chr1B 93.220 118 7 1 467 583 523136941 523137058 3.400000e-39 172.0
13 TraesCS1A01G293000 chr1B 83.041 171 26 2 54 221 523042930 523042760 4.420000e-33 152.0
14 TraesCS1A01G293000 chr1B 96.429 84 2 1 2484 2567 20348094 20348176 1.240000e-28 137.0
15 TraesCS1A01G293000 chr1B 96.429 84 2 1 2484 2567 20387893 20387975 1.240000e-28 137.0
16 TraesCS1A01G293000 chr1B 96.429 84 2 1 2484 2567 20403365 20403447 1.240000e-28 137.0
17 TraesCS1A01G293000 chr1B 100.000 30 0 0 1785 1814 523041594 523041565 3.570000e-04 56.5
18 TraesCS1A01G293000 chr1D 91.055 995 61 14 760 1745 390671847 390670872 0.000000e+00 1319.0
19 TraesCS1A01G293000 chr1D 87.841 1135 80 27 640 1753 390677483 390678580 0.000000e+00 1279.0
20 TraesCS1A01G293000 chr1D 94.131 443 18 4 109 551 390672747 390672313 0.000000e+00 667.0
21 TraesCS1A01G293000 chr1D 86.381 514 37 8 1946 2441 390679158 390679656 4.860000e-147 531.0
22 TraesCS1A01G293000 chr1D 81.559 526 54 17 1947 2440 390668669 390668155 6.660000e-106 394.0
23 TraesCS1A01G293000 chr1D 80.261 537 57 28 49 583 390677169 390677658 2.430000e-95 359.0
24 TraesCS1A01G293000 chr1D 82.045 401 42 16 188 583 390676945 390677320 5.330000e-82 315.0
25 TraesCS1A01G293000 chr1D 82.319 345 40 13 55 393 390676158 390676487 1.940000e-71 279.0
26 TraesCS1A01G293000 chr1D 79.529 425 55 26 144 551 390672312 390671903 9.050000e-70 274.0
27 TraesCS1A01G293000 chr1D 84.884 258 23 11 334 583 390676058 390676307 1.970000e-61 246.0
28 TraesCS1A01G293000 chr1D 87.387 222 15 9 581 800 390672114 390671904 2.550000e-60 243.0
29 TraesCS1A01G293000 chr1D 84.431 167 21 3 55 221 390677515 390677676 2.640000e-35 159.0
30 TraesCS1A01G293000 chr1D 95.062 81 3 1 1 80 390672824 390672744 2.680000e-25 126.0
31 TraesCS1A01G293000 chr1D 87.640 89 11 0 490 578 390672746 390672658 1.260000e-18 104.0
32 TraesCS1A01G293000 chr1D 94.828 58 3 0 524 581 390672312 390672255 9.780000e-15 91.6
33 TraesCS1A01G293000 chr5B 96.429 84 2 1 2484 2567 65274972 65275054 1.240000e-28 137.0
34 TraesCS1A01G293000 chr5B 95.238 84 3 1 2484 2567 65270091 65270173 5.760000e-27 132.0
35 TraesCS1A01G293000 chr3B 95.238 84 3 1 2484 2567 752112302 752112220 5.760000e-27 132.0
36 TraesCS1A01G293000 chr3B 95.238 84 3 1 2484 2567 752117191 752117109 5.760000e-27 132.0


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 TraesCS1A01G293000 chr1A 488218200 488220766 2566 False 1685.666667 4741 90.804667 1 2567 3 chr1A.!!$F3 2566
1 TraesCS1A01G293000 chr1B 523144114 523147603 3489 False 798.000000 1051 88.607500 933 2441 2 chr1B.!!$F5 1508
2 TraesCS1A01G293000 chr1B 523041565 523043119 1554 True 474.875000 1365 88.836750 54 1814 4 chr1B.!!$R2 1760
3 TraesCS1A01G293000 chr1B 523136941 523139184 2243 False 275.000000 344 89.270333 87 940 3 chr1B.!!$F4 853
4 TraesCS1A01G293000 chr1D 390676058 390679656 3598 False 452.571429 1279 84.023143 49 2441 7 chr1D.!!$F1 2392
5 TraesCS1A01G293000 chr1D 390668155 390672824 4669 True 402.325000 1319 88.898875 1 2440 8 chr1D.!!$R1 2439

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
982 3607 1.502231 CAGAGCGCGCATAGGTTTAT 58.498 50.0 35.1 8.99 0.0 1.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1853 8513 0.107993 ATGTCAGGGTGATCAGCGTG 60.108 55.0 31.64 31.64 43.54 5.34 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
74 121 4.871933 TGAAAGAAAATGGGAAAGGAGC 57.128 40.909 0.00 0.00 0.00 4.70
84 131 5.830799 ATGGGAAAGGAGCAAAGAAAAAT 57.169 34.783 0.00 0.00 0.00 1.82
85 132 6.933514 ATGGGAAAGGAGCAAAGAAAAATA 57.066 33.333 0.00 0.00 0.00 1.40
235 286 7.581011 ACGCATTAATGATTGTTTTTCTTCC 57.419 32.000 19.73 0.00 0.00 3.46
595 3120 2.236395 GGTTACTGCCATCCACTACTGT 59.764 50.000 0.00 0.00 0.00 3.55
599 3124 4.408182 ACTGCCATCCACTACTGTATTC 57.592 45.455 0.00 0.00 0.00 1.75
601 3126 2.102420 TGCCATCCACTACTGTATTCGG 59.898 50.000 0.00 0.00 0.00 4.30
602 3127 2.102588 GCCATCCACTACTGTATTCGGT 59.897 50.000 0.00 0.00 37.00 4.69
603 3128 3.319972 GCCATCCACTACTGTATTCGGTA 59.680 47.826 0.00 0.00 34.68 4.02
606 3131 5.926542 CCATCCACTACTGTATTCGGTATTG 59.073 44.000 2.74 2.74 36.48 1.90
609 3134 6.938507 TCCACTACTGTATTCGGTATTGTTT 58.061 36.000 7.56 0.00 35.60 2.83
709 3235 9.553064 AAGCAGGAAAGATAAATATGTACTCAG 57.447 33.333 0.00 0.00 0.00 3.35
777 3392 1.693627 AGAGATACTAGCCACACCCG 58.306 55.000 0.00 0.00 0.00 5.28
843 3458 3.249320 ACAGCTTGCTGCATAATGATACG 59.751 43.478 20.92 0.00 45.94 3.06
898 3521 9.379791 ACAGTATATTTTCAGTTTGGCTACTAC 57.620 33.333 0.00 0.00 0.00 2.73
946 3569 1.839424 CCATCCTTGTGTTCCTTCCC 58.161 55.000 0.00 0.00 0.00 3.97
982 3607 1.502231 CAGAGCGCGCATAGGTTTAT 58.498 50.000 35.10 8.99 0.00 1.40
1051 3677 0.543174 GGTATCTCTCGGGGCCATCT 60.543 60.000 4.39 0.00 0.00 2.90
1562 4191 4.202461 GGGAGGGCTTTCTTTTCCAAAATT 60.202 41.667 0.00 0.00 0.00 1.82
1603 4232 3.165071 GTGGAGATGTGGATTTTGGGTT 58.835 45.455 0.00 0.00 0.00 4.11
1667 4323 6.554334 TTGTAGTTGTCTAGATTTGGTTGC 57.446 37.500 0.00 0.00 0.00 4.17
1679 4336 2.957491 TTGGTTGCAAGGTGTTTCAG 57.043 45.000 0.00 0.00 0.00 3.02
1681 4338 2.665165 TGGTTGCAAGGTGTTTCAGAT 58.335 42.857 0.00 0.00 0.00 2.90
1684 4341 3.256631 GGTTGCAAGGTGTTTCAGATGAT 59.743 43.478 0.00 0.00 0.00 2.45
1753 4417 1.068083 GCTGTAGCATGCGCCTCTA 59.932 57.895 13.01 0.00 41.59 2.43
1755 4419 1.939974 CTGTAGCATGCGCCTCTAAA 58.060 50.000 13.01 0.00 39.83 1.85
1756 4420 1.594862 CTGTAGCATGCGCCTCTAAAC 59.405 52.381 13.01 2.72 39.83 2.01
1758 4422 1.594862 GTAGCATGCGCCTCTAAACTG 59.405 52.381 13.01 0.00 39.83 3.16
1760 4424 0.097674 GCATGCGCCTCTAAACTGTG 59.902 55.000 4.18 0.00 0.00 3.66
1761 4425 1.725641 CATGCGCCTCTAAACTGTGA 58.274 50.000 4.18 0.00 0.00 3.58
1776 8276 1.561076 CTGTGATCCAAGATCACCCCA 59.439 52.381 26.64 13.20 45.70 4.96
1777 8277 1.991813 TGTGATCCAAGATCACCCCAA 59.008 47.619 26.64 11.66 45.70 4.12
1779 8279 2.239654 GTGATCCAAGATCACCCCAAGA 59.760 50.000 21.72 0.00 41.77 3.02
1815 8475 1.402456 GCCGCTTTTGAGTCTAGTCGA 60.402 52.381 0.00 0.00 0.00 4.20
1816 8476 2.520979 CCGCTTTTGAGTCTAGTCGAG 58.479 52.381 0.00 0.00 0.00 4.04
1817 8477 2.520979 CGCTTTTGAGTCTAGTCGAGG 58.479 52.381 0.00 0.00 0.00 4.63
1818 8478 2.161808 CGCTTTTGAGTCTAGTCGAGGA 59.838 50.000 0.00 0.00 0.00 3.71
1820 8480 3.057456 GCTTTTGAGTCTAGTCGAGGACA 60.057 47.826 13.24 0.00 34.60 4.02
1822 8482 4.768130 TTTGAGTCTAGTCGAGGACAAG 57.232 45.455 13.24 0.00 34.60 3.16
1823 8483 3.697619 TGAGTCTAGTCGAGGACAAGA 57.302 47.619 13.24 0.00 34.60 3.02
1824 8484 3.601435 TGAGTCTAGTCGAGGACAAGAG 58.399 50.000 13.24 0.00 34.60 2.85
1825 8485 3.261137 TGAGTCTAGTCGAGGACAAGAGA 59.739 47.826 13.24 0.00 34.60 3.10
1826 8486 4.255301 GAGTCTAGTCGAGGACAAGAGAA 58.745 47.826 13.24 0.00 34.60 2.87
1828 8488 5.258051 AGTCTAGTCGAGGACAAGAGAATT 58.742 41.667 13.24 0.00 34.60 2.17
1829 8489 5.124776 AGTCTAGTCGAGGACAAGAGAATTG 59.875 44.000 13.24 0.00 34.60 2.32
1832 8492 4.962155 AGTCGAGGACAAGAGAATTGTTT 58.038 39.130 0.00 0.00 34.60 2.83
1833 8493 5.368989 AGTCGAGGACAAGAGAATTGTTTT 58.631 37.500 0.00 0.00 34.60 2.43
1834 8494 5.467063 AGTCGAGGACAAGAGAATTGTTTTC 59.533 40.000 0.00 0.00 34.60 2.29
1835 8495 4.755123 TCGAGGACAAGAGAATTGTTTTCC 59.245 41.667 0.00 0.00 31.96 3.13
1836 8496 4.377431 CGAGGACAAGAGAATTGTTTTCCG 60.377 45.833 0.00 0.00 31.96 4.30
1837 8497 4.461198 AGGACAAGAGAATTGTTTTCCGT 58.539 39.130 0.00 0.00 31.96 4.69
1838 8498 4.275936 AGGACAAGAGAATTGTTTTCCGTG 59.724 41.667 0.00 0.00 31.96 4.94
1839 8499 4.537015 GACAAGAGAATTGTTTTCCGTGG 58.463 43.478 0.00 0.00 31.96 4.94
1840 8500 3.951680 ACAAGAGAATTGTTTTCCGTGGT 59.048 39.130 0.00 0.00 0.00 4.16
1841 8501 4.401202 ACAAGAGAATTGTTTTCCGTGGTT 59.599 37.500 0.00 0.00 0.00 3.67
1842 8502 5.591067 ACAAGAGAATTGTTTTCCGTGGTTA 59.409 36.000 0.00 0.00 0.00 2.85
1843 8503 5.684550 AGAGAATTGTTTTCCGTGGTTAC 57.315 39.130 0.00 0.00 0.00 2.50
1844 8504 5.374071 AGAGAATTGTTTTCCGTGGTTACT 58.626 37.500 0.00 0.00 0.00 2.24
1845 8505 5.826208 AGAGAATTGTTTTCCGTGGTTACTT 59.174 36.000 0.00 0.00 0.00 2.24
1846 8506 5.827666 AGAATTGTTTTCCGTGGTTACTTG 58.172 37.500 0.00 0.00 0.00 3.16
1847 8507 3.423996 TTGTTTTCCGTGGTTACTTGC 57.576 42.857 0.00 0.00 0.00 4.01
1848 8508 2.645802 TGTTTTCCGTGGTTACTTGCT 58.354 42.857 0.00 0.00 0.00 3.91
1849 8509 2.356382 TGTTTTCCGTGGTTACTTGCTG 59.644 45.455 0.00 0.00 0.00 4.41
1850 8510 1.600023 TTTCCGTGGTTACTTGCTGG 58.400 50.000 0.00 0.00 0.00 4.85
1851 8511 0.887387 TTCCGTGGTTACTTGCTGGC 60.887 55.000 0.00 0.00 0.00 4.85
1852 8512 2.677003 CCGTGGTTACTTGCTGGCG 61.677 63.158 0.00 0.00 0.00 5.69
1853 8513 2.561373 GTGGTTACTTGCTGGCGC 59.439 61.111 0.00 0.00 0.00 6.53
1854 8514 2.112087 TGGTTACTTGCTGGCGCA 59.888 55.556 10.83 0.00 46.24 6.09
1864 8524 3.857854 CTGGCGCACGCTGATCAC 61.858 66.667 15.36 0.00 41.60 3.06
1868 8528 3.190849 CGCACGCTGATCACCCTG 61.191 66.667 0.00 0.00 0.00 4.45
1869 8529 2.265739 GCACGCTGATCACCCTGA 59.734 61.111 0.00 0.00 0.00 3.86
1870 8530 2.103042 GCACGCTGATCACCCTGAC 61.103 63.158 0.00 0.00 0.00 3.51
1871 8531 1.293179 CACGCTGATCACCCTGACA 59.707 57.895 0.00 0.00 0.00 3.58
1872 8532 0.107993 CACGCTGATCACCCTGACAT 60.108 55.000 0.00 0.00 0.00 3.06
1873 8533 0.107993 ACGCTGATCACCCTGACATG 60.108 55.000 0.00 0.00 0.00 3.21
1875 8535 1.405933 CGCTGATCACCCTGACATGAA 60.406 52.381 0.00 0.00 0.00 2.57
1876 8536 2.286872 GCTGATCACCCTGACATGAAG 58.713 52.381 0.00 0.00 0.00 3.02
1877 8537 2.286872 CTGATCACCCTGACATGAAGC 58.713 52.381 0.00 0.00 0.00 3.86
1879 8539 2.012673 GATCACCCTGACATGAAGCAC 58.987 52.381 0.00 0.00 0.00 4.40
1880 8540 0.764271 TCACCCTGACATGAAGCACA 59.236 50.000 0.00 0.00 0.00 4.57
1881 8541 1.142667 TCACCCTGACATGAAGCACAA 59.857 47.619 0.00 0.00 0.00 3.33
1882 8542 1.267806 CACCCTGACATGAAGCACAAC 59.732 52.381 0.00 0.00 0.00 3.32
1883 8543 0.518636 CCCTGACATGAAGCACAACG 59.481 55.000 0.00 0.00 0.00 4.10
1884 8544 0.110056 CCTGACATGAAGCACAACGC 60.110 55.000 0.00 0.00 42.91 4.84
1894 8554 4.012895 CACAACGCGAGGGCACAC 62.013 66.667 15.93 0.00 39.92 3.82
1901 8561 2.887568 CGAGGGCACACGCTGATC 60.888 66.667 0.00 0.00 39.58 2.92
1902 8562 2.265739 GAGGGCACACGCTGATCA 59.734 61.111 0.00 0.00 39.58 2.92
1903 8563 1.812922 GAGGGCACACGCTGATCAG 60.813 63.158 18.84 18.84 39.58 2.90
1904 8564 2.046892 GGGCACACGCTGATCAGT 60.047 61.111 23.38 2.99 38.60 3.41
1905 8565 2.393768 GGGCACACGCTGATCAGTG 61.394 63.158 30.12 30.12 44.11 3.66
1906 8566 1.374631 GGCACACGCTGATCAGTGA 60.375 57.895 36.45 0.00 41.24 3.41
1907 8567 0.742281 GGCACACGCTGATCAGTGAT 60.742 55.000 36.45 23.13 41.24 3.06
1908 8568 0.649475 GCACACGCTGATCAGTGATC 59.351 55.000 36.45 23.75 41.24 2.92
1909 8569 2.000429 CACACGCTGATCAGTGATCA 58.000 50.000 36.45 29.39 45.35 2.92
1910 8570 1.657594 CACACGCTGATCAGTGATCAC 59.342 52.381 36.45 22.41 43.11 3.06
1926 8586 4.762765 GTGATCACTCATCCGTACTATCCT 59.237 45.833 18.83 0.00 32.98 3.24
1927 8587 5.938710 GTGATCACTCATCCGTACTATCCTA 59.061 44.000 18.83 0.00 32.98 2.94
1930 8591 5.549347 TCACTCATCCGTACTATCCTACTC 58.451 45.833 0.00 0.00 0.00 2.59
1939 8600 4.202440 CGTACTATCCTACTCCTCTTCCCA 60.202 50.000 0.00 0.00 0.00 4.37
1949 8778 1.705186 TCCTCTTCCCAGTTTCCCAAG 59.295 52.381 0.00 0.00 0.00 3.61
1978 8807 1.100510 ATCACGTAGCGGTAAGAGCA 58.899 50.000 14.44 0.00 37.01 4.26
1979 8808 0.450583 TCACGTAGCGGTAAGAGCAG 59.549 55.000 14.44 2.00 37.01 4.24
1980 8809 0.170561 CACGTAGCGGTAAGAGCAGT 59.829 55.000 14.44 0.00 37.01 4.40
2050 8879 4.273480 TCTTTACAGCTCAAAACTCACAGC 59.727 41.667 0.00 0.00 0.00 4.40
2059 8888 5.911838 GCTCAAAACTCACAGCTTCTTAAAG 59.088 40.000 0.00 0.00 35.47 1.85
2083 8912 0.322546 GGGAGAAAACTGGCACGGAT 60.323 55.000 0.00 0.00 38.67 4.18
2108 8937 2.797156 GCATACAGCACTGAGTTATCCG 59.203 50.000 4.31 0.00 44.79 4.18
2154 8987 3.055963 AGTCTCCAAGATCAGCAAGACAG 60.056 47.826 15.99 0.00 36.46 3.51
2155 8988 2.008329 CTCCAAGATCAGCAAGACAGC 58.992 52.381 0.00 0.00 0.00 4.40
2156 8989 1.348696 TCCAAGATCAGCAAGACAGCA 59.651 47.619 0.00 0.00 36.85 4.41
2157 8990 2.156917 CCAAGATCAGCAAGACAGCAA 58.843 47.619 0.00 0.00 36.85 3.91
2158 8991 2.095364 CCAAGATCAGCAAGACAGCAAC 60.095 50.000 0.00 0.00 36.85 4.17
2159 8992 2.551032 CAAGATCAGCAAGACAGCAACA 59.449 45.455 0.00 0.00 36.85 3.33
2160 8993 2.149578 AGATCAGCAAGACAGCAACAC 58.850 47.619 0.00 0.00 36.85 3.32
2161 8994 2.149578 GATCAGCAAGACAGCAACACT 58.850 47.619 0.00 0.00 36.85 3.55
2312 9162 3.736759 GTCTAAGGCAAGACGCTAATAGC 59.263 47.826 1.41 1.41 41.91 2.97
2354 9210 7.872113 AAAGATACTGATCCATCCAAAGTTC 57.128 36.000 0.00 0.00 31.81 3.01
2405 9289 5.988310 AAAATGCAAGACATCCATCAGAA 57.012 34.783 0.00 0.00 38.34 3.02
2452 9336 4.421033 TTGTAAACACTGTTGAACGCAA 57.579 36.364 0.00 0.00 0.00 4.85
2453 9337 4.624336 TGTAAACACTGTTGAACGCAAT 57.376 36.364 0.00 0.00 36.22 3.56
2454 9338 4.346970 TGTAAACACTGTTGAACGCAATG 58.653 39.130 0.00 0.00 36.22 2.82
2455 9339 3.502191 AAACACTGTTGAACGCAATGT 57.498 38.095 0.00 0.00 36.22 2.71
2456 9340 2.473530 ACACTGTTGAACGCAATGTG 57.526 45.000 0.00 0.00 42.08 3.21
2457 9341 1.065401 ACACTGTTGAACGCAATGTGG 59.935 47.619 0.00 0.00 41.39 4.17
2458 9342 1.065401 CACTGTTGAACGCAATGTGGT 59.935 47.619 0.00 0.00 37.52 4.16
2459 9343 1.748493 ACTGTTGAACGCAATGTGGTT 59.252 42.857 0.00 0.00 36.22 3.67
2460 9344 2.118683 CTGTTGAACGCAATGTGGTTG 58.881 47.619 0.00 0.00 40.90 3.77
2485 9369 4.758251 CGTGCGCCATGAGGTCCA 62.758 66.667 4.18 0.00 37.19 4.02
2486 9370 3.127533 GTGCGCCATGAGGTCCAC 61.128 66.667 4.18 0.00 37.19 4.02
2487 9371 4.408821 TGCGCCATGAGGTCCACC 62.409 66.667 4.18 0.00 37.19 4.61
2489 9373 4.838152 CGCCATGAGGTCCACCCG 62.838 72.222 0.00 0.00 38.74 5.28
2490 9374 4.489771 GCCATGAGGTCCACCCGG 62.490 72.222 0.00 0.00 38.74 5.73
2491 9375 4.489771 CCATGAGGTCCACCCGGC 62.490 72.222 0.00 0.00 38.74 6.13
2492 9376 3.402681 CATGAGGTCCACCCGGCT 61.403 66.667 0.00 0.00 38.74 5.52
2493 9377 3.402681 ATGAGGTCCACCCGGCTG 61.403 66.667 0.00 0.00 38.74 4.85
2498 9382 4.408821 GTCCACCCGGCTGCATGA 62.409 66.667 0.50 0.00 0.00 3.07
2499 9383 4.100084 TCCACCCGGCTGCATGAG 62.100 66.667 0.50 0.00 0.00 2.90
2501 9385 4.415150 CACCCGGCTGCATGAGGT 62.415 66.667 0.50 0.00 0.00 3.85
2502 9386 2.687200 ACCCGGCTGCATGAGGTA 60.687 61.111 0.50 0.00 0.00 3.08
2503 9387 2.109799 CCCGGCTGCATGAGGTAG 59.890 66.667 0.50 0.00 0.00 3.18
2504 9388 2.735772 CCCGGCTGCATGAGGTAGT 61.736 63.158 0.50 0.00 0.00 2.73
2505 9389 1.221840 CCGGCTGCATGAGGTAGTT 59.778 57.895 0.50 0.00 0.00 2.24
2506 9390 0.464036 CCGGCTGCATGAGGTAGTTA 59.536 55.000 0.50 0.00 0.00 2.24
2507 9391 1.539065 CCGGCTGCATGAGGTAGTTAG 60.539 57.143 0.50 0.00 0.00 2.34
2508 9392 1.539065 CGGCTGCATGAGGTAGTTAGG 60.539 57.143 0.50 0.00 0.00 2.69
2509 9393 1.762957 GGCTGCATGAGGTAGTTAGGA 59.237 52.381 0.50 0.00 0.00 2.94
2510 9394 2.370189 GGCTGCATGAGGTAGTTAGGAT 59.630 50.000 0.50 0.00 0.00 3.24
2511 9395 3.578716 GGCTGCATGAGGTAGTTAGGATA 59.421 47.826 0.50 0.00 0.00 2.59
2512 9396 4.322349 GGCTGCATGAGGTAGTTAGGATAG 60.322 50.000 0.50 0.00 0.00 2.08
2513 9397 4.524714 GCTGCATGAGGTAGTTAGGATAGA 59.475 45.833 0.00 0.00 0.00 1.98
2514 9398 5.186797 GCTGCATGAGGTAGTTAGGATAGAT 59.813 44.000 0.00 0.00 0.00 1.98
2515 9399 6.378564 GCTGCATGAGGTAGTTAGGATAGATA 59.621 42.308 0.00 0.00 0.00 1.98
2516 9400 7.416213 GCTGCATGAGGTAGTTAGGATAGATAG 60.416 44.444 0.00 0.00 0.00 2.08
2517 9401 7.699878 TGCATGAGGTAGTTAGGATAGATAGA 58.300 38.462 0.00 0.00 0.00 1.98
2518 9402 8.340002 TGCATGAGGTAGTTAGGATAGATAGAT 58.660 37.037 0.00 0.00 0.00 1.98
2519 9403 9.854668 GCATGAGGTAGTTAGGATAGATAGATA 57.145 37.037 0.00 0.00 0.00 1.98
2561 9445 6.723298 TGATCTCCAAGTTCTATCTCTTCC 57.277 41.667 0.00 0.00 0.00 3.46
2562 9446 6.439487 TGATCTCCAAGTTCTATCTCTTCCT 58.561 40.000 0.00 0.00 0.00 3.36
2563 9447 6.900186 TGATCTCCAAGTTCTATCTCTTCCTT 59.100 38.462 0.00 0.00 0.00 3.36
2564 9448 6.537453 TCTCCAAGTTCTATCTCTTCCTTG 57.463 41.667 0.00 0.00 0.00 3.61
2565 9449 6.256819 TCTCCAAGTTCTATCTCTTCCTTGA 58.743 40.000 0.00 0.00 32.96 3.02
2566 9450 6.726299 TCTCCAAGTTCTATCTCTTCCTTGAA 59.274 38.462 0.00 0.00 32.96 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 1.119684 GGAAGAGAGAGGAAGGAGGC 58.880 60.000 0.00 0.00 0.00 4.70
225 276 8.255206 TCAGTAAAAGGGAAAAGGAAGAAAAAC 58.745 33.333 0.00 0.00 0.00 2.43
226 277 8.368962 TCAGTAAAAGGGAAAAGGAAGAAAAA 57.631 30.769 0.00 0.00 0.00 1.94
227 278 7.964666 TCAGTAAAAGGGAAAAGGAAGAAAA 57.035 32.000 0.00 0.00 0.00 2.29
519 2874 4.638421 TGTAGCATTAGTTTATGGGTGTGC 59.362 41.667 0.00 0.00 0.00 4.57
709 3235 9.145865 GTAGCATTAATCTTAATCTAGCTCACC 57.854 37.037 8.44 0.00 34.12 4.02
825 3440 3.883631 TGCGTATCATTATGCAGCAAG 57.116 42.857 0.00 0.00 43.69 4.01
946 3569 2.998670 CTCTGCAACCTCTGTGTGTATG 59.001 50.000 0.00 0.00 0.00 2.39
982 3607 4.718940 TCATGTTTGCTCGATCTCTGTA 57.281 40.909 0.00 0.00 0.00 2.74
1032 3658 0.543174 AGATGGCCCCGAGAGATACC 60.543 60.000 0.00 0.00 0.00 2.73
1051 3677 4.087892 GCTGCCGGAGAGCAAGGA 62.088 66.667 18.39 0.00 43.52 3.36
1562 4191 1.417517 CATCCAGGCAGGCATACTACA 59.582 52.381 0.00 0.00 37.29 2.74
1603 4232 4.779696 GGGTTACCACCGAATTATTACCA 58.220 43.478 2.98 0.00 45.39 3.25
1628 4257 4.385825 ACTACAAATACCACCGCATATGG 58.614 43.478 4.56 0.00 43.43 2.74
1629 4258 5.295787 ACAACTACAAATACCACCGCATATG 59.704 40.000 0.00 0.00 0.00 1.78
1746 4410 2.672961 TGGATCACAGTTTAGAGGCG 57.327 50.000 0.00 0.00 0.00 5.52
1749 4413 6.900568 GTGATCTTGGATCACAGTTTAGAG 57.099 41.667 26.09 0.00 45.61 2.43
1758 4422 2.239654 TCTTGGGGTGATCTTGGATCAC 59.760 50.000 24.19 24.19 45.59 3.06
1760 4424 3.137176 TGATCTTGGGGTGATCTTGGATC 59.863 47.826 0.00 1.04 40.51 3.36
1761 4425 3.117738 GTGATCTTGGGGTGATCTTGGAT 60.118 47.826 0.00 0.00 40.51 3.41
1776 8276 1.271597 GCCCTTGTGTCTGGTGATCTT 60.272 52.381 0.00 0.00 0.00 2.40
1777 8277 0.326264 GCCCTTGTGTCTGGTGATCT 59.674 55.000 0.00 0.00 0.00 2.75
1779 8279 1.380302 GGCCCTTGTGTCTGGTGAT 59.620 57.895 0.00 0.00 0.00 3.06
1815 8475 4.275936 CACGGAAAACAATTCTCTTGTCCT 59.724 41.667 0.00 0.00 0.00 3.85
1816 8476 4.537015 CACGGAAAACAATTCTCTTGTCC 58.463 43.478 0.00 0.00 0.00 4.02
1817 8477 4.036380 ACCACGGAAAACAATTCTCTTGTC 59.964 41.667 0.00 0.00 0.00 3.18
1818 8478 3.951680 ACCACGGAAAACAATTCTCTTGT 59.048 39.130 0.00 0.00 0.00 3.16
1820 8480 5.826208 AGTAACCACGGAAAACAATTCTCTT 59.174 36.000 0.00 0.00 0.00 2.85
1822 8482 5.684550 AGTAACCACGGAAAACAATTCTC 57.315 39.130 0.00 0.00 0.00 2.87
1823 8483 5.735070 GCAAGTAACCACGGAAAACAATTCT 60.735 40.000 0.00 0.00 0.00 2.40
1824 8484 4.443063 GCAAGTAACCACGGAAAACAATTC 59.557 41.667 0.00 0.00 0.00 2.17
1825 8485 4.098807 AGCAAGTAACCACGGAAAACAATT 59.901 37.500 0.00 0.00 0.00 2.32
1826 8486 3.634910 AGCAAGTAACCACGGAAAACAAT 59.365 39.130 0.00 0.00 0.00 2.71
1828 8488 2.356382 CAGCAAGTAACCACGGAAAACA 59.644 45.455 0.00 0.00 0.00 2.83
1829 8489 2.287368 CCAGCAAGTAACCACGGAAAAC 60.287 50.000 0.00 0.00 0.00 2.43
1832 8492 0.887387 GCCAGCAAGTAACCACGGAA 60.887 55.000 0.00 0.00 0.00 4.30
1833 8493 1.302192 GCCAGCAAGTAACCACGGA 60.302 57.895 0.00 0.00 0.00 4.69
1834 8494 2.677003 CGCCAGCAAGTAACCACGG 61.677 63.158 0.00 0.00 0.00 4.94
1835 8495 2.860293 CGCCAGCAAGTAACCACG 59.140 61.111 0.00 0.00 0.00 4.94
1836 8496 2.561373 GCGCCAGCAAGTAACCAC 59.439 61.111 0.00 0.00 44.35 4.16
1847 8507 3.857854 GTGATCAGCGTGCGCCAG 61.858 66.667 13.21 6.62 43.17 4.85
1851 8511 3.190849 CAGGGTGATCAGCGTGCG 61.191 66.667 28.31 11.58 37.77 5.34
1852 8512 2.103042 GTCAGGGTGATCAGCGTGC 61.103 63.158 32.29 25.08 42.38 5.34
1853 8513 0.107993 ATGTCAGGGTGATCAGCGTG 60.108 55.000 31.64 31.64 43.54 5.34
1854 8514 0.107993 CATGTCAGGGTGATCAGCGT 60.108 55.000 18.14 16.10 0.00 5.07
1855 8515 0.176449 TCATGTCAGGGTGATCAGCG 59.824 55.000 18.14 6.17 0.00 5.18
1856 8516 2.286872 CTTCATGTCAGGGTGATCAGC 58.713 52.381 16.65 16.65 0.00 4.26
1857 8517 2.286872 GCTTCATGTCAGGGTGATCAG 58.713 52.381 0.00 0.00 0.00 2.90
1858 8518 1.629861 TGCTTCATGTCAGGGTGATCA 59.370 47.619 0.00 0.00 0.00 2.92
1859 8519 2.012673 GTGCTTCATGTCAGGGTGATC 58.987 52.381 0.00 0.00 0.00 2.92
1861 8521 0.764271 TGTGCTTCATGTCAGGGTGA 59.236 50.000 0.00 0.00 0.00 4.02
1862 8522 1.267806 GTTGTGCTTCATGTCAGGGTG 59.732 52.381 0.00 0.00 0.00 4.61
1864 8524 0.518636 CGTTGTGCTTCATGTCAGGG 59.481 55.000 0.00 0.00 0.00 4.45
1865 8525 0.110056 GCGTTGTGCTTCATGTCAGG 60.110 55.000 0.00 0.00 41.73 3.86
1866 8526 0.451628 CGCGTTGTGCTTCATGTCAG 60.452 55.000 0.00 0.00 43.27 3.51
1868 8528 0.179240 CTCGCGTTGTGCTTCATGTC 60.179 55.000 5.77 0.00 43.27 3.06
1869 8529 1.568612 CCTCGCGTTGTGCTTCATGT 61.569 55.000 5.77 0.00 43.27 3.21
1870 8530 1.133253 CCTCGCGTTGTGCTTCATG 59.867 57.895 5.77 0.00 43.27 3.07
1871 8531 2.034879 CCCTCGCGTTGTGCTTCAT 61.035 57.895 5.77 0.00 43.27 2.57
1872 8532 2.664851 CCCTCGCGTTGTGCTTCA 60.665 61.111 5.77 0.00 43.27 3.02
1873 8533 4.090057 GCCCTCGCGTTGTGCTTC 62.090 66.667 5.77 0.00 43.27 3.86
1877 8537 4.012895 GTGTGCCCTCGCGTTGTG 62.013 66.667 5.77 0.00 38.08 3.33
1884 8544 2.887568 GATCAGCGTGTGCCCTCG 60.888 66.667 0.00 0.00 44.31 4.63
1885 8545 1.812922 CTGATCAGCGTGTGCCCTC 60.813 63.158 10.38 0.00 44.31 4.30
1886 8546 2.267006 CTGATCAGCGTGTGCCCT 59.733 61.111 10.38 0.00 44.31 5.19
1887 8547 2.046892 ACTGATCAGCGTGTGCCC 60.047 61.111 22.83 0.00 44.31 5.36
1888 8548 0.742281 ATCACTGATCAGCGTGTGCC 60.742 55.000 22.83 0.00 44.31 5.01
1889 8549 0.649475 GATCACTGATCAGCGTGTGC 59.351 55.000 22.83 8.09 38.77 4.57
1890 8550 2.000429 TGATCACTGATCAGCGTGTG 58.000 50.000 22.83 13.95 43.11 3.82
1898 8558 3.724508 ACGGATGAGTGATCACTGATC 57.275 47.619 34.36 34.36 46.70 2.92
1899 8559 4.211125 AGTACGGATGAGTGATCACTGAT 58.789 43.478 32.50 28.77 42.66 2.90
1900 8560 3.621558 AGTACGGATGAGTGATCACTGA 58.378 45.455 32.50 25.18 42.66 3.41
1901 8561 5.335269 GGATAGTACGGATGAGTGATCACTG 60.335 48.000 32.50 19.30 42.66 3.66
1902 8562 4.762765 GGATAGTACGGATGAGTGATCACT 59.237 45.833 28.23 28.23 45.84 3.41
1903 8563 4.762765 AGGATAGTACGGATGAGTGATCAC 59.237 45.833 18.47 18.47 31.91 3.06
1904 8564 4.986783 AGGATAGTACGGATGAGTGATCA 58.013 43.478 0.00 0.00 31.91 2.92
1905 8565 6.174760 AGTAGGATAGTACGGATGAGTGATC 58.825 44.000 0.00 0.00 0.00 2.92
1906 8566 6.129414 AGTAGGATAGTACGGATGAGTGAT 57.871 41.667 0.00 0.00 0.00 3.06
1907 8567 5.512749 GGAGTAGGATAGTACGGATGAGTGA 60.513 48.000 0.00 0.00 0.00 3.41
1908 8568 4.696402 GGAGTAGGATAGTACGGATGAGTG 59.304 50.000 0.00 0.00 0.00 3.51
1909 8569 4.598373 AGGAGTAGGATAGTACGGATGAGT 59.402 45.833 0.00 0.00 27.14 3.41
1910 8570 5.046159 AGAGGAGTAGGATAGTACGGATGAG 60.046 48.000 0.00 0.00 27.14 2.90
1926 8586 2.158066 TGGGAAACTGGGAAGAGGAGTA 60.158 50.000 0.00 0.00 0.00 2.59
1927 8587 1.363246 GGGAAACTGGGAAGAGGAGT 58.637 55.000 0.00 0.00 0.00 3.85
1930 8591 1.705186 TCTTGGGAAACTGGGAAGAGG 59.295 52.381 0.00 0.00 0.00 3.69
1939 8600 5.532779 GTGATTTCTTCAGTCTTGGGAAACT 59.467 40.000 0.00 0.00 34.17 2.66
1949 8778 2.599082 CCGCTACGTGATTTCTTCAGTC 59.401 50.000 0.00 0.00 34.17 3.51
1978 8807 5.240844 GGCACAAACTGTCCATTTTACTACT 59.759 40.000 0.00 0.00 0.00 2.57
1979 8808 5.458015 GGCACAAACTGTCCATTTTACTAC 58.542 41.667 0.00 0.00 0.00 2.73
1980 8809 4.521256 GGGCACAAACTGTCCATTTTACTA 59.479 41.667 0.00 0.00 45.18 1.82
2016 8845 4.937620 TGAGCTGTAAAGATGGTAAAGCTG 59.062 41.667 0.89 0.00 41.35 4.24
2050 8879 6.207614 CAGTTTTCTCCCCTTCCTTTAAGAAG 59.792 42.308 0.00 0.00 42.46 2.85
2059 8888 0.112412 TGCCAGTTTTCTCCCCTTCC 59.888 55.000 0.00 0.00 0.00 3.46
2083 8912 3.407424 AACTCAGTGCTGTATGCTTGA 57.593 42.857 0.00 0.00 43.37 3.02
2108 8937 2.764314 CCCTGGCGTGCTATGCAAC 61.764 63.158 0.00 0.00 41.47 4.17
2154 8987 3.354089 TTAAGCTGCTTGAAGTGTTGC 57.646 42.857 24.35 0.00 0.00 4.17
2155 8988 6.363357 GGTTTATTAAGCTGCTTGAAGTGTTG 59.637 38.462 24.35 0.00 0.00 3.33
2156 8989 6.447162 GGTTTATTAAGCTGCTTGAAGTGTT 58.553 36.000 24.35 3.94 0.00 3.32
2157 8990 5.048013 GGGTTTATTAAGCTGCTTGAAGTGT 60.048 40.000 24.35 4.31 32.40 3.55
2158 8991 5.402398 GGGTTTATTAAGCTGCTTGAAGTG 58.598 41.667 24.35 0.00 32.40 3.16
2159 8992 4.462834 GGGGTTTATTAAGCTGCTTGAAGT 59.537 41.667 24.35 9.91 32.40 3.01
2160 8993 4.706962 AGGGGTTTATTAAGCTGCTTGAAG 59.293 41.667 24.35 0.00 32.40 3.02
2161 8994 4.672899 AGGGGTTTATTAAGCTGCTTGAA 58.327 39.130 24.35 14.26 32.40 2.69
2304 9154 4.625607 AGGTGATGTTAGGGCTATTAGC 57.374 45.455 7.16 7.16 41.46 3.09
2312 9162 8.487028 AGTATCTTTTAGAAGGTGATGTTAGGG 58.513 37.037 0.00 0.00 33.56 3.53
2354 9210 3.411446 TGGCTCAGTGTTATGTCCTTTG 58.589 45.455 0.00 0.00 0.00 2.77
2422 9306 4.882671 ACAGTGTTTACAACTTGCTCAG 57.117 40.909 0.00 0.00 0.00 3.35
2441 9325 2.200792 CAACCACATTGCGTTCAACA 57.799 45.000 0.00 0.00 34.60 3.33
2468 9352 4.758251 TGGACCTCATGGCGCACG 62.758 66.667 10.83 0.00 36.63 5.34
2469 9353 3.127533 GTGGACCTCATGGCGCAC 61.128 66.667 10.83 0.00 36.63 5.34
2470 9354 4.408821 GGTGGACCTCATGGCGCA 62.409 66.667 10.83 0.00 36.63 6.09
2472 9356 4.838152 CGGGTGGACCTCATGGCG 62.838 72.222 0.00 0.00 36.97 5.69
2473 9357 4.489771 CCGGGTGGACCTCATGGC 62.490 72.222 0.00 0.00 37.49 4.40
2474 9358 4.489771 GCCGGGTGGACCTCATGG 62.490 72.222 2.18 0.00 37.49 3.66
2475 9359 3.402681 AGCCGGGTGGACCTCATG 61.403 66.667 4.72 0.00 37.49 3.07
2476 9360 3.402681 CAGCCGGGTGGACCTCAT 61.403 66.667 26.09 0.00 37.49 2.90
2481 9365 4.408821 TCATGCAGCCGGGTGGAC 62.409 66.667 33.10 18.88 37.49 4.02
2482 9366 4.100084 CTCATGCAGCCGGGTGGA 62.100 66.667 33.10 31.74 37.49 4.02
2484 9368 2.930385 CTACCTCATGCAGCCGGGTG 62.930 65.000 29.14 29.14 0.00 4.61
2485 9369 2.687200 TACCTCATGCAGCCGGGT 60.687 61.111 0.00 0.00 0.00 5.28
2486 9370 2.109799 CTACCTCATGCAGCCGGG 59.890 66.667 2.18 0.00 0.00 5.73
2487 9371 0.464036 TAACTACCTCATGCAGCCGG 59.536 55.000 0.00 0.00 0.00 6.13
2488 9372 1.539065 CCTAACTACCTCATGCAGCCG 60.539 57.143 0.00 0.00 0.00 5.52
2489 9373 1.762957 TCCTAACTACCTCATGCAGCC 59.237 52.381 0.00 0.00 0.00 4.85
2490 9374 3.760580 ATCCTAACTACCTCATGCAGC 57.239 47.619 0.00 0.00 0.00 5.25
2491 9375 6.849085 ATCTATCCTAACTACCTCATGCAG 57.151 41.667 0.00 0.00 0.00 4.41
2492 9376 7.699878 TCTATCTATCCTAACTACCTCATGCA 58.300 38.462 0.00 0.00 0.00 3.96
2493 9377 8.760980 ATCTATCTATCCTAACTACCTCATGC 57.239 38.462 0.00 0.00 0.00 4.06
2537 9421 6.900186 AGGAAGAGATAGAACTTGGAGATCAA 59.100 38.462 0.00 0.00 0.00 2.57
2538 9422 6.439487 AGGAAGAGATAGAACTTGGAGATCA 58.561 40.000 0.00 0.00 0.00 2.92
2539 9423 6.976934 AGGAAGAGATAGAACTTGGAGATC 57.023 41.667 0.00 0.00 0.00 2.75
2540 9424 6.900186 TCAAGGAAGAGATAGAACTTGGAGAT 59.100 38.462 0.00 0.00 36.78 2.75
2541 9425 6.256819 TCAAGGAAGAGATAGAACTTGGAGA 58.743 40.000 0.00 0.00 36.78 3.71
2542 9426 6.537453 TCAAGGAAGAGATAGAACTTGGAG 57.463 41.667 0.00 0.00 36.78 3.86
2543 9427 6.935240 TTCAAGGAAGAGATAGAACTTGGA 57.065 37.500 0.00 0.00 36.78 3.53


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

AutoCloner maintained by Alex Coulton.