Multiple sequence alignment - TraesCS7B01G144900

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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 TraesCS7B01G144900 chr7B 100.000 6082 0 0 1 6082 187776396 187782477 0.000000e+00 11232.0
1 TraesCS7B01G144900 chr7D 96.632 2939 77 7 3159 6082 213788845 213785914 0.000000e+00 4859.0
2 TraesCS7B01G144900 chr7D 88.005 2326 87 75 1 2184 213792100 213789825 0.000000e+00 2573.0
3 TraesCS7B01G144900 chr7D 91.304 920 68 11 2243 3159 213789798 213788888 0.000000e+00 1245.0
4 TraesCS7B01G144900 chr7D 85.546 339 34 10 2817 3145 573118367 573118034 2.100000e-89 340.0
5 TraesCS7B01G144900 chr7D 83.193 119 20 0 2280 2398 634344287 634344405 6.450000e-20 110.0
6 TraesCS7B01G144900 chr7A 90.793 2748 150 46 3336 6009 225633428 225630710 0.000000e+00 3578.0
7 TraesCS7B01G144900 chr7A 86.758 1465 59 48 711 2072 225636568 225635136 0.000000e+00 1506.0
8 TraesCS7B01G144900 chr7A 91.571 700 31 16 4 690 225637387 225636703 0.000000e+00 941.0
9 TraesCS7B01G144900 chr7A 91.241 411 26 3 2399 2808 225634777 225634376 8.910000e-153 551.0
10 TraesCS7B01G144900 chr7A 90.260 154 7 1 3168 3321 225634067 225633922 1.730000e-45 195.0
11 TraesCS7B01G144900 chr7A 83.051 118 20 0 2283 2400 16307137 16307020 2.320000e-19 108.0
12 TraesCS7B01G144900 chr7A 78.065 155 32 2 1320 1473 685230148 685229995 5.020000e-16 97.1
13 TraesCS7B01G144900 chr3D 84.814 349 36 15 2817 3159 517012055 517011718 9.770000e-88 335.0
14 TraesCS7B01G144900 chr3D 84.034 119 19 0 2280 2398 25580611 25580729 1.390000e-21 115.0
15 TraesCS7B01G144900 chr3D 83.478 115 19 0 2284 2398 582266493 582266379 2.320000e-19 108.0
16 TraesCS7B01G144900 chr3D 82.222 90 14 2 1383 1471 538401378 538401466 6.540000e-10 76.8
17 TraesCS7B01G144900 chr6D 83.714 350 46 9 2816 3157 91846793 91846447 2.740000e-83 320.0
18 TraesCS7B01G144900 chr4D 83.954 349 41 11 2816 3153 323597562 323597218 2.740000e-83 320.0
19 TraesCS7B01G144900 chr1B 84.273 337 38 12 2818 3144 599516407 599516076 1.270000e-81 315.0
20 TraesCS7B01G144900 chr2B 85.623 313 27 14 2818 3126 151646108 151645810 4.580000e-81 313.0
21 TraesCS7B01G144900 chr2B 83.478 115 19 0 2283 2397 545349023 545348909 2.320000e-19 108.0
22 TraesCS7B01G144900 chr5D 82.222 360 45 13 2807 3153 549767768 549767415 5.960000e-75 292.0
23 TraesCS7B01G144900 chr5D 86.420 162 18 4 1317 1476 376939827 376939668 2.250000e-39 174.0
24 TraesCS7B01G144900 chr5D 88.372 86 9 1 4505 4589 376937555 376937470 1.080000e-17 102.0
25 TraesCS7B01G144900 chr2A 81.322 348 53 9 2818 3155 593299594 593299249 7.770000e-69 272.0
26 TraesCS7B01G144900 chr5B 87.582 153 19 0 1319 1471 450107990 450107838 1.740000e-40 178.0
27 TraesCS7B01G144900 chr5B 88.372 86 9 1 4505 4589 450105736 450105651 1.080000e-17 102.0
28 TraesCS7B01G144900 chr5A 87.662 154 16 3 1323 1475 477587136 477586985 6.270000e-40 176.0
29 TraesCS7B01G144900 chr5A 88.372 86 9 1 4505 4589 477584952 477584867 1.080000e-17 102.0
30 TraesCS7B01G144900 chr6B 85.000 120 16 2 2280 2398 90975541 90975659 2.980000e-23 121.0
31 TraesCS7B01G144900 chr6B 84.483 116 18 0 2283 2398 68111925 68111810 1.390000e-21 115.0
32 TraesCS7B01G144900 chr6B 84.483 116 16 2 2286 2400 12514133 12514019 4.980000e-21 113.0
33 TraesCS7B01G144900 chr3B 82.105 95 14 3 1383 1475 713321546 713321639 1.820000e-10 78.7
34 TraesCS7B01G144900 chr3A 82.105 95 14 3 1383 1475 673899292 673899385 1.820000e-10 78.7


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 TraesCS7B01G144900 chr7B 187776396 187782477 6081 False 11232.000000 11232 100.000000 1 6082 1 chr7B.!!$F1 6081
1 TraesCS7B01G144900 chr7D 213785914 213792100 6186 True 2892.333333 4859 91.980333 1 6082 3 chr7D.!!$R2 6081
2 TraesCS7B01G144900 chr7A 225630710 225637387 6677 True 1354.200000 3578 90.124600 4 6009 5 chr7A.!!$R3 6005

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
891 1081 0.106217 GGTCAGGAGGGAGAGAGAGG 60.106 65.000 0.00 0.00 0.00 3.69 F
942 1132 0.179121 GGTCACTCGTGTGTGTGTGA 60.179 55.000 16.49 0.00 44.14 3.58 F
1770 2063 0.322098 TCATTGGGTTGGGTGTAGCG 60.322 55.000 0.00 0.00 0.00 4.26 F
1771 2064 0.322098 CATTGGGTTGGGTGTAGCGA 60.322 55.000 0.00 0.00 0.00 4.93 F
1773 2066 0.402504 TTGGGTTGGGTGTAGCGATT 59.597 50.000 0.00 0.00 0.00 3.34 F
2727 3162 1.004745 CCCCCTCTTGTTGCACAGTAT 59.995 52.381 0.00 0.00 0.00 2.12 F
4179 5193 0.110486 ATCCTTTGGTGAGCAACGGT 59.890 50.000 17.65 4.86 0.00 4.83 F
4662 5679 0.874607 CGAGTAACTACATGCCGCCC 60.875 60.000 0.00 0.00 0.00 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2238 2671 0.179043 TTGGGTGTGCGTGTGTATGT 60.179 50.000 0.00 0.0 0.00 2.29 R
2727 3162 0.908910 ACATCCCCGAGCATACACAA 59.091 50.000 0.00 0.0 0.00 3.33 R
2742 3177 1.308069 ACCATGAGCGCACCAACATC 61.308 55.000 11.47 0.0 0.00 3.06 R
3477 4439 2.027192 GCAGAGGGTTGTCCATCAAGTA 60.027 50.000 1.98 0.0 45.75 2.24 R
3491 4453 2.935481 TCACCAAGGGGCAGAGGG 60.935 66.667 0.00 0.0 37.90 4.30 R
4386 5403 0.456628 GAGGACGCAGGTCTAGGTTC 59.543 60.000 0.00 0.0 42.97 3.62 R
5082 6099 0.179004 TGGGCGCAAATAGTATGGGG 60.179 55.000 10.83 0.0 0.00 4.96 R
5775 6808 0.257039 AGCCAATGCCGGAATCTCTT 59.743 50.000 5.05 0.0 38.69 2.85 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
80 82 0.310543 GAAAGGCACGTGCACATGAA 59.689 50.000 38.60 0.00 44.36 2.57
199 205 0.846015 TAGTAGTAGCCCGTAGCCCA 59.154 55.000 0.00 0.00 45.47 5.36
337 344 2.952978 CACAGGTCTACTAGGTAGCAGG 59.047 54.545 0.00 0.00 36.22 4.85
339 346 3.464080 ACAGGTCTACTAGGTAGCAGGAT 59.536 47.826 0.00 0.00 36.22 3.24
340 347 4.664064 ACAGGTCTACTAGGTAGCAGGATA 59.336 45.833 0.00 0.00 36.22 2.59
380 387 3.442076 GTGTTAAAGGAGGGGAGAGAGA 58.558 50.000 0.00 0.00 0.00 3.10
382 389 3.336997 TGTTAAAGGAGGGGAGAGAGAGA 59.663 47.826 0.00 0.00 0.00 3.10
384 391 0.933700 AAGGAGGGGAGAGAGAGAGG 59.066 60.000 0.00 0.00 0.00 3.69
386 393 1.541672 GAGGGGAGAGAGAGAGGGG 59.458 68.421 0.00 0.00 0.00 4.79
387 394 2.018086 AGGGGAGAGAGAGAGGGGG 61.018 68.421 0.00 0.00 0.00 5.40
430 437 3.054434 CCATGGGAAACATCTACTGTGGA 60.054 47.826 2.85 0.00 37.84 4.02
432 439 2.571653 TGGGAAACATCTACTGTGGAGG 59.428 50.000 4.23 4.23 38.39 4.30
527 536 2.360852 GCAGTGGCAGGTGCAGAT 60.361 61.111 15.18 0.00 44.36 2.90
553 570 1.906253 CAGGGCACTGCTCTCTCAT 59.094 57.895 1.22 0.00 37.20 2.90
592 609 4.517285 GTGATTTGATAAGTGGAGGCAGA 58.483 43.478 0.00 0.00 0.00 4.26
629 647 1.906990 AGATGGCATGAATAGGCAGC 58.093 50.000 3.81 0.00 46.69 5.25
634 652 2.113986 ATGAATAGGCAGCGGGGC 59.886 61.111 0.00 0.00 43.80 5.80
891 1081 0.106217 GGTCAGGAGGGAGAGAGAGG 60.106 65.000 0.00 0.00 0.00 3.69
894 1084 0.859760 CAGGAGGGAGAGAGAGGGAT 59.140 60.000 0.00 0.00 0.00 3.85
942 1132 0.179121 GGTCACTCGTGTGTGTGTGA 60.179 55.000 16.49 0.00 44.14 3.58
948 1138 2.324477 GTGTGTGTGTGAGTGCGC 59.676 61.111 0.00 0.00 0.00 6.09
977 1167 0.541392 CCCATCGTCACCAATCTCCA 59.459 55.000 0.00 0.00 0.00 3.86
1092 1306 1.376543 CTAGCTAGGACCGACGACAA 58.623 55.000 13.32 0.00 0.00 3.18
1223 1437 0.607217 TCTACTTCGAGGACGCCACA 60.607 55.000 0.00 0.00 39.58 4.17
1522 1767 1.448013 GCGTTTCTCTTCTCCCCGG 60.448 63.158 0.00 0.00 0.00 5.73
1546 1791 5.960105 GCAATTTCTTGACGTATTCTGTAGC 59.040 40.000 0.00 0.00 34.04 3.58
1573 1823 6.668645 ACATGGTGTATTCCTAGCCATTTTA 58.331 36.000 0.00 0.00 37.80 1.52
1574 1824 7.122715 ACATGGTGTATTCCTAGCCATTTTAA 58.877 34.615 0.00 0.00 37.80 1.52
1575 1825 7.784550 ACATGGTGTATTCCTAGCCATTTTAAT 59.215 33.333 0.00 0.00 37.80 1.40
1576 1826 8.641541 CATGGTGTATTCCTAGCCATTTTAATT 58.358 33.333 0.00 0.00 37.80 1.40
1577 1827 8.602472 TGGTGTATTCCTAGCCATTTTAATTT 57.398 30.769 0.00 0.00 0.00 1.82
1578 1828 8.474025 TGGTGTATTCCTAGCCATTTTAATTTG 58.526 33.333 0.00 0.00 0.00 2.32
1579 1829 8.474831 GGTGTATTCCTAGCCATTTTAATTTGT 58.525 33.333 0.00 0.00 0.00 2.83
1580 1830 9.301153 GTGTATTCCTAGCCATTTTAATTTGTG 57.699 33.333 0.00 0.00 0.00 3.33
1619 1869 4.993705 AAGGTTTCCTTCTGACCACATA 57.006 40.909 0.00 0.00 40.17 2.29
1626 1876 5.677319 TCCTTCTGACCACATAAGGTAAG 57.323 43.478 11.93 0.00 45.01 2.34
1648 1898 4.137543 GCTGTAGCCCAAGCATTAATAGT 58.862 43.478 0.00 0.00 43.56 2.12
1649 1899 5.071788 AGCTGTAGCCCAAGCATTAATAGTA 59.928 40.000 0.00 0.00 43.56 1.82
1650 1900 5.179555 GCTGTAGCCCAAGCATTAATAGTAC 59.820 44.000 0.00 0.00 43.56 2.73
1651 1901 6.241882 TGTAGCCCAAGCATTAATAGTACA 57.758 37.500 0.00 0.00 43.56 2.90
1652 1902 6.288294 TGTAGCCCAAGCATTAATAGTACAG 58.712 40.000 0.00 0.00 43.56 2.74
1653 1903 5.373812 AGCCCAAGCATTAATAGTACAGT 57.626 39.130 0.00 0.00 43.56 3.55
1655 1905 4.515567 GCCCAAGCATTAATAGTACAGTCC 59.484 45.833 0.00 0.00 39.53 3.85
1656 1906 5.687706 GCCCAAGCATTAATAGTACAGTCCT 60.688 44.000 0.00 0.00 39.53 3.85
1657 1907 5.992217 CCCAAGCATTAATAGTACAGTCCTC 59.008 44.000 0.00 0.00 0.00 3.71
1658 1908 5.992217 CCAAGCATTAATAGTACAGTCCTCC 59.008 44.000 0.00 0.00 0.00 4.30
1730 2023 7.865385 TCAATTGCTTTGCGTCTAATTAGTTTT 59.135 29.630 12.19 0.00 35.16 2.43
1736 2029 7.801783 GCTTTGCGTCTAATTAGTTTTACAAGT 59.198 33.333 12.19 0.00 0.00 3.16
1767 2060 4.119556 TCATTTCATTGGGTTGGGTGTA 57.880 40.909 0.00 0.00 0.00 2.90
1768 2061 4.085733 TCATTTCATTGGGTTGGGTGTAG 58.914 43.478 0.00 0.00 0.00 2.74
1769 2062 1.917872 TTCATTGGGTTGGGTGTAGC 58.082 50.000 0.00 0.00 0.00 3.58
1770 2063 0.322098 TCATTGGGTTGGGTGTAGCG 60.322 55.000 0.00 0.00 0.00 4.26
1771 2064 0.322098 CATTGGGTTGGGTGTAGCGA 60.322 55.000 0.00 0.00 0.00 4.93
1772 2065 0.623723 ATTGGGTTGGGTGTAGCGAT 59.376 50.000 0.00 0.00 0.00 4.58
1773 2066 0.402504 TTGGGTTGGGTGTAGCGATT 59.597 50.000 0.00 0.00 0.00 3.34
1816 2116 4.849111 GCTTGTAGCAGCTTACTACTTG 57.151 45.455 19.47 14.25 41.89 3.16
1817 2117 3.062774 GCTTGTAGCAGCTTACTACTTGC 59.937 47.826 19.47 18.20 41.89 4.01
1818 2118 3.953712 TGTAGCAGCTTACTACTTGCA 57.046 42.857 19.47 0.00 40.56 4.08
1819 2119 4.471904 TGTAGCAGCTTACTACTTGCAT 57.528 40.909 19.47 0.00 40.56 3.96
1821 2121 4.870426 TGTAGCAGCTTACTACTTGCATTC 59.130 41.667 19.47 0.87 40.56 2.67
1822 2122 4.213564 AGCAGCTTACTACTTGCATTCT 57.786 40.909 0.00 0.00 38.97 2.40
1823 2123 5.344743 AGCAGCTTACTACTTGCATTCTA 57.655 39.130 0.00 0.00 38.97 2.10
1824 2124 5.923204 AGCAGCTTACTACTTGCATTCTAT 58.077 37.500 0.00 0.00 38.97 1.98
1825 2125 7.055667 AGCAGCTTACTACTTGCATTCTATA 57.944 36.000 0.00 0.00 38.97 1.31
1826 2126 6.926272 AGCAGCTTACTACTTGCATTCTATAC 59.074 38.462 0.00 0.00 38.97 1.47
1974 2275 9.050601 ACTATACTTGGTAGTTTAGTAGTAGCG 57.949 37.037 6.63 0.00 43.15 4.26
1987 2288 3.819902 AGTAGTAGCGGATTAGTGGTAGC 59.180 47.826 0.00 0.00 0.00 3.58
2039 2341 8.970691 AGTTCTAAAATGGTCAAATCAAATCG 57.029 30.769 0.00 0.00 0.00 3.34
2064 2366 6.183360 GGGAACAGTGAGAAATAACGATCTTG 60.183 42.308 0.00 0.00 0.00 3.02
2094 2521 4.119862 GCATTCTGCTTCGTCATAGGTTA 58.880 43.478 0.00 0.00 40.96 2.85
2095 2522 4.025647 GCATTCTGCTTCGTCATAGGTTAC 60.026 45.833 0.00 0.00 40.96 2.50
2107 2534 8.798859 TCGTCATAGGTTACTAGTCTTAAGTT 57.201 34.615 0.00 0.00 31.54 2.66
2111 2538 9.317827 TCATAGGTTACTAGTCTTAAGTTTGGT 57.682 33.333 0.00 3.22 31.54 3.67
2177 2610 5.223382 GGGCAAGCTTCTCTTTAGTTTTTC 58.777 41.667 0.00 0.00 31.27 2.29
2185 2618 9.174166 AGCTTCTCTTTAGTTTTTCTTAACACA 57.826 29.630 0.00 0.00 0.00 3.72
2192 2625 9.710979 CTTTAGTTTTTCTTAACACATCACGAA 57.289 29.630 0.00 0.00 0.00 3.85
2194 2627 6.189567 AGTTTTTCTTAACACATCACGAACG 58.810 36.000 0.00 0.00 0.00 3.95
2196 2629 2.745102 TCTTAACACATCACGAACGCA 58.255 42.857 0.00 0.00 0.00 5.24
2197 2630 2.729360 TCTTAACACATCACGAACGCAG 59.271 45.455 0.00 0.00 0.00 5.18
2198 2631 2.425578 TAACACATCACGAACGCAGA 57.574 45.000 0.00 0.00 0.00 4.26
2199 2632 1.795768 AACACATCACGAACGCAGAT 58.204 45.000 0.00 0.00 0.00 2.90
2220 2653 3.359654 TGCTCATATATACGCGCATACG 58.640 45.455 5.73 0.00 44.07 3.06
2221 2654 3.064271 TGCTCATATATACGCGCATACGA 59.936 43.478 5.73 0.30 43.93 3.43
2231 2664 2.681344 ACGCGCATACGATCATCCTATA 59.319 45.455 5.73 0.00 43.93 1.31
2235 2668 4.862574 GCGCATACGATCATCCTATAAACA 59.137 41.667 0.30 0.00 43.93 2.83
2236 2669 5.347635 GCGCATACGATCATCCTATAAACAA 59.652 40.000 0.30 0.00 43.93 2.83
2237 2670 6.669977 GCGCATACGATCATCCTATAAACAAC 60.670 42.308 0.30 0.00 43.93 3.32
2238 2671 6.364976 CGCATACGATCATCCTATAAACAACA 59.635 38.462 0.00 0.00 43.93 3.33
2239 2672 7.510630 GCATACGATCATCCTATAAACAACAC 58.489 38.462 0.00 0.00 0.00 3.32
2240 2673 7.170828 GCATACGATCATCCTATAAACAACACA 59.829 37.037 0.00 0.00 0.00 3.72
2241 2674 9.208022 CATACGATCATCCTATAAACAACACAT 57.792 33.333 0.00 0.00 0.00 3.21
2259 2692 1.539388 CATACACACGCACACCCAATT 59.461 47.619 0.00 0.00 0.00 2.32
2264 2697 1.202830 ACACGCACACCCAATTCCTAA 60.203 47.619 0.00 0.00 0.00 2.69
2265 2698 2.091541 CACGCACACCCAATTCCTAAT 58.908 47.619 0.00 0.00 0.00 1.73
2273 2706 4.137543 CACCCAATTCCTAATAGCACCTC 58.862 47.826 0.00 0.00 0.00 3.85
2275 2708 3.403038 CCAATTCCTAATAGCACCTCCG 58.597 50.000 0.00 0.00 0.00 4.63
2276 2709 3.403038 CAATTCCTAATAGCACCTCCGG 58.597 50.000 0.00 0.00 0.00 5.14
2311 2744 7.116233 GCATCGCCGGATATTTTGAAATAAATT 59.884 33.333 5.05 0.00 34.79 1.82
2338 2771 1.089920 AAATGCGAGCACCATGACTC 58.910 50.000 0.00 0.00 0.00 3.36
2347 2780 2.027745 AGCACCATGACTCGAATTCTGT 60.028 45.455 3.52 2.32 0.00 3.41
2351 2784 3.007940 ACCATGACTCGAATTCTGTTGGA 59.992 43.478 18.11 3.93 0.00 3.53
2352 2785 4.194640 CCATGACTCGAATTCTGTTGGAT 58.805 43.478 3.52 0.00 0.00 3.41
2355 2788 6.018425 CCATGACTCGAATTCTGTTGGATTAG 60.018 42.308 3.52 0.00 0.00 1.73
2357 2790 6.333416 TGACTCGAATTCTGTTGGATTAGAG 58.667 40.000 3.52 5.89 0.00 2.43
2364 2797 7.875041 CGAATTCTGTTGGATTAGAGATACCAT 59.125 37.037 3.52 0.00 32.31 3.55
2377 2810 5.529289 AGAGATACCATTGTCCTCCTAACA 58.471 41.667 0.00 0.00 0.00 2.41
2381 2814 4.927267 ACCATTGTCCTCCTAACAATCA 57.073 40.909 0.00 0.00 43.62 2.57
2406 2839 3.016736 CACAGGTTGGTTCACACTTCTT 58.983 45.455 0.00 0.00 0.00 2.52
2420 2853 8.613482 GTTCACACTTCTTTCTTTAGTTAGCTT 58.387 33.333 0.00 0.00 0.00 3.74
2545 2979 8.721478 GGGTTACAGATGTTTATATGTGCTATG 58.279 37.037 0.00 0.00 39.01 2.23
2601 3035 9.289303 CTTCTTTGTATTTCATAAAATGGACGG 57.711 33.333 0.00 0.00 35.84 4.79
2607 3041 2.582052 TCATAAAATGGACGGATGGCC 58.418 47.619 0.00 0.00 0.00 5.36
2727 3162 1.004745 CCCCCTCTTGTTGCACAGTAT 59.995 52.381 0.00 0.00 0.00 2.12
2742 3177 2.158957 ACAGTATTGTGTATGCTCGGGG 60.159 50.000 0.00 0.00 35.83 5.73
2787 3222 2.368011 CCGGGAAGGAGGGGAGAAC 61.368 68.421 0.00 0.00 45.00 3.01
2838 3273 3.621558 GGAGGGGAACTTTTGGTCTATG 58.378 50.000 0.00 0.00 36.15 2.23
2845 3280 5.506708 GGAACTTTTGGTCTATGGGTGTAT 58.493 41.667 0.00 0.00 36.15 2.29
2846 3281 5.589050 GGAACTTTTGGTCTATGGGTGTATC 59.411 44.000 0.00 0.00 36.15 2.24
2847 3282 6.388619 AACTTTTGGTCTATGGGTGTATCT 57.611 37.500 0.00 0.00 0.00 1.98
2848 3283 7.365295 GGAACTTTTGGTCTATGGGTGTATCTA 60.365 40.741 0.00 0.00 36.15 1.98
2849 3284 6.885922 ACTTTTGGTCTATGGGTGTATCTAC 58.114 40.000 0.00 0.00 0.00 2.59
2850 3285 6.442564 ACTTTTGGTCTATGGGTGTATCTACA 59.557 38.462 0.00 0.00 0.00 2.74
3022 3461 4.201910 CGGCCAAAATAGTGTGAATAGTGG 60.202 45.833 2.24 0.00 0.00 4.00
3026 3465 6.403636 GCCAAAATAGTGTGAATAGTGGTCTG 60.404 42.308 0.00 0.00 0.00 3.51
3190 3672 6.774656 AGTTCCCCATATTGATGAGAAATGTC 59.225 38.462 0.00 0.00 34.73 3.06
3200 3682 7.672983 TTGATGAGAAATGTCCAGTTTAGAC 57.327 36.000 0.00 0.00 34.72 2.59
3308 3790 7.327518 CGTAATTTTTCATTCACTAACAACCCC 59.672 37.037 0.00 0.00 0.00 4.95
3452 4413 4.095483 ACAAGAGGCATAATCAGAAAAGCG 59.905 41.667 0.00 0.00 0.00 4.68
3477 4439 6.966637 AGCTAAAATGATATCTCCCTCCAT 57.033 37.500 3.98 0.00 0.00 3.41
4179 5193 0.110486 ATCCTTTGGTGAGCAACGGT 59.890 50.000 17.65 4.86 0.00 4.83
4200 5217 3.430042 TGATTTGCCTCTCTTGCTCTT 57.570 42.857 0.00 0.00 0.00 2.85
4241 5258 2.373540 TGCATTTGCTGATTTGCTCC 57.626 45.000 3.94 0.00 42.66 4.70
4299 5316 1.960417 GCTACCTGCTGGATTTCTCC 58.040 55.000 17.64 0.00 42.45 3.71
4386 5403 0.890683 GTGAAATCCAGTGGCAAGGG 59.109 55.000 3.51 3.53 0.00 3.95
4458 5475 3.880846 GCATACAGCAGCCACGGC 61.881 66.667 0.00 0.00 44.79 5.68
4590 5607 4.722700 GGTGCCAGCCACGACCAT 62.723 66.667 0.00 0.00 45.62 3.55
4619 5636 2.825836 CTTCGATGGCCACCCTGC 60.826 66.667 8.16 0.00 0.00 4.85
4662 5679 0.874607 CGAGTAACTACATGCCGCCC 60.875 60.000 0.00 0.00 0.00 6.13
4665 5682 1.996187 TAACTACATGCCGCCCCCA 60.996 57.895 0.00 0.00 0.00 4.96
4667 5684 3.797353 CTACATGCCGCCCCCAGT 61.797 66.667 0.00 0.00 0.00 4.00
4741 5758 2.433145 AGCTGCCACATGACGTCG 60.433 61.111 11.62 0.00 0.00 5.12
4924 5941 1.612442 TGGTCTCTGTAGGGGCCAC 60.612 63.158 4.39 0.00 0.00 5.01
4958 5975 1.261938 TTACCCTAAGCCTGCGCAGA 61.262 55.000 38.06 17.64 37.52 4.26
4996 6013 4.659172 CCCCTGCCTGCCGTTCAA 62.659 66.667 0.00 0.00 0.00 2.69
5082 6099 6.882610 TCCTTATGCATAATGTCCATGAAC 57.117 37.500 19.17 0.00 0.00 3.18
5083 6100 5.769662 TCCTTATGCATAATGTCCATGAACC 59.230 40.000 19.17 0.00 0.00 3.62
5087 6106 3.233507 GCATAATGTCCATGAACCCCAT 58.766 45.455 0.00 0.00 35.44 4.00
5113 6132 0.808125 TGCGCCCATGTGATGTAAAC 59.192 50.000 4.18 0.00 0.00 2.01
5114 6133 0.100503 GCGCCCATGTGATGTAAACC 59.899 55.000 0.00 0.00 0.00 3.27
5115 6134 1.750193 CGCCCATGTGATGTAAACCT 58.250 50.000 0.00 0.00 0.00 3.50
5142 6164 6.844696 TGAATTTCAAGTATCGGTATGCTC 57.155 37.500 0.00 0.00 0.00 4.26
5156 6178 1.251527 ATGCTCGTCGAGGACCTTGT 61.252 55.000 23.09 2.63 31.84 3.16
5213 6235 5.596361 TGCCAGGAATCTTGTTCTTGTTTAA 59.404 36.000 0.00 0.00 0.00 1.52
5440 6468 6.006449 AGAGACTGCCAAGAATAATGTGTTT 58.994 36.000 0.00 0.00 0.00 2.83
5447 6475 5.567423 GCCAAGAATAATGTGTTTCCAAGCT 60.567 40.000 0.00 0.00 0.00 3.74
5643 6674 2.353958 CAGGGTGGCTGATGCAGT 59.646 61.111 0.00 0.00 41.91 4.40
5775 6808 5.512753 ACACAAATGTAATTGCACTGTGA 57.487 34.783 30.45 0.58 36.10 3.58
5833 6867 3.059982 CAGCCTTCCCACGACTCA 58.940 61.111 0.00 0.00 0.00 3.41
5975 7011 4.307432 TCTTCACAGCTTAACACTACTGC 58.693 43.478 0.00 0.00 33.35 4.40
6073 7109 2.609459 CACCATATGCGAACTCCTGAAC 59.391 50.000 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
80 82 2.821969 CCAGCTTTACCTTTGCATGAGT 59.178 45.455 0.00 0.00 0.00 3.41
199 205 4.332828 CTCAGGGTTAAAATCGGGAAACT 58.667 43.478 0.00 0.00 0.00 2.66
465 474 0.806868 CATGAATGAACAGCACGGCT 59.193 50.000 0.00 0.00 40.77 5.52
592 609 4.961511 TTGGCTTCGCTGCGTCGT 62.962 61.111 22.48 0.00 0.00 4.34
634 652 0.096976 CGTATGGTGAAAAGGCTGCG 59.903 55.000 0.00 0.00 0.00 5.18
635 653 1.165270 ACGTATGGTGAAAAGGCTGC 58.835 50.000 0.00 0.00 0.00 5.25
723 856 3.719144 GGTAAAACGGCTGCGCGT 61.719 61.111 8.43 9.77 0.00 6.01
891 1081 4.080582 CCCTTCAAATTAAAACCCCCATCC 60.081 45.833 0.00 0.00 0.00 3.51
894 1084 3.648545 CACCCTTCAAATTAAAACCCCCA 59.351 43.478 0.00 0.00 0.00 4.96
971 1161 3.586429 GAGAGAGGGGAAAGATGGAGAT 58.414 50.000 0.00 0.00 0.00 2.75
977 1167 1.412361 CGAGGGAGAGAGGGGAAAGAT 60.412 57.143 0.00 0.00 0.00 2.40
1092 1306 2.124570 AATCTCCATTGCGGCGCT 60.125 55.556 33.26 11.23 33.14 5.92
1268 1500 4.667935 TTCCCCTTCCTCCCGCCA 62.668 66.667 0.00 0.00 0.00 5.69
1379 1611 2.203280 CACACCTTGTGGCGGGAA 60.203 61.111 0.00 0.00 44.27 3.97
1522 1767 5.960105 GCTACAGAATACGTCAAGAAATTGC 59.040 40.000 0.00 0.00 0.00 3.56
1546 1791 3.069016 TGGCTAGGAATACACCATGTACG 59.931 47.826 0.00 0.00 35.42 3.67
1573 1823 7.271511 TCAACAAGAAGCCAATAACACAAATT 58.728 30.769 0.00 0.00 0.00 1.82
1574 1824 6.815089 TCAACAAGAAGCCAATAACACAAAT 58.185 32.000 0.00 0.00 0.00 2.32
1575 1825 6.214191 TCAACAAGAAGCCAATAACACAAA 57.786 33.333 0.00 0.00 0.00 2.83
1576 1826 5.843673 TCAACAAGAAGCCAATAACACAA 57.156 34.783 0.00 0.00 0.00 3.33
1577 1827 5.830912 CTTCAACAAGAAGCCAATAACACA 58.169 37.500 0.00 0.00 46.54 3.72
1612 1862 3.118371 GGCTACAGCTTACCTTATGTGGT 60.118 47.826 0.54 0.00 41.44 4.16
1619 1869 1.340114 GCTTGGGCTACAGCTTACCTT 60.340 52.381 0.54 0.00 41.70 3.50
1626 1876 4.137543 ACTATTAATGCTTGGGCTACAGC 58.862 43.478 0.00 0.00 39.59 4.40
1648 1898 6.895756 AGTCACAATAATACTGGAGGACTGTA 59.104 38.462 0.00 0.00 37.80 2.74
1649 1899 5.721960 AGTCACAATAATACTGGAGGACTGT 59.278 40.000 0.00 0.00 35.29 3.55
1650 1900 6.045318 CAGTCACAATAATACTGGAGGACTG 58.955 44.000 0.00 0.00 37.55 3.51
1651 1901 5.958380 TCAGTCACAATAATACTGGAGGACT 59.042 40.000 0.00 0.00 40.79 3.85
1652 1902 6.043411 GTCAGTCACAATAATACTGGAGGAC 58.957 44.000 0.00 0.00 40.79 3.85
1653 1903 5.958380 AGTCAGTCACAATAATACTGGAGGA 59.042 40.000 0.00 0.00 40.79 3.71
1655 1905 7.436673 GCTAAGTCAGTCACAATAATACTGGAG 59.563 40.741 0.00 0.00 40.79 3.86
1656 1906 7.124298 AGCTAAGTCAGTCACAATAATACTGGA 59.876 37.037 0.00 0.00 40.79 3.86
1657 1907 7.268586 AGCTAAGTCAGTCACAATAATACTGG 58.731 38.462 0.00 0.00 40.79 4.00
1658 1908 8.598924 CAAGCTAAGTCAGTCACAATAATACTG 58.401 37.037 0.00 0.00 41.58 2.74
1739 2032 6.060788 CCCAACCCAATGAAATGAAAGAAAA 58.939 36.000 0.00 0.00 0.00 2.29
1740 2033 5.131809 ACCCAACCCAATGAAATGAAAGAAA 59.868 36.000 0.00 0.00 0.00 2.52
1741 2034 4.657969 ACCCAACCCAATGAAATGAAAGAA 59.342 37.500 0.00 0.00 0.00 2.52
1742 2035 4.040217 CACCCAACCCAATGAAATGAAAGA 59.960 41.667 0.00 0.00 0.00 2.52
1743 2036 4.202346 ACACCCAACCCAATGAAATGAAAG 60.202 41.667 0.00 0.00 0.00 2.62
1744 2037 3.713764 ACACCCAACCCAATGAAATGAAA 59.286 39.130 0.00 0.00 0.00 2.69
1745 2038 3.312890 ACACCCAACCCAATGAAATGAA 58.687 40.909 0.00 0.00 0.00 2.57
1746 2039 2.969628 ACACCCAACCCAATGAAATGA 58.030 42.857 0.00 0.00 0.00 2.57
1747 2040 3.368323 GCTACACCCAACCCAATGAAATG 60.368 47.826 0.00 0.00 0.00 2.32
1748 2041 2.831526 GCTACACCCAACCCAATGAAAT 59.168 45.455 0.00 0.00 0.00 2.17
1816 2116 9.967346 TCAGTACACTCAAATAGTATAGAATGC 57.033 33.333 0.00 0.00 35.76 3.56
1825 2125 9.155975 GAACAATCATCAGTACACTCAAATAGT 57.844 33.333 0.00 0.00 39.81 2.12
1826 2126 9.376075 AGAACAATCATCAGTACACTCAAATAG 57.624 33.333 0.00 0.00 0.00 1.73
1847 2147 7.732025 TCAATCAGTCTACCAACTTAAGAACA 58.268 34.615 10.09 0.00 0.00 3.18
1888 2188 1.528824 CGGAAGGCAGGGATGTCAT 59.471 57.895 0.00 0.00 0.00 3.06
2039 2341 5.420409 AGATCGTTATTTCTCACTGTTCCC 58.580 41.667 0.00 0.00 0.00 3.97
2094 2521 8.465201 CGGACTTATACCAAACTTAAGACTAGT 58.535 37.037 10.09 0.00 0.00 2.57
2095 2522 8.465201 ACGGACTTATACCAAACTTAAGACTAG 58.535 37.037 10.09 0.00 0.00 2.57
2177 2610 2.729360 TCTGCGTTCGTGATGTGTTAAG 59.271 45.455 0.00 0.00 0.00 1.85
2183 2616 2.081526 GCATCTGCGTTCGTGATGT 58.918 52.632 20.63 0.00 39.58 3.06
2184 2617 4.961622 GCATCTGCGTTCGTGATG 57.038 55.556 17.90 17.90 40.16 3.07
2194 2627 2.217393 GCGCGTATATATGAGCATCTGC 59.783 50.000 21.51 7.42 37.84 4.26
2196 2629 3.782889 TGCGCGTATATATGAGCATCT 57.217 42.857 24.20 0.00 41.84 2.90
2220 2653 9.325198 TGTGTATGTGTTGTTTATAGGATGATC 57.675 33.333 0.00 0.00 0.00 2.92
2221 2654 9.109393 GTGTGTATGTGTTGTTTATAGGATGAT 57.891 33.333 0.00 0.00 0.00 2.45
2231 2664 2.420372 TGTGCGTGTGTATGTGTTGTTT 59.580 40.909 0.00 0.00 0.00 2.83
2235 2668 0.941542 GGTGTGCGTGTGTATGTGTT 59.058 50.000 0.00 0.00 0.00 3.32
2236 2669 0.882927 GGGTGTGCGTGTGTATGTGT 60.883 55.000 0.00 0.00 0.00 3.72
2237 2670 0.882484 TGGGTGTGCGTGTGTATGTG 60.882 55.000 0.00 0.00 0.00 3.21
2238 2671 0.179043 TTGGGTGTGCGTGTGTATGT 60.179 50.000 0.00 0.00 0.00 2.29
2239 2672 1.164411 ATTGGGTGTGCGTGTGTATG 58.836 50.000 0.00 0.00 0.00 2.39
2240 2673 1.810151 GAATTGGGTGTGCGTGTGTAT 59.190 47.619 0.00 0.00 0.00 2.29
2241 2674 1.231221 GAATTGGGTGTGCGTGTGTA 58.769 50.000 0.00 0.00 0.00 2.90
2311 2744 3.342719 TGGTGCTCGCATTTATTTCTGA 58.657 40.909 0.00 0.00 0.00 3.27
2338 2771 7.210174 TGGTATCTCTAATCCAACAGAATTCG 58.790 38.462 0.00 0.00 0.00 3.34
2343 2776 7.419057 GGACAATGGTATCTCTAATCCAACAGA 60.419 40.741 0.00 0.00 33.55 3.41
2347 2780 6.043243 GGAGGACAATGGTATCTCTAATCCAA 59.957 42.308 3.85 0.00 33.55 3.53
2351 2784 7.789831 TGTTAGGAGGACAATGGTATCTCTAAT 59.210 37.037 3.85 0.00 31.75 1.73
2352 2785 7.130099 TGTTAGGAGGACAATGGTATCTCTAA 58.870 38.462 3.85 0.00 31.75 2.10
2355 2788 5.871396 TGTTAGGAGGACAATGGTATCTC 57.129 43.478 0.00 0.00 0.00 2.75
2357 2790 6.591935 TGATTGTTAGGAGGACAATGGTATC 58.408 40.000 7.15 0.00 45.11 2.24
2364 2797 4.825085 GTGGTTTGATTGTTAGGAGGACAA 59.175 41.667 0.00 0.00 40.86 3.18
2398 2831 9.833917 AAGTAAGCTAACTAAAGAAAGAAGTGT 57.166 29.630 0.00 0.00 0.00 3.55
2406 2839 7.272084 CGCGTAGAAAGTAAGCTAACTAAAGAA 59.728 37.037 0.00 0.00 0.00 2.52
2420 2853 5.300969 AGTTACATGACGCGTAGAAAGTA 57.699 39.130 13.97 8.56 0.00 2.24
2545 2979 7.491048 TCAACAAAGGAAATACAAAGAAGTTGC 59.509 33.333 0.00 0.00 41.31 4.17
2575 3009 9.289303 CCGTCCATTTTATGAAATACAAAGAAG 57.711 33.333 0.00 0.00 33.78 2.85
2607 3041 4.024048 ACAATTAAACAACTCGAGCCACAG 60.024 41.667 13.61 0.31 0.00 3.66
2727 3162 0.908910 ACATCCCCGAGCATACACAA 59.091 50.000 0.00 0.00 0.00 3.33
2742 3177 1.308069 ACCATGAGCGCACCAACATC 61.308 55.000 11.47 0.00 0.00 3.06
2817 3252 3.621558 CATAGACCAAAAGTTCCCCTCC 58.378 50.000 0.00 0.00 0.00 4.30
2915 3351 8.784043 ACAAGTACAATGGAAGATCAAGTTTAC 58.216 33.333 0.00 0.00 0.00 2.01
2990 3426 4.994217 ACACTATTTTGGCCGGAAATTTTG 59.006 37.500 18.55 16.96 0.00 2.44
2993 3429 3.829601 TCACACTATTTTGGCCGGAAATT 59.170 39.130 18.55 5.47 0.00 1.82
3082 3521 9.502091 TGACTTTCTTTTGCACTAGTATGTAAT 57.498 29.630 0.00 0.00 0.00 1.89
3123 3562 8.902540 AAAGGTCAGAAAAGTTTTGAAGTTTT 57.097 26.923 5.36 6.05 44.41 2.43
3164 3646 7.815383 ACATTTCTCATCAATATGGGGAACTA 58.185 34.615 0.00 0.00 33.69 2.24
3166 3648 6.015940 GGACATTTCTCATCAATATGGGGAAC 60.016 42.308 0.00 0.00 33.69 3.62
3190 3672 3.325870 TGAATGCGTCTGTCTAAACTGG 58.674 45.455 0.00 0.00 0.00 4.00
3452 4413 6.773638 TGGAGGGAGATATCATTTTAGCTTC 58.226 40.000 5.32 0.00 0.00 3.86
3477 4439 2.027192 GCAGAGGGTTGTCCATCAAGTA 60.027 50.000 1.98 0.00 45.75 2.24
3491 4453 2.935481 TCACCAAGGGGCAGAGGG 60.935 66.667 0.00 0.00 37.90 4.30
3867 4851 5.358922 TCATGTTGATGCAATACGAGATGA 58.641 37.500 11.86 11.86 31.03 2.92
4179 5193 3.430042 AGAGCAAGAGAGGCAAATCAA 57.570 42.857 0.00 0.00 0.00 2.57
4215 5232 4.250464 CAAATCAGCAAATGCAACTGGAT 58.750 39.130 8.28 0.32 45.16 3.41
4241 5258 2.082231 CTTCTGCACCAAGGATCACAG 58.918 52.381 0.00 0.00 0.00 3.66
4299 5316 1.221021 GCTCGGAACCCTTGGGTAG 59.779 63.158 12.27 6.86 0.00 3.18
4386 5403 0.456628 GAGGACGCAGGTCTAGGTTC 59.543 60.000 0.00 0.00 42.97 3.62
4707 5724 3.656243 CTGCTGATGTGGCGCGTTG 62.656 63.158 8.43 0.00 0.00 4.10
4853 5870 3.857854 CACCGCTGCTGTGATCGC 61.858 66.667 17.81 0.00 35.74 4.58
4854 5871 3.190849 CCACCGCTGCTGTGATCG 61.191 66.667 23.20 5.33 35.74 3.69
4855 5872 3.503363 GCCACCGCTGCTGTGATC 61.503 66.667 23.20 11.89 35.74 2.92
4878 5895 4.096003 CTGCCGGGGTGGTCGAAT 62.096 66.667 2.18 0.00 41.21 3.34
4924 5941 2.749621 AGGGTAACGTACGTAGTTGGAG 59.250 50.000 23.12 0.00 39.46 3.86
4958 5975 3.080319 GCTTCTTCAGTTCCATGCTTCT 58.920 45.455 0.00 0.00 0.00 2.85
5082 6099 0.179004 TGGGCGCAAATAGTATGGGG 60.179 55.000 10.83 0.00 0.00 4.96
5083 6100 1.541147 CATGGGCGCAAATAGTATGGG 59.459 52.381 10.83 0.00 0.00 4.00
5087 6106 2.700722 TCACATGGGCGCAAATAGTA 57.299 45.000 10.83 0.00 0.00 1.82
5113 6132 5.126067 ACCGATACTTGAAATTCATGGAGG 58.874 41.667 12.51 11.18 0.00 4.30
5114 6133 7.571983 GCATACCGATACTTGAAATTCATGGAG 60.572 40.741 12.51 3.19 0.00 3.86
5115 6134 6.204688 GCATACCGATACTTGAAATTCATGGA 59.795 38.462 12.51 5.17 0.00 3.41
5142 6164 1.134901 CGAGACAAGGTCCTCGACG 59.865 63.158 5.95 0.00 36.28 5.12
5156 6178 5.587388 AACAAGGGAATAATACGACGAGA 57.413 39.130 0.00 0.00 0.00 4.04
5213 6235 0.828762 TGGCCTCAACTTTGCATGCT 60.829 50.000 20.33 0.00 0.00 3.79
5643 6674 7.874528 AGCTCAATTATTATGTCATCGTGATGA 59.125 33.333 8.43 8.43 44.83 2.92
5649 6680 7.383300 TCAGTGAGCTCAATTATTATGTCATCG 59.617 37.037 20.19 0.16 0.00 3.84
5775 6808 0.257039 AGCCAATGCCGGAATCTCTT 59.743 50.000 5.05 0.00 38.69 2.85
5975 7011 1.520600 AAGTTACCGCGGCCAAAAGG 61.521 55.000 28.58 1.93 0.00 3.11


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

AutoCloner maintained by Alex Coulton.