Multiple sequence alignment - TraesCS7B01G081800

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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 TraesCS7B01G081800 chr7B 100.000 2705 0 0 1 2705 92310112 92312816 0.000000e+00 4996.0
1 TraesCS7B01G081800 chr7B 89.076 119 10 3 2481 2597 593010618 593010501 7.810000e-31 145.0
2 TraesCS7B01G081800 chr7A 90.430 2184 119 36 11 2145 130221818 130223960 0.000000e+00 2793.0
3 TraesCS7B01G081800 chr7A 84.974 193 15 10 2291 2471 130224288 130224478 1.650000e-42 183.0
4 TraesCS7B01G081800 chr7A 87.943 141 13 1 2131 2271 130223977 130224113 2.150000e-36 163.0
5 TraesCS7B01G081800 chr7A 96.739 92 2 1 2614 2705 130224464 130224554 4.660000e-33 152.0
6 TraesCS7B01G081800 chr7A 87.786 131 12 4 2469 2597 726901613 726901485 1.680000e-32 150.0
7 TraesCS7B01G081800 chr7A 88.235 119 11 3 2481 2597 25136715 25136598 3.630000e-29 139.0
8 TraesCS7B01G081800 chr7D 89.847 2216 111 49 1 2165 131459062 131461214 0.000000e+00 2741.0
9 TraesCS7B01G081800 chr7D 83.939 330 33 12 2150 2471 131461294 131461611 5.660000e-77 298.0
10 TraesCS7B01G081800 chr1A 91.171 589 42 4 1112 1695 7330359 7330942 0.000000e+00 791.0
11 TraesCS7B01G081800 chr4B 90.092 545 31 10 1112 1652 19407097 19407622 0.000000e+00 686.0
12 TraesCS7B01G081800 chr1D 89.313 131 9 5 2469 2597 490440306 490440433 2.790000e-35 159.0
13 TraesCS7B01G081800 chr2D 88.550 131 11 4 2469 2597 43812664 43812536 3.610000e-34 156.0
14 TraesCS7B01G081800 chr3B 91.667 96 6 2 2470 2563 349276250 349276345 6.080000e-27 132.0
15 TraesCS7B01G081800 chr3B 84.211 133 10 5 2473 2595 43323129 43323260 4.730000e-23 119.0
16 TraesCS7B01G081800 chr2A 85.496 131 14 5 2469 2597 603777920 603778047 6.080000e-27 132.0
17 TraesCS7B01G081800 chr2A 87.879 99 10 1 2473 2569 63815231 63815133 6.120000e-22 115.0
18 TraesCS7B01G081800 chr3D 90.476 84 4 4 2482 2561 555332438 555332355 1.020000e-19 108.0
19 TraesCS7B01G081800 chr6B 100.000 35 0 0 2563 2597 194501198 194501232 6.250000e-07 65.8


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 TraesCS7B01G081800 chr7B 92310112 92312816 2704 False 4996.00 4996 100.0000 1 2705 1 chr7B.!!$F1 2704
1 TraesCS7B01G081800 chr7A 130221818 130224554 2736 False 822.75 2793 90.0215 11 2705 4 chr7A.!!$F1 2694
2 TraesCS7B01G081800 chr7D 131459062 131461611 2549 False 1519.50 2741 86.8930 1 2471 2 chr7D.!!$F1 2470
3 TraesCS7B01G081800 chr1A 7330359 7330942 583 False 791.00 791 91.1710 1112 1695 1 chr1A.!!$F1 583
4 TraesCS7B01G081800 chr4B 19407097 19407622 525 False 686.00 686 90.0920 1112 1652 1 chr4B.!!$F1 540

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
234 246 0.462047 GGTGCCCTTGAACGATCGAT 60.462 55.0 24.34 10.66 0.0 3.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1861 1945 1.114627 GAATCCAAGGCATCCAACCC 58.885 55.0 0.0 0.0 0.0 4.11 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
18 19 2.831597 CGATCTCACTGCAGCACAA 58.168 52.632 15.27 0.00 0.00 3.33
45 46 0.738975 ATCCGCAGAGTTTCGATCGA 59.261 50.000 15.15 15.15 0.00 3.59
68 69 1.073025 ATTTCACTGTGCCGCCTCA 59.927 52.632 2.12 0.00 0.00 3.86
74 77 1.867233 CACTGTGCCGCCTCAATATAC 59.133 52.381 0.00 0.00 0.00 1.47
92 99 9.314133 TCAATATACCTCTGTCAGTTGCTATAT 57.686 33.333 0.00 0.35 0.00 0.86
100 107 1.070134 TCAGTTGCTATATGACCGGCC 59.930 52.381 0.00 0.00 0.00 6.13
109 116 4.384208 GCTATATGACCGGCCAATAGGATT 60.384 45.833 0.00 0.00 36.89 3.01
110 117 2.276732 ATGACCGGCCAATAGGATTG 57.723 50.000 0.00 0.00 36.89 2.67
180 188 3.872240 GCTGGTTAGGCCTGTTAACATCA 60.872 47.826 17.99 5.65 38.33 3.07
206 214 4.211920 AGTACTAGCTTGGAGATGTCCTC 58.788 47.826 10.72 0.00 44.30 3.71
226 238 0.690762 GTCCAGTAGGTGCCCTTGAA 59.309 55.000 0.00 0.00 34.61 2.69
234 246 0.462047 GGTGCCCTTGAACGATCGAT 60.462 55.000 24.34 10.66 0.00 3.59
328 342 1.953686 ACACCACAATTGCACTGTACC 59.046 47.619 5.05 0.00 0.00 3.34
451 477 1.153804 GGCGTCGTTCTTCTCCTCC 60.154 63.158 0.00 0.00 0.00 4.30
514 564 5.090083 GTCTGAGCTGAAAGTAACTACTCG 58.910 45.833 0.00 0.00 34.99 4.18
703 760 0.599466 TCTAGACGCCGTCGATCGAT 60.599 55.000 22.50 4.16 42.86 3.59
834 894 3.730761 ACGTCGCCGTCGCTAACT 61.731 61.111 3.22 0.00 46.28 2.24
886 946 3.963687 CTGCACGCCTCTGCCATCA 62.964 63.158 0.00 0.00 36.21 3.07
902 962 2.487934 CATCAGTCGATCCATTGGTCC 58.512 52.381 1.86 0.00 0.00 4.46
940 1000 4.855105 TGTTTGACAGACGCTGCT 57.145 50.000 6.74 0.00 34.37 4.24
941 1001 3.978460 TGTTTGACAGACGCTGCTA 57.022 47.368 6.74 0.00 34.37 3.49
942 1002 1.783284 TGTTTGACAGACGCTGCTAG 58.217 50.000 6.74 0.00 34.37 3.42
943 1003 1.068588 TGTTTGACAGACGCTGCTAGT 59.931 47.619 6.74 0.00 34.37 2.57
959 1019 2.101249 GCTAGTGCAATCTGCTCTCTCT 59.899 50.000 6.49 0.00 42.81 3.10
961 1021 3.699411 AGTGCAATCTGCTCTCTCTTT 57.301 42.857 0.00 0.00 42.81 2.52
986 1046 3.146847 GGTTAGGTTGGTTGAGGACTTG 58.853 50.000 0.00 0.00 0.00 3.16
994 1054 1.202818 GGTTGAGGACTTGAGGTGCTT 60.203 52.381 0.00 0.00 46.56 3.91
997 1057 2.325484 TGAGGACTTGAGGTGCTTGTA 58.675 47.619 0.00 0.00 46.56 2.41
1026 1086 3.357079 GGTGGCAAGTGTCTGGCG 61.357 66.667 0.00 0.00 44.56 5.69
1185 1248 1.143183 CGGTTAGTACATGCCGGCT 59.857 57.895 29.70 10.43 40.45 5.52
1188 1251 0.107848 GTTAGTACATGCCGGCTGGT 60.108 55.000 29.70 26.03 37.67 4.00
1296 1366 0.599204 CAGTGTTCAACTACGCCGGT 60.599 55.000 1.90 0.00 36.83 5.28
1707 1785 1.453379 CGCGGGTCTCTTCTAGGGA 60.453 63.158 0.00 0.00 0.00 4.20
1731 1809 3.644606 CAGGGTGGAGGCAGTGCT 61.645 66.667 16.11 0.33 0.00 4.40
1734 1812 2.592993 GGGTGGAGGCAGTGCTGTA 61.593 63.158 16.11 0.00 0.00 2.74
1736 1814 1.738099 GTGGAGGCAGTGCTGTACG 60.738 63.158 16.11 0.00 0.00 3.67
1737 1815 2.207229 TGGAGGCAGTGCTGTACGT 61.207 57.895 16.11 0.00 0.00 3.57
1738 1816 0.896479 TGGAGGCAGTGCTGTACGTA 60.896 55.000 16.11 0.00 0.00 3.57
1739 1817 0.458025 GGAGGCAGTGCTGTACGTAC 60.458 60.000 18.90 18.90 0.00 3.67
1740 1818 0.797249 GAGGCAGTGCTGTACGTACG 60.797 60.000 20.18 15.01 33.01 3.67
1741 1819 1.080974 GGCAGTGCTGTACGTACGT 60.081 57.895 25.98 25.98 33.01 3.57
1742 1820 0.168788 GGCAGTGCTGTACGTACGTA 59.831 55.000 23.60 23.60 33.01 3.57
1812 1894 3.203716 GTTTCTCGTTTGTTGAGGAGGT 58.796 45.455 0.00 0.00 33.52 3.85
1816 1898 3.830178 TCTCGTTTGTTGAGGAGGTCATA 59.170 43.478 0.00 0.00 34.17 2.15
1861 1945 1.949847 TTTGTTGTGGTTGGCACGGG 61.950 55.000 0.00 0.00 0.00 5.28
1881 1965 1.114627 GGTTGGATGCCTTGGATTCC 58.885 55.000 0.00 0.00 0.00 3.01
1885 1969 0.677842 GGATGCCTTGGATTCCATGC 59.322 55.000 16.79 16.79 31.53 4.06
2086 2173 3.261677 GGTGGCCCCAAGGTACCA 61.262 66.667 15.94 0.00 40.36 3.25
2087 2174 2.355115 GTGGCCCCAAGGTACCAG 59.645 66.667 15.94 6.00 34.57 4.00
2089 2176 1.776710 TGGCCCCAAGGTACCAGTT 60.777 57.895 15.94 0.00 34.57 3.16
2102 2189 3.631686 GGTACCAGTTAACAACCGGTTTT 59.368 43.478 19.55 17.09 39.07 2.43
2170 2382 1.370414 CTGCAAAAACCCTCGCGTG 60.370 57.895 5.77 2.75 0.00 5.34
2259 2474 7.647715 TCCAAGAAATTCAAAATCAAACTCGAC 59.352 33.333 0.00 0.00 0.00 4.20
2265 2480 7.687941 ATTCAAAATCAAACTCGACCTACAT 57.312 32.000 0.00 0.00 0.00 2.29
2271 2486 8.617290 AAATCAAACTCGACCTACATAAAAGT 57.383 30.769 0.00 0.00 0.00 2.66
2272 2487 7.596749 ATCAAACTCGACCTACATAAAAGTG 57.403 36.000 0.00 0.00 0.00 3.16
2274 2489 6.866770 TCAAACTCGACCTACATAAAAGTGAG 59.133 38.462 0.00 0.00 0.00 3.51
2275 2490 4.745649 ACTCGACCTACATAAAAGTGAGC 58.254 43.478 0.00 0.00 0.00 4.26
2276 2491 4.219944 ACTCGACCTACATAAAAGTGAGCA 59.780 41.667 0.00 0.00 0.00 4.26
2277 2492 5.105310 ACTCGACCTACATAAAAGTGAGCAT 60.105 40.000 0.00 0.00 0.00 3.79
2278 2493 5.730550 TCGACCTACATAAAAGTGAGCATT 58.269 37.500 0.00 0.00 0.00 3.56
2280 2495 6.755141 TCGACCTACATAAAAGTGAGCATTAC 59.245 38.462 0.00 0.00 0.00 1.89
2283 2498 7.402862 ACCTACATAAAAGTGAGCATTACCTT 58.597 34.615 0.00 0.00 0.00 3.50
2284 2499 7.553044 ACCTACATAAAAGTGAGCATTACCTTC 59.447 37.037 0.00 0.00 0.00 3.46
2285 2500 6.759497 ACATAAAAGTGAGCATTACCTTCC 57.241 37.500 0.00 0.00 0.00 3.46
2289 2504 6.670695 AAAAGTGAGCATTACCTTCCAAAT 57.329 33.333 0.00 0.00 0.00 2.32
2296 2666 6.998074 TGAGCATTACCTTCCAAATACTATGG 59.002 38.462 0.00 0.00 39.41 2.74
2330 2703 6.911250 TTTTCCCTAAAAGAGATGAAACCC 57.089 37.500 0.00 0.00 30.25 4.11
2332 2705 3.920197 TCCCTAAAAGAGATGAAACCCCA 59.080 43.478 0.00 0.00 0.00 4.96
2412 2788 9.802039 AGAATGAAATTAACACCTACCACTAAA 57.198 29.630 0.00 0.00 36.07 1.85
2415 2791 9.747898 ATGAAATTAACACCTACCACTAAATCA 57.252 29.630 0.00 0.00 0.00 2.57
2423 2799 5.411669 CACCTACCACTAAATCAACTTCCAC 59.588 44.000 0.00 0.00 0.00 4.02
2430 2813 6.073222 CCACTAAATCAACTTCCACACACTAC 60.073 42.308 0.00 0.00 0.00 2.73
2455 2838 6.446318 TCACATCTAAATTTGTCTTGTTGGC 58.554 36.000 0.00 0.00 0.00 4.52
2471 2854 8.531982 GTCTTGTTGGCTCTCCATGTATATATA 58.468 37.037 0.00 0.00 43.05 0.86
2472 2855 9.271921 TCTTGTTGGCTCTCCATGTATATATAT 57.728 33.333 0.00 0.00 43.05 0.86
2473 2856 9.322773 CTTGTTGGCTCTCCATGTATATATATG 57.677 37.037 11.48 11.48 43.05 1.78
2474 2857 8.608185 TGTTGGCTCTCCATGTATATATATGA 57.392 34.615 18.23 6.34 43.05 2.15
2475 2858 8.699130 TGTTGGCTCTCCATGTATATATATGAG 58.301 37.037 18.23 13.60 43.05 2.90
2476 2859 8.918116 GTTGGCTCTCCATGTATATATATGAGA 58.082 37.037 18.23 16.13 43.05 3.27
2477 2860 9.492730 TTGGCTCTCCATGTATATATATGAGAA 57.507 33.333 18.23 5.43 43.05 2.87
2478 2861 9.140874 TGGCTCTCCATGTATATATATGAGAAG 57.859 37.037 18.23 12.77 37.47 2.85
2479 2862 8.087750 GGCTCTCCATGTATATATATGAGAAGC 58.912 40.741 18.23 19.12 0.00 3.86
2480 2863 8.859090 GCTCTCCATGTATATATATGAGAAGCT 58.141 37.037 18.23 0.00 0.00 3.74
2493 2876 3.851051 GAAGCTCTTCTGGGTGGAG 57.149 57.895 2.55 0.00 36.69 3.86
2494 2877 0.980423 GAAGCTCTTCTGGGTGGAGT 59.020 55.000 2.55 0.00 36.69 3.85
2495 2878 0.689623 AAGCTCTTCTGGGTGGAGTG 59.310 55.000 0.00 0.00 0.00 3.51
2496 2879 1.197430 AGCTCTTCTGGGTGGAGTGG 61.197 60.000 0.00 0.00 0.00 4.00
2497 2880 1.484444 GCTCTTCTGGGTGGAGTGGT 61.484 60.000 0.00 0.00 0.00 4.16
2498 2881 1.938585 CTCTTCTGGGTGGAGTGGTA 58.061 55.000 0.00 0.00 0.00 3.25
2499 2882 1.827969 CTCTTCTGGGTGGAGTGGTAG 59.172 57.143 0.00 0.00 0.00 3.18
2500 2883 1.431633 TCTTCTGGGTGGAGTGGTAGA 59.568 52.381 0.00 0.00 0.00 2.59
2501 2884 1.550976 CTTCTGGGTGGAGTGGTAGAC 59.449 57.143 0.00 0.00 0.00 2.59
2502 2885 0.485543 TCTGGGTGGAGTGGTAGACA 59.514 55.000 0.00 0.00 0.00 3.41
2503 2886 1.132977 TCTGGGTGGAGTGGTAGACAA 60.133 52.381 0.00 0.00 0.00 3.18
2504 2887 1.002087 CTGGGTGGAGTGGTAGACAAC 59.998 57.143 0.00 0.00 0.00 3.32
2505 2888 1.053424 GGGTGGAGTGGTAGACAACA 58.947 55.000 0.00 0.00 0.00 3.33
2506 2889 1.270678 GGGTGGAGTGGTAGACAACAC 60.271 57.143 0.00 0.00 37.86 3.32
2507 2890 1.414919 GGTGGAGTGGTAGACAACACA 59.585 52.381 0.00 0.00 39.99 3.72
2508 2891 2.158871 GGTGGAGTGGTAGACAACACAA 60.159 50.000 0.00 0.00 39.99 3.33
2509 2892 3.537580 GTGGAGTGGTAGACAACACAAA 58.462 45.455 0.00 0.00 39.99 2.83
2510 2893 3.560068 GTGGAGTGGTAGACAACACAAAG 59.440 47.826 0.00 0.00 39.99 2.77
2511 2894 3.139077 GGAGTGGTAGACAACACAAAGG 58.861 50.000 0.00 0.00 39.99 3.11
2512 2895 3.433173 GGAGTGGTAGACAACACAAAGGT 60.433 47.826 0.00 0.00 39.99 3.50
2513 2896 4.196971 GAGTGGTAGACAACACAAAGGTT 58.803 43.478 0.00 0.00 39.99 3.50
2521 2904 1.917303 CAACACAAAGGTTGTTGTCGC 59.083 47.619 6.99 0.00 43.23 5.19
2522 2905 0.454196 ACACAAAGGTTGTTGTCGCC 59.546 50.000 0.00 0.00 43.23 5.54
2523 2906 0.248866 CACAAAGGTTGTTGTCGCCC 60.249 55.000 0.00 0.00 43.23 6.13
2524 2907 1.008995 CAAAGGTTGTTGTCGCCCG 60.009 57.895 0.00 0.00 0.00 6.13
2525 2908 2.841160 AAAGGTTGTTGTCGCCCGC 61.841 57.895 0.00 0.00 0.00 6.13
2539 2922 4.136250 CCGCCCGGGTTAATCTTC 57.864 61.111 24.63 0.57 0.00 2.87
2540 2923 1.525442 CCGCCCGGGTTAATCTTCT 59.475 57.895 24.63 0.00 0.00 2.85
2541 2924 0.532196 CCGCCCGGGTTAATCTTCTC 60.532 60.000 24.63 0.00 0.00 2.87
2542 2925 0.177141 CGCCCGGGTTAATCTTCTCA 59.823 55.000 24.63 0.00 0.00 3.27
2543 2926 1.202651 CGCCCGGGTTAATCTTCTCAT 60.203 52.381 24.63 0.00 0.00 2.90
2544 2927 2.495084 GCCCGGGTTAATCTTCTCATC 58.505 52.381 24.63 0.00 0.00 2.92
2545 2928 2.104963 GCCCGGGTTAATCTTCTCATCT 59.895 50.000 24.63 0.00 0.00 2.90
2546 2929 3.804063 GCCCGGGTTAATCTTCTCATCTC 60.804 52.174 24.63 0.00 0.00 2.75
2547 2930 3.244249 CCCGGGTTAATCTTCTCATCTCC 60.244 52.174 14.18 0.00 0.00 3.71
2548 2931 3.643792 CCGGGTTAATCTTCTCATCTCCT 59.356 47.826 0.00 0.00 0.00 3.69
2549 2932 4.833380 CCGGGTTAATCTTCTCATCTCCTA 59.167 45.833 0.00 0.00 0.00 2.94
2550 2933 5.482175 CCGGGTTAATCTTCTCATCTCCTAT 59.518 44.000 0.00 0.00 0.00 2.57
2551 2934 6.663953 CCGGGTTAATCTTCTCATCTCCTATA 59.336 42.308 0.00 0.00 0.00 1.31
2552 2935 7.178628 CCGGGTTAATCTTCTCATCTCCTATAA 59.821 40.741 0.00 0.00 0.00 0.98
2553 2936 8.247562 CGGGTTAATCTTCTCATCTCCTATAAG 58.752 40.741 0.00 0.00 0.00 1.73
2554 2937 9.315363 GGGTTAATCTTCTCATCTCCTATAAGA 57.685 37.037 0.00 0.00 0.00 2.10
2564 2947 9.527157 TCTCATCTCCTATAAGAATAAGACAGG 57.473 37.037 0.00 0.00 0.00 4.00
2565 2948 8.657387 TCATCTCCTATAAGAATAAGACAGGG 57.343 38.462 0.00 0.00 0.00 4.45
2566 2949 7.676043 TCATCTCCTATAAGAATAAGACAGGGG 59.324 40.741 0.00 0.00 0.00 4.79
2567 2950 6.323737 TCTCCTATAAGAATAAGACAGGGGG 58.676 44.000 0.00 0.00 0.00 5.40
2568 2951 6.105740 TCTCCTATAAGAATAAGACAGGGGGA 59.894 42.308 0.00 0.00 0.00 4.81
2569 2952 6.699688 TCCTATAAGAATAAGACAGGGGGAA 58.300 40.000 0.00 0.00 0.00 3.97
2570 2953 6.787957 TCCTATAAGAATAAGACAGGGGGAAG 59.212 42.308 0.00 0.00 0.00 3.46
2571 2954 6.559157 CCTATAAGAATAAGACAGGGGGAAGT 59.441 42.308 0.00 0.00 0.00 3.01
2572 2955 4.846168 AAGAATAAGACAGGGGGAAGTC 57.154 45.455 0.00 0.00 35.02 3.01
2573 2956 4.081695 AGAATAAGACAGGGGGAAGTCT 57.918 45.455 0.00 0.00 46.45 3.24
2574 2957 4.034410 AGAATAAGACAGGGGGAAGTCTC 58.966 47.826 0.00 0.00 43.88 3.36
2575 2958 2.249309 TAAGACAGGGGGAAGTCTCC 57.751 55.000 0.00 0.00 43.88 3.71
2585 2968 1.945580 GGAAGTCTCCCCTCTGTTCT 58.054 55.000 0.00 0.00 35.42 3.01
2586 2969 1.828595 GGAAGTCTCCCCTCTGTTCTC 59.171 57.143 0.00 0.00 35.42 2.87
2587 2970 2.530701 GAAGTCTCCCCTCTGTTCTCA 58.469 52.381 0.00 0.00 0.00 3.27
2588 2971 2.938428 AGTCTCCCCTCTGTTCTCAT 57.062 50.000 0.00 0.00 0.00 2.90
2589 2972 3.197927 AGTCTCCCCTCTGTTCTCATT 57.802 47.619 0.00 0.00 0.00 2.57
2590 2973 3.103742 AGTCTCCCCTCTGTTCTCATTC 58.896 50.000 0.00 0.00 0.00 2.67
2591 2974 3.103742 GTCTCCCCTCTGTTCTCATTCT 58.896 50.000 0.00 0.00 0.00 2.40
2592 2975 3.517500 GTCTCCCCTCTGTTCTCATTCTT 59.482 47.826 0.00 0.00 0.00 2.52
2593 2976 4.019771 GTCTCCCCTCTGTTCTCATTCTTT 60.020 45.833 0.00 0.00 0.00 2.52
2594 2977 4.599241 TCTCCCCTCTGTTCTCATTCTTTT 59.401 41.667 0.00 0.00 0.00 2.27
2595 2978 5.073691 TCTCCCCTCTGTTCTCATTCTTTTT 59.926 40.000 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 1.311859 CCTTTTGTGCTGCAGTGAGA 58.688 50.000 16.64 0.00 0.00 3.27
18 19 2.789409 AACTCTGCGGATAAGCCTTT 57.211 45.000 0.00 0.00 36.02 3.11
68 69 9.314133 TCATATAGCAACTGACAGAGGTATATT 57.686 33.333 24.78 15.82 36.21 1.28
74 77 4.626042 GGTCATATAGCAACTGACAGAGG 58.374 47.826 10.08 1.51 40.80 3.69
92 99 1.208706 TCAATCCTATTGGCCGGTCA 58.791 50.000 3.51 3.51 0.00 4.02
100 107 7.909322 GCCTTTGAGGTGGATCAATCCTATTG 61.909 46.154 10.30 0.00 40.87 1.90
109 116 2.517959 CAAAGCCTTTGAGGTGGATCA 58.482 47.619 11.83 0.00 43.26 2.92
110 117 1.203287 GCAAAGCCTTTGAGGTGGATC 59.797 52.381 21.00 0.00 43.26 3.36
180 188 5.128008 GGACATCTCCAAGCTAGTACTTTCT 59.872 44.000 0.00 0.00 36.42 2.52
328 342 1.448540 ATCGTTCGGCCAGCTCTTG 60.449 57.895 2.24 0.00 0.00 3.02
365 383 6.593770 TGAAGGAGAATTAGTGTACGTACGTA 59.406 38.462 23.60 23.60 0.00 3.57
451 477 2.951676 TCTTGCGATCGAGATCTACG 57.048 50.000 21.57 1.47 35.72 3.51
582 632 5.593679 AGTAATCCCTTCTCGATCGAAAA 57.406 39.130 19.92 11.79 0.00 2.29
598 655 2.218987 GCTAGCTTTCGCGGAAGTAATC 59.781 50.000 27.18 11.39 42.32 1.75
622 679 2.183555 GGCTACCACCGGTCTTCG 59.816 66.667 2.59 0.00 37.09 3.79
629 686 1.107538 TAGCTAGCTGGCTACCACCG 61.108 60.000 26.16 0.00 42.97 4.94
630 687 0.676736 CTAGCTAGCTGGCTACCACC 59.323 60.000 26.16 0.00 42.97 4.61
703 760 3.872728 CCGCGATCGAGTGTCCGA 61.873 66.667 21.57 0.00 43.16 4.55
873 933 2.360949 ATCGACTGATGGCAGAGGCG 62.361 60.000 16.41 16.41 45.17 5.52
886 946 1.759445 CTCTGGACCAATGGATCGACT 59.241 52.381 6.16 0.00 0.00 4.18
902 962 3.367327 CAGTCAATGCGTTTCTCTCTCTG 59.633 47.826 0.00 0.00 0.00 3.35
946 1006 2.569404 ACCGGAAAAGAGAGAGCAGATT 59.431 45.455 9.46 0.00 0.00 2.40
948 1008 1.633774 ACCGGAAAAGAGAGAGCAGA 58.366 50.000 9.46 0.00 0.00 4.26
953 1013 3.007614 CCAACCTAACCGGAAAAGAGAGA 59.992 47.826 9.46 0.00 36.31 3.10
959 1019 3.215975 CTCAACCAACCTAACCGGAAAA 58.784 45.455 9.46 0.00 36.31 2.29
961 1021 1.072648 CCTCAACCAACCTAACCGGAA 59.927 52.381 9.46 0.00 36.31 4.30
986 1046 2.789409 ACCCATCTTACAAGCACCTC 57.211 50.000 0.00 0.00 0.00 3.85
994 1054 1.004277 GCCACCAGAACCCATCTTACA 59.996 52.381 0.00 0.00 35.73 2.41
997 1057 0.482446 TTGCCACCAGAACCCATCTT 59.518 50.000 0.00 0.00 35.73 2.40
1185 1248 6.389830 TGTTACTAGAAAAGTACGTGACCA 57.610 37.500 0.00 0.00 40.48 4.02
1188 1251 8.693504 CGAAAATGTTACTAGAAAAGTACGTGA 58.306 33.333 0.00 0.00 40.48 4.35
1524 1597 4.403502 GAGGGGGTGTCGGGGGTA 62.404 72.222 0.00 0.00 0.00 3.69
1657 1730 2.124403 GATGCCCAGGCCAGTCAG 60.124 66.667 5.01 0.00 41.09 3.51
1744 1822 3.244976 ACATGCAACCTAACGTACGTAC 58.755 45.455 23.12 15.90 0.00 3.67
1745 1823 3.500982 GACATGCAACCTAACGTACGTA 58.499 45.455 23.12 9.19 0.00 3.57
1746 1824 2.331194 GACATGCAACCTAACGTACGT 58.669 47.619 16.72 16.72 0.00 3.57
1747 1825 1.319374 CGACATGCAACCTAACGTACG 59.681 52.381 15.01 15.01 0.00 3.67
1812 1894 4.226394 TCCCCTCCGTCAAAAGAAATATGA 59.774 41.667 0.00 0.00 0.00 2.15
1816 1898 2.375509 AGTCCCCTCCGTCAAAAGAAAT 59.624 45.455 0.00 0.00 0.00 2.17
1861 1945 1.114627 GAATCCAAGGCATCCAACCC 58.885 55.000 0.00 0.00 0.00 4.11
1958 2045 9.512588 AAATCTGCCTATAGATAAATGAACCAG 57.487 33.333 0.00 0.00 36.42 4.00
2086 2173 5.125739 TCAATGACAAAACCGGTTGTTAACT 59.874 36.000 23.08 0.00 41.78 2.24
2087 2174 5.341617 TCAATGACAAAACCGGTTGTTAAC 58.658 37.500 23.08 12.13 41.78 2.01
2089 2176 5.533154 AGATCAATGACAAAACCGGTTGTTA 59.467 36.000 23.08 13.66 41.78 2.41
2102 2189 4.018490 CCAACCATCCAAGATCAATGACA 58.982 43.478 0.00 0.00 0.00 3.58
2170 2382 5.508657 GCATTGAATATTTGGAAGGAGCCTC 60.509 44.000 0.00 0.00 0.00 4.70
2238 2453 8.073768 TGTAGGTCGAGTTTGATTTTGAATTTC 58.926 33.333 0.00 0.00 0.00 2.17
2245 2460 9.063615 ACTTTTATGTAGGTCGAGTTTGATTTT 57.936 29.630 0.00 0.00 0.00 1.82
2259 2474 7.012421 GGAAGGTAATGCTCACTTTTATGTAGG 59.988 40.741 0.00 0.00 0.00 3.18
2265 2480 7.775053 ATTTGGAAGGTAATGCTCACTTTTA 57.225 32.000 0.00 0.00 0.00 1.52
2271 2486 6.998074 CCATAGTATTTGGAAGGTAATGCTCA 59.002 38.462 0.00 0.00 36.26 4.26
2272 2487 7.224297 TCCATAGTATTTGGAAGGTAATGCTC 58.776 38.462 0.00 0.00 40.29 4.26
2274 2489 7.448469 ACATCCATAGTATTTGGAAGGTAATGC 59.552 37.037 0.00 0.00 45.99 3.56
2275 2490 8.924511 ACATCCATAGTATTTGGAAGGTAATG 57.075 34.615 0.00 0.00 45.99 1.90
2276 2491 8.723365 TGACATCCATAGTATTTGGAAGGTAAT 58.277 33.333 0.00 0.00 45.99 1.89
2277 2492 7.990886 GTGACATCCATAGTATTTGGAAGGTAA 59.009 37.037 0.00 0.00 45.99 2.85
2278 2493 7.347222 AGTGACATCCATAGTATTTGGAAGGTA 59.653 37.037 0.00 0.00 45.99 3.08
2280 2495 6.595682 AGTGACATCCATAGTATTTGGAAGG 58.404 40.000 0.00 0.00 45.99 3.46
2283 2498 8.877864 AAAAAGTGACATCCATAGTATTTGGA 57.122 30.769 0.00 0.00 46.86 3.53
2330 2703 1.134367 CACAATGATGCAGAGCCTTGG 59.866 52.381 0.00 0.00 0.00 3.61
2332 2705 2.502142 TCACAATGATGCAGAGCCTT 57.498 45.000 0.00 0.00 0.00 4.35
2412 2788 4.100963 TGTGAGTAGTGTGTGGAAGTTGAT 59.899 41.667 0.00 0.00 0.00 2.57
2415 2791 4.345257 AGATGTGAGTAGTGTGTGGAAGTT 59.655 41.667 0.00 0.00 0.00 2.66
2423 2799 8.539770 AGACAAATTTAGATGTGAGTAGTGTG 57.460 34.615 0.00 0.00 0.00 3.82
2430 2813 6.583806 GCCAACAAGACAAATTTAGATGTGAG 59.416 38.462 0.00 0.00 0.00 3.51
2471 2854 1.558756 CCACCCAGAAGAGCTTCTCAT 59.441 52.381 9.68 0.00 46.13 2.90
2472 2855 0.979665 CCACCCAGAAGAGCTTCTCA 59.020 55.000 9.68 0.00 46.13 3.27
2473 2856 1.206849 CTCCACCCAGAAGAGCTTCTC 59.793 57.143 9.68 0.00 46.13 2.87
2475 2858 0.980423 ACTCCACCCAGAAGAGCTTC 59.020 55.000 2.03 2.03 39.78 3.86
2476 2859 0.689623 CACTCCACCCAGAAGAGCTT 59.310 55.000 0.00 0.00 0.00 3.74
2477 2860 1.197430 CCACTCCACCCAGAAGAGCT 61.197 60.000 0.00 0.00 0.00 4.09
2478 2861 1.298014 CCACTCCACCCAGAAGAGC 59.702 63.158 0.00 0.00 0.00 4.09
2479 2862 1.827969 CTACCACTCCACCCAGAAGAG 59.172 57.143 0.00 0.00 0.00 2.85
2480 2863 1.431633 TCTACCACTCCACCCAGAAGA 59.568 52.381 0.00 0.00 0.00 2.87
2481 2864 1.550976 GTCTACCACTCCACCCAGAAG 59.449 57.143 0.00 0.00 0.00 2.85
2482 2865 1.132977 TGTCTACCACTCCACCCAGAA 60.133 52.381 0.00 0.00 0.00 3.02
2483 2866 0.485543 TGTCTACCACTCCACCCAGA 59.514 55.000 0.00 0.00 0.00 3.86
2484 2867 1.002087 GTTGTCTACCACTCCACCCAG 59.998 57.143 0.00 0.00 0.00 4.45
2485 2868 1.053424 GTTGTCTACCACTCCACCCA 58.947 55.000 0.00 0.00 0.00 4.51
2486 2869 1.053424 TGTTGTCTACCACTCCACCC 58.947 55.000 0.00 0.00 0.00 4.61
2487 2870 1.414919 TGTGTTGTCTACCACTCCACC 59.585 52.381 0.00 0.00 0.00 4.61
2488 2871 2.902705 TGTGTTGTCTACCACTCCAC 57.097 50.000 0.00 0.00 0.00 4.02
2489 2872 3.433031 CCTTTGTGTTGTCTACCACTCCA 60.433 47.826 0.00 0.00 0.00 3.86
2490 2873 3.139077 CCTTTGTGTTGTCTACCACTCC 58.861 50.000 0.00 0.00 0.00 3.85
2491 2874 3.805207 ACCTTTGTGTTGTCTACCACTC 58.195 45.455 0.00 0.00 0.00 3.51
2492 2875 3.926058 ACCTTTGTGTTGTCTACCACT 57.074 42.857 0.00 0.00 0.00 4.00
2493 2876 4.287238 CAACCTTTGTGTTGTCTACCAC 57.713 45.455 0.00 0.00 40.54 4.16
2502 2885 1.135228 GGCGACAACAACCTTTGTGTT 60.135 47.619 0.00 0.00 44.59 3.32
2503 2886 0.454196 GGCGACAACAACCTTTGTGT 59.546 50.000 0.00 0.00 44.59 3.72
2504 2887 0.248866 GGGCGACAACAACCTTTGTG 60.249 55.000 0.00 0.00 44.59 3.33
2506 2889 1.008995 CGGGCGACAACAACCTTTG 60.009 57.895 0.00 0.00 0.00 2.77
2507 2890 2.841160 GCGGGCGACAACAACCTTT 61.841 57.895 0.00 0.00 0.00 3.11
2508 2891 3.284449 GCGGGCGACAACAACCTT 61.284 61.111 0.00 0.00 0.00 3.50
2522 2905 0.532196 GAGAAGATTAACCCGGGCGG 60.532 60.000 24.08 0.00 37.81 6.13
2523 2906 0.177141 TGAGAAGATTAACCCGGGCG 59.823 55.000 24.08 0.00 0.00 6.13
2524 2907 2.104963 AGATGAGAAGATTAACCCGGGC 59.895 50.000 24.08 2.97 0.00 6.13
2525 2908 3.244249 GGAGATGAGAAGATTAACCCGGG 60.244 52.174 22.25 22.25 0.00 5.73
2526 2909 3.643792 AGGAGATGAGAAGATTAACCCGG 59.356 47.826 0.00 0.00 0.00 5.73
2527 2910 4.946478 AGGAGATGAGAAGATTAACCCG 57.054 45.455 0.00 0.00 0.00 5.28
2528 2911 9.315363 TCTTATAGGAGATGAGAAGATTAACCC 57.685 37.037 0.00 0.00 0.00 4.11
2538 2921 9.527157 CCTGTCTTATTCTTATAGGAGATGAGA 57.473 37.037 0.00 0.00 0.00 3.27
2539 2922 8.748412 CCCTGTCTTATTCTTATAGGAGATGAG 58.252 40.741 0.00 0.00 0.00 2.90
2540 2923 7.676043 CCCCTGTCTTATTCTTATAGGAGATGA 59.324 40.741 0.00 0.00 0.00 2.92
2541 2924 7.093112 CCCCCTGTCTTATTCTTATAGGAGATG 60.093 44.444 0.00 0.00 0.00 2.90
2542 2925 6.962902 CCCCCTGTCTTATTCTTATAGGAGAT 59.037 42.308 0.00 0.00 0.00 2.75
2543 2926 6.105740 TCCCCCTGTCTTATTCTTATAGGAGA 59.894 42.308 0.00 0.00 0.00 3.71
2544 2927 6.323737 TCCCCCTGTCTTATTCTTATAGGAG 58.676 44.000 0.00 0.00 0.00 3.69
2545 2928 6.303427 TCCCCCTGTCTTATTCTTATAGGA 57.697 41.667 0.00 0.00 0.00 2.94
2546 2929 6.559157 ACTTCCCCCTGTCTTATTCTTATAGG 59.441 42.308 0.00 0.00 0.00 2.57
2547 2930 7.511028 AGACTTCCCCCTGTCTTATTCTTATAG 59.489 40.741 0.00 0.00 40.21 1.31
2548 2931 7.371043 AGACTTCCCCCTGTCTTATTCTTATA 58.629 38.462 0.00 0.00 40.21 0.98
2549 2932 6.213525 AGACTTCCCCCTGTCTTATTCTTAT 58.786 40.000 0.00 0.00 40.21 1.73
2550 2933 5.600749 AGACTTCCCCCTGTCTTATTCTTA 58.399 41.667 0.00 0.00 40.21 2.10
2551 2934 4.439860 AGACTTCCCCCTGTCTTATTCTT 58.560 43.478 0.00 0.00 40.21 2.52
2552 2935 4.034410 GAGACTTCCCCCTGTCTTATTCT 58.966 47.826 0.00 0.00 42.79 2.40
2553 2936 3.134985 GGAGACTTCCCCCTGTCTTATTC 59.865 52.174 0.00 0.00 42.79 1.75
2554 2937 3.116174 GGAGACTTCCCCCTGTCTTATT 58.884 50.000 0.00 0.00 42.79 1.40
2555 2938 2.765502 GGAGACTTCCCCCTGTCTTAT 58.234 52.381 0.00 0.00 42.79 1.73
2556 2939 2.249309 GGAGACTTCCCCCTGTCTTA 57.751 55.000 0.00 0.00 42.79 2.10
2557 2940 3.090504 GGAGACTTCCCCCTGTCTT 57.909 57.895 0.00 0.00 42.79 3.01
2558 2941 4.899243 GGAGACTTCCCCCTGTCT 57.101 61.111 0.00 0.00 45.06 3.41
2566 2949 1.828595 GAGAACAGAGGGGAGACTTCC 59.171 57.143 0.00 0.00 43.23 3.46
2567 2950 2.530701 TGAGAACAGAGGGGAGACTTC 58.469 52.381 0.00 0.00 0.00 3.01
2568 2951 2.704190 TGAGAACAGAGGGGAGACTT 57.296 50.000 0.00 0.00 0.00 3.01
2569 2952 2.938428 ATGAGAACAGAGGGGAGACT 57.062 50.000 0.00 0.00 0.00 3.24
2570 2953 3.103742 AGAATGAGAACAGAGGGGAGAC 58.896 50.000 0.00 0.00 0.00 3.36
2571 2954 3.481559 AGAATGAGAACAGAGGGGAGA 57.518 47.619 0.00 0.00 0.00 3.71
2572 2955 4.566426 AAAGAATGAGAACAGAGGGGAG 57.434 45.455 0.00 0.00 0.00 4.30
2573 2956 5.324832 AAAAAGAATGAGAACAGAGGGGA 57.675 39.130 0.00 0.00 0.00 4.81
2607 2990 9.851686 AGTTTGATATATACATGGAGAGCAAAA 57.148 29.630 0.00 0.00 0.00 2.44
2608 2991 9.276590 CAGTTTGATATATACATGGAGAGCAAA 57.723 33.333 0.00 0.00 0.00 3.68
2609 2992 7.879677 CCAGTTTGATATATACATGGAGAGCAA 59.120 37.037 0.00 0.00 0.00 3.91
2610 2993 7.235399 TCCAGTTTGATATATACATGGAGAGCA 59.765 37.037 0.00 0.00 32.08 4.26
2611 2994 7.615403 TCCAGTTTGATATATACATGGAGAGC 58.385 38.462 0.00 0.00 32.08 4.09


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

AutoCloner maintained by Alex Coulton.