Multiple sequence alignment - TraesCS5A01G041200

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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 TraesCS5A01G041200 chr5A 100.000 2611 0 0 1 2611 37081184 37083794 0.000000e+00 4822.0
1 TraesCS5A01G041200 chr5A 87.671 1168 105 19 2 1165 528269220 528270352 0.000000e+00 1323.0
2 TraesCS5A01G041200 chr5A 77.173 1599 296 46 31 1594 503050094 503051658 0.000000e+00 867.0
3 TraesCS5A01G041200 chr5A 88.648 599 45 10 1189 1785 528270343 528270920 0.000000e+00 708.0
4 TraesCS5A01G041200 chr5A 78.710 930 154 27 1 915 502501052 502500152 4.840000e-162 580.0
5 TraesCS5A01G041200 chr5A 91.667 60 5 0 2081 2140 37083171 37083230 1.670000e-12 84.2
6 TraesCS5A01G041200 chr5A 91.667 60 5 0 1988 2047 37083264 37083323 1.670000e-12 84.2
7 TraesCS5A01G041200 chr5B 94.066 1921 79 15 4 1916 47122467 47124360 0.000000e+00 2883.0
8 TraesCS5A01G041200 chr5B 89.734 1315 106 14 503 1816 502021495 502022781 0.000000e+00 1653.0
9 TraesCS5A01G041200 chr5B 76.003 1421 264 51 18 1394 477965178 477966565 0.000000e+00 664.0
10 TraesCS5A01G041200 chr5B 78.102 685 126 18 924 1595 476906719 476906046 1.870000e-111 412.0
11 TraesCS5A01G041200 chr5B 80.322 559 97 8 330 877 477984387 477984943 6.730000e-111 411.0
12 TraesCS5A01G041200 chr5B 84.300 414 54 7 87 499 502015304 502015707 6.770000e-106 394.0
13 TraesCS5A01G041200 chr5B 90.000 130 12 1 1194 1322 47129143 47129272 1.610000e-37 167.0
14 TraesCS5A01G041200 chr5B 87.970 133 16 0 2 134 505736590 505736722 9.670000e-35 158.0
15 TraesCS5A01G041200 chr5D 93.939 1881 96 10 1 1877 46067402 46069268 0.000000e+00 2826.0
16 TraesCS5A01G041200 chr5D 77.090 1615 299 48 18 1594 397929797 397931378 0.000000e+00 867.0
17 TraesCS5A01G041200 chr5D 92.612 582 24 7 1871 2452 46074631 46075193 0.000000e+00 819.0
18 TraesCS5A01G041200 chr5D 86.812 690 72 12 2 685 415629611 415630287 0.000000e+00 752.0
19 TraesCS5A01G041200 chr5D 80.442 905 156 11 18 915 396946951 396946061 0.000000e+00 671.0
20 TraesCS5A01G041200 chr5D 85.843 664 57 19 1168 1816 415645140 415645781 0.000000e+00 671.0
21 TraesCS5A01G041200 chr5D 89.455 275 21 6 710 982 415644835 415645103 8.950000e-90 340.0
22 TraesCS5A01G041200 chr7A 88.889 81 7 2 2150 2230 217558059 217557981 5.950000e-17 99.0
23 TraesCS5A01G041200 chr7A 92.683 41 1 2 2160 2200 217558112 217558074 1.010000e-04 58.4
24 TraesCS5A01G041200 chr7D 87.143 70 8 1 2161 2230 205544794 205544726 7.750000e-11 78.7
25 TraesCS5A01G041200 chr4A 95.122 41 2 0 2138 2178 658400235 658400195 6.030000e-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 TraesCS5A01G041200 chr5A 37081184 37083794 2610 False 1663.466667 4822 94.444667 1 2611 3 chr5A.!!$F2 2610
1 TraesCS5A01G041200 chr5A 528269220 528270920 1700 False 1015.500000 1323 88.159500 2 1785 2 chr5A.!!$F3 1783
2 TraesCS5A01G041200 chr5A 503050094 503051658 1564 False 867.000000 867 77.173000 31 1594 1 chr5A.!!$F1 1563
3 TraesCS5A01G041200 chr5A 502500152 502501052 900 True 580.000000 580 78.710000 1 915 1 chr5A.!!$R1 914
4 TraesCS5A01G041200 chr5B 47122467 47124360 1893 False 2883.000000 2883 94.066000 4 1916 1 chr5B.!!$F1 1912
5 TraesCS5A01G041200 chr5B 502021495 502022781 1286 False 1653.000000 1653 89.734000 503 1816 1 chr5B.!!$F6 1313
6 TraesCS5A01G041200 chr5B 477965178 477966565 1387 False 664.000000 664 76.003000 18 1394 1 chr5B.!!$F3 1376
7 TraesCS5A01G041200 chr5B 476906046 476906719 673 True 412.000000 412 78.102000 924 1595 1 chr5B.!!$R1 671
8 TraesCS5A01G041200 chr5B 477984387 477984943 556 False 411.000000 411 80.322000 330 877 1 chr5B.!!$F4 547
9 TraesCS5A01G041200 chr5D 46067402 46069268 1866 False 2826.000000 2826 93.939000 1 1877 1 chr5D.!!$F1 1876
10 TraesCS5A01G041200 chr5D 397929797 397931378 1581 False 867.000000 867 77.090000 18 1594 1 chr5D.!!$F3 1576
11 TraesCS5A01G041200 chr5D 46074631 46075193 562 False 819.000000 819 92.612000 1871 2452 1 chr5D.!!$F2 581
12 TraesCS5A01G041200 chr5D 415629611 415630287 676 False 752.000000 752 86.812000 2 685 1 chr5D.!!$F4 683
13 TraesCS5A01G041200 chr5D 396946061 396946951 890 True 671.000000 671 80.442000 18 915 1 chr5D.!!$R1 897
14 TraesCS5A01G041200 chr5D 415644835 415645781 946 False 505.500000 671 87.649000 710 1816 2 chr5D.!!$F5 1106

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
426 432 0.18135 CAGTCTACTTCCCATGCCCC 59.819 60.0 0.0 0.0 0.0 5.8 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1834 1922 0.109272 TCGCTAGCTGAACCAGTTCG 60.109 55.0 13.93 2.78 42.28 3.95 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
28 30 4.152759 TGAGGGTAAGCGTTTGATTTTACG 59.847 41.667 0.00 0.00 40.55 3.18
137 139 1.070445 GTGCTGCCTGTGTGTCTCT 59.930 57.895 0.00 0.00 0.00 3.10
149 151 1.149148 GTGTCTCTTGCCTTTCGACC 58.851 55.000 0.00 0.00 0.00 4.79
202 204 9.461312 TCACATTTAATAGTCAAACAATAGGCT 57.539 29.630 0.00 0.00 0.00 4.58
220 222 1.532868 GCTTATCACGGGATGACATGC 59.467 52.381 11.33 0.38 41.24 4.06
282 285 1.067635 GGCATTGGCGTGAAGACATTT 60.068 47.619 0.00 0.00 37.96 2.32
302 308 0.942962 GAGATTGATTGCTCCTGCGG 59.057 55.000 0.00 0.00 43.34 5.69
426 432 0.181350 CAGTCTACTTCCCATGCCCC 59.819 60.000 0.00 0.00 0.00 5.80
468 478 4.545610 GAAGCTCGATCTGGTATCTTCAG 58.454 47.826 0.00 0.00 0.00 3.02
694 714 3.614092 CAGGTGTTAGAATGCCACAGAT 58.386 45.455 0.00 0.00 0.00 2.90
922 951 5.763204 TCCAAAACCTCTTGTGACTGATTAC 59.237 40.000 0.00 0.00 0.00 1.89
996 1042 1.518325 TGCAGGTGGTCAATACAACG 58.482 50.000 0.00 0.00 29.28 4.10
1001 1047 2.027192 AGGTGGTCAATACAACGCTGAT 60.027 45.455 0.00 0.00 29.28 2.90
1058 1110 7.480760 ACTTGAGCATTTATGTTAATGGGTT 57.519 32.000 0.00 0.00 36.30 4.11
1688 1757 9.973450 AAGTTCTGTAATCTGTATATACTGCTG 57.027 33.333 13.89 5.42 0.00 4.41
1697 1785 2.867109 ATATACTGCTGGGATGTGCC 57.133 50.000 0.00 0.00 0.00 5.01
1735 1823 6.203530 GCATCATTATGTGCAGAGTTTAGCTA 59.796 38.462 12.42 0.00 40.94 3.32
1736 1824 7.570875 GCATCATTATGTGCAGAGTTTAGCTAG 60.571 40.741 12.42 0.00 40.94 3.42
1737 1825 5.755375 TCATTATGTGCAGAGTTTAGCTAGC 59.245 40.000 6.62 6.62 0.00 3.42
1738 1826 3.902881 ATGTGCAGAGTTTAGCTAGCT 57.097 42.857 23.12 23.12 31.83 3.32
1756 1844 5.278364 GCTAGCTCTGCAATATTTCAATGCT 60.278 40.000 7.70 14.90 40.66 3.79
1768 1856 9.882996 CAATATTTCAATGCTATCGCTTAAAGA 57.117 29.630 0.00 0.00 36.97 2.52
1834 1922 2.859165 TGGTCCAAGGTGTCTGAATC 57.141 50.000 0.00 0.00 0.00 2.52
1846 1934 3.430218 GTGTCTGAATCGAACTGGTTCAG 59.570 47.826 16.21 16.21 46.31 3.02
1916 2004 1.403679 CAAGTTGTTCAGGTTGGCGAA 59.596 47.619 0.00 0.00 0.00 4.70
1936 2024 0.179048 CGCCACAGGATTATCAGCCA 60.179 55.000 0.00 0.00 0.00 4.75
1982 2070 6.528774 TCGTTTTTCCTTTGCTTGTTAAGTTC 59.471 34.615 0.00 0.00 0.00 3.01
1990 2078 6.019881 CCTTTGCTTGTTAAGTTCGGAAAAAG 60.020 38.462 0.00 0.00 0.00 2.27
2021 2109 3.070018 ACTGAAATCTTTGAGTGCTCCG 58.930 45.455 0.00 0.00 33.36 4.63
2024 2112 1.160137 AATCTTTGAGTGCTCCGTGC 58.840 50.000 0.00 0.00 43.25 5.34
2026 2114 2.281484 TTTGAGTGCTCCGTGCCC 60.281 61.111 0.00 0.00 42.00 5.36
2027 2115 4.680237 TTGAGTGCTCCGTGCCCG 62.680 66.667 0.00 0.00 42.00 6.13
2076 2164 7.686438 TTAAATCAATTGCTTCAGCTGTCTA 57.314 32.000 14.67 2.04 42.66 2.59
2080 2168 7.870509 ATCAATTGCTTCAGCTGTCTAATTA 57.129 32.000 14.67 6.78 42.66 1.40
2082 2170 8.109705 TCAATTGCTTCAGCTGTCTAATTAAA 57.890 30.769 14.67 0.00 42.66 1.52
2085 2173 6.486253 TGCTTCAGCTGTCTAATTAAAGTG 57.514 37.500 14.67 0.00 42.66 3.16
2086 2174 6.230472 TGCTTCAGCTGTCTAATTAAAGTGA 58.770 36.000 14.67 0.00 42.66 3.41
2087 2175 6.881065 TGCTTCAGCTGTCTAATTAAAGTGAT 59.119 34.615 14.67 0.00 42.66 3.06
2088 2176 7.065085 TGCTTCAGCTGTCTAATTAAAGTGATC 59.935 37.037 14.67 0.00 42.66 2.92
2089 2177 7.279758 GCTTCAGCTGTCTAATTAAAGTGATCT 59.720 37.037 14.67 0.00 38.21 2.75
2090 2178 8.709386 TTCAGCTGTCTAATTAAAGTGATCTC 57.291 34.615 14.67 0.00 0.00 2.75
2091 2179 8.072321 TCAGCTGTCTAATTAAAGTGATCTCT 57.928 34.615 14.67 0.00 0.00 3.10
2092 2180 7.978414 TCAGCTGTCTAATTAAAGTGATCTCTG 59.022 37.037 14.67 0.00 0.00 3.35
2093 2181 7.978414 CAGCTGTCTAATTAAAGTGATCTCTGA 59.022 37.037 5.25 0.00 0.00 3.27
2094 2182 7.978975 AGCTGTCTAATTAAAGTGATCTCTGAC 59.021 37.037 0.00 0.87 0.00 3.51
2095 2183 7.978975 GCTGTCTAATTAAAGTGATCTCTGACT 59.021 37.037 0.00 0.00 0.00 3.41
2096 2184 9.299963 CTGTCTAATTAAAGTGATCTCTGACTG 57.700 37.037 0.00 1.01 0.00 3.51
2097 2185 9.025041 TGTCTAATTAAAGTGATCTCTGACTGA 57.975 33.333 0.00 0.00 0.00 3.41
2098 2186 9.862371 GTCTAATTAAAGTGATCTCTGACTGAA 57.138 33.333 0.00 0.00 0.00 3.02
2249 2337 2.562738 GGAAGAATGTGGTTTTGGGAGG 59.437 50.000 0.00 0.00 0.00 4.30
2286 2374 2.170397 TCAGTGCTGGTGAAACTTGAGA 59.830 45.455 0.00 0.00 36.74 3.27
2287 2375 2.547211 CAGTGCTGGTGAAACTTGAGAG 59.453 50.000 0.00 0.00 36.74 3.20
2288 2376 2.171448 AGTGCTGGTGAAACTTGAGAGT 59.829 45.455 0.00 0.00 37.87 3.24
2291 2379 4.757149 GTGCTGGTGAAACTTGAGAGTTAT 59.243 41.667 0.00 0.00 45.18 1.89
2292 2380 5.932303 GTGCTGGTGAAACTTGAGAGTTATA 59.068 40.000 0.00 0.00 45.18 0.98
2293 2381 5.932303 TGCTGGTGAAACTTGAGAGTTATAC 59.068 40.000 0.00 0.00 45.18 1.47
2310 2398 8.154856 AGAGTTATACGTTGGGTATGCAATTAT 58.845 33.333 0.00 0.00 41.87 1.28
2321 2409 8.995027 TGGGTATGCAATTATAGACATTTTCT 57.005 30.769 0.00 0.00 38.51 2.52
2335 2423 5.593387 GACATTTTCTGTTGCTTCACAGCG 61.593 45.833 6.44 0.00 43.51 5.18
2353 2441 4.036352 CAGCGGACTAAGACGATTAGTTC 58.964 47.826 15.51 13.40 35.54 3.01
2373 2461 9.567848 TTAGTTCGCCAATTTCTTTGATAAATC 57.432 29.630 0.00 0.00 37.53 2.17
2419 2507 3.934068 AGGCATCATGCTTTTGGAAAAG 58.066 40.909 10.11 7.39 46.25 2.27
2437 2525 2.133281 AGGTTGCATCATGCTTGCTA 57.867 45.000 11.84 10.15 45.31 3.49
2442 2530 0.736636 GCATCATGCTTGCTACTGCA 59.263 50.000 1.02 0.00 43.16 4.41
2453 2541 3.848272 TGCTACTGCATTTTGTTAGCC 57.152 42.857 0.00 0.00 45.31 3.93
2454 2542 2.491693 TGCTACTGCATTTTGTTAGCCC 59.508 45.455 0.00 0.00 45.31 5.19
2455 2543 2.159240 GCTACTGCATTTTGTTAGCCCC 60.159 50.000 0.00 0.00 39.41 5.80
2456 2544 2.008242 ACTGCATTTTGTTAGCCCCA 57.992 45.000 0.00 0.00 0.00 4.96
2457 2545 2.539302 ACTGCATTTTGTTAGCCCCAT 58.461 42.857 0.00 0.00 0.00 4.00
2458 2546 2.234414 ACTGCATTTTGTTAGCCCCATG 59.766 45.455 0.00 0.00 0.00 3.66
2459 2547 1.554160 TGCATTTTGTTAGCCCCATGG 59.446 47.619 4.14 4.14 0.00 3.66
2460 2548 1.554617 GCATTTTGTTAGCCCCATGGT 59.445 47.619 11.73 0.00 0.00 3.55
2461 2549 2.027285 GCATTTTGTTAGCCCCATGGTT 60.027 45.455 11.73 0.00 0.00 3.67
2462 2550 3.196685 GCATTTTGTTAGCCCCATGGTTA 59.803 43.478 11.73 0.00 0.00 2.85
2463 2551 4.141733 GCATTTTGTTAGCCCCATGGTTAT 60.142 41.667 11.73 0.00 0.00 1.89
2464 2552 5.600696 CATTTTGTTAGCCCCATGGTTATC 58.399 41.667 11.73 0.80 0.00 1.75
2465 2553 2.631160 TGTTAGCCCCATGGTTATCG 57.369 50.000 11.73 0.00 0.00 2.92
2466 2554 2.120312 TGTTAGCCCCATGGTTATCGA 58.880 47.619 11.73 0.00 0.00 3.59
2467 2555 2.708861 TGTTAGCCCCATGGTTATCGAT 59.291 45.455 11.73 2.16 0.00 3.59
2468 2556 3.244422 TGTTAGCCCCATGGTTATCGATC 60.244 47.826 11.73 0.00 0.00 3.69
2469 2557 1.734655 AGCCCCATGGTTATCGATCT 58.265 50.000 11.73 0.00 0.00 2.75
2470 2558 1.349026 AGCCCCATGGTTATCGATCTG 59.651 52.381 11.73 0.00 0.00 2.90
2471 2559 1.072331 GCCCCATGGTTATCGATCTGT 59.928 52.381 11.73 0.00 0.00 3.41
2472 2560 2.487265 GCCCCATGGTTATCGATCTGTT 60.487 50.000 11.73 0.00 0.00 3.16
2473 2561 3.820557 CCCCATGGTTATCGATCTGTTT 58.179 45.455 11.73 0.00 0.00 2.83
2474 2562 3.565482 CCCCATGGTTATCGATCTGTTTG 59.435 47.826 11.73 0.00 0.00 2.93
2475 2563 4.199310 CCCATGGTTATCGATCTGTTTGT 58.801 43.478 11.73 0.00 0.00 2.83
2476 2564 4.640201 CCCATGGTTATCGATCTGTTTGTT 59.360 41.667 11.73 0.00 0.00 2.83
2477 2565 5.820423 CCCATGGTTATCGATCTGTTTGTTA 59.180 40.000 11.73 0.00 0.00 2.41
2478 2566 6.017934 CCCATGGTTATCGATCTGTTTGTTAG 60.018 42.308 11.73 0.00 0.00 2.34
2479 2567 6.538742 CCATGGTTATCGATCTGTTTGTTAGT 59.461 38.462 0.00 0.00 0.00 2.24
2480 2568 7.709182 CCATGGTTATCGATCTGTTTGTTAGTA 59.291 37.037 0.00 0.00 0.00 1.82
2481 2569 9.261180 CATGGTTATCGATCTGTTTGTTAGTAT 57.739 33.333 0.00 0.00 0.00 2.12
2482 2570 9.832445 ATGGTTATCGATCTGTTTGTTAGTATT 57.168 29.630 0.00 0.00 0.00 1.89
2483 2571 9.661563 TGGTTATCGATCTGTTTGTTAGTATTT 57.338 29.630 0.00 0.00 0.00 1.40
2489 2577 8.928733 TCGATCTGTTTGTTAGTATTTTGTACC 58.071 33.333 0.00 0.00 0.00 3.34
2490 2578 8.714179 CGATCTGTTTGTTAGTATTTTGTACCA 58.286 33.333 0.00 0.00 0.00 3.25
2493 2581 9.398538 TCTGTTTGTTAGTATTTTGTACCAAGT 57.601 29.630 0.00 0.00 0.00 3.16
2494 2582 9.445786 CTGTTTGTTAGTATTTTGTACCAAGTG 57.554 33.333 0.00 0.00 0.00 3.16
2495 2583 9.175312 TGTTTGTTAGTATTTTGTACCAAGTGA 57.825 29.630 0.00 0.00 0.00 3.41
2513 2601 9.261180 ACCAAGTGAATATATATCGTTTGACTG 57.739 33.333 0.00 0.00 0.00 3.51
2514 2602 9.261180 CCAAGTGAATATATATCGTTTGACTGT 57.739 33.333 0.00 0.00 0.00 3.55
2517 2605 9.627395 AGTGAATATATATCGTTTGACTGTAGC 57.373 33.333 0.00 0.00 0.00 3.58
2518 2606 9.406828 GTGAATATATATCGTTTGACTGTAGCA 57.593 33.333 0.00 0.00 0.00 3.49
2519 2607 9.974980 TGAATATATATCGTTTGACTGTAGCAA 57.025 29.630 0.00 0.00 0.00 3.91
2521 2609 9.982651 AATATATATCGTTTGACTGTAGCAAGT 57.017 29.630 0.00 0.00 0.00 3.16
2526 2614 9.982651 ATATCGTTTGACTGTAGCAAGTATATT 57.017 29.630 0.00 0.00 0.00 1.28
2527 2615 8.718102 ATCGTTTGACTGTAGCAAGTATATTT 57.282 30.769 0.00 0.00 0.00 1.40
2528 2616 9.811995 ATCGTTTGACTGTAGCAAGTATATTTA 57.188 29.630 0.00 0.00 0.00 1.40
2529 2617 9.811995 TCGTTTGACTGTAGCAAGTATATTTAT 57.188 29.630 0.00 0.00 0.00 1.40
2566 2654 9.118236 GAATCTTTAGTTTATCAACAAGTGTGC 57.882 33.333 0.00 0.00 35.05 4.57
2567 2655 6.966021 TCTTTAGTTTATCAACAAGTGTGCC 58.034 36.000 0.00 0.00 35.05 5.01
2568 2656 6.770785 TCTTTAGTTTATCAACAAGTGTGCCT 59.229 34.615 0.00 0.00 35.05 4.75
2569 2657 4.836125 AGTTTATCAACAAGTGTGCCTG 57.164 40.909 0.00 0.00 35.05 4.85
2570 2658 4.460263 AGTTTATCAACAAGTGTGCCTGA 58.540 39.130 0.00 0.00 35.05 3.86
2571 2659 4.887071 AGTTTATCAACAAGTGTGCCTGAA 59.113 37.500 0.00 0.00 35.05 3.02
2572 2660 5.536161 AGTTTATCAACAAGTGTGCCTGAAT 59.464 36.000 0.00 0.00 35.05 2.57
2573 2661 5.627499 TTATCAACAAGTGTGCCTGAATC 57.373 39.130 0.00 0.00 0.00 2.52
2574 2662 2.229792 TCAACAAGTGTGCCTGAATCC 58.770 47.619 0.00 0.00 0.00 3.01
2575 2663 1.955778 CAACAAGTGTGCCTGAATCCA 59.044 47.619 0.00 0.00 0.00 3.41
2576 2664 2.559668 CAACAAGTGTGCCTGAATCCAT 59.440 45.455 0.00 0.00 0.00 3.41
2577 2665 3.719268 ACAAGTGTGCCTGAATCCATA 57.281 42.857 0.00 0.00 0.00 2.74
2578 2666 3.347216 ACAAGTGTGCCTGAATCCATAC 58.653 45.455 0.00 0.00 0.00 2.39
2579 2667 3.009473 ACAAGTGTGCCTGAATCCATACT 59.991 43.478 0.00 0.00 35.34 2.12
2580 2668 4.012374 CAAGTGTGCCTGAATCCATACTT 58.988 43.478 0.00 0.00 41.89 2.24
2581 2669 3.614092 AGTGTGCCTGAATCCATACTTG 58.386 45.455 0.00 0.00 30.61 3.16
2582 2670 2.684881 GTGTGCCTGAATCCATACTTGG 59.315 50.000 0.00 0.00 45.15 3.61
2583 2671 2.301346 GTGCCTGAATCCATACTTGGG 58.699 52.381 0.00 0.00 43.81 4.12
2584 2672 1.322442 GCCTGAATCCATACTTGGGC 58.678 55.000 0.00 0.00 43.81 5.36
2585 2673 1.410083 GCCTGAATCCATACTTGGGCA 60.410 52.381 0.00 0.00 43.81 5.36
2586 2674 2.754186 GCCTGAATCCATACTTGGGCAT 60.754 50.000 0.00 0.00 43.81 4.40
2587 2675 2.889045 CCTGAATCCATACTTGGGCATG 59.111 50.000 0.00 0.00 43.81 4.06
2588 2676 3.559069 CTGAATCCATACTTGGGCATGT 58.441 45.455 0.00 0.00 43.81 3.21
2589 2677 3.956199 CTGAATCCATACTTGGGCATGTT 59.044 43.478 0.00 0.00 43.81 2.71
2590 2678 4.352009 TGAATCCATACTTGGGCATGTTT 58.648 39.130 0.00 0.00 43.81 2.83
2591 2679 4.776837 TGAATCCATACTTGGGCATGTTTT 59.223 37.500 0.00 0.00 43.81 2.43
2592 2680 5.248020 TGAATCCATACTTGGGCATGTTTTT 59.752 36.000 0.00 0.00 43.81 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 7.480542 ACACATTAGAATCGTAAAATCAAACGC 59.519 33.333 0.00 0.00 38.94 4.84
28 30 8.041323 TGGGAGAAGAGTTAACACATTAGAATC 58.959 37.037 8.61 0.00 0.00 2.52
137 139 0.882927 CCACGAAGGTCGAAAGGCAA 60.883 55.000 4.40 0.00 43.74 4.52
149 151 3.057174 GGGATAGTAGCATCTCCACGAAG 60.057 52.174 0.00 0.00 0.00 3.79
202 204 2.998316 TGCATGTCATCCCGTGATAA 57.002 45.000 0.00 0.00 39.48 1.75
220 222 5.199024 TGATCAACTTTGTGGGTGAAATG 57.801 39.130 0.00 0.00 0.00 2.32
282 285 1.660167 CGCAGGAGCAATCAATCTCA 58.340 50.000 0.00 0.00 42.27 3.27
426 432 4.085357 TCCATTCCCATTGGATAGAACG 57.915 45.455 3.62 0.00 41.40 3.95
468 478 2.870411 ACGGAAGACACAGTTAACAAGC 59.130 45.455 8.61 0.00 0.00 4.01
694 714 3.679980 GCTTTGTTCTCTATCGTCTGCAA 59.320 43.478 0.00 0.00 0.00 4.08
908 937 7.116090 GCTCTATGCATAGTAATCAGTCACAAG 59.884 40.741 28.51 16.58 42.31 3.16
968 1014 7.342581 TGTATTGACCACCTGCATAAAGATAA 58.657 34.615 0.00 0.00 0.00 1.75
1058 1110 3.476552 ACCAGAGAAAGACAATCGCAAA 58.523 40.909 0.00 0.00 0.00 3.68
1686 1755 1.915141 AGAAACAAGGCACATCCCAG 58.085 50.000 0.00 0.00 34.51 4.45
1687 1756 1.962807 CAAGAAACAAGGCACATCCCA 59.037 47.619 0.00 0.00 34.51 4.37
1688 1757 1.273327 CCAAGAAACAAGGCACATCCC 59.727 52.381 0.00 0.00 34.51 3.85
1697 1785 6.309494 CACATAATGATGCACCAAGAAACAAG 59.691 38.462 0.00 0.00 36.43 3.16
1726 1814 7.050377 TGAAATATTGCAGAGCTAGCTAAACT 58.950 34.615 19.38 8.03 0.00 2.66
1735 1823 6.348295 CGATAGCATTGAAATATTGCAGAGCT 60.348 38.462 21.49 21.49 37.96 4.09
1736 1824 5.793952 CGATAGCATTGAAATATTGCAGAGC 59.206 40.000 12.10 12.10 37.96 4.09
1756 1844 7.055667 AGAGGTCATCAATCTTTAAGCGATA 57.944 36.000 0.00 0.00 0.00 2.92
1768 1856 9.593565 TGTAGAGTTATATGAGAGGTCATCAAT 57.406 33.333 0.00 0.00 42.80 2.57
1834 1922 0.109272 TCGCTAGCTGAACCAGTTCG 60.109 55.000 13.93 2.78 42.28 3.95
1846 1934 3.188786 CAACCTGCGGTCGCTAGC 61.189 66.667 16.36 4.06 42.51 3.42
1916 2004 0.179045 GGCTGATAATCCTGTGGCGT 60.179 55.000 0.00 0.00 0.00 5.68
1944 2032 6.862711 AGGAAAAACGAGGTTCTAAGAAAG 57.137 37.500 0.00 0.00 0.00 2.62
1982 2070 4.560128 TCAGTCAGAGATCACTTTTTCCG 58.440 43.478 0.00 0.00 0.00 4.30
1990 2078 6.873076 ACTCAAAGATTTCAGTCAGAGATCAC 59.127 38.462 0.00 0.00 39.64 3.06
2027 2115 0.393820 TTCACTTACCCACGGTCCAC 59.606 55.000 0.00 0.00 37.09 4.02
2028 2116 1.129917 TTTCACTTACCCACGGTCCA 58.870 50.000 0.00 0.00 37.09 4.02
2029 2117 1.071228 AGTTTCACTTACCCACGGTCC 59.929 52.381 0.00 0.00 37.09 4.46
2058 2146 8.025445 ACTTTAATTAGACAGCTGAAGCAATTG 58.975 33.333 23.35 0.00 45.16 2.32
2063 2151 6.727824 TCACTTTAATTAGACAGCTGAAGC 57.272 37.500 23.35 9.30 42.49 3.86
2076 2164 9.956640 AGATTTCAGTCAGAGATCACTTTAATT 57.043 29.630 0.00 0.00 39.64 1.40
2080 2168 7.935755 TCAAAGATTTCAGTCAGAGATCACTTT 59.064 33.333 0.00 0.00 39.64 2.66
2082 2170 7.002250 TCAAAGATTTCAGTCAGAGATCACT 57.998 36.000 0.00 0.00 39.64 3.41
2085 2173 6.183360 GCACTCAAAGATTTCAGTCAGAGATC 60.183 42.308 0.00 0.00 37.96 2.75
2086 2174 5.642919 GCACTCAAAGATTTCAGTCAGAGAT 59.357 40.000 0.00 0.00 0.00 2.75
2087 2175 4.993584 GCACTCAAAGATTTCAGTCAGAGA 59.006 41.667 0.00 0.00 0.00 3.10
2088 2176 4.143158 CGCACTCAAAGATTTCAGTCAGAG 60.143 45.833 0.00 0.00 0.00 3.35
2089 2177 3.742882 CGCACTCAAAGATTTCAGTCAGA 59.257 43.478 0.00 0.00 0.00 3.27
2090 2178 3.666374 GCGCACTCAAAGATTTCAGTCAG 60.666 47.826 0.30 0.00 0.00 3.51
2091 2179 2.224079 GCGCACTCAAAGATTTCAGTCA 59.776 45.455 0.30 0.00 0.00 3.41
2092 2180 2.413371 GGCGCACTCAAAGATTTCAGTC 60.413 50.000 10.83 0.00 0.00 3.51
2093 2181 1.537202 GGCGCACTCAAAGATTTCAGT 59.463 47.619 10.83 0.00 0.00 3.41
2094 2182 1.464687 CGGCGCACTCAAAGATTTCAG 60.465 52.381 10.83 0.00 0.00 3.02
2095 2183 0.516877 CGGCGCACTCAAAGATTTCA 59.483 50.000 10.83 0.00 0.00 2.69
2096 2184 0.517316 ACGGCGCACTCAAAGATTTC 59.483 50.000 10.83 0.00 0.00 2.17
2097 2185 0.238289 CACGGCGCACTCAAAGATTT 59.762 50.000 10.83 0.00 0.00 2.17
2098 2186 0.884704 ACACGGCGCACTCAAAGATT 60.885 50.000 10.83 0.00 0.00 2.40
2205 2293 3.776731 TCCATCTAGAAACCCCAGAGA 57.223 47.619 0.00 0.00 0.00 3.10
2249 2337 3.365767 GCACTGAATCTCTCTGCAAAACC 60.366 47.826 0.00 0.00 0.00 3.27
2286 2374 9.431887 CTATAATTGCATACCCAACGTATAACT 57.568 33.333 0.00 0.00 35.35 2.24
2287 2375 9.426837 TCTATAATTGCATACCCAACGTATAAC 57.573 33.333 0.00 0.00 35.35 1.89
2288 2376 9.426837 GTCTATAATTGCATACCCAACGTATAA 57.573 33.333 0.00 0.00 35.35 0.98
2291 2379 6.818233 TGTCTATAATTGCATACCCAACGTA 58.182 36.000 0.00 0.00 0.00 3.57
2292 2380 5.676552 TGTCTATAATTGCATACCCAACGT 58.323 37.500 0.00 0.00 0.00 3.99
2293 2381 6.801539 ATGTCTATAATTGCATACCCAACG 57.198 37.500 0.00 0.00 0.00 4.10
2321 2409 0.391228 TAGTCCGCTGTGAAGCAACA 59.609 50.000 0.00 0.00 34.41 3.33
2353 2441 6.563422 TCCTGATTTATCAAAGAAATTGGCG 58.437 36.000 0.00 0.00 39.62 5.69
2437 2525 2.008242 TGGGGCTAACAAAATGCAGT 57.992 45.000 0.00 0.00 0.00 4.40
2442 2530 4.340950 CGATAACCATGGGGCTAACAAAAT 59.659 41.667 18.09 0.00 37.90 1.82
2452 2540 3.492102 AACAGATCGATAACCATGGGG 57.508 47.619 18.09 0.00 41.29 4.96
2453 2541 4.199310 ACAAACAGATCGATAACCATGGG 58.801 43.478 18.09 0.00 0.00 4.00
2454 2542 5.818136 AACAAACAGATCGATAACCATGG 57.182 39.130 11.19 11.19 0.00 3.66
2455 2543 7.539712 ACTAACAAACAGATCGATAACCATG 57.460 36.000 0.00 0.00 0.00 3.66
2456 2544 9.832445 AATACTAACAAACAGATCGATAACCAT 57.168 29.630 0.00 0.00 0.00 3.55
2457 2545 9.661563 AAATACTAACAAACAGATCGATAACCA 57.338 29.630 0.00 0.00 0.00 3.67
2463 2551 8.928733 GGTACAAAATACTAACAAACAGATCGA 58.071 33.333 0.00 0.00 0.00 3.59
2464 2552 8.714179 TGGTACAAAATACTAACAAACAGATCG 58.286 33.333 0.00 0.00 31.92 3.69
2487 2575 9.261180 CAGTCAAACGATATATATTCACTTGGT 57.739 33.333 0.00 0.00 0.00 3.67
2488 2576 9.261180 ACAGTCAAACGATATATATTCACTTGG 57.739 33.333 0.00 0.00 0.00 3.61
2491 2579 9.627395 GCTACAGTCAAACGATATATATTCACT 57.373 33.333 0.00 0.00 0.00 3.41
2492 2580 9.406828 TGCTACAGTCAAACGATATATATTCAC 57.593 33.333 0.00 0.00 0.00 3.18
2493 2581 9.974980 TTGCTACAGTCAAACGATATATATTCA 57.025 29.630 0.00 0.00 0.00 2.57
2495 2583 9.982651 ACTTGCTACAGTCAAACGATATATATT 57.017 29.630 0.00 0.00 0.00 1.28
2500 2588 9.982651 AATATACTTGCTACAGTCAAACGATAT 57.017 29.630 0.00 0.00 0.00 1.63
2501 2589 9.811995 AAATATACTTGCTACAGTCAAACGATA 57.188 29.630 0.00 0.00 0.00 2.92
2502 2590 8.718102 AAATATACTTGCTACAGTCAAACGAT 57.282 30.769 0.00 0.00 0.00 3.73
2503 2591 9.811995 ATAAATATACTTGCTACAGTCAAACGA 57.188 29.630 0.00 0.00 0.00 3.85
2540 2628 9.118236 GCACACTTGTTGATAAACTAAAGATTC 57.882 33.333 1.00 0.00 0.00 2.52
2541 2629 8.082242 GGCACACTTGTTGATAAACTAAAGATT 58.918 33.333 1.00 0.00 0.00 2.40
2542 2630 7.448469 AGGCACACTTGTTGATAAACTAAAGAT 59.552 33.333 1.00 0.00 0.00 2.40
2543 2631 6.770785 AGGCACACTTGTTGATAAACTAAAGA 59.229 34.615 1.00 0.00 0.00 2.52
2544 2632 6.857964 CAGGCACACTTGTTGATAAACTAAAG 59.142 38.462 0.00 0.00 0.00 1.85
2545 2633 6.544197 TCAGGCACACTTGTTGATAAACTAAA 59.456 34.615 0.00 0.00 0.00 1.85
2546 2634 6.058833 TCAGGCACACTTGTTGATAAACTAA 58.941 36.000 0.00 0.00 0.00 2.24
2547 2635 5.616270 TCAGGCACACTTGTTGATAAACTA 58.384 37.500 0.00 0.00 0.00 2.24
2548 2636 4.460263 TCAGGCACACTTGTTGATAAACT 58.540 39.130 0.00 0.00 0.00 2.66
2549 2637 4.829064 TCAGGCACACTTGTTGATAAAC 57.171 40.909 0.00 0.00 0.00 2.01
2550 2638 5.048083 GGATTCAGGCACACTTGTTGATAAA 60.048 40.000 0.00 0.00 0.00 1.40
2551 2639 4.458989 GGATTCAGGCACACTTGTTGATAA 59.541 41.667 0.00 0.00 0.00 1.75
2552 2640 4.009675 GGATTCAGGCACACTTGTTGATA 58.990 43.478 0.00 0.00 0.00 2.15
2553 2641 2.821969 GGATTCAGGCACACTTGTTGAT 59.178 45.455 0.00 0.00 0.00 2.57
2554 2642 2.229792 GGATTCAGGCACACTTGTTGA 58.770 47.619 0.00 0.00 0.00 3.18
2555 2643 1.955778 TGGATTCAGGCACACTTGTTG 59.044 47.619 0.00 0.00 0.00 3.33
2556 2644 2.363306 TGGATTCAGGCACACTTGTT 57.637 45.000 0.00 0.00 0.00 2.83
2557 2645 2.592102 ATGGATTCAGGCACACTTGT 57.408 45.000 0.00 0.00 0.00 3.16
2558 2646 3.614092 AGTATGGATTCAGGCACACTTG 58.386 45.455 0.00 0.00 0.00 3.16
2559 2647 4.012374 CAAGTATGGATTCAGGCACACTT 58.988 43.478 0.00 0.00 0.00 3.16
2560 2648 3.614092 CAAGTATGGATTCAGGCACACT 58.386 45.455 0.00 0.00 0.00 3.55


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

AutoCloner maintained by Alex Coulton.