Multiple sequence alignment - TraesCS3A01G497200

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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 TraesCS3A01G497200 chr3A 100.000 2543 0 0 1 2543 723179687 723182229 0.000000e+00 4697.0
1 TraesCS3A01G497200 chrUn 91.088 1986 76 33 1 1919 45620728 45618777 0.000000e+00 2593.0
2 TraesCS3A01G497200 chrUn 89.234 548 26 12 1953 2486 45618796 45618268 0.000000e+00 654.0
3 TraesCS3A01G497200 chr3B 88.515 1959 100 45 1 1915 794280817 794282694 0.000000e+00 2255.0
4 TraesCS3A01G497200 chr3B 92.308 39 1 1 1917 1953 133800375 133800413 1.000000e-03 54.7
5 TraesCS3A01G497200 chr3B 92.308 39 2 1 1917 1954 780332110 780332148 1.000000e-03 54.7
6 TraesCS3A01G497200 chr7D 74.731 186 46 1 8 192 46960938 46961123 5.830000e-12 82.4
7 TraesCS3A01G497200 chr2D 89.583 48 5 0 1917 1964 430997675 430997628 7.600000e-06 62.1
8 TraesCS3A01G497200 chr2D 92.500 40 1 1 1917 1954 29668940 29668979 3.530000e-04 56.5
9 TraesCS3A01G497200 chr7B 92.500 40 0 1 1917 1953 1144728 1144767 1.000000e-03 54.7


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 TraesCS3A01G497200 chr3A 723179687 723182229 2542 False 4697.0 4697 100.000 1 2543 1 chr3A.!!$F1 2542
1 TraesCS3A01G497200 chrUn 45618268 45620728 2460 True 1623.5 2593 90.161 1 2486 2 chrUn.!!$R1 2485
2 TraesCS3A01G497200 chr3B 794280817 794282694 1877 False 2255.0 2255 88.515 1 1915 1 chr3B.!!$F3 1914

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
998 1046 0.178843 ACCAACCCCTCCCACATAGT 60.179 55.0 0.0 0.0 0.0 2.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2511 2611 0.104304 AAGATCGACACATACGGGCC 59.896 55.0 0.0 0.0 0.0 5.8 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
21 22 2.614057 GCTTGTCAGTGTGCTTGTAACT 59.386 45.455 0.00 0.00 0.00 2.24
54 55 2.183555 GGAGGTTACCAGCCGACG 59.816 66.667 3.51 0.00 0.00 5.12
85 86 7.872881 TGCATGTAACGAAACAACCTAAATTA 58.127 30.769 0.00 0.00 32.02 1.40
164 166 2.026449 GGCTAGAGGATATGCAGGCAAT 60.026 50.000 0.00 0.00 0.00 3.56
173 175 4.381825 GGATATGCAGGCAATCAAACAACA 60.382 41.667 0.00 0.00 0.00 3.33
181 183 3.615496 GGCAATCAAACAACATGCAGATC 59.385 43.478 0.00 0.00 38.73 2.75
192 194 8.659925 AACAACATGCAGATCATTGTTTTTAA 57.340 26.923 9.48 0.00 34.26 1.52
197 199 9.013229 ACATGCAGATCATTGTTTTTAAGACTA 57.987 29.630 0.00 0.00 31.79 2.59
215 217 7.906199 AAGACTATATTGACTCAACTAGGCT 57.094 36.000 10.79 10.79 34.08 4.58
219 221 8.256356 ACTATATTGACTCAACTAGGCTCAAT 57.744 34.615 0.00 0.00 36.01 2.57
221 223 7.798596 ATATTGACTCAACTAGGCTCAATTG 57.201 36.000 0.00 0.00 34.28 2.32
223 225 3.582647 TGACTCAACTAGGCTCAATTGGA 59.417 43.478 5.42 0.00 32.57 3.53
387 416 3.267483 GCTTTACGCATTTCACTCCCTA 58.733 45.455 0.00 0.00 38.92 3.53
417 446 1.135083 CGGTTGAGTGATTAGCGAGGT 60.135 52.381 0.00 0.00 34.99 3.85
424 453 0.981183 TGATTAGCGAGGTGGGTTGT 59.019 50.000 0.00 0.00 0.00 3.32
547 581 2.890311 CTGTGCCCATGTGTAAAAAGGA 59.110 45.455 0.00 0.00 0.00 3.36
730 767 0.459489 CTTCCCTTCTCCTCTGCTCG 59.541 60.000 0.00 0.00 0.00 5.03
894 942 1.134521 CGCTGCCCACTGGATTAAGTA 60.135 52.381 0.00 0.00 0.00 2.24
895 943 2.289565 GCTGCCCACTGGATTAAGTAC 58.710 52.381 0.00 0.00 0.00 2.73
896 944 2.919228 CTGCCCACTGGATTAAGTACC 58.081 52.381 0.00 0.00 0.00 3.34
928 976 0.315251 CCGAGACAGTCAGCTTCACA 59.685 55.000 2.66 0.00 0.00 3.58
929 977 1.668337 CCGAGACAGTCAGCTTCACAG 60.668 57.143 2.66 0.00 0.00 3.66
942 990 2.289072 GCTTCACAGCCTTCACTACTCA 60.289 50.000 0.00 0.00 40.61 3.41
943 991 3.321497 CTTCACAGCCTTCACTACTCAC 58.679 50.000 0.00 0.00 0.00 3.51
944 992 2.598565 TCACAGCCTTCACTACTCACT 58.401 47.619 0.00 0.00 0.00 3.41
945 993 2.558795 TCACAGCCTTCACTACTCACTC 59.441 50.000 0.00 0.00 0.00 3.51
946 994 2.297315 CACAGCCTTCACTACTCACTCA 59.703 50.000 0.00 0.00 0.00 3.41
947 995 2.297597 ACAGCCTTCACTACTCACTCAC 59.702 50.000 0.00 0.00 0.00 3.51
948 996 2.560542 CAGCCTTCACTACTCACTCACT 59.439 50.000 0.00 0.00 0.00 3.41
949 997 2.823154 AGCCTTCACTACTCACTCACTC 59.177 50.000 0.00 0.00 0.00 3.51
950 998 2.558795 GCCTTCACTACTCACTCACTCA 59.441 50.000 0.00 0.00 0.00 3.41
951 999 3.005897 GCCTTCACTACTCACTCACTCAA 59.994 47.826 0.00 0.00 0.00 3.02
952 1000 4.804108 CCTTCACTACTCACTCACTCAAG 58.196 47.826 0.00 0.00 0.00 3.02
953 1001 3.924918 TCACTACTCACTCACTCAAGC 57.075 47.619 0.00 0.00 0.00 4.01
954 1002 3.491342 TCACTACTCACTCACTCAAGCT 58.509 45.455 0.00 0.00 0.00 3.74
955 1003 3.504134 TCACTACTCACTCACTCAAGCTC 59.496 47.826 0.00 0.00 0.00 4.09
956 1004 2.823154 ACTACTCACTCACTCAAGCTCC 59.177 50.000 0.00 0.00 0.00 4.70
996 1044 0.178858 TCACCAACCCCTCCCACATA 60.179 55.000 0.00 0.00 0.00 2.29
998 1046 0.178843 ACCAACCCCTCCCACATAGT 60.179 55.000 0.00 0.00 0.00 2.12
1026 1074 3.706373 CACCCACCGGTCCTCCTG 61.706 72.222 2.59 0.00 42.04 3.86
1029 1077 2.363795 CCACCGGTCCTCCTGCTA 60.364 66.667 2.59 0.00 0.00 3.49
1206 1254 4.371417 TACCCGTCGCCACCTCCT 62.371 66.667 0.00 0.00 0.00 3.69
1374 1428 0.041982 GAGGACAAGGAGGAGGAGGT 59.958 60.000 0.00 0.00 0.00 3.85
1419 1473 3.708544 CCGCCCAACCCGTTCCTA 61.709 66.667 0.00 0.00 0.00 2.94
1517 1574 2.580867 GACGCTACTGCTGCTCGG 60.581 66.667 0.00 0.00 36.97 4.63
1561 1621 1.212229 GGAGGACGACGGTGAGAAC 59.788 63.158 0.00 0.00 0.00 3.01
1602 1662 2.125552 CGCGCTCAGTGGATCCAA 60.126 61.111 18.20 0.00 0.00 3.53
1719 1789 6.111382 TCCTCTCTGCTTCTGTGATTTATTG 58.889 40.000 0.00 0.00 0.00 1.90
1850 1937 2.346541 GCCAAAGGGAGGAAGCTGC 61.347 63.158 0.00 0.00 35.59 5.25
1915 2002 5.178061 TGTGCATCATATGGATCCGATTAC 58.822 41.667 7.39 6.04 32.57 1.89
1916 2003 5.178061 GTGCATCATATGGATCCGATTACA 58.822 41.667 7.39 2.07 32.57 2.41
1917 2004 5.819379 GTGCATCATATGGATCCGATTACAT 59.181 40.000 7.39 0.00 32.57 2.29
1918 2005 5.818857 TGCATCATATGGATCCGATTACATG 59.181 40.000 7.39 6.19 32.57 3.21
1919 2006 5.277683 GCATCATATGGATCCGATTACATGC 60.278 44.000 7.39 12.11 32.57 4.06
1920 2007 5.419239 TCATATGGATCCGATTACATGCA 57.581 39.130 7.39 0.00 0.00 3.96
1921 2008 5.422145 TCATATGGATCCGATTACATGCAG 58.578 41.667 7.39 0.00 0.00 4.41
1922 2009 5.187576 TCATATGGATCCGATTACATGCAGA 59.812 40.000 7.39 0.00 0.00 4.26
1923 2010 3.391506 TGGATCCGATTACATGCAGAG 57.608 47.619 7.39 0.00 0.00 3.35
1924 2011 2.037641 TGGATCCGATTACATGCAGAGG 59.962 50.000 7.39 0.00 0.00 3.69
1925 2012 2.072298 GATCCGATTACATGCAGAGGC 58.928 52.381 0.00 0.00 41.68 4.70
1926 2013 0.106708 TCCGATTACATGCAGAGGCC 59.893 55.000 0.00 0.00 40.13 5.19
1927 2014 1.224069 CCGATTACATGCAGAGGCCG 61.224 60.000 0.00 0.00 40.13 6.13
1928 2015 1.224069 CGATTACATGCAGAGGCCGG 61.224 60.000 0.00 0.00 40.13 6.13
1929 2016 0.886490 GATTACATGCAGAGGCCGGG 60.886 60.000 2.18 0.00 40.13 5.73
1930 2017 2.343475 ATTACATGCAGAGGCCGGGG 62.343 60.000 2.18 0.00 40.13 5.73
1936 2023 2.445845 CAGAGGCCGGGGGTCATA 60.446 66.667 2.18 0.00 0.00 2.15
1937 2024 2.446036 AGAGGCCGGGGGTCATAC 60.446 66.667 2.18 0.00 0.00 2.39
1938 2025 2.446036 GAGGCCGGGGGTCATACT 60.446 66.667 2.18 0.00 0.00 2.12
1939 2026 2.446036 AGGCCGGGGGTCATACTC 60.446 66.667 2.18 0.00 0.00 2.59
1940 2027 3.557290 GGCCGGGGGTCATACTCC 61.557 72.222 2.18 0.00 38.29 3.85
1941 2028 2.446036 GCCGGGGGTCATACTCCT 60.446 66.667 2.18 0.00 39.27 3.69
1942 2029 2.070650 GCCGGGGGTCATACTCCTT 61.071 63.158 2.18 0.00 39.27 3.36
1943 2030 1.632965 GCCGGGGGTCATACTCCTTT 61.633 60.000 2.18 0.00 39.27 3.11
1944 2031 1.797320 CCGGGGGTCATACTCCTTTA 58.203 55.000 0.00 0.00 39.27 1.85
1945 2032 2.121129 CCGGGGGTCATACTCCTTTAA 58.879 52.381 0.00 0.00 39.27 1.52
1946 2033 2.506644 CCGGGGGTCATACTCCTTTAAA 59.493 50.000 0.00 0.00 39.27 1.52
1947 2034 3.054213 CCGGGGGTCATACTCCTTTAAAA 60.054 47.826 0.00 0.00 39.27 1.52
1948 2035 4.568169 CCGGGGGTCATACTCCTTTAAAAA 60.568 45.833 0.00 0.00 39.27 1.94
1983 2070 4.508971 CGATTACGATGTCATTGTTCTGC 58.491 43.478 11.04 0.00 42.66 4.26
2080 2170 1.268079 GCAGTTCTTCAGTTCTTGGGC 59.732 52.381 0.00 0.00 0.00 5.36
2131 2221 4.916041 ATCTCCTGACATTGGTGAAGAA 57.084 40.909 0.00 0.00 31.96 2.52
2154 2244 3.198409 ACTGTGAGCTGTGAATGTGAA 57.802 42.857 0.00 0.00 0.00 3.18
2155 2245 3.748083 ACTGTGAGCTGTGAATGTGAAT 58.252 40.909 0.00 0.00 0.00 2.57
2156 2246 3.501062 ACTGTGAGCTGTGAATGTGAATG 59.499 43.478 0.00 0.00 0.00 2.67
2157 2247 3.479489 TGTGAGCTGTGAATGTGAATGT 58.521 40.909 0.00 0.00 0.00 2.71
2158 2248 3.251487 TGTGAGCTGTGAATGTGAATGTG 59.749 43.478 0.00 0.00 0.00 3.21
2159 2249 3.499537 GTGAGCTGTGAATGTGAATGTGA 59.500 43.478 0.00 0.00 0.00 3.58
2160 2250 4.023792 GTGAGCTGTGAATGTGAATGTGAA 60.024 41.667 0.00 0.00 0.00 3.18
2161 2251 4.763279 TGAGCTGTGAATGTGAATGTGAAT 59.237 37.500 0.00 0.00 0.00 2.57
2169 2259 7.382759 TGTGAATGTGAATGTGAATGATGTTTG 59.617 33.333 0.00 0.00 0.00 2.93
2235 2325 6.536941 TGCAATACTAGCATTGAACGTCATTA 59.463 34.615 18.18 0.00 38.01 1.90
2244 2334 6.863126 AGCATTGAACGTCATTAAAGGAAAAG 59.137 34.615 0.00 0.00 0.00 2.27
2278 2377 2.414559 CGATGGACTTGGTCAAACATGC 60.415 50.000 0.00 0.00 33.68 4.06
2279 2378 2.064434 TGGACTTGGTCAAACATGCA 57.936 45.000 0.00 0.00 33.68 3.96
2280 2379 2.596346 TGGACTTGGTCAAACATGCAT 58.404 42.857 0.00 0.00 33.68 3.96
2281 2380 2.296752 TGGACTTGGTCAAACATGCATG 59.703 45.455 25.09 25.09 33.68 4.06
2282 2381 2.353011 GGACTTGGTCAAACATGCATGG 60.353 50.000 29.41 12.93 33.68 3.66
2283 2382 2.297033 GACTTGGTCAAACATGCATGGT 59.703 45.455 29.41 22.35 32.09 3.55
2284 2383 2.036217 ACTTGGTCAAACATGCATGGTG 59.964 45.455 29.41 24.63 0.00 4.17
2285 2384 0.317799 TGGTCAAACATGCATGGTGC 59.682 50.000 29.41 19.79 45.29 5.01
2286 2385 0.604578 GGTCAAACATGCATGGTGCT 59.395 50.000 29.41 7.43 45.31 4.40
2287 2386 1.403249 GGTCAAACATGCATGGTGCTC 60.403 52.381 29.41 19.66 45.31 4.26
2288 2387 0.889994 TCAAACATGCATGGTGCTCC 59.110 50.000 29.41 0.00 45.31 4.70
2309 2408 1.518903 GCTCCTGCAGTTGGGAACAC 61.519 60.000 13.81 0.00 38.74 3.32
2311 2410 1.903404 CCTGCAGTTGGGAACACCC 60.903 63.158 13.81 0.00 42.67 4.61
2312 2411 1.151450 CTGCAGTTGGGAACACCCT 59.849 57.895 5.25 0.00 43.80 4.34
2313 2412 1.152777 TGCAGTTGGGAACACCCTG 60.153 57.895 6.85 0.00 43.80 4.45
2314 2413 1.150536 GCAGTTGGGAACACCCTGA 59.849 57.895 6.85 0.00 43.80 3.86
2315 2414 0.890996 GCAGTTGGGAACACCCTGAG 60.891 60.000 6.85 0.00 43.80 3.35
2317 2416 1.133792 CAGTTGGGAACACCCTGAGTT 60.134 52.381 6.85 0.00 43.80 3.01
2335 2435 4.142578 TGAGTTGTTCAGAGTCTCTATCGC 60.143 45.833 0.94 0.00 0.00 4.58
2338 2438 3.879998 TGTTCAGAGTCTCTATCGCTCT 58.120 45.455 0.94 0.00 39.89 4.09
2346 2446 2.477375 GTCTCTATCGCTCTCTGGTACG 59.523 54.545 0.00 0.00 0.00 3.67
2347 2447 1.195900 CTCTATCGCTCTCTGGTACGC 59.804 57.143 0.00 0.00 0.00 4.42
2362 2462 0.948678 TACGCAAACAAGAACCTGCC 59.051 50.000 0.00 0.00 0.00 4.85
2379 2479 2.742372 CGCTACCGTGCAGGCTTT 60.742 61.111 0.00 0.00 46.52 3.51
2414 2514 6.081049 TCTTGTACAAACAAAACAACACTCG 58.919 36.000 10.03 0.00 44.79 4.18
2440 2540 0.727970 GAGTCTCTCTCGCGCTAACA 59.272 55.000 5.56 0.00 33.25 2.41
2454 2554 2.031245 CGCTAACAAAGGCACAACATGA 60.031 45.455 0.00 0.00 0.00 3.07
2455 2555 3.366273 CGCTAACAAAGGCACAACATGAT 60.366 43.478 0.00 0.00 0.00 2.45
2458 2558 3.665745 ACAAAGGCACAACATGATTCC 57.334 42.857 0.00 0.00 0.00 3.01
2468 2568 3.191162 ACAACATGATTCCGGTGAACATG 59.809 43.478 20.55 20.55 41.11 3.21
2488 2588 3.185246 GTCATGGTTCCGATGACATCT 57.815 47.619 13.45 0.00 46.10 2.90
2489 2589 3.126831 GTCATGGTTCCGATGACATCTC 58.873 50.000 13.45 1.98 46.10 2.75
2490 2590 3.033909 TCATGGTTCCGATGACATCTCT 58.966 45.455 13.45 0.00 0.00 3.10
2491 2591 3.068732 TCATGGTTCCGATGACATCTCTC 59.931 47.826 13.45 1.97 0.00 3.20
2492 2592 2.456577 TGGTTCCGATGACATCTCTCA 58.543 47.619 13.45 2.62 0.00 3.27
2493 2593 2.166459 TGGTTCCGATGACATCTCTCAC 59.834 50.000 13.45 4.97 0.00 3.51
2494 2594 2.482142 GGTTCCGATGACATCTCTCACC 60.482 54.545 13.45 9.75 0.00 4.02
2495 2595 1.025041 TCCGATGACATCTCTCACCG 58.975 55.000 13.45 0.00 0.00 4.94
2496 2596 0.741326 CCGATGACATCTCTCACCGT 59.259 55.000 13.45 0.00 0.00 4.83
2497 2597 1.534805 CCGATGACATCTCTCACCGTG 60.535 57.143 13.45 0.00 0.00 4.94
2498 2598 1.401905 CGATGACATCTCTCACCGTGA 59.598 52.381 13.45 0.29 0.00 4.35
2499 2599 2.033927 CGATGACATCTCTCACCGTGAT 59.966 50.000 13.45 0.00 0.00 3.06
2500 2600 3.251004 CGATGACATCTCTCACCGTGATA 59.749 47.826 13.45 0.00 0.00 2.15
2501 2601 4.083057 CGATGACATCTCTCACCGTGATAT 60.083 45.833 13.45 0.00 0.00 1.63
2502 2602 4.574599 TGACATCTCTCACCGTGATATG 57.425 45.455 0.62 8.93 0.00 1.78
2503 2603 3.319122 TGACATCTCTCACCGTGATATGG 59.681 47.826 16.78 2.63 0.00 2.74
2504 2604 3.300388 ACATCTCTCACCGTGATATGGT 58.700 45.455 16.78 5.77 38.21 3.55
2509 2609 3.305314 ACCGTGATATGGTGGCGT 58.695 55.556 0.00 0.00 35.83 5.68
2510 2610 1.600107 ACCGTGATATGGTGGCGTT 59.400 52.632 0.00 0.00 35.83 4.84
2511 2611 0.742990 ACCGTGATATGGTGGCGTTG 60.743 55.000 0.00 0.00 35.83 4.10
2512 2612 1.436195 CCGTGATATGGTGGCGTTGG 61.436 60.000 0.00 0.00 0.00 3.77
2513 2613 1.727467 GTGATATGGTGGCGTTGGC 59.273 57.895 0.00 0.00 38.90 4.52
2523 2623 2.744709 GCGTTGGCCCGTATGTGT 60.745 61.111 0.00 0.00 0.00 3.72
2524 2624 2.746803 GCGTTGGCCCGTATGTGTC 61.747 63.158 0.00 0.00 0.00 3.67
2525 2625 2.449525 CGTTGGCCCGTATGTGTCG 61.450 63.158 0.00 0.00 0.00 4.35
2526 2626 1.079681 GTTGGCCCGTATGTGTCGA 60.080 57.895 0.00 0.00 0.00 4.20
2527 2627 0.461339 GTTGGCCCGTATGTGTCGAT 60.461 55.000 0.00 0.00 0.00 3.59
2528 2628 0.179094 TTGGCCCGTATGTGTCGATC 60.179 55.000 0.00 0.00 0.00 3.69
2529 2629 1.040893 TGGCCCGTATGTGTCGATCT 61.041 55.000 0.00 0.00 0.00 2.75
2530 2630 0.104304 GGCCCGTATGTGTCGATCTT 59.896 55.000 0.00 0.00 0.00 2.40
2531 2631 1.209128 GCCCGTATGTGTCGATCTTG 58.791 55.000 0.00 0.00 0.00 3.02
2532 2632 1.470979 GCCCGTATGTGTCGATCTTGT 60.471 52.381 0.00 0.00 0.00 3.16
2533 2633 2.888594 CCCGTATGTGTCGATCTTGTT 58.111 47.619 0.00 0.00 0.00 2.83
2534 2634 3.259064 CCCGTATGTGTCGATCTTGTTT 58.741 45.455 0.00 0.00 0.00 2.83
2535 2635 4.426416 CCCGTATGTGTCGATCTTGTTTA 58.574 43.478 0.00 0.00 0.00 2.01
2536 2636 4.865925 CCCGTATGTGTCGATCTTGTTTAA 59.134 41.667 0.00 0.00 0.00 1.52
2537 2637 5.220340 CCCGTATGTGTCGATCTTGTTTAAC 60.220 44.000 0.00 0.00 0.00 2.01
2538 2638 5.346551 CCGTATGTGTCGATCTTGTTTAACA 59.653 40.000 0.00 0.00 0.00 2.41
2539 2639 6.035650 CCGTATGTGTCGATCTTGTTTAACAT 59.964 38.462 0.00 0.00 0.00 2.71
2540 2640 6.894517 CGTATGTGTCGATCTTGTTTAACATG 59.105 38.462 0.00 1.31 0.00 3.21
2541 2641 6.801539 ATGTGTCGATCTTGTTTAACATGT 57.198 33.333 10.12 0.00 0.00 3.21
2542 2642 7.899178 ATGTGTCGATCTTGTTTAACATGTA 57.101 32.000 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 3.466881 CCTCGTGGAGGTGGTCAA 58.533 61.111 0.00 0.00 44.25 3.18
85 86 7.341445 TGTGAGCTTGTTTAGGTAAAAACAT 57.659 32.000 3.26 0.00 45.91 2.71
105 106 5.182950 ACAAAGTCATGTTGTTCAGTTGTGA 59.817 36.000 0.00 0.00 35.70 3.58
164 166 5.456548 ACAATGATCTGCATGTTGTTTGA 57.543 34.783 0.00 0.00 37.28 2.69
192 194 7.063593 TGAGCCTAGTTGAGTCAATATAGTCT 58.936 38.462 9.18 9.64 0.00 3.24
197 199 6.769822 CCAATTGAGCCTAGTTGAGTCAATAT 59.230 38.462 9.18 3.89 36.96 1.28
215 217 6.171213 TGCATTGCATATTTGTTCCAATTGA 58.829 32.000 7.38 0.00 31.71 2.57
219 221 4.505808 CCTGCATTGCATATTTGTTCCAA 58.494 39.130 12.53 0.00 38.13 3.53
221 223 2.867975 GCCTGCATTGCATATTTGTTCC 59.132 45.455 12.53 0.00 38.13 3.62
223 225 3.613494 TGCCTGCATTGCATATTTGTT 57.387 38.095 12.53 0.00 38.13 2.83
343 347 2.621055 ACCGCAAAAGTGTGCTGATTAA 59.379 40.909 0.00 0.00 42.62 1.40
417 446 1.452289 CCACGGTGTTCACAACCCA 60.452 57.895 7.45 0.00 0.00 4.51
424 453 1.080093 GAGATCGCCACGGTGTTCA 60.080 57.895 7.45 0.00 0.00 3.18
547 581 1.611491 CCTTGGCGTTTTACACATGGT 59.389 47.619 0.00 0.00 0.00 3.55
895 943 4.715130 TCGGGGTGAGGGGAGTGG 62.715 72.222 0.00 0.00 0.00 4.00
896 944 3.077556 CTCGGGGTGAGGGGAGTG 61.078 72.222 0.00 0.00 41.29 3.51
928 976 2.823154 GAGTGAGTGAGTAGTGAAGGCT 59.177 50.000 0.00 0.00 0.00 4.58
929 977 2.558795 TGAGTGAGTGAGTAGTGAAGGC 59.441 50.000 0.00 0.00 0.00 4.35
934 982 3.366883 GGAGCTTGAGTGAGTGAGTAGTG 60.367 52.174 0.00 0.00 0.00 2.74
935 983 2.823154 GGAGCTTGAGTGAGTGAGTAGT 59.177 50.000 0.00 0.00 0.00 2.73
936 984 2.165437 GGGAGCTTGAGTGAGTGAGTAG 59.835 54.545 0.00 0.00 0.00 2.57
937 985 2.171840 GGGAGCTTGAGTGAGTGAGTA 58.828 52.381 0.00 0.00 0.00 2.59
938 986 0.972883 GGGAGCTTGAGTGAGTGAGT 59.027 55.000 0.00 0.00 0.00 3.41
942 990 0.972883 GAGTGGGAGCTTGAGTGAGT 59.027 55.000 0.00 0.00 0.00 3.41
943 991 0.248843 GGAGTGGGAGCTTGAGTGAG 59.751 60.000 0.00 0.00 0.00 3.51
944 992 1.194781 GGGAGTGGGAGCTTGAGTGA 61.195 60.000 0.00 0.00 0.00 3.41
945 993 1.298014 GGGAGTGGGAGCTTGAGTG 59.702 63.158 0.00 0.00 0.00 3.51
946 994 1.152030 TGGGAGTGGGAGCTTGAGT 60.152 57.895 0.00 0.00 0.00 3.41
947 995 1.197430 AGTGGGAGTGGGAGCTTGAG 61.197 60.000 0.00 0.00 0.00 3.02
948 996 1.152030 AGTGGGAGTGGGAGCTTGA 60.152 57.895 0.00 0.00 0.00 3.02
949 997 1.298014 GAGTGGGAGTGGGAGCTTG 59.702 63.158 0.00 0.00 0.00 4.01
950 998 1.920835 GGAGTGGGAGTGGGAGCTT 60.921 63.158 0.00 0.00 0.00 3.74
951 999 2.284995 GGAGTGGGAGTGGGAGCT 60.285 66.667 0.00 0.00 0.00 4.09
952 1000 3.403558 GGGAGTGGGAGTGGGAGC 61.404 72.222 0.00 0.00 0.00 4.70
953 1001 1.307343 ATGGGAGTGGGAGTGGGAG 60.307 63.158 0.00 0.00 0.00 4.30
954 1002 1.306997 GATGGGAGTGGGAGTGGGA 60.307 63.158 0.00 0.00 0.00 4.37
955 1003 2.378634 GGATGGGAGTGGGAGTGGG 61.379 68.421 0.00 0.00 0.00 4.61
956 1004 2.378634 GGGATGGGAGTGGGAGTGG 61.379 68.421 0.00 0.00 0.00 4.00
996 1044 3.017581 GGGTGGGGAGCCATGACT 61.018 66.667 0.00 0.00 0.00 3.41
998 1046 3.338250 GTGGGTGGGGAGCCATGA 61.338 66.667 0.00 0.00 0.00 3.07
1350 1401 0.251634 CTCCTCCTTGTCCTCCTTGC 59.748 60.000 0.00 0.00 0.00 4.01
1419 1473 3.863538 AGTAGTAGAAGGGGAAGTAGGGT 59.136 47.826 0.00 0.00 0.00 4.34
1506 1563 3.768922 GAGAGCCCGAGCAGCAGT 61.769 66.667 0.00 0.00 43.56 4.40
1530 1587 2.046507 CCTCCTCACCACAGCAGC 60.047 66.667 0.00 0.00 0.00 5.25
1561 1621 2.050895 CGGCAGATCTACCTCGCG 60.051 66.667 10.36 0.00 0.00 5.87
1719 1789 6.600822 TCCTATATAGTTCTATACCGGCACAC 59.399 42.308 0.00 0.00 0.00 3.82
1850 1937 6.404708 TCAACCAATCAAAGAGAGAGATGAG 58.595 40.000 0.00 0.00 0.00 2.90
1919 2006 2.445845 TATGACCCCCGGCCTCTG 60.446 66.667 0.00 0.00 0.00 3.35
1920 2007 2.446036 GTATGACCCCCGGCCTCT 60.446 66.667 0.00 0.00 0.00 3.69
1921 2008 2.446036 AGTATGACCCCCGGCCTC 60.446 66.667 0.00 0.00 0.00 4.70
1922 2009 2.446036 GAGTATGACCCCCGGCCT 60.446 66.667 0.00 0.00 0.00 5.19
1923 2010 3.557290 GGAGTATGACCCCCGGCC 61.557 72.222 0.00 0.00 0.00 6.13
1924 2011 1.632965 AAAGGAGTATGACCCCCGGC 61.633 60.000 0.00 0.00 0.00 6.13
1925 2012 1.797320 TAAAGGAGTATGACCCCCGG 58.203 55.000 0.00 0.00 0.00 5.73
1926 2013 3.918294 TTTAAAGGAGTATGACCCCCG 57.082 47.619 0.00 0.00 0.00 5.73
1948 2035 7.659799 TGACATCGTAATCGGATCCATATTTTT 59.340 33.333 13.41 0.00 37.69 1.94
1949 2036 7.158697 TGACATCGTAATCGGATCCATATTTT 58.841 34.615 13.41 0.00 37.69 1.82
1950 2037 6.697395 TGACATCGTAATCGGATCCATATTT 58.303 36.000 13.41 1.78 37.69 1.40
1951 2038 6.280855 TGACATCGTAATCGGATCCATATT 57.719 37.500 13.41 12.93 37.69 1.28
1952 2039 5.914898 TGACATCGTAATCGGATCCATAT 57.085 39.130 13.41 1.22 37.69 1.78
1953 2040 5.914898 ATGACATCGTAATCGGATCCATA 57.085 39.130 13.41 0.00 37.69 2.74
1954 2041 4.808414 ATGACATCGTAATCGGATCCAT 57.192 40.909 13.41 1.55 37.69 3.41
1955 2042 4.202212 ACAATGACATCGTAATCGGATCCA 60.202 41.667 13.41 0.00 37.69 3.41
1956 2043 4.307432 ACAATGACATCGTAATCGGATCC 58.693 43.478 0.00 0.00 37.69 3.36
1957 2044 5.692204 AGAACAATGACATCGTAATCGGATC 59.308 40.000 0.00 0.00 37.69 3.36
1958 2045 5.463392 CAGAACAATGACATCGTAATCGGAT 59.537 40.000 0.00 0.00 37.69 4.18
1959 2046 4.803613 CAGAACAATGACATCGTAATCGGA 59.196 41.667 0.00 0.00 37.69 4.55
1960 2047 4.550831 GCAGAACAATGACATCGTAATCGG 60.551 45.833 0.00 0.00 37.69 4.18
1961 2048 4.268644 AGCAGAACAATGACATCGTAATCG 59.731 41.667 0.00 0.00 38.55 3.34
1962 2049 5.291858 TCAGCAGAACAATGACATCGTAATC 59.708 40.000 0.00 0.00 0.00 1.75
1963 2050 5.063944 GTCAGCAGAACAATGACATCGTAAT 59.936 40.000 0.00 0.00 42.30 1.89
1964 2051 4.388773 GTCAGCAGAACAATGACATCGTAA 59.611 41.667 0.00 0.00 42.30 3.18
1965 2052 3.926527 GTCAGCAGAACAATGACATCGTA 59.073 43.478 0.00 0.00 42.30 3.43
1966 2053 2.738846 GTCAGCAGAACAATGACATCGT 59.261 45.455 0.00 0.00 42.30 3.73
1983 2070 4.024133 CACGGTGAGAGATAGAGATGTCAG 60.024 50.000 0.74 0.00 0.00 3.51
2027 2114 0.666374 AAACCTTAACCAGCACACGC 59.334 50.000 0.00 0.00 38.99 5.34
2080 2170 0.742281 AAGCTACGCTGCACATCCAG 60.742 55.000 0.00 0.00 39.62 3.86
2131 2221 3.947196 TCACATTCACAGCTCACAGTTTT 59.053 39.130 0.00 0.00 0.00 2.43
2169 2259 8.568794 AGCAAGAACAAGGTAAAAACTAATCTC 58.431 33.333 0.00 0.00 0.00 2.75
2256 2355 2.631160 TGTTTGACCAAGTCCATCGT 57.369 45.000 0.00 0.00 0.00 3.73
2303 2402 2.222027 CTGAACAACTCAGGGTGTTCC 58.778 52.381 19.71 6.85 46.89 3.62
2311 2410 5.568482 CGATAGAGACTCTGAACAACTCAG 58.432 45.833 15.55 0.00 46.71 3.35
2312 2411 4.142578 GCGATAGAGACTCTGAACAACTCA 60.143 45.833 15.55 0.00 39.76 3.41
2313 2412 4.095782 AGCGATAGAGACTCTGAACAACTC 59.904 45.833 15.55 0.00 39.76 3.01
2314 2413 4.013728 AGCGATAGAGACTCTGAACAACT 58.986 43.478 15.55 2.45 39.76 3.16
2315 2414 4.095782 AGAGCGATAGAGACTCTGAACAAC 59.904 45.833 15.55 3.31 39.29 3.32
2317 2416 3.874543 GAGAGCGATAGAGACTCTGAACA 59.125 47.826 15.55 0.00 40.80 3.18
2327 2427 1.195900 GCGTACCAGAGAGCGATAGAG 59.804 57.143 0.00 0.00 39.76 2.43
2331 2431 0.530744 TTTGCGTACCAGAGAGCGAT 59.469 50.000 0.00 0.00 0.00 4.58
2335 2435 3.026630 TCTTGTTTGCGTACCAGAGAG 57.973 47.619 0.00 0.00 0.00 3.20
2338 2438 2.158871 AGGTTCTTGTTTGCGTACCAGA 60.159 45.455 0.00 0.00 0.00 3.86
2346 2446 1.661509 GCGGCAGGTTCTTGTTTGC 60.662 57.895 0.00 0.00 35.87 3.68
2347 2447 1.069227 GTAGCGGCAGGTTCTTGTTTG 60.069 52.381 1.45 0.00 0.00 2.93
2362 2462 2.740714 GAAAGCCTGCACGGTAGCG 61.741 63.158 13.69 13.69 37.31 4.26
2379 2479 9.698309 TTTTGTTTGTACAAGATTCAGTTTTGA 57.302 25.926 8.56 0.00 44.56 2.69
2414 2514 1.062002 CGCGAGAGAGACTCTGAACTC 59.938 57.143 10.44 9.45 41.35 3.01
2440 2540 1.545582 CCGGAATCATGTTGTGCCTTT 59.454 47.619 0.00 0.00 0.00 3.11
2454 2554 2.290896 ACCATGACATGTTCACCGGAAT 60.291 45.455 9.46 0.00 36.92 3.01
2455 2555 1.073125 ACCATGACATGTTCACCGGAA 59.927 47.619 9.46 0.00 36.92 4.30
2458 2558 1.468520 GGAACCATGACATGTTCACCG 59.531 52.381 21.64 8.52 36.92 4.94
2492 2592 0.742990 CAACGCCACCATATCACGGT 60.743 55.000 0.00 0.00 37.16 4.83
2493 2593 1.436195 CCAACGCCACCATATCACGG 61.436 60.000 0.00 0.00 0.00 4.94
2494 2594 2.013807 CCAACGCCACCATATCACG 58.986 57.895 0.00 0.00 0.00 4.35
2495 2595 1.727467 GCCAACGCCACCATATCAC 59.273 57.895 0.00 0.00 0.00 3.06
2496 2596 4.234019 GCCAACGCCACCATATCA 57.766 55.556 0.00 0.00 0.00 2.15
2506 2606 2.744709 ACACATACGGGCCAACGC 60.745 61.111 4.39 0.00 37.37 4.84
2507 2607 2.449525 CGACACATACGGGCCAACG 61.450 63.158 4.39 1.48 40.31 4.10
2508 2608 0.461339 ATCGACACATACGGGCCAAC 60.461 55.000 4.39 0.00 0.00 3.77
2509 2609 0.179094 GATCGACACATACGGGCCAA 60.179 55.000 4.39 0.00 0.00 4.52
2510 2610 1.040893 AGATCGACACATACGGGCCA 61.041 55.000 4.39 0.00 0.00 5.36
2511 2611 0.104304 AAGATCGACACATACGGGCC 59.896 55.000 0.00 0.00 0.00 5.80
2512 2612 1.209128 CAAGATCGACACATACGGGC 58.791 55.000 0.00 0.00 0.00 6.13
2513 2613 2.579207 ACAAGATCGACACATACGGG 57.421 50.000 0.00 0.00 0.00 5.28
2514 2614 5.346551 TGTTAAACAAGATCGACACATACGG 59.653 40.000 0.00 0.00 0.00 4.02
2515 2615 6.384178 TGTTAAACAAGATCGACACATACG 57.616 37.500 0.00 0.00 0.00 3.06
2516 2616 7.739295 ACATGTTAAACAAGATCGACACATAC 58.261 34.615 0.00 0.00 0.00 2.39
2517 2617 7.899178 ACATGTTAAACAAGATCGACACATA 57.101 32.000 0.00 0.00 0.00 2.29
2518 2618 6.801539 ACATGTTAAACAAGATCGACACAT 57.198 33.333 0.00 0.00 0.00 3.21


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

AutoCloner maintained by Alex Coulton.