Multiple sequence alignment - TraesCS3D01G342800

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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 TraesCS3D01G342800 chr3D 100.000 2639 0 0 1 2639 455107943 455105305 0.000000e+00 4874.0
1 TraesCS3D01G342800 chr3D 95.714 70 3 0 2053 2122 341026240 341026309 2.150000e-21 113.0
2 TraesCS3D01G342800 chr3B 90.653 1990 134 27 27 1990 598469565 598467602 0.000000e+00 2597.0
3 TraesCS3D01G342800 chr3B 92.769 484 17 5 2121 2597 598467567 598467095 0.000000e+00 684.0
4 TraesCS3D01G342800 chr3B 87.755 98 12 0 138 235 598483942 598483845 5.970000e-22 115.0
5 TraesCS3D01G342800 chr3B 95.714 70 3 0 2053 2122 426527934 426527865 2.150000e-21 113.0
6 TraesCS3D01G342800 chr3B 91.892 74 2 1 2053 2122 21525470 21525397 1.670000e-17 100.0
7 TraesCS3D01G342800 chr3B 90.789 76 3 1 2051 2122 769594957 769594882 6.010000e-17 99.0
8 TraesCS3D01G342800 chr3A 92.588 1700 76 24 378 2054 597548359 597546687 0.000000e+00 2396.0
9 TraesCS3D01G342800 chr3A 93.908 476 20 5 2121 2592 597546688 597546218 0.000000e+00 710.0
10 TraesCS3D01G342800 chr3A 90.702 527 42 4 1 523 597548778 597548255 0.000000e+00 695.0
11 TraesCS3D01G342800 chr1B 88.221 416 45 4 1084 1497 422563208 422562795 6.560000e-136 494.0
12 TraesCS3D01G342800 chr1B 86.905 420 51 4 1072 1489 529288198 529288615 3.980000e-128 468.0
13 TraesCS3D01G342800 chr1A 88.221 416 45 4 1084 1497 392084936 392084523 6.560000e-136 494.0
14 TraesCS3D01G342800 chr1A 87.112 419 50 4 1072 1488 492046051 492046467 3.070000e-129 472.0
15 TraesCS3D01G342800 chr1D 87.981 416 46 4 1084 1497 311988723 311988310 3.050000e-134 488.0
16 TraesCS3D01G342800 chr1D 87.119 427 51 4 1065 1489 393750495 393750071 5.110000e-132 481.0
17 TraesCS3D01G342800 chr6D 81.671 431 67 10 1044 1471 94602333 94602754 5.410000e-92 348.0
18 TraesCS3D01G342800 chr6D 92.958 71 2 3 2053 2122 389645591 389645659 1.670000e-17 100.0
19 TraesCS3D01G342800 chr2D 94.286 70 4 0 2053 2122 549001741 549001810 9.990000e-20 108.0
20 TraesCS3D01G342800 chr4A 91.139 79 5 2 2048 2125 624263612 624263535 3.590000e-19 106.0
21 TraesCS3D01G342800 chr7A 88.889 81 5 2 2053 2129 79783275 79783195 2.160000e-16 97.1
22 TraesCS3D01G342800 chr2B 91.429 70 6 0 2053 2122 20774937 20774868 2.160000e-16 97.1


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 TraesCS3D01G342800 chr3D 455105305 455107943 2638 True 4874.0 4874 100.000000 1 2639 1 chr3D.!!$R1 2638
1 TraesCS3D01G342800 chr3B 598467095 598469565 2470 True 1640.5 2597 91.711000 27 2597 2 chr3B.!!$R5 2570
2 TraesCS3D01G342800 chr3A 597546218 597548778 2560 True 1267.0 2396 92.399333 1 2592 3 chr3A.!!$R1 2591

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
160 163 1.172812 ACGGGCTGAGTGCTTTTTCC 61.173 55.0 0.0 0.0 42.39 3.13 F
208 211 1.226030 GCGTGCGTTTTGTAGGGACT 61.226 55.0 0.0 0.0 46.37 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1617 1687 0.606401 AAGGGATGTTCGGTGCAGTG 60.606 55.0 0.00 0.0 0.00 3.66 R
2010 2090 0.610174 AGTGCACCGATCACTCACAT 59.390 50.0 14.63 0.0 40.47 3.21 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 2.822215 CAGGTGAGGCGGTAGGTAT 58.178 57.895 0.00 0.00 0.00 2.73
24 25 2.101917 GTGAGGCGGTAGGTATAAAGCA 59.898 50.000 0.00 0.00 0.00 3.91
25 26 2.969950 TGAGGCGGTAGGTATAAAGCAT 59.030 45.455 0.00 0.00 0.00 3.79
71 72 2.112297 GGGTTTCTGTCACCGCCA 59.888 61.111 0.00 0.00 34.79 5.69
136 137 2.936919 AAGAAGGCAGATGTGTGTGA 57.063 45.000 0.00 0.00 0.00 3.58
146 149 2.048127 GTGTGTGAGGAGACGGGC 60.048 66.667 0.00 0.00 0.00 6.13
160 163 1.172812 ACGGGCTGAGTGCTTTTTCC 61.173 55.000 0.00 0.00 42.39 3.13
190 193 1.583194 GTTCTAGACGCGTCGAGGC 60.583 63.158 37.46 28.65 33.85 4.70
208 211 1.226030 GCGTGCGTTTTGTAGGGACT 61.226 55.000 0.00 0.00 46.37 3.85
313 320 1.265905 GGTGTTACCTTTTCCAGCGTG 59.734 52.381 0.00 0.00 34.73 5.34
334 343 3.338250 TGGGGCATGGGGTGAGAC 61.338 66.667 0.00 0.00 0.00 3.36
341 350 2.519013 GCATGGGGTGAGACTCTTTTT 58.481 47.619 3.68 0.00 0.00 1.94
542 594 6.919721 ACATATTTGTTGGATAAGCACGTTT 58.080 32.000 0.00 0.00 29.55 3.60
550 602 8.046294 TGTTGGATAAGCACGTTTGTATAAAT 57.954 30.769 0.00 0.00 0.00 1.40
552 604 6.939627 TGGATAAGCACGTTTGTATAAATCG 58.060 36.000 0.00 5.76 0.00 3.34
564 616 9.592720 CGTTTGTATAAATCGATAAATGCATGA 57.407 29.630 0.00 0.00 0.00 3.07
579 631 5.713792 ATGCATGATTACTAGCTAGACGT 57.286 39.130 27.45 11.50 0.00 4.34
830 887 6.681729 TTTCAGTAGTAACATTCACCTCCT 57.318 37.500 0.00 0.00 0.00 3.69
953 1010 1.541588 CGTCCACTGATCACTCACTCA 59.458 52.381 0.00 0.00 0.00 3.41
954 1011 2.669670 CGTCCACTGATCACTCACTCAC 60.670 54.545 0.00 0.00 0.00 3.51
960 1030 2.890847 GATCACTCACTCACCGCCGG 62.891 65.000 0.00 0.00 0.00 6.13
962 1032 3.681835 ACTCACTCACCGCCGGTC 61.682 66.667 5.41 0.00 31.02 4.79
982 1052 3.404369 GCTAGCTTTGCTCGCTCC 58.596 61.111 7.70 0.00 42.76 4.70
1241 1311 2.639286 CAAGACCAAGGTGCACGC 59.361 61.111 11.45 3.85 0.00 5.34
1518 1588 2.189499 GGCATCTGGTTCATCGGCC 61.189 63.158 0.00 0.00 0.00 6.13
1667 1737 6.166982 AGTAGACTTGCAAACCTTGTCTATC 58.833 40.000 21.46 16.40 40.73 2.08
1672 1742 5.239525 ACTTGCAAACCTTGTCTATCAGTTC 59.760 40.000 0.00 0.00 0.00 3.01
1678 1748 7.288672 CAAACCTTGTCTATCAGTTCGTTTAC 58.711 38.462 0.00 0.00 0.00 2.01
1682 1752 4.478699 TGTCTATCAGTTCGTTTACCGTG 58.521 43.478 0.00 0.00 37.94 4.94
1698 1768 0.249699 CGTGTCCGGCATAGGCATAA 60.250 55.000 0.15 0.00 43.71 1.90
1716 1786 5.336690 GGCATAACAAGATTTGAGCTTTCCA 60.337 40.000 0.00 0.00 0.00 3.53
1735 1805 3.577848 TCCATTTGGTATGCTTTGTTGCT 59.422 39.130 0.00 0.00 36.34 3.91
1837 1907 4.828072 AGTGTTCTAGGGGAAGTGAATC 57.172 45.455 0.00 0.00 34.23 2.52
1851 1921 2.230508 AGTGAATCAATTGGCACAGCTG 59.769 45.455 13.48 13.48 42.39 4.24
1861 1931 1.814394 TGGCACAGCTGATTGTTCATC 59.186 47.619 23.35 0.00 0.00 2.92
1874 1944 7.361542 GCTGATTGTTCATCATCCCATACATAC 60.362 40.741 0.00 0.00 41.35 2.39
1948 2028 2.175202 ACCTCTCAGCTTGATCGAGTT 58.825 47.619 11.71 2.37 0.00 3.01
1994 2074 7.930513 AGAGCTGTTTAATTTTTGCTAACAC 57.069 32.000 0.00 0.00 0.00 3.32
1995 2075 7.488322 AGAGCTGTTTAATTTTTGCTAACACA 58.512 30.769 0.00 0.00 0.00 3.72
1996 2076 8.143835 AGAGCTGTTTAATTTTTGCTAACACAT 58.856 29.630 0.00 0.00 0.00 3.21
1997 2077 8.075593 AGCTGTTTAATTTTTGCTAACACATG 57.924 30.769 0.00 0.00 0.00 3.21
2054 2134 6.316140 TCACTCATACATCCATTGCAAACTAC 59.684 38.462 1.71 0.00 0.00 2.73
2056 2136 6.540189 ACTCATACATCCATTGCAAACTACTC 59.460 38.462 1.71 0.00 0.00 2.59
2057 2137 5.822519 TCATACATCCATTGCAAACTACTCC 59.177 40.000 1.71 0.00 0.00 3.85
2058 2138 3.356290 ACATCCATTGCAAACTACTCCC 58.644 45.455 1.71 0.00 0.00 4.30
2059 2139 3.010584 ACATCCATTGCAAACTACTCCCT 59.989 43.478 1.71 0.00 0.00 4.20
2060 2140 3.350219 TCCATTGCAAACTACTCCCTC 57.650 47.619 1.71 0.00 0.00 4.30
2061 2141 2.026262 TCCATTGCAAACTACTCCCTCC 60.026 50.000 1.71 0.00 0.00 4.30
2062 2142 2.290896 CCATTGCAAACTACTCCCTCCA 60.291 50.000 1.71 0.00 0.00 3.86
2063 2143 3.624777 CATTGCAAACTACTCCCTCCAT 58.375 45.455 1.71 0.00 0.00 3.41
2064 2144 3.806949 TTGCAAACTACTCCCTCCATT 57.193 42.857 0.00 0.00 0.00 3.16
2065 2145 3.350219 TGCAAACTACTCCCTCCATTC 57.650 47.619 0.00 0.00 0.00 2.67
2066 2146 2.026262 TGCAAACTACTCCCTCCATTCC 60.026 50.000 0.00 0.00 0.00 3.01
2067 2147 2.026262 GCAAACTACTCCCTCCATTCCA 60.026 50.000 0.00 0.00 0.00 3.53
2068 2148 3.561313 GCAAACTACTCCCTCCATTCCAA 60.561 47.826 0.00 0.00 0.00 3.53
2069 2149 4.662278 CAAACTACTCCCTCCATTCCAAA 58.338 43.478 0.00 0.00 0.00 3.28
2070 2150 5.264395 CAAACTACTCCCTCCATTCCAAAT 58.736 41.667 0.00 0.00 0.00 2.32
2071 2151 5.536497 AACTACTCCCTCCATTCCAAATT 57.464 39.130 0.00 0.00 0.00 1.82
2072 2152 6.652205 AACTACTCCCTCCATTCCAAATTA 57.348 37.500 0.00 0.00 0.00 1.40
2073 2153 6.002653 ACTACTCCCTCCATTCCAAATTAC 57.997 41.667 0.00 0.00 0.00 1.89
2074 2154 5.731678 ACTACTCCCTCCATTCCAAATTACT 59.268 40.000 0.00 0.00 0.00 2.24
2075 2155 5.117406 ACTCCCTCCATTCCAAATTACTC 57.883 43.478 0.00 0.00 0.00 2.59
2076 2156 4.130118 CTCCCTCCATTCCAAATTACTCG 58.870 47.826 0.00 0.00 0.00 4.18
2077 2157 3.521937 TCCCTCCATTCCAAATTACTCGT 59.478 43.478 0.00 0.00 0.00 4.18
2078 2158 3.877508 CCCTCCATTCCAAATTACTCGTC 59.122 47.826 0.00 0.00 0.00 4.20
2079 2159 4.513442 CCTCCATTCCAAATTACTCGTCA 58.487 43.478 0.00 0.00 0.00 4.35
2080 2160 5.126067 CCTCCATTCCAAATTACTCGTCAT 58.874 41.667 0.00 0.00 0.00 3.06
2081 2161 5.008019 CCTCCATTCCAAATTACTCGTCATG 59.992 44.000 0.00 0.00 0.00 3.07
2082 2162 4.881273 TCCATTCCAAATTACTCGTCATGG 59.119 41.667 0.00 0.00 0.00 3.66
2083 2163 4.640201 CCATTCCAAATTACTCGTCATGGT 59.360 41.667 0.00 0.00 0.00 3.55
2084 2164 5.125417 CCATTCCAAATTACTCGTCATGGTT 59.875 40.000 0.00 0.00 0.00 3.67
2085 2165 6.350110 CCATTCCAAATTACTCGTCATGGTTT 60.350 38.462 0.00 0.00 0.00 3.27
2086 2166 6.642707 TTCCAAATTACTCGTCATGGTTTT 57.357 33.333 0.00 0.00 0.00 2.43
2087 2167 7.747155 TTCCAAATTACTCGTCATGGTTTTA 57.253 32.000 0.00 0.00 0.00 1.52
2088 2168 7.372451 TCCAAATTACTCGTCATGGTTTTAG 57.628 36.000 0.00 0.00 0.00 1.85
2089 2169 6.938030 TCCAAATTACTCGTCATGGTTTTAGT 59.062 34.615 0.00 0.00 0.00 2.24
2090 2170 7.446013 TCCAAATTACTCGTCATGGTTTTAGTT 59.554 33.333 0.00 0.00 0.00 2.24
2091 2171 7.749126 CCAAATTACTCGTCATGGTTTTAGTTC 59.251 37.037 0.00 0.00 0.00 3.01
2092 2172 6.980051 ATTACTCGTCATGGTTTTAGTTCC 57.020 37.500 0.00 0.00 0.00 3.62
2093 2173 4.345859 ACTCGTCATGGTTTTAGTTCCA 57.654 40.909 0.00 0.00 38.14 3.53
2094 2174 4.062991 ACTCGTCATGGTTTTAGTTCCAC 58.937 43.478 0.00 0.00 36.50 4.02
2095 2175 3.061322 TCGTCATGGTTTTAGTTCCACG 58.939 45.455 0.00 0.00 36.50 4.94
2096 2176 3.061322 CGTCATGGTTTTAGTTCCACGA 58.939 45.455 0.00 0.00 36.50 4.35
2097 2177 3.120786 CGTCATGGTTTTAGTTCCACGAC 60.121 47.826 0.00 0.00 41.56 4.34
2098 2178 3.061322 TCATGGTTTTAGTTCCACGACG 58.939 45.455 0.00 0.00 36.50 5.12
2099 2179 2.886862 TGGTTTTAGTTCCACGACGA 57.113 45.000 0.00 0.00 0.00 4.20
2100 2180 2.746269 TGGTTTTAGTTCCACGACGAG 58.254 47.619 0.00 0.00 0.00 4.18
2101 2181 2.101249 TGGTTTTAGTTCCACGACGAGT 59.899 45.455 0.00 0.00 0.00 4.18
2102 2182 3.317711 TGGTTTTAGTTCCACGACGAGTA 59.682 43.478 0.00 0.00 0.00 2.59
2103 2183 4.202101 TGGTTTTAGTTCCACGACGAGTAA 60.202 41.667 0.00 0.00 0.00 2.24
2104 2184 4.925646 GGTTTTAGTTCCACGACGAGTAAT 59.074 41.667 0.00 0.00 0.00 1.89
2105 2185 5.406477 GGTTTTAGTTCCACGACGAGTAATT 59.594 40.000 0.00 0.00 0.00 1.40
2106 2186 6.073602 GGTTTTAGTTCCACGACGAGTAATTT 60.074 38.462 0.00 0.00 0.00 1.82
2107 2187 6.456447 TTTAGTTCCACGACGAGTAATTTG 57.544 37.500 0.00 0.00 0.00 2.32
2108 2188 4.247267 AGTTCCACGACGAGTAATTTGA 57.753 40.909 0.00 0.00 0.00 2.69
2109 2189 4.624015 AGTTCCACGACGAGTAATTTGAA 58.376 39.130 0.00 0.00 0.00 2.69
2110 2190 5.051816 AGTTCCACGACGAGTAATTTGAAA 58.948 37.500 0.00 0.00 0.00 2.69
2111 2191 4.977741 TCCACGACGAGTAATTTGAAAC 57.022 40.909 0.00 0.00 0.00 2.78
2112 2192 3.426191 TCCACGACGAGTAATTTGAAACG 59.574 43.478 0.00 0.00 0.00 3.60
2113 2193 3.422603 CCACGACGAGTAATTTGAAACGG 60.423 47.826 0.00 0.00 0.00 4.44
2114 2194 3.426191 CACGACGAGTAATTTGAAACGGA 59.574 43.478 0.00 0.00 0.00 4.69
2115 2195 3.671928 ACGACGAGTAATTTGAAACGGAG 59.328 43.478 0.00 0.00 0.00 4.63
2116 2196 3.060363 CGACGAGTAATTTGAAACGGAGG 59.940 47.826 0.00 0.00 0.00 4.30
2117 2197 3.332034 ACGAGTAATTTGAAACGGAGGG 58.668 45.455 0.00 0.00 0.00 4.30
2118 2198 3.007182 ACGAGTAATTTGAAACGGAGGGA 59.993 43.478 0.00 0.00 0.00 4.20
2119 2199 3.617263 CGAGTAATTTGAAACGGAGGGAG 59.383 47.826 0.00 0.00 0.00 4.30
2120 2200 4.576879 GAGTAATTTGAAACGGAGGGAGT 58.423 43.478 0.00 0.00 0.00 3.85
2121 2201 5.622914 CGAGTAATTTGAAACGGAGGGAGTA 60.623 44.000 0.00 0.00 0.00 2.59
2122 2202 5.731591 AGTAATTTGAAACGGAGGGAGTAG 58.268 41.667 0.00 0.00 0.00 2.57
2123 2203 2.467566 TTTGAAACGGAGGGAGTAGC 57.532 50.000 0.00 0.00 0.00 3.58
2191 2271 5.914635 CGTTTCTTGCTTAATTTGCAGAAGA 59.085 36.000 6.05 5.19 41.71 2.87
2218 2305 8.680903 ACTGCTTGATGAATGGTTTATTTCTAG 58.319 33.333 0.00 0.00 0.00 2.43
2231 2318 9.263446 TGGTTTATTTCTAGTTTCTCCTAGCTA 57.737 33.333 0.00 0.00 35.43 3.32
2322 2409 2.056223 GGCCAGCCTGCATTGATGT 61.056 57.895 0.00 0.00 0.00 3.06
2323 2410 1.610554 GGCCAGCCTGCATTGATGTT 61.611 55.000 0.00 0.00 0.00 2.71
2506 2593 0.593618 GAGAGAGAGCGTGTGTGTGA 59.406 55.000 0.00 0.00 0.00 3.58
2586 2677 0.537371 AGTTCTTGCGGTTTGAGGGG 60.537 55.000 0.00 0.00 0.00 4.79
2603 2694 4.179599 GGGGAGGGAGGGGGAGAG 62.180 77.778 0.00 0.00 0.00 3.20
2604 2695 3.036959 GGGAGGGAGGGGGAGAGA 61.037 72.222 0.00 0.00 0.00 3.10
2605 2696 2.612251 GGAGGGAGGGGGAGAGAG 59.388 72.222 0.00 0.00 0.00 3.20
2606 2697 2.015726 GGAGGGAGGGGGAGAGAGA 61.016 68.421 0.00 0.00 0.00 3.10
2607 2698 1.541672 GAGGGAGGGGGAGAGAGAG 59.458 68.421 0.00 0.00 0.00 3.20
2608 2699 0.996762 GAGGGAGGGGGAGAGAGAGA 60.997 65.000 0.00 0.00 0.00 3.10
2609 2700 0.998945 AGGGAGGGGGAGAGAGAGAG 60.999 65.000 0.00 0.00 0.00 3.20
2610 2701 0.996762 GGGAGGGGGAGAGAGAGAGA 60.997 65.000 0.00 0.00 0.00 3.10
2611 2702 0.478507 GGAGGGGGAGAGAGAGAGAG 59.521 65.000 0.00 0.00 0.00 3.20
2612 2703 1.518367 GAGGGGGAGAGAGAGAGAGA 58.482 60.000 0.00 0.00 0.00 3.10
2613 2704 2.065799 GAGGGGGAGAGAGAGAGAGAT 58.934 57.143 0.00 0.00 0.00 2.75
2614 2705 2.447047 GAGGGGGAGAGAGAGAGAGATT 59.553 54.545 0.00 0.00 0.00 2.40
2615 2706 2.865165 AGGGGGAGAGAGAGAGAGATTT 59.135 50.000 0.00 0.00 0.00 2.17
2616 2707 4.058731 AGGGGGAGAGAGAGAGAGATTTA 58.941 47.826 0.00 0.00 0.00 1.40
2617 2708 4.106341 AGGGGGAGAGAGAGAGAGATTTAG 59.894 50.000 0.00 0.00 0.00 1.85
2618 2709 4.407365 GGGGAGAGAGAGAGAGATTTAGG 58.593 52.174 0.00 0.00 0.00 2.69
2619 2710 4.407365 GGGAGAGAGAGAGAGATTTAGGG 58.593 52.174 0.00 0.00 0.00 3.53
2620 2711 3.826729 GGAGAGAGAGAGAGATTTAGGGC 59.173 52.174 0.00 0.00 0.00 5.19
2621 2712 4.447762 GGAGAGAGAGAGAGATTTAGGGCT 60.448 50.000 0.00 0.00 0.00 5.19
2622 2713 5.222048 GGAGAGAGAGAGAGATTTAGGGCTA 60.222 48.000 0.00 0.00 0.00 3.93
2623 2714 5.880901 AGAGAGAGAGAGATTTAGGGCTAG 58.119 45.833 0.00 0.00 0.00 3.42
2624 2715 4.998051 AGAGAGAGAGATTTAGGGCTAGG 58.002 47.826 0.00 0.00 0.00 3.02
2625 2716 3.506398 AGAGAGAGATTTAGGGCTAGGC 58.494 50.000 8.00 8.00 0.00 3.93
2626 2717 3.116939 AGAGAGAGATTTAGGGCTAGGCA 60.117 47.826 19.14 0.00 0.00 4.75
2627 2718 3.837731 GAGAGAGATTTAGGGCTAGGCAT 59.162 47.826 19.14 14.26 0.00 4.40
2628 2719 3.582208 AGAGAGATTTAGGGCTAGGCATG 59.418 47.826 19.14 0.00 0.00 4.06
2629 2720 2.039613 AGAGATTTAGGGCTAGGCATGC 59.960 50.000 19.14 9.90 0.00 4.06
2630 2721 1.776667 AGATTTAGGGCTAGGCATGCA 59.223 47.619 21.36 2.37 0.00 3.96
2631 2722 1.882623 GATTTAGGGCTAGGCATGCAC 59.117 52.381 21.36 9.10 0.00 4.57
2632 2723 0.463654 TTTAGGGCTAGGCATGCACG 60.464 55.000 21.36 7.89 39.12 5.34
2633 2724 2.940890 TTAGGGCTAGGCATGCACGC 62.941 60.000 21.36 17.30 39.12 5.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 6.996282 GCTTCCCTTTGTAGGTATATGCTTTA 59.004 38.462 0.00 0.00 40.19 1.85
24 25 6.387220 AGAGTTGCTTCCCTTTGTAGGTATAT 59.613 38.462 0.00 0.00 40.19 0.86
25 26 5.724854 AGAGTTGCTTCCCTTTGTAGGTATA 59.275 40.000 0.00 0.00 40.19 1.47
136 137 3.386237 GCACTCAGCCCGTCTCCT 61.386 66.667 0.00 0.00 37.23 3.69
146 149 2.035066 CACCCAAGGAAAAAGCACTCAG 59.965 50.000 0.00 0.00 0.00 3.35
160 163 1.555533 GTCTAGAACCCCTCACCCAAG 59.444 57.143 0.00 0.00 0.00 3.61
190 193 1.990563 CTAGTCCCTACAAAACGCACG 59.009 52.381 0.00 0.00 0.00 5.34
208 211 3.075005 GCACGCCCCTGGACTCTA 61.075 66.667 0.00 0.00 0.00 2.43
279 282 3.330720 CACCTGGTCCCCCTCCAC 61.331 72.222 0.00 0.00 0.00 4.02
295 302 2.489971 CTCACGCTGGAAAAGGTAACA 58.510 47.619 0.00 0.00 41.41 2.41
307 314 4.415150 ATGCCCCACCTCACGCTG 62.415 66.667 0.00 0.00 0.00 5.18
313 320 4.447342 CACCCCATGCCCCACCTC 62.447 72.222 0.00 0.00 0.00 3.85
341 350 4.449743 GCTCCACGACACACACTTAATTAA 59.550 41.667 0.00 0.00 0.00 1.40
344 353 2.413837 GCTCCACGACACACACTTAAT 58.586 47.619 0.00 0.00 0.00 1.40
446 456 6.411630 AGTTTTATATAAACGCGTCTTGCA 57.588 33.333 14.44 0.00 46.97 4.08
477 487 1.155889 CGTCAAAGCTGGTATGTGCA 58.844 50.000 0.00 0.00 0.00 4.57
550 602 8.739972 TCTAGCTAGTAATCATGCATTTATCGA 58.260 33.333 20.10 0.00 0.00 3.59
552 604 8.802856 CGTCTAGCTAGTAATCATGCATTTATC 58.197 37.037 20.10 0.00 0.00 1.75
1347 1417 3.597728 CCGCTCTCCTCGTAGGCC 61.598 72.222 0.00 0.00 34.61 5.19
1536 1606 2.128290 TACCCTCGACGTCCCTGTCA 62.128 60.000 10.58 0.00 38.84 3.58
1617 1687 0.606401 AAGGGATGTTCGGTGCAGTG 60.606 55.000 0.00 0.00 0.00 3.66
1628 1698 6.041069 GCAAGTCTACTATACTCAAGGGATGT 59.959 42.308 0.00 0.00 0.00 3.06
1682 1752 1.873591 CTTGTTATGCCTATGCCGGAC 59.126 52.381 5.05 0.00 36.33 4.79
1698 1768 5.070847 ACCAAATGGAAAGCTCAAATCTTGT 59.929 36.000 6.42 0.00 38.94 3.16
1807 1877 6.012157 ACTTCCCCTAGAACACTACTACTACA 60.012 42.308 0.00 0.00 0.00 2.74
1837 1907 2.736144 ACAATCAGCTGTGCCAATTG 57.264 45.000 18.55 18.55 37.15 2.32
1851 1921 6.375455 GGGTATGTATGGGATGATGAACAATC 59.625 42.308 0.00 0.00 35.67 2.67
1861 1931 5.779241 ATTACCAGGGTATGTATGGGATG 57.221 43.478 0.00 0.00 38.48 3.51
1997 2077 5.739752 TCACTCACATTATTGCTACATGC 57.260 39.130 0.00 0.00 43.25 4.06
2010 2090 0.610174 AGTGCACCGATCACTCACAT 59.390 50.000 14.63 0.00 40.47 3.21
2012 2092 4.996976 AGTGCACCGATCACTCAC 57.003 55.556 14.63 0.00 40.47 3.51
2015 2095 2.355946 AGTGAGTGCACCGATCACT 58.644 52.632 26.17 26.17 46.71 3.41
2031 2111 6.418101 AGTAGTTTGCAATGGATGTATGAGT 58.582 36.000 0.00 0.00 0.00 3.41
2054 2134 4.130118 CGAGTAATTTGGAATGGAGGGAG 58.870 47.826 0.00 0.00 0.00 4.30
2056 2136 3.877508 GACGAGTAATTTGGAATGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
2057 2137 4.513442 TGACGAGTAATTTGGAATGGAGG 58.487 43.478 0.00 0.00 0.00 4.30
2058 2138 5.008019 CCATGACGAGTAATTTGGAATGGAG 59.992 44.000 0.00 0.00 35.16 3.86
2059 2139 4.881273 CCATGACGAGTAATTTGGAATGGA 59.119 41.667 0.00 0.00 35.16 3.41
2060 2140 4.640201 ACCATGACGAGTAATTTGGAATGG 59.360 41.667 0.00 0.00 38.38 3.16
2061 2141 5.818136 ACCATGACGAGTAATTTGGAATG 57.182 39.130 0.00 0.00 0.00 2.67
2062 2142 6.834168 AAACCATGACGAGTAATTTGGAAT 57.166 33.333 0.00 0.00 0.00 3.01
2063 2143 6.642707 AAAACCATGACGAGTAATTTGGAA 57.357 33.333 0.00 0.00 0.00 3.53
2064 2144 6.938030 ACTAAAACCATGACGAGTAATTTGGA 59.062 34.615 0.00 0.00 0.00 3.53
2065 2145 7.141100 ACTAAAACCATGACGAGTAATTTGG 57.859 36.000 0.00 0.00 0.00 3.28
2066 2146 7.749126 GGAACTAAAACCATGACGAGTAATTTG 59.251 37.037 0.00 0.00 0.00 2.32
2067 2147 7.446013 TGGAACTAAAACCATGACGAGTAATTT 59.554 33.333 0.00 0.00 0.00 1.82
2068 2148 6.938030 TGGAACTAAAACCATGACGAGTAATT 59.062 34.615 0.00 0.00 0.00 1.40
2069 2149 6.370718 GTGGAACTAAAACCATGACGAGTAAT 59.629 38.462 0.00 0.00 38.48 1.89
2070 2150 5.697633 GTGGAACTAAAACCATGACGAGTAA 59.302 40.000 0.00 0.00 38.48 2.24
2071 2151 5.232463 GTGGAACTAAAACCATGACGAGTA 58.768 41.667 0.00 0.00 38.48 2.59
2072 2152 4.062991 GTGGAACTAAAACCATGACGAGT 58.937 43.478 0.00 0.00 38.48 4.18
2073 2153 3.122948 CGTGGAACTAAAACCATGACGAG 59.877 47.826 0.00 0.00 43.47 4.18
2074 2154 3.061322 CGTGGAACTAAAACCATGACGA 58.939 45.455 0.00 0.00 43.47 4.20
2075 2155 3.061322 TCGTGGAACTAAAACCATGACG 58.939 45.455 0.00 0.00 44.15 4.35
2077 2157 3.061322 CGTCGTGGAACTAAAACCATGA 58.939 45.455 0.00 0.00 45.97 3.07
2078 2158 3.061322 TCGTCGTGGAACTAAAACCATG 58.939 45.455 0.00 0.00 42.52 3.66
2079 2159 3.243975 ACTCGTCGTGGAACTAAAACCAT 60.244 43.478 0.00 0.00 38.48 3.55
2080 2160 2.101249 ACTCGTCGTGGAACTAAAACCA 59.899 45.455 0.00 0.00 31.75 3.67
2081 2161 2.747436 ACTCGTCGTGGAACTAAAACC 58.253 47.619 0.00 0.00 31.75 3.27
2082 2162 6.457851 AATTACTCGTCGTGGAACTAAAAC 57.542 37.500 0.00 0.00 31.75 2.43
2083 2163 6.700960 TCAAATTACTCGTCGTGGAACTAAAA 59.299 34.615 0.00 0.00 31.75 1.52
2084 2164 6.215121 TCAAATTACTCGTCGTGGAACTAAA 58.785 36.000 0.00 0.00 31.75 1.85
2085 2165 5.771469 TCAAATTACTCGTCGTGGAACTAA 58.229 37.500 0.00 0.00 31.75 2.24
2086 2166 5.375417 TCAAATTACTCGTCGTGGAACTA 57.625 39.130 0.00 0.00 31.75 2.24
2087 2167 4.247267 TCAAATTACTCGTCGTGGAACT 57.753 40.909 0.00 0.00 31.75 3.01
2088 2168 4.977741 TTCAAATTACTCGTCGTGGAAC 57.022 40.909 0.00 0.00 0.00 3.62
2089 2169 4.084952 CGTTTCAAATTACTCGTCGTGGAA 60.085 41.667 0.00 0.00 0.00 3.53
2090 2170 3.426191 CGTTTCAAATTACTCGTCGTGGA 59.574 43.478 0.00 0.00 0.00 4.02
2091 2171 3.422603 CCGTTTCAAATTACTCGTCGTGG 60.423 47.826 0.00 0.00 0.00 4.94
2092 2172 3.426191 TCCGTTTCAAATTACTCGTCGTG 59.574 43.478 0.00 0.00 0.00 4.35
2093 2173 3.641648 TCCGTTTCAAATTACTCGTCGT 58.358 40.909 0.00 0.00 0.00 4.34
2094 2174 3.060363 CCTCCGTTTCAAATTACTCGTCG 59.940 47.826 0.00 0.00 0.00 5.12
2095 2175 3.370061 CCCTCCGTTTCAAATTACTCGTC 59.630 47.826 0.00 0.00 0.00 4.20
2096 2176 3.007182 TCCCTCCGTTTCAAATTACTCGT 59.993 43.478 0.00 0.00 0.00 4.18
2097 2177 3.592059 TCCCTCCGTTTCAAATTACTCG 58.408 45.455 0.00 0.00 0.00 4.18
2098 2178 4.576879 ACTCCCTCCGTTTCAAATTACTC 58.423 43.478 0.00 0.00 0.00 2.59
2099 2179 4.635699 ACTCCCTCCGTTTCAAATTACT 57.364 40.909 0.00 0.00 0.00 2.24
2100 2180 4.331992 GCTACTCCCTCCGTTTCAAATTAC 59.668 45.833 0.00 0.00 0.00 1.89
2101 2181 4.020039 TGCTACTCCCTCCGTTTCAAATTA 60.020 41.667 0.00 0.00 0.00 1.40
2102 2182 3.244770 TGCTACTCCCTCCGTTTCAAATT 60.245 43.478 0.00 0.00 0.00 1.82
2103 2183 2.304761 TGCTACTCCCTCCGTTTCAAAT 59.695 45.455 0.00 0.00 0.00 2.32
2104 2184 1.695242 TGCTACTCCCTCCGTTTCAAA 59.305 47.619 0.00 0.00 0.00 2.69
2105 2185 1.344065 TGCTACTCCCTCCGTTTCAA 58.656 50.000 0.00 0.00 0.00 2.69
2106 2186 1.344065 TTGCTACTCCCTCCGTTTCA 58.656 50.000 0.00 0.00 0.00 2.69
2107 2187 2.093658 TGATTGCTACTCCCTCCGTTTC 60.094 50.000 0.00 0.00 0.00 2.78
2108 2188 1.906574 TGATTGCTACTCCCTCCGTTT 59.093 47.619 0.00 0.00 0.00 3.60
2109 2189 1.568504 TGATTGCTACTCCCTCCGTT 58.431 50.000 0.00 0.00 0.00 4.44
2110 2190 1.568504 TTGATTGCTACTCCCTCCGT 58.431 50.000 0.00 0.00 0.00 4.69
2111 2191 2.918712 ATTGATTGCTACTCCCTCCG 57.081 50.000 0.00 0.00 0.00 4.63
2112 2192 4.429854 AGAATTGATTGCTACTCCCTCC 57.570 45.455 0.00 0.00 0.00 4.30
2162 2242 4.143326 GCAAATTAAGCAAGAAACGCTTCC 60.143 41.667 0.00 0.00 46.61 3.46
2191 2271 7.899973 AGAAATAAACCATTCATCAAGCAGTT 58.100 30.769 0.00 0.00 0.00 3.16
2231 2318 5.858408 TCTTCCTAGGGATCTACTCCAGTAT 59.142 44.000 9.46 0.00 46.98 2.12
2232 2319 5.233143 TCTTCCTAGGGATCTACTCCAGTA 58.767 45.833 9.46 0.00 46.98 2.74
2246 2333 4.133078 GCACATTCTCCATTCTTCCTAGG 58.867 47.826 0.82 0.82 0.00 3.02
2322 2409 2.096980 CCAGTGAGTGATCGCGTACTAA 59.903 50.000 5.77 0.00 0.00 2.24
2323 2410 1.669265 CCAGTGAGTGATCGCGTACTA 59.331 52.381 5.77 0.00 0.00 1.82
2506 2593 7.577303 AGAACTGTTCATCTATCTCTCTCTCT 58.423 38.462 21.50 0.00 0.00 3.10
2586 2677 4.179599 CTCTCCCCCTCCCTCCCC 62.180 77.778 0.00 0.00 0.00 4.81
2588 2679 2.015726 TCTCTCTCCCCCTCCCTCC 61.016 68.421 0.00 0.00 0.00 4.30
2597 2688 4.407365 CCCTAAATCTCTCTCTCTCTCCC 58.593 52.174 0.00 0.00 0.00 4.30
2598 2689 3.826729 GCCCTAAATCTCTCTCTCTCTCC 59.173 52.174 0.00 0.00 0.00 3.71
2599 2690 4.729868 AGCCCTAAATCTCTCTCTCTCTC 58.270 47.826 0.00 0.00 0.00 3.20
2600 2691 4.814224 AGCCCTAAATCTCTCTCTCTCT 57.186 45.455 0.00 0.00 0.00 3.10
2601 2692 5.010282 CCTAGCCCTAAATCTCTCTCTCTC 58.990 50.000 0.00 0.00 0.00 3.20
2602 2693 4.752903 GCCTAGCCCTAAATCTCTCTCTCT 60.753 50.000 0.00 0.00 0.00 3.10
2603 2694 3.509967 GCCTAGCCCTAAATCTCTCTCTC 59.490 52.174 0.00 0.00 0.00 3.20
2604 2695 3.116939 TGCCTAGCCCTAAATCTCTCTCT 60.117 47.826 0.00 0.00 0.00 3.10
2605 2696 3.235200 TGCCTAGCCCTAAATCTCTCTC 58.765 50.000 0.00 0.00 0.00 3.20
2606 2697 3.336509 TGCCTAGCCCTAAATCTCTCT 57.663 47.619 0.00 0.00 0.00 3.10
2607 2698 3.867984 GCATGCCTAGCCCTAAATCTCTC 60.868 52.174 6.36 0.00 0.00 3.20
2608 2699 2.039613 GCATGCCTAGCCCTAAATCTCT 59.960 50.000 6.36 0.00 0.00 3.10
2609 2700 2.224621 TGCATGCCTAGCCCTAAATCTC 60.225 50.000 16.68 0.00 0.00 2.75
2610 2701 1.776667 TGCATGCCTAGCCCTAAATCT 59.223 47.619 16.68 0.00 0.00 2.40
2611 2702 1.882623 GTGCATGCCTAGCCCTAAATC 59.117 52.381 16.68 0.00 0.00 2.17
2612 2703 1.815408 CGTGCATGCCTAGCCCTAAAT 60.815 52.381 16.68 0.00 0.00 1.40
2613 2704 0.463654 CGTGCATGCCTAGCCCTAAA 60.464 55.000 16.68 0.00 0.00 1.85
2614 2705 1.146041 CGTGCATGCCTAGCCCTAA 59.854 57.895 16.68 0.00 0.00 2.69
2615 2706 2.821685 CGTGCATGCCTAGCCCTA 59.178 61.111 16.68 0.00 0.00 3.53
2616 2707 4.864334 GCGTGCATGCCTAGCCCT 62.864 66.667 20.59 0.00 0.00 5.19


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

AutoCloner maintained by Alex Coulton.