Multiple sequence alignment - TraesCS5A01G540600

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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 TraesCS5A01G540600 chr5A 100.000 2759 0 0 1 2759 697888605 697891363 0.000000e+00 5096.0
1 TraesCS5A01G540600 chr5A 93.729 1802 113 0 1 1802 651582348 651580547 0.000000e+00 2702.0
2 TraesCS5A01G540600 chr1B 91.658 2002 138 22 1 1997 494555810 494553833 0.000000e+00 2745.0
3 TraesCS5A01G540600 chr1B 93.341 1802 120 0 1 1802 414555933 414557734 0.000000e+00 2663.0
4 TraesCS5A01G540600 chr6B 94.118 1802 105 1 1 1802 132659296 132657496 0.000000e+00 2739.0
5 TraesCS5A01G540600 chr4A 91.404 2001 142 23 1 1997 718009351 718007377 0.000000e+00 2715.0
6 TraesCS5A01G540600 chr4A 93.750 80 4 1 1918 1997 709875138 709875060 4.830000e-23 119.0
7 TraesCS5A01G540600 chr4D 92.675 1884 134 4 1 1881 398866317 398868199 0.000000e+00 2712.0
8 TraesCS5A01G540600 chr4D 88.259 247 24 3 2418 2660 509178357 509178602 9.670000e-75 291.0
9 TraesCS5A01G540600 chr4D 80.050 401 54 19 2001 2392 509177892 509178275 9.730000e-70 274.0
10 TraesCS5A01G540600 chr2B 93.487 1827 115 1 1 1827 138738664 138736842 0.000000e+00 2712.0
11 TraesCS5A01G540600 chr3D 93.192 1836 120 2 1 1836 134639019 134640849 0.000000e+00 2693.0
12 TraesCS5A01G540600 chr3D 89.169 397 15 2 1601 1997 55373509 55373877 1.160000e-128 470.0
13 TraesCS5A01G540600 chr4B 93.289 1803 119 2 1 1802 502275561 502277362 0.000000e+00 2658.0
14 TraesCS5A01G540600 chr4B 90.947 243 21 1 2418 2660 657988633 657988392 2.650000e-85 326.0
15 TraesCS5A01G540600 chr3B 93.750 80 4 1 1918 1997 769385250 769385172 4.830000e-23 119.0
16 TraesCS5A01G540600 chr7D 87.500 64 5 3 1936 1997 596643803 596643865 1.370000e-08 71.3
17 TraesCS5A01G540600 chr7A 100.000 30 0 0 2193 2222 151448164 151448135 3.840000e-04 56.5


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 TraesCS5A01G540600 chr5A 697888605 697891363 2758 False 5096.0 5096 100.0000 1 2759 1 chr5A.!!$F1 2758
1 TraesCS5A01G540600 chr5A 651580547 651582348 1801 True 2702.0 2702 93.7290 1 1802 1 chr5A.!!$R1 1801
2 TraesCS5A01G540600 chr1B 494553833 494555810 1977 True 2745.0 2745 91.6580 1 1997 1 chr1B.!!$R1 1996
3 TraesCS5A01G540600 chr1B 414555933 414557734 1801 False 2663.0 2663 93.3410 1 1802 1 chr1B.!!$F1 1801
4 TraesCS5A01G540600 chr6B 132657496 132659296 1800 True 2739.0 2739 94.1180 1 1802 1 chr6B.!!$R1 1801
5 TraesCS5A01G540600 chr4A 718007377 718009351 1974 True 2715.0 2715 91.4040 1 1997 1 chr4A.!!$R2 1996
6 TraesCS5A01G540600 chr4D 398866317 398868199 1882 False 2712.0 2712 92.6750 1 1881 1 chr4D.!!$F1 1880
7 TraesCS5A01G540600 chr4D 509177892 509178602 710 False 282.5 291 84.1545 2001 2660 2 chr4D.!!$F2 659
8 TraesCS5A01G540600 chr2B 138736842 138738664 1822 True 2712.0 2712 93.4870 1 1827 1 chr2B.!!$R1 1826
9 TraesCS5A01G540600 chr3D 134639019 134640849 1830 False 2693.0 2693 93.1920 1 1836 1 chr3D.!!$F2 1835
10 TraesCS5A01G540600 chr4B 502275561 502277362 1801 False 2658.0 2658 93.2890 1 1802 1 chr4B.!!$F1 1801

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
63 64 0.86988 AACGCAACTTGGCTTTTCGC 60.87 50.0 0.0 0.0 38.13 4.7 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1894 1953 0.109964 GTGTTTGTGTGTGCGTGTGT 60.11 50.0 0.0 0.0 0.0 3.72 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
63 64 0.869880 AACGCAACTTGGCTTTTCGC 60.870 50.000 0.00 0.00 38.13 4.70
139 140 5.225899 TGAGATGATTGCAGAATTTGACG 57.774 39.130 0.00 0.00 0.00 4.35
156 157 3.872696 TGACGTGGTAATGCAAGATCAT 58.127 40.909 0.00 0.00 0.00 2.45
174 175 9.689976 CAAGATCATCTTAGACGTATTGAGAAT 57.310 33.333 0.00 0.00 33.78 2.40
248 249 4.401022 TCTCTGTTGGCTTTTGACATCAT 58.599 39.130 0.00 0.00 37.26 2.45
258 259 8.523915 TGGCTTTTGACATCATATGTTCTATT 57.476 30.769 1.90 0.00 45.03 1.73
365 366 7.972832 TTTTAGTCCGATGTGTTAATCTGTT 57.027 32.000 0.00 0.00 0.00 3.16
394 395 7.382898 TGGCAAAATAAAAATTGAGGAGTACC 58.617 34.615 0.00 0.00 0.00 3.34
447 448 7.509318 ACTTCTGGCTTAGGGATTTTTAAAGTT 59.491 33.333 0.00 0.00 0.00 2.66
448 449 7.849322 TCTGGCTTAGGGATTTTTAAAGTTT 57.151 32.000 0.00 0.00 0.00 2.66
454 455 8.495949 GCTTAGGGATTTTTAAAGTTTTGCTTC 58.504 33.333 0.00 0.00 36.17 3.86
646 647 5.068067 TGTGATATGGCAAAATCATGTGAGG 59.932 40.000 16.09 0.00 34.77 3.86
715 717 2.863809 CTGGCTCTACAAAAAGGTGGT 58.136 47.619 0.00 0.00 0.00 4.16
761 763 7.279981 TCCTAGTTTGACCGTGAAATCATTATG 59.720 37.037 0.00 0.00 0.00 1.90
772 774 6.787515 CGTGAAATCATTATGCAATACTCGTC 59.212 38.462 0.00 0.00 0.00 4.20
777 779 4.021456 TCATTATGCAATACTCGTCGGGAT 60.021 41.667 0.00 0.00 0.00 3.85
799 801 9.444600 GGGATAGTAGAATCAAAAGTGTTACAA 57.555 33.333 0.00 0.00 0.00 2.41
830 832 3.857157 TCAAGCCACTGAGTTAAGGTT 57.143 42.857 0.00 0.00 0.00 3.50
876 878 4.867608 GCTTCTGACACTGATCCTAAAGAC 59.132 45.833 0.00 0.00 0.00 3.01
925 928 3.509575 TGCACTTGGTCACTTTGAGTTTT 59.490 39.130 0.00 0.00 0.00 2.43
928 931 5.515270 GCACTTGGTCACTTTGAGTTTTTAC 59.485 40.000 0.00 0.00 0.00 2.01
955 958 9.758021 TTGGTATGATTATCTGGCATGATATTT 57.242 29.630 0.00 1.04 0.00 1.40
966 969 4.930405 TGGCATGATATTTTGTTTGCTGTG 59.070 37.500 0.00 0.00 0.00 3.66
1016 1019 0.036732 ACCATGTGCATTGACTCCGT 59.963 50.000 0.00 0.00 0.00 4.69
1044 1048 9.685828 TTGAAGCAAATAAAAGGTATAACACAC 57.314 29.630 0.00 0.00 0.00 3.82
1069 1073 9.249053 ACTATTTTGAGAAGTACAGAGATGAGA 57.751 33.333 0.00 0.00 0.00 3.27
1151 1155 2.012937 TTTCCAGTGAAACGTCGTGT 57.987 45.000 0.00 0.00 45.86 4.49
1173 1177 7.148787 CGTGTTAAGAGGAAGAAACAGTATGAC 60.149 40.741 0.00 0.00 39.69 3.06
1227 1231 5.523013 CTGAGAAAGCTTTCCGAGTTAAG 57.477 43.478 30.83 13.99 37.92 1.85
1254 1258 3.834489 AATGTTTTGGTTGATGTGGCA 57.166 38.095 0.00 0.00 0.00 4.92
1425 1429 7.379059 TGGTTCATCTGATGTTGAGGTATAT 57.621 36.000 16.66 0.00 0.00 0.86
1527 1531 6.768483 TGTCAGAGAAGTTGATTGTTATCCA 58.232 36.000 0.00 0.00 0.00 3.41
1640 1644 9.565213 GAAGAATTATTTGAGGTCAACAATGAG 57.435 33.333 0.00 0.00 35.88 2.90
1728 1732 3.132289 TCGACCCCATCATAAGTGACTTC 59.868 47.826 0.00 0.00 37.14 3.01
1910 1969 9.699703 ATATATATATACACACGCACACACAAA 57.300 29.630 4.54 0.00 0.00 2.83
1911 1970 2.748461 ATACACACGCACACACAAAC 57.252 45.000 0.00 0.00 0.00 2.93
1912 1971 1.439679 TACACACGCACACACAAACA 58.560 45.000 0.00 0.00 0.00 2.83
1913 1972 0.109964 ACACACGCACACACAAACAC 60.110 50.000 0.00 0.00 0.00 3.32
1914 1973 0.110010 CACACGCACACACAAACACA 60.110 50.000 0.00 0.00 0.00 3.72
1915 1974 0.109964 ACACGCACACACAAACACAC 60.110 50.000 0.00 0.00 0.00 3.82
1916 1975 0.110010 CACGCACACACAAACACACA 60.110 50.000 0.00 0.00 0.00 3.72
1917 1976 0.808125 ACGCACACACAAACACACAT 59.192 45.000 0.00 0.00 0.00 3.21
1923 1982 5.855925 CGCACACACAAACACACATATAATT 59.144 36.000 0.00 0.00 0.00 1.40
1925 1984 7.007009 CGCACACACAAACACACATATAATTAC 59.993 37.037 0.00 0.00 0.00 1.89
1953 2012 5.691896 ACTTGTATATTAAGGGCCCTCAAC 58.308 41.667 28.84 16.81 0.00 3.18
1959 2018 8.337739 TGTATATTAAGGGCCCTCAACTTTTAA 58.662 33.333 28.84 18.49 0.00 1.52
2004 2063 1.144936 GACCGGCCCTGATCTCAAG 59.855 63.158 0.00 0.00 0.00 3.02
2012 2071 2.486191 GCCCTGATCTCAAGGTGTATGG 60.486 54.545 0.00 0.00 30.14 2.74
2015 2076 4.446371 CCTGATCTCAAGGTGTATGGAAC 58.554 47.826 0.00 0.00 0.00 3.62
2036 2097 6.142320 GGAACAAAAACAATGCTAAAGTCTCG 59.858 38.462 0.00 0.00 0.00 4.04
2054 2116 5.237344 AGTCTCGAGAAAGGAAAACAATGTG 59.763 40.000 18.55 0.00 0.00 3.21
2055 2117 5.236478 GTCTCGAGAAAGGAAAACAATGTGA 59.764 40.000 18.55 0.00 0.00 3.58
2077 2139 6.198966 GTGAAGCTTTGAAACATGACGAATTT 59.801 34.615 0.00 0.00 0.00 1.82
2083 2145 7.902403 GCTTTGAAACATGACGAATTTGAAAAA 59.098 29.630 0.00 0.00 0.00 1.94
2086 2148 8.244494 TGAAACATGACGAATTTGAAAAACAA 57.756 26.923 0.00 0.00 36.65 2.83
2087 2149 8.165428 TGAAACATGACGAATTTGAAAAACAAC 58.835 29.630 0.00 0.00 38.29 3.32
2115 2180 1.768112 AAAACACGTGTCCCGAAGCG 61.768 55.000 23.61 0.00 40.70 4.68
2124 2189 0.315568 GTCCCGAAGCGCTCATAGAT 59.684 55.000 12.06 0.00 0.00 1.98
2130 2195 2.030717 CGAAGCGCTCATAGATGGTACT 60.031 50.000 12.06 0.00 0.00 2.73
2131 2196 3.312828 GAAGCGCTCATAGATGGTACTG 58.687 50.000 12.06 0.00 0.00 2.74
2135 2200 3.306364 GCGCTCATAGATGGTACTGGATT 60.306 47.826 0.00 0.00 0.00 3.01
2136 2201 4.800914 GCGCTCATAGATGGTACTGGATTT 60.801 45.833 0.00 0.00 0.00 2.17
2142 2207 7.210174 TCATAGATGGTACTGGATTTTTCTCG 58.790 38.462 0.00 0.00 0.00 4.04
2149 2215 4.853924 ACTGGATTTTTCTCGTTTGCAT 57.146 36.364 0.00 0.00 0.00 3.96
2151 2217 4.278170 ACTGGATTTTTCTCGTTTGCATCA 59.722 37.500 0.00 0.00 0.00 3.07
2154 2220 2.704725 TTTTCTCGTTTGCATCAGGC 57.295 45.000 0.00 0.00 45.13 4.85
2166 2232 3.062323 GCATCAGGCATTTTCTTCTCG 57.938 47.619 0.00 0.00 43.97 4.04
2172 2238 4.578516 TCAGGCATTTTCTTCTCGTTTCAA 59.421 37.500 0.00 0.00 0.00 2.69
2185 2251 8.495949 TCTTCTCGTTTCAAAATGTATCTTGAC 58.504 33.333 0.00 0.00 31.41 3.18
2187 2253 6.422701 TCTCGTTTCAAAATGTATCTTGACGT 59.577 34.615 0.00 0.00 31.41 4.34
2201 2267 4.953269 TCTTGACGTTTCATTTGTATCGC 58.047 39.130 0.00 0.00 0.00 4.58
2202 2268 4.688879 TCTTGACGTTTCATTTGTATCGCT 59.311 37.500 0.00 0.00 0.00 4.93
2204 2270 3.991121 TGACGTTTCATTTGTATCGCTGA 59.009 39.130 0.00 0.00 0.00 4.26
2205 2271 4.629634 TGACGTTTCATTTGTATCGCTGAT 59.370 37.500 0.00 0.00 0.00 2.90
2207 2273 5.323900 ACGTTTCATTTGTATCGCTGATTG 58.676 37.500 0.00 0.00 0.00 2.67
2208 2274 4.730042 CGTTTCATTTGTATCGCTGATTGG 59.270 41.667 0.00 0.00 0.00 3.16
2209 2275 3.969117 TCATTTGTATCGCTGATTGGC 57.031 42.857 0.00 0.00 0.00 4.52
2210 2276 3.544684 TCATTTGTATCGCTGATTGGCT 58.455 40.909 0.00 0.00 0.00 4.75
2211 2277 3.947196 TCATTTGTATCGCTGATTGGCTT 59.053 39.130 0.00 0.00 0.00 4.35
2213 2279 3.763097 TTGTATCGCTGATTGGCTTTG 57.237 42.857 0.00 0.00 0.00 2.77
2214 2280 2.016318 TGTATCGCTGATTGGCTTTGG 58.984 47.619 0.00 0.00 0.00 3.28
2215 2281 2.017049 GTATCGCTGATTGGCTTTGGT 58.983 47.619 0.00 0.00 0.00 3.67
2216 2282 1.549203 ATCGCTGATTGGCTTTGGTT 58.451 45.000 0.00 0.00 0.00 3.67
2217 2283 1.327303 TCGCTGATTGGCTTTGGTTT 58.673 45.000 0.00 0.00 0.00 3.27
2218 2284 1.686052 TCGCTGATTGGCTTTGGTTTT 59.314 42.857 0.00 0.00 0.00 2.43
2219 2285 1.794116 CGCTGATTGGCTTTGGTTTTG 59.206 47.619 0.00 0.00 0.00 2.44
2220 2286 1.532437 GCTGATTGGCTTTGGTTTTGC 59.468 47.619 0.00 0.00 0.00 3.68
2221 2287 2.807837 GCTGATTGGCTTTGGTTTTGCT 60.808 45.455 0.00 0.00 0.00 3.91
2222 2288 3.554752 GCTGATTGGCTTTGGTTTTGCTA 60.555 43.478 0.00 0.00 0.00 3.49
2223 2289 3.988819 TGATTGGCTTTGGTTTTGCTAC 58.011 40.909 0.00 0.00 0.00 3.58
2224 2290 3.386078 TGATTGGCTTTGGTTTTGCTACA 59.614 39.130 0.00 0.00 0.00 2.74
2225 2291 2.880963 TGGCTTTGGTTTTGCTACAC 57.119 45.000 0.00 0.00 0.00 2.90
2226 2292 2.103373 TGGCTTTGGTTTTGCTACACA 58.897 42.857 0.00 0.00 0.00 3.72
2240 2306 2.360801 GCTACACAAACCTGCTCCAAAA 59.639 45.455 0.00 0.00 0.00 2.44
2241 2307 2.959507 ACACAAACCTGCTCCAAAAC 57.040 45.000 0.00 0.00 0.00 2.43
2249 2315 1.342174 CCTGCTCCAAAACAAGTGCAT 59.658 47.619 0.00 0.00 32.61 3.96
2251 2317 3.460103 CTGCTCCAAAACAAGTGCATTT 58.540 40.909 0.00 0.00 32.61 2.32
2252 2318 3.456280 TGCTCCAAAACAAGTGCATTTC 58.544 40.909 0.00 0.00 0.00 2.17
2253 2319 3.132646 TGCTCCAAAACAAGTGCATTTCT 59.867 39.130 0.00 0.00 0.00 2.52
2254 2320 4.122046 GCTCCAAAACAAGTGCATTTCTT 58.878 39.130 0.00 0.00 0.00 2.52
2255 2321 4.571984 GCTCCAAAACAAGTGCATTTCTTT 59.428 37.500 0.00 0.00 0.00 2.52
2295 2361 5.102020 TGAAAACATGGTGATACACGTTG 57.898 39.130 0.00 0.00 34.83 4.10
2306 2372 4.436523 GTGATACACGTTGAAACAAGCAAC 59.563 41.667 0.00 0.00 41.57 4.17
2309 2375 3.643763 ACACGTTGAAACAAGCAACAAA 58.356 36.364 0.00 0.00 44.37 2.83
2310 2376 4.051922 ACACGTTGAAACAAGCAACAAAA 58.948 34.783 0.00 0.00 44.37 2.44
2350 2417 8.955061 ACATTGTGAAACGAGATGAAATTTAG 57.045 30.769 0.00 0.00 42.39 1.85
2360 2427 7.592938 ACGAGATGAAATTTAGCAACAATCAA 58.407 30.769 0.00 0.00 0.00 2.57
2362 2429 7.219535 CGAGATGAAATTTAGCAACAATCAAGG 59.780 37.037 0.00 0.00 0.00 3.61
2392 2460 3.980646 TGAATCTCAAAACAACCACGG 57.019 42.857 0.00 0.00 0.00 4.94
2393 2461 3.546724 TGAATCTCAAAACAACCACGGA 58.453 40.909 0.00 0.00 0.00 4.69
2396 2464 0.306533 CTCAAAACAACCACGGACGG 59.693 55.000 0.00 0.00 0.00 4.79
2444 2568 7.018249 AGGAGATTTCTTTACCAAGGGTTCTAA 59.982 37.037 0.00 0.00 37.09 2.10
2481 2605 6.723298 TTAAATGAGCTTCAAAGGGTTTCA 57.277 33.333 0.00 0.00 0.00 2.69
2486 2610 3.732212 AGCTTCAAAGGGTTTCAAATGC 58.268 40.909 0.00 0.00 0.00 3.56
2488 2612 3.248363 GCTTCAAAGGGTTTCAAATGCAC 59.752 43.478 0.00 0.00 0.00 4.57
2495 2619 3.054166 GGGTTTCAAATGCACGGTAAAC 58.946 45.455 0.00 0.00 0.00 2.01
2496 2620 3.054166 GGTTTCAAATGCACGGTAAACC 58.946 45.455 15.67 15.67 39.13 3.27
2497 2621 3.491104 GGTTTCAAATGCACGGTAAACCA 60.491 43.478 21.67 0.00 43.34 3.67
2498 2622 4.303282 GTTTCAAATGCACGGTAAACCAT 58.697 39.130 0.00 0.00 35.14 3.55
2499 2623 3.840890 TCAAATGCACGGTAAACCATC 57.159 42.857 0.00 0.00 35.14 3.51
2503 2628 4.864704 AATGCACGGTAAACCATCTTTT 57.135 36.364 0.00 0.00 35.14 2.27
2508 2633 5.473846 TGCACGGTAAACCATCTTTTGATTA 59.526 36.000 0.00 0.00 36.97 1.75
2511 2636 7.590279 CACGGTAAACCATCTTTTGATTAACT 58.410 34.615 0.00 0.00 36.97 2.24
2545 2670 9.226606 TCCATTCTTCGAAATAAATTACAGTGT 57.773 29.630 0.00 0.00 0.00 3.55
2563 2688 4.754114 CAGTGTTCTCTTTTCCTTCAGAGG 59.246 45.833 0.00 0.00 45.02 3.69
2574 2701 2.639347 TCCTTCAGAGGTTCTTGCATCA 59.361 45.455 0.00 0.00 43.97 3.07
2587 2714 4.910195 TCTTGCATCAAGCTTCCTCTTTA 58.090 39.130 0.00 0.00 45.94 1.85
2593 2720 6.209192 TGCATCAAGCTTCCTCTTTATTTTCA 59.791 34.615 0.00 0.00 45.94 2.69
2623 2750 0.034198 TCGGCGTCATTGTTTCTCCA 59.966 50.000 6.85 0.00 0.00 3.86
2624 2751 1.086696 CGGCGTCATTGTTTCTCCAT 58.913 50.000 0.00 0.00 0.00 3.41
2633 2760 6.183360 CGTCATTGTTTCTCCATCTTTCTCTC 60.183 42.308 0.00 0.00 0.00 3.20
2635 2762 5.567037 TTGTTTCTCCATCTTTCTCTCCA 57.433 39.130 0.00 0.00 0.00 3.86
2648 2775 9.712305 CATCTTTCTCTCCAGTTAGTTTTTCTA 57.288 33.333 0.00 0.00 0.00 2.10
2653 2780 6.729100 TCTCTCCAGTTAGTTTTTCTATGGGA 59.271 38.462 0.00 0.00 32.51 4.37
2660 2787 7.610305 CAGTTAGTTTTTCTATGGGAAAGGCTA 59.390 37.037 0.00 0.00 43.68 3.93
2661 2788 8.168058 AGTTAGTTTTTCTATGGGAAAGGCTAA 58.832 33.333 0.00 5.45 43.68 3.09
2662 2789 8.967918 GTTAGTTTTTCTATGGGAAAGGCTAAT 58.032 33.333 10.12 0.00 43.68 1.73
2714 2841 9.908152 AATCTAAAGAAATTAGTGGTTTTTCGG 57.092 29.630 0.00 0.00 41.54 4.30
2715 2842 8.454570 TCTAAAGAAATTAGTGGTTTTTCGGT 57.545 30.769 0.00 0.00 41.54 4.69
2716 2843 8.905850 TCTAAAGAAATTAGTGGTTTTTCGGTT 58.094 29.630 0.00 0.00 41.54 4.44
2717 2844 7.764695 AAAGAAATTAGTGGTTTTTCGGTTG 57.235 32.000 0.00 0.00 35.14 3.77
2718 2845 6.702716 AGAAATTAGTGGTTTTTCGGTTGA 57.297 33.333 0.00 0.00 35.14 3.18
2719 2846 7.284919 AGAAATTAGTGGTTTTTCGGTTGAT 57.715 32.000 0.00 0.00 35.14 2.57
2720 2847 8.398878 AGAAATTAGTGGTTTTTCGGTTGATA 57.601 30.769 0.00 0.00 35.14 2.15
2721 2848 9.020731 AGAAATTAGTGGTTTTTCGGTTGATAT 57.979 29.630 0.00 0.00 35.14 1.63
2724 2851 9.457436 AATTAGTGGTTTTTCGGTTGATATAGT 57.543 29.630 0.00 0.00 0.00 2.12
2725 2852 6.980051 AGTGGTTTTTCGGTTGATATAGTC 57.020 37.500 0.00 0.00 0.00 2.59
2726 2853 6.469410 AGTGGTTTTTCGGTTGATATAGTCA 58.531 36.000 0.00 0.00 34.25 3.41
2727 2854 7.110155 AGTGGTTTTTCGGTTGATATAGTCAT 58.890 34.615 0.00 0.00 36.54 3.06
2728 2855 8.262227 AGTGGTTTTTCGGTTGATATAGTCATA 58.738 33.333 0.00 0.00 36.54 2.15
2729 2856 9.052759 GTGGTTTTTCGGTTGATATAGTCATAT 57.947 33.333 0.00 0.00 36.54 1.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 7.027161 GCGTTTACCAAGATATTTCACAACAT 58.973 34.615 0.00 0.00 0.00 2.71
24 25 6.017026 TGCGTTTACCAAGATATTTCACAACA 60.017 34.615 0.00 0.00 0.00 3.33
63 64 3.932710 TGTAAAGCTGCTCACTATTTCCG 59.067 43.478 1.00 0.00 0.00 4.30
139 140 6.074088 CGTCTAAGATGATCTTGCATTACCAC 60.074 42.308 17.50 2.37 37.29 4.16
231 232 6.624423 AGAACATATGATGTCAAAAGCCAAC 58.376 36.000 10.38 0.00 44.07 3.77
348 349 5.572211 CCATCAAACAGATTAACACATCGG 58.428 41.667 0.00 0.00 33.72 4.18
365 366 8.156165 ACTCCTCAATTTTTATTTTGCCATCAA 58.844 29.630 0.00 0.00 0.00 2.57
394 395 3.704061 TCCACTTTCAAGAACCCCAAAAG 59.296 43.478 0.00 0.00 34.05 2.27
397 398 3.117322 TCATCCACTTTCAAGAACCCCAA 60.117 43.478 0.00 0.00 0.00 4.12
447 448 8.084073 CCAAAAGACTCAATAGATTGAAGCAAA 58.916 33.333 6.42 0.00 45.26 3.68
448 449 7.596494 CCAAAAGACTCAATAGATTGAAGCAA 58.404 34.615 6.42 0.00 45.26 3.91
454 455 7.630242 TTAGGCCAAAAGACTCAATAGATTG 57.370 36.000 5.01 0.00 33.64 2.67
486 487 7.022496 TGTCATATCCTTGACCCCTTATATCA 58.978 38.462 2.43 0.00 44.37 2.15
676 677 7.830697 AGAGCCAGCAAATAATACATATATGCA 59.169 33.333 12.79 0.00 0.00 3.96
761 763 3.750130 TCTACTATCCCGACGAGTATTGC 59.250 47.826 0.00 0.00 0.00 3.56
772 774 7.762615 TGTAACACTTTTGATTCTACTATCCCG 59.237 37.037 0.00 0.00 0.00 5.14
799 801 6.893583 ACTCAGTGGCTTGATATCTTATTGT 58.106 36.000 3.98 0.00 0.00 2.71
830 832 4.841443 TGACGTAACTCAGACAAAGCTA 57.159 40.909 0.00 0.00 0.00 3.32
925 928 7.744733 TCATGCCAGATAATCATACCAAGTAA 58.255 34.615 0.00 0.00 0.00 2.24
928 931 8.975663 ATATCATGCCAGATAATCATACCAAG 57.024 34.615 0.07 0.00 34.42 3.61
955 958 6.800543 TGCTAACTTTATTCACAGCAAACAA 58.199 32.000 0.00 0.00 36.18 2.83
957 960 7.138736 TCTTGCTAACTTTATTCACAGCAAAC 58.861 34.615 8.03 0.00 45.37 2.93
1044 1048 9.734620 CTCTCATCTCTGTACTTCTCAAAATAG 57.265 37.037 0.00 0.00 0.00 1.73
1069 1073 5.506317 CGATGCTCAAACTTGAAGAAAACCT 60.506 40.000 0.00 0.00 36.64 3.50
1151 1155 7.223260 TCGTCATACTGTTTCTTCCTCTTAA 57.777 36.000 0.00 0.00 0.00 1.85
1212 1216 9.227777 ACATTAAAATACTTAACTCGGAAAGCT 57.772 29.630 0.00 0.00 0.00 3.74
1227 1231 8.227119 GCCACATCAACCAAAACATTAAAATAC 58.773 33.333 0.00 0.00 0.00 1.89
1249 1253 5.125100 TCATTCAAAGAAGTGATTGCCAC 57.875 39.130 0.00 0.00 46.03 5.01
1481 1485 1.604278 GCCCGAAAATCTCCATAGCAC 59.396 52.381 0.00 0.00 0.00 4.40
1640 1644 5.564848 GCCAAACCATTTAACCTCTCTTGAC 60.565 44.000 0.00 0.00 0.00 3.18
1728 1732 3.706698 TCTTCTAACATTCCTCGATGCG 58.293 45.455 0.00 0.00 0.00 4.73
1775 1779 9.923143 ATCCAAAATCAGTATGCATATCAAATG 57.077 29.630 10.16 0.00 34.76 2.32
1884 1943 9.699703 TTTGTGTGTGCGTGTGTATATATATAT 57.300 29.630 10.10 10.10 0.00 0.86
1885 1944 8.970293 GTTTGTGTGTGCGTGTGTATATATATA 58.030 33.333 0.00 0.00 0.00 0.86
1886 1945 7.492994 TGTTTGTGTGTGCGTGTGTATATATAT 59.507 33.333 0.00 0.00 0.00 0.86
1887 1946 6.812160 TGTTTGTGTGTGCGTGTGTATATATA 59.188 34.615 0.00 0.00 0.00 0.86
1888 1947 5.639931 TGTTTGTGTGTGCGTGTGTATATAT 59.360 36.000 0.00 0.00 0.00 0.86
1889 1948 4.989168 TGTTTGTGTGTGCGTGTGTATATA 59.011 37.500 0.00 0.00 0.00 0.86
1890 1949 3.810386 TGTTTGTGTGTGCGTGTGTATAT 59.190 39.130 0.00 0.00 0.00 0.86
1891 1950 3.001431 GTGTTTGTGTGTGCGTGTGTATA 59.999 43.478 0.00 0.00 0.00 1.47
1892 1951 2.010497 TGTTTGTGTGTGCGTGTGTAT 58.990 42.857 0.00 0.00 0.00 2.29
1893 1952 1.128878 GTGTTTGTGTGTGCGTGTGTA 59.871 47.619 0.00 0.00 0.00 2.90
1894 1953 0.109964 GTGTTTGTGTGTGCGTGTGT 60.110 50.000 0.00 0.00 0.00 3.72
1895 1954 0.110010 TGTGTTTGTGTGTGCGTGTG 60.110 50.000 0.00 0.00 0.00 3.82
1896 1955 0.109964 GTGTGTTTGTGTGTGCGTGT 60.110 50.000 0.00 0.00 0.00 4.49
1897 1956 0.110010 TGTGTGTTTGTGTGTGCGTG 60.110 50.000 0.00 0.00 0.00 5.34
1898 1957 0.808125 ATGTGTGTTTGTGTGTGCGT 59.192 45.000 0.00 0.00 0.00 5.24
1899 1958 2.746623 TATGTGTGTTTGTGTGTGCG 57.253 45.000 0.00 0.00 0.00 5.34
1900 1959 7.805542 TGTAATTATATGTGTGTTTGTGTGTGC 59.194 33.333 0.00 0.00 0.00 4.57
1901 1960 9.670719 TTGTAATTATATGTGTGTTTGTGTGTG 57.329 29.630 0.00 0.00 0.00 3.82
1925 1984 6.306987 AGGGCCCTTAATATACAAGTCATTG 58.693 40.000 22.28 0.00 42.46 2.82
1930 1989 5.432060 AGTTGAGGGCCCTTAATATACAAGT 59.568 40.000 30.04 23.16 0.00 3.16
1942 2001 3.089284 CGAATTAAAAGTTGAGGGCCCT 58.911 45.455 29.18 29.18 0.00 5.19
1953 2012 1.435925 GCCCGGGGCGAATTAAAAG 59.564 57.895 24.63 0.00 39.62 2.27
1974 2033 1.218316 GCCGGTCCTGAGATTTCGT 59.782 57.895 1.90 0.00 0.00 3.85
1997 2056 6.549364 TGTTTTTGTTCCATACACCTTGAGAT 59.451 34.615 0.00 0.00 36.21 2.75
1998 2057 5.888724 TGTTTTTGTTCCATACACCTTGAGA 59.111 36.000 0.00 0.00 36.21 3.27
1999 2058 6.142818 TGTTTTTGTTCCATACACCTTGAG 57.857 37.500 0.00 0.00 36.21 3.02
2004 2063 5.296748 AGCATTGTTTTTGTTCCATACACC 58.703 37.500 0.00 0.00 36.21 4.16
2012 2071 6.910433 TCGAGACTTTAGCATTGTTTTTGTTC 59.090 34.615 0.00 0.00 0.00 3.18
2015 2076 6.658831 TCTCGAGACTTTAGCATTGTTTTTG 58.341 36.000 12.08 0.00 0.00 2.44
2026 2087 7.478520 TTGTTTTCCTTTCTCGAGACTTTAG 57.521 36.000 16.36 9.99 0.00 1.85
2036 2097 5.836347 AGCTTCACATTGTTTTCCTTTCTC 58.164 37.500 0.00 0.00 0.00 2.87
2054 2116 6.417635 TCAAATTCGTCATGTTTCAAAGCTTC 59.582 34.615 0.00 0.00 0.00 3.86
2055 2117 6.272318 TCAAATTCGTCATGTTTCAAAGCTT 58.728 32.000 0.00 0.00 0.00 3.74
2104 2169 1.035385 TCTATGAGCGCTTCGGGACA 61.035 55.000 13.26 3.49 0.00 4.02
2105 2170 0.315568 ATCTATGAGCGCTTCGGGAC 59.684 55.000 13.26 0.00 0.00 4.46
2108 2173 0.032678 ACCATCTATGAGCGCTTCGG 59.967 55.000 13.26 7.23 0.00 4.30
2110 2175 3.312828 CAGTACCATCTATGAGCGCTTC 58.687 50.000 13.26 5.55 0.00 3.86
2115 2180 6.995091 AGAAAAATCCAGTACCATCTATGAGC 59.005 38.462 0.00 0.00 0.00 4.26
2124 2189 4.023536 GCAAACGAGAAAAATCCAGTACCA 60.024 41.667 0.00 0.00 0.00 3.25
2130 2195 4.321156 CCTGATGCAAACGAGAAAAATCCA 60.321 41.667 0.00 0.00 0.00 3.41
2131 2196 4.168760 CCTGATGCAAACGAGAAAAATCC 58.831 43.478 0.00 0.00 0.00 3.01
2135 2200 2.704725 GCCTGATGCAAACGAGAAAA 57.295 45.000 0.00 0.00 40.77 2.29
2149 2215 4.133820 TGAAACGAGAAGAAAATGCCTGA 58.866 39.130 0.00 0.00 0.00 3.86
2151 2217 5.514274 TTTGAAACGAGAAGAAAATGCCT 57.486 34.783 0.00 0.00 0.00 4.75
2165 2231 7.374754 TGAAACGTCAAGATACATTTTGAAACG 59.625 33.333 0.00 2.20 35.29 3.60
2166 2232 8.555166 TGAAACGTCAAGATACATTTTGAAAC 57.445 30.769 0.00 0.00 35.29 2.78
2185 2251 4.730042 CCAATCAGCGATACAAATGAAACG 59.270 41.667 0.00 0.00 0.00 3.60
2187 2253 4.398988 AGCCAATCAGCGATACAAATGAAA 59.601 37.500 0.00 0.00 38.01 2.69
2197 2263 1.549203 AACCAAAGCCAATCAGCGAT 58.451 45.000 0.00 0.00 38.01 4.58
2198 2264 1.327303 AAACCAAAGCCAATCAGCGA 58.673 45.000 0.00 0.00 38.01 4.93
2201 2267 3.116079 AGCAAAACCAAAGCCAATCAG 57.884 42.857 0.00 0.00 0.00 2.90
2202 2268 3.386078 TGTAGCAAAACCAAAGCCAATCA 59.614 39.130 0.00 0.00 0.00 2.57
2204 2270 3.133721 TGTGTAGCAAAACCAAAGCCAAT 59.866 39.130 0.00 0.00 0.00 3.16
2205 2271 2.497675 TGTGTAGCAAAACCAAAGCCAA 59.502 40.909 0.00 0.00 0.00 4.52
2207 2273 2.880963 TGTGTAGCAAAACCAAAGCC 57.119 45.000 0.00 0.00 0.00 4.35
2208 2274 3.308595 GGTTTGTGTAGCAAAACCAAAGC 59.691 43.478 11.45 10.89 46.26 3.51
2216 2282 1.953686 GGAGCAGGTTTGTGTAGCAAA 59.046 47.619 0.00 0.00 44.05 3.68
2217 2283 1.133945 TGGAGCAGGTTTGTGTAGCAA 60.134 47.619 0.00 0.00 34.87 3.91
2218 2284 0.472044 TGGAGCAGGTTTGTGTAGCA 59.528 50.000 0.00 0.00 0.00 3.49
2219 2285 1.604604 TTGGAGCAGGTTTGTGTAGC 58.395 50.000 0.00 0.00 0.00 3.58
2220 2286 3.380004 TGTTTTGGAGCAGGTTTGTGTAG 59.620 43.478 0.00 0.00 0.00 2.74
2221 2287 3.357203 TGTTTTGGAGCAGGTTTGTGTA 58.643 40.909 0.00 0.00 0.00 2.90
2222 2288 2.175202 TGTTTTGGAGCAGGTTTGTGT 58.825 42.857 0.00 0.00 0.00 3.72
2223 2289 2.957491 TGTTTTGGAGCAGGTTTGTG 57.043 45.000 0.00 0.00 0.00 3.33
2224 2290 2.831526 ACTTGTTTTGGAGCAGGTTTGT 59.168 40.909 0.00 0.00 0.00 2.83
2225 2291 3.189285 CACTTGTTTTGGAGCAGGTTTG 58.811 45.455 0.00 0.00 0.00 2.93
2226 2292 2.418609 GCACTTGTTTTGGAGCAGGTTT 60.419 45.455 0.00 0.00 0.00 3.27
2231 2297 3.132646 AGAAATGCACTTGTTTTGGAGCA 59.867 39.130 0.00 0.00 36.34 4.26
2271 2337 5.545658 ACGTGTATCACCATGTTTTCATC 57.454 39.130 0.00 0.00 38.64 2.92
2278 2344 4.130857 TGTTTCAACGTGTATCACCATGT 58.869 39.130 0.00 0.00 36.14 3.21
2316 2382 4.854399 TCGTTTCACAATGTTCCATCAAC 58.146 39.130 0.00 0.00 35.28 3.18
2317 2383 4.819088 TCTCGTTTCACAATGTTCCATCAA 59.181 37.500 0.00 0.00 0.00 2.57
2318 2384 4.384940 TCTCGTTTCACAATGTTCCATCA 58.615 39.130 0.00 0.00 0.00 3.07
2319 2385 5.122239 TCATCTCGTTTCACAATGTTCCATC 59.878 40.000 0.00 0.00 0.00 3.51
2321 2387 4.384940 TCATCTCGTTTCACAATGTTCCA 58.615 39.130 0.00 0.00 0.00 3.53
2322 2388 5.356882 TTCATCTCGTTTCACAATGTTCC 57.643 39.130 0.00 0.00 0.00 3.62
2341 2408 8.954950 TTTTCCTTGATTGTTGCTAAATTTCA 57.045 26.923 0.00 0.00 0.00 2.69
2350 2417 6.101332 TCATGCTATTTTCCTTGATTGTTGC 58.899 36.000 0.00 0.00 0.00 4.17
2360 2427 8.125978 TGTTTTGAGATTCATGCTATTTTCCT 57.874 30.769 0.00 0.00 0.00 3.36
2362 2429 8.650714 GGTTGTTTTGAGATTCATGCTATTTTC 58.349 33.333 0.00 0.00 0.00 2.29
2392 2460 5.476614 ACAAAGAGTGGTTATTCTACCGTC 58.523 41.667 0.00 0.00 41.28 4.79
2393 2461 5.011329 TGACAAAGAGTGGTTATTCTACCGT 59.989 40.000 0.00 0.00 41.28 4.83
2396 2464 7.159372 TCCTTGACAAAGAGTGGTTATTCTAC 58.841 38.462 0.00 0.00 35.19 2.59
2451 2575 6.101997 CCTTTGAAGCTCATTTAAACATCCC 58.898 40.000 0.00 0.00 0.00 3.85
2481 2605 4.864704 AAAGATGGTTTACCGTGCATTT 57.135 36.364 0.00 0.00 39.43 2.32
2486 2610 7.537306 CAGTTAATCAAAAGATGGTTTACCGTG 59.463 37.037 0.00 0.00 33.20 4.94
2488 2612 7.027161 CCAGTTAATCAAAAGATGGTTTACCG 58.973 38.462 0.00 0.00 33.20 4.02
2495 2619 9.971922 GGAATAATCCAGTTAATCAAAAGATGG 57.028 33.333 0.00 0.00 45.79 3.51
2539 2664 5.359194 TCTGAAGGAAAAGAGAACACTGT 57.641 39.130 0.00 0.00 0.00 3.55
2545 2670 5.896073 AGAACCTCTGAAGGAAAAGAGAA 57.104 39.130 0.00 0.00 46.67 2.87
2553 2678 2.639347 TGATGCAAGAACCTCTGAAGGA 59.361 45.455 0.00 0.00 46.67 3.36
2563 2688 3.080319 AGAGGAAGCTTGATGCAAGAAC 58.920 45.455 2.10 1.86 43.42 3.01
2587 2714 7.925993 TGACGCCGATATAAAAGAATGAAAAT 58.074 30.769 0.00 0.00 0.00 1.82
2593 2720 6.861065 ACAATGACGCCGATATAAAAGAAT 57.139 33.333 0.00 0.00 0.00 2.40
2600 2727 4.202172 TGGAGAAACAATGACGCCGATATA 60.202 41.667 0.00 0.00 0.00 0.86
2624 2751 9.712305 CATAGAAAAACTAACTGGAGAGAAAGA 57.288 33.333 0.00 0.00 34.56 2.52
2633 2760 6.350194 GCCTTTCCCATAGAAAAACTAACTGG 60.350 42.308 0.00 0.00 43.84 4.00
2635 2762 6.552932 AGCCTTTCCCATAGAAAAACTAACT 58.447 36.000 0.00 0.00 43.84 2.24
2688 2815 9.908152 CCGAAAAACCACTAATTTCTTTAGATT 57.092 29.630 0.00 0.00 39.86 2.40
2689 2816 9.074576 ACCGAAAAACCACTAATTTCTTTAGAT 57.925 29.630 0.00 0.00 39.86 1.98
2690 2817 8.454570 ACCGAAAAACCACTAATTTCTTTAGA 57.545 30.769 0.00 0.00 39.86 2.10
2691 2818 8.964150 CAACCGAAAAACCACTAATTTCTTTAG 58.036 33.333 0.00 0.00 42.62 1.85
2692 2819 8.684520 TCAACCGAAAAACCACTAATTTCTTTA 58.315 29.630 0.00 0.00 32.28 1.85
2693 2820 7.548967 TCAACCGAAAAACCACTAATTTCTTT 58.451 30.769 0.00 0.00 32.28 2.52
2694 2821 7.102847 TCAACCGAAAAACCACTAATTTCTT 57.897 32.000 0.00 0.00 32.28 2.52
2695 2822 6.702716 TCAACCGAAAAACCACTAATTTCT 57.297 33.333 0.00 0.00 32.28 2.52
2698 2825 9.457436 ACTATATCAACCGAAAAACCACTAATT 57.543 29.630 0.00 0.00 0.00 1.40
2699 2826 9.106070 GACTATATCAACCGAAAAACCACTAAT 57.894 33.333 0.00 0.00 0.00 1.73
2700 2827 8.095792 TGACTATATCAACCGAAAAACCACTAA 58.904 33.333 0.00 0.00 33.02 2.24
2701 2828 7.613585 TGACTATATCAACCGAAAAACCACTA 58.386 34.615 0.00 0.00 33.02 2.74
2702 2829 6.469410 TGACTATATCAACCGAAAAACCACT 58.531 36.000 0.00 0.00 33.02 4.00
2703 2830 6.730960 TGACTATATCAACCGAAAAACCAC 57.269 37.500 0.00 0.00 33.02 4.16


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

AutoCloner maintained by Alex Coulton.