Multiple sequence alignment - TraesCS4A01G314200

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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 TraesCS4A01G314200 chr4A 100.000 2321 0 0 1 2321 604671359 604673679 0.000000e+00 4287
1 TraesCS4A01G314200 chr4A 87.300 937 104 5 4 939 604209855 604208933 0.000000e+00 1057
2 TraesCS4A01G314200 chr4A 81.701 623 79 21 927 1528 604208913 604208305 9.640000e-134 486
3 TraesCS4A01G314200 chr5D 95.731 2038 57 7 1 2030 560008927 560006912 0.000000e+00 3254
4 TraesCS4A01G314200 chr5D 92.247 1509 104 7 1 1500 559960565 559959061 0.000000e+00 2126
5 TraesCS4A01G314200 chr5D 87.455 279 28 3 2024 2301 40782523 40782251 4.810000e-82 315
6 TraesCS4A01G314200 chr5D 87.681 276 26 8 2029 2301 531228485 531228215 4.810000e-82 315
7 TraesCS4A01G314200 chrUn 78.459 1142 218 21 1 1131 284401719 284400595 0.000000e+00 721
8 TraesCS4A01G314200 chrUn 78.459 1142 218 21 1 1131 284408253 284407129 0.000000e+00 721
9 TraesCS4A01G314200 chrUn 78.459 1142 218 21 1 1131 302991878 302990754 0.000000e+00 721
10 TraesCS4A01G314200 chrUn 78.371 1142 219 21 1 1131 257886164 257885040 0.000000e+00 715
11 TraesCS4A01G314200 chr3B 81.047 860 151 11 1 853 13816170 13817024 0.000000e+00 675
12 TraesCS4A01G314200 chr3D 80.958 856 152 8 1 850 4958303 4957453 0.000000e+00 667
13 TraesCS4A01G314200 chr7A 95.318 299 12 2 2025 2321 728872025 728872323 7.510000e-130 473
14 TraesCS4A01G314200 chr2A 93.960 298 11 4 2025 2321 775543855 775543564 5.880000e-121 444
15 TraesCS4A01G314200 chr2A 96.035 227 6 3 2025 2250 693870683 693870907 1.310000e-97 366
16 TraesCS4A01G314200 chr5A 92.982 285 11 4 2017 2299 557712877 557713154 7.720000e-110 407
17 TraesCS4A01G314200 chr5A 91.304 299 22 4 2024 2321 628194311 628194016 2.780000e-109 405
18 TraesCS4A01G314200 chr1A 88.380 284 28 5 2029 2309 593633917 593633636 1.030000e-88 337
19 TraesCS4A01G314200 chr6D 88.686 274 27 3 2029 2301 441628904 441628634 4.780000e-87 331


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 TraesCS4A01G314200 chr4A 604671359 604673679 2320 False 4287.0 4287 100.0000 1 2321 1 chr4A.!!$F1 2320
1 TraesCS4A01G314200 chr4A 604208305 604209855 1550 True 771.5 1057 84.5005 4 1528 2 chr4A.!!$R1 1524
2 TraesCS4A01G314200 chr5D 560006912 560008927 2015 True 3254.0 3254 95.7310 1 2030 1 chr5D.!!$R4 2029
3 TraesCS4A01G314200 chr5D 559959061 559960565 1504 True 2126.0 2126 92.2470 1 1500 1 chr5D.!!$R3 1499
4 TraesCS4A01G314200 chrUn 284400595 284401719 1124 True 721.0 721 78.4590 1 1131 1 chrUn.!!$R2 1130
5 TraesCS4A01G314200 chrUn 284407129 284408253 1124 True 721.0 721 78.4590 1 1131 1 chrUn.!!$R3 1130
6 TraesCS4A01G314200 chrUn 302990754 302991878 1124 True 721.0 721 78.4590 1 1131 1 chrUn.!!$R4 1130
7 TraesCS4A01G314200 chrUn 257885040 257886164 1124 True 715.0 715 78.3710 1 1131 1 chrUn.!!$R1 1130
8 TraesCS4A01G314200 chr3B 13816170 13817024 854 False 675.0 675 81.0470 1 853 1 chr3B.!!$F1 852
9 TraesCS4A01G314200 chr3D 4957453 4958303 850 True 667.0 667 80.9580 1 850 1 chr3D.!!$R1 849

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
412 413 0.032403 CAATGGTGTGGTGGTTGCAG 59.968 55.0 0.0 0.0 0.0 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1382 1449 0.031994 ACCGAAACAAGGTGCATTGC 59.968 50.0 0.46 0.46 41.1 3.56 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
354 355 1.444119 GCGACAGCAACTTGTTGGGA 61.444 55.000 14.30 0.00 44.35 4.37
364 365 1.425066 ACTTGTTGGGATCTGGAAGCA 59.575 47.619 0.00 0.00 0.00 3.91
374 375 4.019174 GGATCTGGAAGCATTGGAAAAGA 58.981 43.478 0.00 0.00 0.00 2.52
412 413 0.032403 CAATGGTGTGGTGGTTGCAG 59.968 55.000 0.00 0.00 0.00 4.41
466 467 0.249073 TAGAAGCTTCGATGCCGAGC 60.249 55.000 20.43 8.77 46.39 5.03
467 468 1.811266 GAAGCTTCGATGCCGAGCA 60.811 57.895 18.70 1.01 46.39 4.26
730 732 2.129607 GAAGCCAAGCAATGTGTTGTG 58.870 47.619 0.00 0.00 37.65 3.33
858 884 2.374184 TGGCACCAGGTATGTAAATGC 58.626 47.619 0.00 0.00 0.00 3.56
890 916 9.814507 TTAATGTAAGCGTTAATTAGTTGTGTG 57.185 29.630 0.00 0.00 32.80 3.82
1034 1094 3.045634 TCTTGACTGGAAAGAGACCCAA 58.954 45.455 0.00 0.00 31.11 4.12
1239 1299 6.057533 CCAGAGAATAACCATGAGCAATGTA 58.942 40.000 0.00 0.00 34.11 2.29
1382 1449 2.503375 GGCACGTACGGAGTGTCG 60.503 66.667 21.06 0.00 45.73 4.35
1584 1666 4.436852 CGACCAAAATATTCCACCTGTTCG 60.437 45.833 0.00 0.00 0.00 3.95
1617 1699 0.321122 CTCTGCTCACCCACCTGTTC 60.321 60.000 0.00 0.00 0.00 3.18
1627 1709 1.335872 CCCACCTGTTCGTTGATTTGC 60.336 52.381 0.00 0.00 0.00 3.68
1628 1710 1.336440 CCACCTGTTCGTTGATTTGCA 59.664 47.619 0.00 0.00 0.00 4.08
1646 1728 1.442567 ACGCCTCGTGTTACAACCA 59.557 52.632 0.00 0.00 39.18 3.67
1773 1862 8.682936 ATGGATTATGAATTAGTGACTCCAAC 57.317 34.615 0.00 0.00 34.23 3.77
1777 1866 4.286297 TGAATTAGTGACTCCAACAGGG 57.714 45.455 0.00 0.00 38.37 4.45
1816 1905 9.032624 ACACAATTAATCTACACCACTACTAGT 57.967 33.333 0.00 0.00 0.00 2.57
1850 1939 8.334632 CCTGTGTTTTGATGGTTTAATTTGTTC 58.665 33.333 0.00 0.00 0.00 3.18
2039 2128 1.257936 CGTAGGTTGAAATCGGATGCG 59.742 52.381 0.00 0.00 0.00 4.73
2040 2129 1.597663 GTAGGTTGAAATCGGATGCGG 59.402 52.381 6.82 0.00 0.00 5.69
2041 2130 0.251916 AGGTTGAAATCGGATGCGGA 59.748 50.000 6.82 0.00 0.00 5.54
2042 2131 1.134098 AGGTTGAAATCGGATGCGGAT 60.134 47.619 6.82 0.00 0.00 4.18
2043 2132 1.676006 GGTTGAAATCGGATGCGGATT 59.324 47.619 6.82 1.82 35.46 3.01
2044 2133 2.099098 GGTTGAAATCGGATGCGGATTT 59.901 45.455 6.82 11.22 42.91 2.17
2045 2134 3.428862 GGTTGAAATCGGATGCGGATTTT 60.429 43.478 6.82 4.85 41.25 1.82
2046 2135 4.201970 GGTTGAAATCGGATGCGGATTTTA 60.202 41.667 6.82 5.94 41.25 1.52
2047 2136 5.336744 GTTGAAATCGGATGCGGATTTTAA 58.663 37.500 6.82 11.12 41.25 1.52
2048 2137 5.766150 TGAAATCGGATGCGGATTTTAAT 57.234 34.783 6.82 0.00 41.25 1.40
2049 2138 6.142818 TGAAATCGGATGCGGATTTTAATT 57.857 33.333 6.82 0.00 41.25 1.40
2050 2139 6.205784 TGAAATCGGATGCGGATTTTAATTC 58.794 36.000 6.82 0.00 41.25 2.17
2051 2140 4.766404 ATCGGATGCGGATTTTAATTCC 57.234 40.909 6.82 0.00 0.00 3.01
2052 2141 2.882137 TCGGATGCGGATTTTAATTCCC 59.118 45.455 6.82 0.00 0.00 3.97
2053 2142 2.884639 CGGATGCGGATTTTAATTCCCT 59.115 45.455 0.00 0.00 0.00 4.20
2054 2143 4.069304 CGGATGCGGATTTTAATTCCCTA 58.931 43.478 0.00 0.00 0.00 3.53
2055 2144 4.083484 CGGATGCGGATTTTAATTCCCTAC 60.083 45.833 0.00 0.00 0.00 3.18
2056 2145 4.825085 GGATGCGGATTTTAATTCCCTACA 59.175 41.667 0.00 0.00 0.00 2.74
2057 2146 5.476945 GGATGCGGATTTTAATTCCCTACAT 59.523 40.000 0.00 2.96 0.00 2.29
2058 2147 6.015434 GGATGCGGATTTTAATTCCCTACATT 60.015 38.462 0.00 0.00 0.00 2.71
2059 2148 6.783708 TGCGGATTTTAATTCCCTACATTT 57.216 33.333 0.91 0.00 0.00 2.32
2060 2149 7.176589 TGCGGATTTTAATTCCCTACATTTT 57.823 32.000 0.91 0.00 0.00 1.82
2061 2150 7.038659 TGCGGATTTTAATTCCCTACATTTTG 58.961 34.615 0.91 0.00 0.00 2.44
2062 2151 7.093727 TGCGGATTTTAATTCCCTACATTTTGA 60.094 33.333 0.91 0.00 0.00 2.69
2063 2152 7.926018 GCGGATTTTAATTCCCTACATTTTGAT 59.074 33.333 0.91 0.00 0.00 2.57
2094 2183 3.692998 TTTTTCCGACATCGCATGC 57.307 47.368 7.91 7.91 38.18 4.06
2095 2184 0.877743 TTTTTCCGACATCGCATGCA 59.122 45.000 19.57 5.34 38.18 3.96
2096 2185 0.877743 TTTTCCGACATCGCATGCAA 59.122 45.000 19.57 0.00 38.18 4.08
2097 2186 0.877743 TTTCCGACATCGCATGCAAA 59.122 45.000 19.57 5.23 38.18 3.68
2098 2187 0.877743 TTCCGACATCGCATGCAAAA 59.122 45.000 19.57 2.32 38.18 2.44
2099 2188 0.877743 TCCGACATCGCATGCAAAAA 59.122 45.000 19.57 0.00 38.18 1.94
2100 2189 1.472082 TCCGACATCGCATGCAAAAAT 59.528 42.857 19.57 2.19 38.18 1.82
2101 2190 2.094803 TCCGACATCGCATGCAAAAATT 60.095 40.909 19.57 0.00 38.18 1.82
2102 2191 3.127721 TCCGACATCGCATGCAAAAATTA 59.872 39.130 19.57 0.00 38.18 1.40
2103 2192 4.043750 CCGACATCGCATGCAAAAATTAT 58.956 39.130 19.57 0.00 38.18 1.28
2104 2193 5.008118 TCCGACATCGCATGCAAAAATTATA 59.992 36.000 19.57 0.00 38.18 0.98
2105 2194 5.340403 CCGACATCGCATGCAAAAATTATAG 59.660 40.000 19.57 0.00 38.18 1.31
2106 2195 5.164254 CGACATCGCATGCAAAAATTATAGC 60.164 40.000 19.57 0.00 0.00 2.97
2107 2196 4.984161 ACATCGCATGCAAAAATTATAGCC 59.016 37.500 19.57 0.00 0.00 3.93
2108 2197 3.626977 TCGCATGCAAAAATTATAGCCG 58.373 40.909 19.57 0.00 0.00 5.52
2109 2198 3.066064 TCGCATGCAAAAATTATAGCCGT 59.934 39.130 19.57 0.00 0.00 5.68
2110 2199 3.796178 CGCATGCAAAAATTATAGCCGTT 59.204 39.130 19.57 0.00 0.00 4.44
2111 2200 4.267452 CGCATGCAAAAATTATAGCCGTTT 59.733 37.500 19.57 0.00 0.00 3.60
2112 2201 5.220378 CGCATGCAAAAATTATAGCCGTTTT 60.220 36.000 19.57 0.00 0.00 2.43
2113 2202 6.020281 CGCATGCAAAAATTATAGCCGTTTTA 60.020 34.615 19.57 0.00 0.00 1.52
2114 2203 7.116819 GCATGCAAAAATTATAGCCGTTTTAC 58.883 34.615 14.21 0.00 0.00 2.01
2115 2204 6.856494 TGCAAAAATTATAGCCGTTTTACG 57.144 33.333 0.00 0.00 42.11 3.18
2116 2205 6.380190 TGCAAAAATTATAGCCGTTTTACGT 58.620 32.000 0.00 0.00 40.58 3.57
2117 2206 6.862090 TGCAAAAATTATAGCCGTTTTACGTT 59.138 30.769 0.00 0.00 40.58 3.99
2118 2207 7.381678 TGCAAAAATTATAGCCGTTTTACGTTT 59.618 29.630 0.00 0.00 40.58 3.60
2119 2208 8.215792 GCAAAAATTATAGCCGTTTTACGTTTT 58.784 29.630 0.00 0.00 40.58 2.43
2120 2209 9.716484 CAAAAATTATAGCCGTTTTACGTTTTC 57.284 29.630 0.00 0.00 40.58 2.29
2121 2210 9.460906 AAAAATTATAGCCGTTTTACGTTTTCA 57.539 25.926 0.00 0.00 40.58 2.69
2122 2211 9.628746 AAAATTATAGCCGTTTTACGTTTTCAT 57.371 25.926 0.00 0.00 40.58 2.57
2123 2212 9.628746 AAATTATAGCCGTTTTACGTTTTCATT 57.371 25.926 0.00 0.00 40.58 2.57
2125 2214 9.706846 ATTATAGCCGTTTTACGTTTTCATTAC 57.293 29.630 0.00 0.00 40.58 1.89
2126 2215 5.421212 AGCCGTTTTACGTTTTCATTACA 57.579 34.783 0.00 0.00 40.58 2.41
2127 2216 5.207033 AGCCGTTTTACGTTTTCATTACAC 58.793 37.500 0.00 0.00 40.58 2.90
2128 2217 5.007921 AGCCGTTTTACGTTTTCATTACACT 59.992 36.000 0.00 0.00 40.58 3.55
2129 2218 5.682422 GCCGTTTTACGTTTTCATTACACTT 59.318 36.000 0.00 0.00 40.58 3.16
2130 2219 6.196910 GCCGTTTTACGTTTTCATTACACTTT 59.803 34.615 0.00 0.00 40.58 2.66
2131 2220 7.253717 GCCGTTTTACGTTTTCATTACACTTTT 60.254 33.333 0.00 0.00 40.58 2.27
2132 2221 8.585436 CCGTTTTACGTTTTCATTACACTTTTT 58.415 29.630 0.00 0.00 40.58 1.94
2207 2296 6.116680 AGTAACATAACTACGTCTCGAAGG 57.883 41.667 0.00 0.00 0.00 3.46
2208 2297 5.877012 AGTAACATAACTACGTCTCGAAGGA 59.123 40.000 0.00 0.00 0.00 3.36
2209 2298 5.831702 AACATAACTACGTCTCGAAGGAT 57.168 39.130 0.00 0.00 0.00 3.24
2210 2299 5.831702 ACATAACTACGTCTCGAAGGATT 57.168 39.130 0.00 0.00 0.00 3.01
2211 2300 6.205101 ACATAACTACGTCTCGAAGGATTT 57.795 37.500 0.00 0.00 0.00 2.17
2212 2301 6.628185 ACATAACTACGTCTCGAAGGATTTT 58.372 36.000 0.00 0.00 0.00 1.82
2213 2302 7.765307 ACATAACTACGTCTCGAAGGATTTTA 58.235 34.615 0.00 0.00 0.00 1.52
2214 2303 8.246180 ACATAACTACGTCTCGAAGGATTTTAA 58.754 33.333 0.00 0.00 0.00 1.52
2215 2304 9.245962 CATAACTACGTCTCGAAGGATTTTAAT 57.754 33.333 0.00 0.00 0.00 1.40
2216 2305 9.813446 ATAACTACGTCTCGAAGGATTTTAATT 57.187 29.630 0.00 0.00 0.00 1.40
2217 2306 8.543862 AACTACGTCTCGAAGGATTTTAATTT 57.456 30.769 0.00 0.00 0.00 1.82
2218 2307 8.543862 ACTACGTCTCGAAGGATTTTAATTTT 57.456 30.769 0.00 0.00 0.00 1.82
2219 2308 8.996271 ACTACGTCTCGAAGGATTTTAATTTTT 58.004 29.630 0.00 0.00 0.00 1.94
2220 2309 9.262472 CTACGTCTCGAAGGATTTTAATTTTTG 57.738 33.333 0.00 0.00 0.00 2.44
2221 2310 7.867752 ACGTCTCGAAGGATTTTAATTTTTGA 58.132 30.769 0.00 0.00 0.00 2.69
2222 2311 8.347035 ACGTCTCGAAGGATTTTAATTTTTGAA 58.653 29.630 0.00 0.00 0.00 2.69
2223 2312 8.840867 CGTCTCGAAGGATTTTAATTTTTGAAG 58.159 33.333 0.00 0.00 0.00 3.02
2224 2313 9.678941 GTCTCGAAGGATTTTAATTTTTGAAGT 57.321 29.630 0.00 0.00 0.00 3.01
2266 2355 4.333633 TTTTTGCAAAACTGAAAAGGCG 57.666 36.364 23.79 0.00 0.00 5.52
2267 2356 2.949451 TTGCAAAACTGAAAAGGCGA 57.051 40.000 0.00 0.00 0.00 5.54
2268 2357 3.451141 TTGCAAAACTGAAAAGGCGAT 57.549 38.095 0.00 0.00 0.00 4.58
2269 2358 4.576216 TTGCAAAACTGAAAAGGCGATA 57.424 36.364 0.00 0.00 0.00 2.92
2270 2359 4.782019 TGCAAAACTGAAAAGGCGATAT 57.218 36.364 0.00 0.00 0.00 1.63
2271 2360 4.484236 TGCAAAACTGAAAAGGCGATATG 58.516 39.130 0.00 0.00 0.00 1.78
2272 2361 3.859386 GCAAAACTGAAAAGGCGATATGG 59.141 43.478 0.00 0.00 0.00 2.74
2273 2362 4.423732 CAAAACTGAAAAGGCGATATGGG 58.576 43.478 0.00 0.00 0.00 4.00
2274 2363 2.348411 ACTGAAAAGGCGATATGGGG 57.652 50.000 0.00 0.00 0.00 4.96
2275 2364 1.133792 ACTGAAAAGGCGATATGGGGG 60.134 52.381 0.00 0.00 0.00 5.40
2294 2383 4.662966 GGGGGAGGGTAGAGTTTAAAAA 57.337 45.455 0.00 0.00 0.00 1.94
2295 2384 5.202746 GGGGGAGGGTAGAGTTTAAAAAT 57.797 43.478 0.00 0.00 0.00 1.82
2296 2385 5.586877 GGGGGAGGGTAGAGTTTAAAAATT 58.413 41.667 0.00 0.00 0.00 1.82
2297 2386 5.421056 GGGGGAGGGTAGAGTTTAAAAATTG 59.579 44.000 0.00 0.00 0.00 2.32
2298 2387 5.105473 GGGGAGGGTAGAGTTTAAAAATTGC 60.105 44.000 0.00 0.00 0.00 3.56
2299 2388 5.105473 GGGAGGGTAGAGTTTAAAAATTGCC 60.105 44.000 0.00 0.00 0.00 4.52
2300 2389 5.105473 GGAGGGTAGAGTTTAAAAATTGCCC 60.105 44.000 10.42 10.42 0.00 5.36
2301 2390 4.775780 AGGGTAGAGTTTAAAAATTGCCCC 59.224 41.667 13.22 8.50 33.16 5.80
2302 2391 4.081309 GGGTAGAGTTTAAAAATTGCCCCC 60.081 45.833 8.27 0.00 0.00 5.40
2303 2392 4.775780 GGTAGAGTTTAAAAATTGCCCCCT 59.224 41.667 0.00 0.00 0.00 4.79
2304 2393 5.247564 GGTAGAGTTTAAAAATTGCCCCCTT 59.752 40.000 0.00 0.00 0.00 3.95
2305 2394 5.483685 AGAGTTTAAAAATTGCCCCCTTC 57.516 39.130 0.00 0.00 0.00 3.46
2306 2395 4.904853 AGAGTTTAAAAATTGCCCCCTTCA 59.095 37.500 0.00 0.00 0.00 3.02
2307 2396 5.012046 AGAGTTTAAAAATTGCCCCCTTCAG 59.988 40.000 0.00 0.00 0.00 3.02
2308 2397 4.658435 AGTTTAAAAATTGCCCCCTTCAGT 59.342 37.500 0.00 0.00 0.00 3.41
2309 2398 4.615588 TTAAAAATTGCCCCCTTCAGTG 57.384 40.909 0.00 0.00 0.00 3.66
2310 2399 2.101640 AAAATTGCCCCCTTCAGTGT 57.898 45.000 0.00 0.00 0.00 3.55
2311 2400 1.341080 AAATTGCCCCCTTCAGTGTG 58.659 50.000 0.00 0.00 0.00 3.82
2312 2401 0.542702 AATTGCCCCCTTCAGTGTGG 60.543 55.000 0.00 0.00 0.00 4.17
2313 2402 2.445492 ATTGCCCCCTTCAGTGTGGG 62.445 60.000 14.37 14.37 42.98 4.61
2314 2403 3.580319 GCCCCCTTCAGTGTGGGT 61.580 66.667 18.07 0.00 41.82 4.51
2315 2404 3.146828 GCCCCCTTCAGTGTGGGTT 62.147 63.158 18.07 0.00 41.82 4.11
2316 2405 1.074951 CCCCCTTCAGTGTGGGTTC 59.925 63.158 18.07 0.00 41.82 3.62
2317 2406 1.302511 CCCCTTCAGTGTGGGTTCG 60.303 63.158 18.07 4.56 41.82 3.95
2318 2407 1.450211 CCCTTCAGTGTGGGTTCGT 59.550 57.895 13.46 0.00 38.65 3.85
2319 2408 0.884704 CCCTTCAGTGTGGGTTCGTG 60.885 60.000 13.46 0.00 38.65 4.35
2320 2409 0.884704 CCTTCAGTGTGGGTTCGTGG 60.885 60.000 0.00 0.00 0.00 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
354 355 6.616237 AAATCTTTTCCAATGCTTCCAGAT 57.384 33.333 0.00 0.00 0.00 2.90
364 365 6.044287 AGTTGGCCCTTAAAATCTTTTCCAAT 59.956 34.615 0.00 0.00 34.03 3.16
374 375 5.338300 CCATTGCTTAGTTGGCCCTTAAAAT 60.338 40.000 0.00 0.00 0.00 1.82
412 413 6.922957 TCCAAATGCATGTCAAGAACTTTTAC 59.077 34.615 0.00 0.00 0.00 2.01
502 503 2.237392 AGCAGGTGTTGAGGATCCTTAC 59.763 50.000 17.42 17.14 0.00 2.34
730 732 1.004185 GTGCTGTCATGTCATCATCGC 60.004 52.381 0.04 0.00 31.15 4.58
912 938 7.881643 TGGAATGAATTCATAAACAAAACGG 57.118 32.000 21.00 0.00 38.53 4.44
1080 1140 1.687297 CCTCCCTAGGAAACGCCTCC 61.687 65.000 11.48 0.00 46.97 4.30
1239 1299 5.651387 TGATCTTCTTCAATCTCACGACT 57.349 39.130 0.00 0.00 0.00 4.18
1311 1372 1.838112 GACAAATCAGTCATGGGGCA 58.162 50.000 0.00 0.00 38.40 5.36
1382 1449 0.031994 ACCGAAACAAGGTGCATTGC 59.968 50.000 0.46 0.46 41.10 3.56
1561 1643 4.436852 CGAACAGGTGGAATATTTTGGTCG 60.437 45.833 9.32 9.32 39.04 4.79
1584 1666 1.066573 AGCAGAGCAGGATACACACAC 60.067 52.381 0.00 0.00 41.41 3.82
1617 1699 1.509787 CGAGGCGTGCAAATCAACG 60.510 57.895 0.00 0.00 0.00 4.10
1628 1710 0.179078 TTGGTTGTAACACGAGGCGT 60.179 50.000 0.00 0.00 42.36 5.68
1646 1728 4.043310 TGGGTTCATGAATCTGAGGAACTT 59.957 41.667 17.99 0.00 41.55 2.66
1767 1856 1.697432 TGTACCAGTTCCCTGTTGGAG 59.303 52.381 0.00 0.00 46.24 3.86
1773 1862 3.283751 TGTGTTTTGTACCAGTTCCCTG 58.716 45.455 0.00 0.00 38.50 4.45
1780 1869 9.607285 GTGTAGATTAATTGTGTTTTGTACCAG 57.393 33.333 0.00 0.00 0.00 4.00
1816 1905 5.197451 ACCATCAAAACACAGGTCTTGTTA 58.803 37.500 0.00 0.00 38.16 2.41
1850 1939 8.251026 GGGGTTATCCTCTTTTAAAATCAACAG 58.749 37.037 0.09 0.00 35.33 3.16
2026 2115 5.766150 ATTAAAATCCGCATCCGATTTCA 57.234 34.783 0.00 0.00 36.29 2.69
2027 2116 5.629435 GGAATTAAAATCCGCATCCGATTTC 59.371 40.000 0.00 0.00 36.29 2.17
2029 2118 4.022329 GGGAATTAAAATCCGCATCCGATT 60.022 41.667 4.98 0.00 37.87 3.34
2030 2119 3.506067 GGGAATTAAAATCCGCATCCGAT 59.494 43.478 4.98 0.00 37.87 4.18
2031 2120 2.882137 GGGAATTAAAATCCGCATCCGA 59.118 45.455 4.98 0.00 37.87 4.55
2032 2121 2.884639 AGGGAATTAAAATCCGCATCCG 59.115 45.455 4.98 0.00 37.87 4.18
2033 2122 4.825085 TGTAGGGAATTAAAATCCGCATCC 59.175 41.667 4.98 0.00 37.87 3.51
2034 2123 6.575162 ATGTAGGGAATTAAAATCCGCATC 57.425 37.500 4.98 0.00 37.87 3.91
2035 2124 6.976934 AATGTAGGGAATTAAAATCCGCAT 57.023 33.333 4.98 6.45 37.87 4.73
2036 2125 6.783708 AAATGTAGGGAATTAAAATCCGCA 57.216 33.333 4.98 4.86 37.87 5.69
2037 2126 7.262048 TCAAAATGTAGGGAATTAAAATCCGC 58.738 34.615 4.98 0.04 37.87 5.54
2076 2165 0.877743 TGCATGCGATGTCGGAAAAA 59.122 45.000 14.09 0.00 44.19 1.94
2077 2166 0.877743 TTGCATGCGATGTCGGAAAA 59.122 45.000 14.09 0.00 44.19 2.29
2078 2167 0.877743 TTTGCATGCGATGTCGGAAA 59.122 45.000 14.09 2.21 44.19 3.13
2079 2168 0.877743 TTTTGCATGCGATGTCGGAA 59.122 45.000 14.09 0.00 44.19 4.30
2080 2169 0.877743 TTTTTGCATGCGATGTCGGA 59.122 45.000 14.09 1.30 45.29 4.55
2081 2170 1.912001 ATTTTTGCATGCGATGTCGG 58.088 45.000 14.09 0.00 40.23 4.79
2082 2171 5.164254 GCTATAATTTTTGCATGCGATGTCG 60.164 40.000 14.09 0.00 43.27 4.35
2083 2172 5.117592 GGCTATAATTTTTGCATGCGATGTC 59.882 40.000 14.09 0.00 0.00 3.06
2084 2173 4.984161 GGCTATAATTTTTGCATGCGATGT 59.016 37.500 14.09 0.00 0.00 3.06
2085 2174 4.088923 CGGCTATAATTTTTGCATGCGATG 59.911 41.667 14.09 0.00 0.00 3.84
2086 2175 4.229096 CGGCTATAATTTTTGCATGCGAT 58.771 39.130 14.09 1.47 0.00 4.58
2087 2176 3.066064 ACGGCTATAATTTTTGCATGCGA 59.934 39.130 14.09 8.74 0.00 5.10
2088 2177 3.371168 ACGGCTATAATTTTTGCATGCG 58.629 40.909 14.09 0.00 0.00 4.73
2089 2178 5.717038 AAACGGCTATAATTTTTGCATGC 57.283 34.783 11.82 11.82 0.00 4.06
2090 2179 7.326645 CGTAAAACGGCTATAATTTTTGCATG 58.673 34.615 4.94 0.00 38.08 4.06
2091 2180 7.444558 CGTAAAACGGCTATAATTTTTGCAT 57.555 32.000 4.94 0.00 38.08 3.96
2092 2181 6.856494 CGTAAAACGGCTATAATTTTTGCA 57.144 33.333 4.94 0.00 38.08 4.08
2175 2264 9.829507 AGACGTAGTTATGTTACTACATCTAGT 57.170 33.333 9.87 2.23 46.46 2.57
2194 2283 9.262472 CAAAAATTAAAATCCTTCGAGACGTAG 57.738 33.333 0.00 0.00 0.00 3.51
2195 2284 8.991026 TCAAAAATTAAAATCCTTCGAGACGTA 58.009 29.630 0.00 0.00 0.00 3.57
2196 2285 7.867752 TCAAAAATTAAAATCCTTCGAGACGT 58.132 30.769 0.00 0.00 0.00 4.34
2197 2286 8.722342 TTCAAAAATTAAAATCCTTCGAGACG 57.278 30.769 0.00 0.00 0.00 4.18
2198 2287 9.678941 ACTTCAAAAATTAAAATCCTTCGAGAC 57.321 29.630 0.00 0.00 0.00 3.36
2245 2334 3.997021 TCGCCTTTTCAGTTTTGCAAAAA 59.003 34.783 25.40 8.42 0.00 1.94
2246 2335 3.589988 TCGCCTTTTCAGTTTTGCAAAA 58.410 36.364 20.46 20.46 0.00 2.44
2247 2336 3.238108 TCGCCTTTTCAGTTTTGCAAA 57.762 38.095 8.05 8.05 0.00 3.68
2248 2337 2.949451 TCGCCTTTTCAGTTTTGCAA 57.051 40.000 0.00 0.00 0.00 4.08
2249 2338 4.484236 CATATCGCCTTTTCAGTTTTGCA 58.516 39.130 0.00 0.00 0.00 4.08
2250 2339 3.859386 CCATATCGCCTTTTCAGTTTTGC 59.141 43.478 0.00 0.00 0.00 3.68
2251 2340 4.423732 CCCATATCGCCTTTTCAGTTTTG 58.576 43.478 0.00 0.00 0.00 2.44
2252 2341 3.447229 CCCCATATCGCCTTTTCAGTTTT 59.553 43.478 0.00 0.00 0.00 2.43
2253 2342 3.023832 CCCCATATCGCCTTTTCAGTTT 58.976 45.455 0.00 0.00 0.00 2.66
2254 2343 2.654863 CCCCATATCGCCTTTTCAGTT 58.345 47.619 0.00 0.00 0.00 3.16
2255 2344 1.133792 CCCCCATATCGCCTTTTCAGT 60.134 52.381 0.00 0.00 0.00 3.41
2256 2345 1.609208 CCCCCATATCGCCTTTTCAG 58.391 55.000 0.00 0.00 0.00 3.02
2257 2346 3.819245 CCCCCATATCGCCTTTTCA 57.181 52.632 0.00 0.00 0.00 2.69
2273 2362 4.662966 TTTTTAAACTCTACCCTCCCCC 57.337 45.455 0.00 0.00 0.00 5.40
2274 2363 5.105473 GCAATTTTTAAACTCTACCCTCCCC 60.105 44.000 0.00 0.00 0.00 4.81
2275 2364 5.105473 GGCAATTTTTAAACTCTACCCTCCC 60.105 44.000 0.00 0.00 0.00 4.30
2276 2365 5.105473 GGGCAATTTTTAAACTCTACCCTCC 60.105 44.000 7.30 0.00 0.00 4.30
2277 2366 5.105473 GGGGCAATTTTTAAACTCTACCCTC 60.105 44.000 12.26 2.88 33.95 4.30
2278 2367 4.775780 GGGGCAATTTTTAAACTCTACCCT 59.224 41.667 12.26 0.00 33.95 4.34
2279 2368 4.081309 GGGGGCAATTTTTAAACTCTACCC 60.081 45.833 6.33 6.33 0.00 3.69
2280 2369 4.775780 AGGGGGCAATTTTTAAACTCTACC 59.224 41.667 0.00 0.00 0.00 3.18
2281 2370 5.995565 AGGGGGCAATTTTTAAACTCTAC 57.004 39.130 0.00 0.00 0.00 2.59
2282 2371 6.078664 TGAAGGGGGCAATTTTTAAACTCTA 58.921 36.000 0.00 0.00 0.00 2.43
2283 2372 4.904853 TGAAGGGGGCAATTTTTAAACTCT 59.095 37.500 0.00 0.00 0.00 3.24
2284 2373 5.221641 ACTGAAGGGGGCAATTTTTAAACTC 60.222 40.000 0.00 0.00 0.00 3.01
2285 2374 4.658435 ACTGAAGGGGGCAATTTTTAAACT 59.342 37.500 0.00 0.00 0.00 2.66
2286 2375 4.754618 CACTGAAGGGGGCAATTTTTAAAC 59.245 41.667 0.00 0.00 0.00 2.01
2287 2376 4.410555 ACACTGAAGGGGGCAATTTTTAAA 59.589 37.500 0.00 0.00 0.00 1.52
2288 2377 3.970640 ACACTGAAGGGGGCAATTTTTAA 59.029 39.130 0.00 0.00 0.00 1.52
2289 2378 3.323403 CACACTGAAGGGGGCAATTTTTA 59.677 43.478 0.00 0.00 0.00 1.52
2290 2379 2.104622 CACACTGAAGGGGGCAATTTTT 59.895 45.455 0.00 0.00 0.00 1.94
2291 2380 1.693606 CACACTGAAGGGGGCAATTTT 59.306 47.619 0.00 0.00 0.00 1.82
2292 2381 1.341080 CACACTGAAGGGGGCAATTT 58.659 50.000 0.00 0.00 0.00 1.82
2293 2382 0.542702 CCACACTGAAGGGGGCAATT 60.543 55.000 0.00 0.00 0.00 2.32
2294 2383 1.077265 CCACACTGAAGGGGGCAAT 59.923 57.895 0.00 0.00 0.00 3.56
2295 2384 2.520458 CCACACTGAAGGGGGCAA 59.480 61.111 0.00 0.00 0.00 4.52
2296 2385 3.579302 CCCACACTGAAGGGGGCA 61.579 66.667 0.00 0.00 41.58 5.36
2301 2390 0.884704 CCACGAACCCACACTGAAGG 60.885 60.000 0.00 0.00 0.00 3.46
2302 2391 2.616969 CCACGAACCCACACTGAAG 58.383 57.895 0.00 0.00 0.00 3.02
2303 2392 4.868026 CCACGAACCCACACTGAA 57.132 55.556 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.