Multiple sequence alignment - TraesCS3B01G095600

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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 TraesCS3B01G095600 chr3B 100.000 2330 0 0 1 2330 64247481 64249810 0.000000e+00 4303
1 TraesCS3B01G095600 chr3B 91.656 815 62 4 550 1359 23474988 23474175 0.000000e+00 1123
2 TraesCS3B01G095600 chr3B 91.857 614 45 3 550 1158 23423533 23422920 0.000000e+00 852
3 TraesCS3B01G095600 chr7B 98.092 1363 23 2 1 1360 234904214 234905576 0.000000e+00 2370
4 TraesCS3B01G095600 chr7B 98.763 485 6 0 881 1365 392671130 392671614 0.000000e+00 863
5 TraesCS3B01G095600 chr4A 97.359 1363 24 5 1 1361 731021853 731020501 0.000000e+00 2307
6 TraesCS3B01G095600 chr4A 93.361 241 15 1 2050 2289 311019164 311019404 2.850000e-94 355
7 TraesCS3B01G095600 chr4A 93.277 238 14 2 2053 2289 503707526 503707762 1.320000e-92 350
8 TraesCS3B01G095600 chr2D 96.718 1371 40 4 1 1369 18898868 18900235 0.000000e+00 2278
9 TraesCS3B01G095600 chr2D 96.769 1362 39 4 1 1360 19003100 19004458 0.000000e+00 2266
10 TraesCS3B01G095600 chr5D 95.815 1362 54 2 1 1360 24877784 24879144 0.000000e+00 2196
11 TraesCS3B01G095600 chr2A 93.129 1368 77 11 1 1361 447991509 447992866 0.000000e+00 1989
12 TraesCS3B01G095600 chr7D 89.540 1348 115 12 17 1358 64477206 64478533 0.000000e+00 1685
13 TraesCS3B01G095600 chr7D 96.793 686 19 2 1 683 41769329 41770014 0.000000e+00 1142
14 TraesCS3B01G095600 chr3A 94.276 594 25 5 1360 1950 52420481 52421068 0.000000e+00 900
15 TraesCS3B01G095600 chr3A 92.958 71 5 0 1941 2011 52421079 52421149 1.140000e-18 104
16 TraesCS3B01G095600 chr3D 93.635 597 25 10 1360 1950 40733831 40734420 0.000000e+00 880
17 TraesCS3B01G095600 chr3D 93.436 259 12 3 2036 2289 367462946 367463204 1.690000e-101 379
18 TraesCS3B01G095600 chr3D 92.509 267 14 4 2029 2289 25211520 25211254 6.080000e-101 377
19 TraesCS3B01G095600 chr3D 91.760 267 16 3 2029 2289 577565096 577565362 1.320000e-97 366
20 TraesCS3B01G095600 chr6D 92.308 260 14 5 2036 2289 21707148 21707407 4.730000e-97 364
21 TraesCS3B01G095600 chr1D 91.506 259 17 3 2036 2289 380017040 380017298 3.680000e-93 351
22 TraesCS3B01G095600 chr6A 91.120 259 18 3 2036 2289 44187883 44188141 1.710000e-91 346
23 TraesCS3B01G095600 chr6A 90.347 259 19 4 2036 2289 44096587 44096844 3.710000e-88 335


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 TraesCS3B01G095600 chr3B 64247481 64249810 2329 False 4303 4303 100.000 1 2330 1 chr3B.!!$F1 2329
1 TraesCS3B01G095600 chr3B 23474175 23474988 813 True 1123 1123 91.656 550 1359 1 chr3B.!!$R2 809
2 TraesCS3B01G095600 chr3B 23422920 23423533 613 True 852 852 91.857 550 1158 1 chr3B.!!$R1 608
3 TraesCS3B01G095600 chr7B 234904214 234905576 1362 False 2370 2370 98.092 1 1360 1 chr7B.!!$F1 1359
4 TraesCS3B01G095600 chr4A 731020501 731021853 1352 True 2307 2307 97.359 1 1361 1 chr4A.!!$R1 1360
5 TraesCS3B01G095600 chr2D 18898868 18900235 1367 False 2278 2278 96.718 1 1369 1 chr2D.!!$F1 1368
6 TraesCS3B01G095600 chr2D 19003100 19004458 1358 False 2266 2266 96.769 1 1360 1 chr2D.!!$F2 1359
7 TraesCS3B01G095600 chr5D 24877784 24879144 1360 False 2196 2196 95.815 1 1360 1 chr5D.!!$F1 1359
8 TraesCS3B01G095600 chr2A 447991509 447992866 1357 False 1989 1989 93.129 1 1361 1 chr2A.!!$F1 1360
9 TraesCS3B01G095600 chr7D 64477206 64478533 1327 False 1685 1685 89.540 17 1358 1 chr7D.!!$F2 1341
10 TraesCS3B01G095600 chr7D 41769329 41770014 685 False 1142 1142 96.793 1 683 1 chr7D.!!$F1 682
11 TraesCS3B01G095600 chr3A 52420481 52421149 668 False 502 900 93.617 1360 2011 2 chr3A.!!$F1 651
12 TraesCS3B01G095600 chr3D 40733831 40734420 589 False 880 880 93.635 1360 1950 1 chr3D.!!$F1 590

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
666 683 1.063174 GAAGATCGCATGAAGGTGTGC 59.937 52.381 0.0 0.0 37.97 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2036 2084 0.658897 CGTTACACACGGGCACTTTT 59.341 50.0 0.0 0.0 45.89 2.27 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
666 683 1.063174 GAAGATCGCATGAAGGTGTGC 59.937 52.381 0.00 0.00 37.97 4.57
710 727 4.340381 GCATGAGAGAAATAAGGCCAATGT 59.660 41.667 5.01 0.00 0.00 2.71
808 825 1.174712 GCAGAGCAGCACCCAGAAAA 61.175 55.000 0.00 0.00 0.00 2.29
1066 1084 5.408299 CGTGTGATATTTGAAACAGACTCCA 59.592 40.000 0.00 0.00 0.00 3.86
1158 1176 7.671495 AATAAAATTTCAGTTGAATGTGGCC 57.329 32.000 0.00 0.00 33.54 5.36
1206 1225 9.331282 GTTTGTCCAAGATCTTGTAATATAGCT 57.669 33.333 29.03 0.00 38.85 3.32
1525 1549 1.391485 CGCAGGATCGAAACACAGAAG 59.609 52.381 0.00 0.00 0.00 2.85
1544 1568 2.151202 AGGAATTGCAGTGTTGGTACG 58.849 47.619 0.00 0.00 0.00 3.67
1545 1569 1.199097 GGAATTGCAGTGTTGGTACGG 59.801 52.381 0.00 0.00 0.00 4.02
1546 1570 1.877443 GAATTGCAGTGTTGGTACGGT 59.123 47.619 0.00 0.00 0.00 4.83
1566 1590 5.012354 ACGGTAGATTTTACTGACAAAGGGA 59.988 40.000 0.48 0.00 0.00 4.20
1573 1597 1.247567 ACTGACAAAGGGAATTGGCG 58.752 50.000 0.00 0.00 41.42 5.69
1834 1861 0.877071 CTGGTCAGCGCAGAAACATT 59.123 50.000 11.47 0.00 0.00 2.71
1866 1894 2.235898 GAGGTAGAGGATGGATGGATGC 59.764 54.545 0.00 0.00 0.00 3.91
1867 1895 1.066573 GGTAGAGGATGGATGGATGCG 60.067 57.143 0.00 0.00 0.00 4.73
1933 1961 1.077429 GAGGTGGAAGGTGGGCATC 60.077 63.158 0.00 0.00 0.00 3.91
1966 2014 3.835978 CTCTCTCCTACCTATCCTCTCGA 59.164 52.174 0.00 0.00 0.00 4.04
1972 2020 4.040217 TCCTACCTATCCTCTCGACTGTAC 59.960 50.000 0.00 0.00 0.00 2.90
1973 2021 4.040706 CCTACCTATCCTCTCGACTGTACT 59.959 50.000 0.00 0.00 0.00 2.73
1974 2022 5.245751 CCTACCTATCCTCTCGACTGTACTA 59.754 48.000 0.00 0.00 0.00 1.82
2006 2054 3.616379 CGATGAAGGAGAGAGAAAAGTGC 59.384 47.826 0.00 0.00 0.00 4.40
2011 2059 3.481453 AGGAGAGAGAAAAGTGCAAACC 58.519 45.455 0.00 0.00 0.00 3.27
2012 2060 3.137360 AGGAGAGAGAAAAGTGCAAACCT 59.863 43.478 0.00 0.00 0.00 3.50
2013 2061 3.885901 GGAGAGAGAAAAGTGCAAACCTT 59.114 43.478 0.00 0.00 0.00 3.50
2014 2062 4.339530 GGAGAGAGAAAAGTGCAAACCTTT 59.660 41.667 0.00 0.00 33.68 3.11
2015 2063 5.506483 GGAGAGAGAAAAGTGCAAACCTTTC 60.506 44.000 1.67 2.93 31.11 2.62
2016 2064 5.196695 AGAGAGAAAAGTGCAAACCTTTCT 58.803 37.500 11.33 11.33 31.11 2.52
2017 2065 5.654209 AGAGAGAAAAGTGCAAACCTTTCTT 59.346 36.000 12.28 0.00 31.11 2.52
2018 2066 6.153510 AGAGAGAAAAGTGCAAACCTTTCTTT 59.846 34.615 12.28 8.52 31.11 2.52
2019 2067 6.701340 AGAGAAAAGTGCAAACCTTTCTTTT 58.299 32.000 8.25 8.25 39.80 2.27
2020 2068 7.161404 AGAGAAAAGTGCAAACCTTTCTTTTT 58.839 30.769 9.48 2.44 38.08 1.94
2021 2069 7.118245 AGAGAAAAGTGCAAACCTTTCTTTTTG 59.882 33.333 9.48 0.00 38.08 2.44
2022 2070 5.878332 AAAGTGCAAACCTTTCTTTTTGG 57.122 34.783 0.00 0.00 33.97 3.28
2023 2071 4.551702 AGTGCAAACCTTTCTTTTTGGT 57.448 36.364 0.00 0.00 33.97 3.67
2024 2072 5.669164 AGTGCAAACCTTTCTTTTTGGTA 57.331 34.783 0.00 0.00 33.97 3.25
2025 2073 6.043854 AGTGCAAACCTTTCTTTTTGGTAA 57.956 33.333 0.00 0.00 33.97 2.85
2026 2074 6.106003 AGTGCAAACCTTTCTTTTTGGTAAG 58.894 36.000 0.00 0.00 33.97 2.34
2027 2075 5.293324 GTGCAAACCTTTCTTTTTGGTAAGG 59.707 40.000 0.00 0.00 42.26 2.69
2028 2076 5.187967 TGCAAACCTTTCTTTTTGGTAAGGA 59.812 36.000 6.72 0.00 39.60 3.36
2029 2077 6.110033 GCAAACCTTTCTTTTTGGTAAGGAA 58.890 36.000 6.72 0.00 39.60 3.36
2030 2078 6.596106 GCAAACCTTTCTTTTTGGTAAGGAAA 59.404 34.615 6.72 0.00 39.60 3.13
2031 2079 7.119992 GCAAACCTTTCTTTTTGGTAAGGAAAA 59.880 33.333 6.72 0.00 39.60 2.29
2032 2080 9.004717 CAAACCTTTCTTTTTGGTAAGGAAAAA 57.995 29.630 6.72 0.00 39.60 1.94
2049 2097 2.753055 AAAAACAAAAGTGCCCGTGT 57.247 40.000 0.00 0.00 0.00 4.49
2050 2098 2.003196 AAAACAAAAGTGCCCGTGTG 57.997 45.000 0.00 0.00 0.00 3.82
2051 2099 0.892063 AAACAAAAGTGCCCGTGTGT 59.108 45.000 0.00 0.00 0.00 3.72
2052 2100 1.752683 AACAAAAGTGCCCGTGTGTA 58.247 45.000 0.00 0.00 0.00 2.90
2053 2101 1.752683 ACAAAAGTGCCCGTGTGTAA 58.247 45.000 0.00 0.00 0.00 2.41
2054 2102 1.402613 ACAAAAGTGCCCGTGTGTAAC 59.597 47.619 0.00 0.00 37.35 2.50
2090 2138 8.546597 TTTTTCATAATCTTCACTGACGATGA 57.453 30.769 0.00 0.00 0.00 2.92
2091 2139 7.525688 TTTCATAATCTTCACTGACGATGAC 57.474 36.000 0.00 0.00 0.00 3.06
2092 2140 5.592054 TCATAATCTTCACTGACGATGACC 58.408 41.667 0.00 0.00 0.00 4.02
2093 2141 3.961480 AATCTTCACTGACGATGACCA 57.039 42.857 0.00 0.00 0.00 4.02
2094 2142 2.724977 TCTTCACTGACGATGACCAC 57.275 50.000 0.00 0.00 0.00 4.16
2095 2143 1.960689 TCTTCACTGACGATGACCACA 59.039 47.619 0.00 0.00 0.00 4.17
2096 2144 2.562738 TCTTCACTGACGATGACCACAT 59.437 45.455 0.00 0.00 39.67 3.21
2097 2145 3.006859 TCTTCACTGACGATGACCACATT 59.993 43.478 0.00 0.00 36.82 2.71
2098 2146 3.401033 TCACTGACGATGACCACATTT 57.599 42.857 0.00 0.00 36.82 2.32
2099 2147 3.738982 TCACTGACGATGACCACATTTT 58.261 40.909 0.00 0.00 36.82 1.82
2100 2148 3.498018 TCACTGACGATGACCACATTTTG 59.502 43.478 0.00 0.00 36.82 2.44
2101 2149 3.250762 CACTGACGATGACCACATTTTGT 59.749 43.478 0.00 0.00 36.82 2.83
2102 2150 3.882888 ACTGACGATGACCACATTTTGTT 59.117 39.130 0.00 0.00 36.82 2.83
2103 2151 4.024048 ACTGACGATGACCACATTTTGTTC 60.024 41.667 0.00 0.00 36.82 3.18
2104 2152 3.879892 TGACGATGACCACATTTTGTTCA 59.120 39.130 0.00 0.00 36.82 3.18
2105 2153 4.219033 GACGATGACCACATTTTGTTCAC 58.781 43.478 0.00 0.00 36.82 3.18
2106 2154 3.629855 ACGATGACCACATTTTGTTCACA 59.370 39.130 0.00 0.00 36.82 3.58
2107 2155 4.278170 ACGATGACCACATTTTGTTCACAT 59.722 37.500 0.00 0.00 36.82 3.21
2108 2156 4.853196 CGATGACCACATTTTGTTCACATC 59.147 41.667 0.00 0.00 36.82 3.06
2109 2157 5.335113 CGATGACCACATTTTGTTCACATCT 60.335 40.000 0.00 0.00 36.82 2.90
2110 2158 5.437289 TGACCACATTTTGTTCACATCTC 57.563 39.130 0.00 0.00 0.00 2.75
2111 2159 4.886489 TGACCACATTTTGTTCACATCTCA 59.114 37.500 0.00 0.00 0.00 3.27
2112 2160 5.535783 TGACCACATTTTGTTCACATCTCAT 59.464 36.000 0.00 0.00 0.00 2.90
2113 2161 6.017400 ACCACATTTTGTTCACATCTCATC 57.983 37.500 0.00 0.00 0.00 2.92
2114 2162 5.090757 CCACATTTTGTTCACATCTCATCG 58.909 41.667 0.00 0.00 0.00 3.84
2115 2163 4.556135 CACATTTTGTTCACATCTCATCGC 59.444 41.667 0.00 0.00 0.00 4.58
2116 2164 4.216042 ACATTTTGTTCACATCTCATCGCA 59.784 37.500 0.00 0.00 0.00 5.10
2117 2165 5.106038 ACATTTTGTTCACATCTCATCGCAT 60.106 36.000 0.00 0.00 0.00 4.73
2118 2166 4.345271 TTTGTTCACATCTCATCGCATG 57.655 40.909 0.00 0.00 0.00 4.06
2119 2167 3.249986 TGTTCACATCTCATCGCATGA 57.750 42.857 0.00 0.05 37.76 3.07
2120 2168 3.800531 TGTTCACATCTCATCGCATGAT 58.199 40.909 0.00 0.00 38.85 2.45
2121 2169 4.193865 TGTTCACATCTCATCGCATGATT 58.806 39.130 0.00 0.00 38.85 2.57
2122 2170 4.637091 TGTTCACATCTCATCGCATGATTT 59.363 37.500 0.00 0.00 38.85 2.17
2123 2171 5.124297 TGTTCACATCTCATCGCATGATTTT 59.876 36.000 0.00 0.00 38.85 1.82
2124 2172 5.164606 TCACATCTCATCGCATGATTTTG 57.835 39.130 0.00 0.00 38.85 2.44
2125 2173 4.877251 TCACATCTCATCGCATGATTTTGA 59.123 37.500 0.00 0.00 38.85 2.69
2126 2174 5.354792 TCACATCTCATCGCATGATTTTGAA 59.645 36.000 0.00 0.00 38.85 2.69
2127 2175 6.031471 CACATCTCATCGCATGATTTTGAAA 58.969 36.000 0.00 0.00 38.85 2.69
2128 2176 6.528774 CACATCTCATCGCATGATTTTGAAAA 59.471 34.615 0.00 0.00 38.85 2.29
2129 2177 7.222031 CACATCTCATCGCATGATTTTGAAAAT 59.778 33.333 2.27 2.27 38.85 1.82
2130 2178 7.762615 ACATCTCATCGCATGATTTTGAAAATT 59.237 29.630 4.46 0.00 38.85 1.82
2131 2179 8.600625 CATCTCATCGCATGATTTTGAAAATTT 58.399 29.630 4.46 0.00 38.85 1.82
2132 2180 7.955502 TCTCATCGCATGATTTTGAAAATTTG 58.044 30.769 4.46 7.26 38.85 2.32
2133 2181 7.599621 TCTCATCGCATGATTTTGAAAATTTGT 59.400 29.630 4.46 0.00 38.85 2.83
2134 2182 8.085720 TCATCGCATGATTTTGAAAATTTGTT 57.914 26.923 4.46 0.00 33.59 2.83
2135 2183 8.222433 TCATCGCATGATTTTGAAAATTTGTTC 58.778 29.630 4.46 0.00 33.59 3.18
2136 2184 7.474398 TCGCATGATTTTGAAAATTTGTTCA 57.526 28.000 4.46 0.00 35.72 3.18
2137 2185 7.343691 TCGCATGATTTTGAAAATTTGTTCAC 58.656 30.769 4.46 0.00 37.24 3.18
2138 2186 7.010830 TCGCATGATTTTGAAAATTTGTTCACA 59.989 29.630 4.46 0.00 37.24 3.58
2139 2187 7.639072 CGCATGATTTTGAAAATTTGTTCACAA 59.361 29.630 4.46 0.00 37.24 3.33
2153 2201 6.981762 TTGTTCACAAATGCAAGAAAATGT 57.018 29.167 0.00 0.00 32.11 2.71
2154 2202 6.981762 TGTTCACAAATGCAAGAAAATGTT 57.018 29.167 0.00 0.00 0.00 2.71
2155 2203 7.375106 TGTTCACAAATGCAAGAAAATGTTT 57.625 28.000 0.00 0.00 0.00 2.83
2156 2204 7.814642 TGTTCACAAATGCAAGAAAATGTTTT 58.185 26.923 0.00 0.00 0.00 2.43
2157 2205 8.295288 TGTTCACAAATGCAAGAAAATGTTTTT 58.705 25.926 0.00 0.00 0.00 1.94
2193 2241 6.586868 TTCACAAATTGAAGCAATGTTCAC 57.413 33.333 0.00 0.00 39.45 3.18
2194 2242 5.658468 TCACAAATTGAAGCAATGTTCACA 58.342 33.333 0.00 0.00 36.15 3.58
2195 2243 6.282167 TCACAAATTGAAGCAATGTTCACAT 58.718 32.000 0.00 0.00 36.15 3.21
2196 2244 6.762187 TCACAAATTGAAGCAATGTTCACATT 59.238 30.769 0.00 0.00 46.62 2.71
2197 2245 7.280428 TCACAAATTGAAGCAATGTTCACATTT 59.720 29.630 0.00 0.00 43.48 2.32
2198 2246 7.911205 CACAAATTGAAGCAATGTTCACATTTT 59.089 29.630 0.00 0.00 43.48 1.82
2199 2247 8.124199 ACAAATTGAAGCAATGTTCACATTTTC 58.876 29.630 0.00 6.35 43.48 2.29
2200 2248 5.886715 TTGAAGCAATGTTCACATTTTCG 57.113 34.783 2.25 0.00 43.48 3.46
2201 2249 5.180367 TGAAGCAATGTTCACATTTTCGA 57.820 34.783 2.25 0.00 43.48 3.71
2202 2250 5.586339 TGAAGCAATGTTCACATTTTCGAA 58.414 33.333 2.25 0.00 43.48 3.71
2203 2251 6.038985 TGAAGCAATGTTCACATTTTCGAAA 58.961 32.000 6.47 6.47 43.48 3.46
2204 2252 6.533012 TGAAGCAATGTTCACATTTTCGAAAA 59.467 30.769 24.43 24.43 43.48 2.29
2205 2253 6.900568 AGCAATGTTCACATTTTCGAAAAA 57.099 29.167 25.77 9.20 43.48 1.94
2226 2274 7.458038 AAAAATATCGTGGTTGTCACAAAAC 57.542 32.000 0.00 0.00 46.36 2.43
2227 2275 4.759516 ATATCGTGGTTGTCACAAAACC 57.240 40.909 0.00 0.00 46.36 3.27
2228 2276 2.116827 TCGTGGTTGTCACAAAACCT 57.883 45.000 0.00 0.00 46.11 3.50
2229 2277 1.740585 TCGTGGTTGTCACAAAACCTG 59.259 47.619 0.00 0.54 46.11 4.00
2230 2278 1.202245 CGTGGTTGTCACAAAACCTGG 60.202 52.381 0.00 0.00 46.11 4.45
2231 2279 1.822371 GTGGTTGTCACAAAACCTGGT 59.178 47.619 0.00 0.00 46.11 4.00
2232 2280 3.018149 GTGGTTGTCACAAAACCTGGTA 58.982 45.455 0.00 0.00 46.11 3.25
2233 2281 3.444388 GTGGTTGTCACAAAACCTGGTAA 59.556 43.478 0.00 0.00 46.11 2.85
2234 2282 4.098807 GTGGTTGTCACAAAACCTGGTAAT 59.901 41.667 0.00 0.00 46.11 1.89
2235 2283 4.712337 TGGTTGTCACAAAACCTGGTAATT 59.288 37.500 0.00 0.00 46.11 1.40
2236 2284 5.163499 TGGTTGTCACAAAACCTGGTAATTC 60.163 40.000 0.00 0.00 46.11 2.17
2237 2285 5.163499 GGTTGTCACAAAACCTGGTAATTCA 60.163 40.000 0.00 0.00 43.20 2.57
2238 2286 6.334202 GTTGTCACAAAACCTGGTAATTCAA 58.666 36.000 0.00 0.00 0.00 2.69
2239 2287 6.531503 TGTCACAAAACCTGGTAATTCAAA 57.468 33.333 0.00 0.00 0.00 2.69
2240 2288 7.118496 TGTCACAAAACCTGGTAATTCAAAT 57.882 32.000 0.00 0.00 0.00 2.32
2241 2289 8.239038 TGTCACAAAACCTGGTAATTCAAATA 57.761 30.769 0.00 0.00 0.00 1.40
2242 2290 8.696374 TGTCACAAAACCTGGTAATTCAAATAA 58.304 29.630 0.00 0.00 0.00 1.40
2243 2291 9.705290 GTCACAAAACCTGGTAATTCAAATAAT 57.295 29.630 0.00 0.00 0.00 1.28
2309 2357 7.962995 ATATATACGTGAAGGTCCATGATCT 57.037 36.000 0.00 0.00 0.00 2.75
2310 2358 9.475620 AATATATACGTGAAGGTCCATGATCTA 57.524 33.333 0.00 0.00 0.00 1.98
2311 2359 7.962995 ATATACGTGAAGGTCCATGATCTAT 57.037 36.000 0.00 0.00 0.00 1.98
2312 2360 6.672266 ATACGTGAAGGTCCATGATCTATT 57.328 37.500 0.00 0.00 0.00 1.73
2313 2361 4.950050 ACGTGAAGGTCCATGATCTATTC 58.050 43.478 0.00 0.00 0.00 1.75
2314 2362 4.651503 ACGTGAAGGTCCATGATCTATTCT 59.348 41.667 0.00 0.00 0.00 2.40
2315 2363 4.987285 CGTGAAGGTCCATGATCTATTCTG 59.013 45.833 0.00 0.00 0.00 3.02
2316 2364 5.303971 GTGAAGGTCCATGATCTATTCTGG 58.696 45.833 0.00 0.00 0.00 3.86
2317 2365 4.202398 TGAAGGTCCATGATCTATTCTGGC 60.202 45.833 0.00 0.00 0.00 4.85
2318 2366 3.321039 AGGTCCATGATCTATTCTGGCA 58.679 45.455 0.00 0.00 0.00 4.92
2319 2367 3.915073 AGGTCCATGATCTATTCTGGCAT 59.085 43.478 0.00 0.00 0.00 4.40
2320 2368 4.008330 GGTCCATGATCTATTCTGGCATG 58.992 47.826 0.00 0.00 36.87 4.06
2321 2369 4.506271 GGTCCATGATCTATTCTGGCATGT 60.506 45.833 0.00 0.00 35.71 3.21
2322 2370 5.280164 GGTCCATGATCTATTCTGGCATGTA 60.280 44.000 0.00 0.00 35.71 2.29
2323 2371 5.641209 GTCCATGATCTATTCTGGCATGTAC 59.359 44.000 0.00 0.00 35.71 2.90
2324 2372 4.628766 CCATGATCTATTCTGGCATGTACG 59.371 45.833 0.00 0.00 35.71 3.67
2325 2373 4.937201 TGATCTATTCTGGCATGTACGT 57.063 40.909 0.00 0.00 0.00 3.57
2326 2374 4.620982 TGATCTATTCTGGCATGTACGTG 58.379 43.478 10.89 10.89 0.00 4.49
2327 2375 4.340950 TGATCTATTCTGGCATGTACGTGA 59.659 41.667 19.38 0.00 0.00 4.35
2328 2376 4.729227 TCTATTCTGGCATGTACGTGAA 57.271 40.909 19.38 4.40 0.00 3.18
2329 2377 5.276461 TCTATTCTGGCATGTACGTGAAT 57.724 39.130 19.38 11.30 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
666 683 2.297033 CCACCACACCCAGAAAAGAATG 59.703 50.000 0.00 0.00 0.00 2.67
710 727 6.538263 TCTAGAGATTTCATCTGATCTCCGA 58.462 40.000 9.14 4.90 46.01 4.55
808 825 8.943085 AGGAGACCAACATATGATAGAATCTTT 58.057 33.333 10.38 0.00 0.00 2.52
1066 1084 0.322816 ATCGCCTGCTTCAACACCAT 60.323 50.000 0.00 0.00 0.00 3.55
1206 1225 0.105593 GTGCTGCTAGGCTATGAGCA 59.894 55.000 18.69 18.69 44.75 4.26
1388 1410 5.048364 CGATTCCAGGTTGGTCAATTGTTAA 60.048 40.000 5.13 0.00 39.03 2.01
1390 1412 3.255642 CGATTCCAGGTTGGTCAATTGTT 59.744 43.478 5.13 0.00 39.03 2.83
1421 1444 0.895530 TCGACTCCAGGAACATCACC 59.104 55.000 0.00 0.00 0.00 4.02
1525 1549 1.199097 CCGTACCAACACTGCAATTCC 59.801 52.381 0.00 0.00 0.00 3.01
1544 1568 7.939784 ATTCCCTTTGTCAGTAAAATCTACC 57.060 36.000 0.00 0.00 0.00 3.18
1545 1569 8.244113 CCAATTCCCTTTGTCAGTAAAATCTAC 58.756 37.037 0.00 0.00 0.00 2.59
1546 1570 7.093945 GCCAATTCCCTTTGTCAGTAAAATCTA 60.094 37.037 0.00 0.00 0.00 1.98
1566 1590 1.577328 CTTGTCGTCAGCCGCCAATT 61.577 55.000 0.00 0.00 33.49 2.32
1573 1597 2.029844 GGTCAGCTTGTCGTCAGCC 61.030 63.158 0.00 0.00 0.00 4.85
1842 1869 1.261480 CATCCATCCTCTACCTCCCG 58.739 60.000 0.00 0.00 0.00 5.14
1843 1870 1.150135 TCCATCCATCCTCTACCTCCC 59.850 57.143 0.00 0.00 0.00 4.30
1891 1919 4.477975 GACCTGCCGTCCGTCTCG 62.478 72.222 0.00 0.00 35.23 4.04
1945 1973 3.579586 GTCGAGAGGATAGGTAGGAGAGA 59.420 52.174 0.00 0.00 0.00 3.10
2006 2054 8.554835 TTTTCCTTACCAAAAAGAAAGGTTTG 57.445 30.769 0.00 0.00 39.62 2.93
2030 2078 2.289133 ACACACGGGCACTTTTGTTTTT 60.289 40.909 0.00 0.00 0.00 1.94
2031 2079 1.273886 ACACACGGGCACTTTTGTTTT 59.726 42.857 0.00 0.00 0.00 2.43
2032 2080 0.892063 ACACACGGGCACTTTTGTTT 59.108 45.000 0.00 0.00 0.00 2.83
2033 2081 1.752683 TACACACGGGCACTTTTGTT 58.247 45.000 0.00 0.00 0.00 2.83
2034 2082 1.402613 GTTACACACGGGCACTTTTGT 59.597 47.619 0.00 0.00 0.00 2.83
2035 2083 1.595976 CGTTACACACGGGCACTTTTG 60.596 52.381 0.00 0.00 45.89 2.44
2036 2084 0.658897 CGTTACACACGGGCACTTTT 59.341 50.000 0.00 0.00 45.89 2.27
2037 2085 2.313267 CGTTACACACGGGCACTTT 58.687 52.632 0.00 0.00 45.89 2.66
2038 2086 4.036977 CGTTACACACGGGCACTT 57.963 55.556 0.00 0.00 45.89 3.16
2065 2113 8.443160 GTCATCGTCAGTGAAGATTATGAAAAA 58.557 33.333 17.58 0.00 29.08 1.94
2066 2114 7.064609 GGTCATCGTCAGTGAAGATTATGAAAA 59.935 37.037 17.58 0.00 29.08 2.29
2067 2115 6.535150 GGTCATCGTCAGTGAAGATTATGAAA 59.465 38.462 17.58 0.00 29.08 2.69
2068 2116 6.042777 GGTCATCGTCAGTGAAGATTATGAA 58.957 40.000 17.58 1.03 29.08 2.57
2069 2117 5.127031 TGGTCATCGTCAGTGAAGATTATGA 59.873 40.000 17.58 11.75 29.08 2.15
2070 2118 5.233050 GTGGTCATCGTCAGTGAAGATTATG 59.767 44.000 17.58 9.75 29.08 1.90
2071 2119 5.105351 TGTGGTCATCGTCAGTGAAGATTAT 60.105 40.000 17.58 0.00 29.08 1.28
2072 2120 4.219725 TGTGGTCATCGTCAGTGAAGATTA 59.780 41.667 17.58 8.62 29.08 1.75
2073 2121 3.006859 TGTGGTCATCGTCAGTGAAGATT 59.993 43.478 17.58 2.65 29.08 2.40
2074 2122 2.562738 TGTGGTCATCGTCAGTGAAGAT 59.437 45.455 14.89 14.89 31.49 2.40
2075 2123 1.960689 TGTGGTCATCGTCAGTGAAGA 59.039 47.619 11.28 11.28 0.00 2.87
2076 2124 2.438868 TGTGGTCATCGTCAGTGAAG 57.561 50.000 0.00 0.00 0.00 3.02
2077 2125 3.401033 AATGTGGTCATCGTCAGTGAA 57.599 42.857 0.00 0.00 32.56 3.18
2078 2126 3.401033 AAATGTGGTCATCGTCAGTGA 57.599 42.857 0.00 0.00 32.56 3.41
2079 2127 3.250762 ACAAAATGTGGTCATCGTCAGTG 59.749 43.478 0.00 0.00 32.56 3.66
2080 2128 3.476552 ACAAAATGTGGTCATCGTCAGT 58.523 40.909 0.00 0.00 32.56 3.41
2081 2129 4.466828 GAACAAAATGTGGTCATCGTCAG 58.533 43.478 0.00 0.00 44.12 3.51
2082 2130 4.481930 GAACAAAATGTGGTCATCGTCA 57.518 40.909 0.00 0.00 44.12 4.35
2089 2137 5.437289 TGAGATGTGAACAAAATGTGGTC 57.563 39.130 0.00 0.00 45.03 4.02
2090 2138 5.335113 CGATGAGATGTGAACAAAATGTGGT 60.335 40.000 0.00 0.00 0.00 4.16
2091 2139 5.090757 CGATGAGATGTGAACAAAATGTGG 58.909 41.667 0.00 0.00 0.00 4.17
2092 2140 4.556135 GCGATGAGATGTGAACAAAATGTG 59.444 41.667 0.00 0.00 0.00 3.21
2093 2141 4.216042 TGCGATGAGATGTGAACAAAATGT 59.784 37.500 0.00 0.00 0.00 2.71
2094 2142 4.725359 TGCGATGAGATGTGAACAAAATG 58.275 39.130 0.00 0.00 0.00 2.32
2095 2143 5.124297 TCATGCGATGAGATGTGAACAAAAT 59.876 36.000 0.00 0.00 33.59 1.82
2096 2144 4.455190 TCATGCGATGAGATGTGAACAAAA 59.545 37.500 0.00 0.00 33.59 2.44
2097 2145 4.002316 TCATGCGATGAGATGTGAACAAA 58.998 39.130 0.00 0.00 33.59 2.83
2098 2146 3.598299 TCATGCGATGAGATGTGAACAA 58.402 40.909 0.00 0.00 33.59 2.83
2099 2147 3.249986 TCATGCGATGAGATGTGAACA 57.750 42.857 0.00 0.00 33.59 3.18
2100 2148 4.808077 AATCATGCGATGAGATGTGAAC 57.192 40.909 5.33 0.00 43.53 3.18
2101 2149 5.354792 TCAAAATCATGCGATGAGATGTGAA 59.645 36.000 5.33 0.00 43.53 3.18
2102 2150 4.877251 TCAAAATCATGCGATGAGATGTGA 59.123 37.500 5.33 5.00 43.53 3.58
2103 2151 5.164606 TCAAAATCATGCGATGAGATGTG 57.835 39.130 5.33 3.28 43.53 3.21
2104 2152 5.823209 TTCAAAATCATGCGATGAGATGT 57.177 34.783 5.33 0.00 43.53 3.06
2105 2153 7.694388 ATTTTCAAAATCATGCGATGAGATG 57.306 32.000 0.00 4.59 43.53 2.90
2106 2154 8.600625 CAAATTTTCAAAATCATGCGATGAGAT 58.399 29.630 0.00 0.00 43.53 2.75
2107 2155 7.599621 ACAAATTTTCAAAATCATGCGATGAGA 59.400 29.630 0.00 0.00 43.53 3.27
2108 2156 7.735500 ACAAATTTTCAAAATCATGCGATGAG 58.264 30.769 0.00 0.00 43.53 2.90
2109 2157 7.655236 ACAAATTTTCAAAATCATGCGATGA 57.345 28.000 0.00 2.05 44.55 2.92
2110 2158 8.010540 TGAACAAATTTTCAAAATCATGCGATG 58.989 29.630 0.00 0.00 32.42 3.84
2111 2159 8.011106 GTGAACAAATTTTCAAAATCATGCGAT 58.989 29.630 0.00 0.00 37.24 4.58
2112 2160 7.010830 TGTGAACAAATTTTCAAAATCATGCGA 59.989 29.630 0.00 0.00 37.24 5.10
2113 2161 7.124471 TGTGAACAAATTTTCAAAATCATGCG 58.876 30.769 0.00 0.00 37.24 4.73
2114 2162 8.838452 TTGTGAACAAATTTTCAAAATCATGC 57.162 26.923 0.00 0.00 37.24 4.06
2130 2178 6.981762 ACATTTTCTTGCATTTGTGAACAA 57.018 29.167 0.00 0.00 0.00 2.83
2131 2179 6.981762 AACATTTTCTTGCATTTGTGAACA 57.018 29.167 0.00 0.00 0.00 3.18
2132 2180 8.672214 AAAAACATTTTCTTGCATTTGTGAAC 57.328 26.923 0.00 0.00 0.00 3.18
2166 2214 9.322773 TGAACATTGCTTCAATTTGTGAATAAA 57.677 25.926 0.00 0.00 45.27 1.40
2167 2215 8.763356 GTGAACATTGCTTCAATTTGTGAATAA 58.237 29.630 0.00 0.00 45.27 1.40
2168 2216 7.924947 TGTGAACATTGCTTCAATTTGTGAATA 59.075 29.630 0.00 0.00 45.27 1.75
2169 2217 6.762187 TGTGAACATTGCTTCAATTTGTGAAT 59.238 30.769 0.00 0.00 45.27 2.57
2170 2218 6.104665 TGTGAACATTGCTTCAATTTGTGAA 58.895 32.000 0.00 0.00 44.20 3.18
2171 2219 5.658468 TGTGAACATTGCTTCAATTTGTGA 58.342 33.333 0.00 0.00 31.05 3.58
2172 2220 5.970140 TGTGAACATTGCTTCAATTTGTG 57.030 34.783 0.00 0.00 31.05 3.33
2173 2221 7.556733 AAATGTGAACATTGCTTCAATTTGT 57.443 28.000 9.34 0.00 45.06 2.83
2174 2222 7.319380 CGAAAATGTGAACATTGCTTCAATTTG 59.681 33.333 9.34 0.00 45.06 2.32
2175 2223 7.224362 TCGAAAATGTGAACATTGCTTCAATTT 59.776 29.630 9.34 0.00 45.06 1.82
2176 2224 6.700960 TCGAAAATGTGAACATTGCTTCAATT 59.299 30.769 9.34 0.00 45.06 2.32
2177 2225 6.215121 TCGAAAATGTGAACATTGCTTCAAT 58.785 32.000 9.34 0.00 45.06 2.57
2178 2226 5.586339 TCGAAAATGTGAACATTGCTTCAA 58.414 33.333 9.34 0.00 45.06 2.69
2179 2227 5.180367 TCGAAAATGTGAACATTGCTTCA 57.820 34.783 9.34 0.96 45.06 3.02
2180 2228 6.509317 TTTCGAAAATGTGAACATTGCTTC 57.491 33.333 8.44 9.27 45.06 3.86
2181 2229 6.900568 TTTTCGAAAATGTGAACATTGCTT 57.099 29.167 19.08 1.61 45.06 3.91
2182 2230 6.900568 TTTTTCGAAAATGTGAACATTGCT 57.099 29.167 23.05 0.73 45.06 3.91
2211 2259 1.822371 ACCAGGTTTTGTGACAACCAC 59.178 47.619 8.97 4.07 45.55 4.16
2212 2260 2.223803 ACCAGGTTTTGTGACAACCA 57.776 45.000 8.97 0.00 45.55 3.67
2213 2261 4.929819 ATTACCAGGTTTTGTGACAACC 57.070 40.909 0.00 0.00 43.73 3.77
2214 2262 5.897050 TGAATTACCAGGTTTTGTGACAAC 58.103 37.500 0.00 0.00 0.00 3.32
2215 2263 6.531503 TTGAATTACCAGGTTTTGTGACAA 57.468 33.333 0.00 0.00 0.00 3.18
2216 2264 6.531503 TTTGAATTACCAGGTTTTGTGACA 57.468 33.333 0.00 0.00 0.00 3.58
2217 2265 9.705290 ATTATTTGAATTACCAGGTTTTGTGAC 57.295 29.630 0.00 0.00 0.00 3.67
2283 2331 9.475620 AGATCATGGACCTTCACGTATATATTA 57.524 33.333 0.00 0.00 0.00 0.98
2284 2332 8.367660 AGATCATGGACCTTCACGTATATATT 57.632 34.615 0.00 0.00 0.00 1.28
2285 2333 7.962995 AGATCATGGACCTTCACGTATATAT 57.037 36.000 0.00 0.00 0.00 0.86
2286 2334 9.475620 AATAGATCATGGACCTTCACGTATATA 57.524 33.333 0.00 0.00 0.00 0.86
2287 2335 7.962995 ATAGATCATGGACCTTCACGTATAT 57.037 36.000 0.00 0.00 0.00 0.86
2288 2336 7.670140 AGAATAGATCATGGACCTTCACGTATA 59.330 37.037 0.00 0.00 0.00 1.47
2289 2337 6.495181 AGAATAGATCATGGACCTTCACGTAT 59.505 38.462 0.00 0.00 0.00 3.06
2290 2338 5.833667 AGAATAGATCATGGACCTTCACGTA 59.166 40.000 0.00 0.00 0.00 3.57
2291 2339 4.651503 AGAATAGATCATGGACCTTCACGT 59.348 41.667 0.00 0.00 0.00 4.49
2292 2340 4.987285 CAGAATAGATCATGGACCTTCACG 59.013 45.833 0.00 0.00 0.00 4.35
2293 2341 5.303971 CCAGAATAGATCATGGACCTTCAC 58.696 45.833 0.00 0.00 34.60 3.18
2294 2342 4.202398 GCCAGAATAGATCATGGACCTTCA 60.202 45.833 0.00 0.00 34.60 3.02
2295 2343 4.202398 TGCCAGAATAGATCATGGACCTTC 60.202 45.833 0.00 0.00 34.60 3.46
2296 2344 3.718434 TGCCAGAATAGATCATGGACCTT 59.282 43.478 0.00 0.00 34.60 3.50
2297 2345 3.321039 TGCCAGAATAGATCATGGACCT 58.679 45.455 0.00 0.00 34.60 3.85
2298 2346 3.777106 TGCCAGAATAGATCATGGACC 57.223 47.619 0.00 0.00 34.60 4.46
2299 2347 4.649692 ACATGCCAGAATAGATCATGGAC 58.350 43.478 0.00 0.00 38.92 4.02
2300 2348 4.987963 ACATGCCAGAATAGATCATGGA 57.012 40.909 0.00 0.00 38.92 3.41
2301 2349 4.628766 CGTACATGCCAGAATAGATCATGG 59.371 45.833 0.00 0.00 38.92 3.66
2302 2350 5.119743 CACGTACATGCCAGAATAGATCATG 59.880 44.000 0.00 0.00 40.07 3.07
2303 2351 5.011023 TCACGTACATGCCAGAATAGATCAT 59.989 40.000 0.00 0.00 0.00 2.45
2304 2352 4.340950 TCACGTACATGCCAGAATAGATCA 59.659 41.667 0.00 0.00 0.00 2.92
2305 2353 4.871513 TCACGTACATGCCAGAATAGATC 58.128 43.478 0.00 0.00 0.00 2.75
2306 2354 4.937201 TCACGTACATGCCAGAATAGAT 57.063 40.909 0.00 0.00 0.00 1.98
2307 2355 4.729227 TTCACGTACATGCCAGAATAGA 57.271 40.909 0.00 0.00 0.00 1.98


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

AutoCloner maintained by Alex Coulton.