Multiple sequence alignment - TraesCS1A01G327600

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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 TraesCS1A01G327600 chr1A 100.000 2318 0 0 1 2318 517095424 517097741 0.000000e+00 4281.0
1 TraesCS1A01G327600 chr1A 88.462 52 2 2 493 544 148958885 148958932 2.490000e-05 60.2
2 TraesCS1A01G327600 chr1D 93.747 2127 78 21 6 2096 420648431 420650538 0.000000e+00 3140.0
3 TraesCS1A01G327600 chr1D 89.583 48 3 1 500 547 141706060 141706015 2.490000e-05 60.2
4 TraesCS1A01G327600 chr1B 93.604 1501 73 17 609 2096 568962579 568964069 0.000000e+00 2218.0
5 TraesCS1A01G327600 chr1B 89.583 48 3 1 500 547 195591284 195591239 2.490000e-05 60.2
6 TraesCS1A01G327600 chr2D 98.507 201 2 1 2109 2308 131459112 131459312 1.020000e-93 353.0
7 TraesCS1A01G327600 chr2D 92.611 203 12 3 2108 2308 255684954 255685155 2.910000e-74 289.0
8 TraesCS1A01G327600 chr3D 97.500 200 4 1 2110 2308 67479953 67479754 7.930000e-90 340.0
9 TraesCS1A01G327600 chr3D 95.477 199 8 1 2111 2308 443355382 443355184 1.340000e-82 316.0
10 TraesCS1A01G327600 chr5D 97.030 202 5 1 2108 2308 7592853 7593054 2.850000e-89 339.0
11 TraesCS1A01G327600 chr5D 91.489 47 2 2 497 543 387683652 387683608 1.920000e-06 63.9
12 TraesCS1A01G327600 chr7A 96.535 202 6 1 2108 2308 409257551 409257350 1.330000e-87 333.0
13 TraesCS1A01G327600 chr7A 95.050 202 9 1 2108 2308 213820349 213820550 1.340000e-82 316.0
14 TraesCS1A01G327600 chr3A 95.050 202 8 2 2108 2308 380875091 380874891 1.340000e-82 316.0
15 TraesCS1A01G327600 chr2A 93.467 199 12 1 2111 2308 57321272 57321470 6.260000e-76 294.0
16 TraesCS1A01G327600 chr6D 92.453 53 2 2 492 544 58245367 58245417 8.880000e-10 75.0
17 TraesCS1A01G327600 chr6A 92.453 53 2 2 492 544 73561984 73562034 8.880000e-10 75.0
18 TraesCS1A01G327600 chr7B 93.617 47 2 1 500 545 668450275 668450229 4.130000e-08 69.4
19 TraesCS1A01G327600 chr4D 91.667 48 2 1 494 541 70354156 70354201 5.350000e-07 65.8


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 TraesCS1A01G327600 chr1A 517095424 517097741 2317 False 4281 4281 100.000 1 2318 1 chr1A.!!$F2 2317
1 TraesCS1A01G327600 chr1D 420648431 420650538 2107 False 3140 3140 93.747 6 2096 1 chr1D.!!$F1 2090
2 TraesCS1A01G327600 chr1B 568962579 568964069 1490 False 2218 2218 93.604 609 2096 1 chr1B.!!$F1 1487

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
245 265 0.672401 ACGTGCATCCACCGGTAAAG 60.672 55.0 6.87 0.0 38.79 1.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2215 2264 0.034767 CACCTCATGGGATGTGCACT 60.035 55.0 19.41 3.19 33.81 4.4 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
34 35 7.173047 GCAATTTTGTGACCATTCCAAATTACT 59.827 33.333 0.00 0.00 0.00 2.24
37 38 6.968263 TTGTGACCATTCCAAATTACTTCA 57.032 33.333 0.00 0.00 0.00 3.02
39 40 5.242838 TGTGACCATTCCAAATTACTTCACC 59.757 40.000 0.00 0.00 31.76 4.02
40 41 4.770010 TGACCATTCCAAATTACTTCACCC 59.230 41.667 0.00 0.00 0.00 4.61
60 61 3.589988 CCCTACACAAGATGACTCACAC 58.410 50.000 0.00 0.00 0.00 3.82
78 79 3.002791 ACACGAGAACAATAGTGCATGG 58.997 45.455 0.00 0.00 38.08 3.66
100 101 1.713647 TCTCAGTCTCAGGGACCTTCT 59.286 52.381 0.00 0.00 45.54 2.85
102 103 0.901124 CAGTCTCAGGGACCTTCTGG 59.099 60.000 0.00 0.00 45.54 3.86
172 173 5.431765 GGTACATCATATCATCCATCCACC 58.568 45.833 0.00 0.00 0.00 4.61
189 190 2.033492 CCACCGTCGTAAAACAGTTCAC 60.033 50.000 0.00 0.00 0.00 3.18
200 220 3.542676 AGTTCACCGGTCGCCACA 61.543 61.111 2.59 0.00 0.00 4.17
240 260 1.214367 GTATTACGTGCATCCACCGG 58.786 55.000 0.00 0.00 38.79 5.28
245 265 0.672401 ACGTGCATCCACCGGTAAAG 60.672 55.000 6.87 0.00 38.79 1.85
280 300 1.610102 GCAAGGCTGAGATGTGACAGT 60.610 52.381 0.00 0.00 36.62 3.55
415 442 7.048512 AGTATAAGGTTACAATGGAGTTGAGC 58.951 38.462 0.00 0.00 40.37 4.26
417 444 4.098914 AGGTTACAATGGAGTTGAGCAA 57.901 40.909 0.00 0.00 40.37 3.91
419 446 4.520492 AGGTTACAATGGAGTTGAGCAAAG 59.480 41.667 0.00 0.00 40.37 2.77
429 456 7.106439 TGGAGTTGAGCAAAGTAAAATTTCA 57.894 32.000 0.00 0.00 0.00 2.69
436 463 7.362662 TGAGCAAAGTAAAATTTCAGCTACTG 58.637 34.615 1.91 0.00 0.00 2.74
459 486 2.138320 GATCCACATGAGCACATACGG 58.862 52.381 0.00 0.58 35.09 4.02
475 502 1.777941 ACGGAAGTAAGGCTCTAGGG 58.222 55.000 0.00 0.00 46.88 3.53
509 547 5.065731 CGACCGTTAAGATGTACTACCTCTT 59.934 44.000 10.50 10.50 37.03 2.85
510 548 6.404074 CGACCGTTAAGATGTACTACCTCTTT 60.404 42.308 10.83 0.00 35.29 2.52
603 641 3.612247 CTGCGCCAGCTGGGTTACT 62.612 63.158 33.46 0.00 45.42 2.24
661 703 0.682852 TCCCACCTGTACCTTCAACG 59.317 55.000 0.00 0.00 0.00 4.10
824 866 8.993852 AATTTCAATAATCGATCAAGCTAACG 57.006 30.769 0.00 0.00 0.00 3.18
903 945 1.152715 CTAGTCCCGAGGTCCCCTC 60.153 68.421 0.00 0.00 46.44 4.30
1008 1050 3.126001 TCAACACTGAAGATGGACACC 57.874 47.619 0.00 0.00 0.00 4.16
1024 1066 2.046023 CCGAGCCAATGAGGTGCA 60.046 61.111 0.00 0.00 40.61 4.57
1146 1188 4.338795 AGGGGATGAACTCAGTAGAGAA 57.661 45.455 0.00 0.00 44.98 2.87
1155 1197 2.384029 ACTCAGTAGAGAAGGAAGGGGT 59.616 50.000 0.00 0.00 44.98 4.95
1184 1226 2.678190 GCGTCAAAGAGGCTATCAAGGT 60.678 50.000 4.60 0.00 39.86 3.50
1340 1382 2.079925 AGGTGAGAAGCTTTTCGATGC 58.920 47.619 11.96 3.10 0.00 3.91
1415 1459 4.629200 GTCTGCCAATCTACTGAAGAGTTG 59.371 45.833 0.00 0.00 37.74 3.16
1473 1517 9.316730 GGCAACATGTCAATTGTAAATATGATT 57.683 29.630 5.13 0.00 0.00 2.57
1532 1576 3.313249 TCCGAATGTATGCAAGCTTCATG 59.687 43.478 16.76 1.23 0.00 3.07
1540 1584 0.815734 GCAAGCTTCATGCACTGGAT 59.184 50.000 3.97 0.00 45.94 3.41
1569 1613 4.405358 TGAAACTGGTTTTCTGCCTTCATT 59.595 37.500 0.13 0.00 43.70 2.57
1584 1628 8.036575 TCTGCCTTCATTTTATTTTTCATGAGG 58.963 33.333 0.00 0.00 0.00 3.86
1586 1630 8.036575 TGCCTTCATTTTATTTTTCATGAGGAG 58.963 33.333 0.00 0.00 0.00 3.69
1605 1649 9.661954 ATGAGGAGAATATAACTTCCTCTACAA 57.338 33.333 21.09 9.13 42.92 2.41
1617 1661 7.497925 ACTTCCTCTACAATTGTTTGTCTTC 57.502 36.000 17.78 0.00 42.43 2.87
1633 1677 9.226606 TGTTTGTCTTCGATTCTAAAATATGGT 57.773 29.630 0.00 0.00 0.00 3.55
1634 1678 9.704098 GTTTGTCTTCGATTCTAAAATATGGTC 57.296 33.333 0.00 0.00 0.00 4.02
1639 1684 7.437267 TCTTCGATTCTAAAATATGGTCGGTTC 59.563 37.037 0.00 0.00 0.00 3.62
1646 1691 7.561251 TCTAAAATATGGTCGGTTCTCATTCA 58.439 34.615 0.00 0.00 0.00 2.57
1650 1695 3.417069 TGGTCGGTTCTCATTCACAAT 57.583 42.857 0.00 0.00 0.00 2.71
1677 1722 9.612066 TGATGCAGTTGATATATAGTGAAAACA 57.388 29.630 0.00 0.00 0.00 2.83
2022 2071 6.808008 ACTCACATTATGAAGTCAGTTTGG 57.192 37.500 0.00 0.00 36.69 3.28
2056 2105 4.445385 GGATGTGTTGTTTCAGAATGTTGC 59.555 41.667 0.00 0.00 37.40 4.17
2096 2145 3.000727 GCATAGGTCAACAGCGTAGTTT 58.999 45.455 0.00 0.00 0.00 2.66
2097 2146 3.435671 GCATAGGTCAACAGCGTAGTTTT 59.564 43.478 0.00 0.00 0.00 2.43
2098 2147 4.435651 GCATAGGTCAACAGCGTAGTTTTC 60.436 45.833 0.00 0.00 0.00 2.29
2099 2148 3.470645 AGGTCAACAGCGTAGTTTTCT 57.529 42.857 0.00 0.00 0.00 2.52
2100 2149 3.805207 AGGTCAACAGCGTAGTTTTCTT 58.195 40.909 0.00 0.00 0.00 2.52
2101 2150 4.196971 AGGTCAACAGCGTAGTTTTCTTT 58.803 39.130 0.00 0.00 0.00 2.52
2102 2151 4.638865 AGGTCAACAGCGTAGTTTTCTTTT 59.361 37.500 0.00 0.00 0.00 2.27
2103 2152 5.124936 AGGTCAACAGCGTAGTTTTCTTTTT 59.875 36.000 0.00 0.00 0.00 1.94
2130 2179 2.880963 TTTTTGAGAAAACGCAGGGG 57.119 45.000 0.00 0.00 30.07 4.79
2131 2180 2.060050 TTTTGAGAAAACGCAGGGGA 57.940 45.000 0.00 0.00 0.00 4.81
2132 2181 1.314730 TTTGAGAAAACGCAGGGGAC 58.685 50.000 0.00 0.00 0.00 4.46
2133 2182 5.050975 TTTTTGAGAAAACGCAGGGGACC 62.051 47.826 0.00 0.00 38.19 4.46
2145 2194 4.337013 GGGACCCATGCGTTTCAT 57.663 55.556 5.33 0.00 35.31 2.57
2146 2195 2.578683 GGGACCCATGCGTTTCATT 58.421 52.632 5.33 0.00 31.79 2.57
2147 2196 0.455815 GGGACCCATGCGTTTCATTC 59.544 55.000 5.33 0.00 31.79 2.67
2148 2197 0.455815 GGACCCATGCGTTTCATTCC 59.544 55.000 0.00 0.00 31.79 3.01
2149 2198 1.173043 GACCCATGCGTTTCATTCCA 58.827 50.000 0.00 0.00 31.79 3.53
2150 2199 1.750778 GACCCATGCGTTTCATTCCAT 59.249 47.619 0.00 0.00 31.79 3.41
2151 2200 2.166254 GACCCATGCGTTTCATTCCATT 59.834 45.455 0.00 0.00 31.79 3.16
2152 2201 2.094078 ACCCATGCGTTTCATTCCATTG 60.094 45.455 0.00 0.00 31.79 2.82
2153 2202 2.166050 CCCATGCGTTTCATTCCATTGA 59.834 45.455 0.00 0.00 31.79 2.57
2154 2203 3.368220 CCCATGCGTTTCATTCCATTGAA 60.368 43.478 0.00 0.00 33.89 2.69
2155 2204 4.244066 CCATGCGTTTCATTCCATTGAAA 58.756 39.130 0.00 0.00 41.92 2.69
2156 2205 4.689812 CCATGCGTTTCATTCCATTGAAAA 59.310 37.500 1.52 0.00 44.71 2.29
2157 2206 5.163933 CCATGCGTTTCATTCCATTGAAAAG 60.164 40.000 8.01 8.01 44.71 2.27
2158 2207 5.193663 TGCGTTTCATTCCATTGAAAAGA 57.806 34.783 14.20 0.00 44.71 2.52
2159 2208 5.221880 TGCGTTTCATTCCATTGAAAAGAG 58.778 37.500 14.20 5.83 44.71 2.85
2160 2209 5.009510 TGCGTTTCATTCCATTGAAAAGAGA 59.990 36.000 14.20 1.07 44.71 3.10
2161 2210 5.570589 GCGTTTCATTCCATTGAAAAGAGAG 59.429 40.000 14.20 2.15 44.71 3.20
2162 2211 6.568462 GCGTTTCATTCCATTGAAAAGAGAGA 60.568 38.462 14.20 0.00 44.71 3.10
2163 2212 7.020010 CGTTTCATTCCATTGAAAAGAGAGAG 58.980 38.462 6.93 0.00 44.71 3.20
2164 2213 7.308229 CGTTTCATTCCATTGAAAAGAGAGAGT 60.308 37.037 6.93 0.00 44.71 3.24
2165 2214 8.355913 GTTTCATTCCATTGAAAAGAGAGAGTT 58.644 33.333 1.52 0.00 44.71 3.01
2166 2215 8.469309 TTCATTCCATTGAAAAGAGAGAGTTT 57.531 30.769 0.00 0.00 32.82 2.66
2167 2216 7.879070 TCATTCCATTGAAAAGAGAGAGTTTG 58.121 34.615 0.00 0.00 33.32 2.93
2168 2217 7.503566 TCATTCCATTGAAAAGAGAGAGTTTGT 59.496 33.333 0.00 0.00 33.32 2.83
2169 2218 8.786898 CATTCCATTGAAAAGAGAGAGTTTGTA 58.213 33.333 0.00 0.00 33.32 2.41
2170 2219 8.746052 TTCCATTGAAAAGAGAGAGTTTGTAA 57.254 30.769 0.00 0.00 0.00 2.41
2171 2220 8.924511 TCCATTGAAAAGAGAGAGTTTGTAAT 57.075 30.769 0.00 0.00 0.00 1.89
2172 2221 9.354673 TCCATTGAAAAGAGAGAGTTTGTAATT 57.645 29.630 0.00 0.00 0.00 1.40
2181 2230 9.660180 AAGAGAGAGTTTGTAATTACAATCCTC 57.340 33.333 29.46 29.46 44.72 3.71
2182 2231 8.261522 AGAGAGAGTTTGTAATTACAATCCTCC 58.738 37.037 31.00 25.88 44.72 4.30
2183 2232 8.152023 AGAGAGTTTGTAATTACAATCCTCCT 57.848 34.615 31.00 26.84 44.72 3.69
2184 2233 9.268282 AGAGAGTTTGTAATTACAATCCTCCTA 57.732 33.333 31.00 17.49 44.72 2.94
2185 2234 9.535878 GAGAGTTTGTAATTACAATCCTCCTAG 57.464 37.037 31.00 0.00 44.72 3.02
2186 2235 8.487028 AGAGTTTGTAATTACAATCCTCCTAGG 58.513 37.037 31.00 0.82 44.72 3.02
2197 2246 2.591915 CTCCTAGGAGGCGGTTTCA 58.408 57.895 28.68 0.00 38.51 2.69
2198 2247 0.461961 CTCCTAGGAGGCGGTTTCAG 59.538 60.000 28.68 1.89 38.51 3.02
2199 2248 0.040646 TCCTAGGAGGCGGTTTCAGA 59.959 55.000 7.62 0.00 34.61 3.27
2200 2249 1.123928 CCTAGGAGGCGGTTTCAGAT 58.876 55.000 1.05 0.00 0.00 2.90
2201 2250 2.091499 TCCTAGGAGGCGGTTTCAGATA 60.091 50.000 7.62 0.00 34.61 1.98
2202 2251 2.297597 CCTAGGAGGCGGTTTCAGATAG 59.702 54.545 1.05 0.00 0.00 2.08
2203 2252 2.160721 AGGAGGCGGTTTCAGATAGA 57.839 50.000 0.00 0.00 0.00 1.98
2204 2253 2.467880 AGGAGGCGGTTTCAGATAGAA 58.532 47.619 0.00 0.00 0.00 2.10
2205 2254 2.838202 AGGAGGCGGTTTCAGATAGAAA 59.162 45.455 0.00 0.00 43.71 2.52
2206 2255 3.118592 AGGAGGCGGTTTCAGATAGAAAG 60.119 47.826 0.00 0.00 46.34 2.62
2207 2256 3.369576 GGAGGCGGTTTCAGATAGAAAGT 60.370 47.826 0.00 0.00 46.34 2.66
2208 2257 4.142004 GGAGGCGGTTTCAGATAGAAAGTA 60.142 45.833 0.00 0.00 46.34 2.24
2209 2258 5.012328 AGGCGGTTTCAGATAGAAAGTAG 57.988 43.478 0.00 0.00 46.34 2.57
2210 2259 4.710375 AGGCGGTTTCAGATAGAAAGTAGA 59.290 41.667 0.00 0.00 46.34 2.59
2211 2260 5.364157 AGGCGGTTTCAGATAGAAAGTAGAT 59.636 40.000 0.00 0.00 46.34 1.98
2212 2261 5.463724 GGCGGTTTCAGATAGAAAGTAGATG 59.536 44.000 0.00 0.00 46.34 2.90
2213 2262 5.050702 GCGGTTTCAGATAGAAAGTAGATGC 60.051 44.000 0.00 0.00 46.34 3.91
2214 2263 6.276847 CGGTTTCAGATAGAAAGTAGATGCT 58.723 40.000 0.00 0.00 46.34 3.79
2215 2264 7.426410 CGGTTTCAGATAGAAAGTAGATGCTA 58.574 38.462 0.00 0.00 46.34 3.49
2216 2265 7.593273 CGGTTTCAGATAGAAAGTAGATGCTAG 59.407 40.741 0.00 0.00 46.34 3.42
2217 2266 8.417884 GGTTTCAGATAGAAAGTAGATGCTAGT 58.582 37.037 0.00 0.00 46.34 2.57
2218 2267 9.243637 GTTTCAGATAGAAAGTAGATGCTAGTG 57.756 37.037 0.00 0.00 46.34 2.74
2219 2268 6.976088 TCAGATAGAAAGTAGATGCTAGTGC 58.024 40.000 0.00 0.00 40.20 4.40
2220 2269 7.068716 TTCAGATAGAAAGTAGATGCTAGTGCA 59.931 37.037 0.00 0.00 42.91 4.57
2229 2278 3.482147 TGCTAGTGCACATCCCATG 57.518 52.632 21.04 1.75 45.31 3.66
2230 2279 0.911053 TGCTAGTGCACATCCCATGA 59.089 50.000 21.04 0.00 45.31 3.07
2231 2280 1.134310 TGCTAGTGCACATCCCATGAG 60.134 52.381 21.04 3.92 45.31 2.90
2232 2281 1.813092 GCTAGTGCACATCCCATGAGG 60.813 57.143 21.04 0.00 39.41 3.86
2233 2282 1.487976 CTAGTGCACATCCCATGAGGT 59.512 52.381 21.04 0.00 35.52 3.85
2242 2291 2.753043 CCATGAGGTGGGCAGCAC 60.753 66.667 0.00 0.00 44.79 4.40
2243 2292 3.129502 CATGAGGTGGGCAGCACG 61.130 66.667 0.00 0.00 0.00 5.34
2244 2293 3.321648 ATGAGGTGGGCAGCACGA 61.322 61.111 0.00 0.00 0.00 4.35
2245 2294 3.612247 ATGAGGTGGGCAGCACGAC 62.612 63.158 0.00 0.00 0.00 4.34
2246 2295 4.008933 GAGGTGGGCAGCACGACT 62.009 66.667 0.00 0.00 0.00 4.18
2247 2296 3.941657 GAGGTGGGCAGCACGACTC 62.942 68.421 2.95 2.95 0.00 3.36
2248 2297 4.008933 GGTGGGCAGCACGACTCT 62.009 66.667 0.00 0.00 0.00 3.24
2249 2298 2.646175 GGTGGGCAGCACGACTCTA 61.646 63.158 0.00 0.00 0.00 2.43
2250 2299 1.292223 GTGGGCAGCACGACTCTAA 59.708 57.895 0.00 0.00 0.00 2.10
2251 2300 0.737715 GTGGGCAGCACGACTCTAAG 60.738 60.000 0.00 0.00 0.00 2.18
2252 2301 1.153549 GGGCAGCACGACTCTAAGG 60.154 63.158 0.00 0.00 0.00 2.69
2253 2302 1.811679 GGCAGCACGACTCTAAGGC 60.812 63.158 0.00 0.00 0.00 4.35
2254 2303 1.811679 GCAGCACGACTCTAAGGCC 60.812 63.158 0.00 0.00 0.00 5.19
2255 2304 1.591703 CAGCACGACTCTAAGGCCA 59.408 57.895 5.01 0.00 0.00 5.36
2256 2305 0.459237 CAGCACGACTCTAAGGCCAG 60.459 60.000 5.01 0.00 0.00 4.85
2257 2306 1.811679 GCACGACTCTAAGGCCAGC 60.812 63.158 5.01 0.00 0.00 4.85
2258 2307 1.591703 CACGACTCTAAGGCCAGCA 59.408 57.895 5.01 0.00 0.00 4.41
2259 2308 0.459237 CACGACTCTAAGGCCAGCAG 60.459 60.000 5.01 0.00 0.00 4.24
2260 2309 1.520342 CGACTCTAAGGCCAGCAGC 60.520 63.158 5.01 0.00 42.60 5.25
2261 2310 1.520342 GACTCTAAGGCCAGCAGCG 60.520 63.158 5.01 0.00 45.17 5.18
2262 2311 2.894387 CTCTAAGGCCAGCAGCGC 60.894 66.667 5.01 0.00 45.17 5.92
2300 2349 2.993539 GCTTCGGCCTTGATCCTAC 58.006 57.895 0.00 0.00 34.32 3.18
2301 2350 0.466124 GCTTCGGCCTTGATCCTACT 59.534 55.000 0.00 0.00 34.32 2.57
2302 2351 1.539280 GCTTCGGCCTTGATCCTACTC 60.539 57.143 0.00 0.00 34.32 2.59
2303 2352 1.757118 CTTCGGCCTTGATCCTACTCA 59.243 52.381 0.00 0.00 0.00 3.41
2304 2353 1.112113 TCGGCCTTGATCCTACTCAC 58.888 55.000 0.00 0.00 0.00 3.51
2305 2354 1.115467 CGGCCTTGATCCTACTCACT 58.885 55.000 0.00 0.00 0.00 3.41
2306 2355 2.092049 TCGGCCTTGATCCTACTCACTA 60.092 50.000 0.00 0.00 0.00 2.74
2307 2356 2.693591 CGGCCTTGATCCTACTCACTAA 59.306 50.000 0.00 0.00 0.00 2.24
2308 2357 3.322254 CGGCCTTGATCCTACTCACTAAT 59.678 47.826 0.00 0.00 0.00 1.73
2309 2358 4.523173 CGGCCTTGATCCTACTCACTAATA 59.477 45.833 0.00 0.00 0.00 0.98
2310 2359 5.565045 CGGCCTTGATCCTACTCACTAATAC 60.565 48.000 0.00 0.00 0.00 1.89
2311 2360 5.540719 GGCCTTGATCCTACTCACTAATACT 59.459 44.000 0.00 0.00 0.00 2.12
2312 2361 6.451393 GCCTTGATCCTACTCACTAATACTG 58.549 44.000 0.00 0.00 0.00 2.74
2313 2362 6.451393 CCTTGATCCTACTCACTAATACTGC 58.549 44.000 0.00 0.00 0.00 4.40
2314 2363 6.266558 CCTTGATCCTACTCACTAATACTGCT 59.733 42.308 0.00 0.00 0.00 4.24
2315 2364 6.885952 TGATCCTACTCACTAATACTGCTC 57.114 41.667 0.00 0.00 0.00 4.26
2316 2365 6.606069 TGATCCTACTCACTAATACTGCTCT 58.394 40.000 0.00 0.00 0.00 4.09
2317 2366 7.746703 TGATCCTACTCACTAATACTGCTCTA 58.253 38.462 0.00 0.00 0.00 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.181488 TGGTCACAAAATTGCTGACTGTG 60.181 43.478 18.96 7.77 38.30 3.66
1 2 3.023119 TGGTCACAAAATTGCTGACTGT 58.977 40.909 18.96 0.00 38.30 3.55
2 3 3.713858 TGGTCACAAAATTGCTGACTG 57.286 42.857 18.96 3.04 38.30 3.51
3 4 4.262164 GGAATGGTCACAAAATTGCTGACT 60.262 41.667 18.96 7.92 38.30 3.41
4 5 3.989817 GGAATGGTCACAAAATTGCTGAC 59.010 43.478 14.81 14.81 37.91 3.51
34 35 3.248024 AGTCATCTTGTGTAGGGGTGAA 58.752 45.455 0.00 0.00 0.00 3.18
37 38 2.567615 GTGAGTCATCTTGTGTAGGGGT 59.432 50.000 0.00 0.00 0.00 4.95
39 40 3.589988 GTGTGAGTCATCTTGTGTAGGG 58.410 50.000 0.00 0.00 0.00 3.53
40 41 3.057526 TCGTGTGAGTCATCTTGTGTAGG 60.058 47.826 0.00 0.00 0.00 3.18
60 61 2.283298 AGCCATGCACTATTGTTCTCG 58.717 47.619 0.00 0.00 0.00 4.04
78 79 0.324275 AGGTCCCTGAGACTGAGAGC 60.324 60.000 0.00 0.00 45.54 4.09
115 116 5.030147 TCAAGGTAGACATGGTAGATTGGT 58.970 41.667 0.00 0.00 0.00 3.67
118 119 6.620877 TGTTCAAGGTAGACATGGTAGATT 57.379 37.500 0.00 0.00 0.00 2.40
119 120 6.620877 TTGTTCAAGGTAGACATGGTAGAT 57.379 37.500 0.00 0.00 0.00 1.98
172 173 1.190763 CCGGTGAACTGTTTTACGACG 59.809 52.381 11.42 0.00 0.00 5.12
209 229 1.203065 CGTAATACCTTCGCGGAACC 58.797 55.000 6.13 0.00 36.31 3.62
212 232 0.526096 GCACGTAATACCTTCGCGGA 60.526 55.000 6.13 0.00 36.31 5.54
213 233 0.802994 TGCACGTAATACCTTCGCGG 60.803 55.000 6.13 0.00 39.35 6.46
214 234 1.189446 GATGCACGTAATACCTTCGCG 59.811 52.381 0.00 0.00 0.00 5.87
215 235 1.525619 GGATGCACGTAATACCTTCGC 59.474 52.381 0.00 0.00 0.00 4.70
216 236 2.538449 GTGGATGCACGTAATACCTTCG 59.462 50.000 0.10 0.00 0.00 3.79
217 237 2.870411 GGTGGATGCACGTAATACCTTC 59.130 50.000 11.52 0.00 0.00 3.46
222 242 0.825410 ACCGGTGGATGCACGTAATA 59.175 50.000 6.12 0.00 0.00 0.98
265 285 1.001293 TGGACACTGTCACATCTCAGC 59.999 52.381 11.34 0.00 35.37 4.26
267 287 3.168292 AGATGGACACTGTCACATCTCA 58.832 45.455 23.84 10.11 41.75 3.27
280 300 1.839994 CCTTGGAGGCTAAGATGGACA 59.160 52.381 0.00 0.00 0.00 4.02
327 349 3.201045 AGTTGAGAATAAGGGGAAGCTCC 59.799 47.826 0.00 0.00 35.23 4.70
415 442 6.208599 TCCCCAGTAGCTGAAATTTTACTTTG 59.791 38.462 0.00 0.00 32.44 2.77
417 444 5.887754 TCCCCAGTAGCTGAAATTTTACTT 58.112 37.500 0.00 0.00 32.44 2.24
419 446 5.299531 GGATCCCCAGTAGCTGAAATTTTAC 59.700 44.000 0.00 0.00 32.44 2.01
429 456 1.135094 CATGTGGATCCCCAGTAGCT 58.865 55.000 9.90 0.00 44.55 3.32
436 463 0.184451 ATGTGCTCATGTGGATCCCC 59.816 55.000 9.90 0.00 32.51 4.81
459 486 4.698575 CATGTTCCCTAGAGCCTTACTTC 58.301 47.826 0.00 0.00 0.00 3.01
474 501 1.149987 TAACGGTCGTTGCATGTTCC 58.850 50.000 17.57 0.00 38.92 3.62
475 502 2.477375 TCTTAACGGTCGTTGCATGTTC 59.523 45.455 17.57 0.00 38.92 3.18
510 548 9.249053 TGCCAAAACATCTTATATTTAGGAACA 57.751 29.630 0.00 0.00 0.00 3.18
521 559 6.996509 ACATTGAACTGCCAAAACATCTTAT 58.003 32.000 0.00 0.00 0.00 1.73
527 565 3.549827 CGCTACATTGAACTGCCAAAACA 60.550 43.478 0.00 0.00 0.00 2.83
533 571 1.060937 CGCGCTACATTGAACTGCC 59.939 57.895 5.56 0.00 0.00 4.85
586 624 3.636231 AGTAACCCAGCTGGCGCA 61.636 61.111 28.39 10.78 39.10 6.09
588 626 1.741770 GACAGTAACCCAGCTGGCG 60.742 63.158 28.39 21.83 37.83 5.69
603 641 8.972127 GGTCTTATTAGCTATGATCCTATGACA 58.028 37.037 0.00 0.00 0.00 3.58
661 703 2.632544 TTCACATGGCTGCAGCTGC 61.633 57.895 35.82 31.89 41.70 5.25
824 866 2.888834 TTTTCCTTTGGCTTGTCTGC 57.111 45.000 0.00 0.00 0.00 4.26
856 898 7.067008 TGCTAGCCTACTTGTATGGAAAATTTC 59.933 37.037 13.29 0.00 0.00 2.17
903 945 1.801913 CGAACAGAAGGGAGCGACG 60.802 63.158 0.00 0.00 0.00 5.12
904 946 0.733223 GACGAACAGAAGGGAGCGAC 60.733 60.000 0.00 0.00 0.00 5.19
1008 1050 1.028330 ATGTGCACCTCATTGGCTCG 61.028 55.000 15.69 0.00 40.22 5.03
1024 1066 1.802960 CTCTTTGAAGTCGCAGCATGT 59.197 47.619 0.00 0.00 39.31 3.21
1146 1188 2.003548 GCCATCCTGACCCCTTCCT 61.004 63.158 0.00 0.00 0.00 3.36
1155 1197 0.250234 CCTCTTTGACGCCATCCTGA 59.750 55.000 0.00 0.00 0.00 3.86
1443 1487 7.701539 ATTTACAATTGACATGTTGCCTAGA 57.298 32.000 13.59 0.00 32.27 2.43
1502 1546 5.455525 GCTTGCATACATTCGGAAACATAAC 59.544 40.000 0.00 0.00 0.00 1.89
1532 1576 7.986085 AACCAGTTTCATATATATCCAGTGC 57.014 36.000 0.00 0.00 0.00 4.40
1540 1584 9.120538 GAAGGCAGAAAACCAGTTTCATATATA 57.879 33.333 0.00 0.00 46.98 0.86
1617 1661 6.700081 TGAGAACCGACCATATTTTAGAATCG 59.300 38.462 0.00 0.00 0.00 3.34
1633 1677 4.142622 GCATCAATTGTGAATGAGAACCGA 60.143 41.667 5.13 0.00 37.30 4.69
1634 1678 4.100529 GCATCAATTGTGAATGAGAACCG 58.899 43.478 5.13 0.00 37.30 4.44
1639 1684 5.705902 TCAACTGCATCAATTGTGAATGAG 58.294 37.500 5.13 4.90 37.30 2.90
1646 1691 9.783081 TCACTATATATCAACTGCATCAATTGT 57.217 29.630 5.13 0.00 0.00 2.71
1844 1892 3.330267 GCAGTAGACAGTTTTCTCTGGG 58.670 50.000 0.00 0.00 39.48 4.45
2056 2105 4.537135 TGCTGTAGACTTTCCCAGTAAG 57.463 45.455 0.00 0.00 35.01 2.34
2111 2160 2.100087 GTCCCCTGCGTTTTCTCAAAAA 59.900 45.455 0.00 0.00 31.13 1.94
2112 2161 1.679153 GTCCCCTGCGTTTTCTCAAAA 59.321 47.619 0.00 0.00 0.00 2.44
2113 2162 1.314730 GTCCCCTGCGTTTTCTCAAA 58.685 50.000 0.00 0.00 0.00 2.69
2114 2163 0.536460 GGTCCCCTGCGTTTTCTCAA 60.536 55.000 0.00 0.00 0.00 3.02
2115 2164 1.072505 GGTCCCCTGCGTTTTCTCA 59.927 57.895 0.00 0.00 0.00 3.27
2116 2165 1.674651 GGGTCCCCTGCGTTTTCTC 60.675 63.158 0.00 0.00 0.00 2.87
2117 2166 1.789576 ATGGGTCCCCTGCGTTTTCT 61.790 55.000 5.13 0.00 36.94 2.52
2118 2167 1.304134 ATGGGTCCCCTGCGTTTTC 60.304 57.895 5.13 0.00 36.94 2.29
2119 2168 1.606313 CATGGGTCCCCTGCGTTTT 60.606 57.895 5.13 0.00 36.94 2.43
2120 2169 2.035626 CATGGGTCCCCTGCGTTT 59.964 61.111 5.13 0.00 36.94 3.60
2121 2170 4.740822 GCATGGGTCCCCTGCGTT 62.741 66.667 20.90 0.00 36.94 4.84
2124 2173 4.740822 AACGCATGGGTCCCCTGC 62.741 66.667 24.41 24.41 37.10 4.85
2125 2174 2.035626 AAACGCATGGGTCCCCTG 59.964 61.111 16.57 7.20 36.94 4.45
2126 2175 1.863155 ATGAAACGCATGGGTCCCCT 61.863 55.000 16.57 0.00 35.42 4.79
2127 2176 0.970427 AATGAAACGCATGGGTCCCC 60.970 55.000 16.57 8.74 37.28 4.81
2128 2177 0.455815 GAATGAAACGCATGGGTCCC 59.544 55.000 16.57 11.13 37.28 4.46
2129 2178 0.455815 GGAATGAAACGCATGGGTCC 59.544 55.000 16.57 11.47 37.28 4.46
2130 2179 1.173043 TGGAATGAAACGCATGGGTC 58.827 50.000 16.57 5.27 37.28 4.46
2131 2180 1.851304 ATGGAATGAAACGCATGGGT 58.149 45.000 10.03 10.03 37.28 4.51
2132 2181 2.166050 TCAATGGAATGAAACGCATGGG 59.834 45.455 8.44 8.44 37.28 4.00
2133 2182 3.507103 TCAATGGAATGAAACGCATGG 57.493 42.857 0.00 0.00 37.28 3.66
2134 2183 5.634439 TCTTTTCAATGGAATGAAACGCATG 59.366 36.000 2.20 0.00 46.06 4.06
2135 2184 5.782047 TCTTTTCAATGGAATGAAACGCAT 58.218 33.333 2.20 0.00 46.06 4.73
2136 2185 5.009510 TCTCTTTTCAATGGAATGAAACGCA 59.990 36.000 2.20 0.00 46.06 5.24
2137 2186 5.460646 TCTCTTTTCAATGGAATGAAACGC 58.539 37.500 2.20 0.00 46.06 4.84
2138 2187 6.902341 TCTCTCTTTTCAATGGAATGAAACG 58.098 36.000 2.20 1.68 46.06 3.60
2139 2188 7.880105 ACTCTCTCTTTTCAATGGAATGAAAC 58.120 34.615 2.20 0.00 46.06 2.78
2140 2189 8.469309 AACTCTCTCTTTTCAATGGAATGAAA 57.531 30.769 0.00 0.00 45.07 2.69
2141 2190 8.355169 CAAACTCTCTCTTTTCAATGGAATGAA 58.645 33.333 0.00 0.00 37.53 2.57
2142 2191 7.503566 ACAAACTCTCTCTTTTCAATGGAATGA 59.496 33.333 0.00 0.00 31.93 2.57
2143 2192 7.655490 ACAAACTCTCTCTTTTCAATGGAATG 58.345 34.615 0.00 0.00 31.93 2.67
2144 2193 7.830099 ACAAACTCTCTCTTTTCAATGGAAT 57.170 32.000 0.00 0.00 31.93 3.01
2145 2194 8.746052 TTACAAACTCTCTCTTTTCAATGGAA 57.254 30.769 0.00 0.00 0.00 3.53
2146 2195 8.924511 ATTACAAACTCTCTCTTTTCAATGGA 57.075 30.769 0.00 0.00 0.00 3.41
2161 2210 8.483758 TCCTAGGAGGATTGTAATTACAAACTC 58.516 37.037 32.67 32.67 44.53 3.01
2162 2211 8.388656 TCCTAGGAGGATTGTAATTACAAACT 57.611 34.615 29.44 27.59 40.06 2.66
2163 2212 8.664211 CTCCTAGGAGGATTGTAATTACAAAC 57.336 38.462 29.44 26.23 44.81 2.93
2179 2228 0.461961 CTGAAACCGCCTCCTAGGAG 59.538 60.000 29.27 29.27 37.67 3.69
2180 2229 0.040646 TCTGAAACCGCCTCCTAGGA 59.959 55.000 11.98 11.98 37.67 2.94
2181 2230 1.123928 ATCTGAAACCGCCTCCTAGG 58.876 55.000 0.82 0.82 38.80 3.02
2182 2231 3.223435 TCTATCTGAAACCGCCTCCTAG 58.777 50.000 0.00 0.00 0.00 3.02
2183 2232 3.308035 TCTATCTGAAACCGCCTCCTA 57.692 47.619 0.00 0.00 0.00 2.94
2184 2233 2.160721 TCTATCTGAAACCGCCTCCT 57.839 50.000 0.00 0.00 0.00 3.69
2185 2234 2.981859 TTCTATCTGAAACCGCCTCC 57.018 50.000 0.00 0.00 0.00 4.30
2186 2235 3.863041 ACTTTCTATCTGAAACCGCCTC 58.137 45.455 0.00 0.00 39.50 4.70
2187 2236 3.983044 ACTTTCTATCTGAAACCGCCT 57.017 42.857 0.00 0.00 39.50 5.52
2188 2237 5.007385 TCTACTTTCTATCTGAAACCGCC 57.993 43.478 0.00 0.00 39.50 6.13
2189 2238 5.050702 GCATCTACTTTCTATCTGAAACCGC 60.051 44.000 0.00 0.00 39.50 5.68
2190 2239 6.276847 AGCATCTACTTTCTATCTGAAACCG 58.723 40.000 0.00 0.00 39.50 4.44
2191 2240 8.417884 ACTAGCATCTACTTTCTATCTGAAACC 58.582 37.037 0.00 0.00 39.50 3.27
2192 2241 9.243637 CACTAGCATCTACTTTCTATCTGAAAC 57.756 37.037 0.00 0.00 39.50 2.78
2193 2242 7.923344 GCACTAGCATCTACTTTCTATCTGAAA 59.077 37.037 0.00 0.00 40.37 2.69
2194 2243 7.429633 GCACTAGCATCTACTTTCTATCTGAA 58.570 38.462 0.00 0.00 41.58 3.02
2195 2244 6.976088 GCACTAGCATCTACTTTCTATCTGA 58.024 40.000 0.00 0.00 41.58 3.27
2210 2259 5.639374 CCTCATGGGATGTGCACTAGCAT 62.639 52.174 19.41 2.32 45.57 3.79
2211 2260 4.390523 CCTCATGGGATGTGCACTAGCA 62.391 54.545 19.41 0.00 43.09 3.49
2212 2261 1.590932 CTCATGGGATGTGCACTAGC 58.409 55.000 19.41 7.19 42.57 3.42
2213 2262 1.487976 ACCTCATGGGATGTGCACTAG 59.512 52.381 19.41 2.77 38.76 2.57
2214 2263 1.210234 CACCTCATGGGATGTGCACTA 59.790 52.381 19.41 4.84 33.81 2.74
2215 2264 0.034767 CACCTCATGGGATGTGCACT 60.035 55.000 19.41 3.19 33.81 4.40
2216 2265 1.033746 CCACCTCATGGGATGTGCAC 61.034 60.000 10.75 10.75 45.95 4.57
2217 2266 1.303948 CCACCTCATGGGATGTGCA 59.696 57.895 0.00 0.00 45.95 4.57
2218 2267 4.247781 CCACCTCATGGGATGTGC 57.752 61.111 0.00 0.00 45.95 4.57
2226 2275 3.129502 CGTGCTGCCCACCTCATG 61.130 66.667 0.00 0.00 41.53 3.07
2227 2276 3.321648 TCGTGCTGCCCACCTCAT 61.322 61.111 0.00 0.00 41.53 2.90
2228 2277 4.314440 GTCGTGCTGCCCACCTCA 62.314 66.667 0.00 0.00 41.53 3.86
2229 2278 3.941657 GAGTCGTGCTGCCCACCTC 62.942 68.421 0.00 0.00 41.53 3.85
2230 2279 4.008933 GAGTCGTGCTGCCCACCT 62.009 66.667 0.00 0.00 41.53 4.00
2231 2280 2.167398 TTAGAGTCGTGCTGCCCACC 62.167 60.000 0.00 0.00 41.53 4.61
2232 2281 0.737715 CTTAGAGTCGTGCTGCCCAC 60.738 60.000 0.00 0.00 41.15 4.61
2233 2282 1.591703 CTTAGAGTCGTGCTGCCCA 59.408 57.895 0.00 0.00 0.00 5.36
2234 2283 1.153549 CCTTAGAGTCGTGCTGCCC 60.154 63.158 0.00 0.00 0.00 5.36
2235 2284 1.811679 GCCTTAGAGTCGTGCTGCC 60.812 63.158 0.00 0.00 0.00 4.85
2236 2285 1.811679 GGCCTTAGAGTCGTGCTGC 60.812 63.158 0.00 0.00 0.00 5.25
2237 2286 0.459237 CTGGCCTTAGAGTCGTGCTG 60.459 60.000 3.32 0.00 0.00 4.41
2238 2287 1.893786 CTGGCCTTAGAGTCGTGCT 59.106 57.895 3.32 0.00 0.00 4.40
2239 2288 1.811679 GCTGGCCTTAGAGTCGTGC 60.812 63.158 3.32 0.00 0.00 5.34
2240 2289 0.459237 CTGCTGGCCTTAGAGTCGTG 60.459 60.000 3.32 0.00 0.00 4.35
2241 2290 1.893786 CTGCTGGCCTTAGAGTCGT 59.106 57.895 3.32 0.00 0.00 4.34
2242 2291 1.520342 GCTGCTGGCCTTAGAGTCG 60.520 63.158 3.32 0.00 34.27 4.18
2243 2292 1.520342 CGCTGCTGGCCTTAGAGTC 60.520 63.158 3.32 0.00 37.74 3.36
2244 2293 2.581354 CGCTGCTGGCCTTAGAGT 59.419 61.111 3.32 0.00 37.74 3.24
2245 2294 2.894387 GCGCTGCTGGCCTTAGAG 60.894 66.667 3.32 2.46 37.74 2.43
2282 2331 0.466124 AGTAGGATCAAGGCCGAAGC 59.534 55.000 0.00 0.00 38.76 3.86
2283 2332 1.757118 TGAGTAGGATCAAGGCCGAAG 59.243 52.381 0.00 0.00 0.00 3.79
2284 2333 1.480954 GTGAGTAGGATCAAGGCCGAA 59.519 52.381 0.00 0.00 0.00 4.30
2285 2334 1.112113 GTGAGTAGGATCAAGGCCGA 58.888 55.000 0.00 0.00 0.00 5.54
2286 2335 1.115467 AGTGAGTAGGATCAAGGCCG 58.885 55.000 0.00 0.00 0.00 6.13
2287 2336 4.965200 ATTAGTGAGTAGGATCAAGGCC 57.035 45.455 0.00 0.00 0.00 5.19
2288 2337 6.451393 CAGTATTAGTGAGTAGGATCAAGGC 58.549 44.000 0.00 0.00 0.00 4.35
2289 2338 6.266558 AGCAGTATTAGTGAGTAGGATCAAGG 59.733 42.308 2.60 0.00 0.00 3.61
2290 2339 7.230510 AGAGCAGTATTAGTGAGTAGGATCAAG 59.769 40.741 2.60 0.00 0.00 3.02
2291 2340 7.063593 AGAGCAGTATTAGTGAGTAGGATCAA 58.936 38.462 2.60 0.00 0.00 2.57
2292 2341 6.606069 AGAGCAGTATTAGTGAGTAGGATCA 58.394 40.000 2.60 0.00 0.00 2.92


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

AutoCloner maintained by Alex Coulton.