Multiple sequence alignment - TraesCS7D01G011500

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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 TraesCS7D01G011500 chr7D 100.000 2777 0 0 1 2777 5125555 5122779 0.000000e+00 5129.0
1 TraesCS7D01G011500 chr7D 84.685 111 16 1 2488 2597 92826341 92826231 2.920000e-20 110.0
2 TraesCS7D01G011500 chr7A 91.385 1451 70 20 1 1407 6352369 6350930 0.000000e+00 1936.0
3 TraesCS7D01G011500 chr7A 92.823 836 21 16 1302 2128 6351116 6350311 0.000000e+00 1175.0
4 TraesCS7D01G011500 chr7A 90.338 207 10 6 2233 2434 6350143 6349942 2.120000e-66 263.0
5 TraesCS7D01G011500 chr7A 90.909 187 9 2 2589 2775 6349679 6349501 7.680000e-61 244.0
6 TraesCS7D01G011500 chr7A 91.209 91 6 2 2416 2506 6349782 6349694 3.760000e-24 122.0
7 TraesCS7D01G011500 chr7A 88.525 61 5 2 2124 2184 721223690 721223748 3.840000e-09 73.1
8 TraesCS7D01G011500 chr4A 92.045 1345 66 14 1 1311 737441795 737443132 0.000000e+00 1853.0
9 TraesCS7D01G011500 chr4A 91.157 769 36 13 1310 2067 737443074 737443821 0.000000e+00 1014.0
10 TraesCS7D01G011500 chr4A 89.404 302 23 4 2416 2717 737444130 737444422 3.380000e-99 372.0
11 TraesCS7D01G011500 chr4A 91.503 153 12 1 2273 2424 737443839 737443991 2.800000e-50 209.0
12 TraesCS7D01G011500 chr4A 87.356 87 11 0 2125 2211 39594270 39594184 1.760000e-17 100.0
13 TraesCS7D01G011500 chr4B 85.586 111 14 2 2489 2597 565943705 565943815 6.290000e-22 115.0
14 TraesCS7D01G011500 chr1B 88.298 94 9 2 2122 2215 53802223 53802314 8.130000e-21 111.0
15 TraesCS7D01G011500 chr1B 81.373 102 17 2 2488 2587 677392639 677392538 6.370000e-12 82.4
16 TraesCS7D01G011500 chr6B 82.569 109 17 2 2488 2594 680723307 680723199 8.190000e-16 95.3
17 TraesCS7D01G011500 chr3B 84.810 79 12 0 2516 2594 741340155 741340233 2.290000e-11 80.5
18 TraesCS7D01G011500 chr6A 93.617 47 3 0 2137 2183 597672470 597672516 1.380000e-08 71.3
19 TraesCS7D01G011500 chr5A 86.667 60 6 2 2529 2587 606204033 606204091 6.420000e-07 65.8
20 TraesCS7D01G011500 chr2A 86.207 58 7 1 2538 2594 714043726 714043783 8.300000e-06 62.1


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7D01G011500 chr7D 5122779 5125555 2776 True 5129 5129 100.00000 1 2777 1 chr7D.!!$R1 2776
1 TraesCS7D01G011500 chr7A 6349501 6352369 2868 True 748 1936 91.33280 1 2775 5 chr7A.!!$R1 2774
2 TraesCS7D01G011500 chr4A 737441795 737444422 2627 False 862 1853 91.02725 1 2717 4 chr4A.!!$F1 2716

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
924 961 2.67107 GGCAGGGCAGCTAACTCA 59.329 61.111 0.0 0.0 34.17 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1930 1978 0.035036 TTAAATCGACACCCGTGGCA 59.965 50.0 0.89 0.0 38.95 4.92 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
35 36 6.156949 TGGTCTTCAATCCAGCTTTACTCTAT 59.843 38.462 0.00 0.00 0.00 1.98
43 44 4.890581 TCCAGCTTTACTCTATCCTCTGAC 59.109 45.833 0.00 0.00 0.00 3.51
546 549 7.722949 AATTCATTTGAGCTTGGGATCTAAA 57.277 32.000 0.00 0.00 0.00 1.85
565 568 9.399403 GATCTAAATTTCTTGAAAACCACACTC 57.601 33.333 0.00 0.00 0.00 3.51
571 574 7.414814 TTTCTTGAAAACCACACTCAAAAAC 57.585 32.000 0.00 0.00 0.00 2.43
572 575 5.474825 TCTTGAAAACCACACTCAAAAACC 58.525 37.500 0.00 0.00 0.00 3.27
573 576 4.873746 TGAAAACCACACTCAAAAACCA 57.126 36.364 0.00 0.00 0.00 3.67
574 577 4.561105 TGAAAACCACACTCAAAAACCAC 58.439 39.130 0.00 0.00 0.00 4.16
650 686 6.589907 GCCCTGTGTGAAAAATATTAGTTTGG 59.410 38.462 0.00 0.00 0.00 3.28
924 961 2.671070 GGCAGGGCAGCTAACTCA 59.329 61.111 0.00 0.00 34.17 3.41
968 1005 2.965572 ACAAAGCAATGCACACAAGT 57.034 40.000 8.35 0.00 0.00 3.16
1053 1091 0.768622 ACATCCTGTTCGGGGACAAA 59.231 50.000 0.00 0.00 35.51 2.83
1183 1221 2.511403 TGCTACGGCAACAACCCA 59.489 55.556 0.00 0.00 46.36 4.51
1236 1274 4.056125 TCACTGGCAGTCGCTCGG 62.056 66.667 19.13 5.55 38.60 4.63
1259 1297 1.968540 GCAACTCAGTGGCAGTCCC 60.969 63.158 0.00 0.00 31.84 4.46
1260 1298 1.757306 CAACTCAGTGGCAGTCCCT 59.243 57.895 0.00 0.00 0.00 4.20
1261 1299 0.321122 CAACTCAGTGGCAGTCCCTC 60.321 60.000 0.00 0.00 0.00 4.30
1262 1300 1.821061 AACTCAGTGGCAGTCCCTCG 61.821 60.000 0.00 0.00 32.31 4.63
1263 1301 2.203640 TCAGTGGCAGTCCCTCGT 60.204 61.111 0.00 0.00 32.31 4.18
1264 1302 2.047844 CAGTGGCAGTCCCTCGTG 60.048 66.667 0.00 0.00 32.31 4.35
1265 1303 3.314331 AGTGGCAGTCCCTCGTGG 61.314 66.667 0.00 0.00 32.31 4.94
1279 1317 4.164252 GTGGGTACGAGCGACAAG 57.836 61.111 0.00 0.00 0.00 3.16
1280 1318 1.445582 GTGGGTACGAGCGACAAGG 60.446 63.158 0.00 0.00 0.00 3.61
1281 1319 2.183555 GGGTACGAGCGACAAGGG 59.816 66.667 0.00 0.00 0.00 3.95
1282 1320 2.183555 GGTACGAGCGACAAGGGG 59.816 66.667 0.00 0.00 0.00 4.79
1283 1321 2.508663 GTACGAGCGACAAGGGGC 60.509 66.667 0.00 0.00 0.00 5.80
1284 1322 4.124351 TACGAGCGACAAGGGGCG 62.124 66.667 0.00 0.00 0.00 6.13
1291 1329 4.740822 GACAAGGGGCGCATGGGT 62.741 66.667 10.83 0.00 0.00 4.51
1292 1330 4.299796 ACAAGGGGCGCATGGGTT 62.300 61.111 10.83 0.00 0.00 4.11
1293 1331 3.451894 CAAGGGGCGCATGGGTTC 61.452 66.667 10.83 4.35 0.00 3.62
1294 1332 4.759205 AAGGGGCGCATGGGTTCC 62.759 66.667 10.83 12.67 0.00 3.62
1297 1335 3.804329 GGGCGCATGGGTTCCCTA 61.804 66.667 10.83 0.00 35.87 3.53
1298 1336 2.203209 GGCGCATGGGTTCCCTAG 60.203 66.667 10.83 3.00 0.00 3.02
1299 1337 2.590092 GCGCATGGGTTCCCTAGT 59.410 61.111 11.82 0.00 0.00 2.57
1300 1338 1.819632 GCGCATGGGTTCCCTAGTG 60.820 63.158 11.82 8.90 0.00 2.74
1301 1339 1.904771 CGCATGGGTTCCCTAGTGA 59.095 57.895 9.43 0.00 0.00 3.41
1302 1340 0.462047 CGCATGGGTTCCCTAGTGAC 60.462 60.000 9.43 2.59 0.00 3.67
1303 1341 0.912486 GCATGGGTTCCCTAGTGACT 59.088 55.000 9.43 0.00 0.00 3.41
1304 1342 1.134371 GCATGGGTTCCCTAGTGACTC 60.134 57.143 9.43 0.00 0.00 3.36
1305 1343 2.187958 CATGGGTTCCCTAGTGACTCA 58.812 52.381 9.43 0.00 0.00 3.41
1306 1344 1.640917 TGGGTTCCCTAGTGACTCAC 58.359 55.000 9.43 0.38 34.10 3.51
1307 1345 0.531200 GGGTTCCCTAGTGACTCACG 59.469 60.000 3.46 0.00 39.64 4.35
1308 1346 0.531200 GGTTCCCTAGTGACTCACGG 59.469 60.000 3.46 0.30 39.64 4.94
1309 1347 0.531200 GTTCCCTAGTGACTCACGGG 59.469 60.000 13.52 13.52 39.64 5.28
1310 1348 1.255667 TTCCCTAGTGACTCACGGGC 61.256 60.000 14.49 0.00 39.64 6.13
1311 1349 1.982395 CCCTAGTGACTCACGGGCA 60.982 63.158 14.80 0.00 39.64 5.36
1312 1350 1.513158 CCTAGTGACTCACGGGCAG 59.487 63.158 3.46 0.96 39.64 4.85
1313 1351 1.251527 CCTAGTGACTCACGGGCAGT 61.252 60.000 3.46 0.00 39.64 4.40
1314 1352 0.171455 CTAGTGACTCACGGGCAGTC 59.829 60.000 9.49 9.49 39.64 3.51
1315 1353 1.248785 TAGTGACTCACGGGCAGTCC 61.249 60.000 12.69 6.34 39.78 3.85
1372 1410 0.538746 TAGTGACTCACTGGCGGTCA 60.539 55.000 20.19 0.00 45.01 4.02
1380 1418 1.531840 ACTGGCGGTCACTCACTCT 60.532 57.895 0.00 0.00 0.00 3.24
1381 1419 1.080230 CTGGCGGTCACTCACTCTG 60.080 63.158 0.00 0.00 0.00 3.35
1382 1420 1.810606 CTGGCGGTCACTCACTCTGT 61.811 60.000 0.00 0.00 0.00 3.41
1406 1444 3.314331 ACTGGCAGTCCCTCGTGG 61.314 66.667 15.88 0.00 0.00 4.94
1590 1637 1.642215 CGACGATGAGGACGACGAT 59.358 57.895 0.00 0.00 46.85 3.73
1591 1638 0.654760 CGACGATGAGGACGACGATG 60.655 60.000 0.00 0.00 46.85 3.84
1592 1639 0.656259 GACGATGAGGACGACGATGA 59.344 55.000 0.00 0.00 34.70 2.92
1593 1640 1.264557 GACGATGAGGACGACGATGAT 59.735 52.381 0.00 0.00 34.70 2.45
1714 1761 1.742880 TTGATGCTGCTGACGCTCC 60.743 57.895 0.00 0.00 36.97 4.70
1715 1762 2.125391 GATGCTGCTGACGCTCCA 60.125 61.111 0.00 0.00 36.97 3.86
1716 1763 2.125229 ATGCTGCTGACGCTCCAG 60.125 61.111 0.00 0.00 36.97 3.86
1930 1978 4.101448 GCAGCCTCACCCGTGGAT 62.101 66.667 0.00 0.00 0.00 3.41
1931 1979 2.124983 CAGCCTCACCCGTGGATG 60.125 66.667 0.00 0.00 36.00 3.51
1932 1980 4.101448 AGCCTCACCCGTGGATGC 62.101 66.667 0.00 0.00 0.00 3.91
1934 1982 3.716195 CCTCACCCGTGGATGCCA 61.716 66.667 0.00 0.00 0.00 4.92
2071 2121 1.825474 CCCTGTGTCGAACCTAGTGAT 59.175 52.381 0.00 0.00 0.00 3.06
2082 2132 2.440409 ACCTAGTGATTCCGTACGTGT 58.560 47.619 15.21 0.00 0.00 4.49
2100 2150 2.615447 GTGTGTGCATGGATAGTGGATG 59.385 50.000 0.00 0.00 0.00 3.51
2124 2174 3.006967 CCTCATTGGCGCTTACTACCTAT 59.993 47.826 7.64 0.00 0.00 2.57
2128 2178 4.843220 TTGGCGCTTACTACCTATCTAC 57.157 45.455 7.64 0.00 0.00 2.59
2129 2179 4.096190 TGGCGCTTACTACCTATCTACT 57.904 45.455 7.64 0.00 0.00 2.57
2130 2180 5.233083 TGGCGCTTACTACCTATCTACTA 57.767 43.478 7.64 0.00 0.00 1.82
2131 2181 4.999950 TGGCGCTTACTACCTATCTACTAC 59.000 45.833 7.64 0.00 0.00 2.73
2136 2186 6.090628 CGCTTACTACCTATCTACTACCTTCG 59.909 46.154 0.00 0.00 0.00 3.79
2138 2188 8.091449 GCTTACTACCTATCTACTACCTTCGTA 58.909 40.741 0.00 0.00 0.00 3.43
2140 2190 6.764379 ACTACCTATCTACTACCTTCGTACC 58.236 44.000 0.00 0.00 0.00 3.34
2141 2191 5.636903 ACCTATCTACTACCTTCGTACCA 57.363 43.478 0.00 0.00 0.00 3.25
2142 2192 6.006275 ACCTATCTACTACCTTCGTACCAA 57.994 41.667 0.00 0.00 0.00 3.67
2143 2193 6.426587 ACCTATCTACTACCTTCGTACCAAA 58.573 40.000 0.00 0.00 0.00 3.28
2144 2194 6.891908 ACCTATCTACTACCTTCGTACCAAAA 59.108 38.462 0.00 0.00 0.00 2.44
2145 2195 7.562821 ACCTATCTACTACCTTCGTACCAAAAT 59.437 37.037 0.00 0.00 0.00 1.82
2146 2196 9.071276 CCTATCTACTACCTTCGTACCAAAATA 57.929 37.037 0.00 0.00 0.00 1.40
2147 2197 9.890352 CTATCTACTACCTTCGTACCAAAATAC 57.110 37.037 0.00 0.00 0.00 1.89
2148 2198 7.944729 TCTACTACCTTCGTACCAAAATACT 57.055 36.000 0.00 0.00 0.00 2.12
2149 2199 8.353423 TCTACTACCTTCGTACCAAAATACTT 57.647 34.615 0.00 0.00 0.00 2.24
2150 2200 8.246180 TCTACTACCTTCGTACCAAAATACTTG 58.754 37.037 0.00 0.00 0.00 3.16
2151 2201 6.762333 ACTACCTTCGTACCAAAATACTTGT 58.238 36.000 0.00 0.00 0.00 3.16
2152 2202 7.895759 ACTACCTTCGTACCAAAATACTTGTA 58.104 34.615 0.00 0.00 0.00 2.41
2153 2203 8.031277 ACTACCTTCGTACCAAAATACTTGTAG 58.969 37.037 0.00 0.00 0.00 2.74
2154 2204 5.640783 ACCTTCGTACCAAAATACTTGTAGC 59.359 40.000 0.00 0.00 0.00 3.58
2155 2205 5.873164 CCTTCGTACCAAAATACTTGTAGCT 59.127 40.000 0.00 0.00 0.00 3.32
2156 2206 6.183360 CCTTCGTACCAAAATACTTGTAGCTG 60.183 42.308 0.00 0.00 0.00 4.24
2157 2207 5.172934 TCGTACCAAAATACTTGTAGCTGG 58.827 41.667 0.00 0.00 0.00 4.85
2158 2208 4.331717 CGTACCAAAATACTTGTAGCTGGG 59.668 45.833 0.00 0.00 0.00 4.45
2159 2209 3.697166 ACCAAAATACTTGTAGCTGGGG 58.303 45.455 0.00 0.00 0.00 4.96
2160 2210 3.332485 ACCAAAATACTTGTAGCTGGGGA 59.668 43.478 0.00 0.00 0.00 4.81
2161 2211 4.202631 ACCAAAATACTTGTAGCTGGGGAA 60.203 41.667 0.00 0.00 0.00 3.97
2162 2212 4.770010 CCAAAATACTTGTAGCTGGGGAAA 59.230 41.667 0.00 0.00 0.00 3.13
2163 2213 5.336451 CCAAAATACTTGTAGCTGGGGAAAC 60.336 44.000 0.00 0.00 0.00 2.78
2164 2214 4.929146 AATACTTGTAGCTGGGGAAACT 57.071 40.909 0.00 0.00 0.00 2.66
2165 2215 6.382919 AAATACTTGTAGCTGGGGAAACTA 57.617 37.500 0.00 0.00 0.00 2.24
2166 2216 6.382919 AATACTTGTAGCTGGGGAAACTAA 57.617 37.500 0.00 0.00 0.00 2.24
2167 2217 4.929146 ACTTGTAGCTGGGGAAACTAAT 57.071 40.909 0.00 0.00 0.00 1.73
2168 2218 7.685849 ATACTTGTAGCTGGGGAAACTAATA 57.314 36.000 0.00 0.00 0.00 0.98
2169 2219 5.742063 ACTTGTAGCTGGGGAAACTAATAC 58.258 41.667 0.00 0.00 0.00 1.89
2170 2220 5.249852 ACTTGTAGCTGGGGAAACTAATACA 59.750 40.000 0.00 0.00 0.00 2.29
2171 2221 5.765576 TGTAGCTGGGGAAACTAATACAA 57.234 39.130 0.00 0.00 0.00 2.41
2172 2222 5.741011 TGTAGCTGGGGAAACTAATACAAG 58.259 41.667 0.00 0.00 0.00 3.16
2173 2223 4.929146 AGCTGGGGAAACTAATACAAGT 57.071 40.909 0.00 0.00 0.00 3.16
2174 2224 5.256806 AGCTGGGGAAACTAATACAAGTT 57.743 39.130 0.00 0.00 41.46 2.66
2175 2225 5.254115 AGCTGGGGAAACTAATACAAGTTC 58.746 41.667 0.00 0.00 38.76 3.01
2176 2226 4.398358 GCTGGGGAAACTAATACAAGTTCC 59.602 45.833 0.00 0.00 38.76 3.62
2177 2227 5.806734 GCTGGGGAAACTAATACAAGTTCCT 60.807 44.000 0.00 0.00 38.76 3.36
2178 2228 5.812286 TGGGGAAACTAATACAAGTTCCTC 58.188 41.667 0.00 0.00 38.76 3.71
2182 2232 6.150641 GGGAAACTAATACAAGTTCCTCCAAC 59.849 42.308 8.82 0.00 37.80 3.77
2195 2245 8.818057 CAAGTTCCTCCAACTATAAGTATTTCG 58.182 37.037 0.00 0.00 45.32 3.46
2196 2246 8.075761 AGTTCCTCCAACTATAAGTATTTCGT 57.924 34.615 0.00 0.00 44.13 3.85
2197 2247 8.537858 AGTTCCTCCAACTATAAGTATTTCGTT 58.462 33.333 0.00 0.00 44.13 3.85
2199 2249 9.807649 TTCCTCCAACTATAAGTATTTCGTTAC 57.192 33.333 0.00 0.00 0.00 2.50
2201 2251 9.245962 CCTCCAACTATAAGTATTTCGTTACAG 57.754 37.037 0.00 0.00 0.00 2.74
2205 2255 8.469902 CAACTATAAGTATTTCGTTACAGAGCG 58.530 37.037 0.00 0.00 0.00 5.03
2207 2257 8.068977 ACTATAAGTATTTCGTTACAGAGCGAG 58.931 37.037 0.00 0.00 38.40 5.03
2208 2258 4.698583 AGTATTTCGTTACAGAGCGAGT 57.301 40.909 0.00 0.00 38.40 4.18
2210 2260 5.808403 AGTATTTCGTTACAGAGCGAGTAG 58.192 41.667 0.00 0.00 38.40 2.57
2212 2262 5.808042 ATTTCGTTACAGAGCGAGTAGTA 57.192 39.130 0.00 0.00 38.40 1.82
2213 2263 5.808042 TTTCGTTACAGAGCGAGTAGTAT 57.192 39.130 0.00 0.00 38.40 2.12
2214 2264 6.908870 TTTCGTTACAGAGCGAGTAGTATA 57.091 37.500 0.00 0.00 38.40 1.47
2217 2267 8.593492 TTCGTTACAGAGCGAGTAGTATATAA 57.407 34.615 0.00 0.00 38.40 0.98
2220 2270 9.823098 CGTTACAGAGCGAGTAGTATATAAATT 57.177 33.333 0.00 0.00 0.00 1.82
2246 2393 7.695480 TGGTACATATATTTTTGCTGTGTGT 57.305 32.000 0.00 0.00 0.00 3.72
2263 2410 1.667724 GTGTATGCATGCAGTCTCACC 59.332 52.381 26.69 8.52 0.00 4.02
2271 2418 1.937191 TGCAGTCTCACCTGTGGATA 58.063 50.000 0.00 0.00 34.84 2.59
2399 2550 5.465056 TGTACCAAGCTTAAATTTGCTTTGC 59.535 36.000 11.86 5.08 45.91 3.68
2401 2552 5.852827 ACCAAGCTTAAATTTGCTTTGCTA 58.147 33.333 11.86 0.00 45.91 3.49
2409 2560 5.886960 AAATTTGCTTTGCTAGATCGAGT 57.113 34.783 4.67 0.00 0.00 4.18
2425 2576 5.879237 GATCGAGTTGATGATCTAGCTAGG 58.121 45.833 20.58 2.51 37.47 3.02
2426 2577 4.720046 TCGAGTTGATGATCTAGCTAGGT 58.280 43.478 20.58 14.33 0.00 3.08
2427 2578 5.866207 TCGAGTTGATGATCTAGCTAGGTA 58.134 41.667 20.58 7.81 0.00 3.08
2439 2767 8.851145 TGATCTAGCTAGGTAAAGATGTAAGTG 58.149 37.037 20.58 0.00 0.00 3.16
2440 2768 7.584122 TCTAGCTAGGTAAAGATGTAAGTGG 57.416 40.000 20.58 0.00 0.00 4.00
2514 2842 9.844257 TTTTTGAAAAAGGGTGAACATCATTAT 57.156 25.926 0.00 0.00 0.00 1.28
2517 2845 8.055279 TGAAAAAGGGTGAACATCATTATCTC 57.945 34.615 0.00 0.00 0.00 2.75
2553 2881 9.586150 CATTAATAGAATACAAACACGATGAGC 57.414 33.333 0.00 0.00 0.00 4.26
2557 2885 4.937620 AGAATACAAACACGATGAGCACAT 59.062 37.500 0.00 0.00 39.67 3.21
2562 2890 0.901827 ACACGATGAGCACATACCCA 59.098 50.000 0.00 0.00 36.82 4.51
2626 2954 3.634448 TGGTGTTATTGGTTGGTGTCAAG 59.366 43.478 0.00 0.00 32.92 3.02
2632 2960 2.807247 GGTTGGTGTCAAGCCTGTT 58.193 52.632 0.00 0.00 43.40 3.16
2676 3004 1.229076 GTGTCAAGGGTTGGTGGGT 59.771 57.895 0.00 0.00 0.00 4.51
2677 3005 0.822121 GTGTCAAGGGTTGGTGGGTC 60.822 60.000 0.00 0.00 0.00 4.46
2678 3006 1.282653 TGTCAAGGGTTGGTGGGTCA 61.283 55.000 0.00 0.00 0.00 4.02
2679 3007 0.537371 GTCAAGGGTTGGTGGGTCAG 60.537 60.000 0.00 0.00 0.00 3.51
2680 3008 1.903404 CAAGGGTTGGTGGGTCAGC 60.903 63.158 0.00 0.00 0.00 4.26
2681 3009 3.491598 AAGGGTTGGTGGGTCAGCG 62.492 63.158 0.00 0.00 34.27 5.18
2739 3067 4.342359 ACACTAGGTGAGAACCGAACTAT 58.658 43.478 4.62 0.00 36.96 2.12
2746 3074 2.024273 TGAGAACCGAACTATCCCCTCT 60.024 50.000 0.00 0.00 0.00 3.69
2751 3079 0.676736 CGAACTATCCCCTCTCCTGC 59.323 60.000 0.00 0.00 0.00 4.85
2775 3103 5.977489 TCTTACCGAACAGAAGAGAATCA 57.023 39.130 0.00 0.00 37.82 2.57
2776 3104 5.955488 TCTTACCGAACAGAAGAGAATCAG 58.045 41.667 0.00 0.00 37.82 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 6.663523 TGACTGAAGTACATATTGTCAGAGGA 59.336 38.462 6.01 0.00 38.37 3.71
80 81 4.884164 GTCTATGCAGGTTAGAGGCAAATT 59.116 41.667 0.00 0.00 41.43 1.82
316 318 5.789643 AAAGCTAGTCATTTTGGCTTCAA 57.210 34.783 0.00 0.00 41.51 2.69
486 489 6.963083 ATCCTCACTCACCTTAGTATGTAC 57.037 41.667 0.00 0.00 0.00 2.90
487 490 7.973048 AAATCCTCACTCACCTTAGTATGTA 57.027 36.000 0.00 0.00 0.00 2.29
546 549 7.119116 GGTTTTTGAGTGTGGTTTTCAAGAAAT 59.881 33.333 0.00 0.00 32.92 2.17
565 568 8.696410 AAGTATTTACTTGTGTGTGGTTTTTG 57.304 30.769 2.25 0.00 44.30 2.44
571 574 9.959749 ATTTACAAAGTATTTACTTGTGTGTGG 57.040 29.630 18.27 4.39 45.17 4.17
619 655 4.864704 ATTTTTCACACAGGGCGTAAAT 57.135 36.364 0.00 0.00 0.00 1.40
893 930 4.182433 TGCCGTGGGTGCAAGTGA 62.182 61.111 0.00 0.00 35.40 3.41
924 961 6.308015 TGGATTGGCTTTATATATAGGCGT 57.692 37.500 17.74 11.30 39.60 5.68
968 1005 7.507277 ACTGTCTGCTTGGTTATCTATCTATGA 59.493 37.037 0.00 0.00 0.00 2.15
1053 1091 1.079266 CAGCTTTCGCTCCTGCTCT 60.079 57.895 0.00 0.00 45.15 4.09
1200 1238 2.104170 GACTCACTAGAGAACCCCTGG 58.896 57.143 0.00 0.00 44.98 4.45
1236 1274 1.287730 CTGCCACTGAGTTGCTCGAC 61.288 60.000 10.13 0.00 32.35 4.20
1262 1300 1.445582 CCTTGTCGCTCGTACCCAC 60.446 63.158 0.00 0.00 0.00 4.61
1263 1301 2.642254 CCCTTGTCGCTCGTACCCA 61.642 63.158 0.00 0.00 0.00 4.51
1264 1302 2.183555 CCCTTGTCGCTCGTACCC 59.816 66.667 0.00 0.00 0.00 3.69
1265 1303 2.183555 CCCCTTGTCGCTCGTACC 59.816 66.667 0.00 0.00 0.00 3.34
1266 1304 2.508663 GCCCCTTGTCGCTCGTAC 60.509 66.667 0.00 0.00 0.00 3.67
1267 1305 4.124351 CGCCCCTTGTCGCTCGTA 62.124 66.667 0.00 0.00 0.00 3.43
1274 1312 4.740822 ACCCATGCGCCCCTTGTC 62.741 66.667 4.18 0.00 0.00 3.18
1275 1313 4.299796 AACCCATGCGCCCCTTGT 62.300 61.111 4.18 0.00 0.00 3.16
1276 1314 3.451894 GAACCCATGCGCCCCTTG 61.452 66.667 4.18 0.00 0.00 3.61
1277 1315 4.759205 GGAACCCATGCGCCCCTT 62.759 66.667 4.18 0.00 0.00 3.95
1285 1323 5.539816 CGTGAGTCACTAGGGAACCCATG 62.540 56.522 20.64 7.44 40.45 3.66
1286 1324 3.474135 CGTGAGTCACTAGGGAACCCAT 61.474 54.545 20.64 0.38 40.45 4.00
1287 1325 2.163449 CGTGAGTCACTAGGGAACCCA 61.163 57.143 20.64 0.00 40.45 4.51
1288 1326 0.531200 CGTGAGTCACTAGGGAACCC 59.469 60.000 20.64 0.94 40.45 4.11
1289 1327 0.531200 CCGTGAGTCACTAGGGAACC 59.469 60.000 20.64 0.00 40.04 3.62
1290 1328 0.531200 CCCGTGAGTCACTAGGGAAC 59.469 60.000 24.71 0.00 44.70 3.62
1291 1329 1.255667 GCCCGTGAGTCACTAGGGAA 61.256 60.000 30.21 0.00 44.70 3.97
1292 1330 1.681327 GCCCGTGAGTCACTAGGGA 60.681 63.158 30.21 0.00 44.70 4.20
1293 1331 1.949847 CTGCCCGTGAGTCACTAGGG 61.950 65.000 24.66 24.66 44.72 3.53
1294 1332 1.251527 ACTGCCCGTGAGTCACTAGG 61.252 60.000 20.64 20.17 31.34 3.02
1295 1333 0.171455 GACTGCCCGTGAGTCACTAG 59.829 60.000 20.64 14.64 39.80 2.57
1296 1334 1.248785 GGACTGCCCGTGAGTCACTA 61.249 60.000 20.64 4.30 41.50 2.74
1297 1335 2.574955 GGACTGCCCGTGAGTCACT 61.575 63.158 20.64 0.70 41.50 3.41
1298 1336 2.048127 GGACTGCCCGTGAGTCAC 60.048 66.667 13.56 13.56 41.50 3.67
1299 1337 3.311110 GGGACTGCCCGTGAGTCA 61.311 66.667 0.00 0.00 46.48 3.41
1372 1410 2.363680 CCAGTGAGTTGACAGAGTGAGT 59.636 50.000 0.00 0.00 0.00 3.41
1380 1418 0.106708 GGACTGCCAGTGAGTTGACA 59.893 55.000 0.00 0.00 0.00 3.58
1381 1419 0.603975 GGGACTGCCAGTGAGTTGAC 60.604 60.000 0.00 0.00 35.15 3.18
1382 1420 0.764369 AGGGACTGCCAGTGAGTTGA 60.764 55.000 0.00 0.00 37.18 3.18
1590 1637 2.291741 CTCATCATCGTCGTCCTCATCA 59.708 50.000 0.00 0.00 0.00 3.07
1591 1638 2.351253 CCTCATCATCGTCGTCCTCATC 60.351 54.545 0.00 0.00 0.00 2.92
1592 1639 1.611006 CCTCATCATCGTCGTCCTCAT 59.389 52.381 0.00 0.00 0.00 2.90
1593 1640 1.025041 CCTCATCATCGTCGTCCTCA 58.975 55.000 0.00 0.00 0.00 3.86
1880 1927 6.142480 CAGACAGCAAACATATACTAGTACGC 59.858 42.308 4.31 0.21 0.00 4.42
1930 1978 0.035036 TTAAATCGACACCCGTGGCA 59.965 50.000 0.89 0.00 38.95 4.92
1931 1979 1.158434 TTTAAATCGACACCCGTGGC 58.842 50.000 0.00 0.00 39.75 5.01
1932 1980 5.548706 TTTATTTAAATCGACACCCGTGG 57.451 39.130 3.39 0.00 39.75 4.94
1933 1981 9.377383 GATTATTTATTTAAATCGACACCCGTG 57.623 33.333 3.39 0.00 37.16 4.94
1934 1982 8.562052 GGATTATTTATTTAAATCGACACCCGT 58.438 33.333 3.39 0.00 37.16 5.28
1935 1983 8.780249 AGGATTATTTATTTAAATCGACACCCG 58.220 33.333 3.39 0.00 37.16 5.28
1999 2047 1.063806 GAGCATCGTCCATACATCGC 58.936 55.000 0.00 0.00 0.00 4.58
2071 2121 0.946700 CCATGCACACACGTACGGAA 60.947 55.000 21.06 0.00 0.00 4.30
2082 2132 2.158769 GGTCATCCACTATCCATGCACA 60.159 50.000 0.00 0.00 0.00 4.57
2100 2150 2.202566 GTAGTAAGCGCCAATGAGGTC 58.797 52.381 2.29 0.00 40.61 3.85
2124 2174 7.944729 AGTATTTTGGTACGAAGGTAGTAGA 57.055 36.000 0.00 0.00 0.00 2.59
2128 2178 7.009907 GCTACAAGTATTTTGGTACGAAGGTAG 59.990 40.741 0.00 0.00 0.00 3.18
2129 2179 6.813152 GCTACAAGTATTTTGGTACGAAGGTA 59.187 38.462 0.00 0.00 0.00 3.08
2130 2180 5.640783 GCTACAAGTATTTTGGTACGAAGGT 59.359 40.000 0.00 0.00 0.00 3.50
2131 2181 5.873164 AGCTACAAGTATTTTGGTACGAAGG 59.127 40.000 0.00 0.00 0.00 3.46
2136 2186 4.638865 CCCCAGCTACAAGTATTTTGGTAC 59.361 45.833 0.00 0.00 0.00 3.34
2138 2188 3.332485 TCCCCAGCTACAAGTATTTTGGT 59.668 43.478 0.00 0.00 0.00 3.67
2140 2190 5.476945 AGTTTCCCCAGCTACAAGTATTTTG 59.523 40.000 0.00 0.00 0.00 2.44
2141 2191 5.641155 AGTTTCCCCAGCTACAAGTATTTT 58.359 37.500 0.00 0.00 0.00 1.82
2142 2192 5.256806 AGTTTCCCCAGCTACAAGTATTT 57.743 39.130 0.00 0.00 0.00 1.40
2143 2193 4.929146 AGTTTCCCCAGCTACAAGTATT 57.071 40.909 0.00 0.00 0.00 1.89
2144 2194 6.576778 ATTAGTTTCCCCAGCTACAAGTAT 57.423 37.500 0.00 0.00 0.00 2.12
2145 2195 6.441284 TGTATTAGTTTCCCCAGCTACAAGTA 59.559 38.462 0.00 0.00 0.00 2.24
2146 2196 4.929146 ATTAGTTTCCCCAGCTACAAGT 57.071 40.909 0.00 0.00 0.00 3.16
2147 2197 5.741011 TGTATTAGTTTCCCCAGCTACAAG 58.259 41.667 0.00 0.00 0.00 3.16
2148 2198 5.765576 TGTATTAGTTTCCCCAGCTACAA 57.234 39.130 0.00 0.00 0.00 2.41
2149 2199 5.249852 ACTTGTATTAGTTTCCCCAGCTACA 59.750 40.000 0.00 0.00 0.00 2.74
2150 2200 5.742063 ACTTGTATTAGTTTCCCCAGCTAC 58.258 41.667 0.00 0.00 0.00 3.58
2151 2201 6.382919 AACTTGTATTAGTTTCCCCAGCTA 57.617 37.500 0.00 0.00 34.81 3.32
2152 2202 4.929146 ACTTGTATTAGTTTCCCCAGCT 57.071 40.909 0.00 0.00 0.00 4.24
2153 2203 4.398358 GGAACTTGTATTAGTTTCCCCAGC 59.602 45.833 0.00 0.00 38.43 4.85
2154 2204 5.816682 AGGAACTTGTATTAGTTTCCCCAG 58.183 41.667 0.00 0.00 38.43 4.45
2155 2205 5.280830 GGAGGAACTTGTATTAGTTTCCCCA 60.281 44.000 0.00 0.00 41.55 4.96
2156 2206 5.191426 GGAGGAACTTGTATTAGTTTCCCC 58.809 45.833 0.00 0.00 41.55 4.81
2157 2207 5.812286 TGGAGGAACTTGTATTAGTTTCCC 58.188 41.667 0.00 0.00 41.55 3.97
2158 2208 6.940867 AGTTGGAGGAACTTGTATTAGTTTCC 59.059 38.462 0.00 0.00 42.70 3.13
2159 2209 7.981102 AGTTGGAGGAACTTGTATTAGTTTC 57.019 36.000 0.00 0.00 42.70 2.78
2168 2218 9.668497 GAAATACTTATAGTTGGAGGAACTTGT 57.332 33.333 0.00 0.00 42.70 3.16
2169 2219 8.818057 CGAAATACTTATAGTTGGAGGAACTTG 58.182 37.037 0.00 0.00 42.70 3.16
2170 2220 8.537858 ACGAAATACTTATAGTTGGAGGAACTT 58.462 33.333 0.00 0.00 42.70 2.66
2172 2222 8.713737 AACGAAATACTTATAGTTGGAGGAAC 57.286 34.615 0.00 0.00 34.40 3.62
2173 2223 9.807649 GTAACGAAATACTTATAGTTGGAGGAA 57.192 33.333 0.00 0.00 0.00 3.36
2174 2224 8.970020 TGTAACGAAATACTTATAGTTGGAGGA 58.030 33.333 0.00 0.00 0.00 3.71
2175 2225 9.245962 CTGTAACGAAATACTTATAGTTGGAGG 57.754 37.037 0.00 0.00 0.00 4.30
2178 2228 8.753175 GCTCTGTAACGAAATACTTATAGTTGG 58.247 37.037 0.00 0.00 0.00 3.77
2182 2232 8.068977 ACTCGCTCTGTAACGAAATACTTATAG 58.931 37.037 0.00 0.00 37.94 1.31
2190 2240 4.698583 ACTACTCGCTCTGTAACGAAAT 57.301 40.909 0.00 0.00 37.94 2.17
2220 2270 9.402320 ACACACAGCAAAAATATATGTACCATA 57.598 29.630 0.00 0.00 0.00 2.74
2221 2271 8.292444 ACACACAGCAAAAATATATGTACCAT 57.708 30.769 0.00 0.00 0.00 3.55
2222 2272 7.695480 ACACACAGCAAAAATATATGTACCA 57.305 32.000 0.00 0.00 0.00 3.25
2223 2273 9.663904 CATACACACAGCAAAAATATATGTACC 57.336 33.333 0.00 0.00 0.00 3.34
2224 2274 9.169468 GCATACACACAGCAAAAATATATGTAC 57.831 33.333 0.00 0.00 0.00 2.90
2225 2275 8.897752 TGCATACACACAGCAAAAATATATGTA 58.102 29.630 0.00 0.00 34.97 2.29
2226 2276 7.770201 TGCATACACACAGCAAAAATATATGT 58.230 30.769 0.00 0.00 34.97 2.29
2227 2277 8.696175 CATGCATACACACAGCAAAAATATATG 58.304 33.333 0.00 0.00 42.15 1.78
2231 2378 4.863689 GCATGCATACACACAGCAAAAATA 59.136 37.500 14.21 0.00 42.15 1.40
2246 2393 1.556451 ACAGGTGAGACTGCATGCATA 59.444 47.619 22.97 0.00 42.21 3.14
2271 2418 0.669318 CGCAGTCCATTACACGTGGT 60.669 55.000 21.57 8.16 37.96 4.16
2409 2560 8.484214 ACATCTTTACCTAGCTAGATCATCAA 57.516 34.615 22.70 5.20 0.00 2.57
2425 2576 4.436332 CCCGTACCCACTTACATCTTTAC 58.564 47.826 0.00 0.00 0.00 2.01
2426 2577 3.451902 CCCCGTACCCACTTACATCTTTA 59.548 47.826 0.00 0.00 0.00 1.85
2427 2578 2.237893 CCCCGTACCCACTTACATCTTT 59.762 50.000 0.00 0.00 0.00 2.52
2439 2767 1.147600 AATTCATCGCCCCGTACCC 59.852 57.895 0.00 0.00 0.00 3.69
2440 2768 0.179067 TCAATTCATCGCCCCGTACC 60.179 55.000 0.00 0.00 0.00 3.34
2533 2861 5.474825 TGTGCTCATCGTGTTTGTATTCTA 58.525 37.500 0.00 0.00 0.00 2.10
2535 2863 4.661993 TGTGCTCATCGTGTTTGTATTC 57.338 40.909 0.00 0.00 0.00 1.75
2553 2881 0.182061 ATGCAGAGGCTGGGTATGTG 59.818 55.000 0.00 0.00 41.91 3.21
2557 2885 1.879575 AACTATGCAGAGGCTGGGTA 58.120 50.000 13.85 0.00 41.91 3.69
2587 2915 1.493022 ACCAGCAGACAGGTTTGGTTA 59.507 47.619 0.00 0.00 38.98 2.85
2592 2920 3.508845 ATAACACCAGCAGACAGGTTT 57.491 42.857 0.00 0.00 32.38 3.27
2626 2954 6.683974 AGATGATGTGTTATACAAACAGGC 57.316 37.500 0.00 0.00 43.77 4.85
2632 2960 6.597672 GTGACCCAAGATGATGTGTTATACAA 59.402 38.462 0.00 0.00 43.77 2.41
2681 3009 4.241681 CTCTTTTATATCTCCCGCTGAGC 58.758 47.826 0.00 0.00 41.18 4.26
2682 3010 4.524714 TCCTCTTTTATATCTCCCGCTGAG 59.475 45.833 0.00 0.00 42.90 3.35
2739 3067 1.692762 GGTAAGATGCAGGAGAGGGGA 60.693 57.143 0.00 0.00 0.00 4.81
2746 3074 2.176045 TCTGTTCGGTAAGATGCAGGA 58.824 47.619 0.00 0.00 34.85 3.86
2751 3079 6.333416 TGATTCTCTTCTGTTCGGTAAGATG 58.667 40.000 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.