Multiple sequence alignment - TraesCS7A01G217500

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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 TraesCS7A01G217500 chr7A 100.000 2816 0 0 1 2816 183950479 183947664 0.000000e+00 5201.0
1 TraesCS7A01G217500 chr7A 85.755 1741 189 32 1 1705 183857931 183856214 0.000000e+00 1786.0
2 TraesCS7A01G217500 chr7A 82.459 1220 192 13 489 1692 183918191 183916978 0.000000e+00 1048.0
3 TraesCS7A01G217500 chr7A 90.756 119 10 1 1909 2027 538102642 538102525 1.040000e-34 158.0
4 TraesCS7A01G217500 chr7A 82.979 94 11 5 2610 2698 117291148 117291241 2.330000e-11 80.5
5 TraesCS7A01G217500 chr7D 94.424 1919 70 16 1 1918 179536338 179534456 0.000000e+00 2916.0
6 TraesCS7A01G217500 chr7D 88.093 1369 149 11 348 1705 179508967 179507602 0.000000e+00 1613.0
7 TraesCS7A01G217500 chr7D 82.438 1452 218 25 266 1692 179522124 179520685 0.000000e+00 1234.0
8 TraesCS7A01G217500 chr7D 95.222 607 22 3 2022 2621 179534458 179533852 0.000000e+00 953.0
9 TraesCS7A01G217500 chr7D 79.146 820 154 12 373 1186 94114614 94113806 4.100000e-153 551.0
10 TraesCS7A01G217500 chr7D 91.892 111 9 0 1917 2027 185178163 185178053 3.760000e-34 156.0
11 TraesCS7A01G217500 chr7D 95.000 40 2 0 2766 2805 64445655 64445616 2.340000e-06 63.9
12 TraesCS7A01G217500 chr7B 87.755 1323 149 10 393 1705 145697362 145696043 0.000000e+00 1533.0
13 TraesCS7A01G217500 chr7B 88.562 1224 113 15 1 1219 145739983 145738782 0.000000e+00 1459.0
14 TraesCS7A01G217500 chr7B 82.000 1450 228 20 266 1692 145710605 145709166 0.000000e+00 1201.0
15 TraesCS7A01G217500 chr7B 87.462 662 57 12 2162 2801 145737617 145736960 0.000000e+00 739.0
16 TraesCS7A01G217500 chr7B 79.218 818 157 11 373 1186 48050322 48049514 8.810000e-155 556.0
17 TraesCS7A01G217500 chr7B 82.420 438 72 4 1269 1705 145738699 145738266 7.360000e-101 377.0
18 TraesCS7A01G217500 chr7B 87.097 155 16 2 2196 2349 145695563 145695412 3.730000e-39 172.0
19 TraesCS7A01G217500 chr7B 84.946 93 10 3 2610 2698 71657453 71657545 1.070000e-14 91.6
20 TraesCS7A01G217500 chr7B 94.872 39 2 0 2769 2807 663110764 663110802 8.420000e-06 62.1
21 TraesCS7A01G217500 chr6A 79.347 857 161 12 373 1219 592500748 592499898 3.120000e-164 588.0
22 TraesCS7A01G217500 chr6A 78.815 439 74 13 1269 1691 592499726 592499291 7.680000e-71 278.0
23 TraesCS7A01G217500 chr6A 79.277 415 70 8 1272 1670 592579992 592580406 2.760000e-70 276.0
24 TraesCS7A01G217500 chr6B 76.887 424 82 6 1279 1687 672885429 672885851 2.820000e-55 226.0
25 TraesCS7A01G217500 chr4B 93.805 113 6 1 1915 2027 315065481 315065370 4.820000e-38 169.0
26 TraesCS7A01G217500 chr4B 88.710 62 6 1 2696 2757 276359708 276359768 1.080000e-09 75.0
27 TraesCS7A01G217500 chr5B 91.597 119 9 1 1910 2027 69548563 69548445 2.240000e-36 163.0
28 TraesCS7A01G217500 chr5B 92.661 109 8 0 1916 2024 51836809 51836917 1.040000e-34 158.0
29 TraesCS7A01G217500 chr5B 89.256 121 11 2 1914 2033 655407527 655407408 1.750000e-32 150.0
30 TraesCS7A01G217500 chr2D 92.174 115 8 1 1910 2024 73968051 73968164 8.070000e-36 161.0
31 TraesCS7A01G217500 chr1D 91.892 111 9 0 1917 2027 41754355 41754465 3.760000e-34 156.0
32 TraesCS7A01G217500 chr1D 100.000 29 0 0 2777 2805 432690248 432690276 1.000000e-03 54.7
33 TraesCS7A01G217500 chr1B 91.964 112 8 1 1917 2027 445431939 445432050 3.760000e-34 156.0
34 TraesCS7A01G217500 chr1A 97.561 41 0 1 2766 2805 139633146 139633186 5.030000e-08 69.4


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 TraesCS7A01G217500 chr7A 183947664 183950479 2815 True 5201.000000 5201 100.000 1 2816 1 chr7A.!!$R3 2815
1 TraesCS7A01G217500 chr7A 183856214 183857931 1717 True 1786.000000 1786 85.755 1 1705 1 chr7A.!!$R1 1704
2 TraesCS7A01G217500 chr7A 183916978 183918191 1213 True 1048.000000 1048 82.459 489 1692 1 chr7A.!!$R2 1203
3 TraesCS7A01G217500 chr7D 179533852 179536338 2486 True 1934.500000 2916 94.823 1 2621 2 chr7D.!!$R6 2620
4 TraesCS7A01G217500 chr7D 179507602 179508967 1365 True 1613.000000 1613 88.093 348 1705 1 chr7D.!!$R3 1357
5 TraesCS7A01G217500 chr7D 179520685 179522124 1439 True 1234.000000 1234 82.438 266 1692 1 chr7D.!!$R4 1426
6 TraesCS7A01G217500 chr7D 94113806 94114614 808 True 551.000000 551 79.146 373 1186 1 chr7D.!!$R2 813
7 TraesCS7A01G217500 chr7B 145709166 145710605 1439 True 1201.000000 1201 82.000 266 1692 1 chr7B.!!$R2 1426
8 TraesCS7A01G217500 chr7B 145736960 145739983 3023 True 858.333333 1459 86.148 1 2801 3 chr7B.!!$R4 2800
9 TraesCS7A01G217500 chr7B 145695412 145697362 1950 True 852.500000 1533 87.426 393 2349 2 chr7B.!!$R3 1956
10 TraesCS7A01G217500 chr7B 48049514 48050322 808 True 556.000000 556 79.218 373 1186 1 chr7B.!!$R1 813
11 TraesCS7A01G217500 chr6A 592499291 592500748 1457 True 433.000000 588 79.081 373 1691 2 chr6A.!!$R1 1318

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
777 791 0.179078 TTTACACTGAACCACGCCGT 60.179 50.0 0.0 0.0 0.0 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1842 2041 0.17668 ATCGCATCCACTCCTCACAC 59.823 55.0 0.0 0.0 0.0 3.82 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
145 146 7.538575 AGTTGCATTTGTTCAAGATACCATAC 58.461 34.615 0.00 0.00 0.00 2.39
160 164 2.305927 ACCATACAAGCTGCAAGTACCT 59.694 45.455 1.02 0.00 35.30 3.08
189 193 4.163078 TGGACCAAAATCAAAAGCTTCCAA 59.837 37.500 0.00 0.00 0.00 3.53
196 200 0.667993 CAAAAGCTTCCAACGCTCCA 59.332 50.000 0.00 0.00 36.56 3.86
197 201 0.954452 AAAAGCTTCCAACGCTCCAG 59.046 50.000 0.00 0.00 36.56 3.86
199 203 2.032681 GCTTCCAACGCTCCAGGT 59.967 61.111 0.00 0.00 0.00 4.00
200 204 2.035442 GCTTCCAACGCTCCAGGTC 61.035 63.158 0.00 0.00 0.00 3.85
201 205 1.376037 CTTCCAACGCTCCAGGTCC 60.376 63.158 0.00 0.00 0.00 4.46
202 206 3.234630 TTCCAACGCTCCAGGTCCG 62.235 63.158 0.80 0.80 0.00 4.79
203 207 4.760047 CCAACGCTCCAGGTCCGG 62.760 72.222 0.00 0.00 0.00 5.14
204 208 3.691342 CAACGCTCCAGGTCCGGA 61.691 66.667 0.00 0.00 0.00 5.14
210 214 3.177291 TCCAGGTCCGGAGACTCA 58.823 61.111 3.06 0.00 43.05 3.41
211 215 1.697910 TCCAGGTCCGGAGACTCAT 59.302 57.895 3.06 0.00 43.05 2.90
212 216 0.684479 TCCAGGTCCGGAGACTCATG 60.684 60.000 3.06 0.00 43.05 3.07
213 217 1.142748 CAGGTCCGGAGACTCATGC 59.857 63.158 3.06 0.00 43.05 4.06
331 342 9.253832 TCCTCTGAAAATCATTGGCTTTAAATA 57.746 29.630 0.00 0.00 0.00 1.40
370 381 1.644509 TACATAGGATGGCAGCGGAT 58.355 50.000 0.00 0.00 33.60 4.18
777 791 0.179078 TTTACACTGAACCACGCCGT 60.179 50.000 0.00 0.00 0.00 5.68
843 864 3.687698 GGTTGCTCCTTTTCGCAGTATTA 59.312 43.478 0.00 0.00 37.46 0.98
857 878 3.055591 CAGTATTAGCTGCGACCATCAG 58.944 50.000 0.00 0.00 34.79 2.90
1068 1089 1.134491 AGGCCAGCCATACGAAGTTAC 60.134 52.381 12.03 0.00 39.70 2.50
1116 1137 1.668826 TGTTTGGTCTGATAGGGGCT 58.331 50.000 0.00 0.00 0.00 5.19
1401 1581 1.561076 AGCAGTTGGTATGATGCAGGA 59.439 47.619 0.00 0.00 41.14 3.86
1516 1696 4.560743 TGCTGCCGCAGTGGTTGA 62.561 61.111 21.29 0.00 42.25 3.18
1581 1773 1.153168 GCTGGATTTGCTCGCCCTA 60.153 57.895 0.00 0.00 0.00 3.53
1641 1833 1.227263 ATCTGTGTATGTCGCCGCC 60.227 57.895 0.00 0.00 0.00 6.13
1713 1905 8.400947 GCATTGTTATGTTGTCATTCTCATAGT 58.599 33.333 0.00 0.00 35.70 2.12
1718 1910 4.256110 TGTTGTCATTCTCATAGTGCTGG 58.744 43.478 0.00 0.00 0.00 4.85
1727 1919 1.839354 TCATAGTGCTGGCATTCCTCA 59.161 47.619 0.00 0.00 0.00 3.86
1736 1928 1.101331 GGCATTCCTCAGCAAAGGAG 58.899 55.000 7.12 0.00 46.02 3.69
1741 1933 1.661463 TCCTCAGCAAAGGAGTCCAT 58.339 50.000 12.86 0.00 40.60 3.41
1809 2001 1.782569 CAGTTTGCTGCAATGTCAACG 59.217 47.619 16.77 4.18 35.77 4.10
1821 2019 4.601019 CAATGTCAACGCCTTGATTATCC 58.399 43.478 1.38 0.00 38.69 2.59
1842 2041 2.097396 CGTGTGTTTGTAGCTCTGTTCG 60.097 50.000 0.00 0.00 0.00 3.95
1845 2044 2.864343 GTGTTTGTAGCTCTGTTCGTGT 59.136 45.455 0.00 0.00 0.00 4.49
1927 2176 9.802039 TTTATTGTTTTTATGTACTCCCTCTGT 57.198 29.630 0.00 0.00 0.00 3.41
1928 2177 9.802039 TTATTGTTTTTATGTACTCCCTCTGTT 57.198 29.630 0.00 0.00 0.00 3.16
1929 2178 7.739498 TTGTTTTTATGTACTCCCTCTGTTC 57.261 36.000 0.00 0.00 0.00 3.18
1930 2179 6.833041 TGTTTTTATGTACTCCCTCTGTTCA 58.167 36.000 0.00 0.00 0.00 3.18
1931 2180 6.708949 TGTTTTTATGTACTCCCTCTGTTCAC 59.291 38.462 0.00 0.00 0.00 3.18
1932 2181 6.681729 TTTTATGTACTCCCTCTGTTCACT 57.318 37.500 0.00 0.00 0.00 3.41
1933 2182 6.681729 TTTATGTACTCCCTCTGTTCACTT 57.318 37.500 0.00 0.00 0.00 3.16
1934 2183 4.810191 ATGTACTCCCTCTGTTCACTTC 57.190 45.455 0.00 0.00 0.00 3.01
1935 2184 3.845860 TGTACTCCCTCTGTTCACTTCT 58.154 45.455 0.00 0.00 0.00 2.85
1936 2185 3.574396 TGTACTCCCTCTGTTCACTTCTG 59.426 47.826 0.00 0.00 0.00 3.02
1937 2186 2.683768 ACTCCCTCTGTTCACTTCTGT 58.316 47.619 0.00 0.00 0.00 3.41
1938 2187 3.845860 ACTCCCTCTGTTCACTTCTGTA 58.154 45.455 0.00 0.00 0.00 2.74
1939 2188 4.223953 ACTCCCTCTGTTCACTTCTGTAA 58.776 43.478 0.00 0.00 0.00 2.41
1940 2189 4.282195 ACTCCCTCTGTTCACTTCTGTAAG 59.718 45.833 0.00 0.00 38.77 2.34
1942 2191 4.281182 TCCCTCTGTTCACTTCTGTAAGTC 59.719 45.833 0.00 0.00 44.28 3.01
1943 2192 4.230657 CCTCTGTTCACTTCTGTAAGTCG 58.769 47.826 0.00 0.00 44.28 4.18
1944 2193 4.261656 CCTCTGTTCACTTCTGTAAGTCGT 60.262 45.833 0.00 0.00 44.28 4.34
1945 2194 5.258456 TCTGTTCACTTCTGTAAGTCGTT 57.742 39.130 0.00 0.00 44.28 3.85
1946 2195 5.657474 TCTGTTCACTTCTGTAAGTCGTTT 58.343 37.500 0.00 0.00 44.28 3.60
1947 2196 6.798482 TCTGTTCACTTCTGTAAGTCGTTTA 58.202 36.000 0.00 0.00 44.28 2.01
1948 2197 7.259882 TCTGTTCACTTCTGTAAGTCGTTTAA 58.740 34.615 0.00 0.00 44.28 1.52
1949 2198 7.434307 TCTGTTCACTTCTGTAAGTCGTTTAAG 59.566 37.037 0.00 0.00 44.28 1.85
1950 2199 7.259882 TGTTCACTTCTGTAAGTCGTTTAAGA 58.740 34.615 0.00 0.00 44.28 2.10
1951 2200 7.221452 TGTTCACTTCTGTAAGTCGTTTAAGAC 59.779 37.037 0.00 0.00 44.28 3.01
1952 2201 6.798482 TCACTTCTGTAAGTCGTTTAAGACA 58.202 36.000 0.00 0.00 44.28 3.41
1953 2202 6.916387 TCACTTCTGTAAGTCGTTTAAGACAG 59.084 38.462 0.00 0.00 44.28 3.51
1954 2203 5.690857 ACTTCTGTAAGTCGTTTAAGACAGC 59.309 40.000 0.00 0.00 42.42 4.40
1955 2204 5.449107 TCTGTAAGTCGTTTAAGACAGCT 57.551 39.130 0.00 0.00 43.24 4.24
1956 2205 5.220381 TCTGTAAGTCGTTTAAGACAGCTG 58.780 41.667 13.48 13.48 43.24 4.24
1957 2206 5.009310 TCTGTAAGTCGTTTAAGACAGCTGA 59.991 40.000 23.35 0.00 43.24 4.26
1958 2207 5.593968 TGTAAGTCGTTTAAGACAGCTGAA 58.406 37.500 23.35 0.04 43.24 3.02
1959 2208 6.044046 TGTAAGTCGTTTAAGACAGCTGAAA 58.956 36.000 23.35 7.52 43.24 2.69
1960 2209 6.704493 TGTAAGTCGTTTAAGACAGCTGAAAT 59.296 34.615 23.35 7.92 43.24 2.17
1961 2210 6.619801 AAGTCGTTTAAGACAGCTGAAATT 57.380 33.333 23.35 13.76 43.24 1.82
1962 2211 5.990408 AGTCGTTTAAGACAGCTGAAATTG 58.010 37.500 23.35 7.48 43.24 2.32
1963 2212 5.758296 AGTCGTTTAAGACAGCTGAAATTGA 59.242 36.000 23.35 9.59 43.24 2.57
1964 2213 5.846473 GTCGTTTAAGACAGCTGAAATTGAC 59.154 40.000 23.35 16.58 40.65 3.18
1965 2214 5.049680 TCGTTTAAGACAGCTGAAATTGACC 60.050 40.000 23.35 0.51 27.41 4.02
1966 2215 5.049405 CGTTTAAGACAGCTGAAATTGACCT 60.049 40.000 23.35 0.00 27.41 3.85
1967 2216 5.947228 TTAAGACAGCTGAAATTGACCTG 57.053 39.130 23.35 0.00 0.00 4.00
1968 2217 3.498774 AGACAGCTGAAATTGACCTGT 57.501 42.857 23.35 0.00 39.27 4.00
1969 2218 3.825328 AGACAGCTGAAATTGACCTGTT 58.175 40.909 23.35 0.00 36.93 3.16
1970 2219 4.210331 AGACAGCTGAAATTGACCTGTTT 58.790 39.130 23.35 0.00 36.93 2.83
1971 2220 4.646492 AGACAGCTGAAATTGACCTGTTTT 59.354 37.500 23.35 0.00 36.93 2.43
1972 2221 5.827797 AGACAGCTGAAATTGACCTGTTTTA 59.172 36.000 23.35 0.00 36.93 1.52
1973 2222 6.016777 AGACAGCTGAAATTGACCTGTTTTAG 60.017 38.462 23.35 0.00 36.93 1.85
1987 2236 6.575162 CCTGTTTTAGGTGCTGTCTTAAAT 57.425 37.500 0.00 0.00 42.00 1.40
1988 2237 6.381801 CCTGTTTTAGGTGCTGTCTTAAATG 58.618 40.000 0.00 0.00 42.00 2.32
1989 2238 6.016276 CCTGTTTTAGGTGCTGTCTTAAATGT 60.016 38.462 0.00 0.00 42.00 2.71
1990 2239 6.966021 TGTTTTAGGTGCTGTCTTAAATGTC 58.034 36.000 0.00 0.00 0.00 3.06
1991 2240 6.770785 TGTTTTAGGTGCTGTCTTAAATGTCT 59.229 34.615 0.00 0.00 0.00 3.41
1992 2241 7.284489 TGTTTTAGGTGCTGTCTTAAATGTCTT 59.716 33.333 0.00 0.00 0.00 3.01
1993 2242 8.780249 GTTTTAGGTGCTGTCTTAAATGTCTTA 58.220 33.333 0.00 0.00 0.00 2.10
1994 2243 8.911918 TTTAGGTGCTGTCTTAAATGTCTTAA 57.088 30.769 0.00 0.00 0.00 1.85
1995 2244 8.911918 TTAGGTGCTGTCTTAAATGTCTTAAA 57.088 30.769 0.00 0.00 0.00 1.52
1996 2245 9.515226 TTAGGTGCTGTCTTAAATGTCTTAAAT 57.485 29.630 0.00 0.00 0.00 1.40
1997 2246 7.820648 AGGTGCTGTCTTAAATGTCTTAAATG 58.179 34.615 0.00 0.00 0.00 2.32
1998 2247 6.528072 GGTGCTGTCTTAAATGTCTTAAATGC 59.472 38.462 0.00 0.00 0.00 3.56
1999 2248 6.528072 GTGCTGTCTTAAATGTCTTAAATGCC 59.472 38.462 0.00 0.00 0.00 4.40
2000 2249 6.434028 TGCTGTCTTAAATGTCTTAAATGCCT 59.566 34.615 0.00 0.00 0.00 4.75
2001 2250 7.039784 TGCTGTCTTAAATGTCTTAAATGCCTT 60.040 33.333 0.00 0.00 0.00 4.35
2002 2251 8.458843 GCTGTCTTAAATGTCTTAAATGCCTTA 58.541 33.333 0.00 0.00 0.00 2.69
2003 2252 9.774742 CTGTCTTAAATGTCTTAAATGCCTTAC 57.225 33.333 0.00 0.00 0.00 2.34
2004 2253 9.290988 TGTCTTAAATGTCTTAAATGCCTTACA 57.709 29.630 0.00 0.00 0.00 2.41
2010 2259 8.816640 AATGTCTTAAATGCCTTACAAAAGTG 57.183 30.769 0.00 0.00 0.00 3.16
2011 2260 7.575414 TGTCTTAAATGCCTTACAAAAGTGA 57.425 32.000 0.00 0.00 0.00 3.41
2012 2261 8.001881 TGTCTTAAATGCCTTACAAAAGTGAA 57.998 30.769 0.00 0.00 0.00 3.18
2013 2262 8.637986 TGTCTTAAATGCCTTACAAAAGTGAAT 58.362 29.630 0.00 0.00 0.00 2.57
2014 2263 8.915654 GTCTTAAATGCCTTACAAAAGTGAATG 58.084 33.333 0.00 0.00 0.00 2.67
2015 2264 8.087750 TCTTAAATGCCTTACAAAAGTGAATGG 58.912 33.333 0.00 0.00 0.00 3.16
2016 2265 6.418057 AAATGCCTTACAAAAGTGAATGGA 57.582 33.333 0.00 0.00 0.00 3.41
2017 2266 5.649782 ATGCCTTACAAAAGTGAATGGAG 57.350 39.130 0.00 0.00 0.00 3.86
2018 2267 3.826157 TGCCTTACAAAAGTGAATGGAGG 59.174 43.478 0.00 0.00 0.00 4.30
2019 2268 3.193479 GCCTTACAAAAGTGAATGGAGGG 59.807 47.826 0.00 0.00 0.00 4.30
2020 2269 4.662278 CCTTACAAAAGTGAATGGAGGGA 58.338 43.478 0.00 0.00 0.00 4.20
2130 2400 1.912043 CTATGCCCTATTCCTCCCCAG 59.088 57.143 0.00 0.00 0.00 4.45
2141 2411 6.787957 CCTATTCCTCCCCAGTTCTAGATTTA 59.212 42.308 0.00 0.00 0.00 1.40
2216 2864 4.092091 GCTAGTATGTTCGAGCATATTGGC 59.908 45.833 26.81 26.81 37.95 4.52
2221 2869 4.511617 TGTTCGAGCATATTGGCAAAAA 57.488 36.364 3.01 0.00 35.83 1.94
2326 2975 3.187700 GGAGCTACGTATGGTTGTTCTG 58.812 50.000 0.00 0.00 33.46 3.02
2507 3160 2.535485 TATGCAGGCACCAGGAACCG 62.535 60.000 0.00 0.00 0.00 4.44
2711 3382 1.064060 GCACTGTTCACGCTCAAAGTT 59.936 47.619 0.00 0.00 0.00 2.66
2721 3392 2.476619 ACGCTCAAAGTTCACGATTCTG 59.523 45.455 0.00 0.00 0.00 3.02
2801 3472 1.964552 GCAGGAGAGCTGCATGTATT 58.035 50.000 1.02 0.00 46.19 1.89
2802 3473 3.117491 GCAGGAGAGCTGCATGTATTA 57.883 47.619 1.02 0.00 46.19 0.98
2803 3474 3.672808 GCAGGAGAGCTGCATGTATTAT 58.327 45.455 1.02 0.00 46.19 1.28
2804 3475 4.825422 GCAGGAGAGCTGCATGTATTATA 58.175 43.478 1.02 0.00 46.19 0.98
2805 3476 4.629200 GCAGGAGAGCTGCATGTATTATAC 59.371 45.833 1.02 0.00 46.19 1.47
2806 3477 5.568423 GCAGGAGAGCTGCATGTATTATACT 60.568 44.000 1.02 0.00 46.19 2.12
2807 3478 6.098679 CAGGAGAGCTGCATGTATTATACTC 58.901 44.000 1.02 0.00 0.00 2.59
2808 3479 5.186797 AGGAGAGCTGCATGTATTATACTCC 59.813 44.000 1.02 0.00 39.98 3.85
2809 3480 5.065704 AGAGCTGCATGTATTATACTCCG 57.934 43.478 1.02 0.00 0.00 4.63
2810 3481 4.524714 AGAGCTGCATGTATTATACTCCGT 59.475 41.667 1.02 0.00 0.00 4.69
2811 3482 5.710567 AGAGCTGCATGTATTATACTCCGTA 59.289 40.000 1.02 0.00 0.00 4.02
2812 3483 6.378564 AGAGCTGCATGTATTATACTCCGTAT 59.621 38.462 1.02 0.00 33.05 3.06
2813 3484 6.936279 AGCTGCATGTATTATACTCCGTATT 58.064 36.000 1.02 0.00 30.79 1.89
2814 3485 8.063200 AGCTGCATGTATTATACTCCGTATTA 57.937 34.615 1.02 0.00 30.79 0.98
2815 3486 8.528643 AGCTGCATGTATTATACTCCGTATTAA 58.471 33.333 1.02 0.00 30.79 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 4.155733 TGCCGGCCGTGTATGAGG 62.156 66.667 26.77 6.93 0.00 3.86
58 59 2.158534 TGCCCACATAGAAGTTGGTGTT 60.159 45.455 0.00 0.00 0.00 3.32
145 146 1.537202 GAACCAGGTACTTGCAGCTTG 59.463 52.381 0.00 0.00 34.60 4.01
196 200 1.000993 AGCATGAGTCTCCGGACCT 59.999 57.895 0.00 0.00 43.05 3.85
197 201 1.142748 CAGCATGAGTCTCCGGACC 59.857 63.158 0.00 0.00 43.05 4.46
199 203 1.000359 TCCAGCATGAGTCTCCGGA 60.000 57.895 2.93 2.93 39.69 5.14
200 204 1.440893 CTCCAGCATGAGTCTCCGG 59.559 63.158 0.00 0.00 39.69 5.14
201 205 1.227205 GCTCCAGCATGAGTCTCCG 60.227 63.158 0.00 0.00 39.69 4.63
202 206 0.540923 AAGCTCCAGCATGAGTCTCC 59.459 55.000 0.00 0.00 45.16 3.71
203 207 1.654317 CAAGCTCCAGCATGAGTCTC 58.346 55.000 0.00 0.00 41.77 3.36
204 208 0.392729 GCAAGCTCCAGCATGAGTCT 60.393 55.000 7.96 0.58 41.77 3.24
205 209 1.375098 GGCAAGCTCCAGCATGAGTC 61.375 60.000 7.96 0.00 41.77 3.36
206 210 1.378250 GGCAAGCTCCAGCATGAGT 60.378 57.895 7.96 0.00 41.77 3.41
207 211 0.963856 TTGGCAAGCTCCAGCATGAG 60.964 55.000 7.96 0.00 41.77 2.90
208 212 0.540133 TTTGGCAAGCTCCAGCATGA 60.540 50.000 7.96 0.00 41.77 3.07
209 213 0.319083 TTTTGGCAAGCTCCAGCATG 59.681 50.000 0.00 0.00 45.16 4.06
210 214 0.606604 CTTTTGGCAAGCTCCAGCAT 59.393 50.000 0.00 0.00 45.16 3.79
211 215 2.043625 CTTTTGGCAAGCTCCAGCA 58.956 52.632 0.00 0.00 45.16 4.41
212 216 1.373873 GCTTTTGGCAAGCTCCAGC 60.374 57.895 3.93 3.37 40.01 4.85
213 217 4.981415 GCTTTTGGCAAGCTCCAG 57.019 55.556 3.93 0.00 40.01 3.86
331 342 2.702270 ATTGGGGAGCAAAAGAGGTT 57.298 45.000 0.00 0.00 0.00 3.50
370 381 1.304962 TACAAGGGAGCGAGCCTGA 60.305 57.895 0.00 0.00 0.00 3.86
527 538 2.028930 CGGAGTTGCAGTAGAAGAAGGT 60.029 50.000 0.00 0.00 0.00 3.50
777 791 3.008375 ACTCAATTTCCTCAGCAGTGCTA 59.992 43.478 19.26 0.44 36.40 3.49
843 864 0.108138 GGTAACTGATGGTCGCAGCT 60.108 55.000 0.00 0.00 36.86 4.24
857 878 1.607148 GTGTCAACCCTGCTTGGTAAC 59.393 52.381 0.00 1.99 37.76 2.50
939 960 2.549349 GCGGGGAAAGTTGTACAAGAGA 60.549 50.000 8.98 0.00 0.00 3.10
1401 1581 2.127271 TGTCATGCATGATCGGGTTT 57.873 45.000 30.89 0.00 39.30 3.27
1513 1693 8.506168 AGCGACCATTCTTTATTCTTATTCAA 57.494 30.769 0.00 0.00 0.00 2.69
1516 1696 8.506168 TTGAGCGACCATTCTTTATTCTTATT 57.494 30.769 0.00 0.00 0.00 1.40
1581 1773 0.179100 CTGCTGCGTATGCCACTAGT 60.179 55.000 4.05 0.00 41.78 2.57
1641 1833 1.300465 CAGGACGGCGATGATCAGG 60.300 63.158 16.62 0.00 0.00 3.86
1718 1910 1.742268 GACTCCTTTGCTGAGGAATGC 59.258 52.381 9.45 0.00 44.92 3.56
1727 1919 2.042831 GCGCATGGACTCCTTTGCT 61.043 57.895 0.30 0.00 33.46 3.91
1736 1928 2.229690 ATTTGCTTGGGCGCATGGAC 62.230 55.000 10.83 0.00 40.04 4.02
1741 1933 1.177895 TGAGAATTTGCTTGGGCGCA 61.178 50.000 10.83 0.00 42.25 6.09
1809 2001 3.190535 ACAAACACACGGATAATCAAGGC 59.809 43.478 0.00 0.00 0.00 4.35
1821 2019 2.097396 CGAACAGAGCTACAAACACACG 60.097 50.000 0.00 0.00 0.00 4.49
1842 2041 0.176680 ATCGCATCCACTCCTCACAC 59.823 55.000 0.00 0.00 0.00 3.82
1845 2044 1.410517 GAAGATCGCATCCACTCCTCA 59.589 52.381 0.00 0.00 0.00 3.86
1915 2164 3.574826 ACAGAAGTGAACAGAGGGAGTAC 59.425 47.826 0.00 0.00 0.00 2.73
1916 2165 3.845860 ACAGAAGTGAACAGAGGGAGTA 58.154 45.455 0.00 0.00 0.00 2.59
1917 2166 2.683768 ACAGAAGTGAACAGAGGGAGT 58.316 47.619 0.00 0.00 0.00 3.85
1918 2167 4.282195 ACTTACAGAAGTGAACAGAGGGAG 59.718 45.833 0.00 0.00 44.50 4.30
1919 2168 4.223953 ACTTACAGAAGTGAACAGAGGGA 58.776 43.478 0.00 0.00 44.50 4.20
1920 2169 4.561105 GACTTACAGAAGTGAACAGAGGG 58.439 47.826 0.00 0.00 46.23 4.30
1921 2170 4.230657 CGACTTACAGAAGTGAACAGAGG 58.769 47.826 0.00 0.00 46.23 3.69
1922 2171 4.861210 ACGACTTACAGAAGTGAACAGAG 58.139 43.478 0.00 0.00 46.23 3.35
1923 2172 4.913335 ACGACTTACAGAAGTGAACAGA 57.087 40.909 0.00 0.00 46.23 3.41
1924 2173 5.968387 AAACGACTTACAGAAGTGAACAG 57.032 39.130 0.00 0.00 46.23 3.16
1925 2174 7.221452 GTCTTAAACGACTTACAGAAGTGAACA 59.779 37.037 0.00 0.00 46.23 3.18
1926 2175 7.221452 TGTCTTAAACGACTTACAGAAGTGAAC 59.779 37.037 0.00 0.00 46.23 3.18
1927 2176 7.259882 TGTCTTAAACGACTTACAGAAGTGAA 58.740 34.615 0.00 0.00 46.23 3.18
1928 2177 6.798482 TGTCTTAAACGACTTACAGAAGTGA 58.202 36.000 0.00 0.00 46.23 3.41
1929 2178 6.345882 GCTGTCTTAAACGACTTACAGAAGTG 60.346 42.308 0.00 0.00 46.23 3.16
1931 2180 5.921408 AGCTGTCTTAAACGACTTACAGAAG 59.079 40.000 0.00 0.00 37.18 2.85
1932 2181 5.690409 CAGCTGTCTTAAACGACTTACAGAA 59.310 40.000 5.25 0.00 37.18 3.02
1933 2182 5.009310 TCAGCTGTCTTAAACGACTTACAGA 59.991 40.000 14.67 0.00 37.18 3.41
1934 2183 5.220381 TCAGCTGTCTTAAACGACTTACAG 58.780 41.667 14.67 0.00 37.87 2.74
1935 2184 5.190992 TCAGCTGTCTTAAACGACTTACA 57.809 39.130 14.67 0.00 35.00 2.41
1936 2185 6.520792 TTTCAGCTGTCTTAAACGACTTAC 57.479 37.500 14.67 0.00 35.00 2.34
1937 2186 7.439955 TCAATTTCAGCTGTCTTAAACGACTTA 59.560 33.333 14.67 0.00 35.00 2.24
1938 2187 6.260050 TCAATTTCAGCTGTCTTAAACGACTT 59.740 34.615 14.67 0.00 35.00 3.01
1939 2188 5.758296 TCAATTTCAGCTGTCTTAAACGACT 59.242 36.000 14.67 0.00 35.00 4.18
1940 2189 5.846473 GTCAATTTCAGCTGTCTTAAACGAC 59.154 40.000 14.67 12.40 34.52 4.34
1941 2190 5.049680 GGTCAATTTCAGCTGTCTTAAACGA 60.050 40.000 14.67 4.79 0.00 3.85
1942 2191 5.049405 AGGTCAATTTCAGCTGTCTTAAACG 60.049 40.000 14.67 2.54 0.00 3.60
1943 2192 6.145535 CAGGTCAATTTCAGCTGTCTTAAAC 58.854 40.000 14.67 6.99 35.13 2.01
1944 2193 6.317789 CAGGTCAATTTCAGCTGTCTTAAA 57.682 37.500 14.67 7.20 35.13 1.52
1945 2194 5.947228 CAGGTCAATTTCAGCTGTCTTAA 57.053 39.130 14.67 4.81 35.13 1.85
1951 2200 5.464168 CCTAAAACAGGTCAATTTCAGCTG 58.536 41.667 7.63 7.63 43.65 4.24
1952 2201 5.712152 CCTAAAACAGGTCAATTTCAGCT 57.288 39.130 0.00 0.00 39.91 4.24
1965 2214 6.970484 ACATTTAAGACAGCACCTAAAACAG 58.030 36.000 0.00 0.00 0.00 3.16
1966 2215 6.770785 AGACATTTAAGACAGCACCTAAAACA 59.229 34.615 0.00 0.00 0.00 2.83
1967 2216 7.203255 AGACATTTAAGACAGCACCTAAAAC 57.797 36.000 0.00 0.00 0.00 2.43
1968 2217 7.817418 AAGACATTTAAGACAGCACCTAAAA 57.183 32.000 0.00 0.00 0.00 1.52
1969 2218 8.911918 TTAAGACATTTAAGACAGCACCTAAA 57.088 30.769 0.00 0.00 0.00 1.85
1970 2219 8.911918 TTTAAGACATTTAAGACAGCACCTAA 57.088 30.769 0.00 0.00 0.00 2.69
1971 2220 8.946085 CATTTAAGACATTTAAGACAGCACCTA 58.054 33.333 0.00 0.00 0.00 3.08
1972 2221 7.575720 GCATTTAAGACATTTAAGACAGCACCT 60.576 37.037 0.00 0.00 0.00 4.00
1973 2222 6.528072 GCATTTAAGACATTTAAGACAGCACC 59.472 38.462 0.00 0.00 0.00 5.01
1974 2223 6.528072 GGCATTTAAGACATTTAAGACAGCAC 59.472 38.462 0.00 0.00 0.00 4.40
1975 2224 6.434028 AGGCATTTAAGACATTTAAGACAGCA 59.566 34.615 0.00 0.00 0.00 4.41
1976 2225 6.856895 AGGCATTTAAGACATTTAAGACAGC 58.143 36.000 0.00 0.00 0.00 4.40
1977 2226 9.774742 GTAAGGCATTTAAGACATTTAAGACAG 57.225 33.333 0.00 0.00 0.00 3.51
1978 2227 9.290988 TGTAAGGCATTTAAGACATTTAAGACA 57.709 29.630 0.00 0.00 0.00 3.41
1984 2233 9.260002 CACTTTTGTAAGGCATTTAAGACATTT 57.740 29.630 0.00 0.00 35.61 2.32
1985 2234 8.637986 TCACTTTTGTAAGGCATTTAAGACATT 58.362 29.630 0.00 0.00 35.61 2.71
1986 2235 8.177119 TCACTTTTGTAAGGCATTTAAGACAT 57.823 30.769 0.00 0.00 35.61 3.06
1987 2236 7.575414 TCACTTTTGTAAGGCATTTAAGACA 57.425 32.000 0.00 0.00 35.61 3.41
1988 2237 8.915654 CATTCACTTTTGTAAGGCATTTAAGAC 58.084 33.333 0.00 0.00 35.61 3.01
1989 2238 8.087750 CCATTCACTTTTGTAAGGCATTTAAGA 58.912 33.333 0.00 0.00 35.61 2.10
1990 2239 8.087750 TCCATTCACTTTTGTAAGGCATTTAAG 58.912 33.333 0.00 0.00 35.61 1.85
1991 2240 7.957002 TCCATTCACTTTTGTAAGGCATTTAA 58.043 30.769 0.00 0.00 35.61 1.52
1992 2241 7.309744 CCTCCATTCACTTTTGTAAGGCATTTA 60.310 37.037 0.00 0.00 35.61 1.40
1993 2242 6.418057 TCCATTCACTTTTGTAAGGCATTT 57.582 33.333 0.00 0.00 35.61 2.32
1994 2243 5.047092 CCTCCATTCACTTTTGTAAGGCATT 60.047 40.000 0.00 0.00 35.61 3.56
1995 2244 4.463891 CCTCCATTCACTTTTGTAAGGCAT 59.536 41.667 0.00 0.00 35.61 4.40
1996 2245 3.826157 CCTCCATTCACTTTTGTAAGGCA 59.174 43.478 0.00 0.00 35.61 4.75
1997 2246 3.193479 CCCTCCATTCACTTTTGTAAGGC 59.807 47.826 0.00 0.00 35.61 4.35
1998 2247 4.662278 TCCCTCCATTCACTTTTGTAAGG 58.338 43.478 0.00 0.00 35.61 2.69
1999 2248 5.316987 ACTCCCTCCATTCACTTTTGTAAG 58.683 41.667 0.00 0.00 37.40 2.34
2000 2249 5.319043 ACTCCCTCCATTCACTTTTGTAA 57.681 39.130 0.00 0.00 0.00 2.41
2001 2250 4.993705 ACTCCCTCCATTCACTTTTGTA 57.006 40.909 0.00 0.00 0.00 2.41
2002 2251 3.884037 ACTCCCTCCATTCACTTTTGT 57.116 42.857 0.00 0.00 0.00 2.83
2003 2252 6.884295 TGTATTACTCCCTCCATTCACTTTTG 59.116 38.462 0.00 0.00 0.00 2.44
2004 2253 7.027874 TGTATTACTCCCTCCATTCACTTTT 57.972 36.000 0.00 0.00 0.00 2.27
2005 2254 6.636454 TGTATTACTCCCTCCATTCACTTT 57.364 37.500 0.00 0.00 0.00 2.66
2006 2255 6.636454 TTGTATTACTCCCTCCATTCACTT 57.364 37.500 0.00 0.00 0.00 3.16
2007 2256 6.636454 TTTGTATTACTCCCTCCATTCACT 57.364 37.500 0.00 0.00 0.00 3.41
2008 2257 8.429641 TCTATTTGTATTACTCCCTCCATTCAC 58.570 37.037 0.00 0.00 0.00 3.18
2009 2258 8.561536 TCTATTTGTATTACTCCCTCCATTCA 57.438 34.615 0.00 0.00 0.00 2.57
2010 2259 9.847224 TTTCTATTTGTATTACTCCCTCCATTC 57.153 33.333 0.00 0.00 0.00 2.67
2011 2260 9.853177 CTTTCTATTTGTATTACTCCCTCCATT 57.147 33.333 0.00 0.00 0.00 3.16
2012 2261 8.440771 CCTTTCTATTTGTATTACTCCCTCCAT 58.559 37.037 0.00 0.00 0.00 3.41
2013 2262 7.626084 TCCTTTCTATTTGTATTACTCCCTCCA 59.374 37.037 0.00 0.00 0.00 3.86
2014 2263 8.030913 TCCTTTCTATTTGTATTACTCCCTCC 57.969 38.462 0.00 0.00 0.00 4.30
2015 2264 8.151596 CCTCCTTTCTATTTGTATTACTCCCTC 58.848 40.741 0.00 0.00 0.00 4.30
2016 2265 7.072581 CCCTCCTTTCTATTTGTATTACTCCCT 59.927 40.741 0.00 0.00 0.00 4.20
2017 2266 7.225011 CCCTCCTTTCTATTTGTATTACTCCC 58.775 42.308 0.00 0.00 0.00 4.30
2018 2267 7.072076 TCCCCTCCTTTCTATTTGTATTACTCC 59.928 40.741 0.00 0.00 0.00 3.85
2019 2268 8.030913 TCCCCTCCTTTCTATTTGTATTACTC 57.969 38.462 0.00 0.00 0.00 2.59
2020 2269 8.440771 CATCCCCTCCTTTCTATTTGTATTACT 58.559 37.037 0.00 0.00 0.00 2.24
2221 2869 4.568152 GCCCGATGCAAAAATGTATAGT 57.432 40.909 0.00 0.00 40.77 2.12
2236 2884 1.270839 CCGAGTCCAAATATGCCCGAT 60.271 52.381 0.00 0.00 0.00 4.18
2326 2975 6.752351 TCTTAGTCTTCGAATCATGTAACTGC 59.248 38.462 0.00 0.00 0.00 4.40
2396 3045 4.098349 ACTGTCTTGTGATGTTTGTGCAAT 59.902 37.500 0.00 0.00 0.00 3.56
2507 3160 4.585955 AGCATTTCATCTTGCATGATCC 57.414 40.909 11.92 0.00 41.35 3.36
2625 3280 8.745464 TTCATCATGAAATTTACACACATGTG 57.255 30.769 24.25 24.25 41.50 3.21
2689 3354 1.331756 CTTTGAGCGTGAACAGTGCTT 59.668 47.619 0.00 0.00 39.49 3.91
2702 3373 4.474226 AACAGAATCGTGAACTTTGAGC 57.526 40.909 0.00 0.00 0.00 4.26
2772 3443 1.074405 AGCTCTCCTGCATGGTTCAAA 59.926 47.619 0.00 0.00 37.07 2.69
2775 3446 2.777969 CAGCTCTCCTGCATGGTTC 58.222 57.895 0.00 0.00 34.21 3.62


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

AutoCloner maintained by Alex Coulton.