Multiple sequence alignment - TraesCS6D01G157400

Loading Multiple Alignment...

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 TraesCS6D01G157400 chr6D 100.000 4628 0 0 1 4628 133479558 133484185 0.000000e+00 8547.0
1 TraesCS6D01G157400 chr6D 77.884 945 144 41 3353 4267 133583241 133584150 1.140000e-145 527.0
2 TraesCS6D01G157400 chr6D 81.382 709 74 27 1024 1690 133882767 133883459 4.100000e-145 525.0
3 TraesCS6D01G157400 chr6D 80.932 708 80 23 1024 1690 133581378 133582071 4.130000e-140 508.0
4 TraesCS6D01G157400 chr6D 77.399 938 152 37 3353 4264 133884621 133885524 1.920000e-138 503.0
5 TraesCS6D01G157400 chr6D 77.365 941 151 43 3353 4267 133956906 133957810 6.910000e-138 501.0
6 TraesCS6D01G157400 chr6D 80.912 702 75 31 1032 1690 133955053 133955738 2.490000e-137 499.0
7 TraesCS6D01G157400 chr6D 80.183 328 40 13 550 869 133580941 133581251 6.030000e-54 222.0
8 TraesCS6D01G157400 chr6D 80.183 328 40 14 550 869 133954614 133954924 6.030000e-54 222.0
9 TraesCS6D01G157400 chr6D 98.333 60 0 1 895 954 133480399 133480457 2.280000e-18 104.0
10 TraesCS6D01G157400 chr6D 98.333 60 0 1 842 900 133480452 133480511 2.280000e-18 104.0
11 TraesCS6D01G157400 chr6A 93.630 2496 96 30 2134 4578 173434700 173437183 0.000000e+00 3670.0
12 TraesCS6D01G157400 chr6A 92.054 1913 75 24 26 1899 173432741 173434615 0.000000e+00 2619.0
13 TraesCS6D01G157400 chr6A 89.612 2012 106 31 2653 4626 173122780 173124726 0.000000e+00 2462.0
14 TraesCS6D01G157400 chr6A 92.326 1251 41 15 670 1899 173113714 173114930 0.000000e+00 1727.0
15 TraesCS6D01G157400 chr6A 80.085 708 85 19 1024 1690 174449755 174450447 4.190000e-130 475.0
16 TraesCS6D01G157400 chr6A 92.604 338 11 5 1 328 173113383 173113716 1.510000e-129 473.0
17 TraesCS6D01G157400 chr6A 77.013 683 109 29 1032 1690 173315238 173315896 9.530000e-92 348.0
18 TraesCS6D01G157400 chr6A 76.862 376 53 28 201 561 173433279 173432923 1.020000e-41 182.0
19 TraesCS6D01G157400 chr6A 86.047 129 15 3 436 563 173113716 173113590 8.080000e-28 135.0
20 TraesCS6D01G157400 chr6A 98.333 60 0 1 895 954 173113877 173113935 2.280000e-18 104.0
21 TraesCS6D01G157400 chr6A 98.333 60 0 1 895 954 173433538 173433596 2.280000e-18 104.0
22 TraesCS6D01G157400 chr6A 96.610 59 1 1 842 900 173433591 173433648 3.810000e-16 97.1
23 TraesCS6D01G157400 chr6B 92.308 1859 90 25 2793 4626 232325419 232327249 0.000000e+00 2591.0
24 TraesCS6D01G157400 chr6B 94.031 1022 34 9 897 1899 232323590 232324603 0.000000e+00 1524.0
25 TraesCS6D01G157400 chr6B 93.647 913 36 9 1 900 232322744 232323647 0.000000e+00 1345.0
26 TraesCS6D01G157400 chr6B 89.820 668 31 20 2134 2794 232324701 232325338 0.000000e+00 822.0
27 TraesCS6D01G157400 chr6B 81.523 709 74 30 1024 1690 232590042 232590735 8.820000e-147 531.0
28 TraesCS6D01G157400 chr6B 77.825 938 155 33 3353 4267 232591906 232592813 8.820000e-147 531.0
29 TraesCS6D01G157400 chr5D 93.548 186 8 4 1897 2079 535728033 535728217 1.640000e-69 274.0
30 TraesCS6D01G157400 chr5D 92.513 187 10 3 1894 2077 344567239 344567424 9.870000e-67 265.0
31 TraesCS6D01G157400 chr5D 97.222 36 1 0 3040 3075 353529371 353529336 1.390000e-05 62.1
32 TraesCS6D01G157400 chr3D 92.513 187 9 4 1898 2080 7021605 7021420 3.550000e-66 263.0
33 TraesCS6D01G157400 chr2D 75.140 535 86 23 3377 3887 593114903 593115414 1.690000e-49 207.0
34 TraesCS6D01G157400 chr2A 74.586 543 97 22 3377 3887 727444609 727445142 2.820000e-47 200.0
35 TraesCS6D01G157400 chr2A 74.217 543 104 20 3377 3887 727392314 727392852 1.310000e-45 195.0
36 TraesCS6D01G157400 chr1D 81.481 189 23 9 1900 2083 240893777 240893596 1.340000e-30 145.0
37 TraesCS6D01G157400 chr1D 80.667 150 19 3 2134 2277 192571127 192570982 1.760000e-19 108.0
38 TraesCS6D01G157400 chr5A 84.211 76 5 4 3004 3075 467388333 467388261 2.990000e-07 67.6


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 TraesCS6D01G157400 chr6D 133479558 133484185 4627 False 2918.333333 8547 98.888667 1 4628 3 chr6D.!!$F1 4627
1 TraesCS6D01G157400 chr6D 133882767 133885524 2757 False 514.000000 525 79.390500 1024 4264 2 chr6D.!!$F3 3240
2 TraesCS6D01G157400 chr6D 133580941 133584150 3209 False 419.000000 527 79.666333 550 4267 3 chr6D.!!$F2 3717
3 TraesCS6D01G157400 chr6D 133954614 133957810 3196 False 407.333333 501 79.486667 550 4267 3 chr6D.!!$F4 3717
4 TraesCS6D01G157400 chr6A 173122780 173124726 1946 False 2462.000000 2462 89.612000 2653 4626 1 chr6A.!!$F1 1973
5 TraesCS6D01G157400 chr6A 173432741 173437183 4442 False 1622.525000 3670 95.156750 26 4578 4 chr6A.!!$F5 4552
6 TraesCS6D01G157400 chr6A 173113383 173114930 1547 False 768.000000 1727 94.421000 1 1899 3 chr6A.!!$F4 1898
7 TraesCS6D01G157400 chr6A 174449755 174450447 692 False 475.000000 475 80.085000 1024 1690 1 chr6A.!!$F3 666
8 TraesCS6D01G157400 chr6A 173315238 173315896 658 False 348.000000 348 77.013000 1032 1690 1 chr6A.!!$F2 658
9 TraesCS6D01G157400 chr6B 232322744 232327249 4505 False 1570.500000 2591 92.451500 1 4626 4 chr6B.!!$F1 4625
10 TraesCS6D01G157400 chr6B 232590042 232592813 2771 False 531.000000 531 79.674000 1024 4267 2 chr6B.!!$F2 3243
11 TraesCS6D01G157400 chr2D 593114903 593115414 511 False 207.000000 207 75.140000 3377 3887 1 chr2D.!!$F1 510

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
400 414 0.169009 GAACAGGCATGAAACGCTCC 59.831 55.0 4.84 0.00 0.00 4.70 F
820 847 0.173708 GACGTCCTTCCAGGTAGCAG 59.826 60.0 3.51 0.00 36.53 4.24 F
1014 1045 0.244450 CGTCAATGGGCATGCTGTTT 59.756 50.0 18.92 5.71 0.00 2.83 F
2263 2633 0.111253 AAGAGGTCAACCTGGCCAAG 59.889 55.0 7.01 2.23 46.77 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1720 1874 0.879765 CCGGCCGTATCCACTACTAG 59.120 60.000 26.12 0.0 0.0 2.57 R
2084 2398 1.541147 CGTTCACAAGGGCATGTTGAT 59.459 47.619 1.85 0.0 0.0 2.57 R
2623 3034 4.086199 TCCGCGGAAATATGACAAAAAC 57.914 40.909 28.99 0.0 0.0 2.43 R
3758 4564 9.621629 ATTATTGAACCAACGGAAATATCAGTA 57.378 29.630 0.00 0.0 32.5 2.74 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
148 149 7.601856 AGCGTATTTGATTCAGGAAATTTCAA 58.398 30.769 19.49 6.24 0.00 2.69
309 323 7.988904 AAATATACGTCTTCACTAGTCTTGC 57.011 36.000 0.00 0.00 0.00 4.01
400 414 0.169009 GAACAGGCATGAAACGCTCC 59.831 55.000 4.84 0.00 0.00 4.70
407 421 0.462759 CATGAAACGCTCCCTCCCTC 60.463 60.000 0.00 0.00 0.00 4.30
428 442 2.035066 CCTCCCTTCAACAAAACTGCAG 59.965 50.000 13.48 13.48 0.00 4.41
580 594 2.794103 AGCACACATGTCCAAATAGCA 58.206 42.857 0.00 0.00 0.00 3.49
582 596 3.765511 AGCACACATGTCCAAATAGCAAT 59.234 39.130 0.00 0.00 0.00 3.56
613 627 7.934855 ACGGAAATAAGAGTAGTGAAGACTA 57.065 36.000 0.00 0.00 33.21 2.59
661 675 3.813529 CATCCGTGGAAAGAAACACTC 57.186 47.619 0.00 0.00 35.51 3.51
820 847 0.173708 GACGTCCTTCCAGGTAGCAG 59.826 60.000 3.51 0.00 36.53 4.24
821 848 0.542232 ACGTCCTTCCAGGTAGCAGT 60.542 55.000 0.00 0.00 36.53 4.40
822 849 1.272313 ACGTCCTTCCAGGTAGCAGTA 60.272 52.381 0.00 0.00 36.53 2.74
823 850 1.405821 CGTCCTTCCAGGTAGCAGTAG 59.594 57.143 0.00 0.00 36.53 2.57
824 851 1.137282 GTCCTTCCAGGTAGCAGTAGC 59.863 57.143 0.00 0.00 36.53 3.58
825 852 1.195115 CCTTCCAGGTAGCAGTAGCA 58.805 55.000 0.00 0.00 45.49 3.49
947 974 4.868450 AGATCTCGTAGCGCTCATATAC 57.132 45.455 16.34 4.88 0.00 1.47
948 975 3.307512 AGATCTCGTAGCGCTCATATACG 59.692 47.826 16.34 19.07 42.70 3.06
949 976 2.410939 TCTCGTAGCGCTCATATACGT 58.589 47.619 24.19 0.00 42.14 3.57
1014 1045 0.244450 CGTCAATGGGCATGCTGTTT 59.756 50.000 18.92 5.71 0.00 2.83
1117 1160 2.482142 CCCTATCTGGTCAAGAACGAGC 60.482 54.545 0.00 0.00 38.79 5.03
1243 1310 5.632959 CGTATAAGCTAGAGCATACTCACC 58.367 45.833 4.01 0.00 46.09 4.02
1277 1362 2.233605 TAACGACGGCTGTGGATGGG 62.234 60.000 15.26 0.00 0.00 4.00
1607 1713 5.001874 CACGTGGCTAGATACTGGAGTATA 58.998 45.833 7.95 0.00 40.99 1.47
1608 1714 5.648526 CACGTGGCTAGATACTGGAGTATAT 59.351 44.000 7.95 0.00 40.99 0.86
1609 1715 6.822170 CACGTGGCTAGATACTGGAGTATATA 59.178 42.308 7.95 0.80 40.99 0.86
1610 1716 7.499563 CACGTGGCTAGATACTGGAGTATATAT 59.500 40.741 7.95 0.00 40.99 0.86
1670 1776 6.448207 AGATCCAACGTTAGAAGGTAGTAC 57.552 41.667 0.00 0.00 0.00 2.73
1671 1777 6.186234 AGATCCAACGTTAGAAGGTAGTACT 58.814 40.000 0.00 0.00 0.00 2.73
1762 2064 1.216122 GCTGATCTGATTGACGGCTC 58.784 55.000 3.42 0.00 0.00 4.70
1893 2207 0.473755 TGGCGCATGACCCATATCTT 59.526 50.000 10.83 0.00 0.00 2.40
1899 2213 3.683340 CGCATGACCCATATCTTGATCAG 59.317 47.826 0.00 0.00 0.00 2.90
1900 2214 4.649692 GCATGACCCATATCTTGATCAGT 58.350 43.478 0.00 0.00 0.00 3.41
1901 2215 5.068636 GCATGACCCATATCTTGATCAGTT 58.931 41.667 0.00 0.00 0.00 3.16
1902 2216 5.533903 GCATGACCCATATCTTGATCAGTTT 59.466 40.000 0.00 0.00 0.00 2.66
1903 2217 6.040166 GCATGACCCATATCTTGATCAGTTTT 59.960 38.462 0.00 0.00 0.00 2.43
1904 2218 7.646314 CATGACCCATATCTTGATCAGTTTTC 58.354 38.462 0.00 0.00 0.00 2.29
1905 2219 6.122277 TGACCCATATCTTGATCAGTTTTCC 58.878 40.000 0.00 0.00 0.00 3.13
1906 2220 6.069440 TGACCCATATCTTGATCAGTTTTCCT 60.069 38.462 0.00 0.00 0.00 3.36
1907 2221 7.127186 TGACCCATATCTTGATCAGTTTTCCTA 59.873 37.037 0.00 0.00 0.00 2.94
1908 2222 7.872138 ACCCATATCTTGATCAGTTTTCCTAA 58.128 34.615 0.00 0.00 0.00 2.69
1909 2223 7.995488 ACCCATATCTTGATCAGTTTTCCTAAG 59.005 37.037 0.00 0.00 0.00 2.18
1910 2224 7.995488 CCCATATCTTGATCAGTTTTCCTAAGT 59.005 37.037 0.00 0.00 0.00 2.24
1911 2225 9.050601 CCATATCTTGATCAGTTTTCCTAAGTC 57.949 37.037 0.00 0.00 0.00 3.01
1912 2226 9.829507 CATATCTTGATCAGTTTTCCTAAGTCT 57.170 33.333 0.00 0.00 0.00 3.24
1914 2228 7.303182 TCTTGATCAGTTTTCCTAAGTCTCA 57.697 36.000 0.00 0.00 0.00 3.27
1915 2229 7.382110 TCTTGATCAGTTTTCCTAAGTCTCAG 58.618 38.462 0.00 0.00 0.00 3.35
1916 2230 6.672266 TGATCAGTTTTCCTAAGTCTCAGT 57.328 37.500 0.00 0.00 0.00 3.41
1917 2231 6.692486 TGATCAGTTTTCCTAAGTCTCAGTC 58.308 40.000 0.00 0.00 0.00 3.51
1918 2232 5.122512 TCAGTTTTCCTAAGTCTCAGTCG 57.877 43.478 0.00 0.00 0.00 4.18
1919 2233 4.825634 TCAGTTTTCCTAAGTCTCAGTCGA 59.174 41.667 0.00 0.00 0.00 4.20
1920 2234 4.918583 CAGTTTTCCTAAGTCTCAGTCGAC 59.081 45.833 7.70 7.70 0.00 4.20
1921 2235 4.828387 AGTTTTCCTAAGTCTCAGTCGACT 59.172 41.667 13.58 13.58 45.73 4.18
1938 2252 6.537466 GTCGACTTAGACTTTCGTTATGTC 57.463 41.667 8.70 0.00 38.09 3.06
1939 2253 6.313252 GTCGACTTAGACTTTCGTTATGTCT 58.687 40.000 8.70 11.38 42.22 3.41
1940 2254 6.465465 GTCGACTTAGACTTTCGTTATGTCTC 59.535 42.308 8.70 0.73 40.57 3.36
1941 2255 6.148315 TCGACTTAGACTTTCGTTATGTCTCA 59.852 38.462 10.43 2.85 40.57 3.27
1942 2256 6.466413 CGACTTAGACTTTCGTTATGTCTCAG 59.534 42.308 10.43 11.23 40.57 3.35
1943 2257 7.216973 ACTTAGACTTTCGTTATGTCTCAGT 57.783 36.000 12.68 12.68 39.11 3.41
1944 2258 7.306953 ACTTAGACTTTCGTTATGTCTCAGTC 58.693 38.462 12.68 0.00 39.44 3.51
1945 2259 4.724303 AGACTTTCGTTATGTCTCAGTCG 58.276 43.478 0.00 0.00 36.78 4.18
1946 2260 4.454847 AGACTTTCGTTATGTCTCAGTCGA 59.545 41.667 0.00 0.00 36.78 4.20
1947 2261 5.124138 AGACTTTCGTTATGTCTCAGTCGAT 59.876 40.000 0.00 0.00 36.78 3.59
1948 2262 5.096169 ACTTTCGTTATGTCTCAGTCGATG 58.904 41.667 0.00 0.00 0.00 3.84
1949 2263 4.696899 TTCGTTATGTCTCAGTCGATGT 57.303 40.909 0.00 0.00 0.00 3.06
1950 2264 4.696899 TCGTTATGTCTCAGTCGATGTT 57.303 40.909 0.00 0.00 0.00 2.71
1951 2265 5.806366 TCGTTATGTCTCAGTCGATGTTA 57.194 39.130 0.00 0.00 0.00 2.41
1952 2266 6.373186 TCGTTATGTCTCAGTCGATGTTAT 57.627 37.500 0.00 0.00 0.00 1.89
1953 2267 6.199393 TCGTTATGTCTCAGTCGATGTTATG 58.801 40.000 0.00 0.00 0.00 1.90
1954 2268 5.971792 CGTTATGTCTCAGTCGATGTTATGT 59.028 40.000 0.00 0.00 0.00 2.29
1955 2269 6.472486 CGTTATGTCTCAGTCGATGTTATGTT 59.528 38.462 0.00 0.00 0.00 2.71
1956 2270 7.642586 CGTTATGTCTCAGTCGATGTTATGTTA 59.357 37.037 0.00 0.00 0.00 2.41
1957 2271 9.464714 GTTATGTCTCAGTCGATGTTATGTTAT 57.535 33.333 0.00 0.00 0.00 1.89
1961 2275 9.463443 TGTCTCAGTCGATGTTATGTTATATTG 57.537 33.333 0.00 0.00 0.00 1.90
1962 2276 9.678941 GTCTCAGTCGATGTTATGTTATATTGA 57.321 33.333 0.00 0.00 0.00 2.57
1968 2282 9.746711 GTCGATGTTATGTTATATTGATCTTGC 57.253 33.333 0.00 0.00 0.00 4.01
1969 2283 9.487790 TCGATGTTATGTTATATTGATCTTGCA 57.512 29.630 0.00 0.00 0.00 4.08
2037 2351 9.449719 TTCATATACTATATCGCTTGACTGAGA 57.550 33.333 0.00 0.00 0.00 3.27
2038 2352 9.620259 TCATATACTATATCGCTTGACTGAGAT 57.380 33.333 0.00 0.00 0.00 2.75
2041 2355 8.978564 ATACTATATCGCTTGACTGAGATTTG 57.021 34.615 0.00 0.00 0.00 2.32
2042 2356 6.219473 ACTATATCGCTTGACTGAGATTTGG 58.781 40.000 0.00 0.00 0.00 3.28
2043 2357 2.839486 TCGCTTGACTGAGATTTGGT 57.161 45.000 0.00 0.00 0.00 3.67
2044 2358 3.126001 TCGCTTGACTGAGATTTGGTT 57.874 42.857 0.00 0.00 0.00 3.67
2045 2359 4.265904 TCGCTTGACTGAGATTTGGTTA 57.734 40.909 0.00 0.00 0.00 2.85
2046 2360 4.637276 TCGCTTGACTGAGATTTGGTTAA 58.363 39.130 0.00 0.00 0.00 2.01
2047 2361 4.690748 TCGCTTGACTGAGATTTGGTTAAG 59.309 41.667 0.00 0.00 32.28 1.85
2048 2362 4.452455 CGCTTGACTGAGATTTGGTTAAGT 59.548 41.667 0.00 0.00 31.92 2.24
2049 2363 5.389935 CGCTTGACTGAGATTTGGTTAAGTC 60.390 44.000 0.00 0.00 35.66 3.01
2050 2364 5.703130 GCTTGACTGAGATTTGGTTAAGTCT 59.297 40.000 0.00 0.00 35.80 3.24
2051 2365 6.874134 GCTTGACTGAGATTTGGTTAAGTCTA 59.126 38.462 0.00 0.00 33.56 2.59
2052 2366 7.387948 GCTTGACTGAGATTTGGTTAAGTCTAA 59.612 37.037 0.00 0.00 33.56 2.10
2053 2367 8.833231 TTGACTGAGATTTGGTTAAGTCTAAG 57.167 34.615 0.00 0.00 37.23 2.18
2054 2368 7.963532 TGACTGAGATTTGGTTAAGTCTAAGT 58.036 34.615 3.12 3.12 43.40 2.24
2055 2369 8.468720 GACTGAGATTTGGTTAAGTCTAAGTC 57.531 38.462 11.79 11.79 45.85 3.01
2056 2370 7.963532 ACTGAGATTTGGTTAAGTCTAAGTCA 58.036 34.615 0.00 0.00 39.07 3.41
2057 2371 8.429641 ACTGAGATTTGGTTAAGTCTAAGTCAA 58.570 33.333 0.00 0.00 39.07 3.18
2058 2372 8.603242 TGAGATTTGGTTAAGTCTAAGTCAAC 57.397 34.615 0.00 0.00 33.56 3.18
2059 2373 8.429641 TGAGATTTGGTTAAGTCTAAGTCAACT 58.570 33.333 0.00 0.00 33.56 3.16
2060 2374 8.608844 AGATTTGGTTAAGTCTAAGTCAACTG 57.391 34.615 0.00 0.00 31.87 3.16
2061 2375 8.429641 AGATTTGGTTAAGTCTAAGTCAACTGA 58.570 33.333 0.00 0.00 31.87 3.41
2062 2376 8.608844 ATTTGGTTAAGTCTAAGTCAACTGAG 57.391 34.615 0.00 0.00 0.00 3.35
2063 2377 6.971726 TGGTTAAGTCTAAGTCAACTGAGA 57.028 37.500 0.00 0.00 31.01 3.27
2064 2378 7.540474 TGGTTAAGTCTAAGTCAACTGAGAT 57.460 36.000 0.52 0.00 35.96 2.75
2065 2379 7.603651 TGGTTAAGTCTAAGTCAACTGAGATC 58.396 38.462 0.52 0.00 35.96 2.75
2066 2380 7.451877 TGGTTAAGTCTAAGTCAACTGAGATCT 59.548 37.037 0.00 0.00 35.96 2.75
2067 2381 8.958506 GGTTAAGTCTAAGTCAACTGAGATCTA 58.041 37.037 0.00 0.00 35.96 1.98
2068 2382 9.997482 GTTAAGTCTAAGTCAACTGAGATCTAG 57.003 37.037 0.00 0.00 35.96 2.43
2069 2383 9.961264 TTAAGTCTAAGTCAACTGAGATCTAGA 57.039 33.333 0.00 0.00 35.96 2.43
2070 2384 7.859325 AGTCTAAGTCAACTGAGATCTAGAC 57.141 40.000 0.00 0.84 35.96 2.59
2071 2385 7.398829 AGTCTAAGTCAACTGAGATCTAGACA 58.601 38.462 14.29 1.10 35.96 3.41
2072 2386 7.335924 AGTCTAAGTCAACTGAGATCTAGACAC 59.664 40.741 14.29 0.00 35.96 3.67
2073 2387 7.119992 GTCTAAGTCAACTGAGATCTAGACACA 59.880 40.741 0.00 0.00 35.96 3.72
2074 2388 5.637006 AGTCAACTGAGATCTAGACACAC 57.363 43.478 0.00 0.00 0.00 3.82
2075 2389 4.461081 AGTCAACTGAGATCTAGACACACC 59.539 45.833 0.00 0.00 0.00 4.16
2076 2390 3.764434 TCAACTGAGATCTAGACACACCC 59.236 47.826 0.00 0.00 0.00 4.61
2077 2391 3.748645 ACTGAGATCTAGACACACCCT 57.251 47.619 0.00 0.00 0.00 4.34
2078 2392 4.864483 ACTGAGATCTAGACACACCCTA 57.136 45.455 0.00 0.00 0.00 3.53
2079 2393 5.396057 ACTGAGATCTAGACACACCCTAT 57.604 43.478 0.00 0.00 0.00 2.57
2080 2394 5.381757 ACTGAGATCTAGACACACCCTATC 58.618 45.833 0.00 0.00 0.00 2.08
2081 2395 5.133660 ACTGAGATCTAGACACACCCTATCT 59.866 44.000 0.00 0.00 0.00 1.98
2082 2396 6.019656 TGAGATCTAGACACACCCTATCTT 57.980 41.667 0.00 0.00 0.00 2.40
2083 2397 5.830457 TGAGATCTAGACACACCCTATCTTG 59.170 44.000 0.00 0.00 0.00 3.02
2084 2398 6.019656 AGATCTAGACACACCCTATCTTGA 57.980 41.667 0.00 0.00 0.00 3.02
2100 2414 2.821378 TCTTGATCAACATGCCCTTGTG 59.179 45.455 3.38 0.00 0.00 3.33
2125 2439 1.144936 CGGAGAGAGGCCAACATCC 59.855 63.158 5.01 6.24 0.00 3.51
2126 2440 1.617018 CGGAGAGAGGCCAACATCCA 61.617 60.000 5.01 0.00 0.00 3.41
2127 2441 0.842635 GGAGAGAGGCCAACATCCAT 59.157 55.000 5.01 0.00 0.00 3.41
2130 2444 3.073650 GGAGAGAGGCCAACATCCATATT 59.926 47.826 5.01 0.00 0.00 1.28
2131 2445 4.322567 GAGAGAGGCCAACATCCATATTC 58.677 47.826 5.01 0.00 0.00 1.75
2132 2446 3.070018 GAGAGGCCAACATCCATATTCG 58.930 50.000 5.01 0.00 0.00 3.34
2263 2633 0.111253 AAGAGGTCAACCTGGCCAAG 59.889 55.000 7.01 2.23 46.77 3.61
2323 2693 2.614446 CGACAGAGGTCACGTCGGT 61.614 63.158 2.73 2.73 46.59 4.69
2497 2877 1.142465 GCCTCCTCATCATGGATGTGT 59.858 52.381 6.15 0.00 40.55 3.72
2498 2878 2.847441 CCTCCTCATCATGGATGTGTG 58.153 52.381 6.15 1.51 40.55 3.82
2595 2977 3.250744 ACGAATTGTGATACCACGAGTG 58.749 45.455 0.00 0.00 46.06 3.51
2623 3034 8.184304 ACTCAGTAAAGTAGCCTTATATCTGG 57.816 38.462 0.00 0.00 0.00 3.86
2673 3085 8.944029 CAGAGCCATATATCAGTCCAAATTAAG 58.056 37.037 0.00 0.00 0.00 1.85
2674 3086 7.609532 AGAGCCATATATCAGTCCAAATTAAGC 59.390 37.037 0.00 0.00 0.00 3.09
2968 3470 6.204882 AGTTTTCTGCGACATTTTAGCTTACT 59.795 34.615 0.00 0.00 0.00 2.24
3254 4025 7.345691 TGACACCATGTATATCCACAGAAAAT 58.654 34.615 0.00 0.00 0.00 1.82
3379 4150 3.671008 ATGTCACATTTGCATGCACTT 57.329 38.095 22.58 7.93 33.05 3.16
3758 4564 5.907662 TCTCATGGTCTAGAGATGGGAAAAT 59.092 40.000 10.60 0.00 36.05 1.82
4062 4881 0.381801 CCGCCATCCAGTTTGTATGC 59.618 55.000 0.00 0.00 0.00 3.14
4127 4948 8.181573 CGCATATTGTTGTGGTCTAAACTTAAT 58.818 33.333 0.00 0.00 0.00 1.40
4193 5025 5.236911 AGGTAACGTATTTTCTTTCGCACAA 59.763 36.000 0.00 0.00 46.39 3.33
4196 5028 7.745594 GGTAACGTATTTTCTTTCGCACAAATA 59.254 33.333 0.00 0.00 0.00 1.40
4269 5101 7.338449 TGCTTTAACTTACACATAGGATTTCCC 59.662 37.037 0.00 0.00 36.42 3.97
4384 5216 6.362016 GTGCTCGAAGATGTGATAGTTGATAG 59.638 42.308 0.00 0.00 33.89 2.08
4626 5471 8.437575 AGTTCTTTAGTTAAGGAAGGACATTCA 58.562 33.333 1.83 0.00 39.91 2.57
4627 5472 8.722394 GTTCTTTAGTTAAGGAAGGACATTCAG 58.278 37.037 1.83 0.00 39.91 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
309 323 7.008447 CGGAAATAAGACTAGTGAAGACGAAAG 59.992 40.741 0.00 0.00 0.00 2.62
400 414 0.547712 TGTTGAAGGGAGGAGGGAGG 60.548 60.000 0.00 0.00 0.00 4.30
407 421 2.031120 TGCAGTTTTGTTGAAGGGAGG 58.969 47.619 0.00 0.00 0.00 4.30
428 442 5.794894 TCCATCTTCACTAGTCTTGTTTCC 58.205 41.667 0.00 0.00 0.00 3.13
580 594 7.807907 CACTACTCTTATTTCCGTTTTTGCATT 59.192 33.333 0.00 0.00 0.00 3.56
582 596 6.483974 TCACTACTCTTATTTCCGTTTTTGCA 59.516 34.615 0.00 0.00 0.00 4.08
613 627 2.599408 TCCAGGAGGAGTACGTCTTT 57.401 50.000 0.00 0.00 39.61 2.52
661 675 0.171455 CACGGAGAGAGAGGGTTTCG 59.829 60.000 0.00 0.00 0.00 3.46
820 847 2.537625 GAGCGATTGACATCTGTGCTAC 59.462 50.000 0.00 0.00 0.00 3.58
821 848 2.796032 CGAGCGATTGACATCTGTGCTA 60.796 50.000 0.00 0.00 0.00 3.49
822 849 1.649664 GAGCGATTGACATCTGTGCT 58.350 50.000 0.00 0.00 0.00 4.40
823 850 0.299895 CGAGCGATTGACATCTGTGC 59.700 55.000 0.00 0.00 0.00 4.57
824 851 1.633561 ACGAGCGATTGACATCTGTG 58.366 50.000 0.00 0.00 0.00 3.66
825 852 2.370281 AACGAGCGATTGACATCTGT 57.630 45.000 0.00 0.00 0.00 3.41
947 974 1.191096 GCAGACACAAGCAAAACACG 58.809 50.000 0.00 0.00 0.00 4.49
948 975 2.187707 CAGCAGACACAAGCAAAACAC 58.812 47.619 0.00 0.00 0.00 3.32
949 976 1.134753 CCAGCAGACACAAGCAAAACA 59.865 47.619 0.00 0.00 0.00 2.83
1117 1160 0.739462 TCGAGGCAGTAATGGTTGCG 60.739 55.000 0.00 0.00 41.17 4.85
1243 1310 2.167861 GTTAGCGCTTGCCGGAGAG 61.168 63.158 18.68 2.17 40.41 3.20
1620 1726 5.030295 CCGTCCAATTCAAAGATCGATTTG 58.970 41.667 0.00 1.85 40.75 2.32
1670 1776 7.356154 GCGAACGTTTCACAAAAAGTTATACAG 60.356 37.037 0.46 0.00 43.88 2.74
1671 1777 6.411492 GCGAACGTTTCACAAAAAGTTATACA 59.589 34.615 0.46 0.00 43.88 2.29
1713 1867 5.106237 GGCCGTATCCACTACTAGTATTCTG 60.106 48.000 2.33 0.00 0.00 3.02
1718 1872 2.550855 CCGGCCGTATCCACTACTAGTA 60.551 54.545 26.12 1.89 0.00 1.82
1719 1873 1.602311 CGGCCGTATCCACTACTAGT 58.398 55.000 19.50 0.00 0.00 2.57
1720 1874 0.879765 CCGGCCGTATCCACTACTAG 59.120 60.000 26.12 0.00 0.00 2.57
1762 2064 3.769369 ATGAGCTGGGCGGCATCAG 62.769 63.158 12.47 11.19 34.17 2.90
1893 2207 6.570571 CGACTGAGACTTAGGAAAACTGATCA 60.571 42.308 0.00 0.00 0.00 2.92
1910 2224 4.063689 ACGAAAGTCTAAGTCGACTGAGA 58.936 43.478 26.12 26.12 44.19 3.27
1911 2225 4.407496 ACGAAAGTCTAAGTCGACTGAG 57.593 45.455 22.32 22.32 44.19 3.35
1917 2231 7.834625 ACTGAGACATAACGAAAGTCTAAGTCG 60.835 40.741 12.84 0.00 46.35 4.18
1918 2232 7.306953 ACTGAGACATAACGAAAGTCTAAGTC 58.693 38.462 12.84 0.00 46.35 3.01
1926 2240 5.096169 ACATCGACTGAGACATAACGAAAG 58.904 41.667 0.00 0.00 33.77 2.62
1927 2241 5.055642 ACATCGACTGAGACATAACGAAA 57.944 39.130 0.00 0.00 33.77 3.46
1928 2242 4.696899 ACATCGACTGAGACATAACGAA 57.303 40.909 0.00 0.00 33.77 3.85
1929 2243 4.696899 AACATCGACTGAGACATAACGA 57.303 40.909 0.00 0.00 0.00 3.85
1930 2244 5.971792 ACATAACATCGACTGAGACATAACG 59.028 40.000 0.00 0.00 0.00 3.18
1931 2245 7.757097 AACATAACATCGACTGAGACATAAC 57.243 36.000 0.00 0.00 0.00 1.89
1935 2249 9.463443 CAATATAACATAACATCGACTGAGACA 57.537 33.333 0.00 0.00 0.00 3.41
1936 2250 9.678941 TCAATATAACATAACATCGACTGAGAC 57.321 33.333 0.00 0.00 0.00 3.36
1942 2256 9.746711 GCAAGATCAATATAACATAACATCGAC 57.253 33.333 0.00 0.00 0.00 4.20
1943 2257 9.487790 TGCAAGATCAATATAACATAACATCGA 57.512 29.630 0.00 0.00 0.00 3.59
2016 2330 8.031864 CCAAATCTCAGTCAAGCGATATAGTAT 58.968 37.037 0.00 0.00 0.00 2.12
2017 2331 7.014326 ACCAAATCTCAGTCAAGCGATATAGTA 59.986 37.037 0.00 0.00 0.00 1.82
2020 2334 6.161855 ACCAAATCTCAGTCAAGCGATATA 57.838 37.500 0.00 0.00 0.00 0.86
2021 2335 5.028549 ACCAAATCTCAGTCAAGCGATAT 57.971 39.130 0.00 0.00 0.00 1.63
2023 2337 3.340814 ACCAAATCTCAGTCAAGCGAT 57.659 42.857 0.00 0.00 0.00 4.58
2024 2338 2.839486 ACCAAATCTCAGTCAAGCGA 57.161 45.000 0.00 0.00 0.00 4.93
2026 2340 5.703130 AGACTTAACCAAATCTCAGTCAAGC 59.297 40.000 0.00 0.00 34.33 4.01
2027 2341 8.833231 TTAGACTTAACCAAATCTCAGTCAAG 57.167 34.615 0.00 0.00 34.33 3.02
2028 2342 8.429641 ACTTAGACTTAACCAAATCTCAGTCAA 58.570 33.333 0.00 0.00 34.33 3.18
2029 2343 7.963532 ACTTAGACTTAACCAAATCTCAGTCA 58.036 34.615 0.00 0.00 34.33 3.41
2030 2344 8.088981 TGACTTAGACTTAACCAAATCTCAGTC 58.911 37.037 7.26 7.26 40.49 3.51
2031 2345 7.963532 TGACTTAGACTTAACCAAATCTCAGT 58.036 34.615 0.00 0.00 30.23 3.41
2032 2346 8.713271 GTTGACTTAGACTTAACCAAATCTCAG 58.287 37.037 0.00 0.00 0.00 3.35
2033 2347 8.429641 AGTTGACTTAGACTTAACCAAATCTCA 58.570 33.333 0.00 0.00 0.00 3.27
2034 2348 8.713271 CAGTTGACTTAGACTTAACCAAATCTC 58.287 37.037 0.00 0.00 0.00 2.75
2035 2349 8.429641 TCAGTTGACTTAGACTTAACCAAATCT 58.570 33.333 0.00 0.00 0.00 2.40
2036 2350 8.603242 TCAGTTGACTTAGACTTAACCAAATC 57.397 34.615 0.00 0.00 0.00 2.17
2037 2351 8.429641 TCTCAGTTGACTTAGACTTAACCAAAT 58.570 33.333 0.00 0.00 0.00 2.32
2038 2352 7.788026 TCTCAGTTGACTTAGACTTAACCAAA 58.212 34.615 0.00 0.00 0.00 3.28
2039 2353 7.356089 TCTCAGTTGACTTAGACTTAACCAA 57.644 36.000 0.00 0.00 0.00 3.67
2040 2354 6.971726 TCTCAGTTGACTTAGACTTAACCA 57.028 37.500 0.00 0.00 0.00 3.67
2041 2355 7.832769 AGATCTCAGTTGACTTAGACTTAACC 58.167 38.462 0.00 0.00 29.94 2.85
2042 2356 9.997482 CTAGATCTCAGTTGACTTAGACTTAAC 57.003 37.037 0.00 0.00 29.94 2.01
2043 2357 9.961264 TCTAGATCTCAGTTGACTTAGACTTAA 57.039 33.333 0.00 0.00 29.94 1.85
2044 2358 9.386010 GTCTAGATCTCAGTTGACTTAGACTTA 57.614 37.037 0.00 1.86 35.12 2.24
2045 2359 7.885922 TGTCTAGATCTCAGTTGACTTAGACTT 59.114 37.037 0.00 4.13 36.83 3.01
2046 2360 7.335924 GTGTCTAGATCTCAGTTGACTTAGACT 59.664 40.741 0.00 9.44 36.83 3.24
2047 2361 7.119992 TGTGTCTAGATCTCAGTTGACTTAGAC 59.880 40.741 0.00 3.20 36.65 2.59
2048 2362 7.119992 GTGTGTCTAGATCTCAGTTGACTTAGA 59.880 40.741 0.00 0.00 31.55 2.10
2049 2363 7.247728 GTGTGTCTAGATCTCAGTTGACTTAG 58.752 42.308 0.00 0.00 0.00 2.18
2050 2364 6.151312 GGTGTGTCTAGATCTCAGTTGACTTA 59.849 42.308 0.00 0.00 0.00 2.24
2051 2365 5.047660 GGTGTGTCTAGATCTCAGTTGACTT 60.048 44.000 0.00 0.00 0.00 3.01
2052 2366 4.461081 GGTGTGTCTAGATCTCAGTTGACT 59.539 45.833 0.00 0.00 0.00 3.41
2053 2367 4.381079 GGGTGTGTCTAGATCTCAGTTGAC 60.381 50.000 0.00 2.43 0.00 3.18
2054 2368 3.764434 GGGTGTGTCTAGATCTCAGTTGA 59.236 47.826 0.00 0.00 0.00 3.18
2055 2369 3.766591 AGGGTGTGTCTAGATCTCAGTTG 59.233 47.826 0.00 0.00 0.00 3.16
2056 2370 4.054359 AGGGTGTGTCTAGATCTCAGTT 57.946 45.455 0.00 0.00 0.00 3.16
2057 2371 3.748645 AGGGTGTGTCTAGATCTCAGT 57.251 47.619 0.00 0.00 0.00 3.41
2058 2372 5.630121 AGATAGGGTGTGTCTAGATCTCAG 58.370 45.833 0.00 0.00 0.00 3.35
2059 2373 5.654901 AGATAGGGTGTGTCTAGATCTCA 57.345 43.478 0.00 0.00 0.00 3.27
2060 2374 6.065374 TCAAGATAGGGTGTGTCTAGATCTC 58.935 44.000 0.00 0.00 0.00 2.75
2061 2375 6.019656 TCAAGATAGGGTGTGTCTAGATCT 57.980 41.667 0.00 0.00 0.00 2.75
2062 2376 6.491745 TGATCAAGATAGGGTGTGTCTAGATC 59.508 42.308 0.00 0.00 0.00 2.75
2063 2377 6.377080 TGATCAAGATAGGGTGTGTCTAGAT 58.623 40.000 0.00 0.00 0.00 1.98
2064 2378 5.766590 TGATCAAGATAGGGTGTGTCTAGA 58.233 41.667 0.00 0.00 0.00 2.43
2065 2379 6.127338 TGTTGATCAAGATAGGGTGTGTCTAG 60.127 42.308 8.80 0.00 0.00 2.43
2066 2380 5.719563 TGTTGATCAAGATAGGGTGTGTCTA 59.280 40.000 8.80 0.00 0.00 2.59
2067 2381 4.532126 TGTTGATCAAGATAGGGTGTGTCT 59.468 41.667 8.80 0.00 0.00 3.41
2068 2382 4.832248 TGTTGATCAAGATAGGGTGTGTC 58.168 43.478 8.80 0.00 0.00 3.67
2069 2383 4.908601 TGTTGATCAAGATAGGGTGTGT 57.091 40.909 8.80 0.00 0.00 3.72
2070 2384 4.036027 GCATGTTGATCAAGATAGGGTGTG 59.964 45.833 16.96 6.73 0.00 3.82
2071 2385 4.202441 GCATGTTGATCAAGATAGGGTGT 58.798 43.478 16.96 0.00 0.00 4.16
2072 2386 3.567164 GGCATGTTGATCAAGATAGGGTG 59.433 47.826 16.96 8.06 0.00 4.61
2073 2387 3.435601 GGGCATGTTGATCAAGATAGGGT 60.436 47.826 16.96 0.00 0.00 4.34
2074 2388 3.152341 GGGCATGTTGATCAAGATAGGG 58.848 50.000 16.96 7.29 0.00 3.53
2075 2389 4.096190 AGGGCATGTTGATCAAGATAGG 57.904 45.455 16.96 7.95 0.00 2.57
2076 2390 4.885907 ACAAGGGCATGTTGATCAAGATAG 59.114 41.667 16.96 12.48 0.00 2.08
2077 2391 4.641541 CACAAGGGCATGTTGATCAAGATA 59.358 41.667 16.96 3.83 0.00 1.98
2078 2392 3.446161 CACAAGGGCATGTTGATCAAGAT 59.554 43.478 12.11 12.11 0.00 2.40
2079 2393 2.821378 CACAAGGGCATGTTGATCAAGA 59.179 45.455 8.80 8.30 0.00 3.02
2080 2394 2.821378 TCACAAGGGCATGTTGATCAAG 59.179 45.455 8.80 0.00 0.00 3.02
2081 2395 2.874014 TCACAAGGGCATGTTGATCAA 58.126 42.857 3.38 3.38 0.00 2.57
2082 2396 2.557924 GTTCACAAGGGCATGTTGATCA 59.442 45.455 0.00 0.00 0.00 2.92
2083 2397 2.414559 CGTTCACAAGGGCATGTTGATC 60.415 50.000 1.85 0.00 0.00 2.92
2084 2398 1.541147 CGTTCACAAGGGCATGTTGAT 59.459 47.619 1.85 0.00 0.00 2.57
2100 2414 4.516195 GCCTCTCTCCGGCCGTTC 62.516 72.222 26.12 0.00 41.73 3.95
2440 2811 7.533426 AGTGATGTTTCAAATGCTAATGACTC 58.467 34.615 0.00 0.00 32.48 3.36
2516 2896 6.642131 CCATTGAAACCAACAAACATCTACAG 59.358 38.462 0.00 0.00 0.00 2.74
2561 2941 7.867445 ATCACAATTCGTTTCACATTTTACC 57.133 32.000 0.00 0.00 0.00 2.85
2623 3034 4.086199 TCCGCGGAAATATGACAAAAAC 57.914 40.909 28.99 0.00 0.00 2.43
2800 3302 5.618561 ACGCTCGTTTCAAATATTTCAGAC 58.381 37.500 0.00 0.00 0.00 3.51
2968 3470 4.243008 TCGCTGGCAAACCCGACA 62.243 61.111 0.00 0.00 35.87 4.35
3758 4564 9.621629 ATTATTGAACCAACGGAAATATCAGTA 57.378 29.630 0.00 0.00 32.50 2.74
4282 5114 7.816031 CAGAAGTCCAAAACTAAATCCTACGTA 59.184 37.037 0.00 0.00 37.17 3.57
4420 5253 8.974060 ATCGCTCCTCCTAAAATGTTATTTTA 57.026 30.769 6.58 6.58 0.00 1.52
4586 5424 4.335647 AACTGTGGCAGCTCCCCG 62.336 66.667 0.00 0.00 34.37 5.73
4596 5441 6.427242 GTCCTTCCTTAACTAAAGAACTGTGG 59.573 42.308 0.00 0.00 37.38 4.17


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

AutoCloner maintained by Alex Coulton.