Multiple sequence alignment - TraesCS7A01G045700

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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 TraesCS7A01G045700 chr7A 100.000 4804 0 0 1 4804 20720433 20725236 0.000000e+00 8872
1 TraesCS7A01G045700 chr7A 95.426 2842 110 2 1842 4663 20660453 20663294 0.000000e+00 4510
2 TraesCS7A01G045700 chr7A 82.582 2130 337 22 1849 3958 20677291 20679406 0.000000e+00 1847
3 TraesCS7A01G045700 chr7A 91.301 1368 86 10 420 1776 20659104 20660449 0.000000e+00 1836
4 TraesCS7A01G045700 chr7A 81.882 2147 334 31 1858 3975 20555926 20558046 0.000000e+00 1759
5 TraesCS7A01G045700 chr7A 81.552 2152 354 33 1855 3981 20651619 20653752 0.000000e+00 1735
6 TraesCS7A01G045700 chr7A 85.670 963 123 6 827 1776 20588592 20589552 0.000000e+00 1000
7 TraesCS7A01G045700 chr7A 84.227 970 132 14 823 1776 20482640 20483604 0.000000e+00 924
8 TraesCS7A01G045700 chr7A 87.089 821 99 4 957 1776 20650788 20651602 0.000000e+00 922
9 TraesCS7A01G045700 chr7A 86.480 821 107 3 957 1776 20910674 20911491 0.000000e+00 898
10 TraesCS7A01G045700 chr7A 85.176 398 24 9 1 383 20658728 20659105 4.540000e-100 375
11 TraesCS7A01G045700 chr7A 89.683 126 13 0 4679 4804 20663374 20663499 1.380000e-35 161
12 TraesCS7A01G045700 chr7D 96.145 2983 90 7 1842 4804 20405107 20408084 0.000000e+00 4848
13 TraesCS7A01G045700 chr7D 95.814 1290 49 4 487 1776 20403819 20405103 0.000000e+00 2078
14 TraesCS7A01G045700 chr7D 84.573 2016 291 11 1842 3842 20947949 20949959 0.000000e+00 1982
15 TraesCS7A01G045700 chr7D 84.651 1948 279 12 1843 3774 555195588 555193645 0.000000e+00 1923
16 TraesCS7A01G045700 chr7D 84.205 1988 289 14 1842 3810 89532238 89530257 0.000000e+00 1908
17 TraesCS7A01G045700 chr7D 83.392 1999 302 18 1858 3837 20311672 20313659 0.000000e+00 1825
18 TraesCS7A01G045700 chr7D 82.296 1977 316 25 1855 3810 20486435 20488398 0.000000e+00 1681
19 TraesCS7A01G045700 chr7D 86.536 817 108 2 961 1776 89533057 89532242 0.000000e+00 898
20 TraesCS7A01G045700 chr7D 86.358 821 110 2 957 1776 555196412 555195593 0.000000e+00 894
21 TraesCS7A01G045700 chr7D 86.553 818 47 24 1 809 20403053 20403816 0.000000e+00 843
22 TraesCS7A01G045700 chr2A 83.326 2267 314 39 1842 4082 733088581 733090809 0.000000e+00 2034
23 TraesCS7A01G045700 chr2D 84.953 2007 281 10 1842 3832 598814879 598816880 0.000000e+00 2013
24 TraesCS7A01G045700 chr2B 84.704 2007 286 11 1842 3832 727686835 727688836 0.000000e+00 1986
25 TraesCS7A01G045700 chr2B 81.868 182 19 9 4316 4495 727735998 727736167 1.800000e-29 141
26 TraesCS7A01G045700 chr7B 83.739 2054 303 20 1843 3878 601115271 601117311 0.000000e+00 1914
27 TraesCS7A01G045700 chr5A 87.430 899 102 10 879 1776 601679803 601680691 0.000000e+00 1024
28 TraesCS7A01G045700 chr3A 91.066 347 17 6 576 914 714515014 714514674 1.580000e-124 457
29 TraesCS7A01G045700 chr3A 86.935 398 23 16 3 396 714515479 714515107 2.070000e-113 420


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 TraesCS7A01G045700 chr7A 20720433 20725236 4803 False 8872.000000 8872 100.000000 1 4804 1 chr7A.!!$F5 4803
1 TraesCS7A01G045700 chr7A 20677291 20679406 2115 False 1847.000000 1847 82.582000 1849 3958 1 chr7A.!!$F4 2109
2 TraesCS7A01G045700 chr7A 20555926 20558046 2120 False 1759.000000 1759 81.882000 1858 3975 1 chr7A.!!$F2 2117
3 TraesCS7A01G045700 chr7A 20658728 20663499 4771 False 1720.500000 4510 90.396500 1 4804 4 chr7A.!!$F8 4803
4 TraesCS7A01G045700 chr7A 20650788 20653752 2964 False 1328.500000 1735 84.320500 957 3981 2 chr7A.!!$F7 3024
5 TraesCS7A01G045700 chr7A 20588592 20589552 960 False 1000.000000 1000 85.670000 827 1776 1 chr7A.!!$F3 949
6 TraesCS7A01G045700 chr7A 20482640 20483604 964 False 924.000000 924 84.227000 823 1776 1 chr7A.!!$F1 953
7 TraesCS7A01G045700 chr7A 20910674 20911491 817 False 898.000000 898 86.480000 957 1776 1 chr7A.!!$F6 819
8 TraesCS7A01G045700 chr7D 20403053 20408084 5031 False 2589.666667 4848 92.837333 1 4804 3 chr7D.!!$F4 4803
9 TraesCS7A01G045700 chr7D 20947949 20949959 2010 False 1982.000000 1982 84.573000 1842 3842 1 chr7D.!!$F3 2000
10 TraesCS7A01G045700 chr7D 20311672 20313659 1987 False 1825.000000 1825 83.392000 1858 3837 1 chr7D.!!$F1 1979
11 TraesCS7A01G045700 chr7D 20486435 20488398 1963 False 1681.000000 1681 82.296000 1855 3810 1 chr7D.!!$F2 1955
12 TraesCS7A01G045700 chr7D 555193645 555196412 2767 True 1408.500000 1923 85.504500 957 3774 2 chr7D.!!$R2 2817
13 TraesCS7A01G045700 chr7D 89530257 89533057 2800 True 1403.000000 1908 85.370500 961 3810 2 chr7D.!!$R1 2849
14 TraesCS7A01G045700 chr2A 733088581 733090809 2228 False 2034.000000 2034 83.326000 1842 4082 1 chr2A.!!$F1 2240
15 TraesCS7A01G045700 chr2D 598814879 598816880 2001 False 2013.000000 2013 84.953000 1842 3832 1 chr2D.!!$F1 1990
16 TraesCS7A01G045700 chr2B 727686835 727688836 2001 False 1986.000000 1986 84.704000 1842 3832 1 chr2B.!!$F1 1990
17 TraesCS7A01G045700 chr7B 601115271 601117311 2040 False 1914.000000 1914 83.739000 1843 3878 1 chr7B.!!$F1 2035
18 TraesCS7A01G045700 chr5A 601679803 601680691 888 False 1024.000000 1024 87.430000 879 1776 1 chr5A.!!$F1 897
19 TraesCS7A01G045700 chr3A 714514674 714515479 805 True 438.500000 457 89.000500 3 914 2 chr3A.!!$R1 911

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
179 192 1.337728 CGGATGTGAAGTGTGGCACTA 60.338 52.381 19.83 2.23 44.62 2.74 F
695 1044 2.105649 GGAAAGTTGGGGCCATTTTTCA 59.894 45.455 4.39 0.00 33.85 2.69 F
1055 1424 1.376609 ATCGGAATCGCCTTGGCAAC 61.377 55.000 12.45 0.00 36.13 4.17 F
1839 2208 2.036346 TCCGCATCATCCATCTGTACAG 59.964 50.000 17.17 17.17 0.00 2.74 F
2939 3322 1.079750 GGTGCTCCCGAAGTCTGTC 60.080 63.158 0.00 0.00 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1055 1424 0.249238 GACATGGTCTGCCGCTCTAG 60.249 60.000 0.00 0.00 37.67 2.43 R
1802 2171 0.594602 CGGATTCTGTACCGCGGATA 59.405 55.000 35.90 17.76 42.55 2.59 R
2456 2825 1.595311 ATGTGCTATCACCCCTTCCA 58.405 50.000 0.00 0.00 42.46 3.53 R
3518 3913 1.001048 GTGCAAAATGTCAGCTGCTCA 60.001 47.619 9.47 11.26 35.78 4.26 R
4568 4977 0.531532 CATCGCCTCCTCCATGTGTC 60.532 60.000 0.00 0.00 0.00 3.67 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
130 134 5.296780 TGAGATAATGGCTTTGAAATCGTCC 59.703 40.000 0.00 0.00 0.00 4.79
148 152 4.935205 TCGTCCGATTTGATCTGATGTTTT 59.065 37.500 0.00 0.00 33.10 2.43
150 154 5.390885 CGTCCGATTTGATCTGATGTTTTGT 60.391 40.000 0.00 0.00 0.00 2.83
179 192 1.337728 CGGATGTGAAGTGTGGCACTA 60.338 52.381 19.83 2.23 44.62 2.74
249 267 6.280643 TGCGTGATTTAGTCTGCAGTAATAT 58.719 36.000 14.67 2.35 35.16 1.28
250 268 7.430441 TGCGTGATTTAGTCTGCAGTAATATA 58.570 34.615 14.67 1.40 35.16 0.86
251 269 7.381408 TGCGTGATTTAGTCTGCAGTAATATAC 59.619 37.037 14.67 2.98 35.16 1.47
252 270 7.595502 GCGTGATTTAGTCTGCAGTAATATACT 59.404 37.037 14.67 11.02 40.28 2.12
379 402 6.104146 TCTGCAGTGTAGTTGTTGGTAATA 57.896 37.500 14.67 0.00 0.00 0.98
384 407 7.094975 TGCAGTGTAGTTGTTGGTAATATTGTC 60.095 37.037 0.00 0.00 0.00 3.18
389 412 9.290988 TGTAGTTGTTGGTAATATTGTCAATGT 57.709 29.630 8.39 0.00 0.00 2.71
390 413 9.554724 GTAGTTGTTGGTAATATTGTCAATGTG 57.445 33.333 8.39 0.00 0.00 3.21
392 415 5.960113 TGTTGGTAATATTGTCAATGTGGC 58.040 37.500 8.39 0.00 0.00 5.01
393 416 5.478332 TGTTGGTAATATTGTCAATGTGGCA 59.522 36.000 8.39 0.00 0.00 4.92
394 417 6.154192 TGTTGGTAATATTGTCAATGTGGCAT 59.846 34.615 8.39 0.00 29.04 4.40
395 418 7.340487 TGTTGGTAATATTGTCAATGTGGCATA 59.660 33.333 8.39 0.00 29.04 3.14
396 419 7.270757 TGGTAATATTGTCAATGTGGCATAC 57.729 36.000 8.39 1.64 29.04 2.39
397 420 7.059788 TGGTAATATTGTCAATGTGGCATACT 58.940 34.615 8.39 0.00 29.04 2.12
398 421 7.559533 TGGTAATATTGTCAATGTGGCATACTT 59.440 33.333 8.39 0.00 29.04 2.24
399 422 9.062524 GGTAATATTGTCAATGTGGCATACTTA 57.937 33.333 8.39 0.00 29.04 2.24
400 423 9.878599 GTAATATTGTCAATGTGGCATACTTAC 57.121 33.333 8.39 0.00 29.04 2.34
401 424 5.835113 ATTGTCAATGTGGCATACTTACC 57.165 39.130 0.00 0.00 29.04 2.85
402 425 4.293662 TGTCAATGTGGCATACTTACCA 57.706 40.909 0.00 0.00 0.00 3.25
452 475 5.934402 AGAAGTTACGACAATGTAGGGAT 57.066 39.130 0.00 0.00 0.00 3.85
503 852 6.664816 TCCTGAAGTGAATATGATGCCTTTTT 59.335 34.615 0.00 0.00 0.00 1.94
546 895 3.940209 TTGATGTTTTGTGATGGCTCC 57.060 42.857 0.00 0.00 0.00 4.70
547 896 3.159213 TGATGTTTTGTGATGGCTCCT 57.841 42.857 0.00 0.00 0.00 3.69
550 899 4.883585 TGATGTTTTGTGATGGCTCCTATC 59.116 41.667 0.00 0.00 0.00 2.08
615 964 4.871993 ACATCTTCTTGCAGCTTAATCG 57.128 40.909 0.00 0.00 0.00 3.34
630 979 5.047847 GCTTAATCGACAACACTGCCTATA 58.952 41.667 0.00 0.00 0.00 1.31
631 980 5.696724 GCTTAATCGACAACACTGCCTATAT 59.303 40.000 0.00 0.00 0.00 0.86
686 1035 2.163613 CGACATTTAGGAAAGTTGGGGC 59.836 50.000 0.00 0.00 0.00 5.80
695 1044 2.105649 GGAAAGTTGGGGCCATTTTTCA 59.894 45.455 4.39 0.00 33.85 2.69
750 1100 3.568007 TGTATGTTCAGTTTGGTTCAGGC 59.432 43.478 0.00 0.00 0.00 4.85
817 1174 4.564769 GCTATAGCAGTCACAAGTGTTCTC 59.435 45.833 20.01 0.00 41.59 2.87
861 1218 4.398044 TGGTTGGAGAGTTTTCAAGTGTTC 59.602 41.667 0.00 0.00 0.00 3.18
863 1220 3.551846 TGGAGAGTTTTCAAGTGTTCCC 58.448 45.455 0.00 0.00 0.00 3.97
954 1311 5.008415 GTGCTCATTCTGACAATATTGAGGG 59.992 44.000 22.16 10.40 33.02 4.30
1055 1424 1.376609 ATCGGAATCGCCTTGGCAAC 61.377 55.000 12.45 0.00 36.13 4.17
1388 1757 5.936956 AGATAGCTGTCAAGGTGAAAGAAAG 59.063 40.000 13.41 0.00 33.50 2.62
1577 1946 2.143876 AAACTTGAGCAGTGGTTGGT 57.856 45.000 0.00 0.00 41.02 3.67
1776 2145 9.173939 GAACTTTTCAAAGATAATGTCAGTGTG 57.826 33.333 6.29 0.00 39.31 3.82
1777 2146 8.450578 ACTTTTCAAAGATAATGTCAGTGTGA 57.549 30.769 6.29 0.00 39.31 3.58
1778 2147 8.345565 ACTTTTCAAAGATAATGTCAGTGTGAC 58.654 33.333 6.29 0.00 41.99 3.67
1789 2158 3.982475 GTCAGTGTGACAGAGAACATCA 58.018 45.455 2.12 0.00 46.22 3.07
1790 2159 4.564041 GTCAGTGTGACAGAGAACATCAT 58.436 43.478 2.12 0.00 46.22 2.45
1791 2160 4.388165 GTCAGTGTGACAGAGAACATCATG 59.612 45.833 2.12 0.00 46.22 3.07
1792 2161 3.124806 CAGTGTGACAGAGAACATCATGC 59.875 47.826 0.00 0.00 0.00 4.06
1793 2162 3.069289 GTGTGACAGAGAACATCATGCA 58.931 45.455 0.00 0.00 0.00 3.96
1794 2163 3.688185 GTGTGACAGAGAACATCATGCAT 59.312 43.478 0.00 0.00 0.00 3.96
1795 2164 4.155462 GTGTGACAGAGAACATCATGCATT 59.845 41.667 0.00 0.00 0.00 3.56
1796 2165 5.352293 GTGTGACAGAGAACATCATGCATTA 59.648 40.000 0.00 0.00 0.00 1.90
1797 2166 6.037940 GTGTGACAGAGAACATCATGCATTAT 59.962 38.462 0.00 0.00 0.00 1.28
1798 2167 6.600427 TGTGACAGAGAACATCATGCATTATT 59.400 34.615 0.00 0.00 0.00 1.40
1799 2168 7.121611 TGTGACAGAGAACATCATGCATTATTT 59.878 33.333 0.00 0.00 0.00 1.40
1800 2169 7.431376 GTGACAGAGAACATCATGCATTATTTG 59.569 37.037 0.00 0.00 0.00 2.32
1801 2170 7.337436 TGACAGAGAACATCATGCATTATTTGA 59.663 33.333 0.00 0.00 0.00 2.69
1802 2171 8.234136 ACAGAGAACATCATGCATTATTTGAT 57.766 30.769 0.00 0.00 0.00 2.57
1803 2172 9.346005 ACAGAGAACATCATGCATTATTTGATA 57.654 29.630 0.00 0.00 0.00 2.15
1806 2175 9.784680 GAGAACATCATGCATTATTTGATATCC 57.215 33.333 0.00 0.00 0.00 2.59
1807 2176 8.456471 AGAACATCATGCATTATTTGATATCCG 58.544 33.333 0.00 0.00 0.00 4.18
1808 2177 6.558009 ACATCATGCATTATTTGATATCCGC 58.442 36.000 0.00 0.00 0.00 5.54
1809 2178 5.220557 TCATGCATTATTTGATATCCGCG 57.779 39.130 0.00 0.00 0.00 6.46
1810 2179 4.094739 TCATGCATTATTTGATATCCGCGG 59.905 41.667 22.12 22.12 0.00 6.46
1811 2180 3.407698 TGCATTATTTGATATCCGCGGT 58.592 40.909 27.15 15.22 0.00 5.68
1812 2181 4.570930 TGCATTATTTGATATCCGCGGTA 58.429 39.130 27.15 17.01 0.00 4.02
1813 2182 4.390603 TGCATTATTTGATATCCGCGGTAC 59.609 41.667 27.15 14.94 0.00 3.34
1814 2183 4.390603 GCATTATTTGATATCCGCGGTACA 59.609 41.667 27.15 17.33 0.00 2.90
1815 2184 5.445939 GCATTATTTGATATCCGCGGTACAG 60.446 44.000 27.15 8.95 0.00 2.74
1816 2185 5.456548 TTATTTGATATCCGCGGTACAGA 57.543 39.130 27.15 15.60 0.00 3.41
1817 2186 3.804786 TTTGATATCCGCGGTACAGAA 57.195 42.857 27.15 11.15 0.00 3.02
1818 2187 4.330944 TTTGATATCCGCGGTACAGAAT 57.669 40.909 27.15 12.75 0.00 2.40
1819 2188 3.570926 TGATATCCGCGGTACAGAATC 57.429 47.619 27.15 18.29 0.00 2.52
1820 2189 2.230508 TGATATCCGCGGTACAGAATCC 59.769 50.000 27.15 6.36 0.00 3.01
1826 2195 3.659850 CGGTACAGAATCCGCATCA 57.340 52.632 0.00 0.00 40.28 3.07
1827 2196 2.154854 CGGTACAGAATCCGCATCAT 57.845 50.000 0.00 0.00 40.28 2.45
1828 2197 2.061773 CGGTACAGAATCCGCATCATC 58.938 52.381 0.00 0.00 40.28 2.92
1829 2198 2.417719 GGTACAGAATCCGCATCATCC 58.582 52.381 0.00 0.00 0.00 3.51
1830 2199 2.224281 GGTACAGAATCCGCATCATCCA 60.224 50.000 0.00 0.00 0.00 3.41
1831 2200 2.945080 ACAGAATCCGCATCATCCAT 57.055 45.000 0.00 0.00 0.00 3.41
1832 2201 2.775890 ACAGAATCCGCATCATCCATC 58.224 47.619 0.00 0.00 0.00 3.51
1833 2202 2.371179 ACAGAATCCGCATCATCCATCT 59.629 45.455 0.00 0.00 0.00 2.90
1834 2203 2.742589 CAGAATCCGCATCATCCATCTG 59.257 50.000 0.00 0.00 0.00 2.90
1835 2204 2.371179 AGAATCCGCATCATCCATCTGT 59.629 45.455 0.00 0.00 0.00 3.41
1836 2205 3.580022 AGAATCCGCATCATCCATCTGTA 59.420 43.478 0.00 0.00 0.00 2.74
1837 2206 2.820059 TCCGCATCATCCATCTGTAC 57.180 50.000 0.00 0.00 0.00 2.90
1838 2207 2.038659 TCCGCATCATCCATCTGTACA 58.961 47.619 0.00 0.00 0.00 2.90
1839 2208 2.036346 TCCGCATCATCCATCTGTACAG 59.964 50.000 17.17 17.17 0.00 2.74
1840 2209 2.036346 CCGCATCATCCATCTGTACAGA 59.964 50.000 27.07 27.07 42.37 3.41
1900 2269 5.312079 AGAGACAATGAAGAGTTTTCTGGG 58.688 41.667 0.00 0.00 32.79 4.45
1941 2310 8.439172 TGATCATATTGGATGATGTTTGGACTA 58.561 33.333 4.81 0.00 38.73 2.59
2074 2443 6.874134 CACATCTTAACACTAGCACCTTTACT 59.126 38.462 0.00 0.00 0.00 2.24
2096 2465 4.637387 AGAAGATAAGGCATGGGATCTG 57.363 45.455 0.00 0.00 0.00 2.90
2142 2511 7.615039 AGAGATACTGATCATGAATGTCCTT 57.385 36.000 0.00 0.00 34.17 3.36
2210 2579 4.081142 GGCTTGCCCCTTGTTATTGTATTT 60.081 41.667 0.00 0.00 0.00 1.40
2456 2825 2.088104 TAGCAGAGGGGTTCATCGAT 57.912 50.000 0.00 0.00 0.00 3.59
2752 3135 1.502231 CACCACCTTCGAACTGTCAG 58.498 55.000 0.00 0.00 0.00 3.51
2939 3322 1.079750 GGTGCTCCCGAAGTCTGTC 60.080 63.158 0.00 0.00 0.00 3.51
3009 3392 1.951209 TGAGTTGCCTAGTGGGATCA 58.049 50.000 0.00 0.00 37.23 2.92
3109 3492 3.434596 GGTATGTGTATCCCCAAAGGTCC 60.435 52.174 0.00 0.00 36.75 4.46
3141 3524 9.959721 ATCTAACAAACCTACAGACATTACAAT 57.040 29.630 0.00 0.00 0.00 2.71
3191 3574 1.600957 CATTTATGGGAGCTGACGCAG 59.399 52.381 0.00 2.92 39.10 5.18
3358 3753 4.096682 GCTGTATTTGAGAGGACGACTAGT 59.903 45.833 0.00 0.00 0.00 2.57
3386 3781 2.008329 GCTTTCGACGAGTCTCCTCTA 58.992 52.381 0.00 0.00 35.43 2.43
3518 3913 4.737855 ATTCACTAGAGCATACAACGGT 57.262 40.909 0.00 0.00 0.00 4.83
3626 4021 2.898920 ATCAAGGTGCCATGGCGAGG 62.899 60.000 30.87 18.02 45.51 4.63
3749 4144 5.408299 CACCGATGACTTCTTGACATTGTTA 59.592 40.000 0.00 0.00 32.71 2.41
3816 4215 3.006859 CCGATATTGACATGCCCAGACTA 59.993 47.826 0.00 0.00 0.00 2.59
3871 4270 3.165875 AGCTACTCACTTGCCAACTAGA 58.834 45.455 0.00 0.00 0.00 2.43
3919 4318 8.243961 TCTCCCTTGTCTCTTATAATCTTCTG 57.756 38.462 0.00 0.00 0.00 3.02
3947 4348 3.441222 TGTTGATGTGATCTGATGTTGGC 59.559 43.478 0.00 0.00 0.00 4.52
3988 4389 3.377346 ACGAAGATGCTTCGCTATGAT 57.623 42.857 24.38 6.01 44.98 2.45
4066 4475 3.128242 GCTGCTGATTGTGCATACTTTCT 59.872 43.478 0.00 0.00 39.86 2.52
4090 4499 5.010617 TGGGTTTCCTCTGCTTTTATTCAAC 59.989 40.000 0.00 0.00 0.00 3.18
4115 4524 3.731089 CACCATTTGTTGCTTGTTCCAT 58.269 40.909 0.00 0.00 0.00 3.41
4277 4686 3.073678 ACTGCTATTTCGTGTGCATTCA 58.926 40.909 0.00 0.00 34.79 2.57
4317 4726 8.856153 TCCAGCTGTGTCTGTTAAATAAATAA 57.144 30.769 13.81 0.00 32.32 1.40
4349 4758 9.066892 TCAGTTTGTGATTCTTAGTTATTGCTT 57.933 29.630 0.00 0.00 0.00 3.91
4384 4793 2.621055 TGTTGTCACTATGGTTGTTGCC 59.379 45.455 0.00 0.00 0.00 4.52
4505 4914 9.415544 GTTTTCTTGAGAAATATGCAGTGAAAT 57.584 29.630 6.98 0.00 42.83 2.17
4574 4983 6.210287 TCCTTTTTAAAAACGTGGACACAT 57.790 33.333 9.31 0.00 0.00 3.21
4718 5191 6.734871 GCCCGATTTATGTAAGATTGGTTTCC 60.735 42.308 0.00 0.00 0.00 3.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
130 134 8.446273 AGTAGAACAAAACATCAGATCAAATCG 58.554 33.333 0.00 0.00 0.00 3.34
148 152 3.572682 ACTTCACATCCGTCAGTAGAACA 59.427 43.478 0.00 0.00 0.00 3.18
150 154 3.572682 ACACTTCACATCCGTCAGTAGAA 59.427 43.478 0.00 0.00 0.00 2.10
179 192 4.471386 AGGCACAACAGAATCTGTATAGGT 59.529 41.667 17.04 9.77 44.62 3.08
252 270 9.976511 GGAATGCATAACTAATAGTACTGTACA 57.023 33.333 19.27 6.64 0.00 2.90
255 273 8.368668 GGAGGAATGCATAACTAATAGTACTGT 58.631 37.037 5.39 0.00 0.00 3.55
256 274 8.589338 AGGAGGAATGCATAACTAATAGTACTG 58.411 37.037 5.39 0.00 0.00 2.74
257 275 8.728596 AGGAGGAATGCATAACTAATAGTACT 57.271 34.615 0.00 0.00 0.00 2.73
258 276 9.780186 AAAGGAGGAATGCATAACTAATAGTAC 57.220 33.333 0.00 0.00 0.00 2.73
300 323 7.465116 AGAACAGGGAATAGGGAATATCAATG 58.535 38.462 0.00 0.00 0.00 2.82
379 402 5.260424 TGGTAAGTATGCCACATTGACAAT 58.740 37.500 0.00 0.00 36.27 2.71
395 418 8.651859 GCATATGCATTCCACTATGTGGTAAGT 61.652 40.741 22.84 3.10 46.21 2.24
396 419 6.348786 GCATATGCATTCCACTATGTGGTAAG 60.349 42.308 22.84 5.60 46.21 2.34
397 420 5.473162 GCATATGCATTCCACTATGTGGTAA 59.527 40.000 22.84 9.48 46.21 2.85
398 421 5.003160 GCATATGCATTCCACTATGTGGTA 58.997 41.667 22.84 7.49 46.21 3.25
399 422 3.822735 GCATATGCATTCCACTATGTGGT 59.177 43.478 22.84 0.00 46.21 4.16
400 423 4.430137 GCATATGCATTCCACTATGTGG 57.570 45.455 22.84 10.24 46.85 4.17
401 424 5.001874 AGAGCATATGCATTCCACTATGTG 58.998 41.667 28.62 0.00 45.16 3.21
402 425 5.238624 AGAGCATATGCATTCCACTATGT 57.761 39.130 28.62 3.88 45.16 2.29
403 426 5.619309 GCAAGAGCATATGCATTCCACTATG 60.619 44.000 28.62 14.12 45.16 2.23
404 427 4.458295 GCAAGAGCATATGCATTCCACTAT 59.542 41.667 28.62 5.21 45.16 2.12
405 428 3.817084 GCAAGAGCATATGCATTCCACTA 59.183 43.478 28.62 0.00 45.16 2.74
406 429 2.621998 GCAAGAGCATATGCATTCCACT 59.378 45.455 28.62 14.13 45.16 4.00
407 430 3.009301 GCAAGAGCATATGCATTCCAC 57.991 47.619 28.62 10.23 45.16 4.02
541 890 6.234177 ACAAAGCTATAATGTGATAGGAGCC 58.766 40.000 0.00 0.00 31.15 4.70
542 891 7.736447 AACAAAGCTATAATGTGATAGGAGC 57.264 36.000 0.00 0.00 31.15 4.70
615 964 6.109359 AGAAACAGATATAGGCAGTGTTGTC 58.891 40.000 0.00 0.00 31.80 3.18
630 979 4.971282 TCCCAGATGTATGGAGAAACAGAT 59.029 41.667 0.00 0.00 43.57 2.90
631 980 4.361783 TCCCAGATGTATGGAGAAACAGA 58.638 43.478 0.00 0.00 43.57 3.41
686 1035 4.402474 GGGTATCAGAGGGTTGAAAAATGG 59.598 45.833 0.00 0.00 0.00 3.16
695 1044 4.753186 CTGTATAGGGGTATCAGAGGGTT 58.247 47.826 0.00 0.00 0.00 4.11
750 1100 7.827236 TGGTATTAACTGATAAGAACAAGTGGG 59.173 37.037 0.00 0.00 29.74 4.61
787 1144 1.936547 GTGACTGCTATAGCCAACTGC 59.063 52.381 21.84 6.27 41.18 4.40
861 1218 4.515404 GCAGTAAGCACCTACGGG 57.485 61.111 0.00 0.00 44.79 5.28
954 1311 1.379044 CTGTTGGATGGTGGCCTCC 60.379 63.158 17.33 17.33 0.00 4.30
1055 1424 0.249238 GACATGGTCTGCCGCTCTAG 60.249 60.000 0.00 0.00 37.67 2.43
1388 1757 4.525100 ACAGGTGAGTAAGGTCTTTCTCTC 59.475 45.833 15.08 12.20 37.71 3.20
1577 1946 3.197766 AGAGTGTCCAAAATCATCGCCTA 59.802 43.478 0.00 0.00 0.00 3.93
1776 2145 7.700505 TCAAATAATGCATGATGTTCTCTGTC 58.299 34.615 0.00 0.00 0.00 3.51
1777 2146 7.634671 TCAAATAATGCATGATGTTCTCTGT 57.365 32.000 0.00 0.00 0.00 3.41
1780 2149 9.784680 GGATATCAAATAATGCATGATGTTCTC 57.215 33.333 0.00 0.00 35.53 2.87
1781 2150 8.456471 CGGATATCAAATAATGCATGATGTTCT 58.544 33.333 0.00 0.00 35.53 3.01
1782 2151 7.219535 GCGGATATCAAATAATGCATGATGTTC 59.780 37.037 0.00 0.00 35.53 3.18
1783 2152 7.031372 GCGGATATCAAATAATGCATGATGTT 58.969 34.615 0.00 0.00 35.53 2.71
1784 2153 6.558009 GCGGATATCAAATAATGCATGATGT 58.442 36.000 0.00 0.00 35.53 3.06
1785 2154 5.679792 CGCGGATATCAAATAATGCATGATG 59.320 40.000 0.00 0.00 35.53 3.07
1786 2155 5.220912 CCGCGGATATCAAATAATGCATGAT 60.221 40.000 24.07 1.99 37.54 2.45
1787 2156 4.094739 CCGCGGATATCAAATAATGCATGA 59.905 41.667 24.07 0.00 0.00 3.07
1788 2157 4.142622 ACCGCGGATATCAAATAATGCATG 60.143 41.667 35.90 0.00 0.00 4.06
1789 2158 4.009675 ACCGCGGATATCAAATAATGCAT 58.990 39.130 35.90 0.00 0.00 3.96
1790 2159 3.407698 ACCGCGGATATCAAATAATGCA 58.592 40.909 35.90 0.00 0.00 3.96
1791 2160 4.390603 TGTACCGCGGATATCAAATAATGC 59.609 41.667 35.90 8.77 0.00 3.56
1792 2161 5.867174 TCTGTACCGCGGATATCAAATAATG 59.133 40.000 35.90 11.13 0.00 1.90
1793 2162 6.032956 TCTGTACCGCGGATATCAAATAAT 57.967 37.500 35.90 6.98 0.00 1.28
1794 2163 5.456548 TCTGTACCGCGGATATCAAATAA 57.543 39.130 35.90 3.05 0.00 1.40
1795 2164 5.456548 TTCTGTACCGCGGATATCAAATA 57.543 39.130 35.90 8.14 31.57 1.40
1796 2165 4.330944 TTCTGTACCGCGGATATCAAAT 57.669 40.909 35.90 9.38 31.57 2.32
1797 2166 3.804786 TTCTGTACCGCGGATATCAAA 57.195 42.857 35.90 15.39 31.57 2.69
1798 2167 3.305813 GGATTCTGTACCGCGGATATCAA 60.306 47.826 35.90 18.47 31.57 2.57
1799 2168 2.230508 GGATTCTGTACCGCGGATATCA 59.769 50.000 35.90 21.68 31.57 2.15
1800 2169 2.731341 CGGATTCTGTACCGCGGATATC 60.731 54.545 35.90 21.32 42.55 1.63
1801 2170 1.201647 CGGATTCTGTACCGCGGATAT 59.798 52.381 35.90 12.99 42.55 1.63
1802 2171 0.594602 CGGATTCTGTACCGCGGATA 59.405 55.000 35.90 17.76 42.55 2.59
1803 2172 1.362717 CGGATTCTGTACCGCGGAT 59.637 57.895 35.90 18.92 42.55 4.18
1804 2173 2.802792 CGGATTCTGTACCGCGGA 59.197 61.111 35.90 13.31 42.55 5.54
1809 2178 2.224281 TGGATGATGCGGATTCTGTACC 60.224 50.000 0.00 0.00 0.00 3.34
1810 2179 3.111853 TGGATGATGCGGATTCTGTAC 57.888 47.619 0.00 0.00 0.00 2.90
1811 2180 3.580022 AGATGGATGATGCGGATTCTGTA 59.420 43.478 0.00 0.00 0.00 2.74
1812 2181 2.371179 AGATGGATGATGCGGATTCTGT 59.629 45.455 0.00 0.00 0.00 3.41
1813 2182 2.742589 CAGATGGATGATGCGGATTCTG 59.257 50.000 0.00 0.00 0.00 3.02
1814 2183 2.371179 ACAGATGGATGATGCGGATTCT 59.629 45.455 0.00 0.00 0.00 2.40
1815 2184 2.775890 ACAGATGGATGATGCGGATTC 58.224 47.619 0.00 0.00 0.00 2.52
1816 2185 2.945080 ACAGATGGATGATGCGGATT 57.055 45.000 0.00 0.00 0.00 3.01
1817 2186 2.634453 TGTACAGATGGATGATGCGGAT 59.366 45.455 0.00 0.00 0.00 4.18
1818 2187 2.036346 CTGTACAGATGGATGATGCGGA 59.964 50.000 18.45 0.00 0.00 5.54
1819 2188 2.036346 TCTGTACAGATGGATGATGCGG 59.964 50.000 21.74 0.00 31.41 5.69
1820 2189 3.375782 TCTGTACAGATGGATGATGCG 57.624 47.619 21.74 0.00 31.41 4.73
1821 2190 5.549347 AGATTCTGTACAGATGGATGATGC 58.451 41.667 25.68 9.46 37.29 3.91
1822 2191 9.551734 TTTTAGATTCTGTACAGATGGATGATG 57.448 33.333 25.68 0.00 37.29 3.07
1823 2192 9.553064 GTTTTAGATTCTGTACAGATGGATGAT 57.447 33.333 25.68 14.97 37.29 2.45
1824 2193 8.762645 AGTTTTAGATTCTGTACAGATGGATGA 58.237 33.333 25.68 10.64 37.29 2.92
1825 2194 8.824781 CAGTTTTAGATTCTGTACAGATGGATG 58.175 37.037 25.68 11.28 37.29 3.51
1826 2195 7.497249 GCAGTTTTAGATTCTGTACAGATGGAT 59.503 37.037 25.68 16.41 37.29 3.41
1827 2196 6.818644 GCAGTTTTAGATTCTGTACAGATGGA 59.181 38.462 25.68 12.14 37.29 3.41
1828 2197 6.595326 TGCAGTTTTAGATTCTGTACAGATGG 59.405 38.462 25.68 0.00 37.29 3.51
1829 2198 7.601073 TGCAGTTTTAGATTCTGTACAGATG 57.399 36.000 25.68 17.52 37.29 2.90
1830 2199 6.314896 GCTGCAGTTTTAGATTCTGTACAGAT 59.685 38.462 25.68 15.53 37.29 2.90
1831 2200 5.639506 GCTGCAGTTTTAGATTCTGTACAGA 59.360 40.000 21.74 21.74 35.27 3.41
1832 2201 5.641209 AGCTGCAGTTTTAGATTCTGTACAG 59.359 40.000 17.17 17.17 0.00 2.74
1833 2202 5.551233 AGCTGCAGTTTTAGATTCTGTACA 58.449 37.500 16.64 0.00 0.00 2.90
1834 2203 7.254590 CCATAGCTGCAGTTTTAGATTCTGTAC 60.255 40.741 16.64 0.00 0.00 2.90
1835 2204 6.763135 CCATAGCTGCAGTTTTAGATTCTGTA 59.237 38.462 16.64 0.00 0.00 2.74
1836 2205 5.587844 CCATAGCTGCAGTTTTAGATTCTGT 59.412 40.000 16.64 0.00 0.00 3.41
1837 2206 5.819379 TCCATAGCTGCAGTTTTAGATTCTG 59.181 40.000 16.64 1.51 0.00 3.02
1838 2207 5.819901 GTCCATAGCTGCAGTTTTAGATTCT 59.180 40.000 16.64 2.70 0.00 2.40
1839 2208 5.586243 TGTCCATAGCTGCAGTTTTAGATTC 59.414 40.000 16.64 0.00 0.00 2.52
1840 2209 5.500234 TGTCCATAGCTGCAGTTTTAGATT 58.500 37.500 16.64 0.00 0.00 2.40
1951 2320 2.499289 AGCACCCTAGACAAGTCATCAG 59.501 50.000 2.72 0.00 0.00 2.90
2074 2443 5.158141 ACAGATCCCATGCCTTATCTTCTA 58.842 41.667 0.00 0.00 0.00 2.10
2142 2511 2.306847 GGACAAAGGCTTCAACTCCAA 58.693 47.619 0.00 0.00 0.00 3.53
2171 2540 4.730600 CAAGCCTTTGCATTTGTTAACC 57.269 40.909 2.48 0.00 41.13 2.85
2210 2579 2.425312 CACACACAAAAGGCTACCAACA 59.575 45.455 0.00 0.00 0.00 3.33
2456 2825 1.595311 ATGTGCTATCACCCCTTCCA 58.405 50.000 0.00 0.00 42.46 3.53
2752 3135 1.808945 GCATGCAGCCATCCAGTATAC 59.191 52.381 14.21 0.00 37.23 1.47
2939 3322 5.743398 TGTCAACAAATTTGAAAGCTTCTCG 59.257 36.000 24.64 0.00 0.00 4.04
3009 3392 3.073062 TGCCTAAGCTTCTTCAGTTTCCT 59.927 43.478 0.00 0.00 40.80 3.36
3109 3492 6.934645 TGTCTGTAGGTTTGTTAGATTTCCAG 59.065 38.462 0.00 0.00 0.00 3.86
3141 3524 4.005650 GACTCATCTTGTGCTTCCAATGA 58.994 43.478 0.00 0.00 0.00 2.57
3191 3574 4.579869 TCCATAACCTCAAACTTCTCAGC 58.420 43.478 0.00 0.00 0.00 4.26
3358 3753 2.167398 CTCGTCGAAAGCCCCTTCCA 62.167 60.000 0.00 0.00 0.00 3.53
3518 3913 1.001048 GTGCAAAATGTCAGCTGCTCA 60.001 47.619 9.47 11.26 35.78 4.26
3626 4021 6.314152 GGTTGACTAAGACTAATCTTTCCAGC 59.686 42.308 0.00 0.00 42.91 4.85
3749 4144 1.464023 CGAATTGCAGAACATTCGCGT 60.464 47.619 15.89 0.00 39.21 6.01
3816 4215 9.515226 ACTTATGTACATACACATTTCCAAACT 57.485 29.630 15.20 0.00 39.77 2.66
3919 4318 7.312657 ACATCAGATCACATCAACACATTAC 57.687 36.000 0.00 0.00 0.00 1.89
3947 4348 1.105167 TCCGCCGGTGACCTACATAG 61.105 60.000 18.79 0.00 0.00 2.23
3988 4389 9.449719 GATACTCCTTTTTCCTTGATCTAAACA 57.550 33.333 0.00 0.00 0.00 2.83
4023 4432 1.625616 GCACGAGCGTACACTAACAT 58.374 50.000 0.00 0.00 0.00 2.71
4066 4475 4.735369 TGAATAAAAGCAGAGGAAACCCA 58.265 39.130 0.00 0.00 0.00 4.51
4115 4524 2.338620 CACGAACAGTGGCGGAGA 59.661 61.111 11.50 0.00 46.77 3.71
4172 4581 4.262420 GCCACAACCAGAACAAACCAATAT 60.262 41.667 0.00 0.00 0.00 1.28
4349 4758 6.403866 AGTGACAACAAAAATGAATGCCTA 57.596 33.333 0.00 0.00 0.00 3.93
4350 4759 5.280654 AGTGACAACAAAAATGAATGCCT 57.719 34.783 0.00 0.00 0.00 4.75
4364 4773 2.884639 AGGCAACAACCATAGTGACAAC 59.115 45.455 0.00 0.00 41.41 3.32
4384 4793 5.182001 ACAAGGCTAGCAATAAAACAGACAG 59.818 40.000 18.24 0.00 0.00 3.51
4563 4972 1.544825 CCTCCTCCATGTGTCCACGT 61.545 60.000 0.00 0.00 0.00 4.49
4568 4977 0.531532 CATCGCCTCCTCCATGTGTC 60.532 60.000 0.00 0.00 0.00 3.67
4574 4983 3.083349 CACCCATCGCCTCCTCCA 61.083 66.667 0.00 0.00 0.00 3.86
4646 5055 5.640732 CATAACATGGTTTGGTACAGCTTC 58.359 41.667 0.00 0.00 42.39 3.86
4718 5191 2.863809 AGCACCAAGGGACAGTTTAAG 58.136 47.619 0.00 0.00 0.00 1.85
4778 5251 0.676184 CCCAGCTAGCGCTTGAGATA 59.324 55.000 23.12 0.00 46.47 1.98


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

AutoCloner maintained by Alex Coulton.