Multiple sequence alignment - TraesCS5D01G474600

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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 TraesCS5D01G474600 chr5D 100.000 2827 0 0 1 2827 514494562 514497388 0.000000e+00 5221
1 TraesCS5D01G474600 chr5D 88.204 746 85 3 1092 1836 445655719 445654976 0.000000e+00 887
2 TraesCS5D01G474600 chr5B 88.849 1103 79 9 1 1086 646521635 646522710 0.000000e+00 1315
3 TraesCS5D01G474600 chr5B 82.638 743 126 3 1092 1833 402727723 402726983 0.000000e+00 654
4 TraesCS5D01G474600 chr5B 79.545 616 121 5 399 1011 691983229 691983842 4.320000e-118 435
5 TraesCS5D01G474600 chr5B 81.930 487 74 10 397 877 40975724 40975246 1.580000e-107 399
6 TraesCS5D01G474600 chr5B 88.571 140 16 0 1131 1270 602788321 602788460 1.350000e-38 171
7 TraesCS5D01G474600 chr3D 93.796 822 49 2 2007 2827 447895281 447896101 0.000000e+00 1234
8 TraesCS5D01G474600 chr3D 93.505 816 52 1 2012 2827 573739155 573738341 0.000000e+00 1212
9 TraesCS5D01G474600 chr3D 93.154 818 56 0 2010 2827 4288553 4287736 0.000000e+00 1201
10 TraesCS5D01G474600 chr3D 89.826 747 73 3 1092 1837 26080354 26079610 0.000000e+00 955
11 TraesCS5D01G474600 chr7D 93.873 816 49 1 2012 2827 372090707 372089893 0.000000e+00 1229
12 TraesCS5D01G474600 chr7D 94.459 740 38 3 1094 1833 541243920 541243184 0.000000e+00 1136
13 TraesCS5D01G474600 chr1D 93.750 816 47 2 2013 2827 437501510 437500698 0.000000e+00 1221
14 TraesCS5D01G474600 chr1D 81.758 751 132 5 1092 1840 75885977 75885230 8.600000e-175 623
15 TraesCS5D01G474600 chr6D 93.212 825 55 1 2003 2827 329888832 329889655 0.000000e+00 1212
16 TraesCS5D01G474600 chr6D 93.252 815 55 0 2013 2827 28968925 28969739 0.000000e+00 1201
17 TraesCS5D01G474600 chr2D 93.260 816 55 0 2012 2827 536974053 536973238 0.000000e+00 1203
18 TraesCS5D01G474600 chr2D 80.697 746 133 5 1092 1836 498279982 498279247 1.140000e-158 569
19 TraesCS5D01G474600 chr2D 81.458 631 97 13 397 1011 389701532 389702158 1.510000e-137 499
20 TraesCS5D01G474600 chr2D 80.983 631 98 10 398 1011 352144584 352143959 5.480000e-132 481
21 TraesCS5D01G474600 chr2D 78.378 629 119 6 397 1010 457852851 457852225 2.640000e-105 392
22 TraesCS5D01G474600 chr2D 79.042 501 77 14 402 888 318247327 318246841 4.540000e-83 318
23 TraesCS5D01G474600 chr2D 76.210 496 94 15 394 884 203751564 203751088 1.010000e-59 241
24 TraesCS5D01G474600 chr2D 91.549 71 6 0 399 469 498111240 498111310 6.450000e-17 99
25 TraesCS5D01G474600 chrUn 93.252 815 55 0 2013 2827 298346440 298347254 0.000000e+00 1201
26 TraesCS5D01G474600 chr4A 85.696 762 89 4 1092 1834 578395351 578394591 0.000000e+00 785
27 TraesCS5D01G474600 chr4A 83.081 727 121 2 1092 1817 19472651 19473376 0.000000e+00 660
28 TraesCS5D01G474600 chr4A 79.384 747 145 8 1092 1834 703880655 703881396 4.170000e-143 518
29 TraesCS5D01G474600 chr4A 84.762 105 15 1 393 497 109938824 109938721 1.390000e-18 104
30 TraesCS5D01G474600 chr5A 89.412 595 55 7 493 1086 642903434 642904021 0.000000e+00 743
31 TraesCS5D01G474600 chr5A 91.164 464 37 4 1 463 642902978 642903438 6.650000e-176 627
32 TraesCS5D01G474600 chr4B 80.189 636 107 10 390 1011 64616279 64616909 2.570000e-125 459
33 TraesCS5D01G474600 chr4B 81.098 492 85 8 523 1011 413773415 413772929 1.230000e-103 387
34 TraesCS5D01G474600 chr7B 79.173 629 112 10 399 1011 377314759 377314134 4.360000e-113 418
35 TraesCS5D01G474600 chr2B 77.083 624 122 13 402 1009 539078905 539078287 9.700000e-90 340
36 TraesCS5D01G474600 chr6B 75.195 512 99 17 398 890 460630021 460630523 1.710000e-52 217


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 TraesCS5D01G474600 chr5D 514494562 514497388 2826 False 5221 5221 100.000 1 2827 1 chr5D.!!$F1 2826
1 TraesCS5D01G474600 chr5D 445654976 445655719 743 True 887 887 88.204 1092 1836 1 chr5D.!!$R1 744
2 TraesCS5D01G474600 chr5B 646521635 646522710 1075 False 1315 1315 88.849 1 1086 1 chr5B.!!$F2 1085
3 TraesCS5D01G474600 chr5B 402726983 402727723 740 True 654 654 82.638 1092 1833 1 chr5B.!!$R2 741
4 TraesCS5D01G474600 chr5B 691983229 691983842 613 False 435 435 79.545 399 1011 1 chr5B.!!$F3 612
5 TraesCS5D01G474600 chr3D 447895281 447896101 820 False 1234 1234 93.796 2007 2827 1 chr3D.!!$F1 820
6 TraesCS5D01G474600 chr3D 573738341 573739155 814 True 1212 1212 93.505 2012 2827 1 chr3D.!!$R3 815
7 TraesCS5D01G474600 chr3D 4287736 4288553 817 True 1201 1201 93.154 2010 2827 1 chr3D.!!$R1 817
8 TraesCS5D01G474600 chr3D 26079610 26080354 744 True 955 955 89.826 1092 1837 1 chr3D.!!$R2 745
9 TraesCS5D01G474600 chr7D 372089893 372090707 814 True 1229 1229 93.873 2012 2827 1 chr7D.!!$R1 815
10 TraesCS5D01G474600 chr7D 541243184 541243920 736 True 1136 1136 94.459 1094 1833 1 chr7D.!!$R2 739
11 TraesCS5D01G474600 chr1D 437500698 437501510 812 True 1221 1221 93.750 2013 2827 1 chr1D.!!$R2 814
12 TraesCS5D01G474600 chr1D 75885230 75885977 747 True 623 623 81.758 1092 1840 1 chr1D.!!$R1 748
13 TraesCS5D01G474600 chr6D 329888832 329889655 823 False 1212 1212 93.212 2003 2827 1 chr6D.!!$F2 824
14 TraesCS5D01G474600 chr6D 28968925 28969739 814 False 1201 1201 93.252 2013 2827 1 chr6D.!!$F1 814
15 TraesCS5D01G474600 chr2D 536973238 536974053 815 True 1203 1203 93.260 2012 2827 1 chr2D.!!$R6 815
16 TraesCS5D01G474600 chr2D 498279247 498279982 735 True 569 569 80.697 1092 1836 1 chr2D.!!$R5 744
17 TraesCS5D01G474600 chr2D 389701532 389702158 626 False 499 499 81.458 397 1011 1 chr2D.!!$F1 614
18 TraesCS5D01G474600 chr2D 352143959 352144584 625 True 481 481 80.983 398 1011 1 chr2D.!!$R3 613
19 TraesCS5D01G474600 chr2D 457852225 457852851 626 True 392 392 78.378 397 1010 1 chr2D.!!$R4 613
20 TraesCS5D01G474600 chrUn 298346440 298347254 814 False 1201 1201 93.252 2013 2827 1 chrUn.!!$F1 814
21 TraesCS5D01G474600 chr4A 578394591 578395351 760 True 785 785 85.696 1092 1834 1 chr4A.!!$R2 742
22 TraesCS5D01G474600 chr4A 19472651 19473376 725 False 660 660 83.081 1092 1817 1 chr4A.!!$F1 725
23 TraesCS5D01G474600 chr4A 703880655 703881396 741 False 518 518 79.384 1092 1834 1 chr4A.!!$F2 742
24 TraesCS5D01G474600 chr5A 642902978 642904021 1043 False 685 743 90.288 1 1086 2 chr5A.!!$F1 1085
25 TraesCS5D01G474600 chr4B 64616279 64616909 630 False 459 459 80.189 390 1011 1 chr4B.!!$F1 621
26 TraesCS5D01G474600 chr7B 377314134 377314759 625 True 418 418 79.173 399 1011 1 chr7B.!!$R1 612
27 TraesCS5D01G474600 chr2B 539078287 539078905 618 True 340 340 77.083 402 1009 1 chr2B.!!$R1 607
28 TraesCS5D01G474600 chr6B 460630021 460630523 502 False 217 217 75.195 398 890 1 chr6B.!!$F1 492

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
691 729 0.17668 ATCACCAGTGATCAGTCCGC 59.823 55.0 7.47 0.0 46.57 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1885 1946 0.168788 TAACGAGCCTTACACGACCG 59.831 55.0 0.0 0.0 36.14 4.79 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
133 149 4.694982 CCTTTGCCAAAAGTGAAACAAACT 59.305 37.500 0.00 0.00 41.12 2.66
134 150 5.872070 CCTTTGCCAAAAGTGAAACAAACTA 59.128 36.000 0.00 0.00 41.12 2.24
162 178 8.891671 AACTAGAAATTTGTTTGCACATTGAT 57.108 26.923 0.00 0.00 31.06 2.57
169 185 6.528014 TTTGTTTGCACATTGATGAATCAC 57.472 33.333 0.00 0.00 36.36 3.06
209 226 7.558161 TGGCACTCATGTATATTTTCTTGAG 57.442 36.000 0.00 12.23 39.83 3.02
240 257 4.260743 CCACACAAGGCAATACACATATCG 60.261 45.833 0.00 0.00 0.00 2.92
250 267 6.915300 GGCAATACACATATCGCAAATGTTTA 59.085 34.615 0.00 0.00 35.39 2.01
254 271 6.735678 ACACATATCGCAAATGTTTACTCA 57.264 33.333 0.00 0.00 35.39 3.41
276 293 1.069090 CATAGCCGGTACCGCATGT 59.931 57.895 29.15 14.09 38.24 3.21
283 300 1.471851 CCGGTACCGCATGTCATACAA 60.472 52.381 29.15 0.00 38.24 2.41
324 341 4.629634 TGCATATATAAAAGCGGTGATCGG 59.370 41.667 0.00 0.00 39.69 4.18
355 372 0.532573 GGAGAGGACATTGACGAGCA 59.467 55.000 0.00 0.00 0.00 4.26
356 373 1.634702 GAGAGGACATTGACGAGCAC 58.365 55.000 0.00 0.00 0.00 4.40
438 456 2.118228 TTGCGATGTTTCACTTGTGC 57.882 45.000 0.00 0.00 0.00 4.57
502 534 1.677552 CCCCACCGTCACTAAAGCT 59.322 57.895 0.00 0.00 0.00 3.74
514 548 6.961554 CCGTCACTAAAGCTTCATCATAAAAC 59.038 38.462 0.00 0.00 0.00 2.43
516 551 8.230486 CGTCACTAAAGCTTCATCATAAAACTT 58.770 33.333 0.00 0.00 0.00 2.66
595 630 5.481473 ACCTAAAATTGTCAATGATGGCTGT 59.519 36.000 0.00 0.00 30.51 4.40
645 680 3.342377 TGATAGGCCAATTTGTCGTCA 57.658 42.857 5.01 0.00 0.00 4.35
667 703 8.471457 CGTCAAAGATAGTTTTTGTTGACAATG 58.529 33.333 13.06 0.00 43.09 2.82
691 729 0.176680 ATCACCAGTGATCAGTCCGC 59.823 55.000 7.47 0.00 46.57 5.54
701 739 2.107041 ATCAGTCCGCGGTTTGACCA 62.107 55.000 27.70 12.99 38.47 4.02
942 983 1.559682 ACGATTCTAACATGTGGGCCT 59.440 47.619 4.53 0.00 0.00 5.19
999 1040 0.321210 TACGTGGGTGATGTGGCTTG 60.321 55.000 0.00 0.00 0.00 4.01
1086 1127 2.284995 GCAGGGGAGTGAGGGAGT 60.285 66.667 0.00 0.00 0.00 3.85
1087 1128 1.001760 GCAGGGGAGTGAGGGAGTA 59.998 63.158 0.00 0.00 0.00 2.59
1088 1129 1.331399 GCAGGGGAGTGAGGGAGTAC 61.331 65.000 0.00 0.00 0.00 2.73
1089 1130 1.038130 CAGGGGAGTGAGGGAGTACG 61.038 65.000 0.00 0.00 0.00 3.67
1090 1131 1.757340 GGGGAGTGAGGGAGTACGG 60.757 68.421 0.00 0.00 0.00 4.02
1145 1186 2.962253 GGAAAGATCGAGCGGCCG 60.962 66.667 24.05 24.05 0.00 6.13
1255 1298 5.580297 GGTTCTAGTGAAAGAGCTCATTCAG 59.420 44.000 29.34 19.72 34.73 3.02
1317 1360 2.907892 TGAGAGGGTGAGATGGAAACT 58.092 47.619 0.00 0.00 0.00 2.66
1366 1409 3.339253 ACTGATGCTGCTGTTGATGTA 57.661 42.857 0.00 0.00 0.00 2.29
1416 1459 3.075005 ACGAGACCATGACGGGGG 61.075 66.667 0.00 0.00 40.22 5.40
1432 1475 0.038310 GGGGACTTTTGCTAGCCAGT 59.962 55.000 13.29 11.53 0.00 4.00
1500 1543 2.753029 GGTCAGGGAAGCTGTGCT 59.247 61.111 0.00 0.00 42.56 4.40
1551 1594 0.179100 ACCATCGAATCGGACTGCAG 60.179 55.000 13.48 13.48 0.00 4.41
1571 1614 5.068329 TGCAGAACTGTCATAGAGGAGTATG 59.932 44.000 3.77 0.00 0.00 2.39
1615 1658 1.162800 GGAGCCCAATCATCAGCGAC 61.163 60.000 0.00 0.00 0.00 5.19
1692 1735 2.777969 CCAATGAGGCTGCTCACTC 58.222 57.895 0.00 0.00 36.05 3.51
1719 1762 0.897863 AGAGAGAGCCTTGCGAGTGT 60.898 55.000 0.00 0.00 0.00 3.55
1766 1809 1.243342 CCCTGCTTCGTTGATTGCCA 61.243 55.000 0.00 0.00 0.00 4.92
1825 1886 2.269241 CCTTGGAGGCCGGTTCTC 59.731 66.667 15.60 15.60 0.00 2.87
1858 1919 4.663636 GACACCTTTGTCCGTTTATGAG 57.336 45.455 0.00 0.00 45.77 2.90
1859 1920 2.812011 ACACCTTTGTCCGTTTATGAGC 59.188 45.455 0.00 0.00 0.00 4.26
1860 1921 2.073816 ACCTTTGTCCGTTTATGAGCG 58.926 47.619 0.00 0.00 0.00 5.03
1861 1922 2.289195 ACCTTTGTCCGTTTATGAGCGA 60.289 45.455 0.00 0.00 0.00 4.93
1862 1923 2.348666 CCTTTGTCCGTTTATGAGCGAG 59.651 50.000 0.00 0.00 0.00 5.03
1863 1924 1.355971 TTGTCCGTTTATGAGCGAGC 58.644 50.000 0.00 0.00 0.00 5.03
1864 1925 0.245266 TGTCCGTTTATGAGCGAGCA 59.755 50.000 0.00 0.00 0.00 4.26
1865 1926 1.134818 TGTCCGTTTATGAGCGAGCAT 60.135 47.619 0.00 0.00 0.00 3.79
1866 1927 1.258982 GTCCGTTTATGAGCGAGCATG 59.741 52.381 0.00 0.00 0.00 4.06
1867 1928 1.134818 TCCGTTTATGAGCGAGCATGT 60.135 47.619 0.00 0.00 0.00 3.21
1868 1929 1.665679 CCGTTTATGAGCGAGCATGTT 59.334 47.619 0.00 0.00 0.00 2.71
1869 1930 2.095853 CCGTTTATGAGCGAGCATGTTT 59.904 45.455 0.00 0.00 0.00 2.83
1870 1931 3.093574 CGTTTATGAGCGAGCATGTTTG 58.906 45.455 0.00 0.00 0.00 2.93
1871 1932 3.429085 GTTTATGAGCGAGCATGTTTGG 58.571 45.455 0.00 0.00 0.00 3.28
1872 1933 1.667236 TATGAGCGAGCATGTTTGGG 58.333 50.000 0.00 0.00 0.00 4.12
1873 1934 0.322816 ATGAGCGAGCATGTTTGGGT 60.323 50.000 0.00 0.00 0.00 4.51
1874 1935 0.537143 TGAGCGAGCATGTTTGGGTT 60.537 50.000 0.00 0.00 0.00 4.11
1875 1936 0.169009 GAGCGAGCATGTTTGGGTTC 59.831 55.000 0.00 0.00 0.00 3.62
1876 1937 1.212751 GCGAGCATGTTTGGGTTCC 59.787 57.895 0.00 0.00 0.00 3.62
1877 1938 1.501741 CGAGCATGTTTGGGTTCCG 59.498 57.895 0.00 0.00 0.00 4.30
1878 1939 1.883021 GAGCATGTTTGGGTTCCGG 59.117 57.895 0.00 0.00 0.00 5.14
1879 1940 2.212900 GAGCATGTTTGGGTTCCGGC 62.213 60.000 0.00 0.00 0.00 6.13
1880 1941 2.569354 GCATGTTTGGGTTCCGGCA 61.569 57.895 0.00 0.00 0.00 5.69
1881 1942 1.586028 CATGTTTGGGTTCCGGCAG 59.414 57.895 0.00 0.00 0.00 4.85
1882 1943 2.275380 ATGTTTGGGTTCCGGCAGC 61.275 57.895 0.00 0.00 0.00 5.25
1883 1944 2.909965 GTTTGGGTTCCGGCAGCA 60.910 61.111 5.49 0.00 0.00 4.41
1884 1945 2.909965 TTTGGGTTCCGGCAGCAC 60.910 61.111 5.49 0.00 0.00 4.40
1885 1946 4.966787 TTGGGTTCCGGCAGCACC 62.967 66.667 5.49 4.58 0.00 5.01
1894 1955 4.367023 GGCAGCACCGGTCGTGTA 62.367 66.667 2.59 0.00 44.97 2.90
1895 1956 2.356553 GCAGCACCGGTCGTGTAA 60.357 61.111 2.59 0.00 44.97 2.41
1896 1957 2.380410 GCAGCACCGGTCGTGTAAG 61.380 63.158 2.59 0.00 44.97 2.34
1897 1958 1.736645 CAGCACCGGTCGTGTAAGG 60.737 63.158 2.59 0.00 44.97 2.69
1898 1959 3.116531 GCACCGGTCGTGTAAGGC 61.117 66.667 2.59 0.00 44.97 4.35
1899 1960 2.654877 CACCGGTCGTGTAAGGCT 59.345 61.111 2.59 0.00 37.73 4.58
1900 1961 1.445582 CACCGGTCGTGTAAGGCTC 60.446 63.158 2.59 0.00 37.73 4.70
1901 1962 2.202570 CCGGTCGTGTAAGGCTCG 60.203 66.667 0.00 0.00 35.64 5.03
1902 1963 2.564975 CGGTCGTGTAAGGCTCGT 59.435 61.111 0.00 0.00 35.78 4.18
1903 1964 1.080974 CGGTCGTGTAAGGCTCGTT 60.081 57.895 0.00 0.00 35.78 3.85
1904 1965 0.168788 CGGTCGTGTAAGGCTCGTTA 59.831 55.000 0.00 0.00 35.78 3.18
1905 1966 1.401409 CGGTCGTGTAAGGCTCGTTAA 60.401 52.381 0.00 0.00 35.78 2.01
1906 1967 1.988467 GGTCGTGTAAGGCTCGTTAAC 59.012 52.381 0.00 0.00 35.78 2.01
1907 1968 1.645751 GTCGTGTAAGGCTCGTTAACG 59.354 52.381 21.85 21.85 41.45 3.18
1908 1969 0.986992 CGTGTAAGGCTCGTTAACGG 59.013 55.000 26.51 17.98 40.29 4.44
1909 1970 0.717784 GTGTAAGGCTCGTTAACGGC 59.282 55.000 26.51 25.26 40.29 5.68
1914 1975 4.143363 GCTCGTTAACGGCCACGC 62.143 66.667 26.51 16.84 46.04 5.34
1915 1976 3.484547 CTCGTTAACGGCCACGCC 61.485 66.667 26.51 0.00 46.75 5.68
1933 1994 4.166011 GTCTGGCGCCGCATTGAC 62.166 66.667 23.90 19.16 0.00 3.18
1938 1999 3.483665 GCGCCGCATTGACGTGTA 61.484 61.111 3.15 0.00 0.00 2.90
1939 2000 2.695055 CGCCGCATTGACGTGTAG 59.305 61.111 0.00 0.00 0.00 2.74
1940 2001 2.399611 GCCGCATTGACGTGTAGC 59.600 61.111 0.00 0.00 0.00 3.58
1941 2002 3.089784 CCGCATTGACGTGTAGCC 58.910 61.111 0.00 0.00 0.00 3.93
1942 2003 1.447838 CCGCATTGACGTGTAGCCT 60.448 57.895 0.00 0.00 0.00 4.58
1943 2004 0.179121 CCGCATTGACGTGTAGCCTA 60.179 55.000 0.00 0.00 0.00 3.93
1944 2005 1.635844 CGCATTGACGTGTAGCCTAA 58.364 50.000 0.00 0.00 0.00 2.69
1945 2006 2.201732 CGCATTGACGTGTAGCCTAAT 58.798 47.619 0.00 0.00 0.00 1.73
1946 2007 2.607635 CGCATTGACGTGTAGCCTAATT 59.392 45.455 0.00 0.00 0.00 1.40
1947 2008 3.544048 CGCATTGACGTGTAGCCTAATTG 60.544 47.826 0.00 0.00 0.00 2.32
1948 2009 3.242739 GCATTGACGTGTAGCCTAATTGG 60.243 47.826 0.00 0.00 39.35 3.16
1957 2018 4.183858 CCTAATTGGCGGCCCGGA 62.184 66.667 17.97 2.63 0.00 5.14
1958 2019 2.124487 CTAATTGGCGGCCCGGAA 60.124 61.111 17.97 4.43 0.00 4.30
1959 2020 2.438795 TAATTGGCGGCCCGGAAC 60.439 61.111 17.97 0.00 0.00 3.62
1974 2035 2.863401 GGAACGTCAAAAACCAGCTT 57.137 45.000 0.00 0.00 0.00 3.74
1975 2036 2.459934 GGAACGTCAAAAACCAGCTTG 58.540 47.619 0.00 0.00 0.00 4.01
1976 2037 2.098443 GGAACGTCAAAAACCAGCTTGA 59.902 45.455 0.00 0.00 0.00 3.02
1977 2038 3.428316 GGAACGTCAAAAACCAGCTTGAA 60.428 43.478 0.00 0.00 33.52 2.69
1978 2039 4.359706 GAACGTCAAAAACCAGCTTGAAT 58.640 39.130 0.00 0.00 33.52 2.57
1979 2040 4.385358 ACGTCAAAAACCAGCTTGAATT 57.615 36.364 0.00 0.00 33.52 2.17
1980 2041 4.111916 ACGTCAAAAACCAGCTTGAATTG 58.888 39.130 0.00 0.00 33.52 2.32
1981 2042 4.111916 CGTCAAAAACCAGCTTGAATTGT 58.888 39.130 0.00 0.00 33.52 2.71
1982 2043 4.566360 CGTCAAAAACCAGCTTGAATTGTT 59.434 37.500 0.00 0.00 33.52 2.83
1983 2044 5.746245 CGTCAAAAACCAGCTTGAATTGTTA 59.254 36.000 0.00 0.00 33.52 2.41
1984 2045 6.074888 CGTCAAAAACCAGCTTGAATTGTTAG 60.075 38.462 0.00 0.00 33.52 2.34
1985 2046 5.752955 TCAAAAACCAGCTTGAATTGTTAGC 59.247 36.000 0.00 0.00 35.16 3.09
1986 2047 4.935352 AAACCAGCTTGAATTGTTAGCA 57.065 36.364 0.00 0.00 37.37 3.49
1987 2048 4.935352 AACCAGCTTGAATTGTTAGCAA 57.065 36.364 0.00 0.00 37.37 3.91
1988 2049 4.243007 ACCAGCTTGAATTGTTAGCAAC 57.757 40.909 0.00 0.00 37.44 4.17
1989 2050 3.636300 ACCAGCTTGAATTGTTAGCAACA 59.364 39.130 0.00 0.00 40.21 3.33
1990 2051 4.232221 CCAGCTTGAATTGTTAGCAACAG 58.768 43.478 0.00 0.00 43.27 3.16
1991 2052 4.261741 CCAGCTTGAATTGTTAGCAACAGT 60.262 41.667 0.00 0.00 43.27 3.55
1992 2053 4.913924 CAGCTTGAATTGTTAGCAACAGTC 59.086 41.667 0.00 0.00 43.27 3.51
1993 2054 3.908382 GCTTGAATTGTTAGCAACAGTCG 59.092 43.478 0.00 0.00 43.27 4.18
1994 2055 4.554723 GCTTGAATTGTTAGCAACAGTCGT 60.555 41.667 0.00 0.00 43.27 4.34
1995 2056 5.493133 TTGAATTGTTAGCAACAGTCGTT 57.507 34.783 0.00 0.00 43.27 3.85
1996 2057 5.493133 TGAATTGTTAGCAACAGTCGTTT 57.507 34.783 0.00 0.00 43.27 3.60
1997 2058 5.885881 TGAATTGTTAGCAACAGTCGTTTT 58.114 33.333 0.00 0.00 43.27 2.43
1998 2059 6.326375 TGAATTGTTAGCAACAGTCGTTTTT 58.674 32.000 0.00 0.00 43.27 1.94
2047 2108 0.546507 TGCCCTCAGTGGTGTCCATA 60.547 55.000 0.00 0.00 35.28 2.74
2054 2115 2.571202 TCAGTGGTGTCCATATGCTCAA 59.429 45.455 0.00 0.00 35.28 3.02
2088 2149 1.066303 TGCGAATTGTGCTCGGTTTTT 59.934 42.857 0.00 0.00 36.80 1.94
2113 2174 3.384789 CCTAGTCCATGCACAGCTACTAA 59.615 47.826 0.00 0.00 0.00 2.24
2517 2578 4.329545 AGGCCGGAGCGCTCAAAA 62.330 61.111 36.27 0.00 41.24 2.44
2616 2678 1.491274 TTGGTGAGGCAGGCATCAGA 61.491 55.000 9.07 0.00 37.42 3.27
2794 2858 0.934436 CGGTTTGCTTTCTTGGTGCG 60.934 55.000 0.00 0.00 0.00 5.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
134 150 9.771915 CAATGTGCAAACAAATTTCTAGTTTTT 57.228 25.926 3.15 0.00 30.89 1.94
142 158 8.283992 TGATTCATCAATGTGCAAACAAATTTC 58.716 29.630 0.00 0.00 30.89 2.17
162 178 5.703978 ATGTTTGACGAAATGGTGATTCA 57.296 34.783 0.00 0.00 0.00 2.57
169 185 2.730928 GTGCCAATGTTTGACGAAATGG 59.269 45.455 0.00 0.00 0.00 3.16
209 226 6.364976 GTGTATTGCCTTGTGTGGTTTATTTC 59.635 38.462 0.00 0.00 0.00 2.17
240 257 5.269313 GCTATGAGCTGAGTAAACATTTGC 58.731 41.667 0.00 0.00 38.45 3.68
254 271 2.857744 GCGGTACCGGCTATGAGCT 61.858 63.158 33.98 0.00 41.99 4.09
315 332 1.852942 CCATTGTCTACCGATCACCG 58.147 55.000 0.00 0.00 38.18 4.94
324 341 1.112113 TCCTCTCCGCCATTGTCTAC 58.888 55.000 0.00 0.00 0.00 2.59
326 343 0.904865 TGTCCTCTCCGCCATTGTCT 60.905 55.000 0.00 0.00 0.00 3.41
355 372 3.637769 GACTGTTCCTCTCCCTATCAGT 58.362 50.000 0.00 0.00 37.37 3.41
356 373 2.621055 CGACTGTTCCTCTCCCTATCAG 59.379 54.545 0.00 0.00 0.00 2.90
514 548 6.598064 AGGAATTGGTACCGTCAAGATTTAAG 59.402 38.462 7.57 0.00 0.00 1.85
516 551 6.057321 AGGAATTGGTACCGTCAAGATTTA 57.943 37.500 7.57 0.00 0.00 1.40
645 680 9.398170 CGATCATTGTCAACAAAAACTATCTTT 57.602 29.630 0.00 0.00 39.55 2.52
685 721 2.030562 CTGGTCAAACCGCGGACT 59.969 61.111 35.90 16.22 42.58 3.85
701 739 5.316987 CCCCACTTGTTAGAATCTTTGACT 58.683 41.667 0.00 0.00 0.00 3.41
942 983 3.430790 GCATCCACATCAGCACTACACTA 60.431 47.826 0.00 0.00 0.00 2.74
979 1020 0.321298 AAGCCACATCACCCACGTAC 60.321 55.000 0.00 0.00 0.00 3.67
999 1040 2.746803 GCCGACGCCCACATGTAAC 61.747 63.158 0.00 0.00 0.00 2.50
1033 1074 2.677836 CTCTCACTCTTCTCTCTGGTCG 59.322 54.545 0.00 0.00 0.00 4.79
1086 1127 0.612732 ATCCCTTGACCACGTCCGTA 60.613 55.000 0.00 0.00 0.00 4.02
1087 1128 1.477685 AATCCCTTGACCACGTCCGT 61.478 55.000 0.00 0.00 0.00 4.69
1088 1129 0.321298 AAATCCCTTGACCACGTCCG 60.321 55.000 0.00 0.00 0.00 4.79
1089 1130 1.165270 CAAATCCCTTGACCACGTCC 58.835 55.000 0.00 0.00 37.17 4.79
1090 1131 0.521735 GCAAATCCCTTGACCACGTC 59.478 55.000 0.00 0.00 37.17 4.34
1255 1298 1.480954 TCGGAAGGAATGTACAGAGCC 59.519 52.381 0.33 2.46 0.00 4.70
1317 1360 3.797353 GCCATCCCTCTTCCGGCA 61.797 66.667 0.00 0.00 42.50 5.69
1366 1409 0.935942 TGGCTGATGATCCCCCATTT 59.064 50.000 0.00 0.00 0.00 2.32
1416 1459 0.523519 GCCACTGGCTAGCAAAAGTC 59.476 55.000 18.24 0.00 46.69 3.01
1500 1543 0.839946 GCCCTTCTCCATAGCCAGAA 59.160 55.000 0.00 0.00 0.00 3.02
1551 1594 5.737635 GCCACATACTCCTCTATGACAGTTC 60.738 48.000 0.00 0.00 0.00 3.01
1615 1658 7.772292 TGAAAGTTCTGGAGATAGGATTTGATG 59.228 37.037 0.00 0.00 0.00 3.07
1692 1735 2.125753 GGCTCTCTCTGGCACACG 60.126 66.667 0.00 0.00 0.00 4.49
1838 1899 2.812011 GCTCATAAACGGACAAAGGTGT 59.188 45.455 0.00 0.00 42.10 4.16
1839 1900 2.159707 CGCTCATAAACGGACAAAGGTG 60.160 50.000 0.00 0.00 0.00 4.00
1840 1901 2.073816 CGCTCATAAACGGACAAAGGT 58.926 47.619 0.00 0.00 0.00 3.50
1841 1902 2.343101 TCGCTCATAAACGGACAAAGG 58.657 47.619 0.00 0.00 0.00 3.11
1842 1903 2.222819 GCTCGCTCATAAACGGACAAAG 60.223 50.000 0.00 0.00 0.00 2.77
1843 1904 1.730064 GCTCGCTCATAAACGGACAAA 59.270 47.619 0.00 0.00 0.00 2.83
1844 1905 1.337354 TGCTCGCTCATAAACGGACAA 60.337 47.619 0.00 0.00 0.00 3.18
1845 1906 0.245266 TGCTCGCTCATAAACGGACA 59.755 50.000 0.00 0.00 0.00 4.02
1846 1907 1.258982 CATGCTCGCTCATAAACGGAC 59.741 52.381 0.00 0.00 0.00 4.79
1847 1908 1.134818 ACATGCTCGCTCATAAACGGA 60.135 47.619 0.00 0.00 0.00 4.69
1848 1909 1.290203 ACATGCTCGCTCATAAACGG 58.710 50.000 0.00 0.00 0.00 4.44
1849 1910 3.093574 CAAACATGCTCGCTCATAAACG 58.906 45.455 0.00 0.00 0.00 3.60
1850 1911 3.429085 CCAAACATGCTCGCTCATAAAC 58.571 45.455 0.00 0.00 0.00 2.01
1851 1912 2.423185 CCCAAACATGCTCGCTCATAAA 59.577 45.455 0.00 0.00 0.00 1.40
1852 1913 2.016318 CCCAAACATGCTCGCTCATAA 58.984 47.619 0.00 0.00 0.00 1.90
1853 1914 1.065491 ACCCAAACATGCTCGCTCATA 60.065 47.619 0.00 0.00 0.00 2.15
1854 1915 0.322816 ACCCAAACATGCTCGCTCAT 60.323 50.000 0.00 0.00 0.00 2.90
1855 1916 0.537143 AACCCAAACATGCTCGCTCA 60.537 50.000 0.00 0.00 0.00 4.26
1856 1917 0.169009 GAACCCAAACATGCTCGCTC 59.831 55.000 0.00 0.00 0.00 5.03
1857 1918 1.244019 GGAACCCAAACATGCTCGCT 61.244 55.000 0.00 0.00 0.00 4.93
1858 1919 1.212751 GGAACCCAAACATGCTCGC 59.787 57.895 0.00 0.00 0.00 5.03
1859 1920 1.501741 CGGAACCCAAACATGCTCG 59.498 57.895 0.00 0.00 0.00 5.03
1860 1921 1.883021 CCGGAACCCAAACATGCTC 59.117 57.895 0.00 0.00 0.00 4.26
1861 1922 2.275380 GCCGGAACCCAAACATGCT 61.275 57.895 5.05 0.00 0.00 3.79
1862 1923 2.261361 GCCGGAACCCAAACATGC 59.739 61.111 5.05 0.00 0.00 4.06
1863 1924 1.586028 CTGCCGGAACCCAAACATG 59.414 57.895 5.05 0.00 0.00 3.21
1864 1925 2.275380 GCTGCCGGAACCCAAACAT 61.275 57.895 5.05 0.00 0.00 2.71
1865 1926 2.909965 GCTGCCGGAACCCAAACA 60.910 61.111 5.05 0.00 0.00 2.83
1866 1927 2.909965 TGCTGCCGGAACCCAAAC 60.910 61.111 5.05 0.00 0.00 2.93
1867 1928 2.909965 GTGCTGCCGGAACCCAAA 60.910 61.111 5.05 0.00 0.00 3.28
1868 1929 4.966787 GGTGCTGCCGGAACCCAA 62.967 66.667 5.05 0.00 37.69 4.12
1883 1944 2.968206 GAGCCTTACACGACCGGT 59.032 61.111 6.92 6.92 0.00 5.28
1884 1945 2.202570 CGAGCCTTACACGACCGG 60.203 66.667 0.00 0.00 33.84 5.28
1885 1946 0.168788 TAACGAGCCTTACACGACCG 59.831 55.000 0.00 0.00 36.14 4.79
1886 1947 1.988467 GTTAACGAGCCTTACACGACC 59.012 52.381 0.00 0.00 36.14 4.79
1887 1948 1.645751 CGTTAACGAGCCTTACACGAC 59.354 52.381 23.35 0.00 43.02 4.34
1888 1949 1.401409 CCGTTAACGAGCCTTACACGA 60.401 52.381 28.79 0.00 43.02 4.35
1889 1950 0.986992 CCGTTAACGAGCCTTACACG 59.013 55.000 28.79 4.44 43.02 4.49
1890 1951 0.717784 GCCGTTAACGAGCCTTACAC 59.282 55.000 28.79 3.39 43.02 2.90
1891 1952 0.390209 GGCCGTTAACGAGCCTTACA 60.390 55.000 34.16 0.00 45.60 2.41
1892 1953 2.377004 GGCCGTTAACGAGCCTTAC 58.623 57.895 34.16 19.11 45.60 2.34
1893 1954 4.917474 GGCCGTTAACGAGCCTTA 57.083 55.556 34.16 0.00 45.60 2.69
1897 1958 4.143363 GCGTGGCCGTTAACGAGC 62.143 66.667 28.79 26.17 42.32 5.03
1898 1959 3.484547 GGCGTGGCCGTTAACGAG 61.485 66.667 28.79 18.81 42.32 4.18
1916 1977 4.166011 GTCAATGCGGCGCCAGAC 62.166 66.667 30.82 27.19 0.00 3.51
1921 1982 3.420222 CTACACGTCAATGCGGCGC 62.420 63.158 27.44 27.44 35.98 6.53
1922 1983 2.695055 CTACACGTCAATGCGGCG 59.305 61.111 0.51 0.51 35.98 6.46
1923 1984 2.399611 GCTACACGTCAATGCGGC 59.600 61.111 0.00 0.00 35.98 6.53
1924 1985 0.179121 TAGGCTACACGTCAATGCGG 60.179 55.000 0.00 0.00 35.98 5.69
1925 1986 1.635844 TTAGGCTACACGTCAATGCG 58.364 50.000 0.00 0.00 37.94 4.73
1926 1987 3.242739 CCAATTAGGCTACACGTCAATGC 60.243 47.826 0.00 0.00 0.00 3.56
1927 1988 4.536364 CCAATTAGGCTACACGTCAATG 57.464 45.455 0.00 0.00 0.00 2.82
1940 2001 3.707640 TTCCGGGCCGCCAATTAGG 62.708 63.158 23.20 4.00 41.84 2.69
1941 2002 2.124487 TTCCGGGCCGCCAATTAG 60.124 61.111 23.20 4.87 0.00 1.73
1942 2003 2.438795 GTTCCGGGCCGCCAATTA 60.439 61.111 23.20 0.00 0.00 1.40
1949 2010 2.544698 TTTTTGACGTTCCGGGCCG 61.545 57.895 21.46 21.46 0.00 6.13
1950 2011 1.008194 GTTTTTGACGTTCCGGGCC 60.008 57.895 0.00 0.00 0.00 5.80
1951 2012 1.008194 GGTTTTTGACGTTCCGGGC 60.008 57.895 0.00 0.00 0.00 6.13
1952 2013 0.309612 CTGGTTTTTGACGTTCCGGG 59.690 55.000 0.00 0.00 0.00 5.73
1953 2014 0.317519 GCTGGTTTTTGACGTTCCGG 60.318 55.000 0.00 0.00 0.00 5.14
1954 2015 0.661020 AGCTGGTTTTTGACGTTCCG 59.339 50.000 0.00 0.00 0.00 4.30
1955 2016 2.098443 TCAAGCTGGTTTTTGACGTTCC 59.902 45.455 0.00 0.00 0.00 3.62
1956 2017 3.414549 TCAAGCTGGTTTTTGACGTTC 57.585 42.857 0.00 0.00 0.00 3.95
1957 2018 3.859411 TTCAAGCTGGTTTTTGACGTT 57.141 38.095 0.00 0.00 33.36 3.99
1958 2019 4.111916 CAATTCAAGCTGGTTTTTGACGT 58.888 39.130 0.00 0.00 33.36 4.34
1959 2020 4.111916 ACAATTCAAGCTGGTTTTTGACG 58.888 39.130 11.38 0.00 33.36 4.35
1960 2021 6.292328 GCTAACAATTCAAGCTGGTTTTTGAC 60.292 38.462 11.38 0.00 33.36 3.18
1961 2022 5.752955 GCTAACAATTCAAGCTGGTTTTTGA 59.247 36.000 11.38 0.00 33.40 2.69
1962 2023 5.523188 TGCTAACAATTCAAGCTGGTTTTTG 59.477 36.000 0.00 0.00 37.16 2.44
1963 2024 5.669477 TGCTAACAATTCAAGCTGGTTTTT 58.331 33.333 0.00 0.00 37.16 1.94
1964 2025 5.275067 TGCTAACAATTCAAGCTGGTTTT 57.725 34.783 0.00 0.00 37.16 2.43
1965 2026 4.935352 TGCTAACAATTCAAGCTGGTTT 57.065 36.364 0.00 0.00 37.16 3.27
1966 2027 4.099266 TGTTGCTAACAATTCAAGCTGGTT 59.901 37.500 0.00 0.00 38.72 3.67
1967 2028 3.636300 TGTTGCTAACAATTCAAGCTGGT 59.364 39.130 0.00 0.00 38.72 4.00
1968 2029 4.232221 CTGTTGCTAACAATTCAAGCTGG 58.768 43.478 0.00 0.00 41.61 4.85
1969 2030 4.863491 ACTGTTGCTAACAATTCAAGCTG 58.137 39.130 0.00 0.00 41.61 4.24
1970 2031 4.319766 CGACTGTTGCTAACAATTCAAGCT 60.320 41.667 5.17 0.00 41.61 3.74
1971 2032 3.908382 CGACTGTTGCTAACAATTCAAGC 59.092 43.478 3.84 0.00 41.61 4.01
1972 2033 5.095691 ACGACTGTTGCTAACAATTCAAG 57.904 39.130 0.00 0.00 41.61 3.02
1973 2034 5.493133 AACGACTGTTGCTAACAATTCAA 57.507 34.783 0.00 0.00 41.61 2.69
1974 2035 5.493133 AAACGACTGTTGCTAACAATTCA 57.507 34.783 0.00 0.00 41.61 2.57
1975 2036 6.806120 AAAAACGACTGTTGCTAACAATTC 57.194 33.333 0.00 3.18 41.61 2.17
2004 2065 8.841300 GCAAAAGGATAATTAACCCAAAACAAA 58.159 29.630 8.09 0.00 0.00 2.83
2005 2066 7.445707 GGCAAAAGGATAATTAACCCAAAACAA 59.554 33.333 8.09 0.00 0.00 2.83
2006 2067 6.937465 GGCAAAAGGATAATTAACCCAAAACA 59.063 34.615 8.09 0.00 0.00 2.83
2007 2068 6.373216 GGGCAAAAGGATAATTAACCCAAAAC 59.627 38.462 8.09 0.00 34.82 2.43
2008 2069 6.273495 AGGGCAAAAGGATAATTAACCCAAAA 59.727 34.615 8.09 0.00 37.28 2.44
2047 2108 2.811410 TCTGAGGGCAAAATTGAGCAT 58.189 42.857 0.00 0.00 0.00 3.79
2054 2115 1.838112 TTCGCATCTGAGGGCAAAAT 58.162 45.000 5.18 0.00 0.00 1.82
2088 2149 1.626356 GCTGTGCATGGACTAGGGGA 61.626 60.000 18.75 0.00 0.00 4.81
2130 2191 3.181479 CGGACGGAATGGACTGAAATCTA 60.181 47.826 0.00 0.00 0.00 1.98
2160 2221 2.281484 CCGGACCCACAACCACTG 60.281 66.667 0.00 0.00 0.00 3.66
2263 2324 1.812093 CGTCGATTTGGCCGGCTAA 60.812 57.895 28.56 25.60 0.00 3.09
2583 2645 2.571653 CTCACCAAATACTCTGGGGTCA 59.428 50.000 0.00 0.00 38.60 4.02
2755 2817 1.066430 GCAACTCCATCCTAACCGACA 60.066 52.381 0.00 0.00 0.00 4.35
2794 2858 1.483415 TGTACCGGTCCCTTCTAATGC 59.517 52.381 12.40 0.00 0.00 3.56


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

AutoCloner maintained by Alex Coulton.