Multiple sequence alignment - TraesCS2A01G518900

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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 TraesCS2A01G518900 chr2A 100.000 2633 0 0 1 2633 742294603 742291971 0.000000e+00 4863.0
1 TraesCS2A01G518900 chr2D 87.606 2243 149 62 33 2221 609516763 609514596 0.000000e+00 2483.0
2 TraesCS2A01G518900 chr2D 86.988 415 31 9 2220 2633 609514562 609514170 1.860000e-121 446.0
3 TraesCS2A01G518900 chr2B 91.762 1141 40 13 737 1855 744058705 744057597 0.000000e+00 1537.0
4 TraesCS2A01G518900 chr2B 85.629 668 75 12 1980 2633 743922644 743921984 0.000000e+00 682.0
5 TraesCS2A01G518900 chr2B 88.435 294 27 5 2219 2508 744057329 744057039 5.390000e-92 348.0
6 TraesCS2A01G518900 chr2B 84.085 377 34 10 2167 2520 743926126 743925753 9.030000e-90 340.0
7 TraesCS2A01G518900 chr2B 88.750 240 18 5 169 407 744059038 744058807 4.290000e-73 285.0
8 TraesCS2A01G518900 chr2B 88.344 163 15 2 1 159 744059239 744059077 2.670000e-45 193.0
9 TraesCS2A01G518900 chr2B 85.034 147 10 7 1721 1855 743926304 743926158 3.530000e-29 139.0
10 TraesCS2A01G518900 chr2B 84.615 91 14 0 613 703 744058791 744058701 1.000000e-14 91.6
11 TraesCS2A01G518900 chr7D 82.873 181 27 4 1022 1200 611135689 611135867 2.710000e-35 159.0
12 TraesCS2A01G518900 chr7D 80.645 186 28 8 1022 1203 91143766 91143585 1.270000e-28 137.0
13 TraesCS2A01G518900 chr7B 82.320 181 28 4 1022 1200 700184178 700184356 1.260000e-33 154.0
14 TraesCS2A01G518900 chr7B 85.385 130 17 2 1075 1203 43754557 43754429 1.640000e-27 134.0
15 TraesCS2A01G518900 chr7A 81.768 181 29 4 1022 1200 701149419 701149597 5.870000e-32 148.0
16 TraesCS2A01G518900 chr7A 81.421 183 26 8 1022 1200 93081906 93082084 2.730000e-30 143.0


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 TraesCS2A01G518900 chr2A 742291971 742294603 2632 True 4863.00 4863 100.0000 1 2633 1 chr2A.!!$R1 2632
1 TraesCS2A01G518900 chr2D 609514170 609516763 2593 True 1464.50 2483 87.2970 33 2633 2 chr2D.!!$R1 2600
2 TraesCS2A01G518900 chr2B 744057039 744059239 2200 True 490.92 1537 88.3812 1 2508 5 chr2B.!!$R2 2507
3 TraesCS2A01G518900 chr2B 743921984 743926304 4320 True 387.00 682 84.9160 1721 2633 3 chr2B.!!$R1 912

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
290 326 0.036164 CCGAGGGAATGTTGGTCACA 59.964 55.0 0.0 0.0 40.71 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1861 1923 0.323957 ACATCTGCTTCTGCTCTGCA 59.676 50.0 0.0 0.0 40.48 4.41 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
98 103 2.210144 TAGCTGAAAATGCCCGCCCT 62.210 55.000 0.00 0.00 0.00 5.19
99 104 2.649129 GCTGAAAATGCCCGCCCTT 61.649 57.895 0.00 0.00 0.00 3.95
118 123 2.450609 TTCGAGCACACTAAACCCTC 57.549 50.000 0.00 0.00 0.00 4.30
123 128 0.391263 GCACACTAAACCCTCCTCCG 60.391 60.000 0.00 0.00 0.00 4.63
140 145 3.365969 CCTCCGGTTGTCTTAAAATGCAC 60.366 47.826 0.00 0.00 0.00 4.57
143 148 3.223157 CGGTTGTCTTAAAATGCACGAC 58.777 45.455 0.00 0.00 0.00 4.34
199 234 2.875296 TCCAACCCTTCAGGATTGTTG 58.125 47.619 0.00 3.41 39.89 3.33
206 241 4.043310 ACCCTTCAGGATTGTTGATCTCAA 59.957 41.667 0.00 0.28 39.89 3.02
272 308 3.820557 TGCAATCTGTATTTAGCCTCCC 58.179 45.455 0.00 0.00 0.00 4.30
285 321 1.224592 CCTCCCGAGGGAATGTTGG 59.775 63.158 12.54 5.70 44.66 3.77
287 323 0.107654 CTCCCGAGGGAATGTTGGTC 60.108 60.000 12.54 0.00 44.66 4.02
290 326 0.036164 CCGAGGGAATGTTGGTCACA 59.964 55.000 0.00 0.00 40.71 3.58
298 334 3.503749 GTTGGTCACAACGCCACA 58.496 55.556 0.00 0.00 46.50 4.17
299 335 1.063488 GTTGGTCACAACGCCACAC 59.937 57.895 0.00 0.00 46.50 3.82
342 378 4.527509 ATTGCTCGAGAGTCTCTTCAAA 57.472 40.909 18.75 7.89 0.00 2.69
367 403 1.087501 CGGTGAGCTAAAGAAAGGCC 58.912 55.000 0.00 0.00 0.00 5.19
404 440 5.305585 TGAACCACATTAGTTCCTCTTCAC 58.694 41.667 1.53 0.00 42.41 3.18
407 443 4.593206 ACCACATTAGTTCCTCTTCACTGA 59.407 41.667 0.00 0.00 0.00 3.41
408 444 5.071788 ACCACATTAGTTCCTCTTCACTGAA 59.928 40.000 0.00 0.00 0.00 3.02
409 445 6.176183 CCACATTAGTTCCTCTTCACTGAAT 58.824 40.000 0.00 0.00 0.00 2.57
420 456 8.267620 TCCTCTTCACTGAATATAATGGACAT 57.732 34.615 0.00 0.00 0.00 3.06
421 457 8.152898 TCCTCTTCACTGAATATAATGGACATG 58.847 37.037 0.00 0.00 0.00 3.21
422 458 7.935755 CCTCTTCACTGAATATAATGGACATGT 59.064 37.037 0.00 0.00 0.00 3.21
423 459 8.667076 TCTTCACTGAATATAATGGACATGTG 57.333 34.615 1.15 0.00 0.00 3.21
424 460 8.485392 TCTTCACTGAATATAATGGACATGTGA 58.515 33.333 1.15 0.00 0.00 3.58
426 462 9.631257 TTCACTGAATATAATGGACATGTGAAT 57.369 29.630 1.15 0.00 36.30 2.57
480 516 5.472137 AGTGTAAAAATAATGCACCGAGTGT 59.528 36.000 0.00 0.00 34.41 3.55
506 542 1.915983 GGTGATGGTTCCTCCCTCC 59.084 63.158 0.00 0.00 34.77 4.30
516 552 0.685097 TCCTCCCTCCGTGTTTGAAG 59.315 55.000 0.00 0.00 0.00 3.02
530 566 0.108520 TTGAAGTGGCCGACGGATAC 60.109 55.000 20.50 15.18 0.00 2.24
547 583 4.276678 CGGATACCGTAGTCAAATACTCCA 59.723 45.833 1.80 0.00 42.73 3.86
551 587 4.028131 ACCGTAGTCAAATACTCCATCCA 58.972 43.478 0.00 0.00 39.80 3.41
554 590 5.011125 CCGTAGTCAAATACTCCATCCATCT 59.989 44.000 0.00 0.00 39.80 2.90
555 591 6.208797 CCGTAGTCAAATACTCCATCCATCTA 59.791 42.308 0.00 0.00 39.80 1.98
567 603 7.731054 ACTCCATCCATCTAGAAATAGTTGTC 58.269 38.462 0.00 0.00 0.00 3.18
571 607 6.392625 TCCATCTAGAAATAGTTGTCGGAG 57.607 41.667 0.00 0.00 0.00 4.63
574 610 7.123697 TCCATCTAGAAATAGTTGTCGGAGAAA 59.876 37.037 0.00 0.00 39.69 2.52
575 611 7.928706 CCATCTAGAAATAGTTGTCGGAGAAAT 59.071 37.037 0.00 0.00 39.69 2.17
577 613 7.265673 TCTAGAAATAGTTGTCGGAGAAATGG 58.734 38.462 0.00 0.00 39.69 3.16
578 614 5.186198 AGAAATAGTTGTCGGAGAAATGGG 58.814 41.667 0.00 0.00 39.69 4.00
579 615 4.569719 AATAGTTGTCGGAGAAATGGGT 57.430 40.909 0.00 0.00 39.69 4.51
580 616 2.474410 AGTTGTCGGAGAAATGGGTC 57.526 50.000 0.00 0.00 39.69 4.46
581 617 1.978580 AGTTGTCGGAGAAATGGGTCT 59.021 47.619 0.00 0.00 39.69 3.85
582 618 3.170717 AGTTGTCGGAGAAATGGGTCTA 58.829 45.455 0.00 0.00 39.69 2.59
583 619 3.775316 AGTTGTCGGAGAAATGGGTCTAT 59.225 43.478 0.00 0.00 39.69 1.98
584 620 4.120589 GTTGTCGGAGAAATGGGTCTATC 58.879 47.826 0.00 0.00 39.69 2.08
585 621 3.643237 TGTCGGAGAAATGGGTCTATCT 58.357 45.455 0.00 0.00 39.69 1.98
586 622 4.800023 TGTCGGAGAAATGGGTCTATCTA 58.200 43.478 0.00 0.00 39.69 1.98
589 625 7.008332 TGTCGGAGAAATGGGTCTATCTAATA 58.992 38.462 0.00 0.00 39.69 0.98
590 626 7.039923 TGTCGGAGAAATGGGTCTATCTAATAC 60.040 40.741 0.00 0.00 39.69 1.89
591 627 6.150641 TCGGAGAAATGGGTCTATCTAATACG 59.849 42.308 0.00 0.00 0.00 3.06
592 628 6.072064 CGGAGAAATGGGTCTATCTAATACGT 60.072 42.308 0.00 0.00 0.00 3.57
593 629 7.120285 CGGAGAAATGGGTCTATCTAATACGTA 59.880 40.741 0.00 0.00 0.00 3.57
599 635 9.635520 AATGGGTCTATCTAATACGTATTTTCG 57.364 33.333 24.81 14.01 0.00 3.46
616 653 8.953990 CGTATTTTCGAACATCCATTTTTATCC 58.046 33.333 0.00 0.00 0.00 2.59
623 660 8.405531 TCGAACATCCATTTTTATCCATTTCTC 58.594 33.333 0.00 0.00 0.00 2.87
624 661 8.190122 CGAACATCCATTTTTATCCATTTCTCA 58.810 33.333 0.00 0.00 0.00 3.27
629 666 9.657419 ATCCATTTTTATCCATTTCTCAACAAC 57.343 29.630 0.00 0.00 0.00 3.32
641 678 5.585500 TTCTCAACAACTATTTTCGGACG 57.415 39.130 0.00 0.00 0.00 4.79
646 683 1.664151 CAACTATTTTCGGACGGAGCC 59.336 52.381 0.00 0.00 0.00 4.70
647 684 1.192428 ACTATTTTCGGACGGAGCCT 58.808 50.000 0.00 0.00 0.00 4.58
661 698 2.354103 CGGAGCCTGTATATGGATGTGG 60.354 54.545 0.00 0.00 0.00 4.17
709 746 8.573035 ACTGCGATTGAATTTTACTCCTTTTAA 58.427 29.630 0.00 0.00 0.00 1.52
729 766 9.710900 CTTTTAAGGCCATAGAAAAGATTGTTT 57.289 29.630 19.02 0.00 39.97 2.83
732 769 6.775594 AGGCCATAGAAAAGATTGTTTACC 57.224 37.500 5.01 0.00 0.00 2.85
733 770 5.656859 AGGCCATAGAAAAGATTGTTTACCC 59.343 40.000 5.01 0.00 0.00 3.69
734 771 5.420739 GGCCATAGAAAAGATTGTTTACCCA 59.579 40.000 0.00 0.00 0.00 4.51
735 772 6.071051 GGCCATAGAAAAGATTGTTTACCCAA 60.071 38.462 0.00 0.00 0.00 4.12
757 794 6.096705 CCAATACCCATAATTTGAAGCTGTGA 59.903 38.462 0.00 0.00 0.00 3.58
776 813 6.621596 GCTGTGATTGCTTTAACAGTCCTTAG 60.622 42.308 10.44 0.00 41.65 2.18
976 1013 2.176055 CTCACGACCGAGTCACCG 59.824 66.667 0.00 0.00 32.09 4.94
984 1021 2.027625 CCGAGTCACCGACAAAGCC 61.028 63.158 0.00 0.00 34.60 4.35
992 1029 2.325082 CCGACAAAGCCAAGACCGG 61.325 63.158 0.00 0.00 0.00 5.28
1003 1040 3.376935 AAGACCGGCTGCTCGATGG 62.377 63.158 0.00 3.62 0.00 3.51
1660 1703 1.134694 GGAACGACCAAGCGATTGC 59.865 57.895 8.15 0.00 39.07 3.56
1772 1822 4.819761 TGCGGCGGCAGATCTGTC 62.820 66.667 23.38 20.66 46.21 3.51
1792 1842 4.163268 TGTCTAAGCATGCCCTGTAATGTA 59.837 41.667 15.66 0.00 0.00 2.29
1809 1859 0.108138 GTAAGCATGGCGACCTCTGT 60.108 55.000 0.00 0.00 0.00 3.41
1810 1860 0.108186 TAAGCATGGCGACCTCTGTG 60.108 55.000 0.00 0.00 0.00 3.66
1812 1862 2.267006 CATGGCGACCTCTGTGCT 59.733 61.111 0.00 0.00 0.00 4.40
1814 1864 1.986757 ATGGCGACCTCTGTGCTCT 60.987 57.895 0.00 0.00 0.00 4.09
1815 1865 2.125753 GGCGACCTCTGTGCTCTG 60.126 66.667 0.00 0.00 0.00 3.35
1816 1866 2.653702 GCGACCTCTGTGCTCTGT 59.346 61.111 0.00 0.00 0.00 3.41
1819 1869 0.665670 CGACCTCTGTGCTCTGTGTG 60.666 60.000 0.00 0.00 0.00 3.82
1820 1870 0.676184 GACCTCTGTGCTCTGTGTGA 59.324 55.000 0.00 0.00 0.00 3.58
1821 1871 1.274728 GACCTCTGTGCTCTGTGTGAT 59.725 52.381 0.00 0.00 0.00 3.06
1834 1896 4.910195 TCTGTGTGATTCTTATGGCAACT 58.090 39.130 0.00 0.00 37.61 3.16
1838 1900 5.181748 GTGTGATTCTTATGGCAACTCTCT 58.818 41.667 0.00 0.00 37.61 3.10
1855 1917 1.344763 CTCTGTTCTTCCTTCCGTGGT 59.655 52.381 0.00 0.00 0.00 4.16
1856 1918 2.561419 CTCTGTTCTTCCTTCCGTGGTA 59.439 50.000 0.00 0.00 0.00 3.25
1857 1919 2.561419 TCTGTTCTTCCTTCCGTGGTAG 59.439 50.000 0.00 0.00 0.00 3.18
1858 1920 2.299297 CTGTTCTTCCTTCCGTGGTAGT 59.701 50.000 0.00 0.00 0.00 2.73
1859 1921 3.499338 TGTTCTTCCTTCCGTGGTAGTA 58.501 45.455 0.00 0.00 0.00 1.82
1860 1922 4.091549 TGTTCTTCCTTCCGTGGTAGTAT 58.908 43.478 0.00 0.00 0.00 2.12
1861 1923 4.529377 TGTTCTTCCTTCCGTGGTAGTATT 59.471 41.667 0.00 0.00 0.00 1.89
1862 1924 4.730949 TCTTCCTTCCGTGGTAGTATTG 57.269 45.455 0.00 0.00 0.00 1.90
1863 1925 2.973694 TCCTTCCGTGGTAGTATTGC 57.026 50.000 0.00 0.00 0.00 3.56
1864 1926 2.181125 TCCTTCCGTGGTAGTATTGCA 58.819 47.619 0.00 0.00 0.00 4.08
1865 1927 2.167693 TCCTTCCGTGGTAGTATTGCAG 59.832 50.000 0.00 0.00 0.00 4.41
1866 1928 2.167693 CCTTCCGTGGTAGTATTGCAGA 59.832 50.000 0.00 0.00 0.00 4.26
1867 1929 3.448686 CTTCCGTGGTAGTATTGCAGAG 58.551 50.000 0.00 0.00 0.00 3.35
1868 1930 1.136305 TCCGTGGTAGTATTGCAGAGC 59.864 52.381 0.00 0.00 0.00 4.09
1869 1931 1.134818 CCGTGGTAGTATTGCAGAGCA 60.135 52.381 0.00 0.00 36.47 4.26
1870 1932 2.196749 CGTGGTAGTATTGCAGAGCAG 58.803 52.381 0.00 0.00 40.61 4.24
1871 1933 2.159240 CGTGGTAGTATTGCAGAGCAGA 60.159 50.000 0.00 0.00 40.61 4.26
1872 1934 3.676049 CGTGGTAGTATTGCAGAGCAGAA 60.676 47.826 0.00 0.00 40.61 3.02
1873 1935 3.868077 GTGGTAGTATTGCAGAGCAGAAG 59.132 47.826 0.00 0.00 40.61 2.85
1874 1936 2.869192 GGTAGTATTGCAGAGCAGAAGC 59.131 50.000 0.00 0.00 40.61 3.86
1875 1937 2.775911 AGTATTGCAGAGCAGAAGCA 57.224 45.000 0.00 0.00 45.49 3.91
1876 1938 2.630158 AGTATTGCAGAGCAGAAGCAG 58.370 47.619 0.00 0.00 45.49 4.24
1877 1939 2.235650 AGTATTGCAGAGCAGAAGCAGA 59.764 45.455 0.00 0.00 45.49 4.26
1878 1940 2.421751 ATTGCAGAGCAGAAGCAGAT 57.578 45.000 0.00 0.00 45.49 2.90
1879 1941 1.450025 TTGCAGAGCAGAAGCAGATG 58.550 50.000 0.00 0.00 45.49 2.90
1880 1942 0.323957 TGCAGAGCAGAAGCAGATGT 59.676 50.000 0.00 0.00 45.49 3.06
1881 1943 1.271217 TGCAGAGCAGAAGCAGATGTT 60.271 47.619 0.00 0.00 45.49 2.71
1882 1944 1.397692 GCAGAGCAGAAGCAGATGTTC 59.602 52.381 0.00 0.00 45.49 3.18
1883 1945 2.936114 GCAGAGCAGAAGCAGATGTTCT 60.936 50.000 0.00 0.00 45.49 3.01
1884 1946 3.336468 CAGAGCAGAAGCAGATGTTCTT 58.664 45.455 0.00 0.00 45.49 2.52
1885 1947 3.752222 CAGAGCAGAAGCAGATGTTCTTT 59.248 43.478 0.00 0.00 45.49 2.52
1886 1948 4.215827 CAGAGCAGAAGCAGATGTTCTTTT 59.784 41.667 0.00 0.00 45.49 2.27
1887 1949 4.826183 AGAGCAGAAGCAGATGTTCTTTTT 59.174 37.500 0.00 0.00 45.49 1.94
1895 1957 7.437267 AGAAGCAGATGTTCTTTTTGACATTTG 59.563 33.333 0.00 0.00 29.57 2.32
1898 1960 7.223387 AGCAGATGTTCTTTTTGACATTTGTTC 59.777 33.333 8.24 0.00 30.45 3.18
1921 5423 3.854784 GCACTCTGTTTCAAACCTGATGC 60.855 47.826 0.00 0.00 0.00 3.91
1923 5425 3.567164 ACTCTGTTTCAAACCTGATGCTG 59.433 43.478 0.00 0.00 0.00 4.41
1924 5426 2.294233 TCTGTTTCAAACCTGATGCTGC 59.706 45.455 0.00 0.00 0.00 5.25
1930 5432 3.719924 TCAAACCTGATGCTGCTTTTTG 58.280 40.909 0.00 2.97 0.00 2.44
1940 5442 4.185467 TGCTGCTTTTTGACTGTTTCAA 57.815 36.364 0.00 0.00 42.83 2.69
1956 5458 6.147821 ACTGTTTCAATCGTCATTCTTGGTAG 59.852 38.462 0.00 0.00 0.00 3.18
1958 5460 7.156000 TGTTTCAATCGTCATTCTTGGTAGTA 58.844 34.615 0.00 0.00 0.00 1.82
1959 5461 7.822334 TGTTTCAATCGTCATTCTTGGTAGTAT 59.178 33.333 0.00 0.00 0.00 2.12
1960 5462 8.665685 GTTTCAATCGTCATTCTTGGTAGTATT 58.334 33.333 0.00 0.00 0.00 1.89
1961 5463 8.420374 TTCAATCGTCATTCTTGGTAGTATTC 57.580 34.615 0.00 0.00 0.00 1.75
1962 5464 6.984474 TCAATCGTCATTCTTGGTAGTATTCC 59.016 38.462 0.00 0.00 0.00 3.01
1963 5465 5.925506 TCGTCATTCTTGGTAGTATTCCA 57.074 39.130 0.00 0.00 0.00 3.53
1964 5466 6.288941 TCGTCATTCTTGGTAGTATTCCAA 57.711 37.500 0.00 0.00 41.84 3.53
1991 5495 4.560513 GCAGAGCAGAAGTAGTGTTCTCTT 60.561 45.833 0.00 0.00 33.63 2.85
1993 5497 5.988561 CAGAGCAGAAGTAGTGTTCTCTTTT 59.011 40.000 0.00 0.00 33.63 2.27
2015 5519 5.403897 TCGAAATCGTGGAATCATAAAGC 57.596 39.130 2.41 0.00 40.80 3.51
2038 5542 3.194062 GGAAGTAGCTGATTGACTCTGC 58.806 50.000 0.00 0.00 46.18 4.26
2076 5583 1.567504 CCGTAATTGGCTCGATCGTT 58.432 50.000 15.94 3.22 0.00 3.85
2098 5605 1.269309 GGTTGGATCGATCAGGACGAG 60.269 57.143 25.93 0.00 42.81 4.18
2122 5629 4.497674 CGTTCTACCTTTCCTGATCGGTAG 60.498 50.000 13.28 13.28 46.55 3.18
2143 5650 2.291465 GACATTGACAAAGAGCAGCACA 59.709 45.455 0.00 0.00 0.00 4.57
2149 5656 4.136796 TGACAAAGAGCAGCACAGTAAAT 58.863 39.130 0.00 0.00 0.00 1.40
2241 5785 3.091545 GAGATTTTCAACTCCATGGCCA 58.908 45.455 8.56 8.56 0.00 5.36
2281 5825 0.398318 AGTTGAGGGTTCTGCCTGAC 59.602 55.000 0.00 0.00 37.43 3.51
2292 5836 0.884514 CTGCCTGACAGTCGAGAGAA 59.115 55.000 0.93 0.00 45.01 2.87
2310 5855 4.219725 AGAGAAGAGCACTCTGAACCTAAC 59.780 45.833 0.00 0.00 42.20 2.34
2335 5882 4.131596 GGTAACTTGCTCAGTAAACCACA 58.868 43.478 12.47 0.00 39.78 4.17
2336 5883 4.213482 GGTAACTTGCTCAGTAAACCACAG 59.787 45.833 12.47 0.00 39.78 3.66
2379 5932 1.001378 CTGCGGAGGAAACTTTTGTGG 60.001 52.381 0.00 0.00 44.43 4.17
2386 5939 4.065789 GAGGAAACTTTTGTGGAGACGAT 58.934 43.478 0.00 0.00 44.43 3.73
2482 6036 1.825090 TTGTCCCAGATGACACATGC 58.175 50.000 0.00 0.00 44.55 4.06
2520 6077 5.416947 GTCAAGGGACGTTATGACAGTTAT 58.583 41.667 14.88 0.00 41.35 1.89
2539 6096 3.784511 ATGAACCTCAGCCCATATCAG 57.215 47.619 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 3.564225 ACAAGTAAAAGGCGAAACAGGAG 59.436 43.478 0.00 0.00 0.00 3.69
17 18 7.764695 ACACATTTTTGTACAAGTAAAAGGC 57.235 32.000 8.56 0.00 0.00 4.35
62 63 1.453155 CTAAAATGAGCGCACCACCT 58.547 50.000 11.47 0.00 0.00 4.00
98 103 2.549349 GGAGGGTTTAGTGTGCTCGAAA 60.549 50.000 0.00 0.00 0.00 3.46
99 104 1.001633 GGAGGGTTTAGTGTGCTCGAA 59.998 52.381 0.00 0.00 0.00 3.71
123 128 3.252458 AGGTCGTGCATTTTAAGACAACC 59.748 43.478 0.00 0.00 33.84 3.77
159 165 1.439644 TTTTTGCGGGTGTTGCCTC 59.560 52.632 0.00 0.00 37.43 4.70
199 234 6.450545 TGACTACCATTGATCGATTGAGATC 58.549 40.000 0.00 0.43 45.35 2.75
206 241 5.798125 AGACATGACTACCATTGATCGAT 57.202 39.130 0.00 0.00 31.94 3.59
272 308 1.890876 TTGTGACCAACATTCCCTCG 58.109 50.000 0.00 0.00 38.99 4.63
285 321 3.645975 CCCGTGTGGCGTTGTGAC 61.646 66.667 0.00 0.00 39.32 3.67
323 359 2.230025 CCTTTGAAGAGACTCTCGAGCA 59.770 50.000 7.81 0.00 35.36 4.26
324 360 2.230266 ACCTTTGAAGAGACTCTCGAGC 59.770 50.000 7.81 0.00 35.36 5.03
342 378 1.192146 TCTTTAGCTCACCGGCACCT 61.192 55.000 0.00 0.00 34.17 4.00
480 516 1.142060 AGGAACCATCACCGACAAACA 59.858 47.619 0.00 0.00 0.00 2.83
506 542 1.278637 GTCGGCCACTTCAAACACG 59.721 57.895 2.24 0.00 0.00 4.49
530 566 4.665833 TGGATGGAGTATTTGACTACGG 57.334 45.455 0.00 0.00 42.78 4.02
534 570 7.921041 TTCTAGATGGATGGAGTATTTGACT 57.079 36.000 0.00 0.00 42.90 3.41
547 583 6.778069 TCTCCGACAACTATTTCTAGATGGAT 59.222 38.462 0.00 0.00 33.32 3.41
551 587 7.928706 CCATTTCTCCGACAACTATTTCTAGAT 59.071 37.037 0.00 0.00 0.00 1.98
554 590 6.070424 ACCCATTTCTCCGACAACTATTTCTA 60.070 38.462 0.00 0.00 0.00 2.10
555 591 5.186198 CCCATTTCTCCGACAACTATTTCT 58.814 41.667 0.00 0.00 0.00 2.52
567 603 6.072064 ACGTATTAGATAGACCCATTTCTCCG 60.072 42.308 0.00 0.00 0.00 4.63
574 610 9.017509 TCGAAAATACGTATTAGATAGACCCAT 57.982 33.333 20.62 0.00 34.70 4.00
575 611 8.394971 TCGAAAATACGTATTAGATAGACCCA 57.605 34.615 20.62 0.00 34.70 4.51
577 613 9.669353 TGTTCGAAAATACGTATTAGATAGACC 57.331 33.333 20.62 9.41 34.70 3.85
582 618 9.706691 ATGGATGTTCGAAAATACGTATTAGAT 57.293 29.630 20.62 8.99 34.70 1.98
583 619 9.537192 AATGGATGTTCGAAAATACGTATTAGA 57.463 29.630 20.62 16.46 34.70 2.10
586 622 9.849166 AAAAATGGATGTTCGAAAATACGTATT 57.151 25.926 15.07 15.07 34.70 1.89
589 625 9.498307 GATAAAAATGGATGTTCGAAAATACGT 57.502 29.630 6.06 2.57 34.70 3.57
590 626 8.953990 GGATAAAAATGGATGTTCGAAAATACG 58.046 33.333 6.06 0.00 0.00 3.06
591 627 9.796120 TGGATAAAAATGGATGTTCGAAAATAC 57.204 29.630 3.31 3.31 0.00 1.89
593 629 9.889128 AATGGATAAAAATGGATGTTCGAAAAT 57.111 25.926 0.00 0.00 0.00 1.82
596 632 8.748412 AGAAATGGATAAAAATGGATGTTCGAA 58.252 29.630 0.00 0.00 0.00 3.71
599 635 9.874205 TTGAGAAATGGATAAAAATGGATGTTC 57.126 29.630 0.00 0.00 0.00 3.18
616 653 6.519761 CGTCCGAAAATAGTTGTTGAGAAATG 59.480 38.462 0.00 0.00 0.00 2.32
623 660 3.424433 GCTCCGTCCGAAAATAGTTGTTG 60.424 47.826 0.00 0.00 0.00 3.33
624 661 2.740447 GCTCCGTCCGAAAATAGTTGTT 59.260 45.455 0.00 0.00 0.00 2.83
629 666 1.134788 ACAGGCTCCGTCCGAAAATAG 60.135 52.381 0.00 0.00 0.00 1.73
641 678 2.906389 TCCACATCCATATACAGGCTCC 59.094 50.000 0.00 0.00 0.00 4.70
709 746 5.656859 GGGTAAACAATCTTTTCTATGGCCT 59.343 40.000 3.32 0.00 0.00 5.19
729 766 6.549364 CAGCTTCAAATTATGGGTATTGGGTA 59.451 38.462 0.00 0.00 0.00 3.69
730 767 5.363580 CAGCTTCAAATTATGGGTATTGGGT 59.636 40.000 0.00 0.00 0.00 4.51
731 768 5.363580 ACAGCTTCAAATTATGGGTATTGGG 59.636 40.000 0.00 0.00 0.00 4.12
732 769 6.096705 TCACAGCTTCAAATTATGGGTATTGG 59.903 38.462 0.00 0.00 0.00 3.16
733 770 7.099266 TCACAGCTTCAAATTATGGGTATTG 57.901 36.000 0.00 0.00 0.00 1.90
734 771 7.902920 ATCACAGCTTCAAATTATGGGTATT 57.097 32.000 0.00 0.00 0.00 1.89
735 772 7.685155 GCAATCACAGCTTCAAATTATGGGTAT 60.685 37.037 0.00 0.00 0.00 2.73
757 794 9.953565 TGTAATACTAAGGACTGTTAAAGCAAT 57.046 29.630 0.00 0.00 0.00 3.56
776 813 4.267349 ACCAGTGGTGAGTGTGTAATAC 57.733 45.455 15.86 0.00 32.98 1.89
984 1021 2.169789 CATCGAGCAGCCGGTCTTG 61.170 63.158 1.90 2.29 37.51 3.02
993 1030 4.957684 ATCGCGCCCATCGAGCAG 62.958 66.667 0.00 0.00 41.67 4.24
1243 1280 3.525545 GGCGGAGGAGGACGTACC 61.526 72.222 0.00 0.00 39.35 3.34
1583 1623 2.989173 TTCCCACTGGACCGTCTCGT 62.989 60.000 0.00 0.00 41.57 4.18
1660 1703 3.787785 TGGTACGTACACCATGCATAAG 58.212 45.455 26.02 0.00 43.76 1.73
1772 1822 4.023707 GCTTACATTACAGGGCATGCTTAG 60.024 45.833 18.92 9.80 0.00 2.18
1792 1842 1.376424 CACAGAGGTCGCCATGCTT 60.376 57.895 0.00 0.00 0.00 3.91
1809 1859 3.273434 GCCATAAGAATCACACAGAGCA 58.727 45.455 0.00 0.00 0.00 4.26
1810 1860 3.273434 TGCCATAAGAATCACACAGAGC 58.727 45.455 0.00 0.00 0.00 4.09
1812 1862 4.910195 AGTTGCCATAAGAATCACACAGA 58.090 39.130 0.00 0.00 0.00 3.41
1814 1864 4.910195 AGAGTTGCCATAAGAATCACACA 58.090 39.130 0.00 0.00 0.00 3.72
1815 1865 5.064452 CAGAGAGTTGCCATAAGAATCACAC 59.936 44.000 0.00 0.00 0.00 3.82
1816 1866 5.181009 CAGAGAGTTGCCATAAGAATCACA 58.819 41.667 0.00 0.00 0.00 3.58
1819 1869 6.112058 AGAACAGAGAGTTGCCATAAGAATC 58.888 40.000 0.00 0.00 41.51 2.52
1820 1870 6.059787 AGAACAGAGAGTTGCCATAAGAAT 57.940 37.500 0.00 0.00 41.51 2.40
1821 1871 5.489792 AGAACAGAGAGTTGCCATAAGAA 57.510 39.130 0.00 0.00 41.51 2.52
1834 1896 1.618837 CCACGGAAGGAAGAACAGAGA 59.381 52.381 0.00 0.00 0.00 3.10
1838 1900 2.322658 ACTACCACGGAAGGAAGAACA 58.677 47.619 0.00 0.00 0.00 3.18
1855 1917 3.448660 TCTGCTTCTGCTCTGCAATACTA 59.551 43.478 0.00 0.00 38.41 1.82
1856 1918 2.235650 TCTGCTTCTGCTCTGCAATACT 59.764 45.455 0.00 0.00 38.41 2.12
1857 1919 2.625737 TCTGCTTCTGCTCTGCAATAC 58.374 47.619 0.00 0.00 38.41 1.89
1858 1920 3.203716 CATCTGCTTCTGCTCTGCAATA 58.796 45.455 0.00 0.00 38.41 1.90
1859 1921 2.017782 CATCTGCTTCTGCTCTGCAAT 58.982 47.619 0.00 0.00 38.41 3.56
1860 1922 1.271217 ACATCTGCTTCTGCTCTGCAA 60.271 47.619 0.00 0.00 38.41 4.08
1861 1923 0.323957 ACATCTGCTTCTGCTCTGCA 59.676 50.000 0.00 0.00 40.48 4.41
1862 1924 1.397692 GAACATCTGCTTCTGCTCTGC 59.602 52.381 0.00 0.00 40.48 4.26
1863 1925 2.975266 AGAACATCTGCTTCTGCTCTG 58.025 47.619 0.00 0.00 40.48 3.35
1864 1926 3.699411 AAGAACATCTGCTTCTGCTCT 57.301 42.857 0.00 0.00 40.48 4.09
1865 1927 4.762956 AAAAGAACATCTGCTTCTGCTC 57.237 40.909 0.00 0.00 40.48 4.26
1866 1928 4.581824 TCAAAAAGAACATCTGCTTCTGCT 59.418 37.500 0.00 0.00 40.48 4.24
1867 1929 4.678742 GTCAAAAAGAACATCTGCTTCTGC 59.321 41.667 0.00 0.00 40.20 4.26
1868 1930 5.824429 TGTCAAAAAGAACATCTGCTTCTG 58.176 37.500 0.00 0.00 0.00 3.02
1869 1931 6.645790 ATGTCAAAAAGAACATCTGCTTCT 57.354 33.333 0.00 0.00 0.00 2.85
1870 1932 7.223387 ACAAATGTCAAAAAGAACATCTGCTTC 59.777 33.333 0.00 0.00 0.00 3.86
1871 1933 7.043565 ACAAATGTCAAAAAGAACATCTGCTT 58.956 30.769 0.00 0.00 0.00 3.91
1872 1934 6.576185 ACAAATGTCAAAAAGAACATCTGCT 58.424 32.000 0.00 0.00 0.00 4.24
1873 1935 6.833342 ACAAATGTCAAAAAGAACATCTGC 57.167 33.333 0.00 0.00 0.00 4.26
1874 1936 7.549649 CGAACAAATGTCAAAAAGAACATCTG 58.450 34.615 0.00 0.00 0.00 2.90
1875 1937 6.198966 GCGAACAAATGTCAAAAAGAACATCT 59.801 34.615 0.00 0.00 0.00 2.90
1876 1938 6.019961 TGCGAACAAATGTCAAAAAGAACATC 60.020 34.615 0.00 0.00 0.00 3.06
1877 1939 5.809562 TGCGAACAAATGTCAAAAAGAACAT 59.190 32.000 0.00 0.00 0.00 2.71
1878 1940 5.061560 GTGCGAACAAATGTCAAAAAGAACA 59.938 36.000 0.00 0.00 0.00 3.18
1879 1941 5.288472 AGTGCGAACAAATGTCAAAAAGAAC 59.712 36.000 0.00 0.00 0.00 3.01
1880 1942 5.406649 AGTGCGAACAAATGTCAAAAAGAA 58.593 33.333 0.00 0.00 0.00 2.52
1881 1943 4.992688 AGTGCGAACAAATGTCAAAAAGA 58.007 34.783 0.00 0.00 0.00 2.52
1882 1944 5.036737 AGAGTGCGAACAAATGTCAAAAAG 58.963 37.500 0.00 0.00 0.00 2.27
1883 1945 4.797868 CAGAGTGCGAACAAATGTCAAAAA 59.202 37.500 0.00 0.00 0.00 1.94
1884 1946 4.142491 ACAGAGTGCGAACAAATGTCAAAA 60.142 37.500 0.00 0.00 0.00 2.44
1885 1947 3.376859 ACAGAGTGCGAACAAATGTCAAA 59.623 39.130 0.00 0.00 0.00 2.69
1886 1948 2.942376 ACAGAGTGCGAACAAATGTCAA 59.058 40.909 0.00 0.00 0.00 3.18
1887 1949 2.560504 ACAGAGTGCGAACAAATGTCA 58.439 42.857 0.00 0.00 0.00 3.58
1895 1957 2.354821 AGGTTTGAAACAGAGTGCGAAC 59.645 45.455 10.53 0.00 0.00 3.95
1898 1960 1.939934 TCAGGTTTGAAACAGAGTGCG 59.060 47.619 10.53 0.00 0.00 5.34
1930 5432 5.049405 ACCAAGAATGACGATTGAAACAGTC 60.049 40.000 0.00 0.00 0.00 3.51
1940 5442 6.479972 TGGAATACTACCAAGAATGACGAT 57.520 37.500 0.00 0.00 34.25 3.73
1956 5458 4.970662 TCTGCTCTGCATTTTGGAATAC 57.029 40.909 0.00 0.00 38.13 1.89
1958 5460 3.830755 ACTTCTGCTCTGCATTTTGGAAT 59.169 39.130 0.00 0.00 38.13 3.01
1959 5461 3.225104 ACTTCTGCTCTGCATTTTGGAA 58.775 40.909 0.00 0.00 38.13 3.53
1960 5462 2.867624 ACTTCTGCTCTGCATTTTGGA 58.132 42.857 0.00 0.00 38.13 3.53
1961 5463 3.755378 ACTACTTCTGCTCTGCATTTTGG 59.245 43.478 0.00 0.00 38.13 3.28
1962 5464 4.214971 ACACTACTTCTGCTCTGCATTTTG 59.785 41.667 0.00 0.00 38.13 2.44
1963 5465 4.392940 ACACTACTTCTGCTCTGCATTTT 58.607 39.130 0.00 0.00 38.13 1.82
1964 5466 4.013267 ACACTACTTCTGCTCTGCATTT 57.987 40.909 0.00 0.00 38.13 2.32
1991 5495 6.093495 AGCTTTATGATTCCACGATTTCGAAA 59.907 34.615 13.91 13.91 43.02 3.46
1993 5497 5.006649 CAGCTTTATGATTCCACGATTTCGA 59.993 40.000 7.01 0.00 43.02 3.71
2015 5519 4.431809 CAGAGTCAATCAGCTACTTCCAG 58.568 47.826 0.00 0.00 0.00 3.86
2029 5533 2.418368 AACCACAACAGCAGAGTCAA 57.582 45.000 0.00 0.00 0.00 3.18
2038 5542 1.873591 GGCTGTGAGTAACCACAACAG 59.126 52.381 0.00 0.00 45.27 3.16
2042 5546 1.330234 TACGGCTGTGAGTAACCACA 58.670 50.000 8.92 0.00 43.98 4.17
2076 5583 1.134818 CGTCCTGATCGATCCAACCAA 60.135 52.381 22.31 1.81 0.00 3.67
2098 5605 2.194271 CGATCAGGAAAGGTAGAACGC 58.806 52.381 0.00 0.00 0.00 4.84
2122 5629 2.291465 TGTGCTGCTCTTTGTCAATGTC 59.709 45.455 0.00 0.00 0.00 3.06
2197 5706 1.247567 CAAAATCCCGACCTGTTGCT 58.752 50.000 0.00 0.00 0.00 3.91
2252 5796 4.399303 CAGAACCCTCAACTGAAACACTTT 59.601 41.667 0.00 0.00 34.07 2.66
2281 5825 2.083774 AGAGTGCTCTTCTCTCGACTG 58.916 52.381 0.00 0.00 37.70 3.51
2285 5829 2.415357 GGTTCAGAGTGCTCTTCTCTCG 60.415 54.545 0.00 0.00 39.84 4.04
2289 5833 3.259625 GGTTAGGTTCAGAGTGCTCTTCT 59.740 47.826 0.00 0.00 37.98 2.85
2292 5836 2.564947 CAGGTTAGGTTCAGAGTGCTCT 59.435 50.000 0.00 0.00 41.37 4.09
2310 5855 3.751698 GGTTTACTGAGCAAGTTACCAGG 59.248 47.826 13.85 0.00 40.00 4.45
2335 5882 4.785511 ATCTCGTACAAGTACAACAGCT 57.214 40.909 10.63 0.00 35.87 4.24
2336 5883 6.033619 CAGTTATCTCGTACAAGTACAACAGC 59.966 42.308 10.63 0.00 35.87 4.40
2379 5932 2.930682 GTTGCTAGGTTGGAATCGTCTC 59.069 50.000 0.00 0.00 0.00 3.36
2386 5939 1.337074 CGTACGGTTGCTAGGTTGGAA 60.337 52.381 7.57 0.00 0.00 3.53
2482 6036 0.172578 TTGACCTGCTATCCGACACG 59.827 55.000 0.00 0.00 0.00 4.49
2520 6077 2.171237 CACTGATATGGGCTGAGGTTCA 59.829 50.000 0.00 0.00 0.00 3.18
2539 6096 6.679327 AGTCCAGTTAGTTTTTCAGTTCAC 57.321 37.500 0.00 0.00 0.00 3.18
2590 6147 2.282391 AGGTTCATTGCTGCGCCA 60.282 55.556 4.18 0.00 0.00 5.69
2591 6148 2.180017 CAGGTTCATTGCTGCGCC 59.820 61.111 4.18 0.00 0.00 6.53
2600 6157 6.240894 ACATATGTTTCACTGTCAGGTTCAT 58.759 36.000 1.41 4.58 0.00 2.57
2601 6158 5.620206 ACATATGTTTCACTGTCAGGTTCA 58.380 37.500 1.41 0.00 0.00 3.18
2602 6159 6.204688 TGAACATATGTTTCACTGTCAGGTTC 59.795 38.462 21.63 5.17 38.56 3.62


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

AutoCloner maintained by Alex Coulton.