Multiple sequence alignment - TraesCS5A01G313500

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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 TraesCS5A01G313500 chr5A 100.000 2657 0 0 1 2657 524388276 524390932 0.000000e+00 4907.0
1 TraesCS5A01G313500 chr5A 88.340 1012 81 17 666 1665 524309063 524310049 0.000000e+00 1181.0
2 TraesCS5A01G313500 chr5A 92.411 224 14 1 2437 2657 524317677 524317900 1.540000e-82 316.0
3 TraesCS5A01G313500 chr5A 84.444 90 14 0 2079 2168 524312097 524312186 3.640000e-14 89.8
4 TraesCS5A01G313500 chr5B 93.750 1184 58 7 642 1812 496569061 496570241 0.000000e+00 1762.0
5 TraesCS5A01G313500 chr5B 92.665 1077 55 5 613 1665 496805633 496806709 0.000000e+00 1530.0
6 TraesCS5A01G313500 chr5B 89.224 1160 91 16 667 1799 496549389 496550541 0.000000e+00 1419.0
7 TraesCS5A01G313500 chr5B 91.707 615 45 6 1 612 524539200 524539811 0.000000e+00 848.0
8 TraesCS5A01G313500 chr5B 91.558 616 46 6 1 613 421161385 421161997 0.000000e+00 845.0
9 TraesCS5A01G313500 chr5B 91.558 616 45 6 1 612 591444311 591443699 0.000000e+00 843.0
10 TraesCS5A01G313500 chr5B 93.576 467 24 1 2191 2657 496570537 496570997 0.000000e+00 691.0
11 TraesCS5A01G313500 chr5B 88.140 371 25 9 2288 2657 496807262 496807614 8.790000e-115 424.0
12 TraesCS5A01G313500 chr5B 91.176 238 10 4 1938 2171 496570315 496570545 1.990000e-81 313.0
13 TraesCS5A01G313500 chr5B 97.126 174 5 0 1795 1968 656461945 656461772 7.190000e-76 294.0
14 TraesCS5A01G313500 chr5D 90.226 1105 75 18 666 1741 412448463 412449563 0.000000e+00 1411.0
15 TraesCS5A01G313500 chr5D 88.429 700 23 13 1963 2657 412449605 412450251 0.000000e+00 791.0
16 TraesCS5A01G313500 chr3B 92.131 610 43 5 1 606 584537163 584537771 0.000000e+00 856.0
17 TraesCS5A01G313500 chr3B 91.158 622 51 4 1 620 661736018 661736637 0.000000e+00 841.0
18 TraesCS5A01G313500 chr3B 91.143 621 51 4 2 620 661768710 661769328 0.000000e+00 839.0
19 TraesCS5A01G313500 chr3B 98.225 169 3 0 1800 1968 703118540 703118708 2.000000e-76 296.0
20 TraesCS5A01G313500 chr7B 91.707 615 44 7 1 612 550507201 550507811 0.000000e+00 846.0
21 TraesCS5A01G313500 chr2A 91.954 609 41 7 1 604 19351917 19352522 0.000000e+00 846.0
22 TraesCS5A01G313500 chr2A 96.571 175 5 1 1798 1972 603083445 603083618 3.350000e-74 289.0
23 TraesCS5A01G313500 chr1D 91.545 615 48 4 1 612 84508997 84508384 0.000000e+00 845.0
24 TraesCS5A01G313500 chr4A 79.918 971 131 29 734 1660 601177938 601178888 0.000000e+00 654.0
25 TraesCS5A01G313500 chr4A 96.552 174 6 0 1791 1964 619191255 619191082 3.350000e-74 289.0
26 TraesCS5A01G313500 chr4A 86.905 84 6 4 721 799 601156179 601156262 3.640000e-14 89.8
27 TraesCS5A01G313500 chrUn 79.938 962 133 27 734 1660 60943090 60944026 0.000000e+00 652.0
28 TraesCS5A01G313500 chrUn 78.983 747 129 20 936 1669 60935620 60936351 3.980000e-133 484.0
29 TraesCS5A01G313500 chrUn 80.275 654 108 14 1000 1653 60947713 60947081 8.610000e-130 473.0
30 TraesCS5A01G313500 chrUn 87.342 79 5 3 726 799 60928430 60928508 4.710000e-13 86.1
31 TraesCS5A01G313500 chr4B 78.763 970 148 26 734 1660 5531714 5532668 4.900000e-167 597.0
32 TraesCS5A01G313500 chr4B 95.604 182 6 2 1795 1975 143898155 143897975 9.300000e-75 291.0
33 TraesCS5A01G313500 chr3A 97.647 170 4 0 1801 1970 542206115 542205946 2.590000e-75 292.0
34 TraesCS5A01G313500 chr3A 97.647 170 4 0 1796 1965 602023227 602023058 2.590000e-75 292.0
35 TraesCS5A01G313500 chr7A 96.045 177 6 1 1796 1972 143080636 143080811 1.200000e-73 287.0
36 TraesCS5A01G313500 chr3D 93.583 187 10 2 1798 1983 214436885 214436700 7.240000e-71 278.0


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 TraesCS5A01G313500 chr5A 524388276 524390932 2656 False 4907.0 4907 100.0000 1 2657 1 chr5A.!!$F2 2656
1 TraesCS5A01G313500 chr5A 524309063 524312186 3123 False 635.4 1181 86.3920 666 2168 2 chr5A.!!$F3 1502
2 TraesCS5A01G313500 chr5B 496549389 496550541 1152 False 1419.0 1419 89.2240 667 1799 1 chr5B.!!$F2 1132
3 TraesCS5A01G313500 chr5B 496805633 496807614 1981 False 977.0 1530 90.4025 613 2657 2 chr5B.!!$F5 2044
4 TraesCS5A01G313500 chr5B 496569061 496570997 1936 False 922.0 1762 92.8340 642 2657 3 chr5B.!!$F4 2015
5 TraesCS5A01G313500 chr5B 524539200 524539811 611 False 848.0 848 91.7070 1 612 1 chr5B.!!$F3 611
6 TraesCS5A01G313500 chr5B 421161385 421161997 612 False 845.0 845 91.5580 1 613 1 chr5B.!!$F1 612
7 TraesCS5A01G313500 chr5B 591443699 591444311 612 True 843.0 843 91.5580 1 612 1 chr5B.!!$R1 611
8 TraesCS5A01G313500 chr5D 412448463 412450251 1788 False 1101.0 1411 89.3275 666 2657 2 chr5D.!!$F1 1991
9 TraesCS5A01G313500 chr3B 584537163 584537771 608 False 856.0 856 92.1310 1 606 1 chr3B.!!$F1 605
10 TraesCS5A01G313500 chr3B 661736018 661736637 619 False 841.0 841 91.1580 1 620 1 chr3B.!!$F2 619
11 TraesCS5A01G313500 chr3B 661768710 661769328 618 False 839.0 839 91.1430 2 620 1 chr3B.!!$F3 618
12 TraesCS5A01G313500 chr7B 550507201 550507811 610 False 846.0 846 91.7070 1 612 1 chr7B.!!$F1 611
13 TraesCS5A01G313500 chr2A 19351917 19352522 605 False 846.0 846 91.9540 1 604 1 chr2A.!!$F1 603
14 TraesCS5A01G313500 chr1D 84508384 84508997 613 True 845.0 845 91.5450 1 612 1 chr1D.!!$R1 611
15 TraesCS5A01G313500 chr4A 601177938 601178888 950 False 654.0 654 79.9180 734 1660 1 chr4A.!!$F2 926
16 TraesCS5A01G313500 chrUn 60943090 60944026 936 False 652.0 652 79.9380 734 1660 1 chrUn.!!$F3 926
17 TraesCS5A01G313500 chrUn 60935620 60936351 731 False 484.0 484 78.9830 936 1669 1 chrUn.!!$F2 733
18 TraesCS5A01G313500 chrUn 60947081 60947713 632 True 473.0 473 80.2750 1000 1653 1 chrUn.!!$R1 653
19 TraesCS5A01G313500 chr4B 5531714 5532668 954 False 597.0 597 78.7630 734 1660 1 chr4B.!!$F1 926

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
380 385 0.884259 TCGACCGTTACGACTGTGGA 60.884 55.0 6.24 0.0 34.85 4.02 F
1199 1281 0.662619 AACATTACCATGCCGATGCG 59.337 50.0 0.00 0.0 41.78 4.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1608 1699 0.037326 CCTTGAGCTTCTGCACGGTA 60.037 55.0 0.0 0.0 42.74 4.02 R
2000 2234 1.399714 ACGGATGGATCTCGTAAGCA 58.600 50.0 0.0 0.0 33.91 3.91 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
65 66 1.371337 CGTCTACGATGTGTCCCCGA 61.371 60.000 0.00 0.00 43.02 5.14
156 159 1.440060 CGCCCATACTAACTCGGCA 59.560 57.895 0.00 0.00 39.69 5.69
192 195 2.599281 TCCACGGCGACTTCCTCA 60.599 61.111 16.62 0.00 0.00 3.86
252 255 3.077519 GCACGGCTACCTCGACCAT 62.078 63.158 0.00 0.00 0.00 3.55
283 286 1.395045 CCATGCTCTCGGCTACCTCA 61.395 60.000 0.00 0.00 42.39 3.86
325 329 1.608025 CGCCTTACTTGAGCAACCTCA 60.608 52.381 0.00 0.00 46.03 3.86
328 332 3.869912 GCCTTACTTGAGCAACCTCATCA 60.870 47.826 0.00 0.00 46.84 3.07
347 351 2.281484 TTTCCACTCCAGCCACGC 60.281 61.111 0.00 0.00 0.00 5.34
380 385 0.884259 TCGACCGTTACGACTGTGGA 60.884 55.000 6.24 0.00 34.85 4.02
414 421 2.087646 GCTTGCCTTCGGATTCTTCTT 58.912 47.619 0.00 0.00 0.00 2.52
473 480 2.483188 GGGGGATGTTGAGTATCGTGAC 60.483 54.545 0.00 0.00 38.61 3.67
490 499 4.334759 TCGTGACTATTAGGAAAGACGAGG 59.665 45.833 0.00 0.00 31.48 4.63
524 533 4.150897 TGTTCTGGCTTGTCTTGTACTT 57.849 40.909 0.00 0.00 0.00 2.24
595 607 4.906618 ACAACGAACTATTCCACCAATCT 58.093 39.130 0.00 0.00 0.00 2.40
604 617 3.481559 TTCCACCAATCTCTCTCTCCT 57.518 47.619 0.00 0.00 0.00 3.69
607 620 4.171234 TCCACCAATCTCTCTCTCCTTTT 58.829 43.478 0.00 0.00 0.00 2.27
608 621 5.342017 TCCACCAATCTCTCTCTCCTTTTA 58.658 41.667 0.00 0.00 0.00 1.52
609 622 5.785423 TCCACCAATCTCTCTCTCCTTTTAA 59.215 40.000 0.00 0.00 0.00 1.52
610 623 5.877564 CCACCAATCTCTCTCTCCTTTTAAC 59.122 44.000 0.00 0.00 0.00 2.01
611 624 6.467677 CACCAATCTCTCTCTCCTTTTAACA 58.532 40.000 0.00 0.00 0.00 2.41
612 625 6.593382 CACCAATCTCTCTCTCCTTTTAACAG 59.407 42.308 0.00 0.00 0.00 3.16
613 626 6.271159 ACCAATCTCTCTCTCCTTTTAACAGT 59.729 38.462 0.00 0.00 0.00 3.55
614 627 7.164803 CCAATCTCTCTCTCCTTTTAACAGTT 58.835 38.462 0.00 0.00 0.00 3.16
684 697 5.009010 ACACTCACACATCCAAGTTTTCATC 59.991 40.000 0.00 0.00 0.00 2.92
685 698 4.214119 ACTCACACATCCAAGTTTTCATCG 59.786 41.667 0.00 0.00 0.00 3.84
691 704 4.218200 ACATCCAAGTTTTCATCGCAATGA 59.782 37.500 0.00 0.00 40.18 2.57
706 719 9.108284 TCATCGCAATGAGAACAGAAATAAATA 57.892 29.630 0.00 0.00 36.98 1.40
1015 1088 1.902938 TTCAATGGCGTCCATCAACA 58.097 45.000 11.08 0.00 44.40 3.33
1199 1281 0.662619 AACATTACCATGCCGATGCG 59.337 50.000 0.00 0.00 41.78 4.73
1608 1699 2.028020 GTCATTCAAGACCGACCTTCCT 60.028 50.000 0.00 0.00 32.36 3.36
1698 1792 5.835257 TCTTGTTGCTCTTCTTTTTCATGG 58.165 37.500 0.00 0.00 0.00 3.66
1803 2021 8.406730 GGCAACTACTCCTACTATGTAATACT 57.593 38.462 0.00 0.00 0.00 2.12
1804 2022 8.513774 GGCAACTACTCCTACTATGTAATACTC 58.486 40.741 0.00 0.00 0.00 2.59
1805 2023 8.513774 GCAACTACTCCTACTATGTAATACTCC 58.486 40.741 0.00 0.00 0.00 3.85
1806 2024 9.012161 CAACTACTCCTACTATGTAATACTCCC 57.988 40.741 0.00 0.00 0.00 4.30
1807 2025 8.522921 ACTACTCCTACTATGTAATACTCCCT 57.477 38.462 0.00 0.00 0.00 4.20
1808 2026 8.605065 ACTACTCCTACTATGTAATACTCCCTC 58.395 40.741 0.00 0.00 0.00 4.30
1809 2027 6.792424 ACTCCTACTATGTAATACTCCCTCC 58.208 44.000 0.00 0.00 0.00 4.30
1810 2028 5.813383 TCCTACTATGTAATACTCCCTCCG 58.187 45.833 0.00 0.00 0.00 4.63
1811 2029 5.311649 TCCTACTATGTAATACTCCCTCCGT 59.688 44.000 0.00 0.00 0.00 4.69
1812 2030 6.008960 CCTACTATGTAATACTCCCTCCGTT 58.991 44.000 0.00 0.00 0.00 4.44
1813 2031 6.150809 CCTACTATGTAATACTCCCTCCGTTC 59.849 46.154 0.00 0.00 0.00 3.95
1814 2032 4.831710 ACTATGTAATACTCCCTCCGTTCC 59.168 45.833 0.00 0.00 0.00 3.62
1815 2033 3.393426 TGTAATACTCCCTCCGTTCCT 57.607 47.619 0.00 0.00 0.00 3.36
1816 2034 4.524802 TGTAATACTCCCTCCGTTCCTA 57.475 45.455 0.00 0.00 0.00 2.94
1817 2035 4.870636 TGTAATACTCCCTCCGTTCCTAA 58.129 43.478 0.00 0.00 0.00 2.69
1818 2036 5.271598 TGTAATACTCCCTCCGTTCCTAAA 58.728 41.667 0.00 0.00 0.00 1.85
1819 2037 5.901276 TGTAATACTCCCTCCGTTCCTAAAT 59.099 40.000 0.00 0.00 0.00 1.40
1820 2038 7.068702 TGTAATACTCCCTCCGTTCCTAAATA 58.931 38.462 0.00 0.00 0.00 1.40
1821 2039 6.416631 AATACTCCCTCCGTTCCTAAATAC 57.583 41.667 0.00 0.00 0.00 1.89
1822 2040 3.991683 ACTCCCTCCGTTCCTAAATACT 58.008 45.455 0.00 0.00 0.00 2.12
1823 2041 4.359996 ACTCCCTCCGTTCCTAAATACTT 58.640 43.478 0.00 0.00 0.00 2.24
1824 2042 4.161754 ACTCCCTCCGTTCCTAAATACTTG 59.838 45.833 0.00 0.00 0.00 3.16
1825 2043 4.098894 TCCCTCCGTTCCTAAATACTTGT 58.901 43.478 0.00 0.00 0.00 3.16
1826 2044 4.533311 TCCCTCCGTTCCTAAATACTTGTT 59.467 41.667 0.00 0.00 0.00 2.83
1827 2045 5.013391 TCCCTCCGTTCCTAAATACTTGTTT 59.987 40.000 0.00 0.00 0.00 2.83
1828 2046 5.708697 CCCTCCGTTCCTAAATACTTGTTTT 59.291 40.000 0.00 0.00 0.00 2.43
1829 2047 6.208007 CCCTCCGTTCCTAAATACTTGTTTTT 59.792 38.462 0.00 0.00 0.00 1.94
1830 2048 7.303261 CCTCCGTTCCTAAATACTTGTTTTTC 58.697 38.462 0.00 0.00 0.00 2.29
1831 2049 7.174426 CCTCCGTTCCTAAATACTTGTTTTTCT 59.826 37.037 0.00 0.00 0.00 2.52
1832 2050 9.211485 CTCCGTTCCTAAATACTTGTTTTTCTA 57.789 33.333 0.00 0.00 0.00 2.10
1833 2051 9.211485 TCCGTTCCTAAATACTTGTTTTTCTAG 57.789 33.333 0.00 0.00 0.00 2.43
1834 2052 8.448615 CCGTTCCTAAATACTTGTTTTTCTAGG 58.551 37.037 0.00 0.00 0.00 3.02
1835 2053 7.961283 CGTTCCTAAATACTTGTTTTTCTAGGC 59.039 37.037 0.00 0.00 0.00 3.93
1836 2054 8.789762 GTTCCTAAATACTTGTTTTTCTAGGCA 58.210 33.333 0.00 0.00 0.00 4.75
1837 2055 9.528489 TTCCTAAATACTTGTTTTTCTAGGCAT 57.472 29.630 0.00 0.00 0.00 4.40
1838 2056 9.528489 TCCTAAATACTTGTTTTTCTAGGCATT 57.472 29.630 0.00 0.00 0.00 3.56
1843 2061 9.476202 AATACTTGTTTTTCTAGGCATTTCAAC 57.524 29.630 0.00 0.00 0.00 3.18
1844 2062 6.872920 ACTTGTTTTTCTAGGCATTTCAACA 58.127 32.000 0.00 0.00 0.00 3.33
1845 2063 6.980397 ACTTGTTTTTCTAGGCATTTCAACAG 59.020 34.615 0.00 0.00 0.00 3.16
1846 2064 5.841810 TGTTTTTCTAGGCATTTCAACAGG 58.158 37.500 0.00 0.00 0.00 4.00
1847 2065 5.362430 TGTTTTTCTAGGCATTTCAACAGGT 59.638 36.000 0.00 0.00 0.00 4.00
1848 2066 5.452078 TTTTCTAGGCATTTCAACAGGTG 57.548 39.130 0.00 0.00 0.00 4.00
1849 2067 4.365514 TTCTAGGCATTTCAACAGGTGA 57.634 40.909 0.00 0.00 0.00 4.02
1850 2068 3.674997 TCTAGGCATTTCAACAGGTGAC 58.325 45.455 0.00 0.00 35.39 3.67
1851 2069 2.664402 AGGCATTTCAACAGGTGACT 57.336 45.000 0.00 0.00 46.44 3.41
1852 2070 3.788227 AGGCATTTCAACAGGTGACTA 57.212 42.857 0.00 0.00 40.21 2.59
1853 2071 3.412386 AGGCATTTCAACAGGTGACTAC 58.588 45.455 0.00 0.00 40.21 2.73
1854 2072 3.146066 GGCATTTCAACAGGTGACTACA 58.854 45.455 0.00 0.00 40.21 2.74
1855 2073 3.758554 GGCATTTCAACAGGTGACTACAT 59.241 43.478 0.00 0.00 40.21 2.29
1856 2074 4.941263 GGCATTTCAACAGGTGACTACATA 59.059 41.667 0.00 0.00 40.21 2.29
1857 2075 5.163754 GGCATTTCAACAGGTGACTACATAC 60.164 44.000 0.00 0.00 40.21 2.39
1858 2076 5.445939 GCATTTCAACAGGTGACTACATACG 60.446 44.000 0.00 0.00 40.21 3.06
1859 2077 3.861276 TCAACAGGTGACTACATACGG 57.139 47.619 0.00 0.00 40.21 4.02
1860 2078 3.423749 TCAACAGGTGACTACATACGGA 58.576 45.455 0.00 0.00 40.21 4.69
1861 2079 3.442625 TCAACAGGTGACTACATACGGAG 59.557 47.826 0.00 0.00 40.21 4.63
1862 2080 1.749634 ACAGGTGACTACATACGGAGC 59.250 52.381 0.00 0.00 40.21 4.70
1863 2081 1.749063 CAGGTGACTACATACGGAGCA 59.251 52.381 0.00 0.00 40.21 4.26
1864 2082 2.165641 CAGGTGACTACATACGGAGCAA 59.834 50.000 0.00 0.00 40.21 3.91
1865 2083 2.829720 AGGTGACTACATACGGAGCAAA 59.170 45.455 0.00 0.00 40.61 3.68
1866 2084 3.259876 AGGTGACTACATACGGAGCAAAA 59.740 43.478 0.00 0.00 40.61 2.44
1867 2085 4.081087 AGGTGACTACATACGGAGCAAAAT 60.081 41.667 0.00 0.00 40.61 1.82
1868 2086 4.034048 GGTGACTACATACGGAGCAAAATG 59.966 45.833 0.00 0.00 0.00 2.32
1869 2087 4.868171 GTGACTACATACGGAGCAAAATGA 59.132 41.667 0.00 0.00 0.00 2.57
1870 2088 5.005779 GTGACTACATACGGAGCAAAATGAG 59.994 44.000 0.00 0.00 0.00 2.90
1871 2089 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
1872 2090 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
1873 2091 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
1874 2092 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
1875 2093 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
1876 2094 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
1877 2095 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
1878 2096 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
1879 2097 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
1880 2098 4.631377 CGGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
1881 2099 5.446473 CGGAGCAAAATGAGTGAATCTACAC 60.446 44.000 0.00 0.00 40.60 2.90
1894 2112 8.764524 AGTGAATCTACACTCTAAAATGTGTC 57.235 34.615 1.91 0.00 46.36 3.67
1895 2113 8.589338 AGTGAATCTACACTCTAAAATGTGTCT 58.411 33.333 1.91 0.00 46.36 3.41
1896 2114 9.856488 GTGAATCTACACTCTAAAATGTGTCTA 57.144 33.333 1.91 0.00 44.94 2.59
1897 2115 9.856488 TGAATCTACACTCTAAAATGTGTCTAC 57.144 33.333 1.91 0.00 44.94 2.59
1898 2116 9.856488 GAATCTACACTCTAAAATGTGTCTACA 57.144 33.333 1.91 0.00 44.94 2.74
1904 2122 9.587772 ACACTCTAAAATGTGTCTACATACATC 57.412 33.333 0.00 0.00 46.54 3.06
1905 2123 9.035607 CACTCTAAAATGTGTCTACATACATCC 57.964 37.037 0.00 0.00 46.54 3.51
1906 2124 7.921214 ACTCTAAAATGTGTCTACATACATCCG 59.079 37.037 0.00 0.00 46.54 4.18
1907 2125 7.778083 TCTAAAATGTGTCTACATACATCCGT 58.222 34.615 0.00 0.00 46.54 4.69
1908 2126 8.905850 TCTAAAATGTGTCTACATACATCCGTA 58.094 33.333 0.00 0.00 46.54 4.02
1909 2127 9.692749 CTAAAATGTGTCTACATACATCCGTAT 57.307 33.333 0.00 0.00 46.54 3.06
1924 2142 7.342769 ACATCCGTATGTAGTAGTCATTTGA 57.657 36.000 0.00 0.00 44.66 2.69
1925 2143 7.778083 ACATCCGTATGTAGTAGTCATTTGAA 58.222 34.615 0.00 0.00 44.66 2.69
1926 2144 8.255206 ACATCCGTATGTAGTAGTCATTTGAAA 58.745 33.333 0.00 0.00 44.66 2.69
1927 2145 9.261180 CATCCGTATGTAGTAGTCATTTGAAAT 57.739 33.333 0.00 0.00 0.00 2.17
1928 2146 8.642908 TCCGTATGTAGTAGTCATTTGAAATG 57.357 34.615 11.54 11.54 0.00 2.32
1929 2147 8.255206 TCCGTATGTAGTAGTCATTTGAAATGT 58.745 33.333 16.62 2.38 0.00 2.71
1930 2148 8.540492 CCGTATGTAGTAGTCATTTGAAATGTC 58.460 37.037 16.62 11.74 0.00 3.06
1931 2149 9.302345 CGTATGTAGTAGTCATTTGAAATGTCT 57.698 33.333 18.62 18.62 0.00 3.41
1999 2233 0.710567 GTCTGAGTCGTGATTGTGCG 59.289 55.000 0.00 0.00 0.00 5.34
2000 2234 0.313987 TCTGAGTCGTGATTGTGCGT 59.686 50.000 0.00 0.00 0.00 5.24
2001 2235 0.436150 CTGAGTCGTGATTGTGCGTG 59.564 55.000 0.00 0.00 0.00 5.34
2002 2236 1.130613 GAGTCGTGATTGTGCGTGC 59.869 57.895 0.00 0.00 0.00 5.34
2034 4131 1.916506 TCCGTTCCCAAATGCATTGA 58.083 45.000 13.82 3.03 41.85 2.57
2039 4136 4.455190 CCGTTCCCAAATGCATTGAAAAAT 59.545 37.500 13.82 0.00 41.85 1.82
2077 4177 9.219497 CGACTAAAAGCTGTTATGTAGTACTAC 57.781 37.037 23.58 23.58 36.63 2.73
2163 4263 4.468510 TCCTAATTTCCTTCAAGCGTCCTA 59.531 41.667 0.00 0.00 0.00 2.94
2164 4264 5.130477 TCCTAATTTCCTTCAAGCGTCCTAT 59.870 40.000 0.00 0.00 0.00 2.57
2166 4266 7.016268 TCCTAATTTCCTTCAAGCGTCCTATAT 59.984 37.037 0.00 0.00 0.00 0.86
2168 4268 9.877178 CTAATTTCCTTCAAGCGTCCTATATAT 57.123 33.333 0.00 0.00 0.00 0.86
2602 4742 2.571216 CCGAACACGTCCTCCCAGT 61.571 63.158 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
101 102 3.119096 GTGCGCCGGGAAGAAGAC 61.119 66.667 4.18 0.00 0.00 3.01
192 195 3.698820 GTCGGGGTAGCCGGTGTT 61.699 66.667 17.03 0.00 0.00 3.32
226 229 0.249398 AGGTAGCCGTGCGAAGAATT 59.751 50.000 0.00 0.00 0.00 2.17
283 286 1.142965 GCCCTTTGTGCCGTTTGTT 59.857 52.632 0.00 0.00 0.00 2.83
325 329 1.067295 TGGCTGGAGTGGAAACTGAT 58.933 50.000 0.00 0.00 0.00 2.90
328 332 1.071471 CGTGGCTGGAGTGGAAACT 59.929 57.895 0.00 0.00 0.00 2.66
380 385 2.526873 AAGCCGACAGACACCCCT 60.527 61.111 0.00 0.00 0.00 4.79
414 421 1.853114 GACGCAGACGGTGAGACTGA 61.853 60.000 0.00 0.00 43.62 3.41
473 480 8.732531 CCTAATCTACCTCGTCTTTCCTAATAG 58.267 40.741 0.00 0.00 0.00 1.73
490 499 6.599638 ACAAGCCAGAACAAATCCTAATCTAC 59.400 38.462 0.00 0.00 0.00 2.59
556 566 3.259064 GTTGTATTGCTTGAGCCTCGTA 58.741 45.455 0.00 0.00 41.18 3.43
595 607 8.483758 ACTTGTTAACTGTTAAAAGGAGAGAGA 58.516 33.333 23.36 4.67 0.00 3.10
604 617 6.094881 AGCTGCTGACTTGTTAACTGTTAAAA 59.905 34.615 14.10 6.81 0.00 1.52
607 620 4.703897 AGCTGCTGACTTGTTAACTGTTA 58.296 39.130 0.00 0.00 0.00 2.41
608 621 3.545703 AGCTGCTGACTTGTTAACTGTT 58.454 40.909 0.00 0.00 0.00 3.16
609 622 3.134458 GAGCTGCTGACTTGTTAACTGT 58.866 45.455 7.01 5.88 0.00 3.55
610 623 2.481952 GGAGCTGCTGACTTGTTAACTG 59.518 50.000 7.01 2.59 0.00 3.16
611 624 2.772287 GGAGCTGCTGACTTGTTAACT 58.228 47.619 7.01 0.00 0.00 2.24
612 625 1.461127 CGGAGCTGCTGACTTGTTAAC 59.539 52.381 7.01 0.00 0.00 2.01
613 626 1.343142 TCGGAGCTGCTGACTTGTTAA 59.657 47.619 7.01 0.00 0.00 2.01
614 627 0.966179 TCGGAGCTGCTGACTTGTTA 59.034 50.000 7.01 0.00 0.00 2.41
659 672 4.335315 TGAAAACTTGGATGTGTGAGTGTC 59.665 41.667 0.00 0.00 0.00 3.67
684 697 9.638300 GTAGTATTTATTTCTGTTCTCATTGCG 57.362 33.333 0.00 0.00 0.00 4.85
685 698 9.638300 CGTAGTATTTATTTCTGTTCTCATTGC 57.362 33.333 0.00 0.00 0.00 3.56
691 704 6.816640 TGCAGCGTAGTATTTATTTCTGTTCT 59.183 34.615 0.00 0.00 0.00 3.01
706 719 5.723672 ATACCTACAATATGCAGCGTAGT 57.276 39.130 0.00 0.00 31.39 2.73
1015 1088 2.567615 CCAACACCAAGGAGTAGTAGCT 59.432 50.000 0.00 0.00 0.00 3.32
1077 1150 2.284625 AGGATGTCAGGGTCGCCA 60.285 61.111 0.00 0.00 0.00 5.69
1356 1447 2.258591 GAGAGCGTGCCGTCAAGA 59.741 61.111 0.00 0.00 0.00 3.02
1608 1699 0.037326 CCTTGAGCTTCTGCACGGTA 60.037 55.000 0.00 0.00 42.74 4.02
1713 1819 7.072263 AGCTCATAGCCTTATTAGTTCATGT 57.928 36.000 0.00 0.00 43.77 3.21
1800 2018 5.134725 AGTATTTAGGAACGGAGGGAGTA 57.865 43.478 0.00 0.00 0.00 2.59
1801 2019 3.991683 AGTATTTAGGAACGGAGGGAGT 58.008 45.455 0.00 0.00 0.00 3.85
1802 2020 4.161754 ACAAGTATTTAGGAACGGAGGGAG 59.838 45.833 0.00 0.00 0.00 4.30
1803 2021 4.098894 ACAAGTATTTAGGAACGGAGGGA 58.901 43.478 0.00 0.00 0.00 4.20
1804 2022 4.482952 ACAAGTATTTAGGAACGGAGGG 57.517 45.455 0.00 0.00 0.00 4.30
1805 2023 6.812879 AAAACAAGTATTTAGGAACGGAGG 57.187 37.500 0.00 0.00 0.00 4.30
1806 2024 8.095937 AGAAAAACAAGTATTTAGGAACGGAG 57.904 34.615 0.00 0.00 0.00 4.63
1807 2025 9.211485 CTAGAAAAACAAGTATTTAGGAACGGA 57.789 33.333 0.00 0.00 0.00 4.69
1808 2026 8.448615 CCTAGAAAAACAAGTATTTAGGAACGG 58.551 37.037 0.00 0.00 0.00 4.44
1809 2027 7.961283 GCCTAGAAAAACAAGTATTTAGGAACG 59.039 37.037 0.00 0.00 0.00 3.95
1810 2028 8.789762 TGCCTAGAAAAACAAGTATTTAGGAAC 58.210 33.333 0.00 0.00 0.00 3.62
1811 2029 8.927675 TGCCTAGAAAAACAAGTATTTAGGAA 57.072 30.769 0.00 0.00 0.00 3.36
1812 2030 9.528489 AATGCCTAGAAAAACAAGTATTTAGGA 57.472 29.630 0.00 0.00 0.00 2.94
1817 2035 9.476202 GTTGAAATGCCTAGAAAAACAAGTATT 57.524 29.630 0.00 0.00 0.00 1.89
1818 2036 8.637986 TGTTGAAATGCCTAGAAAAACAAGTAT 58.362 29.630 0.00 0.00 0.00 2.12
1819 2037 8.001881 TGTTGAAATGCCTAGAAAAACAAGTA 57.998 30.769 0.00 0.00 0.00 2.24
1820 2038 6.872920 TGTTGAAATGCCTAGAAAAACAAGT 58.127 32.000 0.00 0.00 0.00 3.16
1821 2039 6.421801 CCTGTTGAAATGCCTAGAAAAACAAG 59.578 38.462 0.00 0.00 0.00 3.16
1822 2040 6.127196 ACCTGTTGAAATGCCTAGAAAAACAA 60.127 34.615 0.00 0.00 0.00 2.83
1823 2041 5.362430 ACCTGTTGAAATGCCTAGAAAAACA 59.638 36.000 0.00 0.00 0.00 2.83
1824 2042 5.691754 CACCTGTTGAAATGCCTAGAAAAAC 59.308 40.000 0.00 0.00 0.00 2.43
1825 2043 5.596361 TCACCTGTTGAAATGCCTAGAAAAA 59.404 36.000 0.00 0.00 0.00 1.94
1826 2044 5.009610 GTCACCTGTTGAAATGCCTAGAAAA 59.990 40.000 0.00 0.00 35.39 2.29
1827 2045 4.518970 GTCACCTGTTGAAATGCCTAGAAA 59.481 41.667 0.00 0.00 35.39 2.52
1828 2046 4.072131 GTCACCTGTTGAAATGCCTAGAA 58.928 43.478 0.00 0.00 35.39 2.10
1829 2047 3.327757 AGTCACCTGTTGAAATGCCTAGA 59.672 43.478 0.00 0.00 35.39 2.43
1830 2048 3.679389 AGTCACCTGTTGAAATGCCTAG 58.321 45.455 0.00 0.00 35.39 3.02
1831 2049 3.788227 AGTCACCTGTTGAAATGCCTA 57.212 42.857 0.00 0.00 35.39 3.93
1832 2050 2.664402 AGTCACCTGTTGAAATGCCT 57.336 45.000 0.00 0.00 35.39 4.75
1833 2051 3.146066 TGTAGTCACCTGTTGAAATGCC 58.854 45.455 0.00 0.00 35.39 4.40
1834 2052 5.445939 CGTATGTAGTCACCTGTTGAAATGC 60.446 44.000 0.00 0.00 35.39 3.56
1835 2053 5.063438 CCGTATGTAGTCACCTGTTGAAATG 59.937 44.000 0.00 0.00 35.39 2.32
1836 2054 5.046878 TCCGTATGTAGTCACCTGTTGAAAT 60.047 40.000 0.00 0.00 35.39 2.17
1837 2055 4.281435 TCCGTATGTAGTCACCTGTTGAAA 59.719 41.667 0.00 0.00 35.39 2.69
1838 2056 3.827876 TCCGTATGTAGTCACCTGTTGAA 59.172 43.478 0.00 0.00 35.39 2.69
1839 2057 3.423749 TCCGTATGTAGTCACCTGTTGA 58.576 45.455 0.00 0.00 0.00 3.18
1840 2058 3.770666 CTCCGTATGTAGTCACCTGTTG 58.229 50.000 0.00 0.00 0.00 3.33
1841 2059 2.165845 GCTCCGTATGTAGTCACCTGTT 59.834 50.000 0.00 0.00 0.00 3.16
1842 2060 1.749634 GCTCCGTATGTAGTCACCTGT 59.250 52.381 0.00 0.00 0.00 4.00
1843 2061 1.749063 TGCTCCGTATGTAGTCACCTG 59.251 52.381 0.00 0.00 0.00 4.00
1844 2062 2.139323 TGCTCCGTATGTAGTCACCT 57.861 50.000 0.00 0.00 0.00 4.00
1845 2063 2.953466 TTGCTCCGTATGTAGTCACC 57.047 50.000 0.00 0.00 0.00 4.02
1846 2064 4.868171 TCATTTTGCTCCGTATGTAGTCAC 59.132 41.667 0.00 0.00 0.00 3.67
1847 2065 5.079689 TCATTTTGCTCCGTATGTAGTCA 57.920 39.130 0.00 0.00 0.00 3.41
1848 2066 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
1849 2067 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
1850 2068 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
1851 2069 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
1852 2070 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
1853 2071 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
1854 2072 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
1855 2073 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
1856 2074 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
1857 2075 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
1858 2076 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
1859 2077 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
1879 2097 9.035607 GGATGTATGTAGACACATTTTAGAGTG 57.964 37.037 0.00 0.00 42.98 3.51
1880 2098 7.921214 CGGATGTATGTAGACACATTTTAGAGT 59.079 37.037 0.00 0.00 42.98 3.24
1881 2099 7.921214 ACGGATGTATGTAGACACATTTTAGAG 59.079 37.037 0.00 0.00 42.98 2.43
1882 2100 7.778083 ACGGATGTATGTAGACACATTTTAGA 58.222 34.615 0.00 0.00 42.98 2.10
1883 2101 9.692749 ATACGGATGTATGTAGACACATTTTAG 57.307 33.333 0.00 0.00 42.98 1.85
1898 2116 9.074576 TCAAATGACTACTACATACGGATGTAT 57.925 33.333 20.64 13.02 45.42 2.29
1899 2117 8.454570 TCAAATGACTACTACATACGGATGTA 57.545 34.615 19.32 19.32 44.77 2.29
1901 2119 8.642908 TTTCAAATGACTACTACATACGGATG 57.357 34.615 5.94 5.94 39.16 3.51
1902 2120 9.261180 CATTTCAAATGACTACTACATACGGAT 57.739 33.333 3.82 0.00 0.00 4.18
1903 2121 8.255206 ACATTTCAAATGACTACTACATACGGA 58.745 33.333 17.30 0.00 0.00 4.69
1904 2122 8.420374 ACATTTCAAATGACTACTACATACGG 57.580 34.615 17.30 0.00 0.00 4.02
1905 2123 9.302345 AGACATTTCAAATGACTACTACATACG 57.698 33.333 17.30 0.00 0.00 3.06
1929 2147 8.248945 CCGTTCCTAAATACTTGTCTTTCTAGA 58.751 37.037 0.00 0.00 0.00 2.43
1930 2148 8.248945 TCCGTTCCTAAATACTTGTCTTTCTAG 58.751 37.037 0.00 0.00 0.00 2.43
1931 2149 8.125978 TCCGTTCCTAAATACTTGTCTTTCTA 57.874 34.615 0.00 0.00 0.00 2.10
1932 2150 7.001099 TCCGTTCCTAAATACTTGTCTTTCT 57.999 36.000 0.00 0.00 0.00 2.52
1933 2151 6.313164 CCTCCGTTCCTAAATACTTGTCTTTC 59.687 42.308 0.00 0.00 0.00 2.62
1934 2152 6.171213 CCTCCGTTCCTAAATACTTGTCTTT 58.829 40.000 0.00 0.00 0.00 2.52
1935 2153 5.338137 CCCTCCGTTCCTAAATACTTGTCTT 60.338 44.000 0.00 0.00 0.00 3.01
1936 2154 4.161754 CCCTCCGTTCCTAAATACTTGTCT 59.838 45.833 0.00 0.00 0.00 3.41
1937 2155 4.161001 TCCCTCCGTTCCTAAATACTTGTC 59.839 45.833 0.00 0.00 0.00 3.18
1938 2156 4.098894 TCCCTCCGTTCCTAAATACTTGT 58.901 43.478 0.00 0.00 0.00 3.16
1939 2157 4.161754 ACTCCCTCCGTTCCTAAATACTTG 59.838 45.833 0.00 0.00 0.00 3.16
1940 2158 4.359996 ACTCCCTCCGTTCCTAAATACTT 58.640 43.478 0.00 0.00 0.00 2.24
1941 2159 3.991683 ACTCCCTCCGTTCCTAAATACT 58.008 45.455 0.00 0.00 0.00 2.12
1942 2160 4.892345 AGTACTCCCTCCGTTCCTAAATAC 59.108 45.833 0.00 0.00 0.00 1.89
1943 2161 5.134725 AGTACTCCCTCCGTTCCTAAATA 57.865 43.478 0.00 0.00 0.00 1.40
1944 2162 3.991683 AGTACTCCCTCCGTTCCTAAAT 58.008 45.455 0.00 0.00 0.00 1.40
1945 2163 3.463048 AGTACTCCCTCCGTTCCTAAA 57.537 47.619 0.00 0.00 0.00 1.85
1946 2164 4.467769 CATAGTACTCCCTCCGTTCCTAA 58.532 47.826 0.00 0.00 0.00 2.69
1947 2165 3.749954 GCATAGTACTCCCTCCGTTCCTA 60.750 52.174 0.00 0.00 0.00 2.94
1948 2166 2.946785 CATAGTACTCCCTCCGTTCCT 58.053 52.381 0.00 0.00 0.00 3.36
1949 2167 1.340568 GCATAGTACTCCCTCCGTTCC 59.659 57.143 0.00 0.00 0.00 3.62
1950 2168 2.308690 AGCATAGTACTCCCTCCGTTC 58.691 52.381 0.00 0.00 0.00 3.95
1951 2169 2.456073 AGCATAGTACTCCCTCCGTT 57.544 50.000 0.00 0.00 0.00 4.44
1999 2233 1.067212 ACGGATGGATCTCGTAAGCAC 59.933 52.381 0.00 0.00 33.91 4.40
2000 2234 1.399714 ACGGATGGATCTCGTAAGCA 58.600 50.000 0.00 0.00 33.91 3.91
2001 2235 2.395654 GAACGGATGGATCTCGTAAGC 58.604 52.381 0.00 0.00 34.34 3.09
2002 2236 2.288273 GGGAACGGATGGATCTCGTAAG 60.288 54.545 0.00 0.00 34.34 2.34
2034 4131 4.806342 AGTCGTGCGTCAAGTTATTTTT 57.194 36.364 0.00 0.00 0.00 1.94
2039 4136 3.182972 GCTTTTAGTCGTGCGTCAAGTTA 59.817 43.478 0.00 0.00 0.00 2.24
2077 4177 6.649141 TGATTGGTGCTGTTAAGTTGTACTAG 59.351 38.462 0.00 0.00 0.00 2.57
2080 4180 5.008217 TGTGATTGGTGCTGTTAAGTTGTAC 59.992 40.000 0.00 0.00 0.00 2.90
2081 4181 5.126779 TGTGATTGGTGCTGTTAAGTTGTA 58.873 37.500 0.00 0.00 0.00 2.41
2082 4182 3.951037 TGTGATTGGTGCTGTTAAGTTGT 59.049 39.130 0.00 0.00 0.00 3.32
2096 4196 3.004210 TCACGGTGTTCATTTGTGATTGG 59.996 43.478 8.17 0.00 34.85 3.16
2319 4459 2.985282 CACAAGCACCACCGGCAT 60.985 61.111 0.00 0.00 0.00 4.40
2409 4549 2.047844 CACGTCCTCCACAGGCAG 60.048 66.667 0.00 0.00 40.12 4.85
2580 4720 3.998672 GAGGACGTGTTCGGGCCA 61.999 66.667 4.39 0.00 41.85 5.36


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

AutoCloner maintained by Alex Coulton.