Multiple sequence alignment - TraesCS5D01G317400

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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 TraesCS5D01G317400 chr5D 100.000 2828 0 0 1 2828 410619331 410622158 0.000000e+00 5223.0
1 TraesCS5D01G317400 chr5D 88.010 834 82 12 977 1807 410490785 410491603 0.000000e+00 970.0
2 TraesCS5D01G317400 chr5D 88.840 681 70 5 2150 2828 186879553 186878877 0.000000e+00 832.0
3 TraesCS5D01G317400 chr5D 87.812 681 78 5 2150 2828 521961743 521962420 0.000000e+00 793.0
4 TraesCS5D01G317400 chr5D 89.567 393 41 0 1025 1417 410539180 410539572 1.510000e-137 499.0
5 TraesCS5D01G317400 chr5D 90.217 184 18 0 1611 1794 410679751 410679934 1.010000e-59 241.0
6 TraesCS5D01G317400 chr5D 90.506 158 12 1 1424 1578 410620709 410620866 3.690000e-49 206.0
7 TraesCS5D01G317400 chr5D 90.506 158 12 1 1379 1536 410620754 410620908 3.690000e-49 206.0
8 TraesCS5D01G317400 chr5A 93.794 1144 42 13 721 1854 522223460 522224584 0.000000e+00 1692.0
9 TraesCS5D01G317400 chr5A 93.078 679 47 0 2150 2828 522350149 522350827 0.000000e+00 994.0
10 TraesCS5D01G317400 chr5A 86.359 887 91 19 977 1856 522082717 522083580 0.000000e+00 941.0
11 TraesCS5D01G317400 chr5A 87.862 725 45 22 17 716 522222691 522223397 0.000000e+00 811.0
12 TraesCS5D01G317400 chr5A 90.749 454 42 0 966 1419 522425204 522425657 8.660000e-170 606.0
13 TraesCS5D01G317400 chr5A 89.894 188 19 0 1611 1798 522425690 522425877 2.810000e-60 243.0
14 TraesCS5D01G317400 chr5A 90.857 175 8 2 1989 2155 522224661 522224835 7.880000e-56 228.0
15 TraesCS5D01G317400 chr5A 80.000 205 33 6 1643 1843 522357148 522356948 8.170000e-31 145.0
16 TraesCS5D01G317400 chr5B 93.615 877 51 4 726 1601 493086994 493086122 0.000000e+00 1304.0
17 TraesCS5D01G317400 chr5B 95.734 586 25 0 2241 2826 492914565 492913980 0.000000e+00 944.0
18 TraesCS5D01G317400 chr5B 86.380 859 95 13 979 1835 492782477 492783315 0.000000e+00 918.0
19 TraesCS5D01G317400 chr5B 88.218 679 79 1 2150 2828 218321541 218322218 0.000000e+00 809.0
20 TraesCS5D01G317400 chr5B 92.797 472 19 4 1379 1849 493086295 493085838 0.000000e+00 669.0
21 TraesCS5D01G317400 chr5B 90.330 455 43 1 966 1419 493140518 493140972 1.880000e-166 595.0
22 TraesCS5D01G317400 chr5B 82.192 219 33 4 1379 1597 82243157 82242945 1.730000e-42 183.0
23 TraesCS5D01G317400 chr5B 96.000 50 2 0 667 716 493087108 493087059 6.490000e-12 82.4
24 TraesCS5D01G317400 chr7D 88.529 680 75 3 2150 2828 246554382 246555059 0.000000e+00 821.0
25 TraesCS5D01G317400 chr7D 87.776 679 79 4 2150 2828 477926118 477925444 0.000000e+00 791.0
26 TraesCS5D01G317400 chr2D 88.270 682 71 8 2150 2828 351889332 351890007 0.000000e+00 808.0
27 TraesCS5D01G317400 chr6D 87.812 681 75 7 2150 2828 264762103 264761429 0.000000e+00 791.0
28 TraesCS5D01G317400 chr1B 90.132 456 45 0 967 1422 562433872 562433417 6.750000e-166 593.0
29 TraesCS5D01G317400 chr1B 83.673 245 31 4 1617 1855 562433381 562433140 3.670000e-54 222.0


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 TraesCS5D01G317400 chr5D 410619331 410622158 2827 False 1878.333333 5223 93.670667 1 2828 3 chr5D.!!$F5 2827
1 TraesCS5D01G317400 chr5D 410490785 410491603 818 False 970.000000 970 88.010000 977 1807 1 chr5D.!!$F1 830
2 TraesCS5D01G317400 chr5D 186878877 186879553 676 True 832.000000 832 88.840000 2150 2828 1 chr5D.!!$R1 678
3 TraesCS5D01G317400 chr5D 521961743 521962420 677 False 793.000000 793 87.812000 2150 2828 1 chr5D.!!$F4 678
4 TraesCS5D01G317400 chr5A 522350149 522350827 678 False 994.000000 994 93.078000 2150 2828 1 chr5A.!!$F2 678
5 TraesCS5D01G317400 chr5A 522082717 522083580 863 False 941.000000 941 86.359000 977 1856 1 chr5A.!!$F1 879
6 TraesCS5D01G317400 chr5A 522222691 522224835 2144 False 910.333333 1692 90.837667 17 2155 3 chr5A.!!$F3 2138
7 TraesCS5D01G317400 chr5A 522425204 522425877 673 False 424.500000 606 90.321500 966 1798 2 chr5A.!!$F4 832
8 TraesCS5D01G317400 chr5B 492913980 492914565 585 True 944.000000 944 95.734000 2241 2826 1 chr5B.!!$R2 585
9 TraesCS5D01G317400 chr5B 492782477 492783315 838 False 918.000000 918 86.380000 979 1835 1 chr5B.!!$F2 856
10 TraesCS5D01G317400 chr5B 218321541 218322218 677 False 809.000000 809 88.218000 2150 2828 1 chr5B.!!$F1 678
11 TraesCS5D01G317400 chr5B 493085838 493087108 1270 True 685.133333 1304 94.137333 667 1849 3 chr5B.!!$R3 1182
12 TraesCS5D01G317400 chr7D 246554382 246555059 677 False 821.000000 821 88.529000 2150 2828 1 chr7D.!!$F1 678
13 TraesCS5D01G317400 chr7D 477925444 477926118 674 True 791.000000 791 87.776000 2150 2828 1 chr7D.!!$R1 678
14 TraesCS5D01G317400 chr2D 351889332 351890007 675 False 808.000000 808 88.270000 2150 2828 1 chr2D.!!$F1 678
15 TraesCS5D01G317400 chr6D 264761429 264762103 674 True 791.000000 791 87.812000 2150 2828 1 chr6D.!!$R1 678
16 TraesCS5D01G317400 chr1B 562433140 562433872 732 True 407.500000 593 86.902500 967 1855 2 chr1B.!!$R1 888

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
861 946 0.320683 TTCATGTGAGCGTGAGGGTG 60.321 55.0 0.0 0.0 41.18 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1977 2157 0.400213 AGAAGGCGACCAATGACCAA 59.6 50.0 0.0 0.0 0.0 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
126 131 8.856490 ATCACTTCAAATAAACAGTGTGTTTC 57.144 30.769 8.27 0.00 46.61 2.78
155 160 2.753055 AACAAAACGCAAAACCACCT 57.247 40.000 0.00 0.00 0.00 4.00
156 161 2.003196 ACAAAACGCAAAACCACCTG 57.997 45.000 0.00 0.00 0.00 4.00
162 167 1.546476 ACGCAAAACCACCTGAAAACA 59.454 42.857 0.00 0.00 0.00 2.83
178 183 7.549134 ACCTGAAAACAGAAAACCAGAAAAATC 59.451 33.333 0.00 0.00 0.00 2.17
189 194 4.312443 ACCAGAAAAATCGCTAGAAACGA 58.688 39.130 0.00 0.00 44.75 3.85
202 207 2.154427 GAAACGACAACGCACGGGAG 62.154 60.000 0.00 0.00 43.96 4.30
215 220 1.303317 CGGGAGAACAACTTGGGGG 60.303 63.158 0.00 0.00 0.00 5.40
216 221 1.851267 GGGAGAACAACTTGGGGGT 59.149 57.895 0.00 0.00 0.00 4.95
224 231 4.954970 ACTTGGGGGTGCAGTGCG 62.955 66.667 11.20 0.00 0.00 5.34
245 252 4.794439 CCATGTGCGGTCGCTCGA 62.794 66.667 16.36 4.81 42.51 4.04
247 254 2.583319 ATGTGCGGTCGCTCGATG 60.583 61.111 16.36 0.00 42.51 3.84
287 302 1.153842 CACAGCGCGACACATAGGA 60.154 57.895 12.10 0.00 0.00 2.94
297 312 0.629596 ACACATAGGAGGTCCCGAGA 59.370 55.000 0.00 0.00 40.87 4.04
334 350 0.988832 AAAGGGGTGCCGATACAGAA 59.011 50.000 0.00 0.00 0.00 3.02
360 376 7.450074 TGTTGCTGGAAGAAAGAAATAGAGTA 58.550 34.615 0.00 0.00 26.51 2.59
361 377 7.604164 TGTTGCTGGAAGAAAGAAATAGAGTAG 59.396 37.037 0.00 0.00 26.51 2.57
398 414 5.143369 GAGAGCCAATTTGGGATATTTCCT 58.857 41.667 17.03 2.86 42.20 3.36
400 416 5.966319 AGAGCCAATTTGGGATATTTCCTTT 59.034 36.000 17.03 0.00 42.20 3.11
440 462 1.615384 GCCTTGATCAGTGGGAAAGCT 60.615 52.381 15.66 0.00 0.00 3.74
479 501 2.094762 TTCTTAGGCACCGAAGAAGC 57.905 50.000 17.74 0.00 40.76 3.86
527 550 9.338622 CTCCAAAAATAGGTTCTATCCGTTAAT 57.661 33.333 0.00 0.00 0.00 1.40
529 552 8.899771 CCAAAAATAGGTTCTATCCGTTAATGT 58.100 33.333 0.00 0.00 0.00 2.71
575 598 2.170166 GGCACAACCTTGATTGGATCA 58.830 47.619 0.00 0.00 37.55 2.92
580 603 3.691118 ACAACCTTGATTGGATCACATCG 59.309 43.478 0.00 0.00 39.39 3.84
581 604 3.634397 ACCTTGATTGGATCACATCGT 57.366 42.857 0.00 0.00 39.39 3.73
582 605 4.753516 ACCTTGATTGGATCACATCGTA 57.246 40.909 0.00 0.00 39.39 3.43
583 606 5.296151 ACCTTGATTGGATCACATCGTAT 57.704 39.130 0.00 0.00 39.39 3.06
584 607 6.419484 ACCTTGATTGGATCACATCGTATA 57.581 37.500 0.00 0.00 39.39 1.47
585 608 6.223852 ACCTTGATTGGATCACATCGTATAC 58.776 40.000 0.00 0.00 39.39 1.47
588 611 7.542477 CCTTGATTGGATCACATCGTATACTAC 59.458 40.741 0.56 0.00 39.39 2.73
591 614 9.238368 TGATTGGATCACATCGTATACTACATA 57.762 33.333 0.56 0.00 33.59 2.29
618 641 1.084289 GATGTGGTCCAAAGTACGCC 58.916 55.000 0.00 0.00 0.00 5.68
624 647 3.692593 GTGGTCCAAAGTACGCCAATTAT 59.307 43.478 0.00 0.00 0.00 1.28
625 648 4.877251 GTGGTCCAAAGTACGCCAATTATA 59.123 41.667 0.00 0.00 0.00 0.98
626 649 5.529800 GTGGTCCAAAGTACGCCAATTATAT 59.470 40.000 0.00 0.00 0.00 0.86
627 650 5.529430 TGGTCCAAAGTACGCCAATTATATG 59.471 40.000 0.00 0.00 0.00 1.78
628 651 5.449304 GTCCAAAGTACGCCAATTATATGC 58.551 41.667 0.00 0.00 0.00 3.14
686 709 6.023435 CACATAAACAACCAATCTCATGTCG 58.977 40.000 0.00 0.00 0.00 4.35
825 906 4.445545 GAAAAGGACGCGCGCCAG 62.446 66.667 33.53 15.62 0.00 4.85
855 940 1.134075 GCTGCTTCATGTGAGCGTG 59.866 57.895 15.52 12.56 0.00 5.34
856 941 1.293963 GCTGCTTCATGTGAGCGTGA 61.294 55.000 15.52 0.00 38.74 4.35
858 943 0.671472 TGCTTCATGTGAGCGTGAGG 60.671 55.000 15.52 0.00 41.18 3.86
861 946 0.320683 TTCATGTGAGCGTGAGGGTG 60.321 55.000 0.00 0.00 41.18 4.61
994 1085 2.409651 GTCTCCACTAGCGCTCGG 59.590 66.667 16.34 14.18 0.00 4.63
1408 1502 1.204312 GTCGTGGCGTTCAAGAAGC 59.796 57.895 0.00 0.00 35.75 3.86
1425 1522 2.634815 AGCAGCAGATTATCCCAGTG 57.365 50.000 0.00 0.00 0.00 3.66
1470 1567 2.634815 AGCAGCAGATTATCCCAGTG 57.365 50.000 0.00 0.00 0.00 3.66
1546 1685 1.672356 GCGCTCCAGGAAAAGCAGA 60.672 57.895 0.00 0.00 38.45 4.26
1598 1746 2.343758 GCAGCAGGTTCCAGTCGA 59.656 61.111 0.00 0.00 0.00 4.20
1599 1747 2.029844 GCAGCAGGTTCCAGTCGAC 61.030 63.158 7.70 7.70 0.00 4.20
1600 1748 1.734477 CAGCAGGTTCCAGTCGACG 60.734 63.158 10.46 5.16 0.00 5.12
1601 1749 1.901948 AGCAGGTTCCAGTCGACGA 60.902 57.895 10.46 0.00 0.00 4.20
1644 1801 2.076863 AGCGCTCTGTTTTACATGTCC 58.923 47.619 2.64 0.00 0.00 4.02
1843 2010 9.116067 TGTTCAACTAATTTAGCAGTGTAAAGT 57.884 29.630 3.28 0.00 0.00 2.66
1854 2021 6.110411 AGCAGTGTAAAGTTGTACCATAGT 57.890 37.500 0.00 0.00 0.00 2.12
1855 2022 6.164176 AGCAGTGTAAAGTTGTACCATAGTC 58.836 40.000 0.00 0.00 0.00 2.59
1856 2023 5.350640 GCAGTGTAAAGTTGTACCATAGTCC 59.649 44.000 0.00 0.00 0.00 3.85
1857 2024 6.460781 CAGTGTAAAGTTGTACCATAGTCCA 58.539 40.000 0.00 0.00 0.00 4.02
1858 2025 7.103641 CAGTGTAAAGTTGTACCATAGTCCAT 58.896 38.462 0.00 0.00 0.00 3.41
1859 2026 8.255206 CAGTGTAAAGTTGTACCATAGTCCATA 58.745 37.037 0.00 0.00 0.00 2.74
1860 2027 8.475639 AGTGTAAAGTTGTACCATAGTCCATAG 58.524 37.037 0.00 0.00 0.00 2.23
1861 2028 8.472413 GTGTAAAGTTGTACCATAGTCCATAGA 58.528 37.037 0.00 0.00 0.00 1.98
1862 2029 9.209048 TGTAAAGTTGTACCATAGTCCATAGAT 57.791 33.333 0.00 0.00 0.00 1.98
1865 2032 9.435570 AAAGTTGTACCATAGTCCATAGATAGT 57.564 33.333 0.00 0.00 0.00 2.12
1866 2033 9.435570 AAGTTGTACCATAGTCCATAGATAGTT 57.564 33.333 0.00 0.00 0.00 2.24
1867 2034 8.861086 AGTTGTACCATAGTCCATAGATAGTTG 58.139 37.037 0.00 0.00 0.00 3.16
1868 2035 8.639761 GTTGTACCATAGTCCATAGATAGTTGT 58.360 37.037 0.00 0.00 0.00 3.32
1869 2036 8.178313 TGTACCATAGTCCATAGATAGTTGTG 57.822 38.462 0.00 0.00 0.00 3.33
1870 2037 7.783119 TGTACCATAGTCCATAGATAGTTGTGT 59.217 37.037 0.00 0.00 0.00 3.72
1871 2038 7.676683 ACCATAGTCCATAGATAGTTGTGTT 57.323 36.000 0.00 0.00 0.00 3.32
1872 2039 7.727181 ACCATAGTCCATAGATAGTTGTGTTC 58.273 38.462 0.00 0.00 0.00 3.18
1873 2040 7.565398 ACCATAGTCCATAGATAGTTGTGTTCT 59.435 37.037 0.00 0.00 0.00 3.01
1874 2041 8.424918 CCATAGTCCATAGATAGTTGTGTTCTT 58.575 37.037 0.00 0.00 0.00 2.52
1875 2042 9.823647 CATAGTCCATAGATAGTTGTGTTCTTT 57.176 33.333 0.00 0.00 0.00 2.52
1877 2044 8.779354 AGTCCATAGATAGTTGTGTTCTTTTC 57.221 34.615 0.00 0.00 0.00 2.29
1878 2045 8.375506 AGTCCATAGATAGTTGTGTTCTTTTCA 58.624 33.333 0.00 0.00 0.00 2.69
1879 2046 8.999431 GTCCATAGATAGTTGTGTTCTTTTCAA 58.001 33.333 0.00 0.00 0.00 2.69
1880 2047 9.739276 TCCATAGATAGTTGTGTTCTTTTCAAT 57.261 29.630 0.00 0.00 0.00 2.57
1885 2052 8.912988 AGATAGTTGTGTTCTTTTCAATTTGGA 58.087 29.630 0.00 0.00 0.00 3.53
1886 2053 9.185192 GATAGTTGTGTTCTTTTCAATTTGGAG 57.815 33.333 0.00 0.00 0.00 3.86
1887 2054 7.169158 AGTTGTGTTCTTTTCAATTTGGAGA 57.831 32.000 0.00 0.00 0.00 3.71
1888 2055 7.260603 AGTTGTGTTCTTTTCAATTTGGAGAG 58.739 34.615 0.00 0.00 0.00 3.20
1889 2056 7.122650 AGTTGTGTTCTTTTCAATTTGGAGAGA 59.877 33.333 0.00 0.00 0.00 3.10
1890 2057 7.403312 TGTGTTCTTTTCAATTTGGAGAGAA 57.597 32.000 6.57 6.57 0.00 2.87
1891 2058 7.835822 TGTGTTCTTTTCAATTTGGAGAGAAA 58.164 30.769 11.23 2.08 0.00 2.52
1892 2059 7.759433 TGTGTTCTTTTCAATTTGGAGAGAAAC 59.241 33.333 11.23 11.60 30.47 2.78
1893 2060 7.759433 GTGTTCTTTTCAATTTGGAGAGAAACA 59.241 33.333 11.23 9.42 30.47 2.83
1894 2061 7.759433 TGTTCTTTTCAATTTGGAGAGAAACAC 59.241 33.333 11.23 2.93 30.47 3.32
1895 2062 7.403312 TCTTTTCAATTTGGAGAGAAACACA 57.597 32.000 0.00 0.00 30.47 3.72
1896 2063 7.483307 TCTTTTCAATTTGGAGAGAAACACAG 58.517 34.615 0.00 0.00 30.47 3.66
1941 2121 2.403252 ATAAGCTCCCGGTTTGAGTG 57.597 50.000 0.00 0.00 32.31 3.51
1949 2129 1.333619 CCCGGTTTGAGTGTTTGTGAG 59.666 52.381 0.00 0.00 0.00 3.51
1951 2131 2.285083 CGGTTTGAGTGTTTGTGAGGA 58.715 47.619 0.00 0.00 0.00 3.71
1959 2139 2.447047 AGTGTTTGTGAGGAAGGGGATT 59.553 45.455 0.00 0.00 0.00 3.01
1960 2140 2.558359 GTGTTTGTGAGGAAGGGGATTG 59.442 50.000 0.00 0.00 0.00 2.67
1961 2141 1.546029 GTTTGTGAGGAAGGGGATTGC 59.454 52.381 0.00 0.00 0.00 3.56
1962 2142 0.776810 TTGTGAGGAAGGGGATTGCA 59.223 50.000 0.00 0.00 0.00 4.08
1963 2143 1.002069 TGTGAGGAAGGGGATTGCAT 58.998 50.000 0.00 0.00 0.00 3.96
1964 2144 2.204463 TGTGAGGAAGGGGATTGCATA 58.796 47.619 0.00 0.00 0.00 3.14
1965 2145 2.785269 TGTGAGGAAGGGGATTGCATAT 59.215 45.455 0.00 0.00 0.00 1.78
1966 2146 3.205056 TGTGAGGAAGGGGATTGCATATT 59.795 43.478 0.00 0.00 0.00 1.28
1967 2147 4.415179 TGTGAGGAAGGGGATTGCATATTA 59.585 41.667 0.00 0.00 0.00 0.98
1968 2148 4.762251 GTGAGGAAGGGGATTGCATATTAC 59.238 45.833 0.00 0.00 0.00 1.89
1969 2149 4.415179 TGAGGAAGGGGATTGCATATTACA 59.585 41.667 0.00 0.00 0.00 2.41
1970 2150 4.729868 AGGAAGGGGATTGCATATTACAC 58.270 43.478 0.00 0.00 0.00 2.90
1971 2151 3.826729 GGAAGGGGATTGCATATTACACC 59.173 47.826 0.00 0.00 0.00 4.16
1972 2152 4.469657 GAAGGGGATTGCATATTACACCA 58.530 43.478 0.00 0.00 0.00 4.17
1973 2153 4.534647 AGGGGATTGCATATTACACCAA 57.465 40.909 0.00 0.00 0.00 3.67
1974 2154 5.078683 AGGGGATTGCATATTACACCAAT 57.921 39.130 0.00 0.00 0.00 3.16
1975 2155 5.466819 AGGGGATTGCATATTACACCAATT 58.533 37.500 0.00 0.00 0.00 2.32
1976 2156 6.619464 AGGGGATTGCATATTACACCAATTA 58.381 36.000 0.00 0.00 0.00 1.40
1977 2157 7.248237 AGGGGATTGCATATTACACCAATTAT 58.752 34.615 0.00 0.00 0.00 1.28
1978 2158 7.734410 AGGGGATTGCATATTACACCAATTATT 59.266 33.333 0.00 0.00 0.00 1.40
1979 2159 7.818930 GGGGATTGCATATTACACCAATTATTG 59.181 37.037 0.00 0.00 0.00 1.90
2023 2203 4.522789 TGATTTGGGAAAAACAGAGTAGGC 59.477 41.667 0.00 0.00 0.00 3.93
2028 2208 1.804748 GAAAAACAGAGTAGGCGGTGG 59.195 52.381 0.00 0.00 0.00 4.61
2065 2248 4.828829 AGTAGTATTTGTCAAGTTCCCGG 58.171 43.478 0.00 0.00 0.00 5.73
2067 2250 4.094830 AGTATTTGTCAAGTTCCCGGTT 57.905 40.909 0.00 0.00 0.00 4.44
2068 2251 4.466827 AGTATTTGTCAAGTTCCCGGTTT 58.533 39.130 0.00 0.00 0.00 3.27
2069 2252 4.517832 AGTATTTGTCAAGTTCCCGGTTTC 59.482 41.667 0.00 0.00 0.00 2.78
2070 2253 2.721425 TTGTCAAGTTCCCGGTTTCT 57.279 45.000 0.00 0.00 0.00 2.52
2071 2254 3.842007 TTGTCAAGTTCCCGGTTTCTA 57.158 42.857 0.00 0.00 0.00 2.10
2072 2255 3.116079 TGTCAAGTTCCCGGTTTCTAC 57.884 47.619 0.00 0.00 0.00 2.59
2074 2257 3.135167 TGTCAAGTTCCCGGTTTCTACTT 59.865 43.478 0.00 0.00 0.00 2.24
2076 2259 4.212847 GTCAAGTTCCCGGTTTCTACTTTC 59.787 45.833 0.00 0.00 0.00 2.62
2099 2287 3.665173 GCGAAAGGCTAGATTGTTCAG 57.335 47.619 0.00 0.00 39.11 3.02
2118 2306 8.192068 TGTTCAGTACATCAATTATTGGTACG 57.808 34.615 14.27 11.13 39.33 3.67
2128 2316 4.996788 ATTATTGGTACGGAACTCGAGT 57.003 40.909 13.58 13.58 42.43 4.18
2132 2320 2.715046 TGGTACGGAACTCGAGTGTAT 58.285 47.619 20.85 2.73 42.43 2.29
2178 2366 9.146984 CATTATGTTTTGAGATTGATGTTGCTT 57.853 29.630 0.00 0.00 0.00 3.91
2203 2391 3.441572 ACTTTGCTATGCTTAGTGCTTGG 59.558 43.478 8.30 0.00 43.37 3.61
2303 2491 7.959689 ATCTGCTAGTTATATGCACTTCTTG 57.040 36.000 0.00 0.00 32.91 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 9.698309 TGTGAACATTTTCTAAAAAGTTTGTGA 57.302 25.926 9.39 0.00 39.16 3.58
135 140 2.739379 CAGGTGGTTTTGCGTTTTGTTT 59.261 40.909 0.00 0.00 0.00 2.83
136 141 2.028930 TCAGGTGGTTTTGCGTTTTGTT 60.029 40.909 0.00 0.00 0.00 2.83
137 142 1.546476 TCAGGTGGTTTTGCGTTTTGT 59.454 42.857 0.00 0.00 0.00 2.83
155 160 6.035542 GCGATTTTTCTGGTTTTCTGTTTTCA 59.964 34.615 0.00 0.00 0.00 2.69
156 161 6.255670 AGCGATTTTTCTGGTTTTCTGTTTTC 59.744 34.615 0.00 0.00 0.00 2.29
162 167 6.877611 TTCTAGCGATTTTTCTGGTTTTCT 57.122 33.333 0.00 0.00 0.00 2.52
178 183 0.179282 GTGCGTTGTCGTTTCTAGCG 60.179 55.000 0.00 0.00 39.49 4.26
189 194 1.153329 TTGTTCTCCCGTGCGTTGT 60.153 52.632 0.00 0.00 0.00 3.32
202 207 0.755327 ACTGCACCCCCAAGTTGTTC 60.755 55.000 1.45 0.00 0.00 3.18
215 220 3.434319 CATGGGACCGCACTGCAC 61.434 66.667 1.11 0.00 0.00 4.57
216 221 3.952508 ACATGGGACCGCACTGCA 61.953 61.111 1.11 0.00 0.00 4.41
318 333 0.180406 ACATTCTGTATCGGCACCCC 59.820 55.000 0.00 0.00 0.00 4.95
328 344 5.620206 TCTTTCTTCCAGCAACATTCTGTA 58.380 37.500 0.00 0.00 0.00 2.74
334 350 6.944862 ACTCTATTTCTTTCTTCCAGCAACAT 59.055 34.615 0.00 0.00 0.00 2.71
400 416 0.106419 ACGCAAAGGAGACCCCAAAA 60.106 50.000 0.00 0.00 37.41 2.44
403 419 2.429930 CACGCAAAGGAGACCCCA 59.570 61.111 0.00 0.00 37.41 4.96
404 420 3.056328 GCACGCAAAGGAGACCCC 61.056 66.667 0.00 0.00 0.00 4.95
405 421 3.056328 GGCACGCAAAGGAGACCC 61.056 66.667 0.00 0.00 0.00 4.46
406 422 1.600916 AAGGCACGCAAAGGAGACC 60.601 57.895 0.00 0.00 0.00 3.85
440 462 4.162320 AGAATATCCGAGCAGAAGTTGGAA 59.838 41.667 0.00 0.00 31.42 3.53
444 466 5.740513 GCCTAAGAATATCCGAGCAGAAGTT 60.741 44.000 0.00 0.00 0.00 2.66
446 468 4.241681 GCCTAAGAATATCCGAGCAGAAG 58.758 47.826 0.00 0.00 0.00 2.85
479 501 4.084013 AGAGGTTTGTCATTTTCGTAAGCG 60.084 41.667 0.00 0.00 39.92 4.68
527 550 2.422597 CTCTTTTATGGTCACCGCACA 58.577 47.619 0.00 0.00 0.00 4.57
529 552 1.948611 GCCTCTTTTATGGTCACCGCA 60.949 52.381 0.00 0.00 0.00 5.69
618 641 7.481483 CGACCACATATTTTCCGCATATAATTG 59.519 37.037 0.00 0.00 0.00 2.32
624 647 3.135225 CCGACCACATATTTTCCGCATA 58.865 45.455 0.00 0.00 0.00 3.14
625 648 1.946768 CCGACCACATATTTTCCGCAT 59.053 47.619 0.00 0.00 0.00 4.73
626 649 1.374560 CCGACCACATATTTTCCGCA 58.625 50.000 0.00 0.00 0.00 5.69
627 650 0.028902 GCCGACCACATATTTTCCGC 59.971 55.000 0.00 0.00 0.00 5.54
628 651 1.330521 CTGCCGACCACATATTTTCCG 59.669 52.381 0.00 0.00 0.00 4.30
630 653 2.030457 CGACTGCCGACCACATATTTTC 59.970 50.000 0.00 0.00 41.76 2.29
631 654 2.006888 CGACTGCCGACCACATATTTT 58.993 47.619 0.00 0.00 41.76 1.82
632 655 1.206132 TCGACTGCCGACCACATATTT 59.794 47.619 0.00 0.00 43.23 1.40
719 742 3.637273 ACAAGGACCCACGGAGCC 61.637 66.667 0.00 0.00 0.00 4.70
765 846 5.674525 CCACTCAAATATCTTGGCTGTCTA 58.325 41.667 0.00 0.00 0.00 2.59
855 940 2.430921 CGCGTCACTCACACCCTC 60.431 66.667 0.00 0.00 0.00 4.30
856 941 4.664677 GCGCGTCACTCACACCCT 62.665 66.667 8.43 0.00 0.00 4.34
858 943 2.558554 ATAGGCGCGTCACTCACACC 62.559 60.000 15.58 0.00 0.00 4.16
861 946 2.414293 CCTATATAGGCGCGTCACTCAC 60.414 54.545 15.58 0.00 36.53 3.51
896 982 2.900546 TGAGAACTGAGAAGAAGGGGAC 59.099 50.000 0.00 0.00 0.00 4.46
947 1034 1.300931 TCGCTGTGTGCTGAGAACC 60.301 57.895 0.00 0.00 40.11 3.62
994 1085 3.195698 GGCGACGTCCATCTTGGC 61.196 66.667 10.58 5.35 37.47 4.52
1038 1129 4.729918 GTCCTGTGCCCCTGCTGG 62.730 72.222 1.89 1.89 38.71 4.85
1402 1496 3.201708 ACTGGGATAATCTGCTGCTTCTT 59.798 43.478 0.00 0.00 0.00 2.52
1408 1502 1.602311 GCCACTGGGATAATCTGCTG 58.398 55.000 0.00 0.00 35.59 4.41
1540 1679 2.586792 GGCGACTGGGATCTGCTT 59.413 61.111 0.00 0.00 0.00 3.91
1854 2021 9.739276 ATTGAAAAGAACACAACTATCTATGGA 57.261 29.630 0.00 0.00 0.00 3.41
1859 2026 8.912988 TCCAAATTGAAAAGAACACAACTATCT 58.087 29.630 0.00 0.00 0.00 1.98
1860 2027 9.185192 CTCCAAATTGAAAAGAACACAACTATC 57.815 33.333 0.00 0.00 0.00 2.08
1861 2028 8.912988 TCTCCAAATTGAAAAGAACACAACTAT 58.087 29.630 0.00 0.00 0.00 2.12
1862 2029 8.287439 TCTCCAAATTGAAAAGAACACAACTA 57.713 30.769 0.00 0.00 0.00 2.24
1863 2030 7.122650 TCTCTCCAAATTGAAAAGAACACAACT 59.877 33.333 0.00 0.00 0.00 3.16
1864 2031 7.257722 TCTCTCCAAATTGAAAAGAACACAAC 58.742 34.615 0.00 0.00 0.00 3.32
1865 2032 7.403312 TCTCTCCAAATTGAAAAGAACACAA 57.597 32.000 0.00 0.00 0.00 3.33
1866 2033 7.403312 TTCTCTCCAAATTGAAAAGAACACA 57.597 32.000 0.00 0.00 0.00 3.72
1867 2034 7.759433 TGTTTCTCTCCAAATTGAAAAGAACAC 59.241 33.333 0.00 3.29 31.47 3.32
1868 2035 7.759433 GTGTTTCTCTCCAAATTGAAAAGAACA 59.241 33.333 0.00 0.00 31.47 3.18
1869 2036 7.759433 TGTGTTTCTCTCCAAATTGAAAAGAAC 59.241 33.333 0.00 0.00 31.47 3.01
1870 2037 7.835822 TGTGTTTCTCTCCAAATTGAAAAGAA 58.164 30.769 0.00 0.00 31.47 2.52
1871 2038 7.122650 ACTGTGTTTCTCTCCAAATTGAAAAGA 59.877 33.333 0.00 0.00 31.47 2.52
1872 2039 7.260603 ACTGTGTTTCTCTCCAAATTGAAAAG 58.739 34.615 0.00 0.00 31.47 2.27
1873 2040 7.169158 ACTGTGTTTCTCTCCAAATTGAAAA 57.831 32.000 0.00 0.00 31.47 2.29
1874 2041 6.773976 ACTGTGTTTCTCTCCAAATTGAAA 57.226 33.333 0.00 0.00 0.00 2.69
1875 2042 6.017109 GCTACTGTGTTTCTCTCCAAATTGAA 60.017 38.462 0.00 0.00 0.00 2.69
1876 2043 5.470098 GCTACTGTGTTTCTCTCCAAATTGA 59.530 40.000 0.00 0.00 0.00 2.57
1877 2044 5.239306 TGCTACTGTGTTTCTCTCCAAATTG 59.761 40.000 0.00 0.00 0.00 2.32
1878 2045 5.376625 TGCTACTGTGTTTCTCTCCAAATT 58.623 37.500 0.00 0.00 0.00 1.82
1879 2046 4.973168 TGCTACTGTGTTTCTCTCCAAAT 58.027 39.130 0.00 0.00 0.00 2.32
1880 2047 4.415881 TGCTACTGTGTTTCTCTCCAAA 57.584 40.909 0.00 0.00 0.00 3.28
1881 2048 4.284490 AGATGCTACTGTGTTTCTCTCCAA 59.716 41.667 0.00 0.00 0.00 3.53
1882 2049 3.834813 AGATGCTACTGTGTTTCTCTCCA 59.165 43.478 0.00 0.00 0.00 3.86
1883 2050 4.464069 AGATGCTACTGTGTTTCTCTCC 57.536 45.455 0.00 0.00 0.00 3.71
1884 2051 5.233988 ACAAGATGCTACTGTGTTTCTCTC 58.766 41.667 0.00 0.00 0.00 3.20
1885 2052 5.220710 ACAAGATGCTACTGTGTTTCTCT 57.779 39.130 0.00 0.00 0.00 3.10
1886 2053 5.106908 GGAACAAGATGCTACTGTGTTTCTC 60.107 44.000 0.00 0.00 32.75 2.87
1887 2054 4.757149 GGAACAAGATGCTACTGTGTTTCT 59.243 41.667 0.00 0.00 32.75 2.52
1888 2055 4.757149 AGGAACAAGATGCTACTGTGTTTC 59.243 41.667 0.00 0.00 32.75 2.78
1889 2056 4.718961 AGGAACAAGATGCTACTGTGTTT 58.281 39.130 0.00 0.00 32.75 2.83
1890 2057 4.357918 AGGAACAAGATGCTACTGTGTT 57.642 40.909 0.00 0.00 35.20 3.32
1891 2058 4.319177 GAAGGAACAAGATGCTACTGTGT 58.681 43.478 0.00 0.00 0.00 3.72
1892 2059 3.369147 CGAAGGAACAAGATGCTACTGTG 59.631 47.826 0.00 0.00 0.00 3.66
1893 2060 3.006967 ACGAAGGAACAAGATGCTACTGT 59.993 43.478 0.00 0.00 0.00 3.55
1894 2061 3.589988 ACGAAGGAACAAGATGCTACTG 58.410 45.455 0.00 0.00 0.00 2.74
1895 2062 3.963428 ACGAAGGAACAAGATGCTACT 57.037 42.857 0.00 0.00 0.00 2.57
1896 2063 3.746492 ACAACGAAGGAACAAGATGCTAC 59.254 43.478 0.00 0.00 0.00 3.58
1941 2121 1.546029 GCAATCCCCTTCCTCACAAAC 59.454 52.381 0.00 0.00 0.00 2.93
1949 2129 3.826729 GGTGTAATATGCAATCCCCTTCC 59.173 47.826 0.00 0.00 0.00 3.46
1951 2131 4.534647 TGGTGTAATATGCAATCCCCTT 57.465 40.909 0.00 0.00 0.00 3.95
1971 2151 3.381272 AGGCGACCAATGACCAATAATTG 59.619 43.478 0.00 0.00 34.26 2.32
1972 2152 3.631250 AGGCGACCAATGACCAATAATT 58.369 40.909 0.00 0.00 0.00 1.40
1973 2153 3.297134 AGGCGACCAATGACCAATAAT 57.703 42.857 0.00 0.00 0.00 1.28
1974 2154 2.799126 AGGCGACCAATGACCAATAA 57.201 45.000 0.00 0.00 0.00 1.40
1975 2155 2.238646 AGAAGGCGACCAATGACCAATA 59.761 45.455 0.00 0.00 0.00 1.90
1976 2156 1.004745 AGAAGGCGACCAATGACCAAT 59.995 47.619 0.00 0.00 0.00 3.16
1977 2157 0.400213 AGAAGGCGACCAATGACCAA 59.600 50.000 0.00 0.00 0.00 3.67
1978 2158 0.400213 AAGAAGGCGACCAATGACCA 59.600 50.000 0.00 0.00 0.00 4.02
1979 2159 1.087501 GAAGAAGGCGACCAATGACC 58.912 55.000 0.00 0.00 0.00 4.02
1980 2160 1.087501 GGAAGAAGGCGACCAATGAC 58.912 55.000 0.00 0.00 0.00 3.06
1981 2161 0.984230 AGGAAGAAGGCGACCAATGA 59.016 50.000 0.00 0.00 0.00 2.57
1982 2162 1.089920 CAGGAAGAAGGCGACCAATG 58.910 55.000 0.00 0.00 0.00 2.82
1983 2163 0.984230 TCAGGAAGAAGGCGACCAAT 59.016 50.000 0.00 0.00 0.00 3.16
1984 2164 0.984230 ATCAGGAAGAAGGCGACCAA 59.016 50.000 0.00 0.00 0.00 3.67
1985 2165 0.984230 AATCAGGAAGAAGGCGACCA 59.016 50.000 0.00 0.00 0.00 4.02
1986 2166 1.740025 CAAATCAGGAAGAAGGCGACC 59.260 52.381 0.00 0.00 0.00 4.79
1987 2167 1.740025 CCAAATCAGGAAGAAGGCGAC 59.260 52.381 0.00 0.00 0.00 5.19
2023 2203 2.128771 ATGAATGAAGGAACCCACCG 57.871 50.000 0.00 0.00 34.73 4.94
2028 2208 9.614792 ACAAATACTACTATGAATGAAGGAACC 57.385 33.333 0.00 0.00 0.00 3.62
2074 2257 0.539986 AATCTAGCCTTTCGCCCGAA 59.460 50.000 0.00 0.00 38.78 4.30
2076 2259 0.462047 ACAATCTAGCCTTTCGCCCG 60.462 55.000 0.00 0.00 38.78 6.13
2099 2287 7.306399 CGAGTTCCGTACCAATAATTGATGTAC 60.306 40.741 0.00 0.00 0.00 2.90
2118 2306 3.242969 TGCACGATATACACTCGAGTTCC 60.243 47.826 17.26 0.00 39.38 3.62
2128 2316 2.661718 TCCTGGAGTGCACGATATACA 58.338 47.619 12.01 0.00 0.00 2.29
2132 2320 1.412710 GGATTCCTGGAGTGCACGATA 59.587 52.381 12.01 0.25 0.00 2.92
2203 2391 3.833304 GCACTCAGGCCCTAATGC 58.167 61.111 0.00 0.59 0.00 3.56
2270 2458 8.253810 TGCATATAACTAGCAGATAGGATCAAC 58.746 37.037 0.00 0.00 35.63 3.18
2303 2491 2.745821 GGGGTCTACGGATCAAAACAAC 59.254 50.000 0.00 0.00 0.00 3.32
2404 2596 7.057264 GCCTCCTTTTAATAGAGAACCAGAAT 58.943 38.462 0.00 0.00 0.00 2.40
2549 2742 5.221402 TGCACAATAGCTCCAATTCAACAAA 60.221 36.000 0.00 0.00 34.99 2.83


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

AutoCloner maintained by Alex Coulton.