Multiple sequence alignment - TraesCS5D01G026400

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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 TraesCS5D01G026400 chr5D 100.000 2411 0 0 1 2411 23870019 23872429 0.000000e+00 4453.0
1 TraesCS5D01G026400 chr5D 91.001 1389 73 30 298 1664 525387815 525389173 0.000000e+00 1825.0
2 TraesCS5D01G026400 chr5D 89.197 685 35 17 1729 2411 525389188 525389835 0.000000e+00 819.0
3 TraesCS5D01G026400 chr5D 84.169 379 42 10 1039 1411 525317398 525317764 3.810000e-93 351.0
4 TraesCS5D01G026400 chr5D 82.804 378 42 13 998 1356 525226906 525226533 1.390000e-82 316.0
5 TraesCS5D01G026400 chr5D 80.749 374 45 12 1001 1356 525189094 525188730 1.420000e-67 267.0
6 TraesCS5D01G026400 chr5D 81.232 341 24 12 1 306 525381448 525381783 3.100000e-59 239.0
7 TraesCS5D01G026400 chr5B 86.917 1544 103 48 180 1664 659747353 659748856 0.000000e+00 1640.0
8 TraesCS5D01G026400 chr5B 78.805 519 76 20 1920 2411 538045537 538045026 3.870000e-83 318.0
9 TraesCS5D01G026400 chr5B 78.756 386 54 16 1001 1368 659557544 659557169 1.440000e-57 233.0
10 TraesCS5D01G026400 chr5B 85.946 185 14 5 1 185 659747149 659747321 1.140000e-43 187.0
11 TraesCS5D01G026400 chr5A 88.418 1226 82 27 473 1663 651790618 651791818 0.000000e+00 1423.0
12 TraesCS5D01G026400 chr5A 84.450 373 46 3 1039 1411 651755107 651755467 8.200000e-95 357.0
13 TraesCS5D01G026400 chr5A 84.140 372 41 8 1046 1411 651635600 651635959 6.380000e-91 344.0
14 TraesCS5D01G026400 chr5A 82.677 381 41 15 998 1360 651569680 651569307 5.000000e-82 315.0
15 TraesCS5D01G026400 chr5A 82.292 384 47 10 1037 1411 651588641 651589012 1.800000e-81 313.0
16 TraesCS5D01G026400 chr5A 81.117 376 52 13 998 1356 651564362 651563989 1.410000e-72 283.0
17 TraesCS5D01G026400 chr5A 89.000 200 8 6 186 377 651790388 651790581 4.010000e-58 235.0
18 TraesCS5D01G026400 chr5A 86.782 174 14 8 1746 1915 651791839 651792007 4.090000e-43 185.0
19 TraesCS5D01G026400 chr3B 80.732 519 66 17 1920 2411 753267366 753267877 8.140000e-100 374.0
20 TraesCS5D01G026400 chr3B 78.817 524 76 20 1915 2411 825014271 825013756 1.080000e-83 320.0
21 TraesCS5D01G026400 chr3B 84.536 291 35 5 1920 2209 59683168 59683449 1.830000e-71 279.0
22 TraesCS5D01G026400 chr7B 80.422 521 66 21 1920 2411 707963137 707963650 4.900000e-97 364.0
23 TraesCS5D01G026400 chrUn 78.435 524 78 20 1915 2411 158073743 158073228 2.330000e-80 309.0
24 TraesCS5D01G026400 chr6B 78.269 520 77 19 1921 2411 706516530 706517042 3.900000e-78 302.0
25 TraesCS5D01G026400 chr6B 82.215 298 38 9 1920 2209 197228702 197228992 2.390000e-60 243.0
26 TraesCS5D01G026400 chr6B 88.119 202 24 0 2210 2411 710910615 710910816 8.610000e-60 241.0
27 TraesCS5D01G026400 chr6B 81.017 295 43 9 1919 2208 584085125 584084839 3.120000e-54 222.0
28 TraesCS5D01G026400 chr7D 77.438 523 78 22 1920 2411 3463963 3464476 2.360000e-70 276.0
29 TraesCS5D01G026400 chr2B 83.219 292 40 6 1920 2209 779162968 779163252 2.380000e-65 259.0
30 TraesCS5D01G026400 chr4B 89.109 202 22 0 2210 2411 562615510 562615711 3.980000e-63 252.0
31 TraesCS5D01G026400 chr4B 80.678 295 46 8 1918 2209 541847237 541846951 4.040000e-53 219.0
32 TraesCS5D01G026400 chr6D 82.534 292 44 4 1919 2209 456302337 456302052 1.430000e-62 250.0
33 TraesCS5D01G026400 chr3A 82.034 295 33 13 1920 2209 163905859 163905580 1.440000e-57 233.0
34 TraesCS5D01G026400 chr2D 87.192 203 24 2 2210 2411 575827427 575827628 1.860000e-56 230.0
35 TraesCS5D01G026400 chr1D 100.000 28 0 0 1558 1585 124712914 124712941 4.000000e-03 52.8


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 TraesCS5D01G026400 chr5D 23870019 23872429 2410 False 4453.000000 4453 100.000000 1 2411 1 chr5D.!!$F1 2410
1 TraesCS5D01G026400 chr5D 525387815 525389835 2020 False 1322.000000 1825 90.099000 298 2411 2 chr5D.!!$F4 2113
2 TraesCS5D01G026400 chr5B 659747149 659748856 1707 False 913.500000 1640 86.431500 1 1664 2 chr5B.!!$F1 1663
3 TraesCS5D01G026400 chr5B 538045026 538045537 511 True 318.000000 318 78.805000 1920 2411 1 chr5B.!!$R1 491
4 TraesCS5D01G026400 chr5A 651790388 651792007 1619 False 614.333333 1423 88.066667 186 1915 3 chr5A.!!$F4 1729
5 TraesCS5D01G026400 chr3B 753267366 753267877 511 False 374.000000 374 80.732000 1920 2411 1 chr3B.!!$F2 491
6 TraesCS5D01G026400 chr3B 825013756 825014271 515 True 320.000000 320 78.817000 1915 2411 1 chr3B.!!$R1 496
7 TraesCS5D01G026400 chr7B 707963137 707963650 513 False 364.000000 364 80.422000 1920 2411 1 chr7B.!!$F1 491
8 TraesCS5D01G026400 chrUn 158073228 158073743 515 True 309.000000 309 78.435000 1915 2411 1 chrUn.!!$R1 496
9 TraesCS5D01G026400 chr6B 706516530 706517042 512 False 302.000000 302 78.269000 1921 2411 1 chr6B.!!$F2 490
10 TraesCS5D01G026400 chr7D 3463963 3464476 513 False 276.000000 276 77.438000 1920 2411 1 chr7D.!!$F1 491

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
383 433 0.099968 TGCCTATTCTCGTTCGACGG 59.9 55.0 0.0 0.0 42.81 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1674 1839 0.251165 AAATGGGACTTGGGACACCG 60.251 55.0 0.0 0.0 39.29 4.94 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
31 32 2.034432 TGGTGTGTACGTACGTCAATGT 59.966 45.455 26.53 0.86 0.00 2.71
36 37 2.727278 TGTACGTACGTCAATGTGCAAG 59.273 45.455 26.53 0.00 29.52 4.01
51 52 5.880054 TGTGCAAGGAATTTCTTACTAGC 57.120 39.130 0.00 0.00 0.00 3.42
56 57 5.358160 GCAAGGAATTTCTTACTAGCACCAT 59.642 40.000 0.00 0.00 0.00 3.55
64 65 5.531122 TCTTACTAGCACCATACATGTCC 57.469 43.478 0.00 0.00 0.00 4.02
65 66 4.344102 TCTTACTAGCACCATACATGTCCC 59.656 45.833 0.00 0.00 0.00 4.46
66 67 2.477245 ACTAGCACCATACATGTCCCA 58.523 47.619 0.00 0.00 0.00 4.37
67 68 2.170607 ACTAGCACCATACATGTCCCAC 59.829 50.000 0.00 0.00 0.00 4.61
74 75 4.094294 CACCATACATGTCCCACGTTTTAG 59.906 45.833 0.00 0.00 0.00 1.85
86 87 6.091305 GTCCCACGTTTTAGAATTAGTACCAC 59.909 42.308 0.00 0.00 0.00 4.16
100 101 2.834549 AGTACCACACCTGATCCTCAAG 59.165 50.000 0.00 0.00 0.00 3.02
102 103 2.338809 ACCACACCTGATCCTCAAGAA 58.661 47.619 0.00 0.00 0.00 2.52
106 107 4.217118 CCACACCTGATCCTCAAGAAAAAG 59.783 45.833 0.00 0.00 0.00 2.27
107 108 5.065914 CACACCTGATCCTCAAGAAAAAGA 58.934 41.667 0.00 0.00 0.00 2.52
108 109 5.532406 CACACCTGATCCTCAAGAAAAAGAA 59.468 40.000 0.00 0.00 0.00 2.52
109 110 6.039717 CACACCTGATCCTCAAGAAAAAGAAA 59.960 38.462 0.00 0.00 0.00 2.52
110 111 6.607198 ACACCTGATCCTCAAGAAAAAGAAAA 59.393 34.615 0.00 0.00 0.00 2.29
111 112 7.124147 ACACCTGATCCTCAAGAAAAAGAAAAA 59.876 33.333 0.00 0.00 0.00 1.94
112 113 7.650903 CACCTGATCCTCAAGAAAAAGAAAAAG 59.349 37.037 0.00 0.00 0.00 2.27
113 114 7.561356 ACCTGATCCTCAAGAAAAAGAAAAAGA 59.439 33.333 0.00 0.00 0.00 2.52
114 115 8.416329 CCTGATCCTCAAGAAAAAGAAAAAGAA 58.584 33.333 0.00 0.00 0.00 2.52
115 116 9.978044 CTGATCCTCAAGAAAAAGAAAAAGAAT 57.022 29.630 0.00 0.00 0.00 2.40
171 172 2.583868 ACACGAAACACGCTCGCA 60.584 55.556 0.00 0.00 46.94 5.10
177 178 2.695712 GAAACACGCTCGCACACACC 62.696 60.000 0.00 0.00 0.00 4.16
252 290 1.314730 ACAAGTAAACAAGCCCACGG 58.685 50.000 0.00 0.00 0.00 4.94
368 418 1.320344 TAGTCTGGTTCGCGATGCCT 61.320 55.000 24.29 12.14 0.00 4.75
374 424 1.140816 GGTTCGCGATGCCTATTCTC 58.859 55.000 10.88 0.00 0.00 2.87
375 425 0.778815 GTTCGCGATGCCTATTCTCG 59.221 55.000 10.88 0.00 35.57 4.04
376 426 0.384309 TTCGCGATGCCTATTCTCGT 59.616 50.000 10.88 0.00 34.96 4.18
377 427 0.384309 TCGCGATGCCTATTCTCGTT 59.616 50.000 3.71 0.00 34.96 3.85
378 428 0.778815 CGCGATGCCTATTCTCGTTC 59.221 55.000 0.00 0.00 34.96 3.95
379 429 0.778815 GCGATGCCTATTCTCGTTCG 59.221 55.000 0.00 0.00 34.96 3.95
380 430 1.599667 GCGATGCCTATTCTCGTTCGA 60.600 52.381 0.00 0.00 34.96 3.71
381 431 2.044860 CGATGCCTATTCTCGTTCGAC 58.955 52.381 0.00 0.00 0.00 4.20
382 432 2.044860 GATGCCTATTCTCGTTCGACG 58.955 52.381 0.00 0.00 44.19 5.12
383 433 0.099968 TGCCTATTCTCGTTCGACGG 59.900 55.000 0.00 0.00 42.81 4.79
384 434 0.594284 GCCTATTCTCGTTCGACGGG 60.594 60.000 0.00 4.58 44.98 5.28
385 435 0.594284 CCTATTCTCGTTCGACGGGC 60.594 60.000 0.00 0.00 42.90 6.13
386 436 0.928908 CTATTCTCGTTCGACGGGCG 60.929 60.000 0.00 0.00 42.90 6.13
387 437 2.924922 TATTCTCGTTCGACGGGCGC 62.925 60.000 0.00 0.00 42.90 6.53
408 480 0.469331 AGACCACGTCTCCTTGGTGA 60.469 55.000 0.00 0.00 46.56 4.02
731 828 2.046892 CAAGGGTGACTCCTGGCG 60.047 66.667 0.00 0.00 37.20 5.69
1421 1571 7.043961 AGCTGTTCGTCTAGATTGATGAATA 57.956 36.000 0.00 0.50 41.94 1.75
1422 1572 7.665690 AGCTGTTCGTCTAGATTGATGAATAT 58.334 34.615 0.00 0.00 41.94 1.28
1424 1574 8.768955 GCTGTTCGTCTAGATTGATGAATATTT 58.231 33.333 0.00 0.00 41.94 1.40
1459 1615 7.079182 AGTTCTAGTACAGAGTTCTTGATCG 57.921 40.000 2.11 0.00 33.83 3.69
1463 1619 3.444388 AGTACAGAGTTCTTGATCGACCC 59.556 47.826 0.00 0.00 0.00 4.46
1472 1628 0.108992 TTGATCGACCCGTGTAGTGC 60.109 55.000 0.00 0.00 0.00 4.40
1497 1653 2.895062 ACGCGATTTGTTTGTACGTTC 58.105 42.857 15.93 0.00 0.00 3.95
1524 1680 1.469308 GCAGACACACTCGTAGCTAGT 59.531 52.381 0.00 0.00 0.00 2.57
1525 1681 2.676839 GCAGACACACTCGTAGCTAGTA 59.323 50.000 0.00 0.00 0.00 1.82
1533 1689 6.095021 ACACACTCGTAGCTAGTAATTGATCA 59.905 38.462 0.00 0.00 0.00 2.92
1556 1714 5.856126 TTGGTTCATTCATTCGTGTACTC 57.144 39.130 0.00 0.00 0.00 2.59
1570 1731 4.563524 GTGTACTCTTGTGCACGTATTC 57.436 45.455 13.13 2.60 46.41 1.75
1594 1755 5.796935 CGGTGACTTGTTCATTCATTCATTC 59.203 40.000 0.00 0.00 36.32 2.67
1598 1759 8.177663 GTGACTTGTTCATTCATTCATTCGTAT 58.822 33.333 0.00 0.00 36.32 3.06
1599 1760 8.390354 TGACTTGTTCATTCATTCATTCGTATC 58.610 33.333 0.00 0.00 0.00 2.24
1632 1793 9.758651 ATATATACACGTTAACTGATTTGCTCA 57.241 29.630 3.71 0.00 0.00 4.26
1664 1829 1.844289 AACTAGCCCGGTGTCCCAA 60.844 57.895 0.00 0.00 0.00 4.12
1665 1830 1.420532 AACTAGCCCGGTGTCCCAAA 61.421 55.000 0.00 0.00 0.00 3.28
1666 1831 1.377229 CTAGCCCGGTGTCCCAAAA 59.623 57.895 0.00 0.00 0.00 2.44
1667 1832 0.250989 CTAGCCCGGTGTCCCAAAAA 60.251 55.000 0.00 0.00 0.00 1.94
1668 1833 0.537828 TAGCCCGGTGTCCCAAAAAC 60.538 55.000 0.00 0.00 0.00 2.43
1669 1834 1.830847 GCCCGGTGTCCCAAAAACT 60.831 57.895 0.00 0.00 0.00 2.66
1670 1835 0.537828 GCCCGGTGTCCCAAAAACTA 60.538 55.000 0.00 0.00 0.00 2.24
1671 1836 1.530323 CCCGGTGTCCCAAAAACTAG 58.470 55.000 0.00 0.00 0.00 2.57
1672 1837 0.879090 CCGGTGTCCCAAAAACTAGC 59.121 55.000 0.00 0.00 0.00 3.42
1673 1838 0.879090 CGGTGTCCCAAAAACTAGCC 59.121 55.000 0.00 0.00 0.00 3.93
1674 1839 1.254026 GGTGTCCCAAAAACTAGCCC 58.746 55.000 0.00 0.00 0.00 5.19
1675 1840 0.879090 GTGTCCCAAAAACTAGCCCG 59.121 55.000 0.00 0.00 0.00 6.13
1676 1841 0.250989 TGTCCCAAAAACTAGCCCGG 60.251 55.000 0.00 0.00 0.00 5.73
1677 1842 0.251033 GTCCCAAAAACTAGCCCGGT 60.251 55.000 0.00 0.00 0.00 5.28
1678 1843 0.250989 TCCCAAAAACTAGCCCGGTG 60.251 55.000 0.00 0.00 0.00 4.94
1679 1844 0.538746 CCCAAAAACTAGCCCGGTGT 60.539 55.000 0.00 0.00 0.00 4.16
1680 1845 0.879090 CCAAAAACTAGCCCGGTGTC 59.121 55.000 0.00 0.00 0.00 3.67
1681 1846 0.879090 CAAAAACTAGCCCGGTGTCC 59.121 55.000 0.00 0.00 0.00 4.02
1682 1847 0.251033 AAAAACTAGCCCGGTGTCCC 60.251 55.000 0.00 0.00 0.00 4.46
1683 1848 1.420532 AAAACTAGCCCGGTGTCCCA 61.421 55.000 0.00 0.00 0.00 4.37
1684 1849 1.420532 AAACTAGCCCGGTGTCCCAA 61.421 55.000 0.00 0.00 0.00 4.12
1685 1850 1.838073 AACTAGCCCGGTGTCCCAAG 61.838 60.000 0.00 0.00 0.00 3.61
1686 1851 2.203877 TAGCCCGGTGTCCCAAGT 60.204 61.111 0.00 0.00 0.00 3.16
1687 1852 2.240162 CTAGCCCGGTGTCCCAAGTC 62.240 65.000 0.00 0.00 0.00 3.01
1688 1853 4.717313 GCCCGGTGTCCCAAGTCC 62.717 72.222 0.00 0.00 0.00 3.85
1689 1854 4.029809 CCCGGTGTCCCAAGTCCC 62.030 72.222 0.00 0.00 0.00 4.46
1690 1855 3.246112 CCGGTGTCCCAAGTCCCA 61.246 66.667 0.00 0.00 0.00 4.37
1705 1870 1.671293 TCCCATTTTAACGGGGAGGA 58.329 50.000 4.27 0.00 45.83 3.71
1706 1871 1.994047 TCCCATTTTAACGGGGAGGAA 59.006 47.619 4.27 0.00 45.83 3.36
1707 1872 2.097036 CCCATTTTAACGGGGAGGAAC 58.903 52.381 0.00 0.00 45.08 3.62
1708 1873 2.097036 CCATTTTAACGGGGAGGAACC 58.903 52.381 0.00 0.00 38.08 3.62
1709 1874 2.555670 CCATTTTAACGGGGAGGAACCA 60.556 50.000 0.00 0.00 41.20 3.67
1710 1875 2.572209 TTTTAACGGGGAGGAACCAG 57.428 50.000 0.00 0.00 41.20 4.00
1711 1876 1.437397 TTTAACGGGGAGGAACCAGT 58.563 50.000 0.00 0.00 40.78 4.00
1712 1877 0.688487 TTAACGGGGAGGAACCAGTG 59.312 55.000 0.00 0.00 38.95 3.66
1713 1878 0.472352 TAACGGGGAGGAACCAGTGT 60.472 55.000 0.00 0.00 38.95 3.55
1714 1879 2.052047 AACGGGGAGGAACCAGTGTG 62.052 60.000 0.00 0.00 38.95 3.82
1715 1880 2.214216 CGGGGAGGAACCAGTGTGA 61.214 63.158 0.00 0.00 41.20 3.58
1716 1881 1.553690 CGGGGAGGAACCAGTGTGAT 61.554 60.000 0.00 0.00 41.20 3.06
1717 1882 0.035056 GGGGAGGAACCAGTGTGATG 60.035 60.000 0.00 0.00 41.20 3.07
1718 1883 0.984230 GGGAGGAACCAGTGTGATGA 59.016 55.000 0.00 0.00 41.20 2.92
1719 1884 1.339151 GGGAGGAACCAGTGTGATGAC 60.339 57.143 0.00 0.00 41.20 3.06
1720 1885 1.625818 GGAGGAACCAGTGTGATGACT 59.374 52.381 0.00 0.00 38.79 3.41
1721 1886 2.039084 GGAGGAACCAGTGTGATGACTT 59.961 50.000 0.00 0.00 38.79 3.01
1722 1887 3.496870 GGAGGAACCAGTGTGATGACTTT 60.497 47.826 0.00 0.00 38.79 2.66
1723 1888 4.137543 GAGGAACCAGTGTGATGACTTTT 58.862 43.478 0.00 0.00 0.00 2.27
1724 1889 3.885297 AGGAACCAGTGTGATGACTTTTG 59.115 43.478 0.00 0.00 0.00 2.44
1725 1890 3.632145 GGAACCAGTGTGATGACTTTTGT 59.368 43.478 0.00 0.00 0.00 2.83
1726 1891 4.097892 GGAACCAGTGTGATGACTTTTGTT 59.902 41.667 0.00 0.00 0.00 2.83
1727 1892 5.394115 GGAACCAGTGTGATGACTTTTGTTT 60.394 40.000 0.00 0.00 0.00 2.83
1772 1937 8.614469 TGTTCTTTTTGTTCCATGTTTCTTTT 57.386 26.923 0.00 0.00 0.00 2.27
1788 1955 8.364129 TGTTTCTTTTCACTTTATTGATTGGC 57.636 30.769 0.00 0.00 0.00 4.52
1841 2010 0.248539 TTGTAAAACCGTTGCCGCAC 60.249 50.000 0.00 0.00 0.00 5.34
1850 2019 2.593148 TTGCCGCACCAATGTCGT 60.593 55.556 0.00 0.00 0.00 4.34
1868 2037 0.814010 GTATGCACTTAGTGGGGGCG 60.814 60.000 14.63 0.00 33.64 6.13
1883 2052 1.135286 GGGGCGAGAAAGCAAATCTTG 60.135 52.381 0.00 0.00 39.27 3.02
1887 2056 4.496507 GGGCGAGAAAGCAAATCTTGATAC 60.497 45.833 5.19 0.00 39.27 2.24
1890 2059 5.962423 GCGAGAAAGCAAATCTTGATACTTC 59.038 40.000 5.19 0.00 34.67 3.01
1904 2073 6.533012 TCTTGATACTTCGAGATTCTTGCTTG 59.467 38.462 0.00 0.00 37.45 4.01
1910 2079 6.402222 ACTTCGAGATTCTTGCTTGTCTTAT 58.598 36.000 0.00 0.00 0.00 1.73
1918 2087 8.371699 AGATTCTTGCTTGTCTTATAGGGATAC 58.628 37.037 0.00 0.00 0.00 2.24
2016 2185 7.601886 TGACAAAATTGAAAAAGACAGCAGAAA 59.398 29.630 0.00 0.00 0.00 2.52
2023 2192 7.391148 TGAAAAAGACAGCAGAAAACTAGTT 57.609 32.000 1.12 1.12 0.00 2.24
2031 2200 6.483687 ACAGCAGAAAACTAGTTTTTACACG 58.516 36.000 29.26 20.74 42.26 4.49
2201 2374 2.487934 GCGTCTCCATTGCTGATATGT 58.512 47.619 0.00 0.00 0.00 2.29
2241 2440 1.667756 CCGTTGAACGAATCAGACCGA 60.668 52.381 20.47 0.00 46.05 4.69
2249 2448 1.808411 GAATCAGACCGAGGCAACAA 58.192 50.000 0.00 0.00 41.41 2.83
2308 2507 3.735208 CGCACGATTAAGACATCTGAGGT 60.735 47.826 0.00 0.00 0.00 3.85
2326 2525 0.736053 GTGAAAACCGCACCTGTCAA 59.264 50.000 0.00 0.00 0.00 3.18
2327 2526 1.133407 GTGAAAACCGCACCTGTCAAA 59.867 47.619 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 2.034432 ACATTGACGTACGTACACACCA 59.966 45.455 22.87 11.10 0.00 4.17
11 12 2.406024 CACATTGACGTACGTACACACC 59.594 50.000 22.87 8.29 0.00 4.16
31 32 4.700213 GGTGCTAGTAAGAAATTCCTTGCA 59.300 41.667 0.00 3.72 34.24 4.08
36 37 7.499232 ACATGTATGGTGCTAGTAAGAAATTCC 59.501 37.037 0.00 0.00 0.00 3.01
64 65 6.128472 GGTGTGGTACTAATTCTAAAACGTGG 60.128 42.308 0.00 0.00 0.00 4.94
65 66 6.647895 AGGTGTGGTACTAATTCTAAAACGTG 59.352 38.462 0.00 0.00 0.00 4.49
66 67 6.647895 CAGGTGTGGTACTAATTCTAAAACGT 59.352 38.462 0.00 0.00 0.00 3.99
67 68 6.869913 TCAGGTGTGGTACTAATTCTAAAACG 59.130 38.462 0.00 0.00 0.00 3.60
74 75 5.128827 TGAGGATCAGGTGTGGTACTAATTC 59.871 44.000 0.00 0.00 42.56 2.17
106 107 9.444600 TGACAGGTATGGTACTAATTCTTTTTC 57.555 33.333 0.00 0.00 0.00 2.29
107 108 9.975218 ATGACAGGTATGGTACTAATTCTTTTT 57.025 29.630 0.00 0.00 0.00 1.94
108 109 9.396022 CATGACAGGTATGGTACTAATTCTTTT 57.604 33.333 0.00 0.00 0.00 2.27
109 110 8.548877 ACATGACAGGTATGGTACTAATTCTTT 58.451 33.333 0.00 0.00 0.00 2.52
110 111 8.090788 ACATGACAGGTATGGTACTAATTCTT 57.909 34.615 0.00 0.00 0.00 2.52
111 112 7.344612 TGACATGACAGGTATGGTACTAATTCT 59.655 37.037 0.00 0.00 0.00 2.40
112 113 7.497595 TGACATGACAGGTATGGTACTAATTC 58.502 38.462 0.00 0.00 0.00 2.17
113 114 7.432148 TGACATGACAGGTATGGTACTAATT 57.568 36.000 0.00 0.00 0.00 1.40
114 115 7.432148 TTGACATGACAGGTATGGTACTAAT 57.568 36.000 0.00 0.00 0.00 1.73
115 116 6.860790 TTGACATGACAGGTATGGTACTAA 57.139 37.500 0.00 0.00 0.00 2.24
116 117 6.351541 GGTTTGACATGACAGGTATGGTACTA 60.352 42.308 0.00 0.00 0.00 1.82
127 128 7.485913 GCATGTAATTAAGGTTTGACATGACAG 59.514 37.037 15.08 0.00 44.37 3.51
177 178 1.887320 GCTCAAAATACAGCGTGCAG 58.113 50.000 0.00 0.00 0.00 4.41
252 290 1.080025 GCCGGTATGGATACGAGGC 60.080 63.158 1.90 14.91 44.33 4.70
255 293 1.183030 CCAGGCCGGTATGGATACGA 61.183 60.000 19.16 0.00 42.00 3.43
256 294 1.183030 TCCAGGCCGGTATGGATACG 61.183 60.000 21.65 1.37 40.70 3.06
368 418 1.063006 CGCCCGTCGAACGAGAATA 59.937 57.895 8.63 0.00 46.05 1.75
403 475 2.879233 GCCGGGTCAAGTCTCACCA 61.879 63.158 2.18 0.00 33.91 4.17
408 480 4.681978 GTGCGCCGGGTCAAGTCT 62.682 66.667 4.18 0.00 0.00 3.24
532 616 3.777556 CCAAAAAGGGAAGGCGCT 58.222 55.556 7.64 0.00 39.23 5.92
961 1093 4.276926 TGTGATGGATCGACTACTGATCAG 59.723 45.833 21.37 21.37 43.21 2.90
1143 1284 2.986306 GAACGTCGGGAAGGAGCGA 61.986 63.158 0.00 0.00 0.00 4.93
1472 1628 2.288365 ACAAACAAATCGCGTACGTG 57.712 45.000 22.43 22.43 41.18 4.49
1497 1653 0.729478 CGAGTGTGTCTGCGTGTAGG 60.729 60.000 0.00 0.00 0.00 3.18
1524 1680 8.685427 ACGAATGAATGAACCAATGATCAATTA 58.315 29.630 0.00 0.00 0.00 1.40
1525 1681 7.490079 CACGAATGAATGAACCAATGATCAATT 59.510 33.333 0.00 0.00 0.00 2.32
1533 1689 6.173339 AGAGTACACGAATGAATGAACCAAT 58.827 36.000 0.00 0.00 0.00 3.16
1556 1714 1.126113 GTCACCGAATACGTGCACAAG 59.874 52.381 18.64 3.67 37.88 3.16
1565 1726 5.856126 TGAATGAACAAGTCACCGAATAC 57.144 39.130 0.00 0.00 39.72 1.89
1570 1731 4.747540 TGAATGAATGAACAAGTCACCG 57.252 40.909 0.00 0.00 39.72 4.94
1664 1829 1.377612 GGGACACCGGGCTAGTTTT 59.622 57.895 6.32 0.00 0.00 2.43
1665 1830 1.420532 TTGGGACACCGGGCTAGTTT 61.421 55.000 6.32 0.00 39.29 2.66
1666 1831 1.838073 CTTGGGACACCGGGCTAGTT 61.838 60.000 6.32 0.00 39.29 2.24
1667 1832 2.203877 TTGGGACACCGGGCTAGT 60.204 61.111 6.32 0.00 39.29 2.57
1668 1833 2.240162 GACTTGGGACACCGGGCTAG 62.240 65.000 6.32 0.00 39.29 3.42
1669 1834 2.203877 ACTTGGGACACCGGGCTA 60.204 61.111 6.32 0.00 39.29 3.93
1670 1835 3.637273 GACTTGGGACACCGGGCT 61.637 66.667 6.32 0.00 39.29 5.19
1671 1836 4.717313 GGACTTGGGACACCGGGC 62.717 72.222 6.32 0.00 39.29 6.13
1672 1837 4.029809 GGGACTTGGGACACCGGG 62.030 72.222 6.32 0.00 39.29 5.73
1673 1838 2.137177 AATGGGACTTGGGACACCGG 62.137 60.000 0.00 0.00 39.29 5.28
1674 1839 0.251165 AAATGGGACTTGGGACACCG 60.251 55.000 0.00 0.00 39.29 4.94
1675 1840 2.009681 AAAATGGGACTTGGGACACC 57.990 50.000 0.00 0.00 39.29 4.16
1676 1841 3.057806 CGTTAAAATGGGACTTGGGACAC 60.058 47.826 0.00 0.00 39.29 3.67
1677 1842 3.150767 CGTTAAAATGGGACTTGGGACA 58.849 45.455 0.00 0.00 0.00 4.02
1678 1843 2.490509 CCGTTAAAATGGGACTTGGGAC 59.509 50.000 0.00 0.00 0.00 4.46
1679 1844 2.797786 CCGTTAAAATGGGACTTGGGA 58.202 47.619 0.00 0.00 0.00 4.37
1688 1853 2.097036 GGTTCCTCCCCGTTAAAATGG 58.903 52.381 0.00 0.00 34.76 3.16
1689 1854 2.752903 CTGGTTCCTCCCCGTTAAAATG 59.247 50.000 0.00 0.00 34.77 2.32
1690 1855 2.377531 ACTGGTTCCTCCCCGTTAAAAT 59.622 45.455 0.00 0.00 34.77 1.82
1705 1870 5.659440 AAACAAAAGTCATCACACTGGTT 57.341 34.783 0.00 0.00 0.00 3.67
1706 1871 5.650266 TGTAAACAAAAGTCATCACACTGGT 59.350 36.000 0.00 0.00 0.00 4.00
1707 1872 6.130298 TGTAAACAAAAGTCATCACACTGG 57.870 37.500 0.00 0.00 0.00 4.00
1764 1929 8.593492 AGCCAATCAATAAAGTGAAAAGAAAC 57.407 30.769 0.00 0.00 0.00 2.78
1786 1953 4.938226 AGTCAGCACAAGATACTAAAAGCC 59.062 41.667 0.00 0.00 0.00 4.35
1787 1954 5.163814 CCAGTCAGCACAAGATACTAAAAGC 60.164 44.000 0.00 0.00 0.00 3.51
1788 1955 5.352569 CCCAGTCAGCACAAGATACTAAAAG 59.647 44.000 0.00 0.00 0.00 2.27
1841 2010 3.309682 CCACTAAGTGCATACGACATTGG 59.690 47.826 0.00 0.00 31.34 3.16
1850 2019 0.978667 TCGCCCCCACTAAGTGCATA 60.979 55.000 0.00 0.00 31.34 3.14
1868 2037 7.276658 TCTCGAAGTATCAAGATTTGCTTTCTC 59.723 37.037 0.00 0.00 33.60 2.87
1883 2052 6.039616 AGACAAGCAAGAATCTCGAAGTATC 58.960 40.000 0.00 0.00 0.00 2.24
1887 2056 6.900568 ATAAGACAAGCAAGAATCTCGAAG 57.099 37.500 0.00 0.00 0.00 3.79
1890 2059 5.694006 CCCTATAAGACAAGCAAGAATCTCG 59.306 44.000 0.00 0.00 0.00 4.04
1926 2095 5.991328 AAATGAGACACGTATTAGCATGG 57.009 39.130 0.00 0.00 0.00 3.66
2016 2185 6.594937 TGGTGTTCTTCGTGTAAAAACTAGTT 59.405 34.615 1.12 1.12 0.00 2.24
2023 2192 2.614983 GGCTGGTGTTCTTCGTGTAAAA 59.385 45.455 0.00 0.00 0.00 1.52
2031 2200 3.214328 TCTTTCTTGGCTGGTGTTCTTC 58.786 45.455 0.00 0.00 0.00 2.87
2241 2440 1.525995 CGTGTCTGGGTTGTTGCCT 60.526 57.895 0.00 0.00 0.00 4.75
2249 2448 0.889186 GTTTGATGGCGTGTCTGGGT 60.889 55.000 0.00 0.00 0.00 4.51
2308 2507 1.133407 GTTTGACAGGTGCGGTTTTCA 59.867 47.619 0.00 0.00 0.00 2.69
2326 2525 4.644234 TGTGATGAGTTCATGGTTTGTGTT 59.356 37.500 0.00 0.00 36.54 3.32
2327 2526 4.036734 GTGTGATGAGTTCATGGTTTGTGT 59.963 41.667 0.00 0.00 36.54 3.72


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

AutoCloner maintained by Alex Coulton.