Multiple sequence alignment - TraesCS1D01G265700

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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 TraesCS1D01G265700 chr1D 100.000 2927 0 0 1 2927 361356968 361359894 0.000000e+00 5406.0
1 TraesCS1D01G265700 chr1D 76.271 236 51 3 1703 1937 361845142 361845373 1.420000e-23 121.0
2 TraesCS1D01G265700 chr1B 91.002 1756 96 22 1 1705 484006433 484008177 0.000000e+00 2311.0
3 TraesCS1D01G265700 chr1B 87.389 452 38 10 2489 2927 484008572 484009017 4.350000e-138 501.0
4 TraesCS1D01G265700 chr1B 88.442 398 34 4 2055 2444 484008176 484008569 1.230000e-128 470.0
5 TraesCS1D01G265700 chr1B 76.800 250 53 3 1703 1951 484360741 484360986 5.090000e-28 135.0
6 TraesCS1D01G265700 chr1A 91.309 978 59 12 616 1570 460996917 460997891 0.000000e+00 1312.0
7 TraesCS1D01G265700 chr1A 89.819 992 77 8 1956 2927 460997981 460998968 0.000000e+00 1251.0
8 TraesCS1D01G265700 chr1A 83.957 374 44 8 1 368 460990674 460991037 7.770000e-91 344.0
9 TraesCS1D01G265700 chr1A 96.875 64 2 0 1700 1763 460997979 460997916 1.110000e-19 108.0
10 TraesCS1D01G265700 chr3D 83.088 136 20 3 2198 2331 2689839 2689705 1.420000e-23 121.0
11 TraesCS1D01G265700 chr4A 82.443 131 22 1 2203 2332 615953995 615953865 2.380000e-21 113.0
12 TraesCS1D01G265700 chr5A 82.540 126 19 3 2201 2323 356137365 356137240 1.110000e-19 108.0
13 TraesCS1D01G265700 chr5A 80.147 136 26 1 2198 2332 279116409 279116544 1.860000e-17 100.0
14 TraesCS1D01G265700 chr5A 77.941 136 28 2 1701 1835 645000580 645000446 1.870000e-12 84.2
15 TraesCS1D01G265700 chr5B 79.355 155 28 4 2195 2347 680316087 680316239 3.990000e-19 106.0
16 TraesCS1D01G265700 chr5B 80.597 134 23 2 2201 2331 304270739 304270606 1.860000e-17 100.0
17 TraesCS1D01G265700 chr7D 80.741 135 23 3 2199 2331 246034134 246034267 5.160000e-18 102.0
18 TraesCS1D01G265700 chr5D 85.542 83 10 2 2683 2764 536691902 536691821 5.200000e-13 86.1
19 TraesCS1D01G265700 chr2A 84.906 53 8 0 2683 2735 554815367 554815315 1.000000e-03 54.7


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 TraesCS1D01G265700 chr1D 361356968 361359894 2926 False 5406.0 5406 100.000000 1 2927 1 chr1D.!!$F1 2926
1 TraesCS1D01G265700 chr1B 484006433 484009017 2584 False 1094.0 2311 88.944333 1 2927 3 chr1B.!!$F2 2926
2 TraesCS1D01G265700 chr1A 460996917 460998968 2051 False 1281.5 1312 90.564000 616 2927 2 chr1A.!!$F2 2311

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
33 34 0.250234 TTTGACCTCATCTGGGAGCG 59.75 55.0 0.0 0.0 33.47 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1942 1994 0.037882 CACAGTGACCGTGCTCATCT 60.038 55.0 0.0 0.0 0.0 2.9 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
25 26 1.538047 TGGCAAGCTTTGACCTCATC 58.462 50.000 0.00 0.00 38.13 2.92
33 34 0.250234 TTTGACCTCATCTGGGAGCG 59.750 55.000 0.00 0.00 33.47 5.03
34 35 1.617018 TTGACCTCATCTGGGAGCGG 61.617 60.000 0.00 0.00 33.47 5.52
36 37 2.765807 CCTCATCTGGGAGCGGGT 60.766 66.667 0.00 0.00 33.47 5.28
53 54 1.609841 GGGTAAGGGTTGTGTTCTCCG 60.610 57.143 0.00 0.00 0.00 4.63
62 63 3.379445 TGTTCTCCGACTCCGCCC 61.379 66.667 0.00 0.00 0.00 6.13
82 83 2.584391 GCCAGACCAGACCCGAAGT 61.584 63.158 0.00 0.00 0.00 3.01
94 95 2.870411 GACCCGAAGTGTTATACATGCC 59.130 50.000 0.00 0.00 0.00 4.40
101 102 4.568072 AGTGTTATACATGCCCACTTCA 57.432 40.909 0.00 0.00 32.72 3.02
102 103 4.917385 AGTGTTATACATGCCCACTTCAA 58.083 39.130 0.00 0.00 32.72 2.69
106 107 5.125257 TGTTATACATGCCCACTTCAACATG 59.875 40.000 0.00 0.00 44.29 3.21
140 141 4.697352 GGCATGCCGATTTTCTATGTAGAT 59.303 41.667 23.48 0.00 31.40 1.98
143 144 5.673337 TGCCGATTTTCTATGTAGATTGC 57.327 39.130 0.00 0.00 31.40 3.56
144 145 5.122519 TGCCGATTTTCTATGTAGATTGCA 58.877 37.500 0.00 0.00 31.40 4.08
145 146 5.588246 TGCCGATTTTCTATGTAGATTGCAA 59.412 36.000 0.00 0.00 31.40 4.08
147 148 6.138761 CCGATTTTCTATGTAGATTGCAAGC 58.861 40.000 6.58 6.58 31.40 4.01
149 150 6.292328 CGATTTTCTATGTAGATTGCAAGCGA 60.292 38.462 9.38 0.06 31.40 4.93
153 154 1.078709 TGTAGATTGCAAGCGACAGC 58.921 50.000 23.86 8.02 45.58 4.40
230 231 4.748102 TCAACAAGGTTGATACGTTCAGAC 59.252 41.667 7.66 0.00 35.27 3.51
266 267 3.844577 GCAATGATCTTTGCTCACAGT 57.155 42.857 29.43 0.00 46.66 3.55
277 278 1.630244 GCTCACAGTGCACCATCGAC 61.630 60.000 14.63 0.00 0.00 4.20
308 309 3.956744 AGGAATAAGACTTTGGCACTCC 58.043 45.455 0.00 0.00 0.00 3.85
375 377 0.820871 GCTCAGTGCTACTGCTACCT 59.179 55.000 10.36 0.00 45.54 3.08
376 378 2.025155 GCTCAGTGCTACTGCTACCTA 58.975 52.381 10.36 0.00 45.54 3.08
377 379 2.427453 GCTCAGTGCTACTGCTACCTAA 59.573 50.000 10.36 0.00 45.54 2.69
378 380 3.068873 GCTCAGTGCTACTGCTACCTAAT 59.931 47.826 10.36 0.00 45.54 1.73
379 381 4.442192 GCTCAGTGCTACTGCTACCTAATT 60.442 45.833 10.36 0.00 45.54 1.40
380 382 5.665459 CTCAGTGCTACTGCTACCTAATTT 58.335 41.667 10.36 0.00 45.54 1.82
381 383 6.049955 TCAGTGCTACTGCTACCTAATTTT 57.950 37.500 10.36 0.00 45.54 1.82
382 384 5.874810 TCAGTGCTACTGCTACCTAATTTTG 59.125 40.000 10.36 0.00 45.54 2.44
391 411 4.698304 TGCTACCTAATTTTGTACCAGTGC 59.302 41.667 0.00 0.00 0.00 4.40
423 443 8.350722 TGTGGAGTTATACGATCTTGAAGTATC 58.649 37.037 0.00 0.00 33.64 2.24
425 445 9.078990 TGGAGTTATACGATCTTGAAGTATCAT 57.921 33.333 0.00 0.00 34.96 2.45
433 453 5.678483 CGATCTTGAAGTATCATTTTTGCGG 59.322 40.000 0.00 0.00 34.96 5.69
434 454 5.309323 TCTTGAAGTATCATTTTTGCGGG 57.691 39.130 0.00 0.00 34.96 6.13
479 499 1.401552 GCAGAGCACACAAACAAGTCA 59.598 47.619 0.00 0.00 0.00 3.41
508 528 1.135199 ACCCTTATGTACGCACTCACG 60.135 52.381 0.00 0.00 39.50 4.35
521 541 2.924290 GCACTCACGTACATTCTCTTCC 59.076 50.000 0.00 0.00 0.00 3.46
526 546 5.886474 ACTCACGTACATTCTCTTCCTATGA 59.114 40.000 0.00 0.00 0.00 2.15
529 549 4.954202 ACGTACATTCTCTTCCTATGACCA 59.046 41.667 0.00 0.00 0.00 4.02
557 577 2.352817 GACTGAGTCGGTGGGTCTT 58.647 57.895 9.98 0.00 0.00 3.01
565 585 2.158667 AGTCGGTGGGTCTTGAAATTGT 60.159 45.455 0.00 0.00 0.00 2.71
566 586 2.621526 GTCGGTGGGTCTTGAAATTGTT 59.378 45.455 0.00 0.00 0.00 2.83
567 587 2.621055 TCGGTGGGTCTTGAAATTGTTG 59.379 45.455 0.00 0.00 0.00 3.33
570 590 4.620982 GGTGGGTCTTGAAATTGTTGAAG 58.379 43.478 0.00 0.00 29.93 3.02
576 596 6.239008 GGGTCTTGAAATTGTTGAAGTCATCA 60.239 38.462 0.00 0.00 35.85 3.07
586 606 3.717400 TGAAGTCATCATAGACGCCTC 57.283 47.619 0.00 0.00 43.24 4.70
587 607 2.033424 TGAAGTCATCATAGACGCCTCG 59.967 50.000 0.00 0.00 43.24 4.63
588 608 0.312416 AGTCATCATAGACGCCTCGC 59.688 55.000 0.00 0.00 43.24 5.03
590 610 0.312102 TCATCATAGACGCCTCGCAG 59.688 55.000 0.00 0.00 0.00 5.18
597 617 2.141535 AGACGCCTCGCAGAATATTC 57.858 50.000 7.41 7.41 34.09 1.75
599 619 0.597637 ACGCCTCGCAGAATATTCCG 60.598 55.000 11.92 9.47 34.09 4.30
605 625 1.939934 TCGCAGAATATTCCGCCTTTG 59.060 47.619 16.24 6.87 0.00 2.77
613 633 1.523758 ATTCCGCCTTTGTGAGACAC 58.476 50.000 0.00 0.00 34.56 3.67
678 698 2.644798 ACCATTGCCCTCTTAACTGTCT 59.355 45.455 0.00 0.00 0.00 3.41
680 700 4.192317 CCATTGCCCTCTTAACTGTCTAC 58.808 47.826 0.00 0.00 0.00 2.59
686 706 4.618693 GCCCTCTTAACTGTCTACTCACAC 60.619 50.000 0.00 0.00 0.00 3.82
695 715 2.223876 TGTCTACTCACACGTTGGTTCC 60.224 50.000 0.00 0.00 0.00 3.62
841 871 5.178096 TGTCAACTTACATGATGGACCAT 57.822 39.130 6.71 6.71 0.00 3.55
865 895 1.410153 GGTGAATGATGGTTGATGGGC 59.590 52.381 0.00 0.00 0.00 5.36
1339 1370 2.124193 TTCATCATGCCGCTGGGG 60.124 61.111 6.36 6.36 39.58 4.96
1429 1460 2.890808 TATAGAGGTGCTTTCAGCCG 57.109 50.000 0.00 0.00 41.51 5.52
1468 1499 5.106442 ACAAAAACATTCGACTCCAAAACC 58.894 37.500 0.00 0.00 0.00 3.27
1524 1559 5.942872 AGGTAGAAGCAACAATGAAAATCG 58.057 37.500 0.00 0.00 0.00 3.34
1525 1560 5.705441 AGGTAGAAGCAACAATGAAAATCGA 59.295 36.000 0.00 0.00 0.00 3.59
1602 1654 3.181503 GGTCGTCACGCTTAGTCATTCTA 60.182 47.826 0.00 0.00 0.00 2.10
1615 1667 8.730680 GCTTAGTCATTCTATTTGTTTCCTGAA 58.269 33.333 0.00 0.00 0.00 3.02
1707 1759 4.821935 CCATCGGGCTATTTCCCC 57.178 61.111 0.00 0.00 43.56 4.81
1708 1760 1.843421 CCATCGGGCTATTTCCCCA 59.157 57.895 0.00 0.00 43.56 4.96
1709 1761 0.184933 CCATCGGGCTATTTCCCCAA 59.815 55.000 0.00 0.00 43.56 4.12
1710 1762 1.609208 CATCGGGCTATTTCCCCAAG 58.391 55.000 0.00 0.00 43.56 3.61
1711 1763 1.133792 CATCGGGCTATTTCCCCAAGT 60.134 52.381 0.00 0.00 43.56 3.16
1712 1764 0.254747 TCGGGCTATTTCCCCAAGTG 59.745 55.000 0.00 0.00 43.56 3.16
1713 1765 1.384222 CGGGCTATTTCCCCAAGTGC 61.384 60.000 0.00 0.00 43.56 4.40
1714 1766 0.033109 GGGCTATTTCCCCAAGTGCT 60.033 55.000 0.00 0.00 42.36 4.40
1715 1767 1.106285 GGCTATTTCCCCAAGTGCTG 58.894 55.000 0.00 0.00 0.00 4.41
1720 1772 2.616797 TTTCCCCAAGTGCTGCGACA 62.617 55.000 0.00 0.00 0.00 4.35
1721 1773 2.594303 CCCCAAGTGCTGCGACAA 60.594 61.111 0.00 0.00 0.00 3.18
1737 1789 0.034059 ACAACTGCAGGTCCTTCTCG 59.966 55.000 19.93 0.00 0.00 4.04
1741 1793 2.683933 GCAGGTCCTTCTCGGGGA 60.684 66.667 0.00 0.00 0.00 4.81
1742 1794 2.066999 GCAGGTCCTTCTCGGGGAT 61.067 63.158 0.00 0.00 35.15 3.85
1743 1795 2.034048 GCAGGTCCTTCTCGGGGATC 62.034 65.000 0.00 0.00 35.15 3.36
1744 1796 1.455959 AGGTCCTTCTCGGGGATCG 60.456 63.158 0.00 0.00 38.87 3.69
1745 1797 1.455217 GGTCCTTCTCGGGGATCGA 60.455 63.158 0.00 0.00 46.77 3.59
1746 1798 1.734748 GTCCTTCTCGGGGATCGAC 59.265 63.158 0.00 0.00 43.74 4.20
1747 1799 1.822613 TCCTTCTCGGGGATCGACG 60.823 63.158 0.00 1.68 43.74 5.12
1748 1800 2.119655 CCTTCTCGGGGATCGACGT 61.120 63.158 7.42 0.00 43.74 4.34
1749 1801 1.355916 CTTCTCGGGGATCGACGTC 59.644 63.158 5.18 5.18 43.74 4.34
1750 1802 2.376231 CTTCTCGGGGATCGACGTCG 62.376 65.000 31.30 31.30 43.74 5.12
1751 1803 3.950254 CTCGGGGATCGACGTCGG 61.950 72.222 35.05 19.30 43.74 4.79
1752 1804 4.783621 TCGGGGATCGACGTCGGT 62.784 66.667 35.05 31.12 43.74 4.69
1753 1805 4.547905 CGGGGATCGACGTCGGTG 62.548 72.222 35.05 14.79 42.43 4.94
1754 1806 3.136123 GGGGATCGACGTCGGTGA 61.136 66.667 35.05 18.80 40.29 4.02
1755 1807 2.101770 GGGATCGACGTCGGTGAC 59.898 66.667 35.05 23.29 40.29 3.67
1767 1819 3.771160 GGTGACGACGCCCATCCT 61.771 66.667 6.17 0.00 40.47 3.24
1768 1820 2.509336 GTGACGACGCCCATCCTG 60.509 66.667 0.00 0.00 0.00 3.86
1771 1823 2.680352 ACGACGCCCATCCTGAGT 60.680 61.111 0.00 0.00 0.00 3.41
1772 1824 2.202797 CGACGCCCATCCTGAGTG 60.203 66.667 0.00 0.00 0.00 3.51
1775 1827 4.864334 CGCCCATCCTGAGTGCCC 62.864 72.222 0.00 0.00 0.00 5.36
1776 1828 4.512914 GCCCATCCTGAGTGCCCC 62.513 72.222 0.00 0.00 0.00 5.80
1777 1829 3.016971 CCCATCCTGAGTGCCCCA 61.017 66.667 0.00 0.00 0.00 4.96
1780 1832 1.077212 CATCCTGAGTGCCCCAAGG 60.077 63.158 0.00 0.00 0.00 3.61
1791 1843 3.379445 CCCAAGGGCTGCTTGCAG 61.379 66.667 17.34 17.34 45.15 4.41
1793 1845 2.649034 CAAGGGCTGCTTGCAGTG 59.351 61.111 21.55 9.87 45.15 3.66
1794 1846 3.300765 AAGGGCTGCTTGCAGTGC 61.301 61.111 21.55 8.58 45.15 4.40
1815 1867 4.008933 GTGGTGCAGACGAGCCCT 62.009 66.667 0.00 0.00 0.00 5.19
1816 1868 4.007644 TGGTGCAGACGAGCCCTG 62.008 66.667 0.00 0.00 34.88 4.45
1821 1873 2.435586 CAGACGAGCCCTGCCAAG 60.436 66.667 0.00 0.00 0.00 3.61
1822 1874 2.604686 AGACGAGCCCTGCCAAGA 60.605 61.111 0.00 0.00 0.00 3.02
1823 1875 2.435059 GACGAGCCCTGCCAAGAC 60.435 66.667 0.00 0.00 0.00 3.01
1824 1876 4.379243 ACGAGCCCTGCCAAGACG 62.379 66.667 0.00 0.00 0.00 4.18
1825 1877 4.379243 CGAGCCCTGCCAAGACGT 62.379 66.667 0.00 0.00 0.00 4.34
1826 1878 2.032681 GAGCCCTGCCAAGACGTT 59.967 61.111 0.00 0.00 0.00 3.99
1827 1879 2.032681 AGCCCTGCCAAGACGTTC 59.967 61.111 0.00 0.00 0.00 3.95
1828 1880 2.281484 GCCCTGCCAAGACGTTCA 60.281 61.111 0.00 0.00 0.00 3.18
1829 1881 2.328099 GCCCTGCCAAGACGTTCAG 61.328 63.158 0.00 0.00 0.00 3.02
1830 1882 1.672356 CCCTGCCAAGACGTTCAGG 60.672 63.158 12.02 12.02 44.25 3.86
1831 1883 1.071471 CCTGCCAAGACGTTCAGGT 59.929 57.895 11.22 0.00 40.79 4.00
1832 1884 1.230635 CCTGCCAAGACGTTCAGGTG 61.231 60.000 11.22 3.12 40.79 4.00
1833 1885 1.845809 CTGCCAAGACGTTCAGGTGC 61.846 60.000 0.00 0.00 0.00 5.01
1834 1886 2.954753 GCCAAGACGTTCAGGTGCG 61.955 63.158 0.00 0.00 0.00 5.34
1835 1887 2.551270 CAAGACGTTCAGGTGCGC 59.449 61.111 0.00 0.00 0.00 6.09
1836 1888 2.665185 AAGACGTTCAGGTGCGCC 60.665 61.111 8.71 8.71 0.00 6.53
1841 1893 2.260434 GTTCAGGTGCGCCGACTA 59.740 61.111 11.42 0.00 40.50 2.59
1842 1894 2.092882 GTTCAGGTGCGCCGACTAC 61.093 63.158 11.42 4.45 40.50 2.73
1843 1895 3.291101 TTCAGGTGCGCCGACTACC 62.291 63.158 11.42 5.11 40.50 3.18
1853 1905 2.708255 CGACTACCGCGGAGACTC 59.292 66.667 35.90 18.33 0.00 3.36
1854 1906 2.821688 CGACTACCGCGGAGACTCC 61.822 68.421 35.90 11.87 0.00 3.85
1863 1915 2.479650 GGAGACTCCGACGACACG 59.520 66.667 5.55 0.00 0.00 4.49
1864 1916 2.323580 GGAGACTCCGACGACACGT 61.324 63.158 5.55 0.00 45.10 4.49
1865 1917 1.154450 GAGACTCCGACGACACGTG 60.154 63.158 15.48 15.48 41.37 4.49
1866 1918 2.799916 GACTCCGACGACACGTGC 60.800 66.667 17.22 7.72 41.37 5.34
1867 1919 4.678269 ACTCCGACGACACGTGCG 62.678 66.667 24.02 24.02 41.37 5.34
1885 1937 3.302344 GCCCGCCCTGCAAGAAAA 61.302 61.111 0.00 0.00 34.07 2.29
1886 1938 2.866726 GCCCGCCCTGCAAGAAAAA 61.867 57.895 0.00 0.00 34.07 1.94
1887 1939 1.006220 CCCGCCCTGCAAGAAAAAC 60.006 57.895 0.00 0.00 34.07 2.43
1888 1940 1.463553 CCCGCCCTGCAAGAAAAACT 61.464 55.000 0.00 0.00 34.07 2.66
1889 1941 0.318955 CCGCCCTGCAAGAAAAACTG 60.319 55.000 0.00 0.00 34.07 3.16
1890 1942 0.667993 CGCCCTGCAAGAAAAACTGA 59.332 50.000 0.00 0.00 34.07 3.41
1891 1943 1.270550 CGCCCTGCAAGAAAAACTGAT 59.729 47.619 0.00 0.00 34.07 2.90
1892 1944 2.680577 GCCCTGCAAGAAAAACTGATG 58.319 47.619 0.00 0.00 34.07 3.07
1893 1945 2.611224 GCCCTGCAAGAAAAACTGATGG 60.611 50.000 0.00 0.00 34.07 3.51
1894 1946 2.028748 CCCTGCAAGAAAAACTGATGGG 60.029 50.000 0.00 0.00 34.07 4.00
1895 1947 2.629617 CCTGCAAGAAAAACTGATGGGT 59.370 45.455 0.00 0.00 34.07 4.51
1896 1948 3.070015 CCTGCAAGAAAAACTGATGGGTT 59.930 43.478 0.00 0.00 34.07 4.11
1897 1949 4.280677 CCTGCAAGAAAAACTGATGGGTTA 59.719 41.667 0.00 0.00 34.07 2.85
1898 1950 5.221422 CCTGCAAGAAAAACTGATGGGTTAA 60.221 40.000 0.00 0.00 34.07 2.01
1899 1951 5.841810 TGCAAGAAAAACTGATGGGTTAAG 58.158 37.500 0.00 0.00 0.00 1.85
1900 1952 4.686091 GCAAGAAAAACTGATGGGTTAAGC 59.314 41.667 0.00 0.00 0.00 3.09
1901 1953 5.509670 GCAAGAAAAACTGATGGGTTAAGCT 60.510 40.000 4.41 0.00 0.00 3.74
1902 1954 5.966742 AGAAAAACTGATGGGTTAAGCTC 57.033 39.130 4.41 0.00 0.00 4.09
1903 1955 5.385198 AGAAAAACTGATGGGTTAAGCTCA 58.615 37.500 4.41 0.70 0.00 4.26
1904 1956 5.474876 AGAAAAACTGATGGGTTAAGCTCAG 59.525 40.000 17.63 17.63 40.71 3.35
1905 1957 4.640771 AAACTGATGGGTTAAGCTCAGA 57.359 40.909 23.22 4.92 38.74 3.27
1906 1958 4.851639 AACTGATGGGTTAAGCTCAGAT 57.148 40.909 23.22 13.32 38.74 2.90
1907 1959 4.414337 ACTGATGGGTTAAGCTCAGATC 57.586 45.455 23.22 12.45 38.74 2.75
1908 1960 3.776969 ACTGATGGGTTAAGCTCAGATCA 59.223 43.478 23.22 15.26 38.74 2.92
1909 1961 4.125703 CTGATGGGTTAAGCTCAGATCAC 58.874 47.826 15.30 0.00 37.85 3.06
1910 1962 2.672961 TGGGTTAAGCTCAGATCACG 57.327 50.000 4.41 0.00 0.00 4.35
1911 1963 2.176045 TGGGTTAAGCTCAGATCACGA 58.824 47.619 4.41 0.00 0.00 4.35
1912 1964 2.565391 TGGGTTAAGCTCAGATCACGAA 59.435 45.455 4.41 0.00 0.00 3.85
1913 1965 3.007506 TGGGTTAAGCTCAGATCACGAAA 59.992 43.478 4.41 0.00 0.00 3.46
1914 1966 4.192317 GGGTTAAGCTCAGATCACGAAAT 58.808 43.478 4.41 0.00 0.00 2.17
1915 1967 4.034510 GGGTTAAGCTCAGATCACGAAATG 59.965 45.833 4.41 0.00 0.00 2.32
1916 1968 4.631813 GGTTAAGCTCAGATCACGAAATGT 59.368 41.667 0.00 0.00 0.00 2.71
1917 1969 5.122396 GGTTAAGCTCAGATCACGAAATGTT 59.878 40.000 0.00 0.00 0.00 2.71
1918 1970 6.348540 GGTTAAGCTCAGATCACGAAATGTTT 60.349 38.462 0.00 0.00 0.00 2.83
1919 1971 4.935885 AGCTCAGATCACGAAATGTTTC 57.064 40.909 0.00 0.00 0.00 2.78
1934 1986 5.605564 AATGTTTCGCCCAAAATAAAAGC 57.394 34.783 0.00 0.00 0.00 3.51
1935 1987 4.329462 TGTTTCGCCCAAAATAAAAGCT 57.671 36.364 0.00 0.00 0.00 3.74
1936 1988 4.303282 TGTTTCGCCCAAAATAAAAGCTC 58.697 39.130 0.00 0.00 0.00 4.09
1937 1989 4.202161 TGTTTCGCCCAAAATAAAAGCTCA 60.202 37.500 0.00 0.00 0.00 4.26
1938 1990 3.848272 TCGCCCAAAATAAAAGCTCAG 57.152 42.857 0.00 0.00 0.00 3.35
1939 1991 3.417101 TCGCCCAAAATAAAAGCTCAGA 58.583 40.909 0.00 0.00 0.00 3.27
1940 1992 3.190535 TCGCCCAAAATAAAAGCTCAGAC 59.809 43.478 0.00 0.00 0.00 3.51
1941 1993 3.501950 GCCCAAAATAAAAGCTCAGACG 58.498 45.455 0.00 0.00 0.00 4.18
1942 1994 3.190535 GCCCAAAATAAAAGCTCAGACGA 59.809 43.478 0.00 0.00 0.00 4.20
1943 1995 4.672801 GCCCAAAATAAAAGCTCAGACGAG 60.673 45.833 0.00 0.00 42.66 4.18
1944 1996 4.695455 CCCAAAATAAAAGCTCAGACGAGA 59.305 41.667 0.00 0.00 42.34 4.04
1945 1997 5.355350 CCCAAAATAAAAGCTCAGACGAGAT 59.645 40.000 0.00 0.00 42.34 2.75
1946 1998 6.253746 CCAAAATAAAAGCTCAGACGAGATG 58.746 40.000 0.00 0.00 42.34 2.90
1947 1999 6.092670 CCAAAATAAAAGCTCAGACGAGATGA 59.907 38.462 0.00 0.00 42.34 2.92
1948 2000 6.900568 AAATAAAAGCTCAGACGAGATGAG 57.099 37.500 10.54 10.54 45.71 2.90
1952 2004 3.232794 CTCAGACGAGATGAGCACG 57.767 57.895 0.00 0.00 42.34 5.34
1953 2005 0.248417 CTCAGACGAGATGAGCACGG 60.248 60.000 0.00 0.00 42.34 4.94
1954 2006 0.960861 TCAGACGAGATGAGCACGGT 60.961 55.000 0.00 0.00 34.76 4.83
1958 2010 1.244697 ACGAGATGAGCACGGTCACT 61.245 55.000 0.22 1.56 34.76 3.41
1971 2023 2.272678 CGGTCACTGTGTTTGTGTGTA 58.727 47.619 7.79 0.00 36.83 2.90
1990 2042 0.596082 ACATTTGCCCTGCGTTGTAC 59.404 50.000 0.00 0.00 0.00 2.90
2029 2081 6.479331 TCATCATCACCATTGTTGTTGTTTTG 59.521 34.615 0.00 0.00 0.00 2.44
2077 2129 2.158755 GCCTATCAGGTGCCTGTTGTAT 60.159 50.000 16.85 6.73 43.96 2.29
2080 2132 1.656587 TCAGGTGCCTGTTGTATCCT 58.343 50.000 16.85 0.00 43.96 3.24
2092 2144 6.321181 GCCTGTTGTATCCTCCATGAAATAAA 59.679 38.462 0.00 0.00 0.00 1.40
2094 2146 7.339212 CCTGTTGTATCCTCCATGAAATAAACA 59.661 37.037 0.00 0.00 0.00 2.83
2095 2147 8.050778 TGTTGTATCCTCCATGAAATAAACAC 57.949 34.615 0.00 0.00 0.00 3.32
2096 2148 7.122055 TGTTGTATCCTCCATGAAATAAACACC 59.878 37.037 0.00 0.00 0.00 4.16
2097 2149 6.969043 TGTATCCTCCATGAAATAAACACCT 58.031 36.000 0.00 0.00 0.00 4.00
2098 2150 6.828273 TGTATCCTCCATGAAATAAACACCTG 59.172 38.462 0.00 0.00 0.00 4.00
2100 2152 5.253330 TCCTCCATGAAATAAACACCTGAC 58.747 41.667 0.00 0.00 0.00 3.51
2101 2153 5.014123 TCCTCCATGAAATAAACACCTGACT 59.986 40.000 0.00 0.00 0.00 3.41
2122 2183 5.725362 ACTAAAGTGTGTCTCTGCCTAATC 58.275 41.667 0.00 0.00 0.00 1.75
2276 2337 9.667989 ACAAACCGAATAAGTAAACAAATACAC 57.332 29.630 0.00 0.00 0.00 2.90
2399 2460 1.144708 TGAGGGTCAAGTTTGGCATGA 59.855 47.619 0.00 0.00 33.59 3.07
2420 2481 1.247567 GTTGTGCAGCATAACCACCT 58.752 50.000 21.28 0.00 30.98 4.00
2445 2506 8.044574 TGGATTCAATTCCTAGGATTGACATA 57.955 34.615 24.49 16.29 36.68 2.29
2448 2509 9.730705 GATTCAATTCCTAGGATTGACATATGA 57.269 33.333 24.49 14.09 34.47 2.15
2487 2548 9.527157 TCACCATTTATTGAGGATTAAGTTTGA 57.473 29.630 0.00 0.00 0.00 2.69
2566 2627 2.092968 GGACATGGCTTGATCTGTGGTA 60.093 50.000 7.45 0.00 0.00 3.25
2572 2633 4.030216 TGGCTTGATCTGTGGTATGACTA 58.970 43.478 0.00 0.00 0.00 2.59
2578 2639 7.543868 GCTTGATCTGTGGTATGACTACATATC 59.456 40.741 11.90 11.90 40.80 1.63
2632 2694 2.198827 TGTGTGCTCCCTAATTGGTG 57.801 50.000 0.00 0.00 0.00 4.17
2643 2705 2.550699 TAATTGGTGCAGAGGCCGGG 62.551 60.000 2.18 0.00 40.13 5.73
2667 2729 8.539544 GGGAATTGAAATTCTCTCCCAATTTTA 58.460 33.333 17.11 0.00 41.61 1.52
2681 2744 9.681062 TCTCCCAATTTTAAGGTATGTTTAGAG 57.319 33.333 0.00 0.00 0.00 2.43
2720 2783 7.121168 GTCTTTTCACCATTATTGATGACCTCA 59.879 37.037 0.00 0.00 38.03 3.86
2730 2793 5.964958 ATTGATGACCTCAACAAAATCGT 57.035 34.783 2.52 0.00 46.37 3.73
2738 2801 5.230942 ACCTCAACAAAATCGTAGAGACTG 58.769 41.667 0.00 0.00 43.63 3.51
2744 2807 5.462405 ACAAAATCGTAGAGACTGACACTC 58.538 41.667 0.00 0.00 43.63 3.51
2801 2874 3.406728 TCACGTCTATTGCGAGAAGAG 57.593 47.619 0.00 0.00 0.00 2.85
2837 2910 0.028110 GAAGATCCGGTGCGCAATTC 59.972 55.000 14.00 3.82 0.00 2.17
2841 2914 0.381801 ATCCGGTGCGCAATTCATTC 59.618 50.000 14.00 0.00 0.00 2.67
2849 2922 1.027357 CGCAATTCATTCTGGAGGGG 58.973 55.000 0.00 0.00 0.00 4.79
2908 2981 0.459585 CGGCACCGTAAGCAGTGTAT 60.460 55.000 0.00 0.00 36.35 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 2.238319 TACCCGCTCCCAGATGAGGT 62.238 60.000 0.00 0.00 32.81 3.85
25 26 2.298661 AACCCTTACCCGCTCCCAG 61.299 63.158 0.00 0.00 0.00 4.45
33 34 1.609841 CGGAGAACACAACCCTTACCC 60.610 57.143 0.00 0.00 0.00 3.69
34 35 1.345415 TCGGAGAACACAACCCTTACC 59.655 52.381 0.00 0.00 0.00 2.85
36 37 2.298163 GAGTCGGAGAACACAACCCTTA 59.702 50.000 0.00 0.00 39.69 2.69
66 67 0.393077 AACACTTCGGGTCTGGTCTG 59.607 55.000 0.00 0.00 0.00 3.51
75 76 2.218603 GGGCATGTATAACACTTCGGG 58.781 52.381 0.00 0.00 0.00 5.14
76 77 2.612212 GTGGGCATGTATAACACTTCGG 59.388 50.000 0.00 0.00 0.00 4.30
77 78 3.531538 AGTGGGCATGTATAACACTTCG 58.468 45.455 0.00 0.00 39.16 3.79
82 83 4.657013 TGTTGAAGTGGGCATGTATAACA 58.343 39.130 0.00 0.00 0.00 2.41
94 95 5.750067 CCAAAGAAGAAACATGTTGAAGTGG 59.250 40.000 12.82 9.67 0.00 4.00
101 102 4.060205 GCATGCCAAAGAAGAAACATGTT 58.940 39.130 6.36 4.92 37.73 2.71
102 103 3.555586 GGCATGCCAAAGAAGAAACATGT 60.556 43.478 32.08 0.00 37.73 3.21
106 107 1.269448 TCGGCATGCCAAAGAAGAAAC 59.731 47.619 34.93 4.81 35.37 2.78
140 141 1.062440 CGAATATGCTGTCGCTTGCAA 59.938 47.619 0.00 0.00 42.74 4.08
143 144 2.196749 ACTCGAATATGCTGTCGCTTG 58.803 47.619 0.00 0.00 37.19 4.01
144 145 2.099921 AGACTCGAATATGCTGTCGCTT 59.900 45.455 0.00 0.00 37.19 4.68
145 146 1.678627 AGACTCGAATATGCTGTCGCT 59.321 47.619 0.00 0.00 37.19 4.93
147 148 4.210832 TGTAGACTCGAATATGCTGTCG 57.789 45.455 0.00 0.00 38.62 4.35
149 150 4.515567 TCGATGTAGACTCGAATATGCTGT 59.484 41.667 0.00 0.00 41.79 4.40
153 154 6.836953 AGTCATCGATGTAGACTCGAATATG 58.163 40.000 24.09 0.00 46.98 1.78
160 161 5.508200 AAGGAAGTCATCGATGTAGACTC 57.492 43.478 24.09 14.05 41.45 3.36
178 179 5.290493 ACATGGATAAGCAACGATAAGGA 57.710 39.130 0.00 0.00 0.00 3.36
230 231 2.125350 GCTGCCTCTGAACCTCCG 60.125 66.667 0.00 0.00 0.00 4.63
233 234 0.694771 TCATTGCTGCCTCTGAACCT 59.305 50.000 0.00 0.00 0.00 3.50
266 267 1.746787 ACTACATACGTCGATGGTGCA 59.253 47.619 9.90 0.00 0.00 4.57
277 278 7.381678 GCCAAAGTCTTATTCCTACTACATACG 59.618 40.741 0.00 0.00 0.00 3.06
330 331 9.503399 CTTTACAAGTAGACCCTTACAGAAATT 57.497 33.333 0.00 0.00 0.00 1.82
371 373 5.474189 GGTTGCACTGGTACAAAATTAGGTA 59.526 40.000 0.00 0.00 38.70 3.08
372 374 4.279922 GGTTGCACTGGTACAAAATTAGGT 59.720 41.667 0.00 0.00 38.70 3.08
373 375 4.279671 TGGTTGCACTGGTACAAAATTAGG 59.720 41.667 0.00 0.00 38.70 2.69
375 377 5.303078 ACATGGTTGCACTGGTACAAAATTA 59.697 36.000 0.00 0.00 38.70 1.40
376 378 4.100808 ACATGGTTGCACTGGTACAAAATT 59.899 37.500 0.00 0.00 38.70 1.82
377 379 3.640967 ACATGGTTGCACTGGTACAAAAT 59.359 39.130 0.00 0.00 38.70 1.82
378 380 3.027412 ACATGGTTGCACTGGTACAAAA 58.973 40.909 0.00 0.00 38.70 2.44
379 381 2.360483 CACATGGTTGCACTGGTACAAA 59.640 45.455 0.00 0.00 38.70 2.83
380 382 1.952990 CACATGGTTGCACTGGTACAA 59.047 47.619 0.00 0.00 38.70 2.41
381 383 1.603456 CACATGGTTGCACTGGTACA 58.397 50.000 0.00 0.00 0.00 2.90
382 384 0.881118 CCACATGGTTGCACTGGTAC 59.119 55.000 0.00 0.00 0.00 3.34
391 411 5.601662 AGATCGTATAACTCCACATGGTTG 58.398 41.667 0.00 0.00 36.34 3.77
442 462 4.625742 GCTCTGCGTCTTTATTGTGTCTTA 59.374 41.667 0.00 0.00 0.00 2.10
456 476 0.376852 TTGTTTGTGTGCTCTGCGTC 59.623 50.000 0.00 0.00 0.00 5.19
457 477 0.378257 CTTGTTTGTGTGCTCTGCGT 59.622 50.000 0.00 0.00 0.00 5.24
458 478 0.378257 ACTTGTTTGTGTGCTCTGCG 59.622 50.000 0.00 0.00 0.00 5.18
459 479 1.401552 TGACTTGTTTGTGTGCTCTGC 59.598 47.619 0.00 0.00 0.00 4.26
479 499 7.277396 AGTGCGTACATAAGGGTTAATGTATT 58.723 34.615 6.38 0.00 32.91 1.89
508 528 7.296628 AGATGGTCATAGGAAGAGAATGTAC 57.703 40.000 0.00 0.00 0.00 2.90
512 532 4.526262 CGGAGATGGTCATAGGAAGAGAAT 59.474 45.833 0.00 0.00 0.00 2.40
521 541 1.068885 GTCGCTCGGAGATGGTCATAG 60.069 57.143 9.69 0.00 33.89 2.23
526 546 1.378646 TCAGTCGCTCGGAGATGGT 60.379 57.895 9.69 0.00 33.89 3.55
529 549 2.399856 GACTCAGTCGCTCGGAGAT 58.600 57.895 9.69 0.00 40.01 2.75
548 568 4.099419 ACTTCAACAATTTCAAGACCCACC 59.901 41.667 0.00 0.00 0.00 4.61
552 572 6.738114 TGATGACTTCAACAATTTCAAGACC 58.262 36.000 0.00 0.00 0.00 3.85
557 577 7.624134 GCGTCTATGATGACTTCAACAATTTCA 60.624 37.037 0.00 0.00 38.03 2.69
565 585 3.489229 CGAGGCGTCTATGATGACTTCAA 60.489 47.826 4.69 0.00 37.00 2.69
566 586 2.033424 CGAGGCGTCTATGATGACTTCA 59.967 50.000 4.69 0.00 37.00 3.02
567 587 2.656085 CGAGGCGTCTATGATGACTTC 58.344 52.381 4.69 0.00 37.00 3.01
570 590 0.030773 TGCGAGGCGTCTATGATGAC 59.969 55.000 4.69 0.00 0.00 3.06
576 596 3.367498 GGAATATTCTGCGAGGCGTCTAT 60.367 47.826 14.95 0.00 0.00 1.98
588 608 4.034510 GTCTCACAAAGGCGGAATATTCTG 59.965 45.833 18.41 18.41 36.64 3.02
590 610 3.938963 TGTCTCACAAAGGCGGAATATTC 59.061 43.478 6.93 6.93 29.57 1.75
597 617 0.817634 TTGGTGTCTCACAAAGGCGG 60.818 55.000 2.41 0.00 35.86 6.13
599 619 1.269257 GCTTTGGTGTCTCACAAAGGC 60.269 52.381 16.10 11.15 41.69 4.35
605 625 4.278419 AGGTTTTATGCTTTGGTGTCTCAC 59.722 41.667 0.00 0.00 0.00 3.51
841 871 0.037447 TCAACCATCATTCACCGGCA 59.963 50.000 0.00 0.00 0.00 5.69
892 922 7.621832 TGCAAATAATCAGAAAACTTTCACG 57.378 32.000 5.07 0.00 39.61 4.35
896 926 9.328845 ACAACATGCAAATAATCAGAAAACTTT 57.671 25.926 0.00 0.00 0.00 2.66
1251 1282 2.434702 CCGGCCCTTATTAGACTTGTCT 59.565 50.000 8.41 8.41 0.00 3.41
1339 1370 0.249155 CATGCCATCAAATGCCCGTC 60.249 55.000 0.00 0.00 0.00 4.79
1429 1460 5.921408 TGTTTTTGTTGTAGTTGTTGTCCAC 59.079 36.000 0.00 0.00 0.00 4.02
1468 1499 2.675423 TCTCACCCGTCCCGTCTG 60.675 66.667 0.00 0.00 0.00 3.51
1524 1559 0.744771 GGACGGCCAGGAGAACAATC 60.745 60.000 0.00 0.00 0.00 2.67
1525 1560 1.201429 AGGACGGCCAGGAGAACAAT 61.201 55.000 11.69 0.00 36.29 2.71
1530 1582 2.203788 AACAGGACGGCCAGGAGA 60.204 61.111 11.69 0.00 36.29 3.71
1615 1667 1.541588 GCAAAGGCAATCGAACTTCCT 59.458 47.619 0.00 0.00 40.72 3.36
1662 1714 6.609533 CAGCATGGATAGCAATTATTCACTC 58.390 40.000 0.00 0.00 29.91 3.51
1677 1729 1.897137 CGATGGCTGCAGCATGGAT 60.897 57.895 37.63 23.22 44.36 3.41
1703 1755 3.113514 TTGTCGCAGCACTTGGGGA 62.114 57.895 0.00 0.00 40.00 4.81
1704 1756 2.594303 TTGTCGCAGCACTTGGGG 60.594 61.111 0.00 0.00 40.00 4.96
1705 1757 1.893808 AGTTGTCGCAGCACTTGGG 60.894 57.895 0.00 0.00 40.88 4.12
1706 1758 1.280746 CAGTTGTCGCAGCACTTGG 59.719 57.895 0.00 0.00 0.00 3.61
1707 1759 1.369689 GCAGTTGTCGCAGCACTTG 60.370 57.895 0.00 0.00 0.00 3.16
1708 1760 1.819208 TGCAGTTGTCGCAGCACTT 60.819 52.632 0.00 0.00 33.55 3.16
1709 1761 2.203056 TGCAGTTGTCGCAGCACT 60.203 55.556 0.00 0.00 33.55 4.40
1714 1766 2.280797 GGACCTGCAGTTGTCGCA 60.281 61.111 13.81 0.00 37.88 5.10
1715 1767 1.569479 GAAGGACCTGCAGTTGTCGC 61.569 60.000 13.81 7.96 32.19 5.19
1720 1772 1.674057 CCGAGAAGGACCTGCAGTT 59.326 57.895 13.81 0.00 45.00 3.16
1721 1773 2.286523 CCCGAGAAGGACCTGCAGT 61.287 63.158 13.81 0.11 45.00 4.40
1737 1789 3.136123 TCACCGACGTCGATCCCC 61.136 66.667 37.65 0.00 43.02 4.81
1748 1800 4.124351 GATGGGCGTCGTCACCGA 62.124 66.667 0.00 0.00 41.73 4.69
1750 1802 3.771160 AGGATGGGCGTCGTCACC 61.771 66.667 0.00 0.00 33.11 4.02
1751 1803 2.509336 CAGGATGGGCGTCGTCAC 60.509 66.667 0.00 0.00 33.11 3.67
1752 1804 2.678580 TCAGGATGGGCGTCGTCA 60.679 61.111 0.00 0.00 36.16 4.35
1753 1805 2.105128 CTCAGGATGGGCGTCGTC 59.895 66.667 0.00 0.00 36.16 4.20
1754 1806 2.680352 ACTCAGGATGGGCGTCGT 60.680 61.111 0.00 0.00 43.96 4.34
1755 1807 2.202797 CACTCAGGATGGGCGTCG 60.203 66.667 0.00 0.00 43.96 5.12
1756 1808 2.512515 GCACTCAGGATGGGCGTC 60.513 66.667 0.00 0.00 43.96 5.19
1757 1809 4.101448 GGCACTCAGGATGGGCGT 62.101 66.667 0.00 0.00 43.96 5.68
1758 1810 4.864334 GGGCACTCAGGATGGGCG 62.864 72.222 0.00 0.00 43.96 6.13
1759 1811 4.512914 GGGGCACTCAGGATGGGC 62.513 72.222 0.00 0.00 43.96 5.36
1763 1815 2.311854 CCCTTGGGGCACTCAGGAT 61.312 63.158 7.10 0.00 35.35 3.24
1798 1850 4.008933 AGGGCTCGTCTGCACCAC 62.009 66.667 0.00 0.00 36.97 4.16
1799 1851 4.007644 CAGGGCTCGTCTGCACCA 62.008 66.667 0.00 0.00 36.97 4.17
1804 1856 2.435586 CTTGGCAGGGCTCGTCTG 60.436 66.667 0.00 0.00 35.49 3.51
1805 1857 2.604686 TCTTGGCAGGGCTCGTCT 60.605 61.111 0.00 0.00 0.00 4.18
1806 1858 2.435059 GTCTTGGCAGGGCTCGTC 60.435 66.667 0.00 0.00 0.00 4.20
1807 1859 4.379243 CGTCTTGGCAGGGCTCGT 62.379 66.667 0.00 0.00 0.00 4.18
1808 1860 3.883744 AACGTCTTGGCAGGGCTCG 62.884 63.158 0.00 4.20 0.00 5.03
1809 1861 2.032681 AACGTCTTGGCAGGGCTC 59.967 61.111 0.00 0.00 0.00 4.70
1810 1862 2.032681 GAACGTCTTGGCAGGGCT 59.967 61.111 0.00 0.00 0.00 5.19
1811 1863 2.281484 TGAACGTCTTGGCAGGGC 60.281 61.111 0.00 0.00 0.00 5.19
1812 1864 1.672356 CCTGAACGTCTTGGCAGGG 60.672 63.158 0.00 0.00 43.22 4.45
1813 1865 3.972227 CCTGAACGTCTTGGCAGG 58.028 61.111 0.00 0.00 41.62 4.85
1814 1866 1.845809 GCACCTGAACGTCTTGGCAG 61.846 60.000 0.00 0.00 0.00 4.85
1815 1867 1.891919 GCACCTGAACGTCTTGGCA 60.892 57.895 0.00 0.00 0.00 4.92
1816 1868 2.946762 GCACCTGAACGTCTTGGC 59.053 61.111 0.00 0.00 0.00 4.52
1817 1869 2.954753 GCGCACCTGAACGTCTTGG 61.955 63.158 0.30 0.00 0.00 3.61
1818 1870 2.551270 GCGCACCTGAACGTCTTG 59.449 61.111 0.30 0.00 0.00 3.02
1819 1871 2.665185 GGCGCACCTGAACGTCTT 60.665 61.111 10.83 0.00 0.00 3.01
1823 1875 3.620300 TAGTCGGCGCACCTGAACG 62.620 63.158 10.83 0.75 0.00 3.95
1824 1876 2.092882 GTAGTCGGCGCACCTGAAC 61.093 63.158 10.83 0.00 0.00 3.18
1825 1877 2.260434 GTAGTCGGCGCACCTGAA 59.740 61.111 10.83 0.00 0.00 3.02
1826 1878 3.755628 GGTAGTCGGCGCACCTGA 61.756 66.667 10.83 0.00 0.00 3.86
1834 1886 4.549516 GTCTCCGCGGTAGTCGGC 62.550 72.222 27.15 7.50 46.05 5.54
1836 1888 2.708255 GAGTCTCCGCGGTAGTCG 59.292 66.667 27.15 9.75 42.76 4.18
1837 1889 3.109240 GGAGTCTCCGCGGTAGTC 58.891 66.667 27.15 24.00 0.00 2.59
1846 1898 2.323580 ACGTGTCGTCGGAGTCTCC 61.324 63.158 9.05 9.05 33.69 3.71
1847 1899 1.154450 CACGTGTCGTCGGAGTCTC 60.154 63.158 7.58 0.00 38.32 3.36
1848 1900 2.944429 CACGTGTCGTCGGAGTCT 59.056 61.111 7.58 0.00 38.32 3.24
1849 1901 2.799916 GCACGTGTCGTCGGAGTC 60.800 66.667 18.38 0.00 38.32 3.36
1850 1902 4.678269 CGCACGTGTCGTCGGAGT 62.678 66.667 18.38 0.00 38.32 3.85
1868 1920 2.866726 TTTTTCTTGCAGGGCGGGC 61.867 57.895 0.00 0.00 0.00 6.13
1869 1921 1.006220 GTTTTTCTTGCAGGGCGGG 60.006 57.895 0.00 0.00 0.00 6.13
1870 1922 0.318955 CAGTTTTTCTTGCAGGGCGG 60.319 55.000 0.00 0.00 0.00 6.13
1871 1923 0.667993 TCAGTTTTTCTTGCAGGGCG 59.332 50.000 0.00 0.00 0.00 6.13
1872 1924 2.611224 CCATCAGTTTTTCTTGCAGGGC 60.611 50.000 0.00 0.00 0.00 5.19
1873 1925 2.028748 CCCATCAGTTTTTCTTGCAGGG 60.029 50.000 0.00 0.00 0.00 4.45
1874 1926 2.629617 ACCCATCAGTTTTTCTTGCAGG 59.370 45.455 0.00 0.00 0.00 4.85
1875 1927 4.326504 AACCCATCAGTTTTTCTTGCAG 57.673 40.909 0.00 0.00 0.00 4.41
1876 1928 5.738783 GCTTAACCCATCAGTTTTTCTTGCA 60.739 40.000 0.00 0.00 0.00 4.08
1877 1929 4.686091 GCTTAACCCATCAGTTTTTCTTGC 59.314 41.667 0.00 0.00 0.00 4.01
1878 1930 6.089249 AGCTTAACCCATCAGTTTTTCTTG 57.911 37.500 0.00 0.00 0.00 3.02
1879 1931 5.833131 TGAGCTTAACCCATCAGTTTTTCTT 59.167 36.000 0.00 0.00 0.00 2.52
1880 1932 5.385198 TGAGCTTAACCCATCAGTTTTTCT 58.615 37.500 0.00 0.00 0.00 2.52
1881 1933 5.473504 TCTGAGCTTAACCCATCAGTTTTTC 59.526 40.000 0.00 0.00 40.07 2.29
1882 1934 5.385198 TCTGAGCTTAACCCATCAGTTTTT 58.615 37.500 0.00 0.00 40.07 1.94
1883 1935 4.985538 TCTGAGCTTAACCCATCAGTTTT 58.014 39.130 0.00 0.00 40.07 2.43
1884 1936 4.640771 TCTGAGCTTAACCCATCAGTTT 57.359 40.909 0.00 0.00 40.07 2.66
1885 1937 4.225942 TGATCTGAGCTTAACCCATCAGTT 59.774 41.667 0.00 0.00 40.07 3.16
1886 1938 3.776969 TGATCTGAGCTTAACCCATCAGT 59.223 43.478 0.00 0.00 40.07 3.41
1887 1939 4.125703 GTGATCTGAGCTTAACCCATCAG 58.874 47.826 0.00 0.00 40.42 2.90
1888 1940 3.430790 CGTGATCTGAGCTTAACCCATCA 60.431 47.826 0.00 0.00 0.00 3.07
1889 1941 3.126831 CGTGATCTGAGCTTAACCCATC 58.873 50.000 0.00 0.00 0.00 3.51
1890 1942 2.766263 TCGTGATCTGAGCTTAACCCAT 59.234 45.455 0.00 0.00 0.00 4.00
1891 1943 2.176045 TCGTGATCTGAGCTTAACCCA 58.824 47.619 0.00 0.00 0.00 4.51
1892 1944 2.961526 TCGTGATCTGAGCTTAACCC 57.038 50.000 0.00 0.00 0.00 4.11
1893 1945 4.631813 ACATTTCGTGATCTGAGCTTAACC 59.368 41.667 0.00 0.00 0.00 2.85
1894 1946 5.786401 ACATTTCGTGATCTGAGCTTAAC 57.214 39.130 0.00 0.00 0.00 2.01
1895 1947 6.801539 AAACATTTCGTGATCTGAGCTTAA 57.198 33.333 0.00 0.00 0.00 1.85
1896 1948 6.408858 GAAACATTTCGTGATCTGAGCTTA 57.591 37.500 0.00 0.00 0.00 3.09
1897 1949 5.288543 GAAACATTTCGTGATCTGAGCTT 57.711 39.130 0.00 0.00 0.00 3.74
1898 1950 4.935885 GAAACATTTCGTGATCTGAGCT 57.064 40.909 0.00 0.00 0.00 4.09
1910 1962 6.073276 AGCTTTTATTTTGGGCGAAACATTTC 60.073 34.615 0.00 0.00 0.00 2.17
1911 1963 5.762711 AGCTTTTATTTTGGGCGAAACATTT 59.237 32.000 0.00 0.00 0.00 2.32
1912 1964 5.304778 AGCTTTTATTTTGGGCGAAACATT 58.695 33.333 0.00 0.00 0.00 2.71
1913 1965 4.893608 AGCTTTTATTTTGGGCGAAACAT 58.106 34.783 0.00 0.00 0.00 2.71
1914 1966 4.202161 TGAGCTTTTATTTTGGGCGAAACA 60.202 37.500 0.00 0.00 0.00 2.83
1915 1967 4.303282 TGAGCTTTTATTTTGGGCGAAAC 58.697 39.130 0.00 0.00 0.00 2.78
1916 1968 4.279671 TCTGAGCTTTTATTTTGGGCGAAA 59.720 37.500 0.00 0.00 0.00 3.46
1917 1969 3.823873 TCTGAGCTTTTATTTTGGGCGAA 59.176 39.130 0.00 0.00 0.00 4.70
1918 1970 3.190535 GTCTGAGCTTTTATTTTGGGCGA 59.809 43.478 0.00 0.00 0.00 5.54
1919 1971 3.501950 GTCTGAGCTTTTATTTTGGGCG 58.498 45.455 0.00 0.00 0.00 6.13
1920 1972 3.190535 TCGTCTGAGCTTTTATTTTGGGC 59.809 43.478 0.00 0.00 0.00 5.36
1921 1973 4.695455 TCTCGTCTGAGCTTTTATTTTGGG 59.305 41.667 0.00 0.00 42.26 4.12
1922 1974 5.862924 TCTCGTCTGAGCTTTTATTTTGG 57.137 39.130 0.00 0.00 42.26 3.28
1923 1975 7.065216 TCATCTCGTCTGAGCTTTTATTTTG 57.935 36.000 0.00 0.00 42.26 2.44
1924 1976 7.301068 CTCATCTCGTCTGAGCTTTTATTTT 57.699 36.000 0.00 0.00 42.26 1.82
1925 1977 6.900568 CTCATCTCGTCTGAGCTTTTATTT 57.099 37.500 0.00 0.00 42.26 1.40
1934 1986 0.248417 CCGTGCTCATCTCGTCTGAG 60.248 60.000 7.11 7.11 43.99 3.35
1935 1987 0.960861 ACCGTGCTCATCTCGTCTGA 60.961 55.000 0.00 0.00 0.00 3.27
1936 1988 0.524392 GACCGTGCTCATCTCGTCTG 60.524 60.000 0.00 0.00 0.00 3.51
1937 1989 0.960861 TGACCGTGCTCATCTCGTCT 60.961 55.000 0.00 0.00 0.00 4.18
1938 1990 0.798771 GTGACCGTGCTCATCTCGTC 60.799 60.000 0.00 0.00 0.00 4.20
1939 1991 1.213013 GTGACCGTGCTCATCTCGT 59.787 57.895 0.00 0.00 0.00 4.18
1940 1992 0.799917 CAGTGACCGTGCTCATCTCG 60.800 60.000 0.00 0.00 0.00 4.04
1941 1993 0.244994 ACAGTGACCGTGCTCATCTC 59.755 55.000 0.00 0.00 0.00 2.75
1942 1994 0.037882 CACAGTGACCGTGCTCATCT 60.038 55.000 0.00 0.00 0.00 2.90
1943 1995 0.319900 ACACAGTGACCGTGCTCATC 60.320 55.000 7.81 0.00 37.93 2.92
1944 1996 0.106708 AACACAGTGACCGTGCTCAT 59.893 50.000 7.81 0.00 37.93 2.90
1945 1997 0.107897 AAACACAGTGACCGTGCTCA 60.108 50.000 7.81 0.00 37.93 4.26
1946 1998 0.304705 CAAACACAGTGACCGTGCTC 59.695 55.000 7.81 0.00 37.93 4.26
1947 1999 0.392461 ACAAACACAGTGACCGTGCT 60.392 50.000 7.81 0.00 37.93 4.40
1948 2000 0.248054 CACAAACACAGTGACCGTGC 60.248 55.000 7.81 0.00 39.30 5.34
1949 2001 1.083489 ACACAAACACAGTGACCGTG 58.917 50.000 7.81 12.60 40.16 4.94
1950 2002 1.083489 CACACAAACACAGTGACCGT 58.917 50.000 7.81 0.00 40.16 4.83
1951 2003 1.083489 ACACACAAACACAGTGACCG 58.917 50.000 7.81 0.00 40.16 4.79
1952 2004 3.004171 TGTACACACAAACACAGTGACC 58.996 45.455 7.81 0.00 40.16 4.02
1953 2005 4.875544 ATGTACACACAAACACAGTGAC 57.124 40.909 7.81 0.00 40.16 3.67
1954 2006 5.635866 CAAATGTACACACAAACACAGTGA 58.364 37.500 7.81 0.00 40.16 3.41
1958 2010 3.429547 GGGCAAATGTACACACAAACACA 60.430 43.478 0.00 0.00 38.42 3.72
1971 2023 0.596082 GTACAACGCAGGGCAAATGT 59.404 50.000 0.00 0.00 0.00 2.71
2029 2081 6.837992 TCAACAACAACTTACTCTTGAACAC 58.162 36.000 0.00 0.00 0.00 3.32
2077 2129 5.014123 AGTCAGGTGTTTATTTCATGGAGGA 59.986 40.000 0.00 0.00 0.00 3.71
2080 2132 7.942341 ACTTTAGTCAGGTGTTTATTTCATGGA 59.058 33.333 0.00 0.00 0.00 3.41
2092 2144 3.961408 AGAGACACACTTTAGTCAGGTGT 59.039 43.478 4.69 4.69 44.65 4.16
2094 2146 3.243907 GCAGAGACACACTTTAGTCAGGT 60.244 47.826 0.00 0.00 37.23 4.00
2095 2147 3.321497 GCAGAGACACACTTTAGTCAGG 58.679 50.000 0.00 0.00 37.23 3.86
2096 2148 3.006323 AGGCAGAGACACACTTTAGTCAG 59.994 47.826 0.00 0.00 37.23 3.51
2097 2149 2.965831 AGGCAGAGACACACTTTAGTCA 59.034 45.455 0.00 0.00 37.23 3.41
2098 2150 3.669251 AGGCAGAGACACACTTTAGTC 57.331 47.619 0.00 0.00 35.02 2.59
2100 2152 5.724328 TGATTAGGCAGAGACACACTTTAG 58.276 41.667 0.00 0.00 0.00 1.85
2101 2153 5.480422 TCTGATTAGGCAGAGACACACTTTA 59.520 40.000 0.00 0.00 39.84 1.85
2337 2398 9.287373 ACTAAACAAATAAAACGTATTCCCTCA 57.713 29.630 0.00 0.00 0.00 3.86
2382 2443 0.890683 CCTCATGCCAAACTTGACCC 59.109 55.000 0.00 0.00 0.00 4.46
2399 2460 1.247567 GTGGTTATGCTGCACAACCT 58.752 50.000 34.67 10.82 41.89 3.50
2418 2479 5.767168 GTCAATCCTAGGAATTGAATCCAGG 59.233 44.000 25.49 4.20 42.27 4.45
2420 2481 6.325993 TGTCAATCCTAGGAATTGAATCCA 57.674 37.500 25.49 19.78 42.27 3.41
2445 2506 2.898612 TGGTGAAAACCATGTGCATCAT 59.101 40.909 0.00 0.00 34.33 2.45
2549 2610 3.457380 AGTCATACCACAGATCAAGCCAT 59.543 43.478 0.00 0.00 0.00 4.40
2550 2611 2.840038 AGTCATACCACAGATCAAGCCA 59.160 45.455 0.00 0.00 0.00 4.75
2603 2664 6.569179 TTAGGGAGCACACAATCTTTTTAC 57.431 37.500 0.00 0.00 0.00 2.01
2611 2672 3.091545 CACCAATTAGGGAGCACACAAT 58.908 45.455 0.00 0.00 43.89 2.71
2632 2694 0.965363 TTTCAATTCCCGGCCTCTGC 60.965 55.000 0.00 0.00 0.00 4.26
2667 2729 8.568794 GTTGCTTTTCTTCTCTAAACATACCTT 58.431 33.333 0.00 0.00 0.00 3.50
2720 2783 5.844004 AGTGTCAGTCTCTACGATTTTGTT 58.156 37.500 0.00 0.00 0.00 2.83
2738 2801 7.148641 TCAATCTCTTGTTAAGACAGAGTGTC 58.851 38.462 0.00 0.00 39.26 3.67
2801 2874 3.986277 TCTTCGGTACCACTTGAGTTTC 58.014 45.455 13.54 0.00 0.00 2.78
2837 2910 4.942363 ATTGATATCCCCCTCCAGAATG 57.058 45.455 0.00 0.00 0.00 2.67
2841 2914 3.055819 CGTGTATTGATATCCCCCTCCAG 60.056 52.174 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.