Multiple sequence alignment - TraesCS7B01G072100

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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 TraesCS7B01G072100 chr7B 100.000 2291 0 0 1 2291 79314820 79317110 0.000000e+00 4231
1 TraesCS7B01G072100 chr7B 90.528 549 41 9 1 541 155465066 155464521 0.000000e+00 715
2 TraesCS7B01G072100 chr7B 95.683 139 4 2 1565 1702 79313011 79312874 2.960000e-54 222
3 TraesCS7B01G072100 chr7A 87.308 1040 66 18 537 1534 122682868 122683883 0.000000e+00 1129
4 TraesCS7B01G072100 chr7A 92.508 307 23 0 1768 2074 698895438 698895132 7.510000e-120 440
5 TraesCS7B01G072100 chr7A 92.182 307 24 0 1768 2074 698788928 698788622 3.500000e-118 435
6 TraesCS7B01G072100 chr7A 91.429 315 25 2 1759 2073 725206139 725206451 4.520000e-117 431
7 TraesCS7B01G072100 chr7A 91.053 190 13 4 2103 2291 122684591 122684777 1.050000e-63 254
8 TraesCS7B01G072100 chr7A 90.000 170 14 3 1531 1699 122683988 122684155 1.380000e-52 217
9 TraesCS7B01G072100 chr7A 94.776 134 6 1 1567 1700 122682350 122682218 8.290000e-50 207
10 TraesCS7B01G072100 chr7A 82.677 127 14 5 2088 2213 122682171 122682052 3.110000e-19 106
11 TraesCS7B01G072100 chr7D 91.965 809 45 9 743 1534 118161282 118162087 0.000000e+00 1116
12 TraesCS7B01G072100 chr7D 92.810 306 22 0 1768 2073 196009374 196009069 5.810000e-121 444
13 TraesCS7B01G072100 chr7D 91.667 312 26 0 1762 2073 611128829 611129140 1.260000e-117 433
14 TraesCS7B01G072100 chr7D 91.346 312 27 0 1762 2073 611134383 611134694 5.850000e-116 427
15 TraesCS7B01G072100 chr7D 94.375 160 6 3 1531 1689 118162178 118162335 2.270000e-60 243
16 TraesCS7B01G072100 chr7D 94.079 152 6 2 537 685 118161116 118161267 6.370000e-56 228
17 TraesCS7B01G072100 chr7D 93.846 130 5 3 1570 1699 118160573 118160447 2.320000e-45 193
18 TraesCS7B01G072100 chr7D 83.871 124 10 4 2077 2190 118160363 118160240 2.410000e-20 110
19 TraesCS7B01G072100 chr5B 93.370 543 30 4 1 537 293464982 293465524 0.000000e+00 798
20 TraesCS7B01G072100 chr5B 93.223 546 29 6 1 540 409472616 409473159 0.000000e+00 797
21 TraesCS7B01G072100 chr5B 90.580 552 41 9 1 544 376338042 376337494 0.000000e+00 721
22 TraesCS7B01G072100 chr5B 90.328 548 43 9 1 540 689870195 689869650 0.000000e+00 710
23 TraesCS7B01G072100 chr4B 92.661 545 33 6 1 540 507255389 507254847 0.000000e+00 778
24 TraesCS7B01G072100 chr4B 89.599 548 47 8 1 540 134897084 134896539 0.000000e+00 688
25 TraesCS7B01G072100 chr3B 91.486 552 34 6 1 540 817190876 817190326 0.000000e+00 747
26 TraesCS7B01G072100 chr1A 89.725 545 46 8 1 537 348697534 348696992 0.000000e+00 688
27 TraesCS7B01G072100 chr3A 92.880 309 21 1 1765 2073 28326729 28327036 4.490000e-122 448
28 TraesCS7B01G072100 chr5A 91.909 309 23 2 1765 2073 694528963 694528657 4.520000e-117 431
29 TraesCS7B01G072100 chr5A 91.167 317 25 3 1759 2073 607410196 607410511 5.850000e-116 427
30 TraesCS7B01G072100 chrUn 96.040 101 2 2 1583 1681 21199034 21198934 1.820000e-36 163
31 TraesCS7B01G072100 chr6A 96.040 101 2 2 1583 1682 55551265 55551364 1.820000e-36 163
32 TraesCS7B01G072100 chr2B 91.525 118 6 4 1579 1695 175075335 175075221 2.360000e-35 159
33 TraesCS7B01G072100 chr2D 92.035 113 5 3 1584 1695 122055651 122055542 3.050000e-34 156


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 TraesCS7B01G072100 chr7B 79314820 79317110 2290 False 4231.000000 4231 100.000000 1 2291 1 chr7B.!!$F1 2290
1 TraesCS7B01G072100 chr7B 155464521 155465066 545 True 715.000000 715 90.528000 1 541 1 chr7B.!!$R2 540
2 TraesCS7B01G072100 chr7A 122682868 122684777 1909 False 533.333333 1129 89.453667 537 2291 3 chr7A.!!$F2 1754
3 TraesCS7B01G072100 chr7D 118161116 118162335 1219 False 529.000000 1116 93.473000 537 1689 3 chr7D.!!$F3 1152
4 TraesCS7B01G072100 chr5B 293464982 293465524 542 False 798.000000 798 93.370000 1 537 1 chr5B.!!$F1 536
5 TraesCS7B01G072100 chr5B 409472616 409473159 543 False 797.000000 797 93.223000 1 540 1 chr5B.!!$F2 539
6 TraesCS7B01G072100 chr5B 376337494 376338042 548 True 721.000000 721 90.580000 1 544 1 chr5B.!!$R1 543
7 TraesCS7B01G072100 chr5B 689869650 689870195 545 True 710.000000 710 90.328000 1 540 1 chr5B.!!$R2 539
8 TraesCS7B01G072100 chr4B 507254847 507255389 542 True 778.000000 778 92.661000 1 540 1 chr4B.!!$R2 539
9 TraesCS7B01G072100 chr4B 134896539 134897084 545 True 688.000000 688 89.599000 1 540 1 chr4B.!!$R1 539
10 TraesCS7B01G072100 chr3B 817190326 817190876 550 True 747.000000 747 91.486000 1 540 1 chr3B.!!$R1 539
11 TraesCS7B01G072100 chr1A 348696992 348697534 542 True 688.000000 688 89.725000 1 537 1 chr1A.!!$R1 536

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
736 772 0.390735 GGCCATACGGTTCAGTCGTT 60.391 55.0 0.0 0.0 41.38 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2096 2622 0.032416 ATAGGTCTGGCGTACCCACT 60.032 55.0 4.58 0.0 39.18 4.0 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
375 390 3.615709 AAAACAGCTTGCCCCGGC 61.616 61.111 0.00 0.00 42.35 6.13
592 609 4.435970 TGGCCCTGCTGCTCATGG 62.436 66.667 0.00 0.00 34.06 3.66
619 653 1.103803 GTGCCACCTCAGAGACGATA 58.896 55.000 0.00 0.00 0.00 2.92
626 660 2.302260 CCTCAGAGACGATAGCTTCCA 58.698 52.381 0.00 0.00 42.67 3.53
684 720 2.871182 TGTGACAGAGACACAGACAC 57.129 50.000 0.00 0.00 42.20 3.67
685 721 2.099405 TGTGACAGAGACACAGACACA 58.901 47.619 0.00 0.00 42.20 3.72
686 722 2.099756 TGTGACAGAGACACAGACACAG 59.900 50.000 0.00 0.00 42.20 3.66
711 747 0.529337 ACGATGATGAGCGAAGGCAG 60.529 55.000 0.00 0.00 43.41 4.85
726 762 4.569180 CAGGGGCAGGCCATACGG 62.569 72.222 16.36 0.59 37.98 4.02
728 764 4.123545 GGGGCAGGCCATACGGTT 62.124 66.667 16.36 0.00 37.98 4.44
729 765 2.516225 GGGCAGGCCATACGGTTC 60.516 66.667 13.10 0.00 37.98 3.62
730 766 2.270850 GGCAGGCCATACGGTTCA 59.729 61.111 5.01 0.00 35.81 3.18
731 767 1.819632 GGCAGGCCATACGGTTCAG 60.820 63.158 5.01 0.00 35.81 3.02
732 768 1.078426 GCAGGCCATACGGTTCAGT 60.078 57.895 5.01 0.00 33.28 3.41
733 769 1.090052 GCAGGCCATACGGTTCAGTC 61.090 60.000 5.01 0.00 33.28 3.51
734 770 0.806102 CAGGCCATACGGTTCAGTCG 60.806 60.000 5.01 0.00 33.28 4.18
735 771 1.217244 GGCCATACGGTTCAGTCGT 59.783 57.895 0.00 0.00 43.64 4.34
736 772 0.390735 GGCCATACGGTTCAGTCGTT 60.391 55.000 0.00 0.00 41.38 3.85
737 773 0.997196 GCCATACGGTTCAGTCGTTC 59.003 55.000 0.00 0.00 41.38 3.95
738 774 1.670674 GCCATACGGTTCAGTCGTTCA 60.671 52.381 0.00 0.00 41.38 3.18
739 775 2.259618 CCATACGGTTCAGTCGTTCAG 58.740 52.381 0.00 0.00 41.38 3.02
740 776 2.352421 CCATACGGTTCAGTCGTTCAGT 60.352 50.000 0.00 0.00 41.38 3.41
741 777 2.693797 TACGGTTCAGTCGTTCAGTC 57.306 50.000 0.00 0.00 41.38 3.51
761 797 3.433615 GTCGTTCAGATGTGGGAAGAAAG 59.566 47.826 0.00 0.00 0.00 2.62
877 917 9.923143 CCTCTATATATAAACAACGACCAATCA 57.077 33.333 0.00 0.00 0.00 2.57
897 937 0.940126 CACACAGGACACAGAAGCAC 59.060 55.000 0.00 0.00 0.00 4.40
899 939 0.940126 CACAGGACACAGAAGCACAC 59.060 55.000 0.00 0.00 0.00 3.82
900 940 0.530650 ACAGGACACAGAAGCACACG 60.531 55.000 0.00 0.00 0.00 4.49
901 941 1.595382 AGGACACAGAAGCACACGC 60.595 57.895 0.00 0.00 38.99 5.34
936 984 0.921347 GCTACACATTTCGATCGCGT 59.079 50.000 11.09 1.74 38.98 6.01
1326 1393 4.921515 GTGTTGAGCTAATGTACGAGTCAA 59.078 41.667 0.00 0.00 0.00 3.18
1345 1412 1.453155 ATGGTGCGTGCTTTCTTAGG 58.547 50.000 0.00 0.00 0.00 2.69
1432 1499 6.346919 GCTTGTGTGTGTACAGTAGATTGAAG 60.347 42.308 0.00 0.00 37.52 3.02
1443 1510 5.356190 ACAGTAGATTGAAGTGCAATGGATG 59.644 40.000 0.00 0.00 46.90 3.51
1456 1523 7.365741 AGTGCAATGGATGATTCGATTTTATC 58.634 34.615 0.00 0.00 28.89 1.75
1458 1525 7.536622 GTGCAATGGATGATTCGATTTTATCTC 59.463 37.037 0.00 0.00 28.89 2.75
1497 1564 1.271840 TTCTGGCTGCTTATCGGGGT 61.272 55.000 0.00 0.00 0.00 4.95
1501 1571 1.523938 GCTGCTTATCGGGGTGGAC 60.524 63.158 0.00 0.00 0.00 4.02
1581 1760 9.107177 AGACAATTAGCTTATGTGAGAATCTTG 57.893 33.333 0.00 0.00 34.92 3.02
1675 1854 2.031944 CGAATCTCTCAGGCGTCGATAA 60.032 50.000 0.00 0.00 0.00 1.75
1738 2111 7.165485 ACATAAACCGGTATATATGTGCATGT 58.835 34.615 26.92 13.75 37.53 3.21
1771 2297 8.630054 TGGCATTTACACAACTTAAAGATACT 57.370 30.769 0.00 0.00 0.00 2.12
1772 2298 8.726988 TGGCATTTACACAACTTAAAGATACTC 58.273 33.333 0.00 0.00 0.00 2.59
1774 2300 8.182227 GCATTTACACAACTTAAAGATACTCCC 58.818 37.037 0.00 0.00 0.00 4.30
1776 2302 9.668497 ATTTACACAACTTAAAGATACTCCCTC 57.332 33.333 0.00 0.00 0.00 4.30
1777 2303 6.051179 ACACAACTTAAAGATACTCCCTCC 57.949 41.667 0.00 0.00 0.00 4.30
1778 2304 5.546499 ACACAACTTAAAGATACTCCCTCCA 59.454 40.000 0.00 0.00 0.00 3.86
1780 2306 7.112779 CACAACTTAAAGATACTCCCTCCATT 58.887 38.462 0.00 0.00 0.00 3.16
1781 2307 7.611855 CACAACTTAAAGATACTCCCTCCATTT 59.388 37.037 0.00 0.00 0.00 2.32
1782 2308 8.170730 ACAACTTAAAGATACTCCCTCCATTTT 58.829 33.333 0.00 0.00 0.00 1.82
1794 2320 8.114301 ACTCCCTCCATTTTTATATACAAGGT 57.886 34.615 0.00 0.00 0.00 3.50
1795 2321 8.218488 ACTCCCTCCATTTTTATATACAAGGTC 58.782 37.037 0.00 0.00 0.00 3.85
1796 2322 8.108378 TCCCTCCATTTTTATATACAAGGTCA 57.892 34.615 0.00 0.00 0.00 4.02
1797 2323 7.996644 TCCCTCCATTTTTATATACAAGGTCAC 59.003 37.037 0.00 0.00 0.00 3.67
1798 2324 7.998964 CCCTCCATTTTTATATACAAGGTCACT 59.001 37.037 0.00 0.00 0.00 3.41
1817 2343 9.407380 AGGTCACTATGAAATATACATTTTGCA 57.593 29.630 0.00 0.00 34.44 4.08
1830 2356 5.520376 ACATTTTGCATCTATACAAGGCC 57.480 39.130 0.00 0.00 0.00 5.19
1831 2357 4.955450 ACATTTTGCATCTATACAAGGCCA 59.045 37.500 5.01 0.00 0.00 5.36
1832 2358 4.981806 TTTTGCATCTATACAAGGCCAC 57.018 40.909 5.01 0.00 0.00 5.01
1833 2359 2.638480 TGCATCTATACAAGGCCACC 57.362 50.000 5.01 0.00 0.00 4.61
1834 2360 1.843206 TGCATCTATACAAGGCCACCA 59.157 47.619 5.01 0.00 0.00 4.17
1835 2361 2.240921 TGCATCTATACAAGGCCACCAA 59.759 45.455 5.01 0.00 0.00 3.67
1836 2362 2.618709 GCATCTATACAAGGCCACCAAC 59.381 50.000 5.01 0.00 0.00 3.77
1837 2363 3.884895 CATCTATACAAGGCCACCAACA 58.115 45.455 5.01 0.00 0.00 3.33
1838 2364 4.269183 CATCTATACAAGGCCACCAACAA 58.731 43.478 5.01 0.00 0.00 2.83
1839 2365 4.584638 TCTATACAAGGCCACCAACAAT 57.415 40.909 5.01 0.00 0.00 2.71
1840 2366 5.702065 TCTATACAAGGCCACCAACAATA 57.298 39.130 5.01 0.00 0.00 1.90
1841 2367 6.068461 TCTATACAAGGCCACCAACAATAA 57.932 37.500 5.01 0.00 0.00 1.40
1842 2368 6.668645 TCTATACAAGGCCACCAACAATAAT 58.331 36.000 5.01 0.00 0.00 1.28
1843 2369 5.852282 ATACAAGGCCACCAACAATAATC 57.148 39.130 5.01 0.00 0.00 1.75
1844 2370 2.491693 ACAAGGCCACCAACAATAATCG 59.508 45.455 5.01 0.00 0.00 3.34
1845 2371 2.752354 CAAGGCCACCAACAATAATCGA 59.248 45.455 5.01 0.00 0.00 3.59
1846 2372 2.643551 AGGCCACCAACAATAATCGAG 58.356 47.619 5.01 0.00 0.00 4.04
1847 2373 1.676006 GGCCACCAACAATAATCGAGG 59.324 52.381 0.00 0.00 0.00 4.63
1848 2374 1.065551 GCCACCAACAATAATCGAGGC 59.934 52.381 0.00 0.00 0.00 4.70
1849 2375 2.364632 CCACCAACAATAATCGAGGCA 58.635 47.619 0.00 0.00 0.00 4.75
1850 2376 2.752354 CCACCAACAATAATCGAGGCAA 59.248 45.455 0.00 0.00 0.00 4.52
1851 2377 3.192422 CCACCAACAATAATCGAGGCAAA 59.808 43.478 0.00 0.00 0.00 3.68
1852 2378 4.321601 CCACCAACAATAATCGAGGCAAAA 60.322 41.667 0.00 0.00 0.00 2.44
1853 2379 5.410067 CACCAACAATAATCGAGGCAAAAT 58.590 37.500 0.00 0.00 0.00 1.82
1854 2380 5.868801 CACCAACAATAATCGAGGCAAAATT 59.131 36.000 0.00 0.00 0.00 1.82
1855 2381 7.032580 CACCAACAATAATCGAGGCAAAATTA 58.967 34.615 0.00 0.00 0.00 1.40
1856 2382 7.543868 CACCAACAATAATCGAGGCAAAATTAA 59.456 33.333 0.00 0.00 0.00 1.40
1857 2383 8.257306 ACCAACAATAATCGAGGCAAAATTAAT 58.743 29.630 0.00 0.00 0.00 1.40
1858 2384 8.542132 CCAACAATAATCGAGGCAAAATTAATG 58.458 33.333 0.00 0.00 0.00 1.90
1859 2385 9.299963 CAACAATAATCGAGGCAAAATTAATGA 57.700 29.630 0.00 0.00 0.00 2.57
1894 2420 8.455682 TGTAGTAGCAACCTGTTTAATAATTGC 58.544 33.333 0.00 0.00 42.11 3.56
1895 2421 7.461182 AGTAGCAACCTGTTTAATAATTGCA 57.539 32.000 9.21 0.00 43.77 4.08
1896 2422 8.066612 AGTAGCAACCTGTTTAATAATTGCAT 57.933 30.769 9.21 0.00 43.77 3.96
1897 2423 7.975616 AGTAGCAACCTGTTTAATAATTGCATG 59.024 33.333 9.21 0.00 43.77 4.06
1898 2424 5.581874 AGCAACCTGTTTAATAATTGCATGC 59.418 36.000 11.82 11.82 43.77 4.06
1899 2425 5.350914 GCAACCTGTTTAATAATTGCATGCA 59.649 36.000 18.46 18.46 41.56 3.96
1900 2426 6.037391 GCAACCTGTTTAATAATTGCATGCAT 59.963 34.615 23.37 10.46 41.56 3.96
1901 2427 7.403421 CAACCTGTTTAATAATTGCATGCATG 58.597 34.615 23.37 22.70 0.00 4.06
1917 2443 5.528870 CATGCATGCATTCATAATGACAGT 58.471 37.500 30.32 2.29 41.46 3.55
1918 2444 5.177725 TGCATGCATTCATAATGACAGTC 57.822 39.130 18.46 0.00 41.46 3.51
1919 2445 4.641094 TGCATGCATTCATAATGACAGTCA 59.359 37.500 18.46 5.50 41.46 3.41
1920 2446 5.212934 GCATGCATTCATAATGACAGTCAG 58.787 41.667 14.21 0.00 41.46 3.51
1921 2447 4.888038 TGCATTCATAATGACAGTCAGC 57.112 40.909 9.64 4.89 41.46 4.26
1922 2448 4.520179 TGCATTCATAATGACAGTCAGCT 58.480 39.130 9.64 1.33 41.46 4.24
1923 2449 5.673514 TGCATTCATAATGACAGTCAGCTA 58.326 37.500 9.64 3.65 41.46 3.32
1924 2450 5.525012 TGCATTCATAATGACAGTCAGCTAC 59.475 40.000 9.64 0.00 41.46 3.58
1925 2451 5.757320 GCATTCATAATGACAGTCAGCTACT 59.243 40.000 9.64 0.00 41.46 2.57
1926 2452 6.259608 GCATTCATAATGACAGTCAGCTACTT 59.740 38.462 9.64 0.51 41.46 2.24
1927 2453 7.518052 GCATTCATAATGACAGTCAGCTACTTC 60.518 40.741 9.64 0.00 41.46 3.01
1928 2454 5.907207 TCATAATGACAGTCAGCTACTTCC 58.093 41.667 9.64 0.00 35.76 3.46
1929 2455 5.658634 TCATAATGACAGTCAGCTACTTCCT 59.341 40.000 9.64 0.00 35.76 3.36
1930 2456 4.464069 AATGACAGTCAGCTACTTCCTC 57.536 45.455 9.64 0.00 35.76 3.71
1931 2457 2.171840 TGACAGTCAGCTACTTCCTCC 58.828 52.381 0.00 0.00 35.76 4.30
1932 2458 2.171840 GACAGTCAGCTACTTCCTCCA 58.828 52.381 0.00 0.00 35.76 3.86
1933 2459 2.763448 GACAGTCAGCTACTTCCTCCAT 59.237 50.000 0.00 0.00 35.76 3.41
1934 2460 3.177228 ACAGTCAGCTACTTCCTCCATT 58.823 45.455 0.00 0.00 35.76 3.16
1935 2461 3.196685 ACAGTCAGCTACTTCCTCCATTC 59.803 47.826 0.00 0.00 35.76 2.67
1936 2462 3.196469 CAGTCAGCTACTTCCTCCATTCA 59.804 47.826 0.00 0.00 35.76 2.57
1937 2463 3.450457 AGTCAGCTACTTCCTCCATTCAG 59.550 47.826 0.00 0.00 33.35 3.02
1938 2464 3.196685 GTCAGCTACTTCCTCCATTCAGT 59.803 47.826 0.00 0.00 0.00 3.41
1939 2465 3.840666 TCAGCTACTTCCTCCATTCAGTT 59.159 43.478 0.00 0.00 0.00 3.16
1940 2466 4.287067 TCAGCTACTTCCTCCATTCAGTTT 59.713 41.667 0.00 0.00 0.00 2.66
1941 2467 5.006386 CAGCTACTTCCTCCATTCAGTTTT 58.994 41.667 0.00 0.00 0.00 2.43
1942 2468 5.123027 CAGCTACTTCCTCCATTCAGTTTTC 59.877 44.000 0.00 0.00 0.00 2.29
1943 2469 5.013599 AGCTACTTCCTCCATTCAGTTTTCT 59.986 40.000 0.00 0.00 0.00 2.52
1944 2470 5.707764 GCTACTTCCTCCATTCAGTTTTCTT 59.292 40.000 0.00 0.00 0.00 2.52
1945 2471 6.348868 GCTACTTCCTCCATTCAGTTTTCTTG 60.349 42.308 0.00 0.00 0.00 3.02
1946 2472 4.279420 ACTTCCTCCATTCAGTTTTCTTGC 59.721 41.667 0.00 0.00 0.00 4.01
1947 2473 3.831323 TCCTCCATTCAGTTTTCTTGCA 58.169 40.909 0.00 0.00 0.00 4.08
1948 2474 4.410099 TCCTCCATTCAGTTTTCTTGCAT 58.590 39.130 0.00 0.00 0.00 3.96
1949 2475 4.219070 TCCTCCATTCAGTTTTCTTGCATG 59.781 41.667 0.00 0.00 0.00 4.06
1950 2476 3.916761 TCCATTCAGTTTTCTTGCATGC 58.083 40.909 11.82 11.82 0.00 4.06
1951 2477 3.321396 TCCATTCAGTTTTCTTGCATGCA 59.679 39.130 18.46 18.46 0.00 3.96
1952 2478 4.020928 TCCATTCAGTTTTCTTGCATGCAT 60.021 37.500 23.37 0.58 0.00 3.96
1953 2479 4.092821 CCATTCAGTTTTCTTGCATGCATG 59.907 41.667 23.37 23.63 0.00 4.06
1954 2480 4.325028 TTCAGTTTTCTTGCATGCATGT 57.675 36.364 26.79 9.98 0.00 3.21
1955 2481 3.644823 TCAGTTTTCTTGCATGCATGTG 58.355 40.909 26.79 19.38 0.00 3.21
1956 2482 2.734606 CAGTTTTCTTGCATGCATGTGG 59.265 45.455 26.79 16.66 0.00 4.17
1957 2483 2.070783 GTTTTCTTGCATGCATGTGGG 58.929 47.619 26.79 16.34 0.00 4.61
1958 2484 0.609151 TTTCTTGCATGCATGTGGGG 59.391 50.000 26.79 14.73 0.00 4.96
1959 2485 0.542467 TTCTTGCATGCATGTGGGGT 60.542 50.000 26.79 0.00 0.00 4.95
1960 2486 0.330941 TCTTGCATGCATGTGGGGTA 59.669 50.000 26.79 8.63 0.00 3.69
1961 2487 1.063792 TCTTGCATGCATGTGGGGTAT 60.064 47.619 26.79 0.00 0.00 2.73
1962 2488 1.758280 CTTGCATGCATGTGGGGTATT 59.242 47.619 26.79 0.00 0.00 1.89
1963 2489 2.744352 TGCATGCATGTGGGGTATTA 57.256 45.000 26.79 1.42 0.00 0.98
1964 2490 3.023939 TGCATGCATGTGGGGTATTAA 57.976 42.857 26.79 0.00 0.00 1.40
1965 2491 3.574749 TGCATGCATGTGGGGTATTAAT 58.425 40.909 26.79 0.00 0.00 1.40
1966 2492 3.321396 TGCATGCATGTGGGGTATTAATG 59.679 43.478 26.79 0.00 0.00 1.90
1967 2493 3.573538 GCATGCATGTGGGGTATTAATGA 59.426 43.478 26.79 0.00 0.00 2.57
1968 2494 4.221262 GCATGCATGTGGGGTATTAATGAT 59.779 41.667 26.79 0.00 0.00 2.45
1969 2495 5.622914 GCATGCATGTGGGGTATTAATGATC 60.623 44.000 26.79 1.13 0.00 2.92
1970 2496 4.406456 TGCATGTGGGGTATTAATGATCC 58.594 43.478 0.00 0.00 0.00 3.36
1971 2497 3.763897 GCATGTGGGGTATTAATGATCCC 59.236 47.826 13.42 13.42 39.22 3.85
1972 2498 4.752590 GCATGTGGGGTATTAATGATCCCA 60.753 45.833 19.58 18.09 44.59 4.37
1977 2503 6.850263 TGGGGTATTAATGATCCCAGTAAA 57.150 37.500 19.58 3.12 42.21 2.01
1978 2504 7.415004 TGGGGTATTAATGATCCCAGTAAAT 57.585 36.000 19.58 0.00 42.21 1.40
1979 2505 8.527135 TGGGGTATTAATGATCCCAGTAAATA 57.473 34.615 19.58 2.10 42.21 1.40
1980 2506 8.961134 TGGGGTATTAATGATCCCAGTAAATAA 58.039 33.333 19.58 1.58 42.21 1.40
1981 2507 9.816787 GGGGTATTAATGATCCCAGTAAATAAA 57.183 33.333 19.58 0.00 41.51 1.40
1990 2516 9.875691 ATGATCCCAGTAAATAAAAAGAAAAGC 57.124 29.630 0.00 0.00 0.00 3.51
1991 2517 9.088987 TGATCCCAGTAAATAAAAAGAAAAGCT 57.911 29.630 0.00 0.00 0.00 3.74
1992 2518 9.358872 GATCCCAGTAAATAAAAAGAAAAGCTG 57.641 33.333 0.00 0.00 0.00 4.24
1993 2519 8.472007 TCCCAGTAAATAAAAAGAAAAGCTGA 57.528 30.769 0.00 0.00 0.00 4.26
1994 2520 8.357402 TCCCAGTAAATAAAAAGAAAAGCTGAC 58.643 33.333 0.00 0.00 0.00 3.51
1995 2521 8.360390 CCCAGTAAATAAAAAGAAAAGCTGACT 58.640 33.333 0.00 0.00 0.00 3.41
1996 2522 9.750125 CCAGTAAATAAAAAGAAAAGCTGACTT 57.250 29.630 0.00 0.00 37.90 3.01
1998 2524 9.249457 AGTAAATAAAAAGAAAAGCTGACTTGC 57.751 29.630 0.00 0.00 35.85 4.01
1999 2525 9.030301 GTAAATAAAAAGAAAAGCTGACTTGCA 57.970 29.630 0.00 0.00 35.85 4.08
2000 2526 8.491331 AAATAAAAAGAAAAGCTGACTTGCAA 57.509 26.923 0.00 0.00 35.85 4.08
2001 2527 8.491331 AATAAAAAGAAAAGCTGACTTGCAAA 57.509 26.923 0.00 0.00 35.85 3.68
2020 2546 8.654230 TTGCAAAGCAGTCATTAAATTTTACA 57.346 26.923 0.00 0.00 40.61 2.41
2021 2547 8.830201 TGCAAAGCAGTCATTAAATTTTACAT 57.170 26.923 0.00 0.00 33.32 2.29
2022 2548 9.270640 TGCAAAGCAGTCATTAAATTTTACATT 57.729 25.926 0.00 0.00 33.32 2.71
2023 2549 9.532697 GCAAAGCAGTCATTAAATTTTACATTG 57.467 29.630 0.00 0.00 0.00 2.82
2047 2573 9.585099 TTGATATCTGTAATTTGAATTTGTGGC 57.415 29.630 3.98 0.00 0.00 5.01
2048 2574 8.196771 TGATATCTGTAATTTGAATTTGTGGCC 58.803 33.333 3.98 0.00 0.00 5.36
2049 2575 6.610075 ATCTGTAATTTGAATTTGTGGCCT 57.390 33.333 3.32 0.00 0.00 5.19
2050 2576 6.418057 TCTGTAATTTGAATTTGTGGCCTT 57.582 33.333 3.32 0.00 0.00 4.35
2051 2577 6.222389 TCTGTAATTTGAATTTGTGGCCTTG 58.778 36.000 3.32 0.00 0.00 3.61
2052 2578 5.923204 TGTAATTTGAATTTGTGGCCTTGT 58.077 33.333 3.32 0.00 0.00 3.16
2053 2579 6.352516 TGTAATTTGAATTTGTGGCCTTGTT 58.647 32.000 3.32 0.00 0.00 2.83
2054 2580 6.825721 TGTAATTTGAATTTGTGGCCTTGTTT 59.174 30.769 3.32 0.00 0.00 2.83
2055 2581 7.987458 TGTAATTTGAATTTGTGGCCTTGTTTA 59.013 29.630 3.32 0.00 0.00 2.01
2056 2582 8.998377 GTAATTTGAATTTGTGGCCTTGTTTAT 58.002 29.630 3.32 0.00 0.00 1.40
2058 2584 9.566432 AATTTGAATTTGTGGCCTTGTTTATAA 57.434 25.926 3.32 0.00 0.00 0.98
2059 2585 8.964476 TTTGAATTTGTGGCCTTGTTTATAAA 57.036 26.923 3.32 0.00 0.00 1.40
2060 2586 8.964476 TTGAATTTGTGGCCTTGTTTATAAAA 57.036 26.923 3.32 0.00 0.00 1.52
2061 2587 8.964476 TGAATTTGTGGCCTTGTTTATAAAAA 57.036 26.923 3.32 0.00 0.00 1.94
2062 2588 9.566432 TGAATTTGTGGCCTTGTTTATAAAAAT 57.434 25.926 3.32 0.00 0.00 1.82
2063 2589 9.824534 GAATTTGTGGCCTTGTTTATAAAAATG 57.175 29.630 3.32 0.00 0.00 2.32
2064 2590 9.566432 AATTTGTGGCCTTGTTTATAAAAATGA 57.434 25.926 3.32 0.00 0.00 2.57
2065 2591 8.964476 TTTGTGGCCTTGTTTATAAAAATGAA 57.036 26.923 3.32 0.00 0.00 2.57
2066 2592 8.600449 TTGTGGCCTTGTTTATAAAAATGAAG 57.400 30.769 3.32 0.98 0.00 3.02
2067 2593 7.158021 TGTGGCCTTGTTTATAAAAATGAAGG 58.842 34.615 3.32 15.73 38.70 3.46
2068 2594 7.015682 TGTGGCCTTGTTTATAAAAATGAAGGA 59.984 33.333 20.46 7.03 38.33 3.36
2069 2595 7.875554 GTGGCCTTGTTTATAAAAATGAAGGAA 59.124 33.333 20.46 11.10 38.33 3.36
2070 2596 8.093927 TGGCCTTGTTTATAAAAATGAAGGAAG 58.906 33.333 20.46 3.62 38.33 3.46
2071 2597 8.094548 GGCCTTGTTTATAAAAATGAAGGAAGT 58.905 33.333 20.46 0.00 38.33 3.01
2101 2627 6.934048 TTTTGCTAATTTTTGGAAAGTGGG 57.066 33.333 0.00 0.00 0.00 4.61
2105 2631 5.158494 GCTAATTTTTGGAAAGTGGGTACG 58.842 41.667 0.00 0.00 0.00 3.67
2108 2634 0.183014 TTTGGAAAGTGGGTACGCCA 59.817 50.000 7.55 3.19 36.17 5.69
2111 2637 0.672711 GGAAAGTGGGTACGCCAGAC 60.673 60.000 7.55 0.00 36.17 3.51
2125 2651 4.822026 ACGCCAGACCTATTCTATATTGC 58.178 43.478 0.00 0.00 31.12 3.56
2159 2685 7.282332 TGCATAGAGATGGATCTATTATCCG 57.718 40.000 0.00 0.00 39.89 4.18
2171 2697 6.710744 GGATCTATTATCCGGCAAAGAAAAGA 59.289 38.462 0.00 0.00 0.00 2.52
2202 2728 1.442769 CATATGGGCATGACCGCTAC 58.557 55.000 14.43 0.00 40.62 3.58
2213 2740 4.143389 GCATGACCGCTACGACATTTATAC 60.143 45.833 0.00 0.00 0.00 1.47
2241 2768 9.638176 AAAAGATTCTCACATAATATTGGCTCT 57.362 29.630 0.00 0.00 0.00 4.09
2245 2772 5.158141 TCTCACATAATATTGGCTCTCCCT 58.842 41.667 0.00 0.00 0.00 4.20
2264 2791 5.636123 TCCCTTACCAAAATTGCTTCACTA 58.364 37.500 0.00 0.00 0.00 2.74
2265 2792 6.252995 TCCCTTACCAAAATTGCTTCACTAT 58.747 36.000 0.00 0.00 0.00 2.12
2266 2793 7.406916 TCCCTTACCAAAATTGCTTCACTATA 58.593 34.615 0.00 0.00 0.00 1.31
2273 2800 2.254546 TTGCTTCACTATATGGCCCG 57.745 50.000 0.00 0.00 0.00 6.13
2280 2807 2.105649 TCACTATATGGCCCGAAATGCA 59.894 45.455 0.00 0.00 0.00 3.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
118 125 3.249189 GTGCCCAGACCAGTCCCA 61.249 66.667 0.00 0.00 0.00 4.37
234 243 2.086869 CTTGCCATTGATTCCTCACGT 58.913 47.619 0.00 0.00 0.00 4.49
259 268 2.361610 AATGGCAAGGCTGACCGG 60.362 61.111 0.00 0.00 42.76 5.28
261 270 1.135721 GAATCAATGGCAAGGCTGACC 59.864 52.381 0.00 0.00 0.00 4.02
263 272 1.477553 GGAATCAATGGCAAGGCTGA 58.522 50.000 0.00 0.00 0.00 4.26
435 450 1.078426 CCAGGAGCCCGATTTTCGT 60.078 57.895 0.00 0.00 38.40 3.85
501 517 1.925972 GTCCCAGAAAGGCCTCCCT 60.926 63.158 5.23 2.79 45.77 4.20
573 590 4.437587 ATGAGCAGCAGGGCCACC 62.438 66.667 6.18 0.00 0.00 4.61
592 609 3.127533 GAGGTGGCACGCATGACC 61.128 66.667 12.17 0.00 43.02 4.02
593 610 2.358615 TGAGGTGGCACGCATGAC 60.359 61.111 12.17 0.00 43.02 3.06
626 660 0.249911 ACGCTCTGAACTCCGCTTTT 60.250 50.000 0.00 0.00 0.00 2.27
681 717 3.428180 GCTCATCATCGTGTACTCTGTGT 60.428 47.826 0.00 0.00 0.00 3.72
682 718 3.111838 GCTCATCATCGTGTACTCTGTG 58.888 50.000 0.00 0.00 0.00 3.66
683 719 2.223363 CGCTCATCATCGTGTACTCTGT 60.223 50.000 0.00 0.00 0.00 3.41
684 720 2.032178 TCGCTCATCATCGTGTACTCTG 59.968 50.000 0.00 0.00 0.00 3.35
685 721 2.289565 TCGCTCATCATCGTGTACTCT 58.710 47.619 0.00 0.00 0.00 3.24
686 722 2.757686 TCGCTCATCATCGTGTACTC 57.242 50.000 0.00 0.00 0.00 2.59
711 747 4.123545 AACCGTATGGCCTGCCCC 62.124 66.667 3.32 0.00 39.70 5.80
723 759 0.317603 CGACTGAACGACTGAACCGT 60.318 55.000 0.00 0.00 42.61 4.83
724 760 0.317603 ACGACTGAACGACTGAACCG 60.318 55.000 0.00 0.00 37.03 4.44
726 762 2.456989 TGAACGACTGAACGACTGAAC 58.543 47.619 0.00 0.00 37.03 3.18
727 763 2.356695 TCTGAACGACTGAACGACTGAA 59.643 45.455 0.00 0.00 37.03 3.02
728 764 1.944709 TCTGAACGACTGAACGACTGA 59.055 47.619 0.00 0.00 37.03 3.41
729 765 2.401017 TCTGAACGACTGAACGACTG 57.599 50.000 0.00 0.00 37.03 3.51
730 766 2.293677 ACATCTGAACGACTGAACGACT 59.706 45.455 0.00 0.00 37.03 4.18
731 767 2.405357 CACATCTGAACGACTGAACGAC 59.595 50.000 0.00 0.00 37.03 4.34
732 768 2.607038 CCACATCTGAACGACTGAACGA 60.607 50.000 0.00 0.00 37.03 3.85
733 769 1.721389 CCACATCTGAACGACTGAACG 59.279 52.381 0.00 0.00 39.31 3.95
734 770 2.069273 CCCACATCTGAACGACTGAAC 58.931 52.381 0.00 0.00 0.00 3.18
735 771 1.967779 TCCCACATCTGAACGACTGAA 59.032 47.619 0.00 0.00 0.00 3.02
736 772 1.627864 TCCCACATCTGAACGACTGA 58.372 50.000 0.00 0.00 0.00 3.41
737 773 2.029020 TCTTCCCACATCTGAACGACTG 60.029 50.000 0.00 0.00 0.00 3.51
738 774 2.248248 TCTTCCCACATCTGAACGACT 58.752 47.619 0.00 0.00 0.00 4.18
739 775 2.743636 TCTTCCCACATCTGAACGAC 57.256 50.000 0.00 0.00 0.00 4.34
740 776 3.664107 CTTTCTTCCCACATCTGAACGA 58.336 45.455 0.00 0.00 0.00 3.85
741 777 2.160417 GCTTTCTTCCCACATCTGAACG 59.840 50.000 0.00 0.00 0.00 3.95
816 852 1.775208 CTTGCGTCAAGTTGCTTTTCG 59.225 47.619 10.30 0.00 36.79 3.46
877 917 0.541392 TGCTTCTGTGTCCTGTGTGT 59.459 50.000 0.00 0.00 0.00 3.72
878 918 0.940126 GTGCTTCTGTGTCCTGTGTG 59.060 55.000 0.00 0.00 0.00 3.82
897 937 2.510874 CTTACAGTCGAAGAGAGCGTG 58.489 52.381 0.00 0.00 36.95 5.34
899 939 1.131504 AGCTTACAGTCGAAGAGAGCG 59.868 52.381 0.00 0.00 36.95 5.03
900 940 2.931512 AGCTTACAGTCGAAGAGAGC 57.068 50.000 0.00 0.00 36.95 4.09
901 941 4.154375 TGTGTAGCTTACAGTCGAAGAGAG 59.846 45.833 0.00 0.00 39.77 3.20
936 984 0.101219 TCGACGAGACTACGATCCGA 59.899 55.000 0.00 0.00 37.03 4.55
1233 1292 3.518998 ACGGAGGAGACGGCATCG 61.519 66.667 0.00 0.00 43.02 3.84
1326 1393 1.271379 ACCTAAGAAAGCACGCACCAT 60.271 47.619 0.00 0.00 0.00 3.55
1345 1412 4.795278 CCACTACCAACGATAACTACGAAC 59.205 45.833 0.00 0.00 34.70 3.95
1408 1475 6.701841 ACTTCAATCTACTGTACACACACAAG 59.298 38.462 0.00 0.00 0.00 3.16
1432 1499 7.365741 AGATAAAATCGAATCATCCATTGCAC 58.634 34.615 0.00 0.00 0.00 4.57
1443 1510 9.922305 AGATTTCGTTTGAGATAAAATCGAATC 57.078 29.630 0.00 0.00 39.91 2.52
1456 1523 2.225019 ACAGCAGCAGATTTCGTTTGAG 59.775 45.455 0.00 0.00 0.00 3.02
1458 1525 2.693797 ACAGCAGCAGATTTCGTTTG 57.306 45.000 0.00 0.00 0.00 2.93
1497 1564 0.740149 CACAAAGCAACAGCTGTCCA 59.260 50.000 21.95 0.00 38.93 4.02
1501 1571 2.456989 CTGAACACAAAGCAACAGCTG 58.543 47.619 13.48 13.48 38.93 4.24
1554 1732 9.678260 AAGATTCTCACATAAGCTAATTGTCTT 57.322 29.630 0.00 0.00 0.00 3.01
1560 1738 8.887717 GTTGACAAGATTCTCACATAAGCTAAT 58.112 33.333 0.00 0.00 0.00 1.73
1565 1743 7.011773 CGTTGTTGACAAGATTCTCACATAAG 58.988 38.462 0.00 0.00 36.39 1.73
1581 1760 0.928451 GCCAAAGCGTCGTTGTTGAC 60.928 55.000 0.00 0.00 35.49 3.18
1699 1878 6.817140 ACCGGTTTATGTTGCAACTTTTTAAA 59.183 30.769 28.61 21.20 0.00 1.52
1717 2090 6.952773 AAACATGCACATATATACCGGTTT 57.047 33.333 15.04 7.86 0.00 3.27
1746 2272 8.630054 AGTATCTTTAAGTTGTGTAAATGCCA 57.370 30.769 0.00 0.00 0.00 4.92
1749 2275 9.449719 AGGGAGTATCTTTAAGTTGTGTAAATG 57.550 33.333 0.00 0.00 33.73 2.32
1754 2280 5.546499 TGGAGGGAGTATCTTTAAGTTGTGT 59.454 40.000 0.00 0.00 33.73 3.72
1756 2282 6.893020 ATGGAGGGAGTATCTTTAAGTTGT 57.107 37.500 0.00 0.00 33.73 3.32
1769 2295 8.114301 ACCTTGTATATAAAAATGGAGGGAGT 57.886 34.615 0.00 0.00 0.00 3.85
1771 2297 7.996644 GTGACCTTGTATATAAAAATGGAGGGA 59.003 37.037 0.00 0.00 0.00 4.20
1772 2298 7.998964 AGTGACCTTGTATATAAAAATGGAGGG 59.001 37.037 0.00 0.00 0.00 4.30
1791 2317 9.407380 TGCAAAATGTATATTTCATAGTGACCT 57.593 29.630 0.00 0.00 35.50 3.85
1804 2330 8.960591 GGCCTTGTATAGATGCAAAATGTATAT 58.039 33.333 0.00 0.00 32.12 0.86
1805 2331 7.941790 TGGCCTTGTATAGATGCAAAATGTATA 59.058 33.333 3.32 0.00 32.12 1.47
1806 2332 6.777091 TGGCCTTGTATAGATGCAAAATGTAT 59.223 34.615 3.32 0.00 32.12 2.29
1807 2333 6.039270 GTGGCCTTGTATAGATGCAAAATGTA 59.961 38.462 3.32 0.00 32.12 2.29
1808 2334 4.955450 TGGCCTTGTATAGATGCAAAATGT 59.045 37.500 3.32 0.00 32.12 2.71
1809 2335 5.284079 GTGGCCTTGTATAGATGCAAAATG 58.716 41.667 3.32 0.00 32.12 2.32
1810 2336 4.342092 GGTGGCCTTGTATAGATGCAAAAT 59.658 41.667 3.32 0.00 32.12 1.82
1811 2337 3.699038 GGTGGCCTTGTATAGATGCAAAA 59.301 43.478 3.32 0.00 32.12 2.44
1812 2338 3.287222 GGTGGCCTTGTATAGATGCAAA 58.713 45.455 3.32 0.00 32.12 3.68
1813 2339 2.240921 TGGTGGCCTTGTATAGATGCAA 59.759 45.455 3.32 0.00 0.00 4.08
1814 2340 1.843206 TGGTGGCCTTGTATAGATGCA 59.157 47.619 3.32 0.00 0.00 3.96
1815 2341 2.618709 GTTGGTGGCCTTGTATAGATGC 59.381 50.000 3.32 0.00 0.00 3.91
1816 2342 3.884895 TGTTGGTGGCCTTGTATAGATG 58.115 45.455 3.32 0.00 0.00 2.90
1817 2343 4.584638 TTGTTGGTGGCCTTGTATAGAT 57.415 40.909 3.32 0.00 0.00 1.98
1818 2344 4.584638 ATTGTTGGTGGCCTTGTATAGA 57.415 40.909 3.32 0.00 0.00 1.98
1819 2345 6.293407 CGATTATTGTTGGTGGCCTTGTATAG 60.293 42.308 3.32 0.00 0.00 1.31
1820 2346 5.529430 CGATTATTGTTGGTGGCCTTGTATA 59.471 40.000 3.32 0.00 0.00 1.47
1821 2347 4.338118 CGATTATTGTTGGTGGCCTTGTAT 59.662 41.667 3.32 0.00 0.00 2.29
1822 2348 3.692101 CGATTATTGTTGGTGGCCTTGTA 59.308 43.478 3.32 0.00 0.00 2.41
1823 2349 2.491693 CGATTATTGTTGGTGGCCTTGT 59.508 45.455 3.32 0.00 0.00 3.16
1824 2350 2.752354 TCGATTATTGTTGGTGGCCTTG 59.248 45.455 3.32 0.00 0.00 3.61
1825 2351 3.016736 CTCGATTATTGTTGGTGGCCTT 58.983 45.455 3.32 0.00 0.00 4.35
1826 2352 2.643551 CTCGATTATTGTTGGTGGCCT 58.356 47.619 3.32 0.00 0.00 5.19
1827 2353 1.676006 CCTCGATTATTGTTGGTGGCC 59.324 52.381 0.00 0.00 0.00 5.36
1828 2354 1.065551 GCCTCGATTATTGTTGGTGGC 59.934 52.381 0.00 0.00 0.00 5.01
1829 2355 2.364632 TGCCTCGATTATTGTTGGTGG 58.635 47.619 0.00 0.00 0.00 4.61
1830 2356 4.433186 TTTGCCTCGATTATTGTTGGTG 57.567 40.909 0.00 0.00 0.00 4.17
1831 2357 5.659440 ATTTTGCCTCGATTATTGTTGGT 57.341 34.783 0.00 0.00 0.00 3.67
1832 2358 8.542132 CATTAATTTTGCCTCGATTATTGTTGG 58.458 33.333 0.00 0.00 0.00 3.77
1833 2359 9.299963 TCATTAATTTTGCCTCGATTATTGTTG 57.700 29.630 0.00 0.00 0.00 3.33
1868 2394 8.455682 GCAATTATTAAACAGGTTGCTACTACA 58.544 33.333 0.00 0.00 38.97 2.74
1869 2395 8.455682 TGCAATTATTAAACAGGTTGCTACTAC 58.544 33.333 11.09 0.00 41.67 2.73
1870 2396 8.568676 TGCAATTATTAAACAGGTTGCTACTA 57.431 30.769 11.09 0.00 41.67 1.82
1871 2397 7.461182 TGCAATTATTAAACAGGTTGCTACT 57.539 32.000 11.09 0.00 41.67 2.57
1872 2398 7.254084 GCATGCAATTATTAAACAGGTTGCTAC 60.254 37.037 14.21 0.00 41.67 3.58
1873 2399 6.756074 GCATGCAATTATTAAACAGGTTGCTA 59.244 34.615 14.21 2.08 41.67 3.49
1874 2400 5.581874 GCATGCAATTATTAAACAGGTTGCT 59.418 36.000 14.21 0.00 41.67 3.91
1875 2401 5.350914 TGCATGCAATTATTAAACAGGTTGC 59.649 36.000 20.30 0.00 41.53 4.17
1876 2402 6.964741 TGCATGCAATTATTAAACAGGTTG 57.035 33.333 20.30 0.00 0.00 3.77
1877 2403 7.542534 CATGCATGCAATTATTAAACAGGTT 57.457 32.000 26.68 0.00 0.00 3.50
1894 2420 5.528870 ACTGTCATTATGAATGCATGCATG 58.471 37.500 32.79 22.70 38.77 4.06
1895 2421 5.300792 TGACTGTCATTATGAATGCATGCAT 59.699 36.000 27.46 27.46 38.77 3.96
1896 2422 4.641094 TGACTGTCATTATGAATGCATGCA 59.359 37.500 25.04 25.04 38.77 3.96
1897 2423 5.177725 TGACTGTCATTATGAATGCATGC 57.822 39.130 11.82 11.82 38.77 4.06
1898 2424 5.008712 AGCTGACTGTCATTATGAATGCATG 59.991 40.000 11.45 0.00 38.77 4.06
1899 2425 5.131067 AGCTGACTGTCATTATGAATGCAT 58.869 37.500 11.45 0.00 38.77 3.96
1900 2426 4.520179 AGCTGACTGTCATTATGAATGCA 58.480 39.130 11.45 0.00 38.77 3.96
1901 2427 5.757320 AGTAGCTGACTGTCATTATGAATGC 59.243 40.000 11.45 8.48 36.87 3.56
1902 2428 7.042187 GGAAGTAGCTGACTGTCATTATGAATG 60.042 40.741 11.45 0.00 38.87 2.67
1903 2429 6.989169 GGAAGTAGCTGACTGTCATTATGAAT 59.011 38.462 11.45 0.00 38.87 2.57
1904 2430 6.155221 AGGAAGTAGCTGACTGTCATTATGAA 59.845 38.462 11.45 0.00 38.87 2.57
1905 2431 5.658634 AGGAAGTAGCTGACTGTCATTATGA 59.341 40.000 11.45 0.00 38.87 2.15
1906 2432 5.911752 AGGAAGTAGCTGACTGTCATTATG 58.088 41.667 11.45 0.53 38.87 1.90
1907 2433 5.069781 GGAGGAAGTAGCTGACTGTCATTAT 59.930 44.000 11.45 3.10 38.87 1.28
1908 2434 4.402793 GGAGGAAGTAGCTGACTGTCATTA 59.597 45.833 11.45 4.66 38.87 1.90
1909 2435 3.196685 GGAGGAAGTAGCTGACTGTCATT 59.803 47.826 11.45 1.95 38.87 2.57
1910 2436 2.763448 GGAGGAAGTAGCTGACTGTCAT 59.237 50.000 11.45 0.00 38.87 3.06
1911 2437 2.171840 GGAGGAAGTAGCTGACTGTCA 58.828 52.381 10.50 10.50 38.87 3.58
1912 2438 2.171840 TGGAGGAAGTAGCTGACTGTC 58.828 52.381 0.00 0.00 38.87 3.51
1913 2439 2.310779 TGGAGGAAGTAGCTGACTGT 57.689 50.000 0.00 0.00 38.87 3.55
1914 2440 3.196469 TGAATGGAGGAAGTAGCTGACTG 59.804 47.826 0.00 0.00 38.87 3.51
1915 2441 3.445008 TGAATGGAGGAAGTAGCTGACT 58.555 45.455 0.00 0.00 41.56 3.41
1916 2442 3.196685 ACTGAATGGAGGAAGTAGCTGAC 59.803 47.826 0.00 0.00 0.00 3.51
1917 2443 3.445008 ACTGAATGGAGGAAGTAGCTGA 58.555 45.455 0.00 0.00 0.00 4.26
1918 2444 3.902881 ACTGAATGGAGGAAGTAGCTG 57.097 47.619 0.00 0.00 0.00 4.24
1919 2445 4.917906 AAACTGAATGGAGGAAGTAGCT 57.082 40.909 0.00 0.00 0.00 3.32
1920 2446 5.249420 AGAAAACTGAATGGAGGAAGTAGC 58.751 41.667 0.00 0.00 0.00 3.58
1921 2447 6.348868 GCAAGAAAACTGAATGGAGGAAGTAG 60.349 42.308 0.00 0.00 0.00 2.57
1922 2448 5.473504 GCAAGAAAACTGAATGGAGGAAGTA 59.526 40.000 0.00 0.00 0.00 2.24
1923 2449 4.279420 GCAAGAAAACTGAATGGAGGAAGT 59.721 41.667 0.00 0.00 0.00 3.01
1924 2450 4.279169 TGCAAGAAAACTGAATGGAGGAAG 59.721 41.667 0.00 0.00 0.00 3.46
1925 2451 4.214310 TGCAAGAAAACTGAATGGAGGAA 58.786 39.130 0.00 0.00 0.00 3.36
1926 2452 3.831323 TGCAAGAAAACTGAATGGAGGA 58.169 40.909 0.00 0.00 0.00 3.71
1927 2453 4.491676 CATGCAAGAAAACTGAATGGAGG 58.508 43.478 0.00 0.00 0.00 4.30
1928 2454 3.924686 GCATGCAAGAAAACTGAATGGAG 59.075 43.478 14.21 0.00 31.33 3.86
1929 2455 3.321396 TGCATGCAAGAAAACTGAATGGA 59.679 39.130 20.30 0.00 31.33 3.41
1930 2456 3.655486 TGCATGCAAGAAAACTGAATGG 58.345 40.909 20.30 0.00 31.33 3.16
1931 2457 4.688879 ACATGCATGCAAGAAAACTGAATG 59.311 37.500 28.20 17.30 33.51 2.67
1932 2458 4.688879 CACATGCATGCAAGAAAACTGAAT 59.311 37.500 28.20 2.88 0.00 2.57
1933 2459 4.052608 CACATGCATGCAAGAAAACTGAA 58.947 39.130 28.20 0.00 0.00 3.02
1934 2460 3.553302 CCACATGCATGCAAGAAAACTGA 60.553 43.478 28.20 0.00 0.00 3.41
1935 2461 2.734606 CCACATGCATGCAAGAAAACTG 59.265 45.455 28.20 19.88 0.00 3.16
1936 2462 2.289195 CCCACATGCATGCAAGAAAACT 60.289 45.455 28.20 5.86 0.00 2.66
1937 2463 2.070783 CCCACATGCATGCAAGAAAAC 58.929 47.619 28.20 0.00 0.00 2.43
1938 2464 1.002201 CCCCACATGCATGCAAGAAAA 59.998 47.619 28.20 2.35 0.00 2.29
1939 2465 0.609151 CCCCACATGCATGCAAGAAA 59.391 50.000 28.20 3.18 0.00 2.52
1940 2466 0.542467 ACCCCACATGCATGCAAGAA 60.542 50.000 28.20 3.61 0.00 2.52
1941 2467 0.330941 TACCCCACATGCATGCAAGA 59.669 50.000 28.20 4.03 0.00 3.02
1942 2468 1.405872 ATACCCCACATGCATGCAAG 58.594 50.000 26.68 23.45 0.00 4.01
1943 2469 1.863325 AATACCCCACATGCATGCAA 58.137 45.000 26.68 8.49 0.00 4.08
1944 2470 2.744352 TAATACCCCACATGCATGCA 57.256 45.000 26.53 25.04 0.00 3.96
1945 2471 3.573538 TCATTAATACCCCACATGCATGC 59.426 43.478 26.53 11.82 0.00 4.06
1946 2472 5.105635 GGATCATTAATACCCCACATGCATG 60.106 44.000 25.09 25.09 0.00 4.06
1947 2473 5.018809 GGATCATTAATACCCCACATGCAT 58.981 41.667 0.00 0.00 0.00 3.96
1948 2474 4.406456 GGATCATTAATACCCCACATGCA 58.594 43.478 0.00 0.00 0.00 3.96
1949 2475 3.763897 GGGATCATTAATACCCCACATGC 59.236 47.826 11.88 0.00 37.04 4.06
1950 2476 4.996793 TGGGATCATTAATACCCCACATG 58.003 43.478 14.33 0.00 41.78 3.21
1951 2477 4.669768 ACTGGGATCATTAATACCCCACAT 59.330 41.667 14.33 6.45 41.78 3.21
1952 2478 4.051478 ACTGGGATCATTAATACCCCACA 58.949 43.478 14.33 1.04 41.78 4.17
1953 2479 4.724279 ACTGGGATCATTAATACCCCAC 57.276 45.455 14.33 0.00 41.78 4.61
1954 2480 6.850263 TTTACTGGGATCATTAATACCCCA 57.150 37.500 16.34 16.34 44.21 4.96
1955 2481 9.816787 TTTATTTACTGGGATCATTAATACCCC 57.183 33.333 16.71 13.74 37.61 4.95
1964 2490 9.875691 GCTTTTCTTTTTATTTACTGGGATCAT 57.124 29.630 0.00 0.00 0.00 2.45
1965 2491 9.088987 AGCTTTTCTTTTTATTTACTGGGATCA 57.911 29.630 0.00 0.00 0.00 2.92
1966 2492 9.358872 CAGCTTTTCTTTTTATTTACTGGGATC 57.641 33.333 0.00 0.00 0.00 3.36
1967 2493 9.088987 TCAGCTTTTCTTTTTATTTACTGGGAT 57.911 29.630 0.00 0.00 0.00 3.85
1968 2494 8.357402 GTCAGCTTTTCTTTTTATTTACTGGGA 58.643 33.333 0.00 0.00 0.00 4.37
1969 2495 8.360390 AGTCAGCTTTTCTTTTTATTTACTGGG 58.640 33.333 0.00 0.00 0.00 4.45
1970 2496 9.750125 AAGTCAGCTTTTCTTTTTATTTACTGG 57.250 29.630 0.00 0.00 0.00 4.00
1972 2498 9.249457 GCAAGTCAGCTTTTCTTTTTATTTACT 57.751 29.630 0.00 0.00 31.49 2.24
1973 2499 9.030301 TGCAAGTCAGCTTTTCTTTTTATTTAC 57.970 29.630 0.00 0.00 31.49 2.01
1974 2500 9.593134 TTGCAAGTCAGCTTTTCTTTTTATTTA 57.407 25.926 0.00 0.00 31.49 1.40
1975 2501 8.491331 TTGCAAGTCAGCTTTTCTTTTTATTT 57.509 26.923 0.00 0.00 31.49 1.40
1976 2502 8.491331 TTTGCAAGTCAGCTTTTCTTTTTATT 57.509 26.923 0.00 0.00 31.49 1.40
1977 2503 7.254556 GCTTTGCAAGTCAGCTTTTCTTTTTAT 60.255 33.333 13.22 0.00 31.49 1.40
1978 2504 6.035975 GCTTTGCAAGTCAGCTTTTCTTTTTA 59.964 34.615 13.22 0.00 31.49 1.52
1979 2505 5.163824 GCTTTGCAAGTCAGCTTTTCTTTTT 60.164 36.000 13.22 0.00 31.49 1.94
1980 2506 4.330894 GCTTTGCAAGTCAGCTTTTCTTTT 59.669 37.500 13.22 0.00 31.49 2.27
1981 2507 3.867493 GCTTTGCAAGTCAGCTTTTCTTT 59.133 39.130 13.22 0.00 31.49 2.52
1982 2508 3.119029 TGCTTTGCAAGTCAGCTTTTCTT 60.119 39.130 19.45 0.00 34.76 2.52
1983 2509 2.428171 TGCTTTGCAAGTCAGCTTTTCT 59.572 40.909 19.45 0.00 34.76 2.52
1984 2510 2.793232 CTGCTTTGCAAGTCAGCTTTTC 59.207 45.455 19.45 0.00 38.41 2.29
1985 2511 2.167075 ACTGCTTTGCAAGTCAGCTTTT 59.833 40.909 22.21 7.00 38.41 2.27
1986 2512 1.753073 ACTGCTTTGCAAGTCAGCTTT 59.247 42.857 22.21 8.95 38.41 3.51
1987 2513 1.336125 GACTGCTTTGCAAGTCAGCTT 59.664 47.619 22.21 11.23 38.41 3.74
1988 2514 0.950116 GACTGCTTTGCAAGTCAGCT 59.050 50.000 22.21 13.55 38.41 4.24
1989 2515 0.664761 TGACTGCTTTGCAAGTCAGC 59.335 50.000 22.21 18.42 39.62 4.26
1990 2516 3.637998 AATGACTGCTTTGCAAGTCAG 57.362 42.857 20.36 20.83 43.65 3.51
1991 2517 5.512753 TTTAATGACTGCTTTGCAAGTCA 57.487 34.783 18.61 18.61 44.09 3.41
1992 2518 7.412137 AAATTTAATGACTGCTTTGCAAGTC 57.588 32.000 8.97 8.97 38.41 3.01
1993 2519 7.790823 AAAATTTAATGACTGCTTTGCAAGT 57.209 28.000 0.00 0.00 38.41 3.16
1994 2520 8.763356 TGTAAAATTTAATGACTGCTTTGCAAG 58.237 29.630 0.00 0.00 38.41 4.01
1995 2521 8.654230 TGTAAAATTTAATGACTGCTTTGCAA 57.346 26.923 0.00 0.00 38.41 4.08
1996 2522 8.830201 ATGTAAAATTTAATGACTGCTTTGCA 57.170 26.923 0.00 0.00 36.92 4.08
1997 2523 9.532697 CAATGTAAAATTTAATGACTGCTTTGC 57.467 29.630 0.00 0.00 0.00 3.68
2021 2547 9.585099 GCCACAAATTCAAATTACAGATATCAA 57.415 29.630 5.32 0.00 0.00 2.57
2022 2548 8.196771 GGCCACAAATTCAAATTACAGATATCA 58.803 33.333 5.32 0.00 0.00 2.15
2023 2549 8.416329 AGGCCACAAATTCAAATTACAGATATC 58.584 33.333 5.01 0.00 0.00 1.63
2024 2550 8.310122 AGGCCACAAATTCAAATTACAGATAT 57.690 30.769 5.01 0.00 0.00 1.63
2025 2551 7.716799 AGGCCACAAATTCAAATTACAGATA 57.283 32.000 5.01 0.00 0.00 1.98
2026 2552 6.610075 AGGCCACAAATTCAAATTACAGAT 57.390 33.333 5.01 0.00 0.00 2.90
2027 2553 6.183360 ACAAGGCCACAAATTCAAATTACAGA 60.183 34.615 5.01 0.00 0.00 3.41
2028 2554 5.990996 ACAAGGCCACAAATTCAAATTACAG 59.009 36.000 5.01 0.00 0.00 2.74
2029 2555 5.923204 ACAAGGCCACAAATTCAAATTACA 58.077 33.333 5.01 0.00 0.00 2.41
2030 2556 6.859420 AACAAGGCCACAAATTCAAATTAC 57.141 33.333 5.01 0.00 0.00 1.89
2032 2558 9.566432 TTATAAACAAGGCCACAAATTCAAATT 57.434 25.926 5.01 0.00 0.00 1.82
2033 2559 9.566432 TTTATAAACAAGGCCACAAATTCAAAT 57.434 25.926 5.01 0.00 0.00 2.32
2034 2560 8.964476 TTTATAAACAAGGCCACAAATTCAAA 57.036 26.923 5.01 0.00 0.00 2.69
2035 2561 8.964476 TTTTATAAACAAGGCCACAAATTCAA 57.036 26.923 5.01 0.00 0.00 2.69
2036 2562 8.964476 TTTTTATAAACAAGGCCACAAATTCA 57.036 26.923 5.01 0.00 0.00 2.57
2037 2563 9.824534 CATTTTTATAAACAAGGCCACAAATTC 57.175 29.630 5.01 0.00 0.00 2.17
2038 2564 9.566432 TCATTTTTATAAACAAGGCCACAAATT 57.434 25.926 5.01 0.00 0.00 1.82
2039 2565 9.566432 TTCATTTTTATAAACAAGGCCACAAAT 57.434 25.926 5.01 0.00 0.00 2.32
2040 2566 8.964476 TTCATTTTTATAAACAAGGCCACAAA 57.036 26.923 5.01 0.00 0.00 2.83
2041 2567 7.659390 CCTTCATTTTTATAAACAAGGCCACAA 59.341 33.333 5.01 0.00 33.29 3.33
2042 2568 7.015682 TCCTTCATTTTTATAAACAAGGCCACA 59.984 33.333 5.01 2.17 36.97 4.17
2043 2569 7.382898 TCCTTCATTTTTATAAACAAGGCCAC 58.617 34.615 5.01 0.00 36.97 5.01
2044 2570 7.546250 TCCTTCATTTTTATAAACAAGGCCA 57.454 32.000 5.01 0.00 36.97 5.36
2045 2571 8.094548 ACTTCCTTCATTTTTATAAACAAGGCC 58.905 33.333 14.35 0.00 36.97 5.19
2077 2603 6.887002 ACCCACTTTCCAAAAATTAGCAAAAA 59.113 30.769 0.00 0.00 0.00 1.94
2078 2604 6.418946 ACCCACTTTCCAAAAATTAGCAAAA 58.581 32.000 0.00 0.00 0.00 2.44
2079 2605 5.995446 ACCCACTTTCCAAAAATTAGCAAA 58.005 33.333 0.00 0.00 0.00 3.68
2080 2606 5.622346 ACCCACTTTCCAAAAATTAGCAA 57.378 34.783 0.00 0.00 0.00 3.91
2081 2607 5.278561 CGTACCCACTTTCCAAAAATTAGCA 60.279 40.000 0.00 0.00 0.00 3.49
2082 2608 5.158494 CGTACCCACTTTCCAAAAATTAGC 58.842 41.667 0.00 0.00 0.00 3.09
2083 2609 5.158494 GCGTACCCACTTTCCAAAAATTAG 58.842 41.667 0.00 0.00 0.00 1.73
2084 2610 4.022155 GGCGTACCCACTTTCCAAAAATTA 60.022 41.667 0.00 0.00 0.00 1.40
2085 2611 3.243941 GGCGTACCCACTTTCCAAAAATT 60.244 43.478 0.00 0.00 0.00 1.82
2086 2612 2.297880 GGCGTACCCACTTTCCAAAAAT 59.702 45.455 0.00 0.00 0.00 1.82
2087 2613 1.682323 GGCGTACCCACTTTCCAAAAA 59.318 47.619 0.00 0.00 0.00 1.94
2088 2614 1.320507 GGCGTACCCACTTTCCAAAA 58.679 50.000 0.00 0.00 0.00 2.44
2089 2615 0.183014 TGGCGTACCCACTTTCCAAA 59.817 50.000 0.00 0.00 39.18 3.28
2090 2616 0.250553 CTGGCGTACCCACTTTCCAA 60.251 55.000 0.00 0.00 39.18 3.53
2091 2617 1.122632 TCTGGCGTACCCACTTTCCA 61.123 55.000 0.00 0.00 39.18 3.53
2092 2618 0.672711 GTCTGGCGTACCCACTTTCC 60.673 60.000 0.00 0.00 39.18 3.13
2093 2619 0.672711 GGTCTGGCGTACCCACTTTC 60.673 60.000 0.00 0.00 39.18 2.62
2094 2620 1.125711 AGGTCTGGCGTACCCACTTT 61.126 55.000 4.58 0.00 39.18 2.66
2095 2621 0.251922 TAGGTCTGGCGTACCCACTT 60.252 55.000 4.58 0.00 39.18 3.16
2096 2622 0.032416 ATAGGTCTGGCGTACCCACT 60.032 55.000 4.58 0.00 39.18 4.00
2097 2623 0.828677 AATAGGTCTGGCGTACCCAC 59.171 55.000 4.58 0.00 39.18 4.61
2098 2624 1.117150 GAATAGGTCTGGCGTACCCA 58.883 55.000 4.58 3.45 42.79 4.51
2099 2625 1.411041 AGAATAGGTCTGGCGTACCC 58.589 55.000 4.58 0.00 37.77 3.69
2100 2626 6.331061 CAATATAGAATAGGTCTGGCGTACC 58.669 44.000 0.00 0.00 37.12 3.34
2101 2627 5.805994 GCAATATAGAATAGGTCTGGCGTAC 59.194 44.000 0.00 0.00 37.12 3.67
2105 2631 4.184629 CGGCAATATAGAATAGGTCTGGC 58.815 47.826 0.00 0.00 37.12 4.85
2108 2634 4.283467 TGTGCGGCAATATAGAATAGGTCT 59.717 41.667 3.23 0.00 40.71 3.85
2125 2651 9.932824 AGATCCATCTCTATGCATATTGTGCGG 62.933 44.444 6.92 4.58 44.95 5.69
2159 2685 5.277490 GCCAACAGATTTTCTTTTCTTTGCC 60.277 40.000 0.00 0.00 0.00 4.52
2171 2697 3.106054 TGCCCATATGCCAACAGATTTT 58.894 40.909 0.00 0.00 0.00 1.82
2195 2721 6.591062 TCTTTTTGTATAAATGTCGTAGCGGT 59.409 34.615 0.00 0.00 0.00 5.68
2240 2767 4.524328 AGTGAAGCAATTTTGGTAAGGGAG 59.476 41.667 0.00 0.00 38.04 4.30
2241 2768 4.479158 AGTGAAGCAATTTTGGTAAGGGA 58.521 39.130 0.00 0.00 38.04 4.20
2245 2772 7.417342 GGCCATATAGTGAAGCAATTTTGGTAA 60.417 37.037 0.00 0.00 38.04 2.85
2264 2791 1.181098 GGCTGCATTTCGGGCCATAT 61.181 55.000 4.39 0.00 43.59 1.78
2265 2792 1.827789 GGCTGCATTTCGGGCCATA 60.828 57.895 4.39 0.00 43.59 2.74
2266 2793 3.149648 GGCTGCATTTCGGGCCAT 61.150 61.111 4.39 0.00 43.59 4.40


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

AutoCloner maintained by Alex Coulton.