Multiple sequence alignment - TraesCS2A01G443200

Loading Multiple Alignment...

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 TraesCS2A01G443200 chr2A 100.000 2501 0 0 1 2501 693244645 693242145 0.000000e+00 4619.0
1 TraesCS2A01G443200 chr2D 94.742 1008 36 5 763 1768 552607929 552606937 0.000000e+00 1552.0
2 TraesCS2A01G443200 chr2D 91.296 494 33 6 2013 2500 552606934 552606445 0.000000e+00 665.0
3 TraesCS2A01G443200 chr2D 90.647 139 7 3 1877 2009 272810694 272810556 1.980000e-41 180.0
4 TraesCS2A01G443200 chr2B 95.289 849 24 3 764 1612 658211008 658210176 0.000000e+00 1332.0
5 TraesCS2A01G443200 chr2B 90.763 747 64 2 1 747 777842702 777843443 0.000000e+00 992.0
6 TraesCS2A01G443200 chr4D 90.361 747 71 1 1 747 88469776 88469031 0.000000e+00 979.0
7 TraesCS2A01G443200 chr7D 91.870 615 44 3 1 611 371787278 371786666 0.000000e+00 854.0
8 TraesCS2A01G443200 chr7D 90.000 430 42 1 1 429 94928552 94928981 2.810000e-154 555.0
9 TraesCS2A01G443200 chr7D 94.444 324 18 0 424 747 94929705 94930028 1.340000e-137 499.0
10 TraesCS2A01G443200 chr7D 90.141 142 8 3 1874 2009 13690457 13690598 1.980000e-41 180.0
11 TraesCS2A01G443200 chr7D 90.647 139 7 3 1877 2009 231563777 231563639 1.980000e-41 180.0
12 TraesCS2A01G443200 chr6A 91.365 498 43 0 995 1492 494477961 494478458 0.000000e+00 682.0
13 TraesCS2A01G443200 chr6B 90.964 498 45 0 995 1492 530572822 530573319 0.000000e+00 671.0
14 TraesCS2A01G443200 chr6B 94.915 59 3 0 1764 1822 713522702 713522644 2.650000e-15 93.5
15 TraesCS2A01G443200 chr6D 90.763 498 46 0 995 1492 349915386 349914889 0.000000e+00 665.0
16 TraesCS2A01G443200 chr6D 90.647 139 7 3 1877 2009 389244270 389244132 1.980000e-41 180.0
17 TraesCS2A01G443200 chr5B 88.384 198 23 0 1 198 116845769 116845966 3.210000e-59 239.0
18 TraesCS2A01G443200 chr5B 94.059 101 6 0 1765 1865 455637291 455637391 1.200000e-33 154.0
19 TraesCS2A01G443200 chr1D 91.367 139 6 2 1877 2009 51912569 51912431 4.250000e-43 185.0
20 TraesCS2A01G443200 chr1D 90.141 142 8 3 1874 2009 254527155 254527296 1.980000e-41 180.0
21 TraesCS2A01G443200 chr1D 100.000 31 0 0 1776 1806 388621836 388621806 9.660000e-05 58.4
22 TraesCS2A01G443200 chr5D 90.141 142 8 3 1874 2009 503246821 503246962 1.980000e-41 180.0
23 TraesCS2A01G443200 chr5D 90.647 139 7 3 1877 2009 503263224 503263086 1.980000e-41 180.0
24 TraesCS2A01G443200 chr1A 90.141 142 8 3 1874 2009 532075240 532075381 1.980000e-41 180.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2A01G443200 chr2A 693242145 693244645 2500 True 4619.0 4619 100.000 1 2501 1 chr2A.!!$R1 2500
1 TraesCS2A01G443200 chr2D 552606445 552607929 1484 True 1108.5 1552 93.019 763 2500 2 chr2D.!!$R2 1737
2 TraesCS2A01G443200 chr2B 658210176 658211008 832 True 1332.0 1332 95.289 764 1612 1 chr2B.!!$R1 848
3 TraesCS2A01G443200 chr2B 777842702 777843443 741 False 992.0 992 90.763 1 747 1 chr2B.!!$F1 746
4 TraesCS2A01G443200 chr4D 88469031 88469776 745 True 979.0 979 90.361 1 747 1 chr4D.!!$R1 746
5 TraesCS2A01G443200 chr7D 371786666 371787278 612 True 854.0 854 91.870 1 611 1 chr7D.!!$R2 610
6 TraesCS2A01G443200 chr7D 94928552 94930028 1476 False 527.0 555 92.222 1 747 2 chr7D.!!$F2 746

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
756 1492 0.321671 CGAGGGATGCCGGACATAAT 59.678 55.0 5.05 0.0 39.84 1.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1795 2533 0.038166 TTGCAGAGCCTACCCAAAGG 59.962 55.0 0.0 0.0 39.87 3.11 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
72 75 2.207229 CCGATGCCGTCCATCCCTA 61.207 63.158 7.48 0.00 46.17 3.53
75 78 1.758440 GATGCCGTCCATCCCTAGCA 61.758 60.000 2.75 0.00 43.72 3.49
85 88 3.782523 TCCATCCCTAGCAAGAAACTGAT 59.217 43.478 0.00 0.00 0.00 2.90
91 94 3.131223 CCTAGCAAGAAACTGATCCTCGA 59.869 47.826 0.00 0.00 0.00 4.04
101 104 1.411977 CTGATCCTCGACTGCCTGAAT 59.588 52.381 0.00 0.00 0.00 2.57
141 144 2.687935 GAGCAACCCTTCTTTGTGAACA 59.312 45.455 0.00 0.00 0.00 3.18
142 145 3.299503 AGCAACCCTTCTTTGTGAACAT 58.700 40.909 0.00 0.00 0.00 2.71
172 175 4.456280 TTCAAGCTCGAAGATGAAGCTA 57.544 40.909 0.00 0.00 35.15 3.32
211 214 3.019564 AGCATGTGGGCTTTGTAGAATC 58.980 45.455 0.00 0.00 42.71 2.52
217 220 2.919602 TGGGCTTTGTAGAATCCCTTCT 59.080 45.455 10.52 0.00 44.06 2.85
277 280 2.161211 AGTAACGACCAACTCTACGAGC 59.839 50.000 0.00 0.00 32.04 5.03
310 313 3.042887 CAAGTTATCGATCATCGCGACA 58.957 45.455 12.93 0.02 40.94 4.35
321 324 1.590238 CATCGCGACAATCCAACTCTC 59.410 52.381 12.93 0.00 0.00 3.20
367 370 8.186709 ACTCAAAGAGATCAACAATTTCCATT 57.813 30.769 0.31 0.00 33.32 3.16
457 1189 2.188829 GCACAGCTGGCACTTGTCA 61.189 57.895 19.93 0.00 0.00 3.58
502 1238 0.464452 GAACATCCTCCGTCGGGATT 59.536 55.000 12.29 0.00 42.83 3.01
504 1240 1.069765 CATCCTCCGTCGGGATTGG 59.930 63.158 12.29 9.07 42.83 3.16
524 1260 1.429825 CACCTCGCTAGTCTCCACG 59.570 63.158 0.00 0.00 0.00 4.94
564 1300 2.439507 CTGGTACTTCCACTGCCCATAT 59.560 50.000 0.00 0.00 41.93 1.78
623 1359 2.507339 AGTTGCATTGTTTCCCAACG 57.493 45.000 0.00 0.00 41.65 4.10
634 1370 2.011122 TTCCCAACGAGTCCTCTCTT 57.989 50.000 0.00 0.00 38.45 2.85
685 1421 6.704493 GGTATGCGGATCTAACTGTGAAAATA 59.296 38.462 0.00 0.00 0.00 1.40
737 1473 3.567397 TCCTCTAGATTCCTAGTGCACC 58.433 50.000 14.63 0.00 42.33 5.01
747 1483 2.650813 CTAGTGCACCGAGGGATGCC 62.651 65.000 14.63 0.00 41.33 4.40
754 1490 3.455152 CGAGGGATGCCGGACATA 58.545 61.111 5.05 0.00 39.84 2.29
755 1491 1.745890 CGAGGGATGCCGGACATAA 59.254 57.895 5.05 0.00 39.84 1.90
756 1492 0.321671 CGAGGGATGCCGGACATAAT 59.678 55.000 5.05 0.00 39.84 1.28
757 1493 1.270839 CGAGGGATGCCGGACATAATT 60.271 52.381 5.05 0.00 39.84 1.40
758 1494 2.810400 CGAGGGATGCCGGACATAATTT 60.810 50.000 5.05 0.00 39.84 1.82
759 1495 3.222603 GAGGGATGCCGGACATAATTTT 58.777 45.455 5.05 0.00 39.84 1.82
760 1496 3.636764 GAGGGATGCCGGACATAATTTTT 59.363 43.478 5.05 0.00 39.84 1.94
859 1595 1.828979 TAAAGCCCAACCCGAATGAC 58.171 50.000 0.00 0.00 0.00 3.06
951 1687 1.925972 GCCTCTCCCAAACCCTCCT 60.926 63.158 0.00 0.00 0.00 3.69
1230 1966 2.484203 GTCTCCGTCGTCCCTTCG 59.516 66.667 0.00 0.00 0.00 3.79
1563 2299 6.293955 GCTATGCAATGTTGGATTATTACGGT 60.294 38.462 5.08 0.00 39.95 4.83
1593 2329 8.650143 ATTAGTCCATTCTGGTATTTTGTTGT 57.350 30.769 0.00 0.00 39.03 3.32
1598 2334 5.010516 CCATTCTGGTATTTTGTTGTGACCA 59.989 40.000 0.00 0.00 37.85 4.02
1622 2358 7.285401 CCAGTAAAATATGATGTAGCCCTTGTT 59.715 37.037 0.00 0.00 0.00 2.83
1646 2384 3.370527 CCAGACGATGTGGGTAGGAAATT 60.371 47.826 0.00 0.00 0.00 1.82
1649 2387 4.019681 AGACGATGTGGGTAGGAAATTCAA 60.020 41.667 0.00 0.00 0.00 2.69
1652 2390 4.600062 GATGTGGGTAGGAAATTCAACCT 58.400 43.478 13.94 0.00 39.95 3.50
1653 2391 3.761897 TGTGGGTAGGAAATTCAACCTG 58.238 45.455 13.94 0.00 37.68 4.00
1673 2411 3.067684 GCTACAAGCAGTTTCCCCTTA 57.932 47.619 0.00 0.00 41.89 2.69
1674 2412 3.418047 GCTACAAGCAGTTTCCCCTTAA 58.582 45.455 0.00 0.00 41.89 1.85
1705 2443 6.579666 ATTGAATTGCAGAGTATGTGTGTT 57.420 33.333 0.00 0.00 0.00 3.32
1713 2451 5.182950 TGCAGAGTATGTGTGTTAAAATGGG 59.817 40.000 0.00 0.00 0.00 4.00
1719 2457 7.449247 AGTATGTGTGTTAAAATGGGCAAAAT 58.551 30.769 0.00 0.00 0.00 1.82
1745 2483 4.581409 TCAACAGTGCTGTGTGTACTACTA 59.419 41.667 5.53 0.00 44.13 1.82
1748 2486 4.523173 ACAGTGCTGTGTGTACTACTATGT 59.477 41.667 3.80 0.00 43.11 2.29
1764 2502 3.813166 ACTATGTGGACCTGTTTGTTTCG 59.187 43.478 0.00 0.00 0.00 3.46
1768 2506 3.810941 TGTGGACCTGTTTGTTTCGTATC 59.189 43.478 0.00 0.00 0.00 2.24
1769 2507 3.810941 GTGGACCTGTTTGTTTCGTATCA 59.189 43.478 0.00 0.00 0.00 2.15
1770 2508 3.810941 TGGACCTGTTTGTTTCGTATCAC 59.189 43.478 0.00 0.00 0.00 3.06
1771 2509 3.187842 GGACCTGTTTGTTTCGTATCACC 59.812 47.826 0.00 0.00 0.00 4.02
1772 2510 3.143728 ACCTGTTTGTTTCGTATCACCC 58.856 45.455 0.00 0.00 0.00 4.61
1773 2511 3.142951 CCTGTTTGTTTCGTATCACCCA 58.857 45.455 0.00 0.00 0.00 4.51
1774 2512 3.058501 CCTGTTTGTTTCGTATCACCCAC 60.059 47.826 0.00 0.00 0.00 4.61
1775 2513 3.811083 TGTTTGTTTCGTATCACCCACT 58.189 40.909 0.00 0.00 0.00 4.00
1776 2514 4.200874 TGTTTGTTTCGTATCACCCACTT 58.799 39.130 0.00 0.00 0.00 3.16
1777 2515 4.273969 TGTTTGTTTCGTATCACCCACTTC 59.726 41.667 0.00 0.00 0.00 3.01
1778 2516 3.048337 TGTTTCGTATCACCCACTTCC 57.952 47.619 0.00 0.00 0.00 3.46
1779 2517 2.635915 TGTTTCGTATCACCCACTTCCT 59.364 45.455 0.00 0.00 0.00 3.36
1780 2518 3.833650 TGTTTCGTATCACCCACTTCCTA 59.166 43.478 0.00 0.00 0.00 2.94
1781 2519 4.179298 GTTTCGTATCACCCACTTCCTAC 58.821 47.826 0.00 0.00 0.00 3.18
1782 2520 3.090210 TCGTATCACCCACTTCCTACA 57.910 47.619 0.00 0.00 0.00 2.74
1783 2521 3.433343 TCGTATCACCCACTTCCTACAA 58.567 45.455 0.00 0.00 0.00 2.41
1784 2522 4.028131 TCGTATCACCCACTTCCTACAAT 58.972 43.478 0.00 0.00 0.00 2.71
1785 2523 4.098960 TCGTATCACCCACTTCCTACAATC 59.901 45.833 0.00 0.00 0.00 2.67
1786 2524 3.933861 ATCACCCACTTCCTACAATCC 57.066 47.619 0.00 0.00 0.00 3.01
1787 2525 1.553248 TCACCCACTTCCTACAATCCG 59.447 52.381 0.00 0.00 0.00 4.18
1788 2526 0.909623 ACCCACTTCCTACAATCCGG 59.090 55.000 0.00 0.00 0.00 5.14
1789 2527 0.463833 CCCACTTCCTACAATCCGGC 60.464 60.000 0.00 0.00 0.00 6.13
1790 2528 0.463833 CCACTTCCTACAATCCGGCC 60.464 60.000 0.00 0.00 0.00 6.13
1791 2529 0.541863 CACTTCCTACAATCCGGCCT 59.458 55.000 0.00 0.00 0.00 5.19
1792 2530 0.541863 ACTTCCTACAATCCGGCCTG 59.458 55.000 0.00 0.00 0.00 4.85
1793 2531 0.830648 CTTCCTACAATCCGGCCTGA 59.169 55.000 0.00 0.00 0.00 3.86
1794 2532 1.209504 CTTCCTACAATCCGGCCTGAA 59.790 52.381 0.00 0.00 0.00 3.02
1795 2533 0.539986 TCCTACAATCCGGCCTGAAC 59.460 55.000 0.00 0.00 0.00 3.18
1796 2534 0.463833 CCTACAATCCGGCCTGAACC 60.464 60.000 0.00 0.00 0.00 3.62
1797 2535 0.541863 CTACAATCCGGCCTGAACCT 59.458 55.000 0.00 0.00 0.00 3.50
1798 2536 0.988832 TACAATCCGGCCTGAACCTT 59.011 50.000 0.00 0.00 0.00 3.50
1799 2537 0.112412 ACAATCCGGCCTGAACCTTT 59.888 50.000 0.00 0.00 0.00 3.11
1800 2538 0.527565 CAATCCGGCCTGAACCTTTG 59.472 55.000 0.00 0.00 0.00 2.77
1801 2539 0.611896 AATCCGGCCTGAACCTTTGG 60.612 55.000 0.00 0.00 0.00 3.28
1802 2540 2.499303 ATCCGGCCTGAACCTTTGGG 62.499 60.000 0.00 0.00 38.88 4.12
1804 2542 1.377229 CGGCCTGAACCTTTGGGTA 59.623 57.895 0.00 0.00 46.67 3.69
1805 2543 0.676782 CGGCCTGAACCTTTGGGTAG 60.677 60.000 0.00 0.00 46.67 3.18
1806 2544 0.323451 GGCCTGAACCTTTGGGTAGG 60.323 60.000 0.00 0.00 46.67 3.18
1807 2545 3.266240 CCTGAACCTTTGGGTAGGC 57.734 57.895 0.00 0.00 46.67 3.93
1808 2546 0.698818 CCTGAACCTTTGGGTAGGCT 59.301 55.000 0.00 0.00 46.67 4.58
1809 2547 1.340114 CCTGAACCTTTGGGTAGGCTC 60.340 57.143 0.00 0.00 46.67 4.70
1810 2548 1.630878 CTGAACCTTTGGGTAGGCTCT 59.369 52.381 0.00 0.00 46.67 4.09
1811 2549 1.351017 TGAACCTTTGGGTAGGCTCTG 59.649 52.381 0.00 0.00 46.67 3.35
1812 2550 0.038310 AACCTTTGGGTAGGCTCTGC 59.962 55.000 0.00 0.00 46.67 4.26
1813 2551 1.133809 ACCTTTGGGTAGGCTCTGCA 61.134 55.000 0.00 0.00 45.32 4.41
1814 2552 0.038166 CCTTTGGGTAGGCTCTGCAA 59.962 55.000 0.00 0.00 0.00 4.08
1815 2553 1.457346 CTTTGGGTAGGCTCTGCAAG 58.543 55.000 0.00 0.00 0.00 4.01
1816 2554 1.003580 CTTTGGGTAGGCTCTGCAAGA 59.996 52.381 0.00 0.00 43.69 3.02
1817 2555 1.289160 TTGGGTAGGCTCTGCAAGAT 58.711 50.000 0.00 0.00 45.62 2.40
1818 2556 0.833287 TGGGTAGGCTCTGCAAGATC 59.167 55.000 0.00 0.00 45.62 2.75
1819 2557 0.833287 GGGTAGGCTCTGCAAGATCA 59.167 55.000 0.00 0.00 45.62 2.92
1820 2558 1.210478 GGGTAGGCTCTGCAAGATCAA 59.790 52.381 0.00 0.00 45.62 2.57
1821 2559 2.284190 GGTAGGCTCTGCAAGATCAAC 58.716 52.381 0.00 0.00 45.62 3.18
1822 2560 2.355108 GGTAGGCTCTGCAAGATCAACA 60.355 50.000 0.00 0.00 45.62 3.33
1823 2561 2.574006 AGGCTCTGCAAGATCAACAA 57.426 45.000 0.00 0.00 45.62 2.83
1824 2562 2.157738 AGGCTCTGCAAGATCAACAAC 58.842 47.619 0.00 0.00 45.62 3.32
1825 2563 1.200948 GGCTCTGCAAGATCAACAACC 59.799 52.381 0.00 0.00 45.62 3.77
1826 2564 1.881973 GCTCTGCAAGATCAACAACCA 59.118 47.619 0.00 0.00 45.62 3.67
1827 2565 2.490903 GCTCTGCAAGATCAACAACCAT 59.509 45.455 0.00 0.00 45.62 3.55
1828 2566 3.691118 GCTCTGCAAGATCAACAACCATA 59.309 43.478 0.00 0.00 45.62 2.74
1829 2567 4.201891 GCTCTGCAAGATCAACAACCATAG 60.202 45.833 0.00 0.00 45.62 2.23
1830 2568 3.691118 TCTGCAAGATCAACAACCATAGC 59.309 43.478 0.00 0.00 38.67 2.97
1831 2569 2.754552 TGCAAGATCAACAACCATAGCC 59.245 45.455 0.00 0.00 0.00 3.93
1832 2570 2.223340 GCAAGATCAACAACCATAGCCG 60.223 50.000 0.00 0.00 0.00 5.52
1833 2571 1.668419 AGATCAACAACCATAGCCGC 58.332 50.000 0.00 0.00 0.00 6.53
1834 2572 1.065491 AGATCAACAACCATAGCCGCA 60.065 47.619 0.00 0.00 0.00 5.69
1835 2573 1.064060 GATCAACAACCATAGCCGCAC 59.936 52.381 0.00 0.00 0.00 5.34
1836 2574 1.134487 CAACAACCATAGCCGCACG 59.866 57.895 0.00 0.00 0.00 5.34
1837 2575 2.038269 AACAACCATAGCCGCACGG 61.038 57.895 4.30 4.30 38.57 4.94
1838 2576 2.125310 CAACCATAGCCGCACGGA 60.125 61.111 14.43 0.00 37.50 4.69
1839 2577 2.173669 CAACCATAGCCGCACGGAG 61.174 63.158 14.43 0.00 37.50 4.63
1841 2579 1.324740 AACCATAGCCGCACGGAGTA 61.325 55.000 14.43 3.59 41.61 2.59
1842 2580 1.299926 CCATAGCCGCACGGAGTAC 60.300 63.158 14.43 0.00 41.61 2.73
1848 2586 3.489731 CGCACGGAGTACGGTAGA 58.510 61.111 0.00 0.00 44.55 2.59
1849 2587 1.796151 CGCACGGAGTACGGTAGAA 59.204 57.895 0.00 0.00 44.55 2.10
1850 2588 0.379669 CGCACGGAGTACGGTAGAAT 59.620 55.000 0.00 0.00 44.55 2.40
1851 2589 1.202222 CGCACGGAGTACGGTAGAATT 60.202 52.381 0.00 0.00 44.55 2.17
1852 2590 3.103540 CGCACGGAGTACGGTAGAATTC 61.104 54.545 0.00 0.00 44.55 2.17
1854 2592 2.789491 CGGAGTACGGTAGAATTCCC 57.211 55.000 0.65 0.00 39.42 3.97
1855 2593 2.305009 CGGAGTACGGTAGAATTCCCT 58.695 52.381 0.65 0.00 39.42 4.20
1856 2594 2.034305 CGGAGTACGGTAGAATTCCCTG 59.966 54.545 0.65 0.89 39.42 4.45
1857 2595 2.364647 GGAGTACGGTAGAATTCCCTGG 59.635 54.545 0.65 0.00 0.00 4.45
1858 2596 3.029570 GAGTACGGTAGAATTCCCTGGT 58.970 50.000 0.65 0.00 0.00 4.00
1859 2597 4.210331 GAGTACGGTAGAATTCCCTGGTA 58.790 47.826 0.65 0.00 0.00 3.25
1860 2598 4.812653 AGTACGGTAGAATTCCCTGGTAT 58.187 43.478 0.65 0.00 0.00 2.73
1861 2599 4.587684 AGTACGGTAGAATTCCCTGGTATG 59.412 45.833 0.65 0.00 0.00 2.39
1862 2600 2.704065 ACGGTAGAATTCCCTGGTATGG 59.296 50.000 0.65 0.00 0.00 2.74
1863 2601 2.704065 CGGTAGAATTCCCTGGTATGGT 59.296 50.000 0.65 0.00 0.00 3.55
1864 2602 3.244112 CGGTAGAATTCCCTGGTATGGTC 60.244 52.174 0.65 0.00 0.00 4.02
1865 2603 3.072622 GGTAGAATTCCCTGGTATGGTCC 59.927 52.174 0.65 0.00 0.00 4.46
1866 2604 2.136026 AGAATTCCCTGGTATGGTCCC 58.864 52.381 0.65 0.00 0.00 4.46
1867 2605 1.145119 GAATTCCCTGGTATGGTCCCC 59.855 57.143 0.00 0.00 0.00 4.81
1868 2606 0.701310 ATTCCCTGGTATGGTCCCCC 60.701 60.000 0.00 0.00 0.00 5.40
1883 2621 3.478780 CCCCGAGGGTGAACTGAA 58.521 61.111 7.48 0.00 38.25 3.02
1884 2622 1.758592 CCCCGAGGGTGAACTGAAA 59.241 57.895 7.48 0.00 38.25 2.69
1885 2623 0.605589 CCCCGAGGGTGAACTGAAAC 60.606 60.000 7.48 0.00 38.25 2.78
1886 2624 0.107831 CCCGAGGGTGAACTGAAACA 59.892 55.000 0.00 0.00 0.00 2.83
1887 2625 1.271379 CCCGAGGGTGAACTGAAACAT 60.271 52.381 0.00 0.00 0.00 2.71
1888 2626 2.076863 CCGAGGGTGAACTGAAACATC 58.923 52.381 0.00 0.00 0.00 3.06
1889 2627 2.289694 CCGAGGGTGAACTGAAACATCT 60.290 50.000 0.00 0.00 0.00 2.90
1890 2628 3.403038 CGAGGGTGAACTGAAACATCTT 58.597 45.455 0.00 0.00 0.00 2.40
1891 2629 4.562757 CCGAGGGTGAACTGAAACATCTTA 60.563 45.833 0.00 0.00 0.00 2.10
1892 2630 4.627467 CGAGGGTGAACTGAAACATCTTAG 59.373 45.833 0.00 0.00 0.00 2.18
1893 2631 5.552178 GAGGGTGAACTGAAACATCTTAGT 58.448 41.667 0.00 0.00 0.00 2.24
1894 2632 6.571731 CGAGGGTGAACTGAAACATCTTAGTA 60.572 42.308 0.00 0.00 0.00 1.82
1895 2633 6.702329 AGGGTGAACTGAAACATCTTAGTAG 58.298 40.000 0.00 0.00 0.00 2.57
1896 2634 5.351740 GGGTGAACTGAAACATCTTAGTAGC 59.648 44.000 0.00 0.00 0.00 3.58
1897 2635 5.351740 GGTGAACTGAAACATCTTAGTAGCC 59.648 44.000 0.00 0.00 0.00 3.93
1898 2636 5.351740 GTGAACTGAAACATCTTAGTAGCCC 59.648 44.000 0.00 0.00 0.00 5.19
1899 2637 4.124851 ACTGAAACATCTTAGTAGCCCG 57.875 45.455 0.00 0.00 0.00 6.13
1900 2638 3.767673 ACTGAAACATCTTAGTAGCCCGA 59.232 43.478 0.00 0.00 0.00 5.14
1901 2639 4.142138 ACTGAAACATCTTAGTAGCCCGAG 60.142 45.833 0.00 0.00 0.00 4.63
1902 2640 3.132289 TGAAACATCTTAGTAGCCCGAGG 59.868 47.826 0.00 0.00 0.00 4.63
1903 2641 2.750141 ACATCTTAGTAGCCCGAGGA 57.250 50.000 0.00 0.00 0.00 3.71
1904 2642 3.028094 ACATCTTAGTAGCCCGAGGAA 57.972 47.619 0.00 0.00 0.00 3.36
1905 2643 3.371965 ACATCTTAGTAGCCCGAGGAAA 58.628 45.455 0.00 0.00 0.00 3.13
1906 2644 3.773119 ACATCTTAGTAGCCCGAGGAAAA 59.227 43.478 0.00 0.00 0.00 2.29
1907 2645 4.141914 ACATCTTAGTAGCCCGAGGAAAAG 60.142 45.833 0.00 0.00 0.00 2.27
1908 2646 3.705051 TCTTAGTAGCCCGAGGAAAAGA 58.295 45.455 0.00 0.00 0.00 2.52
1909 2647 3.700038 TCTTAGTAGCCCGAGGAAAAGAG 59.300 47.826 0.00 0.00 0.00 2.85
1910 2648 2.233305 AGTAGCCCGAGGAAAAGAGA 57.767 50.000 0.00 0.00 0.00 3.10
1911 2649 2.104170 AGTAGCCCGAGGAAAAGAGAG 58.896 52.381 0.00 0.00 0.00 3.20
1912 2650 0.824759 TAGCCCGAGGAAAAGAGAGC 59.175 55.000 0.00 0.00 0.00 4.09
1913 2651 1.194781 AGCCCGAGGAAAAGAGAGCA 61.195 55.000 0.00 0.00 0.00 4.26
1914 2652 0.321653 GCCCGAGGAAAAGAGAGCAA 60.322 55.000 0.00 0.00 0.00 3.91
1915 2653 1.731720 CCCGAGGAAAAGAGAGCAAG 58.268 55.000 0.00 0.00 0.00 4.01
1916 2654 1.082690 CCGAGGAAAAGAGAGCAAGC 58.917 55.000 0.00 0.00 0.00 4.01
1917 2655 0.718343 CGAGGAAAAGAGAGCAAGCG 59.282 55.000 0.00 0.00 0.00 4.68
1918 2656 1.082690 GAGGAAAAGAGAGCAAGCGG 58.917 55.000 0.00 0.00 0.00 5.52
1919 2657 0.398318 AGGAAAAGAGAGCAAGCGGT 59.602 50.000 0.00 0.00 0.00 5.68
1920 2658 1.202818 AGGAAAAGAGAGCAAGCGGTT 60.203 47.619 0.00 0.00 0.00 4.44
1921 2659 1.197949 GGAAAAGAGAGCAAGCGGTTC 59.802 52.381 0.00 0.00 0.00 3.62
1922 2660 1.197949 GAAAAGAGAGCAAGCGGTTCC 59.802 52.381 0.00 0.00 0.00 3.62
1923 2661 0.606673 AAAGAGAGCAAGCGGTTCCC 60.607 55.000 0.00 0.00 0.00 3.97
1949 2687 3.202706 GGCGAGCGAAATGGGGTC 61.203 66.667 0.00 0.00 0.00 4.46
1950 2688 2.125106 GCGAGCGAAATGGGGTCT 60.125 61.111 0.00 0.00 0.00 3.85
1951 2689 1.143183 GCGAGCGAAATGGGGTCTA 59.857 57.895 0.00 0.00 0.00 2.59
1952 2690 0.461339 GCGAGCGAAATGGGGTCTAA 60.461 55.000 0.00 0.00 0.00 2.10
1953 2691 2.010043 GCGAGCGAAATGGGGTCTAAA 61.010 52.381 0.00 0.00 0.00 1.85
1954 2692 1.664151 CGAGCGAAATGGGGTCTAAAC 59.336 52.381 0.00 0.00 0.00 2.01
1955 2693 2.014857 GAGCGAAATGGGGTCTAAACC 58.985 52.381 0.00 0.00 45.65 3.27
1966 2704 3.842732 GGTCTAAACCGTGAAAATGGG 57.157 47.619 0.00 0.00 35.36 4.00
1967 2705 2.490509 GGTCTAAACCGTGAAAATGGGG 59.509 50.000 0.00 0.00 35.36 4.96
1968 2706 3.151554 GTCTAAACCGTGAAAATGGGGT 58.848 45.455 0.00 0.00 0.00 4.95
1969 2707 3.570975 GTCTAAACCGTGAAAATGGGGTT 59.429 43.478 0.00 0.00 44.29 4.11
1970 2708 2.900716 AAACCGTGAAAATGGGGTTG 57.099 45.000 0.00 0.00 41.70 3.77
1971 2709 1.783071 AACCGTGAAAATGGGGTTGT 58.217 45.000 0.00 0.00 41.04 3.32
1972 2710 1.036707 ACCGTGAAAATGGGGTTGTG 58.963 50.000 0.00 0.00 0.00 3.33
1973 2711 0.316841 CCGTGAAAATGGGGTTGTGG 59.683 55.000 0.00 0.00 0.00 4.17
1974 2712 1.323412 CGTGAAAATGGGGTTGTGGA 58.677 50.000 0.00 0.00 0.00 4.02
1975 2713 1.683917 CGTGAAAATGGGGTTGTGGAA 59.316 47.619 0.00 0.00 0.00 3.53
1976 2714 2.288152 CGTGAAAATGGGGTTGTGGAAG 60.288 50.000 0.00 0.00 0.00 3.46
1977 2715 2.962421 GTGAAAATGGGGTTGTGGAAGA 59.038 45.455 0.00 0.00 0.00 2.87
1978 2716 3.005791 GTGAAAATGGGGTTGTGGAAGAG 59.994 47.826 0.00 0.00 0.00 2.85
1979 2717 1.632589 AAATGGGGTTGTGGAAGAGC 58.367 50.000 0.00 0.00 0.00 4.09
1980 2718 0.482446 AATGGGGTTGTGGAAGAGCA 59.518 50.000 0.00 0.00 0.00 4.26
1981 2719 0.482446 ATGGGGTTGTGGAAGAGCAA 59.518 50.000 0.00 0.00 0.00 3.91
1982 2720 0.482446 TGGGGTTGTGGAAGAGCAAT 59.518 50.000 0.00 0.00 0.00 3.56
1983 2721 1.707989 TGGGGTTGTGGAAGAGCAATA 59.292 47.619 0.00 0.00 0.00 1.90
1984 2722 2.092323 GGGGTTGTGGAAGAGCAATAC 58.908 52.381 0.00 0.00 0.00 1.89
1985 2723 2.554344 GGGGTTGTGGAAGAGCAATACA 60.554 50.000 0.00 0.00 0.00 2.29
1986 2724 3.153919 GGGTTGTGGAAGAGCAATACAA 58.846 45.455 0.00 0.00 0.00 2.41
1987 2725 3.191371 GGGTTGTGGAAGAGCAATACAAG 59.809 47.826 0.00 0.00 32.54 3.16
1988 2726 3.821033 GGTTGTGGAAGAGCAATACAAGT 59.179 43.478 0.00 0.00 32.54 3.16
1989 2727 4.320494 GGTTGTGGAAGAGCAATACAAGTG 60.320 45.833 0.00 0.00 32.54 3.16
1990 2728 4.085357 TGTGGAAGAGCAATACAAGTGT 57.915 40.909 0.00 0.00 0.00 3.55
1991 2729 4.460263 TGTGGAAGAGCAATACAAGTGTT 58.540 39.130 0.00 0.00 0.00 3.32
1992 2730 4.275689 TGTGGAAGAGCAATACAAGTGTTG 59.724 41.667 5.46 5.46 35.22 3.33
1994 2732 4.275689 TGGAAGAGCAATACAAGTGTTGTG 59.724 41.667 10.64 0.00 45.03 3.33
1995 2733 3.904136 AGAGCAATACAAGTGTTGTGC 57.096 42.857 10.64 9.75 45.03 4.57
1996 2734 3.480470 AGAGCAATACAAGTGTTGTGCT 58.520 40.909 16.88 16.88 45.03 4.40
1997 2735 3.251729 AGAGCAATACAAGTGTTGTGCTG 59.748 43.478 20.12 8.27 45.03 4.41
1998 2736 2.053627 GCAATACAAGTGTTGTGCTGC 58.946 47.619 10.64 7.22 45.03 5.25
1999 2737 2.287788 GCAATACAAGTGTTGTGCTGCT 60.288 45.455 15.35 0.00 45.03 4.24
2000 2738 3.058293 GCAATACAAGTGTTGTGCTGCTA 60.058 43.478 15.35 0.00 45.03 3.49
2001 2739 4.715896 CAATACAAGTGTTGTGCTGCTAG 58.284 43.478 0.00 0.00 45.03 3.42
2002 2740 1.597742 ACAAGTGTTGTGCTGCTAGG 58.402 50.000 0.00 0.00 43.48 3.02
2003 2741 0.239347 CAAGTGTTGTGCTGCTAGGC 59.761 55.000 0.00 0.00 0.00 3.93
2004 2742 1.230635 AAGTGTTGTGCTGCTAGGCG 61.231 55.000 0.00 0.00 34.52 5.52
2005 2743 1.667830 GTGTTGTGCTGCTAGGCGA 60.668 57.895 0.00 0.00 34.52 5.54
2006 2744 1.070615 TGTTGTGCTGCTAGGCGAA 59.929 52.632 0.00 0.00 34.52 4.70
2007 2745 0.950555 TGTTGTGCTGCTAGGCGAAG 60.951 55.000 0.00 0.00 34.52 3.79
2054 2792 7.760131 TTTTCTTCTCTGTTGAAATTGCTTG 57.240 32.000 0.00 0.00 31.08 4.01
2056 2794 7.566760 TTCTTCTCTGTTGAAATTGCTTGTA 57.433 32.000 0.00 0.00 0.00 2.41
2093 2831 0.469917 CCTGGTATTGACTGGGCGAT 59.530 55.000 0.00 0.00 0.00 4.58
2095 2833 2.303022 CCTGGTATTGACTGGGCGATAT 59.697 50.000 0.00 0.00 0.00 1.63
2101 2839 2.890808 TGACTGGGCGATATGTTCTC 57.109 50.000 0.00 0.00 0.00 2.87
2106 2844 3.898123 ACTGGGCGATATGTTCTCTGTAT 59.102 43.478 0.00 0.00 0.00 2.29
2148 2886 9.877178 ATAGTTCATTAGTTCTCTTTCAATCGT 57.123 29.630 0.00 0.00 0.00 3.73
2149 2887 8.023050 AGTTCATTAGTTCTCTTTCAATCGTG 57.977 34.615 0.00 0.00 0.00 4.35
2194 2936 0.375106 GCGCTGGTTAATCACTGCTC 59.625 55.000 0.00 0.00 0.00 4.26
2203 2945 4.762251 GGTTAATCACTGCTCCTCTTTTGT 59.238 41.667 0.00 0.00 0.00 2.83
2278 3020 5.295950 AGCTATCATATGCACTCTTGTGAC 58.704 41.667 0.00 0.00 46.55 3.67
2288 3030 4.157472 TGCACTCTTGTGACATTGTTTGAA 59.843 37.500 0.00 0.00 46.55 2.69
2320 3062 4.621769 ACTACTAAATCTACCAGCCCAGT 58.378 43.478 0.00 0.00 0.00 4.00
2439 3181 6.913170 TCTTGAGGATGTATCTTTGTTTTGC 58.087 36.000 0.00 0.00 0.00 3.68
2440 3182 5.295431 TGAGGATGTATCTTTGTTTTGCG 57.705 39.130 0.00 0.00 0.00 4.85
2458 3200 1.344458 CGCTAGCACACAAGAGACAG 58.656 55.000 16.45 0.00 0.00 3.51
2481 3225 9.372369 ACAGACTTTATCTTGCAGATTACTTAC 57.628 33.333 4.35 0.00 36.20 2.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 1.271054 GCTGACAGAGGCTTTTCCAGA 60.271 52.381 6.65 0.00 37.29 3.86
16 17 3.641434 ATACATGCTGACAGAGGCTTT 57.359 42.857 6.65 0.00 0.00 3.51
24 25 4.393680 GTCGGGTTAAAATACATGCTGACA 59.606 41.667 0.00 0.00 0.00 3.58
57 59 1.344953 TTGCTAGGGATGGACGGCAT 61.345 55.000 0.00 0.00 0.00 4.40
72 75 2.564947 AGTCGAGGATCAGTTTCTTGCT 59.435 45.455 0.00 0.00 33.17 3.91
75 78 2.354203 GGCAGTCGAGGATCAGTTTCTT 60.354 50.000 0.00 0.00 33.17 2.52
85 88 1.945819 GCAAATTCAGGCAGTCGAGGA 60.946 52.381 0.00 0.00 0.00 3.71
91 94 1.200716 CGACATGCAAATTCAGGCAGT 59.799 47.619 0.00 4.42 44.24 4.40
101 104 3.857052 CTCCCTTAGTACGACATGCAAA 58.143 45.455 0.00 0.00 0.00 3.68
172 175 4.521130 TGCTACTCATTCTTTCGTGACT 57.479 40.909 0.00 0.00 0.00 3.41
211 214 2.558359 ACGAAAGGCAATTCAAGAAGGG 59.442 45.455 0.00 0.00 0.00 3.95
217 220 1.196808 GCGAGACGAAAGGCAATTCAA 59.803 47.619 0.00 0.00 46.78 2.69
277 280 5.356882 TCGATAACTTGGAGCACAAAAAG 57.643 39.130 0.00 0.00 38.91 2.27
289 292 3.042887 TGTCGCGATGATCGATAACTTG 58.957 45.455 20.25 0.00 43.74 3.16
310 313 2.094675 CCAAATGCCGAGAGTTGGATT 58.905 47.619 6.95 0.00 42.66 3.01
321 324 3.557595 GTCTATGAGAGAACCAAATGCCG 59.442 47.826 0.00 0.00 35.37 5.69
367 370 4.635765 AGATGTATTTGCGCTTTAGCTGAA 59.364 37.500 9.73 0.00 39.32 3.02
457 1189 1.623811 AGTAGAAACATGGCGGACAGT 59.376 47.619 0.00 0.00 0.00 3.55
524 1260 8.857098 AGTACCAGGAAAAATAAGAAACTTTCC 58.143 33.333 0.00 4.59 44.76 3.13
564 1300 3.782523 AGATGCAAGGGAATGGACTTCTA 59.217 43.478 0.00 0.00 34.08 2.10
617 1353 1.474879 GAGAAGAGAGGACTCGTTGGG 59.525 57.143 0.00 0.00 46.64 4.12
623 1359 3.580895 ACCAAAAGGAGAAGAGAGGACTC 59.419 47.826 0.00 0.00 42.90 3.36
634 1370 3.244875 TGCTTGCAGATACCAAAAGGAGA 60.245 43.478 0.00 0.00 0.00 3.71
685 1421 6.352137 GGGCTTGGAATTATGAGAAAAATGGT 60.352 38.462 0.00 0.00 0.00 3.55
737 1473 0.321671 ATTATGTCCGGCATCCCTCG 59.678 55.000 13.58 0.00 38.94 4.63
859 1595 1.159713 TTCCTTGTGCTCGTGCTGTG 61.160 55.000 11.19 0.00 40.48 3.66
891 1627 0.299003 GCACGAAGAGTTATGCGAGC 59.701 55.000 0.00 0.00 33.76 5.03
1077 1813 4.162690 ATCTTGGGGGCGAGCGAC 62.163 66.667 0.00 0.00 0.00 5.19
1107 1843 0.755686 CGATCTTCTTGGGGGAGAGG 59.244 60.000 0.00 0.00 0.00 3.69
1323 2059 1.355563 GGCGATCTCGATGACGTCA 59.644 57.895 22.48 22.48 43.02 4.35
1540 2276 7.575414 AACCGTAATAATCCAACATTGCATA 57.425 32.000 0.00 0.00 0.00 3.14
1589 2325 8.122952 GCTACATCATATTTTACTGGTCACAAC 58.877 37.037 0.00 0.00 0.00 3.32
1593 2329 6.101150 AGGGCTACATCATATTTTACTGGTCA 59.899 38.462 0.00 0.00 0.00 4.02
1598 2334 8.823220 AAACAAGGGCTACATCATATTTTACT 57.177 30.769 0.00 0.00 0.00 2.24
1622 2358 1.191535 CCTACCCACATCGTCTGGAA 58.808 55.000 0.00 0.00 0.00 3.53
1653 2391 1.911057 AAGGGGAAACTGCTTGTAGC 58.089 50.000 0.00 0.00 42.82 3.58
1699 2437 8.316640 TGAATATTTTGCCCATTTTAACACAC 57.683 30.769 0.00 0.00 0.00 3.82
1701 2439 8.778358 TGTTGAATATTTTGCCCATTTTAACAC 58.222 29.630 0.00 0.00 0.00 3.32
1705 2443 7.118971 GCACTGTTGAATATTTTGCCCATTTTA 59.881 33.333 0.00 0.00 0.00 1.52
1713 2451 4.984161 ACACAGCACTGTTGAATATTTTGC 59.016 37.500 0.00 0.00 42.83 3.68
1719 2457 4.956085 AGTACACACAGCACTGTTGAATA 58.044 39.130 15.26 0.54 42.83 1.75
1745 2483 2.650322 ACGAAACAAACAGGTCCACAT 58.350 42.857 0.00 0.00 0.00 3.21
1748 2486 3.810941 GTGATACGAAACAAACAGGTCCA 59.189 43.478 0.00 0.00 0.00 4.02
1764 2502 4.704965 GGATTGTAGGAAGTGGGTGATAC 58.295 47.826 0.00 0.00 0.00 2.24
1768 2506 1.406887 CCGGATTGTAGGAAGTGGGTG 60.407 57.143 0.00 0.00 0.00 4.61
1769 2507 0.909623 CCGGATTGTAGGAAGTGGGT 59.090 55.000 0.00 0.00 0.00 4.51
1770 2508 0.463833 GCCGGATTGTAGGAAGTGGG 60.464 60.000 5.05 0.00 0.00 4.61
1771 2509 0.463833 GGCCGGATTGTAGGAAGTGG 60.464 60.000 5.05 0.00 0.00 4.00
1772 2510 0.541863 AGGCCGGATTGTAGGAAGTG 59.458 55.000 5.05 0.00 0.00 3.16
1773 2511 0.541863 CAGGCCGGATTGTAGGAAGT 59.458 55.000 5.05 0.00 0.00 3.01
1774 2512 0.830648 TCAGGCCGGATTGTAGGAAG 59.169 55.000 5.05 0.00 0.00 3.46
1775 2513 1.065709 GTTCAGGCCGGATTGTAGGAA 60.066 52.381 5.05 0.00 0.00 3.36
1776 2514 0.539986 GTTCAGGCCGGATTGTAGGA 59.460 55.000 5.05 0.00 0.00 2.94
1777 2515 0.463833 GGTTCAGGCCGGATTGTAGG 60.464 60.000 5.05 0.00 0.00 3.18
1778 2516 0.541863 AGGTTCAGGCCGGATTGTAG 59.458 55.000 5.05 0.00 0.00 2.74
1779 2517 0.988832 AAGGTTCAGGCCGGATTGTA 59.011 50.000 5.05 0.00 0.00 2.41
1780 2518 0.112412 AAAGGTTCAGGCCGGATTGT 59.888 50.000 5.05 0.00 0.00 2.71
1781 2519 0.527565 CAAAGGTTCAGGCCGGATTG 59.472 55.000 5.05 4.42 0.00 2.67
1782 2520 0.611896 CCAAAGGTTCAGGCCGGATT 60.612 55.000 5.05 0.00 0.00 3.01
1783 2521 1.000896 CCAAAGGTTCAGGCCGGAT 60.001 57.895 5.05 0.00 0.00 4.18
1784 2522 2.434331 CCAAAGGTTCAGGCCGGA 59.566 61.111 5.05 0.00 0.00 5.14
1785 2523 2.676471 CCCAAAGGTTCAGGCCGG 60.676 66.667 0.00 0.00 0.00 6.13
1795 2533 0.038166 TTGCAGAGCCTACCCAAAGG 59.962 55.000 0.00 0.00 39.87 3.11
1796 2534 1.003580 TCTTGCAGAGCCTACCCAAAG 59.996 52.381 0.00 0.00 0.00 2.77
1797 2535 1.064003 TCTTGCAGAGCCTACCCAAA 58.936 50.000 0.00 0.00 0.00 3.28
1798 2536 1.210478 GATCTTGCAGAGCCTACCCAA 59.790 52.381 0.00 0.00 0.00 4.12
1799 2537 0.833287 GATCTTGCAGAGCCTACCCA 59.167 55.000 0.00 0.00 0.00 4.51
1800 2538 0.833287 TGATCTTGCAGAGCCTACCC 59.167 55.000 0.00 0.00 27.46 3.69
1801 2539 2.284190 GTTGATCTTGCAGAGCCTACC 58.716 52.381 0.00 0.00 27.46 3.18
1802 2540 2.977914 TGTTGATCTTGCAGAGCCTAC 58.022 47.619 0.00 0.00 27.46 3.18
1803 2541 3.338249 GTTGTTGATCTTGCAGAGCCTA 58.662 45.455 0.00 0.00 27.46 3.93
1804 2542 2.157738 GTTGTTGATCTTGCAGAGCCT 58.842 47.619 0.00 0.00 27.46 4.58
1805 2543 1.200948 GGTTGTTGATCTTGCAGAGCC 59.799 52.381 0.00 0.00 27.46 4.70
1806 2544 1.881973 TGGTTGTTGATCTTGCAGAGC 59.118 47.619 0.00 0.00 0.00 4.09
1807 2545 4.201891 GCTATGGTTGTTGATCTTGCAGAG 60.202 45.833 0.00 0.00 0.00 3.35
1808 2546 3.691118 GCTATGGTTGTTGATCTTGCAGA 59.309 43.478 0.00 0.00 0.00 4.26
1809 2547 3.181493 GGCTATGGTTGTTGATCTTGCAG 60.181 47.826 0.00 0.00 0.00 4.41
1810 2548 2.754552 GGCTATGGTTGTTGATCTTGCA 59.245 45.455 0.00 0.00 0.00 4.08
1811 2549 2.223340 CGGCTATGGTTGTTGATCTTGC 60.223 50.000 0.00 0.00 0.00 4.01
1812 2550 2.223340 GCGGCTATGGTTGTTGATCTTG 60.223 50.000 0.00 0.00 0.00 3.02
1813 2551 2.017049 GCGGCTATGGTTGTTGATCTT 58.983 47.619 0.00 0.00 0.00 2.40
1814 2552 1.065491 TGCGGCTATGGTTGTTGATCT 60.065 47.619 0.00 0.00 0.00 2.75
1815 2553 1.064060 GTGCGGCTATGGTTGTTGATC 59.936 52.381 0.00 0.00 0.00 2.92
1816 2554 1.094785 GTGCGGCTATGGTTGTTGAT 58.905 50.000 0.00 0.00 0.00 2.57
1817 2555 1.295357 CGTGCGGCTATGGTTGTTGA 61.295 55.000 0.00 0.00 0.00 3.18
1818 2556 1.134487 CGTGCGGCTATGGTTGTTG 59.866 57.895 0.00 0.00 0.00 3.33
1819 2557 2.038269 CCGTGCGGCTATGGTTGTT 61.038 57.895 0.00 0.00 0.00 2.83
1820 2558 2.435938 CCGTGCGGCTATGGTTGT 60.436 61.111 0.00 0.00 0.00 3.32
1821 2559 2.125310 TCCGTGCGGCTATGGTTG 60.125 61.111 5.64 0.00 34.68 3.77
1822 2560 1.324740 TACTCCGTGCGGCTATGGTT 61.325 55.000 5.64 0.00 34.68 3.67
1823 2561 1.755395 TACTCCGTGCGGCTATGGT 60.755 57.895 5.64 2.78 34.68 3.55
1824 2562 1.299926 GTACTCCGTGCGGCTATGG 60.300 63.158 5.64 3.00 34.68 2.74
1825 2563 1.657487 CGTACTCCGTGCGGCTATG 60.657 63.158 5.64 0.16 37.94 2.23
1826 2564 2.719979 CGTACTCCGTGCGGCTAT 59.280 61.111 5.64 0.00 37.94 2.97
1831 2569 0.379669 ATTCTACCGTACTCCGTGCG 59.620 55.000 0.00 0.00 41.00 5.34
1832 2570 2.457970 GAATTCTACCGTACTCCGTGC 58.542 52.381 0.00 0.00 33.66 5.34
1833 2571 2.223665 GGGAATTCTACCGTACTCCGTG 60.224 54.545 5.23 0.00 33.66 4.94
1834 2572 2.027385 GGGAATTCTACCGTACTCCGT 58.973 52.381 5.23 0.00 33.66 4.69
1835 2573 2.034305 CAGGGAATTCTACCGTACTCCG 59.966 54.545 5.23 0.00 0.00 4.63
1836 2574 2.364647 CCAGGGAATTCTACCGTACTCC 59.635 54.545 5.23 0.00 0.00 3.85
1837 2575 3.029570 ACCAGGGAATTCTACCGTACTC 58.970 50.000 5.23 0.00 0.00 2.59
1838 2576 3.111741 ACCAGGGAATTCTACCGTACT 57.888 47.619 5.23 0.00 0.00 2.73
1839 2577 4.262335 CCATACCAGGGAATTCTACCGTAC 60.262 50.000 5.23 0.00 0.00 3.67
1840 2578 3.899360 CCATACCAGGGAATTCTACCGTA 59.101 47.826 5.23 2.46 0.00 4.02
1841 2579 2.704065 CCATACCAGGGAATTCTACCGT 59.296 50.000 5.23 0.26 0.00 4.83
1842 2580 2.704065 ACCATACCAGGGAATTCTACCG 59.296 50.000 5.23 0.00 0.00 4.02
1843 2581 3.072622 GGACCATACCAGGGAATTCTACC 59.927 52.174 5.23 0.00 0.00 3.18
1844 2582 3.072622 GGGACCATACCAGGGAATTCTAC 59.927 52.174 5.23 0.00 0.00 2.59
1845 2583 3.323775 GGGACCATACCAGGGAATTCTA 58.676 50.000 5.23 0.00 0.00 2.10
1846 2584 2.136026 GGGACCATACCAGGGAATTCT 58.864 52.381 5.23 0.00 0.00 2.40
1847 2585 2.658807 GGGACCATACCAGGGAATTC 57.341 55.000 0.00 0.00 0.00 2.17
1867 2605 0.107831 TGTTTCAGTTCACCCTCGGG 59.892 55.000 0.00 0.00 42.03 5.14
1868 2606 2.076863 GATGTTTCAGTTCACCCTCGG 58.923 52.381 0.00 0.00 0.00 4.63
1869 2607 3.045601 AGATGTTTCAGTTCACCCTCG 57.954 47.619 0.00 0.00 0.00 4.63
1870 2608 5.552178 ACTAAGATGTTTCAGTTCACCCTC 58.448 41.667 0.00 0.00 0.00 4.30
1871 2609 5.568620 ACTAAGATGTTTCAGTTCACCCT 57.431 39.130 0.00 0.00 0.00 4.34
1872 2610 5.351740 GCTACTAAGATGTTTCAGTTCACCC 59.648 44.000 0.00 0.00 0.00 4.61
1873 2611 5.351740 GGCTACTAAGATGTTTCAGTTCACC 59.648 44.000 0.00 0.00 0.00 4.02
1874 2612 5.351740 GGGCTACTAAGATGTTTCAGTTCAC 59.648 44.000 0.00 0.00 0.00 3.18
1875 2613 5.488341 GGGCTACTAAGATGTTTCAGTTCA 58.512 41.667 0.00 0.00 0.00 3.18
1876 2614 4.567159 CGGGCTACTAAGATGTTTCAGTTC 59.433 45.833 0.00 0.00 0.00 3.01
1877 2615 4.222145 TCGGGCTACTAAGATGTTTCAGTT 59.778 41.667 0.00 0.00 0.00 3.16
1878 2616 3.767673 TCGGGCTACTAAGATGTTTCAGT 59.232 43.478 0.00 0.00 0.00 3.41
1879 2617 4.363999 CTCGGGCTACTAAGATGTTTCAG 58.636 47.826 0.00 0.00 0.00 3.02
1880 2618 3.132289 CCTCGGGCTACTAAGATGTTTCA 59.868 47.826 0.00 0.00 0.00 2.69
1881 2619 3.383825 TCCTCGGGCTACTAAGATGTTTC 59.616 47.826 0.00 0.00 0.00 2.78
1882 2620 3.371965 TCCTCGGGCTACTAAGATGTTT 58.628 45.455 0.00 0.00 0.00 2.83
1883 2621 3.028094 TCCTCGGGCTACTAAGATGTT 57.972 47.619 0.00 0.00 0.00 2.71
1884 2622 2.750141 TCCTCGGGCTACTAAGATGT 57.250 50.000 0.00 0.00 0.00 3.06
1885 2623 4.099573 TCTTTTCCTCGGGCTACTAAGATG 59.900 45.833 0.00 0.00 0.00 2.90
1886 2624 4.287552 TCTTTTCCTCGGGCTACTAAGAT 58.712 43.478 0.00 0.00 0.00 2.40
1887 2625 3.700038 CTCTTTTCCTCGGGCTACTAAGA 59.300 47.826 0.00 0.00 0.00 2.10
1888 2626 3.700038 TCTCTTTTCCTCGGGCTACTAAG 59.300 47.826 0.00 0.00 0.00 2.18
1889 2627 3.700038 CTCTCTTTTCCTCGGGCTACTAA 59.300 47.826 0.00 0.00 0.00 2.24
1890 2628 3.288964 CTCTCTTTTCCTCGGGCTACTA 58.711 50.000 0.00 0.00 0.00 1.82
1891 2629 2.104170 CTCTCTTTTCCTCGGGCTACT 58.896 52.381 0.00 0.00 0.00 2.57
1892 2630 1.471851 GCTCTCTTTTCCTCGGGCTAC 60.472 57.143 0.00 0.00 0.00 3.58
1893 2631 0.824759 GCTCTCTTTTCCTCGGGCTA 59.175 55.000 0.00 0.00 0.00 3.93
1894 2632 1.194781 TGCTCTCTTTTCCTCGGGCT 61.195 55.000 0.00 0.00 0.00 5.19
1895 2633 0.321653 TTGCTCTCTTTTCCTCGGGC 60.322 55.000 0.00 0.00 0.00 6.13
1896 2634 1.731720 CTTGCTCTCTTTTCCTCGGG 58.268 55.000 0.00 0.00 0.00 5.14
1897 2635 1.082690 GCTTGCTCTCTTTTCCTCGG 58.917 55.000 0.00 0.00 0.00 4.63
1898 2636 0.718343 CGCTTGCTCTCTTTTCCTCG 59.282 55.000 0.00 0.00 0.00 4.63
1899 2637 1.082690 CCGCTTGCTCTCTTTTCCTC 58.917 55.000 0.00 0.00 0.00 3.71
1900 2638 0.398318 ACCGCTTGCTCTCTTTTCCT 59.602 50.000 0.00 0.00 0.00 3.36
1901 2639 1.197949 GAACCGCTTGCTCTCTTTTCC 59.802 52.381 0.00 0.00 0.00 3.13
1902 2640 1.197949 GGAACCGCTTGCTCTCTTTTC 59.802 52.381 0.00 0.00 0.00 2.29
1903 2641 1.239347 GGAACCGCTTGCTCTCTTTT 58.761 50.000 0.00 0.00 0.00 2.27
1904 2642 0.606673 GGGAACCGCTTGCTCTCTTT 60.607 55.000 0.00 0.00 40.86 2.52
1905 2643 1.003233 GGGAACCGCTTGCTCTCTT 60.003 57.895 0.00 0.00 40.86 2.85
1906 2644 2.665603 GGGAACCGCTTGCTCTCT 59.334 61.111 0.00 0.00 40.86 3.10
1923 2661 2.908088 TTTCGCTCGCCGCTACTACG 62.908 60.000 0.00 0.00 36.73 3.51
1924 2662 0.594284 ATTTCGCTCGCCGCTACTAC 60.594 55.000 0.00 0.00 36.73 2.73
1925 2663 0.594028 CATTTCGCTCGCCGCTACTA 60.594 55.000 0.00 0.00 36.73 1.82
1926 2664 1.878522 CATTTCGCTCGCCGCTACT 60.879 57.895 0.00 0.00 36.73 2.57
1927 2665 2.621000 CATTTCGCTCGCCGCTAC 59.379 61.111 0.00 0.00 36.73 3.58
1928 2666 2.584970 CCATTTCGCTCGCCGCTA 60.585 61.111 0.00 0.00 36.73 4.26
1932 2670 2.306255 TAGACCCCATTTCGCTCGCC 62.306 60.000 0.00 0.00 0.00 5.54
1933 2671 0.461339 TTAGACCCCATTTCGCTCGC 60.461 55.000 0.00 0.00 0.00 5.03
1934 2672 1.664151 GTTTAGACCCCATTTCGCTCG 59.336 52.381 0.00 0.00 0.00 5.03
1935 2673 2.014857 GGTTTAGACCCCATTTCGCTC 58.985 52.381 0.00 0.00 40.25 5.03
1936 2674 1.677820 CGGTTTAGACCCCATTTCGCT 60.678 52.381 0.00 0.00 43.42 4.93
1937 2675 0.730840 CGGTTTAGACCCCATTTCGC 59.269 55.000 0.00 0.00 43.42 4.70
1938 2676 1.735571 CACGGTTTAGACCCCATTTCG 59.264 52.381 0.00 0.00 43.42 3.46
1939 2677 3.062122 TCACGGTTTAGACCCCATTTC 57.938 47.619 0.00 0.00 43.42 2.17
1940 2678 3.512219 TTCACGGTTTAGACCCCATTT 57.488 42.857 0.00 0.00 43.42 2.32
1941 2679 3.512219 TTTCACGGTTTAGACCCCATT 57.488 42.857 0.00 0.00 43.42 3.16
1942 2680 3.512219 TTTTCACGGTTTAGACCCCAT 57.488 42.857 0.00 0.00 43.42 4.00
1943 2681 3.150767 CATTTTCACGGTTTAGACCCCA 58.849 45.455 0.00 0.00 43.42 4.96
1944 2682 2.490509 CCATTTTCACGGTTTAGACCCC 59.509 50.000 0.00 0.00 43.42 4.95
1945 2683 2.490509 CCCATTTTCACGGTTTAGACCC 59.509 50.000 0.00 0.00 43.42 4.46
1946 2684 2.490509 CCCCATTTTCACGGTTTAGACC 59.509 50.000 0.00 0.00 42.87 3.85
1947 2685 3.151554 ACCCCATTTTCACGGTTTAGAC 58.848 45.455 0.00 0.00 0.00 2.59
1948 2686 3.512219 ACCCCATTTTCACGGTTTAGA 57.488 42.857 0.00 0.00 0.00 2.10
1949 2687 3.319689 ACAACCCCATTTTCACGGTTTAG 59.680 43.478 0.00 0.00 36.45 1.85
1950 2688 3.068307 CACAACCCCATTTTCACGGTTTA 59.932 43.478 0.00 0.00 36.45 2.01
1951 2689 2.112190 ACAACCCCATTTTCACGGTTT 58.888 42.857 0.00 0.00 36.45 3.27
1952 2690 1.410882 CACAACCCCATTTTCACGGTT 59.589 47.619 0.00 0.00 39.18 4.44
1953 2691 1.036707 CACAACCCCATTTTCACGGT 58.963 50.000 0.00 0.00 0.00 4.83
1954 2692 0.316841 CCACAACCCCATTTTCACGG 59.683 55.000 0.00 0.00 0.00 4.94
1955 2693 1.323412 TCCACAACCCCATTTTCACG 58.677 50.000 0.00 0.00 0.00 4.35
1956 2694 2.962421 TCTTCCACAACCCCATTTTCAC 59.038 45.455 0.00 0.00 0.00 3.18
1957 2695 3.230134 CTCTTCCACAACCCCATTTTCA 58.770 45.455 0.00 0.00 0.00 2.69
1958 2696 2.029020 GCTCTTCCACAACCCCATTTTC 60.029 50.000 0.00 0.00 0.00 2.29
1959 2697 1.970640 GCTCTTCCACAACCCCATTTT 59.029 47.619 0.00 0.00 0.00 1.82
1960 2698 1.133199 TGCTCTTCCACAACCCCATTT 60.133 47.619 0.00 0.00 0.00 2.32
1961 2699 0.482446 TGCTCTTCCACAACCCCATT 59.518 50.000 0.00 0.00 0.00 3.16
1962 2700 0.482446 TTGCTCTTCCACAACCCCAT 59.518 50.000 0.00 0.00 0.00 4.00
1963 2701 0.482446 ATTGCTCTTCCACAACCCCA 59.518 50.000 0.00 0.00 0.00 4.96
1964 2702 2.092323 GTATTGCTCTTCCACAACCCC 58.908 52.381 0.00 0.00 0.00 4.95
1965 2703 2.790433 TGTATTGCTCTTCCACAACCC 58.210 47.619 0.00 0.00 0.00 4.11
1966 2704 3.821033 ACTTGTATTGCTCTTCCACAACC 59.179 43.478 0.00 0.00 0.00 3.77
1967 2705 4.275936 ACACTTGTATTGCTCTTCCACAAC 59.724 41.667 0.00 0.00 0.00 3.32
1968 2706 4.460263 ACACTTGTATTGCTCTTCCACAA 58.540 39.130 0.00 0.00 0.00 3.33
1969 2707 4.085357 ACACTTGTATTGCTCTTCCACA 57.915 40.909 0.00 0.00 0.00 4.17
1970 2708 4.275936 ACAACACTTGTATTGCTCTTCCAC 59.724 41.667 0.00 0.00 43.27 4.02
1971 2709 4.275689 CACAACACTTGTATTGCTCTTCCA 59.724 41.667 0.00 0.00 43.23 3.53
1972 2710 4.787598 CACAACACTTGTATTGCTCTTCC 58.212 43.478 0.00 0.00 43.23 3.46
1973 2711 4.023707 AGCACAACACTTGTATTGCTCTTC 60.024 41.667 10.48 0.00 43.23 2.87
1974 2712 3.885297 AGCACAACACTTGTATTGCTCTT 59.115 39.130 10.48 0.00 43.23 2.85
1975 2713 3.251729 CAGCACAACACTTGTATTGCTCT 59.748 43.478 12.55 0.00 43.23 4.09
1976 2714 3.558505 CAGCACAACACTTGTATTGCTC 58.441 45.455 12.55 0.00 43.23 4.26
1977 2715 2.287788 GCAGCACAACACTTGTATTGCT 60.288 45.455 10.48 10.48 43.23 3.91
1978 2716 2.053627 GCAGCACAACACTTGTATTGC 58.946 47.619 6.92 6.92 43.23 3.56
1979 2717 3.631145 AGCAGCACAACACTTGTATTG 57.369 42.857 0.00 0.00 43.23 1.90
1980 2718 3.753272 CCTAGCAGCACAACACTTGTATT 59.247 43.478 0.00 0.00 43.23 1.89
1981 2719 3.338249 CCTAGCAGCACAACACTTGTAT 58.662 45.455 0.00 0.00 43.23 2.29
1982 2720 2.766313 CCTAGCAGCACAACACTTGTA 58.234 47.619 0.00 0.00 43.23 2.41
1983 2721 1.597742 CCTAGCAGCACAACACTTGT 58.402 50.000 0.00 0.00 46.75 3.16
1984 2722 0.239347 GCCTAGCAGCACAACACTTG 59.761 55.000 0.00 0.00 0.00 3.16
1985 2723 1.230635 CGCCTAGCAGCACAACACTT 61.231 55.000 0.00 0.00 0.00 3.16
1986 2724 1.669115 CGCCTAGCAGCACAACACT 60.669 57.895 0.00 0.00 0.00 3.55
1987 2725 1.227999 TTCGCCTAGCAGCACAACAC 61.228 55.000 0.00 0.00 0.00 3.32
1988 2726 0.950555 CTTCGCCTAGCAGCACAACA 60.951 55.000 0.00 0.00 0.00 3.33
1989 2727 1.790387 CTTCGCCTAGCAGCACAAC 59.210 57.895 0.00 0.00 0.00 3.32
1990 2728 2.034879 GCTTCGCCTAGCAGCACAA 61.035 57.895 0.00 0.00 40.89 3.33
1991 2729 2.434884 GCTTCGCCTAGCAGCACA 60.435 61.111 0.00 0.00 40.89 4.57
1992 2730 2.434884 TGCTTCGCCTAGCAGCAC 60.435 61.111 3.44 0.00 45.72 4.40
1997 2735 3.971032 ACATAATTTGCTTCGCCTAGC 57.029 42.857 0.00 0.00 41.59 3.42
1998 2736 5.853282 GCAATACATAATTTGCTTCGCCTAG 59.147 40.000 0.64 0.00 0.00 3.02
1999 2737 5.298026 TGCAATACATAATTTGCTTCGCCTA 59.702 36.000 8.84 0.00 0.00 3.93
2000 2738 4.097741 TGCAATACATAATTTGCTTCGCCT 59.902 37.500 8.84 0.00 0.00 5.52
2001 2739 4.358851 TGCAATACATAATTTGCTTCGCC 58.641 39.130 8.84 0.00 0.00 5.54
2002 2740 5.947503 TTGCAATACATAATTTGCTTCGC 57.052 34.783 0.00 0.00 0.00 4.70
2029 2767 7.983484 ACAAGCAATTTCAACAGAGAAGAAAAT 59.017 29.630 0.00 0.00 35.20 1.82
2032 2770 6.455360 ACAAGCAATTTCAACAGAGAAGAA 57.545 33.333 0.00 0.00 0.00 2.52
2037 2775 6.203530 TGTCTCTACAAGCAATTTCAACAGAG 59.796 38.462 0.00 0.00 30.91 3.35
2054 2792 6.322712 ACCAGGATAGAAACTCATGTCTCTAC 59.677 42.308 0.00 0.00 0.00 2.59
2056 2794 5.276440 ACCAGGATAGAAACTCATGTCTCT 58.724 41.667 0.00 0.00 0.00 3.10
2095 2833 9.996554 TTAGAGATCAAAACAATACAGAGAACA 57.003 29.630 0.00 0.00 0.00 3.18
2122 2860 9.877178 ACGATTGAAAGAGAACTAATGAACTAT 57.123 29.630 0.00 0.00 0.00 2.12
2123 2861 9.140286 CACGATTGAAAGAGAACTAATGAACTA 57.860 33.333 0.00 0.00 0.00 2.24
2177 2919 2.093235 AGAGGAGCAGTGATTAACCAGC 60.093 50.000 0.00 0.00 0.00 4.85
2180 2922 4.762251 ACAAAAGAGGAGCAGTGATTAACC 59.238 41.667 0.00 0.00 0.00 2.85
2241 2983 8.300286 GCATATGATAGCTACTTTCACTACAGA 58.700 37.037 6.97 0.00 0.00 3.41
2247 2989 7.151308 AGAGTGCATATGATAGCTACTTTCAC 58.849 38.462 6.97 0.40 0.00 3.18
2252 2994 6.266330 TCACAAGAGTGCATATGATAGCTACT 59.734 38.462 6.97 0.31 45.49 2.57
2255 2997 5.163374 TGTCACAAGAGTGCATATGATAGCT 60.163 40.000 6.97 0.00 45.49 3.32
2312 3054 4.080299 AGGAAATAAGGAACTACTGGGCTG 60.080 45.833 0.00 0.00 38.49 4.85
2320 3062 7.630242 CTGCAATTCAGGAAATAAGGAACTA 57.370 36.000 0.00 0.00 37.02 2.24
2389 3131 1.838345 CACGTCAGTTACTCGCATACG 59.162 52.381 0.00 0.00 42.01 3.06
2406 3148 2.146342 ACATCCTCAAGAACAAGCACG 58.854 47.619 0.00 0.00 0.00 5.34
2439 3181 1.068264 TCTGTCTCTTGTGTGCTAGCG 60.068 52.381 10.77 0.00 0.00 4.26
2440 3182 2.029470 AGTCTGTCTCTTGTGTGCTAGC 60.029 50.000 8.10 8.10 0.00 3.42
2447 3189 5.698089 TGCAAGATAAAGTCTGTCTCTTGTG 59.302 40.000 15.87 0.00 42.92 3.33
2451 3193 5.991933 TCTGCAAGATAAAGTCTGTCTCT 57.008 39.130 0.00 0.00 38.67 3.10


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

AutoCloner maintained by Alex Coulton.