Multiple sequence alignment - TraesCS5D01G369800

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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 TraesCS5D01G369800 chr5D 100.000 2751 0 0 1 2751 445057259 445054509 0.000000e+00 5081.0
1 TraesCS5D01G369800 chr5D 91.200 625 35 7 1078 1690 444976576 444975960 0.000000e+00 832.0
2 TraesCS5D01G369800 chr5D 85.222 609 33 27 1111 1678 445062936 445062344 8.550000e-160 573.0
3 TraesCS5D01G369800 chr5D 85.127 511 47 19 1094 1594 445072948 445072457 1.900000e-136 496.0
4 TraesCS5D01G369800 chr5D 88.177 406 24 11 597 982 444977393 444976992 1.930000e-126 462.0
5 TraesCS5D01G369800 chr5D 91.318 311 14 6 2172 2473 444975931 444975625 1.970000e-111 412.0
6 TraesCS5D01G369800 chr5D 84.815 270 34 6 2465 2732 214927741 214927477 5.840000e-67 265.0
7 TraesCS5D01G369800 chr5D 79.587 436 26 32 163 562 444977798 444977390 1.260000e-63 254.0
8 TraesCS5D01G369800 chr5D 80.980 347 39 15 2087 2415 445061632 445061295 1.640000e-62 250.0
9 TraesCS5D01G369800 chr5D 91.061 179 7 6 1 174 444978439 444978265 1.650000e-57 233.0
10 TraesCS5D01G369800 chr5B 89.427 1135 55 17 597 1707 542296256 542295163 0.000000e+00 1371.0
11 TraesCS5D01G369800 chr5B 82.897 649 46 39 997 1593 542320326 542319691 8.730000e-145 523.0
12 TraesCS5D01G369800 chr5B 83.629 507 53 23 1094 1594 542331437 542330955 1.500000e-122 449.0
13 TraesCS5D01G369800 chr5B 82.780 482 39 21 1992 2461 542295056 542294607 9.240000e-105 390.0
14 TraesCS5D01G369800 chr5B 91.186 295 10 5 286 576 542296525 542296243 1.190000e-103 387.0
15 TraesCS5D01G369800 chr5B 82.918 281 26 10 2087 2352 542319011 542318738 1.650000e-57 233.0
16 TraesCS5D01G369800 chr5B 90.449 178 5 6 1 171 542296716 542296544 9.910000e-55 224.0
17 TraesCS5D01G369800 chr5A 89.041 803 55 8 930 1705 562101221 562100425 0.000000e+00 965.0
18 TraesCS5D01G369800 chr5A 88.462 468 27 10 1223 1677 562108462 562108009 8.670000e-150 540.0
19 TraesCS5D01G369800 chr5A 85.271 516 49 19 1094 1594 562116978 562116475 8.790000e-140 507.0
20 TraesCS5D01G369800 chr5A 84.940 498 55 14 2248 2730 562099723 562099231 1.150000e-133 486.0
21 TraesCS5D01G369800 chr5A 89.855 345 13 11 1930 2252 562100328 562099984 9.110000e-115 424.0
22 TraesCS5D01G369800 chr5A 92.150 293 18 5 286 576 562102564 562102275 2.550000e-110 409.0
23 TraesCS5D01G369800 chr5A 82.867 286 23 12 2087 2352 562107771 562107492 1.650000e-57 233.0
24 TraesCS5D01G369800 chr5A 89.840 187 10 3 595 781 562102290 562102113 5.920000e-57 231.0
25 TraesCS5D01G369800 chr5A 90.058 171 9 4 116 283 562102764 562102599 5.970000e-52 215.0
26 TraesCS5D01G369800 chr5A 92.742 124 7 2 1 123 562103194 562103072 7.830000e-41 178.0
27 TraesCS5D01G369800 chr5A 88.028 142 10 2 780 914 562101466 562101325 7.880000e-36 161.0
28 TraesCS5D01G369800 chr7B 87.037 270 26 7 2465 2732 244757958 244757696 2.070000e-76 296.0
29 TraesCS5D01G369800 chr7B 93.578 109 6 1 1824 1932 750444695 750444588 7.880000e-36 161.0
30 TraesCS5D01G369800 chr7B 89.431 123 12 1 1265 1386 245211853 245211731 1.320000e-33 154.0
31 TraesCS5D01G369800 chr1D 87.023 262 29 4 2471 2730 332066728 332066470 9.640000e-75 291.0
32 TraesCS5D01G369800 chr7A 85.768 267 34 3 2465 2730 19029285 19029022 2.090000e-71 279.0
33 TraesCS5D01G369800 chr7D 85.609 271 32 6 2465 2732 129846733 129846467 7.500000e-71 278.0
34 TraesCS5D01G369800 chr7D 89.431 123 12 1 1265 1386 265004825 265004703 1.320000e-33 154.0
35 TraesCS5D01G369800 chr4A 85.448 268 34 4 2465 2730 728730604 728730868 9.710000e-70 274.0
36 TraesCS5D01G369800 chr1A 84.838 277 35 5 2471 2744 442451410 442451138 3.490000e-69 272.0
37 TraesCS5D01G369800 chr1A 96.000 100 4 0 1830 1929 275355267 275355366 2.190000e-36 163.0
38 TraesCS5D01G369800 chr2D 84.758 269 34 5 2465 2730 172172440 172172176 2.100000e-66 263.0
39 TraesCS5D01G369800 chr2D 90.598 117 10 1 1818 1933 542514793 542514677 1.320000e-33 154.0
40 TraesCS5D01G369800 chr4B 95.146 103 5 0 1830 1932 83187304 83187202 2.190000e-36 163.0
41 TraesCS5D01G369800 chr4B 93.243 74 5 0 1720 1793 137739799 137739726 2.900000e-20 110.0
42 TraesCS5D01G369800 chr3D 93.578 109 7 0 1824 1932 454365994 454365886 2.190000e-36 163.0
43 TraesCS5D01G369800 chr1B 95.146 103 5 0 1830 1932 115915958 115915856 2.190000e-36 163.0
44 TraesCS5D01G369800 chr1B 94.340 106 6 0 1828 1933 224373774 224373879 2.190000e-36 163.0
45 TraesCS5D01G369800 chr6B 94.340 106 5 1 1824 1929 613688890 613688994 7.880000e-36 161.0
46 TraesCS5D01G369800 chr6B 90.769 65 6 0 1731 1795 106518172 106518108 1.360000e-13 87.9
47 TraesCS5D01G369800 chr2B 93.519 108 7 0 1822 1929 213374510 213374617 7.880000e-36 161.0
48 TraesCS5D01G369800 chr6D 94.444 72 4 0 1720 1791 408686914 408686985 8.050000e-21 111.0
49 TraesCS5D01G369800 chr3B 89.041 73 8 0 1720 1792 776994541 776994613 1.050000e-14 91.6


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 TraesCS5D01G369800 chr5D 445054509 445057259 2750 True 5081.000 5081 100.00000 1 2751 1 chr5D.!!$R2 2750
1 TraesCS5D01G369800 chr5D 444975625 444978439 2814 True 438.600 832 88.26860 1 2473 5 chr5D.!!$R4 2472
2 TraesCS5D01G369800 chr5D 445061295 445062936 1641 True 411.500 573 83.10100 1111 2415 2 chr5D.!!$R5 1304
3 TraesCS5D01G369800 chr5B 542294607 542296716 2109 True 593.000 1371 88.46050 1 2461 4 chr5B.!!$R2 2460
4 TraesCS5D01G369800 chr5B 542318738 542320326 1588 True 378.000 523 82.90750 997 2352 2 chr5B.!!$R3 1355
5 TraesCS5D01G369800 chr5A 562116475 562116978 503 True 507.000 507 85.27100 1094 1594 1 chr5A.!!$R1 500
6 TraesCS5D01G369800 chr5A 562107492 562108462 970 True 386.500 540 85.66450 1223 2352 2 chr5A.!!$R3 1129
7 TraesCS5D01G369800 chr5A 562099231 562103194 3963 True 383.625 965 89.58175 1 2730 8 chr5A.!!$R2 2729

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
673 1531 1.122849 ACGTACGTACACACTTTGCG 58.877 50.0 21.41 10.29 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1767 3847 0.036732 TGCCAAATGAAGACCGAGCT 59.963 50.0 0.0 0.0 0.0 4.09 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
27 28 5.422145 TCGGCCTAACTAACTAATTTGTCC 58.578 41.667 0.00 0.00 0.00 4.02
193 995 4.443034 GGGAGGATCACGTTAGTTAGCATT 60.443 45.833 0.00 0.00 36.25 3.56
226 1028 2.641559 GAGCAGTGCAAGTGTGGC 59.358 61.111 19.20 0.00 40.18 5.01
284 1087 6.369615 CGATGCATGTGATTGAGGATACAATA 59.630 38.462 2.46 0.00 40.03 1.90
348 1182 5.463392 ACATCCGAGATATGTGAAAATGACG 59.537 40.000 0.00 0.00 36.24 4.35
349 1183 5.006153 TCCGAGATATGTGAAAATGACGT 57.994 39.130 0.00 0.00 0.00 4.34
398 1240 3.171388 GGCCGGGTCCCTGATGAT 61.171 66.667 6.29 0.00 0.00 2.45
511 1365 3.435186 GCCAGCCGCAGTTTCTCC 61.435 66.667 0.00 0.00 37.47 3.71
572 1426 1.401761 AAGTGTGCATGCACCTTTGA 58.598 45.000 40.01 23.51 45.63 2.69
573 1427 1.624336 AGTGTGCATGCACCTTTGAT 58.376 45.000 40.01 20.68 45.63 2.57
574 1428 1.542915 AGTGTGCATGCACCTTTGATC 59.457 47.619 40.01 22.98 45.63 2.92
575 1429 1.542915 GTGTGCATGCACCTTTGATCT 59.457 47.619 40.01 0.00 45.63 2.75
576 1430 2.029649 GTGTGCATGCACCTTTGATCTT 60.030 45.455 40.01 0.00 45.63 2.40
577 1431 2.629137 TGTGCATGCACCTTTGATCTTT 59.371 40.909 40.01 0.00 45.63 2.52
578 1432 3.069872 TGTGCATGCACCTTTGATCTTTT 59.930 39.130 40.01 0.00 45.63 2.27
579 1433 3.430895 GTGCATGCACCTTTGATCTTTTG 59.569 43.478 35.69 0.00 40.79 2.44
580 1434 3.069872 TGCATGCACCTTTGATCTTTTGT 59.930 39.130 18.46 0.00 0.00 2.83
581 1435 4.060205 GCATGCACCTTTGATCTTTTGTT 58.940 39.130 14.21 0.00 0.00 2.83
582 1436 4.084223 GCATGCACCTTTGATCTTTTGTTG 60.084 41.667 14.21 0.00 0.00 3.33
583 1437 4.734398 TGCACCTTTGATCTTTTGTTGT 57.266 36.364 0.00 0.00 0.00 3.32
584 1438 5.083533 TGCACCTTTGATCTTTTGTTGTT 57.916 34.783 0.00 0.00 0.00 2.83
585 1439 4.869297 TGCACCTTTGATCTTTTGTTGTTG 59.131 37.500 0.00 0.00 0.00 3.33
586 1440 4.869861 GCACCTTTGATCTTTTGTTGTTGT 59.130 37.500 0.00 0.00 0.00 3.32
587 1441 5.351189 GCACCTTTGATCTTTTGTTGTTGTT 59.649 36.000 0.00 0.00 0.00 2.83
588 1442 6.672836 GCACCTTTGATCTTTTGTTGTTGTTG 60.673 38.462 0.00 0.00 0.00 3.33
589 1443 5.351189 ACCTTTGATCTTTTGTTGTTGTTGC 59.649 36.000 0.00 0.00 0.00 4.17
590 1444 5.350914 CCTTTGATCTTTTGTTGTTGTTGCA 59.649 36.000 0.00 0.00 0.00 4.08
591 1445 6.128336 CCTTTGATCTTTTGTTGTTGTTGCAA 60.128 34.615 0.00 0.00 0.00 4.08
592 1446 6.981762 TTGATCTTTTGTTGTTGTTGCAAT 57.018 29.167 0.59 0.00 0.00 3.56
593 1447 6.981762 TGATCTTTTGTTGTTGTTGCAATT 57.018 29.167 0.59 0.00 0.00 2.32
594 1448 7.002816 TGATCTTTTGTTGTTGTTGCAATTC 57.997 32.000 0.59 0.00 0.00 2.17
595 1449 6.592994 TGATCTTTTGTTGTTGTTGCAATTCA 59.407 30.769 0.59 0.00 0.00 2.57
596 1450 6.981762 TCTTTTGTTGTTGTTGCAATTCAT 57.018 29.167 0.59 0.00 0.00 2.57
597 1451 6.773080 TCTTTTGTTGTTGTTGCAATTCATG 58.227 32.000 0.59 0.00 0.00 3.07
612 1466 5.475719 CAATTCATGCACCTTTGATCTGTT 58.524 37.500 0.00 0.00 0.00 3.16
641 1495 2.884827 TCATTCATGACTCAGACGCAG 58.115 47.619 0.00 0.00 0.00 5.18
642 1496 3.118847 ATCATTCATGACTCAGACGCAGT 60.119 43.478 0.00 0.00 42.13 4.40
643 1497 4.098501 ATCATTCATGACTCAGACGCAGTA 59.901 41.667 0.00 0.00 39.98 2.74
644 1498 5.962533 ATCATTCATGACTCAGACGCAGTAC 60.963 44.000 0.00 0.00 39.98 2.73
673 1531 1.122849 ACGTACGTACACACTTTGCG 58.877 50.000 21.41 10.29 0.00 4.85
821 2328 2.733026 CCGCTTTTCTTTTTCATGGCAG 59.267 45.455 0.00 0.00 0.00 4.85
970 2574 2.041976 ACGCTGCACTGTACAGAGT 58.958 52.632 29.30 11.56 42.35 3.24
1014 2644 6.099269 TCACTTCTCCTGTTTATATACCACCC 59.901 42.308 0.00 0.00 0.00 4.61
1016 2646 4.549668 TCTCCTGTTTATATACCACCCGT 58.450 43.478 0.00 0.00 0.00 5.28
1089 3031 1.000843 CTTCCTGATCCACACACACGA 59.999 52.381 0.00 0.00 0.00 4.35
1304 3285 0.394565 ACCGCAAGTTCTTCAGCTCT 59.605 50.000 0.00 0.00 0.00 4.09
1393 3374 4.785453 CTCCCCAGCCTTCGCCAC 62.785 72.222 0.00 0.00 34.57 5.01
1512 3526 3.945434 CGATGGCGCCACTGATGC 61.945 66.667 35.50 15.62 0.00 3.91
1605 3642 3.840890 AGCTCTGAGACGAACTAGTTG 57.159 47.619 14.14 8.09 0.00 3.16
1606 3643 3.413327 AGCTCTGAGACGAACTAGTTGA 58.587 45.455 14.14 1.02 0.00 3.18
1607 3644 3.438781 AGCTCTGAGACGAACTAGTTGAG 59.561 47.826 14.14 12.09 0.00 3.02
1608 3645 3.753842 CTCTGAGACGAACTAGTTGAGC 58.246 50.000 14.14 1.46 0.00 4.26
1609 3646 2.159824 TCTGAGACGAACTAGTTGAGCG 59.840 50.000 14.14 12.98 0.00 5.03
1613 3650 1.467734 GACGAACTAGTTGAGCGGAGA 59.532 52.381 14.14 0.00 0.00 3.71
1716 3796 9.472361 GTACTGATGCTTAATTATTCGGTAGAA 57.528 33.333 6.95 0.00 41.13 2.10
1721 3801 7.618502 TGCTTAATTATTCGGTAGAAGCAAA 57.381 32.000 7.76 0.00 43.38 3.68
1722 3802 8.220755 TGCTTAATTATTCGGTAGAAGCAAAT 57.779 30.769 7.76 0.00 43.38 2.32
1723 3803 8.682710 TGCTTAATTATTCGGTAGAAGCAAATT 58.317 29.630 7.76 0.00 43.38 1.82
1724 3804 8.958043 GCTTAATTATTCGGTAGAAGCAAATTG 58.042 33.333 3.79 0.00 40.09 2.32
1728 3808 9.921637 AATTATTCGGTAGAAGCAAATTGAAAA 57.078 25.926 0.00 0.00 40.09 2.29
1729 3809 8.964420 TTATTCGGTAGAAGCAAATTGAAAAG 57.036 30.769 0.00 0.00 40.09 2.27
1730 3810 6.385649 TTCGGTAGAAGCAAATTGAAAAGT 57.614 33.333 0.00 0.00 31.76 2.66
1731 3811 6.385649 TCGGTAGAAGCAAATTGAAAAGTT 57.614 33.333 0.00 0.00 32.39 2.66
1733 3813 6.695278 TCGGTAGAAGCAAATTGAAAAGTTTG 59.305 34.615 0.00 0.00 38.13 2.93
1767 3847 9.541884 AAGTTTTTAAATAAAGGCCTCCATAGA 57.458 29.630 5.23 0.00 0.00 1.98
1768 3848 9.190317 AGTTTTTAAATAAAGGCCTCCATAGAG 57.810 33.333 5.23 0.00 40.09 2.43
1769 3849 7.582667 TTTTAAATAAAGGCCTCCATAGAGC 57.417 36.000 5.23 0.00 38.96 4.09
1770 3850 6.515512 TTAAATAAAGGCCTCCATAGAGCT 57.484 37.500 5.23 0.00 38.96 4.09
1771 3851 4.632327 AATAAAGGCCTCCATAGAGCTC 57.368 45.455 5.23 5.27 38.96 4.09
1772 3852 0.755686 AAAGGCCTCCATAGAGCTCG 59.244 55.000 5.23 0.00 38.96 5.03
1773 3853 1.118356 AAGGCCTCCATAGAGCTCGG 61.118 60.000 5.23 3.72 38.96 4.63
1774 3854 1.834822 GGCCTCCATAGAGCTCGGT 60.835 63.158 8.37 0.00 38.96 4.69
1775 3855 1.663173 GCCTCCATAGAGCTCGGTC 59.337 63.158 8.37 0.00 38.96 4.79
1776 3856 0.825840 GCCTCCATAGAGCTCGGTCT 60.826 60.000 8.37 3.94 38.96 3.85
1777 3857 1.698506 CCTCCATAGAGCTCGGTCTT 58.301 55.000 8.37 0.00 38.96 3.01
1778 3858 1.611491 CCTCCATAGAGCTCGGTCTTC 59.389 57.143 8.37 0.00 38.96 2.87
1779 3859 2.302260 CTCCATAGAGCTCGGTCTTCA 58.698 52.381 8.37 0.00 32.13 3.02
1780 3860 2.890311 CTCCATAGAGCTCGGTCTTCAT 59.110 50.000 8.37 0.00 32.13 2.57
1781 3861 3.300388 TCCATAGAGCTCGGTCTTCATT 58.700 45.455 8.37 0.00 0.00 2.57
1782 3862 3.706594 TCCATAGAGCTCGGTCTTCATTT 59.293 43.478 8.37 0.00 0.00 2.32
1783 3863 3.806521 CCATAGAGCTCGGTCTTCATTTG 59.193 47.826 8.37 0.00 0.00 2.32
1784 3864 2.393271 AGAGCTCGGTCTTCATTTGG 57.607 50.000 8.37 0.00 0.00 3.28
1785 3865 0.729690 GAGCTCGGTCTTCATTTGGC 59.270 55.000 0.00 0.00 0.00 4.52
1786 3866 0.036732 AGCTCGGTCTTCATTTGGCA 59.963 50.000 0.00 0.00 0.00 4.92
1787 3867 1.098050 GCTCGGTCTTCATTTGGCAT 58.902 50.000 0.00 0.00 0.00 4.40
1788 3868 1.474077 GCTCGGTCTTCATTTGGCATT 59.526 47.619 0.00 0.00 0.00 3.56
1789 3869 2.094545 GCTCGGTCTTCATTTGGCATTT 60.095 45.455 0.00 0.00 0.00 2.32
1790 3870 3.614870 GCTCGGTCTTCATTTGGCATTTT 60.615 43.478 0.00 0.00 0.00 1.82
1791 3871 4.168760 CTCGGTCTTCATTTGGCATTTTC 58.831 43.478 0.00 0.00 0.00 2.29
1792 3872 2.916716 CGGTCTTCATTTGGCATTTTCG 59.083 45.455 0.00 0.00 0.00 3.46
1796 3876 1.695813 TCATTTGGCATTTTCGTGCG 58.304 45.000 0.00 0.00 45.97 5.34
1811 3891 1.002900 CGTGCGGTTGATTGTTTCAGT 60.003 47.619 0.00 0.00 35.27 3.41
1835 3916 9.924010 AGTTCACCATCTATATATACTACTCCC 57.076 37.037 0.00 0.00 0.00 4.30
1836 3917 9.924010 GTTCACCATCTATATATACTACTCCCT 57.076 37.037 0.00 0.00 0.00 4.20
1838 3919 8.725256 TCACCATCTATATATACTACTCCCTCC 58.275 40.741 0.00 0.00 0.00 4.30
1839 3920 7.662258 CACCATCTATATATACTACTCCCTCCG 59.338 44.444 0.00 0.00 0.00 4.63
1840 3921 7.350389 ACCATCTATATATACTACTCCCTCCGT 59.650 40.741 0.00 0.00 0.00 4.69
1841 3922 8.219178 CCATCTATATATACTACTCCCTCCGTT 58.781 40.741 0.00 0.00 0.00 4.44
1842 3923 9.275398 CATCTATATATACTACTCCCTCCGTTC 57.725 40.741 0.00 0.00 0.00 3.95
1843 3924 8.384693 TCTATATATACTACTCCCTCCGTTCA 57.615 38.462 0.00 0.00 0.00 3.18
1844 3925 8.263640 TCTATATATACTACTCCCTCCGTTCAC 58.736 40.741 0.00 0.00 0.00 3.18
1845 3926 3.666345 ATACTACTCCCTCCGTTCACT 57.334 47.619 0.00 0.00 0.00 3.41
1846 3927 2.305858 ACTACTCCCTCCGTTCACTT 57.694 50.000 0.00 0.00 0.00 3.16
1847 3928 2.606378 ACTACTCCCTCCGTTCACTTT 58.394 47.619 0.00 0.00 0.00 2.66
1848 3929 2.970640 ACTACTCCCTCCGTTCACTTTT 59.029 45.455 0.00 0.00 0.00 2.27
1849 3930 2.256117 ACTCCCTCCGTTCACTTTTG 57.744 50.000 0.00 0.00 0.00 2.44
1850 3931 1.489230 ACTCCCTCCGTTCACTTTTGT 59.511 47.619 0.00 0.00 0.00 2.83
1851 3932 2.701951 ACTCCCTCCGTTCACTTTTGTA 59.298 45.455 0.00 0.00 0.00 2.41
1852 3933 3.135167 ACTCCCTCCGTTCACTTTTGTAA 59.865 43.478 0.00 0.00 0.00 2.41
1853 3934 3.735591 TCCCTCCGTTCACTTTTGTAAG 58.264 45.455 0.00 0.00 37.40 2.34
1854 3935 3.135167 TCCCTCCGTTCACTTTTGTAAGT 59.865 43.478 0.00 0.00 45.40 2.24
1855 3936 3.497262 CCCTCCGTTCACTTTTGTAAGTC 59.503 47.826 0.00 0.00 42.67 3.01
1856 3937 4.124238 CCTCCGTTCACTTTTGTAAGTCA 58.876 43.478 0.00 0.00 42.67 3.41
1857 3938 4.755123 CCTCCGTTCACTTTTGTAAGTCAT 59.245 41.667 0.00 0.00 42.67 3.06
1858 3939 5.238650 CCTCCGTTCACTTTTGTAAGTCATT 59.761 40.000 0.00 0.00 42.67 2.57
1859 3940 6.238648 CCTCCGTTCACTTTTGTAAGTCATTT 60.239 38.462 0.00 0.00 42.67 2.32
1860 3941 6.721321 TCCGTTCACTTTTGTAAGTCATTTC 58.279 36.000 0.00 0.00 42.67 2.17
1861 3942 6.316640 TCCGTTCACTTTTGTAAGTCATTTCA 59.683 34.615 0.00 0.00 42.67 2.69
1862 3943 6.632834 CCGTTCACTTTTGTAAGTCATTTCAG 59.367 38.462 0.00 0.00 42.67 3.02
1863 3944 7.406553 CGTTCACTTTTGTAAGTCATTTCAGA 58.593 34.615 0.00 0.00 42.67 3.27
1864 3945 7.373441 CGTTCACTTTTGTAAGTCATTTCAGAC 59.627 37.037 0.00 0.00 42.67 3.51
1865 3946 7.857734 TCACTTTTGTAAGTCATTTCAGACA 57.142 32.000 0.00 0.00 42.67 3.41
1866 3947 7.919690 TCACTTTTGTAAGTCATTTCAGACAG 58.080 34.615 0.00 0.00 42.67 3.51
1867 3948 6.634436 CACTTTTGTAAGTCATTTCAGACAGC 59.366 38.462 0.00 0.00 42.67 4.40
1868 3949 6.543831 ACTTTTGTAAGTCATTTCAGACAGCT 59.456 34.615 0.00 0.00 40.60 4.24
1869 3950 6.942532 TTTGTAAGTCATTTCAGACAGCTT 57.057 33.333 0.00 0.00 40.98 3.74
1870 3951 8.445275 TTTTGTAAGTCATTTCAGACAGCTTA 57.555 30.769 0.00 0.00 40.98 3.09
1871 3952 8.445275 TTTGTAAGTCATTTCAGACAGCTTAA 57.555 30.769 0.00 0.00 40.98 1.85
1872 3953 8.445275 TTGTAAGTCATTTCAGACAGCTTAAA 57.555 30.769 0.00 0.00 40.98 1.52
1873 3954 8.445275 TGTAAGTCATTTCAGACAGCTTAAAA 57.555 30.769 0.00 0.00 40.98 1.52
1874 3955 9.066892 TGTAAGTCATTTCAGACAGCTTAAAAT 57.933 29.630 0.00 0.00 40.98 1.82
1875 3956 9.334693 GTAAGTCATTTCAGACAGCTTAAAATG 57.665 33.333 0.00 8.59 40.98 2.32
1876 3957 6.917533 AGTCATTTCAGACAGCTTAAAATGG 58.082 36.000 12.43 0.00 40.98 3.16
1877 3958 6.716628 AGTCATTTCAGACAGCTTAAAATGGA 59.283 34.615 12.43 0.00 40.98 3.41
1878 3959 6.803807 GTCATTTCAGACAGCTTAAAATGGAC 59.196 38.462 12.43 0.00 37.71 4.02
1879 3960 6.716628 TCATTTCAGACAGCTTAAAATGGACT 59.283 34.615 12.43 0.00 37.71 3.85
1880 3961 5.947228 TTCAGACAGCTTAAAATGGACTG 57.053 39.130 0.00 0.00 0.00 3.51
1881 3962 4.973168 TCAGACAGCTTAAAATGGACTGT 58.027 39.130 0.00 0.00 43.93 3.55
1882 3963 5.376625 TCAGACAGCTTAAAATGGACTGTT 58.623 37.500 0.00 0.00 41.45 3.16
1883 3964 5.827797 TCAGACAGCTTAAAATGGACTGTTT 59.172 36.000 0.00 0.00 41.45 2.83
1884 3965 6.321181 TCAGACAGCTTAAAATGGACTGTTTT 59.679 34.615 0.00 0.00 41.45 2.43
1885 3966 6.418819 CAGACAGCTTAAAATGGACTGTTTTG 59.581 38.462 0.00 0.00 41.45 2.44
1886 3967 5.049828 ACAGCTTAAAATGGACTGTTTTGC 58.950 37.500 0.00 0.00 38.38 3.68
1887 3968 5.049167 CAGCTTAAAATGGACTGTTTTGCA 58.951 37.500 0.00 0.00 31.71 4.08
1888 3969 5.049828 AGCTTAAAATGGACTGTTTTGCAC 58.950 37.500 0.00 0.00 31.71 4.57
1889 3970 4.808364 GCTTAAAATGGACTGTTTTGCACA 59.192 37.500 0.00 0.00 31.71 4.57
1890 3971 5.466393 GCTTAAAATGGACTGTTTTGCACAT 59.534 36.000 0.00 0.00 33.76 3.21
1891 3972 6.018016 GCTTAAAATGGACTGTTTTGCACATT 60.018 34.615 0.00 0.00 33.76 2.71
1892 3973 5.738118 AAAATGGACTGTTTTGCACATTG 57.262 34.783 0.00 0.00 33.76 2.82
1893 3974 4.405116 AATGGACTGTTTTGCACATTGT 57.595 36.364 0.00 0.00 33.76 2.71
1894 3975 3.435105 TGGACTGTTTTGCACATTGTC 57.565 42.857 0.00 0.00 33.76 3.18
1895 3976 3.023119 TGGACTGTTTTGCACATTGTCT 58.977 40.909 0.00 0.00 33.15 3.41
1896 3977 3.181488 TGGACTGTTTTGCACATTGTCTG 60.181 43.478 0.00 0.00 33.15 3.51
1897 3978 3.066621 GGACTGTTTTGCACATTGTCTGA 59.933 43.478 0.00 0.00 33.15 3.27
1898 3979 4.439974 GGACTGTTTTGCACATTGTCTGAA 60.440 41.667 0.00 0.00 33.15 3.02
1899 3980 5.070770 ACTGTTTTGCACATTGTCTGAAA 57.929 34.783 0.00 0.00 33.76 2.69
1900 3981 5.663456 ACTGTTTTGCACATTGTCTGAAAT 58.337 33.333 0.00 0.00 33.76 2.17
1901 3982 5.521010 ACTGTTTTGCACATTGTCTGAAATG 59.479 36.000 0.00 9.50 42.21 2.32
1903 3984 5.873712 TGTTTTGCACATTGTCTGAAATGTT 59.126 32.000 12.41 1.57 46.19 2.71
1904 3985 6.370994 TGTTTTGCACATTGTCTGAAATGTTT 59.629 30.769 12.41 0.00 46.19 2.83
1905 3986 6.981762 TTTGCACATTGTCTGAAATGTTTT 57.018 29.167 12.41 0.00 46.19 2.43
1906 3987 6.586868 TTGCACATTGTCTGAAATGTTTTC 57.413 33.333 12.41 0.00 46.19 2.29
1907 3988 5.658468 TGCACATTGTCTGAAATGTTTTCA 58.342 33.333 12.41 2.96 46.19 2.69
1908 3989 6.104665 TGCACATTGTCTGAAATGTTTTCAA 58.895 32.000 12.41 0.00 46.19 2.69
1909 3990 6.256104 TGCACATTGTCTGAAATGTTTTCAAG 59.744 34.615 12.41 0.45 46.19 3.02
1910 3991 6.292488 GCACATTGTCTGAAATGTTTTCAAGG 60.292 38.462 12.41 0.00 46.19 3.61
1911 3992 6.757947 CACATTGTCTGAAATGTTTTCAAGGT 59.242 34.615 12.41 0.00 46.19 3.50
1912 3993 6.980397 ACATTGTCTGAAATGTTTTCAAGGTC 59.020 34.615 10.41 0.00 46.19 3.85
1913 3994 6.773976 TTGTCTGAAATGTTTTCAAGGTCT 57.226 33.333 4.43 0.00 0.00 3.85
1914 3995 6.773976 TGTCTGAAATGTTTTCAAGGTCTT 57.226 33.333 4.43 0.00 0.00 3.01
1915 3996 7.873719 TGTCTGAAATGTTTTCAAGGTCTTA 57.126 32.000 4.43 0.00 0.00 2.10
1916 3997 8.463930 TGTCTGAAATGTTTTCAAGGTCTTAT 57.536 30.769 4.43 0.00 0.00 1.73
1917 3998 9.567776 TGTCTGAAATGTTTTCAAGGTCTTATA 57.432 29.630 4.43 0.00 0.00 0.98
1938 4019 9.289303 CTTATAAAAATGAACAGTGGATTTCCG 57.711 33.333 0.00 0.00 39.43 4.30
1974 4055 4.381932 CCCTTTGGAGTTTGGATTATGTGC 60.382 45.833 0.00 0.00 0.00 4.57
1990 4071 8.345565 GGATTATGTGCAACCTTAACTAGATTG 58.654 37.037 0.00 0.00 34.36 2.67
2214 4930 1.393487 TTGACGTGAGGTCCGGTTCA 61.393 55.000 0.00 1.25 45.46 3.18
2262 5243 1.715519 GCGTGCTAAGTTTTACGACGA 59.284 47.619 0.00 0.00 38.72 4.20
2272 5254 5.587033 AGTTTTACGACGACATTTTCTCC 57.413 39.130 0.00 0.00 0.00 3.71
2273 5255 5.051816 AGTTTTACGACGACATTTTCTCCA 58.948 37.500 0.00 0.00 0.00 3.86
2378 5372 2.896685 CTCCACAGATCAGATACCCCTC 59.103 54.545 0.00 0.00 0.00 4.30
2404 5398 0.677288 CGTCTAGTCACCCAACACCA 59.323 55.000 0.00 0.00 0.00 4.17
2405 5399 1.336887 CGTCTAGTCACCCAACACCAG 60.337 57.143 0.00 0.00 0.00 4.00
2441 5435 6.261826 ACTTGAGTGCCAGATTTATATGCTTC 59.738 38.462 0.00 0.00 0.00 3.86
2447 5442 6.148480 GTGCCAGATTTATATGCTTCGAGATT 59.852 38.462 0.00 0.00 0.00 2.40
2477 5473 8.258708 AGATACCGCTTTTTAGTGAAGAGTAAT 58.741 33.333 0.00 0.00 0.00 1.89
2505 5501 8.316640 ACACTAGTAATATACTACACGCTACC 57.683 38.462 0.00 0.00 40.14 3.18
2506 5502 7.389053 ACACTAGTAATATACTACACGCTACCC 59.611 40.741 0.00 0.00 40.14 3.69
2507 5503 7.605691 CACTAGTAATATACTACACGCTACCCT 59.394 40.741 0.00 0.00 40.14 4.34
2508 5504 8.816894 ACTAGTAATATACTACACGCTACCCTA 58.183 37.037 0.00 0.00 40.14 3.53
2532 5528 7.291411 AGCTATGTAACTACCTTCATAGTGG 57.709 40.000 11.05 0.00 40.70 4.00
2545 5541 8.562949 ACCTTCATAGTGGGTAGTAACATATT 57.437 34.615 0.00 0.00 0.00 1.28
2550 5546 7.713507 TCATAGTGGGTAGTAACATATTTGTGC 59.286 37.037 0.00 0.00 35.83 4.57
2566 5562 1.337703 TGTGCTGTCATGCAAAGGTTC 59.662 47.619 0.00 0.00 45.12 3.62
2570 5566 3.069872 TGCTGTCATGCAAAGGTTCATTT 59.930 39.130 0.00 0.00 40.29 2.32
2571 5567 4.280425 TGCTGTCATGCAAAGGTTCATTTA 59.720 37.500 0.00 0.00 40.29 1.40
2574 5570 6.183360 GCTGTCATGCAAAGGTTCATTTATTG 60.183 38.462 0.00 0.00 0.00 1.90
2598 5594 9.573166 TTGGGTTATAGAATCATATTGTCTTGG 57.427 33.333 0.00 0.00 0.00 3.61
2612 5608 9.506018 CATATTGTCTTGGGATATGTGATGTTA 57.494 33.333 0.00 0.00 31.99 2.41
2655 5651 8.380742 ACTCAATTTACCTCTCTCCTCATTAA 57.619 34.615 0.00 0.00 0.00 1.40
2663 5659 5.055812 CCTCTCTCCTCATTAACTCATTGC 58.944 45.833 0.00 0.00 0.00 3.56
2666 5662 4.517285 TCTCCTCATTAACTCATTGCCAC 58.483 43.478 0.00 0.00 0.00 5.01
2670 5666 6.604171 TCCTCATTAACTCATTGCCACATAT 58.396 36.000 0.00 0.00 0.00 1.78
2671 5667 7.062322 TCCTCATTAACTCATTGCCACATATT 58.938 34.615 0.00 0.00 0.00 1.28
2672 5668 7.560991 TCCTCATTAACTCATTGCCACATATTT 59.439 33.333 0.00 0.00 0.00 1.40
2673 5669 8.199449 CCTCATTAACTCATTGCCACATATTTT 58.801 33.333 0.00 0.00 0.00 1.82
2674 5670 9.590451 CTCATTAACTCATTGCCACATATTTTT 57.410 29.630 0.00 0.00 0.00 1.94
2695 5692 3.681593 TTTGCTGAATTGAACCCCATG 57.318 42.857 0.00 0.00 0.00 3.66
2701 5698 4.220602 GCTGAATTGAACCCCATGTTACTT 59.779 41.667 0.00 0.00 37.29 2.24
2714 5711 6.072119 CCCCATGTTACTTTTGAAGTTACTCC 60.072 42.308 10.20 0.00 40.62 3.85
2722 5719 7.074653 ACTTTTGAAGTTACTCCCACTATGA 57.925 36.000 0.00 0.00 39.04 2.15
2723 5720 6.935208 ACTTTTGAAGTTACTCCCACTATGAC 59.065 38.462 0.00 0.00 39.04 3.06
2730 5727 3.191888 ACTCCCACTATGACCAGTCTT 57.808 47.619 0.00 0.00 0.00 3.01
2731 5728 4.332683 ACTCCCACTATGACCAGTCTTA 57.667 45.455 0.00 0.00 0.00 2.10
2732 5729 4.884961 ACTCCCACTATGACCAGTCTTAT 58.115 43.478 0.00 0.00 0.00 1.73
2733 5730 6.027025 ACTCCCACTATGACCAGTCTTATA 57.973 41.667 0.00 0.00 0.00 0.98
2734 5731 6.441222 ACTCCCACTATGACCAGTCTTATAA 58.559 40.000 0.00 0.00 0.00 0.98
2735 5732 6.901300 ACTCCCACTATGACCAGTCTTATAAA 59.099 38.462 0.00 0.00 0.00 1.40
2736 5733 7.402071 ACTCCCACTATGACCAGTCTTATAAAA 59.598 37.037 0.00 0.00 0.00 1.52
2737 5734 8.153221 TCCCACTATGACCAGTCTTATAAAAA 57.847 34.615 0.00 0.00 0.00 1.94
2738 5735 8.778059 TCCCACTATGACCAGTCTTATAAAAAT 58.222 33.333 0.00 0.00 0.00 1.82
2739 5736 9.057089 CCCACTATGACCAGTCTTATAAAAATC 57.943 37.037 0.00 0.00 0.00 2.17
2740 5737 9.838339 CCACTATGACCAGTCTTATAAAAATCT 57.162 33.333 0.00 0.00 0.00 2.40
2746 5743 9.886132 TGACCAGTCTTATAAAAATCTTCTACC 57.114 33.333 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 5.594317 CCCCACAAATGATCTTAGTTAAGGG 59.406 44.000 0.00 0.00 34.14 3.95
78 83 4.410743 GGCGCCTTGCTTGCTCAC 62.411 66.667 22.15 0.00 45.43 3.51
193 995 0.101759 GCTCCGCTTGGACGTATGTA 59.898 55.000 0.00 0.00 36.65 2.29
226 1028 4.379813 GCAAATCAAGTGAGGTGTACCATG 60.380 45.833 3.56 0.00 38.89 3.66
267 1069 7.438160 TGTCGTCATTATTGTATCCTCAATCAC 59.562 37.037 0.00 0.00 38.68 3.06
348 1182 0.729116 TACCGCAGTAGCTACGTCAC 59.271 55.000 17.99 8.10 39.10 3.67
349 1183 1.012086 CTACCGCAGTAGCTACGTCA 58.988 55.000 17.99 1.53 39.66 4.35
388 1230 1.966354 CATCGACCAGATCATCAGGGA 59.034 52.381 0.45 0.00 37.52 4.20
398 1240 2.357952 CCTCACGTAATCATCGACCAGA 59.642 50.000 0.00 0.00 0.00 3.86
447 1296 1.033746 TATCTGGGACGACGTGGGTC 61.034 60.000 4.58 5.17 39.89 4.46
511 1365 5.425577 AGATGACATGTACGTACTAGCTG 57.574 43.478 25.12 18.10 0.00 4.24
572 1426 6.981762 TGAATTGCAACAACAACAAAAGAT 57.018 29.167 0.00 0.00 31.03 2.40
573 1427 6.773080 CATGAATTGCAACAACAACAAAAGA 58.227 32.000 0.00 0.00 31.03 2.52
589 1443 5.068234 ACAGATCAAAGGTGCATGAATTG 57.932 39.130 0.00 0.00 0.00 2.32
590 1444 5.475719 CAACAGATCAAAGGTGCATGAATT 58.524 37.500 0.00 0.00 0.00 2.17
591 1445 4.619863 GCAACAGATCAAAGGTGCATGAAT 60.620 41.667 15.29 0.00 0.00 2.57
592 1446 3.305539 GCAACAGATCAAAGGTGCATGAA 60.306 43.478 15.29 0.00 0.00 2.57
593 1447 2.229543 GCAACAGATCAAAGGTGCATGA 59.770 45.455 15.29 0.00 0.00 3.07
594 1448 2.029739 TGCAACAGATCAAAGGTGCATG 60.030 45.455 17.94 0.00 0.00 4.06
595 1449 2.230508 CTGCAACAGATCAAAGGTGCAT 59.769 45.455 20.84 0.00 32.44 3.96
596 1450 1.610038 CTGCAACAGATCAAAGGTGCA 59.390 47.619 19.82 19.82 32.44 4.57
597 1451 1.881973 TCTGCAACAGATCAAAGGTGC 59.118 47.619 13.83 13.83 35.39 5.01
598 1452 2.095364 GCTCTGCAACAGATCAAAGGTG 60.095 50.000 0.00 0.00 39.92 4.00
612 1466 3.203716 GAGTCATGAATGATGCTCTGCA 58.796 45.455 0.00 0.00 44.86 4.41
673 1531 3.474007 GCATCATGCATGTGCTAGC 57.526 52.632 30.37 22.13 44.26 3.42
707 1568 0.944386 ATCATGCGTTTGGCCGATAC 59.056 50.000 0.00 0.00 42.61 2.24
905 2499 2.992543 GCAGTGTACAGCTTCTTCTCTG 59.007 50.000 0.00 0.00 36.45 3.35
1089 3031 3.474570 CCGGAGCTAGCAAGGCCT 61.475 66.667 18.83 0.00 0.00 5.19
1393 3374 1.807573 GAAGAGGAAGCAGTCGCCG 60.808 63.158 0.00 0.00 39.83 6.46
1594 3626 1.199558 GTCTCCGCTCAACTAGTTCGT 59.800 52.381 4.77 0.00 0.00 3.85
1598 3630 1.961394 TGTTGTCTCCGCTCAACTAGT 59.039 47.619 8.96 0.00 42.71 2.57
1605 3642 3.440228 GAATCTAGTGTTGTCTCCGCTC 58.560 50.000 0.00 0.00 0.00 5.03
1606 3643 2.166664 GGAATCTAGTGTTGTCTCCGCT 59.833 50.000 0.00 0.00 0.00 5.52
1607 3644 2.094182 TGGAATCTAGTGTTGTCTCCGC 60.094 50.000 0.00 0.00 0.00 5.54
1608 3645 3.444034 TCTGGAATCTAGTGTTGTCTCCG 59.556 47.826 0.00 0.00 0.00 4.63
1609 3646 5.407407 TTCTGGAATCTAGTGTTGTCTCC 57.593 43.478 0.00 0.00 0.00 3.71
1613 3650 4.623932 TGCTTCTGGAATCTAGTGTTGT 57.376 40.909 0.00 0.00 0.00 3.32
1690 3770 9.472361 TTCTACCGAATAATTAAGCATCAGTAC 57.528 33.333 0.00 0.00 0.00 2.73
1691 3771 9.692749 CTTCTACCGAATAATTAAGCATCAGTA 57.307 33.333 0.00 0.00 0.00 2.74
1692 3772 7.171678 GCTTCTACCGAATAATTAAGCATCAGT 59.828 37.037 0.00 0.00 38.15 3.41
1696 3776 7.801716 TTGCTTCTACCGAATAATTAAGCAT 57.198 32.000 7.58 0.00 44.98 3.79
1707 3787 6.385649 ACTTTTCAATTTGCTTCTACCGAA 57.614 33.333 0.00 0.00 0.00 4.30
1709 3789 6.695278 TCAAACTTTTCAATTTGCTTCTACCG 59.305 34.615 0.00 0.00 36.06 4.02
1741 3821 9.541884 TCTATGGAGGCCTTTATTTAAAAACTT 57.458 29.630 6.77 0.00 0.00 2.66
1743 3823 7.921214 GCTCTATGGAGGCCTTTATTTAAAAAC 59.079 37.037 6.77 0.00 39.80 2.43
1746 3826 6.911308 AGCTCTATGGAGGCCTTTATTTAAA 58.089 36.000 6.77 0.00 39.80 1.52
1749 3829 4.503991 CGAGCTCTATGGAGGCCTTTATTT 60.504 45.833 6.77 0.00 39.80 1.40
1750 3830 3.007398 CGAGCTCTATGGAGGCCTTTATT 59.993 47.826 6.77 0.00 39.80 1.40
1752 3832 1.964223 CGAGCTCTATGGAGGCCTTTA 59.036 52.381 6.77 0.00 39.80 1.85
1753 3833 0.755686 CGAGCTCTATGGAGGCCTTT 59.244 55.000 6.77 0.00 39.80 3.11
1754 3834 1.118356 CCGAGCTCTATGGAGGCCTT 61.118 60.000 6.77 0.00 39.80 4.35
1756 3836 1.811645 GACCGAGCTCTATGGAGGCC 61.812 65.000 12.85 0.00 39.80 5.19
1757 3837 0.825840 AGACCGAGCTCTATGGAGGC 60.826 60.000 12.85 0.56 39.80 4.70
1758 3838 1.611491 GAAGACCGAGCTCTATGGAGG 59.389 57.143 12.85 6.85 39.80 4.30
1761 3841 3.742433 AATGAAGACCGAGCTCTATGG 57.258 47.619 12.85 8.41 0.00 2.74
1762 3842 3.806521 CCAAATGAAGACCGAGCTCTATG 59.193 47.826 12.85 2.63 0.00 2.23
1763 3843 3.742640 GCCAAATGAAGACCGAGCTCTAT 60.743 47.826 12.85 0.00 0.00 1.98
1764 3844 2.418746 GCCAAATGAAGACCGAGCTCTA 60.419 50.000 12.85 0.00 0.00 2.43
1765 3845 1.677217 GCCAAATGAAGACCGAGCTCT 60.677 52.381 12.85 0.00 0.00 4.09
1766 3846 0.729690 GCCAAATGAAGACCGAGCTC 59.270 55.000 2.73 2.73 0.00 4.09
1767 3847 0.036732 TGCCAAATGAAGACCGAGCT 59.963 50.000 0.00 0.00 0.00 4.09
1768 3848 1.098050 ATGCCAAATGAAGACCGAGC 58.902 50.000 0.00 0.00 0.00 5.03
1769 3849 3.855689 AAATGCCAAATGAAGACCGAG 57.144 42.857 0.00 0.00 0.00 4.63
1770 3850 3.365868 CGAAAATGCCAAATGAAGACCGA 60.366 43.478 0.00 0.00 0.00 4.69
1771 3851 2.916716 CGAAAATGCCAAATGAAGACCG 59.083 45.455 0.00 0.00 0.00 4.79
1772 3852 3.674753 CACGAAAATGCCAAATGAAGACC 59.325 43.478 0.00 0.00 0.00 3.85
1773 3853 3.121778 GCACGAAAATGCCAAATGAAGAC 59.878 43.478 0.00 0.00 39.86 3.01
1774 3854 3.316283 GCACGAAAATGCCAAATGAAGA 58.684 40.909 0.00 0.00 39.86 2.87
1775 3855 2.090967 CGCACGAAAATGCCAAATGAAG 59.909 45.455 0.00 0.00 42.99 3.02
1776 3856 2.057316 CGCACGAAAATGCCAAATGAA 58.943 42.857 0.00 0.00 42.99 2.57
1777 3857 1.668337 CCGCACGAAAATGCCAAATGA 60.668 47.619 0.00 0.00 42.99 2.57
1778 3858 0.714994 CCGCACGAAAATGCCAAATG 59.285 50.000 0.00 0.00 42.99 2.32
1779 3859 0.316841 ACCGCACGAAAATGCCAAAT 59.683 45.000 0.00 0.00 42.99 2.32
1780 3860 0.103208 AACCGCACGAAAATGCCAAA 59.897 45.000 0.00 0.00 42.99 3.28
1781 3861 0.596083 CAACCGCACGAAAATGCCAA 60.596 50.000 0.00 0.00 42.99 4.52
1782 3862 1.007964 CAACCGCACGAAAATGCCA 60.008 52.632 0.00 0.00 42.99 4.92
1783 3863 0.109319 ATCAACCGCACGAAAATGCC 60.109 50.000 0.00 0.00 42.99 4.40
1784 3864 1.386412 CAATCAACCGCACGAAAATGC 59.614 47.619 0.00 0.00 42.48 3.56
1785 3865 2.660490 ACAATCAACCGCACGAAAATG 58.340 42.857 0.00 0.00 0.00 2.32
1786 3866 3.363341 AACAATCAACCGCACGAAAAT 57.637 38.095 0.00 0.00 0.00 1.82
1787 3867 2.853731 AACAATCAACCGCACGAAAA 57.146 40.000 0.00 0.00 0.00 2.29
1788 3868 2.097629 TGAAACAATCAACCGCACGAAA 59.902 40.909 0.00 0.00 34.30 3.46
1789 3869 1.671328 TGAAACAATCAACCGCACGAA 59.329 42.857 0.00 0.00 34.30 3.85
1790 3870 1.262950 CTGAAACAATCAACCGCACGA 59.737 47.619 0.00 0.00 37.67 4.35
1791 3871 1.002900 ACTGAAACAATCAACCGCACG 60.003 47.619 0.00 0.00 37.67 5.34
1792 3872 2.774439 ACTGAAACAATCAACCGCAC 57.226 45.000 0.00 0.00 37.67 5.34
1796 3876 4.647424 TGGTGAACTGAAACAATCAACC 57.353 40.909 0.00 0.00 37.67 3.77
1833 3914 3.473625 ACTTACAAAAGTGAACGGAGGG 58.526 45.455 0.00 0.00 44.40 4.30
1834 3915 4.124238 TGACTTACAAAAGTGAACGGAGG 58.876 43.478 0.00 0.00 46.09 4.30
1835 3916 5.924475 ATGACTTACAAAAGTGAACGGAG 57.076 39.130 0.00 0.00 46.09 4.63
1836 3917 6.316640 TGAAATGACTTACAAAAGTGAACGGA 59.683 34.615 0.00 0.00 46.09 4.69
1837 3918 6.491394 TGAAATGACTTACAAAAGTGAACGG 58.509 36.000 0.00 0.00 46.09 4.44
1838 3919 7.373441 GTCTGAAATGACTTACAAAAGTGAACG 59.627 37.037 0.00 0.00 46.09 3.95
1839 3920 8.181573 TGTCTGAAATGACTTACAAAAGTGAAC 58.818 33.333 0.00 0.00 46.09 3.18
1840 3921 8.275015 TGTCTGAAATGACTTACAAAAGTGAA 57.725 30.769 0.00 0.00 46.09 3.18
1841 3922 7.467267 GCTGTCTGAAATGACTTACAAAAGTGA 60.467 37.037 0.00 0.00 46.09 3.41
1842 3923 6.634436 GCTGTCTGAAATGACTTACAAAAGTG 59.366 38.462 0.00 0.00 46.09 3.16
1844 3925 6.963796 AGCTGTCTGAAATGACTTACAAAAG 58.036 36.000 0.00 0.00 37.79 2.27
1845 3926 6.942532 AGCTGTCTGAAATGACTTACAAAA 57.057 33.333 0.00 0.00 37.79 2.44
1846 3927 6.942532 AAGCTGTCTGAAATGACTTACAAA 57.057 33.333 0.00 0.00 37.79 2.83
1847 3928 8.445275 TTTAAGCTGTCTGAAATGACTTACAA 57.555 30.769 0.00 0.00 37.79 2.41
1848 3929 8.445275 TTTTAAGCTGTCTGAAATGACTTACA 57.555 30.769 0.00 0.00 37.79 2.41
1849 3930 9.334693 CATTTTAAGCTGTCTGAAATGACTTAC 57.665 33.333 7.89 0.00 38.06 2.34
1850 3931 8.514594 CCATTTTAAGCTGTCTGAAATGACTTA 58.485 33.333 13.06 0.00 38.06 2.24
1851 3932 7.231317 TCCATTTTAAGCTGTCTGAAATGACTT 59.769 33.333 13.06 0.00 38.06 3.01
1852 3933 6.716628 TCCATTTTAAGCTGTCTGAAATGACT 59.283 34.615 13.06 0.00 38.06 3.41
1853 3934 6.803807 GTCCATTTTAAGCTGTCTGAAATGAC 59.196 38.462 13.06 7.69 38.06 3.06
1854 3935 6.716628 AGTCCATTTTAAGCTGTCTGAAATGA 59.283 34.615 13.06 1.36 38.06 2.57
1855 3936 6.805271 CAGTCCATTTTAAGCTGTCTGAAATG 59.195 38.462 7.00 7.00 36.93 2.32
1856 3937 6.491403 ACAGTCCATTTTAAGCTGTCTGAAAT 59.509 34.615 0.00 0.00 35.78 2.17
1857 3938 5.827797 ACAGTCCATTTTAAGCTGTCTGAAA 59.172 36.000 0.00 0.00 35.78 2.69
1858 3939 5.376625 ACAGTCCATTTTAAGCTGTCTGAA 58.623 37.500 0.00 0.00 35.78 3.02
1859 3940 4.973168 ACAGTCCATTTTAAGCTGTCTGA 58.027 39.130 0.00 0.00 35.78 3.27
1860 3941 5.695851 AACAGTCCATTTTAAGCTGTCTG 57.304 39.130 0.00 0.00 39.19 3.51
1861 3942 6.507023 CAAAACAGTCCATTTTAAGCTGTCT 58.493 36.000 0.00 0.00 39.19 3.41
1862 3943 5.175673 GCAAAACAGTCCATTTTAAGCTGTC 59.824 40.000 0.00 0.00 39.19 3.51
1863 3944 5.049828 GCAAAACAGTCCATTTTAAGCTGT 58.950 37.500 0.00 0.00 41.51 4.40
1864 3945 5.049167 TGCAAAACAGTCCATTTTAAGCTG 58.951 37.500 0.00 0.00 0.00 4.24
1865 3946 5.049828 GTGCAAAACAGTCCATTTTAAGCT 58.950 37.500 0.00 0.00 0.00 3.74
1866 3947 4.808364 TGTGCAAAACAGTCCATTTTAAGC 59.192 37.500 0.00 0.00 33.78 3.09
1867 3948 7.011295 ACAATGTGCAAAACAGTCCATTTTAAG 59.989 33.333 0.00 0.00 43.64 1.85
1868 3949 6.820656 ACAATGTGCAAAACAGTCCATTTTAA 59.179 30.769 0.00 0.00 43.64 1.52
1869 3950 6.344500 ACAATGTGCAAAACAGTCCATTTTA 58.656 32.000 0.00 0.00 43.64 1.52
1870 3951 5.184711 ACAATGTGCAAAACAGTCCATTTT 58.815 33.333 0.00 0.00 43.64 1.82
1871 3952 4.768583 ACAATGTGCAAAACAGTCCATTT 58.231 34.783 0.00 0.00 43.64 2.32
1872 3953 4.099881 AGACAATGTGCAAAACAGTCCATT 59.900 37.500 0.00 0.00 43.64 3.16
1873 3954 3.638160 AGACAATGTGCAAAACAGTCCAT 59.362 39.130 0.00 0.00 43.64 3.41
1874 3955 3.023119 AGACAATGTGCAAAACAGTCCA 58.977 40.909 0.00 0.00 43.64 4.02
1875 3956 3.066621 TCAGACAATGTGCAAAACAGTCC 59.933 43.478 0.00 0.00 43.64 3.85
1876 3957 4.291540 TCAGACAATGTGCAAAACAGTC 57.708 40.909 0.00 0.00 43.64 3.51
1877 3958 4.717233 TTCAGACAATGTGCAAAACAGT 57.283 36.364 0.00 0.00 43.64 3.55
1878 3959 5.521010 ACATTTCAGACAATGTGCAAAACAG 59.479 36.000 0.00 0.00 44.19 3.16
1879 3960 5.417811 ACATTTCAGACAATGTGCAAAACA 58.582 33.333 0.00 0.00 44.19 2.83
1880 3961 5.971895 ACATTTCAGACAATGTGCAAAAC 57.028 34.783 0.00 0.00 44.19 2.43
1881 3962 6.981762 AAACATTTCAGACAATGTGCAAAA 57.018 29.167 10.10 0.00 44.95 2.44
1882 3963 6.592994 TGAAAACATTTCAGACAATGTGCAAA 59.407 30.769 10.10 0.00 44.95 3.68
1883 3964 6.104665 TGAAAACATTTCAGACAATGTGCAA 58.895 32.000 10.10 0.00 44.95 4.08
1884 3965 5.658468 TGAAAACATTTCAGACAATGTGCA 58.342 33.333 10.10 0.00 44.95 4.57
1885 3966 6.292488 CCTTGAAAACATTTCAGACAATGTGC 60.292 38.462 5.75 5.95 44.95 4.57
1886 3967 6.757947 ACCTTGAAAACATTTCAGACAATGTG 59.242 34.615 5.75 0.00 44.95 3.21
1888 3969 7.205297 AGACCTTGAAAACATTTCAGACAATG 58.795 34.615 5.75 0.00 39.67 2.82
1889 3970 7.352079 AGACCTTGAAAACATTTCAGACAAT 57.648 32.000 5.75 0.00 0.00 2.71
1890 3971 6.773976 AGACCTTGAAAACATTTCAGACAA 57.226 33.333 5.75 0.00 0.00 3.18
1891 3972 6.773976 AAGACCTTGAAAACATTTCAGACA 57.226 33.333 5.75 0.00 0.00 3.41
1905 3986 8.792633 CCACTGTTCATTTTTATAAGACCTTGA 58.207 33.333 0.00 0.00 0.00 3.02
1906 3987 8.792633 TCCACTGTTCATTTTTATAAGACCTTG 58.207 33.333 0.00 0.00 0.00 3.61
1907 3988 8.934023 TCCACTGTTCATTTTTATAAGACCTT 57.066 30.769 0.00 0.00 0.00 3.50
1908 3989 9.533831 AATCCACTGTTCATTTTTATAAGACCT 57.466 29.630 0.00 0.00 0.00 3.85
1912 3993 9.289303 CGGAAATCCACTGTTCATTTTTATAAG 57.711 33.333 0.00 0.00 35.14 1.73
1913 3994 8.247562 CCGGAAATCCACTGTTCATTTTTATAA 58.752 33.333 0.00 0.00 35.14 0.98
1914 3995 7.612244 TCCGGAAATCCACTGTTCATTTTTATA 59.388 33.333 0.00 0.00 35.14 0.98
1915 3996 6.435904 TCCGGAAATCCACTGTTCATTTTTAT 59.564 34.615 0.00 0.00 35.14 1.40
1916 3997 5.770663 TCCGGAAATCCACTGTTCATTTTTA 59.229 36.000 0.00 0.00 35.14 1.52
1917 3998 4.586841 TCCGGAAATCCACTGTTCATTTTT 59.413 37.500 0.00 0.00 35.14 1.94
1918 3999 4.148838 TCCGGAAATCCACTGTTCATTTT 58.851 39.130 0.00 0.00 35.14 1.82
1919 4000 3.761897 TCCGGAAATCCACTGTTCATTT 58.238 40.909 0.00 0.00 35.14 2.32
1920 4001 3.433306 TCCGGAAATCCACTGTTCATT 57.567 42.857 0.00 0.00 35.14 2.57
1921 4002 3.652057 ATCCGGAAATCCACTGTTCAT 57.348 42.857 9.01 0.00 35.14 2.57
1922 4003 3.433306 AATCCGGAAATCCACTGTTCA 57.567 42.857 9.01 0.00 35.14 3.18
1923 4004 7.584987 CATATTAATCCGGAAATCCACTGTTC 58.415 38.462 9.01 0.00 35.14 3.18
1924 4005 6.016276 GCATATTAATCCGGAAATCCACTGTT 60.016 38.462 9.01 0.00 35.14 3.16
1925 4006 5.473504 GCATATTAATCCGGAAATCCACTGT 59.526 40.000 9.01 0.00 35.14 3.55
1926 4007 5.106157 GGCATATTAATCCGGAAATCCACTG 60.106 44.000 9.01 2.39 35.14 3.66
1927 4008 5.010282 GGCATATTAATCCGGAAATCCACT 58.990 41.667 9.01 0.00 35.14 4.00
1928 4009 4.157840 GGGCATATTAATCCGGAAATCCAC 59.842 45.833 9.01 0.00 35.14 4.02
1929 4010 4.340617 GGGCATATTAATCCGGAAATCCA 58.659 43.478 9.01 0.00 35.14 3.41
1938 4019 4.089361 CTCCAAAGGGGGCATATTAATCC 58.911 47.826 0.00 0.00 37.22 3.01
1990 4071 4.168760 GCTTGTGTGATTTGTTATCCAGC 58.831 43.478 0.00 0.00 0.00 4.85
2082 4776 3.408634 GGCTGGAGTGTTAAAGTGCTAA 58.591 45.455 0.00 0.00 0.00 3.09
2083 4777 2.290071 GGGCTGGAGTGTTAAAGTGCTA 60.290 50.000 0.00 0.00 0.00 3.49
2085 4779 0.881796 GGGCTGGAGTGTTAAAGTGC 59.118 55.000 0.00 0.00 0.00 4.40
2167 4882 1.409790 ACAGGCACGTACACACTACAA 59.590 47.619 0.00 0.00 0.00 2.41
2214 4930 8.552296 ACTTCCAAGAAATAACTCTATGGACAT 58.448 33.333 0.00 0.00 34.84 3.06
2262 5243 3.421844 GGGTTAGCTGTGGAGAAAATGT 58.578 45.455 0.00 0.00 0.00 2.71
2272 5254 0.743345 GCCGTTAGGGGTTAGCTGTG 60.743 60.000 0.00 0.00 38.20 3.66
2273 5255 1.196104 TGCCGTTAGGGGTTAGCTGT 61.196 55.000 0.00 0.00 38.20 4.40
2359 5343 2.366916 GTGAGGGGTATCTGATCTGTGG 59.633 54.545 0.00 0.00 0.00 4.17
2441 5435 6.771188 AAAAAGCGGTATCTATCAATCTCG 57.229 37.500 0.00 0.00 0.00 4.04
2447 5442 7.778083 TCTTCACTAAAAAGCGGTATCTATCA 58.222 34.615 0.00 0.00 0.00 2.15
2485 5481 6.597280 GCTAGGGTAGCGTGTAGTATATTACT 59.403 42.308 6.91 0.00 42.62 2.24
2502 5498 6.914665 TGAAGGTAGTTACATAGCTAGGGTA 58.085 40.000 10.60 7.12 33.27 3.69
2503 5499 5.774179 TGAAGGTAGTTACATAGCTAGGGT 58.226 41.667 10.60 8.11 33.27 4.34
2504 5500 6.919775 ATGAAGGTAGTTACATAGCTAGGG 57.080 41.667 10.60 1.93 33.27 3.53
2505 5501 8.516234 CACTATGAAGGTAGTTACATAGCTAGG 58.484 40.741 3.34 3.34 43.09 3.02
2506 5502 8.516234 CCACTATGAAGGTAGTTACATAGCTAG 58.484 40.741 0.00 0.00 43.09 3.42
2507 5503 7.450634 CCCACTATGAAGGTAGTTACATAGCTA 59.549 40.741 0.00 0.00 43.09 3.32
2508 5504 6.267928 CCCACTATGAAGGTAGTTACATAGCT 59.732 42.308 0.00 0.00 43.09 3.32
2521 5517 9.273016 CAAATATGTTACTACCCACTATGAAGG 57.727 37.037 0.00 0.00 0.00 3.46
2532 5528 6.978343 TGACAGCACAAATATGTTACTACC 57.022 37.500 0.00 0.00 37.82 3.18
2545 5541 1.401761 ACCTTTGCATGACAGCACAA 58.598 45.000 0.00 0.00 45.61 3.33
2550 5546 6.311935 CCAATAAATGAACCTTTGCATGACAG 59.688 38.462 0.00 0.00 0.00 3.51
2574 5570 8.383175 TCCCAAGACAATATGATTCTATAACCC 58.617 37.037 0.00 0.00 0.00 4.11
2584 5580 8.388589 ACATCACATATCCCAAGACAATATGAT 58.611 33.333 8.21 0.00 37.01 2.45
2598 5594 9.712305 AGCTAGTTATTGTAACATCACATATCC 57.288 33.333 3.05 0.00 0.00 2.59
2631 5627 8.482128 AGTTAATGAGGAGAGAGGTAAATTGAG 58.518 37.037 0.00 0.00 0.00 3.02
2673 5669 4.141528 ACATGGGGTTCAATTCAGCAAAAA 60.142 37.500 0.00 0.00 0.00 1.94
2674 5670 3.390639 ACATGGGGTTCAATTCAGCAAAA 59.609 39.130 0.00 0.00 0.00 2.44
2675 5671 2.971330 ACATGGGGTTCAATTCAGCAAA 59.029 40.909 0.00 0.00 0.00 3.68
2678 5674 3.763897 AGTAACATGGGGTTCAATTCAGC 59.236 43.478 0.00 0.00 40.96 4.26
2679 5675 5.982890 AAGTAACATGGGGTTCAATTCAG 57.017 39.130 0.00 0.00 40.96 3.02
2680 5676 6.325028 TCAAAAGTAACATGGGGTTCAATTCA 59.675 34.615 0.00 0.00 40.96 2.57
2681 5677 6.754193 TCAAAAGTAACATGGGGTTCAATTC 58.246 36.000 0.00 0.00 40.96 2.17
2682 5678 6.739331 TCAAAAGTAACATGGGGTTCAATT 57.261 33.333 0.00 0.00 40.96 2.32
2684 5680 5.659079 ACTTCAAAAGTAACATGGGGTTCAA 59.341 36.000 0.00 0.00 40.69 2.69
2686 5682 5.784578 ACTTCAAAAGTAACATGGGGTTC 57.215 39.130 0.00 0.00 40.69 3.62
2687 5683 6.837048 AGTAACTTCAAAAGTAACATGGGGTT 59.163 34.615 0.00 0.00 41.91 4.11
2688 5684 6.370453 AGTAACTTCAAAAGTAACATGGGGT 58.630 36.000 0.00 0.00 41.91 4.95
2689 5685 6.072119 GGAGTAACTTCAAAAGTAACATGGGG 60.072 42.308 0.00 0.00 41.91 4.96
2692 5688 7.228706 AGTGGGAGTAACTTCAAAAGTAACATG 59.771 37.037 0.00 0.00 41.91 3.21
2695 5692 8.718734 CATAGTGGGAGTAACTTCAAAAGTAAC 58.281 37.037 0.00 0.00 41.91 2.50
2701 5698 5.308497 TGGTCATAGTGGGAGTAACTTCAAA 59.692 40.000 0.00 0.00 0.00 2.69
2714 5711 9.838339 AGATTTTTATAAGACTGGTCATAGTGG 57.162 33.333 3.51 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.