Multiple sequence alignment - TraesCS4B01G281900

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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 TraesCS4B01G281900 chr4B 100.000 5772 0 0 1 5772 564906247 564900476 0.000000e+00 10659.0
1 TraesCS4B01G281900 chr4B 89.041 73 8 0 5700 5772 628115777 628115705 2.210000e-14 91.6
2 TraesCS4B01G281900 chr4B 95.349 43 2 0 3864 3906 660491536 660491578 1.040000e-07 69.4
3 TraesCS4B01G281900 chr4D 95.603 1774 66 8 2079 3850 451298578 451296815 0.000000e+00 2833.0
4 TraesCS4B01G281900 chr4D 93.645 1306 46 12 794 2088 451299884 451298605 0.000000e+00 1917.0
5 TraesCS4B01G281900 chr4D 95.543 920 26 4 3905 4818 451296813 451295903 0.000000e+00 1458.0
6 TraesCS4B01G281900 chr4D 82.845 717 99 13 1 699 451300725 451300015 6.350000e-174 621.0
7 TraesCS4B01G281900 chr4D 81.818 110 14 2 3318 3424 451297382 451297276 2.870000e-13 87.9
8 TraesCS4B01G281900 chr4D 100.000 42 0 0 3865 3906 486185383 486185342 1.720000e-10 78.7
9 TraesCS4B01G281900 chr4D 97.674 43 1 0 3864 3906 79706019 79706061 2.230000e-09 75.0
10 TraesCS4B01G281900 chr4D 97.561 41 1 0 3866 3906 287544124 287544164 2.890000e-08 71.3
11 TraesCS4B01G281900 chr4D 95.556 45 1 1 3862 3906 362116454 362116411 2.890000e-08 71.3
12 TraesCS4B01G281900 chr4A 94.584 1791 71 9 2079 3850 15639535 15641318 0.000000e+00 2747.0
13 TraesCS4B01G281900 chr4A 93.117 1293 62 10 808 2088 15638231 15639508 0.000000e+00 1869.0
14 TraesCS4B01G281900 chr4A 92.308 754 46 8 4070 4818 15641450 15642196 0.000000e+00 1061.0
15 TraesCS4B01G281900 chr4A 83.254 836 115 13 1 821 15637391 15638216 0.000000e+00 745.0
16 TraesCS4B01G281900 chr4A 77.476 737 137 19 1 723 5454832 5455553 1.160000e-111 414.0
17 TraesCS4B01G281900 chr4A 95.455 132 4 2 3905 4035 15641320 15641450 5.860000e-50 209.0
18 TraesCS4B01G281900 chr4A 100.000 42 0 0 3865 3906 638216883 638216924 1.720000e-10 78.7
19 TraesCS4B01G281900 chr2D 92.966 981 41 8 4819 5772 448661811 448662790 0.000000e+00 1404.0
20 TraesCS4B01G281900 chr2D 80.813 787 128 12 1 774 50948296 50949072 3.850000e-166 595.0
21 TraesCS4B01G281900 chr2D 80.207 677 114 13 1 661 642330377 642331049 1.870000e-134 490.0
22 TraesCS4B01G281900 chr7A 92.770 982 43 10 4818 5772 53686310 53685330 0.000000e+00 1395.0
23 TraesCS4B01G281900 chr3D 92.159 982 42 10 4825 5772 598646131 598645151 0.000000e+00 1354.0
24 TraesCS4B01G281900 chr3D 97.619 42 1 0 3865 3906 548728166 548728207 8.020000e-09 73.1
25 TraesCS4B01G281900 chr3D 97.561 41 1 0 3867 3907 420804319 420804279 2.890000e-08 71.3
26 TraesCS4B01G281900 chr1D 93.709 906 35 10 4884 5772 7358226 7357326 0.000000e+00 1338.0
27 TraesCS4B01G281900 chr1D 79.200 750 107 25 1 723 260406554 260405827 5.230000e-130 475.0
28 TraesCS4B01G281900 chr1D 85.897 78 2 3 4819 4887 7358320 7358243 2.230000e-09 75.0
29 TraesCS4B01G281900 chr1D 100.000 33 0 0 3874 3906 298572532 298572564 1.740000e-05 62.1
30 TraesCS4B01G281900 chr3B 95.221 858 17 5 4815 5649 308394435 308395291 0.000000e+00 1336.0
31 TraesCS4B01G281900 chr3B 90.031 983 60 13 4819 5772 679986916 679987889 0.000000e+00 1238.0
32 TraesCS4B01G281900 chr3B 79.911 672 118 9 1 659 182421160 182421827 1.460000e-130 477.0
33 TraesCS4B01G281900 chr3B 96.350 137 5 0 5636 5772 308402003 308402139 5.820000e-55 226.0
34 TraesCS4B01G281900 chr3B 95.918 49 2 0 3865 3913 501117600 501117552 4.790000e-11 80.5
35 TraesCS4B01G281900 chr7D 90.491 978 41 19 4825 5769 414483168 414484126 0.000000e+00 1243.0
36 TraesCS4B01G281900 chr7D 79.079 760 138 12 1 744 118820387 118821141 2.400000e-138 503.0
37 TraesCS4B01G281900 chr7D 77.238 782 149 14 7 776 503922974 503923738 1.150000e-116 431.0
38 TraesCS4B01G281900 chr7D 81.746 126 20 3 566 690 484298663 484298786 1.020000e-17 102.0
39 TraesCS4B01G281900 chr7D 97.561 41 1 0 3866 3906 312543203 312543243 2.890000e-08 71.3
40 TraesCS4B01G281900 chr7B 94.345 672 25 9 5026 5690 351906997 351906332 0.000000e+00 1018.0
41 TraesCS4B01G281900 chr7B 85.477 241 12 3 4819 5037 351908474 351908235 4.500000e-56 230.0
42 TraesCS4B01G281900 chr7B 98.936 94 1 0 5678 5771 351900971 351900878 9.950000e-38 169.0
43 TraesCS4B01G281900 chrUn 83.146 534 76 7 1 522 127023330 127022799 5.230000e-130 475.0
44 TraesCS4B01G281900 chrUn 95.349 43 2 0 3864 3906 110464780 110464822 1.040000e-07 69.4
45 TraesCS4B01G281900 chrUn 100.000 34 0 0 3873 3906 55726298 55726265 4.830000e-06 63.9
46 TraesCS4B01G281900 chr1B 77.806 784 148 14 1 779 531392555 531391793 1.470000e-125 460.0
47 TraesCS4B01G281900 chr1B 81.579 532 79 12 1 520 352524409 352524933 6.920000e-114 422.0
48 TraesCS4B01G281900 chr1B 100.000 43 0 0 3865 3907 386519898 386519940 4.790000e-11 80.5
49 TraesCS4B01G281900 chr1B 97.674 43 1 0 3864 3906 636308020 636308062 2.230000e-09 75.0
50 TraesCS4B01G281900 chr5D 78.641 721 129 12 22 721 112329981 112329265 6.820000e-124 455.0
51 TraesCS4B01G281900 chr5D 78.121 745 130 21 1 723 249880381 249881114 5.310000e-120 442.0
52 TraesCS4B01G281900 chr5D 100.000 42 0 0 3865 3906 533641528 533641487 1.720000e-10 78.7
53 TraesCS4B01G281900 chr5D 97.561 41 1 0 3866 3906 71888893 71888933 2.890000e-08 71.3
54 TraesCS4B01G281900 chr6A 94.643 280 15 0 5122 5401 580956989 580957268 8.880000e-118 435.0
55 TraesCS4B01G281900 chr6A 91.197 284 19 5 5404 5681 581013045 581013328 1.170000e-101 381.0
56 TraesCS4B01G281900 chr6A 91.304 184 13 2 4896 5076 580956818 580957001 1.240000e-61 248.0
57 TraesCS4B01G281900 chr5A 79.233 443 72 17 289 723 596673501 596673071 2.030000e-74 291.0
58 TraesCS4B01G281900 chr5A 97.619 42 1 0 3865 3906 64367709 64367750 8.020000e-09 73.1
59 TraesCS4B01G281900 chr6D 82.550 298 43 2 1 289 309739573 309739870 2.670000e-63 254.0
60 TraesCS4B01G281900 chr6D 97.500 40 1 0 3866 3905 31475309 31475348 1.040000e-07 69.4
61 TraesCS4B01G281900 chr6D 95.238 42 2 0 3866 3907 17354737 17354696 3.730000e-07 67.6
62 TraesCS4B01G281900 chr5B 100.000 42 0 0 3864 3905 82475838 82475879 1.720000e-10 78.7
63 TraesCS4B01G281900 chr5B 100.000 41 0 0 3866 3906 82475807 82475767 6.200000e-10 76.8
64 TraesCS4B01G281900 chr5B 97.674 43 0 1 3865 3907 673688606 673688565 8.020000e-09 73.1
65 TraesCS4B01G281900 chr2A 95.652 46 2 0 3864 3909 706204947 706204992 2.230000e-09 75.0


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 TraesCS4B01G281900 chr4B 564900476 564906247 5771 True 10659.00 10659 100.0000 1 5772 1 chr4B.!!$R1 5771
1 TraesCS4B01G281900 chr4D 451295903 451300725 4822 True 1383.38 2833 89.8908 1 4818 5 chr4D.!!$R3 4817
2 TraesCS4B01G281900 chr4A 15637391 15642196 4805 False 1326.20 2747 91.7436 1 4818 5 chr4A.!!$F3 4817
3 TraesCS4B01G281900 chr4A 5454832 5455553 721 False 414.00 414 77.4760 1 723 1 chr4A.!!$F1 722
4 TraesCS4B01G281900 chr2D 448661811 448662790 979 False 1404.00 1404 92.9660 4819 5772 1 chr2D.!!$F2 953
5 TraesCS4B01G281900 chr2D 50948296 50949072 776 False 595.00 595 80.8130 1 774 1 chr2D.!!$F1 773
6 TraesCS4B01G281900 chr2D 642330377 642331049 672 False 490.00 490 80.2070 1 661 1 chr2D.!!$F3 660
7 TraesCS4B01G281900 chr7A 53685330 53686310 980 True 1395.00 1395 92.7700 4818 5772 1 chr7A.!!$R1 954
8 TraesCS4B01G281900 chr3D 598645151 598646131 980 True 1354.00 1354 92.1590 4825 5772 1 chr3D.!!$R2 947
9 TraesCS4B01G281900 chr1D 7357326 7358320 994 True 706.50 1338 89.8030 4819 5772 2 chr1D.!!$R2 953
10 TraesCS4B01G281900 chr1D 260405827 260406554 727 True 475.00 475 79.2000 1 723 1 chr1D.!!$R1 722
11 TraesCS4B01G281900 chr3B 308394435 308395291 856 False 1336.00 1336 95.2210 4815 5649 1 chr3B.!!$F2 834
12 TraesCS4B01G281900 chr3B 679986916 679987889 973 False 1238.00 1238 90.0310 4819 5772 1 chr3B.!!$F4 953
13 TraesCS4B01G281900 chr3B 182421160 182421827 667 False 477.00 477 79.9110 1 659 1 chr3B.!!$F1 658
14 TraesCS4B01G281900 chr7D 414483168 414484126 958 False 1243.00 1243 90.4910 4825 5769 1 chr7D.!!$F3 944
15 TraesCS4B01G281900 chr7D 118820387 118821141 754 False 503.00 503 79.0790 1 744 1 chr7D.!!$F1 743
16 TraesCS4B01G281900 chr7D 503922974 503923738 764 False 431.00 431 77.2380 7 776 1 chr7D.!!$F5 769
17 TraesCS4B01G281900 chr7B 351906332 351908474 2142 True 624.00 1018 89.9110 4819 5690 2 chr7B.!!$R2 871
18 TraesCS4B01G281900 chrUn 127022799 127023330 531 True 475.00 475 83.1460 1 522 1 chrUn.!!$R2 521
19 TraesCS4B01G281900 chr1B 531391793 531392555 762 True 460.00 460 77.8060 1 779 1 chr1B.!!$R1 778
20 TraesCS4B01G281900 chr1B 352524409 352524933 524 False 422.00 422 81.5790 1 520 1 chr1B.!!$F1 519
21 TraesCS4B01G281900 chr5D 112329265 112329981 716 True 455.00 455 78.6410 22 721 1 chr5D.!!$R1 699
22 TraesCS4B01G281900 chr5D 249880381 249881114 733 False 442.00 442 78.1210 1 723 1 chr5D.!!$F2 722


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
763 896 0.474273 AGGTTTGAGGGTCCGGGTTA 60.474 55.0 0.00 0.0 0.00 2.85 F
1342 1508 0.249955 AATGGCAAATTTGGGCGGAG 59.750 50.0 19.47 0.0 0.00 4.63 F
2416 2648 0.673437 GTGGTGCCAGCTTTGCTTAA 59.327 50.0 6.55 0.0 36.40 1.85 F
3521 3753 0.178967 TTCAAGGTTGCCCATCAGCA 60.179 50.0 0.00 0.0 42.17 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2429 2661 0.177836 TACATGTGATGCGGGTGAGG 59.822 55.0 9.11 0.0 0.0 3.86 R
2642 2874 0.332972 ACCCAGGGATCCTTTTCTGC 59.667 55.0 14.54 0.0 0.0 4.26 R
3853 4106 0.031917 TTACACTATGGGCGGAGGGA 60.032 55.0 0.00 0.0 0.0 4.20 R
5463 7010 0.871722 CTTGCGATGTTCCCACGAAA 59.128 50.0 0.00 0.0 0.0 3.46 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
214 238 2.123251 GAGGAGATGGGGGAGCGA 60.123 66.667 0.00 0.00 0.00 4.93
351 384 2.769095 GAGTAGGGTTCTCAGCTTCCAT 59.231 50.000 0.00 0.00 32.79 3.41
385 418 0.529773 GGTGTATGAATGCGGCGAGA 60.530 55.000 12.98 0.00 0.00 4.04
397 430 2.298593 GGCGAGAAGGCGTATTCAC 58.701 57.895 4.86 0.00 35.04 3.18
463 513 1.676746 CAGATGCAATGGGAGGTCAG 58.323 55.000 0.00 0.00 0.00 3.51
531 583 2.079158 CATGAATGCGGACAACTGACT 58.921 47.619 0.00 0.00 0.00 3.41
532 584 3.261580 CATGAATGCGGACAACTGACTA 58.738 45.455 0.00 0.00 0.00 2.59
533 585 2.959516 TGAATGCGGACAACTGACTAG 58.040 47.619 0.00 0.00 0.00 2.57
543 595 2.158726 ACAACTGACTAGGGGCGAAAAA 60.159 45.455 0.00 0.00 0.00 1.94
629 691 2.852075 ACCCCCGCAAACCTCTCA 60.852 61.111 0.00 0.00 0.00 3.27
763 896 0.474273 AGGTTTGAGGGTCCGGGTTA 60.474 55.000 0.00 0.00 0.00 2.85
786 919 5.799213 AGAGATGCCCTTAATATTTCGAGG 58.201 41.667 0.00 0.00 0.00 4.63
787 920 4.327680 AGATGCCCTTAATATTTCGAGGC 58.672 43.478 10.10 10.10 39.41 4.70
791 929 3.473625 CCCTTAATATTTCGAGGCGGTT 58.526 45.455 0.00 0.00 0.00 4.44
830 996 2.148768 TCGCTCATACGGATCGTACAT 58.851 47.619 2.17 0.00 45.07 2.29
856 1022 5.601662 TCTTAGCAATATTCGGAAGTCAGG 58.398 41.667 0.00 0.00 0.00 3.86
963 1129 4.324022 CCGTTAAACCCTAACTCCCATCTT 60.324 45.833 0.00 0.00 0.00 2.40
1003 1169 4.996434 ACTGCCAGCACGCCACTC 62.996 66.667 0.00 0.00 0.00 3.51
1342 1508 0.249955 AATGGCAAATTTGGGCGGAG 59.750 50.000 19.47 0.00 0.00 4.63
1438 1605 9.525409 AATGATATCTAGTTTTGCTTGCATTTC 57.475 29.630 3.98 0.00 0.00 2.17
1454 1621 7.359014 GCTTGCATTTCTTTTCTGTGAGATTTC 60.359 37.037 0.00 0.00 0.00 2.17
1464 1631 1.270252 TGTGAGATTTCGTGCTGCAGA 60.270 47.619 20.43 0.00 0.00 4.26
1478 1648 3.691118 TGCTGCAGAGTGATATTTTCCAC 59.309 43.478 20.43 0.00 0.00 4.02
1571 1742 6.605471 ACGGAATGAGGACATAGCATTATA 57.395 37.500 0.00 0.00 35.50 0.98
1601 1772 1.341156 GGGGTGAGTGATCAGGGAGG 61.341 65.000 0.00 0.00 0.00 4.30
1644 1820 0.958822 GGCAGGTGGTAGTTTTGGTG 59.041 55.000 0.00 0.00 0.00 4.17
1647 1823 2.650322 CAGGTGGTAGTTTTGGTGTGT 58.350 47.619 0.00 0.00 0.00 3.72
1703 1880 3.189606 TCTGAAGATTAAGGGCCTTCCA 58.810 45.455 24.77 11.58 36.41 3.53
1721 1898 4.524802 TCCATGGGCTCTTTGATGTTAT 57.475 40.909 13.02 0.00 0.00 1.89
1722 1899 4.870636 TCCATGGGCTCTTTGATGTTATT 58.129 39.130 13.02 0.00 0.00 1.40
1723 1900 6.012337 TCCATGGGCTCTTTGATGTTATTA 57.988 37.500 13.02 0.00 0.00 0.98
1774 1953 6.019075 TCTGAAATACAATAATTCAGCGTCCG 60.019 38.462 9.31 0.00 46.06 4.79
1781 1960 5.583061 ACAATAATTCAGCGTCCGTTTATCA 59.417 36.000 0.00 0.00 0.00 2.15
1835 2025 4.155462 TGAATGCACTGAAATCTTGAGCTC 59.845 41.667 6.82 6.82 0.00 4.09
1836 2026 3.130280 TGCACTGAAATCTTGAGCTCA 57.870 42.857 13.74 13.74 0.00 4.26
1837 2027 2.810274 TGCACTGAAATCTTGAGCTCAC 59.190 45.455 18.03 4.16 0.00 3.51
1838 2028 2.161211 GCACTGAAATCTTGAGCTCACC 59.839 50.000 18.03 2.39 0.00 4.02
1839 2029 3.672808 CACTGAAATCTTGAGCTCACCT 58.327 45.455 18.03 0.37 0.00 4.00
1840 2030 4.070716 CACTGAAATCTTGAGCTCACCTT 58.929 43.478 18.03 7.35 0.00 3.50
1841 2031 4.518211 CACTGAAATCTTGAGCTCACCTTT 59.482 41.667 18.03 15.55 0.00 3.11
1842 2032 5.009410 CACTGAAATCTTGAGCTCACCTTTT 59.991 40.000 18.03 15.36 0.00 2.27
1843 2033 6.205464 CACTGAAATCTTGAGCTCACCTTTTA 59.795 38.462 18.03 11.60 0.00 1.52
1844 2034 6.772716 ACTGAAATCTTGAGCTCACCTTTTAA 59.227 34.615 18.03 8.40 0.00 1.52
1845 2035 7.449704 ACTGAAATCTTGAGCTCACCTTTTAAT 59.550 33.333 18.03 0.63 0.00 1.40
1846 2036 8.862325 TGAAATCTTGAGCTCACCTTTTAATA 57.138 30.769 18.03 0.00 0.00 0.98
1847 2037 9.295825 TGAAATCTTGAGCTCACCTTTTAATAA 57.704 29.630 18.03 0.00 0.00 1.40
1850 2040 9.692325 AATCTTGAGCTCACCTTTTAATAATCT 57.308 29.630 18.03 0.00 0.00 2.40
1851 2041 9.692325 ATCTTGAGCTCACCTTTTAATAATCTT 57.308 29.630 18.03 0.00 0.00 2.40
1852 2042 8.950210 TCTTGAGCTCACCTTTTAATAATCTTG 58.050 33.333 18.03 0.00 0.00 3.02
1853 2043 8.862325 TTGAGCTCACCTTTTAATAATCTTGA 57.138 30.769 18.03 0.00 0.00 3.02
1854 2044 8.498054 TGAGCTCACCTTTTAATAATCTTGAG 57.502 34.615 13.74 0.00 33.78 3.02
1923 2113 9.778741 ATATATAACAGATTCAATCGTGTTGGT 57.221 29.630 18.19 12.31 34.67 3.67
1942 2135 7.389607 GTGTTGGTAAAGGCTTGTATTCTCTTA 59.610 37.037 0.00 0.00 0.00 2.10
1960 2153 1.847328 TAGTGTGAGCCCTTCATCGA 58.153 50.000 0.00 0.00 38.29 3.59
2072 2269 2.267006 CTGCTGGTCCTCGCATGT 59.733 61.111 6.84 0.00 35.32 3.21
2115 2347 7.695480 TTTCATGGTTGCTACTTGCTATTAA 57.305 32.000 0.00 0.00 43.37 1.40
2150 2382 6.308015 TCAGCAAGTTATAGCCCTCTTTTA 57.692 37.500 0.00 0.00 0.00 1.52
2160 2392 4.929146 AGCCCTCTTTTATTGTAGGTGT 57.071 40.909 0.00 0.00 0.00 4.16
2167 2399 8.210946 CCCTCTTTTATTGTAGGTGTGATATCA 58.789 37.037 0.00 0.00 0.00 2.15
2219 2451 3.103742 ACAATTGTGTCAAAGTTGGGGT 58.896 40.909 11.07 0.00 29.49 4.95
2245 2477 5.221722 TGCCACTCAGTCTAAAGTTCTCAAT 60.222 40.000 0.00 0.00 0.00 2.57
2257 2489 9.958180 TCTAAAGTTCTCAATGTTGATCCATAA 57.042 29.630 0.00 0.00 36.46 1.90
2265 2497 2.374184 TGTTGATCCATAAAAGGGCCG 58.626 47.619 0.00 0.00 0.00 6.13
2271 2503 1.213182 TCCATAAAAGGGCCGCACATA 59.787 47.619 0.00 0.00 0.00 2.29
2288 2520 6.183360 CCGCACATACATGTAATCCTTCTTTT 60.183 38.462 10.14 0.00 39.39 2.27
2319 2551 5.764686 GGAGGATGCATCATGTAACAATGTA 59.235 40.000 27.25 0.00 0.00 2.29
2392 2624 7.513560 TGGGGGTATAGTTTATTACTGTGTT 57.486 36.000 0.00 0.00 37.73 3.32
2406 2638 3.609853 ACTGTGTTATATGTGGTGCCAG 58.390 45.455 0.00 0.00 0.00 4.85
2409 2641 3.016736 GTGTTATATGTGGTGCCAGCTT 58.983 45.455 0.00 0.00 0.00 3.74
2411 2643 3.443329 TGTTATATGTGGTGCCAGCTTTG 59.557 43.478 0.00 0.00 0.00 2.77
2416 2648 0.673437 GTGGTGCCAGCTTTGCTTAA 59.327 50.000 6.55 0.00 36.40 1.85
2429 2661 8.175716 CCAGCTTTGCTTAACTAACTATTACAC 58.824 37.037 0.00 0.00 36.40 2.90
2438 2670 2.685850 AACTATTACACCTCACCCGC 57.314 50.000 0.00 0.00 0.00 6.13
2642 2874 7.721286 AAAATTGACTAGCTCCATCTAATCG 57.279 36.000 0.00 0.00 0.00 3.34
2753 2985 7.261829 TGTACCGTTAAGTATTGCAAAACTT 57.738 32.000 1.71 3.24 39.25 2.66
2775 3007 1.259609 TTGCTTGCTGATTCCTTGGG 58.740 50.000 0.00 0.00 0.00 4.12
2885 3117 1.546476 ACCTAAGGAGCTCGACACAAG 59.454 52.381 7.83 0.00 0.00 3.16
2944 3176 7.719483 TCCCATGATTTATTTTGAAGCATCTC 58.281 34.615 0.00 0.00 31.34 2.75
3111 3343 3.013921 TCAAGGTCAAACAGGTGAACAC 58.986 45.455 0.00 0.00 37.72 3.32
3147 3379 8.251721 AGATGTAGTTTGTCTATGTTACTGACC 58.748 37.037 0.00 0.00 0.00 4.02
3232 3464 2.877383 TGGGGTGGTAGGGGAGGA 60.877 66.667 0.00 0.00 0.00 3.71
3304 3536 4.971924 GGATATAGCAACCAGGGAGGATAT 59.028 45.833 0.00 0.00 41.22 1.63
3418 3650 1.830408 CGGCCAAAACCAAGGTGGA 60.830 57.895 2.24 0.00 40.96 4.02
3481 3713 7.419172 GGGGGATATGGTAAGTTCTATCATAGC 60.419 44.444 0.00 0.00 0.00 2.97
3492 3724 8.748380 AAGTTCTATCATAGCTTTGTTTTTGC 57.252 30.769 4.00 0.00 0.00 3.68
3521 3753 0.178967 TTCAAGGTTGCCCATCAGCA 60.179 50.000 0.00 0.00 42.17 4.41
3585 3818 4.641989 AGTGTTGACTGCTTCAGTTGATTT 59.358 37.500 0.66 0.00 45.44 2.17
3598 3831 5.055812 TCAGTTGATTTGTTTTTGGATGCC 58.944 37.500 0.00 0.00 0.00 4.40
3769 4022 2.285220 GTGGTATGTACAATCGCAGCAG 59.715 50.000 0.00 0.00 0.00 4.24
3811 4064 7.092716 GCATGAATTGAACTTTCTGTTGGTAT 58.907 34.615 0.00 0.00 39.30 2.73
3850 4103 7.120579 TGCATTTACTCCATCTCGTTACAAATT 59.879 33.333 0.00 0.00 0.00 1.82
3851 4104 8.609176 GCATTTACTCCATCTCGTTACAAATTA 58.391 33.333 0.00 0.00 0.00 1.40
3852 4105 9.916397 CATTTACTCCATCTCGTTACAAATTAC 57.084 33.333 0.00 0.00 0.00 1.89
3853 4106 9.886132 ATTTACTCCATCTCGTTACAAATTACT 57.114 29.630 0.00 0.00 0.00 2.24
3854 4107 8.922058 TTACTCCATCTCGTTACAAATTACTC 57.078 34.615 0.00 0.00 0.00 2.59
3855 4108 6.338937 ACTCCATCTCGTTACAAATTACTCC 58.661 40.000 0.00 0.00 0.00 3.85
3856 4109 5.667466 TCCATCTCGTTACAAATTACTCCC 58.333 41.667 0.00 0.00 0.00 4.30
3857 4110 5.424252 TCCATCTCGTTACAAATTACTCCCT 59.576 40.000 0.00 0.00 0.00 4.20
3858 4111 5.753921 CCATCTCGTTACAAATTACTCCCTC 59.246 44.000 0.00 0.00 0.00 4.30
3859 4112 5.334724 TCTCGTTACAAATTACTCCCTCC 57.665 43.478 0.00 0.00 0.00 4.30
3860 4113 4.110482 CTCGTTACAAATTACTCCCTCCG 58.890 47.826 0.00 0.00 0.00 4.63
3861 4114 2.606272 CGTTACAAATTACTCCCTCCGC 59.394 50.000 0.00 0.00 0.00 5.54
3862 4115 2.941064 GTTACAAATTACTCCCTCCGCC 59.059 50.000 0.00 0.00 0.00 6.13
3863 4116 0.255033 ACAAATTACTCCCTCCGCCC 59.745 55.000 0.00 0.00 0.00 6.13
3864 4117 0.254747 CAAATTACTCCCTCCGCCCA 59.745 55.000 0.00 0.00 0.00 5.36
3865 4118 1.133792 CAAATTACTCCCTCCGCCCAT 60.134 52.381 0.00 0.00 0.00 4.00
3866 4119 2.105821 CAAATTACTCCCTCCGCCCATA 59.894 50.000 0.00 0.00 0.00 2.74
3867 4120 1.645710 ATTACTCCCTCCGCCCATAG 58.354 55.000 0.00 0.00 0.00 2.23
3868 4121 0.263765 TTACTCCCTCCGCCCATAGT 59.736 55.000 0.00 0.00 0.00 2.12
3869 4122 0.469331 TACTCCCTCCGCCCATAGTG 60.469 60.000 0.00 0.00 0.00 2.74
3870 4123 1.762460 CTCCCTCCGCCCATAGTGT 60.762 63.158 0.00 0.00 0.00 3.55
3871 4124 0.469331 CTCCCTCCGCCCATAGTGTA 60.469 60.000 0.00 0.00 0.00 2.90
3872 4125 0.031917 TCCCTCCGCCCATAGTGTAA 60.032 55.000 0.00 0.00 0.00 2.41
3873 4126 0.834612 CCCTCCGCCCATAGTGTAAA 59.165 55.000 0.00 0.00 0.00 2.01
3874 4127 1.210967 CCCTCCGCCCATAGTGTAAAA 59.789 52.381 0.00 0.00 0.00 1.52
3875 4128 2.356330 CCCTCCGCCCATAGTGTAAAAA 60.356 50.000 0.00 0.00 0.00 1.94
3898 4151 8.760980 AAAATGATCTTATATTTTGGGACGGA 57.239 30.769 0.00 0.00 35.73 4.69
3899 4152 7.986085 AATGATCTTATATTTTGGGACGGAG 57.014 36.000 0.00 0.00 0.00 4.63
3900 4153 5.865085 TGATCTTATATTTTGGGACGGAGG 58.135 41.667 0.00 0.00 0.00 4.30
3901 4154 4.699925 TCTTATATTTTGGGACGGAGGG 57.300 45.455 0.00 0.00 0.00 4.30
3902 4155 4.300345 TCTTATATTTTGGGACGGAGGGA 58.700 43.478 0.00 0.00 0.00 4.20
3903 4156 4.347000 TCTTATATTTTGGGACGGAGGGAG 59.653 45.833 0.00 0.00 0.00 4.30
3970 4223 7.847096 TGGCAGAACTTCAGTGAATAGTATTA 58.153 34.615 5.91 0.00 0.00 0.98
3994 4248 9.715121 TTAGTGACGATAGAACAGGTTTTAATT 57.285 29.630 0.00 0.00 41.38 1.40
4031 4285 4.156455 TCAGTGCTAATCTGATTTCCCC 57.844 45.455 8.38 0.00 37.07 4.81
4040 4294 7.093771 TGCTAATCTGATTTCCCCTTTTCTTTC 60.094 37.037 8.38 0.00 0.00 2.62
4057 4311 2.189594 TTCCTTGCTCAGTCACATGG 57.810 50.000 0.00 0.00 33.52 3.66
4067 4321 0.112995 AGTCACATGGGCATTGTGGT 59.887 50.000 16.06 4.74 34.60 4.16
4071 4325 4.141181 AGTCACATGGGCATTGTGGTATAT 60.141 41.667 16.06 0.00 34.60 0.86
4080 4334 5.767665 GGGCATTGTGGTATATACACATTCA 59.232 40.000 14.70 0.34 46.98 2.57
4169 4423 8.662781 TCTCAAGTTGTATATTTAGACCATGC 57.337 34.615 2.11 0.00 0.00 4.06
4179 4433 9.219603 GTATATTTAGACCATGCACATGTGTAT 57.780 33.333 26.01 24.00 37.11 2.29
4235 4490 8.948853 TGAAACAATGATTGAAACGATAACTC 57.051 30.769 12.80 0.00 0.00 3.01
4310 4565 5.612725 AATTCAAAAGGTTTGGAGCTTGA 57.387 34.783 0.00 0.00 42.47 3.02
4363 4620 2.279741 CACCATGTATCAGGTTCGGTG 58.720 52.381 0.00 0.00 35.52 4.94
4668 4930 7.126061 AGGCTTCCCAGTTTTTAGCTATAATT 58.874 34.615 0.00 0.00 32.58 1.40
4909 5201 0.036732 CTAACAGGTTGGCTGCTGGA 59.963 55.000 0.00 0.00 0.00 3.86
4931 5223 4.028852 ACGTTTTGCAAAAGAGACCTTC 57.971 40.909 24.46 9.50 0.00 3.46
4954 5246 5.351465 TCAAGCCTAGCTAAATCAACGAAAG 59.649 40.000 0.00 0.00 38.25 2.62
5231 6778 8.956426 GTACTCCAATGGAAATGTAAAATCTGA 58.044 33.333 2.61 0.00 0.00 3.27
5457 7004 7.493743 TTAGCTGTTTCCATGTAAAAACGTA 57.506 32.000 0.00 2.12 38.03 3.57
5458 7005 5.997385 AGCTGTTTCCATGTAAAAACGTAG 58.003 37.500 0.00 5.48 38.03 3.51
5460 7007 6.707161 AGCTGTTTCCATGTAAAAACGTAGTA 59.293 34.615 0.00 0.00 45.00 1.82
5461 7008 7.389607 AGCTGTTTCCATGTAAAAACGTAGTAT 59.610 33.333 0.00 0.00 45.00 2.12
5463 7010 9.887406 CTGTTTCCATGTAAAAACGTAGTATTT 57.113 29.630 0.00 0.00 45.00 1.40
5645 7213 1.599419 GCCGACGCACAAGAAAACATT 60.599 47.619 0.00 0.00 34.03 2.71
5669 7237 7.185318 TGGTTAATCCTCAATTGCATCAAAT 57.815 32.000 0.00 0.00 37.07 2.32
5706 7274 2.162408 GTCAGGAACAATAGCTGGTTGC 59.838 50.000 12.08 11.01 43.29 4.17
5743 7311 8.147058 TCTAATAGTGAGAATTCTGGCAAGATC 58.853 37.037 14.00 0.00 30.72 2.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 1.063488 GCGCGTGGTTCAACAACTT 59.937 52.632 8.43 0.00 32.50 2.66
85 86 3.385384 CTCGCTGCTCCACCTCCA 61.385 66.667 0.00 0.00 0.00 3.86
138 144 0.521735 GCAGTTCTTTACAAGCCGGG 59.478 55.000 2.18 0.00 0.00 5.73
214 238 1.341383 GCAAGAATCACACCCCTCCAT 60.341 52.381 0.00 0.00 0.00 3.41
351 384 0.402504 ACACCTCCATTAAACCCGCA 59.597 50.000 0.00 0.00 0.00 5.69
385 418 2.587889 CCCCGGTGAATACGCCTT 59.412 61.111 0.00 0.00 43.77 4.35
531 583 1.928706 GCGCACATTTTTCGCCCCTA 61.929 55.000 0.30 0.00 42.71 3.53
532 584 2.961768 CGCACATTTTTCGCCCCT 59.038 55.556 0.00 0.00 0.00 4.79
533 585 2.809174 GCGCACATTTTTCGCCCC 60.809 61.111 0.30 0.00 42.71 5.80
614 671 1.966451 GTGTGAGAGGTTTGCGGGG 60.966 63.158 0.00 0.00 0.00 5.73
629 691 1.404035 GCAAACCGGAGACAAAAGTGT 59.596 47.619 9.46 0.00 42.10 3.55
662 725 4.354155 CTGCGGGACAGTTCGAAA 57.646 55.556 0.00 0.00 41.86 3.46
763 896 5.799213 CCTCGAAATATTAAGGGCATCTCT 58.201 41.667 0.00 0.00 0.00 3.10
786 919 0.178068 TCAAGGGCATCTCTAACCGC 59.822 55.000 0.00 0.00 0.00 5.68
787 920 2.918712 ATCAAGGGCATCTCTAACCG 57.081 50.000 0.00 0.00 0.00 4.44
791 929 4.284490 AGCGAAATATCAAGGGCATCTCTA 59.716 41.667 0.00 0.00 0.00 2.43
830 996 7.872993 CCTGACTTCCGAATATTGCTAAGATAA 59.127 37.037 0.00 0.00 0.00 1.75
1342 1508 4.262506 GCTGTATGGGGTCAGGAAGTATAC 60.263 50.000 0.00 0.00 32.94 1.47
1422 1588 5.876460 ACAGAAAAGAAATGCAAGCAAAACT 59.124 32.000 0.00 0.00 0.00 2.66
1438 1605 4.461405 CAGCACGAAATCTCACAGAAAAG 58.539 43.478 0.00 0.00 0.00 2.27
1454 1621 3.242543 GGAAAATATCACTCTGCAGCACG 60.243 47.826 9.47 2.20 0.00 5.34
1464 1631 2.093658 AGACGGCGTGGAAAATATCACT 60.094 45.455 21.19 0.00 0.00 3.41
1478 1648 2.515912 GCATTCCTTTTTAAGACGGCG 58.484 47.619 4.80 4.80 0.00 6.46
1571 1742 0.252558 ACTCACCCCGGTAGGACAAT 60.253 55.000 0.00 0.00 41.02 2.71
1619 1795 2.200373 AACTACCACCTGCCATCAAC 57.800 50.000 0.00 0.00 0.00 3.18
1621 1797 2.513753 CAAAACTACCACCTGCCATCA 58.486 47.619 0.00 0.00 0.00 3.07
1644 1820 1.544246 GTGGCCCTGTCCAATTAACAC 59.456 52.381 0.00 0.00 37.96 3.32
1647 1823 2.042297 TGATGTGGCCCTGTCCAATTAA 59.958 45.455 0.00 0.00 37.96 1.40
1703 1880 5.829924 CCTGTAATAACATCAAAGAGCCCAT 59.170 40.000 0.00 0.00 34.37 4.00
1721 1898 8.478775 ACAAGAGTATATCATACAGCCTGTAA 57.521 34.615 8.93 0.00 36.31 2.41
1722 1899 8.478775 AACAAGAGTATATCATACAGCCTGTA 57.521 34.615 7.09 7.09 37.24 2.74
1723 1900 6.985653 ACAAGAGTATATCATACAGCCTGT 57.014 37.500 1.54 1.54 0.00 4.00
1774 1953 6.073112 ACAATGCCAATTTGCACTTGATAAAC 60.073 34.615 21.94 0.00 45.48 2.01
1781 1960 3.543665 ACAACAATGCCAATTTGCACTT 58.456 36.364 6.32 0.51 45.48 3.16
1835 2025 9.869844 CGATAAGCTCAAGATTATTAAAAGGTG 57.130 33.333 2.35 0.00 36.83 4.00
1836 2026 9.832445 TCGATAAGCTCAAGATTATTAAAAGGT 57.168 29.630 2.35 0.00 36.83 3.50
1846 2036 8.616076 CCAACTAAATTCGATAAGCTCAAGATT 58.384 33.333 0.00 0.00 0.00 2.40
1847 2037 7.770897 ACCAACTAAATTCGATAAGCTCAAGAT 59.229 33.333 0.00 0.00 0.00 2.40
1848 2038 7.103641 ACCAACTAAATTCGATAAGCTCAAGA 58.896 34.615 0.00 0.00 0.00 3.02
1849 2039 7.308782 ACCAACTAAATTCGATAAGCTCAAG 57.691 36.000 0.00 0.00 0.00 3.02
1850 2040 7.361713 CCAACCAACTAAATTCGATAAGCTCAA 60.362 37.037 0.00 0.00 0.00 3.02
1851 2041 6.093495 CCAACCAACTAAATTCGATAAGCTCA 59.907 38.462 0.00 0.00 0.00 4.26
1852 2042 6.093633 ACCAACCAACTAAATTCGATAAGCTC 59.906 38.462 0.00 0.00 0.00 4.09
1853 2043 5.944007 ACCAACCAACTAAATTCGATAAGCT 59.056 36.000 0.00 0.00 0.00 3.74
1854 2044 6.190954 ACCAACCAACTAAATTCGATAAGC 57.809 37.500 0.00 0.00 0.00 3.09
1855 2045 8.259049 TGTACCAACCAACTAAATTCGATAAG 57.741 34.615 0.00 0.00 0.00 1.73
1856 2046 8.670135 CATGTACCAACCAACTAAATTCGATAA 58.330 33.333 0.00 0.00 0.00 1.75
1916 2106 5.705905 AGAGAATACAAGCCTTTACCAACAC 59.294 40.000 0.00 0.00 0.00 3.32
1923 2113 7.903145 TCACACTAAGAGAATACAAGCCTTTA 58.097 34.615 0.00 0.00 0.00 1.85
1942 2135 0.534412 CTCGATGAAGGGCTCACACT 59.466 55.000 0.00 0.00 36.69 3.55
1960 2153 3.198417 CCTTTTAATGGCAATTGGCTCCT 59.802 43.478 29.53 17.18 44.01 3.69
2048 2245 1.831652 CGAGGACCAGCAGGGAAACT 61.832 60.000 0.00 0.00 41.15 2.66
2072 2269 7.175467 CCATGAAAATGCAATATCAGCTAGGTA 59.825 37.037 0.00 0.00 0.00 3.08
2115 2347 2.372264 ACTTGCTGAAATGGCGATGAT 58.628 42.857 0.00 0.00 0.00 2.45
2160 2392 3.912496 CCAGGAAGTGGTGTGATATCA 57.088 47.619 0.00 0.00 42.17 2.15
2206 2438 1.040339 TGGCACACCCCAACTTTGAC 61.040 55.000 0.00 0.00 33.59 3.18
2219 2451 3.388024 AGAACTTTAGACTGAGTGGCACA 59.612 43.478 21.41 0.00 0.00 4.57
2245 2477 2.374184 CGGCCCTTTTATGGATCAACA 58.626 47.619 0.00 0.00 0.00 3.33
2257 2489 0.323360 ACATGTATGTGCGGCCCTTT 60.323 50.000 0.00 0.00 40.03 3.11
2271 2503 9.753674 TCCTTGATAAAAAGAAGGATTACATGT 57.246 29.630 2.69 2.69 40.30 3.21
2288 2520 5.314718 ACATGATGCATCCTCCTTGATAA 57.685 39.130 23.67 1.25 0.00 1.75
2319 2551 5.733620 TGTAGAAGAACGGTGGAATTACT 57.266 39.130 0.00 0.00 0.00 2.24
2392 2624 2.023673 GCAAAGCTGGCACCACATATA 58.976 47.619 5.80 0.00 0.00 0.86
2406 2638 8.265165 AGGTGTAATAGTTAGTTAAGCAAAGC 57.735 34.615 0.00 0.00 0.00 3.51
2409 2641 7.820872 GGTGAGGTGTAATAGTTAGTTAAGCAA 59.179 37.037 0.00 0.00 0.00 3.91
2411 2643 6.760298 GGGTGAGGTGTAATAGTTAGTTAAGC 59.240 42.308 0.00 0.00 0.00 3.09
2416 2648 3.131755 GCGGGTGAGGTGTAATAGTTAGT 59.868 47.826 0.00 0.00 0.00 2.24
2429 2661 0.177836 TACATGTGATGCGGGTGAGG 59.822 55.000 9.11 0.00 0.00 3.86
2438 2670 7.481275 TGTATGCATACAAGTACATGTGATG 57.519 36.000 32.21 12.93 40.08 3.07
2642 2874 0.332972 ACCCAGGGATCCTTTTCTGC 59.667 55.000 14.54 0.00 0.00 4.26
2753 2985 3.448301 CCCAAGGAATCAGCAAGCAATAA 59.552 43.478 0.00 0.00 0.00 1.40
2885 3117 4.095334 GTCAAACATAATACCCGGGTGAAC 59.905 45.833 36.97 13.79 0.00 3.18
2944 3176 3.797039 TGAAATCAAGGTAGAGCATCCG 58.203 45.455 0.00 0.00 33.66 4.18
3111 3343 9.809096 ATAGACAAACTACATCTAGTGATTGTG 57.191 33.333 3.74 0.00 35.45 3.33
3232 3464 2.716424 CCCACCATAACCTCCACCATAT 59.284 50.000 0.00 0.00 0.00 1.78
3304 3536 2.123511 CCACCTTGGTTGTGGCCA 60.124 61.111 0.00 0.00 46.13 5.36
3418 3650 5.253096 GTCATAACCATAACCCCCTCCATAT 59.747 44.000 0.00 0.00 0.00 1.78
3485 3717 8.539674 CAACCTTGAATAACAGTAAGCAAAAAC 58.460 33.333 0.00 0.00 0.00 2.43
3585 3818 3.054065 ACCCAAAAAGGCATCCAAAAACA 60.054 39.130 0.00 0.00 35.39 2.83
3722 3974 1.674057 CCAGTTGCCTCTTCCTCGT 59.326 57.895 0.00 0.00 0.00 4.18
3769 4022 7.678947 ATTCATGCCTAAATAGACTGTATGC 57.321 36.000 0.00 0.00 0.00 3.14
3811 4064 5.428253 GAGTAAATGCACAAGATAGGTGGA 58.572 41.667 0.00 0.00 40.90 4.02
3850 4103 0.469331 CACTATGGGCGGAGGGAGTA 60.469 60.000 0.00 0.00 0.00 2.59
3851 4104 1.762460 CACTATGGGCGGAGGGAGT 60.762 63.158 0.00 0.00 0.00 3.85
3852 4105 0.469331 TACACTATGGGCGGAGGGAG 60.469 60.000 0.00 0.00 0.00 4.30
3853 4106 0.031917 TTACACTATGGGCGGAGGGA 60.032 55.000 0.00 0.00 0.00 4.20
3854 4107 0.834612 TTTACACTATGGGCGGAGGG 59.165 55.000 0.00 0.00 0.00 4.30
3855 4108 2.702592 TTTTACACTATGGGCGGAGG 57.297 50.000 0.00 0.00 0.00 4.30
3872 4125 9.196139 TCCGTCCCAAAATATAAGATCATTTTT 57.804 29.630 0.00 0.00 33.23 1.94
3873 4126 8.760980 TCCGTCCCAAAATATAAGATCATTTT 57.239 30.769 0.00 0.00 35.30 1.82
3874 4127 7.448469 CCTCCGTCCCAAAATATAAGATCATTT 59.552 37.037 0.00 0.00 0.00 2.32
3875 4128 6.942576 CCTCCGTCCCAAAATATAAGATCATT 59.057 38.462 0.00 0.00 0.00 2.57
3876 4129 6.476378 CCTCCGTCCCAAAATATAAGATCAT 58.524 40.000 0.00 0.00 0.00 2.45
3877 4130 5.221843 CCCTCCGTCCCAAAATATAAGATCA 60.222 44.000 0.00 0.00 0.00 2.92
3878 4131 5.012768 TCCCTCCGTCCCAAAATATAAGATC 59.987 44.000 0.00 0.00 0.00 2.75
3879 4132 4.911522 TCCCTCCGTCCCAAAATATAAGAT 59.088 41.667 0.00 0.00 0.00 2.40
3880 4133 4.300345 TCCCTCCGTCCCAAAATATAAGA 58.700 43.478 0.00 0.00 0.00 2.10
3881 4134 4.102681 ACTCCCTCCGTCCCAAAATATAAG 59.897 45.833 0.00 0.00 0.00 1.73
3882 4135 4.042174 ACTCCCTCCGTCCCAAAATATAA 58.958 43.478 0.00 0.00 0.00 0.98
3883 4136 3.660959 ACTCCCTCCGTCCCAAAATATA 58.339 45.455 0.00 0.00 0.00 0.86
3884 4137 2.488836 ACTCCCTCCGTCCCAAAATAT 58.511 47.619 0.00 0.00 0.00 1.28
3885 4138 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
3886 4139 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
3887 4140 1.626825 CTTACTCCCTCCGTCCCAAAA 59.373 52.381 0.00 0.00 0.00 2.44
3888 4141 1.272807 CTTACTCCCTCCGTCCCAAA 58.727 55.000 0.00 0.00 0.00 3.28
3889 4142 0.115745 ACTTACTCCCTCCGTCCCAA 59.884 55.000 0.00 0.00 0.00 4.12
3890 4143 1.002069 TACTTACTCCCTCCGTCCCA 58.998 55.000 0.00 0.00 0.00 4.37
3891 4144 1.753649 GTTACTTACTCCCTCCGTCCC 59.246 57.143 0.00 0.00 0.00 4.46
3892 4145 2.450476 TGTTACTTACTCCCTCCGTCC 58.550 52.381 0.00 0.00 0.00 4.79
3893 4146 4.732672 ATTGTTACTTACTCCCTCCGTC 57.267 45.455 0.00 0.00 0.00 4.79
3894 4147 6.803366 ATTATTGTTACTTACTCCCTCCGT 57.197 37.500 0.00 0.00 0.00 4.69
3895 4148 7.985752 AGAAATTATTGTTACTTACTCCCTCCG 59.014 37.037 0.00 0.00 0.00 4.63
3896 4149 9.110502 CAGAAATTATTGTTACTTACTCCCTCC 57.889 37.037 0.00 0.00 0.00 4.30
3897 4150 8.613482 GCAGAAATTATTGTTACTTACTCCCTC 58.387 37.037 0.00 0.00 0.00 4.30
3898 4151 8.329502 AGCAGAAATTATTGTTACTTACTCCCT 58.670 33.333 0.00 0.00 0.00 4.20
3899 4152 8.398665 CAGCAGAAATTATTGTTACTTACTCCC 58.601 37.037 0.00 0.00 0.00 4.30
3900 4153 7.910683 GCAGCAGAAATTATTGTTACTTACTCC 59.089 37.037 0.00 0.00 0.00 3.85
3901 4154 8.669243 AGCAGCAGAAATTATTGTTACTTACTC 58.331 33.333 0.00 0.00 0.00 2.59
3902 4155 8.454106 CAGCAGCAGAAATTATTGTTACTTACT 58.546 33.333 0.00 0.00 0.00 2.24
3903 4156 8.450964 TCAGCAGCAGAAATTATTGTTACTTAC 58.549 33.333 0.00 0.00 0.00 2.34
3970 4223 9.148104 GTAATTAAAACCTGTTCTATCGTCACT 57.852 33.333 0.00 0.00 0.00 3.41
4031 4285 4.336433 TGTGACTGAGCAAGGAAAGAAAAG 59.664 41.667 0.00 0.00 0.00 2.27
4040 4294 1.310933 GCCCATGTGACTGAGCAAGG 61.311 60.000 0.00 0.00 0.00 3.61
4057 4311 6.710295 TCTGAATGTGTATATACCACAATGCC 59.290 38.462 16.72 9.97 32.25 4.40
4153 4407 7.496529 ACACATGTGCATGGTCTAAATATAC 57.503 36.000 25.68 0.00 42.91 1.47
4169 4423 9.292846 CTTGGAAATGATTACAATACACATGTG 57.707 33.333 24.25 24.25 38.67 3.21
4179 4433 5.774690 AGTTCAGGCTTGGAAATGATTACAA 59.225 36.000 0.00 0.00 37.02 2.41
4235 4490 5.819379 TGCATCCTTTCTCTAAAGCACATAG 59.181 40.000 0.00 0.00 40.73 2.23
4909 5201 4.082463 TGAAGGTCTCTTTTGCAAAACGTT 60.082 37.500 20.46 17.68 32.52 3.99
4931 5223 5.447818 CCTTTCGTTGATTTAGCTAGGCTTG 60.448 44.000 0.00 0.00 40.44 4.01
4954 5246 1.450025 GAACTGGGTTTCGGATGTCC 58.550 55.000 0.00 0.00 0.00 4.02
5231 6778 9.802039 TTTCCAAATAAGGTTGTACAGTATTCT 57.198 29.630 0.00 0.00 0.00 2.40
5331 6878 5.464965 GCATCTTTTGCCAGAATCATTTG 57.535 39.130 0.00 0.00 46.15 2.32
5457 7004 3.126343 GCGATGTTCCCACGAAAAATACT 59.874 43.478 0.00 0.00 0.00 2.12
5458 7005 3.120130 TGCGATGTTCCCACGAAAAATAC 60.120 43.478 0.00 0.00 0.00 1.89
5459 7006 3.075148 TGCGATGTTCCCACGAAAAATA 58.925 40.909 0.00 0.00 0.00 1.40
5460 7007 1.883275 TGCGATGTTCCCACGAAAAAT 59.117 42.857 0.00 0.00 0.00 1.82
5461 7008 1.309950 TGCGATGTTCCCACGAAAAA 58.690 45.000 0.00 0.00 0.00 1.94
5463 7010 0.871722 CTTGCGATGTTCCCACGAAA 59.128 50.000 0.00 0.00 0.00 3.46
5645 7213 6.602410 TTTGATGCAATTGAGGATTAACCA 57.398 33.333 10.34 0.00 42.04 3.67
5669 7237 4.206375 TCCTGACTTCATTTTTGTGCAGA 58.794 39.130 0.00 0.00 0.00 4.26
5706 7274 9.877178 AATTCTCACTATTAGAACCTGTACTTG 57.123 33.333 0.00 0.00 35.87 3.16
5743 7311 9.350357 CTCACTAATTTTCATGTTCCAGATTTG 57.650 33.333 0.00 0.00 0.00 2.32



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

AutoCloner maintained by Alex Coulton.