Multiple sequence alignment - TraesCS2D01G038800

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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 TraesCS2D01G038800 chr2D 100.000 4850 0 0 1 4850 14257487 14262336 0.000000e+00 8957.0
1 TraesCS2D01G038800 chr2D 93.000 200 10 2 4300 4499 570156086 570156281 6.140000e-74 289.0
2 TraesCS2D01G038800 chr2D 92.090 177 12 1 683 859 516708484 516708310 1.040000e-61 248.0
3 TraesCS2D01G038800 chr2D 80.769 338 39 18 3767 4094 14266337 14266658 1.740000e-59 241.0
4 TraesCS2D01G038800 chr2D 88.832 197 16 5 689 881 602953956 602953762 2.260000e-58 237.0
5 TraesCS2D01G038800 chr2D 94.488 127 6 1 4094 4219 570155962 570156088 1.380000e-45 195.0
6 TraesCS2D01G038800 chr2D 91.150 113 4 2 4515 4627 570156597 570156703 1.090000e-31 148.0
7 TraesCS2D01G038800 chr2A 89.821 3291 176 60 273 3463 16553508 16556739 0.000000e+00 4074.0
8 TraesCS2D01G038800 chr2A 94.876 605 23 4 3468 4065 16556778 16557381 0.000000e+00 939.0
9 TraesCS2D01G038800 chr2A 87.393 468 42 13 1073 1536 481103077 481102623 5.560000e-144 521.0
10 TraesCS2D01G038800 chr2A 87.187 359 22 7 4515 4850 34762790 34763147 2.120000e-103 387.0
11 TraesCS2D01G038800 chr2A 93.000 200 13 1 4300 4499 34762307 34762505 1.710000e-74 291.0
12 TraesCS2D01G038800 chr2A 92.623 122 8 1 4094 4214 34762183 34762304 1.790000e-39 174.0
13 TraesCS2D01G038800 chr2A 100.000 88 0 0 4216 4303 207651879 207651966 3.880000e-36 163.0
14 TraesCS2D01G038800 chr2A 85.827 127 15 3 4094 4218 567566238 567566363 1.100000e-26 132.0
15 TraesCS2D01G038800 chr2B 87.681 2687 176 76 856 3463 26103506 26106116 0.000000e+00 2985.0
16 TraesCS2D01G038800 chr2B 93.785 531 33 0 3465 3995 26106156 26106686 0.000000e+00 798.0
17 TraesCS2D01G038800 chr2B 87.892 223 21 5 11 229 26102179 26102399 1.730000e-64 257.0
18 TraesCS2D01G038800 chr2B 88.298 94 8 3 602 692 26103414 26103507 5.130000e-20 110.0
19 TraesCS2D01G038800 chr3A 91.503 1224 63 25 2261 3455 724634927 724636138 0.000000e+00 1646.0
20 TraesCS2D01G038800 chr3A 88.000 525 29 14 1654 2160 724634355 724634863 1.500000e-164 590.0
21 TraesCS2D01G038800 chr3A 86.131 548 43 19 1009 1544 724633828 724634354 1.180000e-155 560.0
22 TraesCS2D01G038800 chr3A 88.323 471 43 11 3464 3926 724636180 724636646 5.480000e-154 555.0
23 TraesCS2D01G038800 chr3A 89.583 384 27 8 1717 2090 714722066 714721686 4.390000e-130 475.0
24 TraesCS2D01G038800 chr3B 90.711 1238 76 26 2261 3466 796546820 796545590 0.000000e+00 1613.0
25 TraesCS2D01G038800 chr3B 83.543 1191 87 47 1011 2159 796548014 796546891 0.000000e+00 1013.0
26 TraesCS2D01G038800 chr3B 87.885 487 46 13 3464 3942 796545561 796545080 1.180000e-155 560.0
27 TraesCS2D01G038800 chr3B 95.500 200 8 1 4300 4499 41040697 41040895 7.830000e-83 318.0
28 TraesCS2D01G038800 chr3B 94.536 183 8 2 4617 4798 41041619 41041800 1.030000e-71 281.0
29 TraesCS2D01G038800 chr3B 100.000 89 0 0 4216 4304 659068495 659068583 1.080000e-36 165.0
30 TraesCS2D01G038800 chr3B 90.722 97 7 2 593 688 796549552 796549457 1.420000e-25 128.0
31 TraesCS2D01G038800 chr3B 100.000 58 0 0 4793 4850 41042053 41042110 1.850000e-19 108.0
32 TraesCS2D01G038800 chr3B 83.898 118 12 5 4102 4215 776100478 776100592 6.640000e-19 106.0
33 TraesCS2D01G038800 chr3B 100.000 41 0 0 4563 4603 41041542 41041582 5.210000e-10 76.8
34 TraesCS2D01G038800 chr3D 87.853 1276 83 33 1014 2264 3504694 3505922 0.000000e+00 1432.0
35 TraesCS2D01G038800 chr3D 91.974 623 33 13 2854 3466 593346598 593345983 0.000000e+00 857.0
36 TraesCS2D01G038800 chr3D 89.159 618 39 18 2261 2861 593347372 593346766 0.000000e+00 745.0
37 TraesCS2D01G038800 chr3D 89.780 499 26 2 3464 3962 3506306 3506779 2.480000e-172 616.0
38 TraesCS2D01G038800 chr3D 88.358 481 42 12 3464 3937 593345954 593345481 2.530000e-157 566.0
39 TraesCS2D01G038800 chr3D 85.844 551 40 22 1003 1544 593348508 593347987 7.090000e-153 551.0
40 TraesCS2D01G038800 chr3D 91.775 231 19 0 3233 3463 3506044 3506274 6.060000e-84 322.0
41 TraesCS2D01G038800 chr3D 88.542 96 9 2 593 687 593410742 593410648 1.100000e-21 115.0
42 TraesCS2D01G038800 chr6D 87.226 1276 90 35 1014 2263 76563397 76562169 0.000000e+00 1386.0
43 TraesCS2D01G038800 chr6D 84.254 959 87 22 1324 2264 425432978 425433890 0.000000e+00 876.0
44 TraesCS2D01G038800 chr6D 95.591 499 22 0 3464 3962 76561784 76561286 0.000000e+00 800.0
45 TraesCS2D01G038800 chr6D 95.190 499 24 0 3464 3962 425434274 425434772 0.000000e+00 789.0
46 TraesCS2D01G038800 chr6D 93.860 228 14 0 3236 3463 76562043 76561816 1.290000e-90 344.0
47 TraesCS2D01G038800 chr6D 92.641 231 17 0 3233 3463 425434012 425434242 2.800000e-87 333.0
48 TraesCS2D01G038800 chr5A 89.103 468 34 14 1073 1536 431301962 431301508 2.530000e-157 566.0
49 TraesCS2D01G038800 chr5A 89.119 193 15 5 689 877 349787350 349787540 8.120000e-58 235.0
50 TraesCS2D01G038800 chr5A 95.918 98 1 2 4206 4302 76742185 76742090 6.500000e-34 156.0
51 TraesCS2D01G038800 chr5B 88.114 387 33 9 1714 2090 483302523 483302140 9.580000e-122 448.0
52 TraesCS2D01G038800 chr1A 88.301 359 18 14 4515 4850 468652080 468652437 4.520000e-110 409.0
53 TraesCS2D01G038800 chr1A 94.500 200 10 1 4300 4499 468651311 468651509 1.700000e-79 307.0
54 TraesCS2D01G038800 chr1A 87.402 127 13 3 4094 4218 527972727 527972852 5.060000e-30 143.0
55 TraesCS2D01G038800 chr1A 94.231 52 2 1 4795 4845 508553790 508553841 1.450000e-10 78.7
56 TraesCS2D01G038800 chr6A 86.908 359 23 12 4515 4850 337243444 337243087 9.850000e-102 381.0
57 TraesCS2D01G038800 chr6A 94.500 200 10 1 4300 4499 337243931 337243733 1.700000e-79 307.0
58 TraesCS2D01G038800 chr6A 92.529 174 10 2 689 861 222571242 222571413 3.750000e-61 246.0
59 TraesCS2D01G038800 chr5D 92.529 174 11 2 689 862 25040146 25039975 1.040000e-61 248.0
60 TraesCS2D01G038800 chr5D 85.572 201 18 6 4309 4499 393872796 393872597 2.960000e-47 200.0
61 TraesCS2D01G038800 chr5D 100.000 88 0 0 4215 4302 565714523 565714436 3.880000e-36 163.0
62 TraesCS2D01G038800 chr5D 98.889 90 1 0 4216 4305 201522892 201522981 1.400000e-35 161.0
63 TraesCS2D01G038800 chr4A 89.109 202 19 2 670 870 362068096 362067897 1.040000e-61 248.0
64 TraesCS2D01G038800 chr4B 92.486 173 12 1 686 858 53588006 53587835 3.750000e-61 246.0
65 TraesCS2D01G038800 chr7D 91.111 180 14 1 678 857 593376815 593376992 4.850000e-60 243.0
66 TraesCS2D01G038800 chr7D 85.714 210 19 6 4300 4499 509244029 509244237 1.370000e-50 211.0
67 TraesCS2D01G038800 chr7D 98.889 90 1 0 4212 4301 69811304 69811215 1.400000e-35 161.0
68 TraesCS2D01G038800 chr7D 96.875 96 2 1 4208 4303 503689658 503689752 5.020000e-35 159.0
69 TraesCS2D01G038800 chr7D 91.228 57 4 1 4795 4850 168786098 168786042 5.210000e-10 76.8
70 TraesCS2D01G038800 chr7D 97.143 35 1 0 428 462 534653830 534653864 5.240000e-05 60.2
71 TraesCS2D01G038800 chr1D 98.913 92 1 0 4209 4300 296407617 296407526 1.080000e-36 165.0
72 TraesCS2D01G038800 chr7B 98.901 91 1 0 4213 4303 482820129 482820039 3.880000e-36 163.0
73 TraesCS2D01G038800 chr7B 96.000 50 2 0 4798 4847 193724636 193724685 1.120000e-11 82.4
74 TraesCS2D01G038800 chr6B 86.614 127 14 3 4094 4218 172414413 172414538 2.350000e-28 137.0
75 TraesCS2D01G038800 chr6B 92.727 55 3 1 4795 4848 671921551 671921497 1.450000e-10 78.7
76 TraesCS2D01G038800 chr7A 92.982 57 3 1 4795 4850 171255553 171255497 1.120000e-11 82.4


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 TraesCS2D01G038800 chr2D 14257487 14262336 4849 False 8957.000000 8957 100.000000 1 4850 1 chr2D.!!$F1 4849
1 TraesCS2D01G038800 chr2D 570155962 570156703 741 False 210.666667 289 92.879333 4094 4627 3 chr2D.!!$F3 533
2 TraesCS2D01G038800 chr2A 16553508 16557381 3873 False 2506.500000 4074 92.348500 273 4065 2 chr2A.!!$F3 3792
3 TraesCS2D01G038800 chr2A 34762183 34763147 964 False 284.000000 387 90.936667 4094 4850 3 chr2A.!!$F4 756
4 TraesCS2D01G038800 chr2B 26102179 26106686 4507 False 1037.500000 2985 89.414000 11 3995 4 chr2B.!!$F1 3984
5 TraesCS2D01G038800 chr3A 724633828 724636646 2818 False 837.750000 1646 88.489250 1009 3926 4 chr3A.!!$F1 2917
6 TraesCS2D01G038800 chr3B 796545080 796549552 4472 True 828.500000 1613 88.215250 593 3942 4 chr3B.!!$R1 3349
7 TraesCS2D01G038800 chr3D 3504694 3506779 2085 False 790.000000 1432 89.802667 1014 3962 3 chr3D.!!$F1 2948
8 TraesCS2D01G038800 chr3D 593345481 593348508 3027 True 679.750000 857 88.833750 1003 3937 4 chr3D.!!$R2 2934
9 TraesCS2D01G038800 chr6D 76561286 76563397 2111 True 843.333333 1386 92.225667 1014 3962 3 chr6D.!!$R1 2948
10 TraesCS2D01G038800 chr6D 425432978 425434772 1794 False 666.000000 876 90.695000 1324 3962 3 chr6D.!!$F1 2638
11 TraesCS2D01G038800 chr1A 468651311 468652437 1126 False 358.000000 409 91.400500 4300 4850 2 chr1A.!!$F3 550
12 TraesCS2D01G038800 chr6A 337243087 337243931 844 True 344.000000 381 90.704000 4300 4850 2 chr6A.!!$R1 550

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
923 2053 0.253327 GTTGGACTCAAGGCCTAGGG 59.747 60.000 5.16 0.76 32.92 3.53 F
2169 4294 0.596600 TCTCCGTCTTGTGTTCGTGC 60.597 55.000 0.00 0.00 0.00 5.34 F
2475 4643 1.337703 CTTGCTTGCTAACTTGTGCCA 59.662 47.619 0.00 0.00 0.00 4.92 F
2481 4654 1.341852 TGCTAACTTGTGCCACTACGA 59.658 47.619 0.00 0.00 0.00 3.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2481 4654 0.037419 GGAATTGGGCAATGCAACGT 60.037 50.0 7.79 0.0 0.00 3.99 R
3293 5656 0.251787 GTGGCATCCCAAAGACCCTT 60.252 55.0 0.00 0.0 44.33 3.95 R
3537 5952 2.227388 GCCATCTTCAGTCACCTTGTTG 59.773 50.0 0.00 0.0 0.00 3.33 R
4023 6450 2.630098 GAGCAGGCACTCATACTGGATA 59.370 50.0 2.98 0.0 34.60 2.59 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
56 59 1.272807 AAAAATGCAGCTGAGCCCAT 58.727 45.000 20.43 8.41 0.00 4.00
66 69 4.079970 CAGCTGAGCCCATGAATGAATAT 58.920 43.478 8.42 0.00 0.00 1.28
74 77 6.006449 AGCCCATGAATGAATATTAGTCCAC 58.994 40.000 0.00 0.00 0.00 4.02
83 86 1.961793 TATTAGTCCACCGCAATGCC 58.038 50.000 0.00 0.00 0.00 4.40
89 92 2.642129 CACCGCAATGCCGAACAA 59.358 55.556 0.00 0.00 0.00 2.83
163 166 6.699575 ATGTGGAAAAGTATGAGTATTGGC 57.300 37.500 0.00 0.00 0.00 4.52
178 181 2.178912 TTGGCCACGACCTAGAAAAG 57.821 50.000 3.88 0.00 0.00 2.27
323 326 2.116736 AAGCACGTGGACAACATGCG 62.117 55.000 18.88 0.00 41.23 4.73
344 347 5.051039 TGCGCATTTTATACGAGTGATCTTC 60.051 40.000 5.66 0.00 0.00 2.87
717 1829 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
719 1831 6.260271 CCCTCCGTTCCTAAATATTTGTCTTC 59.740 42.308 11.05 0.00 0.00 2.87
796 1908 9.890629 TTAGACTGTATATTCACTCATTTTGCT 57.109 29.630 0.00 0.00 0.00 3.91
797 1909 8.798859 AGACTGTATATTCACTCATTTTGCTT 57.201 30.769 0.00 0.00 0.00 3.91
798 1910 8.887717 AGACTGTATATTCACTCATTTTGCTTC 58.112 33.333 0.00 0.00 0.00 3.86
799 1911 8.565896 ACTGTATATTCACTCATTTTGCTTCA 57.434 30.769 0.00 0.00 0.00 3.02
800 1912 9.182214 ACTGTATATTCACTCATTTTGCTTCAT 57.818 29.630 0.00 0.00 0.00 2.57
803 1915 9.586150 GTATATTCACTCATTTTGCTTCATACG 57.414 33.333 0.00 0.00 0.00 3.06
804 1916 5.940192 TTCACTCATTTTGCTTCATACGT 57.060 34.783 0.00 0.00 0.00 3.57
805 1917 7.609760 ATTCACTCATTTTGCTTCATACGTA 57.390 32.000 0.00 0.00 0.00 3.57
823 1935 7.870954 TCATACGTAGTCAGTTGTTGAAATCTT 59.129 33.333 0.08 0.00 43.93 2.40
852 1964 7.625828 AAGACAAATATTTAGGAACGGAAGG 57.374 36.000 0.00 0.00 0.00 3.46
865 1995 4.440387 GGAACGGAAGGAGTAGATGAGAAC 60.440 50.000 0.00 0.00 0.00 3.01
872 2002 7.413438 CGGAAGGAGTAGATGAGAACAAAAATG 60.413 40.741 0.00 0.00 0.00 2.32
876 2006 6.259550 AGTAGATGAGAACAAAAATGTGGC 57.740 37.500 0.00 0.00 0.00 5.01
896 2026 2.158957 GCTTTGGATCAGACGGACCATA 60.159 50.000 0.00 0.00 32.31 2.74
897 2027 3.681594 GCTTTGGATCAGACGGACCATAA 60.682 47.826 0.00 0.00 32.31 1.90
902 2032 4.058817 GGATCAGACGGACCATAATTCAC 58.941 47.826 0.00 0.00 0.00 3.18
923 2053 0.253327 GTTGGACTCAAGGCCTAGGG 59.747 60.000 5.16 0.76 32.92 3.53
929 2059 1.581149 ACTCAAGGCCTAGGGGAGTAT 59.419 52.381 21.16 4.85 37.08 2.12
933 2063 3.166679 CAAGGCCTAGGGGAGTATAGAC 58.833 54.545 5.16 0.00 33.58 2.59
934 2064 2.440309 AGGCCTAGGGGAGTATAGACA 58.560 52.381 1.29 0.00 33.58 3.41
935 2065 2.380590 AGGCCTAGGGGAGTATAGACAG 59.619 54.545 1.29 0.00 33.58 3.51
984 2117 1.066358 GTGTTAGGGTTTCCTCCTCCG 60.066 57.143 0.00 0.00 43.66 4.63
987 2120 0.976073 TAGGGTTTCCTCCTCCGCTG 60.976 60.000 0.00 0.00 43.66 5.18
991 2124 1.003355 TTTCCTCCTCCGCTGCAAG 60.003 57.895 0.00 0.00 0.00 4.01
1006 2985 1.678635 CAAGCGCCTTCCAATCCCA 60.679 57.895 2.29 0.00 0.00 4.37
1007 2986 1.076549 AAGCGCCTTCCAATCCCAA 59.923 52.632 2.29 0.00 0.00 4.12
1013 2992 0.936691 CCTTCCAATCCCAATCCCCT 59.063 55.000 0.00 0.00 0.00 4.79
1553 3573 1.197492 CGCATCAAAGTGTAAGCAGCA 59.803 47.619 0.00 0.00 0.00 4.41
1556 3576 1.965935 TCAAAGTGTAAGCAGCAGCA 58.034 45.000 3.17 0.00 45.49 4.41
1558 3578 1.875514 CAAAGTGTAAGCAGCAGCAGA 59.124 47.619 3.17 0.00 45.49 4.26
1623 3670 1.611977 TCCTGACGACGAATCTTGTGT 59.388 47.619 0.00 0.00 0.00 3.72
1638 3685 1.734117 GTGTTTCCGCTGCCAATGC 60.734 57.895 0.00 0.00 38.26 3.56
1878 3952 4.641645 CAGAAGGGGTGCGGCACA 62.642 66.667 31.74 0.00 35.86 4.57
1879 3953 4.335647 AGAAGGGGTGCGGCACAG 62.336 66.667 31.74 0.00 35.86 3.66
1881 3955 4.643387 AAGGGGTGCGGCACAGAC 62.643 66.667 31.74 21.03 35.86 3.51
1939 4025 2.415168 CCACTGTGTAAGTAACATGGCG 59.585 50.000 7.08 0.00 41.10 5.69
1940 4026 2.415168 CACTGTGTAAGTAACATGGCGG 59.585 50.000 0.00 0.00 41.10 6.13
1941 4027 2.300723 ACTGTGTAAGTAACATGGCGGA 59.699 45.455 0.00 0.00 41.10 5.54
1942 4028 3.055385 ACTGTGTAAGTAACATGGCGGAT 60.055 43.478 0.00 0.00 41.10 4.18
1954 4049 4.326826 ACATGGCGGATTTATACTGATGG 58.673 43.478 0.00 0.00 0.00 3.51
1958 4053 5.630121 TGGCGGATTTATACTGATGGAATT 58.370 37.500 0.00 0.00 0.00 2.17
2026 4130 4.574828 TCAAGTTTCTGAACAAGTACCTGC 59.425 41.667 0.00 0.00 38.26 4.85
2052 4156 2.819667 CGATGGATCGGCTGATGAC 58.180 57.895 14.17 6.31 45.93 3.06
2143 4254 5.306114 TCTCTATCAGGTACATCCTTCGA 57.694 43.478 0.00 0.00 45.67 3.71
2169 4294 0.596600 TCTCCGTCTTGTGTTCGTGC 60.597 55.000 0.00 0.00 0.00 5.34
2208 4343 5.688176 GGAGACGTAATGCTCTTATGAGTTC 59.312 44.000 7.41 0.00 42.13 3.01
2215 4350 6.841443 AATGCTCTTATGAGTTCGATTCTG 57.159 37.500 7.41 0.00 42.13 3.02
2227 4362 2.610433 TCGATTCTGTGTGAGTGATGC 58.390 47.619 0.00 0.00 0.00 3.91
2230 4365 3.373130 CGATTCTGTGTGAGTGATGCATT 59.627 43.478 0.00 0.00 0.00 3.56
2351 4511 3.619419 TGCTCACATTAGCCTGCAAATA 58.381 40.909 0.00 0.00 42.05 1.40
2352 4512 4.209538 TGCTCACATTAGCCTGCAAATAT 58.790 39.130 0.00 0.00 42.05 1.28
2370 4530 9.995003 TGCAAATATTTAATCTTGTCAACCTTT 57.005 25.926 0.00 0.00 0.00 3.11
2411 4577 2.165641 CAGAGCATGCCAACATTGTGAT 59.834 45.455 15.66 0.00 32.87 3.06
2415 4581 2.861935 GCATGCCAACATTGTGATAAGC 59.138 45.455 6.36 0.00 32.87 3.09
2416 4582 3.676598 GCATGCCAACATTGTGATAAGCA 60.677 43.478 6.36 0.00 32.87 3.91
2417 4583 4.689071 CATGCCAACATTGTGATAAGCAT 58.311 39.130 0.00 0.00 40.15 3.79
2418 4584 4.112716 TGCCAACATTGTGATAAGCATG 57.887 40.909 0.00 0.00 0.00 4.06
2419 4585 3.119065 TGCCAACATTGTGATAAGCATGG 60.119 43.478 0.00 0.00 0.00 3.66
2424 4590 2.057137 TTGTGATAAGCATGGCCCTC 57.943 50.000 0.00 0.00 0.00 4.30
2446 4612 5.410067 TCACAAGCTTTCTTCTTTTGGTTG 58.590 37.500 0.00 0.00 40.54 3.77
2455 4621 5.982890 TCTTCTTTTGGTTGGATGGATTC 57.017 39.130 0.00 0.00 0.00 2.52
2462 4628 2.827322 TGGTTGGATGGATTCTTGCTTG 59.173 45.455 0.00 0.00 0.00 4.01
2464 4630 2.494870 GTTGGATGGATTCTTGCTTGCT 59.505 45.455 0.00 0.00 0.00 3.91
2475 4643 1.337703 CTTGCTTGCTAACTTGTGCCA 59.662 47.619 0.00 0.00 0.00 4.92
2481 4654 1.341852 TGCTAACTTGTGCCACTACGA 59.658 47.619 0.00 0.00 0.00 3.43
2482 4655 1.725164 GCTAACTTGTGCCACTACGAC 59.275 52.381 0.00 0.00 0.00 4.34
2483 4656 1.983605 CTAACTTGTGCCACTACGACG 59.016 52.381 0.00 0.00 0.00 5.12
2559 4733 5.335191 GCCAACAGTAGGTTCTGAAATTCTG 60.335 44.000 0.00 0.85 37.72 3.02
2633 4808 3.556999 TGCCAGTTAAAAACCTAGCACA 58.443 40.909 0.00 0.00 0.00 4.57
2779 4963 6.613271 TGAAGATATTCCTTACTCAGAGGCTT 59.387 38.462 1.53 0.00 34.17 4.35
2815 4999 4.795268 CGTTTCAGACTGCTAACTCTACA 58.205 43.478 14.40 0.00 0.00 2.74
2865 5224 7.573710 TGGTGAACCAATACTAGCAATTCTAT 58.426 34.615 0.00 0.00 44.35 1.98
2893 5252 8.806429 TGCTTCAACTTTTGGATATCTAATGA 57.194 30.769 1.98 0.98 0.00 2.57
2933 5293 3.008923 TGGTTCATGAGGAGTGCATAACA 59.991 43.478 0.00 0.00 0.00 2.41
3021 5381 5.709966 CAATTACAAAAGCCCTTGAGGTAC 58.290 41.667 2.55 0.00 38.26 3.34
3208 5571 4.842531 TGTCAGGTATTCATGTCCACAT 57.157 40.909 0.00 0.00 36.96 3.21
3251 5614 6.220726 ACAGTGTTATGCTTTCCTTTTTGT 57.779 33.333 0.00 0.00 0.00 2.83
3265 5628 9.256477 CTTTCCTTTTTGTTTAATACTTGGTCC 57.744 33.333 0.00 0.00 0.00 4.46
3399 5769 6.915544 TCAGTAGATAATTTTCAGCTGCAG 57.084 37.500 10.11 10.11 0.00 4.41
3537 5952 2.754552 TGCTATCAACACAATCCAAGCC 59.245 45.455 0.00 0.00 0.00 4.35
3770 6188 3.658757 TTTGTAGACAAAAGCCATGCC 57.341 42.857 5.36 0.00 42.26 4.40
3802 6225 4.389077 GCAGTTACTTGTTACAGAATCGCT 59.611 41.667 0.00 0.00 0.00 4.93
3816 6239 5.235186 ACAGAATCGCTATTGTTCATACTGC 59.765 40.000 0.00 0.00 0.00 4.40
3890 6317 9.520204 GGGTTATTGAGAATTTGTATCATGTTG 57.480 33.333 0.00 0.00 0.00 3.33
3939 6366 2.485426 CTGGATGTCGTGTGCTGAAATT 59.515 45.455 0.00 0.00 0.00 1.82
3996 6423 7.335673 TCATCGTTTCCTGCAATAATTGTCTTA 59.664 33.333 0.00 0.00 0.00 2.10
3997 6424 7.072177 TCGTTTCCTGCAATAATTGTCTTAG 57.928 36.000 0.00 0.00 0.00 2.18
4008 6435 7.809806 GCAATAATTGTCTTAGAAGCAAGTTGT 59.190 33.333 4.48 0.00 0.00 3.32
4012 6439 5.484173 TGTCTTAGAAGCAAGTTGTGTTG 57.516 39.130 4.48 0.00 0.00 3.33
4023 6450 4.447389 GCAAGTTGTGTTGTGAGTTTGTTT 59.553 37.500 4.48 0.00 0.00 2.83
4033 6460 7.803189 GTGTTGTGAGTTTGTTTATCCAGTATG 59.197 37.037 0.00 0.00 0.00 2.39
4034 6461 7.717436 TGTTGTGAGTTTGTTTATCCAGTATGA 59.283 33.333 0.00 0.00 39.69 2.15
4035 6462 7.905604 TGTGAGTTTGTTTATCCAGTATGAG 57.094 36.000 0.00 0.00 39.69 2.90
4036 6463 7.450074 TGTGAGTTTGTTTATCCAGTATGAGT 58.550 34.615 0.00 0.00 39.69 3.41
4037 6464 7.387673 TGTGAGTTTGTTTATCCAGTATGAGTG 59.612 37.037 0.00 0.00 39.69 3.51
4038 6465 6.371548 TGAGTTTGTTTATCCAGTATGAGTGC 59.628 38.462 0.00 0.00 39.69 4.40
4049 6483 4.445453 CAGTATGAGTGCCTGCTCAAATA 58.555 43.478 6.79 0.00 46.93 1.40
4068 6502 7.145985 TCAAATAGATTGAGCGTAGTATCACC 58.854 38.462 0.00 0.00 43.08 4.02
4069 6503 6.650427 AATAGATTGAGCGTAGTATCACCA 57.350 37.500 0.00 0.00 0.00 4.17
4070 6504 6.650427 ATAGATTGAGCGTAGTATCACCAA 57.350 37.500 0.00 0.00 0.00 3.67
4071 6505 4.683832 AGATTGAGCGTAGTATCACCAAC 58.316 43.478 0.00 0.00 0.00 3.77
4072 6506 4.402793 AGATTGAGCGTAGTATCACCAACT 59.597 41.667 0.00 0.00 0.00 3.16
4073 6507 3.503827 TGAGCGTAGTATCACCAACTG 57.496 47.619 0.00 0.00 0.00 3.16
4074 6508 2.823747 TGAGCGTAGTATCACCAACTGT 59.176 45.455 0.00 0.00 0.00 3.55
4075 6509 3.257375 TGAGCGTAGTATCACCAACTGTT 59.743 43.478 0.00 0.00 0.00 3.16
4076 6510 4.243270 GAGCGTAGTATCACCAACTGTTT 58.757 43.478 0.00 0.00 0.00 2.83
4077 6511 3.994392 AGCGTAGTATCACCAACTGTTTG 59.006 43.478 0.00 0.00 0.00 2.93
4078 6512 3.991773 GCGTAGTATCACCAACTGTTTGA 59.008 43.478 0.00 0.00 34.24 2.69
4079 6513 4.091509 GCGTAGTATCACCAACTGTTTGAG 59.908 45.833 0.00 0.00 34.24 3.02
4080 6514 5.227908 CGTAGTATCACCAACTGTTTGAGT 58.772 41.667 0.00 0.00 34.24 3.41
4081 6515 5.345202 CGTAGTATCACCAACTGTTTGAGTC 59.655 44.000 0.00 0.00 34.24 3.36
4082 6516 5.552870 AGTATCACCAACTGTTTGAGTCT 57.447 39.130 0.00 0.00 34.24 3.24
4083 6517 5.542779 AGTATCACCAACTGTTTGAGTCTC 58.457 41.667 0.00 0.00 34.24 3.36
4084 6518 4.696479 ATCACCAACTGTTTGAGTCTCT 57.304 40.909 0.65 0.00 34.24 3.10
4085 6519 4.060038 TCACCAACTGTTTGAGTCTCTC 57.940 45.455 0.65 0.00 34.24 3.20
4086 6520 3.450817 TCACCAACTGTTTGAGTCTCTCA 59.549 43.478 0.65 0.00 38.87 3.27
4087 6521 4.081142 TCACCAACTGTTTGAGTCTCTCAA 60.081 41.667 7.92 7.92 46.93 3.02
4096 6530 3.464720 TGAGTCTCTCAATGAGGGTCT 57.535 47.619 9.56 9.56 42.86 3.85
4097 6531 3.784178 TGAGTCTCTCAATGAGGGTCTT 58.216 45.455 10.98 0.00 42.86 3.01
4104 6538 8.166726 AGTCTCTCAATGAGGGTCTTAATTTTT 58.833 33.333 10.28 0.00 42.86 1.94
4202 6636 5.185056 ACTTGCGTCCATTTTAAGCCTTAAT 59.815 36.000 0.00 0.00 0.00 1.40
4218 6652 8.823220 AAGCCTTAATGGTGTTAAATGATACT 57.177 30.769 0.00 0.00 38.35 2.12
4219 6653 8.451908 AGCCTTAATGGTGTTAAATGATACTC 57.548 34.615 0.00 0.00 38.35 2.59
4220 6654 7.502561 AGCCTTAATGGTGTTAAATGATACTCC 59.497 37.037 0.00 0.00 38.35 3.85
4221 6655 7.255486 GCCTTAATGGTGTTAAATGATACTCCC 60.255 40.741 0.00 0.00 38.35 4.30
4222 6656 7.998964 CCTTAATGGTGTTAAATGATACTCCCT 59.001 37.037 0.00 0.00 0.00 4.20
4223 6657 8.974060 TTAATGGTGTTAAATGATACTCCCTC 57.026 34.615 0.00 0.00 0.00 4.30
4224 6658 6.831664 ATGGTGTTAAATGATACTCCCTCT 57.168 37.500 0.00 0.00 0.00 3.69
4225 6659 5.989477 TGGTGTTAAATGATACTCCCTCTG 58.011 41.667 0.00 0.00 0.00 3.35
4226 6660 5.487488 TGGTGTTAAATGATACTCCCTCTGT 59.513 40.000 0.00 0.00 0.00 3.41
4227 6661 6.670464 TGGTGTTAAATGATACTCCCTCTGTA 59.330 38.462 0.00 0.00 0.00 2.74
4228 6662 7.181305 TGGTGTTAAATGATACTCCCTCTGTAA 59.819 37.037 0.00 0.00 0.00 2.41
4229 6663 8.044908 GGTGTTAAATGATACTCCCTCTGTAAA 58.955 37.037 0.00 0.00 0.00 2.01
4230 6664 8.880750 GTGTTAAATGATACTCCCTCTGTAAAC 58.119 37.037 0.00 0.00 0.00 2.01
4231 6665 8.822805 TGTTAAATGATACTCCCTCTGTAAACT 58.177 33.333 0.00 0.00 0.00 2.66
4242 6676 9.939424 ACTCCCTCTGTAAACTAATATAAGAGT 57.061 33.333 0.00 0.00 0.00 3.24
4244 6678 9.710818 TCCCTCTGTAAACTAATATAAGAGTGT 57.289 33.333 0.00 0.00 0.00 3.55
4294 6728 9.490379 AAATGCTCTTATATTAGTTTACGGAGG 57.510 33.333 0.00 0.00 0.00 4.30
4295 6729 6.989659 TGCTCTTATATTAGTTTACGGAGGG 58.010 40.000 0.00 0.00 0.00 4.30
4296 6730 6.779049 TGCTCTTATATTAGTTTACGGAGGGA 59.221 38.462 0.00 0.00 0.00 4.20
4297 6731 7.039923 TGCTCTTATATTAGTTTACGGAGGGAG 60.040 40.741 0.00 0.00 0.00 4.30
4298 6732 7.039853 GCTCTTATATTAGTTTACGGAGGGAGT 60.040 40.741 0.00 0.00 0.00 3.85
4349 6783 5.179182 GGTGGCATGTGACCAAAATTTTAAG 59.821 40.000 2.44 0.94 39.39 1.85
4472 6906 3.650281 ACTCATGGAATGCATGTACCA 57.350 42.857 14.23 18.32 46.21 3.25
4476 6910 5.046288 TCATGGAATGCATGTACCACATA 57.954 39.130 18.36 7.96 46.21 2.29
4499 6933 9.923143 CATAACAATGGCTGATCAATTGATTAT 57.077 29.630 21.57 16.35 34.37 1.28
4527 7554 6.931838 TGACGGTATAGTGAGATTTTGTTCT 58.068 36.000 0.00 0.00 0.00 3.01
4593 7620 4.349342 GGATGTGAGTAGGGATCAGGAAAT 59.651 45.833 0.00 0.00 0.00 2.17
4601 7628 7.037586 TGAGTAGGGATCAGGAAATACTGTTTT 60.038 37.037 0.00 0.00 39.48 2.43
4602 7629 8.388656 AGTAGGGATCAGGAAATACTGTTTTA 57.611 34.615 0.00 0.00 39.48 1.52
4603 7630 8.265764 AGTAGGGATCAGGAAATACTGTTTTAC 58.734 37.037 0.00 0.00 39.48 2.01
4604 7631 7.027874 AGGGATCAGGAAATACTGTTTTACA 57.972 36.000 0.00 0.00 39.48 2.41
4635 7690 2.136878 CCACAGGCCTAGGAGCGAT 61.137 63.158 14.75 0.00 0.00 4.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
56 59 5.029807 TGCGGTGGACTAATATTCATTCA 57.970 39.130 0.00 0.00 0.00 2.57
66 69 1.743623 CGGCATTGCGGTGGACTAA 60.744 57.895 7.96 0.00 0.00 2.24
74 77 0.801836 GGAATTGTTCGGCATTGCGG 60.802 55.000 9.74 9.74 0.00 5.69
105 108 6.823689 AGCATACAAAAGACTCCGACATTTAT 59.176 34.615 0.00 0.00 0.00 1.40
106 109 6.170506 AGCATACAAAAGACTCCGACATTTA 58.829 36.000 0.00 0.00 0.00 1.40
162 165 1.275573 ACCTCTTTTCTAGGTCGTGGC 59.724 52.381 0.00 0.00 44.20 5.01
163 166 3.679824 AACCTCTTTTCTAGGTCGTGG 57.320 47.619 0.00 0.00 46.85 4.94
323 326 6.480320 ACAGGAAGATCACTCGTATAAAATGC 59.520 38.462 0.00 0.00 0.00 3.56
599 1285 5.710513 ATGAAATGTCAAACAGCTTAGCA 57.289 34.783 7.07 0.00 37.30 3.49
639 1326 8.885494 TCTTAATTGTTTGAGGTTTTGGAATG 57.115 30.769 0.00 0.00 0.00 2.67
717 1829 9.581289 TGGTAGTCCATTTGAAATCTTTAAGAA 57.419 29.630 0.00 0.00 39.03 2.52
719 1831 8.792633 TGTGGTAGTCCATTTGAAATCTTTAAG 58.207 33.333 0.00 0.00 46.20 1.85
779 1891 8.213518 ACGTATGAAGCAAAATGAGTGAATAT 57.786 30.769 0.00 0.00 0.00 1.28
782 1894 5.940192 ACGTATGAAGCAAAATGAGTGAA 57.060 34.783 0.00 0.00 0.00 3.18
783 1895 6.163476 ACTACGTATGAAGCAAAATGAGTGA 58.837 36.000 0.00 0.00 0.00 3.41
784 1896 6.090763 TGACTACGTATGAAGCAAAATGAGTG 59.909 38.462 0.00 0.00 0.00 3.51
785 1897 6.163476 TGACTACGTATGAAGCAAAATGAGT 58.837 36.000 0.00 0.00 0.00 3.41
786 1898 6.311445 ACTGACTACGTATGAAGCAAAATGAG 59.689 38.462 0.00 0.00 0.00 2.90
787 1899 6.163476 ACTGACTACGTATGAAGCAAAATGA 58.837 36.000 0.00 0.00 0.00 2.57
788 1900 6.408858 ACTGACTACGTATGAAGCAAAATG 57.591 37.500 0.00 0.00 0.00 2.32
789 1901 6.426937 ACAACTGACTACGTATGAAGCAAAAT 59.573 34.615 0.00 0.00 0.00 1.82
790 1902 5.756347 ACAACTGACTACGTATGAAGCAAAA 59.244 36.000 0.00 0.00 0.00 2.44
791 1903 5.294356 ACAACTGACTACGTATGAAGCAAA 58.706 37.500 0.00 0.00 0.00 3.68
792 1904 4.878439 ACAACTGACTACGTATGAAGCAA 58.122 39.130 0.00 0.00 0.00 3.91
793 1905 4.514781 ACAACTGACTACGTATGAAGCA 57.485 40.909 0.00 0.00 0.00 3.91
794 1906 4.921515 TCAACAACTGACTACGTATGAAGC 59.078 41.667 0.00 0.00 0.00 3.86
795 1907 7.402811 TTTCAACAACTGACTACGTATGAAG 57.597 36.000 0.00 0.00 32.21 3.02
796 1908 7.870954 AGATTTCAACAACTGACTACGTATGAA 59.129 33.333 0.00 0.00 32.21 2.57
797 1909 7.375834 AGATTTCAACAACTGACTACGTATGA 58.624 34.615 0.00 0.00 32.21 2.15
798 1910 7.582435 AGATTTCAACAACTGACTACGTATG 57.418 36.000 0.00 0.00 32.21 2.39
799 1911 8.603242 AAAGATTTCAACAACTGACTACGTAT 57.397 30.769 0.00 0.00 32.21 3.06
800 1912 9.188588 CTAAAGATTTCAACAACTGACTACGTA 57.811 33.333 0.00 0.00 32.21 3.57
801 1913 6.920569 AAAGATTTCAACAACTGACTACGT 57.079 33.333 0.00 0.00 32.21 3.57
802 1914 8.294341 TCTAAAGATTTCAACAACTGACTACG 57.706 34.615 0.00 0.00 32.21 3.51
805 1917 9.396022 TCTTTCTAAAGATTTCAACAACTGACT 57.604 29.630 1.00 0.00 39.95 3.41
823 1935 9.947433 TCCGTTCCTAAATATTTGTCTTTCTAA 57.053 29.630 11.05 0.00 0.00 2.10
848 1960 8.233190 CACATTTTTGTTCTCATCTACTCCTTC 58.767 37.037 0.00 0.00 0.00 3.46
852 1964 6.150140 AGCCACATTTTTGTTCTCATCTACTC 59.850 38.462 0.00 0.00 0.00 2.59
865 1995 4.687483 GTCTGATCCAAAGCCACATTTTTG 59.313 41.667 0.00 0.00 34.79 2.44
872 2002 0.036388 TCCGTCTGATCCAAAGCCAC 60.036 55.000 0.00 0.00 0.00 5.01
876 2006 2.698855 ATGGTCCGTCTGATCCAAAG 57.301 50.000 0.00 0.00 33.55 2.77
896 2026 2.504367 CCTTGAGTCCAACCGTGAATT 58.496 47.619 0.00 0.00 0.00 2.17
897 2027 1.882352 GCCTTGAGTCCAACCGTGAAT 60.882 52.381 0.00 0.00 0.00 2.57
902 2032 0.108138 CTAGGCCTTGAGTCCAACCG 60.108 60.000 12.58 0.00 0.00 4.44
923 2053 4.517453 CAGGTCAGTAGCTGTCTATACTCC 59.483 50.000 0.00 0.00 44.52 3.85
934 2064 2.294078 GGCCCACAGGTCAGTAGCT 61.294 63.158 0.00 0.00 37.86 3.32
935 2065 2.269241 GGCCCACAGGTCAGTAGC 59.731 66.667 0.00 0.00 37.86 3.58
984 2117 2.879039 GATTGGAAGGCGCTTGCAGC 62.879 60.000 7.64 4.18 42.27 5.25
987 2120 2.491621 GGATTGGAAGGCGCTTGC 59.508 61.111 7.64 0.00 38.11 4.01
991 2124 1.735973 GATTGGGATTGGAAGGCGC 59.264 57.895 0.00 0.00 0.00 6.53
992 2125 1.109323 GGGATTGGGATTGGAAGGCG 61.109 60.000 0.00 0.00 0.00 5.52
993 2126 0.760567 GGGGATTGGGATTGGAAGGC 60.761 60.000 0.00 0.00 0.00 4.35
994 2127 0.936691 AGGGGATTGGGATTGGAAGG 59.063 55.000 0.00 0.00 0.00 3.46
995 2128 1.133356 GGAGGGGATTGGGATTGGAAG 60.133 57.143 0.00 0.00 0.00 3.46
996 2129 0.933700 GGAGGGGATTGGGATTGGAA 59.066 55.000 0.00 0.00 0.00 3.53
997 2130 0.047802 AGGAGGGGATTGGGATTGGA 59.952 55.000 0.00 0.00 0.00 3.53
998 2131 0.480252 GAGGAGGGGATTGGGATTGG 59.520 60.000 0.00 0.00 0.00 3.16
999 2132 1.423161 GAGAGGAGGGGATTGGGATTG 59.577 57.143 0.00 0.00 0.00 2.67
1000 2133 1.700576 GGAGAGGAGGGGATTGGGATT 60.701 57.143 0.00 0.00 0.00 3.01
1001 2134 0.104197 GGAGAGGAGGGGATTGGGAT 60.104 60.000 0.00 0.00 0.00 3.85
1006 2985 0.565674 GAGAGGGAGAGGAGGGGATT 59.434 60.000 0.00 0.00 0.00 3.01
1007 2986 1.376249 GGAGAGGGAGAGGAGGGGAT 61.376 65.000 0.00 0.00 0.00 3.85
1013 2992 1.585651 GGAGTGGGAGAGGGAGAGGA 61.586 65.000 0.00 0.00 0.00 3.71
1553 3573 3.474570 GGGATGGTCGCCTCTGCT 61.475 66.667 0.00 0.00 34.43 4.24
1556 3576 3.474570 GCAGGGATGGTCGCCTCT 61.475 66.667 0.00 0.00 0.00 3.69
1638 3685 0.963856 ACAGGCTGCACACATCCATG 60.964 55.000 15.89 0.00 34.33 3.66
1698 3754 0.107654 GCGCCTTCCTGTAGACCAAT 60.108 55.000 0.00 0.00 0.00 3.16
1977 4081 3.087031 CTCCTTGGTCATGCTGTCAATT 58.913 45.455 0.00 0.00 0.00 2.32
2143 4254 3.685139 ACACAAGACGGAGATGTGAAT 57.315 42.857 16.33 0.00 45.61 2.57
2181 4314 4.588951 TCATAAGAGCATTACGTCTCCCAT 59.411 41.667 0.00 0.00 0.00 4.00
2190 4323 7.436673 ACAGAATCGAACTCATAAGAGCATTAC 59.563 37.037 0.00 0.00 46.09 1.89
2208 4343 2.340337 TGCATCACTCACACAGAATCG 58.660 47.619 0.00 0.00 0.00 3.34
2227 4362 6.215121 TGTTCTGGTACAAAGAATGCAAATG 58.785 36.000 11.96 0.00 38.70 2.32
2230 4365 5.534278 TCATGTTCTGGTACAAAGAATGCAA 59.466 36.000 11.96 2.35 38.70 4.08
2335 4495 9.754382 CAAGATTAAATATTTGCAGGCTAATGT 57.246 29.630 11.05 2.14 0.00 2.71
2338 4498 8.965819 TGACAAGATTAAATATTTGCAGGCTAA 58.034 29.630 11.05 0.00 0.00 3.09
2394 4554 2.861935 GCTTATCACAATGTTGGCATGC 59.138 45.455 9.90 9.90 35.15 4.06
2396 4556 4.442332 CCATGCTTATCACAATGTTGGCAT 60.442 41.667 0.00 0.00 39.31 4.40
2411 4577 0.680921 GCTTGTGAGGGCCATGCTTA 60.681 55.000 6.18 0.00 32.11 3.09
2415 4581 0.529378 GAAAGCTTGTGAGGGCCATG 59.471 55.000 6.18 0.00 0.00 3.66
2416 4582 0.407139 AGAAAGCTTGTGAGGGCCAT 59.593 50.000 6.18 0.00 0.00 4.40
2417 4583 0.185901 AAGAAAGCTTGTGAGGGCCA 59.814 50.000 6.18 0.00 31.83 5.36
2418 4584 0.884514 GAAGAAAGCTTGTGAGGGCC 59.115 55.000 0.00 0.00 33.61 5.80
2419 4585 1.902938 AGAAGAAAGCTTGTGAGGGC 58.097 50.000 0.00 0.00 33.61 5.19
2424 4590 4.567959 CCAACCAAAAGAAGAAAGCTTGTG 59.432 41.667 0.00 0.00 33.61 3.33
2446 4612 3.950395 AGTTAGCAAGCAAGAATCCATCC 59.050 43.478 0.00 0.00 0.00 3.51
2455 4621 1.337703 TGGCACAAGTTAGCAAGCAAG 59.662 47.619 0.00 0.00 31.92 4.01
2462 4628 1.725164 GTCGTAGTGGCACAAGTTAGC 59.275 52.381 21.41 0.00 44.16 3.09
2464 4630 1.337703 ACGTCGTAGTGGCACAAGTTA 59.662 47.619 21.41 0.00 44.16 2.24
2475 4643 1.296056 GGGCAATGCAACGTCGTAGT 61.296 55.000 7.79 0.00 0.00 2.73
2481 4654 0.037419 GGAATTGGGCAATGCAACGT 60.037 50.000 7.79 0.00 0.00 3.99
2482 4655 0.247185 AGGAATTGGGCAATGCAACG 59.753 50.000 7.79 0.00 0.00 4.10
2483 4656 1.551883 AGAGGAATTGGGCAATGCAAC 59.448 47.619 7.79 0.00 0.00 4.17
2559 4733 9.582431 GTTAAAACTTGCTAAATAAATCCCTCC 57.418 33.333 0.00 0.00 0.00 4.30
2633 4808 9.605275 CAATACAGTATATAATGTATGCAGCCT 57.395 33.333 27.61 13.96 43.94 4.58
2779 4963 6.535150 CAGTCTGAAACGCTAAATAGGATTCA 59.465 38.462 0.00 0.00 0.00 2.57
2815 4999 4.733165 ACATACCATATCCTTGCAGCAAT 58.267 39.130 8.67 0.00 0.00 3.56
2865 5224 6.899393 AGATATCCAAAAGTTGAAGCAACA 57.101 33.333 12.25 0.00 45.66 3.33
2893 5252 2.919602 ACCAGTCCTGTAAATGGTCCAT 59.080 45.455 0.00 0.00 42.35 3.41
2933 5293 0.532115 GGGACATCAGGCGCATTTTT 59.468 50.000 10.83 0.00 0.00 1.94
3154 5516 4.340666 TGATTAAGCTGGTCAACTTTGCAA 59.659 37.500 0.00 0.00 0.00 4.08
3208 5571 6.878923 CACTGTAATATGGACCAAGAAAGTCA 59.121 38.462 0.00 0.00 35.89 3.41
3251 5614 9.683870 AAATTACATACCGGACCAAGTATTAAA 57.316 29.630 9.46 1.50 0.00 1.52
3265 5628 1.263217 GCCGGCTGAAATTACATACCG 59.737 52.381 22.15 0.00 38.35 4.02
3293 5656 0.251787 GTGGCATCCCAAAGACCCTT 60.252 55.000 0.00 0.00 44.33 3.95
3537 5952 2.227388 GCCATCTTCAGTCACCTTGTTG 59.773 50.000 0.00 0.00 0.00 3.33
3770 6188 5.753438 TGTAACAAGTAACTGCTGACTTCAG 59.247 40.000 1.56 1.56 46.40 3.02
3802 6225 4.525996 ACAGGCATGCAGTATGAACAATA 58.474 39.130 21.36 0.00 39.69 1.90
3816 6239 7.207383 ACAATCATCATGATAAAACAGGCATG 58.793 34.615 8.15 0.00 35.76 4.06
3967 6394 7.151308 ACAATTATTGCAGGAAACGATGAAAA 58.849 30.769 4.68 0.00 0.00 2.29
3977 6404 6.658816 TGCTTCTAAGACAATTATTGCAGGAA 59.341 34.615 4.68 2.94 0.00 3.36
3979 6406 6.441093 TGCTTCTAAGACAATTATTGCAGG 57.559 37.500 4.68 0.00 0.00 4.85
3984 6411 8.850156 ACACAACTTGCTTCTAAGACAATTATT 58.150 29.630 0.00 0.00 0.00 1.40
3996 6423 3.347216 ACTCACAACACAACTTGCTTCT 58.653 40.909 0.00 0.00 0.00 2.85
3997 6424 3.764885 ACTCACAACACAACTTGCTTC 57.235 42.857 0.00 0.00 0.00 3.86
4008 6435 7.717436 TCATACTGGATAAACAAACTCACAACA 59.283 33.333 0.00 0.00 0.00 3.33
4012 6439 7.624344 GCACTCATACTGGATAAACAAACTCAC 60.624 40.741 0.00 0.00 0.00 3.51
4023 6450 2.630098 GAGCAGGCACTCATACTGGATA 59.370 50.000 2.98 0.00 34.60 2.59
4033 6460 4.194640 TCAATCTATTTGAGCAGGCACTC 58.805 43.478 0.95 0.95 39.44 3.51
4034 6461 4.226427 TCAATCTATTTGAGCAGGCACT 57.774 40.909 0.00 0.00 39.44 4.40
4049 6483 4.402793 AGTTGGTGATACTACGCTCAATCT 59.597 41.667 0.00 0.00 0.00 2.40
4065 6499 3.797039 TGAGAGACTCAAACAGTTGGTG 58.203 45.455 5.02 0.00 37.57 4.17
4066 6500 4.487714 TTGAGAGACTCAAACAGTTGGT 57.512 40.909 11.06 0.00 45.84 3.67
4104 6538 7.942341 AGTATTGTCAGTGTCAAATAGGGAAAA 59.058 33.333 6.89 0.00 0.00 2.29
4202 6636 5.487488 ACAGAGGGAGTATCATTTAACACCA 59.513 40.000 0.00 0.00 36.25 4.17
4216 6650 9.939424 ACTCTTATATTAGTTTACAGAGGGAGT 57.061 33.333 0.00 0.00 32.21 3.85
4218 6652 9.710818 ACACTCTTATATTAGTTTACAGAGGGA 57.289 33.333 2.59 0.00 34.50 4.20
4268 6702 9.490379 CCTCCGTAAACTAATATAAGAGCATTT 57.510 33.333 0.00 0.00 0.00 2.32
4269 6703 8.095169 CCCTCCGTAAACTAATATAAGAGCATT 58.905 37.037 0.00 0.00 0.00 3.56
4270 6704 7.453752 TCCCTCCGTAAACTAATATAAGAGCAT 59.546 37.037 0.00 0.00 0.00 3.79
4271 6705 6.779049 TCCCTCCGTAAACTAATATAAGAGCA 59.221 38.462 0.00 0.00 0.00 4.26
4272 6706 7.039853 ACTCCCTCCGTAAACTAATATAAGAGC 60.040 40.741 0.00 0.00 0.00 4.09
4273 6707 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
4274 6708 9.289782 GTACTCCCTCCGTAAACTAATATAAGA 57.710 37.037 0.00 0.00 0.00 2.10
4275 6709 9.294614 AGTACTCCCTCCGTAAACTAATATAAG 57.705 37.037 0.00 0.00 0.00 1.73
4276 6710 9.646522 AAGTACTCCCTCCGTAAACTAATATAA 57.353 33.333 0.00 0.00 0.00 0.98
4277 6711 9.071276 CAAGTACTCCCTCCGTAAACTAATATA 57.929 37.037 0.00 0.00 0.00 0.86
4278 6712 7.781693 TCAAGTACTCCCTCCGTAAACTAATAT 59.218 37.037 0.00 0.00 0.00 1.28
4279 6713 7.118723 TCAAGTACTCCCTCCGTAAACTAATA 58.881 38.462 0.00 0.00 0.00 0.98
4280 6714 5.954150 TCAAGTACTCCCTCCGTAAACTAAT 59.046 40.000 0.00 0.00 0.00 1.73
4281 6715 5.324409 TCAAGTACTCCCTCCGTAAACTAA 58.676 41.667 0.00 0.00 0.00 2.24
4282 6716 4.922206 TCAAGTACTCCCTCCGTAAACTA 58.078 43.478 0.00 0.00 0.00 2.24
4283 6717 3.771216 TCAAGTACTCCCTCCGTAAACT 58.229 45.455 0.00 0.00 0.00 2.66
4284 6718 4.525912 TTCAAGTACTCCCTCCGTAAAC 57.474 45.455 0.00 0.00 0.00 2.01
4285 6719 5.305128 TCTTTTCAAGTACTCCCTCCGTAAA 59.695 40.000 0.00 0.00 0.00 2.01
4286 6720 4.834496 TCTTTTCAAGTACTCCCTCCGTAA 59.166 41.667 0.00 0.00 0.00 3.18
4287 6721 4.219288 GTCTTTTCAAGTACTCCCTCCGTA 59.781 45.833 0.00 0.00 0.00 4.02
4288 6722 3.006644 GTCTTTTCAAGTACTCCCTCCGT 59.993 47.826 0.00 0.00 0.00 4.69
4289 6723 3.586892 GTCTTTTCAAGTACTCCCTCCG 58.413 50.000 0.00 0.00 0.00 4.63
4290 6724 3.307550 GGGTCTTTTCAAGTACTCCCTCC 60.308 52.174 0.00 0.00 0.00 4.30
4291 6725 3.583526 AGGGTCTTTTCAAGTACTCCCTC 59.416 47.826 8.39 0.00 39.68 4.30
4292 6726 3.599348 AGGGTCTTTTCAAGTACTCCCT 58.401 45.455 8.39 8.39 39.11 4.20
4293 6727 4.368565 AAGGGTCTTTTCAAGTACTCCC 57.631 45.455 0.00 0.00 0.00 4.30
4294 6728 5.507482 GCAAAAGGGTCTTTTCAAGTACTCC 60.507 44.000 0.00 0.00 0.00 3.85
4295 6729 5.507482 GGCAAAAGGGTCTTTTCAAGTACTC 60.507 44.000 0.00 0.00 0.00 2.59
4296 6730 4.341235 GGCAAAAGGGTCTTTTCAAGTACT 59.659 41.667 3.00 0.00 0.00 2.73
4297 6731 4.500887 GGGCAAAAGGGTCTTTTCAAGTAC 60.501 45.833 3.00 0.00 0.00 2.73
4298 6732 3.639561 GGGCAAAAGGGTCTTTTCAAGTA 59.360 43.478 3.00 0.00 0.00 2.24
4330 6764 9.865321 ATCATCTCTTAAAATTTTGGTCACATG 57.135 29.630 13.76 8.45 0.00 3.21
4331 6765 9.865321 CATCATCTCTTAAAATTTTGGTCACAT 57.135 29.630 13.76 0.00 0.00 3.21
4428 6862 9.350951 AGTAAACTTTTAACCTGCACTTAGAAT 57.649 29.630 0.00 0.00 0.00 2.40
4472 6906 6.778834 TCAATTGATCAGCCATTGTTATGT 57.221 33.333 15.07 0.00 0.00 2.29
4499 6933 9.661563 AACAAAATCTCACTATACCGTCATAAA 57.338 29.630 0.00 0.00 0.00 1.40
4518 7235 9.753669 GTGTTCGAATTTTCAAAAGAACAAAAT 57.246 25.926 14.48 0.00 45.94 1.82
4523 7550 6.840789 GCATGTGTTCGAATTTTCAAAAGAAC 59.159 34.615 0.00 6.55 38.60 3.01
4527 7554 5.276773 GCTGCATGTGTTCGAATTTTCAAAA 60.277 36.000 0.00 0.00 0.00 2.44
4542 7569 2.675423 AGGCCTGTGCTGCATGTG 60.675 61.111 3.11 0.00 37.74 3.21
4601 7628 1.757699 TGTGGCGTGGCATATACTGTA 59.242 47.619 0.00 0.00 0.00 2.74
4602 7629 0.539518 TGTGGCGTGGCATATACTGT 59.460 50.000 0.00 0.00 0.00 3.55
4603 7630 1.220529 CTGTGGCGTGGCATATACTG 58.779 55.000 0.00 0.00 0.00 2.74
4604 7631 0.106708 CCTGTGGCGTGGCATATACT 59.893 55.000 0.00 0.00 0.00 2.12
4605 7632 2.616969 CCTGTGGCGTGGCATATAC 58.383 57.895 0.00 0.00 0.00 1.47
4635 7690 0.800012 GCACCCGCGATAGAAAACAA 59.200 50.000 8.23 0.00 39.76 2.83
4657 7712 4.759693 TCATCTGGCAAATCACGTTTTAGT 59.240 37.500 0.00 0.00 0.00 2.24
4698 7753 2.456119 CGGCTTCATGAGTGCGTCC 61.456 63.158 13.97 2.99 0.00 4.79
4712 7767 2.106683 GTACATTCGCTTGCCGGCT 61.107 57.895 29.70 6.08 37.59 5.52
4786 7841 8.450578 TTTTGCCCTCATGTAATACTATGAAG 57.549 34.615 0.00 2.67 33.30 3.02


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

AutoCloner maintained by Alex Coulton.