Multiple sequence alignment - TraesCS3D01G337000

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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 TraesCS3D01G337000 chr3D 100.000 5878 0 0 1 5878 448629683 448635560 0.000000e+00 10855.0
1 TraesCS3D01G337000 chr3D 86.752 234 7 1 5168 5401 124798722 124798931 7.610000e-59 239.0
2 TraesCS3D01G337000 chr3D 95.312 128 3 3 3272 3397 407812395 407812521 3.590000e-47 200.0
3 TraesCS3D01G337000 chr3D 90.845 142 10 3 3267 3407 19753259 19753398 2.800000e-43 187.0
4 TraesCS3D01G337000 chr3B 95.735 2040 63 18 685 2718 588859095 588861116 0.000000e+00 3264.0
5 TraesCS3D01G337000 chr3B 96.000 1550 39 6 3412 4958 588862267 588863796 0.000000e+00 2497.0
6 TraesCS3D01G337000 chr3B 90.027 742 40 10 5168 5878 4294258 4293520 0.000000e+00 929.0
7 TraesCS3D01G337000 chr3B 96.601 353 9 2 1 353 588858084 588858433 3.050000e-162 582.0
8 TraesCS3D01G337000 chr3B 85.237 569 54 16 2704 3267 588861734 588862277 5.140000e-155 558.0
9 TraesCS3D01G337000 chr3B 91.860 344 26 2 339 681 588858722 588859064 4.120000e-131 479.0
10 TraesCS3D01G337000 chr3B 94.767 172 4 3 4997 5168 588863797 588863963 4.520000e-66 263.0
11 TraesCS3D01G337000 chr3B 100.000 90 0 0 5168 5257 319028482 319028393 3.640000e-37 167.0
12 TraesCS3D01G337000 chr3A 95.044 1594 51 11 3408 4982 589911202 589912786 0.000000e+00 2481.0
13 TraesCS3D01G337000 chr3A 93.027 1133 41 13 695 1796 589908635 589909760 0.000000e+00 1620.0
14 TraesCS3D01G337000 chr3A 95.266 1014 42 5 1792 2804 589909802 589910810 0.000000e+00 1602.0
15 TraesCS3D01G337000 chr3A 88.712 629 47 13 1 607 589907992 589908618 0.000000e+00 747.0
16 TraesCS3D01G337000 chr3A 91.651 539 23 6 4613 5150 589913260 589913777 0.000000e+00 726.0
17 TraesCS3D01G337000 chr3A 96.765 371 11 1 4613 4982 589912838 589913208 8.370000e-173 617.0
18 TraesCS3D01G337000 chr3A 87.286 409 31 9 2862 3267 589910826 589911216 1.160000e-121 448.0
19 TraesCS3D01G337000 chr1D 93.243 740 19 4 5169 5878 91727482 91726744 0.000000e+00 1061.0
20 TraesCS3D01G337000 chr1D 92.297 740 27 3 5169 5878 429654603 429653864 0.000000e+00 1024.0
21 TraesCS3D01G337000 chr1D 88.435 147 9 3 5168 5306 49869700 49869846 2.820000e-38 171.0
22 TraesCS3D01G337000 chr1D 95.098 102 5 0 5156 5257 420864574 420864473 1.700000e-35 161.0
23 TraesCS3D01G337000 chrUn 92.838 740 17 6 5169 5878 414211837 414212570 0.000000e+00 1040.0
24 TraesCS3D01G337000 chr5D 92.578 741 23 4 5168 5878 423677959 423678697 0.000000e+00 1035.0
25 TraesCS3D01G337000 chr5D 93.333 135 7 2 3264 3397 377147851 377147984 1.290000e-46 198.0
26 TraesCS3D01G337000 chr5D 92.593 54 3 1 4907 4960 367379889 367379941 6.320000e-10 76.8
27 TraesCS3D01G337000 chr5D 94.000 50 3 0 4907 4956 367412971 367413020 6.320000e-10 76.8
28 TraesCS3D01G337000 chr1B 90.983 743 34 6 5169 5878 39153015 39153757 0.000000e+00 970.0
29 TraesCS3D01G337000 chr1B 90.698 43 4 0 4908 4950 133116624 133116582 2.290000e-04 58.4
30 TraesCS3D01G337000 chr5A 94.677 620 32 1 5259 5878 559591915 559592533 0.000000e+00 961.0
31 TraesCS3D01G337000 chr5A 93.846 130 5 3 3270 3397 487945081 487944953 6.010000e-45 193.0
32 TraesCS3D01G337000 chr5A 94.872 39 2 0 642 680 360079050 360079088 1.770000e-05 62.1
33 TraesCS3D01G337000 chr7A 92.526 669 38 7 5210 5878 118781850 118781194 0.000000e+00 948.0
34 TraesCS3D01G337000 chr4A 90.135 740 43 3 5169 5878 345559493 345558754 0.000000e+00 935.0
35 TraesCS3D01G337000 chr6D 92.248 258 6 2 5163 5406 91279840 91279583 2.610000e-93 353.0
36 TraesCS3D01G337000 chr6D 93.182 132 5 4 3267 3397 61175193 61175321 2.160000e-44 191.0
37 TraesCS3D01G337000 chr7D 90.494 263 9 2 5160 5406 288795035 288795297 3.390000e-87 333.0
38 TraesCS3D01G337000 chr4B 89.062 256 12 2 5167 5406 604939165 604938910 2.660000e-78 303.0
39 TraesCS3D01G337000 chr4B 92.424 132 6 4 3268 3398 212173475 212173603 1.010000e-42 185.0
40 TraesCS3D01G337000 chr2B 90.066 151 10 4 3261 3407 755974480 755974331 2.160000e-44 191.0
41 TraesCS3D01G337000 chr2B 90.845 142 9 4 3268 3407 152751986 152752125 2.800000e-43 187.0
42 TraesCS3D01G337000 chr5B 90.210 143 12 2 3267 3408 176237734 176237593 1.010000e-42 185.0
43 TraesCS3D01G337000 chr5B 92.593 54 3 1 4907 4960 434423107 434423159 6.320000e-10 76.8
44 TraesCS3D01G337000 chr5B 93.878 49 3 0 4908 4956 434693902 434693950 2.270000e-09 75.0
45 TraesCS3D01G337000 chr4D 84.906 159 20 3 5169 5326 410843205 410843050 2.190000e-34 158.0
46 TraesCS3D01G337000 chr4D 94.872 39 2 0 642 680 397682337 397682299 1.770000e-05 62.1
47 TraesCS3D01G337000 chr6B 89.216 102 7 4 5143 5244 529207577 529207674 2.220000e-24 124.0
48 TraesCS3D01G337000 chr2A 78.049 164 22 10 424 576 757970302 757970142 2.260000e-14 91.6
49 TraesCS3D01G337000 chr2A 100.000 31 0 0 2862 2892 715403257 715403287 2.290000e-04 58.4
50 TraesCS3D01G337000 chr2D 79.310 145 16 8 424 557 627321055 627320914 8.110000e-14 89.8


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 TraesCS3D01G337000 chr3D 448629683 448635560 5877 False 10855.000000 10855 100.000000 1 5878 1 chr3D.!!$F4 5877
1 TraesCS3D01G337000 chr3B 588858084 588863963 5879 False 1273.833333 3264 93.366667 1 5168 6 chr3B.!!$F1 5167
2 TraesCS3D01G337000 chr3B 4293520 4294258 738 True 929.000000 929 90.027000 5168 5878 1 chr3B.!!$R1 710
3 TraesCS3D01G337000 chr3A 589907992 589913777 5785 False 1177.285714 2481 92.535857 1 5150 7 chr3A.!!$F1 5149
4 TraesCS3D01G337000 chr1D 91726744 91727482 738 True 1061.000000 1061 93.243000 5169 5878 1 chr1D.!!$R1 709
5 TraesCS3D01G337000 chr1D 429653864 429654603 739 True 1024.000000 1024 92.297000 5169 5878 1 chr1D.!!$R3 709
6 TraesCS3D01G337000 chrUn 414211837 414212570 733 False 1040.000000 1040 92.838000 5169 5878 1 chrUn.!!$F1 709
7 TraesCS3D01G337000 chr5D 423677959 423678697 738 False 1035.000000 1035 92.578000 5168 5878 1 chr5D.!!$F4 710
8 TraesCS3D01G337000 chr1B 39153015 39153757 742 False 970.000000 970 90.983000 5169 5878 1 chr1B.!!$F1 709
9 TraesCS3D01G337000 chr5A 559591915 559592533 618 False 961.000000 961 94.677000 5259 5878 1 chr5A.!!$F2 619
10 TraesCS3D01G337000 chr7A 118781194 118781850 656 True 948.000000 948 92.526000 5210 5878 1 chr7A.!!$R1 668
11 TraesCS3D01G337000 chr4A 345558754 345559493 739 True 935.000000 935 90.135000 5169 5878 1 chr4A.!!$R1 709

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
719 1070 0.035439 GATGTTTTCGCCCTCTCCCA 60.035 55.000 0.00 0.00 0.00 4.37 F
823 1175 1.069090 AAGACCACGCGTGTCACAT 59.931 52.632 34.81 19.02 0.00 3.21 F
1796 2224 0.183492 AGGCTTGTTCAGTGCAAGGA 59.817 50.000 11.12 0.00 42.44 3.36 F
2916 3980 0.667487 AACATCTGTGACACGCGAGG 60.667 55.000 15.93 7.12 0.00 4.63 F
3244 4313 0.179124 GCTAGTCCAAGCTCGACTGG 60.179 60.000 21.09 19.43 40.75 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1777 2159 0.183492 TCCTTGCACTGAACAAGCCT 59.817 50.000 8.31 0.00 42.57 4.58 R
2104 2536 3.252701 CGATAGTGAGTGGGCTAACGTAT 59.747 47.826 0.00 0.00 31.18 3.06 R
2936 4000 0.165079 GTGTGCGGGTGTTTCATACG 59.835 55.000 0.00 0.00 0.00 3.06 R
4205 5288 0.460811 TCTGCTGGATGTGCATCGAC 60.461 55.000 6.14 0.00 39.86 4.20 R
5002 6934 1.144936 GGGACATGAAGGAGCTCCG 59.855 63.158 26.95 14.74 42.08 4.63 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
238 251 1.550327 TGTCCACAAAGCAAACACCA 58.450 45.000 0.00 0.00 0.00 4.17
401 715 4.422840 CACACAAACACACATGTCACAAT 58.577 39.130 0.00 0.00 38.45 2.71
412 726 0.313672 TGTCACAATTTTGCTCCGCC 59.686 50.000 0.00 0.00 0.00 6.13
427 741 1.738099 CGCCGAGACAAAGACCCAG 60.738 63.158 0.00 0.00 0.00 4.45
431 745 1.827969 CCGAGACAAAGACCCAGAGAT 59.172 52.381 0.00 0.00 0.00 2.75
432 746 2.417924 CCGAGACAAAGACCCAGAGATG 60.418 54.545 0.00 0.00 0.00 2.90
515 830 9.366216 ACAACTCTAAAACTTTGGAATGTTTTC 57.634 29.630 15.50 0.00 42.00 2.29
538 854 4.295051 CAATTCGGTGTTTTGTAAGGGTG 58.705 43.478 0.00 0.00 0.00 4.61
612 936 9.758651 TTATTCACGTAAATCACATATAGCAGT 57.241 29.630 0.00 0.00 0.00 4.40
631 955 6.987386 AGCAGTCGGGATATCAATATATAGC 58.013 40.000 4.83 0.00 0.00 2.97
652 976 8.930846 ATAGCATATATTATTCCCTGCAATCC 57.069 34.615 0.00 0.00 32.18 3.01
663 987 4.144297 TCCCTGCAATCCATATTACTTGC 58.856 43.478 0.00 0.00 43.25 4.01
664 988 3.256631 CCCTGCAATCCATATTACTTGCC 59.743 47.826 9.29 0.00 42.50 4.52
681 1005 1.533731 TGCCGCAGCTTTAGTACAAAC 59.466 47.619 0.00 0.00 40.80 2.93
683 1007 2.412847 GCCGCAGCTTTAGTACAAACTG 60.413 50.000 0.00 6.02 34.89 3.16
684 1008 2.159627 CCGCAGCTTTAGTACAAACTGG 59.840 50.000 0.00 1.24 36.36 4.00
685 1009 3.064207 CGCAGCTTTAGTACAAACTGGA 58.936 45.455 0.00 0.00 36.36 3.86
687 1011 4.201724 CGCAGCTTTAGTACAAACTGGATC 60.202 45.833 0.00 0.00 36.36 3.36
688 1012 4.201724 GCAGCTTTAGTACAAACTGGATCG 60.202 45.833 0.00 0.00 36.36 3.69
689 1013 4.330074 CAGCTTTAGTACAAACTGGATCGG 59.670 45.833 0.00 0.00 36.36 4.18
691 1015 4.567159 GCTTTAGTACAAACTGGATCGGAG 59.433 45.833 0.00 0.00 36.36 4.63
692 1016 4.730949 TTAGTACAAACTGGATCGGAGG 57.269 45.455 0.00 0.00 36.36 4.30
700 1051 0.669077 CTGGATCGGAGGGAGTAACG 59.331 60.000 0.00 0.00 0.00 3.18
719 1070 0.035439 GATGTTTTCGCCCTCTCCCA 60.035 55.000 0.00 0.00 0.00 4.37
776 1127 2.095768 CGAATACCCTGTTGCACAACTG 60.096 50.000 14.16 13.04 41.67 3.16
807 1159 6.019237 CAGTAGTATATGTTCAGCAGTGCAAG 60.019 42.308 19.20 9.65 0.00 4.01
808 1160 5.089970 AGTATATGTTCAGCAGTGCAAGA 57.910 39.130 19.20 12.08 0.00 3.02
823 1175 1.069090 AAGACCACGCGTGTCACAT 59.931 52.632 34.81 19.02 0.00 3.21
830 1182 2.953821 GCGTGTCACATGTTGGGG 59.046 61.111 0.00 0.00 0.00 4.96
1017 1373 2.519013 TCTCTGCAGCAGTAGACAAGA 58.481 47.619 22.10 13.12 32.77 3.02
1117 1474 3.567478 GAAGGTTTTTGCCGGGCGG 62.567 63.158 15.40 0.00 38.57 6.13
1279 1648 9.057089 ACCAAGAAGTAAGTTTGAGTTTATCAG 57.943 33.333 0.00 0.00 39.68 2.90
1293 1662 6.811665 TGAGTTTATCAGACGATCGAAATTGT 59.188 34.615 24.34 0.00 32.77 2.71
1386 1756 3.252554 AGGTTTGGGGTATTGAAGCAA 57.747 42.857 0.00 0.00 0.00 3.91
1396 1767 8.213489 TGGGGTATTGAAGCAACTATATATGA 57.787 34.615 0.00 0.00 0.00 2.15
1489 1871 3.798878 CGTCCTACTTGCTACATGTGATG 59.201 47.826 9.11 0.00 0.00 3.07
1502 1884 6.201806 GCTACATGTGATGTATTCTCTTGTCC 59.798 42.308 9.11 0.00 44.11 4.02
1790 2218 8.243426 TGCTAATTAATTAAGGCTTGTTCAGTG 58.757 33.333 10.69 0.00 0.00 3.66
1796 2224 0.183492 AGGCTTGTTCAGTGCAAGGA 59.817 50.000 11.12 0.00 42.44 3.36
1843 2272 9.620259 AGTAGTTTCAAAATCTGTTTTCTCTCT 57.380 29.630 0.00 0.00 35.41 3.10
1850 2279 8.830580 TCAAAATCTGTTTTCTCTCTGTAAGTG 58.169 33.333 0.00 0.00 35.41 3.16
1864 2293 7.732025 TCTCTGTAAGTGGTTTGATTTGTAGA 58.268 34.615 0.00 0.00 33.76 2.59
1991 2420 5.562623 CACCTTTACGCTCGAAAACATAAAC 59.437 40.000 0.00 0.00 0.00 2.01
1992 2421 5.467735 ACCTTTACGCTCGAAAACATAAACT 59.532 36.000 0.00 0.00 0.00 2.66
2044 2473 5.843421 AGCCCTTAGTGATGAGATAAGACAT 59.157 40.000 0.00 0.00 0.00 3.06
2104 2536 7.881232 CCTCTCACCTAACTTAAACCAAACATA 59.119 37.037 0.00 0.00 0.00 2.29
2435 2867 2.854185 GGAATCTGCAATTAACAAGCGC 59.146 45.455 0.00 0.00 0.00 5.92
2675 3107 2.156917 CACAATCTGTGCATGACCACT 58.843 47.619 0.00 0.00 41.89 4.00
2760 3824 2.557317 TGGTTTTGTTCCGAGACTGTC 58.443 47.619 0.00 0.00 0.00 3.51
2822 3886 6.325545 TCCCTACGATCCATATTAGTTGTTGT 59.674 38.462 0.00 0.00 0.00 3.32
2823 3887 6.990349 CCCTACGATCCATATTAGTTGTTGTT 59.010 38.462 0.00 0.00 0.00 2.83
2824 3888 7.042051 CCCTACGATCCATATTAGTTGTTGTTG 60.042 40.741 0.00 0.00 0.00 3.33
2827 3891 7.919690 ACGATCCATATTAGTTGTTGTTGATG 58.080 34.615 0.00 0.00 0.00 3.07
2838 3902 6.725246 AGTTGTTGTTGATGTAGTACAAAGC 58.275 36.000 7.16 1.97 33.96 3.51
2839 3903 5.682943 TGTTGTTGATGTAGTACAAAGCC 57.317 39.130 7.16 0.00 33.96 4.35
2840 3904 4.212425 TGTTGTTGATGTAGTACAAAGCCG 59.788 41.667 7.16 0.00 33.96 5.52
2841 3905 3.997762 TGTTGATGTAGTACAAAGCCGT 58.002 40.909 7.16 0.00 0.00 5.68
2842 3906 5.136816 TGTTGATGTAGTACAAAGCCGTA 57.863 39.130 7.16 0.00 0.00 4.02
2843 3907 4.925054 TGTTGATGTAGTACAAAGCCGTAC 59.075 41.667 7.16 1.44 41.75 3.67
2856 3920 9.014533 GTACAAAGCCGTACTAAGTACTAAATC 57.985 37.037 0.00 0.00 38.96 2.17
2858 3922 8.090214 ACAAAGCCGTACTAAGTACTAAATCAA 58.910 33.333 0.00 0.00 36.93 2.57
2860 3924 7.161773 AGCCGTACTAAGTACTAAATCAACA 57.838 36.000 0.00 0.00 36.93 3.33
2912 3976 6.747659 AAATTTAAAACATCTGTGACACGC 57.252 33.333 0.22 0.00 0.00 5.34
2914 3978 1.577468 AAAACATCTGTGACACGCGA 58.423 45.000 15.93 0.43 0.00 5.87
2915 3979 1.139989 AAACATCTGTGACACGCGAG 58.860 50.000 15.93 7.88 0.00 5.03
2916 3980 0.667487 AACATCTGTGACACGCGAGG 60.667 55.000 15.93 7.12 0.00 4.63
2917 3981 2.125912 ATCTGTGACACGCGAGGC 60.126 61.111 15.93 8.23 0.00 4.70
2918 3982 2.931068 ATCTGTGACACGCGAGGCA 61.931 57.895 15.93 11.98 0.00 4.75
2919 3983 2.434658 ATCTGTGACACGCGAGGCAA 62.435 55.000 15.33 0.00 0.00 4.52
2920 3984 2.029288 CTGTGACACGCGAGGCAAT 61.029 57.895 15.33 0.00 0.00 3.56
2921 3985 1.568612 CTGTGACACGCGAGGCAATT 61.569 55.000 15.33 0.00 0.00 2.32
2936 4000 6.128795 GCGAGGCAATTAATGAGTCATACTAC 60.129 42.308 5.94 0.00 0.00 2.73
3056 4123 3.202829 AGTGACGGGAAGCAAAACTTA 57.797 42.857 0.00 0.00 39.29 2.24
3064 4131 4.377021 GGGAAGCAAAACTTAACCAAAGG 58.623 43.478 0.00 0.00 39.29 3.11
3083 4150 6.247176 CAAAGGTTTTGTCAAATTGGTTTCG 58.753 36.000 0.00 0.00 0.00 3.46
3087 4154 4.920640 TTTGTCAAATTGGTTTCGGCTA 57.079 36.364 0.00 0.00 0.00 3.93
3096 4163 8.145122 TCAAATTGGTTTCGGCTAAAACTAAAT 58.855 29.630 13.86 10.94 41.14 1.40
3103 4170 4.444536 TCGGCTAAAACTAAATACGCCAT 58.555 39.130 0.00 0.00 35.89 4.40
3104 4171 5.599732 TCGGCTAAAACTAAATACGCCATA 58.400 37.500 0.00 0.00 35.89 2.74
3107 4174 6.849305 CGGCTAAAACTAAATACGCCATAAAG 59.151 38.462 0.00 0.00 35.89 1.85
3108 4175 7.466320 CGGCTAAAACTAAATACGCCATAAAGT 60.466 37.037 0.00 0.00 35.89 2.66
3244 4313 0.179124 GCTAGTCCAAGCTCGACTGG 60.179 60.000 21.09 19.43 40.75 4.00
3267 4336 2.029110 CCTTGGACGAATTTGGCACATT 60.029 45.455 0.00 0.00 39.30 2.71
3269 4338 3.742433 TGGACGAATTTGGCACATTTT 57.258 38.095 0.00 0.00 39.30 1.82
3270 4339 3.648009 TGGACGAATTTGGCACATTTTC 58.352 40.909 0.00 1.11 39.30 2.29
3272 4341 4.202202 TGGACGAATTTGGCACATTTTCTT 60.202 37.500 0.00 0.00 39.30 2.52
3274 4343 5.236263 GGACGAATTTGGCACATTTTCTTTT 59.764 36.000 0.00 0.00 39.30 2.27
3275 4344 6.238347 GGACGAATTTGGCACATTTTCTTTTT 60.238 34.615 0.00 0.00 39.30 1.94
3276 4345 7.042389 GGACGAATTTGGCACATTTTCTTTTTA 60.042 33.333 0.00 0.00 39.30 1.52
3277 4346 8.202745 ACGAATTTGGCACATTTTCTTTTTAA 57.797 26.923 0.00 0.00 39.30 1.52
3278 4347 8.669243 ACGAATTTGGCACATTTTCTTTTTAAA 58.331 25.926 0.00 0.00 39.30 1.52
3279 4348 9.495754 CGAATTTGGCACATTTTCTTTTTAAAA 57.504 25.926 0.00 0.00 39.30 1.52
3282 4351 9.800433 ATTTGGCACATTTTCTTTTTAAAAAGG 57.200 25.926 30.78 20.46 41.56 3.11
3283 4352 8.567285 TTGGCACATTTTCTTTTTAAAAAGGA 57.433 26.923 30.78 24.34 41.56 3.36
3284 4353 8.207521 TGGCACATTTTCTTTTTAAAAAGGAG 57.792 30.769 30.78 18.38 44.22 3.69
3285 4354 7.281999 TGGCACATTTTCTTTTTAAAAAGGAGG 59.718 33.333 30.78 22.48 44.22 4.30
3286 4355 7.497579 GGCACATTTTCTTTTTAAAAAGGAGGA 59.502 33.333 30.78 19.57 44.22 3.71
3287 4356 9.056005 GCACATTTTCTTTTTAAAAAGGAGGAT 57.944 29.630 30.78 20.58 44.22 3.24
3293 4362 7.786046 TCTTTTTAAAAAGGAGGATTACCCC 57.214 36.000 30.78 0.00 44.22 4.95
3294 4363 6.727231 TCTTTTTAAAAAGGAGGATTACCCCC 59.273 38.462 30.78 0.00 44.22 5.40
3295 4364 2.820728 AAAAAGGAGGATTACCCCCG 57.179 50.000 0.00 0.00 36.73 5.73
3296 4365 0.924090 AAAAGGAGGATTACCCCCGG 59.076 55.000 0.00 0.00 36.73 5.73
3297 4366 1.642513 AAAGGAGGATTACCCCCGGC 61.643 60.000 0.00 0.00 36.73 6.13
3298 4367 3.567209 GGAGGATTACCCCCGGCC 61.567 72.222 0.00 0.00 36.73 6.13
3299 4368 2.447959 GAGGATTACCCCCGGCCT 60.448 66.667 0.00 0.00 36.73 5.19
3300 4369 2.447959 AGGATTACCCCCGGCCTC 60.448 66.667 0.00 0.00 36.73 4.70
3301 4370 2.447959 GGATTACCCCCGGCCTCT 60.448 66.667 0.00 0.00 0.00 3.69
3302 4371 2.819284 GGATTACCCCCGGCCTCTG 61.819 68.421 0.00 0.00 0.00 3.35
3303 4372 3.477578 GATTACCCCCGGCCTCTGC 62.478 68.421 0.00 0.00 0.00 4.26
3305 4374 4.815973 TACCCCCGGCCTCTGCAT 62.816 66.667 0.00 0.00 40.13 3.96
3308 4377 4.559063 CCCCGGCCTCTGCATCTG 62.559 72.222 0.00 0.00 40.13 2.90
3309 4378 4.559063 CCCGGCCTCTGCATCTGG 62.559 72.222 0.00 0.00 40.13 3.86
3310 4379 3.473647 CCGGCCTCTGCATCTGGA 61.474 66.667 0.00 0.00 40.13 3.86
3311 4380 2.202987 CGGCCTCTGCATCTGGAC 60.203 66.667 0.00 0.35 40.13 4.02
3312 4381 2.202987 GGCCTCTGCATCTGGACG 60.203 66.667 0.00 0.00 40.13 4.79
3313 4382 2.725312 GGCCTCTGCATCTGGACGA 61.725 63.158 0.00 0.00 40.13 4.20
3314 4383 1.445095 GCCTCTGCATCTGGACGAT 59.555 57.895 0.00 0.00 37.47 3.73
3321 4390 2.697819 CATCTGGACGATGCATGCA 58.302 52.632 25.04 25.04 42.75 3.96
3322 4391 1.018910 CATCTGGACGATGCATGCAA 58.981 50.000 26.68 8.49 42.75 4.08
3323 4392 1.019673 ATCTGGACGATGCATGCAAC 58.980 50.000 26.68 21.63 0.00 4.17
3324 4393 1.026182 TCTGGACGATGCATGCAACC 61.026 55.000 26.68 23.28 0.00 3.77
3325 4394 1.303155 TGGACGATGCATGCAACCA 60.303 52.632 26.68 25.37 0.00 3.67
3326 4395 0.680601 TGGACGATGCATGCAACCAT 60.681 50.000 26.68 11.85 0.00 3.55
3327 4396 0.457035 GGACGATGCATGCAACCATT 59.543 50.000 26.68 7.61 0.00 3.16
3328 4397 1.135024 GGACGATGCATGCAACCATTT 60.135 47.619 26.68 6.72 0.00 2.32
3329 4398 2.609350 GACGATGCATGCAACCATTTT 58.391 42.857 26.68 5.83 0.00 1.82
3330 4399 2.995258 GACGATGCATGCAACCATTTTT 59.005 40.909 26.68 4.93 0.00 1.94
3331 4400 4.172505 GACGATGCATGCAACCATTTTTA 58.827 39.130 26.68 0.00 0.00 1.52
3332 4401 4.757594 ACGATGCATGCAACCATTTTTAT 58.242 34.783 26.68 3.17 0.00 1.40
3333 4402 5.177326 ACGATGCATGCAACCATTTTTATT 58.823 33.333 26.68 2.55 0.00 1.40
3334 4403 6.336566 ACGATGCATGCAACCATTTTTATTA 58.663 32.000 26.68 0.00 0.00 0.98
3335 4404 6.815641 ACGATGCATGCAACCATTTTTATTAA 59.184 30.769 26.68 0.00 0.00 1.40
3336 4405 7.495279 ACGATGCATGCAACCATTTTTATTAAT 59.505 29.630 26.68 1.01 0.00 1.40
3337 4406 8.336806 CGATGCATGCAACCATTTTTATTAATT 58.663 29.630 26.68 0.55 0.00 1.40
3370 4439 7.793948 AGACCTTACAAAATAGTACTCAGGT 57.206 36.000 0.00 0.00 36.12 4.00
3371 4440 8.890410 AGACCTTACAAAATAGTACTCAGGTA 57.110 34.615 0.00 0.00 34.48 3.08
3372 4441 8.968969 AGACCTTACAAAATAGTACTCAGGTAG 58.031 37.037 0.00 0.00 34.48 3.18
3373 4442 8.661752 ACCTTACAAAATAGTACTCAGGTAGT 57.338 34.615 0.00 0.00 42.62 2.73
3374 4443 8.747471 ACCTTACAAAATAGTACTCAGGTAGTC 58.253 37.037 0.00 0.00 39.80 2.59
3375 4444 8.968969 CCTTACAAAATAGTACTCAGGTAGTCT 58.031 37.037 0.00 0.00 39.80 3.24
3376 4445 9.790389 CTTACAAAATAGTACTCAGGTAGTCTG 57.210 37.037 0.00 0.00 44.68 3.51
3384 4453 3.842869 CAGGTAGTCTGAAGCCACC 57.157 57.895 0.00 0.00 46.18 4.61
3385 4454 0.976641 CAGGTAGTCTGAAGCCACCA 59.023 55.000 0.00 0.00 46.18 4.17
3386 4455 1.556911 CAGGTAGTCTGAAGCCACCAT 59.443 52.381 0.00 0.00 46.18 3.55
3387 4456 1.834263 AGGTAGTCTGAAGCCACCATC 59.166 52.381 0.00 0.00 0.00 3.51
3388 4457 1.834263 GGTAGTCTGAAGCCACCATCT 59.166 52.381 0.00 0.00 0.00 2.90
3389 4458 2.237392 GGTAGTCTGAAGCCACCATCTT 59.763 50.000 0.00 0.00 0.00 2.40
3390 4459 3.451178 GGTAGTCTGAAGCCACCATCTTA 59.549 47.826 0.00 0.00 0.00 2.10
3391 4460 3.902881 AGTCTGAAGCCACCATCTTAG 57.097 47.619 0.00 0.00 0.00 2.18
3392 4461 2.093235 AGTCTGAAGCCACCATCTTAGC 60.093 50.000 0.00 0.00 0.00 3.09
3393 4462 1.908619 TCTGAAGCCACCATCTTAGCA 59.091 47.619 0.00 0.00 0.00 3.49
3394 4463 2.305635 TCTGAAGCCACCATCTTAGCAA 59.694 45.455 0.00 0.00 0.00 3.91
3395 4464 2.421424 CTGAAGCCACCATCTTAGCAAC 59.579 50.000 0.00 0.00 0.00 4.17
3396 4465 2.224744 TGAAGCCACCATCTTAGCAACA 60.225 45.455 0.00 0.00 0.00 3.33
3397 4466 2.814805 AGCCACCATCTTAGCAACAT 57.185 45.000 0.00 0.00 0.00 2.71
3398 4467 3.091633 AGCCACCATCTTAGCAACATT 57.908 42.857 0.00 0.00 0.00 2.71
3399 4468 3.019564 AGCCACCATCTTAGCAACATTC 58.980 45.455 0.00 0.00 0.00 2.67
3400 4469 2.754552 GCCACCATCTTAGCAACATTCA 59.245 45.455 0.00 0.00 0.00 2.57
3401 4470 3.382546 GCCACCATCTTAGCAACATTCAT 59.617 43.478 0.00 0.00 0.00 2.57
3402 4471 4.498682 GCCACCATCTTAGCAACATTCATC 60.499 45.833 0.00 0.00 0.00 2.92
3403 4472 4.260907 CCACCATCTTAGCAACATTCATCG 60.261 45.833 0.00 0.00 0.00 3.84
3404 4473 3.313526 ACCATCTTAGCAACATTCATCGC 59.686 43.478 0.00 0.00 0.00 4.58
3405 4474 3.562973 CCATCTTAGCAACATTCATCGCT 59.437 43.478 0.00 0.00 38.51 4.93
3406 4475 4.751600 CCATCTTAGCAACATTCATCGCTA 59.248 41.667 0.00 0.00 35.93 4.26
3407 4476 5.237127 CCATCTTAGCAACATTCATCGCTAA 59.763 40.000 0.00 0.00 42.91 3.09
3408 4477 5.718649 TCTTAGCAACATTCATCGCTAAC 57.281 39.130 0.00 0.00 40.91 2.34
3409 4478 4.267690 TCTTAGCAACATTCATCGCTAACG 59.732 41.667 0.00 0.00 40.91 3.18
3410 4479 2.346803 AGCAACATTCATCGCTAACGT 58.653 42.857 0.00 0.00 41.18 3.99
3411 4480 3.517602 AGCAACATTCATCGCTAACGTA 58.482 40.909 0.00 0.00 41.18 3.57
3412 4481 4.119862 AGCAACATTCATCGCTAACGTAT 58.880 39.130 0.00 0.00 41.18 3.06
3413 4482 4.570772 AGCAACATTCATCGCTAACGTATT 59.429 37.500 0.00 0.00 41.18 1.89
3414 4483 5.064707 AGCAACATTCATCGCTAACGTATTT 59.935 36.000 0.00 0.00 41.18 1.40
3415 4484 5.169561 GCAACATTCATCGCTAACGTATTTG 59.830 40.000 0.00 0.00 41.18 2.32
3416 4485 6.474364 CAACATTCATCGCTAACGTATTTGA 58.526 36.000 0.00 0.00 41.18 2.69
3417 4486 6.032722 ACATTCATCGCTAACGTATTTGAC 57.967 37.500 0.00 0.00 41.18 3.18
3418 4487 5.579119 ACATTCATCGCTAACGTATTTGACA 59.421 36.000 0.00 0.00 41.18 3.58
3419 4488 5.444586 TTCATCGCTAACGTATTTGACAC 57.555 39.130 0.00 0.00 41.18 3.67
3420 4489 4.487019 TCATCGCTAACGTATTTGACACA 58.513 39.130 0.00 0.00 41.18 3.72
3421 4490 5.106442 TCATCGCTAACGTATTTGACACAT 58.894 37.500 0.00 0.00 41.18 3.21
3422 4491 6.267070 TCATCGCTAACGTATTTGACACATA 58.733 36.000 0.00 0.00 41.18 2.29
3423 4492 6.921307 TCATCGCTAACGTATTTGACACATAT 59.079 34.615 0.00 0.00 41.18 1.78
3424 4493 8.077386 TCATCGCTAACGTATTTGACACATATA 58.923 33.333 0.00 0.00 41.18 0.86
3425 4494 8.860128 CATCGCTAACGTATTTGACACATATAT 58.140 33.333 0.00 0.00 41.18 0.86
3426 4495 8.806177 TCGCTAACGTATTTGACACATATATT 57.194 30.769 0.00 0.00 41.18 1.28
3427 4496 9.251792 TCGCTAACGTATTTGACACATATATTT 57.748 29.630 0.00 0.00 41.18 1.40
3428 4497 9.512287 CGCTAACGTATTTGACACATATATTTC 57.488 33.333 0.00 0.00 33.53 2.17
3452 4521 2.113860 ATCTTAACACACGCATGGCT 57.886 45.000 0.00 0.00 0.00 4.75
3487 4556 4.649218 GGCTAGGATTTTGGCCAATTTAGA 59.351 41.667 21.26 0.00 43.59 2.10
3537 4606 1.682323 CCTCCGAGCTAACCCTAAGAC 59.318 57.143 0.00 0.00 0.00 3.01
3542 4611 4.957954 TCCGAGCTAACCCTAAGACAAATA 59.042 41.667 0.00 0.00 0.00 1.40
3560 4629 7.382218 AGACAAATAGCGATGAAAAACCAAAAG 59.618 33.333 0.00 0.00 0.00 2.27
3575 4647 9.930158 AAAAACCAAAAGGAGCTATATGGTATA 57.070 29.630 8.91 0.00 40.13 1.47
3606 4678 3.072486 GCATGCCCTCACATGGTGC 62.072 63.158 6.36 0.00 46.14 5.01
3607 4679 2.043652 ATGCCCTCACATGGTGCC 60.044 61.111 0.00 0.00 32.98 5.01
3608 4680 2.921500 ATGCCCTCACATGGTGCCA 61.921 57.895 0.00 0.00 32.98 4.92
3609 4681 2.043652 GCCCTCACATGGTGCCAT 60.044 61.111 0.00 0.00 37.08 4.40
3610 4682 1.683365 GCCCTCACATGGTGCCATT 60.683 57.895 0.13 0.00 33.90 3.16
3611 4683 1.952102 GCCCTCACATGGTGCCATTG 61.952 60.000 0.13 4.43 33.90 2.82
3612 4684 0.612732 CCCTCACATGGTGCCATTGT 60.613 55.000 0.13 1.33 33.90 2.71
3613 4685 0.528924 CCTCACATGGTGCCATTGTG 59.471 55.000 18.80 18.80 37.09 3.33
3616 4688 1.610086 ACATGGTGCCATTGTGGGG 60.610 57.895 0.13 0.00 38.19 4.96
3631 4705 2.223745 GTGGGGTTTAAGCGAACTTCA 58.776 47.619 0.00 0.00 37.33 3.02
3904 4987 5.106712 TGTCGGCAAGATTAACAATTCTGAC 60.107 40.000 0.00 0.00 0.00 3.51
4205 5288 0.319040 CATCGGACTACATGGCCTCG 60.319 60.000 3.32 0.00 43.44 4.63
4395 5481 2.538037 TGTGACGTTGTGAAATCTGACG 59.462 45.455 0.00 0.00 39.43 4.35
5024 6956 0.904865 AGCTCCTTCATGTCCCGTCA 60.905 55.000 0.00 0.00 0.00 4.35
5025 6957 0.179000 GCTCCTTCATGTCCCGTCAT 59.821 55.000 0.00 0.00 0.00 3.06
5026 6958 1.412710 GCTCCTTCATGTCCCGTCATA 59.587 52.381 0.00 0.00 0.00 2.15
5046 6978 9.489084 CGTCATAATATTAGGAAGACCATTTCA 57.511 33.333 15.19 0.00 38.94 2.69
5338 7300 0.323360 GCCATTAGTGTGCCTCCCAA 60.323 55.000 0.00 0.00 0.00 4.12
5376 7338 4.949238 ACATGTGCTTTGCCATACTAATGA 59.051 37.500 0.00 0.00 34.84 2.57
5735 7707 1.003118 CTTCATCCGGTTCCTCCAACA 59.997 52.381 0.00 0.00 36.61 3.33
5777 7749 2.983402 TAGCGCGCGTATCTAGATTT 57.017 45.000 32.35 5.80 0.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
192 205 2.572104 AGTTAGGTCCTCGCTTTCCATT 59.428 45.455 0.00 0.00 0.00 3.16
357 671 5.872070 GTGCATGGGATCTAATTCTAGCTAC 59.128 44.000 0.00 0.00 0.00 3.58
412 726 2.417924 CCATCTCTGGGTCTTTGTCTCG 60.418 54.545 0.00 0.00 39.04 4.04
427 741 0.179179 GCAAAGCTCGTTGCCATCTC 60.179 55.000 11.37 0.00 46.69 2.75
515 830 3.319689 ACCCTTACAAAACACCGAATTGG 59.680 43.478 0.00 0.00 46.41 3.16
630 954 7.592885 ATGGATTGCAGGGAATAATATATGC 57.407 36.000 0.00 0.00 0.00 3.14
637 961 7.039784 GCAAGTAATATGGATTGCAGGGAATAA 60.040 37.037 11.93 0.00 45.66 1.40
642 966 4.510038 GCAAGTAATATGGATTGCAGGG 57.490 45.455 11.93 0.00 45.66 4.45
646 970 2.293122 TGCGGCAAGTAATATGGATTGC 59.707 45.455 0.00 9.43 45.64 3.56
652 976 3.698029 AAAGCTGCGGCAAGTAATATG 57.302 42.857 21.93 0.00 41.70 1.78
663 987 2.159627 CCAGTTTGTACTAAAGCTGCGG 59.840 50.000 4.78 0.00 37.14 5.69
664 988 3.064207 TCCAGTTTGTACTAAAGCTGCG 58.936 45.455 4.78 0.58 37.14 5.18
681 1005 0.669077 CGTTACTCCCTCCGATCCAG 59.331 60.000 0.00 0.00 0.00 3.86
683 1007 1.269998 CATCGTTACTCCCTCCGATCC 59.730 57.143 0.00 0.00 37.91 3.36
684 1008 1.955080 ACATCGTTACTCCCTCCGATC 59.045 52.381 0.00 0.00 37.91 3.69
685 1009 2.068834 ACATCGTTACTCCCTCCGAT 57.931 50.000 0.00 0.00 40.39 4.18
687 1011 2.667473 AAACATCGTTACTCCCTCCG 57.333 50.000 0.00 0.00 0.00 4.63
688 1012 2.928116 CGAAAACATCGTTACTCCCTCC 59.072 50.000 0.00 0.00 46.52 4.30
700 1051 0.035439 TGGGAGAGGGCGAAAACATC 60.035 55.000 0.00 0.00 0.00 3.06
719 1070 0.183492 TTTCAGGTGAACAGCAGGCT 59.817 50.000 6.76 0.00 33.13 4.58
776 1127 8.794553 ACTGCTGAACATATACTACTGTATACC 58.205 37.037 0.00 0.00 42.38 2.73
780 1131 6.096282 TGCACTGCTGAACATATACTACTGTA 59.904 38.462 1.98 0.00 0.00 2.74
807 1159 1.495584 AACATGTGACACGCGTGGTC 61.496 55.000 39.21 31.17 35.46 4.02
808 1160 1.522806 AACATGTGACACGCGTGGT 60.523 52.632 39.21 25.96 35.46 4.16
823 1175 0.545171 TTCACCAACGTACCCCAACA 59.455 50.000 0.00 0.00 0.00 3.33
830 1182 5.225899 ACTTTGAAACTTCACCAACGTAC 57.774 39.130 0.00 0.00 36.83 3.67
921 1277 0.036577 GAGCTAGATGGCGCATGGAT 60.037 55.000 10.83 0.00 37.29 3.41
1017 1373 6.100279 TGCTGGAGATGGTGAGTATTATTCTT 59.900 38.462 0.00 0.00 0.00 2.52
1279 1648 5.677178 GGAAGCAATAACAATTTCGATCGTC 59.323 40.000 15.94 0.00 0.00 4.20
1293 1662 4.314522 TGAAGGTCCATGGAAGCAATAA 57.685 40.909 18.20 0.00 0.00 1.40
1344 1713 6.311935 ACCTTGATTGCAAATCATTTCATTCG 59.688 34.615 1.71 0.00 32.73 3.34
1361 1730 4.222810 GCTTCAATACCCCAAACCTTGATT 59.777 41.667 0.00 0.00 0.00 2.57
1396 1767 7.284716 TGAACATCATATAGTACGAGAACCAGT 59.715 37.037 0.00 0.00 0.00 4.00
1514 1896 9.743057 CAAAACCACATTTAGAAACTTATGACA 57.257 29.630 0.00 0.00 0.00 3.58
1777 2159 0.183492 TCCTTGCACTGAACAAGCCT 59.817 50.000 8.31 0.00 42.57 4.58
1823 2252 9.396022 ACTTACAGAGAGAAAACAGATTTTGAA 57.604 29.630 0.00 0.00 38.17 2.69
1825 2254 8.072567 CCACTTACAGAGAGAAAACAGATTTTG 58.927 37.037 0.00 0.00 38.17 2.44
1826 2255 7.775561 ACCACTTACAGAGAGAAAACAGATTTT 59.224 33.333 0.00 0.00 40.83 1.82
1839 2268 7.732025 TCTACAAATCAAACCACTTACAGAGA 58.268 34.615 0.00 0.00 0.00 3.10
1991 2420 4.600062 AGACCCTAATTAACCCAAAGCAG 58.400 43.478 0.00 0.00 0.00 4.24
1992 2421 4.043561 TGAGACCCTAATTAACCCAAAGCA 59.956 41.667 0.00 0.00 0.00 3.91
2104 2536 3.252701 CGATAGTGAGTGGGCTAACGTAT 59.747 47.826 0.00 0.00 31.18 3.06
2246 2678 6.013639 AGCACACTTGGGACTAAAATACTACT 60.014 38.462 0.00 0.00 0.00 2.57
2435 2867 6.690194 TTTTGTTTCCCAATTGGTTCATTG 57.310 33.333 22.91 6.77 31.81 2.82
2675 3107 6.957920 TTCATCTTCAAAAATGTGACCAGA 57.042 33.333 0.00 0.00 0.00 3.86
2742 3806 4.609691 TTTGACAGTCTCGGAACAAAAC 57.390 40.909 1.31 0.00 0.00 2.43
2790 3854 9.716556 ACTAATATGGATCGTAGGGAGAATATT 57.283 33.333 0.00 0.00 0.00 1.28
2815 3879 5.912955 GGCTTTGTACTACATCAACAACAAC 59.087 40.000 0.00 0.00 33.10 3.32
2830 3894 8.917415 ATTTAGTACTTAGTACGGCTTTGTAC 57.083 34.615 15.73 6.40 43.05 2.90
2832 3896 7.605449 TGATTTAGTACTTAGTACGGCTTTGT 58.395 34.615 15.73 0.84 43.05 2.83
2833 3897 8.378421 GTTGATTTAGTACTTAGTACGGCTTTG 58.622 37.037 15.73 0.00 43.05 2.77
2858 3922 9.672673 CTCCCTCCGATCAATATTAATTATTGT 57.327 33.333 0.00 0.00 45.03 2.71
2872 3936 7.664552 TTAAATTTACTACTCCCTCCGATCA 57.335 36.000 0.00 0.00 0.00 2.92
2912 3976 6.088217 CGTAGTATGACTCATTAATTGCCTCG 59.912 42.308 0.00 0.00 0.00 4.63
2914 3978 6.817184 ACGTAGTATGACTCATTAATTGCCT 58.183 36.000 0.00 0.00 41.94 4.75
2936 4000 0.165079 GTGTGCGGGTGTTTCATACG 59.835 55.000 0.00 0.00 0.00 3.06
2947 4011 1.879380 TCTTGAATGAAAGTGTGCGGG 59.121 47.619 0.00 0.00 0.00 6.13
3064 4131 3.868661 AGCCGAAACCAATTTGACAAAAC 59.131 39.130 4.41 0.00 0.00 2.43
3071 4138 7.701809 TTTAGTTTTAGCCGAAACCAATTTG 57.298 32.000 8.45 0.00 39.71 2.32
3072 4139 9.414295 GTATTTAGTTTTAGCCGAAACCAATTT 57.586 29.630 8.45 0.00 39.71 1.82
3073 4140 7.751793 CGTATTTAGTTTTAGCCGAAACCAATT 59.248 33.333 8.45 2.68 39.71 2.32
3083 4150 7.700505 ACTTTATGGCGTATTTAGTTTTAGCC 58.299 34.615 0.00 0.00 43.05 3.93
3087 4154 8.101654 TGTGACTTTATGGCGTATTTAGTTTT 57.898 30.769 0.00 0.00 0.00 2.43
3096 4163 5.334569 GCTTTCTTTGTGACTTTATGGCGTA 60.335 40.000 0.00 0.00 0.00 4.42
3103 4170 4.578928 GGAGTGGCTTTCTTTGTGACTTTA 59.421 41.667 0.00 0.00 0.00 1.85
3104 4171 3.381590 GGAGTGGCTTTCTTTGTGACTTT 59.618 43.478 0.00 0.00 0.00 2.66
3107 4174 2.576615 AGGAGTGGCTTTCTTTGTGAC 58.423 47.619 0.00 0.00 0.00 3.67
3108 4175 4.134563 GTTAGGAGTGGCTTTCTTTGTGA 58.865 43.478 0.00 0.00 0.00 3.58
3189 4258 4.513442 TGCTAGTATCTTGCGGTTCAAAT 58.487 39.130 0.00 0.00 35.17 2.32
3197 4266 8.184848 ACATGTACTATATGCTAGTATCTTGCG 58.815 37.037 0.00 0.00 35.17 4.85
3244 4313 1.215382 GCCAAATTCGTCCAAGGCC 59.785 57.895 0.00 0.00 36.17 5.19
3267 4336 8.653191 GGGGTAATCCTCCTTTTTAAAAAGAAA 58.347 33.333 32.65 21.85 40.60 2.52
3269 4338 7.786046 GGGGTAATCCTCCTTTTTAAAAAGA 57.214 36.000 32.65 20.73 40.60 2.52
3282 4351 2.447959 AGGCCGGGGGTAATCCTC 60.448 66.667 2.18 0.00 35.33 3.71
3283 4352 2.447959 GAGGCCGGGGGTAATCCT 60.448 66.667 2.18 0.00 35.33 3.24
3284 4353 2.447959 AGAGGCCGGGGGTAATCC 60.448 66.667 2.18 0.00 0.00 3.01
3285 4354 2.829592 CAGAGGCCGGGGGTAATC 59.170 66.667 2.18 0.00 0.00 1.75
3286 4355 3.489513 GCAGAGGCCGGGGGTAAT 61.490 66.667 2.18 0.00 0.00 1.89
3288 4357 4.815973 ATGCAGAGGCCGGGGGTA 62.816 66.667 2.18 0.00 40.13 3.69
3291 4360 4.559063 CAGATGCAGAGGCCGGGG 62.559 72.222 2.18 0.00 40.13 5.73
3292 4361 4.559063 CCAGATGCAGAGGCCGGG 62.559 72.222 2.18 0.00 40.13 5.73
3293 4362 3.473647 TCCAGATGCAGAGGCCGG 61.474 66.667 0.00 0.00 40.13 6.13
3294 4363 2.202987 GTCCAGATGCAGAGGCCG 60.203 66.667 0.00 0.00 40.13 6.13
3295 4364 2.037620 ATCGTCCAGATGCAGAGGCC 62.038 60.000 0.00 0.00 38.36 5.19
3296 4365 1.445095 ATCGTCCAGATGCAGAGGC 59.555 57.895 0.00 0.00 38.36 4.70
3304 4373 1.019673 GTTGCATGCATCGTCCAGAT 58.980 50.000 23.37 0.00 41.01 2.90
3305 4374 1.026182 GGTTGCATGCATCGTCCAGA 61.026 55.000 23.37 0.00 0.00 3.86
3306 4375 1.307355 TGGTTGCATGCATCGTCCAG 61.307 55.000 23.37 0.00 0.00 3.86
3307 4376 0.680601 ATGGTTGCATGCATCGTCCA 60.681 50.000 23.37 24.57 0.00 4.02
3308 4377 0.457035 AATGGTTGCATGCATCGTCC 59.543 50.000 23.37 20.20 0.00 4.79
3309 4378 2.282701 AAATGGTTGCATGCATCGTC 57.717 45.000 23.37 12.09 0.00 4.20
3310 4379 2.747396 AAAATGGTTGCATGCATCGT 57.253 40.000 23.37 15.17 0.00 3.73
3311 4380 5.721876 AATAAAAATGGTTGCATGCATCG 57.278 34.783 23.37 0.00 0.00 3.84
3344 4413 8.657712 ACCTGAGTACTATTTTGTAAGGTCTTT 58.342 33.333 0.00 0.00 29.87 2.52
3345 4414 8.203681 ACCTGAGTACTATTTTGTAAGGTCTT 57.796 34.615 0.00 0.00 29.87 3.01
3346 4415 7.793948 ACCTGAGTACTATTTTGTAAGGTCT 57.206 36.000 0.00 0.00 29.87 3.85
3347 4416 8.747471 ACTACCTGAGTACTATTTTGTAAGGTC 58.253 37.037 0.00 0.00 36.27 3.85
3348 4417 8.661752 ACTACCTGAGTACTATTTTGTAAGGT 57.338 34.615 0.00 2.29 36.27 3.50
3349 4418 8.968969 AGACTACCTGAGTACTATTTTGTAAGG 58.031 37.037 0.00 0.00 39.06 2.69
3350 4419 9.790389 CAGACTACCTGAGTACTATTTTGTAAG 57.210 37.037 0.00 0.00 45.78 2.34
3351 4420 9.524496 TCAGACTACCTGAGTACTATTTTGTAA 57.476 33.333 0.00 0.00 46.38 2.41
3366 4435 0.976641 TGGTGGCTTCAGACTACCTG 59.023 55.000 0.00 0.00 44.27 4.00
3367 4436 1.834263 GATGGTGGCTTCAGACTACCT 59.166 52.381 0.00 0.00 32.68 3.08
3368 4437 1.834263 AGATGGTGGCTTCAGACTACC 59.166 52.381 0.00 0.00 0.00 3.18
3369 4438 3.618690 AAGATGGTGGCTTCAGACTAC 57.381 47.619 0.00 0.00 0.00 2.73
3370 4439 3.133003 GCTAAGATGGTGGCTTCAGACTA 59.867 47.826 0.00 0.00 0.00 2.59
3371 4440 2.093235 GCTAAGATGGTGGCTTCAGACT 60.093 50.000 0.00 0.00 0.00 3.24
3372 4441 2.284190 GCTAAGATGGTGGCTTCAGAC 58.716 52.381 0.00 0.00 0.00 3.51
3373 4442 1.908619 TGCTAAGATGGTGGCTTCAGA 59.091 47.619 0.00 0.00 0.00 3.27
3374 4443 2.408271 TGCTAAGATGGTGGCTTCAG 57.592 50.000 0.00 0.00 0.00 3.02
3375 4444 2.224744 TGTTGCTAAGATGGTGGCTTCA 60.225 45.455 0.00 0.00 0.00 3.02
3376 4445 2.436417 TGTTGCTAAGATGGTGGCTTC 58.564 47.619 0.00 0.00 0.00 3.86
3377 4446 2.584835 TGTTGCTAAGATGGTGGCTT 57.415 45.000 0.00 0.00 0.00 4.35
3378 4447 2.814805 ATGTTGCTAAGATGGTGGCT 57.185 45.000 0.00 0.00 0.00 4.75
3379 4448 2.754552 TGAATGTTGCTAAGATGGTGGC 59.245 45.455 0.00 0.00 0.00 5.01
3380 4449 4.260907 CGATGAATGTTGCTAAGATGGTGG 60.261 45.833 0.00 0.00 0.00 4.61
3381 4450 4.787563 GCGATGAATGTTGCTAAGATGGTG 60.788 45.833 0.00 0.00 0.00 4.17
3382 4451 3.313526 GCGATGAATGTTGCTAAGATGGT 59.686 43.478 0.00 0.00 0.00 3.55
3383 4452 3.562973 AGCGATGAATGTTGCTAAGATGG 59.437 43.478 0.00 0.00 37.07 3.51
3384 4453 4.808077 AGCGATGAATGTTGCTAAGATG 57.192 40.909 0.00 0.00 37.07 2.90
3385 4454 5.050769 CGTTAGCGATGAATGTTGCTAAGAT 60.051 40.000 8.44 0.00 46.46 2.40
3386 4455 4.267690 CGTTAGCGATGAATGTTGCTAAGA 59.732 41.667 8.44 0.00 46.46 2.10
3387 4456 4.032900 ACGTTAGCGATGAATGTTGCTAAG 59.967 41.667 5.81 6.41 46.46 2.18
3388 4457 3.930229 ACGTTAGCGATGAATGTTGCTAA 59.070 39.130 5.81 4.84 44.71 3.09
3389 4458 3.517602 ACGTTAGCGATGAATGTTGCTA 58.482 40.909 5.81 0.00 39.52 3.49
3390 4459 2.346803 ACGTTAGCGATGAATGTTGCT 58.653 42.857 5.81 0.00 41.62 3.91
3391 4460 2.806288 ACGTTAGCGATGAATGTTGC 57.194 45.000 5.81 0.00 42.00 4.17
3392 4461 6.408039 GTCAAATACGTTAGCGATGAATGTTG 59.592 38.462 5.81 0.78 42.00 3.33
3393 4462 6.091577 TGTCAAATACGTTAGCGATGAATGTT 59.908 34.615 5.81 0.00 42.00 2.71
3394 4463 5.579119 TGTCAAATACGTTAGCGATGAATGT 59.421 36.000 5.81 0.00 42.00 2.71
3395 4464 5.896432 GTGTCAAATACGTTAGCGATGAATG 59.104 40.000 5.81 0.00 42.00 2.67
3396 4465 5.579119 TGTGTCAAATACGTTAGCGATGAAT 59.421 36.000 5.81 0.00 42.00 2.57
3397 4466 4.924462 TGTGTCAAATACGTTAGCGATGAA 59.076 37.500 5.81 0.00 42.00 2.57
3398 4467 4.487019 TGTGTCAAATACGTTAGCGATGA 58.513 39.130 5.81 1.99 42.00 2.92
3399 4468 4.833469 TGTGTCAAATACGTTAGCGATG 57.167 40.909 5.81 0.00 42.00 3.84
3400 4469 8.981724 ATATATGTGTCAAATACGTTAGCGAT 57.018 30.769 5.81 0.00 42.00 4.58
3401 4470 8.806177 AATATATGTGTCAAATACGTTAGCGA 57.194 30.769 5.81 0.00 42.00 4.93
3402 4471 9.512287 GAAATATATGTGTCAAATACGTTAGCG 57.488 33.333 0.00 0.00 44.93 4.26
3420 4489 9.716507 GCGTGTGTTAAGATTGTTGAAATATAT 57.283 29.630 0.00 0.00 0.00 0.86
3421 4490 8.722394 TGCGTGTGTTAAGATTGTTGAAATATA 58.278 29.630 0.00 0.00 0.00 0.86
3422 4491 7.589395 TGCGTGTGTTAAGATTGTTGAAATAT 58.411 30.769 0.00 0.00 0.00 1.28
3423 4492 6.960468 TGCGTGTGTTAAGATTGTTGAAATA 58.040 32.000 0.00 0.00 0.00 1.40
3424 4493 5.826586 TGCGTGTGTTAAGATTGTTGAAAT 58.173 33.333 0.00 0.00 0.00 2.17
3425 4494 5.236655 TGCGTGTGTTAAGATTGTTGAAA 57.763 34.783 0.00 0.00 0.00 2.69
3426 4495 4.884458 TGCGTGTGTTAAGATTGTTGAA 57.116 36.364 0.00 0.00 0.00 2.69
3427 4496 4.320129 CCATGCGTGTGTTAAGATTGTTGA 60.320 41.667 4.96 0.00 0.00 3.18
3428 4497 3.913763 CCATGCGTGTGTTAAGATTGTTG 59.086 43.478 4.96 0.00 0.00 3.33
3429 4498 3.611530 GCCATGCGTGTGTTAAGATTGTT 60.612 43.478 4.96 0.00 0.00 2.83
3461 4530 1.076995 GGCCAAAATCCTAGCCCGT 60.077 57.895 0.00 0.00 39.60 5.28
3487 4556 5.397672 GGATTGATCTAGCAGGCCATATGAT 60.398 44.000 5.01 1.35 0.00 2.45
3537 4606 6.644592 TCCTTTTGGTTTTTCATCGCTATTTG 59.355 34.615 0.00 0.00 41.38 2.32
3542 4611 3.552890 GCTCCTTTTGGTTTTTCATCGCT 60.553 43.478 0.00 0.00 41.38 4.93
3606 4678 1.540267 TCGCTTAAACCCCACAATGG 58.460 50.000 0.00 0.00 37.25 3.16
3607 4679 2.556622 AGTTCGCTTAAACCCCACAATG 59.443 45.455 0.00 0.00 0.00 2.82
3608 4680 2.871453 AGTTCGCTTAAACCCCACAAT 58.129 42.857 0.00 0.00 0.00 2.71
3609 4681 2.351706 AGTTCGCTTAAACCCCACAA 57.648 45.000 0.00 0.00 0.00 3.33
3610 4682 2.223745 GAAGTTCGCTTAAACCCCACA 58.776 47.619 0.00 0.00 37.61 4.17
3611 4683 2.223745 TGAAGTTCGCTTAAACCCCAC 58.776 47.619 0.00 0.00 37.61 4.61
3612 4684 2.642154 TGAAGTTCGCTTAAACCCCA 57.358 45.000 0.00 0.00 37.61 4.96
3613 4685 3.504520 TGATTGAAGTTCGCTTAAACCCC 59.495 43.478 0.00 0.00 37.61 4.95
3616 4688 4.613031 GCTGTGATTGAAGTTCGCTTAAAC 59.387 41.667 0.00 0.00 37.61 2.01
3631 4705 5.657474 CAGCATAATTTTCCAGCTGTGATT 58.343 37.500 13.81 9.23 45.57 2.57
3904 4987 3.733443 TCGTGTCACATAGATGATGGG 57.267 47.619 3.42 0.00 40.73 4.00
4205 5288 0.460811 TCTGCTGGATGTGCATCGAC 60.461 55.000 6.14 0.00 39.86 4.20
4998 6930 1.227089 CATGAAGGAGCTCCGTCGG 60.227 63.158 34.03 26.92 45.68 4.79
5002 6934 1.144936 GGGACATGAAGGAGCTCCG 59.855 63.158 26.95 14.74 42.08 4.63
5046 6978 1.398692 AACAGCACCAACCGTTCATT 58.601 45.000 0.00 0.00 0.00 2.57
5257 7203 7.980099 GCGCCATTAGTATACCAGATACTAATT 59.020 37.037 20.00 9.00 47.00 1.40
5338 7300 3.476552 CACATGTGTAAATATCGCCCCT 58.523 45.455 18.03 0.00 0.00 4.79
5376 7338 2.032528 CATCACCCCACAGTGCGT 59.967 61.111 0.00 0.00 37.68 5.24
5735 7707 3.011885 CGGGAGAGAGGAGGGAGT 58.988 66.667 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.