Multiple sequence alignment - TraesCS6B01G185300

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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 TraesCS6B01G185300 chr6B 100.000 2810 0 0 1 2810 210607631 210610440 0.000000e+00 5190.0
1 TraesCS6B01G185300 chr6D 91.399 1616 115 18 1 1612 119110894 119112489 0.000000e+00 2193.0
2 TraesCS6B01G185300 chr6D 86.612 859 73 29 1964 2789 377176717 377175868 0.000000e+00 911.0
3 TraesCS6B01G185300 chr6D 92.032 251 16 4 2563 2810 147887760 147887511 1.600000e-92 350.0
4 TraesCS6B01G185300 chr6A 95.393 1324 55 4 537 1860 147252665 147253982 0.000000e+00 2102.0
5 TraesCS6B01G185300 chr6A 88.106 681 56 17 1962 2627 486347425 486346755 0.000000e+00 785.0
6 TraesCS6B01G185300 chr6A 84.942 518 52 13 1 514 147251132 147251627 4.180000e-138 501.0
7 TraesCS6B01G185300 chr6A 86.364 88 11 1 349 436 9461201 9461115 8.290000e-16 95.3
8 TraesCS6B01G185300 chr7A 86.326 841 92 17 1962 2789 732161183 732162013 0.000000e+00 894.0
9 TraesCS6B01G185300 chr4D 88.856 682 50 18 1961 2627 40798942 40799612 0.000000e+00 815.0
10 TraesCS6B01G185300 chr4D 88.467 685 51 18 1961 2627 483163805 483164479 0.000000e+00 802.0
11 TraesCS6B01G185300 chr4D 88.175 685 53 18 1961 2627 483156009 483156683 0.000000e+00 791.0
12 TraesCS6B01G185300 chr4D 74.731 744 151 24 739 1464 3260764 3260040 5.880000e-77 298.0
13 TraesCS6B01G185300 chr4D 73.046 742 158 24 738 1464 2071014 2071728 1.010000e-54 224.0
14 TraesCS6B01G185300 chr4D 97.059 34 0 1 963 995 497224203 497224170 3.910000e-04 56.5
15 TraesCS6B01G185300 chr7D 88.563 682 53 13 1957 2627 560575816 560575149 0.000000e+00 804.0
16 TraesCS6B01G185300 chr7D 76.098 979 178 40 693 1645 624769098 624770046 7.090000e-126 460.0
17 TraesCS6B01G185300 chr7D 92.032 251 17 3 2563 2810 145919698 145919948 1.600000e-92 350.0
18 TraesCS6B01G185300 chr7D 91.600 250 19 2 2563 2810 576644682 576644931 7.450000e-91 344.0
19 TraesCS6B01G185300 chr1D 88.546 681 50 22 1964 2627 463249902 463250571 0.000000e+00 800.0
20 TraesCS6B01G185300 chr1D 92.400 250 16 3 2563 2810 444890544 444890296 1.240000e-93 353.0
21 TraesCS6B01G185300 chr5D 88.218 679 55 17 1965 2627 483581771 483581102 0.000000e+00 787.0
22 TraesCS6B01G185300 chr5D 77.399 938 156 36 727 1648 560224909 560225806 8.980000e-140 507.0
23 TraesCS6B01G185300 chr5D 74.534 483 96 20 920 1395 438519726 438519264 4.780000e-43 185.0
24 TraesCS6B01G185300 chr3A 77.662 958 174 33 709 1648 663441806 663440871 5.290000e-152 547.0
25 TraesCS6B01G185300 chr3A 76.550 968 190 30 696 1648 663451958 663451013 1.940000e-136 496.0
26 TraesCS6B01G185300 chr3B 76.106 1130 220 37 696 1811 700073342 700072249 1.900000e-151 545.0
27 TraesCS6B01G185300 chr3B 91.600 250 18 3 2564 2810 709292226 709292475 2.680000e-90 342.0
28 TraesCS6B01G185300 chr3B 72.868 903 187 37 705 1596 739572752 739573607 9.990000e-65 257.0
29 TraesCS6B01G185300 chr3D 77.381 924 180 24 739 1648 529496477 529495569 3.210000e-144 521.0
30 TraesCS6B01G185300 chr3D 75.284 967 182 37 696 1648 529503770 529502847 2.610000e-110 409.0
31 TraesCS6B01G185300 chr3D 71.881 1106 219 57 705 1786 557461266 557462303 4.680000e-58 235.0
32 TraesCS6B01G185300 chr5B 74.593 1106 218 42 727 1810 711858982 711857918 7.190000e-116 427.0
33 TraesCS6B01G185300 chr4A 74.616 1107 206 57 739 1810 663696119 663695053 4.330000e-113 418.0
34 TraesCS6B01G185300 chr4A 74.677 774 159 24 709 1464 602260039 602260793 2.720000e-80 309.0
35 TraesCS6B01G185300 chr4A 95.000 40 1 1 397 436 136231741 136231779 8.400000e-06 62.1
36 TraesCS6B01G185300 chr2D 91.633 251 17 4 2563 2810 194748470 194748221 7.450000e-91 344.0
37 TraesCS6B01G185300 chr2D 91.566 249 18 3 2563 2810 571192493 571192739 9.640000e-90 340.0
38 TraesCS6B01G185300 chr2D 84.483 116 18 0 709 824 589503629 589503514 6.360000e-22 115.0
39 TraesCS6B01G185300 chr7B 91.600 250 17 3 2563 2810 616548892 616548645 2.680000e-90 342.0
40 TraesCS6B01G185300 chr4B 73.975 976 178 53 727 1657 668873296 668874240 2.700000e-85 326.0
41 TraesCS6B01G185300 chr4B 72.351 774 177 20 709 1464 3784868 3785622 2.840000e-50 209.0
42 TraesCS6B01G185300 chr4B 93.056 72 4 1 364 435 148918181 148918111 1.380000e-18 104.0
43 TraesCS6B01G185300 chrUn 85.417 96 14 0 729 824 28781518 28781613 1.780000e-17 100.0
44 TraesCS6B01G185300 chrUn 75.648 193 42 5 962 1152 47780607 47780418 1.070000e-14 91.6
45 TraesCS6B01G185300 chr2B 97.368 38 1 0 1553 1590 17836048 17836011 6.500000e-07 65.8


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 TraesCS6B01G185300 chr6B 210607631 210610440 2809 False 5190.0 5190 100.0000 1 2810 1 chr6B.!!$F1 2809
1 TraesCS6B01G185300 chr6D 119110894 119112489 1595 False 2193.0 2193 91.3990 1 1612 1 chr6D.!!$F1 1611
2 TraesCS6B01G185300 chr6D 377175868 377176717 849 True 911.0 911 86.6120 1964 2789 1 chr6D.!!$R2 825
3 TraesCS6B01G185300 chr6A 147251132 147253982 2850 False 1301.5 2102 90.1675 1 1860 2 chr6A.!!$F1 1859
4 TraesCS6B01G185300 chr6A 486346755 486347425 670 True 785.0 785 88.1060 1962 2627 1 chr6A.!!$R2 665
5 TraesCS6B01G185300 chr7A 732161183 732162013 830 False 894.0 894 86.3260 1962 2789 1 chr7A.!!$F1 827
6 TraesCS6B01G185300 chr4D 40798942 40799612 670 False 815.0 815 88.8560 1961 2627 1 chr4D.!!$F2 666
7 TraesCS6B01G185300 chr4D 483163805 483164479 674 False 802.0 802 88.4670 1961 2627 1 chr4D.!!$F4 666
8 TraesCS6B01G185300 chr4D 483156009 483156683 674 False 791.0 791 88.1750 1961 2627 1 chr4D.!!$F3 666
9 TraesCS6B01G185300 chr4D 3260040 3260764 724 True 298.0 298 74.7310 739 1464 1 chr4D.!!$R1 725
10 TraesCS6B01G185300 chr4D 2071014 2071728 714 False 224.0 224 73.0460 738 1464 1 chr4D.!!$F1 726
11 TraesCS6B01G185300 chr7D 560575149 560575816 667 True 804.0 804 88.5630 1957 2627 1 chr7D.!!$R1 670
12 TraesCS6B01G185300 chr7D 624769098 624770046 948 False 460.0 460 76.0980 693 1645 1 chr7D.!!$F3 952
13 TraesCS6B01G185300 chr1D 463249902 463250571 669 False 800.0 800 88.5460 1964 2627 1 chr1D.!!$F1 663
14 TraesCS6B01G185300 chr5D 483581102 483581771 669 True 787.0 787 88.2180 1965 2627 1 chr5D.!!$R2 662
15 TraesCS6B01G185300 chr5D 560224909 560225806 897 False 507.0 507 77.3990 727 1648 1 chr5D.!!$F1 921
16 TraesCS6B01G185300 chr3A 663440871 663441806 935 True 547.0 547 77.6620 709 1648 1 chr3A.!!$R1 939
17 TraesCS6B01G185300 chr3A 663451013 663451958 945 True 496.0 496 76.5500 696 1648 1 chr3A.!!$R2 952
18 TraesCS6B01G185300 chr3B 700072249 700073342 1093 True 545.0 545 76.1060 696 1811 1 chr3B.!!$R1 1115
19 TraesCS6B01G185300 chr3B 739572752 739573607 855 False 257.0 257 72.8680 705 1596 1 chr3B.!!$F2 891
20 TraesCS6B01G185300 chr3D 529495569 529496477 908 True 521.0 521 77.3810 739 1648 1 chr3D.!!$R1 909
21 TraesCS6B01G185300 chr3D 529502847 529503770 923 True 409.0 409 75.2840 696 1648 1 chr3D.!!$R2 952
22 TraesCS6B01G185300 chr3D 557461266 557462303 1037 False 235.0 235 71.8810 705 1786 1 chr3D.!!$F1 1081
23 TraesCS6B01G185300 chr5B 711857918 711858982 1064 True 427.0 427 74.5930 727 1810 1 chr5B.!!$R1 1083
24 TraesCS6B01G185300 chr4A 663695053 663696119 1066 True 418.0 418 74.6160 739 1810 1 chr4A.!!$R1 1071
25 TraesCS6B01G185300 chr4A 602260039 602260793 754 False 309.0 309 74.6770 709 1464 1 chr4A.!!$F2 755
26 TraesCS6B01G185300 chr4B 668873296 668874240 944 False 326.0 326 73.9750 727 1657 1 chr4B.!!$F2 930
27 TraesCS6B01G185300 chr4B 3784868 3785622 754 False 209.0 209 72.3510 709 1464 1 chr4B.!!$F1 755

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
879 1919 0.03213 GCTTCGCGATCCCAGTCATA 59.968 55.0 10.88 0.0 0.0 2.15 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1903 3024 0.10412 TCCCATTCTACGGACGCATG 59.896 55.0 0.0 0.0 0.0 4.06 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
47 48 2.151202 GCAGAAACATGGAGACGGAAA 58.849 47.619 0.00 0.00 0.00 3.13
98 99 2.127118 CGACGTACACGGAAGCGT 60.127 61.111 6.72 0.00 44.95 5.07
99 100 1.132436 CGACGTACACGGAAGCGTA 59.868 57.895 6.72 0.00 44.95 4.42
121 123 1.812235 TTCGCTTGCACATGATCAGT 58.188 45.000 0.00 0.00 0.00 3.41
126 128 0.036105 TTGCACATGATCAGTCGGCT 60.036 50.000 0.00 0.00 0.00 5.52
127 129 0.741927 TGCACATGATCAGTCGGCTG 60.742 55.000 11.77 11.77 43.87 4.85
128 130 2.012237 CACATGATCAGTCGGCTGC 58.988 57.895 13.43 0.00 42.29 5.25
209 211 2.360600 GGCGGTGGTGGTTGCATA 60.361 61.111 0.00 0.00 0.00 3.14
211 213 3.051392 GCGGTGGTGGTTGCATAGC 62.051 63.158 0.00 0.00 0.00 2.97
218 220 1.153647 TGGTTGCATAGCGTCGGAG 60.154 57.895 0.00 0.00 0.00 4.63
233 235 0.839946 CGGAGGACATTCAATCCCCT 59.160 55.000 0.00 0.00 36.86 4.79
297 301 3.603965 ATCTTGATACTCGGACCTCCT 57.396 47.619 0.00 0.00 0.00 3.69
309 313 2.261729 GGACCTCCTCCAACTTCTCTT 58.738 52.381 0.00 0.00 39.21 2.85
326 330 8.115490 ACTTCTCTTAGAATTTTGAACCCATG 57.885 34.615 0.00 0.00 33.13 3.66
328 332 9.231297 CTTCTCTTAGAATTTTGAACCCATGTA 57.769 33.333 0.00 0.00 33.13 2.29
329 333 9.581289 TTCTCTTAGAATTTTGAACCCATGTAA 57.419 29.630 0.00 0.00 0.00 2.41
357 361 4.362677 TGACAATCCTAGCTACTCCCTTT 58.637 43.478 0.00 0.00 0.00 3.11
361 365 3.759815 TCCTAGCTACTCCCTTTGTCT 57.240 47.619 0.00 0.00 0.00 3.41
362 366 4.062490 TCCTAGCTACTCCCTTTGTCTT 57.938 45.455 0.00 0.00 0.00 3.01
366 370 7.005296 TCCTAGCTACTCCCTTTGTCTTATAG 58.995 42.308 0.00 0.00 0.00 1.31
454 458 9.403110 GAAGTAGTTACGATGAAAACAACTAGA 57.597 33.333 0.00 0.00 33.59 2.43
508 512 3.003378 GGAAAAGTTGAGTGAAGGTTCGG 59.997 47.826 0.00 0.00 0.00 4.30
514 518 2.833794 TGAGTGAAGGTTCGGTTCTTG 58.166 47.619 0.00 0.00 0.00 3.02
519 524 4.515567 AGTGAAGGTTCGGTTCTTGAATTC 59.484 41.667 0.00 0.00 0.00 2.17
677 1696 1.302351 GCAGCAGCTGTTCACCTCT 60.302 57.895 23.60 0.00 37.91 3.69
689 1708 0.884704 TCACCTCTTTTGCTCACGCC 60.885 55.000 0.00 0.00 34.43 5.68
879 1919 0.032130 GCTTCGCGATCCCAGTCATA 59.968 55.000 10.88 0.00 0.00 2.15
902 1957 3.220999 TTGCTGGAGTGACGACGGG 62.221 63.158 0.00 0.00 0.00 5.28
904 1959 2.989824 CTGGAGTGACGACGGGGT 60.990 66.667 0.00 0.00 0.00 4.95
947 2002 4.379243 CGAGGTGAAGGCAGCCGT 62.379 66.667 5.55 1.27 43.41 5.68
948 2003 2.032681 GAGGTGAAGGCAGCCGTT 59.967 61.111 5.55 0.24 43.41 4.44
949 2004 1.295423 GAGGTGAAGGCAGCCGTTA 59.705 57.895 5.55 0.00 43.41 3.18
1313 2401 4.020617 TGGGTTCCTGGAGCAGCG 62.021 66.667 12.78 0.00 0.00 5.18
1446 2534 0.687757 TGCTCCTCCAGGATAGCGTT 60.688 55.000 15.83 0.00 44.46 4.84
1638 2753 2.032681 GTCTCCGTGGCCTGCTTT 59.967 61.111 3.32 0.00 0.00 3.51
1743 2858 3.005539 AGCGCCACAGTGGAGGAT 61.006 61.111 24.96 9.95 40.96 3.24
1836 2957 4.082733 CGATCCATCAAAGGCTACTCGATA 60.083 45.833 0.00 0.00 0.00 2.92
1865 2986 2.922779 TGTGATCACAGCACAGCAG 58.077 52.632 24.56 0.00 41.00 4.24
1866 2987 1.232621 TGTGATCACAGCACAGCAGC 61.233 55.000 24.56 0.00 41.00 5.25
1868 2989 0.609662 TGATCACAGCACAGCAGCTA 59.390 50.000 0.00 0.00 44.54 3.32
1869 2990 1.288350 GATCACAGCACAGCAGCTAG 58.712 55.000 0.00 0.00 44.54 3.42
1870 2991 0.743701 ATCACAGCACAGCAGCTAGC 60.744 55.000 6.62 6.62 44.54 3.42
1891 3012 3.149899 CAAGCCTGCAAGTCGATCT 57.850 52.632 0.00 0.00 0.00 2.75
1892 3013 2.299993 CAAGCCTGCAAGTCGATCTA 57.700 50.000 0.00 0.00 0.00 1.98
1893 3014 1.929836 CAAGCCTGCAAGTCGATCTAC 59.070 52.381 0.00 0.00 0.00 2.59
1894 3015 1.479709 AGCCTGCAAGTCGATCTACT 58.520 50.000 0.00 0.00 0.00 2.57
1895 3016 1.827969 AGCCTGCAAGTCGATCTACTT 59.172 47.619 6.80 6.80 40.33 2.24
1896 3017 2.234908 AGCCTGCAAGTCGATCTACTTT 59.765 45.455 9.78 0.00 37.61 2.66
1897 3018 2.349886 GCCTGCAAGTCGATCTACTTTG 59.650 50.000 9.78 7.35 37.61 2.77
1898 3019 2.349886 CCTGCAAGTCGATCTACTTTGC 59.650 50.000 18.80 18.80 37.61 3.68
1899 3020 1.992667 TGCAAGTCGATCTACTTTGCG 59.007 47.619 19.57 9.37 37.61 4.85
1900 3021 1.993370 GCAAGTCGATCTACTTTGCGT 59.007 47.619 9.78 0.00 37.61 5.24
1901 3022 2.412089 GCAAGTCGATCTACTTTGCGTT 59.588 45.455 9.78 0.00 37.61 4.84
1902 3023 3.611113 GCAAGTCGATCTACTTTGCGTTA 59.389 43.478 9.78 0.00 37.61 3.18
1903 3024 4.490479 GCAAGTCGATCTACTTTGCGTTAC 60.490 45.833 9.78 0.00 37.61 2.50
1904 3025 4.430137 AGTCGATCTACTTTGCGTTACA 57.570 40.909 0.00 0.00 0.00 2.41
1905 3026 4.995124 AGTCGATCTACTTTGCGTTACAT 58.005 39.130 0.00 0.00 0.00 2.29
1906 3027 4.798907 AGTCGATCTACTTTGCGTTACATG 59.201 41.667 0.00 0.00 0.00 3.21
1907 3028 3.550275 TCGATCTACTTTGCGTTACATGC 59.450 43.478 0.00 0.00 0.00 4.06
1908 3029 3.599339 CGATCTACTTTGCGTTACATGCG 60.599 47.826 0.00 0.00 31.36 4.73
1909 3030 2.679450 TCTACTTTGCGTTACATGCGT 58.321 42.857 0.00 0.00 31.36 5.24
1910 3031 2.664568 TCTACTTTGCGTTACATGCGTC 59.335 45.455 0.00 0.00 31.36 5.19
1911 3032 0.515564 ACTTTGCGTTACATGCGTCC 59.484 50.000 0.00 0.00 31.36 4.79
1912 3033 0.518355 CTTTGCGTTACATGCGTCCG 60.518 55.000 0.00 0.00 31.36 4.79
1913 3034 1.222766 TTTGCGTTACATGCGTCCGT 61.223 50.000 0.00 0.00 31.36 4.69
1914 3035 0.388263 TTGCGTTACATGCGTCCGTA 60.388 50.000 0.00 0.00 31.36 4.02
1915 3036 0.799152 TGCGTTACATGCGTCCGTAG 60.799 55.000 0.00 0.00 31.36 3.51
1916 3037 0.523968 GCGTTACATGCGTCCGTAGA 60.524 55.000 0.00 0.00 0.00 2.59
1917 3038 1.898938 CGTTACATGCGTCCGTAGAA 58.101 50.000 0.00 0.00 0.00 2.10
1918 3039 2.456989 CGTTACATGCGTCCGTAGAAT 58.543 47.619 0.00 0.00 0.00 2.40
1919 3040 2.215587 CGTTACATGCGTCCGTAGAATG 59.784 50.000 0.00 0.00 0.00 2.67
1920 3041 2.502213 TACATGCGTCCGTAGAATGG 57.498 50.000 0.00 0.00 0.00 3.16
1921 3042 0.179084 ACATGCGTCCGTAGAATGGG 60.179 55.000 0.00 0.00 0.00 4.00
1922 3043 0.104120 CATGCGTCCGTAGAATGGGA 59.896 55.000 0.00 0.00 0.00 4.37
1923 3044 0.828022 ATGCGTCCGTAGAATGGGAA 59.172 50.000 0.00 0.00 33.27 3.97
1924 3045 0.609151 TGCGTCCGTAGAATGGGAAA 59.391 50.000 0.00 0.00 33.27 3.13
1925 3046 1.004595 GCGTCCGTAGAATGGGAAAC 58.995 55.000 0.00 0.00 33.27 2.78
1926 3047 1.673626 GCGTCCGTAGAATGGGAAACA 60.674 52.381 0.00 0.00 33.27 2.83
1927 3048 2.690786 CGTCCGTAGAATGGGAAACAA 58.309 47.619 0.00 0.00 33.27 2.83
1928 3049 2.671396 CGTCCGTAGAATGGGAAACAAG 59.329 50.000 0.00 0.00 33.27 3.16
1929 3050 3.671716 GTCCGTAGAATGGGAAACAAGT 58.328 45.455 0.00 0.00 33.27 3.16
1930 3051 3.683340 GTCCGTAGAATGGGAAACAAGTC 59.317 47.826 0.00 0.00 33.27 3.01
1931 3052 3.581332 TCCGTAGAATGGGAAACAAGTCT 59.419 43.478 0.00 0.00 33.53 3.24
1932 3053 4.773674 TCCGTAGAATGGGAAACAAGTCTA 59.226 41.667 0.00 0.00 31.93 2.59
1933 3054 5.424252 TCCGTAGAATGGGAAACAAGTCTAT 59.576 40.000 0.00 0.00 34.33 1.98
1934 3055 5.523916 CCGTAGAATGGGAAACAAGTCTATG 59.476 44.000 0.00 0.00 36.97 2.23
1935 3056 5.006746 CGTAGAATGGGAAACAAGTCTATGC 59.993 44.000 0.00 0.00 34.33 3.14
1936 3057 4.922206 AGAATGGGAAACAAGTCTATGCA 58.078 39.130 0.00 0.00 0.00 3.96
1937 3058 5.513233 AGAATGGGAAACAAGTCTATGCAT 58.487 37.500 3.79 3.79 0.00 3.96
1938 3059 5.359009 AGAATGGGAAACAAGTCTATGCATG 59.641 40.000 10.16 0.00 0.00 4.06
1939 3060 4.032960 TGGGAAACAAGTCTATGCATGT 57.967 40.909 10.16 0.00 0.00 3.21
1940 3061 5.172687 TGGGAAACAAGTCTATGCATGTA 57.827 39.130 10.16 0.00 0.00 2.29
1941 3062 5.754782 TGGGAAACAAGTCTATGCATGTAT 58.245 37.500 10.16 0.82 0.00 2.29
1942 3063 5.589855 TGGGAAACAAGTCTATGCATGTATG 59.410 40.000 10.16 4.00 0.00 2.39
1959 3080 7.052565 CATGTATGCTTTCAACATTGGTTTC 57.947 36.000 0.00 0.00 34.21 2.78
1960 3081 6.403866 TGTATGCTTTCAACATTGGTTTCT 57.596 33.333 0.00 0.00 34.21 2.52
1969 3090 8.758633 TTTCAACATTGGTTTCTTTTACGAAA 57.241 26.923 0.00 0.00 34.21 3.46
2011 3133 3.414700 CGTCTGCCAACTCGCCAC 61.415 66.667 0.00 0.00 0.00 5.01
2012 3134 2.280797 GTCTGCCAACTCGCCACA 60.281 61.111 0.00 0.00 0.00 4.17
2013 3135 2.280797 TCTGCCAACTCGCCACAC 60.281 61.111 0.00 0.00 0.00 3.82
2014 3136 2.591429 CTGCCAACTCGCCACACA 60.591 61.111 0.00 0.00 0.00 3.72
2047 3171 3.438781 GTCCAACCAATTCTGCACGAATA 59.561 43.478 10.51 0.00 41.42 1.75
2082 3207 5.502153 AACAGTTTTTATGTGCCACGTAA 57.498 34.783 5.40 5.40 0.00 3.18
2087 3212 5.049680 AGTTTTTATGTGCCACGTAAGACTG 60.050 40.000 18.95 0.00 43.62 3.51
2106 3231 1.152483 AGCTGGTGTGTGGGCATTT 60.152 52.632 0.00 0.00 0.00 2.32
2154 3282 4.225860 CAGGGGGACTGGTGTGTA 57.774 61.111 0.00 0.00 43.70 2.90
2169 3297 4.890581 TGGTGTGTAGGTGTTTAGCAATTT 59.109 37.500 0.00 0.00 0.00 1.82
2174 3302 1.272212 AGGTGTTTAGCAATTTGCCCG 59.728 47.619 17.51 0.00 46.52 6.13
2237 3367 0.604073 TTATCACTTCGCCCACACGA 59.396 50.000 0.00 0.00 41.04 4.35
2262 3392 1.002134 CCTCGCCCACATCCAAAGT 60.002 57.895 0.00 0.00 0.00 2.66
2265 3395 0.179004 TCGCCCACATCCAAAGTTGT 60.179 50.000 0.00 0.00 0.00 3.32
2318 3451 0.961753 ACTGCCCTAACTTTGCTTGC 59.038 50.000 0.00 0.00 0.00 4.01
2367 3502 3.543665 AGTTGCCATGTGTTTTTGCATT 58.456 36.364 0.00 0.00 0.00 3.56
2406 3541 1.351430 GCGTGCACGTAAGCAGATGA 61.351 55.000 36.80 0.00 46.69 2.92
2433 3570 4.870363 TCTTTCTTTTACATGGCAACTGC 58.130 39.130 0.00 0.00 41.14 4.40
2540 3682 3.775910 ACTGCCTAGTGTTAGTAGGTGT 58.224 45.455 10.53 7.69 42.16 4.16
2550 3692 5.711036 AGTGTTAGTAGGTGTCAACTCCTAG 59.289 44.000 10.46 0.00 41.25 3.02
2551 3693 5.476254 GTGTTAGTAGGTGTCAACTCCTAGT 59.524 44.000 17.98 17.98 43.93 2.57
2555 3697 5.638133 AGTAGGTGTCAACTCCTAGTGTTA 58.362 41.667 14.75 0.00 41.59 2.41
2556 3698 5.711036 AGTAGGTGTCAACTCCTAGTGTTAG 59.289 44.000 14.75 0.00 41.59 2.34
2557 3699 4.481072 AGGTGTCAACTCCTAGTGTTAGT 58.519 43.478 1.98 0.00 38.02 2.24
2558 3700 5.638133 AGGTGTCAACTCCTAGTGTTAGTA 58.362 41.667 1.98 0.00 38.02 1.82
2559 3701 5.711036 AGGTGTCAACTCCTAGTGTTAGTAG 59.289 44.000 1.98 0.00 38.02 2.57
2560 3702 5.105837 GGTGTCAACTCCTAGTGTTAGTAGG 60.106 48.000 3.76 3.76 41.64 3.18
2582 3724 4.339247 GGTGCAATCATGGCAACTATAGTT 59.661 41.667 12.50 12.50 45.37 2.24
2594 3736 3.454371 ACTATAGTTGTCCGACATGGC 57.546 47.619 1.09 0.00 37.80 4.40
2595 3737 2.764010 ACTATAGTTGTCCGACATGGCA 59.236 45.455 1.09 0.00 37.80 4.92
2596 3738 2.779755 ATAGTTGTCCGACATGGCAA 57.220 45.000 1.09 0.00 37.80 4.52
2597 3739 1.803334 TAGTTGTCCGACATGGCAAC 58.197 50.000 1.09 5.44 46.38 4.17
2598 3740 2.629002 GTTGTCCGACATGGCAACT 58.371 52.632 1.09 0.00 44.47 3.16
2599 3741 0.238289 GTTGTCCGACATGGCAACTG 59.762 55.000 1.09 0.00 44.47 3.16
2600 3742 0.179032 TTGTCCGACATGGCAACTGT 60.179 50.000 1.09 0.00 37.80 3.55
2601 3743 0.682292 TGTCCGACATGGCAACTGTA 59.318 50.000 0.00 0.00 37.80 2.74
2602 3744 1.337728 TGTCCGACATGGCAACTGTAG 60.338 52.381 0.00 0.00 37.80 2.74
2603 3745 0.973632 TCCGACATGGCAACTGTAGT 59.026 50.000 0.00 0.00 37.80 2.73
2604 3746 1.346395 TCCGACATGGCAACTGTAGTT 59.654 47.619 0.00 0.00 37.80 2.24
2605 3747 1.732259 CCGACATGGCAACTGTAGTTC 59.268 52.381 0.00 0.00 35.83 3.01
2606 3748 2.412870 CGACATGGCAACTGTAGTTCA 58.587 47.619 0.00 0.00 35.83 3.18
2607 3749 6.878799 TCCGACATGGCAACTGTAGTTCAG 62.879 50.000 0.00 0.00 43.08 3.02
2629 3771 2.031245 CGACATGGCAACTGCAGTTAAA 60.031 45.455 30.67 19.09 44.36 1.52
2630 3772 3.366273 CGACATGGCAACTGCAGTTAAAT 60.366 43.478 30.67 20.35 44.36 1.40
2631 3773 4.559153 GACATGGCAACTGCAGTTAAATT 58.441 39.130 30.67 14.06 44.36 1.82
2632 3774 4.309099 ACATGGCAACTGCAGTTAAATTG 58.691 39.130 30.67 24.78 44.36 2.32
2633 3775 4.039004 ACATGGCAACTGCAGTTAAATTGA 59.961 37.500 30.67 12.55 44.36 2.57
2634 3776 3.976169 TGGCAACTGCAGTTAAATTGAC 58.024 40.909 30.67 21.67 44.36 3.18
2635 3777 3.382865 TGGCAACTGCAGTTAAATTGACA 59.617 39.130 30.67 24.02 44.36 3.58
2636 3778 4.039004 TGGCAACTGCAGTTAAATTGACAT 59.961 37.500 30.67 2.88 44.36 3.06
2637 3779 4.990426 GGCAACTGCAGTTAAATTGACATT 59.010 37.500 30.67 2.31 44.36 2.71
2638 3780 5.107375 GGCAACTGCAGTTAAATTGACATTG 60.107 40.000 30.67 15.99 44.36 2.82
2639 3781 5.691305 GCAACTGCAGTTAAATTGACATTGA 59.309 36.000 30.67 0.00 41.59 2.57
2640 3782 6.200665 GCAACTGCAGTTAAATTGACATTGAA 59.799 34.615 30.67 0.00 41.59 2.69
2641 3783 7.254387 GCAACTGCAGTTAAATTGACATTGAAA 60.254 33.333 30.67 0.00 41.59 2.69
2642 3784 8.602328 CAACTGCAGTTAAATTGACATTGAAAA 58.398 29.630 30.67 0.00 36.32 2.29
2643 3785 8.356533 ACTGCAGTTAAATTGACATTGAAAAG 57.643 30.769 15.25 0.00 0.00 2.27
2644 3786 7.439056 ACTGCAGTTAAATTGACATTGAAAAGG 59.561 33.333 15.25 0.00 0.00 3.11
2645 3787 6.705381 TGCAGTTAAATTGACATTGAAAAGGG 59.295 34.615 0.00 0.00 0.00 3.95
2646 3788 6.705825 GCAGTTAAATTGACATTGAAAAGGGT 59.294 34.615 0.00 0.00 0.00 4.34
2647 3789 7.095649 GCAGTTAAATTGACATTGAAAAGGGTC 60.096 37.037 0.00 0.00 35.41 4.46
2648 3790 7.384932 CAGTTAAATTGACATTGAAAAGGGTCC 59.615 37.037 0.00 0.00 34.34 4.46
2649 3791 4.519540 AATTGACATTGAAAAGGGTCCG 57.480 40.909 0.00 0.00 34.34 4.79
2650 3792 1.904287 TGACATTGAAAAGGGTCCGG 58.096 50.000 0.00 0.00 34.34 5.14
2664 3806 3.443045 CCGGACCATGGCAACTGC 61.443 66.667 13.04 0.00 41.14 4.40
2665 3807 3.803082 CGGACCATGGCAACTGCG 61.803 66.667 13.04 5.52 43.26 5.18
2693 3920 2.733593 GTGACTGTCACGCGGGAC 60.734 66.667 33.90 33.90 37.67 4.46
2722 3949 1.135257 CGTGAGGTAAGTGGCTGAGAG 60.135 57.143 0.00 0.00 0.00 3.20
2723 3950 2.171840 GTGAGGTAAGTGGCTGAGAGA 58.828 52.381 0.00 0.00 0.00 3.10
2724 3951 2.165437 GTGAGGTAAGTGGCTGAGAGAG 59.835 54.545 0.00 0.00 0.00 3.20
2725 3952 1.754226 GAGGTAAGTGGCTGAGAGAGG 59.246 57.143 0.00 0.00 0.00 3.69
2726 3953 1.077993 AGGTAAGTGGCTGAGAGAGGT 59.922 52.381 0.00 0.00 0.00 3.85
2727 3954 2.312140 AGGTAAGTGGCTGAGAGAGGTA 59.688 50.000 0.00 0.00 0.00 3.08
2734 3965 1.617263 GGCTGAGAGAGGTAGTGTGGA 60.617 57.143 0.00 0.00 0.00 4.02
2739 3970 2.161030 AGAGAGGTAGTGTGGACGTTC 58.839 52.381 0.00 0.00 0.00 3.95
2747 3978 5.245526 AGGTAGTGTGGACGTTCTCTATTTT 59.754 40.000 0.00 0.00 0.00 1.82
2757 3988 2.812011 GTTCTCTATTTTGCCCACACGT 59.188 45.455 0.00 0.00 0.00 4.49
2759 3990 3.857052 TCTCTATTTTGCCCACACGTAG 58.143 45.455 0.00 0.00 0.00 3.51
2774 4005 1.511768 GTAGGCGTGTGAGAGGGAC 59.488 63.158 0.00 0.00 0.00 4.46
2802 4033 3.740513 AAAAAGACGGGTGGACGC 58.259 55.556 0.00 0.00 37.37 5.19
2803 4034 1.147600 AAAAAGACGGGTGGACGCT 59.852 52.632 0.00 0.00 37.37 5.07
2804 4035 0.393820 AAAAAGACGGGTGGACGCTA 59.606 50.000 0.00 0.00 37.37 4.26
2805 4036 0.037605 AAAAGACGGGTGGACGCTAG 60.038 55.000 0.00 0.00 37.37 3.42
2806 4037 1.183676 AAAGACGGGTGGACGCTAGT 61.184 55.000 0.00 0.00 37.37 2.57
2807 4038 1.183676 AAGACGGGTGGACGCTAGTT 61.184 55.000 0.00 0.00 37.37 2.24
2808 4039 1.445582 GACGGGTGGACGCTAGTTG 60.446 63.158 0.00 0.00 37.37 3.16
2809 4040 2.151049 GACGGGTGGACGCTAGTTGT 62.151 60.000 0.00 0.00 37.37 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 1.002888 TCAGACGGTCGAGAGTAACCT 59.997 52.381 1.89 0.00 33.14 3.50
98 99 3.795877 TGATCATGTGCAAGCGAATCTA 58.204 40.909 0.00 0.00 0.00 1.98
99 100 2.612672 CTGATCATGTGCAAGCGAATCT 59.387 45.455 0.00 0.00 0.00 2.40
108 110 1.598517 AGCCGACTGATCATGTGCA 59.401 52.632 0.00 0.00 0.00 4.57
121 123 1.302511 GTTTCCCTTCAGCAGCCGA 60.303 57.895 0.00 0.00 0.00 5.54
126 128 1.542547 GGAGAACGTTTCCCTTCAGCA 60.543 52.381 0.46 0.00 0.00 4.41
127 129 1.157585 GGAGAACGTTTCCCTTCAGC 58.842 55.000 0.46 0.00 0.00 4.26
128 130 2.543777 TGGAGAACGTTTCCCTTCAG 57.456 50.000 19.93 0.00 33.62 3.02
178 180 1.072331 CACCGCCTTTGCCCTATATCT 59.928 52.381 0.00 0.00 0.00 1.98
182 184 2.275418 CCACCGCCTTTGCCCTAT 59.725 61.111 0.00 0.00 0.00 2.57
187 189 3.223589 AACCACCACCGCCTTTGC 61.224 61.111 0.00 0.00 0.00 3.68
209 211 0.537188 ATTGAATGTCCTCCGACGCT 59.463 50.000 0.00 0.00 42.37 5.07
211 213 1.571919 GGATTGAATGTCCTCCGACG 58.428 55.000 0.00 0.00 42.37 5.12
218 220 6.544928 AATTTGTAAGGGGATTGAATGTCC 57.455 37.500 0.00 0.00 34.92 4.02
297 301 7.230712 GGGTTCAAAATTCTAAGAGAAGTTGGA 59.769 37.037 2.97 3.01 41.04 3.53
336 340 4.162509 ACAAAGGGAGTAGCTAGGATTGTC 59.837 45.833 0.00 0.00 0.00 3.18
384 388 8.703604 GAGCATCTTTTGACACTACACTAATA 57.296 34.615 0.00 0.00 0.00 0.98
421 425 6.585695 TTCATCGTAACTACTTCCTCTGTT 57.414 37.500 0.00 0.00 0.00 3.16
438 442 6.389622 TGACGATTCTAGTTGTTTTCATCG 57.610 37.500 0.00 0.00 35.46 3.84
476 480 6.778821 TCACTCAACTTTTCCTGGAATCATA 58.221 36.000 10.45 0.00 0.00 2.15
484 488 4.260784 CGAACCTTCACTCAACTTTTCCTG 60.261 45.833 0.00 0.00 0.00 3.86
485 489 3.877508 CGAACCTTCACTCAACTTTTCCT 59.122 43.478 0.00 0.00 0.00 3.36
487 491 3.626217 ACCGAACCTTCACTCAACTTTTC 59.374 43.478 0.00 0.00 0.00 2.29
489 493 3.277142 ACCGAACCTTCACTCAACTTT 57.723 42.857 0.00 0.00 0.00 2.66
493 497 3.118555 TCAAGAACCGAACCTTCACTCAA 60.119 43.478 0.00 0.00 0.00 3.02
508 512 6.313905 TGCCGATTCTTCTAGAATTCAAGAAC 59.686 38.462 17.13 11.99 44.41 3.01
689 1708 4.803426 GGAGGCTGGAGCGTGACG 62.803 72.222 0.00 0.00 43.26 4.35
879 1919 0.827925 TCGTCACTCCAGCAAGGTCT 60.828 55.000 0.00 0.00 39.02 3.85
947 2002 1.002773 GGAAGAAGCCCACGGTCTTAA 59.997 52.381 0.00 0.00 0.00 1.85
948 2003 0.611714 GGAAGAAGCCCACGGTCTTA 59.388 55.000 0.00 0.00 0.00 2.10
949 2004 1.375326 GGAAGAAGCCCACGGTCTT 59.625 57.895 0.00 0.00 0.00 3.01
994 2049 1.141881 GCATCTCCGACATGACCGT 59.858 57.895 0.00 0.00 0.00 4.83
1380 2468 3.127533 GACGTGCCCATGGTGAGC 61.128 66.667 11.73 7.81 0.00 4.26
1416 2504 1.671742 GAGGAGCACCGTCAGGAAA 59.328 57.895 0.00 0.00 41.02 3.13
1478 2566 3.555967 AGACCGGCTGATCATCCC 58.444 61.111 9.98 6.27 0.00 3.85
1743 2858 2.232941 GTCCCTGTAGTGGACGATCAAA 59.767 50.000 0.00 0.00 42.63 2.69
1818 2939 8.818141 TTTATTCTATCGAGTAGCCTTTGATG 57.182 34.615 0.00 0.00 0.00 3.07
1850 2971 1.288350 CTAGCTGCTGTGCTGTGATC 58.712 55.000 13.43 0.00 43.87 2.92
1863 2984 3.499050 CAGGCTTGCAGCTAGCTG 58.501 61.111 35.54 35.54 45.94 4.24
1873 2994 1.929836 GTAGATCGACTTGCAGGCTTG 59.070 52.381 0.00 0.00 0.00 4.01
1874 2995 1.827969 AGTAGATCGACTTGCAGGCTT 59.172 47.619 2.18 0.00 0.00 4.35
1875 2996 1.479709 AGTAGATCGACTTGCAGGCT 58.520 50.000 2.18 0.00 0.00 4.58
1876 2997 2.301577 AAGTAGATCGACTTGCAGGC 57.698 50.000 18.98 0.00 38.25 4.85
1877 2998 2.349886 GCAAAGTAGATCGACTTGCAGG 59.650 50.000 20.15 11.98 39.62 4.85
1878 2999 2.028523 CGCAAAGTAGATCGACTTGCAG 59.971 50.000 26.21 18.99 39.62 4.41
1879 3000 1.992667 CGCAAAGTAGATCGACTTGCA 59.007 47.619 26.21 0.00 39.62 4.08
1880 3001 1.993370 ACGCAAAGTAGATCGACTTGC 59.007 47.619 20.15 21.03 39.62 4.01
1881 3002 4.619760 TGTAACGCAAAGTAGATCGACTTG 59.380 41.667 20.15 14.94 39.62 3.16
1882 3003 4.801891 TGTAACGCAAAGTAGATCGACTT 58.198 39.130 14.70 14.70 41.50 3.01
1883 3004 4.430137 TGTAACGCAAAGTAGATCGACT 57.570 40.909 2.18 2.18 0.00 4.18
1884 3005 4.548346 GCATGTAACGCAAAGTAGATCGAC 60.548 45.833 0.00 0.00 0.00 4.20
1885 3006 3.550275 GCATGTAACGCAAAGTAGATCGA 59.450 43.478 0.00 0.00 0.00 3.59
1886 3007 3.599339 CGCATGTAACGCAAAGTAGATCG 60.599 47.826 0.00 0.00 0.00 3.69
1887 3008 3.306166 ACGCATGTAACGCAAAGTAGATC 59.694 43.478 0.00 0.00 0.00 2.75
1888 3009 3.259064 ACGCATGTAACGCAAAGTAGAT 58.741 40.909 0.00 0.00 0.00 1.98
1889 3010 2.664568 GACGCATGTAACGCAAAGTAGA 59.335 45.455 0.00 0.00 0.00 2.59
1890 3011 2.222729 GGACGCATGTAACGCAAAGTAG 60.223 50.000 0.00 0.00 0.00 2.57
1891 3012 1.727880 GGACGCATGTAACGCAAAGTA 59.272 47.619 0.00 0.00 0.00 2.24
1892 3013 0.515564 GGACGCATGTAACGCAAAGT 59.484 50.000 0.00 0.00 0.00 2.66
1893 3014 0.518355 CGGACGCATGTAACGCAAAG 60.518 55.000 0.00 0.00 0.00 2.77
1894 3015 1.222766 ACGGACGCATGTAACGCAAA 61.223 50.000 0.00 0.00 33.37 3.68
1895 3016 0.388263 TACGGACGCATGTAACGCAA 60.388 50.000 0.00 0.00 33.37 4.85
1896 3017 0.799152 CTACGGACGCATGTAACGCA 60.799 55.000 0.00 0.00 33.37 5.24
1897 3018 0.523968 TCTACGGACGCATGTAACGC 60.524 55.000 0.00 0.00 33.37 4.84
1898 3019 1.898938 TTCTACGGACGCATGTAACG 58.101 50.000 0.00 0.00 35.44 3.18
1899 3020 2.538449 CCATTCTACGGACGCATGTAAC 59.462 50.000 0.00 0.00 0.00 2.50
1900 3021 2.482316 CCCATTCTACGGACGCATGTAA 60.482 50.000 0.00 0.00 0.00 2.41
1901 3022 1.067974 CCCATTCTACGGACGCATGTA 59.932 52.381 0.00 0.00 0.00 2.29
1902 3023 0.179084 CCCATTCTACGGACGCATGT 60.179 55.000 0.00 0.00 0.00 3.21
1903 3024 0.104120 TCCCATTCTACGGACGCATG 59.896 55.000 0.00 0.00 0.00 4.06
1904 3025 0.828022 TTCCCATTCTACGGACGCAT 59.172 50.000 0.00 0.00 0.00 4.73
1905 3026 0.609151 TTTCCCATTCTACGGACGCA 59.391 50.000 0.00 0.00 0.00 5.24
1906 3027 1.004595 GTTTCCCATTCTACGGACGC 58.995 55.000 0.00 0.00 0.00 5.19
1907 3028 2.373540 TGTTTCCCATTCTACGGACG 57.626 50.000 0.00 0.00 0.00 4.79
1908 3029 3.671716 ACTTGTTTCCCATTCTACGGAC 58.328 45.455 0.00 0.00 0.00 4.79
1909 3030 3.581332 AGACTTGTTTCCCATTCTACGGA 59.419 43.478 0.00 0.00 0.00 4.69
1910 3031 3.939066 AGACTTGTTTCCCATTCTACGG 58.061 45.455 0.00 0.00 0.00 4.02
1911 3032 5.006746 GCATAGACTTGTTTCCCATTCTACG 59.993 44.000 0.00 0.00 0.00 3.51
1912 3033 5.880332 TGCATAGACTTGTTTCCCATTCTAC 59.120 40.000 0.00 0.00 0.00 2.59
1913 3034 6.061022 TGCATAGACTTGTTTCCCATTCTA 57.939 37.500 0.00 0.00 0.00 2.10
1914 3035 4.922206 TGCATAGACTTGTTTCCCATTCT 58.078 39.130 0.00 0.00 0.00 2.40
1915 3036 5.126061 ACATGCATAGACTTGTTTCCCATTC 59.874 40.000 0.00 0.00 0.00 2.67
1916 3037 5.018809 ACATGCATAGACTTGTTTCCCATT 58.981 37.500 0.00 0.00 0.00 3.16
1917 3038 4.603131 ACATGCATAGACTTGTTTCCCAT 58.397 39.130 0.00 0.00 0.00 4.00
1918 3039 4.032960 ACATGCATAGACTTGTTTCCCA 57.967 40.909 0.00 0.00 0.00 4.37
1919 3040 6.064846 CATACATGCATAGACTTGTTTCCC 57.935 41.667 0.00 0.00 0.00 3.97
1931 3052 7.579146 AACCAATGTTGAAAGCATACATGCATA 60.579 33.333 16.09 0.00 44.06 3.14
1932 3053 6.798057 AACCAATGTTGAAAGCATACATGCAT 60.798 34.615 16.09 0.00 44.06 3.96
1933 3054 5.511031 AACCAATGTTGAAAGCATACATGCA 60.511 36.000 16.09 0.00 44.06 3.96
1934 3055 4.931002 AACCAATGTTGAAAGCATACATGC 59.069 37.500 6.06 6.06 42.92 4.06
1935 3056 6.869913 AGAAACCAATGTTGAAAGCATACATG 59.130 34.615 0.00 0.00 34.13 3.21
1936 3057 6.996509 AGAAACCAATGTTGAAAGCATACAT 58.003 32.000 0.00 0.00 34.13 2.29
1937 3058 6.403866 AGAAACCAATGTTGAAAGCATACA 57.596 33.333 0.00 0.00 34.13 2.29
1938 3059 7.713764 AAAGAAACCAATGTTGAAAGCATAC 57.286 32.000 0.00 0.00 34.13 2.39
1939 3060 9.255304 GTAAAAGAAACCAATGTTGAAAGCATA 57.745 29.630 0.00 0.00 34.13 3.14
1940 3061 7.042791 CGTAAAAGAAACCAATGTTGAAAGCAT 60.043 33.333 0.00 0.00 34.13 3.79
1941 3062 6.254589 CGTAAAAGAAACCAATGTTGAAAGCA 59.745 34.615 0.00 0.00 34.13 3.91
1942 3063 6.474102 TCGTAAAAGAAACCAATGTTGAAAGC 59.526 34.615 0.00 0.00 34.13 3.51
1943 3064 7.979115 TCGTAAAAGAAACCAATGTTGAAAG 57.021 32.000 0.00 0.00 34.13 2.62
1944 3065 8.758633 TTTCGTAAAAGAAACCAATGTTGAAA 57.241 26.923 0.00 0.00 35.44 2.69
1945 3066 8.758633 TTTTCGTAAAAGAAACCAATGTTGAA 57.241 26.923 0.00 0.00 39.53 2.69
1946 3067 8.758633 TTTTTCGTAAAAGAAACCAATGTTGA 57.241 26.923 0.00 0.00 39.53 3.18
1960 3081 6.869388 GGTGGGCATTAATCTTTTTCGTAAAA 59.131 34.615 0.00 0.00 0.00 1.52
1969 3090 2.099405 CACGGGTGGGCATTAATCTTT 58.901 47.619 0.00 0.00 0.00 2.52
2000 3122 0.317160 TCTACTGTGTGGCGAGTTGG 59.683 55.000 0.00 0.00 0.00 3.77
2010 3132 2.492484 GTTGGACGAGGATCTACTGTGT 59.508 50.000 0.00 0.00 0.00 3.72
2011 3133 2.159226 GGTTGGACGAGGATCTACTGTG 60.159 54.545 0.00 0.00 0.00 3.66
2012 3134 2.100989 GGTTGGACGAGGATCTACTGT 58.899 52.381 0.00 0.00 0.00 3.55
2013 3135 2.100197 TGGTTGGACGAGGATCTACTG 58.900 52.381 0.00 0.00 0.00 2.74
2014 3136 2.526888 TGGTTGGACGAGGATCTACT 57.473 50.000 0.00 0.00 0.00 2.57
2047 3171 4.806342 AAAACTGTTAGAACGCGTCAAT 57.194 36.364 14.44 3.81 0.00 2.57
2082 3207 1.750930 CCACACACCAGCTCAGTCT 59.249 57.895 0.00 0.00 0.00 3.24
2087 3212 1.181098 AAATGCCCACACACCAGCTC 61.181 55.000 0.00 0.00 0.00 4.09
2119 3244 2.450160 CTGTGGTGAAAAAGAACGTGC 58.550 47.619 0.00 0.00 0.00 5.34
2144 3272 2.436542 TGCTAAACACCTACACACCAGT 59.563 45.455 0.00 0.00 0.00 4.00
2154 3282 1.272212 CGGGCAAATTGCTAAACACCT 59.728 47.619 18.04 0.00 44.28 4.00
2169 3297 2.441164 AAAACTGGTGTGCGGGCA 60.441 55.556 0.00 0.00 0.00 5.36
2174 3302 0.865639 GTGCGTGAAAACTGGTGTGC 60.866 55.000 0.00 0.00 0.00 4.57
2237 3367 4.988716 TGTGGGCGAGGAGACGGT 62.989 66.667 0.00 0.00 0.00 4.83
2262 3392 4.749099 GCAAAAACATATGGCAACTGACAA 59.251 37.500 7.80 0.00 36.16 3.18
2265 3395 4.558178 CTGCAAAAACATATGGCAACTGA 58.442 39.130 7.80 0.00 33.58 3.41
2318 3451 5.876612 AAAAGAGAGTTGCTATCTGCTTG 57.123 39.130 0.00 0.00 43.37 4.01
2327 3460 4.810191 ACTCGGATAAAAGAGAGTTGCT 57.190 40.909 0.00 0.00 40.64 3.91
2342 3477 1.686355 AAAACACATGGCAACTCGGA 58.314 45.000 0.00 0.00 37.61 4.55
2406 3541 6.096846 AGTTGCCATGTAAAAGAAAGAGTTGT 59.903 34.615 0.00 0.00 0.00 3.32
2433 3570 1.448540 CTCACAAGCACGCTAGGGG 60.449 63.158 11.95 1.56 0.00 4.79
2535 3677 4.481072 ACTAACACTAGGAGTTGACACCT 58.519 43.478 11.70 5.47 40.15 4.00
2540 3682 4.461781 GCACCTACTAACACTAGGAGTTGA 59.538 45.833 11.70 0.00 31.52 3.18
2550 3692 3.065371 GCCATGATTGCACCTACTAACAC 59.935 47.826 0.00 0.00 0.00 3.32
2551 3693 3.278574 GCCATGATTGCACCTACTAACA 58.721 45.455 0.00 0.00 0.00 2.41
2555 3697 2.094675 GTTGCCATGATTGCACCTACT 58.905 47.619 0.00 0.00 38.72 2.57
2556 3698 2.094675 AGTTGCCATGATTGCACCTAC 58.905 47.619 0.00 0.00 38.72 3.18
2557 3699 2.512692 AGTTGCCATGATTGCACCTA 57.487 45.000 0.00 0.00 38.72 3.08
2558 3700 2.512692 TAGTTGCCATGATTGCACCT 57.487 45.000 0.00 0.00 38.72 4.00
2559 3701 3.885297 ACTATAGTTGCCATGATTGCACC 59.115 43.478 0.00 0.00 38.72 5.01
2560 3702 5.505173 AACTATAGTTGCCATGATTGCAC 57.495 39.130 17.35 0.00 38.72 4.57
2577 3719 2.356135 GTTGCCATGTCGGACAACTAT 58.644 47.619 15.72 0.00 43.12 2.12
2582 3724 0.682292 TACAGTTGCCATGTCGGACA 59.318 50.000 14.01 14.01 36.56 4.02
2584 3726 0.973632 ACTACAGTTGCCATGTCGGA 59.026 50.000 0.00 0.00 36.56 4.55
2598 3740 0.320050 TGCCATGTCGCTGAACTACA 59.680 50.000 0.00 0.00 0.00 2.74
2599 3741 1.128692 GTTGCCATGTCGCTGAACTAC 59.871 52.381 0.00 0.00 0.00 2.73
2600 3742 1.001974 AGTTGCCATGTCGCTGAACTA 59.998 47.619 0.00 0.00 0.00 2.24
2601 3743 0.250467 AGTTGCCATGTCGCTGAACT 60.250 50.000 0.00 0.00 0.00 3.01
2602 3744 0.110056 CAGTTGCCATGTCGCTGAAC 60.110 55.000 0.00 0.00 0.00 3.18
2603 3745 1.855213 GCAGTTGCCATGTCGCTGAA 61.855 55.000 2.90 0.00 34.31 3.02
2604 3746 2.327343 GCAGTTGCCATGTCGCTGA 61.327 57.895 2.90 0.00 34.31 4.26
2605 3747 2.177531 GCAGTTGCCATGTCGCTG 59.822 61.111 0.00 0.00 34.31 5.18
2606 3748 2.281692 TGCAGTTGCCATGTCGCT 60.282 55.556 1.06 0.00 41.18 4.93
2607 3749 2.133742 AACTGCAGTTGCCATGTCGC 62.134 55.000 30.66 0.00 41.18 5.19
2608 3750 1.155889 TAACTGCAGTTGCCATGTCG 58.844 50.000 36.50 0.67 41.18 4.35
2609 3751 3.641437 TTTAACTGCAGTTGCCATGTC 57.359 42.857 36.50 0.00 41.18 3.06
2629 3771 2.825532 CCGGACCCTTTTCAATGTCAAT 59.174 45.455 0.00 0.00 0.00 2.57
2630 3772 2.158593 TCCGGACCCTTTTCAATGTCAA 60.159 45.455 0.00 0.00 0.00 3.18
2631 3773 1.422024 TCCGGACCCTTTTCAATGTCA 59.578 47.619 0.00 0.00 0.00 3.58
2632 3774 1.810755 GTCCGGACCCTTTTCAATGTC 59.189 52.381 24.75 0.00 0.00 3.06
2633 3775 1.546998 GGTCCGGACCCTTTTCAATGT 60.547 52.381 39.24 0.00 45.68 2.71
2634 3776 1.173913 GGTCCGGACCCTTTTCAATG 58.826 55.000 39.24 0.00 45.68 2.82
2635 3777 3.664240 GGTCCGGACCCTTTTCAAT 57.336 52.632 39.24 0.00 45.68 2.57
2645 3787 2.040544 CAGTTGCCATGGTCCGGAC 61.041 63.158 27.04 27.04 0.00 4.79
2646 3788 2.350895 CAGTTGCCATGGTCCGGA 59.649 61.111 14.67 0.00 0.00 5.14
2647 3789 3.443045 GCAGTTGCCATGGTCCGG 61.443 66.667 14.67 0.00 34.31 5.14
2648 3790 3.803082 CGCAGTTGCCATGGTCCG 61.803 66.667 14.67 3.72 37.91 4.79
2649 3791 3.443045 CCGCAGTTGCCATGGTCC 61.443 66.667 14.67 1.25 37.91 4.46
2650 3792 3.443045 CCCGCAGTTGCCATGGTC 61.443 66.667 14.67 6.41 37.91 4.02
2674 3901 4.293648 CCCGCGTGACAGTCACCA 62.294 66.667 25.11 0.00 44.20 4.17
2693 3920 3.271706 TTACCTCACGGTCCGCACG 62.272 63.158 12.28 0.00 44.21 5.34
2701 3928 0.108615 CTCAGCCACTTACCTCACGG 60.109 60.000 0.00 0.00 0.00 4.94
2703 3930 2.165437 CTCTCTCAGCCACTTACCTCAC 59.835 54.545 0.00 0.00 0.00 3.51
2704 3931 2.451490 CTCTCTCAGCCACTTACCTCA 58.549 52.381 0.00 0.00 0.00 3.86
2705 3932 1.754226 CCTCTCTCAGCCACTTACCTC 59.246 57.143 0.00 0.00 0.00 3.85
2706 3933 1.077993 ACCTCTCTCAGCCACTTACCT 59.922 52.381 0.00 0.00 0.00 3.08
2707 3934 1.562783 ACCTCTCTCAGCCACTTACC 58.437 55.000 0.00 0.00 0.00 2.85
2709 3936 3.245300 ACACTACCTCTCTCAGCCACTTA 60.245 47.826 0.00 0.00 0.00 2.24
2710 3937 2.175202 CACTACCTCTCTCAGCCACTT 58.825 52.381 0.00 0.00 0.00 3.16
2712 3939 1.203523 CACACTACCTCTCTCAGCCAC 59.796 57.143 0.00 0.00 0.00 5.01
2713 3940 1.550327 CACACTACCTCTCTCAGCCA 58.450 55.000 0.00 0.00 0.00 4.75
2714 3941 0.820871 CCACACTACCTCTCTCAGCC 59.179 60.000 0.00 0.00 0.00 4.85
2716 3943 1.740585 CGTCCACACTACCTCTCTCAG 59.259 57.143 0.00 0.00 0.00 3.35
2717 3944 1.073444 ACGTCCACACTACCTCTCTCA 59.927 52.381 0.00 0.00 0.00 3.27
2718 3945 1.823797 ACGTCCACACTACCTCTCTC 58.176 55.000 0.00 0.00 0.00 3.20
2719 3946 2.161030 GAACGTCCACACTACCTCTCT 58.839 52.381 0.00 0.00 0.00 3.10
2722 3949 2.161030 AGAGAACGTCCACACTACCTC 58.839 52.381 0.00 0.00 0.00 3.85
2723 3950 2.289592 AGAGAACGTCCACACTACCT 57.710 50.000 0.00 0.00 0.00 3.08
2724 3951 4.715527 AATAGAGAACGTCCACACTACC 57.284 45.455 0.00 0.00 0.00 3.18
2725 3952 5.163982 GCAAAATAGAGAACGTCCACACTAC 60.164 44.000 0.00 0.00 0.00 2.73
2726 3953 4.927425 GCAAAATAGAGAACGTCCACACTA 59.073 41.667 0.00 0.00 0.00 2.74
2727 3954 3.746492 GCAAAATAGAGAACGTCCACACT 59.254 43.478 0.00 0.00 0.00 3.55
2734 3965 2.812011 GTGTGGGCAAAATAGAGAACGT 59.188 45.455 0.00 0.00 0.00 3.99
2739 3970 2.936498 CCTACGTGTGGGCAAAATAGAG 59.064 50.000 0.00 0.00 0.00 2.43
2757 3988 1.681327 GGTCCCTCTCACACGCCTA 60.681 63.158 0.00 0.00 0.00 3.93
2759 3990 4.436998 CGGTCCCTCTCACACGCC 62.437 72.222 0.00 0.00 0.00 5.68
2789 4020 1.605738 AACTAGCGTCCACCCGTCT 60.606 57.895 0.00 0.00 0.00 4.18
2790 4021 1.445582 CAACTAGCGTCCACCCGTC 60.446 63.158 0.00 0.00 0.00 4.79
2791 4022 2.205152 ACAACTAGCGTCCACCCGT 61.205 57.895 0.00 0.00 0.00 5.28
2792 4023 2.654877 ACAACTAGCGTCCACCCG 59.345 61.111 0.00 0.00 0.00 5.28


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

AutoCloner maintained by Alex Coulton.