Multiple sequence alignment - TraesCS4A01G484700

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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 TraesCS4A01G484700 chr4A 100.000 3785 0 0 1 3785 738814226 738818010 0.000000e+00 6990.0
1 TraesCS4A01G484700 chr4A 90.698 43 3 1 3736 3778 638279879 638279920 5.280000e-04 56.5
2 TraesCS4A01G484700 chr7D 95.491 1752 61 13 1058 2803 4877238 4878977 0.000000e+00 2782.0
3 TraesCS4A01G484700 chr7D 93.892 704 36 3 2 700 4875569 4876270 0.000000e+00 1055.0
4 TraesCS4A01G484700 chr7D 76.679 536 121 4 1123 1656 554316584 554317117 1.030000e-75 294.0
5 TraesCS4A01G484700 chr7D 92.157 51 4 0 3735 3785 405798295 405798245 5.240000e-09 73.1
6 TraesCS4A01G484700 chr7A 94.743 1769 73 3 1058 2806 4687769 4686001 0.000000e+00 2734.0
7 TraesCS4A01G484700 chr7A 88.930 813 74 12 2828 3637 4684850 4684051 0.000000e+00 989.0
8 TraesCS4A01G484700 chr7A 89.616 703 60 5 4 705 4689738 4689048 0.000000e+00 881.0
9 TraesCS4A01G484700 chr7A 92.000 100 7 1 3645 3744 4683710 4683612 5.100000e-29 139.0
10 TraesCS4A01G484700 chr5B 75.833 1440 300 35 1201 2622 9417141 9418550 0.000000e+00 688.0
11 TraesCS4A01G484700 chr5B 91.111 360 24 5 43 401 253192690 253192338 7.350000e-132 481.0
12 TraesCS4A01G484700 chr5B 75.714 840 175 16 1200 2035 9334334 9333520 9.850000e-106 394.0
13 TraesCS4A01G484700 chr5B 87.069 116 14 1 43 158 162449979 162449865 3.070000e-26 130.0
14 TraesCS4A01G484700 chr5D 75.897 1365 285 32 1201 2549 9471220 9472556 0.000000e+00 658.0
15 TraesCS4A01G484700 chr5D 77.378 778 139 17 1202 1971 9387039 9386291 9.720000e-116 427.0
16 TraesCS4A01G484700 chr5D 84.646 254 33 4 150 401 170265018 170264769 8.120000e-62 248.0
17 TraesCS4A01G484700 chr5D 83.594 256 36 4 148 401 331578027 331577776 6.320000e-58 235.0
18 TraesCS4A01G484700 chr5D 88.496 113 12 1 46 158 170265162 170265051 6.590000e-28 135.0
19 TraesCS4A01G484700 chr5A 75.191 1443 318 30 1194 2622 7619461 7620877 0.000000e+00 645.0
20 TraesCS4A01G484700 chr5A 75.073 1372 293 31 1201 2549 7506165 7504820 9.050000e-166 593.0
21 TraesCS4A01G484700 chr5A 83.658 257 34 6 148 401 432234454 432234203 6.320000e-58 235.0
22 TraesCS4A01G484700 chr5A 100.000 29 0 0 3735 3763 442105603 442105631 2.000000e-03 54.7
23 TraesCS4A01G484700 chr6D 87.052 363 37 7 43 401 157675934 157676290 5.890000e-108 401.0
24 TraesCS4A01G484700 chr6D 91.837 49 3 1 3738 3785 324558959 324558911 2.440000e-07 67.6
25 TraesCS4A01G484700 chr7B 85.042 361 46 5 43 401 614281411 614281765 1.000000e-95 361.0
26 TraesCS4A01G484700 chr7B 76.330 545 125 4 1123 1665 600597317 600596775 4.780000e-74 289.0
27 TraesCS4A01G484700 chr7B 78.961 385 77 2 1290 1670 140156141 140156525 3.750000e-65 259.0
28 TraesCS4A01G484700 chr7B 96.875 32 1 0 3732 3763 736019696 736019727 2.000000e-03 54.7
29 TraesCS4A01G484700 chr2D 87.815 238 24 5 167 401 638501389 638501154 1.340000e-69 274.0
30 TraesCS4A01G484700 chr2D 84.375 64 6 4 2911 2972 644663116 644663055 4.080000e-05 60.2
31 TraesCS4A01G484700 chr1D 85.098 255 29 7 150 401 78034090 78033842 6.280000e-63 252.0
32 TraesCS4A01G484700 chr1A 87.302 126 16 0 35 160 105306019 105306144 1.100000e-30 145.0
33 TraesCS4A01G484700 chr1A 77.083 144 31 2 1254 1396 579288550 579288408 8.710000e-12 82.4
34 TraesCS4A01G484700 chr1B 85.366 123 17 1 39 160 121560707 121560585 3.970000e-25 126.0
35 TraesCS4A01G484700 chr2A 92.857 56 4 0 3730 3785 672507355 672507300 8.710000e-12 82.4
36 TraesCS4A01G484700 chrUn 85.526 76 11 0 3029 3104 2081709 2081784 3.130000e-11 80.5
37 TraesCS4A01G484700 chrUn 92.105 38 3 0 3735 3772 102653465 102653502 2.000000e-03 54.7
38 TraesCS4A01G484700 chr2B 91.071 56 5 0 3730 3785 797570962 797570907 4.050000e-10 76.8
39 TraesCS4A01G484700 chr4D 90.909 55 2 3 406 459 125074376 125074428 1.890000e-08 71.3


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 TraesCS4A01G484700 chr4A 738814226 738818010 3784 False 6990.00 6990 100.00000 1 3785 1 chr4A.!!$F2 3784
1 TraesCS4A01G484700 chr7D 4875569 4878977 3408 False 1918.50 2782 94.69150 2 2803 2 chr7D.!!$F2 2801
2 TraesCS4A01G484700 chr7D 554316584 554317117 533 False 294.00 294 76.67900 1123 1656 1 chr7D.!!$F1 533
3 TraesCS4A01G484700 chr7A 4683612 4689738 6126 True 1185.75 2734 91.32225 4 3744 4 chr7A.!!$R1 3740
4 TraesCS4A01G484700 chr5B 9417141 9418550 1409 False 688.00 688 75.83300 1201 2622 1 chr5B.!!$F1 1421
5 TraesCS4A01G484700 chr5B 9333520 9334334 814 True 394.00 394 75.71400 1200 2035 1 chr5B.!!$R1 835
6 TraesCS4A01G484700 chr5D 9471220 9472556 1336 False 658.00 658 75.89700 1201 2549 1 chr5D.!!$F1 1348
7 TraesCS4A01G484700 chr5D 9386291 9387039 748 True 427.00 427 77.37800 1202 1971 1 chr5D.!!$R1 769
8 TraesCS4A01G484700 chr5A 7619461 7620877 1416 False 645.00 645 75.19100 1194 2622 1 chr5A.!!$F1 1428
9 TraesCS4A01G484700 chr5A 7504820 7506165 1345 True 593.00 593 75.07300 1201 2549 1 chr5A.!!$R1 1348
10 TraesCS4A01G484700 chr7B 600596775 600597317 542 True 289.00 289 76.33000 1123 1665 1 chr7B.!!$R1 542

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
822 828 0.036875 GGTGGTCTGGAGGTTGAAGG 59.963 60.0 0.00 0.0 0.0 3.46 F
1055 2247 0.239082 TACACGTACGCCAGACACAG 59.761 55.0 16.72 0.0 0.0 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1952 3180 0.449388 GGAGCTTGAAGTTGATGGCG 59.551 55.0 0.0 0.0 0.0 5.69 R
2874 5267 0.097674 GACCATGTGCGATTGACAGC 59.902 55.0 0.0 0.0 0.0 4.40 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
63 68 4.974645 TTGGAGTTGGTAGTGAGTTCAT 57.025 40.909 0.00 0.00 0.00 2.57
108 113 9.349713 TCACAATAAACAAATACACTCCTCTTT 57.650 29.630 0.00 0.00 0.00 2.52
145 150 3.243724 AGTAGCAAACTTCCAGGAGACT 58.756 45.455 0.00 0.00 36.34 3.24
157 162 8.567285 ACTTCCAGGAGACTTATAAACAAATG 57.433 34.615 0.00 0.00 40.21 2.32
164 169 8.540388 AGGAGACTTATAAACAAATGCACTAGA 58.460 33.333 0.00 0.00 37.44 2.43
165 170 8.821894 GGAGACTTATAAACAAATGCACTAGAG 58.178 37.037 0.00 0.00 0.00 2.43
178 183 3.760151 TGCACTAGAGCTACTTTAACGGA 59.240 43.478 13.47 0.00 34.99 4.69
205 210 4.152402 CCAACAGTCATTTAGAAGACACGG 59.848 45.833 0.00 0.00 37.23 4.94
223 228 7.027161 AGACACGGATAACAATTGCAAATAAC 58.973 34.615 1.71 0.00 0.00 1.89
231 236 6.932901 AACAATTGCAAATAACATGACTCG 57.067 33.333 1.71 0.00 0.00 4.18
531 536 3.131396 GTGGCATTGATACTACCCTTCG 58.869 50.000 0.00 0.00 0.00 3.79
705 711 5.335976 GCAATGGTTTACCCTTGAAGAAGAG 60.336 44.000 17.64 0.00 42.08 2.85
706 712 4.367039 TGGTTTACCCTTGAAGAAGAGG 57.633 45.455 0.00 0.00 34.29 3.69
710 716 3.566130 CCCTTGAAGAAGAGGGCAG 57.434 57.895 0.00 0.00 45.72 4.85
711 717 0.679321 CCCTTGAAGAAGAGGGCAGC 60.679 60.000 0.00 0.00 45.72 5.25
712 718 1.023513 CCTTGAAGAAGAGGGCAGCG 61.024 60.000 0.00 0.00 0.00 5.18
714 720 0.036952 TTGAAGAAGAGGGCAGCGAG 60.037 55.000 0.00 0.00 0.00 5.03
715 721 1.153469 GAAGAAGAGGGCAGCGAGG 60.153 63.158 0.00 0.00 0.00 4.63
716 722 3.322318 AAGAAGAGGGCAGCGAGGC 62.322 63.158 0.00 0.00 43.27 4.70
726 732 4.172512 AGCGAGGCTGCATGGGAG 62.173 66.667 0.50 0.00 37.57 4.30
759 765 4.360405 GTGATGGTGGCCGGGGTT 62.360 66.667 2.18 0.00 0.00 4.11
760 766 4.041762 TGATGGTGGCCGGGGTTC 62.042 66.667 2.18 0.00 0.00 3.62
782 788 1.691196 CCGGTGGCATATTTGATGGT 58.309 50.000 0.00 0.00 0.00 3.55
783 789 2.031120 CCGGTGGCATATTTGATGGTT 58.969 47.619 0.00 0.00 0.00 3.67
784 790 2.223782 CCGGTGGCATATTTGATGGTTG 60.224 50.000 0.00 0.00 0.00 3.77
785 791 2.223782 CGGTGGCATATTTGATGGTTGG 60.224 50.000 0.00 0.00 0.00 3.77
786 792 2.102925 GGTGGCATATTTGATGGTTGGG 59.897 50.000 0.00 0.00 0.00 4.12
787 793 2.102925 GTGGCATATTTGATGGTTGGGG 59.897 50.000 0.00 0.00 0.00 4.96
788 794 1.693606 GGCATATTTGATGGTTGGGGG 59.306 52.381 0.00 0.00 0.00 5.40
789 795 2.676748 GCATATTTGATGGTTGGGGGA 58.323 47.619 0.00 0.00 0.00 4.81
790 796 3.037549 GCATATTTGATGGTTGGGGGAA 58.962 45.455 0.00 0.00 0.00 3.97
791 797 3.070015 GCATATTTGATGGTTGGGGGAAG 59.930 47.826 0.00 0.00 0.00 3.46
792 798 4.545678 CATATTTGATGGTTGGGGGAAGA 58.454 43.478 0.00 0.00 0.00 2.87
793 799 3.558608 ATTTGATGGTTGGGGGAAGAA 57.441 42.857 0.00 0.00 0.00 2.52
794 800 2.603075 TTGATGGTTGGGGGAAGAAG 57.397 50.000 0.00 0.00 0.00 2.85
795 801 1.753903 TGATGGTTGGGGGAAGAAGA 58.246 50.000 0.00 0.00 0.00 2.87
796 802 2.069775 TGATGGTTGGGGGAAGAAGAA 58.930 47.619 0.00 0.00 0.00 2.52
797 803 2.448961 TGATGGTTGGGGGAAGAAGAAA 59.551 45.455 0.00 0.00 0.00 2.52
798 804 3.116939 TGATGGTTGGGGGAAGAAGAAAA 60.117 43.478 0.00 0.00 0.00 2.29
799 805 3.406512 TGGTTGGGGGAAGAAGAAAAA 57.593 42.857 0.00 0.00 0.00 1.94
800 806 3.304829 TGGTTGGGGGAAGAAGAAAAAG 58.695 45.455 0.00 0.00 0.00 2.27
801 807 3.052490 TGGTTGGGGGAAGAAGAAAAAGA 60.052 43.478 0.00 0.00 0.00 2.52
802 808 3.964688 GGTTGGGGGAAGAAGAAAAAGAA 59.035 43.478 0.00 0.00 0.00 2.52
803 809 4.039245 GGTTGGGGGAAGAAGAAAAAGAAG 59.961 45.833 0.00 0.00 0.00 2.85
804 810 3.844640 TGGGGGAAGAAGAAAAAGAAGG 58.155 45.455 0.00 0.00 0.00 3.46
805 811 3.206639 TGGGGGAAGAAGAAAAAGAAGGT 59.793 43.478 0.00 0.00 0.00 3.50
806 812 3.574396 GGGGGAAGAAGAAAAAGAAGGTG 59.426 47.826 0.00 0.00 0.00 4.00
807 813 3.574396 GGGGAAGAAGAAAAAGAAGGTGG 59.426 47.826 0.00 0.00 0.00 4.61
808 814 4.215908 GGGAAGAAGAAAAAGAAGGTGGT 58.784 43.478 0.00 0.00 0.00 4.16
809 815 4.278669 GGGAAGAAGAAAAAGAAGGTGGTC 59.721 45.833 0.00 0.00 0.00 4.02
810 816 5.133941 GGAAGAAGAAAAAGAAGGTGGTCT 58.866 41.667 0.00 0.00 0.00 3.85
811 817 5.009110 GGAAGAAGAAAAAGAAGGTGGTCTG 59.991 44.000 0.00 0.00 0.00 3.51
812 818 4.464947 AGAAGAAAAAGAAGGTGGTCTGG 58.535 43.478 0.00 0.00 0.00 3.86
813 819 4.166144 AGAAGAAAAAGAAGGTGGTCTGGA 59.834 41.667 0.00 0.00 0.00 3.86
814 820 4.092116 AGAAAAAGAAGGTGGTCTGGAG 57.908 45.455 0.00 0.00 0.00 3.86
815 821 2.959465 AAAAGAAGGTGGTCTGGAGG 57.041 50.000 0.00 0.00 0.00 4.30
816 822 1.821088 AAAGAAGGTGGTCTGGAGGT 58.179 50.000 0.00 0.00 0.00 3.85
817 823 1.821088 AAGAAGGTGGTCTGGAGGTT 58.179 50.000 0.00 0.00 0.00 3.50
821 827 1.059913 AGGTGGTCTGGAGGTTGAAG 58.940 55.000 0.00 0.00 0.00 3.02
822 828 0.036875 GGTGGTCTGGAGGTTGAAGG 59.963 60.000 0.00 0.00 0.00 3.46
824 830 1.002544 GTGGTCTGGAGGTTGAAGGAG 59.997 57.143 0.00 0.00 0.00 3.69
832 838 1.742268 GAGGTTGAAGGAGCAATCTGC 59.258 52.381 0.00 0.00 39.23 4.26
842 848 1.213537 GCAATCTGCACCGCATGTT 59.786 52.632 0.00 0.00 44.26 2.71
844 850 1.936203 GCAATCTGCACCGCATGTTTT 60.936 47.619 0.00 0.00 44.26 2.43
849 855 0.243365 TGCACCGCATGTTTTCCATC 59.757 50.000 0.00 0.00 31.71 3.51
850 856 0.458370 GCACCGCATGTTTTCCATCC 60.458 55.000 0.00 0.00 0.00 3.51
853 859 1.272212 ACCGCATGTTTTCCATCCAAC 59.728 47.619 0.00 0.00 0.00 3.77
855 861 1.732077 CGCATGTTTTCCATCCAACGG 60.732 52.381 0.00 0.00 0.00 4.44
856 862 1.272212 GCATGTTTTCCATCCAACGGT 59.728 47.619 0.00 0.00 0.00 4.83
857 863 2.288763 GCATGTTTTCCATCCAACGGTT 60.289 45.455 0.00 0.00 0.00 4.44
858 864 3.316283 CATGTTTTCCATCCAACGGTTG 58.684 45.455 13.86 13.86 0.00 3.77
863 1721 1.231221 TCCATCCAACGGTTGAAACG 58.769 50.000 21.88 0.00 37.36 3.60
870 1728 2.303537 CAACGGTTGAAACGAAATCGG 58.696 47.619 15.66 0.00 44.95 4.18
872 1730 0.453782 CGGTTGAAACGAAATCGGCC 60.454 55.000 0.00 0.00 44.95 6.13
875 1733 0.513820 TTGAAACGAAATCGGCCGAC 59.486 50.000 33.75 17.74 44.95 4.79
877 1735 1.004200 AAACGAAATCGGCCGACCT 60.004 52.632 33.75 21.17 44.95 3.85
883 1741 2.286184 CGAAATCGGCCGACCTAAATTG 60.286 50.000 33.75 12.74 35.37 2.32
887 1745 2.993937 TCGGCCGACCTAAATTGAAAT 58.006 42.857 27.28 0.00 0.00 2.17
890 1748 4.102649 CGGCCGACCTAAATTGAAATTTC 58.897 43.478 24.07 11.41 39.24 2.17
893 1751 5.336451 GGCCGACCTAAATTGAAATTTCAGT 60.336 40.000 19.64 15.01 39.24 3.41
906 1764 9.716507 ATTGAAATTTCAGTCGATTTATTACCG 57.283 29.630 19.64 0.00 38.61 4.02
907 1765 7.184106 TGAAATTTCAGTCGATTTATTACCGC 58.816 34.615 16.91 0.00 32.50 5.68
908 1766 6.920569 AATTTCAGTCGATTTATTACCGCT 57.079 33.333 0.00 0.00 0.00 5.52
909 1767 8.428186 AAATTTCAGTCGATTTATTACCGCTA 57.572 30.769 0.00 0.00 0.00 4.26
910 1768 7.639162 ATTTCAGTCGATTTATTACCGCTAG 57.361 36.000 0.00 0.00 0.00 3.42
911 1769 4.543692 TCAGTCGATTTATTACCGCTAGC 58.456 43.478 4.06 4.06 0.00 3.42
912 1770 3.673809 CAGTCGATTTATTACCGCTAGCC 59.326 47.826 9.66 0.00 0.00 3.93
913 1771 3.319972 AGTCGATTTATTACCGCTAGCCA 59.680 43.478 9.66 0.00 0.00 4.75
915 1773 4.689345 GTCGATTTATTACCGCTAGCCATT 59.311 41.667 9.66 0.00 0.00 3.16
916 1774 4.927425 TCGATTTATTACCGCTAGCCATTC 59.073 41.667 9.66 0.00 0.00 2.67
917 1775 4.092968 CGATTTATTACCGCTAGCCATTCC 59.907 45.833 9.66 0.00 0.00 3.01
922 1780 1.209621 ACCGCTAGCCATTCCCTTAA 58.790 50.000 9.66 0.00 0.00 1.85
924 1782 2.222027 CCGCTAGCCATTCCCTTAAAG 58.778 52.381 9.66 0.00 0.00 1.85
925 1783 2.421529 CCGCTAGCCATTCCCTTAAAGT 60.422 50.000 9.66 0.00 0.00 2.66
926 1784 3.181458 CCGCTAGCCATTCCCTTAAAGTA 60.181 47.826 9.66 0.00 0.00 2.24
927 1785 4.505039 CCGCTAGCCATTCCCTTAAAGTAT 60.505 45.833 9.66 0.00 0.00 2.12
928 1786 4.452455 CGCTAGCCATTCCCTTAAAGTATG 59.548 45.833 9.66 0.00 0.00 2.39
929 1787 5.621193 GCTAGCCATTCCCTTAAAGTATGA 58.379 41.667 2.29 0.00 0.00 2.15
930 1788 5.470437 GCTAGCCATTCCCTTAAAGTATGAC 59.530 44.000 2.29 0.00 0.00 3.06
931 1789 4.793201 AGCCATTCCCTTAAAGTATGACC 58.207 43.478 0.00 0.00 0.00 4.02
949 2141 9.645128 AGTATGACCATAATTCATCATGGAAAA 57.355 29.630 11.21 0.00 43.80 2.29
968 2160 7.936584 TGGAAAATAGTTTCACAACGAAGAAT 58.063 30.769 16.69 0.00 44.29 2.40
980 2172 4.081642 ACAACGAAGAATCCTGCTAGCTAA 60.082 41.667 17.23 1.26 0.00 3.09
981 2173 4.314740 ACGAAGAATCCTGCTAGCTAAG 57.685 45.455 17.23 5.63 0.00 2.18
982 2174 3.068873 ACGAAGAATCCTGCTAGCTAAGG 59.931 47.826 17.23 15.29 34.65 2.69
983 2175 3.068873 CGAAGAATCCTGCTAGCTAAGGT 59.931 47.826 17.23 0.00 34.94 3.50
984 2176 4.442192 CGAAGAATCCTGCTAGCTAAGGTT 60.442 45.833 17.23 11.45 34.94 3.50
985 2177 5.221263 CGAAGAATCCTGCTAGCTAAGGTTA 60.221 44.000 17.23 0.60 34.94 2.85
986 2178 5.799827 AGAATCCTGCTAGCTAAGGTTAG 57.200 43.478 17.23 2.46 34.94 2.34
987 2179 4.591072 AGAATCCTGCTAGCTAAGGTTAGG 59.409 45.833 17.23 12.26 34.94 2.69
988 2180 3.399952 TCCTGCTAGCTAAGGTTAGGT 57.600 47.619 17.23 6.68 43.30 3.08
989 2181 3.297736 TCCTGCTAGCTAAGGTTAGGTC 58.702 50.000 17.23 0.00 41.34 3.85
990 2182 3.052793 TCCTGCTAGCTAAGGTTAGGTCT 60.053 47.826 17.23 0.00 41.34 3.85
991 2183 3.707102 CCTGCTAGCTAAGGTTAGGTCTT 59.293 47.826 17.23 0.00 41.34 3.01
992 2184 4.202172 CCTGCTAGCTAAGGTTAGGTCTTC 60.202 50.000 17.23 0.00 41.34 2.87
993 2185 4.611367 TGCTAGCTAAGGTTAGGTCTTCT 58.389 43.478 17.23 0.00 41.34 2.85
994 2186 4.402793 TGCTAGCTAAGGTTAGGTCTTCTG 59.597 45.833 17.23 0.00 41.34 3.02
995 2187 4.403113 GCTAGCTAAGGTTAGGTCTTCTGT 59.597 45.833 7.70 0.00 41.34 3.41
996 2188 5.105269 GCTAGCTAAGGTTAGGTCTTCTGTT 60.105 44.000 7.70 0.00 41.34 3.16
997 2189 5.827326 AGCTAAGGTTAGGTCTTCTGTTT 57.173 39.130 0.00 0.00 36.87 2.83
998 2190 6.930068 AGCTAAGGTTAGGTCTTCTGTTTA 57.070 37.500 0.00 0.00 36.87 2.01
999 2191 7.497773 AGCTAAGGTTAGGTCTTCTGTTTAT 57.502 36.000 0.00 0.00 36.87 1.40
1029 2221 0.744414 AAAGGTATGCATGCGCGTCT 60.744 50.000 14.09 5.43 42.97 4.18
1030 2222 1.154205 AAGGTATGCATGCGCGTCTC 61.154 55.000 14.09 0.00 42.97 3.36
1031 2223 2.598632 GGTATGCATGCGCGTCTCC 61.599 63.158 14.09 5.86 42.97 3.71
1033 2225 3.807631 TATGCATGCGCGTCTCCCC 62.808 63.158 14.09 0.00 42.97 4.81
1036 2228 2.514592 CATGCGCGTCTCCCCAAT 60.515 61.111 8.43 0.00 0.00 3.16
1037 2229 1.227527 CATGCGCGTCTCCCCAATA 60.228 57.895 8.43 0.00 0.00 1.90
1038 2230 1.227556 ATGCGCGTCTCCCCAATAC 60.228 57.895 8.43 0.00 0.00 1.89
1039 2231 1.966901 ATGCGCGTCTCCCCAATACA 61.967 55.000 8.43 0.00 0.00 2.29
1040 2232 2.171725 GCGCGTCTCCCCAATACAC 61.172 63.158 8.43 0.00 0.00 2.90
1041 2233 1.876714 CGCGTCTCCCCAATACACG 60.877 63.158 0.00 0.00 0.00 4.49
1042 2234 1.217244 GCGTCTCCCCAATACACGT 59.783 57.895 0.00 0.00 32.99 4.49
1044 2236 1.800286 GCGTCTCCCCAATACACGTAC 60.800 57.143 0.00 0.00 32.99 3.67
1045 2237 1.532505 CGTCTCCCCAATACACGTACG 60.533 57.143 15.01 15.01 0.00 3.67
1047 2239 0.529119 CTCCCCAATACACGTACGCC 60.529 60.000 16.72 0.00 0.00 5.68
1048 2240 1.218585 CCCCAATACACGTACGCCA 59.781 57.895 16.72 0.16 0.00 5.69
1049 2241 0.808453 CCCCAATACACGTACGCCAG 60.808 60.000 16.72 8.33 0.00 4.85
1051 2243 1.274596 CCAATACACGTACGCCAGAC 58.725 55.000 16.72 0.00 0.00 3.51
1052 2244 1.403116 CCAATACACGTACGCCAGACA 60.403 52.381 16.72 0.36 0.00 3.41
1053 2245 1.652124 CAATACACGTACGCCAGACAC 59.348 52.381 16.72 0.00 0.00 3.67
1055 2247 0.239082 TACACGTACGCCAGACACAG 59.761 55.000 16.72 0.00 0.00 3.66
1500 2728 2.361610 CCAACATCAAGGCCGGCT 60.362 61.111 28.56 9.77 0.00 5.52
1828 3056 1.452108 CCAAGGCGGAAGATCCCAC 60.452 63.158 0.00 0.00 36.56 4.61
1829 3057 1.604378 CAAGGCGGAAGATCCCACT 59.396 57.895 0.00 0.00 31.13 4.00
2504 3750 0.615261 AGAAGTTCGAGGAGGACCCC 60.615 60.000 0.00 0.00 36.73 4.95
2686 3932 3.126831 GCTACTCCATTTCATCACTCGG 58.873 50.000 0.00 0.00 0.00 4.63
2806 4095 0.471617 AAAGGGGCATCTCATCCTCG 59.528 55.000 0.00 0.00 0.00 4.63
2831 4120 0.601558 TCCACTCACTTACCACTCGC 59.398 55.000 0.00 0.00 0.00 5.03
2858 5251 6.493115 AGAACAATGGTTATTGGTTGTGATCA 59.507 34.615 0.00 0.00 44.05 2.92
2872 5265 1.797046 GTGATCATCTACATGCCGCAG 59.203 52.381 0.00 0.00 0.00 5.18
2874 5267 1.797046 GATCATCTACATGCCGCAGTG 59.203 52.381 0.00 0.39 0.00 3.66
2883 5276 1.651240 ATGCCGCAGTGCTGTCAATC 61.651 55.000 14.33 0.00 0.00 2.67
2884 5277 2.780643 CCGCAGTGCTGTCAATCG 59.219 61.111 14.33 0.00 0.00 3.34
2899 5292 3.704231 ATCGCACATGGTCAGGGCC 62.704 63.158 0.00 0.00 0.00 5.80
2924 5317 0.602905 GGCGGCGACCATTTAGCTAT 60.603 55.000 12.98 0.00 0.00 2.97
2928 5321 3.848554 GCGGCGACCATTTAGCTATTTTC 60.849 47.826 12.98 0.00 0.00 2.29
2936 5329 6.852664 ACCATTTAGCTATTTTCGAAAGGTG 58.147 36.000 10.98 6.26 0.00 4.00
2944 5337 3.478857 TTTTCGAAAGGTGTGGCTAGA 57.521 42.857 10.98 0.00 0.00 2.43
2949 5342 2.796383 CGAAAGGTGTGGCTAGATCTCG 60.796 54.545 0.00 0.00 0.00 4.04
2965 5358 3.855159 TCGGTCGACTGAGATCTCA 57.145 52.632 23.11 23.75 38.06 3.27
2973 5366 4.797868 GTCGACTGAGATCTCAATCAAGTG 59.202 45.833 28.22 16.88 35.76 3.16
2985 5378 7.984422 TCTCAATCAAGTGACATAACATGTT 57.016 32.000 16.68 16.68 45.03 2.71
2987 5380 9.500785 TCTCAATCAAGTGACATAACATGTTAA 57.499 29.630 21.57 3.03 45.03 2.01
3029 5422 3.578282 ACAAAGAAGAAAATTGCCCGGAT 59.422 39.130 0.73 0.00 0.00 4.18
3043 5436 8.472007 AATTGCCCGGATCTTAATGTAAAATA 57.528 30.769 0.73 0.00 0.00 1.40
3044 5437 8.650143 ATTGCCCGGATCTTAATGTAAAATAT 57.350 30.769 0.73 0.00 0.00 1.28
3047 5440 7.721842 TGCCCGGATCTTAATGTAAAATATCAA 59.278 33.333 0.73 0.00 0.00 2.57
3074 5467 1.749063 AGCATCGACCGAGACATAACA 59.251 47.619 0.00 0.00 0.00 2.41
3080 5473 5.068234 TCGACCGAGACATAACAAAATCT 57.932 39.130 0.00 0.00 0.00 2.40
3082 5475 4.267928 CGACCGAGACATAACAAAATCTCC 59.732 45.833 0.00 0.00 35.21 3.71
3087 5480 5.661458 GAGACATAACAAAATCTCCCTCGA 58.339 41.667 0.00 0.00 32.97 4.04
3092 5485 6.540189 ACATAACAAAATCTCCCTCGATTGAG 59.460 38.462 2.59 2.59 42.18 3.02
3104 5497 3.691118 CCTCGATTGAGATTTGGCAAGAA 59.309 43.478 11.89 0.00 45.57 2.52
3153 5546 6.693315 TTCTTCAGGTTTTCTTGTTCGAAT 57.307 33.333 0.00 0.00 0.00 3.34
3162 5555 2.888594 TCTTGTTCGAATAAGGCCTCG 58.111 47.619 27.69 5.58 36.39 4.63
3185 5578 7.053498 TCGGACCTATTGATCAAATCATCAAA 58.947 34.615 13.09 0.00 44.18 2.69
3286 5679 3.261897 GGTCATCTTCTTCCTCCAGAACA 59.738 47.826 0.00 0.00 0.00 3.18
3331 5724 2.268920 GGCTCTTCATCGCCCACA 59.731 61.111 0.00 0.00 40.43 4.17
3332 5725 2.109126 GGCTCTTCATCGCCCACAC 61.109 63.158 0.00 0.00 40.43 3.82
3339 5732 1.449601 CATCGCCCACACCACTACC 60.450 63.158 0.00 0.00 0.00 3.18
3352 5745 2.295253 CACTACCGTGGGATCACTTC 57.705 55.000 0.00 0.00 41.53 3.01
3370 5763 1.567357 TCCCACGACCATGAAGATGA 58.433 50.000 0.00 0.00 0.00 2.92
3371 5764 1.207089 TCCCACGACCATGAAGATGAC 59.793 52.381 0.00 0.00 0.00 3.06
3372 5765 1.656652 CCACGACCATGAAGATGACC 58.343 55.000 0.00 0.00 0.00 4.02
3381 5774 0.684535 TGAAGATGACCAACGAGCCA 59.315 50.000 0.00 0.00 0.00 4.75
3389 5782 2.103432 TGACCAACGAGCCAGAGTTAAA 59.897 45.455 0.00 0.00 0.00 1.52
3397 5790 3.862267 CGAGCCAGAGTTAAAGATGTCTG 59.138 47.826 0.00 0.00 36.89 3.51
3409 5802 3.623906 AGATGTCTGTCTTGGTCATGG 57.376 47.619 0.00 0.00 0.00 3.66
3412 5805 1.271001 TGTCTGTCTTGGTCATGGCTG 60.271 52.381 0.00 0.00 0.00 4.85
3444 5837 2.757868 ACGTGAGGAAGAGAAGATCCAG 59.242 50.000 0.00 0.00 38.23 3.86
3446 5839 3.194542 CGTGAGGAAGAGAAGATCCAGTT 59.805 47.826 0.00 0.00 38.23 3.16
3450 5843 5.420421 TGAGGAAGAGAAGATCCAGTTACTG 59.580 44.000 5.22 5.22 38.23 2.74
3571 5964 5.235516 TCGTCTTTCTGTCCCTATTTGTTC 58.764 41.667 0.00 0.00 0.00 3.18
3650 6377 8.630037 CCCTCACACATTTAAAAACTAAGTCTT 58.370 33.333 0.00 0.00 0.00 3.01
3721 6448 4.788521 GCAAACTGTTTTAGGTCGACAAGG 60.789 45.833 18.91 1.90 0.00 3.61
3734 6461 6.926313 AGGTCGACAAGGAATCTAATATAGC 58.074 40.000 18.91 0.00 0.00 2.97
3755 6482 8.753497 ATAGCTAATAATAAAGGGGCTATTGC 57.247 34.615 0.00 0.00 38.01 3.56
3756 6483 6.794534 AGCTAATAATAAAGGGGCTATTGCT 58.205 36.000 0.00 0.00 39.59 3.91
3757 6484 7.241628 AGCTAATAATAAAGGGGCTATTGCTT 58.758 34.615 0.00 0.00 39.59 3.91
3758 6485 7.394641 AGCTAATAATAAAGGGGCTATTGCTTC 59.605 37.037 0.00 0.00 39.59 3.86
3759 6486 7.394641 GCTAATAATAAAGGGGCTATTGCTTCT 59.605 37.037 0.00 0.00 39.59 2.85
3760 6487 9.301897 CTAATAATAAAGGGGCTATTGCTTCTT 57.698 33.333 0.00 0.96 39.59 2.52
3761 6488 5.859205 AATAAAGGGGCTATTGCTTCTTG 57.141 39.130 0.00 0.00 39.59 3.02
3762 6489 1.478631 AAGGGGCTATTGCTTCTTGC 58.521 50.000 0.00 0.00 43.25 4.01
3763 6490 0.749454 AGGGGCTATTGCTTCTTGCG 60.749 55.000 0.00 0.00 46.63 4.85
3764 6491 1.728490 GGGGCTATTGCTTCTTGCGG 61.728 60.000 0.00 0.00 46.63 5.69
3765 6492 1.032114 GGGCTATTGCTTCTTGCGGT 61.032 55.000 0.00 0.00 46.63 5.68
3766 6493 0.099436 GGCTATTGCTTCTTGCGGTG 59.901 55.000 0.00 0.00 46.63 4.94
3767 6494 0.524180 GCTATTGCTTCTTGCGGTGC 60.524 55.000 0.00 0.00 46.63 5.01
3768 6495 0.247814 CTATTGCTTCTTGCGGTGCG 60.248 55.000 0.00 0.00 46.63 5.34
3769 6496 0.953471 TATTGCTTCTTGCGGTGCGT 60.953 50.000 0.00 0.00 46.63 5.24
3770 6497 2.187599 ATTGCTTCTTGCGGTGCGTC 62.188 55.000 0.00 0.00 46.63 5.19
3771 6498 3.345808 GCTTCTTGCGGTGCGTCA 61.346 61.111 0.00 0.00 0.00 4.35
3772 6499 2.680913 GCTTCTTGCGGTGCGTCAT 61.681 57.895 0.00 0.00 0.00 3.06
3773 6500 1.358725 GCTTCTTGCGGTGCGTCATA 61.359 55.000 0.00 0.00 0.00 2.15
3774 6501 0.647410 CTTCTTGCGGTGCGTCATAG 59.353 55.000 0.00 0.00 0.00 2.23
3775 6502 0.245266 TTCTTGCGGTGCGTCATAGA 59.755 50.000 0.00 0.00 0.00 1.98
3776 6503 0.245266 TCTTGCGGTGCGTCATAGAA 59.755 50.000 0.00 0.00 0.00 2.10
3777 6504 1.075542 CTTGCGGTGCGTCATAGAAA 58.924 50.000 0.00 0.00 0.00 2.52
3778 6505 1.665679 CTTGCGGTGCGTCATAGAAAT 59.334 47.619 0.00 0.00 0.00 2.17
3779 6506 1.732941 TGCGGTGCGTCATAGAAATT 58.267 45.000 0.00 0.00 0.00 1.82
3780 6507 1.396648 TGCGGTGCGTCATAGAAATTG 59.603 47.619 0.00 0.00 0.00 2.32
3781 6508 1.856014 GCGGTGCGTCATAGAAATTGC 60.856 52.381 0.00 0.00 0.00 3.56
3782 6509 1.268032 CGGTGCGTCATAGAAATTGCC 60.268 52.381 0.00 0.00 0.00 4.52
3783 6510 1.065551 GGTGCGTCATAGAAATTGCCC 59.934 52.381 0.00 0.00 0.00 5.36
3784 6511 1.065551 GTGCGTCATAGAAATTGCCCC 59.934 52.381 0.00 0.00 0.00 5.80
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 41 6.391227 ACTCACTACCAACTCCAATTTTTG 57.609 37.500 0.00 0.00 0.00 2.44
40 45 5.304686 TGAACTCACTACCAACTCCAATT 57.695 39.130 0.00 0.00 0.00 2.32
108 113 3.578282 TGCTACTTCCACATGTGAAGAGA 59.422 43.478 29.00 17.40 0.00 3.10
145 150 9.667107 AAGTAGCTCTAGTGCATTTGTTTATAA 57.333 29.630 18.36 0.00 34.99 0.98
157 162 4.367386 TCCGTTAAAGTAGCTCTAGTGC 57.633 45.455 8.76 8.76 0.00 4.40
164 169 3.412237 TGGCTTTCCGTTAAAGTAGCT 57.588 42.857 8.70 0.00 45.46 3.32
165 170 3.251487 TGTTGGCTTTCCGTTAAAGTAGC 59.749 43.478 8.70 0.00 45.46 3.58
178 183 5.827797 TGTCTTCTAAATGACTGTTGGCTTT 59.172 36.000 0.00 0.00 34.57 3.51
205 210 8.736742 CGAGTCATGTTATTTGCAATTGTTATC 58.263 33.333 7.40 0.00 0.00 1.75
223 228 9.778993 AAATCATAATTTTGAGTTCGAGTCATG 57.221 29.630 5.87 0.00 28.44 3.07
575 580 6.985645 AGCATTTTTGTGAACATTGTGTACAT 59.014 30.769 0.00 0.00 0.00 2.29
742 748 4.360405 AACCCCGGCCACCATCAC 62.360 66.667 2.24 0.00 0.00 3.06
743 749 4.041762 GAACCCCGGCCACCATCA 62.042 66.667 2.24 0.00 0.00 3.07
763 769 1.691196 ACCATCAAATATGCCACCGG 58.309 50.000 0.00 0.00 0.00 5.28
764 770 2.223782 CCAACCATCAAATATGCCACCG 60.224 50.000 0.00 0.00 0.00 4.94
765 771 2.102925 CCCAACCATCAAATATGCCACC 59.897 50.000 0.00 0.00 0.00 4.61
766 772 2.102925 CCCCAACCATCAAATATGCCAC 59.897 50.000 0.00 0.00 0.00 5.01
767 773 2.396608 CCCCAACCATCAAATATGCCA 58.603 47.619 0.00 0.00 0.00 4.92
768 774 1.693606 CCCCCAACCATCAAATATGCC 59.306 52.381 0.00 0.00 0.00 4.40
769 775 2.676748 TCCCCCAACCATCAAATATGC 58.323 47.619 0.00 0.00 0.00 3.14
770 776 4.545678 TCTTCCCCCAACCATCAAATATG 58.454 43.478 0.00 0.00 0.00 1.78
771 777 4.898014 TCTTCCCCCAACCATCAAATAT 57.102 40.909 0.00 0.00 0.00 1.28
772 778 4.293634 TCTTCTTCCCCCAACCATCAAATA 59.706 41.667 0.00 0.00 0.00 1.40
773 779 3.077391 TCTTCTTCCCCCAACCATCAAAT 59.923 43.478 0.00 0.00 0.00 2.32
774 780 2.448961 TCTTCTTCCCCCAACCATCAAA 59.551 45.455 0.00 0.00 0.00 2.69
775 781 2.069775 TCTTCTTCCCCCAACCATCAA 58.930 47.619 0.00 0.00 0.00 2.57
776 782 1.753903 TCTTCTTCCCCCAACCATCA 58.246 50.000 0.00 0.00 0.00 3.07
777 783 2.899303 TTCTTCTTCCCCCAACCATC 57.101 50.000 0.00 0.00 0.00 3.51
778 784 3.628832 TTTTCTTCTTCCCCCAACCAT 57.371 42.857 0.00 0.00 0.00 3.55
779 785 3.052490 TCTTTTTCTTCTTCCCCCAACCA 60.052 43.478 0.00 0.00 0.00 3.67
780 786 3.572642 TCTTTTTCTTCTTCCCCCAACC 58.427 45.455 0.00 0.00 0.00 3.77
781 787 4.039245 CCTTCTTTTTCTTCTTCCCCCAAC 59.961 45.833 0.00 0.00 0.00 3.77
782 788 4.223144 CCTTCTTTTTCTTCTTCCCCCAA 58.777 43.478 0.00 0.00 0.00 4.12
783 789 3.206639 ACCTTCTTTTTCTTCTTCCCCCA 59.793 43.478 0.00 0.00 0.00 4.96
784 790 3.574396 CACCTTCTTTTTCTTCTTCCCCC 59.426 47.826 0.00 0.00 0.00 5.40
785 791 3.574396 CCACCTTCTTTTTCTTCTTCCCC 59.426 47.826 0.00 0.00 0.00 4.81
786 792 4.215908 ACCACCTTCTTTTTCTTCTTCCC 58.784 43.478 0.00 0.00 0.00 3.97
787 793 5.009110 CAGACCACCTTCTTTTTCTTCTTCC 59.991 44.000 0.00 0.00 0.00 3.46
788 794 5.009110 CCAGACCACCTTCTTTTTCTTCTTC 59.991 44.000 0.00 0.00 0.00 2.87
789 795 4.889995 CCAGACCACCTTCTTTTTCTTCTT 59.110 41.667 0.00 0.00 0.00 2.52
790 796 4.166144 TCCAGACCACCTTCTTTTTCTTCT 59.834 41.667 0.00 0.00 0.00 2.85
791 797 4.461198 TCCAGACCACCTTCTTTTTCTTC 58.539 43.478 0.00 0.00 0.00 2.87
792 798 4.464947 CTCCAGACCACCTTCTTTTTCTT 58.535 43.478 0.00 0.00 0.00 2.52
793 799 3.181439 CCTCCAGACCACCTTCTTTTTCT 60.181 47.826 0.00 0.00 0.00 2.52
794 800 3.149981 CCTCCAGACCACCTTCTTTTTC 58.850 50.000 0.00 0.00 0.00 2.29
795 801 2.514160 ACCTCCAGACCACCTTCTTTTT 59.486 45.455 0.00 0.00 0.00 1.94
796 802 2.136026 ACCTCCAGACCACCTTCTTTT 58.864 47.619 0.00 0.00 0.00 2.27
797 803 1.821088 ACCTCCAGACCACCTTCTTT 58.179 50.000 0.00 0.00 0.00 2.52
798 804 1.421646 CAACCTCCAGACCACCTTCTT 59.578 52.381 0.00 0.00 0.00 2.52
799 805 1.059913 CAACCTCCAGACCACCTTCT 58.940 55.000 0.00 0.00 0.00 2.85
800 806 1.056660 TCAACCTCCAGACCACCTTC 58.943 55.000 0.00 0.00 0.00 3.46
801 807 1.421646 CTTCAACCTCCAGACCACCTT 59.578 52.381 0.00 0.00 0.00 3.50
802 808 1.059913 CTTCAACCTCCAGACCACCT 58.940 55.000 0.00 0.00 0.00 4.00
803 809 0.036875 CCTTCAACCTCCAGACCACC 59.963 60.000 0.00 0.00 0.00 4.61
804 810 1.002544 CTCCTTCAACCTCCAGACCAC 59.997 57.143 0.00 0.00 0.00 4.16
805 811 1.352083 CTCCTTCAACCTCCAGACCA 58.648 55.000 0.00 0.00 0.00 4.02
806 812 0.035915 GCTCCTTCAACCTCCAGACC 60.036 60.000 0.00 0.00 0.00 3.85
807 813 0.687354 TGCTCCTTCAACCTCCAGAC 59.313 55.000 0.00 0.00 0.00 3.51
808 814 1.434188 TTGCTCCTTCAACCTCCAGA 58.566 50.000 0.00 0.00 0.00 3.86
809 815 2.026449 AGATTGCTCCTTCAACCTCCAG 60.026 50.000 0.00 0.00 0.00 3.86
810 816 1.988107 AGATTGCTCCTTCAACCTCCA 59.012 47.619 0.00 0.00 0.00 3.86
811 817 2.363683 CAGATTGCTCCTTCAACCTCC 58.636 52.381 0.00 0.00 0.00 4.30
812 818 1.742268 GCAGATTGCTCCTTCAACCTC 59.258 52.381 0.00 0.00 40.96 3.85
813 819 1.074405 TGCAGATTGCTCCTTCAACCT 59.926 47.619 2.48 0.00 45.31 3.50
814 820 1.200948 GTGCAGATTGCTCCTTCAACC 59.799 52.381 2.48 0.00 45.31 3.77
815 821 2.626088 GTGCAGATTGCTCCTTCAAC 57.374 50.000 2.48 0.00 45.31 3.18
822 828 1.063649 CATGCGGTGCAGATTGCTC 59.936 57.895 2.48 0.00 45.31 4.26
824 830 0.388907 AAACATGCGGTGCAGATTGC 60.389 50.000 0.00 0.00 43.65 3.56
832 838 3.719699 GGATGGAAAACATGCGGTG 57.280 52.632 0.00 0.00 40.72 4.94
836 842 1.272212 ACCGTTGGATGGAAAACATGC 59.728 47.619 0.00 0.00 46.95 4.06
837 843 3.005261 TCAACCGTTGGATGGAAAACATG 59.995 43.478 11.35 0.00 40.72 3.21
838 844 3.226777 TCAACCGTTGGATGGAAAACAT 58.773 40.909 11.35 0.00 44.18 2.71
839 845 2.656002 TCAACCGTTGGATGGAAAACA 58.344 42.857 11.35 0.00 0.00 2.83
842 848 2.033550 CGTTTCAACCGTTGGATGGAAA 59.966 45.455 11.35 1.71 24.69 3.13
844 850 1.202663 TCGTTTCAACCGTTGGATGGA 60.203 47.619 11.35 0.72 0.00 3.41
849 855 2.303537 CGATTTCGTTTCAACCGTTGG 58.696 47.619 11.35 0.00 34.11 3.77
850 856 2.303537 CCGATTTCGTTTCAACCGTTG 58.696 47.619 4.78 4.78 37.74 4.10
853 859 0.453782 GGCCGATTTCGTTTCAACCG 60.454 55.000 0.00 0.00 37.74 4.44
855 861 0.513820 TCGGCCGATTTCGTTTCAAC 59.486 50.000 27.28 0.00 37.74 3.18
856 862 0.513820 GTCGGCCGATTTCGTTTCAA 59.486 50.000 33.58 0.00 37.74 2.69
857 863 1.293267 GGTCGGCCGATTTCGTTTCA 61.293 55.000 33.58 0.18 37.74 2.69
858 864 1.017701 AGGTCGGCCGATTTCGTTTC 61.018 55.000 33.58 15.61 40.50 2.78
863 1721 2.940410 TCAATTTAGGTCGGCCGATTTC 59.060 45.455 33.58 22.81 40.50 2.17
870 1728 5.709966 ACTGAAATTTCAATTTAGGTCGGC 58.290 37.500 20.82 0.00 38.64 5.54
883 1741 7.407337 AGCGGTAATAAATCGACTGAAATTTC 58.593 34.615 11.41 11.41 0.00 2.17
887 1745 5.461078 GCTAGCGGTAATAAATCGACTGAAA 59.539 40.000 0.00 0.00 0.00 2.69
890 1748 3.673809 GGCTAGCGGTAATAAATCGACTG 59.326 47.826 9.00 0.00 0.00 3.51
893 1751 4.530710 ATGGCTAGCGGTAATAAATCGA 57.469 40.909 9.00 0.00 0.00 3.59
895 1753 4.395231 GGGAATGGCTAGCGGTAATAAATC 59.605 45.833 9.00 0.00 0.00 2.17
897 1755 3.393278 AGGGAATGGCTAGCGGTAATAAA 59.607 43.478 9.00 0.00 0.00 1.40
901 1759 1.209621 AAGGGAATGGCTAGCGGTAA 58.790 50.000 9.00 0.00 0.00 2.85
902 1760 2.091098 TAAGGGAATGGCTAGCGGTA 57.909 50.000 9.00 0.00 0.00 4.02
903 1761 1.209621 TTAAGGGAATGGCTAGCGGT 58.790 50.000 9.00 0.00 0.00 5.68
904 1762 2.222027 CTTTAAGGGAATGGCTAGCGG 58.778 52.381 9.00 0.00 0.00 5.52
905 1763 2.919228 ACTTTAAGGGAATGGCTAGCG 58.081 47.619 9.00 0.00 0.00 4.26
906 1764 5.470437 GTCATACTTTAAGGGAATGGCTAGC 59.530 44.000 6.04 6.04 0.00 3.42
907 1765 5.998363 GGTCATACTTTAAGGGAATGGCTAG 59.002 44.000 0.00 0.00 0.00 3.42
908 1766 5.430417 TGGTCATACTTTAAGGGAATGGCTA 59.570 40.000 0.00 0.00 0.00 3.93
909 1767 4.229582 TGGTCATACTTTAAGGGAATGGCT 59.770 41.667 0.00 0.00 0.00 4.75
910 1768 4.532834 TGGTCATACTTTAAGGGAATGGC 58.467 43.478 0.00 0.00 0.00 4.40
911 1769 8.940397 ATTATGGTCATACTTTAAGGGAATGG 57.060 34.615 0.00 0.00 0.00 3.16
915 1773 9.793259 GATGAATTATGGTCATACTTTAAGGGA 57.207 33.333 0.00 0.00 35.84 4.20
916 1774 9.573166 TGATGAATTATGGTCATACTTTAAGGG 57.427 33.333 0.00 0.00 35.84 3.95
922 1780 9.645128 TTTCCATGATGAATTATGGTCATACTT 57.355 29.630 12.39 0.00 42.66 2.24
927 1785 9.645128 ACTATTTTCCATGATGAATTATGGTCA 57.355 29.630 12.39 0.96 42.66 4.02
943 2135 6.928979 TCTTCGTTGTGAAACTATTTTCCA 57.071 33.333 3.38 0.00 40.55 3.53
945 2137 8.290325 AGGATTCTTCGTTGTGAAACTATTTTC 58.710 33.333 0.00 0.00 41.49 2.29
949 2141 5.122396 GCAGGATTCTTCGTTGTGAAACTAT 59.878 40.000 0.00 0.00 38.04 2.12
958 2150 2.898705 AGCTAGCAGGATTCTTCGTTG 58.101 47.619 18.83 0.00 0.00 4.10
968 2160 3.052793 AGACCTAACCTTAGCTAGCAGGA 60.053 47.826 24.11 4.11 33.90 3.86
998 2190 9.481340 CGCATGCATACCTTTCTATATATACAT 57.519 33.333 19.57 0.00 0.00 2.29
999 2191 7.438160 GCGCATGCATACCTTTCTATATATACA 59.562 37.037 19.57 0.00 42.15 2.29
1009 2201 0.316196 GACGCGCATGCATACCTTTC 60.316 55.000 19.57 0.00 42.97 2.62
1012 2204 1.592669 GAGACGCGCATGCATACCT 60.593 57.895 19.57 8.89 42.97 3.08
1029 2221 1.256361 TGGCGTACGTGTATTGGGGA 61.256 55.000 17.90 0.00 0.00 4.81
1030 2222 0.808453 CTGGCGTACGTGTATTGGGG 60.808 60.000 17.90 0.00 0.00 4.96
1031 2223 0.173935 TCTGGCGTACGTGTATTGGG 59.826 55.000 17.90 0.00 0.00 4.12
1033 2225 1.652124 GTGTCTGGCGTACGTGTATTG 59.348 52.381 17.90 2.19 0.00 1.90
1035 2227 0.883153 TGTGTCTGGCGTACGTGTAT 59.117 50.000 17.90 0.00 0.00 2.29
1036 2228 0.239082 CTGTGTCTGGCGTACGTGTA 59.761 55.000 17.90 2.67 0.00 2.90
1037 2229 1.007734 CTGTGTCTGGCGTACGTGT 60.008 57.895 17.90 0.00 0.00 4.49
1038 2230 0.318360 TTCTGTGTCTGGCGTACGTG 60.318 55.000 17.90 7.85 0.00 4.49
1039 2231 0.039437 CTTCTGTGTCTGGCGTACGT 60.039 55.000 17.90 0.00 0.00 3.57
1040 2232 1.344942 GCTTCTGTGTCTGGCGTACG 61.345 60.000 11.84 11.84 0.00 3.67
1041 2233 0.038159 AGCTTCTGTGTCTGGCGTAC 60.038 55.000 0.00 0.00 0.00 3.67
1042 2234 0.243907 GAGCTTCTGTGTCTGGCGTA 59.756 55.000 0.00 0.00 0.00 4.42
1044 2236 1.013005 CAGAGCTTCTGTGTCTGGCG 61.013 60.000 0.00 0.00 39.58 5.69
1045 2237 1.297456 GCAGAGCTTCTGTGTCTGGC 61.297 60.000 12.71 0.00 45.94 4.85
1047 2239 1.672441 GGAGCAGAGCTTCTGTGTCTG 60.672 57.143 12.71 4.25 45.94 3.51
1048 2240 0.607620 GGAGCAGAGCTTCTGTGTCT 59.392 55.000 12.71 4.19 45.94 3.41
1049 2241 0.735632 CGGAGCAGAGCTTCTGTGTC 60.736 60.000 12.71 10.17 45.94 3.67
1051 2243 4.182132 CGGAGCAGAGCTTCTGTG 57.818 61.111 12.71 0.00 45.94 3.66
1075 2300 0.878416 GTTGAACGCCATGGCTTACA 59.122 50.000 33.07 24.56 39.32 2.41
1076 2301 0.179200 CGTTGAACGCCATGGCTTAC 60.179 55.000 33.07 22.46 39.32 2.34
1078 2303 1.599518 TCGTTGAACGCCATGGCTT 60.600 52.632 33.07 23.13 42.21 4.35
1079 2304 2.031919 TCGTTGAACGCCATGGCT 59.968 55.556 33.07 17.14 42.21 4.75
1081 2306 2.024868 TCGTCGTTGAACGCCATGG 61.025 57.895 13.62 7.63 42.21 3.66
1082 2307 1.129809 GTCGTCGTTGAACGCCATG 59.870 57.895 13.62 2.48 42.21 3.66
1952 3180 0.449388 GGAGCTTGAAGTTGATGGCG 59.551 55.000 0.00 0.00 0.00 5.69
2072 3300 3.557290 GGGGAGCGGGGTATCACC 61.557 72.222 0.00 0.00 37.60 4.02
2686 3932 7.364522 TGATGAAACAAACATAGCAGTAGAC 57.635 36.000 0.00 0.00 0.00 2.59
2806 4095 3.067833 GTGGTAAGTGAGTGGAAAGAGC 58.932 50.000 0.00 0.00 0.00 4.09
2831 4120 7.447374 TCACAACCAATAACCATTGTTCTAG 57.553 36.000 0.00 0.00 40.04 2.43
2858 5251 0.812811 CAGCACTGCGGCATGTAGAT 60.813 55.000 1.75 0.00 35.83 1.98
2874 5267 0.097674 GACCATGTGCGATTGACAGC 59.902 55.000 0.00 0.00 0.00 4.40
2905 5298 0.602905 ATAGCTAAATGGTCGCCGCC 60.603 55.000 0.00 0.00 0.00 6.13
2924 5317 3.478857 TCTAGCCACACCTTTCGAAAA 57.521 42.857 12.41 0.00 0.00 2.29
2928 5321 2.796383 CGAGATCTAGCCACACCTTTCG 60.796 54.545 0.00 0.00 0.00 3.46
2936 5329 0.308376 GTCGACCGAGATCTAGCCAC 59.692 60.000 3.51 0.00 0.00 5.01
2949 5342 4.142271 ACTTGATTGAGATCTCAGTCGACC 60.142 45.833 31.32 16.84 45.67 4.79
2961 5354 7.984422 AACATGTTATGTCACTTGATTGAGA 57.016 32.000 9.97 0.00 44.07 3.27
3005 5398 4.126437 CCGGGCAATTTTCTTCTTTGTTT 58.874 39.130 0.00 0.00 0.00 2.83
3006 5399 3.386402 TCCGGGCAATTTTCTTCTTTGTT 59.614 39.130 0.00 0.00 0.00 2.83
3007 5400 2.962421 TCCGGGCAATTTTCTTCTTTGT 59.038 40.909 0.00 0.00 0.00 2.83
3008 5401 3.658757 TCCGGGCAATTTTCTTCTTTG 57.341 42.857 0.00 0.00 0.00 2.77
3010 5403 3.701664 AGATCCGGGCAATTTTCTTCTT 58.298 40.909 0.00 0.00 0.00 2.52
3012 5405 5.576447 TTAAGATCCGGGCAATTTTCTTC 57.424 39.130 0.00 0.00 0.00 2.87
3013 5406 5.422012 ACATTAAGATCCGGGCAATTTTCTT 59.578 36.000 0.00 2.26 0.00 2.52
3015 5408 5.262588 ACATTAAGATCCGGGCAATTTTC 57.737 39.130 0.00 0.00 0.00 2.29
3043 5436 5.416013 TCTCGGTCGATGCTATATTCTTGAT 59.584 40.000 0.00 0.00 0.00 2.57
3044 5437 4.760204 TCTCGGTCGATGCTATATTCTTGA 59.240 41.667 0.00 0.00 0.00 3.02
3047 5440 4.072839 TGTCTCGGTCGATGCTATATTCT 58.927 43.478 0.00 0.00 0.00 2.40
3080 5473 1.559219 TGCCAAATCTCAATCGAGGGA 59.441 47.619 0.00 0.00 39.95 4.20
3082 5475 3.273434 TCTTGCCAAATCTCAATCGAGG 58.727 45.455 0.00 0.00 39.95 4.63
3135 5528 5.154222 GCCTTATTCGAACAAGAAAACCTG 58.846 41.667 17.60 0.23 33.43 4.00
3153 5546 2.464796 TCAATAGGTCCGAGGCCTTA 57.535 50.000 6.77 0.00 37.54 2.69
3196 5589 9.625747 TGGTGTGTATATGTTGATATTTGATGT 57.374 29.630 0.00 0.00 0.00 3.06
3197 5590 9.882996 GTGGTGTGTATATGTTGATATTTGATG 57.117 33.333 0.00 0.00 0.00 3.07
3237 5630 8.472007 AACACCAAAGACCTTGATGTAATTTA 57.528 30.769 0.00 0.00 37.17 1.40
3352 5745 1.656652 GTCATCTTCATGGTCGTGGG 58.343 55.000 0.00 0.00 0.00 4.61
3356 5749 1.660607 CGTTGGTCATCTTCATGGTCG 59.339 52.381 0.00 0.00 0.00 4.79
3370 5763 2.367567 TCTTTAACTCTGGCTCGTTGGT 59.632 45.455 0.00 0.00 0.00 3.67
3371 5764 3.040147 TCTTTAACTCTGGCTCGTTGG 57.960 47.619 0.00 0.00 0.00 3.77
3372 5765 3.997021 ACATCTTTAACTCTGGCTCGTTG 59.003 43.478 0.00 0.00 0.00 4.10
3381 5774 6.042093 TGACCAAGACAGACATCTTTAACTCT 59.958 38.462 0.00 0.00 36.78 3.24
3389 5782 2.355513 GCCATGACCAAGACAGACATCT 60.356 50.000 0.00 0.00 0.00 2.90
3397 5790 1.677217 GGAGACAGCCATGACCAAGAC 60.677 57.143 0.00 0.00 0.00 3.01
3409 5802 2.031163 ACGTGGCAAGGAGACAGC 59.969 61.111 5.22 0.00 34.37 4.40
3412 5805 1.374758 CCTCACGTGGCAAGGAGAC 60.375 63.158 17.00 0.00 31.44 3.36
3424 5817 2.757868 ACTGGATCTTCTCTTCCTCACG 59.242 50.000 0.00 0.00 32.95 4.35
3444 5837 2.354203 CCTCAAGGTCTCCAGCAGTAAC 60.354 54.545 0.00 0.00 0.00 2.50
3446 5839 1.561643 CCTCAAGGTCTCCAGCAGTA 58.438 55.000 0.00 0.00 0.00 2.74
3450 5843 0.747283 CATGCCTCAAGGTCTCCAGC 60.747 60.000 0.00 0.00 37.57 4.85
3533 5926 9.965824 ACAGAAAGACGAAAAACAATGAATATT 57.034 25.926 0.00 0.00 0.00 1.28
3535 5928 8.073768 GGACAGAAAGACGAAAAACAATGAATA 58.926 33.333 0.00 0.00 0.00 1.75
3536 5929 6.918022 GGACAGAAAGACGAAAAACAATGAAT 59.082 34.615 0.00 0.00 0.00 2.57
3537 5930 6.262601 GGACAGAAAGACGAAAAACAATGAA 58.737 36.000 0.00 0.00 0.00 2.57
3538 5931 5.220970 GGGACAGAAAGACGAAAAACAATGA 60.221 40.000 0.00 0.00 0.00 2.57
3539 5932 4.976116 GGGACAGAAAGACGAAAAACAATG 59.024 41.667 0.00 0.00 0.00 2.82
3543 5936 6.555812 AATAGGGACAGAAAGACGAAAAAC 57.444 37.500 0.00 0.00 0.00 2.43
3549 5942 4.392138 GGAACAAATAGGGACAGAAAGACG 59.608 45.833 0.00 0.00 0.00 4.18
3551 5944 5.843019 AGGAACAAATAGGGACAGAAAGA 57.157 39.130 0.00 0.00 0.00 2.52
3623 6017 7.996644 AGACTTAGTTTTTAAATGTGTGAGGGA 59.003 33.333 0.00 0.00 0.00 4.20
3733 6460 7.394641 AGAAGCAATAGCCCCTTTATTATTAGC 59.605 37.037 0.00 0.00 43.56 3.09
3734 6461 8.870075 AGAAGCAATAGCCCCTTTATTATTAG 57.130 34.615 0.00 0.00 43.56 1.73
3744 6471 0.749454 CGCAAGAAGCAATAGCCCCT 60.749 55.000 0.00 0.00 46.13 4.79
3745 6472 1.728490 CCGCAAGAAGCAATAGCCCC 61.728 60.000 0.00 0.00 46.13 5.80
3746 6473 1.032114 ACCGCAAGAAGCAATAGCCC 61.032 55.000 0.00 0.00 46.13 5.19
3747 6474 0.099436 CACCGCAAGAAGCAATAGCC 59.901 55.000 0.00 0.00 46.13 3.93
3748 6475 0.524180 GCACCGCAAGAAGCAATAGC 60.524 55.000 0.00 0.00 46.13 2.97
3749 6476 0.247814 CGCACCGCAAGAAGCAATAG 60.248 55.000 0.00 0.00 46.13 1.73
3750 6477 0.953471 ACGCACCGCAAGAAGCAATA 60.953 50.000 0.00 0.00 46.13 1.90
3751 6478 2.187599 GACGCACCGCAAGAAGCAAT 62.188 55.000 0.00 0.00 46.13 3.56
3752 6479 2.892334 GACGCACCGCAAGAAGCAA 61.892 57.895 0.00 0.00 46.13 3.91
3753 6480 3.345808 GACGCACCGCAAGAAGCA 61.346 61.111 0.00 0.00 46.13 3.91
3754 6481 1.358725 TATGACGCACCGCAAGAAGC 61.359 55.000 0.00 0.00 43.02 3.86
3755 6482 0.647410 CTATGACGCACCGCAAGAAG 59.353 55.000 0.00 0.00 43.02 2.85
3756 6483 0.245266 TCTATGACGCACCGCAAGAA 59.755 50.000 0.00 0.00 43.02 2.52
3757 6484 0.245266 TTCTATGACGCACCGCAAGA 59.755 50.000 0.00 0.00 43.02 3.02
3758 6485 1.075542 TTTCTATGACGCACCGCAAG 58.924 50.000 0.00 0.00 0.00 4.01
3759 6486 1.732941 ATTTCTATGACGCACCGCAA 58.267 45.000 0.00 0.00 0.00 4.85
3760 6487 1.396648 CAATTTCTATGACGCACCGCA 59.603 47.619 0.00 0.00 0.00 5.69
3761 6488 1.856014 GCAATTTCTATGACGCACCGC 60.856 52.381 0.00 0.00 0.00 5.68
3762 6489 1.268032 GGCAATTTCTATGACGCACCG 60.268 52.381 0.00 0.00 0.00 4.94
3763 6490 1.065551 GGGCAATTTCTATGACGCACC 59.934 52.381 0.00 0.00 0.00 5.01
3764 6491 1.065551 GGGGCAATTTCTATGACGCAC 59.934 52.381 0.00 0.00 38.54 5.34
3765 6492 1.388547 GGGGCAATTTCTATGACGCA 58.611 50.000 0.00 0.00 38.54 5.24


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

AutoCloner maintained by Alex Coulton.