Multiple sequence alignment - TraesCS2B01G612300

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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 TraesCS2B01G612300 chr2B 100.000 4751 0 0 1 4751 791482387 791477637 0.000000e+00 8774.0
1 TraesCS2B01G612300 chr2B 82.270 141 20 2 4570 4705 794048316 794048456 3.000000e-22 117.0
2 TraesCS2B01G612300 chr2A 92.818 3091 134 26 837 3885 769494516 769497560 0.000000e+00 4397.0
3 TraesCS2B01G612300 chr2A 86.454 657 63 20 69 716 452785985 452786624 0.000000e+00 697.0
4 TraesCS2B01G612300 chr2A 81.457 755 84 28 1 716 47226023 47226760 6.900000e-158 568.0
5 TraesCS2B01G612300 chr2A 90.551 254 20 2 4011 4264 769497896 769498145 2.740000e-87 333.0
6 TraesCS2B01G612300 chr2A 83.333 282 23 12 4491 4751 769498234 769498512 6.140000e-59 239.0
7 TraesCS2B01G612300 chr2A 93.151 146 7 3 3873 4017 769497712 769497855 1.340000e-50 211.0
8 TraesCS2B01G612300 chr2D 93.183 1511 81 7 2334 3833 644331281 644332780 0.000000e+00 2200.0
9 TraesCS2B01G612300 chr2D 93.048 1309 41 13 837 2124 644329844 644331123 0.000000e+00 1868.0
10 TraesCS2B01G612300 chr2D 90.398 427 25 2 4337 4751 644362340 644362762 8.990000e-152 547.0
11 TraesCS2B01G612300 chr2D 90.000 120 10 2 4011 4129 644360452 644360570 2.290000e-33 154.0
12 TraesCS2B01G612300 chr2D 93.333 105 3 3 3873 3977 644333006 644333106 8.230000e-33 152.0
13 TraesCS2B01G612300 chr2D 81.250 176 24 3 4539 4705 635949273 635949448 2.980000e-27 134.0
14 TraesCS2B01G612300 chr2D 98.571 70 1 0 4260 4329 644361672 644361741 1.800000e-24 124.0
15 TraesCS2B01G612300 chr2D 92.727 55 3 1 4127 4180 644361415 644361469 1.420000e-10 78.7
16 TraesCS2B01G612300 chr7B 86.878 724 75 13 2 716 432495038 432494326 0.000000e+00 793.0
17 TraesCS2B01G612300 chr7B 85.773 724 82 13 1 716 449033819 449033109 0.000000e+00 747.0
18 TraesCS2B01G612300 chr7B 97.273 110 1 2 2132 2241 104069144 104069037 8.120000e-43 185.0
19 TraesCS2B01G612300 chr5D 86.842 722 78 10 1 716 204511783 204511073 0.000000e+00 791.0
20 TraesCS2B01G612300 chr5D 86.546 721 74 13 1 716 19508757 19508055 0.000000e+00 773.0
21 TraesCS2B01G612300 chr5D 85.042 722 89 14 1 716 39698233 39698941 0.000000e+00 717.0
22 TraesCS2B01G612300 chr5D 84.392 724 94 10 1 717 535807787 535807076 0.000000e+00 693.0
23 TraesCS2B01G612300 chr5A 86.149 657 70 16 69 716 602793279 602792635 0.000000e+00 689.0
24 TraesCS2B01G612300 chr4A 86.128 656 65 16 69 716 194759003 194759640 0.000000e+00 684.0
25 TraesCS2B01G612300 chr4A 82.143 336 37 13 465 798 351534428 351534114 2.820000e-67 267.0
26 TraesCS2B01G612300 chr4A 80.838 334 39 14 465 796 206660542 206660232 6.140000e-59 239.0
27 TraesCS2B01G612300 chr7D 84.509 723 77 19 1 716 435509942 435509248 0.000000e+00 682.0
28 TraesCS2B01G612300 chr7D 81.944 720 100 16 2 716 49605879 49606573 2.460000e-162 582.0
29 TraesCS2B01G612300 chr3A 86.385 639 65 14 85 716 164400954 164401577 0.000000e+00 678.0
30 TraesCS2B01G612300 chr3A 84.427 655 79 13 69 716 204880795 204880157 1.450000e-174 623.0
31 TraesCS2B01G612300 chr3A 99.048 105 1 0 2132 2236 64025142 64025038 6.280000e-44 189.0
32 TraesCS2B01G612300 chr6A 86.094 640 69 13 84 716 347599265 347598639 0.000000e+00 671.0
33 TraesCS2B01G612300 chr6A 81.126 604 72 25 120 716 126430009 126430577 3.370000e-121 446.0
34 TraesCS2B01G612300 chr7A 85.849 636 70 16 94 722 725163952 725163330 0.000000e+00 658.0
35 TraesCS2B01G612300 chr7A 83.268 257 27 9 464 716 444906638 444906394 6.190000e-54 222.0
36 TraesCS2B01G612300 chr7A 97.297 111 1 2 2132 2241 639786601 639786710 2.260000e-43 187.0
37 TraesCS2B01G612300 chr1D 84.009 469 54 8 1068 1527 490035075 490034619 9.450000e-117 431.0
38 TraesCS2B01G612300 chr5B 98.165 109 2 0 2132 2240 75535664 75535772 1.750000e-44 191.0
39 TraesCS2B01G612300 chr6B 98.148 108 2 0 2128 2235 548130725 548130618 6.280000e-44 189.0
40 TraesCS2B01G612300 chr6B 98.131 107 1 1 2132 2238 48563291 48563186 8.120000e-43 185.0
41 TraesCS2B01G612300 chr4D 98.131 107 2 0 2132 2238 355283626 355283732 2.260000e-43 187.0
42 TraesCS2B01G612300 chr1B 96.396 111 4 0 2132 2242 409679411 409679301 2.920000e-42 183.0
43 TraesCS2B01G612300 chr1B 77.184 206 23 10 1 203 12596560 12596744 1.090000e-16 99.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2B01G612300 chr2B 791477637 791482387 4750 True 8774.000000 8774 100.00000 1 4751 1 chr2B.!!$R1 4750
1 TraesCS2B01G612300 chr2A 769494516 769498512 3996 False 1295.000000 4397 89.96325 837 4751 4 chr2A.!!$F3 3914
2 TraesCS2B01G612300 chr2A 452785985 452786624 639 False 697.000000 697 86.45400 69 716 1 chr2A.!!$F2 647
3 TraesCS2B01G612300 chr2A 47226023 47226760 737 False 568.000000 568 81.45700 1 716 1 chr2A.!!$F1 715
4 TraesCS2B01G612300 chr2D 644329844 644333106 3262 False 1406.666667 2200 93.18800 837 3977 3 chr2D.!!$F2 3140
5 TraesCS2B01G612300 chr2D 644360452 644362762 2310 False 225.925000 547 92.92400 4011 4751 4 chr2D.!!$F3 740
6 TraesCS2B01G612300 chr7B 432494326 432495038 712 True 793.000000 793 86.87800 2 716 1 chr7B.!!$R2 714
7 TraesCS2B01G612300 chr7B 449033109 449033819 710 True 747.000000 747 85.77300 1 716 1 chr7B.!!$R3 715
8 TraesCS2B01G612300 chr5D 204511073 204511783 710 True 791.000000 791 86.84200 1 716 1 chr5D.!!$R2 715
9 TraesCS2B01G612300 chr5D 19508055 19508757 702 True 773.000000 773 86.54600 1 716 1 chr5D.!!$R1 715
10 TraesCS2B01G612300 chr5D 39698233 39698941 708 False 717.000000 717 85.04200 1 716 1 chr5D.!!$F1 715
11 TraesCS2B01G612300 chr5D 535807076 535807787 711 True 693.000000 693 84.39200 1 717 1 chr5D.!!$R3 716
12 TraesCS2B01G612300 chr5A 602792635 602793279 644 True 689.000000 689 86.14900 69 716 1 chr5A.!!$R1 647
13 TraesCS2B01G612300 chr4A 194759003 194759640 637 False 684.000000 684 86.12800 69 716 1 chr4A.!!$F1 647
14 TraesCS2B01G612300 chr7D 435509248 435509942 694 True 682.000000 682 84.50900 1 716 1 chr7D.!!$R1 715
15 TraesCS2B01G612300 chr7D 49605879 49606573 694 False 582.000000 582 81.94400 2 716 1 chr7D.!!$F1 714
16 TraesCS2B01G612300 chr3A 164400954 164401577 623 False 678.000000 678 86.38500 85 716 1 chr3A.!!$F1 631
17 TraesCS2B01G612300 chr3A 204880157 204880795 638 True 623.000000 623 84.42700 69 716 1 chr3A.!!$R2 647
18 TraesCS2B01G612300 chr6A 347598639 347599265 626 True 671.000000 671 86.09400 84 716 1 chr6A.!!$R1 632
19 TraesCS2B01G612300 chr6A 126430009 126430577 568 False 446.000000 446 81.12600 120 716 1 chr6A.!!$F1 596
20 TraesCS2B01G612300 chr7A 725163330 725163952 622 True 658.000000 658 85.84900 94 722 1 chr7A.!!$R2 628

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
859 920 0.028505 ACCGTCATCGTTCGTATCGG 59.971 55.0 0.00 0.00 41.77 4.18 F
1950 2032 0.609957 TGCTCAAATGGTCAGGCCTG 60.610 55.0 27.87 27.87 38.35 4.85 F
2234 2316 0.108585 GCACTGGGTCTGTCCTTTCA 59.891 55.0 0.00 0.00 36.25 2.69 F
3286 3429 0.942962 GAGGATGCTTTGCTGGATCG 59.057 55.0 0.00 0.00 35.94 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2130 2212 0.037877 AGTGCAATGCAGAGAGGCTT 59.962 50.0 8.73 0.00 40.08 4.35 R
3140 3283 0.247736 GCTCTGGAATGTCGGACACT 59.752 55.0 13.92 1.22 0.00 3.55 R
3432 3586 0.724549 GCATTGTGCATTGCCACATG 59.275 50.0 6.12 6.45 44.44 3.21 R
4576 6555 0.241749 CACCACAAGCATCGCAATGT 59.758 50.0 0.00 0.00 35.18 2.71 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
46 48 5.993748 AGTCCTTTTTGTTTGGTTTGAGA 57.006 34.783 0.00 0.00 0.00 3.27
51 58 4.527509 TTTTGTTTGGTTTGAGAGCACA 57.472 36.364 0.00 0.00 35.04 4.57
88 96 0.970640 TGGCTCGTACACAGGCTAAA 59.029 50.000 14.38 0.00 37.34 1.85
96 104 3.672511 CGTACACAGGCTAAACGATCTGT 60.673 47.826 0.00 0.00 40.62 3.41
116 124 0.794473 GCCAGGTACTTGTACGTTGC 59.206 55.000 11.78 11.78 34.60 4.17
145 153 6.294397 GCCTTTTATGGGCTTTCATAGAGATG 60.294 42.308 0.00 0.00 45.57 2.90
171 182 8.334632 GGCAAATAATTGGGTCAAAATAAATCG 58.665 33.333 0.00 0.00 37.02 3.34
204 215 2.408271 TTGATCACATGACCTCCTGC 57.592 50.000 0.00 0.00 0.00 4.85
216 227 1.045350 CCTCCTGCCTGGATCTTCGA 61.045 60.000 0.00 0.00 45.16 3.71
289 301 3.675698 GCTCTAAATATACGAGTGGCAGC 59.324 47.826 0.00 0.00 0.00 5.25
290 302 4.559704 GCTCTAAATATACGAGTGGCAGCT 60.560 45.833 0.00 0.00 0.00 4.24
301 313 0.790814 GTGGCAGCTCTCGTGTTTAC 59.209 55.000 0.00 0.00 0.00 2.01
485 505 6.140968 AGGCTAATTAAAGGAAGGACTTGT 57.859 37.500 0.00 0.00 0.00 3.16
527 575 4.571366 AAAAGGAGGGGTCTATAGGCTA 57.429 45.455 3.98 0.00 0.00 3.93
528 576 4.571366 AAAGGAGGGGTCTATAGGCTAA 57.429 45.455 3.98 0.00 0.00 3.09
562 613 9.582648 TGGGCTACTAAATTAGAAAAAGAAAGT 57.417 29.630 7.06 0.00 0.00 2.66
605 657 5.510179 CGGGTGAGGACGTTATGGTAATTAT 60.510 44.000 0.00 0.00 0.00 1.28
608 660 7.256083 GGGTGAGGACGTTATGGTAATTATAGT 60.256 40.741 0.00 0.00 0.00 2.12
726 787 8.664798 TGTTCATTTTGTAGAATAGTGAATCGG 58.335 33.333 0.00 0.00 0.00 4.18
727 788 8.879759 GTTCATTTTGTAGAATAGTGAATCGGA 58.120 33.333 0.00 0.00 0.00 4.55
728 789 9.613428 TTCATTTTGTAGAATAGTGAATCGGAT 57.387 29.630 0.00 0.00 0.00 4.18
729 790 9.045223 TCATTTTGTAGAATAGTGAATCGGATG 57.955 33.333 0.00 0.00 0.00 3.51
730 791 8.830580 CATTTTGTAGAATAGTGAATCGGATGT 58.169 33.333 0.00 0.00 0.00 3.06
731 792 8.786826 TTTTGTAGAATAGTGAATCGGATGTT 57.213 30.769 0.00 0.00 0.00 2.71
732 793 7.770801 TTGTAGAATAGTGAATCGGATGTTG 57.229 36.000 0.00 0.00 0.00 3.33
733 794 6.873997 TGTAGAATAGTGAATCGGATGTTGT 58.126 36.000 0.00 0.00 0.00 3.32
734 795 6.756542 TGTAGAATAGTGAATCGGATGTTGTG 59.243 38.462 0.00 0.00 0.00 3.33
735 796 5.977635 AGAATAGTGAATCGGATGTTGTGA 58.022 37.500 0.00 0.00 0.00 3.58
736 797 6.406370 AGAATAGTGAATCGGATGTTGTGAA 58.594 36.000 0.00 0.00 0.00 3.18
737 798 6.878923 AGAATAGTGAATCGGATGTTGTGAAA 59.121 34.615 0.00 0.00 0.00 2.69
738 799 4.749245 AGTGAATCGGATGTTGTGAAAC 57.251 40.909 0.00 0.00 37.35 2.78
756 817 8.346476 TGTGAAACATTATGCTTGTACAAAAC 57.654 30.769 10.03 5.59 45.67 2.43
757 818 7.976175 TGTGAAACATTATGCTTGTACAAAACA 59.024 29.630 10.03 11.20 45.67 2.83
758 819 8.977505 GTGAAACATTATGCTTGTACAAAACAT 58.022 29.630 21.15 21.15 35.45 2.71
759 820 9.539825 TGAAACATTATGCTTGTACAAAACATT 57.460 25.926 22.09 9.48 38.10 2.71
786 847 3.007516 CGTTGAAACGCACGGTCA 58.992 55.556 2.23 0.00 46.06 4.02
787 848 1.567537 CGTTGAAACGCACGGTCAT 59.432 52.632 2.23 0.00 46.06 3.06
788 849 0.785378 CGTTGAAACGCACGGTCATA 59.215 50.000 2.23 0.00 46.06 2.15
789 850 1.392168 CGTTGAAACGCACGGTCATAT 59.608 47.619 2.23 0.00 46.06 1.78
790 851 2.769376 GTTGAAACGCACGGTCATATG 58.231 47.619 0.00 0.00 0.00 1.78
791 852 2.087501 TGAAACGCACGGTCATATGT 57.912 45.000 1.90 0.00 0.00 2.29
792 853 1.729517 TGAAACGCACGGTCATATGTG 59.270 47.619 1.90 0.00 39.10 3.21
800 861 2.807967 CACGGTCATATGTGCTAATGGG 59.192 50.000 1.90 0.00 0.00 4.00
801 862 2.438021 ACGGTCATATGTGCTAATGGGT 59.562 45.455 1.90 0.00 0.00 4.51
802 863 3.118038 ACGGTCATATGTGCTAATGGGTT 60.118 43.478 1.90 0.00 0.00 4.11
803 864 3.882888 CGGTCATATGTGCTAATGGGTTT 59.117 43.478 1.90 0.00 0.00 3.27
804 865 5.060506 CGGTCATATGTGCTAATGGGTTTA 58.939 41.667 1.90 0.00 0.00 2.01
805 866 5.529430 CGGTCATATGTGCTAATGGGTTTAA 59.471 40.000 1.90 0.00 0.00 1.52
806 867 6.038825 CGGTCATATGTGCTAATGGGTTTAAA 59.961 38.462 1.90 0.00 0.00 1.52
807 868 7.200455 GGTCATATGTGCTAATGGGTTTAAAC 58.800 38.462 9.98 9.98 0.00 2.01
808 869 6.910433 GTCATATGTGCTAATGGGTTTAAACG 59.090 38.462 12.07 0.00 0.00 3.60
809 870 4.712122 ATGTGCTAATGGGTTTAAACGG 57.288 40.909 12.07 0.29 0.00 4.44
810 871 2.820787 TGTGCTAATGGGTTTAAACGGG 59.179 45.455 12.07 0.60 0.00 5.28
811 872 2.821378 GTGCTAATGGGTTTAAACGGGT 59.179 45.455 12.07 0.72 0.00 5.28
812 873 3.256383 GTGCTAATGGGTTTAAACGGGTT 59.744 43.478 12.07 8.62 0.00 4.11
813 874 3.896272 TGCTAATGGGTTTAAACGGGTTT 59.104 39.130 12.07 2.05 36.63 3.27
814 875 5.048154 GTGCTAATGGGTTTAAACGGGTTTA 60.048 40.000 12.07 0.05 34.23 2.01
815 876 5.715753 TGCTAATGGGTTTAAACGGGTTTAT 59.284 36.000 12.07 0.00 35.27 1.40
816 877 6.888632 TGCTAATGGGTTTAAACGGGTTTATA 59.111 34.615 12.07 0.00 35.27 0.98
817 878 7.067251 TGCTAATGGGTTTAAACGGGTTTATAG 59.933 37.037 12.07 8.76 35.27 1.31
818 879 6.778834 AATGGGTTTAAACGGGTTTATAGG 57.221 37.500 12.07 0.00 35.27 2.57
819 880 4.598022 TGGGTTTAAACGGGTTTATAGGG 58.402 43.478 12.07 0.00 35.27 3.53
820 881 3.953612 GGGTTTAAACGGGTTTATAGGGG 59.046 47.826 12.07 0.00 35.27 4.79
821 882 3.381272 GGTTTAAACGGGTTTATAGGGGC 59.619 47.826 12.07 0.00 35.27 5.80
822 883 3.295585 TTAAACGGGTTTATAGGGGCC 57.704 47.619 0.00 0.00 35.27 5.80
823 884 0.107066 AAACGGGTTTATAGGGGCCG 60.107 55.000 0.00 0.00 0.00 6.13
824 885 1.273986 AACGGGTTTATAGGGGCCGT 61.274 55.000 3.37 3.37 0.00 5.68
825 886 1.070275 CGGGTTTATAGGGGCCGTC 59.930 63.158 0.00 0.00 0.00 4.79
826 887 1.688269 CGGGTTTATAGGGGCCGTCA 61.688 60.000 0.00 0.00 0.00 4.35
827 888 0.769247 GGGTTTATAGGGGCCGTCAT 59.231 55.000 0.00 0.00 0.00 3.06
828 889 1.271217 GGGTTTATAGGGGCCGTCATC 60.271 57.143 0.00 0.00 0.00 2.92
829 890 1.418637 GGTTTATAGGGGCCGTCATCA 59.581 52.381 0.00 0.00 0.00 3.07
830 891 2.490991 GTTTATAGGGGCCGTCATCAC 58.509 52.381 0.00 0.00 0.00 3.06
831 892 2.097110 TTATAGGGGCCGTCATCACT 57.903 50.000 0.00 0.00 0.00 3.41
832 893 2.984435 TATAGGGGCCGTCATCACTA 57.016 50.000 0.00 0.00 0.00 2.74
833 894 1.339097 ATAGGGGCCGTCATCACTAC 58.661 55.000 0.00 0.00 0.00 2.73
834 895 0.260816 TAGGGGCCGTCATCACTACT 59.739 55.000 0.00 0.00 0.00 2.57
835 896 1.144057 GGGGCCGTCATCACTACTG 59.856 63.158 0.00 0.00 0.00 2.74
840 901 2.947652 GGCCGTCATCACTACTGTACTA 59.052 50.000 0.00 0.00 0.00 1.82
849 910 3.867493 TCACTACTGTACTACCGTCATCG 59.133 47.826 0.00 0.00 0.00 3.84
850 911 3.620374 CACTACTGTACTACCGTCATCGT 59.380 47.826 0.00 0.00 35.01 3.73
859 920 0.028505 ACCGTCATCGTTCGTATCGG 59.971 55.000 0.00 0.00 41.77 4.18
861 922 0.659417 CGTCATCGTTCGTATCGGGG 60.659 60.000 0.00 0.00 0.00 5.73
979 1040 3.166434 TGGATCACCACCACCACC 58.834 61.111 0.00 0.00 41.77 4.61
980 1041 1.772156 TGGATCACCACCACCACCA 60.772 57.895 0.00 0.00 41.77 4.17
981 1042 1.303317 GGATCACCACCACCACCAC 60.303 63.158 0.00 0.00 35.97 4.16
1555 1616 9.427821 ACTACTCCATTAGTGATTATCTGTTCT 57.572 33.333 0.00 0.00 39.39 3.01
1556 1617 9.689976 CTACTCCATTAGTGATTATCTGTTCTG 57.310 37.037 0.00 0.00 39.39 3.02
1557 1618 8.083828 ACTCCATTAGTGATTATCTGTTCTGT 57.916 34.615 0.00 0.00 36.93 3.41
1620 1681 3.221771 TCTGTTCTGGGAATTTGTGGTG 58.778 45.455 0.00 0.00 0.00 4.17
1648 1709 7.773690 AGGTTCAGTTAAACTTGATTACTGTGT 59.226 33.333 0.00 0.00 27.28 3.72
1747 1829 8.476447 GTCCTTTACCTTATAAGTTAGCTCTGT 58.524 37.037 11.50 2.47 0.00 3.41
1772 1854 9.452065 GTTTTTCATTTTACCTCTTTCTCAGTC 57.548 33.333 0.00 0.00 0.00 3.51
1774 1856 6.340962 TCATTTTACCTCTTTCTCAGTCGA 57.659 37.500 0.00 0.00 0.00 4.20
1787 1869 3.763897 TCTCAGTCGAGATGAAATGGTGA 59.236 43.478 2.20 0.00 43.55 4.02
1797 1879 4.398358 AGATGAAATGGTGAGCATGTTCTG 59.602 41.667 11.09 0.00 0.00 3.02
1801 1883 4.558226 AATGGTGAGCATGTTCTGTAGA 57.442 40.909 11.09 0.00 0.00 2.59
1842 1924 6.907212 GGTGAAGTGCATTGAATTAATACTCG 59.093 38.462 0.00 0.00 0.00 4.18
1950 2032 0.609957 TGCTCAAATGGTCAGGCCTG 60.610 55.000 27.87 27.87 38.35 4.85
2194 2276 2.615191 TAATCCCTCCCCAGACCCCG 62.615 65.000 0.00 0.00 0.00 5.73
2234 2316 0.108585 GCACTGGGTCTGTCCTTTCA 59.891 55.000 0.00 0.00 36.25 2.69
2238 2320 2.443255 ACTGGGTCTGTCCTTTCAATGT 59.557 45.455 0.00 0.00 36.25 2.71
2246 2328 6.349363 GGTCTGTCCTTTCAATGTTCCAATAC 60.349 42.308 0.00 0.00 0.00 1.89
2253 2335 6.348950 CCTTTCAATGTTCCAATACTTGCGTA 60.349 38.462 0.00 0.00 0.00 4.42
2282 2364 9.130661 CTGGAATATATGTTAACCCACATTTCA 57.869 33.333 2.48 2.69 38.40 2.69
2418 2560 9.784531 CACTTTCATCCTGTATATCTATTTGGT 57.215 33.333 0.00 0.00 0.00 3.67
2765 2908 2.633509 GCTGCTGGGTTGCTCAAGG 61.634 63.158 0.00 0.00 0.00 3.61
2911 3054 4.123497 CCTCGATGAGGTGAACATTACA 57.877 45.455 4.65 0.00 44.25 2.41
3063 3206 6.292919 GCACTAAACTTGTCTAGTCTTGGTTG 60.293 42.308 0.00 0.00 35.54 3.77
3069 3212 5.365895 ACTTGTCTAGTCTTGGTTGGTTACT 59.634 40.000 0.00 0.00 28.23 2.24
3085 3228 6.165700 TGGTTACTACGAGAAAGAAAACCT 57.834 37.500 0.00 0.00 35.94 3.50
3092 3235 5.548181 ACGAGAAAGAAAACCTCTTACCT 57.452 39.130 0.00 0.00 44.00 3.08
3113 3256 6.913170 ACCTTGTGCTATCTGTTATGTTTTG 58.087 36.000 0.00 0.00 0.00 2.44
3140 3283 4.978099 AGAAATTCTTTGGTCTGAGCTCA 58.022 39.130 17.19 17.19 0.00 4.26
3279 3422 2.576298 AAGCTGGAGGATGCTTTGC 58.424 52.632 0.00 0.00 45.91 3.68
3286 3429 0.942962 GAGGATGCTTTGCTGGATCG 59.057 55.000 0.00 0.00 35.94 3.69
3290 3433 1.534595 GATGCTTTGCTGGATCGGATC 59.465 52.381 9.54 9.54 0.00 3.36
3325 3468 9.259832 AGAGCTTGGATATAAACAAATTTTCCT 57.740 29.630 4.83 0.00 0.00 3.36
3327 3470 9.657419 AGCTTGGATATAAACAAATTTTCCTTG 57.343 29.630 4.83 0.00 0.00 3.61
3387 3530 5.831525 TGCCAGCATGATATCTTCTTCATTT 59.168 36.000 3.98 0.00 39.69 2.32
3451 3605 0.724549 CATGTGGCAATGCACAATGC 59.275 50.000 7.79 11.44 45.29 3.56
3466 3620 4.653893 TGCACAACAGCACAAGGA 57.346 50.000 0.00 0.00 40.11 3.36
3495 3649 4.301027 CGGATAGACTGGCCCGCC 62.301 72.222 0.00 0.00 35.29 6.13
3573 3727 3.005155 ACCTGTACTACGTGAACACCTTC 59.995 47.826 0.00 0.00 0.00 3.46
3634 3788 4.421479 AGAACGTGGCGAGGCTCG 62.421 66.667 31.40 31.40 43.89 5.03
3712 3866 3.243101 TGAGCCTCATATCGAGTCGTTTC 60.243 47.826 13.12 0.00 40.48 2.78
3715 3869 2.361119 CCTCATATCGAGTCGTTTCCCA 59.639 50.000 13.12 0.00 40.48 4.37
3728 3882 1.700186 GTTTCCCAGTGAGGAGGAAGT 59.300 52.381 0.00 0.00 40.63 3.01
3768 3922 3.076621 GTGAGTGAATGTGGAAGATGCA 58.923 45.455 0.00 0.00 0.00 3.96
3833 3987 3.068024 GCCAGTTGTTTCCTCATGTTTCA 59.932 43.478 0.00 0.00 0.00 2.69
3834 3988 4.794003 GCCAGTTGTTTCCTCATGTTTCAG 60.794 45.833 0.00 0.00 0.00 3.02
3836 3990 5.530915 CCAGTTGTTTCCTCATGTTTCAGTA 59.469 40.000 0.00 0.00 0.00 2.74
3837 3991 6.039270 CCAGTTGTTTCCTCATGTTTCAGTAA 59.961 38.462 0.00 0.00 0.00 2.24
3838 3992 6.912591 CAGTTGTTTCCTCATGTTTCAGTAAC 59.087 38.462 0.00 0.00 37.26 2.50
3854 4026 5.237815 TCAGTAACACTAGACAGCAATTGG 58.762 41.667 7.72 0.00 0.00 3.16
3855 4027 4.393062 CAGTAACACTAGACAGCAATTGGG 59.607 45.833 7.72 0.00 0.00 4.12
3862 4034 1.425066 AGACAGCAATTGGGTTCTGGA 59.575 47.619 7.72 0.00 0.00 3.86
3895 4249 5.339008 TGCTACTGTGTATTAGACCCAAG 57.661 43.478 0.00 0.00 0.00 3.61
3921 4275 7.339466 GGAATGTATACAGAAATGAAAGTGGGT 59.661 37.037 11.91 0.00 0.00 4.51
3924 4278 5.964958 ATACAGAAATGAAAGTGGGTGTG 57.035 39.130 0.00 0.00 0.00 3.82
3927 4281 4.097892 ACAGAAATGAAAGTGGGTGTGTTC 59.902 41.667 0.00 0.00 0.00 3.18
3932 4287 5.675684 ATGAAAGTGGGTGTGTTCTTTTT 57.324 34.783 0.00 0.00 31.56 1.94
3988 4343 6.298853 GGCGTGAATGATTTTGTTTCAAATC 58.701 36.000 0.11 0.11 36.29 2.17
4020 4420 5.581085 ACTGTATATTTTTGTCTGCTCGGTC 59.419 40.000 0.00 0.00 0.00 4.79
4072 4472 0.384309 TGCCGCGGATGACTAGTTAG 59.616 55.000 33.48 0.00 0.00 2.34
4110 4510 5.703730 AATGGGGAATGCTTTGATTGATT 57.296 34.783 0.00 0.00 0.00 2.57
4168 5417 1.740380 CGGCGACATGGTCTTCTTCAT 60.740 52.381 0.00 0.00 0.00 2.57
4214 5481 1.554617 AGCTCTGCTTTTCCTCTCCTC 59.445 52.381 0.00 0.00 33.89 3.71
4215 5482 1.406751 GCTCTGCTTTTCCTCTCCTCC 60.407 57.143 0.00 0.00 0.00 4.30
4216 5483 1.209261 CTCTGCTTTTCCTCTCCTCCC 59.791 57.143 0.00 0.00 0.00 4.30
4217 5484 0.254462 CTGCTTTTCCTCTCCTCCCC 59.746 60.000 0.00 0.00 0.00 4.81
4246 5513 7.972277 CCATTCATCTTTTACTTCACAATCTGG 59.028 37.037 0.00 0.00 0.00 3.86
4249 5516 6.430925 TCATCTTTTACTTCACAATCTGGTGG 59.569 38.462 0.00 0.00 39.27 4.61
4279 5657 4.217767 TCACTGTTGTACTGCTAGGTACTG 59.782 45.833 9.73 1.89 41.52 2.74
4329 5707 3.818773 TCCTGCTGATTGATGCATACATG 59.181 43.478 0.00 0.00 38.59 3.21
4387 6356 0.751643 CCTATTTTGTGGCGGAGGGG 60.752 60.000 0.00 0.00 0.00 4.79
4405 6374 5.014228 GGAGGGGGTATTATAACTGATTGCT 59.986 44.000 0.00 0.00 0.00 3.91
4406 6375 6.128138 AGGGGGTATTATAACTGATTGCTC 57.872 41.667 0.00 0.00 0.00 4.26
4441 6410 6.927294 ATCTTAGATCGAATGTTTCAACCC 57.073 37.500 0.00 0.00 0.00 4.11
4455 6424 4.524316 TTCAACCCTCGACGAAAATCTA 57.476 40.909 0.00 0.00 0.00 1.98
4459 6428 1.065102 CCCTCGACGAAAATCTAGCGA 59.935 52.381 0.00 0.00 0.00 4.93
4463 6432 2.161012 TCGACGAAAATCTAGCGACAGT 59.839 45.455 0.00 0.00 0.00 3.55
4464 6433 2.526688 CGACGAAAATCTAGCGACAGTC 59.473 50.000 0.00 0.00 0.00 3.51
4465 6434 2.516923 ACGAAAATCTAGCGACAGTCG 58.483 47.619 19.10 19.10 43.89 4.18
4466 6435 2.161012 ACGAAAATCTAGCGACAGTCGA 59.839 45.455 27.29 5.79 43.74 4.20
4472 6441 5.888691 AATCTAGCGACAGTCGATCATAT 57.111 39.130 27.29 11.55 43.74 1.78
4547 6523 2.223923 TGCATTCCCGTTGTTTTTCCTG 60.224 45.455 0.00 0.00 0.00 3.86
4566 6545 3.509967 CCTGGAAATTGGTTGGGAACTAC 59.490 47.826 0.00 0.00 35.18 2.73
4582 6561 5.353400 GGGAACTACCAGTACTAAACATTGC 59.647 44.000 0.00 0.00 41.20 3.56
4604 6583 2.282462 CTTGTGGTGACAGGGGGC 60.282 66.667 0.00 0.00 44.46 5.80
4642 6621 2.584835 TTGTTGGGACTTGGGAGATG 57.415 50.000 0.00 0.00 0.00 2.90
4663 6654 1.138568 ATGCTCTCCTCCCTCCAATG 58.861 55.000 0.00 0.00 0.00 2.82
4701 6692 0.678048 GATGACCACCAGAGTTGCCC 60.678 60.000 0.00 0.00 0.00 5.36
4737 6728 3.651803 GCTATCGAGCTATGGTGAACT 57.348 47.619 0.00 0.00 45.98 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 48 6.861055 CCAACATTACGAAATTTTAGTGTGCT 59.139 34.615 5.29 0.00 0.00 4.40
51 58 6.072893 ACGAGCCAACATTACGAAATTTTAGT 60.073 34.615 0.00 0.59 0.00 2.24
96 104 1.874739 GCAACGTACAAGTACCTGGCA 60.875 52.381 4.89 0.00 32.61 4.92
145 153 8.334632 CGATTTATTTTGACCCAATTATTTGCC 58.665 33.333 0.00 0.00 0.00 4.52
171 182 9.241317 GTCATGTGATCAATTCCAATAATGTTC 57.759 33.333 0.00 0.00 0.00 3.18
178 189 4.891756 GGAGGTCATGTGATCAATTCCAAT 59.108 41.667 0.00 0.00 0.00 3.16
204 215 4.332819 GGTTGTTACATTCGAAGATCCAGG 59.667 45.833 3.35 0.00 35.04 4.45
216 227 5.615984 CGCATAAGTCGTTGGTTGTTACATT 60.616 40.000 0.00 0.00 0.00 2.71
289 301 0.438830 GCTTGCCGTAAACACGAGAG 59.561 55.000 0.00 0.00 34.64 3.20
290 302 0.032952 AGCTTGCCGTAAACACGAGA 59.967 50.000 0.00 0.00 34.64 4.04
459 479 6.388619 AGTCCTTCCTTTAATTAGCCTCAA 57.611 37.500 0.00 0.00 0.00 3.02
513 561 5.306114 ACACATTTTAGCCTATAGACCCC 57.694 43.478 0.00 0.00 0.00 4.95
527 575 8.644374 TCTAATTTAGTAGCCCAACACATTTT 57.356 30.769 3.45 0.00 0.00 1.82
528 576 8.644374 TTCTAATTTAGTAGCCCAACACATTT 57.356 30.769 3.45 0.00 0.00 2.32
560 611 4.214758 CCGTTTTAGTCGGGAATCAAAACT 59.785 41.667 0.00 0.00 43.68 2.66
562 613 4.752661 CCGTTTTAGTCGGGAATCAAAA 57.247 40.909 0.00 0.00 43.68 2.44
641 699 3.569194 TTGCCGGGCATAATCTTCTAA 57.431 42.857 24.49 0.00 38.76 2.10
718 779 4.481930 TGTTTCACAACATCCGATTCAC 57.518 40.909 0.00 0.00 38.03 3.18
729 790 7.922505 TTGTACAAGCATAATGTTTCACAAC 57.077 32.000 3.59 0.00 32.27 3.32
730 791 8.812329 GTTTTGTACAAGCATAATGTTTCACAA 58.188 29.630 8.56 0.00 32.27 3.33
731 792 7.976175 TGTTTTGTACAAGCATAATGTTTCACA 59.024 29.630 8.56 0.00 32.64 3.58
732 793 8.346476 TGTTTTGTACAAGCATAATGTTTCAC 57.654 30.769 8.56 0.00 32.64 3.18
733 794 9.539825 AATGTTTTGTACAAGCATAATGTTTCA 57.460 25.926 20.60 4.97 40.89 2.69
770 831 2.158841 ACATATGACCGTGCGTTTCAAC 59.841 45.455 10.38 0.00 0.00 3.18
771 832 2.158645 CACATATGACCGTGCGTTTCAA 59.841 45.455 10.38 0.00 0.00 2.69
772 833 1.729517 CACATATGACCGTGCGTTTCA 59.270 47.619 10.38 0.00 0.00 2.69
773 834 2.435685 CACATATGACCGTGCGTTTC 57.564 50.000 10.38 0.00 0.00 2.78
779 840 2.807967 CCCATTAGCACATATGACCGTG 59.192 50.000 10.38 0.00 36.18 4.94
780 841 2.438021 ACCCATTAGCACATATGACCGT 59.562 45.455 10.38 0.00 0.00 4.83
781 842 3.126001 ACCCATTAGCACATATGACCG 57.874 47.619 10.38 0.00 0.00 4.79
782 843 6.952773 TTAAACCCATTAGCACATATGACC 57.047 37.500 10.38 0.00 0.00 4.02
783 844 6.910433 CGTTTAAACCCATTAGCACATATGAC 59.090 38.462 10.38 0.79 0.00 3.06
784 845 6.038825 CCGTTTAAACCCATTAGCACATATGA 59.961 38.462 10.38 0.00 0.00 2.15
785 846 6.205784 CCGTTTAAACCCATTAGCACATATG 58.794 40.000 12.66 0.00 0.00 1.78
786 847 5.300792 CCCGTTTAAACCCATTAGCACATAT 59.699 40.000 12.66 0.00 0.00 1.78
787 848 4.641094 CCCGTTTAAACCCATTAGCACATA 59.359 41.667 12.66 0.00 0.00 2.29
788 849 3.445805 CCCGTTTAAACCCATTAGCACAT 59.554 43.478 12.66 0.00 0.00 3.21
789 850 2.820787 CCCGTTTAAACCCATTAGCACA 59.179 45.455 12.66 0.00 0.00 4.57
790 851 2.821378 ACCCGTTTAAACCCATTAGCAC 59.179 45.455 12.66 0.00 0.00 4.40
791 852 3.157750 ACCCGTTTAAACCCATTAGCA 57.842 42.857 12.66 0.00 0.00 3.49
792 853 4.524316 AAACCCGTTTAAACCCATTAGC 57.476 40.909 12.66 0.00 0.00 3.09
793 854 7.013559 CCCTATAAACCCGTTTAAACCCATTAG 59.986 40.741 12.66 5.40 38.38 1.73
794 855 6.832900 CCCTATAAACCCGTTTAAACCCATTA 59.167 38.462 12.66 7.62 38.38 1.90
795 856 5.657745 CCCTATAAACCCGTTTAAACCCATT 59.342 40.000 12.66 5.82 38.38 3.16
796 857 5.202765 CCCTATAAACCCGTTTAAACCCAT 58.797 41.667 12.66 0.00 38.38 4.00
797 858 4.569440 CCCCTATAAACCCGTTTAAACCCA 60.569 45.833 12.66 0.00 38.38 4.51
798 859 3.953612 CCCCTATAAACCCGTTTAAACCC 59.046 47.826 12.66 0.00 38.38 4.11
799 860 3.381272 GCCCCTATAAACCCGTTTAAACC 59.619 47.826 12.66 0.00 38.38 3.27
800 861 3.381272 GGCCCCTATAAACCCGTTTAAAC 59.619 47.826 8.35 8.35 38.38 2.01
801 862 3.630168 GGCCCCTATAAACCCGTTTAAA 58.370 45.455 4.26 0.00 38.38 1.52
802 863 2.421248 CGGCCCCTATAAACCCGTTTAA 60.421 50.000 0.00 0.00 38.38 1.52
803 864 1.140652 CGGCCCCTATAAACCCGTTTA 59.859 52.381 0.00 2.68 39.12 2.01
804 865 0.107066 CGGCCCCTATAAACCCGTTT 60.107 55.000 0.00 0.00 34.56 3.60
805 866 1.528339 CGGCCCCTATAAACCCGTT 59.472 57.895 0.00 0.00 34.56 4.44
806 867 1.690283 ACGGCCCCTATAAACCCGT 60.690 57.895 0.00 0.00 46.37 5.28
807 868 1.070275 GACGGCCCCTATAAACCCG 59.930 63.158 0.00 0.00 44.19 5.28
808 869 0.769247 ATGACGGCCCCTATAAACCC 59.231 55.000 0.00 0.00 0.00 4.11
809 870 1.418637 TGATGACGGCCCCTATAAACC 59.581 52.381 0.00 0.00 0.00 3.27
810 871 2.104281 AGTGATGACGGCCCCTATAAAC 59.896 50.000 0.00 0.00 0.00 2.01
811 872 2.404559 AGTGATGACGGCCCCTATAAA 58.595 47.619 0.00 0.00 0.00 1.40
812 873 2.097110 AGTGATGACGGCCCCTATAA 57.903 50.000 0.00 0.00 0.00 0.98
813 874 2.109480 AGTAGTGATGACGGCCCCTATA 59.891 50.000 0.00 0.00 0.00 1.31
814 875 1.133136 AGTAGTGATGACGGCCCCTAT 60.133 52.381 0.00 0.00 0.00 2.57
815 876 0.260816 AGTAGTGATGACGGCCCCTA 59.739 55.000 0.00 0.00 0.00 3.53
816 877 1.001760 AGTAGTGATGACGGCCCCT 59.998 57.895 0.00 0.00 0.00 4.79
817 878 1.144057 CAGTAGTGATGACGGCCCC 59.856 63.158 0.00 0.00 0.00 5.80
818 879 1.108776 TACAGTAGTGATGACGGCCC 58.891 55.000 4.09 0.00 0.00 5.80
819 880 1.749634 AGTACAGTAGTGATGACGGCC 59.250 52.381 4.09 0.00 0.00 6.13
820 881 3.243002 GGTAGTACAGTAGTGATGACGGC 60.243 52.174 4.09 0.00 0.00 5.68
821 882 3.002042 CGGTAGTACAGTAGTGATGACGG 59.998 52.174 4.09 0.00 0.00 4.79
822 883 3.620374 ACGGTAGTACAGTAGTGATGACG 59.380 47.826 4.09 3.94 0.00 4.35
823 884 4.633126 TGACGGTAGTACAGTAGTGATGAC 59.367 45.833 6.04 0.00 0.00 3.06
824 885 4.835678 TGACGGTAGTACAGTAGTGATGA 58.164 43.478 6.04 0.00 0.00 2.92
825 886 5.558463 CGATGACGGTAGTACAGTAGTGATG 60.558 48.000 6.04 0.00 35.72 3.07
826 887 4.510711 CGATGACGGTAGTACAGTAGTGAT 59.489 45.833 6.04 0.00 35.72 3.06
827 888 3.867493 CGATGACGGTAGTACAGTAGTGA 59.133 47.826 6.04 0.00 35.72 3.41
828 889 3.620374 ACGATGACGGTAGTACAGTAGTG 59.380 47.826 6.04 0.00 44.46 2.74
829 890 3.866651 ACGATGACGGTAGTACAGTAGT 58.133 45.455 6.04 2.61 44.46 2.73
830 891 4.549680 CGAACGATGACGGTAGTACAGTAG 60.550 50.000 6.04 2.05 40.51 2.57
831 892 3.306973 CGAACGATGACGGTAGTACAGTA 59.693 47.826 6.04 0.00 40.51 2.74
832 893 2.094894 CGAACGATGACGGTAGTACAGT 59.905 50.000 5.73 5.73 40.51 3.55
833 894 2.094894 ACGAACGATGACGGTAGTACAG 59.905 50.000 2.06 0.10 42.55 2.74
834 895 2.076100 ACGAACGATGACGGTAGTACA 58.924 47.619 2.06 0.00 42.55 2.90
835 896 2.813779 ACGAACGATGACGGTAGTAC 57.186 50.000 0.14 0.00 42.55 2.73
840 901 0.028505 CCGATACGAACGATGACGGT 59.971 55.000 0.14 0.00 44.28 4.83
849 910 1.949465 AAATCAGCCCCGATACGAAC 58.051 50.000 0.00 0.00 0.00 3.95
850 911 4.345859 AATAAATCAGCCCCGATACGAA 57.654 40.909 0.00 0.00 0.00 3.85
859 920 5.783111 ACAGTGTCAAAAATAAATCAGCCC 58.217 37.500 0.00 0.00 0.00 5.19
891 952 6.320164 TGTGCTACACTTGTTTTTCCTGTTAT 59.680 34.615 0.00 0.00 35.11 1.89
892 953 5.648526 TGTGCTACACTTGTTTTTCCTGTTA 59.351 36.000 0.00 0.00 35.11 2.41
893 954 4.461081 TGTGCTACACTTGTTTTTCCTGTT 59.539 37.500 0.00 0.00 35.11 3.16
894 955 4.013728 TGTGCTACACTTGTTTTTCCTGT 58.986 39.130 0.00 0.00 35.11 4.00
895 956 4.351192 GTGTGCTACACTTGTTTTTCCTG 58.649 43.478 10.87 0.00 45.27 3.86
904 965 2.170985 GCGCGTGTGCTACACTTG 59.829 61.111 8.43 9.31 46.46 3.16
962 1023 1.772156 TGGTGGTGGTGGTGATCCA 60.772 57.895 0.00 0.00 42.05 3.41
964 1025 1.303317 GGTGGTGGTGGTGGTGATC 60.303 63.158 0.00 0.00 0.00 2.92
976 1037 1.597027 GAGTCAACGGGTGGTGGTG 60.597 63.158 0.00 0.00 0.00 4.17
977 1038 2.814835 GGAGTCAACGGGTGGTGGT 61.815 63.158 0.00 0.00 0.00 4.16
978 1039 2.032071 GGAGTCAACGGGTGGTGG 59.968 66.667 0.00 0.00 0.00 4.61
979 1040 2.357034 CGGAGTCAACGGGTGGTG 60.357 66.667 0.00 0.00 0.00 4.17
1258 1319 3.799755 GTTGCGCGGGTGGATGAC 61.800 66.667 8.83 0.00 0.00 3.06
1553 1614 5.437060 AGGTGAAGTTTTTGCTAGAACAGA 58.563 37.500 4.53 0.00 0.00 3.41
1554 1615 5.757850 AGGTGAAGTTTTTGCTAGAACAG 57.242 39.130 4.53 0.00 0.00 3.16
1555 1616 5.220777 CGAAGGTGAAGTTTTTGCTAGAACA 60.221 40.000 4.53 0.00 0.00 3.18
1556 1617 5.205565 CGAAGGTGAAGTTTTTGCTAGAAC 58.794 41.667 0.00 0.00 0.00 3.01
1557 1618 4.261031 GCGAAGGTGAAGTTTTTGCTAGAA 60.261 41.667 0.00 0.00 0.00 2.10
1620 1681 7.078228 CAGTAATCAAGTTTAACTGAACCTGC 58.922 38.462 0.00 0.00 0.00 4.85
1648 1709 3.072915 TGTTTGCTGAGATCTCAAAGGGA 59.927 43.478 25.09 13.03 39.39 4.20
1737 1819 8.568794 AGAGGTAAAATGAAAAACAGAGCTAAC 58.431 33.333 0.00 0.00 0.00 2.34
1738 1820 8.691661 AGAGGTAAAATGAAAAACAGAGCTAA 57.308 30.769 0.00 0.00 0.00 3.09
1740 1822 7.588497 AAGAGGTAAAATGAAAAACAGAGCT 57.412 32.000 0.00 0.00 0.00 4.09
1747 1829 8.342634 CGACTGAGAAAGAGGTAAAATGAAAAA 58.657 33.333 0.00 0.00 0.00 1.94
1772 1854 2.941064 ACATGCTCACCATTTCATCTCG 59.059 45.455 0.00 0.00 29.71 4.04
1774 1856 4.398358 CAGAACATGCTCACCATTTCATCT 59.602 41.667 0.00 0.00 29.71 2.90
1787 1869 8.043113 TGATTACTGAAATCTACAGAACATGCT 58.957 33.333 0.00 0.00 43.83 3.79
1801 1883 7.557358 TGCACTTCACCATATGATTACTGAAAT 59.443 33.333 3.65 0.00 37.11 2.17
1950 2032 1.227380 CCTGCGAGTGAGCCCATAC 60.227 63.158 0.00 0.00 36.02 2.39
2059 2141 9.877178 GAGTTATCAGTTTAGATGAAAGAAGGA 57.123 33.333 0.00 0.00 0.00 3.36
2130 2212 0.037877 AGTGCAATGCAGAGAGGCTT 59.962 50.000 8.73 0.00 40.08 4.35
2194 2276 0.324943 TAGAAGCTCCCACACAAGGC 59.675 55.000 0.00 0.00 0.00 4.35
2282 2364 5.520748 AAAAGTGGAAGGTGGATATCACT 57.479 39.130 4.83 0.00 45.38 3.41
2366 2508 5.914898 AGGTGGTTATTAACTGAAATGCC 57.085 39.130 6.52 0.47 0.00 4.40
2680 2823 1.738099 AGCTAAAGACACAGCGCCG 60.738 57.895 2.29 0.00 42.74 6.46
2911 3054 6.155393 GTGGAATAGAGATCGGAGGGATAAAT 59.845 42.308 0.00 0.00 34.82 1.40
3009 3152 3.181445 ACAACATGCTACAGGAAGGAACA 60.181 43.478 0.00 0.00 0.00 3.18
3010 3153 3.412386 ACAACATGCTACAGGAAGGAAC 58.588 45.455 0.00 0.00 0.00 3.62
3063 3206 6.453943 AGAGGTTTTCTTTCTCGTAGTAACC 58.546 40.000 0.00 0.00 29.61 2.85
3069 3212 6.661304 AGGTAAGAGGTTTTCTTTCTCGTA 57.339 37.500 0.00 0.00 43.68 3.43
3085 3228 7.182817 ACATAACAGATAGCACAAGGTAAGA 57.817 36.000 0.00 0.00 0.00 2.10
3092 3235 8.109705 ACATCAAAACATAACAGATAGCACAA 57.890 30.769 0.00 0.00 0.00 3.33
3113 3256 6.597280 AGCTCAGACCAAAGAATTTCTACATC 59.403 38.462 0.00 0.00 35.03 3.06
3140 3283 0.247736 GCTCTGGAATGTCGGACACT 59.752 55.000 13.92 1.22 0.00 3.55
3279 3422 3.891977 TCTTACCTGAAGATCCGATCCAG 59.108 47.826 4.67 6.27 39.36 3.86
3286 3429 3.452627 TCCAAGCTCTTACCTGAAGATCC 59.547 47.826 0.00 0.00 43.39 3.36
3290 3433 7.987458 TGTTTATATCCAAGCTCTTACCTGAAG 59.013 37.037 0.00 0.00 36.38 3.02
3325 3468 5.250200 CCATGGCTACTTTAACCACTACAA 58.750 41.667 0.00 0.00 35.99 2.41
3327 3470 3.626217 GCCATGGCTACTTTAACCACTAC 59.374 47.826 29.98 0.00 35.99 2.73
3432 3586 0.724549 GCATTGTGCATTGCCACATG 59.275 50.000 6.12 6.45 44.44 3.21
3433 3587 3.146783 GCATTGTGCATTGCCACAT 57.853 47.368 6.12 0.00 44.44 3.21
3451 3605 1.605710 CTCCTTCCTTGTGCTGTTGTG 59.394 52.381 0.00 0.00 0.00 3.33
3466 3620 2.178106 AGTCTATCCGGATGGTCTCCTT 59.822 50.000 27.55 3.02 42.47 3.36
3495 3649 2.070650 GGCCTGGTAGTGGGGGTAG 61.071 68.421 0.00 0.00 0.00 3.18
3528 3682 4.655527 CCGTCCAGTATGATCGGC 57.344 61.111 0.00 0.00 42.53 5.54
3621 3775 4.498520 ATGACGAGCCTCGCCACG 62.499 66.667 15.20 4.82 45.12 4.94
3634 3788 1.067250 GAGGCAGCCTCGAGATGAC 59.933 63.158 26.09 14.58 41.08 3.06
3712 3866 1.003696 GGAAACTTCCTCCTCACTGGG 59.996 57.143 0.97 0.00 44.11 4.45
3715 3869 0.977395 CGGGAAACTTCCTCCTCACT 59.023 55.000 8.37 0.00 46.72 3.41
3728 3882 4.629523 GGTCCACACGCCGGGAAA 62.630 66.667 2.18 0.00 34.34 3.13
3768 3922 5.132648 TGATCCCAGGCATCAAAACTAGTAT 59.867 40.000 0.00 0.00 0.00 2.12
3833 3987 4.041691 ACCCAATTGCTGTCTAGTGTTACT 59.958 41.667 0.00 0.00 0.00 2.24
3834 3988 4.324267 ACCCAATTGCTGTCTAGTGTTAC 58.676 43.478 0.00 0.00 0.00 2.50
3836 3990 3.508845 ACCCAATTGCTGTCTAGTGTT 57.491 42.857 0.00 0.00 0.00 3.32
3837 3991 3.073062 AGAACCCAATTGCTGTCTAGTGT 59.927 43.478 0.00 0.00 0.00 3.55
3838 3992 3.438087 CAGAACCCAATTGCTGTCTAGTG 59.562 47.826 0.00 0.00 0.00 2.74
3839 3993 3.560025 CCAGAACCCAATTGCTGTCTAGT 60.560 47.826 0.00 0.00 0.00 2.57
3840 3994 3.012518 CCAGAACCCAATTGCTGTCTAG 58.987 50.000 0.00 0.00 0.00 2.43
3841 3995 2.642311 TCCAGAACCCAATTGCTGTCTA 59.358 45.455 0.00 0.00 0.00 2.59
3842 3996 1.425066 TCCAGAACCCAATTGCTGTCT 59.575 47.619 0.00 0.00 0.00 3.41
3847 4019 1.205417 CCACATCCAGAACCCAATTGC 59.795 52.381 0.00 0.00 0.00 3.56
3854 4026 2.360165 GCATTCATCCACATCCAGAACC 59.640 50.000 0.00 0.00 0.00 3.62
3855 4027 3.285484 AGCATTCATCCACATCCAGAAC 58.715 45.455 0.00 0.00 0.00 3.01
3862 4034 4.226427 ACACAGTAGCATTCATCCACAT 57.774 40.909 0.00 0.00 0.00 3.21
3895 4249 7.339466 ACCCACTTTCATTTCTGTATACATTCC 59.661 37.037 5.91 0.00 0.00 3.01
3932 4287 5.399113 ACAAAAATAGGGTCCAAGGCTAAA 58.601 37.500 0.00 0.00 0.00 1.85
4003 4358 2.427506 GAGGACCGAGCAGACAAAAAT 58.572 47.619 0.00 0.00 0.00 1.82
4007 4362 2.283529 GGGAGGACCGAGCAGACAA 61.284 63.158 0.00 0.00 36.97 3.18
4009 4364 1.985116 AAGGGAGGACCGAGCAGAC 60.985 63.158 0.00 0.00 46.96 3.51
4016 4416 1.597742 CATAATGCAAGGGAGGACCG 58.402 55.000 0.00 0.00 46.96 4.79
4072 4472 4.039852 TCCCCATTTCTTTGTTTGGTTAGC 59.960 41.667 0.00 0.00 0.00 3.09
4110 4510 4.558226 ACATGTAGATGACCTGAGCAAA 57.442 40.909 6.90 0.00 33.36 3.68
4193 5460 1.278699 AGGAGAGGAAAAGCAGAGCTG 59.721 52.381 0.00 0.00 39.62 4.24
4195 5462 1.406751 GGAGGAGAGGAAAAGCAGAGC 60.407 57.143 0.00 0.00 0.00 4.09
4214 5481 5.951747 TGAAGTAAAAGATGAATGGAAGGGG 59.048 40.000 0.00 0.00 0.00 4.79
4215 5482 6.434028 TGTGAAGTAAAAGATGAATGGAAGGG 59.566 38.462 0.00 0.00 0.00 3.95
4216 5483 7.452880 TGTGAAGTAAAAGATGAATGGAAGG 57.547 36.000 0.00 0.00 0.00 3.46
4217 5484 9.565213 GATTGTGAAGTAAAAGATGAATGGAAG 57.435 33.333 0.00 0.00 0.00 3.46
4246 5513 5.560183 GCAGTACAACAGTGAAATGTACCAC 60.560 44.000 22.76 16.25 46.65 4.16
4249 5516 5.924475 AGCAGTACAACAGTGAAATGTAC 57.076 39.130 20.71 20.71 46.11 2.90
4279 5657 5.964758 TGTATGGAAGAATGAACAAATGCC 58.035 37.500 0.00 0.00 0.00 4.40
4329 5707 9.229784 CATACAACTTTTATCACATGAGAATGC 57.770 33.333 0.00 0.00 0.00 3.56
4339 5717 8.956426 TCCCTGATTTCATACAACTTTTATCAC 58.044 33.333 0.00 0.00 0.00 3.06
4340 5718 8.956426 GTCCCTGATTTCATACAACTTTTATCA 58.044 33.333 0.00 0.00 0.00 2.15
4387 6356 7.598869 TCGACATGAGCAATCAGTTATAATACC 59.401 37.037 0.00 0.00 0.00 2.73
4405 6374 7.907214 TCGATCTAAGATAATCTCGACATGA 57.093 36.000 0.00 0.00 30.94 3.07
4406 6375 9.008289 CATTCGATCTAAGATAATCTCGACATG 57.992 37.037 0.00 0.00 35.16 3.21
4440 6409 2.110226 GTCGCTAGATTTTCGTCGAGG 58.890 52.381 0.00 0.00 0.00 4.63
4441 6410 2.778928 CTGTCGCTAGATTTTCGTCGAG 59.221 50.000 0.00 0.00 0.00 4.04
4455 6424 6.986904 TCTATAATATGATCGACTGTCGCT 57.013 37.500 24.37 15.98 40.21 4.93
4547 6523 3.502356 TGGTAGTTCCCAACCAATTTCC 58.498 45.455 0.00 0.00 42.74 3.13
4566 6545 3.623060 AGCATCGCAATGTTTAGTACTGG 59.377 43.478 5.39 0.00 35.18 4.00
4567 6546 4.864916 AGCATCGCAATGTTTAGTACTG 57.135 40.909 5.39 0.00 35.18 2.74
4568 6547 4.695455 ACAAGCATCGCAATGTTTAGTACT 59.305 37.500 0.00 0.00 34.48 2.73
4576 6555 0.241749 CACCACAAGCATCGCAATGT 59.758 50.000 0.00 0.00 35.18 2.71
4582 6561 1.300971 CCCTGTCACCACAAGCATCG 61.301 60.000 0.00 0.00 29.82 3.84
4604 6583 2.874701 CAATGTTGCGGATAGGAAGAGG 59.125 50.000 0.00 0.00 0.00 3.69
4642 6621 1.630126 TTGGAGGGAGGAGAGCATGC 61.630 60.000 10.51 10.51 0.00 4.06
4652 6643 1.076485 CCTTGGCCATTGGAGGGAG 60.076 63.158 17.66 4.74 0.00 4.30
4663 6654 2.360475 AAGCTCTTCGCCTTGGCC 60.360 61.111 6.02 0.00 40.39 5.36
4701 6692 3.305361 CGATAGCATCATATGGAGCGTTG 59.695 47.826 2.13 3.08 0.00 4.10


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

AutoCloner maintained by Alex Coulton.