Multiple sequence alignment - TraesCS1A01G032600

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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 TraesCS1A01G032600 chr1A 100.000 2830 0 0 725 3554 15186277 15189106 0.000000e+00 5227.0
1 TraesCS1A01G032600 chr1A 100.000 528 0 0 1 528 15185553 15186080 0.000000e+00 976.0
2 TraesCS1A01G032600 chr1B 87.776 998 60 25 916 1889 20167090 20168049 0.000000e+00 1110.0
3 TraesCS1A01G032600 chr1B 91.413 757 37 5 1973 2722 20168086 20168821 0.000000e+00 1013.0
4 TraesCS1A01G032600 chr1B 86.533 646 40 15 2926 3554 20169197 20169812 0.000000e+00 667.0
5 TraesCS1A01G032600 chr1B 90.000 120 10 2 2814 2931 20169023 20169142 1.710000e-33 154.0
6 TraesCS1A01G032600 chr1B 92.157 51 4 0 2757 2807 20168922 20168972 4.920000e-09 73.1
7 TraesCS1A01G032600 chrUn 94.986 698 33 2 1972 2668 9841146 9840450 0.000000e+00 1094.0
8 TraesCS1A01G032600 chrUn 89.474 646 41 4 2934 3554 9840039 9839396 0.000000e+00 791.0
9 TraesCS1A01G032600 chrUn 88.023 693 36 9 886 1569 9842212 9841558 0.000000e+00 776.0
10 TraesCS1A01G032600 chrUn 92.605 311 19 2 1585 1892 9841488 9841179 9.050000e-121 444.0
11 TraesCS1A01G032600 chrUn 94.776 268 12 2 2666 2931 9840369 9840102 1.970000e-112 416.0
12 TraesCS1A01G032600 chrUn 97.778 45 1 0 725 769 9842254 9842210 1.060000e-10 78.7
13 TraesCS1A01G032600 chr1D 93.260 549 36 1 1991 2539 14204095 14204642 0.000000e+00 808.0
14 TraesCS1A01G032600 chr1D 92.293 532 35 4 1 528 47843248 47842719 0.000000e+00 750.0
15 TraesCS1A01G032600 chr6D 92.075 530 36 6 1 528 246547877 246548402 0.000000e+00 741.0
16 TraesCS1A01G032600 chr6D 91.902 531 37 5 1 528 262264997 262265524 0.000000e+00 737.0
17 TraesCS1A01G032600 chr5D 92.075 530 37 5 1 528 541977041 541976515 0.000000e+00 741.0
18 TraesCS1A01G032600 chr6A 91.902 531 39 4 1 528 572965640 572966169 0.000000e+00 739.0
19 TraesCS1A01G032600 chr6A 91.745 533 36 6 1 528 259916541 259916012 0.000000e+00 734.0
20 TraesCS1A01G032600 chr7D 91.902 531 37 5 1 528 287750130 287749603 0.000000e+00 737.0
21 TraesCS1A01G032600 chr7D 91.887 530 39 3 1 528 510867969 510868496 0.000000e+00 737.0
22 TraesCS1A01G032600 chr2D 91.887 530 37 6 1 528 588254538 588254013 0.000000e+00 736.0


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 TraesCS1A01G032600 chr1A 15185553 15189106 3553 False 3101.50 5227 100.000000 1 3554 2 chr1A.!!$F1 3553
1 TraesCS1A01G032600 chr1B 20167090 20169812 2722 False 603.42 1110 89.575800 916 3554 5 chr1B.!!$F1 2638
2 TraesCS1A01G032600 chrUn 9839396 9842254 2858 True 599.95 1094 92.940333 725 3554 6 chrUn.!!$R1 2829
3 TraesCS1A01G032600 chr1D 14204095 14204642 547 False 808.00 808 93.260000 1991 2539 1 chr1D.!!$F1 548
4 TraesCS1A01G032600 chr1D 47842719 47843248 529 True 750.00 750 92.293000 1 528 1 chr1D.!!$R1 527
5 TraesCS1A01G032600 chr6D 246547877 246548402 525 False 741.00 741 92.075000 1 528 1 chr6D.!!$F1 527
6 TraesCS1A01G032600 chr6D 262264997 262265524 527 False 737.00 737 91.902000 1 528 1 chr6D.!!$F2 527
7 TraesCS1A01G032600 chr5D 541976515 541977041 526 True 741.00 741 92.075000 1 528 1 chr5D.!!$R1 527
8 TraesCS1A01G032600 chr6A 572965640 572966169 529 False 739.00 739 91.902000 1 528 1 chr6A.!!$F1 527
9 TraesCS1A01G032600 chr6A 259916012 259916541 529 True 734.00 734 91.745000 1 528 1 chr6A.!!$R1 527
10 TraesCS1A01G032600 chr7D 287749603 287750130 527 True 737.00 737 91.902000 1 528 1 chr7D.!!$R1 527
11 TraesCS1A01G032600 chr7D 510867969 510868496 527 False 737.00 737 91.887000 1 528 1 chr7D.!!$F1 527
12 TraesCS1A01G032600 chr2D 588254013 588254538 525 True 736.00 736 91.887000 1 528 1 chr2D.!!$R1 527

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
99 100 0.812811 ACCGACGATCGAATCTCGGA 60.813 55.0 36.54 0.36 44.97 4.55 F
1913 2000 0.039618 AAAGATGGGATGGCCGTTGT 59.960 50.0 0.00 0.00 33.83 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2095 2182 0.036732 TGTGAGTGCCCATCAGGAAC 59.963 55.0 0.0 0.0 46.24 3.62 R
3163 3526 0.533755 CCCACCATTCGGATCTCTGC 60.534 60.0 0.0 0.0 35.59 4.26 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
50 51 3.915536 GGAACGAGTAAAGAGACTTGCT 58.084 45.455 0.00 0.00 34.59 3.91
99 100 0.812811 ACCGACGATCGAATCTCGGA 60.813 55.000 36.54 0.36 44.97 4.55
127 128 4.503714 ACATACCGATGACAAAGGGAAT 57.496 40.909 4.83 0.00 36.48 3.01
148 149 7.422399 GGAATAATGTATGTTGTTATGCGGTT 58.578 34.615 0.00 0.00 0.00 4.44
200 203 7.872061 TGTAGGAACCAATATGAGTATCCAT 57.128 36.000 0.00 0.00 0.00 3.41
255 258 6.095580 TGTCTCAGTCATGTCTACATAGTTCC 59.904 42.308 0.00 0.00 34.26 3.62
260 263 5.421056 AGTCATGTCTACATAGTTCCCGAAA 59.579 40.000 0.00 0.00 34.26 3.46
264 267 2.159198 TCTACATAGTTCCCGAAACCGC 60.159 50.000 0.00 0.00 38.76 5.68
266 269 1.065709 ACATAGTTCCCGAAACCGCAT 60.066 47.619 0.00 0.00 38.76 4.73
388 391 3.926616 GAGGAGTCTCGAAATGGTCAAA 58.073 45.455 0.00 0.00 0.00 2.69
397 400 7.228706 AGTCTCGAAATGGTCAAAACATAAAGT 59.771 33.333 0.00 0.00 0.00 2.66
461 464 3.311596 CGGATAGGTTCGGACATTTTTCC 59.688 47.826 0.00 0.00 0.00 3.13
754 762 9.031360 GTCATATCTAAAACTTTGACGATAGCA 57.969 33.333 0.00 0.00 42.67 3.49
766 774 5.791336 TGACGATAGCAGGATATTTGAGT 57.209 39.130 0.00 0.00 42.67 3.41
767 775 5.773575 TGACGATAGCAGGATATTTGAGTC 58.226 41.667 0.00 0.00 42.67 3.36
768 776 5.140747 ACGATAGCAGGATATTTGAGTCC 57.859 43.478 0.00 0.00 42.67 3.85
769 777 4.021016 ACGATAGCAGGATATTTGAGTCCC 60.021 45.833 0.00 0.00 42.67 4.46
770 778 4.221703 CGATAGCAGGATATTTGAGTCCCT 59.778 45.833 0.00 0.00 35.00 4.20
771 779 5.419155 CGATAGCAGGATATTTGAGTCCCTA 59.581 44.000 0.00 0.00 35.00 3.53
772 780 6.071334 CGATAGCAGGATATTTGAGTCCCTAA 60.071 42.308 0.00 0.00 35.00 2.69
773 781 5.975988 AGCAGGATATTTGAGTCCCTAAA 57.024 39.130 0.00 0.00 35.00 1.85
774 782 6.327386 AGCAGGATATTTGAGTCCCTAAAA 57.673 37.500 0.00 0.00 35.00 1.52
775 783 6.915786 AGCAGGATATTTGAGTCCCTAAAAT 58.084 36.000 0.00 0.00 35.00 1.82
776 784 7.357471 AGCAGGATATTTGAGTCCCTAAAATT 58.643 34.615 0.00 0.00 35.00 1.82
777 785 8.502738 AGCAGGATATTTGAGTCCCTAAAATTA 58.497 33.333 0.00 0.00 35.00 1.40
778 786 9.301897 GCAGGATATTTGAGTCCCTAAAATTAT 57.698 33.333 0.00 0.00 35.00 1.28
780 788 9.813826 AGGATATTTGAGTCCCTAAAATTATGG 57.186 33.333 0.00 0.00 35.00 2.74
781 789 9.588096 GGATATTTGAGTCCCTAAAATTATGGT 57.412 33.333 0.00 0.00 28.53 3.55
784 792 8.893563 ATTTGAGTCCCTAAAATTATGGTCAA 57.106 30.769 0.00 0.00 0.00 3.18
785 793 8.713708 TTTGAGTCCCTAAAATTATGGTCAAA 57.286 30.769 8.12 8.12 29.52 2.69
786 794 7.938140 TGAGTCCCTAAAATTATGGTCAAAG 57.062 36.000 0.00 0.00 0.00 2.77
787 795 7.466804 TGAGTCCCTAAAATTATGGTCAAAGT 58.533 34.615 0.00 0.00 0.00 2.66
788 796 7.947890 TGAGTCCCTAAAATTATGGTCAAAGTT 59.052 33.333 0.00 0.00 0.00 2.66
789 797 8.349568 AGTCCCTAAAATTATGGTCAAAGTTC 57.650 34.615 0.00 0.00 0.00 3.01
790 798 7.120726 AGTCCCTAAAATTATGGTCAAAGTTCG 59.879 37.037 0.00 0.00 0.00 3.95
791 799 7.120138 GTCCCTAAAATTATGGTCAAAGTTCGA 59.880 37.037 0.00 0.00 0.00 3.71
792 800 7.120138 TCCCTAAAATTATGGTCAAAGTTCGAC 59.880 37.037 0.00 0.00 0.00 4.20
799 807 3.329929 GGTCAAAGTTCGACCCATAGT 57.670 47.619 1.08 0.00 46.12 2.12
800 808 4.460948 GGTCAAAGTTCGACCCATAGTA 57.539 45.455 1.08 0.00 46.12 1.82
801 809 4.179298 GGTCAAAGTTCGACCCATAGTAC 58.821 47.826 1.08 0.00 46.12 2.73
802 810 4.322198 GGTCAAAGTTCGACCCATAGTACA 60.322 45.833 1.08 0.00 46.12 2.90
803 811 5.232463 GTCAAAGTTCGACCCATAGTACAA 58.768 41.667 0.00 0.00 0.00 2.41
804 812 5.347907 GTCAAAGTTCGACCCATAGTACAAG 59.652 44.000 0.00 0.00 0.00 3.16
805 813 5.244402 TCAAAGTTCGACCCATAGTACAAGA 59.756 40.000 0.00 0.00 0.00 3.02
806 814 4.985538 AGTTCGACCCATAGTACAAGAG 57.014 45.455 0.00 0.00 0.00 2.85
807 815 3.700038 AGTTCGACCCATAGTACAAGAGG 59.300 47.826 0.00 0.00 0.00 3.69
808 816 2.029623 TCGACCCATAGTACAAGAGGC 58.970 52.381 0.00 0.00 0.00 4.70
809 817 2.032620 CGACCCATAGTACAAGAGGCT 58.967 52.381 0.00 0.00 0.00 4.58
810 818 2.431057 CGACCCATAGTACAAGAGGCTT 59.569 50.000 0.00 0.00 0.00 4.35
811 819 3.635373 CGACCCATAGTACAAGAGGCTTA 59.365 47.826 0.00 0.00 0.00 3.09
812 820 4.281182 CGACCCATAGTACAAGAGGCTTAT 59.719 45.833 0.00 0.00 0.00 1.73
813 821 5.475909 CGACCCATAGTACAAGAGGCTTATA 59.524 44.000 0.00 0.00 0.00 0.98
814 822 6.349445 CGACCCATAGTACAAGAGGCTTATAG 60.349 46.154 0.00 0.00 0.00 1.31
815 823 6.621394 ACCCATAGTACAAGAGGCTTATAGA 58.379 40.000 0.00 0.00 0.00 1.98
816 824 7.073854 ACCCATAGTACAAGAGGCTTATAGAA 58.926 38.462 0.00 0.00 0.00 2.10
817 825 7.735321 ACCCATAGTACAAGAGGCTTATAGAAT 59.265 37.037 0.00 0.00 0.00 2.40
818 826 8.037758 CCCATAGTACAAGAGGCTTATAGAATG 58.962 40.741 0.00 0.00 0.00 2.67
819 827 8.589338 CCATAGTACAAGAGGCTTATAGAATGT 58.411 37.037 0.00 0.00 0.00 2.71
820 828 9.988815 CATAGTACAAGAGGCTTATAGAATGTT 57.011 33.333 0.00 0.00 0.00 2.71
822 830 7.501844 AGTACAAGAGGCTTATAGAATGTTCC 58.498 38.462 0.00 0.00 0.00 3.62
823 831 6.567602 ACAAGAGGCTTATAGAATGTTCCT 57.432 37.500 0.00 0.00 0.00 3.36
824 832 7.676683 ACAAGAGGCTTATAGAATGTTCCTA 57.323 36.000 0.00 0.00 0.00 2.94
825 833 8.090788 ACAAGAGGCTTATAGAATGTTCCTAA 57.909 34.615 0.00 0.00 0.00 2.69
826 834 8.548877 ACAAGAGGCTTATAGAATGTTCCTAAA 58.451 33.333 0.00 0.00 0.00 1.85
827 835 8.831550 CAAGAGGCTTATAGAATGTTCCTAAAC 58.168 37.037 0.00 0.00 35.85 2.01
838 846 3.832276 TGTTCCTAAACAAATGATGCGC 58.168 40.909 0.00 0.00 42.34 6.09
839 847 3.254411 TGTTCCTAAACAAATGATGCGCA 59.746 39.130 14.96 14.96 42.34 6.09
840 848 4.082300 TGTTCCTAAACAAATGATGCGCAT 60.082 37.500 25.66 25.66 42.34 4.73
841 849 5.124617 TGTTCCTAAACAAATGATGCGCATA 59.875 36.000 25.40 12.30 42.34 3.14
842 850 6.183360 TGTTCCTAAACAAATGATGCGCATAT 60.183 34.615 25.40 14.08 42.34 1.78
843 851 7.012799 TGTTCCTAAACAAATGATGCGCATATA 59.987 33.333 25.40 16.14 42.34 0.86
844 852 7.686438 TCCTAAACAAATGATGCGCATATAT 57.314 32.000 25.40 17.77 35.78 0.86
845 853 8.785329 TCCTAAACAAATGATGCGCATATATA 57.215 30.769 25.40 10.68 35.78 0.86
846 854 9.225436 TCCTAAACAAATGATGCGCATATATAA 57.775 29.630 25.40 7.26 35.78 0.98
847 855 9.494479 CCTAAACAAATGATGCGCATATATAAG 57.506 33.333 25.40 17.12 35.78 1.73
850 858 9.748708 AAACAAATGATGCGCATATATAAGTTT 57.251 25.926 25.40 24.92 35.78 2.66
851 859 9.748708 AACAAATGATGCGCATATATAAGTTTT 57.251 25.926 25.40 9.44 35.78 2.43
852 860 9.748708 ACAAATGATGCGCATATATAAGTTTTT 57.251 25.926 25.40 8.77 35.78 1.94
877 885 7.728580 TTTTGAATCATTTATACGCGGTTTC 57.271 32.000 12.47 2.22 0.00 2.78
878 886 6.424176 TTGAATCATTTATACGCGGTTTCA 57.576 33.333 12.47 4.94 0.00 2.69
879 887 6.424176 TGAATCATTTATACGCGGTTTCAA 57.576 33.333 12.47 0.00 0.00 2.69
880 888 6.843208 TGAATCATTTATACGCGGTTTCAAA 58.157 32.000 12.47 3.53 0.00 2.69
881 889 7.306213 TGAATCATTTATACGCGGTTTCAAAA 58.694 30.769 12.47 2.39 0.00 2.44
882 890 7.483375 TGAATCATTTATACGCGGTTTCAAAAG 59.517 33.333 12.47 0.69 0.00 2.27
883 891 6.483385 TCATTTATACGCGGTTTCAAAAGA 57.517 33.333 12.47 3.13 0.00 2.52
884 892 7.079182 TCATTTATACGCGGTTTCAAAAGAT 57.921 32.000 12.47 0.00 0.00 2.40
1068 1080 3.151022 GCCGACCTCCTCCTCCTG 61.151 72.222 0.00 0.00 0.00 3.86
1379 1400 2.047274 CGGCCGTGGATTGACAGT 60.047 61.111 19.50 0.00 0.00 3.55
1417 1438 4.161001 GGGATTTGATTCCATTGCAGAAGT 59.839 41.667 0.00 0.00 37.53 3.01
1514 1541 2.204059 AGGCAAGCTCCACTCCCT 60.204 61.111 0.00 0.00 0.00 4.20
1569 1596 3.637273 AGGCCTGGTTGTCCGGAC 61.637 66.667 28.17 28.17 42.46 4.79
1575 1629 3.628982 GGTTGTCCGGACGGGGAA 61.629 66.667 28.70 15.15 37.96 3.97
1578 1632 2.441675 TTGTCCGGACGGGGAACAA 61.442 57.895 28.70 13.91 37.96 2.83
1589 1643 0.608130 GGGGAACAAAAGGGTGATGC 59.392 55.000 0.00 0.00 0.00 3.91
1599 1653 2.634815 AGGGTGATGCTGATGATGAC 57.365 50.000 0.00 0.00 0.00 3.06
1602 1683 2.552743 GGGTGATGCTGATGATGACATG 59.447 50.000 0.00 0.00 36.82 3.21
1617 1698 2.644299 TGACATGGAGAACCTTGGTGAT 59.356 45.455 0.00 0.00 43.06 3.06
1724 1805 1.537135 GGAGCAGAGCATTACCGACTC 60.537 57.143 0.00 0.00 0.00 3.36
1728 1809 2.145397 AGAGCATTACCGACTCTGGA 57.855 50.000 0.00 0.00 39.29 3.86
1790 1871 7.878621 TGGATAACAGGATTATCAAGGAGAT 57.121 36.000 8.50 0.00 40.86 2.75
1802 1883 1.738350 CAAGGAGATGAGCAGCACAAG 59.262 52.381 0.00 0.00 0.00 3.16
1811 1892 1.956477 GAGCAGCACAAGGAGGAAAAA 59.044 47.619 0.00 0.00 0.00 1.94
1885 1972 6.131264 ACATATCAAATGCCAGGATCAGAAA 58.869 36.000 0.00 0.00 0.00 2.52
1886 1973 6.264744 ACATATCAAATGCCAGGATCAGAAAG 59.735 38.462 0.00 0.00 0.00 2.62
1887 1974 4.305539 TCAAATGCCAGGATCAGAAAGA 57.694 40.909 0.00 0.00 0.00 2.52
1888 1975 4.863548 TCAAATGCCAGGATCAGAAAGAT 58.136 39.130 0.00 0.00 40.48 2.40
1910 1997 3.689832 AAAAAGATGGGATGGCCGT 57.310 47.368 0.00 0.00 33.83 5.68
1911 1998 1.937191 AAAAAGATGGGATGGCCGTT 58.063 45.000 0.00 0.00 33.83 4.44
1912 1999 1.185315 AAAAGATGGGATGGCCGTTG 58.815 50.000 0.00 0.00 33.83 4.10
1913 2000 0.039618 AAAGATGGGATGGCCGTTGT 59.960 50.000 0.00 0.00 33.83 3.32
1914 2001 0.916086 AAGATGGGATGGCCGTTGTA 59.084 50.000 0.00 0.00 33.83 2.41
1917 2004 1.676006 GATGGGATGGCCGTTGTAAAG 59.324 52.381 0.00 0.00 33.83 1.85
1923 2010 0.887387 TGGCCGTTGTAAAGTCAGCC 60.887 55.000 0.00 0.00 39.41 4.85
1933 2020 5.356882 TGTAAAGTCAGCCGAAGAAAATG 57.643 39.130 0.00 0.00 0.00 2.32
1934 2021 5.060506 TGTAAAGTCAGCCGAAGAAAATGA 58.939 37.500 0.00 0.00 0.00 2.57
1935 2022 4.756084 AAAGTCAGCCGAAGAAAATGAG 57.244 40.909 0.00 0.00 0.00 2.90
1937 2024 3.330267 AGTCAGCCGAAGAAAATGAGTC 58.670 45.455 0.00 0.00 0.00 3.36
1938 2025 2.416893 GTCAGCCGAAGAAAATGAGTCC 59.583 50.000 0.00 0.00 0.00 3.85
1939 2026 1.740025 CAGCCGAAGAAAATGAGTCCC 59.260 52.381 0.00 0.00 0.00 4.46
1940 2027 1.351017 AGCCGAAGAAAATGAGTCCCA 59.649 47.619 0.00 0.00 0.00 4.37
1941 2028 2.159382 GCCGAAGAAAATGAGTCCCAA 58.841 47.619 0.00 0.00 0.00 4.12
1942 2029 2.162408 GCCGAAGAAAATGAGTCCCAAG 59.838 50.000 0.00 0.00 0.00 3.61
1943 2030 2.749621 CCGAAGAAAATGAGTCCCAAGG 59.250 50.000 0.00 0.00 0.00 3.61
1944 2031 3.412386 CGAAGAAAATGAGTCCCAAGGT 58.588 45.455 0.00 0.00 0.00 3.50
1945 2032 3.189287 CGAAGAAAATGAGTCCCAAGGTG 59.811 47.826 0.00 0.00 0.00 4.00
1946 2033 2.519013 AGAAAATGAGTCCCAAGGTGC 58.481 47.619 0.00 0.00 0.00 5.01
1947 2034 1.546029 GAAAATGAGTCCCAAGGTGCC 59.454 52.381 0.00 0.00 0.00 5.01
1948 2035 0.609131 AAATGAGTCCCAAGGTGCCG 60.609 55.000 0.00 0.00 0.00 5.69
1949 2036 3.628646 ATGAGTCCCAAGGTGCCGC 62.629 63.158 0.00 0.00 0.00 6.53
1950 2037 4.329545 GAGTCCCAAGGTGCCGCA 62.330 66.667 0.00 0.00 0.00 5.69
1951 2038 4.335647 AGTCCCAAGGTGCCGCAG 62.336 66.667 0.00 0.00 0.00 5.18
1952 2039 4.643387 GTCCCAAGGTGCCGCAGT 62.643 66.667 0.00 0.00 0.00 4.40
1953 2040 2.925706 TCCCAAGGTGCCGCAGTA 60.926 61.111 0.00 0.00 0.00 2.74
1954 2041 2.746277 CCCAAGGTGCCGCAGTAC 60.746 66.667 0.00 0.00 0.00 2.73
1955 2042 2.031919 CCAAGGTGCCGCAGTACA 59.968 61.111 0.00 0.00 0.00 2.90
1956 2043 1.599518 CCAAGGTGCCGCAGTACAA 60.600 57.895 0.00 0.00 0.00 2.41
1957 2044 1.577328 CCAAGGTGCCGCAGTACAAG 61.577 60.000 0.00 0.00 0.00 3.16
1958 2045 1.302511 AAGGTGCCGCAGTACAAGG 60.303 57.895 0.00 0.00 0.00 3.61
1959 2046 2.032071 GGTGCCGCAGTACAAGGT 59.968 61.111 0.00 0.00 0.00 3.50
1960 2047 2.033194 GGTGCCGCAGTACAAGGTC 61.033 63.158 0.00 0.00 0.00 3.85
1961 2048 1.301401 GTGCCGCAGTACAAGGTCA 60.301 57.895 0.00 0.00 0.00 4.02
1962 2049 0.673644 GTGCCGCAGTACAAGGTCAT 60.674 55.000 0.00 0.00 0.00 3.06
1963 2050 0.673333 TGCCGCAGTACAAGGTCATG 60.673 55.000 0.00 0.00 0.00 3.07
1964 2051 0.673644 GCCGCAGTACAAGGTCATGT 60.674 55.000 0.00 0.00 37.32 3.21
1965 2052 1.359848 CCGCAGTACAAGGTCATGTC 58.640 55.000 0.00 0.00 34.75 3.06
1966 2053 1.337728 CCGCAGTACAAGGTCATGTCA 60.338 52.381 0.00 0.00 34.75 3.58
1967 2054 1.995484 CGCAGTACAAGGTCATGTCAG 59.005 52.381 0.00 0.00 34.75 3.51
1968 2055 1.734465 GCAGTACAAGGTCATGTCAGC 59.266 52.381 0.00 0.00 34.75 4.26
1969 2056 2.871637 GCAGTACAAGGTCATGTCAGCA 60.872 50.000 0.00 0.00 34.75 4.41
1970 2057 2.738846 CAGTACAAGGTCATGTCAGCAC 59.261 50.000 0.00 0.00 34.75 4.40
2095 2182 1.005340 GGTCAGCGAAGAATGCTCTG 58.995 55.000 0.00 0.00 41.72 3.35
2142 2229 5.495640 CAGCTCTTCAGTAAAAGGAGGATT 58.504 41.667 0.00 0.00 0.00 3.01
2339 2426 3.679824 ACCTTTCTCGGGTTACTCTTG 57.320 47.619 0.00 0.00 32.46 3.02
2422 2512 3.372822 CGGGTGTTGTGGTGAACATATAC 59.627 47.826 0.00 0.00 38.99 1.47
2433 2523 4.993584 GGTGAACATATACTGATGCAGGAG 59.006 45.833 0.00 0.00 35.51 3.69
2445 2535 4.767478 TGATGCAGGAGATTCTGAAGAAG 58.233 43.478 0.00 0.00 37.48 2.85
2478 2568 1.691976 TCGTCAAGGCTGAAAGAAGGA 59.308 47.619 0.00 0.00 34.07 3.36
2511 2601 4.380531 CAGAGTTTTCTAGGCAGACAACA 58.619 43.478 14.15 0.00 41.82 3.33
2516 2606 5.417580 AGTTTTCTAGGCAGACAACAAAACA 59.582 36.000 14.15 0.00 41.82 2.83
2654 2747 5.023533 TCCACTCTGTAATTACTCCATGC 57.976 43.478 16.33 0.00 0.00 4.06
2697 2874 6.611381 TCTTTGTTGATGGCTTATTTTCTCG 58.389 36.000 0.00 0.00 0.00 4.04
2752 2948 5.453567 AAAGTGCTGGTTTCCAATAGTTC 57.546 39.130 0.00 0.00 30.80 3.01
2931 3220 3.827008 TCCTAGTGTTGCATCAGATCC 57.173 47.619 0.00 0.00 0.00 3.36
2947 3296 7.254932 GCATCAGATCCAAGGTGTTAAAGTATC 60.255 40.741 0.00 0.00 0.00 2.24
2975 3324 6.914259 TGATCGATATACAGTAGCAGGAAAG 58.086 40.000 0.00 0.00 0.00 2.62
3001 3350 4.398358 TGTATCTCTCTGGTTCGTTGGTAG 59.602 45.833 0.00 0.00 0.00 3.18
3048 3397 4.547406 TGGTAGATATCTCACGTCAACG 57.453 45.455 8.95 0.12 46.33 4.10
3105 3454 1.072648 ACAAAATGCCCAGCTGCAAAT 59.927 42.857 8.66 0.00 45.84 2.32
3144 3505 6.426937 TGAAAACTCTACACTTTGCAGTATCC 59.573 38.462 0.00 0.00 0.00 2.59
3163 3526 7.550906 CAGTATCCCCTTTTCTTTCTAAGACTG 59.449 40.741 0.00 0.00 37.23 3.51
3164 3527 4.652822 TCCCCTTTTCTTTCTAAGACTGC 58.347 43.478 0.00 0.00 37.23 4.40
3200 3563 3.002348 GTGGGTTTGAACTCGAAGTCTTG 59.998 47.826 0.00 0.00 29.87 3.02
3287 3664 4.584325 TGCATGCTGGATAATAGTTTTCCC 59.416 41.667 20.33 0.00 0.00 3.97
3374 3751 8.723942 ATACAGTAGCAGGAAAACAAGATAAG 57.276 34.615 0.00 0.00 0.00 1.73
3382 3759 4.520492 AGGAAAACAAGATAAGCAGTGTGG 59.480 41.667 0.00 0.00 0.00 4.17
3445 3823 6.625362 TCTATGTCTCTTGTAAAGTGCAGAG 58.375 40.000 0.00 0.00 46.34 3.35
3448 3826 4.061596 GTCTCTTGTAAAGTGCAGAGCTT 58.938 43.478 0.00 0.00 46.34 3.74
3453 3831 6.230472 TCTTGTAAAGTGCAGAGCTTGATTA 58.770 36.000 0.00 0.00 46.34 1.75
3464 3842 4.393062 CAGAGCTTGATTAATTGTCACCGT 59.607 41.667 0.00 0.00 0.00 4.83
3526 3905 6.254804 TCAAACCATACGAGTATGTTTCATCG 59.745 38.462 18.49 7.03 40.90 3.84
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 0.179067 TTCCGTAATGCGTCATCCCC 60.179 55.000 0.00 0.00 39.32 4.81
21 22 3.173599 TCTTTACTCGTTCCGTAATGCG 58.826 45.455 0.00 0.00 40.95 4.73
50 51 8.491045 TCATACCTAGTTCAATATCATCACCA 57.509 34.615 0.00 0.00 0.00 4.17
99 100 5.642063 CCTTTGTCATCGGTATGTTACTTGT 59.358 40.000 0.00 0.00 34.50 3.16
127 128 7.751348 GTCAAAACCGCATAACAACATACATTA 59.249 33.333 0.00 0.00 0.00 1.90
148 149 7.092137 TCTACGAAGATCTTTATCGGTCAAA 57.908 36.000 17.21 0.00 40.71 2.69
180 182 6.431234 GGAACATGGATACTCATATTGGTTCC 59.569 42.308 0.00 0.00 42.34 3.62
194 197 4.431416 AACCAATAGCGGAACATGGATA 57.569 40.909 0.00 0.00 35.16 2.59
264 267 1.423845 GTTAAGCGTGCGGACCATG 59.576 57.895 0.00 0.00 0.00 3.66
266 269 2.735478 CGTTAAGCGTGCGGACCA 60.735 61.111 0.00 0.00 35.54 4.02
435 438 4.417426 AATGTCCGAACCTATCCGAAAT 57.583 40.909 0.00 0.00 0.00 2.17
754 762 9.813826 CCATAATTTTAGGGACTCAAATATCCT 57.186 33.333 0.00 0.00 40.85 3.24
766 774 7.120138 GTCGAACTTTGACCATAATTTTAGGGA 59.880 37.037 7.94 0.00 36.75 4.20
767 775 7.248437 GTCGAACTTTGACCATAATTTTAGGG 58.752 38.462 0.00 0.00 40.29 3.53
780 788 4.813027 TGTACTATGGGTCGAACTTTGAC 58.187 43.478 0.00 0.86 35.60 3.18
781 789 5.244402 TCTTGTACTATGGGTCGAACTTTGA 59.756 40.000 0.00 0.00 0.00 2.69
782 790 5.475719 TCTTGTACTATGGGTCGAACTTTG 58.524 41.667 0.00 0.00 0.00 2.77
783 791 5.337330 CCTCTTGTACTATGGGTCGAACTTT 60.337 44.000 0.00 0.00 0.00 2.66
784 792 4.159879 CCTCTTGTACTATGGGTCGAACTT 59.840 45.833 0.00 0.00 0.00 2.66
785 793 3.700038 CCTCTTGTACTATGGGTCGAACT 59.300 47.826 0.00 0.00 0.00 3.01
786 794 3.737355 GCCTCTTGTACTATGGGTCGAAC 60.737 52.174 0.00 0.00 0.00 3.95
787 795 2.429610 GCCTCTTGTACTATGGGTCGAA 59.570 50.000 0.00 0.00 0.00 3.71
788 796 2.029623 GCCTCTTGTACTATGGGTCGA 58.970 52.381 0.00 0.00 0.00 4.20
789 797 2.032620 AGCCTCTTGTACTATGGGTCG 58.967 52.381 0.00 0.00 0.00 4.79
790 798 5.810080 ATAAGCCTCTTGTACTATGGGTC 57.190 43.478 0.00 0.00 0.00 4.46
791 799 6.621394 TCTATAAGCCTCTTGTACTATGGGT 58.379 40.000 0.00 0.00 0.00 4.51
792 800 7.540474 TTCTATAAGCCTCTTGTACTATGGG 57.460 40.000 0.00 0.00 0.00 4.00
793 801 8.589338 ACATTCTATAAGCCTCTTGTACTATGG 58.411 37.037 0.00 0.00 0.00 2.74
794 802 9.988815 AACATTCTATAAGCCTCTTGTACTATG 57.011 33.333 0.00 0.00 0.00 2.23
796 804 8.639761 GGAACATTCTATAAGCCTCTTGTACTA 58.360 37.037 0.00 0.00 0.00 1.82
797 805 7.345914 AGGAACATTCTATAAGCCTCTTGTACT 59.654 37.037 0.00 0.00 0.00 2.73
798 806 7.501844 AGGAACATTCTATAAGCCTCTTGTAC 58.498 38.462 0.00 0.00 0.00 2.90
799 807 7.676683 AGGAACATTCTATAAGCCTCTTGTA 57.323 36.000 0.00 0.00 0.00 2.41
800 808 6.567602 AGGAACATTCTATAAGCCTCTTGT 57.432 37.500 0.00 0.00 0.00 3.16
801 809 8.831550 GTTTAGGAACATTCTATAAGCCTCTTG 58.168 37.037 0.00 0.00 35.79 3.02
802 810 8.548877 TGTTTAGGAACATTCTATAAGCCTCTT 58.451 33.333 0.00 0.00 40.71 2.85
803 811 8.090788 TGTTTAGGAACATTCTATAAGCCTCT 57.909 34.615 0.00 0.00 40.71 3.69
804 812 8.732746 TTGTTTAGGAACATTCTATAAGCCTC 57.267 34.615 0.00 0.00 44.71 4.70
805 813 9.700831 ATTTGTTTAGGAACATTCTATAAGCCT 57.299 29.630 0.00 0.00 44.71 4.58
806 814 9.736023 CATTTGTTTAGGAACATTCTATAAGCC 57.264 33.333 0.00 0.00 44.71 4.35
811 819 8.131100 CGCATCATTTGTTTAGGAACATTCTAT 58.869 33.333 0.00 0.00 44.71 1.98
812 820 7.471721 CGCATCATTTGTTTAGGAACATTCTA 58.528 34.615 0.00 0.00 44.71 2.10
813 821 6.324819 CGCATCATTTGTTTAGGAACATTCT 58.675 36.000 0.00 0.00 44.71 2.40
814 822 5.004726 GCGCATCATTTGTTTAGGAACATTC 59.995 40.000 0.30 0.00 44.71 2.67
815 823 4.864247 GCGCATCATTTGTTTAGGAACATT 59.136 37.500 0.30 0.00 44.71 2.71
816 824 4.082300 TGCGCATCATTTGTTTAGGAACAT 60.082 37.500 5.66 0.00 44.71 2.71
817 825 3.254411 TGCGCATCATTTGTTTAGGAACA 59.746 39.130 5.66 0.00 43.73 3.18
818 826 3.832276 TGCGCATCATTTGTTTAGGAAC 58.168 40.909 5.66 0.00 36.29 3.62
819 827 4.717233 ATGCGCATCATTTGTTTAGGAA 57.283 36.364 19.28 0.00 29.16 3.36
820 828 7.686438 ATATATGCGCATCATTTGTTTAGGA 57.314 32.000 29.11 4.38 36.63 2.94
821 829 9.494479 CTTATATATGCGCATCATTTGTTTAGG 57.506 33.333 29.11 5.60 36.63 2.69
824 832 9.748708 AAACTTATATATGCGCATCATTTGTTT 57.251 25.926 29.11 25.07 36.63 2.83
825 833 9.748708 AAAACTTATATATGCGCATCATTTGTT 57.251 25.926 29.11 21.78 36.63 2.83
826 834 9.748708 AAAAACTTATATATGCGCATCATTTGT 57.251 25.926 29.11 18.01 36.63 2.83
852 860 7.808381 TGAAACCGCGTATAAATGATTCAAAAA 59.192 29.630 4.92 0.00 0.00 1.94
853 861 7.306213 TGAAACCGCGTATAAATGATTCAAAA 58.694 30.769 4.92 0.00 0.00 2.44
854 862 6.843208 TGAAACCGCGTATAAATGATTCAAA 58.157 32.000 4.92 0.00 0.00 2.69
855 863 6.424176 TGAAACCGCGTATAAATGATTCAA 57.576 33.333 4.92 0.00 0.00 2.69
856 864 6.424176 TTGAAACCGCGTATAAATGATTCA 57.576 33.333 4.92 1.53 0.00 2.57
857 865 7.694784 TCTTTTGAAACCGCGTATAAATGATTC 59.305 33.333 4.92 0.00 0.00 2.52
858 866 7.531716 TCTTTTGAAACCGCGTATAAATGATT 58.468 30.769 4.92 0.00 0.00 2.57
859 867 7.079182 TCTTTTGAAACCGCGTATAAATGAT 57.921 32.000 4.92 0.00 0.00 2.45
860 868 6.483385 TCTTTTGAAACCGCGTATAAATGA 57.517 33.333 4.92 4.53 0.00 2.57
861 869 7.044314 GGAATCTTTTGAAACCGCGTATAAATG 60.044 37.037 4.92 2.33 0.00 2.32
862 870 6.970613 GGAATCTTTTGAAACCGCGTATAAAT 59.029 34.615 4.92 0.00 0.00 1.40
863 871 6.149807 AGGAATCTTTTGAAACCGCGTATAAA 59.850 34.615 4.92 0.00 34.54 1.40
864 872 5.644636 AGGAATCTTTTGAAACCGCGTATAA 59.355 36.000 4.92 0.00 34.54 0.98
865 873 5.180271 AGGAATCTTTTGAAACCGCGTATA 58.820 37.500 4.92 0.00 34.54 1.47
866 874 4.007659 AGGAATCTTTTGAAACCGCGTAT 58.992 39.130 4.92 0.00 34.54 3.06
867 875 3.404899 AGGAATCTTTTGAAACCGCGTA 58.595 40.909 4.92 0.00 34.54 4.42
868 876 2.227194 AGGAATCTTTTGAAACCGCGT 58.773 42.857 4.92 0.00 34.54 6.01
869 877 2.989422 AGGAATCTTTTGAAACCGCG 57.011 45.000 0.00 0.00 34.54 6.46
870 878 3.255888 AGGAAGGAATCTTTTGAAACCGC 59.744 43.478 0.00 0.00 34.54 5.68
871 879 5.222631 CAAGGAAGGAATCTTTTGAAACCG 58.777 41.667 0.00 0.00 34.54 4.44
872 880 5.304357 TCCAAGGAAGGAATCTTTTGAAACC 59.696 40.000 0.00 0.00 33.93 3.27
873 881 6.405278 TCCAAGGAAGGAATCTTTTGAAAC 57.595 37.500 0.00 0.00 33.93 2.78
874 882 7.054491 CTTCCAAGGAAGGAATCTTTTGAAA 57.946 36.000 18.98 0.00 46.05 2.69
875 883 6.655078 CTTCCAAGGAAGGAATCTTTTGAA 57.345 37.500 18.98 0.00 46.05 2.69
994 1006 2.815211 CGTCTCCGCCATGGTGTG 60.815 66.667 23.44 15.48 39.52 3.82
995 1007 4.082523 CCGTCTCCGCCATGGTGT 62.083 66.667 23.44 0.00 39.52 4.16
1242 1263 0.631212 GGGAAGGGTGGTCCATGATT 59.369 55.000 0.00 0.00 36.83 2.57
1243 1264 1.635817 CGGGAAGGGTGGTCCATGAT 61.636 60.000 0.00 0.00 36.83 2.45
1376 1397 3.700538 TCCCCATTGAAGGAAATCACTG 58.299 45.455 0.00 0.00 31.75 3.66
1379 1400 5.340322 TCAAATCCCCATTGAAGGAAATCA 58.660 37.500 0.26 0.00 35.30 2.57
1417 1438 2.185867 GTCGCTGCCCAATCCGTA 59.814 61.111 0.00 0.00 0.00 4.02
1443 1464 1.601419 CGGACCTGTCGGGCTTCTTA 61.601 60.000 0.00 0.00 38.87 2.10
1478 1499 0.178068 TGAATCGTGCCTTAGGAGCC 59.822 55.000 0.69 0.00 0.00 4.70
1491 1518 0.392193 AGTGGAGCTTGCCTGAATCG 60.392 55.000 0.00 0.00 0.00 3.34
1525 1552 4.373116 GTCTCCGGTGGCTTCGCA 62.373 66.667 0.00 0.00 0.00 5.10
1569 1596 0.887933 CATCACCCTTTTGTTCCCCG 59.112 55.000 0.00 0.00 0.00 5.73
1575 1629 3.159213 TCATCAGCATCACCCTTTTGT 57.841 42.857 0.00 0.00 0.00 2.83
1578 1632 3.285484 GTCATCATCAGCATCACCCTTT 58.715 45.455 0.00 0.00 0.00 3.11
1589 1643 4.418973 AGGTTCTCCATGTCATCATCAG 57.581 45.455 0.00 0.00 35.89 2.90
1599 1653 3.641434 AGATCACCAAGGTTCTCCATG 57.359 47.619 0.00 0.00 35.89 3.66
1602 1683 4.398319 TGAAAAGATCACCAAGGTTCTCC 58.602 43.478 0.00 0.00 31.50 3.71
1790 1871 0.473755 TTTCCTCCTTGTGCTGCTCA 59.526 50.000 0.00 0.00 0.00 4.26
1802 1883 3.535280 TGTTTGCCAAGTTTTTCCTCC 57.465 42.857 0.00 0.00 0.00 4.30
1864 1951 6.005066 TCTTTCTGATCCTGGCATTTGATA 57.995 37.500 0.00 0.00 0.00 2.15
1865 1952 4.863548 TCTTTCTGATCCTGGCATTTGAT 58.136 39.130 0.00 0.00 0.00 2.57
1892 1979 1.550072 CAACGGCCATCCCATCTTTTT 59.450 47.619 2.24 0.00 0.00 1.94
1893 1980 1.185315 CAACGGCCATCCCATCTTTT 58.815 50.000 2.24 0.00 0.00 2.27
1894 1981 0.039618 ACAACGGCCATCCCATCTTT 59.960 50.000 2.24 0.00 0.00 2.52
1895 1982 0.916086 TACAACGGCCATCCCATCTT 59.084 50.000 2.24 0.00 0.00 2.40
1896 1983 0.916086 TTACAACGGCCATCCCATCT 59.084 50.000 2.24 0.00 0.00 2.90
1897 1984 1.676006 CTTTACAACGGCCATCCCATC 59.324 52.381 2.24 0.00 0.00 3.51
1898 1985 1.005450 ACTTTACAACGGCCATCCCAT 59.995 47.619 2.24 0.00 0.00 4.00
1899 1986 0.402504 ACTTTACAACGGCCATCCCA 59.597 50.000 2.24 0.00 0.00 4.37
1900 1987 1.092348 GACTTTACAACGGCCATCCC 58.908 55.000 2.24 0.00 0.00 3.85
1901 1988 1.737793 CTGACTTTACAACGGCCATCC 59.262 52.381 2.24 0.00 0.00 3.51
1902 1989 1.130561 GCTGACTTTACAACGGCCATC 59.869 52.381 2.24 0.00 0.00 3.51
1903 1990 1.165270 GCTGACTTTACAACGGCCAT 58.835 50.000 2.24 0.00 0.00 4.40
1904 1991 2.624169 GCTGACTTTACAACGGCCA 58.376 52.632 2.24 0.00 0.00 5.36
1905 1992 1.873863 GGCTGACTTTACAACGGCC 59.126 57.895 0.00 0.00 46.40 6.13
1906 1993 0.947180 TCGGCTGACTTTACAACGGC 60.947 55.000 0.00 0.00 35.49 5.68
1907 1994 1.459592 CTTCGGCTGACTTTACAACGG 59.540 52.381 0.00 0.00 0.00 4.44
1908 1995 2.400399 TCTTCGGCTGACTTTACAACG 58.600 47.619 0.00 0.00 0.00 4.10
1909 1996 4.806342 TTTCTTCGGCTGACTTTACAAC 57.194 40.909 0.00 0.00 0.00 3.32
1910 1997 5.529430 TCATTTTCTTCGGCTGACTTTACAA 59.471 36.000 0.00 0.00 0.00 2.41
1911 1998 5.060506 TCATTTTCTTCGGCTGACTTTACA 58.939 37.500 0.00 0.00 0.00 2.41
1912 1999 5.179555 ACTCATTTTCTTCGGCTGACTTTAC 59.820 40.000 0.00 0.00 0.00 2.01
1913 2000 5.305585 ACTCATTTTCTTCGGCTGACTTTA 58.694 37.500 0.00 0.00 0.00 1.85
1914 2001 4.137543 ACTCATTTTCTTCGGCTGACTTT 58.862 39.130 0.00 0.00 0.00 2.66
1917 2004 2.416893 GGACTCATTTTCTTCGGCTGAC 59.583 50.000 0.00 0.00 0.00 3.51
1923 2010 3.189287 CACCTTGGGACTCATTTTCTTCG 59.811 47.826 0.00 0.00 0.00 3.79
1933 2020 4.329545 TGCGGCACCTTGGGACTC 62.330 66.667 0.00 0.00 0.00 3.36
1934 2021 4.335647 CTGCGGCACCTTGGGACT 62.336 66.667 0.00 0.00 0.00 3.85
1935 2022 3.248446 TACTGCGGCACCTTGGGAC 62.248 63.158 0.00 0.00 0.00 4.46
1937 2024 2.746277 GTACTGCGGCACCTTGGG 60.746 66.667 0.00 0.00 0.00 4.12
1938 2025 1.577328 CTTGTACTGCGGCACCTTGG 61.577 60.000 0.00 0.00 0.00 3.61
1939 2026 1.577328 CCTTGTACTGCGGCACCTTG 61.577 60.000 0.00 0.00 0.00 3.61
1940 2027 1.302511 CCTTGTACTGCGGCACCTT 60.303 57.895 0.00 0.00 0.00 3.50
1941 2028 2.347490 CCTTGTACTGCGGCACCT 59.653 61.111 0.00 0.00 0.00 4.00
1942 2029 2.032071 ACCTTGTACTGCGGCACC 59.968 61.111 0.00 0.00 0.00 5.01
1943 2030 0.673644 ATGACCTTGTACTGCGGCAC 60.674 55.000 0.00 0.00 0.00 5.01
1944 2031 0.673333 CATGACCTTGTACTGCGGCA 60.673 55.000 1.29 1.29 0.00 5.69
1945 2032 0.673644 ACATGACCTTGTACTGCGGC 60.674 55.000 0.00 0.00 0.00 6.53
1946 2033 1.337728 TGACATGACCTTGTACTGCGG 60.338 52.381 0.00 0.00 0.00 5.69
1947 2034 1.995484 CTGACATGACCTTGTACTGCG 59.005 52.381 0.00 0.00 0.00 5.18
1948 2035 1.734465 GCTGACATGACCTTGTACTGC 59.266 52.381 0.00 0.00 0.00 4.40
1949 2036 2.738846 GTGCTGACATGACCTTGTACTG 59.261 50.000 0.00 0.00 0.00 2.74
1950 2037 2.610479 CGTGCTGACATGACCTTGTACT 60.610 50.000 0.00 0.00 34.49 2.73
1951 2038 1.726791 CGTGCTGACATGACCTTGTAC 59.273 52.381 0.00 0.00 34.49 2.90
1952 2039 1.616374 TCGTGCTGACATGACCTTGTA 59.384 47.619 0.00 0.00 36.89 2.41
1953 2040 0.392706 TCGTGCTGACATGACCTTGT 59.607 50.000 0.00 0.00 36.89 3.16
1954 2041 1.730501 ATCGTGCTGACATGACCTTG 58.269 50.000 0.00 0.00 44.46 3.61
1955 2042 2.479566 AATCGTGCTGACATGACCTT 57.520 45.000 0.00 0.00 44.46 3.50
1956 2043 2.027745 AGAAATCGTGCTGACATGACCT 60.028 45.455 0.00 0.00 44.46 3.85
1957 2044 2.349886 GAGAAATCGTGCTGACATGACC 59.650 50.000 0.00 0.00 44.46 4.02
1958 2045 3.257393 AGAGAAATCGTGCTGACATGAC 58.743 45.455 0.00 0.00 44.46 3.06
1959 2046 3.599730 AGAGAAATCGTGCTGACATGA 57.400 42.857 0.00 0.00 45.68 3.07
1960 2047 3.434641 ACAAGAGAAATCGTGCTGACATG 59.565 43.478 0.00 0.00 0.00 3.21
1961 2048 3.434641 CACAAGAGAAATCGTGCTGACAT 59.565 43.478 0.00 0.00 0.00 3.06
1962 2049 2.802247 CACAAGAGAAATCGTGCTGACA 59.198 45.455 0.00 0.00 0.00 3.58
1963 2050 3.059884 TCACAAGAGAAATCGTGCTGAC 58.940 45.455 0.00 0.00 0.00 3.51
1964 2051 3.385193 TCACAAGAGAAATCGTGCTGA 57.615 42.857 0.00 0.00 0.00 4.26
1965 2052 3.496130 AGTTCACAAGAGAAATCGTGCTG 59.504 43.478 0.00 0.00 0.00 4.41
1966 2053 3.733337 AGTTCACAAGAGAAATCGTGCT 58.267 40.909 0.00 0.00 0.00 4.40
1967 2054 4.474226 AAGTTCACAAGAGAAATCGTGC 57.526 40.909 0.00 0.00 0.00 5.34
1968 2055 6.537566 CCATAAGTTCACAAGAGAAATCGTG 58.462 40.000 0.00 0.00 0.00 4.35
1969 2056 5.122396 GCCATAAGTTCACAAGAGAAATCGT 59.878 40.000 0.00 0.00 0.00 3.73
1970 2057 5.122239 TGCCATAAGTTCACAAGAGAAATCG 59.878 40.000 0.00 0.00 0.00 3.34
2095 2182 0.036732 TGTGAGTGCCCATCAGGAAC 59.963 55.000 0.00 0.00 46.24 3.62
2142 2229 2.235650 CTGGGAGCATCTCACTGAGAAA 59.764 50.000 12.83 0.00 36.46 2.52
2172 2259 1.005450 GCCTCCCCAACCTGAACAATA 59.995 52.381 0.00 0.00 0.00 1.90
2339 2426 3.624861 ACTTGAATCATCTTCATCGGCAC 59.375 43.478 0.00 0.00 0.00 5.01
2405 2495 5.353956 TGCATCAGTATATGTTCACCACAAC 59.646 40.000 0.00 0.00 39.50 3.32
2422 2512 4.403585 TCTTCAGAATCTCCTGCATCAG 57.596 45.455 0.00 0.00 34.28 2.90
2478 2568 4.900635 AGAAAACTCTGCAAACGTCATT 57.099 36.364 0.00 0.00 0.00 2.57
2511 2601 5.261216 CCTCCACCACCATAATACTGTTTT 58.739 41.667 0.00 0.00 0.00 2.43
2516 2606 2.487775 TGCCTCCACCACCATAATACT 58.512 47.619 0.00 0.00 0.00 2.12
2544 2634 5.699458 CCATACGTCTTCTGGTTAACTGTTT 59.301 40.000 5.42 0.00 0.00 2.83
2654 2747 7.370383 ACAAAGATAAAAAGTGCATACTGTGG 58.630 34.615 0.00 0.00 37.19 4.17
2696 2873 3.806257 GTGACTTCACAACTGCACG 57.194 52.632 4.43 0.00 45.75 5.34
2718 2914 2.287009 CCAGCACTTTTGAGGTCGAAAC 60.287 50.000 0.00 0.00 0.00 2.78
2752 2948 9.434559 GCTAAACTTACTAACACAAGAACTTTG 57.565 33.333 0.00 0.00 0.00 2.77
2863 3150 4.649692 AGAAACTGAGAATGCAGACACAT 58.350 39.130 0.00 0.00 39.20 3.21
2931 3220 9.476202 TCGATCATATGATACTTTAACACCTTG 57.524 33.333 18.19 0.00 34.37 3.61
2947 3296 8.159344 TCCTGCTACTGTATATCGATCATATG 57.841 38.462 0.00 0.00 0.00 1.78
2975 3324 3.444703 ACGAACCAGAGAGATACATGC 57.555 47.619 0.00 0.00 0.00 4.06
3048 3397 2.496899 TTGCTGGACAGATTTCCTCC 57.503 50.000 3.00 0.00 36.51 4.30
3088 3437 0.978151 TCATTTGCAGCTGGGCATTT 59.022 45.000 17.12 0.00 44.48 2.32
3144 3505 5.308825 TCTGCAGTCTTAGAAAGAAAAGGG 58.691 41.667 14.67 0.00 39.67 3.95
3163 3526 0.533755 CCCACCATTCGGATCTCTGC 60.534 60.000 0.00 0.00 35.59 4.26
3164 3527 0.833287 ACCCACCATTCGGATCTCTG 59.167 55.000 0.00 0.00 35.59 3.35
3200 3563 7.040409 ACACCTCTGATCTGGAACAAAATTAAC 60.040 37.037 0.00 0.00 38.70 2.01
3287 3664 5.184479 ACAGTGGAATTGAATGATTCACAGG 59.816 40.000 7.48 1.40 39.87 4.00
3374 3751 4.083271 GGAAAACAAGATAGACCACACTGC 60.083 45.833 0.00 0.00 0.00 4.40
3407 3785 4.148079 AGACATAGATCATCCTCGCTCAA 58.852 43.478 0.00 0.00 0.00 3.02
3426 3804 3.658709 AGCTCTGCACTTTACAAGAGAC 58.341 45.455 2.81 0.00 0.00 3.36
3445 3823 4.678509 TCACGGTGACAATTAATCAAGC 57.321 40.909 6.76 0.00 0.00 4.01
3448 3826 5.943416 AGGAAATCACGGTGACAATTAATCA 59.057 36.000 13.92 0.00 0.00 2.57
3453 3831 2.228822 GCAGGAAATCACGGTGACAATT 59.771 45.455 13.92 9.01 0.00 2.32
3464 3842 9.693739 TTAAAGGTATAATTCAGCAGGAAATCA 57.306 29.630 0.00 0.00 39.39 2.57
3511 3890 6.812481 TTCATCTTCGATGAAACATACTCG 57.188 37.500 14.85 0.00 35.35 4.18
3526 3905 6.593382 GGCAGAGATACCACATATTCATCTTC 59.407 42.308 0.00 0.00 0.00 2.87


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

AutoCloner maintained by Alex Coulton.