Multiple sequence alignment - TraesCS1B01G332100

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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 TraesCS1B01G332100 chr1B 100.000 2717 0 0 1 2717 558222957 558225673 0.000000e+00 5018.0
1 TraesCS1B01G332100 chr1B 96.308 650 24 0 20 669 642985709 642985060 0.000000e+00 1068.0
2 TraesCS1B01G332100 chr1B 84.966 439 47 9 1307 1743 558504674 558505095 6.950000e-116 427.0
3 TraesCS1B01G332100 chr1B 79.149 235 32 15 1997 2229 558505278 558505497 2.180000e-31 147.0
4 TraesCS1B01G332100 chr1A 94.595 851 43 3 894 1743 510450329 510451177 0.000000e+00 1314.0
5 TraesCS1B01G332100 chr1A 89.857 907 66 6 1827 2717 510451197 510452093 0.000000e+00 1142.0
6 TraesCS1B01G332100 chr1A 93.284 134 7 2 1610 1743 510816702 510816833 2.130000e-46 196.0
7 TraesCS1B01G332100 chr1A 91.667 60 5 0 1774 1833 62352758 62352699 1.730000e-12 84.2
8 TraesCS1B01G332100 chr1D 94.021 853 46 5 893 1743 413697294 413698143 0.000000e+00 1288.0
9 TraesCS1B01G332100 chr1D 90.879 899 57 9 1829 2717 413698166 413699049 0.000000e+00 1182.0
10 TraesCS1B01G332100 chr1D 94.464 289 15 1 1314 1602 403709932 403709645 6.900000e-121 444.0
11 TraesCS1B01G332100 chr1D 80.347 519 77 14 962 1477 413791107 413791603 1.190000e-98 370.0
12 TraesCS1B01G332100 chr1D 91.667 60 5 0 1774 1833 416663281 416663222 1.730000e-12 84.2
13 TraesCS1B01G332100 chr1D 89.231 65 5 2 1997 2060 413811075 413811138 2.240000e-11 80.5
14 TraesCS1B01G332100 chr6B 97.758 669 15 0 1 669 487807556 487806888 0.000000e+00 1153.0
15 TraesCS1B01G332100 chr4B 96.997 666 20 0 1 666 434336259 434336924 0.000000e+00 1120.0
16 TraesCS1B01G332100 chr4B 96.861 669 21 0 1 669 500285304 500284636 0.000000e+00 1120.0
17 TraesCS1B01G332100 chr4B 95.195 666 30 1 1 666 545968574 545969237 0.000000e+00 1051.0
18 TraesCS1B01G332100 chr4B 91.803 61 4 1 1770 1830 186590798 186590739 1.730000e-12 84.2
19 TraesCS1B01G332100 chr3B 96.697 666 21 1 1 666 822745837 822746501 0.000000e+00 1107.0
20 TraesCS1B01G332100 chr3B 90.312 640 58 3 34 669 760400055 760399416 0.000000e+00 835.0
21 TraesCS1B01G332100 chr3B 91.935 62 3 2 1770 1830 188420059 188419999 4.820000e-13 86.1
22 TraesCS1B01G332100 chr3B 91.803 61 4 1 1770 1830 173375741 173375800 1.730000e-12 84.2
23 TraesCS1B01G332100 chr3B 79.487 117 18 5 682 794 357700374 357700488 8.070000e-11 78.7
24 TraesCS1B01G332100 chr3B 78.992 119 19 5 682 796 795047993 795048109 2.900000e-10 76.8
25 TraesCS1B01G332100 chr2B 95.115 655 31 1 13 666 528789043 528789697 0.000000e+00 1031.0
26 TraesCS1B01G332100 chr2B 90.801 674 48 9 1 669 157040075 157039411 0.000000e+00 889.0
27 TraesCS1B01G332100 chr2B 91.667 60 5 0 1774 1833 58987047 58986988 1.730000e-12 84.2
28 TraesCS1B01G332100 chr6D 95.502 289 12 1 1314 1602 58039178 58038891 6.850000e-126 460.0
29 TraesCS1B01G332100 chr6D 92.982 57 4 0 1774 1830 470972960 470972904 1.730000e-12 84.2
30 TraesCS1B01G332100 chr2D 95.156 289 13 1 1314 1602 423279301 423279014 3.190000e-124 455.0
31 TraesCS1B01G332100 chr2D 97.222 36 1 0 1745 1780 427606255 427606290 8.120000e-06 62.1
32 TraesCS1B01G332100 chr2D 97.222 36 1 0 1745 1780 630992294 630992259 8.120000e-06 62.1
33 TraesCS1B01G332100 chr2A 93.220 59 4 0 1774 1832 148025401 148025459 1.340000e-13 87.9
34 TraesCS1B01G332100 chr2A 83.750 80 11 1 1774 1851 63157332 63157253 1.040000e-09 75.0
35 TraesCS1B01G332100 chr2A 93.182 44 3 0 1740 1783 705594332 705594289 6.280000e-07 65.8
36 TraesCS1B01G332100 chr7D 79.845 129 17 9 673 796 158952730 158952606 4.820000e-13 86.1
37 TraesCS1B01G332100 chr7D 97.368 38 1 0 1745 1782 111077550 111077587 6.280000e-07 65.8
38 TraesCS1B01G332100 chr7D 97.222 36 1 0 1745 1780 166263709 166263744 8.120000e-06 62.1
39 TraesCS1B01G332100 chrUn 80.208 96 15 4 682 775 250542980 250543073 4.850000e-08 69.4
40 TraesCS1B01G332100 chrUn 80.208 96 15 4 682 775 261957065 261957158 4.850000e-08 69.4
41 TraesCS1B01G332100 chr6A 95.122 41 2 0 1740 1780 4728931 4728891 6.280000e-07 65.8
42 TraesCS1B01G332100 chr7B 95.000 40 2 0 1744 1783 749484869 749484908 2.260000e-06 63.9
43 TraesCS1B01G332100 chr4D 97.297 37 1 0 1744 1780 206663173 206663137 2.260000e-06 63.9
44 TraesCS1B01G332100 chr5D 97.222 36 1 0 1745 1780 412585966 412585931 8.120000e-06 62.1
45 TraesCS1B01G332100 chr5B 94.737 38 2 0 1745 1782 682036370 682036333 2.920000e-05 60.2
46 TraesCS1B01G332100 chr5B 94.737 38 2 0 1745 1782 682074750 682074713 2.920000e-05 60.2
47 TraesCS1B01G332100 chr5B 94.737 38 2 0 1745 1782 682089587 682089550 2.920000e-05 60.2
48 TraesCS1B01G332100 chr5B 94.737 38 2 0 1745 1782 682127414 682127377 2.920000e-05 60.2
49 TraesCS1B01G332100 chr3D 97.143 35 1 0 1745 1779 204187793 204187827 2.920000e-05 60.2
50 TraesCS1B01G332100 chr7A 94.595 37 2 0 1747 1783 2815335 2815299 1.050000e-04 58.4


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 TraesCS1B01G332100 chr1B 558222957 558225673 2716 False 5018 5018 100.0000 1 2717 1 chr1B.!!$F1 2716
1 TraesCS1B01G332100 chr1B 642985060 642985709 649 True 1068 1068 96.3080 20 669 1 chr1B.!!$R1 649
2 TraesCS1B01G332100 chr1B 558504674 558505497 823 False 287 427 82.0575 1307 2229 2 chr1B.!!$F2 922
3 TraesCS1B01G332100 chr1A 510450329 510452093 1764 False 1228 1314 92.2260 894 2717 2 chr1A.!!$F2 1823
4 TraesCS1B01G332100 chr1D 413697294 413699049 1755 False 1235 1288 92.4500 893 2717 2 chr1D.!!$F3 1824
5 TraesCS1B01G332100 chr6B 487806888 487807556 668 True 1153 1153 97.7580 1 669 1 chr6B.!!$R1 668
6 TraesCS1B01G332100 chr4B 434336259 434336924 665 False 1120 1120 96.9970 1 666 1 chr4B.!!$F1 665
7 TraesCS1B01G332100 chr4B 500284636 500285304 668 True 1120 1120 96.8610 1 669 1 chr4B.!!$R2 668
8 TraesCS1B01G332100 chr4B 545968574 545969237 663 False 1051 1051 95.1950 1 666 1 chr4B.!!$F2 665
9 TraesCS1B01G332100 chr3B 822745837 822746501 664 False 1107 1107 96.6970 1 666 1 chr3B.!!$F4 665
10 TraesCS1B01G332100 chr3B 760399416 760400055 639 True 835 835 90.3120 34 669 1 chr3B.!!$R2 635
11 TraesCS1B01G332100 chr2B 528789043 528789697 654 False 1031 1031 95.1150 13 666 1 chr2B.!!$F1 653
12 TraesCS1B01G332100 chr2B 157039411 157040075 664 True 889 889 90.8010 1 669 1 chr2B.!!$R2 668

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
879 885 0.945099 TTGTTCGTTGTATTGCCGCA 59.055 45.0 0.0 0.0 0.0 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2429 2488 0.031178 CAAGTGCTTGTGGGAAGTGC 59.969 55.0 3.91 0.0 35.92 4.4 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
263 269 6.036953 CGATCTTGAGCTAGCTTCATTTTCTT 59.963 38.462 20.42 0.00 0.00 2.52
493 499 4.954118 AGTGCGGGTCCCAGGTGA 62.954 66.667 9.12 0.00 0.00 4.02
549 555 2.125106 GCGAGAGGGCAACGGAAT 60.125 61.111 0.00 0.00 37.60 3.01
554 560 2.741878 CGAGAGGGCAACGGAATAACAT 60.742 50.000 0.00 0.00 37.60 2.71
640 646 1.949525 CAATATTGGCCGAAGTGGGAG 59.050 52.381 7.62 0.00 38.63 4.30
669 675 4.037690 CACGAAAAAGTTGCCAGAAGAAG 58.962 43.478 0.00 0.00 0.00 2.85
670 676 3.066760 ACGAAAAAGTTGCCAGAAGAAGG 59.933 43.478 0.00 0.00 0.00 3.46
681 687 3.905784 CCAGAAGAAGGCAACATTTGAC 58.094 45.455 0.00 0.00 39.66 3.18
682 688 3.558505 CAGAAGAAGGCAACATTTGACG 58.441 45.455 0.00 0.00 45.70 4.35
683 689 3.250762 CAGAAGAAGGCAACATTTGACGA 59.749 43.478 0.00 0.00 45.70 4.20
684 690 3.251004 AGAAGAAGGCAACATTTGACGAC 59.749 43.478 0.00 0.00 45.70 4.34
685 691 2.851195 AGAAGGCAACATTTGACGACT 58.149 42.857 0.00 0.00 45.70 4.18
686 692 3.214328 AGAAGGCAACATTTGACGACTT 58.786 40.909 0.00 0.00 45.70 3.01
687 693 3.003689 AGAAGGCAACATTTGACGACTTG 59.996 43.478 0.00 0.00 45.70 3.16
688 694 2.297701 AGGCAACATTTGACGACTTGT 58.702 42.857 0.00 0.00 45.70 3.16
689 695 2.687935 AGGCAACATTTGACGACTTGTT 59.312 40.909 0.00 0.00 45.70 2.83
690 696 3.130340 AGGCAACATTTGACGACTTGTTT 59.870 39.130 0.00 0.00 45.70 2.83
691 697 3.862845 GGCAACATTTGACGACTTGTTTT 59.137 39.130 0.00 0.00 30.23 2.43
692 698 4.328712 GGCAACATTTGACGACTTGTTTTT 59.671 37.500 0.00 0.00 30.23 1.94
713 719 5.596836 TTTTGAGACAGGTCAAAATGCTT 57.403 34.783 7.51 0.00 46.57 3.91
714 720 6.707440 TTTTGAGACAGGTCAAAATGCTTA 57.293 33.333 7.51 0.00 46.57 3.09
715 721 6.707440 TTTGAGACAGGTCAAAATGCTTAA 57.293 33.333 1.84 0.00 42.22 1.85
716 722 5.947228 TGAGACAGGTCAAAATGCTTAAG 57.053 39.130 0.00 0.00 0.00 1.85
717 723 4.761739 TGAGACAGGTCAAAATGCTTAAGG 59.238 41.667 4.29 0.00 0.00 2.69
718 724 4.082125 AGACAGGTCAAAATGCTTAAGGG 58.918 43.478 4.29 0.00 0.00 3.95
719 725 3.826729 GACAGGTCAAAATGCTTAAGGGT 59.173 43.478 4.29 0.00 0.00 4.34
720 726 4.223144 ACAGGTCAAAATGCTTAAGGGTT 58.777 39.130 4.29 0.00 0.00 4.11
721 727 4.653801 ACAGGTCAAAATGCTTAAGGGTTT 59.346 37.500 4.29 0.00 0.00 3.27
722 728 5.221441 ACAGGTCAAAATGCTTAAGGGTTTC 60.221 40.000 4.29 0.00 0.00 2.78
723 729 4.283467 AGGTCAAAATGCTTAAGGGTTTCC 59.717 41.667 4.29 0.00 0.00 3.13
724 730 4.562757 GGTCAAAATGCTTAAGGGTTTCCC 60.563 45.833 4.29 0.00 45.90 3.97
754 760 7.481275 AAAATTGAAGTAGCATTTGGTTGTG 57.519 32.000 0.00 0.00 0.00 3.33
755 761 6.403866 AATTGAAGTAGCATTTGGTTGTGA 57.596 33.333 0.00 0.00 0.00 3.58
756 762 4.829064 TGAAGTAGCATTTGGTTGTGAC 57.171 40.909 0.00 0.00 0.00 3.67
757 763 4.203226 TGAAGTAGCATTTGGTTGTGACA 58.797 39.130 0.00 0.00 0.00 3.58
758 764 4.642437 TGAAGTAGCATTTGGTTGTGACAA 59.358 37.500 0.00 0.00 0.00 3.18
759 765 5.301551 TGAAGTAGCATTTGGTTGTGACAAT 59.698 36.000 0.00 0.00 0.00 2.71
760 766 5.125100 AGTAGCATTTGGTTGTGACAATG 57.875 39.130 0.00 0.00 0.00 2.82
761 767 4.826733 AGTAGCATTTGGTTGTGACAATGA 59.173 37.500 0.00 0.00 0.00 2.57
762 768 4.669206 AGCATTTGGTTGTGACAATGAA 57.331 36.364 0.00 0.00 0.00 2.57
763 769 4.370917 AGCATTTGGTTGTGACAATGAAC 58.629 39.130 0.00 0.00 0.00 3.18
764 770 4.118410 GCATTTGGTTGTGACAATGAACA 58.882 39.130 0.00 0.00 0.00 3.18
765 771 4.025813 GCATTTGGTTGTGACAATGAACAC 60.026 41.667 0.00 7.92 37.51 3.32
766 772 4.790765 TTTGGTTGTGACAATGAACACA 57.209 36.364 0.00 11.92 43.73 3.72
767 773 4.998671 TTGGTTGTGACAATGAACACAT 57.001 36.364 15.15 0.00 44.56 3.21
768 774 4.998671 TGGTTGTGACAATGAACACATT 57.001 36.364 15.15 0.00 44.56 2.71
769 775 6.456795 TTGGTTGTGACAATGAACACATTA 57.543 33.333 15.15 3.46 44.56 1.90
770 776 6.647334 TGGTTGTGACAATGAACACATTAT 57.353 33.333 15.15 0.00 44.56 1.28
771 777 7.048629 TGGTTGTGACAATGAACACATTATT 57.951 32.000 15.15 0.00 44.56 1.40
772 778 7.495901 TGGTTGTGACAATGAACACATTATTT 58.504 30.769 15.15 0.00 44.56 1.40
773 779 7.984050 TGGTTGTGACAATGAACACATTATTTT 59.016 29.630 15.15 0.00 44.56 1.82
774 780 8.825745 GGTTGTGACAATGAACACATTATTTTT 58.174 29.630 15.15 0.00 44.56 1.94
802 808 9.593134 TTGTTTTGACATTTGCAAAATACTACT 57.407 25.926 17.19 0.00 44.22 2.57
808 814 8.865978 TGACATTTGCAAAATACTACTAGTACG 58.134 33.333 17.19 0.00 32.84 3.67
809 815 8.767478 ACATTTGCAAAATACTACTAGTACGT 57.233 30.769 17.19 4.58 32.84 3.57
810 816 9.211485 ACATTTGCAAAATACTACTAGTACGTT 57.789 29.630 17.19 0.00 32.84 3.99
811 817 9.685005 CATTTGCAAAATACTACTAGTACGTTC 57.315 33.333 17.19 0.00 32.84 3.95
812 818 9.649167 ATTTGCAAAATACTACTAGTACGTTCT 57.351 29.630 17.19 0.00 32.84 3.01
813 819 8.456904 TTGCAAAATACTACTAGTACGTTCTG 57.543 34.615 4.78 0.00 32.84 3.02
814 820 7.031372 TGCAAAATACTACTAGTACGTTCTGG 58.969 38.462 4.78 4.37 32.84 3.86
815 821 7.094248 TGCAAAATACTACTAGTACGTTCTGGA 60.094 37.037 12.38 0.00 32.84 3.86
816 822 7.431668 GCAAAATACTACTAGTACGTTCTGGAG 59.568 40.741 12.38 7.30 32.84 3.86
817 823 6.616774 AATACTACTAGTACGTTCTGGAGC 57.383 41.667 12.38 0.00 32.84 4.70
818 824 3.277715 ACTACTAGTACGTTCTGGAGCC 58.722 50.000 12.38 0.00 0.00 4.70
819 825 2.211250 ACTAGTACGTTCTGGAGCCA 57.789 50.000 12.38 0.00 0.00 4.75
820 826 2.522185 ACTAGTACGTTCTGGAGCCAA 58.478 47.619 12.38 0.00 0.00 4.52
821 827 2.895404 ACTAGTACGTTCTGGAGCCAAA 59.105 45.455 12.38 0.00 0.00 3.28
822 828 3.514309 ACTAGTACGTTCTGGAGCCAAAT 59.486 43.478 12.38 0.00 0.00 2.32
823 829 3.418684 AGTACGTTCTGGAGCCAAATT 57.581 42.857 0.00 0.00 0.00 1.82
824 830 3.074412 AGTACGTTCTGGAGCCAAATTG 58.926 45.455 0.00 0.00 0.00 2.32
825 831 1.247567 ACGTTCTGGAGCCAAATTGG 58.752 50.000 7.84 7.84 41.55 3.16
826 832 1.202879 ACGTTCTGGAGCCAAATTGGA 60.203 47.619 17.47 0.00 40.96 3.53
827 833 2.094675 CGTTCTGGAGCCAAATTGGAT 58.905 47.619 17.47 10.02 39.95 3.41
828 834 2.493278 CGTTCTGGAGCCAAATTGGATT 59.507 45.455 17.47 2.34 35.51 3.01
829 835 3.056607 CGTTCTGGAGCCAAATTGGATTT 60.057 43.478 17.47 0.00 35.51 2.17
830 836 4.498241 GTTCTGGAGCCAAATTGGATTTC 58.502 43.478 17.47 9.37 35.51 2.17
831 837 2.754552 TCTGGAGCCAAATTGGATTTCG 59.245 45.455 17.47 1.84 35.51 3.46
832 838 2.754552 CTGGAGCCAAATTGGATTTCGA 59.245 45.455 17.47 6.22 35.51 3.71
833 839 3.364549 TGGAGCCAAATTGGATTTCGAT 58.635 40.909 17.47 0.00 35.51 3.59
834 840 4.531854 TGGAGCCAAATTGGATTTCGATA 58.468 39.130 17.47 0.00 35.51 2.92
835 841 5.139727 TGGAGCCAAATTGGATTTCGATAT 58.860 37.500 17.47 0.00 35.51 1.63
836 842 5.241506 TGGAGCCAAATTGGATTTCGATATC 59.758 40.000 17.47 7.27 35.51 1.63
837 843 5.335976 GGAGCCAAATTGGATTTCGATATCC 60.336 44.000 23.51 23.51 35.51 2.59
846 852 5.485209 GGATTTCGATATCCAGGTAAGGT 57.515 43.478 24.82 0.00 43.04 3.50
847 853 5.866207 GGATTTCGATATCCAGGTAAGGTT 58.134 41.667 24.82 0.00 43.04 3.50
848 854 6.296803 GGATTTCGATATCCAGGTAAGGTTT 58.703 40.000 24.82 0.00 43.04 3.27
849 855 6.204882 GGATTTCGATATCCAGGTAAGGTTTG 59.795 42.308 24.82 0.00 43.04 2.93
850 856 5.687166 TTCGATATCCAGGTAAGGTTTGT 57.313 39.130 0.00 0.00 0.00 2.83
851 857 5.687166 TCGATATCCAGGTAAGGTTTGTT 57.313 39.130 0.00 0.00 0.00 2.83
852 858 6.057321 TCGATATCCAGGTAAGGTTTGTTT 57.943 37.500 0.00 0.00 0.00 2.83
853 859 5.878116 TCGATATCCAGGTAAGGTTTGTTTG 59.122 40.000 0.00 0.00 0.00 2.93
854 860 5.646360 CGATATCCAGGTAAGGTTTGTTTGT 59.354 40.000 0.00 0.00 0.00 2.83
855 861 6.150474 CGATATCCAGGTAAGGTTTGTTTGTT 59.850 38.462 0.00 0.00 0.00 2.83
856 862 7.308951 CGATATCCAGGTAAGGTTTGTTTGTTT 60.309 37.037 0.00 0.00 0.00 2.83
857 863 5.331876 TCCAGGTAAGGTTTGTTTGTTTG 57.668 39.130 0.00 0.00 0.00 2.93
858 864 4.773149 TCCAGGTAAGGTTTGTTTGTTTGT 59.227 37.500 0.00 0.00 0.00 2.83
859 865 5.246429 TCCAGGTAAGGTTTGTTTGTTTGTT 59.754 36.000 0.00 0.00 0.00 2.83
860 866 5.935206 CCAGGTAAGGTTTGTTTGTTTGTTT 59.065 36.000 0.00 0.00 0.00 2.83
861 867 6.428465 CCAGGTAAGGTTTGTTTGTTTGTTTT 59.572 34.615 0.00 0.00 0.00 2.43
862 868 7.294473 CAGGTAAGGTTTGTTTGTTTGTTTTG 58.706 34.615 0.00 0.00 0.00 2.44
863 869 6.993308 AGGTAAGGTTTGTTTGTTTGTTTTGT 59.007 30.769 0.00 0.00 0.00 2.83
864 870 7.499563 AGGTAAGGTTTGTTTGTTTGTTTTGTT 59.500 29.630 0.00 0.00 0.00 2.83
865 871 7.799447 GGTAAGGTTTGTTTGTTTGTTTTGTTC 59.201 33.333 0.00 0.00 0.00 3.18
866 872 5.980025 AGGTTTGTTTGTTTGTTTTGTTCG 58.020 33.333 0.00 0.00 0.00 3.95
867 873 5.524281 AGGTTTGTTTGTTTGTTTTGTTCGT 59.476 32.000 0.00 0.00 0.00 3.85
868 874 6.037281 AGGTTTGTTTGTTTGTTTTGTTCGTT 59.963 30.769 0.00 0.00 0.00 3.85
869 875 6.139325 GGTTTGTTTGTTTGTTTTGTTCGTTG 59.861 34.615 0.00 0.00 0.00 4.10
870 876 5.968387 TGTTTGTTTGTTTTGTTCGTTGT 57.032 30.435 0.00 0.00 0.00 3.32
871 877 7.459394 TTGTTTGTTTGTTTTGTTCGTTGTA 57.541 28.000 0.00 0.00 0.00 2.41
872 878 7.639162 TGTTTGTTTGTTTTGTTCGTTGTAT 57.361 28.000 0.00 0.00 0.00 2.29
873 879 8.073355 TGTTTGTTTGTTTTGTTCGTTGTATT 57.927 26.923 0.00 0.00 0.00 1.89
874 880 8.004344 TGTTTGTTTGTTTTGTTCGTTGTATTG 58.996 29.630 0.00 0.00 0.00 1.90
875 881 6.083925 TGTTTGTTTTGTTCGTTGTATTGC 57.916 33.333 0.00 0.00 0.00 3.56
876 882 5.062308 TGTTTGTTTTGTTCGTTGTATTGCC 59.938 36.000 0.00 0.00 0.00 4.52
877 883 3.364062 TGTTTTGTTCGTTGTATTGCCG 58.636 40.909 0.00 0.00 0.00 5.69
878 884 2.039327 TTTGTTCGTTGTATTGCCGC 57.961 45.000 0.00 0.00 0.00 6.53
879 885 0.945099 TTGTTCGTTGTATTGCCGCA 59.055 45.000 0.00 0.00 0.00 5.69
880 886 0.945099 TGTTCGTTGTATTGCCGCAA 59.055 45.000 8.55 8.55 0.00 4.85
881 887 1.333931 TGTTCGTTGTATTGCCGCAAA 59.666 42.857 10.42 0.00 0.00 3.68
882 888 2.223502 TGTTCGTTGTATTGCCGCAAAA 60.224 40.909 10.42 0.00 0.00 2.44
883 889 2.776312 TCGTTGTATTGCCGCAAAAA 57.224 40.000 10.42 2.67 0.00 1.94
979 985 1.444917 CTCCGATCATCCCGTGACGA 61.445 60.000 6.54 0.00 40.28 4.20
988 994 1.592669 CCCGTGACGAGCATGATCC 60.593 63.158 6.54 0.00 35.44 3.36
994 1000 1.337728 TGACGAGCATGATCCAAACGT 60.338 47.619 5.18 0.00 35.31 3.99
995 1001 2.094442 TGACGAGCATGATCCAAACGTA 60.094 45.455 5.18 0.00 32.88 3.57
997 1003 2.671396 ACGAGCATGATCCAAACGTAAC 59.329 45.455 5.18 0.00 0.00 2.50
1050 1057 1.596934 GGTGGATCAGCGAGTCCAA 59.403 57.895 8.29 0.00 45.50 3.53
1142 1149 1.984570 TCTCCACCTCCTGCTTCCG 60.985 63.158 0.00 0.00 0.00 4.30
1288 1295 3.710722 CCACGCTGGCTTCCTCCT 61.711 66.667 0.00 0.00 0.00 3.69
1296 1303 0.837272 TGGCTTCCTCCTTATTCCCG 59.163 55.000 0.00 0.00 0.00 5.14
1727 1744 0.618458 TCAGAGTAATGGCACCACCC 59.382 55.000 0.00 0.00 37.83 4.61
1743 1760 2.202932 CCCTGAACCCGCGATGAG 60.203 66.667 8.23 0.00 0.00 2.90
1744 1761 2.579201 CCTGAACCCGCGATGAGT 59.421 61.111 8.23 0.00 0.00 3.41
1746 1763 1.361668 CCTGAACCCGCGATGAGTTG 61.362 60.000 8.23 0.00 0.00 3.16
1747 1764 0.670546 CTGAACCCGCGATGAGTTGT 60.671 55.000 8.23 0.00 0.00 3.32
1748 1765 0.604073 TGAACCCGCGATGAGTTGTA 59.396 50.000 8.23 0.00 0.00 2.41
1749 1766 1.001068 TGAACCCGCGATGAGTTGTAA 59.999 47.619 8.23 0.00 0.00 2.41
1751 1768 1.651987 ACCCGCGATGAGTTGTAATG 58.348 50.000 8.23 0.00 0.00 1.90
1752 1769 0.937304 CCCGCGATGAGTTGTAATGG 59.063 55.000 8.23 0.00 0.00 3.16
1753 1770 0.937304 CCGCGATGAGTTGTAATGGG 59.063 55.000 8.23 0.00 0.00 4.00
1754 1771 0.937304 CGCGATGAGTTGTAATGGGG 59.063 55.000 0.00 0.00 0.00 4.96
1755 1772 1.472552 CGCGATGAGTTGTAATGGGGA 60.473 52.381 0.00 0.00 0.00 4.81
1756 1773 2.213499 GCGATGAGTTGTAATGGGGAG 58.787 52.381 0.00 0.00 0.00 4.30
1757 1774 2.213499 CGATGAGTTGTAATGGGGAGC 58.787 52.381 0.00 0.00 0.00 4.70
1758 1775 2.419990 CGATGAGTTGTAATGGGGAGCA 60.420 50.000 0.00 0.00 0.00 4.26
1759 1776 3.620488 GATGAGTTGTAATGGGGAGCAA 58.380 45.455 0.00 0.00 0.00 3.91
1760 1777 2.790433 TGAGTTGTAATGGGGAGCAAC 58.210 47.619 0.00 0.00 40.83 4.17
1762 1779 3.525800 AGTTGTAATGGGGAGCAACTT 57.474 42.857 0.00 0.00 46.18 2.66
1763 1780 3.421844 AGTTGTAATGGGGAGCAACTTC 58.578 45.455 0.00 0.00 46.18 3.01
1764 1781 3.074538 AGTTGTAATGGGGAGCAACTTCT 59.925 43.478 0.00 0.00 46.18 2.85
1765 1782 3.806949 TGTAATGGGGAGCAACTTCTT 57.193 42.857 0.00 0.00 0.00 2.52
1766 1783 4.919774 TGTAATGGGGAGCAACTTCTTA 57.080 40.909 0.00 0.00 0.00 2.10
1767 1784 5.249780 TGTAATGGGGAGCAACTTCTTAA 57.750 39.130 0.00 0.00 0.00 1.85
1768 1785 5.253330 TGTAATGGGGAGCAACTTCTTAAG 58.747 41.667 0.00 0.00 0.00 1.85
1769 1786 4.657814 AATGGGGAGCAACTTCTTAAGA 57.342 40.909 0.00 0.00 0.00 2.10
1770 1787 4.657814 ATGGGGAGCAACTTCTTAAGAA 57.342 40.909 16.85 16.85 0.00 2.52
1771 1788 4.657814 TGGGGAGCAACTTCTTAAGAAT 57.342 40.909 18.02 3.17 33.01 2.40
1772 1789 4.335416 TGGGGAGCAACTTCTTAAGAATG 58.665 43.478 18.02 14.95 33.01 2.67
1773 1790 4.202567 TGGGGAGCAACTTCTTAAGAATGT 60.203 41.667 18.02 14.48 33.01 2.71
1774 1791 5.013704 TGGGGAGCAACTTCTTAAGAATGTA 59.986 40.000 18.02 0.00 33.01 2.29
1775 1792 5.944007 GGGGAGCAACTTCTTAAGAATGTAA 59.056 40.000 18.02 0.00 33.01 2.41
1776 1793 6.094186 GGGGAGCAACTTCTTAAGAATGTAAG 59.906 42.308 18.02 8.78 33.01 2.34
1777 1794 6.879458 GGGAGCAACTTCTTAAGAATGTAAGA 59.121 38.462 18.02 0.00 38.14 2.10
1778 1795 7.554476 GGGAGCAACTTCTTAAGAATGTAAGAT 59.446 37.037 18.02 12.28 39.31 2.40
1779 1796 9.601217 GGAGCAACTTCTTAAGAATGTAAGATA 57.399 33.333 18.02 0.00 39.31 1.98
1800 1817 9.751542 AAGATAAGTCTAGATACAACCATTTCG 57.248 33.333 0.00 0.00 33.30 3.46
1801 1818 9.132923 AGATAAGTCTAGATACAACCATTTCGA 57.867 33.333 0.00 0.00 31.36 3.71
1802 1819 9.400638 GATAAGTCTAGATACAACCATTTCGAG 57.599 37.037 0.00 0.00 0.00 4.04
1803 1820 6.150396 AGTCTAGATACAACCATTTCGAGG 57.850 41.667 0.00 0.00 0.00 4.63
1804 1821 5.892119 AGTCTAGATACAACCATTTCGAGGA 59.108 40.000 0.00 0.00 0.00 3.71
1805 1822 6.551601 AGTCTAGATACAACCATTTCGAGGAT 59.448 38.462 0.00 0.00 0.00 3.24
1806 1823 7.724506 AGTCTAGATACAACCATTTCGAGGATA 59.275 37.037 0.00 0.00 0.00 2.59
1807 1824 8.358148 GTCTAGATACAACCATTTCGAGGATAA 58.642 37.037 0.00 0.00 0.00 1.75
1808 1825 8.920174 TCTAGATACAACCATTTCGAGGATAAA 58.080 33.333 0.00 0.00 0.00 1.40
1809 1826 9.712305 CTAGATACAACCATTTCGAGGATAAAT 57.288 33.333 0.00 0.00 0.00 1.40
1815 1832 8.630037 ACAACCATTTCGAGGATAAATATTTCC 58.370 33.333 3.39 0.68 0.00 3.13
1816 1833 7.435068 ACCATTTCGAGGATAAATATTTCCG 57.565 36.000 3.39 2.84 37.10 4.30
1817 1834 6.430000 ACCATTTCGAGGATAAATATTTCCGG 59.570 38.462 3.39 0.00 37.10 5.14
1818 1835 6.653320 CCATTTCGAGGATAAATATTTCCGGA 59.347 38.462 0.00 0.00 37.10 5.14
1819 1836 7.360946 CCATTTCGAGGATAAATATTTCCGGAC 60.361 40.741 1.83 0.00 37.10 4.79
1820 1837 4.801891 TCGAGGATAAATATTTCCGGACG 58.198 43.478 1.83 9.67 37.10 4.79
1821 1838 4.520111 TCGAGGATAAATATTTCCGGACGA 59.480 41.667 1.83 11.51 37.10 4.20
1822 1839 5.009911 TCGAGGATAAATATTTCCGGACGAA 59.990 40.000 1.83 0.00 37.10 3.85
1823 1840 5.345202 CGAGGATAAATATTTCCGGACGAAG 59.655 44.000 1.83 0.00 37.10 3.79
1824 1841 5.548406 AGGATAAATATTTCCGGACGAAGG 58.452 41.667 1.83 0.00 37.10 3.46
1825 1842 4.694037 GGATAAATATTTCCGGACGAAGGG 59.306 45.833 1.83 0.00 0.00 3.95
1835 1852 2.954318 CCGGACGAAGGGAGTAATTCTA 59.046 50.000 0.00 0.00 0.00 2.10
1975 1994 2.175811 GTGCCGGTTGCTTTAGCG 59.824 61.111 1.90 0.00 45.83 4.26
2022 2075 2.851195 AGTTCGATCCTTTTGCTGTGT 58.149 42.857 0.00 0.00 0.00 3.72
2149 2203 3.785038 GCAAACTTGTGCGCTTTTG 57.215 47.368 9.73 11.16 34.21 2.44
2157 2211 5.283060 ACTTGTGCGCTTTTGATAGTTAG 57.717 39.130 9.73 0.00 0.00 2.34
2228 2285 7.714377 ACAGAAATGTGTGAGGAAGATATGATC 59.286 37.037 0.00 0.00 0.00 2.92
2229 2286 7.713942 CAGAAATGTGTGAGGAAGATATGATCA 59.286 37.037 0.00 0.00 0.00 2.92
2230 2287 8.438373 AGAAATGTGTGAGGAAGATATGATCAT 58.562 33.333 13.81 13.81 0.00 2.45
2235 2292 9.716531 TGTGTGAGGAAGATATGATCATTTATC 57.283 33.333 14.65 11.63 34.93 1.75
2356 2414 6.261603 CCGGTCTTGTTTTAAGAAAGGTTAGT 59.738 38.462 0.00 0.00 0.00 2.24
2359 2417 9.297586 GGTCTTGTTTTAAGAAAGGTTAGTTTG 57.702 33.333 0.00 0.00 0.00 2.93
2387 2446 6.311735 AGTTACAAACATTGGTATCCAGGTT 58.688 36.000 0.00 0.00 35.44 3.50
2416 2475 3.509967 GGTGAAGACTAAAAACCCATGGG 59.490 47.826 30.23 30.23 42.03 4.00
2469 2543 5.560722 TGTCTGAAAACTATCAGGTCCAA 57.439 39.130 4.63 0.00 45.55 3.53
2471 2545 7.252612 TGTCTGAAAACTATCAGGTCCAATA 57.747 36.000 4.63 0.00 45.55 1.90
2526 2600 2.094234 GCCTGGACTCTGAAGAGAAGAC 60.094 54.545 14.20 2.24 44.74 3.01
2551 2625 2.182842 GGCTTGCCGTGCATCCTAG 61.183 63.158 0.00 0.00 38.76 3.02
2615 2689 4.139786 ACCTCCAATTTGATCATCATCCG 58.860 43.478 0.00 0.00 0.00 4.18
2651 2725 1.135402 GGCGCACAAATCCTAAACCTG 60.135 52.381 10.83 0.00 0.00 4.00
2682 2756 6.547141 TCTGCCCAAATGAGTCCTAATTATTG 59.453 38.462 0.00 0.00 0.00 1.90
2705 2779 6.430864 TGTACCATCCCAATGTTCAATGTAT 58.569 36.000 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 54 3.343788 CTCCGTGCACGTCTCTCCC 62.344 68.421 34.81 0.00 37.74 4.30
152 157 4.198890 CTAGCGAGCGAGCCTGCA 62.199 66.667 10.88 0.00 38.01 4.41
263 269 1.734137 GCGAGGTCTAAGGATGCGA 59.266 57.895 0.00 0.00 0.00 5.10
549 555 3.466836 GGAGGATGCGAATCACATGTTA 58.533 45.455 5.57 0.00 0.00 2.41
640 646 3.500680 TGGCAACTTTTTCGTGATAGACC 59.499 43.478 0.00 0.00 37.61 3.85
669 675 2.774439 ACAAGTCGTCAAATGTTGCC 57.226 45.000 0.00 0.00 0.00 4.52
670 676 5.448926 AAAAACAAGTCGTCAAATGTTGC 57.551 34.783 0.00 0.00 36.23 4.17
692 698 6.239008 CCTTAAGCATTTTGACCTGTCTCAAA 60.239 38.462 0.00 0.00 38.18 2.69
693 699 5.241506 CCTTAAGCATTTTGACCTGTCTCAA 59.758 40.000 0.00 0.00 0.00 3.02
694 700 4.761739 CCTTAAGCATTTTGACCTGTCTCA 59.238 41.667 0.00 0.00 0.00 3.27
695 701 4.156739 CCCTTAAGCATTTTGACCTGTCTC 59.843 45.833 0.00 0.00 0.00 3.36
696 702 4.082125 CCCTTAAGCATTTTGACCTGTCT 58.918 43.478 0.00 0.00 0.00 3.41
697 703 3.826729 ACCCTTAAGCATTTTGACCTGTC 59.173 43.478 0.00 0.00 0.00 3.51
698 704 3.844640 ACCCTTAAGCATTTTGACCTGT 58.155 40.909 0.00 0.00 0.00 4.00
699 705 4.871933 AACCCTTAAGCATTTTGACCTG 57.128 40.909 0.00 0.00 0.00 4.00
700 706 4.283467 GGAAACCCTTAAGCATTTTGACCT 59.717 41.667 0.00 0.00 0.00 3.85
701 707 4.566004 GGAAACCCTTAAGCATTTTGACC 58.434 43.478 0.00 0.00 0.00 4.02
729 735 7.768120 TCACAACCAAATGCTACTTCAATTTTT 59.232 29.630 0.00 0.00 0.00 1.94
730 736 7.224557 GTCACAACCAAATGCTACTTCAATTTT 59.775 33.333 0.00 0.00 0.00 1.82
731 737 6.701400 GTCACAACCAAATGCTACTTCAATTT 59.299 34.615 0.00 0.00 0.00 1.82
732 738 6.183360 TGTCACAACCAAATGCTACTTCAATT 60.183 34.615 0.00 0.00 0.00 2.32
733 739 5.301551 TGTCACAACCAAATGCTACTTCAAT 59.698 36.000 0.00 0.00 0.00 2.57
734 740 4.642437 TGTCACAACCAAATGCTACTTCAA 59.358 37.500 0.00 0.00 0.00 2.69
735 741 4.203226 TGTCACAACCAAATGCTACTTCA 58.797 39.130 0.00 0.00 0.00 3.02
736 742 4.829064 TGTCACAACCAAATGCTACTTC 57.171 40.909 0.00 0.00 0.00 3.01
737 743 5.301551 TCATTGTCACAACCAAATGCTACTT 59.698 36.000 0.00 0.00 0.00 2.24
738 744 4.826733 TCATTGTCACAACCAAATGCTACT 59.173 37.500 0.00 0.00 0.00 2.57
739 745 5.119931 TCATTGTCACAACCAAATGCTAC 57.880 39.130 0.00 0.00 0.00 3.58
740 746 5.068329 TGTTCATTGTCACAACCAAATGCTA 59.932 36.000 0.00 0.00 0.00 3.49
741 747 4.141981 TGTTCATTGTCACAACCAAATGCT 60.142 37.500 0.00 0.00 0.00 3.79
742 748 4.025813 GTGTTCATTGTCACAACCAAATGC 60.026 41.667 0.00 0.00 35.04 3.56
743 749 5.107824 TGTGTTCATTGTCACAACCAAATG 58.892 37.500 0.00 0.00 40.81 2.32
744 750 5.336150 TGTGTTCATTGTCACAACCAAAT 57.664 34.783 0.00 0.00 40.81 2.32
745 751 4.790765 TGTGTTCATTGTCACAACCAAA 57.209 36.364 0.00 0.00 40.81 3.28
746 752 4.998671 ATGTGTTCATTGTCACAACCAA 57.001 36.364 16.31 0.00 45.51 3.67
747 753 4.998671 AATGTGTTCATTGTCACAACCA 57.001 36.364 16.31 4.15 45.51 3.67
748 754 7.945033 AAATAATGTGTTCATTGTCACAACC 57.055 32.000 16.31 0.00 45.51 3.77
776 782 9.593134 AGTAGTATTTTGCAAATGTCAAAACAA 57.407 25.926 13.65 0.00 43.50 2.83
782 788 8.865978 CGTACTAGTAGTATTTTGCAAATGTCA 58.134 33.333 13.65 0.00 32.65 3.58
783 789 8.866956 ACGTACTAGTAGTATTTTGCAAATGTC 58.133 33.333 13.65 6.33 32.65 3.06
784 790 8.767478 ACGTACTAGTAGTATTTTGCAAATGT 57.233 30.769 13.65 7.72 32.65 2.71
785 791 9.685005 GAACGTACTAGTAGTATTTTGCAAATG 57.315 33.333 13.65 0.00 32.65 2.32
786 792 9.649167 AGAACGTACTAGTAGTATTTTGCAAAT 57.351 29.630 13.65 6.06 32.65 2.32
787 793 8.918658 CAGAACGTACTAGTAGTATTTTGCAAA 58.081 33.333 13.09 8.05 32.65 3.68
788 794 7.543172 CCAGAACGTACTAGTAGTATTTTGCAA 59.457 37.037 13.09 0.00 32.65 4.08
789 795 7.031372 CCAGAACGTACTAGTAGTATTTTGCA 58.969 38.462 13.09 0.00 32.65 4.08
790 796 7.253422 TCCAGAACGTACTAGTAGTATTTTGC 58.747 38.462 13.09 0.00 32.65 3.68
791 797 7.431668 GCTCCAGAACGTACTAGTAGTATTTTG 59.568 40.741 13.09 9.47 32.65 2.44
792 798 7.416101 GGCTCCAGAACGTACTAGTAGTATTTT 60.416 40.741 13.09 9.19 32.65 1.82
793 799 6.039159 GGCTCCAGAACGTACTAGTAGTATTT 59.961 42.308 13.09 9.51 32.65 1.40
794 800 5.530543 GGCTCCAGAACGTACTAGTAGTATT 59.469 44.000 13.09 4.74 32.65 1.89
795 801 5.062528 GGCTCCAGAACGTACTAGTAGTAT 58.937 45.833 13.09 0.00 32.65 2.12
796 802 4.080919 TGGCTCCAGAACGTACTAGTAGTA 60.081 45.833 5.90 5.90 0.00 1.82
797 803 3.277715 GGCTCCAGAACGTACTAGTAGT 58.722 50.000 8.14 8.14 0.00 2.73
798 804 3.276857 TGGCTCCAGAACGTACTAGTAG 58.723 50.000 1.87 0.00 0.00 2.57
799 805 3.354948 TGGCTCCAGAACGTACTAGTA 57.645 47.619 0.00 0.00 0.00 1.82
800 806 2.211250 TGGCTCCAGAACGTACTAGT 57.789 50.000 0.00 0.00 0.00 2.57
801 807 3.587797 TTTGGCTCCAGAACGTACTAG 57.412 47.619 0.00 0.00 0.00 2.57
802 808 4.250464 CAATTTGGCTCCAGAACGTACTA 58.750 43.478 0.00 0.00 0.00 1.82
803 809 3.074412 CAATTTGGCTCCAGAACGTACT 58.926 45.455 0.00 0.00 0.00 2.73
804 810 2.161609 CCAATTTGGCTCCAGAACGTAC 59.838 50.000 1.71 0.00 0.00 3.67
805 811 2.039216 TCCAATTTGGCTCCAGAACGTA 59.961 45.455 10.76 0.00 37.47 3.57
806 812 1.202879 TCCAATTTGGCTCCAGAACGT 60.203 47.619 10.76 0.00 37.47 3.99
807 813 1.533625 TCCAATTTGGCTCCAGAACG 58.466 50.000 10.76 0.00 37.47 3.95
808 814 4.498241 GAAATCCAATTTGGCTCCAGAAC 58.502 43.478 10.76 0.00 37.47 3.01
809 815 3.193267 CGAAATCCAATTTGGCTCCAGAA 59.807 43.478 10.76 0.00 37.47 3.02
810 816 2.754552 CGAAATCCAATTTGGCTCCAGA 59.245 45.455 10.76 0.00 37.47 3.86
811 817 2.754552 TCGAAATCCAATTTGGCTCCAG 59.245 45.455 10.76 2.66 37.47 3.86
812 818 2.801483 TCGAAATCCAATTTGGCTCCA 58.199 42.857 10.76 0.00 37.47 3.86
813 819 5.335976 GGATATCGAAATCCAATTTGGCTCC 60.336 44.000 10.76 2.43 44.26 4.70
814 820 5.703876 GGATATCGAAATCCAATTTGGCTC 58.296 41.667 10.76 6.30 44.26 4.70
815 821 5.712152 GGATATCGAAATCCAATTTGGCT 57.288 39.130 10.76 0.00 44.26 4.75
824 830 5.485209 ACCTTACCTGGATATCGAAATCC 57.515 43.478 0.00 0.00 44.96 3.01
825 831 6.766467 ACAAACCTTACCTGGATATCGAAATC 59.234 38.462 0.00 0.00 0.00 2.17
826 832 6.659824 ACAAACCTTACCTGGATATCGAAAT 58.340 36.000 0.00 0.00 0.00 2.17
827 833 6.057321 ACAAACCTTACCTGGATATCGAAA 57.943 37.500 0.00 0.00 0.00 3.46
828 834 5.687166 ACAAACCTTACCTGGATATCGAA 57.313 39.130 0.00 0.00 0.00 3.71
829 835 5.687166 AACAAACCTTACCTGGATATCGA 57.313 39.130 0.00 0.00 0.00 3.59
830 836 5.646360 ACAAACAAACCTTACCTGGATATCG 59.354 40.000 0.00 0.00 0.00 2.92
831 837 7.462571 AACAAACAAACCTTACCTGGATATC 57.537 36.000 0.00 0.00 0.00 1.63
832 838 7.289084 ACAAACAAACAAACCTTACCTGGATAT 59.711 33.333 0.00 0.00 0.00 1.63
833 839 6.608002 ACAAACAAACAAACCTTACCTGGATA 59.392 34.615 0.00 0.00 0.00 2.59
834 840 5.423931 ACAAACAAACAAACCTTACCTGGAT 59.576 36.000 0.00 0.00 0.00 3.41
835 841 4.773149 ACAAACAAACAAACCTTACCTGGA 59.227 37.500 0.00 0.00 0.00 3.86
836 842 5.079689 ACAAACAAACAAACCTTACCTGG 57.920 39.130 0.00 0.00 0.00 4.45
837 843 7.041712 ACAAAACAAACAAACAAACCTTACCTG 60.042 33.333 0.00 0.00 0.00 4.00
838 844 6.993308 ACAAAACAAACAAACAAACCTTACCT 59.007 30.769 0.00 0.00 0.00 3.08
839 845 7.192148 ACAAAACAAACAAACAAACCTTACC 57.808 32.000 0.00 0.00 0.00 2.85
840 846 7.527849 CGAACAAAACAAACAAACAAACCTTAC 59.472 33.333 0.00 0.00 0.00 2.34
841 847 7.224167 ACGAACAAAACAAACAAACAAACCTTA 59.776 29.630 0.00 0.00 0.00 2.69
842 848 6.037281 ACGAACAAAACAAACAAACAAACCTT 59.963 30.769 0.00 0.00 0.00 3.50
843 849 5.524281 ACGAACAAAACAAACAAACAAACCT 59.476 32.000 0.00 0.00 0.00 3.50
844 850 5.739387 ACGAACAAAACAAACAAACAAACC 58.261 33.333 0.00 0.00 0.00 3.27
845 851 6.683286 ACAACGAACAAAACAAACAAACAAAC 59.317 30.769 0.00 0.00 0.00 2.93
846 852 6.772078 ACAACGAACAAAACAAACAAACAAA 58.228 28.000 0.00 0.00 0.00 2.83
847 853 6.345920 ACAACGAACAAAACAAACAAACAA 57.654 29.167 0.00 0.00 0.00 2.83
848 854 5.968387 ACAACGAACAAAACAAACAAACA 57.032 30.435 0.00 0.00 0.00 2.83
849 855 7.005769 GCAATACAACGAACAAAACAAACAAAC 59.994 33.333 0.00 0.00 0.00 2.93
850 856 7.010023 GCAATACAACGAACAAAACAAACAAA 58.990 30.769 0.00 0.00 0.00 2.83
851 857 6.401153 GGCAATACAACGAACAAAACAAACAA 60.401 34.615 0.00 0.00 0.00 2.83
852 858 5.062308 GGCAATACAACGAACAAAACAAACA 59.938 36.000 0.00 0.00 0.00 2.83
853 859 5.485831 GGCAATACAACGAACAAAACAAAC 58.514 37.500 0.00 0.00 0.00 2.93
854 860 4.265556 CGGCAATACAACGAACAAAACAAA 59.734 37.500 0.00 0.00 0.00 2.83
855 861 3.791887 CGGCAATACAACGAACAAAACAA 59.208 39.130 0.00 0.00 0.00 2.83
856 862 3.364062 CGGCAATACAACGAACAAAACA 58.636 40.909 0.00 0.00 0.00 2.83
857 863 2.152301 GCGGCAATACAACGAACAAAAC 59.848 45.455 0.00 0.00 0.00 2.43
858 864 2.223502 TGCGGCAATACAACGAACAAAA 60.224 40.909 0.00 0.00 0.00 2.44
859 865 1.333931 TGCGGCAATACAACGAACAAA 59.666 42.857 0.00 0.00 0.00 2.83
860 866 0.945099 TGCGGCAATACAACGAACAA 59.055 45.000 0.00 0.00 0.00 2.83
861 867 0.945099 TTGCGGCAATACAACGAACA 59.055 45.000 12.11 0.00 0.00 3.18
862 868 2.039327 TTTGCGGCAATACAACGAAC 57.961 45.000 17.19 0.00 0.00 3.95
863 869 2.776312 TTTTGCGGCAATACAACGAA 57.224 40.000 17.19 2.85 0.00 3.85
864 870 2.776312 TTTTTGCGGCAATACAACGA 57.224 40.000 17.19 0.00 0.00 3.85
884 890 4.678622 CCTTACAACGAACAAGCCTTTTT 58.321 39.130 0.00 0.00 0.00 1.94
885 891 3.490249 GCCTTACAACGAACAAGCCTTTT 60.490 43.478 0.00 0.00 0.00 2.27
886 892 2.034179 GCCTTACAACGAACAAGCCTTT 59.966 45.455 0.00 0.00 0.00 3.11
887 893 1.607148 GCCTTACAACGAACAAGCCTT 59.393 47.619 0.00 0.00 0.00 4.35
888 894 1.235724 GCCTTACAACGAACAAGCCT 58.764 50.000 0.00 0.00 0.00 4.58
889 895 0.240145 GGCCTTACAACGAACAAGCC 59.760 55.000 0.00 0.00 0.00 4.35
890 896 0.240145 GGGCCTTACAACGAACAAGC 59.760 55.000 0.84 0.00 0.00 4.01
891 897 1.600023 TGGGCCTTACAACGAACAAG 58.400 50.000 4.53 0.00 0.00 3.16
898 904 3.629142 ACTCTGTATGGGCCTTACAAC 57.371 47.619 26.55 8.46 0.00 3.32
979 985 2.006888 CGGTTACGTTTGGATCATGCT 58.993 47.619 0.00 0.00 34.81 3.79
988 994 1.015085 TCGGCCATCGGTTACGTTTG 61.015 55.000 2.24 0.00 41.85 2.93
994 1000 0.179067 GTGGAATCGGCCATCGGTTA 60.179 55.000 2.24 0.00 43.00 2.85
995 1001 1.451387 GTGGAATCGGCCATCGGTT 60.451 57.895 2.24 0.00 46.01 4.44
997 1003 2.591715 GGTGGAATCGGCCATCGG 60.592 66.667 2.24 0.00 40.68 4.18
1124 1131 1.984570 CGGAAGCAGGAGGTGGAGA 60.985 63.158 0.00 0.00 0.00 3.71
1157 1164 1.074850 GGGAAGGGAGAGAGAGGGG 60.075 68.421 0.00 0.00 0.00 4.79
1161 1168 2.690452 CGGGGGAAGGGAGAGAGA 59.310 66.667 0.00 0.00 0.00 3.10
1273 1280 0.912486 AATAAGGAGGAAGCCAGCGT 59.088 50.000 0.00 0.00 0.00 5.07
1288 1295 1.227031 CGTGTAGCGGCGGGAATAA 60.227 57.895 9.78 0.00 36.85 1.40
1325 1332 2.756283 AGAGGACGCGGGAAGAGG 60.756 66.667 12.47 0.00 0.00 3.69
1708 1725 0.618458 GGGTGGTGCCATTACTCTGA 59.382 55.000 0.00 0.00 39.65 3.27
1727 1744 1.079127 AACTCATCGCGGGTTCAGG 60.079 57.895 6.13 0.00 0.00 3.86
1743 1760 3.421844 AGAAGTTGCTCCCCATTACAAC 58.578 45.455 0.00 0.00 42.08 3.32
1744 1761 3.806949 AGAAGTTGCTCCCCATTACAA 57.193 42.857 0.00 0.00 0.00 2.41
1746 1763 5.497474 TCTTAAGAAGTTGCTCCCCATTAC 58.503 41.667 1.68 0.00 0.00 1.89
1747 1764 5.772393 TCTTAAGAAGTTGCTCCCCATTA 57.228 39.130 1.68 0.00 0.00 1.90
1748 1765 4.657814 TCTTAAGAAGTTGCTCCCCATT 57.342 40.909 1.68 0.00 0.00 3.16
1749 1766 4.657814 TTCTTAAGAAGTTGCTCCCCAT 57.342 40.909 13.99 0.00 0.00 4.00
1751 1768 4.336280 ACATTCTTAAGAAGTTGCTCCCC 58.664 43.478 21.75 0.00 37.48 4.81
1752 1769 6.879458 TCTTACATTCTTAAGAAGTTGCTCCC 59.121 38.462 21.75 0.00 35.55 4.30
1753 1770 7.907214 TCTTACATTCTTAAGAAGTTGCTCC 57.093 36.000 21.75 0.00 35.55 4.70
1774 1791 9.751542 CGAAATGGTTGTATCTAGACTTATCTT 57.248 33.333 0.00 0.00 36.29 2.40
1775 1792 9.132923 TCGAAATGGTTGTATCTAGACTTATCT 57.867 33.333 0.00 0.00 39.15 1.98
1776 1793 9.400638 CTCGAAATGGTTGTATCTAGACTTATC 57.599 37.037 0.00 0.00 0.00 1.75
1777 1794 8.361139 CCTCGAAATGGTTGTATCTAGACTTAT 58.639 37.037 0.00 0.00 0.00 1.73
1778 1795 7.558807 TCCTCGAAATGGTTGTATCTAGACTTA 59.441 37.037 0.00 0.00 0.00 2.24
1779 1796 6.380274 TCCTCGAAATGGTTGTATCTAGACTT 59.620 38.462 0.00 0.00 0.00 3.01
1780 1797 5.892119 TCCTCGAAATGGTTGTATCTAGACT 59.108 40.000 0.00 0.00 0.00 3.24
1781 1798 6.145338 TCCTCGAAATGGTTGTATCTAGAC 57.855 41.667 0.00 0.00 0.00 2.59
1782 1799 6.978674 ATCCTCGAAATGGTTGTATCTAGA 57.021 37.500 0.00 0.00 0.00 2.43
1783 1800 9.712305 ATTTATCCTCGAAATGGTTGTATCTAG 57.288 33.333 0.00 0.00 0.00 2.43
1789 1806 8.630037 GGAAATATTTATCCTCGAAATGGTTGT 58.370 33.333 0.00 0.00 32.75 3.32
1790 1807 7.803189 CGGAAATATTTATCCTCGAAATGGTTG 59.197 37.037 0.00 0.00 33.36 3.77
1791 1808 7.040686 CCGGAAATATTTATCCTCGAAATGGTT 60.041 37.037 0.00 0.00 33.36 3.67
1792 1809 6.430000 CCGGAAATATTTATCCTCGAAATGGT 59.570 38.462 0.00 0.00 33.36 3.55
1793 1810 6.653320 TCCGGAAATATTTATCCTCGAAATGG 59.347 38.462 0.00 0.00 33.36 3.16
1794 1811 7.519002 GTCCGGAAATATTTATCCTCGAAATG 58.481 38.462 5.23 0.00 33.36 2.32
1795 1812 6.367969 CGTCCGGAAATATTTATCCTCGAAAT 59.632 38.462 5.23 0.00 33.36 2.17
1796 1813 5.693104 CGTCCGGAAATATTTATCCTCGAAA 59.307 40.000 5.23 0.00 33.36 3.46
1797 1814 5.009911 TCGTCCGGAAATATTTATCCTCGAA 59.990 40.000 5.23 0.00 32.57 3.71
1798 1815 4.520111 TCGTCCGGAAATATTTATCCTCGA 59.480 41.667 5.23 2.81 33.36 4.04
1799 1816 4.801891 TCGTCCGGAAATATTTATCCTCG 58.198 43.478 5.23 0.00 33.36 4.63
1800 1817 5.638234 CCTTCGTCCGGAAATATTTATCCTC 59.362 44.000 5.23 0.00 33.34 3.71
1801 1818 5.512576 CCCTTCGTCCGGAAATATTTATCCT 60.513 44.000 5.23 0.00 33.34 3.24
1802 1819 4.694037 CCCTTCGTCCGGAAATATTTATCC 59.306 45.833 5.23 0.00 33.34 2.59
1803 1820 5.544650 TCCCTTCGTCCGGAAATATTTATC 58.455 41.667 5.23 0.00 33.34 1.75
1804 1821 5.071384 ACTCCCTTCGTCCGGAAATATTTAT 59.929 40.000 5.23 0.00 33.34 1.40
1805 1822 4.406649 ACTCCCTTCGTCCGGAAATATTTA 59.593 41.667 5.23 0.00 33.34 1.40
1806 1823 3.199289 ACTCCCTTCGTCCGGAAATATTT 59.801 43.478 5.23 0.00 33.34 1.40
1807 1824 2.770232 ACTCCCTTCGTCCGGAAATATT 59.230 45.455 5.23 0.00 33.34 1.28
1808 1825 2.395619 ACTCCCTTCGTCCGGAAATAT 58.604 47.619 5.23 0.00 33.34 1.28
1809 1826 1.856629 ACTCCCTTCGTCCGGAAATA 58.143 50.000 5.23 0.00 33.34 1.40
1810 1827 1.856629 TACTCCCTTCGTCCGGAAAT 58.143 50.000 5.23 0.00 33.34 2.17
1811 1828 1.631405 TTACTCCCTTCGTCCGGAAA 58.369 50.000 5.23 0.00 33.34 3.13
1812 1829 1.856629 ATTACTCCCTTCGTCCGGAA 58.143 50.000 5.23 0.00 0.00 4.30
1813 1830 1.753073 GAATTACTCCCTTCGTCCGGA 59.247 52.381 0.00 0.00 0.00 5.14
1814 1831 1.755380 AGAATTACTCCCTTCGTCCGG 59.245 52.381 0.00 0.00 0.00 5.14
1815 1832 4.644103 TTAGAATTACTCCCTTCGTCCG 57.356 45.455 0.00 0.00 0.00 4.79
1816 1833 5.915175 ACATTAGAATTACTCCCTTCGTCC 58.085 41.667 0.00 0.00 0.00 4.79
1817 1834 7.039882 TGAACATTAGAATTACTCCCTTCGTC 58.960 38.462 0.00 0.00 0.00 4.20
1818 1835 6.942976 TGAACATTAGAATTACTCCCTTCGT 58.057 36.000 0.00 0.00 0.00 3.85
1819 1836 8.438676 AATGAACATTAGAATTACTCCCTTCG 57.561 34.615 0.00 0.00 0.00 3.79
1879 1897 1.762370 TGCAGAAATCCATAGCTCGGA 59.238 47.619 7.23 7.23 36.84 4.55
1945 1964 1.285641 CGGCACCGCAACAATCTTT 59.714 52.632 0.00 0.00 0.00 2.52
2022 2075 8.325787 TCCTATGGTCATAGCTAGAAAAACAAA 58.674 33.333 11.42 0.00 39.48 2.83
2098 2151 3.433274 AGCGGTGCATATGATTATGAACG 59.567 43.478 6.97 0.00 43.04 3.95
2099 2152 5.362556 AAGCGGTGCATATGATTATGAAC 57.637 39.130 6.97 0.00 41.86 3.18
2101 2154 4.320421 GCAAAGCGGTGCATATGATTATGA 60.320 41.667 6.97 0.00 44.29 2.15
2102 2155 3.916172 GCAAAGCGGTGCATATGATTATG 59.084 43.478 6.97 0.00 44.29 1.90
2103 2156 4.164822 GCAAAGCGGTGCATATGATTAT 57.835 40.909 6.97 0.00 44.29 1.28
2105 2158 2.497107 GCAAAGCGGTGCATATGATT 57.503 45.000 6.97 0.00 44.29 2.57
2149 2203 7.934120 AGTACCATGATCCTTTTGCTAACTATC 59.066 37.037 0.00 0.00 0.00 2.08
2356 2414 8.578151 GGATACCAATGTTTGTAACTAACCAAA 58.422 33.333 0.00 0.00 0.00 3.28
2359 2417 7.148137 CCTGGATACCAATGTTTGTAACTAACC 60.148 40.741 0.00 0.00 30.80 2.85
2387 2446 5.826208 GGGTTTTTAGTCTTCACCTCTTTGA 59.174 40.000 0.00 0.00 0.00 2.69
2416 2475 0.168128 GAAGTGCGTACATGGGTTGC 59.832 55.000 6.38 0.00 0.00 4.17
2429 2488 0.031178 CAAGTGCTTGTGGGAAGTGC 59.969 55.000 3.91 0.00 35.92 4.40
2469 2543 6.102910 AGGAGACTAGTACACCACTATGGTAT 59.897 42.308 0.00 0.00 45.57 2.73
2479 2553 1.404748 GGCGAAGGAGACTAGTACACC 59.595 57.143 0.00 0.00 42.68 4.16
2551 2625 2.432146 GGAATTTGGGATTTCTGAGGGC 59.568 50.000 0.00 0.00 0.00 5.19
2615 2689 4.154347 CCAGAGAGCTCCGGGTGC 62.154 72.222 10.93 13.03 0.00 5.01
2628 2702 1.810151 GTTTAGGATTTGTGCGCCAGA 59.190 47.619 4.18 0.00 0.00 3.86
2630 2704 0.885196 GGTTTAGGATTTGTGCGCCA 59.115 50.000 4.18 0.00 0.00 5.69
2636 2710 4.292306 AGATGACCCAGGTTTAGGATTTGT 59.708 41.667 0.00 0.00 0.00 2.83
2651 2725 1.341383 ACTCATTTGGGCAGATGACCC 60.341 52.381 1.29 3.93 44.80 4.46
2682 2756 6.959639 ATACATTGAACATTGGGATGGTAC 57.040 37.500 0.00 0.00 37.60 3.34


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

AutoCloner maintained by Alex Coulton.