Multiple sequence alignment - TraesCS6A01G281700

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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 TraesCS6A01G281700 chr6A 100.000 2971 0 0 1 2971 511526917 511529887 0.000000e+00 5487.0
1 TraesCS6A01G281700 chr6A 88.034 117 4 5 2477 2586 7373596 7373483 2.400000e-26 130.0
2 TraesCS6A01G281700 chr6D 94.727 1574 39 10 908 2473 370689023 370690560 0.000000e+00 2407.0
3 TraesCS6A01G281700 chr6D 96.460 226 8 0 2746 2971 370690845 370691070 1.010000e-99 374.0
4 TraesCS6A01G281700 chr6D 95.714 210 9 0 2539 2748 370690551 370690760 3.670000e-89 339.0
5 TraesCS6A01G281700 chr6D 90.964 166 9 6 753 916 370581681 370581842 4.990000e-53 219.0
6 TraesCS6A01G281700 chr6D 90.909 66 2 4 2543 2608 249956924 249956985 5.280000e-13 86.1
7 TraesCS6A01G281700 chr6D 95.122 41 2 0 2545 2585 32919203 32919243 6.870000e-07 65.8
8 TraesCS6A01G281700 chr6B 95.785 1210 30 5 999 2208 555805027 555806215 0.000000e+00 1932.0
9 TraesCS6A01G281700 chr6B 93.303 433 18 4 1 424 690877724 690877294 1.940000e-176 628.0
10 TraesCS6A01G281700 chr6B 93.000 400 16 4 2584 2971 555806508 555806907 9.240000e-160 573.0
11 TraesCS6A01G281700 chr6B 90.875 263 17 5 2211 2473 555806252 555806507 2.190000e-91 346.0
12 TraesCS6A01G281700 chr6B 88.462 52 5 1 949 999 555804945 555804996 8.890000e-06 62.1
13 TraesCS6A01G281700 chr6B 100.000 28 0 0 2139 2166 555806229 555806256 5.000000e-03 52.8
14 TraesCS6A01G281700 chr2A 92.702 781 43 5 1 771 173513698 173512922 0.000000e+00 1114.0
15 TraesCS6A01G281700 chr2A 92.138 407 27 2 364 768 572845984 572846387 1.190000e-158 569.0
16 TraesCS6A01G281700 chr3D 93.995 433 15 4 1 424 384009782 384010212 0.000000e+00 645.0
17 TraesCS6A01G281700 chr3D 93.187 411 23 2 364 772 384010205 384010612 1.520000e-167 599.0
18 TraesCS6A01G281700 chr3D 86.885 122 12 3 2467 2585 555010894 555010774 1.860000e-27 134.0
19 TraesCS6A01G281700 chr4B 93.533 433 15 6 1 424 2710910 2710482 1.500000e-177 632.0
20 TraesCS6A01G281700 chr4B 92.575 431 20 6 3 424 97791441 97791014 2.530000e-170 608.0
21 TraesCS6A01G281700 chr4B 91.748 412 29 3 364 773 97879642 97879234 4.300000e-158 568.0
22 TraesCS6A01G281700 chr4B 91.707 410 29 3 364 771 2710489 2710083 5.560000e-157 564.0
23 TraesCS6A01G281700 chr4B 91.687 409 29 2 364 770 535069233 535069638 2.000000e-156 562.0
24 TraesCS6A01G281700 chr4B 91.057 123 6 4 2853 2971 625330743 625330622 8.520000e-36 161.0
25 TraesCS6A01G281700 chr5A 93.303 433 17 5 1 424 354275638 354276067 1.940000e-176 628.0
26 TraesCS6A01G281700 chr4D 93.303 433 18 4 1 424 79010223 79010653 1.940000e-176 628.0
27 TraesCS6A01G281700 chr4D 93.269 104 5 1 2482 2585 135171085 135170984 5.130000e-33 152.0
28 TraesCS6A01G281700 chr1A 93.072 433 18 5 1 424 2283303 2282874 9.040000e-175 623.0
29 TraesCS6A01G281700 chr1A 91.847 417 29 4 364 776 2282881 2282466 7.140000e-161 577.0
30 TraesCS6A01G281700 chr5B 92.841 433 19 5 1 424 345812121 345812550 4.210000e-173 617.0
31 TraesCS6A01G281700 chrUn 92.346 405 26 2 365 767 122648353 122648754 3.320000e-159 571.0
32 TraesCS6A01G281700 chrUn 89.655 116 6 2 2476 2585 65138954 65138839 3.090000e-30 143.0
33 TraesCS6A01G281700 chr7A 91.892 407 28 2 364 768 606194815 606195218 5.560000e-157 564.0
34 TraesCS6A01G281700 chr2D 91.964 112 3 2 2477 2586 79387429 79387322 5.130000e-33 152.0
35 TraesCS6A01G281700 chr2D 95.122 41 2 0 2545 2585 422085571 422085611 6.870000e-07 65.8
36 TraesCS6A01G281700 chr5D 91.071 112 7 2 2477 2586 361674424 361674314 6.630000e-32 148.0
37 TraesCS6A01G281700 chr5D 86.179 123 9 7 2853 2968 499710911 499711032 3.110000e-25 126.0
38 TraesCS6A01G281700 chr3B 91.743 109 4 2 2480 2586 636441639 636441534 2.390000e-31 147.0
39 TraesCS6A01G281700 chr7B 89.474 114 7 2 2477 2585 475307981 475308094 3.990000e-29 139.0
40 TraesCS6A01G281700 chr3A 89.381 113 8 3 2477 2586 18825595 18825484 3.990000e-29 139.0
41 TraesCS6A01G281700 chr7D 94.444 54 3 0 2543 2596 101475417 101475470 1.900000e-12 84.2
42 TraesCS6A01G281700 chr2B 97.368 38 1 0 1343 1380 573814522 573814485 6.870000e-07 65.8
43 TraesCS6A01G281700 chr4A 88.679 53 2 4 2548 2600 516208934 516208886 8.890000e-06 62.1


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 TraesCS6A01G281700 chr6A 511526917 511529887 2970 False 5487.00 5487 100.000000 1 2971 1 chr6A.!!$F1 2970
1 TraesCS6A01G281700 chr6D 370689023 370691070 2047 False 1040.00 2407 95.633667 908 2971 3 chr6D.!!$F4 2063
2 TraesCS6A01G281700 chr6B 555804945 555806907 1962 False 593.18 1932 93.624400 949 2971 5 chr6B.!!$F1 2022
3 TraesCS6A01G281700 chr2A 173512922 173513698 776 True 1114.00 1114 92.702000 1 771 1 chr2A.!!$R1 770
4 TraesCS6A01G281700 chr3D 384009782 384010612 830 False 622.00 645 93.591000 1 772 2 chr3D.!!$F1 771
5 TraesCS6A01G281700 chr4B 2710083 2710910 827 True 598.00 632 92.620000 1 771 2 chr4B.!!$R4 770
6 TraesCS6A01G281700 chr1A 2282466 2283303 837 True 600.00 623 92.459500 1 776 2 chr1A.!!$R1 775

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
833 901 0.110688 CGTTGTCATGCCAACTCGTG 60.111 55.0 16.78 0.0 42.0 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2473 2615 0.338814 ATGGGACGGAGGGAGTAACT 59.661 55.0 0.0 0.0 0.0 2.24 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
124 125 1.886222 GCCATGCTGAAACACACCCTA 60.886 52.381 0.00 0.00 0.00 3.53
258 260 2.448926 TGAAGTCCGAAAAGCATCGA 57.551 45.000 7.97 0.00 45.48 3.59
323 333 3.378512 TGTGCTTGATGAGACTATCCCT 58.621 45.455 0.00 0.00 0.00 4.20
507 571 5.560760 GCTCGAGTTGTTTCATGAATTGTCA 60.561 40.000 15.13 4.26 38.41 3.58
591 659 5.470098 CAGATACAAGCTACCAAACACAGTT 59.530 40.000 0.00 0.00 0.00 3.16
593 661 6.546034 AGATACAAGCTACCAAACACAGTTTT 59.454 34.615 0.00 0.00 0.00 2.43
594 662 4.743493 ACAAGCTACCAAACACAGTTTTG 58.257 39.130 0.00 0.00 36.40 2.44
609 677 3.023119 AGTTTTGGTGCAACATGTCTCA 58.977 40.909 4.62 0.00 39.98 3.27
644 712 3.541996 TCAAACACAGTCTCAGCTCAA 57.458 42.857 0.00 0.00 0.00 3.02
649 717 2.103771 ACACAGTCTCAGCTCAACATGT 59.896 45.455 0.00 0.00 0.00 3.21
656 724 4.565962 GTCTCAGCTCAACATGTATCAGTG 59.434 45.833 0.00 0.00 0.00 3.66
705 773 4.470334 TGCATGTACTGAGCATGTCTAA 57.530 40.909 14.01 0.00 43.93 2.10
717 785 5.352293 TGAGCATGTCTAAACTAAGCATGTG 59.648 40.000 0.00 0.00 39.11 3.21
721 789 6.537566 CATGTCTAAACTAAGCATGTGTCAC 58.462 40.000 0.00 0.00 34.10 3.67
736 804 3.764972 TGTGTCACATGGGAACGACTATA 59.235 43.478 0.00 0.00 0.00 1.31
762 830 2.514803 GTGGGAACAGCTACCAAACAT 58.485 47.619 6.20 0.00 44.46 2.71
776 844 4.403734 ACCAAACATACCCTTAGTGGTTG 58.596 43.478 0.00 0.00 39.60 3.77
777 845 4.141111 ACCAAACATACCCTTAGTGGTTGT 60.141 41.667 0.00 1.60 38.54 3.32
778 846 4.830600 CCAAACATACCCTTAGTGGTTGTT 59.169 41.667 0.00 6.30 38.54 2.83
779 847 5.278758 CCAAACATACCCTTAGTGGTTGTTG 60.279 44.000 14.25 7.63 38.54 3.33
780 848 4.986054 ACATACCCTTAGTGGTTGTTGA 57.014 40.909 0.00 0.00 39.91 3.18
781 849 4.906618 ACATACCCTTAGTGGTTGTTGAG 58.093 43.478 0.00 0.00 39.91 3.02
782 850 2.951229 ACCCTTAGTGGTTGTTGAGG 57.049 50.000 0.00 0.00 33.91 3.86
783 851 2.200373 CCCTTAGTGGTTGTTGAGGG 57.800 55.000 0.00 0.00 38.03 4.30
784 852 1.423921 CCCTTAGTGGTTGTTGAGGGT 59.576 52.381 0.00 0.00 39.18 4.34
785 853 2.158519 CCCTTAGTGGTTGTTGAGGGTT 60.159 50.000 0.00 0.00 39.18 4.11
786 854 2.884639 CCTTAGTGGTTGTTGAGGGTTG 59.115 50.000 0.00 0.00 0.00 3.77
787 855 3.434453 CCTTAGTGGTTGTTGAGGGTTGA 60.434 47.826 0.00 0.00 0.00 3.18
788 856 2.348411 AGTGGTTGTTGAGGGTTGAG 57.652 50.000 0.00 0.00 0.00 3.02
789 857 0.668535 GTGGTTGTTGAGGGTTGAGC 59.331 55.000 0.00 0.00 0.00 4.26
790 858 0.257328 TGGTTGTTGAGGGTTGAGCA 59.743 50.000 0.00 0.00 0.00 4.26
791 859 0.668535 GGTTGTTGAGGGTTGAGCAC 59.331 55.000 0.00 0.00 0.00 4.40
792 860 0.668535 GTTGTTGAGGGTTGAGCACC 59.331 55.000 0.00 0.00 46.46 5.01
803 871 3.972227 GAGCACCACTCGCATGTT 58.028 55.556 0.00 0.00 35.18 2.71
804 872 3.137484 GAGCACCACTCGCATGTTA 57.863 52.632 0.00 0.00 35.18 2.41
805 873 0.721718 GAGCACCACTCGCATGTTAC 59.278 55.000 0.00 0.00 35.18 2.50
806 874 0.321671 AGCACCACTCGCATGTTACT 59.678 50.000 0.00 0.00 0.00 2.24
807 875 0.721718 GCACCACTCGCATGTTACTC 59.278 55.000 0.00 0.00 0.00 2.59
808 876 1.673033 GCACCACTCGCATGTTACTCT 60.673 52.381 0.00 0.00 0.00 3.24
809 877 2.688507 CACCACTCGCATGTTACTCTT 58.311 47.619 0.00 0.00 0.00 2.85
810 878 2.668457 CACCACTCGCATGTTACTCTTC 59.332 50.000 0.00 0.00 0.00 2.87
811 879 1.920574 CCACTCGCATGTTACTCTTCG 59.079 52.381 0.00 0.00 0.00 3.79
812 880 1.321743 CACTCGCATGTTACTCTTCGC 59.678 52.381 0.00 0.00 0.00 4.70
813 881 1.202582 ACTCGCATGTTACTCTTCGCT 59.797 47.619 0.00 0.00 0.00 4.93
814 882 1.849219 CTCGCATGTTACTCTTCGCTC 59.151 52.381 0.00 0.00 0.00 5.03
815 883 0.567968 CGCATGTTACTCTTCGCTCG 59.432 55.000 0.00 0.00 0.00 5.03
816 884 1.630148 GCATGTTACTCTTCGCTCGT 58.370 50.000 0.00 0.00 0.00 4.18
817 885 1.993370 GCATGTTACTCTTCGCTCGTT 59.007 47.619 0.00 0.00 0.00 3.85
818 886 2.222596 GCATGTTACTCTTCGCTCGTTG 60.223 50.000 0.00 0.00 0.00 4.10
819 887 2.787601 TGTTACTCTTCGCTCGTTGT 57.212 45.000 0.00 0.00 0.00 3.32
820 888 2.658285 TGTTACTCTTCGCTCGTTGTC 58.342 47.619 0.00 0.00 0.00 3.18
821 889 2.033675 TGTTACTCTTCGCTCGTTGTCA 59.966 45.455 0.00 0.00 0.00 3.58
822 890 3.243336 GTTACTCTTCGCTCGTTGTCAT 58.757 45.455 0.00 0.00 0.00 3.06
823 891 1.702886 ACTCTTCGCTCGTTGTCATG 58.297 50.000 0.00 0.00 0.00 3.07
824 892 0.368227 CTCTTCGCTCGTTGTCATGC 59.632 55.000 0.00 0.00 0.00 4.06
825 893 1.014044 TCTTCGCTCGTTGTCATGCC 61.014 55.000 0.00 0.00 0.00 4.40
826 894 1.291184 CTTCGCTCGTTGTCATGCCA 61.291 55.000 0.00 0.00 0.00 4.92
827 895 0.882484 TTCGCTCGTTGTCATGCCAA 60.882 50.000 0.00 0.00 0.00 4.52
828 896 1.154413 CGCTCGTTGTCATGCCAAC 60.154 57.895 9.55 9.55 41.01 3.77
829 897 1.568612 CGCTCGTTGTCATGCCAACT 61.569 55.000 16.78 0.00 42.00 3.16
830 898 0.166814 GCTCGTTGTCATGCCAACTC 59.833 55.000 16.78 3.40 42.00 3.01
831 899 0.439985 CTCGTTGTCATGCCAACTCG 59.560 55.000 16.78 5.68 42.00 4.18
832 900 0.249699 TCGTTGTCATGCCAACTCGT 60.250 50.000 16.78 0.00 42.00 4.18
833 901 0.110688 CGTTGTCATGCCAACTCGTG 60.111 55.000 16.78 0.00 42.00 4.35
834 902 0.944386 GTTGTCATGCCAACTCGTGT 59.056 50.000 12.23 0.00 41.17 4.49
835 903 2.139917 GTTGTCATGCCAACTCGTGTA 58.860 47.619 12.23 0.00 41.17 2.90
836 904 1.790755 TGTCATGCCAACTCGTGTAC 58.209 50.000 0.00 0.00 0.00 2.90
837 905 1.069358 TGTCATGCCAACTCGTGTACA 59.931 47.619 0.00 0.00 0.00 2.90
838 906 2.289382 TGTCATGCCAACTCGTGTACAT 60.289 45.455 0.00 0.00 0.00 2.29
839 907 2.094258 GTCATGCCAACTCGTGTACATG 59.906 50.000 8.90 8.90 35.37 3.21
840 908 2.076100 CATGCCAACTCGTGTACATGT 58.924 47.619 14.63 2.69 32.34 3.21
841 909 2.248280 TGCCAACTCGTGTACATGTT 57.752 45.000 14.63 9.88 0.00 2.71
842 910 2.566913 TGCCAACTCGTGTACATGTTT 58.433 42.857 14.63 6.88 0.00 2.83
843 911 2.546368 TGCCAACTCGTGTACATGTTTC 59.454 45.455 14.63 0.00 0.00 2.78
844 912 2.546368 GCCAACTCGTGTACATGTTTCA 59.454 45.455 14.63 1.04 0.00 2.69
845 913 3.606153 GCCAACTCGTGTACATGTTTCAC 60.606 47.826 14.63 17.98 0.00 3.18
846 914 3.807622 CCAACTCGTGTACATGTTTCACT 59.192 43.478 22.29 9.04 0.00 3.41
847 915 4.272504 CCAACTCGTGTACATGTTTCACTT 59.727 41.667 22.29 12.86 0.00 3.16
848 916 5.220777 CCAACTCGTGTACATGTTTCACTTT 60.221 40.000 22.29 14.09 0.00 2.66
849 917 5.652744 ACTCGTGTACATGTTTCACTTTC 57.347 39.130 22.29 5.96 0.00 2.62
850 918 5.357257 ACTCGTGTACATGTTTCACTTTCT 58.643 37.500 22.29 7.68 0.00 2.52
851 919 5.234329 ACTCGTGTACATGTTTCACTTTCTG 59.766 40.000 22.29 12.31 0.00 3.02
852 920 5.113383 TCGTGTACATGTTTCACTTTCTGT 58.887 37.500 22.29 0.00 0.00 3.41
853 921 6.274579 TCGTGTACATGTTTCACTTTCTGTA 58.725 36.000 22.29 0.00 0.00 2.74
854 922 6.199531 TCGTGTACATGTTTCACTTTCTGTAC 59.800 38.462 22.29 0.00 39.41 2.90
855 923 6.200286 CGTGTACATGTTTCACTTTCTGTACT 59.800 38.462 22.29 0.00 39.58 2.73
856 924 7.254319 CGTGTACATGTTTCACTTTCTGTACTT 60.254 37.037 22.29 0.00 39.58 2.24
857 925 9.037737 GTGTACATGTTTCACTTTCTGTACTTA 57.962 33.333 19.62 0.00 39.58 2.24
858 926 9.602568 TGTACATGTTTCACTTTCTGTACTTAA 57.397 29.630 2.30 0.00 39.58 1.85
861 929 8.567948 ACATGTTTCACTTTCTGTACTTAATGG 58.432 33.333 0.00 0.00 0.00 3.16
862 930 8.783093 CATGTTTCACTTTCTGTACTTAATGGA 58.217 33.333 0.00 0.00 0.00 3.41
863 931 8.740123 TGTTTCACTTTCTGTACTTAATGGAA 57.260 30.769 0.00 0.00 0.00 3.53
864 932 9.179909 TGTTTCACTTTCTGTACTTAATGGAAA 57.820 29.630 0.00 0.00 0.00 3.13
865 933 9.665264 GTTTCACTTTCTGTACTTAATGGAAAG 57.335 33.333 10.81 10.81 44.58 2.62
866 934 9.621629 TTTCACTTTCTGTACTTAATGGAAAGA 57.378 29.630 16.97 1.28 42.88 2.52
867 935 9.793259 TTCACTTTCTGTACTTAATGGAAAGAT 57.207 29.630 16.97 3.22 42.88 2.40
870 938 9.668497 ACTTTCTGTACTTAATGGAAAGATACC 57.332 33.333 16.97 0.00 42.88 2.73
871 939 9.667107 CTTTCTGTACTTAATGGAAAGATACCA 57.333 33.333 7.67 0.00 42.88 3.25
874 942 9.832445 TCTGTACTTAATGGAAAGATACCAATC 57.168 33.333 0.00 0.00 40.93 2.67
875 943 9.838339 CTGTACTTAATGGAAAGATACCAATCT 57.162 33.333 0.00 0.00 44.67 2.40
876 944 9.832445 TGTACTTAATGGAAAGATACCAATCTC 57.168 33.333 0.00 0.00 41.81 2.75
877 945 8.979574 GTACTTAATGGAAAGATACCAATCTCG 58.020 37.037 0.00 0.00 41.81 4.04
878 946 7.565680 ACTTAATGGAAAGATACCAATCTCGT 58.434 34.615 0.00 0.00 41.81 4.18
879 947 7.711339 ACTTAATGGAAAGATACCAATCTCGTC 59.289 37.037 0.00 0.00 41.81 4.20
880 948 4.041740 TGGAAAGATACCAATCTCGTCG 57.958 45.455 0.00 0.00 41.81 5.12
881 949 3.446161 TGGAAAGATACCAATCTCGTCGT 59.554 43.478 0.00 0.00 41.81 4.34
882 950 4.641541 TGGAAAGATACCAATCTCGTCGTA 59.358 41.667 0.00 0.00 41.81 3.43
883 951 5.301045 TGGAAAGATACCAATCTCGTCGTAT 59.699 40.000 0.00 0.00 41.81 3.06
884 952 6.183360 TGGAAAGATACCAATCTCGTCGTATT 60.183 38.462 0.00 0.00 41.81 1.89
885 953 6.362820 GGAAAGATACCAATCTCGTCGTATTC 59.637 42.308 0.00 0.00 41.81 1.75
886 954 5.032100 AGATACCAATCTCGTCGTATTCG 57.968 43.478 0.00 0.00 38.04 3.34
887 955 4.514441 AGATACCAATCTCGTCGTATTCGT 59.486 41.667 0.00 0.00 38.04 3.85
888 956 5.698089 AGATACCAATCTCGTCGTATTCGTA 59.302 40.000 0.00 0.00 38.04 3.43
889 957 4.621068 ACCAATCTCGTCGTATTCGTAA 57.379 40.909 0.00 0.00 38.33 3.18
890 958 4.985413 ACCAATCTCGTCGTATTCGTAAA 58.015 39.130 0.00 0.00 38.33 2.01
891 959 5.401550 ACCAATCTCGTCGTATTCGTAAAA 58.598 37.500 0.00 0.00 38.33 1.52
892 960 5.514204 ACCAATCTCGTCGTATTCGTAAAAG 59.486 40.000 0.00 0.00 38.33 2.27
893 961 5.740569 CCAATCTCGTCGTATTCGTAAAAGA 59.259 40.000 0.00 0.00 38.33 2.52
894 962 6.252015 CCAATCTCGTCGTATTCGTAAAAGAA 59.748 38.462 0.00 0.00 38.33 2.52
895 963 7.201376 CCAATCTCGTCGTATTCGTAAAAGAAA 60.201 37.037 0.00 0.00 38.33 2.52
896 964 7.801547 ATCTCGTCGTATTCGTAAAAGAAAA 57.198 32.000 0.00 0.00 38.33 2.29
897 965 7.621832 TCTCGTCGTATTCGTAAAAGAAAAA 57.378 32.000 0.00 0.00 38.33 1.94
983 1051 3.379057 GGCTATTTACGCTTTTGCCCTTA 59.621 43.478 0.00 0.00 43.93 2.69
1065 1165 2.427540 GATGGCGATCTCCCACCTCG 62.428 65.000 0.81 0.00 34.68 4.63
1182 1288 1.306970 CTCCTACTCGACCCCCACT 59.693 63.158 0.00 0.00 0.00 4.00
1272 1378 3.646715 CCCCGGCTCCAGAAACCA 61.647 66.667 0.00 0.00 0.00 3.67
1273 1379 2.359975 CCCGGCTCCAGAAACCAC 60.360 66.667 0.00 0.00 0.00 4.16
1274 1380 2.359975 CCGGCTCCAGAAACCACC 60.360 66.667 0.00 0.00 0.00 4.61
1709 1815 2.903855 TCGGTCGGATCGGTAGCC 60.904 66.667 11.21 1.61 0.00 3.93
1758 1864 0.179051 GCTCTGCTCAGGAAGGATGG 60.179 60.000 0.00 0.00 0.00 3.51
1825 1931 6.937465 AGATTAGACCTTGGAACTCTGAAAAC 59.063 38.462 0.00 0.00 0.00 2.43
2019 2125 5.826737 CCAGCTCCATTTCTCAGTTGATAAT 59.173 40.000 0.00 0.00 0.00 1.28
2082 2188 2.370189 AGTTGCCTACTGAGTTGCTCTT 59.630 45.455 8.03 0.00 35.19 2.85
2095 2201 5.762711 TGAGTTGCTCTTGTATTGCTAAACA 59.237 36.000 0.00 0.00 0.00 2.83
2227 2367 2.770164 AGTTATGGCTTCGCAGTTCT 57.230 45.000 0.00 0.00 0.00 3.01
2265 2405 6.748333 TCATGCCTTCAGAGTTCAATTTAG 57.252 37.500 0.00 0.00 0.00 1.85
2294 2434 8.994429 TCAAAGCTCAGTTTTGAAAATTAACA 57.006 26.923 13.81 0.00 39.16 2.41
2363 2503 8.158025 TCTCAAGGAATTTGGGAATAAGAGTA 57.842 34.615 0.00 0.00 43.28 2.59
2367 2507 8.971073 CAAGGAATTTGGGAATAAGAGTACATT 58.029 33.333 0.00 0.00 32.95 2.71
2400 2540 6.048509 GTGGTGAAATTGGAGATGTTTTTGT 58.951 36.000 0.00 0.00 0.00 2.83
2469 2611 8.639761 AGTAACATTTGTTGTCTCTGTACTAGT 58.360 33.333 0.00 0.00 37.68 2.57
2470 2612 9.903682 GTAACATTTGTTGTCTCTGTACTAGTA 57.096 33.333 6.21 0.00 37.68 1.82
2472 2614 8.179509 ACATTTGTTGTCTCTGTACTAGTAGT 57.820 34.615 8.14 8.14 30.89 2.73
2473 2615 9.293404 ACATTTGTTGTCTCTGTACTAGTAGTA 57.707 33.333 5.90 5.90 30.89 1.82
2474 2616 9.776158 CATTTGTTGTCTCTGTACTAGTAGTAG 57.224 37.037 10.38 5.37 30.12 2.57
2475 2617 8.915057 TTTGTTGTCTCTGTACTAGTAGTAGT 57.085 34.615 14.57 14.57 42.49 2.73
2476 2618 8.915057 TTGTTGTCTCTGTACTAGTAGTAGTT 57.085 34.615 15.34 0.94 40.23 2.24
2478 2620 9.429359 TGTTGTCTCTGTACTAGTAGTAGTTAC 57.571 37.037 15.34 11.44 40.23 2.50
2479 2621 9.651913 GTTGTCTCTGTACTAGTAGTAGTTACT 57.348 37.037 15.34 0.00 44.71 2.24
2480 2622 9.868277 TTGTCTCTGTACTAGTAGTAGTTACTC 57.132 37.037 15.34 5.55 41.70 2.59
2481 2623 8.474025 TGTCTCTGTACTAGTAGTAGTTACTCC 58.526 40.741 15.34 0.00 41.70 3.85
2482 2624 7.926018 GTCTCTGTACTAGTAGTAGTTACTCCC 59.074 44.444 15.34 0.00 41.70 4.30
2483 2625 7.843760 TCTCTGTACTAGTAGTAGTTACTCCCT 59.156 40.741 15.34 0.00 41.70 4.20
2484 2626 8.017418 TCTGTACTAGTAGTAGTTACTCCCTC 57.983 42.308 15.34 0.00 41.70 4.30
2485 2627 7.070571 TCTGTACTAGTAGTAGTTACTCCCTCC 59.929 44.444 15.34 0.00 41.70 4.30
2486 2628 5.289083 ACTAGTAGTAGTTACTCCCTCCG 57.711 47.826 0.00 0.00 41.70 4.63
2487 2629 4.719273 ACTAGTAGTAGTTACTCCCTCCGT 59.281 45.833 0.00 0.00 41.70 4.69
2488 2630 4.149511 AGTAGTAGTTACTCCCTCCGTC 57.850 50.000 0.00 0.00 38.20 4.79
2489 2631 2.433662 AGTAGTTACTCCCTCCGTCC 57.566 55.000 0.00 0.00 0.00 4.79
2490 2632 1.064091 AGTAGTTACTCCCTCCGTCCC 60.064 57.143 0.00 0.00 0.00 4.46
2491 2633 1.002069 TAGTTACTCCCTCCGTCCCA 58.998 55.000 0.00 0.00 0.00 4.37
2492 2634 0.338814 AGTTACTCCCTCCGTCCCAT 59.661 55.000 0.00 0.00 0.00 4.00
2493 2635 1.572415 AGTTACTCCCTCCGTCCCATA 59.428 52.381 0.00 0.00 0.00 2.74
2494 2636 2.023695 AGTTACTCCCTCCGTCCCATAA 60.024 50.000 0.00 0.00 0.00 1.90
2495 2637 2.970640 GTTACTCCCTCCGTCCCATAAT 59.029 50.000 0.00 0.00 0.00 1.28
2496 2638 4.140853 AGTTACTCCCTCCGTCCCATAATA 60.141 45.833 0.00 0.00 0.00 0.98
2497 2639 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
2498 2640 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
2499 2641 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
2500 2642 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
2501 2643 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
2502 2644 5.269991 TCCCTCCGTCCCATAATATAAGAG 58.730 45.833 0.00 0.00 0.00 2.85
2503 2645 4.141914 CCCTCCGTCCCATAATATAAGAGC 60.142 50.000 0.00 0.00 0.00 4.09
2504 2646 4.440250 CCTCCGTCCCATAATATAAGAGCG 60.440 50.000 0.00 0.00 0.00 5.03
2505 2647 4.084287 TCCGTCCCATAATATAAGAGCGT 58.916 43.478 0.00 0.00 0.00 5.07
2506 2648 4.525487 TCCGTCCCATAATATAAGAGCGTT 59.475 41.667 0.00 0.00 0.00 4.84
2507 2649 5.011329 TCCGTCCCATAATATAAGAGCGTTT 59.989 40.000 0.00 0.00 0.00 3.60
2508 2650 5.699458 CCGTCCCATAATATAAGAGCGTTTT 59.301 40.000 0.00 0.00 0.00 2.43
2509 2651 6.204108 CCGTCCCATAATATAAGAGCGTTTTT 59.796 38.462 0.00 0.00 0.00 1.94
2510 2652 7.069569 CGTCCCATAATATAAGAGCGTTTTTG 58.930 38.462 0.00 0.00 0.00 2.44
2511 2653 7.042321 CGTCCCATAATATAAGAGCGTTTTTGA 60.042 37.037 0.00 0.00 0.00 2.69
2512 2654 8.068380 GTCCCATAATATAAGAGCGTTTTTGAC 58.932 37.037 0.00 0.00 0.00 3.18
2513 2655 7.771361 TCCCATAATATAAGAGCGTTTTTGACA 59.229 33.333 0.00 0.00 0.00 3.58
2514 2656 7.855904 CCCATAATATAAGAGCGTTTTTGACAC 59.144 37.037 0.00 0.00 0.00 3.67
2515 2657 8.612619 CCATAATATAAGAGCGTTTTTGACACT 58.387 33.333 0.00 0.00 0.00 3.55
2518 2660 8.773404 AATATAAGAGCGTTTTTGACACTAGT 57.227 30.769 0.00 0.00 0.00 2.57
2519 2661 9.865321 AATATAAGAGCGTTTTTGACACTAGTA 57.135 29.630 0.00 0.00 0.00 1.82
2520 2662 7.813852 ATAAGAGCGTTTTTGACACTAGTAG 57.186 36.000 0.00 0.00 0.00 2.57
2521 2663 5.197682 AGAGCGTTTTTGACACTAGTAGT 57.802 39.130 0.00 0.00 0.00 2.73
2536 2678 7.426929 CACTAGTAGTGTCAAAAATGCTCTT 57.573 36.000 20.29 0.00 41.19 2.85
2537 2679 8.534333 CACTAGTAGTGTCAAAAATGCTCTTA 57.466 34.615 20.29 0.00 41.19 2.10
2538 2680 9.155975 CACTAGTAGTGTCAAAAATGCTCTTAT 57.844 33.333 20.29 0.00 41.19 1.73
2576 2718 5.717078 AACGCTCTTATATTATGGGACGA 57.283 39.130 0.00 0.00 0.00 4.20
2713 2855 6.540914 TCCTCGTTGACAAGTAAATTTTCAGT 59.459 34.615 0.00 0.00 0.00 3.41
2787 3016 0.391661 ACTGCATGCCCTTAGTGACG 60.392 55.000 16.68 0.00 0.00 4.35
2793 3022 1.139095 GCCCTTAGTGACGAGGTCG 59.861 63.158 7.17 0.00 46.33 4.79
2815 3044 7.825270 GGTCGGTTGGGGAATTTTAATAATTTT 59.175 33.333 0.00 0.00 0.00 1.82
2841 3078 0.904649 TAGATCCAGCCACACCACAG 59.095 55.000 0.00 0.00 0.00 3.66
2923 3160 0.618458 TCCACTATGACCTGGGCAAC 59.382 55.000 6.20 0.00 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
124 125 2.548057 CCATGACAGCGTTGTACAAGTT 59.452 45.455 8.98 0.00 37.76 2.66
187 188 8.579850 TTTGCCTTATGTTCTGTGAGATAATT 57.420 30.769 0.00 0.00 0.00 1.40
489 553 9.212687 CAACATTTTGACAATTCATGAAACAAC 57.787 29.630 13.09 5.77 34.24 3.32
546 614 4.260985 TGAGGTATGTTGCATGAACGATT 58.739 39.130 0.00 0.00 37.38 3.34
547 615 3.872696 TGAGGTATGTTGCATGAACGAT 58.127 40.909 0.00 0.00 37.38 3.73
548 616 3.056179 TCTGAGGTATGTTGCATGAACGA 60.056 43.478 0.00 0.00 37.38 3.85
559 627 5.208890 TGGTAGCTTGTATCTGAGGTATGT 58.791 41.667 0.00 0.00 0.00 2.29
591 659 3.253921 CAGATGAGACATGTTGCACCAAA 59.746 43.478 0.00 0.00 0.00 3.28
593 661 2.038820 TCAGATGAGACATGTTGCACCA 59.961 45.455 0.00 0.00 0.00 4.17
594 662 2.703416 TCAGATGAGACATGTTGCACC 58.297 47.619 0.00 0.00 0.00 5.01
609 677 3.881688 GTGTTTGATAGGCTGCATCAGAT 59.118 43.478 0.50 0.00 34.07 2.90
717 785 4.650754 AGTATAGTCGTTCCCATGTGAC 57.349 45.455 0.00 0.00 0.00 3.67
721 789 4.022242 CACCCTAGTATAGTCGTTCCCATG 60.022 50.000 0.00 0.00 36.82 3.66
730 798 3.321396 GCTGTTCCCACCCTAGTATAGTC 59.679 52.174 0.00 0.00 36.82 2.59
736 804 1.569653 GTAGCTGTTCCCACCCTAGT 58.430 55.000 0.00 0.00 0.00 2.57
762 830 2.640826 CCCTCAACAACCACTAAGGGTA 59.359 50.000 0.00 0.00 41.32 3.69
783 851 1.230635 ACATGCGAGTGGTGCTCAAC 61.231 55.000 0.00 0.00 44.33 3.18
784 852 0.534877 AACATGCGAGTGGTGCTCAA 60.535 50.000 0.00 0.00 44.33 3.02
785 853 0.320050 TAACATGCGAGTGGTGCTCA 59.680 50.000 0.00 0.00 44.33 4.26
786 854 0.721718 GTAACATGCGAGTGGTGCTC 59.278 55.000 0.00 0.00 40.77 4.26
787 855 0.321671 AGTAACATGCGAGTGGTGCT 59.678 50.000 0.00 0.00 0.00 4.40
788 856 0.721718 GAGTAACATGCGAGTGGTGC 59.278 55.000 0.00 0.00 0.00 5.01
789 857 2.370281 AGAGTAACATGCGAGTGGTG 57.630 50.000 0.00 0.00 0.00 4.17
790 858 2.671351 CGAAGAGTAACATGCGAGTGGT 60.671 50.000 0.00 0.00 0.00 4.16
791 859 1.920574 CGAAGAGTAACATGCGAGTGG 59.079 52.381 0.00 0.00 0.00 4.00
792 860 1.321743 GCGAAGAGTAACATGCGAGTG 59.678 52.381 0.00 0.00 0.00 3.51
793 861 1.202582 AGCGAAGAGTAACATGCGAGT 59.797 47.619 0.00 0.00 0.00 4.18
794 862 1.849219 GAGCGAAGAGTAACATGCGAG 59.151 52.381 0.00 0.00 0.00 5.03
795 863 1.794076 CGAGCGAAGAGTAACATGCGA 60.794 52.381 0.00 0.00 0.00 5.10
796 864 0.567968 CGAGCGAAGAGTAACATGCG 59.432 55.000 0.00 0.00 0.00 4.73
797 865 1.630148 ACGAGCGAAGAGTAACATGC 58.370 50.000 0.00 0.00 0.00 4.06
798 866 2.987149 ACAACGAGCGAAGAGTAACATG 59.013 45.455 0.00 0.00 0.00 3.21
799 867 3.243336 GACAACGAGCGAAGAGTAACAT 58.757 45.455 0.00 0.00 0.00 2.71
800 868 2.033675 TGACAACGAGCGAAGAGTAACA 59.966 45.455 0.00 0.00 0.00 2.41
801 869 2.658285 TGACAACGAGCGAAGAGTAAC 58.342 47.619 0.00 0.00 0.00 2.50
802 870 3.242518 CATGACAACGAGCGAAGAGTAA 58.757 45.455 0.00 0.00 0.00 2.24
803 871 2.863739 CATGACAACGAGCGAAGAGTA 58.136 47.619 0.00 0.00 0.00 2.59
804 872 1.702886 CATGACAACGAGCGAAGAGT 58.297 50.000 0.00 0.00 0.00 3.24
805 873 0.368227 GCATGACAACGAGCGAAGAG 59.632 55.000 0.00 0.00 0.00 2.85
806 874 1.014044 GGCATGACAACGAGCGAAGA 61.014 55.000 0.00 0.00 0.00 2.87
807 875 1.291184 TGGCATGACAACGAGCGAAG 61.291 55.000 0.00 0.00 0.00 3.79
808 876 0.882484 TTGGCATGACAACGAGCGAA 60.882 50.000 10.79 0.00 0.00 4.70
809 877 1.301322 TTGGCATGACAACGAGCGA 60.301 52.632 10.79 0.00 0.00 4.93
810 878 1.154413 GTTGGCATGACAACGAGCG 60.154 57.895 27.85 0.00 41.00 5.03
811 879 4.847255 GTTGGCATGACAACGAGC 57.153 55.556 27.85 6.26 41.00 5.03
816 884 2.139917 GTACACGAGTTGGCATGACAA 58.860 47.619 10.79 10.79 0.00 3.18
817 885 1.069358 TGTACACGAGTTGGCATGACA 59.931 47.619 0.00 0.00 0.00 3.58
818 886 1.790755 TGTACACGAGTTGGCATGAC 58.209 50.000 0.00 0.00 0.00 3.06
819 887 2.289382 ACATGTACACGAGTTGGCATGA 60.289 45.455 21.48 0.00 41.47 3.07
820 888 2.076100 ACATGTACACGAGTTGGCATG 58.924 47.619 16.64 16.64 43.08 4.06
821 889 2.472695 ACATGTACACGAGTTGGCAT 57.527 45.000 0.00 0.00 0.00 4.40
822 890 2.248280 AACATGTACACGAGTTGGCA 57.752 45.000 0.00 0.00 0.00 4.92
823 891 2.546368 TGAAACATGTACACGAGTTGGC 59.454 45.455 0.00 1.53 0.00 4.52
824 892 3.807622 AGTGAAACATGTACACGAGTTGG 59.192 43.478 21.78 0.00 41.43 3.77
825 893 5.403897 AAGTGAAACATGTACACGAGTTG 57.596 39.130 21.78 0.00 41.43 3.16
826 894 5.815740 AGAAAGTGAAACATGTACACGAGTT 59.184 36.000 21.78 18.24 41.43 3.01
827 895 5.234329 CAGAAAGTGAAACATGTACACGAGT 59.766 40.000 21.78 14.74 41.43 4.18
828 896 5.234329 ACAGAAAGTGAAACATGTACACGAG 59.766 40.000 21.78 15.76 41.43 4.18
829 897 5.113383 ACAGAAAGTGAAACATGTACACGA 58.887 37.500 21.78 0.00 41.43 4.35
830 898 5.403897 ACAGAAAGTGAAACATGTACACG 57.596 39.130 21.78 13.96 41.43 4.49
831 899 7.478520 AGTACAGAAAGTGAAACATGTACAC 57.521 36.000 21.02 21.02 42.22 2.90
832 900 9.602568 TTAAGTACAGAAAGTGAAACATGTACA 57.397 29.630 13.81 0.00 42.22 2.90
835 903 8.567948 CCATTAAGTACAGAAAGTGAAACATGT 58.432 33.333 0.00 0.00 41.43 3.21
836 904 8.783093 TCCATTAAGTACAGAAAGTGAAACATG 58.217 33.333 0.00 0.00 41.43 3.21
837 905 8.918202 TCCATTAAGTACAGAAAGTGAAACAT 57.082 30.769 0.00 0.00 41.43 2.71
838 906 8.740123 TTCCATTAAGTACAGAAAGTGAAACA 57.260 30.769 0.00 0.00 41.43 2.83
839 907 9.665264 CTTTCCATTAAGTACAGAAAGTGAAAC 57.335 33.333 0.00 0.00 38.92 2.78
840 908 9.621629 TCTTTCCATTAAGTACAGAAAGTGAAA 57.378 29.630 9.79 0.00 42.47 2.69
841 909 9.793259 ATCTTTCCATTAAGTACAGAAAGTGAA 57.207 29.630 9.79 0.00 42.47 3.18
844 912 9.668497 GGTATCTTTCCATTAAGTACAGAAAGT 57.332 33.333 9.79 2.50 42.47 2.66
845 913 9.667107 TGGTATCTTTCCATTAAGTACAGAAAG 57.333 33.333 0.00 0.00 42.98 2.62
848 916 9.832445 GATTGGTATCTTTCCATTAAGTACAGA 57.168 33.333 0.00 0.00 34.75 3.41
849 917 9.838339 AGATTGGTATCTTTCCATTAAGTACAG 57.162 33.333 0.00 0.00 37.90 2.74
850 918 9.832445 GAGATTGGTATCTTTCCATTAAGTACA 57.168 33.333 0.00 0.00 41.23 2.90
851 919 8.979574 CGAGATTGGTATCTTTCCATTAAGTAC 58.020 37.037 0.00 0.00 41.23 2.73
852 920 8.701895 ACGAGATTGGTATCTTTCCATTAAGTA 58.298 33.333 0.00 0.00 41.23 2.24
853 921 7.565680 ACGAGATTGGTATCTTTCCATTAAGT 58.434 34.615 0.00 0.00 41.23 2.24
854 922 7.096023 CGACGAGATTGGTATCTTTCCATTAAG 60.096 40.741 0.00 0.00 41.23 1.85
855 923 6.700081 CGACGAGATTGGTATCTTTCCATTAA 59.300 38.462 0.00 0.00 41.23 1.40
856 924 6.183360 ACGACGAGATTGGTATCTTTCCATTA 60.183 38.462 0.00 0.00 41.23 1.90
857 925 5.050490 CGACGAGATTGGTATCTTTCCATT 58.950 41.667 0.00 0.00 41.23 3.16
858 926 4.099573 ACGACGAGATTGGTATCTTTCCAT 59.900 41.667 0.00 0.00 41.23 3.41
859 927 3.446161 ACGACGAGATTGGTATCTTTCCA 59.554 43.478 0.00 0.00 41.23 3.53
860 928 4.043037 ACGACGAGATTGGTATCTTTCC 57.957 45.455 0.00 0.00 41.23 3.13
861 929 6.086502 CGAATACGACGAGATTGGTATCTTTC 59.913 42.308 0.00 0.00 40.44 2.62
862 930 5.913514 CGAATACGACGAGATTGGTATCTTT 59.086 40.000 0.00 0.00 40.44 2.52
863 931 5.008415 ACGAATACGACGAGATTGGTATCTT 59.992 40.000 0.00 0.00 40.44 2.40
864 932 4.514441 ACGAATACGACGAGATTGGTATCT 59.486 41.667 0.00 0.00 41.87 1.98
865 933 4.781071 ACGAATACGACGAGATTGGTATC 58.219 43.478 0.00 0.00 42.66 2.24
866 934 4.825546 ACGAATACGACGAGATTGGTAT 57.174 40.909 0.00 0.00 42.66 2.73
867 935 5.733226 TTACGAATACGACGAGATTGGTA 57.267 39.130 0.00 9.49 42.66 3.25
868 936 4.621068 TTACGAATACGACGAGATTGGT 57.379 40.909 0.00 10.44 42.66 3.67
869 937 5.740569 TCTTTTACGAATACGACGAGATTGG 59.259 40.000 0.00 4.89 42.66 3.16
870 938 6.785633 TCTTTTACGAATACGACGAGATTG 57.214 37.500 0.00 0.00 42.66 2.67
871 939 7.801547 TTTCTTTTACGAATACGACGAGATT 57.198 32.000 0.00 0.12 42.66 2.40
872 940 7.801547 TTTTCTTTTACGAATACGACGAGAT 57.198 32.000 0.00 0.00 42.66 2.75
873 941 7.621832 TTTTTCTTTTACGAATACGACGAGA 57.378 32.000 0.00 0.00 42.66 4.04
894 962 8.835439 CCCAATTACTTATTTGCTTGTGTTTTT 58.165 29.630 0.00 0.00 0.00 1.94
895 963 8.207545 TCCCAATTACTTATTTGCTTGTGTTTT 58.792 29.630 0.00 0.00 0.00 2.43
896 964 7.731054 TCCCAATTACTTATTTGCTTGTGTTT 58.269 30.769 0.00 0.00 0.00 2.83
897 965 7.296628 TCCCAATTACTTATTTGCTTGTGTT 57.703 32.000 0.00 0.00 0.00 3.32
898 966 6.909550 TCCCAATTACTTATTTGCTTGTGT 57.090 33.333 0.00 0.00 0.00 3.72
899 967 6.813152 CCTTCCCAATTACTTATTTGCTTGTG 59.187 38.462 0.00 0.00 0.00 3.33
900 968 6.496911 ACCTTCCCAATTACTTATTTGCTTGT 59.503 34.615 0.00 0.00 0.00 3.16
901 969 6.813152 CACCTTCCCAATTACTTATTTGCTTG 59.187 38.462 0.00 0.00 0.00 4.01
902 970 6.574269 GCACCTTCCCAATTACTTATTTGCTT 60.574 38.462 0.00 0.00 0.00 3.91
903 971 5.105351 GCACCTTCCCAATTACTTATTTGCT 60.105 40.000 0.00 0.00 0.00 3.91
904 972 5.105351 AGCACCTTCCCAATTACTTATTTGC 60.105 40.000 0.00 0.00 0.00 3.68
905 973 6.530019 AGCACCTTCCCAATTACTTATTTG 57.470 37.500 0.00 0.00 0.00 2.32
906 974 6.833933 CCTAGCACCTTCCCAATTACTTATTT 59.166 38.462 0.00 0.00 0.00 1.40
907 975 6.069029 ACCTAGCACCTTCCCAATTACTTATT 60.069 38.462 0.00 0.00 0.00 1.40
908 976 5.432060 ACCTAGCACCTTCCCAATTACTTAT 59.568 40.000 0.00 0.00 0.00 1.73
909 977 4.786454 ACCTAGCACCTTCCCAATTACTTA 59.214 41.667 0.00 0.00 0.00 2.24
910 978 3.591977 ACCTAGCACCTTCCCAATTACTT 59.408 43.478 0.00 0.00 0.00 2.24
911 979 3.054361 CACCTAGCACCTTCCCAATTACT 60.054 47.826 0.00 0.00 0.00 2.24
912 980 3.054655 TCACCTAGCACCTTCCCAATTAC 60.055 47.826 0.00 0.00 0.00 1.89
1098 1204 1.600916 GAAAGAGCTTGGCGGTGGT 60.601 57.895 0.00 0.00 0.00 4.16
1194 1300 3.670377 GGTGGTGTTTGGGCTCGC 61.670 66.667 0.00 0.00 0.00 5.03
1256 1362 2.359975 GTGGTTTCTGGAGCCGGG 60.360 66.667 2.18 0.00 0.00 5.73
1257 1363 2.359975 GGTGGTTTCTGGAGCCGG 60.360 66.667 0.00 0.00 0.00 6.13
1258 1364 2.359975 GGGTGGTTTCTGGAGCCG 60.360 66.667 0.00 0.00 0.00 5.52
1259 1365 2.035783 GGGGTGGTTTCTGGAGCC 59.964 66.667 0.00 0.00 0.00 4.70
1260 1366 2.035783 GGGGGTGGTTTCTGGAGC 59.964 66.667 0.00 0.00 0.00 4.70
1274 1380 1.826024 CTTCATCGACTCCAGGGGG 59.174 63.158 0.00 0.00 0.00 5.40
1709 1815 1.258982 GCTTACCGCATCAAGATCGTG 59.741 52.381 1.76 1.76 38.92 4.35
1758 1864 8.404000 TCTTATTCCTCGAATACTGACACTAAC 58.596 37.037 0.00 0.00 34.73 2.34
1825 1931 3.731652 TCAACATCCAAAAGCACCAAG 57.268 42.857 0.00 0.00 0.00 3.61
1936 2042 5.651530 TGATCCATCTAACAGAAGACGAAC 58.348 41.667 0.00 0.00 0.00 3.95
2082 2188 7.113658 TCCCAAAACTTTGTTTAGCAATACA 57.886 32.000 1.76 0.00 36.89 2.29
2095 2201 7.418254 GCCATATCATGAAGATCCCAAAACTTT 60.418 37.037 0.00 0.00 38.19 2.66
2227 2367 2.099592 GGCATGATTTTTCAGATGGCGA 59.900 45.455 0.00 0.00 32.49 5.54
2294 2434 4.497291 TCTCACAAACCACACTTAACCT 57.503 40.909 0.00 0.00 0.00 3.50
2363 2503 7.016072 TCCAATTTCACCACCTTTTATCAATGT 59.984 33.333 0.00 0.00 0.00 2.71
2367 2507 6.310941 TCTCCAATTTCACCACCTTTTATCA 58.689 36.000 0.00 0.00 0.00 2.15
2469 2611 2.173569 GGGACGGAGGGAGTAACTACTA 59.826 54.545 0.00 0.00 36.50 1.82
2470 2612 1.064091 GGGACGGAGGGAGTAACTACT 60.064 57.143 0.00 0.00 39.71 2.57
2471 2613 1.341383 TGGGACGGAGGGAGTAACTAC 60.341 57.143 0.00 0.00 0.00 2.73
2472 2614 1.002069 TGGGACGGAGGGAGTAACTA 58.998 55.000 0.00 0.00 0.00 2.24
2473 2615 0.338814 ATGGGACGGAGGGAGTAACT 59.661 55.000 0.00 0.00 0.00 2.24
2474 2616 2.077687 TATGGGACGGAGGGAGTAAC 57.922 55.000 0.00 0.00 0.00 2.50
2475 2617 2.852714 TTATGGGACGGAGGGAGTAA 57.147 50.000 0.00 0.00 0.00 2.24
2476 2618 4.687262 ATATTATGGGACGGAGGGAGTA 57.313 45.455 0.00 0.00 0.00 2.59
2477 2619 3.562108 ATATTATGGGACGGAGGGAGT 57.438 47.619 0.00 0.00 0.00 3.85
2478 2620 5.269991 TCTTATATTATGGGACGGAGGGAG 58.730 45.833 0.00 0.00 0.00 4.30
2479 2621 5.269991 CTCTTATATTATGGGACGGAGGGA 58.730 45.833 0.00 0.00 0.00 4.20
2480 2622 4.141914 GCTCTTATATTATGGGACGGAGGG 60.142 50.000 0.00 0.00 0.00 4.30
2481 2623 4.440250 CGCTCTTATATTATGGGACGGAGG 60.440 50.000 0.00 0.00 0.00 4.30
2482 2624 4.158025 ACGCTCTTATATTATGGGACGGAG 59.842 45.833 0.00 0.00 0.00 4.63
2483 2625 4.084287 ACGCTCTTATATTATGGGACGGA 58.916 43.478 0.00 0.00 0.00 4.69
2484 2626 4.451629 ACGCTCTTATATTATGGGACGG 57.548 45.455 0.00 0.00 0.00 4.79
2485 2627 6.780706 AAAACGCTCTTATATTATGGGACG 57.219 37.500 0.00 0.00 0.00 4.79
2486 2628 8.068380 GTCAAAAACGCTCTTATATTATGGGAC 58.932 37.037 0.00 0.00 0.00 4.46
2487 2629 7.771361 TGTCAAAAACGCTCTTATATTATGGGA 59.229 33.333 0.00 0.00 0.00 4.37
2488 2630 7.855904 GTGTCAAAAACGCTCTTATATTATGGG 59.144 37.037 0.00 0.00 35.42 4.00
2489 2631 8.612619 AGTGTCAAAAACGCTCTTATATTATGG 58.387 33.333 0.00 0.00 45.69 2.74
2492 2634 9.865321 ACTAGTGTCAAAAACGCTCTTATATTA 57.135 29.630 0.00 0.00 45.69 0.98
2493 2635 8.773404 ACTAGTGTCAAAAACGCTCTTATATT 57.227 30.769 0.00 0.00 45.69 1.28
2494 2636 9.517609 CTACTAGTGTCAAAAACGCTCTTATAT 57.482 33.333 5.39 0.00 45.69 0.86
2495 2637 8.517878 ACTACTAGTGTCAAAAACGCTCTTATA 58.482 33.333 5.39 0.00 45.69 0.98
2496 2638 7.328737 CACTACTAGTGTCAAAAACGCTCTTAT 59.671 37.037 5.39 0.00 45.69 1.73
2497 2639 6.639686 CACTACTAGTGTCAAAAACGCTCTTA 59.360 38.462 5.39 0.00 45.69 2.10
2498 2640 5.462398 CACTACTAGTGTCAAAAACGCTCTT 59.538 40.000 5.39 0.00 45.69 2.85
2499 2641 4.982916 CACTACTAGTGTCAAAAACGCTCT 59.017 41.667 5.39 0.00 45.69 4.09
2500 2642 5.251999 CACTACTAGTGTCAAAAACGCTC 57.748 43.478 5.39 0.00 45.69 5.03
2533 2675 9.865321 AGCGTTTTTGACACTAGTAATATAAGA 57.135 29.630 0.00 0.00 0.00 2.10
2535 2677 9.865321 AGAGCGTTTTTGACACTAGTAATATAA 57.135 29.630 0.00 0.00 0.00 0.98
2536 2678 9.865321 AAGAGCGTTTTTGACACTAGTAATATA 57.135 29.630 0.00 0.00 0.00 0.86
2537 2679 8.773404 AAGAGCGTTTTTGACACTAGTAATAT 57.227 30.769 0.00 0.00 0.00 1.28
2538 2680 9.865321 ATAAGAGCGTTTTTGACACTAGTAATA 57.135 29.630 0.00 0.00 0.00 0.98
2539 2681 8.773404 ATAAGAGCGTTTTTGACACTAGTAAT 57.227 30.769 0.00 0.00 0.00 1.89
2540 2682 9.865321 ATATAAGAGCGTTTTTGACACTAGTAA 57.135 29.630 0.00 0.00 0.00 2.24
2541 2683 9.865321 AATATAAGAGCGTTTTTGACACTAGTA 57.135 29.630 0.00 0.00 0.00 1.82
2542 2684 8.773404 AATATAAGAGCGTTTTTGACACTAGT 57.227 30.769 0.00 0.00 0.00 2.57
2576 2718 6.814954 ATGTAGATTGTCATGTACTCCCTT 57.185 37.500 0.00 0.00 31.62 3.95
2713 2855 7.344612 TGGTCCAAGCTGATCTATCTAAGTTTA 59.655 37.037 0.00 0.00 0.00 2.01
2787 3016 1.919240 AAAATTCCCCAACCGACCTC 58.081 50.000 0.00 0.00 0.00 3.85
2793 3022 8.735315 CCACAAAATTATTAAAATTCCCCAACC 58.265 33.333 0.00 0.00 0.00 3.77
2815 3044 0.618458 GTGGCTGGATCTAACCCACA 59.382 55.000 18.15 0.00 44.07 4.17
2841 3078 9.132521 CCTCATAAACAACAAAGATCAATTCAC 57.867 33.333 0.00 0.00 0.00 3.18
2923 3160 0.883833 AAGTCAAGCCCTGCATTTCG 59.116 50.000 0.00 0.00 0.00 3.46


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

AutoCloner maintained by Alex Coulton.