Multiple sequence alignment - TraesCS7D01G299800

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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 TraesCS7D01G299800 chr7D 100.000 2762 0 0 1 2762 379824444 379827205 0.000000e+00 5101.0
1 TraesCS7D01G299800 chr7D 92.926 622 44 0 42 663 511635768 511635147 0.000000e+00 905.0
2 TraesCS7D01G299800 chr7D 91.935 620 50 0 44 663 511646262 511645643 0.000000e+00 869.0
3 TraesCS7D01G299800 chr7D 94.444 54 1 2 1 54 511646366 511646315 6.340000e-12 82.4
4 TraesCS7D01G299800 chr7D 92.593 54 2 2 1 54 379777196 379777247 2.950000e-10 76.8
5 TraesCS7D01G299800 chr7B 90.976 1219 64 25 998 2196 374982614 374983806 0.000000e+00 1600.0
6 TraesCS7D01G299800 chr7B 94.082 490 22 4 2278 2762 374983804 374984291 0.000000e+00 737.0
7 TraesCS7D01G299800 chr7B 92.593 54 2 2 1 54 413926731 413926680 2.950000e-10 76.8
8 TraesCS7D01G299800 chr2D 95.375 627 28 1 42 667 113395792 113395166 0.000000e+00 996.0
9 TraesCS7D01G299800 chr2D 94.212 622 36 0 42 663 113426707 113426086 0.000000e+00 950.0
10 TraesCS7D01G299800 chr2D 92.122 622 49 0 42 663 488350132 488349511 0.000000e+00 878.0
11 TraesCS7D01G299800 chr2D 92.982 57 1 3 1 56 113426809 113426755 2.280000e-11 80.5
12 TraesCS7D01G299800 chr7A 93.353 662 26 7 972 1616 428340812 428341472 0.000000e+00 963.0
13 TraesCS7D01G299800 chr7A 94.118 493 20 4 2277 2762 428341992 428342482 0.000000e+00 741.0
14 TraesCS7D01G299800 chr7A 88.625 589 29 10 1612 2193 428341432 428341989 0.000000e+00 682.0
15 TraesCS7D01G299800 chr4A 92.765 622 45 0 42 663 512633329 512633950 0.000000e+00 900.0
16 TraesCS7D01G299800 chr4A 100.000 43 0 0 1 43 512840883 512840925 2.280000e-11 80.5
17 TraesCS7D01G299800 chr4B 92.616 623 42 4 42 663 472889750 472890369 0.000000e+00 893.0
18 TraesCS7D01G299800 chr6D 91.961 622 46 4 43 663 398886098 398885480 0.000000e+00 869.0
19 TraesCS7D01G299800 chr6D 91.814 623 49 2 42 663 377497148 377497769 0.000000e+00 867.0
20 TraesCS7D01G299800 chr6D 98.913 92 0 1 2194 2285 459173414 459173504 2.200000e-36 163.0
21 TraesCS7D01G299800 chr6D 90.909 110 7 3 2172 2280 408688813 408688706 7.970000e-31 145.0
22 TraesCS7D01G299800 chr6D 94.118 51 1 2 4 54 377497049 377497097 2.950000e-10 76.8
23 TraesCS7D01G299800 chr6B 94.444 108 3 3 2195 2300 238156897 238156791 2.200000e-36 163.0
24 TraesCS7D01G299800 chr3B 98.901 91 1 0 2191 2281 689513368 689513458 2.200000e-36 163.0
25 TraesCS7D01G299800 chr3D 97.826 92 1 1 2195 2286 415158283 415158373 1.020000e-34 158.0
26 TraesCS7D01G299800 chr2B 95.833 96 4 0 2195 2290 13713104 13713009 3.680000e-34 156.0
27 TraesCS7D01G299800 chr2B 98.851 87 1 0 2195 2281 40437958 40438044 3.680000e-34 156.0
28 TraesCS7D01G299800 chr2B 90.265 113 9 2 2195 2307 506102678 506102568 2.220000e-31 147.0
29 TraesCS7D01G299800 chr5D 93.204 103 5 2 2195 2297 226705943 226705843 1.710000e-32 150.0
30 TraesCS7D01G299800 chr2A 94.444 54 1 2 1 54 635914801 635914750 6.340000e-12 82.4
31 TraesCS7D01G299800 chr3A 94.340 53 1 2 2 54 43105039 43104989 2.280000e-11 80.5
32 TraesCS7D01G299800 chr3A 94.340 53 1 2 2 54 43713869 43713819 2.280000e-11 80.5
33 TraesCS7D01G299800 chr1D 94.872 39 2 0 925 963 7043489 7043451 8.260000e-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 TraesCS7D01G299800 chr7D 379824444 379827205 2761 False 5101.000000 5101 100.0000 1 2762 1 chr7D.!!$F2 2761
1 TraesCS7D01G299800 chr7D 511635147 511635768 621 True 905.000000 905 92.9260 42 663 1 chr7D.!!$R1 621
2 TraesCS7D01G299800 chr7D 511645643 511646366 723 True 475.700000 869 93.1895 1 663 2 chr7D.!!$R2 662
3 TraesCS7D01G299800 chr7B 374982614 374984291 1677 False 1168.500000 1600 92.5290 998 2762 2 chr7B.!!$F1 1764
4 TraesCS7D01G299800 chr2D 113395166 113395792 626 True 996.000000 996 95.3750 42 667 1 chr2D.!!$R1 625
5 TraesCS7D01G299800 chr2D 488349511 488350132 621 True 878.000000 878 92.1220 42 663 1 chr2D.!!$R2 621
6 TraesCS7D01G299800 chr2D 113426086 113426809 723 True 515.250000 950 93.5970 1 663 2 chr2D.!!$R3 662
7 TraesCS7D01G299800 chr7A 428340812 428342482 1670 False 795.333333 963 92.0320 972 2762 3 chr7A.!!$F1 1790
8 TraesCS7D01G299800 chr4A 512633329 512633950 621 False 900.000000 900 92.7650 42 663 1 chr4A.!!$F1 621
9 TraesCS7D01G299800 chr4B 472889750 472890369 619 False 893.000000 893 92.6160 42 663 1 chr4B.!!$F1 621
10 TraesCS7D01G299800 chr6D 398885480 398886098 618 True 869.000000 869 91.9610 43 663 1 chr6D.!!$R1 620
11 TraesCS7D01G299800 chr6D 377497049 377497769 720 False 471.900000 867 92.9660 4 663 2 chr6D.!!$F2 659

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
966 1031 0.039074 AGAGCGTTCAGAACACGGAG 60.039 55.0 13.82 0.0 38.13 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2263 2375 2.019807 AGTTACTCCCTCCGTTCCAA 57.98 50.0 0.0 0.0 0.0 3.53 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
100 162 1.566298 GCAGGATCTGGACCCAAGGT 61.566 60.000 0.00 0.00 32.88 3.50
139 201 0.749049 GGGGCGGTACTACCACTTAG 59.251 60.000 6.06 0.00 38.47 2.18
164 226 1.677942 GTACTACCGCCTCTACTGCT 58.322 55.000 0.00 0.00 0.00 4.24
242 304 2.386660 GCTCAGAACAGCAGCGGTC 61.387 63.158 0.00 0.00 39.43 4.79
445 508 2.504175 TGTTGATTCCACCCTAGCCTAC 59.496 50.000 0.00 0.00 0.00 3.18
449 512 0.326238 TTCCACCCTAGCCTACCCAG 60.326 60.000 0.00 0.00 0.00 4.45
503 566 4.277423 CCTACGAAACAAGTCCACCAAAAT 59.723 41.667 0.00 0.00 0.00 1.82
552 615 2.597578 TAAAACTCCAAGGGGAAGGC 57.402 50.000 0.00 0.00 44.38 4.35
647 712 9.219603 CATCAATCACCAAAACTACTTAGAGAA 57.780 33.333 0.00 0.00 0.00 2.87
663 728 6.651225 ACTTAGAGAAAGACATGCCTTAACAC 59.349 38.462 0.00 0.00 38.67 3.32
664 729 4.973168 AGAGAAAGACATGCCTTAACACA 58.027 39.130 0.00 0.00 0.00 3.72
665 730 4.757149 AGAGAAAGACATGCCTTAACACAC 59.243 41.667 0.00 0.00 0.00 3.82
666 731 3.498397 AGAAAGACATGCCTTAACACACG 59.502 43.478 0.00 0.00 0.00 4.49
668 733 0.168128 GACATGCCTTAACACACGGC 59.832 55.000 0.00 0.00 44.02 5.68
669 734 1.241315 ACATGCCTTAACACACGGCC 61.241 55.000 0.00 0.00 43.12 6.13
670 735 1.074072 ATGCCTTAACACACGGCCA 59.926 52.632 2.24 0.00 43.12 5.36
671 736 0.538516 ATGCCTTAACACACGGCCAA 60.539 50.000 2.24 0.00 43.12 4.52
672 737 0.752009 TGCCTTAACACACGGCCAAA 60.752 50.000 2.24 0.00 43.12 3.28
673 738 0.318360 GCCTTAACACACGGCCAAAC 60.318 55.000 2.24 0.00 37.86 2.93
674 739 1.314730 CCTTAACACACGGCCAAACT 58.685 50.000 2.24 0.00 0.00 2.66
675 740 1.679153 CCTTAACACACGGCCAAACTT 59.321 47.619 2.24 0.00 0.00 2.66
676 741 2.100087 CCTTAACACACGGCCAAACTTT 59.900 45.455 2.24 0.00 0.00 2.66
677 742 3.429684 CCTTAACACACGGCCAAACTTTT 60.430 43.478 2.24 0.00 0.00 2.27
678 743 2.753055 AACACACGGCCAAACTTTTT 57.247 40.000 2.24 0.00 0.00 1.94
700 765 4.853507 GCGTGTAGCTGTACGTGA 57.146 55.556 20.67 0.00 44.04 4.35
701 766 3.096541 GCGTGTAGCTGTACGTGAA 57.903 52.632 20.67 0.00 44.04 3.18
702 767 1.625616 GCGTGTAGCTGTACGTGAAT 58.374 50.000 20.67 0.00 44.04 2.57
703 768 1.582502 GCGTGTAGCTGTACGTGAATC 59.417 52.381 20.67 5.35 44.04 2.52
704 769 2.858839 CGTGTAGCTGTACGTGAATCA 58.141 47.619 14.20 0.00 35.70 2.57
705 770 3.435566 CGTGTAGCTGTACGTGAATCAT 58.564 45.455 14.20 0.00 35.70 2.45
706 771 3.240631 CGTGTAGCTGTACGTGAATCATG 59.759 47.826 14.20 0.12 35.70 3.07
707 772 4.421058 GTGTAGCTGTACGTGAATCATGA 58.579 43.478 9.74 0.00 30.95 3.07
708 773 5.043903 GTGTAGCTGTACGTGAATCATGAT 58.956 41.667 9.74 1.18 30.95 2.45
709 774 6.206498 GTGTAGCTGTACGTGAATCATGATA 58.794 40.000 9.04 0.00 30.95 2.15
710 775 6.360947 GTGTAGCTGTACGTGAATCATGATAG 59.639 42.308 9.04 0.96 30.95 2.08
711 776 4.302455 AGCTGTACGTGAATCATGATAGC 58.698 43.478 9.04 11.34 0.00 2.97
712 777 4.038522 AGCTGTACGTGAATCATGATAGCT 59.961 41.667 16.15 16.15 33.57 3.32
713 778 4.747108 GCTGTACGTGAATCATGATAGCTT 59.253 41.667 9.04 0.00 0.00 3.74
714 779 5.235186 GCTGTACGTGAATCATGATAGCTTT 59.765 40.000 9.04 0.00 0.00 3.51
715 780 6.563010 GCTGTACGTGAATCATGATAGCTTTC 60.563 42.308 9.04 3.80 0.00 2.62
716 781 6.573434 TGTACGTGAATCATGATAGCTTTCT 58.427 36.000 9.04 0.00 0.00 2.52
717 782 7.041721 TGTACGTGAATCATGATAGCTTTCTT 58.958 34.615 9.04 0.00 0.00 2.52
718 783 6.355397 ACGTGAATCATGATAGCTTTCTTG 57.645 37.500 9.04 12.11 0.00 3.02
719 784 5.877012 ACGTGAATCATGATAGCTTTCTTGT 59.123 36.000 9.04 3.71 0.00 3.16
720 785 6.183360 ACGTGAATCATGATAGCTTTCTTGTG 60.183 38.462 9.04 8.45 0.00 3.33
721 786 6.183360 CGTGAATCATGATAGCTTTCTTGTGT 60.183 38.462 9.04 8.23 0.00 3.72
722 787 7.010460 CGTGAATCATGATAGCTTTCTTGTGTA 59.990 37.037 9.04 2.49 0.00 2.90
723 788 8.834465 GTGAATCATGATAGCTTTCTTGTGTAT 58.166 33.333 9.04 4.30 0.00 2.29
735 800 9.502091 AGCTTTCTTGTGTATATACAGTTTCAA 57.498 29.630 15.93 14.25 36.78 2.69
764 829 3.872459 AAAAACCAAATGAATGGGCCA 57.128 38.095 9.61 9.61 45.18 5.36
765 830 2.857186 AAACCAAATGAATGGGCCAC 57.143 45.000 9.28 0.00 45.18 5.01
766 831 1.727062 AACCAAATGAATGGGCCACA 58.273 45.000 9.28 3.09 45.18 4.17
767 832 1.727062 ACCAAATGAATGGGCCACAA 58.273 45.000 9.28 0.00 45.18 3.33
768 833 2.053244 ACCAAATGAATGGGCCACAAA 58.947 42.857 9.28 0.00 45.18 2.83
769 834 2.224499 ACCAAATGAATGGGCCACAAAC 60.224 45.455 9.28 0.75 45.18 2.93
770 835 2.224475 CCAAATGAATGGGCCACAAACA 60.224 45.455 9.28 7.34 36.79 2.83
771 836 3.068560 CAAATGAATGGGCCACAAACAG 58.931 45.455 9.28 0.00 0.00 3.16
772 837 2.307496 ATGAATGGGCCACAAACAGA 57.693 45.000 9.28 0.00 0.00 3.41
773 838 2.307496 TGAATGGGCCACAAACAGAT 57.693 45.000 9.28 0.00 0.00 2.90
774 839 3.448093 TGAATGGGCCACAAACAGATA 57.552 42.857 9.28 0.00 0.00 1.98
775 840 3.772387 TGAATGGGCCACAAACAGATAA 58.228 40.909 9.28 0.00 0.00 1.75
776 841 4.352009 TGAATGGGCCACAAACAGATAAT 58.648 39.130 9.28 0.00 0.00 1.28
777 842 4.160065 TGAATGGGCCACAAACAGATAATG 59.840 41.667 9.28 0.00 0.00 1.90
778 843 3.448093 TGGGCCACAAACAGATAATGA 57.552 42.857 0.00 0.00 0.00 2.57
779 844 3.772387 TGGGCCACAAACAGATAATGAA 58.228 40.909 0.00 0.00 0.00 2.57
780 845 3.763360 TGGGCCACAAACAGATAATGAAG 59.237 43.478 0.00 0.00 0.00 3.02
781 846 3.763897 GGGCCACAAACAGATAATGAAGT 59.236 43.478 4.39 0.00 0.00 3.01
782 847 4.142381 GGGCCACAAACAGATAATGAAGTC 60.142 45.833 4.39 0.00 0.00 3.01
783 848 4.458989 GGCCACAAACAGATAATGAAGTCA 59.541 41.667 0.00 0.00 0.00 3.41
784 849 5.126061 GGCCACAAACAGATAATGAAGTCAT 59.874 40.000 0.00 0.00 38.41 3.06
785 850 6.032094 GCCACAAACAGATAATGAAGTCATG 58.968 40.000 0.00 0.00 36.56 3.07
786 851 6.127925 GCCACAAACAGATAATGAAGTCATGA 60.128 38.462 0.00 0.00 36.56 3.07
787 852 7.246311 CCACAAACAGATAATGAAGTCATGAC 58.754 38.462 18.47 18.47 36.56 3.06
788 853 7.094677 CCACAAACAGATAATGAAGTCATGACA 60.095 37.037 27.02 7.81 36.56 3.58
789 854 7.961283 CACAAACAGATAATGAAGTCATGACAG 59.039 37.037 27.02 6.50 36.56 3.51
790 855 7.663081 ACAAACAGATAATGAAGTCATGACAGT 59.337 33.333 27.02 14.72 36.56 3.55
791 856 8.509690 CAAACAGATAATGAAGTCATGACAGTT 58.490 33.333 27.02 13.94 36.56 3.16
792 857 8.627208 AACAGATAATGAAGTCATGACAGTTT 57.373 30.769 27.02 13.20 36.56 2.66
793 858 8.627208 ACAGATAATGAAGTCATGACAGTTTT 57.373 30.769 27.02 12.84 36.56 2.43
794 859 8.725148 ACAGATAATGAAGTCATGACAGTTTTC 58.275 33.333 27.02 20.37 36.56 2.29
795 860 8.944029 CAGATAATGAAGTCATGACAGTTTTCT 58.056 33.333 27.02 18.84 36.56 2.52
796 861 9.512588 AGATAATGAAGTCATGACAGTTTTCTT 57.487 29.630 27.02 15.92 36.56 2.52
797 862 9.552114 GATAATGAAGTCATGACAGTTTTCTTG 57.448 33.333 27.02 0.00 36.56 3.02
798 863 6.949352 ATGAAGTCATGACAGTTTTCTTGT 57.051 33.333 27.02 9.74 34.83 3.16
799 864 6.122850 TGAAGTCATGACAGTTTTCTTGTG 57.877 37.500 27.02 0.00 0.00 3.33
800 865 5.647658 TGAAGTCATGACAGTTTTCTTGTGT 59.352 36.000 27.02 0.00 0.00 3.72
801 866 6.821160 TGAAGTCATGACAGTTTTCTTGTGTA 59.179 34.615 27.02 3.32 0.00 2.90
802 867 7.498900 TGAAGTCATGACAGTTTTCTTGTGTAT 59.501 33.333 27.02 0.00 0.00 2.29
803 868 8.902540 AAGTCATGACAGTTTTCTTGTGTATA 57.097 30.769 27.02 0.00 0.00 1.47
804 869 9.507329 AAGTCATGACAGTTTTCTTGTGTATAT 57.493 29.630 27.02 0.00 0.00 0.86
809 874 9.944376 ATGACAGTTTTCTTGTGTATATACTGT 57.056 29.630 13.89 7.28 45.30 3.55
810 875 9.772973 TGACAGTTTTCTTGTGTATATACTGTT 57.227 29.630 13.89 0.00 43.39 3.16
842 907 3.872459 AAAAACAAATGAATGGGGCCA 57.128 38.095 4.39 0.00 0.00 5.36
843 908 2.857186 AAACAAATGAATGGGGCCAC 57.143 45.000 4.39 0.00 0.00 5.01
844 909 1.727062 AACAAATGAATGGGGCCACA 58.273 45.000 11.97 11.97 0.00 4.17
845 910 1.727062 ACAAATGAATGGGGCCACAA 58.273 45.000 14.33 0.00 0.00 3.33
846 911 2.053244 ACAAATGAATGGGGCCACAAA 58.947 42.857 14.33 0.00 0.00 2.83
847 912 2.224499 ACAAATGAATGGGGCCACAAAC 60.224 45.455 14.33 10.16 0.00 2.93
848 913 1.727062 AATGAATGGGGCCACAAACA 58.273 45.000 14.33 16.41 0.00 2.83
849 914 1.269012 ATGAATGGGGCCACAAACAG 58.731 50.000 14.33 0.00 0.00 3.16
850 915 0.187117 TGAATGGGGCCACAAACAGA 59.813 50.000 14.33 0.00 0.00 3.41
851 916 1.203162 TGAATGGGGCCACAAACAGAT 60.203 47.619 14.33 0.00 0.00 2.90
852 917 2.042297 TGAATGGGGCCACAAACAGATA 59.958 45.455 14.33 0.00 0.00 1.98
853 918 2.917713 ATGGGGCCACAAACAGATAA 57.082 45.000 14.33 0.00 0.00 1.75
854 919 2.917713 TGGGGCCACAAACAGATAAT 57.082 45.000 4.31 0.00 0.00 1.28
855 920 4.534647 ATGGGGCCACAAACAGATAATA 57.465 40.909 14.33 0.00 0.00 0.98
856 921 4.323569 TGGGGCCACAAACAGATAATAA 57.676 40.909 4.31 0.00 0.00 1.40
857 922 4.678256 TGGGGCCACAAACAGATAATAAA 58.322 39.130 4.31 0.00 0.00 1.40
858 923 4.709397 TGGGGCCACAAACAGATAATAAAG 59.291 41.667 4.31 0.00 0.00 1.85
859 924 4.709886 GGGGCCACAAACAGATAATAAAGT 59.290 41.667 4.39 0.00 0.00 2.66
860 925 5.163550 GGGGCCACAAACAGATAATAAAGTC 60.164 44.000 4.39 0.00 0.00 3.01
861 926 5.417580 GGGCCACAAACAGATAATAAAGTCA 59.582 40.000 4.39 0.00 0.00 3.41
862 927 6.096846 GGGCCACAAACAGATAATAAAGTCAT 59.903 38.462 4.39 0.00 0.00 3.06
863 928 7.196331 GGCCACAAACAGATAATAAAGTCATC 58.804 38.462 0.00 0.00 0.00 2.92
864 929 7.067494 GGCCACAAACAGATAATAAAGTCATCT 59.933 37.037 0.00 0.00 0.00 2.90
865 930 8.462016 GCCACAAACAGATAATAAAGTCATCTT 58.538 33.333 0.00 0.00 35.14 2.40
883 948 9.821240 AGTCATCTTAGATGTGAGGTATTATCT 57.179 33.333 20.09 0.00 34.51 1.98
885 950 9.813826 TCATCTTAGATGTGAGGTATTATCTCA 57.186 33.333 20.09 2.40 38.75 3.27
895 960 7.846101 TGAGGTATTATCTCACATCACATCT 57.154 36.000 2.40 0.00 36.46 2.90
896 961 8.940397 TGAGGTATTATCTCACATCACATCTA 57.060 34.615 2.40 0.00 36.46 1.98
897 962 9.018582 TGAGGTATTATCTCACATCACATCTAG 57.981 37.037 2.40 0.00 36.46 2.43
898 963 9.237187 GAGGTATTATCTCACATCACATCTAGA 57.763 37.037 0.00 0.00 0.00 2.43
899 964 9.766754 AGGTATTATCTCACATCACATCTAGAT 57.233 33.333 0.00 0.00 0.00 1.98
900 965 9.800433 GGTATTATCTCACATCACATCTAGATG 57.200 37.037 27.63 27.63 46.38 2.90
915 980 7.664082 CATCTAGATGTGACATAATTGGACC 57.336 40.000 22.42 0.00 34.23 4.46
916 981 7.448420 CATCTAGATGTGACATAATTGGACCT 58.552 38.462 22.42 0.00 34.23 3.85
917 982 8.588472 CATCTAGATGTGACATAATTGGACCTA 58.412 37.037 22.42 0.00 34.23 3.08
918 983 8.547481 TCTAGATGTGACATAATTGGACCTAA 57.453 34.615 0.00 0.00 0.00 2.69
919 984 8.988060 TCTAGATGTGACATAATTGGACCTAAA 58.012 33.333 0.00 0.00 0.00 1.85
920 985 9.784531 CTAGATGTGACATAATTGGACCTAAAT 57.215 33.333 0.00 0.00 0.00 1.40
934 999 9.853177 ATTGGACCTAAATAATTACTTCCTCTG 57.147 33.333 0.00 0.00 0.00 3.35
935 1000 8.388656 TGGACCTAAATAATTACTTCCTCTGT 57.611 34.615 0.00 0.00 0.00 3.41
936 1001 9.496710 TGGACCTAAATAATTACTTCCTCTGTA 57.503 33.333 0.00 0.00 0.00 2.74
953 1018 9.736414 TTCCTCTGTATACTAATATAAGAGCGT 57.264 33.333 4.17 0.00 33.14 5.07
954 1019 9.736414 TCCTCTGTATACTAATATAAGAGCGTT 57.264 33.333 4.17 0.00 33.14 4.84
955 1020 9.991388 CCTCTGTATACTAATATAAGAGCGTTC 57.009 37.037 4.17 0.00 33.14 3.95
962 1027 7.988904 ACTAATATAAGAGCGTTCAGAACAC 57.011 36.000 13.82 3.55 0.00 3.32
963 1028 5.950965 AATATAAGAGCGTTCAGAACACG 57.049 39.130 13.82 2.12 40.75 4.49
964 1029 2.060326 TAAGAGCGTTCAGAACACGG 57.940 50.000 13.82 0.00 38.13 4.94
965 1030 0.387929 AAGAGCGTTCAGAACACGGA 59.612 50.000 13.82 0.00 38.13 4.69
966 1031 0.039074 AGAGCGTTCAGAACACGGAG 60.039 55.000 13.82 0.00 38.13 4.63
967 1032 1.006102 AGCGTTCAGAACACGGAGG 60.006 57.895 13.82 0.00 38.13 4.30
968 1033 2.027625 GCGTTCAGAACACGGAGGG 61.028 63.158 13.82 0.00 38.13 4.30
969 1034 1.663739 CGTTCAGAACACGGAGGGA 59.336 57.895 13.82 0.00 33.86 4.20
970 1035 0.388649 CGTTCAGAACACGGAGGGAG 60.389 60.000 13.82 0.00 33.86 4.30
971 1036 0.680061 GTTCAGAACACGGAGGGAGT 59.320 55.000 8.54 0.00 0.00 3.85
972 1037 1.891150 GTTCAGAACACGGAGGGAGTA 59.109 52.381 8.54 0.00 0.00 2.59
973 1038 1.542492 TCAGAACACGGAGGGAGTAC 58.458 55.000 0.00 0.00 0.00 2.73
974 1039 1.075050 TCAGAACACGGAGGGAGTACT 59.925 52.381 0.00 0.00 0.00 2.73
975 1040 1.202582 CAGAACACGGAGGGAGTACTG 59.797 57.143 0.00 0.00 0.00 2.74
976 1041 1.203025 AGAACACGGAGGGAGTACTGT 60.203 52.381 0.00 0.00 0.00 3.55
979 1044 1.617357 ACACGGAGGGAGTACTGTTTC 59.383 52.381 0.00 0.00 0.00 2.78
986 1051 5.393243 CGGAGGGAGTACTGTTTCTTAGAAG 60.393 48.000 0.00 0.00 0.00 2.85
1036 1109 0.252197 GGACGGACTGGGCTTTACAT 59.748 55.000 0.00 0.00 0.00 2.29
1409 1497 0.760945 GGGATGGACGAGATGGAGGT 60.761 60.000 0.00 0.00 0.00 3.85
1481 1569 3.157252 GCGGCTGGAGGATCTGGA 61.157 66.667 0.00 0.00 33.73 3.86
1524 1612 2.109126 GGTGGAGAAGGTGATGCGC 61.109 63.158 0.00 0.00 0.00 6.09
1641 1729 3.006967 CCGAGGACAAGGAAGAAGAAGAA 59.993 47.826 0.00 0.00 0.00 2.52
1680 1768 2.422803 CGAGGAGGATGAGGAAGAGAGT 60.423 54.545 0.00 0.00 0.00 3.24
1690 1778 3.181428 TGAGGAAGAGAGTCTGGAACTGA 60.181 47.826 0.00 0.00 38.74 3.41
1694 1782 3.534357 AGAGAGTCTGGAACTGAAGGA 57.466 47.619 0.00 0.00 38.74 3.36
1695 1783 3.430453 AGAGAGTCTGGAACTGAAGGAG 58.570 50.000 0.00 0.00 38.74 3.69
1696 1784 2.495669 GAGAGTCTGGAACTGAAGGAGG 59.504 54.545 0.00 0.00 38.74 4.30
1697 1785 2.110899 AGAGTCTGGAACTGAAGGAGGA 59.889 50.000 0.00 0.00 38.74 3.71
1698 1786 2.495669 GAGTCTGGAACTGAAGGAGGAG 59.504 54.545 0.00 0.00 38.74 3.69
1699 1787 2.110899 AGTCTGGAACTGAAGGAGGAGA 59.889 50.000 0.00 0.00 38.22 3.71
1716 1810 5.399727 GGAGGAGAAGAAGAGGAAGGAGATA 60.400 48.000 0.00 0.00 0.00 1.98
1803 1897 7.771826 TGATCTCATATCATCACAAGCAAAGAA 59.228 33.333 0.00 0.00 0.00 2.52
1811 1905 4.365514 TCACAAGCAAAGAAGTATCCCA 57.634 40.909 0.00 0.00 0.00 4.37
1813 1907 4.518970 TCACAAGCAAAGAAGTATCCCAAC 59.481 41.667 0.00 0.00 0.00 3.77
1815 1909 4.082125 CAAGCAAAGAAGTATCCCAACCT 58.918 43.478 0.00 0.00 0.00 3.50
1816 1910 3.690460 AGCAAAGAAGTATCCCAACCTG 58.310 45.455 0.00 0.00 0.00 4.00
1875 1969 4.401519 AGAATCCAGCAAGTGAATCCAATG 59.598 41.667 0.00 0.00 0.00 2.82
2021 2116 9.913310 TGTGTTCTTTCCCATCATAATATACAA 57.087 29.630 0.00 0.00 0.00 2.41
2098 2203 6.092122 TGTTGATAATTAACTTGCCGAGTCAG 59.908 38.462 0.00 0.00 37.72 3.51
2137 2242 0.805322 CAGCTAGCAGTCCTTCAGCG 60.805 60.000 18.83 0.00 37.32 5.18
2199 2311 7.823149 AAAACATAACATACAGTCGTACTCC 57.177 36.000 0.00 0.00 0.00 3.85
2200 2312 5.511234 ACATAACATACAGTCGTACTCCC 57.489 43.478 0.00 0.00 0.00 4.30
2201 2313 5.198965 ACATAACATACAGTCGTACTCCCT 58.801 41.667 0.00 0.00 0.00 4.20
2202 2314 5.298777 ACATAACATACAGTCGTACTCCCTC 59.701 44.000 0.00 0.00 0.00 4.30
2203 2315 3.648507 ACATACAGTCGTACTCCCTCT 57.351 47.619 0.00 0.00 0.00 3.69
2204 2316 3.280295 ACATACAGTCGTACTCCCTCTG 58.720 50.000 0.00 0.00 0.00 3.35
2205 2317 3.280295 CATACAGTCGTACTCCCTCTGT 58.720 50.000 0.00 0.00 41.32 3.41
2206 2318 2.289592 ACAGTCGTACTCCCTCTGTT 57.710 50.000 0.00 0.00 36.17 3.16
2207 2319 2.161030 ACAGTCGTACTCCCTCTGTTC 58.839 52.381 0.00 0.00 36.17 3.18
2208 2320 1.473278 CAGTCGTACTCCCTCTGTTCC 59.527 57.143 0.00 0.00 0.00 3.62
2209 2321 1.075050 AGTCGTACTCCCTCTGTTCCA 59.925 52.381 0.00 0.00 0.00 3.53
2210 2322 1.891150 GTCGTACTCCCTCTGTTCCAA 59.109 52.381 0.00 0.00 0.00 3.53
2211 2323 2.298163 GTCGTACTCCCTCTGTTCCAAA 59.702 50.000 0.00 0.00 0.00 3.28
2212 2324 2.967201 TCGTACTCCCTCTGTTCCAAAA 59.033 45.455 0.00 0.00 0.00 2.44
2213 2325 3.581332 TCGTACTCCCTCTGTTCCAAAAT 59.419 43.478 0.00 0.00 0.00 1.82
2214 2326 4.773674 TCGTACTCCCTCTGTTCCAAAATA 59.226 41.667 0.00 0.00 0.00 1.40
2215 2327 5.105473 TCGTACTCCCTCTGTTCCAAAATAG 60.105 44.000 0.00 0.00 0.00 1.73
2216 2328 5.105473 CGTACTCCCTCTGTTCCAAAATAGA 60.105 44.000 0.00 0.00 32.42 1.98
2217 2329 6.407074 CGTACTCCCTCTGTTCCAAAATAGAT 60.407 42.308 0.00 0.00 32.88 1.98
2218 2330 5.749462 ACTCCCTCTGTTCCAAAATAGATG 58.251 41.667 0.00 0.00 32.88 2.90
2219 2331 5.488919 ACTCCCTCTGTTCCAAAATAGATGA 59.511 40.000 0.00 0.00 32.88 2.92
2220 2332 5.745227 TCCCTCTGTTCCAAAATAGATGAC 58.255 41.667 0.00 0.00 32.88 3.06
2221 2333 4.884164 CCCTCTGTTCCAAAATAGATGACC 59.116 45.833 0.00 0.00 32.88 4.02
2222 2334 4.884164 CCTCTGTTCCAAAATAGATGACCC 59.116 45.833 0.00 0.00 32.88 4.46
2223 2335 5.500234 CTCTGTTCCAAAATAGATGACCCA 58.500 41.667 0.00 0.00 32.88 4.51
2224 2336 5.886609 TCTGTTCCAAAATAGATGACCCAA 58.113 37.500 0.00 0.00 28.72 4.12
2225 2337 5.710099 TCTGTTCCAAAATAGATGACCCAAC 59.290 40.000 0.00 0.00 28.72 3.77
2226 2338 5.640147 TGTTCCAAAATAGATGACCCAACT 58.360 37.500 0.00 0.00 0.00 3.16
2227 2339 6.074648 TGTTCCAAAATAGATGACCCAACTT 58.925 36.000 0.00 0.00 0.00 2.66
2228 2340 6.553100 TGTTCCAAAATAGATGACCCAACTTT 59.447 34.615 0.00 0.00 0.00 2.66
2229 2341 6.588719 TCCAAAATAGATGACCCAACTTTG 57.411 37.500 0.00 0.00 0.00 2.77
2230 2342 6.074648 TCCAAAATAGATGACCCAACTTTGT 58.925 36.000 0.00 0.00 0.00 2.83
2231 2343 7.235079 TCCAAAATAGATGACCCAACTTTGTA 58.765 34.615 0.00 0.00 0.00 2.41
2232 2344 7.175990 TCCAAAATAGATGACCCAACTTTGTAC 59.824 37.037 0.00 0.00 0.00 2.90
2233 2345 7.176690 CCAAAATAGATGACCCAACTTTGTACT 59.823 37.037 0.00 0.00 0.00 2.73
2234 2346 9.226606 CAAAATAGATGACCCAACTTTGTACTA 57.773 33.333 0.00 0.00 0.00 1.82
2235 2347 9.802039 AAAATAGATGACCCAACTTTGTACTAA 57.198 29.630 0.00 0.00 0.00 2.24
2236 2348 8.788325 AATAGATGACCCAACTTTGTACTAAC 57.212 34.615 0.00 0.00 0.00 2.34
2237 2349 6.435292 AGATGACCCAACTTTGTACTAACT 57.565 37.500 0.00 0.00 0.00 2.24
2238 2350 6.838382 AGATGACCCAACTTTGTACTAACTT 58.162 36.000 0.00 0.00 0.00 2.66
2239 2351 7.287810 AGATGACCCAACTTTGTACTAACTTT 58.712 34.615 0.00 0.00 0.00 2.66
2240 2352 8.434392 AGATGACCCAACTTTGTACTAACTTTA 58.566 33.333 0.00 0.00 0.00 1.85
2241 2353 8.617290 ATGACCCAACTTTGTACTAACTTTAG 57.383 34.615 0.00 0.00 36.82 1.85
2242 2354 7.567458 TGACCCAACTTTGTACTAACTTTAGT 58.433 34.615 6.85 6.85 45.39 2.24
2243 2355 8.703743 TGACCCAACTTTGTACTAACTTTAGTA 58.296 33.333 4.98 4.98 43.36 1.82
2256 2368 7.567458 ACTAACTTTAGTACAAAGTTGGGTCA 58.433 34.615 28.62 17.50 46.38 4.02
2257 2369 8.215736 ACTAACTTTAGTACAAAGTTGGGTCAT 58.784 33.333 28.62 17.19 46.38 3.06
2258 2370 7.506328 AACTTTAGTACAAAGTTGGGTCATC 57.494 36.000 23.48 0.00 45.58 2.92
2259 2371 6.838382 ACTTTAGTACAAAGTTGGGTCATCT 58.162 36.000 14.04 0.00 37.18 2.90
2260 2372 7.970102 ACTTTAGTACAAAGTTGGGTCATCTA 58.030 34.615 14.04 0.00 37.18 1.98
2261 2373 8.603304 ACTTTAGTACAAAGTTGGGTCATCTAT 58.397 33.333 14.04 0.00 37.18 1.98
2262 2374 9.449719 CTTTAGTACAAAGTTGGGTCATCTATT 57.550 33.333 0.00 0.00 0.00 1.73
2263 2375 9.802039 TTTAGTACAAAGTTGGGTCATCTATTT 57.198 29.630 0.00 0.00 0.00 1.40
2264 2376 9.802039 TTAGTACAAAGTTGGGTCATCTATTTT 57.198 29.630 0.00 0.00 0.00 1.82
2265 2377 8.110860 AGTACAAAGTTGGGTCATCTATTTTG 57.889 34.615 0.00 0.00 0.00 2.44
2266 2378 6.345096 ACAAAGTTGGGTCATCTATTTTGG 57.655 37.500 0.00 0.00 0.00 3.28
2267 2379 6.074648 ACAAAGTTGGGTCATCTATTTTGGA 58.925 36.000 0.00 0.00 0.00 3.53
2268 2380 6.553100 ACAAAGTTGGGTCATCTATTTTGGAA 59.447 34.615 0.00 0.00 0.00 3.53
2269 2381 6.590234 AAGTTGGGTCATCTATTTTGGAAC 57.410 37.500 0.00 0.00 0.00 3.62
2270 2382 4.700213 AGTTGGGTCATCTATTTTGGAACG 59.300 41.667 0.00 0.00 0.00 3.95
2271 2383 3.616219 TGGGTCATCTATTTTGGAACGG 58.384 45.455 0.00 0.00 0.00 4.44
2272 2384 3.264706 TGGGTCATCTATTTTGGAACGGA 59.735 43.478 0.00 0.00 0.00 4.69
2273 2385 3.877508 GGGTCATCTATTTTGGAACGGAG 59.122 47.826 0.00 0.00 0.00 4.63
2274 2386 3.877508 GGTCATCTATTTTGGAACGGAGG 59.122 47.826 0.00 0.00 0.00 4.30
2275 2387 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
2314 2430 5.941058 TCAACAAACAAGTCAACAAGGTCTA 59.059 36.000 0.00 0.00 0.00 2.59
2370 2488 6.769134 TCATCTTGATCAAACATCTTGCAT 57.231 33.333 9.88 0.00 0.00 3.96
2464 2583 2.160219 ACAACGACAAGCTACATGCATG 59.840 45.455 25.09 25.09 44.94 4.06
2480 2599 2.976490 ATGTCAGCCTGGGTGGAGC 61.976 63.158 24.38 15.34 38.35 4.70
2564 2683 3.438360 CTTCACTTTCCACTGCAACAAC 58.562 45.455 0.00 0.00 0.00 3.32
2604 2725 3.903932 GAGGCCTTGTTGCTTGCGC 62.904 63.158 6.77 0.00 0.00 6.09
2634 2755 4.004982 AGCAAAAACATGGATTCAATGGC 58.995 39.130 6.01 0.00 0.00 4.40
2726 2847 9.288576 CTGCCAATTTCCAACATAGATATTAGA 57.711 33.333 0.00 0.00 0.00 2.10
2727 2848 9.812347 TGCCAATTTCCAACATAGATATTAGAT 57.188 29.630 0.00 0.00 0.00 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
100 162 0.323633 TACCACCGCTGCTAGTACCA 60.324 55.000 0.00 0.00 0.00 3.25
449 512 1.335132 TATCAAGAGGGGGTCCGCAC 61.335 60.000 8.40 1.47 38.33 5.34
503 566 2.798283 CGGTGTAGCTCTTTCGTTTCAA 59.202 45.455 0.00 0.00 0.00 2.69
552 615 0.389817 TCCTTTGGCACGAGACGATG 60.390 55.000 0.00 0.00 0.00 3.84
647 712 2.151202 CCGTGTGTTAAGGCATGTCTT 58.849 47.619 18.09 18.09 0.00 3.01
683 748 1.582502 GATTCACGTACAGCTACACGC 59.417 52.381 16.68 0.09 41.80 5.34
684 749 2.858839 TGATTCACGTACAGCTACACG 58.141 47.619 15.52 15.52 43.63 4.49
685 750 4.421058 TCATGATTCACGTACAGCTACAC 58.579 43.478 0.00 0.00 0.00 2.90
686 751 4.712122 TCATGATTCACGTACAGCTACA 57.288 40.909 0.00 0.00 0.00 2.74
687 752 5.343593 GCTATCATGATTCACGTACAGCTAC 59.656 44.000 14.65 0.00 0.00 3.58
688 753 5.241728 AGCTATCATGATTCACGTACAGCTA 59.758 40.000 19.07 0.00 34.08 3.32
689 754 4.038522 AGCTATCATGATTCACGTACAGCT 59.961 41.667 14.65 15.57 0.00 4.24
690 755 4.302455 AGCTATCATGATTCACGTACAGC 58.698 43.478 14.65 13.52 0.00 4.40
691 756 6.699204 AGAAAGCTATCATGATTCACGTACAG 59.301 38.462 14.65 3.49 0.00 2.74
692 757 6.573434 AGAAAGCTATCATGATTCACGTACA 58.427 36.000 14.65 0.00 0.00 2.90
693 758 7.010552 ACAAGAAAGCTATCATGATTCACGTAC 59.989 37.037 14.65 1.42 0.00 3.67
694 759 7.010460 CACAAGAAAGCTATCATGATTCACGTA 59.990 37.037 14.65 0.00 0.00 3.57
695 760 5.877012 ACAAGAAAGCTATCATGATTCACGT 59.123 36.000 14.65 4.31 0.00 4.49
696 761 6.183360 ACACAAGAAAGCTATCATGATTCACG 60.183 38.462 14.65 3.72 0.00 4.35
697 762 7.081526 ACACAAGAAAGCTATCATGATTCAC 57.918 36.000 14.65 3.91 0.00 3.18
698 763 8.969260 ATACACAAGAAAGCTATCATGATTCA 57.031 30.769 14.65 0.00 0.00 2.57
709 774 9.502091 TTGAAACTGTATATACACAAGAAAGCT 57.498 29.630 11.62 0.00 31.93 3.74
744 809 3.117738 TGTGGCCCATTCATTTGGTTTTT 60.118 39.130 0.00 0.00 34.77 1.94
745 810 2.441001 TGTGGCCCATTCATTTGGTTTT 59.559 40.909 0.00 0.00 34.77 2.43
746 811 2.053244 TGTGGCCCATTCATTTGGTTT 58.947 42.857 0.00 0.00 34.77 3.27
747 812 1.727062 TGTGGCCCATTCATTTGGTT 58.273 45.000 0.00 0.00 34.77 3.67
748 813 1.727062 TTGTGGCCCATTCATTTGGT 58.273 45.000 0.00 0.00 34.77 3.67
749 814 2.224475 TGTTTGTGGCCCATTCATTTGG 60.224 45.455 0.00 0.00 36.46 3.28
750 815 3.068560 CTGTTTGTGGCCCATTCATTTG 58.931 45.455 0.00 0.00 0.00 2.32
751 816 2.971330 TCTGTTTGTGGCCCATTCATTT 59.029 40.909 0.00 0.00 0.00 2.32
752 817 2.607499 TCTGTTTGTGGCCCATTCATT 58.393 42.857 0.00 0.00 0.00 2.57
753 818 2.307496 TCTGTTTGTGGCCCATTCAT 57.693 45.000 0.00 0.00 0.00 2.57
754 819 2.307496 ATCTGTTTGTGGCCCATTCA 57.693 45.000 0.00 0.03 0.00 2.57
755 820 4.402155 TCATTATCTGTTTGTGGCCCATTC 59.598 41.667 0.00 0.00 0.00 2.67
756 821 4.352009 TCATTATCTGTTTGTGGCCCATT 58.648 39.130 0.00 0.00 0.00 3.16
757 822 3.979911 TCATTATCTGTTTGTGGCCCAT 58.020 40.909 0.00 0.00 0.00 4.00
758 823 3.448093 TCATTATCTGTTTGTGGCCCA 57.552 42.857 0.00 0.00 0.00 5.36
759 824 3.763897 ACTTCATTATCTGTTTGTGGCCC 59.236 43.478 0.00 0.00 0.00 5.80
760 825 4.458989 TGACTTCATTATCTGTTTGTGGCC 59.541 41.667 0.00 0.00 0.00 5.36
761 826 5.627499 TGACTTCATTATCTGTTTGTGGC 57.373 39.130 0.00 0.00 0.00 5.01
762 827 7.094677 TGTCATGACTTCATTATCTGTTTGTGG 60.095 37.037 25.55 0.00 33.61 4.17
763 828 7.809665 TGTCATGACTTCATTATCTGTTTGTG 58.190 34.615 25.55 0.00 33.61 3.33
764 829 7.663081 ACTGTCATGACTTCATTATCTGTTTGT 59.337 33.333 25.55 0.00 33.61 2.83
765 830 8.037382 ACTGTCATGACTTCATTATCTGTTTG 57.963 34.615 25.55 0.00 33.61 2.93
766 831 8.627208 AACTGTCATGACTTCATTATCTGTTT 57.373 30.769 25.55 0.23 33.61 2.83
767 832 8.627208 AAACTGTCATGACTTCATTATCTGTT 57.373 30.769 25.55 9.83 33.61 3.16
768 833 8.627208 AAAACTGTCATGACTTCATTATCTGT 57.373 30.769 25.55 4.39 33.61 3.41
769 834 8.944029 AGAAAACTGTCATGACTTCATTATCTG 58.056 33.333 25.55 3.79 33.61 2.90
770 835 9.512588 AAGAAAACTGTCATGACTTCATTATCT 57.487 29.630 25.55 16.26 33.61 1.98
771 836 9.552114 CAAGAAAACTGTCATGACTTCATTATC 57.448 33.333 25.55 14.57 33.61 1.75
772 837 9.071276 ACAAGAAAACTGTCATGACTTCATTAT 57.929 29.630 25.55 10.90 33.61 1.28
773 838 8.344831 CACAAGAAAACTGTCATGACTTCATTA 58.655 33.333 25.55 4.32 33.61 1.90
774 839 7.148018 ACACAAGAAAACTGTCATGACTTCATT 60.148 33.333 25.55 15.36 33.61 2.57
775 840 6.319658 ACACAAGAAAACTGTCATGACTTCAT 59.680 34.615 25.55 11.59 36.96 2.57
776 841 5.647658 ACACAAGAAAACTGTCATGACTTCA 59.352 36.000 25.55 5.88 0.00 3.02
777 842 6.124088 ACACAAGAAAACTGTCATGACTTC 57.876 37.500 25.55 19.48 0.00 3.01
778 843 7.807977 ATACACAAGAAAACTGTCATGACTT 57.192 32.000 25.55 12.21 0.00 3.01
783 848 9.944376 ACAGTATATACACAAGAAAACTGTCAT 57.056 29.630 15.18 0.00 41.72 3.06
784 849 9.772973 AACAGTATATACACAAGAAAACTGTCA 57.227 29.630 15.18 0.00 43.94 3.58
822 887 3.117738 TGTGGCCCCATTCATTTGTTTTT 60.118 39.130 0.00 0.00 0.00 1.94
823 888 2.441001 TGTGGCCCCATTCATTTGTTTT 59.559 40.909 0.00 0.00 0.00 2.43
824 889 2.053244 TGTGGCCCCATTCATTTGTTT 58.947 42.857 0.00 0.00 0.00 2.83
825 890 1.727062 TGTGGCCCCATTCATTTGTT 58.273 45.000 0.00 0.00 0.00 2.83
826 891 1.727062 TTGTGGCCCCATTCATTTGT 58.273 45.000 0.00 0.00 0.00 2.83
827 892 2.224475 TGTTTGTGGCCCCATTCATTTG 60.224 45.455 0.00 0.00 0.00 2.32
828 893 2.038820 CTGTTTGTGGCCCCATTCATTT 59.961 45.455 0.00 0.00 0.00 2.32
829 894 1.624813 CTGTTTGTGGCCCCATTCATT 59.375 47.619 0.00 0.00 0.00 2.57
830 895 1.203162 TCTGTTTGTGGCCCCATTCAT 60.203 47.619 0.00 0.00 0.00 2.57
831 896 0.187117 TCTGTTTGTGGCCCCATTCA 59.813 50.000 0.00 0.00 0.00 2.57
832 897 1.560505 ATCTGTTTGTGGCCCCATTC 58.439 50.000 0.00 0.00 0.00 2.67
833 898 2.917713 TATCTGTTTGTGGCCCCATT 57.082 45.000 0.00 0.00 0.00 3.16
834 899 2.917713 TTATCTGTTTGTGGCCCCAT 57.082 45.000 0.00 0.00 0.00 4.00
835 900 2.917713 ATTATCTGTTTGTGGCCCCA 57.082 45.000 0.00 0.00 0.00 4.96
836 901 4.709886 ACTTTATTATCTGTTTGTGGCCCC 59.290 41.667 0.00 0.00 0.00 5.80
837 902 5.417580 TGACTTTATTATCTGTTTGTGGCCC 59.582 40.000 0.00 0.00 0.00 5.80
838 903 6.509418 TGACTTTATTATCTGTTTGTGGCC 57.491 37.500 0.00 0.00 0.00 5.36
839 904 7.989826 AGATGACTTTATTATCTGTTTGTGGC 58.010 34.615 0.00 0.00 30.41 5.01
857 922 9.821240 AGATAATACCTCACATCTAAGATGACT 57.179 33.333 0.00 0.00 0.00 3.41
859 924 9.813826 TGAGATAATACCTCACATCTAAGATGA 57.186 33.333 0.00 0.00 35.89 2.92
871 936 7.846101 AGATGTGATGTGAGATAATACCTCA 57.154 36.000 0.00 0.00 38.24 3.86
872 937 9.237187 TCTAGATGTGATGTGAGATAATACCTC 57.763 37.037 0.00 0.00 0.00 3.85
873 938 9.766754 ATCTAGATGTGATGTGAGATAATACCT 57.233 33.333 3.89 0.00 0.00 3.08
874 939 9.800433 CATCTAGATGTGATGTGAGATAATACC 57.200 37.037 22.42 0.00 37.22 2.73
891 956 7.448420 AGGTCCAATTATGTCACATCTAGATG 58.552 38.462 27.63 27.63 44.15 2.90
892 957 7.623999 AGGTCCAATTATGTCACATCTAGAT 57.376 36.000 0.00 0.00 0.00 1.98
893 958 8.547481 TTAGGTCCAATTATGTCACATCTAGA 57.453 34.615 0.00 0.00 0.00 2.43
894 959 9.784531 ATTTAGGTCCAATTATGTCACATCTAG 57.215 33.333 0.00 0.00 0.00 2.43
908 973 9.853177 CAGAGGAAGTAATTATTTAGGTCCAAT 57.147 33.333 0.00 0.00 29.41 3.16
909 974 8.832735 ACAGAGGAAGTAATTATTTAGGTCCAA 58.167 33.333 0.00 0.00 29.41 3.53
910 975 8.388656 ACAGAGGAAGTAATTATTTAGGTCCA 57.611 34.615 0.00 0.00 29.41 4.02
927 992 9.736414 ACGCTCTTATATTAGTATACAGAGGAA 57.264 33.333 5.50 0.00 33.85 3.36
928 993 9.736414 AACGCTCTTATATTAGTATACAGAGGA 57.264 33.333 5.50 0.00 33.85 3.71
929 994 9.991388 GAACGCTCTTATATTAGTATACAGAGG 57.009 37.037 5.50 4.07 33.85 3.69
936 1001 9.680315 GTGTTCTGAACGCTCTTATATTAGTAT 57.320 33.333 23.02 0.00 38.81 2.12
937 1002 7.854422 CGTGTTCTGAACGCTCTTATATTAGTA 59.146 37.037 26.04 0.00 39.69 1.82
938 1003 6.691818 CGTGTTCTGAACGCTCTTATATTAGT 59.308 38.462 26.04 0.00 39.69 2.24
939 1004 6.142480 CCGTGTTCTGAACGCTCTTATATTAG 59.858 42.308 26.04 10.59 39.69 1.73
940 1005 5.975344 CCGTGTTCTGAACGCTCTTATATTA 59.025 40.000 26.04 0.00 39.69 0.98
941 1006 4.804139 CCGTGTTCTGAACGCTCTTATATT 59.196 41.667 26.04 0.00 39.69 1.28
942 1007 4.097437 TCCGTGTTCTGAACGCTCTTATAT 59.903 41.667 26.04 0.00 39.69 0.86
943 1008 3.441222 TCCGTGTTCTGAACGCTCTTATA 59.559 43.478 26.04 7.39 39.69 0.98
944 1009 2.230508 TCCGTGTTCTGAACGCTCTTAT 59.769 45.455 26.04 0.00 39.69 1.73
945 1010 1.610038 TCCGTGTTCTGAACGCTCTTA 59.390 47.619 26.04 10.26 39.69 2.10
946 1011 0.387929 TCCGTGTTCTGAACGCTCTT 59.612 50.000 26.04 0.00 39.69 2.85
947 1012 0.039074 CTCCGTGTTCTGAACGCTCT 60.039 55.000 26.04 0.00 39.69 4.09
948 1013 1.009389 CCTCCGTGTTCTGAACGCTC 61.009 60.000 26.04 13.78 39.69 5.03
949 1014 1.006102 CCTCCGTGTTCTGAACGCT 60.006 57.895 26.04 0.00 39.69 5.07
950 1015 2.027625 CCCTCCGTGTTCTGAACGC 61.028 63.158 21.04 21.04 39.69 4.84
951 1016 0.388649 CTCCCTCCGTGTTCTGAACG 60.389 60.000 15.18 5.54 40.70 3.95
952 1017 0.680061 ACTCCCTCCGTGTTCTGAAC 59.320 55.000 13.49 13.49 0.00 3.18
953 1018 1.891150 GTACTCCCTCCGTGTTCTGAA 59.109 52.381 0.00 0.00 0.00 3.02
954 1019 1.075050 AGTACTCCCTCCGTGTTCTGA 59.925 52.381 0.00 0.00 0.00 3.27
955 1020 1.202582 CAGTACTCCCTCCGTGTTCTG 59.797 57.143 0.00 0.00 30.38 3.02
956 1021 1.203025 ACAGTACTCCCTCCGTGTTCT 60.203 52.381 0.00 0.00 0.00 3.01
957 1022 1.254954 ACAGTACTCCCTCCGTGTTC 58.745 55.000 0.00 0.00 0.00 3.18
958 1023 1.713297 AACAGTACTCCCTCCGTGTT 58.287 50.000 0.00 0.00 0.00 3.32
959 1024 1.617357 GAAACAGTACTCCCTCCGTGT 59.383 52.381 0.00 0.00 0.00 4.49
960 1025 1.893801 AGAAACAGTACTCCCTCCGTG 59.106 52.381 0.00 0.00 0.00 4.94
961 1026 2.305858 AGAAACAGTACTCCCTCCGT 57.694 50.000 0.00 0.00 0.00 4.69
962 1027 4.015084 TCTAAGAAACAGTACTCCCTCCG 58.985 47.826 0.00 0.00 0.00 4.63
963 1028 5.715753 TCTTCTAAGAAACAGTACTCCCTCC 59.284 44.000 0.00 0.00 30.73 4.30
964 1029 6.837471 TCTTCTAAGAAACAGTACTCCCTC 57.163 41.667 0.00 0.00 30.73 4.30
965 1030 7.613551 TTTCTTCTAAGAAACAGTACTCCCT 57.386 36.000 12.68 0.00 46.80 4.20
979 1044 9.844257 ACCCATTAGAGATCAATTTCTTCTAAG 57.156 33.333 0.00 0.00 0.00 2.18
986 1051 4.279420 GCCCACCCATTAGAGATCAATTTC 59.721 45.833 0.00 0.00 0.00 2.17
996 1061 2.711009 CCAATCTAGCCCACCCATTAGA 59.289 50.000 0.00 0.00 0.00 2.10
1036 1109 2.283388 ACTAGGGCGAACGGTCCA 60.283 61.111 0.00 0.00 45.54 4.02
1263 1351 0.038159 CGTCGAGAGCAAGAGGGTTT 60.038 55.000 0.00 0.00 0.00 3.27
1481 1569 1.001248 TCCTCGTCCGATTCCCCTT 59.999 57.895 0.00 0.00 0.00 3.95
1575 1663 1.666553 CTTGTGGTCGGCGTTGCTA 60.667 57.895 6.85 0.00 0.00 3.49
1641 1729 1.743252 GCTACTGGCGCTGCTCTTT 60.743 57.895 7.64 0.00 0.00 2.52
1660 1748 3.117512 AGACTCTCTTCCTCATCCTCCTC 60.118 52.174 0.00 0.00 0.00 3.71
1661 1749 2.858768 AGACTCTCTTCCTCATCCTCCT 59.141 50.000 0.00 0.00 0.00 3.69
1662 1750 2.958355 CAGACTCTCTTCCTCATCCTCC 59.042 54.545 0.00 0.00 0.00 4.30
1680 1768 3.169099 CTTCTCCTCCTTCAGTTCCAGA 58.831 50.000 0.00 0.00 0.00 3.86
1690 1778 3.078305 TCCTTCCTCTTCTTCTCCTCCTT 59.922 47.826 0.00 0.00 0.00 3.36
1694 1782 4.625225 ATCTCCTTCCTCTTCTTCTCCT 57.375 45.455 0.00 0.00 0.00 3.69
1695 1783 6.553100 TCATTATCTCCTTCCTCTTCTTCTCC 59.447 42.308 0.00 0.00 0.00 3.71
1696 1784 7.595819 TCATTATCTCCTTCCTCTTCTTCTC 57.404 40.000 0.00 0.00 0.00 2.87
1697 1785 6.041979 GCTCATTATCTCCTTCCTCTTCTTCT 59.958 42.308 0.00 0.00 0.00 2.85
1698 1786 6.183360 TGCTCATTATCTCCTTCCTCTTCTTC 60.183 42.308 0.00 0.00 0.00 2.87
1699 1787 5.664908 TGCTCATTATCTCCTTCCTCTTCTT 59.335 40.000 0.00 0.00 0.00 2.52
1716 1810 2.560105 GGCCTTGTTCTTCTTGCTCATT 59.440 45.455 0.00 0.00 0.00 2.57
1811 1905 2.622942 CAAACACACATGTAGCCAGGTT 59.377 45.455 0.00 0.00 38.45 3.50
1813 1907 2.503331 TCAAACACACATGTAGCCAGG 58.497 47.619 0.00 0.00 38.45 4.45
1815 1909 4.002982 GAGATCAAACACACATGTAGCCA 58.997 43.478 0.00 0.00 38.45 4.75
1816 1910 4.002982 TGAGATCAAACACACATGTAGCC 58.997 43.478 0.00 0.00 38.45 3.93
1901 1995 4.212143 TCACAGAGATAGCAATGCAAGT 57.788 40.909 8.35 0.00 0.00 3.16
1990 2085 4.014569 TGATGGGAAAGAACACAATCGA 57.985 40.909 0.00 0.00 0.00 3.59
2027 2122 8.606602 GGGTACAAAGTTCATTATAAACGTAGG 58.393 37.037 0.00 0.00 0.00 3.18
2031 2126 9.590451 TCTAGGGTACAAAGTTCATTATAAACG 57.410 33.333 0.00 0.00 0.00 3.60
2098 2203 4.479619 CTGAAACTGAATTTGCTACCAGC 58.520 43.478 0.00 0.00 42.82 4.85
2137 2242 3.057946 GTGAGACACTTGATTTCCCTTGC 60.058 47.826 0.00 0.00 0.00 4.01
2193 2305 6.295719 TCTATTTTGGAACAGAGGGAGTAC 57.704 41.667 0.00 0.00 42.39 2.73
2195 2307 5.488919 TCATCTATTTTGGAACAGAGGGAGT 59.511 40.000 0.00 0.00 42.39 3.85
2196 2308 5.819901 GTCATCTATTTTGGAACAGAGGGAG 59.180 44.000 0.00 0.00 42.39 4.30
2197 2309 5.339200 GGTCATCTATTTTGGAACAGAGGGA 60.339 44.000 0.00 0.00 42.39 4.20
2198 2310 4.884164 GGTCATCTATTTTGGAACAGAGGG 59.116 45.833 0.00 0.00 42.39 4.30
2199 2311 4.884164 GGGTCATCTATTTTGGAACAGAGG 59.116 45.833 0.00 0.00 42.39 3.69
2200 2312 5.500234 TGGGTCATCTATTTTGGAACAGAG 58.500 41.667 0.00 0.00 42.39 3.35
2201 2313 5.512942 TGGGTCATCTATTTTGGAACAGA 57.487 39.130 0.00 0.00 42.39 3.41
2202 2314 5.711976 AGTTGGGTCATCTATTTTGGAACAG 59.288 40.000 0.00 0.00 42.39 3.16
2203 2315 5.640147 AGTTGGGTCATCTATTTTGGAACA 58.360 37.500 0.00 0.00 0.00 3.18
2204 2316 6.590234 AAGTTGGGTCATCTATTTTGGAAC 57.410 37.500 0.00 0.00 0.00 3.62
2205 2317 6.553100 ACAAAGTTGGGTCATCTATTTTGGAA 59.447 34.615 0.00 0.00 0.00 3.53
2206 2318 6.074648 ACAAAGTTGGGTCATCTATTTTGGA 58.925 36.000 0.00 0.00 0.00 3.53
2207 2319 6.345096 ACAAAGTTGGGTCATCTATTTTGG 57.655 37.500 0.00 0.00 0.00 3.28
2208 2320 8.110860 AGTACAAAGTTGGGTCATCTATTTTG 57.889 34.615 0.00 0.00 0.00 2.44
2209 2321 9.802039 TTAGTACAAAGTTGGGTCATCTATTTT 57.198 29.630 0.00 0.00 0.00 1.82
2210 2322 9.227777 GTTAGTACAAAGTTGGGTCATCTATTT 57.772 33.333 0.00 0.00 0.00 1.40
2211 2323 8.603304 AGTTAGTACAAAGTTGGGTCATCTATT 58.397 33.333 0.00 0.00 0.00 1.73
2212 2324 8.147244 AGTTAGTACAAAGTTGGGTCATCTAT 57.853 34.615 0.00 0.00 0.00 1.98
2213 2325 7.549147 AGTTAGTACAAAGTTGGGTCATCTA 57.451 36.000 0.00 0.00 0.00 1.98
2214 2326 6.435292 AGTTAGTACAAAGTTGGGTCATCT 57.565 37.500 0.00 0.00 0.00 2.90
2215 2327 7.506328 AAAGTTAGTACAAAGTTGGGTCATC 57.494 36.000 0.00 0.00 0.00 2.92
2216 2328 8.215736 ACTAAAGTTAGTACAAAGTTGGGTCAT 58.784 33.333 1.81 0.00 41.92 3.06
2217 2329 7.567458 ACTAAAGTTAGTACAAAGTTGGGTCA 58.433 34.615 1.81 0.00 41.92 4.02
2230 2342 8.703743 TGACCCAACTTTGTACTAAAGTTAGTA 58.296 33.333 23.56 6.81 45.57 1.82
2231 2343 7.567458 TGACCCAACTTTGTACTAAAGTTAGT 58.433 34.615 23.56 22.58 45.57 2.24
2232 2344 8.617290 ATGACCCAACTTTGTACTAAAGTTAG 57.383 34.615 23.56 20.79 45.57 2.34
2233 2345 8.434392 AGATGACCCAACTTTGTACTAAAGTTA 58.566 33.333 23.56 14.79 45.57 2.24
2235 2347 6.838382 AGATGACCCAACTTTGTACTAAAGT 58.162 36.000 14.04 14.04 41.82 2.66
2236 2348 9.449719 AATAGATGACCCAACTTTGTACTAAAG 57.550 33.333 13.08 13.08 0.00 1.85
2237 2349 9.802039 AAATAGATGACCCAACTTTGTACTAAA 57.198 29.630 0.00 0.00 0.00 1.85
2238 2350 9.802039 AAAATAGATGACCCAACTTTGTACTAA 57.198 29.630 0.00 0.00 0.00 2.24
2239 2351 9.226606 CAAAATAGATGACCCAACTTTGTACTA 57.773 33.333 0.00 0.00 0.00 1.82
2240 2352 7.176690 CCAAAATAGATGACCCAACTTTGTACT 59.823 37.037 0.00 0.00 0.00 2.73
2241 2353 7.175990 TCCAAAATAGATGACCCAACTTTGTAC 59.824 37.037 0.00 0.00 0.00 2.90
2242 2354 7.235079 TCCAAAATAGATGACCCAACTTTGTA 58.765 34.615 0.00 0.00 0.00 2.41
2243 2355 6.074648 TCCAAAATAGATGACCCAACTTTGT 58.925 36.000 0.00 0.00 0.00 2.83
2244 2356 6.588719 TCCAAAATAGATGACCCAACTTTG 57.411 37.500 0.00 0.00 0.00 2.77
2245 2357 6.294508 CGTTCCAAAATAGATGACCCAACTTT 60.295 38.462 0.00 0.00 0.00 2.66
2246 2358 5.183140 CGTTCCAAAATAGATGACCCAACTT 59.817 40.000 0.00 0.00 0.00 2.66
2247 2359 4.700213 CGTTCCAAAATAGATGACCCAACT 59.300 41.667 0.00 0.00 0.00 3.16
2248 2360 4.142469 CCGTTCCAAAATAGATGACCCAAC 60.142 45.833 0.00 0.00 0.00 3.77
2249 2361 4.013728 CCGTTCCAAAATAGATGACCCAA 58.986 43.478 0.00 0.00 0.00 4.12
2250 2362 3.264706 TCCGTTCCAAAATAGATGACCCA 59.735 43.478 0.00 0.00 0.00 4.51
2251 2363 3.877508 CTCCGTTCCAAAATAGATGACCC 59.122 47.826 0.00 0.00 0.00 4.46
2252 2364 3.877508 CCTCCGTTCCAAAATAGATGACC 59.122 47.826 0.00 0.00 0.00 4.02
2253 2365 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
2254 2366 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
2255 2367 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
2256 2368 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
2257 2369 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
2258 2370 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
2259 2371 4.533311 AGTTACTCCCTCCGTTCCAAAATA 59.467 41.667 0.00 0.00 0.00 1.40
2260 2372 3.329814 AGTTACTCCCTCCGTTCCAAAAT 59.670 43.478 0.00 0.00 0.00 1.82
2261 2373 2.707257 AGTTACTCCCTCCGTTCCAAAA 59.293 45.455 0.00 0.00 0.00 2.44
2262 2374 2.332117 AGTTACTCCCTCCGTTCCAAA 58.668 47.619 0.00 0.00 0.00 3.28
2263 2375 2.019807 AGTTACTCCCTCCGTTCCAA 57.980 50.000 0.00 0.00 0.00 3.53
2264 2376 2.905415 TAGTTACTCCCTCCGTTCCA 57.095 50.000 0.00 0.00 0.00 3.53
2265 2377 5.738495 GCTTATTAGTTACTCCCTCCGTTCC 60.738 48.000 0.00 0.00 0.00 3.62
2266 2378 5.068855 AGCTTATTAGTTACTCCCTCCGTTC 59.931 44.000 0.00 0.00 0.00 3.95
2267 2379 4.961099 AGCTTATTAGTTACTCCCTCCGTT 59.039 41.667 0.00 0.00 0.00 4.44
2268 2380 4.544683 AGCTTATTAGTTACTCCCTCCGT 58.455 43.478 0.00 0.00 0.00 4.69
2269 2381 4.583489 TGAGCTTATTAGTTACTCCCTCCG 59.417 45.833 0.00 0.00 0.00 4.63
2270 2382 6.127140 TGTTGAGCTTATTAGTTACTCCCTCC 60.127 42.308 0.00 0.00 0.00 4.30
2271 2383 6.875076 TGTTGAGCTTATTAGTTACTCCCTC 58.125 40.000 0.00 0.00 0.00 4.30
2272 2384 6.869206 TGTTGAGCTTATTAGTTACTCCCT 57.131 37.500 0.00 0.00 0.00 4.20
2273 2385 7.389607 TGTTTGTTGAGCTTATTAGTTACTCCC 59.610 37.037 0.00 0.00 0.00 4.30
2274 2386 8.319143 TGTTTGTTGAGCTTATTAGTTACTCC 57.681 34.615 0.00 0.00 0.00 3.85
2275 2387 9.813080 CTTGTTTGTTGAGCTTATTAGTTACTC 57.187 33.333 0.00 0.00 0.00 2.59
2314 2430 6.976088 TCGGTTGTGTTTAATTGACATGAAT 58.024 32.000 0.00 0.00 0.00 2.57
2370 2488 3.981071 AAATCCATTCTGTCGACTCCA 57.019 42.857 17.92 0.02 0.00 3.86
2464 2583 3.640407 TGCTCCACCCAGGCTGAC 61.640 66.667 17.94 0.00 37.29 3.51
2480 2599 4.696877 TGAGCATTCCTGTGATACTTTGTG 59.303 41.667 0.00 0.00 0.00 3.33
2570 2691 6.388394 ACAAGGCCTCTAAATTCTCCTATCTT 59.612 38.462 5.23 0.00 0.00 2.40
2575 2696 4.593956 CAACAAGGCCTCTAAATTCTCCT 58.406 43.478 5.23 0.00 0.00 3.69
2577 2698 4.013050 AGCAACAAGGCCTCTAAATTCTC 58.987 43.478 5.23 0.00 0.00 2.87
2604 2725 5.649782 ATCCATGTTTTTGCTCCTGTAAG 57.350 39.130 0.00 0.00 0.00 2.34


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

AutoCloner maintained by Alex Coulton.