Multiple sequence alignment - TraesCS6A01G345200

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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 TraesCS6A01G345200 chr6A 100.000 2931 0 0 1 2931 578982006 578984936 0.000000e+00 5413.0
1 TraesCS6A01G345200 chr6B 90.888 1284 79 14 888 2160 653014835 653016091 0.000000e+00 1688.0
2 TraesCS6A01G345200 chr6B 93.386 635 22 9 2312 2931 653017876 653018505 0.000000e+00 922.0
3 TraesCS6A01G345200 chr6B 86.159 578 35 22 41 605 653014155 653014700 1.510000e-162 582.0
4 TraesCS6A01G345200 chr6D 87.997 1308 75 29 878 2161 432884308 432885557 0.000000e+00 1471.0
5 TraesCS6A01G345200 chr6D 88.764 623 53 11 2312 2928 432885921 432886532 0.000000e+00 747.0
6 TraesCS6A01G345200 chr6D 76.923 624 64 40 100 702 432883599 432884163 6.180000e-72 281.0
7 TraesCS6A01G345200 chr7B 86.532 297 35 3 1000 1295 31433260 31433552 3.640000e-84 322.0
8 TraesCS6A01G345200 chr7A 88.406 69 4 4 2272 2338 569407155 569407221 2.420000e-11 80.5
9 TraesCS6A01G345200 chr5A 94.340 53 2 1 2265 2316 585148160 585148108 2.420000e-11 80.5
10 TraesCS6A01G345200 chr3B 92.593 54 4 0 2272 2325 495839480 495839427 8.710000e-11 78.7
11 TraesCS6A01G345200 chr1D 91.228 57 5 0 2272 2328 301948758 301948814 8.710000e-11 78.7
12 TraesCS6A01G345200 chr2B 92.593 54 3 1 2272 2324 648069724 648069671 3.130000e-10 76.8
13 TraesCS6A01G345200 chr4D 90.000 60 3 3 2272 2328 175798106 175798165 1.130000e-09 75.0
14 TraesCS6A01G345200 chr4D 84.932 73 7 4 2272 2340 403412949 403412877 1.460000e-08 71.3
15 TraesCS6A01G345200 chr4B 90.000 60 3 3 2272 2328 330777137 330777078 1.130000e-09 75.0
16 TraesCS6A01G345200 chr3D 93.878 49 3 0 2272 2320 537946301 537946253 1.130000e-09 75.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6A01G345200 chr6A 578982006 578984936 2930 False 5413 5413 100.000000 1 2931 1 chr6A.!!$F1 2930
1 TraesCS6A01G345200 chr6B 653014155 653018505 4350 False 1064 1688 90.144333 41 2931 3 chr6B.!!$F1 2890
2 TraesCS6A01G345200 chr6D 432883599 432886532 2933 False 833 1471 84.561333 100 2928 3 chr6D.!!$F1 2828

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
852 1014 0.0297 CGTGCATGTATCGTCGGGTA 59.97 55.0 0.0 0.0 0.0 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2296 4035 0.395312 TGTTCAACTCCCTCCGTTCC 59.605 55.0 0.0 0.0 0.0 3.62 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
23 24 4.643795 TGCCATTCCAGCAGTAGC 57.356 55.556 0.00 0.00 42.56 3.58
24 25 1.077501 TGCCATTCCAGCAGTAGCC 60.078 57.895 0.00 0.00 43.56 3.93
25 26 1.825622 GCCATTCCAGCAGTAGCCC 60.826 63.158 0.00 0.00 43.56 5.19
26 27 1.524621 CCATTCCAGCAGTAGCCCG 60.525 63.158 0.00 0.00 43.56 6.13
27 28 1.524621 CATTCCAGCAGTAGCCCGG 60.525 63.158 0.00 0.00 43.56 5.73
28 29 1.689233 ATTCCAGCAGTAGCCCGGA 60.689 57.895 0.73 0.00 43.56 5.14
29 30 1.690219 ATTCCAGCAGTAGCCCGGAG 61.690 60.000 0.73 0.00 42.04 4.63
30 31 4.537433 CCAGCAGTAGCCCGGAGC 62.537 72.222 0.73 4.57 43.56 4.70
149 151 2.683859 CGGAGGAGACACGTACGCA 61.684 63.158 16.72 0.00 34.04 5.24
206 212 1.885850 GTTTGGTCACGTCACGCCT 60.886 57.895 0.00 0.00 0.00 5.52
228 239 2.508928 CACCCACCACACGTCCTT 59.491 61.111 0.00 0.00 0.00 3.36
353 364 2.664698 GCGTCTTGAAATGAAACCGGTC 60.665 50.000 8.04 0.00 0.00 4.79
392 410 4.233635 CCAAGCTCGCTGCATCGC 62.234 66.667 4.79 0.00 45.94 4.58
403 422 0.099436 CTGCATCGCCTTGGTAAAGC 59.901 55.000 0.00 0.00 31.51 3.51
419 438 5.753438 TGGTAAAGCTATCGAATGTGATCAC 59.247 40.000 19.27 19.27 0.00 3.06
420 439 5.177696 GGTAAAGCTATCGAATGTGATCACC 59.822 44.000 22.85 6.94 0.00 4.02
421 440 3.018598 AGCTATCGAATGTGATCACCG 57.981 47.619 22.85 18.24 0.00 4.94
422 441 2.623416 AGCTATCGAATGTGATCACCGA 59.377 45.455 22.85 22.49 36.79 4.69
423 442 3.256879 AGCTATCGAATGTGATCACCGAT 59.743 43.478 28.92 28.92 41.67 4.18
424 443 3.610242 GCTATCGAATGTGATCACCGATC 59.390 47.826 29.47 20.58 40.44 3.69
425 444 3.733443 ATCGAATGTGATCACCGATCA 57.267 42.857 24.05 8.64 45.35 2.92
458 477 3.524541 GCATGGGGAAAATGTGTGAATC 58.475 45.455 0.00 0.00 0.00 2.52
460 479 4.678840 GCATGGGGAAAATGTGTGAATCTC 60.679 45.833 0.00 0.00 0.00 2.75
461 480 3.081061 TGGGGAAAATGTGTGAATCTCG 58.919 45.455 0.00 0.00 0.00 4.04
462 481 2.159379 GGGGAAAATGTGTGAATCTCGC 60.159 50.000 0.00 0.00 0.00 5.03
463 482 2.487762 GGGAAAATGTGTGAATCTCGCA 59.512 45.455 0.93 0.93 34.04 5.10
464 483 3.426695 GGGAAAATGTGTGAATCTCGCAG 60.427 47.826 4.87 0.00 37.59 5.18
465 484 3.189287 GGAAAATGTGTGAATCTCGCAGT 59.811 43.478 4.87 0.00 37.59 4.40
466 485 4.398247 GAAAATGTGTGAATCTCGCAGTC 58.602 43.478 4.87 0.00 37.59 3.51
494 531 0.930310 CCGACGACATGGCAGTTATG 59.070 55.000 0.00 0.00 0.00 1.90
533 570 2.496291 CGGATCCACCTACCCGTCC 61.496 68.421 13.41 0.00 37.40 4.79
569 606 2.253758 CCCAGCGGTCAACACTGTG 61.254 63.158 6.19 6.19 0.00 3.66
576 613 1.876799 CGGTCAACACTGTGCCATAAA 59.123 47.619 7.90 0.00 0.00 1.40
577 614 2.350388 CGGTCAACACTGTGCCATAAAC 60.350 50.000 7.90 0.00 0.00 2.01
605 645 1.556564 CGTGGGAATGTAGCAGTACG 58.443 55.000 0.00 0.00 30.95 3.67
606 646 1.135199 CGTGGGAATGTAGCAGTACGT 60.135 52.381 0.00 0.00 30.95 3.57
607 647 2.268298 GTGGGAATGTAGCAGTACGTG 58.732 52.381 0.00 0.00 30.95 4.49
608 648 1.206132 TGGGAATGTAGCAGTACGTGG 59.794 52.381 0.00 0.00 30.95 4.94
609 649 1.206371 GGGAATGTAGCAGTACGTGGT 59.794 52.381 0.00 0.00 40.92 4.16
610 650 2.428171 GGGAATGTAGCAGTACGTGGTA 59.572 50.000 0.00 0.00 38.14 3.25
611 651 3.490419 GGGAATGTAGCAGTACGTGGTAG 60.490 52.174 0.00 0.00 39.84 3.18
612 652 3.129988 GGAATGTAGCAGTACGTGGTAGT 59.870 47.826 0.00 0.00 39.84 2.73
613 653 4.336433 GGAATGTAGCAGTACGTGGTAGTA 59.664 45.833 0.00 0.45 39.84 1.82
614 654 5.009410 GGAATGTAGCAGTACGTGGTAGTAT 59.991 44.000 0.00 2.18 39.84 2.12
615 655 5.686159 ATGTAGCAGTACGTGGTAGTATC 57.314 43.478 0.00 0.00 39.84 2.24
616 656 4.516323 TGTAGCAGTACGTGGTAGTATCA 58.484 43.478 0.00 0.00 39.84 2.15
617 657 4.333649 TGTAGCAGTACGTGGTAGTATCAC 59.666 45.833 3.24 3.24 39.84 3.06
647 687 3.249080 ACGGTCACGGAAATTTACACAAG 59.751 43.478 0.39 0.00 46.48 3.16
648 688 3.561503 GGTCACGGAAATTTACACAAGC 58.438 45.455 0.39 0.00 0.00 4.01
653 693 4.214545 CACGGAAATTTACACAAGCACCTA 59.785 41.667 0.39 0.00 0.00 3.08
654 694 4.454504 ACGGAAATTTACACAAGCACCTAG 59.545 41.667 0.39 0.00 0.00 3.02
655 695 4.454504 CGGAAATTTACACAAGCACCTAGT 59.545 41.667 0.39 0.00 0.00 2.57
656 696 5.616866 CGGAAATTTACACAAGCACCTAGTG 60.617 44.000 0.39 0.00 39.12 2.74
684 729 3.227810 ACGTAGGAATGTTTCGTCCTC 57.772 47.619 0.00 0.00 43.44 3.71
685 730 2.182825 CGTAGGAATGTTTCGTCCTCG 58.817 52.381 0.00 0.00 43.44 4.63
721 883 1.616865 CACGACCCAAGTTGGAGTAGA 59.383 52.381 24.06 0.00 40.96 2.59
722 884 1.617357 ACGACCCAAGTTGGAGTAGAC 59.383 52.381 24.06 5.93 40.96 2.59
723 885 1.616865 CGACCCAAGTTGGAGTAGACA 59.383 52.381 24.06 0.00 40.96 3.41
724 886 2.609737 CGACCCAAGTTGGAGTAGACAC 60.610 54.545 24.06 6.34 40.96 3.67
725 887 2.367567 GACCCAAGTTGGAGTAGACACA 59.632 50.000 24.06 0.00 40.96 3.72
729 891 2.800544 CAAGTTGGAGTAGACACAACGG 59.199 50.000 11.89 7.23 46.64 4.44
730 892 2.313317 AGTTGGAGTAGACACAACGGA 58.687 47.619 11.89 0.00 46.64 4.69
731 893 2.696707 AGTTGGAGTAGACACAACGGAA 59.303 45.455 11.89 0.00 46.64 4.30
732 894 3.133362 AGTTGGAGTAGACACAACGGAAA 59.867 43.478 11.89 0.00 46.64 3.13
733 895 4.062991 GTTGGAGTAGACACAACGGAAAT 58.937 43.478 0.00 0.00 35.68 2.17
734 896 5.011329 AGTTGGAGTAGACACAACGGAAATA 59.989 40.000 11.89 0.00 46.64 1.40
735 897 4.813027 TGGAGTAGACACAACGGAAATAC 58.187 43.478 0.00 0.00 0.00 1.89
736 898 4.525487 TGGAGTAGACACAACGGAAATACT 59.475 41.667 0.00 0.00 0.00 2.12
737 899 5.011329 TGGAGTAGACACAACGGAAATACTT 59.989 40.000 0.00 0.00 0.00 2.24
738 900 5.575995 GGAGTAGACACAACGGAAATACTTC 59.424 44.000 0.00 0.00 0.00 3.01
739 901 6.092955 AGTAGACACAACGGAAATACTTCA 57.907 37.500 0.00 0.00 32.75 3.02
740 902 5.924825 AGTAGACACAACGGAAATACTTCAC 59.075 40.000 0.00 0.00 32.75 3.18
741 903 4.699637 AGACACAACGGAAATACTTCACA 58.300 39.130 0.00 0.00 32.75 3.58
742 904 4.750098 AGACACAACGGAAATACTTCACAG 59.250 41.667 0.00 0.00 32.75 3.66
743 905 4.699637 ACACAACGGAAATACTTCACAGA 58.300 39.130 0.00 0.00 32.75 3.41
744 906 5.305585 ACACAACGGAAATACTTCACAGAT 58.694 37.500 0.00 0.00 32.75 2.90
745 907 5.179368 ACACAACGGAAATACTTCACAGATG 59.821 40.000 0.00 0.00 32.75 2.90
746 908 5.408299 CACAACGGAAATACTTCACAGATGA 59.592 40.000 0.00 0.00 32.75 2.92
747 909 6.092670 CACAACGGAAATACTTCACAGATGAT 59.907 38.462 0.00 0.00 33.85 2.45
748 910 7.277760 CACAACGGAAATACTTCACAGATGATA 59.722 37.037 0.00 0.00 33.85 2.15
749 911 7.277981 ACAACGGAAATACTTCACAGATGATAC 59.722 37.037 0.00 0.00 33.85 2.24
750 912 6.873997 ACGGAAATACTTCACAGATGATACA 58.126 36.000 0.00 0.00 33.85 2.29
751 913 6.980978 ACGGAAATACTTCACAGATGATACAG 59.019 38.462 0.00 0.00 33.85 2.74
752 914 6.074088 CGGAAATACTTCACAGATGATACAGC 60.074 42.308 0.00 0.00 33.85 4.40
753 915 6.074088 GGAAATACTTCACAGATGATACAGCG 60.074 42.308 0.00 0.00 33.85 5.18
754 916 2.544685 ACTTCACAGATGATACAGCGC 58.455 47.619 0.00 0.00 33.85 5.92
755 917 2.167281 ACTTCACAGATGATACAGCGCT 59.833 45.455 2.64 2.64 33.85 5.92
756 918 2.214387 TCACAGATGATACAGCGCTG 57.786 50.000 34.89 34.89 0.00 5.18
757 919 1.750778 TCACAGATGATACAGCGCTGA 59.249 47.619 42.03 25.68 0.00 4.26
758 920 2.166254 TCACAGATGATACAGCGCTGAA 59.834 45.455 42.03 23.91 0.00 3.02
759 921 2.283617 CACAGATGATACAGCGCTGAAC 59.716 50.000 42.03 28.91 0.00 3.18
770 932 3.438088 GCTGAACGACACTCGACG 58.562 61.111 0.00 0.00 43.74 5.12
771 933 1.082300 GCTGAACGACACTCGACGA 60.082 57.895 0.00 0.00 43.74 4.20
772 934 0.454620 GCTGAACGACACTCGACGAT 60.455 55.000 0.00 0.00 43.74 3.73
773 935 1.251355 CTGAACGACACTCGACGATG 58.749 55.000 0.00 1.90 43.74 3.84
774 936 0.109919 TGAACGACACTCGACGATGG 60.110 55.000 0.00 0.00 43.74 3.51
775 937 1.403972 GAACGACACTCGACGATGGC 61.404 60.000 0.00 0.39 43.74 4.40
776 938 1.863662 AACGACACTCGACGATGGCT 61.864 55.000 0.00 0.00 43.74 4.75
777 939 1.022982 ACGACACTCGACGATGGCTA 61.023 55.000 0.00 0.00 43.74 3.93
778 940 0.098200 CGACACTCGACGATGGCTAA 59.902 55.000 0.00 0.00 43.74 3.09
779 941 1.268589 CGACACTCGACGATGGCTAAT 60.269 52.381 0.00 0.00 43.74 1.73
780 942 2.794981 CGACACTCGACGATGGCTAATT 60.795 50.000 0.00 0.00 43.74 1.40
781 943 2.789893 GACACTCGACGATGGCTAATTC 59.210 50.000 0.00 0.00 0.00 2.17
782 944 2.165641 ACACTCGACGATGGCTAATTCA 59.834 45.455 0.00 0.00 0.00 2.57
783 945 2.791560 CACTCGACGATGGCTAATTCAG 59.208 50.000 0.00 0.00 0.00 3.02
817 979 6.010294 CTGCTTTAGCTTTATCCATGGATG 57.990 41.667 33.41 19.77 42.66 3.51
818 980 4.828939 TGCTTTAGCTTTATCCATGGATGG 59.171 41.667 33.41 23.25 44.85 3.51
819 981 4.321527 GCTTTAGCTTTATCCATGGATGGC 60.322 45.833 33.41 29.71 41.96 4.40
820 982 6.501752 GCTTTAGCTTTATCCATGGATGGCT 61.502 44.000 33.29 33.29 41.96 4.75
821 983 7.918014 GCTTTAGCTTTATCCATGGATGGCTT 61.918 42.308 34.64 25.10 41.96 4.35
822 984 9.810949 GCTTTAGCTTTATCCATGGATGGCTTG 62.811 44.444 34.64 27.93 41.96 4.01
829 991 2.521126 CCATGGATGGCTTGATATGCA 58.479 47.619 5.56 0.00 41.75 3.96
830 992 3.096852 CCATGGATGGCTTGATATGCAT 58.903 45.455 5.56 3.79 41.75 3.96
831 993 3.119137 CCATGGATGGCTTGATATGCATG 60.119 47.826 5.56 10.51 46.36 4.06
832 994 3.232720 TGGATGGCTTGATATGCATGT 57.767 42.857 10.16 1.23 0.00 3.21
833 995 3.151554 TGGATGGCTTGATATGCATGTC 58.848 45.455 15.93 15.93 0.00 3.06
834 996 2.161012 GGATGGCTTGATATGCATGTCG 59.839 50.000 17.35 6.48 0.00 4.35
835 997 2.330440 TGGCTTGATATGCATGTCGT 57.670 45.000 17.35 0.00 0.00 4.34
836 998 1.941975 TGGCTTGATATGCATGTCGTG 59.058 47.619 17.35 13.26 0.00 4.35
848 1010 1.477105 ATGTCGTGCATGTATCGTCG 58.523 50.000 5.68 0.00 36.26 5.12
849 1011 0.524604 TGTCGTGCATGTATCGTCGG 60.525 55.000 5.68 0.00 0.00 4.79
850 1012 1.065109 TCGTGCATGTATCGTCGGG 59.935 57.895 5.68 0.00 0.00 5.14
851 1013 1.226859 CGTGCATGTATCGTCGGGT 60.227 57.895 0.00 0.00 0.00 5.28
852 1014 0.029700 CGTGCATGTATCGTCGGGTA 59.970 55.000 0.00 0.00 0.00 3.69
853 1015 1.534385 CGTGCATGTATCGTCGGGTAA 60.534 52.381 0.00 0.00 0.00 2.85
854 1016 2.542597 GTGCATGTATCGTCGGGTAAA 58.457 47.619 0.00 0.00 0.00 2.01
855 1017 3.128349 GTGCATGTATCGTCGGGTAAAT 58.872 45.455 0.00 0.00 0.00 1.40
856 1018 3.059868 GTGCATGTATCGTCGGGTAAATG 60.060 47.826 0.00 0.00 0.00 2.32
857 1019 3.128349 GCATGTATCGTCGGGTAAATGT 58.872 45.455 0.00 0.00 0.00 2.71
858 1020 3.183775 GCATGTATCGTCGGGTAAATGTC 59.816 47.826 0.00 1.86 0.00 3.06
859 1021 3.069074 TGTATCGTCGGGTAAATGTCG 57.931 47.619 0.00 0.00 0.00 4.35
860 1022 2.423185 TGTATCGTCGGGTAAATGTCGT 59.577 45.455 0.00 0.00 0.00 4.34
861 1023 2.660189 ATCGTCGGGTAAATGTCGTT 57.340 45.000 0.00 0.00 0.00 3.85
862 1024 1.981254 TCGTCGGGTAAATGTCGTTC 58.019 50.000 0.00 0.00 0.00 3.95
863 1025 1.269174 TCGTCGGGTAAATGTCGTTCA 59.731 47.619 0.00 0.00 0.00 3.18
864 1026 2.094597 TCGTCGGGTAAATGTCGTTCAT 60.095 45.455 0.00 0.00 38.57 2.57
865 1027 2.028763 CGTCGGGTAAATGTCGTTCATG 59.971 50.000 0.00 0.00 36.81 3.07
866 1028 2.997986 GTCGGGTAAATGTCGTTCATGT 59.002 45.455 0.00 0.00 36.81 3.21
867 1029 4.175516 GTCGGGTAAATGTCGTTCATGTA 58.824 43.478 0.00 0.00 36.81 2.29
868 1030 4.266976 GTCGGGTAAATGTCGTTCATGTAG 59.733 45.833 0.00 0.00 36.81 2.74
869 1031 3.000925 CGGGTAAATGTCGTTCATGTAGC 59.999 47.826 11.37 11.37 41.46 3.58
870 1032 3.936453 GGGTAAATGTCGTTCATGTAGCA 59.064 43.478 17.26 0.00 43.00 3.49
871 1033 4.034048 GGGTAAATGTCGTTCATGTAGCAG 59.966 45.833 17.26 0.00 43.00 4.24
872 1034 4.630069 GGTAAATGTCGTTCATGTAGCAGT 59.370 41.667 13.47 0.00 41.67 4.40
873 1035 4.668576 AAATGTCGTTCATGTAGCAGTG 57.331 40.909 0.00 0.00 36.81 3.66
874 1036 1.428448 TGTCGTTCATGTAGCAGTGC 58.572 50.000 7.13 7.13 0.00 4.40
875 1037 1.000843 TGTCGTTCATGTAGCAGTGCT 59.999 47.619 23.44 23.44 43.41 4.40
876 1038 1.656095 GTCGTTCATGTAGCAGTGCTC 59.344 52.381 23.64 13.85 40.44 4.26
884 1046 1.344114 TGTAGCAGTGCTCATGACACA 59.656 47.619 23.64 16.41 40.44 3.72
891 1053 0.890542 TGCTCATGACACAACCCAGC 60.891 55.000 0.00 0.00 0.00 4.85
984 1148 0.250467 AATCGCCTGTTGCTCTGTGT 60.250 50.000 0.00 0.00 38.05 3.72
985 1149 0.671781 ATCGCCTGTTGCTCTGTGTC 60.672 55.000 0.00 0.00 38.05 3.67
986 1150 1.301244 CGCCTGTTGCTCTGTGTCT 60.301 57.895 0.00 0.00 38.05 3.41
987 1151 1.563435 CGCCTGTTGCTCTGTGTCTG 61.563 60.000 0.00 0.00 38.05 3.51
988 1152 0.533755 GCCTGTTGCTCTGTGTCTGT 60.534 55.000 0.00 0.00 36.87 3.41
1013 1180 6.202762 TGAGCTCGCAGTACATATATTTTTGG 59.797 38.462 9.64 0.00 0.00 3.28
1014 1181 5.470098 AGCTCGCAGTACATATATTTTTGGG 59.530 40.000 0.00 0.00 0.00 4.12
1016 1183 6.238648 GCTCGCAGTACATATATTTTTGGGTT 60.239 38.462 0.00 0.00 0.00 4.11
1020 1187 7.264947 GCAGTACATATATTTTTGGGTTGCTT 58.735 34.615 0.00 0.00 0.00 3.91
1040 1207 0.822532 CATCCAATCCCAGCTCTGCC 60.823 60.000 0.00 0.00 0.00 4.85
1044 1211 2.687610 AATCCCAGCTCTGCCCCAG 61.688 63.158 0.00 0.00 0.00 4.45
1048 1215 2.435586 CAGCTCTGCCCCAGAACG 60.436 66.667 0.00 0.00 40.18 3.95
1075 1245 2.158445 ACACTCCACTGACCACTACTCT 60.158 50.000 0.00 0.00 0.00 3.24
1076 1246 2.230025 CACTCCACTGACCACTACTCTG 59.770 54.545 0.00 0.00 0.00 3.35
1079 1249 1.821753 CCACTGACCACTACTCTGGAG 59.178 57.143 0.00 0.00 35.04 3.86
1081 1251 3.157881 CACTGACCACTACTCTGGAGAA 58.842 50.000 4.49 0.00 35.04 2.87
1082 1252 3.766591 CACTGACCACTACTCTGGAGAAT 59.233 47.826 4.49 0.00 35.04 2.40
1083 1253 4.020543 ACTGACCACTACTCTGGAGAATC 58.979 47.826 4.49 0.00 35.04 2.52
1145 1315 0.326904 TCTCCAGCCTCCACATCCAT 60.327 55.000 0.00 0.00 0.00 3.41
1151 1321 0.685458 GCCTCCACATCCATTGCCTT 60.685 55.000 0.00 0.00 0.00 4.35
1157 1327 2.101783 CACATCCATTGCCTTTGCCTA 58.898 47.619 0.00 0.00 36.33 3.93
1174 1344 0.395311 CTACTACTCCGGGGAGCACA 60.395 60.000 9.33 0.00 45.54 4.57
1175 1345 0.260816 TACTACTCCGGGGAGCACAT 59.739 55.000 9.33 0.00 45.54 3.21
1238 1420 2.356553 GTGTACAACGCCTCGGCA 60.357 61.111 8.87 0.00 42.06 5.69
1691 1873 3.255379 GACGGCGGCGTCTTCATC 61.255 66.667 44.95 26.46 36.12 2.92
1694 1876 3.195698 GGCGGCGTCTTCATCACC 61.196 66.667 9.37 0.00 0.00 4.02
1791 1973 6.259638 GCGACATTCTAGGAGCATATACTAC 58.740 44.000 0.00 0.00 0.00 2.73
1815 1997 0.105593 ATATGACACTGGCCTCAGCG 59.894 55.000 3.32 0.00 44.59 5.18
1849 2031 2.128035 CAGTGTTGTTCCTGTCGAGAC 58.872 52.381 0.00 0.00 0.00 3.36
1868 2050 6.771267 TCGAGACTCTAGGAGCATATTGTAAA 59.229 38.462 0.03 0.00 32.04 2.01
1871 2053 8.998277 AGACTCTAGGAGCATATTGTAAACTA 57.002 34.615 0.00 0.00 32.04 2.24
1872 2054 8.852135 AGACTCTAGGAGCATATTGTAAACTAC 58.148 37.037 0.00 0.00 32.04 2.73
1873 2055 8.770010 ACTCTAGGAGCATATTGTAAACTACT 57.230 34.615 0.00 0.00 32.04 2.57
1874 2056 8.852135 ACTCTAGGAGCATATTGTAAACTACTC 58.148 37.037 0.00 0.00 32.04 2.59
1875 2057 8.179509 TCTAGGAGCATATTGTAAACTACTCC 57.820 38.462 0.00 0.00 42.25 3.85
1876 2058 6.808321 AGGAGCATATTGTAAACTACTCCA 57.192 37.500 8.31 0.00 43.95 3.86
1946 2129 7.268586 AGTGTGACAAATAGAGATGGATGTAC 58.731 38.462 0.00 0.00 0.00 2.90
1960 2143 5.394224 TGGATGTACGTAACTCAATGTCA 57.606 39.130 0.00 0.00 0.00 3.58
1984 2167 2.810274 GCTGTGACTGAATGAGCTGAAA 59.190 45.455 0.00 0.00 0.00 2.69
2121 2311 4.070716 CAGAAGTTGAGTGAAGATTGGCT 58.929 43.478 0.00 0.00 0.00 4.75
2154 2344 6.545504 TCATTGCTTGTTTAGACTCTCAAC 57.454 37.500 0.00 0.00 0.00 3.18
2169 3763 8.506168 AGACTCTCAACTTAGATAGAGAACTG 57.494 38.462 13.79 3.48 38.16 3.16
2170 3764 8.325787 AGACTCTCAACTTAGATAGAGAACTGA 58.674 37.037 13.79 0.00 38.16 3.41
2171 3765 9.120538 GACTCTCAACTTAGATAGAGAACTGAT 57.879 37.037 13.79 0.00 38.16 2.90
2172 3766 9.474313 ACTCTCAACTTAGATAGAGAACTGATT 57.526 33.333 13.79 0.00 38.16 2.57
2179 3773 9.868277 ACTTAGATAGAGAACTGATTTCAACTG 57.132 33.333 0.00 0.00 36.57 3.16
2183 3777 9.646427 AGATAGAGAACTGATTTCAACTGTAAC 57.354 33.333 0.00 0.00 36.57 2.50
2184 3778 9.424319 GATAGAGAACTGATTTCAACTGTAACA 57.576 33.333 0.00 0.00 36.57 2.41
2185 3779 9.950496 ATAGAGAACTGATTTCAACTGTAACAT 57.050 29.630 0.00 0.00 36.57 2.71
2187 3781 9.778741 AGAGAACTGATTTCAACTGTAACATAA 57.221 29.630 0.00 0.00 36.57 1.90
2188 3782 9.813080 GAGAACTGATTTCAACTGTAACATAAC 57.187 33.333 0.00 0.00 36.57 1.89
2192 3786 9.337396 ACTGATTTCAACTGTAACATAACTGAA 57.663 29.630 0.00 0.00 0.00 3.02
2194 3788 9.114952 TGATTTCAACTGTAACATAACTGAACA 57.885 29.630 0.00 0.00 0.00 3.18
2199 3793 9.549078 TCAACTGTAACATAACTGAACATTACA 57.451 29.630 0.00 0.00 32.98 2.41
2201 3795 9.772973 AACTGTAACATAACTGAACATTACAGA 57.227 29.630 22.22 0.00 46.42 3.41
2202 3796 9.772973 ACTGTAACATAACTGAACATTACAGAA 57.227 29.630 22.22 0.00 46.42 3.02
2205 3799 9.988350 GTAACATAACTGAACATTACAGAATGG 57.012 33.333 0.00 0.00 45.83 3.16
2207 3801 6.658816 ACATAACTGAACATTACAGAATGGCA 59.341 34.615 0.00 0.00 45.83 4.92
2209 3803 6.403866 AACTGAACATTACAGAATGGCAAA 57.596 33.333 0.00 0.00 45.83 3.68
2210 3804 6.017400 ACTGAACATTACAGAATGGCAAAG 57.983 37.500 0.00 0.00 45.83 2.77
2211 3805 5.536161 ACTGAACATTACAGAATGGCAAAGT 59.464 36.000 0.00 0.00 45.83 2.66
2213 3807 5.301551 TGAACATTACAGAATGGCAAAGTGT 59.698 36.000 0.00 0.00 45.83 3.55
2214 3808 5.789643 ACATTACAGAATGGCAAAGTGTT 57.210 34.783 0.00 0.00 45.83 3.32
2251 3990 5.954150 AGTTGATTGGCCTTGTAATCTTCAT 59.046 36.000 3.32 0.00 35.02 2.57
2252 3991 6.438425 AGTTGATTGGCCTTGTAATCTTCATT 59.562 34.615 3.32 0.00 35.02 2.57
2253 3992 6.211587 TGATTGGCCTTGTAATCTTCATTG 57.788 37.500 3.32 0.00 35.02 2.82
2254 3993 4.454728 TTGGCCTTGTAATCTTCATTGC 57.545 40.909 3.32 0.00 0.00 3.56
2255 3994 2.423185 TGGCCTTGTAATCTTCATTGCG 59.577 45.455 3.32 0.00 0.00 4.85
2256 3995 2.223572 GGCCTTGTAATCTTCATTGCGG 60.224 50.000 0.00 0.00 0.00 5.69
2257 3996 2.682856 GCCTTGTAATCTTCATTGCGGA 59.317 45.455 0.00 0.00 0.00 5.54
2258 3997 3.316308 GCCTTGTAATCTTCATTGCGGAT 59.684 43.478 0.00 0.00 0.00 4.18
2259 3998 4.515191 GCCTTGTAATCTTCATTGCGGATA 59.485 41.667 0.00 0.00 0.00 2.59
2261 4000 6.294176 GCCTTGTAATCTTCATTGCGGATATT 60.294 38.462 0.00 0.00 0.00 1.28
2262 4001 7.651808 CCTTGTAATCTTCATTGCGGATATTT 58.348 34.615 0.00 0.00 0.00 1.40
2263 4002 7.592533 CCTTGTAATCTTCATTGCGGATATTTG 59.407 37.037 0.00 0.00 0.00 2.32
2265 4004 7.995289 TGTAATCTTCATTGCGGATATTTGTT 58.005 30.769 0.00 0.00 0.00 2.83
2267 4006 9.301153 GTAATCTTCATTGCGGATATTTGTTTT 57.699 29.630 0.00 0.00 0.00 2.43
2272 4011 9.352784 CTTCATTGCGGATATTTGTTTTTCTAA 57.647 29.630 0.00 0.00 0.00 2.10
2274 4013 9.868277 TCATTGCGGATATTTGTTTTTCTAAAT 57.132 25.926 0.00 0.00 0.00 1.40
2302 4041 9.595823 TCTAGAAAGACAAATATTTAGGAACGG 57.404 33.333 0.00 0.00 0.00 4.44
2303 4042 9.595823 CTAGAAAGACAAATATTTAGGAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
2304 4043 8.494016 AGAAAGACAAATATTTAGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
2306 4045 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
2307 4046 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
2309 4048 5.191124 ACAAATATTTAGGAACGGAGGGAGT 59.809 40.000 0.00 0.00 0.00 3.85
2310 4049 5.970501 AATATTTAGGAACGGAGGGAGTT 57.029 39.130 0.00 0.00 34.07 3.01
2451 4282 4.870426 TCTCATCGAGCCAAGTTATTTGTC 59.130 41.667 0.00 0.00 34.87 3.18
2521 4355 5.996644 TCAAAGAGTCTTTTGGTGGACTAA 58.003 37.500 15.60 0.00 42.06 2.24
2548 4382 5.034852 TGTGGGAACTGTACATGGATATG 57.965 43.478 0.00 0.00 40.24 1.78
2605 4451 6.016610 TCAGTTTGCTTACCAAGGATGTTAAC 60.017 38.462 0.00 0.00 34.34 2.01
2630 4476 1.790755 TGTCTACAACACGGTGCATC 58.209 50.000 8.30 0.00 31.20 3.91
2751 4597 7.993183 CCTTGTTGTCCTATATTGTTCCACTAT 59.007 37.037 0.00 0.00 0.00 2.12
2831 4677 4.183865 TCAAACCAAGATACGAGCATGAG 58.816 43.478 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.818787 GCTGGAATGGCAGCGGTG 61.819 66.667 10.98 10.98 34.58 4.94
1 2 4.349503 TGCTGGAATGGCAGCGGT 62.350 61.111 0.00 0.00 46.60 5.68
6 7 1.077501 GGCTACTGCTGGAATGGCA 60.078 57.895 0.00 0.00 39.59 4.92
7 8 1.825622 GGGCTACTGCTGGAATGGC 60.826 63.158 0.00 0.00 39.59 4.40
8 9 1.524621 CGGGCTACTGCTGGAATGG 60.525 63.158 0.00 0.00 39.59 3.16
9 10 1.524621 CCGGGCTACTGCTGGAATG 60.525 63.158 0.00 0.00 39.59 2.67
10 11 1.689233 TCCGGGCTACTGCTGGAAT 60.689 57.895 0.00 0.00 39.45 3.01
11 12 2.284331 TCCGGGCTACTGCTGGAA 60.284 61.111 0.00 0.00 39.45 3.53
12 13 2.759973 CTCCGGGCTACTGCTGGA 60.760 66.667 0.00 0.00 39.85 3.86
13 14 4.537433 GCTCCGGGCTACTGCTGG 62.537 72.222 0.00 0.00 39.59 4.85
14 15 4.880537 CGCTCCGGGCTACTGCTG 62.881 72.222 0.00 0.00 39.59 4.41
32 33 2.632544 TACGTGTCTCCACCGCCAG 61.633 63.158 0.00 0.00 38.41 4.85
33 34 2.598099 TACGTGTCTCCACCGCCA 60.598 61.111 0.00 0.00 38.41 5.69
34 35 2.126189 GTACGTGTCTCCACCGCC 60.126 66.667 0.00 0.00 38.41 6.13
35 36 2.126189 GGTACGTGTCTCCACCGC 60.126 66.667 0.00 0.00 38.41 5.68
36 37 1.080974 GTGGTACGTGTCTCCACCG 60.081 63.158 17.18 0.00 43.84 4.94
37 38 4.981415 GTGGTACGTGTCTCCACC 57.019 61.111 17.18 8.83 43.84 4.61
39 40 0.390124 GGTTGTGGTACGTGTCTCCA 59.610 55.000 0.00 0.00 0.00 3.86
42 43 0.313043 CTCGGTTGTGGTACGTGTCT 59.687 55.000 0.00 0.00 0.00 3.41
87 88 1.335810 CAAATCTCGGATGGTGCATGG 59.664 52.381 0.00 0.00 0.00 3.66
130 132 2.393768 GCGTACGTGTCTCCTCCGA 61.394 63.158 17.90 0.00 0.00 4.55
149 151 4.626081 AGGAGCTTGGCGTTGCGT 62.626 61.111 0.00 0.00 0.00 5.24
189 195 1.593209 GAGGCGTGACGTGACCAAA 60.593 57.895 6.91 0.00 0.00 3.28
228 239 2.588596 CGTGCAGCCACTGTGTGA 60.589 61.111 7.08 0.00 39.86 3.58
276 287 4.247380 GCATCGCTAGCTGCCCCT 62.247 66.667 16.11 0.00 38.78 4.79
325 336 2.844946 TCATTTCAAGACGCTTCCACA 58.155 42.857 0.00 0.00 0.00 4.17
364 382 4.643387 AGCTTGGCCCGTGACCAC 62.643 66.667 0.00 0.00 36.76 4.16
375 393 4.233635 GCGATGCAGCGAGCTTGG 62.234 66.667 30.90 0.00 45.94 3.61
388 406 2.364324 TCGATAGCTTTACCAAGGCGAT 59.636 45.455 0.00 0.00 0.00 4.58
392 410 5.116180 TCACATTCGATAGCTTTACCAAGG 58.884 41.667 0.00 0.00 0.00 3.61
403 422 4.798574 TGATCGGTGATCACATTCGATAG 58.201 43.478 27.38 11.01 43.11 2.08
419 438 3.349488 TGCGATACTTGTACTGATCGG 57.651 47.619 15.78 0.00 41.11 4.18
420 439 3.670523 CCATGCGATACTTGTACTGATCG 59.329 47.826 12.08 12.08 43.11 3.69
421 440 3.990469 CCCATGCGATACTTGTACTGATC 59.010 47.826 0.00 0.00 0.00 2.92
422 441 3.244215 CCCCATGCGATACTTGTACTGAT 60.244 47.826 0.00 0.00 0.00 2.90
423 442 2.102420 CCCCATGCGATACTTGTACTGA 59.898 50.000 0.00 0.00 0.00 3.41
424 443 2.102420 TCCCCATGCGATACTTGTACTG 59.898 50.000 0.00 0.00 0.00 2.74
425 444 2.394632 TCCCCATGCGATACTTGTACT 58.605 47.619 0.00 0.00 0.00 2.73
433 452 2.687425 CACACATTTTCCCCATGCGATA 59.313 45.455 0.00 0.00 0.00 2.92
460 479 1.792301 TCGGTAAGACTCGACTGCG 59.208 57.895 0.00 0.00 39.35 5.18
469 488 0.108992 TGCCATGTCGTCGGTAAGAC 60.109 55.000 0.00 0.00 46.16 3.01
476 495 0.301687 GCATAACTGCCATGTCGTCG 59.698 55.000 0.00 0.00 42.88 5.12
494 531 0.528684 GGATCAGCACTCACTACCGC 60.529 60.000 0.00 0.00 0.00 5.68
533 570 0.175073 GGGTTGCCAGAGGTACGTAG 59.825 60.000 0.00 0.00 0.00 3.51
569 606 0.739813 ACGGACAGAGCGTTTATGGC 60.740 55.000 0.00 0.00 0.00 4.40
576 613 2.283529 ATTCCCACGGACAGAGCGT 61.284 57.895 0.00 0.00 0.00 5.07
577 614 1.811266 CATTCCCACGGACAGAGCG 60.811 63.158 0.00 0.00 0.00 5.03
605 645 3.703420 GTGTGGATCGTGATACTACCAC 58.297 50.000 0.00 0.00 45.16 4.16
606 646 2.356695 CGTGTGGATCGTGATACTACCA 59.643 50.000 0.00 0.00 0.00 3.25
607 647 2.287427 CCGTGTGGATCGTGATACTACC 60.287 54.545 0.00 0.00 37.49 3.18
608 648 2.357009 ACCGTGTGGATCGTGATACTAC 59.643 50.000 0.00 0.00 39.21 2.73
609 649 2.615447 GACCGTGTGGATCGTGATACTA 59.385 50.000 0.00 0.00 39.21 1.82
610 650 1.404391 GACCGTGTGGATCGTGATACT 59.596 52.381 0.00 0.00 39.21 2.12
611 651 1.133598 TGACCGTGTGGATCGTGATAC 59.866 52.381 0.00 0.00 39.21 2.24
612 652 1.133598 GTGACCGTGTGGATCGTGATA 59.866 52.381 0.00 0.00 39.21 2.15
613 653 0.108804 GTGACCGTGTGGATCGTGAT 60.109 55.000 0.00 0.00 39.21 3.06
614 654 1.287815 GTGACCGTGTGGATCGTGA 59.712 57.895 0.00 0.00 39.21 4.35
615 655 2.086426 CGTGACCGTGTGGATCGTG 61.086 63.158 0.00 0.00 39.21 4.35
616 656 2.257371 CGTGACCGTGTGGATCGT 59.743 61.111 0.00 0.00 39.21 3.73
617 657 2.480853 TTCCGTGACCGTGTGGATCG 62.481 60.000 0.00 0.00 39.21 3.69
618 658 0.320073 TTTCCGTGACCGTGTGGATC 60.320 55.000 0.00 0.00 39.21 3.36
619 659 0.323629 ATTTCCGTGACCGTGTGGAT 59.676 50.000 0.00 0.00 39.21 3.41
620 660 0.107081 AATTTCCGTGACCGTGTGGA 59.893 50.000 0.00 0.00 39.21 4.02
621 661 0.948678 AAATTTCCGTGACCGTGTGG 59.051 50.000 0.00 0.00 42.84 4.17
624 664 2.544686 TGTGTAAATTTCCGTGACCGTG 59.455 45.455 0.00 0.00 0.00 4.94
648 688 1.939974 ACGTATGCATGCACTAGGTG 58.060 50.000 25.37 12.19 36.51 4.00
653 693 2.979814 TTCCTACGTATGCATGCACT 57.020 45.000 25.37 14.70 0.00 4.40
654 694 2.872245 ACATTCCTACGTATGCATGCAC 59.128 45.455 25.37 10.68 0.00 4.57
655 695 3.192541 ACATTCCTACGTATGCATGCA 57.807 42.857 25.04 25.04 0.00 3.96
656 696 4.527564 GAAACATTCCTACGTATGCATGC 58.472 43.478 11.82 11.82 0.00 4.06
657 697 4.270084 ACGAAACATTCCTACGTATGCATG 59.730 41.667 10.16 8.48 35.49 4.06
658 698 4.439057 ACGAAACATTCCTACGTATGCAT 58.561 39.130 3.79 3.79 35.49 3.96
659 699 3.852286 ACGAAACATTCCTACGTATGCA 58.148 40.909 0.00 0.00 35.49 3.96
660 700 3.244579 GGACGAAACATTCCTACGTATGC 59.755 47.826 0.00 0.00 37.32 3.14
684 729 1.815003 TGGCGACATGGATTCTGCG 60.815 57.895 0.00 0.00 33.40 5.18
685 730 1.723870 GTGGCGACATGGATTCTGC 59.276 57.895 0.00 0.00 46.14 4.26
721 883 4.699637 TCTGTGAAGTATTTCCGTTGTGT 58.300 39.130 0.00 0.00 32.09 3.72
722 884 5.408299 TCATCTGTGAAGTATTTCCGTTGTG 59.592 40.000 0.00 0.00 32.09 3.33
723 885 5.547465 TCATCTGTGAAGTATTTCCGTTGT 58.453 37.500 0.00 0.00 32.09 3.32
724 886 6.668541 ATCATCTGTGAAGTATTTCCGTTG 57.331 37.500 0.00 0.00 38.01 4.10
725 887 7.327975 TGTATCATCTGTGAAGTATTTCCGTT 58.672 34.615 0.00 0.00 38.01 4.44
729 891 6.563010 GCGCTGTATCATCTGTGAAGTATTTC 60.563 42.308 0.00 0.00 38.01 2.17
730 892 5.235186 GCGCTGTATCATCTGTGAAGTATTT 59.765 40.000 0.00 0.00 38.01 1.40
731 893 4.747108 GCGCTGTATCATCTGTGAAGTATT 59.253 41.667 0.00 0.00 38.01 1.89
732 894 4.038522 AGCGCTGTATCATCTGTGAAGTAT 59.961 41.667 10.39 0.00 38.01 2.12
733 895 3.381590 AGCGCTGTATCATCTGTGAAGTA 59.618 43.478 10.39 0.00 38.01 2.24
734 896 2.167281 AGCGCTGTATCATCTGTGAAGT 59.833 45.455 10.39 0.00 38.01 3.01
735 897 2.538861 CAGCGCTGTATCATCTGTGAAG 59.461 50.000 29.24 0.00 38.01 3.02
736 898 2.166254 TCAGCGCTGTATCATCTGTGAA 59.834 45.455 34.70 9.91 38.01 3.18
737 899 1.750778 TCAGCGCTGTATCATCTGTGA 59.249 47.619 34.70 10.38 39.04 3.58
738 900 2.214387 TCAGCGCTGTATCATCTGTG 57.786 50.000 34.70 7.94 0.00 3.66
739 901 2.544685 GTTCAGCGCTGTATCATCTGT 58.455 47.619 34.70 0.00 0.00 3.41
740 902 1.520174 CGTTCAGCGCTGTATCATCTG 59.480 52.381 34.70 14.38 0.00 2.90
741 903 1.405463 TCGTTCAGCGCTGTATCATCT 59.595 47.619 34.70 0.00 41.07 2.90
742 904 1.518929 GTCGTTCAGCGCTGTATCATC 59.481 52.381 34.70 18.47 41.07 2.92
743 905 1.135112 TGTCGTTCAGCGCTGTATCAT 60.135 47.619 34.70 0.00 41.07 2.45
744 906 0.242555 TGTCGTTCAGCGCTGTATCA 59.757 50.000 34.70 23.13 41.07 2.15
745 907 0.640768 GTGTCGTTCAGCGCTGTATC 59.359 55.000 34.70 23.47 41.07 2.24
746 908 0.243907 AGTGTCGTTCAGCGCTGTAT 59.756 50.000 34.70 8.52 41.07 2.29
747 909 0.386858 GAGTGTCGTTCAGCGCTGTA 60.387 55.000 34.70 24.85 41.07 2.74
748 910 1.661821 GAGTGTCGTTCAGCGCTGT 60.662 57.895 34.70 14.99 41.07 4.40
749 911 2.710971 CGAGTGTCGTTCAGCGCTG 61.711 63.158 31.53 31.53 41.07 5.18
750 912 2.429236 CGAGTGTCGTTCAGCGCT 60.429 61.111 2.64 2.64 41.07 5.92
751 913 2.428569 TCGAGTGTCGTTCAGCGC 60.429 61.111 0.00 0.00 41.35 5.92
752 914 2.418333 CGTCGAGTGTCGTTCAGCG 61.418 63.158 0.00 0.00 41.35 5.18
753 915 0.454620 ATCGTCGAGTGTCGTTCAGC 60.455 55.000 0.00 0.00 41.35 4.26
754 916 1.251355 CATCGTCGAGTGTCGTTCAG 58.749 55.000 0.00 0.00 41.35 3.02
755 917 0.109919 CCATCGTCGAGTGTCGTTCA 60.110 55.000 0.00 0.00 41.35 3.18
756 918 1.403972 GCCATCGTCGAGTGTCGTTC 61.404 60.000 0.00 0.00 41.35 3.95
757 919 1.443872 GCCATCGTCGAGTGTCGTT 60.444 57.895 0.00 0.00 41.35 3.85
758 920 1.022982 TAGCCATCGTCGAGTGTCGT 61.023 55.000 0.00 0.00 41.35 4.34
759 921 0.098200 TTAGCCATCGTCGAGTGTCG 59.902 55.000 0.00 0.00 42.10 4.35
760 922 2.493713 ATTAGCCATCGTCGAGTGTC 57.506 50.000 0.00 0.00 0.00 3.67
761 923 2.165641 TGAATTAGCCATCGTCGAGTGT 59.834 45.455 0.00 0.00 0.00 3.55
762 924 2.791560 CTGAATTAGCCATCGTCGAGTG 59.208 50.000 0.00 0.00 0.00 3.51
763 925 3.085443 CTGAATTAGCCATCGTCGAGT 57.915 47.619 0.00 0.00 0.00 4.18
791 953 7.690141 ATCCATGGATAAAGCTAAAGCAGCAG 61.690 42.308 26.25 0.00 42.13 4.24
792 954 5.925160 ATCCATGGATAAAGCTAAAGCAGCA 60.925 40.000 26.25 0.00 42.13 4.41
793 955 4.522022 ATCCATGGATAAAGCTAAAGCAGC 59.478 41.667 26.25 0.00 40.93 5.25
794 956 6.010294 CATCCATGGATAAAGCTAAAGCAG 57.990 41.667 26.87 6.21 37.07 4.24
810 972 3.509967 ACATGCATATCAAGCCATCCATG 59.490 43.478 0.00 0.00 36.00 3.66
811 973 3.762288 GACATGCATATCAAGCCATCCAT 59.238 43.478 0.00 0.00 0.00 3.41
812 974 3.151554 GACATGCATATCAAGCCATCCA 58.848 45.455 0.00 0.00 0.00 3.41
813 975 2.161012 CGACATGCATATCAAGCCATCC 59.839 50.000 5.70 0.00 0.00 3.51
814 976 2.810274 ACGACATGCATATCAAGCCATC 59.190 45.455 5.70 0.00 0.00 3.51
815 977 2.551032 CACGACATGCATATCAAGCCAT 59.449 45.455 5.70 0.00 0.00 4.40
816 978 1.941975 CACGACATGCATATCAAGCCA 59.058 47.619 5.70 0.00 0.00 4.75
817 979 2.675767 CACGACATGCATATCAAGCC 57.324 50.000 5.70 0.00 0.00 4.35
829 991 1.477105 CGACGATACATGCACGACAT 58.523 50.000 12.34 0.00 40.66 3.06
830 992 0.524604 CCGACGATACATGCACGACA 60.525 55.000 12.34 0.00 0.00 4.35
831 993 1.206745 CCCGACGATACATGCACGAC 61.207 60.000 12.34 6.51 0.00 4.34
832 994 1.065109 CCCGACGATACATGCACGA 59.935 57.895 12.34 0.00 0.00 4.35
833 995 0.029700 TACCCGACGATACATGCACG 59.970 55.000 0.00 0.00 0.00 5.34
834 996 2.212869 TTACCCGACGATACATGCAC 57.787 50.000 0.00 0.00 0.00 4.57
835 997 2.963548 TTTACCCGACGATACATGCA 57.036 45.000 0.00 0.00 0.00 3.96
836 998 3.128349 ACATTTACCCGACGATACATGC 58.872 45.455 0.00 0.00 0.00 4.06
837 999 3.424198 CGACATTTACCCGACGATACATG 59.576 47.826 0.00 0.00 0.00 3.21
838 1000 3.067180 ACGACATTTACCCGACGATACAT 59.933 43.478 0.00 0.00 0.00 2.29
839 1001 2.423185 ACGACATTTACCCGACGATACA 59.577 45.455 0.00 0.00 0.00 2.29
840 1002 3.070429 ACGACATTTACCCGACGATAC 57.930 47.619 0.00 0.00 0.00 2.24
841 1003 3.128415 TGAACGACATTTACCCGACGATA 59.872 43.478 0.00 0.00 0.00 2.92
842 1004 2.094597 TGAACGACATTTACCCGACGAT 60.095 45.455 0.00 0.00 0.00 3.73
843 1005 1.269174 TGAACGACATTTACCCGACGA 59.731 47.619 0.00 0.00 0.00 4.20
844 1006 1.700523 TGAACGACATTTACCCGACG 58.299 50.000 0.00 0.00 0.00 5.12
845 1007 2.997986 ACATGAACGACATTTACCCGAC 59.002 45.455 0.00 0.00 37.07 4.79
846 1008 3.322211 ACATGAACGACATTTACCCGA 57.678 42.857 0.00 0.00 37.07 5.14
847 1009 3.000925 GCTACATGAACGACATTTACCCG 59.999 47.826 0.00 0.00 37.07 5.28
848 1010 3.936453 TGCTACATGAACGACATTTACCC 59.064 43.478 0.00 0.00 37.07 3.69
849 1011 4.630069 ACTGCTACATGAACGACATTTACC 59.370 41.667 0.00 0.00 37.07 2.85
850 1012 5.550981 CACTGCTACATGAACGACATTTAC 58.449 41.667 0.00 0.00 37.07 2.01
851 1013 4.092821 GCACTGCTACATGAACGACATTTA 59.907 41.667 0.00 0.00 37.07 1.40
852 1014 3.120199 GCACTGCTACATGAACGACATTT 60.120 43.478 0.00 0.00 37.07 2.32
853 1015 2.416547 GCACTGCTACATGAACGACATT 59.583 45.455 0.00 0.00 37.07 2.71
854 1016 2.002586 GCACTGCTACATGAACGACAT 58.997 47.619 0.00 0.00 40.17 3.06
855 1017 1.000843 AGCACTGCTACATGAACGACA 59.999 47.619 0.21 0.00 36.99 4.35
856 1018 1.656095 GAGCACTGCTACATGAACGAC 59.344 52.381 2.71 0.00 39.88 4.34
857 1019 1.272212 TGAGCACTGCTACATGAACGA 59.728 47.619 2.71 0.00 39.88 3.85
858 1020 1.713597 TGAGCACTGCTACATGAACG 58.286 50.000 2.71 0.00 39.88 3.95
859 1021 3.063180 GTCATGAGCACTGCTACATGAAC 59.937 47.826 28.70 22.61 45.10 3.18
860 1022 3.264947 GTCATGAGCACTGCTACATGAA 58.735 45.455 28.70 18.73 45.10 2.57
861 1023 2.234414 TGTCATGAGCACTGCTACATGA 59.766 45.455 26.04 26.04 43.48 3.07
862 1024 2.350804 GTGTCATGAGCACTGCTACATG 59.649 50.000 23.74 23.74 39.88 3.21
863 1025 2.027837 TGTGTCATGAGCACTGCTACAT 60.028 45.455 21.21 6.81 39.88 2.29
864 1026 1.344114 TGTGTCATGAGCACTGCTACA 59.656 47.619 21.21 1.68 39.88 2.74
865 1027 2.084610 TGTGTCATGAGCACTGCTAC 57.915 50.000 21.21 0.00 39.88 3.58
866 1028 2.416747 GTTGTGTCATGAGCACTGCTA 58.583 47.619 21.21 6.22 39.88 3.49
867 1029 1.233019 GTTGTGTCATGAGCACTGCT 58.767 50.000 21.21 2.22 43.88 4.24
868 1030 0.239347 GGTTGTGTCATGAGCACTGC 59.761 55.000 21.21 15.65 37.70 4.40
869 1031 0.877071 GGGTTGTGTCATGAGCACTG 59.123 55.000 21.21 0.00 37.70 3.66
870 1032 0.473755 TGGGTTGTGTCATGAGCACT 59.526 50.000 21.21 0.00 37.70 4.40
871 1033 0.877071 CTGGGTTGTGTCATGAGCAC 59.123 55.000 16.70 16.70 37.37 4.40
872 1034 0.890542 GCTGGGTTGTGTCATGAGCA 60.891 55.000 0.00 0.00 0.00 4.26
873 1035 0.607489 AGCTGGGTTGTGTCATGAGC 60.607 55.000 0.00 0.00 0.00 4.26
874 1036 1.538512 CAAGCTGGGTTGTGTCATGAG 59.461 52.381 0.00 0.00 0.00 2.90
875 1037 1.142667 TCAAGCTGGGTTGTGTCATGA 59.857 47.619 11.44 0.00 0.00 3.07
876 1038 1.608055 TCAAGCTGGGTTGTGTCATG 58.392 50.000 11.44 0.00 0.00 3.07
884 1046 2.250031 TGCATTTCATCAAGCTGGGTT 58.750 42.857 0.00 0.00 0.00 4.11
984 1148 1.177401 ATGTACTGCGAGCTCACAGA 58.823 50.000 32.81 15.09 37.35 3.41
985 1149 2.851805 TATGTACTGCGAGCTCACAG 57.148 50.000 26.37 26.37 39.86 3.66
986 1150 5.453567 AATATATGTACTGCGAGCTCACA 57.546 39.130 15.40 9.67 0.00 3.58
987 1151 6.771188 AAAATATATGTACTGCGAGCTCAC 57.229 37.500 15.40 4.30 0.00 3.51
988 1152 6.202762 CCAAAAATATATGTACTGCGAGCTCA 59.797 38.462 15.40 0.00 0.00 4.26
1013 1180 1.753073 CTGGGATTGGATGAAGCAACC 59.247 52.381 0.00 0.00 0.00 3.77
1014 1181 1.135721 GCTGGGATTGGATGAAGCAAC 59.864 52.381 0.00 0.00 0.00 4.17
1016 1183 0.627451 AGCTGGGATTGGATGAAGCA 59.373 50.000 0.00 0.00 33.08 3.91
1020 1187 0.182061 GCAGAGCTGGGATTGGATGA 59.818 55.000 0.00 0.00 0.00 2.92
1040 1207 2.978010 GTGTGGGTGCGTTCTGGG 60.978 66.667 0.00 0.00 0.00 4.45
1044 1211 2.110213 TGGAGTGTGGGTGCGTTC 59.890 61.111 0.00 0.00 0.00 3.95
1048 1215 1.598130 GTCAGTGGAGTGTGGGTGC 60.598 63.158 0.00 0.00 0.00 5.01
1075 1245 0.417437 TCACTCCCCCTGATTCTCCA 59.583 55.000 0.00 0.00 0.00 3.86
1076 1246 1.127343 CTCACTCCCCCTGATTCTCC 58.873 60.000 0.00 0.00 0.00 3.71
1079 1249 2.356227 GGTTTCTCACTCCCCCTGATTC 60.356 54.545 0.00 0.00 0.00 2.52
1081 1251 1.290134 GGTTTCTCACTCCCCCTGAT 58.710 55.000 0.00 0.00 0.00 2.90
1082 1252 0.104672 TGGTTTCTCACTCCCCCTGA 60.105 55.000 0.00 0.00 0.00 3.86
1083 1253 0.995024 ATGGTTTCTCACTCCCCCTG 59.005 55.000 0.00 0.00 0.00 4.45
1145 1315 1.066430 CGGAGTAGTAGGCAAAGGCAA 60.066 52.381 0.00 0.00 43.71 4.52
1151 1321 0.396695 CTCCCCGGAGTAGTAGGCAA 60.397 60.000 0.73 0.00 37.47 4.52
1157 1327 1.001760 ATGTGCTCCCCGGAGTAGT 59.998 57.895 0.73 0.00 43.70 2.73
1691 1873 0.739813 GCGGGTAGTAGTTGCAGGTG 60.740 60.000 0.00 0.00 0.00 4.00
1694 1876 1.518572 CGGCGGGTAGTAGTTGCAG 60.519 63.158 0.00 0.00 0.00 4.41
1815 1997 0.604780 ACACTGCCATGACAGACAGC 60.605 55.000 16.61 0.00 40.25 4.40
1849 2031 8.301002 GGAGTAGTTTACAATATGCTCCTAGAG 58.699 40.741 0.00 0.00 38.47 2.43
1868 2050 5.690464 ATCTGCTCTCAAATTGGAGTAGT 57.310 39.130 19.82 10.92 41.06 2.73
1871 2053 6.656902 TCATTATCTGCTCTCAAATTGGAGT 58.343 36.000 9.73 0.00 36.30 3.85
1872 2054 7.747155 ATCATTATCTGCTCTCAAATTGGAG 57.253 36.000 3.13 3.13 36.21 3.86
1873 2055 8.435187 ACTATCATTATCTGCTCTCAAATTGGA 58.565 33.333 0.00 0.00 0.00 3.53
1874 2056 8.504815 CACTATCATTATCTGCTCTCAAATTGG 58.495 37.037 0.00 0.00 0.00 3.16
1875 2057 9.053840 ACACTATCATTATCTGCTCTCAAATTG 57.946 33.333 0.00 0.00 0.00 2.32
1876 2058 9.270640 GACACTATCATTATCTGCTCTCAAATT 57.729 33.333 0.00 0.00 0.00 1.82
1946 2129 4.152223 TCACAGCAATGACATTGAGTTACG 59.848 41.667 28.37 14.70 42.83 3.18
1960 2143 2.747989 CAGCTCATTCAGTCACAGCAAT 59.252 45.455 0.00 0.00 32.17 3.56
1984 2167 8.526147 CCAATTCAGTGATCCAAGTCTAAAAAT 58.474 33.333 0.00 0.00 0.00 1.82
2037 2220 5.938125 TGCTACAGTTTAAATCAGTTCCCTC 59.062 40.000 0.00 0.00 0.00 4.30
2121 2311 9.677567 GTCTAAACAAGCAATGAAGATTACAAA 57.322 29.630 0.00 0.00 0.00 2.83
2154 2344 9.868277 ACAGTTGAAATCAGTTCTCTATCTAAG 57.132 33.333 0.00 0.00 37.13 2.18
2173 3767 9.549078 TGTAATGTTCAGTTATGTTACAGTTGA 57.451 29.630 0.00 0.00 30.96 3.18
2174 3768 9.811655 CTGTAATGTTCAGTTATGTTACAGTTG 57.188 33.333 12.49 0.00 41.60 3.16
2175 3769 9.772973 TCTGTAATGTTCAGTTATGTTACAGTT 57.227 29.630 17.49 0.00 44.42 3.16
2179 3773 9.988350 CCATTCTGTAATGTTCAGTTATGTTAC 57.012 33.333 0.00 0.00 40.84 2.50
2181 3775 7.176515 TGCCATTCTGTAATGTTCAGTTATGTT 59.823 33.333 0.00 0.00 40.84 2.71
2182 3776 6.658816 TGCCATTCTGTAATGTTCAGTTATGT 59.341 34.615 0.00 0.00 40.84 2.29
2183 3777 7.087409 TGCCATTCTGTAATGTTCAGTTATG 57.913 36.000 0.00 0.00 40.84 1.90
2184 3778 7.701539 TTGCCATTCTGTAATGTTCAGTTAT 57.298 32.000 0.00 0.00 40.84 1.89
2185 3779 7.230510 ACTTTGCCATTCTGTAATGTTCAGTTA 59.769 33.333 0.00 0.00 40.84 2.24
2186 3780 6.040842 ACTTTGCCATTCTGTAATGTTCAGTT 59.959 34.615 0.00 0.00 40.84 3.16
2187 3781 5.536161 ACTTTGCCATTCTGTAATGTTCAGT 59.464 36.000 0.00 0.00 40.84 3.41
2188 3782 5.860182 CACTTTGCCATTCTGTAATGTTCAG 59.140 40.000 0.00 0.00 40.84 3.02
2192 3786 5.531634 CAACACTTTGCCATTCTGTAATGT 58.468 37.500 0.00 0.00 40.84 2.71
2216 3810 2.360165 GCCAATCAACTTCTGCCTATGG 59.640 50.000 0.00 0.00 0.00 2.74
2217 3811 2.360165 GGCCAATCAACTTCTGCCTATG 59.640 50.000 0.00 0.00 35.99 2.23
2220 3814 0.407139 AGGCCAATCAACTTCTGCCT 59.593 50.000 5.01 0.00 44.08 4.75
2225 3819 5.904362 AGATTACAAGGCCAATCAACTTC 57.096 39.130 5.01 0.00 34.28 3.01
2226 3820 5.774690 TGAAGATTACAAGGCCAATCAACTT 59.225 36.000 5.01 1.90 34.28 2.66
2227 3821 5.324409 TGAAGATTACAAGGCCAATCAACT 58.676 37.500 5.01 0.00 34.28 3.16
2228 3822 5.643379 TGAAGATTACAAGGCCAATCAAC 57.357 39.130 5.01 4.53 34.28 3.18
2276 4015 9.595823 CCGTTCCTAAATATTTGTCTTTCTAGA 57.404 33.333 11.05 0.00 0.00 2.43
2277 4016 9.595823 TCCGTTCCTAAATATTTGTCTTTCTAG 57.404 33.333 11.05 0.00 0.00 2.43
2280 4019 7.201705 CCCTCCGTTCCTAAATATTTGTCTTTC 60.202 40.741 11.05 0.00 0.00 2.62
2281 4020 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
2283 4022 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
2284 4023 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
2285 4024 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
2286 4025 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
2287 4026 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
2290 4029 4.355549 TCAACTCCCTCCGTTCCTAAATA 58.644 43.478 0.00 0.00 0.00 1.40
2291 4030 3.178865 TCAACTCCCTCCGTTCCTAAAT 58.821 45.455 0.00 0.00 0.00 1.40
2293 4032 2.301009 GTTCAACTCCCTCCGTTCCTAA 59.699 50.000 0.00 0.00 0.00 2.69
2295 4034 0.685660 GTTCAACTCCCTCCGTTCCT 59.314 55.000 0.00 0.00 0.00 3.36
2296 4035 0.395312 TGTTCAACTCCCTCCGTTCC 59.605 55.000 0.00 0.00 0.00 3.62
2297 4036 1.202604 TGTGTTCAACTCCCTCCGTTC 60.203 52.381 0.00 0.00 0.00 3.95
2298 4037 0.834612 TGTGTTCAACTCCCTCCGTT 59.165 50.000 0.00 0.00 0.00 4.44
2299 4038 0.834612 TTGTGTTCAACTCCCTCCGT 59.165 50.000 0.00 0.00 0.00 4.69
2300 4039 2.185004 ATTGTGTTCAACTCCCTCCG 57.815 50.000 0.00 0.00 36.33 4.63
2301 4040 3.222603 ACAATTGTGTTCAACTCCCTCC 58.777 45.455 11.07 0.00 32.58 4.30
2302 4041 4.918810 AACAATTGTGTTCAACTCCCTC 57.081 40.909 12.82 0.00 45.00 4.30
2303 4042 6.976934 AATAACAATTGTGTTCAACTCCCT 57.023 33.333 12.82 0.00 45.00 4.20
2304 4043 7.088272 GGTAATAACAATTGTGTTCAACTCCC 58.912 38.462 12.82 0.50 45.00 4.30
2306 4045 8.964150 GTTGGTAATAACAATTGTGTTCAACTC 58.036 33.333 12.82 0.00 45.00 3.01
2307 4046 8.470805 TGTTGGTAATAACAATTGTGTTCAACT 58.529 29.630 23.70 10.43 45.00 3.16
2421 4252 1.227089 GGCTCGATGAGACGCACAT 60.227 57.895 0.00 0.00 0.00 3.21
2521 4355 3.826157 CCATGTACAGTTCCCACAAATGT 59.174 43.478 0.33 0.00 0.00 2.71
2548 4382 4.484236 TGCATGTACAAGCAATTACAAGC 58.516 39.130 22.48 10.25 41.24 4.01
2577 4415 5.362430 ACATCCTTGGTAAGCAAACTGAAAA 59.638 36.000 0.00 0.00 0.00 2.29
2580 4418 4.098914 ACATCCTTGGTAAGCAAACTGA 57.901 40.909 0.00 0.00 0.00 3.41
2630 4476 2.479566 TGAGCAGCCAACTTTCTAGG 57.520 50.000 0.00 0.00 0.00 3.02
2822 4668 0.800631 ACATTGTGTGCTCATGCTCG 59.199 50.000 0.00 0.00 40.48 5.03
2831 4677 6.007936 TGATAAAACTGGTACATTGTGTGC 57.992 37.500 0.00 0.00 38.20 4.57


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

AutoCloner maintained by Alex Coulton.