Multiple sequence alignment - TraesCS3B01G071200

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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 TraesCS3B01G071200 chr3B 100.000 2846 0 0 1 2846 43056272 43059117 0.000000e+00 5256
1 TraesCS3B01G071200 chr3B 95.886 875 30 4 1975 2846 65208155 65207284 0.000000e+00 1411
2 TraesCS3B01G071200 chr3B 95.074 873 37 4 1975 2846 65202521 65201654 0.000000e+00 1369
3 TraesCS3B01G071200 chr3B 96.399 361 10 3 1 358 31126119 31125759 2.440000e-165 592
4 TraesCS3B01G071200 chr3B 95.223 314 14 1 358 671 31125673 31125361 1.970000e-136 496
5 TraesCS3B01G071200 chr6B 96.449 873 19 4 1975 2846 179719277 179718416 0.000000e+00 1430
6 TraesCS3B01G071200 chr6B 95.862 870 24 5 1974 2842 402220005 402219147 0.000000e+00 1397
7 TraesCS3B01G071200 chr6B 90.556 360 27 6 1 358 200324750 200324396 1.190000e-128 470
8 TraesCS3B01G071200 chr6B 82.396 551 76 12 999 1545 716263192 716263725 7.180000e-126 460
9 TraesCS3B01G071200 chr6B 88.254 315 33 2 358 672 200324312 200324002 9.630000e-100 374
10 TraesCS3B01G071200 chr2B 95.767 874 32 3 1975 2846 672741496 672742366 0.000000e+00 1404
11 TraesCS3B01G071200 chr2B 95.528 872 30 7 1975 2842 117929243 117928377 0.000000e+00 1386
12 TraesCS3B01G071200 chr2B 74.755 511 107 20 1024 1522 794611695 794611195 2.870000e-50 209
13 TraesCS3B01G071200 chr4A 95.397 869 32 5 1975 2842 671508950 671509811 0.000000e+00 1376
14 TraesCS3B01G071200 chr4A 85.669 314 40 3 358 671 648314033 648313725 2.730000e-85 326
15 TraesCS3B01G071200 chr1B 94.898 882 36 7 1966 2842 685085581 685086458 0.000000e+00 1371
16 TraesCS3B01G071200 chr1B 95.074 873 36 4 1975 2846 169020931 169020065 0.000000e+00 1367
17 TraesCS3B01G071200 chr1B 90.000 360 30 6 1 356 591364028 591364385 7.180000e-126 460
18 TraesCS3B01G071200 chr1B 90.159 315 29 2 358 671 591364471 591364784 2.640000e-110 409
19 TraesCS3B01G071200 chr6D 83.927 1095 137 30 913 1976 470046124 470047210 0.000000e+00 1011
20 TraesCS3B01G071200 chr6D 82.057 836 129 15 993 1818 470052763 470053587 0.000000e+00 693
21 TraesCS3B01G071200 chr6D 80.474 886 142 25 952 1811 470104596 470103716 0.000000e+00 649
22 TraesCS3B01G071200 chr6A 82.241 839 128 14 990 1818 614841628 614842455 0.000000e+00 704
23 TraesCS3B01G071200 chr6A 79.617 888 147 23 952 1820 614967868 614966996 8.720000e-170 606
24 TraesCS3B01G071200 chr5B 84.296 675 91 13 1 669 587446181 587445516 0.000000e+00 645
25 TraesCS3B01G071200 chr5B 96.648 358 12 0 1 358 572133036 572132679 1.890000e-166 595
26 TraesCS3B01G071200 chr5B 93.312 314 19 2 358 671 572132594 572132283 2.000000e-126 462
27 TraesCS3B01G071200 chr7A 94.986 359 17 1 1 358 680911948 680912306 1.910000e-156 562
28 TraesCS3B01G071200 chr7A 94.413 358 18 2 1 358 671403671 671404026 1.490000e-152 549
29 TraesCS3B01G071200 chr7A 93.296 358 19 2 1 358 608532121 608532473 9.030000e-145 523
30 TraesCS3B01G071200 chr7A 94.268 314 18 0 358 671 671404111 671404424 5.510000e-132 481
31 TraesCS3B01G071200 chr7A 92.357 314 21 3 358 669 608532558 608532870 7.240000e-121 444
32 TraesCS3B01G071200 chr5A 92.179 358 19 2 1 358 311129054 311129402 5.480000e-137 497
33 TraesCS3B01G071200 chr7D 91.083 314 27 1 358 671 80299996 80300308 9.430000e-115 424
34 TraesCS3B01G071200 chr3A 79.348 276 57 0 1246 1521 13546108 13546383 8.050000e-46 195
35 TraesCS3B01G071200 chr5D 78.746 287 61 0 1246 1532 553910749 553911035 2.890000e-45 193


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 TraesCS3B01G071200 chr3B 43056272 43059117 2845 False 5256.0 5256 100.0000 1 2846 1 chr3B.!!$F1 2845
1 TraesCS3B01G071200 chr3B 65207284 65208155 871 True 1411.0 1411 95.8860 1975 2846 1 chr3B.!!$R2 871
2 TraesCS3B01G071200 chr3B 65201654 65202521 867 True 1369.0 1369 95.0740 1975 2846 1 chr3B.!!$R1 871
3 TraesCS3B01G071200 chr3B 31125361 31126119 758 True 544.0 592 95.8110 1 671 2 chr3B.!!$R3 670
4 TraesCS3B01G071200 chr6B 179718416 179719277 861 True 1430.0 1430 96.4490 1975 2846 1 chr6B.!!$R1 871
5 TraesCS3B01G071200 chr6B 402219147 402220005 858 True 1397.0 1397 95.8620 1974 2842 1 chr6B.!!$R2 868
6 TraesCS3B01G071200 chr6B 716263192 716263725 533 False 460.0 460 82.3960 999 1545 1 chr6B.!!$F1 546
7 TraesCS3B01G071200 chr6B 200324002 200324750 748 True 422.0 470 89.4050 1 672 2 chr6B.!!$R3 671
8 TraesCS3B01G071200 chr2B 672741496 672742366 870 False 1404.0 1404 95.7670 1975 2846 1 chr2B.!!$F1 871
9 TraesCS3B01G071200 chr2B 117928377 117929243 866 True 1386.0 1386 95.5280 1975 2842 1 chr2B.!!$R1 867
10 TraesCS3B01G071200 chr2B 794611195 794611695 500 True 209.0 209 74.7550 1024 1522 1 chr2B.!!$R2 498
11 TraesCS3B01G071200 chr4A 671508950 671509811 861 False 1376.0 1376 95.3970 1975 2842 1 chr4A.!!$F1 867
12 TraesCS3B01G071200 chr1B 685085581 685086458 877 False 1371.0 1371 94.8980 1966 2842 1 chr1B.!!$F1 876
13 TraesCS3B01G071200 chr1B 169020065 169020931 866 True 1367.0 1367 95.0740 1975 2846 1 chr1B.!!$R1 871
14 TraesCS3B01G071200 chr1B 591364028 591364784 756 False 434.5 460 90.0795 1 671 2 chr1B.!!$F2 670
15 TraesCS3B01G071200 chr6D 470046124 470047210 1086 False 1011.0 1011 83.9270 913 1976 1 chr6D.!!$F1 1063
16 TraesCS3B01G071200 chr6D 470052763 470053587 824 False 693.0 693 82.0570 993 1818 1 chr6D.!!$F2 825
17 TraesCS3B01G071200 chr6D 470103716 470104596 880 True 649.0 649 80.4740 952 1811 1 chr6D.!!$R1 859
18 TraesCS3B01G071200 chr6A 614841628 614842455 827 False 704.0 704 82.2410 990 1818 1 chr6A.!!$F1 828
19 TraesCS3B01G071200 chr6A 614966996 614967868 872 True 606.0 606 79.6170 952 1820 1 chr6A.!!$R1 868
20 TraesCS3B01G071200 chr5B 587445516 587446181 665 True 645.0 645 84.2960 1 669 1 chr5B.!!$R1 668
21 TraesCS3B01G071200 chr5B 572132283 572133036 753 True 528.5 595 94.9800 1 671 2 chr5B.!!$R2 670
22 TraesCS3B01G071200 chr7A 671403671 671404424 753 False 515.0 549 94.3405 1 671 2 chr7A.!!$F3 670
23 TraesCS3B01G071200 chr7A 608532121 608532870 749 False 483.5 523 92.8265 1 669 2 chr7A.!!$F2 668

AutoCloner calculated primer pairs

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

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
851 950 0.033306 GGACGGAGGAGGGAGTACTT 60.033 60.0 0.00 0.0 0.0 2.24 F
911 1010 0.107165 AAGTGAGGGCCGGAATTAGC 60.107 55.0 5.05 0.0 0.0 3.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1829 1971 0.456653 CGCTTATTGGTGCCTGCAAC 60.457 55.0 0.0 0.0 0.0 4.17 R
1905 2062 0.462225 TGCGAACGGAAGGAACACAA 60.462 50.0 0.0 0.0 0.0 3.33 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
482 580 3.972276 CGTGTTTGTTGGGCCGGG 61.972 66.667 2.18 0.00 0.00 5.73
527 626 0.178767 CCAGGATTCGATCTGCCACA 59.821 55.000 5.69 0.00 0.00 4.17
556 655 0.593128 CCTGTTTGGAAACGCTCTGG 59.407 55.000 0.00 0.00 41.74 3.86
682 781 5.629079 GGACTTTTTCCATCTCGAAATGT 57.371 39.130 0.00 0.00 45.10 2.71
683 782 5.631992 GGACTTTTTCCATCTCGAAATGTC 58.368 41.667 0.00 0.42 45.10 3.06
684 783 5.392057 GGACTTTTTCCATCTCGAAATGTCC 60.392 44.000 13.66 13.66 45.10 4.02
685 784 5.070001 ACTTTTTCCATCTCGAAATGTCCA 58.930 37.500 0.00 0.00 32.00 4.02
686 785 5.711976 ACTTTTTCCATCTCGAAATGTCCAT 59.288 36.000 0.00 0.00 32.00 3.41
687 786 5.565592 TTTTCCATCTCGAAATGTCCATG 57.434 39.130 0.00 0.00 32.00 3.66
688 787 3.912496 TCCATCTCGAAATGTCCATGT 57.088 42.857 0.00 0.00 0.00 3.21
689 788 4.220693 TCCATCTCGAAATGTCCATGTT 57.779 40.909 0.00 0.00 0.00 2.71
690 789 5.351948 TCCATCTCGAAATGTCCATGTTA 57.648 39.130 0.00 0.00 0.00 2.41
691 790 5.116180 TCCATCTCGAAATGTCCATGTTAC 58.884 41.667 0.00 0.00 0.00 2.50
692 791 5.104941 TCCATCTCGAAATGTCCATGTTACT 60.105 40.000 0.00 0.00 0.00 2.24
693 792 6.097696 TCCATCTCGAAATGTCCATGTTACTA 59.902 38.462 0.00 0.00 0.00 1.82
694 793 6.422100 CCATCTCGAAATGTCCATGTTACTAG 59.578 42.308 0.00 0.00 0.00 2.57
695 794 6.525578 TCTCGAAATGTCCATGTTACTAGT 57.474 37.500 0.00 0.00 0.00 2.57
696 795 6.931838 TCTCGAAATGTCCATGTTACTAGTT 58.068 36.000 0.00 0.00 0.00 2.24
697 796 6.811665 TCTCGAAATGTCCATGTTACTAGTTG 59.188 38.462 0.00 0.00 0.00 3.16
698 797 5.872617 TCGAAATGTCCATGTTACTAGTTGG 59.127 40.000 0.00 2.33 0.00 3.77
699 798 5.642063 CGAAATGTCCATGTTACTAGTTGGT 59.358 40.000 0.00 0.00 0.00 3.67
700 799 6.183360 CGAAATGTCCATGTTACTAGTTGGTC 60.183 42.308 0.00 0.97 0.00 4.02
701 800 5.755409 ATGTCCATGTTACTAGTTGGTCA 57.245 39.130 11.88 11.88 33.09 4.02
702 801 5.554437 TGTCCATGTTACTAGTTGGTCAA 57.446 39.130 0.00 0.00 0.00 3.18
703 802 5.547465 TGTCCATGTTACTAGTTGGTCAAG 58.453 41.667 0.00 0.00 0.00 3.02
704 803 5.071250 TGTCCATGTTACTAGTTGGTCAAGT 59.929 40.000 0.00 0.00 0.00 3.16
705 804 5.638234 GTCCATGTTACTAGTTGGTCAAGTC 59.362 44.000 0.00 0.00 0.00 3.01
706 805 5.305902 TCCATGTTACTAGTTGGTCAAGTCA 59.694 40.000 0.00 0.00 0.00 3.41
707 806 5.995282 CCATGTTACTAGTTGGTCAAGTCAA 59.005 40.000 0.00 0.00 0.00 3.18
708 807 6.147821 CCATGTTACTAGTTGGTCAAGTCAAG 59.852 42.308 0.00 0.00 0.00 3.02
709 808 6.474140 TGTTACTAGTTGGTCAAGTCAAGA 57.526 37.500 0.00 0.00 0.00 3.02
710 809 6.880484 TGTTACTAGTTGGTCAAGTCAAGAA 58.120 36.000 0.00 0.00 0.00 2.52
711 810 7.332557 TGTTACTAGTTGGTCAAGTCAAGAAA 58.667 34.615 0.00 0.00 0.00 2.52
712 811 7.825270 TGTTACTAGTTGGTCAAGTCAAGAAAA 59.175 33.333 0.00 0.00 0.00 2.29
713 812 8.671028 GTTACTAGTTGGTCAAGTCAAGAAAAA 58.329 33.333 0.00 0.00 0.00 1.94
736 835 3.753294 AACTATTAGGCCCACTCATCG 57.247 47.619 0.00 0.00 0.00 3.84
737 836 2.958818 ACTATTAGGCCCACTCATCGA 58.041 47.619 0.00 0.00 0.00 3.59
738 837 2.628657 ACTATTAGGCCCACTCATCGAC 59.371 50.000 0.00 0.00 0.00 4.20
739 838 1.794714 ATTAGGCCCACTCATCGACT 58.205 50.000 0.00 0.00 0.00 4.18
740 839 2.447408 TTAGGCCCACTCATCGACTA 57.553 50.000 0.00 0.00 0.00 2.59
741 840 2.677542 TAGGCCCACTCATCGACTAT 57.322 50.000 0.00 0.00 0.00 2.12
742 841 1.794714 AGGCCCACTCATCGACTATT 58.205 50.000 0.00 0.00 0.00 1.73
743 842 1.414181 AGGCCCACTCATCGACTATTG 59.586 52.381 0.00 0.00 0.00 1.90
744 843 1.412710 GGCCCACTCATCGACTATTGA 59.587 52.381 0.00 0.00 0.00 2.57
745 844 2.158957 GGCCCACTCATCGACTATTGAA 60.159 50.000 0.00 0.00 0.00 2.69
746 845 3.126831 GCCCACTCATCGACTATTGAAG 58.873 50.000 0.00 0.00 0.00 3.02
747 846 3.181475 GCCCACTCATCGACTATTGAAGA 60.181 47.826 0.00 0.00 0.00 2.87
748 847 4.680708 GCCCACTCATCGACTATTGAAGAA 60.681 45.833 0.00 0.00 0.00 2.52
749 848 5.046529 CCCACTCATCGACTATTGAAGAAG 58.953 45.833 0.00 0.00 0.00 2.85
750 849 5.046529 CCACTCATCGACTATTGAAGAAGG 58.953 45.833 0.00 0.00 0.00 3.46
751 850 5.394663 CCACTCATCGACTATTGAAGAAGGT 60.395 44.000 0.00 0.00 0.00 3.50
752 851 6.183360 CCACTCATCGACTATTGAAGAAGGTA 60.183 42.308 0.00 0.00 0.00 3.08
753 852 6.915300 CACTCATCGACTATTGAAGAAGGTAG 59.085 42.308 0.00 0.00 0.00 3.18
754 853 6.603997 ACTCATCGACTATTGAAGAAGGTAGT 59.396 38.462 0.00 0.00 0.00 2.73
755 854 7.774157 ACTCATCGACTATTGAAGAAGGTAGTA 59.226 37.037 0.00 0.00 0.00 1.82
756 855 8.693120 TCATCGACTATTGAAGAAGGTAGTAT 57.307 34.615 0.00 0.00 0.00 2.12
757 856 9.788889 TCATCGACTATTGAAGAAGGTAGTATA 57.211 33.333 0.00 0.00 0.00 1.47
790 889 9.916360 TCCCTATCGTCTTATAATATAAGAGCA 57.084 33.333 19.73 11.49 34.59 4.26
840 939 9.788889 AAAAGGTTTTATATTATAGGACGGAGG 57.211 33.333 0.00 0.00 0.00 4.30
841 940 8.731591 AAGGTTTTATATTATAGGACGGAGGA 57.268 34.615 0.00 0.00 0.00 3.71
842 941 8.363761 AGGTTTTATATTATAGGACGGAGGAG 57.636 38.462 0.00 0.00 0.00 3.69
843 942 7.399478 AGGTTTTATATTATAGGACGGAGGAGG 59.601 40.741 0.00 0.00 0.00 4.30
844 943 7.364497 GGTTTTATATTATAGGACGGAGGAGGG 60.364 44.444 0.00 0.00 0.00 4.30
845 944 6.663336 TTATATTATAGGACGGAGGAGGGA 57.337 41.667 0.00 0.00 0.00 4.20
846 945 2.973983 TTATAGGACGGAGGAGGGAG 57.026 55.000 0.00 0.00 0.00 4.30
847 946 1.830486 TATAGGACGGAGGAGGGAGT 58.170 55.000 0.00 0.00 0.00 3.85
848 947 1.830486 ATAGGACGGAGGAGGGAGTA 58.170 55.000 0.00 0.00 0.00 2.59
849 948 0.842635 TAGGACGGAGGAGGGAGTAC 59.157 60.000 0.00 0.00 0.00 2.73
850 949 0.920271 AGGACGGAGGAGGGAGTACT 60.920 60.000 0.00 0.00 0.00 2.73
851 950 0.033306 GGACGGAGGAGGGAGTACTT 60.033 60.000 0.00 0.00 0.00 2.24
852 951 1.104630 GACGGAGGAGGGAGTACTTG 58.895 60.000 0.00 0.00 0.00 3.16
853 952 0.408700 ACGGAGGAGGGAGTACTTGT 59.591 55.000 0.00 0.00 0.00 3.16
854 953 1.637553 ACGGAGGAGGGAGTACTTGTA 59.362 52.381 0.00 0.00 0.00 2.41
855 954 2.042162 ACGGAGGAGGGAGTACTTGTAA 59.958 50.000 0.00 0.00 0.00 2.41
856 955 3.094572 CGGAGGAGGGAGTACTTGTAAA 58.905 50.000 0.00 0.00 0.00 2.01
857 956 3.705072 CGGAGGAGGGAGTACTTGTAAAT 59.295 47.826 0.00 0.00 0.00 1.40
858 957 4.161754 CGGAGGAGGGAGTACTTGTAAATT 59.838 45.833 0.00 0.00 0.00 1.82
859 958 5.429130 GGAGGAGGGAGTACTTGTAAATTG 58.571 45.833 0.00 0.00 0.00 2.32
860 959 5.189145 GGAGGAGGGAGTACTTGTAAATTGA 59.811 44.000 0.00 0.00 0.00 2.57
861 960 6.301169 AGGAGGGAGTACTTGTAAATTGAG 57.699 41.667 0.00 0.00 0.00 3.02
862 961 6.023603 AGGAGGGAGTACTTGTAAATTGAGA 58.976 40.000 0.00 0.00 0.00 3.27
863 962 6.500751 AGGAGGGAGTACTTGTAAATTGAGAA 59.499 38.462 0.00 0.00 0.00 2.87
864 963 7.017254 AGGAGGGAGTACTTGTAAATTGAGAAA 59.983 37.037 0.00 0.00 0.00 2.52
865 964 7.334671 GGAGGGAGTACTTGTAAATTGAGAAAG 59.665 40.741 0.00 0.00 0.00 2.62
866 965 7.168905 AGGGAGTACTTGTAAATTGAGAAAGG 58.831 38.462 0.00 0.00 0.00 3.11
867 966 6.374613 GGGAGTACTTGTAAATTGAGAAAGGG 59.625 42.308 0.00 0.00 0.00 3.95
868 967 7.166167 GGAGTACTTGTAAATTGAGAAAGGGA 58.834 38.462 0.00 0.00 0.00 4.20
869 968 7.119407 GGAGTACTTGTAAATTGAGAAAGGGAC 59.881 40.741 0.00 0.00 0.00 4.46
870 969 7.514721 AGTACTTGTAAATTGAGAAAGGGACA 58.485 34.615 0.00 0.00 0.00 4.02
871 970 7.996644 AGTACTTGTAAATTGAGAAAGGGACAA 59.003 33.333 0.00 0.00 0.00 3.18
872 971 7.277174 ACTTGTAAATTGAGAAAGGGACAAG 57.723 36.000 9.29 9.29 45.05 3.16
873 972 7.060421 ACTTGTAAATTGAGAAAGGGACAAGA 58.940 34.615 16.02 0.00 43.22 3.02
874 973 6.877611 TGTAAATTGAGAAAGGGACAAGAC 57.122 37.500 0.00 0.00 0.00 3.01
875 974 5.468746 TGTAAATTGAGAAAGGGACAAGACG 59.531 40.000 0.00 0.00 0.00 4.18
876 975 4.351874 AATTGAGAAAGGGACAAGACGA 57.648 40.909 0.00 0.00 0.00 4.20
877 976 3.386768 TTGAGAAAGGGACAAGACGAG 57.613 47.619 0.00 0.00 0.00 4.18
878 977 1.618837 TGAGAAAGGGACAAGACGAGG 59.381 52.381 0.00 0.00 0.00 4.63
879 978 1.893801 GAGAAAGGGACAAGACGAGGA 59.106 52.381 0.00 0.00 0.00 3.71
880 979 1.896465 AGAAAGGGACAAGACGAGGAG 59.104 52.381 0.00 0.00 0.00 3.69
881 980 0.321996 AAAGGGACAAGACGAGGAGC 59.678 55.000 0.00 0.00 0.00 4.70
882 981 0.832135 AAGGGACAAGACGAGGAGCA 60.832 55.000 0.00 0.00 0.00 4.26
883 982 1.216710 GGGACAAGACGAGGAGCAG 59.783 63.158 0.00 0.00 0.00 4.24
884 983 1.251527 GGGACAAGACGAGGAGCAGA 61.252 60.000 0.00 0.00 0.00 4.26
885 984 0.820871 GGACAAGACGAGGAGCAGAT 59.179 55.000 0.00 0.00 0.00 2.90
886 985 1.205893 GGACAAGACGAGGAGCAGATT 59.794 52.381 0.00 0.00 0.00 2.40
887 986 2.427453 GGACAAGACGAGGAGCAGATTA 59.573 50.000 0.00 0.00 0.00 1.75
888 987 3.490078 GGACAAGACGAGGAGCAGATTAG 60.490 52.174 0.00 0.00 0.00 1.73
889 988 2.428890 ACAAGACGAGGAGCAGATTAGG 59.571 50.000 0.00 0.00 0.00 2.69
890 989 1.036707 AGACGAGGAGCAGATTAGGC 58.963 55.000 0.00 0.00 0.00 3.93
891 990 0.747255 GACGAGGAGCAGATTAGGCA 59.253 55.000 0.00 0.00 0.00 4.75
892 991 1.137086 GACGAGGAGCAGATTAGGCAA 59.863 52.381 0.00 0.00 0.00 4.52
893 992 1.555075 ACGAGGAGCAGATTAGGCAAA 59.445 47.619 0.00 0.00 0.00 3.68
894 993 2.208431 CGAGGAGCAGATTAGGCAAAG 58.792 52.381 0.00 0.00 0.00 2.77
895 994 2.419297 CGAGGAGCAGATTAGGCAAAGT 60.419 50.000 0.00 0.00 0.00 2.66
896 995 2.941720 GAGGAGCAGATTAGGCAAAGTG 59.058 50.000 0.00 0.00 0.00 3.16
897 996 2.573462 AGGAGCAGATTAGGCAAAGTGA 59.427 45.455 0.00 0.00 0.00 3.41
898 997 2.941720 GGAGCAGATTAGGCAAAGTGAG 59.058 50.000 0.00 0.00 0.00 3.51
899 998 2.941720 GAGCAGATTAGGCAAAGTGAGG 59.058 50.000 0.00 0.00 0.00 3.86
900 999 2.019984 GCAGATTAGGCAAAGTGAGGG 58.980 52.381 0.00 0.00 0.00 4.30
901 1000 2.019984 CAGATTAGGCAAAGTGAGGGC 58.980 52.381 0.00 0.00 0.00 5.19
905 1004 4.344865 GGCAAAGTGAGGGCCGGA 62.345 66.667 5.05 0.00 38.04 5.14
906 1005 2.282180 GCAAAGTGAGGGCCGGAA 60.282 61.111 5.05 0.00 0.00 4.30
907 1006 1.678970 GCAAAGTGAGGGCCGGAAT 60.679 57.895 5.05 0.00 0.00 3.01
908 1007 1.250840 GCAAAGTGAGGGCCGGAATT 61.251 55.000 5.05 0.00 0.00 2.17
909 1008 1.953311 GCAAAGTGAGGGCCGGAATTA 60.953 52.381 5.05 0.00 0.00 1.40
910 1009 2.017049 CAAAGTGAGGGCCGGAATTAG 58.983 52.381 5.05 0.00 0.00 1.73
911 1010 0.107165 AAGTGAGGGCCGGAATTAGC 60.107 55.000 5.05 0.00 0.00 3.09
923 1022 5.178797 GCCGGAATTAGCAGATACATACAT 58.821 41.667 5.05 0.00 0.00 2.29
924 1023 5.063944 GCCGGAATTAGCAGATACATACATG 59.936 44.000 5.05 0.00 0.00 3.21
925 1024 6.166279 CCGGAATTAGCAGATACATACATGT 58.834 40.000 2.69 2.69 44.48 3.21
927 1026 6.091305 CGGAATTAGCAGATACATACATGTGG 59.909 42.308 9.11 2.98 41.89 4.17
928 1027 6.936900 GGAATTAGCAGATACATACATGTGGT 59.063 38.462 9.11 9.36 41.89 4.16
971 1073 1.684983 ACTTACCTAGTGTGCGTGTGT 59.315 47.619 0.00 0.00 35.19 3.72
972 1074 2.058798 CTTACCTAGTGTGCGTGTGTG 58.941 52.381 0.00 0.00 0.00 3.82
974 1076 0.249322 ACCTAGTGTGCGTGTGTGAC 60.249 55.000 0.00 0.00 0.00 3.67
976 1078 1.566404 CTAGTGTGCGTGTGTGACAA 58.434 50.000 0.00 0.00 0.00 3.18
982 1084 0.813610 TGCGTGTGTGACAAAGGAGG 60.814 55.000 0.00 0.00 0.00 4.30
987 1089 1.351017 TGTGTGACAAAGGAGGGATCC 59.649 52.381 1.92 1.92 0.00 3.36
996 1100 0.725133 AGGAGGGATCCAAGGGAGAA 59.275 55.000 15.23 0.00 34.05 2.87
1022 1126 3.619767 TGTCTCAGGCGCTGTGCT 61.620 61.111 13.46 0.00 45.43 4.40
1030 1134 2.125147 GCGCTGTGCTATGGTGGA 60.125 61.111 5.84 0.00 41.73 4.02
1035 1139 2.014068 GCTGTGCTATGGTGGAAGGAC 61.014 57.143 0.00 0.00 34.91 3.85
1056 1160 2.816958 CAGCTGCGCATCCTCGTT 60.817 61.111 12.24 0.00 0.00 3.85
1060 1164 1.639298 GCTGCGCATCCTCGTTCTTT 61.639 55.000 12.24 0.00 0.00 2.52
1069 1173 1.079503 CCTCGTTCTTTGTAGCCTGC 58.920 55.000 0.00 0.00 0.00 4.85
1081 1185 3.099905 TGTAGCCTGCTGATTCAGTACT 58.900 45.455 14.90 7.64 33.43 2.73
1090 1194 3.181470 GCTGATTCAGTACTTCCTCCTCC 60.181 52.174 14.90 0.00 33.43 4.30
1093 1197 0.338814 TCAGTACTTCCTCCTCCCCC 59.661 60.000 0.00 0.00 0.00 5.40
1123 1231 3.895656 CGTAAGTTCCCCATCAGATCCTA 59.104 47.826 0.00 0.00 0.00 2.94
1124 1232 4.262079 CGTAAGTTCCCCATCAGATCCTAC 60.262 50.000 0.00 0.00 0.00 3.18
1133 1241 4.901849 CCCATCAGATCCTACTTTAGACCA 59.098 45.833 0.00 0.00 0.00 4.02
1166 1274 2.029518 TATCTGGGCAGCGATGCG 59.970 61.111 20.69 6.09 35.24 4.73
1221 1330 2.360852 CAGGAAGCCACAGCAGGG 60.361 66.667 0.00 0.00 43.56 4.45
1231 1340 1.692042 ACAGCAGGGGGATGGAGAG 60.692 63.158 0.00 0.00 37.17 3.20
1268 1404 4.954970 AGGTGTTGTGGGCGCCTG 62.955 66.667 28.56 0.00 44.32 4.85
1279 1415 2.202987 GCGCCTGTCCTCCTGATG 60.203 66.667 0.00 0.00 0.00 3.07
1282 1418 1.530771 GCCTGTCCTCCTGATGCAT 59.469 57.895 0.00 0.00 0.00 3.96
1371 1507 0.251832 ACCTCGGTGTCTCAGGTCAT 60.252 55.000 0.00 0.00 35.47 3.06
1375 1511 0.179161 CGGTGTCTCAGGTCATCGTC 60.179 60.000 0.00 0.00 34.13 4.20
1403 1539 3.703001 ACGTCTTCTGGAAATCATGGT 57.297 42.857 0.00 0.00 0.00 3.55
1416 1555 0.324614 TCATGGTCAGGCAACGACAT 59.675 50.000 0.00 0.00 46.39 3.06
1439 1578 1.717937 CTGCTGCAGGCGACAATAC 59.282 57.895 21.71 0.00 45.43 1.89
1447 1586 2.350522 CAGGCGACAATACTGCTCTTT 58.649 47.619 0.00 0.00 0.00 2.52
1451 1590 3.182572 GGCGACAATACTGCTCTTTATCG 59.817 47.826 0.00 0.00 0.00 2.92
1535 1674 4.699522 GCTCCGGCGACCCTGTTT 62.700 66.667 9.30 0.00 0.00 2.83
1546 1685 2.292828 ACCCTGTTTGGAGGTCAATG 57.707 50.000 0.00 0.00 38.35 2.82
1567 1706 4.060900 TGAACACACAGAAGCTCAAGATC 58.939 43.478 0.00 0.00 0.00 2.75
1568 1707 3.758755 ACACACAGAAGCTCAAGATCA 57.241 42.857 0.00 0.00 0.00 2.92
1587 1726 7.388460 AGATCAATCCACTTGAAGATTTCAC 57.612 36.000 0.00 0.00 46.62 3.18
1600 1739 6.152103 TGAAGATTTCACTGACAAGGCAACT 61.152 40.000 0.00 0.00 42.21 3.16
1601 1740 8.116848 TGAAGATTTCACTGACAAGGCAACTG 62.117 42.308 0.00 0.00 40.10 3.16
1630 1769 5.053811 GCTGAGGAGAATAGCTACCTTTTC 58.946 45.833 0.00 0.00 34.70 2.29
1631 1770 5.263968 TGAGGAGAATAGCTACCTTTTCG 57.736 43.478 0.00 0.00 35.15 3.46
1632 1771 4.099573 TGAGGAGAATAGCTACCTTTTCGG 59.900 45.833 0.00 0.00 35.15 4.30
1645 1784 2.969300 TTTTCGGACCAGCCACACCC 62.969 60.000 0.00 0.00 35.94 4.61
1648 1787 4.265056 GGACCAGCCACACCCGTT 62.265 66.667 0.00 0.00 36.34 4.44
1656 1795 1.507141 GCCACACCCGTTGACTTCAG 61.507 60.000 0.00 0.00 0.00 3.02
1661 1800 1.003718 CCCGTTGACTTCAGTCCCC 60.004 63.158 4.48 0.00 44.15 4.81
1663 1802 0.602905 CCGTTGACTTCAGTCCCCAC 60.603 60.000 4.48 0.00 44.15 4.61
1705 1844 2.382882 TCTCCTTCTGCTGATGATCGT 58.617 47.619 7.90 0.00 0.00 3.73
1723 1862 3.551846 TCGTATCAGGATGCTACTGTCA 58.448 45.455 0.00 0.00 35.66 3.58
1739 1878 5.411831 ACTGTCATTCTCAGCACTTGATA 57.588 39.130 0.00 0.00 36.50 2.15
1758 1897 4.865925 TGATAACAACCATGCGTACTGTAC 59.134 41.667 7.90 7.90 0.00 2.90
1770 1909 2.279136 CGTACTGTACGCTGCAGAATTC 59.721 50.000 25.06 5.18 45.81 2.17
1780 1919 3.391965 GCTGCAGAATTCGATCTCTGAT 58.608 45.455 20.43 0.00 41.38 2.90
1805 1944 3.402628 TTCAGCTCCTCTACACCAAAC 57.597 47.619 0.00 0.00 0.00 2.93
1811 1950 3.883489 GCTCCTCTACACCAAACAAAAGT 59.117 43.478 0.00 0.00 0.00 2.66
1812 1951 4.261197 GCTCCTCTACACCAAACAAAAGTG 60.261 45.833 0.00 0.00 37.53 3.16
1818 1957 4.882842 ACACCAAACAAAAGTGGTTCTT 57.117 36.364 0.00 0.00 46.17 2.52
1819 1958 4.565022 ACACCAAACAAAAGTGGTTCTTG 58.435 39.130 0.00 0.00 46.17 3.02
1821 1960 4.625311 CACCAAACAAAAGTGGTTCTTGAC 59.375 41.667 0.00 0.00 46.17 3.18
1822 1961 4.322424 ACCAAACAAAAGTGGTTCTTGACC 60.322 41.667 0.00 0.00 46.17 4.02
1844 1995 2.339556 GGCGTTGCAGGCACCAATA 61.340 57.895 13.00 0.00 36.61 1.90
1845 1996 1.583986 GCGTTGCAGGCACCAATAA 59.416 52.632 6.92 0.00 0.00 1.40
1846 1997 0.456653 GCGTTGCAGGCACCAATAAG 60.457 55.000 6.92 0.00 0.00 1.73
1848 1999 0.456653 GTTGCAGGCACCAATAAGCG 60.457 55.000 0.00 0.00 0.00 4.68
1851 2002 1.305219 GCAGGCACCAATAAGCGTGA 61.305 55.000 10.77 0.00 46.32 4.35
1858 2009 1.270412 ACCAATAAGCGTGACCGTGAA 60.270 47.619 0.00 0.00 36.15 3.18
1859 2010 1.393539 CCAATAAGCGTGACCGTGAAG 59.606 52.381 0.00 0.00 36.15 3.02
1863 2014 2.933878 AAGCGTGACCGTGAAGGCAA 62.934 55.000 0.00 0.00 46.52 4.52
1867 2018 1.234821 GTGACCGTGAAGGCAAATCA 58.765 50.000 0.00 0.00 46.52 2.57
1869 2020 1.202758 TGACCGTGAAGGCAAATCAGT 60.203 47.619 0.00 0.00 46.52 3.41
1871 2022 0.523072 CCGTGAAGGCAAATCAGTGG 59.477 55.000 0.00 0.00 0.00 4.00
1872 2023 0.523072 CGTGAAGGCAAATCAGTGGG 59.477 55.000 0.00 0.00 0.00 4.61
1874 2025 2.450476 GTGAAGGCAAATCAGTGGGAT 58.550 47.619 0.00 0.00 38.05 3.85
1876 2027 3.091545 TGAAGGCAAATCAGTGGGATTC 58.908 45.455 0.00 0.00 45.46 2.52
1877 2028 3.245371 TGAAGGCAAATCAGTGGGATTCT 60.245 43.478 0.00 0.00 45.46 2.40
1878 2029 4.018506 TGAAGGCAAATCAGTGGGATTCTA 60.019 41.667 0.00 0.00 45.46 2.10
1879 2030 4.803329 AGGCAAATCAGTGGGATTCTAT 57.197 40.909 0.00 0.00 45.46 1.98
1889 2046 4.012374 AGTGGGATTCTATGTTGTTGCTG 58.988 43.478 0.00 0.00 0.00 4.41
1890 2047 2.754552 TGGGATTCTATGTTGTTGCTGC 59.245 45.455 0.00 0.00 0.00 5.25
1892 2049 4.199310 GGGATTCTATGTTGTTGCTGCTA 58.801 43.478 0.00 0.00 0.00 3.49
1897 2054 4.503910 TCTATGTTGTTGCTGCTATTCGT 58.496 39.130 0.00 0.00 0.00 3.85
1902 2059 4.454161 TGTTGTTGCTGCTATTCGTGTATT 59.546 37.500 0.00 0.00 0.00 1.89
1905 2062 4.454161 TGTTGCTGCTATTCGTGTATTTGT 59.546 37.500 0.00 0.00 0.00 2.83
1907 2064 4.968626 TGCTGCTATTCGTGTATTTGTTG 58.031 39.130 0.00 0.00 0.00 3.33
1911 2068 6.307031 TGCTATTCGTGTATTTGTTGTGTT 57.693 33.333 0.00 0.00 0.00 3.32
1934 2091 4.796231 CGTTCGCAGCCGTAGCCT 62.796 66.667 0.00 0.00 41.25 4.58
1935 2092 2.886124 GTTCGCAGCCGTAGCCTC 60.886 66.667 0.00 0.00 41.25 4.70
1936 2093 3.068691 TTCGCAGCCGTAGCCTCT 61.069 61.111 0.00 0.00 41.25 3.69
1939 2096 2.456119 CGCAGCCGTAGCCTCTTTG 61.456 63.158 0.00 0.00 41.25 2.77
1940 2097 1.079127 GCAGCCGTAGCCTCTTTGA 60.079 57.895 0.00 0.00 41.25 2.69
2293 2451 3.321648 TGTCCTCGCCTGCCATGT 61.322 61.111 0.00 0.00 0.00 3.21
2294 2452 2.512515 GTCCTCGCCTGCCATGTC 60.513 66.667 0.00 0.00 0.00 3.06
2295 2453 4.147449 TCCTCGCCTGCCATGTCG 62.147 66.667 0.00 0.00 0.00 4.35
2308 2466 2.762234 ATGTCGTCGTCGAGGAGGC 61.762 63.158 17.34 15.60 46.96 4.70
2347 2506 0.519077 GTCGTCGTCGGGAAGTAGTT 59.481 55.000 1.55 0.00 37.69 2.24
2425 2584 5.325239 CCAAAAACCTTATCACCCTTCTCT 58.675 41.667 0.00 0.00 0.00 3.10
2640 2800 2.999648 AGCGCCAGGAGCTGAAGA 61.000 61.111 18.24 0.00 44.22 2.87
2669 2829 3.555168 GGGAGATGAAACGAACAGACAGT 60.555 47.826 0.00 0.00 0.00 3.55
2671 2831 5.227908 GGAGATGAAACGAACAGACAGTAA 58.772 41.667 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 49 2.172293 TGGGAACAAATTTGCCAAGCTT 59.828 40.909 18.12 3.69 36.96 3.74
482 580 3.947841 TGTGCGTTCGTTGCTGGC 61.948 61.111 0.00 0.00 0.00 4.85
487 585 1.512364 CATTGTTGTGTGCGTTCGTTG 59.488 47.619 0.00 0.00 0.00 4.10
527 626 2.323999 TCCAAACAGGGATTGGCAAT 57.676 45.000 13.54 13.54 45.63 3.56
556 655 3.622166 TCCCGGTCTATTTTGAACCTC 57.378 47.619 0.00 0.00 0.00 3.85
602 701 3.396276 TGAACCCTGAACTTGTAATCCCA 59.604 43.478 0.00 0.00 0.00 4.37
672 771 6.525578 ACTAGTAACATGGACATTTCGAGA 57.474 37.500 0.00 0.00 0.00 4.04
673 772 6.036083 CCAACTAGTAACATGGACATTTCGAG 59.964 42.308 5.51 0.00 34.82 4.04
674 773 5.872617 CCAACTAGTAACATGGACATTTCGA 59.127 40.000 5.51 0.00 34.82 3.71
675 774 5.642063 ACCAACTAGTAACATGGACATTTCG 59.358 40.000 16.58 0.00 36.75 3.46
676 775 6.653320 TGACCAACTAGTAACATGGACATTTC 59.347 38.462 16.58 5.43 33.75 2.17
677 776 6.539173 TGACCAACTAGTAACATGGACATTT 58.461 36.000 16.58 0.00 33.75 2.32
678 777 6.121776 TGACCAACTAGTAACATGGACATT 57.878 37.500 16.58 0.00 33.75 2.71
679 778 5.755409 TGACCAACTAGTAACATGGACAT 57.245 39.130 16.58 0.00 33.75 3.06
680 779 5.071250 ACTTGACCAACTAGTAACATGGACA 59.929 40.000 16.58 13.65 36.18 4.02
681 780 5.548406 ACTTGACCAACTAGTAACATGGAC 58.452 41.667 16.58 11.46 36.75 4.02
682 781 5.305902 TGACTTGACCAACTAGTAACATGGA 59.694 40.000 16.58 0.00 35.01 3.41
683 782 5.547465 TGACTTGACCAACTAGTAACATGG 58.453 41.667 9.38 9.38 35.01 3.66
684 783 6.929049 TCTTGACTTGACCAACTAGTAACATG 59.071 38.462 0.00 0.00 35.01 3.21
685 784 7.062749 TCTTGACTTGACCAACTAGTAACAT 57.937 36.000 0.00 0.00 35.01 2.71
686 785 6.474140 TCTTGACTTGACCAACTAGTAACA 57.526 37.500 0.00 0.00 35.01 2.41
687 786 7.781548 TTTCTTGACTTGACCAACTAGTAAC 57.218 36.000 0.00 0.00 35.01 2.50
688 787 8.795842 TTTTTCTTGACTTGACCAACTAGTAA 57.204 30.769 0.00 0.00 35.01 2.24
713 812 4.881850 CGATGAGTGGGCCTAATAGTTTTT 59.118 41.667 4.53 0.00 0.00 1.94
714 813 4.163458 TCGATGAGTGGGCCTAATAGTTTT 59.837 41.667 4.53 0.00 0.00 2.43
715 814 3.709653 TCGATGAGTGGGCCTAATAGTTT 59.290 43.478 4.53 0.00 0.00 2.66
716 815 3.069729 GTCGATGAGTGGGCCTAATAGTT 59.930 47.826 4.53 0.00 0.00 2.24
717 816 2.628657 GTCGATGAGTGGGCCTAATAGT 59.371 50.000 4.53 0.00 0.00 2.12
718 817 2.894126 AGTCGATGAGTGGGCCTAATAG 59.106 50.000 4.53 0.00 0.00 1.73
719 818 2.958818 AGTCGATGAGTGGGCCTAATA 58.041 47.619 4.53 0.00 0.00 0.98
720 819 1.794714 AGTCGATGAGTGGGCCTAAT 58.205 50.000 4.53 0.00 0.00 1.73
721 820 2.447408 TAGTCGATGAGTGGGCCTAA 57.553 50.000 4.53 0.00 0.00 2.69
722 821 2.628178 CAATAGTCGATGAGTGGGCCTA 59.372 50.000 4.53 0.00 0.00 3.93
723 822 1.414181 CAATAGTCGATGAGTGGGCCT 59.586 52.381 4.53 0.00 0.00 5.19
724 823 1.412710 TCAATAGTCGATGAGTGGGCC 59.587 52.381 0.00 0.00 0.00 5.80
725 824 2.890808 TCAATAGTCGATGAGTGGGC 57.109 50.000 0.00 0.00 0.00 5.36
726 825 4.655762 TCTTCAATAGTCGATGAGTGGG 57.344 45.455 0.00 0.00 0.00 4.61
727 826 5.046529 CCTTCTTCAATAGTCGATGAGTGG 58.953 45.833 0.00 0.00 0.00 4.00
728 827 5.655488 ACCTTCTTCAATAGTCGATGAGTG 58.345 41.667 0.00 0.00 0.00 3.51
729 828 5.923733 ACCTTCTTCAATAGTCGATGAGT 57.076 39.130 0.00 0.00 0.00 3.41
730 829 7.033530 ACTACCTTCTTCAATAGTCGATGAG 57.966 40.000 0.00 0.00 0.00 2.90
731 830 8.693120 ATACTACCTTCTTCAATAGTCGATGA 57.307 34.615 0.00 0.00 0.00 2.92
764 863 9.916360 TGCTCTTATATTATAAGACGATAGGGA 57.084 33.333 18.17 9.11 43.77 4.20
784 883 8.914011 AGTTAGGTTAACTTCAAAAATGCTCTT 58.086 29.630 5.42 0.00 46.27 2.85
785 884 8.465273 AGTTAGGTTAACTTCAAAAATGCTCT 57.535 30.769 5.42 0.00 46.27 4.09
814 913 9.788889 CCTCCGTCCTATAATATAAAACCTTTT 57.211 33.333 0.00 0.00 0.00 2.27
815 914 9.162733 TCCTCCGTCCTATAATATAAAACCTTT 57.837 33.333 0.00 0.00 0.00 3.11
816 915 8.731591 TCCTCCGTCCTATAATATAAAACCTT 57.268 34.615 0.00 0.00 0.00 3.50
817 916 7.399478 CCTCCTCCGTCCTATAATATAAAACCT 59.601 40.741 0.00 0.00 0.00 3.50
818 917 7.364497 CCCTCCTCCGTCCTATAATATAAAACC 60.364 44.444 0.00 0.00 0.00 3.27
819 918 7.398332 TCCCTCCTCCGTCCTATAATATAAAAC 59.602 40.741 0.00 0.00 0.00 2.43
820 919 7.481297 TCCCTCCTCCGTCCTATAATATAAAA 58.519 38.462 0.00 0.00 0.00 1.52
821 920 7.048090 TCCCTCCTCCGTCCTATAATATAAA 57.952 40.000 0.00 0.00 0.00 1.40
822 921 6.219146 ACTCCCTCCTCCGTCCTATAATATAA 59.781 42.308 0.00 0.00 0.00 0.98
823 922 5.735129 ACTCCCTCCTCCGTCCTATAATATA 59.265 44.000 0.00 0.00 0.00 0.86
824 923 4.544968 ACTCCCTCCTCCGTCCTATAATAT 59.455 45.833 0.00 0.00 0.00 1.28
825 924 3.921486 ACTCCCTCCTCCGTCCTATAATA 59.079 47.826 0.00 0.00 0.00 0.98
826 925 2.723010 ACTCCCTCCTCCGTCCTATAAT 59.277 50.000 0.00 0.00 0.00 1.28
827 926 2.141911 ACTCCCTCCTCCGTCCTATAA 58.858 52.381 0.00 0.00 0.00 0.98
828 927 1.830486 ACTCCCTCCTCCGTCCTATA 58.170 55.000 0.00 0.00 0.00 1.31
829 928 1.424684 GTACTCCCTCCTCCGTCCTAT 59.575 57.143 0.00 0.00 0.00 2.57
830 929 0.842635 GTACTCCCTCCTCCGTCCTA 59.157 60.000 0.00 0.00 0.00 2.94
831 930 0.920271 AGTACTCCCTCCTCCGTCCT 60.920 60.000 0.00 0.00 0.00 3.85
832 931 0.033306 AAGTACTCCCTCCTCCGTCC 60.033 60.000 0.00 0.00 0.00 4.79
833 932 1.104630 CAAGTACTCCCTCCTCCGTC 58.895 60.000 0.00 0.00 0.00 4.79
834 933 0.408700 ACAAGTACTCCCTCCTCCGT 59.591 55.000 0.00 0.00 0.00 4.69
835 934 2.431954 TACAAGTACTCCCTCCTCCG 57.568 55.000 0.00 0.00 0.00 4.63
836 935 5.189145 TCAATTTACAAGTACTCCCTCCTCC 59.811 44.000 0.00 0.00 0.00 4.30
837 936 6.154706 TCTCAATTTACAAGTACTCCCTCCTC 59.845 42.308 0.00 0.00 0.00 3.71
838 937 6.023603 TCTCAATTTACAAGTACTCCCTCCT 58.976 40.000 0.00 0.00 0.00 3.69
839 938 6.295719 TCTCAATTTACAAGTACTCCCTCC 57.704 41.667 0.00 0.00 0.00 4.30
840 939 7.334671 CCTTTCTCAATTTACAAGTACTCCCTC 59.665 40.741 0.00 0.00 0.00 4.30
841 940 7.168905 CCTTTCTCAATTTACAAGTACTCCCT 58.831 38.462 0.00 0.00 0.00 4.20
842 941 6.374613 CCCTTTCTCAATTTACAAGTACTCCC 59.625 42.308 0.00 0.00 0.00 4.30
843 942 7.119407 GTCCCTTTCTCAATTTACAAGTACTCC 59.881 40.741 0.00 0.00 0.00 3.85
844 943 7.660208 TGTCCCTTTCTCAATTTACAAGTACTC 59.340 37.037 0.00 0.00 0.00 2.59
845 944 7.514721 TGTCCCTTTCTCAATTTACAAGTACT 58.485 34.615 0.00 0.00 0.00 2.73
846 945 7.739498 TGTCCCTTTCTCAATTTACAAGTAC 57.261 36.000 0.00 0.00 0.00 2.73
847 946 8.215050 TCTTGTCCCTTTCTCAATTTACAAGTA 58.785 33.333 0.00 0.00 41.89 2.24
848 947 7.013369 GTCTTGTCCCTTTCTCAATTTACAAGT 59.987 37.037 0.00 0.00 41.89 3.16
849 948 7.363431 GTCTTGTCCCTTTCTCAATTTACAAG 58.637 38.462 0.00 0.00 42.33 3.16
850 949 6.017440 CGTCTTGTCCCTTTCTCAATTTACAA 60.017 38.462 0.00 0.00 0.00 2.41
851 950 5.468746 CGTCTTGTCCCTTTCTCAATTTACA 59.531 40.000 0.00 0.00 0.00 2.41
852 951 5.699458 TCGTCTTGTCCCTTTCTCAATTTAC 59.301 40.000 0.00 0.00 0.00 2.01
853 952 5.860611 TCGTCTTGTCCCTTTCTCAATTTA 58.139 37.500 0.00 0.00 0.00 1.40
854 953 4.714632 TCGTCTTGTCCCTTTCTCAATTT 58.285 39.130 0.00 0.00 0.00 1.82
855 954 4.319177 CTCGTCTTGTCCCTTTCTCAATT 58.681 43.478 0.00 0.00 0.00 2.32
856 955 3.307059 CCTCGTCTTGTCCCTTTCTCAAT 60.307 47.826 0.00 0.00 0.00 2.57
857 956 2.037251 CCTCGTCTTGTCCCTTTCTCAA 59.963 50.000 0.00 0.00 0.00 3.02
858 957 1.618837 CCTCGTCTTGTCCCTTTCTCA 59.381 52.381 0.00 0.00 0.00 3.27
859 958 1.893801 TCCTCGTCTTGTCCCTTTCTC 59.106 52.381 0.00 0.00 0.00 2.87
860 959 1.896465 CTCCTCGTCTTGTCCCTTTCT 59.104 52.381 0.00 0.00 0.00 2.52
861 960 1.673329 GCTCCTCGTCTTGTCCCTTTC 60.673 57.143 0.00 0.00 0.00 2.62
862 961 0.321996 GCTCCTCGTCTTGTCCCTTT 59.678 55.000 0.00 0.00 0.00 3.11
863 962 0.832135 TGCTCCTCGTCTTGTCCCTT 60.832 55.000 0.00 0.00 0.00 3.95
864 963 1.228894 TGCTCCTCGTCTTGTCCCT 60.229 57.895 0.00 0.00 0.00 4.20
865 964 1.216710 CTGCTCCTCGTCTTGTCCC 59.783 63.158 0.00 0.00 0.00 4.46
866 965 0.820871 ATCTGCTCCTCGTCTTGTCC 59.179 55.000 0.00 0.00 0.00 4.02
867 966 2.663826 AATCTGCTCCTCGTCTTGTC 57.336 50.000 0.00 0.00 0.00 3.18
868 967 2.428890 CCTAATCTGCTCCTCGTCTTGT 59.571 50.000 0.00 0.00 0.00 3.16
869 968 2.801342 GCCTAATCTGCTCCTCGTCTTG 60.801 54.545 0.00 0.00 0.00 3.02
870 969 1.410882 GCCTAATCTGCTCCTCGTCTT 59.589 52.381 0.00 0.00 0.00 3.01
871 970 1.036707 GCCTAATCTGCTCCTCGTCT 58.963 55.000 0.00 0.00 0.00 4.18
872 971 0.747255 TGCCTAATCTGCTCCTCGTC 59.253 55.000 0.00 0.00 0.00 4.20
873 972 1.195115 TTGCCTAATCTGCTCCTCGT 58.805 50.000 0.00 0.00 0.00 4.18
874 973 2.208431 CTTTGCCTAATCTGCTCCTCG 58.792 52.381 0.00 0.00 0.00 4.63
875 974 2.941720 CACTTTGCCTAATCTGCTCCTC 59.058 50.000 0.00 0.00 0.00 3.71
876 975 2.573462 TCACTTTGCCTAATCTGCTCCT 59.427 45.455 0.00 0.00 0.00 3.69
877 976 2.941720 CTCACTTTGCCTAATCTGCTCC 59.058 50.000 0.00 0.00 0.00 4.70
878 977 2.941720 CCTCACTTTGCCTAATCTGCTC 59.058 50.000 0.00 0.00 0.00 4.26
879 978 2.356535 CCCTCACTTTGCCTAATCTGCT 60.357 50.000 0.00 0.00 0.00 4.24
880 979 2.019984 CCCTCACTTTGCCTAATCTGC 58.980 52.381 0.00 0.00 0.00 4.26
881 980 2.019984 GCCCTCACTTTGCCTAATCTG 58.980 52.381 0.00 0.00 0.00 2.90
882 981 1.064389 GGCCCTCACTTTGCCTAATCT 60.064 52.381 0.00 0.00 42.01 2.40
883 982 1.393603 GGCCCTCACTTTGCCTAATC 58.606 55.000 0.00 0.00 42.01 1.75
884 983 0.394352 CGGCCCTCACTTTGCCTAAT 60.394 55.000 0.00 0.00 43.12 1.73
885 984 1.002624 CGGCCCTCACTTTGCCTAA 60.003 57.895 0.00 0.00 43.12 2.69
886 985 2.668632 CGGCCCTCACTTTGCCTA 59.331 61.111 0.00 0.00 43.12 3.93
887 986 4.351054 CCGGCCCTCACTTTGCCT 62.351 66.667 0.00 0.00 43.12 4.75
888 987 3.860930 TTCCGGCCCTCACTTTGCC 62.861 63.158 0.00 0.00 41.85 4.52
889 988 1.250840 AATTCCGGCCCTCACTTTGC 61.251 55.000 0.00 0.00 0.00 3.68
890 989 2.017049 CTAATTCCGGCCCTCACTTTG 58.983 52.381 0.00 0.00 0.00 2.77
891 990 1.682087 GCTAATTCCGGCCCTCACTTT 60.682 52.381 0.00 0.00 0.00 2.66
892 991 0.107165 GCTAATTCCGGCCCTCACTT 60.107 55.000 0.00 0.00 0.00 3.16
893 992 1.271840 TGCTAATTCCGGCCCTCACT 61.272 55.000 0.00 0.00 0.00 3.41
894 993 0.815615 CTGCTAATTCCGGCCCTCAC 60.816 60.000 0.00 0.00 0.00 3.51
895 994 0.980754 TCTGCTAATTCCGGCCCTCA 60.981 55.000 0.00 0.00 0.00 3.86
896 995 0.398318 ATCTGCTAATTCCGGCCCTC 59.602 55.000 0.00 0.00 0.00 4.30
897 996 1.348036 GTATCTGCTAATTCCGGCCCT 59.652 52.381 0.00 0.00 0.00 5.19
898 997 1.071699 TGTATCTGCTAATTCCGGCCC 59.928 52.381 0.00 0.00 0.00 5.80
899 998 2.543777 TGTATCTGCTAATTCCGGCC 57.456 50.000 0.00 0.00 0.00 6.13
900 999 4.566004 TGTATGTATCTGCTAATTCCGGC 58.434 43.478 0.00 0.00 0.00 6.13
901 1000 6.091305 CACATGTATGTATCTGCTAATTCCGG 59.909 42.308 0.00 0.00 39.39 5.14
902 1001 6.091305 CCACATGTATGTATCTGCTAATTCCG 59.909 42.308 0.00 0.00 39.39 4.30
903 1002 6.936900 ACCACATGTATGTATCTGCTAATTCC 59.063 38.462 0.00 0.00 39.39 3.01
904 1003 7.969536 ACCACATGTATGTATCTGCTAATTC 57.030 36.000 0.00 0.00 39.39 2.17
905 1004 8.752005 AAACCACATGTATGTATCTGCTAATT 57.248 30.769 0.00 0.00 39.39 1.40
906 1005 7.171508 CGAAACCACATGTATGTATCTGCTAAT 59.828 37.037 0.00 0.00 39.39 1.73
907 1006 6.478673 CGAAACCACATGTATGTATCTGCTAA 59.521 38.462 0.00 0.00 39.39 3.09
908 1007 5.983118 CGAAACCACATGTATGTATCTGCTA 59.017 40.000 0.00 0.00 39.39 3.49
909 1008 4.811024 CGAAACCACATGTATGTATCTGCT 59.189 41.667 0.00 0.00 39.39 4.24
910 1009 4.570772 ACGAAACCACATGTATGTATCTGC 59.429 41.667 0.00 0.00 39.39 4.26
911 1010 5.006649 CCACGAAACCACATGTATGTATCTG 59.993 44.000 0.00 0.00 39.39 2.90
923 1022 1.525077 GCTGGTCCACGAAACCACA 60.525 57.895 4.58 0.00 41.84 4.17
924 1023 2.258726 GGCTGGTCCACGAAACCAC 61.259 63.158 4.58 3.29 41.84 4.16
925 1024 2.112297 GGCTGGTCCACGAAACCA 59.888 61.111 7.80 7.80 44.46 3.67
927 1026 0.034337 TACTGGCTGGTCCACGAAAC 59.966 55.000 0.00 0.00 40.72 2.78
928 1027 0.320374 CTACTGGCTGGTCCACGAAA 59.680 55.000 0.00 0.00 40.72 3.46
950 1050 2.101917 ACACACGCACACTAGGTAAGTT 59.898 45.455 0.00 0.00 35.76 2.66
956 1056 0.249280 TGTCACACACGCACACTAGG 60.249 55.000 0.00 0.00 0.00 3.02
971 1073 1.635487 CCTTGGATCCCTCCTTTGTCA 59.365 52.381 9.90 0.00 42.59 3.58
972 1074 1.064389 CCCTTGGATCCCTCCTTTGTC 60.064 57.143 9.90 0.00 42.59 3.18
974 1076 1.213926 CTCCCTTGGATCCCTCCTTTG 59.786 57.143 9.90 0.00 42.59 2.77
976 1078 0.725133 TCTCCCTTGGATCCCTCCTT 59.275 55.000 9.90 0.00 42.59 3.36
982 1084 4.140924 ACCCATTATTTCTCCCTTGGATCC 60.141 45.833 4.20 4.20 0.00 3.36
987 1089 4.860022 AGACACCCATTATTTCTCCCTTG 58.140 43.478 0.00 0.00 0.00 3.61
996 1100 1.747206 GCGCCTGAGACACCCATTATT 60.747 52.381 0.00 0.00 0.00 1.40
1022 1126 0.911769 CTGCCAGTCCTTCCACCATA 59.088 55.000 0.00 0.00 0.00 2.74
1056 1160 3.008375 ACTGAATCAGCAGGCTACAAAGA 59.992 43.478 10.62 0.00 40.20 2.52
1060 1164 3.099905 AGTACTGAATCAGCAGGCTACA 58.900 45.455 10.62 0.00 40.20 2.74
1069 1173 3.386402 GGGAGGAGGAAGTACTGAATCAG 59.614 52.174 8.98 8.98 37.52 2.90
1081 1185 4.772231 CGACCGGGGGAGGAGGAA 62.772 72.222 6.32 0.00 34.73 3.36
1093 1197 3.539107 GGAACTTACGCGCGACCG 61.539 66.667 39.36 24.21 37.57 4.79
1133 1241 4.141846 CCCAGATACGCTAGCCATATGAAT 60.142 45.833 16.32 0.00 0.00 2.57
1243 1358 1.302832 CCACAACACCTCCAGGAGC 60.303 63.158 11.57 0.00 38.94 4.70
1244 1359 1.376466 CCCACAACACCTCCAGGAG 59.624 63.158 9.90 9.90 38.94 3.69
1268 1404 0.033228 CCGAGATGCATCAGGAGGAC 59.967 60.000 27.40 10.99 0.00 3.85
1279 1415 0.531532 CATCCTGTCCACCGAGATGC 60.532 60.000 0.00 0.00 0.00 3.91
1282 1418 2.359169 GCCATCCTGTCCACCGAGA 61.359 63.158 0.00 0.00 0.00 4.04
1403 1539 1.375908 GCCTCATGTCGTTGCCTGA 60.376 57.895 0.00 0.00 0.00 3.86
1433 1572 5.488341 ACCAACGATAAAGAGCAGTATTGT 58.512 37.500 0.00 0.00 0.00 2.71
1439 1578 4.950050 AGGATACCAACGATAAAGAGCAG 58.050 43.478 0.00 0.00 37.17 4.24
1447 1586 5.290493 AGCATTTGAGGATACCAACGATA 57.710 39.130 0.00 0.00 37.17 2.92
1451 1590 3.938963 TCGAAGCATTTGAGGATACCAAC 59.061 43.478 0.00 0.00 32.38 3.77
1501 1640 3.678806 CGGAGCTGACAAGGCTGTTAATA 60.679 47.826 0.00 0.00 40.40 0.98
1532 1671 3.380004 TGTGTGTTCATTGACCTCCAAAC 59.620 43.478 0.00 0.00 38.43 2.93
1535 1674 2.437651 TCTGTGTGTTCATTGACCTCCA 59.562 45.455 0.00 0.00 0.00 3.86
1546 1685 4.060900 TGATCTTGAGCTTCTGTGTGTTC 58.939 43.478 0.00 0.00 0.00 3.18
1567 1706 6.016860 TGTCAGTGAAATCTTCAAGTGGATTG 60.017 38.462 0.00 0.00 42.15 2.67
1568 1707 6.064060 TGTCAGTGAAATCTTCAAGTGGATT 58.936 36.000 0.00 0.00 42.15 3.01
1587 1726 2.082231 CAGGATCAGTTGCCTTGTCAG 58.918 52.381 0.00 0.00 30.41 3.51
1631 1770 4.265056 AACGGGTGTGGCTGGTCC 62.265 66.667 0.00 0.00 0.00 4.46
1632 1771 2.978010 CAACGGGTGTGGCTGGTC 60.978 66.667 0.00 0.00 0.00 4.02
1645 1784 0.105964 TGTGGGGACTGAAGTCAACG 59.894 55.000 12.32 0.00 46.47 4.10
1648 1787 1.507140 ACTTGTGGGGACTGAAGTCA 58.493 50.000 12.32 0.00 46.47 3.41
1663 1802 4.944962 TGCGAGATCCACAAATAACTTG 57.055 40.909 0.00 0.00 41.19 3.16
1705 1844 5.835280 TGAGAATGACAGTAGCATCCTGATA 59.165 40.000 4.55 0.00 34.04 2.15
1723 1862 5.316167 TGGTTGTTATCAAGTGCTGAGAAT 58.684 37.500 0.00 0.00 37.58 2.40
1739 1878 2.063266 CGTACAGTACGCATGGTTGTT 58.937 47.619 19.79 0.00 45.81 2.83
1758 1897 1.521840 CAGAGATCGAATTCTGCAGCG 59.478 52.381 9.47 7.01 34.94 5.18
1829 1971 0.456653 CGCTTATTGGTGCCTGCAAC 60.457 55.000 0.00 0.00 0.00 4.17
1839 1990 1.393539 CTTCACGGTCACGCTTATTGG 59.606 52.381 0.00 0.00 46.04 3.16
1842 1993 0.739813 GCCTTCACGGTCACGCTTAT 60.740 55.000 0.00 0.00 46.04 1.73
1844 1995 2.665185 GCCTTCACGGTCACGCTT 60.665 61.111 0.00 0.00 46.04 4.68
1845 1996 2.933878 TTTGCCTTCACGGTCACGCT 62.934 55.000 0.00 0.00 46.04 5.07
1846 1997 1.852067 ATTTGCCTTCACGGTCACGC 61.852 55.000 0.00 0.00 46.04 5.34
1848 1999 1.197721 CTGATTTGCCTTCACGGTCAC 59.802 52.381 0.00 0.00 34.25 3.67
1851 2002 1.238439 CACTGATTTGCCTTCACGGT 58.762 50.000 0.00 0.00 34.25 4.83
1858 2009 4.079558 ACATAGAATCCCACTGATTTGCCT 60.080 41.667 0.00 0.00 43.81 4.75
1859 2010 4.210331 ACATAGAATCCCACTGATTTGCC 58.790 43.478 0.00 0.00 43.81 4.52
1863 2014 5.126061 GCAACAACATAGAATCCCACTGATT 59.874 40.000 0.00 0.00 46.46 2.57
1867 2018 4.012374 CAGCAACAACATAGAATCCCACT 58.988 43.478 0.00 0.00 0.00 4.00
1869 2020 2.754552 GCAGCAACAACATAGAATCCCA 59.245 45.455 0.00 0.00 0.00 4.37
1871 2022 6.382869 AATAGCAGCAACAACATAGAATCC 57.617 37.500 0.00 0.00 0.00 3.01
1872 2023 6.132056 CGAATAGCAGCAACAACATAGAATC 58.868 40.000 0.00 0.00 0.00 2.52
1874 2025 4.935205 ACGAATAGCAGCAACAACATAGAA 59.065 37.500 0.00 0.00 0.00 2.10
1876 2027 4.093408 ACACGAATAGCAGCAACAACATAG 59.907 41.667 0.00 0.00 0.00 2.23
1877 2028 4.000325 ACACGAATAGCAGCAACAACATA 59.000 39.130 0.00 0.00 0.00 2.29
1878 2029 2.813754 ACACGAATAGCAGCAACAACAT 59.186 40.909 0.00 0.00 0.00 2.71
1879 2030 2.217750 ACACGAATAGCAGCAACAACA 58.782 42.857 0.00 0.00 0.00 3.33
1889 2046 5.793457 GGAACACAACAAATACACGAATAGC 59.207 40.000 0.00 0.00 0.00 2.97
1890 2047 7.129109 AGGAACACAACAAATACACGAATAG 57.871 36.000 0.00 0.00 0.00 1.73
1892 2049 6.385649 AAGGAACACAACAAATACACGAAT 57.614 33.333 0.00 0.00 0.00 3.34
1897 2054 4.200874 ACGGAAGGAACACAACAAATACA 58.799 39.130 0.00 0.00 0.00 2.29
1902 2059 1.666700 CGAACGGAAGGAACACAACAA 59.333 47.619 0.00 0.00 0.00 2.83
1905 2062 0.462225 TGCGAACGGAAGGAACACAA 60.462 50.000 0.00 0.00 0.00 3.33
1907 2064 1.860078 CTGCGAACGGAAGGAACAC 59.140 57.895 0.00 0.00 0.00 3.32
1911 2068 4.735132 CGGCTGCGAACGGAAGGA 62.735 66.667 0.00 0.00 0.00 3.36
1934 2091 8.908786 AATTTCTCTGTGACTATGTTCAAAGA 57.091 30.769 0.00 0.00 37.50 2.52
1971 2129 8.416329 GGTAAATTGCTCATATTTCCAACATCT 58.584 33.333 0.00 0.00 0.00 2.90
2295 2453 4.477975 CACGGCCTCCTCGACGAC 62.478 72.222 0.00 0.00 0.00 4.34
2425 2584 2.030185 GCACTCTTTGAGTCCTGTACGA 60.030 50.000 0.00 0.00 41.37 3.43
2629 2789 0.682855 CCTCGGTCTCTTCAGCTCCT 60.683 60.000 0.00 0.00 0.00 3.69
2640 2800 0.818296 CGTTTCATCTCCCTCGGTCT 59.182 55.000 0.00 0.00 0.00 3.85
2669 2829 2.047655 CGCTGCACCCTTCGGTTA 60.048 61.111 0.00 0.00 42.04 2.85
2671 2831 4.250305 AACGCTGCACCCTTCGGT 62.250 61.111 0.00 0.00 46.31 4.69


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

AutoCloner maintained by Alex Coulton.