Multiple sequence alignment - TraesCS6B01G380900

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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 TraesCS6B01G380900 chr6B 100.000 5475 0 0 1 5475 655886953 655892427 0.000000e+00 10111
1 TraesCS6B01G380900 chr6B 88.143 2876 286 24 2474 5323 655867986 655870832 0.000000e+00 3371
2 TraesCS6B01G380900 chr6B 93.480 2224 71 20 3275 5475 655763426 655765598 0.000000e+00 3236
3 TraesCS6B01G380900 chr6B 87.165 2875 310 34 2465 5312 656284035 656281193 0.000000e+00 3210
4 TraesCS6B01G380900 chr6B 88.365 1676 163 14 2484 4150 655311733 655313385 0.000000e+00 1986
5 TraesCS6B01G380900 chr6B 87.325 1144 114 12 4201 5323 655313704 655314837 0.000000e+00 1280
6 TraesCS6B01G380900 chr6B 95.607 774 32 2 2470 3241 655757317 655758090 0.000000e+00 1240
7 TraesCS6B01G380900 chr6B 86.530 928 57 30 994 1879 655752959 655753860 0.000000e+00 959
8 TraesCS6B01G380900 chr6B 100.000 493 0 0 5826 6318 655892778 655893270 0.000000e+00 911
9 TraesCS6B01G380900 chr6B 96.375 469 15 2 5852 6318 655765690 655766158 0.000000e+00 771
10 TraesCS6B01G380900 chr6B 86.299 708 41 20 894 1583 655862850 655863519 0.000000e+00 719
11 TraesCS6B01G380900 chr6B 84.768 604 37 19 894 1479 655300063 655300629 7.160000e-154 555
12 TraesCS6B01G380900 chr6B 94.915 295 13 2 5992 6285 412164562 412164269 1.600000e-125 460
13 TraesCS6B01G380900 chr6B 93.898 295 16 2 5992 6285 106476259 106476552 1.620000e-120 444
14 TraesCS6B01G380900 chr6B 90.970 299 18 7 1079 1368 656286157 656285859 1.650000e-105 394
15 TraesCS6B01G380900 chr6B 86.424 302 38 3 4828 5129 655825201 655825499 1.700000e-85 327
16 TraesCS6B01G380900 chr6B 93.810 210 12 1 2195 2404 655757108 655757316 1.320000e-81 315
17 TraesCS6B01G380900 chr6B 94.030 67 3 1 5826 5891 106476193 106476259 4.030000e-17 100
18 TraesCS6B01G380900 chr6B 94.030 67 3 1 5826 5891 412164628 412164562 4.030000e-17 100
19 TraesCS6B01G380900 chr6A 89.686 3054 251 39 2454 5471 579841990 579845015 0.000000e+00 3836
20 TraesCS6B01G380900 chr6A 86.613 2846 326 31 2493 5312 580206290 580203474 0.000000e+00 3094
21 TraesCS6B01G380900 chr6A 92.617 596 20 6 895 1466 579838964 579839559 0.000000e+00 835
22 TraesCS6B01G380900 chr6A 84.112 428 48 18 954 1369 580213136 580212717 4.590000e-106 396
23 TraesCS6B01G380900 chr6A 84.698 281 15 10 1738 2006 579839741 579840005 8.130000e-64 255
24 TraesCS6B01G380900 chr6A 83.893 149 9 9 1603 1741 579839562 579839705 1.850000e-25 128
25 TraesCS6B01G380900 chr6D 88.162 2889 282 32 2473 5323 433711692 433708826 0.000000e+00 3386
26 TraesCS6B01G380900 chr6D 86.453 2901 312 41 2465 5312 433940071 433937199 0.000000e+00 3105
27 TraesCS6B01G380900 chr6D 84.979 719 55 22 897 1583 433715448 433714751 0.000000e+00 680
28 TraesCS6B01G380900 chr6D 87.135 342 36 8 1034 1368 433942654 433942314 1.290000e-101 381
29 TraesCS6B01G380900 chr7A 94.556 496 24 2 5826 6318 668309014 668309509 0.000000e+00 763
30 TraesCS6B01G380900 chr1D 84.770 696 72 21 1 667 403231817 403232507 0.000000e+00 667
31 TraesCS6B01G380900 chr1D 84.157 688 85 19 1 666 418099340 418100025 0.000000e+00 645
32 TraesCS6B01G380900 chr5D 84.448 688 81 18 1 666 28039758 28039075 0.000000e+00 654
33 TraesCS6B01G380900 chr5D 85.835 593 60 17 93 669 24921168 24920584 5.420000e-170 608
34 TraesCS6B01G380900 chr5D 88.679 159 14 3 667 824 232405228 232405073 2.320000e-44 191
35 TraesCS6B01G380900 chr5D 86.628 172 21 2 667 837 444850871 444850701 8.360000e-44 189
36 TraesCS6B01G380900 chr4D 84.325 689 80 20 1 666 432418551 432417868 0.000000e+00 649
37 TraesCS6B01G380900 chr4D 82.828 693 79 23 1 666 324470977 324470298 9.130000e-163 584
38 TraesCS6B01G380900 chr4D 88.387 155 17 1 667 820 62754362 62754516 1.080000e-42 185
39 TraesCS6B01G380900 chr2B 78.466 1017 196 14 2497 3509 680806421 680805424 1.480000e-180 643
40 TraesCS6B01G380900 chr2B 90.968 155 13 1 667 820 753669857 753670011 2.310000e-49 207
41 TraesCS6B01G380900 chr7B 83.310 707 78 20 1 683 61629924 61629234 3.240000e-172 616
42 TraesCS6B01G380900 chr7B 94.218 294 16 1 5992 6285 320269081 320268789 1.250000e-121 448
43 TraesCS6B01G380900 chr7B 95.455 66 3 0 5826 5891 320269146 320269081 8.660000e-19 106
44 TraesCS6B01G380900 chr2D 77.800 1018 201 16 2497 3509 568252074 568251077 7.010000e-169 604
45 TraesCS6B01G380900 chr2D 79.349 799 141 17 3848 4643 568250677 568249900 2.000000e-149 540
46 TraesCS6B01G380900 chr3A 82.819 681 92 11 1 660 468735525 468736201 2.540000e-163 586
47 TraesCS6B01G380900 chr3D 83.943 629 69 19 1 600 588073970 588073345 1.980000e-159 573
48 TraesCS6B01G380900 chr3D 88.387 155 17 1 667 820 266549041 266548887 1.080000e-42 185
49 TraesCS6B01G380900 chr1A 93.581 296 16 3 5992 6285 412783661 412783955 7.520000e-119 438
50 TraesCS6B01G380900 chr1A 80.652 460 57 14 5828 6281 36189236 36189669 1.700000e-85 327
51 TraesCS6B01G380900 chr1A 90.066 151 14 1 667 816 514053278 514053428 1.800000e-45 195
52 TraesCS6B01G380900 chr1A 95.455 66 3 0 5826 5891 412783596 412783661 8.660000e-19 106
53 TraesCS6B01G380900 chr5B 90.968 155 13 1 667 820 250544425 250544579 2.310000e-49 207
54 TraesCS6B01G380900 chr5B 83.511 188 26 4 6103 6286 648277103 648277289 3.030000e-38 171
55 TraesCS6B01G380900 chr5B 87.097 124 13 2 543 666 276158761 276158881 3.070000e-28 137
56 TraesCS6B01G380900 chr3B 89.032 155 16 1 667 820 773466746 773466592 2.320000e-44 191
57 TraesCS6B01G380900 chr4B 87.117 163 19 2 667 828 69161615 69161454 3.890000e-42 183
58 TraesCS6B01G380900 chr4A 83.422 187 29 2 6102 6286 731593738 731593924 8.420000e-39 172


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 TraesCS6B01G380900 chr6B 655886953 655893270 6317 False 5511.0 10111 100.000000 1 6318 2 chr6B.!!$F9 6317
1 TraesCS6B01G380900 chr6B 655867986 655870832 2846 False 3371.0 3371 88.143000 2474 5323 1 chr6B.!!$F4 2849
2 TraesCS6B01G380900 chr6B 655763426 655766158 2732 False 2003.5 3236 94.927500 3275 6318 2 chr6B.!!$F8 3043
3 TraesCS6B01G380900 chr6B 656281193 656286157 4964 True 1802.0 3210 89.067500 1079 5312 2 chr6B.!!$R2 4233
4 TraesCS6B01G380900 chr6B 655311733 655314837 3104 False 1633.0 1986 87.845000 2484 5323 2 chr6B.!!$F6 2839
5 TraesCS6B01G380900 chr6B 655752959 655758090 5131 False 838.0 1240 91.982333 994 3241 3 chr6B.!!$F7 2247
6 TraesCS6B01G380900 chr6B 655862850 655863519 669 False 719.0 719 86.299000 894 1583 1 chr6B.!!$F3 689
7 TraesCS6B01G380900 chr6B 655300063 655300629 566 False 555.0 555 84.768000 894 1479 1 chr6B.!!$F1 585
8 TraesCS6B01G380900 chr6A 580203474 580206290 2816 True 3094.0 3094 86.613000 2493 5312 1 chr6A.!!$R1 2819
9 TraesCS6B01G380900 chr6A 579838964 579845015 6051 False 1263.5 3836 87.723500 895 5471 4 chr6A.!!$F1 4576
10 TraesCS6B01G380900 chr6D 433708826 433715448 6622 True 2033.0 3386 86.570500 897 5323 2 chr6D.!!$R1 4426
11 TraesCS6B01G380900 chr6D 433937199 433942654 5455 True 1743.0 3105 86.794000 1034 5312 2 chr6D.!!$R2 4278
12 TraesCS6B01G380900 chr1D 403231817 403232507 690 False 667.0 667 84.770000 1 667 1 chr1D.!!$F1 666
13 TraesCS6B01G380900 chr1D 418099340 418100025 685 False 645.0 645 84.157000 1 666 1 chr1D.!!$F2 665
14 TraesCS6B01G380900 chr5D 28039075 28039758 683 True 654.0 654 84.448000 1 666 1 chr5D.!!$R2 665
15 TraesCS6B01G380900 chr5D 24920584 24921168 584 True 608.0 608 85.835000 93 669 1 chr5D.!!$R1 576
16 TraesCS6B01G380900 chr4D 432417868 432418551 683 True 649.0 649 84.325000 1 666 1 chr4D.!!$R2 665
17 TraesCS6B01G380900 chr4D 324470298 324470977 679 True 584.0 584 82.828000 1 666 1 chr4D.!!$R1 665
18 TraesCS6B01G380900 chr2B 680805424 680806421 997 True 643.0 643 78.466000 2497 3509 1 chr2B.!!$R1 1012
19 TraesCS6B01G380900 chr7B 61629234 61629924 690 True 616.0 616 83.310000 1 683 1 chr7B.!!$R1 682
20 TraesCS6B01G380900 chr2D 568249900 568252074 2174 True 572.0 604 78.574500 2497 4643 2 chr2D.!!$R1 2146
21 TraesCS6B01G380900 chr3A 468735525 468736201 676 False 586.0 586 82.819000 1 660 1 chr3A.!!$F1 659
22 TraesCS6B01G380900 chr3D 588073345 588073970 625 True 573.0 573 83.943000 1 600 1 chr3D.!!$R2 599

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
924 974 0.108520 GCCACCGGAATACAAGTCGA 60.109 55.000 9.46 0.00 0.0 4.20 F
1523 2025 1.008424 AGATCGCAGTATCGCACGG 60.008 57.895 0.00 0.00 0.0 4.94 F
2015 3054 0.095589 CAATTGTTAACCGCGCGCTA 59.904 50.000 30.48 15.24 0.0 4.26 F
2017 3056 0.303493 ATTGTTAACCGCGCGCTATG 59.697 50.000 30.48 19.33 0.0 2.23 F
2072 4095 1.517257 CGGCTTAGGTGCGTCTGAG 60.517 63.158 0.00 0.00 0.0 3.35 F
4041 10591 1.290955 CTTCACCGGCTTCGTGGTA 59.709 57.895 0.00 0.00 36.5 3.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1814 2588 0.107410 TGGGCAACACGACAGTTCTT 60.107 50.000 0.00 0.00 39.74 2.52 R
3047 9499 0.532573 GCATGAAGTCGAGGTCCTCA 59.467 55.000 19.15 3.46 0.00 3.86 R
3445 9900 1.290203 CCGTTCCCGATGATGTTCAG 58.710 55.000 0.00 0.00 35.63 3.02 R
4041 10591 2.282180 GTGCCCACGAACACCCAT 60.282 61.111 0.00 0.00 0.00 4.00 R
4048 10598 3.834013 TTGATGCGGTGCCCACGAA 62.834 57.895 0.00 0.00 0.00 3.85 R
5866 12781 0.104671 GCCAGCTGGAGCAAAAACAA 59.895 50.000 37.21 0.00 45.16 2.83 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
42 43 0.392461 AACACCTTGTGCACGTCAGT 60.392 50.000 13.13 4.03 36.98 3.41
60 61 1.885388 TCGTCGGTGCAACAAGTGG 60.885 57.895 0.98 0.00 39.98 4.00
106 121 1.901591 CCCTGCAAGCTTCTTCTTCA 58.098 50.000 0.00 0.00 0.00 3.02
149 164 0.960861 GCCTTGTTCTTCTTCCCGGG 60.961 60.000 16.85 16.85 0.00 5.73
209 226 4.660938 GAGGGGGCACGTGGCTTT 62.661 66.667 36.61 23.77 44.01 3.51
265 282 1.672030 TTGTCTGTGGCGGCATGAG 60.672 57.895 17.19 14.65 0.00 2.90
276 293 2.747460 GCATGAGAAGGCCGCACA 60.747 61.111 0.00 0.00 0.00 4.57
283 300 0.833287 AGAAGGCCGCACATGATACT 59.167 50.000 0.00 0.00 0.00 2.12
299 316 0.545309 TACTGGTGCTTGGAGGAGCT 60.545 55.000 0.00 0.00 43.11 4.09
667 717 1.831580 GGCTGTTGGAGATGCTCTTT 58.168 50.000 0.00 0.00 0.00 2.52
668 718 2.677902 CGGCTGTTGGAGATGCTCTTTA 60.678 50.000 0.00 0.00 0.00 1.85
669 719 2.941720 GGCTGTTGGAGATGCTCTTTAG 59.058 50.000 0.00 0.00 0.00 1.85
670 720 2.941720 GCTGTTGGAGATGCTCTTTAGG 59.058 50.000 0.00 0.00 0.00 2.69
671 721 3.620966 GCTGTTGGAGATGCTCTTTAGGT 60.621 47.826 0.00 0.00 0.00 3.08
672 722 4.583871 CTGTTGGAGATGCTCTTTAGGTT 58.416 43.478 0.00 0.00 0.00 3.50
673 723 4.985538 TGTTGGAGATGCTCTTTAGGTTT 58.014 39.130 0.00 0.00 0.00 3.27
674 724 5.003804 TGTTGGAGATGCTCTTTAGGTTTC 58.996 41.667 0.00 0.00 0.00 2.78
675 725 3.861840 TGGAGATGCTCTTTAGGTTTCG 58.138 45.455 0.00 0.00 0.00 3.46
676 726 3.260884 TGGAGATGCTCTTTAGGTTTCGT 59.739 43.478 0.00 0.00 0.00 3.85
677 727 3.619038 GGAGATGCTCTTTAGGTTTCGTG 59.381 47.826 0.00 0.00 0.00 4.35
678 728 3.003480 AGATGCTCTTTAGGTTTCGTGC 58.997 45.455 0.00 0.00 0.00 5.34
679 729 1.144969 TGCTCTTTAGGTTTCGTGCG 58.855 50.000 0.00 0.00 0.00 5.34
680 730 1.269883 TGCTCTTTAGGTTTCGTGCGA 60.270 47.619 0.00 0.00 0.00 5.10
681 731 2.000447 GCTCTTTAGGTTTCGTGCGAT 59.000 47.619 0.00 0.00 0.00 4.58
682 732 2.222819 GCTCTTTAGGTTTCGTGCGATG 60.223 50.000 0.00 0.00 0.00 3.84
683 733 2.993899 CTCTTTAGGTTTCGTGCGATGT 59.006 45.455 0.00 0.00 0.00 3.06
684 734 3.395639 TCTTTAGGTTTCGTGCGATGTT 58.604 40.909 0.00 0.00 0.00 2.71
685 735 3.810941 TCTTTAGGTTTCGTGCGATGTTT 59.189 39.130 0.00 0.00 0.00 2.83
686 736 3.529634 TTAGGTTTCGTGCGATGTTTG 57.470 42.857 0.00 0.00 0.00 2.93
687 737 1.305201 AGGTTTCGTGCGATGTTTGT 58.695 45.000 0.00 0.00 0.00 2.83
688 738 1.673920 AGGTTTCGTGCGATGTTTGTT 59.326 42.857 0.00 0.00 0.00 2.83
689 739 2.098443 AGGTTTCGTGCGATGTTTGTTT 59.902 40.909 0.00 0.00 0.00 2.83
690 740 2.215363 GGTTTCGTGCGATGTTTGTTTG 59.785 45.455 0.00 0.00 0.00 2.93
691 741 2.112475 TTCGTGCGATGTTTGTTTGG 57.888 45.000 0.00 0.00 0.00 3.28
692 742 0.317436 TCGTGCGATGTTTGTTTGGC 60.317 50.000 0.00 0.00 0.00 4.52
693 743 0.593518 CGTGCGATGTTTGTTTGGCA 60.594 50.000 0.00 0.00 0.00 4.92
694 744 1.782044 GTGCGATGTTTGTTTGGCAT 58.218 45.000 0.00 0.00 32.53 4.40
695 745 2.134346 GTGCGATGTTTGTTTGGCATT 58.866 42.857 0.00 0.00 32.53 3.56
696 746 3.312828 GTGCGATGTTTGTTTGGCATTA 58.687 40.909 0.00 0.00 32.53 1.90
697 747 3.364621 GTGCGATGTTTGTTTGGCATTAG 59.635 43.478 0.00 0.00 32.53 1.73
698 748 2.923020 GCGATGTTTGTTTGGCATTAGG 59.077 45.455 0.00 0.00 0.00 2.69
699 749 2.923020 CGATGTTTGTTTGGCATTAGGC 59.077 45.455 0.00 0.00 43.74 3.93
710 760 1.369625 GCATTAGGCCCGGATATTCG 58.630 55.000 0.73 0.00 36.11 3.34
717 767 4.043168 CCGGATATTCGGCACACC 57.957 61.111 10.13 0.00 43.71 4.16
718 768 1.445942 CCGGATATTCGGCACACCT 59.554 57.895 10.13 0.00 43.71 4.00
719 769 0.179056 CCGGATATTCGGCACACCTT 60.179 55.000 10.13 0.00 43.71 3.50
720 770 1.217882 CGGATATTCGGCACACCTTC 58.782 55.000 0.00 0.00 0.00 3.46
721 771 1.217882 GGATATTCGGCACACCTTCG 58.782 55.000 0.00 0.00 0.00 3.79
722 772 1.472728 GGATATTCGGCACACCTTCGT 60.473 52.381 0.00 0.00 0.00 3.85
723 773 1.859080 GATATTCGGCACACCTTCGTC 59.141 52.381 0.00 0.00 0.00 4.20
724 774 0.604073 TATTCGGCACACCTTCGTCA 59.396 50.000 0.00 0.00 0.00 4.35
725 775 0.250124 ATTCGGCACACCTTCGTCAA 60.250 50.000 0.00 0.00 0.00 3.18
726 776 0.250124 TTCGGCACACCTTCGTCAAT 60.250 50.000 0.00 0.00 0.00 2.57
727 777 0.948623 TCGGCACACCTTCGTCAATG 60.949 55.000 0.00 0.00 0.00 2.82
728 778 1.875963 GGCACACCTTCGTCAATGG 59.124 57.895 0.00 0.00 0.00 3.16
729 779 0.605319 GGCACACCTTCGTCAATGGA 60.605 55.000 0.00 0.00 0.00 3.41
730 780 1.234821 GCACACCTTCGTCAATGGAA 58.765 50.000 0.00 0.00 0.00 3.53
731 781 1.812571 GCACACCTTCGTCAATGGAAT 59.187 47.619 0.00 0.00 0.00 3.01
732 782 3.006940 GCACACCTTCGTCAATGGAATA 58.993 45.455 0.00 0.00 0.00 1.75
733 783 3.063997 GCACACCTTCGTCAATGGAATAG 59.936 47.826 0.00 0.00 0.00 1.73
734 784 3.623060 CACACCTTCGTCAATGGAATAGG 59.377 47.826 0.00 0.00 0.00 2.57
735 785 3.517901 ACACCTTCGTCAATGGAATAGGA 59.482 43.478 0.00 0.00 0.00 2.94
736 786 4.122776 CACCTTCGTCAATGGAATAGGAG 58.877 47.826 0.00 0.00 0.00 3.69
737 787 3.775316 ACCTTCGTCAATGGAATAGGAGT 59.225 43.478 0.00 0.00 0.00 3.85
738 788 4.960469 ACCTTCGTCAATGGAATAGGAGTA 59.040 41.667 0.00 0.00 0.00 2.59
739 789 5.069251 ACCTTCGTCAATGGAATAGGAGTAG 59.931 44.000 0.00 0.00 0.00 2.57
740 790 4.585955 TCGTCAATGGAATAGGAGTAGC 57.414 45.455 0.00 0.00 0.00 3.58
741 791 3.958147 TCGTCAATGGAATAGGAGTAGCA 59.042 43.478 0.00 0.00 0.00 3.49
742 792 4.404394 TCGTCAATGGAATAGGAGTAGCAA 59.596 41.667 0.00 0.00 0.00 3.91
743 793 4.508124 CGTCAATGGAATAGGAGTAGCAAC 59.492 45.833 0.00 0.00 0.00 4.17
744 794 5.428253 GTCAATGGAATAGGAGTAGCAACA 58.572 41.667 0.00 0.00 0.00 3.33
745 795 5.525378 GTCAATGGAATAGGAGTAGCAACAG 59.475 44.000 0.00 0.00 0.00 3.16
746 796 5.425217 TCAATGGAATAGGAGTAGCAACAGA 59.575 40.000 0.00 0.00 0.00 3.41
747 797 6.100279 TCAATGGAATAGGAGTAGCAACAGAT 59.900 38.462 0.00 0.00 0.00 2.90
748 798 5.282055 TGGAATAGGAGTAGCAACAGATG 57.718 43.478 0.00 0.00 0.00 2.90
749 799 4.716784 TGGAATAGGAGTAGCAACAGATGT 59.283 41.667 0.00 0.00 0.00 3.06
750 800 5.189736 TGGAATAGGAGTAGCAACAGATGTT 59.810 40.000 0.00 0.00 39.12 2.71
762 812 3.272574 ACAGATGTTGCCTAGATGGTG 57.727 47.619 0.00 0.00 38.35 4.17
763 813 2.840038 ACAGATGTTGCCTAGATGGTGA 59.160 45.455 0.00 0.00 38.35 4.02
764 814 3.201290 CAGATGTTGCCTAGATGGTGAC 58.799 50.000 0.00 0.00 38.35 3.67
765 815 3.110705 AGATGTTGCCTAGATGGTGACT 58.889 45.455 0.00 0.00 38.35 3.41
766 816 3.521126 AGATGTTGCCTAGATGGTGACTT 59.479 43.478 0.00 0.00 38.35 3.01
767 817 3.334583 TGTTGCCTAGATGGTGACTTC 57.665 47.619 0.00 0.00 38.35 3.01
768 818 2.637382 TGTTGCCTAGATGGTGACTTCA 59.363 45.455 0.00 0.00 36.99 3.02
769 819 3.265791 GTTGCCTAGATGGTGACTTCAG 58.734 50.000 0.00 0.00 36.99 3.02
770 820 2.820178 TGCCTAGATGGTGACTTCAGA 58.180 47.619 0.00 0.00 36.99 3.27
771 821 2.497675 TGCCTAGATGGTGACTTCAGAC 59.502 50.000 0.00 0.00 36.99 3.51
772 822 2.763448 GCCTAGATGGTGACTTCAGACT 59.237 50.000 0.00 0.00 36.99 3.24
773 823 3.430098 GCCTAGATGGTGACTTCAGACTG 60.430 52.174 0.00 0.00 36.99 3.51
774 824 4.019858 CCTAGATGGTGACTTCAGACTGA 58.980 47.826 0.00 0.00 36.99 3.41
775 825 3.951775 AGATGGTGACTTCAGACTGAC 57.048 47.619 4.15 0.00 36.99 3.51
776 826 3.505386 AGATGGTGACTTCAGACTGACT 58.495 45.455 4.15 0.00 36.99 3.41
777 827 3.900601 AGATGGTGACTTCAGACTGACTT 59.099 43.478 4.15 0.00 36.99 3.01
778 828 5.080337 AGATGGTGACTTCAGACTGACTTA 58.920 41.667 4.15 0.00 36.99 2.24
779 829 5.719085 AGATGGTGACTTCAGACTGACTTAT 59.281 40.000 4.15 0.00 36.99 1.73
780 830 5.139435 TGGTGACTTCAGACTGACTTATG 57.861 43.478 4.15 0.00 0.00 1.90
781 831 4.588951 TGGTGACTTCAGACTGACTTATGT 59.411 41.667 4.15 0.00 0.00 2.29
782 832 5.773176 TGGTGACTTCAGACTGACTTATGTA 59.227 40.000 4.15 0.00 0.00 2.29
783 833 6.437477 TGGTGACTTCAGACTGACTTATGTAT 59.563 38.462 4.15 0.00 0.00 2.29
784 834 7.039011 TGGTGACTTCAGACTGACTTATGTATT 60.039 37.037 4.15 0.00 0.00 1.89
785 835 8.467598 GGTGACTTCAGACTGACTTATGTATTA 58.532 37.037 4.15 0.00 0.00 0.98
786 836 9.291664 GTGACTTCAGACTGACTTATGTATTAC 57.708 37.037 4.15 0.00 0.00 1.89
787 837 9.244292 TGACTTCAGACTGACTTATGTATTACT 57.756 33.333 4.15 0.00 0.00 2.24
788 838 9.724839 GACTTCAGACTGACTTATGTATTACTC 57.275 37.037 4.15 0.00 0.00 2.59
789 839 9.469097 ACTTCAGACTGACTTATGTATTACTCT 57.531 33.333 4.15 0.00 0.00 3.24
790 840 9.729023 CTTCAGACTGACTTATGTATTACTCTG 57.271 37.037 4.15 0.00 0.00 3.35
791 841 8.809468 TCAGACTGACTTATGTATTACTCTGT 57.191 34.615 0.00 0.00 0.00 3.41
792 842 9.901172 TCAGACTGACTTATGTATTACTCTGTA 57.099 33.333 0.00 0.00 0.00 2.74
795 845 9.900710 GACTGACTTATGTATTACTCTGTATGG 57.099 37.037 0.00 0.00 0.00 2.74
796 846 9.422681 ACTGACTTATGTATTACTCTGTATGGT 57.577 33.333 0.00 0.00 0.00 3.55
835 885 7.992754 AATAAAATGTCTGGCATCTATCCTC 57.007 36.000 0.00 0.00 36.67 3.71
836 886 4.363991 AAATGTCTGGCATCTATCCTCC 57.636 45.455 0.00 0.00 36.67 4.30
837 887 2.783379 TGTCTGGCATCTATCCTCCT 57.217 50.000 0.00 0.00 0.00 3.69
838 888 3.051940 TGTCTGGCATCTATCCTCCTT 57.948 47.619 0.00 0.00 0.00 3.36
839 889 3.387962 TGTCTGGCATCTATCCTCCTTT 58.612 45.455 0.00 0.00 0.00 3.11
840 890 3.782523 TGTCTGGCATCTATCCTCCTTTT 59.217 43.478 0.00 0.00 0.00 2.27
841 891 4.228210 TGTCTGGCATCTATCCTCCTTTTT 59.772 41.667 0.00 0.00 0.00 1.94
874 924 6.476243 AAAACATAGCTTTCAATCGTACGT 57.524 33.333 16.05 0.00 0.00 3.57
875 925 5.450376 AACATAGCTTTCAATCGTACGTG 57.550 39.130 16.05 7.38 0.00 4.49
876 926 3.306166 ACATAGCTTTCAATCGTACGTGC 59.694 43.478 16.05 9.16 0.00 5.34
877 927 2.080286 AGCTTTCAATCGTACGTGCT 57.920 45.000 16.05 11.07 0.00 4.40
878 928 3.226346 AGCTTTCAATCGTACGTGCTA 57.774 42.857 16.05 0.00 0.00 3.49
879 929 3.179830 AGCTTTCAATCGTACGTGCTAG 58.820 45.455 16.05 8.52 0.00 3.42
880 930 2.921754 GCTTTCAATCGTACGTGCTAGT 59.078 45.455 16.05 0.00 0.00 2.57
881 931 3.241678 GCTTTCAATCGTACGTGCTAGTG 60.242 47.826 16.05 5.46 0.00 2.74
882 932 2.554806 TCAATCGTACGTGCTAGTGG 57.445 50.000 16.05 0.00 0.00 4.00
883 933 0.921347 CAATCGTACGTGCTAGTGGC 59.079 55.000 16.05 0.00 42.22 5.01
884 934 0.179119 AATCGTACGTGCTAGTGGCC 60.179 55.000 16.05 0.00 40.92 5.36
885 935 2.012902 ATCGTACGTGCTAGTGGCCC 62.013 60.000 16.05 0.00 40.92 5.80
886 936 2.975536 GTACGTGCTAGTGGCCCA 59.024 61.111 0.00 0.00 40.92 5.36
887 937 1.294138 GTACGTGCTAGTGGCCCAA 59.706 57.895 0.00 0.00 40.92 4.12
888 938 0.739813 GTACGTGCTAGTGGCCCAAG 60.740 60.000 0.00 0.00 40.92 3.61
889 939 1.895020 TACGTGCTAGTGGCCCAAGG 61.895 60.000 0.00 0.00 40.92 3.61
924 974 0.108520 GCCACCGGAATACAAGTCGA 60.109 55.000 9.46 0.00 0.00 4.20
1365 1484 4.821589 CTTCCGCCGGTGAGCTCC 62.822 72.222 18.79 2.19 0.00 4.70
1514 2016 3.439293 CGATAACACTTCAGATCGCAGT 58.561 45.455 0.00 0.00 35.29 4.40
1515 2017 4.598062 CGATAACACTTCAGATCGCAGTA 58.402 43.478 0.00 0.00 35.29 2.74
1516 2018 5.215903 CGATAACACTTCAGATCGCAGTAT 58.784 41.667 0.00 0.00 35.29 2.12
1517 2019 5.340932 CGATAACACTTCAGATCGCAGTATC 59.659 44.000 0.00 0.00 35.29 2.24
1518 2020 3.071786 ACACTTCAGATCGCAGTATCG 57.928 47.619 0.00 0.00 0.00 2.92
1519 2021 1.783711 CACTTCAGATCGCAGTATCGC 59.216 52.381 0.00 0.00 0.00 4.58
1523 2025 1.008424 AGATCGCAGTATCGCACGG 60.008 57.895 0.00 0.00 0.00 4.94
1559 2068 2.750948 TCTTCCGTCTTGAGTTTTCCG 58.249 47.619 0.00 0.00 0.00 4.30
1568 2077 2.787473 TGAGTTTTCCGATGCTGGAT 57.213 45.000 0.00 0.00 38.00 3.41
1569 2078 2.358957 TGAGTTTTCCGATGCTGGATG 58.641 47.619 0.00 0.00 38.00 3.51
1589 2098 3.403057 CTGCGCGCGTACACAAGT 61.403 61.111 32.35 0.00 0.00 3.16
1590 2099 2.050259 TGCGCGCGTACACAAGTA 60.050 55.556 32.35 0.47 0.00 2.24
1594 2103 1.177668 CGCGCGTACACAAGTAGTAG 58.822 55.000 24.19 0.00 0.00 2.57
1600 2109 5.445939 GCGCGTACACAAGTAGTAGTACTTA 60.446 44.000 20.12 4.87 46.01 2.24
1601 2110 5.954349 CGCGTACACAAGTAGTAGTACTTAC 59.046 44.000 20.12 14.32 46.01 2.34
1640 2149 3.957591 TGGTAGGTACGCACACAATAA 57.042 42.857 0.00 0.00 0.00 1.40
1657 2166 6.144854 CACAATAATTGCGCATATGCTTAGT 58.855 36.000 24.56 12.78 39.32 2.24
1768 2508 3.965292 TCGAATCGTCTGTATCACTCC 57.035 47.619 1.52 0.00 0.00 3.85
1875 2681 4.162690 GCCTCGCCAAGACGGGAT 62.163 66.667 0.00 0.00 34.72 3.85
1876 2682 2.107141 CCTCGCCAAGACGGGATC 59.893 66.667 0.00 0.00 34.72 3.36
1883 2689 0.108992 CCAAGACGGGATCGAACGAA 60.109 55.000 13.29 0.00 40.11 3.85
1884 2690 0.989890 CAAGACGGGATCGAACGAAC 59.010 55.000 13.29 0.00 40.11 3.95
1895 2701 0.738412 CGAACGAACGGGCCACTTAT 60.738 55.000 4.39 0.00 0.00 1.73
1896 2702 1.445871 GAACGAACGGGCCACTTATT 58.554 50.000 4.39 0.00 0.00 1.40
1898 2704 2.014335 ACGAACGGGCCACTTATTAC 57.986 50.000 4.39 0.00 0.00 1.89
1906 2712 2.763448 GGGCCACTTATTACCAATGCAA 59.237 45.455 4.39 0.00 0.00 4.08
1907 2713 3.430236 GGGCCACTTATTACCAATGCAAC 60.430 47.826 4.39 0.00 0.00 4.17
2011 3050 0.386731 ACTGCAATTGTTAACCGCGC 60.387 50.000 7.40 0.00 0.00 6.86
2015 3054 0.095589 CAATTGTTAACCGCGCGCTA 59.904 50.000 30.48 15.24 0.00 4.26
2017 3056 0.303493 ATTGTTAACCGCGCGCTATG 59.697 50.000 30.48 19.33 0.00 2.23
2020 3059 4.516195 TAACCGCGCGCTATGCCA 62.516 61.111 30.48 6.19 42.08 4.92
2021 3060 3.800685 TAACCGCGCGCTATGCCAT 62.801 57.895 30.48 10.33 42.08 4.40
2069 4092 4.452733 GCCGGCTTAGGTGCGTCT 62.453 66.667 22.15 0.00 0.00 4.18
2072 4095 1.517257 CGGCTTAGGTGCGTCTGAG 60.517 63.158 0.00 0.00 0.00 3.35
2113 4169 3.345808 GCTTCTTCACCGCGTGCA 61.346 61.111 4.92 0.00 32.98 4.57
2114 4170 2.551270 CTTCTTCACCGCGTGCAC 59.449 61.111 6.82 6.82 32.98 4.57
2115 4171 3.281751 CTTCTTCACCGCGTGCACG 62.282 63.158 34.01 34.01 43.27 5.34
2116 4172 4.578898 TCTTCACCGCGTGCACGT 62.579 61.111 36.80 17.90 42.22 4.49
2152 4208 3.337398 CTGGTCAAGCTCGCTACTC 57.663 57.895 0.00 0.00 0.00 2.59
2160 4216 3.134262 TCAAGCTCGCTACTCCTACTAGA 59.866 47.826 0.00 0.00 0.00 2.43
2163 4219 5.080969 AGCTCGCTACTCCTACTAGATAG 57.919 47.826 0.00 0.00 0.00 2.08
2374 8269 7.543756 ACACATAAAATGTTAATTTCCCCTCG 58.456 34.615 0.00 0.00 42.70 4.63
2385 8293 2.231716 TTCCCCTCGATCTGACTCAA 57.768 50.000 0.00 0.00 0.00 3.02
2387 8295 2.034878 TCCCCTCGATCTGACTCAATG 58.965 52.381 0.00 0.00 0.00 2.82
2389 8297 2.482664 CCCCTCGATCTGACTCAATGTG 60.483 54.545 0.00 0.00 0.00 3.21
2405 8313 2.959275 GTGTATCGCACTTCCGGAG 58.041 57.895 3.34 1.34 44.41 4.63
2430 8386 3.605634 TCTCTCTCTCTCTCTCGGTTTG 58.394 50.000 0.00 0.00 0.00 2.93
2436 8392 2.761208 TCTCTCTCTCGGTTTGGGATTC 59.239 50.000 0.00 0.00 0.00 2.52
2448 8404 4.156739 GGTTTGGGATTCTAACTGCAAGAG 59.843 45.833 0.00 0.00 37.43 2.85
2450 8406 4.478206 TGGGATTCTAACTGCAAGAGAG 57.522 45.455 0.00 0.00 37.43 3.20
2451 8407 3.840666 TGGGATTCTAACTGCAAGAGAGT 59.159 43.478 0.00 0.00 37.43 3.24
2452 8408 4.287067 TGGGATTCTAACTGCAAGAGAGTT 59.713 41.667 0.00 0.00 37.43 3.01
2457 8613 4.825422 TCTAACTGCAAGAGAGTTCATGG 58.175 43.478 0.00 0.00 37.43 3.66
2460 8616 4.090761 ACTGCAAGAGAGTTCATGGAAA 57.909 40.909 0.00 0.00 37.43 3.13
2462 8618 2.816087 TGCAAGAGAGTTCATGGAAAGC 59.184 45.455 0.00 0.00 0.00 3.51
2468 8624 3.755378 GAGAGTTCATGGAAAGCACATGT 59.245 43.478 0.00 0.00 44.57 3.21
2488 8644 3.326588 TGTGCCTAAAACTCTGCTCCTTA 59.673 43.478 0.00 0.00 0.00 2.69
3047 9499 2.681778 CTGGACAGGCTCGACCCT 60.682 66.667 0.00 0.00 40.58 4.34
3080 9532 3.695606 ATGCAGGGCGTCGTCAGT 61.696 61.111 0.00 0.00 0.00 3.41
3268 9723 3.314331 CCGAGGTGGCCAGTGTCT 61.314 66.667 5.11 0.74 0.00 3.41
4041 10591 1.290955 CTTCACCGGCTTCGTGGTA 59.709 57.895 0.00 0.00 36.50 3.25
4048 10598 1.298667 GGCTTCGTGGTATGGGTGT 59.701 57.895 0.00 0.00 0.00 4.16
4052 10602 0.680618 TTCGTGGTATGGGTGTTCGT 59.319 50.000 0.00 0.00 0.00 3.85
4053 10603 0.038067 TCGTGGTATGGGTGTTCGTG 60.038 55.000 0.00 0.00 0.00 4.35
4054 10604 1.017177 CGTGGTATGGGTGTTCGTGG 61.017 60.000 0.00 0.00 0.00 4.94
4129 10679 3.366396 TCTTCTACTTCGCCTTCTCCAT 58.634 45.455 0.00 0.00 0.00 3.41
4139 10689 1.208293 GCCTTCTCCATCCTCGTCTTT 59.792 52.381 0.00 0.00 0.00 2.52
4182 11043 9.636789 TTGATAACCATCTCATCATCTCAATTT 57.363 29.630 0.00 0.00 31.93 1.82
4187 11048 6.323996 ACCATCTCATCATCTCAATTTTGCAT 59.676 34.615 0.00 0.00 0.00 3.96
4197 11058 8.456471 TCATCTCAATTTTGCATAGTTCTTGAG 58.544 33.333 12.19 12.19 39.46 3.02
4231 11095 4.893608 ACCAAATTAATCAACCTTGGTGC 58.106 39.130 17.01 0.00 46.16 5.01
4236 11100 5.806654 ATTAATCAACCTTGGTGCTGTTT 57.193 34.783 0.00 0.00 0.00 2.83
4622 11513 2.124151 GCTACATGCAGGTGGGGG 60.124 66.667 15.48 2.92 42.31 5.40
4700 11591 2.750637 ACGTGTCGCGGGAGATCT 60.751 61.111 6.13 0.00 46.52 2.75
4753 11644 2.342648 GAGAAGGCGTGGTTCGGT 59.657 61.111 0.00 0.00 40.26 4.69
5134 12046 4.400251 AGGGACGGTGGGGAGGAG 62.400 72.222 0.00 0.00 0.00 3.69
5138 12050 3.083997 ACGGTGGGGAGGAGCATC 61.084 66.667 0.00 0.00 0.00 3.91
5139 12051 3.083349 CGGTGGGGAGGAGCATCA 61.083 66.667 0.00 0.00 36.25 3.07
5141 12053 1.077429 GGTGGGGAGGAGCATCAAC 60.077 63.158 0.00 0.00 36.25 3.18
5143 12055 0.257039 GTGGGGAGGAGCATCAACAT 59.743 55.000 0.00 0.00 36.25 2.71
5385 12300 2.962421 AGAGGAATGCTAGTACAGGAGC 59.038 50.000 7.32 7.32 39.25 4.70
5843 12758 2.591915 ATCCATTCACGTCGGAGGT 58.408 52.632 0.00 0.00 30.84 3.85
5844 12759 0.175760 ATCCATTCACGTCGGAGGTG 59.824 55.000 21.45 21.45 35.48 4.00
5845 12760 2.100631 CCATTCACGTCGGAGGTGC 61.101 63.158 22.38 0.00 34.28 5.01
5846 12761 1.374125 CATTCACGTCGGAGGTGCA 60.374 57.895 22.38 14.60 34.28 4.57
5847 12762 1.374252 ATTCACGTCGGAGGTGCAC 60.374 57.895 22.38 8.80 34.28 4.57
5848 12763 2.781595 ATTCACGTCGGAGGTGCACC 62.782 60.000 29.22 29.22 34.28 5.01
5856 12771 4.436998 GAGGTGCACCCCTCGACG 62.437 72.222 32.29 0.00 41.58 5.12
5882 12797 1.683385 GACCTTGTTTTTGCTCCAGCT 59.317 47.619 0.00 0.00 42.66 4.24
5903 12818 2.093921 TGGCGAAGATTGTAACGGATCA 60.094 45.455 0.00 0.00 0.00 2.92
5918 12833 1.670811 GGATCACCATGGTTTGCTACG 59.329 52.381 16.84 1.62 35.97 3.51
5942 12857 0.518355 CAACGCCGAATGCTACAACG 60.518 55.000 0.00 0.00 38.05 4.10
5948 12863 0.370273 CGAATGCTACAACGACCTGC 59.630 55.000 0.00 0.00 0.00 4.85
5995 12910 1.841663 AAGCTACAACGCGCAACCAG 61.842 55.000 5.73 0.00 34.40 4.00
6027 12942 0.800012 TTGCTACAACCGAATTCGCC 59.200 50.000 22.36 4.59 38.18 5.54
6030 12945 1.467342 GCTACAACCGAATTCGCCTTT 59.533 47.619 22.36 11.45 38.18 3.11
6039 12954 3.365969 CCGAATTCGCCTTTTGCTACTTT 60.366 43.478 22.36 0.00 38.05 2.66
6131 13046 1.614850 GGATCCCGGGTTTTTGCTACA 60.615 52.381 22.86 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 0.238289 GTGCACAAGGTGTTCGATGG 59.762 55.000 13.17 0.00 35.75 3.51
42 43 1.885388 CCACTTGTTGCACCGACGA 60.885 57.895 0.00 0.00 0.00 4.20
265 282 0.940126 CAGTATCATGTGCGGCCTTC 59.060 55.000 0.00 0.00 0.00 3.46
276 293 2.437281 CTCCTCCAAGCACCAGTATCAT 59.563 50.000 0.00 0.00 0.00 2.45
283 300 3.072476 GAGCTCCTCCAAGCACCA 58.928 61.111 0.87 0.00 45.00 4.17
299 316 3.876589 GAGTGTTTGCTCCGCCGGA 62.877 63.158 5.05 5.37 0.00 5.14
346 381 3.910784 TAAACCCGCGACCCCTCCT 62.911 63.158 8.23 0.00 0.00 3.69
362 397 1.084084 CCCCCTCACCCCTTCCTAA 59.916 63.158 0.00 0.00 0.00 2.69
393 429 1.227147 GAATTCGCCCGATGGACGA 60.227 57.895 0.00 0.00 45.77 4.20
667 717 2.485903 ACAAACATCGCACGAAACCTA 58.514 42.857 0.00 0.00 0.00 3.08
668 718 1.305201 ACAAACATCGCACGAAACCT 58.695 45.000 0.00 0.00 0.00 3.50
669 719 2.113910 AACAAACATCGCACGAAACC 57.886 45.000 0.00 0.00 0.00 3.27
670 720 2.215363 CCAAACAAACATCGCACGAAAC 59.785 45.455 0.00 0.00 0.00 2.78
671 721 2.455032 CCAAACAAACATCGCACGAAA 58.545 42.857 0.00 0.00 0.00 3.46
672 722 1.862008 GCCAAACAAACATCGCACGAA 60.862 47.619 0.00 0.00 0.00 3.85
673 723 0.317436 GCCAAACAAACATCGCACGA 60.317 50.000 0.00 0.00 0.00 4.35
674 724 0.593518 TGCCAAACAAACATCGCACG 60.594 50.000 0.00 0.00 0.00 5.34
675 725 1.782044 ATGCCAAACAAACATCGCAC 58.218 45.000 0.00 0.00 0.00 5.34
676 726 2.522836 AATGCCAAACAAACATCGCA 57.477 40.000 0.00 0.00 0.00 5.10
677 727 2.923020 CCTAATGCCAAACAAACATCGC 59.077 45.455 0.00 0.00 0.00 4.58
678 728 2.923020 GCCTAATGCCAAACAAACATCG 59.077 45.455 0.00 0.00 0.00 3.84
691 741 1.369625 CGAATATCCGGGCCTAATGC 58.630 55.000 0.84 0.00 40.16 3.56
692 742 2.024176 CCGAATATCCGGGCCTAATG 57.976 55.000 0.84 0.00 45.43 1.90
701 751 1.217882 GAAGGTGTGCCGAATATCCG 58.782 55.000 0.00 0.00 40.50 4.18
702 752 1.217882 CGAAGGTGTGCCGAATATCC 58.782 55.000 0.00 0.00 40.50 2.59
703 753 1.859080 GACGAAGGTGTGCCGAATATC 59.141 52.381 0.00 0.00 40.50 1.63
704 754 1.206132 TGACGAAGGTGTGCCGAATAT 59.794 47.619 0.00 0.00 40.50 1.28
705 755 0.604073 TGACGAAGGTGTGCCGAATA 59.396 50.000 0.00 0.00 40.50 1.75
706 756 0.250124 TTGACGAAGGTGTGCCGAAT 60.250 50.000 0.00 0.00 40.50 3.34
707 757 0.250124 ATTGACGAAGGTGTGCCGAA 60.250 50.000 0.00 0.00 40.50 4.30
708 758 0.948623 CATTGACGAAGGTGTGCCGA 60.949 55.000 0.00 0.00 40.50 5.54
709 759 1.497278 CATTGACGAAGGTGTGCCG 59.503 57.895 0.00 0.00 40.50 5.69
710 760 0.605319 TCCATTGACGAAGGTGTGCC 60.605 55.000 0.00 0.00 0.00 5.01
711 761 1.234821 TTCCATTGACGAAGGTGTGC 58.765 50.000 0.00 0.00 0.00 4.57
712 762 3.623060 CCTATTCCATTGACGAAGGTGTG 59.377 47.826 0.00 0.00 0.00 3.82
713 763 3.517901 TCCTATTCCATTGACGAAGGTGT 59.482 43.478 0.00 0.00 0.00 4.16
714 764 4.122776 CTCCTATTCCATTGACGAAGGTG 58.877 47.826 0.00 0.00 0.00 4.00
715 765 3.775316 ACTCCTATTCCATTGACGAAGGT 59.225 43.478 0.00 0.00 0.00 3.50
716 766 4.408182 ACTCCTATTCCATTGACGAAGG 57.592 45.455 0.00 0.00 0.00 3.46
717 767 4.985409 GCTACTCCTATTCCATTGACGAAG 59.015 45.833 0.00 0.00 0.00 3.79
718 768 4.404394 TGCTACTCCTATTCCATTGACGAA 59.596 41.667 0.00 0.00 0.00 3.85
719 769 3.958147 TGCTACTCCTATTCCATTGACGA 59.042 43.478 0.00 0.00 0.00 4.20
720 770 4.322080 TGCTACTCCTATTCCATTGACG 57.678 45.455 0.00 0.00 0.00 4.35
721 771 5.428253 TGTTGCTACTCCTATTCCATTGAC 58.572 41.667 0.00 0.00 0.00 3.18
722 772 5.425217 TCTGTTGCTACTCCTATTCCATTGA 59.575 40.000 0.00 0.00 0.00 2.57
723 773 5.674525 TCTGTTGCTACTCCTATTCCATTG 58.325 41.667 0.00 0.00 0.00 2.82
724 774 5.957771 TCTGTTGCTACTCCTATTCCATT 57.042 39.130 0.00 0.00 0.00 3.16
725 775 5.367937 ACATCTGTTGCTACTCCTATTCCAT 59.632 40.000 0.00 0.00 0.00 3.41
726 776 4.716784 ACATCTGTTGCTACTCCTATTCCA 59.283 41.667 0.00 0.00 0.00 3.53
727 777 5.283457 ACATCTGTTGCTACTCCTATTCC 57.717 43.478 0.00 0.00 0.00 3.01
741 791 3.264193 TCACCATCTAGGCAACATCTGTT 59.736 43.478 0.00 0.00 43.14 3.16
742 792 2.840038 TCACCATCTAGGCAACATCTGT 59.160 45.455 0.00 0.00 43.14 3.41
743 793 3.118482 AGTCACCATCTAGGCAACATCTG 60.118 47.826 0.00 0.00 43.14 2.90
744 794 3.110705 AGTCACCATCTAGGCAACATCT 58.889 45.455 0.00 0.00 43.14 2.90
745 795 3.550437 AGTCACCATCTAGGCAACATC 57.450 47.619 0.00 0.00 43.14 3.06
746 796 3.264193 TGAAGTCACCATCTAGGCAACAT 59.736 43.478 0.00 0.00 43.14 2.71
747 797 2.637382 TGAAGTCACCATCTAGGCAACA 59.363 45.455 0.00 0.00 43.14 3.33
748 798 3.055819 TCTGAAGTCACCATCTAGGCAAC 60.056 47.826 0.00 0.00 43.14 4.17
749 799 3.055819 GTCTGAAGTCACCATCTAGGCAA 60.056 47.826 0.00 0.00 43.14 4.52
750 800 2.497675 GTCTGAAGTCACCATCTAGGCA 59.502 50.000 0.00 0.00 43.14 4.75
751 801 2.763448 AGTCTGAAGTCACCATCTAGGC 59.237 50.000 0.00 0.00 43.14 3.93
752 802 4.019858 TCAGTCTGAAGTCACCATCTAGG 58.980 47.826 0.00 0.00 45.67 3.02
753 803 4.704540 AGTCAGTCTGAAGTCACCATCTAG 59.295 45.833 3.51 0.00 0.00 2.43
754 804 4.667573 AGTCAGTCTGAAGTCACCATCTA 58.332 43.478 3.51 0.00 0.00 1.98
755 805 3.505386 AGTCAGTCTGAAGTCACCATCT 58.495 45.455 3.51 0.00 0.00 2.90
756 806 3.951775 AGTCAGTCTGAAGTCACCATC 57.048 47.619 3.51 0.00 0.00 3.51
757 807 5.247110 ACATAAGTCAGTCTGAAGTCACCAT 59.753 40.000 3.51 0.00 0.00 3.55
758 808 4.588951 ACATAAGTCAGTCTGAAGTCACCA 59.411 41.667 3.51 0.00 0.00 4.17
759 809 5.140747 ACATAAGTCAGTCTGAAGTCACC 57.859 43.478 3.51 0.00 0.00 4.02
760 810 9.291664 GTAATACATAAGTCAGTCTGAAGTCAC 57.708 37.037 3.51 0.00 0.00 3.67
761 811 9.244292 AGTAATACATAAGTCAGTCTGAAGTCA 57.756 33.333 3.51 0.00 0.00 3.41
762 812 9.724839 GAGTAATACATAAGTCAGTCTGAAGTC 57.275 37.037 3.51 0.00 0.00 3.01
763 813 9.469097 AGAGTAATACATAAGTCAGTCTGAAGT 57.531 33.333 3.51 0.00 0.00 3.01
764 814 9.729023 CAGAGTAATACATAAGTCAGTCTGAAG 57.271 37.037 3.51 0.00 31.32 3.02
765 815 9.244292 ACAGAGTAATACATAAGTCAGTCTGAA 57.756 33.333 3.51 0.00 33.48 3.02
766 816 8.809468 ACAGAGTAATACATAAGTCAGTCTGA 57.191 34.615 14.25 0.00 33.48 3.27
769 819 9.900710 CCATACAGAGTAATACATAAGTCAGTC 57.099 37.037 0.00 0.00 0.00 3.51
770 820 9.422681 ACCATACAGAGTAATACATAAGTCAGT 57.577 33.333 0.00 0.00 0.00 3.41
809 859 9.507329 GAGGATAGATGCCAGACATTTTATTAA 57.493 33.333 0.00 0.00 39.84 1.40
810 860 8.103305 GGAGGATAGATGCCAGACATTTTATTA 58.897 37.037 0.00 0.00 39.84 0.98
811 861 6.944862 GGAGGATAGATGCCAGACATTTTATT 59.055 38.462 0.00 0.00 39.84 1.40
812 862 6.274200 AGGAGGATAGATGCCAGACATTTTAT 59.726 38.462 0.00 0.00 39.84 1.40
813 863 5.608437 AGGAGGATAGATGCCAGACATTTTA 59.392 40.000 0.00 0.00 39.84 1.52
814 864 4.414846 AGGAGGATAGATGCCAGACATTTT 59.585 41.667 0.00 0.00 39.84 1.82
815 865 3.979347 AGGAGGATAGATGCCAGACATTT 59.021 43.478 0.00 0.00 39.84 2.32
816 866 3.596101 AGGAGGATAGATGCCAGACATT 58.404 45.455 0.00 0.00 39.84 2.71
817 867 3.272716 AGGAGGATAGATGCCAGACAT 57.727 47.619 0.00 0.00 43.54 3.06
818 868 2.783379 AGGAGGATAGATGCCAGACA 57.217 50.000 0.00 0.00 0.00 3.41
819 869 4.429854 AAAAGGAGGATAGATGCCAGAC 57.570 45.455 0.00 0.00 0.00 3.51
850 900 6.795114 CACGTACGATTGAAAGCTATGTTTTT 59.205 34.615 24.41 0.00 0.00 1.94
851 901 6.304126 CACGTACGATTGAAAGCTATGTTTT 58.696 36.000 24.41 0.00 0.00 2.43
852 902 5.670341 GCACGTACGATTGAAAGCTATGTTT 60.670 40.000 24.41 0.00 0.00 2.83
853 903 4.201685 GCACGTACGATTGAAAGCTATGTT 60.202 41.667 24.41 0.00 0.00 2.71
854 904 3.306166 GCACGTACGATTGAAAGCTATGT 59.694 43.478 24.41 0.00 0.00 2.29
855 905 3.551890 AGCACGTACGATTGAAAGCTATG 59.448 43.478 24.41 5.99 0.00 2.23
856 906 3.782046 AGCACGTACGATTGAAAGCTAT 58.218 40.909 24.41 0.00 0.00 2.97
857 907 3.226346 AGCACGTACGATTGAAAGCTA 57.774 42.857 24.41 0.00 0.00 3.32
858 908 2.080286 AGCACGTACGATTGAAAGCT 57.920 45.000 24.41 14.78 0.00 3.74
859 909 2.921754 ACTAGCACGTACGATTGAAAGC 59.078 45.455 24.41 12.88 0.00 3.51
860 910 3.303495 CCACTAGCACGTACGATTGAAAG 59.697 47.826 24.41 13.07 0.00 2.62
861 911 3.247442 CCACTAGCACGTACGATTGAAA 58.753 45.455 24.41 1.62 0.00 2.69
862 912 2.871133 CCACTAGCACGTACGATTGAA 58.129 47.619 24.41 1.97 0.00 2.69
863 913 1.468565 GCCACTAGCACGTACGATTGA 60.469 52.381 24.41 3.40 42.97 2.57
864 914 0.921347 GCCACTAGCACGTACGATTG 59.079 55.000 24.41 12.10 42.97 2.67
865 915 0.179119 GGCCACTAGCACGTACGATT 60.179 55.000 24.41 9.12 46.50 3.34
866 916 1.436336 GGCCACTAGCACGTACGAT 59.564 57.895 24.41 9.86 46.50 3.73
867 917 2.703798 GGGCCACTAGCACGTACGA 61.704 63.158 24.41 0.00 46.50 3.43
868 918 2.202703 GGGCCACTAGCACGTACG 60.203 66.667 15.01 15.01 46.50 3.67
938 992 2.439883 GGACGGGTCTAGCCTCGT 60.440 66.667 0.00 0.00 43.41 4.18
1251 1370 0.755698 TAGTCCTCCACCGCCATCTC 60.756 60.000 0.00 0.00 0.00 2.75
1359 1478 2.123033 GGGAGGGAGAGGGAGCTC 60.123 72.222 4.71 4.71 0.00 4.09
1362 1481 2.612251 GGAGGGAGGGAGAGGGAG 59.388 72.222 0.00 0.00 0.00 4.30
1363 1482 3.036959 GGGAGGGAGGGAGAGGGA 61.037 72.222 0.00 0.00 0.00 4.20
1364 1483 4.179599 GGGGAGGGAGGGAGAGGG 62.180 77.778 0.00 0.00 0.00 4.30
1365 1484 3.039526 AGGGGAGGGAGGGAGAGG 61.040 72.222 0.00 0.00 0.00 3.69
1366 1485 2.285180 CAGGGGAGGGAGGGAGAG 59.715 72.222 0.00 0.00 0.00 3.20
1367 1486 4.095400 GCAGGGGAGGGAGGGAGA 62.095 72.222 0.00 0.00 0.00 3.71
1490 1992 1.188138 CGATCTGAAGTGTTATCGCGC 59.812 52.381 0.00 0.00 35.36 6.86
1512 2014 1.720301 GAGACGACCGTGCGATACT 59.280 57.895 0.00 0.00 34.83 2.12
1513 2015 1.650536 CGAGACGACCGTGCGATAC 60.651 63.158 0.00 0.00 34.83 2.24
1514 2016 1.810853 TCGAGACGACCGTGCGATA 60.811 57.895 11.29 0.00 34.83 2.92
1515 2017 3.122971 TCGAGACGACCGTGCGAT 61.123 61.111 11.29 0.00 34.83 4.58
1537 2039 4.219070 TCGGAAAACTCAAGACGGAAGATA 59.781 41.667 0.00 0.00 0.00 1.98
1559 2068 2.713770 CGCAGCACATCCAGCATC 59.286 61.111 0.00 0.00 0.00 3.91
1584 2093 7.445402 TGAAACGGAGTAAGTACTACTACTTGT 59.555 37.037 8.34 7.77 45.00 3.16
1587 2096 8.572855 AATGAAACGGAGTAAGTACTACTACT 57.427 34.615 6.91 6.91 45.00 2.57
1589 2098 7.067494 GGGAATGAAACGGAGTAAGTACTACTA 59.933 40.741 0.00 0.00 45.00 1.82
1590 2099 6.127507 GGGAATGAAACGGAGTAAGTACTACT 60.128 42.308 0.00 0.00 45.00 2.57
1594 2103 4.824289 TGGGAATGAAACGGAGTAAGTAC 58.176 43.478 0.00 0.00 45.00 2.73
1599 2108 1.626321 TGCTGGGAATGAAACGGAGTA 59.374 47.619 0.00 0.00 45.00 2.59
1601 2110 1.402968 CATGCTGGGAATGAAACGGAG 59.597 52.381 0.00 0.00 0.00 4.63
1650 2159 6.721321 CGTAAGAAAAAGAAACCACTAAGCA 58.279 36.000 0.00 0.00 43.02 3.91
1768 2508 1.728971 GCACAAGACAACAGATCGAGG 59.271 52.381 0.00 0.00 0.00 4.63
1814 2588 0.107410 TGGGCAACACGACAGTTCTT 60.107 50.000 0.00 0.00 39.74 2.52
1872 2678 2.889018 GGCCCGTTCGTTCGATCC 60.889 66.667 0.00 1.72 0.00 3.36
1873 2679 2.125832 TGGCCCGTTCGTTCGATC 60.126 61.111 0.00 0.00 0.00 3.69
1874 2680 2.433664 GTGGCCCGTTCGTTCGAT 60.434 61.111 0.00 0.00 0.00 3.59
1875 2681 1.804396 TAAGTGGCCCGTTCGTTCGA 61.804 55.000 0.00 0.00 0.00 3.71
1876 2682 0.738412 ATAAGTGGCCCGTTCGTTCG 60.738 55.000 0.00 0.00 0.00 3.95
1883 2689 2.650322 CATTGGTAATAAGTGGCCCGT 58.350 47.619 0.00 0.00 0.00 5.28
1884 2690 1.336755 GCATTGGTAATAAGTGGCCCG 59.663 52.381 0.00 0.00 0.00 6.13
1895 2701 2.720659 TGCGTGGTTGCATTGGTAA 58.279 47.368 0.00 0.00 40.62 2.85
1896 2702 4.483090 TGCGTGGTTGCATTGGTA 57.517 50.000 0.00 0.00 40.62 3.25
1927 2959 0.455633 GACTAACACGGACGCATCGT 60.456 55.000 0.00 0.00 45.10 3.73
1928 2960 0.179171 AGACTAACACGGACGCATCG 60.179 55.000 0.00 0.00 0.00 3.84
1929 2961 1.269166 CAGACTAACACGGACGCATC 58.731 55.000 0.00 0.00 0.00 3.91
1930 2962 0.601558 ACAGACTAACACGGACGCAT 59.398 50.000 0.00 0.00 0.00 4.73
1931 2963 0.386476 AACAGACTAACACGGACGCA 59.614 50.000 0.00 0.00 0.00 5.24
1932 2964 1.981533 GTAACAGACTAACACGGACGC 59.018 52.381 0.00 0.00 0.00 5.19
1997 3036 1.011333 ATAGCGCGCGGTTAACAATT 58.989 45.000 40.26 13.05 0.00 2.32
2011 3050 2.865308 CATGGCGATGGCATAGCG 59.135 61.111 23.25 14.32 47.00 4.26
2017 3056 4.241999 GACGTGCATGGCGATGGC 62.242 66.667 11.36 3.77 38.90 4.40
2113 4169 2.503375 GCGCACTAGCACGTACGT 60.503 61.111 16.72 16.72 42.27 3.57
2114 4170 3.594827 CGCGCACTAGCACGTACG 61.595 66.667 15.01 15.01 41.12 3.67
2115 4171 2.202388 TCGCGCACTAGCACGTAC 60.202 61.111 8.75 0.00 45.81 3.67
2116 4172 2.099638 CTCGCGCACTAGCACGTA 59.900 61.111 8.75 0.00 45.81 3.57
2374 8269 4.363138 TGCGATACACATTGAGTCAGATC 58.637 43.478 0.00 0.00 0.00 2.75
2389 8297 4.014065 GCTCCGGAAGTGCGATAC 57.986 61.111 5.23 0.00 0.00 2.24
2400 8308 2.515991 AGAGAGAGAGCGCTCCGG 60.516 66.667 32.94 0.00 41.28 5.14
2405 8313 1.221414 GAGAGAGAGAGAGAGAGCGC 58.779 60.000 0.00 0.00 0.00 5.92
2430 8386 4.479786 ACTCTCTTGCAGTTAGAATCCC 57.520 45.455 0.00 0.00 0.00 3.85
2436 8392 4.825422 TCCATGAACTCTCTTGCAGTTAG 58.175 43.478 0.00 0.00 34.10 2.34
2448 8404 3.829948 CACATGTGCTTTCCATGAACTC 58.170 45.455 13.94 0.00 41.78 3.01
2462 8618 2.816087 AGCAGAGTTTTAGGCACATGTG 59.184 45.455 21.83 21.83 0.00 3.21
2468 8624 3.583086 AGTAAGGAGCAGAGTTTTAGGCA 59.417 43.478 0.00 0.00 0.00 4.75
2488 8644 1.226660 GCGCTGCAACAACAACAGT 60.227 52.632 0.00 0.00 33.87 3.55
3047 9499 0.532573 GCATGAAGTCGAGGTCCTCA 59.467 55.000 19.15 3.46 0.00 3.86
3080 9532 2.599281 TCAACGTGAGGCCGGAGA 60.599 61.111 5.05 0.00 0.00 3.71
3268 9723 4.794648 CCGAAATGCTGGGCCGGA 62.795 66.667 18.84 3.98 42.49 5.14
3357 9812 2.594592 GTGTTGAGCACCGCCCTT 60.595 61.111 0.00 0.00 42.10 3.95
3445 9900 1.290203 CCGTTCCCGATGATGTTCAG 58.710 55.000 0.00 0.00 35.63 3.02
4041 10591 2.282180 GTGCCCACGAACACCCAT 60.282 61.111 0.00 0.00 0.00 4.00
4048 10598 3.834013 TTGATGCGGTGCCCACGAA 62.834 57.895 0.00 0.00 0.00 3.85
4129 10679 0.464036 ACTGTGTGCAAAGACGAGGA 59.536 50.000 0.00 0.00 0.00 3.71
4139 10689 1.347378 TCAAGATGCCTACTGTGTGCA 59.653 47.619 8.23 8.23 39.68 4.57
4182 11043 6.816136 TCGATATTCCTCAAGAACTATGCAA 58.184 36.000 0.00 0.00 37.29 4.08
4187 11048 6.549736 TGGTGATCGATATTCCTCAAGAACTA 59.450 38.462 0.00 0.00 37.29 2.24
4197 11058 9.612620 GTTGATTAATTTGGTGATCGATATTCC 57.387 33.333 0.00 1.85 0.00 3.01
4236 11100 1.270839 CCGGCTTCTCCTCTGTGAAAA 60.271 52.381 0.00 0.00 0.00 2.29
4240 11111 0.967887 TCTCCGGCTTCTCCTCTGTG 60.968 60.000 0.00 0.00 0.00 3.66
4254 11125 1.153939 CTCGACAGGTTGCTCTCCG 60.154 63.158 0.00 0.00 0.00 4.63
4700 11591 4.033776 CCCCTCCGCCAGCTTCAA 62.034 66.667 0.00 0.00 0.00 2.69
5138 12050 0.819582 GTCCCTTCCATGGCATGTTG 59.180 55.000 24.80 11.63 0.00 3.33
5139 12051 0.324645 GGTCCCTTCCATGGCATGTT 60.325 55.000 24.80 0.00 0.00 2.71
5141 12053 0.754217 CTGGTCCCTTCCATGGCATG 60.754 60.000 20.56 20.56 36.84 4.06
5143 12055 3.089838 CTGGTCCCTTCCATGGCA 58.910 61.111 6.96 0.00 36.84 4.92
5219 12131 4.194720 ACTGATCTCCGACGCCGC 62.195 66.667 0.00 0.00 0.00 6.53
5356 12270 3.285484 ACTAGCATTCCTCTGCAAATGG 58.715 45.455 10.12 2.55 44.77 3.16
5825 12740 0.175760 CACCTCCGACGTGAATGGAT 59.824 55.000 0.00 0.00 32.77 3.41
5826 12741 1.589630 CACCTCCGACGTGAATGGA 59.410 57.895 0.00 0.00 32.77 3.41
5827 12742 2.100631 GCACCTCCGACGTGAATGG 61.101 63.158 0.00 0.00 32.77 3.16
5828 12743 1.374125 TGCACCTCCGACGTGAATG 60.374 57.895 0.00 0.00 32.77 2.67
5829 12744 1.374252 GTGCACCTCCGACGTGAAT 60.374 57.895 5.22 0.00 32.77 2.57
5830 12745 2.028484 GTGCACCTCCGACGTGAA 59.972 61.111 5.22 0.00 32.77 3.18
5831 12746 3.986006 GGTGCACCTCCGACGTGA 61.986 66.667 29.12 0.00 32.77 4.35
5854 12769 4.922026 AAACAAGGTCGCCGGCGT 62.922 61.111 44.16 26.54 40.74 5.68
5855 12770 3.189010 AAAAACAAGGTCGCCGGCG 62.189 57.895 42.13 42.13 41.35 6.46
5856 12771 1.660264 CAAAAACAAGGTCGCCGGC 60.660 57.895 19.07 19.07 0.00 6.13
5857 12772 1.660264 GCAAAAACAAGGTCGCCGG 60.660 57.895 0.00 0.00 0.00 6.13
5858 12773 0.660300 GAGCAAAAACAAGGTCGCCG 60.660 55.000 0.00 0.00 0.00 6.46
5859 12774 0.318699 GGAGCAAAAACAAGGTCGCC 60.319 55.000 0.00 0.00 33.28 5.54
5860 12775 0.383949 TGGAGCAAAAACAAGGTCGC 59.616 50.000 0.00 0.00 33.28 5.19
5861 12776 1.600413 GCTGGAGCAAAAACAAGGTCG 60.600 52.381 0.00 0.00 41.59 4.79
5862 12777 1.683385 AGCTGGAGCAAAAACAAGGTC 59.317 47.619 0.65 0.00 45.16 3.85
5863 12778 1.410153 CAGCTGGAGCAAAAACAAGGT 59.590 47.619 5.57 0.00 45.16 3.50
5864 12779 1.269936 CCAGCTGGAGCAAAAACAAGG 60.270 52.381 29.88 0.00 45.16 3.61
5865 12780 1.870993 GCCAGCTGGAGCAAAAACAAG 60.871 52.381 37.21 5.10 45.16 3.16
5866 12781 0.104671 GCCAGCTGGAGCAAAAACAA 59.895 50.000 37.21 0.00 45.16 2.83
5867 12782 1.741525 GCCAGCTGGAGCAAAAACA 59.258 52.632 37.21 0.00 45.16 2.83
5868 12783 1.372128 CGCCAGCTGGAGCAAAAAC 60.372 57.895 37.21 14.63 45.16 2.43
5882 12797 2.093921 TGATCCGTTACAATCTTCGCCA 60.094 45.455 0.00 0.00 0.00 5.69
5903 12818 1.877443 GTGTTCGTAGCAAACCATGGT 59.123 47.619 13.00 13.00 43.54 3.55
5918 12833 4.130857 GCATTCGGCGTTGTGTTC 57.869 55.556 6.85 0.00 0.00 3.18
5942 12857 1.222113 GTAGCTTCCCCTGCAGGTC 59.778 63.158 30.63 13.88 0.00 3.85
5948 12863 0.678048 GCTGGTTGTAGCTTCCCCTG 60.678 60.000 0.00 0.00 40.52 4.45
6116 13031 3.416955 GCATGTAGCAAAAACCCGG 57.583 52.632 0.00 0.00 44.79 5.73
6131 13046 3.573558 CAACGCCGGTTGTAGCAT 58.426 55.556 1.90 0.00 46.69 3.79


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

AutoCloner maintained by Alex Coulton.