Multiple sequence alignment - TraesCS3B01G147300

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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 TraesCS3B01G147300 chr3B 100.000 3904 0 0 1 3904 137748697 137752600 0.000000e+00 7210.0
1 TraesCS3B01G147300 chr3B 91.009 456 39 2 3445 3898 676107545 676107090 7.170000e-172 614.0
2 TraesCS3B01G147300 chr3B 82.353 85 9 5 705 784 42372051 42372134 7.000000e-08 69.4
3 TraesCS3B01G147300 chr3D 93.322 2306 88 18 786 3049 88350968 88353249 0.000000e+00 3345.0
4 TraesCS3B01G147300 chr3A 92.803 2237 92 20 786 3002 105114156 105111969 0.000000e+00 3175.0
5 TraesCS3B01G147300 chr3A 83.404 711 86 17 1 682 562875583 562876290 7.120000e-177 630.0
6 TraesCS3B01G147300 chr3A 96.610 59 1 1 3073 3131 105109653 105109596 3.210000e-16 97.1
7 TraesCS3B01G147300 chr2D 95.497 755 29 4 3153 3904 274730046 274729294 0.000000e+00 1201.0
8 TraesCS3B01G147300 chr2D 85.237 718 69 16 1 683 524150318 524151033 0.000000e+00 704.0
9 TraesCS3B01G147300 chr2D 91.852 270 21 1 3153 3422 274728228 274728496 3.680000e-100 375.0
10 TraesCS3B01G147300 chr7A 95.106 756 32 2 3153 3904 19925127 19925881 0.000000e+00 1186.0
11 TraesCS3B01G147300 chr7A 90.370 270 23 2 3153 3422 19927390 19927124 6.210000e-93 351.0
12 TraesCS3B01G147300 chr7A 81.985 272 34 11 412 683 603521357 603521101 2.360000e-52 217.0
13 TraesCS3B01G147300 chr5A 92.553 752 37 13 3153 3904 57361182 57360450 0.000000e+00 1061.0
14 TraesCS3B01G147300 chr5A 90.741 270 24 1 3153 3422 57358564 57358832 3.710000e-95 359.0
15 TraesCS3B01G147300 chr5A 92.405 237 17 1 3153 3389 339297539 339297774 1.740000e-88 337.0
16 TraesCS3B01G147300 chr5A 88.816 152 15 2 2007 2157 291133328 291133478 6.660000e-43 185.0
17 TraesCS3B01G147300 chr5A 84.795 171 23 2 2011 2181 632836475 632836642 6.710000e-38 169.0
18 TraesCS3B01G147300 chr5A 83.594 128 14 6 1409 1531 34262803 34262928 3.190000e-21 113.0
19 TraesCS3B01G147300 chr2A 96.360 467 17 0 3437 3903 389560634 389561100 0.000000e+00 769.0
20 TraesCS3B01G147300 chr2A 83.151 730 72 31 1 683 478382895 478383620 1.540000e-173 619.0
21 TraesCS3B01G147300 chr2A 96.085 281 10 1 3157 3437 389560309 389560588 1.280000e-124 457.0
22 TraesCS3B01G147300 chr2A 92.222 270 20 1 3153 3422 389563573 389563305 7.920000e-102 381.0
23 TraesCS3B01G147300 chr6D 84.848 693 82 12 3 680 428070604 428071288 0.000000e+00 676.0
24 TraesCS3B01G147300 chr6D 79.126 206 31 10 1337 1536 317005365 317005564 8.800000e-27 132.0
25 TraesCS3B01G147300 chr1B 84.540 718 71 27 4 683 15884409 15885124 0.000000e+00 675.0
26 TraesCS3B01G147300 chr1B 83.747 726 68 29 3 680 329203952 329204675 3.290000e-180 641.0
27 TraesCS3B01G147300 chr1B 89.507 467 45 4 1 465 562451128 562450664 4.350000e-164 588.0
28 TraesCS3B01G147300 chr1B 78.370 319 56 11 1230 1540 416823324 416823011 1.110000e-45 195.0
29 TraesCS3B01G147300 chr1B 83.237 173 25 4 2395 2565 416822564 416822394 5.220000e-34 156.0
30 TraesCS3B01G147300 chr7D 85.075 670 63 19 29 683 268546984 268546337 0.000000e+00 649.0
31 TraesCS3B01G147300 chr7D 85.185 297 39 4 390 683 635667564 635667858 2.280000e-77 300.0
32 TraesCS3B01G147300 chr7D 83.686 331 28 12 375 683 498535181 498535507 4.940000e-74 289.0
33 TraesCS3B01G147300 chr7B 90.909 462 39 3 3445 3904 263148487 263148027 5.540000e-173 617.0
34 TraesCS3B01G147300 chr7B 88.174 482 53 4 3 482 679685304 679685783 4.380000e-159 571.0
35 TraesCS3B01G147300 chr1D 89.002 491 48 6 1 487 440877933 440877445 1.550000e-168 603.0
36 TraesCS3B01G147300 chr1D 90.728 151 12 2 534 683 315999026 315999175 2.380000e-47 200.0
37 TraesCS3B01G147300 chr1D 78.025 314 57 11 1230 1540 307833514 307833210 1.850000e-43 187.0
38 TraesCS3B01G147300 chr1D 84.076 157 24 1 2409 2565 307832754 307832599 2.430000e-32 150.0
39 TraesCS3B01G147300 chr1D 82.166 157 26 2 2400 2555 127504609 127504764 2.450000e-27 134.0
40 TraesCS3B01G147300 chr5B 87.476 519 54 9 1 511 626354475 626354990 4.350000e-164 588.0
41 TraesCS3B01G147300 chr5B 83.077 455 45 13 242 683 263949584 263949149 6.120000e-103 385.0
42 TraesCS3B01G147300 chr5B 88.079 151 18 0 2007 2157 234880144 234880294 3.100000e-41 180.0
43 TraesCS3B01G147300 chr5B 85.380 171 22 2 2011 2181 635194581 635194748 1.440000e-39 174.0
44 TraesCS3B01G147300 chr4B 86.444 509 58 8 1 501 15222680 15222175 7.370000e-152 547.0
45 TraesCS3B01G147300 chr4B 84.211 532 53 11 165 683 621423261 621422748 4.530000e-134 488.0
46 TraesCS3B01G147300 chr4B 85.887 248 33 2 437 683 656997076 656996830 2.990000e-66 263.0
47 TraesCS3B01G147300 chr5D 81.679 262 24 7 434 683 368461127 368460878 3.080000e-46 196.0
48 TraesCS3B01G147300 chr5D 88.079 151 18 0 2007 2157 218189951 218190101 3.100000e-41 180.0
49 TraesCS3B01G147300 chr5D 84.393 173 24 2 2009 2181 505215643 505215812 2.410000e-37 167.0
50 TraesCS3B01G147300 chr1A 77.778 315 56 12 1230 1540 387029935 387029631 8.620000e-42 182.0
51 TraesCS3B01G147300 chr1A 84.076 157 24 1 2409 2565 387029180 387029025 2.430000e-32 150.0
52 TraesCS3B01G147300 chr1A 82.803 157 25 2 2400 2555 186213076 186213231 5.260000e-29 139.0
53 TraesCS3B01G147300 chr6B 87.417 151 16 2 2008 2155 507593471 507593321 1.870000e-38 171.0
54 TraesCS3B01G147300 chr6B 81.043 211 28 10 1332 1536 507594235 507594031 1.450000e-34 158.0
55 TraesCS3B01G147300 chr6A 80.095 211 30 10 1332 1536 454647784 454647988 3.140000e-31 147.0
56 TraesCS3B01G147300 chr4A 80.745 161 29 2 2427 2586 85569776 85569935 1.470000e-24 124.0


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 TraesCS3B01G147300 chr3B 137748697 137752600 3903 False 7210.00 7210 100.0000 1 3904 1 chr3B.!!$F2 3903
1 TraesCS3B01G147300 chr3D 88350968 88353249 2281 False 3345.00 3345 93.3220 786 3049 1 chr3D.!!$F1 2263
2 TraesCS3B01G147300 chr3A 105109596 105114156 4560 True 1636.05 3175 94.7065 786 3131 2 chr3A.!!$R1 2345
3 TraesCS3B01G147300 chr3A 562875583 562876290 707 False 630.00 630 83.4040 1 682 1 chr3A.!!$F1 681
4 TraesCS3B01G147300 chr2D 274729294 274730046 752 True 1201.00 1201 95.4970 3153 3904 1 chr2D.!!$R1 751
5 TraesCS3B01G147300 chr2D 524150318 524151033 715 False 704.00 704 85.2370 1 683 1 chr2D.!!$F2 682
6 TraesCS3B01G147300 chr7A 19925127 19925881 754 False 1186.00 1186 95.1060 3153 3904 1 chr7A.!!$F1 751
7 TraesCS3B01G147300 chr5A 57360450 57361182 732 True 1061.00 1061 92.5530 3153 3904 1 chr5A.!!$R1 751
8 TraesCS3B01G147300 chr2A 478382895 478383620 725 False 619.00 619 83.1510 1 683 1 chr2A.!!$F1 682
9 TraesCS3B01G147300 chr2A 389560309 389561100 791 False 613.00 769 96.2225 3157 3903 2 chr2A.!!$F2 746
10 TraesCS3B01G147300 chr6D 428070604 428071288 684 False 676.00 676 84.8480 3 680 1 chr6D.!!$F2 677
11 TraesCS3B01G147300 chr1B 15884409 15885124 715 False 675.00 675 84.5400 4 683 1 chr1B.!!$F1 679
12 TraesCS3B01G147300 chr1B 329203952 329204675 723 False 641.00 641 83.7470 3 680 1 chr1B.!!$F2 677
13 TraesCS3B01G147300 chr7D 268546337 268546984 647 True 649.00 649 85.0750 29 683 1 chr7D.!!$R1 654
14 TraesCS3B01G147300 chr5B 626354475 626354990 515 False 588.00 588 87.4760 1 511 1 chr5B.!!$F2 510
15 TraesCS3B01G147300 chr4B 15222175 15222680 505 True 547.00 547 86.4440 1 501 1 chr4B.!!$R1 500
16 TraesCS3B01G147300 chr4B 621422748 621423261 513 True 488.00 488 84.2110 165 683 1 chr4B.!!$R2 518

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
379 390 0.539518 TGGTAATAGAGCAAGGCGCA 59.46 50.0 10.83 0.00 46.13 6.09 F
1684 1892 0.459585 GGCCTGAAGATTACGCGTGA 60.46 55.0 24.59 15.72 0.00 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2223 2451 0.445043 CACGACGACGAGTGACCATA 59.555 55.0 15.32 0.0 42.66 2.74 R
3021 3259 0.041238 TCTCCATCTCCGGTCAGGTT 59.959 55.0 0.00 0.0 41.99 3.50 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
35 37 4.124238 CCAGACAGAAACCGTAAAAGTGA 58.876 43.478 0.00 0.00 0.00 3.41
83 88 0.591170 CGAAATGCACACCCGAAACT 59.409 50.000 0.00 0.00 0.00 2.66
97 104 6.070424 ACACCCGAAACTCTTATATTTGGAGA 60.070 38.462 0.00 0.00 0.00 3.71
156 164 1.594293 CCACGTCGGAGCAAACACT 60.594 57.895 0.00 0.00 36.56 3.55
265 273 0.604243 CCACCGGTTCGAATTGGACA 60.604 55.000 21.30 0.00 0.00 4.02
279 287 1.338107 TGGACAAGGTCGACATCACT 58.662 50.000 18.91 1.61 32.65 3.41
379 390 0.539518 TGGTAATAGAGCAAGGCGCA 59.460 50.000 10.83 0.00 46.13 6.09
535 698 3.787001 GCTGGGAGAAGGGACGGG 61.787 72.222 0.00 0.00 0.00 5.28
559 722 1.545706 GCCGGACTTGAGGAAGGAGT 61.546 60.000 5.05 0.00 32.95 3.85
615 790 6.677187 GCCGTAGCTAAAATGAACCCTTAAAG 60.677 42.308 0.00 0.00 35.50 1.85
665 844 7.708998 AGTTTTACAGTTTGCGATTTTAAGGA 58.291 30.769 0.00 0.00 0.00 3.36
683 862 2.091939 AGGAGTCTGCTAGAGATGCTCA 60.092 50.000 0.00 0.00 31.63 4.26
684 863 2.892852 GGAGTCTGCTAGAGATGCTCAT 59.107 50.000 0.00 0.00 31.63 2.90
685 864 3.057315 GGAGTCTGCTAGAGATGCTCATC 60.057 52.174 0.00 1.75 38.09 2.92
686 865 2.553602 AGTCTGCTAGAGATGCTCATCG 59.446 50.000 0.00 0.00 42.48 3.84
687 866 2.293122 GTCTGCTAGAGATGCTCATCGT 59.707 50.000 0.00 0.00 42.48 3.73
688 867 2.292845 TCTGCTAGAGATGCTCATCGTG 59.707 50.000 0.00 0.00 42.48 4.35
689 868 2.027385 TGCTAGAGATGCTCATCGTGT 58.973 47.619 0.00 0.00 42.48 4.49
690 869 2.428530 TGCTAGAGATGCTCATCGTGTT 59.571 45.455 0.00 0.00 42.48 3.32
691 870 3.118992 TGCTAGAGATGCTCATCGTGTTT 60.119 43.478 0.00 0.00 42.48 2.83
692 871 3.244814 GCTAGAGATGCTCATCGTGTTTG 59.755 47.826 0.00 0.00 42.48 2.93
693 872 2.005451 AGAGATGCTCATCGTGTTTGC 58.995 47.619 4.41 0.00 42.48 3.68
694 873 1.733912 GAGATGCTCATCGTGTTTGCA 59.266 47.619 4.41 0.00 42.48 4.08
695 874 2.353889 GAGATGCTCATCGTGTTTGCAT 59.646 45.455 0.00 0.00 45.48 3.96
696 875 2.096980 AGATGCTCATCGTGTTTGCATG 59.903 45.455 3.43 0.00 43.28 4.06
697 876 1.237533 TGCTCATCGTGTTTGCATGT 58.762 45.000 0.00 0.00 33.51 3.21
698 877 1.608109 TGCTCATCGTGTTTGCATGTT 59.392 42.857 0.00 0.00 33.51 2.71
699 878 2.810852 TGCTCATCGTGTTTGCATGTTA 59.189 40.909 0.00 0.00 33.51 2.41
700 879 3.120234 TGCTCATCGTGTTTGCATGTTAG 60.120 43.478 0.00 0.00 33.51 2.34
701 880 3.125146 GCTCATCGTGTTTGCATGTTAGA 59.875 43.478 0.00 0.00 33.51 2.10
702 881 4.378356 GCTCATCGTGTTTGCATGTTAGAA 60.378 41.667 0.00 0.00 33.51 2.10
703 882 5.029650 TCATCGTGTTTGCATGTTAGAAC 57.970 39.130 0.00 0.00 33.51 3.01
704 883 4.513318 TCATCGTGTTTGCATGTTAGAACA 59.487 37.500 0.00 0.00 44.06 3.18
705 884 4.884458 TCGTGTTTGCATGTTAGAACAA 57.116 36.364 1.13 0.00 43.03 2.83
706 885 4.843147 TCGTGTTTGCATGTTAGAACAAG 58.157 39.130 1.13 4.03 43.03 3.16
707 886 4.334203 TCGTGTTTGCATGTTAGAACAAGT 59.666 37.500 10.85 0.00 43.03 3.16
708 887 5.034152 CGTGTTTGCATGTTAGAACAAGTT 58.966 37.500 1.13 0.00 43.03 2.66
709 888 6.037281 TCGTGTTTGCATGTTAGAACAAGTTA 59.963 34.615 10.85 0.00 43.03 2.24
710 889 6.855914 CGTGTTTGCATGTTAGAACAAGTTAT 59.144 34.615 1.13 0.00 43.03 1.89
711 890 8.012809 CGTGTTTGCATGTTAGAACAAGTTATA 58.987 33.333 1.13 0.00 43.03 0.98
712 891 9.672086 GTGTTTGCATGTTAGAACAAGTTATAA 57.328 29.630 1.13 0.00 43.03 0.98
713 892 9.672086 TGTTTGCATGTTAGAACAAGTTATAAC 57.328 29.630 18.52 18.52 43.60 1.89
743 922 9.908152 AATTTCATGTACTTTACAACTTTAGGC 57.092 29.630 0.00 0.00 42.76 3.93
744 923 8.453238 TTTCATGTACTTTACAACTTTAGGCA 57.547 30.769 0.00 0.00 42.76 4.75
745 924 8.630054 TTCATGTACTTTACAACTTTAGGCAT 57.370 30.769 0.00 0.00 42.76 4.40
746 925 8.263940 TCATGTACTTTACAACTTTAGGCATC 57.736 34.615 0.00 0.00 42.76 3.91
747 926 7.880713 TCATGTACTTTACAACTTTAGGCATCA 59.119 33.333 0.00 0.00 42.76 3.07
748 927 8.511321 CATGTACTTTACAACTTTAGGCATCAA 58.489 33.333 0.00 0.00 42.76 2.57
749 928 8.453238 TGTACTTTACAACTTTAGGCATCAAA 57.547 30.769 0.00 0.00 35.38 2.69
750 929 8.904834 TGTACTTTACAACTTTAGGCATCAAAA 58.095 29.630 0.00 0.00 35.38 2.44
751 930 9.908152 GTACTTTACAACTTTAGGCATCAAAAT 57.092 29.630 0.00 0.00 0.00 1.82
752 931 8.816640 ACTTTACAACTTTAGGCATCAAAATG 57.183 30.769 0.00 0.00 35.87 2.32
753 932 8.637986 ACTTTACAACTTTAGGCATCAAAATGA 58.362 29.630 0.00 0.00 34.61 2.57
754 933 9.643693 CTTTACAACTTTAGGCATCAAAATGAT 57.356 29.630 0.00 0.00 37.65 2.45
755 934 9.638239 TTTACAACTTTAGGCATCAAAATGATC 57.362 29.630 0.00 0.00 34.28 2.92
756 935 6.324819 ACAACTTTAGGCATCAAAATGATCG 58.675 36.000 0.00 0.00 34.28 3.69
757 936 6.071952 ACAACTTTAGGCATCAAAATGATCGT 60.072 34.615 0.00 0.00 34.28 3.73
758 937 5.883661 ACTTTAGGCATCAAAATGATCGTG 58.116 37.500 0.00 0.00 34.28 4.35
759 938 5.647658 ACTTTAGGCATCAAAATGATCGTGA 59.352 36.000 0.00 0.00 34.28 4.35
760 939 5.484173 TTAGGCATCAAAATGATCGTGAC 57.516 39.130 0.00 0.00 34.28 3.67
761 940 3.346315 AGGCATCAAAATGATCGTGACA 58.654 40.909 0.00 0.00 34.28 3.58
762 941 3.758023 AGGCATCAAAATGATCGTGACAA 59.242 39.130 0.00 0.00 34.28 3.18
763 942 4.218200 AGGCATCAAAATGATCGTGACAAA 59.782 37.500 0.00 0.00 34.28 2.83
764 943 5.104374 GGCATCAAAATGATCGTGACAAAT 58.896 37.500 0.00 0.00 34.28 2.32
765 944 5.577945 GGCATCAAAATGATCGTGACAAATT 59.422 36.000 0.00 0.00 34.28 1.82
766 945 6.751425 GGCATCAAAATGATCGTGACAAATTA 59.249 34.615 0.00 0.00 34.28 1.40
767 946 7.275341 GGCATCAAAATGATCGTGACAAATTAA 59.725 33.333 0.00 0.00 34.28 1.40
768 947 8.316046 GCATCAAAATGATCGTGACAAATTAAG 58.684 33.333 0.00 0.00 34.28 1.85
769 948 8.800972 CATCAAAATGATCGTGACAAATTAAGG 58.199 33.333 0.00 0.00 34.28 2.69
770 949 6.806249 TCAAAATGATCGTGACAAATTAAGGC 59.194 34.615 0.00 0.00 0.00 4.35
771 950 5.895636 AATGATCGTGACAAATTAAGGCA 57.104 34.783 0.00 0.00 0.00 4.75
772 951 4.678509 TGATCGTGACAAATTAAGGCAC 57.321 40.909 6.71 6.71 0.00 5.01
773 952 3.438781 TGATCGTGACAAATTAAGGCACC 59.561 43.478 10.30 0.00 0.00 5.01
774 953 3.134574 TCGTGACAAATTAAGGCACCT 57.865 42.857 10.30 0.00 0.00 4.00
775 954 4.274602 TCGTGACAAATTAAGGCACCTA 57.725 40.909 10.30 0.00 0.00 3.08
776 955 3.998341 TCGTGACAAATTAAGGCACCTAC 59.002 43.478 10.30 0.00 0.00 3.18
777 956 3.749088 CGTGACAAATTAAGGCACCTACA 59.251 43.478 10.30 0.00 0.00 2.74
778 957 4.142902 CGTGACAAATTAAGGCACCTACAG 60.143 45.833 10.30 0.00 0.00 2.74
779 958 4.760204 GTGACAAATTAAGGCACCTACAGT 59.240 41.667 5.67 0.00 0.00 3.55
1006 1186 2.402564 AGCTAGCTTCTTCCATGGCTA 58.597 47.619 12.68 2.81 36.40 3.93
1155 1335 2.132996 CCACAGCAAGCCCCACAAA 61.133 57.895 0.00 0.00 0.00 2.83
1422 1602 2.206536 GGAGATCCTCCGCTCCCTG 61.207 68.421 0.00 0.00 43.91 4.45
1626 1834 0.681175 GCAAGCACCACCATTTTCCT 59.319 50.000 0.00 0.00 0.00 3.36
1632 1840 3.647590 AGCACCACCATTTTCCTGATTTT 59.352 39.130 0.00 0.00 0.00 1.82
1633 1841 3.747529 GCACCACCATTTTCCTGATTTTG 59.252 43.478 0.00 0.00 0.00 2.44
1674 1882 2.038952 CGAATATCCCATGGCCTGAAGA 59.961 50.000 6.09 0.00 0.00 2.87
1684 1892 0.459585 GGCCTGAAGATTACGCGTGA 60.460 55.000 24.59 15.72 0.00 4.35
1711 1919 5.931146 TGAAAAGCTGAGATTCTCTCTGTTC 59.069 40.000 20.58 20.58 43.73 3.18
1867 2087 3.881952 TTGTCTCGCCGTGCATGCT 62.882 57.895 20.33 0.00 0.00 3.79
1923 2151 1.385528 ATGATTTGAGCTGCGCATGA 58.614 45.000 12.24 0.00 0.00 3.07
1976 2204 4.560743 TGTGTGGCGCTGGCTGAA 62.561 61.111 7.64 0.00 39.81 3.02
1996 2224 2.088423 ACTGATAGAGATCGATCGCCC 58.912 52.381 23.28 14.65 34.49 6.13
1999 2227 2.229062 TGATAGAGATCGATCGCCCAAC 59.771 50.000 23.28 12.17 34.49 3.77
2066 2294 1.000739 CCTGCACATGATGGGGGTT 59.999 57.895 0.00 0.00 0.00 4.11
2163 2391 1.370051 CTCAAGTGCGACGACGTCA 60.370 57.895 26.26 7.04 41.98 4.35
2223 2451 3.322466 CCAACCCGAGCTCCACCT 61.322 66.667 8.47 0.00 0.00 4.00
2246 2474 3.450152 CACTCGTCGTCGTGCGTG 61.450 66.667 1.33 5.01 42.13 5.34
2279 2507 1.582968 GGTGCTGTCATGCCTGTTG 59.417 57.895 0.00 0.00 0.00 3.33
2282 2510 1.542915 GTGCTGTCATGCCTGTTGAAT 59.457 47.619 0.00 0.00 0.00 2.57
2600 2828 4.393155 ATCGTCAGCAAGCGGCCA 62.393 61.111 2.24 0.00 46.50 5.36
2681 2909 3.083349 CAGGACCTCATGGCCCGA 61.083 66.667 0.00 0.00 41.19 5.14
2693 2921 4.388499 GCCCGACTCCTGGCGAAA 62.388 66.667 0.00 0.00 38.00 3.46
2891 3128 2.028748 GCAGCAACATGAGGACCATTTT 60.029 45.455 0.00 0.00 31.94 1.82
2918 3155 6.761714 ACTACTTTTGAGTTGACACCTTGTAG 59.238 38.462 0.00 0.00 0.00 2.74
2938 3175 2.853705 GTCTAGACTAGACGGGCAGAT 58.146 52.381 23.42 0.00 44.90 2.90
2942 3179 1.749334 GACTAGACGGGCAGATGGGG 61.749 65.000 0.00 0.00 0.00 4.96
2947 3184 0.182775 GACGGGCAGATGGGGTTAAT 59.817 55.000 0.00 0.00 0.00 1.40
2948 3185 0.629058 ACGGGCAGATGGGGTTAATT 59.371 50.000 0.00 0.00 0.00 1.40
2949 3186 1.847737 ACGGGCAGATGGGGTTAATTA 59.152 47.619 0.00 0.00 0.00 1.40
2950 3187 2.242708 ACGGGCAGATGGGGTTAATTAA 59.757 45.455 0.00 0.00 0.00 1.40
2951 3188 2.884639 CGGGCAGATGGGGTTAATTAAG 59.115 50.000 0.00 0.00 0.00 1.85
2952 3189 2.628178 GGGCAGATGGGGTTAATTAAGC 59.372 50.000 17.23 17.23 0.00 3.09
2953 3190 3.295973 GGCAGATGGGGTTAATTAAGCA 58.704 45.455 24.50 9.30 35.51 3.91
2954 3191 3.319122 GGCAGATGGGGTTAATTAAGCAG 59.681 47.826 24.50 10.64 35.51 4.24
2955 3192 3.954258 GCAGATGGGGTTAATTAAGCAGT 59.046 43.478 24.50 12.26 35.51 4.40
2956 3193 4.202050 GCAGATGGGGTTAATTAAGCAGTG 60.202 45.833 24.50 15.45 35.51 3.66
2957 3194 4.949856 CAGATGGGGTTAATTAAGCAGTGT 59.050 41.667 24.50 10.46 35.51 3.55
2958 3195 5.418840 CAGATGGGGTTAATTAAGCAGTGTT 59.581 40.000 24.50 8.02 35.51 3.32
2959 3196 5.652452 AGATGGGGTTAATTAAGCAGTGTTC 59.348 40.000 24.50 14.65 35.51 3.18
2960 3197 4.730966 TGGGGTTAATTAAGCAGTGTTCA 58.269 39.130 24.50 11.89 35.51 3.18
2961 3198 5.329399 TGGGGTTAATTAAGCAGTGTTCAT 58.671 37.500 24.50 0.00 35.51 2.57
2962 3199 6.486056 TGGGGTTAATTAAGCAGTGTTCATA 58.514 36.000 24.50 2.00 35.51 2.15
2963 3200 6.948886 TGGGGTTAATTAAGCAGTGTTCATAA 59.051 34.615 24.50 0.20 35.51 1.90
2964 3201 7.451877 TGGGGTTAATTAAGCAGTGTTCATAAA 59.548 33.333 24.50 0.00 35.51 1.40
2965 3202 8.474831 GGGGTTAATTAAGCAGTGTTCATAAAT 58.525 33.333 24.50 0.00 35.51 1.40
3014 3252 6.443934 AAATATTACAGTTTGCATACGCCA 57.556 33.333 1.44 0.00 37.32 5.69
3021 3259 1.268352 GTTTGCATACGCCAAACCAGA 59.732 47.619 5.87 0.00 35.19 3.86
3044 3282 3.140225 GACCGGAGATGGAGACGCC 62.140 68.421 9.46 0.00 37.10 5.68
3050 3288 4.148825 GATGGAGACGCCGTGGCT 62.149 66.667 9.55 0.00 40.66 4.75
3060 3298 3.716006 CCGTGGCTCGTTGCAGTG 61.716 66.667 8.25 0.00 45.15 3.66
3061 3299 2.967076 CGTGGCTCGTTGCAGTGT 60.967 61.111 0.00 0.00 45.15 3.55
3063 3301 1.887242 GTGGCTCGTTGCAGTGTGA 60.887 57.895 5.65 0.00 45.15 3.58
3064 3302 1.071299 TGGCTCGTTGCAGTGTGAT 59.929 52.632 5.65 0.00 45.15 3.06
3065 3303 0.950555 TGGCTCGTTGCAGTGTGATC 60.951 55.000 5.65 0.00 45.15 2.92
3066 3304 1.417592 GCTCGTTGCAGTGTGATCG 59.582 57.895 0.00 0.00 42.31 3.69
3068 3306 0.436150 CTCGTTGCAGTGTGATCGTG 59.564 55.000 0.00 0.00 0.00 4.35
3069 3307 0.943835 TCGTTGCAGTGTGATCGTGG 60.944 55.000 0.00 0.00 0.00 4.94
3070 3308 1.868997 GTTGCAGTGTGATCGTGGG 59.131 57.895 0.00 0.00 0.00 4.61
3071 3309 1.302431 TTGCAGTGTGATCGTGGGG 60.302 57.895 0.00 0.00 0.00 4.96
3126 5609 2.433664 GGATTGGTCGACGGCGTT 60.434 61.111 16.19 0.00 38.98 4.84
3128 5611 2.736682 GATTGGTCGACGGCGTTGG 61.737 63.158 25.85 15.72 38.98 3.77
3129 5612 3.229156 ATTGGTCGACGGCGTTGGA 62.229 57.895 25.85 17.76 38.98 3.53
3130 5613 4.651008 TGGTCGACGGCGTTGGAC 62.651 66.667 26.73 26.73 38.98 4.02
3131 5614 4.353437 GGTCGACGGCGTTGGACT 62.353 66.667 30.40 5.25 38.98 3.85
3132 5615 3.103911 GTCGACGGCGTTGGACTG 61.104 66.667 27.12 10.95 38.98 3.51
3133 5616 4.351938 TCGACGGCGTTGGACTGG 62.352 66.667 25.85 4.94 38.98 4.00
3134 5617 4.351938 CGACGGCGTTGGACTGGA 62.352 66.667 19.51 0.00 0.00 3.86
3135 5618 2.737376 GACGGCGTTGGACTGGAC 60.737 66.667 16.19 0.00 0.00 4.02
3136 5619 4.657824 ACGGCGTTGGACTGGACG 62.658 66.667 6.77 0.00 41.89 4.79
3137 5620 4.351938 CGGCGTTGGACTGGACGA 62.352 66.667 0.00 0.00 41.53 4.20
3138 5621 2.432628 GGCGTTGGACTGGACGAG 60.433 66.667 0.00 0.00 41.53 4.18
3139 5622 2.649034 GCGTTGGACTGGACGAGA 59.351 61.111 0.00 0.00 41.53 4.04
3140 5623 1.006571 GCGTTGGACTGGACGAGAA 60.007 57.895 0.00 0.00 41.53 2.87
3141 5624 1.282930 GCGTTGGACTGGACGAGAAC 61.283 60.000 0.00 0.00 41.53 3.01
3142 5625 0.031585 CGTTGGACTGGACGAGAACA 59.968 55.000 0.00 0.00 41.53 3.18
3143 5626 1.784525 GTTGGACTGGACGAGAACAG 58.215 55.000 0.00 0.00 40.48 3.16
3144 5627 1.340248 GTTGGACTGGACGAGAACAGA 59.660 52.381 0.00 0.00 38.09 3.41
3145 5628 1.248486 TGGACTGGACGAGAACAGAG 58.752 55.000 0.00 0.00 38.09 3.35
3146 5629 0.528470 GGACTGGACGAGAACAGAGG 59.472 60.000 0.00 0.00 38.09 3.69
3147 5630 1.249407 GACTGGACGAGAACAGAGGT 58.751 55.000 0.00 0.00 38.09 3.85
3148 5631 2.434428 GACTGGACGAGAACAGAGGTA 58.566 52.381 0.00 0.00 38.09 3.08
3149 5632 2.818432 GACTGGACGAGAACAGAGGTAA 59.182 50.000 0.00 0.00 38.09 2.85
3150 5633 2.557490 ACTGGACGAGAACAGAGGTAAC 59.443 50.000 0.00 0.00 38.09 2.50
3151 5634 2.557056 CTGGACGAGAACAGAGGTAACA 59.443 50.000 0.00 0.00 36.86 2.41
3171 5654 8.175716 GGTAACAAGAGAATTCCTTATTTGACG 58.824 37.037 0.65 0.00 0.00 4.35
3183 5666 7.982761 TCCTTATTTGACGCTACCTTAAAAA 57.017 32.000 0.00 0.00 0.00 1.94
3201 5684 7.256511 CCTTAAAAATGTGGTTCCCTATTTGGT 60.257 37.037 0.00 0.00 0.00 3.67
3202 5685 6.508030 AAAAATGTGGTTCCCTATTTGGTT 57.492 33.333 0.00 0.00 0.00 3.67
3252 5735 7.886405 GACACGTAGTCTAAATTTCTTTCCT 57.114 36.000 0.00 0.00 41.61 3.36
3289 5772 4.817464 AGTGCATTTTGTTCACTAACGGTA 59.183 37.500 0.00 0.00 39.08 4.02
3334 5817 4.340617 CTTTTTACCCCTGGTGCATAAGA 58.659 43.478 0.00 0.00 36.19 2.10
3410 5893 6.389869 TCATAACCTCCCCTGTAATTTGATCT 59.610 38.462 0.00 0.00 0.00 2.75
3456 5988 3.430042 AGAGTGTTGTACCTCCTCGTA 57.570 47.619 0.00 0.00 0.00 3.43
3460 5992 1.542915 TGTTGTACCTCCTCGTACAGC 59.457 52.381 8.30 8.30 46.84 4.40
3730 6263 8.579006 TCAGCACAATAATGATTTCTCTGTTTT 58.421 29.630 0.00 0.00 0.00 2.43
3748 6281 4.161333 GTTTTGCTTCAGATCATTCCACG 58.839 43.478 0.00 0.00 0.00 4.94
3770 6303 3.561725 GGTGAAAGTGTCTTCAACTCTGG 59.438 47.826 0.00 0.00 39.50 3.86
3781 6314 5.354234 GTCTTCAACTCTGGAAAACTGTTCA 59.646 40.000 0.00 0.00 0.00 3.18
3851 6384 5.545658 ATGGAAGCAACAGTTAACGTATG 57.454 39.130 0.00 1.89 0.00 2.39
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 62 2.268076 GGTGTGCATTTCGGTGGCT 61.268 57.895 0.00 0.00 0.00 4.75
83 88 6.306987 GGCCTTCCAATCTCCAAATATAAGA 58.693 40.000 0.00 0.00 0.00 2.10
248 256 1.519408 CTTGTCCAATTCGAACCGGT 58.481 50.000 0.00 0.00 0.00 5.28
265 273 0.320771 GCCACAGTGATGTCGACCTT 60.321 55.000 14.12 0.00 0.00 3.50
535 698 4.821589 CCTCAAGTCCGGCCGCTC 62.822 72.222 22.85 14.85 0.00 5.03
665 844 2.553602 CGATGAGCATCTCTAGCAGACT 59.446 50.000 8.66 0.00 35.72 3.24
683 862 5.008613 ACTTGTTCTAACATGCAAACACGAT 59.991 36.000 9.39 0.00 38.95 3.73
684 863 4.334203 ACTTGTTCTAACATGCAAACACGA 59.666 37.500 9.39 0.00 38.95 4.35
685 864 4.597079 ACTTGTTCTAACATGCAAACACG 58.403 39.130 8.24 0.00 38.95 4.49
686 865 9.672086 TTATAACTTGTTCTAACATGCAAACAC 57.328 29.630 8.24 0.00 38.95 3.32
687 866 9.672086 GTTATAACTTGTTCTAACATGCAAACA 57.328 29.630 8.41 0.00 38.95 2.83
688 867 9.672086 TGTTATAACTTGTTCTAACATGCAAAC 57.328 29.630 16.33 0.00 38.95 2.93
690 869 9.891828 CTTGTTATAACTTGTTCTAACATGCAA 57.108 29.630 18.41 8.42 38.95 4.08
691 870 9.278978 TCTTGTTATAACTTGTTCTAACATGCA 57.721 29.630 18.41 0.00 38.95 3.96
717 896 9.908152 GCCTAAAGTTGTAAAGTACATGAAATT 57.092 29.630 0.00 0.00 38.68 1.82
718 897 9.073475 TGCCTAAAGTTGTAAAGTACATGAAAT 57.927 29.630 0.00 0.00 38.68 2.17
719 898 8.453238 TGCCTAAAGTTGTAAAGTACATGAAA 57.547 30.769 0.00 0.00 38.68 2.69
720 899 8.630054 ATGCCTAAAGTTGTAAAGTACATGAA 57.370 30.769 0.00 0.00 38.68 2.57
721 900 7.880713 TGATGCCTAAAGTTGTAAAGTACATGA 59.119 33.333 0.00 0.00 38.68 3.07
722 901 8.039603 TGATGCCTAAAGTTGTAAAGTACATG 57.960 34.615 0.00 0.00 38.68 3.21
723 902 8.630054 TTGATGCCTAAAGTTGTAAAGTACAT 57.370 30.769 0.00 0.00 38.68 2.29
724 903 8.453238 TTTGATGCCTAAAGTTGTAAAGTACA 57.547 30.769 0.00 0.00 36.79 2.90
725 904 9.908152 ATTTTGATGCCTAAAGTTGTAAAGTAC 57.092 29.630 0.00 0.00 0.00 2.73
726 905 9.906660 CATTTTGATGCCTAAAGTTGTAAAGTA 57.093 29.630 0.00 0.00 0.00 2.24
727 906 8.637986 TCATTTTGATGCCTAAAGTTGTAAAGT 58.362 29.630 0.00 0.00 0.00 2.66
728 907 9.643693 ATCATTTTGATGCCTAAAGTTGTAAAG 57.356 29.630 0.00 0.00 35.43 1.85
729 908 9.638239 GATCATTTTGATGCCTAAAGTTGTAAA 57.362 29.630 0.00 0.00 37.20 2.01
730 909 7.967854 CGATCATTTTGATGCCTAAAGTTGTAA 59.032 33.333 0.00 0.00 37.20 2.41
731 910 7.120579 ACGATCATTTTGATGCCTAAAGTTGTA 59.879 33.333 0.00 0.00 37.20 2.41
732 911 6.071952 ACGATCATTTTGATGCCTAAAGTTGT 60.072 34.615 0.00 0.00 37.20 3.32
733 912 6.252015 CACGATCATTTTGATGCCTAAAGTTG 59.748 38.462 0.00 0.00 37.20 3.16
734 913 6.150976 TCACGATCATTTTGATGCCTAAAGTT 59.849 34.615 0.00 0.00 37.20 2.66
735 914 5.647658 TCACGATCATTTTGATGCCTAAAGT 59.352 36.000 0.00 0.00 37.20 2.66
736 915 5.967674 GTCACGATCATTTTGATGCCTAAAG 59.032 40.000 0.00 0.00 37.20 1.85
737 916 5.414144 TGTCACGATCATTTTGATGCCTAAA 59.586 36.000 0.00 0.00 37.20 1.85
738 917 4.940654 TGTCACGATCATTTTGATGCCTAA 59.059 37.500 0.00 0.00 37.20 2.69
739 918 4.512484 TGTCACGATCATTTTGATGCCTA 58.488 39.130 0.00 0.00 37.20 3.93
740 919 3.346315 TGTCACGATCATTTTGATGCCT 58.654 40.909 0.00 0.00 37.20 4.75
741 920 3.763097 TGTCACGATCATTTTGATGCC 57.237 42.857 0.00 0.00 37.20 4.40
742 921 6.636666 AATTTGTCACGATCATTTTGATGC 57.363 33.333 0.00 0.00 37.20 3.91
743 922 8.800972 CCTTAATTTGTCACGATCATTTTGATG 58.199 33.333 0.00 0.00 37.20 3.07
744 923 7.489113 GCCTTAATTTGTCACGATCATTTTGAT 59.511 33.333 0.00 0.00 40.34 2.57
745 924 6.806249 GCCTTAATTTGTCACGATCATTTTGA 59.194 34.615 0.00 0.00 0.00 2.69
746 925 6.585702 TGCCTTAATTTGTCACGATCATTTTG 59.414 34.615 0.00 0.00 0.00 2.44
747 926 6.586082 GTGCCTTAATTTGTCACGATCATTTT 59.414 34.615 0.00 0.00 0.00 1.82
748 927 6.092748 GTGCCTTAATTTGTCACGATCATTT 58.907 36.000 0.00 0.00 0.00 2.32
749 928 5.393027 GGTGCCTTAATTTGTCACGATCATT 60.393 40.000 0.00 0.00 0.00 2.57
750 929 4.096382 GGTGCCTTAATTTGTCACGATCAT 59.904 41.667 0.00 0.00 0.00 2.45
751 930 3.438781 GGTGCCTTAATTTGTCACGATCA 59.561 43.478 0.00 0.00 0.00 2.92
752 931 3.689649 AGGTGCCTTAATTTGTCACGATC 59.310 43.478 0.00 0.00 0.00 3.69
753 932 3.686016 AGGTGCCTTAATTTGTCACGAT 58.314 40.909 0.00 0.00 0.00 3.73
754 933 3.134574 AGGTGCCTTAATTTGTCACGA 57.865 42.857 0.00 0.00 0.00 4.35
755 934 3.749088 TGTAGGTGCCTTAATTTGTCACG 59.251 43.478 0.00 0.00 0.00 4.35
756 935 4.760204 ACTGTAGGTGCCTTAATTTGTCAC 59.240 41.667 0.00 0.00 0.00 3.67
757 936 4.759693 CACTGTAGGTGCCTTAATTTGTCA 59.240 41.667 0.00 0.00 39.22 3.58
758 937 5.296813 CACTGTAGGTGCCTTAATTTGTC 57.703 43.478 0.00 0.00 39.22 3.18
771 950 7.841282 ATAGTTGCATAGATACACTGTAGGT 57.159 36.000 0.00 0.00 0.00 3.08
776 955 9.670719 CGGATATATAGTTGCATAGATACACTG 57.329 37.037 0.00 0.00 0.00 3.66
777 956 9.409918 ACGGATATATAGTTGCATAGATACACT 57.590 33.333 0.00 0.00 0.00 3.55
778 957 9.452065 CACGGATATATAGTTGCATAGATACAC 57.548 37.037 0.00 0.00 0.00 2.90
779 958 9.185680 ACACGGATATATAGTTGCATAGATACA 57.814 33.333 0.00 0.00 0.00 2.29
780 959 9.452065 CACACGGATATATAGTTGCATAGATAC 57.548 37.037 0.00 0.00 0.00 2.24
781 960 8.630037 CCACACGGATATATAGTTGCATAGATA 58.370 37.037 0.00 0.00 0.00 1.98
782 961 7.342026 TCCACACGGATATATAGTTGCATAGAT 59.658 37.037 0.00 0.00 35.91 1.98
783 962 6.661805 TCCACACGGATATATAGTTGCATAGA 59.338 38.462 0.00 0.00 35.91 1.98
784 963 6.863275 TCCACACGGATATATAGTTGCATAG 58.137 40.000 0.00 0.00 35.91 2.23
791 970 3.682696 TCGCTCCACACGGATATATAGT 58.317 45.455 0.00 0.00 41.79 2.12
1006 1186 3.288964 AGTCCGATTCATCTCTAACGGT 58.711 45.455 0.00 0.00 40.93 4.83
1155 1335 2.360350 CACTCGGCATGGTTGGCT 60.360 61.111 0.00 0.00 45.85 4.75
1417 1597 2.204090 GAAGGGGTGGTCCAGGGA 60.204 66.667 0.00 0.00 37.22 4.20
1422 1602 4.048470 GGCAGGAAGGGGTGGTCC 62.048 72.222 0.00 0.00 0.00 4.46
1557 1737 0.828022 TTGAATGGTACCTCGCGGAT 59.172 50.000 14.36 0.00 0.00 4.18
1571 1773 4.188462 CAATGCATGCATGGAAGTTGAAT 58.812 39.130 32.79 11.05 36.68 2.57
1626 1834 4.603989 ATGTGAATGTGTGGCAAAATCA 57.396 36.364 0.00 0.00 0.00 2.57
1632 1840 2.492881 GGATCAATGTGAATGTGTGGCA 59.507 45.455 0.00 0.00 0.00 4.92
1633 1841 2.478370 CGGATCAATGTGAATGTGTGGC 60.478 50.000 0.00 0.00 0.00 5.01
1674 1882 3.062639 CAGCTTTTCATCTCACGCGTAAT 59.937 43.478 13.44 2.85 0.00 1.89
1711 1919 1.528129 GAGACAAAGCTTGACCCTGG 58.472 55.000 0.00 0.00 0.00 4.45
1842 2062 0.655733 CACGGCGAGACAAAAAGTGT 59.344 50.000 16.62 0.00 45.74 3.55
1867 2087 6.761714 GGTTCTCAAAAGATCGGCTTAGATAA 59.238 38.462 0.00 0.00 35.24 1.75
1877 2097 3.189287 CCAAGTGGGTTCTCAAAAGATCG 59.811 47.826 0.00 0.00 0.00 3.69
1976 2204 2.088423 GGGCGATCGATCTCTATCAGT 58.912 52.381 21.57 0.00 31.93 3.41
1996 2224 3.837213 AGAATCTGCCGTTCATTGTTG 57.163 42.857 0.00 0.00 0.00 3.33
1999 2227 2.285834 GCGTAGAATCTGCCGTTCATTG 60.286 50.000 0.00 0.00 0.00 2.82
2066 2294 1.823169 GCTTGAGGTCCCGGTACACA 61.823 60.000 0.00 0.00 0.00 3.72
2163 2391 3.483869 GCGGAGGAGCTTGGGGAT 61.484 66.667 0.00 0.00 0.00 3.85
2219 2447 0.809385 ACGACGAGTGACCATAGGTG 59.191 55.000 0.00 0.00 35.25 4.00
2223 2451 0.445043 CACGACGACGAGTGACCATA 59.555 55.000 15.32 0.00 42.66 2.74
2279 2507 1.724654 CGCTTGCGTGTTACACCATTC 60.725 52.381 10.10 3.74 0.00 2.67
2282 2510 2.887889 GCGCTTGCGTGTTACACCA 61.888 57.895 16.38 6.27 0.00 4.17
2489 2717 3.991051 AGCGTCCACCAGTCCACG 61.991 66.667 0.00 0.00 35.32 4.94
2579 2807 1.421485 CCGCTTGCTGACGATGTTC 59.579 57.895 0.00 0.00 0.00 3.18
2738 2966 2.203294 AAGAACCCGTGCCGCTTT 60.203 55.556 0.00 0.00 0.00 3.51
2749 2977 1.072505 TTCACGCCCTGGAAGAACC 59.927 57.895 0.00 0.00 34.07 3.62
2891 3128 5.353394 AGGTGTCAACTCAAAAGTAGTCA 57.647 39.130 0.00 0.00 33.48 3.41
2938 3175 4.730966 TGAACACTGCTTAATTAACCCCA 58.269 39.130 0.00 0.00 0.00 4.96
2948 3185 9.906660 CCAACTTTAATTTATGAACACTGCTTA 57.093 29.630 0.00 0.00 0.00 3.09
2949 3186 8.421002 ACCAACTTTAATTTATGAACACTGCTT 58.579 29.630 0.00 0.00 0.00 3.91
2950 3187 7.951591 ACCAACTTTAATTTATGAACACTGCT 58.048 30.769 0.00 0.00 0.00 4.24
2951 3188 9.341899 CTACCAACTTTAATTTATGAACACTGC 57.658 33.333 0.00 0.00 0.00 4.40
2963 3200 9.744468 GTTGTGAAATCACTACCAACTTTAATT 57.256 29.630 14.54 0.00 46.55 1.40
2964 3201 8.073768 CGTTGTGAAATCACTACCAACTTTAAT 58.926 33.333 18.05 0.00 45.34 1.40
2965 3202 7.280428 TCGTTGTGAAATCACTACCAACTTTAA 59.720 33.333 18.05 0.00 45.34 1.52
2983 3220 6.960468 TGCAAACTGTAATATTTCGTTGTGA 58.040 32.000 0.00 0.00 0.00 3.58
2999 3236 1.000827 TGGTTTGGCGTATGCAAACTG 60.001 47.619 22.63 0.00 45.35 3.16
3014 3252 0.396811 CTCCGGTCAGGTTCTGGTTT 59.603 55.000 0.00 0.00 41.99 3.27
3021 3259 0.041238 TCTCCATCTCCGGTCAGGTT 59.959 55.000 0.00 0.00 41.99 3.50
3044 3282 2.967076 ACACTGCAACGAGCCACG 60.967 61.111 0.00 0.00 44.83 4.94
3050 3288 0.943835 CCACGATCACACTGCAACGA 60.944 55.000 0.00 0.00 0.00 3.85
3055 3293 2.436646 CCCCCACGATCACACTGC 60.437 66.667 0.00 0.00 0.00 4.40
3056 3294 1.079127 GTCCCCCACGATCACACTG 60.079 63.158 0.00 0.00 0.00 3.66
3057 3295 1.535444 TGTCCCCCACGATCACACT 60.535 57.895 0.00 0.00 0.00 3.55
3059 3297 2.290287 CCTGTCCCCCACGATCACA 61.290 63.158 0.00 0.00 0.00 3.58
3060 3298 1.550130 TTCCTGTCCCCCACGATCAC 61.550 60.000 0.00 0.00 0.00 3.06
3061 3299 1.229368 TTCCTGTCCCCCACGATCA 60.229 57.895 0.00 0.00 0.00 2.92
3063 3301 1.131303 TTGTTCCTGTCCCCCACGAT 61.131 55.000 0.00 0.00 0.00 3.73
3064 3302 1.764571 CTTGTTCCTGTCCCCCACGA 61.765 60.000 0.00 0.00 0.00 4.35
3065 3303 1.302511 CTTGTTCCTGTCCCCCACG 60.303 63.158 0.00 0.00 0.00 4.94
3066 3304 1.074951 CCTTGTTCCTGTCCCCCAC 59.925 63.158 0.00 0.00 0.00 4.61
3068 3306 0.539669 CAACCTTGTTCCTGTCCCCC 60.540 60.000 0.00 0.00 0.00 5.40
3069 3307 1.179174 GCAACCTTGTTCCTGTCCCC 61.179 60.000 0.00 0.00 0.00 4.81
3070 3308 1.179174 GGCAACCTTGTTCCTGTCCC 61.179 60.000 0.00 0.00 0.00 4.46
3071 3309 1.515521 CGGCAACCTTGTTCCTGTCC 61.516 60.000 0.00 0.00 0.00 4.02
3111 5594 2.740826 CCAACGCCGTCGACCAAT 60.741 61.111 10.58 0.00 39.41 3.16
3126 5609 1.248486 CTCTGTTCTCGTCCAGTCCA 58.752 55.000 0.00 0.00 0.00 4.02
3128 5611 1.249407 ACCTCTGTTCTCGTCCAGTC 58.751 55.000 0.00 0.00 0.00 3.51
3129 5612 2.557490 GTTACCTCTGTTCTCGTCCAGT 59.443 50.000 0.00 0.00 0.00 4.00
3130 5613 2.557056 TGTTACCTCTGTTCTCGTCCAG 59.443 50.000 0.00 0.00 0.00 3.86
3131 5614 2.589720 TGTTACCTCTGTTCTCGTCCA 58.410 47.619 0.00 0.00 0.00 4.02
3132 5615 3.255149 TCTTGTTACCTCTGTTCTCGTCC 59.745 47.826 0.00 0.00 0.00 4.79
3133 5616 4.215827 TCTCTTGTTACCTCTGTTCTCGTC 59.784 45.833 0.00 0.00 0.00 4.20
3134 5617 4.142790 TCTCTTGTTACCTCTGTTCTCGT 58.857 43.478 0.00 0.00 0.00 4.18
3135 5618 4.768130 TCTCTTGTTACCTCTGTTCTCG 57.232 45.455 0.00 0.00 0.00 4.04
3136 5619 6.592220 GGAATTCTCTTGTTACCTCTGTTCTC 59.408 42.308 5.23 0.00 0.00 2.87
3137 5620 6.271159 AGGAATTCTCTTGTTACCTCTGTTCT 59.729 38.462 5.23 0.00 0.00 3.01
3138 5621 6.468543 AGGAATTCTCTTGTTACCTCTGTTC 58.531 40.000 5.23 0.00 0.00 3.18
3139 5622 6.441088 AGGAATTCTCTTGTTACCTCTGTT 57.559 37.500 5.23 0.00 0.00 3.16
3140 5623 6.441088 AAGGAATTCTCTTGTTACCTCTGT 57.559 37.500 5.23 0.00 0.00 3.41
3141 5624 9.454859 AAATAAGGAATTCTCTTGTTACCTCTG 57.545 33.333 15.42 0.00 0.00 3.35
3142 5625 9.454859 CAAATAAGGAATTCTCTTGTTACCTCT 57.545 33.333 15.42 2.48 0.00 3.69
3143 5626 9.449719 TCAAATAAGGAATTCTCTTGTTACCTC 57.550 33.333 15.42 0.00 0.00 3.85
3144 5627 9.232473 GTCAAATAAGGAATTCTCTTGTTACCT 57.768 33.333 15.42 0.00 0.00 3.08
3145 5628 8.175716 CGTCAAATAAGGAATTCTCTTGTTACC 58.824 37.037 15.42 8.31 0.00 2.85
3146 5629 7.692705 GCGTCAAATAAGGAATTCTCTTGTTAC 59.307 37.037 15.42 11.20 0.00 2.50
3147 5630 7.606456 AGCGTCAAATAAGGAATTCTCTTGTTA 59.394 33.333 15.42 4.29 0.00 2.41
3148 5631 6.431234 AGCGTCAAATAAGGAATTCTCTTGTT 59.569 34.615 15.42 12.97 0.00 2.83
3149 5632 5.940470 AGCGTCAAATAAGGAATTCTCTTGT 59.060 36.000 15.42 8.87 0.00 3.16
3150 5633 6.428385 AGCGTCAAATAAGGAATTCTCTTG 57.572 37.500 15.42 8.45 0.00 3.02
3151 5634 6.539103 GGTAGCGTCAAATAAGGAATTCTCTT 59.461 38.462 5.23 9.48 0.00 2.85
3262 5745 6.293190 CCGTTAGTGAACAAAATGCACTAGAA 60.293 38.462 0.00 0.00 43.55 2.10
3289 5772 6.289064 AGGTCTTTTCACGTCTGTCTTTAAT 58.711 36.000 0.00 0.00 0.00 1.40
3334 5817 7.523293 TTGTCATGTACAGATTTTTGGTCAT 57.477 32.000 0.33 0.00 39.87 3.06
3456 5988 5.188751 AGAAGAGAAATAGTTGCCTAGCTGT 59.811 40.000 0.00 0.00 0.00 4.40
3487 6019 3.517602 CTCACGTTCGATTGACCCAATA 58.482 45.455 0.00 0.00 33.90 1.90
3531 6063 4.160065 TGAATGTGGATTATTTGCCTGTGG 59.840 41.667 0.00 0.00 0.00 4.17
3730 6263 1.278985 ACCGTGGAATGATCTGAAGCA 59.721 47.619 0.00 0.00 0.00 3.91
3748 6281 3.561725 CCAGAGTTGAAGACACTTTCACC 59.438 47.826 0.00 0.00 36.84 4.02
3770 6303 6.806249 TGTGATCAACAAAGTGAACAGTTTTC 59.194 34.615 0.00 2.15 35.24 2.29
3781 6314 6.845758 ATCAATCCATGTGATCAACAAAGT 57.154 33.333 0.00 0.00 43.61 2.66
3851 6384 6.030548 TCTCTTTGATCGTCCATATGATCC 57.969 41.667 3.65 0.00 44.43 3.36


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

AutoCloner maintained by Alex Coulton.