Multiple sequence alignment - TraesCS5D01G450200

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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 TraesCS5D01G450200 chr5D 100.000 6027 0 0 1 6027 498735312 498729286 0.000000e+00 11130.0
1 TraesCS5D01G450200 chr5D 97.096 861 22 2 1 859 9148686 9147827 0.000000e+00 1448.0
2 TraesCS5D01G450200 chr5D 97.096 861 22 3 1 859 415883606 415884465 0.000000e+00 1448.0
3 TraesCS5D01G450200 chr5D 100.000 156 0 0 6382 6537 498728931 498728776 8.290000e-74 289.0
4 TraesCS5D01G450200 chr5D 93.204 103 5 2 5898 5998 498729522 498729420 4.080000e-32 150.0
5 TraesCS5D01G450200 chr5D 98.182 55 1 0 5951 6005 91345452 91345506 5.400000e-16 97.1
6 TraesCS5D01G450200 chr5B 94.168 4287 144 50 1426 5660 618286401 618282169 0.000000e+00 6434.0
7 TraesCS5D01G450200 chr5B 92.974 427 15 5 920 1331 618287134 618286708 5.600000e-170 608.0
8 TraesCS5D01G450200 chr5B 83.085 201 24 9 5656 5852 507804258 507804452 2.420000e-39 174.0
9 TraesCS5D01G450200 chr5A 92.215 3982 155 54 920 4825 623026644 623022742 0.000000e+00 5493.0
10 TraesCS5D01G450200 chr5A 97.143 805 19 2 4856 5660 623022745 623021945 0.000000e+00 1356.0
11 TraesCS5D01G450200 chr5A 97.203 143 4 0 6395 6537 502528328 502528470 6.550000e-60 243.0
12 TraesCS5D01G450200 chr5A 85.366 123 3 1 5920 6027 502528003 502528125 5.360000e-21 113.0
13 TraesCS5D01G450200 chr6D 97.213 861 20 4 1 859 138515078 138515936 0.000000e+00 1454.0
14 TraesCS5D01G450200 chr4D 97.213 861 21 2 1 859 8095570 8094711 0.000000e+00 1454.0
15 TraesCS5D01G450200 chr4D 97.100 862 21 3 1 859 477947832 477948692 0.000000e+00 1450.0
16 TraesCS5D01G450200 chr4D 97.093 860 24 1 1 859 498815642 498814783 0.000000e+00 1448.0
17 TraesCS5D01G450200 chr4D 93.305 239 16 0 5660 5898 211481246 211481484 2.900000e-93 353.0
18 TraesCS5D01G450200 chr4D 96.129 155 6 0 6383 6537 211481747 211481901 3.030000e-63 254.0
19 TraesCS5D01G450200 chr4D 93.103 87 6 0 5898 5984 211481377 211481463 1.910000e-25 128.0
20 TraesCS5D01G450200 chr4D 96.296 54 2 0 5974 6027 211481468 211481521 9.030000e-14 89.8
21 TraesCS5D01G450200 chr7D 97.096 861 23 2 1 859 235297027 235297887 0.000000e+00 1450.0
22 TraesCS5D01G450200 chr7D 86.505 578 43 15 3124 3699 499627168 499626624 2.610000e-168 603.0
23 TraesCS5D01G450200 chr7D 89.011 455 36 10 3866 4309 499626503 499626052 9.580000e-153 551.0
24 TraesCS5D01G450200 chr7D 84.456 193 17 4 2727 2909 499627402 499627213 1.870000e-40 178.0
25 TraesCS5D01G450200 chr1D 97.100 862 22 2 1 859 37617781 37616920 0.000000e+00 1450.0
26 TraesCS5D01G450200 chr1D 97.100 862 22 2 1 859 37658865 37658004 0.000000e+00 1450.0
27 TraesCS5D01G450200 chr1D 90.000 70 3 1 5951 6020 375208694 375208759 3.250000e-13 87.9
28 TraesCS5D01G450200 chr3A 84.393 1416 158 41 3105 4496 734840488 734841864 0.000000e+00 1332.0
29 TraesCS5D01G450200 chr3A 83.969 1416 164 41 3105 4496 734885872 734887248 0.000000e+00 1299.0
30 TraesCS5D01G450200 chr3A 85.393 712 89 14 4630 5333 734842422 734843126 0.000000e+00 725.0
31 TraesCS5D01G450200 chr3A 85.112 712 91 11 4630 5333 734887806 734888510 0.000000e+00 713.0
32 TraesCS5D01G450200 chr3A 85.965 399 49 6 1847 2239 734839312 734839709 2.820000e-113 420.0
33 TraesCS5D01G450200 chr3A 85.965 399 49 6 1847 2239 734884692 734885089 2.820000e-113 420.0
34 TraesCS5D01G450200 chr3A 77.858 691 90 27 2271 2906 734885150 734885832 2.880000e-98 370.0
35 TraesCS5D01G450200 chr3A 77.713 691 87 29 2271 2906 734839770 734840448 1.730000e-95 361.0
36 TraesCS5D01G450200 chr3A 95.673 208 9 0 1124 1331 734838545 734838752 1.050000e-87 335.0
37 TraesCS5D01G450200 chr3A 87.879 198 22 2 5658 5855 28480221 28480026 1.420000e-56 231.0
38 TraesCS5D01G450200 chr3A 87.879 198 19 4 5658 5855 34059077 34058885 1.830000e-55 228.0
39 TraesCS5D01G450200 chr3A 95.385 65 1 2 5898 5962 34058947 34058885 1.160000e-17 102.0
40 TraesCS5D01G450200 chr3D 84.778 1327 150 38 3105 4413 604686049 604687341 0.000000e+00 1284.0
41 TraesCS5D01G450200 chr3D 82.282 666 96 16 4673 5333 604687528 604688176 2.060000e-154 556.0
42 TraesCS5D01G450200 chr3D 86.967 399 47 1 1847 2240 604684863 604685261 1.670000e-120 444.0
43 TraesCS5D01G450200 chr3D 78.775 702 84 32 2264 2906 604685314 604686009 1.700000e-110 411.0
44 TraesCS5D01G450200 chr3D 88.079 302 27 6 1124 1422 604684139 604684434 3.750000e-92 350.0
45 TraesCS5D01G450200 chr3B 83.769 1300 140 46 3149 4427 812459866 812461115 0.000000e+00 1166.0
46 TraesCS5D01G450200 chr3B 85.674 712 90 9 4630 5333 812461519 812462226 0.000000e+00 739.0
47 TraesCS5D01G450200 chr3B 79.446 1119 145 53 1847 2906 812458702 812459794 0.000000e+00 713.0
48 TraesCS5D01G450200 chr3B 87.220 313 32 7 1119 1424 812458053 812458364 3.750000e-92 350.0
49 TraesCS5D01G450200 chr3B 91.213 239 21 0 5660 5898 397427095 397427333 6.320000e-85 326.0
50 TraesCS5D01G450200 chr2B 87.276 558 42 17 3144 3699 30335310 30334780 1.560000e-170 610.0
51 TraesCS5D01G450200 chr2B 89.302 430 36 7 3866 4286 30334660 30334232 1.250000e-146 531.0
52 TraesCS5D01G450200 chr2B 88.500 200 23 0 5656 5855 236810661 236810462 6.550000e-60 243.0
53 TraesCS5D01G450200 chr2B 94.872 156 7 1 6382 6537 638526926 638526772 6.550000e-60 243.0
54 TraesCS5D01G450200 chr2B 95.385 65 3 0 5898 5962 236810526 236810462 3.220000e-18 104.0
55 TraesCS5D01G450200 chr7A 86.505 578 47 18 3124 3699 109230668 109230120 2.020000e-169 606.0
56 TraesCS5D01G450200 chr7A 86.332 578 47 19 3124 3699 61493609 61493062 9.380000e-168 601.0
57 TraesCS5D01G450200 chr7A 88.514 444 40 7 3866 4299 61492944 61492502 1.610000e-145 527.0
58 TraesCS5D01G450200 chr7A 96.129 155 6 0 6382 6536 676069668 676069822 3.030000e-63 254.0
59 TraesCS5D01G450200 chr7A 93.846 65 4 0 5920 5984 676069258 676069322 1.500000e-16 99.0
60 TraesCS5D01G450200 chr4B 89.227 427 36 7 3866 4283 642737942 642738367 5.810000e-145 525.0
61 TraesCS5D01G450200 chr4B 83.889 180 18 3 2727 2896 642737048 642737226 1.890000e-35 161.0
62 TraesCS5D01G450200 chr1B 92.531 241 18 0 5658 5898 628014603 628014363 4.850000e-91 346.0
63 TraesCS5D01G450200 chr1B 98.077 156 3 0 6382 6537 665252625 665252780 8.350000e-69 272.0
64 TraesCS5D01G450200 chr1B 95.946 148 5 1 6390 6537 376051445 376051591 8.470000e-59 239.0
65 TraesCS5D01G450200 chr1B 83.333 192 26 5 5663 5852 125846771 125846958 8.710000e-39 172.0
66 TraesCS5D01G450200 chr1B 95.349 86 4 0 5897 5982 665251735 665251820 3.180000e-28 137.0
67 TraesCS5D01G450200 chr1B 84.553 123 4 1 5920 6027 376050688 376050810 2.490000e-19 108.0
68 TraesCS5D01G450200 chr7B 90.377 239 16 5 5660 5898 703590154 703589923 2.290000e-79 307.0
69 TraesCS5D01G450200 chr7B 97.403 154 4 0 6382 6535 703589695 703589542 5.030000e-66 263.0
70 TraesCS5D01G450200 chr7B 88.489 139 7 7 5898 6027 703590024 703589886 6.780000e-35 159.0
71 TraesCS5D01G450200 chr1A 97.403 154 4 0 6384 6537 583951858 583952011 5.030000e-66 263.0
72 TraesCS5D01G450200 chr1A 86.179 123 2 1 5920 6027 583951493 583951615 1.150000e-22 119.0
73 TraesCS5D01G450200 chr6B 94.872 156 7 1 6382 6537 716387457 716387611 6.550000e-60 243.0
74 TraesCS5D01G450200 chr6B 83.621 116 4 1 5922 6022 716387012 716387127 1.940000e-15 95.3
75 TraesCS5D01G450200 chr6A 85.366 123 3 1 5920 6027 59997611 59997733 5.360000e-21 113.0
76 TraesCS5D01G450200 chr2A 90.244 82 8 0 5816 5897 48481405 48481486 2.490000e-19 108.0
77 TraesCS5D01G450200 chr4A 90.123 81 6 2 5920 5998 621963625 621963545 3.220000e-18 104.0


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 TraesCS5D01G450200 chr5D 498728776 498735312 6536 True 5709.5 11130 100.000000 1 6537 2 chr5D.!!$R3 6536
1 TraesCS5D01G450200 chr5D 9147827 9148686 859 True 1448.0 1448 97.096000 1 859 1 chr5D.!!$R1 858
2 TraesCS5D01G450200 chr5D 415883606 415884465 859 False 1448.0 1448 97.096000 1 859 1 chr5D.!!$F2 858
3 TraesCS5D01G450200 chr5B 618282169 618287134 4965 True 3521.0 6434 93.571000 920 5660 2 chr5B.!!$R1 4740
4 TraesCS5D01G450200 chr5A 623021945 623026644 4699 True 3424.5 5493 94.679000 920 5660 2 chr5A.!!$R1 4740
5 TraesCS5D01G450200 chr6D 138515078 138515936 858 False 1454.0 1454 97.213000 1 859 1 chr6D.!!$F1 858
6 TraesCS5D01G450200 chr4D 8094711 8095570 859 True 1454.0 1454 97.213000 1 859 1 chr4D.!!$R1 858
7 TraesCS5D01G450200 chr4D 477947832 477948692 860 False 1450.0 1450 97.100000 1 859 1 chr4D.!!$F1 858
8 TraesCS5D01G450200 chr4D 498814783 498815642 859 True 1448.0 1448 97.093000 1 859 1 chr4D.!!$R2 858
9 TraesCS5D01G450200 chr4D 211481246 211481901 655 False 206.2 353 94.708250 5660 6537 4 chr4D.!!$F2 877
10 TraesCS5D01G450200 chr7D 235297027 235297887 860 False 1450.0 1450 97.096000 1 859 1 chr7D.!!$F1 858
11 TraesCS5D01G450200 chr7D 499626052 499627402 1350 True 444.0 603 86.657333 2727 4309 3 chr7D.!!$R1 1582
12 TraesCS5D01G450200 chr1D 37616920 37617781 861 True 1450.0 1450 97.100000 1 859 1 chr1D.!!$R1 858
13 TraesCS5D01G450200 chr1D 37658004 37658865 861 True 1450.0 1450 97.100000 1 859 1 chr1D.!!$R2 858
14 TraesCS5D01G450200 chr3A 734884692 734888510 3818 False 700.5 1299 83.226000 1847 5333 4 chr3A.!!$F2 3486
15 TraesCS5D01G450200 chr3A 734838545 734843126 4581 False 634.6 1332 85.827400 1124 5333 5 chr3A.!!$F1 4209
16 TraesCS5D01G450200 chr3D 604684139 604688176 4037 False 609.0 1284 84.176200 1124 5333 5 chr3D.!!$F1 4209
17 TraesCS5D01G450200 chr3B 812458053 812462226 4173 False 742.0 1166 84.027250 1119 5333 4 chr3B.!!$F2 4214
18 TraesCS5D01G450200 chr2B 30334232 30335310 1078 True 570.5 610 88.289000 3144 4286 2 chr2B.!!$R2 1142
19 TraesCS5D01G450200 chr7A 109230120 109230668 548 True 606.0 606 86.505000 3124 3699 1 chr7A.!!$R1 575
20 TraesCS5D01G450200 chr7A 61492502 61493609 1107 True 564.0 601 87.423000 3124 4299 2 chr7A.!!$R2 1175
21 TraesCS5D01G450200 chr4B 642737048 642738367 1319 False 343.0 525 86.558000 2727 4283 2 chr4B.!!$F1 1556
22 TraesCS5D01G450200 chr1B 665251735 665252780 1045 False 204.5 272 96.713000 5897 6537 2 chr1B.!!$F3 640
23 TraesCS5D01G450200 chr7B 703589542 703590154 612 True 243.0 307 92.089667 5660 6535 3 chr7B.!!$R1 875

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
910 921 0.107410 ACAGAGGGTGTGCACGAAAA 60.107 50.000 13.13 0.00 38.28 2.29 F
946 957 0.178068 ATGATACGGAGGGTGTGCAC 59.822 55.000 10.75 10.75 0.00 4.57 F
1755 2063 0.179023 TCATGCTGCGATATTGGGCA 60.179 50.000 0.00 0.00 37.63 5.36 F
2899 3337 0.613260 TGTGCTCTATCCCGTTTGCT 59.387 50.000 0.00 0.00 0.00 3.91 F
2926 3374 0.958382 TGGCGCAACAATGGAGTACC 60.958 55.000 10.83 0.00 0.00 3.34 F
3026 3475 1.216930 ACTTTGTAAACCAGGCACCCT 59.783 47.619 0.00 0.00 0.00 4.34 F
4358 4855 1.466167 GACATGGCAGTACAAGCAGTG 59.534 52.381 11.68 10.98 0.00 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1755 2063 0.537188 CACCGGCCACTAGAGTCAAT 59.463 55.000 0.00 0.0 0.00 2.57 R
2908 3356 0.676782 AGGTACTCCATTGTTGCGCC 60.677 55.000 4.18 0.0 35.89 6.53 R
3516 3973 3.939592 GGGAAAATGGTGTCACTAGCTAC 59.060 47.826 2.35 0.0 0.00 3.58 R
4099 4582 1.089920 CCTCAAAATCAGGACTGCGG 58.910 55.000 0.00 0.0 31.91 5.69 R
4916 5870 2.096220 TTGCGGTTCCGTGCTATTAA 57.904 45.000 12.81 0.0 0.00 1.40 R
4941 5895 0.251634 CCTCTGAAGGAGAAGGGTGC 59.748 60.000 0.00 0.0 46.67 5.01 R
5656 6610 0.101399 ACGCGTGGAGATGCTCTAAG 59.899 55.000 12.93 0.0 31.21 2.18 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 36 1.678970 GGCTGGCCGAGAAAATGGT 60.679 57.895 0.00 0.00 0.00 3.55
695 706 1.003580 TCGTACAGTCGTACTCCCCTT 59.996 52.381 0.00 0.00 44.97 3.95
702 713 2.693762 CGTACTCCCCTTCGCGTGA 61.694 63.158 5.77 0.00 0.00 4.35
725 736 1.738099 CAACTGCCGAGTCTTCCCG 60.738 63.158 0.00 0.00 0.00 5.14
740 751 4.675029 CCGGCCTCCGTGTCGTTT 62.675 66.667 0.00 0.00 46.80 3.60
859 870 4.767255 GAGGCCGACAGCTGGGTG 62.767 72.222 19.93 6.90 43.05 4.61
863 874 4.624364 CCGACAGCTGGGTGTGCA 62.624 66.667 19.93 0.00 0.00 4.57
864 875 3.349006 CGACAGCTGGGTGTGCAC 61.349 66.667 19.93 10.75 0.00 4.57
865 876 3.349006 GACAGCTGGGTGTGCACG 61.349 66.667 19.93 0.00 0.00 5.34
866 877 3.807631 GACAGCTGGGTGTGCACGA 62.808 63.158 19.93 0.00 0.00 4.35
867 878 2.591429 CAGCTGGGTGTGCACGAA 60.591 61.111 13.13 0.00 0.00 3.85
868 879 2.186160 CAGCTGGGTGTGCACGAAA 61.186 57.895 13.13 0.00 0.00 3.46
869 880 1.453015 AGCTGGGTGTGCACGAAAA 60.453 52.632 13.13 0.00 0.00 2.29
870 881 0.823356 AGCTGGGTGTGCACGAAAAT 60.823 50.000 13.13 0.00 0.00 1.82
871 882 0.878416 GCTGGGTGTGCACGAAAATA 59.122 50.000 13.13 0.00 0.00 1.40
872 883 1.401018 GCTGGGTGTGCACGAAAATAC 60.401 52.381 13.13 3.08 0.00 1.89
873 884 1.876799 CTGGGTGTGCACGAAAATACA 59.123 47.619 13.13 3.42 0.00 2.29
874 885 1.876799 TGGGTGTGCACGAAAATACAG 59.123 47.619 13.13 0.00 0.00 2.74
875 886 1.877443 GGGTGTGCACGAAAATACAGT 59.123 47.619 13.13 0.00 0.00 3.55
876 887 2.095919 GGGTGTGCACGAAAATACAGTC 60.096 50.000 13.13 0.00 0.00 3.51
877 888 2.546368 GGTGTGCACGAAAATACAGTCA 59.454 45.455 13.13 0.00 0.00 3.41
878 889 3.188460 GGTGTGCACGAAAATACAGTCAT 59.812 43.478 13.13 0.00 0.00 3.06
879 890 4.390603 GGTGTGCACGAAAATACAGTCATA 59.609 41.667 13.13 0.00 0.00 2.15
880 891 5.064707 GGTGTGCACGAAAATACAGTCATAT 59.935 40.000 13.13 0.00 0.00 1.78
881 892 6.403200 GGTGTGCACGAAAATACAGTCATATT 60.403 38.462 13.13 0.00 0.00 1.28
882 893 7.201574 GGTGTGCACGAAAATACAGTCATATTA 60.202 37.037 13.13 0.00 0.00 0.98
883 894 8.172484 GTGTGCACGAAAATACAGTCATATTAA 58.828 33.333 13.13 0.00 0.00 1.40
884 895 8.888716 TGTGCACGAAAATACAGTCATATTAAT 58.111 29.630 13.13 0.00 0.00 1.40
903 914 7.986085 ATTAATAATGATACAGAGGGTGTGC 57.014 36.000 0.00 0.00 40.69 4.57
904 915 5.372343 AATAATGATACAGAGGGTGTGCA 57.628 39.130 0.00 0.00 40.69 4.57
905 916 2.698855 ATGATACAGAGGGTGTGCAC 57.301 50.000 10.75 10.75 40.69 4.57
906 917 0.246360 TGATACAGAGGGTGTGCACG 59.754 55.000 13.13 0.00 40.69 5.34
907 918 0.530744 GATACAGAGGGTGTGCACGA 59.469 55.000 13.13 0.00 40.69 4.35
908 919 0.973632 ATACAGAGGGTGTGCACGAA 59.026 50.000 13.13 0.00 40.69 3.85
909 920 0.753867 TACAGAGGGTGTGCACGAAA 59.246 50.000 13.13 0.00 40.69 3.46
910 921 0.107410 ACAGAGGGTGTGCACGAAAA 60.107 50.000 13.13 0.00 38.28 2.29
911 922 1.238439 CAGAGGGTGTGCACGAAAAT 58.762 50.000 13.13 0.00 0.00 1.82
912 923 2.224426 ACAGAGGGTGTGCACGAAAATA 60.224 45.455 13.13 0.00 38.28 1.40
913 924 2.159627 CAGAGGGTGTGCACGAAAATAC 59.840 50.000 13.13 3.08 0.00 1.89
914 925 2.147958 GAGGGTGTGCACGAAAATACA 58.852 47.619 13.13 0.00 0.00 2.29
915 926 2.151202 AGGGTGTGCACGAAAATACAG 58.849 47.619 13.13 0.00 0.00 2.74
916 927 1.877443 GGGTGTGCACGAAAATACAGT 59.123 47.619 13.13 0.00 0.00 3.55
917 928 2.292292 GGGTGTGCACGAAAATACAGTT 59.708 45.455 13.13 0.00 0.00 3.16
918 929 3.499157 GGGTGTGCACGAAAATACAGTTA 59.501 43.478 13.13 0.00 0.00 2.24
946 957 0.178068 ATGATACGGAGGGTGTGCAC 59.822 55.000 10.75 10.75 0.00 4.57
955 967 2.147958 GAGGGTGTGCACGAAAATACA 58.852 47.619 13.13 0.00 0.00 2.29
1000 1015 2.759114 CCAGCAGCTTTCCTCCCA 59.241 61.111 0.00 0.00 0.00 4.37
1250 1288 1.439228 CATCAGCGTCACCCTCGAT 59.561 57.895 0.00 0.00 0.00 3.59
1363 1413 0.395862 CCCCTGCCTCGACTCTTCTA 60.396 60.000 0.00 0.00 0.00 2.10
1393 1447 3.431725 CTTTTCGCCCCACGCTCC 61.432 66.667 0.00 0.00 43.23 4.70
1458 1708 3.238788 TCTAGGGTGGATGCTATCGAA 57.761 47.619 0.00 0.00 0.00 3.71
1464 1714 2.564947 GGTGGATGCTATCGAATCCTCT 59.435 50.000 13.62 0.00 42.51 3.69
1468 1718 3.510719 GATGCTATCGAATCCTCTGCTC 58.489 50.000 0.00 0.00 0.00 4.26
1469 1719 1.615883 TGCTATCGAATCCTCTGCTCC 59.384 52.381 0.00 0.00 0.00 4.70
1471 1721 0.598562 TATCGAATCCTCTGCTCCGC 59.401 55.000 0.00 0.00 0.00 5.54
1472 1722 2.093537 ATCGAATCCTCTGCTCCGCC 62.094 60.000 0.00 0.00 0.00 6.13
1473 1723 2.279784 GAATCCTCTGCTCCGCCG 60.280 66.667 0.00 0.00 0.00 6.46
1475 1725 2.691674 GAATCCTCTGCTCCGCCGAG 62.692 65.000 0.00 0.00 39.12 4.63
1476 1726 4.742649 TCCTCTGCTCCGCCGAGT 62.743 66.667 3.98 0.00 38.03 4.18
1477 1727 4.504916 CCTCTGCTCCGCCGAGTG 62.505 72.222 3.98 0.00 38.03 3.51
1478 1728 3.753434 CTCTGCTCCGCCGAGTGT 61.753 66.667 3.98 0.00 38.49 3.55
1535 1785 3.734463 TCTGTCTCGTGTTTTTGGCATA 58.266 40.909 0.00 0.00 0.00 3.14
1544 1798 4.541779 GTGTTTTTGGCATAACACGATGA 58.458 39.130 22.18 0.00 43.03 2.92
1547 1801 5.861251 TGTTTTTGGCATAACACGATGATTC 59.139 36.000 10.53 0.00 29.82 2.52
1561 1815 3.924073 CGATGATTCGGTTAGTGTTGACA 59.076 43.478 0.00 0.00 41.74 3.58
1604 1898 0.613260 TGGATCGGGACCTGTTTGAG 59.387 55.000 0.00 0.00 0.00 3.02
1608 1902 3.243907 GGATCGGGACCTGTTTGAGATAG 60.244 52.174 0.00 0.00 0.00 2.08
1609 1903 1.480954 TCGGGACCTGTTTGAGATAGC 59.519 52.381 0.00 0.00 0.00 2.97
1610 1904 1.473434 CGGGACCTGTTTGAGATAGCC 60.473 57.143 0.00 0.00 0.00 3.93
1653 1947 3.423848 CGGAGCCCTGAAAAATTGC 57.576 52.632 0.00 0.00 0.00 3.56
1680 1975 1.115326 AGAAGGGCCAAAAGGCACAC 61.115 55.000 11.81 4.81 44.77 3.82
1689 1992 3.860641 CCAAAAGGCACACTTCTGTTTT 58.139 40.909 0.00 0.00 38.85 2.43
1709 2012 6.073058 TGTTTTTATTGTCTGCACTAGCTCTG 60.073 38.462 0.00 0.00 42.74 3.35
1710 2013 5.405935 TTTATTGTCTGCACTAGCTCTGA 57.594 39.130 0.00 0.00 42.74 3.27
1711 2014 3.969287 ATTGTCTGCACTAGCTCTGAA 57.031 42.857 0.00 0.00 42.74 3.02
1712 2015 3.309961 TTGTCTGCACTAGCTCTGAAG 57.690 47.619 0.00 0.00 42.74 3.02
1713 2016 2.242926 TGTCTGCACTAGCTCTGAAGT 58.757 47.619 0.00 0.00 42.74 3.01
1714 2017 3.421844 TGTCTGCACTAGCTCTGAAGTA 58.578 45.455 0.00 0.00 42.74 2.24
1715 2018 3.191581 TGTCTGCACTAGCTCTGAAGTAC 59.808 47.826 0.00 0.00 42.74 2.73
1716 2019 3.442273 GTCTGCACTAGCTCTGAAGTACT 59.558 47.826 0.00 0.00 42.74 2.73
1721 2024 5.106118 TGCACTAGCTCTGAAGTACTTACTG 60.106 44.000 8.42 6.82 42.74 2.74
1727 2035 7.469537 AGCTCTGAAGTACTTACTGTATTGT 57.530 36.000 8.42 0.00 36.50 2.71
1733 2041 5.757099 AGTACTTACTGTATTGTTGCCCT 57.243 39.130 0.00 0.00 34.72 5.19
1744 2052 3.066190 TTGCCCTGCTCATGCTGC 61.066 61.111 0.00 0.00 40.48 5.25
1748 2056 1.070275 CCCTGCTCATGCTGCGATA 59.930 57.895 0.00 0.00 40.48 2.92
1749 2057 0.321387 CCCTGCTCATGCTGCGATAT 60.321 55.000 0.00 0.00 40.48 1.63
1753 2061 0.520404 GCTCATGCTGCGATATTGGG 59.480 55.000 0.00 0.00 36.03 4.12
1755 2063 0.179023 TCATGCTGCGATATTGGGCA 60.179 50.000 0.00 0.00 37.63 5.36
1756 2064 0.885879 CATGCTGCGATATTGGGCAT 59.114 50.000 0.00 0.00 43.19 4.40
1758 2066 0.669619 TGCTGCGATATTGGGCATTG 59.330 50.000 0.00 0.00 38.69 2.82
1762 2070 2.221169 TGCGATATTGGGCATTGACTC 58.779 47.619 0.00 0.00 33.52 3.36
1763 2071 2.158769 TGCGATATTGGGCATTGACTCT 60.159 45.455 0.00 0.00 33.52 3.24
1764 2072 3.070878 TGCGATATTGGGCATTGACTCTA 59.929 43.478 0.00 0.00 33.52 2.43
1765 2073 3.681897 GCGATATTGGGCATTGACTCTAG 59.318 47.826 0.00 0.00 0.00 2.43
1800 2111 7.326305 GCAAGATGATTCTATAGCAATGCTTTG 59.674 37.037 14.85 8.23 40.44 2.77
1811 2150 2.483538 GCAATGCTTTGGCCGGAATAAT 60.484 45.455 5.05 0.00 37.74 1.28
2546 2952 3.274288 CAGACTTAGAAATGGCTGGTCC 58.726 50.000 0.00 0.00 0.00 4.46
2549 2955 4.783227 AGACTTAGAAATGGCTGGTCCTAA 59.217 41.667 0.00 0.00 35.26 2.69
2584 2994 7.189087 TGATATACTGCTAATATCTGGTCCCA 58.811 38.462 11.95 0.00 37.27 4.37
2643 3053 8.518702 TCTGCATGCTTGTTTTGTACAAATATA 58.481 29.630 21.17 4.50 45.69 0.86
2869 3307 5.859114 GTCTGTACTGATACATTATGGAGCG 59.141 44.000 5.69 0.00 40.57 5.03
2892 3330 0.755686 CCCTGTCTGTGCTCTATCCC 59.244 60.000 0.00 0.00 0.00 3.85
2899 3337 0.613260 TGTGCTCTATCCCGTTTGCT 59.387 50.000 0.00 0.00 0.00 3.91
2900 3338 1.003118 TGTGCTCTATCCCGTTTGCTT 59.997 47.619 0.00 0.00 0.00 3.91
2901 3339 1.398390 GTGCTCTATCCCGTTTGCTTG 59.602 52.381 0.00 0.00 0.00 4.01
2902 3340 1.277842 TGCTCTATCCCGTTTGCTTGA 59.722 47.619 0.00 0.00 0.00 3.02
2908 3356 5.056480 TCTATCCCGTTTGCTTGATGTATG 58.944 41.667 0.00 0.00 0.00 2.39
2926 3374 0.958382 TGGCGCAACAATGGAGTACC 60.958 55.000 10.83 0.00 0.00 3.34
3026 3475 1.216930 ACTTTGTAAACCAGGCACCCT 59.783 47.619 0.00 0.00 0.00 4.34
3036 3488 1.545841 CAGGCACCCTTCTTTTACCC 58.454 55.000 0.00 0.00 0.00 3.69
3039 3491 2.168496 GGCACCCTTCTTTTACCCTTC 58.832 52.381 0.00 0.00 0.00 3.46
3041 3493 3.009805 GGCACCCTTCTTTTACCCTTCTA 59.990 47.826 0.00 0.00 0.00 2.10
3313 3769 6.137794 TGCTTTTCTGTTGGAAAACGATTA 57.862 33.333 0.00 0.00 45.54 1.75
3431 3887 5.357742 AGCAGTGGTATGTCAATGTGATA 57.642 39.130 0.00 0.00 35.46 2.15
3516 3973 7.432869 TGGTTTCATTTACACCAAATCTCAAG 58.567 34.615 0.00 0.00 37.66 3.02
3536 3995 5.932303 TCAAGTAGCTAGTGACACCATTTTC 59.068 40.000 0.73 0.00 0.00 2.29
3729 4189 9.677567 GTTTTTAACAGTTCACATGATGTACAT 57.322 29.630 8.43 8.43 40.17 2.29
3775 4248 6.282167 TGAAGCTGCAATTTGAAATCTGAAA 58.718 32.000 1.02 0.00 0.00 2.69
4358 4855 1.466167 GACATGGCAGTACAAGCAGTG 59.534 52.381 11.68 10.98 0.00 3.66
4385 4882 3.495331 TGCACTGGACCAAACATGTATT 58.505 40.909 0.00 0.00 0.00 1.89
4473 4970 6.389091 TGCATGTTTCTGAAAAATAGCGAAT 58.611 32.000 4.09 0.00 0.00 3.34
4671 5608 8.752766 AGTTTGAGTTATGAAAAGAATGCATG 57.247 30.769 0.00 0.00 0.00 4.06
4673 5610 9.362539 GTTTGAGTTATGAAAAGAATGCATGAT 57.637 29.630 0.00 0.00 0.00 2.45
4780 5725 4.634004 TCTGGTATGCATTTCACCTAAACG 59.366 41.667 16.29 2.98 33.28 3.60
4804 5754 5.332743 ACAAATCATTGGTACTGGATGGTT 58.667 37.500 0.00 0.00 41.01 3.67
4916 5870 2.982130 CTGGGCCTAACGCTGTCT 59.018 61.111 4.53 0.00 37.74 3.41
4941 5895 1.008995 CACGGAACCGCAAAACTGG 60.009 57.895 13.32 0.00 44.19 4.00
4963 5917 1.284313 CCCTTCTCCTTCAGAGGCTT 58.716 55.000 0.00 0.00 43.44 4.35
5069 6023 9.865321 GTTTCTAGGTATACTACAAACATGTGA 57.135 33.333 0.00 0.00 39.17 3.58
5297 6251 1.820519 GCCTTGATTGATTCAGCCACA 59.179 47.619 0.00 0.00 35.27 4.17
5340 6294 2.267188 TTGGACGACGATAGGTTTCG 57.733 50.000 0.00 0.00 44.56 3.46
5606 6560 9.520204 ACTTTGGCATTCGAAAATAATAATGAG 57.480 29.630 0.00 0.00 32.29 2.90
5607 6561 9.520204 CTTTGGCATTCGAAAATAATAATGAGT 57.480 29.630 0.00 0.00 32.29 3.41
5656 6610 6.144078 ACAAATTGTTACTTCTGGTGTTCC 57.856 37.500 0.00 0.00 0.00 3.62
5737 6691 0.380733 CCGGCGGAAATTTAGGCTTC 59.619 55.000 24.41 0.00 0.00 3.86
5743 6697 2.419574 CGGAAATTTAGGCTTCGGGAGA 60.420 50.000 0.00 0.00 0.00 3.71
5765 6719 2.764637 AATTTTCCCAGCCGTCGCCT 62.765 55.000 0.00 0.00 34.57 5.52
5782 6736 0.036010 CCTCACCCAAGACGCATTCT 60.036 55.000 0.00 0.00 35.32 2.40
5793 6747 2.508891 CGCATTCTGAGGACGCGTC 61.509 63.158 30.67 30.67 38.22 5.19
5865 6819 4.555709 GTCCACCACGCACCACCA 62.556 66.667 0.00 0.00 0.00 4.17
5866 6820 4.248842 TCCACCACGCACCACCAG 62.249 66.667 0.00 0.00 0.00 4.00
5875 6829 4.394712 CACCACCAGCCCTCCGTC 62.395 72.222 0.00 0.00 0.00 4.79
5878 6832 3.775654 CACCAGCCCTCCGTCCTC 61.776 72.222 0.00 0.00 0.00 3.71
5881 6835 4.135153 CAGCCCTCCGTCCTCGTG 62.135 72.222 0.00 0.00 35.01 4.35
5886 6840 3.827898 CTCCGTCCTCGTGCCCTC 61.828 72.222 0.00 0.00 35.01 4.30
5890 6844 4.131088 GTCCTCGTGCCCTCCGTC 62.131 72.222 0.00 0.00 0.00 4.79
5893 6847 4.135153 CTCGTGCCCTCCGTCCAG 62.135 72.222 0.00 0.00 0.00 3.86
5939 6893 2.202797 CCGTCTCCAGCACCATCG 60.203 66.667 0.00 0.00 0.00 3.84
5941 6895 1.215382 CGTCTCCAGCACCATCGAA 59.785 57.895 0.00 0.00 0.00 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 4.166725 AGCCCATTTCTCATTACTGATGGA 59.833 41.667 2.80 0.00 31.95 3.41
657 668 1.670967 CGAGGGTTTACTGGTTCGTCC 60.671 57.143 0.00 0.00 0.00 4.79
695 706 1.495584 GGCAGTTGTTTCTCACGCGA 61.496 55.000 15.93 0.00 0.00 5.87
702 713 2.484889 GAAGACTCGGCAGTTGTTTCT 58.515 47.619 0.00 0.00 30.63 2.52
725 736 2.726822 AAGGAAACGACACGGAGGCC 62.727 60.000 0.00 0.00 0.00 5.19
803 814 0.740868 AGATGCATGTCGGTCGTTGG 60.741 55.000 2.46 0.00 0.00 3.77
877 888 9.672673 GCACACCCTCTGTATCATTATTAATAT 57.327 33.333 0.00 0.00 0.00 1.28
878 889 8.655901 TGCACACCCTCTGTATCATTATTAATA 58.344 33.333 0.00 0.00 0.00 0.98
879 890 7.445402 GTGCACACCCTCTGTATCATTATTAAT 59.555 37.037 13.17 0.00 0.00 1.40
880 891 6.765989 GTGCACACCCTCTGTATCATTATTAA 59.234 38.462 13.17 0.00 0.00 1.40
881 892 6.288294 GTGCACACCCTCTGTATCATTATTA 58.712 40.000 13.17 0.00 0.00 0.98
882 893 5.126067 GTGCACACCCTCTGTATCATTATT 58.874 41.667 13.17 0.00 0.00 1.40
883 894 4.708177 GTGCACACCCTCTGTATCATTAT 58.292 43.478 13.17 0.00 0.00 1.28
884 895 3.430236 CGTGCACACCCTCTGTATCATTA 60.430 47.826 18.64 0.00 0.00 1.90
885 896 2.677902 CGTGCACACCCTCTGTATCATT 60.678 50.000 18.64 0.00 0.00 2.57
886 897 1.134699 CGTGCACACCCTCTGTATCAT 60.135 52.381 18.64 0.00 0.00 2.45
887 898 0.246360 CGTGCACACCCTCTGTATCA 59.754 55.000 18.64 0.00 0.00 2.15
888 899 0.530744 TCGTGCACACCCTCTGTATC 59.469 55.000 18.64 0.00 0.00 2.24
889 900 0.973632 TTCGTGCACACCCTCTGTAT 59.026 50.000 18.64 0.00 0.00 2.29
890 901 0.753867 TTTCGTGCACACCCTCTGTA 59.246 50.000 18.64 0.00 0.00 2.74
891 902 0.107410 TTTTCGTGCACACCCTCTGT 60.107 50.000 18.64 0.00 0.00 3.41
892 903 1.238439 ATTTTCGTGCACACCCTCTG 58.762 50.000 18.64 0.00 0.00 3.35
893 904 2.224426 TGTATTTTCGTGCACACCCTCT 60.224 45.455 18.64 0.00 0.00 3.69
894 905 2.147958 TGTATTTTCGTGCACACCCTC 58.852 47.619 18.64 1.35 0.00 4.30
895 906 2.151202 CTGTATTTTCGTGCACACCCT 58.849 47.619 18.64 0.00 0.00 4.34
896 907 1.877443 ACTGTATTTTCGTGCACACCC 59.123 47.619 18.64 0.00 0.00 4.61
897 908 3.619233 AACTGTATTTTCGTGCACACC 57.381 42.857 18.64 0.00 0.00 4.16
898 909 9.976255 TTAATATAACTGTATTTTCGTGCACAC 57.024 29.630 18.64 6.73 0.00 3.82
918 929 7.769044 GCACACCCTCCGTATCATTATTAATAT 59.231 37.037 0.00 0.00 0.00 1.28
926 937 0.908910 TGCACACCCTCCGTATCATT 59.091 50.000 0.00 0.00 0.00 2.57
955 967 1.450312 GCAGGCCGCAGTAATGACT 60.450 57.895 13.61 0.00 41.79 3.41
1000 1015 1.541620 GGGGAGGGGGAGTGAAGTT 60.542 63.158 0.00 0.00 0.00 2.66
1090 1119 2.928988 ATCTGATCAGGTCCCGCCGA 62.929 60.000 22.42 0.25 43.70 5.54
1103 1141 2.587247 CGCCCCCATCGGATCTGAT 61.587 63.158 11.47 11.47 0.00 2.90
1348 1386 5.186021 AGAAAAGAATAGAAGAGTCGAGGCA 59.814 40.000 0.00 0.00 0.00 4.75
1349 1387 5.656480 AGAAAAGAATAGAAGAGTCGAGGC 58.344 41.667 0.00 0.00 0.00 4.70
1350 1388 7.276878 GGAAAGAAAAGAATAGAAGAGTCGAGG 59.723 40.741 0.00 0.00 0.00 4.63
1363 1413 4.262463 GGGGCGAAAAGGAAAGAAAAGAAT 60.262 41.667 0.00 0.00 0.00 2.40
1418 1490 4.109675 AAACATCTCGGGGGCGGG 62.110 66.667 0.00 0.00 0.00 6.13
1424 1496 2.906354 CCCTAGAACAAACATCTCGGG 58.094 52.381 0.00 0.00 41.79 5.14
1482 1732 5.354234 TCAAGCTTGAAATCTAACGGATTCC 59.646 40.000 26.61 0.00 43.17 3.01
1484 1734 6.817765 TTCAAGCTTGAAATCTAACGGATT 57.182 33.333 34.01 0.00 43.62 3.01
1544 1798 4.695455 CCAATCTGTCAACACTAACCGAAT 59.305 41.667 0.00 0.00 0.00 3.34
1547 1801 2.159627 GCCAATCTGTCAACACTAACCG 59.840 50.000 0.00 0.00 0.00 4.44
1561 1815 1.211457 CTAAGCAGGGACAGCCAATCT 59.789 52.381 0.00 0.00 43.90 2.40
1571 1863 2.242926 CGATCCAGATCTAAGCAGGGA 58.757 52.381 0.00 0.00 35.72 4.20
1604 1898 1.008079 GCAAATGCAGCGGGCTATC 60.008 57.895 0.00 0.00 45.15 2.08
1641 1935 6.424812 CCTTCTTTACAAGGCAATTTTTCAGG 59.575 38.462 0.00 0.00 36.72 3.86
1649 1943 2.179427 GGCCCTTCTTTACAAGGCAAT 58.821 47.619 0.00 0.00 41.69 3.56
1653 1947 3.006859 CCTTTTGGCCCTTCTTTACAAGG 59.993 47.826 0.00 0.00 42.57 3.61
1680 1975 6.798959 GCTAGTGCAGACAATAAAAACAGAAG 59.201 38.462 0.00 0.00 39.41 2.85
1689 1992 5.047021 ACTTCAGAGCTAGTGCAGACAATAA 60.047 40.000 2.75 0.00 42.74 1.40
1709 2012 6.092259 CAGGGCAACAATACAGTAAGTACTTC 59.908 42.308 12.39 4.24 34.49 3.01
1710 2013 5.938125 CAGGGCAACAATACAGTAAGTACTT 59.062 40.000 13.68 13.68 34.49 2.24
1711 2014 5.488341 CAGGGCAACAATACAGTAAGTACT 58.512 41.667 0.00 0.00 34.49 2.73
1712 2015 4.094442 GCAGGGCAACAATACAGTAAGTAC 59.906 45.833 0.00 0.00 34.49 2.73
1713 2016 4.019681 AGCAGGGCAACAATACAGTAAGTA 60.020 41.667 0.00 0.00 35.85 2.24
1714 2017 3.081804 GCAGGGCAACAATACAGTAAGT 58.918 45.455 0.00 0.00 39.74 2.24
1715 2018 3.347216 AGCAGGGCAACAATACAGTAAG 58.653 45.455 0.00 0.00 39.74 2.34
1716 2019 3.244735 TGAGCAGGGCAACAATACAGTAA 60.245 43.478 0.00 0.00 39.74 2.24
1721 2024 1.202336 GCATGAGCAGGGCAACAATAC 60.202 52.381 0.00 0.00 41.58 1.89
1727 2035 3.066190 GCAGCATGAGCAGGGCAA 61.066 61.111 0.00 0.00 45.49 4.52
1733 2041 1.232119 CCAATATCGCAGCATGAGCA 58.768 50.000 10.58 0.00 45.49 4.26
1744 2052 4.687948 CACTAGAGTCAATGCCCAATATCG 59.312 45.833 0.00 0.00 0.00 2.92
1748 2056 2.684927 GCCACTAGAGTCAATGCCCAAT 60.685 50.000 0.00 0.00 0.00 3.16
1749 2057 1.340017 GCCACTAGAGTCAATGCCCAA 60.340 52.381 0.00 0.00 0.00 4.12
1753 2061 0.811616 CCGGCCACTAGAGTCAATGC 60.812 60.000 2.24 0.00 0.00 3.56
1755 2063 0.537188 CACCGGCCACTAGAGTCAAT 59.463 55.000 0.00 0.00 0.00 2.57
1756 2064 1.972198 CACCGGCCACTAGAGTCAA 59.028 57.895 0.00 0.00 0.00 3.18
1758 2066 2.167398 TTGCACCGGCCACTAGAGTC 62.167 60.000 0.00 0.00 40.13 3.36
1762 2070 1.091771 CATCTTGCACCGGCCACTAG 61.092 60.000 0.00 0.00 40.13 2.57
1763 2071 1.078497 CATCTTGCACCGGCCACTA 60.078 57.895 0.00 0.00 40.13 2.74
1764 2072 2.202236 ATCATCTTGCACCGGCCACT 62.202 55.000 0.00 0.00 40.13 4.00
1765 2073 1.315257 AATCATCTTGCACCGGCCAC 61.315 55.000 0.00 0.00 40.13 5.01
1800 2111 1.963515 AGCAATTCCATTATTCCGGCC 59.036 47.619 0.00 0.00 0.00 6.13
1811 2150 3.490439 TCTGAACAGACAGCAATTCCA 57.510 42.857 0.00 0.00 37.75 3.53
2255 2629 4.019321 GCTAGAAATGCATCTACCCCCATA 60.019 45.833 0.00 0.00 0.00 2.74
2546 2952 9.764363 TTAGCAGTATATCATGGAACTTGTTAG 57.236 33.333 0.00 0.00 0.00 2.34
2584 2994 4.536765 ACAATCAGGACAAAACAAGACCT 58.463 39.130 0.00 0.00 0.00 3.85
2725 3153 3.129988 GCTATTGGCATGAAAGCAAGACT 59.870 43.478 0.00 0.00 41.35 3.24
2892 3330 1.813896 CGCCATACATCAAGCAAACG 58.186 50.000 0.00 0.00 0.00 3.60
2899 3337 2.159268 CCATTGTTGCGCCATACATCAA 60.159 45.455 4.18 0.00 32.83 2.57
2900 3338 1.404748 CCATTGTTGCGCCATACATCA 59.595 47.619 4.18 0.00 0.00 3.07
2901 3339 1.675483 TCCATTGTTGCGCCATACATC 59.325 47.619 4.18 0.00 0.00 3.06
2902 3340 1.677576 CTCCATTGTTGCGCCATACAT 59.322 47.619 4.18 0.00 0.00 2.29
2908 3356 0.676782 AGGTACTCCATTGTTGCGCC 60.677 55.000 4.18 0.00 35.89 6.53
3039 3491 9.148104 AGCTTAAAGTTCGGTACAAAGTATTAG 57.852 33.333 0.00 0.00 0.00 1.73
3041 3493 7.974482 AGCTTAAAGTTCGGTACAAAGTATT 57.026 32.000 0.00 0.00 0.00 1.89
3132 3585 5.824624 CCAAGAGAAGCATATAAGGAAAGCA 59.175 40.000 0.00 0.00 0.00 3.91
3516 3973 3.939592 GGGAAAATGGTGTCACTAGCTAC 59.060 47.826 2.35 0.00 0.00 3.58
3775 4248 7.557719 CACAGAACAGGAGGGATAAAATTACAT 59.442 37.037 0.00 0.00 0.00 2.29
4099 4582 1.089920 CCTCAAAATCAGGACTGCGG 58.910 55.000 0.00 0.00 31.91 5.69
4358 4855 2.685897 TGTTTGGTCCAGTGCAGTAAAC 59.314 45.455 9.10 9.10 0.00 2.01
4385 4882 6.599356 TTACTCCAACAAGTGATGCTACTA 57.401 37.500 0.00 0.00 0.00 1.82
4473 4970 8.907222 TTCAAAGCATAAGCATGACTCATATA 57.093 30.769 0.00 0.00 45.49 0.86
4741 5678 8.584157 TGCATACCAGACAAAGACAAATAAAAT 58.416 29.630 0.00 0.00 0.00 1.82
4754 5699 4.032960 AGGTGAAATGCATACCAGACAA 57.967 40.909 17.43 0.00 36.94 3.18
4755 5700 3.719268 AGGTGAAATGCATACCAGACA 57.281 42.857 17.43 2.50 36.94 3.41
4780 5725 4.949856 ACCATCCAGTACCAATGATTTGTC 59.050 41.667 0.00 0.00 0.00 3.18
4804 5754 5.739959 TGGTTTCGGTATCAGATCAATCAA 58.260 37.500 0.00 0.00 0.00 2.57
4916 5870 2.096220 TTGCGGTTCCGTGCTATTAA 57.904 45.000 12.81 0.00 0.00 1.40
4941 5895 0.251634 CCTCTGAAGGAGAAGGGTGC 59.748 60.000 0.00 0.00 46.67 5.01
5069 6023 5.393787 GCCATGATCATGTTTGTCAGATGTT 60.394 40.000 29.23 0.00 37.11 2.71
5297 6251 1.302832 CACTCCTTTCGCAAGCCCT 60.303 57.895 0.00 0.00 37.18 5.19
5340 6294 7.739498 TTAATCTCAACCAAAGACTGTTACC 57.261 36.000 0.00 0.00 0.00 2.85
5536 6490 6.698008 TGCATTGGACTATACAGAAAATGG 57.302 37.500 0.00 0.00 0.00 3.16
5604 6558 6.488683 AGTCCTCATGCTCTTATGTACTACTC 59.511 42.308 0.00 0.00 0.00 2.59
5605 6559 6.369629 AGTCCTCATGCTCTTATGTACTACT 58.630 40.000 0.00 0.00 0.00 2.57
5606 6560 6.642707 AGTCCTCATGCTCTTATGTACTAC 57.357 41.667 0.00 0.00 0.00 2.73
5607 6561 6.833933 TGAAGTCCTCATGCTCTTATGTACTA 59.166 38.462 0.00 0.00 0.00 1.82
5656 6610 0.101399 ACGCGTGGAGATGCTCTAAG 59.899 55.000 12.93 0.00 31.21 2.18
5727 6681 3.713826 TTTGTCTCCCGAAGCCTAAAT 57.286 42.857 0.00 0.00 0.00 1.40
5743 6697 0.596082 CGACGGCTGGGAAAATTTGT 59.404 50.000 0.00 0.00 0.00 2.83
5765 6719 0.684535 TCAGAATGCGTCTTGGGTGA 59.315 50.000 0.00 0.00 32.70 4.02
5803 6757 3.268965 GAGACGGTGTCGAGCTGCA 62.269 63.158 1.02 0.00 37.67 4.41
5858 6812 4.394712 GACGGAGGGCTGGTGGTG 62.395 72.222 0.00 0.00 0.00 4.17
5861 6815 3.775654 GAGGACGGAGGGCTGGTG 61.776 72.222 0.00 0.00 0.00 4.17
5864 6818 4.135153 CACGAGGACGGAGGGCTG 62.135 72.222 0.00 0.00 44.46 4.85
5869 6823 3.827898 GAGGGCACGAGGACGGAG 61.828 72.222 0.00 0.00 44.46 4.63
5873 6827 4.131088 GACGGAGGGCACGAGGAC 62.131 72.222 0.00 0.00 34.93 3.85
5876 6830 4.135153 CTGGACGGAGGGCACGAG 62.135 72.222 0.00 0.00 34.93 4.18
5879 6833 4.459089 GAGCTGGACGGAGGGCAC 62.459 72.222 0.00 0.00 0.00 5.01
5883 6837 4.135153 CACGGAGCTGGACGGAGG 62.135 72.222 0.00 0.00 0.00 4.30
5884 6838 4.135153 CCACGGAGCTGGACGGAG 62.135 72.222 0.00 0.00 31.90 4.63
5910 6864 3.268965 GAGACGGTGTCGAGCTGCA 62.269 63.158 1.02 0.00 37.67 4.41
5924 6878 0.532573 TCTTCGATGGTGCTGGAGAC 59.467 55.000 0.00 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.