Multiple sequence alignment - TraesCS6D01G171100

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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 TraesCS6D01G171100 chr6D 100.000 5654 0 0 1 5654 157589517 157595170 0.000000e+00 10442
1 TraesCS6D01G171100 chr6D 93.976 166 9 1 1 165 168033802 168033637 3.380000e-62 250
2 TraesCS6D01G171100 chr6A 94.960 3988 178 7 750 4724 214563391 214559414 0.000000e+00 6229
3 TraesCS6D01G171100 chr6A 94.872 273 14 0 5233 5505 214481663 214481391 1.460000e-115 427
4 TraesCS6D01G171100 chr6A 97.436 156 4 0 5087 5242 214558805 214558650 3.360000e-67 267
5 TraesCS6D01G171100 chr6A 91.579 190 16 0 4728 4917 214559331 214559142 4.340000e-66 263
6 TraesCS6D01G171100 chr6A 93.000 100 7 0 5555 5654 214435485 214435386 4.560000e-31 147
7 TraesCS6D01G171100 chr6A 93.151 73 2 1 642 714 214563454 214563385 2.790000e-18 104
8 TraesCS6D01G171100 chr6A 95.238 63 3 0 5496 5558 214479697 214479635 3.600000e-17 100
9 TraesCS6D01G171100 chr6B 95.062 3321 147 10 885 4199 281232957 281236266 0.000000e+00 5208
10 TraesCS6D01G171100 chr6B 95.021 723 30 4 4197 4917 281236379 281237097 0.000000e+00 1131
11 TraesCS6D01G171100 chr6B 92.991 214 7 3 647 859 281232324 281232530 7.120000e-79 305
12 TraesCS6D01G171100 chr6B 72.791 996 235 29 3194 4171 715638058 715637081 7.120000e-79 305
13 TraesCS6D01G171100 chrUn 90.815 675 19 10 1 638 26879232 26879900 0.000000e+00 863
14 TraesCS6D01G171100 chr7D 88.018 676 36 12 1 642 241941917 241941253 0.000000e+00 758
15 TraesCS6D01G171100 chr7D 82.317 164 27 2 4269 4431 485028875 485029037 2.120000e-29 141
16 TraesCS6D01G171100 chr3D 87.574 676 46 20 1 638 576277858 576278533 0.000000e+00 749
17 TraesCS6D01G171100 chr4A 86.905 672 55 24 1 646 451013476 451014140 0.000000e+00 723
18 TraesCS6D01G171100 chr5A 85.942 690 45 26 1 638 60747418 60748107 0.000000e+00 689
19 TraesCS6D01G171100 chr5A 87.786 524 40 18 126 641 118417791 118417284 4.880000e-165 592
20 TraesCS6D01G171100 chr2A 85.549 692 48 22 1 641 316793023 316793713 0.000000e+00 676
21 TraesCS6D01G171100 chr1A 84.421 674 65 28 1 644 513000605 512999942 1.340000e-175 627
22 TraesCS6D01G171100 chr3A 88.476 538 32 18 126 645 125831270 125831795 1.730000e-174 623
23 TraesCS6D01G171100 chr3A 88.144 194 18 4 1 189 391096153 391096346 5.700000e-55 226
24 TraesCS6D01G171100 chr7A 87.640 534 44 14 128 644 178237247 178236719 8.110000e-168 601
25 TraesCS6D01G171100 chr7A 82.317 164 27 2 4269 4431 553368286 553368448 2.120000e-29 141
26 TraesCS6D01G171100 chr3B 81.739 690 78 27 1 646 752862705 752862020 3.000000e-147 532
27 TraesCS6D01G171100 chr3B 79.880 333 38 21 1 324 242744004 242743692 3.430000e-52 217
28 TraesCS6D01G171100 chr3B 90.840 131 11 1 1 130 242743195 242743325 2.090000e-39 174
29 TraesCS6D01G171100 chr7B 73.784 370 89 8 4269 4634 663116674 663116309 7.640000e-29 139
30 TraesCS6D01G171100 chr7B 81.212 165 29 2 4269 4432 512698462 512698625 1.280000e-26 132


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 TraesCS6D01G171100 chr6D 157589517 157595170 5653 False 10442.000000 10442 100.0000 1 5654 1 chr6D.!!$F1 5653
1 TraesCS6D01G171100 chr6A 214558650 214563454 4804 True 1715.750000 6229 94.2815 642 5242 4 chr6A.!!$R3 4600
2 TraesCS6D01G171100 chr6A 214479635 214481663 2028 True 263.500000 427 95.0550 5233 5558 2 chr6A.!!$R2 325
3 TraesCS6D01G171100 chr6B 281232324 281237097 4773 False 2214.666667 5208 94.3580 647 4917 3 chr6B.!!$F1 4270
4 TraesCS6D01G171100 chr6B 715637081 715638058 977 True 305.000000 305 72.7910 3194 4171 1 chr6B.!!$R1 977
5 TraesCS6D01G171100 chrUn 26879232 26879900 668 False 863.000000 863 90.8150 1 638 1 chrUn.!!$F1 637
6 TraesCS6D01G171100 chr7D 241941253 241941917 664 True 758.000000 758 88.0180 1 642 1 chr7D.!!$R1 641
7 TraesCS6D01G171100 chr3D 576277858 576278533 675 False 749.000000 749 87.5740 1 638 1 chr3D.!!$F1 637
8 TraesCS6D01G171100 chr4A 451013476 451014140 664 False 723.000000 723 86.9050 1 646 1 chr4A.!!$F1 645
9 TraesCS6D01G171100 chr5A 60747418 60748107 689 False 689.000000 689 85.9420 1 638 1 chr5A.!!$F1 637
10 TraesCS6D01G171100 chr5A 118417284 118417791 507 True 592.000000 592 87.7860 126 641 1 chr5A.!!$R1 515
11 TraesCS6D01G171100 chr2A 316793023 316793713 690 False 676.000000 676 85.5490 1 641 1 chr2A.!!$F1 640
12 TraesCS6D01G171100 chr1A 512999942 513000605 663 True 627.000000 627 84.4210 1 644 1 chr1A.!!$R1 643
13 TraesCS6D01G171100 chr3A 125831270 125831795 525 False 623.000000 623 88.4760 126 645 1 chr3A.!!$F1 519
14 TraesCS6D01G171100 chr7A 178236719 178237247 528 True 601.000000 601 87.6400 128 644 1 chr7A.!!$R1 516
15 TraesCS6D01G171100 chr3B 752862020 752862705 685 True 532.000000 532 81.7390 1 646 1 chr3B.!!$R2 645

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
842 1009 0.165944 GACGAAACAAGCCACGGATG 59.834 55.0 0.00 0.0 0.00 3.51 F
1826 2407 0.536006 GCTTCCAACCAGCTGTCAGT 60.536 55.0 13.81 0.0 34.15 3.41 F
2124 2705 0.393944 AGCTCGTCGGACAGATACCA 60.394 55.0 9.10 0.0 0.00 3.25 F
3243 3824 0.250513 GCATTCCTGAGTTCCTCGGT 59.749 55.0 0.00 0.0 35.27 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2109 2690 0.027716 CGTCTGGTATCTGTCCGACG 59.972 60.000 11.89 11.89 41.28 5.12 R
3096 3677 0.458025 GTAAGCTTCGACACTCCCCG 60.458 60.000 0.00 0.00 0.00 5.73 R
4005 4592 2.260869 GCTTGGCTTGAGGTCGCAA 61.261 57.895 0.00 0.00 0.00 4.85 R
4955 5741 0.250124 TTTGCGGAACCTCGTCACAT 60.250 50.000 0.00 0.00 0.00 3.21 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
112 114 6.618287 TGACATCTGAAAAGACGATTTTGT 57.382 33.333 7.63 1.31 0.00 2.83
519 681 6.833933 AGTCTTTTCAGGTGTCATTTAGGTTT 59.166 34.615 0.00 0.00 0.00 3.27
677 843 3.963428 GATAGGATAGCGGTTGTGGAT 57.037 47.619 0.00 0.00 0.00 3.41
724 890 3.350612 CAAAAAGGTCCGGCGCGA 61.351 61.111 12.10 0.00 0.00 5.87
725 891 2.359478 AAAAAGGTCCGGCGCGAT 60.359 55.556 12.10 0.00 0.00 4.58
726 892 1.969589 AAAAAGGTCCGGCGCGATT 60.970 52.632 12.10 0.00 0.00 3.34
738 905 0.453782 GCGCGATTAACTTTTGCCGT 60.454 50.000 12.10 0.00 0.00 5.68
739 906 1.958417 CGCGATTAACTTTTGCCGTT 58.042 45.000 0.00 0.00 0.00 4.44
740 907 2.725452 GCGCGATTAACTTTTGCCGTTA 60.725 45.455 12.10 0.00 0.00 3.18
741 908 2.836161 CGCGATTAACTTTTGCCGTTAC 59.164 45.455 0.00 0.00 0.00 2.50
780 947 3.466836 CCGCCAGCTTTTCATATCACTA 58.533 45.455 0.00 0.00 0.00 2.74
842 1009 0.165944 GACGAAACAAGCCACGGATG 59.834 55.000 0.00 0.00 0.00 3.51
958 1529 3.068560 GTTTATACGCAACACTCACCCA 58.931 45.455 0.00 0.00 0.00 4.51
966 1537 1.480137 CAACACTCACCCAAGCCAAAA 59.520 47.619 0.00 0.00 0.00 2.44
1147 1728 4.057428 GCTCCGTCGCCACTCACT 62.057 66.667 0.00 0.00 0.00 3.41
1148 1729 2.651361 CTCCGTCGCCACTCACTT 59.349 61.111 0.00 0.00 0.00 3.16
1429 2010 3.357079 CCAACCTCACGCACCTGC 61.357 66.667 0.00 0.00 37.78 4.85
1569 2150 4.767255 CTCTCCCGGTGCAGGCAC 62.767 72.222 15.78 15.78 45.49 5.01
1630 2211 2.670148 ATCCCACCGGAGCTGTTCC 61.670 63.158 9.46 0.00 43.12 3.62
1631 2212 3.322466 CCCACCGGAGCTGTTCCT 61.322 66.667 9.46 0.00 44.41 3.36
1641 2222 1.213013 GCTGTTCCTCTCGCTTCGA 59.787 57.895 0.00 0.00 0.00 3.71
1826 2407 0.536006 GCTTCCAACCAGCTGTCAGT 60.536 55.000 13.81 0.00 34.15 3.41
1881 2462 1.823169 TAACCGCTCTCACCGCCTTT 61.823 55.000 0.00 0.00 0.00 3.11
1941 2522 1.985614 CCTGTCATCCCTCAGCACA 59.014 57.895 0.00 0.00 0.00 4.57
2034 2615 3.562176 CCTTAAACCTCCAGAGCAATGGT 60.562 47.826 7.06 0.00 41.43 3.55
2037 2618 1.915141 ACCTCCAGAGCAATGGTTTG 58.085 50.000 7.06 0.00 41.43 2.93
2044 2625 0.831711 GAGCAATGGTTTGGTGGGGT 60.832 55.000 0.00 0.00 43.35 4.95
2092 2673 1.008995 TTGCTTGAAGCCGTTTCGC 60.009 52.632 15.43 0.00 41.51 4.70
2109 2690 2.448705 GCTCGCGGAGAACAAGCTC 61.449 63.158 6.13 0.00 0.00 4.09
2115 2696 1.585006 GGAGAACAAGCTCGTCGGA 59.415 57.895 0.00 0.00 35.74 4.55
2116 2697 0.733223 GGAGAACAAGCTCGTCGGAC 60.733 60.000 0.00 0.00 35.74 4.79
2124 2705 0.393944 AGCTCGTCGGACAGATACCA 60.394 55.000 9.10 0.00 0.00 3.25
2157 2738 2.586245 CTCCATGCCCTCGCTGAA 59.414 61.111 0.00 0.00 35.36 3.02
2190 2771 0.548510 ACAATGAGCTAGAAGGCCCC 59.451 55.000 0.00 0.00 0.00 5.80
2313 2894 3.612955 CGAGTCTCCAGTCCTTTCTTGTC 60.613 52.174 0.00 0.00 0.00 3.18
2370 2951 0.901114 TGTGCAATGCCTCCATGCTT 60.901 50.000 1.53 0.00 0.00 3.91
2379 2960 1.964552 CCTCCATGCTTCAGATGGTC 58.035 55.000 0.00 0.00 41.19 4.02
2400 2981 5.221581 GGTCCAGACAGTAAACAACTTCCTA 60.222 44.000 0.00 0.00 35.76 2.94
2439 3020 3.801997 CTGGGGGCTCGCCAAGAT 61.802 66.667 10.51 0.00 45.61 2.40
2448 3029 1.938926 GCTCGCCAAGATATGCTCTCC 60.939 57.143 0.00 0.00 31.03 3.71
2517 3098 1.644337 TGGGGCTTCCTGACTAGTCTA 59.356 52.381 23.01 9.26 36.20 2.59
2563 3144 5.036117 AGTGGATGTTAGTGACAACAAGT 57.964 39.130 5.07 0.00 42.62 3.16
2712 3293 9.565213 GAACTTGACATGGAAAATAATCTTCTG 57.435 33.333 0.00 0.00 0.00 3.02
2713 3294 8.059798 ACTTGACATGGAAAATAATCTTCTGG 57.940 34.615 0.00 0.00 0.00 3.86
2766 3347 5.049680 GCTTAAGAAGTTGAATCGGTTGTCA 60.050 40.000 6.67 0.00 0.00 3.58
2767 3348 6.348540 GCTTAAGAAGTTGAATCGGTTGTCAT 60.349 38.462 6.67 0.00 0.00 3.06
2769 3350 8.610248 TTAAGAAGTTGAATCGGTTGTCATTA 57.390 30.769 0.00 0.00 0.00 1.90
2844 3425 2.420372 GCTTACAACCCTTCTGCTTAGC 59.580 50.000 0.00 0.00 0.00 3.09
2947 3528 2.124695 GCCCAACGCCTAAGGAGG 60.125 66.667 0.00 0.00 46.93 4.30
3063 3644 6.430864 TCTAGGTGAACTTGATCTCTCTGAT 58.569 40.000 0.00 0.00 38.27 2.90
3066 3647 6.872920 AGGTGAACTTGATCTCTCTGATAAC 58.127 40.000 0.00 0.00 35.14 1.89
3096 3677 3.790152 GGAAAGATTCCTGCCAACATC 57.210 47.619 1.86 0.00 46.57 3.06
3117 3698 1.001633 GGGGAGTGTCGAAGCTTACAA 59.998 52.381 0.00 0.00 0.00 2.41
3183 3764 1.355381 TCACTAGGACAGTTACGGGGA 59.645 52.381 0.00 0.00 34.26 4.81
3243 3824 0.250513 GCATTCCTGAGTTCCTCGGT 59.749 55.000 0.00 0.00 35.27 4.69
3545 4132 1.139853 GCCACAGATAACTCTCCCCAG 59.860 57.143 0.00 0.00 0.00 4.45
3558 4145 4.289672 ACTCTCCCCAGTGACAAATACATT 59.710 41.667 0.00 0.00 0.00 2.71
3602 4189 2.364970 CCAAGGCAACAGATGGTTTCAA 59.635 45.455 0.00 0.00 37.72 2.69
3835 4422 2.328099 GGTGGCGACTTCAAGGCTG 61.328 63.158 0.00 0.00 0.00 4.85
3846 4433 3.701040 ACTTCAAGGCTGTTGTGTTTGAT 59.299 39.130 0.00 0.00 0.00 2.57
4005 4592 3.573967 AGAAGCCGTTTCCAATTGTTCAT 59.426 39.130 4.43 0.00 36.40 2.57
4372 5077 1.071071 TCACCGGTAAAAGACCCACAG 59.929 52.381 6.87 0.00 46.81 3.66
4374 5079 0.958876 CCGGTAAAAGACCCACAGGC 60.959 60.000 0.00 0.00 46.81 4.85
4488 5193 3.766545 AGCAGAAAGTAATGGCAAAGGA 58.233 40.909 0.00 0.00 0.00 3.36
4491 5196 4.475944 CAGAAAGTAATGGCAAAGGAACG 58.524 43.478 0.00 0.00 0.00 3.95
4520 5225 1.656095 GTATCACAGCAGCGAAGACAC 59.344 52.381 0.00 0.00 0.00 3.67
4578 5283 4.460382 GGAATTTCATGCTCCAAAGAGACA 59.540 41.667 0.00 0.00 43.39 3.41
4747 5531 8.082242 GGTAACCTAGTCGTTTTAACTCTGTAA 58.918 37.037 0.00 0.00 0.00 2.41
4800 5584 3.118956 AGAGGCATCTTAAGGAGTCAACG 60.119 47.826 1.85 0.00 28.57 4.10
4837 5621 0.033504 TCAGTGTCGACAGGAAAGCC 59.966 55.000 20.73 5.13 0.00 4.35
4917 5703 1.697982 GGTGTGGGGTTAGTCTCACTT 59.302 52.381 0.00 0.00 0.00 3.16
4918 5704 2.550208 GGTGTGGGGTTAGTCTCACTTG 60.550 54.545 0.00 0.00 0.00 3.16
4919 5705 1.697432 TGTGGGGTTAGTCTCACTTGG 59.303 52.381 0.00 0.00 0.00 3.61
4920 5706 1.975680 GTGGGGTTAGTCTCACTTGGA 59.024 52.381 0.00 0.00 0.00 3.53
4921 5707 2.572104 GTGGGGTTAGTCTCACTTGGAT 59.428 50.000 0.00 0.00 0.00 3.41
4922 5708 3.009143 GTGGGGTTAGTCTCACTTGGATT 59.991 47.826 0.00 0.00 0.00 3.01
4923 5709 3.655777 TGGGGTTAGTCTCACTTGGATTT 59.344 43.478 0.00 0.00 0.00 2.17
4924 5710 4.105697 TGGGGTTAGTCTCACTTGGATTTT 59.894 41.667 0.00 0.00 0.00 1.82
4925 5711 5.077564 GGGGTTAGTCTCACTTGGATTTTT 58.922 41.667 0.00 0.00 0.00 1.94
4926 5712 5.183331 GGGGTTAGTCTCACTTGGATTTTTC 59.817 44.000 0.00 0.00 0.00 2.29
4927 5713 6.004574 GGGTTAGTCTCACTTGGATTTTTCT 58.995 40.000 0.00 0.00 0.00 2.52
4928 5714 6.490381 GGGTTAGTCTCACTTGGATTTTTCTT 59.510 38.462 0.00 0.00 0.00 2.52
4929 5715 7.664318 GGGTTAGTCTCACTTGGATTTTTCTTA 59.336 37.037 0.00 0.00 0.00 2.10
4930 5716 9.063615 GGTTAGTCTCACTTGGATTTTTCTTAA 57.936 33.333 0.00 0.00 0.00 1.85
4931 5717 9.880064 GTTAGTCTCACTTGGATTTTTCTTAAC 57.120 33.333 0.00 0.00 0.00 2.01
4932 5718 9.847224 TTAGTCTCACTTGGATTTTTCTTAACT 57.153 29.630 0.00 0.00 0.00 2.24
4935 5721 8.621286 GTCTCACTTGGATTTTTCTTAACTGAA 58.379 33.333 0.00 0.00 0.00 3.02
4936 5722 9.184523 TCTCACTTGGATTTTTCTTAACTGAAA 57.815 29.630 0.00 0.00 34.55 2.69
4940 5726 9.045223 ACTTGGATTTTTCTTAACTGAAATTGC 57.955 29.630 0.00 0.00 36.07 3.56
4941 5727 8.954950 TTGGATTTTTCTTAACTGAAATTGCA 57.045 26.923 0.00 0.00 36.07 4.08
4943 5729 7.656948 TGGATTTTTCTTAACTGAAATTGCAGG 59.343 33.333 18.01 0.00 40.20 4.85
4944 5730 7.872483 GGATTTTTCTTAACTGAAATTGCAGGA 59.128 33.333 18.01 2.32 40.20 3.86
4945 5731 9.260002 GATTTTTCTTAACTGAAATTGCAGGAA 57.740 29.630 18.01 10.09 40.20 3.36
4947 5733 6.707440 TTCTTAACTGAAATTGCAGGAACA 57.293 33.333 18.01 0.00 40.20 3.18
4948 5734 6.072112 TCTTAACTGAAATTGCAGGAACAC 57.928 37.500 18.01 0.00 40.20 3.32
4950 5736 3.715628 ACTGAAATTGCAGGAACACAC 57.284 42.857 18.01 0.00 40.20 3.82
4951 5737 3.290710 ACTGAAATTGCAGGAACACACT 58.709 40.909 18.01 0.00 40.20 3.55
4954 5740 3.890756 TGAAATTGCAGGAACACACTGAT 59.109 39.130 0.00 0.00 38.20 2.90
4955 5741 5.069318 TGAAATTGCAGGAACACACTGATA 58.931 37.500 0.00 0.00 38.20 2.15
4956 5742 5.711506 TGAAATTGCAGGAACACACTGATAT 59.288 36.000 0.00 0.00 38.20 1.63
4957 5743 5.571784 AATTGCAGGAACACACTGATATG 57.428 39.130 0.00 0.00 38.20 1.78
4958 5744 3.701205 TGCAGGAACACACTGATATGT 57.299 42.857 0.00 0.00 38.20 2.29
4968 5754 4.111375 ACACTGATATGTGACGAGGTTC 57.889 45.455 1.47 0.00 40.12 3.62
4969 5755 3.119101 ACACTGATATGTGACGAGGTTCC 60.119 47.826 1.47 0.00 40.12 3.62
4970 5756 2.099263 ACTGATATGTGACGAGGTTCCG 59.901 50.000 0.00 0.00 0.00 4.30
4971 5757 1.202371 TGATATGTGACGAGGTTCCGC 60.202 52.381 0.00 0.00 0.00 5.54
4972 5758 0.821517 ATATGTGACGAGGTTCCGCA 59.178 50.000 0.00 0.00 0.00 5.69
4973 5759 0.604073 TATGTGACGAGGTTCCGCAA 59.396 50.000 0.00 0.00 0.00 4.85
4974 5760 0.250124 ATGTGACGAGGTTCCGCAAA 60.250 50.000 0.00 0.00 0.00 3.68
4975 5761 0.462225 TGTGACGAGGTTCCGCAAAA 60.462 50.000 0.00 0.00 0.00 2.44
4976 5762 0.872388 GTGACGAGGTTCCGCAAAAT 59.128 50.000 0.00 0.00 0.00 1.82
4977 5763 2.070783 GTGACGAGGTTCCGCAAAATA 58.929 47.619 0.00 0.00 0.00 1.40
4983 5769 4.920927 ACGAGGTTCCGCAAAATATTTTTG 59.079 37.500 10.77 6.80 0.00 2.44
5019 5807 5.888161 AGTATTCTTGCAGATTTTACCCCAG 59.112 40.000 0.00 0.00 0.00 4.45
5021 5809 2.041620 TCTTGCAGATTTTACCCCAGCT 59.958 45.455 0.00 0.00 0.00 4.24
5053 5882 3.242446 GGCTTATCGCAAGCTGAAAGTAC 60.242 47.826 17.50 0.00 42.62 2.73
5073 5902 5.600484 AGTACATGCCTCTAATGAAGCTAGT 59.400 40.000 0.00 0.00 31.28 2.57
5085 5914 5.667539 ATGAAGCTAGTCTGACTAAGCAA 57.332 39.130 26.27 17.74 31.66 3.91
5110 6081 5.479124 AGTCTAACCATACTTTCCACGTT 57.521 39.130 0.00 0.00 0.00 3.99
5142 6113 5.053145 CGTTGAAGAAGAAGATATCCTGGG 58.947 45.833 0.00 0.00 0.00 4.45
5219 6190 2.283532 ACCTCCGTCAGCTCAGCT 60.284 61.111 0.00 0.00 40.77 4.24
5281 6252 1.300697 GTAGCCCATCGCCCGTAAG 60.301 63.158 0.00 0.00 38.78 2.34
5287 6258 0.460311 CCATCGCCCGTAAGAAGAGT 59.540 55.000 0.00 0.00 43.02 3.24
5288 6259 1.679680 CCATCGCCCGTAAGAAGAGTA 59.320 52.381 0.00 0.00 43.02 2.59
5290 6261 3.243771 CCATCGCCCGTAAGAAGAGTAAT 60.244 47.826 0.00 0.00 43.02 1.89
5312 6283 0.670162 GACGGCCAATTGGATCCATG 59.330 55.000 29.02 12.00 37.39 3.66
5330 6301 0.793861 TGTTGATCAAGTAACGCCGC 59.206 50.000 8.80 0.00 0.00 6.53
5355 6326 3.686241 CCAACACGAGTTCATGTCATCAT 59.314 43.478 0.00 0.00 35.28 2.45
5380 6351 1.913778 TCTTGTAGTACCAGCGTCCA 58.086 50.000 0.00 0.00 0.00 4.02
5381 6352 2.241160 TCTTGTAGTACCAGCGTCCAA 58.759 47.619 0.00 0.00 0.00 3.53
5478 6449 2.432510 AGGAAGGATTTACCGAGAGCAG 59.567 50.000 0.00 0.00 44.74 4.24
5506 8180 4.856801 ATCGGGCATGCCGGTGAC 62.857 66.667 35.08 19.63 37.63 3.67
5567 8241 4.980805 GGGCACGGCGTCTTGACA 62.981 66.667 10.85 0.00 0.00 3.58
5568 8242 2.742372 GGCACGGCGTCTTGACAT 60.742 61.111 10.85 0.00 0.00 3.06
5569 8243 2.476051 GCACGGCGTCTTGACATG 59.524 61.111 10.85 0.00 0.00 3.21
5570 8244 3.027170 GCACGGCGTCTTGACATGG 62.027 63.158 10.85 0.00 0.00 3.66
5571 8245 1.667830 CACGGCGTCTTGACATGGT 60.668 57.895 10.85 0.00 0.00 3.55
5572 8246 1.374252 ACGGCGTCTTGACATGGTC 60.374 57.895 6.77 0.00 0.00 4.02
5573 8247 2.100631 CGGCGTCTTGACATGGTCC 61.101 63.158 0.00 0.00 0.00 4.46
5574 8248 2.100631 GGCGTCTTGACATGGTCCG 61.101 63.158 0.00 0.00 0.00 4.79
5575 8249 1.374252 GCGTCTTGACATGGTCCGT 60.374 57.895 0.00 0.00 0.00 4.69
5576 8250 1.626654 GCGTCTTGACATGGTCCGTG 61.627 60.000 9.71 9.71 0.00 4.94
5577 8251 0.319555 CGTCTTGACATGGTCCGTGT 60.320 55.000 16.96 16.96 36.19 4.49
5578 8252 1.429463 GTCTTGACATGGTCCGTGTC 58.571 55.000 30.11 30.11 46.84 3.67
5579 8253 0.320374 TCTTGACATGGTCCGTGTCC 59.680 55.000 32.32 19.29 46.32 4.02
5580 8254 0.034756 CTTGACATGGTCCGTGTCCA 59.965 55.000 32.32 24.14 46.32 4.02
5581 8255 0.690192 TTGACATGGTCCGTGTCCAT 59.310 50.000 32.32 6.69 46.32 3.41
5586 8260 1.910580 ATGGTCCGTGTCCATGACCC 61.911 60.000 13.27 3.22 46.45 4.46
5587 8261 2.589157 GGTCCGTGTCCATGACCCA 61.589 63.158 0.00 0.00 42.21 4.51
5588 8262 1.079127 GTCCGTGTCCATGACCCAG 60.079 63.158 0.00 0.00 0.00 4.45
5589 8263 1.229051 TCCGTGTCCATGACCCAGA 60.229 57.895 0.00 0.00 0.00 3.86
5590 8264 0.834261 TCCGTGTCCATGACCCAGAA 60.834 55.000 0.00 0.00 0.00 3.02
5591 8265 0.673644 CCGTGTCCATGACCCAGAAC 60.674 60.000 0.00 0.00 0.00 3.01
5592 8266 0.034756 CGTGTCCATGACCCAGAACA 59.965 55.000 0.00 0.00 0.00 3.18
5593 8267 1.339055 CGTGTCCATGACCCAGAACAT 60.339 52.381 0.00 0.00 0.00 2.71
5594 8268 2.086869 GTGTCCATGACCCAGAACATG 58.913 52.381 0.00 0.00 42.12 3.21
5595 8269 1.098050 GTCCATGACCCAGAACATGC 58.902 55.000 0.00 0.00 41.43 4.06
5596 8270 0.392863 TCCATGACCCAGAACATGCG 60.393 55.000 0.00 0.00 41.43 4.73
5597 8271 1.430632 CATGACCCAGAACATGCGC 59.569 57.895 0.00 0.00 37.62 6.09
5598 8272 1.750399 ATGACCCAGAACATGCGCC 60.750 57.895 4.18 0.00 0.00 6.53
5599 8273 3.134127 GACCCAGAACATGCGCCC 61.134 66.667 4.18 0.00 0.00 6.13
5600 8274 4.740822 ACCCAGAACATGCGCCCC 62.741 66.667 4.18 0.00 0.00 5.80
5601 8275 4.431131 CCCAGAACATGCGCCCCT 62.431 66.667 4.18 0.00 0.00 4.79
5602 8276 2.361610 CCAGAACATGCGCCCCTT 60.362 61.111 4.18 0.00 0.00 3.95
5603 8277 2.703798 CCAGAACATGCGCCCCTTG 61.704 63.158 4.18 0.00 0.00 3.61
5604 8278 1.675310 CAGAACATGCGCCCCTTGA 60.675 57.895 4.18 0.00 0.00 3.02
5605 8279 1.675641 AGAACATGCGCCCCTTGAC 60.676 57.895 4.18 0.00 0.00 3.18
5606 8280 2.676471 AACATGCGCCCCTTGACC 60.676 61.111 4.18 0.00 0.00 4.02
5608 8282 4.776322 CATGCGCCCCTTGACCGA 62.776 66.667 4.18 0.00 0.00 4.69
5609 8283 3.797353 ATGCGCCCCTTGACCGAT 61.797 61.111 4.18 0.00 0.00 4.18
5610 8284 3.344137 ATGCGCCCCTTGACCGATT 62.344 57.895 4.18 0.00 0.00 3.34
5611 8285 2.750237 GCGCCCCTTGACCGATTT 60.750 61.111 0.00 0.00 0.00 2.17
5612 8286 3.051392 GCGCCCCTTGACCGATTTG 62.051 63.158 0.00 0.00 0.00 2.32
5613 8287 1.376683 CGCCCCTTGACCGATTTGA 60.377 57.895 0.00 0.00 0.00 2.69
5614 8288 1.644786 CGCCCCTTGACCGATTTGAC 61.645 60.000 0.00 0.00 0.00 3.18
5615 8289 1.313091 GCCCCTTGACCGATTTGACC 61.313 60.000 0.00 0.00 0.00 4.02
5616 8290 1.024579 CCCCTTGACCGATTTGACCG 61.025 60.000 0.00 0.00 0.00 4.79
5617 8291 0.321298 CCCTTGACCGATTTGACCGT 60.321 55.000 0.00 0.00 0.00 4.83
5618 8292 1.076332 CCTTGACCGATTTGACCGTC 58.924 55.000 0.00 0.00 0.00 4.79
5619 8293 1.606994 CCTTGACCGATTTGACCGTCA 60.607 52.381 0.00 0.00 0.00 4.35
5620 8294 1.726791 CTTGACCGATTTGACCGTCAG 59.273 52.381 0.64 0.00 0.00 3.51
5621 8295 0.669318 TGACCGATTTGACCGTCAGC 60.669 55.000 0.64 0.00 0.00 4.26
5622 8296 1.359459 GACCGATTTGACCGTCAGCC 61.359 60.000 0.64 0.00 0.00 4.85
5623 8297 1.375396 CCGATTTGACCGTCAGCCA 60.375 57.895 0.64 0.00 0.00 4.75
5624 8298 1.635663 CCGATTTGACCGTCAGCCAC 61.636 60.000 0.64 0.00 0.00 5.01
5625 8299 0.670546 CGATTTGACCGTCAGCCACT 60.671 55.000 0.64 0.00 0.00 4.00
5626 8300 1.079503 GATTTGACCGTCAGCCACTC 58.920 55.000 0.64 0.00 0.00 3.51
5627 8301 0.670546 ATTTGACCGTCAGCCACTCG 60.671 55.000 0.64 0.00 0.00 4.18
5648 8322 4.963428 GGCGGGTAAGGCGGATCG 62.963 72.222 0.00 0.00 0.00 3.69
5649 8323 4.963428 GCGGGTAAGGCGGATCGG 62.963 72.222 0.00 0.00 0.00 4.18
5650 8324 3.534056 CGGGTAAGGCGGATCGGT 61.534 66.667 1.93 0.00 0.00 4.69
5651 8325 2.108362 GGGTAAGGCGGATCGGTG 59.892 66.667 1.93 0.00 0.00 4.94
5652 8326 2.108362 GGTAAGGCGGATCGGTGG 59.892 66.667 1.93 0.00 0.00 4.61
5653 8327 2.588034 GTAAGGCGGATCGGTGGC 60.588 66.667 1.93 0.00 0.00 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
112 114 0.177836 CGCACATACCACATGAGGGA 59.822 55.000 14.11 5.16 0.00 4.20
519 681 7.663905 CCCTATATGACATTTCCGTCCATTTTA 59.336 37.037 0.00 0.00 34.88 1.52
585 751 6.486253 TCTGCTTCATTATTTGACACTGAC 57.514 37.500 0.00 0.00 32.84 3.51
623 789 8.625571 TCCCCTTAGGACAAAATTCCTTATTTA 58.374 33.333 0.00 0.00 44.22 1.40
676 842 1.066858 CGTTCACACTGACCCTGCTAT 60.067 52.381 0.00 0.00 0.00 2.97
677 843 0.317160 CGTTCACACTGACCCTGCTA 59.683 55.000 0.00 0.00 0.00 3.49
678 844 1.069765 CGTTCACACTGACCCTGCT 59.930 57.895 0.00 0.00 0.00 4.24
724 890 7.331193 TGTTTGTTTGTAACGGCAAAAGTTAAT 59.669 29.630 4.16 0.00 39.65 1.40
725 891 6.643770 TGTTTGTTTGTAACGGCAAAAGTTAA 59.356 30.769 4.16 0.00 39.65 2.01
726 892 6.154445 TGTTTGTTTGTAACGGCAAAAGTTA 58.846 32.000 4.16 0.00 39.65 2.24
738 905 4.299978 GGCCGCTATTTGTTTGTTTGTAA 58.700 39.130 0.00 0.00 0.00 2.41
739 906 3.609644 CGGCCGCTATTTGTTTGTTTGTA 60.610 43.478 14.67 0.00 0.00 2.41
740 907 2.749776 GGCCGCTATTTGTTTGTTTGT 58.250 42.857 0.00 0.00 0.00 2.83
741 908 1.718711 CGGCCGCTATTTGTTTGTTTG 59.281 47.619 14.67 0.00 0.00 2.93
780 947 1.751924 GAGCCATGAGTAGTCGAGGTT 59.248 52.381 0.00 4.11 0.00 3.50
919 1490 0.534203 ACAAACTGTAGCCACCGGTG 60.534 55.000 28.26 28.26 0.00 4.94
920 1491 0.181824 AACAAACTGTAGCCACCGGT 59.818 50.000 0.00 0.00 0.00 5.28
921 1492 1.314730 AAACAAACTGTAGCCACCGG 58.685 50.000 0.00 0.00 0.00 5.28
922 1493 4.201647 CGTATAAACAAACTGTAGCCACCG 60.202 45.833 0.00 0.00 0.00 4.94
958 1529 7.346960 AGGTAGATAGAGAGAGATTTTTGGCTT 59.653 37.037 0.00 0.00 0.00 4.35
966 1537 7.514127 AGACAGAGAGGTAGATAGAGAGAGATT 59.486 40.741 0.00 0.00 0.00 2.40
1182 1763 1.944676 GTAATCCTCGACGCTGGCG 60.945 63.158 13.56 13.56 46.03 5.69
1193 1774 1.079127 AGCAGCGCGTTGTAATCCT 60.079 52.632 23.96 9.39 0.00 3.24
1641 2222 0.896226 GGTTGAGTACCTCGAGGCTT 59.104 55.000 31.56 16.76 44.10 4.35
1653 2234 1.371558 GTTCTGGCCGAGGTTGAGT 59.628 57.895 0.00 0.00 0.00 3.41
1677 2258 3.987594 GGAAGGGATGCTTCCTGTT 57.012 52.632 17.48 11.53 45.05 3.16
1806 2387 0.535780 CTGACAGCTGGTTGGAAGCA 60.536 55.000 19.93 2.11 43.37 3.91
1809 2390 1.070758 GAGACTGACAGCTGGTTGGAA 59.929 52.381 19.93 0.00 0.00 3.53
1941 2522 3.222603 GTGGTTGTCTTCCAAATGGAGT 58.777 45.455 1.86 0.00 46.36 3.85
2044 2625 1.550179 CCCTATAGACTCGGGGATGCA 60.550 57.143 0.00 0.00 41.25 3.96
2052 2633 2.628657 CCCAAGGTTCCCTATAGACTCG 59.371 54.545 0.00 0.00 31.13 4.18
2092 2673 2.155194 CGAGCTTGTTCTCCGCGAG 61.155 63.158 8.23 3.02 0.00 5.03
2109 2690 0.027716 CGTCTGGTATCTGTCCGACG 59.972 60.000 11.89 11.89 41.28 5.12
2115 2696 1.134401 CCAATGGCGTCTGGTATCTGT 60.134 52.381 0.00 0.00 0.00 3.41
2116 2697 1.586422 CCAATGGCGTCTGGTATCTG 58.414 55.000 0.00 0.00 0.00 2.90
2124 2705 1.299976 GAGGTTCCCAATGGCGTCT 59.700 57.895 0.00 0.00 0.00 4.18
2157 2738 6.115448 AGCTCATTGTTGTCTAGGTAAAGT 57.885 37.500 0.00 0.00 0.00 2.66
2241 2822 1.153046 CCCGGTGAGGTTGTTGTGT 60.153 57.895 0.00 0.00 38.74 3.72
2269 2850 4.429212 CGTGTCGCCCATGTCGGA 62.429 66.667 5.03 0.00 36.56 4.55
2270 2851 3.716539 ATCGTGTCGCCCATGTCGG 62.717 63.158 5.03 0.00 0.00 4.79
2313 2894 3.310774 CGCCATGAAACTGGTTATCAGAG 59.689 47.826 0.00 0.00 46.18 3.35
2370 2951 3.901222 TGTTTACTGTCTGGACCATCTGA 59.099 43.478 0.00 0.00 0.00 3.27
2379 2960 5.577164 CGATAGGAAGTTGTTTACTGTCTGG 59.423 44.000 0.00 0.00 36.10 3.86
2439 3020 1.557099 AGTTCACCACGGAGAGCATA 58.443 50.000 0.71 0.00 0.00 3.14
2448 3029 2.637025 CCCGCAAAGTTCACCACG 59.363 61.111 0.00 0.00 0.00 4.94
2517 3098 6.720112 AATATCATATTGCTGCAGTTGGTT 57.280 33.333 16.64 0.00 0.00 3.67
2563 3144 2.047655 CGGTAGCACGCCTTGGAA 60.048 61.111 0.00 0.00 0.00 3.53
2800 3381 5.105595 GCTTTGTAAGATTTCCAAGAGCCAT 60.106 40.000 0.00 0.00 0.00 4.40
2844 3425 1.284657 CTCCACTGAGCGCATTAGTG 58.715 55.000 23.42 23.42 41.04 2.74
2947 3528 4.377841 CGACAAGCTTGAGATGAGGAAAAC 60.378 45.833 32.50 6.39 0.00 2.43
3088 3669 1.745489 GACACTCCCCGATGTTGGC 60.745 63.158 0.00 0.00 0.00 4.52
3093 3674 1.519455 GCTTCGACACTCCCCGATG 60.519 63.158 0.00 0.00 34.58 3.84
3096 3677 0.458025 GTAAGCTTCGACACTCCCCG 60.458 60.000 0.00 0.00 0.00 5.73
3117 3698 6.590656 TGGTTCCCAGATAAATTGAGGTAT 57.409 37.500 0.00 0.00 0.00 2.73
3183 3764 4.142271 CGAGAAAGATCAAGCACTAGGAGT 60.142 45.833 0.00 0.00 0.00 3.85
3243 3824 5.499004 AACTAGCAAGACCTTTCATGGTA 57.501 39.130 0.00 0.00 41.00 3.25
3558 4145 5.590259 GGCCAATTCAGCATAAGAAACTCTA 59.410 40.000 0.00 0.00 0.00 2.43
3835 4422 5.793026 TTTGGCAGAAAATCAAACACAAC 57.207 34.783 0.00 0.00 0.00 3.32
3846 4433 6.071391 GGTCTAGATTTCCATTTGGCAGAAAA 60.071 38.462 0.00 0.00 33.53 2.29
4005 4592 2.260869 GCTTGGCTTGAGGTCGCAA 61.261 57.895 0.00 0.00 0.00 4.85
4222 4924 5.298026 GCTTCCTTGGATGGAGAGTAAAATC 59.702 44.000 4.98 0.00 37.43 2.17
4302 5007 5.027293 TGTAGACATCACCATGGATTGAG 57.973 43.478 21.47 9.12 33.82 3.02
4372 5077 2.032675 GCAATTCTCCGAATTCAGAGCC 59.967 50.000 13.01 0.00 0.00 4.70
4374 5079 5.277250 GCTAAGCAATTCTCCGAATTCAGAG 60.277 44.000 11.81 11.81 0.00 3.35
4512 5217 3.673338 TGCAACTAATTCTCGTGTCTTCG 59.327 43.478 0.00 0.00 0.00 3.79
4520 5225 3.178618 CGAGACGATGCAACTAATTCTCG 59.821 47.826 14.80 14.80 43.35 4.04
4572 5277 0.464036 TGCGTTCAGTTGGTGTCTCT 59.536 50.000 0.00 0.00 0.00 3.10
4578 5283 4.050553 CAATTTGAATGCGTTCAGTTGGT 58.949 39.130 25.85 11.33 44.62 3.67
4721 5426 6.450545 ACAGAGTTAAAACGACTAGGTTACC 58.549 40.000 0.00 0.00 0.00 2.85
4747 5531 5.764192 GGATCTTCAGCTTTCAGCATCTTAT 59.236 40.000 0.00 0.00 45.56 1.73
4786 5570 6.159988 AGAGAATTGTCGTTGACTCCTTAAG 58.840 40.000 0.00 0.00 33.15 1.85
4800 5584 7.322222 CGACACTGAAAAATCAAGAGAATTGTC 59.678 37.037 0.00 0.00 0.00 3.18
4837 5621 7.928307 TCAGTTCCTTATCTGGAATTTCTTG 57.072 36.000 0.00 0.00 46.36 3.02
4904 5690 7.511959 AAGAAAAATCCAAGTGAGACTAACC 57.488 36.000 0.00 0.00 0.00 2.85
4917 5703 7.656948 CCTGCAATTTCAGTTAAGAAAAATCCA 59.343 33.333 4.38 0.00 40.54 3.41
4918 5704 7.872483 TCCTGCAATTTCAGTTAAGAAAAATCC 59.128 33.333 4.38 0.00 40.54 3.01
4919 5705 8.816640 TCCTGCAATTTCAGTTAAGAAAAATC 57.183 30.769 4.38 0.00 40.54 2.17
4920 5706 9.045223 GTTCCTGCAATTTCAGTTAAGAAAAAT 57.955 29.630 4.38 0.00 40.54 1.82
4921 5707 8.037758 TGTTCCTGCAATTTCAGTTAAGAAAAA 58.962 29.630 4.38 0.00 40.54 1.94
4922 5708 7.491048 GTGTTCCTGCAATTTCAGTTAAGAAAA 59.509 33.333 4.38 0.00 40.54 2.29
4923 5709 6.978080 GTGTTCCTGCAATTTCAGTTAAGAAA 59.022 34.615 4.38 0.00 41.31 2.52
4924 5710 6.096141 TGTGTTCCTGCAATTTCAGTTAAGAA 59.904 34.615 4.38 0.00 32.32 2.52
4925 5711 5.592282 TGTGTTCCTGCAATTTCAGTTAAGA 59.408 36.000 4.38 0.00 32.32 2.10
4926 5712 5.687285 GTGTGTTCCTGCAATTTCAGTTAAG 59.313 40.000 4.38 0.00 32.32 1.85
4927 5713 5.359576 AGTGTGTTCCTGCAATTTCAGTTAA 59.640 36.000 4.38 0.00 32.32 2.01
4928 5714 4.887071 AGTGTGTTCCTGCAATTTCAGTTA 59.113 37.500 4.38 0.00 32.32 2.24
4929 5715 3.701040 AGTGTGTTCCTGCAATTTCAGTT 59.299 39.130 4.38 0.00 32.32 3.16
4930 5716 3.067180 CAGTGTGTTCCTGCAATTTCAGT 59.933 43.478 4.38 0.00 32.32 3.41
4931 5717 3.316029 TCAGTGTGTTCCTGCAATTTCAG 59.684 43.478 0.00 0.00 0.00 3.02
4932 5718 3.286353 TCAGTGTGTTCCTGCAATTTCA 58.714 40.909 0.00 0.00 0.00 2.69
4935 5721 5.012239 ACATATCAGTGTGTTCCTGCAATT 58.988 37.500 0.00 0.00 0.00 2.32
4936 5722 4.397103 CACATATCAGTGTGTTCCTGCAAT 59.603 41.667 0.00 0.00 43.43 3.56
4938 5724 3.337358 CACATATCAGTGTGTTCCTGCA 58.663 45.455 0.00 0.00 43.43 4.41
4947 5733 3.119101 GGAACCTCGTCACATATCAGTGT 60.119 47.826 0.00 0.00 40.37 3.55
4948 5734 3.448686 GGAACCTCGTCACATATCAGTG 58.551 50.000 0.00 0.00 40.85 3.66
4950 5736 2.732366 CGGAACCTCGTCACATATCAG 58.268 52.381 0.00 0.00 0.00 2.90
4951 5737 1.202371 GCGGAACCTCGTCACATATCA 60.202 52.381 0.00 0.00 0.00 2.15
4954 5740 0.604073 TTGCGGAACCTCGTCACATA 59.396 50.000 0.00 0.00 0.00 2.29
4955 5741 0.250124 TTTGCGGAACCTCGTCACAT 60.250 50.000 0.00 0.00 0.00 3.21
4956 5742 0.462225 TTTTGCGGAACCTCGTCACA 60.462 50.000 0.00 0.00 0.00 3.58
4957 5743 0.872388 ATTTTGCGGAACCTCGTCAC 59.128 50.000 0.00 0.00 0.00 3.67
4958 5744 2.459060 TATTTTGCGGAACCTCGTCA 57.541 45.000 0.00 0.00 0.00 4.35
4959 5745 4.351131 AAATATTTTGCGGAACCTCGTC 57.649 40.909 0.00 0.00 0.00 4.20
4960 5746 4.776795 AAAATATTTTGCGGAACCTCGT 57.223 36.364 12.62 0.00 0.00 4.18
4961 5747 4.201580 GCAAAAATATTTTGCGGAACCTCG 60.202 41.667 20.62 0.00 44.13 4.63
4962 5748 5.203358 GCAAAAATATTTTGCGGAACCTC 57.797 39.130 20.62 0.00 44.13 3.85
4983 5769 6.258727 TCTGCAAGAATACTAATACAAGCTGC 59.741 38.462 0.00 0.00 42.31 5.25
4984 5770 7.776933 TCTGCAAGAATACTAATACAAGCTG 57.223 36.000 0.00 0.00 42.31 4.24
5001 5789 2.450476 AGCTGGGGTAAAATCTGCAAG 58.550 47.619 0.00 0.00 0.00 4.01
5014 5802 0.466124 GCCTCTTGTACTAGCTGGGG 59.534 60.000 0.85 8.64 0.00 4.96
5019 5807 3.310246 GCGATAAGCCTCTTGTACTAGC 58.690 50.000 0.00 0.00 40.81 3.42
5073 5902 7.476540 TGGTTAGACTTATTGCTTAGTCAGA 57.523 36.000 0.00 0.00 42.51 3.27
5085 5914 7.179076 ACGTGGAAAGTATGGTTAGACTTAT 57.821 36.000 0.00 0.00 37.37 1.73
5142 6113 2.467826 GCACCTTCGAGCCTCATGC 61.468 63.158 0.00 0.00 41.71 4.06
5231 6202 3.612717 CGCATCACATTCTCTACCGCTAT 60.613 47.826 0.00 0.00 0.00 2.97
5266 6237 1.887707 CTTCTTACGGGCGATGGGC 60.888 63.158 0.00 0.00 42.51 5.36
5273 6244 3.869832 GTCCAATTACTCTTCTTACGGGC 59.130 47.826 0.00 0.00 0.00 6.13
5281 6252 2.396590 TGGCCGTCCAATTACTCTTC 57.603 50.000 0.00 0.00 39.99 2.87
5312 6283 1.060698 GAGCGGCGTTACTTGATCAAC 59.939 52.381 9.37 0.00 0.00 3.18
5330 6301 2.069273 GACATGAACTCGTGTTGGGAG 58.931 52.381 7.72 0.00 45.32 4.30
5355 6326 3.699538 ACGCTGGTACTACAAGATGATGA 59.300 43.478 0.00 0.00 0.00 2.92
5380 6351 1.973281 CCGCAGCCTGTGTCCATTT 60.973 57.895 4.32 0.00 0.00 2.32
5381 6352 2.360350 CCGCAGCCTGTGTCCATT 60.360 61.111 4.32 0.00 0.00 3.16
5414 6385 0.673644 TTTGCCTGGTCGCTTCTAGC 60.674 55.000 0.00 0.00 38.02 3.42
5478 6449 2.822701 GCCCGATTCGTTGGACCC 60.823 66.667 5.20 0.00 0.00 4.46
5506 8180 1.615107 GGAAGACGAGACGTTTGGCG 61.615 60.000 0.00 0.00 41.37 5.69
5551 8225 2.742372 ATGTCAAGACGCCGTGCC 60.742 61.111 0.00 0.00 0.00 5.01
5555 8229 2.100631 GGACCATGTCAAGACGCCG 61.101 63.158 0.00 0.00 33.68 6.46
5558 8232 0.319555 ACACGGACCATGTCAAGACG 60.320 55.000 0.00 0.00 33.68 4.18
5559 8233 1.429463 GACACGGACCATGTCAAGAC 58.571 55.000 15.68 0.00 44.87 3.01
5560 8234 0.320374 GGACACGGACCATGTCAAGA 59.680 55.000 21.44 0.00 46.89 3.02
5561 8235 0.034756 TGGACACGGACCATGTCAAG 59.965 55.000 21.44 0.00 46.89 3.02
5562 8236 0.690192 ATGGACACGGACCATGTCAA 59.310 50.000 21.44 11.76 46.89 3.18
5563 8237 2.371784 ATGGACACGGACCATGTCA 58.628 52.632 21.44 8.83 46.89 3.58
5569 8243 2.521958 CTGGGTCATGGACACGGACC 62.522 65.000 13.66 13.66 44.42 4.46
5570 8244 1.079127 CTGGGTCATGGACACGGAC 60.079 63.158 1.14 0.00 44.42 4.79
5571 8245 3.387716 CTGGGTCATGGACACGGA 58.612 61.111 1.14 0.00 44.42 4.69
5572 8246 0.673644 GTTCTGGGTCATGGACACGG 60.674 60.000 0.96 0.96 43.14 4.94
5573 8247 0.034756 TGTTCTGGGTCATGGACACG 59.965 55.000 0.00 0.00 39.08 4.49
5574 8248 2.086869 CATGTTCTGGGTCATGGACAC 58.913 52.381 0.00 0.00 38.10 3.67
5575 8249 1.614051 GCATGTTCTGGGTCATGGACA 60.614 52.381 7.15 0.00 40.91 4.02
5576 8250 1.098050 GCATGTTCTGGGTCATGGAC 58.902 55.000 7.15 0.00 40.91 4.02
5577 8251 0.392863 CGCATGTTCTGGGTCATGGA 60.393 55.000 7.15 0.00 40.91 3.41
5578 8252 1.996786 GCGCATGTTCTGGGTCATGG 61.997 60.000 0.30 0.28 40.91 3.66
5579 8253 1.430632 GCGCATGTTCTGGGTCATG 59.569 57.895 0.30 0.00 42.71 3.07
5580 8254 1.750399 GGCGCATGTTCTGGGTCAT 60.750 57.895 10.83 0.00 41.76 3.06
5581 8255 2.359850 GGCGCATGTTCTGGGTCA 60.360 61.111 10.83 0.00 41.76 4.02
5582 8256 3.134127 GGGCGCATGTTCTGGGTC 61.134 66.667 10.83 0.00 41.44 4.46
5583 8257 4.740822 GGGGCGCATGTTCTGGGT 62.741 66.667 10.83 0.00 39.88 4.51
5584 8258 3.944250 AAGGGGCGCATGTTCTGGG 62.944 63.158 10.83 0.00 40.65 4.45
5585 8259 2.361610 AAGGGGCGCATGTTCTGG 60.362 61.111 10.83 0.00 0.00 3.86
5586 8260 1.675310 TCAAGGGGCGCATGTTCTG 60.675 57.895 10.83 0.00 0.00 3.02
5587 8261 1.675641 GTCAAGGGGCGCATGTTCT 60.676 57.895 10.83 0.00 0.00 3.01
5588 8262 2.700773 GGTCAAGGGGCGCATGTTC 61.701 63.158 10.83 0.00 0.00 3.18
5589 8263 2.676471 GGTCAAGGGGCGCATGTT 60.676 61.111 10.83 0.00 0.00 2.71
5591 8265 4.776322 TCGGTCAAGGGGCGCATG 62.776 66.667 10.83 1.66 0.00 4.06
5592 8266 2.837031 AAATCGGTCAAGGGGCGCAT 62.837 55.000 10.83 0.00 0.00 4.73
5593 8267 3.561120 AAATCGGTCAAGGGGCGCA 62.561 57.895 10.83 0.00 0.00 6.09
5594 8268 2.750237 AAATCGGTCAAGGGGCGC 60.750 61.111 0.00 0.00 0.00 6.53
5595 8269 1.376683 TCAAATCGGTCAAGGGGCG 60.377 57.895 0.00 0.00 0.00 6.13
5596 8270 1.313091 GGTCAAATCGGTCAAGGGGC 61.313 60.000 0.00 0.00 0.00 5.80
5597 8271 1.024579 CGGTCAAATCGGTCAAGGGG 61.025 60.000 0.00 0.00 0.00 4.79
5598 8272 0.321298 ACGGTCAAATCGGTCAAGGG 60.321 55.000 0.00 0.00 0.00 3.95
5599 8273 1.076332 GACGGTCAAATCGGTCAAGG 58.924 55.000 2.62 0.00 37.52 3.61
5600 8274 1.726791 CTGACGGTCAAATCGGTCAAG 59.273 52.381 12.54 0.00 43.35 3.02
5601 8275 1.790755 CTGACGGTCAAATCGGTCAA 58.209 50.000 12.54 0.00 43.35 3.18
5602 8276 0.669318 GCTGACGGTCAAATCGGTCA 60.669 55.000 12.54 6.84 42.38 4.02
5603 8277 1.359459 GGCTGACGGTCAAATCGGTC 61.359 60.000 12.54 0.00 37.89 4.79
5604 8278 1.375523 GGCTGACGGTCAAATCGGT 60.376 57.895 12.54 0.00 0.00 4.69
5605 8279 1.375396 TGGCTGACGGTCAAATCGG 60.375 57.895 12.54 1.15 0.00 4.18
5606 8280 0.670546 AGTGGCTGACGGTCAAATCG 60.671 55.000 12.54 1.54 0.00 3.34
5607 8281 1.079503 GAGTGGCTGACGGTCAAATC 58.920 55.000 12.54 2.77 0.00 2.17
5608 8282 0.670546 CGAGTGGCTGACGGTCAAAT 60.671 55.000 12.54 0.00 0.00 2.32
5609 8283 1.300620 CGAGTGGCTGACGGTCAAA 60.301 57.895 12.54 0.00 0.00 2.69
5610 8284 2.338620 CGAGTGGCTGACGGTCAA 59.661 61.111 12.54 0.00 0.00 3.18
5611 8285 3.680786 CCGAGTGGCTGACGGTCA 61.681 66.667 10.88 10.88 41.47 4.02
5630 8304 4.963428 GATCCGCCTTACCCGCCG 62.963 72.222 0.00 0.00 0.00 6.46
5631 8305 4.963428 CGATCCGCCTTACCCGCC 62.963 72.222 0.00 0.00 0.00 6.13
5632 8306 4.963428 CCGATCCGCCTTACCCGC 62.963 72.222 0.00 0.00 0.00 6.13
5633 8307 3.534056 ACCGATCCGCCTTACCCG 61.534 66.667 0.00 0.00 0.00 5.28
5634 8308 2.108362 CACCGATCCGCCTTACCC 59.892 66.667 0.00 0.00 0.00 3.69
5635 8309 2.108362 CCACCGATCCGCCTTACC 59.892 66.667 0.00 0.00 0.00 2.85
5636 8310 2.588034 GCCACCGATCCGCCTTAC 60.588 66.667 0.00 0.00 0.00 2.34


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

AutoCloner maintained by Alex Coulton.