Multiple sequence alignment - TraesCS2B01G364200

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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 TraesCS2B01G364200 chr2B 100.000 5708 0 0 1 5708 518512704 518518411 0.000000e+00 10541
1 TraesCS2B01G364200 chr2B 97.273 110 3 0 5098 5207 764550660 764550769 2.720000e-43 187
2 TraesCS2B01G364200 chr2B 96.429 112 4 0 5098 5209 131311723 131311834 9.770000e-43 185
3 TraesCS2B01G364200 chr2A 94.154 4379 154 43 796 5100 584062685 584067035 0.000000e+00 6575
4 TraesCS2B01G364200 chr2A 94.040 302 15 3 5409 5708 584067320 584067620 6.740000e-124 455
5 TraesCS2B01G364200 chr2A 94.366 213 12 0 5203 5415 584067033 584067245 1.530000e-85 327
6 TraesCS2B01G364200 chr2A 98.165 109 2 0 5098 5206 758757139 758757247 2.100000e-44 191
7 TraesCS2B01G364200 chr2D 95.312 2944 76 22 796 3697 440607962 440610885 0.000000e+00 4615
8 TraesCS2B01G364200 chr2D 98.552 829 9 2 3917 4744 440610888 440611714 0.000000e+00 1461
9 TraesCS2B01G364200 chr2D 84.366 710 85 21 88 775 544204584 544205289 0.000000e+00 673
10 TraesCS2B01G364200 chr2D 87.162 444 36 14 5203 5628 440612387 440612827 8.600000e-133 484
11 TraesCS2B01G364200 chr2D 95.455 88 4 0 5621 5708 440614932 440615019 2.140000e-29 141
12 TraesCS2B01G364200 chr7B 85.655 718 77 7 84 775 715364753 715365470 0.000000e+00 732
13 TraesCS2B01G364200 chr7B 84.211 627 72 6 88 688 711737220 711736595 8.240000e-163 584
14 TraesCS2B01G364200 chr7B 95.536 112 5 0 5098 5209 695049395 695049284 4.540000e-41 180
15 TraesCS2B01G364200 chr6B 87.652 575 68 3 202 774 681075886 681075313 0.000000e+00 665
16 TraesCS2B01G364200 chr6B 97.273 110 3 0 5098 5207 460495302 460495411 2.720000e-43 187
17 TraesCS2B01G364200 chr3D 86.855 601 70 8 104 696 515704796 515704197 0.000000e+00 664
18 TraesCS2B01G364200 chr3D 82.143 308 30 6 82 366 6025241 6024936 2.060000e-59 241
19 TraesCS2B01G364200 chrUn 83.170 713 93 9 88 775 98340195 98340905 1.350000e-175 627
20 TraesCS2B01G364200 chrUn 95.536 112 5 0 5098 5209 347838625 347838514 4.540000e-41 180
21 TraesCS2B01G364200 chrUn 93.388 121 8 0 5089 5209 441816721 441816841 4.540000e-41 180
22 TraesCS2B01G364200 chr5D 83.191 702 94 6 98 775 369106187 369105486 6.280000e-174 621
23 TraesCS2B01G364200 chr5A 83.006 712 94 11 88 774 471402601 471401892 2.260000e-173 619
24 TraesCS2B01G364200 chr5A 82.270 705 98 8 86 763 580409740 580410444 8.240000e-163 584
25 TraesCS2B01G364200 chr1A 82.402 716 77 19 86 777 50834347 50835037 3.830000e-161 579
26 TraesCS2B01G364200 chr1A 94.872 117 5 1 5098 5214 584968576 584968691 1.260000e-41 182
27 TraesCS2B01G364200 chr3B 81.062 697 100 13 89 759 822004377 822005067 1.410000e-145 527
28 TraesCS2B01G364200 chr3B 81.062 697 100 12 89 759 822019350 822020040 1.410000e-145 527
29 TraesCS2B01G364200 chr3B 83.908 261 19 2 88 325 409536837 409536577 1.600000e-55 228
30 TraesCS2B01G364200 chr7D 81.042 691 101 20 108 775 61232848 61232165 1.820000e-144 523
31 TraesCS2B01G364200 chr7A 83.206 262 19 8 88 325 269965211 269965471 3.460000e-52 217
32 TraesCS2B01G364200 chr7A 98.148 108 2 0 5098 5205 442030115 442030008 7.550000e-44 189


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 TraesCS2B01G364200 chr2B 518512704 518518411 5707 False 10541.000000 10541 100.000000 1 5708 1 chr2B.!!$F2 5707
1 TraesCS2B01G364200 chr2A 584062685 584067620 4935 False 2452.333333 6575 94.186667 796 5708 3 chr2A.!!$F2 4912
2 TraesCS2B01G364200 chr2D 440607962 440615019 7057 False 1675.250000 4615 94.120250 796 5708 4 chr2D.!!$F2 4912
3 TraesCS2B01G364200 chr2D 544204584 544205289 705 False 673.000000 673 84.366000 88 775 1 chr2D.!!$F1 687
4 TraesCS2B01G364200 chr7B 715364753 715365470 717 False 732.000000 732 85.655000 84 775 1 chr7B.!!$F1 691
5 TraesCS2B01G364200 chr7B 711736595 711737220 625 True 584.000000 584 84.211000 88 688 1 chr7B.!!$R2 600
6 TraesCS2B01G364200 chr6B 681075313 681075886 573 True 665.000000 665 87.652000 202 774 1 chr6B.!!$R1 572
7 TraesCS2B01G364200 chr3D 515704197 515704796 599 True 664.000000 664 86.855000 104 696 1 chr3D.!!$R2 592
8 TraesCS2B01G364200 chrUn 98340195 98340905 710 False 627.000000 627 83.170000 88 775 1 chrUn.!!$F1 687
9 TraesCS2B01G364200 chr5D 369105486 369106187 701 True 621.000000 621 83.191000 98 775 1 chr5D.!!$R1 677
10 TraesCS2B01G364200 chr5A 471401892 471402601 709 True 619.000000 619 83.006000 88 774 1 chr5A.!!$R1 686
11 TraesCS2B01G364200 chr5A 580409740 580410444 704 False 584.000000 584 82.270000 86 763 1 chr5A.!!$F1 677
12 TraesCS2B01G364200 chr1A 50834347 50835037 690 False 579.000000 579 82.402000 86 777 1 chr1A.!!$F1 691
13 TraesCS2B01G364200 chr3B 822004377 822005067 690 False 527.000000 527 81.062000 89 759 1 chr3B.!!$F1 670
14 TraesCS2B01G364200 chr3B 822019350 822020040 690 False 527.000000 527 81.062000 89 759 1 chr3B.!!$F2 670
15 TraesCS2B01G364200 chr7D 61232165 61232848 683 True 523.000000 523 81.042000 108 775 1 chr7D.!!$R1 667

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
82 83 0.110192 GTAAAAGCAGCGCACCTGTC 60.110 55.0 11.47 0.0 43.71 3.51 F
382 428 0.390866 AAGCGACGAGACCGAGACTA 60.391 55.0 0.00 0.0 39.50 2.59 F
1411 1516 0.940126 AGTGCTTGACTCGCAACTTG 59.060 50.0 0.00 0.0 39.39 3.16 F
1507 1612 0.730494 GCTTGCTTCGTGTGGCAATC 60.730 55.0 0.00 0.0 45.47 2.67 F
3126 3247 0.038159 GGAGCGAGATACCAATCCCG 60.038 60.0 0.00 0.0 36.51 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1411 1516 0.107654 AACTGCATTAGGTCGAGGGC 60.108 55.000 0.00 0.0 0.00 5.19 R
1441 1546 1.167851 ACAATCAAGCACACGATGGG 58.832 50.000 0.00 0.0 0.00 4.00 R
3087 3208 1.065102 CTCCATTCTTGCTCCAATGCG 59.935 52.381 0.00 0.0 35.36 4.73 R
3308 3435 5.505181 TCTTGCCCAGAACTTATTCTTCT 57.495 39.130 0.00 0.0 42.91 2.85 R
5101 5553 1.479323 TGAGTAATTCCGAACGGAGGG 59.521 52.381 15.34 0.0 46.06 4.30 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
18 19 3.690487 TCCTTTGTGTACCACCACG 57.310 52.632 0.00 0.00 38.20 4.94
19 20 0.533308 TCCTTTGTGTACCACCACGC 60.533 55.000 0.00 0.00 38.20 5.34
20 21 1.512156 CCTTTGTGTACCACCACGCC 61.512 60.000 0.00 0.00 38.20 5.68
21 22 0.816018 CTTTGTGTACCACCACGCCA 60.816 55.000 0.00 0.00 38.20 5.69
22 23 0.179015 TTTGTGTACCACCACGCCAT 60.179 50.000 0.00 0.00 38.20 4.40
23 24 0.604243 TTGTGTACCACCACGCCATC 60.604 55.000 0.00 0.00 38.20 3.51
24 25 2.098233 GTGTACCACCACGCCATCG 61.098 63.158 0.00 0.00 42.43 3.84
25 26 3.192922 GTACCACCACGCCATCGC 61.193 66.667 0.00 0.00 39.84 4.58
26 27 4.460683 TACCACCACGCCATCGCC 62.461 66.667 0.00 0.00 39.84 5.54
30 31 4.467084 ACCACGCCATCGCCGAAT 62.467 61.111 0.00 0.00 39.84 3.34
31 32 2.279851 CCACGCCATCGCCGAATA 60.280 61.111 0.00 0.00 39.84 1.75
32 33 2.594962 CCACGCCATCGCCGAATAC 61.595 63.158 0.00 0.00 39.84 1.89
33 34 2.279918 ACGCCATCGCCGAATACC 60.280 61.111 0.00 0.00 39.84 2.73
34 35 3.041940 CGCCATCGCCGAATACCC 61.042 66.667 0.00 0.00 0.00 3.69
35 36 2.426023 GCCATCGCCGAATACCCT 59.574 61.111 0.00 0.00 0.00 4.34
36 37 1.227853 GCCATCGCCGAATACCCTT 60.228 57.895 0.00 0.00 0.00 3.95
37 38 0.818040 GCCATCGCCGAATACCCTTT 60.818 55.000 0.00 0.00 0.00 3.11
38 39 1.675552 CCATCGCCGAATACCCTTTT 58.324 50.000 0.00 0.00 0.00 2.27
39 40 2.021457 CCATCGCCGAATACCCTTTTT 58.979 47.619 0.00 0.00 0.00 1.94
40 41 3.207778 CCATCGCCGAATACCCTTTTTA 58.792 45.455 0.00 0.00 0.00 1.52
41 42 3.628487 CCATCGCCGAATACCCTTTTTAA 59.372 43.478 0.00 0.00 0.00 1.52
42 43 4.261031 CCATCGCCGAATACCCTTTTTAAG 60.261 45.833 0.00 0.00 0.00 1.85
60 61 9.875691 CTTTTTAAGGAAGGATTTTTATGGGAG 57.124 33.333 0.00 0.00 0.00 4.30
61 62 7.418337 TTTAAGGAAGGATTTTTATGGGAGC 57.582 36.000 0.00 0.00 0.00 4.70
62 63 3.555966 AGGAAGGATTTTTATGGGAGCG 58.444 45.455 0.00 0.00 0.00 5.03
63 64 2.623416 GGAAGGATTTTTATGGGAGCGG 59.377 50.000 0.00 0.00 0.00 5.52
64 65 3.288092 GAAGGATTTTTATGGGAGCGGT 58.712 45.455 0.00 0.00 0.00 5.68
65 66 4.457466 GAAGGATTTTTATGGGAGCGGTA 58.543 43.478 0.00 0.00 0.00 4.02
66 67 4.513406 AGGATTTTTATGGGAGCGGTAA 57.487 40.909 0.00 0.00 0.00 2.85
67 68 4.862371 AGGATTTTTATGGGAGCGGTAAA 58.138 39.130 0.00 0.00 0.00 2.01
68 69 5.265989 AGGATTTTTATGGGAGCGGTAAAA 58.734 37.500 0.00 0.00 0.00 1.52
69 70 5.359860 AGGATTTTTATGGGAGCGGTAAAAG 59.640 40.000 0.00 0.00 31.33 2.27
70 71 4.443913 TTTTTATGGGAGCGGTAAAAGC 57.556 40.909 0.00 0.00 31.33 3.51
71 72 2.791347 TTATGGGAGCGGTAAAAGCA 57.209 45.000 0.00 0.00 37.01 3.91
72 73 2.325583 TATGGGAGCGGTAAAAGCAG 57.674 50.000 0.00 0.00 37.01 4.24
73 74 1.032114 ATGGGAGCGGTAAAAGCAGC 61.032 55.000 0.00 0.00 37.01 5.25
74 75 2.750888 GGGAGCGGTAAAAGCAGCG 61.751 63.158 0.00 0.00 42.13 5.18
78 79 2.175811 CGGTAAAAGCAGCGCACC 59.824 61.111 11.47 5.30 32.13 5.01
79 80 2.325082 CGGTAAAAGCAGCGCACCT 61.325 57.895 11.47 1.13 32.13 4.00
80 81 1.210155 GGTAAAAGCAGCGCACCTG 59.790 57.895 11.47 0.00 44.67 4.00
81 82 1.515521 GGTAAAAGCAGCGCACCTGT 61.516 55.000 11.47 0.00 43.71 4.00
82 83 0.110192 GTAAAAGCAGCGCACCTGTC 60.110 55.000 11.47 0.00 43.71 3.51
83 84 0.533978 TAAAAGCAGCGCACCTGTCA 60.534 50.000 11.47 0.00 43.71 3.58
84 85 1.383456 AAAAGCAGCGCACCTGTCAA 61.383 50.000 11.47 0.00 43.71 3.18
209 239 4.142988 TGCATTAAAGACTTAACTTCGGCG 60.143 41.667 0.00 0.00 29.82 6.46
217 247 4.159135 AGACTTAACTTCGGCGGAATCTTA 59.841 41.667 7.21 4.11 0.00 2.10
247 277 0.608035 AAACATCGCCCACCATCGTT 60.608 50.000 0.00 0.00 0.00 3.85
258 288 0.968901 ACCATCGTTCTCCACCGCTA 60.969 55.000 0.00 0.00 0.00 4.26
269 315 2.094659 CACCGCTACTGAGGCAACG 61.095 63.158 0.00 0.00 46.39 4.10
271 317 2.094659 CCGCTACTGAGGCAACGTG 61.095 63.158 0.00 0.00 46.39 4.49
382 428 0.390866 AAGCGACGAGACCGAGACTA 60.391 55.000 0.00 0.00 39.50 2.59
415 462 1.666872 GTGGTTCTTCCCCGTGTCG 60.667 63.158 0.00 0.00 34.77 4.35
417 464 2.739132 GTTCTTCCCCGTGTCGGT 59.261 61.111 7.40 0.00 46.80 4.69
523 570 2.951642 AGACATCAAACACAACCACAGG 59.048 45.455 0.00 0.00 0.00 4.00
574 621 1.369091 GAGCGCCGACCATCAAACAT 61.369 55.000 2.29 0.00 0.00 2.71
577 624 1.268032 GCGCCGACCATCAAACATAAG 60.268 52.381 0.00 0.00 0.00 1.73
691 740 2.726681 GCAAATTATTTCGACACGGCGT 60.727 45.455 6.77 6.77 0.00 5.68
715 764 5.248477 TCCTCTCTACCATTAAAGCAACACT 59.752 40.000 0.00 0.00 0.00 3.55
738 795 8.299570 CACTTTTGAGAACAAACTATGCCTATT 58.700 33.333 0.00 0.00 44.22 1.73
753 810 8.837737 ACTATGCCTATTCTATACCTCTACTGA 58.162 37.037 0.00 0.00 0.00 3.41
757 814 8.225416 TGCCTATTCTATACCTCTACTGAAGAA 58.775 37.037 0.00 0.00 32.46 2.52
779 836 4.660611 TGCCGGGGTCCCCACTTA 62.661 66.667 27.45 6.92 45.83 2.24
780 837 3.094498 GCCGGGGTCCCCACTTAT 61.094 66.667 27.45 0.00 45.83 1.73
781 838 2.915869 CCGGGGTCCCCACTTATG 59.084 66.667 27.45 9.03 45.83 1.90
782 839 2.752807 CCGGGGTCCCCACTTATGG 61.753 68.421 27.45 14.58 45.83 2.74
794 851 3.313012 CACTTATGGACACCTCGTGAA 57.687 47.619 0.00 0.00 36.96 3.18
834 893 4.672542 CGGTAATTGTTGGTGATGCTCTTG 60.673 45.833 0.00 0.00 0.00 3.02
887 946 7.778470 ATAATTCCAAGAGCTCTAACGAAAG 57.222 36.000 18.59 1.09 0.00 2.62
909 968 2.069277 CGTTTTGTTCTCTGCGCGC 61.069 57.895 27.26 27.26 0.00 6.86
1373 1472 5.392811 GCAGAGTAGAAATTCATTTGCTGCT 60.393 40.000 15.33 0.00 0.00 4.24
1411 1516 0.940126 AGTGCTTGACTCGCAACTTG 59.060 50.000 0.00 0.00 39.39 3.16
1441 1546 1.151668 AATGCAGTTCACTCGAGCAC 58.848 50.000 13.61 7.13 38.12 4.40
1479 1584 8.006298 TGATTGTTAGGTGTGAACTTTGAAAT 57.994 30.769 0.00 0.00 0.00 2.17
1507 1612 0.730494 GCTTGCTTCGTGTGGCAATC 60.730 55.000 0.00 0.00 45.47 2.67
1516 1621 3.937814 TCGTGTGGCAATCTAGATGTTT 58.062 40.909 5.86 0.00 0.00 2.83
1538 1643 4.569943 TGAGTCTCTAATTGCAGAACACC 58.430 43.478 0.65 0.00 0.00 4.16
1726 1837 3.937814 TGTCATGACCTATGTTGTGACC 58.062 45.455 22.85 0.00 37.89 4.02
2090 2201 8.540388 TGCCTATTTTTCTGTACTGTCTAAGAT 58.460 33.333 0.00 0.00 0.00 2.40
2091 2202 9.036671 GCCTATTTTTCTGTACTGTCTAAGATC 57.963 37.037 0.00 0.00 0.00 2.75
2191 2302 1.513858 TGTTGTAGTTGTGGAGGGGT 58.486 50.000 0.00 0.00 0.00 4.95
2401 2512 7.677454 TGCATGACCTCATTATAAATAGCTG 57.323 36.000 0.00 0.00 33.61 4.24
2415 2533 7.873739 ATAAATAGCTGCGATAAATTTTGCC 57.126 32.000 0.00 0.00 0.00 4.52
2828 2946 6.616947 ACGAGTCTTGTTTCATTTTTCACAA 58.383 32.000 0.00 0.00 0.00 3.33
3050 3171 1.677217 GGAGGACAGACATGAACCTGC 60.677 57.143 0.00 2.18 37.07 4.85
3087 3208 2.280628 CTCGCAGTTAAGGATGGGAAC 58.719 52.381 4.33 0.00 37.84 3.62
3126 3247 0.038159 GGAGCGAGATACCAATCCCG 60.038 60.000 0.00 0.00 36.51 5.14
3174 3295 1.065199 TCCCCTTCATGTGACATCTGC 60.065 52.381 0.00 0.00 0.00 4.26
3175 3296 1.340308 CCCCTTCATGTGACATCTGCA 60.340 52.381 0.00 0.00 0.00 4.41
3176 3297 2.439409 CCCTTCATGTGACATCTGCAA 58.561 47.619 0.00 0.00 0.00 4.08
3538 3665 8.254508 AGAAGAAGTGAGGTATGTTGATACTTC 58.745 37.037 0.00 0.00 40.15 3.01
3646 3773 1.650314 TTGCGCATCTCAGCCATGTG 61.650 55.000 12.75 0.00 35.27 3.21
3649 3776 0.376152 CGCATCTCAGCCATGTGTTC 59.624 55.000 0.00 0.00 0.00 3.18
3728 3855 3.560636 ACTAGTGTGGACTGCAGTTTT 57.439 42.857 22.65 0.00 33.21 2.43
3737 3864 4.515191 GTGGACTGCAGTTTTGATACAGAA 59.485 41.667 22.65 0.00 32.67 3.02
3767 3894 7.173907 AGGTCTGTTTTTCTATGAGTGATTGTG 59.826 37.037 0.00 0.00 0.00 3.33
3848 3975 6.216801 TCGTATGGTACCATAATAGGATGC 57.783 41.667 31.64 17.55 40.15 3.91
3854 3981 6.717289 TGGTACCATAATAGGATGCATTACC 58.283 40.000 11.60 5.31 31.78 2.85
3901 4028 6.976349 TCGCGTGTTTATCAACATAGATACTT 59.024 34.615 5.77 0.00 44.85 2.24
4587 4715 1.003118 CCTTTCCGGATCAAGACCACA 59.997 52.381 16.06 0.00 33.16 4.17
4744 4872 5.356470 AGAACTGATTTTAGCAGAGCATTCC 59.644 40.000 0.00 0.00 36.86 3.01
4759 4887 7.249147 CAGAGCATTCCTTCAGTATTCTTTTG 58.751 38.462 0.00 0.00 0.00 2.44
4770 4898 9.449719 CTTCAGTATTCTTTTGGGTACATAACT 57.550 33.333 0.00 0.00 0.00 2.24
4823 4951 8.395633 AGTTAGTTTATTGTCATACGAATTGGC 58.604 33.333 0.00 0.00 0.00 4.52
4875 5311 5.642063 GCCACTTACTCTGTTGTATGCTTAA 59.358 40.000 0.00 0.00 0.00 1.85
4999 5448 9.383519 TCTTGTGTTTCTTGATGTTCCTATATC 57.616 33.333 0.00 0.00 0.00 1.63
5029 5481 0.238553 GCAGTTCGTGGGAGAAAAGC 59.761 55.000 0.00 0.00 0.00 3.51
5039 5491 3.440522 GTGGGAGAAAAGCATCTTGTACC 59.559 47.826 0.00 0.00 0.00 3.34
5091 5543 0.951558 ATTCTCGCCGTTGCTTGTTT 59.048 45.000 0.00 0.00 34.43 2.83
5097 5549 1.263217 CGCCGTTGCTTGTTTACTCTT 59.737 47.619 0.00 0.00 34.43 2.85
5098 5550 2.477375 CGCCGTTGCTTGTTTACTCTTA 59.523 45.455 0.00 0.00 34.43 2.10
5099 5551 3.663493 CGCCGTTGCTTGTTTACTCTTAC 60.663 47.826 0.00 0.00 34.43 2.34
5100 5552 3.497262 GCCGTTGCTTGTTTACTCTTACT 59.503 43.478 0.00 0.00 33.53 2.24
5101 5553 4.377124 GCCGTTGCTTGTTTACTCTTACTC 60.377 45.833 0.00 0.00 33.53 2.59
5102 5554 4.151867 CCGTTGCTTGTTTACTCTTACTCC 59.848 45.833 0.00 0.00 0.00 3.85
5103 5555 4.151867 CGTTGCTTGTTTACTCTTACTCCC 59.848 45.833 0.00 0.00 0.00 4.30
5104 5556 5.306394 GTTGCTTGTTTACTCTTACTCCCT 58.694 41.667 0.00 0.00 0.00 4.20
5105 5557 5.148651 TGCTTGTTTACTCTTACTCCCTC 57.851 43.478 0.00 0.00 0.00 4.30
5106 5558 4.020485 TGCTTGTTTACTCTTACTCCCTCC 60.020 45.833 0.00 0.00 0.00 4.30
5107 5559 4.745649 CTTGTTTACTCTTACTCCCTCCG 58.254 47.826 0.00 0.00 0.00 4.63
5108 5560 3.771216 TGTTTACTCTTACTCCCTCCGT 58.229 45.455 0.00 0.00 0.00 4.69
5109 5561 4.154942 TGTTTACTCTTACTCCCTCCGTT 58.845 43.478 0.00 0.00 0.00 4.44
5110 5562 4.219288 TGTTTACTCTTACTCCCTCCGTTC 59.781 45.833 0.00 0.00 0.00 3.95
5111 5563 1.461559 ACTCTTACTCCCTCCGTTCG 58.538 55.000 0.00 0.00 0.00 3.95
5112 5564 0.739561 CTCTTACTCCCTCCGTTCGG 59.260 60.000 4.74 4.74 0.00 4.30
5113 5565 0.329261 TCTTACTCCCTCCGTTCGGA 59.671 55.000 13.34 13.34 0.00 4.55
5114 5566 1.180029 CTTACTCCCTCCGTTCGGAA 58.820 55.000 14.79 0.04 33.41 4.30
5115 5567 1.755380 CTTACTCCCTCCGTTCGGAAT 59.245 52.381 14.79 2.09 33.41 3.01
5116 5568 1.856629 TACTCCCTCCGTTCGGAATT 58.143 50.000 14.79 0.00 33.41 2.17
5117 5569 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
5118 5570 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
5119 5571 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
5120 5572 1.753073 TCCCTCCGTTCGGAATTACTC 59.247 52.381 14.79 0.00 33.41 2.59
5121 5573 1.479323 CCCTCCGTTCGGAATTACTCA 59.521 52.381 14.79 0.00 33.41 3.41
5122 5574 2.102588 CCCTCCGTTCGGAATTACTCAT 59.897 50.000 14.79 0.00 33.41 2.90
5123 5575 3.381949 CCTCCGTTCGGAATTACTCATC 58.618 50.000 14.79 0.00 33.41 2.92
5124 5576 3.068307 CCTCCGTTCGGAATTACTCATCT 59.932 47.826 14.79 0.00 33.41 2.90
5125 5577 4.277672 CCTCCGTTCGGAATTACTCATCTA 59.722 45.833 14.79 0.00 33.41 1.98
5126 5578 5.221185 CCTCCGTTCGGAATTACTCATCTAA 60.221 44.000 14.79 0.00 33.41 2.10
5127 5579 5.828747 TCCGTTCGGAATTACTCATCTAAG 58.171 41.667 11.66 0.00 0.00 2.18
5128 5580 5.591472 TCCGTTCGGAATTACTCATCTAAGA 59.409 40.000 11.66 0.00 0.00 2.10
5129 5581 6.095860 TCCGTTCGGAATTACTCATCTAAGAA 59.904 38.462 11.66 0.00 0.00 2.52
5130 5582 6.755141 CCGTTCGGAATTACTCATCTAAGAAA 59.245 38.462 5.19 0.00 0.00 2.52
5131 5583 7.438459 CCGTTCGGAATTACTCATCTAAGAAAT 59.562 37.037 5.19 0.00 0.00 2.17
5132 5584 8.269424 CGTTCGGAATTACTCATCTAAGAAATG 58.731 37.037 0.00 0.00 0.00 2.32
5133 5585 9.314321 GTTCGGAATTACTCATCTAAGAAATGA 57.686 33.333 0.00 0.00 0.00 2.57
5134 5586 9.884636 TTCGGAATTACTCATCTAAGAAATGAA 57.115 29.630 0.00 0.00 32.96 2.57
5143 5595 9.775854 ACTCATCTAAGAAATGAATGTATCCAG 57.224 33.333 0.00 0.00 32.96 3.86
5144 5596 9.993454 CTCATCTAAGAAATGAATGTATCCAGA 57.007 33.333 0.00 0.00 32.96 3.86
5178 5630 8.862325 AGTTGTAGATACATCCATTTTTGTGA 57.138 30.769 0.00 0.00 35.89 3.58
5179 5631 8.730680 AGTTGTAGATACATCCATTTTTGTGAC 58.269 33.333 0.00 0.00 35.89 3.67
5180 5632 8.511321 GTTGTAGATACATCCATTTTTGTGACA 58.489 33.333 0.00 0.00 35.89 3.58
5181 5633 8.628630 TGTAGATACATCCATTTTTGTGACAA 57.371 30.769 0.00 0.00 0.00 3.18
5182 5634 8.729756 TGTAGATACATCCATTTTTGTGACAAG 58.270 33.333 0.00 0.00 0.00 3.16
5183 5635 7.765695 AGATACATCCATTTTTGTGACAAGT 57.234 32.000 0.00 0.00 0.00 3.16
5184 5636 8.862325 AGATACATCCATTTTTGTGACAAGTA 57.138 30.769 0.00 0.00 0.00 2.24
5185 5637 9.295825 AGATACATCCATTTTTGTGACAAGTAA 57.704 29.630 0.00 0.00 0.00 2.24
5188 5640 8.816640 ACATCCATTTTTGTGACAAGTAATTC 57.183 30.769 0.00 0.00 0.00 2.17
5189 5641 7.872483 ACATCCATTTTTGTGACAAGTAATTCC 59.128 33.333 0.00 0.00 0.00 3.01
5190 5642 6.442952 TCCATTTTTGTGACAAGTAATTCCG 58.557 36.000 0.00 0.00 0.00 4.30
5191 5643 6.263392 TCCATTTTTGTGACAAGTAATTCCGA 59.737 34.615 0.00 0.00 0.00 4.55
5192 5644 6.920758 CCATTTTTGTGACAAGTAATTCCGAA 59.079 34.615 0.00 0.00 0.00 4.30
5193 5645 7.096230 CCATTTTTGTGACAAGTAATTCCGAAC 60.096 37.037 0.00 0.00 0.00 3.95
5194 5646 4.718858 TTGTGACAAGTAATTCCGAACG 57.281 40.909 0.00 0.00 0.00 3.95
5195 5647 3.061322 TGTGACAAGTAATTCCGAACGG 58.939 45.455 6.94 6.94 0.00 4.44
5196 5648 3.243805 TGTGACAAGTAATTCCGAACGGA 60.244 43.478 12.04 12.04 43.52 4.69
5197 5649 3.367025 GTGACAAGTAATTCCGAACGGAG 59.633 47.826 15.34 5.60 46.06 4.63
5198 5650 2.928116 GACAAGTAATTCCGAACGGAGG 59.072 50.000 15.34 4.52 46.06 4.30
5199 5651 2.277084 CAAGTAATTCCGAACGGAGGG 58.723 52.381 15.34 0.00 46.06 4.30
5200 5652 1.856629 AGTAATTCCGAACGGAGGGA 58.143 50.000 15.34 2.49 46.06 4.20
5201 5653 1.755380 AGTAATTCCGAACGGAGGGAG 59.245 52.381 15.34 0.00 46.06 4.30
5208 5660 2.958379 CCGAACGGAGGGAGTACATCC 61.958 61.905 7.53 0.00 42.14 3.51
5260 5712 5.185454 CAGGTAGTTTTCATATGCACTCCA 58.815 41.667 0.00 0.00 0.00 3.86
5295 5747 4.214971 CAGAAACACCTCTCATCCAAACAG 59.785 45.833 0.00 0.00 0.00 3.16
5300 5752 2.290577 ACCTCTCATCCAAACAGCTTCC 60.291 50.000 0.00 0.00 0.00 3.46
5358 5810 6.276847 CAGTAGTAGCTTCTAAACTGGATGG 58.723 44.000 12.96 0.00 0.00 3.51
5427 5959 3.508012 TCCTACAGTTGACTTGAGCTCTC 59.492 47.826 16.19 4.81 0.00 3.20
5439 5971 1.268079 TGAGCTCTCTCAACTCACACG 59.732 52.381 16.19 0.00 45.69 4.49
5467 5999 2.344950 CTCTCACATGCCTTCTGTGAC 58.655 52.381 2.19 0.00 45.97 3.67
5477 6009 2.875672 GCCTTCTGTGACATGGCAAGTA 60.876 50.000 0.58 0.00 42.79 2.24
5570 6103 8.485976 TGTGATTACGATGATCAACACATTTA 57.514 30.769 0.00 0.00 35.46 1.40
5587 6121 8.017418 ACACATTTATGTTTTCTTTCCCTTCA 57.983 30.769 0.00 0.00 39.39 3.02
5618 6152 3.338249 AGCTACCGAGAAGTACGTACAA 58.662 45.455 26.55 0.00 0.00 2.41
5654 8300 5.163343 ACCTCTTGCTTTATGCCGTAGATTA 60.163 40.000 0.00 0.00 42.00 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 2.263227 CGATGGCGTGGTGGTACA 59.737 61.111 0.00 0.00 0.00 2.90
8 9 3.192922 GCGATGGCGTGGTGGTAC 61.193 66.667 0.00 0.00 40.36 3.34
9 10 4.460683 GGCGATGGCGTGGTGGTA 62.461 66.667 0.00 0.00 41.24 3.25
18 19 0.818040 AAAGGGTATTCGGCGATGGC 60.818 55.000 11.76 3.32 38.90 4.40
19 20 1.675552 AAAAGGGTATTCGGCGATGG 58.324 50.000 11.76 0.00 0.00 3.51
20 21 4.261031 CCTTAAAAAGGGTATTCGGCGATG 60.261 45.833 11.76 0.00 45.27 3.84
21 22 3.881089 CCTTAAAAAGGGTATTCGGCGAT 59.119 43.478 11.76 3.57 45.27 4.58
22 23 3.272581 CCTTAAAAAGGGTATTCGGCGA 58.727 45.455 4.99 4.99 45.27 5.54
23 24 3.685836 CCTTAAAAAGGGTATTCGGCG 57.314 47.619 0.00 0.00 45.27 6.46
34 35 9.875691 CTCCCATAAAAATCCTTCCTTAAAAAG 57.124 33.333 0.00 0.00 0.00 2.27
35 36 8.318412 GCTCCCATAAAAATCCTTCCTTAAAAA 58.682 33.333 0.00 0.00 0.00 1.94
36 37 7.363443 CGCTCCCATAAAAATCCTTCCTTAAAA 60.363 37.037 0.00 0.00 0.00 1.52
37 38 6.096282 CGCTCCCATAAAAATCCTTCCTTAAA 59.904 38.462 0.00 0.00 0.00 1.52
38 39 5.592688 CGCTCCCATAAAAATCCTTCCTTAA 59.407 40.000 0.00 0.00 0.00 1.85
39 40 5.130350 CGCTCCCATAAAAATCCTTCCTTA 58.870 41.667 0.00 0.00 0.00 2.69
40 41 3.954258 CGCTCCCATAAAAATCCTTCCTT 59.046 43.478 0.00 0.00 0.00 3.36
41 42 3.555966 CGCTCCCATAAAAATCCTTCCT 58.444 45.455 0.00 0.00 0.00 3.36
42 43 2.623416 CCGCTCCCATAAAAATCCTTCC 59.377 50.000 0.00 0.00 0.00 3.46
43 44 3.288092 ACCGCTCCCATAAAAATCCTTC 58.712 45.455 0.00 0.00 0.00 3.46
44 45 3.382083 ACCGCTCCCATAAAAATCCTT 57.618 42.857 0.00 0.00 0.00 3.36
45 46 4.513406 TTACCGCTCCCATAAAAATCCT 57.487 40.909 0.00 0.00 0.00 3.24
46 47 5.585820 TTTTACCGCTCCCATAAAAATCC 57.414 39.130 0.00 0.00 0.00 3.01
47 48 5.041287 GCTTTTACCGCTCCCATAAAAATC 58.959 41.667 0.00 0.00 29.79 2.17
48 49 4.464597 TGCTTTTACCGCTCCCATAAAAAT 59.535 37.500 0.00 0.00 29.79 1.82
49 50 3.827302 TGCTTTTACCGCTCCCATAAAAA 59.173 39.130 0.00 0.00 29.79 1.94
50 51 3.422796 TGCTTTTACCGCTCCCATAAAA 58.577 40.909 0.00 0.00 0.00 1.52
51 52 3.013921 CTGCTTTTACCGCTCCCATAAA 58.986 45.455 0.00 0.00 0.00 1.40
52 53 2.639065 CTGCTTTTACCGCTCCCATAA 58.361 47.619 0.00 0.00 0.00 1.90
53 54 1.745827 GCTGCTTTTACCGCTCCCATA 60.746 52.381 0.00 0.00 0.00 2.74
54 55 1.032114 GCTGCTTTTACCGCTCCCAT 61.032 55.000 0.00 0.00 0.00 4.00
55 56 1.674322 GCTGCTTTTACCGCTCCCA 60.674 57.895 0.00 0.00 0.00 4.37
56 57 2.750888 CGCTGCTTTTACCGCTCCC 61.751 63.158 0.00 0.00 0.00 4.30
57 58 2.785258 CGCTGCTTTTACCGCTCC 59.215 61.111 0.00 0.00 0.00 4.70
58 59 2.098489 GCGCTGCTTTTACCGCTC 59.902 61.111 0.00 0.00 42.83 5.03
59 60 2.668212 TGCGCTGCTTTTACCGCT 60.668 55.556 9.73 0.00 45.97 5.52
60 61 2.501865 GTGCGCTGCTTTTACCGC 60.502 61.111 9.73 0.00 45.99 5.68
61 62 2.175811 GGTGCGCTGCTTTTACCG 59.824 61.111 9.73 0.00 0.00 4.02
62 63 1.210155 CAGGTGCGCTGCTTTTACC 59.790 57.895 9.73 5.73 0.00 2.85
63 64 0.110192 GACAGGTGCGCTGCTTTTAC 60.110 55.000 9.73 0.00 0.00 2.01
64 65 0.533978 TGACAGGTGCGCTGCTTTTA 60.534 50.000 9.73 0.00 0.00 1.52
65 66 1.383456 TTGACAGGTGCGCTGCTTTT 61.383 50.000 9.73 0.00 0.00 2.27
66 67 1.174712 ATTGACAGGTGCGCTGCTTT 61.175 50.000 9.73 0.00 0.00 3.51
67 68 1.580845 GATTGACAGGTGCGCTGCTT 61.581 55.000 9.73 0.00 0.00 3.91
68 69 2.033141 ATTGACAGGTGCGCTGCT 59.967 55.556 9.73 0.00 0.00 4.24
69 70 1.580845 AAGATTGACAGGTGCGCTGC 61.581 55.000 9.73 0.69 0.00 5.25
70 71 0.877071 AAAGATTGACAGGTGCGCTG 59.123 50.000 9.73 0.08 0.00 5.18
71 72 1.609208 AAAAGATTGACAGGTGCGCT 58.391 45.000 9.73 0.00 0.00 5.92
72 73 2.422276 AAAAAGATTGACAGGTGCGC 57.578 45.000 0.00 0.00 0.00 6.09
130 131 7.334421 GTGATGACCACATATGTACTCTTTGTT 59.666 37.037 8.32 0.00 45.03 2.83
191 197 3.940209 TCCGCCGAAGTTAAGTCTTTA 57.060 42.857 0.00 0.00 0.00 1.85
200 207 1.940613 GCATAAGATTCCGCCGAAGTT 59.059 47.619 0.00 0.00 0.00 2.66
209 239 1.388547 TTGGCGTGGCATAAGATTCC 58.611 50.000 0.00 0.00 0.00 3.01
217 247 1.212490 CGATGTTTTGGCGTGGCAT 59.788 52.632 0.00 0.00 0.00 4.40
247 277 2.052690 GCCTCAGTAGCGGTGGAGA 61.053 63.158 12.45 0.61 0.00 3.71
258 288 0.468226 TTCTTCCACGTTGCCTCAGT 59.532 50.000 0.00 0.00 0.00 3.41
269 315 0.988063 AGCTCCCCTCTTTCTTCCAC 59.012 55.000 0.00 0.00 0.00 4.02
271 317 0.393673 GCAGCTCCCCTCTTTCTTCC 60.394 60.000 0.00 0.00 0.00 3.46
398 445 2.738480 CGACACGGGGAAGAACCA 59.262 61.111 0.00 0.00 41.20 3.67
415 462 1.618837 TGATGGCGCTAGGATCTAACC 59.381 52.381 7.64 0.00 0.00 2.85
417 464 2.965831 AGTTGATGGCGCTAGGATCTAA 59.034 45.455 7.64 0.00 0.00 2.10
492 539 0.961019 TTTGATGTCTTGCAGTGGGC 59.039 50.000 0.00 0.00 45.13 5.36
523 570 1.146358 GATAGCGTTGGTGTCGGCTC 61.146 60.000 0.00 0.00 0.00 4.70
574 621 3.638860 TCTTCAGATCCGGTAAGGCTTA 58.361 45.455 2.04 2.04 40.77 3.09
577 624 2.608261 CGATCTTCAGATCCGGTAAGGC 60.608 54.545 10.62 0.00 46.16 4.35
600 648 0.390472 CAGGTGGCTCGGTCTTCTTC 60.390 60.000 0.00 0.00 0.00 2.87
691 740 5.248477 AGTGTTGCTTTAATGGTAGAGAGGA 59.752 40.000 0.00 0.00 0.00 3.71
715 764 8.635765 AGAATAGGCATAGTTTGTTCTCAAAA 57.364 30.769 0.00 0.00 43.78 2.44
738 795 8.251721 GCAGTTTTTCTTCAGTAGAGGTATAGA 58.748 37.037 0.00 0.00 33.51 1.98
753 810 0.826256 GGACCCCGGCAGTTTTTCTT 60.826 55.000 0.00 0.00 0.00 2.52
777 834 4.202315 CCCATATTCACGAGGTGTCCATAA 60.202 45.833 0.00 0.00 34.79 1.90
778 835 3.323691 CCCATATTCACGAGGTGTCCATA 59.676 47.826 0.00 0.00 34.79 2.74
779 836 2.104792 CCCATATTCACGAGGTGTCCAT 59.895 50.000 0.00 0.00 34.79 3.41
780 837 1.484653 CCCATATTCACGAGGTGTCCA 59.515 52.381 0.00 0.00 34.79 4.02
781 838 1.202651 CCCCATATTCACGAGGTGTCC 60.203 57.143 0.00 0.00 34.79 4.02
782 839 1.485066 ACCCCATATTCACGAGGTGTC 59.515 52.381 0.00 0.00 34.79 3.67
783 840 1.209504 CACCCCATATTCACGAGGTGT 59.790 52.381 0.00 0.00 39.91 4.16
784 841 1.953559 CACCCCATATTCACGAGGTG 58.046 55.000 0.00 0.00 38.89 4.00
785 842 1.580059 ACACCCCATATTCACGAGGT 58.420 50.000 0.00 0.00 0.00 3.85
786 843 2.710096 AACACCCCATATTCACGAGG 57.290 50.000 0.00 0.00 0.00 4.63
817 874 6.839124 AATTATCAAGAGCATCACCAACAA 57.161 33.333 0.00 0.00 37.82 2.83
854 913 7.057264 AGAGCTCTTGGAATTATTAGGGTTTC 58.943 38.462 11.45 0.00 0.00 2.78
855 914 6.974795 AGAGCTCTTGGAATTATTAGGGTTT 58.025 36.000 11.45 0.00 0.00 3.27
856 915 6.582929 AGAGCTCTTGGAATTATTAGGGTT 57.417 37.500 11.45 0.00 0.00 4.11
857 916 7.510407 GTTAGAGCTCTTGGAATTATTAGGGT 58.490 38.462 23.84 0.00 0.00 4.34
887 946 0.657368 CGCAGAGAACAAAACGGCAC 60.657 55.000 0.00 0.00 0.00 5.01
909 968 0.921347 CCGAGTTTAGATTCACGGCG 59.079 55.000 4.80 4.80 34.36 6.46
974 1053 1.681793 GATCGCTAGAACCTACAGGCA 59.318 52.381 0.00 0.00 39.32 4.75
1055 1134 4.570663 GTCCGAGGATGGCGACGG 62.571 72.222 0.00 0.00 45.61 4.79
1120 1199 2.444706 CGAGGGCCAGATGGAGGA 60.445 66.667 6.18 0.00 37.39 3.71
1411 1516 0.107654 AACTGCATTAGGTCGAGGGC 60.108 55.000 0.00 0.00 0.00 5.19
1441 1546 1.167851 ACAATCAAGCACACGATGGG 58.832 50.000 0.00 0.00 0.00 4.00
1479 1584 2.621055 ACACGAAGCAAGCATAACCAAA 59.379 40.909 0.00 0.00 0.00 3.28
1507 1612 7.978414 TCTGCAATTAGAGACTCAAACATCTAG 59.022 37.037 5.02 0.00 0.00 2.43
1516 1621 4.569943 GGTGTTCTGCAATTAGAGACTCA 58.430 43.478 5.02 0.00 0.00 3.41
1538 1643 4.695455 AGTAACATGACCAACCAGAAATCG 59.305 41.667 0.00 0.00 0.00 3.34
1612 1721 4.160252 GTGAATGTACATTGCCATTTCCCT 59.840 41.667 25.42 0.00 31.67 4.20
1726 1837 7.445121 TCCAAGTTATAGACCATAGCAATCTG 58.555 38.462 0.00 0.00 0.00 2.90
1827 1938 6.598753 TTGTTTGCTGTACAAGAGAAGTAC 57.401 37.500 0.00 0.00 40.06 2.73
1960 2071 5.869649 TCTTAATCTGTATAGCAGCACCA 57.130 39.130 0.00 0.00 44.66 4.17
2112 2223 9.983804 CATCTTAAGCATTAGCATGTGTATATG 57.016 33.333 0.00 0.00 45.49 1.78
2163 2274 7.083858 CCTCCACAACTACAACATTTTATGTG 58.916 38.462 0.00 0.00 44.07 3.21
2219 2330 4.737054 GTGCAACCATTCAGATACCAAAG 58.263 43.478 0.00 0.00 0.00 2.77
2305 2416 4.674101 GCACGCTTGAACTTTGGCATAATA 60.674 41.667 0.00 0.00 0.00 0.98
2401 2512 3.753842 TGAACTCGGCAAAATTTATCGC 58.246 40.909 0.00 0.00 0.00 4.58
2410 2528 9.352784 CTCATTAAATTAATTGAACTCGGCAAA 57.647 29.630 0.39 0.00 0.00 3.68
2415 2533 7.432252 GTGGCCTCATTAAATTAATTGAACTCG 59.568 37.037 3.32 0.00 0.00 4.18
2538 2656 3.608316 ACATCAGAAGGTCTCAAGAGC 57.392 47.619 0.94 0.94 42.47 4.09
2788 2906 1.822990 CTCGTACCTAGGAACTGGCAA 59.177 52.381 17.98 0.00 41.52 4.52
3050 3171 1.466167 CGAGGCTCCAATGTTCAAGTG 59.534 52.381 9.32 0.00 0.00 3.16
3087 3208 1.065102 CTCCATTCTTGCTCCAATGCG 59.935 52.381 0.00 0.00 35.36 4.73
3174 3295 9.933723 AATCTAACTTCCATTTCCAAAGAATTG 57.066 29.630 0.00 0.00 34.54 2.32
3176 3297 8.753133 GGAATCTAACTTCCATTTCCAAAGAAT 58.247 33.333 0.00 0.00 43.56 2.40
3308 3435 5.505181 TCTTGCCCAGAACTTATTCTTCT 57.495 39.130 0.00 0.00 42.91 2.85
3538 3665 9.750882 CAATTCAGCATGTATACTGATTAATCG 57.249 33.333 10.80 8.09 42.26 3.34
3737 3864 6.042093 TCACTCATAGAAAAACAGACCTGTCT 59.958 38.462 2.84 0.00 44.13 3.41
3756 3883 6.318648 GGGCATTAACTATTCACAATCACTCA 59.681 38.462 0.00 0.00 0.00 3.41
3767 3894 8.345565 CAATTGACTGTAGGGCATTAACTATTC 58.654 37.037 0.00 0.00 30.17 1.75
3799 3926 9.851686 ATATGATAGATTTTTCACTAAGTGCCA 57.148 29.630 0.00 0.00 32.98 4.92
4475 4603 5.456497 CGCAATTCATGATTTACGAATGCTT 59.544 36.000 14.82 0.00 30.17 3.91
4587 4715 2.644798 GCCATCCCAGTATCCTACCAAT 59.355 50.000 0.00 0.00 0.00 3.16
4744 4872 9.449719 AGTTATGTACCCAAAAGAATACTGAAG 57.550 33.333 0.00 0.00 0.00 3.02
4759 4887 4.124970 GGGAATCGAACAGTTATGTACCC 58.875 47.826 0.00 0.00 39.29 3.69
4785 4913 2.902705 AACTAACTCGCTCACCAACA 57.097 45.000 0.00 0.00 0.00 3.33
4793 4921 6.558009 TCGTATGACAATAAACTAACTCGCT 58.442 36.000 0.00 0.00 0.00 4.93
4823 4951 2.195922 GAAAGTGCACAACAAAGCCAG 58.804 47.619 21.04 0.00 0.00 4.85
4875 5311 8.076178 GCTATTCTGTGATATAACCGCAAAAAT 58.924 33.333 0.00 0.00 0.00 1.82
4967 5416 7.095439 GGAACATCAAGAAACACAAGAGTAGAG 60.095 40.741 0.00 0.00 0.00 2.43
4999 5448 4.038763 TCCCACGAACTGCTATATACAAGG 59.961 45.833 0.00 0.00 0.00 3.61
5006 5458 4.755411 CTTTTCTCCCACGAACTGCTATA 58.245 43.478 0.00 0.00 0.00 1.31
5013 5465 2.427506 AGATGCTTTTCTCCCACGAAC 58.572 47.619 0.00 0.00 0.00 3.95
5039 5491 3.562973 CCTGATGTGGCTAGCAGTATTTG 59.437 47.826 18.24 1.38 0.00 2.32
5091 5543 2.636830 CGAACGGAGGGAGTAAGAGTA 58.363 52.381 0.00 0.00 0.00 2.59
5097 5549 1.856629 AATTCCGAACGGAGGGAGTA 58.143 50.000 15.34 1.05 46.06 2.59
5098 5550 1.479730 GTAATTCCGAACGGAGGGAGT 59.520 52.381 15.34 4.12 46.06 3.85
5099 5551 1.755380 AGTAATTCCGAACGGAGGGAG 59.245 52.381 15.34 0.00 46.06 4.30
5100 5552 1.753073 GAGTAATTCCGAACGGAGGGA 59.247 52.381 15.34 2.49 46.06 4.20
5101 5553 1.479323 TGAGTAATTCCGAACGGAGGG 59.521 52.381 15.34 0.00 46.06 4.30
5102 5554 2.953466 TGAGTAATTCCGAACGGAGG 57.047 50.000 15.34 0.00 46.06 4.30
5103 5555 4.308899 AGATGAGTAATTCCGAACGGAG 57.691 45.455 15.34 0.00 46.06 4.63
5104 5556 5.591472 TCTTAGATGAGTAATTCCGAACGGA 59.409 40.000 12.04 12.04 43.52 4.69
5105 5557 5.828747 TCTTAGATGAGTAATTCCGAACGG 58.171 41.667 6.94 6.94 0.00 4.44
5106 5558 7.751047 TTTCTTAGATGAGTAATTCCGAACG 57.249 36.000 0.00 0.00 0.00 3.95
5107 5559 9.314321 TCATTTCTTAGATGAGTAATTCCGAAC 57.686 33.333 0.00 0.00 0.00 3.95
5108 5560 9.884636 TTCATTTCTTAGATGAGTAATTCCGAA 57.115 29.630 0.00 0.00 35.17 4.30
5152 5604 9.952030 TCACAAAAATGGATGTATCTACAACTA 57.048 29.630 0.00 0.00 39.99 2.24
5153 5605 8.730680 GTCACAAAAATGGATGTATCTACAACT 58.269 33.333 0.00 0.00 39.99 3.16
5154 5606 8.511321 TGTCACAAAAATGGATGTATCTACAAC 58.489 33.333 0.00 0.00 39.99 3.32
5155 5607 8.628630 TGTCACAAAAATGGATGTATCTACAA 57.371 30.769 0.00 0.00 39.99 2.41
5156 5608 8.628630 TTGTCACAAAAATGGATGTATCTACA 57.371 30.769 0.00 0.00 40.98 2.74
5157 5609 8.730680 ACTTGTCACAAAAATGGATGTATCTAC 58.269 33.333 0.00 0.00 0.00 2.59
5158 5610 8.862325 ACTTGTCACAAAAATGGATGTATCTA 57.138 30.769 0.00 0.00 0.00 1.98
5159 5611 7.765695 ACTTGTCACAAAAATGGATGTATCT 57.234 32.000 0.00 0.00 0.00 1.98
5162 5614 9.906660 GAATTACTTGTCACAAAAATGGATGTA 57.093 29.630 0.00 0.00 0.00 2.29
5163 5615 7.872483 GGAATTACTTGTCACAAAAATGGATGT 59.128 33.333 0.00 0.00 0.00 3.06
5164 5616 7.062138 CGGAATTACTTGTCACAAAAATGGATG 59.938 37.037 0.00 0.00 0.00 3.51
5165 5617 7.040062 TCGGAATTACTTGTCACAAAAATGGAT 60.040 33.333 0.00 0.00 0.00 3.41
5166 5618 6.263392 TCGGAATTACTTGTCACAAAAATGGA 59.737 34.615 0.00 0.00 0.00 3.41
5167 5619 6.442952 TCGGAATTACTTGTCACAAAAATGG 58.557 36.000 0.00 0.00 0.00 3.16
5168 5620 7.357206 CGTTCGGAATTACTTGTCACAAAAATG 60.357 37.037 0.00 0.00 0.00 2.32
5169 5621 6.635239 CGTTCGGAATTACTTGTCACAAAAAT 59.365 34.615 0.00 0.00 0.00 1.82
5170 5622 5.966503 CGTTCGGAATTACTTGTCACAAAAA 59.033 36.000 0.00 0.00 0.00 1.94
5171 5623 5.503498 CGTTCGGAATTACTTGTCACAAAA 58.497 37.500 0.00 0.00 0.00 2.44
5172 5624 4.024725 CCGTTCGGAATTACTTGTCACAAA 60.025 41.667 5.19 0.00 0.00 2.83
5173 5625 3.495377 CCGTTCGGAATTACTTGTCACAA 59.505 43.478 5.19 0.00 0.00 3.33
5174 5626 3.061322 CCGTTCGGAATTACTTGTCACA 58.939 45.455 5.19 0.00 0.00 3.58
5175 5627 3.319755 TCCGTTCGGAATTACTTGTCAC 58.680 45.455 11.66 0.00 0.00 3.67
5176 5628 3.581755 CTCCGTTCGGAATTACTTGTCA 58.418 45.455 14.79 0.00 33.41 3.58
5177 5629 2.928116 CCTCCGTTCGGAATTACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
5178 5630 2.354403 CCCTCCGTTCGGAATTACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
5179 5631 2.093869 TCCCTCCGTTCGGAATTACTTG 60.094 50.000 14.79 1.97 33.41 3.16
5180 5632 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
5181 5633 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
5182 5634 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
5183 5635 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
5184 5636 1.479730 GTACTCCCTCCGTTCGGAATT 59.520 52.381 14.79 0.00 33.41 2.17
5185 5637 1.109609 GTACTCCCTCCGTTCGGAAT 58.890 55.000 14.79 2.09 33.41 3.01
5186 5638 0.251297 TGTACTCCCTCCGTTCGGAA 60.251 55.000 14.79 0.04 33.41 4.30
5187 5639 0.033796 ATGTACTCCCTCCGTTCGGA 60.034 55.000 13.34 13.34 0.00 4.55
5188 5640 0.384669 GATGTACTCCCTCCGTTCGG 59.615 60.000 4.74 4.74 0.00 4.30
5189 5641 0.384669 GGATGTACTCCCTCCGTTCG 59.615 60.000 0.00 0.00 38.19 3.95
5190 5642 0.384669 CGGATGTACTCCCTCCGTTC 59.615 60.000 14.50 0.00 45.30 3.95
5191 5643 2.501492 CGGATGTACTCCCTCCGTT 58.499 57.895 14.50 0.00 45.30 4.44
5192 5644 4.254721 CGGATGTACTCCCTCCGT 57.745 61.111 14.50 0.00 45.30 4.69
5194 5646 1.611519 CTCTCGGATGTACTCCCTCC 58.388 60.000 0.00 0.00 41.49 4.30
5195 5647 1.133730 ACCTCTCGGATGTACTCCCTC 60.134 57.143 0.00 0.00 41.49 4.30
5196 5648 0.927767 ACCTCTCGGATGTACTCCCT 59.072 55.000 0.00 0.00 41.49 4.20
5197 5649 1.033574 CACCTCTCGGATGTACTCCC 58.966 60.000 0.00 0.00 41.49 4.30
5198 5650 1.765230 ACACCTCTCGGATGTACTCC 58.235 55.000 0.00 0.00 41.07 3.85
5199 5651 2.753452 TGAACACCTCTCGGATGTACTC 59.247 50.000 0.00 0.00 0.00 2.59
5200 5652 2.755655 CTGAACACCTCTCGGATGTACT 59.244 50.000 0.00 0.00 0.00 2.73
5201 5653 2.753452 TCTGAACACCTCTCGGATGTAC 59.247 50.000 0.00 0.00 0.00 2.90
5208 5660 2.101582 CCCCTTATCTGAACACCTCTCG 59.898 54.545 0.00 0.00 0.00 4.04
5260 5712 8.822805 TGAGAGGTGTTTCTGGTTAACTAATAT 58.177 33.333 5.42 0.00 0.00 1.28
5295 5747 6.723131 AAAATACGTCTTAGTCTTGGAAGC 57.277 37.500 0.00 0.00 0.00 3.86
5300 5752 8.744008 TGAGAGAAAAATACGTCTTAGTCTTG 57.256 34.615 0.00 0.00 0.00 3.02
5358 5810 3.003480 CAGAGGAAACGAACTGGATTCC 58.997 50.000 0.00 0.00 41.32 3.01
5372 5824 0.976641 ACGTTGATGCCTCAGAGGAA 59.023 50.000 21.89 10.89 37.67 3.36
5467 5999 4.201753 CGTCAGAGAACAATACTTGCCATG 60.202 45.833 0.00 0.00 0.00 3.66
5477 6009 2.146342 CAGCAACCGTCAGAGAACAAT 58.854 47.619 0.00 0.00 0.00 2.71
5570 6103 6.051074 CAGCTTTTGAAGGGAAAGAAAACAT 58.949 36.000 1.11 0.00 36.45 2.71
5581 6114 2.270959 GCTCCCAGCTTTTGAAGGG 58.729 57.895 0.00 0.00 42.86 3.95
5638 8284 5.398711 GTCGTGAGTAATCTACGGCATAAAG 59.601 44.000 12.48 0.00 41.60 1.85
5676 8322 0.246635 AGGAATCGGTTCTGTGGTCG 59.753 55.000 8.59 0.00 34.68 4.79


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

AutoCloner maintained by Alex Coulton.