Multiple sequence alignment - TraesCS3D01G310700

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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 TraesCS3D01G310700 chr3D 100.000 3886 0 0 1 3886 425117999 425121884 0.000000e+00 7177.0
1 TraesCS3D01G310700 chr3D 83.736 787 103 18 1086 1861 424486792 424486020 0.000000e+00 721.0
2 TraesCS3D01G310700 chr3D 81.277 235 40 3 1173 1404 253605321 253605088 1.840000e-43 187.0
3 TraesCS3D01G310700 chr3B 89.543 1291 82 21 1450 2714 555063551 555064814 0.000000e+00 1587.0
4 TraesCS3D01G310700 chr3B 89.775 890 54 24 576 1452 555062721 555063586 0.000000e+00 1105.0
5 TraesCS3D01G310700 chr3B 91.854 356 25 3 3193 3545 555095097 555095451 9.700000e-136 494.0
6 TraesCS3D01G310700 chr3B 90.831 349 18 9 2779 3126 555094762 555095097 4.580000e-124 455.0
7 TraesCS3D01G310700 chr3B 87.464 351 21 6 232 582 555060951 555061278 2.190000e-102 383.0
8 TraesCS3D01G310700 chr3B 94.538 238 5 3 3654 3886 555107609 555107843 1.030000e-95 361.0
9 TraesCS3D01G310700 chr3B 78.440 218 24 12 2296 2503 555110405 555110609 1.900000e-23 121.0
10 TraesCS3D01G310700 chr3B 91.429 70 3 3 3593 3661 555095436 555095503 4.130000e-15 93.5
11 TraesCS3D01G310700 chr3A 95.135 966 41 2 906 1868 563411305 563410343 0.000000e+00 1519.0
12 TraesCS3D01G310700 chr3A 89.922 893 59 12 1 886 563412543 563411675 0.000000e+00 1122.0
13 TraesCS3D01G310700 chr3A 88.175 871 95 8 948 1815 563402578 563401713 0.000000e+00 1031.0
14 TraesCS3D01G310700 chr3A 85.531 781 55 21 1950 2692 563410261 563409501 0.000000e+00 763.0
15 TraesCS3D01G310700 chr3A 79.909 219 24 8 2295 2506 563401344 563401139 4.050000e-30 143.0
16 TraesCS3D01G310700 chr3A 95.588 68 1 1 3819 3886 563406782 563406717 1.480000e-19 108.0
17 TraesCS3D01G310700 chr3A 91.549 71 5 1 3446 3515 563409460 563409390 3.200000e-16 97.1
18 TraesCS3D01G310700 chr2B 90.116 516 44 6 1 513 23640564 23641075 0.000000e+00 664.0
19 TraesCS3D01G310700 chr2B 80.682 176 22 3 3215 3378 773006356 773006531 4.080000e-25 126.0
20 TraesCS3D01G310700 chr2B 80.469 128 22 2 1157 1284 584873778 584873902 1.150000e-15 95.3
21 TraesCS3D01G310700 chr4A 89.126 515 50 6 1 512 40794044 40794555 1.520000e-178 636.0
22 TraesCS3D01G310700 chr2A 88.932 515 49 7 1 512 515938749 515938240 2.550000e-176 628.0
23 TraesCS3D01G310700 chr2A 87.500 536 54 11 1 532 502817269 502816743 1.190000e-169 606.0
24 TraesCS3D01G310700 chr2A 85.294 238 31 2 1171 1404 712055149 712055386 3.880000e-60 243.0
25 TraesCS3D01G310700 chr2A 79.646 113 20 2 1172 1284 643007926 643008035 1.160000e-10 78.7
26 TraesCS3D01G310700 chr7D 88.566 516 52 6 1 512 534631001 534630489 1.530000e-173 619.0
27 TraesCS3D01G310700 chr7D 89.868 227 20 2 1261 1487 63456918 63457141 4.910000e-74 289.0
28 TraesCS3D01G310700 chr6D 88.521 514 52 6 3 512 102465464 102465974 1.980000e-172 616.0
29 TraesCS3D01G310700 chr2D 88.417 518 51 8 1 512 498811625 498812139 1.980000e-172 616.0
30 TraesCS3D01G310700 chr2D 87.850 214 26 0 1288 1501 518799989 518799776 6.450000e-63 252.0
31 TraesCS3D01G310700 chr2D 81.564 179 21 3 3212 3378 629976825 629977003 1.880000e-28 137.0
32 TraesCS3D01G310700 chr2D 81.818 176 20 4 3215 3378 630044566 630044741 1.880000e-28 137.0
33 TraesCS3D01G310700 chr2D 74.717 265 51 10 1157 1413 498276279 498276535 1.910000e-18 104.0
34 TraesCS3D01G310700 chr2D 81.061 132 11 6 3261 3378 600425370 600425239 4.130000e-15 93.5
35 TraesCS3D01G310700 chr7B 88.372 516 50 8 1 512 749122780 749122271 2.570000e-171 612.0
36 TraesCS3D01G310700 chr4D 88.201 517 53 8 1 513 443799356 443798844 9.230000e-171 610.0
37 TraesCS3D01G310700 chrUn 82.988 241 34 3 1171 1404 110476798 110476558 1.090000e-50 211.0
38 TraesCS3D01G310700 chr4B 81.068 206 28 9 994 1197 607672465 607672661 1.870000e-33 154.0
39 TraesCS3D01G310700 chr4B 80.583 206 29 9 994 1197 607660338 607660534 8.700000e-32 148.0


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 TraesCS3D01G310700 chr3D 425117999 425121884 3885 False 7177.00 7177 100.000000 1 3886 1 chr3D.!!$F1 3885
1 TraesCS3D01G310700 chr3D 424486020 424486792 772 True 721.00 721 83.736000 1086 1861 1 chr3D.!!$R2 775
2 TraesCS3D01G310700 chr3B 555060951 555064814 3863 False 1025.00 1587 88.927333 232 2714 3 chr3B.!!$F1 2482
3 TraesCS3D01G310700 chr3B 555094762 555095503 741 False 347.50 494 91.371333 2779 3661 3 chr3B.!!$F2 882
4 TraesCS3D01G310700 chr3B 555107609 555110609 3000 False 241.00 361 86.489000 2296 3886 2 chr3B.!!$F3 1590
5 TraesCS3D01G310700 chr3A 563406717 563412543 5826 True 721.82 1519 91.545000 1 3886 5 chr3A.!!$R2 3885
6 TraesCS3D01G310700 chr3A 563401139 563402578 1439 True 587.00 1031 84.042000 948 2506 2 chr3A.!!$R1 1558
7 TraesCS3D01G310700 chr2B 23640564 23641075 511 False 664.00 664 90.116000 1 513 1 chr2B.!!$F1 512
8 TraesCS3D01G310700 chr4A 40794044 40794555 511 False 636.00 636 89.126000 1 512 1 chr4A.!!$F1 511
9 TraesCS3D01G310700 chr2A 515938240 515938749 509 True 628.00 628 88.932000 1 512 1 chr2A.!!$R2 511
10 TraesCS3D01G310700 chr2A 502816743 502817269 526 True 606.00 606 87.500000 1 532 1 chr2A.!!$R1 531
11 TraesCS3D01G310700 chr7D 534630489 534631001 512 True 619.00 619 88.566000 1 512 1 chr7D.!!$R1 511
12 TraesCS3D01G310700 chr6D 102465464 102465974 510 False 616.00 616 88.521000 3 512 1 chr6D.!!$F1 509
13 TraesCS3D01G310700 chr2D 498811625 498812139 514 False 616.00 616 88.417000 1 512 1 chr2D.!!$F2 511
14 TraesCS3D01G310700 chr7B 749122271 749122780 509 True 612.00 612 88.372000 1 512 1 chr7B.!!$R1 511
15 TraesCS3D01G310700 chr4D 443798844 443799356 512 True 610.00 610 88.201000 1 513 1 chr4D.!!$R1 512

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
781 2280 0.457851 ACGCTACAGTCATCAGAGCC 59.542 55.0 0.0 0.0 0.0 4.70 F
1794 3649 0.037326 TCGGCTACAACTGCTTCCTG 60.037 55.0 0.0 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2385 4297 0.035881 CCTCAGTTTGCAGCAGGAGA 59.964 55.0 13.85 3.76 0.0 3.71 R
3274 5229 0.895530 ACATCATCGGTCGGAGTTGT 59.104 50.0 0.00 0.00 0.0 3.32 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
133 136 1.526455 ACGCTCTCGGCTACCTAGG 60.526 63.158 7.41 7.41 40.69 3.02
282 288 3.953612 CTGCTATTCTCTCCAGTCTGACT 59.046 47.826 4.06 4.06 0.00 3.41
296 302 4.400109 GACTGTCCGCGACGCTCA 62.400 66.667 19.02 12.77 34.95 4.26
317 323 2.311701 TTGTTCGCAACGCTACCGG 61.312 57.895 0.00 0.00 39.22 5.28
697 2164 8.445275 TCACATTACACTTGCTCTAAAAAGAA 57.555 30.769 0.00 0.00 0.00 2.52
773 2272 2.363038 AGTACCAACAACGCTACAGTCA 59.637 45.455 0.00 0.00 0.00 3.41
774 2273 2.543777 ACCAACAACGCTACAGTCAT 57.456 45.000 0.00 0.00 0.00 3.06
775 2274 2.413837 ACCAACAACGCTACAGTCATC 58.586 47.619 0.00 0.00 0.00 2.92
776 2275 2.224185 ACCAACAACGCTACAGTCATCA 60.224 45.455 0.00 0.00 0.00 3.07
777 2276 2.413112 CCAACAACGCTACAGTCATCAG 59.587 50.000 0.00 0.00 0.00 2.90
778 2277 3.317150 CAACAACGCTACAGTCATCAGA 58.683 45.455 0.00 0.00 0.00 3.27
779 2278 3.223423 ACAACGCTACAGTCATCAGAG 57.777 47.619 0.00 0.00 0.00 3.35
780 2279 1.923204 CAACGCTACAGTCATCAGAGC 59.077 52.381 0.00 0.00 0.00 4.09
781 2280 0.457851 ACGCTACAGTCATCAGAGCC 59.542 55.000 0.00 0.00 0.00 4.70
782 2281 0.593518 CGCTACAGTCATCAGAGCCG 60.594 60.000 0.00 0.00 0.00 5.52
783 2282 0.741326 GCTACAGTCATCAGAGCCGA 59.259 55.000 0.00 0.00 0.00 5.54
784 2283 1.339610 GCTACAGTCATCAGAGCCGAT 59.660 52.381 0.00 0.00 0.00 4.18
785 2284 2.223923 GCTACAGTCATCAGAGCCGATT 60.224 50.000 0.00 0.00 0.00 3.34
786 2285 3.739519 GCTACAGTCATCAGAGCCGATTT 60.740 47.826 0.00 0.00 0.00 2.17
787 2286 2.898705 ACAGTCATCAGAGCCGATTTC 58.101 47.619 0.00 0.00 0.00 2.17
788 2287 2.234661 ACAGTCATCAGAGCCGATTTCA 59.765 45.455 0.00 0.00 0.00 2.69
789 2288 2.864946 CAGTCATCAGAGCCGATTTCAG 59.135 50.000 0.00 0.00 0.00 3.02
790 2289 1.596727 GTCATCAGAGCCGATTTCAGC 59.403 52.381 0.00 0.00 0.00 4.26
791 2290 1.483827 TCATCAGAGCCGATTTCAGCT 59.516 47.619 0.00 0.00 43.55 4.24
792 2291 2.695147 TCATCAGAGCCGATTTCAGCTA 59.305 45.455 0.00 0.00 40.11 3.32
793 2292 3.323115 TCATCAGAGCCGATTTCAGCTAT 59.677 43.478 0.00 0.00 40.11 2.97
794 2293 3.377346 TCAGAGCCGATTTCAGCTATC 57.623 47.619 0.00 0.00 40.11 2.08
795 2294 2.057316 CAGAGCCGATTTCAGCTATCG 58.943 52.381 9.88 9.88 43.32 2.92
800 2299 2.509052 CGATTTCAGCTATCGGTCCA 57.491 50.000 9.11 0.00 40.78 4.02
801 2300 2.398498 CGATTTCAGCTATCGGTCCAG 58.602 52.381 9.11 0.00 40.78 3.86
829 2328 3.524606 GGCGCGCAGTAGGGAGTA 61.525 66.667 34.42 0.00 0.00 2.59
842 2341 5.705441 CAGTAGGGAGTATTGCACAGAAAAA 59.295 40.000 0.00 0.00 0.00 1.94
1794 3649 0.037326 TCGGCTACAACTGCTTCCTG 60.037 55.000 0.00 0.00 0.00 3.86
1852 3707 5.052304 GCGAAATATGTCAGTGAGTAGTTCG 60.052 44.000 26.94 26.94 43.34 3.95
1881 3736 7.957002 TCTTCTCAGAAGTTGATACAAGTTCT 58.043 34.615 21.35 21.35 39.72 3.01
1882 3737 8.424918 TCTTCTCAGAAGTTGATACAAGTTCTT 58.575 33.333 23.30 11.99 37.72 2.52
1886 3741 9.657121 CTCAGAAGTTGATACAAGTTCTTTTTC 57.343 33.333 23.30 5.50 37.72 2.29
1893 3748 6.970484 TGATACAAGTTCTTTTTCTTCCAGC 58.030 36.000 0.00 0.00 0.00 4.85
1894 3749 6.545666 TGATACAAGTTCTTTTTCTTCCAGCA 59.454 34.615 0.00 0.00 0.00 4.41
1895 3750 5.659440 ACAAGTTCTTTTTCTTCCAGCAA 57.341 34.783 0.00 0.00 0.00 3.91
1897 3752 4.313277 AGTTCTTTTTCTTCCAGCAAGC 57.687 40.909 0.00 0.00 31.26 4.01
1906 3761 1.066908 CTTCCAGCAAGCAAACGGAAA 59.933 47.619 0.00 0.00 0.00 3.13
1961 3824 1.149361 CGCCACCATGAATGCAATGC 61.149 55.000 0.00 0.00 0.00 3.56
2006 3902 0.734889 AGTTAATGCCATCTGTGCGC 59.265 50.000 0.00 0.00 0.00 6.09
2054 3955 1.869132 CATCGAGCATGTGTGGTATGG 59.131 52.381 0.00 0.00 35.91 2.74
2062 3963 3.508012 GCATGTGTGGTATGGGTTGTAAA 59.492 43.478 0.00 0.00 0.00 2.01
2089 3990 3.165058 TCTAATCAAGCGCGTCTCATT 57.835 42.857 8.43 9.77 0.00 2.57
2092 3993 5.289595 TCTAATCAAGCGCGTCTCATTAAT 58.710 37.500 8.43 0.00 0.00 1.40
2162 4063 1.808411 CTGGTTGTAACAGCGGTGAT 58.192 50.000 23.44 12.76 0.00 3.06
2205 4106 3.965258 ACCGGGAATGTGGCAGCA 61.965 61.111 6.32 0.00 0.00 4.41
2257 4167 2.730090 CGGCTACGTACGTGTTCTCAAT 60.730 50.000 30.25 2.64 34.81 2.57
2262 4172 6.141369 GGCTACGTACGTGTTCTCAATATTAC 59.859 42.308 30.25 3.63 0.00 1.89
2291 4201 1.814394 GCATTCATGGCTGACTGTCAA 59.186 47.619 12.16 0.00 35.19 3.18
2292 4202 2.426024 GCATTCATGGCTGACTGTCAAT 59.574 45.455 12.16 0.00 35.19 2.57
2293 4203 3.119245 GCATTCATGGCTGACTGTCAATT 60.119 43.478 12.16 0.00 35.19 2.32
2299 4209 4.558226 TGGCTGACTGTCAATTATCAGT 57.442 40.909 12.16 12.49 45.81 3.41
2316 4226 8.722480 ATTATCAGTCTGTCATTCGATTTGAA 57.278 30.769 0.00 0.00 41.81 2.69
2334 4244 3.064207 TGAATGTTGAGCACGGTCTAAC 58.936 45.455 0.00 2.18 0.00 2.34
2335 4245 2.094762 ATGTTGAGCACGGTCTAACC 57.905 50.000 0.00 0.00 34.05 2.85
2344 4254 1.686110 CGGTCTAACCTGGGCCTCT 60.686 63.158 4.53 0.00 35.66 3.69
2383 4295 1.082756 CAGGTCAGCAAACGAACGC 60.083 57.895 0.00 0.00 0.00 4.84
2384 4296 1.227556 AGGTCAGCAAACGAACGCT 60.228 52.632 0.00 0.00 39.66 5.07
2385 4297 0.814010 AGGTCAGCAAACGAACGCTT 60.814 50.000 0.00 0.00 35.96 4.68
2386 4298 0.384353 GGTCAGCAAACGAACGCTTC 60.384 55.000 0.00 0.00 35.96 3.86
2387 4299 0.582005 GTCAGCAAACGAACGCTTCT 59.418 50.000 0.00 0.00 35.96 2.85
2388 4300 0.859232 TCAGCAAACGAACGCTTCTC 59.141 50.000 0.00 0.00 35.96 2.87
2435 4347 3.867783 CGGTCACCACCACCACCA 61.868 66.667 0.00 0.00 44.02 4.17
2535 4460 6.409524 TTTTCTGTTTGAGATCCATGCTTT 57.590 33.333 0.00 0.00 0.00 3.51
2566 4497 8.215926 CTAGTAGCTGAACTAGTAGTGATTGT 57.784 38.462 13.48 0.00 44.78 2.71
2567 4498 7.090953 AGTAGCTGAACTAGTAGTGATTGTC 57.909 40.000 2.90 0.00 32.44 3.18
2568 4499 5.984695 AGCTGAACTAGTAGTGATTGTCA 57.015 39.130 2.90 2.65 0.00 3.58
2569 4500 6.346477 AGCTGAACTAGTAGTGATTGTCAA 57.654 37.500 2.90 0.00 0.00 3.18
2570 4501 6.159988 AGCTGAACTAGTAGTGATTGTCAAC 58.840 40.000 2.90 0.00 0.00 3.18
2574 4505 9.639601 CTGAACTAGTAGTGATTGTCAACATTA 57.360 33.333 2.90 0.00 0.00 1.90
2583 4530 7.272244 AGTGATTGTCAACATTATATCGTCCA 58.728 34.615 0.00 0.00 0.00 4.02
2648 4595 5.584253 TGTCCTAGATCAGTTTCAGTAGC 57.416 43.478 0.00 0.00 0.00 3.58
2649 4596 5.265191 TGTCCTAGATCAGTTTCAGTAGCT 58.735 41.667 0.00 0.00 0.00 3.32
2710 4664 3.235200 AGAGCAATTCTAGCGGATACCT 58.765 45.455 0.00 0.00 33.23 3.08
2714 4668 6.663953 AGAGCAATTCTAGCGGATACCTTATA 59.336 38.462 0.00 0.00 33.23 0.98
2715 4669 7.343316 AGAGCAATTCTAGCGGATACCTTATAT 59.657 37.037 0.00 0.00 33.23 0.86
2716 4670 7.493367 AGCAATTCTAGCGGATACCTTATATC 58.507 38.462 0.00 0.00 37.01 1.63
2717 4671 6.418226 GCAATTCTAGCGGATACCTTATATCG 59.582 42.308 0.00 0.00 0.00 2.92
2718 4672 5.496133 TTCTAGCGGATACCTTATATCGC 57.504 43.478 0.00 0.00 39.54 4.58
2719 4673 3.881688 TCTAGCGGATACCTTATATCGCC 59.118 47.826 0.00 0.00 39.85 5.54
2720 4674 1.755380 AGCGGATACCTTATATCGCCC 59.245 52.381 0.00 0.00 39.85 6.13
2721 4675 1.755380 GCGGATACCTTATATCGCCCT 59.245 52.381 0.00 0.00 35.97 5.19
2722 4676 2.954318 GCGGATACCTTATATCGCCCTA 59.046 50.000 0.00 0.00 35.97 3.53
2723 4677 3.243334 GCGGATACCTTATATCGCCCTAC 60.243 52.174 0.00 0.00 35.97 3.18
2724 4678 4.205587 CGGATACCTTATATCGCCCTACT 58.794 47.826 0.00 0.00 0.00 2.57
2725 4679 4.036498 CGGATACCTTATATCGCCCTACTG 59.964 50.000 0.00 0.00 0.00 2.74
2726 4680 4.954826 GGATACCTTATATCGCCCTACTGT 59.045 45.833 0.00 0.00 0.00 3.55
2727 4681 6.125029 GGATACCTTATATCGCCCTACTGTA 58.875 44.000 0.00 0.00 0.00 2.74
2728 4682 6.604795 GGATACCTTATATCGCCCTACTGTAA 59.395 42.308 0.00 0.00 0.00 2.41
2729 4683 7.123247 GGATACCTTATATCGCCCTACTGTAAA 59.877 40.741 0.00 0.00 0.00 2.01
2730 4684 6.736110 ACCTTATATCGCCCTACTGTAAAA 57.264 37.500 0.00 0.00 0.00 1.52
2731 4685 7.312415 ACCTTATATCGCCCTACTGTAAAAT 57.688 36.000 0.00 0.00 0.00 1.82
2732 4686 7.384477 ACCTTATATCGCCCTACTGTAAAATC 58.616 38.462 0.00 0.00 0.00 2.17
2733 4687 7.015877 ACCTTATATCGCCCTACTGTAAAATCA 59.984 37.037 0.00 0.00 0.00 2.57
2734 4688 7.545965 CCTTATATCGCCCTACTGTAAAATCAG 59.454 40.741 0.00 0.00 40.80 2.90
2736 4690 4.546829 TCGCCCTACTGTAAAATCAGTT 57.453 40.909 4.72 0.00 44.92 3.16
2737 4691 4.901868 TCGCCCTACTGTAAAATCAGTTT 58.098 39.130 4.72 0.00 44.92 2.66
2738 4692 6.040209 TCGCCCTACTGTAAAATCAGTTTA 57.960 37.500 4.72 0.00 44.92 2.01
2747 4701 5.287170 GTAAAATCAGTTTACCGGTCACC 57.713 43.478 12.40 0.00 43.98 4.02
2748 4702 4.143052 GTAAAATCAGTTTACCGGTCACCG 60.143 45.833 12.40 10.12 43.98 4.94
2749 4703 0.971386 ATCAGTTTACCGGTCACCGT 59.029 50.000 16.87 6.00 46.80 4.83
2750 4704 1.614996 TCAGTTTACCGGTCACCGTA 58.385 50.000 16.87 4.91 46.80 4.02
2751 4705 1.959985 TCAGTTTACCGGTCACCGTAA 59.040 47.619 16.87 11.03 46.80 3.18
2752 4706 2.363680 TCAGTTTACCGGTCACCGTAAA 59.636 45.455 16.87 16.12 46.80 2.01
2753 4707 2.476241 CAGTTTACCGGTCACCGTAAAC 59.524 50.000 28.62 28.62 46.80 2.01
2754 4708 2.365293 AGTTTACCGGTCACCGTAAACT 59.635 45.455 30.74 30.74 46.00 2.66
2755 4709 2.437200 TTACCGGTCACCGTAAACTG 57.563 50.000 16.87 0.15 46.80 3.16
2756 4710 1.327303 TACCGGTCACCGTAAACTGT 58.673 50.000 16.87 7.16 46.80 3.55
2757 4711 0.465287 ACCGGTCACCGTAAACTGTT 59.535 50.000 16.87 0.00 46.80 3.16
2758 4712 1.134431 ACCGGTCACCGTAAACTGTTT 60.134 47.619 16.87 10.98 46.80 2.83
2759 4713 1.941975 CCGGTCACCGTAAACTGTTTT 59.058 47.619 16.87 0.00 46.80 2.43
2760 4714 2.355444 CCGGTCACCGTAAACTGTTTTT 59.645 45.455 16.87 0.00 46.80 1.94
2761 4715 3.356145 CGGTCACCGTAAACTGTTTTTG 58.644 45.455 8.54 4.47 42.73 2.44
2762 4716 3.110358 GGTCACCGTAAACTGTTTTTGC 58.890 45.455 11.48 2.16 0.00 3.68
2763 4717 2.779471 GTCACCGTAAACTGTTTTTGCG 59.221 45.455 11.48 12.82 0.00 4.85
2764 4718 2.113289 CACCGTAAACTGTTTTTGCGG 58.887 47.619 26.48 26.48 42.70 5.69
2765 4719 1.744522 ACCGTAAACTGTTTTTGCGGT 59.255 42.857 27.34 27.34 43.92 5.68
2766 4720 2.941720 ACCGTAAACTGTTTTTGCGGTA 59.058 40.909 29.52 6.53 45.38 4.02
2767 4721 3.565063 ACCGTAAACTGTTTTTGCGGTAT 59.435 39.130 29.52 16.98 45.38 2.73
2768 4722 4.754114 ACCGTAAACTGTTTTTGCGGTATA 59.246 37.500 29.52 5.37 45.38 1.47
2769 4723 5.238214 ACCGTAAACTGTTTTTGCGGTATAA 59.762 36.000 29.52 4.78 45.38 0.98
2770 4724 6.141462 CCGTAAACTGTTTTTGCGGTATAAA 58.859 36.000 23.09 0.00 37.31 1.40
2771 4725 6.636044 CCGTAAACTGTTTTTGCGGTATAAAA 59.364 34.615 23.09 0.00 37.31 1.52
2772 4726 7.326547 CCGTAAACTGTTTTTGCGGTATAAAAT 59.673 33.333 23.09 0.00 37.31 1.82
2773 4727 8.692615 CGTAAACTGTTTTTGCGGTATAAAATT 58.307 29.630 11.48 0.00 0.00 1.82
2774 4728 9.786224 GTAAACTGTTTTTGCGGTATAAAATTG 57.214 29.630 11.48 0.00 0.00 2.32
2775 4729 7.414814 AACTGTTTTTGCGGTATAAAATTGG 57.585 32.000 0.00 0.00 0.00 3.16
2776 4730 5.929415 ACTGTTTTTGCGGTATAAAATTGGG 59.071 36.000 0.00 0.00 0.00 4.12
2777 4731 5.855045 TGTTTTTGCGGTATAAAATTGGGT 58.145 33.333 0.00 0.00 0.00 4.51
2909 4863 7.977293 GGCATTTAATATTTTACGGTTCACCTT 59.023 33.333 0.00 0.00 0.00 3.50
2918 4873 6.857777 TTTACGGTTCACCTTAAAAATCGA 57.142 33.333 5.42 0.00 36.97 3.59
2929 4884 5.528320 ACCTTAAAAATCGACTCGAAAACCA 59.472 36.000 5.00 0.00 39.99 3.67
2937 4892 7.837202 AATCGACTCGAAAACCACAAATATA 57.163 32.000 5.00 0.00 39.99 0.86
2938 4893 6.880822 TCGACTCGAAAACCACAAATATAG 57.119 37.500 0.00 0.00 31.06 1.31
2939 4894 5.808540 TCGACTCGAAAACCACAAATATAGG 59.191 40.000 0.00 0.00 31.06 2.57
2946 4901 8.484575 TCGAAAACCACAAATATAGGGTATGTA 58.515 33.333 0.00 0.00 32.21 2.29
2971 4926 6.044287 AGGTGATAATATATGGTGACCTGCAA 59.956 38.462 2.11 0.00 31.27 4.08
2972 4927 6.714810 GGTGATAATATATGGTGACCTGCAAA 59.285 38.462 2.11 0.00 0.00 3.68
3025 4980 9.906660 TTTTTGCAACCTATACTGTGAATTTAG 57.093 29.630 0.00 0.00 0.00 1.85
3026 4981 8.856153 TTTGCAACCTATACTGTGAATTTAGA 57.144 30.769 0.00 0.00 0.00 2.10
3027 4982 8.492673 TTGCAACCTATACTGTGAATTTAGAG 57.507 34.615 0.00 0.00 0.00 2.43
3028 4983 7.847096 TGCAACCTATACTGTGAATTTAGAGA 58.153 34.615 1.07 0.00 0.00 3.10
3071 5026 3.735591 TGCTAGAGTTGCTTTTACCGTT 58.264 40.909 0.00 0.00 0.00 4.44
3138 5093 1.139163 CAAGGAAAATTGCACGTGGC 58.861 50.000 18.88 10.30 45.13 5.01
3151 5106 3.121030 GTGGCACTGCGCGAGAAT 61.121 61.111 12.10 0.00 43.84 2.40
3152 5107 3.120385 TGGCACTGCGCGAGAATG 61.120 61.111 12.10 2.55 43.84 2.67
3153 5108 4.527157 GGCACTGCGCGAGAATGC 62.527 66.667 12.10 13.55 43.84 3.56
3154 5109 3.792047 GCACTGCGCGAGAATGCA 61.792 61.111 12.10 0.00 39.13 3.96
3155 5110 2.097160 CACTGCGCGAGAATGCAC 59.903 61.111 12.10 0.00 35.90 4.57
3156 5111 3.121030 ACTGCGCGAGAATGCACC 61.121 61.111 12.10 0.00 35.90 5.01
3157 5112 2.816958 CTGCGCGAGAATGCACCT 60.817 61.111 12.10 0.00 35.90 4.00
3158 5113 2.358615 TGCGCGAGAATGCACCTT 60.359 55.556 12.10 0.00 35.90 3.50
3159 5114 1.915614 CTGCGCGAGAATGCACCTTT 61.916 55.000 12.10 0.00 35.90 3.11
3160 5115 1.512734 GCGCGAGAATGCACCTTTG 60.513 57.895 12.10 0.00 34.15 2.77
3161 5116 1.135315 CGCGAGAATGCACCTTTGG 59.865 57.895 0.00 0.00 34.15 3.28
3162 5117 1.577328 CGCGAGAATGCACCTTTGGT 61.577 55.000 0.00 0.00 35.62 3.67
3171 5126 3.175710 ACCTTTGGTGCCCGGTCT 61.176 61.111 0.00 0.00 32.98 3.85
3172 5127 2.359975 CCTTTGGTGCCCGGTCTC 60.360 66.667 0.00 0.00 0.00 3.36
3173 5128 2.359975 CTTTGGTGCCCGGTCTCC 60.360 66.667 0.00 0.00 0.00 3.71
3174 5129 3.172106 TTTGGTGCCCGGTCTCCA 61.172 61.111 1.34 1.34 0.00 3.86
3175 5130 3.485346 TTTGGTGCCCGGTCTCCAC 62.485 63.158 5.64 4.62 30.23 4.02
3176 5131 4.954118 TGGTGCCCGGTCTCCACT 62.954 66.667 1.34 0.00 0.00 4.00
3177 5132 2.682494 GGTGCCCGGTCTCCACTA 60.682 66.667 0.00 0.00 0.00 2.74
3178 5133 2.064581 GGTGCCCGGTCTCCACTAT 61.065 63.158 0.00 0.00 0.00 2.12
3179 5134 1.144057 GTGCCCGGTCTCCACTATG 59.856 63.158 0.00 0.00 0.00 2.23
3180 5135 1.001120 TGCCCGGTCTCCACTATGA 59.999 57.895 0.00 0.00 0.00 2.15
3181 5136 1.043116 TGCCCGGTCTCCACTATGAG 61.043 60.000 0.00 0.00 0.00 2.90
3182 5137 1.742768 CCCGGTCTCCACTATGAGC 59.257 63.158 0.00 0.00 32.22 4.26
3183 5138 1.043116 CCCGGTCTCCACTATGAGCA 61.043 60.000 0.00 0.00 32.22 4.26
3184 5139 1.043816 CCGGTCTCCACTATGAGCAT 58.956 55.000 0.00 0.00 32.22 3.79
3185 5140 1.000283 CCGGTCTCCACTATGAGCATC 60.000 57.143 0.00 0.00 32.22 3.91
3186 5141 1.959985 CGGTCTCCACTATGAGCATCT 59.040 52.381 0.00 0.00 34.92 2.90
3187 5142 2.363680 CGGTCTCCACTATGAGCATCTT 59.636 50.000 0.00 0.00 34.92 2.40
3188 5143 3.551863 CGGTCTCCACTATGAGCATCTTC 60.552 52.174 0.00 0.00 34.92 2.87
3189 5144 3.386078 GGTCTCCACTATGAGCATCTTCA 59.614 47.826 0.00 0.00 34.92 3.02
3190 5145 4.141846 GGTCTCCACTATGAGCATCTTCAA 60.142 45.833 0.00 0.00 34.92 2.69
3191 5146 5.454471 GGTCTCCACTATGAGCATCTTCAAT 60.454 44.000 0.00 0.00 34.92 2.57
3192 5147 6.239430 GGTCTCCACTATGAGCATCTTCAATA 60.239 42.308 0.00 0.00 34.92 1.90
3265 5220 8.415950 TCACTAAAATGTGGGTTTTACATCAT 57.584 30.769 0.00 0.00 37.77 2.45
3271 5226 7.961325 AATGTGGGTTTTACATCATCAAAAC 57.039 32.000 0.00 0.00 41.67 2.43
3272 5227 6.723298 TGTGGGTTTTACATCATCAAAACT 57.277 33.333 9.12 0.00 41.94 2.66
3273 5228 7.118496 TGTGGGTTTTACATCATCAAAACTT 57.882 32.000 9.12 0.00 41.94 2.66
3274 5229 8.239038 TGTGGGTTTTACATCATCAAAACTTA 57.761 30.769 9.12 0.00 41.94 2.24
3275 5230 8.138712 TGTGGGTTTTACATCATCAAAACTTAC 58.861 33.333 9.12 8.85 41.94 2.34
3276 5231 8.138712 GTGGGTTTTACATCATCAAAACTTACA 58.861 33.333 9.12 4.91 41.94 2.41
3278 5233 8.974408 GGGTTTTACATCATCAAAACTTACAAC 58.026 33.333 9.12 0.00 41.94 3.32
3279 5234 9.744468 GGTTTTACATCATCAAAACTTACAACT 57.256 29.630 9.12 0.00 41.94 3.16
3282 5237 6.241207 ACATCATCAAAACTTACAACTCCG 57.759 37.500 0.00 0.00 0.00 4.63
3284 5239 5.917541 TCATCAAAACTTACAACTCCGAC 57.082 39.130 0.00 0.00 0.00 4.79
3286 5241 3.125316 TCAAAACTTACAACTCCGACCG 58.875 45.455 0.00 0.00 0.00 4.79
3305 5260 4.787551 ACCGATGATGTAAAATAGGGCAA 58.212 39.130 0.00 0.00 0.00 4.52
3306 5261 5.385198 ACCGATGATGTAAAATAGGGCAAT 58.615 37.500 0.00 0.00 0.00 3.56
3463 5420 8.816894 GTCACCCTATATCTCAAATCAATCCTA 58.183 37.037 0.00 0.00 0.00 2.94
3583 6291 0.601046 TGAACTTGCCAGACGCTCAG 60.601 55.000 0.00 0.00 38.78 3.35
3599 6307 4.230314 GCTCAGCGAGTATCTGAACATA 57.770 45.455 7.27 0.00 39.77 2.29
3606 6314 5.127194 AGCGAGTATCTGAACATACAGGAAA 59.873 40.000 0.00 0.00 38.31 3.13
3668 6376 1.372499 GTGCTTGTAGTCGTCGCCA 60.372 57.895 0.00 0.00 0.00 5.69
3698 6406 8.738199 CACTTCTCGTGTTCTTTGTACTATAA 57.262 34.615 0.00 0.00 38.84 0.98
3699 6407 9.355215 CACTTCTCGTGTTCTTTGTACTATAAT 57.645 33.333 0.00 0.00 38.84 1.28
3700 6408 9.355215 ACTTCTCGTGTTCTTTGTACTATAATG 57.645 33.333 0.00 0.00 0.00 1.90
3701 6409 9.355215 CTTCTCGTGTTCTTTGTACTATAATGT 57.645 33.333 0.00 0.00 0.00 2.71
3702 6410 9.701098 TTCTCGTGTTCTTTGTACTATAATGTT 57.299 29.630 0.00 0.00 0.00 2.71
3757 6465 7.934855 AGATATTCTGGGATGTGAAATATGC 57.065 36.000 0.00 0.00 0.00 3.14
3770 6478 4.082300 GTGAAATATGCCATGGACAACACA 60.082 41.667 18.40 2.37 0.00 3.72
3772 6480 4.659111 AATATGCCATGGACAACACATG 57.341 40.909 18.40 0.00 44.03 3.21
3808 6518 8.910944 CAGATCTTCCCAATCACTTTCATATTT 58.089 33.333 0.00 0.00 0.00 1.40
3842 8162 9.612620 CATTAGTTGAATAAAGTGTGTTCTTCC 57.387 33.333 0.00 0.00 0.00 3.46
3843 8163 6.300354 AGTTGAATAAAGTGTGTTCTTCCG 57.700 37.500 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
133 136 1.130561 GATAGCCCTTTGTGTCGTTGC 59.869 52.381 0.00 0.00 0.00 4.17
282 288 3.567478 AACATGAGCGTCGCGGACA 62.567 57.895 12.30 13.65 32.09 4.02
317 323 3.693085 TCTAACATCCCTCACAGTCGTAC 59.307 47.826 0.00 0.00 0.00 3.67
328 335 8.525729 AACCCAAATATATCTCTAACATCCCT 57.474 34.615 0.00 0.00 0.00 4.20
379 387 7.034967 AGAGATAAGGTAGGAGACGGATTAT 57.965 40.000 0.00 0.00 0.00 1.28
465 473 6.741992 TTGACGGAATATGATGGATATTGC 57.258 37.500 0.00 0.00 40.35 3.56
642 2100 6.860023 GTGATGTAAGCATGCCATAAAGATTC 59.140 38.462 15.66 1.11 30.84 2.52
697 2164 0.038159 CTTCCTCGCAACTTCCGTCT 60.038 55.000 0.00 0.00 0.00 4.18
781 2280 2.398498 CTGGACCGATAGCTGAAATCG 58.602 52.381 9.88 9.88 44.51 3.34
782 2281 2.139118 GCTGGACCGATAGCTGAAATC 58.861 52.381 0.00 0.00 36.99 2.17
783 2282 1.486310 TGCTGGACCGATAGCTGAAAT 59.514 47.619 0.00 0.00 40.52 2.17
784 2283 0.901827 TGCTGGACCGATAGCTGAAA 59.098 50.000 0.00 0.00 40.52 2.69
785 2284 0.175760 GTGCTGGACCGATAGCTGAA 59.824 55.000 0.00 0.00 40.52 3.02
786 2285 1.676678 GGTGCTGGACCGATAGCTGA 61.677 60.000 1.54 0.00 40.52 4.26
787 2286 1.227380 GGTGCTGGACCGATAGCTG 60.227 63.158 1.54 0.00 40.52 4.24
788 2287 3.221222 GGTGCTGGACCGATAGCT 58.779 61.111 1.54 0.00 40.52 3.32
795 2294 2.262915 CTCGTGAGGTGCTGGACC 59.737 66.667 10.74 10.74 46.58 4.46
796 2295 2.262915 CCTCGTGAGGTGCTGGAC 59.737 66.667 7.79 0.00 43.61 4.02
829 2328 2.545742 GGCGTTCCTTTTTCTGTGCAAT 60.546 45.455 0.00 0.00 0.00 3.56
842 2341 2.349590 GTAATTGTTACGGGCGTTCCT 58.650 47.619 0.00 0.00 0.00 3.36
893 2393 3.039202 CTGACCGCACCGATTTGCC 62.039 63.158 0.00 0.00 39.53 4.52
1285 3140 3.730761 GCACGCCAGGCAGTCTTG 61.731 66.667 13.30 0.89 0.00 3.02
1836 3691 2.812591 GAGGACGAACTACTCACTGACA 59.187 50.000 0.00 0.00 0.00 3.58
1852 3707 6.274157 TGTATCAACTTCTGAGAAGAGGAC 57.726 41.667 27.49 18.25 37.52 3.85
1881 3736 3.186119 CGTTTGCTTGCTGGAAGAAAAA 58.814 40.909 15.58 10.43 40.37 1.94
1882 3737 2.481104 CCGTTTGCTTGCTGGAAGAAAA 60.481 45.455 13.43 11.95 36.92 2.29
1886 3741 0.667993 TTCCGTTTGCTTGCTGGAAG 59.332 50.000 4.37 4.37 33.95 3.46
1889 3744 0.667993 TCTTTCCGTTTGCTTGCTGG 59.332 50.000 0.00 0.00 0.00 4.85
1893 3748 4.858935 TCAGATTTCTTTCCGTTTGCTTG 58.141 39.130 0.00 0.00 0.00 4.01
1894 3749 5.712152 ATCAGATTTCTTTCCGTTTGCTT 57.288 34.783 0.00 0.00 0.00 3.91
1895 3750 6.655003 TCTTATCAGATTTCTTTCCGTTTGCT 59.345 34.615 0.00 0.00 0.00 3.91
1897 3752 8.256611 TCTCTTATCAGATTTCTTTCCGTTTG 57.743 34.615 0.00 0.00 0.00 2.93
1961 3824 6.875195 ACTTAAATGTTCCATGAAATGCCAAG 59.125 34.615 0.00 0.00 44.97 3.61
1977 3873 8.677300 CACAGATGGCATTAACTACTTAAATGT 58.323 33.333 0.00 0.00 0.00 2.71
2006 3902 1.589803 TCTGCATGCCGATCATCTTG 58.410 50.000 16.68 0.00 31.79 3.02
2054 3955 6.582672 GCTTGATTAGAACTTGCTTTACAACC 59.417 38.462 0.00 0.00 33.68 3.77
2062 3963 1.394917 CGCGCTTGATTAGAACTTGCT 59.605 47.619 5.56 0.00 0.00 3.91
2065 3966 2.924290 GAGACGCGCTTGATTAGAACTT 59.076 45.455 5.73 0.00 0.00 2.66
2089 3990 2.153645 CACAGGTTGCTCTGCACATTA 58.846 47.619 0.00 0.00 38.71 1.90
2092 3993 1.526686 CCACAGGTTGCTCTGCACA 60.527 57.895 0.00 0.00 38.71 4.57
2162 4063 1.275471 CTTCTTTCTCACGCACGCGA 61.275 55.000 19.66 0.00 42.83 5.87
2202 4103 2.438614 CCTGATGCTGCTGCTGCT 60.439 61.111 27.67 15.76 40.48 4.24
2257 4167 5.614308 CCATGAATGCACTCCAGAGTAATA 58.386 41.667 0.00 0.00 40.20 0.98
2262 4172 1.022735 GCCATGAATGCACTCCAGAG 58.977 55.000 0.00 0.00 0.00 3.35
2291 4201 8.722480 TTCAAATCGAATGACAGACTGATAAT 57.278 30.769 10.08 0.00 0.00 1.28
2292 4202 8.722480 ATTCAAATCGAATGACAGACTGATAA 57.278 30.769 10.08 0.00 42.95 1.75
2316 4226 1.623811 AGGTTAGACCGTGCTCAACAT 59.376 47.619 0.00 0.00 44.90 2.71
2325 4235 1.988406 GAGGCCCAGGTTAGACCGT 60.988 63.158 0.00 0.00 44.90 4.83
2344 4254 3.189495 TGCTTTATTCGTTTTGCATCGGA 59.811 39.130 0.00 0.00 0.00 4.55
2383 4295 1.805345 CTCAGTTTGCAGCAGGAGAAG 59.195 52.381 0.00 0.00 0.00 2.85
2384 4296 1.544093 CCTCAGTTTGCAGCAGGAGAA 60.544 52.381 13.85 0.00 0.00 2.87
2385 4297 0.035881 CCTCAGTTTGCAGCAGGAGA 59.964 55.000 13.85 3.76 0.00 3.71
2386 4298 0.959372 CCCTCAGTTTGCAGCAGGAG 60.959 60.000 0.00 2.04 0.00 3.69
2387 4299 1.073722 CCCTCAGTTTGCAGCAGGA 59.926 57.895 0.00 0.00 0.00 3.86
2388 4300 0.959372 CTCCCTCAGTTTGCAGCAGG 60.959 60.000 0.00 0.00 0.00 4.85
2435 4347 2.028385 GTGGTCGTATGACTCCAAAGGT 60.028 50.000 14.61 0.00 44.83 3.50
2514 4438 4.154737 CGAAAGCATGGATCTCAAACAGAA 59.845 41.667 0.00 0.00 33.62 3.02
2562 4493 5.997746 CCCTGGACGATATAATGTTGACAAT 59.002 40.000 0.00 0.00 0.00 2.71
2563 4494 5.104693 ACCCTGGACGATATAATGTTGACAA 60.105 40.000 0.00 0.00 0.00 3.18
2564 4495 4.407621 ACCCTGGACGATATAATGTTGACA 59.592 41.667 0.00 0.00 0.00 3.58
2565 4496 4.750098 CACCCTGGACGATATAATGTTGAC 59.250 45.833 0.00 0.00 0.00 3.18
2566 4497 4.651962 TCACCCTGGACGATATAATGTTGA 59.348 41.667 0.00 0.00 0.00 3.18
2567 4498 4.956085 TCACCCTGGACGATATAATGTTG 58.044 43.478 0.00 0.00 0.00 3.33
2568 4499 5.825593 ATCACCCTGGACGATATAATGTT 57.174 39.130 0.00 0.00 0.00 2.71
2569 4500 5.187186 GGTATCACCCTGGACGATATAATGT 59.813 44.000 0.00 0.00 30.04 2.71
2570 4501 5.186992 TGGTATCACCCTGGACGATATAATG 59.813 44.000 0.00 0.00 37.50 1.90
2574 4505 3.254093 TGGTATCACCCTGGACGATAT 57.746 47.619 0.00 0.00 37.50 1.63
2575 4506 2.696707 GTTGGTATCACCCTGGACGATA 59.303 50.000 0.00 0.00 37.50 2.92
2576 4507 1.485066 GTTGGTATCACCCTGGACGAT 59.515 52.381 0.00 0.00 37.50 3.73
2583 4530 2.025321 GGGTTCATGTTGGTATCACCCT 60.025 50.000 0.00 0.00 39.55 4.34
2692 4640 6.418226 CGATATAAGGTATCCGCTAGAATTGC 59.582 42.308 0.00 0.00 0.00 3.56
2693 4641 6.418226 GCGATATAAGGTATCCGCTAGAATTG 59.582 42.308 0.00 0.00 37.38 2.32
2725 4679 4.143052 CGGTGACCGGTAAACTGATTTTAC 60.143 45.833 17.80 0.00 46.25 2.01
2726 4680 3.995705 CGGTGACCGGTAAACTGATTTTA 59.004 43.478 17.80 0.00 44.15 1.52
2727 4681 2.809696 CGGTGACCGGTAAACTGATTTT 59.190 45.455 17.80 0.00 44.15 1.82
2728 4682 2.419667 CGGTGACCGGTAAACTGATTT 58.580 47.619 17.80 0.00 44.15 2.17
2729 4683 2.088950 CGGTGACCGGTAAACTGATT 57.911 50.000 17.80 0.00 44.15 2.57
2730 4684 3.826637 CGGTGACCGGTAAACTGAT 57.173 52.632 17.80 0.00 44.15 2.90
2741 4695 3.110358 GCAAAAACAGTTTACGGTGACC 58.890 45.455 0.00 0.00 0.00 4.02
2742 4696 2.779471 CGCAAAAACAGTTTACGGTGAC 59.221 45.455 0.00 0.00 0.00 3.67
2743 4697 2.223294 CCGCAAAAACAGTTTACGGTGA 60.223 45.455 19.66 0.00 39.76 4.02
2744 4698 2.113289 CCGCAAAAACAGTTTACGGTG 58.887 47.619 19.66 10.63 39.76 4.94
2745 4699 1.744522 ACCGCAAAAACAGTTTACGGT 59.255 42.857 24.50 24.50 46.72 4.83
2746 4700 2.478547 ACCGCAAAAACAGTTTACGG 57.521 45.000 23.55 23.55 45.41 4.02
2747 4701 7.606132 TTTTATACCGCAAAAACAGTTTACG 57.394 32.000 0.00 4.21 0.00 3.18
2748 4702 9.786224 CAATTTTATACCGCAAAAACAGTTTAC 57.214 29.630 0.00 0.00 0.00 2.01
2749 4703 8.979574 CCAATTTTATACCGCAAAAACAGTTTA 58.020 29.630 0.00 0.00 0.00 2.01
2750 4704 7.041712 CCCAATTTTATACCGCAAAAACAGTTT 60.042 33.333 0.00 0.00 0.00 2.66
2751 4705 6.425417 CCCAATTTTATACCGCAAAAACAGTT 59.575 34.615 0.00 0.00 0.00 3.16
2752 4706 5.929415 CCCAATTTTATACCGCAAAAACAGT 59.071 36.000 0.00 0.00 0.00 3.55
2753 4707 5.929415 ACCCAATTTTATACCGCAAAAACAG 59.071 36.000 0.00 0.00 0.00 3.16
2754 4708 5.696724 CACCCAATTTTATACCGCAAAAACA 59.303 36.000 0.00 0.00 0.00 2.83
2755 4709 5.697178 ACACCCAATTTTATACCGCAAAAAC 59.303 36.000 0.00 0.00 0.00 2.43
2756 4710 5.855045 ACACCCAATTTTATACCGCAAAAA 58.145 33.333 0.00 0.00 0.00 1.94
2757 4711 5.470047 ACACCCAATTTTATACCGCAAAA 57.530 34.783 0.00 0.00 0.00 2.44
2758 4712 5.711036 AGTACACCCAATTTTATACCGCAAA 59.289 36.000 0.00 0.00 0.00 3.68
2759 4713 5.124138 CAGTACACCCAATTTTATACCGCAA 59.876 40.000 0.00 0.00 0.00 4.85
2760 4714 4.636648 CAGTACACCCAATTTTATACCGCA 59.363 41.667 0.00 0.00 0.00 5.69
2761 4715 4.496840 GCAGTACACCCAATTTTATACCGC 60.497 45.833 0.00 0.00 0.00 5.68
2762 4716 4.636648 TGCAGTACACCCAATTTTATACCG 59.363 41.667 0.00 0.00 0.00 4.02
2763 4717 5.883673 TCTGCAGTACACCCAATTTTATACC 59.116 40.000 14.67 0.00 0.00 2.73
2764 4718 6.995511 TCTGCAGTACACCCAATTTTATAC 57.004 37.500 14.67 0.00 0.00 1.47
2765 4719 7.172342 AGTTCTGCAGTACACCCAATTTTATA 58.828 34.615 23.33 0.00 0.00 0.98
2766 4720 6.010219 AGTTCTGCAGTACACCCAATTTTAT 58.990 36.000 23.33 0.00 0.00 1.40
2767 4721 5.381757 AGTTCTGCAGTACACCCAATTTTA 58.618 37.500 23.33 0.00 0.00 1.52
2768 4722 4.215109 AGTTCTGCAGTACACCCAATTTT 58.785 39.130 23.33 0.00 0.00 1.82
2769 4723 3.832527 AGTTCTGCAGTACACCCAATTT 58.167 40.909 23.33 0.00 0.00 1.82
2770 4724 3.508845 AGTTCTGCAGTACACCCAATT 57.491 42.857 23.33 0.15 0.00 2.32
2771 4725 4.844349 ATAGTTCTGCAGTACACCCAAT 57.156 40.909 23.33 6.14 0.00 3.16
2772 4726 4.775780 AGTATAGTTCTGCAGTACACCCAA 59.224 41.667 23.33 2.01 0.00 4.12
2773 4727 4.159693 CAGTATAGTTCTGCAGTACACCCA 59.840 45.833 23.33 7.68 0.00 4.51
2774 4728 4.683832 CAGTATAGTTCTGCAGTACACCC 58.316 47.826 23.33 9.55 0.00 4.61
2898 4852 4.383173 AGTCGATTTTTAAGGTGAACCGT 58.617 39.130 0.00 0.00 42.08 4.83
2899 4853 4.433805 CGAGTCGATTTTTAAGGTGAACCG 60.434 45.833 6.73 0.00 42.08 4.44
2909 4863 5.987777 TGTGGTTTTCGAGTCGATTTTTA 57.012 34.783 17.34 0.00 35.23 1.52
2918 4873 5.812286 ACCCTATATTTGTGGTTTTCGAGT 58.188 37.500 0.00 0.00 0.00 4.18
2937 4892 9.213777 CACCATATATTATCACCTACATACCCT 57.786 37.037 0.00 0.00 0.00 4.34
2938 4893 9.209048 TCACCATATATTATCACCTACATACCC 57.791 37.037 0.00 0.00 0.00 3.69
2946 4901 5.547666 TGCAGGTCACCATATATTATCACCT 59.452 40.000 0.00 0.00 33.07 4.00
3024 4979 9.041354 AGATACTCTAAAAGTGGTCAAATCTCT 57.959 33.333 0.00 0.00 39.11 3.10
3025 4980 9.092876 CAGATACTCTAAAAGTGGTCAAATCTC 57.907 37.037 0.00 0.00 39.11 2.75
3026 4981 7.550906 GCAGATACTCTAAAAGTGGTCAAATCT 59.449 37.037 0.00 0.00 39.11 2.40
3027 4982 7.550906 AGCAGATACTCTAAAAGTGGTCAAATC 59.449 37.037 0.00 0.00 39.11 2.17
3028 4983 7.398024 AGCAGATACTCTAAAAGTGGTCAAAT 58.602 34.615 0.00 0.00 39.11 2.32
3071 5026 3.888323 TGCAGCAAGTCTAATTTGGAACA 59.112 39.130 0.00 0.00 0.00 3.18
3119 5074 1.139163 GCCACGTGCAATTTTCCTTG 58.861 50.000 10.91 0.00 40.77 3.61
3134 5089 3.121030 ATTCTCGCGCAGTGCCAC 61.121 61.111 10.11 0.56 42.08 5.01
3135 5090 3.120385 CATTCTCGCGCAGTGCCA 61.120 61.111 10.11 0.00 42.08 4.92
3136 5091 4.527157 GCATTCTCGCGCAGTGCC 62.527 66.667 10.11 1.23 42.08 5.01
3137 5092 3.792047 TGCATTCTCGCGCAGTGC 61.792 61.111 8.75 15.42 38.30 4.40
3138 5093 2.097160 GTGCATTCTCGCGCAGTG 59.903 61.111 8.75 0.00 42.07 3.66
3139 5094 3.121030 GGTGCATTCTCGCGCAGT 61.121 61.111 8.75 0.00 44.30 4.40
3140 5095 1.915614 AAAGGTGCATTCTCGCGCAG 61.916 55.000 8.75 4.17 44.30 5.18
3141 5096 1.965930 AAAGGTGCATTCTCGCGCA 60.966 52.632 8.75 0.00 44.30 6.09
3142 5097 1.512734 CAAAGGTGCATTCTCGCGC 60.513 57.895 0.00 0.00 41.75 6.86
3143 5098 1.135315 CCAAAGGTGCATTCTCGCG 59.865 57.895 0.00 0.00 33.35 5.87
3144 5099 2.257353 ACCAAAGGTGCATTCTCGC 58.743 52.632 0.00 0.00 32.98 5.03
3161 5116 1.144057 CATAGTGGAGACCGGGCAC 59.856 63.158 11.69 1.47 0.00 5.01
3162 5117 1.001120 TCATAGTGGAGACCGGGCA 59.999 57.895 11.69 0.00 0.00 5.36
3163 5118 1.742768 CTCATAGTGGAGACCGGGC 59.257 63.158 6.32 0.52 37.05 6.13
3164 5119 1.043116 TGCTCATAGTGGAGACCGGG 61.043 60.000 6.32 0.00 37.05 5.73
3165 5120 1.000283 GATGCTCATAGTGGAGACCGG 60.000 57.143 0.00 0.00 37.05 5.28
3166 5121 1.959985 AGATGCTCATAGTGGAGACCG 59.040 52.381 0.00 0.00 37.05 4.79
3167 5122 3.386078 TGAAGATGCTCATAGTGGAGACC 59.614 47.826 0.00 0.00 37.05 3.85
3168 5123 4.662468 TGAAGATGCTCATAGTGGAGAC 57.338 45.455 0.00 0.00 37.05 3.36
3169 5124 5.883685 ATTGAAGATGCTCATAGTGGAGA 57.116 39.130 0.00 0.00 37.05 3.71
3170 5125 6.990798 TCTATTGAAGATGCTCATAGTGGAG 58.009 40.000 0.00 0.00 37.97 3.86
3171 5126 6.983906 TCTATTGAAGATGCTCATAGTGGA 57.016 37.500 0.00 0.00 0.00 4.02
3203 5158 9.146984 ACTCAAAGCAAAATTTGATGATGTATG 57.853 29.630 10.26 4.96 45.50 2.39
3252 5207 8.974408 GTTGTAAGTTTTGATGATGTAAAACCC 58.026 33.333 0.00 0.00 44.00 4.11
3265 5220 3.125316 CGGTCGGAGTTGTAAGTTTTGA 58.875 45.455 0.00 0.00 0.00 2.69
3271 5226 2.933495 TCATCGGTCGGAGTTGTAAG 57.067 50.000 0.00 0.00 0.00 2.34
3272 5227 2.494471 ACATCATCGGTCGGAGTTGTAA 59.506 45.455 0.00 0.00 0.00 2.41
3273 5228 2.097036 ACATCATCGGTCGGAGTTGTA 58.903 47.619 0.00 0.00 0.00 2.41
3274 5229 0.895530 ACATCATCGGTCGGAGTTGT 59.104 50.000 0.00 0.00 0.00 3.32
3275 5230 2.863401 TACATCATCGGTCGGAGTTG 57.137 50.000 0.00 0.00 0.00 3.16
3276 5231 3.880047 TTTACATCATCGGTCGGAGTT 57.120 42.857 0.00 0.00 0.00 3.01
3278 5233 4.923871 CCTATTTTACATCATCGGTCGGAG 59.076 45.833 0.00 0.00 0.00 4.63
3279 5234 4.262292 CCCTATTTTACATCATCGGTCGGA 60.262 45.833 0.00 0.00 0.00 4.55
3282 5237 4.385825 TGCCCTATTTTACATCATCGGTC 58.614 43.478 0.00 0.00 0.00 4.79
3284 5239 5.964958 ATTGCCCTATTTTACATCATCGG 57.035 39.130 0.00 0.00 0.00 4.18
3286 5241 9.289782 AGAACTATTGCCCTATTTTACATCATC 57.710 33.333 0.00 0.00 0.00 2.92
3414 5371 4.260212 CCCGGCGCGAGATATTTATTTATG 60.260 45.833 12.10 0.00 0.00 1.90
3415 5372 3.869246 CCCGGCGCGAGATATTTATTTAT 59.131 43.478 12.10 0.00 0.00 1.40
3475 5432 8.680903 CCTATAGCAGCCCTGATAAAATTATTG 58.319 37.037 0.00 0.00 34.93 1.90
3478 5435 6.721318 CCCTATAGCAGCCCTGATAAAATTA 58.279 40.000 0.00 0.00 34.93 1.40
3486 5443 1.074547 TGCCCTATAGCAGCCCTGA 60.075 57.895 9.70 0.00 38.00 3.86
3558 6266 2.094417 GCGTCTGGCAAGTTCAGATAAC 59.906 50.000 0.00 0.00 42.36 1.89
3583 6291 4.569761 TCCTGTATGTTCAGATACTCGC 57.430 45.455 0.00 0.00 37.61 5.03
3599 6307 3.285484 CCTGCTATGCTCAATTTCCTGT 58.715 45.455 0.00 0.00 0.00 4.00
3606 6314 1.842562 AGTGTCCCTGCTATGCTCAAT 59.157 47.619 0.00 0.00 0.00 2.57
3731 6439 8.800332 GCATATTTCACATCCCAGAATATCTTT 58.200 33.333 0.00 0.00 0.00 2.52
3732 6440 7.395489 GGCATATTTCACATCCCAGAATATCTT 59.605 37.037 0.00 0.00 0.00 2.40
3733 6441 6.888632 GGCATATTTCACATCCCAGAATATCT 59.111 38.462 0.00 0.00 0.00 1.98
3734 6442 6.660521 TGGCATATTTCACATCCCAGAATATC 59.339 38.462 0.00 0.00 0.00 1.63
3735 6443 6.554784 TGGCATATTTCACATCCCAGAATAT 58.445 36.000 0.00 0.00 0.00 1.28
3736 6444 5.951204 TGGCATATTTCACATCCCAGAATA 58.049 37.500 0.00 0.00 0.00 1.75
3737 6445 4.806892 TGGCATATTTCACATCCCAGAAT 58.193 39.130 0.00 0.00 0.00 2.40
3738 6446 4.248174 TGGCATATTTCACATCCCAGAA 57.752 40.909 0.00 0.00 0.00 3.02
3739 6447 3.949586 TGGCATATTTCACATCCCAGA 57.050 42.857 0.00 0.00 0.00 3.86
3740 6448 3.257375 CCATGGCATATTTCACATCCCAG 59.743 47.826 0.00 0.00 0.00 4.45
3741 6449 3.117208 TCCATGGCATATTTCACATCCCA 60.117 43.478 6.96 0.00 0.00 4.37
3749 6457 4.717233 TGTGTTGTCCATGGCATATTTC 57.283 40.909 6.96 0.00 0.00 2.17
3757 6465 2.162208 GCTACACATGTGTTGTCCATGG 59.838 50.000 34.66 12.52 43.15 3.66
3770 6478 3.640967 GGGAAGATCTGAGAGCTACACAT 59.359 47.826 0.00 0.00 0.00 3.21
3772 6480 3.027412 TGGGAAGATCTGAGAGCTACAC 58.973 50.000 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.