Multiple sequence alignment - TraesCS5A01G443100

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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 TraesCS5A01G443100 chr5A 100.000 3080 0 0 1 3080 623216859 623213780 0.000000e+00 5688
1 TraesCS5A01G443100 chr5A 95.556 90 4 0 37 126 623216735 623216646 8.900000e-31 145
2 TraesCS5A01G443100 chr5B 94.247 1634 45 22 778 2394 618476945 618475344 0.000000e+00 2451
3 TraesCS5A01G443100 chr5B 92.017 476 30 6 2607 3080 618475286 618474817 0.000000e+00 662
4 TraesCS5A01G443100 chr5B 82.653 490 62 14 304 783 91934094 91934570 2.210000e-111 412
5 TraesCS5A01G443100 chr5D 94.579 1605 43 16 804 2394 498778985 498777411 0.000000e+00 2442
6 TraesCS5A01G443100 chr5D 90.108 465 30 6 2617 3079 498777374 498776924 9.510000e-165 590
7 TraesCS5A01G443100 chr2A 91.594 690 26 5 125 782 763942679 763941990 0.000000e+00 924
8 TraesCS5A01G443100 chr2A 91.608 572 26 6 235 784 104987673 104987102 0.000000e+00 771
9 TraesCS5A01G443100 chr2A 81.818 297 37 12 1177 1461 490665338 490665047 1.850000e-57 233
10 TraesCS5A01G443100 chr2A 96.032 126 5 0 1 126 763942715 763942590 4.030000e-49 206
11 TraesCS5A01G443100 chr2A 94.915 118 6 0 125 242 104989236 104989119 5.240000e-43 185
12 TraesCS5A01G443100 chr1D 89.420 690 19 14 125 783 252546817 252546151 0.000000e+00 821
13 TraesCS5A01G443100 chr1D 96.825 126 4 0 1 126 252546853 252546728 8.650000e-51 211
14 TraesCS5A01G443100 chr6A 91.219 558 37 9 125 681 560564878 560564332 0.000000e+00 749
15 TraesCS5A01G443100 chr6A 82.340 470 70 7 304 772 609788659 609789116 2.230000e-106 396
16 TraesCS5A01G443100 chr6A 95.238 126 6 0 1 126 560564914 560564789 1.870000e-47 200
17 TraesCS5A01G443100 chr7D 93.182 352 20 3 300 648 451038498 451038848 5.890000e-142 514
18 TraesCS5A01G443100 chr7D 95.732 164 7 0 125 288 451032956 451033119 6.550000e-67 265
19 TraesCS5A01G443100 chr7D 96.032 126 5 0 1 126 451032920 451033045 4.030000e-49 206
20 TraesCS5A01G443100 chr7B 87.760 433 23 9 125 527 740003189 740002757 2.150000e-131 479
21 TraesCS5A01G443100 chr7B 82.857 490 62 13 304 783 328590684 328590207 1.320000e-113 420
22 TraesCS5A01G443100 chr7B 95.349 215 10 0 513 727 740001331 740001117 2.940000e-90 342
23 TraesCS5A01G443100 chr7B 88.806 134 7 1 1 126 740003225 740003092 1.140000e-34 158
24 TraesCS5A01G443100 chr6B 89.083 229 20 5 558 783 703151603 703151377 2.340000e-71 279
25 TraesCS5A01G443100 chr1A 82.263 327 48 7 457 782 332380913 332381230 1.090000e-69 274
26 TraesCS5A01G443100 chr6D 88.106 227 26 1 556 782 28664934 28665159 5.060000e-68 268
27 TraesCS5A01G443100 chr2D 81.879 298 35 14 1177 1461 364169572 364169281 1.850000e-57 233
28 TraesCS5A01G443100 chr2B 81.879 298 35 14 1177 1461 432559136 432558845 1.850000e-57 233
29 TraesCS5A01G443100 chr3D 75.854 410 61 22 130 516 105177573 105177179 1.140000e-39 174
30 TraesCS5A01G443100 chr3D 76.119 402 57 23 130 507 105199571 105199185 1.140000e-39 174
31 TraesCS5A01G443100 chr3D 75.610 410 62 21 130 516 105255322 105254928 5.280000e-38 169
32 TraesCS5A01G443100 chr3D 75.610 410 62 21 130 516 105282753 105282359 5.280000e-38 169


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 TraesCS5A01G443100 chr5A 623213780 623216859 3079 True 2916.500000 5688 97.778000 1 3080 2 chr5A.!!$R1 3079
1 TraesCS5A01G443100 chr5B 618474817 618476945 2128 True 1556.500000 2451 93.132000 778 3080 2 chr5B.!!$R1 2302
2 TraesCS5A01G443100 chr5D 498776924 498778985 2061 True 1516.000000 2442 92.343500 804 3079 2 chr5D.!!$R1 2275
3 TraesCS5A01G443100 chr2A 763941990 763942715 725 True 565.000000 924 93.813000 1 782 2 chr2A.!!$R3 781
4 TraesCS5A01G443100 chr2A 104987102 104989236 2134 True 478.000000 771 93.261500 125 784 2 chr2A.!!$R2 659
5 TraesCS5A01G443100 chr1D 252546151 252546853 702 True 516.000000 821 93.122500 1 783 2 chr1D.!!$R1 782
6 TraesCS5A01G443100 chr6A 560564332 560564914 582 True 474.500000 749 93.228500 1 681 2 chr6A.!!$R1 680
7 TraesCS5A01G443100 chr7B 740001117 740003225 2108 True 326.333333 479 90.638333 1 727 3 chr7B.!!$R2 726

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
881 3815 0.042708 CCGCTTCATTCGCTCATTCG 60.043 55.0 0.0 0.0 0.0 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2655 5607 0.039617 TTGAAAAACAGATGCCCGCG 60.04 50.0 0.0 0.0 0.0 6.46 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
40 41 1.357907 TTCGGTCAAAAACGTCACGT 58.642 45.000 0.00 0.00 43.97 4.49
56 57 6.870517 ACGTCACGTTCTGTTTCTATAAAAC 58.129 36.000 0.00 0.00 36.35 2.43
57 58 6.476380 ACGTCACGTTCTGTTTCTATAAAACA 59.524 34.615 0.00 3.59 36.35 2.83
58 59 7.010367 ACGTCACGTTCTGTTTCTATAAAACAA 59.990 33.333 0.00 0.00 36.89 2.83
59 60 8.007716 CGTCACGTTCTGTTTCTATAAAACAAT 58.992 33.333 5.03 0.00 39.36 2.71
60 61 9.314501 GTCACGTTCTGTTTCTATAAAACAATC 57.685 33.333 5.03 0.00 39.36 2.67
61 62 9.047371 TCACGTTCTGTTTCTATAAAACAATCA 57.953 29.630 5.03 0.00 39.36 2.57
62 63 9.825972 CACGTTCTGTTTCTATAAAACAATCAT 57.174 29.630 5.03 0.00 39.36 2.45
73 74 9.665719 TCTATAAAACAATCATCACTACAAGCA 57.334 29.630 0.00 0.00 0.00 3.91
74 75 9.708222 CTATAAAACAATCATCACTACAAGCAC 57.292 33.333 0.00 0.00 0.00 4.40
75 76 6.389830 AAAACAATCATCACTACAAGCACA 57.610 33.333 0.00 0.00 0.00 4.57
76 77 6.389830 AAACAATCATCACTACAAGCACAA 57.610 33.333 0.00 0.00 0.00 3.33
77 78 6.579666 AACAATCATCACTACAAGCACAAT 57.420 33.333 0.00 0.00 0.00 2.71
78 79 5.946298 ACAATCATCACTACAAGCACAATG 58.054 37.500 0.00 0.00 0.00 2.82
79 80 4.627611 ATCATCACTACAAGCACAATGC 57.372 40.909 0.00 0.00 45.46 3.56
94 95 6.956299 GCACAATGCAAATTCATCTACTTT 57.044 33.333 0.00 0.00 44.26 2.66
96 97 8.638685 GCACAATGCAAATTCATCTACTTTAT 57.361 30.769 0.00 0.00 44.26 1.40
97 98 9.090692 GCACAATGCAAATTCATCTACTTTATT 57.909 29.630 0.00 0.00 44.26 1.40
114 115 9.788960 CTACTTTATTTCTGAAATTAACAGGCC 57.211 33.333 19.68 0.00 36.22 5.19
115 116 8.189119 ACTTTATTTCTGAAATTAACAGGCCA 57.811 30.769 19.68 0.00 36.22 5.36
116 117 8.306761 ACTTTATTTCTGAAATTAACAGGCCAG 58.693 33.333 19.68 0.00 36.22 4.85
117 118 7.775053 TTATTTCTGAAATTAACAGGCCAGT 57.225 32.000 19.68 0.00 36.22 4.00
118 119 5.705609 TTTCTGAAATTAACAGGCCAGTC 57.294 39.130 5.01 0.00 36.22 3.51
119 120 4.365514 TCTGAAATTAACAGGCCAGTCA 57.634 40.909 5.01 0.00 36.22 3.41
120 121 4.922206 TCTGAAATTAACAGGCCAGTCAT 58.078 39.130 5.01 0.00 36.22 3.06
121 122 4.943705 TCTGAAATTAACAGGCCAGTCATC 59.056 41.667 5.01 0.00 36.22 2.92
122 123 4.922206 TGAAATTAACAGGCCAGTCATCT 58.078 39.130 5.01 0.00 0.00 2.90
123 124 4.701651 TGAAATTAACAGGCCAGTCATCTG 59.298 41.667 5.01 0.00 41.01 2.90
127 128 2.104859 CAGGCCAGTCATCTGCACG 61.105 63.158 5.01 0.00 40.09 5.34
164 165 5.308014 AGACAATCATCAGTACAAGCACAA 58.692 37.500 0.00 0.00 0.00 3.33
205 214 1.459450 TCTGAAATTAACAGGCCGGC 58.541 50.000 21.18 21.18 36.22 6.13
266 1728 2.609002 GCTATCACGAACACATGATGCA 59.391 45.455 0.00 0.00 36.26 3.96
335 1807 1.065926 AGCCATCGCTTGATTCTGACA 60.066 47.619 0.00 0.00 45.55 3.58
340 1812 4.334759 CCATCGCTTGATTCTGACAAAGAT 59.665 41.667 0.00 0.00 33.93 2.40
416 1888 0.683973 CGCTTCCTCTATCCCATGCT 59.316 55.000 0.00 0.00 0.00 3.79
489 1982 2.094675 GCAATTGCAGTAGGTGTGGAT 58.905 47.619 25.36 0.00 41.59 3.41
541 3474 1.003118 TGCACTAGGAAGGCGAAACAT 59.997 47.619 0.00 0.00 0.00 2.71
622 3555 3.935203 AGTGACAAATCAGTGCCTAATCG 59.065 43.478 0.00 0.00 37.11 3.34
784 3718 9.286170 GAGGGTGAAAACTATACTTCTTTCTTT 57.714 33.333 0.00 0.00 0.00 2.52
800 3734 2.706890 TCTTTATGAAAGGGCCGACAC 58.293 47.619 0.00 0.00 39.01 3.67
878 3812 1.091771 CACCCGCTTCATTCGCTCAT 61.092 55.000 0.00 0.00 0.00 2.90
879 3813 0.392998 ACCCGCTTCATTCGCTCATT 60.393 50.000 0.00 0.00 0.00 2.57
880 3814 0.305922 CCCGCTTCATTCGCTCATTC 59.694 55.000 0.00 0.00 0.00 2.67
881 3815 0.042708 CCGCTTCATTCGCTCATTCG 60.043 55.000 0.00 0.00 0.00 3.34
882 3816 0.652751 CGCTTCATTCGCTCATTCGC 60.653 55.000 0.00 0.00 0.00 4.70
883 3817 0.654683 GCTTCATTCGCTCATTCGCT 59.345 50.000 0.00 0.00 0.00 4.93
884 3818 1.332728 GCTTCATTCGCTCATTCGCTC 60.333 52.381 0.00 0.00 0.00 5.03
885 3819 1.929169 CTTCATTCGCTCATTCGCTCA 59.071 47.619 0.00 0.00 0.00 4.26
886 3820 2.008752 TCATTCGCTCATTCGCTCAA 57.991 45.000 0.00 0.00 0.00 3.02
887 3821 2.345876 TCATTCGCTCATTCGCTCAAA 58.654 42.857 0.00 0.00 0.00 2.69
888 3822 2.741517 TCATTCGCTCATTCGCTCAAAA 59.258 40.909 0.00 0.00 0.00 2.44
889 3823 2.880822 TTCGCTCATTCGCTCAAAAG 57.119 45.000 0.00 0.00 0.00 2.27
890 3824 1.078709 TCGCTCATTCGCTCAAAAGG 58.921 50.000 0.00 0.00 0.00 3.11
891 3825 1.078709 CGCTCATTCGCTCAAAAGGA 58.921 50.000 0.00 0.00 0.00 3.36
1545 4479 1.278413 CGCATGGAGGAGGATGATGAT 59.722 52.381 0.00 0.00 0.00 2.45
1787 4736 1.824230 ACAGCAAGGCACAACAAAAGA 59.176 42.857 0.00 0.00 0.00 2.52
1823 4772 1.228367 AAGGCAGCACCAAGACAGG 60.228 57.895 0.00 0.00 43.14 4.00
1836 4785 1.979693 GACAGGAGGCTCACCGACT 60.980 63.158 17.69 0.09 42.76 4.18
1873 4822 2.765250 GAAGAGACAGCGAACCGGCA 62.765 60.000 0.00 0.00 34.64 5.69
2096 5046 0.397254 TAGCTACCTGGACTGGAGCC 60.397 60.000 0.00 0.00 33.67 4.70
2190 5141 9.971922 ATTCCTTTTTCTCTTTGTGATAAACTG 57.028 29.630 0.00 0.00 0.00 3.16
2246 5197 9.424319 GATTTATCATGTACTGTATGTAGGGTG 57.576 37.037 0.00 0.00 0.00 4.61
2330 5282 3.798878 AGATCTTGATTGTGTATGCGTCG 59.201 43.478 0.00 0.00 0.00 5.12
2350 5302 5.640732 GTCGTGTGCTGAAATGGAAATATT 58.359 37.500 0.00 0.00 0.00 1.28
2351 5303 5.739161 GTCGTGTGCTGAAATGGAAATATTC 59.261 40.000 0.00 0.00 0.00 1.75
2416 5368 8.702163 AAGTGATAAAATAAATTCCTTTGCGG 57.298 30.769 0.00 0.00 0.00 5.69
2417 5369 7.264947 AGTGATAAAATAAATTCCTTTGCGGG 58.735 34.615 0.00 0.00 0.00 6.13
2418 5370 7.123547 AGTGATAAAATAAATTCCTTTGCGGGA 59.876 33.333 0.00 0.00 0.00 5.14
2419 5371 7.435192 GTGATAAAATAAATTCCTTTGCGGGAG 59.565 37.037 0.00 0.00 36.66 4.30
2420 5372 5.993748 AAAATAAATTCCTTTGCGGGAGA 57.006 34.783 0.00 0.00 36.66 3.71
2421 5373 5.993748 AAATAAATTCCTTTGCGGGAGAA 57.006 34.783 0.00 0.00 36.66 2.87
2422 5374 6.544928 AAATAAATTCCTTTGCGGGAGAAT 57.455 33.333 0.00 0.00 36.66 2.40
2423 5375 6.544928 AATAAATTCCTTTGCGGGAGAATT 57.455 33.333 0.00 0.00 39.89 2.17
2424 5376 4.890158 AAATTCCTTTGCGGGAGAATTT 57.110 36.364 10.00 10.00 41.65 1.82
2425 5377 4.890158 AATTCCTTTGCGGGAGAATTTT 57.110 36.364 0.00 0.00 35.89 1.82
2426 5378 3.658757 TTCCTTTGCGGGAGAATTTTG 57.341 42.857 0.00 0.00 36.66 2.44
2427 5379 2.870175 TCCTTTGCGGGAGAATTTTGA 58.130 42.857 0.00 0.00 0.00 2.69
2428 5380 3.226777 TCCTTTGCGGGAGAATTTTGAA 58.773 40.909 0.00 0.00 0.00 2.69
2429 5381 3.255642 TCCTTTGCGGGAGAATTTTGAAG 59.744 43.478 0.00 0.00 0.00 3.02
2430 5382 3.578688 CTTTGCGGGAGAATTTTGAAGG 58.421 45.455 0.00 0.00 0.00 3.46
2431 5383 0.887933 TGCGGGAGAATTTTGAAGGC 59.112 50.000 0.00 0.00 0.00 4.35
2432 5384 1.177401 GCGGGAGAATTTTGAAGGCT 58.823 50.000 0.00 0.00 0.00 4.58
2433 5385 1.133216 GCGGGAGAATTTTGAAGGCTC 59.867 52.381 0.00 0.00 0.00 4.70
2434 5386 1.398390 CGGGAGAATTTTGAAGGCTCG 59.602 52.381 0.00 0.00 0.00 5.03
2435 5387 1.133216 GGGAGAATTTTGAAGGCTCGC 59.867 52.381 0.00 0.00 0.00 5.03
2436 5388 2.087646 GGAGAATTTTGAAGGCTCGCT 58.912 47.619 0.00 0.00 0.00 4.93
2437 5389 2.489722 GGAGAATTTTGAAGGCTCGCTT 59.510 45.455 0.00 0.00 0.00 4.68
2438 5390 3.496155 GAGAATTTTGAAGGCTCGCTTG 58.504 45.455 0.00 0.00 0.00 4.01
2439 5391 1.988467 GAATTTTGAAGGCTCGCTTGC 59.012 47.619 0.00 0.00 0.00 4.01
2440 5392 1.251251 ATTTTGAAGGCTCGCTTGCT 58.749 45.000 0.00 0.00 0.00 3.91
2441 5393 0.593128 TTTTGAAGGCTCGCTTGCTC 59.407 50.000 0.00 0.00 0.00 4.26
2442 5394 0.534877 TTTGAAGGCTCGCTTGCTCA 60.535 50.000 0.00 0.00 0.00 4.26
2443 5395 0.952497 TTGAAGGCTCGCTTGCTCAG 60.952 55.000 0.00 0.00 0.00 3.35
2444 5396 2.745492 AAGGCTCGCTTGCTCAGC 60.745 61.111 0.00 0.00 46.31 4.26
2456 5408 4.959596 CTTGCTCAGCACTATGACAAAT 57.040 40.909 0.00 0.00 38.71 2.32
2457 5409 4.659088 CTTGCTCAGCACTATGACAAATG 58.341 43.478 0.00 0.00 38.71 2.32
2458 5410 3.011818 TGCTCAGCACTATGACAAATGG 58.988 45.455 0.00 0.00 31.71 3.16
2459 5411 2.357009 GCTCAGCACTATGACAAATGGG 59.643 50.000 0.00 0.00 0.00 4.00
2460 5412 2.947652 CTCAGCACTATGACAAATGGGG 59.052 50.000 0.00 0.00 0.00 4.96
2461 5413 2.026641 CAGCACTATGACAAATGGGGG 58.973 52.381 0.00 0.00 0.00 5.40
2462 5414 0.746659 GCACTATGACAAATGGGGGC 59.253 55.000 0.00 0.00 0.00 5.80
2463 5415 1.959508 GCACTATGACAAATGGGGGCA 60.960 52.381 0.00 0.00 0.00 5.36
2464 5416 2.455557 CACTATGACAAATGGGGGCAA 58.544 47.619 0.00 0.00 0.00 4.52
2465 5417 3.033184 CACTATGACAAATGGGGGCAAT 58.967 45.455 0.00 0.00 0.00 3.56
2466 5418 4.214310 CACTATGACAAATGGGGGCAATA 58.786 43.478 0.00 0.00 0.00 1.90
2467 5419 4.834496 CACTATGACAAATGGGGGCAATAT 59.166 41.667 0.00 0.00 0.00 1.28
2468 5420 6.009589 CACTATGACAAATGGGGGCAATATA 58.990 40.000 0.00 0.00 0.00 0.86
2469 5421 6.664816 CACTATGACAAATGGGGGCAATATAT 59.335 38.462 0.00 0.00 0.00 0.86
2470 5422 7.178983 CACTATGACAAATGGGGGCAATATATT 59.821 37.037 0.00 0.00 0.00 1.28
2471 5423 6.610075 ATGACAAATGGGGGCAATATATTC 57.390 37.500 0.00 0.00 0.00 1.75
2472 5424 5.714863 TGACAAATGGGGGCAATATATTCT 58.285 37.500 0.00 0.00 0.00 2.40
2473 5425 5.774690 TGACAAATGGGGGCAATATATTCTC 59.225 40.000 0.00 0.00 0.00 2.87
2474 5426 4.766891 ACAAATGGGGGCAATATATTCTCG 59.233 41.667 0.00 0.00 0.00 4.04
2475 5427 3.652057 ATGGGGGCAATATATTCTCGG 57.348 47.619 0.00 0.00 0.00 4.63
2476 5428 2.344592 TGGGGGCAATATATTCTCGGT 58.655 47.619 0.00 0.00 0.00 4.69
2477 5429 2.039746 TGGGGGCAATATATTCTCGGTG 59.960 50.000 0.00 0.00 0.00 4.94
2478 5430 2.304761 GGGGGCAATATATTCTCGGTGA 59.695 50.000 0.00 0.00 0.00 4.02
2479 5431 3.244770 GGGGGCAATATATTCTCGGTGAA 60.245 47.826 0.00 0.00 39.24 3.18
2480 5432 4.394729 GGGGCAATATATTCTCGGTGAAA 58.605 43.478 0.00 0.00 38.29 2.69
2481 5433 5.010282 GGGGCAATATATTCTCGGTGAAAT 58.990 41.667 0.00 0.00 38.29 2.17
2482 5434 5.123979 GGGGCAATATATTCTCGGTGAAATC 59.876 44.000 0.00 0.00 38.29 2.17
2483 5435 5.940470 GGGCAATATATTCTCGGTGAAATCT 59.060 40.000 0.00 0.00 38.29 2.40
2484 5436 6.128172 GGGCAATATATTCTCGGTGAAATCTG 60.128 42.308 0.00 0.00 38.29 2.90
2485 5437 6.310197 GCAATATATTCTCGGTGAAATCTGC 58.690 40.000 0.00 0.00 38.29 4.26
2486 5438 6.148480 GCAATATATTCTCGGTGAAATCTGCT 59.852 38.462 0.00 0.00 38.29 4.24
2487 5439 7.308229 GCAATATATTCTCGGTGAAATCTGCTT 60.308 37.037 0.00 0.00 38.29 3.91
2488 5440 9.208022 CAATATATTCTCGGTGAAATCTGCTTA 57.792 33.333 0.00 0.00 38.29 3.09
2489 5441 8.764524 ATATATTCTCGGTGAAATCTGCTTAC 57.235 34.615 0.00 0.00 38.29 2.34
2490 5442 3.953712 TCTCGGTGAAATCTGCTTACA 57.046 42.857 0.00 0.00 0.00 2.41
2491 5443 3.849911 TCTCGGTGAAATCTGCTTACAG 58.150 45.455 0.00 0.00 45.95 2.74
2495 5447 2.680339 GGTGAAATCTGCTTACAGGCTC 59.320 50.000 0.00 0.00 44.59 4.70
2496 5448 3.604582 GTGAAATCTGCTTACAGGCTCT 58.395 45.455 0.00 0.00 44.59 4.09
2500 5452 6.986817 GTGAAATCTGCTTACAGGCTCTATAA 59.013 38.462 0.00 0.00 44.59 0.98
2502 5454 7.658982 TGAAATCTGCTTACAGGCTCTATAATG 59.341 37.037 0.00 0.00 44.59 1.90
2508 5460 8.422577 TGCTTACAGGCTCTATAATGAAGATA 57.577 34.615 0.00 0.00 0.00 1.98
2514 5466 8.718656 ACAGGCTCTATAATGAAGATAAACCTT 58.281 33.333 0.00 0.00 0.00 3.50
2527 5479 9.529325 TGAAGATAAACCTTAATCGTGATACTG 57.471 33.333 0.00 0.00 0.00 2.74
2528 5480 8.888579 AAGATAAACCTTAATCGTGATACTGG 57.111 34.615 0.00 0.00 0.00 4.00
2529 5481 7.442656 AGATAAACCTTAATCGTGATACTGGG 58.557 38.462 0.00 0.00 0.00 4.45
2530 5482 5.687166 AAACCTTAATCGTGATACTGGGA 57.313 39.130 0.00 0.00 0.00 4.37
2531 5483 4.939052 ACCTTAATCGTGATACTGGGAG 57.061 45.455 0.00 0.00 0.00 4.30
2532 5484 3.069729 ACCTTAATCGTGATACTGGGAGC 59.930 47.826 0.00 0.00 0.00 4.70
2533 5485 3.555168 CCTTAATCGTGATACTGGGAGCC 60.555 52.174 0.00 0.00 0.00 4.70
2534 5486 0.759346 AATCGTGATACTGGGAGCCC 59.241 55.000 0.00 0.00 0.00 5.19
2535 5487 1.122019 ATCGTGATACTGGGAGCCCC 61.122 60.000 2.49 3.42 45.71 5.80
2536 5488 1.762460 CGTGATACTGGGAGCCCCT 60.762 63.158 11.10 0.00 45.70 4.79
2537 5489 1.749334 CGTGATACTGGGAGCCCCTC 61.749 65.000 11.10 2.02 45.70 4.30
2538 5490 0.399233 GTGATACTGGGAGCCCCTCT 60.399 60.000 11.10 0.08 45.70 3.69
2539 5491 1.133136 GTGATACTGGGAGCCCCTCTA 60.133 57.143 11.10 2.05 45.70 2.43
2540 5492 1.148027 TGATACTGGGAGCCCCTCTAG 59.852 57.143 11.10 3.79 45.70 2.43
2541 5493 0.178918 ATACTGGGAGCCCCTCTAGC 60.179 60.000 11.10 0.00 45.70 3.42
2542 5494 1.297409 TACTGGGAGCCCCTCTAGCT 61.297 60.000 11.10 0.00 45.70 3.32
2548 5500 3.839979 AGCCCCTCTAGCTCTAGTG 57.160 57.895 0.00 2.12 34.91 2.74
2549 5501 0.930726 AGCCCCTCTAGCTCTAGTGT 59.069 55.000 0.00 0.00 34.91 3.55
2550 5502 1.289530 AGCCCCTCTAGCTCTAGTGTT 59.710 52.381 0.00 0.00 34.91 3.32
2551 5503 1.410882 GCCCCTCTAGCTCTAGTGTTG 59.589 57.143 0.00 0.00 34.84 3.33
2552 5504 1.410882 CCCCTCTAGCTCTAGTGTTGC 59.589 57.143 0.00 0.00 34.84 4.17
2553 5505 2.103373 CCCTCTAGCTCTAGTGTTGCA 58.897 52.381 0.00 0.00 34.84 4.08
2554 5506 2.100584 CCCTCTAGCTCTAGTGTTGCAG 59.899 54.545 0.00 0.00 34.84 4.41
2555 5507 3.020274 CCTCTAGCTCTAGTGTTGCAGA 58.980 50.000 0.00 0.00 34.84 4.26
2556 5508 3.445450 CCTCTAGCTCTAGTGTTGCAGAA 59.555 47.826 0.00 0.00 34.84 3.02
2557 5509 4.081972 CCTCTAGCTCTAGTGTTGCAGAAA 60.082 45.833 0.00 0.00 34.84 2.52
2558 5510 5.468540 TCTAGCTCTAGTGTTGCAGAAAA 57.531 39.130 0.00 0.00 34.84 2.29
2559 5511 5.473931 TCTAGCTCTAGTGTTGCAGAAAAG 58.526 41.667 0.00 0.00 34.84 2.27
2560 5512 2.810852 AGCTCTAGTGTTGCAGAAAAGC 59.189 45.455 0.00 0.00 0.00 3.51
2561 5513 2.095516 GCTCTAGTGTTGCAGAAAAGCC 60.096 50.000 0.00 0.00 0.00 4.35
2562 5514 3.406764 CTCTAGTGTTGCAGAAAAGCCT 58.593 45.455 0.00 0.00 0.00 4.58
2563 5515 3.403038 TCTAGTGTTGCAGAAAAGCCTC 58.597 45.455 0.00 0.00 0.00 4.70
2564 5516 1.322442 AGTGTTGCAGAAAAGCCTCC 58.678 50.000 0.00 0.00 0.00 4.30
2565 5517 1.032014 GTGTTGCAGAAAAGCCTCCA 58.968 50.000 0.00 0.00 0.00 3.86
2566 5518 1.032014 TGTTGCAGAAAAGCCTCCAC 58.968 50.000 0.00 0.00 0.00 4.02
2567 5519 0.315251 GTTGCAGAAAAGCCTCCACC 59.685 55.000 0.00 0.00 0.00 4.61
2568 5520 0.185901 TTGCAGAAAAGCCTCCACCT 59.814 50.000 0.00 0.00 0.00 4.00
2569 5521 0.185901 TGCAGAAAAGCCTCCACCTT 59.814 50.000 0.00 0.00 0.00 3.50
2570 5522 0.600057 GCAGAAAAGCCTCCACCTTG 59.400 55.000 0.00 0.00 0.00 3.61
2571 5523 1.251251 CAGAAAAGCCTCCACCTTGG 58.749 55.000 0.00 0.00 39.43 3.61
2576 5528 2.757099 GCCTCCACCTTGGCCATG 60.757 66.667 6.09 9.47 43.11 3.66
2577 5529 2.765969 CCTCCACCTTGGCCATGT 59.234 61.111 6.09 4.01 37.47 3.21
2578 5530 1.998530 CCTCCACCTTGGCCATGTA 59.001 57.895 6.09 0.00 37.47 2.29
2579 5531 0.552848 CCTCCACCTTGGCCATGTAT 59.447 55.000 6.09 0.00 37.47 2.29
2580 5532 1.477558 CCTCCACCTTGGCCATGTATC 60.478 57.143 6.09 0.00 37.47 2.24
2581 5533 1.492176 CTCCACCTTGGCCATGTATCT 59.508 52.381 6.09 0.00 37.47 1.98
2582 5534 1.212688 TCCACCTTGGCCATGTATCTG 59.787 52.381 6.09 0.00 37.47 2.90
2583 5535 1.683943 CACCTTGGCCATGTATCTGG 58.316 55.000 6.09 3.18 39.45 3.86
2584 5536 1.212688 CACCTTGGCCATGTATCTGGA 59.787 52.381 6.09 0.00 38.69 3.86
2585 5537 1.922447 ACCTTGGCCATGTATCTGGAA 59.078 47.619 6.09 0.00 38.69 3.53
2586 5538 2.311542 ACCTTGGCCATGTATCTGGAAA 59.688 45.455 6.09 0.00 38.69 3.13
2587 5539 2.954318 CCTTGGCCATGTATCTGGAAAG 59.046 50.000 6.09 0.00 38.69 2.62
2588 5540 3.624777 CTTGGCCATGTATCTGGAAAGT 58.375 45.455 6.09 0.00 38.69 2.66
2589 5541 3.737559 TGGCCATGTATCTGGAAAGTT 57.262 42.857 0.00 0.00 38.69 2.66
2590 5542 4.853468 TGGCCATGTATCTGGAAAGTTA 57.147 40.909 0.00 0.00 38.69 2.24
2591 5543 5.186256 TGGCCATGTATCTGGAAAGTTAA 57.814 39.130 0.00 0.00 38.69 2.01
2592 5544 4.947388 TGGCCATGTATCTGGAAAGTTAAC 59.053 41.667 0.00 0.00 38.69 2.01
2593 5545 5.193679 GGCCATGTATCTGGAAAGTTAACT 58.806 41.667 1.12 1.12 38.69 2.24
2594 5546 5.066505 GGCCATGTATCTGGAAAGTTAACTG 59.933 44.000 9.34 0.00 38.69 3.16
2595 5547 5.648092 GCCATGTATCTGGAAAGTTAACTGT 59.352 40.000 9.34 2.64 38.69 3.55
2596 5548 6.151144 GCCATGTATCTGGAAAGTTAACTGTT 59.849 38.462 9.34 5.86 38.69 3.16
2597 5549 7.626452 GCCATGTATCTGGAAAGTTAACTGTTC 60.626 40.741 9.34 13.79 38.69 3.18
2598 5550 7.148239 CCATGTATCTGGAAAGTTAACTGTTCC 60.148 40.741 26.34 26.34 41.09 3.62
2599 5551 6.833041 TGTATCTGGAAAGTTAACTGTTCCA 58.167 36.000 29.84 29.84 46.66 3.53
2604 5556 6.591750 TGGAAAGTTAACTGTTCCAAACAA 57.408 33.333 29.87 17.62 46.03 2.83
2605 5557 6.994221 TGGAAAGTTAACTGTTCCAAACAAA 58.006 32.000 29.87 17.18 46.03 2.83
2615 5567 7.161773 ACTGTTCCAAACAAAGATGGATATG 57.838 36.000 0.00 0.00 44.83 1.78
2623 5575 6.530019 AACAAAGATGGATATGAACCCAAC 57.470 37.500 0.00 0.00 35.85 3.77
2633 5585 5.163519 GGATATGAACCCAACATGTTTCCTG 60.164 44.000 8.77 0.00 0.00 3.86
2655 5607 1.468914 GCAACAGGGATTTCGAAGACC 59.531 52.381 12.33 12.33 34.32 3.85
2656 5608 1.732259 CAACAGGGATTTCGAAGACCG 59.268 52.381 13.72 9.41 34.32 4.79
2672 5624 1.154035 CCGCGGGCATCTGTTTTTC 60.154 57.895 20.10 0.00 0.00 2.29
2673 5625 1.578926 CGCGGGCATCTGTTTTTCA 59.421 52.632 0.00 0.00 0.00 2.69
2676 5628 1.000274 GCGGGCATCTGTTTTTCAAGT 60.000 47.619 0.00 0.00 0.00 3.16
2728 5681 2.562738 GTGGATTGGAAGAACAAAGGGG 59.437 50.000 0.00 0.00 33.48 4.79
2881 5835 4.144297 TCAACAAAATCAGAGAAGTGGGG 58.856 43.478 0.00 0.00 0.00 4.96
2887 5841 0.473694 TCAGAGAAGTGGGGAAGGCA 60.474 55.000 0.00 0.00 0.00 4.75
2888 5842 0.401738 CAGAGAAGTGGGGAAGGCAA 59.598 55.000 0.00 0.00 0.00 4.52
2929 5883 4.654915 AGTGTGGATGATGATCAAACACA 58.345 39.130 26.72 24.98 43.56 3.72
2954 5908 2.874701 CAGCGGAGTTCCTGGAAATATG 59.125 50.000 11.40 7.06 0.00 1.78
2959 5913 5.186198 CGGAGTTCCTGGAAATATGAGTTT 58.814 41.667 11.40 0.00 0.00 2.66
3040 5994 5.070981 TCCTGGAAACTGATGATATGGAGTC 59.929 44.000 0.00 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 9.665719 TGCTTGTAGTGATGATTGTTTTATAGA 57.334 29.630 0.00 0.00 0.00 1.98
48 49 9.708222 GTGCTTGTAGTGATGATTGTTTTATAG 57.292 33.333 0.00 0.00 0.00 1.31
49 50 9.225436 TGTGCTTGTAGTGATGATTGTTTTATA 57.775 29.630 0.00 0.00 0.00 0.98
50 51 8.109705 TGTGCTTGTAGTGATGATTGTTTTAT 57.890 30.769 0.00 0.00 0.00 1.40
51 52 7.503521 TGTGCTTGTAGTGATGATTGTTTTA 57.496 32.000 0.00 0.00 0.00 1.52
52 53 6.389830 TGTGCTTGTAGTGATGATTGTTTT 57.610 33.333 0.00 0.00 0.00 2.43
53 54 6.389830 TTGTGCTTGTAGTGATGATTGTTT 57.610 33.333 0.00 0.00 0.00 2.83
54 55 6.384224 CATTGTGCTTGTAGTGATGATTGTT 58.616 36.000 0.00 0.00 0.00 2.83
55 56 5.620654 GCATTGTGCTTGTAGTGATGATTGT 60.621 40.000 0.00 0.00 40.96 2.71
56 57 4.796830 GCATTGTGCTTGTAGTGATGATTG 59.203 41.667 0.00 0.00 40.96 2.67
57 58 4.460034 TGCATTGTGCTTGTAGTGATGATT 59.540 37.500 3.41 0.00 45.31 2.57
58 59 4.011698 TGCATTGTGCTTGTAGTGATGAT 58.988 39.130 3.41 0.00 45.31 2.45
59 60 3.410508 TGCATTGTGCTTGTAGTGATGA 58.589 40.909 3.41 0.00 45.31 2.92
60 61 3.835378 TGCATTGTGCTTGTAGTGATG 57.165 42.857 3.41 0.00 45.31 3.07
61 62 4.852134 TTTGCATTGTGCTTGTAGTGAT 57.148 36.364 3.41 0.00 45.31 3.06
62 63 4.852134 ATTTGCATTGTGCTTGTAGTGA 57.148 36.364 3.41 0.00 45.31 3.41
63 64 4.983538 TGAATTTGCATTGTGCTTGTAGTG 59.016 37.500 3.41 0.00 45.31 2.74
64 65 5.199024 TGAATTTGCATTGTGCTTGTAGT 57.801 34.783 3.41 0.00 45.31 2.73
65 66 6.097356 AGATGAATTTGCATTGTGCTTGTAG 58.903 36.000 3.41 0.00 45.31 2.74
66 67 6.028146 AGATGAATTTGCATTGTGCTTGTA 57.972 33.333 3.41 0.00 45.31 2.41
67 68 4.890088 AGATGAATTTGCATTGTGCTTGT 58.110 34.783 3.41 0.00 45.31 3.16
68 69 6.097356 AGTAGATGAATTTGCATTGTGCTTG 58.903 36.000 3.41 0.00 45.31 4.01
69 70 6.276832 AGTAGATGAATTTGCATTGTGCTT 57.723 33.333 3.41 0.00 45.31 3.91
70 71 5.909621 AGTAGATGAATTTGCATTGTGCT 57.090 34.783 3.41 0.00 45.31 4.40
71 72 6.956299 AAAGTAGATGAATTTGCATTGTGC 57.044 33.333 0.00 0.00 45.29 4.57
88 89 9.788960 GGCCTGTTAATTTCAGAAATAAAGTAG 57.211 33.333 8.88 4.91 35.20 2.57
89 90 9.303116 TGGCCTGTTAATTTCAGAAATAAAGTA 57.697 29.630 8.88 0.00 35.20 2.24
90 91 8.189119 TGGCCTGTTAATTTCAGAAATAAAGT 57.811 30.769 8.88 0.00 35.20 2.66
91 92 8.306761 ACTGGCCTGTTAATTTCAGAAATAAAG 58.693 33.333 9.88 0.00 35.20 1.85
92 93 8.189119 ACTGGCCTGTTAATTTCAGAAATAAA 57.811 30.769 9.88 0.00 35.20 1.40
93 94 7.450014 TGACTGGCCTGTTAATTTCAGAAATAA 59.550 33.333 17.25 2.10 35.20 1.40
94 95 6.945435 TGACTGGCCTGTTAATTTCAGAAATA 59.055 34.615 17.25 0.00 35.20 1.40
95 96 5.774690 TGACTGGCCTGTTAATTTCAGAAAT 59.225 36.000 17.25 2.20 35.20 2.17
96 97 5.136828 TGACTGGCCTGTTAATTTCAGAAA 58.863 37.500 17.25 0.00 35.20 2.52
97 98 4.724399 TGACTGGCCTGTTAATTTCAGAA 58.276 39.130 17.25 0.00 35.20 3.02
98 99 4.365514 TGACTGGCCTGTTAATTTCAGA 57.634 40.909 17.25 0.00 35.20 3.27
99 100 4.946157 AGATGACTGGCCTGTTAATTTCAG 59.054 41.667 17.25 0.00 0.00 3.02
100 101 4.701651 CAGATGACTGGCCTGTTAATTTCA 59.298 41.667 17.25 9.22 40.14 2.69
101 102 4.439289 GCAGATGACTGGCCTGTTAATTTC 60.439 45.833 17.25 7.54 43.62 2.17
102 103 3.445096 GCAGATGACTGGCCTGTTAATTT 59.555 43.478 17.25 6.66 43.62 1.82
103 104 3.019564 GCAGATGACTGGCCTGTTAATT 58.980 45.455 17.25 2.78 43.62 1.40
104 105 2.025981 TGCAGATGACTGGCCTGTTAAT 60.026 45.455 17.25 13.34 43.62 1.40
105 106 1.350684 TGCAGATGACTGGCCTGTTAA 59.649 47.619 17.25 9.00 43.62 2.01
106 107 0.983467 TGCAGATGACTGGCCTGTTA 59.017 50.000 17.25 13.39 43.62 2.41
107 108 0.607489 GTGCAGATGACTGGCCTGTT 60.607 55.000 17.25 1.15 43.62 3.16
108 109 1.002868 GTGCAGATGACTGGCCTGT 60.003 57.895 16.10 16.10 43.62 4.00
109 110 2.104859 CGTGCAGATGACTGGCCTG 61.105 63.158 8.29 8.29 43.62 4.85
110 111 2.116983 AACGTGCAGATGACTGGCCT 62.117 55.000 3.32 0.00 43.62 5.19
111 112 1.639298 GAACGTGCAGATGACTGGCC 61.639 60.000 0.00 0.00 43.62 5.36
112 113 0.671781 AGAACGTGCAGATGACTGGC 60.672 55.000 0.00 0.00 43.62 4.85
113 114 1.073964 CAGAACGTGCAGATGACTGG 58.926 55.000 0.00 0.00 43.62 4.00
114 115 1.788258 ACAGAACGTGCAGATGACTG 58.212 50.000 0.00 0.00 45.91 3.51
115 116 2.533266 AACAGAACGTGCAGATGACT 57.467 45.000 0.00 0.00 0.00 3.41
116 117 2.802816 AGAAACAGAACGTGCAGATGAC 59.197 45.455 0.00 0.00 0.00 3.06
117 118 3.111853 AGAAACAGAACGTGCAGATGA 57.888 42.857 0.00 0.00 0.00 2.92
118 119 6.531594 TCTTATAGAAACAGAACGTGCAGATG 59.468 38.462 0.00 0.00 0.00 2.90
119 120 6.531948 GTCTTATAGAAACAGAACGTGCAGAT 59.468 38.462 0.00 0.00 0.00 2.90
120 121 5.862323 GTCTTATAGAAACAGAACGTGCAGA 59.138 40.000 0.00 0.00 0.00 4.26
121 122 5.633601 TGTCTTATAGAAACAGAACGTGCAG 59.366 40.000 0.00 0.00 0.00 4.41
122 123 5.534407 TGTCTTATAGAAACAGAACGTGCA 58.466 37.500 0.00 0.00 0.00 4.57
123 124 6.462073 TTGTCTTATAGAAACAGAACGTGC 57.538 37.500 0.00 0.00 0.00 5.34
153 154 5.865552 AGATGAATTTGCATTGTGCTTGTAC 59.134 36.000 3.41 0.00 45.31 2.90
205 214 4.411256 AAATGGGCTAATTTGCAGATGG 57.589 40.909 13.80 0.00 34.04 3.51
266 1728 3.335579 GTGTTAAGGACGAGGCTTGATT 58.664 45.455 9.20 3.05 0.00 2.57
278 1740 5.048083 ACCGTAGTAATGTTCGTGTTAAGGA 60.048 40.000 0.00 0.00 0.00 3.36
331 1803 0.601057 TCGCGAGTCCATCTTTGTCA 59.399 50.000 3.71 0.00 0.00 3.58
335 1807 0.456221 ATCGTCGCGAGTCCATCTTT 59.544 50.000 10.24 0.00 39.91 2.52
340 1812 1.136774 CTCAATCGTCGCGAGTCCA 59.863 57.895 10.24 0.00 39.91 4.02
416 1888 3.483421 TCTCTCACTTGACGTCACCTTA 58.517 45.455 19.90 2.05 0.00 2.69
465 1958 0.447801 CACCTACTGCAATTGCGTCC 59.552 55.000 24.58 0.00 45.83 4.79
541 3474 2.049802 GGGCGTTCGTCTTCGTCA 60.050 61.111 0.00 0.00 38.33 4.35
583 3516 0.528924 ACTGACGTGGCGTGCTTATA 59.471 50.000 0.00 0.00 41.37 0.98
622 3555 4.060205 AGTGGTTTTGCATCTGATTTTGC 58.940 39.130 0.00 0.00 39.33 3.68
737 3671 2.679837 CAAATCCTGTCCAATGTCTCCG 59.320 50.000 0.00 0.00 0.00 4.63
784 3718 1.219664 CCGTGTCGGCCCTTTCATA 59.780 57.895 0.00 0.00 41.17 2.15
785 3719 2.046314 CCGTGTCGGCCCTTTCAT 60.046 61.111 0.00 0.00 41.17 2.57
786 3720 4.323477 CCCGTGTCGGCCCTTTCA 62.323 66.667 0.00 0.00 46.86 2.69
1419 4353 1.801913 CACCTCGCGGTCGAAGAAG 60.802 63.158 6.13 0.00 43.24 2.85
1545 4479 2.944954 TCCTCCCCCGTCTCCTCA 60.945 66.667 0.00 0.00 0.00 3.86
1787 4736 1.792757 TTGATGCCCTCCTTGCCTGT 61.793 55.000 0.00 0.00 0.00 4.00
1823 4772 2.183046 GCAGAGTCGGTGAGCCTC 59.817 66.667 0.00 0.00 0.00 4.70
1873 4822 1.668294 CTCTGGGCTCACTGTCGTT 59.332 57.895 0.00 0.00 0.00 3.85
1879 4828 1.551908 CCTTCTGCTCTGGGCTCACT 61.552 60.000 0.00 0.00 42.39 3.41
1992 4941 0.819259 CCTGCTCTCTCCTCTCCTCG 60.819 65.000 0.00 0.00 0.00 4.63
2096 5046 0.674581 TTCTTCTGTCCAGGCATGCG 60.675 55.000 12.44 0.00 0.00 4.73
2185 5136 3.146847 GACTGAATTCCGGAACCAGTTT 58.853 45.455 35.23 23.45 37.54 2.66
2390 5342 9.796120 CCGCAAAGGAATTTATTTTATCACTTA 57.204 29.630 0.00 0.00 45.00 2.24
2391 5343 7.763985 CCCGCAAAGGAATTTATTTTATCACTT 59.236 33.333 0.00 0.00 45.00 3.16
2392 5344 7.123547 TCCCGCAAAGGAATTTATTTTATCACT 59.876 33.333 0.00 0.00 45.00 3.41
2393 5345 7.262048 TCCCGCAAAGGAATTTATTTTATCAC 58.738 34.615 0.00 0.00 45.00 3.06
2394 5346 7.340743 TCTCCCGCAAAGGAATTTATTTTATCA 59.659 33.333 0.00 0.00 45.00 2.15
2395 5347 7.712797 TCTCCCGCAAAGGAATTTATTTTATC 58.287 34.615 0.00 0.00 45.00 1.75
2396 5348 7.654022 TCTCCCGCAAAGGAATTTATTTTAT 57.346 32.000 0.00 0.00 45.00 1.40
2398 5350 5.993748 TCTCCCGCAAAGGAATTTATTTT 57.006 34.783 0.00 0.00 45.00 1.82
2399 5351 5.993748 TTCTCCCGCAAAGGAATTTATTT 57.006 34.783 0.00 0.00 45.00 1.40
2400 5352 6.544928 AATTCTCCCGCAAAGGAATTTATT 57.455 33.333 0.00 0.00 45.00 1.40
2401 5353 6.544928 AAATTCTCCCGCAAAGGAATTTAT 57.455 33.333 12.52 0.00 42.66 1.40
2403 5355 4.890158 AAATTCTCCCGCAAAGGAATTT 57.110 36.364 0.00 0.00 45.00 1.82
2404 5356 4.283212 TCAAAATTCTCCCGCAAAGGAATT 59.717 37.500 0.00 0.00 45.00 2.17
2405 5357 3.831911 TCAAAATTCTCCCGCAAAGGAAT 59.168 39.130 0.00 0.00 45.00 3.01
2406 5358 3.226777 TCAAAATTCTCCCGCAAAGGAA 58.773 40.909 0.00 0.00 45.00 3.36
2407 5359 2.870175 TCAAAATTCTCCCGCAAAGGA 58.130 42.857 0.00 0.00 45.00 3.36
2408 5360 3.578688 CTTCAAAATTCTCCCGCAAAGG 58.421 45.455 0.00 0.00 40.63 3.11
2409 5361 3.578688 CCTTCAAAATTCTCCCGCAAAG 58.421 45.455 0.00 0.00 0.00 2.77
2410 5362 2.288763 GCCTTCAAAATTCTCCCGCAAA 60.289 45.455 0.00 0.00 0.00 3.68
2412 5364 0.887933 GCCTTCAAAATTCTCCCGCA 59.112 50.000 0.00 0.00 0.00 5.69
2413 5365 1.133216 GAGCCTTCAAAATTCTCCCGC 59.867 52.381 0.00 0.00 0.00 6.13
2414 5366 1.398390 CGAGCCTTCAAAATTCTCCCG 59.602 52.381 0.00 0.00 0.00 5.14
2415 5367 1.133216 GCGAGCCTTCAAAATTCTCCC 59.867 52.381 0.00 0.00 0.00 4.30
2416 5368 2.087646 AGCGAGCCTTCAAAATTCTCC 58.912 47.619 0.00 0.00 0.00 3.71
2417 5369 3.496155 CAAGCGAGCCTTCAAAATTCTC 58.504 45.455 0.00 0.00 0.00 2.87
2418 5370 2.352127 GCAAGCGAGCCTTCAAAATTCT 60.352 45.455 0.00 0.00 0.00 2.40
2419 5371 1.988467 GCAAGCGAGCCTTCAAAATTC 59.012 47.619 0.00 0.00 0.00 2.17
2420 5372 1.615392 AGCAAGCGAGCCTTCAAAATT 59.385 42.857 0.00 0.00 34.23 1.82
2421 5373 1.200948 GAGCAAGCGAGCCTTCAAAAT 59.799 47.619 0.00 0.00 34.23 1.82
2422 5374 0.593128 GAGCAAGCGAGCCTTCAAAA 59.407 50.000 0.00 0.00 34.23 2.44
2423 5375 0.534877 TGAGCAAGCGAGCCTTCAAA 60.535 50.000 0.00 0.00 34.23 2.69
2424 5376 0.952497 CTGAGCAAGCGAGCCTTCAA 60.952 55.000 0.00 0.00 34.23 2.69
2425 5377 1.375140 CTGAGCAAGCGAGCCTTCA 60.375 57.895 0.00 0.00 34.23 3.02
2426 5378 2.748843 GCTGAGCAAGCGAGCCTTC 61.749 63.158 0.00 0.00 43.45 3.46
2427 5379 2.745492 GCTGAGCAAGCGAGCCTT 60.745 61.111 0.00 0.00 43.45 4.35
2435 5387 4.438336 CCATTTGTCATAGTGCTGAGCAAG 60.438 45.833 9.51 0.00 41.47 4.01
2436 5388 3.441222 CCATTTGTCATAGTGCTGAGCAA 59.559 43.478 9.51 0.00 41.47 3.91
2437 5389 3.011818 CCATTTGTCATAGTGCTGAGCA 58.988 45.455 1.40 1.40 35.60 4.26
2438 5390 2.357009 CCCATTTGTCATAGTGCTGAGC 59.643 50.000 0.00 0.00 0.00 4.26
2439 5391 2.947652 CCCCATTTGTCATAGTGCTGAG 59.052 50.000 0.00 0.00 0.00 3.35
2440 5392 2.357050 CCCCCATTTGTCATAGTGCTGA 60.357 50.000 0.00 0.00 0.00 4.26
2441 5393 2.026641 CCCCCATTTGTCATAGTGCTG 58.973 52.381 0.00 0.00 0.00 4.41
2442 5394 1.686115 GCCCCCATTTGTCATAGTGCT 60.686 52.381 0.00 0.00 0.00 4.40
2443 5395 0.746659 GCCCCCATTTGTCATAGTGC 59.253 55.000 0.00 0.00 0.00 4.40
2444 5396 2.142356 TGCCCCCATTTGTCATAGTG 57.858 50.000 0.00 0.00 0.00 2.74
2445 5397 2.917713 TTGCCCCCATTTGTCATAGT 57.082 45.000 0.00 0.00 0.00 2.12
2446 5398 7.616935 AGAATATATTGCCCCCATTTGTCATAG 59.383 37.037 1.78 0.00 0.00 2.23
2447 5399 7.477864 AGAATATATTGCCCCCATTTGTCATA 58.522 34.615 1.78 0.00 0.00 2.15
2448 5400 6.325352 AGAATATATTGCCCCCATTTGTCAT 58.675 36.000 1.78 0.00 0.00 3.06
2449 5401 5.714863 AGAATATATTGCCCCCATTTGTCA 58.285 37.500 1.78 0.00 0.00 3.58
2450 5402 5.106157 CGAGAATATATTGCCCCCATTTGTC 60.106 44.000 1.78 0.00 0.00 3.18
2451 5403 4.766891 CGAGAATATATTGCCCCCATTTGT 59.233 41.667 1.78 0.00 0.00 2.83
2452 5404 4.158394 CCGAGAATATATTGCCCCCATTTG 59.842 45.833 1.78 0.00 0.00 2.32
2453 5405 4.202673 ACCGAGAATATATTGCCCCCATTT 60.203 41.667 1.78 0.00 0.00 2.32
2454 5406 3.333680 ACCGAGAATATATTGCCCCCATT 59.666 43.478 1.78 0.00 0.00 3.16
2455 5407 2.919602 ACCGAGAATATATTGCCCCCAT 59.080 45.455 1.78 0.00 0.00 4.00
2456 5408 2.039746 CACCGAGAATATATTGCCCCCA 59.960 50.000 1.78 0.00 0.00 4.96
2457 5409 2.304761 TCACCGAGAATATATTGCCCCC 59.695 50.000 1.78 0.00 0.00 5.40
2458 5410 3.695830 TCACCGAGAATATATTGCCCC 57.304 47.619 1.78 0.00 0.00 5.80
2459 5411 5.940470 AGATTTCACCGAGAATATATTGCCC 59.060 40.000 1.78 0.00 35.83 5.36
2460 5412 6.621596 GCAGATTTCACCGAGAATATATTGCC 60.622 42.308 1.78 0.00 35.83 4.52
2461 5413 6.148480 AGCAGATTTCACCGAGAATATATTGC 59.852 38.462 1.78 0.00 35.83 3.56
2462 5414 7.664082 AGCAGATTTCACCGAGAATATATTG 57.336 36.000 1.78 0.00 35.83 1.90
2463 5415 9.209175 GTAAGCAGATTTCACCGAGAATATATT 57.791 33.333 0.00 0.00 35.83 1.28
2464 5416 8.367911 TGTAAGCAGATTTCACCGAGAATATAT 58.632 33.333 0.00 0.00 35.83 0.86
2465 5417 7.722363 TGTAAGCAGATTTCACCGAGAATATA 58.278 34.615 0.00 0.00 35.83 0.86
2466 5418 6.582636 TGTAAGCAGATTTCACCGAGAATAT 58.417 36.000 0.00 0.00 35.83 1.28
2467 5419 5.972935 TGTAAGCAGATTTCACCGAGAATA 58.027 37.500 0.00 0.00 35.83 1.75
2468 5420 4.832248 TGTAAGCAGATTTCACCGAGAAT 58.168 39.130 0.00 0.00 35.83 2.40
2469 5421 4.245660 CTGTAAGCAGATTTCACCGAGAA 58.754 43.478 0.00 0.00 45.28 2.87
2470 5422 3.368427 CCTGTAAGCAGATTTCACCGAGA 60.368 47.826 0.00 0.00 45.28 4.04
2471 5423 2.932614 CCTGTAAGCAGATTTCACCGAG 59.067 50.000 0.00 0.00 45.28 4.63
2472 5424 2.935238 GCCTGTAAGCAGATTTCACCGA 60.935 50.000 0.00 0.00 45.28 4.69
2473 5425 1.398390 GCCTGTAAGCAGATTTCACCG 59.602 52.381 0.00 0.00 45.28 4.94
2474 5426 2.680339 GAGCCTGTAAGCAGATTTCACC 59.320 50.000 0.00 0.00 45.28 4.02
2475 5427 3.604582 AGAGCCTGTAAGCAGATTTCAC 58.395 45.455 0.00 0.00 45.28 3.18
2476 5428 3.988976 AGAGCCTGTAAGCAGATTTCA 57.011 42.857 0.00 0.00 45.28 2.69
2477 5429 7.875041 TCATTATAGAGCCTGTAAGCAGATTTC 59.125 37.037 0.00 0.00 45.28 2.17
2478 5430 7.739825 TCATTATAGAGCCTGTAAGCAGATTT 58.260 34.615 0.00 0.00 45.28 2.17
2479 5431 7.308450 TCATTATAGAGCCTGTAAGCAGATT 57.692 36.000 0.00 0.00 45.28 2.40
2480 5432 6.924913 TCATTATAGAGCCTGTAAGCAGAT 57.075 37.500 0.00 0.00 45.28 2.90
2481 5433 6.551227 TCTTCATTATAGAGCCTGTAAGCAGA 59.449 38.462 0.00 0.00 45.28 4.26
2482 5434 6.753180 TCTTCATTATAGAGCCTGTAAGCAG 58.247 40.000 0.00 0.00 42.22 4.24
2483 5435 6.731292 TCTTCATTATAGAGCCTGTAAGCA 57.269 37.500 0.00 0.00 34.23 3.91
2484 5436 9.712305 TTTATCTTCATTATAGAGCCTGTAAGC 57.288 33.333 0.00 0.00 0.00 3.09
2486 5438 9.998106 GGTTTATCTTCATTATAGAGCCTGTAA 57.002 33.333 0.00 0.00 0.00 2.41
2487 5439 9.381038 AGGTTTATCTTCATTATAGAGCCTGTA 57.619 33.333 0.00 0.00 0.00 2.74
2488 5440 8.268878 AGGTTTATCTTCATTATAGAGCCTGT 57.731 34.615 0.00 0.00 0.00 4.00
2502 5454 8.979574 CCAGTATCACGATTAAGGTTTATCTTC 58.020 37.037 0.00 0.00 0.00 2.87
2508 5460 5.671493 CTCCCAGTATCACGATTAAGGTTT 58.329 41.667 0.00 0.00 0.00 3.27
2514 5466 1.968493 GGGCTCCCAGTATCACGATTA 59.032 52.381 0.00 0.00 35.81 1.75
2530 5482 0.930726 ACACTAGAGCTAGAGGGGCT 59.069 55.000 11.28 0.00 43.26 5.19
2531 5483 1.410882 CAACACTAGAGCTAGAGGGGC 59.589 57.143 11.28 0.00 36.97 5.80
2532 5484 1.410882 GCAACACTAGAGCTAGAGGGG 59.589 57.143 11.28 2.16 36.97 4.79
2533 5485 2.100584 CTGCAACACTAGAGCTAGAGGG 59.899 54.545 11.28 0.00 36.97 4.30
2534 5486 3.020274 TCTGCAACACTAGAGCTAGAGG 58.980 50.000 11.28 5.68 36.97 3.69
2535 5487 4.710423 TTCTGCAACACTAGAGCTAGAG 57.290 45.455 11.28 6.03 36.97 2.43
2536 5488 5.468540 TTTTCTGCAACACTAGAGCTAGA 57.531 39.130 11.28 0.00 36.97 2.43
2537 5489 4.092675 GCTTTTCTGCAACACTAGAGCTAG 59.907 45.833 0.00 3.06 39.04 3.42
2538 5490 3.997021 GCTTTTCTGCAACACTAGAGCTA 59.003 43.478 0.00 0.00 0.00 3.32
2539 5491 2.810852 GCTTTTCTGCAACACTAGAGCT 59.189 45.455 0.00 0.00 0.00 4.09
2540 5492 2.095516 GGCTTTTCTGCAACACTAGAGC 60.096 50.000 0.00 0.00 34.04 4.09
2541 5493 3.406764 AGGCTTTTCTGCAACACTAGAG 58.593 45.455 0.00 0.00 34.04 2.43
2542 5494 3.403038 GAGGCTTTTCTGCAACACTAGA 58.597 45.455 0.00 0.00 34.04 2.43
2543 5495 2.485814 GGAGGCTTTTCTGCAACACTAG 59.514 50.000 0.00 0.00 34.04 2.57
2544 5496 2.158682 TGGAGGCTTTTCTGCAACACTA 60.159 45.455 0.00 0.00 32.21 2.74
2545 5497 1.322442 GGAGGCTTTTCTGCAACACT 58.678 50.000 0.00 0.00 34.04 3.55
2546 5498 1.032014 TGGAGGCTTTTCTGCAACAC 58.968 50.000 0.00 0.00 32.21 3.32
2547 5499 1.032014 GTGGAGGCTTTTCTGCAACA 58.968 50.000 0.00 0.00 36.87 3.33
2548 5500 0.315251 GGTGGAGGCTTTTCTGCAAC 59.685 55.000 0.00 0.00 36.87 4.17
2549 5501 0.185901 AGGTGGAGGCTTTTCTGCAA 59.814 50.000 0.00 0.00 36.87 4.08
2550 5502 0.185901 AAGGTGGAGGCTTTTCTGCA 59.814 50.000 0.00 0.00 32.71 4.41
2551 5503 0.600057 CAAGGTGGAGGCTTTTCTGC 59.400 55.000 0.00 0.00 0.00 4.26
2552 5504 1.251251 CCAAGGTGGAGGCTTTTCTG 58.749 55.000 0.00 0.00 40.96 3.02
2553 5505 3.753787 CCAAGGTGGAGGCTTTTCT 57.246 52.632 0.00 0.00 40.96 2.52
2560 5512 0.552848 ATACATGGCCAAGGTGGAGG 59.447 55.000 20.36 0.00 40.96 4.30
2561 5513 1.492176 AGATACATGGCCAAGGTGGAG 59.508 52.381 20.36 4.00 40.96 3.86
2562 5514 1.212688 CAGATACATGGCCAAGGTGGA 59.787 52.381 20.36 7.91 40.96 4.02
2563 5515 1.683943 CAGATACATGGCCAAGGTGG 58.316 55.000 20.36 6.88 41.55 4.61
2564 5516 1.212688 TCCAGATACATGGCCAAGGTG 59.787 52.381 20.36 12.82 40.41 4.00
2565 5517 1.595311 TCCAGATACATGGCCAAGGT 58.405 50.000 10.96 14.56 40.41 3.50
2566 5518 2.734755 TTCCAGATACATGGCCAAGG 57.265 50.000 10.96 8.08 40.41 3.61
2567 5519 3.624777 ACTTTCCAGATACATGGCCAAG 58.375 45.455 10.96 8.43 40.41 3.61
2568 5520 3.737559 ACTTTCCAGATACATGGCCAA 57.262 42.857 10.96 0.00 40.41 4.52
2569 5521 3.737559 AACTTTCCAGATACATGGCCA 57.262 42.857 8.56 8.56 40.41 5.36
2570 5522 5.066505 CAGTTAACTTTCCAGATACATGGCC 59.933 44.000 5.07 0.00 40.41 5.36
2571 5523 5.648092 ACAGTTAACTTTCCAGATACATGGC 59.352 40.000 5.07 0.00 40.41 4.40
2572 5524 7.148239 GGAACAGTTAACTTTCCAGATACATGG 60.148 40.741 27.22 9.96 38.98 3.66
2573 5525 7.390440 TGGAACAGTTAACTTTCCAGATACATG 59.610 37.037 29.10 12.10 43.13 3.21
2574 5526 7.458397 TGGAACAGTTAACTTTCCAGATACAT 58.542 34.615 29.10 3.38 43.13 2.29
2575 5527 6.833041 TGGAACAGTTAACTTTCCAGATACA 58.167 36.000 29.10 16.74 43.13 2.29
2581 5533 6.591750 TTGTTTGGAACAGTTAACTTTCCA 57.408 33.333 29.10 29.10 45.69 3.53
2582 5534 7.317390 TCTTTGTTTGGAACAGTTAACTTTCC 58.683 34.615 26.34 26.34 43.27 3.13
2583 5535 8.807581 CATCTTTGTTTGGAACAGTTAACTTTC 58.192 33.333 5.07 12.46 43.27 2.62
2584 5536 7.763985 CCATCTTTGTTTGGAACAGTTAACTTT 59.236 33.333 5.07 4.17 43.27 2.66
2585 5537 7.123547 TCCATCTTTGTTTGGAACAGTTAACTT 59.876 33.333 5.07 0.00 43.27 2.66
2586 5538 6.605594 TCCATCTTTGTTTGGAACAGTTAACT 59.394 34.615 1.12 1.12 43.27 2.24
2587 5539 6.801575 TCCATCTTTGTTTGGAACAGTTAAC 58.198 36.000 0.00 0.00 43.27 2.01
2588 5540 7.595819 ATCCATCTTTGTTTGGAACAGTTAA 57.404 32.000 0.00 0.00 44.83 2.01
2589 5541 8.739039 CATATCCATCTTTGTTTGGAACAGTTA 58.261 33.333 0.00 0.00 44.83 2.24
2590 5542 7.451255 TCATATCCATCTTTGTTTGGAACAGTT 59.549 33.333 0.00 0.00 44.83 3.16
2591 5543 6.947733 TCATATCCATCTTTGTTTGGAACAGT 59.052 34.615 0.00 0.00 44.83 3.55
2592 5544 7.395190 TCATATCCATCTTTGTTTGGAACAG 57.605 36.000 0.00 0.00 44.83 3.16
2593 5545 7.309744 GGTTCATATCCATCTTTGTTTGGAACA 60.310 37.037 0.00 0.00 44.83 3.18
2594 5546 7.035612 GGTTCATATCCATCTTTGTTTGGAAC 58.964 38.462 0.00 0.00 44.83 3.62
2595 5547 6.154363 GGGTTCATATCCATCTTTGTTTGGAA 59.846 38.462 0.00 0.00 44.83 3.53
2596 5548 5.656416 GGGTTCATATCCATCTTTGTTTGGA 59.344 40.000 0.00 0.00 45.69 3.53
2597 5549 5.421693 TGGGTTCATATCCATCTTTGTTTGG 59.578 40.000 0.00 0.00 0.00 3.28
2598 5550 6.528537 TGGGTTCATATCCATCTTTGTTTG 57.471 37.500 0.00 0.00 0.00 2.93
2599 5551 6.496565 TGTTGGGTTCATATCCATCTTTGTTT 59.503 34.615 0.00 0.00 32.48 2.83
2600 5552 6.015918 TGTTGGGTTCATATCCATCTTTGTT 58.984 36.000 0.00 0.00 32.48 2.83
2601 5553 5.579047 TGTTGGGTTCATATCCATCTTTGT 58.421 37.500 0.00 0.00 32.48 2.83
2602 5554 6.097270 ACATGTTGGGTTCATATCCATCTTTG 59.903 38.462 0.00 0.00 32.48 2.77
2603 5555 6.197168 ACATGTTGGGTTCATATCCATCTTT 58.803 36.000 0.00 0.00 32.48 2.52
2604 5556 5.769835 ACATGTTGGGTTCATATCCATCTT 58.230 37.500 0.00 0.00 32.48 2.40
2605 5557 5.393068 ACATGTTGGGTTCATATCCATCT 57.607 39.130 0.00 0.00 32.48 2.90
2615 5567 2.545742 GCACAGGAAACATGTTGGGTTC 60.546 50.000 12.82 5.63 0.00 3.62
2633 5585 2.095718 GTCTTCGAAATCCCTGTTGCAC 60.096 50.000 0.00 0.00 0.00 4.57
2655 5607 0.039617 TTGAAAAACAGATGCCCGCG 60.040 50.000 0.00 0.00 0.00 6.46
2656 5608 1.000274 ACTTGAAAAACAGATGCCCGC 60.000 47.619 0.00 0.00 0.00 6.13
2672 5624 6.974622 ACACTTGCTTCACTAATTTGAACTTG 59.025 34.615 0.00 0.00 32.02 3.16
2673 5625 6.974622 CACACTTGCTTCACTAATTTGAACTT 59.025 34.615 0.00 0.00 32.02 2.66
2676 5628 5.592282 TCCACACTTGCTTCACTAATTTGAA 59.408 36.000 0.00 0.00 34.30 2.69
2929 5883 0.832135 TCCAGGAACTCCGCTGTCTT 60.832 55.000 0.00 0.00 42.08 3.01
2954 5908 2.032681 ACCCGCAGCCTGAAACTC 59.967 61.111 0.00 0.00 0.00 3.01
2959 5913 4.704833 GCTTCACCCGCAGCCTGA 62.705 66.667 0.00 0.00 0.00 3.86
2994 5948 0.835971 ACCTTTGCCCATTCCCAACC 60.836 55.000 0.00 0.00 0.00 3.77
2997 5951 1.912763 GCACCTTTGCCCATTCCCA 60.913 57.895 0.00 0.00 43.66 4.37
3008 5962 1.494721 TCAGTTTCCAGGAGCACCTTT 59.505 47.619 0.00 0.00 45.36 3.11
3040 5994 1.227674 GCCTCCATACCCTGCTTCG 60.228 63.158 0.00 0.00 0.00 3.79


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

AutoCloner maintained by Alex Coulton.