Multiple sequence alignment - TraesCS5B01G146900

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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 TraesCS5B01G146900 chr5B 100.000 2696 0 0 1 2696 275172286 275174981 0.000000e+00 4979
1 TraesCS5B01G146900 chr5B 82.353 153 23 4 2069 2218 706718016 706717865 2.180000e-26 130
2 TraesCS5B01G146900 chr5A 90.242 2275 94 42 1 2217 325995323 325997527 0.000000e+00 2854
3 TraesCS5B01G146900 chr5D 91.951 1317 52 23 927 2220 231322213 231320928 0.000000e+00 1796
4 TraesCS5B01G146900 chr5D 92.489 932 31 7 1 913 231323180 231322269 0.000000e+00 1297
5 TraesCS5B01G146900 chr5D 85.106 141 19 2 2079 2217 300935230 300935370 2.800000e-30 143
6 TraesCS5B01G146900 chr7B 93.376 468 31 0 2221 2688 641732383 641732850 0.000000e+00 693
7 TraesCS5B01G146900 chr7B 90.966 476 42 1 2221 2696 659409948 659410422 8.140000e-180 640
8 TraesCS5B01G146900 chr4B 95.033 302 15 0 949 1250 139769315 139769014 2.430000e-130 475
9 TraesCS5B01G146900 chr4D 94.702 302 16 0 949 1250 98482062 98481761 1.130000e-128 470
10 TraesCS5B01G146900 chr4A 94.371 302 17 0 949 1250 477833810 477834111 5.260000e-127 464
11 TraesCS5B01G146900 chr4A 86.364 132 18 0 1120 1251 477830556 477830687 7.780000e-31 145
12 TraesCS5B01G146900 chr4A 83.660 153 21 4 2069 2218 608187771 608187922 1.010000e-29 141
13 TraesCS5B01G146900 chr1B 81.818 451 80 2 2228 2677 578536150 578536599 7.050000e-101 377
14 TraesCS5B01G146900 chr2D 77.828 442 84 9 2223 2657 57315053 57314619 7.400000e-66 261


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 TraesCS5B01G146900 chr5B 275172286 275174981 2695 False 4979.0 4979 100.0000 1 2696 1 chr5B.!!$F1 2695
1 TraesCS5B01G146900 chr5A 325995323 325997527 2204 False 2854.0 2854 90.2420 1 2217 1 chr5A.!!$F1 2216
2 TraesCS5B01G146900 chr5D 231320928 231323180 2252 True 1546.5 1796 92.2200 1 2220 2 chr5D.!!$R1 2219
3 TraesCS5B01G146900 chr4A 477830556 477834111 3555 False 304.5 464 90.3675 949 1251 2 chr4A.!!$F2 302

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
251 270 1.607148 GGCTGTGCCGTAAAGTTTCTT 59.393 47.619 0.0 0.0 39.62 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2244 4591 0.039618 GATGTGGTGGGGGATGTGTT 59.96 55.0 0.0 0.0 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
135 154 4.014406 GTTGTTCCGGGAATATTGGTTCT 58.986 43.478 13.48 0.00 0.00 3.01
251 270 1.607148 GGCTGTGCCGTAAAGTTTCTT 59.393 47.619 0.00 0.00 39.62 2.52
252 271 2.034179 GGCTGTGCCGTAAAGTTTCTTT 59.966 45.455 0.00 0.59 39.62 2.52
329 348 8.848474 AGTGTTAAACTATGCTGATAGTGTTT 57.152 30.769 0.00 0.00 43.46 2.83
330 349 9.284968 AGTGTTAAACTATGCTGATAGTGTTTT 57.715 29.630 0.00 0.00 43.46 2.43
395 414 3.396560 TGTCAGCTTGATCACACTCTTG 58.603 45.455 0.00 0.00 0.00 3.02
405 424 5.056480 TGATCACACTCTTGTCGTTGAAAT 58.944 37.500 0.00 0.00 31.66 2.17
504 523 4.162888 ACATGATGCACTGACCAATCTAGA 59.837 41.667 0.00 0.00 0.00 2.43
673 692 2.671070 CTGGTCCGGTTGGCATCT 59.329 61.111 0.00 0.00 34.14 2.90
674 693 1.746615 CTGGTCCGGTTGGCATCTG 60.747 63.158 0.00 0.00 34.14 2.90
706 725 4.746115 TCAATGCTGCATGAAAAACAAGAC 59.254 37.500 17.00 0.00 0.00 3.01
707 726 2.730069 TGCTGCATGAAAAACAAGACG 58.270 42.857 0.00 0.00 0.00 4.18
1361 3671 2.635229 CTAGCACTAGCAGCGGGTGG 62.635 65.000 18.03 0.00 45.49 4.61
1700 4017 0.965866 AGCTACACTGGCTAGTCGCA 60.966 55.000 15.01 0.00 41.67 5.10
1755 4072 7.413475 GAGCTTCTCGATTTATAGCATGAAA 57.587 36.000 0.00 0.00 34.37 2.69
1770 4087 3.604772 GCATGAAACTCACCGATTATCGC 60.605 47.826 9.34 0.00 38.82 4.58
1920 4237 1.691196 TGAAAGTGGAAAGCAGGTGG 58.309 50.000 0.00 0.00 0.00 4.61
1924 4241 1.067295 AGTGGAAAGCAGGTGGATGA 58.933 50.000 0.00 0.00 0.00 2.92
1938 4255 3.941483 GGTGGATGACATTGTGGAGTTAG 59.059 47.826 0.00 0.00 0.00 2.34
1939 4256 3.941483 GTGGATGACATTGTGGAGTTAGG 59.059 47.826 0.00 0.00 0.00 2.69
1955 4272 4.589908 AGTTAGGGGAACATTACTTGCTG 58.410 43.478 0.00 0.00 40.86 4.41
1980 4297 6.809196 GTGCAAATCATTTACGGGTTATTTGA 59.191 34.615 9.18 0.00 36.77 2.69
2099 4439 9.535170 TTGTGGAATTAATTCTTGTATTACCCA 57.465 29.630 23.85 10.16 37.00 4.51
2118 4458 6.220726 ACCCAATTAAAGTACAATCATGCC 57.779 37.500 0.00 0.00 0.00 4.40
2169 4516 1.098050 CCCAAGCCATACTGCAGTTC 58.902 55.000 27.06 11.91 0.00 3.01
2183 4530 0.390472 CAGTTCGGCCTTGAGTCCTC 60.390 60.000 0.00 0.00 0.00 3.71
2184 4531 1.446272 GTTCGGCCTTGAGTCCTCG 60.446 63.158 0.00 0.00 0.00 4.63
2223 4570 9.965902 AAACATGACTAGAAGAATTACAATCCT 57.034 29.630 0.00 0.00 0.00 3.24
2224 4571 9.606631 AACATGACTAGAAGAATTACAATCCTC 57.393 33.333 0.00 0.00 0.00 3.71
2225 4572 7.923344 ACATGACTAGAAGAATTACAATCCTCG 59.077 37.037 0.00 0.00 0.00 4.63
2226 4573 6.273825 TGACTAGAAGAATTACAATCCTCGC 58.726 40.000 0.00 0.00 0.00 5.03
2227 4574 5.602628 ACTAGAAGAATTACAATCCTCGCC 58.397 41.667 0.00 0.00 0.00 5.54
2228 4575 4.487714 AGAAGAATTACAATCCTCGCCA 57.512 40.909 0.00 0.00 0.00 5.69
2229 4576 4.843728 AGAAGAATTACAATCCTCGCCAA 58.156 39.130 0.00 0.00 0.00 4.52
2230 4577 5.253330 AGAAGAATTACAATCCTCGCCAAA 58.747 37.500 0.00 0.00 0.00 3.28
2231 4578 5.355350 AGAAGAATTACAATCCTCGCCAAAG 59.645 40.000 0.00 0.00 0.00 2.77
2232 4579 4.589908 AGAATTACAATCCTCGCCAAAGT 58.410 39.130 0.00 0.00 0.00 2.66
2233 4580 4.636206 AGAATTACAATCCTCGCCAAAGTC 59.364 41.667 0.00 0.00 0.00 3.01
2234 4581 2.004583 TACAATCCTCGCCAAAGTCG 57.995 50.000 0.00 0.00 0.00 4.18
2235 4582 0.320374 ACAATCCTCGCCAAAGTCGA 59.680 50.000 0.00 0.00 34.52 4.20
2242 4589 3.793144 GCCAAAGTCGAGGCGCTG 61.793 66.667 7.64 0.00 41.70 5.18
2243 4590 3.793144 CCAAAGTCGAGGCGCTGC 61.793 66.667 7.64 0.00 0.00 5.25
2244 4591 3.043713 CAAAGTCGAGGCGCTGCA 61.044 61.111 7.64 0.00 0.00 4.41
2245 4592 2.280797 AAAGTCGAGGCGCTGCAA 60.281 55.556 7.64 0.00 0.00 4.08
2246 4593 2.607892 AAAGTCGAGGCGCTGCAAC 61.608 57.895 7.64 1.03 0.00 4.17
2247 4594 3.807631 AAGTCGAGGCGCTGCAACA 62.808 57.895 7.64 0.00 0.00 3.33
2248 4595 4.077188 GTCGAGGCGCTGCAACAC 62.077 66.667 7.64 0.00 0.00 3.32
2249 4596 4.600576 TCGAGGCGCTGCAACACA 62.601 61.111 7.64 0.00 0.00 3.72
2250 4597 3.425713 CGAGGCGCTGCAACACAT 61.426 61.111 7.64 0.00 0.00 3.21
2251 4598 2.482374 GAGGCGCTGCAACACATC 59.518 61.111 7.64 0.00 0.00 3.06
2252 4599 3.044059 GAGGCGCTGCAACACATCC 62.044 63.158 7.64 0.00 0.00 3.51
2253 4600 4.120331 GGCGCTGCAACACATCCC 62.120 66.667 7.64 0.00 0.00 3.85
2254 4601 4.120331 GCGCTGCAACACATCCCC 62.120 66.667 0.00 0.00 0.00 4.81
2255 4602 3.443045 CGCTGCAACACATCCCCC 61.443 66.667 0.00 0.00 0.00 5.40
2256 4603 2.283101 GCTGCAACACATCCCCCA 60.283 61.111 0.00 0.00 0.00 4.96
2257 4604 2.639327 GCTGCAACACATCCCCCAC 61.639 63.158 0.00 0.00 0.00 4.61
2258 4605 1.978617 CTGCAACACATCCCCCACC 60.979 63.158 0.00 0.00 0.00 4.61
2259 4606 2.117206 GCAACACATCCCCCACCA 59.883 61.111 0.00 0.00 0.00 4.17
2260 4607 2.275380 GCAACACATCCCCCACCAC 61.275 63.158 0.00 0.00 0.00 4.16
2261 4608 1.152599 CAACACATCCCCCACCACA 59.847 57.895 0.00 0.00 0.00 4.17
2262 4609 0.251742 CAACACATCCCCCACCACAT 60.252 55.000 0.00 0.00 0.00 3.21
2263 4610 0.039618 AACACATCCCCCACCACATC 59.960 55.000 0.00 0.00 0.00 3.06
2264 4611 1.451927 CACATCCCCCACCACATCG 60.452 63.158 0.00 0.00 0.00 3.84
2265 4612 2.516930 CATCCCCCACCACATCGC 60.517 66.667 0.00 0.00 0.00 4.58
2266 4613 3.809013 ATCCCCCACCACATCGCC 61.809 66.667 0.00 0.00 0.00 5.54
2269 4616 4.715523 CCCCACCACATCGCCGTT 62.716 66.667 0.00 0.00 0.00 4.44
2270 4617 3.124921 CCCACCACATCGCCGTTC 61.125 66.667 0.00 0.00 0.00 3.95
2271 4618 2.358125 CCACCACATCGCCGTTCA 60.358 61.111 0.00 0.00 0.00 3.18
2272 4619 2.677003 CCACCACATCGCCGTTCAC 61.677 63.158 0.00 0.00 0.00 3.18
2273 4620 2.358247 ACCACATCGCCGTTCACC 60.358 61.111 0.00 0.00 0.00 4.02
2274 4621 3.487202 CCACATCGCCGTTCACCG 61.487 66.667 0.00 0.00 0.00 4.94
2275 4622 4.147322 CACATCGCCGTTCACCGC 62.147 66.667 0.00 0.00 34.38 5.68
2276 4623 4.373116 ACATCGCCGTTCACCGCT 62.373 61.111 0.00 0.00 34.38 5.52
2277 4624 3.118454 CATCGCCGTTCACCGCTT 61.118 61.111 0.00 0.00 34.38 4.68
2278 4625 2.813908 ATCGCCGTTCACCGCTTC 60.814 61.111 0.00 0.00 34.38 3.86
2281 4628 3.774702 GCCGTTCACCGCTTCGAC 61.775 66.667 0.00 0.00 34.38 4.20
2282 4629 3.467119 CCGTTCACCGCTTCGACG 61.467 66.667 0.00 0.00 34.38 5.12
2313 4660 2.809174 CGCCGACGTGCTGATCAA 60.809 61.111 0.00 0.00 33.53 2.57
2314 4661 2.778679 GCCGACGTGCTGATCAAC 59.221 61.111 0.00 0.00 0.00 3.18
2315 4662 3.071459 GCCGACGTGCTGATCAACG 62.071 63.158 16.40 16.40 0.00 4.10
2316 4663 1.443702 CCGACGTGCTGATCAACGA 60.444 57.895 23.06 0.00 0.00 3.85
2317 4664 1.406219 CCGACGTGCTGATCAACGAG 61.406 60.000 23.06 16.14 0.00 4.18
2318 4665 0.454452 CGACGTGCTGATCAACGAGA 60.454 55.000 23.06 0.00 0.00 4.04
2319 4666 1.795525 CGACGTGCTGATCAACGAGAT 60.796 52.381 23.06 4.40 40.48 2.75
2330 4677 1.931841 TCAACGAGATCTAGGACGTCG 59.068 52.381 9.92 2.42 38.00 5.12
2331 4678 0.656785 AACGAGATCTAGGACGTCGC 59.343 55.000 9.92 2.53 38.00 5.19
2332 4679 1.202072 CGAGATCTAGGACGTCGCG 59.798 63.158 9.92 0.00 0.00 5.87
2333 4680 1.082627 GAGATCTAGGACGTCGCGC 60.083 63.158 9.92 0.00 0.00 6.86
2335 4682 2.879070 GATCTAGGACGTCGCGCGA 61.879 63.158 31.40 31.40 44.77 5.87
2336 4683 2.172719 GATCTAGGACGTCGCGCGAT 62.173 60.000 37.03 22.09 44.77 4.58
2337 4684 2.172719 ATCTAGGACGTCGCGCGATC 62.173 60.000 37.03 28.66 44.77 3.69
2338 4685 4.289379 TAGGACGTCGCGCGATCG 62.289 66.667 35.33 35.33 44.77 3.69
2365 4712 4.308458 CCGTCCGCACCTCCACAA 62.308 66.667 0.00 0.00 0.00 3.33
2366 4713 3.041940 CGTCCGCACCTCCACAAC 61.042 66.667 0.00 0.00 0.00 3.32
2367 4714 2.668550 GTCCGCACCTCCACAACC 60.669 66.667 0.00 0.00 0.00 3.77
2368 4715 3.948719 TCCGCACCTCCACAACCC 61.949 66.667 0.00 0.00 0.00 4.11
2371 4718 3.897122 GCACCTCCACAACCCCCA 61.897 66.667 0.00 0.00 0.00 4.96
2372 4719 3.180282 CACCTCCACAACCCCCAT 58.820 61.111 0.00 0.00 0.00 4.00
2373 4720 1.000896 CACCTCCACAACCCCCATC 60.001 63.158 0.00 0.00 0.00 3.51
2374 4721 2.238701 ACCTCCACAACCCCCATCC 61.239 63.158 0.00 0.00 0.00 3.51
2375 4722 2.272146 CTCCACAACCCCCATCCG 59.728 66.667 0.00 0.00 0.00 4.18
2376 4723 3.995506 CTCCACAACCCCCATCCGC 62.996 68.421 0.00 0.00 0.00 5.54
2377 4724 4.358841 CCACAACCCCCATCCGCA 62.359 66.667 0.00 0.00 0.00 5.69
2378 4725 3.061848 CACAACCCCCATCCGCAC 61.062 66.667 0.00 0.00 0.00 5.34
2379 4726 4.715523 ACAACCCCCATCCGCACG 62.716 66.667 0.00 0.00 0.00 5.34
2411 4758 3.866582 GAGGGGGATCCGGTGCTG 61.867 72.222 5.45 0.00 41.52 4.41
2423 4770 3.426568 GTGCTGGGCGTGCTCTTC 61.427 66.667 0.00 0.00 0.00 2.87
2424 4771 4.704833 TGCTGGGCGTGCTCTTCC 62.705 66.667 0.00 0.00 0.00 3.46
2425 4772 4.400961 GCTGGGCGTGCTCTTCCT 62.401 66.667 0.00 0.00 0.00 3.36
2426 4773 2.125350 CTGGGCGTGCTCTTCCTC 60.125 66.667 0.00 0.00 0.00 3.71
2427 4774 3.997064 CTGGGCGTGCTCTTCCTCG 62.997 68.421 0.00 0.00 0.00 4.63
2428 4775 4.821589 GGGCGTGCTCTTCCTCGG 62.822 72.222 0.00 0.00 0.00 4.63
2429 4776 3.760035 GGCGTGCTCTTCCTCGGA 61.760 66.667 0.00 0.00 0.00 4.55
2430 4777 2.507324 GCGTGCTCTTCCTCGGAC 60.507 66.667 0.00 0.00 0.00 4.79
2431 4778 2.182030 CGTGCTCTTCCTCGGACC 59.818 66.667 0.00 0.00 0.00 4.46
2432 4779 2.579738 GTGCTCTTCCTCGGACCC 59.420 66.667 0.00 0.00 0.00 4.46
2433 4780 1.985116 GTGCTCTTCCTCGGACCCT 60.985 63.158 0.00 0.00 0.00 4.34
2434 4781 1.984570 TGCTCTTCCTCGGACCCTG 60.985 63.158 0.00 0.00 0.00 4.45
2435 4782 2.896443 CTCTTCCTCGGACCCTGC 59.104 66.667 0.00 0.00 0.00 4.85
2436 4783 2.683933 TCTTCCTCGGACCCTGCC 60.684 66.667 0.00 0.00 0.00 4.85
2437 4784 2.685380 CTTCCTCGGACCCTGCCT 60.685 66.667 0.00 0.00 0.00 4.75
2438 4785 2.683933 TTCCTCGGACCCTGCCTC 60.684 66.667 0.00 0.00 0.00 4.70
2466 4813 3.787001 CTCCTTGGCCCGGGACTC 61.787 72.222 30.93 15.00 0.00 3.36
2491 4838 4.603535 GCACCAGGTGGCCAGGTT 62.604 66.667 21.77 0.00 40.64 3.50
2492 4839 2.598394 CACCAGGTGGCCAGGTTG 60.598 66.667 12.37 8.11 40.64 3.77
2493 4840 2.776526 ACCAGGTGGCCAGGTTGA 60.777 61.111 5.11 0.00 40.64 3.18
2494 4841 2.391130 ACCAGGTGGCCAGGTTGAA 61.391 57.895 5.11 0.00 40.64 2.69
2495 4842 1.604593 CCAGGTGGCCAGGTTGAAG 60.605 63.158 5.11 0.00 0.00 3.02
2496 4843 1.455849 CAGGTGGCCAGGTTGAAGA 59.544 57.895 5.11 0.00 0.00 2.87
2497 4844 0.890996 CAGGTGGCCAGGTTGAAGAC 60.891 60.000 5.11 0.00 0.00 3.01
2498 4845 1.966451 GGTGGCCAGGTTGAAGACG 60.966 63.158 5.11 0.00 0.00 4.18
2499 4846 1.070786 GTGGCCAGGTTGAAGACGA 59.929 57.895 5.11 0.00 0.00 4.20
2500 4847 0.321653 GTGGCCAGGTTGAAGACGAT 60.322 55.000 5.11 0.00 0.00 3.73
2501 4848 0.321564 TGGCCAGGTTGAAGACGATG 60.322 55.000 0.00 0.00 0.00 3.84
2502 4849 1.026718 GGCCAGGTTGAAGACGATGG 61.027 60.000 0.00 0.00 38.29 3.51
2503 4850 2.471255 CCAGGTTGAAGACGATGGC 58.529 57.895 0.00 0.00 31.52 4.40
2504 4851 0.321564 CCAGGTTGAAGACGATGGCA 60.322 55.000 0.00 0.00 31.52 4.92
2505 4852 1.679944 CCAGGTTGAAGACGATGGCAT 60.680 52.381 0.00 0.00 31.52 4.40
2506 4853 1.399440 CAGGTTGAAGACGATGGCATG 59.601 52.381 3.81 0.00 0.00 4.06
2507 4854 0.734889 GGTTGAAGACGATGGCATGG 59.265 55.000 3.81 6.26 0.00 3.66
2508 4855 0.099436 GTTGAAGACGATGGCATGGC 59.901 55.000 13.29 13.29 0.00 4.40
2534 4881 3.849953 CGTACCGCGCTTTCCTGC 61.850 66.667 5.56 0.00 0.00 4.85
2535 4882 2.740826 GTACCGCGCTTTCCTGCA 60.741 61.111 5.56 0.00 0.00 4.41
2536 4883 2.434185 TACCGCGCTTTCCTGCAG 60.434 61.111 6.78 6.78 0.00 4.41
2542 4889 3.066814 GCTTTCCTGCAGCCCCAG 61.067 66.667 8.66 2.08 0.00 4.45
2543 4890 2.759114 CTTTCCTGCAGCCCCAGA 59.241 61.111 8.66 0.00 34.77 3.86
2544 4891 1.305623 CTTTCCTGCAGCCCCAGAT 59.694 57.895 8.66 0.00 34.77 2.90
2545 4892 0.750911 CTTTCCTGCAGCCCCAGATC 60.751 60.000 8.66 0.00 34.77 2.75
2546 4893 2.541547 TTTCCTGCAGCCCCAGATCG 62.542 60.000 8.66 0.00 34.77 3.69
2550 4897 4.925861 GCAGCCCCAGATCGCCTC 62.926 72.222 0.00 0.00 0.00 4.70
2551 4898 4.247380 CAGCCCCAGATCGCCTCC 62.247 72.222 0.00 0.00 0.00 4.30
2561 4908 3.708210 TCGCCTCCGACCAAGATT 58.292 55.556 0.00 0.00 38.82 2.40
2562 4909 1.980052 TCGCCTCCGACCAAGATTT 59.020 52.632 0.00 0.00 38.82 2.17
2563 4910 0.108329 TCGCCTCCGACCAAGATTTC 60.108 55.000 0.00 0.00 38.82 2.17
2564 4911 0.391130 CGCCTCCGACCAAGATTTCA 60.391 55.000 0.00 0.00 36.29 2.69
2565 4912 1.743772 CGCCTCCGACCAAGATTTCAT 60.744 52.381 0.00 0.00 36.29 2.57
2566 4913 1.672881 GCCTCCGACCAAGATTTCATG 59.327 52.381 0.00 0.00 0.00 3.07
2567 4914 2.292267 CCTCCGACCAAGATTTCATGG 58.708 52.381 0.42 0.42 40.34 3.66
2568 4915 1.672881 CTCCGACCAAGATTTCATGGC 59.327 52.381 1.85 0.00 38.21 4.40
2569 4916 0.740737 CCGACCAAGATTTCATGGCC 59.259 55.000 0.00 0.00 38.21 5.36
2570 4917 1.462616 CGACCAAGATTTCATGGCCA 58.537 50.000 8.56 8.56 38.21 5.36
2571 4918 2.026641 CGACCAAGATTTCATGGCCAT 58.973 47.619 14.09 14.09 38.21 4.40
2572 4919 2.223641 CGACCAAGATTTCATGGCCATG 60.224 50.000 35.76 35.76 38.21 3.66
2573 4920 1.483415 ACCAAGATTTCATGGCCATGC 59.517 47.619 36.47 23.83 38.21 4.06
2574 4921 1.760613 CCAAGATTTCATGGCCATGCT 59.239 47.619 36.47 25.55 38.65 3.79
2575 4922 2.483013 CCAAGATTTCATGGCCATGCTG 60.483 50.000 36.47 23.87 38.65 4.41
2576 4923 2.429250 CAAGATTTCATGGCCATGCTGA 59.571 45.455 36.47 24.81 38.65 4.26
2577 4924 2.742348 AGATTTCATGGCCATGCTGAA 58.258 42.857 36.47 28.53 38.65 3.02
2578 4925 2.693591 AGATTTCATGGCCATGCTGAAG 59.306 45.455 36.47 15.96 38.65 3.02
2579 4926 2.219080 TTTCATGGCCATGCTGAAGA 57.781 45.000 36.47 18.67 38.65 2.87
2580 4927 2.447408 TTCATGGCCATGCTGAAGAT 57.553 45.000 36.47 1.74 38.65 2.40
2581 4928 1.977056 TCATGGCCATGCTGAAGATC 58.023 50.000 36.47 0.00 38.65 2.75
2582 4929 1.493446 TCATGGCCATGCTGAAGATCT 59.507 47.619 36.47 0.27 38.65 2.75
2583 4930 1.880675 CATGGCCATGCTGAAGATCTC 59.119 52.381 31.95 0.00 31.39 2.75
2584 4931 0.182061 TGGCCATGCTGAAGATCTCC 59.818 55.000 0.00 0.00 0.00 3.71
2585 4932 0.473326 GGCCATGCTGAAGATCTCCT 59.527 55.000 0.00 0.00 0.00 3.69
2586 4933 1.133853 GGCCATGCTGAAGATCTCCTT 60.134 52.381 0.00 0.00 37.93 3.36
2596 4943 3.362870 AAGATCTCCTTCAAGCCCAAG 57.637 47.619 0.00 0.00 0.00 3.61
2597 4944 1.064832 AGATCTCCTTCAAGCCCAAGC 60.065 52.381 0.00 0.00 40.32 4.01
2607 4954 3.930504 GCCCAAGCTCATCAAGGG 58.069 61.111 0.00 0.00 42.55 3.95
2608 4955 1.755783 GCCCAAGCTCATCAAGGGG 60.756 63.158 0.00 0.00 39.96 4.79
2609 4956 1.076485 CCCAAGCTCATCAAGGGGG 60.076 63.158 0.00 0.00 35.83 5.40
2610 4957 1.755783 CCAAGCTCATCAAGGGGGC 60.756 63.158 0.00 0.00 0.00 5.80
2611 4958 1.305623 CAAGCTCATCAAGGGGGCT 59.694 57.895 0.00 0.00 34.52 5.19
2612 4959 0.750911 CAAGCTCATCAAGGGGGCTC 60.751 60.000 0.00 0.00 32.46 4.70
2613 4960 1.931007 AAGCTCATCAAGGGGGCTCC 61.931 60.000 0.00 0.00 32.46 4.70
2621 4968 2.286502 AGGGGGCTCCTTTCTCCC 60.287 66.667 0.00 0.00 45.47 4.30
2622 4969 2.286502 GGGGGCTCCTTTCTCCCT 60.287 66.667 0.52 0.00 39.95 4.20
2623 4970 2.379459 GGGGGCTCCTTTCTCCCTC 61.379 68.421 0.52 0.00 39.95 4.30
2624 4971 2.379459 GGGGCTCCTTTCTCCCTCC 61.379 68.421 0.00 0.00 39.95 4.30
2625 4972 2.379459 GGGCTCCTTTCTCCCTCCC 61.379 68.421 0.00 0.00 37.08 4.30
2626 4973 2.379459 GGCTCCTTTCTCCCTCCCC 61.379 68.421 0.00 0.00 0.00 4.81
2627 4974 1.616628 GCTCCTTTCTCCCTCCCCA 60.617 63.158 0.00 0.00 0.00 4.96
2628 4975 1.916206 GCTCCTTTCTCCCTCCCCAC 61.916 65.000 0.00 0.00 0.00 4.61
2629 4976 1.612442 TCCTTTCTCCCTCCCCACG 60.612 63.158 0.00 0.00 0.00 4.94
2630 4977 2.670148 CCTTTCTCCCTCCCCACGG 61.670 68.421 0.00 0.00 0.00 4.94
2631 4978 1.918800 CTTTCTCCCTCCCCACGGT 60.919 63.158 0.00 0.00 0.00 4.83
2632 4979 1.900545 CTTTCTCCCTCCCCACGGTC 61.901 65.000 0.00 0.00 0.00 4.79
2633 4980 4.753662 TCTCCCTCCCCACGGTCG 62.754 72.222 0.00 0.00 0.00 4.79
2634 4981 4.753662 CTCCCTCCCCACGGTCGA 62.754 72.222 0.00 0.00 0.00 4.20
2635 4982 4.753662 TCCCTCCCCACGGTCGAG 62.754 72.222 0.00 0.00 0.00 4.04
2638 4985 4.135153 CTCCCCACGGTCGAGCAG 62.135 72.222 15.89 9.92 0.00 4.24
2641 4988 4.803426 CCCACGGTCGAGCAGCTC 62.803 72.222 15.89 12.94 0.00 4.09
2657 5004 4.854784 TCGCGCACGAGGATGAGC 62.855 66.667 8.75 0.00 45.12 4.26
2658 5005 4.862092 CGCGCACGAGGATGAGCT 62.862 66.667 8.75 0.00 42.57 4.09
2659 5006 2.413351 GCGCACGAGGATGAGCTA 59.587 61.111 0.30 0.00 41.63 3.32
2660 5007 1.946650 GCGCACGAGGATGAGCTAC 60.947 63.158 0.30 0.00 41.63 3.58
2661 5008 1.655654 CGCACGAGGATGAGCTACG 60.656 63.158 0.00 0.00 0.00 3.51
2662 5009 1.728069 GCACGAGGATGAGCTACGA 59.272 57.895 0.00 0.00 0.00 3.43
2663 5010 0.317436 GCACGAGGATGAGCTACGAG 60.317 60.000 0.00 0.00 0.00 4.18
2664 5011 0.309302 CACGAGGATGAGCTACGAGG 59.691 60.000 0.00 0.00 0.00 4.63
2665 5012 0.180642 ACGAGGATGAGCTACGAGGA 59.819 55.000 0.00 0.00 0.00 3.71
2666 5013 1.202830 ACGAGGATGAGCTACGAGGAT 60.203 52.381 0.00 0.00 0.00 3.24
2667 5014 1.198867 CGAGGATGAGCTACGAGGATG 59.801 57.143 0.00 0.00 0.00 3.51
2668 5015 0.965439 AGGATGAGCTACGAGGATGC 59.035 55.000 0.00 0.00 0.00 3.91
2669 5016 0.037790 GGATGAGCTACGAGGATGCC 60.038 60.000 0.00 0.00 0.00 4.40
2670 5017 0.965439 GATGAGCTACGAGGATGCCT 59.035 55.000 0.00 0.00 36.03 4.75
2671 5018 0.678395 ATGAGCTACGAGGATGCCTG 59.322 55.000 0.00 0.00 31.76 4.85
2672 5019 1.300542 GAGCTACGAGGATGCCTGC 60.301 63.158 0.00 0.00 31.76 4.85
2673 5020 2.659897 GCTACGAGGATGCCTGCG 60.660 66.667 0.00 0.00 31.76 5.18
2674 5021 2.659897 CTACGAGGATGCCTGCGC 60.660 66.667 0.00 0.00 31.76 6.09
2675 5022 3.144120 CTACGAGGATGCCTGCGCT 62.144 63.158 9.73 0.00 31.76 5.92
2676 5023 3.138930 TACGAGGATGCCTGCGCTC 62.139 63.158 9.73 0.00 31.76 5.03
2678 5025 3.859414 GAGGATGCCTGCGCTCCT 61.859 66.667 14.45 14.45 42.10 3.69
2679 5026 3.805891 GAGGATGCCTGCGCTCCTC 62.806 68.421 22.32 22.32 44.67 3.71
2680 5027 4.925861 GGATGCCTGCGCTCCTCC 62.926 72.222 9.73 6.22 35.36 4.30
2681 5028 4.925861 GATGCCTGCGCTCCTCCC 62.926 72.222 9.73 0.00 35.36 4.30
2686 5033 4.093291 CTGCGCTCCTCCCTGCTT 62.093 66.667 9.73 0.00 0.00 3.91
2687 5034 4.399395 TGCGCTCCTCCCTGCTTG 62.399 66.667 9.73 0.00 0.00 4.01
2688 5035 4.087892 GCGCTCCTCCCTGCTTGA 62.088 66.667 0.00 0.00 0.00 3.02
2689 5036 2.906458 CGCTCCTCCCTGCTTGAT 59.094 61.111 0.00 0.00 0.00 2.57
2690 5037 2.032860 GCGCTCCTCCCTGCTTGATA 62.033 60.000 0.00 0.00 0.00 2.15
2691 5038 0.249657 CGCTCCTCCCTGCTTGATAC 60.250 60.000 0.00 0.00 0.00 2.24
2692 5039 0.249657 GCTCCTCCCTGCTTGATACG 60.250 60.000 0.00 0.00 0.00 3.06
2693 5040 0.390860 CTCCTCCCTGCTTGATACGG 59.609 60.000 0.00 0.00 0.00 4.02
2694 5041 0.032515 TCCTCCCTGCTTGATACGGA 60.033 55.000 0.00 0.00 0.00 4.69
2695 5042 0.830648 CCTCCCTGCTTGATACGGAA 59.169 55.000 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
135 154 7.392953 TCTGTTGCCATCAATGACTAAATACAA 59.607 33.333 0.00 0.00 34.29 2.41
251 270 9.619316 CTTTATTTCATCCGTGAATGTAACAAA 57.381 29.630 0.00 0.00 43.49 2.83
252 271 8.788806 ACTTTATTTCATCCGTGAATGTAACAA 58.211 29.630 0.00 0.00 43.49 2.83
281 300 7.006210 CACTAAGATTTCGTGCGAATACAAAAC 59.994 37.037 7.87 0.00 33.79 2.43
291 310 5.912528 AGTTTAACACTAAGATTTCGTGCG 58.087 37.500 0.00 0.00 31.97 5.34
330 349 2.880963 AAGCTTAACCGCAGCAAAAA 57.119 40.000 0.00 0.00 39.99 1.94
395 414 9.314501 GTATTTAAGTGTTCAGATTTCAACGAC 57.685 33.333 0.00 0.00 0.00 4.34
405 424 8.097038 AGAGCAGATTGTATTTAAGTGTTCAGA 58.903 33.333 0.00 0.00 0.00 3.27
504 523 4.844349 ACCAACTTACCATACAGCTGAT 57.156 40.909 23.35 6.78 0.00 2.90
566 585 2.704464 TCAGATGCAGTCATGAAGGG 57.296 50.000 0.00 0.00 31.96 3.95
567 586 4.638865 TGAATTCAGATGCAGTCATGAAGG 59.361 41.667 3.38 0.00 31.96 3.46
673 692 0.953727 GCAGCATTGACACCTTGACA 59.046 50.000 0.00 0.00 0.00 3.58
674 693 0.953727 TGCAGCATTGACACCTTGAC 59.046 50.000 0.00 0.00 0.00 3.18
706 725 5.234329 ACAGTTGTGTTTCTCTGATGTTACG 59.766 40.000 0.00 0.00 30.30 3.18
707 726 6.604735 ACAGTTGTGTTTCTCTGATGTTAC 57.395 37.500 0.00 0.00 30.30 2.50
916 943 5.935789 CCCACATTGCTCTTTTGAATTTGAT 59.064 36.000 0.00 0.00 0.00 2.57
1400 3713 2.048222 CTCGCTTCAAGCCGTCCA 60.048 61.111 3.08 0.00 38.18 4.02
1556 3869 4.758251 CTGCGATGGTGGTGGCGA 62.758 66.667 0.00 0.00 0.00 5.54
1576 3889 2.746277 GGTCGTGATGGTGGTGGC 60.746 66.667 0.00 0.00 0.00 5.01
1577 3890 1.375908 CTGGTCGTGATGGTGGTGG 60.376 63.158 0.00 0.00 0.00 4.61
1578 3891 2.034879 GCTGGTCGTGATGGTGGTG 61.035 63.158 0.00 0.00 0.00 4.17
1662 3975 1.066587 CGATCTTCCGCTCCTGTCC 59.933 63.158 0.00 0.00 0.00 4.02
1700 4017 2.102357 CGTCATCGTACAGCGGCT 59.898 61.111 0.00 0.00 41.72 5.52
1717 4034 2.029221 GCTCGCCGGATTACTCCC 59.971 66.667 5.05 0.00 38.45 4.30
1750 4067 3.792401 TGCGATAATCGGTGAGTTTCAT 58.208 40.909 0.00 0.00 40.84 2.57
1755 4072 2.051879 CGATGCGATAATCGGTGAGT 57.948 50.000 7.46 0.00 44.49 3.41
1770 4087 4.154015 TGCCAGTCACTTGTAATTTCGATG 59.846 41.667 0.00 0.00 0.00 3.84
1893 4210 3.195396 TGCTTTCCACTTTCATAATGCCC 59.805 43.478 0.00 0.00 0.00 5.36
1920 4237 3.199946 TCCCCTAACTCCACAATGTCATC 59.800 47.826 0.00 0.00 0.00 2.92
1924 4241 2.714250 TGTTCCCCTAACTCCACAATGT 59.286 45.455 0.00 0.00 38.99 2.71
1938 4255 1.202348 GCACAGCAAGTAATGTTCCCC 59.798 52.381 0.00 0.00 0.00 4.81
1939 4256 1.885887 TGCACAGCAAGTAATGTTCCC 59.114 47.619 0.00 0.00 34.76 3.97
1955 4272 6.809196 TCAAATAACCCGTAAATGATTTGCAC 59.191 34.615 6.79 0.00 35.33 4.57
2043 4375 3.491447 GGGCATGTGCATACAAAATCCTC 60.491 47.826 7.36 0.00 44.36 3.71
2097 4437 8.465999 TGTTAGGCATGATTGTACTTTAATTGG 58.534 33.333 0.00 0.00 0.00 3.16
2102 4442 7.045416 ACGATGTTAGGCATGATTGTACTTTA 58.955 34.615 0.00 0.00 38.06 1.85
2115 4455 4.453136 GGTTGTTTTAGACGATGTTAGGCA 59.547 41.667 0.00 0.00 0.00 4.75
2118 4458 6.090898 CCAGAGGTTGTTTTAGACGATGTTAG 59.909 42.308 0.00 0.00 0.00 2.34
2124 4464 3.243975 GGACCAGAGGTTGTTTTAGACGA 60.244 47.826 0.00 0.00 35.25 4.20
2154 4501 1.450312 GCCGAACTGCAGTATGGCT 60.450 57.895 36.72 18.89 42.05 4.75
2169 4516 3.589654 TTGCGAGGACTCAAGGCCG 62.590 63.158 0.00 0.00 0.00 6.13
2225 4572 3.793144 CAGCGCCTCGACTTTGGC 61.793 66.667 2.29 3.38 45.25 4.52
2226 4573 3.793144 GCAGCGCCTCGACTTTGG 61.793 66.667 2.29 0.00 0.00 3.28
2227 4574 2.606961 TTGCAGCGCCTCGACTTTG 61.607 57.895 2.29 0.00 0.00 2.77
2228 4575 2.280797 TTGCAGCGCCTCGACTTT 60.281 55.556 2.29 0.00 0.00 2.66
2229 4576 3.044305 GTTGCAGCGCCTCGACTT 61.044 61.111 2.29 0.00 0.00 3.01
2230 4577 4.299547 TGTTGCAGCGCCTCGACT 62.300 61.111 2.29 0.00 0.00 4.18
2231 4578 4.077188 GTGTTGCAGCGCCTCGAC 62.077 66.667 2.29 6.87 0.00 4.20
2232 4579 3.881952 ATGTGTTGCAGCGCCTCGA 62.882 57.895 11.79 0.00 0.00 4.04
2233 4580 3.372676 GATGTGTTGCAGCGCCTCG 62.373 63.158 11.79 0.00 0.00 4.63
2234 4581 2.482374 GATGTGTTGCAGCGCCTC 59.518 61.111 11.79 7.61 0.00 4.70
2235 4582 3.058160 GGATGTGTTGCAGCGCCT 61.058 61.111 11.79 1.12 33.59 5.52
2236 4583 4.120331 GGGATGTGTTGCAGCGCC 62.120 66.667 11.79 2.60 40.03 6.53
2237 4584 4.120331 GGGGATGTGTTGCAGCGC 62.120 66.667 7.21 7.21 44.32 5.92
2238 4585 3.443045 GGGGGATGTGTTGCAGCG 61.443 66.667 0.00 0.00 33.59 5.18
2239 4586 2.283101 TGGGGGATGTGTTGCAGC 60.283 61.111 0.00 0.00 0.00 5.25
2240 4587 1.978617 GGTGGGGGATGTGTTGCAG 60.979 63.158 0.00 0.00 0.00 4.41
2241 4588 2.117206 GGTGGGGGATGTGTTGCA 59.883 61.111 0.00 0.00 0.00 4.08
2242 4589 2.117206 TGGTGGGGGATGTGTTGC 59.883 61.111 0.00 0.00 0.00 4.17
2243 4590 0.251742 ATGTGGTGGGGGATGTGTTG 60.252 55.000 0.00 0.00 0.00 3.33
2244 4591 0.039618 GATGTGGTGGGGGATGTGTT 59.960 55.000 0.00 0.00 0.00 3.32
2245 4592 1.691219 GATGTGGTGGGGGATGTGT 59.309 57.895 0.00 0.00 0.00 3.72
2246 4593 1.451927 CGATGTGGTGGGGGATGTG 60.452 63.158 0.00 0.00 0.00 3.21
2247 4594 2.998097 CGATGTGGTGGGGGATGT 59.002 61.111 0.00 0.00 0.00 3.06
2248 4595 2.516930 GCGATGTGGTGGGGGATG 60.517 66.667 0.00 0.00 0.00 3.51
2249 4596 3.809013 GGCGATGTGGTGGGGGAT 61.809 66.667 0.00 0.00 0.00 3.85
2252 4599 4.715523 AACGGCGATGTGGTGGGG 62.716 66.667 16.62 0.00 0.00 4.96
2253 4600 3.124921 GAACGGCGATGTGGTGGG 61.125 66.667 16.62 0.00 0.00 4.61
2254 4601 2.358125 TGAACGGCGATGTGGTGG 60.358 61.111 16.62 0.00 0.00 4.61
2255 4602 2.677003 GGTGAACGGCGATGTGGTG 61.677 63.158 16.62 0.00 0.00 4.17
2256 4603 2.358247 GGTGAACGGCGATGTGGT 60.358 61.111 16.62 0.00 0.00 4.16
2257 4604 3.487202 CGGTGAACGGCGATGTGG 61.487 66.667 16.62 0.00 39.42 4.17
2258 4605 4.147322 GCGGTGAACGGCGATGTG 62.147 66.667 16.62 0.00 44.51 3.21
2259 4606 3.876589 AAGCGGTGAACGGCGATGT 62.877 57.895 16.62 0.00 45.36 3.06
2260 4607 3.083600 GAAGCGGTGAACGGCGATG 62.084 63.158 16.62 0.00 45.36 3.84
2261 4608 2.813908 GAAGCGGTGAACGGCGAT 60.814 61.111 16.62 0.00 45.36 4.58
2264 4611 3.774702 GTCGAAGCGGTGAACGGC 61.775 66.667 4.94 4.94 44.51 5.68
2265 4612 3.467119 CGTCGAAGCGGTGAACGG 61.467 66.667 0.00 0.00 44.51 4.44
2266 4613 3.467119 CCGTCGAAGCGGTGAACG 61.467 66.667 6.32 9.02 46.11 3.95
2296 4643 2.809174 TTGATCAGCACGTCGGCG 60.809 61.111 8.42 8.42 44.93 6.46
2297 4644 2.778679 GTTGATCAGCACGTCGGC 59.221 61.111 4.47 0.00 0.00 5.54
2298 4645 1.406219 CTCGTTGATCAGCACGTCGG 61.406 60.000 17.09 7.52 0.00 4.79
2299 4646 0.454452 TCTCGTTGATCAGCACGTCG 60.454 55.000 17.09 11.02 0.00 5.12
2300 4647 1.914634 ATCTCGTTGATCAGCACGTC 58.085 50.000 17.09 0.00 0.00 4.34
2309 4656 2.544686 CGACGTCCTAGATCTCGTTGAT 59.455 50.000 10.58 0.00 39.21 2.57
2310 4657 1.931841 CGACGTCCTAGATCTCGTTGA 59.068 52.381 10.58 0.00 39.21 3.18
2311 4658 1.595003 GCGACGTCCTAGATCTCGTTG 60.595 57.143 10.58 14.55 39.66 4.10
2312 4659 0.656785 GCGACGTCCTAGATCTCGTT 59.343 55.000 10.58 0.00 36.67 3.85
2313 4660 1.489070 CGCGACGTCCTAGATCTCGT 61.489 60.000 10.58 6.88 39.21 4.18
2314 4661 1.202072 CGCGACGTCCTAGATCTCG 59.798 63.158 10.58 0.00 0.00 4.04
2315 4662 1.082627 GCGCGACGTCCTAGATCTC 60.083 63.158 12.10 0.00 0.00 2.75
2316 4663 2.883468 CGCGCGACGTCCTAGATCT 61.883 63.158 28.94 0.00 36.87 2.75
2317 4664 2.172719 ATCGCGCGACGTCCTAGATC 62.173 60.000 37.37 0.00 44.19 2.75
2318 4665 2.172719 GATCGCGCGACGTCCTAGAT 62.173 60.000 37.37 16.52 44.19 1.98
2319 4666 2.879070 GATCGCGCGACGTCCTAGA 61.879 63.158 37.37 10.06 44.19 2.43
2320 4667 2.425448 GATCGCGCGACGTCCTAG 60.425 66.667 37.37 0.00 44.19 3.02
2321 4668 4.289379 CGATCGCGCGACGTCCTA 62.289 66.667 37.37 11.87 44.19 2.94
2348 4695 4.308458 TTGTGGAGGTGCGGACGG 62.308 66.667 0.00 0.00 0.00 4.79
2349 4696 3.041940 GTTGTGGAGGTGCGGACG 61.042 66.667 0.00 0.00 0.00 4.79
2350 4697 2.668550 GGTTGTGGAGGTGCGGAC 60.669 66.667 0.00 0.00 0.00 4.79
2351 4698 3.948719 GGGTTGTGGAGGTGCGGA 61.949 66.667 0.00 0.00 0.00 5.54
2354 4701 3.224007 ATGGGGGTTGTGGAGGTGC 62.224 63.158 0.00 0.00 0.00 5.01
2355 4702 1.000896 GATGGGGGTTGTGGAGGTG 60.001 63.158 0.00 0.00 0.00 4.00
2356 4703 2.238701 GGATGGGGGTTGTGGAGGT 61.239 63.158 0.00 0.00 0.00 3.85
2357 4704 2.683475 GGATGGGGGTTGTGGAGG 59.317 66.667 0.00 0.00 0.00 4.30
2358 4705 2.272146 CGGATGGGGGTTGTGGAG 59.728 66.667 0.00 0.00 0.00 3.86
2359 4706 4.041762 GCGGATGGGGGTTGTGGA 62.042 66.667 0.00 0.00 0.00 4.02
2360 4707 4.358841 TGCGGATGGGGGTTGTGG 62.359 66.667 0.00 0.00 0.00 4.17
2361 4708 3.061848 GTGCGGATGGGGGTTGTG 61.062 66.667 0.00 0.00 0.00 3.33
2362 4709 4.715523 CGTGCGGATGGGGGTTGT 62.716 66.667 0.00 0.00 0.00 3.32
2394 4741 3.866582 CAGCACCGGATCCCCCTC 61.867 72.222 9.46 0.00 0.00 4.30
2406 4753 3.426568 GAAGAGCACGCCCAGCAC 61.427 66.667 0.00 0.00 0.00 4.40
2407 4754 4.704833 GGAAGAGCACGCCCAGCA 62.705 66.667 0.00 0.00 0.00 4.41
2408 4755 4.400961 AGGAAGAGCACGCCCAGC 62.401 66.667 0.00 0.00 0.00 4.85
2409 4756 2.125350 GAGGAAGAGCACGCCCAG 60.125 66.667 0.00 0.00 0.00 4.45
2410 4757 4.069232 CGAGGAAGAGCACGCCCA 62.069 66.667 0.00 0.00 0.00 5.36
2411 4758 4.821589 CCGAGGAAGAGCACGCCC 62.822 72.222 0.00 0.00 0.00 6.13
2412 4759 3.760035 TCCGAGGAAGAGCACGCC 61.760 66.667 0.00 0.00 0.00 5.68
2413 4760 2.507324 GTCCGAGGAAGAGCACGC 60.507 66.667 0.00 0.00 0.00 5.34
2414 4761 2.182030 GGTCCGAGGAAGAGCACG 59.818 66.667 0.00 0.00 0.00 5.34
2415 4762 1.985116 AGGGTCCGAGGAAGAGCAC 60.985 63.158 0.00 0.00 33.37 4.40
2416 4763 1.984570 CAGGGTCCGAGGAAGAGCA 60.985 63.158 0.00 0.00 33.37 4.26
2417 4764 2.896443 CAGGGTCCGAGGAAGAGC 59.104 66.667 0.00 0.00 0.00 4.09
2418 4765 2.726351 GGCAGGGTCCGAGGAAGAG 61.726 68.421 0.00 0.00 0.00 2.85
2419 4766 2.683933 GGCAGGGTCCGAGGAAGA 60.684 66.667 0.00 0.00 0.00 2.87
2420 4767 2.685380 AGGCAGGGTCCGAGGAAG 60.685 66.667 0.00 0.00 0.00 3.46
2421 4768 2.683933 GAGGCAGGGTCCGAGGAA 60.684 66.667 0.00 0.00 0.00 3.36
2449 4796 3.787001 GAGTCCCGGGCCAAGGAG 61.787 72.222 18.49 8.06 31.17 3.69
2477 4824 1.604593 CTTCAACCTGGCCACCTGG 60.605 63.158 0.00 4.17 46.30 4.45
2478 4825 0.890996 GTCTTCAACCTGGCCACCTG 60.891 60.000 0.00 0.00 0.00 4.00
2479 4826 1.456287 GTCTTCAACCTGGCCACCT 59.544 57.895 0.00 0.00 0.00 4.00
2480 4827 1.966451 CGTCTTCAACCTGGCCACC 60.966 63.158 0.00 0.00 0.00 4.61
2481 4828 0.321653 ATCGTCTTCAACCTGGCCAC 60.322 55.000 0.00 0.00 0.00 5.01
2482 4829 0.321564 CATCGTCTTCAACCTGGCCA 60.322 55.000 4.71 4.71 0.00 5.36
2483 4830 1.026718 CCATCGTCTTCAACCTGGCC 61.027 60.000 0.00 0.00 0.00 5.36
2484 4831 1.648467 GCCATCGTCTTCAACCTGGC 61.648 60.000 0.00 0.00 42.61 4.85
2485 4832 0.321564 TGCCATCGTCTTCAACCTGG 60.322 55.000 0.00 0.00 32.67 4.45
2486 4833 1.399440 CATGCCATCGTCTTCAACCTG 59.601 52.381 0.00 0.00 0.00 4.00
2487 4834 1.679944 CCATGCCATCGTCTTCAACCT 60.680 52.381 0.00 0.00 0.00 3.50
2488 4835 0.734889 CCATGCCATCGTCTTCAACC 59.265 55.000 0.00 0.00 0.00 3.77
2489 4836 0.099436 GCCATGCCATCGTCTTCAAC 59.901 55.000 0.00 0.00 0.00 3.18
2490 4837 2.481212 GCCATGCCATCGTCTTCAA 58.519 52.632 0.00 0.00 0.00 2.69
2491 4838 4.223800 GCCATGCCATCGTCTTCA 57.776 55.556 0.00 0.00 0.00 3.02
2518 4865 2.740714 CTGCAGGAAAGCGCGGTAC 61.741 63.158 12.91 9.17 37.31 3.34
2519 4866 2.434185 CTGCAGGAAAGCGCGGTA 60.434 61.111 12.91 0.00 37.31 4.02
2525 4872 2.850828 ATCTGGGGCTGCAGGAAAGC 62.851 60.000 17.12 0.13 40.06 3.51
2526 4873 0.750911 GATCTGGGGCTGCAGGAAAG 60.751 60.000 17.12 0.00 0.00 2.62
2527 4874 1.304282 GATCTGGGGCTGCAGGAAA 59.696 57.895 17.12 0.00 0.00 3.13
2528 4875 3.001514 GATCTGGGGCTGCAGGAA 58.998 61.111 17.12 0.00 0.00 3.36
2529 4876 3.473647 CGATCTGGGGCTGCAGGA 61.474 66.667 17.12 3.73 0.00 3.86
2533 4880 4.925861 GAGGCGATCTGGGGCTGC 62.926 72.222 0.00 0.00 40.78 5.25
2534 4881 4.247380 GGAGGCGATCTGGGGCTG 62.247 72.222 0.00 0.00 40.78 4.85
2537 4884 3.917760 GTCGGAGGCGATCTGGGG 61.918 72.222 0.00 0.00 34.76 4.96
2538 4885 3.917760 GGTCGGAGGCGATCTGGG 61.918 72.222 0.00 0.00 34.76 4.45
2539 4886 2.635229 CTTGGTCGGAGGCGATCTGG 62.635 65.000 0.00 0.00 34.76 3.86
2540 4887 1.227089 CTTGGTCGGAGGCGATCTG 60.227 63.158 0.00 0.00 35.40 2.90
2541 4888 0.757188 ATCTTGGTCGGAGGCGATCT 60.757 55.000 0.00 0.00 0.00 2.75
2542 4889 0.105039 AATCTTGGTCGGAGGCGATC 59.895 55.000 0.00 0.00 0.00 3.69
2543 4890 0.541863 AAATCTTGGTCGGAGGCGAT 59.458 50.000 0.00 0.00 0.00 4.58
2544 4891 0.108329 GAAATCTTGGTCGGAGGCGA 60.108 55.000 0.00 0.00 0.00 5.54
2545 4892 0.391130 TGAAATCTTGGTCGGAGGCG 60.391 55.000 0.00 0.00 0.00 5.52
2546 4893 1.672881 CATGAAATCTTGGTCGGAGGC 59.327 52.381 0.00 0.00 0.00 4.70
2547 4894 2.292267 CCATGAAATCTTGGTCGGAGG 58.708 52.381 0.00 0.00 36.67 4.30
2548 4895 1.672881 GCCATGAAATCTTGGTCGGAG 59.327 52.381 14.62 0.00 41.65 4.63
2549 4896 1.681780 GGCCATGAAATCTTGGTCGGA 60.682 52.381 14.62 0.00 41.65 4.55
2550 4897 0.740737 GGCCATGAAATCTTGGTCGG 59.259 55.000 14.62 0.00 41.65 4.79
2551 4898 1.462616 TGGCCATGAAATCTTGGTCG 58.537 50.000 0.00 0.00 45.53 4.79
2552 4899 2.482490 GCATGGCCATGAAATCTTGGTC 60.482 50.000 43.18 20.97 43.62 4.02
2553 4900 1.483415 GCATGGCCATGAAATCTTGGT 59.517 47.619 43.18 5.46 41.65 3.67
2554 4901 1.760613 AGCATGGCCATGAAATCTTGG 59.239 47.619 43.18 18.56 41.20 3.61
2555 4902 2.429250 TCAGCATGGCCATGAAATCTTG 59.571 45.455 43.18 28.08 41.20 3.02
2556 4903 2.742348 TCAGCATGGCCATGAAATCTT 58.258 42.857 43.18 20.28 41.20 2.40
2557 4904 2.447408 TCAGCATGGCCATGAAATCT 57.553 45.000 43.18 28.98 41.20 2.40
2558 4905 2.691526 TCTTCAGCATGGCCATGAAATC 59.308 45.455 43.18 27.35 41.20 2.17
2559 4906 2.742348 TCTTCAGCATGGCCATGAAAT 58.258 42.857 43.18 27.00 41.20 2.17
2560 4907 2.219080 TCTTCAGCATGGCCATGAAA 57.781 45.000 43.18 30.43 41.20 2.69
2561 4908 2.092049 AGATCTTCAGCATGGCCATGAA 60.092 45.455 43.18 29.78 41.20 2.57
2562 4909 1.493446 AGATCTTCAGCATGGCCATGA 59.507 47.619 43.18 25.30 41.20 3.07
2563 4910 1.880675 GAGATCTTCAGCATGGCCATG 59.119 52.381 36.80 36.80 41.60 3.66
2564 4911 1.202903 GGAGATCTTCAGCATGGCCAT 60.203 52.381 14.09 14.09 36.16 4.40
2565 4912 0.182061 GGAGATCTTCAGCATGGCCA 59.818 55.000 8.56 8.56 36.16 5.36
2566 4913 0.473326 AGGAGATCTTCAGCATGGCC 59.527 55.000 3.21 0.00 36.16 5.36
2567 4914 2.345124 AAGGAGATCTTCAGCATGGC 57.655 50.000 3.21 0.00 36.16 4.40
2575 4922 4.488662 GCTTGGGCTTGAAGGAGATCTTC 61.489 52.174 0.00 0.00 42.40 2.87
2576 4923 2.620108 GCTTGGGCTTGAAGGAGATCTT 60.620 50.000 0.00 0.00 35.35 2.40
2577 4924 1.064832 GCTTGGGCTTGAAGGAGATCT 60.065 52.381 0.00 0.00 35.22 2.75
2578 4925 1.387539 GCTTGGGCTTGAAGGAGATC 58.612 55.000 0.00 0.00 35.22 2.75
2579 4926 3.584947 GCTTGGGCTTGAAGGAGAT 57.415 52.632 0.00 0.00 35.22 2.75
2590 4937 1.755783 CCCCTTGATGAGCTTGGGC 60.756 63.158 0.00 0.00 36.66 5.36
2591 4938 1.076485 CCCCCTTGATGAGCTTGGG 60.076 63.158 0.00 0.00 37.68 4.12
2592 4939 1.755783 GCCCCCTTGATGAGCTTGG 60.756 63.158 0.00 0.00 0.00 3.61
2593 4940 0.750911 GAGCCCCCTTGATGAGCTTG 60.751 60.000 0.00 0.00 32.97 4.01
2594 4941 1.611965 GAGCCCCCTTGATGAGCTT 59.388 57.895 0.00 0.00 32.97 3.74
2595 4942 2.381941 GGAGCCCCCTTGATGAGCT 61.382 63.158 0.00 0.00 36.25 4.09
2596 4943 2.194326 GGAGCCCCCTTGATGAGC 59.806 66.667 0.00 0.00 0.00 4.26
2597 4944 4.079827 AGGAGCCCCCTTGATGAG 57.920 61.111 0.00 0.00 44.85 2.90
2605 4952 2.286502 AGGGAGAAAGGAGCCCCC 60.287 66.667 0.00 0.00 43.08 5.40
2606 4953 2.379459 GGAGGGAGAAAGGAGCCCC 61.379 68.421 0.00 0.00 43.08 5.80
2607 4954 2.379459 GGGAGGGAGAAAGGAGCCC 61.379 68.421 0.00 0.00 42.37 5.19
2608 4955 2.379459 GGGGAGGGAGAAAGGAGCC 61.379 68.421 0.00 0.00 0.00 4.70
2609 4956 1.616628 TGGGGAGGGAGAAAGGAGC 60.617 63.158 0.00 0.00 0.00 4.70
2610 4957 1.617947 CGTGGGGAGGGAGAAAGGAG 61.618 65.000 0.00 0.00 0.00 3.69
2611 4958 1.612442 CGTGGGGAGGGAGAAAGGA 60.612 63.158 0.00 0.00 0.00 3.36
2612 4959 2.670148 CCGTGGGGAGGGAGAAAGG 61.670 68.421 0.00 0.00 34.06 3.11
2613 4960 1.900545 GACCGTGGGGAGGGAGAAAG 61.901 65.000 0.00 0.00 36.97 2.62
2614 4961 1.916777 GACCGTGGGGAGGGAGAAA 60.917 63.158 0.00 0.00 36.97 2.52
2615 4962 2.284405 GACCGTGGGGAGGGAGAA 60.284 66.667 0.00 0.00 36.97 2.87
2616 4963 4.753662 CGACCGTGGGGAGGGAGA 62.754 72.222 0.00 0.00 36.97 3.71
2617 4964 4.753662 TCGACCGTGGGGAGGGAG 62.754 72.222 0.00 0.00 36.97 4.30
2618 4965 4.753662 CTCGACCGTGGGGAGGGA 62.754 72.222 0.00 0.00 36.97 4.20
2621 4968 4.135153 CTGCTCGACCGTGGGGAG 62.135 72.222 5.22 5.22 36.97 4.30
2624 4971 4.803426 GAGCTGCTCGACCGTGGG 62.803 72.222 14.68 0.00 0.00 4.61
2640 4987 4.854784 GCTCATCCTCGTGCGCGA 62.855 66.667 22.60 22.60 45.79 5.87
2641 4988 3.469754 TAGCTCATCCTCGTGCGCG 62.470 63.158 14.79 14.79 35.12 6.86
2642 4989 1.946650 GTAGCTCATCCTCGTGCGC 60.947 63.158 0.00 0.00 0.00 6.09
2643 4990 1.655654 CGTAGCTCATCCTCGTGCG 60.656 63.158 0.00 0.00 0.00 5.34
2644 4991 0.317436 CTCGTAGCTCATCCTCGTGC 60.317 60.000 0.00 0.00 0.00 5.34
2645 4992 0.309302 CCTCGTAGCTCATCCTCGTG 59.691 60.000 0.00 0.00 0.00 4.35
2646 4993 0.180642 TCCTCGTAGCTCATCCTCGT 59.819 55.000 0.00 0.00 0.00 4.18
2647 4994 1.198867 CATCCTCGTAGCTCATCCTCG 59.801 57.143 0.00 0.00 0.00 4.63
2648 4995 1.067915 GCATCCTCGTAGCTCATCCTC 60.068 57.143 0.00 0.00 0.00 3.71
2649 4996 0.965439 GCATCCTCGTAGCTCATCCT 59.035 55.000 0.00 0.00 0.00 3.24
2650 4997 0.037790 GGCATCCTCGTAGCTCATCC 60.038 60.000 0.00 0.00 0.00 3.51
2651 4998 0.965439 AGGCATCCTCGTAGCTCATC 59.035 55.000 0.00 0.00 0.00 2.92
2652 4999 0.678395 CAGGCATCCTCGTAGCTCAT 59.322 55.000 0.00 0.00 0.00 2.90
2653 5000 2.021068 GCAGGCATCCTCGTAGCTCA 62.021 60.000 0.00 0.00 0.00 4.26
2654 5001 1.300542 GCAGGCATCCTCGTAGCTC 60.301 63.158 0.00 0.00 0.00 4.09
2655 5002 2.818132 GCAGGCATCCTCGTAGCT 59.182 61.111 0.00 0.00 0.00 3.32
2656 5003 2.659897 CGCAGGCATCCTCGTAGC 60.660 66.667 0.00 0.00 0.00 3.58
2657 5004 2.659897 GCGCAGGCATCCTCGTAG 60.660 66.667 0.30 0.00 39.62 3.51
2658 5005 3.138930 GAGCGCAGGCATCCTCGTA 62.139 63.158 11.47 0.00 43.41 3.43
2659 5006 4.521062 GAGCGCAGGCATCCTCGT 62.521 66.667 11.47 0.00 43.41 4.18
2661 5008 3.805891 GAGGAGCGCAGGCATCCTC 62.806 68.421 22.32 22.32 46.47 3.71
2662 5009 3.859414 GAGGAGCGCAGGCATCCT 61.859 66.667 14.45 14.45 44.34 3.24
2663 5010 4.925861 GGAGGAGCGCAGGCATCC 62.926 72.222 11.47 11.63 43.41 3.51
2664 5011 4.925861 GGGAGGAGCGCAGGCATC 62.926 72.222 11.47 5.54 43.41 3.91
2669 5016 4.093291 AAGCAGGGAGGAGCGCAG 62.093 66.667 11.47 0.00 35.48 5.18
2670 5017 4.399395 CAAGCAGGGAGGAGCGCA 62.399 66.667 11.47 0.00 35.48 6.09
2671 5018 2.032860 TATCAAGCAGGGAGGAGCGC 62.033 60.000 0.00 0.00 35.48 5.92
2672 5019 0.249657 GTATCAAGCAGGGAGGAGCG 60.250 60.000 0.00 0.00 35.48 5.03
2673 5020 0.249657 CGTATCAAGCAGGGAGGAGC 60.250 60.000 0.00 0.00 0.00 4.70
2674 5021 0.390860 CCGTATCAAGCAGGGAGGAG 59.609 60.000 0.00 0.00 0.00 3.69
2675 5022 0.032515 TCCGTATCAAGCAGGGAGGA 60.033 55.000 0.00 0.00 0.00 3.71
2676 5023 0.830648 TTCCGTATCAAGCAGGGAGG 59.169 55.000 0.00 0.00 31.94 4.30


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

AutoCloner maintained by Alex Coulton.