Multiple sequence alignment - TraesCS1D01G116900

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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 TraesCS1D01G116900 chr1D 100.000 4608 0 0 1 4608 112766428 112771035 0.000000e+00 8510.0
1 TraesCS1D01G116900 chr1D 92.308 533 21 12 345 862 112752031 112752558 0.000000e+00 739.0
2 TraesCS1D01G116900 chr1D 93.175 337 22 1 1 336 165477039 165477375 1.150000e-135 494.0
3 TraesCS1D01G116900 chr1D 94.811 212 10 1 1 211 216126268 216126479 3.440000e-86 329.0
4 TraesCS1D01G116900 chr1D 94.872 39 2 0 4032 4070 112770418 112770456 1.380000e-05 62.1
5 TraesCS1D01G116900 chr1D 94.872 39 2 0 3991 4029 112770459 112770497 1.380000e-05 62.1
6 TraesCS1D01G116900 chr1A 90.231 2508 153 33 2158 4604 120009322 120011798 0.000000e+00 3190.0
7 TraesCS1D01G116900 chr1A 91.502 1671 63 27 345 2003 120002246 120003849 0.000000e+00 2226.0
8 TraesCS1D01G116900 chr1A 91.964 112 8 1 2046 2157 120009173 120009283 6.170000e-34 156.0
9 TraesCS1D01G116900 chr1B 92.263 1719 86 15 2733 4419 172380386 172382089 0.000000e+00 2394.0
10 TraesCS1D01G116900 chr1B 91.425 1726 92 30 440 2157 172378180 172379857 0.000000e+00 2316.0
11 TraesCS1D01G116900 chr1B 85.135 518 40 14 2158 2666 172379896 172380385 3.200000e-136 496.0
12 TraesCS1D01G116900 chr1B 94.631 149 8 0 4456 4604 172387189 172387337 9.970000e-57 231.0
13 TraesCS1D01G116900 chr5D 95.335 343 14 2 1 342 416003086 416002745 1.130000e-150 544.0
14 TraesCS1D01G116900 chr7A 95.252 337 15 1 1 336 520874709 520875045 2.440000e-147 532.0
15 TraesCS1D01G116900 chr7A 90.448 335 20 2 3 336 707329126 707328803 9.160000e-117 431.0
16 TraesCS1D01G116900 chr6D 95.252 337 15 1 1 336 329897239 329897575 2.440000e-147 532.0
17 TraesCS1D01G116900 chr5A 91.988 337 14 6 1 336 513720552 513720876 1.170000e-125 460.0
18 TraesCS1D01G116900 chr2D 95.755 212 8 1 1 211 8395010 8394799 1.590000e-89 340.0
19 TraesCS1D01G116900 chr4D 95.283 212 9 1 1 211 374822403 374822614 7.390000e-88 335.0
20 TraesCS1D01G116900 chr4D 96.947 131 4 0 212 342 374825723 374825853 2.160000e-53 220.0
21 TraesCS1D01G116900 chr2B 93.868 212 12 1 1 211 697460924 697460713 7.440000e-83 318.0
22 TraesCS1D01G116900 chr7D 96.183 131 5 0 212 342 100648401 100648271 1.000000e-51 215.0


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 TraesCS1D01G116900 chr1D 112766428 112771035 4607 False 2878.066667 8510 96.581333 1 4608 3 chr1D.!!$F4 4607
1 TraesCS1D01G116900 chr1D 112752031 112752558 527 False 739.000000 739 92.308000 345 862 1 chr1D.!!$F1 517
2 TraesCS1D01G116900 chr1A 120002246 120003849 1603 False 2226.000000 2226 91.502000 345 2003 1 chr1A.!!$F1 1658
3 TraesCS1D01G116900 chr1A 120009173 120011798 2625 False 1673.000000 3190 91.097500 2046 4604 2 chr1A.!!$F2 2558
4 TraesCS1D01G116900 chr1B 172378180 172382089 3909 False 1735.333333 2394 89.607667 440 4419 3 chr1B.!!$F2 3979
5 TraesCS1D01G116900 chr4D 374822403 374825853 3450 False 277.500000 335 96.115000 1 342 2 chr4D.!!$F1 341

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
46 48 0.798771 GCTCCAGCGACTCGTGTAAG 60.799 60.0 0.00 0.00 0.00 2.34 F
1458 4589 0.176910 TGTCAAGGACAGTTGTCGCA 59.823 50.0 6.21 0.00 45.65 5.10 F
2542 5715 0.250234 CTGCCAAAGTCTCCGGATGA 59.750 55.0 3.57 1.41 0.00 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1558 4689 0.318614 ACAAAATTGCCGCGGAACAG 60.319 50.0 33.48 13.43 0.00 3.16 R
3403 6583 0.952497 CAGCTCCGACTTGCATGTGT 60.952 55.0 10.37 0.00 0.00 3.72 R
4062 7260 0.112995 TTGTCTGGAAGGCTTGCCAT 59.887 50.0 16.49 0.98 41.06 4.40 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
26 27 3.206150 ACACGATGTGAGCTGAAAAACT 58.794 40.909 3.61 0.00 36.96 2.66
46 48 0.798771 GCTCCAGCGACTCGTGTAAG 60.799 60.000 0.00 0.00 0.00 2.34
116 118 0.804544 TATACACGAGCAAGCCACGC 60.805 55.000 8.64 0.00 0.00 5.34
204 206 4.096003 CCCCCAAGTCGCCGTCAT 62.096 66.667 0.00 0.00 0.00 3.06
251 3361 3.340034 ACACGTTCCACTGAAAAACTGA 58.660 40.909 0.00 0.00 30.79 3.41
272 3382 7.275920 ACTGAGAGGTGTATAATTTAGCAAGG 58.724 38.462 0.00 0.00 0.00 3.61
326 3436 4.379394 CGTCCAAATTTACACCATCCACTG 60.379 45.833 0.00 0.00 0.00 3.66
365 3475 3.059800 GCGAAACTGTTCTTGTGGAGTAC 60.060 47.826 0.00 0.00 0.00 2.73
366 3476 4.369182 CGAAACTGTTCTTGTGGAGTACT 58.631 43.478 0.00 0.00 0.00 2.73
367 3477 5.526115 CGAAACTGTTCTTGTGGAGTACTA 58.474 41.667 0.00 0.00 0.00 1.82
377 3487 6.491383 TCTTGTGGAGTACTAGTACCAATCT 58.509 40.000 25.97 10.08 36.75 2.40
410 3523 3.332761 CTGAGCTAGCAAGTACTCGAG 57.667 52.381 18.83 11.84 31.64 4.04
411 3524 1.402259 TGAGCTAGCAAGTACTCGAGC 59.598 52.381 18.83 8.16 31.64 5.03
456 3573 3.130164 GGAGGAACGGGAGAAGTAAGTAC 59.870 52.174 0.00 0.00 0.00 2.73
464 3581 3.619419 GGAGAAGTAAGTACGAGGGAGT 58.381 50.000 0.00 0.00 0.00 3.85
668 3795 4.690719 TCCAAATCGCGCCGTGGT 62.691 61.111 17.58 0.00 32.68 4.16
743 3873 3.935315 CAGATTCCTTTGACTGCTCTGA 58.065 45.455 0.00 0.00 32.36 3.27
1018 4149 1.300971 GATGAGCAACAAGAGCGGCA 61.301 55.000 1.45 0.00 37.01 5.69
1240 4371 4.150454 CGGCCTCCTCCTCCTCCT 62.150 72.222 0.00 0.00 0.00 3.69
1241 4372 2.123033 GGCCTCCTCCTCCTCCTC 60.123 72.222 0.00 0.00 0.00 3.71
1242 4373 2.710826 GGCCTCCTCCTCCTCCTCT 61.711 68.421 0.00 0.00 0.00 3.69
1458 4589 0.176910 TGTCAAGGACAGTTGTCGCA 59.823 50.000 6.21 0.00 45.65 5.10
1530 4661 2.872732 TCTACGGAGGTGTTTGAGTCT 58.127 47.619 0.00 0.00 0.00 3.24
1554 4685 4.785301 TCATGAAGAATGAAGGATGGACC 58.215 43.478 0.00 0.00 42.49 4.46
1558 4689 0.819666 GAATGAAGGATGGACCGGGC 60.820 60.000 6.32 0.21 44.74 6.13
1677 4808 2.697751 CACCATGGTTCCCTTGTTTTGA 59.302 45.455 16.84 0.00 0.00 2.69
1680 4811 5.011533 CACCATGGTTCCCTTGTTTTGAATA 59.988 40.000 16.84 0.00 0.00 1.75
1681 4812 5.784906 ACCATGGTTCCCTTGTTTTGAATAT 59.215 36.000 13.00 0.00 0.00 1.28
1682 4813 6.108015 CCATGGTTCCCTTGTTTTGAATATG 58.892 40.000 2.57 0.00 0.00 1.78
1768 4899 3.808728 TGTTATGAGTCCTTGCCTATGC 58.191 45.455 0.00 0.00 38.26 3.14
1788 4919 8.814235 CCTATGCTTTTTCTTTTGATTAGCATG 58.186 33.333 14.83 0.00 42.10 4.06
1806 4937 3.490761 GCATGTAAATGCACATACCCACC 60.491 47.826 13.25 0.00 46.25 4.61
1817 4948 3.694072 CACATACCCACCCACATACAAAG 59.306 47.826 0.00 0.00 0.00 2.77
1824 4956 4.079253 CCACCCACATACAAAGTTAAGCT 58.921 43.478 0.00 0.00 0.00 3.74
1830 4962 7.174426 ACCCACATACAAAGTTAAGCTTTACTC 59.826 37.037 17.78 0.79 44.95 2.59
1848 4980 3.660865 ACTCGTTGTAAATCAGTGTCCC 58.339 45.455 0.00 0.00 0.00 4.46
1860 4992 2.507886 TCAGTGTCCCTTTCTGTCCAAA 59.492 45.455 0.00 0.00 0.00 3.28
1865 4997 4.340950 GTGTCCCTTTCTGTCCAAATTTCA 59.659 41.667 0.00 0.00 0.00 2.69
1868 5000 3.575687 CCCTTTCTGTCCAAATTTCAGCT 59.424 43.478 1.44 0.00 0.00 4.24
1869 5001 4.039609 CCCTTTCTGTCCAAATTTCAGCTT 59.960 41.667 1.44 0.00 0.00 3.74
1870 5002 5.243730 CCCTTTCTGTCCAAATTTCAGCTTA 59.756 40.000 1.44 0.00 0.00 3.09
1871 5003 6.385033 CCTTTCTGTCCAAATTTCAGCTTAG 58.615 40.000 1.44 0.13 0.00 2.18
1872 5004 5.964958 TTCTGTCCAAATTTCAGCTTAGG 57.035 39.130 1.44 0.00 0.00 2.69
1873 5005 4.985538 TCTGTCCAAATTTCAGCTTAGGT 58.014 39.130 1.44 0.00 0.00 3.08
1874 5006 5.003804 TCTGTCCAAATTTCAGCTTAGGTC 58.996 41.667 1.44 0.00 0.00 3.85
1875 5007 4.079253 TGTCCAAATTTCAGCTTAGGTCC 58.921 43.478 0.00 0.00 0.00 4.46
1876 5008 4.079253 GTCCAAATTTCAGCTTAGGTCCA 58.921 43.478 0.00 0.00 0.00 4.02
1877 5009 4.706962 GTCCAAATTTCAGCTTAGGTCCAT 59.293 41.667 0.00 0.00 0.00 3.41
1878 5010 5.185828 GTCCAAATTTCAGCTTAGGTCCATT 59.814 40.000 0.00 0.00 0.00 3.16
1882 5014 7.118245 CCAAATTTCAGCTTAGGTCCATTTTTC 59.882 37.037 0.00 0.00 0.00 2.29
1892 5024 8.406297 GCTTAGGTCCATTTTTCTTACTATTGG 58.594 37.037 0.00 0.00 0.00 3.16
1895 5027 6.603599 AGGTCCATTTTTCTTACTATTGGCTC 59.396 38.462 0.00 0.00 0.00 4.70
1905 5037 6.860034 TCTTACTATTGGCTCAGGTCCTATA 58.140 40.000 0.00 0.00 0.00 1.31
1907 5039 5.081315 ACTATTGGCTCAGGTCCTATACT 57.919 43.478 0.00 0.00 0.00 2.12
1910 5042 1.062886 TGGCTCAGGTCCTATACTGCT 60.063 52.381 0.00 0.00 34.76 4.24
1912 5044 3.181417 TGGCTCAGGTCCTATACTGCTAT 60.181 47.826 0.00 0.00 34.76 2.97
1913 5045 3.835395 GGCTCAGGTCCTATACTGCTATT 59.165 47.826 0.00 0.00 34.76 1.73
1914 5046 4.284746 GGCTCAGGTCCTATACTGCTATTT 59.715 45.833 0.00 0.00 34.76 1.40
1915 5047 5.233988 GCTCAGGTCCTATACTGCTATTTG 58.766 45.833 0.00 0.00 34.76 2.32
1916 5048 5.788450 CTCAGGTCCTATACTGCTATTTGG 58.212 45.833 0.00 0.00 34.76 3.28
1917 5049 4.040461 TCAGGTCCTATACTGCTATTTGGC 59.960 45.833 0.00 0.00 34.76 4.52
1918 5050 3.973973 AGGTCCTATACTGCTATTTGGCA 59.026 43.478 0.00 0.00 40.15 4.92
1919 5051 4.065789 GGTCCTATACTGCTATTTGGCAC 58.934 47.826 0.00 0.00 37.29 5.01
1972 5104 9.671279 GTTTACTATTTAACCTGGGCTAACTTA 57.329 33.333 0.00 0.00 0.00 2.24
2006 5138 8.883789 TTTTGTTTAAAACTGAAGTACTGTCG 57.116 30.769 0.00 0.00 31.13 4.35
2007 5139 6.039781 TGTTTAAAACTGAAGTACTGTCGC 57.960 37.500 0.00 0.00 0.00 5.19
2010 5142 2.726832 AACTGAAGTACTGTCGCTCC 57.273 50.000 0.00 0.00 0.00 4.70
2015 5147 4.463186 ACTGAAGTACTGTCGCTCCTATTT 59.537 41.667 0.00 0.00 0.00 1.40
2017 5149 3.802948 AGTACTGTCGCTCCTATTTGG 57.197 47.619 0.00 0.00 37.10 3.28
2018 5150 2.159085 AGTACTGTCGCTCCTATTTGGC 60.159 50.000 0.00 0.00 35.26 4.52
2020 5152 1.003118 ACTGTCGCTCCTATTTGGCAA 59.997 47.619 0.00 0.00 35.26 4.52
2021 5153 2.083774 CTGTCGCTCCTATTTGGCAAA 58.916 47.619 16.01 16.01 35.26 3.68
2022 5154 2.083774 TGTCGCTCCTATTTGGCAAAG 58.916 47.619 18.61 5.37 35.26 2.77
2023 5155 2.084546 GTCGCTCCTATTTGGCAAAGT 58.915 47.619 18.61 9.08 35.26 2.66
2024 5156 2.083774 TCGCTCCTATTTGGCAAAGTG 58.916 47.619 18.61 10.58 35.26 3.16
2025 5157 1.468054 CGCTCCTATTTGGCAAAGTGC 60.468 52.381 18.61 14.81 44.08 4.40
2064 5196 2.989422 AGCTGGATTTACGCAAACAC 57.011 45.000 0.00 0.00 0.00 3.32
2095 5227 1.280421 CTTTCCTGAGCTAGGCCACTT 59.720 52.381 5.01 0.00 46.87 3.16
2096 5228 0.615331 TTCCTGAGCTAGGCCACTTG 59.385 55.000 5.01 0.00 46.87 3.16
2128 5260 7.164230 TCCTTCAATCTAGTTCAGAAGAGAC 57.836 40.000 13.50 0.00 38.30 3.36
2133 5265 6.894654 TCAATCTAGTTCAGAAGAGACCTCAT 59.105 38.462 0.00 0.00 36.67 2.90
2153 5285 7.443575 ACCTCATGCTTTGATGTACTTCATATC 59.556 37.037 11.84 4.60 36.83 1.63
2154 5286 7.443272 CCTCATGCTTTGATGTACTTCATATCA 59.557 37.037 11.84 9.51 36.83 2.15
2155 5287 8.913487 TCATGCTTTGATGTACTTCATATCAT 57.087 30.769 11.84 11.11 35.02 2.45
2286 5455 3.504375 AGGAGTCGTTGTAGTTTACCCT 58.496 45.455 0.00 0.00 0.00 4.34
2303 5476 9.100197 AGTTTACCCTATGAAATTGATTTTGGT 57.900 29.630 0.00 0.00 0.00 3.67
2304 5477 9.150348 GTTTACCCTATGAAATTGATTTTGGTG 57.850 33.333 0.00 0.00 0.00 4.17
2329 5502 1.073897 AACTTGCCTGTCCTCTGCC 59.926 57.895 0.00 0.00 0.00 4.85
2342 5515 0.615331 CTCTGCCCAAGCTGGTCTAA 59.385 55.000 0.00 0.00 40.80 2.10
2345 5518 2.158534 TCTGCCCAAGCTGGTCTAAAAA 60.159 45.455 0.00 0.00 40.80 1.94
2373 5546 6.495706 AGTAGCTTCAACACTTAAACAAAGC 58.504 36.000 0.00 0.00 38.93 3.51
2374 5547 5.582689 AGCTTCAACACTTAAACAAAGCT 57.417 34.783 0.00 0.00 42.16 3.74
2375 5548 5.582550 AGCTTCAACACTTAAACAAAGCTC 58.417 37.500 0.00 0.00 43.11 4.09
2376 5549 5.358160 AGCTTCAACACTTAAACAAAGCTCT 59.642 36.000 0.00 0.00 43.11 4.09
2377 5550 5.456822 GCTTCAACACTTAAACAAAGCTCTG 59.543 40.000 0.00 0.00 38.93 3.35
2378 5551 5.499139 TCAACACTTAAACAAAGCTCTGG 57.501 39.130 0.00 0.00 38.93 3.86
2379 5552 5.189928 TCAACACTTAAACAAAGCTCTGGA 58.810 37.500 0.00 0.00 38.93 3.86
2380 5553 5.827797 TCAACACTTAAACAAAGCTCTGGAT 59.172 36.000 0.00 0.00 38.93 3.41
2381 5554 6.321181 TCAACACTTAAACAAAGCTCTGGATT 59.679 34.615 0.00 0.00 38.93 3.01
2382 5555 6.076981 ACACTTAAACAAAGCTCTGGATTG 57.923 37.500 0.00 0.00 38.93 2.67
2383 5556 4.919754 CACTTAAACAAAGCTCTGGATTGC 59.080 41.667 0.00 0.00 38.93 3.56
2384 5557 4.584325 ACTTAAACAAAGCTCTGGATTGCA 59.416 37.500 0.00 0.00 38.93 4.08
2385 5558 5.244626 ACTTAAACAAAGCTCTGGATTGCAT 59.755 36.000 0.00 0.00 38.93 3.96
2386 5559 6.434028 ACTTAAACAAAGCTCTGGATTGCATA 59.566 34.615 0.00 0.00 38.93 3.14
2387 5560 5.726980 AAACAAAGCTCTGGATTGCATAA 57.273 34.783 0.00 0.00 0.00 1.90
2388 5561 5.726980 AACAAAGCTCTGGATTGCATAAA 57.273 34.783 0.00 0.00 0.00 1.40
2389 5562 5.927281 ACAAAGCTCTGGATTGCATAAAT 57.073 34.783 0.00 0.00 0.00 1.40
2390 5563 6.290294 ACAAAGCTCTGGATTGCATAAATT 57.710 33.333 0.00 0.00 0.00 1.82
2391 5564 7.408756 ACAAAGCTCTGGATTGCATAAATTA 57.591 32.000 0.00 0.00 0.00 1.40
2392 5565 7.486647 ACAAAGCTCTGGATTGCATAAATTAG 58.513 34.615 0.00 0.00 0.00 1.73
2399 5572 6.835488 TCTGGATTGCATAAATTAGAGGCTTT 59.165 34.615 0.00 0.00 0.00 3.51
2408 5581 7.577616 GCATAAATTAGAGGCTTTGAACCACTT 60.578 37.037 0.00 0.00 30.26 3.16
2410 5583 1.986882 AGAGGCTTTGAACCACTTGG 58.013 50.000 0.00 0.00 42.17 3.61
2452 5625 8.922237 AGATCAGTCAAGATAACATATCAGTGT 58.078 33.333 0.00 0.00 0.00 3.55
2468 5641 9.293404 CATATCAGTGTCTATTCCAATTTCCAT 57.707 33.333 0.00 0.00 0.00 3.41
2471 5644 6.767902 TCAGTGTCTATTCCAATTTCCATAGC 59.232 38.462 0.00 0.00 0.00 2.97
2487 5660 6.763715 TCCATAGCCCATAATCCATATACC 57.236 41.667 0.00 0.00 0.00 2.73
2500 5673 4.116961 TCCATATACCAAGAAACTTCGCG 58.883 43.478 0.00 0.00 0.00 5.87
2541 5714 0.745845 CCTGCCAAAGTCTCCGGATG 60.746 60.000 3.57 0.00 0.00 3.51
2542 5715 0.250234 CTGCCAAAGTCTCCGGATGA 59.750 55.000 3.57 1.41 0.00 2.92
2543 5716 0.911769 TGCCAAAGTCTCCGGATGAT 59.088 50.000 3.57 0.00 0.00 2.45
2582 5755 5.130292 AGATTTTCATGCCTGAAGTGTTG 57.870 39.130 4.57 0.00 42.19 3.33
2583 5756 3.731652 TTTTCATGCCTGAAGTGTTGG 57.268 42.857 4.57 0.00 42.19 3.77
2595 5768 1.059098 AGTGTTGGATGTGAGCAGGA 58.941 50.000 0.00 0.00 0.00 3.86
2608 5784 5.809001 TGTGAGCAGGAATAACTTCAATCT 58.191 37.500 0.00 0.00 32.70 2.40
2699 5876 6.017275 AGCTGCAGATCATTAGCATTAGTTTC 60.017 38.462 20.43 0.00 38.59 2.78
2703 5882 5.237127 CAGATCATTAGCATTAGTTTCGCCA 59.763 40.000 0.00 0.00 0.00 5.69
2724 5903 7.019418 CGCCACTTTTCTGTACCTTTATTTAC 58.981 38.462 0.00 0.00 0.00 2.01
2926 6106 2.359900 CAAATCTGGGGAAGAACGGAG 58.640 52.381 0.00 0.00 38.79 4.63
3142 6322 2.559440 CCTCTAATTGTGCAGAGAGGC 58.441 52.381 12.89 0.00 46.42 4.70
3178 6358 5.075858 TCCTCCATGCATTTGTGAAAATC 57.924 39.130 0.00 0.00 0.00 2.17
3196 6376 2.046217 GTCCGTGAAGAAGGCCCC 60.046 66.667 0.00 0.00 0.00 5.80
3208 6388 4.840005 GGCCCCGCTGAGCTGTAC 62.840 72.222 1.78 0.00 0.00 2.90
3320 6500 9.820725 AGAAAATGTTCAAGACAAATGAAATCA 57.179 25.926 0.00 0.00 42.62 2.57
3373 6553 0.747283 CAGGAGCCATCTCAAGCACC 60.747 60.000 0.00 0.00 41.13 5.01
3586 6766 5.073311 ACGAAGCTTGCAAGAAGATACTA 57.927 39.130 30.39 0.00 0.00 1.82
3604 6784 4.993029 ACTAATTGAGGAAGAGGACGAG 57.007 45.455 0.00 0.00 0.00 4.18
3622 6802 0.387929 AGTGAAGCGTTCCTCGACAA 59.612 50.000 0.00 0.00 42.86 3.18
3624 6804 0.103390 TGAAGCGTTCCTCGACAACA 59.897 50.000 3.93 0.00 42.86 3.33
3627 6807 1.664965 GCGTTCCTCGACAACAGCT 60.665 57.895 3.93 0.00 42.86 4.24
3628 6808 1.618640 GCGTTCCTCGACAACAGCTC 61.619 60.000 3.93 0.00 42.86 4.09
3635 6815 3.007506 TCCTCGACAACAGCTCCATAAAA 59.992 43.478 0.00 0.00 0.00 1.52
3650 6830 3.947834 CCATAAAAGGGTAGTGGCTTGAG 59.052 47.826 0.00 0.00 0.00 3.02
3663 6843 2.204237 GGCTTGAGTTTTGTTTGCTGG 58.796 47.619 0.00 0.00 0.00 4.85
3674 6860 5.913137 TTTGTTTGCTGGTCCTATTATGG 57.087 39.130 0.00 0.00 0.00 2.74
3706 6892 1.512735 GGCCTTCCTCCCAAGATACT 58.487 55.000 0.00 0.00 0.00 2.12
3715 6907 3.705072 CCTCCCAAGATACTAGGTTTCGT 59.295 47.826 0.00 0.00 0.00 3.85
3719 6911 4.081862 CCCAAGATACTAGGTTTCGTGACA 60.082 45.833 0.00 0.00 28.76 3.58
3725 6917 2.957006 ACTAGGTTTCGTGACAGACAGT 59.043 45.455 0.00 0.00 0.00 3.55
3729 6921 0.828022 TTTCGTGACAGACAGTGGGT 59.172 50.000 0.00 0.00 0.00 4.51
3738 6930 5.124936 GTGACAGACAGTGGGTAAACTTTTT 59.875 40.000 0.00 0.00 0.00 1.94
3770 6962 7.861629 TCTTTGGATGATGTTACCTGACTAAT 58.138 34.615 0.00 0.00 0.00 1.73
3822 7014 4.830046 ACTCTTTCTGTAGTCTCAGCTTGA 59.170 41.667 0.00 0.00 35.63 3.02
3828 7020 3.435275 TGTAGTCTCAGCTTGACCTGAT 58.565 45.455 11.69 0.00 40.77 2.90
3888 7084 2.406024 GCATGAATGAAGCGTGTGTTTG 59.594 45.455 0.00 0.00 0.00 2.93
3891 7087 2.286125 TGAATGAAGCGTGTGTTTGTCG 60.286 45.455 0.00 0.00 0.00 4.35
3892 7088 1.295792 ATGAAGCGTGTGTTTGTCGT 58.704 45.000 0.00 0.00 0.00 4.34
3905 7101 6.579666 GTGTGTTTGTCGTAAAGTCTTTGTTT 59.420 34.615 8.14 0.00 0.00 2.83
3909 7105 3.065648 TGTCGTAAAGTCTTTGTTTGGGC 59.934 43.478 8.14 0.00 0.00 5.36
3934 7132 6.953743 CGTATGAAACCAGTGAAATTAACTCG 59.046 38.462 0.00 0.00 0.00 4.18
3935 7133 6.877611 ATGAAACCAGTGAAATTAACTCGT 57.122 33.333 0.00 0.00 0.00 4.18
3949 7147 9.267096 GAAATTAACTCGTGAGACATCAAATTC 57.733 33.333 3.44 0.00 37.14 2.17
3965 7163 4.571984 TCAAATTCTACATGAGTGGCATCG 59.428 41.667 0.00 0.00 34.15 3.84
3967 7165 3.885724 TTCTACATGAGTGGCATCGAA 57.114 42.857 0.00 0.00 34.15 3.71
3971 7169 3.770263 ACATGAGTGGCATCGAAATTG 57.230 42.857 0.00 0.00 34.15 2.32
3977 7175 4.095334 TGAGTGGCATCGAAATTGATCTTG 59.905 41.667 0.00 0.00 0.00 3.02
3985 7183 6.033196 GCATCGAAATTGATCTTGTTCAGTTG 59.967 38.462 0.00 0.07 0.00 3.16
4038 7236 2.573462 ACTCATGGCAAGTCTGGTATGT 59.427 45.455 0.00 0.00 0.00 2.29
4050 7248 8.082242 GCAAGTCTGGTATGTACTTTTGATTTT 58.918 33.333 0.00 0.00 31.21 1.82
4062 7260 5.916318 ACTTTTGATTTTGATGCCAACTCA 58.084 33.333 0.00 0.00 30.88 3.41
4064 7262 6.425721 ACTTTTGATTTTGATGCCAACTCATG 59.574 34.615 0.00 0.00 30.88 3.07
4079 7277 0.322816 TCATGGCAAGCCTTCCAGAC 60.323 55.000 12.96 0.00 35.57 3.51
4080 7278 0.609957 CATGGCAAGCCTTCCAGACA 60.610 55.000 12.96 0.00 35.57 3.41
4081 7279 0.112995 ATGGCAAGCCTTCCAGACAA 59.887 50.000 12.96 0.00 35.57 3.18
4093 7291 6.775629 AGCCTTCCAGACAAACACTTAAATTA 59.224 34.615 0.00 0.00 0.00 1.40
4106 7304 5.065218 ACACTTAAATTATCAGCTCTTGCCG 59.935 40.000 0.00 0.00 40.80 5.69
4281 7493 5.596836 ACAAAAGAAAACAGAAGCCATCA 57.403 34.783 0.00 0.00 0.00 3.07
4470 7699 9.241919 TCTGAATGATATCCTGCTAAAAACAAA 57.758 29.630 0.00 0.00 0.00 2.83
4556 7785 4.582869 TCTCATCCTTGATTTCCACAGTG 58.417 43.478 0.00 0.00 0.00 3.66
4581 7810 5.538849 TGTCGTAATCCCTGCACATATTA 57.461 39.130 0.00 0.00 0.00 0.98
4588 7817 7.387673 CGTAATCCCTGCACATATTATTCTTGA 59.612 37.037 0.00 0.00 0.00 3.02
4606 7835 6.500684 TCTTGATTAGAGAATGTTTGTGCC 57.499 37.500 0.00 0.00 0.00 5.01
4607 7836 6.003326 TCTTGATTAGAGAATGTTTGTGCCA 58.997 36.000 0.00 0.00 0.00 4.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 1.520600 TTACACGAGTCGCTGGAGCA 61.521 55.000 13.59 0.00 42.21 4.26
46 48 1.084289 GTGGATGTTTACACGCCCTC 58.916 55.000 0.00 0.00 0.00 4.30
127 129 1.668151 GCAGCGGTCTCCTTTTCGT 60.668 57.895 0.00 0.00 0.00 3.85
163 165 1.152735 TCCTCCGATCCTTCCTCCG 60.153 63.158 0.00 0.00 0.00 4.63
177 179 4.168291 CTTGGGGGCGAGCTCCTC 62.168 72.222 14.32 4.81 36.64 3.71
193 195 2.736144 TTAGAAACATGACGGCGACT 57.264 45.000 16.62 0.00 0.00 4.18
251 3361 6.958767 ACACCTTGCTAAATTATACACCTCT 58.041 36.000 0.00 0.00 0.00 3.69
272 3382 7.387119 TCTCCATATACACGTCCATATACAC 57.613 40.000 0.00 0.00 0.00 2.90
336 3446 3.560068 ACAAGAACAGTTTCGCCTACTTG 59.440 43.478 0.00 0.00 39.17 3.16
342 3452 1.264288 CTCCACAAGAACAGTTTCGCC 59.736 52.381 0.00 0.00 36.78 5.54
343 3453 1.940613 ACTCCACAAGAACAGTTTCGC 59.059 47.619 0.00 0.00 36.78 4.70
365 3475 6.518537 GCCCAGTAATGGTAGATTGGTACTAG 60.519 46.154 8.66 0.00 0.00 2.57
366 3476 5.306160 GCCCAGTAATGGTAGATTGGTACTA 59.694 44.000 8.66 0.00 0.00 1.82
367 3477 4.102681 GCCCAGTAATGGTAGATTGGTACT 59.897 45.833 8.66 0.00 0.00 2.73
377 3487 1.879575 AGCTCAGCCCAGTAATGGTA 58.120 50.000 8.66 0.00 0.00 3.25
423 3536 1.605712 CCGTTCCTCCACTGAAGACAC 60.606 57.143 0.00 0.00 0.00 3.67
456 3573 1.131883 CGTTGTACCTACACTCCCTCG 59.868 57.143 0.00 0.00 35.64 4.63
464 3581 0.166597 CTCGCGACGTTGTACCTACA 59.833 55.000 3.71 0.00 0.00 2.74
668 3795 0.991920 AAGATTCGGAGGCCCTTTCA 59.008 50.000 0.00 0.00 0.00 2.69
863 3993 1.772182 GACAGCGACGGATATCAAGG 58.228 55.000 4.83 0.00 0.00 3.61
1065 4196 0.972983 CGGAGAGGGAGAGGAAGCAA 60.973 60.000 0.00 0.00 0.00 3.91
1129 4260 1.548081 CATGCCAGGTTGAATCCACA 58.452 50.000 0.00 0.00 0.00 4.17
1237 4368 4.147449 CGATGTGGCGCCAGAGGA 62.147 66.667 33.73 15.00 0.00 3.71
1238 4369 4.457496 ACGATGTGGCGCCAGAGG 62.457 66.667 33.73 26.14 33.86 3.69
1239 4370 2.887568 GACGATGTGGCGCCAGAG 60.888 66.667 33.73 20.71 33.86 3.35
1240 4371 4.794439 CGACGATGTGGCGCCAGA 62.794 66.667 33.73 31.82 33.86 3.86
1434 4565 0.947244 CAACTGTCCTTGACACTGCC 59.053 55.000 0.00 0.00 37.67 4.85
1458 4589 3.056035 GTGTCCTAATCGTCTCCAAAGGT 60.056 47.826 0.00 0.00 0.00 3.50
1530 4661 6.537355 GGTCCATCCTTCATTCTTCATGATA 58.463 40.000 0.00 0.00 41.82 2.15
1558 4689 0.318614 ACAAAATTGCCGCGGAACAG 60.319 50.000 33.48 13.43 0.00 3.16
1705 4836 9.740239 CTCCTGCTTAGTACGTATACATTAAAA 57.260 33.333 0.00 0.00 33.30 1.52
1709 4840 6.771749 AGTCTCCTGCTTAGTACGTATACATT 59.228 38.462 0.00 0.00 33.30 2.71
1710 4841 6.297582 AGTCTCCTGCTTAGTACGTATACAT 58.702 40.000 0.00 0.00 33.30 2.29
1713 4844 8.915057 AATAAGTCTCCTGCTTAGTACGTATA 57.085 34.615 0.00 0.00 32.72 1.47
1714 4845 7.820578 AATAAGTCTCCTGCTTAGTACGTAT 57.179 36.000 0.00 0.00 32.72 3.06
1715 4846 7.636150 AAATAAGTCTCCTGCTTAGTACGTA 57.364 36.000 0.00 0.00 32.72 3.57
1716 4847 6.527057 AAATAAGTCTCCTGCTTAGTACGT 57.473 37.500 0.00 0.00 32.72 3.57
1717 4848 6.916932 GGTAAATAAGTCTCCTGCTTAGTACG 59.083 42.308 0.00 0.00 32.72 3.67
1718 4849 7.779073 TGGTAAATAAGTCTCCTGCTTAGTAC 58.221 38.462 0.00 0.00 32.72 2.73
1720 4851 6.869206 TGGTAAATAAGTCTCCTGCTTAGT 57.131 37.500 0.00 0.00 32.72 2.24
1722 4853 9.778741 CATTATGGTAAATAAGTCTCCTGCTTA 57.221 33.333 0.00 0.00 33.59 3.09
1723 4854 8.275040 ACATTATGGTAAATAAGTCTCCTGCTT 58.725 33.333 0.00 0.00 0.00 3.91
1752 4883 3.439857 AAAAGCATAGGCAAGGACTCA 57.560 42.857 0.67 0.00 44.61 3.41
1788 4919 2.425668 GTGGGTGGGTATGTGCATTTAC 59.574 50.000 0.00 0.00 0.00 2.01
1803 4934 5.705609 AAGCTTAACTTTGTATGTGGGTG 57.294 39.130 0.00 0.00 33.71 4.61
1826 4958 4.525487 AGGGACACTGATTTACAACGAGTA 59.475 41.667 0.00 0.00 0.00 2.59
1830 4962 4.755123 AGAAAGGGACACTGATTTACAACG 59.245 41.667 0.00 0.00 0.00 4.10
1848 4980 6.015940 ACCTAAGCTGAAATTTGGACAGAAAG 60.016 38.462 9.03 3.59 34.07 2.62
1860 4992 7.544804 AAGAAAAATGGACCTAAGCTGAAAT 57.455 32.000 0.00 0.00 0.00 2.17
1865 4997 9.178758 CAATAGTAAGAAAAATGGACCTAAGCT 57.821 33.333 0.00 0.00 0.00 3.74
1868 5000 8.113462 AGCCAATAGTAAGAAAAATGGACCTAA 58.887 33.333 0.00 0.00 0.00 2.69
1869 5001 7.639378 AGCCAATAGTAAGAAAAATGGACCTA 58.361 34.615 0.00 0.00 0.00 3.08
1870 5002 6.494059 AGCCAATAGTAAGAAAAATGGACCT 58.506 36.000 0.00 0.00 0.00 3.85
1871 5003 6.377146 TGAGCCAATAGTAAGAAAAATGGACC 59.623 38.462 0.00 0.00 0.00 4.46
1872 5004 7.391148 TGAGCCAATAGTAAGAAAAATGGAC 57.609 36.000 0.00 0.00 0.00 4.02
1873 5005 6.603201 CCTGAGCCAATAGTAAGAAAAATGGA 59.397 38.462 0.00 0.00 0.00 3.41
1874 5006 6.378280 ACCTGAGCCAATAGTAAGAAAAATGG 59.622 38.462 0.00 0.00 0.00 3.16
1875 5007 7.396540 ACCTGAGCCAATAGTAAGAAAAATG 57.603 36.000 0.00 0.00 0.00 2.32
1876 5008 6.603599 GGACCTGAGCCAATAGTAAGAAAAAT 59.396 38.462 0.00 0.00 0.00 1.82
1877 5009 5.944007 GGACCTGAGCCAATAGTAAGAAAAA 59.056 40.000 0.00 0.00 0.00 1.94
1878 5010 5.250774 AGGACCTGAGCCAATAGTAAGAAAA 59.749 40.000 0.00 0.00 0.00 2.29
1882 5014 6.722129 AGTATAGGACCTGAGCCAATAGTAAG 59.278 42.308 3.53 0.00 0.00 2.34
1892 5024 5.233988 CAAATAGCAGTATAGGACCTGAGC 58.766 45.833 3.53 0.85 0.00 4.26
1895 5027 4.202357 TGCCAAATAGCAGTATAGGACCTG 60.202 45.833 3.53 0.00 38.00 4.00
1905 5037 0.883833 GCACTGTGCCAAATAGCAGT 59.116 50.000 21.78 0.00 45.14 4.40
1916 5048 5.991606 TGAAGAATATATGTAGGCACTGTGC 59.008 40.000 24.02 24.02 44.08 4.57
1917 5049 7.712639 AGTTGAAGAATATATGTAGGCACTGTG 59.287 37.037 2.76 2.76 41.52 3.66
1918 5050 7.796054 AGTTGAAGAATATATGTAGGCACTGT 58.204 34.615 0.00 0.00 41.52 3.55
1919 5051 9.764363 TTAGTTGAAGAATATATGTAGGCACTG 57.236 33.333 0.00 0.00 41.52 3.66
1980 5112 8.782327 CGACAGTACTTCAGTTTTAAACAAAAC 58.218 33.333 10.60 1.89 41.62 2.43
2003 5135 2.084546 ACTTTGCCAAATAGGAGCGAC 58.915 47.619 0.00 0.00 41.22 5.19
2005 5137 1.468054 GCACTTTGCCAAATAGGAGCG 60.468 52.381 0.00 0.00 41.22 5.03
2006 5138 2.284263 GCACTTTGCCAAATAGGAGC 57.716 50.000 0.00 0.00 41.22 4.70
2017 5149 7.832503 AAAAATTCATATGTAGGCACTTTGC 57.167 32.000 1.90 0.00 44.08 3.68
2039 5171 6.199342 GTGTTTGCGTAAATCCAGCTTAAAAA 59.801 34.615 0.99 0.00 0.00 1.94
2042 5174 4.276183 TGTGTTTGCGTAAATCCAGCTTAA 59.724 37.500 0.99 0.00 0.00 1.85
2050 5182 8.122952 AGCTCTTAATATGTGTTTGCGTAAATC 58.877 33.333 0.99 0.00 0.00 2.17
2057 5189 6.749118 CAGGAAAGCTCTTAATATGTGTTTGC 59.251 38.462 0.00 0.00 0.00 3.68
2059 5191 7.148171 GCTCAGGAAAGCTCTTAATATGTGTTT 60.148 37.037 0.00 0.00 39.27 2.83
2095 5227 8.134202 TGAACTAGATTGAAGGATTAGTCACA 57.866 34.615 0.00 0.00 0.00 3.58
2096 5228 8.470805 TCTGAACTAGATTGAAGGATTAGTCAC 58.529 37.037 0.00 0.00 0.00 3.67
2128 5260 7.443272 TGATATGAAGTACATCAAAGCATGAGG 59.557 37.037 4.69 3.07 45.24 3.86
2213 5382 9.720769 CTGTTAACATAAAAGGTCTCTAAGGAA 57.279 33.333 9.13 0.00 0.00 3.36
2247 5416 7.123847 ACGACTCCTTGTTATATGAACCTAACT 59.876 37.037 0.00 0.00 0.00 2.24
2248 5417 7.263496 ACGACTCCTTGTTATATGAACCTAAC 58.737 38.462 0.00 0.00 0.00 2.34
2249 5418 7.414222 ACGACTCCTTGTTATATGAACCTAA 57.586 36.000 0.00 0.00 0.00 2.69
2256 5425 8.475331 AAACTACAACGACTCCTTGTTATATG 57.525 34.615 0.00 0.00 33.79 1.78
2286 5455 5.936956 GGCAACCACCAAAATCAATTTCATA 59.063 36.000 0.00 0.00 0.00 2.15
2303 5476 1.381056 ACAGGCAAGTTGGCAACCA 60.381 52.632 28.85 0.00 46.46 3.67
2304 5477 1.363807 GACAGGCAAGTTGGCAACC 59.636 57.895 28.85 11.50 46.46 3.77
2354 5527 5.973565 CCAGAGCTTTGTTTAAGTGTTGAAG 59.026 40.000 3.25 0.00 36.19 3.02
2357 5530 5.499139 TCCAGAGCTTTGTTTAAGTGTTG 57.501 39.130 3.25 0.00 36.19 3.33
2360 5533 4.919754 GCAATCCAGAGCTTTGTTTAAGTG 59.080 41.667 3.25 0.00 36.19 3.16
2361 5534 4.584325 TGCAATCCAGAGCTTTGTTTAAGT 59.416 37.500 3.25 0.00 36.19 2.24
2370 5543 6.489361 CCTCTAATTTATGCAATCCAGAGCTT 59.511 38.462 0.00 0.00 34.96 3.74
2371 5544 6.002704 CCTCTAATTTATGCAATCCAGAGCT 58.997 40.000 0.00 0.00 34.96 4.09
2372 5545 5.335504 GCCTCTAATTTATGCAATCCAGAGC 60.336 44.000 0.00 0.00 34.96 4.09
2373 5546 6.002704 AGCCTCTAATTTATGCAATCCAGAG 58.997 40.000 0.00 0.00 35.52 3.35
2374 5547 5.945310 AGCCTCTAATTTATGCAATCCAGA 58.055 37.500 0.00 0.00 0.00 3.86
2375 5548 6.645790 AAGCCTCTAATTTATGCAATCCAG 57.354 37.500 0.00 0.00 0.00 3.86
2376 5549 6.606796 TCAAAGCCTCTAATTTATGCAATCCA 59.393 34.615 0.00 0.00 0.00 3.41
2377 5550 7.042797 TCAAAGCCTCTAATTTATGCAATCC 57.957 36.000 0.00 0.00 0.00 3.01
2378 5551 7.436376 GGTTCAAAGCCTCTAATTTATGCAATC 59.564 37.037 0.00 0.00 0.00 2.67
2379 5552 7.093377 TGGTTCAAAGCCTCTAATTTATGCAAT 60.093 33.333 0.00 0.00 0.00 3.56
2380 5553 6.210385 TGGTTCAAAGCCTCTAATTTATGCAA 59.790 34.615 0.00 0.00 0.00 4.08
2381 5554 5.714333 TGGTTCAAAGCCTCTAATTTATGCA 59.286 36.000 0.00 0.00 0.00 3.96
2382 5555 6.036470 GTGGTTCAAAGCCTCTAATTTATGC 58.964 40.000 0.00 0.00 0.00 3.14
2383 5556 7.396540 AGTGGTTCAAAGCCTCTAATTTATG 57.603 36.000 0.00 0.00 0.00 1.90
2384 5557 7.093771 CCAAGTGGTTCAAAGCCTCTAATTTAT 60.094 37.037 0.00 0.00 30.58 1.40
2385 5558 6.208599 CCAAGTGGTTCAAAGCCTCTAATTTA 59.791 38.462 0.00 0.00 30.58 1.40
2386 5559 5.011023 CCAAGTGGTTCAAAGCCTCTAATTT 59.989 40.000 0.00 0.00 30.58 1.82
2387 5560 4.524328 CCAAGTGGTTCAAAGCCTCTAATT 59.476 41.667 0.00 0.00 30.58 1.40
2388 5561 4.082125 CCAAGTGGTTCAAAGCCTCTAAT 58.918 43.478 0.00 0.00 30.58 1.73
2389 5562 3.486383 CCAAGTGGTTCAAAGCCTCTAA 58.514 45.455 0.00 0.00 30.58 2.10
2390 5563 3.140325 CCAAGTGGTTCAAAGCCTCTA 57.860 47.619 0.00 0.00 30.58 2.43
2391 5564 1.986882 CCAAGTGGTTCAAAGCCTCT 58.013 50.000 0.00 0.00 0.00 3.69
2408 5581 7.054124 ACTGATCTTGTACAAAGAAAGAACCA 58.946 34.615 10.03 5.12 33.86 3.67
2410 5583 8.142994 TGACTGATCTTGTACAAAGAAAGAAC 57.857 34.615 10.03 2.55 33.86 3.01
2412 5585 8.204160 TCTTGACTGATCTTGTACAAAGAAAGA 58.796 33.333 10.03 13.91 34.61 2.52
2417 5590 9.208022 TGTTATCTTGACTGATCTTGTACAAAG 57.792 33.333 10.03 6.62 0.00 2.77
2452 5625 5.661503 TGGGCTATGGAAATTGGAATAGA 57.338 39.130 5.97 0.00 0.00 1.98
2461 5634 8.227507 GGTATATGGATTATGGGCTATGGAAAT 58.772 37.037 0.00 0.00 0.00 2.17
2468 5641 7.822749 TTCTTGGTATATGGATTATGGGCTA 57.177 36.000 0.00 0.00 0.00 3.93
2471 5644 8.940397 AAGTTTCTTGGTATATGGATTATGGG 57.060 34.615 0.00 0.00 0.00 4.00
2487 5660 2.783440 GGCAACGCGAAGTTTCTTG 58.217 52.632 15.93 5.98 42.02 3.02
2500 5673 1.393196 GCATGGCAATAAAACGGCAAC 59.607 47.619 0.00 0.00 41.43 4.17
2582 5755 4.517285 TGAAGTTATTCCTGCTCACATCC 58.483 43.478 0.00 0.00 34.28 3.51
2583 5756 6.541641 AGATTGAAGTTATTCCTGCTCACATC 59.458 38.462 0.00 0.00 34.28 3.06
2595 5768 6.710744 ACGGTCAAGACAAGATTGAAGTTATT 59.289 34.615 2.29 0.00 38.34 1.40
2608 5784 1.410004 AGACTGGACGGTCAAGACAA 58.590 50.000 19.25 0.00 38.57 3.18
2669 5846 3.204526 GCTAATGATCTGCAGCTCAGTT 58.795 45.455 23.52 18.43 43.32 3.16
2699 5876 5.622770 AATAAAGGTACAGAAAAGTGGCG 57.377 39.130 0.00 0.00 0.00 5.69
2703 5882 9.856162 TCAAGGTAAATAAAGGTACAGAAAAGT 57.144 29.630 0.00 0.00 0.00 2.66
2724 5903 8.697507 AAGGGTAAATAGAATTAGCATCAAGG 57.302 34.615 0.00 0.00 35.50 3.61
2813 5992 6.327386 AGCATTAAGGAAGAGGATAAACCA 57.673 37.500 0.00 0.00 42.04 3.67
3043 6223 1.527034 GCATCCAGACAGTTCTTGCA 58.473 50.000 0.00 0.00 34.48 4.08
3078 6258 9.990360 TTCATGTGTTGTAATAGAACTCTAACA 57.010 29.630 2.03 0.00 31.39 2.41
3081 6261 9.639601 CACTTCATGTGTTGTAATAGAACTCTA 57.360 33.333 2.03 0.00 41.53 2.43
3123 6303 2.200067 CGCCTCTCTGCACAATTAGAG 58.800 52.381 0.00 0.00 41.36 2.43
3142 6322 4.449068 GCATGGAGGAAGTTATCATACACG 59.551 45.833 0.00 0.00 35.01 4.49
3178 6358 2.434359 GGGCCTTCTTCACGGACG 60.434 66.667 0.84 0.00 0.00 4.79
3196 6376 1.518133 GCCTCTGTACAGCTCAGCG 60.518 63.158 18.45 6.18 33.48 5.18
3208 6388 1.630878 AGACTTGGGGTTAAGCCTCTG 59.369 52.381 22.42 14.28 38.99 3.35
3320 6500 2.193536 GCAGGGTTGGAACGTTGCT 61.194 57.895 20.82 0.00 36.57 3.91
3403 6583 0.952497 CAGCTCCGACTTGCATGTGT 60.952 55.000 10.37 0.00 0.00 3.72
3433 6613 6.128282 CGTGAAGCATGTTCTTGTATACCTTT 60.128 38.462 0.00 0.00 0.00 3.11
3586 6766 3.165875 TCACTCGTCCTCTTCCTCAATT 58.834 45.455 0.00 0.00 0.00 2.32
3604 6784 0.507358 GTTGTCGAGGAACGCTTCAC 59.493 55.000 0.00 0.00 42.26 3.18
3622 6802 3.054361 CCACTACCCTTTTATGGAGCTGT 60.054 47.826 0.00 0.00 31.69 4.40
3624 6804 2.092375 GCCACTACCCTTTTATGGAGCT 60.092 50.000 0.00 0.00 31.69 4.09
3627 6807 3.589735 TCAAGCCACTACCCTTTTATGGA 59.410 43.478 0.00 0.00 31.69 3.41
3628 6808 3.947834 CTCAAGCCACTACCCTTTTATGG 59.052 47.826 0.00 0.00 0.00 2.74
3635 6815 2.174854 ACAAAACTCAAGCCACTACCCT 59.825 45.455 0.00 0.00 0.00 4.34
3650 6830 6.071616 TCCATAATAGGACCAGCAAACAAAAC 60.072 38.462 0.00 0.00 31.23 2.43
3674 6860 1.905894 GGAAGGCCCTAGGATCAGATC 59.094 57.143 11.48 1.18 0.00 2.75
3706 6892 2.035449 CCACTGTCTGTCACGAAACCTA 59.965 50.000 0.00 0.00 0.00 3.08
3715 6907 4.497291 AAAGTTTACCCACTGTCTGTCA 57.503 40.909 0.00 0.00 0.00 3.58
3738 6930 5.710099 GGTAACATCATCCAAAGAAGACCAA 59.290 40.000 0.00 0.00 0.00 3.67
3739 6931 5.014123 AGGTAACATCATCCAAAGAAGACCA 59.986 40.000 0.00 0.00 41.41 4.02
3742 6934 6.013379 AGTCAGGTAACATCATCCAAAGAAGA 60.013 38.462 0.00 0.00 41.41 2.87
3745 6937 5.762179 AGTCAGGTAACATCATCCAAAGA 57.238 39.130 0.00 0.00 41.41 2.52
3756 6948 8.812972 ACAGTTATTGAGATTAGTCAGGTAACA 58.187 33.333 10.92 0.00 34.75 2.41
3770 6962 8.621532 AAATCTTGTAGCAACAGTTATTGAGA 57.378 30.769 0.00 0.00 36.83 3.27
3888 7084 3.624900 GCCCAAACAAAGACTTTACGAC 58.375 45.455 0.00 0.00 0.00 4.34
3891 7087 3.703286 ACGCCCAAACAAAGACTTTAC 57.297 42.857 0.00 0.00 0.00 2.01
3892 7088 5.064558 TCATACGCCCAAACAAAGACTTTA 58.935 37.500 0.00 0.00 0.00 1.85
3905 7101 0.687920 TCACTGGTTTCATACGCCCA 59.312 50.000 0.00 0.00 0.00 5.36
3909 7105 6.953743 CGAGTTAATTTCACTGGTTTCATACG 59.046 38.462 0.00 0.00 0.00 3.06
3934 7132 7.201591 CCACTCATGTAGAATTTGATGTCTCAC 60.202 40.741 0.00 0.00 0.00 3.51
3935 7133 6.820152 CCACTCATGTAGAATTTGATGTCTCA 59.180 38.462 0.00 0.00 0.00 3.27
3949 7147 4.571984 TCAATTTCGATGCCACTCATGTAG 59.428 41.667 0.00 0.00 35.05 2.74
3965 7163 8.697067 CACAATCAACTGAACAAGATCAATTTC 58.303 33.333 0.00 0.00 0.00 2.17
3967 7165 7.719483 ACACAATCAACTGAACAAGATCAATT 58.281 30.769 0.00 0.00 0.00 2.32
3971 7169 7.752239 CCATAACACAATCAACTGAACAAGATC 59.248 37.037 0.00 0.00 0.00 2.75
3977 7175 6.560253 AGTCCATAACACAATCAACTGAAC 57.440 37.500 0.00 0.00 0.00 3.18
3985 7183 9.474920 TCAAAATCAAAAGTCCATAACACAATC 57.525 29.630 0.00 0.00 0.00 2.67
4038 7236 7.048629 TGAGTTGGCATCAAAATCAAAAGTA 57.951 32.000 0.00 0.00 34.28 2.24
4062 7260 0.112995 TTGTCTGGAAGGCTTGCCAT 59.887 50.000 16.49 0.98 41.06 4.40
4064 7262 0.315251 GTTTGTCTGGAAGGCTTGCC 59.685 55.000 16.49 11.84 41.06 4.52
4070 7268 8.792633 TGATAATTTAAGTGTTTGTCTGGAAGG 58.207 33.333 0.00 0.00 0.00 3.46
4079 7277 7.274250 GGCAAGAGCTGATAATTTAAGTGTTTG 59.726 37.037 0.00 0.00 41.70 2.93
4080 7278 7.315890 GGCAAGAGCTGATAATTTAAGTGTTT 58.684 34.615 0.00 0.00 41.70 2.83
4081 7279 6.856895 GGCAAGAGCTGATAATTTAAGTGTT 58.143 36.000 0.00 0.00 41.70 3.32
4488 7717 5.314306 AGGCCAAGGTCAGAATAATCCATAT 59.686 40.000 5.01 0.00 0.00 1.78
4493 7722 5.394553 CCAAAAGGCCAAGGTCAGAATAATC 60.395 44.000 5.01 0.00 0.00 1.75
4556 7785 1.134521 TGTGCAGGGATTACGACATCC 60.135 52.381 8.60 8.60 42.09 3.51
4563 7792 8.621532 TCAAGAATAATATGTGCAGGGATTAC 57.378 34.615 0.00 0.00 0.00 1.89
4581 7810 7.177216 TGGCACAAACATTCTCTAATCAAGAAT 59.823 33.333 0.00 0.00 38.64 2.40


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

AutoCloner maintained by Alex Coulton.