Multiple sequence alignment - TraesCS3A01G218800

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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 TraesCS3A01G218800 chr3A 100.000 4409 0 0 1 4409 401566561 401562153 0.000000e+00 8142.0
1 TraesCS3A01G218800 chr3B 96.826 3119 75 8 881 3989 397410273 397413377 0.000000e+00 5190.0
2 TraesCS3A01G218800 chr3B 89.139 267 9 4 4016 4262 397413360 397413626 9.210000e-82 315.0
3 TraesCS3A01G218800 chr3B 93.000 100 5 1 4260 4357 397413987 397414086 1.280000e-30 145.0
4 TraesCS3A01G218800 chr3B 100.000 43 0 0 4258 4300 397413943 397413985 3.660000e-11 80.5
5 TraesCS3A01G218800 chr3D 97.265 3035 63 7 902 3926 322068286 322071310 0.000000e+00 5127.0
6 TraesCS3A01G218800 chr3D 97.479 238 5 1 4018 4255 322071462 322071698 5.310000e-109 405.0
7 TraesCS3A01G218800 chr3D 74.485 388 65 24 443 808 548595360 548595735 2.140000e-28 137.0
8 TraesCS3A01G218800 chr4D 85.135 888 104 16 1 876 477919914 477919043 0.000000e+00 883.0
9 TraesCS3A01G218800 chr4D 86.819 789 87 11 1 780 70672284 70671504 0.000000e+00 865.0
10 TraesCS3A01G218800 chr5D 84.537 886 114 14 1 867 467843731 467842850 0.000000e+00 856.0
11 TraesCS3A01G218800 chrUn 85.954 776 86 10 1 762 11016210 11016976 0.000000e+00 808.0
12 TraesCS3A01G218800 chr1D 83.465 883 128 11 1 870 175038585 175039462 0.000000e+00 806.0
13 TraesCS3A01G218800 chr1B 84.841 818 102 12 1 808 630254546 630255351 0.000000e+00 804.0
14 TraesCS3A01G218800 chr5A 83.465 883 120 16 1 870 425562587 425563456 0.000000e+00 798.0
15 TraesCS3A01G218800 chr6D 82.619 886 123 21 1 867 287380245 287381118 0.000000e+00 754.0
16 TraesCS3A01G218800 chr6B 82.300 887 124 19 1 869 683574290 683573419 0.000000e+00 737.0
17 TraesCS3A01G218800 chr6B 82.432 148 13 8 4220 4357 274126271 274126415 2.790000e-22 117.0
18 TraesCS3A01G218800 chr6B 92.308 52 4 0 4358 4409 717102559 717102508 1.700000e-09 75.0
19 TraesCS3A01G218800 chr2B 77.957 186 21 11 4118 4303 373727060 373727225 1.010000e-16 99.0
20 TraesCS3A01G218800 chr7D 90.385 52 5 0 4358 4409 28334642 28334591 7.910000e-08 69.4


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 TraesCS3A01G218800 chr3A 401562153 401566561 4408 True 8142.000 8142 100.00000 1 4409 1 chr3A.!!$R1 4408
1 TraesCS3A01G218800 chr3B 397410273 397414086 3813 False 1432.625 5190 94.74125 881 4357 4 chr3B.!!$F1 3476
2 TraesCS3A01G218800 chr3D 322068286 322071698 3412 False 2766.000 5127 97.37200 902 4255 2 chr3D.!!$F2 3353
3 TraesCS3A01G218800 chr4D 477919043 477919914 871 True 883.000 883 85.13500 1 876 1 chr4D.!!$R2 875
4 TraesCS3A01G218800 chr4D 70671504 70672284 780 True 865.000 865 86.81900 1 780 1 chr4D.!!$R1 779
5 TraesCS3A01G218800 chr5D 467842850 467843731 881 True 856.000 856 84.53700 1 867 1 chr5D.!!$R1 866
6 TraesCS3A01G218800 chrUn 11016210 11016976 766 False 808.000 808 85.95400 1 762 1 chrUn.!!$F1 761
7 TraesCS3A01G218800 chr1D 175038585 175039462 877 False 806.000 806 83.46500 1 870 1 chr1D.!!$F1 869
8 TraesCS3A01G218800 chr1B 630254546 630255351 805 False 804.000 804 84.84100 1 808 1 chr1B.!!$F1 807
9 TraesCS3A01G218800 chr5A 425562587 425563456 869 False 798.000 798 83.46500 1 870 1 chr5A.!!$F1 869
10 TraesCS3A01G218800 chr6D 287380245 287381118 873 False 754.000 754 82.61900 1 867 1 chr6D.!!$F1 866
11 TraesCS3A01G218800 chr6B 683573419 683574290 871 True 737.000 737 82.30000 1 869 1 chr6B.!!$R1 868

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
796 831 0.390603 TCGATGTTTTGGGTCGCGAT 60.391 50.0 14.06 0.0 35.48 4.58 F
990 1034 1.132500 CCCTAGCTAAACCCCTCCTG 58.868 60.0 0.00 0.0 0.00 3.86 F
1848 1898 0.969917 AGGACGAGATGCTGTCTGCT 60.970 55.0 3.20 0.0 43.37 4.24 F
2126 2176 1.579084 TTGTGCGATAAACGGTGGGC 61.579 55.0 0.00 0.0 42.83 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1777 1827 1.538512 CTTGACAAGCACATCCACCAG 59.461 52.381 1.43 0.0 0.00 4.00 R
2146 2196 2.289569 GCCTAGAATCAGCCATCTCCAG 60.290 54.545 0.00 0.0 0.00 3.86 R
3203 3253 0.617820 AGGGCGTACATCCAACCTCT 60.618 55.000 4.56 0.0 0.00 3.69 R
4010 4165 0.036010 ACACACAGCTCTATGCACCC 60.036 55.000 0.00 0.0 45.94 4.61 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
162 163 4.957759 AACGGCGCTGAAATACTTTATT 57.042 36.364 25.98 0.00 0.00 1.40
182 183 4.700365 CGTGCAGTGGAGCGTCGA 62.700 66.667 0.00 0.00 36.89 4.20
287 289 2.431430 GCGGCTTTGCTTTGCTCC 60.431 61.111 0.00 0.00 0.00 4.70
296 298 1.600916 GCTTTGCTCCCGAACAGGT 60.601 57.895 0.00 0.00 38.74 4.00
305 307 2.342279 CGAACAGGTCGGCCAGAA 59.658 61.111 9.71 0.00 46.45 3.02
362 370 2.964310 GCTTCCTCCTCCAGCAGCA 61.964 63.158 0.00 0.00 33.45 4.41
531 541 2.184579 CGGCGGAACCCTCTCTTC 59.815 66.667 0.00 0.00 33.26 2.87
545 557 2.184579 CTTCTCCGGCGAGGGAAC 59.815 66.667 9.30 0.00 41.52 3.62
547 559 4.728110 TCTCCGGCGAGGGAACGA 62.728 66.667 9.30 0.00 41.52 3.85
654 678 5.682234 TCTGAATCTGGAAGTGCAAGATA 57.318 39.130 0.00 0.00 33.76 1.98
774 807 0.610785 AAATGGGCCAATTCGACGGT 60.611 50.000 11.89 0.00 0.00 4.83
781 814 1.129811 GCCAATTCGACGGTTTTCGAT 59.870 47.619 0.00 0.00 46.94 3.59
790 824 2.025898 ACGGTTTTCGATGTTTTGGGT 58.974 42.857 0.00 0.00 42.43 4.51
796 831 0.390603 TCGATGTTTTGGGTCGCGAT 60.391 50.000 14.06 0.00 35.48 4.58
850 891 4.738998 CCGAGGCATGTTGGGGCA 62.739 66.667 0.00 0.00 0.00 5.36
873 914 4.700692 ACGAGTGAAGATGCTCTAAGTACA 59.299 41.667 0.00 0.00 0.00 2.90
875 916 5.513495 CGAGTGAAGATGCTCTAAGTACAAC 59.487 44.000 0.00 0.00 0.00 3.32
876 917 6.597832 AGTGAAGATGCTCTAAGTACAACT 57.402 37.500 0.00 0.00 0.00 3.16
877 918 6.998802 AGTGAAGATGCTCTAAGTACAACTT 58.001 36.000 0.00 0.00 41.97 2.66
878 919 8.123639 AGTGAAGATGCTCTAAGTACAACTTA 57.876 34.615 0.00 0.03 39.51 2.24
879 920 8.030106 AGTGAAGATGCTCTAAGTACAACTTAC 58.970 37.037 0.00 0.00 39.51 2.34
882 923 8.709386 AAGATGCTCTAAGTACAACTTACATG 57.291 34.615 0.00 0.00 39.51 3.21
887 928 6.406624 GCTCTAAGTACAACTTACATGGGCTA 60.407 42.308 0.00 0.00 39.51 3.93
892 933 6.958767 AGTACAACTTACATGGGCTAAGAAT 58.041 36.000 8.20 0.00 0.00 2.40
945 986 1.235724 GAAGTTCTTGGGGGTCAACG 58.764 55.000 0.00 0.00 0.00 4.10
990 1034 1.132500 CCCTAGCTAAACCCCTCCTG 58.868 60.000 0.00 0.00 0.00 3.86
1848 1898 0.969917 AGGACGAGATGCTGTCTGCT 60.970 55.000 3.20 0.00 43.37 4.24
2126 2176 1.579084 TTGTGCGATAAACGGTGGGC 61.579 55.000 0.00 0.00 42.83 5.36
2201 2251 6.588756 GTCTTCACGTACAATGGTCTAATTCA 59.411 38.462 0.00 0.00 0.00 2.57
2397 2447 8.671028 GGATTTGTACCTAATGTTTTCACGTAT 58.329 33.333 0.00 0.00 0.00 3.06
2559 2609 8.066612 ACCGGATTTATGAAGTTGATGAAATT 57.933 30.769 9.46 0.00 0.00 1.82
2814 2864 1.610038 CTTCAACCTGACATTGCTGCA 59.390 47.619 0.00 0.00 0.00 4.41
3009 3059 6.606395 AGAGCATGATTAAAGAAGGAATTGCT 59.394 34.615 0.00 0.00 33.76 3.91
3180 3230 1.838112 TTGGAGACATTGATGGTGCC 58.162 50.000 0.00 0.00 42.32 5.01
3207 3257 7.052873 AGAAGTTATTGGATGACATGAAGAGG 58.947 38.462 0.00 0.00 0.00 3.69
3458 3508 5.654209 GGCTTAAGAAGATTGAAGGTTCCAT 59.346 40.000 6.67 0.00 0.00 3.41
3472 3522 3.194116 AGGTTCCATTGCATGACAACATC 59.806 43.478 0.00 0.00 42.27 3.06
3704 3755 8.272173 ACCACCAACTATATTGTGTAGCTTAAT 58.728 33.333 0.00 0.00 0.00 1.40
3748 3799 7.712639 TCCTGATGCTTTGTGATTATTCTACTC 59.287 37.037 0.00 0.00 0.00 2.59
3753 3804 9.717942 ATGCTTTGTGATTATTCTACTCTATCC 57.282 33.333 0.00 0.00 0.00 2.59
3754 3805 8.928448 TGCTTTGTGATTATTCTACTCTATCCT 58.072 33.333 0.00 0.00 0.00 3.24
3755 3806 9.771534 GCTTTGTGATTATTCTACTCTATCCTT 57.228 33.333 0.00 0.00 0.00 3.36
3768 3819 9.036980 TCTACTCTATCCTTTAAGCTTTTCTGT 57.963 33.333 3.20 0.00 0.00 3.41
3896 3947 9.716531 TTTATATATGCTTGAGATGTTCCTCAG 57.283 33.333 0.00 0.00 43.28 3.35
3980 4135 3.815856 TGGCTTCTTCTCATAGAGCTG 57.184 47.619 0.00 0.00 0.00 4.24
3984 4139 3.864583 GCTTCTTCTCATAGAGCTGTGTG 59.135 47.826 0.70 0.70 0.00 3.82
3985 4140 4.620332 GCTTCTTCTCATAGAGCTGTGTGT 60.620 45.833 7.49 0.00 0.00 3.72
3986 4141 5.474578 TTCTTCTCATAGAGCTGTGTGTT 57.525 39.130 7.49 0.00 0.00 3.32
3987 4142 5.474578 TCTTCTCATAGAGCTGTGTGTTT 57.525 39.130 7.49 0.00 0.00 2.83
3988 4143 5.473931 TCTTCTCATAGAGCTGTGTGTTTC 58.526 41.667 7.49 0.00 0.00 2.78
3989 4144 5.244851 TCTTCTCATAGAGCTGTGTGTTTCT 59.755 40.000 7.49 0.00 0.00 2.52
3990 4145 5.474578 TCTCATAGAGCTGTGTGTTTCTT 57.525 39.130 7.49 0.00 0.00 2.52
3991 4146 5.858381 TCTCATAGAGCTGTGTGTTTCTTT 58.142 37.500 7.49 0.00 0.00 2.52
3992 4147 6.291377 TCTCATAGAGCTGTGTGTTTCTTTT 58.709 36.000 7.49 0.00 0.00 2.27
3993 4148 6.767902 TCTCATAGAGCTGTGTGTTTCTTTTT 59.232 34.615 7.49 0.00 0.00 1.94
4025 4180 2.187946 GCGGGTGCATAGAGCTGT 59.812 61.111 0.00 0.00 45.94 4.40
4026 4181 2.176273 GCGGGTGCATAGAGCTGTG 61.176 63.158 0.00 0.00 45.94 3.66
4027 4182 1.219124 CGGGTGCATAGAGCTGTGT 59.781 57.895 0.00 0.00 45.94 3.72
4197 4371 6.972722 ACAACGAGTAGATTAGATTAGAGGC 58.027 40.000 0.00 0.00 0.00 4.70
4203 4377 2.900546 AGATTAGATTAGAGGCCCCGTG 59.099 50.000 0.00 0.00 0.00 4.94
4316 4854 4.504858 AGACTTCCGATGTAATGTTGGAC 58.495 43.478 0.00 0.00 0.00 4.02
4320 4858 4.022413 TCCGATGTAATGTTGGACCAAA 57.978 40.909 8.94 0.00 0.00 3.28
4327 4865 2.917713 ATGTTGGACCAAATGGCCTA 57.082 45.000 8.94 4.43 39.32 3.93
4330 4868 2.042297 TGTTGGACCAAATGGCCTATGA 59.958 45.455 8.94 0.00 39.32 2.15
4357 4897 2.754946 ATTTGCATCTTGGCACTTGG 57.245 45.000 0.00 0.00 44.86 3.61
4358 4898 1.702182 TTTGCATCTTGGCACTTGGA 58.298 45.000 0.00 0.00 44.86 3.53
4359 4899 1.250328 TTGCATCTTGGCACTTGGAG 58.750 50.000 0.00 0.00 44.86 3.86
4360 4900 1.246056 TGCATCTTGGCACTTGGAGC 61.246 55.000 0.00 0.00 39.25 4.70
4361 4901 1.246056 GCATCTTGGCACTTGGAGCA 61.246 55.000 0.00 0.00 0.00 4.26
4362 4902 1.250328 CATCTTGGCACTTGGAGCAA 58.750 50.000 0.00 0.00 0.00 3.91
4363 4903 1.068055 CATCTTGGCACTTGGAGCAAC 60.068 52.381 0.00 0.00 0.00 4.17
4364 4904 0.183492 TCTTGGCACTTGGAGCAACT 59.817 50.000 0.00 0.00 0.00 3.16
4365 4905 0.595095 CTTGGCACTTGGAGCAACTC 59.405 55.000 0.00 0.00 0.00 3.01
4366 4906 1.165907 TTGGCACTTGGAGCAACTCG 61.166 55.000 0.00 0.00 0.00 4.18
4367 4907 1.301716 GGCACTTGGAGCAACTCGA 60.302 57.895 0.00 0.00 0.00 4.04
4368 4908 0.884704 GGCACTTGGAGCAACTCGAA 60.885 55.000 0.00 0.00 0.00 3.71
4369 4909 0.235926 GCACTTGGAGCAACTCGAAC 59.764 55.000 0.00 0.00 0.00 3.95
4370 4910 0.508641 CACTTGGAGCAACTCGAACG 59.491 55.000 0.00 0.00 0.00 3.95
4371 4911 0.600255 ACTTGGAGCAACTCGAACGG 60.600 55.000 0.00 0.00 0.00 4.44
4372 4912 1.291877 CTTGGAGCAACTCGAACGGG 61.292 60.000 0.00 0.00 0.00 5.28
4373 4913 2.035237 TTGGAGCAACTCGAACGGGT 62.035 55.000 0.00 0.00 0.00 5.28
4374 4914 1.737008 GGAGCAACTCGAACGGGTC 60.737 63.158 0.00 0.00 0.00 4.46
4389 4929 3.357504 GGTCGACCCAAATAGACGG 57.642 57.895 24.75 0.00 34.68 4.79
4390 4930 0.808847 GGTCGACCCAAATAGACGGC 60.809 60.000 24.75 0.00 34.68 5.68
4391 4931 1.140161 TCGACCCAAATAGACGGCG 59.860 57.895 4.80 4.80 0.00 6.46
4392 4932 1.140161 CGACCCAAATAGACGGCGA 59.860 57.895 16.62 0.00 0.00 5.54
4393 4933 0.249322 CGACCCAAATAGACGGCGAT 60.249 55.000 16.62 3.89 0.00 4.58
4394 4934 1.805120 CGACCCAAATAGACGGCGATT 60.805 52.381 16.62 0.00 0.00 3.34
4395 4935 2.285977 GACCCAAATAGACGGCGATTT 58.714 47.619 16.62 3.19 30.75 2.17
4396 4936 2.285977 ACCCAAATAGACGGCGATTTC 58.714 47.619 16.62 0.00 28.56 2.17
4397 4937 1.260561 CCCAAATAGACGGCGATTTCG 59.739 52.381 16.62 0.12 43.27 3.46
4398 4938 1.931172 CCAAATAGACGGCGATTTCGT 59.069 47.619 16.62 0.00 44.03 3.85
4404 4944 3.161817 CGGCGATTTCGTCCGTTT 58.838 55.556 20.13 0.00 46.11 3.60
4405 4945 1.494189 CGGCGATTTCGTCCGTTTT 59.506 52.632 20.13 0.00 46.11 2.43
4406 4946 0.110554 CGGCGATTTCGTCCGTTTTT 60.111 50.000 20.13 0.00 46.11 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 3.005897 AGAAGTGCACGACAACTATGAGT 59.994 43.478 12.01 0.00 0.00 3.41
65 66 1.728971 CGGCTACTTCAAGTGCAAGAG 59.271 52.381 0.00 0.00 0.00 2.85
269 271 2.431430 GAGCAAAGCAAAGCCGCC 60.431 61.111 0.00 0.00 0.00 6.13
280 282 1.301401 CGACCTGTTCGGGAGCAAA 60.301 57.895 4.54 0.00 44.60 3.68
305 307 1.758514 ATCTCATGGTCCTCGCCGT 60.759 57.895 0.00 0.00 0.00 5.68
531 541 3.486252 GATCGTTCCCTCGCCGGAG 62.486 68.421 5.05 0.00 40.14 4.63
545 557 0.179187 CACCGCCGCTAGATAGATCG 60.179 60.000 0.00 0.00 0.00 3.69
547 559 1.251527 CCCACCGCCGCTAGATAGAT 61.252 60.000 0.00 0.00 0.00 1.98
631 655 4.564782 TCTTGCACTTCCAGATTCAGAT 57.435 40.909 0.00 0.00 0.00 2.90
632 656 4.564782 ATCTTGCACTTCCAGATTCAGA 57.435 40.909 0.00 0.00 0.00 3.27
633 657 5.426504 AGTATCTTGCACTTCCAGATTCAG 58.573 41.667 3.29 0.00 0.00 3.02
654 678 2.556622 CACCATTGTTAGGCGGAAAAGT 59.443 45.455 0.00 0.00 0.00 2.66
739 772 2.034999 TTTTTGGCCCGGCGATCT 59.965 55.556 9.30 0.00 0.00 2.75
770 803 2.025898 ACCCAAAACATCGAAAACCGT 58.974 42.857 0.00 0.00 39.75 4.83
774 807 1.334239 CGCGACCCAAAACATCGAAAA 60.334 47.619 0.00 0.00 38.10 2.29
781 814 1.270947 ACCTAATCGCGACCCAAAACA 60.271 47.619 12.93 0.00 0.00 2.83
832 869 4.424711 GCCCCAACATGCCTCGGA 62.425 66.667 0.00 0.00 0.00 4.55
834 871 3.443045 GTGCCCCAACATGCCTCG 61.443 66.667 0.00 0.00 0.00 4.63
873 914 6.321821 TGGTATTCTTAGCCCATGTAAGTT 57.678 37.500 0.00 0.00 0.00 2.66
875 916 6.808008 CATGGTATTCTTAGCCCATGTAAG 57.192 41.667 8.92 0.00 45.97 2.34
882 923 3.139077 CGTTCCATGGTATTCTTAGCCC 58.861 50.000 12.58 0.00 0.00 5.19
887 928 4.553330 ACTGTCGTTCCATGGTATTCTT 57.447 40.909 12.58 0.00 0.00 2.52
892 933 2.105134 ACCAAACTGTCGTTCCATGGTA 59.895 45.455 12.58 0.00 39.04 3.25
898 939 0.041576 GCGAACCAAACTGTCGTTCC 60.042 55.000 8.76 1.62 33.81 3.62
927 968 0.549469 ACGTTGACCCCCAAGAACTT 59.451 50.000 0.00 0.00 35.03 2.66
1671 1721 2.738139 CACAGTGCCGCGATCACA 60.738 61.111 25.40 9.89 36.93 3.58
1777 1827 1.538512 CTTGACAAGCACATCCACCAG 59.461 52.381 1.43 0.00 0.00 4.00
1848 1898 2.513753 ACGACATCCATTTTCTTGCCA 58.486 42.857 0.00 0.00 0.00 4.92
2126 2176 3.124806 CAGACACAAGCTTACAGCATCTG 59.875 47.826 0.00 3.50 45.56 2.90
2146 2196 2.289569 GCCTAGAATCAGCCATCTCCAG 60.290 54.545 0.00 0.00 0.00 3.86
2814 2864 9.651913 CAAAACCCACTTATTAAAGCATTGTAT 57.348 29.630 0.00 0.00 36.05 2.29
3009 3059 6.605995 AGGTAGTGTATGTTACTGTATCAGCA 59.394 38.462 5.01 4.11 34.37 4.41
3121 3171 5.176958 GTGTTAACGCTGTGAAAGTGATACT 59.823 40.000 11.93 0.00 38.83 2.12
3122 3172 5.050634 TGTGTTAACGCTGTGAAAGTGATAC 60.051 40.000 19.29 0.00 38.83 2.24
3180 3230 8.272545 TCTTCATGTCATCCAATAACTTCTTG 57.727 34.615 0.00 0.00 0.00 3.02
3203 3253 0.617820 AGGGCGTACATCCAACCTCT 60.618 55.000 4.56 0.00 0.00 3.69
3207 3257 1.602377 GCATTAGGGCGTACATCCAAC 59.398 52.381 4.56 0.00 0.00 3.77
3362 3412 1.187087 ACTGTCACCTTCCGGAGATC 58.813 55.000 3.34 0.00 32.39 2.75
3442 3492 4.773674 TCATGCAATGGAACCTTCAATCTT 59.226 37.500 0.00 0.00 46.73 2.40
3452 3502 3.173599 CGATGTTGTCATGCAATGGAAC 58.826 45.455 0.00 0.00 46.73 3.62
3458 3508 1.902938 TTCCCGATGTTGTCATGCAA 58.097 45.000 0.00 0.00 34.06 4.08
3472 3522 9.184062 GGTTTTACTTTATTTAACAGTTTCCCG 57.816 33.333 0.00 0.00 0.00 5.14
3598 3649 8.948631 TTCCTGTATCAAGCTCTTATACTTTG 57.051 34.615 11.92 0.00 0.00 2.77
3704 3755 7.485810 CATCAGGAACAATGCAGATATCAAAA 58.514 34.615 5.32 0.00 0.00 2.44
3748 3799 7.596749 TTCGACAGAAAAGCTTAAAGGATAG 57.403 36.000 0.00 0.00 32.65 2.08
3751 3802 9.314321 CTATATTCGACAGAAAAGCTTAAAGGA 57.686 33.333 0.00 0.00 40.15 3.36
3752 3803 8.064814 GCTATATTCGACAGAAAAGCTTAAAGG 58.935 37.037 0.00 0.00 40.15 3.11
3753 3804 8.604035 TGCTATATTCGACAGAAAAGCTTAAAG 58.396 33.333 0.00 0.00 40.15 1.85
3754 3805 8.487313 TGCTATATTCGACAGAAAAGCTTAAA 57.513 30.769 0.00 0.00 40.15 1.52
3755 3806 8.487313 TTGCTATATTCGACAGAAAAGCTTAA 57.513 30.769 0.00 0.00 40.15 1.85
3756 3807 8.487313 TTTGCTATATTCGACAGAAAAGCTTA 57.513 30.769 0.00 0.00 40.15 3.09
3757 3808 6.985188 TTGCTATATTCGACAGAAAAGCTT 57.015 33.333 0.00 0.00 40.15 3.74
3768 3819 4.574828 GCCTCAAGGTTTTGCTATATTCGA 59.425 41.667 0.00 0.00 37.57 3.71
3850 3901 4.766404 AATTGAAACGTCCAGTTCATCC 57.234 40.909 1.48 0.00 43.37 3.51
3896 3947 5.967088 TGTAACCTGTAAGATCAGAAGAGC 58.033 41.667 0.00 0.00 37.61 4.09
3963 4118 5.070770 ACACACAGCTCTATGAGAAGAAG 57.929 43.478 0.00 0.00 0.00 2.85
4008 4163 2.176273 CACAGCTCTATGCACCCGC 61.176 63.158 0.00 0.00 45.94 6.13
4009 4164 1.086067 CACACAGCTCTATGCACCCG 61.086 60.000 0.00 0.00 45.94 5.28
4010 4165 0.036010 ACACACAGCTCTATGCACCC 60.036 55.000 0.00 0.00 45.94 4.61
4011 4166 1.813513 AACACACAGCTCTATGCACC 58.186 50.000 0.00 0.00 45.94 5.01
4012 4167 2.159787 CGAAACACACAGCTCTATGCAC 60.160 50.000 0.00 0.00 45.94 4.57
4013 4168 2.068519 CGAAACACACAGCTCTATGCA 58.931 47.619 0.00 0.00 45.94 3.96
4014 4169 2.069273 ACGAAACACACAGCTCTATGC 58.931 47.619 0.00 0.00 43.29 3.14
4015 4170 4.486090 ACTACGAAACACACAGCTCTATG 58.514 43.478 0.00 0.00 0.00 2.23
4016 4171 4.785511 ACTACGAAACACACAGCTCTAT 57.214 40.909 0.00 0.00 0.00 1.98
4017 4172 5.694231 TTACTACGAAACACACAGCTCTA 57.306 39.130 0.00 0.00 0.00 2.43
4018 4173 4.579454 TTACTACGAAACACACAGCTCT 57.421 40.909 0.00 0.00 0.00 4.09
4019 4174 7.521509 AATATTACTACGAAACACACAGCTC 57.478 36.000 0.00 0.00 0.00 4.09
4020 4175 8.248945 ACTAATATTACTACGAAACACACAGCT 58.751 33.333 0.00 0.00 0.00 4.24
4021 4176 8.403606 ACTAATATTACTACGAAACACACAGC 57.596 34.615 0.00 0.00 0.00 4.40
4316 4854 9.480053 CAAATTTATTACTCATAGGCCATTTGG 57.520 33.333 5.01 0.00 38.53 3.28
4320 4858 7.838079 TGCAAATTTATTACTCATAGGCCAT 57.162 32.000 5.01 0.00 0.00 4.40
4327 4865 7.707893 GTGCCAAGATGCAAATTTATTACTCAT 59.292 33.333 0.00 0.00 44.11 2.90
4330 4868 7.174107 AGTGCCAAGATGCAAATTTATTACT 57.826 32.000 0.00 0.00 44.11 2.24
4357 4897 3.857909 GACCCGTTCGAGTTGCTC 58.142 61.111 0.00 0.00 0.00 4.26
4371 4911 0.808847 GCCGTCTATTTGGGTCGACC 60.809 60.000 27.04 27.04 40.81 4.79
4372 4912 1.143969 CGCCGTCTATTTGGGTCGAC 61.144 60.000 7.13 7.13 0.00 4.20
4373 4913 1.140161 CGCCGTCTATTTGGGTCGA 59.860 57.895 0.00 0.00 0.00 4.20
4374 4914 0.249322 ATCGCCGTCTATTTGGGTCG 60.249 55.000 0.00 0.00 0.00 4.79
4375 4915 1.949465 AATCGCCGTCTATTTGGGTC 58.051 50.000 0.00 0.00 0.00 4.46
4376 4916 2.285977 GAAATCGCCGTCTATTTGGGT 58.714 47.619 0.00 0.00 0.00 4.51
4377 4917 1.260561 CGAAATCGCCGTCTATTTGGG 59.739 52.381 0.00 0.00 0.00 4.12
4378 4918 1.931172 ACGAAATCGCCGTCTATTTGG 59.069 47.619 2.15 0.00 44.43 3.28
4388 4928 3.759550 AAAAACGGACGAAATCGCC 57.240 47.368 2.15 4.66 44.43 5.54


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

AutoCloner maintained by Alex Coulton.