Multiple sequence alignment - TraesCS5B01G395700

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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 TraesCS5B01G395700 chr5B 100.000 6676 0 0 1 6676 572946056 572952731 0.000000e+00 12329
1 TraesCS5B01G395700 chr5B 84.553 246 33 3 5594 5838 479631443 479631202 8.650000e-59 239
2 TraesCS5B01G395700 chr5D 96.745 6698 150 23 1 6676 465713704 465720355 0.000000e+00 11099
3 TraesCS5B01G395700 chr5D 86.531 245 29 2 5594 5838 399222956 399222716 3.970000e-67 267
4 TraesCS5B01G395700 chr5A 95.097 6710 260 30 1 6676 586144089 586150763 0.000000e+00 10504


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 TraesCS5B01G395700 chr5B 572946056 572952731 6675 False 12329 12329 100.000 1 6676 1 chr5B.!!$F1 6675
1 TraesCS5B01G395700 chr5D 465713704 465720355 6651 False 11099 11099 96.745 1 6676 1 chr5D.!!$F1 6675
2 TraesCS5B01G395700 chr5A 586144089 586150763 6674 False 10504 10504 95.097 1 6676 1 chr5A.!!$F1 6675

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
564 580 2.208132 TTTTGGATGGGTGCACGTAT 57.792 45.000 11.45 7.49 0.00 3.06 F
1032 1049 0.464193 TCATCATGGCACCATCACCG 60.464 55.000 0.00 0.00 33.90 4.94 F
1349 1366 1.427020 GCTCGAATGTGAAGCAGGC 59.573 57.895 0.00 0.00 0.00 4.85 F
2221 2238 1.912043 ACCAGAGCCTTATTCAGCTGT 59.088 47.619 14.67 0.00 40.11 4.40 F
3868 3901 1.271543 TGGAGAACTGGTGCATCCTTG 60.272 52.381 0.00 0.00 37.07 3.61 F
4189 4226 0.461693 TTGTGGCTTTGCAAACCAGC 60.462 50.000 24.63 19.32 33.12 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1647 1664 1.134580 GCCAGCACAGCAGAGATAAGA 60.135 52.381 0.00 0.00 0.00 2.10 R
2229 2246 1.799403 GATCTCAGGCTTGCATCATCG 59.201 52.381 0.00 0.00 0.00 3.84 R
3308 3341 1.689813 TCTGAGCCTTTGTACAACGGA 59.310 47.619 29.77 15.90 31.98 4.69 R
3969 4002 0.178932 AGCCCCTCCTTTGTTTTCCC 60.179 55.000 0.00 0.00 0.00 3.97 R
5222 5265 0.249784 CCACCTGGATCAGATCGCAG 60.250 60.000 16.46 16.46 37.39 5.18 R
6039 6082 0.254462 TCAATTACCCGATGCAGCCA 59.746 50.000 0.00 0.00 0.00 4.75 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
310 315 6.094048 GCATCCTGCACTTATTCTTTACTTCA 59.906 38.462 0.00 0.00 44.26 3.02
337 342 6.311055 ACACTTCTGAGAATCTTTTTCTGC 57.689 37.500 0.00 0.00 34.92 4.26
449 457 9.947433 TTTATTTCCAGAATTCTGCAATGAAAT 57.053 25.926 31.13 31.13 42.47 2.17
564 580 2.208132 TTTTGGATGGGTGCACGTAT 57.792 45.000 11.45 7.49 0.00 3.06
873 890 6.252599 TCTTTCCAGTTGCCATATATGACT 57.747 37.500 14.54 6.98 0.00 3.41
988 1005 3.264947 TGATTCAACTGCTCTTCATCGG 58.735 45.455 0.00 0.00 0.00 4.18
1032 1049 0.464193 TCATCATGGCACCATCACCG 60.464 55.000 0.00 0.00 33.90 4.94
1104 1121 2.743664 CAAGGACATTGAGAACATCGCA 59.256 45.455 0.00 0.00 41.83 5.10
1349 1366 1.427020 GCTCGAATGTGAAGCAGGC 59.573 57.895 0.00 0.00 0.00 4.85
1447 1464 3.782889 ACACCTTGAAAGCAGTTGTTC 57.217 42.857 0.00 0.00 0.00 3.18
1647 1664 2.688666 TCCATTCCAGCGGCTCCT 60.689 61.111 0.00 0.00 0.00 3.69
1875 1892 2.457598 GACATGACAGGTGTCCCTCTA 58.542 52.381 7.64 0.00 44.15 2.43
2039 2056 3.091545 GCTTGACTTTGGATGGGAATCA 58.908 45.455 0.00 0.00 0.00 2.57
2082 2099 4.860022 AGCATTTGTTATGCCCTCTTAGT 58.140 39.130 6.15 0.00 45.59 2.24
2221 2238 1.912043 ACCAGAGCCTTATTCAGCTGT 59.088 47.619 14.67 0.00 40.11 4.40
2229 2246 4.518211 AGCCTTATTCAGCTGTCAATATGC 59.482 41.667 14.67 15.12 38.11 3.14
2595 2612 4.648651 TCAGTACCCTCCTTTTTGCTAAC 58.351 43.478 0.00 0.00 0.00 2.34
2871 2898 3.423539 TGTGCTCTCAGGTAAAAGCAT 57.576 42.857 0.00 0.00 45.61 3.79
3051 3078 4.827284 TCTTGGTGGAAATGAAGGAAGTTC 59.173 41.667 0.00 0.00 35.48 3.01
3592 3625 5.682234 TTCCAGTGCTAAGATTGAGATCA 57.318 39.130 0.00 0.00 34.60 2.92
3697 3730 2.368875 TGAGGAACTTGGACTTCTGGTC 59.631 50.000 0.00 0.00 41.55 4.02
3736 3769 1.440893 CCGAGATGTCCTCAGCCAG 59.559 63.158 0.00 0.00 42.06 4.85
3748 3781 2.630098 CCTCAGCCAGCTAGCTACATTA 59.370 50.000 18.86 2.47 42.61 1.90
3762 3795 8.331742 GCTAGCTACATTAAAGTCAATCAAGAC 58.668 37.037 7.70 0.00 38.81 3.01
3808 3841 4.161189 CACAAAGAGGAGCTGGAGAAGATA 59.839 45.833 0.00 0.00 0.00 1.98
3868 3901 1.271543 TGGAGAACTGGTGCATCCTTG 60.272 52.381 0.00 0.00 37.07 3.61
3880 3913 3.052909 ATCCTTGCAGGCCAGCGAT 62.053 57.895 16.10 9.27 34.61 4.58
3969 4002 4.080863 ACTCTTACTACCAGCCATTCTTGG 60.081 45.833 0.00 0.00 46.66 3.61
4053 4086 2.789893 GGCGTCTCGAATGTGAAGATAC 59.210 50.000 0.00 0.00 0.00 2.24
4114 4147 5.009210 GCAGGTAAAAACATACACCAACAGA 59.991 40.000 0.00 0.00 33.27 3.41
4128 4161 9.817809 ATACACCAACAGATAATTACTACTGTG 57.182 33.333 16.85 10.98 41.73 3.66
4144 4177 3.149196 ACTGTGGTTTGTATCTGCCAAG 58.851 45.455 0.00 0.00 32.26 3.61
4145 4178 3.149196 CTGTGGTTTGTATCTGCCAAGT 58.851 45.455 0.00 0.00 32.26 3.16
4146 4179 2.884012 TGTGGTTTGTATCTGCCAAGTG 59.116 45.455 0.00 0.00 32.26 3.16
4150 4183 4.458989 TGGTTTGTATCTGCCAAGTGATTC 59.541 41.667 0.00 0.00 0.00 2.52
4151 4184 4.702131 GGTTTGTATCTGCCAAGTGATTCT 59.298 41.667 0.00 0.00 0.00 2.40
4152 4185 5.183904 GGTTTGTATCTGCCAAGTGATTCTT 59.816 40.000 0.00 0.00 36.75 2.52
4153 4186 6.294731 GGTTTGTATCTGCCAAGTGATTCTTT 60.295 38.462 0.00 0.00 33.63 2.52
4154 4187 6.899393 TTGTATCTGCCAAGTGATTCTTTT 57.101 33.333 0.00 0.00 33.63 2.27
4155 4188 6.500684 TGTATCTGCCAAGTGATTCTTTTC 57.499 37.500 0.00 0.00 33.63 2.29
4158 4195 6.661304 ATCTGCCAAGTGATTCTTTTCTTT 57.339 33.333 0.00 0.00 33.63 2.52
4160 4197 6.507023 TCTGCCAAGTGATTCTTTTCTTTTC 58.493 36.000 0.00 0.00 33.63 2.29
4164 4201 7.492344 TGCCAAGTGATTCTTTTCTTTTCTTTC 59.508 33.333 0.00 0.00 33.63 2.62
4166 4203 9.369904 CCAAGTGATTCTTTTCTTTTCTTTCAA 57.630 29.630 0.00 0.00 33.63 2.69
4185 4222 3.434984 TCAAAACTTGTGGCTTTGCAAAC 59.565 39.130 8.05 5.54 31.51 2.93
4186 4223 2.022764 AACTTGTGGCTTTGCAAACC 57.977 45.000 8.05 14.70 0.00 3.27
4187 4224 0.901124 ACTTGTGGCTTTGCAAACCA 59.099 45.000 21.93 21.93 0.00 3.67
4188 4225 1.134729 ACTTGTGGCTTTGCAAACCAG 60.135 47.619 24.63 18.23 33.12 4.00
4189 4226 0.461693 TTGTGGCTTTGCAAACCAGC 60.462 50.000 24.63 19.32 33.12 4.85
4213 4252 2.539274 CGCAATTGTTGTGGTTTTCTGG 59.461 45.455 7.40 0.00 37.51 3.86
4225 4264 9.059260 GTTGTGGTTTTCTGGTATTTACTCTTA 57.941 33.333 0.00 0.00 0.00 2.10
4268 4309 7.620491 TGGTTACACCTGGATATTACTTCAGTA 59.380 37.037 0.00 0.00 39.58 2.74
4273 4314 9.435570 ACACCTGGATATTACTTCAGTATAGTT 57.564 33.333 0.00 0.00 0.00 2.24
4302 4343 8.894768 ATACAGATTCGATTTTCTAAGGGAAG 57.105 34.615 0.00 0.00 35.16 3.46
4346 4389 6.015603 TGCATAACAAAATCATGTGTCTTGGA 60.016 34.615 0.00 0.00 32.81 3.53
4468 4511 2.332362 GATGTGCTTGCATGCTCCGG 62.332 60.000 23.31 0.00 0.00 5.14
4481 4524 4.994852 GCATGCTCCGGTAGAAATATTACA 59.005 41.667 11.37 0.00 0.00 2.41
4511 4554 3.067833 GAGGCTACTCCACAAGTTTGTC 58.932 50.000 0.00 0.00 39.55 3.18
4714 4757 3.503363 TGGAGTGCAGTTGAAAGCAATAG 59.497 43.478 0.00 0.00 43.20 1.73
4739 4782 4.531732 AGGCTCATCTTAAGATCAGGATCC 59.468 45.833 16.99 14.62 38.58 3.36
4748 4791 0.683973 GATCAGGATCCGACCATGCT 59.316 55.000 5.98 0.00 31.76 3.79
4760 4803 2.607526 CGACCATGCTAGAGATCTGCTG 60.608 54.545 0.00 0.00 0.00 4.41
4913 4956 3.933722 ATCCTGGGCATCGCGAGG 61.934 66.667 17.78 17.78 0.00 4.63
4928 4971 3.140225 GAGGGGCGTCGAGATGGTC 62.140 68.421 0.00 0.00 0.00 4.02
5222 5265 1.369321 GGTGGAGGATCAGATCGGC 59.631 63.158 4.23 0.00 36.25 5.54
5300 5343 4.153117 AGCAAGTTCATGAAGCTCTTAACG 59.847 41.667 8.80 0.00 0.00 3.18
5351 5394 1.500736 GTTGGGATGGGGGAGATGATT 59.499 52.381 0.00 0.00 0.00 2.57
5403 5446 0.613572 TGACTCCTCGGCCATGTACA 60.614 55.000 2.24 0.00 0.00 2.90
5407 5450 3.264897 CTCGGCCATGTACAGCGC 61.265 66.667 2.24 0.00 0.00 5.92
5408 5451 4.075854 TCGGCCATGTACAGCGCA 62.076 61.111 11.47 0.00 0.00 6.09
5492 5535 1.635817 CCAACGACATGGGGGAGGAT 61.636 60.000 0.00 0.00 36.79 3.24
5540 5583 0.627986 ATTTCCTGAGAGGGCAAGGG 59.372 55.000 0.00 0.00 35.59 3.95
5679 5722 3.317571 AGCTGCCGCTCTGAACCT 61.318 61.111 0.00 0.00 45.15 3.50
5689 5732 1.067821 GCTCTGAACCTATCCACTCCG 59.932 57.143 0.00 0.00 0.00 4.63
5764 5807 3.305950 GCTGATAGCCTGATAGGTGACAG 60.306 52.174 0.00 0.00 37.80 3.51
5777 5820 3.931578 AGGTGACAGTTGAGAATAGTGC 58.068 45.455 0.00 0.00 0.00 4.40
5778 5821 3.324846 AGGTGACAGTTGAGAATAGTGCA 59.675 43.478 0.00 0.00 0.00 4.57
5779 5822 3.681897 GGTGACAGTTGAGAATAGTGCAG 59.318 47.826 0.00 0.00 0.00 4.41
5780 5823 4.310769 GTGACAGTTGAGAATAGTGCAGT 58.689 43.478 0.00 0.00 0.00 4.40
5781 5824 4.752101 GTGACAGTTGAGAATAGTGCAGTT 59.248 41.667 0.00 0.00 0.00 3.16
5782 5825 4.751600 TGACAGTTGAGAATAGTGCAGTTG 59.248 41.667 0.00 0.00 0.00 3.16
5783 5826 4.708177 ACAGTTGAGAATAGTGCAGTTGT 58.292 39.130 0.00 0.00 0.00 3.32
5784 5827 4.512944 ACAGTTGAGAATAGTGCAGTTGTG 59.487 41.667 0.00 0.00 0.00 3.33
5785 5828 4.512944 CAGTTGAGAATAGTGCAGTTGTGT 59.487 41.667 0.00 0.00 0.00 3.72
5786 5829 4.512944 AGTTGAGAATAGTGCAGTTGTGTG 59.487 41.667 0.00 0.00 0.00 3.82
5787 5830 4.335400 TGAGAATAGTGCAGTTGTGTGA 57.665 40.909 0.00 0.00 0.00 3.58
5788 5831 4.898320 TGAGAATAGTGCAGTTGTGTGAT 58.102 39.130 0.00 0.00 0.00 3.06
5789 5832 4.692155 TGAGAATAGTGCAGTTGTGTGATG 59.308 41.667 0.00 0.00 0.00 3.07
5790 5833 3.438087 AGAATAGTGCAGTTGTGTGATGC 59.562 43.478 0.00 0.00 40.40 3.91
5845 5888 6.017192 TCTGTCAAATTGTGTGTATTCCTGTG 60.017 38.462 0.00 0.00 0.00 3.66
5937 5980 2.578021 AGGGTGTGATTTGCCTATGAGT 59.422 45.455 0.00 0.00 0.00 3.41
5938 5981 3.780294 AGGGTGTGATTTGCCTATGAGTA 59.220 43.478 0.00 0.00 0.00 2.59
5939 5982 4.413520 AGGGTGTGATTTGCCTATGAGTAT 59.586 41.667 0.00 0.00 0.00 2.12
5940 5983 5.606749 AGGGTGTGATTTGCCTATGAGTATA 59.393 40.000 0.00 0.00 0.00 1.47
6009 6052 6.203723 CCTTGGAGAAAAACAAAACACACAAA 59.796 34.615 0.00 0.00 0.00 2.83
6035 6078 0.391661 CAATGTGACTCAGGACGGGG 60.392 60.000 0.00 0.00 0.00 5.73
6036 6079 1.553690 AATGTGACTCAGGACGGGGG 61.554 60.000 0.00 0.00 0.00 5.40
6309 6356 4.066139 AGCACCCCCATGAAGGCC 62.066 66.667 0.00 0.00 35.39 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
310 315 7.174599 CAGAAAAAGATTCTCAGAAGTGTCCAT 59.825 37.037 0.00 0.00 0.00 3.41
379 385 6.210584 TGTCTTACATCACTGGTAATCACTGA 59.789 38.462 0.00 0.00 30.93 3.41
382 388 7.201644 CCATTGTCTTACATCACTGGTAATCAC 60.202 40.741 0.00 0.00 32.28 3.06
432 440 8.579006 TGTTCACTTATTTCATTGCAGAATTCT 58.421 29.630 0.88 0.88 0.00 2.40
542 558 2.733956 ACGTGCACCCATCCAAAATAT 58.266 42.857 12.15 0.00 0.00 1.28
543 559 2.208132 ACGTGCACCCATCCAAAATA 57.792 45.000 12.15 0.00 0.00 1.40
544 560 2.208132 TACGTGCACCCATCCAAAAT 57.792 45.000 12.15 0.00 0.00 1.82
545 561 2.208132 ATACGTGCACCCATCCAAAA 57.792 45.000 12.15 0.00 0.00 2.44
546 562 2.208132 AATACGTGCACCCATCCAAA 57.792 45.000 12.15 0.00 0.00 3.28
547 563 2.208132 AAATACGTGCACCCATCCAA 57.792 45.000 12.15 0.00 0.00 3.53
548 564 2.420827 CCTAAATACGTGCACCCATCCA 60.421 50.000 12.15 0.00 0.00 3.41
549 565 2.158871 TCCTAAATACGTGCACCCATCC 60.159 50.000 12.15 0.00 0.00 3.51
564 580 9.782900 TCCACTATATGTATGATCCATCCTAAA 57.217 33.333 0.00 0.00 0.00 1.85
873 890 4.402155 ACAAAACAGATTTCACAGGCAGAA 59.598 37.500 0.00 0.00 0.00 3.02
988 1005 0.618458 TCACCCATACTTGGAGGTGC 59.382 55.000 3.13 0.00 46.92 5.01
1032 1049 7.668052 ACATCTCTGATATACTCCTGGTTAGAC 59.332 40.741 0.00 0.00 0.00 2.59
1104 1121 2.558359 GTTTGCTGCAACCTGGTAGAAT 59.442 45.455 15.72 0.00 0.00 2.40
1447 1464 6.726230 CAGCTCCAATTCTACAATCATTGAG 58.274 40.000 3.79 0.00 30.66 3.02
1647 1664 1.134580 GCCAGCACAGCAGAGATAAGA 60.135 52.381 0.00 0.00 0.00 2.10
2039 2056 2.176798 TCCAATCCAACTCCACCAAAGT 59.823 45.455 0.00 0.00 0.00 2.66
2082 2099 4.343814 TGTGTCTGAAGTGGTGAGAATGTA 59.656 41.667 0.00 0.00 0.00 2.29
2221 2238 2.227149 GGCTTGCATCATCGCATATTGA 59.773 45.455 0.00 0.00 42.62 2.57
2229 2246 1.799403 GATCTCAGGCTTGCATCATCG 59.201 52.381 0.00 0.00 0.00 3.84
2296 2313 5.711976 ACCCTCTGAATGACAAAATTCGAAT 59.288 36.000 4.39 4.39 39.06 3.34
2430 2447 7.669722 AGTTTCTCATAAATTTGGCCTGTCTTA 59.330 33.333 3.32 0.00 0.00 2.10
2595 2612 7.398024 AGTATTGCCTTATTTCTGCCTATAGG 58.602 38.462 15.01 15.01 38.53 2.57
3013 3040 6.009589 TCCACCAAGATTACACATTGTCAAT 58.990 36.000 0.00 0.00 0.00 2.57
3308 3341 1.689813 TCTGAGCCTTTGTACAACGGA 59.310 47.619 29.77 15.90 31.98 4.69
3406 3439 0.880278 TTCGCAAGTGGTGAGTGAGC 60.880 55.000 0.00 0.00 37.32 4.26
3491 3524 2.622942 TCAACCTCCAGTCATGCAAAAC 59.377 45.455 0.00 0.00 0.00 2.43
3592 3625 3.627395 TTCTCCACATTATCACGCCTT 57.373 42.857 0.00 0.00 0.00 4.35
3697 3730 4.178540 GGCAGAACCATTCACAATTCATG 58.821 43.478 0.00 0.00 38.86 3.07
3736 3769 8.331742 GTCTTGATTGACTTTAATGTAGCTAGC 58.668 37.037 6.62 6.62 34.39 3.42
3748 3781 7.151308 CACTACTCTCTGTCTTGATTGACTTT 58.849 38.462 0.00 0.00 37.79 2.66
3762 3795 4.058817 GACAAAACCACCACTACTCTCTG 58.941 47.826 0.00 0.00 0.00 3.35
3808 3841 3.963222 CGCAGCTTCTCTTGCAGT 58.037 55.556 0.00 0.00 0.00 4.40
3868 3901 2.099141 TTATGATATCGCTGGCCTGC 57.901 50.000 23.78 23.78 0.00 4.85
3904 3937 5.132648 AGGGTCCTGTTCATAGCATAATTCA 59.867 40.000 0.00 0.00 0.00 2.57
3969 4002 0.178932 AGCCCCTCCTTTGTTTTCCC 60.179 55.000 0.00 0.00 0.00 3.97
4053 4086 3.620374 GTCACTTGTCAGGAGCATATGTG 59.380 47.826 4.29 0.00 0.00 3.21
4057 4090 3.834813 AGAAGTCACTTGTCAGGAGCATA 59.165 43.478 0.00 0.00 0.00 3.14
4114 4147 9.326413 GCAGATACAAACCACAGTAGTAATTAT 57.674 33.333 0.00 0.00 0.00 1.28
4124 4157 3.058016 CACTTGGCAGATACAAACCACAG 60.058 47.826 0.00 0.00 0.00 3.66
4128 4161 4.702131 AGAATCACTTGGCAGATACAAACC 59.298 41.667 0.00 0.00 0.00 3.27
4136 4169 6.322201 AGAAAAGAAAAGAATCACTTGGCAGA 59.678 34.615 0.00 0.00 38.98 4.26
4150 4183 7.746034 GCCACAAGTTTTGAAAGAAAAGAAAAG 59.254 33.333 0.00 0.00 0.00 2.27
4151 4184 7.443879 AGCCACAAGTTTTGAAAGAAAAGAAAA 59.556 29.630 0.00 0.00 0.00 2.29
4152 4185 6.934083 AGCCACAAGTTTTGAAAGAAAAGAAA 59.066 30.769 0.00 0.00 0.00 2.52
4153 4186 6.463360 AGCCACAAGTTTTGAAAGAAAAGAA 58.537 32.000 0.00 0.00 0.00 2.52
4154 4187 6.036577 AGCCACAAGTTTTGAAAGAAAAGA 57.963 33.333 0.00 0.00 0.00 2.52
4155 4188 6.726258 AAGCCACAAGTTTTGAAAGAAAAG 57.274 33.333 0.00 0.00 0.00 2.27
4158 4195 4.391523 GCAAAGCCACAAGTTTTGAAAGAA 59.608 37.500 6.24 0.00 46.41 2.52
4160 4197 3.683822 TGCAAAGCCACAAGTTTTGAAAG 59.316 39.130 6.24 0.00 46.41 2.62
4164 4201 3.746089 GTTTGCAAAGCCACAAGTTTTG 58.254 40.909 13.26 0.00 46.28 2.44
4185 4222 2.806198 CAACAATTGCGGCGCTGG 60.806 61.111 33.26 20.34 0.00 4.85
4186 4223 2.050168 ACAACAATTGCGGCGCTG 60.050 55.556 33.26 24.46 0.00 5.18
4187 4224 2.050168 CACAACAATTGCGGCGCT 60.050 55.556 33.26 11.23 0.00 5.92
4188 4225 3.105157 CCACAACAATTGCGGCGC 61.105 61.111 27.44 27.44 0.00 6.53
4189 4226 0.873743 AAACCACAACAATTGCGGCG 60.874 50.000 5.05 0.51 36.32 6.46
4196 4234 8.245195 AGTAAATACCAGAAAACCACAACAAT 57.755 30.769 0.00 0.00 0.00 2.71
4225 4264 7.430441 GTGTAACCACCAGTCAATTTATGTTT 58.570 34.615 0.00 0.00 35.44 2.83
4273 4314 9.982651 CCCTTAGAAAATCGAATCTGTATAGAA 57.017 33.333 8.51 0.00 36.32 2.10
4275 4316 9.982651 TTCCCTTAGAAAATCGAATCTGTATAG 57.017 33.333 8.51 2.68 0.00 1.31
4276 4317 9.982651 CTTCCCTTAGAAAATCGAATCTGTATA 57.017 33.333 8.51 0.00 32.88 1.47
4297 4338 2.552743 CGAACCTGGAAAGAAACTTCCC 59.447 50.000 0.00 0.00 43.78 3.97
4302 4343 2.031944 GCAGACGAACCTGGAAAGAAAC 60.032 50.000 0.00 0.00 34.82 2.78
4366 4409 9.681062 CTGTATAAATAAGGTTTTTCTCCAGGA 57.319 33.333 0.00 0.00 0.00 3.86
4397 4440 3.193267 CCACCTTTACATGGACACCATTG 59.807 47.826 0.00 0.69 42.23 2.82
4468 4511 7.171678 GCCTCACCATGTCTGTAATATTTCTAC 59.828 40.741 0.00 0.00 0.00 2.59
4481 4524 1.273267 TGGAGTAGCCTCACCATGTCT 60.273 52.381 0.00 0.00 39.64 3.41
4511 4554 3.879295 ACAAATTCAGTATCGCTGGGATG 59.121 43.478 16.51 2.74 45.08 3.51
4529 4572 4.900684 TGAACGTCATATTGGGAGACAAA 58.099 39.130 0.00 0.00 43.46 2.83
4673 4716 5.184096 ACTCCAGGTATGCTGATAATCGTAG 59.816 44.000 0.00 0.00 0.00 3.51
4676 4719 4.240888 CACTCCAGGTATGCTGATAATCG 58.759 47.826 0.00 0.00 0.00 3.34
4714 4757 5.543507 TCCTGATCTTAAGATGAGCCTTC 57.456 43.478 22.61 7.79 34.96 3.46
4739 4782 1.612950 AGCAGATCTCTAGCATGGTCG 59.387 52.381 0.00 0.00 0.00 4.79
4913 4956 3.140225 GAGGACCATCTCGACGCCC 62.140 68.421 0.00 0.00 0.00 6.13
4916 4959 0.530744 TTTGGAGGACCATCTCGACG 59.469 55.000 0.00 0.00 46.34 5.12
4928 4971 6.928492 GCTCTATTATCTTCAGTCTTTGGAGG 59.072 42.308 0.00 0.00 32.77 4.30
5078 5121 1.834263 AGGTAGAACATCTGAGGCACC 59.166 52.381 0.00 0.00 0.00 5.01
5222 5265 0.249784 CCACCTGGATCAGATCGCAG 60.250 60.000 16.46 16.46 37.39 5.18
5300 5343 2.174319 GCCGATCTTCAGGGCGAAC 61.174 63.158 0.00 0.00 37.06 3.95
5492 5535 1.451927 CTGCCTGGCCGCTTTCATA 60.452 57.895 17.53 0.00 0.00 2.15
5540 5583 0.984230 TGTCCATCCCTGTCAGAACC 59.016 55.000 0.00 0.00 0.00 3.62
5637 5680 2.820479 CTCGTCTCCTCTCGCGGT 60.820 66.667 6.13 0.00 0.00 5.68
5679 5722 3.845259 GGCACGCCGGAGTGGATA 61.845 66.667 34.76 0.00 42.09 2.59
5710 5753 4.394712 GGGAGGCACCTGTGGTCG 62.395 72.222 0.00 0.00 38.98 4.79
5764 5807 4.511454 TCACACAACTGCACTATTCTCAAC 59.489 41.667 0.00 0.00 0.00 3.18
5845 5888 4.152938 GCAAGCAAATCAATCCCAAAGAAC 59.847 41.667 0.00 0.00 0.00 3.01
6009 6052 4.690748 CGTCCTGAGTCACATTGTAAACAT 59.309 41.667 0.00 0.00 0.00 2.71
6014 6057 1.548719 CCCGTCCTGAGTCACATTGTA 59.451 52.381 0.00 0.00 0.00 2.41
6036 6079 2.624674 ATTACCCGATGCAGCCACCC 62.625 60.000 0.00 0.00 0.00 4.61
6037 6080 0.751643 AATTACCCGATGCAGCCACC 60.752 55.000 0.00 0.00 0.00 4.61
6038 6081 0.381801 CAATTACCCGATGCAGCCAC 59.618 55.000 0.00 0.00 0.00 5.01
6039 6082 0.254462 TCAATTACCCGATGCAGCCA 59.746 50.000 0.00 0.00 0.00 4.75
6552 6599 1.822186 GGTGTGGCTGTTCGTGGTT 60.822 57.895 0.00 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.