Multiple sequence alignment - TraesCS1B01G210300

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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 TraesCS1B01G210300 chr1B 100.000 4735 0 0 1 4735 382214601 382219335 0.000000e+00 8745
1 TraesCS1B01G210300 chr1D 95.413 4055 138 24 5 4031 281406483 281402449 0.000000e+00 6414
2 TraesCS1B01G210300 chr1D 91.803 244 10 1 4502 4735 281402013 281401770 9.820000e-87 331
3 TraesCS1B01G210300 chr1D 84.926 272 13 12 4047 4308 281402379 281402126 2.830000e-62 250
4 TraesCS1B01G210300 chr1A 95.071 3895 126 34 164 4025 353252795 353256656 0.000000e+00 6069
5 TraesCS1B01G210300 chr1A 88.088 638 42 11 4116 4733 353256876 353257499 0.000000e+00 726
6 TraesCS1B01G210300 chr6B 90.826 109 8 2 4365 4473 672366958 672367064 1.370000e-30 145
7 TraesCS1B01G210300 chr5B 85.965 114 15 1 4365 4478 103481055 103481167 2.310000e-23 121
8 TraesCS1B01G210300 chr3D 87.273 110 8 3 4365 4473 325979853 325979957 2.310000e-23 121
9 TraesCS1B01G210300 chr3B 85.965 114 15 1 4365 4478 753131537 753131649 2.310000e-23 121
10 TraesCS1B01G210300 chr5D 86.239 109 14 1 4365 4473 192080531 192080638 2.990000e-22 117
11 TraesCS1B01G210300 chr2A 86.239 109 14 1 4365 4473 40225082 40225189 2.990000e-22 117
12 TraesCS1B01G210300 chr7A 85.088 114 16 1 4365 4478 26675593 26675705 1.080000e-21 115
13 TraesCS1B01G210300 chr3A 85.088 114 16 1 4365 4478 120806223 120806111 1.080000e-21 115


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 TraesCS1B01G210300 chr1B 382214601 382219335 4734 False 8745.000000 8745 100.0000 1 4735 1 chr1B.!!$F1 4734
1 TraesCS1B01G210300 chr1D 281401770 281406483 4713 True 2331.666667 6414 90.7140 5 4735 3 chr1D.!!$R1 4730
2 TraesCS1B01G210300 chr1A 353252795 353257499 4704 False 3397.500000 6069 91.5795 164 4733 2 chr1A.!!$F1 4569

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
214 218 0.249398 AGCCCAGTTAACGCACTAGG 59.751 55.000 0.00 0.00 0.00 3.02 F
552 578 0.673644 ACTCAAGCGCGCTAAATGGT 60.674 50.000 36.73 23.31 0.00 3.55 F
1199 1225 0.796312 ATCGCGTGCCACTTTAACAG 59.204 50.000 5.77 0.00 0.00 3.16 F
2961 2992 1.378119 TTGGAGCAGCAGGAGCATG 60.378 57.895 0.00 0.00 45.49 4.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1915 1941 2.824341 CTGCCTGCTTTTGGAAGAGATT 59.176 45.455 0.0 0.0 34.71 2.40 R
2456 2487 1.312371 CCCATTACAACCCGGCACAG 61.312 60.000 0.0 0.0 0.00 3.66 R
3140 3171 2.541588 CCTGTTTCCACACAAAAGAGCG 60.542 50.000 0.0 0.0 0.00 5.03 R
4473 4732 0.029834 GCCGCCTCATGCTACATTTG 59.970 55.000 0.0 0.0 38.05 2.32 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
22 23 1.283613 TGTCTTGTTTGTGTGGGGAGT 59.716 47.619 0.00 0.00 0.00 3.85
24 25 2.876550 GTCTTGTTTGTGTGGGGAGTAC 59.123 50.000 0.00 0.00 0.00 2.73
41 42 7.349859 TGGGGAGTACCTAGTTATTTTCATCAT 59.650 37.037 0.00 0.00 40.03 2.45
65 66 8.725148 CATAACTTTGCTAGATTCAACTTGAGT 58.275 33.333 0.00 0.00 0.00 3.41
70 71 5.423015 TGCTAGATTCAACTTGAGTCATCC 58.577 41.667 14.71 4.80 35.82 3.51
81 82 4.038402 ACTTGAGTCATCCTTTGCCTTTTG 59.962 41.667 0.00 0.00 0.00 2.44
90 91 2.803956 CCTTTGCCTTTTGCTTCATGTG 59.196 45.455 0.00 0.00 42.00 3.21
106 107 5.378230 TCATGTGATTTCCTGATTAGGCT 57.622 39.130 0.00 0.00 44.22 4.58
123 124 8.623903 TGATTAGGCTAGCTGTTTCAAATAATG 58.376 33.333 15.72 0.00 0.00 1.90
133 134 7.930865 AGCTGTTTCAAATAATGTTTGGCTTAA 59.069 29.630 2.74 0.00 0.00 1.85
156 157 2.005537 CATATTTTCGCGCGCAGGC 61.006 57.895 32.61 1.90 0.00 4.85
200 201 5.758296 GTCATAATCGTAATTTCTGAGCCCA 59.242 40.000 0.00 0.00 0.00 5.36
210 214 0.320421 TCTGAGCCCAGTTAACGCAC 60.320 55.000 0.00 0.00 41.16 5.34
214 218 0.249398 AGCCCAGTTAACGCACTAGG 59.751 55.000 0.00 0.00 0.00 3.02
276 282 4.414852 CCAGCTGTTCAAATATTTGGTCG 58.585 43.478 24.40 13.35 38.66 4.79
284 290 3.997681 TCAAATATTTGGTCGACGAAGCA 59.002 39.130 24.40 5.84 38.66 3.91
382 397 5.365403 TTTTTAAAGCCCTGTATCACGTG 57.635 39.130 9.94 9.94 0.00 4.49
383 398 3.688694 TTAAAGCCCTGTATCACGTGT 57.311 42.857 16.51 5.66 0.00 4.49
387 402 1.623811 AGCCCTGTATCACGTGTTCTT 59.376 47.619 16.51 2.02 0.00 2.52
404 419 2.636830 TCTTCTGATTAGGCAAGCTGC 58.363 47.619 0.00 0.00 44.08 5.25
415 430 4.119442 AGGCAAGCTGCTTCAAATATTG 57.881 40.909 12.82 0.24 44.28 1.90
428 443 6.625081 GCTTCAAATATTGGGTTTACGAAGCT 60.625 38.462 11.84 0.00 45.76 3.74
446 461 1.123396 GCTTAATTTTCGCGCGCAAAA 59.877 42.857 29.41 30.69 0.00 2.44
522 537 2.094659 GCTGTCTCAAGCGCGCTAA 61.095 57.895 36.73 24.18 32.56 3.09
537 552 3.796717 CGCGCTAAATATGACTGAACTCA 59.203 43.478 5.56 0.00 0.00 3.41
538 553 4.267690 CGCGCTAAATATGACTGAACTCAA 59.732 41.667 5.56 0.00 0.00 3.02
540 555 5.732288 CGCTAAATATGACTGAACTCAAGC 58.268 41.667 0.00 0.00 0.00 4.01
543 558 1.629013 TATGACTGAACTCAAGCGCG 58.371 50.000 0.00 0.00 0.00 6.86
545 560 2.024319 GACTGAACTCAAGCGCGCT 61.024 57.895 31.32 31.32 0.00 5.92
552 578 0.673644 ACTCAAGCGCGCTAAATGGT 60.674 50.000 36.73 23.31 0.00 3.55
591 617 5.105228 AGGACTTTATGGGTGCAAATCAATG 60.105 40.000 0.00 0.00 0.00 2.82
598 624 5.534207 TGGGTGCAAATCAATGGATAATC 57.466 39.130 0.00 0.00 32.09 1.75
692 718 7.767198 TGATAGTTTTGGGGAATTTACTCGTAG 59.233 37.037 0.00 0.00 0.00 3.51
749 775 6.890663 TTTGCATATATTCTGTTTGCTTGC 57.109 33.333 0.00 0.00 34.47 4.01
765 791 9.231297 TGTTTGCTTGCTTTAAGATATTCTAGT 57.769 29.630 0.00 0.00 38.76 2.57
805 831 2.114825 GTTCGTCGCTTATAAGACCGG 58.885 52.381 16.85 0.00 34.10 5.28
806 832 1.382522 TCGTCGCTTATAAGACCGGT 58.617 50.000 16.85 6.92 34.10 5.28
809 835 3.376859 TCGTCGCTTATAAGACCGGTTAA 59.623 43.478 16.85 1.85 34.10 2.01
871 897 4.034048 CACCCGACCGATATTCTTTTTCTG 59.966 45.833 0.00 0.00 0.00 3.02
947 973 8.456471 GTGTAAATATTAGACTTGTTGGGGTTC 58.544 37.037 0.00 0.00 0.00 3.62
1150 1176 4.414337 ACTGGAAACTCTGATATCAGGC 57.586 45.455 28.30 14.55 43.91 4.85
1199 1225 0.796312 ATCGCGTGCCACTTTAACAG 59.204 50.000 5.77 0.00 0.00 3.16
1643 1669 4.039245 CAGTACTGAAGAGGTTTCCAGTGA 59.961 45.833 18.45 0.00 39.83 3.41
2136 2162 2.760650 TGTGCTCCTGTCTCGTATCATT 59.239 45.455 0.00 0.00 0.00 2.57
2190 2216 2.235898 GCATCTACTCCCCTCCATCATC 59.764 54.545 0.00 0.00 0.00 2.92
2197 2223 2.507058 CTCCCCTCCATCATCTTTGTGA 59.493 50.000 0.00 0.00 0.00 3.58
2237 2264 6.763135 TCTGTCTTATCTTGCCATATGTGTTC 59.237 38.462 1.24 0.00 0.00 3.18
2268 2295 9.686683 ATTTGTAGATAAATAGTTTCTGGCACT 57.313 29.630 0.00 0.00 0.00 4.40
2295 2322 4.481930 TTTACTTCCACTTGCATGTTCG 57.518 40.909 1.83 0.00 0.00 3.95
2321 2348 7.043656 GCATGTTTTTAGTTGTCAACTTACCAC 60.044 37.037 22.81 14.75 42.81 4.16
2324 2351 5.744666 TTTAGTTGTCAACTTACCACTGC 57.255 39.130 22.81 0.00 42.81 4.40
2326 2353 2.943033 AGTTGTCAACTTACCACTGCAC 59.057 45.455 12.62 0.00 39.04 4.57
2332 2359 4.798387 GTCAACTTACCACTGCACTTTTTG 59.202 41.667 0.00 0.00 0.00 2.44
2333 2360 4.461081 TCAACTTACCACTGCACTTTTTGT 59.539 37.500 0.00 0.00 0.00 2.83
2334 2361 4.632538 ACTTACCACTGCACTTTTTGTC 57.367 40.909 0.00 0.00 0.00 3.18
2357 2388 9.739276 TGTCTATTTGTTTCTATTCCTTGACAT 57.261 29.630 0.00 0.00 0.00 3.06
2388 2419 5.994668 TCCCTAACCATTGCAAAAATTCAAC 59.005 36.000 1.71 0.00 0.00 3.18
2397 2428 8.956014 CCATTGCAAAAATTCAACATTTTGTAC 58.044 29.630 1.71 0.00 44.45 2.90
2551 2582 7.497595 AGTATTTTGATAGCGGTGTAGATGAA 58.502 34.615 0.00 0.00 0.00 2.57
2554 2585 5.339008 TTGATAGCGGTGTAGATGAACTT 57.661 39.130 0.00 0.00 0.00 2.66
2575 2606 2.939460 AAAACCCGCAGCATTACATC 57.061 45.000 0.00 0.00 0.00 3.06
2668 2699 4.798387 GCCAAAGGTAATTAATCGCAACTG 59.202 41.667 0.00 0.00 0.00 3.16
2674 2705 2.549633 ATTAATCGCAACTGCTGTGC 57.450 45.000 0.00 2.77 39.32 4.57
2688 2719 4.708421 ACTGCTGTGCCATCATTTTAGAAT 59.292 37.500 0.00 0.00 0.00 2.40
2761 2792 6.604735 TTTCTTACAAGTCAGCTTTCTCAC 57.395 37.500 0.00 0.00 31.49 3.51
2815 2846 3.204306 TGTCAGGATTCATCTGATGCC 57.796 47.619 12.78 8.50 42.36 4.40
2961 2992 1.378119 TTGGAGCAGCAGGAGCATG 60.378 57.895 0.00 0.00 45.49 4.06
3140 3171 2.490115 TCACAAAACACCAGTTGACACC 59.510 45.455 0.00 0.00 38.17 4.16
3142 3173 0.454196 AAAACACCAGTTGACACCGC 59.546 50.000 0.00 0.00 38.17 5.68
3147 3178 0.180406 ACCAGTTGACACCGCTCTTT 59.820 50.000 0.00 0.00 0.00 2.52
3379 3410 4.764823 TCAGTTCTTGGTTGTTGTGTTCTT 59.235 37.500 0.00 0.00 0.00 2.52
3486 3517 1.142748 CCTAGTGAAGAGGCTGCGG 59.857 63.158 0.00 0.00 0.00 5.69
3608 3640 1.944024 TCTGCCCGTTTAACACACAAG 59.056 47.619 0.00 0.00 0.00 3.16
3609 3641 1.944024 CTGCCCGTTTAACACACAAGA 59.056 47.619 0.00 0.00 0.00 3.02
3632 3664 1.123077 TGCTCCTGTGGCACTATAGG 58.877 55.000 19.83 16.94 34.56 2.57
3704 3736 2.892640 CCTCCGATGGTGAAGCGA 59.107 61.111 0.00 0.00 0.00 4.93
3732 3764 1.455217 GATGCTCCAGCCAAGGCAT 60.455 57.895 14.40 0.00 46.24 4.40
3829 3861 6.365247 GTCTTCTGAGTTTATTTGCGTCTGTA 59.635 38.462 0.00 0.00 0.00 2.74
3968 4011 8.450180 GTTTTTGTCCAATCAACATTGAGTTTT 58.550 29.630 0.23 0.00 41.97 2.43
3969 4012 9.658799 TTTTTGTCCAATCAACATTGAGTTTTA 57.341 25.926 0.23 0.00 41.97 1.52
3970 4013 8.870160 TTTGTCCAATCAACATTGAGTTTTAG 57.130 30.769 0.23 0.00 41.97 1.85
3972 4015 8.006298 TGTCCAATCAACATTGAGTTTTAGTT 57.994 30.769 0.23 0.00 41.97 2.24
4028 4071 1.724623 TCTGTGTTTATTCTCGCGTGC 59.275 47.619 5.77 0.00 0.00 5.34
4031 4074 0.711670 TGTTTATTCTCGCGTGCGTC 59.288 50.000 14.47 0.00 40.74 5.19
4032 4075 0.024619 GTTTATTCTCGCGTGCGTCC 59.975 55.000 14.47 0.00 40.74 4.79
4033 4076 1.407721 TTTATTCTCGCGTGCGTCCG 61.408 55.000 14.47 4.57 40.74 4.79
4034 4077 2.531927 TTATTCTCGCGTGCGTCCGT 62.532 55.000 14.47 2.61 40.74 4.69
4035 4078 2.531927 TATTCTCGCGTGCGTCCGTT 62.532 55.000 14.47 0.09 40.74 4.44
4041 4084 4.953868 CGTGCGTCCGTTGGTGGA 62.954 66.667 0.00 0.00 35.04 4.02
4042 4085 2.358247 GTGCGTCCGTTGGTGGAT 60.358 61.111 0.00 0.00 40.91 3.41
4043 4086 2.047655 TGCGTCCGTTGGTGGATC 60.048 61.111 0.00 0.00 40.91 3.36
4044 4087 3.186047 GCGTCCGTTGGTGGATCG 61.186 66.667 0.00 0.00 40.91 3.69
4045 4088 2.508439 CGTCCGTTGGTGGATCGG 60.508 66.667 0.00 0.00 40.91 4.18
4049 4216 1.302192 CCGTTGGTGGATCGGTTGT 60.302 57.895 0.00 0.00 39.51 3.32
4101 4286 1.093159 GGCTGTCTGAGGCTTGAATG 58.907 55.000 0.00 0.00 44.09 2.67
4102 4287 1.612726 GGCTGTCTGAGGCTTGAATGT 60.613 52.381 0.00 0.00 44.09 2.71
4103 4288 2.157738 GCTGTCTGAGGCTTGAATGTT 58.842 47.619 0.00 0.00 0.00 2.71
4104 4289 2.555757 GCTGTCTGAGGCTTGAATGTTT 59.444 45.455 0.00 0.00 0.00 2.83
4105 4290 3.005155 GCTGTCTGAGGCTTGAATGTTTT 59.995 43.478 0.00 0.00 0.00 2.43
4106 4291 4.543692 CTGTCTGAGGCTTGAATGTTTTG 58.456 43.478 0.00 0.00 0.00 2.44
4107 4292 3.243501 TGTCTGAGGCTTGAATGTTTTGC 60.244 43.478 0.00 0.00 0.00 3.68
4108 4293 2.957680 TCTGAGGCTTGAATGTTTTGCA 59.042 40.909 0.00 0.00 0.00 4.08
4109 4294 3.054878 CTGAGGCTTGAATGTTTTGCAC 58.945 45.455 0.00 0.00 0.00 4.57
4110 4295 2.053627 GAGGCTTGAATGTTTTGCACG 58.946 47.619 0.00 0.00 0.00 5.34
4126 4311 0.392327 CACGGGCATGTGTACATCCA 60.392 55.000 0.00 0.00 33.61 3.41
4141 4327 7.497579 TGTGTACATCCATAAGCAACGAATAAT 59.502 33.333 0.00 0.00 0.00 1.28
4146 4332 6.844696 TCCATAAGCAACGAATAATGTCTC 57.155 37.500 0.00 0.00 0.00 3.36
4193 4387 2.540383 AGCTGGACTAGATGTTGGTGA 58.460 47.619 0.00 0.00 0.00 4.02
4194 4388 3.110705 AGCTGGACTAGATGTTGGTGAT 58.889 45.455 0.00 0.00 0.00 3.06
4195 4389 3.118482 AGCTGGACTAGATGTTGGTGATG 60.118 47.826 0.00 0.00 0.00 3.07
4196 4390 3.369892 GCTGGACTAGATGTTGGTGATGT 60.370 47.826 0.00 0.00 0.00 3.06
4197 4391 4.836825 CTGGACTAGATGTTGGTGATGTT 58.163 43.478 0.00 0.00 0.00 2.71
4198 4392 4.578871 TGGACTAGATGTTGGTGATGTTG 58.421 43.478 0.00 0.00 0.00 3.33
4199 4393 3.941483 GGACTAGATGTTGGTGATGTTGG 59.059 47.826 0.00 0.00 0.00 3.77
4200 4394 4.565652 GGACTAGATGTTGGTGATGTTGGT 60.566 45.833 0.00 0.00 0.00 3.67
4201 4395 4.326826 ACTAGATGTTGGTGATGTTGGTG 58.673 43.478 0.00 0.00 0.00 4.17
4246 4440 2.046314 CCGGGTGGCTCGATGTTT 60.046 61.111 0.00 0.00 0.00 2.83
4339 4582 7.122501 TCAATTTTCTTGCAGATATGCACCTAA 59.877 33.333 15.91 6.79 45.32 2.69
4379 4638 2.357034 TTCGCTCCACAACTCCGC 60.357 61.111 0.00 0.00 0.00 5.54
4380 4639 3.158537 TTCGCTCCACAACTCCGCA 62.159 57.895 0.00 0.00 0.00 5.69
4410 4669 3.461843 CGGAGCTGCAGTTCAAAAC 57.538 52.632 28.64 12.64 0.00 2.43
4412 4671 0.040067 GGAGCTGCAGTTCAAAACGG 60.040 55.000 28.64 0.00 36.23 4.44
4430 4689 1.179174 GGTGGAGTTGCAGTTTCCCC 61.179 60.000 9.80 7.48 0.00 4.81
4435 4694 2.282180 TTGCAGTTTCCCCGCTCC 60.282 61.111 0.00 0.00 0.00 4.70
4452 4711 4.803426 CGCAGACTCCGGGAGTGC 62.803 72.222 33.29 27.40 43.53 4.40
4473 4732 1.182667 GTGATTACCAAACAGGGCCC 58.817 55.000 16.46 16.46 43.89 5.80
4484 4743 0.336048 ACAGGGCCCAAATGTAGCAT 59.664 50.000 27.56 0.00 0.00 3.79
4619 4878 1.603455 CACCACCACATCCGCCTTT 60.603 57.895 0.00 0.00 0.00 3.11
4706 4978 1.712977 GCATAGCAGCAGGTCAGCAC 61.713 60.000 0.00 0.00 36.85 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.562008 TCCCCACACAAACAAGACAGA 59.438 47.619 0.00 0.00 0.00 3.41
1 2 1.949525 CTCCCCACACAAACAAGACAG 59.050 52.381 0.00 0.00 0.00 3.51
2 3 1.283613 ACTCCCCACACAAACAAGACA 59.716 47.619 0.00 0.00 0.00 3.41
3 4 2.052782 ACTCCCCACACAAACAAGAC 57.947 50.000 0.00 0.00 0.00 3.01
41 42 7.931407 TGACTCAAGTTGAATCTAGCAAAGTTA 59.069 33.333 14.84 0.00 0.00 2.24
81 82 5.506982 GCCTAATCAGGAAATCACATGAAGC 60.507 44.000 0.00 0.00 45.91 3.86
90 91 4.967036 ACAGCTAGCCTAATCAGGAAATC 58.033 43.478 12.13 0.00 45.91 2.17
106 107 6.991938 AGCCAAACATTATTTGAAACAGCTA 58.008 32.000 0.98 0.00 0.00 3.32
133 134 0.316196 GCGCGCGAAAATATGCTTCT 60.316 50.000 37.18 0.00 0.00 2.85
156 157 5.452777 TGACGCAGAACTATCATCTATTCG 58.547 41.667 0.00 0.00 0.00 3.34
162 163 5.859114 ACGATTATGACGCAGAACTATCATC 59.141 40.000 0.00 0.00 33.84 2.92
235 240 4.340381 GCTGGCCTAATGAGAAAATCACAT 59.660 41.667 3.32 0.00 41.91 3.21
284 290 0.167908 TTCATCTGCGCGCGAAAAAT 59.832 45.000 37.18 17.25 0.00 1.82
375 390 4.184629 GCCTAATCAGAAGAACACGTGAT 58.815 43.478 25.01 11.26 0.00 3.06
376 391 3.006430 TGCCTAATCAGAAGAACACGTGA 59.994 43.478 25.01 0.00 0.00 4.35
377 392 3.325870 TGCCTAATCAGAAGAACACGTG 58.674 45.455 15.48 15.48 0.00 4.49
378 393 3.678056 TGCCTAATCAGAAGAACACGT 57.322 42.857 0.00 0.00 0.00 4.49
379 394 3.181516 GCTTGCCTAATCAGAAGAACACG 60.182 47.826 0.00 0.00 0.00 4.49
380 395 4.006319 AGCTTGCCTAATCAGAAGAACAC 58.994 43.478 0.00 0.00 0.00 3.32
381 396 4.005650 CAGCTTGCCTAATCAGAAGAACA 58.994 43.478 0.00 0.00 0.00 3.18
382 397 3.181502 GCAGCTTGCCTAATCAGAAGAAC 60.182 47.826 0.00 0.00 37.42 3.01
383 398 3.012518 GCAGCTTGCCTAATCAGAAGAA 58.987 45.455 0.00 0.00 37.42 2.52
387 402 2.026915 TGAAGCAGCTTGCCTAATCAGA 60.027 45.455 13.91 0.00 46.52 3.27
404 419 6.852664 AGCTTCGTAAACCCAATATTTGAAG 58.147 36.000 0.00 0.00 34.83 3.02
415 430 4.556135 GCGAAAATTAAGCTTCGTAAACCC 59.444 41.667 17.88 2.92 44.82 4.11
428 443 2.980476 TCATTTTGCGCGCGAAAATTAA 59.020 36.364 40.85 27.53 31.96 1.40
446 461 5.306937 TCACCCGGAACTATCATGTATTCAT 59.693 40.000 0.73 0.00 34.21 2.57
522 537 2.604914 CGCGCTTGAGTTCAGTCATATT 59.395 45.455 5.56 0.00 0.00 1.28
537 552 1.241315 AACCACCATTTAGCGCGCTT 61.241 50.000 41.04 19.99 0.00 4.68
538 553 1.241315 AAACCACCATTTAGCGCGCT 61.241 50.000 38.01 38.01 0.00 5.92
540 555 0.802494 AGAAACCACCATTTAGCGCG 59.198 50.000 0.00 0.00 0.00 6.86
543 558 3.874392 ATGCAGAAACCACCATTTAGC 57.126 42.857 0.00 0.00 0.00 3.09
545 560 5.593909 CCTCATATGCAGAAACCACCATTTA 59.406 40.000 0.00 0.00 0.00 1.40
552 578 4.574674 AAGTCCTCATATGCAGAAACCA 57.425 40.909 0.00 0.00 0.00 3.67
591 617 9.860898 GCAAAATACTTCAATATGGGATTATCC 57.139 33.333 1.91 1.91 35.23 2.59
642 668 2.273370 ACATTAGCACGACGAACGAT 57.727 45.000 0.00 0.00 45.77 3.73
692 718 0.037232 ACTCTGTCGGCAGCTAAACC 60.037 55.000 13.43 0.00 42.29 3.27
805 831 5.597182 AGGAAACCTGAAAAGGGAAGTTAAC 59.403 40.000 0.00 0.00 29.57 2.01
806 832 5.773091 AGGAAACCTGAAAAGGGAAGTTAA 58.227 37.500 0.00 0.00 29.57 2.01
809 835 3.973472 AGGAAACCTGAAAAGGGAAGT 57.027 42.857 0.00 0.00 29.57 3.01
871 897 5.098218 AGACTACTTCAATATCGACGAGC 57.902 43.478 3.01 0.00 0.00 5.03
947 973 7.277539 CAGAGACTAATTCCTTCTAGCAAACTG 59.722 40.741 0.00 0.00 0.00 3.16
1150 1176 3.261580 TGCGATCTTCACCAACATACAG 58.738 45.455 0.00 0.00 0.00 2.74
1199 1225 5.605534 TCTGATAGCTCTGTAAAATCTGCC 58.394 41.667 0.00 0.00 0.00 4.85
1643 1669 4.825085 CCTTCTCGGCTCTAACTCTCTTAT 59.175 45.833 0.00 0.00 0.00 1.73
1915 1941 2.824341 CTGCCTGCTTTTGGAAGAGATT 59.176 45.455 0.00 0.00 34.71 2.40
2038 2064 4.202631 TGGACACCTAGTGGGCTTTTTAAT 60.203 41.667 0.00 0.00 37.94 1.40
2295 2322 6.975772 TGGTAAGTTGACAACTAAAAACATGC 59.024 34.615 20.85 7.28 41.91 4.06
2321 2348 7.992180 AGAAACAAATAGACAAAAAGTGCAG 57.008 32.000 0.00 0.00 0.00 4.41
2350 2381 8.408601 CAATGGTTAGGGAAGAAATATGTCAAG 58.591 37.037 0.00 0.00 0.00 3.02
2357 2388 7.546250 TTTTGCAATGGTTAGGGAAGAAATA 57.454 32.000 0.00 0.00 0.00 1.40
2358 2389 6.432403 TTTTGCAATGGTTAGGGAAGAAAT 57.568 33.333 0.00 0.00 0.00 2.17
2360 2391 5.878406 TTTTTGCAATGGTTAGGGAAGAA 57.122 34.783 0.00 0.00 0.00 2.52
2362 2393 6.229733 TGAATTTTTGCAATGGTTAGGGAAG 58.770 36.000 0.00 0.00 0.00 3.46
2363 2394 6.179906 TGAATTTTTGCAATGGTTAGGGAA 57.820 33.333 0.00 0.00 0.00 3.97
2388 2419 6.852853 CACACTGCAGAAAGTAGTACAAAATG 59.147 38.462 23.35 4.42 41.58 2.32
2397 2428 6.870965 AGAGTAATTCACACTGCAGAAAGTAG 59.129 38.462 23.35 10.33 35.87 2.57
2456 2487 1.312371 CCCATTACAACCCGGCACAG 61.312 60.000 0.00 0.00 0.00 3.66
2551 2582 3.570550 TGTAATGCTGCGGGTTTTTAAGT 59.429 39.130 0.00 0.00 0.00 2.24
2554 2585 3.181505 CGATGTAATGCTGCGGGTTTTTA 60.182 43.478 0.00 0.00 0.00 1.52
2575 2606 8.470002 TGACTATTCAGATTCATATCCCATACG 58.530 37.037 0.00 0.00 0.00 3.06
2710 2741 8.554835 TTAGATTGACATTTGTTATGAACGGA 57.445 30.769 0.00 0.00 0.00 4.69
2754 2785 6.129179 AGGGAATCTGAAACAAAGTGAGAAA 58.871 36.000 0.00 0.00 0.00 2.52
2761 2792 5.532406 TGTGAAGAGGGAATCTGAAACAAAG 59.468 40.000 0.00 0.00 38.67 2.77
2800 2831 3.139850 CAGTGAGGCATCAGATGAATCC 58.860 50.000 15.12 6.03 35.66 3.01
2961 2992 3.372206 AGACACGCAATCTGAATAACTGC 59.628 43.478 0.00 0.00 0.00 4.40
3090 3121 4.701651 CCAACATAACTGACATGACATGGT 59.298 41.667 19.39 5.28 33.60 3.55
3092 3123 4.701651 ACCCAACATAACTGACATGACATG 59.298 41.667 14.02 14.02 0.00 3.21
3140 3171 2.541588 CCTGTTTCCACACAAAAGAGCG 60.542 50.000 0.00 0.00 0.00 5.03
3142 3173 3.694072 TGTCCTGTTTCCACACAAAAGAG 59.306 43.478 0.00 0.00 0.00 2.85
3147 3178 3.289407 TCATGTCCTGTTTCCACACAA 57.711 42.857 0.00 0.00 0.00 3.33
3350 3381 5.688621 CACAACAACCAAGAACTGATGAATG 59.311 40.000 0.00 0.00 0.00 2.67
3379 3410 2.247358 GGGAAGGCCAGTTTTCAATCA 58.753 47.619 5.01 0.00 35.15 2.57
3486 3517 3.064545 GCATTCTGTCACCAACTATGAGC 59.935 47.826 0.00 0.00 0.00 4.26
3554 3585 1.673033 GCTAACAGCGCCTCAGAAGAA 60.673 52.381 2.29 0.00 0.00 2.52
3608 3640 4.402851 TGCCACAGGAGCACAATC 57.597 55.556 0.00 0.00 34.69 2.67
3620 3652 4.336889 TGTTGCTATCCTATAGTGCCAC 57.663 45.455 0.00 0.00 0.00 5.01
3621 3653 5.567037 AATGTTGCTATCCTATAGTGCCA 57.433 39.130 0.00 0.00 0.00 4.92
3714 3746 1.455217 ATGCCTTGGCTGGAGCATC 60.455 57.895 13.18 0.00 42.05 3.91
3829 3861 0.829333 AGACAGAGCGGCAGATTCAT 59.171 50.000 1.45 0.00 0.00 2.57
4009 4052 1.524986 CGCACGCGAGAATAAACACAG 60.525 52.381 15.93 0.00 42.83 3.66
4032 4075 0.601576 TGACAACCGATCCACCAACG 60.602 55.000 0.00 0.00 0.00 4.10
4033 4076 1.821216 ATGACAACCGATCCACCAAC 58.179 50.000 0.00 0.00 0.00 3.77
4034 4077 2.577606 AATGACAACCGATCCACCAA 57.422 45.000 0.00 0.00 0.00 3.67
4035 4078 2.224646 TGAAATGACAACCGATCCACCA 60.225 45.455 0.00 0.00 0.00 4.17
4036 4079 2.432444 TGAAATGACAACCGATCCACC 58.568 47.619 0.00 0.00 0.00 4.61
4037 4080 4.876107 AGTATGAAATGACAACCGATCCAC 59.124 41.667 0.00 0.00 0.00 4.02
4039 4082 5.360591 AGAGTATGAAATGACAACCGATCC 58.639 41.667 0.00 0.00 0.00 3.36
4040 4083 6.238211 CCAAGAGTATGAAATGACAACCGATC 60.238 42.308 0.00 0.00 0.00 3.69
4041 4084 5.586243 CCAAGAGTATGAAATGACAACCGAT 59.414 40.000 0.00 0.00 0.00 4.18
4042 4085 4.935205 CCAAGAGTATGAAATGACAACCGA 59.065 41.667 0.00 0.00 0.00 4.69
4043 4086 4.695455 ACCAAGAGTATGAAATGACAACCG 59.305 41.667 0.00 0.00 0.00 4.44
4044 4087 5.123979 GGACCAAGAGTATGAAATGACAACC 59.876 44.000 0.00 0.00 0.00 3.77
4045 4088 5.940470 AGGACCAAGAGTATGAAATGACAAC 59.060 40.000 0.00 0.00 0.00 3.32
4049 4216 6.373005 TTCAGGACCAAGAGTATGAAATGA 57.627 37.500 0.00 0.00 33.51 2.57
4096 4281 2.119009 TGCCCGTGCAAAACATTCA 58.881 47.368 0.00 0.00 46.66 2.57
4106 4291 1.714899 GGATGTACACATGCCCGTGC 61.715 60.000 0.00 0.00 40.73 5.34
4107 4292 0.392327 TGGATGTACACATGCCCGTG 60.392 55.000 10.81 1.29 43.00 4.94
4108 4293 0.546122 ATGGATGTACACATGCCCGT 59.454 50.000 10.81 1.04 43.00 5.28
4109 4294 2.542020 TATGGATGTACACATGCCCG 57.458 50.000 10.81 0.00 43.00 6.13
4110 4295 2.554032 GCTTATGGATGTACACATGCCC 59.446 50.000 10.81 2.84 43.00 5.36
4114 4299 4.765273 TCGTTGCTTATGGATGTACACAT 58.235 39.130 0.00 0.38 39.70 3.21
4126 4311 7.534085 TTTCGAGACATTATTCGTTGCTTAT 57.466 32.000 0.00 0.00 37.99 1.73
4199 4393 3.721370 AATCAGATGCCCCGCCCAC 62.721 63.158 0.00 0.00 0.00 4.61
4200 4394 3.419580 AATCAGATGCCCCGCCCA 61.420 61.111 0.00 0.00 0.00 5.36
4201 4395 2.908940 CAATCAGATGCCCCGCCC 60.909 66.667 0.00 0.00 0.00 6.13
4246 4440 4.631740 TGTCGAGGGGACTGGCCA 62.632 66.667 4.71 4.71 46.24 5.36
4339 4582 2.173569 AGCGCCTTAGATTCCCTTTCAT 59.826 45.455 2.29 0.00 0.00 2.57
4379 4638 3.121030 CTCCGCCAACTCCGCTTG 61.121 66.667 0.00 0.00 0.00 4.01
4394 4653 0.663153 ACCGTTTTGAACTGCAGCTC 59.337 50.000 15.27 12.53 0.00 4.09
4397 4656 1.002468 CTCCACCGTTTTGAACTGCAG 60.002 52.381 13.48 13.48 0.00 4.41
4410 4669 1.515521 GGGAAACTGCAACTCCACCG 61.516 60.000 9.84 0.00 0.00 4.94
4412 4671 1.515521 CGGGGAAACTGCAACTCCAC 61.516 60.000 9.84 5.81 0.00 4.02
4435 4694 4.803426 GCACTCCCGGAGTCTGCG 62.803 72.222 17.77 6.80 41.37 5.18
4463 4722 1.266178 GCTACATTTGGGCCCTGTTT 58.734 50.000 25.70 6.01 0.00 2.83
4473 4732 0.029834 GCCGCCTCATGCTACATTTG 59.970 55.000 0.00 0.00 38.05 2.32
4484 4743 0.887387 GTAAAACACCAGCCGCCTCA 60.887 55.000 0.00 0.00 0.00 3.86
4498 4757 4.997395 CAGACAAGAAGCTAGCAGGTAAAA 59.003 41.667 18.83 0.00 0.00 1.52
4568 4827 4.487412 GACCCGGAGTACACGCGG 62.487 72.222 12.47 11.38 0.00 6.46
4619 4878 2.124736 GGGAGCGTGGCTTATGCA 60.125 61.111 2.72 0.00 43.98 3.96
4706 4978 4.764679 TGATGATTGTTTGGTTCTTCCG 57.235 40.909 0.00 0.00 39.52 4.30


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

AutoCloner maintained by Alex Coulton.