Multiple sequence alignment - TraesCS5D01G120400

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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 TraesCS5D01G120400 chr5D 100.000 4073 0 0 1 4073 170317661 170313589 0.000000e+00 7522.0
1 TraesCS5D01G120400 chr5B 95.691 3922 116 20 1 3891 162494418 162490519 0.000000e+00 6257.0
2 TraesCS5D01G120400 chr5A 96.137 3598 94 16 1 3568 176445915 176449497 0.000000e+00 5832.0
3 TraesCS5D01G120400 chr5A 85.519 366 47 3 3625 3987 176449836 176450198 1.070000e-100 377.0
4 TraesCS5D01G120400 chr6D 77.966 177 29 9 3815 3986 472524544 472524373 7.200000e-18 102.0
5 TraesCS5D01G120400 chr6D 100.000 35 0 0 3882 3916 465799484 465799450 9.450000e-07 65.8
6 TraesCS5D01G120400 chr1B 81.395 86 12 4 3869 3952 588847326 588847409 2.630000e-07 67.6


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 TraesCS5D01G120400 chr5D 170313589 170317661 4072 True 7522.0 7522 100.000 1 4073 1 chr5D.!!$R1 4072
1 TraesCS5D01G120400 chr5B 162490519 162494418 3899 True 6257.0 6257 95.691 1 3891 1 chr5B.!!$R1 3890
2 TraesCS5D01G120400 chr5A 176445915 176450198 4283 False 3104.5 5832 90.828 1 3987 2 chr5A.!!$F1 3986

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
630 640 0.597637 GGAGATCACGGCCGTGTATG 60.598 60.000 46.56 29.17 45.55 2.39 F
1529 1548 1.473434 GCCATGAGGACTAGTTTCCCG 60.473 57.143 0.00 0.00 36.12 5.14 F
1815 1838 0.900182 TCTCCGATCCGCCAGCATAT 60.900 55.000 0.00 0.00 0.00 1.78 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1554 1573 1.295423 CAAGGTCACGTAGGGGTGG 59.705 63.158 0.0 0.0 38.46 4.61 R
2721 2744 0.625316 CCATGACATTCCCCTCCACA 59.375 55.000 0.0 0.0 0.00 4.17 R
3672 3996 0.468226 TGCTAGGGATGGGTTTAGCG 59.532 55.000 0.0 0.0 41.00 4.26 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
49 50 1.133761 ACCCCTCGATCTGATCTCGAA 60.134 52.381 15.16 0.00 43.85 3.71
52 53 2.159585 CCCTCGATCTGATCTCGAATCG 60.160 54.545 15.16 8.29 43.85 3.34
273 274 3.898123 TGGTGGCTCTGAGATCCTATTAC 59.102 47.826 9.28 0.00 0.00 1.89
375 376 2.688446 CTCATCGCCAGTAAGTAGTCCA 59.312 50.000 0.00 0.00 0.00 4.02
435 438 3.477210 AGATCTAAAATCGACCAGGCC 57.523 47.619 0.00 0.00 0.00 5.19
437 440 3.456277 AGATCTAAAATCGACCAGGCCTT 59.544 43.478 0.00 0.00 0.00 4.35
440 443 2.286365 AAAATCGACCAGGCCTTGAA 57.714 45.000 11.55 0.00 0.00 2.69
441 444 1.534729 AAATCGACCAGGCCTTGAAC 58.465 50.000 11.55 3.47 0.00 3.18
442 445 0.693049 AATCGACCAGGCCTTGAACT 59.307 50.000 11.55 0.00 0.00 3.01
460 463 7.441458 CCTTGAACTATCGGGACCTTAATTTAG 59.559 40.741 0.00 0.00 0.00 1.85
498 501 3.246619 TGCGGCGAATTTAATTTTGACC 58.753 40.909 12.98 2.61 0.00 4.02
630 640 0.597637 GGAGATCACGGCCGTGTATG 60.598 60.000 46.56 29.17 45.55 2.39
873 886 8.978564 TTGCAATTGGTATAAGTAACACAATG 57.021 30.769 7.72 0.00 0.00 2.82
903 916 5.188327 TCTTCAAGATGTGTAGCTATCGG 57.812 43.478 0.00 0.00 0.00 4.18
908 921 5.826208 TCAAGATGTGTAGCTATCGGTCTAA 59.174 40.000 0.00 0.00 0.00 2.10
1043 1056 1.812571 GGTTTATGTGAGGCACCACTG 59.187 52.381 10.57 0.00 37.89 3.66
1269 1282 8.752187 TCCTAATTTTGGAATTTCAGAATGGAG 58.248 33.333 3.35 4.73 36.82 3.86
1502 1520 5.072741 ACACTTTGCTTCCATACACTTGAT 58.927 37.500 0.00 0.00 0.00 2.57
1529 1548 1.473434 GCCATGAGGACTAGTTTCCCG 60.473 57.143 0.00 0.00 36.12 5.14
1554 1573 8.989980 CGAAAGGGTTCTATTAAATCTATCCAC 58.010 37.037 0.00 0.00 0.00 4.02
1591 1610 7.940688 TGACCTTGTTATGCATGATTGAGATAT 59.059 33.333 10.16 0.00 0.00 1.63
1598 1617 8.680001 GTTATGCATGATTGAGATATTATGGCA 58.320 33.333 10.16 0.00 0.00 4.92
1667 1686 1.610522 GGATGTCCATTACTGCCATGC 59.389 52.381 0.00 0.00 35.64 4.06
1732 1755 6.656902 TCCATTTCAGCTGTATCTGAGAAAT 58.343 36.000 14.67 6.76 43.23 2.17
1815 1838 0.900182 TCTCCGATCCGCCAGCATAT 60.900 55.000 0.00 0.00 0.00 1.78
2071 2094 6.982724 TGATGTGTCATCATCTTCTCACATAC 59.017 38.462 8.14 4.47 43.41 2.39
2178 2201 3.311322 TGAAACCTGTTTGCTGTAAGACG 59.689 43.478 0.00 0.00 30.64 4.18
2408 2431 2.414806 GAACTTCTGGGACGAACTTCC 58.585 52.381 0.00 0.00 34.52 3.46
2721 2744 2.694628 TGACAGGCAAGAAAATTGCTGT 59.305 40.909 11.90 12.88 44.36 4.40
2925 2948 1.750778 CATGGATACTTTGGTGGCCAC 59.249 52.381 28.57 28.57 34.50 5.01
2964 2987 3.560068 GGGATATTGGTTTCAGTAGCGTG 59.440 47.826 0.00 0.00 0.00 5.34
3427 3469 4.942761 TGCTTTCCTTGCATCTTTTCTT 57.057 36.364 0.00 0.00 35.31 2.52
3473 3515 3.583086 AGCAGGGTTGTGTTACTATGAGT 59.417 43.478 0.00 0.00 0.00 3.41
3531 3573 4.273969 CGGTTCTAGGTTGCACAAGTTTTA 59.726 41.667 0.00 0.00 0.00 1.52
3532 3574 5.516996 GGTTCTAGGTTGCACAAGTTTTAC 58.483 41.667 0.00 0.00 0.00 2.01
3540 3582 2.757868 TGCACAAGTTTTACTGGCAAGT 59.242 40.909 0.00 0.00 40.67 3.16
3541 3583 3.194542 TGCACAAGTTTTACTGGCAAGTT 59.805 39.130 0.00 0.00 37.88 2.66
3542 3584 4.180817 GCACAAGTTTTACTGGCAAGTTT 58.819 39.130 0.00 0.00 37.88 2.66
3658 3982 2.999185 TCTTTGAAAAGCCCATCCCT 57.001 45.000 0.00 0.00 35.99 4.20
3672 3996 3.181433 CCCATCCCTACTTTTGATACCCC 60.181 52.174 0.00 0.00 0.00 4.95
3732 4059 1.697432 TGGATGGTTCGGAGAACAGTT 59.303 47.619 13.89 0.00 45.90 3.16
3735 4062 1.948104 TGGTTCGGAGAACAGTTGTG 58.052 50.000 13.89 0.00 45.90 3.33
3753 4080 2.258109 GTGTCCCTTCAAGTCCTAGGT 58.742 52.381 9.08 0.00 0.00 3.08
3839 4166 1.978580 AGAAGACATTCCCACCGACTT 59.021 47.619 0.00 0.00 35.94 3.01
3846 4173 3.691342 CCCACCGACTTCGAGGCA 61.691 66.667 0.00 0.00 43.02 4.75
3847 4174 2.579201 CCACCGACTTCGAGGCAT 59.421 61.111 0.00 0.00 43.02 4.40
3861 4188 3.638627 TCGAGGCATGTATGATGACTTCT 59.361 43.478 0.00 0.00 37.55 2.85
3888 4215 5.878332 TCAATGTTAATATGCTATGCCGG 57.122 39.130 0.00 0.00 0.00 6.13
3894 4221 0.979665 ATATGCTATGCCGGCTCAGT 59.020 50.000 29.70 13.44 0.00 3.41
3897 4224 1.300542 GCTATGCCGGCTCAGTCTC 60.301 63.158 29.70 7.98 0.00 3.36
3899 4226 0.749649 CTATGCCGGCTCAGTCTCTT 59.250 55.000 29.70 3.51 0.00 2.85
3907 4234 1.346068 GGCTCAGTCTCTTGAAGGTGT 59.654 52.381 0.00 0.00 0.00 4.16
3909 4236 3.063485 GCTCAGTCTCTTGAAGGTGTTC 58.937 50.000 0.00 0.00 0.00 3.18
3919 4246 3.695830 TGAAGGTGTTCATAGGGTCAC 57.304 47.619 0.00 0.00 37.79 3.67
3927 4254 3.386402 TGTTCATAGGGTCACGATATGCA 59.614 43.478 0.00 0.00 0.00 3.96
3929 4256 4.192429 TCATAGGGTCACGATATGCATG 57.808 45.455 10.16 0.00 0.00 4.06
3931 4258 0.601046 AGGGTCACGATATGCATGCG 60.601 55.000 14.09 18.40 0.00 4.73
3938 4265 2.545731 ACGATATGCATGCGTGTGTTA 58.454 42.857 22.77 1.82 36.83 2.41
3939 4266 2.933260 ACGATATGCATGCGTGTGTTAA 59.067 40.909 22.77 1.00 36.83 2.01
3940 4267 3.559655 ACGATATGCATGCGTGTGTTAAT 59.440 39.130 22.77 6.48 36.83 1.40
3949 4276 3.845178 TGCGTGTGTTAATAGAGGTGAG 58.155 45.455 0.00 0.00 0.00 3.51
3959 4286 4.576216 AATAGAGGTGAGTGTATGCTCG 57.424 45.455 0.00 0.00 38.28 5.03
3962 4289 0.108615 AGGTGAGTGTATGCTCGTGC 60.109 55.000 1.71 1.71 38.28 5.34
3981 4308 3.246226 GTGCATGTAAGCGATTTCGATCT 59.754 43.478 3.77 0.00 43.02 2.75
3987 4314 4.503007 TGTAAGCGATTTCGATCTTACTGC 59.497 41.667 20.73 1.85 41.31 4.40
3988 4315 2.120232 AGCGATTTCGATCTTACTGCG 58.880 47.619 3.77 0.00 43.02 5.18
3989 4316 2.117137 GCGATTTCGATCTTACTGCGA 58.883 47.619 3.77 0.00 43.02 5.10
3990 4317 2.726760 GCGATTTCGATCTTACTGCGAT 59.273 45.455 3.77 0.00 43.02 4.58
3991 4318 3.182572 GCGATTTCGATCTTACTGCGATT 59.817 43.478 3.77 0.00 43.02 3.34
3992 4319 4.318121 GCGATTTCGATCTTACTGCGATTT 60.318 41.667 3.77 0.00 43.02 2.17
3993 4320 5.358691 CGATTTCGATCTTACTGCGATTTC 58.641 41.667 0.00 0.00 43.02 2.17
3994 4321 4.755191 TTTCGATCTTACTGCGATTTCG 57.245 40.909 0.00 0.00 43.27 3.46
3995 4322 3.685836 TCGATCTTACTGCGATTTCGA 57.314 42.857 3.77 0.00 43.02 3.71
3996 4323 4.224715 TCGATCTTACTGCGATTTCGAT 57.775 40.909 3.77 0.00 43.02 3.59
3997 4324 4.219802 TCGATCTTACTGCGATTTCGATC 58.780 43.478 3.77 0.00 43.02 3.69
3998 4325 3.975035 CGATCTTACTGCGATTTCGATCA 59.025 43.478 3.77 0.00 43.02 2.92
3999 4326 4.618912 CGATCTTACTGCGATTTCGATCAT 59.381 41.667 3.77 0.00 43.02 2.45
4000 4327 5.795441 CGATCTTACTGCGATTTCGATCATA 59.205 40.000 3.77 0.00 43.02 2.15
4001 4328 6.470556 CGATCTTACTGCGATTTCGATCATAT 59.529 38.462 3.77 0.00 43.02 1.78
4002 4329 7.008719 CGATCTTACTGCGATTTCGATCATATT 59.991 37.037 3.77 0.00 43.02 1.28
4003 4330 7.338440 TCTTACTGCGATTTCGATCATATTG 57.662 36.000 3.77 0.00 43.02 1.90
4004 4331 6.923508 TCTTACTGCGATTTCGATCATATTGT 59.076 34.615 3.77 0.00 43.02 2.71
4005 4332 5.991328 ACTGCGATTTCGATCATATTGTT 57.009 34.783 3.77 0.00 43.02 2.83
4006 4333 6.363577 ACTGCGATTTCGATCATATTGTTT 57.636 33.333 3.77 0.00 43.02 2.83
4007 4334 6.422223 ACTGCGATTTCGATCATATTGTTTC 58.578 36.000 3.77 0.00 43.02 2.78
4008 4335 6.037062 ACTGCGATTTCGATCATATTGTTTCA 59.963 34.615 3.77 0.00 43.02 2.69
4009 4336 6.780127 TGCGATTTCGATCATATTGTTTCAA 58.220 32.000 3.77 0.00 43.02 2.69
4010 4337 7.247019 TGCGATTTCGATCATATTGTTTCAAA 58.753 30.769 3.77 0.00 43.02 2.69
4011 4338 7.218014 TGCGATTTCGATCATATTGTTTCAAAC 59.782 33.333 3.77 0.00 43.02 2.93
4012 4339 7.218014 GCGATTTCGATCATATTGTTTCAAACA 59.782 33.333 0.00 0.00 43.02 2.83
4013 4340 8.515473 CGATTTCGATCATATTGTTTCAAACAC 58.485 33.333 1.28 0.00 40.79 3.32
4014 4341 9.340695 GATTTCGATCATATTGTTTCAAACACA 57.659 29.630 1.28 0.00 41.97 3.72
4015 4342 8.500837 TTTCGATCATATTGTTTCAAACACAC 57.499 30.769 1.28 0.00 41.97 3.82
4016 4343 7.195839 TCGATCATATTGTTTCAAACACACA 57.804 32.000 1.28 0.00 41.97 3.72
4017 4344 7.815641 TCGATCATATTGTTTCAAACACACAT 58.184 30.769 1.28 0.00 41.97 3.21
4018 4345 8.940952 TCGATCATATTGTTTCAAACACACATA 58.059 29.630 1.28 0.00 41.97 2.29
4019 4346 9.553418 CGATCATATTGTTTCAAACACACATAA 57.447 29.630 1.28 0.00 41.97 1.90
4022 4349 9.891828 TCATATTGTTTCAAACACACATAACTC 57.108 29.630 1.28 0.00 41.97 3.01
4023 4350 9.897744 CATATTGTTTCAAACACACATAACTCT 57.102 29.630 1.28 0.00 41.97 3.24
4026 4353 6.939627 TGTTTCAAACACACATAACTCTACG 58.060 36.000 0.00 0.00 36.25 3.51
4027 4354 6.535865 TGTTTCAAACACACATAACTCTACGT 59.464 34.615 0.00 0.00 36.25 3.57
4028 4355 6.758593 TTCAAACACACATAACTCTACGTC 57.241 37.500 0.00 0.00 0.00 4.34
4029 4356 5.834169 TCAAACACACATAACTCTACGTCA 58.166 37.500 0.00 0.00 0.00 4.35
4030 4357 6.274579 TCAAACACACATAACTCTACGTCAA 58.725 36.000 0.00 0.00 0.00 3.18
4031 4358 6.926826 TCAAACACACATAACTCTACGTCAAT 59.073 34.615 0.00 0.00 0.00 2.57
4032 4359 7.439955 TCAAACACACATAACTCTACGTCAATT 59.560 33.333 0.00 0.00 0.00 2.32
4033 4360 6.946229 ACACACATAACTCTACGTCAATTC 57.054 37.500 0.00 0.00 0.00 2.17
4034 4361 6.452242 ACACACATAACTCTACGTCAATTCA 58.548 36.000 0.00 0.00 0.00 2.57
4035 4362 6.926826 ACACACATAACTCTACGTCAATTCAA 59.073 34.615 0.00 0.00 0.00 2.69
4036 4363 7.439955 ACACACATAACTCTACGTCAATTCAAA 59.560 33.333 0.00 0.00 0.00 2.69
4037 4364 8.443160 CACACATAACTCTACGTCAATTCAAAT 58.557 33.333 0.00 0.00 0.00 2.32
4038 4365 8.656849 ACACATAACTCTACGTCAATTCAAATC 58.343 33.333 0.00 0.00 0.00 2.17
4039 4366 8.116753 CACATAACTCTACGTCAATTCAAATCC 58.883 37.037 0.00 0.00 0.00 3.01
4040 4367 7.822334 ACATAACTCTACGTCAATTCAAATCCA 59.178 33.333 0.00 0.00 0.00 3.41
4041 4368 6.481954 AACTCTACGTCAATTCAAATCCAC 57.518 37.500 0.00 0.00 0.00 4.02
4042 4369 4.625742 ACTCTACGTCAATTCAAATCCACG 59.374 41.667 0.00 5.37 32.58 4.94
4043 4370 4.811908 TCTACGTCAATTCAAATCCACGA 58.188 39.130 0.00 0.00 31.48 4.35
4044 4371 3.806316 ACGTCAATTCAAATCCACGAC 57.194 42.857 11.32 0.00 31.48 4.34
4045 4372 3.135225 ACGTCAATTCAAATCCACGACA 58.865 40.909 11.32 0.00 31.48 4.35
4046 4373 3.751175 ACGTCAATTCAAATCCACGACAT 59.249 39.130 11.32 0.00 31.48 3.06
4047 4374 4.932799 ACGTCAATTCAAATCCACGACATA 59.067 37.500 11.32 0.00 31.48 2.29
4048 4375 5.063438 ACGTCAATTCAAATCCACGACATAG 59.937 40.000 11.32 0.00 31.48 2.23
4049 4376 5.266242 GTCAATTCAAATCCACGACATAGC 58.734 41.667 0.00 0.00 0.00 2.97
4050 4377 4.940654 TCAATTCAAATCCACGACATAGCA 59.059 37.500 0.00 0.00 0.00 3.49
4051 4378 5.414144 TCAATTCAAATCCACGACATAGCAA 59.586 36.000 0.00 0.00 0.00 3.91
4052 4379 6.095300 TCAATTCAAATCCACGACATAGCAAT 59.905 34.615 0.00 0.00 0.00 3.56
4053 4380 5.895636 TTCAAATCCACGACATAGCAATT 57.104 34.783 0.00 0.00 0.00 2.32
4054 4381 5.895636 TCAAATCCACGACATAGCAATTT 57.104 34.783 0.00 0.00 0.00 1.82
4055 4382 6.993786 TCAAATCCACGACATAGCAATTTA 57.006 33.333 0.00 0.00 0.00 1.40
4056 4383 7.384439 TCAAATCCACGACATAGCAATTTAA 57.616 32.000 0.00 0.00 0.00 1.52
4057 4384 7.821652 TCAAATCCACGACATAGCAATTTAAA 58.178 30.769 0.00 0.00 0.00 1.52
4058 4385 8.465999 TCAAATCCACGACATAGCAATTTAAAT 58.534 29.630 0.00 0.00 0.00 1.40
4059 4386 9.729023 CAAATCCACGACATAGCAATTTAAATA 57.271 29.630 0.01 0.00 0.00 1.40
4061 4388 9.897744 AATCCACGACATAGCAATTTAAATATG 57.102 29.630 0.01 4.31 0.00 1.78
4062 4389 8.669946 TCCACGACATAGCAATTTAAATATGA 57.330 30.769 13.24 0.00 31.52 2.15
4063 4390 9.114952 TCCACGACATAGCAATTTAAATATGAA 57.885 29.630 13.24 3.49 31.52 2.57
4064 4391 9.169468 CCACGACATAGCAATTTAAATATGAAC 57.831 33.333 13.24 7.57 31.52 3.18
4065 4392 9.715123 CACGACATAGCAATTTAAATATGAACA 57.285 29.630 13.24 0.00 31.52 3.18
4066 4393 9.716507 ACGACATAGCAATTTAAATATGAACAC 57.283 29.630 13.24 4.19 31.52 3.32
4067 4394 9.715123 CGACATAGCAATTTAAATATGAACACA 57.285 29.630 13.24 0.00 31.52 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 3.271225 GGAGGGGAAAGAGGGGAAATTTA 59.729 47.826 0.00 0.00 0.00 1.40
49 50 0.479378 GGGGAGGAGAGGTAGACGAT 59.521 60.000 0.00 0.00 0.00 3.73
52 53 0.258194 TTCGGGGAGGAGAGGTAGAC 59.742 60.000 0.00 0.00 0.00 2.59
273 274 3.747099 ATTCGATGAAAAGAACCGCAG 57.253 42.857 0.00 0.00 0.00 5.18
435 438 7.985752 ACTAAATTAAGGTCCCGATAGTTCAAG 59.014 37.037 0.00 0.00 0.00 3.02
437 440 7.427989 ACTAAATTAAGGTCCCGATAGTTCA 57.572 36.000 0.00 0.00 0.00 3.18
440 443 7.767659 GTCAAACTAAATTAAGGTCCCGATAGT 59.232 37.037 0.00 0.00 0.00 2.12
441 444 7.985752 AGTCAAACTAAATTAAGGTCCCGATAG 59.014 37.037 0.00 0.00 0.00 2.08
442 445 7.854337 AGTCAAACTAAATTAAGGTCCCGATA 58.146 34.615 0.00 0.00 0.00 2.92
460 463 4.201485 CGCCGCATGAAAAATAAGTCAAAC 60.201 41.667 0.00 0.00 0.00 2.93
630 640 1.250154 TATGGGCAAACACAGGCAGC 61.250 55.000 0.00 0.00 0.00 5.25
750 760 3.181504 TGCACAAATCGATTGCATCTCAG 60.182 43.478 17.14 2.26 41.29 3.35
873 886 2.808543 ACACATCTTGAAGAGGAAACGC 59.191 45.455 14.29 0.00 29.42 4.84
903 916 3.868077 GTGATCACTGCACAGGATTAGAC 59.132 47.826 18.83 0.00 36.31 2.59
908 921 0.254178 GGGTGATCACTGCACAGGAT 59.746 55.000 24.50 2.38 37.99 3.24
1043 1056 2.202440 CACATGCAAGCTGCTCGC 60.202 61.111 5.45 5.45 45.31 5.03
1269 1282 7.488471 CAGTATTAACTAGACAAGCTGTGGTAC 59.512 40.741 0.00 0.00 33.48 3.34
1502 1520 2.307768 CTAGTCCTCATGGCGGAAGTA 58.692 52.381 6.28 2.20 31.13 2.24
1529 1548 9.286170 GGTGGATAGATTTAATAGAACCCTTTC 57.714 37.037 0.00 0.00 0.00 2.62
1554 1573 1.295423 CAAGGTCACGTAGGGGTGG 59.705 63.158 0.00 0.00 38.46 4.61
1598 1617 4.159557 ACACAAAGATGGCCAAAATACCT 58.840 39.130 10.96 0.00 0.00 3.08
1667 1686 6.664515 TCAGCACTTTGGTTTTATAGAAACG 58.335 36.000 0.00 0.00 0.00 3.60
1815 1838 4.782691 TCATCCTCACTTTCCTCATTACCA 59.217 41.667 0.00 0.00 0.00 3.25
1820 1843 3.848975 ACCTTCATCCTCACTTTCCTCAT 59.151 43.478 0.00 0.00 0.00 2.90
2071 2094 4.230657 CTCTCGGCTTCCTTTATATCACG 58.769 47.826 0.00 0.00 0.00 4.35
2178 2201 3.921119 TCATCAACACAACTGCAATCC 57.079 42.857 0.00 0.00 0.00 3.01
2400 2423 1.497722 GAAGGCAAGCGGAAGTTCG 59.502 57.895 0.00 0.00 0.00 3.95
2408 2431 2.266070 TTCAATGGGAAGGCAAGCG 58.734 52.632 0.00 0.00 0.00 4.68
2721 2744 0.625316 CCATGACATTCCCCTCCACA 59.375 55.000 0.00 0.00 0.00 4.17
2925 2948 1.501741 CCATGTTTTCGGGTCGCAG 59.498 57.895 0.00 0.00 0.00 5.18
2964 2987 5.690997 AAAGAAATTCGTCTTTCTCCCAC 57.309 39.130 12.92 0.00 42.88 4.61
3427 3469 7.769044 GCTTTGGGAAGTGTCATCTACTTATAA 59.231 37.037 0.00 0.00 38.42 0.98
3473 3515 3.289407 TGGTTGACCATCTGTTGACAA 57.711 42.857 0.00 0.00 42.01 3.18
3562 3604 8.082242 GGAAGTATTTGCAGTTCAGTATTTGTT 58.918 33.333 0.00 0.00 30.73 2.83
3658 3982 4.516323 GGTTTAGCGGGGTATCAAAAGTA 58.484 43.478 0.00 0.00 0.00 2.24
3672 3996 0.468226 TGCTAGGGATGGGTTTAGCG 59.532 55.000 0.00 0.00 41.00 4.26
3732 4059 2.257207 CCTAGGACTTGAAGGGACACA 58.743 52.381 1.05 0.00 0.00 3.72
3735 4062 3.326880 TCAAACCTAGGACTTGAAGGGAC 59.673 47.826 17.98 0.00 34.52 4.46
3798 4125 4.649218 TCTCCCACTCAACGAATATCATCA 59.351 41.667 0.00 0.00 0.00 3.07
3833 4160 1.067060 TCATACATGCCTCGAAGTCGG 59.933 52.381 0.11 0.00 40.29 4.79
3839 4166 3.638627 AGAAGTCATCATACATGCCTCGA 59.361 43.478 0.00 0.00 0.00 4.04
3846 4173 9.404848 ACATTGATTGAAGAAGTCATCATACAT 57.595 29.630 0.00 0.00 35.70 2.29
3847 4174 8.797350 ACATTGATTGAAGAAGTCATCATACA 57.203 30.769 0.00 0.00 35.70 2.29
3861 4188 8.022550 CGGCATAGCATATTAACATTGATTGAA 58.977 33.333 0.00 0.00 0.00 2.69
3888 4215 2.829741 ACACCTTCAAGAGACTGAGC 57.170 50.000 0.00 0.00 0.00 4.26
3894 4221 4.168101 ACCCTATGAACACCTTCAAGAGA 58.832 43.478 0.00 0.00 39.90 3.10
3897 4224 4.003648 GTGACCCTATGAACACCTTCAAG 58.996 47.826 0.00 0.00 39.90 3.02
3899 4226 2.028476 CGTGACCCTATGAACACCTTCA 60.028 50.000 0.00 0.00 40.77 3.02
3907 4234 4.568956 CATGCATATCGTGACCCTATGAA 58.431 43.478 0.00 0.00 33.49 2.57
3909 4236 2.674852 GCATGCATATCGTGACCCTATG 59.325 50.000 14.21 0.00 33.49 2.23
3919 4246 3.584095 TTAACACACGCATGCATATCG 57.416 42.857 19.57 16.08 0.00 2.92
3927 4254 4.081642 ACTCACCTCTATTAACACACGCAT 60.082 41.667 0.00 0.00 0.00 4.73
3929 4256 3.612860 CACTCACCTCTATTAACACACGC 59.387 47.826 0.00 0.00 0.00 5.34
3931 4258 6.255887 GCATACACTCACCTCTATTAACACAC 59.744 42.308 0.00 0.00 0.00 3.82
3934 4261 6.459710 CGAGCATACACTCACCTCTATTAACA 60.460 42.308 0.00 0.00 36.42 2.41
3938 4265 3.954904 ACGAGCATACACTCACCTCTATT 59.045 43.478 0.00 0.00 36.42 1.73
3939 4266 3.316588 CACGAGCATACACTCACCTCTAT 59.683 47.826 0.00 0.00 36.42 1.98
3940 4267 2.683362 CACGAGCATACACTCACCTCTA 59.317 50.000 0.00 0.00 36.42 2.43
3959 4286 3.246226 AGATCGAAATCGCTTACATGCAC 59.754 43.478 0.00 0.00 39.60 4.57
3962 4289 6.576021 CAGTAAGATCGAAATCGCTTACATG 58.424 40.000 23.06 17.33 42.21 3.21
3970 4297 4.956034 AATCGCAGTAAGATCGAAATCG 57.044 40.909 0.00 0.00 36.97 3.34
3981 4308 7.477144 AACAATATGATCGAAATCGCAGTAA 57.523 32.000 0.00 0.00 39.60 2.24
3987 4314 8.515473 GTGTTTGAAACAATATGATCGAAATCG 58.485 33.333 12.89 0.00 44.16 3.34
3988 4315 9.340695 TGTGTTTGAAACAATATGATCGAAATC 57.659 29.630 12.89 0.00 44.16 2.17
3989 4316 9.128107 GTGTGTTTGAAACAATATGATCGAAAT 57.872 29.630 12.89 0.00 44.16 2.17
3990 4317 8.131731 TGTGTGTTTGAAACAATATGATCGAAA 58.868 29.630 12.89 0.00 44.16 3.46
3991 4318 7.643579 TGTGTGTTTGAAACAATATGATCGAA 58.356 30.769 12.89 0.00 44.16 3.71
3992 4319 7.195839 TGTGTGTTTGAAACAATATGATCGA 57.804 32.000 12.89 0.00 44.16 3.59
3993 4320 9.553418 TTATGTGTGTTTGAAACAATATGATCG 57.447 29.630 12.89 0.00 44.16 3.69
3996 4323 9.891828 GAGTTATGTGTGTTTGAAACAATATGA 57.108 29.630 12.89 2.18 44.16 2.15
3997 4324 9.897744 AGAGTTATGTGTGTTTGAAACAATATG 57.102 29.630 12.89 0.00 44.16 1.78
4000 4327 8.067784 CGTAGAGTTATGTGTGTTTGAAACAAT 58.932 33.333 12.89 5.69 44.16 2.71
4001 4328 7.064847 ACGTAGAGTTATGTGTGTTTGAAACAA 59.935 33.333 12.89 0.00 44.16 2.83
4002 4329 6.535865 ACGTAGAGTTATGTGTGTTTGAAACA 59.464 34.615 6.66 6.66 39.52 2.83
4003 4330 6.940714 ACGTAGAGTTATGTGTGTTTGAAAC 58.059 36.000 0.14 0.14 0.00 2.78
4004 4331 6.757478 TGACGTAGAGTTATGTGTGTTTGAAA 59.243 34.615 0.00 0.00 0.00 2.69
4005 4332 6.274579 TGACGTAGAGTTATGTGTGTTTGAA 58.725 36.000 0.00 0.00 0.00 2.69
4006 4333 5.834169 TGACGTAGAGTTATGTGTGTTTGA 58.166 37.500 0.00 0.00 0.00 2.69
4007 4334 6.519353 TTGACGTAGAGTTATGTGTGTTTG 57.481 37.500 0.00 0.00 0.00 2.93
4008 4335 7.439955 TGAATTGACGTAGAGTTATGTGTGTTT 59.560 33.333 0.00 0.00 0.00 2.83
4009 4336 6.926826 TGAATTGACGTAGAGTTATGTGTGTT 59.073 34.615 0.00 0.00 0.00 3.32
4010 4337 6.452242 TGAATTGACGTAGAGTTATGTGTGT 58.548 36.000 0.00 0.00 0.00 3.72
4011 4338 6.944557 TGAATTGACGTAGAGTTATGTGTG 57.055 37.500 0.00 0.00 0.00 3.82
4012 4339 7.956420 TTTGAATTGACGTAGAGTTATGTGT 57.044 32.000 0.00 0.00 0.00 3.72
4013 4340 8.116753 GGATTTGAATTGACGTAGAGTTATGTG 58.883 37.037 0.00 0.00 0.00 3.21
4014 4341 7.822334 TGGATTTGAATTGACGTAGAGTTATGT 59.178 33.333 0.00 0.00 0.00 2.29
4015 4342 8.116753 GTGGATTTGAATTGACGTAGAGTTATG 58.883 37.037 0.00 0.00 0.00 1.90
4016 4343 7.010183 CGTGGATTTGAATTGACGTAGAGTTAT 59.990 37.037 0.00 0.00 0.00 1.89
4017 4344 6.309494 CGTGGATTTGAATTGACGTAGAGTTA 59.691 38.462 0.00 0.00 0.00 2.24
4018 4345 5.120208 CGTGGATTTGAATTGACGTAGAGTT 59.880 40.000 0.00 0.00 0.00 3.01
4019 4346 4.625742 CGTGGATTTGAATTGACGTAGAGT 59.374 41.667 0.00 0.00 0.00 3.24
4020 4347 4.862574 TCGTGGATTTGAATTGACGTAGAG 59.137 41.667 0.00 0.00 0.00 2.43
4021 4348 4.624024 GTCGTGGATTTGAATTGACGTAGA 59.376 41.667 0.00 0.00 0.00 2.59
4022 4349 4.387559 TGTCGTGGATTTGAATTGACGTAG 59.612 41.667 0.00 0.00 0.00 3.51
4023 4350 4.308265 TGTCGTGGATTTGAATTGACGTA 58.692 39.130 0.00 0.00 0.00 3.57
4024 4351 3.135225 TGTCGTGGATTTGAATTGACGT 58.865 40.909 0.00 0.00 0.00 4.34
4025 4352 3.804518 TGTCGTGGATTTGAATTGACG 57.195 42.857 0.00 0.00 0.00 4.35
4026 4353 5.163764 TGCTATGTCGTGGATTTGAATTGAC 60.164 40.000 0.00 0.00 0.00 3.18
4027 4354 4.940654 TGCTATGTCGTGGATTTGAATTGA 59.059 37.500 0.00 0.00 0.00 2.57
4028 4355 5.233957 TGCTATGTCGTGGATTTGAATTG 57.766 39.130 0.00 0.00 0.00 2.32
4029 4356 5.895636 TTGCTATGTCGTGGATTTGAATT 57.104 34.783 0.00 0.00 0.00 2.17
4030 4357 6.455360 AATTGCTATGTCGTGGATTTGAAT 57.545 33.333 0.00 0.00 0.00 2.57
4031 4358 5.895636 AATTGCTATGTCGTGGATTTGAA 57.104 34.783 0.00 0.00 0.00 2.69
4032 4359 5.895636 AAATTGCTATGTCGTGGATTTGA 57.104 34.783 0.00 0.00 0.00 2.69
4033 4360 8.633075 ATTTAAATTGCTATGTCGTGGATTTG 57.367 30.769 0.00 0.00 0.00 2.32
4035 4362 9.897744 CATATTTAAATTGCTATGTCGTGGATT 57.102 29.630 5.91 0.00 0.00 3.01
4036 4363 9.283768 TCATATTTAAATTGCTATGTCGTGGAT 57.716 29.630 5.91 0.00 0.00 3.41
4037 4364 8.669946 TCATATTTAAATTGCTATGTCGTGGA 57.330 30.769 5.91 0.00 0.00 4.02
4038 4365 9.169468 GTTCATATTTAAATTGCTATGTCGTGG 57.831 33.333 5.91 0.00 0.00 4.94
4039 4366 9.715123 TGTTCATATTTAAATTGCTATGTCGTG 57.285 29.630 5.91 0.00 0.00 4.35
4040 4367 9.716507 GTGTTCATATTTAAATTGCTATGTCGT 57.283 29.630 5.91 0.00 0.00 4.34
4041 4368 9.715123 TGTGTTCATATTTAAATTGCTATGTCG 57.285 29.630 5.91 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.