Multiple sequence alignment - TraesCS4B01G207700

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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 TraesCS4B01G207700 chr4B 100.000 5378 0 0 1 5378 443818776 443813399 0.000000e+00 9932
1 TraesCS4B01G207700 chr4A 96.116 5304 155 21 4 5278 105596603 105601884 0.000000e+00 8606
2 TraesCS4B01G207700 chr4D 96.015 5295 163 23 4 5278 359420758 359415492 0.000000e+00 8565
3 TraesCS4B01G207700 chr4D 97.260 73 2 0 5293 5365 359415504 359415432 2.030000e-24 124
4 TraesCS4B01G207700 chr2B 87.102 597 69 7 3075 3667 519684847 519685439 0.000000e+00 669
5 TraesCS4B01G207700 chr2B 87.220 313 27 6 3748 4059 519685532 519685832 1.430000e-90 344


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 TraesCS4B01G207700 chr4B 443813399 443818776 5377 True 9932.0 9932 100.0000 1 5378 1 chr4B.!!$R1 5377
1 TraesCS4B01G207700 chr4A 105596603 105601884 5281 False 8606.0 8606 96.1160 4 5278 1 chr4A.!!$F1 5274
2 TraesCS4B01G207700 chr4D 359415432 359420758 5326 True 4344.5 8565 96.6375 4 5365 2 chr4D.!!$R1 5361
3 TraesCS4B01G207700 chr2B 519684847 519685832 985 False 506.5 669 87.1610 3075 4059 2 chr2B.!!$F1 984

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
717 728 0.038310 CTCCTGGGGTTTTGGGACTC 59.962 60.000 0.00 0.0 0.00 3.36 F
1478 1489 0.620556 ACTGGCGGATCACCATTCTT 59.379 50.000 0.00 0.0 36.36 2.52 F
1696 1707 0.958876 CCTACAACAAGAACGCCCCC 60.959 60.000 0.00 0.0 0.00 5.40 F
3012 3026 1.508256 ACCCCTAGCAAGGTATGGAC 58.492 55.000 2.71 0.0 41.89 4.02 F
3662 3680 1.402968 GCACATAGCTGTCACCCATTG 59.597 52.381 0.00 0.0 41.15 2.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1813 1824 0.035739 CTTTCGGACCCCTCGGAAAA 59.964 55.000 5.35 0.00 42.18 2.29 R
2990 3004 1.202651 CCATACCTTGCTAGGGGTTCG 60.203 57.143 18.75 2.28 46.58 3.95 R
3502 3518 1.944709 CTCGCCATCTGCATGAAATCA 59.055 47.619 0.00 0.00 41.33 2.57 R
4082 4126 0.321671 GTTGCCTACAGGTGCTGAGA 59.678 55.000 0.00 0.00 37.57 3.27 R
5037 5101 2.108075 TCCCAAGCAGGATCACTTTCAA 59.892 45.455 0.00 0.00 41.22 2.69 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
103 104 1.979155 GGCTGCCTGGGGTTTTCTC 60.979 63.158 12.43 0.00 0.00 2.87
113 114 2.045242 GTTTTCTCCCGGCCTCCC 60.045 66.667 0.00 0.00 0.00 4.30
133 134 1.687297 GGGAGGTCTCGGGTCCATTC 61.687 65.000 0.25 0.00 31.31 2.67
141 142 2.276740 GGGTCCATTCCTGCCTGG 59.723 66.667 0.00 0.00 37.10 4.45
154 155 0.250467 TGCCTGGAACTCTGTTGCTC 60.250 55.000 0.00 0.00 0.00 4.26
155 156 0.957888 GCCTGGAACTCTGTTGCTCC 60.958 60.000 0.00 0.00 0.00 4.70
157 158 0.671781 CTGGAACTCTGTTGCTCCGG 60.672 60.000 0.00 0.00 0.00 5.14
207 208 1.533965 GCGGAGAATTCGGGCAATTTC 60.534 52.381 11.78 0.00 37.77 2.17
215 216 3.518068 GGGCAATTTCGAGCGGGG 61.518 66.667 0.00 0.00 0.00 5.73
246 247 1.581954 CGAGCTGTTCGTCTCAGGT 59.418 57.895 5.71 8.15 44.27 4.00
257 258 0.322546 GTCTCAGGTCGCCCCATTTT 60.323 55.000 0.00 0.00 34.66 1.82
314 315 3.928779 GATCCGATCTGGCGCCCA 61.929 66.667 26.77 11.47 37.80 5.36
447 449 4.380867 GGATTCCGATGCATGTGAGTTTTT 60.381 41.667 2.46 0.00 0.00 1.94
559 567 6.693315 TTTCAACCGAAAGATTGTTCTCTT 57.307 33.333 0.00 0.00 35.58 2.85
593 604 1.534175 GGATCACGAGAGCAAGTACGG 60.534 57.143 0.00 0.00 0.00 4.02
598 609 2.093106 ACGAGAGCAAGTACGGATTCT 58.907 47.619 0.00 0.00 0.00 2.40
717 728 0.038310 CTCCTGGGGTTTTGGGACTC 59.962 60.000 0.00 0.00 0.00 3.36
851 862 9.733556 TGATCTTTCCTTTTTGTACTATAGCAA 57.266 29.630 0.00 0.00 0.00 3.91
853 864 8.331730 TCTTTCCTTTTTGTACTATAGCAACC 57.668 34.615 0.00 0.00 0.00 3.77
854 865 6.730960 TTCCTTTTTGTACTATAGCAACCG 57.269 37.500 0.00 0.00 0.00 4.44
855 866 5.180271 TCCTTTTTGTACTATAGCAACCGG 58.820 41.667 0.00 0.00 0.00 5.28
856 867 5.046448 TCCTTTTTGTACTATAGCAACCGGA 60.046 40.000 9.46 1.07 0.00 5.14
857 868 5.293569 CCTTTTTGTACTATAGCAACCGGAG 59.706 44.000 9.46 0.15 0.00 4.63
858 869 5.410355 TTTTGTACTATAGCAACCGGAGT 57.590 39.130 9.46 0.68 0.00 3.85
875 886 5.048083 ACCGGAGTACGTATCTTTTGTTGTA 60.048 40.000 9.46 0.00 42.24 2.41
930 941 3.332919 CAGATCTGTGTTCTGGGACAAG 58.667 50.000 14.95 0.00 38.70 3.16
937 948 1.144708 TGTTCTGGGACAAGCCATGAA 59.855 47.619 0.00 0.00 38.70 2.57
943 954 1.503542 GACAAGCCATGAACAGCGG 59.496 57.895 0.00 0.00 0.00 5.52
1127 1138 4.379499 CCTTTCAGCGTCTAAATTTGGTCC 60.379 45.833 0.00 0.00 0.00 4.46
1339 1350 2.264166 GTCCTCGCTGCTTCTGCT 59.736 61.111 0.00 0.00 40.48 4.24
1478 1489 0.620556 ACTGGCGGATCACCATTCTT 59.379 50.000 0.00 0.00 36.36 2.52
1483 1494 2.091541 GCGGATCACCATTCTTGGAAA 58.908 47.619 0.00 0.00 46.92 3.13
1696 1707 0.958876 CCTACAACAAGAACGCCCCC 60.959 60.000 0.00 0.00 0.00 5.40
1747 1758 2.892425 GATGTGAAGCCGCCTCCG 60.892 66.667 0.00 0.00 0.00 4.63
1813 1824 3.251004 GCAAAATTCACAAGTCCGTCTCT 59.749 43.478 0.00 0.00 0.00 3.10
2050 2061 3.117888 CCTATAGTGGTGAGCATTGGGTT 60.118 47.826 0.00 0.00 0.00 4.11
2051 2062 4.102524 CCTATAGTGGTGAGCATTGGGTTA 59.897 45.833 0.00 0.00 0.00 2.85
2066 2077 8.275040 AGCATTGGGTTATCTCACTATACTTTT 58.725 33.333 0.00 0.00 0.00 2.27
2130 2141 6.479884 ACCAGCTTAATCTCACTTGAATTCT 58.520 36.000 7.05 0.00 0.00 2.40
2346 2357 4.382577 GCTTCCTTGGAAGGTTTGTTTTGA 60.383 41.667 25.34 0.00 46.54 2.69
2410 2421 4.393680 TCTTGTAACTTATTTCGGCGCAAT 59.606 37.500 10.83 10.05 0.00 3.56
2653 2665 6.542821 TCACTGAAGGTATTTCCAGACATTT 58.457 36.000 0.00 0.00 39.02 2.32
2875 2889 3.025978 CCTTAATGCAAGCTGGGATTGA 58.974 45.455 17.53 8.78 32.41 2.57
2894 2908 6.773200 GGATTGATCATGATGATATGCTGGAT 59.227 38.462 14.30 0.00 37.20 3.41
2990 3004 4.457466 TCCTAGAAACTGTTGAAACCACC 58.543 43.478 0.00 0.00 0.00 4.61
3012 3026 1.508256 ACCCCTAGCAAGGTATGGAC 58.492 55.000 2.71 0.00 41.89 4.02
3215 3229 4.139786 ACCAGGGAAATGATCATGATTCG 58.860 43.478 9.46 0.83 0.00 3.34
3332 3346 2.356665 TAGTTCCAGCAAACAAGGCA 57.643 45.000 0.00 0.00 0.00 4.75
3466 3480 1.909700 TTCCTCATTCAACCTGGCAC 58.090 50.000 0.00 0.00 0.00 5.01
3478 3494 3.064900 ACCTGGCACTGAAAATCTCTC 57.935 47.619 0.00 0.00 0.00 3.20
3479 3495 2.641815 ACCTGGCACTGAAAATCTCTCT 59.358 45.455 0.00 0.00 0.00 3.10
3480 3496 3.840666 ACCTGGCACTGAAAATCTCTCTA 59.159 43.478 0.00 0.00 0.00 2.43
3512 3528 6.845302 TCTGACTAATTGTGTGATTTCATGC 58.155 36.000 0.00 0.00 0.00 4.06
3662 3680 1.402968 GCACATAGCTGTCACCCATTG 59.597 52.381 0.00 0.00 41.15 2.82
3675 3717 8.998377 GCTGTCACCCATTGTTAAAATTTTATT 58.002 29.630 11.33 0.00 0.00 1.40
3709 3751 4.092968 CGACTATTTTACTCCTGTGGCAAC 59.907 45.833 0.00 0.00 0.00 4.17
3802 3844 2.572104 ACCATGAAGGACAGTCTAACCC 59.428 50.000 0.00 0.00 41.22 4.11
3971 4015 5.240713 GCAGAATGGTTCACCTAGAAATG 57.759 43.478 0.00 0.00 35.31 2.32
4036 4080 7.659652 CTTTAGAAAAAGTCTCATCGAAGGT 57.340 36.000 0.00 0.00 37.83 3.50
4067 4111 4.460505 CCTTTGGTTCGTTTACTAAAGCG 58.539 43.478 13.84 0.00 42.12 4.68
4148 4203 7.490402 GGTCAAATTTGATGAATGAAGATGGTC 59.510 37.037 23.05 5.15 39.73 4.02
4394 4449 4.101585 CACCTAATAACTCCCATCTCAGCA 59.898 45.833 0.00 0.00 0.00 4.41
4695 4752 2.896044 TGAACTGAGATCTGCAGTGACT 59.104 45.455 21.12 11.30 45.27 3.41
4997 5056 4.644103 AAATTATGTCTCTGGCATGTGC 57.356 40.909 0.00 0.00 41.14 4.57
4998 5057 2.785540 TTATGTCTCTGGCATGTGCA 57.214 45.000 7.36 0.00 44.36 4.57
4999 5058 3.286329 TTATGTCTCTGGCATGTGCAT 57.714 42.857 7.36 0.00 44.36 3.96
5000 5059 1.676746 ATGTCTCTGGCATGTGCATC 58.323 50.000 7.36 0.00 44.36 3.91
5020 5084 8.229811 GTGCATCTTTGTTATTGCGATCATATA 58.770 33.333 0.00 0.00 37.92 0.86
5129 5193 6.205658 GCCAGAGGGTTTGATTATTGTAGATC 59.794 42.308 0.00 0.00 36.17 2.75
5180 5244 1.751924 TGTGCCAAAAGTTTACCGCTT 59.248 42.857 0.00 0.00 0.00 4.68
5181 5245 2.124122 GTGCCAAAAGTTTACCGCTTG 58.876 47.619 0.00 0.00 0.00 4.01
5195 5259 0.989164 CGCTTGCAATGCTGATTGTG 59.011 50.000 6.82 0.00 41.09 3.33
5199 5263 3.737047 GCTTGCAATGCTGATTGTGCTAT 60.737 43.478 6.82 0.00 41.09 2.97
5253 5318 5.420409 AGGAAAAGCGGTAGTTAGATCTTG 58.580 41.667 0.00 0.00 0.00 3.02
5266 5331 9.331282 GTAGTTAGATCTTGACTTGCCATAATT 57.669 33.333 14.38 0.00 0.00 1.40
5267 5332 8.443953 AGTTAGATCTTGACTTGCCATAATTC 57.556 34.615 0.00 0.00 0.00 2.17
5268 5333 8.049117 AGTTAGATCTTGACTTGCCATAATTCA 58.951 33.333 0.00 0.00 0.00 2.57
5269 5334 8.844244 GTTAGATCTTGACTTGCCATAATTCAT 58.156 33.333 0.00 0.00 0.00 2.57
5271 5336 8.618702 AGATCTTGACTTGCCATAATTCATAG 57.381 34.615 0.00 0.00 0.00 2.23
5272 5337 8.435187 AGATCTTGACTTGCCATAATTCATAGA 58.565 33.333 0.00 0.00 0.00 1.98
5273 5338 8.985315 ATCTTGACTTGCCATAATTCATAGAA 57.015 30.769 0.00 0.00 0.00 2.10
5274 5339 8.806429 TCTTGACTTGCCATAATTCATAGAAA 57.194 30.769 0.00 0.00 0.00 2.52
5275 5340 9.412460 TCTTGACTTGCCATAATTCATAGAAAT 57.588 29.630 0.00 0.00 0.00 2.17
5278 5343 9.288576 TGACTTGCCATAATTCATAGAAATAGG 57.711 33.333 0.00 0.00 0.00 2.57
5279 5344 9.289782 GACTTGCCATAATTCATAGAAATAGGT 57.710 33.333 0.00 0.00 0.00 3.08
5280 5345 9.646522 ACTTGCCATAATTCATAGAAATAGGTT 57.353 29.630 0.00 0.00 0.00 3.50
5281 5346 9.903682 CTTGCCATAATTCATAGAAATAGGTTG 57.096 33.333 0.00 0.00 0.00 3.77
5282 5347 9.639563 TTGCCATAATTCATAGAAATAGGTTGA 57.360 29.630 0.00 0.00 0.00 3.18
5283 5348 9.812347 TGCCATAATTCATAGAAATAGGTTGAT 57.188 29.630 0.00 0.00 0.00 2.57
5291 5356 9.618890 TTCATAGAAATAGGTTGATCCAAGAAG 57.381 33.333 0.00 0.00 39.02 2.85
5292 5357 8.772250 TCATAGAAATAGGTTGATCCAAGAAGT 58.228 33.333 0.00 0.00 39.02 3.01
5325 5390 8.422577 AATAGCAGTGTTCTAAAATTTTCCCT 57.577 30.769 6.72 0.00 0.00 4.20
5369 5434 8.578151 ACTAGTATCTAATTTAGCACTACCAGC 58.422 37.037 0.00 0.00 0.00 4.85
5370 5435 7.361457 AGTATCTAATTTAGCACTACCAGCA 57.639 36.000 8.10 0.00 0.00 4.41
5371 5436 7.210873 AGTATCTAATTTAGCACTACCAGCAC 58.789 38.462 8.10 0.00 0.00 4.40
5372 5437 5.414789 TCTAATTTAGCACTACCAGCACA 57.585 39.130 0.00 0.00 0.00 4.57
5373 5438 5.989477 TCTAATTTAGCACTACCAGCACAT 58.011 37.500 0.00 0.00 0.00 3.21
5374 5439 6.414732 TCTAATTTAGCACTACCAGCACATT 58.585 36.000 0.00 0.00 0.00 2.71
5375 5440 5.982890 AATTTAGCACTACCAGCACATTT 57.017 34.783 0.00 0.00 0.00 2.32
5376 5441 5.982890 ATTTAGCACTACCAGCACATTTT 57.017 34.783 0.00 0.00 0.00 1.82
5377 5442 4.764679 TTAGCACTACCAGCACATTTTG 57.235 40.909 0.00 0.00 0.00 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 1.428448 TTCAGCACAATTCGACGGAG 58.572 50.000 0.00 0.00 0.00 4.63
43 44 1.589716 CCCAAGCAAAGAAGGCGAGG 61.590 60.000 0.00 0.00 36.08 4.63
113 114 4.753662 TGGACCCGAGACCTCCCG 62.754 72.222 0.00 0.00 0.00 5.14
120 121 2.367202 GGCAGGAATGGACCCGAGA 61.367 63.158 0.00 0.00 0.00 4.04
124 125 2.276740 CCAGGCAGGAATGGACCC 59.723 66.667 0.00 0.00 41.22 4.46
133 134 1.239968 GCAACAGAGTTCCAGGCAGG 61.240 60.000 0.00 0.00 39.47 4.85
141 142 0.249911 ACACCGGAGCAACAGAGTTC 60.250 55.000 9.46 0.00 0.00 3.01
148 149 3.474806 CGATCACACCGGAGCAAC 58.525 61.111 9.46 0.00 0.00 4.17
155 156 4.752879 AACCCGCCGATCACACCG 62.753 66.667 0.00 0.00 0.00 4.94
157 158 2.100631 CAGAACCCGCCGATCACAC 61.101 63.158 0.00 0.00 0.00 3.82
182 183 1.893808 CCCGAATTCTCCGCATGGG 60.894 63.158 2.06 2.06 35.24 4.00
188 189 1.268032 CGAAATTGCCCGAATTCTCCG 60.268 52.381 3.52 0.00 32.76 4.63
215 216 4.223964 GCTCGAAATGCGCGACCC 62.224 66.667 12.10 0.00 40.61 4.46
218 219 1.955529 GAACAGCTCGAAATGCGCGA 61.956 55.000 12.10 0.00 40.61 5.87
281 282 1.202818 GGATCTTGGCGCCTAATTCCT 60.203 52.381 29.70 5.51 0.00 3.36
314 315 4.380233 CCAAGCAAGAATTCTCAAATCGCT 60.380 41.667 8.78 7.41 0.00 4.93
447 449 6.016276 AGCGATCAAAGAGAAAAGCCTTTAAA 60.016 34.615 0.00 0.00 31.98 1.52
559 567 5.001237 TCGTGATCCAAATTACTAAGCGA 57.999 39.130 0.00 0.00 0.00 4.93
593 604 5.495640 AGAACACAGGAAATGGAGAGAATC 58.504 41.667 0.00 0.00 0.00 2.52
598 609 5.445069 TCAAAAGAACACAGGAAATGGAGA 58.555 37.500 0.00 0.00 0.00 3.71
849 860 4.240096 ACAAAAGATACGTACTCCGGTTG 58.760 43.478 0.00 0.00 42.24 3.77
851 862 4.240096 CAACAAAAGATACGTACTCCGGT 58.760 43.478 0.00 0.00 42.24 5.28
853 864 6.932901 TTACAACAAAAGATACGTACTCCG 57.067 37.500 0.00 0.00 44.03 4.63
930 941 1.971167 TGGTTCCGCTGTTCATGGC 60.971 57.895 0.00 0.00 0.00 4.40
943 954 2.546789 CAGAGTTAACAACCGGTGGTTC 59.453 50.000 30.59 17.34 43.05 3.62
1116 1127 2.446435 GGAGCAGCAGGACCAAATTTA 58.554 47.619 0.00 0.00 0.00 1.40
1147 1158 2.887568 GACGCCATCGCTGTCAGG 60.888 66.667 1.14 0.00 37.98 3.86
1339 1350 1.275010 TGCTTCACGCAGACATCCTTA 59.725 47.619 0.00 0.00 45.47 2.69
1478 1489 4.365368 TCATTCAGATCCTCTCCTTTCCA 58.635 43.478 0.00 0.00 0.00 3.53
1483 1494 3.704545 ACCTCATTCAGATCCTCTCCT 57.295 47.619 0.00 0.00 0.00 3.69
1680 1691 2.593436 CGGGGGCGTTCTTGTTGT 60.593 61.111 0.00 0.00 0.00 3.32
1696 1707 3.791887 GGTCGAGAAGATTGTACATGTCG 59.208 47.826 0.00 7.26 0.00 4.35
1813 1824 0.035739 CTTTCGGACCCCTCGGAAAA 59.964 55.000 5.35 0.00 42.18 2.29
1866 1877 9.110502 CGGAAGATTTATCATCATCATCATCAT 57.889 33.333 0.00 0.00 0.00 2.45
1867 1878 7.551617 CCGGAAGATTTATCATCATCATCATCA 59.448 37.037 0.00 0.00 0.00 3.07
1868 1879 7.012138 CCCGGAAGATTTATCATCATCATCATC 59.988 40.741 0.73 0.00 0.00 2.92
1930 1941 1.098050 CAGCTGTACAATTGGGCCTC 58.902 55.000 10.83 0.00 0.00 4.70
2066 2077 5.620206 TCAATGAAGTGCTACTTGAAAGGA 58.380 37.500 6.31 0.00 38.80 3.36
2410 2421 5.163519 GCCCTTATTTGCTGCAGAAGAAATA 60.164 40.000 20.43 17.63 0.00 1.40
2586 2597 5.726308 TGGGATCTCAATTAGAAGTTCAGGA 59.274 40.000 5.50 0.00 37.89 3.86
2628 2639 5.762179 TGTCTGGAAATACCTTCAGTGAT 57.238 39.130 0.00 0.00 39.86 3.06
2875 2889 9.780186 CTATGTTATCCAGCATATCATCATGAT 57.220 33.333 5.24 5.24 40.72 2.45
2894 2908 5.007682 GGTTCCAGTGAAAAGCCTATGTTA 58.992 41.667 0.00 0.00 30.79 2.41
2990 3004 1.202651 CCATACCTTGCTAGGGGTTCG 60.203 57.143 18.75 2.28 46.58 3.95
3068 3082 6.151144 GCACCAATAAGACTCAGGTTACAAAT 59.849 38.462 0.00 0.00 0.00 2.32
3215 3229 3.721706 CCCCCAGGAGAGTGCACC 61.722 72.222 14.63 5.12 33.47 5.01
3332 3346 2.171448 CCCCTGTTCCGATGATCTCTTT 59.829 50.000 0.00 0.00 0.00 2.52
3502 3518 1.944709 CTCGCCATCTGCATGAAATCA 59.055 47.619 0.00 0.00 41.33 2.57
3512 3528 4.259970 CGAAGTTTAACATCTCGCCATCTG 60.260 45.833 0.00 0.00 0.00 2.90
3675 3717 6.759827 GGAGTAAAATAGTCGAGCCAAACATA 59.240 38.462 0.00 0.00 0.00 2.29
3709 3751 1.476488 CCCAAACCCCGAAATTAGCTG 59.524 52.381 0.00 0.00 0.00 4.24
3802 3844 9.562583 CTTCTAGTACTAACAGAAAAGCAGTAG 57.437 37.037 3.76 0.00 0.00 2.57
4031 4075 3.956744 ACCAAAGGCTATCTCAACCTTC 58.043 45.455 0.00 0.00 42.99 3.46
4036 4080 3.695830 ACGAACCAAAGGCTATCTCAA 57.304 42.857 0.00 0.00 0.00 3.02
4050 4094 3.424039 GCTTCCGCTTTAGTAAACGAACC 60.424 47.826 14.91 0.00 0.00 3.62
4082 4126 0.321671 GTTGCCTACAGGTGCTGAGA 59.678 55.000 0.00 0.00 37.57 3.27
4269 4324 2.418910 CCGGTCGAGCAGATCCTGT 61.419 63.158 15.89 0.00 33.43 4.00
4695 4752 7.462571 TGCAGAGAATTGTGAGTTAGTAGTA 57.537 36.000 0.00 0.00 0.00 1.82
4738 4795 6.769822 TGAACAAAAGAATCTGAAGCTTCTCT 59.230 34.615 26.09 17.41 30.15 3.10
4739 4796 6.963796 TGAACAAAAGAATCTGAAGCTTCTC 58.036 36.000 26.09 15.49 30.15 2.87
4740 4797 6.545298 ACTGAACAAAAGAATCTGAAGCTTCT 59.455 34.615 26.09 6.84 32.49 2.85
4741 4798 6.733145 ACTGAACAAAAGAATCTGAAGCTTC 58.267 36.000 19.89 19.89 0.00 3.86
4742 4799 6.705863 ACTGAACAAAAGAATCTGAAGCTT 57.294 33.333 0.00 0.00 0.00 3.74
4969 5028 4.229582 TGCCAGAGACATAATTTAAGGGGT 59.770 41.667 0.00 0.00 0.00 4.95
5029 5093 5.474876 AGCAGGATCACTTTCAAAACTAAGG 59.525 40.000 0.00 0.00 0.00 2.69
5037 5101 2.108075 TCCCAAGCAGGATCACTTTCAA 59.892 45.455 0.00 0.00 41.22 2.69
5129 5193 2.213499 GATTGACGCCAGTGGATAAGG 58.787 52.381 15.20 0.00 0.00 2.69
5180 5244 4.822896 TCATATAGCACAATCAGCATTGCA 59.177 37.500 11.91 0.00 43.03 4.08
5181 5245 5.048921 ACTCATATAGCACAATCAGCATTGC 60.049 40.000 0.00 0.00 43.03 3.56
5253 5318 9.289782 ACCTATTTCTATGAATTATGGCAAGTC 57.710 33.333 0.00 0.00 0.00 3.01
5266 5331 8.772250 ACTTCTTGGATCAACCTATTTCTATGA 58.228 33.333 0.00 0.00 39.86 2.15
5267 5332 8.970859 ACTTCTTGGATCAACCTATTTCTATG 57.029 34.615 0.00 0.00 39.86 2.23
5268 5333 9.620259 GAACTTCTTGGATCAACCTATTTCTAT 57.380 33.333 0.00 0.00 39.86 1.98
5269 5334 8.047310 GGAACTTCTTGGATCAACCTATTTCTA 58.953 37.037 0.00 0.00 39.86 2.10
5270 5335 6.887002 GGAACTTCTTGGATCAACCTATTTCT 59.113 38.462 0.00 0.00 39.86 2.52
5271 5336 6.887002 AGGAACTTCTTGGATCAACCTATTTC 59.113 38.462 0.00 0.00 35.19 2.17
5272 5337 6.794534 AGGAACTTCTTGGATCAACCTATTT 58.205 36.000 0.00 0.00 35.19 1.40
5273 5338 6.394345 AGGAACTTCTTGGATCAACCTATT 57.606 37.500 0.00 0.00 35.19 1.73
5274 5339 6.903534 TCTAGGAACTTCTTGGATCAACCTAT 59.096 38.462 0.00 0.00 41.75 2.57
5275 5340 6.261435 TCTAGGAACTTCTTGGATCAACCTA 58.739 40.000 0.00 0.00 41.75 3.08
5276 5341 5.094387 TCTAGGAACTTCTTGGATCAACCT 58.906 41.667 0.00 0.00 41.75 3.50
5277 5342 5.422214 TCTAGGAACTTCTTGGATCAACC 57.578 43.478 0.00 0.00 41.75 3.77
5278 5343 7.929941 ATTTCTAGGAACTTCTTGGATCAAC 57.070 36.000 0.00 0.00 41.75 3.18
5279 5344 7.770897 GCTATTTCTAGGAACTTCTTGGATCAA 59.229 37.037 0.00 0.00 41.75 2.57
5280 5345 7.092891 TGCTATTTCTAGGAACTTCTTGGATCA 60.093 37.037 0.00 0.00 41.75 2.92
5281 5346 7.275920 TGCTATTTCTAGGAACTTCTTGGATC 58.724 38.462 0.00 0.00 41.75 3.36
5282 5347 7.092668 ACTGCTATTTCTAGGAACTTCTTGGAT 60.093 37.037 0.00 0.00 41.75 3.41
5283 5348 6.213600 ACTGCTATTTCTAGGAACTTCTTGGA 59.786 38.462 0.00 0.00 41.75 3.53
5284 5349 6.314896 CACTGCTATTTCTAGGAACTTCTTGG 59.685 42.308 0.00 0.00 41.75 3.61
5285 5350 6.876257 ACACTGCTATTTCTAGGAACTTCTTG 59.124 38.462 0.00 0.00 41.75 3.02
5286 5351 7.010339 ACACTGCTATTTCTAGGAACTTCTT 57.990 36.000 0.00 0.00 41.75 2.52
5287 5352 6.613153 ACACTGCTATTTCTAGGAACTTCT 57.387 37.500 0.00 0.00 41.75 2.85
5288 5353 7.100409 AGAACACTGCTATTTCTAGGAACTTC 58.900 38.462 0.00 0.00 41.75 3.01
5289 5354 7.010339 AGAACACTGCTATTTCTAGGAACTT 57.990 36.000 0.00 0.00 41.75 2.66
5290 5355 6.613153 AGAACACTGCTATTTCTAGGAACT 57.387 37.500 0.00 0.00 46.37 3.01
5291 5356 8.773404 TTTAGAACACTGCTATTTCTAGGAAC 57.227 34.615 0.00 0.00 34.22 3.62
5292 5357 9.959721 ATTTTAGAACACTGCTATTTCTAGGAA 57.040 29.630 0.00 0.00 34.22 3.36
5353 5418 5.982890 AAATGTGCTGGTAGTGCTAAATT 57.017 34.783 0.00 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.