Multiple sequence alignment - TraesCS5B01G296100

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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 TraesCS5B01G296100 chr5B 100.000 4502 0 0 1 4502 479630606 479626105 0.000000e+00 8314.0
1 TraesCS5B01G296100 chr5B 96.154 130 5 0 4142 4271 411518928 411518799 3.530000e-51 213.0
2 TraesCS5B01G296100 chr5A 96.252 3922 136 10 230 4144 504868014 504864097 0.000000e+00 6418.0
3 TraesCS5B01G296100 chr5A 92.958 213 11 3 4268 4480 504864096 504863888 1.570000e-79 307.0
4 TraesCS5B01G296100 chr5A 87.983 233 19 5 2 234 504868481 504868258 2.670000e-67 267.0
5 TraesCS5B01G296100 chr5A 95.455 132 6 0 4140 4271 652657843 652657712 1.270000e-50 211.0
6 TraesCS5B01G296100 chr5D 97.213 3229 88 2 918 4146 399221049 399217823 0.000000e+00 5463.0
7 TraesCS5B01G296100 chr5D 84.722 648 74 17 217 845 399221809 399221168 3.820000e-175 625.0
8 TraesCS5B01G296100 chr5D 85.156 128 18 1 2 129 399222075 399221949 3.650000e-26 130.0
9 TraesCS5B01G296100 chr5D 100.000 28 0 0 4475 4502 399217458 399217431 8.000000e-03 52.8
10 TraesCS5B01G296100 chr3D 90.330 455 31 8 2917 3367 480417187 480417632 6.490000e-163 584.0
11 TraesCS5B01G296100 chr3D 90.314 382 35 2 3764 4145 543810589 543810968 2.420000e-137 499.0
12 TraesCS5B01G296100 chr3D 95.522 134 5 1 4140 4273 84562607 84562739 3.530000e-51 213.0
13 TraesCS5B01G296100 chr3D 81.102 254 23 9 3679 3930 480417660 480417890 3.580000e-41 180.0
14 TraesCS5B01G296100 chr3B 87.234 470 33 13 2912 3377 640973160 640973606 1.120000e-140 510.0
15 TraesCS5B01G296100 chr3B 80.782 307 37 11 3843 4145 640973786 640974074 2.110000e-53 220.0
16 TraesCS5B01G296100 chr3A 81.511 503 57 13 3654 4145 623530317 623530794 9.140000e-102 381.0
17 TraesCS5B01G296100 chr7D 78.406 389 57 16 173 542 561709865 561709485 1.260000e-55 228.0
18 TraesCS5B01G296100 chr7A 77.835 388 60 16 173 542 646548647 646548268 2.730000e-52 217.0
19 TraesCS5B01G296100 chr7A 96.183 131 4 1 4143 4273 121932679 121932808 3.530000e-51 213.0
20 TraesCS5B01G296100 chr7B 95.489 133 5 1 4142 4274 332242889 332242758 1.270000e-50 211.0
21 TraesCS5B01G296100 chr1B 95.489 133 5 1 4143 4275 41782684 41782553 1.270000e-50 211.0
22 TraesCS5B01G296100 chr1B 94.203 138 6 2 4138 4275 572202435 572202570 4.560000e-50 209.0
23 TraesCS5B01G296100 chr1B 92.414 145 10 1 4126 4270 659726045 659725902 5.900000e-49 206.0
24 TraesCS5B01G296100 chr6D 78.717 343 52 11 174 498 16140668 16141007 4.560000e-50 209.0
25 TraesCS5B01G296100 chr6B 94.161 137 7 1 4134 4270 678328945 678328810 1.640000e-49 207.0
26 TraesCS5B01G296100 chr6A 78.006 341 56 9 174 497 16440413 16440751 3.550000e-46 196.0


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 TraesCS5B01G296100 chr5B 479626105 479630606 4501 True 8314.000000 8314 100.000000 1 4502 1 chr5B.!!$R2 4501
1 TraesCS5B01G296100 chr5A 504863888 504868481 4593 True 2330.666667 6418 92.397667 2 4480 3 chr5A.!!$R2 4478
2 TraesCS5B01G296100 chr5D 399217431 399222075 4644 True 1567.700000 5463 91.772750 2 4502 4 chr5D.!!$R1 4500
3 TraesCS5B01G296100 chr3D 480417187 480417890 703 False 382.000000 584 85.716000 2917 3930 2 chr3D.!!$F3 1013
4 TraesCS5B01G296100 chr3B 640973160 640974074 914 False 365.000000 510 84.008000 2912 4145 2 chr3B.!!$F1 1233

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
536 858 0.031449 AATTGTGGGTTGCGAAACGG 59.969 50.000 0.00 0.0 0.00 4.44 F
1809 2192 0.101759 GCAGCATGATTTCGGCATGT 59.898 50.000 0.00 0.0 43.79 3.21 F
1818 2201 1.171549 TTTCGGCATGTGCAGAGCAA 61.172 50.000 7.36 0.0 45.26 3.91 F
2737 3120 1.686052 GCCATGTTGGTCTGGTGAAAA 59.314 47.619 0.00 0.0 40.46 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1818 2201 0.755686 GCCCGAATCTGACTGATCCT 59.244 55.000 0.00 0.0 33.57 3.24 R
2709 3092 1.369091 GACCAACATGGCTACAGGCG 61.369 60.000 0.00 0.0 42.67 5.52 R
3126 3509 2.266554 CCAGCTCTGAACTCGTGAATC 58.733 52.381 0.00 0.0 0.00 2.52 R
4246 4642 0.032813 TCCCTCCGTCCGGAATTACT 60.033 55.000 5.23 0.0 44.66 2.24 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
109 110 1.228154 GGAAACCAACCCGCAGTCT 60.228 57.895 0.00 0.00 0.00 3.24
126 127 7.307396 CCCGCAGTCTGTTATATTGTAATTGAG 60.307 40.741 0.93 0.00 0.00 3.02
129 160 7.065894 CAGTCTGTTATATTGTAATTGAGCGC 58.934 38.462 0.00 0.00 0.00 5.92
137 168 0.524816 GTAATTGAGCGCGAGTCGGA 60.525 55.000 12.10 0.00 38.94 4.55
155 186 2.576615 GGAGATGTTATTGGGCCTCAC 58.423 52.381 4.53 0.00 0.00 3.51
156 187 2.173569 GGAGATGTTATTGGGCCTCACT 59.826 50.000 4.53 0.00 0.00 3.41
157 188 3.209410 GAGATGTTATTGGGCCTCACTG 58.791 50.000 4.53 0.00 0.00 3.66
158 189 1.678101 GATGTTATTGGGCCTCACTGC 59.322 52.381 4.53 0.00 0.00 4.40
159 190 0.676466 TGTTATTGGGCCTCACTGCG 60.676 55.000 4.53 0.00 0.00 5.18
160 191 0.392461 GTTATTGGGCCTCACTGCGA 60.392 55.000 4.53 0.00 0.00 5.10
161 192 0.107703 TTATTGGGCCTCACTGCGAG 60.108 55.000 4.53 0.00 41.89 5.03
162 193 1.264749 TATTGGGCCTCACTGCGAGT 61.265 55.000 4.53 0.00 40.48 4.18
203 234 2.378038 GGCCAAGTTGCATAGATTCCA 58.622 47.619 0.00 0.00 0.00 3.53
212 243 3.736720 TGCATAGATTCCACTCATGCTC 58.263 45.455 6.43 0.00 41.94 4.26
249 557 1.513858 ACAGGTTACAAGTCCCACCA 58.486 50.000 0.00 0.00 0.00 4.17
265 573 3.317993 CCCACCAAACTTCTTTACACCTG 59.682 47.826 0.00 0.00 0.00 4.00
300 608 9.809096 AATTTATATATGCTCGTGAGTATGAGG 57.191 33.333 10.25 0.00 39.79 3.86
321 629 8.190326 TGAGGATTAACAAGTAGTCTGAGAAA 57.810 34.615 0.00 0.00 0.00 2.52
450 771 3.323403 TGGGTTGCGAAATGAAAAATCCT 59.677 39.130 0.00 0.00 0.00 3.24
455 776 3.056891 TGCGAAATGAAAAATCCTGGTCC 60.057 43.478 0.00 0.00 0.00 4.46
487 809 1.818674 GGGAATTGTGGACTGCGAAAT 59.181 47.619 0.00 0.00 0.00 2.17
536 858 0.031449 AATTGTGGGTTGCGAAACGG 59.969 50.000 0.00 0.00 0.00 4.44
568 891 4.354893 TGAAAACGGGGTTGTAGTATGT 57.645 40.909 0.00 0.00 0.00 2.29
572 895 3.323751 ACGGGGTTGTAGTATGTGAAC 57.676 47.619 0.00 0.00 0.00 3.18
573 896 2.264813 CGGGGTTGTAGTATGTGAACG 58.735 52.381 0.00 0.00 0.00 3.95
574 897 2.094597 CGGGGTTGTAGTATGTGAACGA 60.095 50.000 0.00 0.00 0.00 3.85
625 950 6.017192 GGATTTTGGTCCATGAAACAAAAAGG 60.017 38.462 12.13 0.00 43.41 3.11
684 1009 7.435068 AAAGGCTATGTTGCGGTATAAATAG 57.565 36.000 0.00 0.00 0.00 1.73
689 1014 6.649557 GCTATGTTGCGGTATAAATAGAAGGT 59.350 38.462 0.00 0.00 0.00 3.50
690 1015 6.861065 ATGTTGCGGTATAAATAGAAGGTG 57.139 37.500 0.00 0.00 0.00 4.00
696 1021 5.813672 GCGGTATAAATAGAAGGTGTTGTGA 59.186 40.000 0.00 0.00 0.00 3.58
801 1129 3.631250 ACACTGGGTGAACAATTTCAGT 58.369 40.909 4.62 0.00 42.60 3.41
808 1136 8.576442 ACTGGGTGAACAATTTCAGTATTTTAG 58.424 33.333 0.00 0.00 42.60 1.85
855 1183 5.967674 GGCTGAATTATGTCGACAATTTCAG 59.032 40.000 35.16 35.16 39.92 3.02
897 1266 7.256286 GGTGCTACTCTTATCTAAAGTTTCGA 58.744 38.462 0.00 0.00 0.00 3.71
980 1363 4.988598 ACGGCTGTCAGTTGCCCG 62.989 66.667 13.22 13.22 45.90 6.13
1013 1396 3.483869 GCCGATGCCCTCTCCCTT 61.484 66.667 0.00 0.00 0.00 3.95
1122 1505 1.586154 GCCACTTCAACCCACGGATG 61.586 60.000 0.00 0.00 0.00 3.51
1686 2069 1.179814 GGACAGTGGTCGTCTGGACT 61.180 60.000 0.00 0.00 45.28 3.85
1759 2142 8.065473 TGAATTATTTCTTGGCATGCTAGAAA 57.935 30.769 31.51 31.51 40.84 2.52
1809 2192 0.101759 GCAGCATGATTTCGGCATGT 59.898 50.000 0.00 0.00 43.79 3.21
1818 2201 1.171549 TTTCGGCATGTGCAGAGCAA 61.172 50.000 7.36 0.00 45.26 3.91
1923 2306 5.239744 ACTTGTGGACATGTACGCAAAATTA 59.760 36.000 31.25 14.25 42.66 1.40
2082 2465 5.953183 TGCGAAATGTTAAATGAGAGCATT 58.047 33.333 0.00 0.00 46.35 3.56
2098 2481 2.030007 AGCATTGAACCAAACCACATCG 60.030 45.455 0.00 0.00 0.00 3.84
2286 2669 3.181520 CGTTCGACCAGCTTTATGAAAGG 60.182 47.826 1.42 0.00 38.93 3.11
2485 2868 2.399916 AGCAGGCTTTGAGTCTGATC 57.600 50.000 13.32 0.00 44.01 2.92
2709 3092 5.353956 TGTCACATACATTGCTGTGTTATCC 59.646 40.000 15.56 5.39 42.62 2.59
2737 3120 1.686052 GCCATGTTGGTCTGGTGAAAA 59.314 47.619 0.00 0.00 40.46 2.29
2834 3217 2.497273 TGGATCTTCTTGCACGATCAGA 59.503 45.455 13.30 6.86 36.22 3.27
2884 3267 2.192664 TGAAATGCCCTGTAAAGCGA 57.807 45.000 0.00 0.00 0.00 4.93
3436 3823 3.381335 TCCACTGGAAGGGAGGTAATAC 58.619 50.000 0.00 0.00 43.23 1.89
3489 3876 0.106569 ATGGGAAATGCTCATGCGGA 60.107 50.000 0.00 0.00 43.34 5.54
3591 3978 2.900716 TGGCCTTTTTGCTGGTAAAC 57.099 45.000 3.32 0.00 0.00 2.01
3595 3982 3.319689 GGCCTTTTTGCTGGTAAACACTA 59.680 43.478 0.00 0.00 0.00 2.74
3751 4138 6.458210 CAGCATGTTTCTTATCTTTTTGGGT 58.542 36.000 0.00 0.00 0.00 4.51
3922 4309 4.039004 TGTTTACATGGAAAATGCTGCACT 59.961 37.500 4.20 0.00 0.00 4.40
3981 4374 4.387026 AGGTTGAGGGTGATCAAAATGA 57.613 40.909 0.00 0.00 40.72 2.57
4025 4418 9.519191 TGAAGACAAAAATTCATTCTAGATCCA 57.481 29.630 0.00 0.00 30.67 3.41
4054 4449 0.887387 ACCGTTTGAACCCATGGTCG 60.887 55.000 11.73 0.00 33.12 4.79
4115 4511 6.286240 AGACAAGCTGACTGAATACATACA 57.714 37.500 0.00 0.00 0.00 2.29
4151 4547 6.969993 GAGTATATGGATCATACTCCCTCC 57.030 45.833 15.87 0.00 44.74 4.30
4152 4548 5.450453 AGTATATGGATCATACTCCCTCCG 58.550 45.833 0.00 0.00 34.80 4.63
4153 4549 2.704190 ATGGATCATACTCCCTCCGT 57.296 50.000 0.00 0.00 34.12 4.69
4154 4550 1.996798 TGGATCATACTCCCTCCGTC 58.003 55.000 0.00 0.00 34.12 4.79
4155 4551 1.258676 GGATCATACTCCCTCCGTCC 58.741 60.000 0.00 0.00 0.00 4.79
4156 4552 0.882474 GATCATACTCCCTCCGTCCG 59.118 60.000 0.00 0.00 0.00 4.79
4157 4553 0.477204 ATCATACTCCCTCCGTCCGA 59.523 55.000 0.00 0.00 0.00 4.55
4158 4554 0.256752 TCATACTCCCTCCGTCCGAA 59.743 55.000 0.00 0.00 0.00 4.30
4159 4555 1.108776 CATACTCCCTCCGTCCGAAA 58.891 55.000 0.00 0.00 0.00 3.46
4160 4556 1.479323 CATACTCCCTCCGTCCGAAAA 59.521 52.381 0.00 0.00 0.00 2.29
4161 4557 1.856629 TACTCCCTCCGTCCGAAAAT 58.143 50.000 0.00 0.00 0.00 1.82
4162 4558 1.856629 ACTCCCTCCGTCCGAAAATA 58.143 50.000 0.00 0.00 0.00 1.40
4163 4559 1.479730 ACTCCCTCCGTCCGAAAATAC 59.520 52.381 0.00 0.00 0.00 1.89
4164 4560 1.755380 CTCCCTCCGTCCGAAAATACT 59.245 52.381 0.00 0.00 0.00 2.12
4165 4561 2.167900 CTCCCTCCGTCCGAAAATACTT 59.832 50.000 0.00 0.00 0.00 2.24
4166 4562 2.093869 TCCCTCCGTCCGAAAATACTTG 60.094 50.000 0.00 0.00 0.00 3.16
4167 4563 2.354403 CCCTCCGTCCGAAAATACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
4168 4564 2.928116 CCTCCGTCCGAAAATACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
4169 4565 3.581755 CTCCGTCCGAAAATACTTGTCA 58.418 45.455 0.00 0.00 0.00 3.58
4170 4566 4.181578 CTCCGTCCGAAAATACTTGTCAT 58.818 43.478 0.00 0.00 0.00 3.06
4171 4567 4.178540 TCCGTCCGAAAATACTTGTCATC 58.821 43.478 0.00 0.00 0.00 2.92
4172 4568 3.930229 CCGTCCGAAAATACTTGTCATCA 59.070 43.478 0.00 0.00 0.00 3.07
4173 4569 4.390603 CCGTCCGAAAATACTTGTCATCAA 59.609 41.667 0.00 0.00 0.00 2.57
4174 4570 5.106869 CCGTCCGAAAATACTTGTCATCAAA 60.107 40.000 0.00 0.00 32.87 2.69
4175 4571 6.367421 CGTCCGAAAATACTTGTCATCAAAA 58.633 36.000 0.00 0.00 32.87 2.44
4176 4572 7.021196 CGTCCGAAAATACTTGTCATCAAAAT 58.979 34.615 0.00 0.00 32.87 1.82
4177 4573 7.007367 CGTCCGAAAATACTTGTCATCAAAATG 59.993 37.037 0.00 0.00 32.87 2.32
4178 4574 7.273381 GTCCGAAAATACTTGTCATCAAAATGG 59.727 37.037 0.00 0.00 33.42 3.16
4179 4575 7.175816 TCCGAAAATACTTGTCATCAAAATGGA 59.824 33.333 0.00 0.00 33.42 3.41
4180 4576 7.975616 CCGAAAATACTTGTCATCAAAATGGAT 59.024 33.333 0.00 0.00 33.42 3.41
4225 4621 8.120140 ACTAAAATACGTCTAGATACATCCCC 57.880 38.462 0.00 0.00 0.00 4.81
4226 4622 7.949006 ACTAAAATACGTCTAGATACATCCCCT 59.051 37.037 0.00 0.00 0.00 4.79
4227 4623 7.613551 AAAATACGTCTAGATACATCCCCTT 57.386 36.000 0.00 0.00 0.00 3.95
4228 4624 7.613551 AAATACGTCTAGATACATCCCCTTT 57.386 36.000 0.00 0.00 0.00 3.11
4229 4625 7.613551 AATACGTCTAGATACATCCCCTTTT 57.386 36.000 0.00 0.00 0.00 2.27
4230 4626 8.716674 AATACGTCTAGATACATCCCCTTTTA 57.283 34.615 0.00 0.00 0.00 1.52
4231 4627 8.896722 ATACGTCTAGATACATCCCCTTTTAT 57.103 34.615 0.00 0.00 0.00 1.40
4232 4628 7.613551 ACGTCTAGATACATCCCCTTTTATT 57.386 36.000 0.00 0.00 0.00 1.40
4233 4629 8.030913 ACGTCTAGATACATCCCCTTTTATTT 57.969 34.615 0.00 0.00 0.00 1.40
4234 4630 9.151177 ACGTCTAGATACATCCCCTTTTATTTA 57.849 33.333 0.00 0.00 0.00 1.40
4248 4644 9.942850 CCCCTTTTATTTATTTTGATGACAAGT 57.057 29.630 0.00 0.00 37.32 3.16
4256 4652 9.801873 ATTTATTTTGATGACAAGTAATTCCGG 57.198 29.630 0.00 0.00 37.32 5.14
4257 4653 8.568676 TTATTTTGATGACAAGTAATTCCGGA 57.431 30.769 0.00 0.00 37.32 5.14
4258 4654 5.873179 TTTGATGACAAGTAATTCCGGAC 57.127 39.130 1.83 0.00 37.32 4.79
4259 4655 3.517602 TGATGACAAGTAATTCCGGACG 58.482 45.455 1.83 0.00 0.00 4.79
4260 4656 2.373540 TGACAAGTAATTCCGGACGG 57.626 50.000 1.83 3.96 0.00 4.79
4261 4657 1.894466 TGACAAGTAATTCCGGACGGA 59.106 47.619 1.83 9.76 43.52 4.69
4262 4658 2.094390 TGACAAGTAATTCCGGACGGAG 60.094 50.000 13.64 3.15 46.06 4.63
4263 4659 1.206371 ACAAGTAATTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
4264 4660 0.828677 AAGTAATTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
4265 4661 0.032813 AGTAATTCCGGACGGAGGGA 60.033 55.000 13.64 0.00 46.06 4.20
4266 4662 0.388294 GTAATTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
4276 4672 2.015587 GACGGAGGGAGTACTGTACAG 58.984 57.143 21.44 21.44 0.00 2.74
4304 4700 9.591792 CTAATTCTTCATATCACAACTGTCAGA 57.408 33.333 6.91 0.00 0.00 3.27
4386 4782 3.802685 ACTGAAGTGCACGAGAAAAGTAC 59.197 43.478 12.01 0.00 0.00 2.73
4387 4783 4.051922 CTGAAGTGCACGAGAAAAGTACT 58.948 43.478 12.01 0.00 0.00 2.73
4388 4784 5.190992 TGAAGTGCACGAGAAAAGTACTA 57.809 39.130 12.01 0.00 0.00 1.82
4389 4785 5.593968 TGAAGTGCACGAGAAAAGTACTAA 58.406 37.500 12.01 0.00 0.00 2.24
4390 4786 6.044046 TGAAGTGCACGAGAAAAGTACTAAA 58.956 36.000 12.01 0.00 0.00 1.85
4391 4787 6.704493 TGAAGTGCACGAGAAAAGTACTAAAT 59.296 34.615 12.01 0.00 0.00 1.40
4417 4813 5.250313 AGAACTTGTCTCATTCCATCCTTCT 59.750 40.000 0.00 0.00 0.00 2.85
4453 4849 1.827315 CGCACACCGTGTAACACTGG 61.827 60.000 3.25 0.00 35.74 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.712305 GTAGGTGCAGATTCAATATAGTACAAT 57.288 33.333 0.00 0.00 0.00 2.71
19 20 5.985911 TCACTTCCCTTTATTAGTAGGTGC 58.014 41.667 0.00 0.00 0.00 5.01
50 51 4.960938 TCTGCAAAAGTACATGTCTGACT 58.039 39.130 0.00 0.00 0.00 3.41
54 55 6.150140 GGAGATTTCTGCAAAAGTACATGTCT 59.850 38.462 0.00 0.00 34.20 3.41
109 110 5.751509 ACTCGCGCTCAATTACAATATAACA 59.248 36.000 5.56 0.00 0.00 2.41
126 127 0.317938 ATAACATCTCCGACTCGCGC 60.318 55.000 0.00 0.00 39.11 6.86
129 160 2.743938 CCCAATAACATCTCCGACTCG 58.256 52.381 0.00 0.00 0.00 4.18
137 168 2.684927 GCAGTGAGGCCCAATAACATCT 60.685 50.000 0.00 0.00 0.00 2.90
162 193 2.286713 CCAAAAACATCAACGTCGCAGA 60.287 45.455 0.00 0.00 0.00 4.26
203 234 7.042797 ACAAACTTGTTTTATGAGCATGAGT 57.957 32.000 0.00 0.00 38.47 3.41
249 557 6.605594 TGGTGAAATCAGGTGTAAAGAAGTTT 59.394 34.615 0.00 0.00 0.00 2.66
265 573 9.546909 CACGAGCATATATAAATTGGTGAAATC 57.453 33.333 0.00 0.00 0.00 2.17
300 608 9.262358 AGTTGTTTCTCAGACTACTTGTTAATC 57.738 33.333 0.00 0.00 30.76 1.75
321 629 4.021102 CAACTCACCCTCCATTAGTTGT 57.979 45.455 0.00 0.00 41.21 3.32
420 741 1.182385 TTTCGCAACCCACAATCCCC 61.182 55.000 0.00 0.00 0.00 4.81
450 771 3.935818 TCCCTTTATTTATGCGGACCA 57.064 42.857 0.00 0.00 0.00 4.02
455 776 5.977129 GTCCACAATTCCCTTTATTTATGCG 59.023 40.000 0.00 0.00 0.00 4.73
516 838 1.537135 CCGTTTCGCAACCCACAATTT 60.537 47.619 0.00 0.00 0.00 1.82
549 872 4.354893 TCACATACTACAACCCCGTTTT 57.645 40.909 0.00 0.00 0.00 2.43
550 873 4.067192 GTTCACATACTACAACCCCGTTT 58.933 43.478 0.00 0.00 0.00 3.60
586 910 8.983789 TGGACCAAAATCCCTTTTATTTATACC 58.016 33.333 0.00 0.00 38.06 2.73
625 950 4.929211 GCCAATGGGAAGACATTTGTTTAC 59.071 41.667 0.00 0.00 38.94 2.01
660 985 7.221450 TCTATTTATACCGCAACATAGCCTTT 58.779 34.615 0.00 0.00 0.00 3.11
661 986 6.765403 TCTATTTATACCGCAACATAGCCTT 58.235 36.000 0.00 0.00 0.00 4.35
684 1009 0.880278 TCGCAGCTCACAACACCTTC 60.880 55.000 0.00 0.00 0.00 3.46
689 1014 1.090728 TTTGTTCGCAGCTCACAACA 58.909 45.000 5.89 0.09 30.12 3.33
690 1015 2.187351 TTTTGTTCGCAGCTCACAAC 57.813 45.000 5.89 0.00 30.12 3.32
720 1048 6.418057 TTTGTTTATGCCAACCAAGAGATT 57.582 33.333 0.00 0.00 0.00 2.40
808 1136 6.019075 GCCTTTGAACGAAAATAATATTGGCC 60.019 38.462 0.00 0.00 0.00 5.36
827 1155 4.944962 TGTCGACATAATTCAGCCTTTG 57.055 40.909 15.76 0.00 0.00 2.77
855 1183 1.598601 CACCCAGTGTTGCAAAAATGC 59.401 47.619 11.60 0.00 0.00 3.56
1488 1871 3.793144 GGAAAGCAGGCACGAGCG 61.793 66.667 0.00 0.00 43.41 5.03
1575 1958 4.293648 CAGCCCACCGACACGTCA 62.294 66.667 0.00 0.00 0.00 4.35
1759 2142 1.241315 CCGTCGGGCTCAAAACCATT 61.241 55.000 2.34 0.00 0.00 3.16
1809 2192 0.978907 TGACTGATCCTTGCTCTGCA 59.021 50.000 0.00 0.00 36.47 4.41
1818 2201 0.755686 GCCCGAATCTGACTGATCCT 59.244 55.000 0.00 0.00 33.57 3.24
2082 2465 1.614996 ATGCGATGTGGTTTGGTTCA 58.385 45.000 0.00 0.00 0.00 3.18
2098 2481 6.648725 CAGGCCTTAAGAAGACTAGAATATGC 59.351 42.308 0.00 0.00 0.00 3.14
2286 2669 5.305585 TCAGAACTGGTGGAAAGTATGTTC 58.694 41.667 1.93 0.00 0.00 3.18
2709 3092 1.369091 GACCAACATGGCTACAGGCG 61.369 60.000 0.00 0.00 42.67 5.52
2737 3120 8.964772 CATTGATCTGAAGTATTCCTTTCCTTT 58.035 33.333 0.00 0.00 46.93 3.11
2834 3217 2.376518 TCCAGGGCTTCTTGAACAAGAT 59.623 45.455 16.29 0.79 45.78 2.40
2884 3267 5.126707 GGAGAGTCTTCCAAATCAATGCATT 59.873 40.000 5.99 5.99 37.20 3.56
3048 3431 4.686972 TCATCAGACTCCTTATTCTTGCG 58.313 43.478 0.00 0.00 0.00 4.85
3126 3509 2.266554 CCAGCTCTGAACTCGTGAATC 58.733 52.381 0.00 0.00 0.00 2.52
3436 3823 3.196469 TGGAACCTGTTGCTATCTCTCAG 59.804 47.826 3.22 0.00 0.00 3.35
3489 3876 2.294449 TCACAGCTCACCAGTACTCT 57.706 50.000 0.00 0.00 0.00 3.24
3701 4088 9.708222 GCTAGTCAAGTTTGTATTGTTCATATG 57.292 33.333 0.00 0.00 0.00 1.78
3922 4309 2.044793 ACCCAAGGAGAGTCCATGAA 57.955 50.000 0.00 0.00 37.42 2.57
3981 4374 8.791327 TGTCTTCATCATGTGTATGTATTTGT 57.209 30.769 0.00 0.00 35.73 2.83
4011 4404 6.490241 TGATGCTTCTGGATCTAGAATGAA 57.510 37.500 20.40 10.71 40.95 2.57
4016 4409 3.068732 CGGTTGATGCTTCTGGATCTAGA 59.931 47.826 4.39 4.39 40.95 2.43
4024 4417 3.300009 GTTCAAACGGTTGATGCTTCTG 58.700 45.455 18.16 0.00 43.29 3.02
4025 4418 2.293399 GGTTCAAACGGTTGATGCTTCT 59.707 45.455 18.16 0.00 43.29 2.85
4054 4449 6.473455 GGCTTTTGTATTATGTTGTCAGATGC 59.527 38.462 0.00 0.00 0.00 3.91
4115 4511 9.539194 TGATCCATATACTCTTGTGATACTGAT 57.461 33.333 0.00 0.00 0.00 2.90
4146 4542 2.277084 CAAGTATTTTCGGACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
4147 4543 2.928116 GACAAGTATTTTCGGACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
4148 4544 3.581755 TGACAAGTATTTTCGGACGGAG 58.418 45.455 0.00 0.00 0.00 4.63
4149 4545 3.663995 TGACAAGTATTTTCGGACGGA 57.336 42.857 0.00 0.00 0.00 4.69
4150 4546 3.930229 TGATGACAAGTATTTTCGGACGG 59.070 43.478 0.00 0.00 0.00 4.79
4151 4547 5.524511 TTGATGACAAGTATTTTCGGACG 57.475 39.130 0.00 0.00 0.00 4.79
4152 4548 7.273381 CCATTTTGATGACAAGTATTTTCGGAC 59.727 37.037 0.00 0.00 37.32 4.79
4153 4549 7.175816 TCCATTTTGATGACAAGTATTTTCGGA 59.824 33.333 0.00 0.00 37.32 4.55
4154 4550 7.312154 TCCATTTTGATGACAAGTATTTTCGG 58.688 34.615 0.00 0.00 37.32 4.30
4155 4551 8.915871 ATCCATTTTGATGACAAGTATTTTCG 57.084 30.769 0.00 0.00 37.32 3.46
4199 4595 8.583296 GGGGATGTATCTAGACGTATTTTAGTT 58.417 37.037 0.00 0.00 0.00 2.24
4200 4596 7.949006 AGGGGATGTATCTAGACGTATTTTAGT 59.051 37.037 0.00 0.00 0.00 2.24
4201 4597 8.350852 AGGGGATGTATCTAGACGTATTTTAG 57.649 38.462 0.00 0.00 0.00 1.85
4202 4598 8.716674 AAGGGGATGTATCTAGACGTATTTTA 57.283 34.615 0.00 0.00 0.00 1.52
4203 4599 7.613551 AAGGGGATGTATCTAGACGTATTTT 57.386 36.000 0.00 0.00 0.00 1.82
4204 4600 7.613551 AAAGGGGATGTATCTAGACGTATTT 57.386 36.000 0.00 0.00 0.00 1.40
4205 4601 7.613551 AAAAGGGGATGTATCTAGACGTATT 57.386 36.000 0.00 0.00 0.00 1.89
4206 4602 8.896722 ATAAAAGGGGATGTATCTAGACGTAT 57.103 34.615 0.00 0.00 0.00 3.06
4207 4603 8.716674 AATAAAAGGGGATGTATCTAGACGTA 57.283 34.615 0.00 0.00 0.00 3.57
4208 4604 7.613551 AATAAAAGGGGATGTATCTAGACGT 57.386 36.000 0.00 0.00 0.00 4.34
4222 4618 9.942850 ACTTGTCATCAAAATAAATAAAAGGGG 57.057 29.630 0.00 0.00 32.87 4.79
4230 4626 9.801873 CCGGAATTACTTGTCATCAAAATAAAT 57.198 29.630 0.00 0.00 32.87 1.40
4231 4627 9.015367 TCCGGAATTACTTGTCATCAAAATAAA 57.985 29.630 0.00 0.00 32.87 1.40
4232 4628 8.455682 GTCCGGAATTACTTGTCATCAAAATAA 58.544 33.333 5.23 0.00 32.87 1.40
4233 4629 7.201574 CGTCCGGAATTACTTGTCATCAAAATA 60.202 37.037 5.23 0.00 32.87 1.40
4234 4630 6.403200 CGTCCGGAATTACTTGTCATCAAAAT 60.403 38.462 5.23 0.00 32.87 1.82
4235 4631 5.106869 CGTCCGGAATTACTTGTCATCAAAA 60.107 40.000 5.23 0.00 32.87 2.44
4236 4632 4.390603 CGTCCGGAATTACTTGTCATCAAA 59.609 41.667 5.23 0.00 32.87 2.69
4237 4633 3.930229 CGTCCGGAATTACTTGTCATCAA 59.070 43.478 5.23 0.00 0.00 2.57
4238 4634 3.517602 CGTCCGGAATTACTTGTCATCA 58.482 45.455 5.23 0.00 0.00 3.07
4239 4635 2.864343 CCGTCCGGAATTACTTGTCATC 59.136 50.000 5.23 0.00 37.50 2.92
4240 4636 2.498481 TCCGTCCGGAATTACTTGTCAT 59.502 45.455 5.23 0.00 42.05 3.06
4241 4637 1.894466 TCCGTCCGGAATTACTTGTCA 59.106 47.619 5.23 0.00 42.05 3.58
4242 4638 2.537401 CTCCGTCCGGAATTACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
4243 4639 1.206371 CCTCCGTCCGGAATTACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
4244 4640 1.472728 CCCTCCGTCCGGAATTACTTG 60.473 57.143 5.23 0.00 44.66 3.16
4245 4641 0.828677 CCCTCCGTCCGGAATTACTT 59.171 55.000 5.23 0.00 44.66 2.24
4246 4642 0.032813 TCCCTCCGTCCGGAATTACT 60.033 55.000 5.23 0.00 44.66 2.24
4247 4643 0.388294 CTCCCTCCGTCCGGAATTAC 59.612 60.000 5.23 0.00 44.66 1.89
4248 4644 0.032813 ACTCCCTCCGTCCGGAATTA 60.033 55.000 5.23 0.00 44.66 1.40
4249 4645 0.032813 TACTCCCTCCGTCCGGAATT 60.033 55.000 5.23 0.00 44.66 2.17
4250 4646 0.754587 GTACTCCCTCCGTCCGGAAT 60.755 60.000 5.23 0.00 44.66 3.01
4251 4647 1.379044 GTACTCCCTCCGTCCGGAA 60.379 63.158 5.23 0.00 44.66 4.30
4252 4648 2.273449 GTACTCCCTCCGTCCGGA 59.727 66.667 0.00 0.00 42.90 5.14
4253 4649 2.119655 CAGTACTCCCTCCGTCCGG 61.120 68.421 0.00 0.00 0.00 5.14
4254 4650 0.107508 TACAGTACTCCCTCCGTCCG 60.108 60.000 0.00 0.00 0.00 4.79
4255 4651 1.340405 TGTACAGTACTCCCTCCGTCC 60.340 57.143 12.07 0.00 0.00 4.79
4256 4652 2.015587 CTGTACAGTACTCCCTCCGTC 58.984 57.143 15.06 0.00 0.00 4.79
4257 4653 1.340795 CCTGTACAGTACTCCCTCCGT 60.341 57.143 21.18 0.00 0.00 4.69
4258 4654 1.390565 CCTGTACAGTACTCCCTCCG 58.609 60.000 21.18 0.00 0.00 4.63
4259 4655 1.112950 GCCTGTACAGTACTCCCTCC 58.887 60.000 21.18 0.00 0.00 4.30
4260 4656 2.146920 AGCCTGTACAGTACTCCCTC 57.853 55.000 21.18 0.89 0.00 4.30
4261 4657 3.752359 TTAGCCTGTACAGTACTCCCT 57.248 47.619 21.18 9.59 0.00 4.20
4262 4658 4.650131 AGAATTAGCCTGTACAGTACTCCC 59.350 45.833 21.18 5.37 0.00 4.30
4263 4659 5.855740 AGAATTAGCCTGTACAGTACTCC 57.144 43.478 21.18 8.66 0.00 3.85
4264 4660 6.864342 TGAAGAATTAGCCTGTACAGTACTC 58.136 40.000 21.18 8.82 0.00 2.59
4265 4661 6.852420 TGAAGAATTAGCCTGTACAGTACT 57.148 37.500 21.18 18.85 0.00 2.73
4266 4662 9.413048 GATATGAAGAATTAGCCTGTACAGTAC 57.587 37.037 21.18 12.87 0.00 2.73
4276 4672 7.280876 TGACAGTTGTGATATGAAGAATTAGCC 59.719 37.037 0.00 0.00 0.00 3.93
4353 4749 1.615392 GCACTTCAGTCTGGGCATTTT 59.385 47.619 0.00 0.00 0.00 1.82
4386 4782 7.912056 TGGAATGAGACAAGTTCTGATTTAG 57.088 36.000 0.00 0.00 38.20 1.85
4387 4783 7.554118 GGATGGAATGAGACAAGTTCTGATTTA 59.446 37.037 0.00 0.00 38.20 1.40
4388 4784 6.376581 GGATGGAATGAGACAAGTTCTGATTT 59.623 38.462 0.00 0.00 38.20 2.17
4389 4785 5.884792 GGATGGAATGAGACAAGTTCTGATT 59.115 40.000 0.00 0.00 40.54 2.57
4390 4786 5.191323 AGGATGGAATGAGACAAGTTCTGAT 59.809 40.000 0.00 0.00 33.22 2.90
4391 4787 4.533707 AGGATGGAATGAGACAAGTTCTGA 59.466 41.667 0.00 0.00 33.22 3.27
4417 4813 1.371183 CGGCTTCCACCAGAACTGA 59.629 57.895 3.19 0.00 0.00 3.41
4442 4838 3.746045 TCCAAGACTCCAGTGTTACAC 57.254 47.619 7.50 7.50 29.85 2.90


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

AutoCloner maintained by Alex Coulton.