Multiple sequence alignment - TraesCS1A01G227300

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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 TraesCS1A01G227300 chr1A 100.000 4679 0 0 1 4679 398049613 398054291 0.000000e+00 8641.0
1 TraesCS1A01G227300 chr1D 93.159 4634 223 36 1 4600 316855726 316860299 0.000000e+00 6715.0
2 TraesCS1A01G227300 chr1B 92.622 3768 193 35 594 4342 429001777 429005478 0.000000e+00 5339.0
3 TraesCS1A01G227300 chr1B 83.613 476 60 6 1 476 429000064 429000521 9.300000e-117 431.0
4 TraesCS1A01G227300 chr1B 88.364 275 15 6 4328 4594 429005502 429005767 9.770000e-82 315.0
5 TraesCS1A01G227300 chr1B 95.192 104 3 1 483 584 429001454 429001557 3.750000e-36 163.0
6 TraesCS1A01G227300 chr1B 88.636 88 3 7 4595 4679 429005816 429005899 2.980000e-17 100.0
7 TraesCS1A01G227300 chr4A 89.640 3224 268 33 830 4018 181707762 181710954 0.000000e+00 4043.0
8 TraesCS1A01G227300 chr4D 89.508 3231 255 41 833 4021 301009164 301005976 0.000000e+00 4012.0
9 TraesCS1A01G227300 chr4D 95.745 47 2 0 310 356 464658360 464658406 5.020000e-10 76.8
10 TraesCS1A01G227300 chr4B 88.964 3235 284 38 833 4021 374630012 374626805 0.000000e+00 3928.0
11 TraesCS1A01G227300 chrUn 90.931 419 38 0 2216 2634 476932637 476932219 8.790000e-157 564.0
12 TraesCS1A01G227300 chr5D 83.929 224 31 4 1 220 233391320 233391542 4.740000e-50 209.0
13 TraesCS1A01G227300 chr5D 83.857 223 31 4 1 219 233400297 233400518 1.710000e-49 207.0
14 TraesCS1A01G227300 chr5D 82.063 223 36 3 1 220 224226681 224226902 2.220000e-43 187.0
15 TraesCS1A01G227300 chr5D 83.007 153 24 2 221 371 13723456 13723608 2.270000e-28 137.0
16 TraesCS1A01G227300 chr2B 82.511 223 32 4 1 220 532076347 532076129 6.180000e-44 189.0
17 TraesCS1A01G227300 chr2D 82.143 224 35 4 1 220 165829892 165829670 2.220000e-43 187.0
18 TraesCS1A01G227300 chr7A 81.624 234 33 8 1 227 636209713 636209483 8.000000e-43 185.0
19 TraesCS1A01G227300 chr7A 81.197 234 34 8 1 227 636147869 636147639 3.720000e-41 180.0
20 TraesCS1A01G227300 chr5B 77.459 244 52 3 236 476 477494357 477494600 4.880000e-30 143.0
21 TraesCS1A01G227300 chr6B 74.775 222 50 6 218 436 655273406 655273624 1.390000e-15 95.3


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 TraesCS1A01G227300 chr1A 398049613 398054291 4678 False 8641.0 8641 100.0000 1 4679 1 chr1A.!!$F1 4678
1 TraesCS1A01G227300 chr1D 316855726 316860299 4573 False 6715.0 6715 93.1590 1 4600 1 chr1D.!!$F1 4599
2 TraesCS1A01G227300 chr1B 429000064 429005899 5835 False 1269.6 5339 89.6854 1 4679 5 chr1B.!!$F1 4678
3 TraesCS1A01G227300 chr4A 181707762 181710954 3192 False 4043.0 4043 89.6400 830 4018 1 chr4A.!!$F1 3188
4 TraesCS1A01G227300 chr4D 301005976 301009164 3188 True 4012.0 4012 89.5080 833 4021 1 chr4D.!!$R1 3188
5 TraesCS1A01G227300 chr4B 374626805 374630012 3207 True 3928.0 3928 88.9640 833 4021 1 chr4B.!!$R1 3188

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
201 202 0.832135 GACCCCATAGGCGAGATCCA 60.832 60.0 0.00 0.0 40.58 3.41 F
1617 2786 0.186386 TCTCCTCCCCGGATCTCTTC 59.814 60.0 0.73 0.0 42.12 2.87 F
2308 3477 0.325933 TGTCCCAAGTGCTGATCCAG 59.674 55.0 0.00 0.0 34.12 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1875 3044 0.465705 CCGTGGCATAGACATCCAGT 59.534 55.000 0.0 0.0 0.00 4.00 R
2791 3960 2.037902 TGTCCTCGCAGTAACCAATCAA 59.962 45.455 0.0 0.0 0.00 2.57 R
3764 4945 0.395724 CCCCCAGTCCATAACTTGCC 60.396 60.000 0.0 0.0 35.45 4.52 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
32 33 7.888546 AGCTTTAGGGTTTAGAACACAACATAT 59.111 33.333 0.00 0.00 37.23 1.78
42 43 9.725019 TTTAGAACACAACATATGATCTTGAGT 57.275 29.630 10.38 5.82 0.00 3.41
65 66 7.921787 AGTTAGATCATCTTGTACTCAGTACG 58.078 38.462 10.46 0.00 41.41 3.67
69 70 4.733850 TCATCTTGTACTCAGTACGCAAG 58.266 43.478 10.46 9.26 41.41 4.01
99 100 2.633967 TCAAAGCAGGACGTAGGGTTTA 59.366 45.455 9.48 0.00 31.71 2.01
107 108 3.513119 AGGACGTAGGGTTTAACCTCTTC 59.487 47.826 14.27 6.63 42.09 2.87
112 113 5.070847 ACGTAGGGTTTAACCTCTTCAAGAA 59.929 40.000 14.27 0.00 42.09 2.52
115 116 4.415846 AGGGTTTAACCTCTTCAAGAAGGT 59.584 41.667 14.27 3.41 38.64 3.50
116 117 4.760715 GGGTTTAACCTCTTCAAGAAGGTC 59.239 45.833 14.27 0.00 38.64 3.85
172 173 4.500887 CGTGTTACCCATCGTTCCAGATAT 60.501 45.833 0.00 0.00 0.00 1.63
192 193 2.122813 AGCTCGGGACCCCATAGG 60.123 66.667 4.46 0.00 43.78 2.57
201 202 0.832135 GACCCCATAGGCGAGATCCA 60.832 60.000 0.00 0.00 40.58 3.41
256 257 2.991076 GCCGCTATACCTCGCCGAT 61.991 63.158 0.00 0.00 0.00 4.18
319 320 1.226888 CCCGCTCGCCTTGTACTAC 60.227 63.158 0.00 0.00 0.00 2.73
371 372 1.988406 GTACCTCCGCCCTCCTGTT 60.988 63.158 0.00 0.00 0.00 3.16
377 378 0.982852 TCCGCCCTCCTGTTGATGAT 60.983 55.000 0.00 0.00 0.00 2.45
385 386 3.118149 CCTCCTGTTGATGATGTCCATGA 60.118 47.826 0.00 0.00 35.17 3.07
405 406 2.994995 ATCACCACGCCCGACAGA 60.995 61.111 0.00 0.00 0.00 3.41
410 411 1.671054 CCACGCCCGACAGATGTTT 60.671 57.895 0.00 0.00 0.00 2.83
424 425 2.299867 AGATGTTTGGTCAAATGCCACC 59.700 45.455 0.00 0.00 35.46 4.61
440 441 2.354821 GCCACCGAGCTTATTTTCGAAT 59.645 45.455 0.00 0.00 39.06 3.34
446 447 7.330946 CCACCGAGCTTATTTTCGAATATCATA 59.669 37.037 4.27 0.00 39.06 2.15
449 450 8.262588 CCGAGCTTATTTTCGAATATCATATCG 58.737 37.037 4.27 10.44 39.06 2.92
467 469 7.532571 TCATATCGTTTTTGAGAGTACGAAGA 58.467 34.615 0.00 0.00 44.85 2.87
472 474 5.176958 CGTTTTTGAGAGTACGAAGAATGGT 59.823 40.000 0.00 0.00 36.16 3.55
588 1733 1.550327 TCTCTGAGACGGCACTGATT 58.450 50.000 2.58 0.00 0.00 2.57
589 1734 1.203287 TCTCTGAGACGGCACTGATTG 59.797 52.381 2.58 0.00 0.00 2.67
775 1924 1.401199 CCGTAGTCTCCGAAACCTCTC 59.599 57.143 0.00 0.00 0.00 3.20
816 1965 4.806339 CCTCCCCGGCCCTTCTCT 62.806 72.222 0.00 0.00 0.00 3.10
817 1966 3.157949 CTCCCCGGCCCTTCTCTC 61.158 72.222 0.00 0.00 0.00 3.20
819 1968 4.806339 CCCCGGCCCTTCTCTCCT 62.806 72.222 0.00 0.00 0.00 3.69
822 1971 3.157949 CGGCCCTTCTCTCCTCCC 61.158 72.222 0.00 0.00 0.00 4.30
1378 2547 2.012902 CTACCCGGCCAACTACTCCG 62.013 65.000 2.24 0.00 42.58 4.63
1617 2786 0.186386 TCTCCTCCCCGGATCTCTTC 59.814 60.000 0.73 0.00 42.12 2.87
1677 2846 2.511600 CAGCCGTTCCCGATGGAC 60.512 66.667 0.00 0.00 41.57 4.02
1704 2873 3.840831 TGCTCTGCAGACCATGTAC 57.159 52.632 13.74 0.00 33.32 2.90
1791 2960 1.922545 GACGACACGCCCTACATTTAC 59.077 52.381 0.00 0.00 0.00 2.01
1849 3018 3.914426 ATGTCACAATCACCTACCCTC 57.086 47.619 0.00 0.00 0.00 4.30
1850 3019 1.906574 TGTCACAATCACCTACCCTCC 59.093 52.381 0.00 0.00 0.00 4.30
1875 3044 4.248842 CCGGGATATGTGGCGCCA 62.249 66.667 29.03 29.03 0.00 5.69
1876 3045 2.972505 CGGGATATGTGGCGCCAC 60.973 66.667 45.20 45.20 46.33 5.01
1998 3167 1.471684 CTTGTGAGGCTCCATTTCTGC 59.528 52.381 12.86 0.00 0.00 4.26
2086 3255 1.878775 GTGGAAGGTGCTGATGTGC 59.121 57.895 0.00 0.00 0.00 4.57
2112 3281 1.361632 GGTGGATCCGCGTAGTACC 59.638 63.158 18.92 9.21 0.00 3.34
2135 3304 4.606210 GGTACCCCATTGTACAAGGATTT 58.394 43.478 21.22 7.17 42.31 2.17
2136 3305 4.643334 GGTACCCCATTGTACAAGGATTTC 59.357 45.833 21.22 7.61 42.31 2.17
2308 3477 0.325933 TGTCCCAAGTGCTGATCCAG 59.674 55.000 0.00 0.00 34.12 3.86
2336 3505 1.078143 CCGGGCAAGGGAAGAAGAG 60.078 63.158 0.00 0.00 0.00 2.85
2340 3509 1.443802 GGCAAGGGAAGAAGAGTTCG 58.556 55.000 0.00 0.00 34.02 3.95
2607 3776 1.396301 GAGATCAAGGCTGCAACGAAG 59.604 52.381 0.50 0.00 0.00 3.79
2791 3960 1.667830 CACCGCCATCTTGTGTCGT 60.668 57.895 0.00 0.00 0.00 4.34
2889 4058 3.181465 ACCTATACAAGACCCAGAATGCG 60.181 47.826 0.00 0.00 31.97 4.73
2997 4166 0.320374 TCCACCGTGATGTGAAGACC 59.680 55.000 0.00 0.00 38.55 3.85
3111 4280 2.024414 ACAGTTGTCAAGGGCAGTTTC 58.976 47.619 0.00 0.00 0.00 2.78
3159 4328 2.099431 GCAGCAGCTCACCGAGAAG 61.099 63.158 0.00 0.00 37.91 2.85
3502 4671 2.427540 GATGTCGGATGAGGAGGGCG 62.428 65.000 0.00 0.00 0.00 6.13
3692 4861 1.947212 GCGGTGAGGTAAAAATCCGGT 60.947 52.381 0.00 0.00 38.63 5.28
3753 4934 7.603024 TCAGCATATTTTTCATGAATTTGTGCA 59.397 29.630 23.55 10.93 0.00 4.57
3764 4945 7.085746 TCATGAATTTGTGCACTTGTTATCTG 58.914 34.615 19.41 7.15 0.00 2.90
3808 4989 7.064728 GGTCAGAGAATTGTTTCATACTGTACC 59.935 40.741 0.00 0.00 34.51 3.34
3834 5015 2.819608 GACATTTCTGCCTTGCCTTGTA 59.180 45.455 0.00 0.00 0.00 2.41
3838 5019 4.953940 TTTCTGCCTTGCCTTGTATTTT 57.046 36.364 0.00 0.00 0.00 1.82
3839 5020 4.519540 TTCTGCCTTGCCTTGTATTTTC 57.480 40.909 0.00 0.00 0.00 2.29
3840 5021 3.766545 TCTGCCTTGCCTTGTATTTTCT 58.233 40.909 0.00 0.00 0.00 2.52
3841 5022 4.151883 TCTGCCTTGCCTTGTATTTTCTT 58.848 39.130 0.00 0.00 0.00 2.52
3842 5023 4.218417 TCTGCCTTGCCTTGTATTTTCTTC 59.782 41.667 0.00 0.00 0.00 2.87
3843 5024 4.151883 TGCCTTGCCTTGTATTTTCTTCT 58.848 39.130 0.00 0.00 0.00 2.85
3844 5025 4.588528 TGCCTTGCCTTGTATTTTCTTCTT 59.411 37.500 0.00 0.00 0.00 2.52
3845 5026 5.164233 GCCTTGCCTTGTATTTTCTTCTTC 58.836 41.667 0.00 0.00 0.00 2.87
3922 5124 0.802494 GCCACGTGTTATTGACCCAG 59.198 55.000 15.65 0.00 0.00 4.45
4063 5287 2.831685 TTGTTACCAGTCGTGCTCAT 57.168 45.000 0.00 0.00 0.00 2.90
4064 5288 2.831685 TGTTACCAGTCGTGCTCATT 57.168 45.000 0.00 0.00 0.00 2.57
4072 5296 2.222678 CAGTCGTGCTCATTCATATGCC 59.777 50.000 0.00 0.00 0.00 4.40
4086 5310 4.024143 TGCCGTGTTGCATGTCGC 62.024 61.111 0.00 0.00 42.89 5.19
4159 5386 2.970974 GCTGAACCGGAGCTTGTGC 61.971 63.158 9.46 0.00 40.05 4.57
4160 5387 2.281484 TGAACCGGAGCTTGTGCC 60.281 61.111 9.46 0.00 40.80 5.01
4161 5388 3.056328 GAACCGGAGCTTGTGCCC 61.056 66.667 9.46 0.00 40.80 5.36
4162 5389 3.842925 GAACCGGAGCTTGTGCCCA 62.843 63.158 9.46 0.00 40.80 5.36
4163 5390 3.850098 AACCGGAGCTTGTGCCCAG 62.850 63.158 9.46 0.00 40.80 4.45
4165 5392 4.711949 CGGAGCTTGTGCCCAGCT 62.712 66.667 1.20 1.20 42.13 4.24
4166 5393 3.060615 GGAGCTTGTGCCCAGCTG 61.061 66.667 6.78 6.78 39.21 4.24
4167 5394 2.282040 GAGCTTGTGCCCAGCTGT 60.282 61.111 13.81 0.00 39.21 4.40
4168 5395 1.900498 GAGCTTGTGCCCAGCTGTT 60.900 57.895 13.81 0.00 39.21 3.16
4169 5396 1.860484 GAGCTTGTGCCCAGCTGTTC 61.860 60.000 13.81 4.17 39.21 3.18
4170 5397 2.195567 GCTTGTGCCCAGCTGTTCA 61.196 57.895 13.81 7.01 0.00 3.18
4171 5398 1.656441 CTTGTGCCCAGCTGTTCAC 59.344 57.895 21.70 21.70 0.00 3.18
4172 5399 0.820891 CTTGTGCCCAGCTGTTCACT 60.821 55.000 25.85 0.00 0.00 3.41
4173 5400 0.395586 TTGTGCCCAGCTGTTCACTT 60.396 50.000 25.85 0.00 0.00 3.16
4174 5401 1.102809 TGTGCCCAGCTGTTCACTTG 61.103 55.000 25.85 6.94 0.00 3.16
4195 5422 3.432517 GCTGTAGAGCACTGTCCAG 57.567 57.895 7.06 0.00 45.46 3.86
4200 5427 1.889829 GTAGAGCACTGTCCAGTCTGT 59.110 52.381 0.00 0.45 40.20 3.41
4201 5428 0.965439 AGAGCACTGTCCAGTCTGTC 59.035 55.000 0.00 0.00 40.20 3.51
4204 5431 1.274728 AGCACTGTCCAGTCTGTCATC 59.725 52.381 0.00 0.00 40.20 2.92
4210 5437 4.182339 CTGTCCAGTCTGTCATCTTGATG 58.818 47.826 4.35 4.35 0.00 3.07
4213 5440 2.937149 CCAGTCTGTCATCTTGATGCAG 59.063 50.000 19.32 19.32 0.00 4.41
4219 5446 4.001652 CTGTCATCTTGATGCAGTCAACT 58.998 43.478 18.15 0.00 41.79 3.16
4225 5452 3.578282 TCTTGATGCAGTCAACTCACCTA 59.422 43.478 7.27 0.00 41.79 3.08
4231 5458 2.037251 GCAGTCAACTCACCTACTTCCA 59.963 50.000 0.00 0.00 0.00 3.53
4232 5459 3.862642 GCAGTCAACTCACCTACTTCCAG 60.863 52.174 0.00 0.00 0.00 3.86
4233 5460 2.300437 AGTCAACTCACCTACTTCCAGC 59.700 50.000 0.00 0.00 0.00 4.85
4234 5461 1.272490 TCAACTCACCTACTTCCAGCG 59.728 52.381 0.00 0.00 0.00 5.18
4235 5462 1.272490 CAACTCACCTACTTCCAGCGA 59.728 52.381 0.00 0.00 0.00 4.93
4236 5463 1.853963 ACTCACCTACTTCCAGCGAT 58.146 50.000 0.00 0.00 0.00 4.58
4237 5464 3.014304 ACTCACCTACTTCCAGCGATA 57.986 47.619 0.00 0.00 0.00 2.92
4238 5465 3.567397 ACTCACCTACTTCCAGCGATAT 58.433 45.455 0.00 0.00 0.00 1.63
4239 5466 4.726583 ACTCACCTACTTCCAGCGATATA 58.273 43.478 0.00 0.00 0.00 0.86
4240 5467 4.519730 ACTCACCTACTTCCAGCGATATAC 59.480 45.833 0.00 0.00 0.00 1.47
4241 5468 4.466827 TCACCTACTTCCAGCGATATACA 58.533 43.478 0.00 0.00 0.00 2.29
4242 5469 4.519350 TCACCTACTTCCAGCGATATACAG 59.481 45.833 0.00 0.00 0.00 2.74
4243 5470 3.256136 ACCTACTTCCAGCGATATACAGC 59.744 47.826 0.00 0.00 0.00 4.40
4295 5525 5.886960 ACTGCTTGTCTTCCATGTTATTC 57.113 39.130 0.00 0.00 0.00 1.75
4300 5530 6.821160 TGCTTGTCTTCCATGTTATTCGATTA 59.179 34.615 0.00 0.00 0.00 1.75
4335 5604 2.031682 GCTGTGCACGTCTGAAGAAATT 60.032 45.455 13.13 0.00 0.00 1.82
4342 5611 4.451096 GCACGTCTGAAGAAATTAGTGGAA 59.549 41.667 0.00 0.00 0.00 3.53
4399 5668 3.944015 AGAATGAGCACTTGAATACTGCC 59.056 43.478 0.00 0.00 0.00 4.85
4400 5669 3.641434 ATGAGCACTTGAATACTGCCT 57.359 42.857 0.00 0.00 0.00 4.75
4401 5670 2.977914 TGAGCACTTGAATACTGCCTC 58.022 47.619 0.00 0.00 0.00 4.70
4402 5671 2.284190 GAGCACTTGAATACTGCCTCC 58.716 52.381 0.00 0.00 0.00 4.30
4470 5739 1.407299 CCAGCATCGTGAAATCTCCCA 60.407 52.381 0.00 0.00 0.00 4.37
4471 5740 2.358957 CAGCATCGTGAAATCTCCCAA 58.641 47.619 0.00 0.00 0.00 4.12
4472 5741 2.353889 CAGCATCGTGAAATCTCCCAAG 59.646 50.000 0.00 0.00 0.00 3.61
4473 5742 2.026822 AGCATCGTGAAATCTCCCAAGT 60.027 45.455 0.00 0.00 0.00 3.16
4474 5743 2.096496 GCATCGTGAAATCTCCCAAGTG 59.904 50.000 0.00 0.00 0.00 3.16
4475 5744 2.472695 TCGTGAAATCTCCCAAGTGG 57.527 50.000 0.00 0.00 0.00 4.00
4476 5745 1.974957 TCGTGAAATCTCCCAAGTGGA 59.025 47.619 0.00 0.00 42.41 4.02
4477 5746 2.076863 CGTGAAATCTCCCAAGTGGAC 58.923 52.381 0.00 0.00 38.61 4.02
4481 5750 0.613777 AATCTCCCAAGTGGACGGAC 59.386 55.000 0.00 0.00 38.61 4.79
4522 5799 1.142748 CGTTTTGCTTGCCCAACCA 59.857 52.632 0.00 0.00 0.00 3.67
4568 5845 1.405105 CCAACCCTAAATCATGTGCCG 59.595 52.381 0.00 0.00 0.00 5.69
4584 5861 1.743252 CCGGTCTTGCTTCCTCTGC 60.743 63.158 0.00 0.00 0.00 4.26
4589 5866 1.067495 GTCTTGCTTCCTCTGCGTAGT 60.067 52.381 0.00 0.00 0.00 2.73
4603 5911 1.337447 GCGTAGTGTAGGTCTTTGCCA 60.337 52.381 0.00 0.00 0.00 4.92
4604 5912 2.607187 CGTAGTGTAGGTCTTTGCCAG 58.393 52.381 0.00 0.00 0.00 4.85
4649 5971 1.363246 GGAAGGAGTGAAGGAGGGTT 58.637 55.000 0.00 0.00 0.00 4.11
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 9.747898 ATCATATGTTGTGTTCTAAACCCTAAA 57.252 29.630 1.90 0.00 0.00 1.85
42 43 6.317893 TGCGTACTGAGTACAAGATGATCTAA 59.682 38.462 21.34 0.00 38.77 2.10
65 66 5.689068 GTCCTGCTTTGATTATATTGCTTGC 59.311 40.000 0.00 0.00 0.00 4.01
69 70 5.424121 ACGTCCTGCTTTGATTATATTGC 57.576 39.130 0.00 0.00 0.00 3.56
99 100 2.326428 TCGGACCTTCTTGAAGAGGTT 58.674 47.619 14.55 0.00 34.38 3.50
115 116 4.998672 CACAATGTTTTACCTAGGTTCGGA 59.001 41.667 22.11 0.00 0.00 4.55
116 117 4.758165 ACACAATGTTTTACCTAGGTTCGG 59.242 41.667 22.11 4.27 0.00 4.30
172 173 0.469331 CTATGGGGTCCCGAGCTGTA 60.469 60.000 0.48 0.00 39.42 2.74
192 193 1.287425 CTAAAACCGGTGGATCTCGC 58.713 55.000 8.52 0.00 0.00 5.03
222 223 1.821332 GGCGGCATTGGAAGAGGAG 60.821 63.158 3.07 0.00 0.00 3.69
279 280 3.632080 TGGGTCGTGGTTGCGGAT 61.632 61.111 0.00 0.00 0.00 4.18
319 320 4.189188 CCTAGGTGGACGGCGTCG 62.189 72.222 31.02 17.24 43.02 5.12
365 366 3.679639 CGTCATGGACATCATCAACAGGA 60.680 47.826 0.00 0.00 32.92 3.86
371 372 3.493176 GGTGATCGTCATGGACATCATCA 60.493 47.826 12.77 7.41 34.53 3.07
377 378 0.108851 CGTGGTGATCGTCATGGACA 60.109 55.000 0.00 0.00 32.09 4.02
385 386 4.430765 GTCGGGCGTGGTGATCGT 62.431 66.667 0.00 0.00 0.00 3.73
405 406 1.000731 CGGTGGCATTTGACCAAACAT 59.999 47.619 0.00 0.00 39.39 2.71
410 411 1.971167 GCTCGGTGGCATTTGACCA 60.971 57.895 0.00 0.00 33.84 4.02
424 425 8.799091 ACGATATGATATTCGAAAATAAGCTCG 58.201 33.333 0.00 9.36 38.67 5.03
440 441 9.447040 CTTCGTACTCTCAAAAACGATATGATA 57.553 33.333 0.00 0.00 43.16 2.15
446 447 6.090898 CCATTCTTCGTACTCTCAAAAACGAT 59.909 38.462 0.00 0.00 43.16 3.73
449 450 6.363473 CACCATTCTTCGTACTCTCAAAAAC 58.637 40.000 0.00 0.00 0.00 2.43
455 457 2.758979 TCCCACCATTCTTCGTACTCTC 59.241 50.000 0.00 0.00 0.00 3.20
467 469 0.620410 TCGTCCTCCATCCCACCATT 60.620 55.000 0.00 0.00 0.00 3.16
472 474 0.684479 CTGTCTCGTCCTCCATCCCA 60.684 60.000 0.00 0.00 0.00 4.37
507 1437 1.453197 CCCCGCTAACATGGGTTCC 60.453 63.158 0.00 0.00 44.44 3.62
806 1955 2.770475 GGGGAGGAGAGAAGGGCC 60.770 72.222 0.00 0.00 0.00 5.80
807 1956 2.770475 GGGGGAGGAGAGAAGGGC 60.770 72.222 0.00 0.00 0.00 5.19
852 2001 2.440247 GGTGGGATTTGAGGGCGG 60.440 66.667 0.00 0.00 0.00 6.13
854 2003 0.394899 CTGAGGTGGGATTTGAGGGC 60.395 60.000 0.00 0.00 0.00 5.19
1350 2519 2.125106 GCCGGGTAGAAGTGCAGG 60.125 66.667 2.18 0.00 0.00 4.85
1422 2591 2.925170 AGGAGCGTGACCTTGGCT 60.925 61.111 0.00 0.00 40.29 4.75
1474 2643 0.963962 ACGAGGTAGGCGAAGTTGAA 59.036 50.000 0.00 0.00 0.00 2.69
1617 2786 4.657824 AACGGTGTGGCGAGGTCG 62.658 66.667 0.00 0.00 43.27 4.79
1704 2873 4.796231 CCTCCGACGTTGAGCCGG 62.796 72.222 3.74 5.20 44.22 6.13
1782 2951 1.663695 CCCCTGCACCGTAAATGTAG 58.336 55.000 0.00 0.00 0.00 2.74
1850 3019 0.815213 CACATATCCCGGCACACTGG 60.815 60.000 0.00 0.00 42.66 4.00
1875 3044 0.465705 CCGTGGCATAGACATCCAGT 59.534 55.000 0.00 0.00 0.00 4.00
1876 3045 0.882042 GCCGTGGCATAGACATCCAG 60.882 60.000 5.89 0.00 41.49 3.86
1877 3046 1.146041 GCCGTGGCATAGACATCCA 59.854 57.895 5.89 0.00 41.49 3.41
1998 3167 6.128172 GCTTATCAATTGGGGATTGTATCTCG 60.128 42.308 5.42 0.00 44.46 4.04
2336 3505 0.743345 AATAGGCCCGACAAGCGAAC 60.743 55.000 0.00 0.00 44.57 3.95
2340 3509 1.452108 AGCAATAGGCCCGACAAGC 60.452 57.895 0.00 0.00 46.50 4.01
2343 3512 2.297895 ACCAGCAATAGGCCCGACA 61.298 57.895 0.00 0.00 46.50 4.35
2607 3776 2.129823 TCCGTGACTCGTCAAAGTTC 57.870 50.000 0.64 0.00 41.85 3.01
2709 3878 2.673523 CCCTGCTCAGACAAGGGG 59.326 66.667 5.08 0.00 36.21 4.79
2791 3960 2.037902 TGTCCTCGCAGTAACCAATCAA 59.962 45.455 0.00 0.00 0.00 2.57
2889 4058 4.473520 TGCCTCCAGCTAAGCGGC 62.474 66.667 9.46 9.46 44.23 6.53
3111 4280 6.651975 AAGTATTCAGGATCTAGGTAACCG 57.348 41.667 0.00 0.00 37.17 4.44
3159 4328 4.094887 ACGCCAAATGAATACACATCAGAC 59.905 41.667 0.00 0.00 0.00 3.51
3502 4671 3.415087 AGCCATCACCAGGGGAGC 61.415 66.667 0.00 0.00 0.00 4.70
3600 4769 4.888741 TCGATGCTCGCGACGCTC 62.889 66.667 24.04 18.49 40.21 5.03
3645 4814 2.208431 GGGTTCATGATCTGCGAGAAG 58.792 52.381 0.00 0.00 0.00 2.85
3764 4945 0.395724 CCCCCAGTCCATAACTTGCC 60.396 60.000 0.00 0.00 35.45 4.52
3808 4989 3.698040 AGGCAAGGCAGAAATGTCTAATG 59.302 43.478 0.00 0.00 30.85 1.90
3834 5015 6.484977 ACGCTGAAGAAGAAGAAGAAGAAAAT 59.515 34.615 0.00 0.00 0.00 1.82
3838 5019 4.592485 ACGCTGAAGAAGAAGAAGAAGA 57.408 40.909 0.00 0.00 0.00 2.87
3839 5020 4.509600 ACAACGCTGAAGAAGAAGAAGAAG 59.490 41.667 0.00 0.00 0.00 2.85
3840 5021 4.271049 CACAACGCTGAAGAAGAAGAAGAA 59.729 41.667 0.00 0.00 0.00 2.52
3841 5022 3.804325 CACAACGCTGAAGAAGAAGAAGA 59.196 43.478 0.00 0.00 0.00 2.87
3842 5023 3.804325 TCACAACGCTGAAGAAGAAGAAG 59.196 43.478 0.00 0.00 0.00 2.85
3843 5024 3.792401 TCACAACGCTGAAGAAGAAGAA 58.208 40.909 0.00 0.00 0.00 2.52
3844 5025 3.452755 TCACAACGCTGAAGAAGAAGA 57.547 42.857 0.00 0.00 0.00 2.87
3845 5026 3.742882 TCATCACAACGCTGAAGAAGAAG 59.257 43.478 0.00 0.00 0.00 2.85
3905 5107 1.518325 TGCTGGGTCAATAACACGTG 58.482 50.000 15.48 15.48 32.08 4.49
3922 5124 9.151471 TCACTTTCTCATACAGTATTTACTTGC 57.849 33.333 0.00 0.00 33.46 4.01
4028 5252 3.641437 AACAATCAACATCAACACGGG 57.359 42.857 0.00 0.00 0.00 5.28
4029 5253 4.472286 GGTAACAATCAACATCAACACGG 58.528 43.478 0.00 0.00 0.00 4.94
4159 5386 1.954528 CTGCAAGTGAACAGCTGGG 59.045 57.895 19.93 0.00 0.00 4.45
4164 5391 2.735663 CTCTACAGCTGCAAGTGAACAG 59.264 50.000 15.27 1.04 35.30 3.16
4165 5392 2.759191 CTCTACAGCTGCAAGTGAACA 58.241 47.619 15.27 0.00 35.30 3.18
4166 5393 1.462670 GCTCTACAGCTGCAAGTGAAC 59.537 52.381 15.27 0.00 43.09 3.18
4167 5394 1.800805 GCTCTACAGCTGCAAGTGAA 58.199 50.000 15.27 0.00 43.09 3.18
4168 5395 3.521995 GCTCTACAGCTGCAAGTGA 57.478 52.632 15.27 4.18 43.09 3.41
4189 5416 3.618263 GCATCAAGATGACAGACTGGACA 60.618 47.826 13.93 7.20 41.20 4.02
4195 5422 3.593096 TGACTGCATCAAGATGACAGAC 58.407 45.455 26.30 22.56 41.28 3.51
4210 5437 2.037251 TGGAAGTAGGTGAGTTGACTGC 59.963 50.000 0.00 0.00 0.00 4.40
4213 5440 2.689646 GCTGGAAGTAGGTGAGTTGAC 58.310 52.381 0.00 0.00 35.30 3.18
4219 5446 4.466827 TGTATATCGCTGGAAGTAGGTGA 58.533 43.478 0.00 0.00 35.30 4.02
4225 5452 2.695666 ACTGCTGTATATCGCTGGAAGT 59.304 45.455 0.00 0.00 35.30 3.01
4231 5458 3.757270 ACTCCTACTGCTGTATATCGCT 58.243 45.455 3.72 0.00 0.00 4.93
4232 5459 5.821516 ATACTCCTACTGCTGTATATCGC 57.178 43.478 3.72 0.00 0.00 4.58
4239 5466 8.091449 GCAGAAATTATATACTCCTACTGCTGT 58.909 37.037 0.00 0.66 42.06 4.40
4240 5467 8.472683 GCAGAAATTATATACTCCTACTGCTG 57.527 38.462 0.00 0.00 42.06 4.41
4242 5469 8.307483 TGAGCAGAAATTATATACTCCTACTGC 58.693 37.037 0.00 0.00 44.47 4.40
4335 5604 6.174720 AGCCAGAATTATTCGATTCCACTA 57.825 37.500 0.00 0.00 36.84 2.74
4399 5668 2.036475 CTGGACACCGGAATCATAGGAG 59.964 54.545 9.46 0.00 29.82 3.69
4400 5669 2.039418 CTGGACACCGGAATCATAGGA 58.961 52.381 9.46 0.00 29.82 2.94
4401 5670 1.070758 CCTGGACACCGGAATCATAGG 59.929 57.143 9.46 12.39 29.82 2.57
4402 5671 1.762957 ACCTGGACACCGGAATCATAG 59.237 52.381 9.46 7.28 29.82 2.23
4470 5739 3.677648 CCGTCCGTCCGTCCACTT 61.678 66.667 0.00 0.00 0.00 3.16
4474 5743 4.446413 AATGCCGTCCGTCCGTCC 62.446 66.667 0.00 0.00 0.00 4.79
4475 5744 3.186047 CAATGCCGTCCGTCCGTC 61.186 66.667 0.00 0.00 0.00 4.79
4476 5745 2.999739 AAACAATGCCGTCCGTCCGT 63.000 55.000 0.00 0.00 0.00 4.69
4477 5746 2.235536 GAAACAATGCCGTCCGTCCG 62.236 60.000 0.00 0.00 0.00 4.79
4481 5750 1.434555 TAGTGAAACAATGCCGTCCG 58.565 50.000 0.00 0.00 41.43 4.79
4522 5799 0.107081 TCATCGACCCCAAAACGTGT 59.893 50.000 0.00 0.00 0.00 4.49
4568 5845 0.246635 TACGCAGAGGAAGCAAGACC 59.753 55.000 0.00 0.00 0.00 3.85
4584 5861 2.230508 TCTGGCAAAGACCTACACTACG 59.769 50.000 0.00 0.00 0.00 3.51
4589 5866 2.038557 GGAACTCTGGCAAAGACCTACA 59.961 50.000 0.00 0.00 0.00 2.74
4603 5911 1.004918 CGGGCAAAGACGGAACTCT 60.005 57.895 0.00 0.00 0.00 3.24
4604 5912 3.562635 CGGGCAAAGACGGAACTC 58.437 61.111 0.00 0.00 0.00 3.01
4649 5971 1.032014 GCTCTCAAAACAGTTGGGCA 58.968 50.000 0.00 0.00 0.00 5.36


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

AutoCloner maintained by Alex Coulton.