Multiple sequence alignment - TraesCS4D01G305400

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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 TraesCS4D01G305400 chr4D 100.000 6299 0 0 1 6299 473833995 473840293 0.000000e+00 11633.0
1 TraesCS4D01G305400 chr4D 93.122 567 24 12 5741 6299 464684463 464683904 0.000000e+00 817.0
2 TraesCS4D01G305400 chr4D 97.279 147 3 1 4197 4342 473838051 473838197 1.360000e-61 248.0
3 TraesCS4D01G305400 chr4D 97.279 147 3 1 4057 4203 473838191 473838336 1.360000e-61 248.0
4 TraesCS4D01G305400 chr4B 91.987 3095 105 46 2632 5642 596650761 596653796 0.000000e+00 4209.0
5 TraesCS4D01G305400 chr4B 93.017 2678 80 38 3 2632 596648114 596650732 0.000000e+00 3810.0
6 TraesCS4D01G305400 chr4B 89.175 582 47 13 5727 6299 142040945 142041519 0.000000e+00 712.0
7 TraesCS4D01G305400 chr4B 96.599 147 4 1 4057 4203 596652372 596652517 6.310000e-60 243.0
8 TraesCS4D01G305400 chr4B 95.918 147 5 1 4197 4342 596652232 596652378 2.940000e-58 237.0
9 TraesCS4D01G305400 chr4A 92.572 2531 118 32 136 2632 680397376 680399870 0.000000e+00 3568.0
10 TraesCS4D01G305400 chr4A 95.124 1292 41 12 4202 5490 680401741 680403013 0.000000e+00 2017.0
11 TraesCS4D01G305400 chr4A 88.153 1494 68 49 2800 4203 680400399 680401873 0.000000e+00 1677.0
12 TraesCS4D01G305400 chr4A 88.072 503 20 10 2632 3102 680399899 680400393 1.530000e-155 560.0
13 TraesCS4D01G305400 chr4A 89.759 166 12 2 2142 2307 17978104 17977944 2.300000e-49 207.0
14 TraesCS4D01G305400 chr4A 100.000 60 0 0 2303 2362 17976545 17976486 1.860000e-20 111.0
15 TraesCS4D01G305400 chr6D 98.630 657 9 0 5643 6299 433634034 433634690 0.000000e+00 1164.0
16 TraesCS4D01G305400 chr5D 98.326 657 11 0 5643 6299 368740375 368739719 0.000000e+00 1153.0
17 TraesCS4D01G305400 chr1B 91.793 658 49 4 5643 6299 467901685 467901032 0.000000e+00 911.0
18 TraesCS4D01G305400 chr1B 90.563 657 61 1 5643 6299 1265319 1264664 0.000000e+00 869.0
19 TraesCS4D01G305400 chr2D 93.298 567 23 12 5741 6299 260849379 260849938 0.000000e+00 822.0
20 TraesCS4D01G305400 chr2D 91.031 223 19 1 2142 2363 245669725 245669503 3.690000e-77 300.0
21 TraesCS4D01G305400 chr3D 90.076 655 31 22 5659 6299 561721830 561721196 0.000000e+00 819.0
22 TraesCS4D01G305400 chr6B 89.660 648 56 9 5645 6291 229134150 229133513 0.000000e+00 815.0
23 TraesCS4D01G305400 chr6B 80.657 274 27 21 5659 5918 223418316 223418577 8.340000e-44 189.0
24 TraesCS4D01G305400 chr6B 85.981 107 7 8 5655 5757 223434036 223434138 2.400000e-19 108.0
25 TraesCS4D01G305400 chr6B 95.000 60 1 2 5659 5716 447435679 447435620 6.720000e-15 93.5
26 TraesCS4D01G305400 chr7D 93.243 222 12 1 2142 2363 159000671 159000889 2.190000e-84 324.0
27 TraesCS4D01G305400 chr2B 87.755 98 9 3 5661 5757 793265502 793265407 1.860000e-20 111.0


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 TraesCS4D01G305400 chr4D 473833995 473840293 6298 False 4043.00 11633 98.18600 1 6299 3 chr4D.!!$F1 6298
1 TraesCS4D01G305400 chr4D 464683904 464684463 559 True 817.00 817 93.12200 5741 6299 1 chr4D.!!$R1 558
2 TraesCS4D01G305400 chr4B 596648114 596653796 5682 False 2124.75 4209 94.38025 3 5642 4 chr4B.!!$F2 5639
3 TraesCS4D01G305400 chr4B 142040945 142041519 574 False 712.00 712 89.17500 5727 6299 1 chr4B.!!$F1 572
4 TraesCS4D01G305400 chr4A 680397376 680403013 5637 False 1955.50 3568 90.98025 136 5490 4 chr4A.!!$F1 5354
5 TraesCS4D01G305400 chr6D 433634034 433634690 656 False 1164.00 1164 98.63000 5643 6299 1 chr6D.!!$F1 656
6 TraesCS4D01G305400 chr5D 368739719 368740375 656 True 1153.00 1153 98.32600 5643 6299 1 chr5D.!!$R1 656
7 TraesCS4D01G305400 chr1B 467901032 467901685 653 True 911.00 911 91.79300 5643 6299 1 chr1B.!!$R2 656
8 TraesCS4D01G305400 chr1B 1264664 1265319 655 True 869.00 869 90.56300 5643 6299 1 chr1B.!!$R1 656
9 TraesCS4D01G305400 chr2D 260849379 260849938 559 False 822.00 822 93.29800 5741 6299 1 chr2D.!!$F1 558
10 TraesCS4D01G305400 chr3D 561721196 561721830 634 True 819.00 819 90.07600 5659 6299 1 chr3D.!!$R1 640
11 TraesCS4D01G305400 chr6B 229133513 229134150 637 True 815.00 815 89.66000 5645 6291 1 chr6B.!!$R1 646

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
209 216 0.105593 CCGGTCAGTCATCCATCCAG 59.894 60.0 0.0 0.0 0.00 3.86 F
1637 1735 0.324275 ACTGGAGCTGGAGAGTCCTC 60.324 60.0 0.0 0.0 37.46 3.71 F
2849 2986 0.755698 TGGGATCTGGACGACTAGGC 60.756 60.0 0.0 0.0 0.00 3.93 F
3856 4417 1.168714 AACCGATCTTTTGCTGGAGC 58.831 50.0 0.0 0.0 42.50 4.70 F
4587 5154 1.696063 AAGTGAGCAGCAATGTGGTT 58.304 45.0 0.0 0.0 0.00 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1732 1830 1.291877 CGTGTTGCTTCCCTTCCTCG 61.292 60.000 0.00 0.00 0.0 4.63 R
2996 3489 2.069165 GAGGGGCACAAAGGGTCACT 62.069 60.000 0.00 0.00 0.0 3.41 R
4152 4715 2.840651 CAGGTTGGGGATGTCTAACTCT 59.159 50.000 0.00 0.00 0.0 3.24 R
4928 5495 2.192664 TACAGATTTCTTTGGCGCCA 57.807 45.000 29.03 29.03 0.0 5.69 R
6048 6640 1.476891 ACAATCACAGTATCGCGTCCT 59.523 47.619 5.77 0.00 0.0 3.85 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
123 129 5.277683 GGCGTACGTAGAAAGATCATCTACA 60.278 44.000 25.76 13.23 46.19 2.74
143 149 5.606348 ACATTTGTTGTTGGTGTTGGTAT 57.394 34.783 0.00 0.00 33.74 2.73
200 207 2.283676 GTCCCCTCCGGTCAGTCA 60.284 66.667 0.00 0.00 0.00 3.41
209 216 0.105593 CCGGTCAGTCATCCATCCAG 59.894 60.000 0.00 0.00 0.00 3.86
246 261 2.069430 GGGGAAGAGCTGAGGGAGG 61.069 68.421 0.00 0.00 0.00 4.30
247 262 2.069430 GGGAAGAGCTGAGGGAGGG 61.069 68.421 0.00 0.00 0.00 4.30
248 263 1.002274 GGAAGAGCTGAGGGAGGGA 59.998 63.158 0.00 0.00 0.00 4.20
249 264 1.048160 GGAAGAGCTGAGGGAGGGAG 61.048 65.000 0.00 0.00 0.00 4.30
264 279 2.445654 GAGCAGGGAGGAGGGGAG 60.446 72.222 0.00 0.00 0.00 4.30
265 280 4.101077 AGCAGGGAGGAGGGGAGG 62.101 72.222 0.00 0.00 0.00 4.30
266 281 4.095400 GCAGGGAGGAGGGGAGGA 62.095 72.222 0.00 0.00 0.00 3.71
267 282 2.285180 CAGGGAGGAGGGGAGGAG 59.715 72.222 0.00 0.00 0.00 3.69
268 283 3.039526 AGGGAGGAGGGGAGGAGG 61.040 72.222 0.00 0.00 0.00 4.30
269 284 4.890306 GGGAGGAGGGGAGGAGGC 62.890 77.778 0.00 0.00 0.00 4.70
270 285 4.890306 GGAGGAGGGGAGGAGGCC 62.890 77.778 0.00 0.00 0.00 5.19
271 286 4.095400 GAGGAGGGGAGGAGGCCA 62.095 72.222 5.01 0.00 0.00 5.36
272 287 4.101077 AGGAGGGGAGGAGGCCAG 62.101 72.222 5.01 0.00 0.00 4.85
290 305 4.633769 GCCAAGCCAAGAGAGAGG 57.366 61.111 0.00 0.00 0.00 3.69
549 612 3.680920 TTCCTCCGCCTCCTCTCCC 62.681 68.421 0.00 0.00 0.00 4.30
561 624 0.391793 CCTCTCCCTCTTGGTTTCGC 60.392 60.000 0.00 0.00 34.77 4.70
1237 1335 3.011517 AGCGGCCTGGAGGTCAAT 61.012 61.111 0.00 0.00 40.62 2.57
1402 1500 1.153349 GACTGGTCCGATTGCCCTC 60.153 63.158 0.00 0.00 0.00 4.30
1489 1587 2.017049 GGCAATCGCTACATGAAAGGT 58.983 47.619 0.00 0.00 38.60 3.50
1540 1638 1.439679 GCGAGGACGGTCAGAATTTT 58.560 50.000 10.76 0.00 40.15 1.82
1637 1735 0.324275 ACTGGAGCTGGAGAGTCCTC 60.324 60.000 0.00 0.00 37.46 3.71
1732 1830 1.069636 CGGTTCTTGCAGCAGAAGTTC 60.070 52.381 0.97 0.00 33.29 3.01
1765 1863 3.068024 AGCAACACGTGGATGTGATTTTT 59.932 39.130 21.57 0.00 42.55 1.94
1837 1935 6.822676 CCAACTATCTCATTCAGAAGCTTCTT 59.177 38.462 26.44 9.87 34.74 2.52
1873 1971 5.545162 GAGGATCAGAGGCTGAGGATCATT 61.545 50.000 16.70 8.05 44.08 2.57
1955 2053 6.835819 AATTTACCTTCTCTTGCCTAAACC 57.164 37.500 0.00 0.00 0.00 3.27
2116 2215 7.254185 CCATGATGCTTACATTGCAACATAAAC 60.254 37.037 0.00 0.00 46.87 2.01
2124 2223 3.760580 TTGCAACATAAACCCCCTTTG 57.239 42.857 0.00 0.00 0.00 2.77
2125 2224 2.683768 TGCAACATAAACCCCCTTTGT 58.316 42.857 0.00 0.00 0.00 2.83
2127 2226 4.223953 TGCAACATAAACCCCCTTTGTTA 58.776 39.130 0.00 0.00 0.00 2.41
2128 2227 4.039366 TGCAACATAAACCCCCTTTGTTAC 59.961 41.667 0.00 0.00 0.00 2.50
2129 2228 4.282449 GCAACATAAACCCCCTTTGTTACT 59.718 41.667 0.00 0.00 0.00 2.24
2130 2229 5.477637 GCAACATAAACCCCCTTTGTTACTA 59.522 40.000 0.00 0.00 0.00 1.82
2131 2230 6.570957 GCAACATAAACCCCCTTTGTTACTAC 60.571 42.308 0.00 0.00 0.00 2.73
2132 2231 5.247862 ACATAAACCCCCTTTGTTACTACG 58.752 41.667 0.00 0.00 0.00 3.51
2140 2239 4.939439 CCCCTTTGTTACTACGTAAATGCT 59.061 41.667 0.00 0.00 29.42 3.79
2215 2314 6.257630 GGCAGTTCAGAAATTGATAGAGACTC 59.742 42.308 0.00 0.00 35.27 3.36
2394 2493 9.937175 GCTATTTTTGGTCATATAACTGACTTC 57.063 33.333 6.46 0.00 44.05 3.01
2567 2669 5.945784 ACCTACACATGTGCATAAACTCATT 59.054 36.000 25.68 4.13 0.00 2.57
2568 2670 7.109501 ACCTACACATGTGCATAAACTCATTA 58.890 34.615 25.68 5.11 0.00 1.90
2569 2671 7.280876 ACCTACACATGTGCATAAACTCATTAG 59.719 37.037 25.68 13.78 0.00 1.73
2572 2674 7.530010 ACACATGTGCATAAACTCATTAGAAC 58.470 34.615 25.68 0.00 0.00 3.01
2581 2686 8.893727 GCATAAACTCATTAGAACTATGTTGGT 58.106 33.333 0.00 0.00 0.00 3.67
2647 2781 8.631797 TGTAAATTTGCATCAGTATGTGCATAT 58.368 29.630 4.71 0.31 46.62 1.78
2716 2850 4.565022 GCTAGCCAATATTCAGGAGACTC 58.435 47.826 2.29 0.00 40.21 3.36
2744 2878 9.638239 GTTTGCTGATTGTTATCTTAATTCCAA 57.362 29.630 0.00 0.00 0.00 3.53
2767 2901 9.800433 CCAAATGCATCACTGTATATACAAAAA 57.200 29.630 16.17 5.33 35.50 1.94
2778 2912 9.813446 ACTGTATATACAAAAAGTACCTAGCAC 57.187 33.333 16.17 0.00 35.05 4.40
2783 2917 7.907214 ATACAAAAAGTACCTAGCACTTGAG 57.093 36.000 8.29 5.25 36.38 3.02
2784 2918 5.681639 ACAAAAAGTACCTAGCACTTGAGT 58.318 37.500 8.29 5.72 36.38 3.41
2849 2986 0.755698 TGGGATCTGGACGACTAGGC 60.756 60.000 0.00 0.00 0.00 3.93
2850 2987 1.655329 GGATCTGGACGACTAGGCG 59.345 63.158 18.57 18.57 37.29 5.52
2869 3006 6.229936 AGGCGTAACTAAAATATGACCTGA 57.770 37.500 0.00 0.00 0.00 3.86
2887 3024 8.463930 TGACCTGAAATTTGAGTTAACAGATT 57.536 30.769 8.61 0.00 0.00 2.40
2986 3123 4.828072 AGGTTCTCCAGTGGACTAATTC 57.172 45.455 8.12 3.31 35.89 2.17
2996 3489 5.070001 CAGTGGACTAATTCTTGGTTTGGA 58.930 41.667 0.00 0.00 0.00 3.53
3008 3501 1.286553 TGGTTTGGAGTGACCCTTTGT 59.713 47.619 0.00 0.00 38.00 2.83
3014 3507 2.069165 GAGTGACCCTTTGTGCCCCT 62.069 60.000 0.00 0.00 0.00 4.79
3092 3588 8.827177 TTGTCTTTTACATATCTCTGAACGTT 57.173 30.769 0.00 0.00 38.10 3.99
3097 3593 8.842358 TTTTACATATCTCTGAACGTTCCTTT 57.158 30.769 24.78 8.40 0.00 3.11
3225 3721 8.368668 AGACCTTATACAAGTATATTCTGCACC 58.631 37.037 1.11 0.00 0.00 5.01
3249 3745 4.410099 ACAGTTGATCCAATGGTGAATGT 58.590 39.130 0.00 0.00 0.00 2.71
3317 3821 6.262944 ACAAACTGTCAATAGCTCAATGAACA 59.737 34.615 0.00 0.00 0.00 3.18
3324 3828 8.833493 TGTCAATAGCTCAATGAACATCATAAG 58.167 33.333 0.00 0.00 35.76 1.73
3353 3866 7.090173 TGTCGGGTAAATTAGTAGTGTGTTAC 58.910 38.462 0.00 0.00 0.00 2.50
3699 4238 4.508861 CCCAATTCTTTTGTGAAGCAGTTG 59.491 41.667 0.00 0.00 0.00 3.16
3856 4417 1.168714 AACCGATCTTTTGCTGGAGC 58.831 50.000 0.00 0.00 42.50 4.70
4046 4609 9.926158 TTTGCATTTCACAGACAATACAATAAT 57.074 25.926 0.00 0.00 0.00 1.28
4063 4626 7.421530 ACAATAATCGTGCTGATAATGGTAC 57.578 36.000 0.00 0.00 35.84 3.34
4116 4679 9.471084 AACCTTTGTTGTAATAACTATTTGCAC 57.529 29.630 0.00 0.00 32.13 4.57
4117 4680 8.634444 ACCTTTGTTGTAATAACTATTTGCACA 58.366 29.630 0.00 0.00 0.00 4.57
4152 4715 8.415950 TTTTCTTGCTCCCTTGTATAATTTGA 57.584 30.769 0.00 0.00 0.00 2.69
4325 4888 5.022787 TCCCCAACCTGATTTATCTTTTGG 58.977 41.667 9.05 9.05 33.87 3.28
4351 4914 9.875691 GCAAGTAGTGAATGTATATCCATCATA 57.124 33.333 0.00 0.00 0.00 2.15
4392 4956 8.442632 TCATGAGATAGCTTGGTATTTTTCAG 57.557 34.615 0.00 0.00 0.00 3.02
4587 5154 1.696063 AAGTGAGCAGCAATGTGGTT 58.304 45.000 0.00 0.00 0.00 3.67
4928 5495 4.505039 GGAGGTGAAAGGTGTACAATCTGT 60.505 45.833 0.00 0.00 0.00 3.41
5149 5716 8.617809 GTGATGGTGTAGAGTTGTAAAGAAAAA 58.382 33.333 0.00 0.00 0.00 1.94
5177 5744 3.059597 CGTGTGCTTTCCAAGTTGTCTAG 60.060 47.826 1.45 0.00 0.00 2.43
5253 5820 6.349300 AGTAATGGTGGACAAGTTGCTATAG 58.651 40.000 1.81 0.00 0.00 1.31
5254 5821 4.844349 ATGGTGGACAAGTTGCTATAGT 57.156 40.909 1.81 0.00 0.00 2.12
5255 5822 4.634012 TGGTGGACAAGTTGCTATAGTT 57.366 40.909 1.81 0.00 0.00 2.24
5334 5901 9.797642 TGGTAATGAAATAATAGCTCATCATGT 57.202 29.630 0.00 0.00 0.00 3.21
5427 5995 2.006888 CGGGCGTTTCATTCAGTACAT 58.993 47.619 0.00 0.00 0.00 2.29
5428 5996 3.191669 CGGGCGTTTCATTCAGTACATA 58.808 45.455 0.00 0.00 0.00 2.29
5431 5999 4.634443 GGGCGTTTCATTCAGTACATAGTT 59.366 41.667 0.00 0.00 0.00 2.24
5435 6003 6.901887 GCGTTTCATTCAGTACATAGTTGATG 59.098 38.462 0.00 0.00 41.79 3.07
5465 6033 7.067372 TGTTGGACCAAAGCTGATTGATTATAG 59.933 37.037 8.94 0.00 31.84 1.31
5491 6059 8.730680 GGAGTATATCACAATTGAACAACTTGT 58.269 33.333 13.59 0.00 34.61 3.16
5565 6151 9.948964 TCATAGAGATATGGTGTGGATAATTTG 57.051 33.333 0.00 0.00 0.00 2.32
5580 6166 7.486232 GTGGATAATTTGACTAAAAGAAGCTGC 59.514 37.037 0.00 0.00 0.00 5.25
5582 6168 8.893727 GGATAATTTGACTAAAAGAAGCTGCTA 58.106 33.333 0.90 0.00 0.00 3.49
5589 6175 8.340618 TGACTAAAAGAAGCTGCTATTTTCAT 57.659 30.769 21.58 14.36 0.00 2.57
5590 6176 8.796475 TGACTAAAAGAAGCTGCTATTTTCATT 58.204 29.630 21.58 11.79 0.00 2.57
5591 6177 8.976986 ACTAAAAGAAGCTGCTATTTTCATTG 57.023 30.769 21.58 15.07 0.00 2.82
5592 6178 8.796475 ACTAAAAGAAGCTGCTATTTTCATTGA 58.204 29.630 21.58 9.20 0.00 2.57
5593 6179 9.798994 CTAAAAGAAGCTGCTATTTTCATTGAT 57.201 29.630 21.58 6.32 0.00 2.57
5619 6205 4.698583 AATTTGCTTGTTTTGCTTTGCA 57.301 31.818 0.00 0.00 36.47 4.08
5641 6227 7.672983 GCAATAGCATACTTAGCTTGGATAA 57.327 36.000 0.00 0.00 43.25 1.75
6048 6640 7.094334 ACGAATGGAGATATTCTAACTATCGCA 60.094 37.037 0.00 0.00 35.42 5.10
6070 6662 3.129813 AGGACGCGATACTGTGATTGTTA 59.870 43.478 15.93 0.00 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
87 93 0.653636 CGTACGCCACGCCATAAAAT 59.346 50.000 0.52 0.00 45.03 1.82
89 95 3.783393 CGTACGCCACGCCATAAA 58.217 55.556 0.52 0.00 45.03 1.40
98 104 3.630769 AGATGATCTTTCTACGTACGCCA 59.369 43.478 16.72 2.17 0.00 5.69
100 106 5.745514 TGTAGATGATCTTTCTACGTACGC 58.254 41.667 16.72 0.00 45.56 4.42
200 207 2.191375 CCGCACTGCTGGATGGAT 59.809 61.111 6.14 0.00 0.00 3.41
246 261 4.095400 TCCCCTCCTCCCTGCTCC 62.095 72.222 0.00 0.00 0.00 4.70
247 262 2.445654 CTCCCCTCCTCCCTGCTC 60.446 72.222 0.00 0.00 0.00 4.26
248 263 4.101077 CCTCCCCTCCTCCCTGCT 62.101 72.222 0.00 0.00 0.00 4.24
249 264 4.095400 TCCTCCCCTCCTCCCTGC 62.095 72.222 0.00 0.00 0.00 4.85
273 288 1.077858 CCCTCTCTCTTGGCTTGGC 60.078 63.158 0.00 0.00 0.00 4.52
274 289 0.540923 CTCCCTCTCTCTTGGCTTGG 59.459 60.000 0.00 0.00 0.00 3.61
275 290 0.540923 CCTCCCTCTCTCTTGGCTTG 59.459 60.000 0.00 0.00 0.00 4.01
276 291 0.415429 TCCTCCCTCTCTCTTGGCTT 59.585 55.000 0.00 0.00 0.00 4.35
277 292 0.415429 TTCCTCCCTCTCTCTTGGCT 59.585 55.000 0.00 0.00 0.00 4.75
278 293 0.829990 CTTCCTCCCTCTCTCTTGGC 59.170 60.000 0.00 0.00 0.00 4.52
279 294 0.829990 GCTTCCTCCCTCTCTCTTGG 59.170 60.000 0.00 0.00 0.00 3.61
280 295 0.829990 GGCTTCCTCCCTCTCTCTTG 59.170 60.000 0.00 0.00 0.00 3.02
281 296 0.326143 GGGCTTCCTCCCTCTCTCTT 60.326 60.000 0.00 0.00 43.13 2.85
282 297 1.313129 GGGCTTCCTCCCTCTCTCT 59.687 63.158 0.00 0.00 43.13 3.10
283 298 3.964108 GGGCTTCCTCCCTCTCTC 58.036 66.667 0.00 0.00 43.13 3.20
495 544 0.911769 ATCAGAGATTGCAACCGGGA 59.088 50.000 6.32 0.00 0.00 5.14
500 552 4.125703 AGAATCCGATCAGAGATTGCAAC 58.874 43.478 0.00 0.00 32.91 4.17
549 612 2.391389 GGCGAGGCGAAACCAAGAG 61.391 63.158 0.00 0.00 43.14 2.85
961 1059 3.358076 CTGCTTCTCCGGGTCGTCC 62.358 68.421 0.00 0.00 0.00 4.79
1489 1587 4.659115 CCTCCATCTGATTATTCATGCCA 58.341 43.478 0.00 0.00 0.00 4.92
1637 1735 2.101415 TGTTCTCATACCTCAGCATCCG 59.899 50.000 0.00 0.00 0.00 4.18
1732 1830 1.291877 CGTGTTGCTTCCCTTCCTCG 61.292 60.000 0.00 0.00 0.00 4.63
1765 1863 4.018490 CCATGTGGTCAATGATTCCTTCA 58.982 43.478 0.00 0.00 39.12 3.02
1837 1935 3.770933 TCTGATCCTCATCACACACATCA 59.229 43.478 0.00 0.00 33.80 3.07
1955 2053 4.880886 TCATGGTGCAGTTAATTGATCG 57.119 40.909 1.56 0.00 0.00 3.69
2002 2100 2.987413 TTTGTGACAATTGGCTAGCG 57.013 45.000 13.62 0.00 0.00 4.26
2007 2105 9.801873 ATACAGTAATAATTTGTGACAATTGGC 57.198 29.630 10.83 7.53 0.00 4.52
2128 2227 6.020440 CCAATCATTTGCAAGCATTTACGTAG 60.020 38.462 0.00 0.00 0.00 3.51
2129 2228 5.804473 CCAATCATTTGCAAGCATTTACGTA 59.196 36.000 0.00 0.00 0.00 3.57
2130 2229 4.626604 CCAATCATTTGCAAGCATTTACGT 59.373 37.500 0.00 0.00 0.00 3.57
2131 2230 4.626604 ACCAATCATTTGCAAGCATTTACG 59.373 37.500 0.00 0.00 0.00 3.18
2132 2231 5.638657 TCACCAATCATTTGCAAGCATTTAC 59.361 36.000 0.00 0.00 0.00 2.01
2140 2239 5.644206 CCAAATCATCACCAATCATTTGCAA 59.356 36.000 0.00 0.00 34.47 4.08
2215 2314 5.355596 CACTATCTGCTTCCTGACCTTAAG 58.644 45.833 0.00 0.00 0.00 1.85
2572 2674 9.834628 ACGTGTTATAAATTCAAACCAACATAG 57.165 29.630 0.00 0.00 0.00 2.23
2716 2850 9.294030 GGAATTAAGATAACAATCAGCAAACAG 57.706 33.333 0.00 0.00 0.00 3.16
2767 2901 4.408276 TCAAGACTCAAGTGCTAGGTACT 58.592 43.478 0.00 0.00 46.37 2.73
2778 2912 6.181908 AGTACTACCTACCTCAAGACTCAAG 58.818 44.000 0.00 0.00 0.00 3.02
2779 2913 6.137104 AGTACTACCTACCTCAAGACTCAA 57.863 41.667 0.00 0.00 0.00 3.02
2780 2914 5.775813 AGTACTACCTACCTCAAGACTCA 57.224 43.478 0.00 0.00 0.00 3.41
2781 2915 6.126796 ACCTAGTACTACCTACCTCAAGACTC 60.127 46.154 0.00 0.00 0.00 3.36
2782 2916 5.730697 ACCTAGTACTACCTACCTCAAGACT 59.269 44.000 0.00 0.00 0.00 3.24
2783 2917 6.000246 ACCTAGTACTACCTACCTCAAGAC 58.000 45.833 0.00 0.00 0.00 3.01
2784 2918 5.969402 AGACCTAGTACTACCTACCTCAAGA 59.031 44.000 0.00 0.00 0.00 3.02
2818 2953 3.843619 TCCAGATCCCAAGTATCACACAA 59.156 43.478 0.00 0.00 0.00 3.33
2869 3006 7.595819 TGTCCCAATCTGTTAACTCAAATTT 57.404 32.000 7.22 0.00 0.00 1.82
2986 3123 2.362077 CAAAGGGTCACTCCAAACCAAG 59.638 50.000 0.00 0.00 37.28 3.61
2996 3489 2.069165 GAGGGGCACAAAGGGTCACT 62.069 60.000 0.00 0.00 0.00 3.41
3082 3578 3.625764 TCCAACAAAAGGAACGTTCAGAG 59.374 43.478 28.24 15.28 30.71 3.35
3092 3588 3.053245 TGGGTTCTTCTCCAACAAAAGGA 60.053 43.478 0.00 0.00 0.00 3.36
3097 3593 5.073144 AGTCTTATGGGTTCTTCTCCAACAA 59.927 40.000 0.00 0.00 36.54 2.83
3139 3635 9.346725 GTTAAAAGAAACCTTAGCATCAATCAG 57.653 33.333 0.00 0.00 0.00 2.90
3176 3672 7.653713 GTCTGGTACATTAACTTCATGATCGAT 59.346 37.037 0.00 0.00 38.20 3.59
3225 3721 5.649395 ACATTCACCATTGGATCAACTGTAG 59.351 40.000 10.37 0.00 0.00 2.74
3324 3828 7.761249 ACACACTACTAATTTACCCGACATTAC 59.239 37.037 0.00 0.00 0.00 1.89
3699 4238 6.910995 TCTCTACAAGTAAGCAGACAAGTAC 58.089 40.000 0.00 0.00 0.00 2.73
3828 4368 7.012327 TCCAGCAAAAGATCGGTTAATGATAAG 59.988 37.037 0.00 0.00 0.00 1.73
3856 4417 5.188751 AGAAGGGAGGTGAAGATAACTCTTG 59.811 44.000 0.00 0.00 41.87 3.02
4013 4575 3.286353 TCTGTGAAATGCAAACAGACCA 58.714 40.909 16.41 1.33 44.01 4.02
4046 4609 3.129813 AGTTCGTACCATTATCAGCACGA 59.870 43.478 0.00 0.00 36.70 4.35
4063 4626 5.778161 TCATGTAATTAGCACACAGTTCG 57.222 39.130 0.00 0.00 0.00 3.95
4152 4715 2.840651 CAGGTTGGGGATGTCTAACTCT 59.159 50.000 0.00 0.00 0.00 3.24
4325 4888 8.783833 ATGATGGATATACATTCACTACTTGC 57.216 34.615 0.86 0.00 0.00 4.01
4587 5154 3.328931 AGAAGACCTTCAGGCATTTCTCA 59.671 43.478 11.80 0.00 41.84 3.27
4754 5321 6.611381 TGCATGCTGTAATTTGAAGTACTTC 58.389 36.000 25.73 25.73 39.91 3.01
4761 5328 6.831727 GCAATATGCATGCTGTAATTTGAA 57.168 33.333 20.33 0.00 44.26 2.69
4928 5495 2.192664 TACAGATTTCTTTGGCGCCA 57.807 45.000 29.03 29.03 0.00 5.69
4969 5536 9.529325 TGCAGATACATCATAGTAAACAACTAC 57.471 33.333 0.00 0.00 43.47 2.73
4973 5540 7.010091 CGTGTGCAGATACATCATAGTAAACAA 59.990 37.037 0.00 0.00 32.43 2.83
5167 5734 6.525629 ACAGCAGATACAAACTAGACAACTT 58.474 36.000 0.00 0.00 0.00 2.66
5177 5744 6.092259 AGGAAAACGATACAGCAGATACAAAC 59.908 38.462 0.00 0.00 0.00 2.93
5253 5820 8.129211 GGAGTGACCAAAATATATAGCAACAAC 58.871 37.037 0.00 0.00 38.79 3.32
5254 5821 7.831690 TGGAGTGACCAAAATATATAGCAACAA 59.168 33.333 0.00 0.00 46.75 2.83
5255 5822 7.342581 TGGAGTGACCAAAATATATAGCAACA 58.657 34.615 0.00 0.00 46.75 3.33
5360 5927 5.390991 GCAAAACAGGTGAGCTCTACAATAC 60.391 44.000 16.19 2.99 0.00 1.89
5427 5995 5.554437 TTGGTCCAACAGTACATCAACTA 57.446 39.130 0.00 0.00 0.00 2.24
5428 5996 4.431416 TTGGTCCAACAGTACATCAACT 57.569 40.909 0.00 0.00 0.00 3.16
5431 5999 3.146066 GCTTTGGTCCAACAGTACATCA 58.854 45.455 2.98 0.00 0.00 3.07
5435 6003 2.846193 TCAGCTTTGGTCCAACAGTAC 58.154 47.619 2.98 0.00 0.00 2.73
5465 6033 8.730680 ACAAGTTGTTCAATTGTGATATACTCC 58.269 33.333 1.64 0.00 35.89 3.85
5550 6134 8.698973 TTCTTTTAGTCAAATTATCCACACCA 57.301 30.769 0.00 0.00 0.00 4.17
5555 6141 7.394359 AGCAGCTTCTTTTAGTCAAATTATCCA 59.606 33.333 0.00 0.00 0.00 3.41
5556 6142 7.766283 AGCAGCTTCTTTTAGTCAAATTATCC 58.234 34.615 0.00 0.00 0.00 2.59
5565 6151 9.070149 CAATGAAAATAGCAGCTTCTTTTAGTC 57.930 33.333 0.00 0.00 0.00 2.59
5619 6205 9.799106 AACATTATCCAAGCTAAGTATGCTATT 57.201 29.630 0.00 0.00 40.22 1.73
6048 6640 1.476891 ACAATCACAGTATCGCGTCCT 59.523 47.619 5.77 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.