Multiple sequence alignment - TraesCS3A01G170500

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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 TraesCS3A01G170500 chr3A 100.000 2828 0 0 1 2828 178256480 178253653 0.000000e+00 5223
1 TraesCS3A01G170500 chr3B 90.336 2204 108 28 1 2141 222803237 222805398 0.000000e+00 2793
2 TraesCS3A01G170500 chr3B 83.834 433 49 6 2404 2828 222813577 222813996 2.640000e-105 392
3 TraesCS3A01G170500 chr3D 91.356 2013 77 23 1 1954 152481651 152483625 0.000000e+00 2663
4 TraesCS3A01G170500 chr3D 93.750 848 45 5 1986 2828 152483706 152484550 0.000000e+00 1266


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 TraesCS3A01G170500 chr3A 178253653 178256480 2827 True 5223.0 5223 100.000 1 2828 1 chr3A.!!$R1 2827
1 TraesCS3A01G170500 chr3B 222803237 222805398 2161 False 2793.0 2793 90.336 1 2141 1 chr3B.!!$F1 2140
2 TraesCS3A01G170500 chr3D 152481651 152484550 2899 False 1964.5 2663 92.553 1 2828 2 chr3D.!!$F1 2827


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
225 227 1.064017 TGTGTGAGGAAAAAGCCCTGT 60.064 47.619 0.00 0.00 33.36 4.00 F
776 787 1.529010 GCGTCACGTGACATAATTGCC 60.529 52.381 39.14 18.66 44.99 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1411 1464 0.109272 TTGTAAGCCGAGACGAGCAG 60.109 55.0 0.0 0.0 0.00 4.24 R
2345 2504 0.253160 TATGAGTTCCACCAGGGCCT 60.253 55.0 0.0 0.0 36.21 5.19 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
26 27 7.430502 CCTGCTTGATTTATCGATTCAACTTTC 59.569 37.037 1.71 0.00 0.00 2.62
37 39 4.447724 CGATTCAACTTTCGTCAGGAGAAA 59.552 41.667 0.00 0.00 36.34 2.52
42 44 1.623811 CTTTCGTCAGGAGAAAGGGGA 59.376 52.381 9.98 0.00 46.38 4.81
55 57 3.384467 AGAAAGGGGAATGTTGTGTTGTG 59.616 43.478 0.00 0.00 0.00 3.33
84 86 3.552604 GCACAAAGCACCTCGAAATTA 57.447 42.857 0.00 0.00 44.79 1.40
105 107 6.721571 TTAGCTAATTGGTTTCTTCTGTCG 57.278 37.500 0.86 0.00 0.00 4.35
119 121 4.923871 TCTTCTGTCGCAGTTCTTTGATAC 59.076 41.667 6.72 0.00 32.61 2.24
121 123 4.237724 TCTGTCGCAGTTCTTTGATACTG 58.762 43.478 6.72 0.00 43.58 2.74
186 188 5.039920 TGGTTGATCCATTAGACATCCTG 57.960 43.478 0.00 0.00 41.93 3.86
187 189 4.721274 TGGTTGATCCATTAGACATCCTGA 59.279 41.667 0.00 0.00 41.93 3.86
223 225 2.452600 TTGTGTGAGGAAAAAGCCCT 57.547 45.000 0.00 0.00 36.57 5.19
225 227 1.064017 TGTGTGAGGAAAAAGCCCTGT 60.064 47.619 0.00 0.00 33.36 4.00
288 290 6.252995 TGAATGTATTCTTACTTTGGGCCTT 58.747 36.000 4.53 0.00 37.67 4.35
289 291 6.723977 TGAATGTATTCTTACTTTGGGCCTTT 59.276 34.615 4.53 0.00 37.67 3.11
290 292 7.234577 TGAATGTATTCTTACTTTGGGCCTTTT 59.765 33.333 4.53 0.00 37.67 2.27
355 357 4.202567 GGGCTCCCAACAGATTATTATCCA 60.203 45.833 0.00 0.00 35.81 3.41
374 376 5.726980 TCCAAAATTTCTCCTCAACCATG 57.273 39.130 0.00 0.00 0.00 3.66
375 377 5.147032 TCCAAAATTTCTCCTCAACCATGT 58.853 37.500 0.00 0.00 0.00 3.21
376 378 6.310941 TCCAAAATTTCTCCTCAACCATGTA 58.689 36.000 0.00 0.00 0.00 2.29
409 411 6.215121 GTGATCCATTGTGAGAGACTGATAG 58.785 44.000 0.00 0.00 0.00 2.08
479 483 3.840831 ACACATATGCGAGCTGTGT 57.159 47.368 13.48 13.48 46.37 3.72
580 591 6.543465 ACAACTGATGTCATGTTCTTTTCTGA 59.457 34.615 0.00 0.00 37.96 3.27
697 708 7.202526 TCTTGCAGTGTTTCCTTGAATAAAAG 58.797 34.615 0.00 0.00 0.00 2.27
755 766 2.358957 TGCATGAGTTACTCCATGCAC 58.641 47.619 29.80 15.48 43.09 4.57
776 787 1.529010 GCGTCACGTGACATAATTGCC 60.529 52.381 39.14 18.66 44.99 4.52
784 795 3.609853 GTGACATAATTGCCTGGTCTGA 58.390 45.455 0.00 0.00 0.00 3.27
918 959 4.621510 CGTAAACCCTACTTCCACCTTACC 60.622 50.000 0.00 0.00 0.00 2.85
983 1024 2.573915 TCTCTCTCCTCTCTGCACTGTA 59.426 50.000 0.00 0.00 0.00 2.74
984 1025 2.945008 CTCTCTCCTCTCTGCACTGTAG 59.055 54.545 0.00 0.00 0.00 2.74
985 1026 2.573915 TCTCTCCTCTCTGCACTGTAGA 59.426 50.000 0.00 0.00 0.00 2.59
986 1027 2.682856 CTCTCCTCTCTGCACTGTAGAC 59.317 54.545 0.00 0.00 0.00 2.59
987 1028 2.040412 TCTCCTCTCTGCACTGTAGACA 59.960 50.000 0.00 0.00 0.00 3.41
1411 1464 2.015382 CAGCAGCAGCAGCAGATAC 58.985 57.895 12.92 0.00 45.49 2.24
1777 1853 7.125811 TGGTGGATATATATGGGCTTCTTCTAC 59.874 40.741 0.00 0.00 0.00 2.59
1782 1858 0.179108 ATGGGCTTCTTCTACGCGTC 60.179 55.000 18.63 0.00 0.00 5.19
1791 1868 1.519758 CTTCTACGCGTCGTGTTTTGT 59.480 47.619 18.63 0.00 41.39 2.83
1794 1871 3.111838 TCTACGCGTCGTGTTTTGTAAA 58.888 40.909 18.63 0.00 41.39 2.01
1855 1932 2.903798 CAGTGAGAGAAGATGAAGGCC 58.096 52.381 0.00 0.00 0.00 5.19
1856 1933 1.836802 AGTGAGAGAAGATGAAGGCCC 59.163 52.381 0.00 0.00 0.00 5.80
1857 1934 1.134250 GTGAGAGAAGATGAAGGCCCC 60.134 57.143 0.00 0.00 0.00 5.80
1858 1935 1.207791 GAGAGAAGATGAAGGCCCCA 58.792 55.000 0.00 0.00 0.00 4.96
1859 1936 1.561542 GAGAGAAGATGAAGGCCCCAA 59.438 52.381 0.00 0.00 0.00 4.12
1860 1937 1.995542 AGAGAAGATGAAGGCCCCAAA 59.004 47.619 0.00 0.00 0.00 3.28
1861 1938 2.095461 GAGAAGATGAAGGCCCCAAAC 58.905 52.381 0.00 0.00 0.00 2.93
1862 1939 1.186200 GAAGATGAAGGCCCCAAACC 58.814 55.000 0.00 0.00 0.00 3.27
1863 1940 0.252239 AAGATGAAGGCCCCAAACCC 60.252 55.000 0.00 0.00 0.00 4.11
1864 1941 1.149133 AGATGAAGGCCCCAAACCCT 61.149 55.000 0.00 0.00 0.00 4.34
1865 1942 0.629058 GATGAAGGCCCCAAACCCTA 59.371 55.000 0.00 0.00 0.00 3.53
1866 1943 0.631212 ATGAAGGCCCCAAACCCTAG 59.369 55.000 0.00 0.00 0.00 3.02
1867 1944 1.306633 GAAGGCCCCAAACCCTAGG 59.693 63.158 0.06 0.06 0.00 3.02
1868 1945 2.856039 GAAGGCCCCAAACCCTAGGC 62.856 65.000 2.05 0.00 44.99 3.93
1869 1946 3.347590 GGCCCCAAACCCTAGGCT 61.348 66.667 2.05 0.00 45.07 4.58
1870 1947 2.043953 GCCCCAAACCCTAGGCTG 60.044 66.667 2.05 0.00 42.34 4.85
1871 1948 2.612493 GCCCCAAACCCTAGGCTGA 61.612 63.158 2.05 0.00 42.34 4.26
1872 1949 1.303282 CCCCAAACCCTAGGCTGAC 59.697 63.158 2.05 0.00 0.00 3.51
1873 1950 1.208165 CCCCAAACCCTAGGCTGACT 61.208 60.000 2.05 0.00 0.00 3.41
1874 1951 1.580059 CCCAAACCCTAGGCTGACTA 58.420 55.000 2.05 0.00 0.00 2.59
1875 1952 1.209747 CCCAAACCCTAGGCTGACTAC 59.790 57.143 2.05 0.00 0.00 2.73
1893 1970 7.259290 TGACTACAGAAATTCAACTGTTTCC 57.741 36.000 14.72 7.72 43.52 3.13
2176 2331 6.595716 AGAACCTCAGTTGCATTCAGTATTAC 59.404 38.462 0.00 0.00 35.94 1.89
2211 2366 3.119459 AGCACATGAACTGGAGTAGTACG 60.119 47.826 0.00 0.00 39.18 3.67
2236 2394 6.595682 CCTCACAAGTCACAAATATAGGGAT 58.404 40.000 0.00 0.00 0.00 3.85
2252 2410 9.762381 AATATAGGGATTAAAAACACAGGAACA 57.238 29.630 0.00 0.00 0.00 3.18
2254 2412 5.454966 AGGGATTAAAAACACAGGAACAGT 58.545 37.500 0.00 0.00 0.00 3.55
2255 2413 5.897250 AGGGATTAAAAACACAGGAACAGTT 59.103 36.000 0.00 0.00 0.00 3.16
2276 2435 1.359474 AGAGTAGCTTGGAGGGACAGA 59.641 52.381 0.00 0.00 0.00 3.41
2283 2442 2.260822 CTTGGAGGGACAGAAGGAGAA 58.739 52.381 0.00 0.00 0.00 2.87
2286 2445 0.174617 GAGGGACAGAAGGAGAAGCG 59.825 60.000 0.00 0.00 0.00 4.68
2291 2450 0.394565 ACAGAAGGAGAAGCGTTGCT 59.605 50.000 0.00 0.00 42.56 3.91
2319 2478 6.828502 TGTATTGCTACTCGATGAAATCAC 57.171 37.500 0.00 0.00 45.97 3.06
2326 2485 7.142021 TGCTACTCGATGAAATCACTAAGATC 58.858 38.462 0.00 0.00 45.97 2.75
2337 2496 9.521503 TGAAATCACTAAGATCATCTAAACTCG 57.478 33.333 0.00 0.00 35.39 4.18
2345 2504 7.392494 AAGATCATCTAAACTCGTGAGTACA 57.608 36.000 2.42 0.00 41.58 2.90
2356 2515 1.918293 TGAGTACAGGCCCTGGTGG 60.918 63.158 16.70 0.00 35.51 4.61
2361 2520 1.198759 TACAGGCCCTGGTGGAACTC 61.199 60.000 16.70 0.00 35.51 3.01
2375 2534 5.874810 TGGTGGAACTCATAAAGATTTCTCG 59.125 40.000 0.00 0.00 36.47 4.04
2377 2536 5.582665 GTGGAACTCATAAAGATTTCTCGCT 59.417 40.000 0.00 0.00 36.47 4.93
2380 2539 7.492669 TGGAACTCATAAAGATTTCTCGCTAAG 59.507 37.037 0.00 0.00 36.47 2.18
2391 2550 0.179161 CTCGCTAAGTGTGACCGAGG 60.179 60.000 0.00 0.00 41.04 4.63
2392 2551 1.153823 CGCTAAGTGTGACCGAGGG 60.154 63.158 0.00 0.00 0.00 4.30
2395 2554 1.404315 GCTAAGTGTGACCGAGGGAAG 60.404 57.143 0.00 0.00 0.00 3.46
2399 2558 1.075050 AGTGTGACCGAGGGAAGACTA 59.925 52.381 0.00 0.00 0.00 2.59
2404 2563 3.385111 GTGACCGAGGGAAGACTAATGAT 59.615 47.826 0.00 0.00 0.00 2.45
2405 2564 4.030913 TGACCGAGGGAAGACTAATGATT 58.969 43.478 0.00 0.00 0.00 2.57
2406 2565 5.068723 GTGACCGAGGGAAGACTAATGATTA 59.931 44.000 0.00 0.00 0.00 1.75
2445 2604 3.494924 CCACAAACTGGAGATGACTCACA 60.495 47.826 0.00 0.00 43.95 3.58
2450 2609 6.014242 ACAAACTGGAGATGACTCACAATAGA 60.014 38.462 0.00 0.00 44.22 1.98
2479 2638 2.076863 CAGACCGGTTGGATCAAACTC 58.923 52.381 9.42 3.04 39.21 3.01
2581 2740 2.555325 CAAATATCAGCATGCGGATGGT 59.445 45.455 34.46 23.16 41.09 3.55
2651 2810 4.274147 TCCTTGTGCTACAACCTCAAAAA 58.726 39.130 0.00 0.00 33.96 1.94
2669 2828 8.958043 CCTCAAAAAGAAACTGAAAATTCTACG 58.042 33.333 0.00 0.00 34.90 3.51
2672 2831 7.914537 AAAAGAAACTGAAAATTCTACGCTG 57.085 32.000 0.00 0.00 34.90 5.18
2708 2867 2.034558 AGATGTTCACCAAAACCAAGCG 59.965 45.455 0.00 0.00 0.00 4.68
2731 2890 0.177141 TACTGCGGGAACAGCCATAC 59.823 55.000 0.00 0.00 41.60 2.39
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 1.279271 ACATTCCCCTTTCTCCTGACG 59.721 52.381 0.00 0.00 0.00 4.35
37 39 1.216678 TCCACAACACAACATTCCCCT 59.783 47.619 0.00 0.00 0.00 4.79
42 44 5.163468 TGCATAAACTCCACAACACAACATT 60.163 36.000 0.00 0.00 0.00 2.71
84 86 3.437049 GCGACAGAAGAAACCAATTAGCT 59.563 43.478 0.00 0.00 0.00 3.32
105 107 4.253685 TGGCTACAGTATCAAAGAACTGC 58.746 43.478 2.52 0.00 45.65 4.40
119 121 2.062971 AAGAATGGGCATGGCTACAG 57.937 50.000 19.78 0.00 0.00 2.74
121 123 1.410153 CCAAAGAATGGGCATGGCTAC 59.590 52.381 19.78 3.75 46.27 3.58
185 187 9.447157 TCACACAATCACACTATTATTTCATCA 57.553 29.630 0.00 0.00 0.00 3.07
186 188 9.926751 CTCACACAATCACACTATTATTTCATC 57.073 33.333 0.00 0.00 0.00 2.92
187 189 8.896744 CCTCACACAATCACACTATTATTTCAT 58.103 33.333 0.00 0.00 0.00 2.57
223 225 4.612264 GGTCACTTACCCAGAAGTAACA 57.388 45.455 0.00 0.00 43.16 2.41
288 290 4.517453 ACTTATGTGTTAGCGAGCCAAAAA 59.483 37.500 0.00 0.00 0.00 1.94
289 291 4.069304 ACTTATGTGTTAGCGAGCCAAAA 58.931 39.130 0.00 0.00 0.00 2.44
290 292 3.435327 CACTTATGTGTTAGCGAGCCAAA 59.565 43.478 0.62 0.00 39.24 3.28
355 357 8.960591 CATACTACATGGTTGAGGAGAAATTTT 58.039 33.333 0.00 0.00 0.00 1.82
374 376 4.745125 CACAATGGATCACCGACATACTAC 59.255 45.833 0.00 0.00 39.42 2.73
375 377 4.647399 TCACAATGGATCACCGACATACTA 59.353 41.667 0.00 0.00 39.42 1.82
376 378 3.450817 TCACAATGGATCACCGACATACT 59.549 43.478 0.00 0.00 39.42 2.12
409 411 3.626028 AACCGTTTCATTCTGACTTGC 57.374 42.857 0.00 0.00 0.00 4.01
453 457 5.200454 CAGCTCGCATATGTGTTCAATAAC 58.800 41.667 15.62 0.00 36.07 1.89
456 460 3.064408 CACAGCTCGCATATGTGTTCAAT 59.936 43.478 15.62 0.00 39.54 2.57
457 461 2.416202 CACAGCTCGCATATGTGTTCAA 59.584 45.455 15.62 0.00 39.54 2.69
470 474 4.896562 TCGTTTACAAATACACAGCTCG 57.103 40.909 0.00 0.00 0.00 5.03
580 591 3.321111 GCAATCCTTCCAGAATGCATCAT 59.679 43.478 0.00 0.00 41.42 2.45
776 787 6.528423 CGTAGTAGTTTCATTTCTCAGACCAG 59.472 42.308 0.00 0.00 0.00 4.00
784 795 7.879070 TCAGTACACGTAGTAGTTTCATTTCT 58.121 34.615 0.00 0.00 41.61 2.52
918 959 4.268644 CGTATATATGCGCTCCCAAAGATG 59.731 45.833 9.73 0.00 0.00 2.90
1411 1464 0.109272 TTGTAAGCCGAGACGAGCAG 60.109 55.000 0.00 0.00 0.00 4.24
1777 1853 1.377505 GCATTTACAAAACACGACGCG 59.622 47.619 3.53 3.53 0.00 6.01
1782 1858 3.485378 CACACCTGCATTTACAAAACACG 59.515 43.478 0.00 0.00 0.00 4.49
1791 1868 1.270571 TGAGCGTCACACCTGCATTTA 60.271 47.619 0.00 0.00 0.00 1.40
1794 1871 1.375140 CTGAGCGTCACACCTGCAT 60.375 57.895 0.00 0.00 0.00 3.96
1836 1913 1.836802 GGGCCTTCATCTTCTCTCACT 59.163 52.381 0.84 0.00 0.00 3.41
1837 1914 1.134250 GGGGCCTTCATCTTCTCTCAC 60.134 57.143 0.84 0.00 0.00 3.51
1840 1917 1.673767 TTGGGGCCTTCATCTTCTCT 58.326 50.000 0.84 0.00 0.00 3.10
1855 1932 1.209747 GTAGTCAGCCTAGGGTTTGGG 59.790 57.143 11.77 0.00 0.00 4.12
1856 1933 1.906574 TGTAGTCAGCCTAGGGTTTGG 59.093 52.381 11.77 0.00 0.00 3.28
1857 1934 2.832129 TCTGTAGTCAGCCTAGGGTTTG 59.168 50.000 11.77 0.66 41.10 2.93
1858 1935 3.185880 TCTGTAGTCAGCCTAGGGTTT 57.814 47.619 11.77 2.61 41.10 3.27
1859 1936 2.921834 TCTGTAGTCAGCCTAGGGTT 57.078 50.000 11.77 0.00 41.10 4.11
1860 1937 2.921834 TTCTGTAGTCAGCCTAGGGT 57.078 50.000 7.93 7.93 41.10 4.34
1861 1938 4.162320 TGAATTTCTGTAGTCAGCCTAGGG 59.838 45.833 11.72 0.00 41.10 3.53
1862 1939 5.344743 TGAATTTCTGTAGTCAGCCTAGG 57.655 43.478 3.67 3.67 41.10 3.02
1863 1940 6.312426 CAGTTGAATTTCTGTAGTCAGCCTAG 59.688 42.308 0.00 0.00 41.10 3.02
1864 1941 6.166279 CAGTTGAATTTCTGTAGTCAGCCTA 58.834 40.000 0.00 0.00 41.10 3.93
1865 1942 4.999950 CAGTTGAATTTCTGTAGTCAGCCT 59.000 41.667 0.00 0.00 41.10 4.58
1866 1943 4.757149 ACAGTTGAATTTCTGTAGTCAGCC 59.243 41.667 9.16 0.00 42.13 4.85
1867 1944 5.931441 ACAGTTGAATTTCTGTAGTCAGC 57.069 39.130 9.16 0.00 42.13 4.26
1868 1945 7.227512 AGGAAACAGTTGAATTTCTGTAGTCAG 59.772 37.037 10.64 0.00 42.95 3.51
1869 1946 7.054124 AGGAAACAGTTGAATTTCTGTAGTCA 58.946 34.615 10.64 0.00 42.95 3.41
1870 1947 7.497925 AGGAAACAGTTGAATTTCTGTAGTC 57.502 36.000 10.64 10.69 42.95 2.59
1871 1948 9.003658 CATAGGAAACAGTTGAATTTCTGTAGT 57.996 33.333 10.64 4.69 42.95 2.73
1872 1949 9.219603 TCATAGGAAACAGTTGAATTTCTGTAG 57.780 33.333 10.64 0.00 42.95 2.74
1873 1950 9.567776 TTCATAGGAAACAGTTGAATTTCTGTA 57.432 29.630 10.64 0.00 42.95 2.74
1874 1951 8.463930 TTCATAGGAAACAGTTGAATTTCTGT 57.536 30.769 0.00 6.21 45.21 3.41
1875 1952 9.918630 ATTTCATAGGAAACAGTTGAATTTCTG 57.081 29.630 4.42 5.21 45.22 3.02
1975 2117 2.677836 GCAGAAGAGAAACACACACACA 59.322 45.455 0.00 0.00 0.00 3.72
1976 2118 2.939103 AGCAGAAGAGAAACACACACAC 59.061 45.455 0.00 0.00 0.00 3.82
1977 2119 3.266510 AGCAGAAGAGAAACACACACA 57.733 42.857 0.00 0.00 0.00 3.72
1978 2120 3.623060 TCAAGCAGAAGAGAAACACACAC 59.377 43.478 0.00 0.00 0.00 3.82
1979 2121 3.872696 TCAAGCAGAAGAGAAACACACA 58.127 40.909 0.00 0.00 0.00 3.72
1980 2122 3.303659 GCTCAAGCAGAAGAGAAACACAC 60.304 47.826 0.00 0.00 41.59 3.82
1981 2123 2.874701 GCTCAAGCAGAAGAGAAACACA 59.125 45.455 0.00 0.00 41.59 3.72
1982 2124 3.534524 GCTCAAGCAGAAGAGAAACAC 57.465 47.619 0.00 0.00 41.59 3.32
2081 2236 9.525409 GCTTGAAATAATCTCTAAAATGCATGT 57.475 29.630 0.00 0.00 0.00 3.21
2176 2331 2.827322 TCATGTGCTTTTCCTGAATGGG 59.173 45.455 0.00 0.00 36.20 4.00
2211 2366 4.576463 CCCTATATTTGTGACTTGTGAGGC 59.424 45.833 0.00 0.00 0.00 4.70
2236 2394 9.321562 CTACTCTAACTGTTCCTGTGTTTTTAA 57.678 33.333 0.00 0.00 0.00 1.52
2252 2410 3.245658 TGTCCCTCCAAGCTACTCTAACT 60.246 47.826 0.00 0.00 0.00 2.24
2254 2412 3.011369 TCTGTCCCTCCAAGCTACTCTAA 59.989 47.826 0.00 0.00 0.00 2.10
2255 2413 2.581246 TCTGTCCCTCCAAGCTACTCTA 59.419 50.000 0.00 0.00 0.00 2.43
2283 2442 2.489329 AGCAATACATCAAAGCAACGCT 59.511 40.909 0.00 0.00 42.56 5.07
2286 2445 5.063438 TCGAGTAGCAATACATCAAAGCAAC 59.937 40.000 0.00 0.00 0.00 4.17
2291 2450 7.841915 TTTCATCGAGTAGCAATACATCAAA 57.158 32.000 0.00 0.00 0.00 2.69
2294 2453 7.383572 AGTGATTTCATCGAGTAGCAATACATC 59.616 37.037 0.00 0.00 0.00 3.06
2319 2478 8.613482 TGTACTCACGAGTTTAGATGATCTTAG 58.387 37.037 4.79 0.00 42.54 2.18
2326 2485 4.106197 GCCTGTACTCACGAGTTTAGATG 58.894 47.826 4.79 0.00 42.54 2.90
2337 2496 1.296715 CACCAGGGCCTGTACTCAC 59.703 63.158 30.68 0.00 0.00 3.51
2345 2504 0.253160 TATGAGTTCCACCAGGGCCT 60.253 55.000 0.00 0.00 36.21 5.19
2356 2515 8.324567 CACTTAGCGAGAAATCTTTATGAGTTC 58.675 37.037 0.95 0.95 46.53 3.01
2361 2520 7.394872 GTCACACTTAGCGAGAAATCTTTATG 58.605 38.462 0.00 0.00 0.00 1.90
2375 2534 0.606604 TTCCCTCGGTCACACTTAGC 59.393 55.000 0.00 0.00 0.00 3.09
2377 2536 1.891150 GTCTTCCCTCGGTCACACTTA 59.109 52.381 0.00 0.00 0.00 2.24
2380 2539 1.542492 TAGTCTTCCCTCGGTCACAC 58.458 55.000 0.00 0.00 0.00 3.82
2399 2558 8.530311 TGGCAACATAGAATTTGTGTAATCATT 58.470 29.630 0.00 0.00 46.17 2.57
2445 2604 2.271800 CGGTCTGAGCGCTTTTCTATT 58.728 47.619 13.26 0.00 30.39 1.73
2450 2609 1.227853 AACCGGTCTGAGCGCTTTT 60.228 52.632 22.59 12.32 37.85 2.27
2479 2638 1.271001 TGACCCTTGTCATGCACTCTG 60.271 52.381 0.00 0.00 46.40 3.35
2617 2776 8.903820 GTTGTAGCACAAGGAATCCTAATATTT 58.096 33.333 0.46 0.00 39.00 1.40
2651 2810 6.566753 GCTTCAGCGTAGAATTTTCAGTTTCT 60.567 38.462 0.00 0.00 36.26 2.52
2669 2828 5.303971 ACATCTGAGTTATATGGCTTCAGC 58.696 41.667 0.00 0.00 41.14 4.26
2672 2831 6.203723 GGTGAACATCTGAGTTATATGGCTTC 59.796 42.308 0.00 0.00 0.00 3.86
2708 2867 1.523938 GCTGTTCCCGCAGTATCCC 60.524 63.158 0.00 0.00 38.65 3.85
2731 2890 3.043586 CCGATGAGACTCGTTAAATCCG 58.956 50.000 0.00 0.00 36.93 4.18



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

AutoCloner maintained by Alex Coulton.