Multiple sequence alignment - TraesCS3A01G309400

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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 TraesCS3A01G309400 chr3A 100.000 2369 0 0 1 2369 547405056 547407424 0.000000e+00 4375.0
1 TraesCS3A01G309400 chr3A 87.974 923 57 20 7 914 547471851 547472734 0.000000e+00 1040.0
2 TraesCS3A01G309400 chr3A 93.137 408 20 4 507 914 547413440 547413839 2.030000e-165 592.0
3 TraesCS3A01G309400 chr3A 81.174 579 77 21 942 1492 547414432 547415006 1.010000e-118 436.0
4 TraesCS3A01G309400 chr3B 87.985 799 52 14 7 802 144809356 144810113 0.000000e+00 904.0
5 TraesCS3A01G309400 chr3B 90.785 586 42 3 227 811 144780102 144780676 0.000000e+00 773.0
6 TraesCS3A01G309400 chr3B 85.246 488 55 9 942 1420 144800105 144800584 9.840000e-134 486.0
7 TraesCS3A01G309400 chr3B 84.615 481 55 13 942 1413 144781144 144781614 5.970000e-126 460.0
8 TraesCS3A01G309400 chr3B 83.028 436 63 8 942 1368 144777219 144777652 3.690000e-103 385.0
9 TraesCS3A01G309400 chr3B 88.038 209 11 9 7 208 144779908 144780109 3.940000e-58 235.0
10 TraesCS3A01G309400 chr3B 82.609 253 44 0 1000 1252 144244719 144244467 8.520000e-55 224.0
11 TraesCS3A01G309400 chr3B 78.916 332 62 6 976 1300 143620963 143621293 3.960000e-53 219.0
12 TraesCS3A01G309400 chr1A 93.849 504 25 5 1499 1999 554032476 554032976 0.000000e+00 754.0
13 TraesCS3A01G309400 chr1A 93.265 490 30 3 1500 1988 19083781 19083294 0.000000e+00 719.0
14 TraesCS3A01G309400 chr2D 94.309 492 25 3 1499 1989 612336566 612337055 0.000000e+00 750.0
15 TraesCS3A01G309400 chr3D 93.902 492 28 2 1499 1989 52854064 52854554 0.000000e+00 741.0
16 TraesCS3A01G309400 chr3D 93.509 493 29 3 1499 1989 59301687 59301196 0.000000e+00 730.0
17 TraesCS3A01G309400 chr3D 92.445 503 32 6 1499 1999 462832029 462832527 0.000000e+00 713.0
18 TraesCS3A01G309400 chr3D 88.346 532 45 5 945 1475 94245379 94245894 7.190000e-175 623.0
19 TraesCS3A01G309400 chr3D 83.544 316 44 6 942 1252 94026246 94026558 2.980000e-74 289.0
20 TraesCS3A01G309400 chr3D 81.690 142 14 7 2236 2369 94246646 94246783 8.950000e-20 108.0
21 TraesCS3A01G309400 chr3D 100.000 28 0 0 1467 1494 94246287 94246314 4.000000e-03 52.8
22 TraesCS3A01G309400 chr2A 93.496 492 30 2 1499 1989 163044864 163044374 0.000000e+00 730.0
23 TraesCS3A01G309400 chr5D 93.306 493 28 5 1499 1989 260868511 260868022 0.000000e+00 723.0
24 TraesCS3A01G309400 chr4D 91.939 521 32 8 1499 2018 499450861 499451372 0.000000e+00 721.0
25 TraesCS3A01G309400 chr4B 77.329 322 48 8 982 1300 50177714 50177415 1.460000e-37 167.0


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 TraesCS3A01G309400 chr3A 547405056 547407424 2368 False 4375.000000 4375 100.0000 1 2369 1 chr3A.!!$F1 2368
1 TraesCS3A01G309400 chr3A 547471851 547472734 883 False 1040.000000 1040 87.9740 7 914 1 chr3A.!!$F2 907
2 TraesCS3A01G309400 chr3A 547413440 547415006 1566 False 514.000000 592 87.1555 507 1492 2 chr3A.!!$F3 985
3 TraesCS3A01G309400 chr3B 144809356 144810113 757 False 904.000000 904 87.9850 7 802 1 chr3B.!!$F3 795
4 TraesCS3A01G309400 chr3B 144777219 144781614 4395 False 463.250000 773 86.6165 7 1413 4 chr3B.!!$F4 1406
5 TraesCS3A01G309400 chr1A 554032476 554032976 500 False 754.000000 754 93.8490 1499 1999 1 chr1A.!!$F1 500
6 TraesCS3A01G309400 chr3D 94245379 94246783 1404 False 261.266667 623 90.0120 945 2369 3 chr3D.!!$F4 1424
7 TraesCS3A01G309400 chr4D 499450861 499451372 511 False 721.000000 721 91.9390 1499 2018 1 chr4D.!!$F1 519

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
140 2824 0.531311 AACGACAAGAACACCGGGAC 60.531 55.0 6.32 0.0 0.0 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1926 5662 0.994247 ATGCCAGAGTGGTGATCCAA 59.006 50.0 0.0 0.0 46.15 3.53 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
139 2823 1.039068 TAACGACAAGAACACCGGGA 58.961 50.000 6.32 0.00 0.00 5.14
140 2824 0.531311 AACGACAAGAACACCGGGAC 60.531 55.000 6.32 0.00 0.00 4.46
180 2882 1.750351 GCCGGAAAAGTTTTCGACAC 58.250 50.000 19.48 7.14 41.61 3.67
183 2885 3.103007 CCGGAAAAGTTTTCGACACAAC 58.897 45.455 19.48 5.59 41.61 3.32
209 2911 3.870422 CGCGCGCAGAGAGAGAGA 61.870 66.667 32.61 0.00 0.00 3.10
210 2912 2.024588 GCGCGCAGAGAGAGAGAG 59.975 66.667 29.10 0.00 0.00 3.20
211 2913 2.468670 GCGCGCAGAGAGAGAGAGA 61.469 63.158 29.10 0.00 0.00 3.10
212 2914 1.643292 CGCGCAGAGAGAGAGAGAG 59.357 63.158 8.75 0.00 0.00 3.20
213 2915 0.809636 CGCGCAGAGAGAGAGAGAGA 60.810 60.000 8.75 0.00 0.00 3.10
214 2916 0.940126 GCGCAGAGAGAGAGAGAGAG 59.060 60.000 0.30 0.00 0.00 3.20
215 2917 1.473257 GCGCAGAGAGAGAGAGAGAGA 60.473 57.143 0.30 0.00 0.00 3.10
216 2918 2.477825 CGCAGAGAGAGAGAGAGAGAG 58.522 57.143 0.00 0.00 0.00 3.20
275 2988 2.103934 CTCTCTTCTGGGAGCGCG 59.896 66.667 0.00 0.00 33.70 6.86
286 2999 1.226717 GGAGCGCGTCGAGAATTCT 60.227 57.895 7.95 7.95 0.00 2.40
418 3131 1.474478 GTCTCGCTGATTGGAGAGTCA 59.526 52.381 0.00 0.00 39.80 3.41
475 3188 2.650778 CTGTTTTCCGGCCTTGGC 59.349 61.111 0.00 2.49 0.00 4.52
943 4238 1.079819 CAACGCCGTGATGTCCTCT 60.080 57.895 0.00 0.00 0.00 3.69
949 4244 1.079819 CGTGATGTCCTCTGCCGTT 60.080 57.895 0.00 0.00 0.00 4.44
958 4253 0.955919 CCTCTGCCGTTTGGGAACTC 60.956 60.000 0.00 0.00 38.47 3.01
976 4273 2.609759 CCCGTAGCGCCGTGTTTTT 61.610 57.895 2.29 0.00 0.00 1.94
989 4286 2.478894 CGTGTTTTTGTAGCGTGGAGAT 59.521 45.455 0.00 0.00 0.00 2.75
1091 4388 2.577059 GCCATCGGACGGTGAAGA 59.423 61.111 6.53 0.00 0.00 2.87
1117 4414 3.073503 CCCCATATGCTTGGATCAAGAGA 59.926 47.826 11.35 0.00 43.42 3.10
1121 4418 1.661463 TGCTTGGATCAAGAGAGGGT 58.339 50.000 11.35 0.00 43.42 4.34
1169 4466 1.272037 TGGGCACATCTTTCATGAGCA 60.272 47.619 0.00 0.00 37.36 4.26
1200 4497 3.068691 TGGCTCGAGACGAAGGGG 61.069 66.667 18.75 0.00 34.74 4.79
1206 4503 0.538977 TCGAGACGAAGGGGAGTTGT 60.539 55.000 0.00 0.00 31.06 3.32
1237 4534 1.160137 GCGTCAGCTTCAAGAACCAT 58.840 50.000 0.00 0.00 41.01 3.55
1241 4538 3.141398 GTCAGCTTCAAGAACCATGTGA 58.859 45.455 0.00 0.00 0.00 3.58
1263 4560 5.299028 TGATGCTGCAAAATATGGTATTCGT 59.701 36.000 6.36 0.00 0.00 3.85
1279 4579 0.253894 TCGTCGTAGTCCCCTCATCA 59.746 55.000 0.00 0.00 0.00 3.07
1288 4588 1.303074 CCCCTCATCATGATGGCGG 60.303 63.158 30.54 27.77 39.24 6.13
1294 4594 0.949397 CATCATGATGGCGGTGGAAG 59.051 55.000 25.37 0.00 35.24 3.46
1332 4632 5.579564 ACCTTCCAGATCGAAGTAACTAC 57.420 43.478 8.86 0.00 38.05 2.73
1348 4648 9.205719 GAAGTAACTACTTTAGGCAATATAGGC 57.794 37.037 3.71 0.00 45.84 3.93
1365 4665 0.391263 GGCAGGAGACGTTTGTAGGG 60.391 60.000 0.00 0.00 0.00 3.53
1366 4666 0.320697 GCAGGAGACGTTTGTAGGGT 59.679 55.000 0.00 0.00 0.00 4.34
1367 4667 1.939838 GCAGGAGACGTTTGTAGGGTG 60.940 57.143 0.00 0.00 0.00 4.61
1368 4668 1.616865 CAGGAGACGTTTGTAGGGTGA 59.383 52.381 0.00 0.00 0.00 4.02
1369 4669 1.617357 AGGAGACGTTTGTAGGGTGAC 59.383 52.381 0.00 0.00 0.00 3.67
1370 4670 1.342174 GGAGACGTTTGTAGGGTGACA 59.658 52.381 0.00 0.00 0.00 3.58
1401 4735 3.871006 ACAATGTCGACATATGCAACGAT 59.129 39.130 30.16 9.53 35.10 3.73
1402 4736 4.332543 ACAATGTCGACATATGCAACGATT 59.667 37.500 30.16 9.56 35.10 3.34
1403 4737 5.163764 ACAATGTCGACATATGCAACGATTT 60.164 36.000 30.16 9.03 35.10 2.17
1404 4738 4.257536 TGTCGACATATGCAACGATTTG 57.742 40.909 15.76 0.00 37.14 2.32
1405 4739 3.682377 TGTCGACATATGCAACGATTTGT 59.318 39.130 15.76 0.00 37.14 2.83
1406 4740 4.021822 GTCGACATATGCAACGATTTGTG 58.978 43.478 11.55 0.00 37.14 3.33
1407 4741 3.682377 TCGACATATGCAACGATTTGTGT 59.318 39.130 13.48 0.00 34.90 3.72
1408 4742 4.865365 TCGACATATGCAACGATTTGTGTA 59.135 37.500 13.48 0.00 34.90 2.90
1409 4743 4.955590 CGACATATGCAACGATTTGTGTAC 59.044 41.667 1.58 0.00 34.90 2.90
1410 4744 5.220397 CGACATATGCAACGATTTGTGTACT 60.220 40.000 1.58 0.00 34.90 2.73
1426 4760 7.571089 TTGTGTACTTTATTGTAGCTGTACG 57.429 36.000 0.00 0.00 34.70 3.67
1519 5254 0.392461 GCGGCTCAGGTTGGTAATGA 60.392 55.000 0.00 0.00 0.00 2.57
1545 5280 3.772025 CTCAAGACCCTCTCATGGTTACT 59.228 47.826 0.00 0.00 35.85 2.24
1559 5294 0.378962 GTTACTGTTGTGTTGCGGCA 59.621 50.000 0.00 0.00 0.00 5.69
1611 5346 2.588146 CTTTGCTCAAGGATGGCGCG 62.588 60.000 0.00 0.00 0.00 6.86
1864 5600 0.247537 GCCTTGTACGATTTTCGGCG 60.248 55.000 0.00 0.00 45.59 6.46
1917 5653 7.104290 TGTTTAAGGTTTTTGATCCGGTTTTT 58.896 30.769 0.00 0.00 0.00 1.94
1947 5683 1.355381 TGGATCACCACTCTGGCATTT 59.645 47.619 0.00 0.00 42.67 2.32
1949 5685 2.827921 GGATCACCACTCTGGCATTTTT 59.172 45.455 0.00 0.00 42.67 1.94
2063 5799 1.154225 CGTTAAAGCAGGGCAAGCG 60.154 57.895 0.00 0.00 37.01 4.68
2078 5814 4.990543 GCAAGCGCCTTTTTCTAAAAAT 57.009 36.364 2.29 0.00 37.27 1.82
2108 5846 8.545229 AACATGAGATTGTAAGAAGAACTCTG 57.455 34.615 0.00 0.00 33.37 3.35
2116 5854 9.587772 GATTGTAAGAAGAACTCTGCAACTATA 57.412 33.333 0.00 0.00 34.61 1.31
2153 5891 6.594788 ATGGTTGCAATTTGAACTATGACT 57.405 33.333 0.59 0.00 0.00 3.41
2154 5892 5.771469 TGGTTGCAATTTGAACTATGACTG 58.229 37.500 0.59 0.00 0.00 3.51
2155 5893 5.534278 TGGTTGCAATTTGAACTATGACTGA 59.466 36.000 0.59 0.00 0.00 3.41
2201 5939 6.210584 TGGTTTGTCTTTTCAGGTTTTCTCTT 59.789 34.615 0.00 0.00 0.00 2.85
2202 5940 6.531594 GGTTTGTCTTTTCAGGTTTTCTCTTG 59.468 38.462 0.00 0.00 0.00 3.02
2207 5945 6.469275 GTCTTTTCAGGTTTTCTCTTGAAACG 59.531 38.462 4.07 3.48 41.34 3.60
2210 5948 1.954382 AGGTTTTCTCTTGAAACGGGC 59.046 47.619 0.00 0.00 41.34 6.13
2214 5952 2.457366 TTCTCTTGAAACGGGCTCTC 57.543 50.000 0.00 0.00 0.00 3.20
2233 5971 6.146347 GGCTCTCGCTCCACTTTATAAATAAG 59.854 42.308 0.00 0.00 36.09 1.73
2262 6113 5.320549 GCCAATGGCCTGAATATAATGAG 57.679 43.478 14.47 0.00 44.06 2.90
2263 6114 5.012239 GCCAATGGCCTGAATATAATGAGA 58.988 41.667 14.47 0.00 44.06 3.27
2279 6130 5.344743 AATGAGACGACACACATTAGGAT 57.655 39.130 0.00 0.00 32.35 3.24
2294 6145 2.750141 AGGATACCTAAGCTCCACGA 57.250 50.000 0.00 0.00 28.47 4.35
2297 6148 2.223758 GGATACCTAAGCTCCACGACAC 60.224 54.545 0.00 0.00 0.00 3.67
2298 6149 1.180029 TACCTAAGCTCCACGACACC 58.820 55.000 0.00 0.00 0.00 4.16
2302 6161 1.000955 CTAAGCTCCACGACACCAAGT 59.999 52.381 0.00 0.00 0.00 3.16
2310 6169 0.834612 ACGACACCAAGTGGAAAGGA 59.165 50.000 3.83 0.00 37.94 3.36
2313 6172 0.818040 ACACCAAGTGGAAAGGACGC 60.818 55.000 3.83 0.00 37.94 5.19
2314 6173 0.817634 CACCAAGTGGAAAGGACGCA 60.818 55.000 3.83 0.00 38.94 5.24
2319 6178 1.301716 GTGGAAAGGACGCAGAGCA 60.302 57.895 0.00 0.00 0.00 4.26
2325 6184 2.512515 GGACGCAGAGCATCACCC 60.513 66.667 0.00 0.00 37.82 4.61
2326 6185 2.887568 GACGCAGAGCATCACCCG 60.888 66.667 0.00 0.00 37.82 5.28
2328 6187 4.827087 CGCAGAGCATCACCCGCT 62.827 66.667 0.00 0.00 44.10 5.52
2329 6188 2.501128 GCAGAGCATCACCCGCTA 59.499 61.111 0.00 0.00 40.63 4.26
2334 6193 0.664767 GAGCATCACCCGCTATCGAC 60.665 60.000 0.00 0.00 40.63 4.20
2338 6197 0.467474 ATCACCCGCTATCGACTCCA 60.467 55.000 0.00 0.00 38.10 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.458342 GCGGTAGAAAAATTAAGTGGAGGATG 60.458 42.308 0.00 0.00 0.00 3.51
1 2 5.589050 GCGGTAGAAAAATTAAGTGGAGGAT 59.411 40.000 0.00 0.00 0.00 3.24
2 3 4.939439 GCGGTAGAAAAATTAAGTGGAGGA 59.061 41.667 0.00 0.00 0.00 3.71
3 4 4.201783 CGCGGTAGAAAAATTAAGTGGAGG 60.202 45.833 0.00 0.00 0.00 4.30
10 11 1.463831 TGCGCGCGGTAGAAAAATTAA 59.536 42.857 33.06 0.00 0.00 1.40
43 2727 0.032130 CGACTATCCATCCCGGTGTG 59.968 60.000 0.00 0.00 35.57 3.82
46 2730 4.192950 CCGACTATCCATCCCGGT 57.807 61.111 0.00 0.00 35.83 5.28
139 2823 4.648626 TCTCCCGTGTCGTCCCGT 62.649 66.667 0.00 0.00 0.00 5.28
140 2824 4.112341 GTCTCCCGTGTCGTCCCG 62.112 72.222 0.00 0.00 0.00 5.14
141 2825 4.112341 CGTCTCCCGTGTCGTCCC 62.112 72.222 0.00 0.00 0.00 4.46
142 2826 4.773117 GCGTCTCCCGTGTCGTCC 62.773 72.222 0.00 0.00 39.32 4.79
143 2827 4.773117 GGCGTCTCCCGTGTCGTC 62.773 72.222 0.00 0.00 39.32 4.20
199 2901 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
201 2903 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
203 2905 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
205 2907 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
206 2908 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
207 2909 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
208 2910 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
209 2911 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
210 2912 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
211 2913 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
212 2914 5.279406 CCATCTCTCTCTCTCTCTCTCTCTC 60.279 52.000 0.00 0.00 0.00 3.20
213 2915 4.592351 CCATCTCTCTCTCTCTCTCTCTCT 59.408 50.000 0.00 0.00 0.00 3.10
214 2916 4.802248 GCCATCTCTCTCTCTCTCTCTCTC 60.802 54.167 0.00 0.00 0.00 3.20
215 2917 3.072184 GCCATCTCTCTCTCTCTCTCTCT 59.928 52.174 0.00 0.00 0.00 3.10
216 2918 3.072184 AGCCATCTCTCTCTCTCTCTCTC 59.928 52.174 0.00 0.00 0.00 3.20
281 2994 2.125106 GGCGAGGGCACGAGAATT 60.125 61.111 7.45 0.00 42.47 2.17
339 3052 4.838152 CGAGGTGGATGGTGGCGG 62.838 72.222 0.00 0.00 0.00 6.13
341 3054 4.408821 TGCGAGGTGGATGGTGGC 62.409 66.667 0.00 0.00 0.00 5.01
342 3055 2.436646 GTGCGAGGTGGATGGTGG 60.437 66.667 0.00 0.00 0.00 4.61
343 3056 1.448540 GAGTGCGAGGTGGATGGTG 60.449 63.158 0.00 0.00 0.00 4.17
378 3091 4.907034 CGCGATCGAGGTCACCGG 62.907 72.222 21.57 0.00 38.10 5.28
397 3110 0.453793 ACTCTCCAATCAGCGAGACG 59.546 55.000 0.00 0.00 31.86 4.18
418 3131 2.359230 GCGGCAAGCTTGTCCTCT 60.359 61.111 24.68 0.00 44.04 3.69
449 3162 0.313987 CCGGAAAACAGGAAGGCAAC 59.686 55.000 0.00 0.00 0.00 4.17
455 3168 0.825840 CCAAGGCCGGAAAACAGGAA 60.826 55.000 5.05 0.00 0.00 3.36
461 3174 2.915137 GGTGCCAAGGCCGGAAAA 60.915 61.111 5.05 0.00 41.09 2.29
936 3691 1.701031 TTCCCAAACGGCAGAGGACA 61.701 55.000 0.00 0.00 0.00 4.02
958 4253 2.609759 AAAAACACGGCGCTACGGG 61.610 57.895 6.90 7.14 44.31 5.28
976 4273 1.550524 AGAAGCAATCTCCACGCTACA 59.449 47.619 0.00 0.00 34.11 2.74
989 4286 0.178967 TGGTTCCATGGCAGAAGCAA 60.179 50.000 16.10 0.00 45.78 3.91
1091 4388 2.158279 TGATCCAAGCATATGGGGCATT 60.158 45.455 4.56 0.00 41.05 3.56
1169 4466 2.045926 GCCACCTCTCCACGCATT 60.046 61.111 0.00 0.00 0.00 3.56
1206 4503 3.295304 CTGACGCCGACACATGGGA 62.295 63.158 0.00 0.00 0.00 4.37
1237 4534 6.468333 AATACCATATTTTGCAGCATCACA 57.532 33.333 0.00 0.00 0.00 3.58
1241 4538 5.560760 CGACGAATACCATATTTTGCAGCAT 60.561 40.000 0.00 0.00 0.00 3.79
1263 4560 2.748209 TCATGATGAGGGGACTACGA 57.252 50.000 0.00 0.00 44.43 3.43
1279 4579 2.575532 CATTACTTCCACCGCCATCAT 58.424 47.619 0.00 0.00 0.00 2.45
1288 4588 3.000727 CGGAGTTGTCCATTACTTCCAC 58.999 50.000 0.00 0.00 44.18 4.02
1294 4594 3.259902 GAAGGTCGGAGTTGTCCATTAC 58.740 50.000 0.00 0.00 44.18 1.89
1332 4632 5.241662 GTCTCCTGCCTATATTGCCTAAAG 58.758 45.833 0.00 0.00 0.00 1.85
1348 4648 1.616865 TCACCCTACAAACGTCTCCTG 59.383 52.381 0.00 0.00 0.00 3.86
1365 4665 3.366121 CGACATTGTCTCATCACTGTCAC 59.634 47.826 14.54 0.00 43.39 3.67
1366 4666 3.255642 TCGACATTGTCTCATCACTGTCA 59.744 43.478 14.54 3.31 43.39 3.58
1367 4667 3.610242 GTCGACATTGTCTCATCACTGTC 59.390 47.826 11.55 6.97 41.40 3.51
1368 4668 3.005791 TGTCGACATTGTCTCATCACTGT 59.994 43.478 15.76 0.00 34.73 3.55
1369 4669 3.578688 TGTCGACATTGTCTCATCACTG 58.421 45.455 15.76 0.00 0.00 3.66
1370 4670 3.942130 TGTCGACATTGTCTCATCACT 57.058 42.857 15.76 0.00 0.00 3.41
1401 4735 7.652909 ACGTACAGCTACAATAAAGTACACAAA 59.347 33.333 0.00 0.00 33.35 2.83
1402 4736 7.115236 CACGTACAGCTACAATAAAGTACACAA 59.885 37.037 0.00 0.00 33.35 3.33
1403 4737 6.583427 CACGTACAGCTACAATAAAGTACACA 59.417 38.462 0.00 0.00 33.35 3.72
1404 4738 6.583806 ACACGTACAGCTACAATAAAGTACAC 59.416 38.462 0.00 0.00 33.35 2.90
1405 4739 6.583427 CACACGTACAGCTACAATAAAGTACA 59.417 38.462 0.00 0.00 33.35 2.90
1406 4740 6.803320 TCACACGTACAGCTACAATAAAGTAC 59.197 38.462 0.00 0.00 0.00 2.73
1407 4741 6.912082 TCACACGTACAGCTACAATAAAGTA 58.088 36.000 0.00 0.00 0.00 2.24
1408 4742 5.775686 TCACACGTACAGCTACAATAAAGT 58.224 37.500 0.00 0.00 0.00 2.66
1409 4743 6.090783 TCTCACACGTACAGCTACAATAAAG 58.909 40.000 0.00 0.00 0.00 1.85
1410 4744 6.016213 TCTCACACGTACAGCTACAATAAA 57.984 37.500 0.00 0.00 0.00 1.40
1494 5229 1.210931 CAACCTGAGCCGCACAATG 59.789 57.895 0.00 0.00 0.00 2.82
1495 5230 1.973281 CCAACCTGAGCCGCACAAT 60.973 57.895 0.00 0.00 0.00 2.71
1496 5231 2.046009 TACCAACCTGAGCCGCACAA 62.046 55.000 0.00 0.00 0.00 3.33
1497 5232 2.046009 TTACCAACCTGAGCCGCACA 62.046 55.000 0.00 0.00 0.00 4.57
1519 5254 2.092538 CCATGAGAGGGTCTTGAGCAAT 60.093 50.000 0.00 0.00 33.05 3.56
1545 5280 1.943116 AAGCTTGCCGCAACACAACA 61.943 50.000 0.38 0.00 42.61 3.33
1565 5300 3.316308 GTCAAGACAACACCAAGAGCATT 59.684 43.478 0.00 0.00 0.00 3.56
1566 5301 2.880890 GTCAAGACAACACCAAGAGCAT 59.119 45.455 0.00 0.00 0.00 3.79
1855 5591 2.564458 GGAAACCGCGCCGAAAAT 59.436 55.556 0.00 0.00 0.00 1.82
1896 5632 6.718522 AGAAAAACCGGATCAAAAACCTTA 57.281 33.333 9.46 0.00 0.00 2.69
1917 5653 7.282585 CCAGAGTGGTGATCCAATTTATAAGA 58.717 38.462 0.00 0.00 46.15 2.10
1926 5662 0.994247 ATGCCAGAGTGGTGATCCAA 59.006 50.000 0.00 0.00 46.15 3.53
1949 5685 8.892723 CACTTGAATATATTACTCAAAGTGGCA 58.107 33.333 18.45 0.00 31.66 4.92
2045 5781 1.154225 CGCTTGCCCTGCTTTAACG 60.154 57.895 0.00 0.00 0.00 3.18
2097 5835 8.097038 TGACAAATATAGTTGCAGAGTTCTTCT 58.903 33.333 12.62 0.00 32.15 2.85
2101 5839 9.118236 GTTTTGACAAATATAGTTGCAGAGTTC 57.882 33.333 12.62 2.93 31.29 3.01
2107 5845 8.986847 CCATTTGTTTTGACAAATATAGTTGCA 58.013 29.630 12.62 8.94 45.34 4.08
2108 5846 8.987890 ACCATTTGTTTTGACAAATATAGTTGC 58.012 29.630 12.62 6.61 45.34 4.17
2131 5869 5.534278 TCAGTCATAGTTCAAATTGCAACCA 59.466 36.000 0.00 0.00 0.00 3.67
2167 5905 9.533831 ACCTGAAAAGACAAACCATTCTAATAT 57.466 29.630 0.00 0.00 0.00 1.28
2168 5906 8.934023 ACCTGAAAAGACAAACCATTCTAATA 57.066 30.769 0.00 0.00 0.00 0.98
2172 5910 6.544928 AAACCTGAAAAGACAAACCATTCT 57.455 33.333 0.00 0.00 0.00 2.40
2180 5918 7.461182 TTCAAGAGAAAACCTGAAAAGACAA 57.539 32.000 0.00 0.00 0.00 3.18
2190 5928 1.954382 GCCCGTTTCAAGAGAAAACCT 59.046 47.619 0.00 0.00 44.75 3.50
2210 5948 6.146347 GCCTTATTTATAAAGTGGAGCGAGAG 59.854 42.308 14.36 0.00 0.00 3.20
2214 5952 5.295787 TGTGCCTTATTTATAAAGTGGAGCG 59.704 40.000 14.36 0.00 0.00 5.03
2245 5983 4.343814 TGTCGTCTCATTATATTCAGGCCA 59.656 41.667 5.01 0.00 0.00 5.36
2247 5985 5.175856 GTGTGTCGTCTCATTATATTCAGGC 59.824 44.000 0.00 0.00 0.00 4.85
2248 5986 6.273071 TGTGTGTCGTCTCATTATATTCAGG 58.727 40.000 0.00 0.00 0.00 3.86
2256 6107 5.907866 TCCTAATGTGTGTCGTCTCATTA 57.092 39.130 0.00 0.00 34.70 1.90
2262 6113 4.650754 AGGTATCCTAATGTGTGTCGTC 57.349 45.455 0.00 0.00 28.47 4.20
2263 6114 5.451520 GCTTAGGTATCCTAATGTGTGTCGT 60.452 44.000 8.43 0.00 44.01 4.34
2279 6130 1.180029 GGTGTCGTGGAGCTTAGGTA 58.820 55.000 0.00 0.00 0.00 3.08
2294 6145 0.818040 GCGTCCTTTCCACTTGGTGT 60.818 55.000 0.00 0.00 36.34 4.16
2297 6148 0.250295 TCTGCGTCCTTTCCACTTGG 60.250 55.000 0.00 0.00 0.00 3.61
2298 6149 1.151668 CTCTGCGTCCTTTCCACTTG 58.848 55.000 0.00 0.00 0.00 3.16
2302 6161 0.391661 GATGCTCTGCGTCCTTTCCA 60.392 55.000 0.66 0.00 38.50 3.53
2313 6172 0.665670 CGATAGCGGGTGATGCTCTG 60.666 60.000 0.00 0.00 42.85 3.35
2314 6173 0.823769 TCGATAGCGGGTGATGCTCT 60.824 55.000 0.00 0.00 42.85 4.09
2319 6178 0.467474 TGGAGTCGATAGCGGGTGAT 60.467 55.000 0.00 0.00 38.28 3.06
2325 6184 1.671328 TCTGTCTTGGAGTCGATAGCG 59.329 52.381 0.00 0.00 39.35 4.26
2326 6185 2.539953 CGTCTGTCTTGGAGTCGATAGC 60.540 54.545 0.00 0.00 0.00 2.97
2327 6186 2.937149 TCGTCTGTCTTGGAGTCGATAG 59.063 50.000 0.00 0.00 0.00 2.08
2328 6187 2.937149 CTCGTCTGTCTTGGAGTCGATA 59.063 50.000 0.00 0.00 32.06 2.92
2329 6188 1.740585 CTCGTCTGTCTTGGAGTCGAT 59.259 52.381 0.00 0.00 32.06 3.59
2334 6193 0.528470 GACCCTCGTCTGTCTTGGAG 59.472 60.000 0.00 0.00 35.99 3.86


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

AutoCloner maintained by Alex Coulton.