Multiple sequence alignment - TraesCS6B01G149200

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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 TraesCS6B01G149200 chr6B 100.000 2703 0 0 1 2703 150153061 150150359 0.000000e+00 4992.0
1 TraesCS6B01G149200 chr6B 100.000 340 0 0 3117 3456 150149945 150149606 2.260000e-176 628.0
2 TraesCS6B01G149200 chr6B 84.615 78 10 2 154 231 127369166 127369241 3.700000e-10 76.8
3 TraesCS6B01G149200 chr6D 93.829 794 33 8 1434 2216 77524646 77523858 0.000000e+00 1181.0
4 TraesCS6B01G149200 chr6D 91.725 713 39 13 415 1117 77525729 77525027 0.000000e+00 972.0
5 TraesCS6B01G149200 chr6D 94.010 384 22 1 2236 2619 77519962 77519580 6.430000e-162 580.0
6 TraesCS6B01G149200 chr6D 96.034 353 14 0 1105 1457 77525009 77524657 2.990000e-160 575.0
7 TraesCS6B01G149200 chr6D 90.289 381 29 5 1 379 77526097 77525723 3.100000e-135 492.0
8 TraesCS6B01G149200 chr6D 92.400 250 15 3 3208 3456 77519139 77518893 1.530000e-93 353.0
9 TraesCS6B01G149200 chr6A 91.725 713 35 8 1526 2214 92853207 92852495 0.000000e+00 968.0
10 TraesCS6B01G149200 chr6A 94.340 424 14 2 1105 1524 92853670 92853253 2.910000e-180 641.0
11 TraesCS6B01G149200 chr6A 90.544 349 23 3 3117 3456 92851769 92851422 1.460000e-123 453.0
12 TraesCS6B01G149200 chr6A 93.704 270 15 2 2238 2507 92852325 92852058 1.490000e-108 403.0
13 TraesCS6B01G149200 chr6A 89.048 210 8 4 912 1117 92853886 92853688 2.660000e-61 246.0
14 TraesCS6B01G149200 chr6A 97.436 78 2 0 1 78 92853965 92853888 2.160000e-27 134.0
15 TraesCS6B01G149200 chr4A 79.545 220 30 6 1807 2015 167305722 167305937 3.600000e-30 143.0
16 TraesCS6B01G149200 chr4A 82.143 84 11 4 529 610 715768663 715768744 6.190000e-08 69.4
17 TraesCS6B01G149200 chr5D 82.659 173 16 7 1807 1969 426475629 426475797 1.290000e-29 141.0
18 TraesCS6B01G149200 chr7B 90.110 91 5 2 1829 1918 268457254 268457341 7.840000e-22 115.0
19 TraesCS6B01G149200 chr7B 81.884 138 21 2 1805 1942 211421939 211421806 2.820000e-21 113.0
20 TraesCS6B01G149200 chr7B 83.750 80 11 2 152 231 624942562 624942639 1.330000e-09 75.0
21 TraesCS6B01G149200 chr1B 82.707 133 19 2 1805 1937 659726162 659726290 7.840000e-22 115.0
22 TraesCS6B01G149200 chr1B 80.583 103 18 2 154 256 15285317 15285217 1.030000e-10 78.7
23 TraesCS6B01G149200 chr7A 83.740 123 13 5 1804 1924 638488910 638489027 3.650000e-20 110.0
24 TraesCS6B01G149200 chr3B 77.665 197 29 8 1807 1992 791757801 791757993 4.720000e-19 106.0
25 TraesCS6B01G149200 chr5A 85.106 94 12 2 154 247 88349722 88349813 1.020000e-15 95.3
26 TraesCS6B01G149200 chr1A 83.495 103 15 1 154 256 204618373 204618273 1.020000e-15 95.3
27 TraesCS6B01G149200 chr3A 87.692 65 8 0 192 256 379825568 379825504 3.700000e-10 76.8
28 TraesCS6B01G149200 chr2B 84.810 79 9 3 154 231 25954292 25954368 3.700000e-10 76.8
29 TraesCS6B01G149200 chr4D 95.652 46 2 0 189 234 237553148 237553103 1.330000e-09 75.0


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 TraesCS6B01G149200 chr6B 150149606 150153061 3455 True 2810.000000 4992 100.000000 1 3456 2 chr6B.!!$R1 3455
1 TraesCS6B01G149200 chr6D 77518893 77526097 7204 True 692.166667 1181 93.047833 1 3456 6 chr6D.!!$R1 3455
2 TraesCS6B01G149200 chr6A 92851422 92853965 2543 True 474.166667 968 92.799500 1 3456 6 chr6A.!!$R1 3455

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
552 556 0.758123 CTGGTTTGGGTGGCATTTGT 59.242 50.0 0.0 0.0 0.0 2.83 F
1776 1902 0.532115 AAATGGCGCATGGGAAACTC 59.468 50.0 14.9 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1937 2071 0.918799 AGGTGGGGCCATACACATGA 60.919 55.0 21.22 0.0 39.31 3.07 R
3391 7590 1.070038 CCCATTTTGCATGTGTTCGC 58.930 50.0 0.00 0.0 0.00 4.70 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
21 22 4.402056 GACCTCCCAACATCGATCTTTA 57.598 45.455 0.00 0.00 0.00 1.85
108 110 5.063880 ACAGGAAAGACTTGTGAATGTACC 58.936 41.667 0.00 0.00 37.43 3.34
150 152 5.571784 TGATGTTTAGGTCACTACGGTAG 57.428 43.478 13.49 13.49 0.00 3.18
161 163 4.514816 GTCACTACGGTAGATTACTCCCTC 59.485 50.000 21.39 0.00 0.00 4.30
178 180 2.222027 CCTCCATCCCGAATTACTTGC 58.778 52.381 0.00 0.00 0.00 4.01
187 189 6.121776 TCCCGAATTACTTGCCACATATAT 57.878 37.500 0.00 0.00 0.00 0.86
188 190 7.247456 TCCCGAATTACTTGCCACATATATA 57.753 36.000 0.00 0.00 0.00 0.86
204 206 9.093458 CCACATATATATGGATGTATCTAGGCA 57.907 37.037 23.44 0.00 38.34 4.75
215 217 9.944376 TGGATGTATCTAGGCATATTTTAGTTC 57.056 33.333 0.00 0.00 0.00 3.01
237 240 6.621316 TCTAGAGACATCCATTTCTACGAC 57.379 41.667 0.00 0.00 0.00 4.34
247 250 9.010029 ACATCCATTTCTACGACAAGTAATTTT 57.990 29.630 0.00 0.00 34.45 1.82
251 254 9.968743 CCATTTCTACGACAAGTAATTTTAGAC 57.031 33.333 0.00 0.00 34.45 2.59
253 256 7.801547 TTCTACGACAAGTAATTTTAGACGG 57.198 36.000 0.00 0.00 34.45 4.79
282 285 8.962679 CATGGAGGGAGTAGTTTATAGAGATAC 58.037 40.741 0.00 0.00 0.00 2.24
326 329 9.947669 CTGAATGAAGCAAAATTAGAGGAATAG 57.052 33.333 0.00 0.00 0.00 1.73
331 334 7.822334 TGAAGCAAAATTAGAGGAATAGAACGA 59.178 33.333 0.00 0.00 0.00 3.85
346 349 7.065923 GGAATAGAACGAGATTTTGTTTAGGCT 59.934 37.037 0.00 0.00 30.90 4.58
349 352 6.228258 AGAACGAGATTTTGTTTAGGCTACA 58.772 36.000 0.00 0.00 30.90 2.74
354 357 7.985184 ACGAGATTTTGTTTAGGCTACATGATA 59.015 33.333 0.00 0.00 0.00 2.15
392 395 9.547753 AATGATGATACAAGTAGTATGTTGACC 57.452 33.333 0.00 0.00 43.39 4.02
393 396 8.306313 TGATGATACAAGTAGTATGTTGACCT 57.694 34.615 0.00 0.00 43.39 3.85
394 397 9.416284 TGATGATACAAGTAGTATGTTGACCTA 57.584 33.333 0.00 0.00 43.39 3.08
395 398 9.680315 GATGATACAAGTAGTATGTTGACCTAC 57.320 37.037 0.00 0.00 43.39 3.18
396 399 8.584063 TGATACAAGTAGTATGTTGACCTACA 57.416 34.615 0.00 0.00 43.39 2.74
397 400 8.464404 TGATACAAGTAGTATGTTGACCTACAC 58.536 37.037 0.00 0.00 43.39 2.90
398 401 6.912951 ACAAGTAGTATGTTGACCTACACT 57.087 37.500 0.00 0.00 34.78 3.55
399 402 9.690913 ATACAAGTAGTATGTTGACCTACACTA 57.309 33.333 0.00 0.00 41.81 2.74
400 403 8.413309 ACAAGTAGTATGTTGACCTACACTAA 57.587 34.615 0.00 0.00 34.78 2.24
401 404 8.863086 ACAAGTAGTATGTTGACCTACACTAAA 58.137 33.333 0.00 0.00 34.78 1.85
402 405 9.136952 CAAGTAGTATGTTGACCTACACTAAAC 57.863 37.037 0.00 0.00 34.78 2.01
403 406 7.533426 AGTAGTATGTTGACCTACACTAAACG 58.467 38.462 0.00 0.00 34.78 3.60
404 407 5.166398 AGTATGTTGACCTACACTAAACGC 58.834 41.667 0.61 0.00 0.00 4.84
405 408 3.738830 TGTTGACCTACACTAAACGCT 57.261 42.857 0.00 0.00 0.00 5.07
406 409 4.852134 TGTTGACCTACACTAAACGCTA 57.148 40.909 0.00 0.00 0.00 4.26
407 410 4.801891 TGTTGACCTACACTAAACGCTAG 58.198 43.478 0.00 0.00 0.00 3.42
408 411 3.498927 TGACCTACACTAAACGCTAGC 57.501 47.619 4.06 4.06 0.00 3.42
409 412 2.159476 TGACCTACACTAAACGCTAGCG 60.159 50.000 34.27 34.27 46.03 4.26
410 413 2.086869 ACCTACACTAAACGCTAGCGA 58.913 47.619 41.33 20.03 42.83 4.93
411 414 2.686915 ACCTACACTAAACGCTAGCGAT 59.313 45.455 41.33 29.11 42.83 4.58
412 415 3.879295 ACCTACACTAAACGCTAGCGATA 59.121 43.478 41.33 29.15 42.83 2.92
413 416 4.336433 ACCTACACTAAACGCTAGCGATAA 59.664 41.667 41.33 23.57 42.83 1.75
414 417 4.910456 CCTACACTAAACGCTAGCGATAAG 59.090 45.833 41.33 31.50 42.83 1.73
415 418 4.627611 ACACTAAACGCTAGCGATAAGA 57.372 40.909 41.33 20.13 42.83 2.10
416 419 5.184340 ACACTAAACGCTAGCGATAAGAT 57.816 39.130 41.33 22.31 42.83 2.40
417 420 4.976731 ACACTAAACGCTAGCGATAAGATG 59.023 41.667 41.33 29.35 42.83 2.90
418 421 3.982058 ACTAAACGCTAGCGATAAGATGC 59.018 43.478 41.33 0.00 42.83 3.91
419 422 2.509052 AACGCTAGCGATAAGATGCA 57.491 45.000 41.33 0.00 42.83 3.96
420 423 2.509052 ACGCTAGCGATAAGATGCAA 57.491 45.000 41.33 0.00 42.83 4.08
421 424 2.821546 ACGCTAGCGATAAGATGCAAA 58.178 42.857 41.33 0.00 42.83 3.68
422 425 3.393800 ACGCTAGCGATAAGATGCAAAT 58.606 40.909 41.33 13.19 42.83 2.32
423 426 3.430218 ACGCTAGCGATAAGATGCAAATC 59.570 43.478 41.33 0.00 42.83 2.17
524 528 9.739276 ATTTGTAATGGACTTTCTTATCTCACA 57.261 29.630 0.00 0.00 0.00 3.58
527 531 8.253810 TGTAATGGACTTTCTTATCTCACAGAG 58.746 37.037 0.00 0.00 0.00 3.35
531 535 6.103330 GGACTTTCTTATCTCACAGAGGTTC 58.897 44.000 0.00 0.00 0.00 3.62
552 556 0.758123 CTGGTTTGGGTGGCATTTGT 59.242 50.000 0.00 0.00 0.00 2.83
556 560 2.224499 GGTTTGGGTGGCATTTGTGAAT 60.224 45.455 0.00 0.00 0.00 2.57
587 591 8.258007 TGATGACTATTTTAGTTGTTCGGAGAT 58.742 33.333 0.00 0.00 39.59 2.75
591 595 7.490000 ACTATTTTAGTTGTTCGGAGATCGAT 58.510 34.615 0.00 0.00 41.16 3.59
592 596 8.627403 ACTATTTTAGTTGTTCGGAGATCGATA 58.373 33.333 0.00 0.00 41.16 2.92
612 616 6.036300 TCGATAGTTTCTTCAAAACAACACGT 59.964 34.615 3.75 0.00 32.81 4.49
613 617 6.685403 CGATAGTTTCTTCAAAACAACACGTT 59.315 34.615 3.75 0.00 40.50 3.99
660 664 4.873827 TGAGTAAAAACGAGCAGAAACTGT 59.126 37.500 0.00 0.00 33.43 3.55
665 669 2.086054 ACGAGCAGAAACTGTCATCC 57.914 50.000 0.00 0.00 33.43 3.51
676 680 4.543590 AACTGTCATCCTTTGATCTCGT 57.456 40.909 0.00 0.00 36.54 4.18
692 696 5.865013 TGATCTCGTGTCGCAACTAAAATTA 59.135 36.000 0.00 0.00 0.00 1.40
827 833 7.619366 GCCTATGTTATAACGTGATTCACATCG 60.619 40.741 18.67 5.69 33.40 3.84
836 842 3.964347 CGTGATTCACATCGATGCATTTC 59.036 43.478 25.11 16.51 33.40 2.17
837 843 4.260497 CGTGATTCACATCGATGCATTTCT 60.260 41.667 25.11 5.47 33.40 2.52
838 844 4.968181 GTGATTCACATCGATGCATTTCTG 59.032 41.667 25.11 14.39 34.08 3.02
839 845 4.877251 TGATTCACATCGATGCATTTCTGA 59.123 37.500 25.11 16.43 31.08 3.27
840 846 4.870221 TTCACATCGATGCATTTCTGAG 57.130 40.909 25.11 4.53 0.00 3.35
841 847 4.127566 TCACATCGATGCATTTCTGAGA 57.872 40.909 25.11 6.65 0.00 3.27
843 849 4.569564 TCACATCGATGCATTTCTGAGAAG 59.430 41.667 25.11 0.00 0.00 2.85
857 864 9.552114 CATTTCTGAGAAGTTTTTAGTGCATAG 57.448 33.333 0.00 0.00 0.00 2.23
860 867 9.772973 TTCTGAGAAGTTTTTAGTGCATAGTTA 57.227 29.630 0.00 0.00 0.00 2.24
869 876 3.840124 AGTGCATAGTTAGGTAAGCCC 57.160 47.619 0.00 0.00 34.57 5.19
877 884 4.057063 AGTTAGGTAAGCCCTGTACTCA 57.943 45.455 0.00 0.00 45.81 3.41
882 889 3.452627 AGGTAAGCCCTGTACTCAATGAG 59.547 47.826 8.98 8.98 44.08 2.90
883 890 3.451178 GGTAAGCCCTGTACTCAATGAGA 59.549 47.826 18.20 0.00 33.32 3.27
886 893 2.906389 AGCCCTGTACTCAATGAGACAA 59.094 45.455 18.20 0.00 33.32 3.18
887 894 3.521126 AGCCCTGTACTCAATGAGACAAT 59.479 43.478 18.20 0.00 33.32 2.71
888 895 3.624861 GCCCTGTACTCAATGAGACAATG 59.375 47.826 18.20 10.69 33.32 2.82
889 896 4.623886 GCCCTGTACTCAATGAGACAATGA 60.624 45.833 18.20 0.00 33.32 2.57
890 897 4.872691 CCCTGTACTCAATGAGACAATGAC 59.127 45.833 18.20 5.46 33.32 3.06
891 898 5.337894 CCCTGTACTCAATGAGACAATGACT 60.338 44.000 18.20 0.00 33.32 3.41
892 899 5.809562 CCTGTACTCAATGAGACAATGACTC 59.190 44.000 18.20 5.80 33.32 3.36
893 900 6.345096 TGTACTCAATGAGACAATGACTCA 57.655 37.500 18.20 16.70 46.17 3.41
894 901 6.159293 TGTACTCAATGAGACAATGACTCAC 58.841 40.000 18.20 4.34 45.19 3.51
895 902 4.573900 ACTCAATGAGACAATGACTCACC 58.426 43.478 18.20 0.00 45.19 4.02
947 954 7.985184 TCAGTTTGGCTTAGTACACTATTATGG 59.015 37.037 0.00 0.00 0.00 2.74
978 985 5.135383 GGTTTTACTTTTGTAGAGGGTGGT 58.865 41.667 0.00 0.00 36.14 4.16
1038 1045 0.698238 CCCCAAATCTCCTGTGACCA 59.302 55.000 0.00 0.00 0.00 4.02
1045 1052 2.254152 TCTCCTGTGACCAGCCTAAT 57.746 50.000 0.00 0.00 37.38 1.73
1303 1344 2.125106 GCAACGGCCTCCTTCGAT 60.125 61.111 0.00 0.00 0.00 3.59
1471 1544 1.391577 TGTTTGTCTGCACTGCACAT 58.608 45.000 0.00 0.00 33.79 3.21
1551 1668 4.380531 TGTCATTGCTTCGTCTTCTTCTT 58.619 39.130 0.00 0.00 0.00 2.52
1635 1760 1.344191 AAGATCTCTCCCTGCTGCCC 61.344 60.000 0.00 0.00 0.00 5.36
1654 1779 2.026169 CCCTTTCCCCCTCTTCTTACAC 60.026 54.545 0.00 0.00 0.00 2.90
1728 1854 1.654023 GGCACGGGAAACAGTATGCC 61.654 60.000 0.00 0.00 42.53 4.40
1737 1863 6.485648 ACGGGAAACAGTATGCCTTTTATATC 59.514 38.462 0.00 0.00 42.53 1.63
1775 1901 0.975887 AAAATGGCGCATGGGAAACT 59.024 45.000 14.90 0.00 0.00 2.66
1776 1902 0.532115 AAATGGCGCATGGGAAACTC 59.468 50.000 14.90 0.00 0.00 3.01
1858 1984 4.171005 GCATCACATGTTCAGTTTGATGG 58.829 43.478 17.14 4.75 42.50 3.51
1937 2071 3.788227 ATGGTCATATGTGGGCGTATT 57.212 42.857 1.90 0.00 0.00 1.89
2008 2142 5.782047 CATTTTTGCATAAGACACCCTTGA 58.218 37.500 0.00 0.00 36.34 3.02
2010 2144 6.418057 TTTTTGCATAAGACACCCTTGAAT 57.582 33.333 0.00 0.00 36.34 2.57
2011 2145 6.418057 TTTTGCATAAGACACCCTTGAATT 57.582 33.333 0.00 0.00 36.34 2.17
2133 2275 4.558860 GCTCATGATGCGAAAAGTAAAACC 59.441 41.667 0.00 0.00 0.00 3.27
2145 2288 2.156917 AGTAAAACCAAAGGGCTACGC 58.843 47.619 0.00 0.00 37.90 4.42
2227 2370 6.924913 TCACATTTGAATGGGTAAATTGGA 57.075 33.333 5.92 0.00 40.68 3.53
2228 2371 7.308450 TCACATTTGAATGGGTAAATTGGAA 57.692 32.000 5.92 0.00 40.68 3.53
2230 2373 6.933521 CACATTTGAATGGGTAAATTGGAACA 59.066 34.615 8.44 0.00 40.70 3.18
2232 2375 7.995488 ACATTTGAATGGGTAAATTGGAACAAA 59.005 29.630 8.44 0.00 41.89 2.83
2285 6304 3.745480 GCTTATCTGGGCTGCAGATACAA 60.745 47.826 20.43 0.00 40.24 2.41
2318 6337 7.579589 TTTACACGCGCTATCTTTTTAAGTA 57.420 32.000 5.73 0.00 0.00 2.24
3154 7343 9.295214 TGTGCGTATATTTATTGAAATGTTTGG 57.705 29.630 0.00 0.00 35.96 3.28
3413 7612 0.763652 AACACATGCAAAATGGGCCA 59.236 45.000 9.61 9.61 0.00 5.36
3416 7615 1.549620 CACATGCAAAATGGGCCACTA 59.450 47.619 9.28 0.00 0.00 2.74
3422 7621 4.144297 TGCAAAATGGGCCACTATATCTC 58.856 43.478 9.28 0.00 0.00 2.75
3423 7622 3.507622 GCAAAATGGGCCACTATATCTCC 59.492 47.826 9.28 0.00 0.00 3.71
3425 7624 5.139727 CAAAATGGGCCACTATATCTCCAA 58.860 41.667 9.28 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
78 80 5.984725 TCACAAGTCTTTCCTGTACAAGAA 58.015 37.500 2.67 2.67 30.76 2.52
87 89 4.506802 GGGGTACATTCACAAGTCTTTCCT 60.507 45.833 0.00 0.00 0.00 3.36
89 91 3.756963 GGGGGTACATTCACAAGTCTTTC 59.243 47.826 0.00 0.00 0.00 2.62
131 133 6.886459 AGTAATCTACCGTAGTGACCTAAACA 59.114 38.462 5.46 0.00 0.00 2.83
136 138 4.459330 GGAGTAATCTACCGTAGTGACCT 58.541 47.826 5.46 0.00 0.00 3.85
146 148 3.174779 GGGATGGAGGGAGTAATCTACC 58.825 54.545 0.00 0.00 44.87 3.18
150 152 2.011122 TCGGGATGGAGGGAGTAATC 57.989 55.000 0.00 0.00 0.00 1.75
161 163 1.676006 GTGGCAAGTAATTCGGGATGG 59.324 52.381 0.00 0.00 0.00 3.51
178 180 9.093458 TGCCTAGATACATCCATATATATGTGG 57.907 37.037 19.72 19.72 40.08 4.17
215 217 6.378710 TGTCGTAGAAATGGATGTCTCTAG 57.621 41.667 0.00 0.00 39.69 2.43
220 222 7.772332 ATTACTTGTCGTAGAAATGGATGTC 57.228 36.000 0.00 0.00 39.69 3.06
237 240 5.584649 TCCATGCTCCGTCTAAAATTACTTG 59.415 40.000 0.00 0.00 0.00 3.16
247 250 0.468214 CTCCCTCCATGCTCCGTCTA 60.468 60.000 0.00 0.00 0.00 2.59
251 254 0.757188 ACTACTCCCTCCATGCTCCG 60.757 60.000 0.00 0.00 0.00 4.63
253 256 4.965200 ATAAACTACTCCCTCCATGCTC 57.035 45.455 0.00 0.00 0.00 4.26
305 308 7.822334 TCGTTCTATTCCTCTAATTTTGCTTCA 59.178 33.333 0.00 0.00 0.00 3.02
326 329 6.476243 TGTAGCCTAAACAAAATCTCGTTC 57.524 37.500 0.00 0.00 0.00 3.95
366 369 9.547753 GGTCAACATACTACTTGTATCATCATT 57.452 33.333 0.00 0.00 39.66 2.57
372 375 8.684520 AGTGTAGGTCAACATACTACTTGTATC 58.315 37.037 6.53 0.00 39.66 2.24
373 376 8.591114 AGTGTAGGTCAACATACTACTTGTAT 57.409 34.615 6.53 0.00 42.18 2.29
374 377 9.519191 TTAGTGTAGGTCAACATACTACTTGTA 57.481 33.333 6.53 0.00 38.27 2.41
376 379 9.136952 GTTTAGTGTAGGTCAACATACTACTTG 57.863 37.037 6.53 0.00 38.27 3.16
377 380 8.025445 CGTTTAGTGTAGGTCAACATACTACTT 58.975 37.037 6.53 0.00 38.27 2.24
378 381 7.533426 CGTTTAGTGTAGGTCAACATACTACT 58.467 38.462 6.53 9.61 38.27 2.57
379 382 6.252228 GCGTTTAGTGTAGGTCAACATACTAC 59.748 42.308 6.53 0.00 38.02 2.73
380 383 6.151648 AGCGTTTAGTGTAGGTCAACATACTA 59.848 38.462 6.53 0.00 34.54 1.82
381 384 5.047519 AGCGTTTAGTGTAGGTCAACATACT 60.048 40.000 6.53 0.00 34.54 2.12
382 385 5.166398 AGCGTTTAGTGTAGGTCAACATAC 58.834 41.667 0.00 0.00 34.08 2.39
383 386 5.395682 AGCGTTTAGTGTAGGTCAACATA 57.604 39.130 0.00 0.00 0.00 2.29
384 387 4.267349 AGCGTTTAGTGTAGGTCAACAT 57.733 40.909 0.00 0.00 0.00 2.71
385 388 3.738830 AGCGTTTAGTGTAGGTCAACA 57.261 42.857 0.00 0.00 0.00 3.33
386 389 3.611549 GCTAGCGTTTAGTGTAGGTCAAC 59.388 47.826 0.00 0.00 0.00 3.18
387 390 3.671433 CGCTAGCGTTTAGTGTAGGTCAA 60.671 47.826 28.66 0.00 34.35 3.18
388 391 2.159476 CGCTAGCGTTTAGTGTAGGTCA 60.159 50.000 28.66 0.00 34.35 4.02
389 392 2.096496 TCGCTAGCGTTTAGTGTAGGTC 59.904 50.000 34.10 0.00 40.74 3.85
390 393 2.086869 TCGCTAGCGTTTAGTGTAGGT 58.913 47.619 34.10 0.00 40.74 3.08
391 394 2.838386 TCGCTAGCGTTTAGTGTAGG 57.162 50.000 34.10 4.25 40.74 3.18
392 395 5.745514 TCTTATCGCTAGCGTTTAGTGTAG 58.254 41.667 34.10 19.81 40.74 2.74
393 396 5.739752 TCTTATCGCTAGCGTTTAGTGTA 57.260 39.130 34.10 14.90 40.74 2.90
394 397 4.627611 TCTTATCGCTAGCGTTTAGTGT 57.372 40.909 34.10 15.62 40.74 3.55
395 398 4.143514 GCATCTTATCGCTAGCGTTTAGTG 60.144 45.833 34.10 25.27 40.74 2.74
396 399 3.982058 GCATCTTATCGCTAGCGTTTAGT 59.018 43.478 34.10 18.73 40.74 2.24
397 400 3.981416 TGCATCTTATCGCTAGCGTTTAG 59.019 43.478 34.10 27.41 40.74 1.85
398 401 3.972403 TGCATCTTATCGCTAGCGTTTA 58.028 40.909 34.10 23.70 40.74 2.01
399 402 2.821546 TGCATCTTATCGCTAGCGTTT 58.178 42.857 34.10 24.68 40.74 3.60
400 403 2.509052 TGCATCTTATCGCTAGCGTT 57.491 45.000 34.10 28.35 40.74 4.84
401 404 2.509052 TTGCATCTTATCGCTAGCGT 57.491 45.000 34.10 23.62 40.74 5.07
402 405 3.181526 GGATTTGCATCTTATCGCTAGCG 60.182 47.826 30.91 30.91 41.35 4.26
403 406 3.748048 TGGATTTGCATCTTATCGCTAGC 59.252 43.478 4.06 4.06 0.00 3.42
404 407 4.993584 AGTGGATTTGCATCTTATCGCTAG 59.006 41.667 0.00 0.00 0.00 3.42
405 408 4.960938 AGTGGATTTGCATCTTATCGCTA 58.039 39.130 0.00 0.00 0.00 4.26
406 409 3.813443 AGTGGATTTGCATCTTATCGCT 58.187 40.909 0.00 0.00 0.00 4.93
407 410 4.558538 AAGTGGATTTGCATCTTATCGC 57.441 40.909 0.00 0.00 0.00 4.58
408 411 7.225538 ACTTCTAAGTGGATTTGCATCTTATCG 59.774 37.037 0.00 0.00 37.98 2.92
409 412 8.443953 ACTTCTAAGTGGATTTGCATCTTATC 57.556 34.615 0.00 0.00 37.98 1.75
411 414 9.330063 CATACTTCTAAGTGGATTTGCATCTTA 57.670 33.333 5.62 0.00 40.07 2.10
412 415 7.831193 ACATACTTCTAAGTGGATTTGCATCTT 59.169 33.333 5.62 0.00 40.07 2.40
413 416 7.341805 ACATACTTCTAAGTGGATTTGCATCT 58.658 34.615 5.62 0.00 40.07 2.90
414 417 7.559590 ACATACTTCTAAGTGGATTTGCATC 57.440 36.000 5.62 0.00 40.07 3.91
415 418 9.632638 ATTACATACTTCTAAGTGGATTTGCAT 57.367 29.630 5.62 0.00 40.07 3.96
416 419 8.892723 CATTACATACTTCTAAGTGGATTTGCA 58.107 33.333 5.62 0.00 40.07 4.08
417 420 9.109393 TCATTACATACTTCTAAGTGGATTTGC 57.891 33.333 5.62 0.00 40.07 3.68
420 423 9.331282 GCTTCATTACATACTTCTAAGTGGATT 57.669 33.333 5.62 0.00 40.07 3.01
421 424 7.934120 GGCTTCATTACATACTTCTAAGTGGAT 59.066 37.037 5.62 0.00 40.07 3.41
422 425 7.272978 GGCTTCATTACATACTTCTAAGTGGA 58.727 38.462 5.62 0.00 40.07 4.02
423 426 6.201044 CGGCTTCATTACATACTTCTAAGTGG 59.799 42.308 5.62 0.97 40.07 4.00
470 474 2.308866 CTGACAGGTCCCCCTTAACATT 59.691 50.000 0.00 0.00 39.89 2.71
503 507 7.400339 ACCTCTGTGAGATAAGAAAGTCCATTA 59.600 37.037 0.00 0.00 0.00 1.90
524 528 1.073199 CCCAAACCAGCGAACCTCT 59.927 57.895 0.00 0.00 0.00 3.69
527 531 2.561037 CCACCCAAACCAGCGAACC 61.561 63.158 0.00 0.00 0.00 3.62
531 535 2.098426 AAATGCCACCCAAACCAGCG 62.098 55.000 0.00 0.00 0.00 5.18
556 560 9.658475 CGAACAACTAAAATAGTCATCAAAACA 57.342 29.630 0.00 0.00 38.26 2.83
581 585 6.310467 TGTTTTGAAGAAACTATCGATCTCCG 59.690 38.462 0.00 0.00 40.25 4.63
587 591 6.036300 ACGTGTTGTTTTGAAGAAACTATCGA 59.964 34.615 14.24 0.00 0.00 3.59
591 595 8.031848 ACTAACGTGTTGTTTTGAAGAAACTA 57.968 30.769 0.00 0.00 42.09 2.24
592 596 6.905578 ACTAACGTGTTGTTTTGAAGAAACT 58.094 32.000 0.00 0.00 42.09 2.66
660 664 2.735444 GCGACACGAGATCAAAGGATGA 60.735 50.000 0.00 0.00 43.67 2.92
665 669 2.061773 AGTTGCGACACGAGATCAAAG 58.938 47.619 6.90 0.00 0.00 2.77
676 680 5.425577 TGCTTGTAATTTTAGTTGCGACA 57.574 34.783 6.90 0.00 0.00 4.35
692 696 2.418060 CGTTGGAAAAGGGTTTGCTTGT 60.418 45.455 0.00 0.00 36.14 3.16
758 762 4.470334 AAAATTGGCACACACAAACTCT 57.530 36.364 0.00 0.00 39.29 3.24
827 833 7.061557 GCACTAAAAACTTCTCAGAAATGCATC 59.938 37.037 0.00 0.00 0.00 3.91
836 842 8.660373 CCTAACTATGCACTAAAAACTTCTCAG 58.340 37.037 0.00 0.00 0.00 3.35
837 843 8.154856 ACCTAACTATGCACTAAAAACTTCTCA 58.845 33.333 0.00 0.00 0.00 3.27
838 844 8.549338 ACCTAACTATGCACTAAAAACTTCTC 57.451 34.615 0.00 0.00 0.00 2.87
841 847 8.727910 GCTTACCTAACTATGCACTAAAAACTT 58.272 33.333 0.00 0.00 0.00 2.66
843 849 7.414873 GGGCTTACCTAACTATGCACTAAAAAC 60.415 40.741 0.00 0.00 35.85 2.43
869 876 6.309980 GTGAGTCATTGTCTCATTGAGTACAG 59.690 42.308 15.07 6.43 42.63 2.74
877 884 3.755378 GCAAGGTGAGTCATTGTCTCATT 59.245 43.478 15.07 5.65 42.63 2.57
882 889 1.195448 CGTGCAAGGTGAGTCATTGTC 59.805 52.381 8.00 2.55 39.61 3.18
883 890 1.229428 CGTGCAAGGTGAGTCATTGT 58.771 50.000 8.00 0.00 39.61 2.71
886 893 1.343142 TGTACGTGCAAGGTGAGTCAT 59.657 47.619 3.02 0.00 35.89 3.06
887 894 0.747852 TGTACGTGCAAGGTGAGTCA 59.252 50.000 3.02 0.00 35.89 3.41
888 895 1.726791 CATGTACGTGCAAGGTGAGTC 59.273 52.381 11.22 0.00 35.89 3.36
889 896 1.070134 ACATGTACGTGCAAGGTGAGT 59.930 47.619 11.22 0.25 35.89 3.41
890 897 1.795768 ACATGTACGTGCAAGGTGAG 58.204 50.000 11.22 0.00 35.89 3.51
891 898 2.248280 AACATGTACGTGCAAGGTGA 57.752 45.000 11.22 0.00 35.89 4.02
892 899 3.347958 AAAACATGTACGTGCAAGGTG 57.652 42.857 11.22 7.32 35.89 4.00
893 900 4.757657 TGATAAAACATGTACGTGCAAGGT 59.242 37.500 11.22 9.42 39.04 3.50
894 901 5.289917 TGATAAAACATGTACGTGCAAGG 57.710 39.130 11.22 8.74 0.00 3.61
895 902 7.795431 ATTTGATAAAACATGTACGTGCAAG 57.205 32.000 11.22 9.11 0.00 4.01
947 954 7.181143 TCTACAAAAGTAAAACCACATCGAC 57.819 36.000 0.00 0.00 0.00 4.20
1551 1668 5.120399 ACTAGTCCACGATGAAAACACAAA 58.880 37.500 0.00 0.00 0.00 2.83
1635 1760 4.576330 ATGTGTAAGAAGAGGGGGAAAG 57.424 45.455 0.00 0.00 0.00 2.62
1654 1779 7.834068 TCTTCAGAAAGACGAAAGGATAATG 57.166 36.000 0.00 0.00 36.59 1.90
1737 1863 7.967303 GCCATTTTAGTCTGAAGAAATCAAGAG 59.033 37.037 0.00 0.00 37.67 2.85
1754 1880 2.166254 AGTTTCCCATGCGCCATTTTAG 59.834 45.455 4.18 0.00 0.00 1.85
1858 1984 8.739461 CACAAAACCGTATTTTCAAAGTTCTAC 58.261 33.333 0.00 0.00 0.00 2.59
1937 2071 0.918799 AGGTGGGGCCATACACATGA 60.919 55.000 21.22 0.00 39.31 3.07
2145 2288 3.699038 TGGGTCTCTTGTTTGAGTTTTGG 59.301 43.478 0.00 0.00 35.68 3.28
2285 6304 2.682876 CGCGTGTAAAATGGGCCGT 61.683 57.895 0.00 0.00 0.00 5.68
3391 7590 1.070038 CCCATTTTGCATGTGTTCGC 58.930 50.000 0.00 0.00 0.00 4.70
3399 7598 4.744237 AGATATAGTGGCCCATTTTGCAT 58.256 39.130 0.00 0.00 0.00 3.96
3400 7599 4.144297 GAGATATAGTGGCCCATTTTGCA 58.856 43.478 0.00 0.00 0.00 4.08
3413 7612 7.304497 AGCTTAAATCGGTTGGAGATATAGT 57.696 36.000 0.00 0.00 0.00 2.12
3416 7615 5.071788 TGGAGCTTAAATCGGTTGGAGATAT 59.928 40.000 0.00 0.00 0.00 1.63
3422 7621 2.432444 TGTGGAGCTTAAATCGGTTGG 58.568 47.619 0.00 0.00 0.00 3.77
3423 7622 3.731867 GCATGTGGAGCTTAAATCGGTTG 60.732 47.826 0.00 0.00 0.00 3.77
3425 7624 2.017049 GCATGTGGAGCTTAAATCGGT 58.983 47.619 0.00 0.00 0.00 4.69


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

AutoCloner maintained by Alex Coulton.