Multiple sequence alignment - TraesCS2D01G119800

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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 TraesCS2D01G119800 chr2D 100.000 2735 0 0 1 2735 69029365 69026631 0.000000e+00 5051.0
1 TraesCS2D01G119800 chr2D 78.709 883 119 35 577 1426 67447829 67448675 2.410000e-145 525.0
2 TraesCS2D01G119800 chr2D 77.567 896 110 52 577 1426 67445143 67445993 8.930000e-125 457.0
3 TraesCS2D01G119800 chr2D 89.691 97 10 0 1922 2018 433984750 433984846 1.030000e-24 124.0
4 TraesCS2D01G119800 chr2D 100.000 28 0 0 1 28 68811670 68811697 5.000000e-03 52.8
5 TraesCS2D01G119800 chr2B 88.783 1471 95 29 1 1429 101543988 101542546 0.000000e+00 1738.0
6 TraesCS2D01G119800 chr2B 90.693 548 46 2 2188 2735 101541826 101541284 0.000000e+00 725.0
7 TraesCS2D01G119800 chr2B 89.906 426 34 4 1431 1853 101542481 101542062 8.620000e-150 540.0
8 TraesCS2D01G119800 chr2B 78.621 856 110 39 621 1434 103845839 103845015 1.460000e-137 499.0
9 TraesCS2D01G119800 chr2B 77.336 1006 113 61 495 1434 104052989 104052033 3.170000e-134 488.0
10 TraesCS2D01G119800 chr2B 77.740 885 124 33 589 1434 103901174 103900324 2.460000e-130 475.0
11 TraesCS2D01G119800 chr2B 77.841 880 116 38 589 1429 103956347 103955508 3.190000e-129 472.0
12 TraesCS2D01G119800 chr2B 93.382 272 18 0 2464 2735 101529218 101528947 1.180000e-108 403.0
13 TraesCS2D01G119800 chr2B 76.379 707 98 35 780 1434 104005871 104005182 1.580000e-82 316.0
14 TraesCS2D01G119800 chr2B 77.536 552 69 22 780 1299 104019277 104018749 5.770000e-72 281.0
15 TraesCS2D01G119800 chr2B 77.751 418 45 25 621 1018 103709570 103709181 2.130000e-51 213.0
16 TraesCS2D01G119800 chr2B 89.583 96 3 1 1842 1937 101542041 101541953 6.190000e-22 115.0
17 TraesCS2D01G119800 chr2B 85.075 67 9 1 1342 1407 104018724 104018658 1.760000e-07 67.6
18 TraesCS2D01G119800 chr2A 93.458 963 49 6 472 1429 66004754 66003801 0.000000e+00 1417.0
19 TraesCS2D01G119800 chr2A 93.388 968 42 9 476 1429 65954238 65953279 0.000000e+00 1413.0
20 TraesCS2D01G119800 chr2A 92.135 445 25 8 1 442 66005291 66004854 1.080000e-173 619.0
21 TraesCS2D01G119800 chr2A 89.914 466 33 5 1431 1893 65953208 65952754 3.030000e-164 588.0
22 TraesCS2D01G119800 chr2A 92.954 369 19 2 1431 1796 66003736 66003372 5.190000e-147 531.0
23 TraesCS2D01G119800 chr2A 87.746 457 36 5 2188 2644 65952507 65952071 1.450000e-142 516.0
24 TraesCS2D01G119800 chr2A 89.160 369 25 10 72 432 65954741 65954380 1.930000e-121 446.0
25 TraesCS2D01G119800 chr2A 78.244 763 112 27 703 1429 66909636 66908892 8.990000e-120 440.0
26 TraesCS2D01G119800 chr2A 78.902 692 85 27 775 1434 66915225 66914563 1.960000e-111 412.0
27 TraesCS2D01G119800 chr2A 92.517 147 10 1 2013 2159 65952640 65952495 2.760000e-50 209.0
28 TraesCS2D01G119800 chr2A 94.318 88 5 0 1928 2015 592785589 592785676 4.750000e-28 135.0
29 TraesCS2D01G119800 chr2A 80.620 129 24 1 10 137 738028836 738028708 6.230000e-17 99.0
30 TraesCS2D01G119800 chr6A 91.304 92 8 0 1928 2019 31750247 31750156 2.860000e-25 126.0
31 TraesCS2D01G119800 chr6A 85.841 113 13 3 1920 2030 258133057 258133168 1.720000e-22 117.0
32 TraesCS2D01G119800 chr3B 93.023 86 6 0 1930 2015 54592460 54592545 2.860000e-25 126.0
33 TraesCS2D01G119800 chr3B 91.398 93 7 1 1930 2022 748777091 748777182 2.860000e-25 126.0
34 TraesCS2D01G119800 chr1A 92.135 89 7 0 1930 2018 498400930 498400842 2.860000e-25 126.0
35 TraesCS2D01G119800 chr7B 90.426 94 9 0 1929 2022 726227063 726226970 1.030000e-24 124.0
36 TraesCS2D01G119800 chr4B 91.954 87 7 0 1928 2014 565213463 565213377 3.700000e-24 122.0
37 TraesCS2D01G119800 chr4A 78.261 184 30 7 1 182 631904999 631904824 2.880000e-20 110.0


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 TraesCS2D01G119800 chr2D 69026631 69029365 2734 True 5051.000000 5051 100.00000 1 2735 1 chr2D.!!$R1 2734
1 TraesCS2D01G119800 chr2D 67445143 67448675 3532 False 491.000000 525 78.13800 577 1426 2 chr2D.!!$F3 849
2 TraesCS2D01G119800 chr2B 101541284 101543988 2704 True 779.500000 1738 89.74125 1 2735 4 chr2B.!!$R8 2734
3 TraesCS2D01G119800 chr2B 103845015 103845839 824 True 499.000000 499 78.62100 621 1434 1 chr2B.!!$R3 813
4 TraesCS2D01G119800 chr2B 104052033 104052989 956 True 488.000000 488 77.33600 495 1434 1 chr2B.!!$R7 939
5 TraesCS2D01G119800 chr2B 103900324 103901174 850 True 475.000000 475 77.74000 589 1434 1 chr2B.!!$R4 845
6 TraesCS2D01G119800 chr2B 103955508 103956347 839 True 472.000000 472 77.84100 589 1429 1 chr2B.!!$R5 840
7 TraesCS2D01G119800 chr2B 104005182 104005871 689 True 316.000000 316 76.37900 780 1434 1 chr2B.!!$R6 654
8 TraesCS2D01G119800 chr2A 66003372 66005291 1919 True 855.666667 1417 92.84900 1 1796 3 chr2A.!!$R5 1795
9 TraesCS2D01G119800 chr2A 65952071 65954741 2670 True 634.400000 1413 90.54500 72 2644 5 chr2A.!!$R4 2572
10 TraesCS2D01G119800 chr2A 66908892 66909636 744 True 440.000000 440 78.24400 703 1429 1 chr2A.!!$R1 726
11 TraesCS2D01G119800 chr2A 66914563 66915225 662 True 412.000000 412 78.90200 775 1434 1 chr2A.!!$R2 659

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
95 96 1.146041 GTATGGGCGCCATGTCTGA 59.854 57.895 30.85 2.17 44.84 3.27 F
1300 4335 1.153349 GGCGAGGTGTTCATCCCTC 60.153 63.158 0.00 0.00 43.20 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1429 4473 0.679505 GGATAGTACTGCCATGGCGA 59.320 55.0 30.87 18.84 45.51 5.54 R
2242 5425 0.246635 AGTTTGATCCGACGACCCTG 59.753 55.0 0.00 0.00 0.00 4.45 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
95 96 1.146041 GTATGGGCGCCATGTCTGA 59.854 57.895 30.85 2.17 44.84 3.27
114 120 5.892119 GTCTGATTAGGATATCCCGGTGATA 59.108 44.000 18.56 13.06 40.20 2.15
130 136 4.261867 CGGTGATATTGTATTCGTCCCTGA 60.262 45.833 0.00 0.00 0.00 3.86
168 174 5.548406 ACGGAGTAATAAAGCTTTGTGAGT 58.452 37.500 22.02 11.15 41.94 3.41
170 176 6.147328 ACGGAGTAATAAAGCTTTGTGAGTTC 59.853 38.462 22.02 9.02 41.94 3.01
171 177 6.369065 CGGAGTAATAAAGCTTTGTGAGTTCT 59.631 38.462 22.02 4.45 0.00 3.01
172 178 7.544566 CGGAGTAATAAAGCTTTGTGAGTTCTA 59.455 37.037 22.02 0.48 0.00 2.10
329 366 7.439157 TGTAAGTTCAGTTTGAGGAATGATG 57.561 36.000 0.00 0.00 0.00 3.07
417 456 9.965824 AATTCACAAGGTTAATCAAGTAACTTG 57.034 29.630 0.00 0.00 42.25 3.16
418 457 8.514330 TTCACAAGGTTAATCAAGTAACTTGT 57.486 30.769 4.01 4.01 41.66 3.16
420 459 9.616156 TCACAAGGTTAATCAAGTAACTTGTTA 57.384 29.630 5.52 2.10 41.66 2.41
421 460 9.659830 CACAAGGTTAATCAAGTAACTTGTTAC 57.340 33.333 13.89 13.89 41.66 2.50
423 462 9.063615 CAAGGTTAATCAAGTAACTTGTTACCT 57.936 33.333 17.02 1.80 41.66 3.08
431 529 8.115490 TCAAGTAACTTGTTACCTACTACTCC 57.885 38.462 17.02 0.00 41.66 3.85
511 737 2.441532 GGCATGCAGCTGGTCCAT 60.442 61.111 21.36 7.69 44.79 3.41
669 903 8.723942 AACAGTCCTATACAATTCACTGATTC 57.276 34.615 3.96 0.00 35.77 2.52
670 904 7.851228 ACAGTCCTATACAATTCACTGATTCA 58.149 34.615 3.96 0.00 35.77 2.57
1059 4082 4.074970 GTCACAACCTGAAGGATGTCAAT 58.925 43.478 9.15 0.00 46.49 2.57
1300 4335 1.153349 GGCGAGGTGTTCATCCCTC 60.153 63.158 0.00 0.00 43.20 4.30
1429 4473 4.778143 GCTTCGGCCCCGTGATGT 62.778 66.667 6.61 0.00 40.74 3.06
1445 4558 1.068588 GATGTCGCCATGGCAGTACTA 59.931 52.381 34.93 18.86 42.06 1.82
1508 4621 3.699894 CCCTCAGGCGTGTGCTCT 61.700 66.667 6.26 0.00 42.25 4.09
1704 4817 0.617820 ATGACTCCGGGTACAAGCCT 60.618 55.000 0.00 0.00 32.48 4.58
1758 4874 7.286087 TGAAAACTTCCCATATTCATCAGGATG 59.714 37.037 2.84 2.84 40.09 3.51
1796 4914 8.524870 AGTACGTACGTCAAACTTGAATAAAT 57.475 30.769 26.53 0.00 39.21 1.40
1797 4915 9.624697 AGTACGTACGTCAAACTTGAATAAATA 57.375 29.630 26.53 0.00 39.21 1.40
1859 5009 4.051922 GTCCAGATAGCTTGGTACATTCG 58.948 47.826 2.88 0.00 39.30 3.34
1864 5014 2.386661 AGCTTGGTACATTCGGTCAG 57.613 50.000 0.00 0.00 39.30 3.51
1882 5032 4.156373 GGTCAGTCCTGTAGTCTACTTGTC 59.844 50.000 11.28 1.18 0.00 3.18
1883 5033 5.005094 GTCAGTCCTGTAGTCTACTTGTCT 58.995 45.833 11.28 3.22 0.00 3.41
1884 5034 5.004448 TCAGTCCTGTAGTCTACTTGTCTG 58.996 45.833 11.28 13.22 0.00 3.51
1885 5035 4.762765 CAGTCCTGTAGTCTACTTGTCTGT 59.237 45.833 11.28 0.00 0.00 3.41
1886 5036 5.938710 CAGTCCTGTAGTCTACTTGTCTGTA 59.061 44.000 11.28 0.00 0.00 2.74
1887 5037 5.939296 AGTCCTGTAGTCTACTTGTCTGTAC 59.061 44.000 11.28 0.00 0.00 2.90
1888 5038 5.939296 GTCCTGTAGTCTACTTGTCTGTACT 59.061 44.000 11.28 0.00 0.00 2.73
1931 5114 0.443869 CGCTGTCCATTGCAGTGTAC 59.556 55.000 8.53 3.06 39.02 2.90
1933 5116 2.154462 GCTGTCCATTGCAGTGTACTT 58.846 47.619 8.53 0.00 36.42 2.24
1935 5118 2.744202 CTGTCCATTGCAGTGTACTTCC 59.256 50.000 8.53 0.00 0.00 3.46
1937 5120 3.003480 GTCCATTGCAGTGTACTTCCTC 58.997 50.000 8.53 0.00 0.00 3.71
1939 5122 2.290260 CCATTGCAGTGTACTTCCTCCA 60.290 50.000 8.53 0.00 0.00 3.86
1943 5126 4.901197 TGCAGTGTACTTCCTCCATAAA 57.099 40.909 0.00 0.00 0.00 1.40
1944 5127 5.435686 TGCAGTGTACTTCCTCCATAAAT 57.564 39.130 0.00 0.00 0.00 1.40
1945 5128 5.815581 TGCAGTGTACTTCCTCCATAAATT 58.184 37.500 0.00 0.00 0.00 1.82
1946 5129 6.953101 TGCAGTGTACTTCCTCCATAAATTA 58.047 36.000 0.00 0.00 0.00 1.40
1947 5130 7.398829 TGCAGTGTACTTCCTCCATAAATTAA 58.601 34.615 0.00 0.00 0.00 1.40
1949 5132 9.555727 GCAGTGTACTTCCTCCATAAATTAATA 57.444 33.333 0.00 0.00 0.00 0.98
2022 5205 5.656213 TTACAGAGGGAGTACTTGCTTAC 57.344 43.478 0.00 0.00 0.00 2.34
2035 5218 4.499183 ACTTGCTTACTCGATTCCTTCTG 58.501 43.478 0.00 0.00 0.00 3.02
2105 5288 0.952280 CAGCATGCATCTGTGATCCC 59.048 55.000 21.98 0.00 0.00 3.85
2131 5314 3.210857 GCTGTGGAAGCGAAGTGTA 57.789 52.632 0.00 0.00 43.45 2.90
2146 5329 3.444703 AGTGTAAGAGCATCGATCCAC 57.555 47.619 0.00 0.00 42.67 4.02
2147 5330 2.760650 AGTGTAAGAGCATCGATCCACA 59.239 45.455 0.00 0.00 42.67 4.17
2148 5331 3.195610 AGTGTAAGAGCATCGATCCACAA 59.804 43.478 0.00 0.00 42.67 3.33
2149 5332 3.307242 GTGTAAGAGCATCGATCCACAAC 59.693 47.826 0.00 0.00 42.67 3.32
2150 5333 2.768253 AAGAGCATCGATCCACAACA 57.232 45.000 0.00 0.00 42.67 3.33
2151 5334 2.768253 AGAGCATCGATCCACAACAA 57.232 45.000 0.00 0.00 42.67 2.83
2152 5335 3.272574 AGAGCATCGATCCACAACAAT 57.727 42.857 0.00 0.00 42.67 2.71
2153 5336 2.941064 AGAGCATCGATCCACAACAATG 59.059 45.455 0.00 0.00 42.67 2.82
2154 5337 2.679837 GAGCATCGATCCACAACAATGT 59.320 45.455 0.00 0.00 41.61 2.71
2155 5338 3.084039 AGCATCGATCCACAACAATGTT 58.916 40.909 0.00 0.00 37.82 2.71
2156 5339 3.507233 AGCATCGATCCACAACAATGTTT 59.493 39.130 0.00 0.00 37.82 2.83
2157 5340 4.699735 AGCATCGATCCACAACAATGTTTA 59.300 37.500 0.00 0.00 37.82 2.01
2158 5341 5.357878 AGCATCGATCCACAACAATGTTTAT 59.642 36.000 0.00 0.00 37.82 1.40
2159 5342 6.542005 AGCATCGATCCACAACAATGTTTATA 59.458 34.615 0.00 0.00 37.82 0.98
2160 5343 7.229306 AGCATCGATCCACAACAATGTTTATAT 59.771 33.333 0.00 0.00 37.82 0.86
2161 5344 7.862372 GCATCGATCCACAACAATGTTTATATT 59.138 33.333 0.00 0.00 37.82 1.28
2162 5345 9.734620 CATCGATCCACAACAATGTTTATATTT 57.265 29.630 0.00 0.00 37.82 1.40
2219 5402 0.669318 TGGAGGCGACGTTTGTGATC 60.669 55.000 0.00 0.00 0.00 2.92
2228 5411 3.173599 GACGTTTGTGATCCAATGCATG 58.826 45.455 0.00 0.00 31.81 4.06
2232 5415 4.142622 CGTTTGTGATCCAATGCATGTACT 60.143 41.667 0.00 0.00 31.81 2.73
2234 5417 4.968812 TGTGATCCAATGCATGTACTTG 57.031 40.909 0.00 4.42 0.00 3.16
2242 5425 5.097529 CCAATGCATGTACTTGTGACAATC 58.902 41.667 0.00 0.00 0.00 2.67
2249 5432 2.169832 ACTTGTGACAATCAGGGTCG 57.830 50.000 0.00 0.00 38.10 4.79
2250 5433 1.416401 ACTTGTGACAATCAGGGTCGT 59.584 47.619 0.00 0.00 38.10 4.34
2257 5440 0.459899 CAATCAGGGTCGTCGGATCA 59.540 55.000 0.00 0.00 0.00 2.92
2269 5452 2.604914 CGTCGGATCAAACTCAAGATGG 59.395 50.000 0.00 0.00 0.00 3.51
2270 5453 2.939103 GTCGGATCAAACTCAAGATGGG 59.061 50.000 0.00 0.00 0.00 4.00
2280 5463 6.761242 TCAAACTCAAGATGGGTAACGATATG 59.239 38.462 0.00 0.00 33.87 1.78
2293 5476 6.124759 GGTAACGATATGTTTTTCGAATCGG 58.875 40.000 16.60 2.82 42.73 4.18
2389 5572 1.354101 ACCCGGATGTACTCAAACCA 58.646 50.000 0.73 0.00 0.00 3.67
2413 5596 1.957877 GTCGATGGCTACTCTAAGGCT 59.042 52.381 0.00 0.00 42.33 4.58
2419 5602 1.957877 GGCTACTCTAAGGCTCGACAT 59.042 52.381 0.00 0.00 38.92 3.06
2449 5632 6.715280 ACAAGACAAACCATATCATGAGACT 58.285 36.000 0.09 0.00 0.00 3.24
2480 5663 6.435591 TGATGTTGATTAGGGTTGCATTTGTA 59.564 34.615 0.00 0.00 0.00 2.41
2536 5719 9.801873 ATTCCAGGAATAACAAACAAATATTCG 57.198 29.630 13.56 0.00 37.06 3.34
2662 5845 1.739338 ATGTCGAGCTGATCCCGGAC 61.739 60.000 0.73 0.00 0.00 4.79
2664 5847 4.271816 CGAGCTGATCCCGGACCG 62.272 72.222 6.99 6.99 0.00 4.79
2668 5851 2.505982 CTGATCCCGGACCGCATT 59.494 61.111 8.86 0.00 0.00 3.56
2682 5865 2.620112 GCATTGACGTGGCAGCAGT 61.620 57.895 0.00 0.00 0.00 4.40
2704 5887 5.893824 AGTCAAAGAAGAGGTGGAAACAATT 59.106 36.000 0.00 0.00 46.06 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
76 77 2.108976 AGACATGGCGCCCATACG 59.891 61.111 26.77 10.11 43.15 3.06
95 96 8.798975 ATACAATATCACCGGGATATCCTAAT 57.201 34.615 21.18 10.03 46.23 1.73
114 120 5.064707 CGATGTTTTCAGGGACGAATACAAT 59.935 40.000 0.00 0.00 39.30 2.71
181 192 6.053005 TCAAACTTAAAGACACCAATCGAGT 58.947 36.000 0.00 0.00 0.00 4.18
198 209 9.277565 CGAATCGAATGTTGAATAATCAAACTT 57.722 29.630 0.00 0.00 46.66 2.66
223 234 8.789881 TTTTGGAACTGTTAACAATACATTCG 57.210 30.769 10.03 0.00 0.00 3.34
466 689 3.864921 GCCCATGAAGAACTAACAGACGT 60.865 47.826 0.00 0.00 0.00 4.34
467 690 2.673368 GCCCATGAAGAACTAACAGACG 59.327 50.000 0.00 0.00 0.00 4.18
468 691 3.674997 TGCCCATGAAGAACTAACAGAC 58.325 45.455 0.00 0.00 0.00 3.51
474 697 3.364549 CCCAATTGCCCATGAAGAACTA 58.635 45.455 0.00 0.00 0.00 2.24
586 812 3.660501 TCCCACTGATGCGACATATAC 57.339 47.619 0.00 0.00 0.00 1.47
669 903 5.147330 TCTAGAATACCTGTGGTTGTGTG 57.853 43.478 0.00 0.00 37.09 3.82
670 904 5.542635 TCTTCTAGAATACCTGTGGTTGTGT 59.457 40.000 5.44 0.00 37.09 3.72
740 997 5.233902 CAGCTAGCTTGTTACTGATGACATC 59.766 44.000 16.46 8.59 0.00 3.06
950 3940 3.164268 TGGGAAACTACGTGGCTACTAA 58.836 45.455 0.00 0.00 0.00 2.24
951 3941 2.806434 TGGGAAACTACGTGGCTACTA 58.194 47.619 0.00 0.00 0.00 1.82
952 3942 1.636148 TGGGAAACTACGTGGCTACT 58.364 50.000 0.00 0.00 0.00 2.57
953 3943 2.685850 ATGGGAAACTACGTGGCTAC 57.314 50.000 0.00 0.00 0.00 3.58
1059 4082 1.672030 CTCCATGCGGCTGAACACA 60.672 57.895 0.00 0.00 0.00 3.72
1281 4316 1.899437 GAGGGATGAACACCTCGCCA 61.899 60.000 0.00 0.00 43.37 5.69
1429 4473 0.679505 GGATAGTACTGCCATGGCGA 59.320 55.000 30.87 18.84 45.51 5.54
1434 4478 2.240279 GTCGGAGGATAGTACTGCCAT 58.760 52.381 16.19 1.97 0.00 4.40
1567 4680 6.411652 CGTTCCTTACGCAATAATTCTTCTC 58.588 40.000 0.00 0.00 44.26 2.87
1641 4754 1.669760 GTCGCCGAACACCATTCCA 60.670 57.895 0.00 0.00 0.00 3.53
1644 4757 1.922135 GCATGTCGCCGAACACCATT 61.922 55.000 0.00 0.00 32.94 3.16
1715 4828 4.021925 AGAAGGCGACCCCTGCAC 62.022 66.667 0.00 0.00 45.62 4.57
1716 4829 4.020617 CAGAAGGCGACCCCTGCA 62.021 66.667 0.00 0.00 45.62 4.41
1722 4838 1.535896 GGAAGTTTTCAGAAGGCGACC 59.464 52.381 0.00 0.00 0.00 4.79
1725 4841 1.604604 TGGGAAGTTTTCAGAAGGCG 58.395 50.000 0.00 0.00 0.00 5.52
1796 4914 7.815840 TCCTGATGAACATGTCAAGTTTTTA 57.184 32.000 0.00 0.00 40.50 1.52
1797 4915 6.713762 TCCTGATGAACATGTCAAGTTTTT 57.286 33.333 0.00 0.00 40.50 1.94
1798 4916 6.348786 CGATCCTGATGAACATGTCAAGTTTT 60.349 38.462 0.00 0.00 40.50 2.43
1799 4917 5.122869 CGATCCTGATGAACATGTCAAGTTT 59.877 40.000 0.00 0.00 40.50 2.66
1810 4928 2.799412 GCATCTCACGATCCTGATGAAC 59.201 50.000 12.87 1.79 38.72 3.18
1859 5009 4.080687 ACAAGTAGACTACAGGACTGACC 58.919 47.826 14.95 0.00 39.35 4.02
1864 5014 5.939296 AGTACAGACAAGTAGACTACAGGAC 59.061 44.000 14.95 6.64 0.00 3.85
1882 5032 3.284323 ACAACGCAGTACAGAGTACAG 57.716 47.619 9.68 3.13 45.00 2.74
1883 5033 3.720949 AACAACGCAGTACAGAGTACA 57.279 42.857 9.68 0.00 45.00 2.90
1884 5034 4.791974 AGTAACAACGCAGTACAGAGTAC 58.208 43.478 0.00 0.00 45.00 2.73
1885 5035 5.443185 AAGTAACAACGCAGTACAGAGTA 57.557 39.130 0.00 0.00 45.00 2.59
1886 5036 4.317671 AAGTAACAACGCAGTACAGAGT 57.682 40.909 0.00 0.00 45.00 3.24
1887 5037 5.164215 CGTAAAGTAACAACGCAGTACAGAG 60.164 44.000 0.00 0.00 45.00 3.35
1888 5038 4.676471 CGTAAAGTAACAACGCAGTACAGA 59.324 41.667 0.00 0.00 45.00 3.41
1992 5175 8.422566 GCAAGTACTCCCTCTGTAAACTTATAT 58.577 37.037 0.00 0.00 0.00 0.86
1993 5176 7.618512 AGCAAGTACTCCCTCTGTAAACTTATA 59.381 37.037 0.00 0.00 0.00 0.98
1994 5177 6.440965 AGCAAGTACTCCCTCTGTAAACTTAT 59.559 38.462 0.00 0.00 0.00 1.73
1995 5178 5.778750 AGCAAGTACTCCCTCTGTAAACTTA 59.221 40.000 0.00 0.00 0.00 2.24
1996 5179 4.593634 AGCAAGTACTCCCTCTGTAAACTT 59.406 41.667 0.00 0.00 0.00 2.66
1997 5180 4.161102 AGCAAGTACTCCCTCTGTAAACT 58.839 43.478 0.00 0.00 0.00 2.66
1998 5181 4.538746 AGCAAGTACTCCCTCTGTAAAC 57.461 45.455 0.00 0.00 0.00 2.01
1999 5182 5.778750 AGTAAGCAAGTACTCCCTCTGTAAA 59.221 40.000 0.00 0.00 27.56 2.01
2000 5183 5.331069 AGTAAGCAAGTACTCCCTCTGTAA 58.669 41.667 0.00 0.00 27.56 2.41
2001 5184 4.931914 AGTAAGCAAGTACTCCCTCTGTA 58.068 43.478 0.00 0.00 27.56 2.74
2002 5185 3.764972 GAGTAAGCAAGTACTCCCTCTGT 59.235 47.826 0.00 0.00 42.82 3.41
2003 5186 3.181495 CGAGTAAGCAAGTACTCCCTCTG 60.181 52.174 13.52 0.00 44.84 3.35
2004 5187 3.018149 CGAGTAAGCAAGTACTCCCTCT 58.982 50.000 13.52 0.00 44.84 3.69
2005 5188 3.015327 TCGAGTAAGCAAGTACTCCCTC 58.985 50.000 13.52 0.00 44.84 4.30
2006 5189 3.083122 TCGAGTAAGCAAGTACTCCCT 57.917 47.619 13.52 0.00 44.84 4.20
2007 5190 4.361420 GAATCGAGTAAGCAAGTACTCCC 58.639 47.826 13.52 0.00 44.84 4.30
2008 5191 4.098196 AGGAATCGAGTAAGCAAGTACTCC 59.902 45.833 13.52 0.00 44.84 3.85
2009 5192 5.251601 AGGAATCGAGTAAGCAAGTACTC 57.748 43.478 0.00 10.60 44.41 2.59
2010 5193 5.419471 AGAAGGAATCGAGTAAGCAAGTACT 59.581 40.000 0.00 0.00 37.02 2.73
2011 5194 5.517054 CAGAAGGAATCGAGTAAGCAAGTAC 59.483 44.000 0.00 0.00 0.00 2.73
2022 5205 2.094286 ACTCACAGCAGAAGGAATCGAG 60.094 50.000 0.00 0.00 0.00 4.04
2035 5218 6.729187 ACTTTGAAGTTTAATCACTCACAGC 58.271 36.000 0.00 0.00 35.21 4.40
2078 5261 1.067846 CAGATGCATGCTGCTGTTGTT 60.068 47.619 23.55 0.00 45.31 2.83
2083 5266 1.002359 GATCACAGATGCATGCTGCTG 60.002 52.381 27.47 27.47 45.31 4.41
2105 5288 1.285023 GCTTCCACAGCTGCACTTG 59.715 57.895 15.27 4.12 46.27 3.16
2131 5314 2.768253 TGTTGTGGATCGATGCTCTT 57.232 45.000 18.23 0.00 0.00 2.85
2175 5358 2.456577 ACATTGTTGCAGGGGTAATCC 58.543 47.619 0.00 0.00 0.00 3.01
2176 5359 4.535526 AAACATTGTTGCAGGGGTAATC 57.464 40.909 2.13 0.00 0.00 1.75
2177 5360 6.405538 CAATAAACATTGTTGCAGGGGTAAT 58.594 36.000 2.13 0.00 0.00 1.89
2178 5361 5.279708 CCAATAAACATTGTTGCAGGGGTAA 60.280 40.000 2.13 0.00 31.31 2.85
2179 5362 4.221703 CCAATAAACATTGTTGCAGGGGTA 59.778 41.667 2.13 0.00 31.31 3.69
2180 5363 3.007831 CCAATAAACATTGTTGCAGGGGT 59.992 43.478 2.13 0.00 31.31 4.95
2181 5364 3.260380 TCCAATAAACATTGTTGCAGGGG 59.740 43.478 2.13 2.51 31.31 4.79
2182 5365 4.497300 CTCCAATAAACATTGTTGCAGGG 58.503 43.478 2.13 3.85 31.31 4.45
2183 5366 4.497300 CCTCCAATAAACATTGTTGCAGG 58.503 43.478 2.13 3.87 34.09 4.85
2184 5367 3.928375 GCCTCCAATAAACATTGTTGCAG 59.072 43.478 2.13 0.00 31.31 4.41
2185 5368 3.613671 CGCCTCCAATAAACATTGTTGCA 60.614 43.478 2.13 0.00 31.31 4.08
2186 5369 2.923020 CGCCTCCAATAAACATTGTTGC 59.077 45.455 2.13 0.00 31.31 4.17
2219 5402 4.502171 TTGTCACAAGTACATGCATTGG 57.498 40.909 0.00 0.00 0.00 3.16
2228 5411 2.993899 CGACCCTGATTGTCACAAGTAC 59.006 50.000 0.00 0.00 32.91 2.73
2232 5415 1.604438 CGACGACCCTGATTGTCACAA 60.604 52.381 0.00 0.00 33.16 3.33
2234 5417 0.736325 CCGACGACCCTGATTGTCAC 60.736 60.000 0.00 0.00 33.16 3.67
2242 5425 0.246635 AGTTTGATCCGACGACCCTG 59.753 55.000 0.00 0.00 0.00 4.45
2249 5432 2.939103 CCCATCTTGAGTTTGATCCGAC 59.061 50.000 0.00 0.00 0.00 4.79
2250 5433 2.571653 ACCCATCTTGAGTTTGATCCGA 59.428 45.455 0.00 0.00 0.00 4.55
2257 5440 6.650120 ACATATCGTTACCCATCTTGAGTTT 58.350 36.000 0.00 0.00 0.00 2.66
2269 5452 6.124759 CCGATTCGAAAAACATATCGTTACC 58.875 40.000 7.83 0.00 36.59 2.85
2270 5453 6.699063 ACCGATTCGAAAAACATATCGTTAC 58.301 36.000 7.83 0.00 36.59 2.50
2293 5476 0.806492 GGATTCTCTTCCGCGGTGAC 60.806 60.000 27.15 11.97 0.00 3.67
2389 5572 2.616634 TAGAGTAGCCATCGACTCGT 57.383 50.000 0.00 0.00 45.75 4.18
2413 5596 4.272504 GGTTTGTCTTGTTCAAGATGTCGA 59.727 41.667 16.55 3.73 0.00 4.20
2419 5602 7.665145 TCATGATATGGTTTGTCTTGTTCAAGA 59.335 33.333 10.67 10.67 0.00 3.02
2449 5632 7.342581 TGCAACCCTAATCAACATCATTAGTA 58.657 34.615 0.00 0.00 33.56 1.82
2480 5663 3.074412 GTTCCATGACATCGACCAACTT 58.926 45.455 0.00 0.00 0.00 2.66
2504 5687 5.163513 GTTTGTTATTCCTGGAATGCACAG 58.836 41.667 28.00 0.00 33.95 3.66
2536 5719 1.701545 TTTGATCGTCGCAATCCCGC 61.702 55.000 0.00 0.00 0.00 6.13
2646 5829 2.833582 GGTCCGGGATCAGCTCGA 60.834 66.667 0.00 0.00 45.56 4.04
2647 5830 4.271816 CGGTCCGGGATCAGCTCG 62.272 72.222 8.26 0.00 41.20 5.03
2662 5845 4.465512 GCTGCCACGTCAATGCGG 62.466 66.667 0.00 0.00 35.98 5.69
2664 5847 2.177531 CTGCTGCCACGTCAATGC 59.822 61.111 0.00 0.00 0.00 3.56
2668 5851 1.153269 TTTGACTGCTGCCACGTCA 60.153 52.632 10.97 10.97 36.02 4.35
2682 5865 6.790232 AAATTGTTTCCACCTCTTCTTTGA 57.210 33.333 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.