Multiple sequence alignment - TraesCS7D01G156300

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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 TraesCS7D01G156300 chr7D 100.000 2532 0 0 1 2532 104568146 104565615 0.000000e+00 4676
1 TraesCS7D01G156300 chr7A 91.031 1795 98 20 7 1776 108810303 108808547 0.000000e+00 2364
2 TraesCS7D01G156300 chr7A 86.667 855 86 15 985 1820 418348125 418348970 0.000000e+00 922
3 TraesCS7D01G156300 chr7A 86.242 487 35 10 2068 2532 108808209 108807733 1.350000e-137 499
4 TraesCS7D01G156300 chr7B 88.159 1841 147 38 3 1807 62688889 62687084 0.000000e+00 2126
5 TraesCS7D01G156300 chr7B 92.642 299 10 2 2235 2532 62686653 62686366 1.080000e-113 420
6 TraesCS7D01G156300 chr3B 86.839 889 82 17 980 1849 632817296 632818168 0.000000e+00 961
7 TraesCS7D01G156300 chr5B 85.407 884 79 18 985 1849 453116865 453116013 0.000000e+00 872
8 TraesCS7D01G156300 chr5B 87.333 450 31 13 1283 1728 546011949 546012376 2.260000e-135 492
9 TraesCS7D01G156300 chr3A 86.430 818 79 16 1051 1849 56494202 56495006 0.000000e+00 867
10 TraesCS7D01G156300 chr3A 85.978 271 21 9 985 1243 71904660 71904925 8.920000e-70 274
11 TraesCS7D01G156300 chr1D 90.541 518 40 4 1121 1633 10037466 10037979 0.000000e+00 676
12 TraesCS7D01G156300 chr1D 90.347 518 41 4 1121 1633 9923760 9923247 0.000000e+00 671
13 TraesCS7D01G156300 chrUn 82.294 401 51 13 1001 1398 74596104 74596487 1.880000e-86 329
14 TraesCS7D01G156300 chr5A 85.556 270 24 7 985 1243 43682909 43682644 4.150000e-68 268
15 TraesCS7D01G156300 chr5A 85.556 270 24 7 985 1243 43768965 43768700 4.150000e-68 268
16 TraesCS7D01G156300 chr4A 85.185 270 25 7 985 1243 590625478 590625743 1.930000e-66 263
17 TraesCS7D01G156300 chr2A 85.185 270 25 7 985 1243 779538102 779537837 1.930000e-66 263
18 TraesCS7D01G156300 chr2A 85.992 257 21 7 998 1243 779441332 779441080 6.950000e-66 261
19 TraesCS7D01G156300 chr2A 83.026 271 29 9 985 1243 35027171 35027436 1.960000e-56 230


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 TraesCS7D01G156300 chr7D 104565615 104568146 2531 True 4676.0 4676 100.0000 1 2532 1 chr7D.!!$R1 2531
1 TraesCS7D01G156300 chr7A 108807733 108810303 2570 True 1431.5 2364 88.6365 7 2532 2 chr7A.!!$R1 2525
2 TraesCS7D01G156300 chr7A 418348125 418348970 845 False 922.0 922 86.6670 985 1820 1 chr7A.!!$F1 835
3 TraesCS7D01G156300 chr7B 62686366 62688889 2523 True 1273.0 2126 90.4005 3 2532 2 chr7B.!!$R1 2529
4 TraesCS7D01G156300 chr3B 632817296 632818168 872 False 961.0 961 86.8390 980 1849 1 chr3B.!!$F1 869
5 TraesCS7D01G156300 chr5B 453116013 453116865 852 True 872.0 872 85.4070 985 1849 1 chr5B.!!$R1 864
6 TraesCS7D01G156300 chr3A 56494202 56495006 804 False 867.0 867 86.4300 1051 1849 1 chr3A.!!$F1 798
7 TraesCS7D01G156300 chr1D 10037466 10037979 513 False 676.0 676 90.5410 1121 1633 1 chr1D.!!$F1 512
8 TraesCS7D01G156300 chr1D 9923247 9923760 513 True 671.0 671 90.3470 1121 1633 1 chr1D.!!$R1 512

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
378 381 0.366871 CAAATTCGCGACCGACAGAG 59.633 55.0 9.15 0.0 44.3 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2073 2276 0.86973 CCAGCTTGCCAACAATTTGC 59.13 50.0 0.0 0.0 34.61 3.68 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
56 57 6.718454 AGATGATGAACAGAACTTTCTTCG 57.282 37.500 0.00 0.00 34.74 3.79
67 68 4.335315 AGAACTTTCTTCGTGCATTTCACA 59.665 37.500 0.00 0.00 38.89 3.58
75 76 0.664166 GTGCATTTCACACGGCCTTG 60.664 55.000 7.87 7.87 44.98 3.61
77 78 0.387239 GCATTTCACACGGCCTTGTC 60.387 55.000 12.77 0.00 0.00 3.18
147 149 7.669089 TGGATGGTGACTAGAATGTATACAA 57.331 36.000 10.14 0.00 0.00 2.41
148 150 7.726216 TGGATGGTGACTAGAATGTATACAAG 58.274 38.462 10.14 5.21 0.00 3.16
236 238 1.379527 CGGCCATAAGAAGGGTGAAC 58.620 55.000 2.24 0.00 0.00 3.18
283 286 2.553172 AGCTATTCGAACCCTAGTAGCG 59.447 50.000 16.42 0.00 39.47 4.26
344 347 3.751479 ACCAAAATTGCAGGTTTCCTC 57.249 42.857 0.39 0.00 29.58 3.71
346 349 2.061028 CAAAATTGCAGGTTTCCTCGC 58.939 47.619 0.39 0.00 0.00 5.03
378 381 0.366871 CAAATTCGCGACCGACAGAG 59.633 55.000 9.15 0.00 44.30 3.35
451 454 5.254115 AGGTGAAATTAGGGCTTACAGTTC 58.746 41.667 0.00 0.00 0.00 3.01
534 538 3.878519 GAGGAGCGGACCTCGTCG 61.879 72.222 10.74 0.00 45.30 5.12
754 771 4.974721 AACAAGCCCACCGCCCAG 62.975 66.667 0.00 0.00 38.78 4.45
1011 1032 2.757099 GCAGCCATGGTGAAGGGG 60.757 66.667 14.67 0.00 32.22 4.79
1098 1143 2.279784 CCTTCTCGCCGGATCTGC 60.280 66.667 5.05 0.00 0.00 4.26
1111 1157 3.344904 GGATCTGCCGTTCATTTCATG 57.655 47.619 0.00 0.00 0.00 3.07
1112 1158 2.033801 GGATCTGCCGTTCATTTCATGG 59.966 50.000 0.00 0.00 0.00 3.66
1113 1159 0.810648 TCTGCCGTTCATTTCATGGC 59.189 50.000 0.00 0.00 45.42 4.40
1116 1162 1.226660 CCGTTCATTTCATGGCGGC 60.227 57.895 0.00 0.00 40.24 6.53
1423 1469 2.711542 CCCGCCTCTAGTTTTTGATGT 58.288 47.619 0.00 0.00 0.00 3.06
1441 1491 2.737376 GCTGCTTGCTTGCTTGCC 60.737 61.111 0.00 0.00 38.95 4.52
1475 1525 0.528249 AGGCTGTTTGTTGCTTTGCG 60.528 50.000 0.00 0.00 0.00 4.85
1477 1527 0.998669 GCTGTTTGTTGCTTTGCGTT 59.001 45.000 0.00 0.00 0.00 4.84
1478 1528 1.393196 GCTGTTTGTTGCTTTGCGTTT 59.607 42.857 0.00 0.00 0.00 3.60
1545 1595 2.810852 GCATCTAAGGTTAGCATCTGCC 59.189 50.000 0.00 0.00 43.38 4.85
1577 1630 5.049828 GCTGATGTTTGTTTAAGGCTGTTT 58.950 37.500 0.00 0.00 0.00 2.83
1598 1652 4.970662 TCTTTGCTCTGCATGATTTACC 57.029 40.909 0.00 0.00 38.76 2.85
1602 1656 3.808728 TGCTCTGCATGATTTACCCTAC 58.191 45.455 0.00 0.00 31.71 3.18
1612 1666 4.584874 TGATTTACCCTACCATGTGTGTG 58.415 43.478 0.00 0.00 0.00 3.82
1628 1682 3.558418 GTGTGTGACATTTTGTCCTACGT 59.442 43.478 5.27 0.00 46.40 3.57
1658 1712 8.372877 AGAATGACTAGGATGGATGTTATAGG 57.627 38.462 0.00 0.00 0.00 2.57
1695 1767 6.881065 AGTCGCAATATATAACATGCCTGAAT 59.119 34.615 10.95 3.40 35.41 2.57
1750 1829 2.969628 TGATGGTTTGGTTTGGGTCAT 58.030 42.857 0.00 0.00 0.00 3.06
1752 1831 3.713764 TGATGGTTTGGTTTGGGTCATTT 59.286 39.130 0.00 0.00 0.00 2.32
1753 1832 4.901849 TGATGGTTTGGTTTGGGTCATTTA 59.098 37.500 0.00 0.00 0.00 1.40
1755 1834 4.290942 TGGTTTGGTTTGGGTCATTTAGT 58.709 39.130 0.00 0.00 0.00 2.24
1756 1835 4.100189 TGGTTTGGTTTGGGTCATTTAGTG 59.900 41.667 0.00 0.00 0.00 2.74
1757 1836 4.100344 GGTTTGGTTTGGGTCATTTAGTGT 59.900 41.667 0.00 0.00 0.00 3.55
1758 1837 5.395879 GGTTTGGTTTGGGTCATTTAGTGTT 60.396 40.000 0.00 0.00 0.00 3.32
1759 1838 4.927978 TGGTTTGGGTCATTTAGTGTTG 57.072 40.909 0.00 0.00 0.00 3.33
1760 1839 3.068873 TGGTTTGGGTCATTTAGTGTTGC 59.931 43.478 0.00 0.00 0.00 4.17
1781 1860 4.202295 TGCTGATGTAGGATTCTGTGATCC 60.202 45.833 0.00 5.16 44.91 3.36
1792 1873 4.524316 TTCTGTGATCCTGCCATTTTTG 57.476 40.909 0.00 0.00 0.00 2.44
1809 1890 6.351202 CCATTTTTGTCCCTGAAAGATGCATA 60.351 38.462 0.00 0.00 34.07 3.14
1810 1891 5.643379 TTTTGTCCCTGAAAGATGCATAC 57.357 39.130 0.00 0.00 34.07 2.39
1811 1892 4.574674 TTGTCCCTGAAAGATGCATACT 57.425 40.909 0.00 0.00 34.07 2.12
1812 1893 4.142609 TGTCCCTGAAAGATGCATACTC 57.857 45.455 0.00 0.00 34.07 2.59
1813 1894 3.126831 GTCCCTGAAAGATGCATACTCG 58.873 50.000 0.00 0.00 34.07 4.18
1819 1900 3.384789 TGAAAGATGCATACTCGGCTAGT 59.615 43.478 0.00 0.00 42.62 2.57
1832 1913 5.533482 ACTCGGCTAGTCAATATTGTCATC 58.467 41.667 14.97 5.28 30.33 2.92
1851 1932 9.623000 TTGTCATCATGAGTTATCAATCTGAAT 57.377 29.630 0.09 0.00 39.39 2.57
1857 1938 8.886719 TCATGAGTTATCAATCTGAATTGTGTC 58.113 33.333 0.00 0.00 42.46 3.67
1858 1939 7.615582 TGAGTTATCAATCTGAATTGTGTCC 57.384 36.000 0.00 0.00 42.46 4.02
1859 1940 7.167535 TGAGTTATCAATCTGAATTGTGTCCA 58.832 34.615 0.00 0.00 42.46 4.02
1874 1955 2.616842 GTGTCCACAGTTTGATCCGTTT 59.383 45.455 0.00 0.00 0.00 3.60
1880 1961 5.533154 TCCACAGTTTGATCCGTTTACATTT 59.467 36.000 0.00 0.00 0.00 2.32
1881 1962 6.711194 TCCACAGTTTGATCCGTTTACATTTA 59.289 34.615 0.00 0.00 0.00 1.40
1882 1963 7.021196 CCACAGTTTGATCCGTTTACATTTAG 58.979 38.462 0.00 0.00 0.00 1.85
1883 1964 7.308348 CCACAGTTTGATCCGTTTACATTTAGT 60.308 37.037 0.00 0.00 0.00 2.24
1886 1967 9.916397 CAGTTTGATCCGTTTACATTTAGTATC 57.084 33.333 0.00 0.00 31.53 2.24
1915 2116 2.285827 TTTTGGTGCCGTTTGTCAAG 57.714 45.000 0.00 0.00 0.00 3.02
1916 2117 1.178276 TTTGGTGCCGTTTGTCAAGT 58.822 45.000 0.00 0.00 0.00 3.16
1919 2120 2.577700 TGGTGCCGTTTGTCAAGTTAT 58.422 42.857 0.00 0.00 0.00 1.89
1921 2122 4.328536 TGGTGCCGTTTGTCAAGTTATAT 58.671 39.130 0.00 0.00 0.00 0.86
1922 2123 4.762765 TGGTGCCGTTTGTCAAGTTATATT 59.237 37.500 0.00 0.00 0.00 1.28
1925 2126 4.216472 TGCCGTTTGTCAAGTTATATTGCA 59.784 37.500 0.00 0.00 0.00 4.08
1930 2131 6.634837 CGTTTGTCAAGTTATATTGCACACAA 59.365 34.615 0.00 0.00 40.87 3.33
1931 2132 7.357206 CGTTTGTCAAGTTATATTGCACACAAC 60.357 37.037 0.00 0.00 38.99 3.32
1932 2133 6.875948 TGTCAAGTTATATTGCACACAACT 57.124 33.333 0.00 0.00 38.99 3.16
1933 2134 7.270757 TGTCAAGTTATATTGCACACAACTT 57.729 32.000 8.39 8.39 38.99 2.66
1934 2135 7.711846 TGTCAAGTTATATTGCACACAACTTT 58.288 30.769 10.57 0.00 38.99 2.66
1935 2136 8.841300 TGTCAAGTTATATTGCACACAACTTTA 58.159 29.630 10.57 3.43 38.99 1.85
1936 2137 9.840427 GTCAAGTTATATTGCACACAACTTTAT 57.160 29.630 10.57 0.00 38.99 1.40
2012 2214 8.871686 ATCTGATTTCACTTTGGTGTTTTTAC 57.128 30.769 0.00 0.00 43.41 2.01
2032 2235 3.467803 ACTTGTACCTCAAACTGCTGAC 58.532 45.455 0.00 0.00 35.48 3.51
2038 2241 6.999950 TGTACCTCAAACTGCTGACTATTTA 58.000 36.000 0.00 0.00 0.00 1.40
2045 2248 9.534565 CTCAAACTGCTGACTATTTAGCTATTA 57.465 33.333 0.00 0.00 40.52 0.98
2085 2288 6.092533 ACAAATAGCTATTGCAAATTGTTGGC 59.907 34.615 19.53 0.00 42.74 4.52
2090 2293 2.328819 TTGCAAATTGTTGGCAAGCT 57.671 40.000 0.00 0.00 38.10 3.74
2099 2302 3.433306 TGTTGGCAAGCTGGTATTAGT 57.567 42.857 0.00 0.00 0.00 2.24
2102 2305 4.022416 TGTTGGCAAGCTGGTATTAGTTTG 60.022 41.667 0.00 0.00 40.51 2.93
2126 2329 7.517320 TGGATGTTATGGTAGAGTTGCATAAT 58.483 34.615 0.00 0.00 0.00 1.28
2127 2330 7.998383 TGGATGTTATGGTAGAGTTGCATAATT 59.002 33.333 0.00 0.00 0.00 1.40
2128 2331 9.502091 GGATGTTATGGTAGAGTTGCATAATTA 57.498 33.333 0.00 0.00 0.00 1.40
2160 2363 8.950208 AAGATTAGAAGTCACCTAACTAATGC 57.050 34.615 0.00 0.00 34.02 3.56
2173 2376 7.281774 CACCTAACTAATGCTTTGACATCAGAT 59.718 37.037 0.00 0.00 0.00 2.90
2177 2380 8.565896 AACTAATGCTTTGACATCAGATGTTA 57.434 30.769 17.43 10.72 45.03 2.41
2178 2381 8.743085 ACTAATGCTTTGACATCAGATGTTAT 57.257 30.769 17.43 0.26 45.03 1.89
2179 2382 8.618677 ACTAATGCTTTGACATCAGATGTTATG 58.381 33.333 17.43 10.15 45.03 1.90
2191 2414 3.319972 CAGATGTTATGGGGCATTCCTTG 59.680 47.826 0.00 0.00 35.33 3.61
2221 2445 5.046376 AGCAGCATAAAGTGGCCTTATTTTT 60.046 36.000 3.32 0.12 0.00 1.94
2222 2446 5.063817 GCAGCATAAAGTGGCCTTATTTTTG 59.936 40.000 3.32 8.82 0.00 2.44
2225 2449 6.013812 AGCATAAAGTGGCCTTATTTTTGGAA 60.014 34.615 3.32 0.00 0.00 3.53
2247 2472 6.150140 GGAAATGAGATACTGTCTTTGTTGCT 59.850 38.462 0.00 0.00 37.29 3.91
2258 2483 7.491682 ACTGTCTTTGTTGCTTCAAATTATGT 58.508 30.769 7.17 3.77 36.83 2.29
2278 2503 9.882996 ATTATGTACATGATTTGCTATTTGTCG 57.117 29.630 18.81 0.00 0.00 4.35
2291 2516 4.025647 GCTATTTGTCGTTCTAGCCATGTC 60.026 45.833 0.00 0.00 32.32 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 6.347969 CCTTGATAATCACATGCTTATGTCGG 60.348 42.308 0.00 0.00 31.37 4.79
5 6 7.734924 TCCTTGATAATCACATGCTTATGTC 57.265 36.000 0.00 0.00 31.37 3.06
67 68 5.353394 TGATTTATTCTAGACAAGGCCGT 57.647 39.130 0.00 0.00 0.00 5.68
147 149 2.867109 AGGCATGTCTACTTTGTGCT 57.133 45.000 0.00 0.00 36.15 4.40
148 150 3.861840 TCTAGGCATGTCTACTTTGTGC 58.138 45.455 2.01 0.00 35.17 4.57
236 238 6.869913 TGGTAACTAGTCTATTTTGTTCGTGG 59.130 38.462 0.00 0.00 37.61 4.94
283 286 2.735134 CTGTAAATCCGGGCGCTATTAC 59.265 50.000 7.64 8.64 0.00 1.89
344 347 3.722082 CGAATTTGGAAGTTTCTCTCGCG 60.722 47.826 0.00 0.00 0.00 5.87
346 349 3.722082 CGCGAATTTGGAAGTTTCTCTCG 60.722 47.826 0.00 0.00 0.00 4.04
451 454 4.436998 GTCGCCTGACCGGGTCTG 62.437 72.222 26.41 24.58 39.30 3.51
504 508 3.612247 CTCCTCCCGTGCCCAGTTG 62.612 68.421 0.00 0.00 0.00 3.16
534 538 3.160748 GAGCTCTCCCTCCCAGGC 61.161 72.222 6.43 0.00 32.73 4.85
757 776 2.585247 GTCACGGCGGTAGATGGC 60.585 66.667 13.24 0.00 0.00 4.40
818 838 2.822399 GGGATGGACGGCTCGATT 59.178 61.111 1.50 0.00 0.00 3.34
852 872 4.201679 CGGTATCTGGACGGCGCA 62.202 66.667 10.83 0.00 0.00 6.09
870 890 1.676014 GGCTTATATGTAGGCAGCGGG 60.676 57.143 5.95 0.00 38.03 6.13
1059 1080 2.035442 GGCCGCTCACCTCTTGAAC 61.035 63.158 0.00 0.00 32.21 3.18
1144 1190 0.967380 CCTGCAGAAATTTCCCCGCT 60.967 55.000 17.39 0.00 0.00 5.52
1409 1455 4.557296 GCAAGCAGCACATCAAAAACTAGA 60.557 41.667 0.00 0.00 44.79 2.43
1410 1456 3.671928 GCAAGCAGCACATCAAAAACTAG 59.328 43.478 0.00 0.00 44.79 2.57
1475 1525 1.227234 GCCCCTGCACACAACAAAC 60.227 57.895 0.00 0.00 37.47 2.93
1477 1527 3.215568 CGCCCCTGCACACAACAA 61.216 61.111 0.00 0.00 37.32 2.83
1545 1595 1.660607 ACAAACATCAGCGATAGTGCG 59.339 47.619 0.00 0.00 40.67 5.34
1577 1630 3.696051 GGGTAAATCATGCAGAGCAAAGA 59.304 43.478 0.00 0.00 43.62 2.52
1598 1652 4.278170 ACAAAATGTCACACACATGGTAGG 59.722 41.667 0.00 0.00 45.77 3.18
1612 1666 5.227908 TCTCAAGACGTAGGACAAAATGTC 58.772 41.667 1.88 1.88 46.23 3.06
1628 1682 5.901853 ACATCCATCCTAGTCATTCTCAAGA 59.098 40.000 0.00 0.00 0.00 3.02
1658 1712 9.850628 TTATATATTGCGACTACACTTGGTATC 57.149 33.333 0.00 0.00 0.00 2.24
1661 1715 7.494211 TGTTATATATTGCGACTACACTTGGT 58.506 34.615 0.00 0.00 0.00 3.67
1695 1767 5.356751 GGACACATTGCACAAGTCCATATAA 59.643 40.000 17.32 0.00 46.15 0.98
1750 1829 6.595326 CAGAATCCTACATCAGCAACACTAAA 59.405 38.462 0.00 0.00 0.00 1.85
1752 1831 5.187772 ACAGAATCCTACATCAGCAACACTA 59.812 40.000 0.00 0.00 0.00 2.74
1753 1832 4.019860 ACAGAATCCTACATCAGCAACACT 60.020 41.667 0.00 0.00 0.00 3.55
1755 1834 4.020307 TCACAGAATCCTACATCAGCAACA 60.020 41.667 0.00 0.00 0.00 3.33
1756 1835 4.507710 TCACAGAATCCTACATCAGCAAC 58.492 43.478 0.00 0.00 0.00 4.17
1757 1836 4.824479 TCACAGAATCCTACATCAGCAA 57.176 40.909 0.00 0.00 0.00 3.91
1758 1837 4.202295 GGATCACAGAATCCTACATCAGCA 60.202 45.833 0.00 0.00 41.78 4.41
1759 1838 4.314121 GGATCACAGAATCCTACATCAGC 58.686 47.826 0.00 0.00 41.78 4.26
1781 1860 3.321682 TCTTTCAGGGACAAAAATGGCAG 59.678 43.478 0.00 0.00 0.00 4.85
1792 1873 3.126831 CGAGTATGCATCTTTCAGGGAC 58.873 50.000 0.19 0.00 0.00 4.46
1809 1890 5.069119 TGATGACAATATTGACTAGCCGAGT 59.931 40.000 22.16 0.00 42.90 4.18
1810 1891 5.532557 TGATGACAATATTGACTAGCCGAG 58.467 41.667 22.16 0.00 0.00 4.63
1811 1892 5.529581 TGATGACAATATTGACTAGCCGA 57.470 39.130 22.16 0.00 0.00 5.54
1812 1893 5.928264 TCATGATGACAATATTGACTAGCCG 59.072 40.000 22.16 6.66 0.00 5.52
1813 1894 6.933521 ACTCATGATGACAATATTGACTAGCC 59.066 38.462 22.16 7.28 0.00 3.93
1832 1913 8.127327 GGACACAATTCAGATTGATAACTCATG 58.873 37.037 6.17 0.00 44.37 3.07
1849 1930 3.253188 CGGATCAAACTGTGGACACAATT 59.747 43.478 6.60 0.00 41.33 2.32
1851 1932 2.217750 CGGATCAAACTGTGGACACAA 58.782 47.619 6.60 0.00 41.33 3.33
1857 1938 5.371115 AATGTAAACGGATCAAACTGTGG 57.629 39.130 0.00 0.00 0.00 4.17
1858 1939 7.581476 ACTAAATGTAAACGGATCAAACTGTG 58.419 34.615 0.00 0.00 0.00 3.66
1859 1940 7.739498 ACTAAATGTAAACGGATCAAACTGT 57.261 32.000 0.00 0.00 0.00 3.55
1880 1961 6.094881 GGCACCAAAATAGCAACAAGATACTA 59.905 38.462 0.00 0.00 0.00 1.82
1881 1962 5.105756 GGCACCAAAATAGCAACAAGATACT 60.106 40.000 0.00 0.00 0.00 2.12
1882 1963 5.102313 GGCACCAAAATAGCAACAAGATAC 58.898 41.667 0.00 0.00 0.00 2.24
1883 1964 4.142491 CGGCACCAAAATAGCAACAAGATA 60.142 41.667 0.00 0.00 0.00 1.98
1886 1967 2.288152 ACGGCACCAAAATAGCAACAAG 60.288 45.455 0.00 0.00 0.00 3.16
1896 1987 1.546476 ACTTGACAAACGGCACCAAAA 59.454 42.857 0.00 0.00 0.00 2.44
1900 1991 4.957759 ATATAACTTGACAAACGGCACC 57.042 40.909 0.00 0.00 0.00 5.01
1930 2131 7.033185 GTGTTTCCAACTTCACACAATAAAGT 58.967 34.615 0.00 0.00 39.51 2.66
1931 2132 7.032580 TGTGTTTCCAACTTCACACAATAAAG 58.967 34.615 1.56 0.00 45.01 1.85
1932 2133 6.925211 TGTGTTTCCAACTTCACACAATAAA 58.075 32.000 1.56 0.00 45.01 1.40
1933 2134 6.516739 TGTGTTTCCAACTTCACACAATAA 57.483 33.333 1.56 0.00 45.01 1.40
1941 2142 8.740123 TTAATCTAAGTGTGTTTCCAACTTCA 57.260 30.769 0.00 0.00 35.77 3.02
2001 2203 6.660094 AGTTTGAGGTACAAGTAAAAACACCA 59.340 34.615 0.00 0.00 39.77 4.17
2002 2204 6.970613 CAGTTTGAGGTACAAGTAAAAACACC 59.029 38.462 0.00 0.00 39.77 4.16
2008 2210 5.526111 GTCAGCAGTTTGAGGTACAAGTAAA 59.474 40.000 0.00 0.00 39.77 2.01
2012 2214 3.733337 AGTCAGCAGTTTGAGGTACAAG 58.267 45.455 0.00 0.00 39.77 3.16
2057 2260 9.881529 CAACAATTTGCAATAGCTATTTGTTTT 57.118 25.926 21.21 9.55 46.94 2.43
2058 2261 8.505625 CCAACAATTTGCAATAGCTATTTGTTT 58.494 29.630 21.21 9.02 46.94 2.83
2060 2263 6.092533 GCCAACAATTTGCAATAGCTATTTGT 59.907 34.615 16.46 13.68 45.17 2.83
2061 2264 6.092396 TGCCAACAATTTGCAATAGCTATTTG 59.908 34.615 16.46 13.07 42.74 2.32
2062 2265 6.171921 TGCCAACAATTTGCAATAGCTATTT 58.828 32.000 16.46 0.00 42.74 1.40
2063 2266 5.732633 TGCCAACAATTTGCAATAGCTATT 58.267 33.333 13.37 13.37 42.74 1.73
2064 2267 5.341872 TGCCAACAATTTGCAATAGCTAT 57.658 34.783 0.00 0.00 42.74 2.97
2065 2268 4.797800 TGCCAACAATTTGCAATAGCTA 57.202 36.364 0.00 0.00 42.74 3.32
2066 2269 3.681593 TGCCAACAATTTGCAATAGCT 57.318 38.095 0.00 0.00 42.74 3.32
2067 2270 3.425227 GCTTGCCAACAATTTGCAATAGC 60.425 43.478 0.00 0.00 36.80 2.97
2068 2271 3.998341 AGCTTGCCAACAATTTGCAATAG 59.002 39.130 0.00 0.00 34.61 1.73
2069 2272 3.747010 CAGCTTGCCAACAATTTGCAATA 59.253 39.130 0.00 0.00 34.61 1.90
2070 2273 2.550606 CAGCTTGCCAACAATTTGCAAT 59.449 40.909 0.00 0.00 34.61 3.56
2071 2274 1.941294 CAGCTTGCCAACAATTTGCAA 59.059 42.857 0.00 0.00 34.61 4.08
2072 2275 1.584175 CAGCTTGCCAACAATTTGCA 58.416 45.000 0.00 0.00 34.61 4.08
2073 2276 0.869730 CCAGCTTGCCAACAATTTGC 59.130 50.000 0.00 0.00 34.61 3.68
2074 2277 2.243602 ACCAGCTTGCCAACAATTTG 57.756 45.000 0.00 0.00 34.61 2.32
2075 2278 4.622260 AATACCAGCTTGCCAACAATTT 57.378 36.364 0.00 0.00 34.61 1.82
2076 2279 4.772100 ACTAATACCAGCTTGCCAACAATT 59.228 37.500 0.00 0.00 34.61 2.32
2077 2280 4.344104 ACTAATACCAGCTTGCCAACAAT 58.656 39.130 0.00 0.00 34.61 2.71
2078 2281 3.761897 ACTAATACCAGCTTGCCAACAA 58.238 40.909 0.00 0.00 0.00 2.83
2079 2282 3.433306 ACTAATACCAGCTTGCCAACA 57.567 42.857 0.00 0.00 0.00 3.33
2080 2283 4.485163 CAAACTAATACCAGCTTGCCAAC 58.515 43.478 0.00 0.00 0.00 3.77
2085 2288 6.515272 AACATCCAAACTAATACCAGCTTG 57.485 37.500 0.00 0.00 0.00 4.01
2090 2293 8.994500 TCTACCATAACATCCAAACTAATACCA 58.006 33.333 0.00 0.00 0.00 3.25
2099 2302 5.565509 TGCAACTCTACCATAACATCCAAA 58.434 37.500 0.00 0.00 0.00 3.28
2102 2305 7.986085 ATTATGCAACTCTACCATAACATCC 57.014 36.000 0.00 0.00 35.13 3.51
2141 2344 6.651225 GTCAAAGCATTAGTTAGGTGACTTCT 59.349 38.462 0.00 0.00 43.67 2.85
2154 2357 8.074370 CCATAACATCTGATGTCAAAGCATTAG 58.926 37.037 22.47 5.38 44.07 1.73
2160 2363 4.037208 GCCCCATAACATCTGATGTCAAAG 59.963 45.833 22.47 12.88 44.07 2.77
2173 2376 2.917713 ACAAGGAATGCCCCATAACA 57.082 45.000 0.00 0.00 34.66 2.41
2177 2380 3.055167 GCTAAAAACAAGGAATGCCCCAT 60.055 43.478 0.00 0.00 34.66 4.00
2178 2381 2.301583 GCTAAAAACAAGGAATGCCCCA 59.698 45.455 0.00 0.00 34.66 4.96
2179 2382 2.301583 TGCTAAAAACAAGGAATGCCCC 59.698 45.455 0.00 0.00 34.66 5.80
2191 2414 3.926527 GGCCACTTTATGCTGCTAAAAAC 59.073 43.478 0.00 0.00 0.00 2.43
2221 2445 6.072508 GCAACAAAGACAGTATCTCATTTCCA 60.073 38.462 0.00 0.00 36.27 3.53
2222 2446 6.150140 AGCAACAAAGACAGTATCTCATTTCC 59.850 38.462 0.00 0.00 36.27 3.13
2225 2449 6.712095 TGAAGCAACAAAGACAGTATCTCATT 59.288 34.615 0.00 0.00 36.27 2.57
2258 2483 7.609760 AGAACGACAAATAGCAAATCATGTA 57.390 32.000 0.00 0.00 0.00 2.29
2278 2503 3.319137 TGTGTCAGACATGGCTAGAAC 57.681 47.619 0.00 0.23 30.13 3.01
2291 2516 1.820519 CCAACCCAATGGATGTGTCAG 59.179 52.381 0.00 0.00 43.54 3.51
2327 2552 7.293402 TGCATTGAACAAAACAAAAAGAGAG 57.707 32.000 0.00 0.00 0.00 3.20
2360 2585 4.716784 ACAAGCATTACTGTCCCTAGATCA 59.283 41.667 0.00 0.00 0.00 2.92


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

AutoCloner maintained by Alex Coulton.