Multiple sequence alignment - TraesCS4B01G220000

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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 TraesCS4B01G220000 chr4B 100.000 2695 0 0 1 2695 462591162 462593856 0.000000e+00 4977.0
1 TraesCS4B01G220000 chr4B 76.868 562 87 30 1130 1652 462696856 462697413 7.350000e-71 278.0
2 TraesCS4B01G220000 chr4A 94.850 932 28 8 941 1852 88705202 88704271 0.000000e+00 1437.0
3 TraesCS4B01G220000 chr4A 91.841 527 32 4 391 910 88705812 88705290 0.000000e+00 725.0
4 TraesCS4B01G220000 chr4A 83.039 566 63 17 1925 2486 88704235 88703699 1.450000e-132 483.0
5 TraesCS4B01G220000 chr4A 77.661 573 87 29 1130 1666 88541338 88540771 7.250000e-81 311.0
6 TraesCS4B01G220000 chr4A 100.000 39 0 0 1999 2037 617439330 617439368 3.720000e-09 73.1
7 TraesCS4B01G220000 chr4D 92.005 888 51 13 38 910 375444206 375445088 0.000000e+00 1229.0
8 TraesCS4B01G220000 chr4D 94.026 703 38 3 1993 2695 375446360 375447058 0.000000e+00 1062.0
9 TraesCS4B01G220000 chr4D 96.123 619 14 3 937 1554 375445166 375445775 0.000000e+00 1002.0
10 TraesCS4B01G220000 chr4D 88.406 276 9 8 1592 1844 375445771 375446046 7.250000e-81 311.0
11 TraesCS4B01G220000 chr4D 77.020 557 89 27 1130 1652 375508845 375509396 1.580000e-72 283.0
12 TraesCS4B01G220000 chr7A 85.398 678 76 9 1999 2672 668991518 668992176 0.000000e+00 682.0
13 TraesCS4B01G220000 chr3A 80.029 696 129 8 1999 2692 119277644 119278331 8.610000e-140 507.0
14 TraesCS4B01G220000 chr1D 77.714 700 134 15 1999 2695 439885505 439886185 2.500000e-110 409.0
15 TraesCS4B01G220000 chr1D 96.429 56 1 1 2001 2055 394948019 394947964 1.030000e-14 91.6


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 TraesCS4B01G220000 chr4B 462591162 462593856 2694 False 4977.000000 4977 100.000 1 2695 1 chr4B.!!$F1 2694
1 TraesCS4B01G220000 chr4B 462696856 462697413 557 False 278.000000 278 76.868 1130 1652 1 chr4B.!!$F2 522
2 TraesCS4B01G220000 chr4A 88703699 88705812 2113 True 881.666667 1437 89.910 391 2486 3 chr4A.!!$R2 2095
3 TraesCS4B01G220000 chr4A 88540771 88541338 567 True 311.000000 311 77.661 1130 1666 1 chr4A.!!$R1 536
4 TraesCS4B01G220000 chr4D 375444206 375447058 2852 False 901.000000 1229 92.640 38 2695 4 chr4D.!!$F2 2657
5 TraesCS4B01G220000 chr4D 375508845 375509396 551 False 283.000000 283 77.020 1130 1652 1 chr4D.!!$F1 522
6 TraesCS4B01G220000 chr7A 668991518 668992176 658 False 682.000000 682 85.398 1999 2672 1 chr7A.!!$F1 673
7 TraesCS4B01G220000 chr3A 119277644 119278331 687 False 507.000000 507 80.029 1999 2692 1 chr3A.!!$F1 693
8 TraesCS4B01G220000 chr1D 439885505 439886185 680 False 409.000000 409 77.714 1999 2695 1 chr1D.!!$F1 696

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
36 37 0.039764 TCAGGTCTCCGATGTCTGGT 59.960 55.0 0.0 0.0 0.0 4.00 F
1023 1099 0.031010 ACCTCCACCTCCCCATAGTC 60.031 60.0 0.0 0.0 0.0 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1580 1691 0.390860 CCCAGACGAGGATGTCCATC 59.609 60.0 1.3 0.0 39.77 3.51 R
2604 2939 0.034896 GACGCACCTTTCTCCTCCAA 59.965 55.0 0.0 0.0 0.00 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
20 21 3.085443 CCTTAGCTATCACCGTGTCAG 57.915 52.381 0.00 0.00 0.00 3.51
21 22 2.223829 CCTTAGCTATCACCGTGTCAGG 60.224 54.545 0.00 0.00 37.30 3.86
23 24 0.818296 AGCTATCACCGTGTCAGGTC 59.182 55.000 0.00 0.00 43.89 3.85
24 25 0.818296 GCTATCACCGTGTCAGGTCT 59.182 55.000 0.00 0.00 43.89 3.85
25 26 1.202313 GCTATCACCGTGTCAGGTCTC 60.202 57.143 0.00 0.00 43.89 3.36
26 27 1.405821 CTATCACCGTGTCAGGTCTCC 59.594 57.143 0.00 0.00 43.89 3.71
27 28 1.595993 ATCACCGTGTCAGGTCTCCG 61.596 60.000 0.00 0.00 43.89 4.63
28 29 2.114625 ACCGTGTCAGGTCTCCGA 59.885 61.111 0.00 0.00 41.46 4.55
29 30 1.304217 ACCGTGTCAGGTCTCCGAT 60.304 57.895 0.00 0.00 41.46 4.18
30 31 1.139734 CCGTGTCAGGTCTCCGATG 59.860 63.158 0.00 0.00 0.00 3.84
31 32 1.595993 CCGTGTCAGGTCTCCGATGT 61.596 60.000 0.00 0.00 0.00 3.06
32 33 0.179161 CGTGTCAGGTCTCCGATGTC 60.179 60.000 0.00 0.00 0.00 3.06
33 34 1.178276 GTGTCAGGTCTCCGATGTCT 58.822 55.000 0.00 0.00 0.00 3.41
34 35 1.135257 GTGTCAGGTCTCCGATGTCTG 60.135 57.143 0.00 0.00 0.00 3.51
35 36 0.457851 GTCAGGTCTCCGATGTCTGG 59.542 60.000 0.00 0.00 0.00 3.86
36 37 0.039764 TCAGGTCTCCGATGTCTGGT 59.960 55.000 0.00 0.00 0.00 4.00
37 38 0.898320 CAGGTCTCCGATGTCTGGTT 59.102 55.000 0.00 0.00 0.00 3.67
38 39 0.898320 AGGTCTCCGATGTCTGGTTG 59.102 55.000 0.00 0.00 0.00 3.77
39 40 0.895530 GGTCTCCGATGTCTGGTTGA 59.104 55.000 0.00 0.00 0.00 3.18
40 41 1.134965 GGTCTCCGATGTCTGGTTGAG 60.135 57.143 0.00 0.00 0.00 3.02
41 42 1.546476 GTCTCCGATGTCTGGTTGAGT 59.454 52.381 0.00 0.00 0.00 3.41
42 43 2.753452 GTCTCCGATGTCTGGTTGAGTA 59.247 50.000 0.00 0.00 0.00 2.59
61 62 0.837272 ACCATGCGTAGTTAGCCCAT 59.163 50.000 0.00 0.00 0.00 4.00
62 63 1.229428 CCATGCGTAGTTAGCCCATG 58.771 55.000 0.00 0.00 34.55 3.66
69 70 2.565841 GTAGTTAGCCCATGCCTTCTG 58.434 52.381 0.00 0.00 38.69 3.02
133 136 3.007635 CGTTCCATGTTTCCCTTAGACC 58.992 50.000 0.00 0.00 0.00 3.85
153 156 1.066143 CAGTGAGCCCCAATACGAACT 60.066 52.381 0.00 0.00 0.00 3.01
166 169 6.204108 CCCAATACGAACTAAGTGTTTCTTGT 59.796 38.462 0.00 0.00 39.30 3.16
175 178 4.983671 AAGTGTTTCTTGTGTTTCTCCC 57.016 40.909 0.00 0.00 34.77 4.30
181 184 1.699634 TCTTGTGTTTCTCCCCTCTGG 59.300 52.381 0.00 0.00 0.00 3.86
182 185 0.110486 TTGTGTTTCTCCCCTCTGGC 59.890 55.000 0.00 0.00 0.00 4.85
188 191 0.343372 TTCTCCCCTCTGGCATAGGT 59.657 55.000 16.76 0.00 31.70 3.08
198 201 5.380043 CCTCTGGCATAGGTTTCATTGTAT 58.620 41.667 10.63 0.00 0.00 2.29
199 202 5.829924 CCTCTGGCATAGGTTTCATTGTATT 59.170 40.000 10.63 0.00 0.00 1.89
216 219 1.358830 ATTCCCTCCATCAGCCCAGG 61.359 60.000 0.00 0.00 0.00 4.45
218 221 2.367377 CCTCCATCAGCCCAGGGA 60.367 66.667 10.89 0.00 0.00 4.20
220 223 1.530771 CTCCATCAGCCCAGGGAAG 59.469 63.158 10.89 0.00 0.00 3.46
246 249 0.115349 ACCACACTCTAGCTCCACCT 59.885 55.000 0.00 0.00 0.00 4.00
251 254 4.246458 CACACTCTAGCTCCACCTTTAAC 58.754 47.826 0.00 0.00 0.00 2.01
255 258 4.398673 ACTCTAGCTCCACCTTTAACGTAG 59.601 45.833 0.00 0.00 0.00 3.51
264 267 2.160417 ACCTTTAACGTAGACGACCTCG 59.840 50.000 9.41 0.00 43.02 4.63
293 296 4.778415 CAGTCCACCCTCGCGTCG 62.778 72.222 5.77 0.00 0.00 5.12
382 385 1.808945 CATGCCTCAGAAGTTGGACAC 59.191 52.381 0.00 0.00 0.00 3.67
385 388 1.059913 CCTCAGAAGTTGGACACCCT 58.940 55.000 0.00 0.00 0.00 4.34
387 390 0.679505 TCAGAAGTTGGACACCCTCG 59.320 55.000 0.00 0.00 0.00 4.63
398 406 0.754217 ACACCCTCGGCGCTCTTATA 60.754 55.000 7.64 0.00 0.00 0.98
419 427 6.990908 ATATCATCCTCTGTGATCTCAACA 57.009 37.500 0.00 0.00 37.48 3.33
437 445 7.151976 TCTCAACATTATCTTTCGTTCTGACA 58.848 34.615 0.00 0.00 0.00 3.58
459 467 1.666872 GTCCCCGTCCGTCAAACTG 60.667 63.158 0.00 0.00 0.00 3.16
492 500 2.622436 GCAGGAGCTTACGAAGATTGT 58.378 47.619 0.00 0.00 37.91 2.71
530 538 8.671921 CAGTTAGAATTTGTTATGCTCTCATGT 58.328 33.333 0.00 0.00 34.22 3.21
572 584 4.519540 ATTTTTCACTTAATGCACCGCT 57.480 36.364 0.00 0.00 0.00 5.52
579 591 2.211619 TTAATGCACCGCTGCTTGGC 62.212 55.000 4.05 0.00 44.57 4.52
591 603 2.867429 CTGCTTGGCTAATGTTTTCCG 58.133 47.619 0.00 0.00 0.00 4.30
599 611 2.908626 GCTAATGTTTTCCGCAAAGTCG 59.091 45.455 0.00 0.00 0.00 4.18
684 700 1.000607 GTGTTGGAGAGAGCACGTACA 60.001 52.381 0.00 0.00 0.00 2.90
722 738 1.687612 CTGGAGCCCACAGGTCAAT 59.312 57.895 0.00 0.00 45.21 2.57
726 742 1.589716 GAGCCCACAGGTCAATGCAC 61.590 60.000 0.00 0.00 42.81 4.57
730 746 1.575922 CACAGGTCAATGCACACGG 59.424 57.895 0.00 0.00 0.00 4.94
748 764 1.363807 GCACAGGTTGCCAAAGACC 59.636 57.895 0.00 0.00 46.63 3.85
855 871 1.130373 ACGACGCGGTTATTTCTACGA 59.870 47.619 12.47 0.00 0.00 3.43
924 956 4.884744 ACAGAGCTCTATATATGCCCTACG 59.115 45.833 17.75 0.86 0.00 3.51
925 957 4.884744 CAGAGCTCTATATATGCCCTACGT 59.115 45.833 17.75 0.00 0.00 3.57
927 959 6.203915 CAGAGCTCTATATATGCCCTACGTAG 59.796 46.154 17.75 15.92 0.00 3.51
928 960 6.099990 AGAGCTCTATATATGCCCTACGTAGA 59.900 42.308 24.15 4.43 0.00 2.59
929 961 6.056884 AGCTCTATATATGCCCTACGTAGAC 58.943 44.000 24.15 15.28 0.00 2.59
931 963 6.543100 GCTCTATATATGCCCTACGTAGACTT 59.457 42.308 24.15 14.73 0.00 3.01
932 964 7.254863 GCTCTATATATGCCCTACGTAGACTTC 60.255 44.444 24.15 9.73 0.00 3.01
933 965 7.627311 TCTATATATGCCCTACGTAGACTTCA 58.373 38.462 24.15 14.58 0.00 3.02
934 966 4.850347 ATATGCCCTACGTAGACTTCAC 57.150 45.455 24.15 6.81 0.00 3.18
935 967 2.211250 TGCCCTACGTAGACTTCACT 57.789 50.000 24.15 0.00 0.00 3.41
1023 1099 0.031010 ACCTCCACCTCCCCATAGTC 60.031 60.000 0.00 0.00 0.00 2.59
1218 1297 1.153842 CACGCTGATCACCACGCTA 60.154 57.895 7.70 0.00 0.00 4.26
1685 1796 2.750637 GCACTCTGCTGCAGCCAT 60.751 61.111 34.64 15.25 40.96 4.40
1695 1806 0.742281 CTGCAGCCATCGCAACTAGT 60.742 55.000 0.00 0.00 39.30 2.57
1715 1826 1.961277 GTTGACTGGCGGGTGACTG 60.961 63.158 0.00 0.00 40.79 3.51
1733 1844 1.611977 CTGTATCGTCCAGCCGGATAA 59.388 52.381 5.05 0.00 45.33 1.75
1736 1847 0.389391 ATCGTCCAGCCGGATAAGTG 59.611 55.000 5.05 0.00 45.33 3.16
1804 1938 9.476202 CAGTGAATTAGTTATCGATGATTACCA 57.524 33.333 8.54 0.00 0.00 3.25
1828 1962 6.691754 TTTTCTTCAAGCTGTGTGACATAA 57.308 33.333 0.00 0.00 0.00 1.90
1854 2022 5.745294 GCTGATGTTAATGAATTGACGCAAT 59.255 36.000 0.09 0.09 35.39 3.56
1856 2024 6.264832 TGATGTTAATGAATTGACGCAATCC 58.735 36.000 5.70 0.00 32.43 3.01
1857 2025 5.895636 TGTTAATGAATTGACGCAATCCT 57.104 34.783 5.70 0.00 32.43 3.24
1859 2027 6.321717 TGTTAATGAATTGACGCAATCCTTC 58.678 36.000 5.70 2.78 32.43 3.46
1862 2030 2.162208 TGAATTGACGCAATCCTTCTGC 59.838 45.455 5.70 0.00 32.43 4.26
1865 2033 0.955428 TGACGCAATCCTTCTGCCAC 60.955 55.000 0.00 0.00 36.40 5.01
1866 2034 0.674895 GACGCAATCCTTCTGCCACT 60.675 55.000 0.00 0.00 36.40 4.00
1867 2035 0.613260 ACGCAATCCTTCTGCCACTA 59.387 50.000 0.00 0.00 36.40 2.74
1869 2037 1.869767 CGCAATCCTTCTGCCACTATC 59.130 52.381 0.00 0.00 36.40 2.08
1870 2038 2.484417 CGCAATCCTTCTGCCACTATCT 60.484 50.000 0.00 0.00 36.40 1.98
1872 2040 3.950395 GCAATCCTTCTGCCACTATCTTT 59.050 43.478 0.00 0.00 33.51 2.52
1873 2041 4.400567 GCAATCCTTCTGCCACTATCTTTT 59.599 41.667 0.00 0.00 33.51 2.27
1898 2066 9.679661 TTTTCCTGATATAAAATCTAGTGCACA 57.320 29.630 21.04 4.13 0.00 4.57
1899 2067 9.679661 TTTCCTGATATAAAATCTAGTGCACAA 57.320 29.630 21.04 4.16 0.00 3.33
1900 2068 8.662781 TCCTGATATAAAATCTAGTGCACAAC 57.337 34.615 21.04 0.00 0.00 3.32
1901 2069 7.715249 TCCTGATATAAAATCTAGTGCACAACC 59.285 37.037 21.04 0.00 0.00 3.77
1902 2070 7.307396 CCTGATATAAAATCTAGTGCACAACCG 60.307 40.741 21.04 3.98 0.00 4.44
1903 2071 7.045416 TGATATAAAATCTAGTGCACAACCGT 58.955 34.615 21.04 0.00 0.00 4.83
1904 2072 7.551262 TGATATAAAATCTAGTGCACAACCGTT 59.449 33.333 21.04 8.14 0.00 4.44
1905 2073 4.483476 AAAATCTAGTGCACAACCGTTC 57.517 40.909 21.04 0.00 0.00 3.95
1906 2074 1.710013 ATCTAGTGCACAACCGTTCG 58.290 50.000 21.04 0.00 0.00 3.95
1907 2075 0.942410 TCTAGTGCACAACCGTTCGC 60.942 55.000 21.04 0.00 0.00 4.70
1908 2076 1.897398 CTAGTGCACAACCGTTCGCC 61.897 60.000 21.04 0.00 0.00 5.54
1909 2077 2.372040 TAGTGCACAACCGTTCGCCT 62.372 55.000 21.04 0.00 0.00 5.52
1910 2078 2.515057 TGCACAACCGTTCGCCTT 60.515 55.556 0.00 0.00 0.00 4.35
1911 2079 2.251371 GCACAACCGTTCGCCTTC 59.749 61.111 0.00 0.00 0.00 3.46
1912 2080 2.251642 GCACAACCGTTCGCCTTCT 61.252 57.895 0.00 0.00 0.00 2.85
1913 2081 0.947180 GCACAACCGTTCGCCTTCTA 60.947 55.000 0.00 0.00 0.00 2.10
1914 2082 1.068474 CACAACCGTTCGCCTTCTAG 58.932 55.000 0.00 0.00 0.00 2.43
1915 2083 0.963962 ACAACCGTTCGCCTTCTAGA 59.036 50.000 0.00 0.00 0.00 2.43
1916 2084 1.336609 ACAACCGTTCGCCTTCTAGAC 60.337 52.381 0.00 0.00 0.00 2.59
1917 2085 0.109412 AACCGTTCGCCTTCTAGACG 60.109 55.000 0.00 0.00 0.00 4.18
1920 2088 0.248134 CGTTCGCCTTCTAGACGGAG 60.248 60.000 19.09 15.50 0.00 4.63
1935 2103 2.658707 GGAGTGAACAGTCGCGTGC 61.659 63.158 5.77 0.00 39.38 5.34
1966 2135 1.606903 ACACGGCAAAAATAACGGGA 58.393 45.000 0.00 0.00 33.29 5.14
1973 2281 3.368013 GGCAAAAATAACGGGAAAGGAGG 60.368 47.826 0.00 0.00 0.00 4.30
2128 2463 0.540365 CCAAGACATGGCAACCACCT 60.540 55.000 0.00 0.00 43.80 4.00
2192 2527 4.899352 ACAAGGTTCAGAAGCATAGTCT 57.101 40.909 14.73 0.00 0.00 3.24
2248 2583 2.737252 CGTTCCTAGAGTGCCAAGTTTC 59.263 50.000 0.00 0.00 0.00 2.78
2330 2665 4.279169 GCTATATCCCAAATTGCAGCAAGA 59.721 41.667 14.47 5.23 0.00 3.02
2344 2679 1.668294 CAAGAGAGAGTGGTGCGGT 59.332 57.895 0.00 0.00 0.00 5.68
2382 2717 2.620115 CAGGTCTGAACTGCAAACATGT 59.380 45.455 10.18 0.00 0.00 3.21
2500 2835 5.598005 TGGTGTTGAGACAATCCTTGAAAAT 59.402 36.000 0.00 0.00 37.57 1.82
2578 2913 2.307049 GAAGGCGTCGATGTTGTTTTG 58.693 47.619 6.48 0.00 0.00 2.44
2604 2939 2.171448 GTGATGATGGAGTAGGCCTGTT 59.829 50.000 17.99 2.26 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.223829 CCTGACACGGTGATAGCTAAGG 60.224 54.545 16.29 0.00 0.00 2.69
1 2 2.427453 ACCTGACACGGTGATAGCTAAG 59.573 50.000 16.29 0.00 35.52 2.18
4 5 0.818296 GACCTGACACGGTGATAGCT 59.182 55.000 16.29 0.00 37.42 3.32
5 6 0.818296 AGACCTGACACGGTGATAGC 59.182 55.000 16.29 1.92 37.42 2.97
6 7 1.405821 GGAGACCTGACACGGTGATAG 59.594 57.143 16.29 11.63 37.42 2.08
7 8 1.471119 GGAGACCTGACACGGTGATA 58.529 55.000 16.29 2.07 37.42 2.15
8 9 1.595993 CGGAGACCTGACACGGTGAT 61.596 60.000 16.29 0.00 37.42 3.06
9 10 2.265904 CGGAGACCTGACACGGTGA 61.266 63.158 16.29 0.00 37.42 4.02
10 11 1.595993 ATCGGAGACCTGACACGGTG 61.596 60.000 6.58 6.58 42.51 4.94
11 12 1.304217 ATCGGAGACCTGACACGGT 60.304 57.895 0.00 0.00 42.51 4.83
12 13 1.139734 CATCGGAGACCTGACACGG 59.860 63.158 0.00 0.00 42.51 4.94
13 14 0.179161 GACATCGGAGACCTGACACG 60.179 60.000 0.00 0.00 42.51 4.49
14 15 1.135257 CAGACATCGGAGACCTGACAC 60.135 57.143 0.00 0.00 42.51 3.67
15 16 1.177401 CAGACATCGGAGACCTGACA 58.823 55.000 0.00 0.00 42.51 3.58
16 17 0.457851 CCAGACATCGGAGACCTGAC 59.542 60.000 0.00 0.00 42.51 3.51
17 18 0.039764 ACCAGACATCGGAGACCTGA 59.960 55.000 0.00 0.00 42.51 3.86
18 19 0.898320 AACCAGACATCGGAGACCTG 59.102 55.000 0.00 0.00 42.51 4.00
19 20 0.898320 CAACCAGACATCGGAGACCT 59.102 55.000 0.00 0.00 42.51 3.85
20 21 0.895530 TCAACCAGACATCGGAGACC 59.104 55.000 0.00 0.00 42.51 3.85
21 22 1.546476 ACTCAACCAGACATCGGAGAC 59.454 52.381 0.00 0.00 42.51 3.36
22 23 1.924731 ACTCAACCAGACATCGGAGA 58.075 50.000 0.00 0.00 45.75 3.71
23 24 3.152261 GTACTCAACCAGACATCGGAG 57.848 52.381 0.00 0.00 0.00 4.63
35 36 3.550678 GCTAACTACGCATGGTACTCAAC 59.449 47.826 0.00 0.00 0.00 3.18
36 37 3.429822 GGCTAACTACGCATGGTACTCAA 60.430 47.826 0.00 0.00 0.00 3.02
37 38 2.100252 GGCTAACTACGCATGGTACTCA 59.900 50.000 0.00 0.00 0.00 3.41
38 39 2.545322 GGGCTAACTACGCATGGTACTC 60.545 54.545 0.00 0.00 0.00 2.59
39 40 1.411612 GGGCTAACTACGCATGGTACT 59.588 52.381 0.00 0.00 0.00 2.73
40 41 1.137479 TGGGCTAACTACGCATGGTAC 59.863 52.381 0.00 0.00 0.00 3.34
41 42 1.487300 TGGGCTAACTACGCATGGTA 58.513 50.000 0.00 0.00 0.00 3.25
42 43 0.837272 ATGGGCTAACTACGCATGGT 59.163 50.000 0.00 0.00 39.03 3.55
69 70 1.615424 TTCTCTGTACTGGGGGCCC 60.615 63.158 15.76 15.76 0.00 5.80
81 82 4.097437 CCAATGGTGAATGATGGTTCTCTG 59.903 45.833 0.00 0.00 0.00 3.35
133 136 1.066143 AGTTCGTATTGGGGCTCACTG 60.066 52.381 0.00 0.00 0.00 3.66
153 156 4.885325 GGGGAGAAACACAAGAAACACTTA 59.115 41.667 0.00 0.00 37.03 2.24
166 169 1.839994 CTATGCCAGAGGGGAGAAACA 59.160 52.381 0.00 0.00 38.23 2.83
175 178 3.624777 ACAATGAAACCTATGCCAGAGG 58.375 45.455 3.24 3.24 40.22 3.69
181 184 5.241728 GGAGGGAATACAATGAAACCTATGC 59.758 44.000 0.00 0.00 0.00 3.14
182 185 6.364701 TGGAGGGAATACAATGAAACCTATG 58.635 40.000 0.00 0.00 0.00 2.23
188 191 4.889409 GCTGATGGAGGGAATACAATGAAA 59.111 41.667 0.00 0.00 0.00 2.69
198 201 2.002977 CCTGGGCTGATGGAGGGAA 61.003 63.158 0.00 0.00 0.00 3.97
199 202 2.367377 CCTGGGCTGATGGAGGGA 60.367 66.667 0.00 0.00 0.00 4.20
216 219 4.930405 GCTAGAGTGTGGTAAAAGACTTCC 59.070 45.833 0.00 0.00 0.00 3.46
218 221 5.279556 GGAGCTAGAGTGTGGTAAAAGACTT 60.280 44.000 0.00 0.00 0.00 3.01
220 223 4.021368 TGGAGCTAGAGTGTGGTAAAAGAC 60.021 45.833 0.00 0.00 0.00 3.01
269 272 0.390860 CGAGGGTGGACTGATCATCC 59.609 60.000 14.03 14.03 35.69 3.51
293 296 0.250901 TTGGGAGCTTGAAGTCAGCC 60.251 55.000 0.00 0.00 0.00 4.85
296 299 2.507484 CACATTGGGAGCTTGAAGTCA 58.493 47.619 0.00 0.00 0.00 3.41
354 357 1.728971 CTTCTGAGGCATGACAACGAC 59.271 52.381 0.00 0.00 0.00 4.34
382 385 0.888619 TGATATAAGAGCGCCGAGGG 59.111 55.000 2.29 0.00 0.00 4.30
385 388 2.423892 GAGGATGATATAAGAGCGCCGA 59.576 50.000 2.29 0.00 0.00 5.54
387 390 3.194542 ACAGAGGATGATATAAGAGCGCC 59.805 47.826 2.29 0.00 0.00 6.53
398 406 5.890752 ATGTTGAGATCACAGAGGATGAT 57.109 39.130 0.00 0.00 39.54 2.45
419 427 6.758886 GGACATCTGTCAGAACGAAAGATAAT 59.241 38.462 6.64 0.00 45.55 1.28
437 445 1.189524 TTTGACGGACGGGGACATCT 61.190 55.000 0.00 0.00 0.00 2.90
459 467 1.265365 GCTCCTGCTTGTTGTCTTGAC 59.735 52.381 0.00 0.00 36.03 3.18
503 511 8.886719 CATGAGAGCATAACAAATTCTAACTGA 58.113 33.333 0.00 0.00 32.27 3.41
525 533 7.581213 AACTCAAAATTCTTGGTACACATGA 57.419 32.000 0.00 0.00 39.29 3.07
572 584 1.067915 GCGGAAAACATTAGCCAAGCA 60.068 47.619 0.00 0.00 0.00 3.91
579 591 4.084013 AGACGACTTTGCGGAAAACATTAG 60.084 41.667 3.02 0.00 35.12 1.73
599 611 8.332996 TGGTTCCATATAGTCTTCGTATAGAC 57.667 38.462 0.00 0.00 43.90 2.59
684 700 1.620822 GAGTTGTTGGGCACTTGGAT 58.379 50.000 0.00 0.00 0.00 3.41
748 764 1.131883 GCATTTGCTACAGCTGACTGG 59.868 52.381 23.35 1.34 42.41 4.00
855 871 6.090898 GTCTACGATGCAGTGTTTTGTTATCT 59.909 38.462 0.00 0.00 0.00 1.98
924 956 4.054780 TGTGGTGACAAGTGAAGTCTAC 57.945 45.455 0.00 0.00 46.06 2.59
925 957 4.439057 GTTGTGGTGACAAGTGAAGTCTA 58.561 43.478 0.00 0.00 42.87 2.59
927 959 2.030457 CGTTGTGGTGACAAGTGAAGTC 59.970 50.000 0.00 0.00 42.87 3.01
928 960 2.006888 CGTTGTGGTGACAAGTGAAGT 58.993 47.619 0.00 0.00 42.87 3.01
929 961 2.276201 TCGTTGTGGTGACAAGTGAAG 58.724 47.619 0.00 0.00 42.87 3.02
931 963 2.276201 CTTCGTTGTGGTGACAAGTGA 58.724 47.619 0.00 0.00 42.87 3.41
932 964 1.268032 GCTTCGTTGTGGTGACAAGTG 60.268 52.381 0.00 0.00 42.87 3.16
933 965 1.014352 GCTTCGTTGTGGTGACAAGT 58.986 50.000 0.00 0.00 42.87 3.16
934 966 1.013596 TGCTTCGTTGTGGTGACAAG 58.986 50.000 0.00 0.00 42.87 3.16
935 967 0.730265 GTGCTTCGTTGTGGTGACAA 59.270 50.000 0.00 0.00 46.06 3.18
1071 1147 3.663176 TTCACGGCTGCTGCTTGC 61.663 61.111 15.64 5.42 43.25 4.01
1218 1297 2.663196 GTGCCGAGCTGGTAGGTT 59.337 61.111 7.81 0.00 41.21 3.50
1580 1691 0.390860 CCCAGACGAGGATGTCCATC 59.609 60.000 1.30 0.00 39.77 3.51
1695 1806 0.830444 AGTCACCCGCCAGTCAACTA 60.830 55.000 0.00 0.00 0.00 2.24
1733 1844 1.992557 TCCCTAGCCAATCAAACCACT 59.007 47.619 0.00 0.00 0.00 4.00
1736 1847 4.038042 GCTAATTCCCTAGCCAATCAAACC 59.962 45.833 0.00 0.00 38.72 3.27
1804 1938 5.779529 ATGTCACACAGCTTGAAGAAAAT 57.220 34.783 0.00 0.00 0.00 1.82
1828 1962 5.163632 TGCGTCAATTCATTAACATCAGCAT 60.164 36.000 0.00 0.00 0.00 3.79
1872 2040 9.679661 TGTGCACTAGATTTTATATCAGGAAAA 57.320 29.630 19.41 0.00 0.00 2.29
1873 2041 9.679661 TTGTGCACTAGATTTTATATCAGGAAA 57.320 29.630 19.41 0.00 0.00 3.13
1876 2044 7.307396 CGGTTGTGCACTAGATTTTATATCAGG 60.307 40.741 19.41 0.00 0.00 3.86
1877 2045 7.224753 ACGGTTGTGCACTAGATTTTATATCAG 59.775 37.037 19.41 0.00 0.00 2.90
1878 2046 7.045416 ACGGTTGTGCACTAGATTTTATATCA 58.955 34.615 19.41 0.00 0.00 2.15
1880 2048 7.254319 CGAACGGTTGTGCACTAGATTTTATAT 60.254 37.037 19.41 0.00 0.00 0.86
1881 2049 6.035220 CGAACGGTTGTGCACTAGATTTTATA 59.965 38.462 19.41 0.00 0.00 0.98
1882 2050 5.163893 CGAACGGTTGTGCACTAGATTTTAT 60.164 40.000 19.41 0.00 0.00 1.40
1883 2051 4.150980 CGAACGGTTGTGCACTAGATTTTA 59.849 41.667 19.41 0.00 0.00 1.52
1884 2052 3.059188 CGAACGGTTGTGCACTAGATTTT 60.059 43.478 19.41 4.21 0.00 1.82
1885 2053 2.478894 CGAACGGTTGTGCACTAGATTT 59.521 45.455 19.41 5.86 0.00 2.17
1886 2054 2.066262 CGAACGGTTGTGCACTAGATT 58.934 47.619 19.41 6.04 0.00 2.40
1887 2055 1.710013 CGAACGGTTGTGCACTAGAT 58.290 50.000 19.41 1.27 0.00 1.98
1888 2056 0.942410 GCGAACGGTTGTGCACTAGA 60.942 55.000 19.41 0.90 0.00 2.43
1889 2057 1.491563 GCGAACGGTTGTGCACTAG 59.508 57.895 19.41 8.95 0.00 2.57
1890 2058 1.957186 GGCGAACGGTTGTGCACTA 60.957 57.895 19.41 7.83 0.00 2.74
1891 2059 3.276846 GGCGAACGGTTGTGCACT 61.277 61.111 19.41 0.00 0.00 4.40
1892 2060 2.711185 GAAGGCGAACGGTTGTGCAC 62.711 60.000 10.75 10.75 0.00 4.57
1893 2061 2.515057 AAGGCGAACGGTTGTGCA 60.515 55.556 14.36 0.00 0.00 4.57
1894 2062 0.947180 TAGAAGGCGAACGGTTGTGC 60.947 55.000 0.00 1.86 0.00 4.57
1895 2063 1.068474 CTAGAAGGCGAACGGTTGTG 58.932 55.000 0.00 0.00 0.00 3.33
1896 2064 0.963962 TCTAGAAGGCGAACGGTTGT 59.036 50.000 0.00 0.00 0.00 3.32
1897 2065 1.347320 GTCTAGAAGGCGAACGGTTG 58.653 55.000 0.00 0.00 0.00 3.77
1898 2066 3.808583 GTCTAGAAGGCGAACGGTT 57.191 52.632 0.00 0.00 0.00 4.44
1905 2073 0.809385 TTCACTCCGTCTAGAAGGCG 59.191 55.000 18.93 15.64 44.05 5.52
1906 2074 1.544691 TGTTCACTCCGTCTAGAAGGC 59.455 52.381 18.93 5.47 0.00 4.35
1907 2075 2.820787 ACTGTTCACTCCGTCTAGAAGG 59.179 50.000 17.80 17.80 0.00 3.46
1908 2076 3.425094 CGACTGTTCACTCCGTCTAGAAG 60.425 52.174 0.00 0.00 0.00 2.85
1909 2077 2.483106 CGACTGTTCACTCCGTCTAGAA 59.517 50.000 0.00 0.00 0.00 2.10
1910 2078 2.074576 CGACTGTTCACTCCGTCTAGA 58.925 52.381 0.00 0.00 0.00 2.43
1911 2079 1.466024 GCGACTGTTCACTCCGTCTAG 60.466 57.143 0.00 0.00 0.00 2.43
1912 2080 0.520404 GCGACTGTTCACTCCGTCTA 59.480 55.000 0.00 0.00 0.00 2.59
1913 2081 1.286260 GCGACTGTTCACTCCGTCT 59.714 57.895 0.00 0.00 0.00 4.18
1914 2082 2.081212 CGCGACTGTTCACTCCGTC 61.081 63.158 0.00 0.00 0.00 4.79
1915 2083 2.050351 CGCGACTGTTCACTCCGT 60.050 61.111 0.00 0.00 0.00 4.69
1916 2084 2.050351 ACGCGACTGTTCACTCCG 60.050 61.111 15.93 0.00 0.00 4.63
1917 2085 2.658707 GCACGCGACTGTTCACTCC 61.659 63.158 15.93 0.00 0.00 3.85
1920 2088 1.083401 CTTGCACGCGACTGTTCAC 60.083 57.895 15.93 0.00 0.00 3.18
2150 2485 9.393512 CCTTGTAAATGATTTCTCTCTCTGAAT 57.606 33.333 0.00 0.00 0.00 2.57
2192 2527 4.233789 GCAAATGAAAATCACACGCCTAA 58.766 39.130 0.00 0.00 0.00 2.69
2248 2583 1.164411 TGTGCTCGCTATTTTGTGGG 58.836 50.000 0.00 0.00 0.00 4.61
2330 2665 2.936912 GCTCACCGCACCACTCTCT 61.937 63.158 0.00 0.00 38.92 3.10
2344 2679 1.649321 CTGGGATGCCCTATAGCTCA 58.351 55.000 0.00 0.00 45.70 4.26
2365 2700 2.287644 CACGACATGTTTGCAGTTCAGA 59.712 45.455 0.00 0.00 0.00 3.27
2382 2717 2.684001 ACTCACTTGTTTGTCCACGA 57.316 45.000 0.00 0.00 0.00 4.35
2500 2835 3.069443 GGTCAAGATTTTTGGTTGGCTCA 59.931 43.478 0.00 0.00 0.00 4.26
2563 2898 2.032894 ACTGAGCAAAACAACATCGACG 60.033 45.455 0.00 0.00 0.00 5.12
2578 2913 2.547642 GCCTACTCCATCATCACTGAGC 60.548 54.545 0.00 0.00 34.12 4.26
2604 2939 0.034896 GACGCACCTTTCTCCTCCAA 59.965 55.000 0.00 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.