Multiple sequence alignment - TraesCS2B01G178700

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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 TraesCS2B01G178700 chr2B 100.000 3806 0 0 1 3806 153759061 153762866 0.000000e+00 7029.0
1 TraesCS2B01G178700 chr2B 97.826 92 1 1 1846 1936 77856059 77856150 1.420000e-34 158.0
2 TraesCS2B01G178700 chr2B 83.444 151 18 4 3658 3804 531163624 531163771 2.390000e-27 134.0
3 TraesCS2B01G178700 chr2B 93.103 58 3 1 1972 2029 508955320 508955264 2.440000e-12 84.2
4 TraesCS2B01G178700 chr2D 94.273 1816 74 11 43 1851 102540566 102542358 0.000000e+00 2750.0
5 TraesCS2B01G178700 chr2D 95.975 1590 57 6 2051 3637 102542776 102544361 0.000000e+00 2575.0
6 TraesCS2B01G178700 chr2D 95.210 167 8 0 3640 3806 102544430 102544596 8.110000e-67 265.0
7 TraesCS2B01G178700 chr2D 96.694 121 3 1 1933 2052 102542354 102542474 2.320000e-47 200.0
8 TraesCS2B01G178700 chr2D 82.524 103 11 3 1936 2038 558334705 558334800 2.440000e-12 84.2
9 TraesCS2B01G178700 chr2A 92.459 1724 85 7 1933 3637 101536172 101537869 0.000000e+00 2422.0
10 TraesCS2B01G178700 chr2A 95.386 1127 49 1 728 1851 101535050 101536176 0.000000e+00 1790.0
11 TraesCS2B01G178700 chr2A 91.610 739 40 12 1 735 101534464 101535184 0.000000e+00 1002.0
12 TraesCS2B01G178700 chr2A 94.186 172 5 2 3640 3806 101537937 101538108 1.360000e-64 257.0
13 TraesCS2B01G178700 chr2A 92.857 56 4 0 1969 2024 555339563 555339618 8.760000e-12 82.4
14 TraesCS2B01G178700 chr4D 83.505 194 25 5 1936 2124 482705730 482705539 1.410000e-39 174.0
15 TraesCS2B01G178700 chr4D 93.069 101 6 1 1838 1937 426582352 426582252 3.060000e-31 147.0
16 TraesCS2B01G178700 chr4B 82.474 194 27 5 1936 2124 612276438 612276247 3.040000e-36 163.0
17 TraesCS2B01G178700 chr4B 92.453 106 6 2 1841 1944 58761315 58761420 2.370000e-32 150.0
18 TraesCS2B01G178700 chr4B 82.581 155 21 3 3654 3804 393397802 393397650 8.580000e-27 132.0
19 TraesCS2B01G178700 chr4B 84.946 93 13 1 1938 2030 75204544 75204453 4.050000e-15 93.5
20 TraesCS2B01G178700 chr5B 96.907 97 0 2 1842 1937 556628617 556628711 3.940000e-35 159.0
21 TraesCS2B01G178700 chr1B 96.875 96 2 1 1843 1937 248358698 248358603 3.940000e-35 159.0
22 TraesCS2B01G178700 chr7D 97.826 92 1 1 1847 1937 311872938 311872847 1.420000e-34 158.0
23 TraesCS2B01G178700 chr7D 82.667 150 21 2 3658 3804 475721343 475721196 1.110000e-25 128.0
24 TraesCS2B01G178700 chr3B 94.118 102 5 1 1841 1941 541515367 541515266 1.830000e-33 154.0
25 TraesCS2B01G178700 chr7B 94.949 99 2 2 1848 1945 450280555 450280651 6.590000e-33 152.0
26 TraesCS2B01G178700 chr3A 93.000 100 5 2 1839 1937 444255873 444255775 1.100000e-30 145.0
27 TraesCS2B01G178700 chr4A 83.333 150 20 2 3658 3804 536785218 536785071 2.390000e-27 134.0
28 TraesCS2B01G178700 chr4A 83.444 151 18 4 3658 3804 629510945 629510798 2.390000e-27 134.0
29 TraesCS2B01G178700 chr4A 83.444 151 18 4 3658 3804 629516077 629515930 2.390000e-27 134.0
30 TraesCS2B01G178700 chr1D 82.667 150 21 2 3658 3804 362328035 362328182 1.110000e-25 128.0
31 TraesCS2B01G178700 chr5D 83.784 74 7 2 1989 2062 244710630 244710698 8.830000e-07 65.8


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 TraesCS2B01G178700 chr2B 153759061 153762866 3805 False 7029.00 7029 100.00000 1 3806 1 chr2B.!!$F2 3805
1 TraesCS2B01G178700 chr2D 102540566 102544596 4030 False 1447.50 2750 95.53800 43 3806 4 chr2D.!!$F2 3763
2 TraesCS2B01G178700 chr2A 101534464 101538108 3644 False 1367.75 2422 93.41025 1 3806 4 chr2A.!!$F2 3805

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
499 503 0.239347 CTCCTTGCCGTCTTTTGCTG 59.761 55.0 0.0 0.0 0.00 4.41 F
2108 2420 0.754472 AGTGCAATGTTGGCTGCTTT 59.246 45.0 0.0 0.0 39.38 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2189 2501 0.931005 CCGAGCTTTGCTACGGAATC 59.069 55.000 18.4 0.0 45.13 2.52 R
3417 3747 1.141881 AGACGGGCAAGTATGAGCG 59.858 57.895 0.0 0.0 0.00 5.03 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
24 25 6.786967 ATCTCAAAAGGATTCCCTGAATTG 57.213 37.500 0.00 0.00 43.48 2.32
26 27 5.711976 TCTCAAAAGGATTCCCTGAATTGTC 59.288 40.000 0.00 0.00 43.48 3.18
29 30 4.934797 AAGGATTCCCTGAATTGTCTCA 57.065 40.909 0.00 0.00 43.48 3.27
209 213 1.528309 CTTTTGGCGGTGTCCAGGT 60.528 57.895 0.00 0.00 37.44 4.00
423 427 4.436998 GCGTCCTCACGGGTCTGG 62.437 72.222 0.00 0.00 46.80 3.86
473 477 1.520342 GGACCGCAGATGAGCTCAC 60.520 63.158 20.97 13.11 0.00 3.51
474 478 1.875813 GACCGCAGATGAGCTCACG 60.876 63.158 20.97 17.64 0.00 4.35
476 480 3.260483 CGCAGATGAGCTCACGGC 61.260 66.667 20.97 21.61 42.19 5.68
497 501 1.581447 CCTCCTTGCCGTCTTTTGC 59.419 57.895 0.00 0.00 0.00 3.68
499 503 0.239347 CTCCTTGCCGTCTTTTGCTG 59.761 55.000 0.00 0.00 0.00 4.41
503 507 1.267806 CTTGCCGTCTTTTGCTGTGAT 59.732 47.619 0.00 0.00 0.00 3.06
554 558 4.652679 AAGATTACGACTTTCCCCCTTT 57.347 40.909 0.00 0.00 0.00 3.11
565 569 0.772384 TCCCCCTTTTTACCTGCGAA 59.228 50.000 0.00 0.00 0.00 4.70
625 629 1.512734 GCGAGCAGCGTTTTGATGG 60.513 57.895 0.00 0.00 43.41 3.51
759 763 2.097142 GCAGCGCTTTGATGAATTCTCT 59.903 45.455 7.50 0.00 35.47 3.10
762 766 3.373439 AGCGCTTTGATGAATTCTCTGTC 59.627 43.478 2.64 1.02 0.00 3.51
775 779 8.463930 TGAATTCTCTGTCTTTTGTTACCAAT 57.536 30.769 7.05 0.00 0.00 3.16
786 791 8.626526 GTCTTTTGTTACCAATTTCTCCAGTTA 58.373 33.333 0.00 0.00 0.00 2.24
807 812 6.147821 AGTTATGTAGCTGCAGTTTGTTGTAG 59.852 38.462 16.64 0.00 34.39 2.74
834 839 3.910648 TGAAATTTCAATGCGTCATGCA 58.089 36.364 18.45 0.00 45.18 3.96
944 949 4.725304 AGGTTATTCCGGGGAGTTAGATTT 59.275 41.667 0.00 0.00 41.99 2.17
1027 1032 1.225704 GCTTCCCATCAGTCCCCAG 59.774 63.158 0.00 0.00 0.00 4.45
1043 1048 1.566563 CAGTAATGATGAGCGGCGC 59.433 57.895 26.86 26.86 0.00 6.53
1107 1112 3.883489 GGTACCCTATGATTGCCAACTTC 59.117 47.826 0.00 0.00 0.00 3.01
1291 1296 0.913934 TTCTCATGGGTGCAGGCCTA 60.914 55.000 3.98 0.00 0.00 3.93
1390 1395 3.071023 TGCGAGGGAAGAAGAAAAAGAGA 59.929 43.478 0.00 0.00 0.00 3.10
1498 1503 9.757227 GTTACTGATCAGCTTCTCAAGTATATT 57.243 33.333 22.83 0.00 0.00 1.28
1677 1682 4.938080 AGTTCGCATAGATGAGATTCGTT 58.062 39.130 0.00 0.00 36.51 3.85
1698 1703 3.614092 TCAGGGATTTCTGAGTGAATGC 58.386 45.455 0.00 0.00 38.70 3.56
1858 1866 5.514500 AGATCATCTCTACTACTCCCTCC 57.486 47.826 0.00 0.00 30.26 4.30
1859 1867 3.773418 TCATCTCTACTACTCCCTCCG 57.227 52.381 0.00 0.00 0.00 4.63
1860 1868 3.047115 TCATCTCTACTACTCCCTCCGT 58.953 50.000 0.00 0.00 0.00 4.69
1861 1869 3.458857 TCATCTCTACTACTCCCTCCGTT 59.541 47.826 0.00 0.00 0.00 4.44
1862 1870 3.557228 TCTCTACTACTCCCTCCGTTC 57.443 52.381 0.00 0.00 0.00 3.95
1863 1871 2.172293 TCTCTACTACTCCCTCCGTTCC 59.828 54.545 0.00 0.00 0.00 3.62
1864 1872 1.918262 TCTACTACTCCCTCCGTTCCA 59.082 52.381 0.00 0.00 0.00 3.53
1865 1873 2.309755 TCTACTACTCCCTCCGTTCCAA 59.690 50.000 0.00 0.00 0.00 3.53
1866 1874 2.019807 ACTACTCCCTCCGTTCCAAA 57.980 50.000 0.00 0.00 0.00 3.28
1867 1875 2.332117 ACTACTCCCTCCGTTCCAAAA 58.668 47.619 0.00 0.00 0.00 2.44
1868 1876 2.910977 ACTACTCCCTCCGTTCCAAAAT 59.089 45.455 0.00 0.00 0.00 1.82
1869 1877 4.098894 ACTACTCCCTCCGTTCCAAAATA 58.901 43.478 0.00 0.00 0.00 1.40
1870 1878 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
1871 1879 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
1872 1880 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
1873 1881 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
1874 1882 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
1875 1883 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
1876 1884 4.384208 CCCTCCGTTCCAAAATAGATGACT 60.384 45.833 0.00 0.00 0.00 3.41
1877 1885 4.811557 CCTCCGTTCCAAAATAGATGACTC 59.188 45.833 0.00 0.00 0.00 3.36
1878 1886 5.414789 TCCGTTCCAAAATAGATGACTCA 57.585 39.130 0.00 0.00 0.00 3.41
1879 1887 5.800296 TCCGTTCCAAAATAGATGACTCAA 58.200 37.500 0.00 0.00 0.00 3.02
1880 1888 5.642063 TCCGTTCCAAAATAGATGACTCAAC 59.358 40.000 0.00 0.00 0.00 3.18
1881 1889 5.643777 CCGTTCCAAAATAGATGACTCAACT 59.356 40.000 0.00 0.00 0.00 3.16
1882 1890 6.149474 CCGTTCCAAAATAGATGACTCAACTT 59.851 38.462 0.00 0.00 0.00 2.66
1883 1891 7.308589 CCGTTCCAAAATAGATGACTCAACTTT 60.309 37.037 0.00 0.00 0.00 2.66
1884 1892 8.717821 CGTTCCAAAATAGATGACTCAACTTTA 58.282 33.333 0.00 0.00 0.00 1.85
1921 1929 9.739276 ATACAAAGTTGAGTCATCTATTTTGGA 57.261 29.630 14.35 9.09 40.00 3.53
1922 1930 8.463930 ACAAAGTTGAGTCATCTATTTTGGAA 57.536 30.769 14.35 0.00 40.00 3.53
1923 1931 8.352942 ACAAAGTTGAGTCATCTATTTTGGAAC 58.647 33.333 14.35 0.00 40.00 3.62
1924 1932 6.727824 AGTTGAGTCATCTATTTTGGAACG 57.272 37.500 1.70 0.00 0.00 3.95
1925 1933 5.643777 AGTTGAGTCATCTATTTTGGAACGG 59.356 40.000 1.70 0.00 0.00 4.44
1926 1934 5.414789 TGAGTCATCTATTTTGGAACGGA 57.585 39.130 0.00 0.00 0.00 4.69
1927 1935 5.419542 TGAGTCATCTATTTTGGAACGGAG 58.580 41.667 0.00 0.00 0.00 4.63
1928 1936 4.770795 AGTCATCTATTTTGGAACGGAGG 58.229 43.478 0.00 0.00 0.00 4.30
1929 1937 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
1930 1938 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
1931 1939 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
1932 1940 3.178865 TCTATTTTGGAACGGAGGGAGT 58.821 45.455 0.00 0.00 0.00 3.85
1933 1941 4.355549 TCTATTTTGGAACGGAGGGAGTA 58.644 43.478 0.00 0.00 0.00 2.59
1934 1942 2.845363 TTTTGGAACGGAGGGAGTAC 57.155 50.000 0.00 0.00 0.00 2.73
1935 1943 1.719529 TTTGGAACGGAGGGAGTACA 58.280 50.000 0.00 0.00 0.00 2.90
2108 2420 0.754472 AGTGCAATGTTGGCTGCTTT 59.246 45.000 0.00 0.00 39.38 3.51
2118 2430 3.261580 GTTGGCTGCTTTGTTGAGTTTT 58.738 40.909 0.00 0.00 0.00 2.43
2167 2479 7.414222 TGGTTGTTATCTACTACTAACCCAG 57.586 40.000 0.00 0.00 36.22 4.45
2307 2619 3.173853 TTTTTCCGCAGATCGCCG 58.826 55.556 4.37 3.07 37.30 6.46
2310 2622 2.501223 TTTTCCGCAGATCGCCGTCT 62.501 55.000 7.17 0.00 37.30 4.18
2400 2712 2.894126 TCCTCTGCTCGAAGAACTTCTT 59.106 45.455 3.55 3.55 39.87 2.52
2459 2771 0.604780 GTCACCAGCAGAGCATGTGT 60.605 55.000 0.00 0.00 35.13 3.72
2491 2803 3.346631 CTCATGTTGCGGCAAGGGC 62.347 63.158 16.97 5.21 40.13 5.19
2526 2838 1.642762 AGAGATGGGGCACTTGGAATT 59.357 47.619 0.00 0.00 0.00 2.17
2569 2881 6.364261 CGATACCTTACTCTCGTCAATAGTG 58.636 44.000 0.00 0.00 0.00 2.74
2576 2888 8.735315 CCTTACTCTCGTCAATAGTGATATCAT 58.265 37.037 9.02 1.07 35.80 2.45
2767 3079 4.336433 ACATTTTTCACCCTGATGATAGCG 59.664 41.667 0.00 0.00 0.00 4.26
2825 3137 6.825213 TCCTAAATGTGATGATTTGTCTCCAG 59.175 38.462 0.00 0.00 0.00 3.86
3175 3505 2.352960 GGAGCATTTTGGACTAGAAGCG 59.647 50.000 0.00 0.00 0.00 4.68
3192 3522 9.227777 ACTAGAAGCGGTTCTTTGTAAATTTAT 57.772 29.630 32.36 8.48 40.35 1.40
3281 3611 7.943079 TCATTTGGAGATGTGATTGTATGTT 57.057 32.000 0.00 0.00 0.00 2.71
3295 3625 9.953697 GTGATTGTATGTTGGTAAAAACTAACA 57.046 29.630 9.42 9.42 43.36 2.41
3386 3716 5.675684 TTGTTGGTGCTGAGTATCTGATA 57.324 39.130 0.00 0.00 35.94 2.15
3417 3747 2.007547 GCCTTTACCTCCGCAGTCTTC 61.008 57.143 0.00 0.00 0.00 2.87
3432 3762 0.179111 TCTTCGCTCATACTTGCCCG 60.179 55.000 0.00 0.00 0.00 6.13
3512 3842 6.128418 GCAATCTGAAGTCTTCTACAAACTCC 60.128 42.308 13.67 0.00 0.00 3.85
3594 3924 7.497595 TGATCAATACCGCTGTTACTTAGAAT 58.502 34.615 0.00 0.00 0.00 2.40
3637 3967 5.958380 TGTGACCTAGAAATGACCAGATACT 59.042 40.000 0.00 0.00 0.00 2.12
3638 3968 6.127338 TGTGACCTAGAAATGACCAGATACTG 60.127 42.308 0.00 0.00 0.00 2.74
3680 4076 6.071672 TCAGATCTCAGGTAGTTCTTCAACAG 60.072 42.308 0.00 0.00 32.88 3.16
3788 4189 7.817418 AGGATAACAAGCTACTTTGACAAAA 57.183 32.000 1.62 0.00 0.00 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 5.644188 AGACAATTCAGGGAATCCTTTTGA 58.356 37.500 0.00 0.00 42.67 2.69
140 141 0.754957 CTGGCGAGAGAGAGGTGGAT 60.755 60.000 0.00 0.00 0.00 3.41
141 142 1.379176 CTGGCGAGAGAGAGGTGGA 60.379 63.158 0.00 0.00 0.00 4.02
192 196 1.826054 CACCTGGACACCGCCAAAA 60.826 57.895 0.00 0.00 37.52 2.44
215 219 2.758737 AGGAAGACGGCGGTAGGG 60.759 66.667 13.24 0.00 0.00 3.53
228 232 2.989253 TCACGCTCGGAGCAGGAA 60.989 61.111 27.83 8.78 42.58 3.36
290 294 4.643387 GCACCCACGCCTGGTCTT 62.643 66.667 0.86 0.00 35.46 3.01
492 496 8.354426 GGTAAAAGTTACCTAATCACAGCAAAA 58.646 33.333 9.49 0.00 34.82 2.44
497 501 9.503399 AAGAAGGTAAAAGTTACCTAATCACAG 57.497 33.333 17.82 0.00 46.52 3.66
503 507 7.387673 GCGGTTAAGAAGGTAAAAGTTACCTAA 59.612 37.037 17.82 7.77 46.52 2.69
514 518 6.887626 ATCTTTTTGCGGTTAAGAAGGTAA 57.112 33.333 0.00 0.00 32.20 2.85
515 519 6.887626 AATCTTTTTGCGGTTAAGAAGGTA 57.112 33.333 0.00 0.00 32.20 3.08
525 529 4.319984 GGAAAGTCGTAATCTTTTTGCGGT 60.320 41.667 0.00 0.00 35.62 5.68
554 558 7.539366 CGATTTTTATCCTTTTTCGCAGGTAAA 59.461 33.333 0.00 0.00 32.59 2.01
591 595 2.320587 CGCAGTCACAGGAAGGCAC 61.321 63.158 0.00 0.00 0.00 5.01
775 779 4.551702 TGCAGCTACATAACTGGAGAAA 57.448 40.909 0.00 0.00 35.02 2.52
786 791 4.641396 TCTACAACAAACTGCAGCTACAT 58.359 39.130 15.27 0.00 0.00 2.29
807 812 6.932901 TGACGCATTGAAATTTCAGATTTC 57.067 33.333 19.64 13.92 38.61 2.17
834 839 2.489329 CACCAAAATGAGTGAGCCGAAT 59.511 45.455 0.00 0.00 36.01 3.34
1016 1021 3.072184 GCTCATCATTACTGGGGACTGAT 59.928 47.826 0.00 0.00 0.00 2.90
1027 1032 1.560860 GAGGCGCCGCTCATCATTAC 61.561 60.000 24.06 0.00 0.00 1.89
1043 1048 1.487231 CGCGAGACAACAAACGAGG 59.513 57.895 0.00 0.00 0.00 4.63
1107 1112 4.931601 TCGGACTGATTGATCAAAGAACAG 59.068 41.667 13.09 19.01 36.18 3.16
1367 1372 3.403038 TCTTTTTCTTCTTCCCTCGCAG 58.597 45.455 0.00 0.00 0.00 5.18
1390 1395 1.157257 TTGCACACAAGACATCGCGT 61.157 50.000 5.77 0.00 0.00 6.01
1498 1503 6.354130 ACTAAAACAAGAGTACCTTTCTGCA 58.646 36.000 0.00 0.00 31.42 4.41
1532 1537 5.411669 GTGGTCAGATTTGGAATTTAGACGT 59.588 40.000 0.00 0.00 0.00 4.34
1586 1591 1.580059 AGAGGCCACCCGATTTTAGA 58.420 50.000 5.01 0.00 35.76 2.10
1660 1665 3.993081 CCCTGAACGAATCTCATCTATGC 59.007 47.826 0.00 0.00 0.00 3.14
1677 1682 3.009363 TGCATTCACTCAGAAATCCCTGA 59.991 43.478 0.00 0.00 40.22 3.86
1851 1859 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
1852 1860 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
1853 1861 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
1854 1862 4.770795 AGTCATCTATTTTGGAACGGAGG 58.229 43.478 0.00 0.00 0.00 4.30
1855 1863 5.419542 TGAGTCATCTATTTTGGAACGGAG 58.580 41.667 0.00 0.00 0.00 4.63
1856 1864 5.414789 TGAGTCATCTATTTTGGAACGGA 57.585 39.130 0.00 0.00 0.00 4.69
1857 1865 5.643777 AGTTGAGTCATCTATTTTGGAACGG 59.356 40.000 1.70 0.00 0.00 4.44
1858 1866 6.727824 AGTTGAGTCATCTATTTTGGAACG 57.272 37.500 1.70 0.00 0.00 3.95
1895 1903 9.739276 TCCAAAATAGATGACTCAACTTTGTAT 57.261 29.630 0.00 0.00 0.00 2.29
1896 1904 9.567776 TTCCAAAATAGATGACTCAACTTTGTA 57.432 29.630 0.00 0.00 0.00 2.41
1897 1905 8.352942 GTTCCAAAATAGATGACTCAACTTTGT 58.647 33.333 0.00 0.00 0.00 2.83
1898 1906 7.535258 CGTTCCAAAATAGATGACTCAACTTTG 59.465 37.037 0.00 0.00 0.00 2.77
1899 1907 7.308589 CCGTTCCAAAATAGATGACTCAACTTT 60.309 37.037 0.00 0.00 0.00 2.66
1900 1908 6.149474 CCGTTCCAAAATAGATGACTCAACTT 59.851 38.462 0.00 0.00 0.00 2.66
1901 1909 5.643777 CCGTTCCAAAATAGATGACTCAACT 59.356 40.000 0.00 0.00 0.00 3.16
1902 1910 5.642063 TCCGTTCCAAAATAGATGACTCAAC 59.358 40.000 0.00 0.00 0.00 3.18
1903 1911 5.800296 TCCGTTCCAAAATAGATGACTCAA 58.200 37.500 0.00 0.00 0.00 3.02
1904 1912 5.414789 TCCGTTCCAAAATAGATGACTCA 57.585 39.130 0.00 0.00 0.00 3.41
1905 1913 4.811557 CCTCCGTTCCAAAATAGATGACTC 59.188 45.833 0.00 0.00 0.00 3.36
1906 1914 4.384208 CCCTCCGTTCCAAAATAGATGACT 60.384 45.833 0.00 0.00 0.00 3.41
1907 1915 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
1908 1916 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
1909 1917 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
1910 1918 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
1911 1919 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
1912 1920 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
1913 1921 3.839490 TGTACTCCCTCCGTTCCAAAATA 59.161 43.478 0.00 0.00 0.00 1.40
1914 1922 2.640826 TGTACTCCCTCCGTTCCAAAAT 59.359 45.455 0.00 0.00 0.00 1.82
1915 1923 2.048601 TGTACTCCCTCCGTTCCAAAA 58.951 47.619 0.00 0.00 0.00 2.44
1916 1924 1.719529 TGTACTCCCTCCGTTCCAAA 58.280 50.000 0.00 0.00 0.00 3.28
1917 1925 1.829222 GATGTACTCCCTCCGTTCCAA 59.171 52.381 0.00 0.00 0.00 3.53
1918 1926 1.006758 AGATGTACTCCCTCCGTTCCA 59.993 52.381 0.00 0.00 0.00 3.53
1919 1927 1.777941 AGATGTACTCCCTCCGTTCC 58.222 55.000 0.00 0.00 0.00 3.62
1920 1928 6.645790 TTATAAGATGTACTCCCTCCGTTC 57.354 41.667 0.00 0.00 0.00 3.95
1921 1929 7.613551 ATTTATAAGATGTACTCCCTCCGTT 57.386 36.000 0.00 0.00 0.00 4.44
1922 1930 7.442656 CAATTTATAAGATGTACTCCCTCCGT 58.557 38.462 0.00 0.00 0.00 4.69
1923 1931 6.874134 CCAATTTATAAGATGTACTCCCTCCG 59.126 42.308 0.00 0.00 0.00 4.63
1924 1932 7.974504 TCCAATTTATAAGATGTACTCCCTCC 58.025 38.462 0.00 0.00 0.00 4.30
1925 1933 8.652290 ACTCCAATTTATAAGATGTACTCCCTC 58.348 37.037 0.00 0.00 0.00 4.30
1926 1934 8.568617 ACTCCAATTTATAAGATGTACTCCCT 57.431 34.615 0.00 0.00 0.00 4.20
1932 1940 9.555727 GCCACTAACTCCAATTTATAAGATGTA 57.444 33.333 0.00 0.00 0.00 2.29
1933 1941 8.052748 TGCCACTAACTCCAATTTATAAGATGT 58.947 33.333 0.00 0.00 0.00 3.06
1934 1942 8.450578 TGCCACTAACTCCAATTTATAAGATG 57.549 34.615 0.00 0.00 0.00 2.90
1935 1943 8.275040 ACTGCCACTAACTCCAATTTATAAGAT 58.725 33.333 0.00 0.00 0.00 2.40
2068 2379 1.153066 TGAAAACTGCAGCGGTGGA 60.153 52.632 15.27 13.36 0.00 4.02
2138 2450 7.985752 GGTTAGTAGTAGATAACAACCAATGCT 59.014 37.037 0.00 0.00 35.21 3.79
2189 2501 0.931005 CCGAGCTTTGCTACGGAATC 59.069 55.000 18.40 0.00 45.13 2.52
2234 2546 2.536928 GGCATAACGAGAATCAACGTGC 60.537 50.000 6.32 6.03 42.43 5.34
2237 2549 2.550978 AGGGCATAACGAGAATCAACG 58.449 47.619 0.00 0.00 33.17 4.10
2310 2622 2.234908 GTCAAGGCTGAGGCTCTTAAGA 59.765 50.000 16.72 4.81 37.50 2.10
2400 2712 8.236585 CATCAACAAATGGACATAGGGAAATA 57.763 34.615 0.00 0.00 0.00 1.40
2459 2771 1.017701 CATGAGACGCTTCAGCTGCA 61.018 55.000 9.47 0.00 39.32 4.41
2491 2803 3.451178 CCATCTCTTATACCCCCATACGG 59.549 52.174 0.00 0.00 0.00 4.02
2526 2838 3.357504 CAGCTCGTGCATCATCTCA 57.642 52.632 12.58 0.00 42.74 3.27
2569 2881 3.577848 ACCAGCTCCTCTGTCATGATATC 59.422 47.826 0.00 0.00 41.25 1.63
2576 2888 1.372683 GCAACCAGCTCCTCTGTCA 59.627 57.895 0.00 0.00 41.25 3.58
2644 2956 1.167851 CCATCCACAACGATGTTGCT 58.832 50.000 9.45 0.00 37.82 3.91
2767 3079 4.965062 TCGTCAAACTTGTCAGTGAAAAC 58.035 39.130 0.00 0.00 31.60 2.43
2825 3137 9.579768 CCAATATATAGATAGATTGATAGCCGC 57.420 37.037 15.30 0.00 41.87 6.53
2931 3243 2.169561 TCCGCATTTGGTCTGCAGTATA 59.830 45.455 14.67 0.00 39.64 1.47
3175 3505 8.024865 AGCGGTACAATAAATTTACAAAGAACC 58.975 33.333 0.00 3.67 0.00 3.62
3192 3522 6.407299 CCCCTACTAATCTTAAAGCGGTACAA 60.407 42.308 0.00 0.00 0.00 2.41
3281 3611 8.798402 CAATATCCAACCTGTTAGTTTTTACCA 58.202 33.333 0.00 0.00 0.00 3.25
3295 3625 3.117738 CCCTGCTCTTCAATATCCAACCT 60.118 47.826 0.00 0.00 0.00 3.50
3386 3716 5.705905 GCGGAGGTAAAGGCTTTATATGATT 59.294 40.000 21.59 5.52 0.00 2.57
3417 3747 1.141881 AGACGGGCAAGTATGAGCG 59.858 57.895 0.00 0.00 0.00 5.03
3512 3842 4.162640 TCGAATGTCGACAAGGCG 57.837 55.556 24.13 23.69 44.82 5.52


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

AutoCloner maintained by Alex Coulton.