Multiple sequence alignment - TraesCS6B01G082200

Loading Multiple Alignment...

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 TraesCS6B01G082200 chr6B 100.000 2787 0 0 1 2787 59025160 59027946 0.000000e+00 5147.0
1 TraesCS6B01G082200 chr6B 93.011 930 20 10 1900 2784 58311484 58312413 0.000000e+00 1315.0
2 TraesCS6B01G082200 chr6B 93.159 804 33 13 912 1695 58309670 58310471 0.000000e+00 1160.0
3 TraesCS6B01G082200 chr6B 90.979 654 44 9 1060 1698 58777632 58778285 0.000000e+00 867.0
4 TraesCS6B01G082200 chr6B 83.944 928 99 24 30 925 58308716 58309625 0.000000e+00 843.0
5 TraesCS6B01G082200 chr6B 94.759 477 23 2 1224 1698 61796058 61795582 0.000000e+00 741.0
6 TraesCS6B01G082200 chr6B 95.584 385 8 3 2409 2784 59582999 59583383 2.370000e-170 608.0
7 TraesCS6B01G082200 chr6B 92.388 381 14 6 2414 2784 58779340 58779715 1.900000e-146 529.0
8 TraesCS6B01G082200 chr6B 88.066 243 22 4 1905 2146 720616758 720616522 5.880000e-72 281.0
9 TraesCS6B01G082200 chr6B 92.969 128 8 1 1699 1825 58310532 58310659 4.740000e-43 185.0
10 TraesCS6B01G082200 chr6B 89.286 112 12 0 1700 1811 61795522 61795411 1.040000e-29 141.0
11 TraesCS6B01G082200 chr6B 88.496 113 13 0 1699 1811 58778344 58778456 1.350000e-28 137.0
12 TraesCS6B01G082200 chr6B 90.909 55 4 1 30 84 59561729 59561782 3.850000e-09 73.1
13 TraesCS6B01G082200 chr6B 100.000 33 0 0 1 33 58120976 58121008 8.330000e-06 62.1
14 TraesCS6B01G082200 chr6A 88.466 919 74 15 30 930 33000279 33001183 0.000000e+00 1081.0
15 TraesCS6B01G082200 chr6A 86.765 952 74 37 912 1825 33001225 33002162 0.000000e+00 1013.0
16 TraesCS6B01G082200 chr6A 84.122 888 83 34 985 1823 33964464 33963586 0.000000e+00 806.0
17 TraesCS6B01G082200 chr6A 85.422 734 89 14 30 749 32938468 32939197 0.000000e+00 747.0
18 TraesCS6B01G082200 chr6A 96.512 86 2 1 2112 2196 33003663 33003748 1.040000e-29 141.0
19 TraesCS6B01G082200 chr6D 86.594 1007 76 40 859 1825 29392313 29391326 0.000000e+00 1057.0
20 TraesCS6B01G082200 chr6D 87.179 897 90 13 30 905 29393210 29392318 0.000000e+00 996.0
21 TraesCS6B01G082200 chr6D 87.646 599 46 21 1224 1811 28688071 28688652 0.000000e+00 671.0
22 TraesCS6B01G082200 chr6D 95.349 86 3 1 2112 2196 29389422 29389337 4.840000e-28 135.0
23 TraesCS6B01G082200 chr6D 100.000 33 0 0 1 33 29734628 29734596 8.330000e-06 62.1
24 TraesCS6B01G082200 chr1D 91.239 468 31 6 1224 1688 321704952 321704492 1.820000e-176 628.0
25 TraesCS6B01G082200 chr1D 90.385 156 14 1 1905 2059 393297271 393297426 1.310000e-48 204.0
26 TraesCS6B01G082200 chr1A 91.026 468 37 4 1224 1690 400975349 400974886 6.550000e-176 627.0
27 TraesCS6B01G082200 chr1B 82.869 753 74 25 982 1690 434408804 434409545 2.360000e-175 625.0
28 TraesCS6B01G082200 chr1B 87.866 239 22 2 1909 2146 426931007 426930775 9.830000e-70 274.0
29 TraesCS6B01G082200 chrUn 89.121 239 19 2 1909 2146 68837710 68837478 9.770000e-75 291.0
30 TraesCS6B01G082200 chrUn 85.135 74 7 2 589 658 332816838 332816911 3.850000e-09 73.1
31 TraesCS6B01G082200 chrUn 85.135 74 7 2 589 658 332825214 332825287 3.850000e-09 73.1
32 TraesCS6B01G082200 chrUn 75.294 170 32 7 589 748 343436192 343436023 3.850000e-09 73.1
33 TraesCS6B01G082200 chr5B 87.654 243 23 2 1905 2146 606627543 606627779 2.730000e-70 276.0
34 TraesCS6B01G082200 chr2B 85.263 95 10 2 1731 1825 2243949 2243859 8.220000e-16 95.3
35 TraesCS6B01G082200 chr3D 84.884 86 10 2 1740 1825 19667309 19667227 1.780000e-12 84.2
36 TraesCS6B01G082200 chr2D 75.691 181 35 5 590 761 24221051 24221231 6.400000e-12 82.4
37 TraesCS6B01G082200 chr2D 79.167 120 16 6 547 658 23079675 23079793 1.070000e-09 75.0
38 TraesCS6B01G082200 chr4D 83.721 86 10 2 1740 1825 273376549 273376468 8.280000e-11 78.7
39 TraesCS6B01G082200 chr4A 87.931 58 3 4 987 1042 23611515 23611460 6.440000e-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 TraesCS6B01G082200 chr6B 59025160 59027946 2786 False 5147.000000 5147 100.000000 1 2787 1 chr6B.!!$F2 2786
1 TraesCS6B01G082200 chr6B 58308716 58312413 3697 False 875.750000 1315 90.770750 30 2784 4 chr6B.!!$F5 2754
2 TraesCS6B01G082200 chr6B 58777632 58779715 2083 False 511.000000 867 90.621000 1060 2784 3 chr6B.!!$F6 1724
3 TraesCS6B01G082200 chr6B 61795411 61796058 647 True 441.000000 741 92.022500 1224 1811 2 chr6B.!!$R2 587
4 TraesCS6B01G082200 chr6A 33963586 33964464 878 True 806.000000 806 84.122000 985 1823 1 chr6A.!!$R1 838
5 TraesCS6B01G082200 chr6A 32938468 32939197 729 False 747.000000 747 85.422000 30 749 1 chr6A.!!$F1 719
6 TraesCS6B01G082200 chr6A 33000279 33003748 3469 False 745.000000 1081 90.581000 30 2196 3 chr6A.!!$F2 2166
7 TraesCS6B01G082200 chr6D 29389337 29393210 3873 True 729.333333 1057 89.707333 30 2196 3 chr6D.!!$R2 2166
8 TraesCS6B01G082200 chr6D 28688071 28688652 581 False 671.000000 671 87.646000 1224 1811 1 chr6D.!!$F1 587
9 TraesCS6B01G082200 chr1B 434408804 434409545 741 False 625.000000 625 82.869000 982 1690 1 chr1B.!!$F1 708

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
899 955 0.66102 AAACGACAGTCTTTTGGGCG 59.339 50.0 4.28 0.0 0.0 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2600 5011 1.16342 TGTTCTTGTGCGGCATTCGT 61.163 50.0 5.72 0.0 41.72 3.85 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
108 109 1.301479 GACGATATGGGGCGGGAAC 60.301 63.158 0.00 0.00 0.00 3.62
109 110 2.035237 GACGATATGGGGCGGGAACA 62.035 60.000 0.00 0.00 0.00 3.18
137 139 3.266964 GTGCAAATCAGGCAGCGA 58.733 55.556 0.00 0.00 42.85 4.93
183 195 2.687200 TCATGGCGGTGGCTACCT 60.687 61.111 18.03 0.00 45.22 3.08
224 238 2.141011 CTGAGGGTGGGTGGCAATCA 62.141 60.000 0.00 0.00 0.00 2.57
252 276 4.736631 GTGCGGCGGCGAGTTTTC 62.737 66.667 36.87 16.62 44.10 2.29
253 277 4.980805 TGCGGCGGCGAGTTTTCT 62.981 61.111 36.87 0.00 44.10 2.52
254 278 4.148645 GCGGCGGCGAGTTTTCTC 62.149 66.667 36.87 10.85 43.01 2.87
255 279 3.488090 CGGCGGCGAGTTTTCTCC 61.488 66.667 29.19 0.00 43.49 3.71
286 310 2.156051 GAAGTGAAGGCGGGTCGAGT 62.156 60.000 0.00 0.00 0.00 4.18
297 321 1.729284 GGGTCGAGTAATGCGGAAAA 58.271 50.000 0.00 0.00 0.00 2.29
481 509 2.951229 AGGGAATTTGTTGAGGACGT 57.049 45.000 0.00 0.00 0.00 4.34
528 556 5.505780 TCAGGGGATGAACAATAAAATCGT 58.494 37.500 0.00 0.00 34.02 3.73
585 622 4.649845 TGCTCCTGCATGTGATGG 57.350 55.556 0.00 0.00 45.31 3.51
587 624 1.453379 GCTCCTGCATGTGATGGCT 60.453 57.895 0.00 0.00 39.41 4.75
599 636 3.806380 TGTGATGGCTGTGCAAAATTTT 58.194 36.364 0.00 0.00 0.00 1.82
703 748 3.577649 TTTTGTCGTTTCTGCCACAAA 57.422 38.095 0.00 0.00 37.04 2.83
709 754 2.354510 TCGTTTCTGCCACAAACTTCTG 59.645 45.455 0.00 0.00 32.46 3.02
736 784 5.045869 TCCAAACACCCCAAAATTTTACACA 60.046 36.000 2.44 0.00 0.00 3.72
749 797 4.403015 TTTTACACAGACATCACGCATG 57.597 40.909 0.00 0.00 38.64 4.06
778 826 9.903682 AGCATCTTGGATGAAAAATAATAATCG 57.096 29.630 11.16 0.00 0.00 3.34
832 888 2.146342 CTGTTCACCGTTTGAGCATCT 58.854 47.619 2.02 0.00 43.76 2.90
844 900 7.028962 CCGTTTGAGCATCTTTTGAATTATCA 58.971 34.615 0.00 0.00 34.92 2.15
899 955 0.661020 AAACGACAGTCTTTTGGGCG 59.339 50.000 4.28 0.00 0.00 6.13
905 961 2.040544 AGTCTTTTGGGCGCATCCG 61.041 57.895 10.83 0.00 34.94 4.18
921 1085 4.233789 GCATCCGTTTTGCTACAAATTGA 58.766 39.130 0.00 0.00 37.14 2.57
973 1144 8.943002 ACCAACCAATCGTTACTTATAAAGAAG 58.057 33.333 0.00 0.00 33.33 2.85
1080 1262 2.109126 GGCTGGCAGATCCAACGAC 61.109 63.158 20.86 0.00 46.01 4.34
1114 1296 0.817634 CCTTCCCGAAACACACAGCA 60.818 55.000 0.00 0.00 0.00 4.41
1115 1297 1.238439 CTTCCCGAAACACACAGCAT 58.762 50.000 0.00 0.00 0.00 3.79
1122 1304 3.155998 CGAAACACACAGCATCGAAATC 58.844 45.455 0.00 0.00 35.65 2.17
1132 1322 1.524621 ATCGAAATCTGGCCAGGCG 60.525 57.895 32.23 26.74 0.00 5.52
1133 1323 1.971505 ATCGAAATCTGGCCAGGCGA 61.972 55.000 32.23 30.24 0.00 5.54
1161 1360 4.324641 GCCCACTCCTCTTCTCCTTAAAAT 60.325 45.833 0.00 0.00 0.00 1.82
1704 2029 5.582665 GTGTAGAGATCTTGTTGTGATTCCC 59.417 44.000 0.00 0.00 0.00 3.97
1713 2038 1.060729 TTGTGATTCCCCGTTCCAGA 58.939 50.000 0.00 0.00 0.00 3.86
1726 2066 5.238650 CCCCGTTCCAGATAATGTTATGTTC 59.761 44.000 0.00 0.00 0.00 3.18
1784 2124 4.630644 TCTGAATCAAAGTTGGCTCTCT 57.369 40.909 0.00 0.00 0.00 3.10
1825 2167 4.101942 GTTCTTGTGACGCATTTTGTTGA 58.898 39.130 0.00 0.00 0.00 3.18
1826 2168 3.690422 TCTTGTGACGCATTTTGTTGAC 58.310 40.909 0.00 0.00 0.00 3.18
1828 2170 3.332761 TGTGACGCATTTTGTTGACTC 57.667 42.857 0.00 0.00 0.00 3.36
1830 2172 3.002246 TGTGACGCATTTTGTTGACTCTC 59.998 43.478 0.00 0.00 0.00 3.20
1831 2173 2.220824 TGACGCATTTTGTTGACTCTCG 59.779 45.455 0.00 0.00 0.00 4.04
1832 2174 1.531149 ACGCATTTTGTTGACTCTCGG 59.469 47.619 0.00 0.00 0.00 4.63
1833 2175 1.135972 CGCATTTTGTTGACTCTCGGG 60.136 52.381 0.00 0.00 0.00 5.14
1834 2176 2.151202 GCATTTTGTTGACTCTCGGGA 58.849 47.619 0.00 0.00 0.00 5.14
1836 2178 3.181506 GCATTTTGTTGACTCTCGGGATC 60.182 47.826 0.00 0.00 0.00 3.36
1838 2180 3.319137 TTTGTTGACTCTCGGGATCAG 57.681 47.619 0.00 0.00 0.00 2.90
1840 2182 2.095461 TGTTGACTCTCGGGATCAGAG 58.905 52.381 10.22 10.22 42.84 3.35
1842 2184 2.755655 GTTGACTCTCGGGATCAGAGAA 59.244 50.000 17.26 4.58 43.30 2.87
1843 2185 3.304911 TGACTCTCGGGATCAGAGAAT 57.695 47.619 17.26 10.33 43.30 2.40
1844 2186 3.218453 TGACTCTCGGGATCAGAGAATC 58.782 50.000 16.84 16.84 43.30 2.52
1846 2188 3.634448 GACTCTCGGGATCAGAGAATCAA 59.366 47.826 18.05 1.69 43.30 2.57
1847 2189 3.383185 ACTCTCGGGATCAGAGAATCAAC 59.617 47.826 17.26 0.00 43.30 3.18
1848 2190 3.636300 CTCTCGGGATCAGAGAATCAACT 59.364 47.826 17.26 0.00 43.30 3.16
1849 2191 4.026744 TCTCGGGATCAGAGAATCAACTT 58.973 43.478 15.14 0.00 41.29 2.66
1852 2194 4.222810 TCGGGATCAGAGAATCAACTTTGA 59.777 41.667 0.00 0.00 42.14 2.69
1853 2195 4.331168 CGGGATCAGAGAATCAACTTTGAC 59.669 45.833 0.00 0.00 40.49 3.18
1854 2196 5.248640 GGGATCAGAGAATCAACTTTGACA 58.751 41.667 0.00 0.00 40.49 3.58
1855 2197 5.707298 GGGATCAGAGAATCAACTTTGACAA 59.293 40.000 0.00 0.00 40.49 3.18
1856 2198 6.376581 GGGATCAGAGAATCAACTTTGACAAT 59.623 38.462 0.00 0.00 40.49 2.71
1857 2199 7.414984 GGGATCAGAGAATCAACTTTGACAATC 60.415 40.741 0.00 0.00 40.49 2.67
1858 2200 7.120285 GGATCAGAGAATCAACTTTGACAATCA 59.880 37.037 0.00 0.00 40.49 2.57
1859 2201 7.194607 TCAGAGAATCAACTTTGACAATCAC 57.805 36.000 0.00 0.00 40.49 3.06
1860 2202 6.205464 TCAGAGAATCAACTTTGACAATCACC 59.795 38.462 0.00 0.00 40.49 4.02
1861 2203 6.206243 CAGAGAATCAACTTTGACAATCACCT 59.794 38.462 0.00 0.00 40.49 4.00
1868 3278 8.099364 TCAACTTTGACAATCACCTTAGATTC 57.901 34.615 0.00 0.00 32.44 2.52
1876 3286 6.240894 ACAATCACCTTAGATTCAGCAAAGA 58.759 36.000 0.00 0.00 36.13 2.52
1877 3287 6.716628 ACAATCACCTTAGATTCAGCAAAGAA 59.283 34.615 0.00 0.00 36.13 2.52
1878 3288 6.998968 ATCACCTTAGATTCAGCAAAGAAG 57.001 37.500 0.00 0.00 0.00 2.85
1880 3290 4.013050 ACCTTAGATTCAGCAAAGAAGCC 58.987 43.478 0.00 0.00 34.59 4.35
1882 3292 4.643784 CCTTAGATTCAGCAAAGAAGCCAT 59.356 41.667 0.00 0.00 34.59 4.40
1885 3295 5.479124 AGATTCAGCAAAGAAGCCATTTT 57.521 34.783 0.00 0.00 34.59 1.82
1886 3296 5.235516 AGATTCAGCAAAGAAGCCATTTTG 58.764 37.500 0.00 1.31 34.59 2.44
1889 3299 3.132646 TCAGCAAAGAAGCCATTTTGTGT 59.867 39.130 6.36 0.00 36.81 3.72
1891 3301 4.025480 CAGCAAAGAAGCCATTTTGTGTTC 60.025 41.667 6.36 0.00 36.81 3.18
1894 3304 5.502869 GCAAAGAAGCCATTTTGTGTTCTTG 60.503 40.000 0.00 0.00 34.92 3.02
1896 3306 4.685924 AGAAGCCATTTTGTGTTCTTGTG 58.314 39.130 0.00 0.00 0.00 3.33
1897 3307 4.402155 AGAAGCCATTTTGTGTTCTTGTGA 59.598 37.500 0.00 0.00 0.00 3.58
1898 3308 4.734398 AGCCATTTTGTGTTCTTGTGAA 57.266 36.364 0.00 0.00 0.00 3.18
1921 4266 3.066342 GCCAATGAGTCTGATGAACATGG 59.934 47.826 0.00 0.00 0.00 3.66
2092 4441 1.133976 GTTCAGTATGCCCCTGCTCAT 60.134 52.381 0.00 0.00 38.71 2.90
2107 4456 4.098960 CCTGCTCATTTAATTCAGGCACAT 59.901 41.667 5.23 0.00 38.00 3.21
2213 4589 5.702065 TGCTAATGTATCCCCACTAACAA 57.298 39.130 0.00 0.00 0.00 2.83
2343 4730 5.304614 TGCTAGGAGTTCATACTGGATTACC 59.695 44.000 0.00 0.00 33.84 2.85
2366 4753 1.077169 GGAGGGGATTTTTGTCCTGGT 59.923 52.381 0.00 0.00 38.38 4.00
2455 4842 6.481954 ACTCTAGCGTGAAACTTTATTTGG 57.518 37.500 0.00 0.00 31.75 3.28
2600 5011 3.227614 TGAGTACAGTACAGAAGGCACA 58.772 45.455 13.37 0.00 0.00 4.57
2693 5104 7.235399 TCACCTGTGATAATCATCTTAGCCATA 59.765 37.037 0.00 0.00 34.14 2.74
2702 5113 3.069586 TCATCTTAGCCATACTCGGTTGG 59.930 47.826 0.00 0.00 36.03 3.77
2784 5204 7.149351 CGTTACTCTTACAACGCAATTTTGAAG 60.149 37.037 0.00 0.00 40.76 3.02
2785 5205 6.371809 ACTCTTACAACGCAATTTTGAAGA 57.628 33.333 0.00 1.24 0.00 2.87
2786 5206 6.970484 ACTCTTACAACGCAATTTTGAAGAT 58.030 32.000 0.00 0.00 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 9.739276 ATGTACCAATTTGTTTCTCTATTGAGA 57.261 29.630 2.49 2.49 46.58 3.27
45 46 8.817100 CACTAGCGAAAGTTATGTGAATTATCA 58.183 33.333 0.00 0.00 32.28 2.15
46 47 8.276325 CCACTAGCGAAAGTTATGTGAATTATC 58.724 37.037 0.00 0.00 32.28 1.75
50 51 4.332819 GCCACTAGCGAAAGTTATGTGAAT 59.667 41.667 0.00 0.00 32.28 2.57
53 54 3.658351 GCCACTAGCGAAAGTTATGTG 57.342 47.619 0.00 0.00 0.00 3.21
108 109 2.228582 TGATTTGCACCGATTCTGGTTG 59.771 45.455 0.00 0.00 41.38 3.77
109 110 2.489329 CTGATTTGCACCGATTCTGGTT 59.511 45.455 0.00 0.00 41.38 3.67
183 195 1.985662 CGTAGCCACCCCACCACTA 60.986 63.158 0.00 0.00 0.00 2.74
246 270 1.630878 AGGCCGATTCTGGAGAAAACT 59.369 47.619 0.00 0.00 37.61 2.66
247 271 1.740025 CAGGCCGATTCTGGAGAAAAC 59.260 52.381 0.00 0.00 37.61 2.43
248 272 1.628340 TCAGGCCGATTCTGGAGAAAA 59.372 47.619 0.00 0.00 37.61 2.29
249 273 1.275666 TCAGGCCGATTCTGGAGAAA 58.724 50.000 0.00 0.00 37.61 2.52
250 274 1.208052 CTTCAGGCCGATTCTGGAGAA 59.792 52.381 0.00 0.00 39.60 2.87
251 275 0.826715 CTTCAGGCCGATTCTGGAGA 59.173 55.000 0.00 0.00 39.60 3.71
252 276 0.539051 ACTTCAGGCCGATTCTGGAG 59.461 55.000 0.00 0.00 42.19 3.86
253 277 0.250234 CACTTCAGGCCGATTCTGGA 59.750 55.000 0.00 0.00 33.36 3.86
254 278 0.250234 TCACTTCAGGCCGATTCTGG 59.750 55.000 0.00 0.00 33.36 3.86
255 279 2.005451 CTTCACTTCAGGCCGATTCTG 58.995 52.381 0.00 0.00 0.00 3.02
286 310 4.946772 TGATGAGGTGAATTTTCCGCATTA 59.053 37.500 15.72 11.30 42.48 1.90
297 321 3.350833 GAAGCCAACTGATGAGGTGAAT 58.649 45.455 0.00 0.00 39.56 2.57
410 435 3.828451 CCCTATTCATATTTGGTGCCCAG 59.172 47.826 0.00 0.00 33.81 4.45
481 509 3.417101 CCGGGTGCATATTAATTAGCCA 58.583 45.455 0.00 0.00 0.00 4.75
578 615 3.472283 AAATTTTGCACAGCCATCACA 57.528 38.095 0.00 0.00 0.00 3.58
585 622 6.852345 CCAAACTTCATAAAATTTTGCACAGC 59.148 34.615 13.76 0.00 0.00 4.40
587 624 7.550551 TGTCCAAACTTCATAAAATTTTGCACA 59.449 29.630 13.76 0.00 27.89 4.57
599 636 5.945784 CCTCCTTGAATGTCCAAACTTCATA 59.054 40.000 0.00 0.00 0.00 2.15
639 676 0.547075 TGTTCCTCAAACACCCGGAA 59.453 50.000 0.73 0.00 42.95 4.30
671 716 3.555917 ACGACAAAAACGGTTGTGAAA 57.444 38.095 11.17 0.00 41.78 2.69
709 754 5.906113 AAAATTTTGGGGTGTTTGGAAAC 57.094 34.783 1.75 0.00 39.33 2.78
736 784 2.169789 GCTCGCATGCGTGATGTCT 61.170 57.895 37.76 0.00 40.74 3.41
749 797 3.492421 TTTTTCATCCAAGATGCTCGC 57.508 42.857 0.00 0.00 0.00 5.03
805 860 4.675114 GCTCAAACGGTGAACAGTAAAATG 59.325 41.667 0.00 0.00 35.22 2.32
844 900 4.923281 GCCGAAAATACTGCTCAACAATTT 59.077 37.500 0.00 0.00 0.00 1.82
846 902 3.119495 GGCCGAAAATACTGCTCAACAAT 60.119 43.478 0.00 0.00 0.00 2.71
899 955 4.233789 TCAATTTGTAGCAAAACGGATGC 58.766 39.130 0.00 1.61 44.15 3.91
905 961 8.922058 AGATCATCATCAATTTGTAGCAAAAC 57.078 30.769 0.00 0.00 0.00 2.43
940 1104 1.078708 CGATTGGTTGGTAGCCGGT 60.079 57.895 1.90 0.00 0.00 5.28
973 1144 5.614013 CGTTCTGATTGGTTAGTCGGTTTTC 60.614 44.000 0.00 0.00 0.00 2.29
978 1149 1.659098 GCGTTCTGATTGGTTAGTCGG 59.341 52.381 0.00 0.00 0.00 4.79
979 1150 2.333926 TGCGTTCTGATTGGTTAGTCG 58.666 47.619 0.00 0.00 0.00 4.18
980 1151 2.673368 CCTGCGTTCTGATTGGTTAGTC 59.327 50.000 0.00 0.00 0.00 2.59
1080 1262 0.038310 GAAGGGGAGGTGAGTTTGGG 59.962 60.000 0.00 0.00 0.00 4.12
1114 1296 1.524621 CGCCTGGCCAGATTTCGAT 60.525 57.895 34.91 0.00 0.00 3.59
1115 1297 2.125147 CGCCTGGCCAGATTTCGA 60.125 61.111 34.91 0.00 0.00 3.71
1278 1527 4.357279 GGTGGCCAGCTGCTTCCT 62.357 66.667 27.63 0.00 40.92 3.36
1704 2029 7.926555 ACTAGAACATAACATTATCTGGAACGG 59.073 37.037 0.00 0.00 0.00 4.44
1770 2110 3.933955 CAGAGATCAGAGAGCCAACTTTG 59.066 47.826 0.00 0.00 0.00 2.77
1784 2124 5.624159 AGAACACAAAATGGACAGAGATCA 58.376 37.500 0.00 0.00 0.00 2.92
1825 2167 3.304911 TGATTCTCTGATCCCGAGAGT 57.695 47.619 10.55 8.69 38.62 3.24
1826 2168 3.636300 AGTTGATTCTCTGATCCCGAGAG 59.364 47.826 10.55 6.98 38.62 3.20
1828 2170 4.399004 AAGTTGATTCTCTGATCCCGAG 57.601 45.455 3.39 3.39 0.00 4.63
1830 2172 4.331168 GTCAAAGTTGATTCTCTGATCCCG 59.669 45.833 0.00 0.00 39.73 5.14
1831 2173 5.248640 TGTCAAAGTTGATTCTCTGATCCC 58.751 41.667 0.00 0.00 39.73 3.85
1832 2174 6.808008 TTGTCAAAGTTGATTCTCTGATCC 57.192 37.500 0.00 0.00 39.73 3.36
1833 2175 7.961827 GTGATTGTCAAAGTTGATTCTCTGATC 59.038 37.037 0.00 0.00 39.73 2.92
1834 2176 7.094463 GGTGATTGTCAAAGTTGATTCTCTGAT 60.094 37.037 0.00 0.00 39.73 2.90
1836 2178 6.206243 AGGTGATTGTCAAAGTTGATTCTCTG 59.794 38.462 0.00 0.00 39.73 3.35
1838 2180 6.566197 AGGTGATTGTCAAAGTTGATTCTC 57.434 37.500 0.00 0.00 39.73 2.87
1840 2182 8.099364 TCTAAGGTGATTGTCAAAGTTGATTC 57.901 34.615 0.00 0.00 39.73 2.52
1842 2184 8.641498 AATCTAAGGTGATTGTCAAAGTTGAT 57.359 30.769 0.00 0.00 35.57 2.57
1843 2185 7.719193 TGAATCTAAGGTGATTGTCAAAGTTGA 59.281 33.333 0.00 0.00 36.86 3.18
1844 2186 7.874940 TGAATCTAAGGTGATTGTCAAAGTTG 58.125 34.615 0.00 0.00 36.86 3.16
1846 2188 6.150140 GCTGAATCTAAGGTGATTGTCAAAGT 59.850 38.462 0.00 0.00 36.86 2.66
1847 2189 6.149973 TGCTGAATCTAAGGTGATTGTCAAAG 59.850 38.462 0.00 0.00 36.86 2.77
1848 2190 6.003326 TGCTGAATCTAAGGTGATTGTCAAA 58.997 36.000 0.00 0.00 36.86 2.69
1849 2191 5.559770 TGCTGAATCTAAGGTGATTGTCAA 58.440 37.500 0.00 0.00 36.86 3.18
1852 2194 6.240894 TCTTTGCTGAATCTAAGGTGATTGT 58.759 36.000 0.00 0.00 36.86 2.71
1853 2195 6.748333 TCTTTGCTGAATCTAAGGTGATTG 57.252 37.500 0.00 0.00 36.86 2.67
1854 2196 6.127786 GCTTCTTTGCTGAATCTAAGGTGATT 60.128 38.462 0.00 0.00 39.14 2.57
1855 2197 5.356470 GCTTCTTTGCTGAATCTAAGGTGAT 59.644 40.000 0.00 0.00 0.00 3.06
1856 2198 4.697352 GCTTCTTTGCTGAATCTAAGGTGA 59.303 41.667 0.00 0.00 0.00 4.02
1857 2199 4.142513 GGCTTCTTTGCTGAATCTAAGGTG 60.143 45.833 0.00 0.00 0.00 4.00
1858 2200 4.013050 GGCTTCTTTGCTGAATCTAAGGT 58.987 43.478 0.00 0.00 0.00 3.50
1859 2201 4.012374 TGGCTTCTTTGCTGAATCTAAGG 58.988 43.478 0.00 0.00 0.00 2.69
1860 2202 5.831702 ATGGCTTCTTTGCTGAATCTAAG 57.168 39.130 0.00 0.00 0.00 2.18
1861 2203 6.594788 AAATGGCTTCTTTGCTGAATCTAA 57.405 33.333 0.00 0.00 0.00 2.10
1868 3278 3.460103 ACACAAAATGGCTTCTTTGCTG 58.540 40.909 6.48 6.85 36.24 4.41
1876 3286 4.734398 TCACAAGAACACAAAATGGCTT 57.266 36.364 0.00 0.00 0.00 4.35
1877 3287 4.685924 CTTCACAAGAACACAAAATGGCT 58.314 39.130 0.00 0.00 0.00 4.75
1878 3288 3.245990 GCTTCACAAGAACACAAAATGGC 59.754 43.478 0.00 0.00 0.00 4.40
1880 3290 4.431809 TGGCTTCACAAGAACACAAAATG 58.568 39.130 0.00 0.00 0.00 2.32
1882 3292 4.527509 TTGGCTTCACAAGAACACAAAA 57.472 36.364 0.00 0.00 0.00 2.44
1885 3295 3.286353 TCATTGGCTTCACAAGAACACA 58.714 40.909 0.00 0.00 33.23 3.72
1886 3296 3.316308 ACTCATTGGCTTCACAAGAACAC 59.684 43.478 0.00 0.00 33.23 3.32
1889 3299 3.817084 CAGACTCATTGGCTTCACAAGAA 59.183 43.478 0.00 0.00 33.23 2.52
1891 3301 3.405831 TCAGACTCATTGGCTTCACAAG 58.594 45.455 0.00 0.00 33.23 3.16
1894 3304 3.603532 TCATCAGACTCATTGGCTTCAC 58.396 45.455 0.00 0.00 0.00 3.18
1896 3306 4.005650 TGTTCATCAGACTCATTGGCTTC 58.994 43.478 0.00 0.00 0.00 3.86
1897 3307 4.025040 TGTTCATCAGACTCATTGGCTT 57.975 40.909 0.00 0.00 0.00 4.35
1898 3308 3.708403 TGTTCATCAGACTCATTGGCT 57.292 42.857 0.00 0.00 0.00 4.75
1921 4266 8.258708 ACTGAACTTTAGTATATGAAGGTCACC 58.741 37.037 8.50 0.00 44.00 4.02
2092 4441 4.406456 AGACCACATGTGCCTGAATTAAA 58.594 39.130 20.81 0.00 0.00 1.52
2107 4456 1.490490 ACAGCCAAAGAAGAGACCACA 59.510 47.619 0.00 0.00 0.00 4.17
2230 4607 4.545823 TTTTCCAACAGAACTACAAGCG 57.454 40.909 0.00 0.00 32.95 4.68
2343 4730 2.762327 CAGGACAAAAATCCCCTCCATG 59.238 50.000 0.00 0.00 39.91 3.66
2455 4842 3.561725 GGTATAGCAACTGAAGCATCCAC 59.438 47.826 0.00 0.00 0.00 4.02
2600 5011 1.163420 TGTTCTTGTGCGGCATTCGT 61.163 50.000 5.72 0.00 41.72 3.85
2693 5104 2.600769 AGAGCGACCCAACCGAGT 60.601 61.111 0.00 0.00 0.00 4.18


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

AutoCloner maintained by Alex Coulton.