Multiple sequence alignment - TraesCS5D01G432700

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 TraesCS5D01G432700 chr5D 100.000 2669 0 0 1 2669 488836809 488839477 0.000000e+00 4929.0
1 TraesCS5D01G432700 chr5D 86.516 838 97 10 865 1689 488783555 488784389 0.000000e+00 907.0
2 TraesCS5D01G432700 chr5D 88.978 744 57 14 1940 2659 378673327 378672585 0.000000e+00 896.0
3 TraesCS5D01G432700 chr5B 90.383 1934 113 30 54 1938 602137148 602139057 0.000000e+00 2473.0
4 TraesCS5D01G432700 chr5B 84.084 999 126 24 708 1686 602066680 602067665 0.000000e+00 933.0
5 TraesCS5D01G432700 chr5A 89.974 1157 67 30 764 1874 609812746 609813899 0.000000e+00 1448.0
6 TraesCS5D01G432700 chr5A 86.420 810 71 22 867 1668 609789713 609790491 0.000000e+00 850.0
7 TraesCS5D01G432700 chr5A 90.875 263 19 4 431 690 609812455 609812715 5.470000e-92 348.0
8 TraesCS5D01G432700 chr5A 89.286 84 4 3 233 316 76124967 76125045 1.690000e-17 100.0
9 TraesCS5D01G432700 chr1A 88.172 744 63 15 1940 2659 546220284 546221026 0.000000e+00 863.0
10 TraesCS5D01G432700 chr7D 87.110 737 71 13 1940 2656 38625038 38624306 0.000000e+00 813.0
11 TraesCS5D01G432700 chr7D 86.796 568 60 12 2100 2654 59987289 59986724 1.050000e-173 619.0
12 TraesCS5D01G432700 chr4A 86.667 735 72 13 1947 2657 26987921 26988653 0.000000e+00 791.0
13 TraesCS5D01G432700 chr6A 86.575 730 79 10 1936 2657 594235835 594236553 0.000000e+00 787.0
14 TraesCS5D01G432700 chr6A 79.096 177 34 3 15 190 77058008 77058182 4.670000e-23 119.0
15 TraesCS5D01G432700 chr2A 85.887 744 77 17 1939 2657 503471866 503472606 0.000000e+00 767.0
16 TraesCS5D01G432700 chr7B 85.542 747 79 17 1936 2657 2137601 2138343 0.000000e+00 754.0
17 TraesCS5D01G432700 chr2D 87.097 558 55 11 2106 2653 608563161 608563711 1.360000e-172 616.0
18 TraesCS5D01G432700 chr2D 91.935 124 9 1 1 124 347462997 347463119 3.530000e-39 172.0
19 TraesCS5D01G432700 chr2D 82.840 169 25 4 24 190 623270058 623269892 5.950000e-32 148.0
20 TraesCS5D01G432700 chr3D 80.707 679 121 9 1000 1670 482501344 482502020 1.100000e-143 520.0
21 TraesCS5D01G432700 chr3A 80.572 664 120 9 1012 1669 625405493 625406153 1.100000e-138 503.0
22 TraesCS5D01G432700 chr3B 83.957 187 15 7 4 190 69617826 69617997 5.910000e-37 165.0
23 TraesCS5D01G432700 chr3B 83.616 177 26 3 1000 1173 644839414 644839590 2.130000e-36 163.0
24 TraesCS5D01G432700 chr2B 90.164 122 10 2 3 124 412767220 412767339 9.890000e-35 158.0
25 TraesCS5D01G432700 chr4D 84.932 73 6 4 229 300 404676561 404676629 4.770000e-08 69.4


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 TraesCS5D01G432700 chr5D 488836809 488839477 2668 False 4929 4929 100.0000 1 2669 1 chr5D.!!$F2 2668
1 TraesCS5D01G432700 chr5D 488783555 488784389 834 False 907 907 86.5160 865 1689 1 chr5D.!!$F1 824
2 TraesCS5D01G432700 chr5D 378672585 378673327 742 True 896 896 88.9780 1940 2659 1 chr5D.!!$R1 719
3 TraesCS5D01G432700 chr5B 602137148 602139057 1909 False 2473 2473 90.3830 54 1938 1 chr5B.!!$F2 1884
4 TraesCS5D01G432700 chr5B 602066680 602067665 985 False 933 933 84.0840 708 1686 1 chr5B.!!$F1 978
5 TraesCS5D01G432700 chr5A 609812455 609813899 1444 False 898 1448 90.4245 431 1874 2 chr5A.!!$F3 1443
6 TraesCS5D01G432700 chr5A 609789713 609790491 778 False 850 850 86.4200 867 1668 1 chr5A.!!$F2 801
7 TraesCS5D01G432700 chr1A 546220284 546221026 742 False 863 863 88.1720 1940 2659 1 chr1A.!!$F1 719
8 TraesCS5D01G432700 chr7D 38624306 38625038 732 True 813 813 87.1100 1940 2656 1 chr7D.!!$R1 716
9 TraesCS5D01G432700 chr7D 59986724 59987289 565 True 619 619 86.7960 2100 2654 1 chr7D.!!$R2 554
10 TraesCS5D01G432700 chr4A 26987921 26988653 732 False 791 791 86.6670 1947 2657 1 chr4A.!!$F1 710
11 TraesCS5D01G432700 chr6A 594235835 594236553 718 False 787 787 86.5750 1936 2657 1 chr6A.!!$F2 721
12 TraesCS5D01G432700 chr2A 503471866 503472606 740 False 767 767 85.8870 1939 2657 1 chr2A.!!$F1 718
13 TraesCS5D01G432700 chr7B 2137601 2138343 742 False 754 754 85.5420 1936 2657 1 chr7B.!!$F1 721
14 TraesCS5D01G432700 chr2D 608563161 608563711 550 False 616 616 87.0970 2106 2653 1 chr2D.!!$F2 547
15 TraesCS5D01G432700 chr3D 482501344 482502020 676 False 520 520 80.7070 1000 1670 1 chr3D.!!$F1 670
16 TraesCS5D01G432700 chr3A 625405493 625406153 660 False 503 503 80.5720 1012 1669 1 chr3A.!!$F1 657

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
20 21 0.036765 GTGTGCGTGGGTAATGGAGA 60.037 55.0 0.0 0.0 0.0 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1797 1891 0.179067 ACTACCACCAACCACACACG 60.179 55.0 0.0 0.0 0.0 4.49 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
17 18 3.585856 GGTGTGCGTGGGTAATGG 58.414 61.111 0.00 0.00 0.00 3.16
18 19 1.003112 GGTGTGCGTGGGTAATGGA 60.003 57.895 0.00 0.00 0.00 3.41
19 20 1.024579 GGTGTGCGTGGGTAATGGAG 61.025 60.000 0.00 0.00 0.00 3.86
20 21 0.036765 GTGTGCGTGGGTAATGGAGA 60.037 55.000 0.00 0.00 0.00 3.71
21 22 0.687920 TGTGCGTGGGTAATGGAGAA 59.312 50.000 0.00 0.00 0.00 2.87
22 23 1.084289 GTGCGTGGGTAATGGAGAAC 58.916 55.000 0.00 0.00 0.00 3.01
23 24 0.390603 TGCGTGGGTAATGGAGAACG 60.391 55.000 0.00 0.00 0.00 3.95
24 25 0.108520 GCGTGGGTAATGGAGAACGA 60.109 55.000 0.00 0.00 33.03 3.85
25 26 1.922570 CGTGGGTAATGGAGAACGAG 58.077 55.000 0.00 0.00 33.03 4.18
26 27 1.470979 CGTGGGTAATGGAGAACGAGG 60.471 57.143 0.00 0.00 33.03 4.63
27 28 1.829222 GTGGGTAATGGAGAACGAGGA 59.171 52.381 0.00 0.00 0.00 3.71
28 29 2.108168 TGGGTAATGGAGAACGAGGAG 58.892 52.381 0.00 0.00 0.00 3.69
29 30 1.413077 GGGTAATGGAGAACGAGGAGG 59.587 57.143 0.00 0.00 0.00 4.30
30 31 2.385803 GGTAATGGAGAACGAGGAGGA 58.614 52.381 0.00 0.00 0.00 3.71
31 32 2.101082 GGTAATGGAGAACGAGGAGGAC 59.899 54.545 0.00 0.00 0.00 3.85
32 33 0.818296 AATGGAGAACGAGGAGGACG 59.182 55.000 0.00 0.00 0.00 4.79
33 34 1.038130 ATGGAGAACGAGGAGGACGG 61.038 60.000 0.00 0.00 34.93 4.79
34 35 2.416432 GGAGAACGAGGAGGACGGG 61.416 68.421 0.00 0.00 34.93 5.28
35 36 2.362632 AGAACGAGGAGGACGGGG 60.363 66.667 0.00 0.00 34.93 5.73
36 37 3.459063 GAACGAGGAGGACGGGGG 61.459 72.222 0.00 0.00 34.93 5.40
87 88 2.394563 GCTGCTGCTTTCTCCCGTC 61.395 63.158 8.53 0.00 36.03 4.79
92 93 1.372087 CTGCTTTCTCCCGTCCATGC 61.372 60.000 0.00 0.00 0.00 4.06
94 95 2.435938 TTTCTCCCGTCCATGCGC 60.436 61.111 0.00 0.00 0.00 6.09
111 112 2.281345 CGCAGGGGCATCTCCATC 60.281 66.667 0.00 0.00 41.24 3.51
113 114 2.760378 GCAGGGGCATCTCCATCCA 61.760 63.158 0.00 0.00 40.72 3.41
121 122 1.404391 GCATCTCCATCCACAAAGCAG 59.596 52.381 0.00 0.00 0.00 4.24
147 148 4.081972 AGCTAGTCCATATCTTGGTATGCG 60.082 45.833 0.00 0.00 46.52 4.73
160 161 1.153249 TATGCGGGCTGGTGCTTAC 60.153 57.895 0.00 0.00 39.59 2.34
216 217 8.584157 TGTCACAAAGCTTATATTGTTGGATTT 58.416 29.630 0.00 0.00 37.66 2.17
305 306 6.405278 AATTTGACCCAAACTACAAAGAGG 57.595 37.500 0.00 0.00 36.13 3.69
319 320 7.621796 ACTACAAAGAGGACTAATAAACCAGG 58.378 38.462 0.00 0.00 0.00 4.45
324 325 6.793505 AGAGGACTAATAAACCAGGTAGTG 57.206 41.667 0.00 0.00 0.00 2.74
335 336 3.154827 CCAGGTAGTGGTTGATTTGGT 57.845 47.619 0.00 0.00 42.17 3.67
341 342 2.328319 AGTGGTTGATTTGGTGCCAAT 58.672 42.857 4.32 0.00 35.70 3.16
347 348 4.111916 GTTGATTTGGTGCCAATAATCGG 58.888 43.478 4.32 0.00 35.70 4.18
418 419 4.103153 AGTTCTCACCCATCTCTCAACAAA 59.897 41.667 0.00 0.00 0.00 2.83
419 420 4.705110 TCTCACCCATCTCTCAACAAAA 57.295 40.909 0.00 0.00 0.00 2.44
423 424 4.022068 TCACCCATCTCTCAACAAAATTGC 60.022 41.667 0.00 0.00 0.00 3.56
427 428 6.095377 CCCATCTCTCAACAAAATTGCTAAC 58.905 40.000 0.00 0.00 0.00 2.34
442 443 4.053469 TGCTAACTTTTGGCAACTTTCC 57.947 40.909 0.00 0.00 44.47 3.13
484 485 8.087750 TCTTGGCATCAAACCAAAAATAACTAG 58.912 33.333 0.00 0.00 46.24 2.57
579 591 0.041090 TCTTTTCCCCAATCCCAGGC 59.959 55.000 0.00 0.00 0.00 4.85
583 595 1.574526 TTCCCCAATCCCAGGCTCAG 61.575 60.000 0.00 0.00 0.00 3.35
600 612 2.336809 GCGATCTTCTCCGCCGAT 59.663 61.111 0.00 0.00 45.06 4.18
601 613 1.731257 GCGATCTTCTCCGCCGATC 60.731 63.158 0.00 0.00 45.06 3.69
701 713 1.604378 CTCGTGCTGGGATTCCCTT 59.396 57.895 22.38 0.00 45.70 3.95
702 714 0.462759 CTCGTGCTGGGATTCCCTTC 60.463 60.000 22.38 13.81 45.70 3.46
710 722 3.044703 GGATTCCCTTCCCTTCCCT 57.955 57.895 0.00 0.00 0.00 4.20
711 723 1.309876 GGATTCCCTTCCCTTCCCTT 58.690 55.000 0.00 0.00 0.00 3.95
712 724 1.646447 GGATTCCCTTCCCTTCCCTTT 59.354 52.381 0.00 0.00 0.00 3.11
715 727 1.071314 TCCCTTCCCTTCCCTTTGCA 61.071 55.000 0.00 0.00 0.00 4.08
717 729 1.244019 CCTTCCCTTCCCTTTGCACG 61.244 60.000 0.00 0.00 0.00 5.34
753 765 3.268603 CGCAAGCGGTGACACACA 61.269 61.111 8.08 0.00 35.86 3.72
793 809 1.153289 CAGAATCCTCCAGCCGGTG 60.153 63.158 1.90 0.00 0.00 4.94
905 936 3.079843 CCCTCTCCCCTATAAATCCTCCT 59.920 52.174 0.00 0.00 0.00 3.69
909 940 4.675065 TCTCCCCTATAAATCCTCCTCTCA 59.325 45.833 0.00 0.00 0.00 3.27
947 990 1.293963 CTCATCACCCACACAGCGTG 61.294 60.000 7.07 7.07 45.92 5.34
1706 1772 3.986006 CCATGCATGCGCCATCCC 61.986 66.667 21.69 0.00 37.32 3.85
1749 1830 2.332654 GCGTTTGGGTGGCCTACAG 61.333 63.158 3.32 0.00 0.00 2.74
1759 1840 1.080298 GGCCTACAGTGCGTACGTT 60.080 57.895 17.90 0.00 0.00 3.99
1761 1842 0.712222 GCCTACAGTGCGTACGTTTC 59.288 55.000 17.90 7.67 0.00 2.78
1763 1844 0.979811 CTACAGTGCGTACGTTTCGG 59.020 55.000 17.90 10.43 0.00 4.30
1764 1845 0.590682 TACAGTGCGTACGTTTCGGA 59.409 50.000 17.90 8.54 0.00 4.55
1765 1846 0.038892 ACAGTGCGTACGTTTCGGAT 60.039 50.000 17.90 0.00 0.00 4.18
1766 1847 1.199789 ACAGTGCGTACGTTTCGGATA 59.800 47.619 17.90 0.00 0.00 2.59
1769 1862 2.855963 AGTGCGTACGTTTCGGATATTG 59.144 45.455 17.90 0.00 0.00 1.90
1770 1863 2.853594 GTGCGTACGTTTCGGATATTGA 59.146 45.455 17.90 0.00 0.00 2.57
1783 1876 5.289595 TCGGATATTGATTTCTTCGTGGAG 58.710 41.667 0.00 0.00 0.00 3.86
1785 1878 5.175856 CGGATATTGATTTCTTCGTGGAGTC 59.824 44.000 0.00 0.00 0.00 3.36
1786 1879 6.284459 GGATATTGATTTCTTCGTGGAGTCT 58.716 40.000 0.00 0.00 0.00 3.24
1797 1891 1.699343 GTGGAGTCTAGTGTTCGTGC 58.301 55.000 0.00 0.00 0.00 5.34
1819 1913 1.282447 TGTGTGGTTGGTGGTAGTTGT 59.718 47.619 0.00 0.00 0.00 3.32
1824 1918 2.291670 TGGTTGGTGGTAGTTGTTTGGT 60.292 45.455 0.00 0.00 0.00 3.67
1826 1920 3.196039 GGTTGGTGGTAGTTGTTTGGTTT 59.804 43.478 0.00 0.00 0.00 3.27
1827 1921 4.322877 GGTTGGTGGTAGTTGTTTGGTTTT 60.323 41.667 0.00 0.00 0.00 2.43
1830 1924 4.283722 TGGTGGTAGTTGTTTGGTTTTGTT 59.716 37.500 0.00 0.00 0.00 2.83
1837 1931 6.334102 AGTTGTTTGGTTTTGTTAGTGTGA 57.666 33.333 0.00 0.00 0.00 3.58
1844 1938 3.545426 GGTTTTGTTAGTGTGAGTGCGTC 60.545 47.826 0.00 0.00 0.00 5.19
1845 1939 1.483316 TTGTTAGTGTGAGTGCGTCG 58.517 50.000 0.00 0.00 0.00 5.12
1851 1956 3.036084 GTGAGTGCGTCGTGGGTG 61.036 66.667 0.00 0.00 0.00 4.61
1859 1964 2.735857 GTCGTGGGTGCCGTGTAC 60.736 66.667 0.00 0.00 0.00 2.90
1860 1965 2.913578 TCGTGGGTGCCGTGTACT 60.914 61.111 0.00 0.00 0.00 2.73
1861 1966 2.431942 CGTGGGTGCCGTGTACTC 60.432 66.667 0.00 0.00 0.00 2.59
1862 1967 2.047560 GTGGGTGCCGTGTACTCC 60.048 66.667 0.00 0.00 0.00 3.85
1880 2005 1.277842 TCCTGTGTGTGTGTCAAGTGT 59.722 47.619 0.00 0.00 0.00 3.55
1883 2008 1.198867 TGTGTGTGTGTCAAGTGTTGC 59.801 47.619 0.00 0.00 0.00 4.17
1886 2011 0.808125 TGTGTGTCAAGTGTTGCCAC 59.192 50.000 0.00 0.00 42.17 5.01
1890 2015 1.360192 GTCAAGTGTTGCCACCTGC 59.640 57.895 0.00 0.00 42.88 4.85
1895 2020 1.210155 GTGTTGCCACCTGCGATTC 59.790 57.895 0.00 0.00 45.60 2.52
1901 2026 0.532115 GCCACCTGCGATTCCATTTT 59.468 50.000 0.00 0.00 0.00 1.82
1928 2053 6.912203 TCCGTGCGATGAATAAATTAAGAA 57.088 33.333 0.00 0.00 0.00 2.52
1999 2124 4.373116 GCGGCCCGACACTTCAGA 62.373 66.667 7.68 0.00 0.00 3.27
2006 2131 3.312697 GGCCCGACACTTCAGATAATTTC 59.687 47.826 0.00 0.00 0.00 2.17
2014 2140 7.543868 CGACACTTCAGATAATTTCTTGTCTCT 59.456 37.037 12.83 0.00 36.77 3.10
2058 2184 7.565398 TCATCTAGTAGTCCCTTTTTCTGCTAT 59.435 37.037 0.00 0.00 0.00 2.97
2069 2195 9.474313 TCCCTTTTTCTGCTATGTATTAAATGT 57.526 29.630 0.00 0.00 0.00 2.71
2090 2232 8.727100 AATGTCAACATATGTATCTCCTCCTA 57.273 34.615 9.21 0.00 35.10 2.94
2158 2301 3.689649 AGGCATAACTTTCAATCCGTGTC 59.310 43.478 0.00 0.00 0.00 3.67
2160 2303 4.156008 GGCATAACTTTCAATCCGTGTCTT 59.844 41.667 0.00 0.00 0.00 3.01
2257 2401 3.196469 TGATGAACTAGTCTTCCTGCCAG 59.804 47.826 0.00 0.00 30.90 4.85
2301 2447 2.359354 ACTACATGCCGCGCCAAA 60.359 55.556 0.00 0.00 0.00 3.28
2309 2455 1.009675 GCCGCGCCAAATGAGTATG 60.010 57.895 0.00 0.00 0.00 2.39
2319 2469 5.619757 CGCCAAATGAGTATGTGTGTCAATT 60.620 40.000 0.00 0.00 0.00 2.32
2326 2476 6.061441 TGAGTATGTGTGTCAATTGTCCTTT 58.939 36.000 5.13 0.00 0.00 3.11
2428 2586 5.532779 TGCCAACTAAACATCAATGTGTGTA 59.467 36.000 0.00 0.00 41.61 2.90
2440 2598 8.531982 ACATCAATGTGTGTACAACTAGACTAT 58.468 33.333 0.00 0.00 40.84 2.12
2445 2603 9.817809 AATGTGTGTACAACTAGACTATATTGG 57.182 33.333 0.00 0.00 40.84 3.16
2491 2649 2.095059 GCAATTAGTGTCCTGCCAACTG 60.095 50.000 0.00 0.00 0.00 3.16
2541 2699 9.238368 ACTAAATTACAAGCCAACTAAGCATAA 57.762 29.630 0.00 0.00 0.00 1.90
2568 2726 2.040278 TGCAACTAGTCCTTCTGCCAAT 59.960 45.455 12.70 0.00 31.92 3.16
2605 2765 9.577110 TGTGTGTAACTATACTACATTACAAGC 57.423 33.333 0.00 0.00 38.79 4.01
2659 2820 5.817816 ACTATATTACAAGCCAACTGAGCAC 59.182 40.000 0.00 0.00 0.00 4.40
2660 2821 2.340210 TTACAAGCCAACTGAGCACA 57.660 45.000 0.00 0.00 0.00 4.57
2661 2822 2.340210 TACAAGCCAACTGAGCACAA 57.660 45.000 0.00 0.00 0.00 3.33
2662 2823 1.473258 ACAAGCCAACTGAGCACAAA 58.527 45.000 0.00 0.00 0.00 2.83
2663 2824 1.406539 ACAAGCCAACTGAGCACAAAG 59.593 47.619 0.00 0.00 0.00 2.77
2664 2825 1.406539 CAAGCCAACTGAGCACAAAGT 59.593 47.619 0.00 0.00 0.00 2.66
2665 2826 2.618241 CAAGCCAACTGAGCACAAAGTA 59.382 45.455 0.00 0.00 0.00 2.24
2666 2827 2.498167 AGCCAACTGAGCACAAAGTAG 58.502 47.619 0.00 0.00 0.00 2.57
2667 2828 1.068954 GCCAACTGAGCACAAAGTAGC 60.069 52.381 0.00 0.00 0.00 3.58
2668 2829 2.498167 CCAACTGAGCACAAAGTAGCT 58.502 47.619 0.00 0.00 45.25 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 0.036765 TCTCCATTACCCACGCACAC 60.037 55.000 0.00 0.00 0.00 3.82
6 7 1.470979 CCTCGTTCTCCATTACCCACG 60.471 57.143 0.00 0.00 0.00 4.94
7 8 1.829222 TCCTCGTTCTCCATTACCCAC 59.171 52.381 0.00 0.00 0.00 4.61
8 9 2.108168 CTCCTCGTTCTCCATTACCCA 58.892 52.381 0.00 0.00 0.00 4.51
9 10 1.413077 CCTCCTCGTTCTCCATTACCC 59.587 57.143 0.00 0.00 0.00 3.69
10 11 2.101082 GTCCTCCTCGTTCTCCATTACC 59.899 54.545 0.00 0.00 0.00 2.85
11 12 2.223525 CGTCCTCCTCGTTCTCCATTAC 60.224 54.545 0.00 0.00 0.00 1.89
12 13 2.022195 CGTCCTCCTCGTTCTCCATTA 58.978 52.381 0.00 0.00 0.00 1.90
13 14 0.818296 CGTCCTCCTCGTTCTCCATT 59.182 55.000 0.00 0.00 0.00 3.16
14 15 1.038130 CCGTCCTCCTCGTTCTCCAT 61.038 60.000 0.00 0.00 0.00 3.41
15 16 1.677966 CCGTCCTCCTCGTTCTCCA 60.678 63.158 0.00 0.00 0.00 3.86
16 17 2.416432 CCCGTCCTCCTCGTTCTCC 61.416 68.421 0.00 0.00 0.00 3.71
17 18 2.416432 CCCCGTCCTCCTCGTTCTC 61.416 68.421 0.00 0.00 0.00 2.87
18 19 2.362632 CCCCGTCCTCCTCGTTCT 60.363 66.667 0.00 0.00 0.00 3.01
19 20 3.459063 CCCCCGTCCTCCTCGTTC 61.459 72.222 0.00 0.00 0.00 3.95
44 45 3.857038 GCCCCATGCAGCCATTGG 61.857 66.667 0.00 0.00 40.77 3.16
94 95 2.281345 GATGGAGATGCCCCTGCG 60.281 66.667 0.00 0.00 41.78 5.18
109 110 3.690745 GCTGCCTGCTTTGTGGAT 58.309 55.556 0.00 0.00 38.95 3.41
135 136 1.149174 CCAGCCCGCATACCAAGAT 59.851 57.895 0.00 0.00 0.00 2.40
175 176 6.623767 GCTTTGTGACATACTCCCTTTGATTC 60.624 42.308 0.00 0.00 0.00 2.52
181 182 4.373156 AAGCTTTGTGACATACTCCCTT 57.627 40.909 0.00 0.00 0.00 3.95
183 184 7.499232 ACAATATAAGCTTTGTGACATACTCCC 59.501 37.037 3.20 0.00 34.87 4.30
185 186 9.708222 CAACAATATAAGCTTTGTGACATACTC 57.292 33.333 3.20 0.00 36.26 2.59
294 295 7.237055 ACCTGGTTTATTAGTCCTCTTTGTAGT 59.763 37.037 0.00 0.00 0.00 2.73
319 320 2.235016 TGGCACCAAATCAACCACTAC 58.765 47.619 0.00 0.00 0.00 2.73
324 325 4.111916 CGATTATTGGCACCAAATCAACC 58.888 43.478 6.14 0.00 39.55 3.77
325 326 4.111916 CCGATTATTGGCACCAAATCAAC 58.888 43.478 6.14 0.00 39.55 3.18
341 342 6.404184 CCTGTCAACAAATAACATGCCGATTA 60.404 38.462 0.00 0.00 0.00 1.75
347 348 5.376854 AGACCTGTCAACAAATAACATGC 57.623 39.130 0.00 0.00 0.00 4.06
423 424 5.402270 CGAATGGAAAGTTGCCAAAAGTTAG 59.598 40.000 6.69 0.00 39.21 2.34
427 428 2.476241 GCGAATGGAAAGTTGCCAAAAG 59.524 45.455 6.69 2.10 39.21 2.27
442 443 2.114056 CAAGATTCGGCATTGCGAATG 58.886 47.619 23.61 13.29 41.85 2.67
484 485 3.748568 TGCATTTAATTTTGCGGGGAAAC 59.251 39.130 0.00 0.00 41.80 2.78
701 713 2.282180 GCGTGCAAAGGGAAGGGA 60.282 61.111 0.00 0.00 0.00 4.20
702 714 3.737172 CGCGTGCAAAGGGAAGGG 61.737 66.667 0.00 0.00 0.00 3.95
704 716 4.741781 CGCGCGTGCAAAGGGAAG 62.742 66.667 24.19 0.00 42.97 3.46
767 783 1.281925 TGGAGGATTCTGGGCCTTCC 61.282 60.000 4.53 6.19 33.84 3.46
793 809 2.824071 ATCGAACGGGTGGTGTACGC 62.824 60.000 0.00 0.00 38.76 4.42
905 936 3.840078 TGAGGATGAACATGAGGTTGAGA 59.160 43.478 0.00 0.00 40.63 3.27
909 940 3.584406 TGAGTGAGGATGAACATGAGGTT 59.416 43.478 0.00 0.00 44.10 3.50
947 990 2.797156 TGTGTTTGTGTTTGTGTTGTGC 59.203 40.909 0.00 0.00 0.00 4.57
1715 1781 1.680338 ACGCTCCCTGATTTATTGGC 58.320 50.000 0.00 0.00 0.00 4.52
1749 1830 2.853594 TCAATATCCGAAACGTACGCAC 59.146 45.455 16.72 6.03 0.00 5.34
1759 1840 5.666462 TCCACGAAGAAATCAATATCCGAA 58.334 37.500 0.00 0.00 0.00 4.30
1761 1842 5.050490 ACTCCACGAAGAAATCAATATCCG 58.950 41.667 0.00 0.00 0.00 4.18
1763 1844 8.138712 ACTAGACTCCACGAAGAAATCAATATC 58.861 37.037 0.00 0.00 0.00 1.63
1764 1845 7.923344 CACTAGACTCCACGAAGAAATCAATAT 59.077 37.037 0.00 0.00 0.00 1.28
1765 1846 7.093902 ACACTAGACTCCACGAAGAAATCAATA 60.094 37.037 0.00 0.00 0.00 1.90
1766 1847 6.102663 CACTAGACTCCACGAAGAAATCAAT 58.897 40.000 0.00 0.00 0.00 2.57
1769 1862 5.061920 ACACTAGACTCCACGAAGAAATC 57.938 43.478 0.00 0.00 0.00 2.17
1770 1863 5.470047 AACACTAGACTCCACGAAGAAAT 57.530 39.130 0.00 0.00 0.00 2.17
1783 1876 0.776451 CACACGCACGAACACTAGAC 59.224 55.000 0.00 0.00 0.00 2.59
1785 1878 0.502695 CACACACGCACGAACACTAG 59.497 55.000 0.00 0.00 0.00 2.57
1786 1879 0.872451 CCACACACGCACGAACACTA 60.872 55.000 0.00 0.00 0.00 2.74
1797 1891 0.179067 ACTACCACCAACCACACACG 60.179 55.000 0.00 0.00 0.00 4.49
1819 1913 4.673061 CGCACTCACACTAACAAAACCAAA 60.673 41.667 0.00 0.00 0.00 3.28
1824 1918 2.283086 CGACGCACTCACACTAACAAAA 59.717 45.455 0.00 0.00 0.00 2.44
1826 1920 1.202325 ACGACGCACTCACACTAACAA 60.202 47.619 0.00 0.00 0.00 2.83
1827 1921 0.382873 ACGACGCACTCACACTAACA 59.617 50.000 0.00 0.00 0.00 2.41
1830 1924 1.284715 CCACGACGCACTCACACTA 59.715 57.895 0.00 0.00 0.00 2.74
1844 1938 2.431942 GAGTACACGGCACCCACG 60.432 66.667 0.00 0.00 37.36 4.94
1845 1939 2.047560 GGAGTACACGGCACCCAC 60.048 66.667 0.00 0.00 0.00 4.61
1851 1956 0.944311 CACACACAGGAGTACACGGC 60.944 60.000 0.00 0.00 0.00 5.68
1853 1958 1.202371 ACACACACACAGGAGTACACG 60.202 52.381 0.00 0.00 0.00 4.49
1854 1959 2.159156 TGACACACACACAGGAGTACAC 60.159 50.000 0.00 0.00 0.00 2.90
1855 1960 2.104170 TGACACACACACAGGAGTACA 58.896 47.619 0.00 0.00 0.00 2.90
1856 1961 2.882927 TGACACACACACAGGAGTAC 57.117 50.000 0.00 0.00 0.00 2.73
1857 1962 2.764010 ACTTGACACACACACAGGAGTA 59.236 45.455 0.00 0.00 0.00 2.59
1859 1964 1.935873 CACTTGACACACACACAGGAG 59.064 52.381 0.00 0.00 0.00 3.69
1860 1965 1.277842 ACACTTGACACACACACAGGA 59.722 47.619 0.00 0.00 0.00 3.86
1861 1966 1.737838 ACACTTGACACACACACAGG 58.262 50.000 0.00 0.00 0.00 4.00
1862 1967 2.728846 GCAACACTTGACACACACACAG 60.729 50.000 0.00 0.00 0.00 3.66
1880 2005 0.611618 AATGGAATCGCAGGTGGCAA 60.612 50.000 0.00 0.00 45.17 4.52
1883 2008 1.818060 TGAAAATGGAATCGCAGGTGG 59.182 47.619 0.00 0.00 0.00 4.61
1886 2011 3.709987 GGAATGAAAATGGAATCGCAGG 58.290 45.455 0.00 0.00 0.00 4.85
1890 2015 3.108144 GCACGGAATGAAAATGGAATCG 58.892 45.455 0.00 0.00 0.00 3.34
1895 2020 2.097304 TCATCGCACGGAATGAAAATGG 59.903 45.455 0.00 0.00 0.00 3.16
1901 2026 5.749596 AATTTATTCATCGCACGGAATGA 57.250 34.783 0.00 0.00 35.49 2.57
1928 2053 3.382832 CGCGTCCAGAAGACCCCT 61.383 66.667 0.00 0.00 43.08 4.79
1990 2115 7.821846 GGAGAGACAAGAAATTATCTGAAGTGT 59.178 37.037 0.00 0.00 38.79 3.55
2023 2149 9.802039 AAAGGGACTACTAGATGACTATTCTAG 57.198 37.037 0.00 6.25 42.85 2.43
2069 2195 6.725834 TGCATAGGAGGAGATACATATGTTGA 59.274 38.462 14.77 0.00 34.61 3.18
2090 2232 8.755696 AAATAAATACGAACAAACACATGCAT 57.244 26.923 0.00 0.00 0.00 3.96
2158 2301 8.019094 ACGGTGAAAACGGATCTTAATTTTAAG 58.981 33.333 4.07 4.07 37.58 1.85
2160 2303 7.437793 ACGGTGAAAACGGATCTTAATTTTA 57.562 32.000 0.00 0.00 35.23 1.52
2194 2337 2.206750 ACTTTTAAAGAGCACGTCGCA 58.793 42.857 12.02 0.00 46.13 5.10
2257 2401 9.817365 CTAGTTGCACACATATTGATATTTAGC 57.183 33.333 0.00 0.00 0.00 3.09
2301 2447 5.809001 AGGACAATTGACACACATACTCAT 58.191 37.500 13.59 0.00 0.00 2.90
2309 2455 4.045636 AGCAAAAGGACAATTGACACAC 57.954 40.909 13.59 0.00 0.00 3.82
2319 2469 7.575414 TTGATGTTTAGTTAGCAAAAGGACA 57.425 32.000 0.00 0.00 0.00 4.02
2326 2476 7.138081 CACACACATTGATGTTTAGTTAGCAA 58.862 34.615 0.00 0.00 39.39 3.91
2428 2586 3.067742 ACGCGCCAATATAGTCTAGTTGT 59.932 43.478 5.73 0.00 0.00 3.32
2440 2598 1.061729 CGCAATTGACGCGCCAATA 59.938 52.632 21.04 0.00 46.98 1.90
2474 2632 2.171659 TGTTCAGTTGGCAGGACACTAA 59.828 45.455 0.00 0.00 0.00 2.24
2491 2649 5.869344 TCTAGTTGCACACATACTGATGTTC 59.131 40.000 0.00 0.00 44.18 3.18
2541 2699 2.700897 AGAAGGACTAGTTGCACACACT 59.299 45.455 0.00 0.00 0.00 3.55
2591 2751 9.158233 GATGTTTAGTTGGCTTGTAATGTAGTA 57.842 33.333 0.00 0.00 0.00 1.82
2601 2761 5.403166 CACACATTGATGTTTAGTTGGCTTG 59.597 40.000 0.00 0.00 39.39 4.01
2605 2765 4.681025 GCACACACATTGATGTTTAGTTGG 59.319 41.667 0.00 0.00 39.39 3.77


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

AutoCloner maintained by Alex Coulton.