Multiple sequence alignment - TraesCS1A01G334100

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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 TraesCS1A01G334100 chr1A 100.000 2925 0 0 1 2925 521737723 521740647 0.000000e+00 5402
1 TraesCS1A01G334100 chr1B 90.470 2214 118 36 15 2200 576520493 576522641 0.000000e+00 2833
2 TraesCS1A01G334100 chr1D 95.338 1094 38 4 773 1866 426651781 426652861 0.000000e+00 1725
3 TraesCS1A01G334100 chr1D 92.736 592 23 12 72 644 426650967 426651557 0.000000e+00 837
4 TraesCS1A01G334100 chr1D 86.455 347 40 4 1854 2200 426659846 426660185 9.900000e-100 374
5 TraesCS1A01G334100 chr6D 89.943 696 66 4 2233 2925 129739470 129738776 0.000000e+00 894
6 TraesCS1A01G334100 chr6D 89.784 695 61 10 2233 2921 472764465 472765155 0.000000e+00 881
7 TraesCS1A01G334100 chr7A 88.728 692 70 7 2238 2925 594432372 594431685 0.000000e+00 839
8 TraesCS1A01G334100 chr3D 89.593 663 61 7 2269 2925 10387218 10387878 0.000000e+00 835
9 TraesCS1A01G334100 chr3D 88.785 214 18 3 1220 1433 406772760 406772553 1.040000e-64 257
10 TraesCS1A01G334100 chr3D 81.726 197 27 8 1234 1422 376169979 376169784 3.900000e-34 156
11 TraesCS1A01G334100 chr2D 90.792 619 54 3 2310 2925 209133236 209133854 0.000000e+00 824
12 TraesCS1A01G334100 chr2D 89.736 643 57 6 2279 2917 111987781 111987144 0.000000e+00 813
13 TraesCS1A01G334100 chr5B 87.391 690 76 6 2238 2924 523368107 523367426 0.000000e+00 782
14 TraesCS1A01G334100 chr5B 89.071 183 18 2 1246 1428 488559779 488559959 2.930000e-55 226
15 TraesCS1A01G334100 chr6A 86.782 696 88 4 2231 2924 19265184 19264491 0.000000e+00 773
16 TraesCS1A01G334100 chr2B 86.900 687 83 6 2237 2919 775071497 775070814 0.000000e+00 763
17 TraesCS1A01G334100 chr3A 89.252 214 17 3 1220 1433 544969600 544969807 2.240000e-66 263
18 TraesCS1A01G334100 chr3A 81.557 244 28 5 2227 2469 699171888 699172115 4.980000e-43 185
19 TraesCS1A01G334100 chr3B 88.785 214 18 3 1220 1433 532667438 532667231 1.040000e-64 257
20 TraesCS1A01G334100 chr7B 87.560 209 20 3 1220 1428 712841420 712841622 1.350000e-58 237
21 TraesCS1A01G334100 chr7B 89.071 183 18 2 1246 1428 712841873 712842053 2.930000e-55 226


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 TraesCS1A01G334100 chr1A 521737723 521740647 2924 False 5402.0 5402 100.0000 1 2925 1 chr1A.!!$F1 2924
1 TraesCS1A01G334100 chr1B 576520493 576522641 2148 False 2833.0 2833 90.4700 15 2200 1 chr1B.!!$F1 2185
2 TraesCS1A01G334100 chr1D 426650967 426652861 1894 False 1281.0 1725 94.0370 72 1866 2 chr1D.!!$F2 1794
3 TraesCS1A01G334100 chr6D 129738776 129739470 694 True 894.0 894 89.9430 2233 2925 1 chr6D.!!$R1 692
4 TraesCS1A01G334100 chr6D 472764465 472765155 690 False 881.0 881 89.7840 2233 2921 1 chr6D.!!$F1 688
5 TraesCS1A01G334100 chr7A 594431685 594432372 687 True 839.0 839 88.7280 2238 2925 1 chr7A.!!$R1 687
6 TraesCS1A01G334100 chr3D 10387218 10387878 660 False 835.0 835 89.5930 2269 2925 1 chr3D.!!$F1 656
7 TraesCS1A01G334100 chr2D 209133236 209133854 618 False 824.0 824 90.7920 2310 2925 1 chr2D.!!$F1 615
8 TraesCS1A01G334100 chr2D 111987144 111987781 637 True 813.0 813 89.7360 2279 2917 1 chr2D.!!$R1 638
9 TraesCS1A01G334100 chr5B 523367426 523368107 681 True 782.0 782 87.3910 2238 2924 1 chr5B.!!$R1 686
10 TraesCS1A01G334100 chr6A 19264491 19265184 693 True 773.0 773 86.7820 2231 2924 1 chr6A.!!$R1 693
11 TraesCS1A01G334100 chr2B 775070814 775071497 683 True 763.0 763 86.9000 2237 2919 1 chr2B.!!$R1 682
12 TraesCS1A01G334100 chr7B 712841420 712842053 633 False 231.5 237 88.3155 1220 1428 2 chr7B.!!$F1 208

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
395 415 0.179222 GCCAAAGCGAGTAAAGCGAC 60.179 55.0 0.0 0.0 40.04 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2109 2259 0.03601 ACACTTCGCTTCCATCCCTG 60.036 55.0 0.0 0.0 0.0 4.45 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 7.919313 CATATTGTGAATGCCATGTTTACTC 57.081 36.000 0.00 0.00 0.00 2.59
138 139 8.871686 TTTCAACAGAAAGAAATAAAGAAGCC 57.128 30.769 0.00 0.00 0.00 4.35
139 140 6.981722 TCAACAGAAAGAAATAAAGAAGCCC 58.018 36.000 0.00 0.00 0.00 5.19
156 166 6.007076 AGAAGCCCTAAAGAAAGAAAGAAGG 58.993 40.000 0.00 0.00 0.00 3.46
196 206 3.601443 AGTCTAGCTACAAAGTGGCAG 57.399 47.619 8.19 4.03 42.47 4.85
237 248 2.345760 CGCATTGGCAGGGAAAGCT 61.346 57.895 0.00 0.00 41.24 3.74
239 250 1.252904 GCATTGGCAGGGAAAGCTCA 61.253 55.000 0.00 0.00 40.72 4.26
395 415 0.179222 GCCAAAGCGAGTAAAGCGAC 60.179 55.000 0.00 0.00 40.04 5.19
403 423 0.438830 GAGTAAAGCGACGCACCTTG 59.561 55.000 23.70 0.00 0.00 3.61
504 525 4.578601 CCATCTTTCGTCGCTTTTACATC 58.421 43.478 0.00 0.00 0.00 3.06
608 629 1.428448 GAAAATGGGCCGTTTCTTGC 58.572 50.000 23.32 10.18 32.18 4.01
609 630 1.000843 GAAAATGGGCCGTTTCTTGCT 59.999 47.619 23.32 8.10 32.18 3.91
628 649 4.947645 TGCTGCTGAAACAAGCTTAATTT 58.052 34.783 0.00 2.80 43.90 1.82
633 654 3.996363 CTGAAACAAGCTTAATTTGGCCC 59.004 43.478 11.53 0.54 0.00 5.80
644 665 0.678950 ATTTGGCCCTGTTTGGAACG 59.321 50.000 0.00 0.00 38.35 3.95
648 672 3.361977 CCCTGTTTGGAACGCGGG 61.362 66.667 12.47 0.00 38.05 6.13
650 674 2.325082 CCTGTTTGGAACGCGGGAG 61.325 63.158 12.47 0.00 38.35 4.30
671 695 2.697431 TTTTTGGTCGATTTCAGCGG 57.303 45.000 0.00 0.00 0.00 5.52
672 696 1.885560 TTTTGGTCGATTTCAGCGGA 58.114 45.000 0.00 0.00 0.00 5.54
673 697 1.885560 TTTGGTCGATTTCAGCGGAA 58.114 45.000 0.00 0.00 0.00 4.30
682 706 2.147436 TTTCAGCGGAAATTTGGCAC 57.853 45.000 8.00 0.00 38.07 5.01
683 707 0.316841 TTCAGCGGAAATTTGGCACC 59.683 50.000 12.00 0.00 0.00 5.01
684 708 1.444212 CAGCGGAAATTTGGCACCG 60.444 57.895 10.77 10.77 46.74 4.94
688 782 0.525761 CGGAAATTTGGCACCGTGAT 59.474 50.000 1.65 0.00 40.42 3.06
703 815 3.820467 ACCGTGATCTTGATCTTTTTGCA 59.180 39.130 11.31 0.00 0.00 4.08
736 855 2.292267 CCAAATGGGTCCTTGATCGAG 58.708 52.381 2.59 2.59 0.00 4.04
866 985 5.390991 GCAGTTAGATGTTCCTTTTCCTTCG 60.391 44.000 0.00 0.00 0.00 3.79
944 1063 3.300857 CACAGAGCACGTATCCTATTCG 58.699 50.000 0.00 0.00 0.00 3.34
1006 1125 1.079819 ACACTTCTCCGTGGCATCG 60.080 57.895 0.00 0.00 39.19 3.84
1528 1653 4.299796 GGGCTTGGCTTCCACCCA 62.300 66.667 6.65 0.00 39.03 4.51
1771 1896 2.670414 CAGCTCCTGTCGATTGAAACTC 59.330 50.000 0.00 0.00 0.00 3.01
1782 1907 1.028905 TTGAAACTCCGGGTTTGCTG 58.971 50.000 21.11 0.00 46.77 4.41
1787 1912 0.182775 ACTCCGGGTTTGCTGTTTCT 59.817 50.000 0.00 0.00 0.00 2.52
1788 1913 0.875059 CTCCGGGTTTGCTGTTTCTC 59.125 55.000 0.00 0.00 0.00 2.87
1789 1914 0.181587 TCCGGGTTTGCTGTTTCTCA 59.818 50.000 0.00 0.00 0.00 3.27
1790 1915 1.028905 CCGGGTTTGCTGTTTCTCAA 58.971 50.000 0.00 0.00 0.00 3.02
1791 1916 1.613437 CCGGGTTTGCTGTTTCTCAAT 59.387 47.619 0.00 0.00 0.00 2.57
1792 1917 2.351738 CCGGGTTTGCTGTTTCTCAATC 60.352 50.000 0.00 0.00 0.00 2.67
1793 1918 2.665519 CGGGTTTGCTGTTTCTCAATCG 60.666 50.000 0.00 0.00 0.00 3.34
1794 1919 2.552315 GGGTTTGCTGTTTCTCAATCGA 59.448 45.455 0.00 0.00 0.00 3.59
1795 1920 3.191371 GGGTTTGCTGTTTCTCAATCGAT 59.809 43.478 0.00 0.00 0.00 3.59
1796 1921 4.406943 GGTTTGCTGTTTCTCAATCGATC 58.593 43.478 0.00 0.00 0.00 3.69
1797 1922 3.997319 TTGCTGTTTCTCAATCGATCG 57.003 42.857 9.36 9.36 0.00 3.69
1798 1923 2.270923 TGCTGTTTCTCAATCGATCGG 58.729 47.619 16.41 0.00 0.00 4.18
1799 1924 1.594862 GCTGTTTCTCAATCGATCGGG 59.405 52.381 16.41 5.65 0.00 5.14
1800 1925 2.205074 CTGTTTCTCAATCGATCGGGG 58.795 52.381 16.41 5.27 0.00 5.73
1801 1926 1.828595 TGTTTCTCAATCGATCGGGGA 59.171 47.619 16.41 9.46 0.00 4.81
1802 1927 2.235155 TGTTTCTCAATCGATCGGGGAA 59.765 45.455 16.41 8.18 0.00 3.97
1803 1928 3.118408 TGTTTCTCAATCGATCGGGGAAT 60.118 43.478 16.41 0.00 0.00 3.01
1804 1929 4.100344 TGTTTCTCAATCGATCGGGGAATA 59.900 41.667 16.41 1.18 0.00 1.75
1805 1930 4.521130 TTCTCAATCGATCGGGGAATAG 57.479 45.455 16.41 6.08 0.00 1.73
1834 1978 4.559502 GCTCAATCGATGCTATAGTGGTCA 60.560 45.833 0.00 0.00 0.00 4.02
1981 2131 0.754472 AAAGAGTGGGAACGGACGAA 59.246 50.000 0.00 0.00 0.00 3.85
1989 2139 0.519961 GGAACGGACGAAATTGGGTG 59.480 55.000 0.00 0.00 0.00 4.61
1990 2140 0.109919 GAACGGACGAAATTGGGTGC 60.110 55.000 0.00 0.00 0.00 5.01
1997 2147 1.102154 CGAAATTGGGTGCTGCCATA 58.898 50.000 0.00 0.00 39.65 2.74
1998 2148 1.682854 CGAAATTGGGTGCTGCCATAT 59.317 47.619 0.00 0.00 39.65 1.78
1999 2149 2.884012 CGAAATTGGGTGCTGCCATATA 59.116 45.455 0.00 0.00 39.65 0.86
2014 2164 6.310224 GCTGCCATATATGTTTTCGTGTTTTT 59.690 34.615 11.73 0.00 0.00 1.94
2040 2190 4.693283 TCTGAATACGGAAGCCAATACAG 58.307 43.478 0.00 0.00 0.00 2.74
2066 2216 3.231160 GCCGGAAACAAATACAGAAACG 58.769 45.455 5.05 0.00 0.00 3.60
2068 2218 4.708601 CCGGAAACAAATACAGAAACGAG 58.291 43.478 0.00 0.00 0.00 4.18
2075 2225 7.880059 AACAAATACAGAAACGAGTACTACC 57.120 36.000 0.00 0.00 0.00 3.18
2076 2226 7.224522 ACAAATACAGAAACGAGTACTACCT 57.775 36.000 0.00 0.00 0.00 3.08
2089 2239 8.488651 ACGAGTACTACCTAAAATGAAAATGG 57.511 34.615 0.00 0.00 0.00 3.16
2093 2243 8.329502 AGTACTACCTAAAATGAAAATGGAGCT 58.670 33.333 0.00 0.00 0.00 4.09
2109 2259 4.513442 TGGAGCTAATACAACATGGACAC 58.487 43.478 0.00 0.00 0.00 3.67
2112 2262 4.517285 AGCTAATACAACATGGACACAGG 58.483 43.478 0.00 0.00 0.00 4.00
2115 2265 4.591321 AATACAACATGGACACAGGGAT 57.409 40.909 0.00 0.00 31.42 3.85
2123 2273 1.596934 GACACAGGGATGGAAGCGA 59.403 57.895 0.00 0.00 0.00 4.93
2133 2283 1.126846 GATGGAAGCGAAGTGTTCACG 59.873 52.381 0.00 0.00 0.00 4.35
2167 2323 7.584987 AGATCCGTTGAAACATAGACAAAAAG 58.415 34.615 0.00 0.00 0.00 2.27
2181 2337 6.544928 AGACAAAAAGACAAGGAAACCAAT 57.455 33.333 0.00 0.00 0.00 3.16
2186 2342 9.981114 ACAAAAAGACAAGGAAACCAATATAAG 57.019 29.630 0.00 0.00 0.00 1.73
2202 2358 8.695456 ACCAATATAAGTTGTTCAATTGATCCC 58.305 33.333 9.40 1.31 0.00 3.85
2203 2359 8.143835 CCAATATAAGTTGTTCAATTGATCCCC 58.856 37.037 9.40 2.12 0.00 4.81
2204 2360 7.839680 ATATAAGTTGTTCAATTGATCCCCC 57.160 36.000 9.40 0.00 0.00 5.40
2205 2361 3.541242 AGTTGTTCAATTGATCCCCCA 57.459 42.857 9.40 0.00 0.00 4.96
2206 2362 3.165071 AGTTGTTCAATTGATCCCCCAC 58.835 45.455 9.40 3.86 0.00 4.61
2207 2363 1.832883 TGTTCAATTGATCCCCCACG 58.167 50.000 9.40 0.00 0.00 4.94
2208 2364 1.074727 TGTTCAATTGATCCCCCACGT 59.925 47.619 9.40 0.00 0.00 4.49
2209 2365 1.743394 GTTCAATTGATCCCCCACGTC 59.257 52.381 9.40 0.00 0.00 4.34
2210 2366 0.107897 TCAATTGATCCCCCACGTCG 60.108 55.000 3.38 0.00 0.00 5.12
2211 2367 1.451387 AATTGATCCCCCACGTCGC 60.451 57.895 0.00 0.00 0.00 5.19
2212 2368 2.886730 AATTGATCCCCCACGTCGCC 62.887 60.000 0.00 0.00 0.00 5.54
2217 2373 4.733542 CCCCCACGTCGCCCAATT 62.734 66.667 0.00 0.00 0.00 2.32
2218 2374 2.675075 CCCCACGTCGCCCAATTT 60.675 61.111 0.00 0.00 0.00 1.82
2219 2375 2.272447 CCCCACGTCGCCCAATTTT 61.272 57.895 0.00 0.00 0.00 1.82
2220 2376 0.961358 CCCCACGTCGCCCAATTTTA 60.961 55.000 0.00 0.00 0.00 1.52
2221 2377 0.450184 CCCACGTCGCCCAATTTTAG 59.550 55.000 0.00 0.00 0.00 1.85
2222 2378 1.444836 CCACGTCGCCCAATTTTAGA 58.555 50.000 0.00 0.00 0.00 2.10
2223 2379 1.129811 CCACGTCGCCCAATTTTAGAC 59.870 52.381 0.00 0.00 0.00 2.59
2224 2380 1.801771 CACGTCGCCCAATTTTAGACA 59.198 47.619 0.00 0.00 32.57 3.41
2225 2381 1.802365 ACGTCGCCCAATTTTAGACAC 59.198 47.619 0.00 0.00 32.57 3.67
2226 2382 1.129811 CGTCGCCCAATTTTAGACACC 59.870 52.381 0.00 0.00 32.57 4.16
2227 2383 1.471287 GTCGCCCAATTTTAGACACCC 59.529 52.381 0.00 0.00 32.57 4.61
2228 2384 0.815095 CGCCCAATTTTAGACACCCC 59.185 55.000 0.00 0.00 0.00 4.95
2229 2385 1.191535 GCCCAATTTTAGACACCCCC 58.808 55.000 0.00 0.00 0.00 5.40
2368 2528 1.332144 TTATAACGCGGGGGCTGACT 61.332 55.000 12.47 0.00 0.00 3.41
2369 2529 0.467844 TATAACGCGGGGGCTGACTA 60.468 55.000 12.47 0.00 0.00 2.59
2377 2537 3.702048 GGGCTGACTACGGTGGCA 61.702 66.667 0.00 0.00 0.00 4.92
2561 2727 3.053896 GCGGCCTTGGCTACGTTT 61.054 61.111 11.71 0.00 0.00 3.60
2562 2728 1.742510 GCGGCCTTGGCTACGTTTA 60.743 57.895 11.71 0.00 0.00 2.01
2684 2850 2.432146 CCTCCGGACAAATCTGATCTGA 59.568 50.000 0.00 4.63 32.26 3.27
2732 2898 3.770040 CAGATCGGCGGTGACCCA 61.770 66.667 7.21 0.00 0.00 4.51
2778 2950 0.807667 CGAGCGGATCTGGGTGAAAG 60.808 60.000 3.14 0.00 0.00 2.62
2779 2951 0.462759 GAGCGGATCTGGGTGAAAGG 60.463 60.000 3.14 0.00 0.00 3.11
2889 3061 3.205507 AGACCTCTATCTGCTACCTCCAA 59.794 47.826 0.00 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 7.886629 AGAGTAAACATGGCATTCACAATAT 57.113 32.000 0.00 0.00 0.00 1.28
2 3 7.701539 AAGAGTAAACATGGCATTCACAATA 57.298 32.000 0.00 0.00 0.00 1.90
3 4 6.594788 AAGAGTAAACATGGCATTCACAAT 57.405 33.333 0.00 0.00 0.00 2.71
4 5 6.403866 AAAGAGTAAACATGGCATTCACAA 57.596 33.333 0.00 0.00 0.00 3.33
5 6 6.714810 AGTAAAGAGTAAACATGGCATTCACA 59.285 34.615 0.00 0.00 0.00 3.58
7 8 6.939730 TGAGTAAAGAGTAAACATGGCATTCA 59.060 34.615 0.00 0.00 0.00 2.57
8 9 7.377766 TGAGTAAAGAGTAAACATGGCATTC 57.622 36.000 0.00 0.00 0.00 2.67
9 10 7.148018 CCATGAGTAAAGAGTAAACATGGCATT 60.148 37.037 0.00 0.00 43.81 3.56
10 11 6.319658 CCATGAGTAAAGAGTAAACATGGCAT 59.680 38.462 0.00 0.00 43.81 4.40
11 12 5.647658 CCATGAGTAAAGAGTAAACATGGCA 59.352 40.000 0.00 0.00 43.81 4.92
12 13 6.124088 CCATGAGTAAAGAGTAAACATGGC 57.876 41.667 0.00 0.00 43.81 4.40
129 130 8.990163 TTCTTTCTTTCTTTAGGGCTTCTTTA 57.010 30.769 0.00 0.00 0.00 1.85
130 131 7.014711 CCTTCTTTCTTTCTTTAGGGCTTCTTT 59.985 37.037 0.00 0.00 0.00 2.52
137 138 8.465273 TTTCTTCCTTCTTTCTTTCTTTAGGG 57.535 34.615 0.00 0.00 0.00 3.53
138 139 9.343539 TCTTTCTTCCTTCTTTCTTTCTTTAGG 57.656 33.333 0.00 0.00 0.00 2.69
167 177 9.220767 CCACTTTGTAGCTAGACTTAGATTTTT 57.779 33.333 0.00 0.00 0.00 1.94
196 206 3.667497 AGCTTTGCTTTAGGGCTTTTC 57.333 42.857 0.00 0.00 33.89 2.29
219 230 2.182537 GCTTTCCCTGCCAATGCG 59.817 61.111 0.00 0.00 41.78 4.73
237 248 1.678627 CTCCTCGCTAGCTAGCTTTGA 59.321 52.381 36.02 27.18 46.85 2.69
239 250 1.679153 GACTCCTCGCTAGCTAGCTTT 59.321 52.381 36.02 17.67 46.85 3.51
245 265 1.169661 CGATGGACTCCTCGCTAGCT 61.170 60.000 13.93 0.00 0.00 3.32
258 278 3.385749 GAAAGGCTCCGGCGATGGA 62.386 63.158 9.30 0.00 39.81 3.41
395 415 1.006832 CTATCCGAAACCAAGGTGCG 58.993 55.000 7.53 7.53 0.00 5.34
403 423 4.618965 AGCGATAAAGACTATCCGAAACC 58.381 43.478 0.00 0.00 0.00 3.27
504 525 1.535204 AATCACTTTTGCGGCAGGGG 61.535 55.000 1.67 0.00 0.00 4.79
608 629 4.151157 GCCAAATTAAGCTTGTTTCAGCAG 59.849 41.667 9.86 0.00 42.84 4.24
609 630 4.057432 GCCAAATTAAGCTTGTTTCAGCA 58.943 39.130 9.86 0.00 42.84 4.41
628 649 2.909965 GCGTTCCAAACAGGGCCA 60.910 61.111 6.18 0.00 38.24 5.36
633 654 1.164041 AACTCCCGCGTTCCAAACAG 61.164 55.000 4.92 0.00 0.00 3.16
656 680 2.107950 ATTTCCGCTGAAATCGACCA 57.892 45.000 10.00 0.00 45.87 4.02
668 692 1.732683 CACGGTGCCAAATTTCCGC 60.733 57.895 14.12 7.68 45.76 5.54
670 694 1.818674 AGATCACGGTGCCAAATTTCC 59.181 47.619 2.51 0.00 0.00 3.13
671 695 3.057596 TCAAGATCACGGTGCCAAATTTC 60.058 43.478 2.51 0.00 0.00 2.17
672 696 2.890311 TCAAGATCACGGTGCCAAATTT 59.110 40.909 2.51 0.00 0.00 1.82
673 697 2.513753 TCAAGATCACGGTGCCAAATT 58.486 42.857 2.51 0.00 0.00 1.82
675 699 2.083774 GATCAAGATCACGGTGCCAAA 58.916 47.619 2.51 0.00 37.74 3.28
677 701 0.904649 AGATCAAGATCACGGTGCCA 59.095 50.000 12.21 0.00 40.22 4.92
678 702 2.029838 AAGATCAAGATCACGGTGCC 57.970 50.000 12.21 0.00 40.22 5.01
681 705 3.820467 TGCAAAAAGATCAAGATCACGGT 59.180 39.130 12.21 0.00 40.22 4.83
682 706 4.424061 TGCAAAAAGATCAAGATCACGG 57.576 40.909 12.21 0.00 40.22 4.94
683 707 5.916883 ACTTTGCAAAAAGATCAAGATCACG 59.083 36.000 13.84 0.00 40.22 4.35
684 708 7.436080 TGAACTTTGCAAAAAGATCAAGATCAC 59.564 33.333 13.84 0.00 38.21 3.06
688 782 5.743398 CGTGAACTTTGCAAAAAGATCAAGA 59.257 36.000 13.84 0.00 41.23 3.02
703 815 2.556622 CCCATTTGGCTACGTGAACTTT 59.443 45.455 0.00 0.00 0.00 2.66
736 855 2.511600 ATTGCCGCCACGACTAGC 60.512 61.111 0.00 0.00 0.00 3.42
747 866 3.443045 GGCCACACTCCATTGCCG 61.443 66.667 0.00 0.00 31.55 5.69
794 913 4.204891 CGATGCCGTTCGGTTCGC 62.205 66.667 19.05 5.38 35.50 4.70
866 985 0.322187 TTCCTTTAACAGGGCGAGGC 60.322 55.000 0.00 0.00 44.12 4.70
947 1066 0.318614 GCTCGCTTGCTAGCTAGGAG 60.319 60.000 25.52 25.52 45.51 3.69
1015 1134 3.936203 TCGGTCAGTGTGTGCCCC 61.936 66.667 0.00 0.00 0.00 5.80
1189 1314 4.831307 CGCCCCGAAGACGACGAG 62.831 72.222 0.00 0.00 42.66 4.18
1528 1653 1.698532 GCCTGAGACCATCCATGATCT 59.301 52.381 0.00 0.00 0.00 2.75
1698 1823 4.202161 TGTTGGAACATACGGCAACAAATT 60.202 37.500 0.00 0.00 39.30 1.82
1715 1840 7.856145 ATTTGCAACTTTTTACATTGTTGGA 57.144 28.000 0.00 0.00 39.82 3.53
1771 1896 1.028905 TTGAGAAACAGCAAACCCGG 58.971 50.000 0.00 0.00 0.00 5.73
1782 1907 2.596904 TCCCCGATCGATTGAGAAAC 57.403 50.000 18.66 0.00 0.00 2.78
1787 1912 5.995565 ATAACTATTCCCCGATCGATTGA 57.004 39.130 18.66 6.89 0.00 2.57
1788 1913 5.749109 GCTATAACTATTCCCCGATCGATTG 59.251 44.000 18.66 5.59 0.00 2.67
1789 1914 5.657302 AGCTATAACTATTCCCCGATCGATT 59.343 40.000 18.66 0.00 0.00 3.34
1790 1915 5.202004 AGCTATAACTATTCCCCGATCGAT 58.798 41.667 18.66 0.00 0.00 3.59
1791 1916 4.597004 AGCTATAACTATTCCCCGATCGA 58.403 43.478 18.66 0.00 0.00 3.59
1792 1917 4.398358 TGAGCTATAACTATTCCCCGATCG 59.602 45.833 8.51 8.51 0.00 3.69
1793 1918 5.916661 TGAGCTATAACTATTCCCCGATC 57.083 43.478 0.00 0.00 0.00 3.69
1794 1919 6.405953 CGATTGAGCTATAACTATTCCCCGAT 60.406 42.308 0.00 0.00 0.00 4.18
1795 1920 5.105877 CGATTGAGCTATAACTATTCCCCGA 60.106 44.000 0.00 0.00 0.00 5.14
1796 1921 5.103000 CGATTGAGCTATAACTATTCCCCG 58.897 45.833 0.00 0.00 0.00 5.73
1797 1922 6.282199 TCGATTGAGCTATAACTATTCCCC 57.718 41.667 0.00 0.00 0.00 4.81
1798 1923 6.256757 GCATCGATTGAGCTATAACTATTCCC 59.743 42.308 0.00 0.00 0.00 3.97
1799 1924 7.038659 AGCATCGATTGAGCTATAACTATTCC 58.961 38.462 6.92 0.00 36.73 3.01
1800 1925 9.743057 ATAGCATCGATTGAGCTATAACTATTC 57.257 33.333 21.05 0.00 46.52 1.75
1803 1928 9.397280 ACTATAGCATCGATTGAGCTATAACTA 57.603 33.333 24.65 13.01 46.93 2.24
1804 1929 8.187480 CACTATAGCATCGATTGAGCTATAACT 58.813 37.037 24.65 15.77 46.93 2.24
1805 1930 7.433719 CCACTATAGCATCGATTGAGCTATAAC 59.566 40.741 24.65 0.00 46.93 1.89
1834 1978 3.784701 ACGAATCTCTGCGTACAATCT 57.215 42.857 0.00 0.00 39.21 2.40
1885 2035 9.793259 ATTGTCTCCAATAAAAACAGTAGAAGA 57.207 29.630 0.00 0.00 39.52 2.87
1965 2115 1.463444 CAATTTCGTCCGTTCCCACTC 59.537 52.381 0.00 0.00 0.00 3.51
1971 2121 0.109919 GCACCCAATTTCGTCCGTTC 60.110 55.000 0.00 0.00 0.00 3.95
1972 2122 0.536460 AGCACCCAATTTCGTCCGTT 60.536 50.000 0.00 0.00 0.00 4.44
1981 2131 3.848303 ACATATATGGCAGCACCCAATT 58.152 40.909 16.96 0.00 38.61 2.32
1989 2139 4.552166 ACACGAAAACATATATGGCAGC 57.448 40.909 16.96 3.29 0.00 5.25
1990 2140 7.810766 AAAAACACGAAAACATATATGGCAG 57.189 32.000 16.96 6.13 0.00 4.85
2014 2164 5.975693 ATTGGCTTCCGTATTCAGAAAAA 57.024 34.783 0.00 0.00 0.00 1.94
2017 2167 5.092554 TGTATTGGCTTCCGTATTCAGAA 57.907 39.130 0.00 0.00 0.00 3.02
2019 2169 4.693283 TCTGTATTGGCTTCCGTATTCAG 58.307 43.478 0.00 0.00 0.00 3.02
2020 2170 4.746535 TCTGTATTGGCTTCCGTATTCA 57.253 40.909 0.00 0.00 0.00 2.57
2021 2171 6.430451 CATTTCTGTATTGGCTTCCGTATTC 58.570 40.000 0.00 0.00 0.00 1.75
2024 2174 3.625764 GCATTTCTGTATTGGCTTCCGTA 59.374 43.478 0.00 0.00 0.00 4.02
2025 2175 2.423538 GCATTTCTGTATTGGCTTCCGT 59.576 45.455 0.00 0.00 0.00 4.69
2026 2176 2.223572 GGCATTTCTGTATTGGCTTCCG 60.224 50.000 0.00 0.00 33.51 4.30
2027 2177 2.223572 CGGCATTTCTGTATTGGCTTCC 60.224 50.000 0.00 0.00 34.08 3.46
2028 2178 2.223572 CCGGCATTTCTGTATTGGCTTC 60.224 50.000 0.00 0.00 34.08 3.86
2029 2179 1.750778 CCGGCATTTCTGTATTGGCTT 59.249 47.619 0.00 0.00 34.08 4.35
2030 2180 1.064758 TCCGGCATTTCTGTATTGGCT 60.065 47.619 0.00 0.00 34.08 4.75
2032 2182 3.192422 TGTTTCCGGCATTTCTGTATTGG 59.808 43.478 0.00 0.00 0.00 3.16
2033 2183 4.433186 TGTTTCCGGCATTTCTGTATTG 57.567 40.909 0.00 0.00 0.00 1.90
2034 2184 5.461032 TTTGTTTCCGGCATTTCTGTATT 57.539 34.783 0.00 0.00 0.00 1.89
2040 2190 5.054390 TCTGTATTTGTTTCCGGCATTTC 57.946 39.130 0.00 0.00 0.00 2.17
2066 2216 8.613482 GCTCCATTTTCATTTTAGGTAGTACTC 58.387 37.037 0.00 0.00 0.00 2.59
2068 2218 8.507524 AGCTCCATTTTCATTTTAGGTAGTAC 57.492 34.615 0.00 0.00 0.00 2.73
2088 2238 4.513442 TGTGTCCATGTTGTATTAGCTCC 58.487 43.478 0.00 0.00 0.00 4.70
2089 2239 4.572389 CCTGTGTCCATGTTGTATTAGCTC 59.428 45.833 0.00 0.00 0.00 4.09
2093 2243 5.436175 CATCCCTGTGTCCATGTTGTATTA 58.564 41.667 0.00 0.00 0.00 0.98
2109 2259 0.036010 ACACTTCGCTTCCATCCCTG 60.036 55.000 0.00 0.00 0.00 4.45
2112 2262 1.464997 GTGAACACTTCGCTTCCATCC 59.535 52.381 0.00 0.00 37.22 3.51
2115 2265 0.878523 CCGTGAACACTTCGCTTCCA 60.879 55.000 3.51 0.00 38.02 3.53
2123 2273 5.469084 GGATCTTTAGTTTCCGTGAACACTT 59.531 40.000 3.51 0.00 31.94 3.16
2133 2283 6.308371 TGTTTCAACGGATCTTTAGTTTCC 57.692 37.500 0.00 0.00 0.00 3.13
2148 2298 8.188139 TCCTTGTCTTTTTGTCTATGTTTCAAC 58.812 33.333 0.00 0.00 0.00 3.18
2167 2323 8.573035 TGAACAACTTATATTGGTTTCCTTGTC 58.427 33.333 0.00 0.00 33.63 3.18
2181 2337 6.605594 GTGGGGGATCAATTGAACAACTTATA 59.394 38.462 13.09 0.00 0.00 0.98
2186 2342 2.094752 CGTGGGGGATCAATTGAACAAC 60.095 50.000 13.09 6.66 0.00 3.32
2200 2356 4.733542 AATTGGGCGACGTGGGGG 62.734 66.667 0.00 0.00 0.00 5.40
2201 2357 0.961358 TAAAATTGGGCGACGTGGGG 60.961 55.000 0.00 0.00 0.00 4.96
2202 2358 0.450184 CTAAAATTGGGCGACGTGGG 59.550 55.000 0.00 0.00 0.00 4.61
2203 2359 1.129811 GTCTAAAATTGGGCGACGTGG 59.870 52.381 0.00 0.00 0.00 4.94
2204 2360 1.801771 TGTCTAAAATTGGGCGACGTG 59.198 47.619 0.00 0.00 0.00 4.49
2205 2361 1.802365 GTGTCTAAAATTGGGCGACGT 59.198 47.619 0.00 0.00 0.00 4.34
2206 2362 1.129811 GGTGTCTAAAATTGGGCGACG 59.870 52.381 0.00 0.00 0.00 5.12
2207 2363 1.471287 GGGTGTCTAAAATTGGGCGAC 59.529 52.381 0.00 0.00 0.00 5.19
2208 2364 1.614850 GGGGTGTCTAAAATTGGGCGA 60.615 52.381 0.00 0.00 0.00 5.54
2209 2365 0.815095 GGGGTGTCTAAAATTGGGCG 59.185 55.000 0.00 0.00 0.00 6.13
2210 2366 1.191535 GGGGGTGTCTAAAATTGGGC 58.808 55.000 0.00 0.00 0.00 5.36
2274 2431 2.359975 GCGGCTAGGGTTGCAACT 60.360 61.111 27.64 12.75 0.00 3.16
2385 2545 3.350031 ATGGCGCAGGAAAGAGGGG 62.350 63.158 10.83 0.00 0.00 4.79
2778 2950 1.153549 ATCAAGCCGAGAACGAGCC 60.154 57.895 0.00 0.00 42.66 4.70
2779 2951 2.002127 CATCAAGCCGAGAACGAGC 58.998 57.895 0.00 0.00 42.66 5.03
2889 3061 5.399113 GATCTACTGATCTAGGGTTTCCCT 58.601 45.833 12.22 12.22 46.36 4.20


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

AutoCloner maintained by Alex Coulton.