Multiple sequence alignment - TraesCS1D01G384500

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 TraesCS1D01G384500 chr1D 100.000 2490 0 0 1 2490 458279217 458281706 0.000000e+00 4599
1 TraesCS1D01G384500 chr1D 91.562 1280 80 4 536 1815 458169038 458170289 0.000000e+00 1740
2 TraesCS1D01G384500 chr1D 94.715 492 23 1 2002 2490 458170555 458171046 0.000000e+00 761
3 TraesCS1D01G384500 chr1D 94.819 193 10 0 1808 2000 458170543 458170735 4.020000e-78 302
4 TraesCS1D01G384500 chr1D 95.028 181 9 0 1820 2000 458281218 458281398 4.050000e-73 285
5 TraesCS1D01G384500 chr1A 96.729 2507 59 11 1 2490 550828614 550831114 0.000000e+00 4154
6 TraesCS1D01G384500 chr1A 87.102 1287 113 13 738 1996 550700138 550701399 0.000000e+00 1408
7 TraesCS1D01G384500 chr1A 91.318 933 50 15 3 934 550659565 550660467 0.000000e+00 1245
8 TraesCS1D01G384500 chr1A 89.076 952 59 16 3 940 550673296 550674216 0.000000e+00 1140
9 TraesCS1D01G384500 chr1A 88.080 948 62 16 13 940 550692693 550693609 0.000000e+00 1077
10 TraesCS1D01G384500 chr1A 90.027 742 46 11 199 940 550683276 550683989 0.000000e+00 935
11 TraesCS1D01G384500 chr1A 89.676 494 41 5 2000 2490 550701222 550701708 2.720000e-174 621
12 TraesCS1D01G384500 chr1A 86.364 484 57 8 2 479 550691411 550691891 1.020000e-143 520
13 TraesCS1D01G384500 chr1A 85.451 488 58 10 2 479 550681778 550682262 1.720000e-136 496
14 TraesCS1D01G384500 chr1B 88.701 1593 124 24 222 1810 628903147 628904687 0.000000e+00 1893
15 TraesCS1D01G384500 chr1B 84.638 1380 156 19 452 1793 629095916 629097277 0.000000e+00 1323
16 TraesCS1D01G384500 chr1B 91.735 859 65 4 955 1810 628860939 628861794 0.000000e+00 1188
17 TraesCS1D01G384500 chr1B 91.628 860 65 5 955 1810 628930325 628931181 0.000000e+00 1182
18 TraesCS1D01G384500 chr1B 91.036 859 70 5 955 1810 628979933 628980787 0.000000e+00 1153
19 TraesCS1D01G384500 chr1B 90.930 860 71 5 955 1810 628816984 628817840 0.000000e+00 1149
20 TraesCS1D01G384500 chr1B 90.056 885 58 5 1 881 628814681 628815539 0.000000e+00 1120
21 TraesCS1D01G384500 chr1B 90.934 728 39 11 207 933 628860248 628860949 0.000000e+00 953
22 TraesCS1D01G384500 chr1B 89.900 703 43 11 232 933 628979268 628979943 0.000000e+00 880
23 TraesCS1D01G384500 chr1B 93.902 492 27 3 2002 2490 628904904 628905395 0.000000e+00 739
24 TraesCS1D01G384500 chr1B 82.735 863 111 16 1 861 628688773 628689599 0.000000e+00 734
25 TraesCS1D01G384500 chr1B 93.293 492 29 4 2002 2490 628867397 628867887 0.000000e+00 723
26 TraesCS1D01G384500 chr1B 92.073 492 35 2 2002 2490 628818055 628818545 0.000000e+00 689
27 TraesCS1D01G384500 chr1B 92.073 492 35 2 2002 2490 628931396 628931886 0.000000e+00 689
28 TraesCS1D01G384500 chr1B 86.420 486 54 10 1 479 629071291 629071771 2.840000e-144 521
29 TraesCS1D01G384500 chr1B 86.279 481 62 4 2 479 628910852 628911331 1.020000e-143 520
30 TraesCS1D01G384500 chr1B 86.279 481 62 4 2 479 628986858 628987337 1.020000e-143 520
31 TraesCS1D01G384500 chr1B 88.078 411 23 13 1590 2000 628867192 628867576 4.850000e-127 464
32 TraesCS1D01G384500 chr1B 87.409 413 25 13 1590 2000 628904697 628905084 1.360000e-122 449
33 TraesCS1D01G384500 chr1B 87.409 413 25 13 1590 2000 628980797 628981184 1.360000e-122 449
34 TraesCS1D01G384500 chr1B 87.105 411 27 8 1590 2000 628817850 628818234 2.270000e-120 442
35 TraesCS1D01G384500 chr1B 86.618 411 29 8 1590 2000 628931191 628931575 4.920000e-117 431
36 TraesCS1D01G384500 chr1B 84.104 346 44 6 2002 2338 628921851 628922194 8.590000e-85 324
37 TraesCS1D01G384500 chr1B 83.668 349 46 6 1999 2338 629057533 629057879 4.000000e-83 318
38 TraesCS1D01G384500 chr1B 93.210 162 10 1 2330 2490 628981221 628981382 1.150000e-58 237


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 TraesCS1D01G384500 chr1D 458279217 458281706 2489 False 2442.000000 4599 97.514000 1 2490 2 chr1D.!!$F2 2489
1 TraesCS1D01G384500 chr1D 458169038 458171046 2008 False 934.333333 1740 93.698667 536 2490 3 chr1D.!!$F1 1954
2 TraesCS1D01G384500 chr1A 550828614 550831114 2500 False 4154.000000 4154 96.729000 1 2490 1 chr1A.!!$F3 2489
3 TraesCS1D01G384500 chr1A 550659565 550660467 902 False 1245.000000 1245 91.318000 3 934 1 chr1A.!!$F1 931
4 TraesCS1D01G384500 chr1A 550673296 550674216 920 False 1140.000000 1140 89.076000 3 940 1 chr1A.!!$F2 937
5 TraesCS1D01G384500 chr1A 550700138 550701708 1570 False 1014.500000 1408 88.389000 738 2490 2 chr1A.!!$F6 1752
6 TraesCS1D01G384500 chr1A 550691411 550693609 2198 False 798.500000 1077 87.222000 2 940 2 chr1A.!!$F5 938
7 TraesCS1D01G384500 chr1A 550681778 550683989 2211 False 715.500000 935 87.739000 2 940 2 chr1A.!!$F4 938
8 TraesCS1D01G384500 chr1B 629095916 629097277 1361 False 1323.000000 1323 84.638000 452 1793 1 chr1B.!!$F7 1341
9 TraesCS1D01G384500 chr1B 628860248 628861794 1546 False 1070.500000 1188 91.334500 207 1810 2 chr1B.!!$F9 1603
10 TraesCS1D01G384500 chr1B 628903147 628905395 2248 False 1027.000000 1893 90.004000 222 2490 3 chr1B.!!$F11 2268
11 TraesCS1D01G384500 chr1B 628814681 628818545 3864 False 850.000000 1149 90.041000 1 2490 4 chr1B.!!$F8 2489
12 TraesCS1D01G384500 chr1B 628930325 628931886 1561 False 767.333333 1182 90.106333 955 2490 3 chr1B.!!$F12 1535
13 TraesCS1D01G384500 chr1B 628688773 628689599 826 False 734.000000 734 82.735000 1 861 1 chr1B.!!$F1 860
14 TraesCS1D01G384500 chr1B 628979268 628981382 2114 False 679.750000 1153 90.388750 232 2490 4 chr1B.!!$F13 2258
15 TraesCS1D01G384500 chr1B 628867192 628867887 695 False 593.500000 723 90.685500 1590 2490 2 chr1B.!!$F10 900

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
369 1717 0.461548 TATGCAGAGACGAAGGGCAG 59.538 55.0 0.0 0.0 37.96 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1923 5417 0.536724 GGGTGGTTCCAAATCATGCC 59.463 55.0 0.0 0.0 38.11 4.4 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
258 1604 8.722394 CCTTCTCTACTTTTACCAGATGAAAAC 58.278 37.037 0.00 0.00 0.00 2.43
369 1717 0.461548 TATGCAGAGACGAAGGGCAG 59.538 55.000 0.00 0.00 37.96 4.85
444 1792 6.560253 ATTGCTAGGTCTGTACAAAAGTTG 57.440 37.500 0.00 0.00 0.00 3.16
651 2007 5.126061 CCGATGAAGATTTGTCCCAAAGAAT 59.874 40.000 0.00 0.00 0.00 2.40
1206 3992 5.107298 GCAGAGCGGTTCTTAATCATATCAC 60.107 44.000 0.00 0.00 32.41 3.06
1459 4251 2.691011 GAGCTACTCCCAGAACTTCGAT 59.309 50.000 0.00 0.00 0.00 3.59
1463 4255 2.248248 ACTCCCAGAACTTCGATGACA 58.752 47.619 5.16 0.00 0.00 3.58
1883 5377 9.797642 AAGTTGTTTGATATATATGCATCCAGA 57.202 29.630 0.19 0.00 0.00 3.86
1884 5378 9.970553 AGTTGTTTGATATATATGCATCCAGAT 57.029 29.630 0.19 0.00 0.00 2.90
1887 5381 9.181061 TGTTTGATATATATGCATCCAGATTGG 57.819 33.333 0.19 0.00 39.43 3.16
1888 5382 8.627403 GTTTGATATATATGCATCCAGATTGGG 58.373 37.037 0.19 0.00 38.32 4.12
1889 5383 7.695074 TGATATATATGCATCCAGATTGGGA 57.305 36.000 0.19 0.00 42.21 4.37
1890 5384 8.104838 TGATATATATGCATCCAGATTGGGAA 57.895 34.615 0.19 0.00 41.12 3.97
1891 5385 8.215736 TGATATATATGCATCCAGATTGGGAAG 58.784 37.037 0.19 0.00 41.12 3.46
1892 5386 4.736611 ATATGCATCCAGATTGGGAAGT 57.263 40.909 0.19 0.00 41.12 3.01
1893 5387 2.133281 TGCATCCAGATTGGGAAGTG 57.867 50.000 0.00 0.00 41.12 3.16
1894 5388 1.634973 TGCATCCAGATTGGGAAGTGA 59.365 47.619 0.00 0.00 41.12 3.41
1895 5389 2.041485 TGCATCCAGATTGGGAAGTGAA 59.959 45.455 0.00 0.00 41.12 3.18
1896 5390 2.686915 GCATCCAGATTGGGAAGTGAAG 59.313 50.000 0.00 0.00 41.12 3.02
1897 5391 3.875369 GCATCCAGATTGGGAAGTGAAGT 60.875 47.826 0.00 0.00 41.12 3.01
1898 5392 3.423539 TCCAGATTGGGAAGTGAAGTG 57.576 47.619 0.00 0.00 38.32 3.16
1899 5393 2.040278 TCCAGATTGGGAAGTGAAGTGG 59.960 50.000 0.00 0.00 38.32 4.00
1900 5394 2.040278 CCAGATTGGGAAGTGAAGTGGA 59.960 50.000 0.00 0.00 32.67 4.02
1901 5395 3.308688 CCAGATTGGGAAGTGAAGTGGAT 60.309 47.826 0.00 0.00 32.67 3.41
1902 5396 4.338879 CAGATTGGGAAGTGAAGTGGATT 58.661 43.478 0.00 0.00 0.00 3.01
1903 5397 4.768968 CAGATTGGGAAGTGAAGTGGATTT 59.231 41.667 0.00 0.00 0.00 2.17
1904 5398 5.012893 AGATTGGGAAGTGAAGTGGATTTC 58.987 41.667 0.00 0.00 0.00 2.17
1905 5399 3.154827 TGGGAAGTGAAGTGGATTTCC 57.845 47.619 0.00 0.00 37.23 3.13
1906 5400 2.445145 TGGGAAGTGAAGTGGATTTCCA 59.555 45.455 0.00 0.00 45.30 3.53
1922 5416 8.200024 TGGATTTCCAATGTAAATTTTCAGGA 57.800 30.769 0.00 0.00 44.35 3.86
1923 5417 8.313292 TGGATTTCCAATGTAAATTTTCAGGAG 58.687 33.333 0.00 0.00 44.35 3.69
1924 5418 7.765819 GGATTTCCAATGTAAATTTTCAGGAGG 59.234 37.037 0.00 1.68 35.64 4.30
1925 5419 5.659440 TCCAATGTAAATTTTCAGGAGGC 57.341 39.130 0.00 0.00 0.00 4.70
1926 5420 5.083122 TCCAATGTAAATTTTCAGGAGGCA 58.917 37.500 0.00 0.00 0.00 4.75
1927 5421 5.721000 TCCAATGTAAATTTTCAGGAGGCAT 59.279 36.000 0.00 0.00 0.00 4.40
1928 5422 5.813672 CCAATGTAAATTTTCAGGAGGCATG 59.186 40.000 0.00 0.00 0.00 4.06
1929 5423 6.351202 CCAATGTAAATTTTCAGGAGGCATGA 60.351 38.462 0.00 0.00 0.00 3.07
1930 5424 7.270047 CAATGTAAATTTTCAGGAGGCATGAT 58.730 34.615 0.00 0.00 0.00 2.45
1931 5425 6.855763 TGTAAATTTTCAGGAGGCATGATT 57.144 33.333 0.00 0.00 0.00 2.57
1932 5426 7.243604 TGTAAATTTTCAGGAGGCATGATTT 57.756 32.000 0.00 0.00 0.00 2.17
1933 5427 7.098477 TGTAAATTTTCAGGAGGCATGATTTG 58.902 34.615 0.00 0.00 0.00 2.32
1934 5428 4.748277 ATTTTCAGGAGGCATGATTTGG 57.252 40.909 0.00 0.00 0.00 3.28
1935 5429 3.454719 TTTCAGGAGGCATGATTTGGA 57.545 42.857 0.00 0.00 0.00 3.53
1936 5430 3.454719 TTCAGGAGGCATGATTTGGAA 57.545 42.857 0.00 0.00 0.00 3.53
1937 5431 2.726821 TCAGGAGGCATGATTTGGAAC 58.273 47.619 0.00 0.00 0.00 3.62
1938 5432 1.753073 CAGGAGGCATGATTTGGAACC 59.247 52.381 0.00 0.00 0.00 3.62
1939 5433 1.358787 AGGAGGCATGATTTGGAACCA 59.641 47.619 0.00 0.00 0.00 3.67
1940 5434 1.478105 GGAGGCATGATTTGGAACCAC 59.522 52.381 0.00 0.00 0.00 4.16
1941 5435 1.478105 GAGGCATGATTTGGAACCACC 59.522 52.381 0.00 0.00 39.54 4.61
1942 5436 0.536724 GGCATGATTTGGAACCACCC 59.463 55.000 0.00 0.00 38.00 4.61
1943 5437 1.560505 GCATGATTTGGAACCACCCT 58.439 50.000 0.00 0.00 38.00 4.34
1944 5438 1.901833 GCATGATTTGGAACCACCCTT 59.098 47.619 0.00 0.00 38.00 3.95
1945 5439 3.096092 GCATGATTTGGAACCACCCTTA 58.904 45.455 0.00 0.00 38.00 2.69
1946 5440 3.706086 GCATGATTTGGAACCACCCTTAT 59.294 43.478 0.00 0.00 38.00 1.73
1947 5441 4.892934 GCATGATTTGGAACCACCCTTATA 59.107 41.667 0.00 0.00 38.00 0.98
1948 5442 5.362430 GCATGATTTGGAACCACCCTTATAA 59.638 40.000 0.00 0.00 38.00 0.98
1949 5443 6.127196 GCATGATTTGGAACCACCCTTATAAA 60.127 38.462 0.00 0.00 38.00 1.40
1950 5444 7.580495 GCATGATTTGGAACCACCCTTATAAAA 60.580 37.037 0.00 0.00 38.00 1.52
1951 5445 7.475137 TGATTTGGAACCACCCTTATAAAAG 57.525 36.000 0.00 0.00 38.00 2.27
1952 5446 7.013834 TGATTTGGAACCACCCTTATAAAAGT 58.986 34.615 0.00 0.00 38.00 2.66
1953 5447 7.511028 TGATTTGGAACCACCCTTATAAAAGTT 59.489 33.333 0.00 0.00 38.00 2.66
1954 5448 7.678207 TTTGGAACCACCCTTATAAAAGTTT 57.322 32.000 0.00 0.00 38.00 2.66
1955 5449 8.779096 TTTGGAACCACCCTTATAAAAGTTTA 57.221 30.769 0.00 0.00 38.00 2.01
1956 5450 8.959676 TTGGAACCACCCTTATAAAAGTTTAT 57.040 30.769 2.11 2.11 38.00 1.40
1957 5451 8.356000 TGGAACCACCCTTATAAAAGTTTATG 57.644 34.615 6.56 0.00 38.00 1.90
1958 5452 8.171400 TGGAACCACCCTTATAAAAGTTTATGA 58.829 33.333 6.56 0.00 38.00 2.15
1959 5453 9.197306 GGAACCACCCTTATAAAAGTTTATGAT 57.803 33.333 6.56 0.00 35.20 2.45
1978 5472 9.613428 TTTATGATTTTGTAGGTAGATCAGTGG 57.387 33.333 0.00 0.00 31.05 4.00
1979 5473 6.867519 TGATTTTGTAGGTAGATCAGTGGA 57.132 37.500 0.00 0.00 0.00 4.02
1980 5474 6.878317 TGATTTTGTAGGTAGATCAGTGGAG 58.122 40.000 0.00 0.00 0.00 3.86
1981 5475 6.667848 TGATTTTGTAGGTAGATCAGTGGAGA 59.332 38.462 0.00 0.00 0.00 3.71
1982 5476 6.531503 TTTTGTAGGTAGATCAGTGGAGAG 57.468 41.667 0.00 0.00 0.00 3.20
1983 5477 5.452341 TTGTAGGTAGATCAGTGGAGAGA 57.548 43.478 0.00 0.00 0.00 3.10
1984 5478 5.654901 TGTAGGTAGATCAGTGGAGAGAT 57.345 43.478 0.00 0.00 0.00 2.75
1985 5479 6.019656 TGTAGGTAGATCAGTGGAGAGATT 57.980 41.667 0.00 0.00 0.00 2.40
1986 5480 7.150447 TGTAGGTAGATCAGTGGAGAGATTA 57.850 40.000 0.00 0.00 0.00 1.75
1987 5481 7.583625 TGTAGGTAGATCAGTGGAGAGATTAA 58.416 38.462 0.00 0.00 0.00 1.40
1988 5482 8.059461 TGTAGGTAGATCAGTGGAGAGATTAAA 58.941 37.037 0.00 0.00 0.00 1.52
1989 5483 9.084533 GTAGGTAGATCAGTGGAGAGATTAAAT 57.915 37.037 0.00 0.00 0.00 1.40
1990 5484 8.189119 AGGTAGATCAGTGGAGAGATTAAATC 57.811 38.462 0.00 0.00 0.00 2.17
1991 5485 8.010105 AGGTAGATCAGTGGAGAGATTAAATCT 58.990 37.037 0.00 0.00 43.70 2.40
1992 5486 8.646900 GGTAGATCAGTGGAGAGATTAAATCTT 58.353 37.037 0.00 0.00 40.38 2.40
1997 5491 9.995003 ATCAGTGGAGAGATTAAATCTTATCAC 57.005 33.333 0.00 0.00 40.38 3.06
1998 5492 9.206690 TCAGTGGAGAGATTAAATCTTATCACT 57.793 33.333 13.51 13.51 40.38 3.41
1999 5493 9.829507 CAGTGGAGAGATTAAATCTTATCACTT 57.170 33.333 15.08 6.35 40.38 3.16
2019 5513 8.115491 TCACTTATCATTTTATTCACGAGACG 57.885 34.615 0.00 0.00 0.00 4.18
2020 5514 7.971722 TCACTTATCATTTTATTCACGAGACGA 59.028 33.333 0.00 0.00 0.00 4.20
2021 5515 8.592155 CACTTATCATTTTATTCACGAGACGAA 58.408 33.333 0.00 0.00 0.00 3.85
2022 5516 9.146984 ACTTATCATTTTATTCACGAGACGAAA 57.853 29.630 0.00 0.00 0.00 3.46
2023 5517 9.409949 CTTATCATTTTATTCACGAGACGAAAC 57.590 33.333 0.00 0.00 0.00 2.78
2024 5518 6.160664 TCATTTTATTCACGAGACGAAACC 57.839 37.500 0.00 0.00 0.00 3.27
2025 5519 5.697178 TCATTTTATTCACGAGACGAAACCA 59.303 36.000 0.00 0.00 0.00 3.67
2026 5520 5.987777 TTTTATTCACGAGACGAAACCAA 57.012 34.783 0.00 0.00 0.00 3.67
2027 5521 6.548441 TTTTATTCACGAGACGAAACCAAT 57.452 33.333 0.00 0.00 0.00 3.16
2028 5522 5.524511 TTATTCACGAGACGAAACCAATG 57.475 39.130 0.00 0.00 0.00 2.82
2029 5523 2.519377 TCACGAGACGAAACCAATGT 57.481 45.000 0.00 0.00 0.00 2.71
2030 5524 3.646611 TCACGAGACGAAACCAATGTA 57.353 42.857 0.00 0.00 0.00 2.29
2031 5525 3.571571 TCACGAGACGAAACCAATGTAG 58.428 45.455 0.00 0.00 0.00 2.74
2032 5526 3.005050 TCACGAGACGAAACCAATGTAGT 59.995 43.478 0.00 0.00 0.00 2.73
2033 5527 3.121279 CACGAGACGAAACCAATGTAGTG 59.879 47.826 0.00 0.00 0.00 2.74
2034 5528 3.243636 ACGAGACGAAACCAATGTAGTGT 60.244 43.478 0.00 0.00 0.00 3.55
2035 5529 4.022935 ACGAGACGAAACCAATGTAGTGTA 60.023 41.667 0.00 0.00 0.00 2.90
2036 5530 4.919168 CGAGACGAAACCAATGTAGTGTAA 59.081 41.667 0.00 0.00 0.00 2.41
2037 5531 5.164119 CGAGACGAAACCAATGTAGTGTAAC 60.164 44.000 0.00 0.00 0.00 2.50
2124 5800 0.679640 GGCATGATTCGGAACCACCA 60.680 55.000 0.00 0.00 38.90 4.17
2268 5947 7.169035 TGGTAGATAATTGATCGTTTTACGC 57.831 36.000 0.00 0.00 42.21 4.42
2364 6043 2.418628 CGTTACTTGCCACGATGGAATT 59.581 45.455 8.04 0.00 40.96 2.17
2430 6109 3.394836 GCACCGGGGCTTCTCTCT 61.395 66.667 24.98 0.00 0.00 3.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
258 1604 7.316393 TCCAATAGGAGTCCATAATTGTAGG 57.684 40.000 21.22 12.27 39.61 3.18
369 1717 2.618053 AGTACCTACTGACGCATTTGC 58.382 47.619 0.00 0.00 34.72 3.68
444 1792 5.758784 ACTTTTGTACAGACCTAGCACTTTC 59.241 40.000 0.00 0.00 0.00 2.62
1206 3992 1.450312 GCGAATGGGAGGTCACTGG 60.450 63.158 0.00 0.00 0.00 4.00
1459 4251 3.695606 GCAGGGACGAGGCTGTCA 61.696 66.667 15.59 0.00 40.72 3.58
1879 5373 2.040278 TCCACTTCACTTCCCAATCTGG 59.960 50.000 0.00 0.00 37.25 3.86
1880 5374 3.423539 TCCACTTCACTTCCCAATCTG 57.576 47.619 0.00 0.00 0.00 2.90
1881 5375 4.664688 AATCCACTTCACTTCCCAATCT 57.335 40.909 0.00 0.00 0.00 2.40
1882 5376 4.158579 GGAAATCCACTTCACTTCCCAATC 59.841 45.833 0.00 0.00 35.64 2.67
1883 5377 4.089361 GGAAATCCACTTCACTTCCCAAT 58.911 43.478 0.00 0.00 35.64 3.16
1884 5378 3.117322 TGGAAATCCACTTCACTTCCCAA 60.117 43.478 0.00 0.00 42.01 4.12
1885 5379 2.445145 TGGAAATCCACTTCACTTCCCA 59.555 45.455 0.00 0.00 42.01 4.37
1886 5380 3.154827 TGGAAATCCACTTCACTTCCC 57.845 47.619 0.00 0.00 42.01 3.97
1897 5391 8.200024 TCCTGAAAATTTACATTGGAAATCCA 57.800 30.769 7.30 0.00 45.94 3.41
1898 5392 7.765819 CCTCCTGAAAATTTACATTGGAAATCC 59.234 37.037 7.30 1.87 0.00 3.01
1899 5393 7.278646 GCCTCCTGAAAATTTACATTGGAAATC 59.721 37.037 7.30 0.00 0.00 2.17
1900 5394 7.105588 GCCTCCTGAAAATTTACATTGGAAAT 58.894 34.615 0.73 0.73 0.00 2.17
1901 5395 6.042552 TGCCTCCTGAAAATTTACATTGGAAA 59.957 34.615 0.00 0.00 0.00 3.13
1902 5396 5.541868 TGCCTCCTGAAAATTTACATTGGAA 59.458 36.000 0.00 0.00 0.00 3.53
1903 5397 5.083122 TGCCTCCTGAAAATTTACATTGGA 58.917 37.500 0.00 0.00 0.00 3.53
1904 5398 5.404466 TGCCTCCTGAAAATTTACATTGG 57.596 39.130 0.00 0.00 0.00 3.16
1905 5399 6.632909 TCATGCCTCCTGAAAATTTACATTG 58.367 36.000 0.00 0.00 0.00 2.82
1906 5400 6.855763 TCATGCCTCCTGAAAATTTACATT 57.144 33.333 0.00 0.00 0.00 2.71
1907 5401 7.427989 AATCATGCCTCCTGAAAATTTACAT 57.572 32.000 0.00 0.00 0.00 2.29
1908 5402 6.855763 AATCATGCCTCCTGAAAATTTACA 57.144 33.333 0.00 0.00 0.00 2.41
1909 5403 6.536224 CCAAATCATGCCTCCTGAAAATTTAC 59.464 38.462 0.00 0.00 0.00 2.01
1910 5404 6.440010 TCCAAATCATGCCTCCTGAAAATTTA 59.560 34.615 0.00 0.00 0.00 1.40
1911 5405 5.248934 TCCAAATCATGCCTCCTGAAAATTT 59.751 36.000 0.00 0.00 0.00 1.82
1912 5406 4.778958 TCCAAATCATGCCTCCTGAAAATT 59.221 37.500 0.00 0.00 0.00 1.82
1913 5407 4.355549 TCCAAATCATGCCTCCTGAAAAT 58.644 39.130 0.00 0.00 0.00 1.82
1914 5408 3.777087 TCCAAATCATGCCTCCTGAAAA 58.223 40.909 0.00 0.00 0.00 2.29
1915 5409 3.454719 TCCAAATCATGCCTCCTGAAA 57.545 42.857 0.00 0.00 0.00 2.69
1916 5410 3.091545 GTTCCAAATCATGCCTCCTGAA 58.908 45.455 0.00 0.00 0.00 3.02
1917 5411 2.621407 GGTTCCAAATCATGCCTCCTGA 60.621 50.000 0.00 0.00 0.00 3.86
1918 5412 1.753073 GGTTCCAAATCATGCCTCCTG 59.247 52.381 0.00 0.00 0.00 3.86
1919 5413 1.358787 TGGTTCCAAATCATGCCTCCT 59.641 47.619 0.00 0.00 0.00 3.69
1920 5414 1.478105 GTGGTTCCAAATCATGCCTCC 59.522 52.381 0.00 0.00 0.00 4.30
1921 5415 1.478105 GGTGGTTCCAAATCATGCCTC 59.522 52.381 0.00 0.00 35.97 4.70
1922 5416 1.560505 GGTGGTTCCAAATCATGCCT 58.439 50.000 0.00 0.00 35.97 4.75
1923 5417 0.536724 GGGTGGTTCCAAATCATGCC 59.463 55.000 0.00 0.00 38.11 4.40
1924 5418 1.560505 AGGGTGGTTCCAAATCATGC 58.439 50.000 0.00 0.00 38.11 4.06
1925 5419 7.416964 TTTATAAGGGTGGTTCCAAATCATG 57.583 36.000 0.00 0.00 38.11 3.07
1926 5420 7.678171 ACTTTTATAAGGGTGGTTCCAAATCAT 59.322 33.333 0.00 0.00 38.11 2.45
1927 5421 7.013834 ACTTTTATAAGGGTGGTTCCAAATCA 58.986 34.615 0.00 0.00 38.11 2.57
1928 5422 7.476540 ACTTTTATAAGGGTGGTTCCAAATC 57.523 36.000 0.00 0.00 38.11 2.17
1929 5423 7.865530 AACTTTTATAAGGGTGGTTCCAAAT 57.134 32.000 0.00 0.00 38.11 2.32
1930 5424 7.678207 AAACTTTTATAAGGGTGGTTCCAAA 57.322 32.000 0.00 0.00 38.11 3.28
1931 5425 8.808092 CATAAACTTTTATAAGGGTGGTTCCAA 58.192 33.333 0.00 0.00 35.61 3.53
1932 5426 8.171400 TCATAAACTTTTATAAGGGTGGTTCCA 58.829 33.333 0.00 0.00 35.61 3.53
1933 5427 8.584063 TCATAAACTTTTATAAGGGTGGTTCC 57.416 34.615 0.00 0.00 35.61 3.62
1952 5446 9.613428 CCACTGATCTACCTACAAAATCATAAA 57.387 33.333 0.00 0.00 0.00 1.40
1953 5447 8.988060 TCCACTGATCTACCTACAAAATCATAA 58.012 33.333 0.00 0.00 0.00 1.90
1954 5448 8.547481 TCCACTGATCTACCTACAAAATCATA 57.453 34.615 0.00 0.00 0.00 2.15
1955 5449 7.345653 TCTCCACTGATCTACCTACAAAATCAT 59.654 37.037 0.00 0.00 0.00 2.45
1956 5450 6.667848 TCTCCACTGATCTACCTACAAAATCA 59.332 38.462 0.00 0.00 0.00 2.57
1957 5451 7.068839 TCTCTCCACTGATCTACCTACAAAATC 59.931 40.741 0.00 0.00 0.00 2.17
1958 5452 6.897966 TCTCTCCACTGATCTACCTACAAAAT 59.102 38.462 0.00 0.00 0.00 1.82
1959 5453 6.253758 TCTCTCCACTGATCTACCTACAAAA 58.746 40.000 0.00 0.00 0.00 2.44
1960 5454 5.827756 TCTCTCCACTGATCTACCTACAAA 58.172 41.667 0.00 0.00 0.00 2.83
1961 5455 5.452341 TCTCTCCACTGATCTACCTACAA 57.548 43.478 0.00 0.00 0.00 2.41
1962 5456 5.654901 ATCTCTCCACTGATCTACCTACA 57.345 43.478 0.00 0.00 0.00 2.74
1963 5457 8.466617 TTTAATCTCTCCACTGATCTACCTAC 57.533 38.462 0.00 0.00 0.00 3.18
1964 5458 9.303116 GATTTAATCTCTCCACTGATCTACCTA 57.697 37.037 0.00 0.00 0.00 3.08
1965 5459 8.010105 AGATTTAATCTCTCCACTGATCTACCT 58.990 37.037 0.99 0.00 33.42 3.08
1966 5460 8.189119 AGATTTAATCTCTCCACTGATCTACC 57.811 38.462 0.99 0.00 33.42 3.18
1971 5465 9.995003 GTGATAAGATTTAATCTCTCCACTGAT 57.005 33.333 8.00 0.00 39.08 2.90
1972 5466 9.206690 AGTGATAAGATTTAATCTCTCCACTGA 57.793 33.333 22.59 4.18 38.88 3.41
1973 5467 9.829507 AAGTGATAAGATTTAATCTCTCCACTG 57.170 33.333 23.29 0.00 39.54 3.66
1993 5487 8.755941 CGTCTCGTGAATAAAATGATAAGTGAT 58.244 33.333 0.00 0.00 0.00 3.06
1994 5488 7.971722 TCGTCTCGTGAATAAAATGATAAGTGA 59.028 33.333 0.00 0.00 0.00 3.41
1995 5489 8.115491 TCGTCTCGTGAATAAAATGATAAGTG 57.885 34.615 0.00 0.00 0.00 3.16
1996 5490 8.697846 TTCGTCTCGTGAATAAAATGATAAGT 57.302 30.769 0.00 0.00 0.00 2.24
1997 5491 9.409949 GTTTCGTCTCGTGAATAAAATGATAAG 57.590 33.333 0.00 0.00 0.00 1.73
1998 5492 8.385111 GGTTTCGTCTCGTGAATAAAATGATAA 58.615 33.333 0.00 0.00 0.00 1.75
1999 5493 7.546316 TGGTTTCGTCTCGTGAATAAAATGATA 59.454 33.333 0.00 0.00 0.00 2.15
2000 5494 6.370442 TGGTTTCGTCTCGTGAATAAAATGAT 59.630 34.615 0.00 0.00 0.00 2.45
2001 5495 5.697178 TGGTTTCGTCTCGTGAATAAAATGA 59.303 36.000 0.00 0.00 0.00 2.57
2002 5496 5.922546 TGGTTTCGTCTCGTGAATAAAATG 58.077 37.500 0.00 0.00 0.00 2.32
2003 5497 6.548441 TTGGTTTCGTCTCGTGAATAAAAT 57.452 33.333 0.00 0.00 0.00 1.82
2004 5498 5.987777 TTGGTTTCGTCTCGTGAATAAAA 57.012 34.783 0.00 0.00 0.00 1.52
2005 5499 5.467399 ACATTGGTTTCGTCTCGTGAATAAA 59.533 36.000 0.00 0.00 0.00 1.40
2006 5500 4.992319 ACATTGGTTTCGTCTCGTGAATAA 59.008 37.500 0.00 0.00 0.00 1.40
2007 5501 4.562082 ACATTGGTTTCGTCTCGTGAATA 58.438 39.130 0.00 0.00 0.00 1.75
2008 5502 3.399330 ACATTGGTTTCGTCTCGTGAAT 58.601 40.909 0.00 0.00 0.00 2.57
2009 5503 2.828877 ACATTGGTTTCGTCTCGTGAA 58.171 42.857 0.00 0.00 0.00 3.18
2010 5504 2.519377 ACATTGGTTTCGTCTCGTGA 57.481 45.000 0.00 0.00 0.00 4.35
2011 5505 3.121279 CACTACATTGGTTTCGTCTCGTG 59.879 47.826 0.00 0.00 0.00 4.35
2012 5506 3.243636 ACACTACATTGGTTTCGTCTCGT 60.244 43.478 0.00 0.00 0.00 4.18
2013 5507 3.314553 ACACTACATTGGTTTCGTCTCG 58.685 45.455 0.00 0.00 0.00 4.04
2014 5508 5.924825 AGTTACACTACATTGGTTTCGTCTC 59.075 40.000 0.00 0.00 0.00 3.36
2015 5509 5.850614 AGTTACACTACATTGGTTTCGTCT 58.149 37.500 0.00 0.00 0.00 4.18
2016 5510 7.383300 ACTTAGTTACACTACATTGGTTTCGTC 59.617 37.037 0.00 0.00 28.93 4.20
2017 5511 7.212274 ACTTAGTTACACTACATTGGTTTCGT 58.788 34.615 0.00 0.00 28.93 3.85
2018 5512 7.647907 ACTTAGTTACACTACATTGGTTTCG 57.352 36.000 0.00 0.00 28.93 3.46
2019 5513 8.833493 ACAACTTAGTTACACTACATTGGTTTC 58.167 33.333 0.00 0.00 33.39 2.78
2020 5514 8.741603 ACAACTTAGTTACACTACATTGGTTT 57.258 30.769 0.00 0.00 33.39 3.27
2021 5515 8.741603 AACAACTTAGTTACACTACATTGGTT 57.258 30.769 0.00 0.00 33.39 3.67
2022 5516 8.617809 CAAACAACTTAGTTACACTACATTGGT 58.382 33.333 0.00 2.85 33.39 3.67
2023 5517 8.832521 TCAAACAACTTAGTTACACTACATTGG 58.167 33.333 0.00 0.00 33.39 3.16
2036 5530 9.204570 GGACGCATATATATCAAACAACTTAGT 57.795 33.333 0.00 0.00 0.00 2.24
2037 5531 9.203421 TGGACGCATATATATCAAACAACTTAG 57.797 33.333 0.00 0.00 0.00 2.18
2038 5532 9.719355 ATGGACGCATATATATCAAACAACTTA 57.281 29.630 0.00 0.00 0.00 2.24
2039 5533 8.621532 ATGGACGCATATATATCAAACAACTT 57.378 30.769 0.00 0.00 0.00 2.66
2040 5534 9.890629 ATATGGACGCATATATATCAAACAACT 57.109 29.630 0.00 0.00 0.00 3.16
2043 5537 9.108284 CCAATATGGACGCATATATATCAAACA 57.892 33.333 0.00 0.00 40.96 2.83
2044 5538 8.559536 CCCAATATGGACGCATATATATCAAAC 58.440 37.037 0.00 0.00 40.96 2.93
2045 5539 8.490311 TCCCAATATGGACGCATATATATCAAA 58.510 33.333 0.00 0.00 40.96 2.69
2046 5540 8.028652 TCCCAATATGGACGCATATATATCAA 57.971 34.615 0.00 0.00 40.96 2.57
2047 5541 7.610580 TCCCAATATGGACGCATATATATCA 57.389 36.000 0.00 0.00 40.96 2.15
2048 5542 8.150945 ACTTCCCAATATGGACGCATATATATC 58.849 37.037 0.00 0.00 40.96 1.63
2049 5543 7.933577 CACTTCCCAATATGGACGCATATATAT 59.066 37.037 0.00 0.00 40.96 0.86
2050 5544 7.125053 TCACTTCCCAATATGGACGCATATATA 59.875 37.037 0.00 0.00 40.96 0.86
2051 5545 6.070251 TCACTTCCCAATATGGACGCATATAT 60.070 38.462 0.00 0.00 40.96 0.86
2052 5546 5.247337 TCACTTCCCAATATGGACGCATATA 59.753 40.000 0.00 0.00 40.96 0.86
2053 5547 4.041567 TCACTTCCCAATATGGACGCATAT 59.958 41.667 0.00 0.00 40.96 1.78
2054 5548 3.389656 TCACTTCCCAATATGGACGCATA 59.610 43.478 0.00 0.00 40.96 3.14
2055 5549 2.172505 TCACTTCCCAATATGGACGCAT 59.827 45.455 0.00 0.00 40.96 4.73
2056 5550 1.557371 TCACTTCCCAATATGGACGCA 59.443 47.619 0.00 0.00 40.96 5.24
2057 5551 2.325583 TCACTTCCCAATATGGACGC 57.674 50.000 0.00 0.00 40.96 5.19
2058 5552 3.623060 CACTTCACTTCCCAATATGGACG 59.377 47.826 0.00 0.00 40.96 4.79
2059 5553 3.947834 CCACTTCACTTCCCAATATGGAC 59.052 47.826 0.00 0.00 40.96 4.02
2060 5554 3.849574 TCCACTTCACTTCCCAATATGGA 59.150 43.478 0.00 0.00 40.96 3.41
2268 5947 5.047021 TGCTTCTAATAAGGATGGATCTCGG 60.047 44.000 0.00 0.00 0.00 4.63
2301 5980 4.127907 TGTAATTCAACGGTGCTACAACA 58.872 39.130 0.00 0.00 0.00 3.33
2430 6109 3.243873 GCACCGATATCAACCATGAGAGA 60.244 47.826 3.12 0.00 39.39 3.10


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

AutoCloner maintained by Alex Coulton.