Multiple sequence alignment - TraesCS3D01G227800

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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 TraesCS3D01G227800 chr3D 100.000 2633 0 0 1 2633 309774593 309771961 0.000000e+00 4863.0
1 TraesCS3D01G227800 chr3D 78.914 313 38 18 2340 2627 591387760 591388069 1.240000e-43 187.0
2 TraesCS3D01G227800 chr3D 84.810 158 22 1 2472 2629 359914076 359914231 9.760000e-35 158.0
3 TraesCS3D01G227800 chr3D 79.828 233 31 12 2386 2609 563429837 563429612 3.510000e-34 156.0
4 TraesCS3D01G227800 chr3D 84.146 164 21 4 2468 2627 597863303 597863141 1.260000e-33 154.0
5 TraesCS3D01G227800 chr3B 93.071 1905 79 16 1 1862 411451158 411453052 0.000000e+00 2737.0
6 TraesCS3D01G227800 chr3B 92.086 139 8 3 1985 2122 411453071 411453207 2.670000e-45 193.0
7 TraesCS3D01G227800 chr3A 91.558 1836 94 16 1 1791 423128555 423130374 0.000000e+00 2475.0
8 TraesCS3D01G227800 chr3A 84.234 685 66 23 1969 2632 423130395 423131058 1.720000e-176 628.0
9 TraesCS3D01G227800 chr6D 83.826 643 82 12 2 623 412770969 412770328 2.260000e-165 592.0
10 TraesCS3D01G227800 chr2A 85.868 559 68 6 2 553 164769895 164769341 3.780000e-163 584.0
11 TraesCS3D01G227800 chr2A 81.071 560 96 7 2 553 442514499 442513942 3.110000e-119 438.0
12 TraesCS3D01G227800 chr2A 84.795 171 23 3 2464 2632 617056885 617056716 4.510000e-38 169.0
13 TraesCS3D01G227800 chr2B 85.246 549 59 10 2 547 424509439 424509968 1.780000e-151 545.0
14 TraesCS3D01G227800 chr2B 80.556 216 22 10 2395 2592 447866357 447866570 5.870000e-32 148.0
15 TraesCS3D01G227800 chr2B 86.667 75 3 5 2361 2428 263825987 263825913 2.810000e-10 76.8
16 TraesCS3D01G227800 chr5D 84.436 559 78 5 2 553 504022813 504022257 2.310000e-150 542.0
17 TraesCS3D01G227800 chr2D 84.712 556 66 12 2 553 356729713 356730253 2.980000e-149 538.0
18 TraesCS3D01G227800 chr2D 84.337 166 20 6 2468 2628 469774598 469774434 9.760000e-35 158.0
19 TraesCS3D01G227800 chr2D 85.714 63 7 2 2368 2428 127992343 127992281 6.080000e-07 65.8
20 TraesCS3D01G227800 chr4B 81.488 551 93 7 9 553 142544111 142544658 6.690000e-121 444.0
21 TraesCS3D01G227800 chr4B 77.348 181 21 11 2335 2497 19734071 19734249 3.610000e-14 89.8
22 TraesCS3D01G227800 chr6A 81.227 554 97 6 2 551 567940190 567940740 8.650000e-120 440.0
23 TraesCS3D01G227800 chr7D 85.354 198 23 6 2395 2586 586027758 586027561 1.600000e-47 200.0
24 TraesCS3D01G227800 chr7A 83.511 188 16 12 2432 2610 653618949 653618768 7.540000e-36 161.0
25 TraesCS3D01G227800 chr7A 82.888 187 18 12 2432 2610 653635446 653635266 3.510000e-34 156.0
26 TraesCS3D01G227800 chr7A 81.481 189 26 6 2444 2629 522928889 522929071 2.110000e-31 147.0
27 TraesCS3D01G227800 chrUn 74.321 405 65 22 2144 2524 331160278 331160667 4.570000e-28 135.0
28 TraesCS3D01G227800 chrUn 74.138 406 66 22 2144 2524 33334889 33334498 5.910000e-27 132.0


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 TraesCS3D01G227800 chr3D 309771961 309774593 2632 True 4863.0 4863 100.0000 1 2633 1 chr3D.!!$R1 2632
1 TraesCS3D01G227800 chr3B 411451158 411453207 2049 False 1465.0 2737 92.5785 1 2122 2 chr3B.!!$F1 2121
2 TraesCS3D01G227800 chr3A 423128555 423131058 2503 False 1551.5 2475 87.8960 1 2632 2 chr3A.!!$F1 2631
3 TraesCS3D01G227800 chr6D 412770328 412770969 641 True 592.0 592 83.8260 2 623 1 chr6D.!!$R1 621
4 TraesCS3D01G227800 chr2A 164769341 164769895 554 True 584.0 584 85.8680 2 553 1 chr2A.!!$R1 551
5 TraesCS3D01G227800 chr2A 442513942 442514499 557 True 438.0 438 81.0710 2 553 1 chr2A.!!$R2 551
6 TraesCS3D01G227800 chr2B 424509439 424509968 529 False 545.0 545 85.2460 2 547 1 chr2B.!!$F1 545
7 TraesCS3D01G227800 chr5D 504022257 504022813 556 True 542.0 542 84.4360 2 553 1 chr5D.!!$R1 551
8 TraesCS3D01G227800 chr2D 356729713 356730253 540 False 538.0 538 84.7120 2 553 1 chr2D.!!$F1 551
9 TraesCS3D01G227800 chr4B 142544111 142544658 547 False 444.0 444 81.4880 9 553 1 chr4B.!!$F2 544
10 TraesCS3D01G227800 chr6A 567940190 567940740 550 False 440.0 440 81.2270 2 551 1 chr6A.!!$F1 549

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
625 678 0.035439 GTTTGAGGGCTCGGATTGGA 60.035 55.0 0.0 0.0 0.0 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1919 2012 0.036875 GCCAACACTACTTCAGGGCT 59.963 55.0 0.0 0.0 37.0 5.19 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
229 249 3.063084 GACCACGGCTCCTCGTCT 61.063 66.667 0.00 0.00 41.86 4.18
231 251 3.374402 CCACGGCTCCTCGTCTGT 61.374 66.667 0.00 0.00 41.86 3.41
315 338 1.378762 GGCCAGCAAGGAAGTGGTA 59.621 57.895 0.00 0.00 41.22 3.25
403 426 8.365210 CGTTTATGTGAATTATGTGAACTTTGC 58.635 33.333 0.00 0.00 0.00 3.68
414 437 3.380004 TGTGAACTTTGCCGATCTTTTGT 59.620 39.130 0.00 0.00 0.00 2.83
562 610 2.866762 GAGATACACGGACAGGATTTGC 59.133 50.000 0.00 0.00 0.00 3.68
566 614 2.028130 ACACGGACAGGATTTGCAAAA 58.972 42.857 17.19 0.00 0.00 2.44
623 676 1.982073 GCGTTTGAGGGCTCGGATTG 61.982 60.000 0.00 0.00 0.00 2.67
624 677 1.369091 CGTTTGAGGGCTCGGATTGG 61.369 60.000 0.00 0.00 0.00 3.16
625 678 0.035439 GTTTGAGGGCTCGGATTGGA 60.035 55.000 0.00 0.00 0.00 3.53
626 679 0.918983 TTTGAGGGCTCGGATTGGAT 59.081 50.000 0.00 0.00 0.00 3.41
627 680 0.918983 TTGAGGGCTCGGATTGGATT 59.081 50.000 0.00 0.00 0.00 3.01
651 704 1.202463 AGCGGCTGTAGATGCTGTAAG 60.202 52.381 0.00 0.00 38.90 2.34
744 797 2.224744 TGCACATGGTACCACTGTGAAT 60.225 45.455 36.06 15.90 37.50 2.57
779 832 2.913578 ACTGCACGTGGGACCGTA 60.914 61.111 18.88 0.00 39.45 4.02
999 1066 1.002069 ATTCCATCCAGCCACCAAGA 58.998 50.000 0.00 0.00 0.00 3.02
1043 1110 1.371267 CGACGACGGCAGAACAAGA 60.371 57.895 0.00 0.00 35.72 3.02
1681 1771 1.203313 ACCTTACCTTCTGGCCTCTGA 60.203 52.381 3.32 0.00 36.63 3.27
1738 1828 6.753744 GTGGATGCCTGTTGAAATTAGATTTC 59.246 38.462 6.48 6.48 46.75 2.17
1813 1903 2.743664 CGAAAATCCATCTCTGCACACA 59.256 45.455 0.00 0.00 0.00 3.72
1816 1906 1.747709 ATCCATCTCTGCACACAAGC 58.252 50.000 0.00 0.00 0.00 4.01
1822 1912 1.622312 TCTCTGCACACAAGCTCATCT 59.378 47.619 0.00 0.00 34.99 2.90
1826 1916 0.809385 GCACACAAGCTCATCTGCAT 59.191 50.000 0.00 0.00 34.99 3.96
1904 1997 8.446489 TTTTATGATAGACAATTTGTTGCGTG 57.554 30.769 3.08 0.00 0.00 5.34
1905 1998 5.878332 ATGATAGACAATTTGTTGCGTGA 57.122 34.783 3.08 0.00 0.00 4.35
1906 1999 5.281693 TGATAGACAATTTGTTGCGTGAG 57.718 39.130 3.08 0.00 0.00 3.51
1907 2000 4.994217 TGATAGACAATTTGTTGCGTGAGA 59.006 37.500 3.08 0.00 0.00 3.27
1908 2001 3.609103 AGACAATTTGTTGCGTGAGAC 57.391 42.857 3.08 0.00 0.00 3.36
1909 2002 2.290641 AGACAATTTGTTGCGTGAGACC 59.709 45.455 3.08 0.00 0.00 3.85
1910 2003 2.290641 GACAATTTGTTGCGTGAGACCT 59.709 45.455 3.08 0.00 0.00 3.85
1911 2004 2.033299 ACAATTTGTTGCGTGAGACCTG 59.967 45.455 0.00 0.00 0.00 4.00
1912 2005 2.254546 ATTTGTTGCGTGAGACCTGA 57.745 45.000 0.00 0.00 0.00 3.86
1913 2006 2.031258 TTTGTTGCGTGAGACCTGAA 57.969 45.000 0.00 0.00 0.00 3.02
1914 2007 1.581934 TTGTTGCGTGAGACCTGAAG 58.418 50.000 0.00 0.00 0.00 3.02
1915 2008 0.464036 TGTTGCGTGAGACCTGAAGT 59.536 50.000 0.00 0.00 0.00 3.01
1916 2009 1.684450 TGTTGCGTGAGACCTGAAGTA 59.316 47.619 0.00 0.00 0.00 2.24
1917 2010 2.288213 TGTTGCGTGAGACCTGAAGTAG 60.288 50.000 0.00 0.00 0.00 2.57
1918 2011 1.617322 TGCGTGAGACCTGAAGTAGT 58.383 50.000 0.00 0.00 0.00 2.73
1919 2012 2.786777 TGCGTGAGACCTGAAGTAGTA 58.213 47.619 0.00 0.00 0.00 1.82
1920 2013 2.747989 TGCGTGAGACCTGAAGTAGTAG 59.252 50.000 0.00 0.00 0.00 2.57
1921 2014 2.478200 GCGTGAGACCTGAAGTAGTAGC 60.478 54.545 0.00 0.00 0.00 3.58
1922 2015 2.097791 CGTGAGACCTGAAGTAGTAGCC 59.902 54.545 0.00 0.00 0.00 3.93
1923 2016 2.427812 GTGAGACCTGAAGTAGTAGCCC 59.572 54.545 0.00 0.00 0.00 5.19
1924 2017 2.312140 TGAGACCTGAAGTAGTAGCCCT 59.688 50.000 0.00 0.00 0.00 5.19
1925 2018 2.691011 GAGACCTGAAGTAGTAGCCCTG 59.309 54.545 0.00 0.00 0.00 4.45
1926 2019 2.312140 AGACCTGAAGTAGTAGCCCTGA 59.688 50.000 0.00 0.00 0.00 3.86
1927 2020 3.097614 GACCTGAAGTAGTAGCCCTGAA 58.902 50.000 0.00 0.00 0.00 3.02
1928 2021 3.100671 ACCTGAAGTAGTAGCCCTGAAG 58.899 50.000 0.00 0.00 0.00 3.02
1929 2022 3.100671 CCTGAAGTAGTAGCCCTGAAGT 58.899 50.000 0.00 0.00 0.00 3.01
1930 2023 4.264262 ACCTGAAGTAGTAGCCCTGAAGTA 60.264 45.833 0.00 0.00 0.00 2.24
1931 2024 4.339814 CCTGAAGTAGTAGCCCTGAAGTAG 59.660 50.000 0.00 0.00 0.00 2.57
1932 2025 4.931914 TGAAGTAGTAGCCCTGAAGTAGT 58.068 43.478 0.00 0.00 0.00 2.73
1933 2026 4.705507 TGAAGTAGTAGCCCTGAAGTAGTG 59.294 45.833 0.00 0.00 0.00 2.74
1934 2027 4.319037 AGTAGTAGCCCTGAAGTAGTGT 57.681 45.455 0.00 0.00 0.00 3.55
1935 2028 4.675038 AGTAGTAGCCCTGAAGTAGTGTT 58.325 43.478 0.00 0.00 0.00 3.32
1936 2029 3.963428 AGTAGCCCTGAAGTAGTGTTG 57.037 47.619 0.00 0.00 0.00 3.33
1937 2030 2.567615 AGTAGCCCTGAAGTAGTGTTGG 59.432 50.000 0.00 0.00 0.00 3.77
1938 2031 0.036875 AGCCCTGAAGTAGTGTTGGC 59.963 55.000 0.00 0.00 37.68 4.52
1939 2032 0.960861 GCCCTGAAGTAGTGTTGGCC 60.961 60.000 0.00 0.00 0.00 5.36
1940 2033 0.673644 CCCTGAAGTAGTGTTGGCCG 60.674 60.000 0.00 0.00 0.00 6.13
1941 2034 0.673644 CCTGAAGTAGTGTTGGCCGG 60.674 60.000 0.00 0.00 0.00 6.13
1942 2035 0.673644 CTGAAGTAGTGTTGGCCGGG 60.674 60.000 2.18 0.00 0.00 5.73
1943 2036 1.373812 GAAGTAGTGTTGGCCGGGT 59.626 57.895 2.18 0.00 0.00 5.28
1944 2037 0.250597 GAAGTAGTGTTGGCCGGGTT 60.251 55.000 2.18 0.00 0.00 4.11
1945 2038 0.536460 AAGTAGTGTTGGCCGGGTTG 60.536 55.000 2.18 0.00 0.00 3.77
1946 2039 1.228033 GTAGTGTTGGCCGGGTTGT 60.228 57.895 2.18 0.00 0.00 3.32
1947 2040 0.820482 GTAGTGTTGGCCGGGTTGTT 60.820 55.000 2.18 0.00 0.00 2.83
1948 2041 0.820074 TAGTGTTGGCCGGGTTGTTG 60.820 55.000 2.18 0.00 0.00 3.33
1949 2042 2.122167 GTGTTGGCCGGGTTGTTGA 61.122 57.895 2.18 0.00 0.00 3.18
1950 2043 2.122167 TGTTGGCCGGGTTGTTGAC 61.122 57.895 2.18 0.00 0.00 3.18
1962 2055 2.152016 GTTGTTGACCAGTCTAAGGCC 58.848 52.381 0.00 0.00 0.00 5.19
1963 2056 0.690762 TGTTGACCAGTCTAAGGCCC 59.309 55.000 0.00 0.00 0.00 5.80
1964 2057 0.690762 GTTGACCAGTCTAAGGCCCA 59.309 55.000 0.00 0.00 0.00 5.36
1965 2058 0.984230 TTGACCAGTCTAAGGCCCAG 59.016 55.000 0.00 0.00 0.00 4.45
1966 2059 1.222113 GACCAGTCTAAGGCCCAGC 59.778 63.158 0.00 0.00 0.00 4.85
2025 2119 6.038714 CCATCTAGTTGCAAAATCTTCCCTAC 59.961 42.308 0.00 0.00 0.00 3.18
2029 2123 5.842907 AGTTGCAAAATCTTCCCTACAAAC 58.157 37.500 0.00 0.00 0.00 2.93
2034 2128 7.106239 TGCAAAATCTTCCCTACAAACAAAAA 58.894 30.769 0.00 0.00 0.00 1.94
2124 2218 0.329261 TTCACTTGGGATGGGCTGAG 59.671 55.000 0.00 0.00 0.00 3.35
2126 2220 0.107312 CACTTGGGATGGGCTGAGAG 60.107 60.000 0.00 0.00 0.00 3.20
2129 2223 3.474570 GGGATGGGCTGAGAGCGT 61.475 66.667 0.00 0.00 43.62 5.07
2131 2225 2.894387 GATGGGCTGAGAGCGTGC 60.894 66.667 0.00 0.00 43.62 5.34
2152 2246 2.731691 ATTTGGCGCTCAGTCACCGT 62.732 55.000 7.64 0.00 31.94 4.83
2155 2249 3.106407 GCGCTCAGTCACCGTCAC 61.106 66.667 0.00 0.00 0.00 3.67
2160 2254 0.660595 CTCAGTCACCGTCACGTGTC 60.661 60.000 16.51 9.31 35.18 3.67
2165 2259 2.028484 ACCGTCACGTGTCGCATT 59.972 55.556 26.15 11.91 0.00 3.56
2166 2260 1.004785 CACCGTCACGTGTCGCATTA 61.005 55.000 26.15 0.00 0.00 1.90
2168 2262 0.297525 CCGTCACGTGTCGCATTATG 59.702 55.000 26.15 10.41 0.00 1.90
2181 2275 1.953686 GCATTATGGGCGCTTCCTTTA 59.046 47.619 7.64 0.00 34.39 1.85
2284 2384 8.357402 GTCTTTCTTAGCTTTTGGACCAATTTA 58.643 33.333 7.99 0.00 0.00 1.40
2285 2385 8.919145 TCTTTCTTAGCTTTTGGACCAATTTAA 58.081 29.630 7.99 0.00 0.00 1.52
2286 2386 9.541143 CTTTCTTAGCTTTTGGACCAATTTAAA 57.459 29.630 7.99 0.00 0.00 1.52
2328 2433 2.048503 ACGTTTTCCCGCGAGAGG 60.049 61.111 8.23 0.00 0.00 3.69
2346 2451 2.050442 GGTGGTTTTGCTTCCGCG 60.050 61.111 0.00 0.00 39.65 6.46
2347 2452 2.050442 GTGGTTTTGCTTCCGCGG 60.050 61.111 22.12 22.12 39.65 6.46
2348 2453 3.291383 TGGTTTTGCTTCCGCGGG 61.291 61.111 27.83 11.74 39.65 6.13
2374 2479 1.377202 GCCATGCCTCTCGGAAACA 60.377 57.895 0.00 0.00 0.00 2.83
2428 2535 0.033504 AGTTTTGCTTCCGCGAGAGA 59.966 50.000 8.23 0.00 39.65 3.10
2446 2562 1.978580 AGAGCCTCTCGGAAAGGAAAA 59.021 47.619 0.36 0.00 35.83 2.29
2472 2588 6.954487 ACACGTTCTCCCTTTTTATTTTCT 57.046 33.333 0.00 0.00 0.00 2.52
2476 2592 7.112984 CACGTTCTCCCTTTTTATTTTCTTTCG 59.887 37.037 0.00 0.00 0.00 3.46
2478 2594 7.112984 CGTTCTCCCTTTTTATTTTCTTTCGTG 59.887 37.037 0.00 0.00 0.00 4.35
2483 2599 7.040686 TCCCTTTTTATTTTCTTTCGTGAGAGG 60.041 37.037 0.00 0.00 43.69 3.69
2486 2602 6.817765 TTTATTTTCTTTCGTGAGAGGCAT 57.182 33.333 0.00 0.00 43.69 4.40
2487 2603 4.691860 ATTTTCTTTCGTGAGAGGCATG 57.308 40.909 0.00 0.00 43.69 4.06
2501 2617 2.088178 GCATGGTTTTGCTTCCGCG 61.088 57.895 0.00 0.00 39.57 6.46
2586 2702 2.496341 CTTCCGCGAGAGGCATGA 59.504 61.111 8.23 0.00 43.84 3.07
2595 2711 2.793933 GCGAGAGGCATGATTTTGCTTC 60.794 50.000 0.00 0.80 46.00 3.86
2599 2715 2.231964 GAGGCATGATTTTGCTTCCACA 59.768 45.455 0.00 0.00 41.44 4.17
2632 2748 0.889186 TGCCTCTTGGAAACGGCTTC 60.889 55.000 0.00 0.00 37.97 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
177 182 0.686224 GGAGAGGATGATGAGCCCTG 59.314 60.000 0.00 0.00 0.00 4.45
229 249 1.078637 AGGATCGTCCGAGTCGACA 60.079 57.895 19.50 0.00 42.75 4.35
231 251 1.523258 GGAGGATCGTCCGAGTCGA 60.523 63.158 18.18 0.00 42.75 4.20
483 521 9.840427 GCAACATACAAGTAAACAACATAGATT 57.160 29.630 0.00 0.00 0.00 2.40
562 610 2.667171 CGAACACTAACCGGGCATTTTG 60.667 50.000 6.32 0.00 0.00 2.44
566 614 1.078708 CCGAACACTAACCGGGCAT 60.079 57.895 6.32 0.00 39.59 4.40
623 676 0.744414 TCTACAGCCGCTGCAAATCC 60.744 55.000 20.56 0.00 41.13 3.01
624 677 1.003116 CATCTACAGCCGCTGCAAATC 60.003 52.381 20.56 0.00 41.13 2.17
625 678 1.019673 CATCTACAGCCGCTGCAAAT 58.980 50.000 20.56 8.09 41.13 2.32
626 679 1.647545 GCATCTACAGCCGCTGCAAA 61.648 55.000 20.56 5.99 41.13 3.68
627 680 2.108514 GCATCTACAGCCGCTGCAA 61.109 57.895 20.56 8.01 41.13 4.08
884 937 0.753848 GGAGAGGAACCGAGGAGAGG 60.754 65.000 0.00 0.00 0.00 3.69
885 938 2.801859 GGAGAGGAACCGAGGAGAG 58.198 63.158 0.00 0.00 0.00 3.20
959 1022 2.877582 CGGCCGGTTCTTACGTCG 60.878 66.667 20.10 0.00 0.00 5.12
966 1029 1.376812 GGAATCAACGGCCGGTTCT 60.377 57.895 31.76 9.67 36.49 3.01
999 1066 2.285368 TCCTCTCCCGTGCCCATT 60.285 61.111 0.00 0.00 0.00 3.16
1043 1110 1.039068 CTGCTCATCATCCTCTCCGT 58.961 55.000 0.00 0.00 0.00 4.69
1073 1140 0.563173 CATCACCCCTCCTCCTCCTA 59.437 60.000 0.00 0.00 0.00 2.94
1494 1584 2.801631 CCAGTCCCCGCTCAGATCC 61.802 68.421 0.00 0.00 0.00 3.36
1813 1903 0.177373 TCAGCGATGCAGATGAGCTT 59.823 50.000 0.00 0.00 35.82 3.74
1816 1906 0.248784 TCGTCAGCGATGCAGATGAG 60.249 55.000 0.00 0.00 42.81 2.90
1878 1971 8.910666 CACGCAACAAATTGTCTATCATAAAAA 58.089 29.630 0.00 0.00 38.17 1.94
1879 1972 8.293157 TCACGCAACAAATTGTCTATCATAAAA 58.707 29.630 0.00 0.00 38.17 1.52
1880 1973 7.811653 TCACGCAACAAATTGTCTATCATAAA 58.188 30.769 0.00 0.00 38.17 1.40
1881 1974 7.333174 TCTCACGCAACAAATTGTCTATCATAA 59.667 33.333 0.00 0.00 38.17 1.90
1882 1975 6.816140 TCTCACGCAACAAATTGTCTATCATA 59.184 34.615 0.00 0.00 38.17 2.15
1883 1976 5.643348 TCTCACGCAACAAATTGTCTATCAT 59.357 36.000 0.00 0.00 38.17 2.45
1884 1977 4.994217 TCTCACGCAACAAATTGTCTATCA 59.006 37.500 0.00 0.00 38.17 2.15
1885 1978 5.316770 GTCTCACGCAACAAATTGTCTATC 58.683 41.667 0.00 0.00 38.17 2.08
1886 1979 4.154195 GGTCTCACGCAACAAATTGTCTAT 59.846 41.667 0.00 0.00 38.17 1.98
1887 1980 3.496884 GGTCTCACGCAACAAATTGTCTA 59.503 43.478 0.00 0.00 38.17 2.59
1888 1981 2.290641 GGTCTCACGCAACAAATTGTCT 59.709 45.455 0.00 0.00 38.17 3.41
1889 1982 2.290641 AGGTCTCACGCAACAAATTGTC 59.709 45.455 0.00 0.00 38.17 3.18
1890 1983 2.033299 CAGGTCTCACGCAACAAATTGT 59.967 45.455 0.00 0.00 38.17 2.71
1891 1984 2.290367 TCAGGTCTCACGCAACAAATTG 59.710 45.455 0.00 0.00 38.99 2.32
1892 1985 2.571212 TCAGGTCTCACGCAACAAATT 58.429 42.857 0.00 0.00 0.00 1.82
1893 1986 2.254546 TCAGGTCTCACGCAACAAAT 57.745 45.000 0.00 0.00 0.00 2.32
1894 1987 1.939934 CTTCAGGTCTCACGCAACAAA 59.060 47.619 0.00 0.00 0.00 2.83
1895 1988 1.134521 ACTTCAGGTCTCACGCAACAA 60.135 47.619 0.00 0.00 0.00 2.83
1896 1989 0.464036 ACTTCAGGTCTCACGCAACA 59.536 50.000 0.00 0.00 0.00 3.33
1897 1990 2.288273 ACTACTTCAGGTCTCACGCAAC 60.288 50.000 0.00 0.00 0.00 4.17
1898 1991 1.961394 ACTACTTCAGGTCTCACGCAA 59.039 47.619 0.00 0.00 0.00 4.85
1899 1992 1.617322 ACTACTTCAGGTCTCACGCA 58.383 50.000 0.00 0.00 0.00 5.24
1900 1993 2.478200 GCTACTACTTCAGGTCTCACGC 60.478 54.545 0.00 0.00 0.00 5.34
1901 1994 2.097791 GGCTACTACTTCAGGTCTCACG 59.902 54.545 0.00 0.00 0.00 4.35
1902 1995 2.427812 GGGCTACTACTTCAGGTCTCAC 59.572 54.545 0.00 0.00 0.00 3.51
1903 1996 2.312140 AGGGCTACTACTTCAGGTCTCA 59.688 50.000 0.00 0.00 0.00 3.27
1904 1997 2.691011 CAGGGCTACTACTTCAGGTCTC 59.309 54.545 0.00 0.00 0.00 3.36
1905 1998 2.312140 TCAGGGCTACTACTTCAGGTCT 59.688 50.000 0.00 0.00 0.00 3.85
1906 1999 2.736347 TCAGGGCTACTACTTCAGGTC 58.264 52.381 0.00 0.00 0.00 3.85
1907 2000 2.921834 TCAGGGCTACTACTTCAGGT 57.078 50.000 0.00 0.00 0.00 4.00
1908 2001 3.100671 ACTTCAGGGCTACTACTTCAGG 58.899 50.000 0.00 0.00 0.00 3.86
1909 2002 4.951094 ACTACTTCAGGGCTACTACTTCAG 59.049 45.833 0.00 0.00 0.00 3.02
1910 2003 4.705507 CACTACTTCAGGGCTACTACTTCA 59.294 45.833 0.00 0.00 0.00 3.02
1911 2004 4.705991 ACACTACTTCAGGGCTACTACTTC 59.294 45.833 0.00 0.00 0.00 3.01
1912 2005 4.675038 ACACTACTTCAGGGCTACTACTT 58.325 43.478 0.00 0.00 0.00 2.24
1913 2006 4.319037 ACACTACTTCAGGGCTACTACT 57.681 45.455 0.00 0.00 0.00 2.57
1914 2007 4.381718 CCAACACTACTTCAGGGCTACTAC 60.382 50.000 0.00 0.00 0.00 2.73
1915 2008 3.767673 CCAACACTACTTCAGGGCTACTA 59.232 47.826 0.00 0.00 0.00 1.82
1916 2009 2.567615 CCAACACTACTTCAGGGCTACT 59.432 50.000 0.00 0.00 0.00 2.57
1917 2010 2.935676 GCCAACACTACTTCAGGGCTAC 60.936 54.545 0.00 0.00 37.00 3.58
1918 2011 1.278127 GCCAACACTACTTCAGGGCTA 59.722 52.381 0.00 0.00 37.00 3.93
1919 2012 0.036875 GCCAACACTACTTCAGGGCT 59.963 55.000 0.00 0.00 37.00 5.19
1920 2013 0.960861 GGCCAACACTACTTCAGGGC 60.961 60.000 0.00 0.00 39.18 5.19
1921 2014 0.673644 CGGCCAACACTACTTCAGGG 60.674 60.000 2.24 0.00 0.00 4.45
1922 2015 0.673644 CCGGCCAACACTACTTCAGG 60.674 60.000 2.24 0.00 0.00 3.86
1923 2016 0.673644 CCCGGCCAACACTACTTCAG 60.674 60.000 2.24 0.00 0.00 3.02
1924 2017 1.373435 CCCGGCCAACACTACTTCA 59.627 57.895 2.24 0.00 0.00 3.02
1925 2018 0.250597 AACCCGGCCAACACTACTTC 60.251 55.000 2.24 0.00 0.00 3.01
1926 2019 0.536460 CAACCCGGCCAACACTACTT 60.536 55.000 2.24 0.00 0.00 2.24
1927 2020 1.072505 CAACCCGGCCAACACTACT 59.927 57.895 2.24 0.00 0.00 2.57
1928 2021 0.820482 AACAACCCGGCCAACACTAC 60.820 55.000 2.24 0.00 0.00 2.73
1929 2022 0.820074 CAACAACCCGGCCAACACTA 60.820 55.000 2.24 0.00 0.00 2.74
1930 2023 2.124693 CAACAACCCGGCCAACACT 61.125 57.895 2.24 0.00 0.00 3.55
1931 2024 2.122167 TCAACAACCCGGCCAACAC 61.122 57.895 2.24 0.00 0.00 3.32
1932 2025 2.122167 GTCAACAACCCGGCCAACA 61.122 57.895 2.24 0.00 0.00 3.33
1933 2026 2.725641 GTCAACAACCCGGCCAAC 59.274 61.111 2.24 0.00 0.00 3.77
1934 2027 2.519780 GGTCAACAACCCGGCCAA 60.520 61.111 2.24 0.00 42.85 4.52
1942 2035 2.152016 GGCCTTAGACTGGTCAACAAC 58.848 52.381 0.00 0.00 0.00 3.32
1943 2036 1.073284 GGGCCTTAGACTGGTCAACAA 59.927 52.381 0.84 0.00 0.00 2.83
1944 2037 0.690762 GGGCCTTAGACTGGTCAACA 59.309 55.000 0.84 0.00 0.00 3.33
1945 2038 0.690762 TGGGCCTTAGACTGGTCAAC 59.309 55.000 4.53 0.00 0.00 3.18
1946 2039 0.984230 CTGGGCCTTAGACTGGTCAA 59.016 55.000 4.53 0.00 0.00 3.18
1947 2040 1.553690 GCTGGGCCTTAGACTGGTCA 61.554 60.000 4.53 0.00 0.00 4.02
1948 2041 1.222113 GCTGGGCCTTAGACTGGTC 59.778 63.158 4.53 0.00 0.00 4.02
1949 2042 2.301738 GGCTGGGCCTTAGACTGGT 61.302 63.158 4.53 0.00 46.69 4.00
1950 2043 2.592308 GGCTGGGCCTTAGACTGG 59.408 66.667 4.53 0.00 46.69 4.00
1960 2053 6.901081 ATAAAATTTACTAGATGGCTGGGC 57.099 37.500 0.00 0.00 0.00 5.36
1971 2064 9.623000 GGGCTGACTCCTAAATAAAATTTACTA 57.377 33.333 0.00 0.00 0.00 1.82
1972 2065 8.113462 TGGGCTGACTCCTAAATAAAATTTACT 58.887 33.333 0.00 0.00 0.00 2.24
1973 2066 8.288689 TGGGCTGACTCCTAAATAAAATTTAC 57.711 34.615 0.00 0.00 0.00 2.01
1974 2067 7.068226 GCTGGGCTGACTCCTAAATAAAATTTA 59.932 37.037 0.00 0.00 0.00 1.40
1975 2068 6.127338 GCTGGGCTGACTCCTAAATAAAATTT 60.127 38.462 0.00 0.00 0.00 1.82
1982 2075 0.548510 GGCTGGGCTGACTCCTAAAT 59.451 55.000 0.00 0.00 0.00 1.40
1993 2086 1.225704 GCAACTAGATGGCTGGGCT 59.774 57.895 0.00 0.00 0.00 5.19
2025 2119 9.437045 GGAGATTTTGCAACTAATTTTTGTTTG 57.563 29.630 0.00 0.00 0.00 2.93
2029 2123 7.501515 GTCGGAGATTTTGCAACTAATTTTTG 58.498 34.615 0.00 0.00 40.67 2.44
2034 2128 3.181510 GCGTCGGAGATTTTGCAACTAAT 60.182 43.478 0.00 0.00 40.67 1.73
2131 2225 1.503542 GTGACTGAGCGCCAAATGG 59.496 57.895 2.29 0.00 38.53 3.16
2134 2228 2.664851 CGGTGACTGAGCGCCAAA 60.665 61.111 2.29 0.00 39.02 3.28
2152 2246 1.087202 GCCCATAATGCGACACGTGA 61.087 55.000 25.01 0.00 0.00 4.35
2165 2259 5.669164 AAAATTTAAAGGAAGCGCCCATA 57.331 34.783 2.29 0.00 37.37 2.74
2166 2260 4.551702 AAAATTTAAAGGAAGCGCCCAT 57.448 36.364 2.29 0.00 37.37 4.00
2248 2348 3.813724 AGCTAAGAAAGACCGGTGAAAAC 59.186 43.478 14.63 0.00 0.00 2.43
2257 2357 4.142038 TGGTCCAAAAGCTAAGAAAGACC 58.858 43.478 11.59 11.59 42.32 3.85
2393 2500 0.753262 AACTATGCCTCTCGCGGAAT 59.247 50.000 6.13 0.00 42.08 3.01
2398 2505 3.905900 GCAAAACTATGCCTCTCGC 57.094 52.632 0.00 0.00 40.49 5.03
2446 2562 8.255206 AGAAAATAAAAAGGGAGAACGTGTTTT 58.745 29.630 0.00 0.00 0.00 2.43
2448 2564 7.342769 AGAAAATAAAAAGGGAGAACGTGTT 57.657 32.000 0.00 0.00 0.00 3.32
2449 2565 6.954487 AGAAAATAAAAAGGGAGAACGTGT 57.046 33.333 0.00 0.00 0.00 4.49
2450 2566 7.112984 CGAAAGAAAATAAAAAGGGAGAACGTG 59.887 37.037 0.00 0.00 0.00 4.49
2451 2567 7.136772 CGAAAGAAAATAAAAAGGGAGAACGT 58.863 34.615 0.00 0.00 0.00 3.99
2452 2568 7.112984 CACGAAAGAAAATAAAAAGGGAGAACG 59.887 37.037 0.00 0.00 0.00 3.95
2453 2569 8.132995 TCACGAAAGAAAATAAAAAGGGAGAAC 58.867 33.333 0.00 0.00 0.00 3.01
2454 2570 8.228035 TCACGAAAGAAAATAAAAAGGGAGAA 57.772 30.769 0.00 0.00 0.00 2.87
2455 2571 7.717875 TCTCACGAAAGAAAATAAAAAGGGAGA 59.282 33.333 0.00 0.00 0.00 3.71
2456 2572 7.871853 TCTCACGAAAGAAAATAAAAAGGGAG 58.128 34.615 0.00 0.00 0.00 4.30
2457 2573 7.040686 CCTCTCACGAAAGAAAATAAAAAGGGA 60.041 37.037 0.00 0.00 0.00 4.20
2458 2574 7.084486 CCTCTCACGAAAGAAAATAAAAAGGG 58.916 38.462 0.00 0.00 0.00 3.95
2459 2575 6.582672 GCCTCTCACGAAAGAAAATAAAAAGG 59.417 38.462 0.00 0.00 0.00 3.11
2460 2576 7.138736 TGCCTCTCACGAAAGAAAATAAAAAG 58.861 34.615 0.00 0.00 0.00 2.27
2461 2577 7.033530 TGCCTCTCACGAAAGAAAATAAAAA 57.966 32.000 0.00 0.00 0.00 1.94
2462 2578 6.627395 TGCCTCTCACGAAAGAAAATAAAA 57.373 33.333 0.00 0.00 0.00 1.52
2463 2579 6.349280 CCATGCCTCTCACGAAAGAAAATAAA 60.349 38.462 0.00 0.00 0.00 1.40
2464 2580 5.123820 CCATGCCTCTCACGAAAGAAAATAA 59.876 40.000 0.00 0.00 0.00 1.40
2472 2588 2.270352 AAACCATGCCTCTCACGAAA 57.730 45.000 0.00 0.00 0.00 3.46
2476 2592 3.800628 GCAAAACCATGCCTCTCAC 57.199 52.632 0.00 0.00 40.49 3.51
2586 2702 2.036346 GTGCCTCTTGTGGAAGCAAAAT 59.964 45.455 0.00 0.00 42.24 1.82


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

AutoCloner maintained by Alex Coulton.