Multiple sequence alignment - TraesCS4A01G434300

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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 TraesCS4A01G434300 chr4A 100.000 2753 0 0 1 2753 705056103 705053351 0.000000e+00 5084.0
1 TraesCS4A01G434300 chr4A 93.889 1882 82 15 1 1869 704808829 704806968 0.000000e+00 2808.0
2 TraesCS4A01G434300 chr4A 91.275 1169 72 14 776 1921 705170664 705169503 0.000000e+00 1567.0
3 TraesCS4A01G434300 chr4A 96.512 430 6 6 2325 2753 705169193 705168772 0.000000e+00 702.0
4 TraesCS4A01G434300 chr4A 95.556 270 11 1 2058 2326 705169502 705169233 5.450000e-117 431.0
5 TraesCS4A01G434300 chr4A 84.568 162 22 3 2587 2748 704806267 704806109 1.020000e-34 158.0
6 TraesCS4A01G434300 chr7D 87.583 1208 67 25 573 1725 22510210 22509031 0.000000e+00 1323.0
7 TraesCS4A01G434300 chr7D 86.606 1202 96 39 776 1921 22523175 22521983 0.000000e+00 1267.0
8 TraesCS4A01G434300 chr7D 87.177 1162 64 28 776 1869 22270428 22269284 0.000000e+00 1242.0
9 TraesCS4A01G434300 chr7D 85.664 286 24 11 2478 2750 22521560 22521279 4.490000e-73 285.0
10 TraesCS4A01G434300 chr7D 93.846 130 6 2 1920 2047 554237141 554237012 7.780000e-46 195.0
11 TraesCS4A01G434300 chr7D 89.630 135 14 0 2058 2192 22508789 22508655 3.640000e-39 172.0
12 TraesCS4A01G434300 chr7D 89.394 132 14 0 2058 2189 22521982 22521851 1.700000e-37 167.0
13 TraesCS4A01G434300 chr7D 83.333 162 24 3 2587 2748 22268540 22268382 2.210000e-31 147.0
14 TraesCS4A01G434300 chr7A 92.132 788 41 9 776 1542 22898542 22897755 0.000000e+00 1092.0
15 TraesCS4A01G434300 chr7A 87.848 971 59 30 775 1725 22916650 22915719 0.000000e+00 1085.0
16 TraesCS4A01G434300 chr7A 81.924 343 34 17 1603 1921 22897733 22897395 5.850000e-67 265.0
17 TraesCS4A01G434300 chr3D 95.841 577 20 4 1 575 8303313 8302739 0.000000e+00 929.0
18 TraesCS4A01G434300 chr3D 95.321 577 24 3 1 575 611606109 611606684 0.000000e+00 913.0
19 TraesCS4A01G434300 chr6D 95.660 576 22 3 1 575 427235430 427234857 0.000000e+00 922.0
20 TraesCS4A01G434300 chr6D 95.296 574 24 3 1 574 57995700 57995130 0.000000e+00 907.0
21 TraesCS4A01G434300 chr6D 100.000 28 0 0 2299 2326 459399165 459399192 5.000000e-03 52.8
22 TraesCS4A01G434300 chr2D 95.462 573 23 3 1 571 16905786 16906357 0.000000e+00 911.0
23 TraesCS4A01G434300 chr2D 95.455 572 24 2 2 571 476880160 476880731 0.000000e+00 911.0
24 TraesCS4A01G434300 chr2D 95.455 572 23 3 1 571 605105014 605105583 0.000000e+00 909.0
25 TraesCS4A01G434300 chr2D 88.667 150 13 4 1920 2067 619720672 619720525 2.180000e-41 180.0
26 TraesCS4A01G434300 chr2D 96.610 59 1 1 1464 1522 392441150 392441093 2.260000e-16 97.1
27 TraesCS4A01G434300 chr5D 94.983 578 28 1 1 577 304882931 304882354 0.000000e+00 905.0
28 TraesCS4A01G434300 chr5B 93.320 494 32 1 965 1457 469337832 469338325 0.000000e+00 728.0
29 TraesCS4A01G434300 chr5B 93.182 132 7 2 1920 2049 557532292 557532161 2.800000e-45 193.0
30 TraesCS4A01G434300 chr6B 90.233 215 21 0 1102 1316 138522222 138522436 5.800000e-72 281.0
31 TraesCS4A01G434300 chr6B 89.865 148 10 4 1920 2065 674714763 674714619 4.680000e-43 185.0
32 TraesCS4A01G434300 chr5A 91.608 143 9 3 1916 2055 427320024 427319882 7.780000e-46 195.0
33 TraesCS4A01G434300 chr4D 91.912 136 8 3 1920 2052 505937323 505937188 1.300000e-43 187.0
34 TraesCS4A01G434300 chr4D 90.714 140 11 2 1917 2055 165913229 165913367 4.680000e-43 185.0
35 TraesCS4A01G434300 chr2B 90.210 143 12 2 1920 2060 550044179 550044037 4.680000e-43 185.0
36 TraesCS4A01G434300 chr1B 87.742 155 15 4 1920 2070 625574601 625574755 7.830000e-41 178.0
37 TraesCS4A01G434300 chr7B 87.755 147 15 3 1920 2064 369812027 369812172 4.720000e-38 169.0
38 TraesCS4A01G434300 chr4B 86.061 165 14 9 1913 2071 360232867 360233028 4.720000e-38 169.0
39 TraesCS4A01G434300 chr2A 85.256 156 16 6 1920 2068 1220517 1220362 1.320000e-33 154.0
40 TraesCS4A01G434300 chr1A 98.246 57 1 0 1466 1522 27383212 27383156 1.740000e-17 100.0
41 TraesCS4A01G434300 chr3A 100.000 28 0 0 2299 2326 574335720 574335693 5.000000e-03 52.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4A01G434300 chr4A 705053351 705056103 2752 True 5084.0 5084 100.000000 1 2753 1 chr4A.!!$R1 2752
1 TraesCS4A01G434300 chr4A 704806109 704808829 2720 True 1483.0 2808 89.228500 1 2748 2 chr4A.!!$R2 2747
2 TraesCS4A01G434300 chr4A 705168772 705170664 1892 True 900.0 1567 94.447667 776 2753 3 chr4A.!!$R3 1977
3 TraesCS4A01G434300 chr7D 22508655 22510210 1555 True 747.5 1323 88.606500 573 2192 2 chr7D.!!$R3 1619
4 TraesCS4A01G434300 chr7D 22268382 22270428 2046 True 694.5 1242 85.255000 776 2748 2 chr7D.!!$R2 1972
5 TraesCS4A01G434300 chr7D 22521279 22523175 1896 True 573.0 1267 87.221333 776 2750 3 chr7D.!!$R4 1974
6 TraesCS4A01G434300 chr7A 22915719 22916650 931 True 1085.0 1085 87.848000 775 1725 1 chr7A.!!$R1 950
7 TraesCS4A01G434300 chr7A 22897395 22898542 1147 True 678.5 1092 87.028000 776 1921 2 chr7A.!!$R2 1145
8 TraesCS4A01G434300 chr3D 8302739 8303313 574 True 929.0 929 95.841000 1 575 1 chr3D.!!$R1 574
9 TraesCS4A01G434300 chr3D 611606109 611606684 575 False 913.0 913 95.321000 1 575 1 chr3D.!!$F1 574
10 TraesCS4A01G434300 chr6D 427234857 427235430 573 True 922.0 922 95.660000 1 575 1 chr6D.!!$R2 574
11 TraesCS4A01G434300 chr6D 57995130 57995700 570 True 907.0 907 95.296000 1 574 1 chr6D.!!$R1 573
12 TraesCS4A01G434300 chr2D 16905786 16906357 571 False 911.0 911 95.462000 1 571 1 chr2D.!!$F1 570
13 TraesCS4A01G434300 chr2D 476880160 476880731 571 False 911.0 911 95.455000 2 571 1 chr2D.!!$F2 569
14 TraesCS4A01G434300 chr2D 605105014 605105583 569 False 909.0 909 95.455000 1 571 1 chr2D.!!$F3 570
15 TraesCS4A01G434300 chr5D 304882354 304882931 577 True 905.0 905 94.983000 1 577 1 chr5D.!!$R1 576

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
454 457 2.037251 TGTGGGAGGAGAGACGAAAAAG 59.963 50.0 0.0 0.0 0.0 2.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1773 1934 0.032952 GTACAGCCACCGAACTGACA 59.967 55.0 0.0 0.0 37.35 3.58 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
178 179 7.947282 TCCGTTTCCTGAAAATCTGTTATTTT 58.053 30.769 0.00 0.00 34.30 1.82
417 418 5.646360 GGAGAGAAAAATAAACCGATGGACA 59.354 40.000 0.00 0.00 0.00 4.02
433 434 2.863988 CAAGGGTGGGAGGGGGTT 60.864 66.667 0.00 0.00 0.00 4.11
454 457 2.037251 TGTGGGAGGAGAGACGAAAAAG 59.963 50.000 0.00 0.00 0.00 2.27
635 647 7.931578 ATGAATACACGATTTGGGTAAGAAA 57.068 32.000 0.00 0.00 0.00 2.52
672 684 4.063335 CCACCTGCAGGGAGAGAT 57.937 61.111 35.42 11.84 40.27 2.75
856 908 3.132289 CGCCTCTCTTCCACCTATAAACA 59.868 47.826 0.00 0.00 0.00 2.83
1755 1916 0.247460 CGAGGTCCAAGCACTGATGA 59.753 55.000 0.00 0.00 0.00 2.92
1756 1917 1.134580 CGAGGTCCAAGCACTGATGAT 60.135 52.381 0.00 0.00 0.00 2.45
1757 1918 2.286872 GAGGTCCAAGCACTGATGATG 58.713 52.381 0.00 0.00 0.00 3.07
1773 1934 6.436532 ACTGATGATGGATTTCTGCTCTTTTT 59.563 34.615 0.00 0.00 0.00 1.94
1774 1935 6.627243 TGATGATGGATTTCTGCTCTTTTTG 58.373 36.000 0.00 0.00 0.00 2.44
1775 1936 6.209986 TGATGATGGATTTCTGCTCTTTTTGT 59.790 34.615 0.00 0.00 0.00 2.83
1776 1937 6.017400 TGATGGATTTCTGCTCTTTTTGTC 57.983 37.500 0.00 0.00 0.00 3.18
1777 1938 5.535783 TGATGGATTTCTGCTCTTTTTGTCA 59.464 36.000 0.00 0.00 0.00 3.58
1778 1939 5.443185 TGGATTTCTGCTCTTTTTGTCAG 57.557 39.130 0.00 0.00 0.00 3.51
1779 1940 4.889409 TGGATTTCTGCTCTTTTTGTCAGT 59.111 37.500 0.00 0.00 0.00 3.41
1780 1941 5.360714 TGGATTTCTGCTCTTTTTGTCAGTT 59.639 36.000 0.00 0.00 0.00 3.16
1781 1942 5.917447 GGATTTCTGCTCTTTTTGTCAGTTC 59.083 40.000 0.00 0.00 0.00 3.01
1782 1943 4.536364 TTCTGCTCTTTTTGTCAGTTCG 57.464 40.909 0.00 0.00 0.00 3.95
1783 1944 2.872245 TCTGCTCTTTTTGTCAGTTCGG 59.128 45.455 0.00 0.00 0.00 4.30
1787 1957 1.673920 TCTTTTTGTCAGTTCGGTGGC 59.326 47.619 0.00 0.00 0.00 5.01
1789 1959 1.021202 TTTTGTCAGTTCGGTGGCTG 58.979 50.000 0.00 0.00 0.00 4.85
1792 1978 0.032952 TGTCAGTTCGGTGGCTGTAC 59.967 55.000 0.00 0.00 34.57 2.90
1793 1979 1.007336 GTCAGTTCGGTGGCTGTACG 61.007 60.000 0.00 0.00 34.57 3.67
1854 2040 5.163513 GTTTGTTGAAATGCTCGAATGGAT 58.836 37.500 0.00 0.00 0.00 3.41
1921 2168 8.779354 AATGTCTCTGGTTAACTCTGAATTAC 57.221 34.615 5.42 5.25 0.00 1.89
1922 2169 7.540474 TGTCTCTGGTTAACTCTGAATTACT 57.460 36.000 5.42 0.00 0.00 2.24
1923 2170 8.645814 TGTCTCTGGTTAACTCTGAATTACTA 57.354 34.615 5.42 0.00 0.00 1.82
1924 2171 8.521176 TGTCTCTGGTTAACTCTGAATTACTAC 58.479 37.037 5.42 0.00 0.00 2.73
1925 2172 8.741841 GTCTCTGGTTAACTCTGAATTACTACT 58.258 37.037 5.42 0.00 0.00 2.57
1926 2173 9.310449 TCTCTGGTTAACTCTGAATTACTACTT 57.690 33.333 5.42 0.00 0.00 2.24
1927 2174 9.575783 CTCTGGTTAACTCTGAATTACTACTTC 57.424 37.037 5.42 0.00 0.00 3.01
1928 2175 8.529476 TCTGGTTAACTCTGAATTACTACTTCC 58.471 37.037 5.42 0.00 0.00 3.46
1929 2176 7.318141 TGGTTAACTCTGAATTACTACTTCCG 58.682 38.462 5.42 0.00 0.00 4.30
1930 2177 7.039504 TGGTTAACTCTGAATTACTACTTCCGT 60.040 37.037 5.42 0.00 0.00 4.69
1931 2178 7.487509 GGTTAACTCTGAATTACTACTTCCGTC 59.512 40.741 5.42 0.00 0.00 4.79
1932 2179 5.579564 ACTCTGAATTACTACTTCCGTCC 57.420 43.478 0.00 0.00 0.00 4.79
1933 2180 4.096081 ACTCTGAATTACTACTTCCGTCCG 59.904 45.833 0.00 0.00 0.00 4.79
1934 2181 3.379372 TCTGAATTACTACTTCCGTCCGG 59.621 47.826 0.00 0.00 0.00 5.14
1935 2182 3.355378 TGAATTACTACTTCCGTCCGGA 58.645 45.455 0.00 0.00 43.52 5.14
1945 2192 2.660189 TCCGTCCGGAAATACTTGTC 57.340 50.000 5.23 0.00 42.05 3.18
1946 2193 1.894466 TCCGTCCGGAAATACTTGTCA 59.106 47.619 5.23 0.00 42.05 3.58
1947 2194 2.498481 TCCGTCCGGAAATACTTGTCAT 59.502 45.455 5.23 0.00 42.05 3.06
1948 2195 2.864343 CCGTCCGGAAATACTTGTCATC 59.136 50.000 5.23 0.00 37.50 2.92
1949 2196 3.517602 CGTCCGGAAATACTTGTCATCA 58.482 45.455 5.23 0.00 0.00 3.07
1950 2197 3.930229 CGTCCGGAAATACTTGTCATCAA 59.070 43.478 5.23 0.00 0.00 2.57
1951 2198 4.390603 CGTCCGGAAATACTTGTCATCAAA 59.609 41.667 5.23 0.00 32.87 2.69
1952 2199 5.106869 CGTCCGGAAATACTTGTCATCAAAA 60.107 40.000 5.23 0.00 32.87 2.44
1953 2200 6.403200 CGTCCGGAAATACTTGTCATCAAAAT 60.403 38.462 5.23 0.00 32.87 1.82
1954 2201 7.312899 GTCCGGAAATACTTGTCATCAAAATT 58.687 34.615 5.23 0.00 32.87 1.82
1955 2202 8.455682 GTCCGGAAATACTTGTCATCAAAATTA 58.544 33.333 5.23 0.00 32.87 1.40
1956 2203 9.015367 TCCGGAAATACTTGTCATCAAAATTAA 57.985 29.630 0.00 0.00 32.87 1.40
1957 2204 9.801873 CCGGAAATACTTGTCATCAAAATTAAT 57.198 29.630 0.00 0.00 32.87 1.40
1999 2246 9.614792 AGATGTATTTTAGTTTAGACACATCCC 57.385 33.333 7.54 0.00 41.08 3.85
2000 2247 9.614792 GATGTATTTTAGTTTAGACACATCCCT 57.385 33.333 0.00 0.00 36.59 4.20
2001 2248 9.975218 ATGTATTTTAGTTTAGACACATCCCTT 57.025 29.630 0.00 0.00 0.00 3.95
2002 2249 9.802039 TGTATTTTAGTTTAGACACATCCCTTT 57.198 29.630 0.00 0.00 0.00 3.11
2008 2255 7.939784 AGTTTAGACACATCCCTTTTTATCC 57.060 36.000 0.00 0.00 0.00 2.59
2009 2256 7.466804 AGTTTAGACACATCCCTTTTTATCCA 58.533 34.615 0.00 0.00 0.00 3.41
2010 2257 8.116026 AGTTTAGACACATCCCTTTTTATCCAT 58.884 33.333 0.00 0.00 0.00 3.41
2011 2258 8.749354 GTTTAGACACATCCCTTTTTATCCATT 58.251 33.333 0.00 0.00 0.00 3.16
2012 2259 8.893563 TTAGACACATCCCTTTTTATCCATTT 57.106 30.769 0.00 0.00 0.00 2.32
2013 2260 7.797121 AGACACATCCCTTTTTATCCATTTT 57.203 32.000 0.00 0.00 0.00 1.82
2014 2261 8.893563 AGACACATCCCTTTTTATCCATTTTA 57.106 30.769 0.00 0.00 0.00 1.52
2015 2262 9.320295 AGACACATCCCTTTTTATCCATTTTAA 57.680 29.630 0.00 0.00 0.00 1.52
2017 2264 9.889128 ACACATCCCTTTTTATCCATTTTAATG 57.111 29.630 0.00 0.00 36.17 1.90
2035 2282 8.676454 TTTTAATGACAAATATTTTCGGACGG 57.324 30.769 0.00 0.00 0.00 4.79
2036 2283 7.612668 TTAATGACAAATATTTTCGGACGGA 57.387 32.000 0.00 0.00 0.00 4.69
2037 2284 5.734855 ATGACAAATATTTTCGGACGGAG 57.265 39.130 0.00 0.00 0.00 4.63
2038 2285 3.936453 TGACAAATATTTTCGGACGGAGG 59.064 43.478 0.00 0.00 0.00 4.30
2039 2286 3.275999 ACAAATATTTTCGGACGGAGGG 58.724 45.455 0.00 0.00 0.00 4.30
2040 2287 3.054948 ACAAATATTTTCGGACGGAGGGA 60.055 43.478 0.00 0.00 0.00 4.20
2041 2288 3.470645 AATATTTTCGGACGGAGGGAG 57.529 47.619 0.00 0.00 0.00 4.30
2042 2289 1.856629 TATTTTCGGACGGAGGGAGT 58.143 50.000 0.00 0.00 0.00 3.85
2043 2290 1.856629 ATTTTCGGACGGAGGGAGTA 58.143 50.000 0.00 0.00 0.00 2.59
2044 2291 1.856629 TTTTCGGACGGAGGGAGTAT 58.143 50.000 0.00 0.00 0.00 2.12
2045 2292 1.108776 TTTCGGACGGAGGGAGTATG 58.891 55.000 0.00 0.00 0.00 2.39
2046 2293 0.256752 TTCGGACGGAGGGAGTATGA 59.743 55.000 0.00 0.00 0.00 2.15
2047 2294 0.256752 TCGGACGGAGGGAGTATGAA 59.743 55.000 0.00 0.00 0.00 2.57
2048 2295 1.108776 CGGACGGAGGGAGTATGAAA 58.891 55.000 0.00 0.00 0.00 2.69
2049 2296 1.479323 CGGACGGAGGGAGTATGAAAA 59.521 52.381 0.00 0.00 0.00 2.29
2050 2297 2.102588 CGGACGGAGGGAGTATGAAAAT 59.897 50.000 0.00 0.00 0.00 1.82
2051 2298 3.319972 CGGACGGAGGGAGTATGAAAATA 59.680 47.826 0.00 0.00 0.00 1.40
2052 2299 4.202182 CGGACGGAGGGAGTATGAAAATAA 60.202 45.833 0.00 0.00 0.00 1.40
2053 2300 5.510861 CGGACGGAGGGAGTATGAAAATAAT 60.511 44.000 0.00 0.00 0.00 1.28
2054 2301 6.294899 CGGACGGAGGGAGTATGAAAATAATA 60.295 42.308 0.00 0.00 0.00 0.98
2055 2302 7.097834 GGACGGAGGGAGTATGAAAATAATAG 58.902 42.308 0.00 0.00 0.00 1.73
2056 2303 7.256225 GGACGGAGGGAGTATGAAAATAATAGT 60.256 40.741 0.00 0.00 0.00 2.12
2210 2506 7.615757 TCTGAATCTTCCTGTACTGTGATCTTA 59.384 37.037 0.00 0.00 0.00 2.10
2253 2549 2.248248 AGTAGTTCCTGTACTGCTGCA 58.752 47.619 0.88 0.88 39.25 4.41
2310 2606 0.248621 GGCTGCGTGCAATTGGTATC 60.249 55.000 7.72 0.00 45.15 2.24
2315 2611 1.856014 GCGTGCAATTGGTATCTTCGC 60.856 52.381 7.72 7.63 34.93 4.70
2318 2614 2.287915 GTGCAATTGGTATCTTCGCGAT 59.712 45.455 10.88 0.00 36.11 4.58
2319 2615 3.493129 GTGCAATTGGTATCTTCGCGATA 59.507 43.478 10.88 0.85 33.48 2.92
2322 2618 5.929415 TGCAATTGGTATCTTCGCGATATTA 59.071 36.000 10.88 0.00 36.99 0.98
2380 2718 9.830975 TGTTTATCAAGCTCAGTTAATGCTATA 57.169 29.630 0.00 0.00 35.85 1.31
2471 2809 9.783081 AAATGTTCCATTTCTTGCTTATTTTCT 57.217 25.926 0.00 0.00 0.00 2.52
2575 3025 7.125391 TGCCTGATCAAACCTAAAATATCCTT 58.875 34.615 0.00 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
417 418 2.863988 CAACCCCCTCCCACCCTT 60.864 66.667 0.00 0.00 0.00 3.95
433 434 1.712056 TTTTCGTCTCTCCTCCCACA 58.288 50.000 0.00 0.00 0.00 4.17
454 457 1.789054 CGCGGTTTATTTTCGCTGGTC 60.789 52.381 0.00 0.00 46.23 4.02
492 496 2.044793 TTTGTCTCTCCTCCCACCAT 57.955 50.000 0.00 0.00 0.00 3.55
547 553 5.296283 GTCTCTACTCCTAATGCACGAGTTA 59.704 44.000 11.47 0.00 37.93 2.24
605 612 5.101628 CCCAAATCGTGTATTCATTTGTGG 58.898 41.667 0.00 0.00 32.18 4.17
672 684 3.134804 GCTTTCCTTCACCTATCCAGCTA 59.865 47.826 0.00 0.00 0.00 3.32
872 926 2.427002 GGAGGGGATGGATGAGAGAGAA 60.427 54.545 0.00 0.00 0.00 2.87
1464 1574 2.029844 GAGCTTCCTGACGCGCTTT 61.030 57.895 5.73 0.00 31.96 3.51
1522 1632 3.077907 CTTCTTCTTCCCGCCCCA 58.922 61.111 0.00 0.00 0.00 4.96
1524 1634 2.438614 GGCTTCTTCTTCCCGCCC 60.439 66.667 0.00 0.00 34.75 6.13
1677 1790 2.282958 TTCGGTGAGGTCCTCGCT 60.283 61.111 27.55 0.00 40.43 4.93
1755 1916 5.537674 ACTGACAAAAAGAGCAGAAATCCAT 59.462 36.000 0.00 0.00 32.86 3.41
1756 1917 4.889409 ACTGACAAAAAGAGCAGAAATCCA 59.111 37.500 0.00 0.00 32.86 3.41
1757 1918 5.444663 ACTGACAAAAAGAGCAGAAATCC 57.555 39.130 0.00 0.00 32.86 3.01
1773 1934 0.032952 GTACAGCCACCGAACTGACA 59.967 55.000 0.00 0.00 37.35 3.58
1774 1935 1.007336 CGTACAGCCACCGAACTGAC 61.007 60.000 0.00 0.00 37.35 3.51
1775 1936 1.287815 CGTACAGCCACCGAACTGA 59.712 57.895 0.00 0.00 37.35 3.41
1776 1937 1.736645 CCGTACAGCCACCGAACTG 60.737 63.158 0.00 0.00 39.86 3.16
1777 1938 2.654877 CCGTACAGCCACCGAACT 59.345 61.111 0.00 0.00 0.00 3.01
1778 1939 2.433664 CCCGTACAGCCACCGAAC 60.434 66.667 0.00 0.00 0.00 3.95
1779 1940 2.438951 GAACCCGTACAGCCACCGAA 62.439 60.000 0.00 0.00 0.00 4.30
1780 1941 2.918802 AACCCGTACAGCCACCGA 60.919 61.111 0.00 0.00 0.00 4.69
1781 1942 2.433664 GAACCCGTACAGCCACCG 60.434 66.667 0.00 0.00 0.00 4.94
1782 1943 1.375523 CTGAACCCGTACAGCCACC 60.376 63.158 0.00 0.00 0.00 4.61
1783 1944 1.375523 CCTGAACCCGTACAGCCAC 60.376 63.158 0.00 0.00 33.40 5.01
1787 1957 0.677288 TCACACCTGAACCCGTACAG 59.323 55.000 0.00 0.00 0.00 2.74
1789 1959 3.714391 GATATCACACCTGAACCCGTAC 58.286 50.000 0.00 0.00 0.00 3.67
1792 1978 1.538204 CCGATATCACACCTGAACCCG 60.538 57.143 3.12 0.00 0.00 5.28
1793 1979 1.760613 TCCGATATCACACCTGAACCC 59.239 52.381 3.12 0.00 0.00 4.11
1854 2040 9.836864 ATATACAGAAATAAGCATGACACTGAA 57.163 29.630 0.00 0.00 0.00 3.02
1926 2173 1.894466 TGACAAGTATTTCCGGACGGA 59.106 47.619 1.83 9.76 43.52 4.69
1927 2174 2.373540 TGACAAGTATTTCCGGACGG 57.626 50.000 1.83 3.96 0.00 4.79
1928 2175 3.517602 TGATGACAAGTATTTCCGGACG 58.482 45.455 1.83 0.00 0.00 4.79
1929 2176 5.873179 TTTGATGACAAGTATTTCCGGAC 57.127 39.130 1.83 0.00 37.32 4.79
1930 2177 7.461182 AATTTTGATGACAAGTATTTCCGGA 57.539 32.000 0.00 0.00 37.32 5.14
1931 2178 9.801873 ATTAATTTTGATGACAAGTATTTCCGG 57.198 29.630 0.00 0.00 37.32 5.14
1973 2220 9.614792 GGGATGTGTCTAAACTAAAATACATCT 57.385 33.333 0.00 0.00 41.55 2.90
1974 2221 9.614792 AGGGATGTGTCTAAACTAAAATACATC 57.385 33.333 0.00 0.00 41.27 3.06
1975 2222 9.975218 AAGGGATGTGTCTAAACTAAAATACAT 57.025 29.630 0.00 0.00 0.00 2.29
1976 2223 9.802039 AAAGGGATGTGTCTAAACTAAAATACA 57.198 29.630 0.00 0.00 0.00 2.29
1982 2229 9.457436 GGATAAAAAGGGATGTGTCTAAACTAA 57.543 33.333 0.00 0.00 0.00 2.24
1983 2230 8.607713 TGGATAAAAAGGGATGTGTCTAAACTA 58.392 33.333 0.00 0.00 0.00 2.24
1984 2231 7.466804 TGGATAAAAAGGGATGTGTCTAAACT 58.533 34.615 0.00 0.00 0.00 2.66
1985 2232 7.696992 TGGATAAAAAGGGATGTGTCTAAAC 57.303 36.000 0.00 0.00 0.00 2.01
1986 2233 8.893563 AATGGATAAAAAGGGATGTGTCTAAA 57.106 30.769 0.00 0.00 0.00 1.85
1987 2234 8.893563 AAATGGATAAAAAGGGATGTGTCTAA 57.106 30.769 0.00 0.00 0.00 2.10
1988 2235 8.893563 AAAATGGATAAAAAGGGATGTGTCTA 57.106 30.769 0.00 0.00 0.00 2.59
1989 2236 7.797121 AAAATGGATAAAAAGGGATGTGTCT 57.203 32.000 0.00 0.00 0.00 3.41
1991 2238 9.889128 CATTAAAATGGATAAAAAGGGATGTGT 57.111 29.630 0.00 0.00 32.78 3.72
2009 2256 9.296400 CCGTCCGAAAATATTTGTCATTAAAAT 57.704 29.630 0.39 0.00 0.00 1.82
2010 2257 8.512956 TCCGTCCGAAAATATTTGTCATTAAAA 58.487 29.630 0.39 0.00 0.00 1.52
2011 2258 8.041829 TCCGTCCGAAAATATTTGTCATTAAA 57.958 30.769 0.39 0.00 0.00 1.52
2012 2259 7.201661 CCTCCGTCCGAAAATATTTGTCATTAA 60.202 37.037 0.39 0.00 0.00 1.40
2013 2260 6.259167 CCTCCGTCCGAAAATATTTGTCATTA 59.741 38.462 0.39 0.00 0.00 1.90
2014 2261 5.065988 CCTCCGTCCGAAAATATTTGTCATT 59.934 40.000 0.39 0.00 0.00 2.57
2015 2262 4.574828 CCTCCGTCCGAAAATATTTGTCAT 59.425 41.667 0.39 0.00 0.00 3.06
2016 2263 3.936453 CCTCCGTCCGAAAATATTTGTCA 59.064 43.478 0.39 0.00 0.00 3.58
2017 2264 3.311596 CCCTCCGTCCGAAAATATTTGTC 59.688 47.826 0.39 1.54 0.00 3.18
2018 2265 3.054948 TCCCTCCGTCCGAAAATATTTGT 60.055 43.478 0.39 0.00 0.00 2.83
2019 2266 3.537580 TCCCTCCGTCCGAAAATATTTG 58.462 45.455 0.39 0.00 0.00 2.32
2020 2267 3.199289 ACTCCCTCCGTCCGAAAATATTT 59.801 43.478 0.00 0.00 0.00 1.40
2021 2268 2.770232 ACTCCCTCCGTCCGAAAATATT 59.230 45.455 0.00 0.00 0.00 1.28
2022 2269 2.395619 ACTCCCTCCGTCCGAAAATAT 58.604 47.619 0.00 0.00 0.00 1.28
2023 2270 1.856629 ACTCCCTCCGTCCGAAAATA 58.143 50.000 0.00 0.00 0.00 1.40
2024 2271 1.856629 TACTCCCTCCGTCCGAAAAT 58.143 50.000 0.00 0.00 0.00 1.82
2025 2272 1.479323 CATACTCCCTCCGTCCGAAAA 59.521 52.381 0.00 0.00 0.00 2.29
2026 2273 1.108776 CATACTCCCTCCGTCCGAAA 58.891 55.000 0.00 0.00 0.00 3.46
2027 2274 0.256752 TCATACTCCCTCCGTCCGAA 59.743 55.000 0.00 0.00 0.00 4.30
2028 2275 0.256752 TTCATACTCCCTCCGTCCGA 59.743 55.000 0.00 0.00 0.00 4.55
2029 2276 1.108776 TTTCATACTCCCTCCGTCCG 58.891 55.000 0.00 0.00 0.00 4.79
2030 2277 3.840124 ATTTTCATACTCCCTCCGTCC 57.160 47.619 0.00 0.00 0.00 4.79
2031 2278 7.668492 ACTATTATTTTCATACTCCCTCCGTC 58.332 38.462 0.00 0.00 0.00 4.79
2032 2279 7.613551 ACTATTATTTTCATACTCCCTCCGT 57.386 36.000 0.00 0.00 0.00 4.69
2033 2280 8.368668 AGAACTATTATTTTCATACTCCCTCCG 58.631 37.037 0.00 0.00 0.00 4.63
2115 2365 0.325933 TCCAGACCATGCCTCAACAG 59.674 55.000 0.00 0.00 0.00 3.16
2165 2415 9.784531 GATTCAGATATAGAAAGAAACATGGGA 57.215 33.333 0.00 0.00 0.00 4.37
2293 2589 2.537529 CGAAGATACCAATTGCACGCAG 60.538 50.000 0.00 0.00 0.00 5.18
2380 2718 7.496591 ACTTGAATTCACTTTGCAATTCACATT 59.503 29.630 7.89 2.69 44.77 2.71
2470 2808 5.026462 CAGCATTTCGACAAAGAAGCATAG 58.974 41.667 0.00 0.00 0.00 2.23
2471 2809 4.142622 CCAGCATTTCGACAAAGAAGCATA 60.143 41.667 0.00 0.00 0.00 3.14


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

AutoCloner maintained by Alex Coulton.