Multiple sequence alignment - TraesCS3D01G156400

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 TraesCS3D01G156400 chr3D 100.000 2675 0 0 1 2675 123779512 123776838 0.000000e+00 4940.0
1 TraesCS3D01G156400 chr3D 90.582 1582 148 1 1 1581 123689652 123688071 0.000000e+00 2095.0
2 TraesCS3D01G156400 chr3A 95.578 1696 71 2 1 1692 131425350 131423655 0.000000e+00 2713.0
3 TraesCS3D01G156400 chr3A 89.910 1774 173 4 1 1768 131343904 131345677 0.000000e+00 2279.0
4 TraesCS3D01G156400 chr3A 87.726 554 52 8 2130 2675 131423198 131422653 1.350000e-177 632.0
5 TraesCS3D01G156400 chr3A 91.960 199 13 1 1951 2146 131423410 131423212 2.620000e-70 276.0
6 TraesCS3D01G156400 chr3A 94.615 130 7 0 1772 1901 131423542 131423413 4.520000e-48 202.0
7 TraesCS3D01G156400 chr3B 93.556 1769 100 3 1 1768 177917659 177915904 0.000000e+00 2623.0
8 TraesCS3D01G156400 chr3B 89.373 1769 186 2 1 1768 177088299 177086532 0.000000e+00 2224.0
9 TraesCS3D01G156400 chr3B 85.417 96 14 0 1787 1882 177086317 177086222 1.690000e-17 100.0
10 TraesCS3D01G156400 chr2D 84.291 261 35 5 2289 2543 31671274 31671534 1.590000e-62 250.0
11 TraesCS3D01G156400 chr2D 83.333 144 21 3 2506 2647 579590046 579589904 2.160000e-26 130.0
12 TraesCS3D01G156400 chr2B 83.212 137 20 3 2506 2640 697589228 697589093 3.620000e-24 122.0
13 TraesCS3D01G156400 chrUn 78.107 169 25 6 2457 2623 39710942 39711100 2.190000e-16 97.1
14 TraesCS3D01G156400 chr5D 88.636 44 4 1 1308 1351 350682171 350682129 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 TraesCS3D01G156400 chr3D 123776838 123779512 2674 True 4940.00 4940 100.00000 1 2675 1 chr3D.!!$R2 2674
1 TraesCS3D01G156400 chr3D 123688071 123689652 1581 True 2095.00 2095 90.58200 1 1581 1 chr3D.!!$R1 1580
2 TraesCS3D01G156400 chr3A 131343904 131345677 1773 False 2279.00 2279 89.91000 1 1768 1 chr3A.!!$F1 1767
3 TraesCS3D01G156400 chr3A 131422653 131425350 2697 True 955.75 2713 92.46975 1 2675 4 chr3A.!!$R1 2674
4 TraesCS3D01G156400 chr3B 177915904 177917659 1755 True 2623.00 2623 93.55600 1 1768 1 chr3B.!!$R1 1767
5 TraesCS3D01G156400 chr3B 177086222 177088299 2077 True 1162.00 2224 87.39500 1 1882 2 chr3B.!!$R2 1881

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
789 805 1.004745 AGCCACCATGAATTTCTCCGT 59.995 47.619 0.0 0.0 0.0 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2650 2912 0.038166 ACATTTGCACCCGGATGACT 59.962 50.0 0.0 0.0 0.0 3.41 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
132 133 1.826921 GGTACTCGGAGCCGGATCA 60.827 63.158 23.22 0.00 40.25 2.92
303 304 2.437895 GGGGCTTGGGTACTTCGC 60.438 66.667 0.00 0.00 0.00 4.70
323 324 1.677966 AACGGCTGCTCGAGGTCTA 60.678 57.895 15.58 0.00 0.00 2.59
514 530 3.079578 CCATGGATGCAAGCTATGGTAG 58.920 50.000 20.37 3.23 34.88 3.18
628 644 3.054878 GCAAACAAGAGGAATTGCACTG 58.945 45.455 0.00 0.00 45.61 3.66
675 691 6.624352 TGCTTCTTTGATACTGATAATGGC 57.376 37.500 0.00 0.00 0.00 4.40
789 805 1.004745 AGCCACCATGAATTTCTCCGT 59.995 47.619 0.00 0.00 0.00 4.69
971 988 3.636300 CTGTTGGGATTTTGTGTCAAGGA 59.364 43.478 0.00 0.00 0.00 3.36
1131 1149 2.681848 GCATGAAGAATGTGAGGACTGG 59.318 50.000 0.00 0.00 38.65 4.00
1197 1215 0.819582 AATTCTGCCCCAAGATTGCG 59.180 50.000 0.00 0.00 0.00 4.85
1298 1316 3.948719 GGAGTGGTTGTCCGGGCA 61.949 66.667 3.51 3.51 36.30 5.36
1694 1716 5.495640 CTGAAGGAGGTTGCTAGAGAATTT 58.504 41.667 0.00 0.00 0.00 1.82
1729 1754 6.974932 TTGAGTTAAGATCTGAATCTGTGC 57.025 37.500 0.00 0.00 41.54 4.57
1746 1772 3.351740 TGTGCTCTGTTTTGTTTCCAGA 58.648 40.909 0.00 0.00 34.28 3.86
1752 1778 5.279156 GCTCTGTTTTGTTTCCAGATCCAAT 60.279 40.000 0.00 0.00 34.90 3.16
1753 1779 6.071952 GCTCTGTTTTGTTTCCAGATCCAATA 60.072 38.462 0.00 0.00 34.90 1.90
1757 1783 9.740239 CTGTTTTGTTTCCAGATCCAATATATG 57.260 33.333 0.00 0.00 0.00 1.78
1763 1789 6.940430 TTCCAGATCCAATATATGAGCTCA 57.060 37.500 20.79 20.79 0.00 4.26
1768 1794 7.093596 CCAGATCCAATATATGAGCTCACTACA 60.094 40.741 20.97 5.02 0.00 2.74
1769 1795 7.758980 CAGATCCAATATATGAGCTCACTACAC 59.241 40.741 20.97 3.51 0.00 2.90
1770 1796 6.346477 TCCAATATATGAGCTCACTACACC 57.654 41.667 20.97 0.00 0.00 4.16
1771 1797 5.246203 TCCAATATATGAGCTCACTACACCC 59.754 44.000 20.97 0.00 0.00 4.61
1774 1800 6.747414 ATATATGAGCTCACTACACCCAAA 57.253 37.500 20.97 0.00 0.00 3.28
1776 1802 3.788227 TGAGCTCACTACACCCAAATT 57.212 42.857 13.74 0.00 0.00 1.82
1778 1804 4.072131 TGAGCTCACTACACCCAAATTTC 58.928 43.478 13.74 0.00 0.00 2.17
1889 2110 3.363787 ACAAAGATGTCCAAGGCCC 57.636 52.632 0.00 0.00 33.41 5.80
1896 2117 3.692406 GTCCAAGGCCCGTCGACT 61.692 66.667 14.70 0.00 0.00 4.18
1901 2122 2.932234 AAGGCCCGTCGACTGACTG 61.932 63.158 14.70 0.00 43.21 3.51
1902 2123 3.371063 GGCCCGTCGACTGACTGA 61.371 66.667 14.70 0.00 43.21 3.41
1903 2124 2.179517 GCCCGTCGACTGACTGAG 59.820 66.667 14.70 0.00 43.21 3.35
1904 2125 2.333417 GCCCGTCGACTGACTGAGA 61.333 63.158 14.70 0.00 43.21 3.27
1905 2126 1.658686 GCCCGTCGACTGACTGAGAT 61.659 60.000 14.70 0.00 43.21 2.75
1906 2127 0.811915 CCCGTCGACTGACTGAGATT 59.188 55.000 14.70 0.00 43.21 2.40
1907 2128 1.202200 CCCGTCGACTGACTGAGATTC 60.202 57.143 14.70 0.00 43.21 2.52
1908 2129 1.468914 CCGTCGACTGACTGAGATTCA 59.531 52.381 14.70 0.00 43.21 2.57
1921 2142 5.686159 CTGAGATTCAGTGACTTTGCTTT 57.314 39.130 0.00 0.00 39.58 3.51
1922 2143 5.428496 TGAGATTCAGTGACTTTGCTTTG 57.572 39.130 0.00 0.00 0.00 2.77
1923 2144 4.883585 TGAGATTCAGTGACTTTGCTTTGT 59.116 37.500 0.00 0.00 0.00 2.83
1924 2145 5.179045 AGATTCAGTGACTTTGCTTTGTG 57.821 39.130 0.00 0.00 0.00 3.33
1925 2146 4.883585 AGATTCAGTGACTTTGCTTTGTGA 59.116 37.500 0.00 0.00 0.00 3.58
1926 2147 5.357878 AGATTCAGTGACTTTGCTTTGTGAA 59.642 36.000 0.00 0.00 0.00 3.18
1927 2148 4.621068 TCAGTGACTTTGCTTTGTGAAG 57.379 40.909 0.00 0.00 35.92 3.02
1928 2149 4.009675 TCAGTGACTTTGCTTTGTGAAGT 58.990 39.130 0.00 0.00 36.40 3.01
1929 2150 4.094887 TCAGTGACTTTGCTTTGTGAAGTC 59.905 41.667 8.17 8.17 45.86 3.01
1930 2151 4.095483 CAGTGACTTTGCTTTGTGAAGTCT 59.905 41.667 14.31 0.00 45.85 3.24
1931 2152 4.095483 AGTGACTTTGCTTTGTGAAGTCTG 59.905 41.667 14.31 0.00 45.85 3.51
1932 2153 4.094887 GTGACTTTGCTTTGTGAAGTCTGA 59.905 41.667 14.31 0.00 45.85 3.27
1933 2154 4.333649 TGACTTTGCTTTGTGAAGTCTGAG 59.666 41.667 14.31 0.00 45.85 3.35
1934 2155 3.065925 ACTTTGCTTTGTGAAGTCTGAGC 59.934 43.478 0.00 0.00 35.25 4.26
1935 2156 2.627515 TGCTTTGTGAAGTCTGAGCT 57.372 45.000 0.00 0.00 35.25 4.09
1936 2157 2.923121 TGCTTTGTGAAGTCTGAGCTT 58.077 42.857 0.00 0.00 35.25 3.74
1937 2158 2.615447 TGCTTTGTGAAGTCTGAGCTTG 59.385 45.455 0.00 0.00 35.25 4.01
1938 2159 2.874701 GCTTTGTGAAGTCTGAGCTTGA 59.125 45.455 0.00 0.00 35.25 3.02
1939 2160 3.303659 GCTTTGTGAAGTCTGAGCTTGAC 60.304 47.826 11.41 11.41 35.25 3.18
1940 2161 3.827008 TTGTGAAGTCTGAGCTTGACT 57.173 42.857 14.93 14.93 45.55 3.41
1944 2165 3.621953 AGTCTGAGCTTGACTTGGC 57.378 52.632 14.93 0.00 41.45 4.52
1945 2166 0.036022 AGTCTGAGCTTGACTTGGCC 59.964 55.000 14.93 0.00 41.45 5.36
1946 2167 0.957888 GTCTGAGCTTGACTTGGCCC 60.958 60.000 0.00 0.00 0.00 5.80
1947 2168 1.676967 CTGAGCTTGACTTGGCCCC 60.677 63.158 0.00 0.00 0.00 5.80
1948 2169 2.134630 CTGAGCTTGACTTGGCCCCT 62.135 60.000 0.00 0.00 0.00 4.79
1949 2170 0.840288 TGAGCTTGACTTGGCCCCTA 60.840 55.000 0.00 0.00 0.00 3.53
1985 2206 0.776810 TGTGATCCAAAGGCCCAGAA 59.223 50.000 0.00 0.00 0.00 3.02
1986 2207 1.358787 TGTGATCCAAAGGCCCAGAAT 59.641 47.619 0.00 0.00 0.00 2.40
1990 2211 4.023291 TGATCCAAAGGCCCAGAATTTAC 58.977 43.478 0.00 0.00 0.00 2.01
2011 2232 4.532834 ACAAAGTCAAAACTGAAGCCCTA 58.467 39.130 0.00 0.00 35.36 3.53
2015 2236 4.390264 AGTCAAAACTGAAGCCCTAACTC 58.610 43.478 0.00 0.00 33.32 3.01
2028 2249 5.828871 AGCCCTAACTCTCTAGACTTGTAA 58.171 41.667 0.00 0.00 0.00 2.41
2029 2250 5.653330 AGCCCTAACTCTCTAGACTTGTAAC 59.347 44.000 0.00 0.00 0.00 2.50
2056 2277 6.486253 TCAGCAGATTCAGTGATAAAACAC 57.514 37.500 0.00 0.00 40.60 3.32
2069 2290 5.335583 GTGATAAAACACCAGCAACTATGCA 60.336 40.000 3.41 0.00 43.33 3.96
2087 2308 1.060698 GCACTCCACGCTACGAAAATC 59.939 52.381 0.00 0.00 0.00 2.17
2122 2346 5.645624 TGGTATTCGTTGCAAATATGGTTG 58.354 37.500 0.00 0.00 0.00 3.77
2173 2427 2.835605 GCAAGTGCTACTGCCGTAA 58.164 52.632 0.00 0.00 38.71 3.18
2179 2433 3.473625 AGTGCTACTGCCGTAAAAACTT 58.526 40.909 0.00 0.00 38.71 2.66
2180 2434 3.250040 AGTGCTACTGCCGTAAAAACTTG 59.750 43.478 0.00 0.00 38.71 3.16
2181 2435 3.249080 GTGCTACTGCCGTAAAAACTTGA 59.751 43.478 0.00 0.00 38.71 3.02
2182 2436 3.249080 TGCTACTGCCGTAAAAACTTGAC 59.751 43.478 0.00 0.00 38.71 3.18
2184 2438 4.260866 GCTACTGCCGTAAAAACTTGACAA 60.261 41.667 0.00 0.00 0.00 3.18
2185 2439 4.023739 ACTGCCGTAAAAACTTGACAAC 57.976 40.909 0.00 0.00 0.00 3.32
2186 2440 3.440872 ACTGCCGTAAAAACTTGACAACA 59.559 39.130 0.00 0.00 0.00 3.33
2187 2441 4.082679 ACTGCCGTAAAAACTTGACAACAA 60.083 37.500 0.00 0.00 34.65 2.83
2219 2473 5.869753 ATGTGAACAGATTGTAGAAGCAC 57.130 39.130 0.00 0.00 0.00 4.40
2229 2483 5.712446 AGATTGTAGAAGCACAGAGTACAGA 59.288 40.000 0.00 0.00 0.00 3.41
2234 2488 3.505680 AGAAGCACAGAGTACAGACTGAG 59.494 47.826 10.08 12.20 35.45 3.35
2249 2503 7.158099 ACAGACTGAGCAAAGTAAAAACTTT 57.842 32.000 10.08 0.00 40.22 2.66
2256 2510 7.603651 TGAGCAAAGTAAAAACTTTACACCAA 58.396 30.769 10.91 0.00 37.80 3.67
2276 2530 0.530744 TGCTACTGCTCTACCAACCG 59.469 55.000 0.00 0.00 40.48 4.44
2329 2585 3.335737 CTCTCAAATGAGCTCGCGA 57.664 52.632 9.26 9.26 41.80 5.87
2336 2592 1.284657 AATGAGCTCGCGATGAACAG 58.715 50.000 10.36 0.00 0.00 3.16
2340 2596 2.259618 GAGCTCGCGATGAACAGTAAA 58.740 47.619 10.36 0.00 0.00 2.01
2341 2597 1.993370 AGCTCGCGATGAACAGTAAAC 59.007 47.619 10.36 0.00 0.00 2.01
2343 2599 1.320555 CTCGCGATGAACAGTAAACCG 59.679 52.381 10.36 0.00 0.00 4.44
2345 2601 1.320555 CGCGATGAACAGTAAACCGAG 59.679 52.381 0.00 0.00 0.00 4.63
2349 2605 4.665897 GCGATGAACAGTAAACCGAGAAAC 60.666 45.833 0.00 0.00 0.00 2.78
2353 2612 6.055231 TGAACAGTAAACCGAGAAACATTG 57.945 37.500 0.00 0.00 0.00 2.82
2357 2616 7.090953 ACAGTAAACCGAGAAACATTGAAAA 57.909 32.000 0.00 0.00 0.00 2.29
2417 2676 8.603181 ACTTTGACAAATTTTCTATGTGTTTGC 58.397 29.630 0.05 0.00 34.12 3.68
2436 2695 7.795272 GTGTTTGCAAAGTTTCATGATGAAATC 59.205 33.333 21.91 15.39 46.55 2.17
2452 2711 7.558161 GATGAAATCACATATGTGGAAGTCA 57.442 36.000 30.56 25.98 44.70 3.41
2454 2713 7.324354 TGAAATCACATATGTGGAAGTCATG 57.676 36.000 30.56 6.89 45.65 3.07
2459 2719 6.244654 TCACATATGTGGAAGTCATGGAAAA 58.755 36.000 30.56 7.84 45.65 2.29
2510 2770 9.434420 TTTTGAAAGTAATATTTTGGGAGCATG 57.566 29.630 0.00 0.00 0.00 4.06
2531 2791 4.979388 TGCATTTTGTTTCTTTTTGGCAC 58.021 34.783 0.00 0.00 0.00 5.01
2585 2845 7.038154 ACTTTGCAAGCACTTAGAACATTTA 57.962 32.000 0.00 0.00 0.00 1.40
2587 2847 7.809806 ACTTTGCAAGCACTTAGAACATTTATC 59.190 33.333 0.00 0.00 0.00 1.75
2632 2894 9.874205 AATCAGAATTTTGTGAACTCTTTTCAA 57.126 25.926 0.00 0.00 33.95 2.69
2636 2898 9.305925 AGAATTTTGTGAACTCTTTTCAATGTC 57.694 29.630 0.00 0.00 0.00 3.06
2642 2904 6.315144 TGTGAACTCTTTTCAATGTCTTTCGA 59.685 34.615 0.00 0.00 0.00 3.71
2650 2912 9.483916 TCTTTTCAATGTCTTTCGATGTTACTA 57.516 29.630 0.00 0.00 0.00 1.82
2662 2924 3.550233 CGATGTTACTAGTCATCCGGGTG 60.550 52.174 8.97 8.97 37.67 4.61
2670 2932 1.280710 AGTCATCCGGGTGCAAATGTA 59.719 47.619 10.80 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
303 304 4.379243 ACCTCGAGCAGCCGTTGG 62.379 66.667 6.99 12.48 0.00 3.77
514 530 2.160417 GCTCAGATTGTACAGGTTGTGC 59.840 50.000 0.00 4.99 33.42 4.57
626 642 4.036027 GCATATCAATCCAGTGACCAACAG 59.964 45.833 0.00 0.00 0.00 3.16
628 644 4.202441 AGCATATCAATCCAGTGACCAAC 58.798 43.478 0.00 0.00 0.00 3.77
675 691 1.342496 TCCTGAATCTCCATAGCAGCG 59.658 52.381 0.00 0.00 0.00 5.18
789 805 0.930726 ATCCCCCTGGCCGATTTTAA 59.069 50.000 0.00 0.00 0.00 1.52
971 988 0.398318 GACCAGCAACCTTCTGTCCT 59.602 55.000 0.00 0.00 0.00 3.85
1131 1149 4.260375 GGTTTGATGTCGCAGTGTATGATC 60.260 45.833 0.00 0.00 0.00 2.92
1197 1215 1.356624 CTTCGCCATGCCGAAATCC 59.643 57.895 12.94 0.00 45.37 3.01
1298 1316 2.988839 GCCTTCCTGGTGATGGGCT 61.989 63.158 0.00 0.00 38.45 5.19
1427 1445 1.775934 AACCTCCCCTTCGTTCACCC 61.776 60.000 0.00 0.00 0.00 4.61
1713 1738 4.822685 ACAGAGCACAGATTCAGATCTT 57.177 40.909 0.00 0.00 40.67 2.40
1729 1754 5.772825 TTGGATCTGGAAACAAAACAGAG 57.227 39.130 0.00 0.00 43.67 3.35
1746 1772 6.070538 GGGTGTAGTGAGCTCATATATTGGAT 60.071 42.308 21.47 0.69 0.00 3.41
1752 1778 6.747414 ATTTGGGTGTAGTGAGCTCATATA 57.253 37.500 21.47 13.28 0.00 0.86
1753 1779 5.636903 ATTTGGGTGTAGTGAGCTCATAT 57.363 39.130 21.47 14.35 0.00 1.78
1757 1783 4.327680 AGAAATTTGGGTGTAGTGAGCTC 58.672 43.478 6.82 6.82 0.00 4.09
1763 1789 4.827284 CCACAGAAGAAATTTGGGTGTAGT 59.173 41.667 0.00 0.00 0.00 2.73
1768 1794 4.901250 ACAATCCACAGAAGAAATTTGGGT 59.099 37.500 0.00 0.00 0.00 4.51
1769 1795 5.473066 ACAATCCACAGAAGAAATTTGGG 57.527 39.130 0.00 0.00 0.00 4.12
1770 1796 6.282930 ACAACAATCCACAGAAGAAATTTGG 58.717 36.000 0.00 0.00 0.00 3.28
1771 1797 7.596248 CCTACAACAATCCACAGAAGAAATTTG 59.404 37.037 0.00 0.00 0.00 2.32
1774 1800 5.711976 CCCTACAACAATCCACAGAAGAAAT 59.288 40.000 0.00 0.00 0.00 2.17
1776 1802 4.349636 TCCCTACAACAATCCACAGAAGAA 59.650 41.667 0.00 0.00 0.00 2.52
1778 1804 4.286297 TCCCTACAACAATCCACAGAAG 57.714 45.455 0.00 0.00 0.00 2.85
1901 2122 5.008019 TCACAAAGCAAAGTCACTGAATCTC 59.992 40.000 0.00 0.00 0.00 2.75
1902 2123 4.883585 TCACAAAGCAAAGTCACTGAATCT 59.116 37.500 0.00 0.00 0.00 2.40
1903 2124 5.173774 TCACAAAGCAAAGTCACTGAATC 57.826 39.130 0.00 0.00 0.00 2.52
1904 2125 5.126061 ACTTCACAAAGCAAAGTCACTGAAT 59.874 36.000 0.00 0.00 35.81 2.57
1905 2126 4.458989 ACTTCACAAAGCAAAGTCACTGAA 59.541 37.500 0.00 0.00 35.81 3.02
1906 2127 4.009675 ACTTCACAAAGCAAAGTCACTGA 58.990 39.130 0.00 0.00 35.81 3.41
1907 2128 4.346129 GACTTCACAAAGCAAAGTCACTG 58.654 43.478 9.05 0.00 45.23 3.66
1908 2129 4.622701 GACTTCACAAAGCAAAGTCACT 57.377 40.909 9.05 0.00 45.23 3.41
1911 2132 4.787882 GCTCAGACTTCACAAAGCAAAGTC 60.788 45.833 6.41 6.41 45.90 3.01
1912 2133 3.065925 GCTCAGACTTCACAAAGCAAAGT 59.934 43.478 0.00 0.00 35.81 2.66
1913 2134 3.314635 AGCTCAGACTTCACAAAGCAAAG 59.685 43.478 0.00 0.00 35.81 2.77
1914 2135 3.282021 AGCTCAGACTTCACAAAGCAAA 58.718 40.909 0.00 0.00 35.81 3.68
1915 2136 2.923121 AGCTCAGACTTCACAAAGCAA 58.077 42.857 0.00 0.00 35.81 3.91
1916 2137 2.615447 CAAGCTCAGACTTCACAAAGCA 59.385 45.455 0.00 0.00 35.81 3.91
1917 2138 2.874701 TCAAGCTCAGACTTCACAAAGC 59.125 45.455 0.00 0.00 35.81 3.51
1918 2139 4.125703 AGTCAAGCTCAGACTTCACAAAG 58.874 43.478 14.20 0.00 43.47 2.77
1919 2140 4.142609 AGTCAAGCTCAGACTTCACAAA 57.857 40.909 14.20 0.00 43.47 2.83
1920 2141 3.827008 AGTCAAGCTCAGACTTCACAA 57.173 42.857 14.20 0.00 43.47 3.33
1927 2148 0.957888 GGGCCAAGTCAAGCTCAGAC 60.958 60.000 4.39 10.42 36.26 3.51
1928 2149 1.376466 GGGCCAAGTCAAGCTCAGA 59.624 57.895 4.39 0.00 0.00 3.27
1929 2150 1.676967 GGGGCCAAGTCAAGCTCAG 60.677 63.158 4.39 0.00 0.00 3.35
1930 2151 0.840288 TAGGGGCCAAGTCAAGCTCA 60.840 55.000 4.39 0.00 0.00 4.26
1931 2152 0.393132 GTAGGGGCCAAGTCAAGCTC 60.393 60.000 4.39 0.00 0.00 4.09
1932 2153 1.685820 GTAGGGGCCAAGTCAAGCT 59.314 57.895 4.39 0.00 0.00 3.74
1933 2154 1.378646 GGTAGGGGCCAAGTCAAGC 60.379 63.158 4.39 0.00 0.00 4.01
1934 2155 0.625849 ATGGTAGGGGCCAAGTCAAG 59.374 55.000 4.39 0.00 42.48 3.02
1935 2156 1.080638 AATGGTAGGGGCCAAGTCAA 58.919 50.000 4.39 0.00 42.48 3.18
1936 2157 0.331278 CAATGGTAGGGGCCAAGTCA 59.669 55.000 4.39 0.00 42.48 3.41
1937 2158 0.623723 TCAATGGTAGGGGCCAAGTC 59.376 55.000 4.39 0.00 42.48 3.01
1938 2159 0.625849 CTCAATGGTAGGGGCCAAGT 59.374 55.000 4.39 0.00 42.48 3.16
1939 2160 0.106519 CCTCAATGGTAGGGGCCAAG 60.107 60.000 4.39 0.00 42.48 3.61
1940 2161 2.006748 CCTCAATGGTAGGGGCCAA 58.993 57.895 4.39 0.00 42.48 4.52
1941 2162 3.754043 CCTCAATGGTAGGGGCCA 58.246 61.111 4.39 0.00 43.48 5.36
1964 2185 2.204463 TCTGGGCCTTTGGATCACATA 58.796 47.619 4.53 0.00 0.00 2.29
1966 2187 0.776810 TTCTGGGCCTTTGGATCACA 59.223 50.000 4.53 0.00 0.00 3.58
1985 2206 6.098266 AGGGCTTCAGTTTTGACTTTGTAAAT 59.902 34.615 0.00 0.00 31.71 1.40
1986 2207 5.420739 AGGGCTTCAGTTTTGACTTTGTAAA 59.579 36.000 0.00 0.00 31.71 2.01
1990 2211 5.067805 AGTTAGGGCTTCAGTTTTGACTTTG 59.932 40.000 0.00 0.00 31.71 2.77
2011 2232 7.654116 GCTGAAAAGTTACAAGTCTAGAGAGTT 59.346 37.037 0.00 0.00 38.16 3.01
2015 2236 7.148641 TCTGCTGAAAAGTTACAAGTCTAGAG 58.851 38.462 0.00 0.00 0.00 2.43
2028 2249 7.750229 TTTATCACTGAATCTGCTGAAAAGT 57.250 32.000 0.00 0.00 0.00 2.66
2029 2250 8.077991 TGTTTTATCACTGAATCTGCTGAAAAG 58.922 33.333 0.00 0.00 0.00 2.27
2069 2290 1.274167 TGGATTTTCGTAGCGTGGAGT 59.726 47.619 0.00 0.00 0.00 3.85
2087 2308 5.447279 GCAACGAATACCAGTTATCTGTTGG 60.447 44.000 0.00 0.00 39.82 3.77
2179 2433 8.246871 TGTTCACATTTAATTCACTTGTTGTCA 58.753 29.630 0.00 0.00 0.00 3.58
2180 2434 8.627487 TGTTCACATTTAATTCACTTGTTGTC 57.373 30.769 0.00 0.00 0.00 3.18
2181 2435 8.465999 TCTGTTCACATTTAATTCACTTGTTGT 58.534 29.630 0.00 0.00 0.00 3.32
2182 2436 8.854979 TCTGTTCACATTTAATTCACTTGTTG 57.145 30.769 0.00 0.00 0.00 3.33
2184 2438 9.467258 CAATCTGTTCACATTTAATTCACTTGT 57.533 29.630 0.00 0.00 0.00 3.16
2185 2439 9.467258 ACAATCTGTTCACATTTAATTCACTTG 57.533 29.630 0.00 0.00 0.00 3.16
2219 2473 4.250116 ACTTTGCTCAGTCTGTACTCTG 57.750 45.455 0.00 0.95 31.97 3.35
2229 2483 7.094118 TGGTGTAAAGTTTTTACTTTGCTCAGT 60.094 33.333 16.09 0.00 41.03 3.41
2234 2488 7.011016 AGCATTGGTGTAAAGTTTTTACTTTGC 59.989 33.333 12.25 11.39 39.89 3.68
2249 2503 3.132289 GGTAGAGCAGTAGCATTGGTGTA 59.868 47.826 0.00 0.00 45.49 2.90
2256 2510 1.137086 CGGTTGGTAGAGCAGTAGCAT 59.863 52.381 0.00 0.00 45.49 3.79
2276 2530 5.277683 GGGACTTCCGTTTTGTACTTTTCTC 60.278 44.000 0.00 0.00 36.71 2.87
2324 2580 1.068402 TCGGTTTACTGTTCATCGCGA 60.068 47.619 13.09 13.09 0.00 5.87
2327 2583 4.446385 TGTTTCTCGGTTTACTGTTCATCG 59.554 41.667 0.00 0.00 0.00 3.84
2329 2585 6.485313 TCAATGTTTCTCGGTTTACTGTTCAT 59.515 34.615 0.00 0.00 0.00 2.57
2384 2643 6.421377 AGAAAATTTGTCAAAGTTTGCCAC 57.579 33.333 24.03 12.21 38.60 5.01
2401 2660 8.715191 TGAAACTTTGCAAACACATAGAAAAT 57.285 26.923 8.05 0.00 0.00 1.82
2406 2665 7.595875 TCATCATGAAACTTTGCAAACACATAG 59.404 33.333 8.05 0.00 0.00 2.23
2407 2666 7.432059 TCATCATGAAACTTTGCAAACACATA 58.568 30.769 8.05 0.00 0.00 2.29
2436 2695 6.513806 TTTTCCATGACTTCCACATATGTG 57.486 37.500 26.02 26.02 45.23 3.21
2459 2719 5.694458 GCATTTTGGAGTACCGATTTTGTTT 59.306 36.000 0.00 0.00 39.42 2.83
2495 2755 5.747342 ACAAAATGCATGCTCCCAAAATAT 58.253 33.333 20.33 0.00 0.00 1.28
2496 2756 5.163281 ACAAAATGCATGCTCCCAAAATA 57.837 34.783 20.33 0.00 0.00 1.40
2502 2762 3.323751 AGAAACAAAATGCATGCTCCC 57.676 42.857 20.33 0.00 0.00 4.30
2510 2770 4.027724 CGTGCCAAAAAGAAACAAAATGC 58.972 39.130 0.00 0.00 0.00 3.56
2531 2791 1.062587 GAATCACATTCGTGGAAGCCG 59.937 52.381 0.00 0.00 43.79 5.52
2613 2873 9.657419 AAAGACATTGAAAAGAGTTCACAAAAT 57.343 25.926 0.00 0.00 0.00 1.82
2618 2880 6.715464 TCGAAAGACATTGAAAAGAGTTCAC 58.285 36.000 0.00 0.00 33.31 3.18
2625 2887 9.746711 CTAGTAACATCGAAAGACATTGAAAAG 57.253 33.333 0.00 0.00 46.97 2.27
2632 2894 7.203910 GGATGACTAGTAACATCGAAAGACAT 58.796 38.462 14.93 2.50 46.97 3.06
2636 2898 4.976731 CCGGATGACTAGTAACATCGAAAG 59.023 45.833 14.93 8.60 42.34 2.62
2642 2904 2.102588 GCACCCGGATGACTAGTAACAT 59.897 50.000 0.00 0.00 0.00 2.71
2650 2912 0.038166 ACATTTGCACCCGGATGACT 59.962 50.000 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.