Multiple sequence alignment - TraesCS7D01G099900

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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 TraesCS7D01G099900 chr7D 100.000 3681 0 0 1 3681 59940538 59936858 0.000000e+00 6798
1 TraesCS7D01G099900 chr7D 94.859 1595 71 3 2098 3681 64246362 64247956 0.000000e+00 2481
2 TraesCS7D01G099900 chr7D 93.958 1473 75 8 2219 3681 64266853 64268321 0.000000e+00 2215
3 TraesCS7D01G099900 chr7D 96.639 1339 34 6 2093 3422 64223777 64225113 0.000000e+00 2213
4 TraesCS7D01G099900 chr7D 91.597 1083 84 5 867 1944 64222707 64223787 0.000000e+00 1489
5 TraesCS7D01G099900 chr7D 86.461 1263 160 11 690 1944 63944046 63942787 0.000000e+00 1375
6 TraesCS7D01G099900 chr7D 86.410 1273 145 15 679 1944 64245117 64246368 0.000000e+00 1367
7 TraesCS7D01G099900 chr7D 86.434 1231 140 13 720 1936 64265529 64266746 0.000000e+00 1323
8 TraesCS7D01G099900 chr7D 86.734 897 106 11 2094 2983 59906859 59905969 0.000000e+00 985
9 TraesCS7D01G099900 chr7D 84.615 169 12 3 1942 2097 116693747 116693914 4.920000e-34 156
10 TraesCS7D01G099900 chr7D 92.381 105 5 3 1996 2097 352097197 352097301 2.960000e-31 147
11 TraesCS7D01G099900 chr7A 92.736 1597 107 3 2093 3681 67986066 67987661 0.000000e+00 2298
12 TraesCS7D01G099900 chr7A 90.653 1562 131 9 2131 3681 68030153 68031710 0.000000e+00 2061
13 TraesCS7D01G099900 chr7A 90.102 1566 126 13 2093 3647 68044068 68045615 0.000000e+00 2006
14 TraesCS7D01G099900 chr7A 90.725 1186 103 6 765 1944 67593225 67592041 0.000000e+00 1574
15 TraesCS7D01G099900 chr7A 89.336 1219 115 10 678 1889 68076779 68077989 0.000000e+00 1517
16 TraesCS7D01G099900 chr7A 82.239 1599 231 33 2120 3678 68023458 68025043 0.000000e+00 1330
17 TraesCS7D01G099900 chr7A 92.237 760 51 2 2093 2845 67592051 67591293 0.000000e+00 1070
18 TraesCS7D01G099900 chr7A 92.888 464 24 4 1 455 68028221 68028684 0.000000e+00 665
19 TraesCS7D01G099900 chr7A 93.089 463 6 2 513 949 68028705 68029167 0.000000e+00 654
20 TraesCS7D01G099900 chr7A 89.809 157 5 5 1941 2096 467427155 467427009 1.350000e-44 191
21 TraesCS7D01G099900 chr7A 76.636 321 43 19 180 483 67984378 67984683 8.240000e-32 148
22 TraesCS7D01G099900 chr7A 76.873 307 39 18 200 489 67593755 67593464 1.070000e-30 145
23 TraesCS7D01G099900 chr7B 91.280 1594 110 8 2098 3681 5217494 5219068 0.000000e+00 2146
24 TraesCS7D01G099900 chr7B 88.770 1594 166 9 2098 3681 5283076 5284666 0.000000e+00 1940
25 TraesCS7D01G099900 chr7B 90.292 1473 127 11 2219 3681 5504232 5505698 0.000000e+00 1914
26 TraesCS7D01G099900 chr7B 87.068 1593 156 25 2098 3681 5338025 5339576 0.000000e+00 1755
27 TraesCS7D01G099900 chr7B 92.546 1033 66 3 2098 3120 5511098 5512129 0.000000e+00 1471
28 TraesCS7D01G099900 chr7B 87.943 1269 123 13 679 1944 5216260 5217501 0.000000e+00 1469
29 TraesCS7D01G099900 chr7B 86.871 1272 146 12 679 1944 5509848 5511104 0.000000e+00 1404
30 TraesCS7D01G099900 chr7B 84.825 1285 170 20 647 1916 5195373 5196647 0.000000e+00 1269
31 TraesCS7D01G099900 chr7B 82.615 1392 180 42 566 1915 5267164 5268535 0.000000e+00 1173
32 TraesCS7D01G099900 chr5D 91.824 159 9 2 1945 2099 557197321 557197479 6.190000e-53 219
33 TraesCS7D01G099900 chr5B 88.312 154 6 5 1945 2097 617706414 617706272 1.360000e-39 174
34 TraesCS7D01G099900 chr6A 88.276 145 16 1 1942 2086 10140306 10140449 4.890000e-39 172
35 TraesCS7D01G099900 chr6A 85.207 169 12 6 1930 2086 111742733 111742566 1.060000e-35 161
36 TraesCS7D01G099900 chr3D 86.503 163 11 2 1945 2096 40010238 40010400 6.320000e-38 169
37 TraesCS7D01G099900 chr5A 89.630 135 3 5 1941 2074 130533123 130533247 1.060000e-35 161
38 TraesCS7D01G099900 chr3A 85.542 166 11 6 1933 2086 217823802 217823638 1.060000e-35 161
39 TraesCS7D01G099900 chr2D 87.333 150 7 5 1948 2096 185386245 185386107 1.060000e-35 161
40 TraesCS7D01G099900 chr6B 87.248 149 6 5 1939 2074 239363445 239363593 1.370000e-34 158
41 TraesCS7D01G099900 chr4A 91.453 117 6 4 1984 2096 92743737 92743853 1.370000e-34 158
42 TraesCS7D01G099900 chr2B 87.413 143 5 5 1945 2074 288941224 288941082 6.370000e-33 152
43 TraesCS7D01G099900 chr2B 88.889 117 8 5 1984 2096 305318942 305319057 4.960000e-29 139


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 TraesCS7D01G099900 chr7D 59936858 59940538 3680 True 6798.000000 6798 100.000000 1 3681 1 chr7D.!!$R2 3680
1 TraesCS7D01G099900 chr7D 64245117 64247956 2839 False 1924.000000 2481 90.634500 679 3681 2 chr7D.!!$F4 3002
2 TraesCS7D01G099900 chr7D 64222707 64225113 2406 False 1851.000000 2213 94.118000 867 3422 2 chr7D.!!$F3 2555
3 TraesCS7D01G099900 chr7D 64265529 64268321 2792 False 1769.000000 2215 90.196000 720 3681 2 chr7D.!!$F5 2961
4 TraesCS7D01G099900 chr7D 63942787 63944046 1259 True 1375.000000 1375 86.461000 690 1944 1 chr7D.!!$R3 1254
5 TraesCS7D01G099900 chr7D 59905969 59906859 890 True 985.000000 985 86.734000 2094 2983 1 chr7D.!!$R1 889
6 TraesCS7D01G099900 chr7A 68044068 68045615 1547 False 2006.000000 2006 90.102000 2093 3647 1 chr7A.!!$F1 1554
7 TraesCS7D01G099900 chr7A 68076779 68077989 1210 False 1517.000000 1517 89.336000 678 1889 1 chr7A.!!$F2 1211
8 TraesCS7D01G099900 chr7A 67984378 67987661 3283 False 1223.000000 2298 84.686000 180 3681 2 chr7A.!!$F3 3501
9 TraesCS7D01G099900 chr7A 68023458 68031710 8252 False 1177.500000 2061 89.717250 1 3681 4 chr7A.!!$F4 3680
10 TraesCS7D01G099900 chr7A 67591293 67593755 2462 True 929.666667 1574 86.611667 200 2845 3 chr7A.!!$R2 2645
11 TraesCS7D01G099900 chr7B 5283076 5284666 1590 False 1940.000000 1940 88.770000 2098 3681 1 chr7B.!!$F3 1583
12 TraesCS7D01G099900 chr7B 5504232 5505698 1466 False 1914.000000 1914 90.292000 2219 3681 1 chr7B.!!$F5 1462
13 TraesCS7D01G099900 chr7B 5216260 5219068 2808 False 1807.500000 2146 89.611500 679 3681 2 chr7B.!!$F6 3002
14 TraesCS7D01G099900 chr7B 5338025 5339576 1551 False 1755.000000 1755 87.068000 2098 3681 1 chr7B.!!$F4 1583
15 TraesCS7D01G099900 chr7B 5509848 5512129 2281 False 1437.500000 1471 89.708500 679 3120 2 chr7B.!!$F7 2441
16 TraesCS7D01G099900 chr7B 5195373 5196647 1274 False 1269.000000 1269 84.825000 647 1916 1 chr7B.!!$F1 1269
17 TraesCS7D01G099900 chr7B 5267164 5268535 1371 False 1173.000000 1173 82.615000 566 1915 1 chr7B.!!$F2 1349

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
974 5914 0.107066 TAGTGGTGCGTAGATCGGGA 60.107 55.0 0.00 0.0 40.26 5.14 F
980 5920 0.179111 TGCGTAGATCGGGAGCAAAG 60.179 55.0 5.89 0.0 40.26 2.77 F
1298 6281 0.321653 AAGCCAACGGACATGAGGAC 60.322 55.0 0.00 0.0 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1964 6956 1.508088 CCCAGCGCCTTAAAGCAAG 59.492 57.895 2.29 0.00 35.48 4.01 R
1965 6957 1.976474 CCCCAGCGCCTTAAAGCAA 60.976 57.895 2.29 0.00 35.48 3.91 R
3113 8134 2.438868 ACCTGCGAAATTTCTTTGCC 57.561 45.000 15.92 0.77 0.00 4.52 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
25 4789 3.314080 AGCTCTCGATCTAGTTAGTGCAC 59.686 47.826 9.40 9.40 32.38 4.57
27 4791 4.788201 GCTCTCGATCTAGTTAGTGCACAG 60.788 50.000 21.04 7.24 0.00 3.66
34 4798 4.082845 TCTAGTTAGTGCACAGCTCTCTT 58.917 43.478 21.04 0.00 34.22 2.85
61 4825 2.679837 CCTGTTCTGATTTGGATCCGTG 59.320 50.000 7.39 0.00 0.00 4.94
67 4831 3.055167 TCTGATTTGGATCCGTGATGTGT 60.055 43.478 7.39 0.00 0.00 3.72
80 4844 4.338400 CCGTGATGTGTAGAGTTGGATCTA 59.662 45.833 0.00 0.00 0.00 1.98
147 4911 4.025396 CAGAGTTGCTGTGTAGTGTTGAAG 60.025 45.833 0.00 0.00 39.85 3.02
175 4939 1.064758 TCTTCAACTTGTGCCACCTGT 60.065 47.619 0.00 0.00 0.00 4.00
227 4997 0.979665 CAGAGCAAGGAGAGGGTCAA 59.020 55.000 0.00 0.00 34.11 3.18
276 5047 9.912634 CTCCTTAATCTTTTGTTGCTATTTTCA 57.087 29.630 0.00 0.00 0.00 2.69
393 5168 4.769345 AAAGCAAAGGGAAAATGGTCAA 57.231 36.364 0.00 0.00 0.00 3.18
400 5175 3.855668 AGGGAAAATGGTCAATGGTCAA 58.144 40.909 0.00 0.00 0.00 3.18
463 5319 3.541632 TCCTTTTCACTCTGTGACCAAC 58.458 45.455 0.00 0.00 42.60 3.77
489 5345 7.173562 CCAAAATCAGATCATGCTTTTCCAAAA 59.826 33.333 0.00 0.00 35.57 2.44
490 5346 8.726988 CAAAATCAGATCATGCTTTTCCAAAAT 58.273 29.630 0.00 0.00 35.57 1.82
491 5347 8.488651 AAATCAGATCATGCTTTTCCAAAATC 57.511 30.769 0.00 0.00 0.00 2.17
493 5349 6.627243 TCAGATCATGCTTTTCCAAAATCAG 58.373 36.000 0.00 0.00 28.94 2.90
494 5350 6.434965 TCAGATCATGCTTTTCCAAAATCAGA 59.565 34.615 0.00 0.00 28.94 3.27
495 5351 7.123697 TCAGATCATGCTTTTCCAAAATCAGAT 59.876 33.333 0.00 0.00 28.94 2.90
496 5352 7.435488 CAGATCATGCTTTTCCAAAATCAGATC 59.565 37.037 0.00 13.37 34.09 2.75
498 5354 6.860080 TCATGCTTTTCCAAAATCAGATCTC 58.140 36.000 0.00 0.00 28.94 2.75
499 5355 6.662234 TCATGCTTTTCCAAAATCAGATCTCT 59.338 34.615 0.00 0.00 28.94 3.10
501 5357 6.684686 TGCTTTTCCAAAATCAGATCTCTTG 58.315 36.000 0.00 0.00 0.00 3.02
502 5358 6.266103 TGCTTTTCCAAAATCAGATCTCTTGT 59.734 34.615 0.00 0.00 0.00 3.16
503 5359 7.150640 GCTTTTCCAAAATCAGATCTCTTGTT 58.849 34.615 0.00 0.00 0.00 2.83
504 5360 7.115947 GCTTTTCCAAAATCAGATCTCTTGTTG 59.884 37.037 0.00 0.00 0.00 3.33
544 5422 5.703130 TCATTCCATCACGTGTTGTTATTCA 59.297 36.000 21.74 0.00 0.00 2.57
632 5512 2.189594 TTGCTCATCCAGTGGTTCTG 57.810 50.000 9.54 5.97 43.27 3.02
811 5727 7.418025 GCTGATATTCAGGGTACACTTCTACTT 60.418 40.741 0.00 0.00 44.43 2.24
814 5730 5.723672 TTCAGGGTACACTTCTACTTCTG 57.276 43.478 0.00 0.00 0.00 3.02
892 5832 1.202521 CCACCAAGTTCAGGTTTTGCC 60.203 52.381 0.00 0.00 37.23 4.52
946 5886 4.781775 TTACAGAAGTTCAACCCAAGGA 57.218 40.909 5.50 0.00 0.00 3.36
947 5887 2.932261 ACAGAAGTTCAACCCAAGGAC 58.068 47.619 5.50 0.00 0.00 3.85
948 5888 2.241176 ACAGAAGTTCAACCCAAGGACA 59.759 45.455 5.50 0.00 0.00 4.02
949 5889 2.880890 CAGAAGTTCAACCCAAGGACAG 59.119 50.000 5.50 0.00 0.00 3.51
950 5890 2.509964 AGAAGTTCAACCCAAGGACAGT 59.490 45.455 5.50 0.00 0.00 3.55
951 5891 2.348411 AGTTCAACCCAAGGACAGTG 57.652 50.000 0.00 0.00 0.00 3.66
952 5892 1.133792 AGTTCAACCCAAGGACAGTGG 60.134 52.381 0.00 0.00 35.77 4.00
953 5893 0.923358 TTCAACCCAAGGACAGTGGT 59.077 50.000 0.00 0.00 34.01 4.16
954 5894 1.809133 TCAACCCAAGGACAGTGGTA 58.191 50.000 0.00 0.00 34.01 3.25
955 5895 2.344592 TCAACCCAAGGACAGTGGTAT 58.655 47.619 0.00 0.00 34.01 2.73
956 5896 3.522759 TCAACCCAAGGACAGTGGTATA 58.477 45.455 0.00 0.00 34.01 1.47
957 5897 3.517901 TCAACCCAAGGACAGTGGTATAG 59.482 47.826 0.00 0.00 34.01 1.31
958 5898 3.200958 ACCCAAGGACAGTGGTATAGT 57.799 47.619 0.00 0.00 34.01 2.12
959 5899 2.838202 ACCCAAGGACAGTGGTATAGTG 59.162 50.000 0.00 0.00 34.01 2.74
960 5900 2.170607 CCCAAGGACAGTGGTATAGTGG 59.829 54.545 0.00 0.00 34.01 4.00
961 5901 2.838202 CCAAGGACAGTGGTATAGTGGT 59.162 50.000 0.00 0.00 33.84 4.16
962 5902 3.369471 CCAAGGACAGTGGTATAGTGGTG 60.369 52.174 0.00 0.00 33.84 4.17
963 5903 1.831736 AGGACAGTGGTATAGTGGTGC 59.168 52.381 0.00 0.00 33.84 5.01
964 5904 1.470979 GGACAGTGGTATAGTGGTGCG 60.471 57.143 0.00 0.00 33.84 5.34
965 5905 1.203994 GACAGTGGTATAGTGGTGCGT 59.796 52.381 0.00 0.00 33.84 5.24
966 5906 2.424601 GACAGTGGTATAGTGGTGCGTA 59.575 50.000 0.00 0.00 33.84 4.42
967 5907 2.426024 ACAGTGGTATAGTGGTGCGTAG 59.574 50.000 0.00 0.00 33.84 3.51
968 5908 2.686405 CAGTGGTATAGTGGTGCGTAGA 59.314 50.000 0.00 0.00 0.00 2.59
969 5909 3.318275 CAGTGGTATAGTGGTGCGTAGAT 59.682 47.826 0.00 0.00 0.00 1.98
970 5910 3.568853 AGTGGTATAGTGGTGCGTAGATC 59.431 47.826 0.00 0.00 0.00 2.75
971 5911 2.551032 TGGTATAGTGGTGCGTAGATCG 59.449 50.000 0.00 0.00 43.12 3.69
972 5912 2.095364 GGTATAGTGGTGCGTAGATCGG 60.095 54.545 0.00 0.00 40.26 4.18
973 5913 0.959553 ATAGTGGTGCGTAGATCGGG 59.040 55.000 0.00 0.00 40.26 5.14
974 5914 0.107066 TAGTGGTGCGTAGATCGGGA 60.107 55.000 0.00 0.00 40.26 5.14
975 5915 1.065928 GTGGTGCGTAGATCGGGAG 59.934 63.158 0.00 0.00 40.26 4.30
976 5916 2.027751 GGTGCGTAGATCGGGAGC 59.972 66.667 0.00 0.00 40.26 4.70
977 5917 2.782222 GGTGCGTAGATCGGGAGCA 61.782 63.158 4.54 4.54 40.26 4.26
978 5918 1.141019 GTGCGTAGATCGGGAGCAA 59.859 57.895 9.13 0.00 39.67 3.91
979 5919 0.459585 GTGCGTAGATCGGGAGCAAA 60.460 55.000 9.13 0.00 39.67 3.68
980 5920 0.179111 TGCGTAGATCGGGAGCAAAG 60.179 55.000 5.89 0.00 40.26 2.77
1117 6100 7.749627 AAGGTGTACAGTCACTCCTTATAGAGT 60.750 40.741 10.58 0.00 45.82 3.24
1260 6243 1.594293 CGACTTCCTGGTGCGTGTT 60.594 57.895 0.00 0.00 0.00 3.32
1298 6281 0.321653 AAGCCAACGGACATGAGGAC 60.322 55.000 0.00 0.00 0.00 3.85
1454 6437 3.592898 TGACATGTGTAGCACTACCAG 57.407 47.619 1.15 0.00 35.11 4.00
1748 6731 4.434520 GACTTACTCTATGGCCTTGACAC 58.565 47.826 3.32 0.00 0.00 3.67
1962 6954 9.417284 CTTTTATACTATGTTTTAAAGGCGACG 57.583 33.333 0.00 0.00 0.00 5.12
1963 6955 3.734776 ACTATGTTTTAAAGGCGACGC 57.265 42.857 12.43 12.43 0.00 5.19
1973 6965 3.259930 GGCGACGCCTTGCTTTAA 58.740 55.556 31.30 0.00 46.69 1.52
1974 6966 1.134694 GGCGACGCCTTGCTTTAAG 59.865 57.895 31.30 0.00 46.69 1.85
1982 6974 1.508088 CTTGCTTTAAGGCGCTGGG 59.492 57.895 7.64 0.00 32.56 4.45
1983 6975 1.937546 CTTGCTTTAAGGCGCTGGGG 61.938 60.000 7.64 0.00 32.56 4.96
1984 6976 3.140814 GCTTTAAGGCGCTGGGGG 61.141 66.667 7.64 0.00 0.00 5.40
1985 6977 3.140814 CTTTAAGGCGCTGGGGGC 61.141 66.667 7.64 3.15 40.84 5.80
2046 7038 1.563111 CATATTTGCAAAGCGCTGGG 58.437 50.000 12.58 7.58 43.06 4.45
2047 7039 0.461135 ATATTTGCAAAGCGCTGGGG 59.539 50.000 12.58 4.50 43.06 4.96
2048 7040 1.603236 TATTTGCAAAGCGCTGGGGG 61.603 55.000 12.58 1.49 43.06 5.40
2084 7076 3.198582 GTCGCCTTAGAGACGCCT 58.801 61.111 0.00 0.00 32.96 5.52
2085 7077 1.511768 GTCGCCTTAGAGACGCCTT 59.488 57.895 0.00 0.00 32.96 4.35
2086 7078 0.108756 GTCGCCTTAGAGACGCCTTT 60.109 55.000 0.00 0.00 32.96 3.11
2087 7079 1.133790 GTCGCCTTAGAGACGCCTTTA 59.866 52.381 0.00 0.00 32.96 1.85
2088 7080 1.820519 TCGCCTTAGAGACGCCTTTAA 59.179 47.619 0.00 0.00 0.00 1.52
2089 7081 2.231964 TCGCCTTAGAGACGCCTTTAAA 59.768 45.455 0.00 0.00 0.00 1.52
2090 7082 2.997986 CGCCTTAGAGACGCCTTTAAAA 59.002 45.455 0.00 0.00 0.00 1.52
2091 7083 3.181523 CGCCTTAGAGACGCCTTTAAAAC 60.182 47.826 0.00 0.00 0.00 2.43
2092 7084 3.749609 GCCTTAGAGACGCCTTTAAAACA 59.250 43.478 0.00 0.00 0.00 2.83
2093 7085 4.395231 GCCTTAGAGACGCCTTTAAAACAT 59.605 41.667 0.00 0.00 0.00 2.71
2094 7086 5.583457 GCCTTAGAGACGCCTTTAAAACATA 59.417 40.000 0.00 0.00 0.00 2.29
2095 7087 6.238130 GCCTTAGAGACGCCTTTAAAACATAG 60.238 42.308 0.00 0.00 0.00 2.23
2096 7088 6.238130 CCTTAGAGACGCCTTTAAAACATAGC 60.238 42.308 0.00 0.00 0.00 2.97
3113 8134 2.213499 GGAGTGGAATGCACCTAATCG 58.787 52.381 0.07 0.00 0.00 3.34
3523 8545 3.477530 GTGTCAATTATAGGGTGAGGCC 58.522 50.000 0.00 0.00 0.00 5.19
3579 8601 2.742589 GTGCTGGAACAAGTAGGCTTAC 59.257 50.000 0.00 0.00 38.70 2.34
3610 8632 1.065926 TCACATTGCGGAAGAGCTGAT 60.066 47.619 0.00 0.00 38.13 2.90
3666 8688 3.935203 CTGTGCTAACATGAACGAGGATT 59.065 43.478 0.00 0.00 35.22 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 3.065510 TGTGCACTAACTAGATCGAGAGC 59.934 47.826 19.41 6.06 0.00 4.09
21 4785 2.105477 AGGAAAAGAAGAGAGCTGTGCA 59.895 45.455 0.00 0.00 0.00 4.57
25 4789 4.451774 CAGAACAGGAAAAGAAGAGAGCTG 59.548 45.833 0.00 0.00 0.00 4.24
27 4791 4.636249 TCAGAACAGGAAAAGAAGAGAGC 58.364 43.478 0.00 0.00 0.00 4.09
34 4798 5.711976 GGATCCAAATCAGAACAGGAAAAGA 59.288 40.000 6.95 0.00 33.21 2.52
61 4825 7.981789 TGTTCAATAGATCCAACTCTACACATC 59.018 37.037 0.00 0.00 30.77 3.06
67 4831 7.201741 CGAGAGTGTTCAATAGATCCAACTCTA 60.202 40.741 2.23 0.00 31.92 2.43
80 4844 1.001293 TGCTGAGCGAGAGTGTTCAAT 59.999 47.619 0.00 0.00 0.00 2.57
147 4911 2.287248 GCACAAGTTGAAGAAGAGCACC 60.287 50.000 10.54 0.00 0.00 5.01
227 4997 2.569404 GGAGAACAGATGGACCAAGAGT 59.431 50.000 0.00 0.00 0.00 3.24
234 5004 0.833949 GGAGGGGAGAACAGATGGAC 59.166 60.000 0.00 0.00 0.00 4.02
444 5221 3.278574 TGGTTGGTCACAGAGTGAAAAG 58.721 45.455 0.82 0.00 44.49 2.27
457 5234 4.159135 AGCATGATCTGATTTTGGTTGGTC 59.841 41.667 0.00 0.00 0.00 4.02
458 5235 4.091549 AGCATGATCTGATTTTGGTTGGT 58.908 39.130 0.00 0.00 0.00 3.67
489 5345 6.767456 AGAGTGAAACAACAAGAGATCTGAT 58.233 36.000 0.00 0.00 41.43 2.90
490 5346 6.166984 AGAGTGAAACAACAAGAGATCTGA 57.833 37.500 0.00 0.00 41.43 3.27
491 5347 6.857777 AAGAGTGAAACAACAAGAGATCTG 57.142 37.500 0.00 0.00 41.43 2.90
493 5349 8.371770 ACTAAAGAGTGAAACAACAAGAGATC 57.628 34.615 0.00 0.00 41.43 2.75
494 5350 8.738645 AACTAAAGAGTGAAACAACAAGAGAT 57.261 30.769 0.00 0.00 41.43 2.75
495 5351 8.561738 AAACTAAAGAGTGAAACAACAAGAGA 57.438 30.769 0.00 0.00 41.43 3.10
496 5352 8.450964 TGAAACTAAAGAGTGAAACAACAAGAG 58.549 33.333 0.00 0.00 41.43 2.85
498 5354 9.573133 AATGAAACTAAAGAGTGAAACAACAAG 57.427 29.630 0.00 0.00 41.43 3.16
499 5355 9.567848 GAATGAAACTAAAGAGTGAAACAACAA 57.432 29.630 0.00 0.00 41.43 2.83
501 5357 8.188139 TGGAATGAAACTAAAGAGTGAAACAAC 58.812 33.333 0.00 0.00 41.43 3.32
502 5358 8.287439 TGGAATGAAACTAAAGAGTGAAACAA 57.713 30.769 0.00 0.00 41.43 2.83
503 5359 7.873719 TGGAATGAAACTAAAGAGTGAAACA 57.126 32.000 0.00 0.00 41.43 2.83
504 5360 8.567948 TGATGGAATGAAACTAAAGAGTGAAAC 58.432 33.333 0.00 0.00 35.52 2.78
544 5422 7.828223 TGCATTGCATTACCTTTCCAATAAATT 59.172 29.630 7.38 0.00 31.71 1.82
632 5512 4.381411 ACAGAGGAGCTAACTGTTTTCAC 58.619 43.478 12.20 0.00 41.21 3.18
892 5832 9.793252 CATAAAGGTTTTCAGAAGACATAATGG 57.207 33.333 6.19 0.00 0.00 3.16
946 5886 1.263356 ACGCACCACTATACCACTGT 58.737 50.000 0.00 0.00 0.00 3.55
947 5887 2.686405 TCTACGCACCACTATACCACTG 59.314 50.000 0.00 0.00 0.00 3.66
948 5888 3.008835 TCTACGCACCACTATACCACT 57.991 47.619 0.00 0.00 0.00 4.00
949 5889 3.608707 CGATCTACGCACCACTATACCAC 60.609 52.174 0.00 0.00 34.51 4.16
950 5890 2.551032 CGATCTACGCACCACTATACCA 59.449 50.000 0.00 0.00 34.51 3.25
951 5891 2.095364 CCGATCTACGCACCACTATACC 60.095 54.545 0.00 0.00 41.07 2.73
952 5892 2.095364 CCCGATCTACGCACCACTATAC 60.095 54.545 0.00 0.00 41.07 1.47
953 5893 2.156917 CCCGATCTACGCACCACTATA 58.843 52.381 0.00 0.00 41.07 1.31
954 5894 0.959553 CCCGATCTACGCACCACTAT 59.040 55.000 0.00 0.00 41.07 2.12
955 5895 0.107066 TCCCGATCTACGCACCACTA 60.107 55.000 0.00 0.00 41.07 2.74
956 5896 1.379443 TCCCGATCTACGCACCACT 60.379 57.895 0.00 0.00 41.07 4.00
957 5897 1.065928 CTCCCGATCTACGCACCAC 59.934 63.158 0.00 0.00 41.07 4.16
958 5898 2.782222 GCTCCCGATCTACGCACCA 61.782 63.158 0.00 0.00 41.07 4.17
959 5899 2.027751 GCTCCCGATCTACGCACC 59.972 66.667 0.00 0.00 41.07 5.01
960 5900 0.459585 TTTGCTCCCGATCTACGCAC 60.460 55.000 0.00 0.00 41.07 5.34
961 5901 0.179111 CTTTGCTCCCGATCTACGCA 60.179 55.000 0.00 0.00 41.07 5.24
962 5902 0.102481 TCTTTGCTCCCGATCTACGC 59.898 55.000 0.00 0.00 41.07 4.42
963 5903 1.134367 TGTCTTTGCTCCCGATCTACG 59.866 52.381 0.00 0.00 42.18 3.51
964 5904 2.961526 TGTCTTTGCTCCCGATCTAC 57.038 50.000 0.00 0.00 0.00 2.59
965 5905 3.973206 TTTGTCTTTGCTCCCGATCTA 57.027 42.857 0.00 0.00 0.00 1.98
966 5906 2.859165 TTTGTCTTTGCTCCCGATCT 57.141 45.000 0.00 0.00 0.00 2.75
967 5907 5.449177 CCTTTATTTGTCTTTGCTCCCGATC 60.449 44.000 0.00 0.00 0.00 3.69
968 5908 4.399303 CCTTTATTTGTCTTTGCTCCCGAT 59.601 41.667 0.00 0.00 0.00 4.18
969 5909 3.756434 CCTTTATTTGTCTTTGCTCCCGA 59.244 43.478 0.00 0.00 0.00 5.14
970 5910 3.756434 TCCTTTATTTGTCTTTGCTCCCG 59.244 43.478 0.00 0.00 0.00 5.14
971 5911 5.921962 ATCCTTTATTTGTCTTTGCTCCC 57.078 39.130 0.00 0.00 0.00 4.30
972 5912 6.587608 CACAATCCTTTATTTGTCTTTGCTCC 59.412 38.462 0.00 0.00 0.00 4.70
973 5913 7.370383 TCACAATCCTTTATTTGTCTTTGCTC 58.630 34.615 0.00 0.00 0.00 4.26
974 5914 7.288810 TCACAATCCTTTATTTGTCTTTGCT 57.711 32.000 0.00 0.00 0.00 3.91
975 5915 9.807649 ATATCACAATCCTTTATTTGTCTTTGC 57.192 29.630 0.00 0.00 0.00 3.68
978 5918 9.699410 TCCATATCACAATCCTTTATTTGTCTT 57.301 29.630 0.00 0.00 0.00 3.01
979 5919 9.347240 CTCCATATCACAATCCTTTATTTGTCT 57.653 33.333 0.00 0.00 0.00 3.41
980 5920 8.571336 CCTCCATATCACAATCCTTTATTTGTC 58.429 37.037 0.00 0.00 0.00 3.18
1117 6100 1.815003 CGGCGTGCATCATCTCCAA 60.815 57.895 0.00 0.00 0.00 3.53
1260 6243 0.472925 TACTGCCTGAACCCTCACCA 60.473 55.000 0.00 0.00 0.00 4.17
1298 6281 3.924918 TGAGGAACTTCTTGACTCGAG 57.075 47.619 11.84 11.84 41.55 4.04
1454 6437 2.112815 GGGTCAATGGTAGCACCGC 61.113 63.158 0.00 0.00 42.58 5.68
1944 6936 3.047613 GGCGTCGCCTTTAAAACATAG 57.952 47.619 28.98 0.00 46.69 2.23
1957 6949 4.745549 CTTAAAGCAAGGCGTCGC 57.254 55.556 9.22 9.22 0.00 5.19
1964 6956 1.508088 CCCAGCGCCTTAAAGCAAG 59.492 57.895 2.29 0.00 35.48 4.01
1965 6957 1.976474 CCCCAGCGCCTTAAAGCAA 60.976 57.895 2.29 0.00 35.48 3.91
1966 6958 2.361104 CCCCAGCGCCTTAAAGCA 60.361 61.111 2.29 0.00 35.48 3.91
1967 6959 3.140814 CCCCCAGCGCCTTAAAGC 61.141 66.667 2.29 0.00 0.00 3.51
1968 6960 3.140814 GCCCCCAGCGCCTTAAAG 61.141 66.667 2.29 0.00 0.00 1.85
2066 7058 2.278013 GGCGTCTCTAAGGCGACG 60.278 66.667 4.97 10.21 43.54 5.12
2070 7062 3.749609 TGTTTTAAAGGCGTCTCTAAGGC 59.250 43.478 0.00 0.00 38.05 4.35
2071 7063 6.238130 GCTATGTTTTAAAGGCGTCTCTAAGG 60.238 42.308 0.00 0.00 0.00 2.69
2072 7064 6.535508 AGCTATGTTTTAAAGGCGTCTCTAAG 59.464 38.462 0.00 0.00 0.00 2.18
2073 7065 6.403878 AGCTATGTTTTAAAGGCGTCTCTAA 58.596 36.000 0.00 0.00 0.00 2.10
2074 7066 5.974108 AGCTATGTTTTAAAGGCGTCTCTA 58.026 37.500 0.00 0.00 0.00 2.43
2075 7067 4.833390 AGCTATGTTTTAAAGGCGTCTCT 58.167 39.130 0.00 0.00 0.00 3.10
2076 7068 5.547181 AAGCTATGTTTTAAAGGCGTCTC 57.453 39.130 0.00 0.00 0.00 3.36
2077 7069 5.959618 AAAGCTATGTTTTAAAGGCGTCT 57.040 34.783 0.00 0.00 0.00 4.18
2078 7070 9.946165 ATATAAAAGCTATGTTTTAAAGGCGTC 57.054 29.630 0.00 0.00 35.91 5.19
2079 7071 9.946165 GATATAAAAGCTATGTTTTAAAGGCGT 57.054 29.630 0.00 0.00 35.91 5.68
2548 7562 7.041780 TCCTCGCTTTGAAATATTCTTCTATGC 60.042 37.037 0.00 0.00 32.08 3.14
3113 8134 2.438868 ACCTGCGAAATTTCTTTGCC 57.561 45.000 15.92 0.77 0.00 4.52
3523 8545 1.948721 GCTCCCCATTCCTTTTGGCG 61.949 60.000 0.00 0.00 40.12 5.69
3579 8601 1.809271 CGCAATGTGAGGAGATGAGGG 60.809 57.143 0.00 0.00 0.00 4.30
3610 8632 4.220821 GTGTCCTAACCTCTGTCAGATGAA 59.779 45.833 11.63 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.