Multiple sequence alignment - TraesCS2A01G358500

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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 TraesCS2A01G358500 chr2A 100.000 2877 0 0 1 2877 602689864 602686988 0.000000e+00 5313.0
1 TraesCS2A01G358500 chr2A 91.587 939 52 11 852 1775 602766972 602766046 0.000000e+00 1271.0
2 TraesCS2A01G358500 chr2A 90.536 951 63 15 890 1834 602718868 602717939 0.000000e+00 1232.0
3 TraesCS2A01G358500 chr2A 89.249 986 96 9 1899 2877 163664103 163665085 0.000000e+00 1225.0
4 TraesCS2A01G358500 chr2A 88.708 983 103 7 1901 2877 489835154 489836134 0.000000e+00 1194.0
5 TraesCS2A01G358500 chr2A 89.912 912 89 2 1895 2803 541193049 541193960 0.000000e+00 1171.0
6 TraesCS2A01G358500 chr2A 83.723 983 111 25 1901 2877 90608448 90607509 0.000000e+00 883.0
7 TraesCS2A01G358500 chr2A 92.459 305 19 4 589 889 602719430 602719126 1.580000e-117 433.0
8 TraesCS2A01G358500 chr2D 89.980 988 88 9 1897 2877 623460685 623459702 0.000000e+00 1266.0
9 TraesCS2A01G358500 chr2D 86.132 1060 98 29 727 1775 459344344 459343323 0.000000e+00 1098.0
10 TraesCS2A01G358500 chr2D 93.407 273 16 1 83 353 81971602 81971874 1.240000e-108 403.0
11 TraesCS2A01G358500 chr2D 95.378 238 11 0 352 589 81971912 81972149 2.090000e-101 379.0
12 TraesCS2A01G358500 chr6A 89.024 984 99 7 1899 2877 214183319 214184298 0.000000e+00 1210.0
13 TraesCS2A01G358500 chr6A 95.472 265 10 2 88 351 84049307 84049044 3.430000e-114 422.0
14 TraesCS2A01G358500 chr6A 94.118 238 13 1 353 590 84049004 84048768 7.580000e-96 361.0
15 TraesCS2A01G358500 chr6D 88.618 984 100 10 1901 2877 455734777 455733799 0.000000e+00 1186.0
16 TraesCS2A01G358500 chr5D 88.170 989 99 16 1899 2877 425072705 425073685 0.000000e+00 1162.0
17 TraesCS2A01G358500 chr5D 94.361 266 15 0 88 353 400282937 400282672 2.670000e-110 409.0
18 TraesCS2A01G358500 chr5D 95.378 238 11 0 352 589 400282634 400282397 2.090000e-101 379.0
19 TraesCS2A01G358500 chr5D 94.231 52 3 0 2 53 494470027 494469976 2.380000e-11 80.5
20 TraesCS2A01G358500 chr7A 87.755 980 114 6 1901 2875 57178059 57179037 0.000000e+00 1140.0
21 TraesCS2A01G358500 chr7A 81.923 520 70 12 1106 1619 700685332 700684831 4.430000e-113 418.0
22 TraesCS2A01G358500 chr7A 87.778 90 5 5 1639 1722 700684838 700684749 1.820000e-17 100.0
23 TraesCS2A01G358500 chr7D 87.691 983 112 8 1901 2877 426190379 426191358 0.000000e+00 1136.0
24 TraesCS2A01G358500 chr2B 89.491 904 64 15 923 1821 540813879 540813002 0.000000e+00 1114.0
25 TraesCS2A01G358500 chr3A 97.284 589 16 0 1 589 682753312 682753900 0.000000e+00 1000.0
26 TraesCS2A01G358500 chr7B 82.287 621 104 2 1077 1697 699524618 699524004 1.520000e-147 532.0
27 TraesCS2A01G358500 chr7B 80.838 668 96 17 1077 1732 699562559 699561912 1.990000e-136 496.0
28 TraesCS2A01G358500 chr7B 79.167 672 98 29 1112 1771 699354569 699355210 7.370000e-116 427.0
29 TraesCS2A01G358500 chr7B 83.421 380 51 5 1077 1456 699361925 699362292 2.740000e-90 342.0
30 TraesCS2A01G358500 chr1D 94.139 273 14 1 83 353 10775763 10776035 5.740000e-112 414.0
31 TraesCS2A01G358500 chr1D 93.985 266 16 0 88 353 370321796 370321531 1.240000e-108 403.0
32 TraesCS2A01G358500 chr1D 94.958 238 12 0 352 589 10776073 10776310 9.730000e-100 374.0
33 TraesCS2A01G358500 chr1D 94.118 238 14 0 352 589 370321493 370321256 2.110000e-96 363.0
34 TraesCS2A01G358500 chr4D 94.361 266 15 0 88 353 455762064 455761799 2.670000e-110 409.0
35 TraesCS2A01G358500 chr4D 95.378 238 11 0 352 589 455761761 455761524 2.090000e-101 379.0
36 TraesCS2A01G358500 chr3B 90.037 271 26 1 88 357 800934692 800934962 1.640000e-92 350.0
37 TraesCS2A01G358500 chr3B 88.235 238 28 0 352 589 800934996 800935233 4.690000e-73 285.0
38 TraesCS2A01G358500 chrUn 88.696 230 24 2 361 589 29857681 29857453 2.180000e-71 279.0
39 TraesCS2A01G358500 chr5A 86.100 259 33 2 95 353 337647742 337647997 2.820000e-70 276.0


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 TraesCS2A01G358500 chr2A 602686988 602689864 2876 True 5313.0 5313 100.0000 1 2877 1 chr2A.!!$R2 2876
1 TraesCS2A01G358500 chr2A 602766046 602766972 926 True 1271.0 1271 91.5870 852 1775 1 chr2A.!!$R3 923
2 TraesCS2A01G358500 chr2A 163664103 163665085 982 False 1225.0 1225 89.2490 1899 2877 1 chr2A.!!$F1 978
3 TraesCS2A01G358500 chr2A 489835154 489836134 980 False 1194.0 1194 88.7080 1901 2877 1 chr2A.!!$F2 976
4 TraesCS2A01G358500 chr2A 541193049 541193960 911 False 1171.0 1171 89.9120 1895 2803 1 chr2A.!!$F3 908
5 TraesCS2A01G358500 chr2A 90607509 90608448 939 True 883.0 883 83.7230 1901 2877 1 chr2A.!!$R1 976
6 TraesCS2A01G358500 chr2A 602717939 602719430 1491 True 832.5 1232 91.4975 589 1834 2 chr2A.!!$R4 1245
7 TraesCS2A01G358500 chr2D 623459702 623460685 983 True 1266.0 1266 89.9800 1897 2877 1 chr2D.!!$R2 980
8 TraesCS2A01G358500 chr2D 459343323 459344344 1021 True 1098.0 1098 86.1320 727 1775 1 chr2D.!!$R1 1048
9 TraesCS2A01G358500 chr2D 81971602 81972149 547 False 391.0 403 94.3925 83 589 2 chr2D.!!$F1 506
10 TraesCS2A01G358500 chr6A 214183319 214184298 979 False 1210.0 1210 89.0240 1899 2877 1 chr6A.!!$F1 978
11 TraesCS2A01G358500 chr6A 84048768 84049307 539 True 391.5 422 94.7950 88 590 2 chr6A.!!$R1 502
12 TraesCS2A01G358500 chr6D 455733799 455734777 978 True 1186.0 1186 88.6180 1901 2877 1 chr6D.!!$R1 976
13 TraesCS2A01G358500 chr5D 425072705 425073685 980 False 1162.0 1162 88.1700 1899 2877 1 chr5D.!!$F1 978
14 TraesCS2A01G358500 chr5D 400282397 400282937 540 True 394.0 409 94.8695 88 589 2 chr5D.!!$R2 501
15 TraesCS2A01G358500 chr7A 57178059 57179037 978 False 1140.0 1140 87.7550 1901 2875 1 chr7A.!!$F1 974
16 TraesCS2A01G358500 chr7A 700684749 700685332 583 True 259.0 418 84.8505 1106 1722 2 chr7A.!!$R1 616
17 TraesCS2A01G358500 chr7D 426190379 426191358 979 False 1136.0 1136 87.6910 1901 2877 1 chr7D.!!$F1 976
18 TraesCS2A01G358500 chr2B 540813002 540813879 877 True 1114.0 1114 89.4910 923 1821 1 chr2B.!!$R1 898
19 TraesCS2A01G358500 chr3A 682753312 682753900 588 False 1000.0 1000 97.2840 1 589 1 chr3A.!!$F1 588
20 TraesCS2A01G358500 chr7B 699524004 699524618 614 True 532.0 532 82.2870 1077 1697 1 chr7B.!!$R1 620
21 TraesCS2A01G358500 chr7B 699561912 699562559 647 True 496.0 496 80.8380 1077 1732 1 chr7B.!!$R2 655
22 TraesCS2A01G358500 chr7B 699354569 699355210 641 False 427.0 427 79.1670 1112 1771 1 chr7B.!!$F1 659
23 TraesCS2A01G358500 chr1D 10775763 10776310 547 False 394.0 414 94.5485 83 589 2 chr1D.!!$F1 506
24 TraesCS2A01G358500 chr1D 370321256 370321796 540 True 383.0 403 94.0515 88 589 2 chr1D.!!$R1 501
25 TraesCS2A01G358500 chr4D 455761524 455762064 540 True 394.0 409 94.8695 88 589 2 chr4D.!!$R1 501
26 TraesCS2A01G358500 chr3B 800934692 800935233 541 False 317.5 350 89.1360 88 589 2 chr3B.!!$F1 501

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
810 860 0.179073 CCAAGTCATACCGGAGCCAG 60.179 60.0 9.46 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1879 2254 0.399454 ACAGCAGATGGAGCAGTGTT 59.601 50.0 0.0 0.0 30.16 3.32 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
154 155 4.052518 GGCACCATGGGAGGCTGT 62.053 66.667 18.09 0.00 36.09 4.40
168 169 2.592993 GCTGTAGGCAGGGTCACCA 61.593 63.158 0.00 0.00 42.78 4.17
597 640 1.350684 TGCAATTGACTCCCTGCTACA 59.649 47.619 10.34 0.00 35.78 2.74
638 682 2.309755 TGCTGATTTCTCACCCCAGATT 59.690 45.455 0.00 0.00 0.00 2.40
760 804 1.070821 ATCATCACGTTGCAGACACG 58.929 50.000 7.83 7.83 0.00 4.49
764 808 0.317854 TCACGTTGCAGACACGAGAG 60.318 55.000 15.82 5.85 0.00 3.20
776 820 2.186384 CGAGAGCTTGAGGCCCAG 59.814 66.667 0.00 0.00 43.05 4.45
803 853 1.876799 TGTTGCAACCAAGTCATACCG 59.123 47.619 26.14 0.00 0.00 4.02
806 856 1.338674 TGCAACCAAGTCATACCGGAG 60.339 52.381 9.46 0.00 0.00 4.63
807 857 1.369625 CAACCAAGTCATACCGGAGC 58.630 55.000 9.46 0.00 0.00 4.70
808 858 0.252197 AACCAAGTCATACCGGAGCC 59.748 55.000 9.46 0.00 0.00 4.70
809 859 0.907704 ACCAAGTCATACCGGAGCCA 60.908 55.000 9.46 0.00 0.00 4.75
810 860 0.179073 CCAAGTCATACCGGAGCCAG 60.179 60.000 9.46 0.00 0.00 4.85
811 861 0.824109 CAAGTCATACCGGAGCCAGA 59.176 55.000 9.46 0.00 0.00 3.86
831 881 0.535102 CGCCCCCATACCAGATTGTC 60.535 60.000 0.00 0.00 0.00 3.18
835 885 2.423373 CCCCCATACCAGATTGTCTTGG 60.423 54.545 0.00 0.00 0.00 3.61
995 1322 3.114616 CCTGTCGCACAGCTTCGG 61.115 66.667 9.88 0.00 44.63 4.30
1028 1355 1.734707 GCACATCATCAGCAAGCAACC 60.735 52.381 0.00 0.00 0.00 3.77
1044 1371 1.815003 CAACCAGCAGGAAAGTCATCC 59.185 52.381 0.35 0.00 39.96 3.51
1267 1600 0.813610 CGGCCGCTGATCATACCAAA 60.814 55.000 14.67 0.00 0.00 3.28
1306 1639 1.213296 ACCCTTCTGCACGGGATTAT 58.787 50.000 15.91 0.00 43.44 1.28
1313 1646 2.146342 CTGCACGGGATTATGTGATCC 58.854 52.381 0.00 0.00 44.03 3.36
1355 1688 2.118076 CCAGGGCCAAGGCAAAGA 59.882 61.111 13.87 0.00 44.11 2.52
1362 1695 1.172812 GCCAAGGCAAAGACGGAAGT 61.173 55.000 6.14 0.00 44.78 3.01
1460 1799 1.910580 TAGCAGCAAGGTACAGGGCC 61.911 60.000 0.00 0.00 0.00 5.80
1545 1899 1.523711 GCATGCCGGGAAGATTCGA 60.524 57.895 6.36 0.00 0.00 3.71
1551 1905 1.519455 CGGGAAGATTCGAAGCGCT 60.519 57.895 2.64 2.64 0.00 5.92
1668 2028 0.103208 CCGAGCCTAGATGACACCAC 59.897 60.000 0.00 0.00 0.00 4.16
1689 2049 1.433534 GAGTTCCCTTCGCTGAAGTG 58.566 55.000 14.33 6.14 37.92 3.16
1756 2131 6.008875 CGATTTTTAATCGGCTTGCTTTTTG 58.991 36.000 12.63 0.00 37.84 2.44
1779 2154 3.119628 CGACATGTTCGTGTAGTTCAGTG 59.880 47.826 0.00 0.00 43.24 3.66
1780 2155 4.049186 GACATGTTCGTGTAGTTCAGTGT 58.951 43.478 0.00 0.00 31.16 3.55
1794 2169 6.354794 AGTTCAGTGTAGGTGCTATACAAA 57.645 37.500 0.00 0.00 35.04 2.83
1799 2174 6.872020 TCAGTGTAGGTGCTATACAAACTTTC 59.128 38.462 0.00 0.00 35.04 2.62
1805 2180 7.733402 AGGTGCTATACAAACTTTCGTTTTA 57.267 32.000 0.00 0.00 41.23 1.52
1834 2209 5.178797 CAATTGTCTTGGGACTACTCGATT 58.821 41.667 0.00 0.00 42.54 3.34
1835 2210 4.884668 TTGTCTTGGGACTACTCGATTT 57.115 40.909 0.00 0.00 42.54 2.17
1836 2211 4.188247 TGTCTTGGGACTACTCGATTTG 57.812 45.455 0.00 0.00 42.54 2.32
1837 2212 3.576982 TGTCTTGGGACTACTCGATTTGT 59.423 43.478 0.00 0.00 42.54 2.83
1838 2213 4.768448 TGTCTTGGGACTACTCGATTTGTA 59.232 41.667 0.00 0.00 42.54 2.41
1839 2214 5.100943 GTCTTGGGACTACTCGATTTGTAC 58.899 45.833 0.00 0.00 39.24 2.90
1840 2215 5.014858 TCTTGGGACTACTCGATTTGTACT 58.985 41.667 0.09 0.00 0.00 2.73
1841 2216 6.094603 GTCTTGGGACTACTCGATTTGTACTA 59.905 42.308 0.09 0.00 39.24 1.82
1842 2217 6.832384 TCTTGGGACTACTCGATTTGTACTAT 59.168 38.462 0.09 0.00 0.00 2.12
1843 2218 6.387041 TGGGACTACTCGATTTGTACTATG 57.613 41.667 0.09 0.00 0.00 2.23
1844 2219 6.124340 TGGGACTACTCGATTTGTACTATGA 58.876 40.000 0.09 0.00 0.00 2.15
1845 2220 6.776116 TGGGACTACTCGATTTGTACTATGAT 59.224 38.462 0.09 0.00 0.00 2.45
1846 2221 7.040617 TGGGACTACTCGATTTGTACTATGATC 60.041 40.741 0.09 0.00 0.00 2.92
1847 2222 7.175293 GGGACTACTCGATTTGTACTATGATCT 59.825 40.741 0.09 0.00 0.00 2.75
1848 2223 8.569641 GGACTACTCGATTTGTACTATGATCTT 58.430 37.037 0.00 0.00 0.00 2.40
1849 2224 9.953697 GACTACTCGATTTGTACTATGATCTTT 57.046 33.333 0.00 0.00 0.00 2.52
1858 2233 8.575565 TTTGTACTATGATCTTTATGAGACGC 57.424 34.615 0.00 0.00 37.17 5.19
1859 2234 6.371389 TGTACTATGATCTTTATGAGACGCG 58.629 40.000 3.53 3.53 37.17 6.01
1860 2235 5.440234 ACTATGATCTTTATGAGACGCGT 57.560 39.130 13.85 13.85 37.17 6.01
1861 2236 6.555812 ACTATGATCTTTATGAGACGCGTA 57.444 37.500 13.97 0.00 37.17 4.42
1862 2237 7.147143 ACTATGATCTTTATGAGACGCGTAT 57.853 36.000 13.97 9.93 37.17 3.06
1863 2238 7.594714 ACTATGATCTTTATGAGACGCGTATT 58.405 34.615 13.97 2.79 37.17 1.89
1864 2239 8.727910 ACTATGATCTTTATGAGACGCGTATTA 58.272 33.333 13.97 6.16 37.17 0.98
1865 2240 7.798486 ATGATCTTTATGAGACGCGTATTAC 57.202 36.000 13.97 0.00 37.17 1.89
1866 2241 6.147581 TGATCTTTATGAGACGCGTATTACC 58.852 40.000 13.97 0.00 37.17 2.85
1867 2242 5.503662 TCTTTATGAGACGCGTATTACCA 57.496 39.130 13.97 3.45 0.00 3.25
1868 2243 6.080648 TCTTTATGAGACGCGTATTACCAT 57.919 37.500 13.97 11.89 0.00 3.55
1869 2244 5.918576 TCTTTATGAGACGCGTATTACCATG 59.081 40.000 13.97 0.03 0.00 3.66
1870 2245 1.847818 TGAGACGCGTATTACCATGC 58.152 50.000 13.97 0.00 0.00 4.06
1871 2246 1.135333 TGAGACGCGTATTACCATGCA 59.865 47.619 13.97 0.00 0.00 3.96
1872 2247 2.198406 GAGACGCGTATTACCATGCAA 58.802 47.619 13.97 0.00 0.00 4.08
1873 2248 2.605818 GAGACGCGTATTACCATGCAAA 59.394 45.455 13.97 0.00 0.00 3.68
1874 2249 3.004171 AGACGCGTATTACCATGCAAAA 58.996 40.909 13.97 0.00 0.00 2.44
1875 2250 3.437395 AGACGCGTATTACCATGCAAAAA 59.563 39.130 13.97 0.00 0.00 1.94
1921 2296 4.845580 CATCTTCAGCCGCGGCCT 62.846 66.667 44.47 29.19 43.17 5.19
1992 2368 3.386237 GTCACGCCTCAGGAGCCT 61.386 66.667 0.00 0.00 0.00 4.58
2093 2473 1.358759 CACAAGCGAAAAGGGCGTT 59.641 52.632 0.00 0.00 35.00 4.84
2107 2487 4.680237 CGTTGGGCCGCTCTGTCA 62.680 66.667 0.00 0.00 0.00 3.58
2109 2489 3.241530 TTGGGCCGCTCTGTCAGT 61.242 61.111 0.00 0.00 0.00 3.41
2196 2579 3.089874 CCCGCCAATCTCCCTCCA 61.090 66.667 0.00 0.00 0.00 3.86
2301 2686 1.595993 CGAACCAGAGGAAGCCGAGA 61.596 60.000 0.00 0.00 0.00 4.04
2522 2908 3.454573 CGCCCAGCACGTACCCTA 61.455 66.667 0.00 0.00 0.00 3.53
2702 3090 0.815734 CCTTCGTCGGTGTGGAGTAT 59.184 55.000 0.00 0.00 0.00 2.12
2728 3116 4.430765 CAACTACTCGCCGCCGGT 62.431 66.667 4.45 0.00 34.56 5.28
2733 3121 2.275547 CTACTCGCCGCCGGTTTACT 62.276 60.000 4.45 0.00 34.56 2.24
2747 3135 1.880819 TTTACTCGTGCTCCCCGACC 61.881 60.000 0.00 0.00 0.00 4.79
2804 3192 2.507110 CTTCCATGTCGCACCTCGGT 62.507 60.000 0.00 0.00 39.05 4.69
2844 3232 0.530431 CGACATGGACGGCATCATCA 60.530 55.000 0.00 0.00 0.00 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
82 83 1.515020 CTGCTTCTCGTCCTCCCAG 59.485 63.158 0.00 0.00 0.00 4.45
140 141 2.378634 GCCTACAGCCTCCCATGGT 61.379 63.158 11.73 0.00 34.35 3.55
227 228 1.377725 CTCCGCCACTTGCCTCAAT 60.378 57.895 0.00 0.00 36.24 2.57
491 534 7.908827 AAAACACCGGAAAATTTGTTAAGTT 57.091 28.000 9.46 0.00 31.92 2.66
523 566 6.513720 GCAGAAAACCACCAACTCGTTAATAA 60.514 38.462 0.00 0.00 0.00 1.40
524 567 5.049267 GCAGAAAACCACCAACTCGTTAATA 60.049 40.000 0.00 0.00 0.00 0.98
597 640 3.868062 CAAAGGGAGGAGGAGGAGATAT 58.132 50.000 0.00 0.00 0.00 1.63
638 682 7.009179 ACAACAATTGAGAGATACAAGGAGA 57.991 36.000 13.59 0.00 0.00 3.71
760 804 1.220477 GACTGGGCCTCAAGCTCTC 59.780 63.158 4.53 0.00 45.11 3.20
764 808 2.035442 GTTCGACTGGGCCTCAAGC 61.035 63.158 4.53 0.00 42.60 4.01
776 820 1.400494 ACTTGGTTGCAACAGTTCGAC 59.600 47.619 29.55 11.84 0.00 4.20
806 856 4.564110 GGTATGGGGGCGTCTGGC 62.564 72.222 0.00 0.00 42.51 4.85
807 857 3.087253 TGGTATGGGGGCGTCTGG 61.087 66.667 0.00 0.00 0.00 3.86
808 858 1.410850 ATCTGGTATGGGGGCGTCTG 61.411 60.000 0.00 0.00 0.00 3.51
809 859 0.694444 AATCTGGTATGGGGGCGTCT 60.694 55.000 0.00 0.00 0.00 4.18
810 860 0.535102 CAATCTGGTATGGGGGCGTC 60.535 60.000 0.00 0.00 0.00 5.19
811 861 1.279025 ACAATCTGGTATGGGGGCGT 61.279 55.000 0.00 0.00 0.00 5.68
835 885 2.003301 GCTGTTCGAATTGGAGGACTC 58.997 52.381 0.00 0.00 0.00 3.36
845 898 1.089920 GGTCTGCATGCTGTTCGAAT 58.910 50.000 20.33 0.00 0.00 3.34
850 903 1.975407 GCTGGGTCTGCATGCTGTT 60.975 57.895 20.33 0.00 0.00 3.16
854 907 1.078214 TAGTGCTGGGTCTGCATGC 60.078 57.895 11.82 11.82 40.15 4.06
1002 1329 3.766151 CTTGCTGATGATGTGCGATTTT 58.234 40.909 0.00 0.00 0.00 1.82
1013 1340 0.537828 TGCTGGTTGCTTGCTGATGA 60.538 50.000 0.00 0.00 43.37 2.92
1028 1355 1.363744 GACGGATGACTTTCCTGCTG 58.636 55.000 0.00 0.00 33.30 4.41
1033 1360 2.733517 GAGATCGACGGATGACTTTCC 58.266 52.381 0.00 0.00 31.51 3.13
1034 1361 2.223294 ACGAGATCGACGGATGACTTTC 60.223 50.000 9.58 0.00 43.02 2.62
1035 1362 1.743958 ACGAGATCGACGGATGACTTT 59.256 47.619 9.58 0.00 43.02 2.66
1036 1363 1.331138 GACGAGATCGACGGATGACTT 59.669 52.381 9.58 0.00 43.02 3.01
1255 1588 5.279006 GCCGAGTAGATCTTTGGTATGATCA 60.279 44.000 0.00 0.00 40.92 2.92
1267 1600 1.834822 GGCCTGGCCGAGTAGATCT 60.835 63.158 24.16 0.00 39.62 2.75
1306 1639 1.202879 AGCTGGTTTTTCCGGATCACA 60.203 47.619 4.15 0.00 45.09 3.58
1313 1646 1.160137 CTCTCCAGCTGGTTTTTCCG 58.840 55.000 31.58 12.45 39.52 4.30
1355 1688 2.657237 CTTCGCCTCCACTTCCGT 59.343 61.111 0.00 0.00 0.00 4.69
1362 1695 4.033776 CCCTTGCCTTCGCCTCCA 62.034 66.667 0.00 0.00 0.00 3.86
1460 1799 5.822519 TGTAATATCTACCTTGCTTTGCTGG 59.177 40.000 0.00 0.00 0.00 4.85
1545 1899 2.124942 GCTGCCTCCTTAGCGCTT 60.125 61.111 18.68 0.00 0.00 4.68
1551 1905 1.300963 CTGCCTTGCTGCCTCCTTA 59.699 57.895 0.00 0.00 0.00 2.69
1668 2028 0.737715 CTTCAGCGAAGGGAACTCGG 60.738 60.000 9.54 0.00 42.68 4.63
1689 2049 2.546162 GGGAAAGCTATCGTCTAGCACC 60.546 54.545 17.70 16.09 42.68 5.01
1794 2169 9.634163 AAGACAATTGTTTCTTAAAACGAAAGT 57.366 25.926 13.36 0.00 46.39 2.66
1799 2174 6.975772 TCCCAAGACAATTGTTTCTTAAAACG 59.024 34.615 13.36 0.75 46.39 3.60
1805 2180 6.365520 AGTAGTCCCAAGACAATTGTTTCTT 58.634 36.000 13.36 9.51 46.15 2.52
1834 2209 6.856426 CGCGTCTCATAAAGATCATAGTACAA 59.144 38.462 0.00 0.00 36.11 2.41
1835 2210 6.017357 ACGCGTCTCATAAAGATCATAGTACA 60.017 38.462 5.58 0.00 36.11 2.90
1836 2211 6.372185 ACGCGTCTCATAAAGATCATAGTAC 58.628 40.000 5.58 0.00 36.11 2.73
1837 2212 6.555812 ACGCGTCTCATAAAGATCATAGTA 57.444 37.500 5.58 0.00 36.11 1.82
1838 2213 5.440234 ACGCGTCTCATAAAGATCATAGT 57.560 39.130 5.58 0.00 36.11 2.12
1839 2214 9.001049 GTAATACGCGTCTCATAAAGATCATAG 57.999 37.037 18.63 0.00 36.11 2.23
1840 2215 7.966753 GGTAATACGCGTCTCATAAAGATCATA 59.033 37.037 18.63 0.00 36.11 2.15
1841 2216 6.807230 GGTAATACGCGTCTCATAAAGATCAT 59.193 38.462 18.63 0.00 36.11 2.45
1842 2217 6.147581 GGTAATACGCGTCTCATAAAGATCA 58.852 40.000 18.63 0.00 36.11 2.92
1843 2218 6.147581 TGGTAATACGCGTCTCATAAAGATC 58.852 40.000 18.63 0.00 36.11 2.75
1844 2219 6.080648 TGGTAATACGCGTCTCATAAAGAT 57.919 37.500 18.63 0.00 36.11 2.40
1845 2220 5.503662 TGGTAATACGCGTCTCATAAAGA 57.496 39.130 18.63 0.00 0.00 2.52
1846 2221 5.388475 GCATGGTAATACGCGTCTCATAAAG 60.388 44.000 18.63 2.80 0.00 1.85
1847 2222 4.446385 GCATGGTAATACGCGTCTCATAAA 59.554 41.667 18.63 0.00 0.00 1.40
1848 2223 3.985279 GCATGGTAATACGCGTCTCATAA 59.015 43.478 18.63 0.00 0.00 1.90
1849 2224 3.004944 TGCATGGTAATACGCGTCTCATA 59.995 43.478 18.63 0.00 0.00 2.15
1850 2225 2.223947 TGCATGGTAATACGCGTCTCAT 60.224 45.455 18.63 10.79 0.00 2.90
1851 2226 1.135333 TGCATGGTAATACGCGTCTCA 59.865 47.619 18.63 8.74 0.00 3.27
1852 2227 1.847818 TGCATGGTAATACGCGTCTC 58.152 50.000 18.63 4.56 0.00 3.36
1853 2228 2.303163 TTGCATGGTAATACGCGTCT 57.697 45.000 18.63 1.73 0.00 4.18
1854 2229 3.392769 TTTTGCATGGTAATACGCGTC 57.607 42.857 18.63 0.00 0.00 5.19
1855 2230 3.833545 TTTTTGCATGGTAATACGCGT 57.166 38.095 19.17 19.17 0.00 6.01
1876 2251 2.295349 CAGCAGATGGAGCAGTGTTTTT 59.705 45.455 0.00 0.00 0.00 1.94
1877 2252 1.884579 CAGCAGATGGAGCAGTGTTTT 59.115 47.619 0.00 0.00 0.00 2.43
1878 2253 1.202855 ACAGCAGATGGAGCAGTGTTT 60.203 47.619 0.00 0.00 30.16 2.83
1879 2254 0.399454 ACAGCAGATGGAGCAGTGTT 59.601 50.000 0.00 0.00 30.16 3.32
1880 2255 0.399454 AACAGCAGATGGAGCAGTGT 59.601 50.000 0.00 0.00 31.82 3.55
1881 2256 2.093816 TCTAACAGCAGATGGAGCAGTG 60.094 50.000 0.00 0.00 31.82 3.66
1882 2257 2.168106 CTCTAACAGCAGATGGAGCAGT 59.832 50.000 0.00 0.00 32.84 4.40
1883 2258 2.823984 CTCTAACAGCAGATGGAGCAG 58.176 52.381 0.00 0.00 0.00 4.24
1884 2259 2.975732 CTCTAACAGCAGATGGAGCA 57.024 50.000 0.00 0.00 0.00 4.26
1992 2368 2.265182 CCCAAGCCGGCGAAAAAGA 61.265 57.895 23.20 0.00 0.00 2.52
2093 2473 4.007644 CACTGACAGAGCGGCCCA 62.008 66.667 10.08 0.00 0.00 5.36
2167 2549 1.131303 TTGGCGGGAGGAAAGGAGAA 61.131 55.000 0.00 0.00 0.00 2.87
2274 2659 4.785453 CTCTGGTTCGGCTGGGCC 62.785 72.222 0.00 0.00 46.75 5.80
2512 2898 1.320344 TGCTGGCTCTAGGGTACGTG 61.320 60.000 0.00 0.00 0.00 4.49
2522 2908 1.670406 CTGACGCTTTGCTGGCTCT 60.670 57.895 0.00 0.00 0.00 4.09
2702 3090 2.029623 GGCGAGTAGTTGTATGGAGGA 58.970 52.381 0.00 0.00 0.00 3.71
2728 3116 1.588082 GTCGGGGAGCACGAGTAAA 59.412 57.895 0.00 0.00 41.50 2.01


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

AutoCloner maintained by Alex Coulton.