Multiple sequence alignment - TraesCS1D01G269900

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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 TraesCS1D01G269900 chr1D 100.000 2516 0 0 1 2516 365082068 365084583 0.000000e+00 4647.0
1 TraesCS1D01G269900 chr1D 80.800 125 21 3 2055 2178 405380590 405380468 7.410000e-16 95.3
2 TraesCS1D01G269900 chr1B 93.062 1816 80 30 1 1799 488473769 488475555 0.000000e+00 2614.0
3 TraesCS1D01G269900 chr1B 78.107 676 126 21 129 790 488395963 488396630 2.330000e-110 409.0
4 TraesCS1D01G269900 chr1B 84.516 155 21 3 1644 1796 328643830 328643677 1.560000e-32 150.0
5 TraesCS1D01G269900 chr1B 91.304 46 2 2 2371 2416 494600173 494600216 7.510000e-06 62.1
6 TraesCS1D01G269900 chr1A 93.731 1643 77 13 25 1666 463958500 463960117 0.000000e+00 2440.0
7 TraesCS1D01G269900 chr1A 75.726 758 87 50 1819 2510 463960455 463961181 8.800000e-75 291.0
8 TraesCS1D01G269900 chr1A 85.161 155 21 2 1643 1796 395177448 395177601 9.320000e-35 158.0
9 TraesCS1D01G269900 chr3B 80.229 698 122 16 138 827 651427238 651426549 6.210000e-141 510.0
10 TraesCS1D01G269900 chr3B 84.985 333 41 7 1112 1441 651426305 651425979 1.870000e-86 329.0
11 TraesCS1D01G269900 chr3B 84.132 334 42 9 1112 1441 489350608 489350282 1.880000e-81 313.0
12 TraesCS1D01G269900 chr3B 77.143 175 32 6 2028 2199 821589306 821589137 7.410000e-16 95.3
13 TraesCS1D01G269900 chr3A 79.799 698 125 15 138 827 632041222 632040533 6.250000e-136 494.0
14 TraesCS1D01G269900 chr3A 84.985 333 41 7 1112 1441 632040298 632039972 1.870000e-86 329.0
15 TraesCS1D01G269900 chr3D 80.000 670 122 12 138 801 488950102 488950765 3.760000e-133 484.0
16 TraesCS1D01G269900 chr3D 77.424 753 150 20 84 826 488902978 488903720 4.970000e-117 431.0
17 TraesCS1D01G269900 chr3D 84.685 333 42 7 1112 1441 488951035 488951361 8.680000e-85 324.0
18 TraesCS1D01G269900 chr3D 83.871 155 22 3 1644 1796 288550458 288550611 7.250000e-31 145.0
19 TraesCS1D01G269900 chr3D 80.986 142 21 5 2035 2173 532862633 532862771 9.520000e-20 108.0
20 TraesCS1D01G269900 chr4B 79.708 685 125 14 150 827 46934226 46933549 1.350000e-132 483.0
21 TraesCS1D01G269900 chr4B 85.050 301 37 7 1112 1408 46933305 46933009 1.460000e-77 300.0
22 TraesCS1D01G269900 chr4B 82.738 168 25 4 1647 1811 146469365 146469199 2.020000e-31 147.0
23 TraesCS1D01G269900 chr4B 89.655 58 6 0 139 196 672128282 672128339 9.650000e-10 75.0
24 TraesCS1D01G269900 chr2B 79.762 672 120 16 149 812 254626190 254626853 8.150000e-130 473.0
25 TraesCS1D01G269900 chr2B 84.731 334 40 9 1112 1441 254627112 254627438 8.680000e-85 324.0
26 TraesCS1D01G269900 chr2B 83.030 165 23 5 1643 1806 288939923 288939763 7.250000e-31 145.0
27 TraesCS1D01G269900 chr2B 82.524 103 11 5 2102 2199 199400680 199400780 1.600000e-12 84.2
28 TraesCS1D01G269900 chr7D 84.950 299 41 3 1112 1408 89311902 89312198 1.460000e-77 300.0
29 TraesCS1D01G269900 chr7D 84.416 154 22 2 1644 1796 34373470 34373318 1.560000e-32 150.0
30 TraesCS1D01G269900 chr7D 83.766 154 23 2 1644 1796 34756866 34757018 7.250000e-31 145.0
31 TraesCS1D01G269900 chr7D 79.231 130 21 3 2054 2177 622361497 622361626 4.460000e-13 86.1
32 TraesCS1D01G269900 chr5D 83.051 177 27 3 1628 1802 220683175 220683350 9.320000e-35 158.0
33 TraesCS1D01G269900 chr5D 76.562 192 36 8 2014 2199 412110197 412110385 2.060000e-16 97.1
34 TraesCS1D01G269900 chr2D 85.161 155 21 2 1644 1797 241661894 241662047 9.320000e-35 158.0
35 TraesCS1D01G269900 chr6D 79.739 153 21 6 2028 2179 381975004 381975147 4.430000e-18 102.0
36 TraesCS1D01G269900 chr7A 77.005 187 31 8 2008 2187 512258909 512259090 2.060000e-16 97.1
37 TraesCS1D01G269900 chr6B 77.465 142 25 7 2039 2174 710661068 710660928 7.460000e-11 78.7


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 TraesCS1D01G269900 chr1D 365082068 365084583 2515 False 4647.0 4647 100.0000 1 2516 1 chr1D.!!$F1 2515
1 TraesCS1D01G269900 chr1B 488473769 488475555 1786 False 2614.0 2614 93.0620 1 1799 1 chr1B.!!$F2 1798
2 TraesCS1D01G269900 chr1B 488395963 488396630 667 False 409.0 409 78.1070 129 790 1 chr1B.!!$F1 661
3 TraesCS1D01G269900 chr1A 463958500 463961181 2681 False 1365.5 2440 84.7285 25 2510 2 chr1A.!!$F2 2485
4 TraesCS1D01G269900 chr3B 651425979 651427238 1259 True 419.5 510 82.6070 138 1441 2 chr3B.!!$R3 1303
5 TraesCS1D01G269900 chr3A 632039972 632041222 1250 True 411.5 494 82.3920 138 1441 2 chr3A.!!$R1 1303
6 TraesCS1D01G269900 chr3D 488902978 488903720 742 False 431.0 431 77.4240 84 826 1 chr3D.!!$F2 742
7 TraesCS1D01G269900 chr3D 488950102 488951361 1259 False 404.0 484 82.3425 138 1441 2 chr3D.!!$F4 1303
8 TraesCS1D01G269900 chr4B 46933009 46934226 1217 True 391.5 483 82.3790 150 1408 2 chr4B.!!$R2 1258
9 TraesCS1D01G269900 chr2B 254626190 254627438 1248 False 398.5 473 82.2465 149 1441 2 chr2B.!!$F2 1292

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
905 921 0.173029 AGCAGAGCAGTGAGACATCG 59.827 55.0 0.0 0.0 0.0 3.84 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1853 2296 1.196104 TACAGTACTTGGCCGGCCTT 61.196 55.0 43.34 29.57 36.94 4.35 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
30 31 9.646427 GTACACCTTGAATTCATATCTATCCTC 57.354 37.037 9.40 0.00 0.00 3.71
51 61 4.008330 TCTGCCTAGCACGAGTATATACC 58.992 47.826 9.32 0.83 33.79 2.73
870 886 1.857318 CTCGTCGACCTGAGCACTGT 61.857 60.000 10.58 0.00 0.00 3.55
871 887 0.604511 TCGTCGACCTGAGCACTGTA 60.605 55.000 10.58 0.00 0.00 2.74
875 891 1.269723 TCGACCTGAGCACTGTACAAG 59.730 52.381 0.00 0.00 0.00 3.16
876 892 1.269723 CGACCTGAGCACTGTACAAGA 59.730 52.381 0.00 0.00 0.00 3.02
881 897 4.202357 ACCTGAGCACTGTACAAGATTTGA 60.202 41.667 0.00 0.00 0.00 2.69
882 898 4.756642 CCTGAGCACTGTACAAGATTTGAA 59.243 41.667 0.00 0.00 0.00 2.69
883 899 5.334414 CCTGAGCACTGTACAAGATTTGAAC 60.334 44.000 0.00 0.00 0.00 3.18
890 906 6.415867 CACTGTACAAGATTTGAACAAAGCAG 59.584 38.462 15.87 10.84 39.00 4.24
892 908 6.728200 TGTACAAGATTTGAACAAAGCAGAG 58.272 36.000 15.87 8.58 39.00 3.35
895 911 4.500603 AGATTTGAACAAAGCAGAGCAG 57.499 40.909 15.87 0.00 39.00 4.24
898 914 2.330440 TGAACAAAGCAGAGCAGTGA 57.670 45.000 0.00 0.00 0.00 3.41
899 915 2.216046 TGAACAAAGCAGAGCAGTGAG 58.784 47.619 0.00 0.00 0.00 3.51
900 916 2.158914 TGAACAAAGCAGAGCAGTGAGA 60.159 45.455 0.00 0.00 0.00 3.27
901 917 1.876322 ACAAAGCAGAGCAGTGAGAC 58.124 50.000 0.00 0.00 0.00 3.36
902 918 1.139654 ACAAAGCAGAGCAGTGAGACA 59.860 47.619 0.00 0.00 0.00 3.41
903 919 2.224475 ACAAAGCAGAGCAGTGAGACAT 60.224 45.455 0.00 0.00 0.00 3.06
904 920 2.383368 AAGCAGAGCAGTGAGACATC 57.617 50.000 0.00 0.00 0.00 3.06
905 921 0.173029 AGCAGAGCAGTGAGACATCG 59.827 55.000 0.00 0.00 0.00 3.84
906 922 1.419874 GCAGAGCAGTGAGACATCGC 61.420 60.000 0.00 0.00 36.12 4.58
908 924 1.153939 GAGCAGTGAGACATCGCGT 60.154 57.895 5.77 0.00 41.02 6.01
910 926 0.734253 AGCAGTGAGACATCGCGTTC 60.734 55.000 5.77 1.06 41.02 3.95
911 927 0.734253 GCAGTGAGACATCGCGTTCT 60.734 55.000 5.77 6.68 41.02 3.01
913 929 1.651138 CAGTGAGACATCGCGTTCTTC 59.349 52.381 5.77 0.00 41.02 2.87
914 930 0.992802 GTGAGACATCGCGTTCTTCC 59.007 55.000 5.77 0.00 0.00 3.46
915 931 0.888619 TGAGACATCGCGTTCTTCCT 59.111 50.000 5.77 0.00 0.00 3.36
916 932 1.135373 TGAGACATCGCGTTCTTCCTC 60.135 52.381 5.77 7.44 0.00 3.71
918 934 1.546476 AGACATCGCGTTCTTCCTCTT 59.454 47.619 5.77 0.00 0.00 2.85
919 935 1.656095 GACATCGCGTTCTTCCTCTTG 59.344 52.381 5.77 0.00 0.00 3.02
920 936 0.371645 CATCGCGTTCTTCCTCTTGC 59.628 55.000 5.77 0.00 0.00 4.01
921 937 0.247736 ATCGCGTTCTTCCTCTTGCT 59.752 50.000 5.77 0.00 0.00 3.91
922 938 0.667487 TCGCGTTCTTCCTCTTGCTG 60.667 55.000 5.77 0.00 0.00 4.41
923 939 1.499502 GCGTTCTTCCTCTTGCTGC 59.500 57.895 0.00 0.00 0.00 5.25
924 940 0.952984 GCGTTCTTCCTCTTGCTGCT 60.953 55.000 0.00 0.00 0.00 4.24
925 941 1.517242 CGTTCTTCCTCTTGCTGCTT 58.483 50.000 0.00 0.00 0.00 3.91
926 942 1.196354 CGTTCTTCCTCTTGCTGCTTG 59.804 52.381 0.00 0.00 0.00 4.01
927 943 2.225467 GTTCTTCCTCTTGCTGCTTGT 58.775 47.619 0.00 0.00 0.00 3.16
928 944 3.403038 GTTCTTCCTCTTGCTGCTTGTA 58.597 45.455 0.00 0.00 0.00 2.41
931 947 2.299993 TCCTCTTGCTGCTTGTATCG 57.700 50.000 0.00 0.00 0.00 2.92
932 948 1.134699 TCCTCTTGCTGCTTGTATCGG 60.135 52.381 0.00 0.00 0.00 4.18
937 953 0.459899 TGCTGCTTGTATCGGTCGAT 59.540 50.000 10.75 10.75 38.54 3.59
941 957 1.002792 TGCTTGTATCGGTCGATCGAG 60.003 52.381 26.45 13.13 42.69 4.04
944 960 1.235724 TGTATCGGTCGATCGAGCAT 58.764 50.000 37.34 30.28 42.69 3.79
945 961 1.197036 TGTATCGGTCGATCGAGCATC 59.803 52.381 37.34 25.59 42.69 3.91
961 977 1.901591 CATCCTGCCAAACACTCTGT 58.098 50.000 0.00 0.00 0.00 3.41
962 978 2.875672 GCATCCTGCCAAACACTCTGTA 60.876 50.000 0.00 0.00 37.42 2.74
963 979 3.614092 CATCCTGCCAAACACTCTGTAT 58.386 45.455 0.00 0.00 0.00 2.29
964 980 3.788227 TCCTGCCAAACACTCTGTATT 57.212 42.857 0.00 0.00 0.00 1.89
965 981 4.098914 TCCTGCCAAACACTCTGTATTT 57.901 40.909 0.00 0.00 0.00 1.40
1180 1396 3.075998 CAGAGCATCACGACGCAC 58.924 61.111 0.00 0.00 37.82 5.34
1476 1692 3.435327 TCGGTGTTACTGCATTTGTGATC 59.565 43.478 0.00 0.00 0.00 2.92
1477 1693 3.426159 CGGTGTTACTGCATTTGTGATCC 60.426 47.826 0.00 0.00 0.00 3.36
1510 1726 0.104487 ATGTCGAGAGAGCCAGCATG 59.896 55.000 0.00 0.00 43.49 4.06
1526 1742 0.676466 CATGCCTAAACCCTGCACGA 60.676 55.000 0.00 0.00 37.92 4.35
1535 1751 1.166531 ACCCTGCACGAAGTTTCAGC 61.167 55.000 0.00 0.85 41.61 4.26
1536 1752 1.165907 CCCTGCACGAAGTTTCAGCA 61.166 55.000 8.19 8.19 41.61 4.41
1538 1754 0.940126 CTGCACGAAGTTTCAGCAGT 59.060 50.000 19.76 0.00 44.32 4.40
1595 1812 5.400066 TCCTGTCTCGTGAATCAAACATA 57.600 39.130 0.00 0.00 0.00 2.29
1603 1820 6.590292 TCTCGTGAATCAAACATAGGAGAAAC 59.410 38.462 0.00 0.00 0.00 2.78
1613 1830 5.489792 ACATAGGAGAAACAAGAGCAGAA 57.510 39.130 0.00 0.00 0.00 3.02
1627 1844 2.537625 GAGCAGAATGAAATCTCGTCCG 59.462 50.000 0.00 0.00 39.69 4.79
1628 1845 2.093973 AGCAGAATGAAATCTCGTCCGT 60.094 45.455 0.00 0.00 39.69 4.69
1658 1875 1.254954 ACAGTACTCCCTCCGTTCAC 58.745 55.000 0.00 0.00 0.00 3.18
1661 1878 2.036733 CAGTACTCCCTCCGTTCACAAA 59.963 50.000 0.00 0.00 0.00 2.83
1725 2083 8.020244 ACAAATTCAAACAAATGAACAAACACC 58.980 29.630 0.00 0.00 41.78 4.16
1731 2089 9.273016 TCAAACAAATGAACAAACACCTTAAAA 57.727 25.926 0.00 0.00 0.00 1.52
1803 2246 8.890410 TTATGAACAAAGGGAGTACTACTACT 57.110 34.615 4.77 0.00 35.77 2.57
1804 2247 9.979897 TTATGAACAAAGGGAGTACTACTACTA 57.020 33.333 4.77 0.00 32.96 1.82
1805 2248 7.693969 TGAACAAAGGGAGTACTACTACTAC 57.306 40.000 4.77 0.00 32.96 2.73
1806 2249 7.465116 TGAACAAAGGGAGTACTACTACTACT 58.535 38.462 4.77 0.00 34.48 2.57
1807 2250 8.605947 TGAACAAAGGGAGTACTACTACTACTA 58.394 37.037 4.77 0.00 34.48 1.82
1808 2251 8.800370 AACAAAGGGAGTACTACTACTACTAC 57.200 38.462 4.77 0.00 34.48 2.73
1809 2252 8.156822 ACAAAGGGAGTACTACTACTACTACT 57.843 38.462 4.77 0.00 34.48 2.57
1810 2253 9.273137 ACAAAGGGAGTACTACTACTACTACTA 57.727 37.037 4.77 0.00 34.48 1.82
1811 2254 9.541143 CAAAGGGAGTACTACTACTACTACTAC 57.459 40.741 4.77 0.00 34.48 2.73
1812 2255 9.500701 AAAGGGAGTACTACTACTACTACTACT 57.499 37.037 4.77 0.00 34.48 2.57
1849 2292 2.695147 TCATGCCTCTTATCAAGCGAGA 59.305 45.455 0.00 0.00 0.00 4.04
1850 2293 2.879002 TGCCTCTTATCAAGCGAGAG 57.121 50.000 0.00 0.00 37.30 3.20
1866 2309 3.330720 AGCTAAGGCCGGCCAAGT 61.331 61.111 45.13 31.25 39.73 3.16
1871 2314 1.196104 TAAGGCCGGCCAAGTACTGT 61.196 55.000 45.13 21.51 38.92 3.55
1873 2316 1.153429 GGCCGGCCAAGTACTGTAG 60.153 63.158 40.73 0.00 35.81 2.74
1877 2320 0.246635 CGGCCAAGTACTGTAGCTGT 59.753 55.000 2.24 0.00 0.00 4.40
1879 2322 1.275291 GGCCAAGTACTGTAGCTGTCA 59.725 52.381 0.00 0.00 0.00 3.58
1881 2324 2.288825 GCCAAGTACTGTAGCTGTCACA 60.289 50.000 0.00 0.00 0.00 3.58
1882 2325 3.318017 CCAAGTACTGTAGCTGTCACAC 58.682 50.000 0.00 0.00 0.00 3.82
1883 2326 3.243737 CCAAGTACTGTAGCTGTCACACA 60.244 47.826 0.00 0.00 0.00 3.72
1926 2376 4.744631 GGTTTTCACTGTTTGCATCGATTT 59.255 37.500 0.00 0.00 0.00 2.17
1930 2380 6.552859 TTCACTGTTTGCATCGATTTCTTA 57.447 33.333 0.00 0.00 0.00 2.10
1941 2391 6.030228 GCATCGATTTCTTAGGGTCTTTTTG 58.970 40.000 0.00 0.00 0.00 2.44
1946 2396 8.132995 TCGATTTCTTAGGGTCTTTTTGTTTTC 58.867 33.333 0.00 0.00 0.00 2.29
1947 2397 8.135529 CGATTTCTTAGGGTCTTTTTGTTTTCT 58.864 33.333 0.00 0.00 0.00 2.52
1948 2398 9.464714 GATTTCTTAGGGTCTTTTTGTTTTCTC 57.535 33.333 0.00 0.00 0.00 2.87
1949 2399 8.589701 TTTCTTAGGGTCTTTTTGTTTTCTCT 57.410 30.769 0.00 0.00 0.00 3.10
1951 2401 8.589701 TCTTAGGGTCTTTTTGTTTTCTCTTT 57.410 30.769 0.00 0.00 0.00 2.52
2004 2465 6.633500 TTCTTCGATTTTCATCAGGTTTGT 57.367 33.333 0.00 0.00 0.00 2.83
2010 2471 6.712998 TCGATTTTCATCAGGTTTGTCCTTTA 59.287 34.615 0.00 0.00 45.67 1.85
2031 2500 6.701145 TTAACAACACAGGTCTGCATTTTA 57.299 33.333 0.00 0.00 0.00 1.52
2040 2509 5.945784 ACAGGTCTGCATTTTACATACACAT 59.054 36.000 0.00 0.00 0.00 3.21
2042 2511 7.039784 ACAGGTCTGCATTTTACATACACATTT 60.040 33.333 0.00 0.00 0.00 2.32
2080 2549 8.948853 ATACATCAAGAACATTTTTACACACG 57.051 30.769 0.00 0.00 0.00 4.49
2084 2553 7.728580 TCAAGAACATTTTTACACACGTTTC 57.271 32.000 0.00 0.00 0.00 2.78
2091 2560 7.670916 ACATTTTTACACACGTTTCACATTTG 58.329 30.769 0.00 0.00 0.00 2.32
2095 2564 8.912787 TTTTACACACGTTTCACATTTGTTAT 57.087 26.923 0.00 0.00 0.00 1.89
2116 2585 8.710551 TGTTATGTTCATGATTGACATTTTTGC 58.289 29.630 14.94 4.76 37.07 3.68
2117 2586 8.928733 GTTATGTTCATGATTGACATTTTTGCT 58.071 29.630 14.94 0.00 37.07 3.91
2121 2590 9.491675 TGTTCATGATTGACATTTTTGCTAAAT 57.508 25.926 0.00 0.00 37.07 1.40
2155 2625 7.933396 TCATGGCTATTTCTTCATACACATTG 58.067 34.615 0.00 0.00 0.00 2.82
2195 2666 8.730680 ACATCTAAAAGATACTTTCGCATGTTT 58.269 29.630 0.00 0.00 32.12 2.83
2339 2839 6.810888 ATTGTGAAACTCGTGAACATTTTG 57.189 33.333 0.00 0.00 38.04 2.44
2341 2841 5.704888 TGTGAAACTCGTGAACATTTTGTT 58.295 33.333 0.00 0.00 40.01 2.83
2352 2852 9.175060 TCGTGAACATTTTGTTAATGTAACATG 57.825 29.630 15.57 15.57 46.89 3.21
2353 2853 9.175060 CGTGAACATTTTGTTAATGTAACATGA 57.825 29.630 0.00 0.00 46.89 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 1.539388 CTCGTGCTAGGCAGAGGATAG 59.461 57.143 0.00 0.00 40.08 2.08
30 31 3.181509 CGGTATATACTCGTGCTAGGCAG 60.182 52.174 12.54 0.00 40.08 4.85
51 61 3.244579 GCTACCGTTGGTTAGAATTAGCG 59.755 47.826 0.00 0.00 37.09 4.26
870 886 5.299028 TGCTCTGCTTTGTTCAAATCTTGTA 59.701 36.000 0.00 0.00 0.00 2.41
871 887 4.098349 TGCTCTGCTTTGTTCAAATCTTGT 59.902 37.500 0.00 0.00 0.00 3.16
875 891 3.979495 CACTGCTCTGCTTTGTTCAAATC 59.021 43.478 0.00 0.00 0.00 2.17
876 892 3.633525 TCACTGCTCTGCTTTGTTCAAAT 59.366 39.130 0.00 0.00 0.00 2.32
881 897 2.216898 GTCTCACTGCTCTGCTTTGTT 58.783 47.619 0.00 0.00 0.00 2.83
882 898 1.139654 TGTCTCACTGCTCTGCTTTGT 59.860 47.619 0.00 0.00 0.00 2.83
883 899 1.875009 TGTCTCACTGCTCTGCTTTG 58.125 50.000 0.00 0.00 0.00 2.77
890 906 0.734253 AACGCGATGTCTCACTGCTC 60.734 55.000 15.93 0.00 0.00 4.26
892 908 0.734253 AGAACGCGATGTCTCACTGC 60.734 55.000 15.93 0.00 0.00 4.40
895 911 0.992802 GGAAGAACGCGATGTCTCAC 59.007 55.000 15.93 9.84 0.00 3.51
898 914 1.178276 AGAGGAAGAACGCGATGTCT 58.822 50.000 15.93 9.69 0.00 3.41
899 915 1.656095 CAAGAGGAAGAACGCGATGTC 59.344 52.381 15.93 7.15 0.00 3.06
900 916 1.714794 CAAGAGGAAGAACGCGATGT 58.285 50.000 15.93 0.00 0.00 3.06
901 917 0.371645 GCAAGAGGAAGAACGCGATG 59.628 55.000 15.93 0.00 0.00 3.84
902 918 0.247736 AGCAAGAGGAAGAACGCGAT 59.752 50.000 15.93 0.00 0.00 4.58
903 919 0.667487 CAGCAAGAGGAAGAACGCGA 60.667 55.000 15.93 0.00 0.00 5.87
904 920 1.784062 CAGCAAGAGGAAGAACGCG 59.216 57.895 3.53 3.53 0.00 6.01
905 921 0.952984 AGCAGCAAGAGGAAGAACGC 60.953 55.000 0.00 0.00 0.00 4.84
906 922 1.196354 CAAGCAGCAAGAGGAAGAACG 59.804 52.381 0.00 0.00 0.00 3.95
908 924 2.645838 ACAAGCAGCAAGAGGAAGAA 57.354 45.000 0.00 0.00 0.00 2.52
910 926 2.606725 CGATACAAGCAGCAAGAGGAAG 59.393 50.000 0.00 0.00 0.00 3.46
911 927 2.621338 CGATACAAGCAGCAAGAGGAA 58.379 47.619 0.00 0.00 0.00 3.36
913 929 1.293924 CCGATACAAGCAGCAAGAGG 58.706 55.000 0.00 0.00 0.00 3.69
914 930 1.929836 GACCGATACAAGCAGCAAGAG 59.070 52.381 0.00 0.00 0.00 2.85
915 931 1.735700 CGACCGATACAAGCAGCAAGA 60.736 52.381 0.00 0.00 0.00 3.02
916 932 0.647410 CGACCGATACAAGCAGCAAG 59.353 55.000 0.00 0.00 0.00 4.01
918 934 0.459899 ATCGACCGATACAAGCAGCA 59.540 50.000 2.75 0.00 32.36 4.41
919 935 1.132588 GATCGACCGATACAAGCAGC 58.867 55.000 4.78 0.00 34.60 5.25
920 936 1.002792 TCGATCGACCGATACAAGCAG 60.003 52.381 15.15 0.00 34.60 4.24
921 937 1.002792 CTCGATCGACCGATACAAGCA 60.003 52.381 15.15 0.00 37.96 3.91
922 938 1.676057 CTCGATCGACCGATACAAGC 58.324 55.000 15.15 0.00 37.96 4.01
923 939 1.002792 TGCTCGATCGACCGATACAAG 60.003 52.381 15.15 2.05 37.96 3.16
924 940 1.018910 TGCTCGATCGACCGATACAA 58.981 50.000 15.15 0.00 37.96 2.41
925 941 1.197036 GATGCTCGATCGACCGATACA 59.803 52.381 15.15 4.71 37.96 2.29
926 942 1.466024 GGATGCTCGATCGACCGATAC 60.466 57.143 15.15 0.00 37.96 2.24
927 943 0.803117 GGATGCTCGATCGACCGATA 59.197 55.000 15.15 0.00 37.96 2.92
928 944 0.891449 AGGATGCTCGATCGACCGAT 60.891 55.000 15.15 6.09 37.96 4.18
931 947 4.643733 CAGGATGCTCGATCGACC 57.356 61.111 15.15 13.99 30.87 4.79
941 957 7.793398 TAAATACAGAGTGTTTGGCAGGATGC 61.793 42.308 2.70 0.00 43.17 3.91
944 960 3.788227 AATACAGAGTGTTTGGCAGGA 57.212 42.857 0.00 0.00 0.00 3.86
945 961 6.515272 AATAAATACAGAGTGTTTGGCAGG 57.485 37.500 2.70 0.00 30.19 4.85
961 977 4.931002 GCGCCGGAATACAGGTAATAAATA 59.069 41.667 5.05 0.00 33.97 1.40
962 978 3.749609 GCGCCGGAATACAGGTAATAAAT 59.250 43.478 5.05 0.00 33.97 1.40
963 979 3.132925 GCGCCGGAATACAGGTAATAAA 58.867 45.455 5.05 0.00 33.97 1.40
964 980 2.548493 GGCGCCGGAATACAGGTAATAA 60.548 50.000 12.58 0.00 33.97 1.40
965 981 1.001181 GGCGCCGGAATACAGGTAATA 59.999 52.381 12.58 0.00 33.97 0.98
1476 1692 2.317149 GACATTGCTCTCCTCCGGGG 62.317 65.000 0.00 0.00 0.00 5.73
1477 1693 1.144936 GACATTGCTCTCCTCCGGG 59.855 63.158 0.00 0.00 0.00 5.73
1510 1726 0.605589 ACTTCGTGCAGGGTTTAGGC 60.606 55.000 6.56 0.00 0.00 3.93
1526 1742 1.027357 CACTGGCACTGCTGAAACTT 58.973 50.000 0.00 0.00 0.00 2.66
1535 1751 5.947228 TTCTAAATTTCTCACTGGCACTG 57.053 39.130 0.00 0.00 0.00 3.66
1536 1752 6.491403 ACATTTCTAAATTTCTCACTGGCACT 59.509 34.615 0.00 0.00 0.00 4.40
1538 1754 6.489700 TCACATTTCTAAATTTCTCACTGGCA 59.510 34.615 0.00 0.00 0.00 4.92
1595 1812 4.630644 TCATTCTGCTCTTGTTTCTCCT 57.369 40.909 0.00 0.00 0.00 3.69
1603 1820 4.033817 GGACGAGATTTCATTCTGCTCTTG 59.966 45.833 0.00 0.00 0.00 3.02
1613 1830 3.328382 TTTGGACGGACGAGATTTCAT 57.672 42.857 0.00 0.00 0.00 2.57
1627 1844 6.990939 GGAGGGAGTACTGTATAATTTTGGAC 59.009 42.308 0.00 0.00 0.00 4.02
1628 1845 6.183360 CGGAGGGAGTACTGTATAATTTTGGA 60.183 42.308 0.00 0.00 0.00 3.53
1706 2059 9.323963 GTTTTAAGGTGTTTGTTCATTTGTTTG 57.676 29.630 0.00 0.00 0.00 2.93
1766 2208 9.793259 TCCCTTTGTTCATAAATATAGGATGTC 57.207 33.333 0.00 0.00 29.80 3.06
1785 2228 9.541143 GTAGTAGTAGTAGTAGTACTCCCTTTG 57.459 40.741 22.85 0.00 42.27 2.77
1849 2292 1.993391 TACTTGGCCGGCCTTAGCT 60.993 57.895 43.34 28.28 39.73 3.32
1850 2293 1.818363 GTACTTGGCCGGCCTTAGC 60.818 63.158 43.34 25.77 36.94 3.09
1853 2296 1.196104 TACAGTACTTGGCCGGCCTT 61.196 55.000 43.34 29.57 36.94 4.35
1854 2297 1.611261 TACAGTACTTGGCCGGCCT 60.611 57.895 43.34 27.93 36.94 5.19
1861 2304 3.243737 TGTGTGACAGCTACAGTACTTGG 60.244 47.826 0.00 0.00 0.00 3.61
1891 2334 8.813282 CAAACAGTGAAAACCAATAAAACTACC 58.187 33.333 0.00 0.00 0.00 3.18
1892 2335 8.325282 GCAAACAGTGAAAACCAATAAAACTAC 58.675 33.333 0.00 0.00 0.00 2.73
1894 2337 6.876257 TGCAAACAGTGAAAACCAATAAAACT 59.124 30.769 0.00 0.00 0.00 2.66
1895 2338 7.066374 TGCAAACAGTGAAAACCAATAAAAC 57.934 32.000 0.00 0.00 0.00 2.43
1896 2339 7.254252 CGATGCAAACAGTGAAAACCAATAAAA 60.254 33.333 0.00 0.00 0.00 1.52
1902 2352 2.685388 TCGATGCAAACAGTGAAAACCA 59.315 40.909 0.00 0.00 0.00 3.67
1906 2356 5.437289 AGAAATCGATGCAAACAGTGAAA 57.563 34.783 0.00 0.00 0.00 2.69
1926 2376 8.589701 AAAGAGAAAACAAAAAGACCCTAAGA 57.410 30.769 0.00 0.00 0.00 2.10
2004 2465 3.211045 GCAGACCTGTGTTGTTAAAGGA 58.789 45.455 0.00 0.00 33.78 3.36
2010 2471 4.400884 TGTAAAATGCAGACCTGTGTTGTT 59.599 37.500 0.00 0.00 0.00 2.83
2055 2524 8.564574 ACGTGTGTAAAAATGTTCTTGATGTAT 58.435 29.630 0.00 0.00 0.00 2.29
2056 2525 7.921787 ACGTGTGTAAAAATGTTCTTGATGTA 58.078 30.769 0.00 0.00 0.00 2.29
2057 2526 6.791303 ACGTGTGTAAAAATGTTCTTGATGT 58.209 32.000 0.00 0.00 0.00 3.06
2058 2527 7.678194 AACGTGTGTAAAAATGTTCTTGATG 57.322 32.000 0.00 0.00 0.00 3.07
2060 2529 7.271653 GTGAAACGTGTGTAAAAATGTTCTTGA 59.728 33.333 0.00 0.00 0.00 3.02
2061 2530 7.061210 TGTGAAACGTGTGTAAAAATGTTCTTG 59.939 33.333 0.00 0.00 42.39 3.02
2062 2531 7.085116 TGTGAAACGTGTGTAAAAATGTTCTT 58.915 30.769 0.00 0.00 42.39 2.52
2063 2532 6.613233 TGTGAAACGTGTGTAAAAATGTTCT 58.387 32.000 0.00 0.00 42.39 3.01
2064 2533 6.856494 TGTGAAACGTGTGTAAAAATGTTC 57.144 33.333 0.00 0.00 42.39 3.18
2066 2535 7.670916 CAAATGTGAAACGTGTGTAAAAATGT 58.329 30.769 0.00 0.00 42.39 2.71
2075 2544 6.470556 TGAACATAACAAATGTGAAACGTGTG 59.529 34.615 0.00 0.00 46.70 3.82
2076 2545 6.556212 TGAACATAACAAATGTGAAACGTGT 58.444 32.000 0.00 0.00 42.39 4.49
2084 2553 8.745464 TGTCAATCATGAACATAACAAATGTG 57.255 30.769 0.00 0.00 37.30 3.21
2091 2560 8.928733 AGCAAAAATGTCAATCATGAACATAAC 58.071 29.630 11.05 2.05 37.30 1.89
2095 2564 8.883954 TTTAGCAAAAATGTCAATCATGAACA 57.116 26.923 0.00 0.00 37.30 3.18
2131 2601 7.709947 ACAATGTGTATGAAGAAATAGCCATG 58.290 34.615 0.00 0.00 0.00 3.66
2134 2604 8.208718 TGTACAATGTGTATGAAGAAATAGCC 57.791 34.615 0.00 0.00 35.05 3.93
2319 2818 7.728580 TTAACAAAATGTTCACGAGTTTCAC 57.271 32.000 0.00 0.00 40.22 3.18


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

AutoCloner maintained by Alex Coulton.