Multiple sequence alignment - TraesCS2B01G015800

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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 TraesCS2B01G015800 chr2B 100.000 2414 0 0 1 2414 7583245 7580832 0.000000e+00 4458
1 TraesCS2B01G015800 chr2B 97.429 1439 37 0 1 1439 705366377 705367815 0.000000e+00 2453
2 TraesCS2B01G015800 chr2B 87.643 526 57 3 1543 2067 7646728 7646210 2.650000e-169 604
3 TraesCS2B01G015800 chr5B 96.877 1441 37 1 1 1441 350409322 350410754 0.000000e+00 2405
4 TraesCS2B01G015800 chr4B 90.264 1438 140 0 1 1438 581946026 581944589 0.000000e+00 1881
5 TraesCS2B01G015800 chr7B 89.786 1449 142 6 1 1446 732589353 732590798 0.000000e+00 1851
6 TraesCS2B01G015800 chr7B 95.098 102 4 1 2066 2167 706811142 706811042 2.480000e-35 159
7 TraesCS2B01G015800 chr6B 89.507 1439 137 2 1 1439 659669307 659670731 0.000000e+00 1808
8 TraesCS2B01G015800 chr6B 88.501 687 78 1 1 686 94007851 94007165 0.000000e+00 830
9 TraesCS2B01G015800 chr6B 85.636 731 102 3 711 1440 94007172 94006444 0.000000e+00 765
10 TraesCS2B01G015800 chr2D 84.364 1439 223 2 1 1438 442006890 442005453 0.000000e+00 1410
11 TraesCS2B01G015800 chr2D 86.859 624 70 10 1448 2068 3079021 3079635 0.000000e+00 688
12 TraesCS2B01G015800 chr2D 85.514 214 31 0 2201 2414 3079680 3079893 8.680000e-55 224
13 TraesCS2B01G015800 chr2D 84.579 214 33 0 2201 2414 3623604 3623817 1.880000e-51 213
14 TraesCS2B01G015800 chr2D 86.667 150 20 0 1918 2067 3032517 3032666 1.480000e-37 167
15 TraesCS2B01G015800 chr2D 94.393 107 4 2 2065 2170 107204079 107204184 1.920000e-36 163
16 TraesCS2B01G015800 chr2D 95.146 103 4 1 2065 2167 532305999 532305898 6.910000e-36 161
17 TraesCS2B01G015800 chr3A 83.777 752 121 1 690 1440 23297301 23296550 0.000000e+00 712
18 TraesCS2B01G015800 chr3A 95.098 102 4 1 2066 2167 712147991 712148091 2.480000e-35 159
19 TraesCS2B01G015800 chr2A 86.598 582 59 13 1497 2067 2659128 2658555 2.040000e-175 625
20 TraesCS2B01G015800 chr2A 87.008 254 30 3 2162 2414 2658556 2658305 1.410000e-72 283
21 TraesCS2B01G015800 chr1B 84.420 552 86 0 889 1440 648706116 648706667 5.870000e-151 544
22 TraesCS2B01G015800 chr3D 95.327 107 3 2 2065 2170 495531608 495531503 4.130000e-38 169
23 TraesCS2B01G015800 chr7D 95.050 101 4 1 2066 2166 60439692 60439593 8.930000e-35 158
24 TraesCS2B01G015800 chr7D 92.661 109 6 2 2059 2167 545268996 545269102 3.210000e-34 156
25 TraesCS2B01G015800 chr7D 92.727 110 5 2 2059 2168 635688986 635688880 3.210000e-34 156
26 TraesCS2B01G015800 chr7D 92.727 110 5 2 2059 2168 636310151 636310257 3.210000e-34 156


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 TraesCS2B01G015800 chr2B 7580832 7583245 2413 True 4458.0 4458 100.0000 1 2414 1 chr2B.!!$R1 2413
1 TraesCS2B01G015800 chr2B 705366377 705367815 1438 False 2453.0 2453 97.4290 1 1439 1 chr2B.!!$F1 1438
2 TraesCS2B01G015800 chr2B 7646210 7646728 518 True 604.0 604 87.6430 1543 2067 1 chr2B.!!$R2 524
3 TraesCS2B01G015800 chr5B 350409322 350410754 1432 False 2405.0 2405 96.8770 1 1441 1 chr5B.!!$F1 1440
4 TraesCS2B01G015800 chr4B 581944589 581946026 1437 True 1881.0 1881 90.2640 1 1438 1 chr4B.!!$R1 1437
5 TraesCS2B01G015800 chr7B 732589353 732590798 1445 False 1851.0 1851 89.7860 1 1446 1 chr7B.!!$F1 1445
6 TraesCS2B01G015800 chr6B 659669307 659670731 1424 False 1808.0 1808 89.5070 1 1439 1 chr6B.!!$F1 1438
7 TraesCS2B01G015800 chr6B 94006444 94007851 1407 True 797.5 830 87.0685 1 1440 2 chr6B.!!$R1 1439
8 TraesCS2B01G015800 chr2D 442005453 442006890 1437 True 1410.0 1410 84.3640 1 1438 1 chr2D.!!$R1 1437
9 TraesCS2B01G015800 chr2D 3079021 3079893 872 False 456.0 688 86.1865 1448 2414 2 chr2D.!!$F4 966
10 TraesCS2B01G015800 chr3A 23296550 23297301 751 True 712.0 712 83.7770 690 1440 1 chr3A.!!$R1 750
11 TraesCS2B01G015800 chr2A 2658305 2659128 823 True 454.0 625 86.8030 1497 2414 2 chr2A.!!$R1 917
12 TraesCS2B01G015800 chr1B 648706116 648706667 551 False 544.0 544 84.4200 889 1440 1 chr1B.!!$F1 551

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
375 376 0.525668 GTGCGTCCAGTACTCATCCG 60.526 60.0 0.0 0.0 32.41 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2279 2302 0.179089 CGCCCACCTCTCTTGATGAG 60.179 60.0 0.0 0.0 43.96 2.9 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
146 147 1.102978 AATTGCCGTCTACATTGGGC 58.897 50.000 0.00 0.00 45.76 5.36
212 213 2.838637 AGGGAACACTTTTGGGAACA 57.161 45.000 0.00 0.00 39.83 3.18
375 376 0.525668 GTGCGTCCAGTACTCATCCG 60.526 60.000 0.00 0.00 32.41 4.18
420 421 6.183360 GGCAATGTATTTGGAATGCTAGAGTT 60.183 38.462 0.00 0.00 35.75 3.01
964 965 5.592104 TGCTTCGTTATCAGTAGATGGAA 57.408 39.130 0.00 0.00 35.67 3.53
977 978 7.461749 TCAGTAGATGGAACCTTTTCTCAAAT 58.538 34.615 0.00 0.00 31.71 2.32
1013 1014 2.691526 CAGCAGGTATGGTACTACGGAA 59.308 50.000 0.00 0.00 34.74 4.30
1461 1462 1.403323 GAAAAGGAGGCACATAGCTGC 59.597 52.381 0.00 0.00 44.79 5.25
1471 1472 5.792741 AGGCACATAGCTGCAAAATTTTAA 58.207 33.333 2.44 0.00 44.79 1.52
1491 1492 4.525912 AATGAAAATTGAGTCCCTGCAC 57.474 40.909 0.00 0.00 0.00 4.57
1501 1502 1.079503 GTCCCTGCACGAAGTTCATC 58.920 55.000 3.32 0.00 41.61 2.92
1506 1507 0.038251 TGCACGAAGTTCATCGCTCT 60.038 50.000 3.32 0.00 46.51 4.09
1537 1538 2.099141 TAGATGCCAACACACTGAGC 57.901 50.000 0.00 0.00 0.00 4.26
1539 1540 1.202855 AGATGCCAACACACTGAGCTT 60.203 47.619 0.00 0.00 0.00 3.74
1541 1552 1.882912 TGCCAACACACTGAGCTTAG 58.117 50.000 3.53 3.53 0.00 2.18
1566 1577 6.446781 AAATGCAGATAATCAACACTGAGG 57.553 37.500 0.00 0.00 34.23 3.86
1612 1623 3.758554 CCACTAACTGAATTTGACAGGGG 59.241 47.826 0.00 0.00 39.38 4.79
1669 1680 5.046950 AGGTAAAACCACTTTGTTTTGCTCA 60.047 36.000 14.12 0.00 45.40 4.26
1677 1688 6.546034 ACCACTTTGTTTTGCTCACTTATACT 59.454 34.615 0.00 0.00 0.00 2.12
1681 1692 8.903820 ACTTTGTTTTGCTCACTTATACTTTCT 58.096 29.630 0.00 0.00 0.00 2.52
1726 1738 4.081406 TCATGTTCTACTTGCAATGCCTT 58.919 39.130 1.53 0.00 0.00 4.35
1736 1748 4.951715 ACTTGCAATGCCTTCAGATATTCA 59.048 37.500 1.53 0.00 0.00 2.57
1776 1788 5.946377 GGATGTACCTTGGAGAAATTGTTCT 59.054 40.000 0.00 0.00 40.20 3.01
1819 1831 3.057245 CACAAGAGTCTCATCTGTTCGGA 60.057 47.826 1.94 0.00 0.00 4.55
1829 1841 2.810486 CTGTTCGGACAGTCGTTCC 58.190 57.895 16.21 0.00 46.57 3.62
1848 1860 1.354040 CCTGACAAACTAGCTGAGCG 58.646 55.000 0.00 0.00 0.00 5.03
1866 1878 2.295909 AGCGCATTTGTTCTAAGGCAAA 59.704 40.909 11.47 0.00 38.68 3.68
1870 1882 5.347364 GCGCATTTGTTCTAAGGCAAATTAA 59.653 36.000 0.30 0.00 41.62 1.40
1873 1885 7.489113 CGCATTTGTTCTAAGGCAAATTAATCT 59.511 33.333 0.00 0.00 41.62 2.40
1946 1959 1.126846 CGTTCTAAGCTGAACCGCAAG 59.873 52.381 10.43 0.00 42.22 4.01
1949 1962 1.089920 CTAAGCTGAACCGCAAGCAT 58.910 50.000 0.00 0.00 0.00 3.79
1955 1968 2.792542 GCTGAACCGCAAGCATGATTAC 60.793 50.000 0.00 0.00 0.00 1.89
1991 2004 5.956068 TGTGTGCTATGCAACAAGATAAA 57.044 34.783 0.00 0.00 41.47 1.40
2019 2032 6.238049 CGATGATCTTGGAGAAGTTGAATCAC 60.238 42.308 0.00 0.00 27.36 3.06
2025 2038 6.603201 TCTTGGAGAAGTTGAATCACTTTTGT 59.397 34.615 0.00 0.00 37.11 2.83
2062 2076 6.769341 GGGGTAAGTTTCTACACTTTTTCAGA 59.231 38.462 0.00 0.00 38.07 3.27
2068 2082 9.614792 AAGTTTCTACACTTTTTCAGACATACT 57.385 29.630 0.00 0.00 32.81 2.12
2069 2083 9.262358 AGTTTCTACACTTTTTCAGACATACTC 57.738 33.333 0.00 0.00 0.00 2.59
2070 2084 8.496751 GTTTCTACACTTTTTCAGACATACTCC 58.503 37.037 0.00 0.00 0.00 3.85
2071 2085 6.698380 TCTACACTTTTTCAGACATACTCCC 58.302 40.000 0.00 0.00 0.00 4.30
2072 2086 5.568620 ACACTTTTTCAGACATACTCCCT 57.431 39.130 0.00 0.00 0.00 4.20
2073 2087 5.552178 ACACTTTTTCAGACATACTCCCTC 58.448 41.667 0.00 0.00 0.00 4.30
2074 2088 4.938226 CACTTTTTCAGACATACTCCCTCC 59.062 45.833 0.00 0.00 0.00 4.30
2075 2089 3.887621 TTTTCAGACATACTCCCTCCG 57.112 47.619 0.00 0.00 0.00 4.63
2076 2090 2.526888 TTCAGACATACTCCCTCCGT 57.473 50.000 0.00 0.00 0.00 4.69
2077 2091 2.526888 TCAGACATACTCCCTCCGTT 57.473 50.000 0.00 0.00 0.00 4.44
2078 2092 2.376109 TCAGACATACTCCCTCCGTTC 58.624 52.381 0.00 0.00 0.00 3.95
2079 2093 1.409427 CAGACATACTCCCTCCGTTCC 59.591 57.143 0.00 0.00 0.00 3.62
2080 2094 1.006758 AGACATACTCCCTCCGTTCCA 59.993 52.381 0.00 0.00 0.00 3.53
2081 2095 1.829222 GACATACTCCCTCCGTTCCAA 59.171 52.381 0.00 0.00 0.00 3.53
2082 2096 2.235402 GACATACTCCCTCCGTTCCAAA 59.765 50.000 0.00 0.00 0.00 3.28
2083 2097 2.640826 ACATACTCCCTCCGTTCCAAAA 59.359 45.455 0.00 0.00 0.00 2.44
2084 2098 3.265995 ACATACTCCCTCCGTTCCAAAAT 59.734 43.478 0.00 0.00 0.00 1.82
2085 2099 4.472108 ACATACTCCCTCCGTTCCAAAATA 59.528 41.667 0.00 0.00 0.00 1.40
2086 2100 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
2087 2101 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
2088 2102 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
2089 2103 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
2090 2104 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
2091 2105 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
2092 2106 4.384208 CCCTCCGTTCCAAAATAGATGACT 60.384 45.833 0.00 0.00 0.00 3.41
2093 2107 4.811557 CCTCCGTTCCAAAATAGATGACTC 59.188 45.833 0.00 0.00 0.00 3.36
2094 2108 5.414789 TCCGTTCCAAAATAGATGACTCA 57.585 39.130 0.00 0.00 0.00 3.41
2095 2109 5.800296 TCCGTTCCAAAATAGATGACTCAA 58.200 37.500 0.00 0.00 0.00 3.02
2096 2110 5.642063 TCCGTTCCAAAATAGATGACTCAAC 59.358 40.000 0.00 0.00 0.00 3.18
2097 2111 5.643777 CCGTTCCAAAATAGATGACTCAACT 59.356 40.000 0.00 0.00 0.00 3.16
2098 2112 6.149474 CCGTTCCAAAATAGATGACTCAACTT 59.851 38.462 0.00 0.00 0.00 2.66
2099 2113 7.308589 CCGTTCCAAAATAGATGACTCAACTTT 60.309 37.037 0.00 0.00 0.00 2.66
2100 2114 7.535258 CGTTCCAAAATAGATGACTCAACTTTG 59.465 37.037 0.00 0.00 0.00 2.77
2101 2115 8.352942 GTTCCAAAATAGATGACTCAACTTTGT 58.647 33.333 0.00 0.00 0.00 2.83
2102 2116 9.567776 TTCCAAAATAGATGACTCAACTTTGTA 57.432 29.630 0.00 0.00 0.00 2.41
2103 2117 8.999431 TCCAAAATAGATGACTCAACTTTGTAC 58.001 33.333 0.00 0.00 0.00 2.90
2104 2118 9.003658 CCAAAATAGATGACTCAACTTTGTACT 57.996 33.333 0.00 0.00 0.00 2.73
2134 2148 8.801715 TTAGTACGAAGTTAGTACAAAGTTGG 57.198 34.615 23.02 0.00 44.92 3.77
2135 2149 6.218746 AGTACGAAGTTAGTACAAAGTTGGG 58.781 40.000 23.02 0.00 44.92 4.12
2136 2150 5.027293 ACGAAGTTAGTACAAAGTTGGGT 57.973 39.130 0.00 0.00 37.78 4.51
2137 2151 5.052481 ACGAAGTTAGTACAAAGTTGGGTC 58.948 41.667 0.00 0.00 37.78 4.46
2138 2152 4.450080 CGAAGTTAGTACAAAGTTGGGTCC 59.550 45.833 0.00 0.00 0.00 4.46
2139 2153 5.618236 GAAGTTAGTACAAAGTTGGGTCCT 58.382 41.667 0.00 0.00 0.00 3.85
2140 2154 5.224821 AGTTAGTACAAAGTTGGGTCCTC 57.775 43.478 0.00 0.00 0.00 3.71
2141 2155 4.906060 AGTTAGTACAAAGTTGGGTCCTCT 59.094 41.667 0.00 0.00 0.00 3.69
2142 2156 6.080009 AGTTAGTACAAAGTTGGGTCCTCTA 58.920 40.000 0.00 0.00 0.00 2.43
2143 2157 6.729569 AGTTAGTACAAAGTTGGGTCCTCTAT 59.270 38.462 0.00 0.00 0.00 1.98
2144 2158 7.237055 AGTTAGTACAAAGTTGGGTCCTCTATT 59.763 37.037 0.00 0.00 0.00 1.73
2145 2159 6.449830 AGTACAAAGTTGGGTCCTCTATTT 57.550 37.500 0.00 0.00 0.00 1.40
2146 2160 6.849151 AGTACAAAGTTGGGTCCTCTATTTT 58.151 36.000 0.00 0.00 0.00 1.82
2147 2161 6.715264 AGTACAAAGTTGGGTCCTCTATTTTG 59.285 38.462 0.00 0.00 0.00 2.44
2148 2162 4.832823 ACAAAGTTGGGTCCTCTATTTTGG 59.167 41.667 11.24 0.00 0.00 3.28
2149 2163 5.076873 CAAAGTTGGGTCCTCTATTTTGGA 58.923 41.667 0.00 0.00 0.00 3.53
2150 2164 5.333566 AAGTTGGGTCCTCTATTTTGGAA 57.666 39.130 0.00 0.00 33.72 3.53
2151 2165 5.333566 AGTTGGGTCCTCTATTTTGGAAA 57.666 39.130 0.00 0.00 33.72 3.13
2152 2166 5.077564 AGTTGGGTCCTCTATTTTGGAAAC 58.922 41.667 0.00 0.00 33.72 2.78
2153 2167 3.681593 TGGGTCCTCTATTTTGGAAACG 58.318 45.455 0.00 0.00 33.72 3.60
2154 2168 3.328343 TGGGTCCTCTATTTTGGAAACGA 59.672 43.478 0.00 0.00 33.72 3.85
2155 2169 4.202482 TGGGTCCTCTATTTTGGAAACGAA 60.202 41.667 0.00 0.00 33.72 3.85
2156 2170 4.395231 GGGTCCTCTATTTTGGAAACGAAG 59.605 45.833 0.00 0.00 34.49 3.79
2157 2171 4.395231 GGTCCTCTATTTTGGAAACGAAGG 59.605 45.833 0.00 0.00 34.49 3.46
2158 2172 4.395231 GTCCTCTATTTTGGAAACGAAGGG 59.605 45.833 0.00 0.00 34.49 3.95
2159 2173 4.287585 TCCTCTATTTTGGAAACGAAGGGA 59.712 41.667 0.00 0.00 34.49 4.20
2160 2174 4.636206 CCTCTATTTTGGAAACGAAGGGAG 59.364 45.833 0.00 0.00 34.49 4.30
2161 2175 5.237236 TCTATTTTGGAAACGAAGGGAGT 57.763 39.130 0.00 0.00 34.49 3.85
2162 2176 6.363167 TCTATTTTGGAAACGAAGGGAGTA 57.637 37.500 0.00 0.00 34.49 2.59
2169 2183 3.181458 GGAAACGAAGGGAGTATATGGCA 60.181 47.826 0.00 0.00 0.00 4.92
2186 2200 1.732417 GCAATCTTAGCCAGCCAGCC 61.732 60.000 0.00 0.00 0.00 4.85
2187 2201 0.106819 CAATCTTAGCCAGCCAGCCT 60.107 55.000 0.00 0.00 0.00 4.58
2188 2202 0.182299 AATCTTAGCCAGCCAGCCTC 59.818 55.000 0.00 0.00 0.00 4.70
2192 2206 1.200760 TTAGCCAGCCAGCCTCTGAA 61.201 55.000 0.00 0.00 32.44 3.02
2194 2208 2.045536 CCAGCCAGCCTCTGAACC 60.046 66.667 0.00 0.00 32.44 3.62
2198 2212 3.076092 CCAGCCTCTGAACCTGCT 58.924 61.111 0.00 0.00 32.44 4.24
2212 2235 5.684704 TGAACCTGCTATTTTCTCCCATAG 58.315 41.667 0.00 0.00 0.00 2.23
2225 2248 1.228367 CCATAGCCATGGTCCCAGC 60.228 63.158 14.67 0.00 45.92 4.85
2238 2261 1.815003 GTCCCAGCTCAACCAATCTTG 59.185 52.381 0.00 0.00 0.00 3.02
2244 2267 4.318332 CAGCTCAACCAATCTTGTGTAGA 58.682 43.478 0.00 0.00 37.28 2.59
2249 2272 4.012374 CAACCAATCTTGTGTAGAGGCAT 58.988 43.478 0.00 0.00 36.02 4.40
2252 2275 3.624861 CCAATCTTGTGTAGAGGCATGAC 59.375 47.826 0.00 0.00 36.02 3.06
2260 2283 4.189231 GTGTAGAGGCATGACGGTTTATT 58.811 43.478 0.00 0.00 0.00 1.40
2279 2302 4.965119 ATTGTAGAAGTTTCCGATTGCC 57.035 40.909 0.00 0.00 0.00 4.52
2282 2305 2.859165 AGAAGTTTCCGATTGCCTCA 57.141 45.000 0.00 0.00 0.00 3.86
2343 2366 4.165565 TGGCATTCTTCAGAAGATGGAGAT 59.834 41.667 13.86 1.24 43.42 2.75
2345 2368 6.126681 TGGCATTCTTCAGAAGATGGAGATTA 60.127 38.462 13.86 0.00 43.42 1.75
2363 2386 5.946486 AGATTAATTCCAAGGGACTGATCC 58.054 41.667 0.00 0.00 45.42 3.36
2392 2415 2.111384 AGAACAGTGGTAGCGATGGAT 58.889 47.619 0.00 0.00 0.00 3.41
2395 2418 0.465705 CAGTGGTAGCGATGGATGGT 59.534 55.000 0.00 0.00 0.00 3.55
2404 2427 2.439507 AGCGATGGATGGTGGACTTTAT 59.560 45.455 0.00 0.00 0.00 1.40
2405 2428 3.646162 AGCGATGGATGGTGGACTTTATA 59.354 43.478 0.00 0.00 0.00 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
146 147 4.604843 TGCTCGTCAATAAAATCTGCTG 57.395 40.909 0.00 0.00 0.00 4.41
212 213 6.633500 TTTTCAAAATCTCACGAACATCCT 57.367 33.333 0.00 0.00 0.00 3.24
375 376 0.822121 AAACAGGCCTTTGTCCGGTC 60.822 55.000 0.00 0.00 30.83 4.79
964 965 4.089361 GACCCATCCATTTGAGAAAAGGT 58.911 43.478 0.00 0.00 0.00 3.50
977 978 2.672908 CTGCAGCTGACCCATCCA 59.327 61.111 20.43 2.50 0.00 3.41
1013 1014 5.641209 GCGAAGATAATACTTCCATCATGCT 59.359 40.000 0.00 0.00 41.99 3.79
1101 1102 2.433145 ATCGCTATCGCCATGCCG 60.433 61.111 0.00 0.00 35.26 5.69
1122 1123 0.252761 TGATGGGAAGCTCGCAATGA 59.747 50.000 6.93 0.00 42.66 2.57
1261 1262 3.944650 TGCAAGCGGCTAATTTTCATAGA 59.055 39.130 1.35 0.00 45.15 1.98
1441 1442 1.403323 GCAGCTATGTGCCTCCTTTTC 59.597 52.381 0.00 0.00 44.23 2.29
1443 1444 0.329261 TGCAGCTATGTGCCTCCTTT 59.671 50.000 0.00 0.00 43.28 3.11
1446 1447 1.176527 TTTTGCAGCTATGTGCCTCC 58.823 50.000 0.00 0.00 43.28 4.30
1449 1450 6.313411 TCATTAAAATTTTGCAGCTATGTGCC 59.687 34.615 13.76 0.00 43.28 5.01
1471 1472 2.489329 CGTGCAGGGACTCAATTTTCAT 59.511 45.455 0.00 0.00 34.60 2.57
1478 1479 0.468226 AACTTCGTGCAGGGACTCAA 59.532 50.000 6.56 0.00 34.60 3.02
1485 1486 1.016130 AGCGATGAACTTCGTGCAGG 61.016 55.000 0.00 0.00 41.16 4.85
1491 1492 5.037385 TCTTATTCAGAGCGATGAACTTCG 58.963 41.667 8.54 5.88 41.76 3.79
1506 1507 7.280876 GTGTGTTGGCATCTATTCTCTTATTCA 59.719 37.037 0.00 0.00 0.00 2.57
1537 1538 9.499585 CAGTGTTGATTATCTGCATTTTCTAAG 57.500 33.333 0.00 0.00 0.00 2.18
1539 1540 8.791327 TCAGTGTTGATTATCTGCATTTTCTA 57.209 30.769 0.00 0.00 0.00 2.10
1541 1552 6.971184 CCTCAGTGTTGATTATCTGCATTTTC 59.029 38.462 0.00 0.00 31.68 2.29
1566 1577 1.272704 ACCATCTGAAAAAGCTCCCCC 60.273 52.381 0.00 0.00 0.00 5.40
1654 1665 8.856490 AAAGTATAAGTGAGCAAAACAAAGTG 57.144 30.769 0.00 0.00 0.00 3.16
1692 1704 8.834465 GCAAGTAGAACATGACATCAAGATAAT 58.166 33.333 0.00 0.00 0.00 1.28
1693 1705 7.823799 TGCAAGTAGAACATGACATCAAGATAA 59.176 33.333 0.00 0.00 0.00 1.75
1694 1706 7.330262 TGCAAGTAGAACATGACATCAAGATA 58.670 34.615 0.00 0.00 0.00 1.98
1695 1707 6.175471 TGCAAGTAGAACATGACATCAAGAT 58.825 36.000 0.00 0.00 0.00 2.40
1696 1708 5.550290 TGCAAGTAGAACATGACATCAAGA 58.450 37.500 0.00 0.00 0.00 3.02
1697 1709 5.868043 TGCAAGTAGAACATGACATCAAG 57.132 39.130 0.00 0.00 0.00 3.02
1704 1716 3.689347 AGGCATTGCAAGTAGAACATGA 58.311 40.909 11.39 0.00 0.00 3.07
1713 1725 4.951715 TGAATATCTGAAGGCATTGCAAGT 59.048 37.500 11.39 0.00 0.00 3.16
1726 1738 6.697455 CGGAAATCGTCTTCTTGAATATCTGA 59.303 38.462 0.54 0.00 0.00 3.27
1736 1748 2.236395 ACATCCCGGAAATCGTCTTCTT 59.764 45.455 0.73 0.00 37.11 2.52
1776 1788 4.980592 TCCTGGCCAGCACCCTCA 62.981 66.667 28.39 1.07 0.00 3.86
1798 1810 3.057174 GTCCGAACAGATGAGACTCTTGT 60.057 47.826 3.68 3.34 0.00 3.16
1819 1831 1.485066 AGTTTGTCAGGGAACGACTGT 59.515 47.619 0.00 0.00 37.25 3.55
1822 1834 2.067013 GCTAGTTTGTCAGGGAACGAC 58.933 52.381 0.00 0.00 35.42 4.34
1829 1841 1.354040 CGCTCAGCTAGTTTGTCAGG 58.646 55.000 0.00 0.00 0.00 3.86
1848 1860 8.707938 AGATTAATTTGCCTTAGAACAAATGC 57.292 30.769 11.82 5.27 43.76 3.56
1866 1878 7.108841 TCTGGAAGCTACAACGTAGATTAAT 57.891 36.000 4.76 0.00 0.00 1.40
1870 1882 4.017808 ACTCTGGAAGCTACAACGTAGAT 58.982 43.478 5.35 0.00 0.00 1.98
1873 1885 2.490903 GGACTCTGGAAGCTACAACGTA 59.509 50.000 0.00 0.00 0.00 3.57
1946 1959 5.824904 AATGTGGAGTTCTGTAATCATGC 57.175 39.130 0.00 0.00 0.00 4.06
1949 1962 6.558771 CACAAATGTGGAGTTCTGTAATCA 57.441 37.500 5.63 0.00 42.10 2.57
1991 2004 4.406972 TCAACTTCTCCAAGATCATCGGAT 59.593 41.667 0.00 0.00 36.13 4.18
2019 2032 3.258498 CGATGACGTCGCACAAAAG 57.742 52.632 11.62 0.00 44.33 2.27
2031 2044 4.081807 AGTGTAGAAACTTACCCCGATGAC 60.082 45.833 0.00 0.00 0.00 3.06
2062 2076 1.946984 TTGGAACGGAGGGAGTATGT 58.053 50.000 0.00 0.00 0.00 2.29
2067 2081 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
2068 2082 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
2069 2083 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
2070 2084 4.770795 AGTCATCTATTTTGGAACGGAGG 58.229 43.478 0.00 0.00 0.00 4.30
2071 2085 5.419542 TGAGTCATCTATTTTGGAACGGAG 58.580 41.667 0.00 0.00 0.00 4.63
2072 2086 5.414789 TGAGTCATCTATTTTGGAACGGA 57.585 39.130 0.00 0.00 0.00 4.69
2073 2087 5.643777 AGTTGAGTCATCTATTTTGGAACGG 59.356 40.000 1.70 0.00 0.00 4.44
2074 2088 6.727824 AGTTGAGTCATCTATTTTGGAACG 57.272 37.500 1.70 0.00 0.00 3.95
2075 2089 8.352942 ACAAAGTTGAGTCATCTATTTTGGAAC 58.647 33.333 14.35 0.00 40.00 3.62
2076 2090 8.463930 ACAAAGTTGAGTCATCTATTTTGGAA 57.536 30.769 14.35 0.00 40.00 3.53
2077 2091 8.999431 GTACAAAGTTGAGTCATCTATTTTGGA 58.001 33.333 14.35 6.88 40.00 3.53
2078 2092 9.003658 AGTACAAAGTTGAGTCATCTATTTTGG 57.996 33.333 14.35 0.00 40.00 3.28
2108 2122 9.248291 CCAACTTTGTACTAACTTCGTACTAAA 57.752 33.333 5.48 4.32 38.39 1.85
2109 2123 7.867403 CCCAACTTTGTACTAACTTCGTACTAA 59.133 37.037 5.48 3.76 38.39 2.24
2110 2124 7.014230 ACCCAACTTTGTACTAACTTCGTACTA 59.986 37.037 5.48 0.00 38.39 1.82
2111 2125 6.183360 ACCCAACTTTGTACTAACTTCGTACT 60.183 38.462 5.48 0.00 38.39 2.73
2112 2126 5.985530 ACCCAACTTTGTACTAACTTCGTAC 59.014 40.000 0.00 0.00 38.13 3.67
2113 2127 6.160576 ACCCAACTTTGTACTAACTTCGTA 57.839 37.500 0.00 0.00 0.00 3.43
2114 2128 5.027293 ACCCAACTTTGTACTAACTTCGT 57.973 39.130 0.00 0.00 0.00 3.85
2115 2129 4.450080 GGACCCAACTTTGTACTAACTTCG 59.550 45.833 0.00 0.00 0.00 3.79
2116 2130 5.618236 AGGACCCAACTTTGTACTAACTTC 58.382 41.667 0.00 0.00 0.00 3.01
2117 2131 5.368816 AGAGGACCCAACTTTGTACTAACTT 59.631 40.000 0.00 0.00 0.00 2.66
2118 2132 4.906060 AGAGGACCCAACTTTGTACTAACT 59.094 41.667 0.00 0.00 0.00 2.24
2119 2133 5.224821 AGAGGACCCAACTTTGTACTAAC 57.775 43.478 0.00 0.00 0.00 2.34
2120 2134 7.563724 AATAGAGGACCCAACTTTGTACTAA 57.436 36.000 0.00 0.00 0.00 2.24
2121 2135 7.563724 AAATAGAGGACCCAACTTTGTACTA 57.436 36.000 0.00 0.00 0.00 1.82
2122 2136 6.449830 AAATAGAGGACCCAACTTTGTACT 57.550 37.500 0.00 0.00 0.00 2.73
2123 2137 6.072119 CCAAAATAGAGGACCCAACTTTGTAC 60.072 42.308 0.00 0.00 0.00 2.90
2124 2138 6.007703 CCAAAATAGAGGACCCAACTTTGTA 58.992 40.000 0.00 0.00 0.00 2.41
2125 2139 4.832823 CCAAAATAGAGGACCCAACTTTGT 59.167 41.667 0.00 0.00 0.00 2.83
2126 2140 5.076873 TCCAAAATAGAGGACCCAACTTTG 58.923 41.667 0.00 0.00 0.00 2.77
2127 2141 5.333566 TCCAAAATAGAGGACCCAACTTT 57.666 39.130 0.00 0.00 0.00 2.66
2128 2142 5.333566 TTCCAAAATAGAGGACCCAACTT 57.666 39.130 0.00 0.00 32.62 2.66
2129 2143 5.077564 GTTTCCAAAATAGAGGACCCAACT 58.922 41.667 0.00 0.00 32.62 3.16
2130 2144 4.082949 CGTTTCCAAAATAGAGGACCCAAC 60.083 45.833 0.00 0.00 32.62 3.77
2131 2145 4.076394 CGTTTCCAAAATAGAGGACCCAA 58.924 43.478 0.00 0.00 32.62 4.12
2132 2146 3.328343 TCGTTTCCAAAATAGAGGACCCA 59.672 43.478 0.00 0.00 32.62 4.51
2133 2147 3.946606 TCGTTTCCAAAATAGAGGACCC 58.053 45.455 0.00 0.00 32.62 4.46
2134 2148 4.395231 CCTTCGTTTCCAAAATAGAGGACC 59.605 45.833 0.00 0.00 32.62 4.46
2135 2149 4.395231 CCCTTCGTTTCCAAAATAGAGGAC 59.605 45.833 0.00 0.00 32.62 3.85
2136 2150 4.287585 TCCCTTCGTTTCCAAAATAGAGGA 59.712 41.667 0.00 0.00 0.00 3.71
2137 2151 4.585879 TCCCTTCGTTTCCAAAATAGAGG 58.414 43.478 0.00 0.00 0.00 3.69
2138 2152 5.246307 ACTCCCTTCGTTTCCAAAATAGAG 58.754 41.667 0.00 0.00 0.00 2.43
2139 2153 5.237236 ACTCCCTTCGTTTCCAAAATAGA 57.763 39.130 0.00 0.00 0.00 1.98
2140 2154 8.774586 CATATACTCCCTTCGTTTCCAAAATAG 58.225 37.037 0.00 0.00 0.00 1.73
2141 2155 7.717875 CCATATACTCCCTTCGTTTCCAAAATA 59.282 37.037 0.00 0.00 0.00 1.40
2142 2156 6.546034 CCATATACTCCCTTCGTTTCCAAAAT 59.454 38.462 0.00 0.00 0.00 1.82
2143 2157 5.883673 CCATATACTCCCTTCGTTTCCAAAA 59.116 40.000 0.00 0.00 0.00 2.44
2144 2158 5.433526 CCATATACTCCCTTCGTTTCCAAA 58.566 41.667 0.00 0.00 0.00 3.28
2145 2159 4.685030 GCCATATACTCCCTTCGTTTCCAA 60.685 45.833 0.00 0.00 0.00 3.53
2146 2160 3.181458 GCCATATACTCCCTTCGTTTCCA 60.181 47.826 0.00 0.00 0.00 3.53
2147 2161 3.181458 TGCCATATACTCCCTTCGTTTCC 60.181 47.826 0.00 0.00 0.00 3.13
2148 2162 4.067972 TGCCATATACTCCCTTCGTTTC 57.932 45.455 0.00 0.00 0.00 2.78
2149 2163 4.497291 TTGCCATATACTCCCTTCGTTT 57.503 40.909 0.00 0.00 0.00 3.60
2150 2164 4.348168 AGATTGCCATATACTCCCTTCGTT 59.652 41.667 0.00 0.00 0.00 3.85
2151 2165 3.904339 AGATTGCCATATACTCCCTTCGT 59.096 43.478 0.00 0.00 0.00 3.85
2152 2166 4.543590 AGATTGCCATATACTCCCTTCG 57.456 45.455 0.00 0.00 0.00 3.79
2153 2167 5.877564 GCTAAGATTGCCATATACTCCCTTC 59.122 44.000 0.00 0.00 0.00 3.46
2154 2168 5.810095 GCTAAGATTGCCATATACTCCCTT 58.190 41.667 0.00 0.00 0.00 3.95
2155 2169 5.428184 GCTAAGATTGCCATATACTCCCT 57.572 43.478 0.00 0.00 0.00 4.20
2169 2183 4.995594 GGCTGGCTGGCTAAGATT 57.004 55.556 10.74 0.00 38.32 2.40
2186 2200 4.195416 GGGAGAAAATAGCAGGTTCAGAG 58.805 47.826 0.00 0.00 0.00 3.35
2187 2201 3.587061 TGGGAGAAAATAGCAGGTTCAGA 59.413 43.478 0.00 0.00 0.00 3.27
2188 2202 3.955471 TGGGAGAAAATAGCAGGTTCAG 58.045 45.455 0.00 0.00 0.00 3.02
2192 2206 4.092116 GCTATGGGAGAAAATAGCAGGT 57.908 45.455 9.25 0.00 46.89 4.00
2212 2235 2.048603 GTTGAGCTGGGACCATGGC 61.049 63.158 13.04 4.47 0.00 4.40
2220 2243 1.542915 CACAAGATTGGTTGAGCTGGG 59.457 52.381 0.00 0.00 0.00 4.45
2221 2244 2.233271 ACACAAGATTGGTTGAGCTGG 58.767 47.619 0.00 0.00 0.00 4.85
2225 2248 3.686726 GCCTCTACACAAGATTGGTTGAG 59.313 47.826 13.36 13.36 34.50 3.02
2238 2261 2.094762 AAACCGTCATGCCTCTACAC 57.905 50.000 0.00 0.00 0.00 2.90
2244 2267 4.481368 TCTACAATAAACCGTCATGCCT 57.519 40.909 0.00 0.00 0.00 4.75
2249 2272 5.406175 CGGAAACTTCTACAATAAACCGTCA 59.594 40.000 0.00 0.00 33.44 4.35
2252 2275 6.657836 ATCGGAAACTTCTACAATAAACCG 57.342 37.500 0.00 0.00 38.31 4.44
2260 2283 3.007506 TGAGGCAATCGGAAACTTCTACA 59.992 43.478 0.00 0.00 0.00 2.74
2279 2302 0.179089 CGCCCACCTCTCTTGATGAG 60.179 60.000 0.00 0.00 43.96 2.90
2282 2305 1.201429 AACCGCCCACCTCTCTTGAT 61.201 55.000 0.00 0.00 0.00 2.57
2343 2366 5.369699 CCTAGGATCAGTCCCTTGGAATTAA 59.630 44.000 1.05 0.00 45.59 1.40
2345 2368 3.718956 CCTAGGATCAGTCCCTTGGAATT 59.281 47.826 1.05 0.00 45.59 2.17
2363 2386 3.131400 GCTACCACTGTTCTTCTCCCTAG 59.869 52.174 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.