Multiple sequence alignment - TraesCS2B01G108900

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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 TraesCS2B01G108900 chr2B 100.000 2252 0 0 1 2252 69416481 69418732 0.000000e+00 4159.0
1 TraesCS2B01G108900 chr2B 80.769 156 11 6 1511 1664 69631547 69631685 1.100000e-18 104.0
2 TraesCS2B01G108900 chr2D 89.186 1683 58 60 602 2242 44082313 44083913 0.000000e+00 1986.0
3 TraesCS2B01G108900 chr2D 85.767 541 31 20 40 577 44081622 44082119 4.260000e-147 531.0
4 TraesCS2B01G108900 chr2A 83.382 1709 106 74 34 1663 47912753 47914362 0.000000e+00 1419.0
5 TraesCS2B01G108900 chr2A 86.076 79 1 2 1914 1991 47914575 47914644 2.400000e-10 76.8
6 TraesCS2B01G108900 chr6D 83.333 174 13 7 40 212 335166359 335166201 1.800000e-31 147.0
7 TraesCS2B01G108900 chr1D 83.333 174 13 7 40 212 293924074 293923916 1.800000e-31 147.0
8 TraesCS2B01G108900 chr1D 83.333 174 13 7 40 212 368919202 368919360 1.800000e-31 147.0
9 TraesCS2B01G108900 chr4D 82.759 174 14 7 40 212 38580446 38580604 8.390000e-30 141.0
10 TraesCS2B01G108900 chr4D 82.759 174 14 7 40 212 54782971 54782813 8.390000e-30 141.0
11 TraesCS2B01G108900 chr4D 82.184 174 15 7 40 212 231624487 231624645 3.900000e-28 135.0
12 TraesCS2B01G108900 chr4D 82.184 174 15 10 40 212 272817617 272817459 3.900000e-28 135.0
13 TraesCS2B01G108900 chr7A 93.548 93 5 1 2151 2243 83278942 83279033 1.080000e-28 137.0
14 TraesCS2B01G108900 chr7D 90.722 97 4 1 2147 2243 45273676 45273585 8.450000e-25 124.0
15 TraesCS2B01G108900 chr5D 90.196 102 1 5 2147 2248 459067134 459067226 8.450000e-25 124.0
16 TraesCS2B01G108900 chr6B 89.899 99 4 2 2149 2247 60630266 60630174 3.040000e-24 122.0
17 TraesCS2B01G108900 chr6A 91.398 93 2 2 2149 2241 33391289 33391203 3.040000e-24 122.0
18 TraesCS2B01G108900 chr5B 90.526 95 1 4 2151 2244 563122937 563123024 3.930000e-23 119.0
19 TraesCS2B01G108900 chr4A 86.726 113 6 5 2131 2242 656553661 656553557 1.410000e-22 117.0
20 TraesCS2B01G108900 chr4A 93.590 78 0 1 2164 2241 655621483 655621555 6.570000e-21 111.0


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 TraesCS2B01G108900 chr2B 69416481 69418732 2251 False 4159.0 4159 100.0000 1 2252 1 chr2B.!!$F1 2251
1 TraesCS2B01G108900 chr2D 44081622 44083913 2291 False 1258.5 1986 87.4765 40 2242 2 chr2D.!!$F1 2202
2 TraesCS2B01G108900 chr2A 47912753 47914644 1891 False 747.9 1419 84.7290 34 1991 2 chr2A.!!$F1 1957

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
321 324 0.169009 CTTACGAAGCAAGGCAAGGC 59.831 55.0 0.0 0.0 0.0 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1873 2175 0.535102 ACAGGGTTTCACCGAGCTTG 60.535 55.0 0.0 0.0 39.83 4.01 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
27 28 8.925700 TCTTTCAGTTTTCTTTTTCTTTTCTGC 58.074 29.630 0.00 0.00 0.00 4.26
28 29 6.869421 TCAGTTTTCTTTTTCTTTTCTGCG 57.131 33.333 0.00 0.00 0.00 5.18
29 30 5.804979 TCAGTTTTCTTTTTCTTTTCTGCGG 59.195 36.000 0.00 0.00 0.00 5.69
30 31 5.005682 CAGTTTTCTTTTTCTTTTCTGCGGG 59.994 40.000 0.00 0.00 0.00 6.13
31 32 4.993029 TTTCTTTTTCTTTTCTGCGGGA 57.007 36.364 0.00 0.00 0.00 5.14
32 33 4.993029 TTCTTTTTCTTTTCTGCGGGAA 57.007 36.364 0.00 0.00 0.00 3.97
33 34 4.301637 TCTTTTTCTTTTCTGCGGGAAC 57.698 40.909 0.00 0.00 33.13 3.62
34 35 3.951680 TCTTTTTCTTTTCTGCGGGAACT 59.048 39.130 0.00 0.00 33.13 3.01
35 36 4.401202 TCTTTTTCTTTTCTGCGGGAACTT 59.599 37.500 0.00 0.00 33.13 2.66
36 37 4.729227 TTTTCTTTTCTGCGGGAACTTT 57.271 36.364 0.00 0.00 33.13 2.66
37 38 3.982576 TTCTTTTCTGCGGGAACTTTC 57.017 42.857 0.00 0.00 33.13 2.62
38 39 2.925724 TCTTTTCTGCGGGAACTTTCA 58.074 42.857 0.00 0.00 33.13 2.69
44 45 4.237349 TCTGCGGGAACTTTCATTTTTC 57.763 40.909 0.00 0.00 0.00 2.29
110 112 0.329261 CCCAGTTGCAATCAGAGGGA 59.671 55.000 15.41 0.00 36.96 4.20
120 122 3.243434 GCAATCAGAGGGATTTGCATCTG 60.243 47.826 7.33 7.33 43.76 2.90
121 123 2.723322 TCAGAGGGATTTGCATCTGG 57.277 50.000 12.68 0.00 39.69 3.86
122 124 1.030457 CAGAGGGATTTGCATCTGGC 58.970 55.000 5.92 0.00 45.13 4.85
123 125 6.710771 AATCAGAGGGATTTGCATCTGGCA 62.711 45.833 12.68 0.00 43.76 4.92
124 126 7.931418 AATCAGAGGGATTTGCATCTGGCAT 62.931 44.000 12.68 0.00 43.76 4.40
134 136 2.590821 GCATCTGGCATCATAAAGGGT 58.409 47.619 0.00 0.00 43.97 4.34
139 141 1.476085 TGGCATCATAAAGGGTTTGCG 59.524 47.619 0.00 0.00 0.00 4.85
154 156 3.924507 GCGACTGGCATCCCAATT 58.075 55.556 0.00 0.00 41.58 2.32
155 157 1.729881 GCGACTGGCATCCCAATTC 59.270 57.895 0.00 0.00 41.58 2.17
156 158 1.728490 GCGACTGGCATCCCAATTCC 61.728 60.000 0.00 0.00 41.58 3.01
157 159 1.103398 CGACTGGCATCCCAATTCCC 61.103 60.000 0.00 0.00 41.58 3.97
198 200 4.796110 AGGGATAAAGCAGCAAATCCTA 57.204 40.909 16.21 0.00 38.37 2.94
203 205 1.089920 AAGCAGCAAATCCTAGCACG 58.910 50.000 0.00 0.00 0.00 5.34
217 219 5.892568 TCCTAGCACGAAAGAAGAGAATAC 58.107 41.667 0.00 0.00 0.00 1.89
236 238 9.593134 GAGAATACATATCTCTCTCTCTCTCTC 57.407 40.741 0.00 0.00 40.14 3.20
237 239 9.331466 AGAATACATATCTCTCTCTCTCTCTCT 57.669 37.037 0.00 0.00 0.00 3.10
238 240 9.593134 GAATACATATCTCTCTCTCTCTCTCTC 57.407 40.741 0.00 0.00 0.00 3.20
239 241 8.907829 ATACATATCTCTCTCTCTCTCTCTCT 57.092 38.462 0.00 0.00 0.00 3.10
240 242 7.238486 ACATATCTCTCTCTCTCTCTCTCTC 57.762 44.000 0.00 0.00 0.00 3.20
241 243 7.015680 ACATATCTCTCTCTCTCTCTCTCTCT 58.984 42.308 0.00 0.00 0.00 3.10
242 244 7.178274 ACATATCTCTCTCTCTCTCTCTCTCTC 59.822 44.444 0.00 0.00 0.00 3.20
243 245 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
244 246 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
245 247 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
246 248 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
258 260 9.401058 CTCTCTCTCTCTCTCTTCTCTTTTTAT 57.599 37.037 0.00 0.00 0.00 1.40
259 261 9.753674 TCTCTCTCTCTCTCTTCTCTTTTTATT 57.246 33.333 0.00 0.00 0.00 1.40
318 321 2.806244 GTTCTCTTACGAAGCAAGGCAA 59.194 45.455 0.00 0.00 0.00 4.52
320 323 1.734465 CTCTTACGAAGCAAGGCAAGG 59.266 52.381 0.00 0.00 0.00 3.61
321 324 0.169009 CTTACGAAGCAAGGCAAGGC 59.831 55.000 0.00 0.00 0.00 4.35
368 371 3.545703 CCAAGCTGAAGGAACGGATATT 58.454 45.455 0.00 0.00 0.00 1.28
418 421 2.100584 CTCAGAGGGGAAAGATGTCTCG 59.899 54.545 0.00 0.00 0.00 4.04
426 429 0.173708 AAAGATGTCTCGGGTCTCGC 59.826 55.000 0.00 0.00 39.05 5.03
474 478 0.468226 GTGGTGAGGTTCCAGTCACA 59.532 55.000 11.48 0.00 44.17 3.58
516 520 2.279120 GCATCCAGCCTCGTCTCG 60.279 66.667 0.00 0.00 37.23 4.04
519 523 2.122167 ATCCAGCCTCGTCTCGGTC 61.122 63.158 0.00 0.00 0.00 4.79
533 537 3.673484 GGTCCCGTTCGTGTCCGA 61.673 66.667 0.00 0.00 42.41 4.55
568 572 4.687948 AGTTGAACATCGATCTGTCAACAG 59.312 41.667 29.13 3.69 45.08 3.16
737 913 0.598419 TCTGCACAGTTGAGTGAGCG 60.598 55.000 0.00 0.72 42.05 5.03
761 937 2.686118 GCTTCCAAGGCATCAGATTCCT 60.686 50.000 0.00 0.00 0.00 3.36
776 952 1.929806 TTCCTGATCGGACGGTCGTG 61.930 60.000 2.08 0.00 42.97 4.35
802 978 3.348236 GCCAAGCGCCATATGAGG 58.652 61.111 2.29 0.00 0.00 3.86
934 1131 2.787249 CTGGCCTTCATTGTCGCG 59.213 61.111 3.32 0.00 0.00 5.87
955 1152 1.394151 CACCTCCCTCTCCCCTCTT 59.606 63.158 0.00 0.00 0.00 2.85
969 1169 1.437160 CTCTTCTCTCCTCCAGCGC 59.563 63.158 0.00 0.00 0.00 5.92
970 1170 2.103934 CTTCTCTCCTCCAGCGCG 59.896 66.667 0.00 0.00 0.00 6.86
971 1171 4.135153 TTCTCTCCTCCAGCGCGC 62.135 66.667 26.66 26.66 0.00 6.86
1252 1452 1.511305 CACATCGTCCACCGCTAGT 59.489 57.895 0.00 0.00 36.19 2.57
1257 1457 3.450115 GTCCACCGCTAGTCCGCT 61.450 66.667 0.00 0.00 0.00 5.52
1430 1660 3.838271 GGCTCATCAGGCGGACGA 61.838 66.667 0.00 0.00 35.07 4.20
1547 1801 2.658285 TCATCATGCATGGGTCCTTTC 58.342 47.619 25.97 0.00 32.64 2.62
1585 1839 2.861147 TCCTGTTGTCGAGAGAGAGA 57.139 50.000 0.00 0.00 43.49 3.10
1587 1841 2.303311 TCCTGTTGTCGAGAGAGAGAGA 59.697 50.000 0.00 0.00 43.49 3.10
1588 1842 2.677836 CCTGTTGTCGAGAGAGAGAGAG 59.322 54.545 0.00 0.00 43.49 3.20
1589 1843 3.595173 CTGTTGTCGAGAGAGAGAGAGA 58.405 50.000 0.00 0.00 43.49 3.10
1590 1844 3.595173 TGTTGTCGAGAGAGAGAGAGAG 58.405 50.000 0.00 0.00 43.49 3.20
1591 1845 2.936498 GTTGTCGAGAGAGAGAGAGAGG 59.064 54.545 0.00 0.00 43.49 3.69
1592 1846 2.462723 TGTCGAGAGAGAGAGAGAGGA 58.537 52.381 0.00 0.00 43.49 3.71
1593 1847 2.430694 TGTCGAGAGAGAGAGAGAGGAG 59.569 54.545 0.00 0.00 43.49 3.69
1594 1848 2.039418 TCGAGAGAGAGAGAGAGGAGG 58.961 57.143 0.00 0.00 34.84 4.30
1595 1849 1.070758 CGAGAGAGAGAGAGAGGAGGG 59.929 61.905 0.00 0.00 0.00 4.30
1596 1850 1.421646 GAGAGAGAGAGAGAGGAGGGG 59.578 61.905 0.00 0.00 0.00 4.79
1597 1851 0.478507 GAGAGAGAGAGAGGAGGGGG 59.521 65.000 0.00 0.00 0.00 5.40
1653 1915 1.289276 CCATCAATCATCACACGCGA 58.711 50.000 15.93 0.00 0.00 5.87
1682 1944 7.173907 CCTTTCTTTCTGCTTCAGTTTCAGATA 59.826 37.037 0.00 0.00 36.81 1.98
1683 1945 7.664082 TTCTTTCTGCTTCAGTTTCAGATAG 57.336 36.000 0.00 0.00 36.81 2.08
1712 1974 3.370366 CGTGAGATTCCTTTCTGCTTCAG 59.630 47.826 0.00 0.00 0.00 3.02
1741 2007 3.221964 GCTTCTGCAAAACATACCTGG 57.778 47.619 0.00 0.00 39.41 4.45
1866 2168 2.202932 CGCTCCAGAATCACGGGG 60.203 66.667 0.00 0.00 34.65 5.73
1868 2170 2.989639 CTCCAGAATCACGGGGCA 59.010 61.111 0.00 0.00 34.65 5.36
1869 2171 1.528824 CTCCAGAATCACGGGGCAT 59.471 57.895 0.00 0.00 34.65 4.40
1870 2172 0.816825 CTCCAGAATCACGGGGCATG 60.817 60.000 0.00 0.00 34.65 4.06
1871 2173 1.224315 CCAGAATCACGGGGCATGA 59.776 57.895 0.00 0.00 0.00 3.07
1872 2174 0.816825 CCAGAATCACGGGGCATGAG 60.817 60.000 0.00 0.00 0.00 2.90
1873 2175 1.153086 AGAATCACGGGGCATGAGC 60.153 57.895 0.00 0.00 41.10 4.26
1874 2176 1.451927 GAATCACGGGGCATGAGCA 60.452 57.895 0.00 0.00 44.61 4.26
1875 2177 1.001020 AATCACGGGGCATGAGCAA 60.001 52.632 0.00 0.00 44.61 3.91
1876 2178 1.033746 AATCACGGGGCATGAGCAAG 61.034 55.000 0.00 0.00 44.61 4.01
1877 2179 3.818787 CACGGGGCATGAGCAAGC 61.819 66.667 0.00 0.00 44.61 4.01
1878 2180 4.039092 ACGGGGCATGAGCAAGCT 62.039 61.111 0.00 0.00 44.61 3.74
1901 2203 1.822186 GAAACCCTGTGGCACGTGT 60.822 57.895 18.38 6.91 33.59 4.49
1902 2204 2.058829 GAAACCCTGTGGCACGTGTG 62.059 60.000 18.38 3.99 33.59 3.82
1904 2206 4.248842 CCCTGTGGCACGTGTGGA 62.249 66.667 18.38 0.00 0.00 4.02
1905 2207 2.972505 CCTGTGGCACGTGTGGAC 60.973 66.667 18.38 11.60 0.00 4.02
1906 2208 2.203001 CTGTGGCACGTGTGGACA 60.203 61.111 18.38 15.37 0.00 4.02
1907 2209 1.817520 CTGTGGCACGTGTGGACAA 60.818 57.895 18.38 0.00 0.00 3.18
1908 2210 2.047151 CTGTGGCACGTGTGGACAAC 62.047 60.000 18.38 4.42 0.00 3.32
1909 2211 2.515057 TGGCACGTGTGGACAACC 60.515 61.111 18.38 8.29 0.00 3.77
1910 2212 2.203153 GGCACGTGTGGACAACCT 60.203 61.111 18.38 0.00 37.04 3.50
1911 2213 2.542907 GGCACGTGTGGACAACCTG 61.543 63.158 18.38 0.00 37.04 4.00
1912 2214 1.817941 GCACGTGTGGACAACCTGT 60.818 57.895 18.38 0.00 37.04 4.00
1953 2255 2.738521 CGCTGGTCCCAGTCAACG 60.739 66.667 14.56 6.02 45.24 4.10
1954 2256 3.050275 GCTGGTCCCAGTCAACGC 61.050 66.667 14.56 0.00 45.24 4.84
1955 2257 2.738521 CTGGTCCCAGTCAACGCG 60.739 66.667 3.53 3.53 39.10 6.01
1956 2258 4.980805 TGGTCCCAGTCAACGCGC 62.981 66.667 5.73 0.00 0.00 6.86
1961 2263 4.025401 CCAGTCAACGCGCCCAAC 62.025 66.667 5.73 0.00 0.00 3.77
2015 2317 1.967535 CCGTCAGAGGCTCAGAACA 59.032 57.895 18.26 0.00 0.00 3.18
2017 2329 1.638133 CGTCAGAGGCTCAGAACATG 58.362 55.000 18.26 5.01 0.00 3.21
2031 2343 2.584418 CATGCCTGCGGACGAGAG 60.584 66.667 0.00 0.00 0.00 3.20
2035 2347 3.068691 CCTGCGGACGAGAGGGAA 61.069 66.667 0.00 0.00 0.00 3.97
2036 2348 2.646175 CCTGCGGACGAGAGGGAAA 61.646 63.158 0.00 0.00 0.00 3.13
2194 2507 2.559026 GGGTATCGATCCCCATACCTCA 60.559 54.545 20.60 0.00 42.97 3.86
2195 2508 2.496470 GGTATCGATCCCCATACCTCAC 59.504 54.545 0.00 0.00 41.00 3.51
2196 2509 1.645710 ATCGATCCCCATACCTCACC 58.354 55.000 0.00 0.00 0.00 4.02
2197 2510 0.561184 TCGATCCCCATACCTCACCT 59.439 55.000 0.00 0.00 0.00 4.00
2198 2511 0.969894 CGATCCCCATACCTCACCTC 59.030 60.000 0.00 0.00 0.00 3.85
2242 2555 2.053244 CCATCTGAGCTACATCCCCTT 58.947 52.381 0.00 0.00 0.00 3.95
2243 2556 2.224475 CCATCTGAGCTACATCCCCTTG 60.224 54.545 0.00 0.00 0.00 3.61
2244 2557 0.833287 TCTGAGCTACATCCCCTTGC 59.167 55.000 0.00 0.00 0.00 4.01
2245 2558 0.835941 CTGAGCTACATCCCCTTGCT 59.164 55.000 0.00 0.00 36.63 3.91
2246 2559 0.543277 TGAGCTACATCCCCTTGCTG 59.457 55.000 0.00 0.00 33.83 4.41
2247 2560 0.543749 GAGCTACATCCCCTTGCTGT 59.456 55.000 0.00 0.00 33.83 4.40
2248 2561 1.762957 GAGCTACATCCCCTTGCTGTA 59.237 52.381 0.00 0.00 33.83 2.74
2249 2562 2.170607 GAGCTACATCCCCTTGCTGTAA 59.829 50.000 0.00 0.00 33.83 2.41
2250 2563 2.092914 AGCTACATCCCCTTGCTGTAAC 60.093 50.000 0.00 0.00 32.32 2.50
2251 2564 2.550978 CTACATCCCCTTGCTGTAACG 58.449 52.381 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 7.894753 CGCAGAAAAGAAAAAGAAAACTGAAAG 59.105 33.333 0.00 0.00 42.29 2.62
4 5 6.310224 CCGCAGAAAAGAAAAAGAAAACTGAA 59.690 34.615 0.00 0.00 0.00 3.02
5 6 5.804979 CCGCAGAAAAGAAAAAGAAAACTGA 59.195 36.000 0.00 0.00 0.00 3.41
6 7 5.005682 CCCGCAGAAAAGAAAAAGAAAACTG 59.994 40.000 0.00 0.00 0.00 3.16
7 8 5.105513 TCCCGCAGAAAAGAAAAAGAAAACT 60.106 36.000 0.00 0.00 0.00 2.66
8 9 5.106442 TCCCGCAGAAAAGAAAAAGAAAAC 58.894 37.500 0.00 0.00 0.00 2.43
9 10 5.331876 TCCCGCAGAAAAGAAAAAGAAAA 57.668 34.783 0.00 0.00 0.00 2.29
10 11 4.993029 TCCCGCAGAAAAGAAAAAGAAA 57.007 36.364 0.00 0.00 0.00 2.52
11 12 4.401202 AGTTCCCGCAGAAAAGAAAAAGAA 59.599 37.500 0.00 0.00 35.85 2.52
12 13 3.951680 AGTTCCCGCAGAAAAGAAAAAGA 59.048 39.130 0.00 0.00 35.85 2.52
13 14 4.307443 AGTTCCCGCAGAAAAGAAAAAG 57.693 40.909 0.00 0.00 35.85 2.27
14 15 4.729227 AAGTTCCCGCAGAAAAGAAAAA 57.271 36.364 0.00 0.00 35.85 1.94
15 16 4.158764 TGAAAGTTCCCGCAGAAAAGAAAA 59.841 37.500 0.00 0.00 35.85 2.29
16 17 3.697045 TGAAAGTTCCCGCAGAAAAGAAA 59.303 39.130 0.00 0.00 35.85 2.52
17 18 3.283751 TGAAAGTTCCCGCAGAAAAGAA 58.716 40.909 0.00 0.00 35.85 2.52
18 19 2.925724 TGAAAGTTCCCGCAGAAAAGA 58.074 42.857 0.00 0.00 35.85 2.52
19 20 3.923017 ATGAAAGTTCCCGCAGAAAAG 57.077 42.857 0.00 0.00 35.85 2.27
20 21 4.664150 AAATGAAAGTTCCCGCAGAAAA 57.336 36.364 0.00 0.00 35.85 2.29
21 22 4.664150 AAAATGAAAGTTCCCGCAGAAA 57.336 36.364 0.00 0.00 35.85 2.52
22 23 4.340950 AGAAAAATGAAAGTTCCCGCAGAA 59.659 37.500 0.00 0.00 0.00 3.02
23 24 3.888930 AGAAAAATGAAAGTTCCCGCAGA 59.111 39.130 0.00 0.00 0.00 4.26
24 25 4.243007 AGAAAAATGAAAGTTCCCGCAG 57.757 40.909 0.00 0.00 0.00 5.18
25 26 4.664150 AAGAAAAATGAAAGTTCCCGCA 57.336 36.364 0.00 0.00 0.00 5.69
26 27 5.753438 AGAAAAGAAAAATGAAAGTTCCCGC 59.247 36.000 0.00 0.00 0.00 6.13
27 28 7.770801 AAGAAAAGAAAAATGAAAGTTCCCG 57.229 32.000 0.00 0.00 0.00 5.14
71 72 8.320338 ACTGGGTAAGATATTGCTAGTAAACT 57.680 34.615 0.00 0.00 0.00 2.66
120 122 1.748493 TCGCAAACCCTTTATGATGCC 59.252 47.619 0.00 0.00 0.00 4.40
121 123 2.423538 AGTCGCAAACCCTTTATGATGC 59.576 45.455 0.00 0.00 0.00 3.91
122 124 3.181497 CCAGTCGCAAACCCTTTATGATG 60.181 47.826 0.00 0.00 0.00 3.07
123 125 3.016736 CCAGTCGCAAACCCTTTATGAT 58.983 45.455 0.00 0.00 0.00 2.45
124 126 2.432444 CCAGTCGCAAACCCTTTATGA 58.568 47.619 0.00 0.00 0.00 2.15
125 127 1.135402 GCCAGTCGCAAACCCTTTATG 60.135 52.381 0.00 0.00 37.47 1.90
126 128 1.173913 GCCAGTCGCAAACCCTTTAT 58.826 50.000 0.00 0.00 37.47 1.40
139 141 0.033208 TGGGAATTGGGATGCCAGTC 60.033 55.000 5.91 8.22 32.87 3.51
151 153 1.678970 GCAGACGGGCTTGGGAATT 60.679 57.895 0.00 0.00 0.00 2.17
152 154 2.044946 GCAGACGGGCTTGGGAAT 60.045 61.111 0.00 0.00 0.00 3.01
153 155 2.819984 GATGCAGACGGGCTTGGGAA 62.820 60.000 0.00 0.00 34.04 3.97
154 156 3.329542 GATGCAGACGGGCTTGGGA 62.330 63.158 0.00 0.00 34.04 4.37
155 157 2.825836 GATGCAGACGGGCTTGGG 60.826 66.667 0.00 0.00 34.04 4.12
156 158 2.046023 TGATGCAGACGGGCTTGG 60.046 61.111 0.00 0.00 34.04 3.61
157 159 2.110967 CCTGATGCAGACGGGCTTG 61.111 63.158 8.32 0.00 32.44 4.01
198 200 7.721402 AGATATGTATTCTCTTCTTTCGTGCT 58.279 34.615 0.00 0.00 0.00 4.40
217 219 7.396907 AGAGAGAGAGAGAGAGAGAGAGATATG 59.603 44.444 0.00 0.00 0.00 1.78
225 227 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
230 232 5.867903 AGAGAAGAGAGAGAGAGAGAGAG 57.132 47.826 0.00 0.00 0.00 3.20
231 233 6.627087 AAAGAGAAGAGAGAGAGAGAGAGA 57.373 41.667 0.00 0.00 0.00 3.10
232 234 7.693969 AAAAAGAGAAGAGAGAGAGAGAGAG 57.306 40.000 0.00 0.00 0.00 3.20
233 235 9.753674 AATAAAAAGAGAAGAGAGAGAGAGAGA 57.246 33.333 0.00 0.00 0.00 3.10
258 260 9.211485 GGTGTTGCTTTATTGTCTAACTAGTAA 57.789 33.333 0.00 0.00 0.00 2.24
259 261 7.820872 GGGTGTTGCTTTATTGTCTAACTAGTA 59.179 37.037 0.00 0.00 0.00 1.82
260 262 6.653740 GGGTGTTGCTTTATTGTCTAACTAGT 59.346 38.462 0.00 0.00 0.00 2.57
261 263 6.879458 AGGGTGTTGCTTTATTGTCTAACTAG 59.121 38.462 0.00 0.00 0.00 2.57
262 264 6.775708 AGGGTGTTGCTTTATTGTCTAACTA 58.224 36.000 0.00 0.00 0.00 2.24
263 265 5.631119 AGGGTGTTGCTTTATTGTCTAACT 58.369 37.500 0.00 0.00 0.00 2.24
264 266 5.959618 AGGGTGTTGCTTTATTGTCTAAC 57.040 39.130 0.00 0.00 0.00 2.34
318 321 4.406456 TGAAAAGGAACACATGTATGCCT 58.594 39.130 0.00 0.00 0.00 4.75
320 323 5.973565 GCTATGAAAAGGAACACATGTATGC 59.026 40.000 0.00 0.00 0.00 3.14
321 324 6.498304 GGCTATGAAAAGGAACACATGTATG 58.502 40.000 0.00 0.00 0.00 2.39
368 371 0.961019 AAAGGCTGCTTGCGAAATGA 59.039 45.000 0.00 0.00 44.05 2.57
426 429 4.697756 TGGTGGAGCCGAAAGCCG 62.698 66.667 0.00 0.00 45.47 5.52
502 506 2.750637 GACCGAGACGAGGCTGGA 60.751 66.667 2.65 0.00 0.00 3.86
533 537 1.135527 TGTTCAACTTGTCCTCGTCGT 59.864 47.619 0.00 0.00 0.00 4.34
681 853 3.191669 CCTTTCCGCGTCACATTGTATA 58.808 45.455 4.92 0.00 0.00 1.47
682 854 2.006888 CCTTTCCGCGTCACATTGTAT 58.993 47.619 4.92 0.00 0.00 2.29
683 855 1.270412 ACCTTTCCGCGTCACATTGTA 60.270 47.619 4.92 0.00 0.00 2.41
684 856 0.534203 ACCTTTCCGCGTCACATTGT 60.534 50.000 4.92 0.00 0.00 2.71
686 858 2.396590 ATACCTTTCCGCGTCACATT 57.603 45.000 4.92 0.00 0.00 2.71
737 913 0.679002 TCTGATGCCTTGGAAGCAGC 60.679 55.000 7.99 0.00 46.58 5.25
761 937 2.360225 TCCACGACCGTCCGATCA 60.360 61.111 0.00 0.00 0.00 2.92
802 978 2.336809 CTATGCTCGGGACCTCGC 59.663 66.667 0.00 0.00 0.00 5.03
950 1147 2.015227 GCGCTGGAGGAGAGAAGAGG 62.015 65.000 0.00 0.00 0.00 3.69
980 1180 2.477845 CTTGCTTTGCTCCGCGAG 59.522 61.111 8.23 4.18 0.00 5.03
981 1181 3.049674 CCTTGCTTTGCTCCGCGA 61.050 61.111 8.23 0.00 0.00 5.87
982 1182 4.107051 CCCTTGCTTTGCTCCGCG 62.107 66.667 0.00 0.00 0.00 6.46
983 1183 2.048603 ATCCCTTGCTTTGCTCCGC 61.049 57.895 0.00 0.00 0.00 5.54
984 1184 1.660560 CCATCCCTTGCTTTGCTCCG 61.661 60.000 0.00 0.00 0.00 4.63
1327 1539 3.357079 CACGCAAGGTGGTGGAGC 61.357 66.667 0.00 0.00 43.16 4.70
1335 1547 1.510480 GAAAGAGCAGCACGCAAGGT 61.510 55.000 0.00 0.00 46.13 3.50
1430 1660 3.138930 CTCGCCACCATCGATCGGT 62.139 63.158 16.41 4.70 37.16 4.69
1547 1801 9.508567 CAACAGGAAAACTAGAAAAAGAAGAAG 57.491 33.333 0.00 0.00 0.00 2.85
1567 1821 2.677836 CTCTCTCTCTCTCGACAACAGG 59.322 54.545 0.00 0.00 0.00 4.00
1594 1848 1.544246 CGGAAACAAACATTCTCCCCC 59.456 52.381 0.00 0.00 0.00 5.40
1595 1849 1.544246 CCGGAAACAAACATTCTCCCC 59.456 52.381 0.00 0.00 0.00 4.81
1596 1850 1.544246 CCCGGAAACAAACATTCTCCC 59.456 52.381 0.73 0.00 0.00 4.30
1597 1851 1.544246 CCCCGGAAACAAACATTCTCC 59.456 52.381 0.73 0.00 0.00 3.71
1653 1915 6.322201 TGAAACTGAAGCAGAAAGAAAGGAAT 59.678 34.615 0.82 0.00 35.18 3.01
1682 1944 1.846007 AGGAATCTCACGAGCAGACT 58.154 50.000 0.00 0.00 0.00 3.24
1683 1945 2.663826 AAGGAATCTCACGAGCAGAC 57.336 50.000 0.00 0.00 0.00 3.51
1741 2007 2.806244 AGTATCAAGCGGACACAACAAC 59.194 45.455 0.00 0.00 0.00 3.32
1814 2080 2.094803 TCATTTTCATTCGTGCGCCAAT 60.095 40.909 4.18 0.00 0.00 3.16
1866 2168 1.300971 TTCACCGAGCTTGCTCATGC 61.301 55.000 20.59 0.09 40.20 4.06
1868 2170 1.160137 GTTTCACCGAGCTTGCTCAT 58.840 50.000 20.59 6.95 0.00 2.90
1869 2171 0.884704 GGTTTCACCGAGCTTGCTCA 60.885 55.000 20.59 0.30 0.00 4.26
1870 2172 1.578206 GGGTTTCACCGAGCTTGCTC 61.578 60.000 12.20 12.20 39.83 4.26
1871 2173 1.600916 GGGTTTCACCGAGCTTGCT 60.601 57.895 0.00 0.00 39.83 3.91
1872 2174 1.600916 AGGGTTTCACCGAGCTTGC 60.601 57.895 0.00 0.00 39.83 4.01
1873 2175 0.535102 ACAGGGTTTCACCGAGCTTG 60.535 55.000 0.00 0.00 39.83 4.01
1874 2176 0.535102 CACAGGGTTTCACCGAGCTT 60.535 55.000 0.00 0.00 39.83 3.74
1875 2177 1.071471 CACAGGGTTTCACCGAGCT 59.929 57.895 0.00 0.00 39.83 4.09
1876 2178 1.966451 CCACAGGGTTTCACCGAGC 60.966 63.158 0.00 0.00 39.83 5.03
1877 2179 1.966451 GCCACAGGGTTTCACCGAG 60.966 63.158 0.00 0.00 39.83 4.63
1878 2180 2.112297 GCCACAGGGTTTCACCGA 59.888 61.111 0.00 0.00 39.83 4.69
1901 2203 2.203280 CGGCCAACAGGTTGTCCA 60.203 61.111 12.16 0.00 38.42 4.02
1902 2204 3.670377 GCGGCCAACAGGTTGTCC 61.670 66.667 2.24 6.78 38.85 4.02
1905 2207 4.974721 AGGGCGGCCAACAGGTTG 62.975 66.667 31.59 5.19 40.13 3.77
1906 2208 4.974721 CAGGGCGGCCAACAGGTT 62.975 66.667 31.59 3.91 0.00 3.50
1953 2255 3.670377 GGACAACCTGTTGGGCGC 61.670 66.667 14.05 0.00 44.45 6.53
1954 2256 2.203280 TGGACAACCTGTTGGGCG 60.203 61.111 14.05 0.00 44.45 6.13
1955 2257 1.454847 TGTGGACAACCTGTTGGGC 60.455 57.895 14.05 5.92 44.45 5.36
1956 2258 1.444119 CGTGTGGACAACCTGTTGGG 61.444 60.000 14.05 0.00 44.45 4.12
1957 2259 1.444119 CCGTGTGGACAACCTGTTGG 61.444 60.000 14.05 0.00 44.45 3.77
1958 2260 1.444119 CCCGTGTGGACAACCTGTTG 61.444 60.000 8.42 8.42 45.58 3.33
1959 2261 1.153046 CCCGTGTGGACAACCTGTT 60.153 57.895 0.00 0.00 37.49 3.16
1960 2262 2.508928 CCCGTGTGGACAACCTGT 59.491 61.111 0.00 0.00 37.49 4.00
1961 2263 2.978010 GCCCGTGTGGACAACCTG 60.978 66.667 0.00 0.00 37.49 4.00
2042 2354 3.117131 TGTGAGGGGATGTAGCTCAGATA 60.117 47.826 0.00 0.00 0.00 1.98
2148 2461 9.354673 CCCACTTCTCCAATATGTATTATTTGT 57.645 33.333 0.00 0.00 0.00 2.83
2149 2462 8.796475 CCCCACTTCTCCAATATGTATTATTTG 58.204 37.037 0.00 0.00 0.00 2.32
2150 2463 8.511126 ACCCCACTTCTCCAATATGTATTATTT 58.489 33.333 0.00 0.00 0.00 1.40
2151 2464 8.057246 ACCCCACTTCTCCAATATGTATTATT 57.943 34.615 0.00 0.00 0.00 1.40
2152 2465 7.648177 ACCCCACTTCTCCAATATGTATTAT 57.352 36.000 0.00 0.00 0.00 1.28
2153 2466 8.751215 ATACCCCACTTCTCCAATATGTATTA 57.249 34.615 0.00 0.00 0.00 0.98
2154 2467 5.994416 ACCCCACTTCTCCAATATGTATT 57.006 39.130 0.00 0.00 0.00 1.89
2155 2468 6.070767 CGATACCCCACTTCTCCAATATGTAT 60.071 42.308 0.00 0.00 0.00 2.29
2156 2469 5.245301 CGATACCCCACTTCTCCAATATGTA 59.755 44.000 0.00 0.00 0.00 2.29
2157 2470 4.040461 CGATACCCCACTTCTCCAATATGT 59.960 45.833 0.00 0.00 0.00 2.29
2158 2471 4.283467 TCGATACCCCACTTCTCCAATATG 59.717 45.833 0.00 0.00 0.00 1.78
2159 2472 4.489737 TCGATACCCCACTTCTCCAATAT 58.510 43.478 0.00 0.00 0.00 1.28
2160 2473 3.918566 TCGATACCCCACTTCTCCAATA 58.081 45.455 0.00 0.00 0.00 1.90
2194 2507 4.844420 GCTTAGCATGCGAGAGGT 57.156 55.556 22.95 4.38 0.00 3.85


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

AutoCloner maintained by Alex Coulton.