Multiple sequence alignment - TraesCS7D01G506700

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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 TraesCS7D01G506700 chr7D 100.000 1183 0 0 938 2120 611331771 611332953 0.000000e+00 2185.0
1 TraesCS7D01G506700 chr7D 100.000 426 0 0 1 426 611330834 611331259 0.000000e+00 787.0
2 TraesCS7D01G506700 chr7D 87.821 156 19 0 972 1127 611294549 611294704 1.290000e-42 183.0
3 TraesCS7D01G506700 chr7D 83.974 156 8 10 1 155 611294134 611294273 1.320000e-27 134.0
4 TraesCS7D01G506700 chr7D 91.667 60 4 1 2053 2111 249770 249829 4.850000e-12 82.4
5 TraesCS7D01G506700 chr7B 83.709 798 58 37 958 1720 700551409 700552169 0.000000e+00 688.0
6 TraesCS7D01G506700 chr7B 89.583 432 21 10 1 426 700551001 700551414 5.180000e-146 527.0
7 TraesCS7D01G506700 chr7B 87.730 163 20 0 970 1132 700439974 700440136 7.720000e-45 191.0
8 TraesCS7D01G506700 chr7A 86.525 423 32 16 2 414 701390897 701391304 1.930000e-120 442.0
9 TraesCS7D01G506700 chr7A 84.254 362 21 13 962 1307 701391319 701391660 9.440000e-84 320.0
10 TraesCS7D01G506700 chr7A 79.318 440 47 22 1 410 701360163 701360588 3.470000e-68 268.0
11 TraesCS7D01G506700 chr7A 81.279 219 23 12 1916 2120 701392354 701392568 6.050000e-36 161.0
12 TraesCS7D01G506700 chr3D 91.549 71 4 2 2049 2118 580430709 580430640 1.730000e-16 97.1
13 TraesCS7D01G506700 chr3D 86.585 82 8 3 2039 2120 11436199 11436277 1.040000e-13 87.9
14 TraesCS7D01G506700 chr3D 78.000 150 21 7 1966 2109 123774725 123774868 1.350000e-12 84.2
15 TraesCS7D01G506700 chr4D 90.909 66 5 1 2054 2119 509834644 509834708 1.040000e-13 87.9
16 TraesCS7D01G506700 chr1D 84.783 92 8 6 1054 1143 452762517 452762430 1.040000e-13 87.9
17 TraesCS7D01G506700 chr1D 84.783 92 8 6 1054 1143 452858223 452858136 1.040000e-13 87.9
18 TraesCS7D01G506700 chr3B 88.732 71 4 3 2049 2118 160391780 160391847 1.350000e-12 84.2
19 TraesCS7D01G506700 chr1B 94.545 55 1 2 1054 1106 623224817 623224763 1.350000e-12 84.2
20 TraesCS7D01G506700 chr1B 95.833 48 2 0 1054 1101 623317865 623317912 6.270000e-11 78.7
21 TraesCS7D01G506700 chr3A 76.064 188 28 12 1940 2120 687531104 687530927 4.850000e-12 82.4
22 TraesCS7D01G506700 chr1A 85.185 81 6 6 1054 1132 547591994 547591918 6.270000e-11 78.7
23 TraesCS7D01G506700 chr6D 89.286 56 6 0 2060 2115 42477431 42477486 1.050000e-08 71.3


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 TraesCS7D01G506700 chr7D 611330834 611332953 2119 False 1486.000000 2185 100.000000 1 2120 2 chr7D.!!$F3 2119
1 TraesCS7D01G506700 chr7B 700551001 700552169 1168 False 607.500000 688 86.646000 1 1720 2 chr7B.!!$F2 1719
2 TraesCS7D01G506700 chr7A 701390897 701392568 1671 False 307.666667 442 84.019333 2 2120 3 chr7A.!!$F2 2118

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
252 266 0.250513 ATCTCCTTCACGGCTTCACC 59.749 55.0 0.0 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1898 2136 0.108138 GCGTATCTGTGGGCTTCTGT 60.108 55.0 0.0 0.0 0.0 3.41 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
205 217 2.217112 GCTCGCTCGCGTTATCAAT 58.783 52.632 5.77 0.00 40.74 2.57
216 230 2.544267 GCGTTATCAATTCTAAGCCGCT 59.456 45.455 0.00 0.00 36.03 5.52
233 247 1.335964 CGCTGTCGTCTTCTTCCTTCA 60.336 52.381 0.00 0.00 0.00 3.02
234 248 2.672478 CGCTGTCGTCTTCTTCCTTCAT 60.672 50.000 0.00 0.00 0.00 2.57
236 250 3.367910 GCTGTCGTCTTCTTCCTTCATCT 60.368 47.826 0.00 0.00 0.00 2.90
237 251 4.420168 CTGTCGTCTTCTTCCTTCATCTC 58.580 47.826 0.00 0.00 0.00 2.75
241 255 4.158764 TCGTCTTCTTCCTTCATCTCCTTC 59.841 45.833 0.00 0.00 0.00 3.46
242 256 4.081972 CGTCTTCTTCCTTCATCTCCTTCA 60.082 45.833 0.00 0.00 0.00 3.02
243 257 5.175127 GTCTTCTTCCTTCATCTCCTTCAC 58.825 45.833 0.00 0.00 0.00 3.18
244 258 3.876274 TCTTCCTTCATCTCCTTCACG 57.124 47.619 0.00 0.00 0.00 4.35
245 259 2.497675 TCTTCCTTCATCTCCTTCACGG 59.502 50.000 0.00 0.00 0.00 4.94
247 261 0.539051 CCTTCATCTCCTTCACGGCT 59.461 55.000 0.00 0.00 0.00 5.52
249 263 2.275318 CTTCATCTCCTTCACGGCTTC 58.725 52.381 0.00 0.00 0.00 3.86
250 264 1.266178 TCATCTCCTTCACGGCTTCA 58.734 50.000 0.00 0.00 0.00 3.02
251 265 1.066858 TCATCTCCTTCACGGCTTCAC 60.067 52.381 0.00 0.00 0.00 3.18
252 266 0.250513 ATCTCCTTCACGGCTTCACC 59.749 55.000 0.00 0.00 0.00 4.02
254 268 2.359975 CCTTCACGGCTTCACCCC 60.360 66.667 0.00 0.00 33.26 4.95
255 269 2.750350 CTTCACGGCTTCACCCCT 59.250 61.111 0.00 0.00 33.26 4.79
256 270 1.550130 CCTTCACGGCTTCACCCCTA 61.550 60.000 0.00 0.00 33.26 3.53
277 291 1.174783 CACCTACCTAGCTCGTGTGT 58.825 55.000 0.00 0.00 0.00 3.72
300 314 3.261390 GCCATCTGGATCTGAATCTAGCT 59.739 47.826 0.00 0.00 39.63 3.32
342 360 4.760047 CCCACCCGTTGCCGAGAG 62.760 72.222 0.00 0.00 35.63 3.20
361 379 5.289083 AGAGGAAATCATTAGCCAGAGTC 57.711 43.478 0.00 0.00 0.00 3.36
385 403 1.604278 GTTCAGCAACACTCCTTCACC 59.396 52.381 0.00 0.00 32.14 4.02
397 415 0.859232 CCTTCACCACACTTCGTTCG 59.141 55.000 0.00 0.00 0.00 3.95
406 424 1.217882 CACTTCGTTCGCTTCCAACT 58.782 50.000 0.00 0.00 0.00 3.16
959 985 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
960 986 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
961 987 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
962 988 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
981 1007 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
983 1009 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
985 1011 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
989 1015 3.708631 AGAGAGAGAGAGAGAGAGAGTGG 59.291 52.174 0.00 0.00 0.00 4.00
1150 1188 1.817357 CATGGATGGATGGACGGATG 58.183 55.000 0.00 0.00 0.00 3.51
1151 1189 0.694771 ATGGATGGATGGACGGATGG 59.305 55.000 0.00 0.00 0.00 3.51
1152 1190 1.302832 GGATGGATGGACGGATGGC 60.303 63.158 0.00 0.00 0.00 4.40
1189 1227 3.581755 CATGGATGGTGTTTGAAGCAAG 58.418 45.455 0.00 0.00 0.00 4.01
1190 1228 1.340889 TGGATGGTGTTTGAAGCAAGC 59.659 47.619 0.00 0.00 0.00 4.01
1191 1229 1.340889 GGATGGTGTTTGAAGCAAGCA 59.659 47.619 0.00 0.00 32.55 3.91
1192 1230 2.224018 GGATGGTGTTTGAAGCAAGCAA 60.224 45.455 0.00 0.00 36.44 3.91
1193 1231 2.582728 TGGTGTTTGAAGCAAGCAAG 57.417 45.000 0.00 0.00 36.44 4.01
1222 1260 6.405278 ACTTTTTGATTTTGGGTCTGTAGG 57.595 37.500 0.00 0.00 0.00 3.18
1223 1261 6.133356 ACTTTTTGATTTTGGGTCTGTAGGA 58.867 36.000 0.00 0.00 0.00 2.94
1224 1262 6.609616 ACTTTTTGATTTTGGGTCTGTAGGAA 59.390 34.615 0.00 0.00 0.00 3.36
1225 1263 6.648879 TTTTGATTTTGGGTCTGTAGGAAG 57.351 37.500 0.00 0.00 0.00 3.46
1227 1265 3.913799 TGATTTTGGGTCTGTAGGAAGGA 59.086 43.478 0.00 0.00 0.00 3.36
1228 1266 4.352595 TGATTTTGGGTCTGTAGGAAGGAA 59.647 41.667 0.00 0.00 0.00 3.36
1230 1268 1.952621 TGGGTCTGTAGGAAGGAAGG 58.047 55.000 0.00 0.00 0.00 3.46
1231 1269 1.151413 TGGGTCTGTAGGAAGGAAGGT 59.849 52.381 0.00 0.00 0.00 3.50
1232 1270 1.555533 GGGTCTGTAGGAAGGAAGGTG 59.444 57.143 0.00 0.00 0.00 4.00
1233 1271 2.258109 GGTCTGTAGGAAGGAAGGTGT 58.742 52.381 0.00 0.00 0.00 4.16
1236 1274 3.087031 TCTGTAGGAAGGAAGGTGTACG 58.913 50.000 0.00 0.00 0.00 3.67
1237 1275 1.547372 TGTAGGAAGGAAGGTGTACGC 59.453 52.381 0.00 0.00 0.00 4.42
1238 1276 1.547372 GTAGGAAGGAAGGTGTACGCA 59.453 52.381 8.97 0.00 0.00 5.24
1239 1277 0.320697 AGGAAGGAAGGTGTACGCAC 59.679 55.000 8.97 0.00 44.53 5.34
1240 1278 0.320697 GGAAGGAAGGTGTACGCACT 59.679 55.000 8.97 0.14 44.65 4.40
1241 1279 1.672145 GGAAGGAAGGTGTACGCACTC 60.672 57.143 8.97 3.72 44.65 3.51
1246 1288 2.049433 GGTGTACGCACTCGCAGT 60.049 61.111 8.97 0.00 44.65 4.40
1273 1315 7.603651 AGTACTTGTACATAAGAGGTCAGTTG 58.396 38.462 12.64 0.00 0.00 3.16
1297 1345 8.698973 TGATTATAGAAGTAGAAGTAGCAGCT 57.301 34.615 0.00 0.00 0.00 4.24
1316 1364 5.393569 GCAGCTAAGCAATAGGATCGATCTA 60.394 44.000 23.96 14.52 31.83 1.98
1322 1370 5.777802 AGCAATAGGATCGATCTAGTGTTG 58.222 41.667 23.96 20.78 35.84 3.33
1325 1373 6.516718 CAATAGGATCGATCTAGTGTTGGTT 58.483 40.000 23.96 5.08 30.85 3.67
1344 1392 2.030027 TGATTCACCACCTCCTCTGT 57.970 50.000 0.00 0.00 0.00 3.41
1349 1397 1.304547 ACCACCTCCTCTGTCCTCG 60.305 63.158 0.00 0.00 0.00 4.63
1395 1448 5.125257 CCATTGTACAATTACATCAGTGCCA 59.875 40.000 18.50 0.00 38.05 4.92
1433 1491 7.880195 GCAATATAGGCTGAAAGAGAAGGAATA 59.120 37.037 0.00 0.00 34.07 1.75
1434 1492 9.784531 CAATATAGGCTGAAAGAGAAGGAATAA 57.215 33.333 0.00 0.00 34.07 1.40
1438 1496 6.355747 AGGCTGAAAGAGAAGGAATAATCAG 58.644 40.000 0.00 0.00 34.07 2.90
1445 1503 6.432403 AGAGAAGGAATAATCAGTGGATCC 57.568 41.667 4.20 4.20 31.88 3.36
1480 1540 0.250252 TCCAAAGCTCGTGTGATGCA 60.250 50.000 0.00 0.00 0.00 3.96
1501 1561 4.245660 CAAGCTGATCTCGGTGTTTCTTA 58.754 43.478 0.00 0.00 0.00 2.10
1503 1563 3.258372 AGCTGATCTCGGTGTTTCTTACA 59.742 43.478 0.00 0.00 0.00 2.41
1598 1702 1.672881 CCATCGTGCTCCAAGAAATCC 59.327 52.381 0.00 0.00 0.00 3.01
1609 1713 2.622436 CAAGAAATCCGAGGAGTCCAC 58.378 52.381 12.86 3.83 0.00 4.02
1612 1716 0.905357 AAATCCGAGGAGTCCACAGG 59.095 55.000 12.86 11.37 0.00 4.00
1616 1720 2.716017 CGAGGAGTCCACAGGGAGC 61.716 68.421 12.86 0.00 46.12 4.70
1617 1721 1.610673 GAGGAGTCCACAGGGAGCA 60.611 63.158 12.86 0.00 46.12 4.26
1618 1722 1.893919 GAGGAGTCCACAGGGAGCAC 61.894 65.000 12.86 0.00 46.12 4.40
1723 1838 3.007920 CCCAGGAGCAGCAGGTCT 61.008 66.667 8.27 0.00 41.89 3.85
1724 1839 2.268280 CCAGGAGCAGCAGGTCTG 59.732 66.667 8.27 4.84 45.62 3.51
1725 1840 2.288778 CCAGGAGCAGCAGGTCTGA 61.289 63.158 8.27 0.00 45.72 3.27
1726 1841 1.675801 CAGGAGCAGCAGGTCTGAA 59.324 57.895 8.27 0.00 45.72 3.02
1727 1842 0.673022 CAGGAGCAGCAGGTCTGAAC 60.673 60.000 8.27 0.00 45.72 3.18
1728 1843 0.835543 AGGAGCAGCAGGTCTGAACT 60.836 55.000 8.27 0.00 45.72 3.01
1730 1845 1.544314 GGAGCAGCAGGTCTGAACTTT 60.544 52.381 8.27 0.00 45.72 2.66
1731 1846 1.534595 GAGCAGCAGGTCTGAACTTTG 59.465 52.381 0.45 0.00 45.72 2.77
1732 1847 1.141657 AGCAGCAGGTCTGAACTTTGA 59.858 47.619 7.88 0.00 45.72 2.69
1733 1848 1.949525 GCAGCAGGTCTGAACTTTGAA 59.050 47.619 7.88 0.00 45.72 2.69
1734 1849 2.031333 GCAGCAGGTCTGAACTTTGAAG 60.031 50.000 7.88 0.00 45.72 3.02
1736 1851 1.069636 GCAGGTCTGAACTTTGAAGCG 60.070 52.381 1.65 0.00 0.00 4.68
1737 1852 1.069636 CAGGTCTGAACTTTGAAGCGC 60.070 52.381 0.00 0.00 0.00 5.92
1738 1853 0.944386 GGTCTGAACTTTGAAGCGCA 59.056 50.000 11.47 0.00 0.00 6.09
1739 1854 1.333619 GGTCTGAACTTTGAAGCGCAA 59.666 47.619 11.47 0.00 33.88 4.85
1741 1856 2.032178 GTCTGAACTTTGAAGCGCAACT 59.968 45.455 11.47 0.00 35.91 3.16
1742 1857 2.287915 TCTGAACTTTGAAGCGCAACTC 59.712 45.455 11.47 3.36 35.91 3.01
1743 1858 1.003972 TGAACTTTGAAGCGCAACTCG 60.004 47.619 11.47 0.00 35.91 4.18
1744 1859 0.307760 AACTTTGAAGCGCAACTCGG 59.692 50.000 11.47 0.00 35.91 4.63
1763 1954 1.918293 TGAACACCCGGATGGCTCT 60.918 57.895 0.73 0.00 37.83 4.09
1834 2034 0.817654 TCAAGACGCTCACGGATGAT 59.182 50.000 0.00 0.00 46.04 2.45
1848 2086 2.338500 GGATGATCCGGCGATCTTAAC 58.662 52.381 9.30 1.95 44.61 2.01
1870 2108 9.918630 TTAACGCTAGTGTCTATTTACTTCTTT 57.081 29.630 9.86 0.00 0.00 2.52
1871 2109 8.828688 AACGCTAGTGTCTATTTACTTCTTTT 57.171 30.769 9.86 0.00 0.00 2.27
1872 2110 8.828688 ACGCTAGTGTCTATTTACTTCTTTTT 57.171 30.769 2.24 0.00 0.00 1.94
1873 2111 8.923683 ACGCTAGTGTCTATTTACTTCTTTTTC 58.076 33.333 2.24 0.00 0.00 2.29
1898 2136 9.231297 TCTTTTCTTTTCTTCTTCTTCAGTTCA 57.769 29.630 0.00 0.00 0.00 3.18
1899 2137 9.283420 CTTTTCTTTTCTTCTTCTTCAGTTCAC 57.717 33.333 0.00 0.00 0.00 3.18
1900 2138 7.921786 TTCTTTTCTTCTTCTTCAGTTCACA 57.078 32.000 0.00 0.00 0.00 3.58
1901 2139 7.545362 TCTTTTCTTCTTCTTCAGTTCACAG 57.455 36.000 0.00 0.00 0.00 3.66
1902 2140 7.331026 TCTTTTCTTCTTCTTCAGTTCACAGA 58.669 34.615 0.00 0.00 0.00 3.41
1903 2141 7.824289 TCTTTTCTTCTTCTTCAGTTCACAGAA 59.176 33.333 0.00 0.00 0.00 3.02
1904 2142 7.545362 TTTCTTCTTCTTCAGTTCACAGAAG 57.455 36.000 5.89 5.89 43.38 2.85
1905 2143 5.053145 TCTTCTTCTTCAGTTCACAGAAGC 58.947 41.667 7.12 0.00 42.25 3.86
1906 2144 3.733337 TCTTCTTCAGTTCACAGAAGCC 58.267 45.455 7.12 0.00 42.25 4.35
1907 2145 2.550830 TCTTCAGTTCACAGAAGCCC 57.449 50.000 7.12 0.00 38.76 5.19
1908 2146 1.768275 TCTTCAGTTCACAGAAGCCCA 59.232 47.619 7.12 0.00 38.76 5.36
1909 2147 1.876156 CTTCAGTTCACAGAAGCCCAC 59.124 52.381 0.00 0.00 33.75 4.61
1910 2148 0.836606 TCAGTTCACAGAAGCCCACA 59.163 50.000 0.00 0.00 0.00 4.17
1911 2149 1.202687 TCAGTTCACAGAAGCCCACAG 60.203 52.381 0.00 0.00 0.00 3.66
1912 2150 1.131638 AGTTCACAGAAGCCCACAGA 58.868 50.000 0.00 0.00 0.00 3.41
1913 2151 1.701847 AGTTCACAGAAGCCCACAGAT 59.298 47.619 0.00 0.00 0.00 2.90
1914 2152 2.906389 AGTTCACAGAAGCCCACAGATA 59.094 45.455 0.00 0.00 0.00 1.98
1926 2164 3.536917 CAGATACGCTGGGCCGGA 61.537 66.667 18.84 0.00 41.07 5.14
1945 2187 2.159037 GGACCATCGTCGAACCTTTTTC 59.841 50.000 0.00 0.00 40.17 2.29
1951 2193 1.529865 CGTCGAACCTTTTTCCCACTC 59.470 52.381 0.00 0.00 0.00 3.51
1960 2202 6.222038 ACCTTTTTCCCACTCTTTCTTTTC 57.778 37.500 0.00 0.00 0.00 2.29
1964 2206 6.699575 TTTTCCCACTCTTTCTTTTCTCAG 57.300 37.500 0.00 0.00 0.00 3.35
2003 2249 8.732531 TCTTTTTCTGTTTTTCCTTCTTCGTTA 58.267 29.630 0.00 0.00 0.00 3.18
2005 2251 5.996669 TCTGTTTTTCCTTCTTCGTTACC 57.003 39.130 0.00 0.00 0.00 2.85
2006 2252 5.430007 TCTGTTTTTCCTTCTTCGTTACCA 58.570 37.500 0.00 0.00 0.00 3.25
2010 2256 7.197703 TGTTTTTCCTTCTTCGTTACCATTTC 58.802 34.615 0.00 0.00 0.00 2.17
2012 2258 4.903045 TCCTTCTTCGTTACCATTTCCT 57.097 40.909 0.00 0.00 0.00 3.36
2015 2261 5.704053 TCCTTCTTCGTTACCATTTCCTTTC 59.296 40.000 0.00 0.00 0.00 2.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 1.248101 GGTGGAAAATGTGTCGGGGG 61.248 60.000 0.00 0.00 0.00 5.40
64 65 2.049985 GTCAGAGAGCGTGCGTGT 60.050 61.111 0.00 0.00 0.00 4.49
193 205 2.792674 CGGCTTAGAATTGATAACGCGA 59.207 45.455 15.93 0.00 0.00 5.87
195 207 2.544267 AGCGGCTTAGAATTGATAACGC 59.456 45.455 0.00 0.00 44.20 4.84
196 208 3.555956 ACAGCGGCTTAGAATTGATAACG 59.444 43.478 0.00 0.00 0.00 3.18
197 209 4.318121 CGACAGCGGCTTAGAATTGATAAC 60.318 45.833 0.00 0.00 0.00 1.89
198 210 3.802139 CGACAGCGGCTTAGAATTGATAA 59.198 43.478 0.00 0.00 0.00 1.75
200 212 2.205074 CGACAGCGGCTTAGAATTGAT 58.795 47.619 0.00 0.00 0.00 2.57
201 213 1.067142 ACGACAGCGGCTTAGAATTGA 60.067 47.619 0.00 0.00 43.17 2.57
202 214 1.324736 GACGACAGCGGCTTAGAATTG 59.675 52.381 0.00 0.00 43.91 2.32
203 215 1.641577 GACGACAGCGGCTTAGAATT 58.358 50.000 0.00 0.00 43.91 2.17
205 217 4.883026 GACGACAGCGGCTTAGAA 57.117 55.556 0.00 0.00 43.91 2.10
216 230 3.193691 GGAGATGAAGGAAGAAGACGACA 59.806 47.826 0.00 0.00 0.00 4.35
233 247 0.250513 GGTGAAGCCGTGAAGGAGAT 59.749 55.000 0.00 0.00 45.00 2.75
234 248 1.671742 GGTGAAGCCGTGAAGGAGA 59.328 57.895 0.00 0.00 45.00 3.71
236 250 2.747686 GGGTGAAGCCGTGAAGGA 59.252 61.111 0.00 0.00 45.00 3.36
237 251 1.550130 TAGGGGTGAAGCCGTGAAGG 61.550 60.000 4.08 0.00 44.97 3.46
241 255 2.267961 GGTAGGGGTGAAGCCGTG 59.732 66.667 4.08 0.00 38.44 4.94
242 256 2.203877 TGGTAGGGGTGAAGCCGT 60.204 61.111 0.00 0.00 38.44 5.68
243 257 2.267961 GTGGTAGGGGTGAAGCCG 59.732 66.667 0.00 0.00 38.44 5.52
244 258 0.619543 TAGGTGGTAGGGGTGAAGCC 60.620 60.000 0.00 0.00 0.00 4.35
245 259 0.540454 GTAGGTGGTAGGGGTGAAGC 59.460 60.000 0.00 0.00 0.00 3.86
247 261 0.794934 AGGTAGGTGGTAGGGGTGAA 59.205 55.000 0.00 0.00 0.00 3.18
249 263 2.033208 GCTAGGTAGGTGGTAGGGGTG 61.033 61.905 0.00 0.00 0.00 4.61
250 264 0.264062 GCTAGGTAGGTGGTAGGGGT 59.736 60.000 0.00 0.00 0.00 4.95
251 265 0.561680 AGCTAGGTAGGTGGTAGGGG 59.438 60.000 0.00 0.00 31.96 4.79
252 266 1.818522 CGAGCTAGGTAGGTGGTAGGG 60.819 61.905 0.00 0.00 33.58 3.53
254 268 1.948145 CACGAGCTAGGTAGGTGGTAG 59.052 57.143 14.63 0.00 40.04 3.18
255 269 1.283029 ACACGAGCTAGGTAGGTGGTA 59.717 52.381 22.27 0.00 40.04 3.25
256 270 0.039326 ACACGAGCTAGGTAGGTGGT 59.961 55.000 22.27 9.44 42.18 4.16
277 291 3.007723 GCTAGATTCAGATCCAGATGGCA 59.992 47.826 0.00 0.00 32.44 4.92
300 314 6.413325 GCTTATATATAGGGATGGAGGAGGGA 60.413 46.154 4.23 0.00 0.00 4.20
342 360 5.028549 TCTGACTCTGGCTAATGATTTCC 57.971 43.478 0.00 0.00 0.00 3.13
361 379 2.540265 AGGAGTGTTGCTGAACTCTG 57.460 50.000 11.34 0.00 42.07 3.35
385 403 0.934496 TTGGAAGCGAACGAAGTGTG 59.066 50.000 0.00 0.00 45.00 3.82
397 415 2.027192 TGGTGTGGAGATAGTTGGAAGC 60.027 50.000 0.00 0.00 0.00 3.86
937 963 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
938 964 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
939 965 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
940 966 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
941 967 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
942 968 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
943 969 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
944 970 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
945 971 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
946 972 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
947 973 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
948 974 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
949 975 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
950 976 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
951 977 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
952 978 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
953 979 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
954 980 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
955 981 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
956 982 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
957 983 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
958 984 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
959 985 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
960 986 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
961 987 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
962 988 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
981 1007 3.326006 TCATCTTTGCTTCACCACTCTCT 59.674 43.478 0.00 0.00 0.00 3.10
983 1009 3.777106 TCATCTTTGCTTCACCACTCT 57.223 42.857 0.00 0.00 0.00 3.24
985 1011 2.555757 GCTTCATCTTTGCTTCACCACT 59.444 45.455 0.00 0.00 0.00 4.00
989 1015 5.338365 CCATAAGCTTCATCTTTGCTTCAC 58.662 41.667 0.00 0.00 44.59 3.18
1146 1184 1.700042 ATGGAAGGACGGAGCCATCC 61.700 60.000 8.11 8.11 44.24 3.51
1147 1185 0.181350 AATGGAAGGACGGAGCCATC 59.819 55.000 0.00 0.00 40.09 3.51
1148 1186 0.181350 GAATGGAAGGACGGAGCCAT 59.819 55.000 0.00 0.00 42.66 4.40
1149 1187 1.602237 GAATGGAAGGACGGAGCCA 59.398 57.895 0.00 0.00 34.45 4.75
1150 1188 1.153147 GGAATGGAAGGACGGAGCC 60.153 63.158 0.00 0.00 0.00 4.70
1151 1189 0.181350 ATGGAATGGAAGGACGGAGC 59.819 55.000 0.00 0.00 0.00 4.70
1152 1190 1.959042 CATGGAATGGAAGGACGGAG 58.041 55.000 0.00 0.00 41.79 4.63
1189 1227 8.040727 ACCCAAAATCAAAAAGTATATCCTTGC 58.959 33.333 0.00 0.00 0.00 4.01
1190 1228 9.586435 GACCCAAAATCAAAAAGTATATCCTTG 57.414 33.333 0.00 0.00 0.00 3.61
1191 1229 9.547279 AGACCCAAAATCAAAAAGTATATCCTT 57.453 29.630 0.00 0.00 0.00 3.36
1192 1230 8.971073 CAGACCCAAAATCAAAAAGTATATCCT 58.029 33.333 0.00 0.00 0.00 3.24
1193 1231 8.749354 ACAGACCCAAAATCAAAAAGTATATCC 58.251 33.333 0.00 0.00 0.00 2.59
1220 1258 0.320697 GTGCGTACACCTTCCTTCCT 59.679 55.000 0.00 0.00 41.21 3.36
1221 1259 2.836944 GTGCGTACACCTTCCTTCC 58.163 57.895 0.00 0.00 41.21 3.46
1233 1271 8.729129 GTACAAGTACTAACTGCGAGTGCGTA 62.729 46.154 0.00 0.00 37.19 4.42
1236 1274 2.673833 ACAAGTACTAACTGCGAGTGC 58.326 47.619 0.00 0.00 43.20 4.40
1237 1275 4.790878 TGTACAAGTACTAACTGCGAGTG 58.209 43.478 11.27 0.00 35.62 3.51
1238 1276 5.640189 ATGTACAAGTACTAACTGCGAGT 57.360 39.130 0.00 0.00 35.62 4.18
1239 1277 7.470079 TCTTATGTACAAGTACTAACTGCGAG 58.530 38.462 0.00 0.00 35.62 5.03
1240 1278 7.381766 TCTTATGTACAAGTACTAACTGCGA 57.618 36.000 0.00 1.01 35.62 5.10
1241 1279 6.691818 CCTCTTATGTACAAGTACTAACTGCG 59.308 42.308 0.00 0.00 35.62 5.18
1246 1288 8.874744 ACTGACCTCTTATGTACAAGTACTAA 57.125 34.615 0.00 6.90 37.00 2.24
1297 1345 7.371159 CAACACTAGATCGATCCTATTGCTTA 58.629 38.462 21.66 4.36 0.00 3.09
1322 1370 1.630878 AGAGGAGGTGGTGAATCAACC 59.369 52.381 0.00 0.00 40.94 3.77
1325 1373 1.902508 GACAGAGGAGGTGGTGAATCA 59.097 52.381 0.00 0.00 0.00 2.57
1344 1392 2.683933 GCTGAAGGGGGTCGAGGA 60.684 66.667 0.00 0.00 0.00 3.71
1349 1397 0.890996 CACACTTGCTGAAGGGGGTC 60.891 60.000 0.00 0.00 36.85 4.46
1395 1448 7.233632 TCAGCCTATATTGCATTCCAGTATTT 58.766 34.615 0.00 0.00 30.15 1.40
1415 1471 6.038050 CACTGATTATTCCTTCTCTTTCAGCC 59.962 42.308 0.00 0.00 34.19 4.85
1433 1491 2.092753 ACAAGCGATGGATCCACTGATT 60.093 45.455 18.99 14.58 0.00 2.57
1434 1492 1.487976 ACAAGCGATGGATCCACTGAT 59.512 47.619 18.99 8.45 0.00 2.90
1435 1493 0.904649 ACAAGCGATGGATCCACTGA 59.095 50.000 18.99 0.00 0.00 3.41
1438 1496 0.815615 GGGACAAGCGATGGATCCAC 60.816 60.000 18.99 10.34 0.00 4.02
1445 1503 2.106683 GGAACGGGGACAAGCGATG 61.107 63.158 0.00 0.00 0.00 3.84
1480 1540 3.409026 AAGAAACACCGAGATCAGCTT 57.591 42.857 0.00 0.00 0.00 3.74
1598 1702 2.716017 GCTCCCTGTGGACTCCTCG 61.716 68.421 0.00 0.00 35.03 4.63
1609 1713 1.326213 ACTCGAGGATGTGCTCCCTG 61.326 60.000 18.41 0.00 46.27 4.45
1625 1730 3.788672 CCATGTTGGCCTCCTACTC 57.211 57.895 3.32 0.00 30.94 2.59
1723 1838 1.003972 CGAGTTGCGCTTCAAAGTTCA 60.004 47.619 9.73 0.00 36.26 3.18
1724 1839 1.660333 CCGAGTTGCGCTTCAAAGTTC 60.660 52.381 9.73 0.00 39.11 3.01
1725 1840 0.307760 CCGAGTTGCGCTTCAAAGTT 59.692 50.000 9.73 0.00 39.11 2.66
1726 1841 0.814010 ACCGAGTTGCGCTTCAAAGT 60.814 50.000 9.73 0.00 39.11 2.66
1727 1842 0.384725 CACCGAGTTGCGCTTCAAAG 60.385 55.000 9.73 0.00 39.11 2.77
1728 1843 0.812014 TCACCGAGTTGCGCTTCAAA 60.812 50.000 9.73 0.00 39.11 2.69
1730 1845 1.227409 TTCACCGAGTTGCGCTTCA 60.227 52.632 9.73 0.00 39.11 3.02
1731 1846 1.204312 GTTCACCGAGTTGCGCTTC 59.796 57.895 9.73 2.80 39.11 3.86
1732 1847 1.522806 TGTTCACCGAGTTGCGCTT 60.523 52.632 9.73 0.00 39.11 4.68
1733 1848 2.108157 TGTTCACCGAGTTGCGCT 59.892 55.556 9.73 0.00 39.11 5.92
1734 1849 2.248431 GTGTTCACCGAGTTGCGC 59.752 61.111 0.00 0.00 39.11 6.09
1736 1851 3.340789 GGGTGTTCACCGAGTTGC 58.659 61.111 14.63 0.00 0.00 4.17
1743 1858 2.750237 GCCATCCGGGTGTTCACC 60.750 66.667 15.03 12.99 39.65 4.02
1744 1859 1.745489 GAGCCATCCGGGTGTTCAC 60.745 63.158 15.03 0.00 45.28 3.18
1745 1860 1.488705 AAGAGCCATCCGGGTGTTCA 61.489 55.000 15.03 0.00 42.23 3.18
1746 1861 1.026718 CAAGAGCCATCCGGGTGTTC 61.027 60.000 15.03 11.05 42.23 3.18
1747 1862 1.002134 CAAGAGCCATCCGGGTGTT 60.002 57.895 15.03 0.47 46.50 3.32
1795 1992 0.674581 TCCTGGAAAGATGTGCGCTG 60.675 55.000 9.73 0.00 0.00 5.18
1796 1993 0.254178 ATCCTGGAAAGATGTGCGCT 59.746 50.000 9.73 0.00 0.00 5.92
1799 1996 3.376546 GTCTTGATCCTGGAAAGATGTGC 59.623 47.826 12.65 0.00 32.85 4.57
1807 2007 1.066858 GTGAGCGTCTTGATCCTGGAA 60.067 52.381 0.00 0.00 29.76 3.53
1845 2083 9.918630 AAAAGAAGTAAATAGACACTAGCGTTA 57.081 29.630 0.00 0.00 0.00 3.18
1848 2086 9.141400 AGAAAAAGAAGTAAATAGACACTAGCG 57.859 33.333 0.00 0.00 0.00 4.26
1872 2110 9.231297 TGAACTGAAGAAGAAGAAAAGAAAAGA 57.769 29.630 0.00 0.00 0.00 2.52
1873 2111 9.283420 GTGAACTGAAGAAGAAGAAAAGAAAAG 57.717 33.333 0.00 0.00 0.00 2.27
1877 2115 7.331026 TCTGTGAACTGAAGAAGAAGAAAAGA 58.669 34.615 0.00 0.00 0.00 2.52
1891 2129 0.836606 TGTGGGCTTCTGTGAACTGA 59.163 50.000 0.00 0.00 0.00 3.41
1893 2131 1.131638 TCTGTGGGCTTCTGTGAACT 58.868 50.000 0.00 0.00 0.00 3.01
1897 2135 1.645034 CGTATCTGTGGGCTTCTGTG 58.355 55.000 0.00 0.00 0.00 3.66
1898 2136 0.108138 GCGTATCTGTGGGCTTCTGT 60.108 55.000 0.00 0.00 0.00 3.41
1899 2137 0.176680 AGCGTATCTGTGGGCTTCTG 59.823 55.000 0.00 0.00 30.04 3.02
1900 2138 0.176680 CAGCGTATCTGTGGGCTTCT 59.823 55.000 0.00 0.00 38.02 2.85
1901 2139 0.811616 CCAGCGTATCTGTGGGCTTC 60.812 60.000 0.00 0.00 41.25 3.86
1902 2140 1.221840 CCAGCGTATCTGTGGGCTT 59.778 57.895 0.00 0.00 41.25 4.35
1903 2141 2.735772 CCCAGCGTATCTGTGGGCT 61.736 63.158 0.00 0.00 44.60 5.19
1904 2142 2.203070 CCCAGCGTATCTGTGGGC 60.203 66.667 0.00 0.00 44.60 5.36
1906 2144 2.203070 GGCCCAGCGTATCTGTGG 60.203 66.667 0.00 0.00 41.25 4.17
1907 2145 2.586079 CGGCCCAGCGTATCTGTG 60.586 66.667 0.00 0.00 41.25 3.66
1908 2146 3.849951 CCGGCCCAGCGTATCTGT 61.850 66.667 0.00 0.00 41.25 3.41
1909 2147 3.536917 TCCGGCCCAGCGTATCTG 61.537 66.667 0.00 0.00 42.49 2.90
1910 2148 3.537874 GTCCGGCCCAGCGTATCT 61.538 66.667 0.00 0.00 0.00 1.98
1911 2149 4.603946 GGTCCGGCCCAGCGTATC 62.604 72.222 0.00 0.00 0.00 2.24
1924 2162 1.804601 AAAAGGTTCGACGATGGTCC 58.195 50.000 0.00 0.00 40.17 4.46
1926 2164 2.148768 GGAAAAAGGTTCGACGATGGT 58.851 47.619 0.00 0.00 0.00 3.55
1931 2169 1.529865 GAGTGGGAAAAAGGTTCGACG 59.470 52.381 0.00 0.00 0.00 5.12
1945 2187 6.456795 AAAACTGAGAAAAGAAAGAGTGGG 57.543 37.500 0.00 0.00 0.00 4.61
1971 2213 9.996554 AGAAGGAAAAACAGAAAAAGAAAAAGA 57.003 25.926 0.00 0.00 0.00 2.52
1977 2223 7.153217 ACGAAGAAGGAAAAACAGAAAAAGA 57.847 32.000 0.00 0.00 0.00 2.52
1978 2224 7.812309 AACGAAGAAGGAAAAACAGAAAAAG 57.188 32.000 0.00 0.00 0.00 2.27
1984 2230 5.744666 TGGTAACGAAGAAGGAAAAACAG 57.255 39.130 0.00 0.00 42.51 3.16
1991 2237 4.903045 AGGAAATGGTAACGAAGAAGGA 57.097 40.909 0.00 0.00 42.51 3.36
1996 2242 6.554334 TTGAGAAAGGAAATGGTAACGAAG 57.446 37.500 0.00 0.00 42.51 3.79


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

AutoCloner maintained by Alex Coulton.