Multiple sequence alignment - TraesCS2A01G582200

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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 TraesCS2A01G582200 chr2A 100.000 2357 0 0 1 2357 774574830 774572474 0.000000e+00 4353
1 TraesCS2A01G582200 chr2D 87.500 1960 158 51 1 1916 650321593 650323509 0.000000e+00 2182
2 TraesCS2A01G582200 chr2D 92.414 145 9 2 2214 2357 650323836 650323979 3.070000e-49 206
3 TraesCS2A01G582200 chr2B 86.592 1969 178 48 1 1942 786225634 786227543 0.000000e+00 2095
4 TraesCS2A01G582200 chr2B 89.051 137 12 3 2218 2352 786227850 786227985 1.450000e-37 167
5 TraesCS2A01G582200 chrUn 87.705 366 31 9 303 659 96707904 96707544 4.690000e-112 414
6 TraesCS2A01G582200 chrUn 83.453 139 18 5 659 794 96702250 96702114 8.840000e-25 124
7 TraesCS2A01G582200 chr6B 86.792 371 38 11 248 618 47899090 47898731 1.010000e-108 403
8 TraesCS2A01G582200 chr6A 86.636 217 28 1 18 234 27197730 27197515 3.030000e-59 239


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 TraesCS2A01G582200 chr2A 774572474 774574830 2356 True 4353 4353 100.0000 1 2357 1 chr2A.!!$R1 2356
1 TraesCS2A01G582200 chr2D 650321593 650323979 2386 False 1194 2182 89.9570 1 2357 2 chr2D.!!$F1 2356
2 TraesCS2A01G582200 chr2B 786225634 786227985 2351 False 1131 2095 87.8215 1 2352 2 chr2B.!!$F1 2351

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
854 870 0.245266 ACATACACATGACACGCCGA 59.755 50.0 0.0 0.0 35.96 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2298 2437 0.395312 CCAACTACACGGAACTGGGT 59.605 55.0 0.0 0.0 0.0 4.51 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
145 149 1.098050 GGCATGTCATTGGAGGTGTC 58.902 55.000 0.00 0.00 0.00 3.67
163 167 1.679977 CCTGGGTGGAGCATTGGTG 60.680 63.158 0.00 0.00 38.35 4.17
203 207 7.043961 CAGGTAACAGCAATCTACTAGATCA 57.956 40.000 0.00 0.00 33.74 2.92
204 208 7.144661 CAGGTAACAGCAATCTACTAGATCAG 58.855 42.308 0.00 0.00 33.74 2.90
210 214 5.047164 CAGCAATCTACTAGATCAGCCTCAT 60.047 44.000 15.03 1.13 36.75 2.90
214 218 4.078537 TCTACTAGATCAGCCTCATCTGC 58.921 47.826 0.00 0.00 32.61 4.26
215 219 2.961510 ACTAGATCAGCCTCATCTGCT 58.038 47.619 0.00 0.00 40.41 4.24
241 245 1.003580 TCAGACATGGAACCAAGCTCC 59.996 52.381 0.00 0.00 0.00 4.70
248 253 1.034292 GGAACCAAGCTCCTGCATCC 61.034 60.000 0.00 0.00 42.74 3.51
250 255 0.323178 AACCAAGCTCCTGCATCCAG 60.323 55.000 0.00 0.00 42.74 3.86
251 256 1.203441 ACCAAGCTCCTGCATCCAGA 61.203 55.000 0.00 0.00 41.77 3.86
253 258 1.595466 CAAGCTCCTGCATCCAGATC 58.405 55.000 0.00 0.00 41.77 2.75
255 260 1.210538 AGCTCCTGCATCCAGATCAA 58.789 50.000 0.00 0.00 41.77 2.57
256 261 1.134159 AGCTCCTGCATCCAGATCAAC 60.134 52.381 0.00 0.00 41.77 3.18
257 262 1.964552 CTCCTGCATCCAGATCAACC 58.035 55.000 0.00 0.00 41.77 3.77
259 264 1.487976 TCCTGCATCCAGATCAACCTC 59.512 52.381 0.00 0.00 41.77 3.85
260 265 1.211212 CCTGCATCCAGATCAACCTCA 59.789 52.381 0.00 0.00 41.77 3.86
262 267 3.552875 CTGCATCCAGATCAACCTCATT 58.447 45.455 0.00 0.00 41.77 2.57
263 268 3.952323 CTGCATCCAGATCAACCTCATTT 59.048 43.478 0.00 0.00 41.77 2.32
264 269 3.697542 TGCATCCAGATCAACCTCATTTG 59.302 43.478 0.00 0.00 0.00 2.32
265 270 3.490419 GCATCCAGATCAACCTCATTTGC 60.490 47.826 0.00 0.00 0.00 3.68
266 271 3.726557 TCCAGATCAACCTCATTTGCT 57.273 42.857 0.00 0.00 0.00 3.91
269 274 5.188434 TCCAGATCAACCTCATTTGCTAAG 58.812 41.667 0.00 0.00 0.00 2.18
271 276 5.826737 CCAGATCAACCTCATTTGCTAAGAT 59.173 40.000 0.00 0.00 0.00 2.40
272 277 6.320672 CCAGATCAACCTCATTTGCTAAGATT 59.679 38.462 0.00 0.00 0.00 2.40
273 278 7.416022 CAGATCAACCTCATTTGCTAAGATTC 58.584 38.462 0.00 0.00 0.00 2.52
283 295 8.791327 TCATTTGCTAAGATTCAGACATACAA 57.209 30.769 0.00 0.00 0.00 2.41
288 300 9.665719 TTGCTAAGATTCAGACATACAACATAA 57.334 29.630 0.00 0.00 0.00 1.90
348 360 1.478654 GGGACTTTTGTGCAAGGAGGA 60.479 52.381 0.00 0.00 42.95 3.71
428 440 4.415150 CGCTGGGCCAGATGTGGT 62.415 66.667 37.07 0.00 46.96 4.16
519 531 4.101585 CCTAGCTCTGGGATATTTGACACA 59.898 45.833 0.00 0.00 32.26 3.72
586 598 4.336889 TTTGTCGACACTTCCATCTCTT 57.663 40.909 19.90 0.00 0.00 2.85
698 712 1.130955 GGCTGTGTTTTGTTGCATCG 58.869 50.000 0.00 0.00 0.00 3.84
854 870 0.245266 ACATACACATGACACGCCGA 59.755 50.000 0.00 0.00 35.96 5.54
874 894 0.755079 CGCATGATCTTCCCTGGAGA 59.245 55.000 0.00 0.00 0.00 3.71
875 895 1.347050 CGCATGATCTTCCCTGGAGAT 59.653 52.381 0.00 0.00 0.00 2.75
916 936 2.223203 GCTTCTTGATGTCATTCTGCGG 60.223 50.000 0.00 0.00 0.00 5.69
919 939 3.673902 TCTTGATGTCATTCTGCGGAAA 58.326 40.909 12.96 0.00 34.90 3.13
932 956 1.751351 TGCGGAAACAACATTCACCAA 59.249 42.857 0.00 0.00 0.00 3.67
933 957 2.223688 TGCGGAAACAACATTCACCAAG 60.224 45.455 0.00 0.00 0.00 3.61
949 973 3.813166 CACCAAGTGAATTACCGTTCTGT 59.187 43.478 0.00 0.00 35.23 3.41
959 983 0.314302 ACCGTTCTGTTGGAGACGAG 59.686 55.000 0.00 0.00 31.01 4.18
960 984 0.388649 CCGTTCTGTTGGAGACGAGG 60.389 60.000 0.00 0.00 31.01 4.63
965 989 4.174762 GTTCTGTTGGAGACGAGGAATAC 58.825 47.826 0.00 0.00 0.00 1.89
966 990 3.427573 TCTGTTGGAGACGAGGAATACA 58.572 45.455 0.00 0.00 0.00 2.29
970 994 4.282449 TGTTGGAGACGAGGAATACAGAAA 59.718 41.667 0.00 0.00 0.00 2.52
1089 1113 3.070446 TGGTGAAGTTCCACTTGATACGT 59.930 43.478 0.00 0.00 38.80 3.57
1107 1131 1.664873 GTTCTCCAAATAGACCGCCC 58.335 55.000 0.00 0.00 0.00 6.13
1134 1158 6.096987 TCTCTGACTTCAAGAACTTGTACAGT 59.903 38.462 13.15 12.86 41.16 3.55
1161 1185 0.306228 CATTGTTGCCGTTCACGTCA 59.694 50.000 0.00 0.00 37.74 4.35
1170 1194 1.003851 CGTTCACGTCAACCTGTTGT 58.996 50.000 9.65 0.00 41.16 3.32
1191 1215 9.554395 TGTTGTCAACTCAGAAATGTTTAGATA 57.446 29.630 16.45 0.00 0.00 1.98
1226 1250 1.225855 TGTGTTTGGAAGCTAGCACG 58.774 50.000 18.83 0.00 0.00 5.34
1238 1265 1.464687 GCTAGCACGCACACAGAAATG 60.465 52.381 10.63 0.00 0.00 2.32
1243 1270 2.384382 CACGCACACAGAAATGGAAAC 58.616 47.619 0.00 0.00 0.00 2.78
1259 1286 3.634448 TGGAAACAAAGATTTTCGCTGGA 59.366 39.130 0.00 0.00 37.44 3.86
1344 1371 2.363680 CTCATCGCTATCTGGTTCCTGT 59.636 50.000 0.00 0.00 0.00 4.00
1347 1374 0.824109 CGCTATCTGGTTCCTGTCCA 59.176 55.000 0.00 0.00 0.00 4.02
1353 1380 1.915141 CTGGTTCCTGTCCAGCAAAT 58.085 50.000 0.00 0.00 44.46 2.32
1404 1431 4.503741 TCCTAATTGCAGCAGAAAACAC 57.496 40.909 0.00 0.00 0.00 3.32
1409 1437 0.525242 TGCAGCAGAAAACACGCAAC 60.525 50.000 0.00 0.00 0.00 4.17
1534 1563 5.643777 ACTTGCAGCCTAACATAAACTGTAG 59.356 40.000 0.00 0.00 36.98 2.74
1585 1617 8.160106 AGGTCTTCTATCATTATTTAGCCCAAG 58.840 37.037 0.00 0.00 0.00 3.61
1587 1619 7.939588 GTCTTCTATCATTATTTAGCCCAAGGT 59.060 37.037 0.00 0.00 0.00 3.50
1589 1621 8.463930 TTCTATCATTATTTAGCCCAAGGTTG 57.536 34.615 0.00 0.00 0.00 3.77
1601 1634 2.875296 CCAAGGTTGGTTCCAATCTCA 58.125 47.619 16.38 0.00 43.43 3.27
1643 1676 7.781324 AACTTGAATAGTTGGATCCAAACAT 57.219 32.000 28.64 20.18 45.33 2.71
1649 1682 8.217111 TGAATAGTTGGATCCAAACATAGCATA 58.783 33.333 28.64 11.36 37.70 3.14
1689 1722 3.499338 TGATGGGAAGCAAACTGTTGAT 58.501 40.909 0.00 0.00 36.83 2.57
1695 1728 3.057946 GGAAGCAAACTGTTGATCAGGTC 60.058 47.826 0.00 0.00 44.18 3.85
1697 1730 1.541588 GCAAACTGTTGATCAGGTCCC 59.458 52.381 0.00 0.00 44.18 4.46
1723 1763 4.703897 TCTAGGACTTTTTGACACCACTG 58.296 43.478 0.00 0.00 0.00 3.66
1724 1764 3.366052 AGGACTTTTTGACACCACTGT 57.634 42.857 0.00 0.00 0.00 3.55
1731 1771 5.354234 ACTTTTTGACACCACTGTAGTCTTG 59.646 40.000 8.15 0.00 33.56 3.02
1738 1778 4.814771 ACACCACTGTAGTCTTGTAAAAGC 59.185 41.667 0.00 0.00 0.00 3.51
1743 1788 7.883311 ACCACTGTAGTCTTGTAAAAGCAATAT 59.117 33.333 0.00 0.00 0.00 1.28
1802 1847 2.008329 CTGAGAAGCCATGCTCTTGAC 58.992 52.381 3.58 0.00 38.25 3.18
1811 1856 0.179936 ATGCTCTTGACCAGCTAGGC 59.820 55.000 2.50 0.00 43.14 3.93
1828 1873 3.336138 AGGCAAGCTACAGGTAAGTTC 57.664 47.619 0.00 0.00 0.00 3.01
1829 1874 2.907042 AGGCAAGCTACAGGTAAGTTCT 59.093 45.455 0.00 0.00 0.00 3.01
1830 1875 3.003480 GGCAAGCTACAGGTAAGTTCTG 58.997 50.000 0.00 0.00 38.16 3.02
1832 1877 3.866449 GCAAGCTACAGGTAAGTTCTGCT 60.866 47.826 0.00 0.00 35.78 4.24
1833 1878 3.601443 AGCTACAGGTAAGTTCTGCTG 57.399 47.619 0.00 0.00 35.78 4.41
1834 1879 2.003301 GCTACAGGTAAGTTCTGCTGC 58.997 52.381 0.00 0.00 35.78 5.25
1835 1880 2.354203 GCTACAGGTAAGTTCTGCTGCT 60.354 50.000 0.00 0.00 35.78 4.24
1836 1881 2.175878 ACAGGTAAGTTCTGCTGCTG 57.824 50.000 0.00 0.00 35.78 4.41
1837 1882 0.801251 CAGGTAAGTTCTGCTGCTGC 59.199 55.000 8.89 8.89 40.20 5.25
1890 1939 3.181510 GCACACATTATGACCGAGAAACC 60.182 47.826 0.00 0.00 0.00 3.27
1897 1946 1.699730 TGACCGAGAAACCACTCAGA 58.300 50.000 0.00 0.00 36.80 3.27
1903 1952 2.079925 GAGAAACCACTCAGATGCCAC 58.920 52.381 0.00 0.00 36.95 5.01
1929 1984 3.007074 TGTTGTGCTGATTGGATTGCATT 59.993 39.130 0.00 0.00 37.76 3.56
1931 1986 3.852286 TGTGCTGATTGGATTGCATTTC 58.148 40.909 0.00 0.00 37.76 2.17
1942 1997 8.937634 ATTGGATTGCATTTCTTATGAGTTTC 57.062 30.769 0.00 0.00 0.00 2.78
1943 1998 7.707624 TGGATTGCATTTCTTATGAGTTTCT 57.292 32.000 0.00 0.00 0.00 2.52
1945 2000 8.677300 TGGATTGCATTTCTTATGAGTTTCTAC 58.323 33.333 0.00 0.00 0.00 2.59
1964 2084 5.571285 TCTACTCTCTAGTGAAGGCAAAGA 58.429 41.667 0.00 0.00 36.36 2.52
1971 2091 3.228188 AGTGAAGGCAAAGACAATGGA 57.772 42.857 0.00 0.00 0.00 3.41
1974 2094 4.590222 AGTGAAGGCAAAGACAATGGATTT 59.410 37.500 0.00 0.00 0.00 2.17
2006 2127 3.420943 GGAACATTCCCCGCGATG 58.579 61.111 8.23 5.70 41.62 3.84
2009 2130 0.935196 GAACATTCCCCGCGATGTAC 59.065 55.000 8.23 0.00 0.00 2.90
2030 2151 4.067896 ACAAAAGTGATGCATCGAAGAGT 58.932 39.130 21.34 12.38 43.63 3.24
2033 2154 5.695851 AAAGTGATGCATCGAAGAGTTTT 57.304 34.783 21.34 10.50 43.63 2.43
2036 2157 6.992063 AGTGATGCATCGAAGAGTTTTAAT 57.008 33.333 21.34 0.00 43.63 1.40
2049 2170 6.590234 AGAGTTTTAATCATTCCCCACAAC 57.410 37.500 0.00 0.00 0.00 3.32
2050 2171 6.074648 AGAGTTTTAATCATTCCCCACAACA 58.925 36.000 0.00 0.00 0.00 3.33
2052 2175 6.758254 AGTTTTAATCATTCCCCACAACAAG 58.242 36.000 0.00 0.00 0.00 3.16
2056 2179 8.837099 TTTAATCATTCCCCACAACAAGATAT 57.163 30.769 0.00 0.00 0.00 1.63
2062 2185 5.725551 TCCCCACAACAAGATATAACCAT 57.274 39.130 0.00 0.00 0.00 3.55
2121 2253 8.775527 TCGTGTTCAGTTTTAATACAAATAGCA 58.224 29.630 0.00 0.00 0.00 3.49
2161 2298 4.295051 GTTAAGAACCGTACAACGTACCA 58.705 43.478 0.00 0.00 40.58 3.25
2165 2302 4.379652 AGAACCGTACAACGTACCAAATT 58.620 39.130 0.00 0.00 40.58 1.82
2168 2305 5.132897 ACCGTACAACGTACCAAATTAGA 57.867 39.130 0.00 0.00 40.58 2.10
2169 2306 5.537188 ACCGTACAACGTACCAAATTAGAA 58.463 37.500 0.00 0.00 40.58 2.10
2170 2307 6.165577 ACCGTACAACGTACCAAATTAGAAT 58.834 36.000 0.00 0.00 40.58 2.40
2171 2308 6.311200 ACCGTACAACGTACCAAATTAGAATC 59.689 38.462 0.00 0.00 40.58 2.52
2172 2309 6.532657 CCGTACAACGTACCAAATTAGAATCT 59.467 38.462 0.00 0.00 40.58 2.40
2173 2310 7.388712 CGTACAACGTACCAAATTAGAATCTG 58.611 38.462 0.00 0.00 36.74 2.90
2174 2311 6.178239 ACAACGTACCAAATTAGAATCTGC 57.822 37.500 0.00 0.00 0.00 4.26
2175 2312 5.938125 ACAACGTACCAAATTAGAATCTGCT 59.062 36.000 0.00 0.00 0.00 4.24
2176 2313 7.101054 ACAACGTACCAAATTAGAATCTGCTA 58.899 34.615 0.00 0.00 0.00 3.49
2177 2314 7.604927 ACAACGTACCAAATTAGAATCTGCTAA 59.395 33.333 0.00 0.00 35.06 3.09
2178 2315 8.447833 CAACGTACCAAATTAGAATCTGCTAAA 58.552 33.333 0.00 0.00 34.33 1.85
2179 2316 7.971455 ACGTACCAAATTAGAATCTGCTAAAC 58.029 34.615 0.00 0.00 34.33 2.01
2180 2317 7.822822 ACGTACCAAATTAGAATCTGCTAAACT 59.177 33.333 0.00 0.00 34.33 2.66
2181 2318 9.309516 CGTACCAAATTAGAATCTGCTAAACTA 57.690 33.333 0.00 0.00 34.33 2.24
2192 2329 9.549078 AGAATCTGCTAAACTACTAAATAAGGC 57.451 33.333 0.00 0.00 0.00 4.35
2193 2330 9.549078 GAATCTGCTAAACTACTAAATAAGGCT 57.451 33.333 0.00 0.00 0.00 4.58
2194 2331 8.894768 ATCTGCTAAACTACTAAATAAGGCTG 57.105 34.615 0.00 0.00 0.00 4.85
2195 2332 7.272978 TCTGCTAAACTACTAAATAAGGCTGG 58.727 38.462 0.00 0.00 0.00 4.85
2196 2333 6.354130 TGCTAAACTACTAAATAAGGCTGGG 58.646 40.000 0.00 0.00 0.00 4.45
2197 2334 5.763698 GCTAAACTACTAAATAAGGCTGGGG 59.236 44.000 0.00 0.00 0.00 4.96
2198 2335 5.791303 AAACTACTAAATAAGGCTGGGGT 57.209 39.130 0.00 0.00 0.00 4.95
2199 2336 4.772886 ACTACTAAATAAGGCTGGGGTG 57.227 45.455 0.00 0.00 0.00 4.61
2200 2337 4.368067 ACTACTAAATAAGGCTGGGGTGA 58.632 43.478 0.00 0.00 0.00 4.02
2201 2338 4.786454 ACTACTAAATAAGGCTGGGGTGAA 59.214 41.667 0.00 0.00 0.00 3.18
2202 2339 4.881157 ACTAAATAAGGCTGGGGTGAAT 57.119 40.909 0.00 0.00 0.00 2.57
2203 2340 5.987019 ACTAAATAAGGCTGGGGTGAATA 57.013 39.130 0.00 0.00 0.00 1.75
2204 2341 6.530601 ACTAAATAAGGCTGGGGTGAATAT 57.469 37.500 0.00 0.00 0.00 1.28
2205 2342 7.642094 ACTAAATAAGGCTGGGGTGAATATA 57.358 36.000 0.00 0.00 0.00 0.86
2206 2343 8.052621 ACTAAATAAGGCTGGGGTGAATATAA 57.947 34.615 0.00 0.00 0.00 0.98
2207 2344 8.678798 ACTAAATAAGGCTGGGGTGAATATAAT 58.321 33.333 0.00 0.00 0.00 1.28
2208 2345 7.781324 AAATAAGGCTGGGGTGAATATAATG 57.219 36.000 0.00 0.00 0.00 1.90
2209 2346 3.160679 AGGCTGGGGTGAATATAATGC 57.839 47.619 0.00 0.00 0.00 3.56
2210 2347 2.446666 AGGCTGGGGTGAATATAATGCA 59.553 45.455 0.00 0.00 0.00 3.96
2211 2348 3.076484 AGGCTGGGGTGAATATAATGCAT 59.924 43.478 0.00 0.00 0.00 3.96
2212 2349 3.834231 GGCTGGGGTGAATATAATGCATT 59.166 43.478 17.56 17.56 0.00 3.56
2213 2350 5.016173 GGCTGGGGTGAATATAATGCATTA 58.984 41.667 20.95 20.95 0.00 1.90
2214 2351 5.126061 GGCTGGGGTGAATATAATGCATTAG 59.874 44.000 22.76 8.82 0.00 1.73
2215 2352 5.945784 GCTGGGGTGAATATAATGCATTAGA 59.054 40.000 22.76 19.35 0.00 2.10
2262 2401 6.845302 TGACATGTGCAAAGCTATAGAAAAG 58.155 36.000 1.15 0.00 0.00 2.27
2263 2402 6.430925 TGACATGTGCAAAGCTATAGAAAAGT 59.569 34.615 1.15 0.00 0.00 2.66
2265 2404 7.978982 ACATGTGCAAAGCTATAGAAAAGTAG 58.021 34.615 3.21 0.00 0.00 2.57
2295 2434 6.412362 TTCTCCCTGTATTTCTCATAGAGC 57.588 41.667 0.00 0.00 0.00 4.09
2298 2437 5.458595 TCCCTGTATTTCTCATAGAGCTGA 58.541 41.667 0.00 0.00 0.00 4.26
2304 2443 2.836636 TCTCATAGAGCTGACCCAGT 57.163 50.000 0.00 0.00 33.43 4.00
2322 2461 3.188460 CCAGTTCCGTGTAGTTGGAATTG 59.812 47.826 8.90 8.90 46.04 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 8.695456 GGATTTCATACAATCCCTACAAACATT 58.305 33.333 1.52 0.00 44.71 2.71
131 135 0.035056 CCCAGGACACCTCCAATGAC 60.035 60.000 0.00 0.00 39.39 3.06
145 149 1.679977 CACCAATGCTCCACCCAGG 60.680 63.158 0.00 0.00 39.47 4.45
163 167 2.032528 TGCACAGTACTGGCAGCC 59.967 61.111 25.71 3.66 33.85 4.85
197 201 4.734266 TCTTAGCAGATGAGGCTGATCTA 58.266 43.478 16.25 0.00 42.62 1.98
201 205 3.708121 TGAATCTTAGCAGATGAGGCTGA 59.292 43.478 0.00 0.00 42.62 4.26
202 206 4.059511 CTGAATCTTAGCAGATGAGGCTG 58.940 47.826 0.00 0.00 42.62 4.85
203 207 3.966006 TCTGAATCTTAGCAGATGAGGCT 59.034 43.478 0.00 0.00 39.00 4.58
204 208 4.057432 GTCTGAATCTTAGCAGATGAGGC 58.943 47.826 0.00 0.00 42.51 4.70
210 214 5.423015 GTTCCATGTCTGAATCTTAGCAGA 58.577 41.667 0.00 0.00 38.72 4.26
214 218 5.065731 GCTTGGTTCCATGTCTGAATCTTAG 59.934 44.000 6.60 0.00 0.00 2.18
215 219 4.943705 GCTTGGTTCCATGTCTGAATCTTA 59.056 41.667 6.60 0.00 0.00 2.10
241 245 2.704464 TGAGGTTGATCTGGATGCAG 57.296 50.000 8.12 8.12 0.00 4.41
248 253 6.939132 ATCTTAGCAAATGAGGTTGATCTG 57.061 37.500 0.00 0.00 0.00 2.90
250 255 7.281774 TCTGAATCTTAGCAAATGAGGTTGATC 59.718 37.037 0.00 0.00 0.00 2.92
251 256 7.066766 GTCTGAATCTTAGCAAATGAGGTTGAT 59.933 37.037 0.00 0.00 0.00 2.57
253 258 6.149973 TGTCTGAATCTTAGCAAATGAGGTTG 59.850 38.462 0.00 0.00 0.00 3.77
255 260 5.809001 TGTCTGAATCTTAGCAAATGAGGT 58.191 37.500 0.00 0.00 0.00 3.85
256 261 6.939132 ATGTCTGAATCTTAGCAAATGAGG 57.061 37.500 0.00 0.00 0.00 3.86
257 262 8.429493 TGTATGTCTGAATCTTAGCAAATGAG 57.571 34.615 0.00 0.00 0.00 2.90
259 264 8.453320 TGTTGTATGTCTGAATCTTAGCAAATG 58.547 33.333 0.00 0.00 0.00 2.32
260 265 8.565896 TGTTGTATGTCTGAATCTTAGCAAAT 57.434 30.769 0.00 0.00 0.00 2.32
262 267 9.665719 TTATGTTGTATGTCTGAATCTTAGCAA 57.334 29.630 0.00 0.00 0.00 3.91
263 268 9.665719 TTTATGTTGTATGTCTGAATCTTAGCA 57.334 29.630 0.00 0.00 0.00 3.49
283 295 8.088365 GCCAAACAGGATTAGAAACTTTTATGT 58.912 33.333 0.00 0.00 41.22 2.29
288 300 6.670695 ATGCCAAACAGGATTAGAAACTTT 57.329 33.333 0.00 0.00 41.22 2.66
348 360 5.279657 GGCTTTCTTGGACTTTGATTTGGAT 60.280 40.000 0.00 0.00 0.00 3.41
423 435 4.314440 GAGCTGGGCGACACCACA 62.314 66.667 0.00 0.00 42.05 4.17
428 440 3.695606 GTCCTGAGCTGGGCGACA 61.696 66.667 0.00 0.00 0.00 4.35
519 531 6.655003 AGTTGATATCAATGTTGGAACTTCGT 59.345 34.615 20.65 0.00 38.24 3.85
586 598 7.341769 TCTTTTTGGGAACAGAAAAATCTCTCA 59.658 33.333 0.00 0.00 43.00 3.27
632 644 4.398044 TCTCAAAAACCGAATGGGCTATTC 59.602 41.667 13.07 13.07 41.46 1.75
720 734 5.619086 CGGTGAAAGGAAATAACATTTCGCT 60.619 40.000 15.12 2.57 44.64 4.93
728 742 6.790285 TTCTACACGGTGAAAGGAAATAAC 57.210 37.500 16.29 0.00 0.00 1.89
729 743 7.282675 TGTTTTCTACACGGTGAAAGGAAATAA 59.717 33.333 16.29 8.58 34.29 1.40
731 745 5.591067 TGTTTTCTACACGGTGAAAGGAAAT 59.409 36.000 16.29 0.00 34.29 2.17
736 752 4.809426 ACTCTGTTTTCTACACGGTGAAAG 59.191 41.667 16.29 11.52 34.29 2.62
819 835 6.524734 TGTGTATGTGTCATCTGTTCTTTCT 58.475 36.000 0.00 0.00 0.00 2.52
820 836 6.785488 TGTGTATGTGTCATCTGTTCTTTC 57.215 37.500 0.00 0.00 0.00 2.62
854 870 0.467384 CTCCAGGGAAGATCATGCGT 59.533 55.000 0.00 0.00 0.00 5.24
874 894 4.475016 AGCTGTTGGAGGTTTGAGGTATAT 59.525 41.667 0.00 0.00 0.00 0.86
875 895 3.844211 AGCTGTTGGAGGTTTGAGGTATA 59.156 43.478 0.00 0.00 0.00 1.47
932 956 4.039973 TCTCCAACAGAACGGTAATTCACT 59.960 41.667 0.00 0.00 0.00 3.41
933 957 4.151867 GTCTCCAACAGAACGGTAATTCAC 59.848 45.833 0.00 0.00 30.72 3.18
943 967 2.814280 TTCCTCGTCTCCAACAGAAC 57.186 50.000 0.00 0.00 30.72 3.01
945 969 3.427573 TGTATTCCTCGTCTCCAACAGA 58.572 45.455 0.00 0.00 0.00 3.41
949 973 5.477607 TTTTCTGTATTCCTCGTCTCCAA 57.522 39.130 0.00 0.00 0.00 3.53
965 989 8.559536 TGCTCTAACTCAACAGTTTATTTTCTG 58.440 33.333 0.00 0.00 40.16 3.02
966 990 8.677148 TGCTCTAACTCAACAGTTTATTTTCT 57.323 30.769 0.00 0.00 40.16 2.52
970 994 7.119846 GGTGATGCTCTAACTCAACAGTTTATT 59.880 37.037 0.00 0.00 40.16 1.40
1080 1104 6.830114 GGTCTATTTGGAGAACGTATCAAG 57.170 41.667 0.00 0.00 0.00 3.02
1089 1113 0.544697 GGGGCGGTCTATTTGGAGAA 59.455 55.000 0.00 0.00 0.00 2.87
1107 1131 4.954875 ACAAGTTCTTGAAGTCAGAGAGG 58.045 43.478 17.75 0.00 0.00 3.69
1152 1176 2.004017 TGACAACAGGTTGACGTGAAC 58.996 47.619 18.28 9.59 42.93 3.18
1161 1185 4.949856 ACATTTCTGAGTTGACAACAGGTT 59.050 37.500 20.08 0.00 33.19 3.50
1192 1216 7.856145 TCCAAACACAAATGCACTTATTTTT 57.144 28.000 0.00 0.00 0.00 1.94
1226 1250 4.681744 TCTTTGTTTCCATTTCTGTGTGC 58.318 39.130 0.00 0.00 0.00 4.57
1238 1265 4.237349 TCCAGCGAAAATCTTTGTTTCC 57.763 40.909 0.00 0.00 32.40 3.13
1243 1270 5.355350 AGGTCTATTCCAGCGAAAATCTTTG 59.645 40.000 0.00 0.00 0.00 2.77
1244 1271 5.501156 AGGTCTATTCCAGCGAAAATCTTT 58.499 37.500 0.00 0.00 0.00 2.52
1245 1272 5.104259 AGGTCTATTCCAGCGAAAATCTT 57.896 39.130 0.00 0.00 0.00 2.40
1247 1274 4.496507 GCAAGGTCTATTCCAGCGAAAATC 60.497 45.833 0.00 0.00 0.00 2.17
1248 1275 3.378427 GCAAGGTCTATTCCAGCGAAAAT 59.622 43.478 0.00 0.00 0.00 1.82
1254 1281 2.024176 TTCGCAAGGTCTATTCCAGC 57.976 50.000 0.00 0.00 38.47 4.85
1255 1282 5.567138 ATTTTTCGCAAGGTCTATTCCAG 57.433 39.130 0.00 0.00 38.47 3.86
1256 1283 5.588648 CCTATTTTTCGCAAGGTCTATTCCA 59.411 40.000 0.00 0.00 38.47 3.53
1257 1284 5.820947 TCCTATTTTTCGCAAGGTCTATTCC 59.179 40.000 0.00 0.00 38.47 3.01
1259 1286 7.393515 AGTTTCCTATTTTTCGCAAGGTCTATT 59.606 33.333 0.00 0.00 38.47 1.73
1353 1380 1.976474 GGCGTTCCCCTGCAATCAA 60.976 57.895 0.00 0.00 0.00 2.57
1404 1431 6.409185 GTCTTCAATCTTCATTTATCGTTGCG 59.591 38.462 0.00 0.00 0.00 4.85
1409 1437 7.899974 ACTTCGTCTTCAATCTTCATTTATCG 58.100 34.615 0.00 0.00 0.00 2.92
1454 1483 0.251474 AGATGTGCCATTGTGCAGGT 60.251 50.000 0.00 0.00 43.02 4.00
1495 1524 5.236047 GGCTGCAAGTCTTTAGTATGATGAG 59.764 44.000 0.50 0.00 34.11 2.90
1496 1525 5.118990 GGCTGCAAGTCTTTAGTATGATGA 58.881 41.667 0.50 0.00 34.11 2.92
1497 1526 5.415415 GGCTGCAAGTCTTTAGTATGATG 57.585 43.478 0.50 0.00 34.11 3.07
1557 1589 9.166222 TGGGCTAAATAATGATAGAAGACCTTA 57.834 33.333 0.00 0.00 0.00 2.69
1558 1590 8.045720 TGGGCTAAATAATGATAGAAGACCTT 57.954 34.615 0.00 0.00 0.00 3.50
1559 1591 7.633018 TGGGCTAAATAATGATAGAAGACCT 57.367 36.000 0.00 0.00 0.00 3.85
1560 1592 7.391833 CCTTGGGCTAAATAATGATAGAAGACC 59.608 40.741 0.00 0.00 0.00 3.85
1561 1593 7.939588 ACCTTGGGCTAAATAATGATAGAAGAC 59.060 37.037 0.00 0.00 0.00 3.01
1562 1594 8.045720 ACCTTGGGCTAAATAATGATAGAAGA 57.954 34.615 0.00 0.00 0.00 2.87
1563 1595 8.571336 CAACCTTGGGCTAAATAATGATAGAAG 58.429 37.037 0.00 0.00 0.00 2.85
1564 1596 7.505585 CCAACCTTGGGCTAAATAATGATAGAA 59.494 37.037 0.00 0.00 44.70 2.10
1565 1597 7.004086 CCAACCTTGGGCTAAATAATGATAGA 58.996 38.462 0.00 0.00 44.70 1.98
1566 1598 7.219484 CCAACCTTGGGCTAAATAATGATAG 57.781 40.000 0.00 0.00 44.70 2.08
1585 1617 4.766891 TCAGATTTGAGATTGGAACCAACC 59.233 41.667 8.50 0.00 38.88 3.77
1587 1619 6.975196 TTTCAGATTTGAGATTGGAACCAA 57.025 33.333 8.75 8.75 36.08 3.67
1589 1621 6.986250 AGTTTTCAGATTTGAGATTGGAACC 58.014 36.000 0.00 0.00 34.15 3.62
1643 1676 9.481340 CAAACAGATATTACAGAAGCTATGCTA 57.519 33.333 0.00 0.00 38.25 3.49
1649 1682 6.769822 CCCATCAAACAGATATTACAGAAGCT 59.230 38.462 0.00 0.00 34.43 3.74
1689 1722 2.233305 GTCCTAGAAGTGGGACCTGA 57.767 55.000 0.00 0.00 46.38 3.86
1695 1728 4.515567 GTGTCAAAAAGTCCTAGAAGTGGG 59.484 45.833 0.00 0.00 0.00 4.61
1697 1730 5.007724 GTGGTGTCAAAAAGTCCTAGAAGTG 59.992 44.000 0.00 0.00 0.00 3.16
1713 1746 5.601583 TTTACAAGACTACAGTGGTGTCA 57.398 39.130 16.45 0.00 38.19 3.58
1714 1747 5.050295 GCTTTTACAAGACTACAGTGGTGTC 60.050 44.000 0.00 9.00 33.20 3.67
1723 1763 9.974750 GAAGTCATATTGCTTTTACAAGACTAC 57.025 33.333 0.00 0.00 33.77 2.73
1724 1764 9.719355 TGAAGTCATATTGCTTTTACAAGACTA 57.281 29.630 0.00 0.00 33.77 2.59
1731 1771 9.243637 TGTGTTTTGAAGTCATATTGCTTTTAC 57.756 29.630 0.00 0.00 0.00 2.01
1738 1778 9.121517 GACTGAATGTGTTTTGAAGTCATATTG 57.878 33.333 0.00 0.00 34.19 1.90
1743 1788 6.698008 ATGACTGAATGTGTTTTGAAGTCA 57.302 33.333 5.20 5.20 44.60 3.41
1811 1856 3.681897 CAGCAGAACTTACCTGTAGCTTG 59.318 47.826 0.00 0.00 34.29 4.01
1819 1864 0.689623 AGCAGCAGCAGAACTTACCT 59.310 50.000 3.17 0.00 45.49 3.08
1825 1870 4.333633 CTTACTAAAGCAGCAGCAGAAC 57.666 45.455 3.17 0.00 45.49 3.01
1837 1882 7.819900 AGAATACACTTCACCTGCTTACTAAAG 59.180 37.037 0.00 0.00 35.68 1.85
1890 1939 2.398252 ACAGATGTGGCATCTGAGTG 57.602 50.000 32.84 16.31 46.25 3.51
1903 1952 4.421058 CAATCCAATCAGCACAACAGATG 58.579 43.478 0.00 0.00 0.00 2.90
1942 1997 5.184096 TGTCTTTGCCTTCACTAGAGAGTAG 59.816 44.000 0.00 0.00 33.32 2.57
1943 1998 5.077564 TGTCTTTGCCTTCACTAGAGAGTA 58.922 41.667 0.00 0.00 33.32 2.59
1945 2000 4.527509 TGTCTTTGCCTTCACTAGAGAG 57.472 45.455 0.00 0.00 0.00 3.20
1949 2069 4.326826 TCCATTGTCTTTGCCTTCACTAG 58.673 43.478 0.00 0.00 0.00 2.57
1954 2074 6.226052 AGAAAAATCCATTGTCTTTGCCTTC 58.774 36.000 0.00 0.00 0.00 3.46
2001 2122 3.469899 TGCATCACTTTTGTACATCGC 57.530 42.857 0.00 0.00 0.00 4.58
2002 2123 4.032786 TCGATGCATCACTTTTGTACATCG 59.967 41.667 25.70 14.39 43.88 3.84
2005 2126 4.994217 TCTTCGATGCATCACTTTTGTACA 59.006 37.500 25.70 0.00 0.00 2.90
2006 2127 5.120830 ACTCTTCGATGCATCACTTTTGTAC 59.879 40.000 25.70 0.00 0.00 2.90
2009 2130 4.675190 ACTCTTCGATGCATCACTTTTG 57.325 40.909 25.70 12.90 0.00 2.44
2030 2151 6.985653 TCTTGTTGTGGGGAATGATTAAAA 57.014 33.333 0.00 0.00 0.00 1.52
2033 2154 9.349713 GTTATATCTTGTTGTGGGGAATGATTA 57.650 33.333 0.00 0.00 0.00 1.75
2036 2157 6.126409 GGTTATATCTTGTTGTGGGGAATGA 58.874 40.000 0.00 0.00 0.00 2.57
2056 2179 8.865420 TGCTTTGTACTTAAATGGTATGGTTA 57.135 30.769 0.00 0.00 0.00 2.85
2096 2228 8.942669 TGCTATTTGTATTAAAACTGAACACG 57.057 30.769 0.00 0.00 0.00 4.49
2154 2291 7.822822 AGTTTAGCAGATTCTAATTTGGTACGT 59.177 33.333 5.04 0.00 34.52 3.57
2155 2292 8.197988 AGTTTAGCAGATTCTAATTTGGTACG 57.802 34.615 5.04 0.00 34.52 3.67
2168 2305 9.331282 CAGCCTTATTTAGTAGTTTAGCAGATT 57.669 33.333 0.00 0.00 0.00 2.40
2169 2306 7.934120 CCAGCCTTATTTAGTAGTTTAGCAGAT 59.066 37.037 0.00 0.00 0.00 2.90
2170 2307 7.272978 CCAGCCTTATTTAGTAGTTTAGCAGA 58.727 38.462 0.00 0.00 0.00 4.26
2171 2308 6.483640 CCCAGCCTTATTTAGTAGTTTAGCAG 59.516 42.308 0.00 0.00 0.00 4.24
2172 2309 6.354130 CCCAGCCTTATTTAGTAGTTTAGCA 58.646 40.000 0.00 0.00 0.00 3.49
2173 2310 5.763698 CCCCAGCCTTATTTAGTAGTTTAGC 59.236 44.000 0.00 0.00 0.00 3.09
2174 2311 6.766467 CACCCCAGCCTTATTTAGTAGTTTAG 59.234 42.308 0.00 0.00 0.00 1.85
2175 2312 6.444493 TCACCCCAGCCTTATTTAGTAGTTTA 59.556 38.462 0.00 0.00 0.00 2.01
2176 2313 5.252164 TCACCCCAGCCTTATTTAGTAGTTT 59.748 40.000 0.00 0.00 0.00 2.66
2177 2314 4.786454 TCACCCCAGCCTTATTTAGTAGTT 59.214 41.667 0.00 0.00 0.00 2.24
2178 2315 4.368067 TCACCCCAGCCTTATTTAGTAGT 58.632 43.478 0.00 0.00 0.00 2.73
2179 2316 5.367945 TTCACCCCAGCCTTATTTAGTAG 57.632 43.478 0.00 0.00 0.00 2.57
2180 2317 5.987019 ATTCACCCCAGCCTTATTTAGTA 57.013 39.130 0.00 0.00 0.00 1.82
2181 2318 4.881157 ATTCACCCCAGCCTTATTTAGT 57.119 40.909 0.00 0.00 0.00 2.24
2182 2319 8.960591 CATTATATTCACCCCAGCCTTATTTAG 58.039 37.037 0.00 0.00 0.00 1.85
2183 2320 7.396055 GCATTATATTCACCCCAGCCTTATTTA 59.604 37.037 0.00 0.00 0.00 1.40
2184 2321 6.211384 GCATTATATTCACCCCAGCCTTATTT 59.789 38.462 0.00 0.00 0.00 1.40
2185 2322 5.716703 GCATTATATTCACCCCAGCCTTATT 59.283 40.000 0.00 0.00 0.00 1.40
2186 2323 5.222316 TGCATTATATTCACCCCAGCCTTAT 60.222 40.000 0.00 0.00 0.00 1.73
2187 2324 4.105537 TGCATTATATTCACCCCAGCCTTA 59.894 41.667 0.00 0.00 0.00 2.69
2188 2325 3.117169 TGCATTATATTCACCCCAGCCTT 60.117 43.478 0.00 0.00 0.00 4.35
2189 2326 2.446666 TGCATTATATTCACCCCAGCCT 59.553 45.455 0.00 0.00 0.00 4.58
2190 2327 2.875296 TGCATTATATTCACCCCAGCC 58.125 47.619 0.00 0.00 0.00 4.85
2191 2328 5.945784 TCTAATGCATTATATTCACCCCAGC 59.054 40.000 19.17 0.00 0.00 4.85
2192 2329 9.334947 CTATCTAATGCATTATATTCACCCCAG 57.665 37.037 19.17 5.45 0.00 4.45
2193 2330 9.056799 TCTATCTAATGCATTATATTCACCCCA 57.943 33.333 19.17 1.25 0.00 4.96
2194 2331 9.553064 CTCTATCTAATGCATTATATTCACCCC 57.447 37.037 19.17 0.00 0.00 4.95
2195 2332 9.050601 GCTCTATCTAATGCATTATATTCACCC 57.949 37.037 19.17 2.53 0.00 4.61
2196 2333 9.829507 AGCTCTATCTAATGCATTATATTCACC 57.170 33.333 19.17 7.02 0.00 4.02
2228 2365 5.066375 GCTTTGCACATGTCATTCCACTATA 59.934 40.000 0.00 0.00 0.00 1.31
2262 2401 6.383436 AGAAATACAGGGAGAAAGGTACCTAC 59.617 42.308 16.67 12.66 0.00 3.18
2263 2402 6.509386 AGAAATACAGGGAGAAAGGTACCTA 58.491 40.000 16.67 0.00 0.00 3.08
2265 2404 5.189145 TGAGAAATACAGGGAGAAAGGTACC 59.811 44.000 2.73 2.73 0.00 3.34
2295 2434 0.966920 ACTACACGGAACTGGGTCAG 59.033 55.000 0.00 0.00 37.52 3.51
2298 2437 0.395312 CCAACTACACGGAACTGGGT 59.605 55.000 0.00 0.00 0.00 4.51
2304 2443 2.156098 GCCAATTCCAACTACACGGAA 58.844 47.619 0.00 0.00 45.12 4.30
2322 2461 4.729918 CCCTGCAGTGGTCTGGCC 62.730 72.222 13.81 0.00 41.57 5.36


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

AutoCloner maintained by Alex Coulton.