Multiple sequence alignment - TraesCS7B01G094200

Loading Multiple Alignment...

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 TraesCS7B01G094200 chr7B 100.000 2072 0 0 750 2821 107974936 107977007 0.000000e+00 3827
1 TraesCS7B01G094200 chr7B 100.000 298 0 0 1 298 107974187 107974484 4.110000e-153 551
2 TraesCS7B01G094200 chr7D 92.431 1123 62 13 762 1865 145906056 145907174 0.000000e+00 1581
3 TraesCS7B01G094200 chr7D 90.368 924 70 9 1911 2821 145907264 145908181 0.000000e+00 1195
4 TraesCS7B01G094200 chr7D 93.289 298 20 0 1 298 145905650 145905947 9.280000e-120 440
5 TraesCS7B01G094200 chr7A 90.679 987 72 14 1849 2821 146678479 146679459 0.000000e+00 1295
6 TraesCS7B01G094200 chr7A 92.911 790 45 6 750 1529 146677306 146678094 0.000000e+00 1138
7 TraesCS7B01G094200 chr7A 92.898 352 22 1 1517 1865 146678115 146678466 2.510000e-140 508
8 TraesCS7B01G094200 chr7A 83.660 306 13 4 1 298 146676938 146677214 1.300000e-63 254


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 TraesCS7B01G094200 chr7B 107974187 107977007 2820 False 2189.00 3827 100.000000 1 2821 2 chr7B.!!$F1 2820
1 TraesCS7B01G094200 chr7D 145905650 145908181 2531 False 1072.00 1581 92.029333 1 2821 3 chr7D.!!$F1 2820
2 TraesCS7B01G094200 chr7A 146676938 146679459 2521 False 798.75 1295 90.037000 1 2821 4 chr7A.!!$F1 2820

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
222 231 1.070821 CGAATCAACTCGCTTCTGCA 58.929 50.0 0.0 0.0 39.64 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2196 2313 0.036732 TGGCAGAAGTAGCACCCTTG 59.963 55.0 0.0 0.0 0.0 3.61 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
56 57 2.742053 TCAAGGAATCGTTTGCTAGTGC 59.258 45.455 0.33 0.00 31.50 4.40
120 129 2.398498 CGAGTCAACTCAGAACAGGTG 58.602 52.381 10.56 0.00 43.00 4.00
184 193 1.332375 CGCGGTTCTTTCAGTTGGAAA 59.668 47.619 0.00 0.00 43.07 3.13
187 196 3.796717 GCGGTTCTTTCAGTTGGAAAAAG 59.203 43.478 0.00 0.00 44.52 2.27
189 198 3.796717 GGTTCTTTCAGTTGGAAAAAGCG 59.203 43.478 0.00 0.00 44.52 4.68
222 231 1.070821 CGAATCAACTCGCTTCTGCA 58.929 50.000 0.00 0.00 39.64 4.41
235 244 2.614057 GCTTCTGCATAAATGGCGTACT 59.386 45.455 0.00 0.00 39.41 2.73
772 787 1.376543 CTGAATGGAACGATGCAGCT 58.623 50.000 0.00 0.00 0.00 4.24
785 802 1.196766 TGCAGCTGTCTCCATGGAGT 61.197 55.000 35.34 17.64 42.49 3.85
884 902 8.821686 TGTAACATCAAATTGACCTAATCCAT 57.178 30.769 0.00 0.00 0.00 3.41
906 924 1.442769 GCAGTCCGCCCATGTATATG 58.557 55.000 0.00 0.00 32.94 1.78
936 954 1.457346 CAGGGAGCATGGACTGTTTC 58.543 55.000 0.00 0.00 0.00 2.78
975 993 6.610741 ACAGTTTTGAGTCTTTGATCAGTC 57.389 37.500 0.00 0.00 0.00 3.51
1220 1238 2.874780 GGCTCTCACGTACGTGCG 60.875 66.667 37.13 32.49 45.04 5.34
1224 1242 0.793478 CTCTCACGTACGTGCGGAAG 60.793 60.000 37.13 29.09 45.04 3.46
1228 1246 0.638746 CACGTACGTGCGGAAGAATC 59.361 55.000 32.93 0.00 39.39 2.52
1235 1254 2.230508 ACGTGCGGAAGAATCTTCAGTA 59.769 45.455 22.71 16.17 0.00 2.74
1247 1266 8.484214 AAGAATCTTCAGTACCTGATAGCATA 57.516 34.615 0.00 0.00 40.39 3.14
1302 1321 8.149647 TGATGCTCCAACTGTTTGAATTTTATT 58.850 29.630 0.00 0.00 34.24 1.40
1332 1358 1.879380 TCTTCGTGGTGGCAAATTCTG 59.121 47.619 0.00 0.00 0.00 3.02
1365 1391 0.826715 TCTCATCCTTTCGCTCCCAG 59.173 55.000 0.00 0.00 0.00 4.45
1427 1453 3.056322 GCAGGCTGGTCTTGATCATTTTT 60.056 43.478 17.64 0.00 0.00 1.94
1443 1469 4.624024 TCATTTTTGACGCGGTAAGACTAG 59.376 41.667 12.47 0.00 0.00 2.57
1446 1472 4.445452 TTTGACGCGGTAAGACTAGATT 57.555 40.909 12.47 0.00 0.00 2.40
1455 1481 6.633634 CGCGGTAAGACTAGATTTTTCTCTAG 59.366 42.308 0.00 6.58 46.75 2.43
1467 1493 6.543831 AGATTTTTCTCTAGTGCAAAGTGTGT 59.456 34.615 0.00 0.00 0.00 3.72
1472 1498 4.122776 CTCTAGTGCAAAGTGTGTCAGTT 58.877 43.478 0.00 0.00 0.00 3.16
1473 1499 4.513442 TCTAGTGCAAAGTGTGTCAGTTT 58.487 39.130 0.00 0.00 37.47 2.66
1474 1500 3.764885 AGTGCAAAGTGTGTCAGTTTC 57.235 42.857 0.00 0.00 35.17 2.78
1475 1501 3.081061 AGTGCAAAGTGTGTCAGTTTCA 58.919 40.909 0.00 0.94 35.17 2.69
1479 1505 4.233789 GCAAAGTGTGTCAGTTTCAAACA 58.766 39.130 2.41 0.00 35.17 2.83
1480 1506 4.089923 GCAAAGTGTGTCAGTTTCAAACAC 59.910 41.667 2.41 0.00 42.80 3.32
1484 1510 4.088648 GTGTGTCAGTTTCAAACACTTCG 58.911 43.478 2.41 0.00 42.89 3.79
1489 1515 6.627671 GTGTCAGTTTCAAACACTTCGATTAC 59.372 38.462 2.41 0.00 40.07 1.89
1497 1523 8.771920 TTCAAACACTTCGATTACTATCATGT 57.228 30.769 0.00 0.00 0.00 3.21
1534 1593 9.982651 GAAACTATGCATGGTTACTAATCTAGA 57.017 33.333 26.27 0.00 30.91 2.43
1559 1618 5.916661 ATTGAAGAAAGAGAAGCATGCAT 57.083 34.783 21.98 8.13 0.00 3.96
1568 1627 5.752892 AGAGAAGCATGCATCAATAACTG 57.247 39.130 23.62 0.00 0.00 3.16
1580 1639 7.951591 TGCATCAATAACTGTATCAGCTACTA 58.048 34.615 0.00 0.00 34.37 1.82
1581 1640 8.421002 TGCATCAATAACTGTATCAGCTACTAA 58.579 33.333 0.00 0.00 34.37 2.24
1582 1641 8.920665 GCATCAATAACTGTATCAGCTACTAAG 58.079 37.037 0.00 0.00 34.37 2.18
1592 1657 7.097192 TGTATCAGCTACTAAGTTTCCTTGTG 58.903 38.462 0.00 0.00 31.89 3.33
1622 1687 0.179936 AGGCAATGCTAGCTCTGGTC 59.820 55.000 17.23 2.39 0.00 4.02
1661 1726 4.436584 GCAGCAACAGCTATTGTCTACTTG 60.437 45.833 6.59 0.00 39.73 3.16
1700 1765 5.972952 TCAGGGCAAACTGGCTTGCTATT 62.973 47.826 13.97 1.58 46.99 1.73
1732 1797 2.159099 TGGATTCTTTCTGCGAGCGTAT 60.159 45.455 0.00 0.00 0.00 3.06
1770 1835 1.247567 CTCGTTTGGAGCCATGGTTT 58.752 50.000 14.67 1.53 35.63 3.27
1788 1853 3.691118 GGTTTTGCTGATACTGCTCATCA 59.309 43.478 0.00 0.00 0.00 3.07
1802 1867 3.390311 TGCTCATCATACTCTCAGCCATT 59.610 43.478 0.00 0.00 0.00 3.16
1808 1873 0.543277 TACTCTCAGCCATTGCCCTG 59.457 55.000 0.00 0.00 38.69 4.45
1829 1894 0.734889 CCAGGCGCTAGACCAAATTG 59.265 55.000 7.64 0.00 0.00 2.32
1865 1930 6.870965 GCTCCCTGAAGTATAAGTGTGATATG 59.129 42.308 0.00 0.00 0.00 1.78
1866 1931 7.303182 TCCCTGAAGTATAAGTGTGATATGG 57.697 40.000 0.00 0.00 0.00 2.74
1867 1932 6.844388 TCCCTGAAGTATAAGTGTGATATGGT 59.156 38.462 0.00 0.00 0.00 3.55
1885 1978 1.263217 GGTGTGGTTCTTGTACTTGCG 59.737 52.381 0.00 0.00 0.00 4.85
1887 1980 1.937223 TGTGGTTCTTGTACTTGCGTG 59.063 47.619 0.00 0.00 0.00 5.34
1891 1984 2.803956 GGTTCTTGTACTTGCGTGCTTA 59.196 45.455 0.00 0.00 0.00 3.09
1902 1995 8.332464 TGTACTTGCGTGCTTAATGTAATAATC 58.668 33.333 0.00 0.00 0.00 1.75
1907 2000 6.536941 TGCGTGCTTAATGTAATAATCTGTGA 59.463 34.615 0.00 0.00 0.00 3.58
1931 2045 2.057137 ATATTGTGCACCGCCTTGAT 57.943 45.000 15.69 0.00 0.00 2.57
1933 2047 1.597797 ATTGTGCACCGCCTTGATGG 61.598 55.000 15.69 0.00 39.35 3.51
1934 2048 2.672996 GTGCACCGCCTTGATGGT 60.673 61.111 5.22 0.00 39.66 3.55
1947 2061 4.083271 GCCTTGATGGTGTGTTACTTCTTC 60.083 45.833 0.00 0.00 38.35 2.87
1957 2071 4.219944 TGTGTTACTTCTTCTGTATCGGCT 59.780 41.667 0.00 0.00 0.00 5.52
1974 2088 6.823678 ATCGGCTTTTGTACTTCTTATACG 57.176 37.500 0.00 0.00 0.00 3.06
1978 2092 6.540205 GGCTTTTGTACTTCTTATACGGTTG 58.460 40.000 0.00 0.00 0.00 3.77
2020 2136 7.608761 TCATGGTTTGGGTACTATACTTTTCAC 59.391 37.037 0.00 0.00 0.00 3.18
2021 2137 7.081857 TGGTTTGGGTACTATACTTTTCACT 57.918 36.000 0.00 0.00 0.00 3.41
2023 2139 6.373495 GGTTTGGGTACTATACTTTTCACTGG 59.627 42.308 0.00 0.00 0.00 4.00
2026 2142 5.105064 TGGGTACTATACTTTTCACTGGAGC 60.105 44.000 0.00 0.00 0.00 4.70
2029 2145 5.746990 ACTATACTTTTCACTGGAGCTGT 57.253 39.130 0.00 0.00 0.00 4.40
2036 2152 3.569194 TTCACTGGAGCTGTTGGTAAA 57.431 42.857 0.00 0.00 0.00 2.01
2084 2200 5.164620 TGAGACATGTCATTAGCTGGAAA 57.835 39.130 27.02 0.00 0.00 3.13
2130 2246 2.290514 TGCTGCTAGCTCCAAGTGAAAT 60.291 45.455 17.23 0.00 42.97 2.17
2133 2249 4.197750 CTGCTAGCTCCAAGTGAAATCAT 58.802 43.478 17.23 0.00 0.00 2.45
2136 2252 4.637534 GCTAGCTCCAAGTGAAATCATCAA 59.362 41.667 7.70 0.00 40.50 2.57
2139 2255 4.217118 AGCTCCAAGTGAAATCATCAACAC 59.783 41.667 0.00 0.00 40.50 3.32
2141 2257 5.618640 GCTCCAAGTGAAATCATCAACACTC 60.619 44.000 0.00 0.00 41.73 3.51
2143 2259 4.452114 CCAAGTGAAATCATCAACACTCGA 59.548 41.667 0.00 0.00 41.73 4.04
2154 2271 4.190304 TCAACACTCGACGTTTTGAATG 57.810 40.909 11.58 0.00 38.86 2.67
2164 2281 6.359545 TCGACGTTTTGAATGTGATTTACTG 58.640 36.000 0.00 0.00 0.00 2.74
2171 2288 8.784043 GTTTTGAATGTGATTTACTGTCTAGGT 58.216 33.333 0.00 0.00 0.00 3.08
2182 2299 3.358118 ACTGTCTAGGTCTCCTTGCTAC 58.642 50.000 0.00 0.00 34.61 3.58
2190 2307 3.031736 GGTCTCCTTGCTACTGGTATCA 58.968 50.000 0.00 0.00 0.00 2.15
2192 2309 2.695666 TCTCCTTGCTACTGGTATCAGC 59.304 50.000 1.90 0.00 44.59 4.26
2193 2310 2.432146 CTCCTTGCTACTGGTATCAGCA 59.568 50.000 1.90 0.00 44.59 4.41
2196 2313 4.039245 TCCTTGCTACTGGTATCAGCATAC 59.961 45.833 1.90 0.00 44.29 2.39
2197 2314 4.202253 CCTTGCTACTGGTATCAGCATACA 60.202 45.833 1.90 0.00 44.29 2.29
2211 2328 3.268023 GCATACAAGGGTGCTACTTCT 57.732 47.619 0.00 0.00 38.30 2.85
2212 2329 2.939103 GCATACAAGGGTGCTACTTCTG 59.061 50.000 0.00 0.00 38.30 3.02
2225 2343 2.736670 ACTTCTGCCACTTTCTGGTT 57.263 45.000 0.00 0.00 42.99 3.67
2230 2348 0.250553 TGCCACTTTCTGGTTACCGG 60.251 55.000 3.32 3.32 42.99 5.28
2241 2359 2.360801 CTGGTTACCGGGCATAAAATGG 59.639 50.000 6.32 0.00 0.00 3.16
2242 2360 2.025226 TGGTTACCGGGCATAAAATGGA 60.025 45.455 6.32 0.00 0.00 3.41
2245 2363 4.081586 GGTTACCGGGCATAAAATGGAAAA 60.082 41.667 6.32 0.00 0.00 2.29
2247 2365 2.900546 ACCGGGCATAAAATGGAAAACA 59.099 40.909 6.32 0.00 0.00 2.83
2262 2380 3.550842 GGAAAACAGAGCATGGACACAAC 60.551 47.826 0.00 0.00 0.00 3.32
2265 2383 0.037303 CAGAGCATGGACACAACCCT 59.963 55.000 0.00 0.00 0.00 4.34
2266 2384 1.278985 CAGAGCATGGACACAACCCTA 59.721 52.381 0.00 0.00 0.00 3.53
2267 2385 1.556911 AGAGCATGGACACAACCCTAG 59.443 52.381 0.00 0.00 0.00 3.02
2268 2386 1.279271 GAGCATGGACACAACCCTAGT 59.721 52.381 0.00 0.00 0.00 2.57
2269 2387 2.500098 GAGCATGGACACAACCCTAGTA 59.500 50.000 0.00 0.00 0.00 1.82
2281 2399 6.761714 ACACAACCCTAGTATTCATCGAATTC 59.238 38.462 0.00 0.00 33.95 2.17
2284 2402 6.688073 ACCCTAGTATTCATCGAATTCCAT 57.312 37.500 0.00 0.00 33.95 3.41
2453 2579 3.806380 CCAGAGAGCAGCACATAATCTT 58.194 45.455 0.00 0.00 0.00 2.40
2569 2695 3.068165 TCCATATGACTGCACTAGGTTCG 59.932 47.826 3.65 0.00 0.00 3.95
2781 2907 1.276989 AGCATTTGGGCACATTCCTTG 59.723 47.619 0.00 0.00 35.83 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
162 171 1.082104 CAACTGAAAGAACCGCGCC 60.082 57.895 0.00 0.00 37.43 6.53
166 175 3.796717 GCTTTTTCCAACTGAAAGAACCG 59.203 43.478 0.00 0.00 43.57 4.44
184 193 2.995938 GCGTATTGTTTCGCGCTTT 58.004 47.368 5.56 0.00 45.48 3.51
235 244 4.344104 CTTTTTCATAAGAGGAAGGGGCA 58.656 43.478 0.00 0.00 0.00 5.36
785 802 1.209504 GCTGGTACCTGCTCCACATAA 59.790 52.381 30.48 0.00 37.80 1.90
904 922 6.616959 TCCATGCTCCCTGCTTATATATACAT 59.383 38.462 0.00 0.00 43.37 2.29
906 924 6.098982 AGTCCATGCTCCCTGCTTATATATAC 59.901 42.308 0.00 0.00 43.37 1.47
936 954 1.421646 ACTGTTTCCCAGGTCTGAAGG 59.578 52.381 0.00 0.00 46.06 3.46
975 993 5.415701 TCTGGTATTTTTCTTAAGCTGCTGG 59.584 40.000 1.35 0.00 0.00 4.85
1235 1254 9.760926 TCTATCTGAAAGTATATGCTATCAGGT 57.239 33.333 0.00 0.00 35.99 4.00
1260 1279 5.238214 GGAGCATCAGATCATAACCTTGTTC 59.762 44.000 0.00 0.00 36.25 3.18
1263 1282 4.711399 TGGAGCATCAGATCATAACCTTG 58.289 43.478 0.00 0.00 36.25 3.61
1302 1321 2.285083 CACCACGAAGAACCTGTCAAA 58.715 47.619 0.00 0.00 0.00 2.69
1332 1358 2.131183 GATGAGATAGGCGCTCACAAC 58.869 52.381 7.64 0.00 44.39 3.32
1365 1391 4.734854 CCTAATTATGTGCGCAATTGACAC 59.265 41.667 14.00 19.59 34.86 3.67
1427 1453 4.445452 AAAATCTAGTCTTACCGCGTCA 57.555 40.909 4.92 0.00 0.00 4.35
1443 1469 6.729187 ACACACTTTGCACTAGAGAAAAATC 58.271 36.000 0.00 0.00 0.00 2.17
1446 1472 5.182487 TGACACACTTTGCACTAGAGAAAA 58.818 37.500 0.00 0.00 0.00 2.29
1455 1481 3.485947 TGAAACTGACACACTTTGCAC 57.514 42.857 0.00 0.00 0.00 4.57
1457 1483 4.089923 GTGTTTGAAACTGACACACTTTGC 59.910 41.667 9.69 0.00 42.36 3.68
1467 1493 8.827177 ATAGTAATCGAAGTGTTTGAAACTGA 57.173 30.769 9.69 0.65 30.46 3.41
1472 1498 8.771920 ACATGATAGTAATCGAAGTGTTTGAA 57.228 30.769 0.00 0.00 34.60 2.69
1473 1499 8.032451 TGACATGATAGTAATCGAAGTGTTTGA 58.968 33.333 0.00 0.00 34.60 2.69
1474 1500 8.185003 TGACATGATAGTAATCGAAGTGTTTG 57.815 34.615 0.00 0.00 34.60 2.93
1475 1501 8.948631 ATGACATGATAGTAATCGAAGTGTTT 57.051 30.769 0.00 0.00 34.60 2.83
1479 1505 7.374272 CAGGATGACATGATAGTAATCGAAGT 58.626 38.462 0.00 0.00 39.69 3.01
1480 1506 6.309980 GCAGGATGACATGATAGTAATCGAAG 59.690 42.308 0.00 0.00 39.69 3.79
1484 1510 7.101700 TCATGCAGGATGACATGATAGTAATC 58.898 38.462 0.00 0.00 46.66 1.75
1534 1593 7.400599 TGCATGCTTCTCTTTCTTCAATATT 57.599 32.000 20.33 0.00 0.00 1.28
1538 1597 4.763279 TGATGCATGCTTCTCTTTCTTCAA 59.237 37.500 27.81 6.91 0.00 2.69
1580 1639 6.389906 CTTCACAAGAAACACAAGGAAACTT 58.610 36.000 0.00 0.00 42.06 2.66
1581 1640 5.105756 CCTTCACAAGAAACACAAGGAAACT 60.106 40.000 0.00 0.00 35.98 2.66
1582 1641 5.102313 CCTTCACAAGAAACACAAGGAAAC 58.898 41.667 0.00 0.00 33.50 2.78
1592 1657 3.375782 AGCATTGCCTTCACAAGAAAC 57.624 42.857 4.70 0.00 32.35 2.78
1661 1726 1.290009 GACATTGCCCTTGTGTGCC 59.710 57.895 0.00 0.00 0.00 5.01
1673 1738 0.037975 GCCAGTTTGCCCTGACATTG 60.038 55.000 0.00 0.00 34.23 2.82
1700 1765 3.579586 AGAAAGAATCCAATTGCTGGCAA 59.420 39.130 10.48 10.48 45.98 4.52
1709 1774 1.667724 CGCTCGCAGAAAGAATCCAAT 59.332 47.619 0.00 0.00 34.09 3.16
1732 1797 1.920325 CCAACCAGGGAGCCAGAGA 60.920 63.158 0.00 0.00 0.00 3.10
1788 1853 1.142465 CAGGGCAATGGCTGAGAGTAT 59.858 52.381 6.78 0.00 40.87 2.12
1808 1873 2.893682 ATTTGGTCTAGCGCCTGGCC 62.894 60.000 14.12 13.16 45.17 5.36
1824 1889 4.081309 CAGGGAGCAAATGATGGACAATTT 60.081 41.667 0.00 0.00 0.00 1.82
1829 1894 2.425143 TCAGGGAGCAAATGATGGAC 57.575 50.000 0.00 0.00 0.00 4.02
1865 1930 1.263217 CGCAAGTACAAGAACCACACC 59.737 52.381 0.00 0.00 0.00 4.16
1866 1931 2.663279 CGCAAGTACAAGAACCACAC 57.337 50.000 0.00 0.00 0.00 3.82
1885 1978 7.227512 AGGCTCACAGATTATTACATTAAGCAC 59.772 37.037 0.00 0.00 0.00 4.40
1887 1980 7.736447 AGGCTCACAGATTATTACATTAAGC 57.264 36.000 0.00 0.00 0.00 3.09
1902 1995 2.874701 GGTGCACAATATAGGCTCACAG 59.125 50.000 20.43 0.00 0.00 3.66
1907 2000 0.535102 GGCGGTGCACAATATAGGCT 60.535 55.000 20.43 0.00 0.00 4.58
1931 2045 5.466819 CGATACAGAAGAAGTAACACACCA 58.533 41.667 0.00 0.00 0.00 4.17
1933 2047 4.326548 GCCGATACAGAAGAAGTAACACAC 59.673 45.833 0.00 0.00 0.00 3.82
1934 2048 4.219944 AGCCGATACAGAAGAAGTAACACA 59.780 41.667 0.00 0.00 0.00 3.72
1947 2061 7.772332 ATAAGAAGTACAAAAGCCGATACAG 57.228 36.000 0.00 0.00 0.00 2.74
1957 2071 9.539825 TGTAACAACCGTATAAGAAGTACAAAA 57.460 29.630 0.00 0.00 0.00 2.44
1993 2109 8.333235 TGAAAAGTATAGTACCCAAACCATGAT 58.667 33.333 0.00 0.00 0.00 2.45
2000 2116 7.319052 TCCAGTGAAAAGTATAGTACCCAAA 57.681 36.000 0.00 0.00 0.00 3.28
2004 2120 6.043411 CAGCTCCAGTGAAAAGTATAGTACC 58.957 44.000 0.00 0.00 0.00 3.34
2020 2136 4.616835 GCAGAAATTTACCAACAGCTCCAG 60.617 45.833 0.00 0.00 0.00 3.86
2021 2137 3.255642 GCAGAAATTTACCAACAGCTCCA 59.744 43.478 0.00 0.00 0.00 3.86
2023 2139 4.503741 TGCAGAAATTTACCAACAGCTC 57.496 40.909 0.00 0.00 0.00 4.09
2026 2142 8.946085 TCTAGTTATGCAGAAATTTACCAACAG 58.054 33.333 0.00 0.00 0.00 3.16
2062 2178 4.824479 TTCCAGCTAATGACATGTCTCA 57.176 40.909 25.55 8.56 0.00 3.27
2066 2182 4.263462 TGGAGTTTCCAGCTAATGACATGT 60.263 41.667 0.00 0.00 42.67 3.21
2084 2200 2.990066 GCAACTAGCAGGTATGGAGT 57.010 50.000 0.00 0.00 44.79 3.85
2117 2233 4.217118 AGTGTTGATGATTTCACTTGGAGC 59.783 41.667 0.00 0.00 37.81 4.70
2136 2252 3.191669 TCACATTCAAAACGTCGAGTGT 58.808 40.909 0.00 5.32 32.91 3.55
2139 2255 6.516355 CAGTAAATCACATTCAAAACGTCGAG 59.484 38.462 0.00 0.00 0.00 4.04
2141 2257 6.133392 ACAGTAAATCACATTCAAAACGTCG 58.867 36.000 0.00 0.00 0.00 5.12
2143 2259 7.259290 AGACAGTAAATCACATTCAAAACGT 57.741 32.000 0.00 0.00 0.00 3.99
2154 2271 6.334202 CAAGGAGACCTAGACAGTAAATCAC 58.666 44.000 0.00 0.00 31.13 3.06
2164 2281 2.691011 CCAGTAGCAAGGAGACCTAGAC 59.309 54.545 0.00 0.00 31.13 2.59
2171 2288 2.695666 GCTGATACCAGTAGCAAGGAGA 59.304 50.000 0.00 0.00 42.35 3.71
2182 2299 3.470709 CACCCTTGTATGCTGATACCAG 58.529 50.000 0.00 0.00 43.22 4.00
2192 2309 2.939103 GCAGAAGTAGCACCCTTGTATG 59.061 50.000 0.00 0.00 0.00 2.39
2193 2310 2.092914 GGCAGAAGTAGCACCCTTGTAT 60.093 50.000 0.00 0.00 0.00 2.29
2196 2313 0.036732 TGGCAGAAGTAGCACCCTTG 59.963 55.000 0.00 0.00 0.00 3.61
2197 2314 0.036875 GTGGCAGAAGTAGCACCCTT 59.963 55.000 0.00 0.00 0.00 3.95
2225 2343 4.087182 TGTTTTCCATTTTATGCCCGGTA 58.913 39.130 0.00 0.00 0.00 4.02
2230 2348 4.819769 TGCTCTGTTTTCCATTTTATGCC 58.180 39.130 0.00 0.00 0.00 4.40
2241 2359 3.550842 GGTTGTGTCCATGCTCTGTTTTC 60.551 47.826 0.00 0.00 0.00 2.29
2242 2360 2.362077 GGTTGTGTCCATGCTCTGTTTT 59.638 45.455 0.00 0.00 0.00 2.43
2245 2363 0.250901 GGGTTGTGTCCATGCTCTGT 60.251 55.000 0.00 0.00 0.00 3.41
2247 2365 1.556911 CTAGGGTTGTGTCCATGCTCT 59.443 52.381 0.00 0.00 0.00 4.09
2262 2380 6.936900 ACAATGGAATTCGATGAATACTAGGG 59.063 38.462 3.50 0.00 31.22 3.53
2265 2383 8.866093 TCCTACAATGGAATTCGATGAATACTA 58.134 33.333 3.50 0.00 31.22 1.82
2266 2384 7.735917 TCCTACAATGGAATTCGATGAATACT 58.264 34.615 3.50 0.00 31.22 2.12
2267 2385 7.962964 TCCTACAATGGAATTCGATGAATAC 57.037 36.000 3.50 0.00 31.22 1.89
2269 2387 9.388506 GATATCCTACAATGGAATTCGATGAAT 57.611 33.333 3.50 0.00 39.85 2.57
2281 2399 5.702670 GTGATGTGTGGATATCCTACAATGG 59.297 44.000 25.79 0.00 37.35 3.16
2284 2402 5.948742 TGTGATGTGTGGATATCCTACAA 57.051 39.130 25.79 16.93 37.35 2.41
2453 2579 4.707030 AAATGAATGAAGATGCAAGCGA 57.293 36.364 0.00 0.00 0.00 4.93
2696 2822 6.705381 GGATTAGTTGAAGATGGTCAGAGATG 59.295 42.308 0.00 0.00 0.00 2.90
2781 2907 9.206870 TCCAATTCTTCAATAAAATGCTTCAAC 57.793 29.630 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.