Multiple sequence alignment - TraesCS6A01G260500

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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 TraesCS6A01G260500 chr6A 100.000 2177 0 0 461 2637 484038596 484040772 0.000000e+00 4021.0
1 TraesCS6A01G260500 chr6A 100.000 76 0 0 1 76 484038136 484038211 9.840000e-30 141.0
2 TraesCS6A01G260500 chr6B 93.728 1419 76 10 463 1876 518591376 518592786 0.000000e+00 2115.0
3 TraesCS6A01G260500 chr6B 97.368 76 2 0 1 76 518591202 518591277 2.130000e-26 130.0
4 TraesCS6A01G260500 chr6D 94.034 1341 59 13 463 1787 343616625 343617960 0.000000e+00 2013.0
5 TraesCS6A01G260500 chr6D 77.188 377 32 28 2261 2595 343621571 343621935 1.260000e-38 171.0
6 TraesCS6A01G260500 chr6D 94.737 76 4 0 1 76 343616382 343616457 4.610000e-23 119.0
7 TraesCS6A01G260500 chr6D 95.522 67 2 1 1879 1945 343619759 343619824 3.590000e-19 106.0
8 TraesCS6A01G260500 chr6D 92.857 56 4 0 1823 1878 343619388 343619443 6.050000e-12 82.4
9 TraesCS6A01G260500 chr2D 79.878 164 26 6 2059 2221 57255122 57255279 2.150000e-21 113.0
10 TraesCS6A01G260500 chr3B 87.342 79 10 0 2047 2125 744183589 744183667 1.010000e-14 91.6
11 TraesCS6A01G260500 chr3B 77.215 158 33 3 2065 2221 20157908 20157753 3.620000e-14 89.8


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 TraesCS6A01G260500 chr6A 484038136 484040772 2636 False 2081.00 4021 100.0000 1 2637 2 chr6A.!!$F1 2636
1 TraesCS6A01G260500 chr6B 518591202 518592786 1584 False 1122.50 2115 95.5480 1 1876 2 chr6B.!!$F1 1875
2 TraesCS6A01G260500 chr6D 343616382 343621935 5553 False 498.28 2013 90.8676 1 2595 5 chr6D.!!$F1 2594

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
821 825 1.069535 AAAGGGGGAAACGGAAGGGA 61.07 55.0 0.0 0.0 0.0 4.2 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1756 1774 0.240945 CATGGTTCGGAGTGGTTTGC 59.759 55.0 0.0 0.0 0.0 3.68 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
50 51 6.515272 TCATAAGCAACTGAATTTCCCTTC 57.485 37.500 0.00 0.00 0.00 3.46
653 656 6.533723 ACGAACAAATATGATAAACTCGCTCA 59.466 34.615 0.00 0.00 0.00 4.26
805 809 5.835113 TGAAGACCAGGACAAAAGAAAAG 57.165 39.130 0.00 0.00 0.00 2.27
821 825 1.069535 AAAGGGGGAAACGGAAGGGA 61.070 55.000 0.00 0.00 0.00 4.20
830 834 1.639722 AACGGAAGGGAAAAATGGGG 58.360 50.000 0.00 0.00 0.00 4.96
880 884 6.157211 AGTAAACTACATGTGTCGAAGGAAG 58.843 40.000 9.11 0.00 0.00 3.46
883 887 2.457366 ACATGTGTCGAAGGAAGACC 57.543 50.000 0.00 0.00 37.80 3.85
896 900 1.542547 GGAAGACCGAGTTTGCAGGAA 60.543 52.381 0.00 0.00 0.00 3.36
943 947 4.226761 CTCCAAATAAACGCCAACAAGAC 58.773 43.478 0.00 0.00 0.00 3.01
1018 1022 3.387699 TCCATACATGTAGCTGCTTAGCA 59.612 43.478 7.79 6.76 37.25 3.49
1075 1079 3.654414 AGAGAGTGAATCAACGACCAAC 58.346 45.455 0.00 0.00 0.00 3.77
1081 1085 4.398044 AGTGAATCAACGACCAACAAACTT 59.602 37.500 0.00 0.00 0.00 2.66
1102 1106 3.846180 ATGGCATCCAACCATCGC 58.154 55.556 0.00 0.00 44.85 4.58
1291 1295 2.743928 CTGGTGAAGGAGCGGTGC 60.744 66.667 0.00 0.00 0.00 5.01
1554 1566 1.173043 TTGCCCAAGTAATGAAGCGG 58.827 50.000 0.00 0.00 32.57 5.52
1584 1596 2.761208 ACTGGCAGATGGAGTACTGTAC 59.239 50.000 23.66 9.93 36.62 2.90
1631 1643 9.677567 TGAGAACAAATAAATAAAGCTTGTGAC 57.322 29.630 0.00 0.00 30.90 3.67
1632 1644 9.899226 GAGAACAAATAAATAAAGCTTGTGACT 57.101 29.630 0.00 0.00 30.90 3.41
1636 1648 9.248291 ACAAATAAATAAAGCTTGTGACTTGTG 57.752 29.630 0.00 0.00 0.00 3.33
1637 1649 9.462174 CAAATAAATAAAGCTTGTGACTTGTGA 57.538 29.630 0.00 0.00 0.00 3.58
1640 1652 2.338577 AAGCTTGTGACTTGTGAGCT 57.661 45.000 0.00 0.00 44.95 4.09
1641 1653 1.590932 AGCTTGTGACTTGTGAGCTG 58.409 50.000 0.00 0.00 41.75 4.24
1668 1686 5.040635 GGTGTGGACTGTTAAATTGTTGTG 58.959 41.667 0.00 0.00 0.00 3.33
1756 1774 4.527564 GGAAATTACAGATTTGATCGCCG 58.472 43.478 0.00 0.00 0.00 6.46
1782 1800 0.247736 ACTCCGAACCATGAGTCTGC 59.752 55.000 0.00 0.00 37.24 4.26
1815 1834 9.935241 TGATTAGCATATTGGATTCTCTAACTC 57.065 33.333 0.00 0.00 0.00 3.01
1893 3640 3.258123 AGCATCCTTTGTTTTTACCGCAT 59.742 39.130 0.00 0.00 0.00 4.73
1932 3679 1.633774 TTTTCGCATTGGCCCCTTTA 58.366 45.000 0.00 0.00 36.38 1.85
1940 4854 3.679639 GCATTGGCCCCTTTATGTTTCTG 60.680 47.826 0.00 0.00 0.00 3.02
1946 4860 3.306019 GCCCCTTTATGTTTCTGTGTTGG 60.306 47.826 0.00 0.00 0.00 3.77
1963 4877 0.536460 TGGGTCGTTTGGGCTTTCTC 60.536 55.000 0.00 0.00 0.00 2.87
1981 4928 7.094634 GGCTTTCTCTGTTTTCATGTCTATTGA 60.095 37.037 0.00 0.00 0.00 2.57
1989 4936 5.426689 TTTCATGTCTATTGAGCTGAGGT 57.573 39.130 0.00 0.00 0.00 3.85
1990 4937 4.397481 TCATGTCTATTGAGCTGAGGTG 57.603 45.455 0.00 0.00 0.00 4.00
2025 4972 2.291153 TGTTACGGAGGTAGTAGCTGGT 60.291 50.000 6.60 7.19 0.00 4.00
2046 5011 0.599204 ACATATTCCGCTAACGCCCG 60.599 55.000 0.00 0.00 38.22 6.13
2050 5015 4.781959 TCCGCTAACGCCCGAACG 62.782 66.667 0.00 0.00 38.22 3.95
2064 5029 2.713927 CGAACGTTCGGGATTTGATC 57.286 50.000 36.53 4.10 46.30 2.92
2069 5034 1.002468 CGTTCGGGATTTGATCATGGC 60.002 52.381 0.00 0.00 0.00 4.40
2080 5045 4.987408 TTGATCATGGCAAATCGAATGT 57.013 36.364 0.00 0.00 0.00 2.71
2084 5049 5.806502 TGATCATGGCAAATCGAATGTTTTC 59.193 36.000 0.00 0.00 0.00 2.29
2085 5050 5.131594 TCATGGCAAATCGAATGTTTTCA 57.868 34.783 0.00 0.00 0.00 2.69
2089 5054 4.689812 TGGCAAATCGAATGTTTTCAATGG 59.310 37.500 0.00 0.00 0.00 3.16
2090 5055 4.435917 GGCAAATCGAATGTTTTCAATGGC 60.436 41.667 0.00 0.00 0.00 4.40
2097 5062 6.886307 TCGAATGTTTTCAATGGCAATTTTC 58.114 32.000 0.00 0.00 0.00 2.29
2099 5064 6.563753 CGAATGTTTTCAATGGCAATTTTCGT 60.564 34.615 6.44 0.00 28.57 3.85
2102 5067 5.006165 TGTTTTCAATGGCAATTTTCGTGAC 59.994 36.000 0.00 0.00 0.00 3.67
2105 5070 0.454285 ATGGCAATTTTCGTGACGCG 60.454 50.000 3.53 3.53 43.01 6.01
2116 5081 0.366871 CGTGACGCGAGGATGAAAAG 59.633 55.000 15.93 0.00 44.77 2.27
2124 5089 4.084013 ACGCGAGGATGAAAAGTTTAGTTG 60.084 41.667 15.93 0.00 0.00 3.16
2134 5099 4.935352 AAAGTTTAGTTGGCAAGCATGA 57.065 36.364 0.00 0.00 0.00 3.07
2190 5155 5.220700 GGAATTGTCGTGTGTGTCAACTAAA 60.221 40.000 0.00 0.00 0.00 1.85
2198 5163 5.390040 CGTGTGTGTCAACTAAACTTGTCAA 60.390 40.000 0.00 0.00 0.00 3.18
2202 5167 5.123186 TGTGTCAACTAAACTTGTCAACCTG 59.877 40.000 0.00 0.00 0.00 4.00
2204 5169 4.638865 GTCAACTAAACTTGTCAACCTGGT 59.361 41.667 0.00 0.00 0.00 4.00
2205 5170 4.638421 TCAACTAAACTTGTCAACCTGGTG 59.362 41.667 0.00 0.00 0.00 4.17
2208 5173 2.799126 AACTTGTCAACCTGGTGTCA 57.201 45.000 0.00 0.00 0.00 3.58
2221 5186 3.320541 CCTGGTGTCACTAAAATTGCCAA 59.679 43.478 2.35 0.00 0.00 4.52
2222 5187 4.549458 CTGGTGTCACTAAAATTGCCAAG 58.451 43.478 2.35 0.00 0.00 3.61
2226 5191 5.462068 GGTGTCACTAAAATTGCCAAGAAAC 59.538 40.000 2.35 0.00 0.00 2.78
2227 5192 5.173131 GTGTCACTAAAATTGCCAAGAAACG 59.827 40.000 0.00 0.00 0.00 3.60
2228 5193 4.679654 GTCACTAAAATTGCCAAGAAACGG 59.320 41.667 0.00 0.00 0.00 4.44
2229 5194 4.339814 TCACTAAAATTGCCAAGAAACGGT 59.660 37.500 0.00 0.00 0.00 4.83
2230 5195 5.531659 TCACTAAAATTGCCAAGAAACGGTA 59.468 36.000 0.00 0.00 0.00 4.02
2231 5196 6.039493 TCACTAAAATTGCCAAGAAACGGTAA 59.961 34.615 0.00 0.00 32.38 2.85
2232 5197 6.866248 CACTAAAATTGCCAAGAAACGGTAAT 59.134 34.615 0.00 0.00 40.14 1.89
2233 5198 7.383843 CACTAAAATTGCCAAGAAACGGTAATT 59.616 33.333 0.00 0.00 46.73 1.40
2236 5201 6.779115 AATTGCCAAGAAACGGTAATTTTC 57.221 33.333 0.00 0.00 43.65 2.29
2237 5202 4.920640 TGCCAAGAAACGGTAATTTTCA 57.079 36.364 0.00 0.00 35.72 2.69
2239 5204 4.339814 TGCCAAGAAACGGTAATTTTCAGT 59.660 37.500 0.00 0.00 35.72 3.41
2240 5205 5.163499 TGCCAAGAAACGGTAATTTTCAGTT 60.163 36.000 0.00 0.00 35.72 3.16
2243 5208 7.597369 GCCAAGAAACGGTAATTTTCAGTTATT 59.403 33.333 0.00 0.00 35.72 1.40
2244 5209 9.471084 CCAAGAAACGGTAATTTTCAGTTATTT 57.529 29.630 0.00 0.00 35.72 1.40
2246 5211 9.471084 AAGAAACGGTAATTTTCAGTTATTTGG 57.529 29.630 0.00 0.00 35.72 3.28
2247 5212 8.085909 AGAAACGGTAATTTTCAGTTATTTGGG 58.914 33.333 0.00 0.00 35.72 4.12
2248 5213 6.904463 ACGGTAATTTTCAGTTATTTGGGT 57.096 33.333 0.00 0.00 0.00 4.51
2249 5214 6.916440 ACGGTAATTTTCAGTTATTTGGGTC 58.084 36.000 0.00 0.00 0.00 4.46
2250 5215 6.071784 ACGGTAATTTTCAGTTATTTGGGTCC 60.072 38.462 0.00 0.00 0.00 4.46
2251 5216 6.327154 GGTAATTTTCAGTTATTTGGGTCCG 58.673 40.000 0.00 0.00 0.00 4.79
2252 5217 5.400066 AATTTTCAGTTATTTGGGTCCGG 57.600 39.130 0.00 0.00 0.00 5.14
2254 5219 0.034863 TCAGTTATTTGGGTCCGGCC 60.035 55.000 0.00 0.36 0.00 6.13
2272 5456 3.021695 GGCCCAATTAGGTGTAAGGAAC 58.978 50.000 0.00 0.00 34.66 3.62
2275 5459 3.275999 CCAATTAGGTGTAAGGAACCCG 58.724 50.000 0.00 0.00 38.57 5.28
2295 5479 3.922850 CCGGTTTTACGAACCTTCTAGAC 59.077 47.826 6.40 0.00 38.15 2.59
2296 5480 4.321527 CCGGTTTTACGAACCTTCTAGACT 60.322 45.833 6.40 0.00 38.15 3.24
2297 5481 5.225642 CGGTTTTACGAACCTTCTAGACTT 58.774 41.667 6.40 0.00 38.15 3.01
2300 5484 7.568315 CGGTTTTACGAACCTTCTAGACTTTTC 60.568 40.741 6.40 0.00 38.15 2.29
2301 5485 7.307632 GGTTTTACGAACCTTCTAGACTTTTCC 60.308 40.741 0.00 0.00 37.34 3.13
2302 5486 6.661304 TTACGAACCTTCTAGACTTTTCCT 57.339 37.500 0.00 0.00 0.00 3.36
2303 5487 5.548181 ACGAACCTTCTAGACTTTTCCTT 57.452 39.130 0.00 0.00 0.00 3.36
2304 5488 5.926663 ACGAACCTTCTAGACTTTTCCTTT 58.073 37.500 0.00 0.00 0.00 3.11
2305 5489 7.059202 ACGAACCTTCTAGACTTTTCCTTTA 57.941 36.000 0.00 0.00 0.00 1.85
2306 5490 6.927936 ACGAACCTTCTAGACTTTTCCTTTAC 59.072 38.462 0.00 0.00 0.00 2.01
2307 5491 6.089150 CGAACCTTCTAGACTTTTCCTTTACG 59.911 42.308 0.00 0.00 0.00 3.18
2308 5492 5.791666 ACCTTCTAGACTTTTCCTTTACGG 58.208 41.667 0.00 0.00 0.00 4.02
2309 5493 4.630505 CCTTCTAGACTTTTCCTTTACGGC 59.369 45.833 0.00 0.00 0.00 5.68
2312 5496 1.422402 AGACTTTTCCTTTACGGCCCA 59.578 47.619 0.00 0.00 0.00 5.36
2326 5510 2.966516 ACGGCCCAATTTGGTCTTTTTA 59.033 40.909 14.26 0.00 35.17 1.52
2331 5518 5.825679 GGCCCAATTTGGTCTTTTTAGTTTT 59.174 36.000 14.26 0.00 35.17 2.43
2610 5840 9.780413 TTTTAAAAATGTTCCTGATTTGTTTGC 57.220 25.926 0.00 0.00 0.00 3.68
2611 5841 6.998968 AAAAATGTTCCTGATTTGTTTGCA 57.001 29.167 0.00 0.00 0.00 4.08
2612 5842 5.989551 AAATGTTCCTGATTTGTTTGCAC 57.010 34.783 0.00 0.00 0.00 4.57
2613 5843 4.942761 ATGTTCCTGATTTGTTTGCACT 57.057 36.364 0.00 0.00 0.00 4.40
2614 5844 6.403866 AATGTTCCTGATTTGTTTGCACTA 57.596 33.333 0.00 0.00 0.00 2.74
2615 5845 6.594788 ATGTTCCTGATTTGTTTGCACTAT 57.405 33.333 0.00 0.00 0.00 2.12
2616 5846 6.403866 TGTTCCTGATTTGTTTGCACTATT 57.596 33.333 0.00 0.00 0.00 1.73
2617 5847 6.815089 TGTTCCTGATTTGTTTGCACTATTT 58.185 32.000 0.00 0.00 0.00 1.40
2618 5848 6.922957 TGTTCCTGATTTGTTTGCACTATTTC 59.077 34.615 0.00 0.00 0.00 2.17
2619 5849 6.647334 TCCTGATTTGTTTGCACTATTTCA 57.353 33.333 0.00 0.00 0.00 2.69
2620 5850 7.048629 TCCTGATTTGTTTGCACTATTTCAA 57.951 32.000 0.00 0.00 0.00 2.69
2621 5851 7.495901 TCCTGATTTGTTTGCACTATTTCAAA 58.504 30.769 0.00 0.00 0.00 2.69
2622 5852 7.984050 TCCTGATTTGTTTGCACTATTTCAAAA 59.016 29.630 0.00 0.00 34.44 2.44
2623 5853 8.610896 CCTGATTTGTTTGCACTATTTCAAAAA 58.389 29.630 0.00 0.00 34.44 1.94
2625 5855 9.932699 TGATTTGTTTGCACTATTTCAAAAATG 57.067 25.926 0.00 0.00 34.44 2.32
2626 5856 9.934190 GATTTGTTTGCACTATTTCAAAAATGT 57.066 25.926 0.00 0.00 34.44 2.71
2629 5859 8.055609 TGTTTGCACTATTTCAAAAATGTACG 57.944 30.769 0.00 0.00 34.44 3.67
2630 5860 6.683090 TTGCACTATTTCAAAAATGTACGC 57.317 33.333 0.00 0.00 0.00 4.42
2631 5861 5.763088 TGCACTATTTCAAAAATGTACGCA 58.237 33.333 0.00 0.00 0.00 5.24
2632 5862 6.385843 TGCACTATTTCAAAAATGTACGCAT 58.614 32.000 0.00 0.00 36.80 4.73
2633 5863 6.865726 TGCACTATTTCAAAAATGTACGCATT 59.134 30.769 0.00 0.00 46.38 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 51 2.222213 TCGTTTTGAACACTGCCATACG 59.778 45.455 0.00 0.00 0.00 3.06
460 461 8.081633 TGTGTGAACATTTTATTTGACTGATCC 58.918 33.333 0.00 0.00 0.00 3.36
461 462 9.462174 TTGTGTGAACATTTTATTTGACTGATC 57.538 29.630 0.00 0.00 0.00 2.92
767 770 8.184192 CCTGGTCTTCATGTGTTTCAATAATAC 58.816 37.037 0.00 0.00 0.00 1.89
772 776 4.520492 GTCCTGGTCTTCATGTGTTTCAAT 59.480 41.667 0.00 0.00 0.00 2.57
790 794 2.957474 TCCCCCTTTTCTTTTGTCCTG 58.043 47.619 0.00 0.00 0.00 3.86
805 809 0.178955 TTTTCCCTTCCGTTTCCCCC 60.179 55.000 0.00 0.00 0.00 5.40
821 825 8.443979 TCTTTGGATAACATTTTCCCCATTTTT 58.556 29.630 0.00 0.00 0.00 1.94
880 884 0.878961 ACGTTCCTGCAAACTCGGTC 60.879 55.000 0.13 0.00 0.00 4.79
883 887 0.234884 GGAACGTTCCTGCAAACTCG 59.765 55.000 34.98 0.45 44.11 4.18
896 900 3.380004 TCTTGCAACTGAATTTGGAACGT 59.620 39.130 0.00 0.00 33.71 3.99
1059 1063 4.287238 AGTTTGTTGGTCGTTGATTCAC 57.713 40.909 0.00 0.00 0.00 3.18
1075 1079 3.747529 GGTTGGATGCCATTGAAAGTTTG 59.252 43.478 0.00 0.00 31.53 2.93
1081 1085 1.750206 CGATGGTTGGATGCCATTGAA 59.250 47.619 5.82 0.00 46.12 2.69
1102 1106 3.532155 CCGGAGAGGAGGAAGCGG 61.532 72.222 0.00 0.00 45.00 5.52
1426 1430 4.070552 GCGGCGAACTCCCTCTGT 62.071 66.667 12.98 0.00 0.00 3.41
1489 1493 0.037605 CACCAAGTGTACTCCCGACC 60.038 60.000 0.00 0.00 0.00 4.79
1554 1566 3.556999 TCCATCTGCCAGTAGAGTACTC 58.443 50.000 15.41 15.41 36.76 2.59
1631 1643 2.079158 CCACACCATACAGCTCACAAG 58.921 52.381 0.00 0.00 0.00 3.16
1632 1644 1.696884 TCCACACCATACAGCTCACAA 59.303 47.619 0.00 0.00 0.00 3.33
1636 1648 1.276421 ACAGTCCACACCATACAGCTC 59.724 52.381 0.00 0.00 0.00 4.09
1637 1649 1.352083 ACAGTCCACACCATACAGCT 58.648 50.000 0.00 0.00 0.00 4.24
1640 1652 6.065374 ACAATTTAACAGTCCACACCATACA 58.935 36.000 0.00 0.00 0.00 2.29
1641 1653 6.569179 ACAATTTAACAGTCCACACCATAC 57.431 37.500 0.00 0.00 0.00 2.39
1668 1686 5.247337 TCCAACCCTTTTTATTCATCAACCC 59.753 40.000 0.00 0.00 0.00 4.11
1756 1774 0.240945 CATGGTTCGGAGTGGTTTGC 59.759 55.000 0.00 0.00 0.00 3.68
1782 1800 9.376075 AGAATCCAATATGCTAATCAGTAATCG 57.624 33.333 0.00 0.00 0.00 3.34
1855 3287 3.593096 GATGCTTCATATCGGATGCTGA 58.407 45.455 0.00 1.10 38.40 4.26
1893 3640 1.918868 ATGACGACGACGCACTAGCA 61.919 55.000 7.30 0.00 43.96 3.49
1932 3679 2.341846 ACGACCCAACACAGAAACAT 57.658 45.000 0.00 0.00 0.00 2.71
1940 4854 1.388837 AAGCCCAAACGACCCAACAC 61.389 55.000 0.00 0.00 0.00 3.32
1946 4860 0.875059 CAGAGAAAGCCCAAACGACC 59.125 55.000 0.00 0.00 0.00 4.79
1963 4877 6.183360 CCTCAGCTCAATAGACATGAAAACAG 60.183 42.308 0.00 0.00 0.00 3.16
2001 4948 4.322198 CCAGCTACTACCTCCGTAACAAAA 60.322 45.833 0.00 0.00 0.00 2.44
2002 4949 3.194116 CCAGCTACTACCTCCGTAACAAA 59.806 47.826 0.00 0.00 0.00 2.83
2003 4950 2.756760 CCAGCTACTACCTCCGTAACAA 59.243 50.000 0.00 0.00 0.00 2.83
2004 4951 2.291153 ACCAGCTACTACCTCCGTAACA 60.291 50.000 0.00 0.00 0.00 2.41
2005 4952 2.373224 ACCAGCTACTACCTCCGTAAC 58.627 52.381 0.00 0.00 0.00 2.50
2006 4953 2.814805 ACCAGCTACTACCTCCGTAA 57.185 50.000 0.00 0.00 0.00 3.18
2007 4954 3.054434 TGTTACCAGCTACTACCTCCGTA 60.054 47.826 0.00 0.00 0.00 4.02
2009 4956 2.372264 TGTTACCAGCTACTACCTCCG 58.628 52.381 0.00 0.00 0.00 4.63
2010 4957 6.295180 GGAATATGTTACCAGCTACTACCTCC 60.295 46.154 0.00 0.00 0.00 4.30
2011 4958 6.569994 CGGAATATGTTACCAGCTACTACCTC 60.570 46.154 0.00 0.00 0.00 3.85
2012 4959 5.243283 CGGAATATGTTACCAGCTACTACCT 59.757 44.000 0.00 0.00 0.00 3.08
2013 4960 5.467705 CGGAATATGTTACCAGCTACTACC 58.532 45.833 0.00 0.00 0.00 3.18
2025 4972 2.758009 GGGCGTTAGCGGAATATGTTA 58.242 47.619 0.00 0.00 46.35 2.41
2046 5011 3.242739 CCATGATCAAATCCCGAACGTTC 60.243 47.826 18.47 18.47 0.00 3.95
2050 5015 2.023673 TGCCATGATCAAATCCCGAAC 58.976 47.619 0.00 0.00 0.00 3.95
2062 5027 5.722263 TGAAAACATTCGATTTGCCATGAT 58.278 33.333 0.00 0.00 0.00 2.45
2063 5028 5.131594 TGAAAACATTCGATTTGCCATGA 57.868 34.783 0.00 0.00 0.00 3.07
2064 5029 5.842619 TTGAAAACATTCGATTTGCCATG 57.157 34.783 0.00 0.00 0.00 3.66
2069 5034 5.842619 TGCCATTGAAAACATTCGATTTG 57.157 34.783 0.00 0.00 0.00 2.32
2074 5039 5.784625 CGAAAATTGCCATTGAAAACATTCG 59.215 36.000 0.00 0.00 0.00 3.34
2080 5045 4.208047 CGTCACGAAAATTGCCATTGAAAA 59.792 37.500 0.00 0.00 0.00 2.29
2084 5049 1.386412 GCGTCACGAAAATTGCCATTG 59.614 47.619 0.00 0.00 0.00 2.82
2085 5050 1.696988 GCGTCACGAAAATTGCCATT 58.303 45.000 0.00 0.00 0.00 3.16
2097 5062 0.366871 CTTTTCATCCTCGCGTCACG 59.633 55.000 5.77 0.00 45.62 4.35
2099 5064 2.163818 AACTTTTCATCCTCGCGTCA 57.836 45.000 5.77 0.00 0.00 4.35
2102 5067 4.394795 CAACTAAACTTTTCATCCTCGCG 58.605 43.478 0.00 0.00 0.00 5.87
2105 5070 5.705609 TGCCAACTAAACTTTTCATCCTC 57.294 39.130 0.00 0.00 0.00 3.71
2107 5072 4.686091 GCTTGCCAACTAAACTTTTCATCC 59.314 41.667 0.00 0.00 0.00 3.51
2112 5077 5.049828 GTCATGCTTGCCAACTAAACTTTT 58.950 37.500 0.00 0.00 0.00 2.27
2116 5081 3.641437 TGTCATGCTTGCCAACTAAAC 57.359 42.857 0.00 0.00 0.00 2.01
2157 5122 3.066064 CACACGACAATTCCCAGACAAAA 59.934 43.478 0.00 0.00 0.00 2.44
2164 5129 1.134371 TGACACACACGACAATTCCCA 60.134 47.619 0.00 0.00 0.00 4.37
2175 5140 5.539582 TGACAAGTTTAGTTGACACACAC 57.460 39.130 4.40 0.00 29.04 3.82
2190 5155 1.559682 AGTGACACCAGGTTGACAAGT 59.440 47.619 0.84 0.00 0.00 3.16
2198 5163 2.890945 GGCAATTTTAGTGACACCAGGT 59.109 45.455 0.84 0.00 0.00 4.00
2202 5167 4.846779 TCTTGGCAATTTTAGTGACACC 57.153 40.909 0.00 0.00 32.35 4.16
2204 5169 5.277825 CGTTTCTTGGCAATTTTAGTGACA 58.722 37.500 0.00 0.00 30.04 3.58
2205 5170 4.679654 CCGTTTCTTGGCAATTTTAGTGAC 59.320 41.667 0.00 0.00 0.00 3.67
2208 5173 4.929819 ACCGTTTCTTGGCAATTTTAGT 57.070 36.364 0.00 0.00 0.00 2.24
2221 5186 8.085909 CCCAAATAACTGAAAATTACCGTTTCT 58.914 33.333 0.00 0.00 36.22 2.52
2222 5187 7.868922 ACCCAAATAACTGAAAATTACCGTTTC 59.131 33.333 0.00 0.00 35.87 2.78
2226 5191 6.327154 GGACCCAAATAACTGAAAATTACCG 58.673 40.000 0.00 0.00 0.00 4.02
2227 5192 6.327154 CGGACCCAAATAACTGAAAATTACC 58.673 40.000 0.00 0.00 0.00 2.85
2228 5193 6.327154 CCGGACCCAAATAACTGAAAATTAC 58.673 40.000 0.00 0.00 0.00 1.89
2229 5194 5.105675 GCCGGACCCAAATAACTGAAAATTA 60.106 40.000 5.05 0.00 0.00 1.40
2230 5195 4.322424 GCCGGACCCAAATAACTGAAAATT 60.322 41.667 5.05 0.00 0.00 1.82
2231 5196 3.194755 GCCGGACCCAAATAACTGAAAAT 59.805 43.478 5.05 0.00 0.00 1.82
2232 5197 2.559231 GCCGGACCCAAATAACTGAAAA 59.441 45.455 5.05 0.00 0.00 2.29
2233 5198 2.164338 GCCGGACCCAAATAACTGAAA 58.836 47.619 5.05 0.00 0.00 2.69
2234 5199 1.614850 GGCCGGACCCAAATAACTGAA 60.615 52.381 5.05 0.00 0.00 3.02
2236 5201 2.489040 GGCCGGACCCAAATAACTG 58.511 57.895 5.05 0.00 0.00 3.16
2246 5211 1.453197 CACCTAATTGGGCCGGACC 60.453 63.158 23.70 23.70 41.11 4.46
2247 5212 0.542805 TACACCTAATTGGGCCGGAC 59.457 55.000 5.05 0.00 41.11 4.79
2248 5213 1.210967 CTTACACCTAATTGGGCCGGA 59.789 52.381 5.05 0.00 41.11 5.14
2249 5214 1.675552 CTTACACCTAATTGGGCCGG 58.324 55.000 7.93 0.00 41.11 6.13
2250 5215 1.210967 TCCTTACACCTAATTGGGCCG 59.789 52.381 7.93 1.91 41.11 6.13
2251 5216 3.021695 GTTCCTTACACCTAATTGGGCC 58.978 50.000 7.93 0.00 41.11 5.80
2252 5217 3.021695 GGTTCCTTACACCTAATTGGGC 58.978 50.000 7.93 0.00 41.11 5.36
2254 5219 3.275999 CGGGTTCCTTACACCTAATTGG 58.724 50.000 0.00 0.00 42.93 3.16
2255 5220 3.275999 CCGGGTTCCTTACACCTAATTG 58.724 50.000 0.00 0.00 34.36 2.32
2257 5222 2.554563 ACCGGGTTCCTTACACCTAAT 58.445 47.619 6.32 0.00 34.36 1.73
2258 5223 2.028561 ACCGGGTTCCTTACACCTAA 57.971 50.000 6.32 0.00 34.36 2.69
2262 5446 2.480037 CGTAAAACCGGGTTCCTTACAC 59.520 50.000 23.93 12.25 0.00 2.90
2272 5456 2.174363 AGAAGGTTCGTAAAACCGGG 57.826 50.000 6.32 0.00 44.82 5.73
2275 5459 7.307632 GGAAAAGTCTAGAAGGTTCGTAAAACC 60.308 40.741 0.00 0.00 40.58 3.27
2295 5479 3.953712 AATTGGGCCGTAAAGGAAAAG 57.046 42.857 0.00 0.00 45.00 2.27
2296 5480 3.244249 CCAAATTGGGCCGTAAAGGAAAA 60.244 43.478 3.60 0.00 43.43 2.29
2297 5481 2.300437 CCAAATTGGGCCGTAAAGGAAA 59.700 45.455 3.60 0.00 43.43 3.13
2300 5484 1.203758 GACCAAATTGGGCCGTAAAGG 59.796 52.381 17.27 0.20 40.64 3.11
2301 5485 2.647529 GACCAAATTGGGCCGTAAAG 57.352 50.000 17.27 0.00 40.64 1.85
2336 5523 9.374838 CCTTACGAACTTGTAAATATAACAGGT 57.625 33.333 0.00 1.39 38.64 4.00
2463 5667 9.617523 AATCTGAACATTTTTGGAACTTTTGAT 57.382 25.926 0.00 0.00 0.00 2.57
2587 5817 7.768120 AGTGCAAACAAATCAGGAACATTTTTA 59.232 29.630 0.00 0.00 0.00 1.52
2588 5818 6.598850 AGTGCAAACAAATCAGGAACATTTTT 59.401 30.769 0.00 0.00 0.00 1.94
2592 5822 4.942761 AGTGCAAACAAATCAGGAACAT 57.057 36.364 0.00 0.00 0.00 2.71
2593 5823 6.403866 AATAGTGCAAACAAATCAGGAACA 57.596 33.333 0.00 0.00 0.00 3.18
2594 5824 6.922957 TGAAATAGTGCAAACAAATCAGGAAC 59.077 34.615 0.00 0.00 0.00 3.62
2595 5825 7.048629 TGAAATAGTGCAAACAAATCAGGAA 57.951 32.000 0.00 0.00 0.00 3.36
2596 5826 6.647334 TGAAATAGTGCAAACAAATCAGGA 57.353 33.333 0.00 0.00 0.00 3.86
2597 5827 7.712264 TTTGAAATAGTGCAAACAAATCAGG 57.288 32.000 0.00 0.00 0.00 3.86
2599 5829 9.932699 CATTTTTGAAATAGTGCAAACAAATCA 57.067 25.926 0.00 0.00 34.09 2.57
2600 5830 9.934190 ACATTTTTGAAATAGTGCAAACAAATC 57.066 25.926 0.00 0.00 34.09 2.17
2603 5833 8.535592 CGTACATTTTTGAAATAGTGCAAACAA 58.464 29.630 0.00 0.00 34.09 2.83
2604 5834 7.306283 GCGTACATTTTTGAAATAGTGCAAACA 60.306 33.333 0.00 0.00 34.09 2.83
2605 5835 7.001347 GCGTACATTTTTGAAATAGTGCAAAC 58.999 34.615 0.00 0.00 34.09 2.93
2606 5836 6.697455 TGCGTACATTTTTGAAATAGTGCAAA 59.303 30.769 0.00 0.00 32.63 3.68
2607 5837 6.209361 TGCGTACATTTTTGAAATAGTGCAA 58.791 32.000 0.00 0.00 0.00 4.08
2608 5838 5.763088 TGCGTACATTTTTGAAATAGTGCA 58.237 33.333 0.00 0.00 0.00 4.57
2609 5839 6.869421 ATGCGTACATTTTTGAAATAGTGC 57.131 33.333 0.00 0.00 30.07 4.40


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

AutoCloner maintained by Alex Coulton.