Multiple sequence alignment - TraesCS2D01G544100

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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 TraesCS2D01G544100 chr2D 100.000 2702 0 0 1 2702 621495181 621497882 0.000000e+00 4990.0
1 TraesCS2D01G544100 chr2D 87.013 77 9 1 2195 2271 621502193 621502268 4.790000e-13 86.1
2 TraesCS2D01G544100 chr2A 85.732 2453 161 92 135 2480 753228235 753230605 0.000000e+00 2416.0
3 TraesCS2D01G544100 chr2B 85.602 2417 148 92 1 2324 762428792 762431101 0.000000e+00 2351.0
4 TraesCS2D01G544100 chr2B 82.162 370 24 21 2362 2702 762431109 762431465 2.050000e-71 279.0
5 TraesCS2D01G544100 chr3D 94.558 147 8 0 1183 1329 554140244 554140390 7.530000e-56 228.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G544100 chr2D 621495181 621497882 2701 False 4990 4990 100.000 1 2702 1 chr2D.!!$F1 2701
1 TraesCS2D01G544100 chr2A 753228235 753230605 2370 False 2416 2416 85.732 135 2480 1 chr2A.!!$F1 2345
2 TraesCS2D01G544100 chr2B 762428792 762431465 2673 False 1315 2351 83.882 1 2702 2 chr2B.!!$F1 2701

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
205 224 0.552848 ACCCATCCACATCCACATCC 59.447 55.0 0.0 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2052 2192 0.109132 GTTTTGCTCCTCAATGGCGG 60.109 55.0 0.0 0.0 34.12 6.13 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
18 19 1.306141 TCTTCGGCCTCATCCACCT 60.306 57.895 0.00 0.00 0.00 4.00
59 60 1.530771 GGAGATGACATGCTGGCCT 59.469 57.895 3.32 0.00 0.00 5.19
73 74 3.925090 GCCTACGACATCCCCGGG 61.925 72.222 15.80 15.80 0.00 5.73
205 224 0.552848 ACCCATCCACATCCACATCC 59.447 55.000 0.00 0.00 0.00 3.51
207 226 1.683943 CCATCCACATCCACATCCAC 58.316 55.000 0.00 0.00 0.00 4.02
208 227 1.064537 CCATCCACATCCACATCCACA 60.065 52.381 0.00 0.00 0.00 4.17
211 230 1.914798 TCCACATCCACATCCACATCA 59.085 47.619 0.00 0.00 0.00 3.07
212 231 2.092807 TCCACATCCACATCCACATCAG 60.093 50.000 0.00 0.00 0.00 2.90
213 232 2.092807 CCACATCCACATCCACATCAGA 60.093 50.000 0.00 0.00 0.00 3.27
214 233 2.941064 CACATCCACATCCACATCAGAC 59.059 50.000 0.00 0.00 0.00 3.51
215 234 2.092753 ACATCCACATCCACATCAGACC 60.093 50.000 0.00 0.00 0.00 3.85
216 235 1.956869 TCCACATCCACATCAGACCT 58.043 50.000 0.00 0.00 0.00 3.85
217 236 1.833630 TCCACATCCACATCAGACCTC 59.166 52.381 0.00 0.00 0.00 3.85
218 237 1.556451 CCACATCCACATCAGACCTCA 59.444 52.381 0.00 0.00 0.00 3.86
224 249 1.474677 CCACATCAGACCTCATCAGCC 60.475 57.143 0.00 0.00 0.00 4.85
233 258 1.002134 CTCATCAGCCAACCCCGTT 60.002 57.895 0.00 0.00 0.00 4.44
258 283 3.124921 CCGGAATTTCGCGGCACT 61.125 61.111 6.13 0.00 0.00 4.40
308 343 2.175621 GTACGTGGCCGGGCAATAC 61.176 63.158 34.51 30.23 38.78 1.89
344 379 2.112297 ACGGCACCACCACGAAAT 59.888 55.556 0.00 0.00 39.03 2.17
373 408 2.046604 GGGACGGCACTTGGTACC 60.047 66.667 4.43 4.43 0.00 3.34
410 449 1.306226 GACCTGCCTGACCCCTACT 60.306 63.158 0.00 0.00 0.00 2.57
414 453 1.913419 CCTGCCTGACCCCTACTAAAA 59.087 52.381 0.00 0.00 0.00 1.52
418 457 3.850173 TGCCTGACCCCTACTAAAATCTT 59.150 43.478 0.00 0.00 0.00 2.40
438 477 9.803315 AAATCTTCAAAAAGGTCTGAACTTAAC 57.197 29.630 8.63 0.00 33.03 2.01
439 478 7.931578 TCTTCAAAAAGGTCTGAACTTAACA 57.068 32.000 8.63 0.00 33.03 2.41
440 479 7.985476 TCTTCAAAAAGGTCTGAACTTAACAG 58.015 34.615 8.63 1.67 33.85 3.16
441 480 6.693315 TCAAAAAGGTCTGAACTTAACAGG 57.307 37.500 8.63 0.00 36.22 4.00
524 571 2.202531 GGCGACCGTCCTACGTTC 60.203 66.667 0.00 0.00 40.58 3.95
612 676 2.148768 CGACTACCCAAACCAAAGACC 58.851 52.381 0.00 0.00 0.00 3.85
633 697 3.445096 CCAAGTTGGACCAATGGAGATTC 59.555 47.826 17.60 0.57 40.96 2.52
661 725 2.607750 TCGCCTTGGCTTCTCCCT 60.608 61.111 10.12 0.00 0.00 4.20
671 735 1.664321 GCTTCTCCCTGGCTGCAATG 61.664 60.000 0.50 0.00 0.00 2.82
672 736 1.664321 CTTCTCCCTGGCTGCAATGC 61.664 60.000 0.00 0.00 0.00 3.56
673 737 2.361992 CTCCCTGGCTGCAATGCA 60.362 61.111 7.99 7.99 36.92 3.96
674 738 1.980232 CTCCCTGGCTGCAATGCAA 60.980 57.895 9.92 0.00 38.41 4.08
675 739 1.305465 TCCCTGGCTGCAATGCAAT 60.305 52.632 9.92 0.00 38.41 3.56
781 854 2.773053 GTTAGCCCCTCCCCTCCC 60.773 72.222 0.00 0.00 0.00 4.30
859 938 2.461110 CCGCCATACAGCAACGTCC 61.461 63.158 0.00 0.00 0.00 4.79
892 971 4.875301 ACCCACCCCACCAACCCT 62.875 66.667 0.00 0.00 0.00 4.34
973 1057 1.759445 CCAGCCAGTGAGCACTACTAT 59.241 52.381 2.36 0.00 40.20 2.12
980 1064 5.724328 CCAGTGAGCACTACTATTTCTTCA 58.276 41.667 2.36 0.00 40.20 3.02
981 1065 6.166279 CCAGTGAGCACTACTATTTCTTCAA 58.834 40.000 2.36 0.00 40.20 2.69
985 1069 6.868864 GTGAGCACTACTATTTCTTCAACTGA 59.131 38.462 0.00 0.00 0.00 3.41
988 1072 5.064071 GCACTACTATTTCTTCAACTGAGGC 59.936 44.000 0.00 0.00 0.00 4.70
990 1074 4.537135 ACTATTTCTTCAACTGAGGCGA 57.463 40.909 0.00 0.00 0.00 5.54
991 1075 4.499183 ACTATTTCTTCAACTGAGGCGAG 58.501 43.478 0.00 0.00 0.00 5.03
1161 1251 2.586792 CTGGCCTACCTGCTGTCC 59.413 66.667 3.32 0.00 36.63 4.02
1580 1688 3.506096 CGCGGACAGCCTCTACGA 61.506 66.667 0.00 0.00 44.76 3.43
1751 1865 6.319405 AGAACTTCTCGTAGATTAGGGAGAAC 59.681 42.308 0.00 0.00 39.78 3.01
1798 1934 1.545706 GGTCAGGTCAGGTCAGGTCC 61.546 65.000 0.00 0.00 0.00 4.46
1810 1946 1.342174 GTCAGGTCCGTGAAACCAGTA 59.658 52.381 0.00 0.00 39.39 2.74
1811 1947 1.616865 TCAGGTCCGTGAAACCAGTAG 59.383 52.381 0.00 0.00 39.39 2.57
1812 1948 1.343465 CAGGTCCGTGAAACCAGTAGT 59.657 52.381 0.00 0.00 39.39 2.73
1820 1956 5.877012 TCCGTGAAACCAGTAGTAGTAGTAG 59.123 44.000 0.00 0.00 0.00 2.57
1839 1979 2.583143 AGTAGCAGTTGGTTTTGTCCC 58.417 47.619 0.00 0.00 0.00 4.46
1850 1990 0.104671 TTTTGTCCCAGCAAGCAAGC 59.895 50.000 0.00 0.00 0.00 4.01
1851 1991 1.042003 TTTGTCCCAGCAAGCAAGCA 61.042 50.000 3.19 0.00 36.85 3.91
1852 1992 1.042003 TTGTCCCAGCAAGCAAGCAA 61.042 50.000 3.19 0.00 36.85 3.91
1853 1993 1.288127 GTCCCAGCAAGCAAGCAAG 59.712 57.895 3.19 0.00 36.85 4.01
1854 1994 2.048503 CCCAGCAAGCAAGCAAGC 60.049 61.111 3.19 0.00 36.85 4.01
1855 1995 2.732016 CCAGCAAGCAAGCAAGCA 59.268 55.556 10.52 0.00 36.85 3.91
1856 1996 1.068417 CCAGCAAGCAAGCAAGCAA 59.932 52.632 10.52 0.00 36.85 3.91
1858 1998 1.300697 AGCAAGCAAGCAAGCAAGC 60.301 52.632 10.52 6.16 36.99 4.01
1859 1999 1.593209 GCAAGCAAGCAAGCAAGCA 60.593 52.632 10.52 0.00 36.81 3.91
1860 2000 1.155424 GCAAGCAAGCAAGCAAGCAA 61.155 50.000 10.52 0.00 36.81 3.91
1861 2001 0.859232 CAAGCAAGCAAGCAAGCAAG 59.141 50.000 10.52 0.00 36.85 4.01
1862 2002 0.748450 AAGCAAGCAAGCAAGCAAGA 59.252 45.000 10.52 0.00 36.85 3.02
1863 2003 0.314302 AGCAAGCAAGCAAGCAAGAG 59.686 50.000 10.52 0.00 36.85 2.85
1864 2004 1.282930 GCAAGCAAGCAAGCAAGAGC 61.283 55.000 3.19 0.00 42.56 4.09
1865 2005 0.031585 CAAGCAAGCAAGCAAGAGCA 59.968 50.000 3.19 0.00 45.49 4.26
1866 2006 0.966920 AAGCAAGCAAGCAAGAGCAT 59.033 45.000 3.19 0.00 45.49 3.79
1867 2007 0.526662 AGCAAGCAAGCAAGAGCATC 59.473 50.000 3.19 0.00 45.49 3.91
1868 2008 0.458025 GCAAGCAAGCAAGAGCATCC 60.458 55.000 0.00 0.00 45.49 3.51
1869 2009 0.179171 CAAGCAAGCAAGAGCATCCG 60.179 55.000 0.00 0.00 45.49 4.18
1870 2010 1.930908 AAGCAAGCAAGAGCATCCGC 61.931 55.000 0.00 0.00 45.49 5.54
1907 2047 6.275335 CCTTTTGATTTCTTGCAACTCTGAA 58.725 36.000 0.00 0.00 0.00 3.02
1945 2085 1.618143 TCCGGATGGGGGTTGTGAT 60.618 57.895 0.00 0.00 36.01 3.06
1949 2089 0.041090 GGATGGGGGTTGTGATGGTT 59.959 55.000 0.00 0.00 0.00 3.67
1973 2113 0.679960 CCGACCAAAATCTCCCCACC 60.680 60.000 0.00 0.00 0.00 4.61
1975 2115 1.271926 CGACCAAAATCTCCCCACCTT 60.272 52.381 0.00 0.00 0.00 3.50
1976 2116 2.171003 GACCAAAATCTCCCCACCTTG 58.829 52.381 0.00 0.00 0.00 3.61
1977 2117 1.203174 ACCAAAATCTCCCCACCTTGG 60.203 52.381 0.00 0.00 39.38 3.61
1978 2118 0.897621 CAAAATCTCCCCACCTTGGC 59.102 55.000 0.00 0.00 35.79 4.52
2040 2180 2.623418 AACTTTCCCCATTTCCCCTC 57.377 50.000 0.00 0.00 0.00 4.30
2047 2187 1.925959 CCCCATTTCCCCTCTCTTTCT 59.074 52.381 0.00 0.00 0.00 2.52
2049 2189 3.527665 CCCCATTTCCCCTCTCTTTCTTA 59.472 47.826 0.00 0.00 0.00 2.10
2050 2190 4.017499 CCCCATTTCCCCTCTCTTTCTTAA 60.017 45.833 0.00 0.00 0.00 1.85
2051 2191 4.950475 CCCATTTCCCCTCTCTTTCTTAAC 59.050 45.833 0.00 0.00 0.00 2.01
2052 2192 4.950475 CCATTTCCCCTCTCTTTCTTAACC 59.050 45.833 0.00 0.00 0.00 2.85
2062 2202 3.343617 TCTTTCTTAACCCGCCATTGAG 58.656 45.455 0.00 0.00 0.00 3.02
2071 2220 0.109132 CCGCCATTGAGGAGCAAAAC 60.109 55.000 0.00 0.00 40.48 2.43
2271 2428 1.153628 CCCTCGCTAACCCTGTTCG 60.154 63.158 0.00 0.00 0.00 3.95
2272 2429 1.590147 CCTCGCTAACCCTGTTCGT 59.410 57.895 0.00 0.00 0.00 3.85
2278 2435 0.688487 CTAACCCTGTTCGTTCCCCA 59.312 55.000 0.00 0.00 0.00 4.96
2296 2453 3.291584 CCCAGCTACTCACTCACTCATA 58.708 50.000 0.00 0.00 0.00 2.15
2313 2470 2.308570 TCATAGTGGGCTTTGGTGACAT 59.691 45.455 0.00 0.00 42.32 3.06
2314 2471 2.489938 TAGTGGGCTTTGGTGACATC 57.510 50.000 0.00 0.00 42.32 3.06
2317 2474 0.409092 TGGGCTTTGGTGACATCCAT 59.591 50.000 0.00 0.00 42.32 3.41
2324 2481 0.106569 TGGTGACATCCATCCATGCC 60.107 55.000 0.00 0.00 33.40 4.40
2327 2484 1.679680 GTGACATCCATCCATGCCTTG 59.320 52.381 0.00 0.00 0.00 3.61
2328 2485 0.672342 GACATCCATCCATGCCTTGC 59.328 55.000 0.00 0.00 0.00 4.01
2334 2491 3.384555 ATCCATGCCTTGCCCCCTG 62.385 63.158 0.00 0.00 0.00 4.45
2351 2508 1.262417 CCTGAACGATGGAATCATGCG 59.738 52.381 0.00 0.00 45.97 4.73
2360 2524 3.728076 TGGAATCATGCGTACTACTCC 57.272 47.619 0.00 0.00 0.00 3.85
2377 2541 6.768029 CTACTCCTAGTAGCAAGTACTACG 57.232 45.833 0.00 0.00 45.87 3.51
2378 2542 5.350504 ACTCCTAGTAGCAAGTACTACGA 57.649 43.478 0.00 0.00 45.87 3.43
2396 2566 3.421741 ACGATCGTTGTTGTTGTTGTTG 58.578 40.909 16.60 0.00 0.00 3.33
2436 2611 0.823460 GAGCTGGCTAGAGCAGTTCT 59.177 55.000 0.00 0.00 44.36 3.01
2443 2626 1.354040 CTAGAGCAGTTCTTGGCACG 58.646 55.000 0.00 0.00 37.36 5.34
2538 2734 1.265905 GTGCGAATTTGACCCGAAAGT 59.734 47.619 0.00 0.00 0.00 2.66
2573 2769 4.790962 CTGCACTGCGGCTCCCAT 62.791 66.667 0.00 0.00 34.04 4.00
2576 2772 2.360350 CACTGCGGCTCCCATGTT 60.360 61.111 0.00 0.00 0.00 2.71
2584 2780 2.162681 CGGCTCCCATGTTTCTCTTTT 58.837 47.619 0.00 0.00 0.00 2.27
2598 2794 3.326836 CTCTTTTCTCGAAAGGGAGCT 57.673 47.619 0.00 0.00 46.84 4.09
2601 2797 3.833070 TCTTTTCTCGAAAGGGAGCTACT 59.167 43.478 0.00 0.00 44.69 2.57
2602 2798 5.014858 TCTTTTCTCGAAAGGGAGCTACTA 58.985 41.667 0.00 0.00 44.69 1.82
2603 2799 4.715527 TTTCTCGAAAGGGAGCTACTAC 57.284 45.455 0.00 0.00 44.69 2.73
2604 2800 2.286872 TCTCGAAAGGGAGCTACTACG 58.713 52.381 0.00 3.80 34.08 3.51
2625 2821 3.727673 CGTACCATCTTTTGAACCATGCG 60.728 47.826 0.00 0.00 0.00 4.73
2634 2830 7.861176 TCTTTTGAACCATGCGTTTTATTAC 57.139 32.000 1.80 0.00 33.74 1.89
2636 2832 8.784994 TCTTTTGAACCATGCGTTTTATTACTA 58.215 29.630 1.80 0.00 33.74 1.82
2637 2833 8.958175 TTTTGAACCATGCGTTTTATTACTAG 57.042 30.769 1.80 0.00 33.74 2.57
2639 2835 8.774890 TTGAACCATGCGTTTTATTACTAGTA 57.225 30.769 0.00 0.00 33.74 1.82
2640 2836 8.951787 TGAACCATGCGTTTTATTACTAGTAT 57.048 30.769 2.79 0.00 33.74 2.12
2645 2845 9.864034 CCATGCGTTTTATTACTAGTATTTCTG 57.136 33.333 2.79 0.00 0.00 3.02
2658 2858 5.489792 AGTATTTCTGTGCTTTGAGAGGA 57.510 39.130 0.00 0.00 0.00 3.71
2667 2867 6.205464 TCTGTGCTTTGAGAGGAGTATTTTTG 59.795 38.462 0.00 0.00 0.00 2.44
2668 2868 5.827797 TGTGCTTTGAGAGGAGTATTTTTGT 59.172 36.000 0.00 0.00 0.00 2.83
2669 2869 6.145535 GTGCTTTGAGAGGAGTATTTTTGTG 58.854 40.000 0.00 0.00 0.00 3.33
2670 2870 5.827797 TGCTTTGAGAGGAGTATTTTTGTGT 59.172 36.000 0.00 0.00 0.00 3.72
2671 2871 6.995686 TGCTTTGAGAGGAGTATTTTTGTGTA 59.004 34.615 0.00 0.00 0.00 2.90
2672 2872 7.665559 TGCTTTGAGAGGAGTATTTTTGTGTAT 59.334 33.333 0.00 0.00 0.00 2.29
2675 2875 9.567776 TTTGAGAGGAGTATTTTTGTGTATTCA 57.432 29.630 0.00 0.00 0.00 2.57
2676 2876 9.567776 TTGAGAGGAGTATTTTTGTGTATTCAA 57.432 29.630 0.00 0.00 0.00 2.69
2677 2877 8.999431 TGAGAGGAGTATTTTTGTGTATTCAAC 58.001 33.333 0.00 0.00 0.00 3.18
2691 2891 5.574055 GTGTATTCAACTCAATTGTGGCATG 59.426 40.000 11.89 7.83 39.54 4.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 4.899239 GCGAGGTGGATGAGGCCG 62.899 72.222 0.00 0.00 0.00 6.13
5 6 3.453070 GAGCGAGGTGGATGAGGCC 62.453 68.421 0.00 0.00 0.00 5.19
18 19 3.966104 CGAGCATAGCCCGAGCGA 61.966 66.667 0.00 0.00 46.67 4.93
59 60 4.468769 AGGCCCGGGGATGTCGTA 62.469 66.667 25.28 0.00 0.00 3.43
77 78 1.107538 TTGATCGAGGTAGGAGGCGG 61.108 60.000 0.00 0.00 0.00 6.13
78 79 0.312416 CTTGATCGAGGTAGGAGGCG 59.688 60.000 1.50 0.00 0.00 5.52
86 87 1.949847 CTGGACGGCTTGATCGAGGT 61.950 60.000 12.06 1.92 0.00 3.85
205 224 1.208776 TGGCTGATGAGGTCTGATGTG 59.791 52.381 0.00 0.00 0.00 3.21
207 226 2.286872 GTTGGCTGATGAGGTCTGATG 58.713 52.381 0.00 0.00 0.00 3.07
208 227 1.211457 GGTTGGCTGATGAGGTCTGAT 59.789 52.381 0.00 0.00 0.00 2.90
211 230 1.566298 GGGGTTGGCTGATGAGGTCT 61.566 60.000 0.00 0.00 0.00 3.85
212 231 1.077429 GGGGTTGGCTGATGAGGTC 60.077 63.158 0.00 0.00 0.00 3.85
213 232 2.971598 CGGGGTTGGCTGATGAGGT 61.972 63.158 0.00 0.00 0.00 3.85
214 233 2.124570 CGGGGTTGGCTGATGAGG 60.125 66.667 0.00 0.00 0.00 3.86
215 234 1.002134 AACGGGGTTGGCTGATGAG 60.002 57.895 0.00 0.00 0.00 2.90
216 235 1.303236 CAACGGGGTTGGCTGATGA 60.303 57.895 0.61 0.00 39.56 2.92
217 236 3.277133 CAACGGGGTTGGCTGATG 58.723 61.111 0.61 0.00 39.56 3.07
233 258 1.003112 CGAAATTCCGGTGTCCCCA 60.003 57.895 0.00 0.00 0.00 4.96
258 283 4.651008 GGGACGTGCGTGGTTCGA 62.651 66.667 0.67 0.00 42.86 3.71
279 308 2.182284 CACGTACGGGGATTCGCA 59.818 61.111 21.06 0.00 0.00 5.10
281 310 2.584143 GCCACGTACGGGGATTCG 60.584 66.667 39.88 13.76 42.48 3.34
303 332 1.567504 GTGGTCGGTCGATGGTATTG 58.432 55.000 0.00 0.00 0.00 1.90
344 379 1.894756 CCGTCCCGCTGGTGAAAAA 60.895 57.895 0.00 0.00 0.00 1.94
391 430 2.363795 TAGGGGTCAGGCAGGTCG 60.364 66.667 0.00 0.00 0.00 4.79
414 453 8.519799 TGTTAAGTTCAGACCTTTTTGAAGAT 57.480 30.769 0.00 0.00 34.25 2.40
418 457 6.094881 CACCTGTTAAGTTCAGACCTTTTTGA 59.905 38.462 0.00 0.00 35.20 2.69
436 475 0.182775 GTGGTTGGACCTCACCTGTT 59.817 55.000 13.02 0.00 39.58 3.16
437 476 1.837090 GTGGTTGGACCTCACCTGT 59.163 57.895 13.02 0.00 39.58 4.00
438 477 1.301716 CGTGGTTGGACCTCACCTG 60.302 63.158 13.02 4.23 39.58 4.00
439 478 1.458777 TCGTGGTTGGACCTCACCT 60.459 57.895 13.02 0.00 39.58 4.00
440 479 1.301479 GTCGTGGTTGGACCTCACC 60.301 63.158 6.50 6.50 39.58 4.02
441 480 0.878961 GTGTCGTGGTTGGACCTCAC 60.879 60.000 0.00 0.00 39.58 3.51
612 676 3.127548 CGAATCTCCATTGGTCCAACTTG 59.872 47.826 6.41 2.07 0.00 3.16
661 725 2.629137 CCCTATTATTGCATTGCAGCCA 59.371 45.455 11.76 0.00 40.61 4.75
671 735 2.556286 GCTCCGGCCCTATTATTGC 58.444 57.895 0.00 0.00 0.00 3.56
772 845 1.557371 GAAGAGAACAAGGGAGGGGAG 59.443 57.143 0.00 0.00 0.00 4.30
777 850 1.557371 GGGAGGAAGAGAACAAGGGAG 59.443 57.143 0.00 0.00 0.00 4.30
779 852 1.557371 GAGGGAGGAAGAGAACAAGGG 59.443 57.143 0.00 0.00 0.00 3.95
781 854 2.027653 GGTGAGGGAGGAAGAGAACAAG 60.028 54.545 0.00 0.00 0.00 3.16
949 1032 4.648626 TGCTCACTGGCTGGTGGC 62.649 66.667 10.25 11.84 37.75 5.01
952 1036 0.833834 AGTAGTGCTCACTGGCTGGT 60.834 55.000 12.43 0.00 42.52 4.00
965 1049 5.289675 CGCCTCAGTTGAAGAAATAGTAGTG 59.710 44.000 0.00 0.00 0.00 2.74
973 1057 1.070758 AGCTCGCCTCAGTTGAAGAAA 59.929 47.619 0.00 0.00 0.00 2.52
980 1064 4.749310 CCGCAGCTCGCCTCAGTT 62.749 66.667 3.09 0.00 37.30 3.16
988 1072 2.578163 TTCTTCATCCCCGCAGCTCG 62.578 60.000 0.00 0.00 38.08 5.03
990 1074 1.222936 CTTCTTCATCCCCGCAGCT 59.777 57.895 0.00 0.00 0.00 4.24
991 1075 2.476320 GCTTCTTCATCCCCGCAGC 61.476 63.158 0.00 0.00 0.00 5.25
1751 1865 2.040278 TCTTGGTGGTCTCCATTCTTGG 59.960 50.000 0.00 0.00 45.15 3.61
1798 1934 6.734104 ACTACTACTACTACTGGTTTCACG 57.266 41.667 0.00 0.00 0.00 4.35
1810 1946 7.015001 ACAAAACCAACTGCTACTACTACTACT 59.985 37.037 0.00 0.00 0.00 2.57
1811 1947 7.150640 ACAAAACCAACTGCTACTACTACTAC 58.849 38.462 0.00 0.00 0.00 2.73
1812 1948 7.294017 ACAAAACCAACTGCTACTACTACTA 57.706 36.000 0.00 0.00 0.00 1.82
1820 1956 2.293399 CTGGGACAAAACCAACTGCTAC 59.707 50.000 0.00 0.00 38.70 3.58
1839 1979 1.557443 GCTTGCTTGCTTGCTTGCTG 61.557 55.000 10.35 6.09 0.00 4.41
1850 1990 0.179171 CGGATGCTCTTGCTTGCTTG 60.179 55.000 0.00 0.00 40.48 4.01
1851 1991 1.930908 GCGGATGCTCTTGCTTGCTT 61.931 55.000 0.00 0.00 40.48 3.91
1852 1992 2.404995 GCGGATGCTCTTGCTTGCT 61.405 57.895 0.00 0.00 40.48 3.91
1853 1993 2.101770 GCGGATGCTCTTGCTTGC 59.898 61.111 0.00 0.00 40.48 4.01
1863 2003 0.389687 GGCATAGAGAGAGCGGATGC 60.390 60.000 0.00 0.00 41.73 3.91
1864 2004 0.246086 GGGCATAGAGAGAGCGGATG 59.754 60.000 0.00 0.00 0.00 3.51
1865 2005 0.902516 GGGGCATAGAGAGAGCGGAT 60.903 60.000 0.00 0.00 0.00 4.18
1866 2006 1.531840 GGGGCATAGAGAGAGCGGA 60.532 63.158 0.00 0.00 0.00 5.54
1867 2007 1.118356 AAGGGGCATAGAGAGAGCGG 61.118 60.000 0.00 0.00 0.00 5.52
1868 2008 0.755686 AAAGGGGCATAGAGAGAGCG 59.244 55.000 0.00 0.00 0.00 5.03
1869 2009 2.171448 TCAAAAGGGGCATAGAGAGAGC 59.829 50.000 0.00 0.00 0.00 4.09
1870 2010 4.703379 ATCAAAAGGGGCATAGAGAGAG 57.297 45.455 0.00 0.00 0.00 3.20
1871 2011 5.192522 AGAAATCAAAAGGGGCATAGAGAGA 59.807 40.000 0.00 0.00 0.00 3.10
1872 2012 5.444176 AGAAATCAAAAGGGGCATAGAGAG 58.556 41.667 0.00 0.00 0.00 3.20
1873 2013 5.456921 AGAAATCAAAAGGGGCATAGAGA 57.543 39.130 0.00 0.00 0.00 3.10
1907 2047 2.657237 CTCGGGGTTGCTCGTTCT 59.343 61.111 0.00 0.00 0.00 3.01
1932 2072 0.783206 TGAACCATCACAACCCCCAT 59.217 50.000 0.00 0.00 0.00 4.00
1938 2078 2.161609 GGTCGGATTGAACCATCACAAC 59.838 50.000 0.00 0.00 34.61 3.32
1945 2085 3.756434 GAGATTTTGGTCGGATTGAACCA 59.244 43.478 0.00 0.00 31.20 3.67
1949 2089 2.356741 GGGGAGATTTTGGTCGGATTGA 60.357 50.000 0.00 0.00 0.00 2.57
1973 2113 1.819632 GTACATGGGAGGCGCCAAG 60.820 63.158 31.54 13.44 38.95 3.61
1975 2115 3.792736 GGTACATGGGAGGCGCCA 61.793 66.667 31.54 8.23 38.95 5.69
1976 2116 3.792736 TGGTACATGGGAGGCGCC 61.793 66.667 21.89 21.89 0.00 6.53
2040 2180 3.343617 TCAATGGCGGGTTAAGAAAGAG 58.656 45.455 0.00 0.00 0.00 2.85
2047 2187 0.393808 GCTCCTCAATGGCGGGTTAA 60.394 55.000 0.00 0.00 35.26 2.01
2049 2189 2.044946 GCTCCTCAATGGCGGGTT 60.045 61.111 0.00 0.00 35.26 4.11
2050 2190 2.424842 TTTGCTCCTCAATGGCGGGT 62.425 55.000 0.00 0.00 34.12 5.28
2051 2191 1.250154 TTTTGCTCCTCAATGGCGGG 61.250 55.000 0.00 0.00 34.12 6.13
2052 2192 0.109132 GTTTTGCTCCTCAATGGCGG 60.109 55.000 0.00 0.00 34.12 6.13
2071 2220 1.920574 CGACAGTTCATACGAGCAAGG 59.079 52.381 0.00 0.00 0.00 3.61
2079 2228 5.277058 GCAGGAATCAATCGACAGTTCATAC 60.277 44.000 0.00 0.00 0.00 2.39
2150 2307 4.036144 GCACTTAATCATTTCCAGAGGCTC 59.964 45.833 6.34 6.34 0.00 4.70
2271 2428 1.066787 GTGAGTGAGTAGCTGGGGAAC 60.067 57.143 0.00 0.00 0.00 3.62
2272 2429 1.203187 AGTGAGTGAGTAGCTGGGGAA 60.203 52.381 0.00 0.00 0.00 3.97
2296 2453 0.251341 GGATGTCACCAAAGCCCACT 60.251 55.000 0.00 0.00 0.00 4.00
2313 2470 2.279743 GGGCAAGGCATGGATGGA 59.720 61.111 0.00 0.00 0.00 3.41
2314 2471 2.841044 GGGGCAAGGCATGGATGG 60.841 66.667 0.00 0.00 0.00 3.51
2317 2474 4.064768 CAGGGGGCAAGGCATGGA 62.065 66.667 0.00 0.00 0.00 3.41
2324 2481 1.750399 CCATCGTTCAGGGGGCAAG 60.750 63.158 0.00 0.00 0.00 4.01
2327 2484 0.819666 GATTCCATCGTTCAGGGGGC 60.820 60.000 0.00 0.00 0.00 5.80
2328 2485 0.546122 TGATTCCATCGTTCAGGGGG 59.454 55.000 0.00 0.00 0.00 5.40
2334 2491 3.123804 AGTACGCATGATTCCATCGTTC 58.876 45.455 0.00 0.00 37.54 3.95
2360 2524 5.903764 ACGATCGTAGTACTTGCTACTAG 57.096 43.478 21.32 0.00 38.42 2.57
2374 2538 4.494362 CCAACAACAACAACAACGATCGTA 60.494 41.667 23.04 0.00 0.00 3.43
2376 2540 2.781101 CCAACAACAACAACAACGATCG 59.219 45.455 14.88 14.88 0.00 3.69
2377 2541 3.765026 ACCAACAACAACAACAACGATC 58.235 40.909 0.00 0.00 0.00 3.69
2378 2542 3.859411 ACCAACAACAACAACAACGAT 57.141 38.095 0.00 0.00 0.00 3.73
2396 2566 6.647895 AGCTCAAATCAAATCAATCAACAACC 59.352 34.615 0.00 0.00 0.00 3.77
2436 2611 0.248012 TCGAGCTTTATCCGTGCCAA 59.752 50.000 0.00 0.00 0.00 4.52
2511 2699 2.126502 CAAATTCGCACCGGCACC 60.127 61.111 0.00 0.00 41.24 5.01
2513 2701 2.622011 GGTCAAATTCGCACCGGCA 61.622 57.895 0.00 0.00 41.24 5.69
2514 2702 2.178273 GGTCAAATTCGCACCGGC 59.822 61.111 0.00 0.00 0.00 6.13
2516 2704 1.570347 TTCGGGTCAAATTCGCACCG 61.570 55.000 0.00 0.00 42.45 4.94
2565 2761 3.425659 AGAAAAGAGAAACATGGGAGCC 58.574 45.455 0.00 0.00 0.00 4.70
2573 2769 5.031066 TCCCTTTCGAGAAAAGAGAAACA 57.969 39.130 0.00 0.00 46.18 2.83
2574 2770 4.083749 GCTCCCTTTCGAGAAAAGAGAAAC 60.084 45.833 20.40 7.19 46.18 2.78
2576 2772 3.325135 AGCTCCCTTTCGAGAAAAGAGAA 59.675 43.478 20.40 0.35 46.18 2.87
2584 2780 2.286872 CGTAGTAGCTCCCTTTCGAGA 58.713 52.381 0.00 0.00 30.97 4.04
2598 2794 6.343716 TGGTTCAAAAGATGGTACGTAGTA 57.656 37.500 0.00 0.00 45.11 1.82
2601 2797 4.393680 GCATGGTTCAAAAGATGGTACGTA 59.606 41.667 0.00 0.00 0.00 3.57
2602 2798 3.190535 GCATGGTTCAAAAGATGGTACGT 59.809 43.478 0.00 0.00 0.00 3.57
2603 2799 3.727673 CGCATGGTTCAAAAGATGGTACG 60.728 47.826 0.00 0.00 0.00 3.67
2604 2800 3.190535 ACGCATGGTTCAAAAGATGGTAC 59.809 43.478 0.00 0.00 0.00 3.34
2634 2830 6.634805 TCCTCTCAAAGCACAGAAATACTAG 58.365 40.000 0.00 0.00 0.00 2.57
2636 2832 5.012561 ACTCCTCTCAAAGCACAGAAATACT 59.987 40.000 0.00 0.00 0.00 2.12
2637 2833 5.241662 ACTCCTCTCAAAGCACAGAAATAC 58.758 41.667 0.00 0.00 0.00 1.89
2639 2835 4.363991 ACTCCTCTCAAAGCACAGAAAT 57.636 40.909 0.00 0.00 0.00 2.17
2640 2836 3.845781 ACTCCTCTCAAAGCACAGAAA 57.154 42.857 0.00 0.00 0.00 2.52
2645 2845 6.145535 CACAAAAATACTCCTCTCAAAGCAC 58.854 40.000 0.00 0.00 0.00 4.40
2667 2867 5.119931 TGCCACAATTGAGTTGAATACAC 57.880 39.130 13.59 0.00 40.37 2.90
2668 2868 5.336610 CCATGCCACAATTGAGTTGAATACA 60.337 40.000 13.59 0.00 40.37 2.29
2669 2869 5.104374 CCATGCCACAATTGAGTTGAATAC 58.896 41.667 13.59 0.00 40.37 1.89
2670 2870 4.160065 CCCATGCCACAATTGAGTTGAATA 59.840 41.667 13.59 0.00 40.37 1.75
2671 2871 3.055675 CCCATGCCACAATTGAGTTGAAT 60.056 43.478 13.59 0.00 40.37 2.57
2672 2872 2.299582 CCCATGCCACAATTGAGTTGAA 59.700 45.455 13.59 0.00 40.37 2.69
2674 2874 1.894466 TCCCATGCCACAATTGAGTTG 59.106 47.619 13.59 0.00 43.64 3.16
2675 2875 2.173519 CTCCCATGCCACAATTGAGTT 58.826 47.619 13.59 0.00 0.00 3.01
2676 2876 1.617804 CCTCCCATGCCACAATTGAGT 60.618 52.381 13.59 0.00 0.00 3.41
2677 2877 1.108776 CCTCCCATGCCACAATTGAG 58.891 55.000 13.59 3.79 0.00 3.02


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

AutoCloner maintained by Alex Coulton.