Multiple sequence alignment - TraesCS3B01G383200

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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 TraesCS3B01G383200 chr3B 100.000 2546 0 0 1 2546 603373483 603376028 0.000000e+00 4702
1 TraesCS3B01G383200 chr3D 90.414 2514 135 48 1 2480 456319450 456317009 0.000000e+00 3210
2 TraesCS3B01G383200 chr3A 90.927 1025 41 22 872 1869 598989275 598988276 0.000000e+00 1330
3 TraesCS3B01G383200 chr3A 94.794 557 21 6 222 770 598990188 598989632 0.000000e+00 861
4 TraesCS3B01G383200 chr3A 93.631 157 8 1 1 157 598990344 598990190 1.520000e-57 233
5 TraesCS3B01G383200 chr1D 80.874 183 23 10 2269 2441 396317138 396317318 1.590000e-27 134


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 TraesCS3B01G383200 chr3B 603373483 603376028 2545 False 4702 4702 100.000000 1 2546 1 chr3B.!!$F1 2545
1 TraesCS3B01G383200 chr3D 456317009 456319450 2441 True 3210 3210 90.414000 1 2480 1 chr3D.!!$R1 2479
2 TraesCS3B01G383200 chr3A 598988276 598990344 2068 True 808 1330 93.117333 1 1869 3 chr3A.!!$R1 1868

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
66 67 0.1792 GAGGTTAAACATGTGGCGCG 60.179 55.0 0.0 0.0 0.0 6.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2024 2341 0.240411 GCTCGTGTCAGTACTTCGGT 59.76 55.0 0.0 0.0 0.0 4.69 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
21 22 1.681666 CCTGCCTCTCTTTCTGCCA 59.318 57.895 0.00 0.00 0.00 4.92
65 66 1.165270 AGAGGTTAAACATGTGGCGC 58.835 50.000 0.00 0.00 0.00 6.53
66 67 0.179200 GAGGTTAAACATGTGGCGCG 60.179 55.000 0.00 0.00 0.00 6.86
67 68 1.799916 GGTTAAACATGTGGCGCGC 60.800 57.895 25.94 25.94 0.00 6.86
110 111 1.237285 TGGCTTCTTTTGAGCTCGGC 61.237 55.000 9.64 5.70 0.00 5.54
113 114 1.400759 GCTTCTTTTGAGCTCGGCAAG 60.401 52.381 9.64 10.70 0.00 4.01
140 141 9.813446 ACCAAAAATATACTAGTAGGTTCTTCG 57.187 33.333 8.85 0.00 0.00 3.79
147 148 1.254954 AGTAGGTTCTTCGTTCGGCT 58.745 50.000 0.00 0.00 0.00 5.52
181 182 2.235402 GCCACTGCACCTAACCTTACTA 59.765 50.000 0.00 0.00 37.47 1.82
191 192 7.038048 GCACCTAACCTTACTAAACGAGTATT 58.962 38.462 0.00 0.00 40.43 1.89
310 313 6.366332 CCATACGAACTTTCTGGAGTATATGC 59.634 42.308 0.00 0.00 0.00 3.14
339 342 2.421775 ACACGCATGAAAACAGAACACA 59.578 40.909 0.00 0.00 0.00 3.72
355 359 4.454161 AGAACACACAGTTTATGCGCATAA 59.546 37.500 33.26 33.26 41.51 1.90
415 423 2.047213 GATTAATCCCCGGCCGTCCA 62.047 60.000 26.12 7.05 0.00 4.02
424 432 2.845550 CGGCCGTCCATCGAGATGA 61.846 63.158 19.50 0.00 41.20 2.92
440 448 4.394300 CGAGATGATTCCTTGCTTCAACTT 59.606 41.667 0.00 0.00 0.00 2.66
447 455 4.292186 TCCTTGCTTCAACTTCTAGCAT 57.708 40.909 0.00 0.00 43.72 3.79
473 481 0.307760 GTTCCGTGGTTCTGTGCAAG 59.692 55.000 0.00 0.00 0.00 4.01
492 500 2.575532 AGCAGCATTGTAATGGCGTAT 58.424 42.857 6.72 0.00 36.90 3.06
614 623 0.249031 CGCCTGCGTGAGACATCATA 60.249 55.000 2.83 0.00 37.87 2.15
642 652 4.101856 TCTAATTCTCTTTCGGGTCCCTT 58.898 43.478 6.29 0.00 0.00 3.95
693 703 3.106407 GACAGTCGCTGCCACGTC 61.106 66.667 6.74 6.62 34.37 4.34
840 850 6.758886 GTCCACTTGAATACTACTTGATCTGG 59.241 42.308 0.00 0.00 0.00 3.86
862 872 3.052082 CGCACACTGGGGAAGCAG 61.052 66.667 0.00 0.00 0.00 4.24
950 1215 1.866925 GCGCGCTTAGTTTTGTCCT 59.133 52.632 26.67 0.00 0.00 3.85
996 1261 2.764010 GAGGAGGAAGAGGAAGAGGAAC 59.236 54.545 0.00 0.00 0.00 3.62
1005 1274 2.436646 AAGAGGAACGGCATGGCG 60.437 61.111 36.56 36.56 0.00 5.69
1197 1466 2.184322 GCGACGCTTCCCATCTCA 59.816 61.111 13.73 0.00 0.00 3.27
1382 1651 1.735376 ATATGCCTCGGCGAGTTCGT 61.735 55.000 32.41 25.28 45.51 3.85
1386 1655 2.202492 CTCGGCGAGTTCGTGGAG 60.202 66.667 27.92 0.16 42.22 3.86
1556 1825 1.226802 CTGTCTGATCGACCCTGCG 60.227 63.158 12.89 0.00 42.13 5.18
1618 1894 2.109126 GCGACTGACATTGGAGCCC 61.109 63.158 0.00 0.00 0.00 5.19
1619 1895 1.811266 CGACTGACATTGGAGCCCG 60.811 63.158 0.00 0.00 0.00 6.13
1623 1899 4.424711 GACATTGGAGCCCGGCCA 62.425 66.667 5.55 0.00 0.00 5.36
1625 1901 4.431131 CATTGGAGCCCGGCCACT 62.431 66.667 5.55 0.00 34.56 4.00
1631 1907 0.683179 GGAGCCCGGCCACTAATTTT 60.683 55.000 5.55 0.00 0.00 1.82
1643 1919 4.414852 CCACTAATTTTCATTGCACCGAG 58.585 43.478 0.00 0.00 0.00 4.63
1644 1920 4.082787 CCACTAATTTTCATTGCACCGAGT 60.083 41.667 0.00 0.00 0.00 4.18
1645 1921 5.088739 CACTAATTTTCATTGCACCGAGTC 58.911 41.667 0.00 0.00 0.00 3.36
1647 1923 3.559238 ATTTTCATTGCACCGAGTCAC 57.441 42.857 0.00 0.00 0.00 3.67
1648 1924 2.254546 TTTCATTGCACCGAGTCACT 57.745 45.000 0.00 0.00 0.00 3.41
1650 1926 0.678950 TCATTGCACCGAGTCACTGA 59.321 50.000 0.00 0.00 0.00 3.41
1651 1927 1.276138 TCATTGCACCGAGTCACTGAT 59.724 47.619 0.00 0.00 0.00 2.90
1652 1928 1.662629 CATTGCACCGAGTCACTGATC 59.337 52.381 0.00 0.00 0.00 2.92
1653 1929 0.388520 TTGCACCGAGTCACTGATCG 60.389 55.000 0.00 4.72 38.65 3.69
1654 1930 1.241315 TGCACCGAGTCACTGATCGA 61.241 55.000 10.59 0.00 41.40 3.59
1655 1931 0.101399 GCACCGAGTCACTGATCGAT 59.899 55.000 0.00 0.00 41.40 3.59
1656 1932 1.832600 CACCGAGTCACTGATCGATG 58.167 55.000 0.54 0.00 41.40 3.84
1657 1933 0.741326 ACCGAGTCACTGATCGATGG 59.259 55.000 0.54 0.00 41.40 3.51
1658 1934 0.596083 CCGAGTCACTGATCGATGGC 60.596 60.000 0.54 0.00 41.40 4.40
1659 1935 0.383590 CGAGTCACTGATCGATGGCT 59.616 55.000 0.54 0.00 41.40 4.75
1660 1936 1.850377 GAGTCACTGATCGATGGCTG 58.150 55.000 0.54 0.00 28.73 4.85
1661 1937 1.135915 GAGTCACTGATCGATGGCTGT 59.864 52.381 0.54 0.00 28.73 4.40
1664 1940 0.376152 CACTGATCGATGGCTGTTGC 59.624 55.000 0.54 0.00 38.76 4.17
1682 1958 1.005037 CTGCTGGAGTACGTGCCAA 60.005 57.895 0.00 0.00 32.95 4.52
1734 2013 5.117592 CCGATCATTTTTGCTGAGTGTTTTC 59.882 40.000 0.00 0.00 0.00 2.29
1775 2054 8.934825 GGATCATTTTTGCTTAGTTAATTTGCA 58.065 29.630 0.00 0.00 0.00 4.08
1823 2115 9.410556 GTTTGATATTGCCCACATCAATAATAC 57.589 33.333 0.00 0.00 39.13 1.89
1824 2116 7.376435 TGATATTGCCCACATCAATAATACG 57.624 36.000 0.00 0.00 39.13 3.06
1825 2117 6.939730 TGATATTGCCCACATCAATAATACGT 59.060 34.615 0.00 0.00 39.13 3.57
1827 2119 6.801539 ATTGCCCACATCAATAATACGTAG 57.198 37.500 0.08 0.00 32.84 3.51
1849 2141 0.392193 ACGAGCTGCATCTTTCCCTG 60.392 55.000 1.02 0.00 0.00 4.45
1875 2167 3.662713 CGTTTGCATCATATCTGCTACGC 60.663 47.826 15.32 0.00 39.50 4.42
1894 2186 1.548132 CCTTTCGCCGTTTTTGCAGC 61.548 55.000 0.00 0.00 0.00 5.25
1975 2292 1.081840 GCTTTCAGTTGCAGGCGAC 60.082 57.895 3.39 3.39 0.00 5.19
2024 2341 0.881118 GGAAAACCTGCATGCTTCGA 59.119 50.000 20.33 0.00 0.00 3.71
2027 2344 1.577328 AAACCTGCATGCTTCGACCG 61.577 55.000 20.33 0.76 0.00 4.79
2028 2345 2.125552 CCTGCATGCTTCGACCGA 60.126 61.111 20.33 0.00 0.00 4.69
2071 2388 1.351017 CTAAACCTCTCCAGCCCACAA 59.649 52.381 0.00 0.00 0.00 3.33
2073 2390 0.038744 AACCTCTCCAGCCCACAATG 59.961 55.000 0.00 0.00 0.00 2.82
2074 2391 1.136329 ACCTCTCCAGCCCACAATGT 61.136 55.000 0.00 0.00 0.00 2.71
2075 2392 0.679002 CCTCTCCAGCCCACAATGTG 60.679 60.000 6.37 6.37 0.00 3.21
2078 2395 1.278985 TCTCCAGCCCACAATGTGTAG 59.721 52.381 12.79 4.53 0.00 2.74
2079 2396 0.327924 TCCAGCCCACAATGTGTAGG 59.672 55.000 12.79 8.37 0.00 3.18
2080 2397 0.038166 CCAGCCCACAATGTGTAGGT 59.962 55.000 12.79 6.11 0.00 3.08
2081 2398 1.547675 CCAGCCCACAATGTGTAGGTT 60.548 52.381 12.79 2.49 0.00 3.50
2082 2399 2.238521 CAGCCCACAATGTGTAGGTTT 58.761 47.619 12.79 0.00 0.00 3.27
2083 2400 3.417101 CAGCCCACAATGTGTAGGTTTA 58.583 45.455 12.79 0.00 0.00 2.01
2084 2401 4.016444 CAGCCCACAATGTGTAGGTTTAT 58.984 43.478 12.79 0.00 0.00 1.40
2085 2402 4.462483 CAGCCCACAATGTGTAGGTTTATT 59.538 41.667 12.79 0.00 0.00 1.40
2086 2403 5.650266 CAGCCCACAATGTGTAGGTTTATTA 59.350 40.000 12.79 0.00 0.00 0.98
2087 2404 6.321181 CAGCCCACAATGTGTAGGTTTATTAT 59.679 38.462 12.79 0.00 0.00 1.28
2088 2405 6.895204 AGCCCACAATGTGTAGGTTTATTATT 59.105 34.615 12.79 0.00 0.00 1.40
2113 2430 0.728466 GGAACGAAGACTCACGACGG 60.728 60.000 0.00 0.00 0.00 4.79
2146 2464 1.972872 CTGTGATCCTGGCCATAACC 58.027 55.000 5.51 0.00 0.00 2.85
2167 2485 2.272471 GCCGGGCCTAAAAGAGCT 59.728 61.111 8.12 0.00 0.00 4.09
2176 2494 2.430465 CCTAAAAGAGCTTGCAGCAGA 58.570 47.619 10.16 0.00 45.56 4.26
2181 2499 1.683943 AGAGCTTGCAGCAGAAAACA 58.316 45.000 10.16 0.00 45.56 2.83
2182 2500 1.336125 AGAGCTTGCAGCAGAAAACAC 59.664 47.619 10.16 0.00 45.56 3.32
2183 2501 1.066002 GAGCTTGCAGCAGAAAACACA 59.934 47.619 10.16 0.00 45.56 3.72
2185 2503 1.866880 GCTTGCAGCAGAAAACACAGG 60.867 52.381 0.00 0.00 41.89 4.00
2188 2506 1.662044 CAGCAGAAAACACAGGCCC 59.338 57.895 0.00 0.00 0.00 5.80
2190 2508 0.825010 AGCAGAAAACACAGGCCCAG 60.825 55.000 0.00 0.00 0.00 4.45
2191 2509 1.109323 GCAGAAAACACAGGCCCAGT 61.109 55.000 0.00 0.00 0.00 4.00
2193 2511 0.846693 AGAAAACACAGGCCCAGTCT 59.153 50.000 0.00 0.00 0.00 3.24
2234 2552 4.856801 CCCAAGCCCGGACCATCG 62.857 72.222 0.73 0.00 0.00 3.84
2245 2563 1.534729 GGACCATCGGTGAAAAAGCT 58.465 50.000 0.00 0.00 35.25 3.74
2246 2564 1.468914 GGACCATCGGTGAAAAAGCTC 59.531 52.381 0.00 0.00 35.25 4.09
2249 2567 1.535462 CCATCGGTGAAAAAGCTCGTT 59.465 47.619 0.00 0.00 0.00 3.85
2250 2568 2.574322 CATCGGTGAAAAAGCTCGTTG 58.426 47.619 0.00 0.00 0.00 4.10
2256 2574 0.673985 GAAAAAGCTCGTTGGGCCTT 59.326 50.000 4.53 0.00 0.00 4.35
2257 2575 1.883926 GAAAAAGCTCGTTGGGCCTTA 59.116 47.619 4.53 0.00 0.00 2.69
2263 2581 0.175989 CTCGTTGGGCCTTAGGTCTC 59.824 60.000 4.53 0.00 0.00 3.36
2264 2582 0.543410 TCGTTGGGCCTTAGGTCTCA 60.543 55.000 4.53 0.00 0.00 3.27
2305 2623 1.338294 ACGCACGTATGTCAATCCCAA 60.338 47.619 0.00 0.00 0.00 4.12
2312 2630 3.140814 GTCAATCCCAAGCCCGGC 61.141 66.667 0.00 0.00 0.00 6.13
2343 2661 4.413520 AGCATTAGGGCTCAAAATCTAGGA 59.586 41.667 0.00 0.00 41.05 2.94
2344 2662 4.517075 GCATTAGGGCTCAAAATCTAGGAC 59.483 45.833 0.00 0.00 0.00 3.85
2345 2663 5.688766 GCATTAGGGCTCAAAATCTAGGACT 60.689 44.000 0.00 0.00 0.00 3.85
2351 2669 3.389656 GCTCAAAATCTAGGACTAGGCCT 59.610 47.826 23.94 23.94 42.15 5.19
2396 2714 1.904771 GGGTTGGGCTATTTTGGGC 59.095 57.895 0.00 0.00 0.00 5.36
2401 2719 2.043349 GGCTATTTTGGGCCGGGT 60.043 61.111 2.18 0.00 38.91 5.28
2402 2720 2.125326 GGCTATTTTGGGCCGGGTC 61.125 63.158 2.18 0.00 38.91 4.46
2403 2721 2.478033 GCTATTTTGGGCCGGGTCG 61.478 63.158 2.18 0.00 0.00 4.79
2442 2761 3.479489 CATGGCCAGTATAATCACAGCA 58.521 45.455 13.05 0.00 0.00 4.41
2447 2766 3.066760 GCCAGTATAATCACAGCAAACCC 59.933 47.826 0.00 0.00 0.00 4.11
2465 2784 4.513406 ACCCCAACTTACAAACAGAAGA 57.487 40.909 0.00 0.00 0.00 2.87
2520 2839 4.993705 AAAGTAGAGGATCCACAAACCA 57.006 40.909 15.82 0.00 33.66 3.67
2521 2840 4.993705 AAGTAGAGGATCCACAAACCAA 57.006 40.909 15.82 0.00 33.66 3.67
2522 2841 4.993705 AGTAGAGGATCCACAAACCAAA 57.006 40.909 15.82 0.00 33.66 3.28
2523 2842 4.652822 AGTAGAGGATCCACAAACCAAAC 58.347 43.478 15.82 0.00 33.66 2.93
2524 2843 3.593442 AGAGGATCCACAAACCAAACA 57.407 42.857 15.82 0.00 33.66 2.83
2525 2844 3.490348 AGAGGATCCACAAACCAAACAG 58.510 45.455 15.82 0.00 33.66 3.16
2526 2845 2.558359 GAGGATCCACAAACCAAACAGG 59.442 50.000 15.82 0.00 45.67 4.00
2528 2847 8.875604 TAGAGGATCCACAAACCAAACAGGTG 62.876 46.154 15.82 0.00 44.64 4.00
2539 2858 4.701956 CCAAACAGGTGATACAATGTCC 57.298 45.455 0.00 0.00 0.00 4.02
2540 2859 4.335416 CCAAACAGGTGATACAATGTCCT 58.665 43.478 0.00 0.00 0.00 3.85
2541 2860 5.496556 CCAAACAGGTGATACAATGTCCTA 58.503 41.667 0.00 0.00 0.00 2.94
2542 2861 5.354234 CCAAACAGGTGATACAATGTCCTAC 59.646 44.000 0.00 0.00 0.00 3.18
2543 2862 5.755409 AACAGGTGATACAATGTCCTACA 57.245 39.130 0.00 0.00 0.00 2.74
2544 2863 5.957771 ACAGGTGATACAATGTCCTACAT 57.042 39.130 0.00 0.00 41.31 2.29
2545 2864 5.674525 ACAGGTGATACAATGTCCTACATG 58.325 41.667 0.00 0.00 37.97 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 2.165998 ACAAATGGCAGAAAGAGAGGC 58.834 47.619 0.00 0.00 0.00 4.70
8 9 5.302357 GGTAACAAATGGCAGAAAGAGAG 57.698 43.478 0.00 0.00 0.00 3.20
65 66 5.580691 TCACATGGAAAGAAATACTGTAGCG 59.419 40.000 0.00 0.00 0.00 4.26
66 67 6.985188 TCACATGGAAAGAAATACTGTAGC 57.015 37.500 0.00 0.00 0.00 3.58
140 141 3.879351 CTGCACGCCAAAGCCGAAC 62.879 63.158 0.00 0.00 34.57 3.95
161 162 4.546829 TTAGTAAGGTTAGGTGCAGTGG 57.453 45.455 0.00 0.00 0.00 4.00
310 313 3.188254 TGTTTTCATGCGTGTACTCCATG 59.812 43.478 5.68 14.87 38.10 3.66
339 342 8.601845 TCTGTATATTTATGCGCATAAACTGT 57.398 30.769 42.31 33.26 43.54 3.55
415 423 4.412796 TGAAGCAAGGAATCATCTCGAT 57.587 40.909 0.00 0.00 35.12 3.59
424 432 4.655963 TGCTAGAAGTTGAAGCAAGGAAT 58.344 39.130 6.32 0.00 42.96 3.01
440 448 2.688446 CACGGAACCAGAGTATGCTAGA 59.312 50.000 0.00 0.00 0.00 2.43
447 455 1.616865 CAGAACCACGGAACCAGAGTA 59.383 52.381 0.00 0.00 0.00 2.59
473 481 3.354089 AATACGCCATTACAATGCTGC 57.646 42.857 0.00 0.00 35.08 5.25
492 500 0.179137 CTGTCATGAGGTCGCGCTAA 60.179 55.000 5.56 0.00 0.00 3.09
614 623 8.541234 GGGACCCGAAAGAGAATTAGAATATAT 58.459 37.037 0.00 0.00 0.00 0.86
693 703 1.002659 TGCCATATCCCGGGTAATTCG 59.997 52.381 22.86 6.12 0.00 3.34
840 850 3.825160 TTCCCCAGTGTGCGCTCAC 62.825 63.158 29.91 29.91 43.40 3.51
862 872 1.610554 TTCCTGGGCCTGCTACGTAC 61.611 60.000 4.53 0.00 0.00 3.67
1197 1466 0.935194 ACGAGGAGGGGTAGGAGAAT 59.065 55.000 0.00 0.00 0.00 2.40
1382 1651 3.539593 TTCACCCTCTCGCCCTCCA 62.540 63.158 0.00 0.00 0.00 3.86
1386 1655 4.475135 GCCTTCACCCTCTCGCCC 62.475 72.222 0.00 0.00 0.00 6.13
1458 1727 4.802051 GGGCAGCTGGGATGCGAA 62.802 66.667 17.12 0.00 44.80 4.70
1513 1782 1.148310 CTCGCGTCCACAGTTTTGAT 58.852 50.000 5.77 0.00 0.00 2.57
1571 1847 2.171489 GAGCGGTGCAGTTTCGAACC 62.171 60.000 0.00 0.00 0.00 3.62
1618 1894 2.923020 GTGCAATGAAAATTAGTGGCCG 59.077 45.455 0.00 0.00 0.00 6.13
1619 1895 3.261580 GGTGCAATGAAAATTAGTGGCC 58.738 45.455 0.00 0.00 0.00 5.36
1623 1899 4.759693 TGACTCGGTGCAATGAAAATTAGT 59.240 37.500 0.00 0.00 0.00 2.24
1625 1901 4.759693 AGTGACTCGGTGCAATGAAAATTA 59.240 37.500 0.00 0.00 0.00 1.40
1631 1907 0.678950 TCAGTGACTCGGTGCAATGA 59.321 50.000 0.00 0.00 36.85 2.57
1643 1919 1.662629 CAACAGCCATCGATCAGTGAC 59.337 52.381 0.00 0.00 0.00 3.67
1644 1920 2.008543 GCAACAGCCATCGATCAGTGA 61.009 52.381 0.00 0.00 0.00 3.41
1645 1921 0.376152 GCAACAGCCATCGATCAGTG 59.624 55.000 0.00 0.00 0.00 3.66
1647 1923 0.656259 CAGCAACAGCCATCGATCAG 59.344 55.000 0.00 0.00 0.00 2.90
1648 1924 1.371337 GCAGCAACAGCCATCGATCA 61.371 55.000 0.00 0.00 0.00 2.92
1650 1926 1.077930 AGCAGCAACAGCCATCGAT 60.078 52.632 0.00 0.00 0.00 3.59
1651 1927 2.036571 CAGCAGCAACAGCCATCGA 61.037 57.895 0.00 0.00 0.00 3.59
1652 1928 2.483745 CAGCAGCAACAGCCATCG 59.516 61.111 0.00 0.00 0.00 3.84
1653 1929 1.654954 CTCCAGCAGCAACAGCCATC 61.655 60.000 0.00 0.00 0.00 3.51
1654 1930 1.677966 CTCCAGCAGCAACAGCCAT 60.678 57.895 0.00 0.00 0.00 4.40
1655 1931 1.767654 TACTCCAGCAGCAACAGCCA 61.768 55.000 0.00 0.00 0.00 4.75
1656 1932 1.003355 TACTCCAGCAGCAACAGCC 60.003 57.895 0.00 0.00 0.00 4.85
1657 1933 1.630244 CGTACTCCAGCAGCAACAGC 61.630 60.000 0.00 0.00 0.00 4.40
1658 1934 0.319900 ACGTACTCCAGCAGCAACAG 60.320 55.000 0.00 0.00 0.00 3.16
1659 1935 0.599991 CACGTACTCCAGCAGCAACA 60.600 55.000 0.00 0.00 0.00 3.33
1660 1936 1.901650 GCACGTACTCCAGCAGCAAC 61.902 60.000 0.00 0.00 0.00 4.17
1661 1937 1.667830 GCACGTACTCCAGCAGCAA 60.668 57.895 0.00 0.00 0.00 3.91
1664 1940 0.391661 ATTGGCACGTACTCCAGCAG 60.392 55.000 0.00 0.00 33.32 4.24
1682 1958 2.498481 CCAATCAACCATGCCTGAACAT 59.502 45.455 0.00 0.00 0.00 2.71
1734 2013 8.482429 CAAAAATGATCCGTTCAAAGAAAAGAG 58.518 33.333 0.00 0.00 38.03 2.85
1775 2054 3.340928 GCCCGTAAAAACTCACTGGTAT 58.659 45.455 0.00 0.00 0.00 2.73
1777 2056 1.601166 GCCCGTAAAAACTCACTGGT 58.399 50.000 0.00 0.00 0.00 4.00
1778 2057 0.515564 CGCCCGTAAAAACTCACTGG 59.484 55.000 0.00 0.00 0.00 4.00
1824 2116 3.062774 GGAAAGATGCAGCTCGTTTCTAC 59.937 47.826 4.22 0.00 0.00 2.59
1825 2117 3.262420 GGAAAGATGCAGCTCGTTTCTA 58.738 45.455 4.22 0.00 0.00 2.10
1827 2119 1.131315 GGGAAAGATGCAGCTCGTTTC 59.869 52.381 4.22 5.56 0.00 2.78
1849 2141 1.267806 CAGATATGATGCAAACGGGGC 59.732 52.381 0.00 0.00 0.00 5.80
1875 2167 1.548132 GCTGCAAAAACGGCGAAAGG 61.548 55.000 16.62 0.00 31.03 3.11
1894 2186 7.115520 CCACATAGTAGCATTTGTTCTATCGAG 59.884 40.741 0.00 0.00 0.00 4.04
1911 2228 1.552578 AGTGCACGGTCCACATAGTA 58.447 50.000 12.01 0.00 35.69 1.82
2024 2341 0.240411 GCTCGTGTCAGTACTTCGGT 59.760 55.000 0.00 0.00 0.00 4.69
2027 2344 1.197264 ACTCGCTCGTGTCAGTACTTC 59.803 52.381 0.00 0.00 0.00 3.01
2028 2345 1.236628 ACTCGCTCGTGTCAGTACTT 58.763 50.000 0.00 0.00 0.00 2.24
2031 2348 3.790091 AGTATACTCGCTCGTGTCAGTA 58.210 45.455 0.00 0.00 0.00 2.74
2088 2405 2.536803 CGTGAGTCTTCGTTCCGAAAAA 59.463 45.455 0.47 0.00 45.23 1.94
2093 2410 1.058590 CGTCGTGAGTCTTCGTTCCG 61.059 60.000 7.81 6.07 0.00 4.30
2099 2416 2.126031 GCCCCGTCGTGAGTCTTC 60.126 66.667 0.00 0.00 0.00 2.87
2113 2430 2.710096 TCACAGCTTAGTTATGGCCC 57.290 50.000 0.00 0.00 0.00 5.80
2167 2485 0.102844 GCCTGTGTTTTCTGCTGCAA 59.897 50.000 3.02 0.00 0.00 4.08
2176 2494 0.258774 ACAGACTGGGCCTGTGTTTT 59.741 50.000 21.65 3.31 42.68 2.43
2181 2499 0.398318 GAAGAACAGACTGGGCCTGT 59.602 55.000 16.65 16.65 45.88 4.00
2182 2500 0.671781 CGAAGAACAGACTGGGCCTG 60.672 60.000 9.11 9.11 37.64 4.85
2183 2501 1.674057 CGAAGAACAGACTGGGCCT 59.326 57.895 4.53 0.00 0.00 5.19
2185 2503 1.376037 CCCGAAGAACAGACTGGGC 60.376 63.158 7.51 0.00 0.00 5.36
2188 2506 0.895530 TAGGCCCGAAGAACAGACTG 59.104 55.000 0.00 0.00 0.00 3.51
2190 2508 2.467566 TTTAGGCCCGAAGAACAGAC 57.532 50.000 0.00 0.00 0.00 3.51
2191 2509 3.713826 AATTTAGGCCCGAAGAACAGA 57.286 42.857 0.00 0.00 0.00 3.41
2193 2511 3.756434 CTGAAATTTAGGCCCGAAGAACA 59.244 43.478 0.00 0.00 0.00 3.18
2195 2513 3.352648 CCTGAAATTTAGGCCCGAAGAA 58.647 45.455 0.00 0.00 0.00 2.52
2234 2552 0.318699 GCCCAACGAGCTTTTTCACC 60.319 55.000 0.00 0.00 0.00 4.02
2238 2556 1.886542 CTAAGGCCCAACGAGCTTTTT 59.113 47.619 0.00 0.00 31.37 1.94
2239 2557 1.534729 CTAAGGCCCAACGAGCTTTT 58.465 50.000 0.00 0.00 31.37 2.27
2245 2563 0.543410 TGAGACCTAAGGCCCAACGA 60.543 55.000 0.00 0.00 0.00 3.85
2246 2564 0.108138 CTGAGACCTAAGGCCCAACG 60.108 60.000 0.00 0.00 0.00 4.10
2249 2567 4.480480 CCTGAGACCTAAGGCCCA 57.520 61.111 0.00 0.00 0.00 5.36
2256 2574 2.365635 GGCCCAGCCTGAGACCTA 60.366 66.667 0.00 0.00 46.69 3.08
2385 2703 2.478033 CGACCCGGCCCAAAATAGC 61.478 63.158 0.00 0.00 0.00 2.97
2404 2722 0.898326 ATGGAAAACCGGGCTCAACC 60.898 55.000 6.32 1.85 37.93 3.77
2405 2723 0.243636 CATGGAAAACCGGGCTCAAC 59.756 55.000 6.32 0.00 0.00 3.18
2406 2724 0.897863 CCATGGAAAACCGGGCTCAA 60.898 55.000 5.56 0.00 0.00 3.02
2407 2725 1.304052 CCATGGAAAACCGGGCTCA 60.304 57.895 5.56 0.00 0.00 4.26
2408 2726 2.710902 GCCATGGAAAACCGGGCTC 61.711 63.158 18.40 0.00 41.39 4.70
2409 2727 2.679996 GCCATGGAAAACCGGGCT 60.680 61.111 18.40 0.00 41.39 5.19
2410 2728 3.770040 GGCCATGGAAAACCGGGC 61.770 66.667 18.40 11.51 43.86 6.13
2411 2729 2.283532 TGGCCATGGAAAACCGGG 60.284 61.111 18.40 0.00 0.00 5.73
2412 2730 0.322997 TACTGGCCATGGAAAACCGG 60.323 55.000 18.40 14.61 34.56 5.28
2413 2731 1.762708 ATACTGGCCATGGAAAACCG 58.237 50.000 18.40 6.21 0.00 4.44
2414 2732 4.892934 TGATTATACTGGCCATGGAAAACC 59.107 41.667 18.40 7.65 0.00 3.27
2415 2733 5.359576 TGTGATTATACTGGCCATGGAAAAC 59.640 40.000 18.40 2.31 0.00 2.43
2419 2737 3.496692 GCTGTGATTATACTGGCCATGGA 60.497 47.826 18.40 0.00 0.00 3.41
2442 2761 5.265989 TCTTCTGTTTGTAAGTTGGGGTTT 58.734 37.500 0.00 0.00 0.00 3.27
2497 2816 5.701224 TGGTTTGTGGATCCTCTACTTTTT 58.299 37.500 14.23 0.00 0.00 1.94
2498 2817 5.319043 TGGTTTGTGGATCCTCTACTTTT 57.681 39.130 14.23 0.00 0.00 2.27
2499 2818 4.993705 TGGTTTGTGGATCCTCTACTTT 57.006 40.909 14.23 0.00 0.00 2.66
2500 2819 4.993705 TTGGTTTGTGGATCCTCTACTT 57.006 40.909 14.23 0.00 0.00 2.24
2501 2820 4.104102 TGTTTGGTTTGTGGATCCTCTACT 59.896 41.667 14.23 0.00 0.00 2.57
2502 2821 4.394729 TGTTTGGTTTGTGGATCCTCTAC 58.605 43.478 14.23 11.41 0.00 2.59
2503 2822 4.506625 CCTGTTTGGTTTGTGGATCCTCTA 60.507 45.833 14.23 3.28 0.00 2.43
2504 2823 3.490348 CTGTTTGGTTTGTGGATCCTCT 58.510 45.455 14.23 0.00 0.00 3.69
2505 2824 2.558359 CCTGTTTGGTTTGTGGATCCTC 59.442 50.000 14.23 10.39 0.00 3.71
2506 2825 2.597455 CCTGTTTGGTTTGTGGATCCT 58.403 47.619 14.23 0.00 0.00 3.24
2518 2837 4.335416 AGGACATTGTATCACCTGTTTGG 58.665 43.478 0.00 0.00 42.93 3.28
2519 2838 5.937540 TGTAGGACATTGTATCACCTGTTTG 59.062 40.000 5.29 0.00 32.90 2.93
2520 2839 6.121776 TGTAGGACATTGTATCACCTGTTT 57.878 37.500 5.29 0.00 32.90 2.83
2521 2840 5.755409 TGTAGGACATTGTATCACCTGTT 57.245 39.130 5.29 0.00 32.90 3.16
2522 2841 5.674525 CATGTAGGACATTGTATCACCTGT 58.325 41.667 5.29 0.00 36.53 4.00


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

AutoCloner maintained by Alex Coulton.