Multiple sequence alignment - TraesCS7A01G143500

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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 TraesCS7A01G143500 chr7A 100.000 2555 0 0 1 2555 94451814 94454368 0.000000e+00 4719.0
1 TraesCS7A01G143500 chr7A 85.411 802 107 6 405 1200 94436861 94437658 0.000000e+00 824.0
2 TraesCS7A01G143500 chr7A 90.878 592 54 0 1964 2555 94778559 94779150 0.000000e+00 795.0
3 TraesCS7A01G143500 chr7A 84.760 584 77 8 1971 2552 94700798 94701371 2.200000e-160 575.0
4 TraesCS7A01G143500 chr7A 73.514 555 128 16 984 1530 632908558 632908015 2.590000e-45 193.0
5 TraesCS7A01G143500 chr7A 73.429 557 128 15 984 1530 631966921 631967467 9.330000e-45 191.0
6 TraesCS7A01G143500 chr7A 73.285 554 129 17 985 1530 633037551 633037009 4.340000e-43 185.0
7 TraesCS7A01G143500 chr7A 72.163 564 129 17 984 1530 632971111 632970559 5.700000e-32 148.0
8 TraesCS7A01G143500 chr7D 92.075 1918 109 17 1 1897 92274270 92276165 0.000000e+00 2660.0
9 TraesCS7A01G143500 chr7D 92.399 592 45 0 1964 2555 92599826 92600417 0.000000e+00 845.0
10 TraesCS7A01G143500 chr7D 82.678 814 96 16 394 1200 92266245 92267020 0.000000e+00 680.0
11 TraesCS7A01G143500 chr7B 91.017 1180 87 3 656 1833 44398194 44399356 0.000000e+00 1574.0
12 TraesCS7A01G143500 chr7B 81.882 1700 224 54 18 1677 44384189 44385844 0.000000e+00 1356.0
13 TraesCS7A01G143500 chr7B 91.511 589 46 4 1969 2555 44881309 44881895 0.000000e+00 808.0
14 TraesCS7A01G143500 chr7B 81.905 840 115 15 397 1200 44327466 44328304 0.000000e+00 675.0
15 TraesCS7A01G143500 chr7B 86.186 333 31 9 331 651 44396917 44397246 1.880000e-91 346.0
16 TraesCS7A01G143500 chr3A 76.868 562 114 12 984 1537 685780814 685781367 1.150000e-78 303.0
17 TraesCS7A01G143500 chr5D 74.785 698 151 21 984 1668 388038463 388039148 8.940000e-75 291.0
18 TraesCS7A01G143500 chr5D 82.927 164 24 4 825 986 388092181 388092342 7.370000e-31 145.0
19 TraesCS7A01G143500 chr5D 83.226 155 26 0 826 980 388051548 388051702 2.650000e-30 143.0
20 TraesCS7A01G143500 chr5B 84.242 165 20 6 825 986 470115565 470115726 3.400000e-34 156.0
21 TraesCS7A01G143500 chr5B 86.364 88 12 0 656 743 265429831 265429918 2.090000e-16 97.1
22 TraesCS7A01G143500 chr5B 82.609 92 14 2 659 749 264936500 264936410 2.110000e-11 80.5
23 TraesCS7A01G143500 chr5A 82.927 164 24 4 825 986 491251896 491252057 7.370000e-31 145.0


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 TraesCS7A01G143500 chr7A 94451814 94454368 2554 False 4719 4719 100.0000 1 2555 1 chr7A.!!$F2 2554
1 TraesCS7A01G143500 chr7A 94436861 94437658 797 False 824 824 85.4110 405 1200 1 chr7A.!!$F1 795
2 TraesCS7A01G143500 chr7A 94778559 94779150 591 False 795 795 90.8780 1964 2555 1 chr7A.!!$F4 591
3 TraesCS7A01G143500 chr7A 94700798 94701371 573 False 575 575 84.7600 1971 2552 1 chr7A.!!$F3 581
4 TraesCS7A01G143500 chr7D 92274270 92276165 1895 False 2660 2660 92.0750 1 1897 1 chr7D.!!$F2 1896
5 TraesCS7A01G143500 chr7D 92599826 92600417 591 False 845 845 92.3990 1964 2555 1 chr7D.!!$F3 591
6 TraesCS7A01G143500 chr7D 92266245 92267020 775 False 680 680 82.6780 394 1200 1 chr7D.!!$F1 806
7 TraesCS7A01G143500 chr7B 44384189 44385844 1655 False 1356 1356 81.8820 18 1677 1 chr7B.!!$F2 1659
8 TraesCS7A01G143500 chr7B 44396917 44399356 2439 False 960 1574 88.6015 331 1833 2 chr7B.!!$F4 1502
9 TraesCS7A01G143500 chr7B 44881309 44881895 586 False 808 808 91.5110 1969 2555 1 chr7B.!!$F3 586
10 TraesCS7A01G143500 chr7B 44327466 44328304 838 False 675 675 81.9050 397 1200 1 chr7B.!!$F1 803
11 TraesCS7A01G143500 chr3A 685780814 685781367 553 False 303 303 76.8680 984 1537 1 chr3A.!!$F1 553
12 TraesCS7A01G143500 chr5D 388038463 388039148 685 False 291 291 74.7850 984 1668 1 chr5D.!!$F1 684

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
930 1928 0.455815 TGCGGGATGATATCGATCCG 59.544 55.0 19.51 19.51 40.47 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1959 3011 0.034896 AACCATGCTCCGACGAGTTT 59.965 50.0 0.0 0.0 38.49 2.66 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
107 112 3.027675 GCGGGGTGGAAGAGGTACC 62.028 68.421 2.73 2.73 0.00 3.34
109 114 2.582978 GGGTGGAAGAGGTACCGC 59.417 66.667 7.70 7.70 35.31 5.68
110 115 2.183555 GGTGGAAGAGGTACCGCG 59.816 66.667 10.22 0.00 37.53 6.46
168 177 1.262417 GGGAGGAGATCGGAGGATTC 58.738 60.000 0.00 0.00 31.51 2.52
169 178 1.262417 GGAGGAGATCGGAGGATTCC 58.738 60.000 0.00 0.00 40.33 3.01
183 196 5.489249 GGAGGATTCCGTTTTCTTCTAACT 58.511 41.667 0.00 0.00 32.79 2.24
265 278 3.068691 TTCTCCTCCGACGCCCTG 61.069 66.667 0.00 0.00 0.00 4.45
290 303 3.790437 CACCGCTCCAGCCCTCAT 61.790 66.667 0.00 0.00 37.91 2.90
291 304 3.790437 ACCGCTCCAGCCCTCATG 61.790 66.667 0.00 0.00 37.91 3.07
292 305 4.559063 CCGCTCCAGCCCTCATGG 62.559 72.222 0.00 0.00 39.33 3.66
400 418 1.450531 GGCGGCCTTCATCAATCCAG 61.451 60.000 12.87 0.00 0.00 3.86
554 579 0.965439 TCCAAGGGCAACGAAAATGG 59.035 50.000 0.00 0.00 37.60 3.16
559 584 1.538075 AGGGCAACGAAAATGGTAACG 59.462 47.619 0.00 0.00 36.80 3.18
562 587 2.227556 GCAACGAAAATGGTAACGTCG 58.772 47.619 0.00 0.00 38.00 5.12
618 673 3.000727 GGATCTGACGGTTGAAATCGTT 58.999 45.455 2.45 0.00 39.88 3.85
619 674 3.435671 GGATCTGACGGTTGAAATCGTTT 59.564 43.478 2.45 0.00 39.88 3.60
756 1754 2.178521 CGTACAGAGACGCGGCTT 59.821 61.111 19.64 1.63 35.79 4.35
930 1928 0.455815 TGCGGGATGATATCGATCCG 59.544 55.000 19.51 19.51 40.47 4.18
1238 2259 0.456628 GAGGCGACTGTAGAGGTTCC 59.543 60.000 0.00 0.00 44.43 3.62
1239 2260 1.139095 GGCGACTGTAGAGGTTCCG 59.861 63.158 0.00 0.00 0.00 4.30
1275 2296 6.421501 TGCAAAGCAGTTTCAATTTGTCTATG 59.578 34.615 0.00 0.00 35.55 2.23
1364 2385 3.477530 GCTTAAAGAGGTCTGTGGTTGT 58.522 45.455 0.00 0.00 0.00 3.32
1406 2428 5.643777 CGATAGATTTGGAGTTCAAGGTTGT 59.356 40.000 0.00 0.00 35.58 3.32
1444 2466 1.001815 CCGACCACCAACATTGTTGTC 60.002 52.381 24.01 15.39 34.06 3.18
1451 2476 4.362279 CACCAACATTGTTGTCCTTTCAG 58.638 43.478 24.01 11.31 34.06 3.02
1541 2566 1.005867 GGTCGACGTTGCCTGGTAA 60.006 57.895 9.92 0.00 0.00 2.85
1624 2655 7.008810 CAGATTAAGAACTTCGACAGTCTTAGC 59.991 40.741 0.00 7.46 32.94 3.09
1784 2816 5.984926 ACCATGTTTTGACATGTAAGCAAAG 59.015 36.000 15.85 0.00 44.29 2.77
1836 2870 6.644248 ATGTCCATGTGTTCAATATCCATG 57.356 37.500 0.00 0.00 34.18 3.66
1843 2895 6.073447 TGTGTTCAATATCCATGGGTTAGT 57.927 37.500 13.02 0.62 0.00 2.24
1844 2896 6.489603 TGTGTTCAATATCCATGGGTTAGTT 58.510 36.000 13.02 0.00 0.00 2.24
1850 2902 2.917713 TCCATGGGTTAGTTGGCAAT 57.082 45.000 13.02 0.00 0.00 3.56
1851 2903 3.182887 TCCATGGGTTAGTTGGCAATT 57.817 42.857 13.02 0.69 0.00 2.32
1874 2926 7.766219 TTTCATGCCGTCTATTAAGTCTTAC 57.234 36.000 0.00 0.00 0.00 2.34
1897 2949 6.410540 ACTTCTTGGAGGATTAGCTTAGTTG 58.589 40.000 0.00 0.00 0.00 3.16
1898 2950 6.013293 ACTTCTTGGAGGATTAGCTTAGTTGT 60.013 38.462 0.00 0.00 0.00 3.32
1899 2951 7.180408 ACTTCTTGGAGGATTAGCTTAGTTGTA 59.820 37.037 0.00 0.00 0.00 2.41
1900 2952 7.676683 TCTTGGAGGATTAGCTTAGTTGTAT 57.323 36.000 0.00 0.00 0.00 2.29
1901 2953 7.500992 TCTTGGAGGATTAGCTTAGTTGTATG 58.499 38.462 0.00 0.00 0.00 2.39
1902 2954 5.611374 TGGAGGATTAGCTTAGTTGTATGC 58.389 41.667 0.00 0.00 0.00 3.14
1903 2955 5.366768 TGGAGGATTAGCTTAGTTGTATGCT 59.633 40.000 0.00 0.00 41.36 3.79
1904 2956 6.126768 TGGAGGATTAGCTTAGTTGTATGCTT 60.127 38.462 0.00 0.00 39.65 3.91
1905 2957 6.768381 GGAGGATTAGCTTAGTTGTATGCTTT 59.232 38.462 0.00 0.00 39.65 3.51
1906 2958 7.254932 GGAGGATTAGCTTAGTTGTATGCTTTG 60.255 40.741 0.00 0.00 39.65 2.77
1907 2959 7.112779 AGGATTAGCTTAGTTGTATGCTTTGT 58.887 34.615 0.00 0.00 39.65 2.83
1908 2960 7.611855 AGGATTAGCTTAGTTGTATGCTTTGTT 59.388 33.333 0.00 0.00 39.65 2.83
1909 2961 8.244113 GGATTAGCTTAGTTGTATGCTTTGTTT 58.756 33.333 0.00 0.00 39.65 2.83
1910 2962 8.970691 ATTAGCTTAGTTGTATGCTTTGTTTG 57.029 30.769 0.00 0.00 39.65 2.93
1911 2963 5.772521 AGCTTAGTTGTATGCTTTGTTTGG 58.227 37.500 0.00 0.00 36.49 3.28
1912 2964 4.923281 GCTTAGTTGTATGCTTTGTTTGGG 59.077 41.667 0.00 0.00 0.00 4.12
1913 2965 5.278758 GCTTAGTTGTATGCTTTGTTTGGGA 60.279 40.000 0.00 0.00 0.00 4.37
1914 2966 4.853924 AGTTGTATGCTTTGTTTGGGAG 57.146 40.909 0.00 0.00 0.00 4.30
1915 2967 4.469657 AGTTGTATGCTTTGTTTGGGAGA 58.530 39.130 0.00 0.00 0.00 3.71
1916 2968 4.892934 AGTTGTATGCTTTGTTTGGGAGAA 59.107 37.500 0.00 0.00 0.00 2.87
1917 2969 5.010012 AGTTGTATGCTTTGTTTGGGAGAAG 59.990 40.000 0.00 0.00 0.00 2.85
1918 2970 4.469657 TGTATGCTTTGTTTGGGAGAAGT 58.530 39.130 0.00 0.00 0.00 3.01
1919 2971 4.278170 TGTATGCTTTGTTTGGGAGAAGTG 59.722 41.667 0.00 0.00 0.00 3.16
1920 2972 1.408702 TGCTTTGTTTGGGAGAAGTGC 59.591 47.619 0.00 0.00 0.00 4.40
1921 2973 1.683385 GCTTTGTTTGGGAGAAGTGCT 59.317 47.619 0.00 0.00 0.00 4.40
1922 2974 2.101415 GCTTTGTTTGGGAGAAGTGCTT 59.899 45.455 0.00 0.00 0.00 3.91
1923 2975 3.796844 GCTTTGTTTGGGAGAAGTGCTTC 60.797 47.826 3.89 3.89 39.78 3.86
1937 2989 7.510549 AGAAGTGCTTCTTTTTGCTATACAA 57.489 32.000 8.51 0.00 46.95 2.41
1938 2990 7.940850 AGAAGTGCTTCTTTTTGCTATACAAA 58.059 30.769 8.51 0.00 46.95 2.83
1939 2991 8.579863 AGAAGTGCTTCTTTTTGCTATACAAAT 58.420 29.630 8.51 0.00 46.95 2.32
1940 2992 9.840427 GAAGTGCTTCTTTTTGCTATACAAATA 57.160 29.630 4.80 0.00 40.75 1.40
1958 3010 9.895138 ATACAAATACTATTAAACTCGGTGGTT 57.105 29.630 0.00 0.00 0.00 3.67
1960 3012 9.723601 ACAAATACTATTAAACTCGGTGGTTAA 57.276 29.630 3.10 3.10 41.46 2.01
1967 3019 2.428888 ACTCGGTGGTTAAACTCGTC 57.571 50.000 6.70 0.00 0.00 4.20
1991 3043 4.290155 GAGCATGGTTAATATTGGCAACG 58.710 43.478 0.00 0.00 42.51 4.10
2003 3055 2.042831 GGCAACGCATTCAGCCTCT 61.043 57.895 0.00 0.00 43.70 3.69
2022 3074 7.119407 CAGCCTCTGGTATGATAAATTCATCTG 59.881 40.741 0.00 0.00 44.13 2.90
2152 3204 1.955778 CTTGAGTGACCCAAATGCACA 59.044 47.619 0.00 0.00 35.08 4.57
2154 3206 0.238289 GAGTGACCCAAATGCACACG 59.762 55.000 0.00 0.00 36.71 4.49
2156 3208 1.202710 AGTGACCCAAATGCACACGTA 60.203 47.619 0.00 0.00 36.71 3.57
2157 3209 1.196808 GTGACCCAAATGCACACGTAG 59.803 52.381 0.00 0.00 32.96 3.51
2162 3214 0.452618 CAAATGCACACGTAGCGGTG 60.453 55.000 0.00 3.79 43.54 4.94
2167 3219 1.286570 CACACGTAGCGGTGGTACA 59.713 57.895 0.00 0.00 42.23 2.90
2171 3223 0.668401 ACGTAGCGGTGGTACAAAGC 60.668 55.000 0.00 0.00 44.16 3.51
2172 3224 0.668096 CGTAGCGGTGGTACAAAGCA 60.668 55.000 0.00 0.00 44.16 3.91
2189 3241 6.449698 ACAAAGCAAAGAATGTCTATGGTTG 58.550 36.000 0.00 0.00 32.62 3.77
2207 3259 4.766891 TGGTTGAACAATTCCTTCTCATCC 59.233 41.667 0.00 0.00 0.00 3.51
2212 3264 6.487828 TGAACAATTCCTTCTCATCCTGAAT 58.512 36.000 0.00 0.00 0.00 2.57
2250 3302 6.348786 CCACTCATTTAAATGACACCTCACAG 60.349 42.308 23.86 14.42 40.32 3.66
2415 3468 0.808755 GGGACACGTAGGCCATTTTG 59.191 55.000 5.01 0.00 0.00 2.44
2430 3483 4.923281 GCCATTTTGACGTTCTAAAGCATT 59.077 37.500 0.00 0.00 0.00 3.56
2432 3485 6.584563 GCCATTTTGACGTTCTAAAGCATTAA 59.415 34.615 0.00 0.00 0.00 1.40
2434 3487 8.020819 CCATTTTGACGTTCTAAAGCATTAAGA 58.979 33.333 0.00 0.00 0.00 2.10
2473 3526 2.936032 GACCCCTCCCAACCAGCT 60.936 66.667 0.00 0.00 0.00 4.24
2483 3536 4.331968 CTCCCAACCAGCTAACACAAATA 58.668 43.478 0.00 0.00 0.00 1.40
2510 3563 3.191162 CCGAAGATCAAAATCAACAGCCA 59.809 43.478 0.00 0.00 34.07 4.75
2520 3573 3.650281 ATCAACAGCCACCATCACATA 57.350 42.857 0.00 0.00 0.00 2.29
2525 3578 3.966979 ACAGCCACCATCACATATTGAA 58.033 40.909 0.00 0.00 37.92 2.69
2532 3585 6.375174 GCCACCATCACATATTGAATAGCATA 59.625 38.462 0.00 0.00 37.92 3.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
86 87 3.646715 CCTCTTCCACCCCGCCAA 61.647 66.667 0.00 0.00 0.00 4.52
107 112 4.514577 CCAGACCCTAGTGCCGCG 62.515 72.222 0.00 0.00 0.00 6.46
109 114 1.742768 GATCCAGACCCTAGTGCCG 59.257 63.158 0.00 0.00 0.00 5.69
110 115 0.755698 TCGATCCAGACCCTAGTGCC 60.756 60.000 0.00 0.00 0.00 5.01
168 177 5.338822 GCGCTTTTTAGTTAGAAGAAAACGG 59.661 40.000 0.00 0.00 32.00 4.44
169 178 5.905181 TGCGCTTTTTAGTTAGAAGAAAACG 59.095 36.000 9.73 0.00 32.00 3.60
170 179 7.642586 TCTTGCGCTTTTTAGTTAGAAGAAAAC 59.357 33.333 9.73 0.00 0.00 2.43
171 180 7.699566 TCTTGCGCTTTTTAGTTAGAAGAAAA 58.300 30.769 9.73 0.00 0.00 2.29
172 181 7.254227 TCTTGCGCTTTTTAGTTAGAAGAAA 57.746 32.000 9.73 0.00 0.00 2.52
183 196 6.978080 GGGAATATCAATTCTTGCGCTTTTTA 59.022 34.615 9.73 0.00 41.18 1.52
232 245 5.368989 GAGGAGAACTTGGAAAAGAACTCA 58.631 41.667 0.00 0.00 32.27 3.41
290 303 4.212913 GCGAGCGAGATGAGGCCA 62.213 66.667 5.01 0.00 0.00 5.36
292 305 4.257510 TCGCGAGCGAGATGAGGC 62.258 66.667 16.64 0.00 44.01 4.70
389 407 1.141657 GGGCAGTAGCTGGATTGATGA 59.858 52.381 0.00 0.00 41.70 2.92
390 408 1.602311 GGGCAGTAGCTGGATTGATG 58.398 55.000 0.00 0.00 41.70 3.07
391 409 0.107456 CGGGCAGTAGCTGGATTGAT 59.893 55.000 0.00 0.00 41.70 2.57
574 621 2.510012 TGCGCTGCTCCGATCTTG 60.510 61.111 9.73 0.00 0.00 3.02
618 673 0.970937 ATCCGTCCTCCTCGCTGAAA 60.971 55.000 0.00 0.00 0.00 2.69
619 674 0.106868 TATCCGTCCTCCTCGCTGAA 60.107 55.000 0.00 0.00 0.00 3.02
756 1754 1.630223 TTGACAATGCCATTGCCTCA 58.370 45.000 17.14 11.38 43.98 3.86
797 1795 4.200838 TGAGTTATGCAAGTTCCATCGA 57.799 40.909 0.00 0.00 0.00 3.59
1022 2037 8.746751 CAATTAGAACACTATCCGCGATATATG 58.253 37.037 8.23 2.50 0.00 1.78
1024 2039 8.047413 TCAATTAGAACACTATCCGCGATATA 57.953 34.615 8.23 4.16 0.00 0.86
1137 2152 2.142356 ATGTGAATGGCCGATTCCAA 57.858 45.000 19.08 11.28 40.00 3.53
1238 2259 1.933181 TGCTTTGCACTTCCGATATCG 59.067 47.619 18.31 18.31 31.71 2.92
1239 2260 2.939103 ACTGCTTTGCACTTCCGATATC 59.061 45.455 0.00 0.00 33.79 1.63
1275 2296 4.600692 AAACCCACTGCTTAAACATTCC 57.399 40.909 0.00 0.00 0.00 3.01
1541 2566 5.337330 CCGGACAAACCTTAGTCAGATAAGT 60.337 44.000 0.00 0.00 36.50 2.24
1624 2655 1.433053 TTTGTCACAAGCCCACGACG 61.433 55.000 0.00 0.00 0.00 5.12
1685 2717 5.535753 AAGGACAAGGAAATGACAAAAGG 57.464 39.130 0.00 0.00 0.00 3.11
1819 2853 6.672593 ACTAACCCATGGATATTGAACACAT 58.327 36.000 15.22 0.00 0.00 3.21
1826 2860 4.214310 TGCCAACTAACCCATGGATATTG 58.786 43.478 15.22 9.90 36.27 1.90
1833 2867 4.533919 TGAAATTGCCAACTAACCCATG 57.466 40.909 0.00 0.00 0.00 3.66
1834 2868 4.623647 GCATGAAATTGCCAACTAACCCAT 60.624 41.667 0.00 0.00 36.60 4.00
1835 2869 3.306641 GCATGAAATTGCCAACTAACCCA 60.307 43.478 0.00 0.00 36.60 4.51
1836 2870 3.261580 GCATGAAATTGCCAACTAACCC 58.738 45.455 0.00 0.00 36.60 4.11
1850 2902 7.553334 AGTAAGACTTAATAGACGGCATGAAA 58.447 34.615 0.00 0.00 0.00 2.69
1851 2903 7.108841 AGTAAGACTTAATAGACGGCATGAA 57.891 36.000 0.00 0.00 0.00 2.57
1874 2926 6.410540 ACAACTAAGCTAATCCTCCAAGAAG 58.589 40.000 0.00 0.00 0.00 2.85
1897 2949 4.798574 CACTTCTCCCAAACAAAGCATAC 58.201 43.478 0.00 0.00 0.00 2.39
1898 2950 3.255642 GCACTTCTCCCAAACAAAGCATA 59.744 43.478 0.00 0.00 0.00 3.14
1899 2951 2.036346 GCACTTCTCCCAAACAAAGCAT 59.964 45.455 0.00 0.00 0.00 3.79
1900 2952 1.408702 GCACTTCTCCCAAACAAAGCA 59.591 47.619 0.00 0.00 0.00 3.91
1901 2953 1.683385 AGCACTTCTCCCAAACAAAGC 59.317 47.619 0.00 0.00 0.00 3.51
1902 2954 3.633986 AGAAGCACTTCTCCCAAACAAAG 59.366 43.478 7.10 0.00 46.13 2.77
1903 2955 3.631250 AGAAGCACTTCTCCCAAACAAA 58.369 40.909 7.10 0.00 46.13 2.83
1904 2956 3.297134 AGAAGCACTTCTCCCAAACAA 57.703 42.857 7.10 0.00 46.13 2.83
1911 2963 7.308589 TTGTATAGCAAAAAGAAGCACTTCTCC 60.309 37.037 13.08 1.38 40.38 3.71
1912 2964 7.584987 TTGTATAGCAAAAAGAAGCACTTCTC 58.415 34.615 13.08 1.22 40.38 2.87
1913 2965 7.510549 TTGTATAGCAAAAAGAAGCACTTCT 57.489 32.000 7.10 7.10 41.75 2.85
1932 2984 9.895138 AACCACCGAGTTTAATAGTATTTGTAT 57.105 29.630 0.00 0.00 0.00 2.29
1934 2986 9.723601 TTAACCACCGAGTTTAATAGTATTTGT 57.276 29.630 0.00 0.00 0.00 2.83
1937 2989 9.948964 AGTTTAACCACCGAGTTTAATAGTATT 57.051 29.630 0.17 0.17 0.00 1.89
1938 2990 9.591792 GAGTTTAACCACCGAGTTTAATAGTAT 57.408 33.333 0.00 0.00 0.00 2.12
1939 2991 7.754924 CGAGTTTAACCACCGAGTTTAATAGTA 59.245 37.037 0.00 0.00 0.00 1.82
1940 2992 6.587608 CGAGTTTAACCACCGAGTTTAATAGT 59.412 38.462 0.00 0.00 0.00 2.12
1941 2993 6.587608 ACGAGTTTAACCACCGAGTTTAATAG 59.412 38.462 8.58 0.00 0.00 1.73
1942 2994 6.454795 ACGAGTTTAACCACCGAGTTTAATA 58.545 36.000 8.58 0.00 0.00 0.98
1943 2995 5.299949 ACGAGTTTAACCACCGAGTTTAAT 58.700 37.500 8.58 0.00 0.00 1.40
1944 2996 4.692228 ACGAGTTTAACCACCGAGTTTAA 58.308 39.130 8.58 0.00 0.00 1.52
1945 2997 4.298332 GACGAGTTTAACCACCGAGTTTA 58.702 43.478 8.58 0.00 0.00 2.01
1946 2998 3.126073 GACGAGTTTAACCACCGAGTTT 58.874 45.455 8.58 0.00 0.00 2.66
1947 2999 2.747436 GACGAGTTTAACCACCGAGTT 58.253 47.619 8.58 0.00 0.00 3.01
1948 3000 1.335324 CGACGAGTTTAACCACCGAGT 60.335 52.381 8.58 0.00 0.00 4.18
1949 3001 1.334054 CGACGAGTTTAACCACCGAG 58.666 55.000 8.58 0.89 0.00 4.63
1950 3002 0.039256 CCGACGAGTTTAACCACCGA 60.039 55.000 0.00 0.00 0.00 4.69
1951 3003 0.039256 TCCGACGAGTTTAACCACCG 60.039 55.000 0.00 0.00 0.00 4.94
1952 3004 1.706443 CTCCGACGAGTTTAACCACC 58.294 55.000 0.00 0.00 0.00 4.61
1953 3005 1.066136 GCTCCGACGAGTTTAACCAC 58.934 55.000 0.00 0.00 38.49 4.16
1954 3006 0.675083 TGCTCCGACGAGTTTAACCA 59.325 50.000 0.00 0.00 38.49 3.67
1955 3007 1.659098 CATGCTCCGACGAGTTTAACC 59.341 52.381 0.00 0.00 38.49 2.85
1956 3008 1.659098 CCATGCTCCGACGAGTTTAAC 59.341 52.381 0.00 0.00 38.49 2.01
1957 3009 1.274167 ACCATGCTCCGACGAGTTTAA 59.726 47.619 0.00 0.00 38.49 1.52
1958 3010 0.892755 ACCATGCTCCGACGAGTTTA 59.107 50.000 0.00 0.00 38.49 2.01
1959 3011 0.034896 AACCATGCTCCGACGAGTTT 59.965 50.000 0.00 0.00 38.49 2.66
1960 3012 0.892755 TAACCATGCTCCGACGAGTT 59.107 50.000 0.00 0.00 38.49 3.01
1961 3013 0.892755 TTAACCATGCTCCGACGAGT 59.107 50.000 0.00 0.00 38.49 4.18
1962 3014 2.225068 ATTAACCATGCTCCGACGAG 57.775 50.000 0.00 0.00 39.33 4.18
1967 3019 2.884012 TGCCAATATTAACCATGCTCCG 59.116 45.455 0.00 0.00 0.00 4.63
1991 3043 2.627515 TCATACCAGAGGCTGAATGC 57.372 50.000 0.00 0.00 41.94 3.56
2003 3055 7.758609 ATGGGACAGATGAATTTATCATACCA 58.241 34.615 16.32 16.32 45.42 3.25
2022 3074 7.069331 TCACAATTGGGTTATAAATGATGGGAC 59.931 37.037 7.75 0.00 0.00 4.46
2113 3165 5.264395 TCAAGGGGAGATTCAAAATCCTTC 58.736 41.667 0.00 0.00 31.56 3.46
2152 3204 0.668401 GCTTTGTACCACCGCTACGT 60.668 55.000 0.00 0.00 0.00 3.57
2154 3206 1.515081 TTGCTTTGTACCACCGCTAC 58.485 50.000 0.00 0.00 0.00 3.58
2156 3208 0.951558 CTTTGCTTTGTACCACCGCT 59.048 50.000 0.00 0.00 0.00 5.52
2157 3209 0.948678 TCTTTGCTTTGTACCACCGC 59.051 50.000 0.00 0.00 0.00 5.68
2162 3214 6.151144 ACCATAGACATTCTTTGCTTTGTACC 59.849 38.462 0.00 0.00 0.00 3.34
2167 3219 6.899393 TCAACCATAGACATTCTTTGCTTT 57.101 33.333 0.00 0.00 0.00 3.51
2171 3223 9.132521 GAATTGTTCAACCATAGACATTCTTTG 57.867 33.333 0.00 0.00 0.00 2.77
2172 3224 8.306761 GGAATTGTTCAACCATAGACATTCTTT 58.693 33.333 0.00 0.00 0.00 2.52
2222 3274 4.044065 AGGTGTCATTTAAATGAGTGGGGA 59.956 41.667 27.26 5.39 45.38 4.81
2250 3302 0.951558 TTCTTGCCTCCTTTTCGTGC 59.048 50.000 0.00 0.00 0.00 5.34
2407 3460 3.896122 TGCTTTAGAACGTCAAAATGGC 58.104 40.909 0.00 0.00 0.00 4.40
2415 3468 9.447040 AAGTTTTTCTTAATGCTTTAGAACGTC 57.553 29.630 0.00 0.00 34.23 4.34
2430 3483 7.275888 ACACATGATGCTCAAGTTTTTCTTA 57.724 32.000 0.00 0.00 34.66 2.10
2432 3485 5.779529 ACACATGATGCTCAAGTTTTTCT 57.220 34.783 0.00 0.00 0.00 2.52
2434 3487 5.750067 GTCAACACATGATGCTCAAGTTTTT 59.250 36.000 0.00 0.00 40.97 1.94
2454 3507 2.840753 GCTGGTTGGGAGGGGTCAA 61.841 63.158 0.00 0.00 0.00 3.18
2473 3526 8.554835 TTGATCTTCGGTTCATATTTGTGTTA 57.445 30.769 0.00 0.00 0.00 2.41
2483 3536 6.573664 TGTTGATTTTGATCTTCGGTTCAT 57.426 33.333 0.00 0.00 0.00 2.57
2510 3563 7.693132 ACCTATGCTATTCAATATGTGATGGT 58.307 34.615 0.00 0.00 35.70 3.55
2520 3573 7.934120 GTGGTAGAAAGACCTATGCTATTCAAT 59.066 37.037 0.00 0.00 40.46 2.57
2525 3578 5.009811 GTCGTGGTAGAAAGACCTATGCTAT 59.990 44.000 0.00 0.00 40.46 2.97
2532 3585 1.272769 GCTGTCGTGGTAGAAAGACCT 59.727 52.381 0.00 0.00 40.46 3.85


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

AutoCloner maintained by Alex Coulton.