Multiple sequence alignment - TraesCS2A01G096400

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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 TraesCS2A01G096400 chr2A 100.000 2597 0 0 1 2597 50132348 50134944 0.000000e+00 4796.0
1 TraesCS2A01G096400 chr2B 86.164 2067 130 49 602 2579 74203774 74205773 0.000000e+00 2089.0
2 TraesCS2A01G096400 chr2B 81.834 589 42 30 66 598 74203124 74203703 3.970000e-118 435.0
3 TraesCS2A01G096400 chr2D 87.912 1820 127 41 794 2579 46825743 46827503 0.000000e+00 2056.0
4 TraesCS2A01G096400 chr2D 85.891 567 33 24 62 598 46824923 46825472 6.280000e-156 560.0
5 TraesCS2A01G096400 chr2D 94.366 142 7 1 647 787 46825555 46825696 1.570000e-52 217.0
6 TraesCS2A01G096400 chr7D 78.161 261 39 12 1313 1561 605168645 605168899 1.610000e-32 150.0
7 TraesCS2A01G096400 chr7A 85.366 123 12 3 947 1063 675923409 675923531 3.510000e-24 122.0
8 TraesCS2A01G096400 chrUn 88.235 68 8 0 1424 1491 23302263 23302330 5.960000e-12 82.4
9 TraesCS2A01G096400 chr1B 86.301 73 10 0 1427 1499 27674475 27674403 2.140000e-11 80.5


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 TraesCS2A01G096400 chr2A 50132348 50134944 2596 False 4796.000000 4796 100.000000 1 2597 1 chr2A.!!$F1 2596
1 TraesCS2A01G096400 chr2B 74203124 74205773 2649 False 1262.000000 2089 83.999000 66 2579 2 chr2B.!!$F1 2513
2 TraesCS2A01G096400 chr2D 46824923 46827503 2580 False 944.333333 2056 89.389667 62 2579 3 chr2D.!!$F1 2517

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
478 540 0.193069 AGCTATCCCTCATGCCTCCT 59.807 55.0 0.0 0.0 0.0 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2305 2548 0.035056 CAGGTTTACTGGAGCCTGGG 60.035 60.0 0.0 0.0 43.39 4.45 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
29 30 2.922740 TTACCGAACCATGATAGGGC 57.077 50.000 0.00 0.00 0.00 5.19
30 31 1.796017 TACCGAACCATGATAGGGCA 58.204 50.000 0.00 0.00 0.00 5.36
31 32 1.140312 ACCGAACCATGATAGGGCAT 58.860 50.000 0.00 0.00 0.00 4.40
32 33 2.334977 ACCGAACCATGATAGGGCATA 58.665 47.619 0.00 0.00 0.00 3.14
33 34 2.912956 ACCGAACCATGATAGGGCATAT 59.087 45.455 0.00 0.00 0.00 1.78
34 35 3.330701 ACCGAACCATGATAGGGCATATT 59.669 43.478 0.00 0.00 0.00 1.28
35 36 4.534500 ACCGAACCATGATAGGGCATATTA 59.466 41.667 0.00 0.00 0.00 0.98
36 37 5.191722 ACCGAACCATGATAGGGCATATTAT 59.808 40.000 0.00 0.00 0.00 1.28
37 38 5.528690 CCGAACCATGATAGGGCATATTATG 59.471 44.000 14.74 14.74 37.52 1.90
51 52 6.456795 GCATATTATGGCTAAAGAATCCCC 57.543 41.667 5.84 0.00 0.00 4.81
52 53 6.190587 GCATATTATGGCTAAAGAATCCCCT 58.809 40.000 5.84 0.00 0.00 4.79
53 54 7.346471 GCATATTATGGCTAAAGAATCCCCTA 58.654 38.462 5.84 0.00 0.00 3.53
54 55 7.834181 GCATATTATGGCTAAAGAATCCCCTAA 59.166 37.037 5.84 0.00 0.00 2.69
55 56 9.178758 CATATTATGGCTAAAGAATCCCCTAAC 57.821 37.037 0.00 0.00 0.00 2.34
56 57 6.584471 TTATGGCTAAAGAATCCCCTAACA 57.416 37.500 0.00 0.00 0.00 2.41
57 58 4.503714 TGGCTAAAGAATCCCCTAACAG 57.496 45.455 0.00 0.00 0.00 3.16
58 59 3.202151 TGGCTAAAGAATCCCCTAACAGG 59.798 47.826 0.00 0.00 34.30 4.00
59 60 3.458487 GGCTAAAGAATCCCCTAACAGGA 59.542 47.826 0.00 0.00 37.67 3.86
60 61 4.445019 GGCTAAAGAATCCCCTAACAGGAG 60.445 50.000 0.00 0.00 37.67 3.69
110 113 4.929479 AGCCACCATTTGATTTACCTACA 58.071 39.130 0.00 0.00 0.00 2.74
172 180 2.095461 GGGGAAGACATGAGCTTTTCC 58.905 52.381 0.00 8.38 37.23 3.13
186 194 3.891977 AGCTTTTCCTTCCTTTTGACCTC 59.108 43.478 0.00 0.00 0.00 3.85
198 206 3.975168 TTTGACCTCCTTACACTAGCC 57.025 47.619 0.00 0.00 0.00 3.93
202 210 3.301274 GACCTCCTTACACTAGCCAGAT 58.699 50.000 0.00 0.00 0.00 2.90
220 235 7.049799 GCCAGATTATTATTACCTTTTGGCA 57.950 36.000 0.00 0.00 44.98 4.92
228 243 6.969993 TTATTACCTTTTGGCAGAAAGTGT 57.030 33.333 15.84 14.91 45.59 3.55
245 262 2.106684 AGTGTGACTTTTTCCCCTCTCC 59.893 50.000 0.00 0.00 0.00 3.71
248 265 2.910977 GTGACTTTTTCCCCTCTCCCTA 59.089 50.000 0.00 0.00 0.00 3.53
267 284 2.426023 GGTGGAGCGTTCACTGGT 59.574 61.111 0.53 0.00 35.61 4.00
292 339 3.764293 CGTATATACGGCCGTAGGTGCT 61.764 54.545 38.09 25.49 45.99 4.40
315 363 3.797524 GCATGATGGGACGATACGTACAA 60.798 47.826 8.71 0.00 43.28 2.41
465 527 4.392940 ACATGGCATGTAGGAAAGCTATC 58.607 43.478 30.56 0.00 42.78 2.08
474 536 1.423161 AGGAAAGCTATCCCTCATGCC 59.577 52.381 0.00 0.00 40.59 4.40
475 537 1.423161 GGAAAGCTATCCCTCATGCCT 59.577 52.381 0.00 0.00 33.05 4.75
476 538 2.551938 GGAAAGCTATCCCTCATGCCTC 60.552 54.545 0.00 0.00 33.05 4.70
477 539 1.063183 AAGCTATCCCTCATGCCTCC 58.937 55.000 0.00 0.00 0.00 4.30
478 540 0.193069 AGCTATCCCTCATGCCTCCT 59.807 55.000 0.00 0.00 0.00 3.69
479 541 0.612744 GCTATCCCTCATGCCTCCTC 59.387 60.000 0.00 0.00 0.00 3.71
480 542 2.021262 CTATCCCTCATGCCTCCTCA 57.979 55.000 0.00 0.00 0.00 3.86
481 543 2.549082 CTATCCCTCATGCCTCCTCAT 58.451 52.381 0.00 0.00 0.00 2.90
482 544 1.065647 ATCCCTCATGCCTCCTCATG 58.934 55.000 0.00 0.00 43.84 3.07
483 545 1.228184 CCCTCATGCCTCCTCATGC 60.228 63.158 0.00 0.00 42.58 4.06
536 610 1.862138 TCACTCCCTCCCTCCCTCA 60.862 63.158 0.00 0.00 0.00 3.86
538 612 2.443016 CTCCCTCCCTCCCTCACG 60.443 72.222 0.00 0.00 0.00 4.35
539 613 3.273654 TCCCTCCCTCCCTCACGT 61.274 66.667 0.00 0.00 0.00 4.49
543 617 2.044650 TCCCTCCCTCACGTACGG 60.045 66.667 21.06 8.79 0.00 4.02
544 618 3.834799 CCCTCCCTCACGTACGGC 61.835 72.222 21.06 0.00 0.00 5.68
598 674 1.600916 GAGCTCCACGGCAAAACCT 60.601 57.895 0.87 0.00 35.61 3.50
600 743 0.605589 AGCTCCACGGCAAAACCTAC 60.606 55.000 0.00 0.00 35.61 3.18
605 748 1.665599 ACGGCAAAACCTACGGACG 60.666 57.895 0.00 0.00 35.61 4.79
712 856 2.401766 GGTGGCTGAGCGTGGATTG 61.402 63.158 0.00 0.00 0.00 2.67
719 863 2.045926 AGCGTGGATTGGTCTGGC 60.046 61.111 0.00 0.00 0.00 4.85
787 931 7.148656 CGAGGACAAGAAAACAACAAAACAAAT 60.149 33.333 0.00 0.00 0.00 2.32
788 932 7.805700 AGGACAAGAAAACAACAAAACAAATG 58.194 30.769 0.00 0.00 0.00 2.32
789 933 7.020602 GGACAAGAAAACAACAAAACAAATGG 58.979 34.615 0.00 0.00 0.00 3.16
790 934 6.907741 ACAAGAAAACAACAAAACAAATGGG 58.092 32.000 0.00 0.00 0.00 4.00
792 936 6.983474 AGAAAACAACAAAACAAATGGGAG 57.017 33.333 0.00 0.00 0.00 4.30
889 1073 1.383803 GCTCCCTCCCACTCATCCT 60.384 63.158 0.00 0.00 0.00 3.24
892 1082 1.231751 TCCCTCCCACTCATCCTCCT 61.232 60.000 0.00 0.00 0.00 3.69
930 1120 2.353607 CGTCGTCCATCGGCTAGC 60.354 66.667 6.04 6.04 42.47 3.42
932 1122 4.266070 TCGTCCATCGGCTAGCGC 62.266 66.667 9.00 0.00 40.32 5.92
933 1123 4.569023 CGTCCATCGGCTAGCGCA 62.569 66.667 11.47 0.00 38.10 6.09
935 1125 4.221422 TCCATCGGCTAGCGCACC 62.221 66.667 11.47 7.18 38.10 5.01
967 1173 4.326766 CAACAACACAGCCGGCCG 62.327 66.667 26.15 21.04 0.00 6.13
1032 1244 4.954118 TCCACCTCCACCACGGCT 62.954 66.667 0.00 0.00 33.14 5.52
1033 1245 4.704833 CCACCTCCACCACGGCTG 62.705 72.222 0.00 0.00 33.14 4.85
1491 1712 3.249189 AGGAAGCTGCCGTTCCCA 61.249 61.111 14.88 0.00 44.12 4.37
1500 1721 4.821589 CCGTTCCCAGCGCTCCTC 62.822 72.222 7.13 0.00 0.00 3.71
1686 1907 0.315059 CGTCGGCGCATGTACATTTC 60.315 55.000 10.83 0.09 0.00 2.17
1725 1946 0.248743 TCCAGTGTGTGACGACGAAC 60.249 55.000 0.00 0.00 0.00 3.95
1822 2046 5.178809 AGAAACAGTAGCCGTTCATTTGTAC 59.821 40.000 0.00 0.00 0.00 2.90
1823 2047 4.267349 ACAGTAGCCGTTCATTTGTACT 57.733 40.909 0.00 0.00 0.00 2.73
1824 2048 4.638304 ACAGTAGCCGTTCATTTGTACTT 58.362 39.130 0.00 0.00 0.00 2.24
1825 2049 5.786311 ACAGTAGCCGTTCATTTGTACTTA 58.214 37.500 0.00 0.00 0.00 2.24
1841 2071 7.807687 TTGTACTTAGATTCTTGTTAGCGTC 57.192 36.000 0.00 0.00 0.00 5.19
1850 2080 3.537580 TCTTGTTAGCGTCTTGGTTTGT 58.462 40.909 0.00 0.00 0.00 2.83
1889 2119 6.000219 AGCTAAATCCGTAAATGCATGAGAT 59.000 36.000 0.00 0.00 0.00 2.75
1890 2120 6.488006 AGCTAAATCCGTAAATGCATGAGATT 59.512 34.615 0.00 2.19 0.00 2.40
1891 2121 7.013655 AGCTAAATCCGTAAATGCATGAGATTT 59.986 33.333 18.52 18.52 36.65 2.17
1892 2122 7.649306 GCTAAATCCGTAAATGCATGAGATTTT 59.351 33.333 19.18 6.87 35.00 1.82
1894 2124 7.992180 AATCCGTAAATGCATGAGATTTTTC 57.008 32.000 0.00 0.00 0.00 2.29
1895 2125 5.890334 TCCGTAAATGCATGAGATTTTTCC 58.110 37.500 0.00 0.00 0.00 3.13
1900 2133 4.900635 ATGCATGAGATTTTTCCGTACC 57.099 40.909 0.00 0.00 0.00 3.34
1918 2151 0.804989 CCATCTTTCCGGAGTGTTGC 59.195 55.000 3.34 0.00 0.00 4.17
1919 2152 0.804989 CATCTTTCCGGAGTGTTGCC 59.195 55.000 3.34 0.00 0.00 4.52
1937 2170 1.817357 CCTTCTCATCAGCAAGCACA 58.183 50.000 0.00 0.00 0.00 4.57
1938 2171 2.156917 CCTTCTCATCAGCAAGCACAA 58.843 47.619 0.00 0.00 0.00 3.33
1962 2197 3.314080 AGATCGCCGTTTTCTTTGACAAA 59.686 39.130 0.00 0.00 0.00 2.83
1978 2221 0.600782 CAAATGTTGGTGCCAGTGCC 60.601 55.000 0.00 0.00 36.33 5.01
1982 2225 3.225798 TTGGTGCCAGTGCCTTGC 61.226 61.111 0.00 0.00 36.33 4.01
2060 2303 6.939730 TCAGAAGGACAAGTGCAATGTTAATA 59.060 34.615 7.73 0.00 0.00 0.98
2065 2308 7.989826 AGGACAAGTGCAATGTTAATAATCTC 58.010 34.615 7.73 0.00 0.00 2.75
2071 2314 8.565896 AGTGCAATGTTAATAATCTCTGACAA 57.434 30.769 0.00 0.00 0.00 3.18
2103 2346 9.112725 CAAGATTTTTCAAATCTTTTCCCTTGT 57.887 29.630 17.90 0.00 42.52 3.16
2116 2359 3.095912 TCCCTTGTCCTAATCGAGACA 57.904 47.619 1.40 1.40 41.13 3.41
2137 2380 0.179145 ACGGGATCGAGCTTTGTACG 60.179 55.000 0.00 0.00 40.11 3.67
2140 2383 1.278238 GGATCGAGCTTTGTACGGTG 58.722 55.000 0.00 0.00 0.00 4.94
2145 2388 1.897398 GAGCTTTGTACGGTGCGGTG 61.897 60.000 0.00 0.00 0.00 4.94
2146 2389 2.961669 GCTTTGTACGGTGCGGTGG 61.962 63.158 0.00 0.00 0.00 4.61
2147 2390 2.961669 CTTTGTACGGTGCGGTGGC 61.962 63.158 0.00 0.00 40.52 5.01
2148 2391 4.992511 TTGTACGGTGCGGTGGCC 62.993 66.667 0.00 0.00 38.85 5.36
2310 2553 3.127533 CGCGCTTTTCTCCCCAGG 61.128 66.667 5.56 0.00 0.00 4.45
2311 2570 3.443925 GCGCTTTTCTCCCCAGGC 61.444 66.667 0.00 0.00 0.00 4.85
2313 2572 1.746991 CGCTTTTCTCCCCAGGCTC 60.747 63.158 0.00 0.00 0.00 4.70
2322 2581 1.205460 TCCCCAGGCTCCAGTAAACC 61.205 60.000 0.00 0.00 0.00 3.27
2376 2636 3.250280 TCGATGTAGAGATACGTTGAGGC 59.750 47.826 0.00 0.00 0.00 4.70
2411 2671 3.123620 GACAAGGGCAGCTCGCAG 61.124 66.667 9.78 0.00 45.17 5.18
2412 2672 4.711949 ACAAGGGCAGCTCGCAGG 62.712 66.667 9.78 1.70 45.17 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 7.773690 GCCCTATCATGGTTCGGTAATAATAAT 59.226 37.037 0.00 0.00 0.00 1.28
4 5 7.107542 GCCCTATCATGGTTCGGTAATAATAA 58.892 38.462 0.00 0.00 0.00 1.40
5 6 6.213802 TGCCCTATCATGGTTCGGTAATAATA 59.786 38.462 0.00 0.00 0.00 0.98
6 7 5.013704 TGCCCTATCATGGTTCGGTAATAAT 59.986 40.000 0.00 0.00 0.00 1.28
7 8 4.348461 TGCCCTATCATGGTTCGGTAATAA 59.652 41.667 0.00 0.00 0.00 1.40
8 9 3.904965 TGCCCTATCATGGTTCGGTAATA 59.095 43.478 0.00 0.00 0.00 0.98
9 10 2.708861 TGCCCTATCATGGTTCGGTAAT 59.291 45.455 0.00 0.00 0.00 1.89
10 11 2.120312 TGCCCTATCATGGTTCGGTAA 58.880 47.619 0.00 0.00 0.00 2.85
11 12 1.796017 TGCCCTATCATGGTTCGGTA 58.204 50.000 0.00 0.00 0.00 4.02
12 13 1.140312 ATGCCCTATCATGGTTCGGT 58.860 50.000 0.00 0.00 0.00 4.69
13 14 3.634397 ATATGCCCTATCATGGTTCGG 57.366 47.619 0.00 0.00 0.00 4.30
14 15 5.528690 CCATAATATGCCCTATCATGGTTCG 59.471 44.000 0.00 0.00 0.00 3.95
15 16 5.300286 GCCATAATATGCCCTATCATGGTTC 59.700 44.000 7.18 0.00 35.07 3.62
16 17 5.043881 AGCCATAATATGCCCTATCATGGTT 60.044 40.000 7.18 0.30 35.07 3.67
17 18 4.479796 AGCCATAATATGCCCTATCATGGT 59.520 41.667 7.18 0.00 35.07 3.55
18 19 5.057843 AGCCATAATATGCCCTATCATGG 57.942 43.478 0.00 2.46 35.59 3.66
19 20 7.994911 TCTTTAGCCATAATATGCCCTATCATG 59.005 37.037 0.00 0.00 0.00 3.07
20 21 8.106017 TCTTTAGCCATAATATGCCCTATCAT 57.894 34.615 0.00 0.00 0.00 2.45
21 22 7.509236 TCTTTAGCCATAATATGCCCTATCA 57.491 36.000 0.00 0.00 0.00 2.15
22 23 8.986929 ATTCTTTAGCCATAATATGCCCTATC 57.013 34.615 0.00 0.00 0.00 2.08
23 24 8.001292 GGATTCTTTAGCCATAATATGCCCTAT 58.999 37.037 0.00 0.00 0.00 2.57
24 25 7.346471 GGATTCTTTAGCCATAATATGCCCTA 58.654 38.462 0.00 0.00 0.00 3.53
25 26 6.190587 GGATTCTTTAGCCATAATATGCCCT 58.809 40.000 0.00 0.00 0.00 5.19
26 27 5.360999 GGGATTCTTTAGCCATAATATGCCC 59.639 44.000 0.00 0.00 0.00 5.36
27 28 5.360999 GGGGATTCTTTAGCCATAATATGCC 59.639 44.000 0.00 0.00 0.00 4.40
28 29 6.190587 AGGGGATTCTTTAGCCATAATATGC 58.809 40.000 0.00 0.00 0.00 3.14
29 30 9.178758 GTTAGGGGATTCTTTAGCCATAATATG 57.821 37.037 0.00 0.00 0.00 1.78
30 31 8.900802 TGTTAGGGGATTCTTTAGCCATAATAT 58.099 33.333 0.00 0.00 0.00 1.28
31 32 8.282801 TGTTAGGGGATTCTTTAGCCATAATA 57.717 34.615 0.00 0.00 0.00 0.98
32 33 7.161715 TGTTAGGGGATTCTTTAGCCATAAT 57.838 36.000 0.00 0.00 0.00 1.28
33 34 6.410388 CCTGTTAGGGGATTCTTTAGCCATAA 60.410 42.308 0.00 0.00 0.00 1.90
34 35 5.073144 CCTGTTAGGGGATTCTTTAGCCATA 59.927 44.000 0.00 0.00 0.00 2.74
35 36 4.141158 CCTGTTAGGGGATTCTTTAGCCAT 60.141 45.833 0.00 0.00 0.00 4.40
36 37 3.202151 CCTGTTAGGGGATTCTTTAGCCA 59.798 47.826 0.00 0.00 0.00 4.75
37 38 3.458487 TCCTGTTAGGGGATTCTTTAGCC 59.542 47.826 0.00 0.00 35.59 3.93
38 39 4.709250 CTCCTGTTAGGGGATTCTTTAGC 58.291 47.826 0.00 0.00 38.47 3.09
39 40 4.164221 TGCTCCTGTTAGGGGATTCTTTAG 59.836 45.833 0.00 0.00 38.47 1.85
40 41 4.108570 TGCTCCTGTTAGGGGATTCTTTA 58.891 43.478 0.00 0.00 38.47 1.85
41 42 2.919602 TGCTCCTGTTAGGGGATTCTTT 59.080 45.455 0.00 0.00 38.47 2.52
42 43 2.562296 TGCTCCTGTTAGGGGATTCTT 58.438 47.619 0.00 0.00 38.47 2.52
43 44 2.270434 TGCTCCTGTTAGGGGATTCT 57.730 50.000 0.00 0.00 38.47 2.40
44 45 3.584733 AATGCTCCTGTTAGGGGATTC 57.415 47.619 0.00 0.00 38.47 2.52
45 46 4.337264 AAAATGCTCCTGTTAGGGGATT 57.663 40.909 0.00 0.00 38.47 3.01
46 47 4.337264 AAAAATGCTCCTGTTAGGGGAT 57.663 40.909 0.00 0.00 38.47 3.85
47 48 3.825908 AAAAATGCTCCTGTTAGGGGA 57.174 42.857 0.00 0.00 38.47 4.81
84 87 3.429410 GGTAAATCAAATGGTGGCTCAGC 60.429 47.826 0.00 0.00 0.00 4.26
110 113 5.428253 ACTCATGTTTGGCGATAGTGTAAT 58.572 37.500 0.00 0.00 39.35 1.89
140 148 1.161563 TCTTCCCCGCAACAACGAAC 61.162 55.000 0.00 0.00 34.06 3.95
141 149 1.146485 TCTTCCCCGCAACAACGAA 59.854 52.632 0.00 0.00 34.06 3.85
142 150 1.595929 GTCTTCCCCGCAACAACGA 60.596 57.895 0.00 0.00 34.06 3.85
143 151 1.234615 ATGTCTTCCCCGCAACAACG 61.235 55.000 0.00 0.00 0.00 4.10
172 180 4.974399 AGTGTAAGGAGGTCAAAAGGAAG 58.026 43.478 0.00 0.00 0.00 3.46
186 194 9.654663 GGTAATAATAATCTGGCTAGTGTAAGG 57.345 37.037 0.00 0.00 0.00 2.69
202 210 9.084533 ACACTTTCTGCCAAAAGGTAATAATAA 57.915 29.630 11.33 0.00 39.96 1.40
220 235 4.079730 AGAGGGGAAAAAGTCACACTTTCT 60.080 41.667 2.19 0.00 46.78 2.52
228 243 2.133858 AGGGAGAGGGGAAAAAGTCA 57.866 50.000 0.00 0.00 0.00 3.41
248 265 2.029073 CAGTGAACGCTCCACCGT 59.971 61.111 0.00 0.00 44.41 4.83
280 313 2.947938 ATCATGCAGCACCTACGGCC 62.948 60.000 0.00 0.00 0.00 6.13
281 314 1.524621 ATCATGCAGCACCTACGGC 60.525 57.895 0.00 0.00 0.00 5.68
282 315 1.162181 CCATCATGCAGCACCTACGG 61.162 60.000 0.00 0.00 0.00 4.02
292 339 0.750249 ACGTATCGTCCCATCATGCA 59.250 50.000 0.00 0.00 33.69 3.96
315 363 1.751927 CGCCACCTACTACCTCCGT 60.752 63.158 0.00 0.00 0.00 4.69
465 527 1.228184 GCATGAGGAGGCATGAGGG 60.228 63.158 8.40 0.00 46.64 4.30
474 536 0.394192 TGATTAGGCGGCATGAGGAG 59.606 55.000 13.08 0.00 0.00 3.69
475 537 1.059098 ATGATTAGGCGGCATGAGGA 58.941 50.000 13.08 0.00 0.00 3.71
476 538 1.162698 CATGATTAGGCGGCATGAGG 58.837 55.000 13.08 0.00 41.35 3.86
477 539 0.520404 GCATGATTAGGCGGCATGAG 59.480 55.000 13.08 0.00 41.35 2.90
478 540 0.890542 GGCATGATTAGGCGGCATGA 60.891 55.000 13.08 0.00 41.35 3.07
479 541 1.582968 GGCATGATTAGGCGGCATG 59.417 57.895 13.08 6.82 41.66 4.06
480 542 1.604593 GGGCATGATTAGGCGGCAT 60.605 57.895 13.08 0.00 33.61 4.40
481 543 2.203337 GGGCATGATTAGGCGGCA 60.203 61.111 13.08 0.00 33.61 5.69
482 544 2.203337 TGGGCATGATTAGGCGGC 60.203 61.111 0.00 0.00 33.61 6.53
483 545 1.898574 GGTGGGCATGATTAGGCGG 60.899 63.158 0.00 0.00 33.61 6.13
584 660 4.364817 CGTAGGTTTTGCCGTGGA 57.635 55.556 0.00 0.00 43.70 4.02
605 748 3.467119 CGCAGGCGACGTGTACAC 61.467 66.667 16.32 16.32 42.83 2.90
631 774 0.639392 AGACCTAGATCACCAGCCCT 59.361 55.000 0.00 0.00 0.00 5.19
638 781 3.648009 GCTGCATGTAGACCTAGATCAC 58.352 50.000 15.68 0.00 0.00 3.06
698 842 1.078848 AGACCAATCCACGCTCAGC 60.079 57.895 0.00 0.00 0.00 4.26
700 844 1.296392 CCAGACCAATCCACGCTCA 59.704 57.895 0.00 0.00 0.00 4.26
702 846 2.045926 GCCAGACCAATCCACGCT 60.046 61.111 0.00 0.00 0.00 5.07
719 863 3.109612 CTACGTGGCCTCGTCTCCG 62.110 68.421 33.82 17.70 43.12 4.63
789 933 4.176752 AAGATTCCGGGCCGCTCC 62.177 66.667 23.20 9.09 0.00 4.70
790 934 2.897350 CAAGATTCCGGGCCGCTC 60.897 66.667 23.20 16.36 0.00 5.03
889 1073 0.967380 TGCGAGTCAGATGCAGAGGA 60.967 55.000 0.00 0.00 34.03 3.71
892 1082 1.718396 CTTTGCGAGTCAGATGCAGA 58.282 50.000 0.00 0.00 40.15 4.26
1365 1583 3.869272 GAAGCGCGATGTGGCAGG 61.869 66.667 12.10 0.00 0.00 4.85
1500 1721 2.513204 TAGTCGGACGCCTCGGAG 60.513 66.667 1.89 0.00 0.00 4.63
1822 2046 5.869888 ACCAAGACGCTAACAAGAATCTAAG 59.130 40.000 0.00 0.00 0.00 2.18
1823 2047 5.790593 ACCAAGACGCTAACAAGAATCTAA 58.209 37.500 0.00 0.00 0.00 2.10
1824 2048 5.401531 ACCAAGACGCTAACAAGAATCTA 57.598 39.130 0.00 0.00 0.00 1.98
1825 2049 4.273148 ACCAAGACGCTAACAAGAATCT 57.727 40.909 0.00 0.00 0.00 2.40
1841 2071 0.744281 GGACACACCCACAAACCAAG 59.256 55.000 0.00 0.00 0.00 3.61
1850 2080 0.901114 TAGCTTAGCGGACACACCCA 60.901 55.000 0.00 0.00 34.64 4.51
1894 2124 0.822164 ACTCCGGAAAGATGGTACGG 59.178 55.000 5.23 0.00 45.52 4.02
1895 2125 1.203994 ACACTCCGGAAAGATGGTACG 59.796 52.381 5.23 0.00 0.00 3.67
1900 2133 0.804989 GGCAACACTCCGGAAAGATG 59.195 55.000 5.23 7.15 0.00 2.90
1918 2151 1.817357 TGTGCTTGCTGATGAGAAGG 58.183 50.000 0.00 0.00 0.00 3.46
1919 2152 3.909776 TTTGTGCTTGCTGATGAGAAG 57.090 42.857 0.00 0.00 0.00 2.85
1937 2170 4.201970 TGTCAAAGAAAACGGCGATCTTTT 60.202 37.500 25.32 17.67 40.44 2.27
1938 2171 3.314080 TGTCAAAGAAAACGGCGATCTTT 59.686 39.130 23.54 23.54 42.49 2.52
1962 2197 1.152483 AAGGCACTGGCACCAACAT 60.152 52.632 5.25 0.00 40.86 2.71
2060 2303 3.995199 TCTTGCGAACTTGTCAGAGATT 58.005 40.909 0.00 0.00 0.00 2.40
2065 2308 5.273170 TGAAAAATCTTGCGAACTTGTCAG 58.727 37.500 0.00 0.00 0.00 3.51
2071 2314 8.424274 AAAAGATTTGAAAAATCTTGCGAACT 57.576 26.923 22.22 8.33 43.87 3.01
2087 2330 6.374333 TCGATTAGGACAAGGGAAAAGATTTG 59.626 38.462 0.00 0.00 0.00 2.32
2088 2331 6.481643 TCGATTAGGACAAGGGAAAAGATTT 58.518 36.000 0.00 0.00 0.00 2.17
2103 2346 2.449464 TCCCGTTTGTCTCGATTAGGA 58.551 47.619 0.00 0.00 0.00 2.94
2116 2359 2.344025 GTACAAAGCTCGATCCCGTTT 58.656 47.619 0.00 0.00 37.05 3.60
2296 2539 1.379176 GGAGCCTGGGGAGAAAAGC 60.379 63.158 0.00 0.00 0.00 3.51
2302 2545 0.253327 GTTTACTGGAGCCTGGGGAG 59.747 60.000 0.00 0.00 0.00 4.30
2304 2547 1.208165 AGGTTTACTGGAGCCTGGGG 61.208 60.000 0.00 0.00 0.00 4.96
2305 2548 0.035056 CAGGTTTACTGGAGCCTGGG 60.035 60.000 0.00 0.00 43.39 4.45
2306 2549 3.558674 CAGGTTTACTGGAGCCTGG 57.441 57.895 7.86 0.00 43.39 4.45


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

AutoCloner maintained by Alex Coulton.