Multiple sequence alignment - TraesCS3D01G344500

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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 TraesCS3D01G344500 chr3D 100.000 2546 0 0 1 2546 456319473 456316928 0.000000e+00 4702
1 TraesCS3D01G344500 chr3D 78.927 261 33 12 2136 2382 114203571 114203823 9.430000e-35 158
2 TraesCS3D01G344500 chr3B 89.769 2639 141 54 3 2546 603373462 603376066 0.000000e+00 3258
3 TraesCS3D01G344500 chr3A 91.304 1012 49 13 868 1852 598989275 598988276 0.000000e+00 1345
4 TraesCS3D01G344500 chr3A 89.445 559 22 12 243 766 598990188 598989632 0.000000e+00 671
5 TraesCS3D01G344500 chr3A 97.159 176 5 0 3 178 598990365 598990190 5.330000e-77 298
6 TraesCS3D01G344500 chr1D 83.571 140 14 7 2269 2399 396317138 396317277 3.440000e-24 122


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 TraesCS3D01G344500 chr3D 456316928 456319473 2545 True 4702.000000 4702 100.000 1 2546 1 chr3D.!!$R1 2545
1 TraesCS3D01G344500 chr3B 603373462 603376066 2604 False 3258.000000 3258 89.769 3 2546 1 chr3B.!!$F1 2543
2 TraesCS3D01G344500 chr3A 598988276 598990365 2089 True 771.333333 1345 92.636 3 1852 3 chr3A.!!$R1 1849

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
468 497 0.602905 CACTCTGGTTCCGTGGTTCC 60.603 60.0 0.0 0.0 0.0 3.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2035 2367 0.039978 CTCGCTCGTGTCAGTTCTGT 60.04 55.0 0.0 0.0 0.0 3.41 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
82 83 4.380867 CCATGTGCCAAGAGGTTAAACATC 60.381 45.833 0.00 0.00 37.19 3.06
202 205 1.238439 CACTGCACCCAACCTTACTG 58.762 55.000 0.00 0.00 0.00 2.74
212 215 4.081807 ACCCAACCTTACTGAACGAGTATC 60.082 45.833 0.00 0.00 37.01 2.24
310 313 2.617308 CCTTGCTAACTCTGATGCCATG 59.383 50.000 0.00 0.00 0.00 3.66
311 314 3.276857 CTTGCTAACTCTGATGCCATGT 58.723 45.455 0.00 0.00 0.00 3.21
321 324 4.005650 TCTGATGCCATGTGAACTTTCTC 58.994 43.478 0.00 0.00 0.00 2.87
345 350 5.638783 GAGTATATGTATGGAGTACACGCC 58.361 45.833 0.00 0.00 45.59 5.68
375 404 2.710096 ACACCCAGTTTATGCGCTAT 57.290 45.000 9.73 3.00 0.00 2.97
440 469 3.012518 CGAGATGGTTCCTTGCTTCAAT 58.987 45.455 0.00 0.00 0.00 2.57
445 474 6.012745 AGATGGTTCCTTGCTTCAATTACTT 58.987 36.000 0.00 0.00 0.00 2.24
468 497 0.602905 CACTCTGGTTCCGTGGTTCC 60.603 60.000 0.00 0.00 0.00 3.62
470 499 3.047877 CTGGTTCCGTGGTTCCGC 61.048 66.667 0.00 0.00 0.00 5.54
538 575 5.847304 CTTGATAAGGAGGAACATCGATCA 58.153 41.667 0.00 0.00 0.00 2.92
557 594 5.757320 CGATCAACTAAGATGCTTCCAGAAT 59.243 40.000 5.99 0.00 0.00 2.40
559 596 7.439356 CGATCAACTAAGATGCTTCCAGAATTA 59.561 37.037 5.99 0.00 0.00 1.40
560 597 9.282569 GATCAACTAAGATGCTTCCAGAATTAT 57.717 33.333 5.99 0.00 0.00 1.28
562 599 9.547753 TCAACTAAGATGCTTCCAGAATTATAC 57.452 33.333 5.99 0.00 0.00 1.47
563 600 9.330063 CAACTAAGATGCTTCCAGAATTATACA 57.670 33.333 5.99 0.00 0.00 2.29
564 601 9.905713 AACTAAGATGCTTCCAGAATTATACAA 57.094 29.630 5.99 0.00 0.00 2.41
565 602 9.553064 ACTAAGATGCTTCCAGAATTATACAAG 57.447 33.333 5.99 0.00 0.00 3.16
687 724 4.662961 CGGACAGTCGCTGCCACA 62.663 66.667 0.00 0.00 34.37 4.17
836 873 7.548097 GTCCACTTGAATACTACTTGATCTGA 58.452 38.462 0.00 0.00 0.00 3.27
858 895 3.357079 CGCACACTGGGGAAGCAC 61.357 66.667 0.00 0.00 0.00 4.40
908 1200 3.181967 GTGCCGACGTGCAGCTAG 61.182 66.667 10.64 0.00 43.02 3.42
945 1237 2.380410 CGCGCGCCTAGTTTTGTCT 61.380 57.895 27.72 0.00 0.00 3.41
1182 1474 2.162754 CCGATACAACACCGACGCC 61.163 63.158 0.00 0.00 0.00 5.68
1218 1510 1.152715 CTCCTACCCCTCCTCGTCC 60.153 68.421 0.00 0.00 0.00 4.79
1434 1726 4.284550 GGGCACTGCTTCCACCCA 62.285 66.667 0.00 0.00 40.52 4.51
1520 1812 1.876416 CGACACCTCCACCGTCAAAAT 60.876 52.381 0.00 0.00 0.00 1.82
1530 1822 3.835686 CGTCAAAATTGTGGACGCA 57.164 47.368 12.02 0.00 46.25 5.24
1611 1911 1.467543 GCGACTCTGCGACTGACATTA 60.468 52.381 0.00 0.00 0.00 1.90
1616 1916 2.095461 TCTGCGACTGACATTAGAGCT 58.905 47.619 0.00 0.00 0.00 4.09
1666 1980 2.033194 GTTGCTGGAGTACGTGCCC 61.033 63.158 0.00 0.74 0.00 5.36
1760 2077 8.110002 GGATCATTTTTGCTTAGTTAATTTGCG 58.890 33.333 0.00 0.00 0.00 4.85
1807 2137 7.539710 CGTTTGATATTGCCCTCATCAATAATG 59.460 37.037 0.00 0.00 39.13 1.90
1809 2139 6.792424 TGATATTGCCCTCATCAATAATGGA 58.208 36.000 0.00 0.00 39.13 3.41
1812 2142 5.596836 TTGCCCTCATCAATAATGGAAAC 57.403 39.130 0.00 0.00 35.94 2.78
1813 2143 3.631686 TGCCCTCATCAATAATGGAAACG 59.368 43.478 0.00 0.00 35.94 3.60
1818 2150 4.438148 TCATCAATAATGGAAACGCGAGA 58.562 39.130 15.93 0.00 35.94 4.04
1858 2190 3.120889 CGTTTGCATCATATCTGCTACGG 60.121 47.826 17.57 7.67 40.86 4.02
1877 2209 1.548132 GCTTTCGCCGTTTTTGCAGG 61.548 55.000 0.00 0.00 0.00 4.85
1883 2215 0.454452 GCCGTTTTTGCAGGTCGATC 60.454 55.000 0.00 0.00 0.00 3.69
1884 2216 0.179225 CCGTTTTTGCAGGTCGATCG 60.179 55.000 9.36 9.36 0.00 3.69
1885 2217 0.179225 CGTTTTTGCAGGTCGATCGG 60.179 55.000 16.41 0.00 0.00 4.18
1886 2218 0.872388 GTTTTTGCAGGTCGATCGGT 59.128 50.000 16.41 0.00 0.00 4.69
1887 2219 0.871722 TTTTTGCAGGTCGATCGGTG 59.128 50.000 16.41 11.55 0.00 4.94
1888 2220 0.953471 TTTTGCAGGTCGATCGGTGG 60.953 55.000 16.41 4.02 0.00 4.61
1889 2221 1.822114 TTTGCAGGTCGATCGGTGGA 61.822 55.000 16.41 9.08 0.00 4.02
1890 2222 2.105128 GCAGGTCGATCGGTGGAG 59.895 66.667 16.41 3.32 0.00 3.86
1891 2223 2.808315 CAGGTCGATCGGTGGAGG 59.192 66.667 16.41 0.00 0.00 4.30
1892 2224 1.753078 CAGGTCGATCGGTGGAGGA 60.753 63.158 16.41 0.00 0.00 3.71
1893 2225 1.454111 AGGTCGATCGGTGGAGGAG 60.454 63.158 16.41 0.00 0.00 3.69
1894 2226 2.491022 GGTCGATCGGTGGAGGAGG 61.491 68.421 16.41 0.00 0.00 4.30
1895 2227 2.123854 TCGATCGGTGGAGGAGGG 60.124 66.667 16.41 0.00 0.00 4.30
1896 2228 2.123854 CGATCGGTGGAGGAGGGA 60.124 66.667 7.38 0.00 0.00 4.20
1897 2229 1.531840 CGATCGGTGGAGGAGGGAT 60.532 63.158 7.38 0.00 0.00 3.85
1898 2230 1.810606 CGATCGGTGGAGGAGGGATG 61.811 65.000 7.38 0.00 0.00 3.51
1899 2231 0.470080 GATCGGTGGAGGAGGGATGA 60.470 60.000 0.00 0.00 0.00 2.92
1900 2232 0.760945 ATCGGTGGAGGAGGGATGAC 60.761 60.000 0.00 0.00 0.00 3.06
1901 2233 1.381872 CGGTGGAGGAGGGATGACT 60.382 63.158 0.00 0.00 0.00 3.41
1902 2234 0.978146 CGGTGGAGGAGGGATGACTT 60.978 60.000 0.00 0.00 0.00 3.01
1903 2235 0.543749 GGTGGAGGAGGGATGACTTG 59.456 60.000 0.00 0.00 0.00 3.16
1904 2236 0.107459 GTGGAGGAGGGATGACTTGC 60.107 60.000 0.00 0.00 0.00 4.01
1905 2237 0.252881 TGGAGGAGGGATGACTTGCT 60.253 55.000 0.00 0.00 0.00 3.91
1906 2238 0.915364 GGAGGAGGGATGACTTGCTT 59.085 55.000 0.00 0.00 0.00 3.91
1907 2239 1.134250 GGAGGAGGGATGACTTGCTTC 60.134 57.143 0.00 0.00 0.00 3.86
1919 2251 3.243501 TGACTTGCTTCAGAACAAATGCC 60.244 43.478 0.00 0.00 0.00 4.40
1925 2257 5.252547 TGCTTCAGAACAAATGCCACTATA 58.747 37.500 0.00 0.00 0.00 1.31
1983 2315 1.208614 GCTTTCAGTTGCAGGCGAG 59.791 57.895 0.00 0.00 0.00 5.03
2032 2364 0.109132 GGAAAACCTGCATGCTTCGG 60.109 55.000 20.33 17.94 0.00 4.30
2035 2367 3.866379 AACCTGCATGCTTCGGCCA 62.866 57.895 20.33 0.00 40.91 5.36
2036 2368 3.818787 CCTGCATGCTTCGGCCAC 61.819 66.667 20.33 0.00 40.91 5.01
2039 2371 2.747460 GCATGCTTCGGCCACAGA 60.747 61.111 11.37 0.00 40.91 3.41
2079 2411 1.561542 CTAAACCTCTCCAGCCCACAT 59.438 52.381 0.00 0.00 0.00 3.21
2081 2413 0.779997 AACCTCTCCAGCCCACATTT 59.220 50.000 0.00 0.00 0.00 2.32
2082 2414 1.668826 ACCTCTCCAGCCCACATTTA 58.331 50.000 0.00 0.00 0.00 1.40
2083 2415 2.208872 ACCTCTCCAGCCCACATTTAT 58.791 47.619 0.00 0.00 0.00 1.40
2086 2418 4.416848 ACCTCTCCAGCCCACATTTATTAT 59.583 41.667 0.00 0.00 0.00 1.28
2087 2419 5.103515 ACCTCTCCAGCCCACATTTATTATT 60.104 40.000 0.00 0.00 0.00 1.40
2088 2420 6.102615 ACCTCTCCAGCCCACATTTATTATTA 59.897 38.462 0.00 0.00 0.00 0.98
2113 2453 1.406180 TGGAACAAAGACTCACGACGA 59.594 47.619 0.00 0.00 31.92 4.20
2125 2465 2.293677 CTCACGACGAGGCCATAACTAT 59.706 50.000 5.01 0.00 38.18 2.12
2147 2487 1.133976 GCTGTGATCCTGGCCATAACT 60.134 52.381 5.51 0.00 0.00 2.24
2183 2523 4.079446 GCCTGCAGCAGTAAACCA 57.921 55.556 21.26 0.00 42.97 3.67
2184 2524 1.878775 GCCTGCAGCAGTAAACCAG 59.121 57.895 21.26 4.98 42.97 4.00
2186 2526 1.589716 CCTGCAGCAGTAAACCAGGC 61.590 60.000 21.26 0.00 36.94 4.85
2189 2529 2.040544 CAGCAGTAAACCAGGCCCG 61.041 63.158 0.00 0.00 0.00 6.13
2191 2531 1.077716 GCAGTAAACCAGGCCCGAT 60.078 57.895 0.00 0.00 0.00 4.18
2192 2532 1.095807 GCAGTAAACCAGGCCCGATC 61.096 60.000 0.00 0.00 0.00 3.69
2194 2534 0.912487 AGTAAACCAGGCCCGATCCA 60.912 55.000 0.00 0.00 0.00 3.41
2234 2575 2.445845 CCTAGGCCCGGACCATCA 60.446 66.667 10.37 0.00 0.00 3.07
2249 2590 1.457346 CATCAGTGGGAAAGCCTGTC 58.543 55.000 0.00 0.00 0.00 3.51
2250 2591 1.067295 ATCAGTGGGAAAGCCTGTCA 58.933 50.000 0.00 0.00 0.00 3.58
2263 2604 2.203788 TGTCAGGCCTCGGGTCTT 60.204 61.111 0.00 0.00 34.19 3.01
2264 2605 1.831652 CTGTCAGGCCTCGGGTCTTT 61.832 60.000 0.00 0.00 34.19 2.52
2305 2646 0.930310 CGCACGTATGTCAATCCCAG 59.070 55.000 0.00 0.00 0.00 4.45
2312 2653 3.728373 GTCAATCCCAGGCCCGGT 61.728 66.667 3.77 0.00 0.00 5.28
2314 2655 3.411517 CAATCCCAGGCCCGGTCT 61.412 66.667 3.77 0.00 0.00 3.85
2343 2684 3.254411 GCATTAGGGCTCAAAATCTAGGC 59.746 47.826 0.00 0.00 37.55 3.93
2344 2685 2.910688 TAGGGCTCAAAATCTAGGCG 57.089 50.000 0.00 0.00 39.08 5.52
2345 2686 0.464554 AGGGCTCAAAATCTAGGCGC 60.465 55.000 0.00 0.00 39.08 6.53
2391 2733 2.789842 GGCCGGGTTGGACTATTTC 58.210 57.895 2.18 0.00 45.46 2.17
2395 2737 0.251073 CGGGTTGGACTATTTCGGGT 59.749 55.000 0.00 0.00 0.00 5.28
2399 2741 1.205417 GTTGGACTATTTCGGGTCGGA 59.795 52.381 0.00 0.00 33.70 4.55
2403 2760 3.129109 GGACTATTTCGGGTCGGATTTC 58.871 50.000 0.00 0.00 33.70 2.17
2414 2771 1.829533 CGGATTTCCCATGGCCAGG 60.830 63.158 13.05 12.17 34.14 4.45
2427 2784 1.202639 TGGCCAGGTATAATCACAGCG 60.203 52.381 0.00 0.00 0.00 5.18
2432 2789 3.431626 CCAGGTATAATCACAGCGAACCA 60.432 47.826 0.00 0.00 0.00 3.67
2450 2807 5.576447 AACCACAACTTACAAACAGAAGG 57.424 39.130 0.00 0.00 0.00 3.46
2460 2817 8.757164 ACTTACAAACAGAAGGAAAAACAAAG 57.243 30.769 0.00 0.00 0.00 2.77
2465 2822 8.556194 ACAAACAGAAGGAAAAACAAAGAAAAC 58.444 29.630 0.00 0.00 0.00 2.43
2466 2823 8.773645 CAAACAGAAGGAAAAACAAAGAAAACT 58.226 29.630 0.00 0.00 0.00 2.66
2467 2824 9.990360 AAACAGAAGGAAAAACAAAGAAAACTA 57.010 25.926 0.00 0.00 0.00 2.24
2484 2864 7.716612 AGAAAACTAAGGATTCACAAACCAAG 58.283 34.615 0.00 0.00 0.00 3.61
2506 2886 4.122776 GCAGGTGATACAATGTCCTACAG 58.877 47.826 0.00 0.00 0.00 2.74
2529 2909 6.198966 CAGGAAGCTAACAACAAATCAACAAC 59.801 38.462 0.00 0.00 0.00 3.32
2542 2922 8.506168 ACAAATCAACAACAGAAACTAAGAGA 57.494 30.769 0.00 0.00 0.00 3.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.182537 CAAATTGCTCGGGCTGGC 59.817 61.111 9.62 0.00 39.59 4.85
1 2 2.887360 CCAAATTGCTCGGGCTGG 59.113 61.111 9.62 3.25 39.59 4.85
6 7 0.169672 CACTCTGCCAAATTGCTCGG 59.830 55.000 0.00 0.00 0.00 4.63
82 83 4.693566 TGGAAAGAAATACTGTAACGCCAG 59.306 41.667 0.00 0.00 38.45 4.85
182 185 0.537371 AGTAAGGTTGGGTGCAGTGC 60.537 55.000 8.58 8.58 0.00 4.40
192 195 6.565234 AGATGATACTCGTTCAGTAAGGTTG 58.435 40.000 0.00 0.00 41.17 3.77
262 265 1.023502 GACGTGGGCTACTCCTACTC 58.976 60.000 0.00 0.00 43.52 2.59
310 313 8.350722 TCCATACATATACTCGAGAAAGTTCAC 58.649 37.037 21.68 0.00 0.00 3.18
311 314 8.459911 TCCATACATATACTCGAGAAAGTTCA 57.540 34.615 21.68 0.00 0.00 3.18
321 324 5.322310 GCGTGTACTCCATACATATACTCG 58.678 45.833 0.00 0.00 45.59 4.18
375 404 3.075283 AGTGTATGGGGTCATTTTCACCA 59.925 43.478 0.00 0.00 42.89 4.17
440 469 2.805295 CGGAACCAGAGTGTGCAAGTAA 60.805 50.000 0.00 0.00 0.00 2.24
445 474 1.227527 CACGGAACCAGAGTGTGCA 60.228 57.895 0.00 0.00 0.00 4.57
536 573 9.547753 GTATAATTCTGGAAGCATCTTAGTTGA 57.452 33.333 0.00 0.00 0.00 3.18
537 574 9.330063 TGTATAATTCTGGAAGCATCTTAGTTG 57.670 33.333 0.00 0.00 0.00 3.16
538 575 9.905713 TTGTATAATTCTGGAAGCATCTTAGTT 57.094 29.630 0.00 0.00 0.00 2.24
557 594 8.160521 TGTTCTTAGCTTGCAAACTTGTATAA 57.839 30.769 7.82 0.00 0.00 0.98
559 596 6.633500 TGTTCTTAGCTTGCAAACTTGTAT 57.367 33.333 7.82 0.00 0.00 2.29
560 597 6.094881 AGTTGTTCTTAGCTTGCAAACTTGTA 59.905 34.615 7.82 0.00 0.00 2.41
562 599 5.343249 AGTTGTTCTTAGCTTGCAAACTTG 58.657 37.500 7.82 2.27 0.00 3.16
563 600 5.582689 AGTTGTTCTTAGCTTGCAAACTT 57.417 34.783 7.82 0.00 0.00 2.66
564 601 5.582689 AAGTTGTTCTTAGCTTGCAAACT 57.417 34.783 7.62 7.62 34.23 2.66
565 602 7.149128 CGATTAAGTTGTTCTTAGCTTGCAAAC 60.149 37.037 0.00 0.00 39.42 2.93
687 724 3.075283 TGCCATATCCCGGGTAATTCAAT 59.925 43.478 22.86 7.15 0.00 2.57
836 873 2.809861 CTTCCCCAGTGTGCGCTCAT 62.810 60.000 16.02 2.19 0.00 2.90
858 895 1.327690 TTCCTGGGCCTGCTACGTAG 61.328 60.000 18.47 18.47 0.00 3.51
934 1226 1.068474 CCGTGGCGAGACAAAACTAG 58.932 55.000 0.00 0.00 0.00 2.57
945 1237 4.069232 CCTTCTCTGCCGTGGCGA 62.069 66.667 6.37 5.89 45.51 5.54
1167 1459 1.735198 CGTGGCGTCGGTGTTGTAT 60.735 57.895 0.00 0.00 0.00 2.29
1182 1474 1.743252 GAAGGAGCTGGGAAGCGTG 60.743 63.158 0.00 0.00 40.27 5.34
1193 1485 0.761323 GGAGGGGTAGGAGAAGGAGC 60.761 65.000 0.00 0.00 0.00 4.70
1197 1489 0.259356 ACGAGGAGGGGTAGGAGAAG 59.741 60.000 0.00 0.00 0.00 2.85
1218 1510 4.821589 GCAGCGGAGGAAGACGGG 62.822 72.222 0.00 0.00 0.00 5.28
1389 1681 2.284258 AGCGCCTTCACCCTCTCT 60.284 61.111 2.29 0.00 0.00 3.10
1520 1812 2.892334 GCTTCGCTTGCGTCCACAA 61.892 57.895 14.70 0.78 0.00 3.33
1530 1822 0.528017 TCGATCAGACAGCTTCGCTT 59.472 50.000 0.00 0.00 36.40 4.68
1596 1896 2.095461 AGCTCTAATGTCAGTCGCAGA 58.905 47.619 0.00 0.00 0.00 4.26
1616 1916 0.246086 GTGCAATGGAAATTGGCGGA 59.754 50.000 0.00 0.00 32.43 5.54
1666 1980 1.167851 ATCAACCATGCCTGAACACG 58.832 50.000 0.00 0.00 0.00 4.49
1730 2047 8.687824 ATTAACTAAGCAAAAATGATCCGTTG 57.312 30.769 0.00 0.00 0.00 4.10
1760 2077 3.061697 CGCCCGTAAAAACTCACTGATAC 59.938 47.826 0.00 0.00 0.00 2.24
1796 2126 4.438148 TCTCGCGTTTCCATTATTGATGA 58.562 39.130 5.77 0.00 38.03 2.92
1807 2137 1.009829 AAGATGCATCTCGCGTTTCC 58.990 50.000 28.83 0.00 46.97 3.13
1809 2139 1.398390 GGAAAGATGCATCTCGCGTTT 59.602 47.619 28.83 18.75 46.97 3.60
1812 2142 0.531532 AGGGAAAGATGCATCTCGCG 60.532 55.000 28.83 0.00 46.97 5.87
1813 2143 2.139118 GTAGGGAAAGATGCATCTCGC 58.861 52.381 28.83 23.38 42.89 5.03
1818 2150 0.474184 CGGGGTAGGGAAAGATGCAT 59.526 55.000 0.00 0.00 0.00 3.96
1877 2209 2.491022 CCCTCCTCCACCGATCGAC 61.491 68.421 18.66 0.00 0.00 4.20
1883 2215 0.978146 AAGTCATCCCTCCTCCACCG 60.978 60.000 0.00 0.00 0.00 4.94
1884 2216 0.543749 CAAGTCATCCCTCCTCCACC 59.456 60.000 0.00 0.00 0.00 4.61
1885 2217 0.107459 GCAAGTCATCCCTCCTCCAC 60.107 60.000 0.00 0.00 0.00 4.02
1886 2218 0.252881 AGCAAGTCATCCCTCCTCCA 60.253 55.000 0.00 0.00 0.00 3.86
1887 2219 0.915364 AAGCAAGTCATCCCTCCTCC 59.085 55.000 0.00 0.00 0.00 4.30
1888 2220 1.556911 TGAAGCAAGTCATCCCTCCTC 59.443 52.381 0.00 0.00 0.00 3.71
1889 2221 1.558756 CTGAAGCAAGTCATCCCTCCT 59.441 52.381 0.00 0.00 0.00 3.69
1890 2222 1.556911 TCTGAAGCAAGTCATCCCTCC 59.443 52.381 0.00 0.00 0.00 4.30
1891 2223 3.006247 GTTCTGAAGCAAGTCATCCCTC 58.994 50.000 0.00 0.00 0.00 4.30
1892 2224 2.373169 TGTTCTGAAGCAAGTCATCCCT 59.627 45.455 0.00 0.00 0.00 4.20
1893 2225 2.783135 TGTTCTGAAGCAAGTCATCCC 58.217 47.619 0.00 0.00 0.00 3.85
1894 2226 4.836125 TTTGTTCTGAAGCAAGTCATCC 57.164 40.909 0.00 0.00 0.00 3.51
1895 2227 4.620184 GCATTTGTTCTGAAGCAAGTCATC 59.380 41.667 0.00 0.00 0.00 2.92
1896 2228 4.553323 GCATTTGTTCTGAAGCAAGTCAT 58.447 39.130 0.00 0.00 0.00 3.06
1897 2229 3.243501 GGCATTTGTTCTGAAGCAAGTCA 60.244 43.478 0.00 0.00 0.00 3.41
1898 2230 3.243501 TGGCATTTGTTCTGAAGCAAGTC 60.244 43.478 0.00 0.00 0.00 3.01
1899 2231 2.694628 TGGCATTTGTTCTGAAGCAAGT 59.305 40.909 0.00 0.00 0.00 3.16
1900 2232 3.054878 GTGGCATTTGTTCTGAAGCAAG 58.945 45.455 0.00 0.00 0.00 4.01
1901 2233 2.694628 AGTGGCATTTGTTCTGAAGCAA 59.305 40.909 0.00 0.00 0.00 3.91
1902 2234 2.309613 AGTGGCATTTGTTCTGAAGCA 58.690 42.857 0.00 0.00 0.00 3.91
1903 2235 4.708726 ATAGTGGCATTTGTTCTGAAGC 57.291 40.909 0.00 0.00 0.00 3.86
1904 2236 6.732154 CCATATAGTGGCATTTGTTCTGAAG 58.268 40.000 0.00 0.00 42.12 3.02
1905 2237 6.698008 CCATATAGTGGCATTTGTTCTGAA 57.302 37.500 0.00 0.00 42.12 3.02
1919 2251 2.866156 CAAGTGCACGGTCCATATAGTG 59.134 50.000 12.01 0.00 37.63 2.74
2032 2364 1.560860 GCTCGTGTCAGTTCTGTGGC 61.561 60.000 0.00 0.00 0.00 5.01
2035 2367 0.039978 CTCGCTCGTGTCAGTTCTGT 60.040 55.000 0.00 0.00 0.00 3.41
2036 2368 0.039978 ACTCGCTCGTGTCAGTTCTG 60.040 55.000 0.00 0.00 0.00 3.02
2039 2371 3.008330 AGTATACTCGCTCGTGTCAGTT 58.992 45.455 0.00 0.00 0.00 3.16
2083 2415 9.672086 CGTGAGTCTTTGTTCCAAAAATAATAA 57.328 29.630 0.00 0.00 0.00 1.40
2086 2418 7.190871 GTCGTGAGTCTTTGTTCCAAAAATAA 58.809 34.615 0.00 0.00 0.00 1.40
2087 2419 6.510478 CGTCGTGAGTCTTTGTTCCAAAAATA 60.510 38.462 0.00 0.00 0.00 1.40
2088 2420 5.578776 GTCGTGAGTCTTTGTTCCAAAAAT 58.421 37.500 0.00 0.00 0.00 1.82
2093 2433 1.406180 TCGTCGTGAGTCTTTGTTCCA 59.594 47.619 0.00 0.00 0.00 3.53
2099 2439 1.289380 GGCCTCGTCGTGAGTCTTT 59.711 57.895 0.00 0.00 43.64 2.52
2113 2453 4.223923 GGATCACAGCTATAGTTATGGCCT 59.776 45.833 3.32 0.00 40.57 5.19
2125 2465 2.101640 TATGGCCAGGATCACAGCTA 57.898 50.000 13.05 0.00 0.00 3.32
2164 2504 0.178992 TGGTTTACTGCTGCAGGCTT 60.179 50.000 31.00 14.74 42.39 4.35
2168 2508 1.589716 GGCCTGGTTTACTGCTGCAG 61.590 60.000 27.02 27.02 37.52 4.41
2177 2517 0.912487 ACTGGATCGGGCCTGGTTTA 60.912 55.000 12.87 0.00 0.00 2.01
2182 2522 1.144936 GAAGACTGGATCGGGCCTG 59.855 63.158 4.71 4.71 0.00 4.85
2183 2523 2.427245 CGAAGACTGGATCGGGCCT 61.427 63.158 0.84 0.00 35.49 5.19
2184 2524 2.107141 CGAAGACTGGATCGGGCC 59.893 66.667 0.00 0.00 35.49 5.80
2189 2529 1.120530 TTAGGCCCGAAGACTGGATC 58.879 55.000 0.00 0.00 0.00 3.36
2191 2531 1.580059 ATTTAGGCCCGAAGACTGGA 58.420 50.000 0.00 0.00 0.00 3.86
2192 2532 2.420058 AATTTAGGCCCGAAGACTGG 57.580 50.000 0.00 0.00 0.00 4.00
2194 2534 3.610911 CTGAAATTTAGGCCCGAAGACT 58.389 45.455 0.00 0.00 0.00 3.24
2219 2560 2.063979 CACTGATGGTCCGGGCCTA 61.064 63.158 28.64 13.55 0.00 3.93
2221 2562 4.489771 CCACTGATGGTCCGGGCC 62.490 72.222 21.35 21.35 41.64 5.80
2234 2575 1.763770 CCTGACAGGCTTTCCCACT 59.236 57.895 8.99 0.00 35.39 4.00
2245 2586 1.831652 AAAGACCCGAGGCCTGACAG 61.832 60.000 12.00 0.00 0.00 3.51
2246 2587 1.841556 AAAGACCCGAGGCCTGACA 60.842 57.895 12.00 0.00 0.00 3.58
2249 2590 2.045926 CCAAAGACCCGAGGCCTG 60.046 66.667 12.00 1.85 0.00 4.85
2250 2591 4.035102 GCCAAAGACCCGAGGCCT 62.035 66.667 3.86 3.86 41.25 5.19
2384 2726 2.158856 GGGAAATCCGACCCGAAATAGT 60.159 50.000 0.00 0.00 36.56 2.12
2395 2737 1.227102 CTGGCCATGGGAAATCCGA 59.773 57.895 15.13 0.00 38.76 4.55
2399 2741 4.107798 TGATTATACCTGGCCATGGGAAAT 59.892 41.667 17.65 14.76 0.00 2.17
2403 2760 2.108075 TGTGATTATACCTGGCCATGGG 59.892 50.000 20.97 16.10 0.00 4.00
2414 2771 4.630069 AGTTGTGGTTCGCTGTGATTATAC 59.370 41.667 0.00 0.00 0.00 1.47
2427 2784 5.355910 TCCTTCTGTTTGTAAGTTGTGGTTC 59.644 40.000 0.00 0.00 0.00 3.62
2432 2789 7.662897 TGTTTTTCCTTCTGTTTGTAAGTTGT 58.337 30.769 0.00 0.00 0.00 3.32
2460 2817 6.420903 GCTTGGTTTGTGAATCCTTAGTTTTC 59.579 38.462 0.00 0.00 0.00 2.29
2465 2822 4.082571 CCTGCTTGGTTTGTGAATCCTTAG 60.083 45.833 0.00 0.00 0.00 2.18
2466 2823 3.826157 CCTGCTTGGTTTGTGAATCCTTA 59.174 43.478 0.00 0.00 0.00 2.69
2467 2824 2.629617 CCTGCTTGGTTTGTGAATCCTT 59.370 45.455 0.00 0.00 0.00 3.36
2484 2864 4.122776 CTGTAGGACATTGTATCACCTGC 58.877 47.826 5.29 4.69 34.77 4.85
2506 2886 6.039616 TGTTGTTGATTTGTTGTTAGCTTCC 58.960 36.000 0.00 0.00 0.00 3.46
2518 2898 8.616076 ACTCTCTTAGTTTCTGTTGTTGATTTG 58.384 33.333 0.00 0.00 33.35 2.32


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

AutoCloner maintained by Alex Coulton.