Multiple sequence alignment - TraesCS3A01G182600

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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 TraesCS3A01G182600 chr3A 100.000 2792 0 0 1 2792 212085482 212088273 0.000000e+00 5156
1 TraesCS3A01G182600 chr3D 89.529 1041 84 11 1 1023 173613102 173614135 0.000000e+00 1295
2 TraesCS3A01G182600 chr3D 89.528 869 41 20 1038 1881 173614415 173615258 0.000000e+00 1055
3 TraesCS3A01G182600 chr3D 88.561 542 25 16 1942 2453 173615261 173615795 8.490000e-175 623
4 TraesCS3A01G182600 chr3D 90.504 337 17 5 2471 2792 173616067 173616403 5.520000e-117 431
5 TraesCS3A01G182600 chr3B 92.334 861 34 6 1045 1881 252355488 252356340 0.000000e+00 1195
6 TraesCS3A01G182600 chr3B 91.506 624 28 8 2189 2792 252356646 252357264 0.000000e+00 835
7 TraesCS3A01G182600 chr3B 86.783 628 72 7 1 622 252354041 252354663 0.000000e+00 689
8 TraesCS3A01G182600 chr3B 82.255 479 50 15 606 1058 252354907 252355376 5.640000e-102 381
9 TraesCS3A01G182600 chr3B 91.566 249 12 2 1941 2189 252356342 252356581 4.460000e-88 335
10 TraesCS3A01G182600 chr5D 96.875 64 2 0 1882 1945 505361897 505361960 1.060000e-19 108
11 TraesCS3A01G182600 chr5A 95.455 66 3 0 1882 1947 248535389 248535324 3.800000e-19 106
12 TraesCS3A01G182600 chr5A 94.118 68 4 0 1882 1949 428970152 428970085 1.370000e-18 104
13 TraesCS3A01G182600 chr1D 96.825 63 2 0 1882 1944 216133274 216133336 3.800000e-19 106
14 TraesCS3A01G182600 chr1A 96.825 63 2 0 1882 1944 50284453 50284391 3.800000e-19 106
15 TraesCS3A01G182600 chr6D 95.385 65 3 0 1882 1946 25851309 25851373 1.370000e-18 104
16 TraesCS3A01G182600 chr2A 94.118 68 4 0 1882 1949 659096385 659096318 1.370000e-18 104
17 TraesCS3A01G182600 chr1B 94.118 68 4 0 1882 1949 492329900 492329967 1.370000e-18 104
18 TraesCS3A01G182600 chr7A 83.186 113 17 2 302 413 195328268 195328379 4.920000e-18 102
19 TraesCS3A01G182600 chr4A 91.781 73 6 0 1882 1954 574539948 574539876 4.920000e-18 102


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 TraesCS3A01G182600 chr3A 212085482 212088273 2791 False 5156 5156 100.0000 1 2792 1 chr3A.!!$F1 2791
1 TraesCS3A01G182600 chr3D 173613102 173616403 3301 False 851 1295 89.5305 1 2792 4 chr3D.!!$F1 2791
2 TraesCS3A01G182600 chr3B 252354041 252357264 3223 False 687 1195 88.8888 1 2792 5 chr3B.!!$F1 2791

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
77 78 1.152902 TGCATAGCCATGGAGCACC 60.153 57.895 18.4 0.0 34.23 5.01 F
1102 1660 0.695924 TTCGAATGGGGCTGGAAAGA 59.304 50.000 0.0 0.0 0.00 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1293 1857 0.034670 ACGAAGCGTAGGTAGGAGGT 60.035 55.0 0.0 0.0 38.73 3.85 R
1936 2530 0.036671 CCGGGGAAACTGGTACTCAC 60.037 60.0 0.0 0.0 41.03 3.51 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
77 78 1.152902 TGCATAGCCATGGAGCACC 60.153 57.895 18.40 0.00 34.23 5.01
90 91 2.087646 GGAGCACCTCTCACCAAATTC 58.912 52.381 0.00 0.00 43.70 2.17
128 133 8.701908 ACGAGGATTAATATACTAACCAGTCA 57.298 34.615 0.00 0.00 36.14 3.41
158 166 5.338381 GCATGGCTAGCAATAAGTCCCTATA 60.338 44.000 18.24 0.00 0.00 1.31
159 167 6.711277 CATGGCTAGCAATAAGTCCCTATAA 58.289 40.000 18.24 0.00 0.00 0.98
160 168 6.952605 TGGCTAGCAATAAGTCCCTATAAT 57.047 37.500 18.24 0.00 0.00 1.28
217 225 2.161211 GTGTCATCAGCAAAGAGAAGGC 59.839 50.000 0.00 0.00 0.00 4.35
227 235 2.683362 CAAAGAGAAGGCGGGAAATACC 59.317 50.000 0.00 0.00 38.08 2.73
268 276 9.023962 AGATTTTTAGTGGATCAAAAGCACATA 57.976 29.630 6.32 0.00 29.99 2.29
277 285 6.127281 TGGATCAAAAGCACATATTTCTGCAT 60.127 34.615 0.00 0.00 35.73 3.96
283 291 4.989277 AGCACATATTTCTGCATCCCATA 58.011 39.130 0.00 0.00 35.73 2.74
294 302 2.289010 TGCATCCCATATGAGTAGCACG 60.289 50.000 3.65 0.00 0.00 5.34
307 315 1.732259 GTAGCACGGACAAACCATCAG 59.268 52.381 0.00 0.00 38.90 2.90
413 423 8.054572 TCCATTGAATTTCATGGAGTATCTCAA 58.945 33.333 18.62 0.00 38.19 3.02
421 431 7.776933 TTCATGGAGTATCTCAAAAAGATCG 57.223 36.000 0.00 0.00 43.90 3.69
434 444 8.551205 TCTCAAAAAGATCGCATATGTCATTAC 58.449 33.333 4.29 0.00 0.00 1.89
456 466 1.438651 GCAGTACGATTTGGTGAGCA 58.561 50.000 0.00 0.00 0.00 4.26
473 483 3.134442 TGAGCAAAGCCAAACTTTTCCAT 59.866 39.130 0.00 0.00 46.73 3.41
489 501 2.733956 TCCATCGCCTGCCTTAAAAAT 58.266 42.857 0.00 0.00 0.00 1.82
498 510 4.080919 GCCTGCCTTAAAAATTCCCAATCT 60.081 41.667 0.00 0.00 0.00 2.40
503 515 5.792741 CCTTAAAAATTCCCAATCTGCACA 58.207 37.500 0.00 0.00 0.00 4.57
519 531 4.821260 TCTGCACAGTCAAATGCTTTAGAA 59.179 37.500 0.00 0.00 42.55 2.10
557 571 3.119708 GCACAAAAGCTATTCCCTGAGTG 60.120 47.826 0.00 0.00 0.00 3.51
559 573 4.520492 CACAAAAGCTATTCCCTGAGTGTT 59.480 41.667 0.00 0.00 0.00 3.32
592 661 8.265055 TCTTTAGTGATAAAATGGATCGAAGGT 58.735 33.333 0.00 0.00 0.00 3.50
647 919 5.827568 ATTTGCAACGAACACATCAATTC 57.172 34.783 0.00 0.00 0.00 2.17
769 1063 7.107542 TGTTGGGTTAAATATAGGAGTCACAC 58.892 38.462 0.00 0.00 0.00 3.82
771 1065 7.260387 TGGGTTAAATATAGGAGTCACACAA 57.740 36.000 0.00 0.00 0.00 3.33
827 1121 7.573283 GCACGTGCATGATTACTAGAGTCTATA 60.573 40.741 34.52 0.00 41.59 1.31
901 1195 4.817318 AAGAAAACTTGTTTTCCCAGCA 57.183 36.364 25.90 0.00 40.75 4.41
957 1251 5.458069 CCAGGGCCTATTCCAATCAATAGAA 60.458 44.000 5.28 0.00 38.25 2.10
1018 1313 9.860898 AAACTAGAATGCTCCATTTTTATGTTC 57.139 29.630 0.00 0.00 33.90 3.18
1059 1617 3.539842 GGGGGCGAAGAGAGTAGG 58.460 66.667 0.00 0.00 0.00 3.18
1102 1660 0.695924 TTCGAATGGGGCTGGAAAGA 59.304 50.000 0.00 0.00 0.00 2.52
1106 1664 1.561542 GAATGGGGCTGGAAAGAGAGA 59.438 52.381 0.00 0.00 0.00 3.10
1125 1683 1.602377 GACTTTCGGGTGTGGAAACAG 59.398 52.381 0.00 0.00 44.46 3.16
1293 1857 2.060383 CGCCTCCACCCTCTCATCA 61.060 63.158 0.00 0.00 0.00 3.07
1302 1866 1.062810 ACCCTCTCATCACCTCCTACC 60.063 57.143 0.00 0.00 0.00 3.18
1303 1867 1.219213 CCCTCTCATCACCTCCTACCT 59.781 57.143 0.00 0.00 0.00 3.08
1324 1888 4.624024 CCTACGCTTCGTCATTTTTGACTA 59.376 41.667 4.76 0.00 41.54 2.59
1392 1956 0.250295 CCGGTGTTGCTTTCCTCTCA 60.250 55.000 0.00 0.00 0.00 3.27
1530 2094 4.513442 ACAATAATAGCACGAGCAAGGAA 58.487 39.130 7.77 0.00 45.49 3.36
1533 2097 6.072175 ACAATAATAGCACGAGCAAGGAAAAA 60.072 34.615 7.77 0.00 45.49 1.94
1855 2449 5.310451 TGGGTGTGAGACTAAAATTGTACC 58.690 41.667 0.00 0.00 0.00 3.34
1893 2487 6.604735 CCTTTGGGACGAGATGTATTTTAG 57.395 41.667 0.00 0.00 33.58 1.85
1894 2488 6.113411 CCTTTGGGACGAGATGTATTTTAGT 58.887 40.000 0.00 0.00 33.58 2.24
1895 2489 6.598064 CCTTTGGGACGAGATGTATTTTAGTT 59.402 38.462 0.00 0.00 33.58 2.24
1896 2490 7.201617 CCTTTGGGACGAGATGTATTTTAGTTC 60.202 40.741 0.00 0.00 33.58 3.01
1897 2491 6.540438 TGGGACGAGATGTATTTTAGTTCT 57.460 37.500 0.00 0.00 0.00 3.01
1898 2492 7.649533 TGGGACGAGATGTATTTTAGTTCTA 57.350 36.000 0.00 0.00 0.00 2.10
1899 2493 7.713750 TGGGACGAGATGTATTTTAGTTCTAG 58.286 38.462 0.00 0.00 0.00 2.43
1900 2494 7.558807 TGGGACGAGATGTATTTTAGTTCTAGA 59.441 37.037 0.00 0.00 0.00 2.43
1901 2495 8.578151 GGGACGAGATGTATTTTAGTTCTAGAT 58.422 37.037 0.00 0.00 0.00 1.98
1918 2512 9.632807 AGTTCTAGATATATTCATTTCTGCGAC 57.367 33.333 0.00 0.00 0.00 5.19
1919 2513 8.579600 GTTCTAGATATATTCATTTCTGCGACG 58.420 37.037 0.00 0.00 0.00 5.12
1920 2514 8.040716 TCTAGATATATTCATTTCTGCGACGA 57.959 34.615 0.00 0.00 0.00 4.20
1921 2515 8.178313 TCTAGATATATTCATTTCTGCGACGAG 58.822 37.037 0.00 0.00 0.00 4.18
1922 2516 6.682746 AGATATATTCATTTCTGCGACGAGT 58.317 36.000 0.00 0.00 0.00 4.18
1923 2517 7.817641 AGATATATTCATTTCTGCGACGAGTA 58.182 34.615 0.00 0.00 0.00 2.59
1924 2518 8.297426 AGATATATTCATTTCTGCGACGAGTAA 58.703 33.333 0.00 0.00 0.00 2.24
1925 2519 8.988064 ATATATTCATTTCTGCGACGAGTAAT 57.012 30.769 0.00 0.00 0.00 1.89
1926 2520 7.715265 ATATTCATTTCTGCGACGAGTAATT 57.285 32.000 0.00 0.00 0.00 1.40
1927 2521 5.856126 TTCATTTCTGCGACGAGTAATTT 57.144 34.783 0.00 0.00 0.00 1.82
1928 2522 5.203358 TCATTTCTGCGACGAGTAATTTG 57.797 39.130 0.00 0.00 0.00 2.32
1929 2523 4.092821 TCATTTCTGCGACGAGTAATTTGG 59.907 41.667 0.00 0.00 0.00 3.28
1930 2524 3.306917 TTCTGCGACGAGTAATTTGGA 57.693 42.857 0.00 0.00 0.00 3.53
1931 2525 3.306917 TCTGCGACGAGTAATTTGGAA 57.693 42.857 0.00 0.00 0.00 3.53
1932 2526 2.991190 TCTGCGACGAGTAATTTGGAAC 59.009 45.455 0.00 0.00 0.00 3.62
1933 2527 1.722464 TGCGACGAGTAATTTGGAACG 59.278 47.619 0.00 0.00 0.00 3.95
1934 2528 1.060122 GCGACGAGTAATTTGGAACGG 59.940 52.381 0.00 0.00 0.00 4.44
1935 2529 2.598589 CGACGAGTAATTTGGAACGGA 58.401 47.619 0.00 0.00 0.00 4.69
1936 2530 2.597305 CGACGAGTAATTTGGAACGGAG 59.403 50.000 0.00 0.00 0.00 4.63
1938 2532 3.323243 ACGAGTAATTTGGAACGGAGTG 58.677 45.455 0.00 0.00 45.00 3.51
1939 2533 3.006110 ACGAGTAATTTGGAACGGAGTGA 59.994 43.478 0.00 0.00 45.00 3.41
1940 2534 3.612860 CGAGTAATTTGGAACGGAGTGAG 59.387 47.826 0.00 0.00 45.00 3.51
1941 2535 4.566987 GAGTAATTTGGAACGGAGTGAGT 58.433 43.478 0.00 0.00 45.00 3.41
1942 2536 5.620654 CGAGTAATTTGGAACGGAGTGAGTA 60.621 44.000 0.00 0.00 45.00 2.59
1943 2537 5.476614 AGTAATTTGGAACGGAGTGAGTAC 58.523 41.667 0.00 0.00 45.00 2.73
1944 2538 2.825861 TTTGGAACGGAGTGAGTACC 57.174 50.000 0.00 0.00 45.00 3.34
1972 2566 3.515104 CCCCGGGTAATATACGTACCAAT 59.485 47.826 21.85 0.00 42.51 3.16
1987 2581 4.387862 CGTACCAATTCGAAGCTTTGTAGT 59.612 41.667 13.49 0.20 0.00 2.73
1988 2582 5.574055 CGTACCAATTCGAAGCTTTGTAGTA 59.426 40.000 13.49 6.74 0.00 1.82
1989 2583 6.237490 CGTACCAATTCGAAGCTTTGTAGTAG 60.237 42.308 13.49 0.00 0.00 2.57
1990 2584 5.548406 ACCAATTCGAAGCTTTGTAGTAGT 58.452 37.500 13.49 0.00 0.00 2.73
1991 2585 6.694447 ACCAATTCGAAGCTTTGTAGTAGTA 58.306 36.000 13.49 0.00 0.00 1.82
1992 2586 6.812160 ACCAATTCGAAGCTTTGTAGTAGTAG 59.188 38.462 13.49 0.09 0.00 2.57
1993 2587 6.812160 CCAATTCGAAGCTTTGTAGTAGTAGT 59.188 38.462 13.49 0.00 0.00 2.73
2054 2658 3.620488 TGAAACCATAGCCAGAATCCAC 58.380 45.455 0.00 0.00 0.00 4.02
2074 2678 1.156736 GCCGTGTTGCTTGTATGTCT 58.843 50.000 0.00 0.00 0.00 3.41
2075 2679 2.343101 GCCGTGTTGCTTGTATGTCTA 58.657 47.619 0.00 0.00 0.00 2.59
2076 2680 2.093783 GCCGTGTTGCTTGTATGTCTAC 59.906 50.000 0.00 0.00 0.00 2.59
2088 2692 5.120054 TGTATGTCTACTACCAGGCAGTA 57.880 43.478 0.00 0.00 32.72 2.74
2093 2697 6.650427 TGTCTACTACCAGGCAGTATTATG 57.350 41.667 0.00 0.00 0.00 1.90
2123 2727 4.711399 ACACCAGTTTTAGTAACTCCCAC 58.289 43.478 0.00 0.00 0.00 4.61
2199 2868 3.305950 GCTATGCAAGTGAGATCGATCCT 60.306 47.826 21.66 9.21 0.00 3.24
2201 2870 2.897436 TGCAAGTGAGATCGATCCTTG 58.103 47.619 26.01 26.01 36.47 3.61
2202 2871 2.208431 GCAAGTGAGATCGATCCTTGG 58.792 52.381 28.68 17.99 34.51 3.61
2207 2876 4.222336 AGTGAGATCGATCCTTGGATCTT 58.778 43.478 21.66 12.84 44.57 2.40
2211 2880 6.012745 TGAGATCGATCCTTGGATCTTCATA 58.987 40.000 21.66 11.88 44.57 2.15
2290 2959 3.571828 AGGTCTCACATATCGGACAGATG 59.428 47.826 0.00 0.00 40.40 2.90
2318 2987 2.533916 AGTGATTCAGTGCTCCTCTCA 58.466 47.619 0.00 0.00 0.00 3.27
2319 2988 2.233431 AGTGATTCAGTGCTCCTCTCAC 59.767 50.000 0.00 0.00 33.46 3.51
2320 2989 2.028658 GTGATTCAGTGCTCCTCTCACA 60.029 50.000 0.00 0.00 36.93 3.58
2465 3379 7.824289 AGCTAAAGAACATAACTGTATCAGCAA 59.176 33.333 0.00 0.00 33.36 3.91
2492 3419 8.739039 CAGTAATGGTGATTAAGACCAATTTCA 58.261 33.333 12.03 0.00 46.57 2.69
2531 3472 9.726438 ATTCCACATATAACTAATGCTAGAACC 57.274 33.333 0.00 0.00 0.00 3.62
2535 3476 8.993121 CACATATAACTAATGCTAGAACCAAGG 58.007 37.037 0.00 0.00 0.00 3.61
2537 3478 9.778741 CATATAACTAATGCTAGAACCAAGGAA 57.221 33.333 0.00 0.00 0.00 3.36
2546 3487 4.454847 GCTAGAACCAAGGAACACTAAACC 59.545 45.833 0.00 0.00 0.00 3.27
2710 3652 2.037772 ACTGAGAGCTCGTTGTTTCCAT 59.962 45.455 8.37 0.00 0.00 3.41
2772 3714 1.079612 CGGAGTGCTGCACATCTCA 60.080 57.895 31.90 0.00 36.74 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 9.017509 ACAATGTGAGTACTGAATTTGAATCAT 57.982 29.630 0.00 0.00 0.00 2.45
72 73 4.851639 ATAGAATTTGGTGAGAGGTGCT 57.148 40.909 0.00 0.00 0.00 4.40
128 133 2.953284 ATTGCTAGCCATGCTCAGAT 57.047 45.000 13.29 0.00 40.44 2.90
158 166 3.244181 GGTGAACCCACATCAAGCAAATT 60.244 43.478 0.00 0.00 44.93 1.82
159 167 2.299867 GGTGAACCCACATCAAGCAAAT 59.700 45.455 0.00 0.00 44.93 2.32
160 168 1.686052 GGTGAACCCACATCAAGCAAA 59.314 47.619 0.00 0.00 44.93 3.68
227 235 4.399004 AAAATCTGTCGGAGATCTCTGG 57.601 45.455 27.57 17.34 40.89 3.86
233 241 5.677319 TCCACTAAAAATCTGTCGGAGAT 57.323 39.130 0.00 0.00 43.91 2.75
268 276 5.221986 TGCTACTCATATGGGATGCAGAAAT 60.222 40.000 18.25 0.00 0.00 2.17
277 285 1.961394 GTCCGTGCTACTCATATGGGA 59.039 52.381 10.29 0.00 0.00 4.37
283 291 1.346395 TGGTTTGTCCGTGCTACTCAT 59.654 47.619 0.00 0.00 39.52 2.90
294 302 0.539438 TGGTGGCTGATGGTTTGTCC 60.539 55.000 0.00 0.00 0.00 4.02
307 315 5.007724 CCTCGTTCTTATTCTTATTGGTGGC 59.992 44.000 0.00 0.00 0.00 5.01
413 423 5.179368 CGGGTAATGACATATGCGATCTTTT 59.821 40.000 1.58 0.00 0.00 2.27
421 431 2.494059 ACTGCGGGTAATGACATATGC 58.506 47.619 1.58 0.00 0.00 3.14
434 444 0.390603 TCACCAAATCGTACTGCGGG 60.391 55.000 0.00 0.00 41.72 6.13
473 483 1.822371 GGGAATTTTTAAGGCAGGCGA 59.178 47.619 0.00 0.00 0.00 5.54
489 501 2.655090 TTGACTGTGCAGATTGGGAA 57.345 45.000 6.17 0.00 0.00 3.97
498 510 5.512753 TTTCTAAAGCATTTGACTGTGCA 57.487 34.783 0.00 0.00 43.63 4.57
503 515 9.822185 AACTTGATTTTTCTAAAGCATTTGACT 57.178 25.926 0.00 0.00 39.21 3.41
519 531 7.334171 AGCTTTTGTGCTTACAAACTTGATTTT 59.666 29.630 5.20 0.00 40.93 1.82
549 561 6.148480 CACTAAAGATTCTTCAACACTCAGGG 59.852 42.308 0.00 0.00 0.00 4.45
609 881 9.249457 TCGTTGCAAATTCAGACTATCTTATAG 57.751 33.333 0.00 0.00 0.00 1.31
632 904 3.140325 ACCTGGAATTGATGTGTTCGT 57.860 42.857 0.00 0.00 0.00 3.85
633 905 5.818136 ATAACCTGGAATTGATGTGTTCG 57.182 39.130 0.00 0.00 0.00 3.95
827 1121 5.999205 TTTCACAGCCATATTTGGAACAT 57.001 34.783 6.35 0.00 46.92 2.71
901 1195 1.765904 GTCCCATGGGTTTGGTTGTTT 59.234 47.619 30.28 0.00 34.77 2.83
992 1286 9.860898 GAACATAAAAATGGAGCATTCTAGTTT 57.139 29.630 0.00 0.00 34.24 2.66
1045 1343 2.223845 GTCGTATCCTACTCTCTTCGCC 59.776 54.545 0.00 0.00 0.00 5.54
1046 1344 2.223845 GGTCGTATCCTACTCTCTTCGC 59.776 54.545 0.00 0.00 0.00 4.70
1048 1346 3.494251 GTCGGTCGTATCCTACTCTCTTC 59.506 52.174 0.00 0.00 0.00 2.87
1050 1348 2.224257 GGTCGGTCGTATCCTACTCTCT 60.224 54.545 0.00 0.00 0.00 3.10
1051 1349 2.142319 GGTCGGTCGTATCCTACTCTC 58.858 57.143 0.00 0.00 0.00 3.20
1058 1616 2.864343 CTGAATTTGGTCGGTCGTATCC 59.136 50.000 0.00 0.00 0.00 2.59
1059 1617 3.777478 TCTGAATTTGGTCGGTCGTATC 58.223 45.455 0.00 0.00 0.00 2.24
1064 1622 3.120649 CGAAACTCTGAATTTGGTCGGTC 60.121 47.826 0.00 0.00 0.00 4.79
1102 1660 1.420430 TTCCACACCCGAAAGTCTCT 58.580 50.000 0.00 0.00 0.00 3.10
1106 1664 1.675552 CTGTTTCCACACCCGAAAGT 58.324 50.000 0.00 0.00 30.11 2.66
1112 1670 3.670377 GGCGCTGTTTCCACACCC 61.670 66.667 7.64 0.00 0.00 4.61
1114 1672 1.444119 TTCAGGCGCTGTTTCCACAC 61.444 55.000 7.64 0.00 32.61 3.82
1125 1683 2.751837 CCTCCCCTTTTCAGGCGC 60.752 66.667 0.00 0.00 39.20 6.53
1293 1857 0.034670 ACGAAGCGTAGGTAGGAGGT 60.035 55.000 0.00 0.00 38.73 3.85
1302 1866 4.647291 AGTCAAAAATGACGAAGCGTAG 57.353 40.909 3.54 0.00 41.37 3.51
1303 1867 7.997107 ATATAGTCAAAAATGACGAAGCGTA 57.003 32.000 3.54 0.00 41.37 4.42
1324 1888 0.250166 GCACGCCGGGGAGTAAATAT 60.250 55.000 27.23 0.00 0.00 1.28
1533 2097 0.984230 TGGTGATCTCGCCCTTCTTT 59.016 50.000 7.30 0.00 45.66 2.52
1549 2113 0.898320 CTGTCTCGGATGGTCTTGGT 59.102 55.000 0.00 0.00 0.00 3.67
1841 2435 6.963049 ATGTCTCGTGGTACAATTTTAGTC 57.037 37.500 0.00 0.00 44.16 2.59
1855 2449 0.609131 AAAGGGGGCAATGTCTCGTG 60.609 55.000 0.00 0.00 0.00 4.35
1892 2486 9.632807 GTCGCAGAAATGAATATATCTAGAACT 57.367 33.333 0.00 0.00 39.69 3.01
1893 2487 8.579600 CGTCGCAGAAATGAATATATCTAGAAC 58.420 37.037 0.00 0.00 39.69 3.01
1894 2488 8.512138 TCGTCGCAGAAATGAATATATCTAGAA 58.488 33.333 0.00 0.00 39.69 2.10
1895 2489 8.040716 TCGTCGCAGAAATGAATATATCTAGA 57.959 34.615 0.00 0.00 39.69 2.43
1896 2490 7.965655 ACTCGTCGCAGAAATGAATATATCTAG 59.034 37.037 0.00 0.00 39.69 2.43
1897 2491 7.817641 ACTCGTCGCAGAAATGAATATATCTA 58.182 34.615 0.00 0.00 39.69 1.98
1898 2492 6.682746 ACTCGTCGCAGAAATGAATATATCT 58.317 36.000 0.00 0.00 39.69 1.98
1899 2493 6.936222 ACTCGTCGCAGAAATGAATATATC 57.064 37.500 0.00 0.00 39.69 1.63
1900 2494 8.988064 ATTACTCGTCGCAGAAATGAATATAT 57.012 30.769 0.00 0.00 39.69 0.86
1901 2495 8.812147 AATTACTCGTCGCAGAAATGAATATA 57.188 30.769 0.00 0.00 39.69 0.86
1902 2496 7.715265 AATTACTCGTCGCAGAAATGAATAT 57.285 32.000 0.00 0.00 39.69 1.28
1903 2497 7.398746 CAAATTACTCGTCGCAGAAATGAATA 58.601 34.615 0.00 0.00 39.69 1.75
1904 2498 6.250819 CAAATTACTCGTCGCAGAAATGAAT 58.749 36.000 0.00 0.00 39.69 2.57
1905 2499 5.390461 CCAAATTACTCGTCGCAGAAATGAA 60.390 40.000 0.00 0.00 39.69 2.57
1906 2500 4.092821 CCAAATTACTCGTCGCAGAAATGA 59.907 41.667 0.00 0.00 39.69 2.57
1907 2501 4.092821 TCCAAATTACTCGTCGCAGAAATG 59.907 41.667 0.00 0.00 39.69 2.32
1908 2502 4.250464 TCCAAATTACTCGTCGCAGAAAT 58.750 39.130 0.00 0.00 39.69 2.17
1909 2503 3.655486 TCCAAATTACTCGTCGCAGAAA 58.345 40.909 0.00 0.00 39.69 2.52
1910 2504 3.306917 TCCAAATTACTCGTCGCAGAA 57.693 42.857 0.00 0.00 39.69 3.02
1911 2505 2.991190 GTTCCAAATTACTCGTCGCAGA 59.009 45.455 0.00 0.00 0.00 4.26
1912 2506 2.222508 CGTTCCAAATTACTCGTCGCAG 60.223 50.000 0.00 0.00 0.00 5.18
1913 2507 1.722464 CGTTCCAAATTACTCGTCGCA 59.278 47.619 0.00 0.00 0.00 5.10
1914 2508 1.060122 CCGTTCCAAATTACTCGTCGC 59.940 52.381 0.00 0.00 0.00 5.19
1915 2509 2.597305 CTCCGTTCCAAATTACTCGTCG 59.403 50.000 0.00 0.00 0.00 5.12
1916 2510 3.367025 CACTCCGTTCCAAATTACTCGTC 59.633 47.826 0.00 0.00 0.00 4.20
1917 2511 3.006110 TCACTCCGTTCCAAATTACTCGT 59.994 43.478 0.00 0.00 0.00 4.18
1918 2512 3.581755 TCACTCCGTTCCAAATTACTCG 58.418 45.455 0.00 0.00 0.00 4.18
1919 2513 4.566987 ACTCACTCCGTTCCAAATTACTC 58.433 43.478 0.00 0.00 0.00 2.59
1920 2514 4.618920 ACTCACTCCGTTCCAAATTACT 57.381 40.909 0.00 0.00 0.00 2.24
1921 2515 4.628766 GGTACTCACTCCGTTCCAAATTAC 59.371 45.833 0.00 0.00 0.00 1.89
1922 2516 4.283978 TGGTACTCACTCCGTTCCAAATTA 59.716 41.667 0.00 0.00 30.28 1.40
1923 2517 3.071892 TGGTACTCACTCCGTTCCAAATT 59.928 43.478 0.00 0.00 30.28 1.82
1924 2518 2.635915 TGGTACTCACTCCGTTCCAAAT 59.364 45.455 0.00 0.00 30.28 2.32
1925 2519 2.036733 CTGGTACTCACTCCGTTCCAAA 59.963 50.000 0.00 0.00 32.51 3.28
1926 2520 1.616865 CTGGTACTCACTCCGTTCCAA 59.383 52.381 0.00 0.00 32.51 3.53
1927 2521 1.254026 CTGGTACTCACTCCGTTCCA 58.746 55.000 0.00 0.00 32.07 3.53
1928 2522 1.254954 ACTGGTACTCACTCCGTTCC 58.745 55.000 0.00 0.00 0.00 3.62
1929 2523 3.315418 GAAACTGGTACTCACTCCGTTC 58.685 50.000 0.00 0.00 0.00 3.95
1930 2524 2.036862 GGAAACTGGTACTCACTCCGTT 59.963 50.000 0.00 0.00 0.00 4.44
1931 2525 1.617357 GGAAACTGGTACTCACTCCGT 59.383 52.381 0.00 0.00 0.00 4.69
1932 2526 1.067071 GGGAAACTGGTACTCACTCCG 60.067 57.143 0.00 0.00 0.00 4.63
1933 2527 1.278413 GGGGAAACTGGTACTCACTCC 59.722 57.143 0.00 0.00 0.00 3.85
1934 2528 1.067071 CGGGGAAACTGGTACTCACTC 60.067 57.143 0.00 0.00 0.00 3.51
1935 2529 0.974383 CGGGGAAACTGGTACTCACT 59.026 55.000 0.00 0.00 0.00 3.41
1936 2530 0.036671 CCGGGGAAACTGGTACTCAC 60.037 60.000 0.00 0.00 41.03 3.51
1937 2531 1.196104 CCCGGGGAAACTGGTACTCA 61.196 60.000 14.71 0.00 44.78 3.41
1938 2532 1.196766 ACCCGGGGAAACTGGTACTC 61.197 60.000 27.92 0.00 44.78 2.59
1939 2533 0.116940 TACCCGGGGAAACTGGTACT 59.883 55.000 27.92 0.33 44.78 2.73
1940 2534 0.983467 TTACCCGGGGAAACTGGTAC 59.017 55.000 27.92 0.00 44.78 3.34
1941 2535 1.969713 ATTACCCGGGGAAACTGGTA 58.030 50.000 25.54 0.00 44.78 3.25
1942 2536 1.969713 TATTACCCGGGGAAACTGGT 58.030 50.000 25.54 8.20 44.78 4.00
1943 2537 3.555586 CGTATATTACCCGGGGAAACTGG 60.556 52.174 25.54 7.39 45.92 4.00
1944 2538 3.070015 ACGTATATTACCCGGGGAAACTG 59.930 47.826 25.54 14.48 0.00 3.16
1972 2566 7.678947 ACTACTACTACTACAAAGCTTCGAA 57.321 36.000 0.00 0.00 0.00 3.71
1988 2582 9.720769 ATTGCACAATTTTGTACTACTACTACT 57.279 29.630 0.00 0.00 39.91 2.57
2054 2658 0.179225 GACATACAAGCAACACGGCG 60.179 55.000 4.80 4.80 39.27 6.46
2074 2678 4.899457 ACTGCATAATACTGCCTGGTAGTA 59.101 41.667 23.93 23.93 41.58 1.82
2075 2679 3.711704 ACTGCATAATACTGCCTGGTAGT 59.288 43.478 21.18 21.18 41.58 2.73
2076 2680 4.310769 GACTGCATAATACTGCCTGGTAG 58.689 47.826 10.48 10.48 41.58 3.18
2088 2692 3.887621 ACTGGTGTACGACTGCATAAT 57.112 42.857 0.00 0.00 0.00 1.28
2093 2697 3.387397 ACTAAAACTGGTGTACGACTGC 58.613 45.455 0.00 0.00 0.00 4.40
2123 2727 0.318441 TCGACAGAGAGGCACTTTGG 59.682 55.000 7.35 0.00 41.55 3.28
2199 2868 8.827832 ATCTGTTTTCCATTATGAAGATCCAA 57.172 30.769 0.00 0.00 0.00 3.53
2201 2870 8.689972 ACAATCTGTTTTCCATTATGAAGATCC 58.310 33.333 0.00 0.00 0.00 3.36
2202 2871 9.727627 GACAATCTGTTTTCCATTATGAAGATC 57.272 33.333 0.00 0.00 0.00 2.75
2207 2876 6.127647 GCCAGACAATCTGTTTTCCATTATGA 60.128 38.462 5.18 0.00 42.80 2.15
2211 2880 3.896888 TGCCAGACAATCTGTTTTCCATT 59.103 39.130 5.18 0.00 42.80 3.16
2290 2959 2.079925 GCACTGAATCACTTCTCACCC 58.920 52.381 0.00 0.00 32.29 4.61
2318 2987 8.485392 AGGTTTTATTTATATGCATTGCCTTGT 58.515 29.630 3.54 0.00 0.00 3.16
2319 2988 8.767085 CAGGTTTTATTTATATGCATTGCCTTG 58.233 33.333 3.54 0.00 0.00 3.61
2320 2989 8.485392 ACAGGTTTTATTTATATGCATTGCCTT 58.515 29.630 3.54 0.00 0.00 4.35
2456 3370 6.683974 AATCACCATTACTGTTGCTGATAC 57.316 37.500 0.00 0.00 0.00 2.24
2465 3379 8.650143 AAATTGGTCTTAATCACCATTACTGT 57.350 30.769 7.15 0.00 43.66 3.55
2531 3472 5.122396 GTGCTAGATGGTTTAGTGTTCCTTG 59.878 44.000 0.00 0.00 0.00 3.61
2535 3476 6.554334 TTTGTGCTAGATGGTTTAGTGTTC 57.446 37.500 0.00 0.00 0.00 3.18
2537 3478 5.049680 CGTTTTGTGCTAGATGGTTTAGTGT 60.050 40.000 0.00 0.00 0.00 3.55
2546 3487 1.131126 CTGCCCGTTTTGTGCTAGATG 59.869 52.381 0.00 0.00 0.00 2.90
2577 3519 0.242825 CAAGTAGTCCGCACGGAGAA 59.757 55.000 12.96 0.17 46.16 2.87
2710 3652 0.965866 AGACGGCATCTCCAAGACGA 60.966 55.000 0.00 0.00 28.16 4.20


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

AutoCloner maintained by Alex Coulton.