Multiple sequence alignment - TraesCS4D01G240400

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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 TraesCS4D01G240400 chr4D 100.000 2961 0 0 1 2961 402970158 402973118 0.000000e+00 5469
1 TraesCS4D01G240400 chr4D 86.468 1175 88 35 791 1954 383782809 383783923 0.000000e+00 1223
2 TraesCS4D01G240400 chr4D 88.904 757 68 12 2218 2961 415247082 415246329 0.000000e+00 918
3 TraesCS4D01G240400 chr4D 92.033 364 18 6 1 354 402947010 402947372 4.410000e-138 501
4 TraesCS4D01G240400 chr4A 91.381 1311 49 29 605 1908 60343961 60345214 0.000000e+00 1736
5 TraesCS4D01G240400 chr4A 87.419 1081 77 27 791 1868 65466320 65467344 0.000000e+00 1188
6 TraesCS4D01G240400 chr4B 88.736 1092 73 25 791 1872 470971853 470972904 0.000000e+00 1290
7 TraesCS4D01G240400 chr4B 90.781 781 37 15 476 1233 499059267 499060035 0.000000e+00 1011
8 TraesCS4D01G240400 chr4B 91.746 739 40 10 1258 1983 499060034 499060764 0.000000e+00 1007
9 TraesCS4D01G240400 chr4B 86.858 487 47 9 1 485 499057732 499058203 2.020000e-146 529
10 TraesCS4D01G240400 chr4B 85.475 179 22 3 2031 2208 499062657 499062832 1.810000e-42 183
11 TraesCS4D01G240400 chr7D 93.378 740 41 3 2229 2961 140551600 140552338 0.000000e+00 1088
12 TraesCS4D01G240400 chr7D 86.939 490 51 6 2218 2697 115530489 115530003 3.360000e-149 538
13 TraesCS4D01G240400 chr1D 89.460 759 55 8 2226 2961 243257744 243256988 0.000000e+00 935
14 TraesCS4D01G240400 chr1D 88.787 767 63 5 2218 2961 75273338 75274104 0.000000e+00 918
15 TraesCS4D01G240400 chr1D 88.787 767 62 9 2218 2961 189495786 189496551 0.000000e+00 918
16 TraesCS4D01G240400 chr1D 88.598 763 65 7 2218 2958 161672182 161672944 0.000000e+00 907
17 TraesCS4D01G240400 chr1D 88.248 451 47 2 1351 1795 410472045 410471595 4.340000e-148 534
18 TraesCS4D01G240400 chr1D 87.582 459 51 2 1351 1803 410482675 410482217 7.270000e-146 527
19 TraesCS4D01G240400 chr1D 87.387 444 50 3 1351 1788 410490874 410490431 3.410000e-139 505
20 TraesCS4D01G240400 chr3D 89.164 766 60 7 2219 2961 161041718 161040953 0.000000e+00 933
21 TraesCS4D01G240400 chr3D 88.527 767 65 8 2218 2961 314171743 314172509 0.000000e+00 907
22 TraesCS4D01G240400 chr6D 88.527 767 65 9 2218 2961 123599268 123600034 0.000000e+00 907
23 TraesCS4D01G240400 chr6D 88.149 751 79 5 2218 2961 241082697 241083444 0.000000e+00 885
24 TraesCS4D01G240400 chr6D 85.470 702 91 4 2218 2910 251100853 251100154 0.000000e+00 721
25 TraesCS4D01G240400 chr5D 88.005 767 69 12 2218 2961 280130159 280130925 0.000000e+00 885
26 TraesCS4D01G240400 chr2A 86.881 747 90 5 2222 2961 479984279 479983534 0.000000e+00 830
27 TraesCS4D01G240400 chr2D 86.232 552 67 3 2218 2762 257735456 257734907 9.140000e-165 590
28 TraesCS4D01G240400 chr1A 87.140 451 52 2 1351 1795 506288704 506288254 9.470000e-140 507
29 TraesCS4D01G240400 chr2B 77.869 244 32 17 288 525 246376039 246376266 6.660000e-27 132


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 TraesCS4D01G240400 chr4D 402970158 402973118 2960 False 5469.0 5469 100.000 1 2961 1 chr4D.!!$F3 2960
1 TraesCS4D01G240400 chr4D 383782809 383783923 1114 False 1223.0 1223 86.468 791 1954 1 chr4D.!!$F1 1163
2 TraesCS4D01G240400 chr4D 415246329 415247082 753 True 918.0 918 88.904 2218 2961 1 chr4D.!!$R1 743
3 TraesCS4D01G240400 chr4A 60343961 60345214 1253 False 1736.0 1736 91.381 605 1908 1 chr4A.!!$F1 1303
4 TraesCS4D01G240400 chr4A 65466320 65467344 1024 False 1188.0 1188 87.419 791 1868 1 chr4A.!!$F2 1077
5 TraesCS4D01G240400 chr4B 470971853 470972904 1051 False 1290.0 1290 88.736 791 1872 1 chr4B.!!$F1 1081
6 TraesCS4D01G240400 chr4B 499057732 499062832 5100 False 682.5 1011 88.715 1 2208 4 chr4B.!!$F2 2207
7 TraesCS4D01G240400 chr7D 140551600 140552338 738 False 1088.0 1088 93.378 2229 2961 1 chr7D.!!$F1 732
8 TraesCS4D01G240400 chr1D 243256988 243257744 756 True 935.0 935 89.460 2226 2961 1 chr1D.!!$R1 735
9 TraesCS4D01G240400 chr1D 75273338 75274104 766 False 918.0 918 88.787 2218 2961 1 chr1D.!!$F1 743
10 TraesCS4D01G240400 chr1D 189495786 189496551 765 False 918.0 918 88.787 2218 2961 1 chr1D.!!$F3 743
11 TraesCS4D01G240400 chr1D 161672182 161672944 762 False 907.0 907 88.598 2218 2958 1 chr1D.!!$F2 740
12 TraesCS4D01G240400 chr3D 161040953 161041718 765 True 933.0 933 89.164 2219 2961 1 chr3D.!!$R1 742
13 TraesCS4D01G240400 chr3D 314171743 314172509 766 False 907.0 907 88.527 2218 2961 1 chr3D.!!$F1 743
14 TraesCS4D01G240400 chr6D 123599268 123600034 766 False 907.0 907 88.527 2218 2961 1 chr6D.!!$F1 743
15 TraesCS4D01G240400 chr6D 241082697 241083444 747 False 885.0 885 88.149 2218 2961 1 chr6D.!!$F2 743
16 TraesCS4D01G240400 chr6D 251100154 251100853 699 True 721.0 721 85.470 2218 2910 1 chr6D.!!$R1 692
17 TraesCS4D01G240400 chr5D 280130159 280130925 766 False 885.0 885 88.005 2218 2961 1 chr5D.!!$F1 743
18 TraesCS4D01G240400 chr2A 479983534 479984279 745 True 830.0 830 86.881 2222 2961 1 chr2A.!!$R1 739
19 TraesCS4D01G240400 chr2D 257734907 257735456 549 True 590.0 590 86.232 2218 2762 1 chr2D.!!$R1 544

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
585 1657 0.110486 AACACTGGATTGCCGGAAGT 59.89 50.0 5.05 0.0 43.76 3.01 F
1235 2336 0.720027 GGTAAGCCTCTTTTCGTCGC 59.28 55.0 0.00 0.0 0.00 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1654 2768 0.034616 ACTTGCTCTCCACACTCTGC 59.965 55.0 0.00 0.00 0.0 4.26 R
2205 5171 0.475475 TTATGCAGGCCTCCTCATGG 59.525 55.0 17.51 1.34 0.0 3.66 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
48 49 7.891183 TGGCAAATGTATTACCCTTAAAGAAGA 59.109 33.333 0.00 0.00 34.25 2.87
132 133 9.742144 TTTGTAGCATTGGTATTAACCTTAAGA 57.258 29.630 3.36 0.00 46.91 2.10
134 135 9.391006 TGTAGCATTGGTATTAACCTTAAGAAG 57.609 33.333 3.36 0.00 46.91 2.85
135 136 9.609346 GTAGCATTGGTATTAACCTTAAGAAGA 57.391 33.333 3.36 0.00 46.91 2.87
137 138 9.528489 AGCATTGGTATTAACCTTAAGAAGAAA 57.472 29.630 3.36 0.00 46.91 2.52
361 362 4.060288 CGCACAGAAACAGCGTAATAAA 57.940 40.909 0.00 0.00 45.82 1.40
362 363 4.459606 CGCACAGAAACAGCGTAATAAAA 58.540 39.130 0.00 0.00 45.82 1.52
381 382 0.242555 AAAACGCGTAATGGGCAAGG 59.757 50.000 14.46 0.00 0.00 3.61
403 404 3.938963 GCCAATAAAGAATCGACTGACCA 59.061 43.478 0.00 0.00 0.00 4.02
404 405 4.394920 GCCAATAAAGAATCGACTGACCAA 59.605 41.667 0.00 0.00 0.00 3.67
414 415 2.640826 TCGACTGACCAAAAATAGGGGT 59.359 45.455 0.00 0.00 37.70 4.95
427 428 6.658188 AAAATAGGGGTCAATCGAAAACAA 57.342 33.333 0.00 0.00 0.00 2.83
428 429 6.850752 AAATAGGGGTCAATCGAAAACAAT 57.149 33.333 0.00 0.00 0.00 2.71
439 441 7.008628 GTCAATCGAAAACAATTCAGCCAATAG 59.991 37.037 0.00 0.00 0.00 1.73
442 444 4.157656 CGAAAACAATTCAGCCAATAGGGA 59.842 41.667 0.00 0.00 40.01 4.20
445 447 4.046286 ACAATTCAGCCAATAGGGACAA 57.954 40.909 0.00 0.00 40.01 3.18
448 450 2.489938 TCAGCCAATAGGGACAACAC 57.510 50.000 0.00 0.00 40.01 3.32
498 1568 2.089201 CACATCTTGGAGCAGCAATCA 58.911 47.619 0.00 0.00 0.00 2.57
508 1578 3.306225 GGAGCAGCAATCAATGGTCAAAA 60.306 43.478 0.00 0.00 43.91 2.44
542 1613 6.709846 TGACCCAATTTTAAAAATCAGGCAAG 59.290 34.615 4.44 0.00 0.00 4.01
545 1616 7.559533 ACCCAATTTTAAAAATCAGGCAAGTTT 59.440 29.630 4.44 0.00 0.00 2.66
575 1647 4.666512 AGGCTGTCATTTAAACACTGGAT 58.333 39.130 0.00 0.00 0.00 3.41
582 1654 2.570415 TTAAACACTGGATTGCCGGA 57.430 45.000 5.05 0.00 43.76 5.14
585 1657 0.110486 AACACTGGATTGCCGGAAGT 59.890 50.000 5.05 0.00 43.76 3.01
609 1694 5.777526 AAACAATGGAATAATTGCCCCTT 57.222 34.783 0.00 0.00 40.54 3.95
676 1761 2.605366 GCGTGTCTCTCTAATTGCTTCC 59.395 50.000 0.00 0.00 0.00 3.46
695 1780 1.520368 CCGTTATCTCGCGCAAAAAC 58.480 50.000 8.75 2.59 0.00 2.43
699 1784 2.892373 TATCTCGCGCAAAAACCAAG 57.108 45.000 8.75 0.00 0.00 3.61
841 1933 2.358247 TTTTGGCGAGCTCCGGAC 60.358 61.111 8.47 0.00 39.04 4.79
842 1934 2.879233 TTTTGGCGAGCTCCGGACT 61.879 57.895 8.47 2.58 39.04 3.85
843 1935 2.781595 TTTTGGCGAGCTCCGGACTC 62.782 60.000 18.62 18.62 39.04 3.36
888 1980 2.663852 CGTCCACGTTGTGACCCC 60.664 66.667 0.00 0.00 35.23 4.95
1212 2313 2.765807 CCTCGTCAGGGCCCAGAT 60.766 66.667 27.56 0.00 35.89 2.90
1234 2335 2.365408 AGGTAAGCCTCTTTTCGTCG 57.635 50.000 0.00 0.00 42.67 5.12
1235 2336 0.720027 GGTAAGCCTCTTTTCGTCGC 59.280 55.000 0.00 0.00 0.00 5.19
1253 2354 1.001746 CGCCTGACTCTGCCATCATAT 59.998 52.381 0.00 0.00 0.00 1.78
1280 2381 8.662781 TTGTTTACTCCGTATACTCTACGTAT 57.337 34.615 0.00 0.00 41.57 3.06
1352 2457 3.068691 TCGAGCCGACCAAGGAGG 61.069 66.667 0.00 0.00 45.67 4.30
1353 2458 3.068691 CGAGCCGACCAAGGAGGA 61.069 66.667 8.99 0.00 41.22 3.71
1381 2486 2.029666 GCATCGACATCCTCCCCG 59.970 66.667 0.00 0.00 0.00 5.73
1803 2917 4.162096 ACGTCTGAAACTAGCTAGTGTG 57.838 45.455 26.70 15.99 36.50 3.82
1804 2918 3.568853 ACGTCTGAAACTAGCTAGTGTGT 59.431 43.478 26.70 15.02 36.50 3.72
1805 2919 4.758674 ACGTCTGAAACTAGCTAGTGTGTA 59.241 41.667 26.70 11.60 36.50 2.90
1806 2920 5.087397 CGTCTGAAACTAGCTAGTGTGTAC 58.913 45.833 26.70 18.34 36.50 2.90
1955 3077 2.289382 TGGAGCTTCGAATTACTGCACA 60.289 45.455 11.41 6.43 0.00 4.57
1956 3078 2.094417 GGAGCTTCGAATTACTGCACAC 59.906 50.000 0.00 0.00 0.00 3.82
1993 4860 8.662781 TCATTCCACTGTATATGTTTCTTAGC 57.337 34.615 0.00 0.00 0.00 3.09
1995 4862 9.060347 CATTCCACTGTATATGTTTCTTAGCAT 57.940 33.333 0.00 0.00 0.00 3.79
2016 4883 6.575083 CATATACAGTATATGCTTGGTCGC 57.425 41.667 22.31 0.00 40.90 5.19
2029 4896 3.949031 GGTCGCAGAGATGTAGACC 57.051 57.895 8.48 8.48 43.55 3.85
2146 5112 8.606040 ATCACAATTTGAAATTTTGGGTACAG 57.394 30.769 14.61 0.00 37.92 2.74
2160 5126 4.208746 TGGGTACAGGTTTGAAATTCGTT 58.791 39.130 0.00 0.00 0.00 3.85
2163 5129 6.320672 TGGGTACAGGTTTGAAATTCGTTAAA 59.679 34.615 0.00 0.00 0.00 1.52
2166 5132 8.558700 GGTACAGGTTTGAAATTCGTTAAAGTA 58.441 33.333 0.00 0.00 0.00 2.24
2192 5158 6.903883 TTCTAAAAGGACGATGATAGTTGC 57.096 37.500 0.00 0.00 0.00 4.17
2193 5159 5.357257 TCTAAAAGGACGATGATAGTTGCC 58.643 41.667 0.00 0.00 0.00 4.52
2194 5160 2.225068 AAGGACGATGATAGTTGCCG 57.775 50.000 0.00 0.00 0.00 5.69
2195 5161 0.389391 AGGACGATGATAGTTGCCGG 59.611 55.000 0.00 0.00 0.00 6.13
2196 5162 1.222115 GGACGATGATAGTTGCCGGC 61.222 60.000 22.73 22.73 0.00 6.13
2197 5163 1.222115 GACGATGATAGTTGCCGGCC 61.222 60.000 26.77 9.73 0.00 6.13
2198 5164 1.069765 CGATGATAGTTGCCGGCCT 59.930 57.895 26.77 17.64 0.00 5.19
2199 5165 0.317160 CGATGATAGTTGCCGGCCTA 59.683 55.000 26.77 19.40 0.00 3.93
2200 5166 1.670087 CGATGATAGTTGCCGGCCTAG 60.670 57.143 26.77 2.82 0.00 3.02
2201 5167 1.618837 GATGATAGTTGCCGGCCTAGA 59.381 52.381 26.77 7.40 0.00 2.43
2202 5168 1.040646 TGATAGTTGCCGGCCTAGAG 58.959 55.000 26.77 0.00 0.00 2.43
2203 5169 0.318762 GATAGTTGCCGGCCTAGAGG 59.681 60.000 26.77 0.00 38.53 3.69
2214 5180 2.757313 CCTAGAGGCCCATGAGGAG 58.243 63.158 0.00 0.00 38.24 3.69
2215 5181 0.835543 CCTAGAGGCCCATGAGGAGG 60.836 65.000 0.00 0.00 38.24 4.30
2224 5190 0.475475 CCATGAGGAGGCCTGCATAA 59.525 55.000 27.56 11.54 36.89 1.90
2359 5344 2.122167 TTTTCACCTTGCCGGCGTT 61.122 52.632 23.90 1.91 35.61 4.84
2408 5400 2.358003 GCTCCGCTGTCACTGCTT 60.358 61.111 5.02 0.00 0.00 3.91
2433 5425 3.053544 TCTTCCTCGAGTTCCCTCTATGT 60.054 47.826 12.31 0.00 35.43 2.29
2517 5510 3.313526 GGTTTAGGTGCGACTAGTATCGA 59.686 47.826 8.07 0.00 45.13 3.59
2522 5515 2.289820 GGTGCGACTAGTATCGATGTGA 59.710 50.000 8.54 0.00 45.13 3.58
2728 5722 4.464951 TCAATCTGCTCAATGGCTTTGATT 59.535 37.500 15.20 4.98 43.30 2.57
2764 5758 1.215647 GATCCCGCGTTGAGACACT 59.784 57.895 4.92 0.00 0.00 3.55
2818 5812 1.045407 ACACGCACTTCTCTGGGTTA 58.955 50.000 0.00 0.00 35.25 2.85
2925 5919 9.539825 CACTATATCATCCATATAAGCTTCCAC 57.460 37.037 0.00 0.00 30.73 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 9.474313 ACATTTGCCACTAATTAATTCCTTCTA 57.526 29.630 3.39 0.00 0.00 2.10
180 181 2.443887 ACATGTTCAAATGGTGCAGC 57.556 45.000 9.47 9.47 31.46 5.25
276 277 5.274015 TGGATGTAGGGTGAGTGTAACATA 58.726 41.667 0.00 0.00 41.43 2.29
279 280 4.546829 TTGGATGTAGGGTGAGTGTAAC 57.453 45.455 0.00 0.00 0.00 2.50
280 281 5.570205 TTTTGGATGTAGGGTGAGTGTAA 57.430 39.130 0.00 0.00 0.00 2.41
283 284 4.335416 ACATTTTGGATGTAGGGTGAGTG 58.665 43.478 0.00 0.00 0.00 3.51
285 286 4.881850 GGTACATTTTGGATGTAGGGTGAG 59.118 45.833 0.00 0.00 35.43 3.51
290 291 7.889873 TTTATGGGTACATTTTGGATGTAGG 57.110 36.000 0.00 0.00 38.53 3.18
327 328 3.502191 TCTGTGCGTTTTGCTTCTTTT 57.498 38.095 0.00 0.00 46.63 2.27
328 329 3.502191 TTCTGTGCGTTTTGCTTCTTT 57.498 38.095 0.00 0.00 46.63 2.52
329 330 3.179048 GTTTCTGTGCGTTTTGCTTCTT 58.821 40.909 0.00 0.00 46.63 2.52
332 333 2.529151 CTGTTTCTGTGCGTTTTGCTT 58.471 42.857 0.00 0.00 46.63 3.91
361 362 1.336424 CCTTGCCCATTACGCGTTTTT 60.336 47.619 20.78 0.00 0.00 1.94
362 363 0.242555 CCTTGCCCATTACGCGTTTT 59.757 50.000 20.78 1.48 0.00 2.43
381 382 3.938963 TGGTCAGTCGATTCTTTATTGGC 59.061 43.478 0.00 0.00 0.00 4.52
403 404 6.658188 TGTTTTCGATTGACCCCTATTTTT 57.342 33.333 0.00 0.00 0.00 1.94
404 405 6.658188 TTGTTTTCGATTGACCCCTATTTT 57.342 33.333 0.00 0.00 0.00 1.82
409 410 4.148838 TGAATTGTTTTCGATTGACCCCT 58.851 39.130 0.00 0.00 34.36 4.79
410 411 4.485163 CTGAATTGTTTTCGATTGACCCC 58.515 43.478 0.00 0.00 34.36 4.95
414 415 4.844998 TGGCTGAATTGTTTTCGATTGA 57.155 36.364 0.00 0.00 34.36 2.57
427 428 3.245229 TGTGTTGTCCCTATTGGCTGAAT 60.245 43.478 0.00 0.00 0.00 2.57
428 429 2.107378 TGTGTTGTCCCTATTGGCTGAA 59.893 45.455 0.00 0.00 0.00 3.02
439 441 0.738389 CCTGTTGTGTGTGTTGTCCC 59.262 55.000 0.00 0.00 0.00 4.46
442 444 4.592485 TTTTTCCTGTTGTGTGTGTTGT 57.408 36.364 0.00 0.00 0.00 3.32
465 467 3.047796 CAAGATGTGTGCTGCTTGTTTC 58.952 45.455 0.00 0.00 34.54 2.78
466 468 2.223876 CCAAGATGTGTGCTGCTTGTTT 60.224 45.455 0.00 0.00 36.81 2.83
469 471 1.199327 CTCCAAGATGTGTGCTGCTTG 59.801 52.381 0.00 0.00 37.93 4.01
470 472 1.531423 CTCCAAGATGTGTGCTGCTT 58.469 50.000 0.00 0.00 0.00 3.91
472 474 1.239296 TGCTCCAAGATGTGTGCTGC 61.239 55.000 0.00 0.00 0.00 5.25
475 477 1.239296 TGCTGCTCCAAGATGTGTGC 61.239 55.000 0.00 0.00 0.00 4.57
478 480 2.089201 TGATTGCTGCTCCAAGATGTG 58.911 47.619 0.00 0.00 0.00 3.21
511 1581 9.323985 CTGATTTTTAAAATTGGGTCAGTCAAA 57.676 29.630 4.32 0.00 0.00 2.69
517 1588 6.179906 TGCCTGATTTTTAAAATTGGGTCA 57.820 33.333 17.96 14.37 0.00 4.02
545 1616 7.232534 AGTGTTTAAATGACAGCCTCCATTTAA 59.767 33.333 16.86 16.86 45.64 1.52
550 1621 3.820467 CAGTGTTTAAATGACAGCCTCCA 59.180 43.478 0.00 0.00 0.00 3.86
551 1622 3.191371 CCAGTGTTTAAATGACAGCCTCC 59.809 47.826 0.00 0.00 0.00 4.30
575 1647 3.223435 TCCATTGTTTTACTTCCGGCAA 58.777 40.909 0.00 0.00 0.00 4.52
582 1654 7.037658 AGGGGCAATTATTCCATTGTTTTACTT 60.038 33.333 0.00 0.00 36.63 2.24
585 1657 6.882768 AGGGGCAATTATTCCATTGTTTTA 57.117 33.333 0.00 0.00 36.63 1.52
609 1694 0.109272 GTCCAGACGCACGATGAGAA 60.109 55.000 0.00 0.00 0.00 2.87
649 1734 1.934220 TTAGAGAGACACGCAGGCCG 61.934 60.000 0.00 0.00 44.21 6.13
676 1761 1.520368 GTTTTTGCGCGAGATAACGG 58.480 50.000 12.10 0.00 0.00 4.44
695 1780 1.234821 TGCGTTTAGGTCTTGCTTGG 58.765 50.000 0.00 0.00 0.00 3.61
699 1784 2.289547 TGAGTTTGCGTTTAGGTCTTGC 59.710 45.455 0.00 0.00 0.00 4.01
754 1846 1.014564 GGAAGACTCCGGAAAGTGCG 61.015 60.000 5.23 0.00 30.03 5.34
842 1934 4.804420 ATGCAGAGGGCCTCCGGA 62.804 66.667 29.62 21.89 43.89 5.14
843 1935 4.559063 CATGCAGAGGGCCTCCGG 62.559 72.222 29.62 22.37 43.89 5.14
844 1936 4.559063 CCATGCAGAGGGCCTCCG 62.559 72.222 29.62 21.34 43.89 4.63
845 1937 3.415087 ACCATGCAGAGGGCCTCC 61.415 66.667 29.62 16.01 43.89 4.30
846 1938 2.124403 CACCATGCAGAGGGCCTC 60.124 66.667 26.42 26.42 43.89 4.70
847 1939 4.437587 GCACCATGCAGAGGGCCT 62.438 66.667 5.25 5.25 44.26 5.19
977 2069 2.123640 GGGGAGGACGAGCTAGCT 60.124 66.667 19.45 19.45 0.00 3.32
1012 2105 1.959899 CTGTTGCCGATGACGAGTGC 61.960 60.000 0.00 0.00 42.66 4.40
1231 2332 1.520342 GATGGCAGAGTCAGGCGAC 60.520 63.158 4.63 1.99 42.95 5.19
1232 2333 1.332889 ATGATGGCAGAGTCAGGCGA 61.333 55.000 4.63 0.00 0.00 5.54
1233 2334 0.390492 TATGATGGCAGAGTCAGGCG 59.610 55.000 4.63 0.00 0.00 5.52
1234 2335 2.302445 AGATATGATGGCAGAGTCAGGC 59.698 50.000 1.77 1.77 0.00 4.85
1235 2336 4.202336 ACAAGATATGATGGCAGAGTCAGG 60.202 45.833 0.00 0.00 0.00 3.86
1273 2374 7.007188 CACACTCGAAACTTGACTTATACGTAG 59.993 40.741 0.08 0.00 0.00 3.51
1280 2381 3.802139 CAGCACACTCGAAACTTGACTTA 59.198 43.478 0.00 0.00 0.00 2.24
1283 2384 1.933853 ACAGCACACTCGAAACTTGAC 59.066 47.619 0.00 0.00 0.00 3.18
1293 2394 0.249615 TGAGTCAGCACAGCACACTC 60.250 55.000 11.33 11.33 38.86 3.51
1352 2457 3.013990 CGATGCGCTCGTCGTCTC 61.014 66.667 9.73 0.00 44.39 3.36
1654 2768 0.034616 ACTTGCTCTCCACACTCTGC 59.965 55.000 0.00 0.00 0.00 4.26
1803 2917 3.000724 CGCACGTACAGGAGTACTAGTAC 59.999 52.174 23.03 23.03 46.68 2.73
1804 2918 3.190079 CGCACGTACAGGAGTACTAGTA 58.810 50.000 0.00 0.00 46.68 1.82
1805 2919 2.005451 CGCACGTACAGGAGTACTAGT 58.995 52.381 0.00 0.00 46.68 2.57
1806 2920 2.005451 ACGCACGTACAGGAGTACTAG 58.995 52.381 0.00 0.00 46.68 2.57
1930 3052 3.873952 GCAGTAATTCGAAGCTCCAAGAT 59.126 43.478 3.35 0.00 0.00 2.40
1993 4860 6.099341 TGCGACCAAGCATATACTGTATATG 58.901 40.000 30.30 30.30 46.82 1.78
1995 4862 5.475564 TCTGCGACCAAGCATATACTGTATA 59.524 40.000 9.78 9.78 46.97 1.47
1996 4863 4.280929 TCTGCGACCAAGCATATACTGTAT 59.719 41.667 5.53 5.53 46.97 2.29
1997 4864 3.634910 TCTGCGACCAAGCATATACTGTA 59.365 43.478 0.00 0.00 46.97 2.74
1998 4865 2.430694 TCTGCGACCAAGCATATACTGT 59.569 45.455 0.00 0.00 46.97 3.55
1999 4866 3.055591 CTCTGCGACCAAGCATATACTG 58.944 50.000 0.00 0.00 46.97 2.74
2001 4868 3.371102 TCTCTGCGACCAAGCATATAC 57.629 47.619 0.00 0.00 46.97 1.47
2016 4883 8.200120 TGTTCATATTCTTGGTCTACATCTCTG 58.800 37.037 0.00 0.00 0.00 3.35
2055 4922 8.341903 CGGAACATGCATACATTACTGAAAATA 58.658 33.333 0.00 0.00 32.87 1.40
2056 4923 7.066887 TCGGAACATGCATACATTACTGAAAAT 59.933 33.333 0.00 0.00 32.87 1.82
2057 4924 6.372937 TCGGAACATGCATACATTACTGAAAA 59.627 34.615 0.00 0.00 32.87 2.29
2060 4927 5.017294 TCGGAACATGCATACATTACTGA 57.983 39.130 0.00 0.00 32.87 3.41
2061 4928 5.733226 TTCGGAACATGCATACATTACTG 57.267 39.130 0.00 0.00 32.87 2.74
2064 4931 4.450976 AGCTTCGGAACATGCATACATTA 58.549 39.130 0.00 0.00 32.87 1.90
2065 4932 3.282021 AGCTTCGGAACATGCATACATT 58.718 40.909 0.00 0.00 32.87 2.71
2066 4933 2.923121 AGCTTCGGAACATGCATACAT 58.077 42.857 0.00 0.00 36.79 2.29
2068 4935 2.677836 TGAAGCTTCGGAACATGCATAC 59.322 45.455 21.11 0.00 0.00 2.39
2131 5097 8.445275 AATTTCAAACCTGTACCCAAAATTTC 57.555 30.769 0.00 0.00 0.00 2.17
2166 5132 8.398665 GCAACTATCATCGTCCTTTTAGAAAAT 58.601 33.333 0.00 0.00 0.00 1.82
2171 5137 4.209288 CGGCAACTATCATCGTCCTTTTAG 59.791 45.833 0.00 0.00 0.00 1.85
2172 5138 4.116961 CGGCAACTATCATCGTCCTTTTA 58.883 43.478 0.00 0.00 0.00 1.52
2173 5139 2.936498 CGGCAACTATCATCGTCCTTTT 59.064 45.455 0.00 0.00 0.00 2.27
2179 5145 1.227556 GGCCGGCAACTATCATCGT 60.228 57.895 30.85 0.00 0.00 3.73
2181 5147 1.618837 TCTAGGCCGGCAACTATCATC 59.381 52.381 30.85 7.16 0.00 2.92
2183 5149 1.040646 CTCTAGGCCGGCAACTATCA 58.959 55.000 30.85 9.65 0.00 2.15
2196 5162 0.835543 CCTCCTCATGGGCCTCTAGG 60.836 65.000 4.53 8.69 38.53 3.02
2197 5163 1.479368 GCCTCCTCATGGGCCTCTAG 61.479 65.000 4.53 0.00 42.30 2.43
2198 5164 1.460305 GCCTCCTCATGGGCCTCTA 60.460 63.158 4.53 0.00 42.30 2.43
2199 5165 2.771762 GCCTCCTCATGGGCCTCT 60.772 66.667 4.53 0.00 42.30 3.69
2204 5170 1.421346 TATGCAGGCCTCCTCATGGG 61.421 60.000 17.51 0.00 0.00 4.00
2205 5171 0.475475 TTATGCAGGCCTCCTCATGG 59.525 55.000 17.51 1.34 0.00 3.66
2206 5172 1.134007 TGTTATGCAGGCCTCCTCATG 60.134 52.381 17.51 2.90 0.00 3.07
2207 5173 1.142465 CTGTTATGCAGGCCTCCTCAT 59.858 52.381 0.00 9.65 41.42 2.90
2208 5174 0.543277 CTGTTATGCAGGCCTCCTCA 59.457 55.000 0.00 0.92 41.42 3.86
2209 5175 0.833287 TCTGTTATGCAGGCCTCCTC 59.167 55.000 0.00 0.00 45.08 3.71
2210 5176 0.835941 CTCTGTTATGCAGGCCTCCT 59.164 55.000 0.00 0.00 45.08 3.69
2211 5177 0.543749 ACTCTGTTATGCAGGCCTCC 59.456 55.000 0.00 0.00 45.08 4.30
2212 5178 2.804933 GCTACTCTGTTATGCAGGCCTC 60.805 54.545 0.00 0.00 45.08 4.70
2213 5179 1.139853 GCTACTCTGTTATGCAGGCCT 59.860 52.381 0.00 0.00 45.08 5.19
2214 5180 1.139853 AGCTACTCTGTTATGCAGGCC 59.860 52.381 0.00 0.00 45.08 5.19
2215 5181 2.611225 AGCTACTCTGTTATGCAGGC 57.389 50.000 0.00 0.00 45.08 4.85
2216 5182 4.128925 TCAAGCTACTCTGTTATGCAGG 57.871 45.455 0.00 0.00 45.08 4.85
2232 5198 5.127031 CCTCTTATAGGGAGCTAGATCAAGC 59.873 48.000 10.68 0.00 42.32 4.01
2400 5392 2.230025 CTCGAGGAAGAAGAAGCAGTGA 59.770 50.000 3.91 0.00 0.00 3.41
2408 5400 2.606751 AGGGAACTCGAGGAAGAAGA 57.393 50.000 18.41 0.00 32.90 2.87
2517 5510 4.597507 TGAAGAGGTACCTTTCCTTCACAT 59.402 41.667 28.21 5.64 38.49 3.21
2522 5515 6.455690 AGATTTGAAGAGGTACCTTTCCTT 57.544 37.500 17.53 14.81 35.20 3.36
2728 5722 1.885560 TCGAAGCAAATCCCGACAAA 58.114 45.000 0.00 0.00 0.00 2.83
2764 5758 2.882137 CGGCAAACTTCTTGGGTTCTTA 59.118 45.455 0.00 0.00 0.00 2.10
2818 5812 1.808945 CGCAAGATCAACCTCAAGCTT 59.191 47.619 0.00 0.00 43.02 3.74
2925 5919 0.672342 GCCCCAGCTGCATAGAAATG 59.328 55.000 8.66 0.00 35.50 2.32


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

AutoCloner maintained by Alex Coulton.