Multiple sequence alignment - TraesCS2D01G389000

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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 TraesCS2D01G389000 chr2D 100.000 3113 0 0 1 3113 495397678 495400790 0.000000e+00 5749.0
1 TraesCS2D01G389000 chr2B 91.766 1421 89 15 228 1635 583061548 583062953 0.000000e+00 1951.0
2 TraesCS2D01G389000 chr2B 85.745 919 54 29 1664 2578 583062934 583063779 0.000000e+00 900.0
3 TraesCS2D01G389000 chr2B 96.471 340 11 1 2571 2910 583063829 583064167 7.540000e-156 560.0
4 TraesCS2D01G389000 chr2B 94.662 281 8 3 2833 3113 583064160 583064433 2.220000e-116 429.0
5 TraesCS2D01G389000 chr2B 92.079 202 13 3 1 199 583061155 583061356 6.570000e-72 281.0
6 TraesCS2D01G389000 chr2A 95.033 906 36 2 2207 3111 638310843 638309946 0.000000e+00 1415.0
7 TraesCS2D01G389000 chr2A 90.039 1034 55 12 1111 2139 638320458 638319468 0.000000e+00 1295.0
8 TraesCS2D01G389000 chr2A 87.748 555 43 11 1653 2206 638311406 638310876 2.640000e-175 625.0
9 TraesCS2D01G389000 chr2A 91.758 364 22 1 2205 2568 638319395 638319040 1.670000e-137 499.0
10 TraesCS2D01G389000 chrUn 87.623 711 76 8 209 909 71102376 71103084 0.000000e+00 815.0
11 TraesCS2D01G389000 chrUn 87.623 711 76 8 209 909 281490935 281490227 0.000000e+00 815.0
12 TraesCS2D01G389000 chrUn 84.932 73 11 0 2490 2562 319858113 319858041 1.200000e-09 75.0
13 TraesCS2D01G389000 chr3B 86.857 700 71 9 207 896 723662913 723662225 0.000000e+00 763.0
14 TraesCS2D01G389000 chr1B 85.784 619 73 10 258 864 589705685 589705070 2.620000e-180 641.0
15 TraesCS2D01G389000 chr3A 86.691 556 66 5 361 909 377805953 377805399 7.380000e-171 610.0
16 TraesCS2D01G389000 chr3A 86.280 328 37 4 589 909 141823338 141823664 1.780000e-92 350.0
17 TraesCS2D01G389000 chr3A 87.218 266 30 4 210 473 726988822 726988559 1.810000e-77 300.0
18 TraesCS2D01G389000 chr3D 83.453 556 67 10 361 909 288121285 288120748 7.760000e-136 494.0
19 TraesCS2D01G389000 chr5B 88.957 326 29 7 209 531 662963874 662963553 2.250000e-106 396.0
20 TraesCS2D01G389000 chr5B 82.500 160 24 3 234 389 398795655 398795814 1.510000e-28 137.0
21 TraesCS2D01G389000 chr5B 87.324 71 9 0 2489 2559 567154082 567154152 7.160000e-12 82.4
22 TraesCS2D01G389000 chr7D 85.030 334 28 13 229 559 450255885 450256199 1.390000e-83 320.0
23 TraesCS2D01G389000 chr1D 89.333 75 8 0 2492 2566 69266556 69266630 9.190000e-16 95.3
24 TraesCS2D01G389000 chr4D 86.585 82 11 0 2479 2560 32768492 32768411 1.190000e-14 91.6
25 TraesCS2D01G389000 chr5A 88.732 71 8 0 2489 2559 581300953 581301023 1.540000e-13 87.9
26 TraesCS2D01G389000 chr5A 84.000 75 11 1 2486 2560 19104988 19105061 1.550000e-08 71.3
27 TraesCS2D01G389000 chr5D 84.000 75 11 1 2486 2560 28479945 28480018 1.550000e-08 71.3


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 TraesCS2D01G389000 chr2D 495397678 495400790 3112 False 5749.0 5749 100.0000 1 3113 1 chr2D.!!$F1 3112
1 TraesCS2D01G389000 chr2B 583061155 583064433 3278 False 824.2 1951 92.1446 1 3113 5 chr2B.!!$F1 3112
2 TraesCS2D01G389000 chr2A 638309946 638311406 1460 True 1020.0 1415 91.3905 1653 3111 2 chr2A.!!$R1 1458
3 TraesCS2D01G389000 chr2A 638319040 638320458 1418 True 897.0 1295 90.8985 1111 2568 2 chr2A.!!$R2 1457
4 TraesCS2D01G389000 chrUn 71102376 71103084 708 False 815.0 815 87.6230 209 909 1 chrUn.!!$F1 700
5 TraesCS2D01G389000 chrUn 281490227 281490935 708 True 815.0 815 87.6230 209 909 1 chrUn.!!$R1 700
6 TraesCS2D01G389000 chr3B 723662225 723662913 688 True 763.0 763 86.8570 207 896 1 chr3B.!!$R1 689
7 TraesCS2D01G389000 chr1B 589705070 589705685 615 True 641.0 641 85.7840 258 864 1 chr1B.!!$R1 606
8 TraesCS2D01G389000 chr3A 377805399 377805953 554 True 610.0 610 86.6910 361 909 1 chr3A.!!$R1 548
9 TraesCS2D01G389000 chr3D 288120748 288121285 537 True 494.0 494 83.4530 361 909 1 chr3D.!!$R1 548

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
369 539 0.029834 CATGTGCGGCCTTATTCTGC 59.970 55.0 0.00 0.00 36.41 4.26 F
1852 2060 0.107459 GGAGCAGTTGATCTGGGTCC 60.107 60.0 8.28 8.28 43.78 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1909 2117 0.391661 ATCACGGCTCGCACTGAAAT 60.392 50.0 0.00 0.0 0.00 2.17 R
2703 3051 0.108396 TGTTTGGCTCTACAGCTGCA 59.892 50.0 15.27 0.0 46.03 4.41 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
120 124 3.744426 CGGTAACACTTTTAGTGGTCTGG 59.256 47.826 11.17 0.00 44.04 3.86
125 129 6.844097 AACACTTTTAGTGGTCTGGAAAAA 57.156 33.333 11.17 0.00 44.04 1.94
126 130 7.418337 AACACTTTTAGTGGTCTGGAAAAAT 57.582 32.000 11.17 0.00 44.04 1.82
143 147 8.321650 TGGAAAAATGATAGCAAAACCAAATC 57.678 30.769 0.00 0.00 0.00 2.17
148 152 8.866970 AAATGATAGCAAAACCAAATCCATTT 57.133 26.923 0.00 0.00 0.00 2.32
165 169 9.476202 AAATCCATTTTAATAAAATAGGAGCGC 57.524 29.630 21.94 0.00 38.97 5.92
199 203 0.033504 GTTCGTCAGGAAGAGTGGCA 59.966 55.000 0.00 0.00 34.69 4.92
200 204 0.756294 TTCGTCAGGAAGAGTGGCAA 59.244 50.000 0.00 0.00 0.00 4.52
201 205 0.756294 TCGTCAGGAAGAGTGGCAAA 59.244 50.000 0.00 0.00 0.00 3.68
202 206 1.347707 TCGTCAGGAAGAGTGGCAAAT 59.652 47.619 0.00 0.00 0.00 2.32
203 207 2.154462 CGTCAGGAAGAGTGGCAAATT 58.846 47.619 0.00 0.00 0.00 1.82
204 208 2.554032 CGTCAGGAAGAGTGGCAAATTT 59.446 45.455 0.00 0.00 0.00 1.82
205 209 3.004734 CGTCAGGAAGAGTGGCAAATTTT 59.995 43.478 0.00 0.00 0.00 1.82
213 217 7.710907 AGGAAGAGTGGCAAATTTTAGTTTTTC 59.289 33.333 0.00 0.00 0.00 2.29
220 224 6.313905 TGGCAAATTTTAGTTTTTCTTTGCGA 59.686 30.769 10.55 5.36 45.69 5.10
224 228 5.838531 TTTTAGTTTTTCTTTGCGAGGGA 57.161 34.783 0.00 0.00 0.00 4.20
235 402 3.848272 TTGCGAGGGAAAATCATGTTC 57.152 42.857 0.00 0.00 0.00 3.18
369 539 0.029834 CATGTGCGGCCTTATTCTGC 59.970 55.000 0.00 0.00 36.41 4.26
385 556 9.706691 CCTTATTCTGCGATCTACCTATTTTTA 57.293 33.333 0.00 0.00 0.00 1.52
425 597 2.542020 TGCAACATCTTTGAGACGGA 57.458 45.000 0.00 0.00 0.00 4.69
454 626 8.971073 CCACCTAAAACATATTCCTTGATCTTT 58.029 33.333 0.00 0.00 0.00 2.52
483 655 4.104383 ACCTGATTCAAGGAGCTTCAAA 57.896 40.909 0.00 0.00 40.02 2.69
586 758 3.626996 CTCCGCCTCCAATGCACCA 62.627 63.158 0.00 0.00 0.00 4.17
601 773 1.915141 CACCAAGGCAGTTCTGGATT 58.085 50.000 1.97 0.00 0.00 3.01
656 828 5.049198 GTGTGATCACGTAGGATTATACCGA 60.049 44.000 20.54 0.00 34.79 4.69
666 856 2.360165 GGATTATACCGACACCGACTGT 59.640 50.000 0.00 0.00 38.22 3.55
667 857 3.181483 GGATTATACCGACACCGACTGTT 60.181 47.826 0.00 0.00 38.22 3.16
668 858 3.492421 TTATACCGACACCGACTGTTC 57.508 47.619 0.00 0.00 38.22 3.18
669 859 0.529378 ATACCGACACCGACTGTTCC 59.471 55.000 0.00 0.00 38.22 3.62
670 860 0.822944 TACCGACACCGACTGTTCCA 60.823 55.000 0.00 0.00 38.22 3.53
671 861 1.292223 CCGACACCGACTGTTCCAT 59.708 57.895 0.00 0.00 38.22 3.41
672 862 0.736325 CCGACACCGACTGTTCCATC 60.736 60.000 0.00 0.00 38.22 3.51
673 863 0.243907 CGACACCGACTGTTCCATCT 59.756 55.000 0.00 0.00 38.22 2.90
674 864 1.471287 CGACACCGACTGTTCCATCTA 59.529 52.381 0.00 0.00 38.22 1.98
697 887 3.302870 CCTGTACAAACGAACCGTCAAAG 60.303 47.826 0.00 0.00 39.99 2.77
791 984 6.801539 TCATTGTTGGATAATAGAATCGGC 57.198 37.500 0.00 0.00 0.00 5.54
849 1051 6.992123 TGTTTGATAGCAAGGAATCGACATAT 59.008 34.615 0.00 0.00 35.04 1.78
853 1055 8.298729 TGATAGCAAGGAATCGACATATCTAT 57.701 34.615 0.00 0.00 0.00 1.98
924 1126 7.930865 TGGGTGAGTTCAAAATTTTATTTGAGG 59.069 33.333 2.44 0.00 46.63 3.86
1005 1207 4.330074 CGTTTGATCTGGCCTAACAACTAG 59.670 45.833 3.32 0.00 0.00 2.57
1006 1208 5.246307 GTTTGATCTGGCCTAACAACTAGT 58.754 41.667 3.32 0.00 0.00 2.57
1008 1210 6.614694 TTGATCTGGCCTAACAACTAGTAA 57.385 37.500 3.32 0.00 0.00 2.24
1009 1211 6.614694 TGATCTGGCCTAACAACTAGTAAA 57.385 37.500 3.32 0.00 0.00 2.01
1010 1212 7.011499 TGATCTGGCCTAACAACTAGTAAAA 57.989 36.000 3.32 0.00 0.00 1.52
1012 1214 6.429521 TCTGGCCTAACAACTAGTAAAACT 57.570 37.500 3.32 0.00 0.00 2.66
1013 1215 6.228258 TCTGGCCTAACAACTAGTAAAACTG 58.772 40.000 3.32 0.00 0.00 3.16
1014 1216 5.932455 TGGCCTAACAACTAGTAAAACTGT 58.068 37.500 3.32 0.00 0.00 3.55
1015 1217 5.761234 TGGCCTAACAACTAGTAAAACTGTG 59.239 40.000 3.32 0.00 0.00 3.66
1016 1218 5.993441 GGCCTAACAACTAGTAAAACTGTGA 59.007 40.000 0.00 0.00 0.00 3.58
1017 1219 6.147328 GGCCTAACAACTAGTAAAACTGTGAG 59.853 42.308 0.00 0.00 0.00 3.51
1018 1220 6.927381 GCCTAACAACTAGTAAAACTGTGAGA 59.073 38.462 9.71 0.00 0.00 3.27
1047 1249 0.469144 TTGTTTGCCACCCTCTTCCC 60.469 55.000 0.00 0.00 0.00 3.97
1072 1274 2.289195 TGACGTCCGCCAAGTAATTTCT 60.289 45.455 14.12 0.00 0.00 2.52
1243 1451 3.876300 CGCAGCCCTAAGTGTGAC 58.124 61.111 0.00 0.00 0.00 3.67
1299 1507 0.802222 AAGACATCGACATGGACGCG 60.802 55.000 3.53 3.53 33.82 6.01
1628 1836 2.513204 CCATGCTGGCGACTGGAG 60.513 66.667 0.00 0.00 32.19 3.86
1629 1837 3.200593 CATGCTGGCGACTGGAGC 61.201 66.667 0.00 0.00 32.19 4.70
1630 1838 4.827087 ATGCTGGCGACTGGAGCG 62.827 66.667 0.00 0.00 35.36 5.03
1822 2030 1.357258 GCGTGGTGAGATCACTGCTG 61.357 60.000 12.43 2.68 45.73 4.41
1847 2055 6.072175 GGAGTATAGTAGGAGCAGTTGATCTG 60.072 46.154 0.00 0.00 46.12 2.90
1848 2056 5.772672 AGTATAGTAGGAGCAGTTGATCTGG 59.227 44.000 0.00 0.00 43.78 3.86
1849 2057 2.114616 AGTAGGAGCAGTTGATCTGGG 58.885 52.381 0.00 0.00 43.78 4.45
1850 2058 1.834263 GTAGGAGCAGTTGATCTGGGT 59.166 52.381 0.00 0.00 43.78 4.51
1851 2059 0.908198 AGGAGCAGTTGATCTGGGTC 59.092 55.000 0.00 0.00 43.78 4.46
1852 2060 0.107459 GGAGCAGTTGATCTGGGTCC 60.107 60.000 8.28 8.28 43.78 4.46
1853 2061 0.908198 GAGCAGTTGATCTGGGTCCT 59.092 55.000 0.00 0.00 43.78 3.85
1854 2062 0.908198 AGCAGTTGATCTGGGTCCTC 59.092 55.000 0.00 0.00 43.78 3.71
1899 2107 4.871933 TGTTCAACTCTGTCTATCTGCA 57.128 40.909 0.00 0.00 0.00 4.41
1909 2117 7.161404 ACTCTGTCTATCTGCATGTGTTAAAA 58.839 34.615 0.00 0.00 0.00 1.52
1918 2126 5.691305 TCTGCATGTGTTAAAATTTCAGTGC 59.309 36.000 0.00 0.71 0.00 4.40
1923 2131 3.668656 GTGTTAAAATTTCAGTGCGAGCC 59.331 43.478 0.00 0.00 0.00 4.70
1950 2158 0.952280 TCGTAGCACGATCTGGATCC 59.048 55.000 4.20 4.20 46.73 3.36
1953 2161 1.000283 GTAGCACGATCTGGATCCTGG 60.000 57.143 17.73 8.65 34.40 4.45
1954 2162 1.070445 GCACGATCTGGATCCTGGG 59.930 63.158 17.73 10.35 34.40 4.45
1962 2170 3.199442 TCTGGATCCTGGGTCTTGTAA 57.801 47.619 17.73 0.00 0.00 2.41
1964 2172 3.455910 TCTGGATCCTGGGTCTTGTAATG 59.544 47.826 17.73 0.00 0.00 1.90
1968 2176 5.071788 TGGATCCTGGGTCTTGTAATGATAC 59.928 44.000 14.23 0.00 0.00 2.24
1974 2182 4.780554 TGGGTCTTGTAATGATACTGTGGA 59.219 41.667 0.00 0.00 32.98 4.02
1975 2183 5.428457 TGGGTCTTGTAATGATACTGTGGAT 59.572 40.000 0.00 0.00 32.98 3.41
1976 2184 5.992217 GGGTCTTGTAATGATACTGTGGATC 59.008 44.000 0.00 0.00 32.98 3.36
1977 2185 6.408092 GGGTCTTGTAATGATACTGTGGATCA 60.408 42.308 0.00 0.00 37.70 2.92
1979 2187 7.268586 GTCTTGTAATGATACTGTGGATCACT 58.731 38.462 0.00 0.00 36.18 3.41
1983 2191 5.824904 AATGATACTGTGGATCACTTTGC 57.175 39.130 0.00 0.00 36.18 3.68
1988 2196 4.019792 ACTGTGGATCACTTTGCATGTA 57.980 40.909 0.00 0.00 35.11 2.29
1989 2197 3.753272 ACTGTGGATCACTTTGCATGTAC 59.247 43.478 0.00 0.00 35.11 2.90
1990 2198 3.749226 TGTGGATCACTTTGCATGTACA 58.251 40.909 0.00 0.00 35.11 2.90
1998 2206 4.637977 TCACTTTGCATGTACAAGTGTTCA 59.362 37.500 21.60 6.19 33.84 3.18
2102 2310 4.705991 TCATGTAGCTTCATGGCAAAATCA 59.294 37.500 26.99 7.94 43.52 2.57
2119 2327 3.904136 ATCACAGCAAGAAAAACGGAG 57.096 42.857 0.00 0.00 0.00 4.63
2154 2365 4.963318 TCTTCTGTTTGAGGTCACATCT 57.037 40.909 0.00 0.00 0.00 2.90
2182 2393 3.497227 GCCCAGGTTACAGGTTCAAGTTA 60.497 47.826 0.00 0.00 0.00 2.24
2196 2407 9.755064 CAGGTTCAAGTTATACAAAGAAATACG 57.245 33.333 0.00 0.00 0.00 3.06
2228 2503 2.738135 GAGATCCTACGCTCTTTGCTC 58.262 52.381 0.00 0.00 40.11 4.26
2270 2545 1.741145 TGCATACATTCTGTGCAGCTG 59.259 47.619 10.11 10.11 43.30 4.24
2272 2547 1.065102 CATACATTCTGTGCAGCTGGC 59.935 52.381 17.12 8.54 45.13 4.85
2326 2601 5.441500 TGAGTCAACACCTGGATTTTTACA 58.558 37.500 0.00 0.00 0.00 2.41
2365 2640 8.103948 ACTCAGAAACACAAATTATCAGAAGG 57.896 34.615 0.00 0.00 0.00 3.46
2423 2698 3.730061 GCTGCACGAAAATCTTCCATGAG 60.730 47.826 0.00 0.00 0.00 2.90
2424 2699 3.673902 TGCACGAAAATCTTCCATGAGA 58.326 40.909 0.00 0.00 0.00 3.27
2428 2703 5.008415 GCACGAAAATCTTCCATGAGATCAT 59.992 40.000 0.00 0.00 35.37 2.45
2443 2718 4.610605 AGATCATGATCTCAAGAGGCTG 57.389 45.455 28.92 0.00 44.37 4.85
2444 2719 4.224762 AGATCATGATCTCAAGAGGCTGA 58.775 43.478 28.92 0.00 44.37 4.26
2445 2720 4.282449 AGATCATGATCTCAAGAGGCTGAG 59.718 45.833 28.92 0.00 44.37 3.35
2446 2721 3.372897 TCATGATCTCAAGAGGCTGAGT 58.627 45.455 0.00 0.00 42.93 3.41
2447 2722 3.132467 TCATGATCTCAAGAGGCTGAGTG 59.868 47.826 0.00 0.00 42.93 3.51
2448 2723 2.812658 TGATCTCAAGAGGCTGAGTGA 58.187 47.619 0.00 0.00 42.93 3.41
2449 2724 2.495270 TGATCTCAAGAGGCTGAGTGAC 59.505 50.000 0.00 0.00 42.93 3.67
2676 3024 1.915266 TGTCTCTGTGAGGCCTGGG 60.915 63.158 12.00 0.00 32.68 4.45
3001 3419 9.810545 CTGAAAGAAAGTACTAGGAAGGAATAG 57.189 37.037 0.00 0.00 34.07 1.73
3074 3493 6.181255 GCAACGCAAATATATCGATCTGATC 58.819 40.000 0.00 7.60 38.57 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 1.665442 CCCGCCCTTCTTTGTTTGG 59.335 57.895 0.00 0.00 0.00 3.28
11 12 3.623703 GACCTTCACCCCGCCCTTC 62.624 68.421 0.00 0.00 0.00 3.46
84 87 7.870509 AAGTGTTACCGATACATGAGTAGTA 57.129 36.000 0.00 0.00 32.86 1.82
115 119 6.454795 TGGTTTTGCTATCATTTTTCCAGAC 58.545 36.000 0.00 0.00 0.00 3.51
120 124 8.321650 TGGATTTGGTTTTGCTATCATTTTTC 57.678 30.769 0.00 0.00 0.00 2.29
125 129 9.956640 TTAAAATGGATTTGGTTTTGCTATCAT 57.043 25.926 0.00 0.00 32.27 2.45
126 130 9.956640 ATTAAAATGGATTTGGTTTTGCTATCA 57.043 25.926 0.00 0.00 32.27 2.15
143 147 6.435428 ACGCGCTCCTATTTTATTAAAATGG 58.565 36.000 19.88 17.33 41.01 3.16
148 152 5.987347 AGCTAACGCGCTCCTATTTTATTAA 59.013 36.000 5.73 0.00 42.32 1.40
188 192 7.710907 AGAAAAACTAAAATTTGCCACTCTTCC 59.289 33.333 0.00 0.00 0.00 3.46
199 203 7.269316 TCCCTCGCAAAGAAAAACTAAAATTT 58.731 30.769 0.00 0.00 0.00 1.82
200 204 6.811954 TCCCTCGCAAAGAAAAACTAAAATT 58.188 32.000 0.00 0.00 0.00 1.82
201 205 6.399639 TCCCTCGCAAAGAAAAACTAAAAT 57.600 33.333 0.00 0.00 0.00 1.82
202 206 5.838531 TCCCTCGCAAAGAAAAACTAAAA 57.161 34.783 0.00 0.00 0.00 1.52
203 207 5.838531 TTCCCTCGCAAAGAAAAACTAAA 57.161 34.783 0.00 0.00 0.00 1.85
204 208 5.838531 TTTCCCTCGCAAAGAAAAACTAA 57.161 34.783 0.00 0.00 0.00 2.24
205 209 5.838531 TTTTCCCTCGCAAAGAAAAACTA 57.161 34.783 0.00 0.00 36.75 2.24
213 217 3.855689 ACATGATTTTCCCTCGCAAAG 57.144 42.857 0.00 0.00 0.00 2.77
235 402 7.219484 ACTCCCACTGTTGATTAAATGAAAG 57.781 36.000 0.00 0.00 0.00 2.62
250 417 6.573664 TTTCAAATGATTGTACTCCCACTG 57.426 37.500 0.00 0.00 37.79 3.66
385 556 6.403049 TGCAAGAAAGATCAATGCAAATCAT 58.597 32.000 0.00 0.00 43.36 2.45
425 597 4.230745 AGGAATATGTTTTAGGTGGCGT 57.769 40.909 0.00 0.00 0.00 5.68
483 655 3.976339 GCAGACTATGCGGAGATGT 57.024 52.632 0.00 0.00 46.99 3.06
501 673 0.471617 CCTGCCTATCCAGGTGAAGG 59.528 60.000 0.10 0.00 45.87 3.46
519 691 0.678048 GACATTGCACTGGACTCCCC 60.678 60.000 9.06 0.00 0.00 4.81
586 758 3.618351 CAGATGAATCCAGAACTGCCTT 58.382 45.455 0.00 0.00 0.00 4.35
601 773 1.592400 CTACGCGGCATGCAGATGA 60.592 57.895 22.57 4.03 46.97 2.92
649 821 1.745087 GGAACAGTCGGTGTCGGTATA 59.255 52.381 0.00 0.00 39.03 1.47
666 856 5.232463 GTTCGTTTGTACAGGTAGATGGAA 58.768 41.667 0.00 0.00 0.00 3.53
667 857 4.322198 GGTTCGTTTGTACAGGTAGATGGA 60.322 45.833 0.00 0.00 0.00 3.41
668 858 3.930848 GGTTCGTTTGTACAGGTAGATGG 59.069 47.826 0.00 0.00 0.00 3.51
669 859 3.611113 CGGTTCGTTTGTACAGGTAGATG 59.389 47.826 0.00 0.00 0.00 2.90
670 860 3.256631 ACGGTTCGTTTGTACAGGTAGAT 59.743 43.478 0.00 0.00 36.35 1.98
671 861 2.622942 ACGGTTCGTTTGTACAGGTAGA 59.377 45.455 0.00 0.00 36.35 2.59
672 862 2.982470 GACGGTTCGTTTGTACAGGTAG 59.018 50.000 0.00 0.00 41.37 3.18
673 863 2.360483 TGACGGTTCGTTTGTACAGGTA 59.640 45.455 0.00 0.00 41.37 3.08
674 864 1.136695 TGACGGTTCGTTTGTACAGGT 59.863 47.619 0.00 0.00 41.37 4.00
849 1051 8.294954 AGGTGTCGAAGAAATTTCTCTATAGA 57.705 34.615 20.71 12.45 39.69 1.98
871 1073 2.052690 CACTGATCCCGGTCGAGGT 61.053 63.158 0.00 0.00 0.00 3.85
964 1166 3.547649 ACGGCGACAGGTTTTAAATTC 57.452 42.857 16.62 0.00 0.00 2.17
965 1167 3.994204 AACGGCGACAGGTTTTAAATT 57.006 38.095 16.62 0.00 0.00 1.82
968 1170 2.286872 TCAAACGGCGACAGGTTTTAA 58.713 42.857 16.62 0.00 34.33 1.52
1024 1226 2.159179 AGAGGGTGGCAAACAAAAGT 57.841 45.000 0.00 0.00 0.00 2.66
1029 1231 1.152830 GGGAAGAGGGTGGCAAACA 59.847 57.895 0.00 0.00 0.00 2.83
1047 1249 0.172578 TACTTGGCGGACGTCAGATG 59.827 55.000 20.25 5.95 0.00 2.90
1243 1451 1.218763 CGCAGATTGCAGAGATGGAG 58.781 55.000 1.69 0.00 45.36 3.86
1512 1720 4.150454 CCTCCGCCTCCTCCTCCT 62.150 72.222 0.00 0.00 0.00 3.69
1822 2030 6.007703 AGATCAACTGCTCCTACTATACTCC 58.992 44.000 0.00 0.00 0.00 3.85
1847 2055 1.687493 CTCCCAGACCTGAGGACCC 60.687 68.421 4.99 0.00 0.00 4.46
1848 2056 4.042251 CTCCCAGACCTGAGGACC 57.958 66.667 4.99 0.00 0.00 4.46
1852 2060 1.693062 CATCATCCTCCCAGACCTGAG 59.307 57.143 0.00 0.00 0.00 3.35
1853 2061 1.008815 ACATCATCCTCCCAGACCTGA 59.991 52.381 0.00 0.00 0.00 3.86
1854 2062 1.140452 CACATCATCCTCCCAGACCTG 59.860 57.143 0.00 0.00 0.00 4.00
1869 2077 4.576463 AGACAGAGTTGAACAAACCACATC 59.424 41.667 0.00 0.00 39.85 3.06
1899 2107 4.917415 GCTCGCACTGAAATTTTAACACAT 59.083 37.500 0.00 0.00 0.00 3.21
1909 2117 0.391661 ATCACGGCTCGCACTGAAAT 60.392 50.000 0.00 0.00 0.00 2.17
1918 2126 0.999228 GCTACGATCATCACGGCTCG 60.999 60.000 0.00 0.00 37.17 5.03
1923 2131 3.526825 TCGTGCTACGATCATCACG 57.473 52.632 15.40 15.40 46.73 4.35
1950 2158 5.104941 TCCACAGTATCATTACAAGACCCAG 60.105 44.000 0.00 0.00 0.00 4.45
1953 2161 6.480320 GTGATCCACAGTATCATTACAAGACC 59.520 42.308 0.00 0.00 35.87 3.85
1954 2162 7.268586 AGTGATCCACAGTATCATTACAAGAC 58.731 38.462 0.00 0.00 35.87 3.01
1962 2170 4.847198 TGCAAAGTGATCCACAGTATCAT 58.153 39.130 0.00 0.00 35.87 2.45
1964 2172 4.637534 ACATGCAAAGTGATCCACAGTATC 59.362 41.667 0.00 0.00 36.74 2.24
1968 2176 3.752747 TGTACATGCAAAGTGATCCACAG 59.247 43.478 5.51 0.00 36.74 3.66
1974 2182 5.299028 TGAACACTTGTACATGCAAAGTGAT 59.701 36.000 28.58 21.81 34.61 3.06
1975 2183 4.637977 TGAACACTTGTACATGCAAAGTGA 59.362 37.500 28.58 13.44 34.61 3.41
1976 2184 4.919206 TGAACACTTGTACATGCAAAGTG 58.081 39.130 23.73 23.73 35.58 3.16
1977 2185 5.574891 TTGAACACTTGTACATGCAAAGT 57.425 34.783 8.58 0.01 0.00 2.66
1979 2187 7.038048 TGAAATTGAACACTTGTACATGCAAA 58.962 30.769 8.58 0.00 0.00 3.68
1988 2196 9.337396 TCTGTTATACTGAAATTGAACACTTGT 57.663 29.630 0.00 0.00 0.00 3.16
2026 2234 5.163632 CCAGCAGCACATGTTGATTATGTAA 60.164 40.000 0.00 0.00 42.36 2.41
2102 2310 1.388547 TGCTCCGTTTTTCTTGCTGT 58.611 45.000 0.00 0.00 0.00 4.40
2119 2327 1.135575 CAGAAGAATGAGCCCGTTTGC 60.136 52.381 0.00 0.00 0.00 3.68
2154 2365 1.369692 CTGTAACCTGGGCACGACA 59.630 57.895 0.00 0.00 0.00 4.35
2182 2393 8.019094 CGGGTTTTTCTTCGTATTTCTTTGTAT 58.981 33.333 0.00 0.00 0.00 2.29
2196 2407 3.864003 CGTAGGATCTCGGGTTTTTCTTC 59.136 47.826 0.00 0.00 0.00 2.87
2228 2503 6.088824 GCAAGTTTGTCTTCTATGGTTGATG 58.911 40.000 0.00 0.00 33.63 3.07
2270 2545 0.459934 CAGAGTGCTGAGCTACTGCC 60.460 60.000 12.90 2.18 45.17 4.85
2272 2547 2.029560 TCAACAGAGTGCTGAGCTACTG 60.030 50.000 18.34 18.34 45.17 2.74
2304 2579 6.575162 ATGTAAAAATCCAGGTGTTGACTC 57.425 37.500 0.00 0.00 0.00 3.36
2326 2601 1.611977 TCTGAGTCCGACGTTGTCAAT 59.388 47.619 1.30 0.00 32.09 2.57
2423 2698 4.039488 ACTCAGCCTCTTGAGATCATGATC 59.961 45.833 25.42 25.42 45.95 2.92
2424 2699 3.968649 ACTCAGCCTCTTGAGATCATGAT 59.031 43.478 8.25 8.25 45.95 2.45
2428 2703 2.495270 GTCACTCAGCCTCTTGAGATCA 59.505 50.000 9.78 0.00 45.95 2.92
2429 2704 2.479389 CGTCACTCAGCCTCTTGAGATC 60.479 54.545 9.78 0.00 45.95 2.75
2430 2705 1.476085 CGTCACTCAGCCTCTTGAGAT 59.524 52.381 9.78 0.00 45.95 2.75
2431 2706 0.884514 CGTCACTCAGCCTCTTGAGA 59.115 55.000 9.78 0.00 45.95 3.27
2433 2708 0.884514 CTCGTCACTCAGCCTCTTGA 59.115 55.000 0.00 0.00 0.00 3.02
2434 2709 0.108898 CCTCGTCACTCAGCCTCTTG 60.109 60.000 0.00 0.00 0.00 3.02
2435 2710 1.882989 GCCTCGTCACTCAGCCTCTT 61.883 60.000 0.00 0.00 0.00 2.85
2436 2711 2.347322 GCCTCGTCACTCAGCCTCT 61.347 63.158 0.00 0.00 0.00 3.69
2437 2712 1.882989 AAGCCTCGTCACTCAGCCTC 61.883 60.000 0.00 0.00 0.00 4.70
2438 2713 1.882989 GAAGCCTCGTCACTCAGCCT 61.883 60.000 0.00 0.00 0.00 4.58
2439 2714 1.446966 GAAGCCTCGTCACTCAGCC 60.447 63.158 0.00 0.00 0.00 4.85
2440 2715 0.037790 AAGAAGCCTCGTCACTCAGC 60.038 55.000 0.00 0.00 0.00 4.26
2441 2716 1.543802 AGAAGAAGCCTCGTCACTCAG 59.456 52.381 1.05 0.00 32.96 3.35
2442 2717 1.621992 AGAAGAAGCCTCGTCACTCA 58.378 50.000 1.05 0.00 32.96 3.41
2443 2718 2.478879 GCTAGAAGAAGCCTCGTCACTC 60.479 54.545 1.05 0.00 36.45 3.51
2444 2719 1.474879 GCTAGAAGAAGCCTCGTCACT 59.525 52.381 1.05 0.00 36.45 3.41
2445 2720 1.915952 GCTAGAAGAAGCCTCGTCAC 58.084 55.000 1.05 0.00 36.45 3.67
2676 3024 0.536915 GAGCTTGGATCCTGGATGCC 60.537 60.000 23.25 18.41 29.18 4.40
2703 3051 0.108396 TGTTTGGCTCTACAGCTGCA 59.892 50.000 15.27 0.00 46.03 4.41
3001 3419 4.338400 GGTGTCCCAAAGCCAGTTATAATC 59.662 45.833 0.00 0.00 0.00 1.75
3005 3423 1.427368 TGGTGTCCCAAAGCCAGTTAT 59.573 47.619 0.00 0.00 37.98 1.89
3054 3473 6.698766 TGGATGATCAGATCGATATATTTGCG 59.301 38.462 0.00 0.00 33.17 4.85
3074 3493 4.445452 AAAATGCAGTTACAGCTGGATG 57.555 40.909 19.93 6.95 44.82 3.51


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

AutoCloner maintained by Alex Coulton.