Multiple sequence alignment - TraesCS5D01G478500

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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 TraesCS5D01G478500 chr5D 100.000 2600 0 0 1 2600 517269633 517272232 0.000000e+00 4802.0
1 TraesCS5D01G478500 chr5D 89.720 1537 77 17 124 1610 517316907 517318412 0.000000e+00 1888.0
2 TraesCS5D01G478500 chr5D 98.392 995 16 0 1606 2600 300774283 300773289 0.000000e+00 1749.0
3 TraesCS5D01G478500 chr5D 82.597 724 87 24 434 1129 517360753 517360041 1.030000e-168 603.0
4 TraesCS5D01G478500 chr5D 84.533 375 35 13 1160 1531 517360046 517359692 1.480000e-92 350.0
5 TraesCS5D01G478500 chr5D 97.561 41 1 0 1 41 517316868 517316908 1.290000e-08 71.3
6 TraesCS5D01G478500 chr1D 98.991 991 10 0 1610 2600 289519656 289520646 0.000000e+00 1775.0
7 TraesCS5D01G478500 chr1D 98.587 991 13 1 1610 2600 67686316 67687305 0.000000e+00 1751.0
8 TraesCS5D01G478500 chr7D 98.794 995 11 1 1607 2600 518648639 518649633 0.000000e+00 1770.0
9 TraesCS5D01G478500 chrUn 98.687 990 13 0 1611 2600 238793435 238792446 0.000000e+00 1757.0
10 TraesCS5D01G478500 chr3D 98.688 991 12 1 1611 2600 584959024 584958034 0.000000e+00 1757.0
11 TraesCS5D01G478500 chr3D 98.395 997 12 3 1608 2600 505968742 505967746 0.000000e+00 1749.0
12 TraesCS5D01G478500 chr4D 98.586 990 14 0 1611 2600 480137037 480136048 0.000000e+00 1751.0
13 TraesCS5D01G478500 chr2D 98.108 1004 16 3 1599 2600 20699694 20700696 0.000000e+00 1746.0
14 TraesCS5D01G478500 chr5B 88.966 1305 69 24 77 1338 649539558 649540830 0.000000e+00 1543.0
15 TraesCS5D01G478500 chr5B 90.010 1001 53 21 559 1536 649729275 649730251 0.000000e+00 1251.0
16 TraesCS5D01G478500 chr5B 86.156 744 43 22 693 1432 649859562 649858875 0.000000e+00 749.0
17 TraesCS5D01G478500 chr5B 89.757 371 14 8 1 370 649728767 649729114 1.100000e-123 453.0
18 TraesCS5D01G478500 chr5B 93.421 76 5 0 1 76 649537294 649537369 2.110000e-21 113.0
19 TraesCS5D01G478500 chr5B 95.833 48 2 0 438 485 649729233 649729280 7.710000e-11 78.7
20 TraesCS5D01G478500 chr5A 88.620 993 50 26 641 1608 644358389 644359343 0.000000e+00 1149.0
21 TraesCS5D01G478500 chr5A 86.556 662 39 16 693 1336 644456299 644455670 0.000000e+00 684.0
22 TraesCS5D01G478500 chr5A 90.287 453 20 7 891 1336 644501720 644501285 2.900000e-159 571.0
23 TraesCS5D01G478500 chr5A 83.670 643 61 21 697 1338 644445324 644444725 1.350000e-157 566.0
24 TraesCS5D01G478500 chr5A 83.566 572 36 23 123 640 644357595 644358162 1.400000e-132 483.0
25 TraesCS5D01G478500 chr5A 92.000 100 5 1 1 97 644357416 644357515 1.250000e-28 137.0
26 TraesCS5D01G478500 chr4A 96.078 51 2 0 1 51 388678747 388678797 1.660000e-12 84.2
27 TraesCS5D01G478500 chr3A 94.444 54 3 0 1 54 435387163 435387110 1.660000e-12 84.2
28 TraesCS5D01G478500 chr2A 92.593 54 4 0 1 54 69376072 69376019 7.710000e-11 78.7


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 TraesCS5D01G478500 chr5D 517269633 517272232 2599 False 4802.000000 4802 100.000000 1 2600 1 chr5D.!!$F1 2599
1 TraesCS5D01G478500 chr5D 300773289 300774283 994 True 1749.000000 1749 98.392000 1606 2600 1 chr5D.!!$R1 994
2 TraesCS5D01G478500 chr5D 517316868 517318412 1544 False 979.650000 1888 93.640500 1 1610 2 chr5D.!!$F2 1609
3 TraesCS5D01G478500 chr5D 517359692 517360753 1061 True 476.500000 603 83.565000 434 1531 2 chr5D.!!$R2 1097
4 TraesCS5D01G478500 chr1D 289519656 289520646 990 False 1775.000000 1775 98.991000 1610 2600 1 chr1D.!!$F2 990
5 TraesCS5D01G478500 chr1D 67686316 67687305 989 False 1751.000000 1751 98.587000 1610 2600 1 chr1D.!!$F1 990
6 TraesCS5D01G478500 chr7D 518648639 518649633 994 False 1770.000000 1770 98.794000 1607 2600 1 chr7D.!!$F1 993
7 TraesCS5D01G478500 chrUn 238792446 238793435 989 True 1757.000000 1757 98.687000 1611 2600 1 chrUn.!!$R1 989
8 TraesCS5D01G478500 chr3D 584958034 584959024 990 True 1757.000000 1757 98.688000 1611 2600 1 chr3D.!!$R2 989
9 TraesCS5D01G478500 chr3D 505967746 505968742 996 True 1749.000000 1749 98.395000 1608 2600 1 chr3D.!!$R1 992
10 TraesCS5D01G478500 chr4D 480136048 480137037 989 True 1751.000000 1751 98.586000 1611 2600 1 chr4D.!!$R1 989
11 TraesCS5D01G478500 chr2D 20699694 20700696 1002 False 1746.000000 1746 98.108000 1599 2600 1 chr2D.!!$F1 1001
12 TraesCS5D01G478500 chr5B 649537294 649540830 3536 False 828.000000 1543 91.193500 1 1338 2 chr5B.!!$F1 1337
13 TraesCS5D01G478500 chr5B 649858875 649859562 687 True 749.000000 749 86.156000 693 1432 1 chr5B.!!$R1 739
14 TraesCS5D01G478500 chr5B 649728767 649730251 1484 False 594.233333 1251 91.866667 1 1536 3 chr5B.!!$F2 1535
15 TraesCS5D01G478500 chr5A 644455670 644456299 629 True 684.000000 684 86.556000 693 1336 1 chr5A.!!$R2 643
16 TraesCS5D01G478500 chr5A 644357416 644359343 1927 False 589.666667 1149 88.062000 1 1608 3 chr5A.!!$F1 1607
17 TraesCS5D01G478500 chr5A 644444725 644445324 599 True 566.000000 566 83.670000 697 1338 1 chr5A.!!$R1 641

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
352 2668 0.251341 ATCCTTTTGTCCTTGCGGCT 60.251 50.0 0.0 0.0 0.0 5.52 F
877 3538 0.251916 CTCGCCTAACCAACCATCCA 59.748 55.0 0.0 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1181 3875 0.250295 GTGTTGGTACCTCTGCTGCA 60.25 55.000 14.36 0.88 0.00 4.41 R
1708 4421 1.009900 CGTAAGAGGCGCGACTAGG 60.01 63.158 18.29 0.01 43.02 3.02 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
44 2317 4.904466 GCAATTGCCCAGAGCTTG 57.096 55.556 20.06 0.00 44.23 4.01
45 2318 1.447314 GCAATTGCCCAGAGCTTGC 60.447 57.895 20.06 0.00 43.00 4.01
46 2319 1.885163 GCAATTGCCCAGAGCTTGCT 61.885 55.000 20.06 0.00 44.88 3.91
47 2320 1.466856 CAATTGCCCAGAGCTTGCTA 58.533 50.000 0.00 0.00 44.23 3.49
48 2321 1.404391 CAATTGCCCAGAGCTTGCTAG 59.596 52.381 0.00 0.00 44.23 3.42
49 2322 0.622665 ATTGCCCAGAGCTTGCTAGT 59.377 50.000 0.00 0.00 44.23 2.57
50 2323 1.275666 TTGCCCAGAGCTTGCTAGTA 58.724 50.000 0.00 0.00 44.23 1.82
51 2324 1.275666 TGCCCAGAGCTTGCTAGTAA 58.724 50.000 0.00 0.00 44.23 2.24
52 2325 1.839994 TGCCCAGAGCTTGCTAGTAAT 59.160 47.619 0.00 0.00 44.23 1.89
53 2326 3.038280 TGCCCAGAGCTTGCTAGTAATA 58.962 45.455 0.00 0.00 44.23 0.98
54 2327 3.070159 TGCCCAGAGCTTGCTAGTAATAG 59.930 47.826 0.00 0.00 44.23 1.73
55 2328 3.322254 GCCCAGAGCTTGCTAGTAATAGA 59.678 47.826 0.38 0.00 38.99 1.98
56 2329 4.020662 GCCCAGAGCTTGCTAGTAATAGAT 60.021 45.833 0.38 0.00 38.99 1.98
57 2330 5.719173 CCCAGAGCTTGCTAGTAATAGATC 58.281 45.833 0.38 0.00 0.00 2.75
58 2331 5.398169 CCAGAGCTTGCTAGTAATAGATCG 58.602 45.833 0.38 0.00 0.00 3.69
59 2332 5.398169 CAGAGCTTGCTAGTAATAGATCGG 58.602 45.833 0.38 0.00 0.00 4.18
60 2333 5.048364 CAGAGCTTGCTAGTAATAGATCGGT 60.048 44.000 0.38 0.00 0.00 4.69
61 2334 5.536916 AGAGCTTGCTAGTAATAGATCGGTT 59.463 40.000 0.38 0.00 0.00 4.44
62 2335 6.715718 AGAGCTTGCTAGTAATAGATCGGTTA 59.284 38.462 0.38 0.00 0.00 2.85
63 2336 7.230913 AGAGCTTGCTAGTAATAGATCGGTTAA 59.769 37.037 0.38 0.00 0.00 2.01
64 2337 7.897864 AGCTTGCTAGTAATAGATCGGTTAAT 58.102 34.615 0.38 0.00 0.00 1.40
65 2338 8.368668 AGCTTGCTAGTAATAGATCGGTTAATT 58.631 33.333 0.38 0.00 0.00 1.40
66 2339 9.635520 GCTTGCTAGTAATAGATCGGTTAATTA 57.364 33.333 0.38 0.00 0.00 1.40
77 2350 7.605410 AGATCGGTTAATTAATTCGTTGTGT 57.395 32.000 3.39 6.95 0.00 3.72
78 2351 7.461107 AGATCGGTTAATTAATTCGTTGTGTG 58.539 34.615 3.39 0.00 0.00 3.82
79 2352 5.929278 TCGGTTAATTAATTCGTTGTGTGG 58.071 37.500 3.39 0.00 0.00 4.17
80 2353 5.469421 TCGGTTAATTAATTCGTTGTGTGGT 59.531 36.000 3.39 0.00 0.00 4.16
81 2354 6.648310 TCGGTTAATTAATTCGTTGTGTGGTA 59.352 34.615 3.39 0.80 0.00 3.25
82 2355 6.957077 CGGTTAATTAATTCGTTGTGTGGTAG 59.043 38.462 3.39 0.00 0.00 3.18
83 2356 7.148606 CGGTTAATTAATTCGTTGTGTGGTAGA 60.149 37.037 3.39 0.00 0.00 2.59
84 2357 8.671028 GGTTAATTAATTCGTTGTGTGGTAGAT 58.329 33.333 3.39 0.00 0.00 1.98
87 2360 6.489127 TTAATTCGTTGTGTGGTAGATTGG 57.511 37.500 0.00 0.00 0.00 3.16
88 2361 3.478857 TTCGTTGTGTGGTAGATTGGT 57.521 42.857 0.00 0.00 0.00 3.67
89 2362 2.761559 TCGTTGTGTGGTAGATTGGTG 58.238 47.619 0.00 0.00 0.00 4.17
90 2363 2.103432 TCGTTGTGTGGTAGATTGGTGT 59.897 45.455 0.00 0.00 0.00 4.16
91 2364 2.875933 CGTTGTGTGGTAGATTGGTGTT 59.124 45.455 0.00 0.00 0.00 3.32
92 2365 4.059511 CGTTGTGTGGTAGATTGGTGTTA 58.940 43.478 0.00 0.00 0.00 2.41
93 2366 4.084223 CGTTGTGTGGTAGATTGGTGTTAC 60.084 45.833 0.00 0.00 0.00 2.50
94 2367 4.967084 TGTGTGGTAGATTGGTGTTACT 57.033 40.909 0.00 0.00 0.00 2.24
95 2368 6.225318 GTTGTGTGGTAGATTGGTGTTACTA 58.775 40.000 0.00 0.00 0.00 1.82
96 2369 5.786311 TGTGTGGTAGATTGGTGTTACTAC 58.214 41.667 0.00 0.00 35.79 2.73
97 2370 4.860907 GTGTGGTAGATTGGTGTTACTACG 59.139 45.833 0.00 0.00 36.91 3.51
98 2371 4.766373 TGTGGTAGATTGGTGTTACTACGA 59.234 41.667 0.00 0.00 36.91 3.43
99 2372 5.106038 TGTGGTAGATTGGTGTTACTACGAG 60.106 44.000 0.00 0.00 36.91 4.18
100 2373 5.012239 TGGTAGATTGGTGTTACTACGAGT 58.988 41.667 0.00 0.00 36.91 4.18
101 2374 6.094048 GTGGTAGATTGGTGTTACTACGAGTA 59.906 42.308 0.00 0.00 36.91 2.59
102 2375 6.830324 TGGTAGATTGGTGTTACTACGAGTAT 59.170 38.462 0.00 0.00 36.91 2.12
103 2376 7.992608 TGGTAGATTGGTGTTACTACGAGTATA 59.007 37.037 0.00 0.00 36.91 1.47
104 2377 9.007901 GGTAGATTGGTGTTACTACGAGTATAT 57.992 37.037 0.00 0.00 36.91 0.86
107 2380 9.790344 AGATTGGTGTTACTACGAGTATATACT 57.210 33.333 15.37 15.37 39.71 2.12
110 2383 8.539770 TGGTGTTACTACGAGTATATACTAGC 57.460 38.462 19.43 9.83 36.50 3.42
111 2384 7.604164 TGGTGTTACTACGAGTATATACTAGCC 59.396 40.741 19.43 11.89 36.50 3.93
112 2385 7.604164 GGTGTTACTACGAGTATATACTAGCCA 59.396 40.741 19.43 9.40 36.50 4.75
113 2386 8.439286 GTGTTACTACGAGTATATACTAGCCAC 58.561 40.741 19.43 14.12 36.50 5.01
114 2387 8.150296 TGTTACTACGAGTATATACTAGCCACA 58.850 37.037 19.43 13.93 36.50 4.17
115 2388 8.993121 GTTACTACGAGTATATACTAGCCACAA 58.007 37.037 19.43 8.87 36.50 3.33
116 2389 7.670009 ACTACGAGTATATACTAGCCACAAG 57.330 40.000 19.43 12.63 36.50 3.16
117 2390 5.961396 ACGAGTATATACTAGCCACAAGG 57.039 43.478 19.43 3.90 36.50 3.61
118 2391 5.383476 ACGAGTATATACTAGCCACAAGGT 58.617 41.667 19.43 4.39 36.50 3.50
119 2392 5.832060 ACGAGTATATACTAGCCACAAGGTT 59.168 40.000 19.43 0.00 36.50 3.50
120 2393 7.000472 ACGAGTATATACTAGCCACAAGGTTA 59.000 38.462 19.43 0.00 36.50 2.85
177 2485 3.870419 GTGCACCTTTTGAAAATTCTGCA 59.130 39.130 5.22 10.94 0.00 4.41
178 2486 4.025480 GTGCACCTTTTGAAAATTCTGCAG 60.025 41.667 7.63 7.63 34.22 4.41
179 2487 4.122046 GCACCTTTTGAAAATTCTGCAGT 58.878 39.130 14.67 0.00 0.00 4.40
180 2488 4.571984 GCACCTTTTGAAAATTCTGCAGTT 59.428 37.500 14.67 0.00 0.00 3.16
181 2489 5.065090 GCACCTTTTGAAAATTCTGCAGTTT 59.935 36.000 14.67 7.07 0.00 2.66
231 2547 1.073025 ATGCAGCCAACAACTCCGA 59.927 52.632 0.00 0.00 0.00 4.55
279 2595 2.076100 TGCTTGATGCGTTTTCTCGAT 58.924 42.857 0.00 0.00 46.63 3.59
302 2618 4.002982 TGACTGTCGATTTCAAGATTGGG 58.997 43.478 2.98 0.00 0.00 4.12
352 2668 0.251341 ATCCTTTTGTCCTTGCGGCT 60.251 50.000 0.00 0.00 0.00 5.52
362 2678 2.747446 GTCCTTGCGGCTTCTCATTTAA 59.253 45.455 0.00 0.00 0.00 1.52
363 2679 3.009723 TCCTTGCGGCTTCTCATTTAAG 58.990 45.455 0.00 0.00 0.00 1.85
364 2680 2.478539 CCTTGCGGCTTCTCATTTAAGC 60.479 50.000 0.00 0.00 46.90 3.09
381 2727 2.859165 AGCCAGCTAGCTGTTTGTAA 57.141 45.000 36.14 0.00 42.95 2.41
504 2876 2.459934 GTTTTTGTTTCAGCTCACGGG 58.540 47.619 0.00 0.00 0.00 5.28
510 2882 3.876589 TTCAGCTCACGGGCGGTTC 62.877 63.158 0.00 0.00 37.29 3.62
523 2895 1.073199 CGGTTCCTCTGCCCAACTT 59.927 57.895 0.00 0.00 0.00 2.66
664 3309 2.386661 ATCATCGACCAGGTCAACAC 57.613 50.000 20.13 0.00 32.09 3.32
665 3310 1.044611 TCATCGACCAGGTCAACACA 58.955 50.000 20.13 0.00 32.09 3.72
730 3375 3.367806 CGAGTGTCCATCTGATCACTTGT 60.368 47.826 10.64 0.00 40.53 3.16
745 3390 8.669946 TGATCACTTGTTTGTCAACACTAATA 57.330 30.769 0.00 0.00 42.87 0.98
787 3432 2.961721 CGATGGATCACACGGCCG 60.962 66.667 26.86 26.86 0.00 6.13
792 3444 4.832608 GATCACACGGCCGGGTCC 62.833 72.222 34.54 19.36 0.00 4.46
870 3531 3.410631 TCAAATCACTCGCCTAACCAA 57.589 42.857 0.00 0.00 0.00 3.67
874 3535 0.981183 TCACTCGCCTAACCAACCAT 59.019 50.000 0.00 0.00 0.00 3.55
875 3536 1.066430 TCACTCGCCTAACCAACCATC 60.066 52.381 0.00 0.00 0.00 3.51
876 3537 0.252197 ACTCGCCTAACCAACCATCC 59.748 55.000 0.00 0.00 0.00 3.51
877 3538 0.251916 CTCGCCTAACCAACCATCCA 59.748 55.000 0.00 0.00 0.00 3.41
897 3558 3.554692 CGACTGCGGCGATTGTCC 61.555 66.667 12.98 0.00 0.00 4.02
1053 3741 6.142818 CTAAGCTTAGCTAGAGCAAGAGAA 57.857 41.667 20.13 6.96 45.16 2.87
1061 3749 6.047511 AGCTAGAGCAAGAGAAATTTCTGA 57.952 37.500 25.12 0.12 45.16 3.27
1142 3830 0.693767 CAGGAGGAGGAAGAGGCCAT 60.694 60.000 5.01 0.00 0.00 4.40
1215 3909 0.179032 AACACATTCACAGGGTGCGA 60.179 50.000 0.00 0.00 36.00 5.10
1343 4037 3.846360 AGCAAGACGGATAGTACAACAC 58.154 45.455 0.00 0.00 0.00 3.32
1369 4063 1.376466 GATCCAGCTGTGTGGGTGT 59.624 57.895 13.81 0.00 38.26 4.16
1384 4078 1.409427 GGGTGTTCTATCTGGTCGAGG 59.591 57.143 0.00 0.00 0.00 4.63
1397 4091 1.079127 TCGAGGTTTGCTGCTAGCC 60.079 57.895 13.29 8.78 41.51 3.93
1545 4253 8.150945 GGATGTGTATGTAACTATCTGATGGTT 58.849 37.037 20.75 20.75 37.70 3.67
1781 4494 1.900545 GCTGACCGGGACTAAAGGCT 61.901 60.000 6.32 0.00 0.00 4.58
2438 5151 3.438087 AGCTCATGTTTGAATTCACCGAG 59.562 43.478 7.89 10.32 0.00 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 2324 9.321562 ACACAACGAATTAATTAACCGATCTAT 57.678 29.630 21.38 7.39 0.00 1.98
52 2325 8.597227 CACACAACGAATTAATTAACCGATCTA 58.403 33.333 21.38 0.00 0.00 1.98
53 2326 7.413657 CCACACAACGAATTAATTAACCGATCT 60.414 37.037 21.38 8.42 0.00 2.75
54 2327 6.685403 CCACACAACGAATTAATTAACCGATC 59.315 38.462 21.38 9.28 0.00 3.69
55 2328 6.149807 ACCACACAACGAATTAATTAACCGAT 59.850 34.615 21.38 11.67 0.00 4.18
56 2329 5.469421 ACCACACAACGAATTAATTAACCGA 59.531 36.000 21.38 0.00 0.00 4.69
57 2330 5.691815 ACCACACAACGAATTAATTAACCG 58.308 37.500 15.90 15.90 0.00 4.44
58 2331 8.031848 TCTACCACACAACGAATTAATTAACC 57.968 34.615 0.00 0.00 0.00 2.85
61 2334 8.670135 CCAATCTACCACACAACGAATTAATTA 58.330 33.333 0.00 0.00 0.00 1.40
62 2335 7.175990 ACCAATCTACCACACAACGAATTAATT 59.824 33.333 0.00 0.00 0.00 1.40
63 2336 6.657541 ACCAATCTACCACACAACGAATTAAT 59.342 34.615 0.00 0.00 0.00 1.40
64 2337 5.998981 ACCAATCTACCACACAACGAATTAA 59.001 36.000 0.00 0.00 0.00 1.40
65 2338 5.410132 CACCAATCTACCACACAACGAATTA 59.590 40.000 0.00 0.00 0.00 1.40
66 2339 4.215399 CACCAATCTACCACACAACGAATT 59.785 41.667 0.00 0.00 0.00 2.17
67 2340 3.751175 CACCAATCTACCACACAACGAAT 59.249 43.478 0.00 0.00 0.00 3.34
68 2341 3.135225 CACCAATCTACCACACAACGAA 58.865 45.455 0.00 0.00 0.00 3.85
69 2342 2.103432 ACACCAATCTACCACACAACGA 59.897 45.455 0.00 0.00 0.00 3.85
70 2343 2.489971 ACACCAATCTACCACACAACG 58.510 47.619 0.00 0.00 0.00 4.10
71 2344 5.061179 AGTAACACCAATCTACCACACAAC 58.939 41.667 0.00 0.00 0.00 3.32
72 2345 5.298989 AGTAACACCAATCTACCACACAA 57.701 39.130 0.00 0.00 0.00 3.33
73 2346 4.967084 AGTAACACCAATCTACCACACA 57.033 40.909 0.00 0.00 0.00 3.72
74 2347 4.860907 CGTAGTAACACCAATCTACCACAC 59.139 45.833 0.00 0.00 31.97 3.82
75 2348 4.766373 TCGTAGTAACACCAATCTACCACA 59.234 41.667 0.00 0.00 31.97 4.17
76 2349 5.105997 ACTCGTAGTAACACCAATCTACCAC 60.106 44.000 0.00 0.00 31.97 4.16
77 2350 5.012239 ACTCGTAGTAACACCAATCTACCA 58.988 41.667 0.00 0.00 31.97 3.25
78 2351 5.573337 ACTCGTAGTAACACCAATCTACC 57.427 43.478 0.00 0.00 31.97 3.18
81 2354 9.790344 AGTATATACTCGTAGTAACACCAATCT 57.210 33.333 9.71 0.00 33.89 2.40
84 2357 8.993121 GCTAGTATATACTCGTAGTAACACCAA 58.007 37.037 18.68 0.00 37.73 3.67
85 2358 7.604164 GGCTAGTATATACTCGTAGTAACACCA 59.396 40.741 18.68 0.00 37.73 4.17
86 2359 7.604164 TGGCTAGTATATACTCGTAGTAACACC 59.396 40.741 18.68 7.88 37.73 4.16
87 2360 8.439286 GTGGCTAGTATATACTCGTAGTAACAC 58.561 40.741 18.68 15.34 37.73 3.32
88 2361 8.150296 TGTGGCTAGTATATACTCGTAGTAACA 58.850 37.037 18.68 14.63 37.73 2.41
89 2362 8.539770 TGTGGCTAGTATATACTCGTAGTAAC 57.460 38.462 18.68 12.69 37.73 2.50
90 2363 9.212641 CTTGTGGCTAGTATATACTCGTAGTAA 57.787 37.037 18.68 8.48 37.73 2.24
91 2364 7.821359 CCTTGTGGCTAGTATATACTCGTAGTA 59.179 40.741 18.68 0.00 37.73 1.82
92 2365 6.654161 CCTTGTGGCTAGTATATACTCGTAGT 59.346 42.308 18.68 0.00 37.73 2.73
93 2366 6.654161 ACCTTGTGGCTAGTATATACTCGTAG 59.346 42.308 18.68 11.96 35.81 3.51
94 2367 6.537355 ACCTTGTGGCTAGTATATACTCGTA 58.463 40.000 18.68 1.27 35.81 3.43
95 2368 5.383476 ACCTTGTGGCTAGTATATACTCGT 58.617 41.667 18.68 0.00 35.81 4.18
96 2369 5.961396 ACCTTGTGGCTAGTATATACTCG 57.039 43.478 18.68 13.71 35.81 4.18
97 2370 8.406730 ACTAACCTTGTGGCTAGTATATACTC 57.593 38.462 18.68 5.90 41.84 2.59
98 2371 9.517868 CTACTAACCTTGTGGCTAGTATATACT 57.482 37.037 19.07 19.07 42.93 2.12
99 2372 9.294614 ACTACTAACCTTGTGGCTAGTATATAC 57.705 37.037 4.60 4.60 42.93 1.47
101 2374 9.872684 TTACTACTAACCTTGTGGCTAGTATAT 57.127 33.333 6.01 2.30 42.93 0.86
102 2375 9.347240 CTTACTACTAACCTTGTGGCTAGTATA 57.653 37.037 6.01 1.12 42.93 1.47
103 2376 7.201893 GCTTACTACTAACCTTGTGGCTAGTAT 60.202 40.741 6.01 1.79 42.93 2.12
104 2377 6.096001 GCTTACTACTAACCTTGTGGCTAGTA 59.904 42.308 5.57 5.57 41.84 1.82
105 2378 5.105432 GCTTACTACTAACCTTGTGGCTAGT 60.105 44.000 4.01 4.01 44.68 2.57
106 2379 5.127356 AGCTTACTACTAACCTTGTGGCTAG 59.873 44.000 0.00 0.00 37.86 3.42
107 2380 5.021458 AGCTTACTACTAACCTTGTGGCTA 58.979 41.667 0.00 0.00 36.63 3.93
108 2381 3.838903 AGCTTACTACTAACCTTGTGGCT 59.161 43.478 0.00 0.00 36.63 4.75
109 2382 4.182339 GAGCTTACTACTAACCTTGTGGC 58.818 47.826 0.00 0.00 36.63 5.01
110 2383 5.401531 TGAGCTTACTACTAACCTTGTGG 57.598 43.478 0.00 0.00 39.83 4.17
111 2384 6.313905 CCATTGAGCTTACTACTAACCTTGTG 59.686 42.308 0.00 0.00 0.00 3.33
112 2385 6.013639 ACCATTGAGCTTACTACTAACCTTGT 60.014 38.462 0.00 0.00 0.00 3.16
113 2386 6.313905 CACCATTGAGCTTACTACTAACCTTG 59.686 42.308 0.00 0.00 0.00 3.61
114 2387 6.013639 ACACCATTGAGCTTACTACTAACCTT 60.014 38.462 0.00 0.00 0.00 3.50
115 2388 5.484290 ACACCATTGAGCTTACTACTAACCT 59.516 40.000 0.00 0.00 0.00 3.50
116 2389 5.581085 CACACCATTGAGCTTACTACTAACC 59.419 44.000 0.00 0.00 0.00 2.85
117 2390 6.395629 TCACACCATTGAGCTTACTACTAAC 58.604 40.000 0.00 0.00 0.00 2.34
118 2391 6.599356 TCACACCATTGAGCTTACTACTAA 57.401 37.500 0.00 0.00 0.00 2.24
119 2392 6.599356 TTCACACCATTGAGCTTACTACTA 57.401 37.500 0.00 0.00 0.00 1.82
120 2393 5.483685 TTCACACCATTGAGCTTACTACT 57.516 39.130 0.00 0.00 0.00 2.57
121 2394 6.258068 GGTATTCACACCATTGAGCTTACTAC 59.742 42.308 0.00 0.00 38.55 2.73
122 2395 6.070481 TGGTATTCACACCATTGAGCTTACTA 60.070 38.462 0.00 0.00 43.76 1.82
123 2396 5.186198 GGTATTCACACCATTGAGCTTACT 58.814 41.667 0.00 0.00 38.55 2.24
124 2397 4.941263 TGGTATTCACACCATTGAGCTTAC 59.059 41.667 0.00 0.00 43.76 2.34
125 2398 5.172687 TGGTATTCACACCATTGAGCTTA 57.827 39.130 0.00 0.00 43.76 3.09
126 2399 4.032960 TGGTATTCACACCATTGAGCTT 57.967 40.909 0.00 0.00 43.76 3.74
231 2547 5.585047 GCCATGTTTTTCGTAGTAGGATTCT 59.415 40.000 0.00 0.00 0.00 2.40
279 2595 4.455533 CCCAATCTTGAAATCGACAGTCAA 59.544 41.667 0.41 6.97 0.00 3.18
352 2668 4.194640 CAGCTAGCTGGCTTAAATGAGAA 58.805 43.478 33.06 0.00 41.00 2.87
381 2727 8.752254 CGACGTGTACACATATATTTCAAATCT 58.248 33.333 24.98 0.00 0.00 2.40
504 2876 3.056328 GTTGGGCAGAGGAACCGC 61.056 66.667 0.00 0.00 0.00 5.68
664 3309 0.535102 ACGACAAAAGGTGGGAGCTG 60.535 55.000 0.00 0.00 0.00 4.24
665 3310 0.250338 GACGACAAAAGGTGGGAGCT 60.250 55.000 0.00 0.00 0.00 4.09
730 3375 5.366460 TCCGTGGTTATTAGTGTTGACAAA 58.634 37.500 0.00 0.00 0.00 2.83
745 3390 6.683715 CCATTTGTTTAGTTAATCCGTGGTT 58.316 36.000 0.00 0.00 0.00 3.67
787 3432 1.536662 ACTGGACACTCCTGGACCC 60.537 63.158 0.00 0.00 39.50 4.46
792 3444 2.291741 GCTTTTTGACTGGACACTCCTG 59.708 50.000 0.00 0.00 40.80 3.86
800 3452 1.021202 CGTGGTGCTTTTTGACTGGA 58.979 50.000 0.00 0.00 0.00 3.86
870 3531 2.048222 CGCAGTCGTGTGGATGGT 60.048 61.111 0.00 0.00 0.00 3.55
876 3537 3.112075 AATCGCCGCAGTCGTGTG 61.112 61.111 0.00 0.00 0.00 3.82
877 3538 3.112075 CAATCGCCGCAGTCGTGT 61.112 61.111 0.00 0.00 0.00 4.49
897 3558 3.375299 CGCCTTGAGAGTTTGATTAAGGG 59.625 47.826 0.00 0.00 36.17 3.95
1053 3741 3.593328 TCCCACTTCCCATCTCAGAAATT 59.407 43.478 0.00 0.00 0.00 1.82
1061 3749 2.843113 CTCTTCTTCCCACTTCCCATCT 59.157 50.000 0.00 0.00 0.00 2.90
1120 3808 1.334384 GCCTCTTCCTCCTCCTGTCC 61.334 65.000 0.00 0.00 0.00 4.02
1181 3875 0.250295 GTGTTGGTACCTCTGCTGCA 60.250 55.000 14.36 0.88 0.00 4.41
1343 4037 2.664185 CAGCTGGATCCATCGGCG 60.664 66.667 16.63 0.00 33.57 6.46
1369 4063 2.832129 AGCAAACCTCGACCAGATAGAA 59.168 45.455 0.00 0.00 0.00 2.10
1384 4078 1.497722 GACGTGGCTAGCAGCAAAC 59.502 57.895 18.24 5.45 44.75 2.93
1397 4091 4.450122 GCCTGCATGCACGACGTG 62.450 66.667 23.43 23.43 38.41 4.49
1545 4253 8.691797 GGCATCTGTAAATTTAGGAAAATACCA 58.308 33.333 0.00 0.00 34.12 3.25
1708 4421 1.009900 CGTAAGAGGCGCGACTAGG 60.010 63.158 18.29 0.01 43.02 3.02
1709 4422 2.012237 TCGTAAGAGGCGCGACTAG 58.988 57.895 18.29 4.24 45.01 2.57
2438 5151 5.771602 GAGACGGTTCTCAGAAGAAATTC 57.228 43.478 0.00 0.00 46.84 2.17


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

AutoCloner maintained by Alex Coulton.