Multiple sequence alignment - TraesCS4D01G141500

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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 TraesCS4D01G141500 chr4D 100.000 2480 0 0 1 2480 126216212 126218691 0.000000e+00 4580.0
1 TraesCS4D01G141500 chr4A 94.161 1353 60 11 809 2155 444157761 444156422 0.000000e+00 2043.0
2 TraesCS4D01G141500 chr4A 95.796 452 14 3 31 481 444158830 444158383 0.000000e+00 725.0
3 TraesCS4D01G141500 chr4A 88.796 357 29 7 466 817 444158368 444158018 6.340000e-116 427.0
4 TraesCS4D01G141500 chr4A 91.623 191 3 4 2303 2480 444156419 444156229 4.090000e-63 252.0
5 TraesCS4D01G141500 chr4B 95.197 937 28 6 516 1441 190170110 190171040 0.000000e+00 1465.0
6 TraesCS4D01G141500 chr4B 96.454 282 7 1 234 515 190166665 190166387 1.740000e-126 462.0
7 TraesCS4D01G141500 chr4B 81.920 448 63 12 1688 2130 190180712 190181146 1.810000e-96 363.0
8 TraesCS4D01G141500 chr4B 85.019 267 23 5 1437 1686 190173559 190173825 3.170000e-64 255.0
9 TraesCS4D01G141500 chr4B 91.538 130 6 2 1 125 190166257 190166386 9.120000e-40 174.0
10 TraesCS4D01G141500 chr4B 89.565 115 5 2 127 234 190168372 190168258 3.330000e-29 139.0
11 TraesCS4D01G141500 chr4B 89.565 115 5 2 127 234 190170111 190169997 3.330000e-29 139.0
12 TraesCS4D01G141500 chr4B 98.630 73 1 0 516 588 190168371 190168443 2.000000e-26 130.0
13 TraesCS4D01G141500 chr4B 92.308 65 5 0 2153 2217 190181147 190181211 2.630000e-15 93.5
14 TraesCS4D01G141500 chr2B 82.997 347 43 15 1827 2160 363485118 363485461 1.440000e-77 300.0
15 TraesCS4D01G141500 chr2D 81.638 354 48 16 1827 2166 298839704 298839354 6.760000e-71 278.0
16 TraesCS4D01G141500 chr2D 76.240 383 76 11 1789 2159 592182847 592182468 3.260000e-44 189.0
17 TraesCS4D01G141500 chrUn 79.769 346 55 13 1827 2160 85460051 85460393 1.150000e-58 237.0
18 TraesCS4D01G141500 chrUn 87.931 58 7 0 1153 1210 67240943 67241000 4.430000e-08 69.4
19 TraesCS4D01G141500 chr7A 77.451 408 73 18 1773 2167 427556196 427555795 2.480000e-55 226.0
20 TraesCS4D01G141500 chr7A 77.684 354 66 11 1782 2125 725327292 725326942 1.160000e-48 204.0
21 TraesCS4D01G141500 chr7A 79.208 303 50 12 1782 2075 450961268 450961566 5.410000e-47 198.0
22 TraesCS4D01G141500 chr1A 75.987 304 62 10 1774 2071 9243869 9244167 1.990000e-31 147.0
23 TraesCS4D01G141500 chr1A 83.333 108 17 1 1132 1238 482964240 482964133 5.640000e-17 99.0
24 TraesCS4D01G141500 chr1A 82.716 81 10 4 1318 1396 482964081 482964003 4.430000e-08 69.4
25 TraesCS4D01G141500 chr3B 80.337 178 29 6 1875 2049 59359591 59359417 2.000000e-26 130.0
26 TraesCS4D01G141500 chr5D 74.324 222 41 10 1153 1360 525188963 525188744 2.040000e-11 80.5
27 TraesCS4D01G141500 chr5D 89.286 56 6 0 1155 1210 525226764 525226709 1.230000e-08 71.3
28 TraesCS4D01G141500 chr5D 85.075 67 10 0 1144 1210 525253901 525253967 4.430000e-08 69.4
29 TraesCS4D01G141500 chr5D 100.000 35 0 0 1176 1210 525250468 525250502 5.730000e-07 65.8
30 TraesCS4D01G141500 chr5B 88.060 67 8 0 1144 1210 659704592 659704658 2.040000e-11 80.5
31 TraesCS4D01G141500 chr5B 87.931 58 7 0 1153 1210 659557413 659557356 4.430000e-08 69.4
32 TraesCS4D01G141500 chr5B 82.857 70 12 0 1291 1360 659586526 659586457 2.060000e-06 63.9
33 TraesCS4D01G141500 chr5A 73.991 223 40 16 1153 1360 651564222 651564003 9.510000e-10 75.0
34 TraesCS4D01G141500 chr5A 87.931 58 7 0 1153 1210 651555837 651555780 4.430000e-08 69.4
35 TraesCS4D01G141500 chr5A 81.707 82 15 0 1129 1210 651635659 651635740 4.430000e-08 69.4
36 TraesCS4D01G141500 chr1D 90.000 50 5 0 1318 1367 383177944 383177895 5.730000e-07 65.8


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 TraesCS4D01G141500 chr4D 126216212 126218691 2479 False 4580.000000 4580 100.000000 1 2480 1 chr4D.!!$F1 2479
1 TraesCS4D01G141500 chr4A 444156229 444158830 2601 True 861.750000 2043 92.594000 31 2480 4 chr4A.!!$R1 2449
2 TraesCS4D01G141500 chr4B 190166257 190173825 7568 False 506.000000 1465 92.596000 1 1686 4 chr4B.!!$F1 1685
3 TraesCS4D01G141500 chr4B 190166387 190170111 3724 True 246.666667 462 91.861333 127 515 3 chr4B.!!$R1 388


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
552 5039 0.782384 CGAGCTTACCAACACGTCAC 59.218 55.0 0.0 0.0 0.0 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2233 9552 0.031857 TCGCACGGAAAAGGTTCGTA 59.968 50.0 0.0 0.0 34.28 3.43 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
100 106 7.069852 CTGATGAGTTTCACCAGTCAATTAG 57.930 40.000 0.00 0.00 33.27 1.73
157 163 5.399301 CAGTACGAACTGCATTTCTTTTTGG 59.601 40.000 14.08 1.27 46.28 3.28
158 164 4.385358 ACGAACTGCATTTCTTTTTGGT 57.615 36.364 14.08 1.84 0.00 3.67
159 165 4.359706 ACGAACTGCATTTCTTTTTGGTC 58.640 39.130 14.08 0.00 0.00 4.02
160 166 4.097892 ACGAACTGCATTTCTTTTTGGTCT 59.902 37.500 14.08 0.00 0.00 3.85
231 2514 1.335689 GCCACACGGTATAGGACGATC 60.336 57.143 0.00 0.00 33.28 3.69
552 5039 0.782384 CGAGCTTACCAACACGTCAC 59.218 55.000 0.00 0.00 0.00 3.67
834 5603 5.047660 AGCTTAGCTTAAGAATCGGATCGAT 60.048 40.000 6.67 0.00 41.89 3.59
1007 5780 6.392625 AATCTAGCTCGCTAGTATGACAAA 57.607 37.500 21.54 4.46 44.59 2.83
1031 5804 0.036164 GTGGCCAGTGGTGATACACA 59.964 55.000 5.11 0.00 43.72 3.72
1113 5886 0.602638 TGATCGGCAAGAACAAGCGT 60.603 50.000 0.00 0.00 0.00 5.07
1433 6207 2.313172 CGTGCCTGTCTGTGTCTGC 61.313 63.158 0.00 0.00 0.00 4.26
1506 8804 9.075678 GGGATTAGTGCTACTGTCTATAAGTTA 57.924 37.037 0.00 0.00 0.00 2.24
1682 8996 4.002906 ACTCAGTTTGAAATCGCCTACA 57.997 40.909 0.00 0.00 0.00 2.74
1729 9043 8.699749 GGAGATGTGCTTAATAACAAAACAAAC 58.300 33.333 0.00 0.00 0.00 2.93
1743 9057 6.172630 ACAAAACAAACAAGCATTTTCTCCT 58.827 32.000 0.00 0.00 0.00 3.69
1771 9085 3.987220 GTGTGAATAGGTGCGCAATTTTT 59.013 39.130 14.00 4.59 0.00 1.94
1774 9088 4.683781 GTGAATAGGTGCGCAATTTTTGAA 59.316 37.500 14.00 0.00 0.00 2.69
1775 9089 5.348451 GTGAATAGGTGCGCAATTTTTGAAT 59.652 36.000 14.00 0.00 0.00 2.57
1779 9093 5.329035 AGGTGCGCAATTTTTGAATATCT 57.671 34.783 14.00 0.00 0.00 1.98
1786 9100 9.022915 TGCGCAATTTTTGAATATCTATTTCTG 57.977 29.630 8.16 0.00 0.00 3.02
1873 9188 8.893563 AAAATCCATCTTTTTACATGGTAGGA 57.106 30.769 0.00 0.00 35.74 2.94
1892 9207 0.673437 AAATTTGGTGCGTGAGGTGG 59.327 50.000 0.00 0.00 0.00 4.61
1905 9220 1.186200 GAGGTGGGCTCCAAATTTCC 58.814 55.000 0.00 0.00 34.18 3.13
1906 9221 0.611896 AGGTGGGCTCCAAATTTCCG 60.612 55.000 0.00 0.00 34.18 4.30
1915 9230 4.555262 GCTCCAAATTTCCGAACATTTGA 58.445 39.130 19.54 11.20 41.18 2.69
1968 9283 3.417069 TTGGGGTCAGAACAGTACATG 57.583 47.619 0.00 0.00 0.00 3.21
1976 9291 5.634020 GGTCAGAACAGTACATGAACAGTAC 59.366 44.000 0.00 0.00 41.59 2.73
1979 9294 6.923508 TCAGAACAGTACATGAACAGTACAAG 59.076 38.462 0.00 1.58 43.24 3.16
1998 9313 6.994421 ACAAGAAATTACAGACCCCAAATT 57.006 33.333 0.00 0.00 0.00 1.82
2057 9373 3.250762 TCTGAAATTTGAAGTGGCTCACG 59.749 43.478 0.00 0.00 39.64 4.35
2166 9485 4.481112 GGGCACCGAATTGCTGCG 62.481 66.667 0.00 0.00 42.56 5.18
2168 9487 4.403137 GCACCGAATTGCTGCGCA 62.403 61.111 10.98 10.98 39.59 6.09
2179 9498 3.641437 TTGCTGCGCAATTTTAGACTT 57.359 38.095 13.05 0.00 43.99 3.01
2180 9499 4.757799 TTGCTGCGCAATTTTAGACTTA 57.242 36.364 13.05 0.00 43.99 2.24
2181 9500 4.757799 TGCTGCGCAATTTTAGACTTAA 57.242 36.364 13.05 0.00 34.76 1.85
2182 9501 5.114785 TGCTGCGCAATTTTAGACTTAAA 57.885 34.783 13.05 0.00 34.76 1.52
2183 9502 5.153513 TGCTGCGCAATTTTAGACTTAAAG 58.846 37.500 13.05 0.00 34.76 1.85
2184 9503 5.154222 GCTGCGCAATTTTAGACTTAAAGT 58.846 37.500 13.05 0.00 30.84 2.66
2185 9504 5.629435 GCTGCGCAATTTTAGACTTAAAGTT 59.371 36.000 13.05 0.00 31.28 2.66
2186 9505 6.398935 GCTGCGCAATTTTAGACTTAAAGTTG 60.399 38.462 13.05 9.53 43.64 3.16
2249 9568 5.010249 GTTTAGTACGAACCTTTTCCGTG 57.990 43.478 0.00 0.00 0.00 4.94
2250 9569 1.505425 AGTACGAACCTTTTCCGTGC 58.495 50.000 0.00 0.00 0.00 5.34
2251 9570 0.162294 GTACGAACCTTTTCCGTGCG 59.838 55.000 0.00 0.00 38.29 5.34
2252 9571 0.031857 TACGAACCTTTTCCGTGCGA 59.968 50.000 0.00 0.00 35.73 5.10
2253 9572 1.203313 CGAACCTTTTCCGTGCGAC 59.797 57.895 0.00 0.00 33.92 5.19
2254 9573 1.492319 CGAACCTTTTCCGTGCGACA 61.492 55.000 0.00 0.00 33.92 4.35
2255 9574 0.041576 GAACCTTTTCCGTGCGACAC 60.042 55.000 0.00 0.00 0.00 3.67
2256 9575 0.745128 AACCTTTTCCGTGCGACACA 60.745 50.000 9.95 0.00 33.40 3.72
2257 9576 0.745128 ACCTTTTCCGTGCGACACAA 60.745 50.000 9.95 0.00 33.40 3.33
2258 9577 0.316689 CCTTTTCCGTGCGACACAAC 60.317 55.000 9.95 0.00 33.40 3.32
2259 9578 0.653323 CTTTTCCGTGCGACACAACG 60.653 55.000 9.95 0.00 33.40 4.10
2260 9579 1.082679 TTTTCCGTGCGACACAACGA 61.083 50.000 9.95 0.82 33.40 3.85
2261 9580 1.484227 TTTCCGTGCGACACAACGAG 61.484 55.000 9.95 0.00 33.40 4.18
2262 9581 4.059459 CCGTGCGACACAACGAGC 62.059 66.667 9.95 0.00 33.40 5.03
2263 9582 3.326981 CGTGCGACACAACGAGCA 61.327 61.111 9.95 0.00 37.26 4.26
2264 9583 2.546321 GTGCGACACAACGAGCAG 59.454 61.111 5.30 0.00 40.53 4.24
2265 9584 2.661537 TGCGACACAACGAGCAGG 60.662 61.111 0.00 0.00 34.39 4.85
2266 9585 2.661866 GCGACACAACGAGCAGGT 60.662 61.111 0.00 0.00 35.09 4.00
2267 9586 2.943345 GCGACACAACGAGCAGGTG 61.943 63.158 0.00 0.00 44.94 4.00
2268 9587 2.310233 CGACACAACGAGCAGGTGG 61.310 63.158 2.37 0.00 43.31 4.61
2269 9588 1.069090 GACACAACGAGCAGGTGGA 59.931 57.895 2.37 0.00 43.31 4.02
2270 9589 0.320771 GACACAACGAGCAGGTGGAT 60.321 55.000 2.37 0.00 43.31 3.41
2271 9590 0.108585 ACACAACGAGCAGGTGGATT 59.891 50.000 2.37 0.00 43.31 3.01
2272 9591 1.238439 CACAACGAGCAGGTGGATTT 58.762 50.000 2.37 0.00 43.31 2.17
2273 9592 2.224426 ACACAACGAGCAGGTGGATTTA 60.224 45.455 2.37 0.00 43.31 1.40
2274 9593 2.416547 CACAACGAGCAGGTGGATTTAG 59.583 50.000 2.37 0.00 43.31 1.85
2275 9594 2.301870 ACAACGAGCAGGTGGATTTAGA 59.698 45.455 2.37 0.00 43.31 2.10
2276 9595 2.673368 CAACGAGCAGGTGGATTTAGAC 59.327 50.000 0.00 0.00 32.78 2.59
2277 9596 1.135083 ACGAGCAGGTGGATTTAGACG 60.135 52.381 0.00 0.00 0.00 4.18
2278 9597 1.135083 CGAGCAGGTGGATTTAGACGT 60.135 52.381 0.00 0.00 0.00 4.34
2279 9598 2.674177 CGAGCAGGTGGATTTAGACGTT 60.674 50.000 0.00 0.00 0.00 3.99
2280 9599 2.673368 GAGCAGGTGGATTTAGACGTTG 59.327 50.000 0.00 0.00 0.00 4.10
2281 9600 1.130561 GCAGGTGGATTTAGACGTTGC 59.869 52.381 0.00 0.00 0.00 4.17
2282 9601 1.737793 CAGGTGGATTTAGACGTTGCC 59.262 52.381 0.00 0.00 0.00 4.52
2283 9602 1.349688 AGGTGGATTTAGACGTTGCCA 59.650 47.619 0.00 0.00 0.00 4.92
2284 9603 1.737793 GGTGGATTTAGACGTTGCCAG 59.262 52.381 0.00 0.00 0.00 4.85
2285 9604 1.737793 GTGGATTTAGACGTTGCCAGG 59.262 52.381 0.00 0.00 0.00 4.45
2286 9605 1.339631 TGGATTTAGACGTTGCCAGGG 60.340 52.381 0.00 0.00 0.00 4.45
2287 9606 1.065709 GGATTTAGACGTTGCCAGGGA 60.066 52.381 0.00 0.00 0.00 4.20
2288 9607 2.007608 GATTTAGACGTTGCCAGGGAC 58.992 52.381 0.00 0.00 0.00 4.46
2289 9608 0.035739 TTTAGACGTTGCCAGGGACC 59.964 55.000 0.00 0.00 0.00 4.46
2290 9609 1.833787 TTAGACGTTGCCAGGGACCC 61.834 60.000 0.59 0.59 0.00 4.46
2291 9610 2.741878 TAGACGTTGCCAGGGACCCT 62.742 60.000 7.44 7.44 0.00 4.34
2300 9619 2.538760 AGGGACCCTGAAGCCAGA 59.461 61.111 13.95 0.00 43.02 3.86
2301 9620 1.151810 AGGGACCCTGAAGCCAGAA 60.152 57.895 13.95 0.00 43.02 3.02
2371 9690 2.136298 TTTGACTTTGCCTGGACACA 57.864 45.000 0.00 0.00 0.00 3.72
2387 9706 7.095910 CCTGGACACACATAAAATATTTGCAA 58.904 34.615 0.39 0.00 0.00 4.08
2393 9712 7.930865 ACACACATAAAATATTTGCAACCAAGT 59.069 29.630 0.00 0.00 31.52 3.16
2394 9713 9.416794 CACACATAAAATATTTGCAACCAAGTA 57.583 29.630 0.00 0.00 31.52 2.24
2396 9715 8.594687 CACATAAAATATTTGCAACCAAGTAGC 58.405 33.333 0.00 0.00 31.52 3.58
2397 9716 8.531146 ACATAAAATATTTGCAACCAAGTAGCT 58.469 29.630 0.00 0.00 31.52 3.32
2439 9771 4.152223 CACAGTGTTGTCGCAGATGAAATA 59.848 41.667 0.00 0.00 40.67 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 3.215244 CAACTGTCACAACGTTATTCGC 58.785 45.455 0.00 0.00 44.19 4.70
25 26 4.446857 ACAACTGTCACAACGTTATTCG 57.553 40.909 0.00 0.00 46.00 3.34
38 44 7.639113 TTATTATTGGGATCCAACAACTGTC 57.361 36.000 15.23 0.00 46.95 3.51
80 86 5.305585 GGACTAATTGACTGGTGAAACTCA 58.694 41.667 0.00 0.00 36.74 3.41
100 106 6.541086 ACGTATATATCGATTCAACTCGGAC 58.459 40.000 1.71 0.00 39.13 4.79
157 163 1.466024 CCTAGCGTGTCGTCTTGAGAC 60.466 57.143 1.00 1.00 41.47 3.36
158 164 0.803117 CCTAGCGTGTCGTCTTGAGA 59.197 55.000 0.00 0.00 0.00 3.27
159 165 0.803117 TCCTAGCGTGTCGTCTTGAG 59.197 55.000 0.00 0.00 0.00 3.02
160 166 0.803117 CTCCTAGCGTGTCGTCTTGA 59.197 55.000 0.00 0.00 0.00 3.02
211 2494 0.672342 ATCGTCCTATACCGTGTGGC 59.328 55.000 0.00 0.00 39.70 5.01
388 4845 1.921243 TGCATATCGAACGACTGGTG 58.079 50.000 0.00 0.00 0.00 4.17
389 4846 2.094182 ACTTGCATATCGAACGACTGGT 60.094 45.455 0.00 0.00 0.00 4.00
390 4847 2.535984 GACTTGCATATCGAACGACTGG 59.464 50.000 0.00 0.00 0.00 4.00
391 4848 3.439293 AGACTTGCATATCGAACGACTG 58.561 45.455 0.00 2.06 0.00 3.51
552 5039 5.058613 CGATCTTGAAGCGACGTATGAATAG 59.941 44.000 0.00 0.00 39.75 1.73
654 5141 0.179161 AGCGAGCACTACGTCACATC 60.179 55.000 0.00 0.00 0.00 3.06
655 5142 1.092348 TAGCGAGCACTACGTCACAT 58.908 50.000 0.00 0.00 0.00 3.21
656 5143 1.063616 GATAGCGAGCACTACGTCACA 59.936 52.381 0.00 0.00 0.00 3.58
834 5603 3.396611 GGGGTTTAAGGTGGATATGGCTA 59.603 47.826 0.00 0.00 0.00 3.93
869 5638 5.281727 TGCTTATATATAGGCGCGAATGAG 58.718 41.667 12.10 0.00 38.09 2.90
1007 5780 3.941188 CACCACTGGCCACGTCCT 61.941 66.667 0.00 0.00 0.00 3.85
1031 5804 2.688446 TCTATCAACTTGATCGGCGACT 59.312 45.455 13.76 0.78 38.26 4.18
1506 8804 4.151883 ACCACTACAAATCAACCAATGCT 58.848 39.130 0.00 0.00 0.00 3.79
1608 8921 3.987868 CGCGTATTGGCACTACAATAGAT 59.012 43.478 14.34 0.00 42.24 1.98
1682 8996 4.101585 TCCAAGCGAAATAGATCACCTGAT 59.898 41.667 0.00 0.00 37.51 2.90
1791 9105 5.908268 CTTGAGCAAGTGCAGATGAGTCTG 61.908 50.000 6.00 1.17 45.16 3.51
1851 9166 9.492730 AATTTCCTACCATGTAAAAAGATGGAT 57.507 29.630 8.40 0.00 41.63 3.41
1868 9183 2.161609 CCTCACGCACCAAATTTCCTAC 59.838 50.000 0.00 0.00 0.00 3.18
1873 9188 0.673437 CCACCTCACGCACCAAATTT 59.327 50.000 0.00 0.00 0.00 1.82
1892 9207 3.592898 AATGTTCGGAAATTTGGAGCC 57.407 42.857 0.00 0.00 0.00 4.70
1896 9211 4.742659 ACGTTCAAATGTTCGGAAATTTGG 59.257 37.500 17.61 6.11 41.83 3.28
1905 9220 7.045725 AGTTACTCATACGTTCAAATGTTCG 57.954 36.000 0.00 0.00 0.00 3.95
1906 9221 8.240883 AGAGTTACTCATACGTTCAAATGTTC 57.759 34.615 15.23 0.00 32.06 3.18
1944 9259 4.141287 TGTACTGTTCTGACCCCAATTTG 58.859 43.478 0.00 0.00 0.00 2.32
1953 9268 6.213677 TGTACTGTTCATGTACTGTTCTGAC 58.786 40.000 17.65 11.44 40.44 3.51
1968 9283 6.148976 GGGGTCTGTAATTTCTTGTACTGTTC 59.851 42.308 0.00 0.00 0.00 3.18
1976 9291 7.216494 ACAAATTTGGGGTCTGTAATTTCTTG 58.784 34.615 21.74 0.00 30.17 3.02
1979 9294 6.993079 AGACAAATTTGGGGTCTGTAATTTC 58.007 36.000 21.74 5.91 40.21 2.17
2010 9325 6.104665 TCATTTGACATCTGAGTAGCTCTTG 58.895 40.000 0.00 0.00 0.00 3.02
2011 9326 6.291648 TCATTTGACATCTGAGTAGCTCTT 57.708 37.500 0.00 0.00 0.00 2.85
2128 9446 3.561528 CCTGGCTCATCTGCATCCATAAT 60.562 47.826 0.00 0.00 34.04 1.28
2129 9447 2.224695 CCTGGCTCATCTGCATCCATAA 60.225 50.000 0.00 0.00 34.04 1.90
2131 9449 0.110678 CCTGGCTCATCTGCATCCAT 59.889 55.000 0.00 0.00 34.04 3.41
2162 9481 6.398935 GCAACTTTAAGTCTAAAATTGCGCAG 60.399 38.462 11.31 0.00 45.11 5.18
2163 9482 5.401079 GCAACTTTAAGTCTAAAATTGCGCA 59.599 36.000 5.66 5.66 45.11 6.09
2164 9483 5.832840 GCAACTTTAAGTCTAAAATTGCGC 58.167 37.500 0.00 0.00 45.11 6.09
2210 9529 9.920826 CGTACTAAACGTCAGTTCTATACATAA 57.079 33.333 7.95 0.00 46.72 1.90
2227 9546 4.609113 GCACGGAAAAGGTTCGTACTAAAC 60.609 45.833 0.00 0.00 34.28 2.01
2228 9547 3.494251 GCACGGAAAAGGTTCGTACTAAA 59.506 43.478 0.00 0.00 34.28 1.85
2229 9548 3.059166 GCACGGAAAAGGTTCGTACTAA 58.941 45.455 0.00 0.00 34.28 2.24
2230 9549 2.676076 GCACGGAAAAGGTTCGTACTA 58.324 47.619 0.00 0.00 34.28 1.82
2231 9550 1.505425 GCACGGAAAAGGTTCGTACT 58.495 50.000 0.00 0.00 34.28 2.73
2232 9551 0.162294 CGCACGGAAAAGGTTCGTAC 59.838 55.000 0.00 0.00 34.28 3.67
2233 9552 0.031857 TCGCACGGAAAAGGTTCGTA 59.968 50.000 0.00 0.00 34.28 3.43
2234 9553 1.227321 TCGCACGGAAAAGGTTCGT 60.227 52.632 0.00 0.00 34.28 3.85
2235 9554 1.203313 GTCGCACGGAAAAGGTTCG 59.797 57.895 0.00 0.00 34.28 3.95
2236 9555 0.041576 GTGTCGCACGGAAAAGGTTC 60.042 55.000 0.00 0.00 0.00 3.62
2237 9556 0.745128 TGTGTCGCACGGAAAAGGTT 60.745 50.000 5.69 0.00 37.14 3.50
2238 9557 0.745128 TTGTGTCGCACGGAAAAGGT 60.745 50.000 5.69 0.00 37.14 3.50
2239 9558 0.316689 GTTGTGTCGCACGGAAAAGG 60.317 55.000 5.69 0.00 37.14 3.11
2240 9559 0.653323 CGTTGTGTCGCACGGAAAAG 60.653 55.000 5.69 0.00 37.14 2.27
2241 9560 1.082679 TCGTTGTGTCGCACGGAAAA 61.083 50.000 5.69 0.00 37.14 2.29
2242 9561 1.484227 CTCGTTGTGTCGCACGGAAA 61.484 55.000 5.69 0.00 37.14 3.13
2243 9562 1.947146 CTCGTTGTGTCGCACGGAA 60.947 57.895 5.69 0.00 37.14 4.30
2244 9563 2.354188 CTCGTTGTGTCGCACGGA 60.354 61.111 5.69 3.08 37.14 4.69
2245 9564 4.059459 GCTCGTTGTGTCGCACGG 62.059 66.667 5.69 0.00 37.14 4.94
2246 9565 3.268446 CTGCTCGTTGTGTCGCACG 62.268 63.158 5.69 0.00 37.14 5.34
2247 9566 2.546321 CTGCTCGTTGTGTCGCAC 59.454 61.111 3.44 3.44 34.56 5.34
2248 9567 2.661537 CCTGCTCGTTGTGTCGCA 60.662 61.111 0.00 0.00 0.00 5.10
2249 9568 2.661866 ACCTGCTCGTTGTGTCGC 60.662 61.111 0.00 0.00 0.00 5.19
2250 9569 2.310233 CCACCTGCTCGTTGTGTCG 61.310 63.158 0.00 0.00 0.00 4.35
2251 9570 0.320771 ATCCACCTGCTCGTTGTGTC 60.321 55.000 0.00 0.00 0.00 3.67
2252 9571 0.108585 AATCCACCTGCTCGTTGTGT 59.891 50.000 0.00 0.00 0.00 3.72
2253 9572 1.238439 AAATCCACCTGCTCGTTGTG 58.762 50.000 0.00 0.00 0.00 3.33
2254 9573 2.301870 TCTAAATCCACCTGCTCGTTGT 59.698 45.455 0.00 0.00 0.00 3.32
2255 9574 2.673368 GTCTAAATCCACCTGCTCGTTG 59.327 50.000 0.00 0.00 0.00 4.10
2256 9575 2.674177 CGTCTAAATCCACCTGCTCGTT 60.674 50.000 0.00 0.00 0.00 3.85
2257 9576 1.135083 CGTCTAAATCCACCTGCTCGT 60.135 52.381 0.00 0.00 0.00 4.18
2258 9577 1.135083 ACGTCTAAATCCACCTGCTCG 60.135 52.381 0.00 0.00 0.00 5.03
2259 9578 2.673368 CAACGTCTAAATCCACCTGCTC 59.327 50.000 0.00 0.00 0.00 4.26
2260 9579 2.699954 CAACGTCTAAATCCACCTGCT 58.300 47.619 0.00 0.00 0.00 4.24
2261 9580 1.130561 GCAACGTCTAAATCCACCTGC 59.869 52.381 0.00 0.00 0.00 4.85
2262 9581 1.737793 GGCAACGTCTAAATCCACCTG 59.262 52.381 0.00 0.00 0.00 4.00
2263 9582 1.349688 TGGCAACGTCTAAATCCACCT 59.650 47.619 0.00 0.00 42.51 4.00
2264 9583 1.737793 CTGGCAACGTCTAAATCCACC 59.262 52.381 0.00 0.00 42.51 4.61
2265 9584 1.737793 CCTGGCAACGTCTAAATCCAC 59.262 52.381 0.00 0.00 42.51 4.02
2266 9585 1.339631 CCCTGGCAACGTCTAAATCCA 60.340 52.381 0.00 0.00 42.51 3.41
2267 9586 1.065709 TCCCTGGCAACGTCTAAATCC 60.066 52.381 0.00 0.00 42.51 3.01
2268 9587 2.007608 GTCCCTGGCAACGTCTAAATC 58.992 52.381 0.00 0.00 42.51 2.17
2269 9588 1.339727 GGTCCCTGGCAACGTCTAAAT 60.340 52.381 0.00 0.00 42.51 1.40
2270 9589 0.035739 GGTCCCTGGCAACGTCTAAA 59.964 55.000 0.00 0.00 42.51 1.85
2271 9590 1.675219 GGTCCCTGGCAACGTCTAA 59.325 57.895 0.00 0.00 42.51 2.10
2272 9591 2.288025 GGGTCCCTGGCAACGTCTA 61.288 63.158 0.00 0.00 42.51 2.59
2273 9592 3.637273 GGGTCCCTGGCAACGTCT 61.637 66.667 0.00 0.00 42.51 4.18
2274 9593 3.637273 AGGGTCCCTGGCAACGTC 61.637 66.667 10.61 0.00 42.51 4.34
2283 9602 0.772124 TTTCTGGCTTCAGGGTCCCT 60.772 55.000 3.85 3.85 38.96 4.20
2284 9603 0.332972 ATTTCTGGCTTCAGGGTCCC 59.667 55.000 0.00 0.00 38.96 4.46
2285 9604 3.584733 ATATTTCTGGCTTCAGGGTCC 57.415 47.619 0.00 0.00 38.96 4.46
2286 9605 4.096984 CACAATATTTCTGGCTTCAGGGTC 59.903 45.833 0.00 0.00 38.96 4.46
2287 9606 4.019174 CACAATATTTCTGGCTTCAGGGT 58.981 43.478 0.00 0.00 38.96 4.34
2288 9607 3.382546 CCACAATATTTCTGGCTTCAGGG 59.617 47.826 0.00 0.00 38.96 4.45
2289 9608 3.181483 GCCACAATATTTCTGGCTTCAGG 60.181 47.826 20.25 0.00 46.05 3.86
2290 9609 4.037858 GCCACAATATTTCTGGCTTCAG 57.962 45.455 20.25 0.00 46.05 3.02
2371 9690 8.531146 AGCTACTTGGTTGCAAATATTTTATGT 58.469 29.630 0.00 0.00 36.81 2.29
2387 9706 5.479375 TGTTTAGCAGTACTAGCTACTTGGT 59.521 40.000 19.94 5.72 43.71 3.67
2393 9712 7.039882 GTGGAATTGTTTAGCAGTACTAGCTA 58.960 38.462 17.64 17.64 43.25 3.32
2394 9713 5.875359 GTGGAATTGTTTAGCAGTACTAGCT 59.125 40.000 19.21 19.21 45.77 3.32
2396 9715 6.874134 ACTGTGGAATTGTTTAGCAGTACTAG 59.126 38.462 0.00 0.00 34.47 2.57
2397 9716 6.649141 CACTGTGGAATTGTTTAGCAGTACTA 59.351 38.462 0.00 0.00 34.47 1.82
2398 9717 5.470098 CACTGTGGAATTGTTTAGCAGTACT 59.530 40.000 0.00 0.00 34.47 2.73
2399 9718 5.238650 ACACTGTGGAATTGTTTAGCAGTAC 59.761 40.000 13.09 0.00 34.47 2.73
2439 9771 7.712205 GCATATTTTGGAATGGTTTGCTTATCT 59.288 33.333 0.00 0.00 0.00 1.98



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

AutoCloner maintained by Alex Coulton.