Multiple sequence alignment - TraesCS3D01G426100

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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 TraesCS3D01G426100 chr3D 100.000 2261 0 0 1 2261 538688419 538686159 0.000000e+00 4176.0
1 TraesCS3D01G426100 chr3D 87.535 1420 105 29 399 1805 538700117 538698757 0.000000e+00 1576.0
2 TraesCS3D01G426100 chr3D 78.598 1341 164 71 446 1744 538516249 538514990 0.000000e+00 773.0
3 TraesCS3D01G426100 chr3D 82.968 775 89 27 871 1622 538574192 538573438 0.000000e+00 660.0
4 TraesCS3D01G426100 chr3D 97.826 46 1 0 276 321 538688090 538688045 1.860000e-11 80.5
5 TraesCS3D01G426100 chr3D 97.826 46 1 0 330 375 538688144 538688099 1.860000e-11 80.5
6 TraesCS3D01G426100 chr3B 94.529 1444 62 14 376 1805 713969403 713967963 0.000000e+00 2213.0
7 TraesCS3D01G426100 chr3B 93.418 1185 46 7 376 1555 713988809 713987652 0.000000e+00 1727.0
8 TraesCS3D01G426100 chr3B 78.216 1345 170 60 446 1738 713392472 713391199 0.000000e+00 747.0
9 TraesCS3D01G426100 chr3B 81.725 777 85 33 871 1630 713492956 713492220 1.490000e-166 595.0
10 TraesCS3D01G426100 chr3B 85.470 351 43 5 1810 2152 713967901 713967551 2.140000e-95 359.0
11 TraesCS3D01G426100 chr3A 90.524 1583 109 19 190 1760 674026320 674024767 0.000000e+00 2054.0
12 TraesCS3D01G426100 chr3A 90.512 938 68 13 874 1805 674061300 674060378 0.000000e+00 1219.0
13 TraesCS3D01G426100 chr3A 92.435 423 28 4 399 819 674061737 674061317 3.210000e-168 601.0
14 TraesCS3D01G426100 chr3A 93.651 189 12 0 2 190 674026621 674026433 1.320000e-72 283.0
15 TraesCS3D01G426100 chr3A 88.679 106 7 1 1 106 674068276 674068176 8.480000e-25 124.0
16 TraesCS3D01G426100 chr2D 90.291 103 9 1 2148 2249 559322414 559322516 1.410000e-27 134.0
17 TraesCS3D01G426100 chr2D 98.039 51 1 0 403 453 615472775 615472725 3.090000e-14 89.8
18 TraesCS3D01G426100 chr6B 88.000 100 10 2 2153 2250 698408174 698408075 1.420000e-22 117.0
19 TraesCS3D01G426100 chr6B 85.981 107 10 4 2153 2255 698838128 698838233 2.370000e-20 110.0
20 TraesCS3D01G426100 chr7D 89.024 82 5 4 2153 2231 252052604 252052524 5.140000e-17 99.0
21 TraesCS3D01G426100 chr1A 85.393 89 6 5 2172 2255 541395960 541396046 4.000000e-13 86.1
22 TraesCS3D01G426100 chrUn 79.646 113 12 11 2153 2261 470751613 470751508 1.120000e-08 71.3
23 TraesCS3D01G426100 chr2B 80.374 107 10 11 2153 2255 762069257 762069158 1.120000e-08 71.3
24 TraesCS3D01G426100 chr2A 97.222 36 1 0 418 453 745431456 745431421 6.740000e-06 62.1
25 TraesCS3D01G426100 chr5D 78.302 106 11 12 2153 2258 508569863 508569770 8.720000e-05 58.4
26 TraesCS3D01G426100 chr1D 83.077 65 9 2 1964 2026 400179023 400178959 8.720000e-05 58.4
27 TraesCS3D01G426100 chr1D 78.641 103 10 12 2153 2255 490362819 490362909 8.720000e-05 58.4


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 TraesCS3D01G426100 chr3D 538686159 538688419 2260 True 1445.666667 4176 98.550667 1 2261 3 chr3D.!!$R4 2260
1 TraesCS3D01G426100 chr3D 538698757 538700117 1360 True 1576.000000 1576 87.535000 399 1805 1 chr3D.!!$R3 1406
2 TraesCS3D01G426100 chr3D 538514990 538516249 1259 True 773.000000 773 78.598000 446 1744 1 chr3D.!!$R1 1298
3 TraesCS3D01G426100 chr3D 538573438 538574192 754 True 660.000000 660 82.968000 871 1622 1 chr3D.!!$R2 751
4 TraesCS3D01G426100 chr3B 713987652 713988809 1157 True 1727.000000 1727 93.418000 376 1555 1 chr3B.!!$R3 1179
5 TraesCS3D01G426100 chr3B 713967551 713969403 1852 True 1286.000000 2213 89.999500 376 2152 2 chr3B.!!$R4 1776
6 TraesCS3D01G426100 chr3B 713391199 713392472 1273 True 747.000000 747 78.216000 446 1738 1 chr3B.!!$R1 1292
7 TraesCS3D01G426100 chr3B 713492220 713492956 736 True 595.000000 595 81.725000 871 1630 1 chr3B.!!$R2 759
8 TraesCS3D01G426100 chr3A 674024767 674026621 1854 True 1168.500000 2054 92.087500 2 1760 2 chr3A.!!$R2 1758
9 TraesCS3D01G426100 chr3A 674060378 674061737 1359 True 910.000000 1219 91.473500 399 1805 2 chr3A.!!$R3 1406

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
126 127 0.026803 GCGTCGATGGATTGCTTGAC 59.973 55.0 6.79 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1844 2135 0.512952 CACGCCTTTCCAACTCGAAG 59.487 55.0 0.0 0.0 0.0 3.79 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
25 26 1.741770 CACTTGCTAGTGGGCGTCC 60.742 63.158 19.06 0.00 46.52 4.79
82 83 3.107642 ACGTCTTGTTTCCTCATTCGT 57.892 42.857 0.00 0.00 0.00 3.85
91 92 1.244816 TCCTCATTCGTGACTCGTGT 58.755 50.000 0.00 0.00 40.80 4.49
102 103 0.776451 GACTCGTGTACGTGCAACTG 59.224 55.000 8.25 3.77 40.80 3.16
115 116 2.434884 AACTGGCCTGCGTCGATG 60.435 61.111 9.95 0.00 0.00 3.84
121 122 3.017323 CCTGCGTCGATGGATTGC 58.983 61.111 6.79 0.00 0.00 3.56
126 127 0.026803 GCGTCGATGGATTGCTTGAC 59.973 55.000 6.79 0.00 0.00 3.18
127 128 1.358877 CGTCGATGGATTGCTTGACA 58.641 50.000 0.00 0.00 0.00 3.58
150 151 9.268268 GACACTCCATCCGTATCAAAATATAAA 57.732 33.333 0.00 0.00 0.00 1.40
205 319 5.360999 TGGTACAGAGTCAGGATACAAGATG 59.639 44.000 0.00 0.00 41.41 2.90
251 365 8.425577 ACAAGATGAAATTAACCTGATAGTCG 57.574 34.615 0.00 0.00 0.00 4.18
280 394 3.195825 GTCACAGGTTCAGGCTAGTACAT 59.804 47.826 0.00 0.00 0.00 2.29
332 446 3.055385 TCCTTAGCCTCAACACCATGTAC 60.055 47.826 0.00 0.00 0.00 2.90
333 447 3.307410 CCTTAGCCTCAACACCATGTACA 60.307 47.826 0.00 0.00 0.00 2.90
335 449 2.991250 AGCCTCAACACCATGTACATC 58.009 47.619 5.07 0.00 0.00 3.06
336 450 2.017049 GCCTCAACACCATGTACATCC 58.983 52.381 5.07 0.00 0.00 3.51
339 453 2.679837 CTCAACACCATGTACATCCAGC 59.320 50.000 5.07 0.00 0.00 4.85
341 455 2.679837 CAACACCATGTACATCCAGCTC 59.320 50.000 5.07 0.00 0.00 4.09
344 458 2.941064 CACCATGTACATCCAGCTCTTG 59.059 50.000 5.07 0.00 0.00 3.02
345 459 1.945394 CCATGTACATCCAGCTCTTGC 59.055 52.381 5.07 0.00 40.05 4.01
527 641 3.243434 ACAGAATATCCGAAGCGACGATT 60.243 43.478 0.00 0.00 35.09 3.34
697 840 2.289819 CCAGCTTAGGTTTCGTTGGGTA 60.290 50.000 0.00 0.00 0.00 3.69
702 845 4.383173 CTTAGGTTTCGTTGGGTAACACT 58.617 43.478 0.00 0.00 36.58 3.55
780 928 0.329261 CCTCCCAGATCCACTTTGCA 59.671 55.000 0.00 0.00 0.00 4.08
854 1009 3.196254 GCCAAGATGTGAAATGGAATGGT 59.804 43.478 0.00 0.00 34.82 3.55
867 1022 8.328758 TGAAATGGAATGGTATAGTCTTCAGTT 58.671 33.333 0.00 0.00 0.00 3.16
984 1154 1.451028 GCCACAGAGCTTAGGCAGG 60.451 63.158 12.86 1.64 46.26 4.85
987 1157 2.042464 CCACAGAGCTTAGGCAGGATA 58.958 52.381 0.00 0.00 41.70 2.59
988 1158 2.636893 CCACAGAGCTTAGGCAGGATAT 59.363 50.000 0.00 0.00 41.70 1.63
991 1161 5.221722 CCACAGAGCTTAGGCAGGATATAAA 60.222 44.000 0.00 0.00 41.70 1.40
1278 1462 3.069980 GATGAGCTCCGTCGTGGCT 62.070 63.158 12.15 8.57 39.16 4.75
1359 1549 8.314751 GGGTAGCCATGGATATATACATACATC 58.685 40.741 18.40 0.00 28.03 3.06
1603 1836 4.153117 CAGTTCCTTTTTGGATGTCGAGAG 59.847 45.833 0.00 0.00 45.68 3.20
1636 1869 6.312918 ACAAGTGCCGTATCAAAATACAGTAG 59.687 38.462 0.00 0.00 38.11 2.57
1637 1870 5.974108 AGTGCCGTATCAAAATACAGTAGT 58.026 37.500 0.00 0.00 38.11 2.73
1681 1914 7.542890 TCACATCTTGTTTTTGCTTGAAACTA 58.457 30.769 10.10 4.04 37.75 2.24
1714 1947 1.060729 TCGTCTGGTTCCCATCCAAA 58.939 50.000 0.00 0.00 34.35 3.28
1829 2120 4.783621 TGAGCTCGCCCATGCACC 62.784 66.667 9.64 0.00 37.32 5.01
1848 2139 2.268298 CCGGCCGGATATAATTCTTCG 58.732 52.381 41.82 6.03 37.50 3.79
1866 2157 0.882927 CGAGTTGGAAAGGCGTGGAA 60.883 55.000 0.00 0.00 0.00 3.53
1871 2162 1.344065 TGGAAAGGCGTGGAAGACTA 58.656 50.000 0.00 0.00 0.00 2.59
1877 2168 1.405821 AGGCGTGGAAGACTAATCGAG 59.594 52.381 0.00 0.00 0.00 4.04
1938 2229 1.379044 GCATCCCCACCCACTCAAG 60.379 63.158 0.00 0.00 0.00 3.02
1945 2236 2.121963 ACCCACTCAAGGCCTCCA 60.122 61.111 5.23 0.00 0.00 3.86
1950 2241 4.101448 CTCAAGGCCTCCACCCCG 62.101 72.222 5.23 0.00 0.00 5.73
1968 2259 1.985116 GTGCTTCCTCTCCCCTCGT 60.985 63.158 0.00 0.00 0.00 4.18
2037 2335 1.379977 CTGGGCTCTGACGTCCCTA 60.380 63.158 14.12 3.72 40.69 3.53
2040 2338 2.128507 GGCTCTGACGTCCCTAGGG 61.129 68.421 23.22 23.22 0.00 3.53
2047 2345 3.296054 CGTCCCTAGGGCGGCTAG 61.296 72.222 27.32 8.58 33.48 3.42
2053 2351 2.894565 CTAGGGCGGCTAGTCGTCG 61.895 68.421 19.35 0.00 45.28 5.12
2054 2352 3.687321 TAGGGCGGCTAGTCGTCGT 62.687 63.158 20.92 20.92 44.09 4.34
2067 2365 2.358737 GTCGTGTGGGGGCTCTTG 60.359 66.667 0.00 0.00 0.00 3.02
2103 2401 2.887568 CGCTCCTCCATGCGTGTC 60.888 66.667 4.96 0.00 46.09 3.67
2159 2458 4.091939 GGTGGTGGAGCCCCGTAC 62.092 72.222 0.00 0.00 36.04 3.67
2160 2459 4.091939 GTGGTGGAGCCCCGTACC 62.092 72.222 0.00 0.00 36.04 3.34
2164 2463 4.791069 TGGAGCCCCGTACCCCTC 62.791 72.222 0.00 0.00 34.29 4.30
2169 2468 3.455469 CCCCGTACCCCTCGTGTC 61.455 72.222 0.00 0.00 0.00 3.67
2170 2469 3.818787 CCCGTACCCCTCGTGTCG 61.819 72.222 0.00 0.00 0.00 4.35
2171 2470 4.487412 CCGTACCCCTCGTGTCGC 62.487 72.222 0.00 0.00 0.00 5.19
2172 2471 4.487412 CGTACCCCTCGTGTCGCC 62.487 72.222 0.00 0.00 0.00 5.54
2173 2472 3.066814 GTACCCCTCGTGTCGCCT 61.067 66.667 0.00 0.00 0.00 5.52
2174 2473 2.753043 TACCCCTCGTGTCGCCTC 60.753 66.667 0.00 0.00 0.00 4.70
2211 2510 3.855853 GCGGCCTCTCCTTCCCTC 61.856 72.222 0.00 0.00 0.00 4.30
2212 2511 3.532155 CGGCCTCTCCTTCCCTCG 61.532 72.222 0.00 0.00 0.00 4.63
2213 2512 3.855853 GGCCTCTCCTTCCCTCGC 61.856 72.222 0.00 0.00 0.00 5.03
2214 2513 3.855853 GCCTCTCCTTCCCTCGCC 61.856 72.222 0.00 0.00 0.00 5.54
2215 2514 2.364317 CCTCTCCTTCCCTCGCCA 60.364 66.667 0.00 0.00 0.00 5.69
2216 2515 2.726351 CCTCTCCTTCCCTCGCCAC 61.726 68.421 0.00 0.00 0.00 5.01
2217 2516 2.683933 TCTCCTTCCCTCGCCACC 60.684 66.667 0.00 0.00 0.00 4.61
2218 2517 2.685380 CTCCTTCCCTCGCCACCT 60.685 66.667 0.00 0.00 0.00 4.00
2219 2518 1.381327 CTCCTTCCCTCGCCACCTA 60.381 63.158 0.00 0.00 0.00 3.08
2220 2519 0.976073 CTCCTTCCCTCGCCACCTAA 60.976 60.000 0.00 0.00 0.00 2.69
2221 2520 0.976073 TCCTTCCCTCGCCACCTAAG 60.976 60.000 0.00 0.00 0.00 2.18
2222 2521 1.153349 CTTCCCTCGCCACCTAAGC 60.153 63.158 0.00 0.00 0.00 3.09
2223 2522 2.595009 CTTCCCTCGCCACCTAAGCC 62.595 65.000 0.00 0.00 0.00 4.35
2224 2523 4.176752 CCCTCGCCACCTAAGCCC 62.177 72.222 0.00 0.00 0.00 5.19
2225 2524 4.176752 CCTCGCCACCTAAGCCCC 62.177 72.222 0.00 0.00 0.00 5.80
2226 2525 4.176752 CTCGCCACCTAAGCCCCC 62.177 72.222 0.00 0.00 0.00 5.40
2227 2526 4.733725 TCGCCACCTAAGCCCCCT 62.734 66.667 0.00 0.00 0.00 4.79
2228 2527 4.176752 CGCCACCTAAGCCCCCTC 62.177 72.222 0.00 0.00 0.00 4.30
2229 2528 3.810188 GCCACCTAAGCCCCCTCC 61.810 72.222 0.00 0.00 0.00 4.30
2230 2529 3.097162 CCACCTAAGCCCCCTCCC 61.097 72.222 0.00 0.00 0.00 4.30
2231 2530 2.286121 CACCTAAGCCCCCTCCCA 60.286 66.667 0.00 0.00 0.00 4.37
2232 2531 2.286197 ACCTAAGCCCCCTCCCAC 60.286 66.667 0.00 0.00 0.00 4.61
2233 2532 3.097162 CCTAAGCCCCCTCCCACC 61.097 72.222 0.00 0.00 0.00 4.61
2234 2533 3.097162 CTAAGCCCCCTCCCACCC 61.097 72.222 0.00 0.00 0.00 4.61
2235 2534 4.771745 TAAGCCCCCTCCCACCCC 62.772 72.222 0.00 0.00 0.00 4.95
2241 2540 4.371231 CCCTCCCACCCCCTTCCT 62.371 72.222 0.00 0.00 0.00 3.36
2242 2541 3.017581 CCTCCCACCCCCTTCCTG 61.018 72.222 0.00 0.00 0.00 3.86
2243 2542 2.204151 CTCCCACCCCCTTCCTGT 60.204 66.667 0.00 0.00 0.00 4.00
2244 2543 2.204090 TCCCACCCCCTTCCTGTC 60.204 66.667 0.00 0.00 0.00 3.51
2245 2544 3.717294 CCCACCCCCTTCCTGTCG 61.717 72.222 0.00 0.00 0.00 4.35
2246 2545 4.410400 CCACCCCCTTCCTGTCGC 62.410 72.222 0.00 0.00 0.00 5.19
2247 2546 3.322466 CACCCCCTTCCTGTCGCT 61.322 66.667 0.00 0.00 0.00 4.93
2248 2547 3.322466 ACCCCCTTCCTGTCGCTG 61.322 66.667 0.00 0.00 0.00 5.18
2249 2548 4.785453 CCCCCTTCCTGTCGCTGC 62.785 72.222 0.00 0.00 0.00 5.25
2250 2549 4.785453 CCCCTTCCTGTCGCTGCC 62.785 72.222 0.00 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 1.595466 ACGATAGGGCTAGAGACACG 58.405 55.000 0.00 0.00 43.77 4.49
82 83 0.382873 AGTTGCACGTACACGAGTCA 59.617 50.000 9.04 1.01 43.02 3.41
91 92 2.668212 GCAGGCCAGTTGCACGTA 60.668 61.111 5.01 0.00 43.89 3.57
102 103 2.203070 AATCCATCGACGCAGGCC 60.203 61.111 0.00 0.00 0.00 5.19
121 122 3.801114 TGATACGGATGGAGTGTCAAG 57.199 47.619 0.00 0.00 36.92 3.02
127 128 9.847224 ACTTTTATATTTTGATACGGATGGAGT 57.153 29.630 0.00 0.00 0.00 3.85
251 365 2.417515 GCCTGAACCTGTGACTAGCTAC 60.418 54.545 0.00 0.00 0.00 3.58
298 412 6.875972 TGAGGCTAAGGAAGAGAAATAACT 57.124 37.500 0.00 0.00 0.00 2.24
350 464 8.529476 ACGAAGCTAAGGAAGAGAAATAACTAA 58.471 33.333 0.00 0.00 0.00 2.24
351 465 7.974501 CACGAAGCTAAGGAAGAGAAATAACTA 59.025 37.037 0.00 0.00 0.00 2.24
352 466 6.814146 CACGAAGCTAAGGAAGAGAAATAACT 59.186 38.462 0.00 0.00 0.00 2.24
353 467 6.455780 GCACGAAGCTAAGGAAGAGAAATAAC 60.456 42.308 0.00 0.00 41.15 1.89
354 468 5.581085 GCACGAAGCTAAGGAAGAGAAATAA 59.419 40.000 0.00 0.00 41.15 1.40
355 469 5.109903 GCACGAAGCTAAGGAAGAGAAATA 58.890 41.667 0.00 0.00 41.15 1.40
356 470 3.935828 GCACGAAGCTAAGGAAGAGAAAT 59.064 43.478 0.00 0.00 41.15 2.17
357 471 3.244078 TGCACGAAGCTAAGGAAGAGAAA 60.244 43.478 6.22 0.00 45.94 2.52
358 472 2.299013 TGCACGAAGCTAAGGAAGAGAA 59.701 45.455 6.22 0.00 45.94 2.87
359 473 1.893137 TGCACGAAGCTAAGGAAGAGA 59.107 47.619 6.22 0.00 45.94 3.10
360 474 2.370281 TGCACGAAGCTAAGGAAGAG 57.630 50.000 6.22 0.00 45.94 2.85
361 475 2.037251 AGTTGCACGAAGCTAAGGAAGA 59.963 45.455 6.22 0.00 45.94 2.87
362 476 2.158449 CAGTTGCACGAAGCTAAGGAAG 59.842 50.000 6.22 0.00 45.94 3.46
363 477 2.143122 CAGTTGCACGAAGCTAAGGAA 58.857 47.619 6.22 0.00 45.94 3.36
364 478 1.070134 ACAGTTGCACGAAGCTAAGGA 59.930 47.619 6.22 0.00 45.94 3.36
365 479 1.195448 CACAGTTGCACGAAGCTAAGG 59.805 52.381 6.22 0.00 45.94 2.69
366 480 1.195448 CCACAGTTGCACGAAGCTAAG 59.805 52.381 6.22 0.00 45.94 2.18
367 481 1.225855 CCACAGTTGCACGAAGCTAA 58.774 50.000 6.22 0.00 45.94 3.09
368 482 1.227999 GCCACAGTTGCACGAAGCTA 61.228 55.000 6.22 0.00 45.94 3.32
369 483 2.546494 GCCACAGTTGCACGAAGCT 61.546 57.895 6.22 0.00 45.94 3.74
370 484 2.050985 GCCACAGTTGCACGAAGC 60.051 61.111 0.00 0.00 45.96 3.86
371 485 0.317269 CAAGCCACAGTTGCACGAAG 60.317 55.000 0.00 0.00 0.00 3.79
372 486 1.029408 ACAAGCCACAGTTGCACGAA 61.029 50.000 0.00 0.00 0.00 3.85
373 487 0.179070 TACAAGCCACAGTTGCACGA 60.179 50.000 0.00 0.00 0.00 4.35
374 488 0.660488 TTACAAGCCACAGTTGCACG 59.340 50.000 0.00 0.00 0.00 5.34
527 641 4.469227 CCCTTTCCAGATCAGAGAGAGAAA 59.531 45.833 0.00 0.00 0.00 2.52
563 677 1.615392 ACATGCTTGCCAAGGTTCTTC 59.385 47.619 6.57 0.00 0.00 2.87
697 840 0.180406 AAGTGGCACGAGGAAGTGTT 59.820 50.000 12.71 0.00 43.61 3.32
702 845 1.153066 TGCAAAGTGGCACGAGGAA 60.153 52.632 12.71 0.00 39.25 3.36
780 928 2.735762 GCATCGACGAAACTTAGCTCCT 60.736 50.000 0.00 0.00 0.00 3.69
867 1022 5.675684 TTGTGCATGAGATAGGTAGACAA 57.324 39.130 0.00 0.00 0.00 3.18
922 1083 0.039256 TTGCTTTGCGATGCTGGAAC 60.039 50.000 12.65 0.00 0.00 3.62
972 1142 6.203723 CACTGTTTTATATCCTGCCTAAGCTC 59.796 42.308 0.00 0.00 40.80 4.09
984 1154 5.827797 TCCCTCCATTGCACTGTTTTATATC 59.172 40.000 3.14 0.00 0.00 1.63
987 1157 4.046286 TCCCTCCATTGCACTGTTTTAT 57.954 40.909 3.14 0.00 0.00 1.40
988 1158 3.517296 TCCCTCCATTGCACTGTTTTA 57.483 42.857 3.14 0.00 0.00 1.52
991 1161 1.620822 GTTCCCTCCATTGCACTGTT 58.379 50.000 3.14 0.00 0.00 3.16
1278 1462 2.603473 CCTGGACCGACCTGACCA 60.603 66.667 0.00 0.00 39.52 4.02
1657 1890 6.651755 AGTTTCAAGCAAAAACAAGATGTG 57.348 33.333 10.11 0.00 38.73 3.21
1681 1914 7.480810 GGAACCAGACGATTGCTTATTTTTAT 58.519 34.615 0.00 0.00 0.00 1.40
1762 1996 8.820831 AGTGATAATCCATATGTAGAGGGAAAG 58.179 37.037 1.24 0.00 32.25 2.62
1808 2099 0.533531 TGCATGGGCGAGCTCATTAG 60.534 55.000 15.40 0.00 45.35 1.73
1829 2120 3.179830 CTCGAAGAATTATATCCGGCCG 58.820 50.000 21.04 21.04 34.09 6.13
1844 2135 0.512952 CACGCCTTTCCAACTCGAAG 59.487 55.000 0.00 0.00 0.00 3.79
1846 2137 1.301401 CCACGCCTTTCCAACTCGA 60.301 57.895 0.00 0.00 0.00 4.04
1848 2139 0.875059 CTTCCACGCCTTTCCAACTC 59.125 55.000 0.00 0.00 0.00 3.01
1877 2168 1.736365 GCAGGGGCTACGAGTACTCC 61.736 65.000 17.23 3.08 36.96 3.85
1945 2236 3.003763 GGAGAGGAAGCACGGGGT 61.004 66.667 0.00 0.00 0.00 4.95
1950 2241 1.950973 GACGAGGGGAGAGGAAGCAC 61.951 65.000 0.00 0.00 0.00 4.40
1953 2244 2.776913 GCGACGAGGGGAGAGGAAG 61.777 68.421 0.00 0.00 0.00 3.46
1992 2283 2.414594 GATCCGCATGGGCTTTGC 59.585 61.111 3.80 2.69 38.10 3.68
1993 2284 2.837883 CGGATCCGCATGGGCTTTG 61.838 63.158 23.37 0.00 38.10 2.77
1994 2285 2.516930 CGGATCCGCATGGGCTTT 60.517 61.111 23.37 0.00 38.10 3.51
1995 2286 4.569180 CCGGATCCGCATGGGCTT 62.569 66.667 29.12 0.00 38.10 4.35
2018 2316 4.459089 GGGACGTCAGAGCCCAGC 62.459 72.222 18.91 0.00 41.64 4.85
2020 2318 1.379977 CTAGGGACGTCAGAGCCCA 60.380 63.158 18.91 0.00 44.55 5.36
2021 2319 2.128507 CCTAGGGACGTCAGAGCCC 61.129 68.421 18.91 9.71 42.37 5.19
2026 2324 3.528370 CCGCCCTAGGGACGTCAG 61.528 72.222 33.21 16.49 37.50 3.51
2029 2327 4.133373 TAGCCGCCCTAGGGACGT 62.133 66.667 33.21 19.57 37.50 4.34
2040 2338 2.874780 CACACGACGACTAGCCGC 60.875 66.667 0.00 0.00 0.00 6.53
2047 2345 4.736896 GAGCCCCCACACGACGAC 62.737 72.222 0.00 0.00 0.00 4.34
2099 2397 4.814294 CCTAGGCACCCGCGACAC 62.814 72.222 8.23 0.00 39.92 3.67
2142 2441 4.091939 GTACGGGGCTCCACCACC 62.092 72.222 1.96 0.00 39.56 4.61
2152 2451 3.455469 GACACGAGGGGTACGGGG 61.455 72.222 0.00 0.00 38.55 5.73
2153 2452 3.818787 CGACACGAGGGGTACGGG 61.819 72.222 0.00 0.00 40.19 5.28
2154 2453 4.487412 GCGACACGAGGGGTACGG 62.487 72.222 0.00 0.00 34.93 4.02
2155 2454 4.487412 GGCGACACGAGGGGTACG 62.487 72.222 0.00 0.00 0.00 3.67
2156 2455 3.061260 GAGGCGACACGAGGGGTAC 62.061 68.421 0.00 0.00 0.00 3.34
2157 2456 2.753043 GAGGCGACACGAGGGGTA 60.753 66.667 0.00 0.00 0.00 3.69
2194 2493 3.855853 GAGGGAAGGAGAGGCCGC 61.856 72.222 0.00 0.00 43.43 6.53
2195 2494 3.532155 CGAGGGAAGGAGAGGCCG 61.532 72.222 0.00 0.00 43.43 6.13
2196 2495 3.855853 GCGAGGGAAGGAGAGGCC 61.856 72.222 0.00 0.00 0.00 5.19
2197 2496 3.855853 GGCGAGGGAAGGAGAGGC 61.856 72.222 0.00 0.00 0.00 4.70
2198 2497 2.364317 TGGCGAGGGAAGGAGAGG 60.364 66.667 0.00 0.00 0.00 3.69
2199 2498 2.726351 GGTGGCGAGGGAAGGAGAG 61.726 68.421 0.00 0.00 0.00 3.20
2200 2499 1.870941 TAGGTGGCGAGGGAAGGAGA 61.871 60.000 0.00 0.00 0.00 3.71
2201 2500 0.976073 TTAGGTGGCGAGGGAAGGAG 60.976 60.000 0.00 0.00 0.00 3.69
2202 2501 0.976073 CTTAGGTGGCGAGGGAAGGA 60.976 60.000 0.00 0.00 0.00 3.36
2203 2502 1.522569 CTTAGGTGGCGAGGGAAGG 59.477 63.158 0.00 0.00 0.00 3.46
2204 2503 1.153349 GCTTAGGTGGCGAGGGAAG 60.153 63.158 0.00 0.00 0.00 3.46
2205 2504 2.666098 GGCTTAGGTGGCGAGGGAA 61.666 63.158 0.00 0.00 0.00 3.97
2206 2505 3.081409 GGCTTAGGTGGCGAGGGA 61.081 66.667 0.00 0.00 0.00 4.20
2207 2506 4.176752 GGGCTTAGGTGGCGAGGG 62.177 72.222 0.00 0.00 0.00 4.30
2208 2507 4.176752 GGGGCTTAGGTGGCGAGG 62.177 72.222 0.00 0.00 0.00 4.63
2209 2508 4.176752 GGGGGCTTAGGTGGCGAG 62.177 72.222 0.00 0.00 0.00 5.03
2210 2509 4.733725 AGGGGGCTTAGGTGGCGA 62.734 66.667 0.00 0.00 0.00 5.54
2211 2510 4.176752 GAGGGGGCTTAGGTGGCG 62.177 72.222 0.00 0.00 0.00 5.69
2212 2511 3.810188 GGAGGGGGCTTAGGTGGC 61.810 72.222 0.00 0.00 0.00 5.01
2213 2512 3.097162 GGGAGGGGGCTTAGGTGG 61.097 72.222 0.00 0.00 0.00 4.61
2214 2513 2.286121 TGGGAGGGGGCTTAGGTG 60.286 66.667 0.00 0.00 0.00 4.00
2215 2514 2.286197 GTGGGAGGGGGCTTAGGT 60.286 66.667 0.00 0.00 0.00 3.08
2216 2515 3.097162 GGTGGGAGGGGGCTTAGG 61.097 72.222 0.00 0.00 0.00 2.69
2217 2516 3.097162 GGGTGGGAGGGGGCTTAG 61.097 72.222 0.00 0.00 0.00 2.18
2218 2517 4.771745 GGGGTGGGAGGGGGCTTA 62.772 72.222 0.00 0.00 0.00 3.09
2224 2523 4.371231 AGGAAGGGGGTGGGAGGG 62.371 72.222 0.00 0.00 0.00 4.30
2225 2524 3.017581 CAGGAAGGGGGTGGGAGG 61.018 72.222 0.00 0.00 0.00 4.30
2226 2525 2.204151 ACAGGAAGGGGGTGGGAG 60.204 66.667 0.00 0.00 0.00 4.30
2227 2526 2.204090 GACAGGAAGGGGGTGGGA 60.204 66.667 0.00 0.00 0.00 4.37
2228 2527 3.717294 CGACAGGAAGGGGGTGGG 61.717 72.222 0.00 0.00 0.00 4.61
2229 2528 4.410400 GCGACAGGAAGGGGGTGG 62.410 72.222 0.00 0.00 0.00 4.61
2230 2529 3.322466 AGCGACAGGAAGGGGGTG 61.322 66.667 0.00 0.00 0.00 4.61
2231 2530 3.322466 CAGCGACAGGAAGGGGGT 61.322 66.667 0.00 0.00 0.00 4.95
2232 2531 4.785453 GCAGCGACAGGAAGGGGG 62.785 72.222 0.00 0.00 0.00 5.40
2233 2532 4.785453 GGCAGCGACAGGAAGGGG 62.785 72.222 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.