Multiple sequence alignment - TraesCS1B01G331800

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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 TraesCS1B01G331800 chr1B 100.000 2315 0 0 1 2315 557923168 557920854 0.000000e+00 4276.0
1 TraesCS1B01G331800 chr1B 79.920 249 43 6 569 814 60547762 60548006 2.360000e-40 176.0
2 TraesCS1B01G331800 chr1B 92.135 89 7 0 2080 2168 164770454 164770366 2.410000e-25 126.0
3 TraesCS1B01G331800 chr1B 88.660 97 11 0 2081 2177 631232764 631232668 4.040000e-23 119.0
4 TraesCS1B01G331800 chr1A 87.576 2149 147 38 1 2085 510374631 510372539 0.000000e+00 2379.0
5 TraesCS1B01G331800 chr1D 92.431 1189 56 13 920 2084 413416225 413415047 0.000000e+00 1666.0
6 TraesCS1B01G331800 chr1D 81.745 619 76 18 227 814 413417228 413416616 1.240000e-132 483.0
7 TraesCS1B01G331800 chr1D 91.111 225 20 0 1 225 413572480 413572256 2.890000e-79 305.0
8 TraesCS1B01G331800 chr1D 94.558 147 7 1 2169 2315 413415045 413414900 2.310000e-55 226.0
9 TraesCS1B01G331800 chr1D 92.135 89 7 0 2080 2168 436100586 436100498 2.410000e-25 126.0
10 TraesCS1B01G331800 chr1D 87.379 103 12 1 2084 2186 308266881 308266780 1.450000e-22 117.0
11 TraesCS1B01G331800 chr3D 78.351 388 76 4 504 884 74318331 74318717 6.390000e-61 244.0
12 TraesCS1B01G331800 chr3D 74.427 524 78 25 407 879 433315908 433316426 8.500000e-40 174.0
13 TraesCS1B01G331800 chr5B 80.212 283 44 7 409 681 677805582 677805862 3.900000e-48 202.0
14 TraesCS1B01G331800 chr4A 76.000 300 49 12 606 884 632865564 632865267 1.440000e-27 134.0
15 TraesCS1B01G331800 chr5A 90.816 98 9 0 2084 2181 678203657 678203560 5.190000e-27 132.0
16 TraesCS1B01G331800 chr2D 90.722 97 9 0 2082 2178 25037882 25037978 1.870000e-26 130.0
17 TraesCS1B01G331800 chr3B 89.899 99 8 2 2084 2182 420875914 420876010 2.410000e-25 126.0
18 TraesCS1B01G331800 chr3B 86.792 106 11 3 2079 2182 467226384 467226488 5.230000e-22 115.0
19 TraesCS1B01G331800 chr5D 91.209 91 8 0 2078 2168 223649888 223649978 8.680000e-25 124.0
20 TraesCS1B01G331800 chr2B 75.969 129 23 7 760 882 229779877 229779751 2.480000e-05 60.2


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 TraesCS1B01G331800 chr1B 557920854 557923168 2314 True 4276.000000 4276 100.000 1 2315 1 chr1B.!!$R2 2314
1 TraesCS1B01G331800 chr1A 510372539 510374631 2092 True 2379.000000 2379 87.576 1 2085 1 chr1A.!!$R1 2084
2 TraesCS1B01G331800 chr1D 413414900 413417228 2328 True 791.666667 1666 89.578 227 2315 3 chr1D.!!$R4 2088

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
866 906 0.108329 CCACCCATGTCTCACGGTAC 60.108 60.0 0.0 0.0 0.0 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2284 2636 0.185901 AACTGACATGGGCCAACAGT 59.814 50.0 26.81 26.81 42.4 3.55 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
43 44 1.687493 GGACCCCTCCTCCACTCAG 60.687 68.421 0.00 0.00 33.07 3.35
58 59 3.196463 CACTCAGCTCTCCAATGACATC 58.804 50.000 0.00 0.00 0.00 3.06
60 61 3.118702 ACTCAGCTCTCCAATGACATCAG 60.119 47.826 0.00 0.00 0.00 2.90
157 158 3.102972 TCTGAGGCTGAGCAATCTTACT 58.897 45.455 6.82 0.00 0.00 2.24
175 176 6.297582 TCTTACTCCCTCTCTACTTAATCCG 58.702 44.000 0.00 0.00 0.00 4.18
176 177 3.224269 ACTCCCTCTCTACTTAATCCGC 58.776 50.000 0.00 0.00 0.00 5.54
189 190 1.164411 AATCCGCGCTTTTGATGTCA 58.836 45.000 5.56 0.00 0.00 3.58
213 214 2.566913 TGCTTGTGTACGTCACCAAAT 58.433 42.857 13.24 0.00 45.61 2.32
220 221 3.682858 GTGTACGTCACCAAATGTAGCAT 59.317 43.478 0.00 0.00 40.84 3.79
302 304 6.089954 GCAAATAAAGCTTCACCAGATTCAAC 59.910 38.462 0.00 0.00 27.99 3.18
307 309 3.054802 AGCTTCACCAGATTCAACCCTAG 60.055 47.826 0.00 0.00 0.00 3.02
325 327 4.141528 CCCTAGCTCTTGAAGTTGGATGAT 60.142 45.833 0.00 0.00 0.00 2.45
330 332 4.498241 CTCTTGAAGTTGGATGATGACGA 58.502 43.478 0.00 0.00 0.00 4.20
331 333 4.245660 TCTTGAAGTTGGATGATGACGAC 58.754 43.478 0.00 0.00 0.00 4.34
349 351 5.122554 TGACGACTAAGCTTTTGTTGACAAA 59.877 36.000 19.86 5.25 43.36 2.83
368 370 7.802738 TGACAAACGTTGTGATAGATAAAAGG 58.197 34.615 0.00 0.00 45.52 3.11
399 401 6.546972 TTGCACATTTAATACGTCAACTCA 57.453 33.333 0.00 0.00 0.00 3.41
418 420 1.520174 CACTGACGCATTAGAGCATCG 59.480 52.381 0.00 0.00 42.67 3.84
430 432 0.602562 GAGCATCGCTAGCAGATCCT 59.397 55.000 16.45 13.37 39.88 3.24
458 460 5.694231 AACGGTCAAACCTTGGTATTTAC 57.306 39.130 0.00 0.00 35.66 2.01
460 462 3.995705 CGGTCAAACCTTGGTATTTACGA 59.004 43.478 0.00 0.00 35.66 3.43
470 472 5.236478 CCTTGGTATTTACGATACAAGCTGG 59.764 44.000 0.00 0.00 0.00 4.85
486 488 1.067846 GCTGGAAAAATCACCCCGAAC 60.068 52.381 0.00 0.00 0.00 3.95
534 555 1.550976 CCTATATTCGAGCCCCAGTCC 59.449 57.143 0.00 0.00 0.00 3.85
557 578 5.125739 CCGTTATATCTAGAGGATTTCGGCT 59.874 44.000 0.00 0.00 35.98 5.52
584 605 2.257409 GAGGATCCTGCAAAGCCGGA 62.257 60.000 22.02 4.64 45.26 5.14
588 609 0.539438 ATCCTGCAAAGCCGGACAAA 60.539 50.000 5.05 0.00 44.10 2.83
648 669 3.385384 CAGGCGGAGGAGCTCACA 61.385 66.667 17.19 0.00 37.29 3.58
654 675 4.154347 GAGGAGCTCACAGGCGGG 62.154 72.222 17.19 0.00 37.29 6.13
709 741 2.226330 GTGTGTCACCAATGTAGGCAA 58.774 47.619 0.00 0.00 0.00 4.52
757 789 4.680237 CGCTGTTCTGGCCGACCA 62.680 66.667 0.00 0.00 46.51 4.02
789 821 4.758251 CCATGCGTGCGTCCCAGA 62.758 66.667 0.00 0.00 0.00 3.86
808 840 4.395542 CCAGAAAAGAAGAAGCATGAGGAG 59.604 45.833 0.00 0.00 0.00 3.69
814 851 5.956068 AGAAGAAGCATGAGGAGAAAAAC 57.044 39.130 0.00 0.00 0.00 2.43
833 870 8.357402 AGAAAAACAATGTTTACTGTATGGGTC 58.643 33.333 12.11 0.00 0.00 4.46
836 873 9.528489 AAAACAATGTTTACTGTATGGGTCTAT 57.472 29.630 12.11 0.00 0.00 1.98
839 876 9.778741 ACAATGTTTACTGTATGGGTCTATATG 57.221 33.333 0.00 0.00 0.00 1.78
849 886 7.016296 TGTATGGGTCTATATGATCTGTTCCA 58.984 38.462 0.00 0.00 0.00 3.53
856 896 5.846164 TCTATATGATCTGTTCCACCCATGT 59.154 40.000 0.00 0.00 0.00 3.21
860 900 1.728323 TCTGTTCCACCCATGTCTCA 58.272 50.000 0.00 0.00 0.00 3.27
866 906 0.108329 CCACCCATGTCTCACGGTAC 60.108 60.000 0.00 0.00 0.00 3.34
884 924 4.492409 CGGTACCGTAAATTCGTTTTAGGC 60.492 45.833 26.39 0.00 35.36 3.93
886 926 3.066380 ACCGTAAATTCGTTTTAGGCGT 58.934 40.909 7.39 0.00 35.36 5.68
889 929 4.456914 CGTAAATTCGTTTTAGGCGTGTT 58.543 39.130 0.00 0.00 31.19 3.32
891 931 5.396070 CGTAAATTCGTTTTAGGCGTGTTTT 59.604 36.000 0.00 0.00 31.19 2.43
894 934 6.736807 AATTCGTTTTAGGCGTGTTTTTAC 57.263 33.333 0.00 0.00 0.00 2.01
910 1234 3.293311 TTTACACGTGGTGCTAGAGAC 57.707 47.619 21.57 0.00 36.98 3.36
917 1241 1.743958 GTGGTGCTAGAGACGCTCTTA 59.256 52.381 13.34 1.06 41.50 2.10
942 1266 3.684788 CCAAACCCTCGTCTAGATTGTTG 59.315 47.826 0.00 0.00 0.00 3.33
1379 1704 0.324738 TTGGGTGTTGCCAGGTTTCA 60.325 50.000 0.00 0.00 39.65 2.69
1396 1721 2.577606 TCATGGGTACAAAGGTGTGG 57.422 50.000 0.00 0.00 38.82 4.17
1491 1816 1.999648 ACATGTGCTGGTTGGAATGT 58.000 45.000 0.00 0.00 0.00 2.71
1533 1859 7.440198 TGTGATGAACAAATTAGCCAATTTCA 58.560 30.769 0.00 0.00 41.41 2.69
1540 1866 5.185635 ACAAATTAGCCAATTTCAGCAGCTA 59.814 36.000 0.00 0.00 41.41 3.32
1588 1916 8.579850 TTATCTTGATGGATTGCTGTACTTTT 57.420 30.769 0.00 0.00 0.00 2.27
1589 1917 6.899393 TCTTGATGGATTGCTGTACTTTTT 57.101 33.333 0.00 0.00 0.00 1.94
1753 2096 4.331168 GCATTGTTAGACATGAGTCCAGAC 59.669 45.833 0.00 0.00 46.15 3.51
1759 2102 6.321435 TGTTAGACATGAGTCCAGACGATATT 59.679 38.462 0.00 0.00 46.15 1.28
1760 2103 5.860941 AGACATGAGTCCAGACGATATTT 57.139 39.130 0.00 0.00 46.15 1.40
1761 2104 5.837437 AGACATGAGTCCAGACGATATTTC 58.163 41.667 0.00 0.00 46.15 2.17
1762 2105 4.950050 ACATGAGTCCAGACGATATTTCC 58.050 43.478 0.00 0.00 36.20 3.13
1763 2106 4.651503 ACATGAGTCCAGACGATATTTCCT 59.348 41.667 0.00 0.00 36.20 3.36
1786 2134 2.686915 CCTGGACTTGAATTGCTCCATC 59.313 50.000 0.00 0.00 32.27 3.51
1846 2194 5.210715 CGAGCAATAATTTCCTCATTGAGC 58.789 41.667 8.23 0.00 32.54 4.26
1847 2195 5.008415 CGAGCAATAATTTCCTCATTGAGCT 59.992 40.000 8.23 0.00 32.54 4.09
1848 2196 6.203530 CGAGCAATAATTTCCTCATTGAGCTA 59.796 38.462 8.23 0.00 32.54 3.32
1860 2211 5.027293 TCATTGAGCTACACATATGCAGT 57.973 39.130 1.58 4.63 0.00 4.40
2015 2367 7.448420 AGCTTATCATGATGTATTGCTGTACT 58.552 34.615 18.72 0.00 0.00 2.73
2075 2427 6.935771 AGCCATTTGTTGAAATATTTGCAAGA 59.064 30.769 5.17 5.90 30.20 3.02
2091 2443 4.284378 GCAAGATGCAAACTACTCCATC 57.716 45.455 0.00 0.00 44.26 3.51
2092 2444 3.065925 GCAAGATGCAAACTACTCCATCC 59.934 47.826 0.00 0.00 44.26 3.51
2093 2445 3.185246 AGATGCAAACTACTCCATCCG 57.815 47.619 0.00 0.00 35.78 4.18
2094 2446 2.766263 AGATGCAAACTACTCCATCCGA 59.234 45.455 0.00 0.00 35.78 4.55
2095 2447 2.380084 TGCAAACTACTCCATCCGAC 57.620 50.000 0.00 0.00 0.00 4.79
2096 2448 1.066430 TGCAAACTACTCCATCCGACC 60.066 52.381 0.00 0.00 0.00 4.79
2097 2449 1.742750 GCAAACTACTCCATCCGACCC 60.743 57.143 0.00 0.00 0.00 4.46
2098 2450 1.553248 CAAACTACTCCATCCGACCCA 59.447 52.381 0.00 0.00 0.00 4.51
2099 2451 1.946984 AACTACTCCATCCGACCCAA 58.053 50.000 0.00 0.00 0.00 4.12
2100 2452 1.946984 ACTACTCCATCCGACCCAAA 58.053 50.000 0.00 0.00 0.00 3.28
2101 2453 2.262637 ACTACTCCATCCGACCCAAAA 58.737 47.619 0.00 0.00 0.00 2.44
2102 2454 2.844348 ACTACTCCATCCGACCCAAAAT 59.156 45.455 0.00 0.00 0.00 1.82
2103 2455 2.128771 ACTCCATCCGACCCAAAATG 57.871 50.000 0.00 0.00 0.00 2.32
2104 2456 1.354368 ACTCCATCCGACCCAAAATGT 59.646 47.619 0.00 0.00 0.00 2.71
2105 2457 2.574369 ACTCCATCCGACCCAAAATGTA 59.426 45.455 0.00 0.00 0.00 2.29
2106 2458 3.009695 ACTCCATCCGACCCAAAATGTAA 59.990 43.478 0.00 0.00 0.00 2.41
2107 2459 3.616219 TCCATCCGACCCAAAATGTAAG 58.384 45.455 0.00 0.00 0.00 2.34
2108 2460 3.264706 TCCATCCGACCCAAAATGTAAGA 59.735 43.478 0.00 0.00 0.00 2.10
2109 2461 3.377172 CCATCCGACCCAAAATGTAAGAC 59.623 47.826 0.00 0.00 0.00 3.01
2110 2462 2.690786 TCCGACCCAAAATGTAAGACG 58.309 47.619 0.00 0.00 0.00 4.18
2111 2463 2.037511 TCCGACCCAAAATGTAAGACGT 59.962 45.455 0.00 0.00 0.00 4.34
2112 2464 2.809696 CCGACCCAAAATGTAAGACGTT 59.190 45.455 0.00 0.00 0.00 3.99
2113 2465 3.251487 CCGACCCAAAATGTAAGACGTTT 59.749 43.478 0.00 0.00 38.84 3.60
2114 2466 4.261280 CCGACCCAAAATGTAAGACGTTTT 60.261 41.667 4.14 4.14 45.25 2.43
2115 2467 5.275494 CGACCCAAAATGTAAGACGTTTTT 58.725 37.500 6.77 0.00 42.72 1.94
2157 2509 5.952526 AAAAACGTCTTACATTTCGGGAT 57.047 34.783 0.00 0.00 0.00 3.85
2158 2510 4.939509 AAACGTCTTACATTTCGGGATG 57.060 40.909 0.00 0.00 0.00 3.51
2159 2511 2.901249 ACGTCTTACATTTCGGGATGG 58.099 47.619 4.40 0.00 0.00 3.51
2160 2512 2.498481 ACGTCTTACATTTCGGGATGGA 59.502 45.455 4.40 0.00 0.00 3.41
2161 2513 3.123804 CGTCTTACATTTCGGGATGGAG 58.876 50.000 4.40 2.62 0.00 3.86
2162 2514 3.467803 GTCTTACATTTCGGGATGGAGG 58.532 50.000 4.40 0.00 0.00 4.30
2163 2515 2.438021 TCTTACATTTCGGGATGGAGGG 59.562 50.000 4.40 0.00 0.00 4.30
2164 2516 2.184088 TACATTTCGGGATGGAGGGA 57.816 50.000 4.40 0.00 0.00 4.20
2165 2517 0.839946 ACATTTCGGGATGGAGGGAG 59.160 55.000 4.40 0.00 0.00 4.30
2166 2518 0.839946 CATTTCGGGATGGAGGGAGT 59.160 55.000 0.00 0.00 0.00 3.85
2167 2519 2.047061 CATTTCGGGATGGAGGGAGTA 58.953 52.381 0.00 0.00 0.00 2.59
2174 2526 3.136626 CGGGATGGAGGGAGTAAATCTTT 59.863 47.826 0.00 0.00 0.00 2.52
2179 2531 7.458170 GGGATGGAGGGAGTAAATCTTTATAGA 59.542 40.741 0.00 0.00 34.21 1.98
2210 2562 0.038744 ATGGAACCTTGCTCACTGGG 59.961 55.000 0.00 0.00 0.00 4.45
2241 2593 5.175388 GGAGTGTTATCCTTACCTTTGGT 57.825 43.478 0.00 0.00 36.70 3.67
2284 2636 6.613699 AGCACATCCATAAAGATCCCAAATA 58.386 36.000 0.00 0.00 0.00 1.40
2285 2637 6.491403 AGCACATCCATAAAGATCCCAAATAC 59.509 38.462 0.00 0.00 0.00 1.89
2287 2639 7.522725 GCACATCCATAAAGATCCCAAATACTG 60.523 40.741 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 6.206634 GGTCCATCAGAAAGTTTGACATTACA 59.793 38.462 0.00 0.00 0.00 2.41
11 12 2.716424 AGGGGTCCATCAGAAAGTTTGA 59.284 45.455 0.00 0.00 0.00 2.69
22 23 1.003573 AGTGGAGGAGGGGTCCATC 59.996 63.158 0.00 0.00 45.91 3.51
43 44 3.626670 CCTTTCTGATGTCATTGGAGAGC 59.373 47.826 0.00 0.00 0.00 4.09
103 104 9.778741 GTTCAGGTTACATGGATTAATCTATCA 57.221 33.333 14.95 5.49 0.00 2.15
157 158 2.228059 CGCGGATTAAGTAGAGAGGGA 58.772 52.381 0.00 0.00 0.00 4.20
189 190 3.999821 TGACGTACACAAGCATGGT 57.000 47.368 0.00 0.00 0.00 3.55
213 214 6.668283 GGGAGATAGTTTATAGGGATGCTACA 59.332 42.308 0.00 0.00 0.00 2.74
220 221 7.431936 AAGTAGGGGAGATAGTTTATAGGGA 57.568 40.000 0.00 0.00 0.00 4.20
270 271 6.058833 TGGTGAAGCTTTATTTGCGGATATA 58.941 36.000 0.00 0.00 35.28 0.86
275 276 2.487762 TCTGGTGAAGCTTTATTTGCGG 59.512 45.455 0.00 0.00 35.28 5.69
278 279 6.587608 GGTTGAATCTGGTGAAGCTTTATTTG 59.412 38.462 0.00 0.00 0.00 2.32
302 304 3.198635 TCATCCAACTTCAAGAGCTAGGG 59.801 47.826 0.00 0.00 0.00 3.53
307 309 3.063180 CGTCATCATCCAACTTCAAGAGC 59.937 47.826 0.00 0.00 0.00 4.09
325 327 4.185394 TGTCAACAAAAGCTTAGTCGTCA 58.815 39.130 0.00 0.00 0.00 4.35
330 332 5.305139 ACGTTTGTCAACAAAAGCTTAGT 57.695 34.783 17.59 0.00 46.08 2.24
331 333 5.571357 ACAACGTTTGTCAACAAAAGCTTAG 59.429 36.000 17.59 0.00 46.08 2.18
349 351 6.170506 TGCTTCCTTTTATCTATCACAACGT 58.829 36.000 0.00 0.00 0.00 3.99
368 370 7.061673 TGACGTATTAAATGTGCAATTTGCTTC 59.938 33.333 21.19 14.46 45.31 3.86
399 401 1.845266 CGATGCTCTAATGCGTCAGT 58.155 50.000 9.00 0.00 46.16 3.41
418 420 3.309954 CCGTTTTTACAGGATCTGCTAGC 59.690 47.826 8.10 8.10 34.37 3.42
430 432 3.762823 ACCAAGGTTTGACCGTTTTTACA 59.237 39.130 0.00 0.00 44.90 2.41
458 460 4.438744 GGGTGATTTTTCCAGCTTGTATCG 60.439 45.833 0.00 0.00 33.02 2.92
460 462 3.769300 GGGGTGATTTTTCCAGCTTGTAT 59.231 43.478 0.00 0.00 33.02 2.29
470 472 3.128764 GGATCTGTTCGGGGTGATTTTTC 59.871 47.826 0.00 0.00 0.00 2.29
534 555 6.030849 CAGCCGAAATCCTCTAGATATAACG 58.969 44.000 0.00 0.98 33.66 3.18
557 578 2.673775 TGCAGGATCCTCCAAAAACA 57.326 45.000 12.69 0.00 39.61 2.83
575 596 2.255252 CGGCTTTGTCCGGCTTTG 59.745 61.111 0.00 0.00 45.38 2.77
584 605 2.282462 CCCCTGCTTCGGCTTTGT 60.282 61.111 0.00 0.00 42.37 2.83
661 682 2.816958 CGTGCTCTGGCGATGCTT 60.817 61.111 0.00 0.00 42.25 3.91
681 702 4.344865 GGTGACACACCGGGCCAT 62.345 66.667 6.32 0.00 44.95 4.40
690 722 2.226330 GTTGCCTACATTGGTGACACA 58.774 47.619 8.08 0.00 42.67 3.72
692 724 1.518325 CGTTGCCTACATTGGTGACA 58.482 50.000 0.00 0.00 39.83 3.58
756 788 2.254459 CATGGACGAACTCGAACTCTG 58.746 52.381 6.05 0.00 43.02 3.35
757 789 1.402984 GCATGGACGAACTCGAACTCT 60.403 52.381 6.05 0.00 43.02 3.24
758 790 0.992802 GCATGGACGAACTCGAACTC 59.007 55.000 6.05 0.00 43.02 3.01
789 821 6.966534 TTTTCTCCTCATGCTTCTTCTTTT 57.033 33.333 0.00 0.00 0.00 2.27
808 840 8.357402 AGACCCATACAGTAAACATTGTTTTTC 58.643 33.333 19.15 12.80 0.00 2.29
814 851 9.996554 TCATATAGACCCATACAGTAAACATTG 57.003 33.333 0.00 0.00 0.00 2.82
833 870 6.013898 AGACATGGGTGGAACAGATCATATAG 60.014 42.308 0.00 0.00 41.80 1.31
836 873 4.040047 AGACATGGGTGGAACAGATCATA 58.960 43.478 0.00 0.00 41.80 2.15
838 875 2.237143 GAGACATGGGTGGAACAGATCA 59.763 50.000 0.00 0.00 41.80 2.92
839 876 2.237143 TGAGACATGGGTGGAACAGATC 59.763 50.000 0.00 0.00 41.80 2.75
849 886 1.601419 CGGTACCGTGAGACATGGGT 61.601 60.000 26.39 8.31 44.23 4.51
866 906 3.120580 ACACGCCTAAAACGAATTTACGG 60.121 43.478 0.00 0.40 37.61 4.02
886 926 3.794717 TCTAGCACCACGTGTAAAAACA 58.205 40.909 15.65 0.00 35.75 2.83
889 929 3.645884 GTCTCTAGCACCACGTGTAAAA 58.354 45.455 15.65 0.00 35.75 1.52
891 931 1.198408 CGTCTCTAGCACCACGTGTAA 59.802 52.381 15.65 0.00 35.75 2.41
894 934 1.801913 GCGTCTCTAGCACCACGTG 60.802 63.158 9.08 9.08 34.69 4.49
897 937 0.528470 AAGAGCGTCTCTAGCACCAC 59.472 55.000 9.33 0.00 40.28 4.16
898 938 1.743958 GTAAGAGCGTCTCTAGCACCA 59.256 52.381 9.33 0.00 40.28 4.17
899 939 1.743958 TGTAAGAGCGTCTCTAGCACC 59.256 52.381 9.33 0.00 40.28 5.01
900 940 2.478200 GGTGTAAGAGCGTCTCTAGCAC 60.478 54.545 21.21 21.21 40.28 4.40
910 1234 1.439679 GAGGGTTTGGTGTAAGAGCG 58.560 55.000 0.00 0.00 0.00 5.03
917 1241 2.005370 TCTAGACGAGGGTTTGGTGT 57.995 50.000 0.00 0.00 0.00 4.16
942 1266 2.100197 GATTCTAGGGTTTTGGTGGGC 58.900 52.381 0.00 0.00 0.00 5.36
1379 1704 2.062636 AGACCACACCTTTGTACCCAT 58.937 47.619 0.00 0.00 33.30 4.00
1396 1721 2.678336 GCACCAGTATACAGCCAAAGAC 59.322 50.000 5.50 0.00 0.00 3.01
1491 1816 1.034838 ACAAACGACAGCAAGCCCAA 61.035 50.000 0.00 0.00 0.00 4.12
1570 1897 4.082026 AGCCAAAAAGTACAGCAATCCATC 60.082 41.667 0.00 0.00 0.00 3.51
1588 1916 4.662468 TTTCAGTGCATACAAAAGCCAA 57.338 36.364 0.00 0.00 0.00 4.52
1589 1917 4.870123 ATTTCAGTGCATACAAAAGCCA 57.130 36.364 0.00 0.00 0.00 4.75
1654 1982 8.765517 ACGGTTTCCTAATCCTTAAGAAGATAA 58.234 33.333 3.36 0.00 0.00 1.75
1655 1983 8.202137 CACGGTTTCCTAATCCTTAAGAAGATA 58.798 37.037 3.36 0.00 0.00 1.98
1662 1990 4.566070 CCACCACGGTTTCCTAATCCTTAA 60.566 45.833 0.00 0.00 0.00 1.85
1665 1993 1.280998 CCACCACGGTTTCCTAATCCT 59.719 52.381 0.00 0.00 0.00 3.24
1760 2103 1.887956 GCAATTCAAGTCCAGGCAGGA 60.888 52.381 0.00 0.00 46.75 3.86
1761 2104 0.529378 GCAATTCAAGTCCAGGCAGG 59.471 55.000 0.00 0.00 39.47 4.85
1762 2105 1.471684 GAGCAATTCAAGTCCAGGCAG 59.528 52.381 0.00 0.00 0.00 4.85
1763 2106 1.538047 GAGCAATTCAAGTCCAGGCA 58.462 50.000 0.00 0.00 0.00 4.75
1786 2134 3.005367 GGTGTTTGTCCTTACCATTGGTG 59.995 47.826 18.83 2.29 36.19 4.17
1804 2152 0.677842 GGACAGTCGTGGTAAGGTGT 59.322 55.000 0.00 0.00 0.00 4.16
1846 2194 6.296365 CAGGAAATGACTGCATATGTGTAG 57.704 41.667 6.01 6.01 42.93 2.74
1878 2229 4.163649 AGCCCAAAGGTAAGGTACAGATAC 59.836 45.833 0.00 0.00 34.57 2.24
2015 2367 3.386078 TCAGTGCATACCAAAGCCAAAAA 59.614 39.130 0.00 0.00 0.00 1.94
2075 2427 2.420129 GGTCGGATGGAGTAGTTTGCAT 60.420 50.000 0.00 0.00 0.00 3.96
2085 2437 2.128771 ACATTTTGGGTCGGATGGAG 57.871 50.000 0.00 0.00 0.00 3.86
2086 2438 3.264706 TCTTACATTTTGGGTCGGATGGA 59.735 43.478 0.00 0.00 0.00 3.41
2087 2439 3.377172 GTCTTACATTTTGGGTCGGATGG 59.623 47.826 0.00 0.00 0.00 3.51
2088 2440 3.063452 CGTCTTACATTTTGGGTCGGATG 59.937 47.826 0.00 0.00 0.00 3.51
2089 2441 3.267483 CGTCTTACATTTTGGGTCGGAT 58.733 45.455 0.00 0.00 0.00 4.18
2090 2442 2.037511 ACGTCTTACATTTTGGGTCGGA 59.962 45.455 0.00 0.00 0.00 4.55
2091 2443 2.419667 ACGTCTTACATTTTGGGTCGG 58.580 47.619 0.00 0.00 0.00 4.79
2092 2444 4.477302 AAACGTCTTACATTTTGGGTCG 57.523 40.909 0.00 0.00 0.00 4.79
2135 2487 5.335348 CCATCCCGAAATGTAAGACGTTTTT 60.335 40.000 0.00 0.00 37.43 1.94
2136 2488 4.155280 CCATCCCGAAATGTAAGACGTTTT 59.845 41.667 0.00 0.00 37.43 2.43
2137 2489 3.687698 CCATCCCGAAATGTAAGACGTTT 59.312 43.478 0.00 0.00 39.79 3.60
2138 2490 3.055675 TCCATCCCGAAATGTAAGACGTT 60.056 43.478 0.00 0.00 0.00 3.99
2139 2491 2.498481 TCCATCCCGAAATGTAAGACGT 59.502 45.455 0.00 0.00 0.00 4.34
2140 2492 3.123804 CTCCATCCCGAAATGTAAGACG 58.876 50.000 0.00 0.00 0.00 4.18
2141 2493 3.467803 CCTCCATCCCGAAATGTAAGAC 58.532 50.000 0.00 0.00 0.00 3.01
2142 2494 2.438021 CCCTCCATCCCGAAATGTAAGA 59.562 50.000 0.00 0.00 0.00 2.10
2143 2495 2.438021 TCCCTCCATCCCGAAATGTAAG 59.562 50.000 0.00 0.00 0.00 2.34
2144 2496 2.438021 CTCCCTCCATCCCGAAATGTAA 59.562 50.000 0.00 0.00 0.00 2.41
2145 2497 2.047061 CTCCCTCCATCCCGAAATGTA 58.953 52.381 0.00 0.00 0.00 2.29
2146 2498 0.839946 CTCCCTCCATCCCGAAATGT 59.160 55.000 0.00 0.00 0.00 2.71
2147 2499 0.839946 ACTCCCTCCATCCCGAAATG 59.160 55.000 0.00 0.00 0.00 2.32
2148 2500 2.489528 TACTCCCTCCATCCCGAAAT 57.510 50.000 0.00 0.00 0.00 2.17
2149 2501 2.257391 TTACTCCCTCCATCCCGAAA 57.743 50.000 0.00 0.00 0.00 3.46
2150 2502 2.257391 TTTACTCCCTCCATCCCGAA 57.743 50.000 0.00 0.00 0.00 4.30
2151 2503 2.090719 AGATTTACTCCCTCCATCCCGA 60.091 50.000 0.00 0.00 0.00 5.14
2152 2504 2.330216 AGATTTACTCCCTCCATCCCG 58.670 52.381 0.00 0.00 0.00 5.14
2153 2505 4.797912 AAAGATTTACTCCCTCCATCCC 57.202 45.455 0.00 0.00 0.00 3.85
2154 2506 8.437274 TCTATAAAGATTTACTCCCTCCATCC 57.563 38.462 0.00 0.00 0.00 3.51
2155 2507 9.315363 TCTCTATAAAGATTTACTCCCTCCATC 57.685 37.037 0.00 0.00 0.00 3.51
2156 2508 9.320295 CTCTCTATAAAGATTTACTCCCTCCAT 57.680 37.037 0.00 0.00 0.00 3.41
2157 2509 8.511969 TCTCTCTATAAAGATTTACTCCCTCCA 58.488 37.037 0.00 0.00 0.00 3.86
2158 2510 8.943594 TCTCTCTATAAAGATTTACTCCCTCC 57.056 38.462 0.00 0.00 0.00 4.30
2179 2531 6.430007 AGCAAGGTTCCATCATAATTTCTCT 58.570 36.000 0.00 0.00 0.00 3.10
2188 2540 2.619849 CCAGTGAGCAAGGTTCCATCAT 60.620 50.000 0.00 0.00 0.00 2.45
2210 2562 6.706716 GGTAAGGATAACACTCCTAGCATTTC 59.293 42.308 0.00 0.00 45.15 2.17
2284 2636 0.185901 AACTGACATGGGCCAACAGT 59.814 50.000 26.81 26.81 42.40 3.55
2285 2637 0.599558 CAACTGACATGGGCCAACAG 59.400 55.000 25.85 25.85 35.14 3.16
2287 2639 0.539438 TCCAACTGACATGGGCCAAC 60.539 55.000 11.89 6.02 38.54 3.77


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

AutoCloner maintained by Alex Coulton.