Multiple sequence alignment - TraesCS1B01G098000

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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 TraesCS1B01G098000 chr1B 100.000 2772 0 0 1 2772 104723018 104720247 0.000000e+00 5120.0
1 TraesCS1B01G098000 chr1B 89.706 136 13 1 2638 2772 555781153 555781018 3.670000e-39 172.0
2 TraesCS1B01G098000 chr1B 97.872 47 1 0 2253 2299 555781559 555781513 6.360000e-12 82.4
3 TraesCS1B01G098000 chr1D 89.648 2299 137 47 1 2239 63924183 63921926 0.000000e+00 2833.0
4 TraesCS1B01G098000 chr1D 82.595 316 23 11 2457 2772 63921419 63921136 1.650000e-62 250.0
5 TraesCS1B01G098000 chr1D 84.496 129 18 2 2290 2418 63921827 63921701 2.900000e-25 126.0
6 TraesCS1B01G098000 chr1A 92.623 1803 77 19 472 2248 63006087 63004315 0.000000e+00 2542.0
7 TraesCS1B01G098000 chr1A 91.209 273 24 0 2500 2772 63003627 63003355 3.370000e-99 372.0
8 TraesCS1B01G098000 chr1A 89.600 250 19 3 71 315 63009803 63009556 7.450000e-81 311.0
9 TraesCS1B01G098000 chr1A 89.041 73 3 1 403 475 63006184 63006117 4.920000e-13 86.1
10 TraesCS1B01G098000 chr1A 97.297 37 1 0 1 37 63011616 63011580 2.300000e-06 63.9
11 TraesCS1B01G098000 chr3D 83.240 358 58 2 2416 2772 243244366 243244722 7.400000e-86 327.0
12 TraesCS1B01G098000 chr3D 97.500 40 1 0 2251 2290 25783608 25783569 4.950000e-08 69.4
13 TraesCS1B01G098000 chr2B 82.065 368 42 10 2414 2772 475629031 475628679 2.700000e-75 292.0
14 TraesCS1B01G098000 chr2B 80.793 328 41 6 2446 2771 225815287 225814980 1.280000e-58 237.0
15 TraesCS1B01G098000 chr7A 81.111 360 54 9 2413 2771 179888110 179887764 2.720000e-70 276.0
16 TraesCS1B01G098000 chr7A 87.195 164 19 2 2413 2575 540954788 540954950 4.710000e-43 185.0
17 TraesCS1B01G098000 chr7A 93.182 44 1 2 2252 2295 180160477 180160436 2.300000e-06 63.9
18 TraesCS1B01G098000 chr7A 94.872 39 1 1 2257 2295 180340974 180340937 2.980000e-05 60.2
19 TraesCS1B01G098000 chrUn 79.832 357 67 5 1365 1718 79450121 79449767 3.540000e-64 255.0
20 TraesCS1B01G098000 chr6D 80.332 361 49 14 2414 2772 62328997 62329337 1.270000e-63 254.0
21 TraesCS1B01G098000 chr6D 97.778 45 1 0 2251 2295 62328732 62328776 8.230000e-11 78.7
22 TraesCS1B01G098000 chr6B 80.851 329 57 6 1374 1699 692044350 692044025 1.270000e-63 254.0
23 TraesCS1B01G098000 chr6B 75.889 506 113 9 1227 1727 691945132 691945633 1.650000e-62 250.0
24 TraesCS1B01G098000 chr6B 93.651 63 4 0 2709 2771 668037946 668038008 8.170000e-16 95.3
25 TraesCS1B01G098000 chr2D 79.942 344 48 14 2429 2771 352120738 352120415 1.660000e-57 233.0
26 TraesCS1B01G098000 chr2D 81.229 293 35 8 2486 2772 648153192 648153470 4.650000e-53 219.0
27 TraesCS1B01G098000 chr5D 80.547 329 41 12 2446 2772 447897027 447896720 5.970000e-57 231.0
28 TraesCS1B01G098000 chr7D 89.744 117 11 1 2413 2528 630301953 630301837 6.190000e-32 148.0
29 TraesCS1B01G098000 chr7D 89.744 117 11 1 2413 2528 630510485 630510369 6.190000e-32 148.0
30 TraesCS1B01G098000 chr7D 83.333 156 25 1 2617 2771 630301827 630301672 2.880000e-30 143.0
31 TraesCS1B01G098000 chr6A 94.118 51 2 1 2248 2297 536430686 536430736 2.960000e-10 76.8
32 TraesCS1B01G098000 chr6A 95.455 44 1 1 2423 2465 594465628 594465671 4.950000e-08 69.4
33 TraesCS1B01G098000 chr5A 95.000 40 2 0 2256 2295 388163658 388163697 2.300000e-06 63.9
34 TraesCS1B01G098000 chr5B 92.683 41 3 0 2256 2296 634069980 634069940 2.980000e-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 TraesCS1B01G098000 chr1B 104720247 104723018 2771 True 5120.000000 5120 100.000000 1 2772 1 chr1B.!!$R1 2771
1 TraesCS1B01G098000 chr1D 63921136 63924183 3047 True 1069.666667 2833 85.579667 1 2772 3 chr1D.!!$R1 2771
2 TraesCS1B01G098000 chr1A 63003355 63011616 8261 True 675.000000 2542 91.954000 1 2772 5 chr1A.!!$R1 2771
3 TraesCS1B01G098000 chr6B 691945132 691945633 501 False 250.000000 250 75.889000 1227 1727 1 chr6B.!!$F2 500

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
307 3831 0.165944 GACGCACAATGAAACCCTCG 59.834 55.0 0.00 0.0 0.0 4.63 F
453 5502 0.452184 TCCTCGCGCAAAACAAAACA 59.548 45.0 8.75 0.0 0.0 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1480 6569 0.524816 TTATGAAGCCGACGTCGAGC 60.525 55.0 37.65 33.79 43.02 5.03 R
2341 7524 0.591170 CGCGCAGAAAGGAAAGGAAA 59.409 50.0 8.75 0.00 0.00 3.13 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
111 1855 5.758784 GGCAACTGGAGGTATAGTTACAATC 59.241 44.000 0.00 0.00 35.50 2.67
122 1866 8.265764 AGGTATAGTTACAATCCCAAAGAAGAC 58.734 37.037 0.00 0.00 0.00 3.01
223 1976 5.469084 ACTGGTATCTTCGACCAAAGAAAAC 59.531 40.000 0.00 0.00 46.27 2.43
229 1982 2.567985 TCGACCAAAGAAAACTGGACC 58.432 47.619 0.00 0.00 36.49 4.46
262 2015 7.010023 GCTGAAAAGACGCCTATAATAATTCG 58.990 38.462 0.00 0.00 0.00 3.34
265 2018 7.496591 TGAAAAGACGCCTATAATAATTCGGTT 59.503 33.333 0.00 0.00 0.00 4.44
291 2044 0.297820 GCTTTTAGATGGTCGCGACG 59.702 55.000 30.99 15.82 0.00 5.12
301 2054 1.203065 GTCGCGACGCACAATGAAA 59.797 52.632 25.19 0.00 0.00 2.69
307 3831 0.165944 GACGCACAATGAAACCCTCG 59.834 55.000 0.00 0.00 0.00 4.63
315 3839 3.315191 ACAATGAAACCCTCGTCTTGTTG 59.685 43.478 0.00 0.00 0.00 3.33
347 3873 5.687285 CAGTTCCTCCTTTTCGATGTTTTTG 59.313 40.000 0.00 0.00 0.00 2.44
372 3898 9.361315 TGATCTGCAATCAAATGAAATAACTTG 57.639 29.630 8.52 0.00 0.00 3.16
411 5460 9.490663 CGTTTTTCATATAGCTCTTACTTTTGG 57.509 33.333 0.00 0.00 0.00 3.28
427 5476 2.570415 TTGGCCGTCAAGTCCATTTA 57.430 45.000 0.00 0.00 0.00 1.40
451 5500 1.402259 TCTTCCTCGCGCAAAACAAAA 59.598 42.857 8.75 0.00 0.00 2.44
452 5501 1.516864 CTTCCTCGCGCAAAACAAAAC 59.483 47.619 8.75 0.00 0.00 2.43
453 5502 0.452184 TCCTCGCGCAAAACAAAACA 59.548 45.000 8.75 0.00 0.00 2.83
454 5503 1.135373 TCCTCGCGCAAAACAAAACAA 60.135 42.857 8.75 0.00 0.00 2.83
455 5504 1.656095 CCTCGCGCAAAACAAAACAAA 59.344 42.857 8.75 0.00 0.00 2.83
479 5561 2.466846 CTGAATGCAAATGATTCGCCC 58.533 47.619 0.00 0.00 33.25 6.13
494 5576 4.829872 TTCGCCCTACCAAAAATCTCTA 57.170 40.909 0.00 0.00 0.00 2.43
495 5577 4.133013 TCGCCCTACCAAAAATCTCTAC 57.867 45.455 0.00 0.00 0.00 2.59
499 5581 5.497474 GCCCTACCAAAAATCTCTACTCAA 58.503 41.667 0.00 0.00 0.00 3.02
543 5625 1.380650 AAACACCACCACCACCACC 60.381 57.895 0.00 0.00 0.00 4.61
544 5626 2.156496 AAACACCACCACCACCACCA 62.156 55.000 0.00 0.00 0.00 4.17
545 5627 2.518349 CACCACCACCACCACCAC 60.518 66.667 0.00 0.00 0.00 4.16
548 5630 2.124693 CCACCACCACCACCACAAC 61.125 63.158 0.00 0.00 0.00 3.32
563 5645 5.656416 CCACCACAACCCTACATTATTCATT 59.344 40.000 0.00 0.00 0.00 2.57
581 5663 0.828022 TTAGATCGACATTGCGGGGT 59.172 50.000 0.00 0.00 0.00 4.95
636 5718 5.471116 CAGATCAAAATCAAGAGGTGTGTGA 59.529 40.000 0.00 0.00 34.07 3.58
657 5739 9.840427 GTGTGAGCAATAAAATAGTAACAACAT 57.160 29.630 0.00 0.00 0.00 2.71
786 5873 4.944317 TCACATCACTCACTCCTACTACTG 59.056 45.833 0.00 0.00 0.00 2.74
789 5876 3.611970 TCACTCACTCCTACTACTGCTC 58.388 50.000 0.00 0.00 0.00 4.26
791 5878 2.309162 ACTCACTCCTACTACTGCTCCA 59.691 50.000 0.00 0.00 0.00 3.86
792 5879 2.948979 CTCACTCCTACTACTGCTCCAG 59.051 54.545 0.00 0.00 37.52 3.86
794 5881 2.685897 CACTCCTACTACTGCTCCAGTC 59.314 54.545 0.48 0.00 41.21 3.51
1000 6087 2.347490 GGAGGACCAAGCTCGCAA 59.653 61.111 0.00 0.00 35.97 4.85
1001 6088 1.078143 GGAGGACCAAGCTCGCAAT 60.078 57.895 0.00 0.00 35.97 3.56
1002 6089 1.372087 GGAGGACCAAGCTCGCAATG 61.372 60.000 0.00 0.00 35.97 2.82
1003 6090 1.372087 GAGGACCAAGCTCGCAATGG 61.372 60.000 10.89 10.89 40.16 3.16
1004 6091 2.409870 GGACCAAGCTCGCAATGGG 61.410 63.158 15.24 0.00 38.58 4.00
1005 6092 3.056313 GACCAAGCTCGCAATGGGC 62.056 63.158 15.24 10.26 38.58 5.36
1013 6100 4.517815 CGCAATGGGCATGGGCAC 62.518 66.667 0.00 0.00 46.33 5.01
1138 6225 2.047443 GTCGCCGACCTCTCTTCCT 61.047 63.158 5.81 0.00 0.00 3.36
1186 6273 1.448189 GCTCTCTGCTGCTCACAGG 60.448 63.158 0.00 0.00 44.63 4.00
1199 6286 2.354259 CTCACAGGTCAGAAAGATGGC 58.646 52.381 0.00 0.00 0.00 4.40
1209 6296 4.558860 GTCAGAAAGATGGCGCAAATTAAC 59.441 41.667 10.83 0.00 0.00 2.01
1387 6476 2.113139 CTCAACACCCTGGGCGTT 59.887 61.111 13.31 13.31 0.00 4.84
1522 6611 1.664649 CGGCAACAAGCTCGTCTCA 60.665 57.895 0.00 0.00 44.79 3.27
1784 6873 2.440409 AGGCCTGACTAAACAATGCTG 58.560 47.619 3.11 0.00 0.00 4.41
1882 7009 7.174413 TCTTGATTTGTTGGATCCTCATTGTA 58.826 34.615 14.23 0.00 0.00 2.41
1883 7010 7.835682 TCTTGATTTGTTGGATCCTCATTGTAT 59.164 33.333 14.23 4.53 0.00 2.29
1884 7011 7.959658 TGATTTGTTGGATCCTCATTGTATT 57.040 32.000 14.23 0.00 0.00 1.89
1885 7012 7.774134 TGATTTGTTGGATCCTCATTGTATTG 58.226 34.615 14.23 0.00 0.00 1.90
1886 7013 7.396907 TGATTTGTTGGATCCTCATTGTATTGT 59.603 33.333 14.23 0.00 0.00 2.71
1892 7019 9.337396 GTTGGATCCTCATTGTATTGTGTAATA 57.663 33.333 14.23 0.00 0.00 0.98
1901 7028 4.196193 TGTATTGTGTAATACTGCCCTGC 58.804 43.478 10.45 0.00 45.71 4.85
1951 7078 7.227512 GGTCTGTGCTGCTTGTAATAATAAGAT 59.772 37.037 0.00 0.00 0.00 2.40
1987 7114 9.699410 TGTTGGTTCTAAATCTAATCATTCCAT 57.301 29.630 0.00 0.00 0.00 3.41
2180 7315 3.884693 CACCAATGCCACATTAGAGCATA 59.115 43.478 0.00 0.00 46.17 3.14
2183 7318 5.008331 CCAATGCCACATTAGAGCATATCT 58.992 41.667 0.00 0.00 46.17 1.98
2185 7320 6.315642 CCAATGCCACATTAGAGCATATCTAG 59.684 42.308 0.00 0.00 46.17 2.43
2191 7326 8.307483 GCCACATTAGAGCATATCTAGTAGAAA 58.693 37.037 3.45 0.00 41.57 2.52
2230 7365 2.337583 CGAACTTTTGCATCTCCGAGA 58.662 47.619 0.00 0.00 0.00 4.04
2293 7451 4.322499 CCGGAGATGTAAACTACAACACCT 60.322 45.833 0.00 0.00 42.76 4.00
2295 7453 4.863131 GGAGATGTAAACTACAACACCTCG 59.137 45.833 4.16 0.00 42.76 4.63
2311 7494 3.941483 CACCTCGCAGGAGATGTAAAAAT 59.059 43.478 8.91 0.00 43.27 1.82
2313 7496 4.191544 CCTCGCAGGAGATGTAAAAATGA 58.808 43.478 0.00 0.00 43.27 2.57
2319 7502 4.034510 CAGGAGATGTAAAAATGAGACCGC 59.965 45.833 0.00 0.00 0.00 5.68
2337 7520 2.587889 CCGCCGGATACCCAACTT 59.412 61.111 5.05 0.00 0.00 2.66
2338 7521 1.817941 CCGCCGGATACCCAACTTG 60.818 63.158 5.05 0.00 0.00 3.16
2339 7522 1.078708 CGCCGGATACCCAACTTGT 60.079 57.895 5.05 0.00 0.00 3.16
2341 7524 0.252197 GCCGGATACCCAACTTGTCT 59.748 55.000 5.05 0.00 0.00 3.41
2351 7534 3.052869 ACCCAACTTGTCTTTCCTTTCCT 60.053 43.478 0.00 0.00 0.00 3.36
2410 7593 0.975887 AGCCAAATCCGCACCAAATT 59.024 45.000 0.00 0.00 0.00 1.82
2435 7618 4.776322 CCCACAGCCGCCGATTCA 62.776 66.667 0.00 0.00 0.00 2.57
2436 7619 3.499737 CCACAGCCGCCGATTCAC 61.500 66.667 0.00 0.00 0.00 3.18
2437 7620 2.434884 CACAGCCGCCGATTCACT 60.435 61.111 0.00 0.00 0.00 3.41
2438 7621 2.034879 CACAGCCGCCGATTCACTT 61.035 57.895 0.00 0.00 0.00 3.16
2439 7622 1.302511 ACAGCCGCCGATTCACTTT 60.303 52.632 0.00 0.00 0.00 2.66
2440 7623 1.298859 ACAGCCGCCGATTCACTTTC 61.299 55.000 0.00 0.00 0.00 2.62
2441 7624 2.100631 AGCCGCCGATTCACTTTCG 61.101 57.895 0.00 0.00 36.38 3.46
2447 7630 1.425428 CGATTCACTTTCGGCTGCC 59.575 57.895 9.11 9.11 33.05 4.85
2465 7891 3.475944 GCCGAACGAAGCTTCTCC 58.524 61.111 23.50 11.34 0.00 3.71
2469 7895 1.079750 GAACGAAGCTTCTCCGGCT 60.080 57.895 23.50 4.01 42.31 5.52
2471 7897 1.816863 AACGAAGCTTCTCCGGCTGA 61.817 55.000 23.50 0.00 40.19 4.26
2518 8091 0.875728 CGAGGTCTACGATGGGCTAG 59.124 60.000 0.00 0.00 0.00 3.42
2530 8103 1.497161 TGGGCTAGGCTTCTTCCTAC 58.503 55.000 16.80 0.00 37.66 3.18
2540 8113 2.359461 GCTTCTTCCTACCCTAGACCCT 60.359 54.545 0.00 0.00 0.00 4.34
2563 8136 2.978824 GGAGTTAGTGGAGGCGCA 59.021 61.111 10.83 0.00 0.00 6.09
2690 8263 0.814457 ATCTCCTCTGTCGTGCAGTC 59.186 55.000 8.95 0.00 45.23 3.51
2755 8328 2.822701 GGCCGATTTCGTCCACCC 60.823 66.667 0.00 0.00 37.34 4.61
2768 8341 3.447040 CACCCCACAAGCAAGGTG 58.553 61.111 0.00 0.00 43.50 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
98 1842 7.254353 GCGTCTTCTTTGGGATTGTAACTATAC 60.254 40.741 0.00 0.00 0.00 1.47
111 1855 1.470098 CCATCTTGCGTCTTCTTTGGG 59.530 52.381 0.00 0.00 0.00 4.12
223 1976 4.504916 CAGCTCTCCGCGGTCCAG 62.505 72.222 27.15 19.39 45.59 3.86
229 1982 1.678269 CGTCTTTTCAGCTCTCCGCG 61.678 60.000 0.00 0.00 45.59 6.46
262 2015 7.411588 CGCGACCATCTAAAAGCTTATATAACC 60.412 40.741 0.00 0.00 0.00 2.85
265 2018 6.805271 GTCGCGACCATCTAAAAGCTTATATA 59.195 38.462 28.61 0.00 0.00 0.86
291 2044 1.523758 AGACGAGGGTTTCATTGTGC 58.476 50.000 0.00 0.00 0.00 4.57
301 2054 0.759346 AGCTTCAACAAGACGAGGGT 59.241 50.000 0.00 0.00 0.00 4.34
307 3831 3.002759 GGAACTGTCAGCTTCAACAAGAC 59.997 47.826 0.00 0.00 0.00 3.01
315 3839 2.849294 AAGGAGGAACTGTCAGCTTC 57.151 50.000 0.00 3.49 41.55 3.86
347 3873 8.814235 CCAAGTTATTTCATTTGATTGCAGATC 58.186 33.333 0.00 0.00 0.00 2.75
386 5435 9.290483 GCCAAAAGTAAGAGCTATATGAAAAAC 57.710 33.333 0.00 0.00 0.00 2.43
391 5440 5.163343 ACGGCCAAAAGTAAGAGCTATATGA 60.163 40.000 2.24 0.00 0.00 2.15
411 5460 5.310720 AGAAATTAAATGGACTTGACGGC 57.689 39.130 0.00 0.00 0.00 5.68
427 5476 2.034053 TGTTTTGCGCGAGGAAGAAATT 59.966 40.909 12.10 0.00 44.06 1.82
451 5500 4.669206 TCATTTGCATTCAGGTGTTTGT 57.331 36.364 0.00 0.00 0.00 2.83
452 5501 5.164031 CGAATCATTTGCATTCAGGTGTTTG 60.164 40.000 0.00 0.00 31.53 2.93
453 5502 4.925054 CGAATCATTTGCATTCAGGTGTTT 59.075 37.500 0.00 0.00 31.53 2.83
454 5503 4.487948 CGAATCATTTGCATTCAGGTGTT 58.512 39.130 0.00 0.00 31.53 3.32
455 5504 3.674138 GCGAATCATTTGCATTCAGGTGT 60.674 43.478 4.56 0.00 39.91 4.16
494 5576 7.342026 GGGTAATTGGAGGTGATTAATTTGAGT 59.658 37.037 0.00 0.00 0.00 3.41
495 5577 7.468631 CGGGTAATTGGAGGTGATTAATTTGAG 60.469 40.741 0.00 0.00 0.00 3.02
499 5581 5.762279 ACGGGTAATTGGAGGTGATTAATT 58.238 37.500 0.00 0.00 0.00 1.40
517 5599 2.193786 GGTGGTGTTTGGACGGGT 59.806 61.111 0.00 0.00 0.00 5.28
543 5625 8.712363 CGATCTAATGAATAATGTAGGGTTGTG 58.288 37.037 0.00 0.00 0.00 3.33
544 5626 8.647796 TCGATCTAATGAATAATGTAGGGTTGT 58.352 33.333 0.00 0.00 0.00 3.32
545 5627 8.926710 GTCGATCTAATGAATAATGTAGGGTTG 58.073 37.037 0.00 0.00 0.00 3.77
548 5630 9.658799 AATGTCGATCTAATGAATAATGTAGGG 57.341 33.333 0.00 0.00 0.00 3.53
563 5645 0.828022 AACCCCGCAATGTCGATCTA 59.172 50.000 0.00 0.00 0.00 1.98
581 5663 1.880646 GCTTAGGCCGTGAACCAGAAA 60.881 52.381 0.00 0.00 0.00 2.52
657 5739 6.013725 AGGAGTACACAAGGAACAATGTCATA 60.014 38.462 0.00 0.00 0.00 2.15
659 5741 4.102524 AGGAGTACACAAGGAACAATGTCA 59.897 41.667 0.00 0.00 0.00 3.58
786 5873 1.711060 CGGAGAGAGACGACTGGAGC 61.711 65.000 0.00 0.00 0.00 4.70
789 5876 1.377463 ACCGGAGAGAGACGACTGG 60.377 63.158 9.46 0.00 34.44 4.00
791 5878 2.041686 GCACCGGAGAGAGACGACT 61.042 63.158 9.46 0.00 0.00 4.18
792 5879 2.486042 GCACCGGAGAGAGACGAC 59.514 66.667 9.46 0.00 0.00 4.34
793 5880 2.750637 GGCACCGGAGAGAGACGA 60.751 66.667 9.46 0.00 0.00 4.20
794 5881 3.827898 GGGCACCGGAGAGAGACG 61.828 72.222 9.46 0.00 40.86 4.18
882 5969 1.446272 GCGCACGCTCCTTTACTCT 60.446 57.895 7.96 0.00 38.26 3.24
1013 6100 3.350031 AAGGGAGAAGCCATGCCCG 62.350 63.158 0.00 0.00 45.40 6.13
1186 6273 2.927553 ATTTGCGCCATCTTTCTGAC 57.072 45.000 4.18 0.00 0.00 3.51
1199 6286 5.920273 ACAAGTCCAAGATTGTTAATTTGCG 59.080 36.000 0.00 0.00 36.23 4.85
1209 6296 2.606308 GCTGCACACAAGTCCAAGATTG 60.606 50.000 0.00 0.00 0.00 2.67
1387 6476 4.828925 TCGATGCGCGCCATGGAA 62.829 61.111 30.77 9.22 35.99 3.53
1480 6569 0.524816 TTATGAAGCCGACGTCGAGC 60.525 55.000 37.65 33.79 43.02 5.03
1522 6611 2.436646 CCGGCGCTGATGGTCTTT 60.437 61.111 20.25 0.00 0.00 2.52
1642 6731 2.982130 GTCATGGCGAGGGACTGT 59.018 61.111 0.00 0.00 41.55 3.55
1723 6812 3.517500 ACTTGATCTTCTCCACCTCCTTC 59.482 47.826 0.00 0.00 0.00 3.46
1784 6873 6.095160 TCGGAAGAAACATCTTAGGAGTACTC 59.905 42.308 14.87 14.87 37.03 2.59
1882 7009 3.364460 TGCAGGGCAGTATTACACAAT 57.636 42.857 0.00 0.00 33.32 2.71
1883 7010 2.869101 TGCAGGGCAGTATTACACAA 57.131 45.000 0.00 0.00 33.32 3.33
1901 7028 2.658285 CAGCTTTTGTACTTGCTGCTG 58.342 47.619 13.61 12.60 44.72 4.41
1951 7078 8.463930 AGATTTAGAACCAACAAATGACTTGA 57.536 30.769 0.00 0.00 38.50 3.02
1987 7114 2.133281 AGCTGCTGCAACCATAATGA 57.867 45.000 18.42 0.00 42.74 2.57
2201 7336 7.309920 GGAGATGCAAAAGTTCGGTATTTTTA 58.690 34.615 0.00 0.00 0.00 1.52
2211 7346 2.095053 GCTCTCGGAGATGCAAAAGTTC 59.905 50.000 18.38 0.00 36.27 3.01
2239 7374 7.119846 CGGAGATGTAATTTTTCTGAGAGGTTT 59.880 37.037 0.00 0.00 0.00 3.27
2241 7376 6.109359 CGGAGATGTAATTTTTCTGAGAGGT 58.891 40.000 0.00 0.00 0.00 3.85
2243 7378 5.007136 GGCGGAGATGTAATTTTTCTGAGAG 59.993 44.000 0.00 0.00 0.00 3.20
2244 7379 4.876107 GGCGGAGATGTAATTTTTCTGAGA 59.124 41.667 0.00 0.00 0.00 3.27
2245 7380 4.878397 AGGCGGAGATGTAATTTTTCTGAG 59.122 41.667 0.00 0.00 0.00 3.35
2246 7381 4.843728 AGGCGGAGATGTAATTTTTCTGA 58.156 39.130 0.00 0.00 0.00 3.27
2273 7431 4.326548 GCGAGGTGTTGTAGTTTACATCTC 59.673 45.833 0.00 0.00 45.01 2.75
2293 7451 4.870426 GTCTCATTTTTACATCTCCTGCGA 59.130 41.667 0.00 0.00 0.00 5.10
2295 7453 4.034510 CGGTCTCATTTTTACATCTCCTGC 59.965 45.833 0.00 0.00 0.00 4.85
2319 7502 3.038945 AAGTTGGGTATCCGGCGGG 62.039 63.158 27.98 7.65 35.24 6.13
2325 7508 4.302559 AGGAAAGACAAGTTGGGTATCC 57.697 45.455 7.96 9.45 0.00 2.59
2327 7510 5.077564 GGAAAGGAAAGACAAGTTGGGTAT 58.922 41.667 7.96 0.00 0.00 2.73
2329 7512 3.052869 AGGAAAGGAAAGACAAGTTGGGT 60.053 43.478 7.96 0.00 0.00 4.51
2337 7520 2.878406 CGCAGAAAGGAAAGGAAAGACA 59.122 45.455 0.00 0.00 0.00 3.41
2338 7521 2.350868 GCGCAGAAAGGAAAGGAAAGAC 60.351 50.000 0.30 0.00 0.00 3.01
2339 7522 1.880027 GCGCAGAAAGGAAAGGAAAGA 59.120 47.619 0.30 0.00 0.00 2.52
2341 7524 0.591170 CGCGCAGAAAGGAAAGGAAA 59.409 50.000 8.75 0.00 0.00 3.13
2384 7567 2.513666 CGGATTTGGCTAGCGGCA 60.514 61.111 9.00 0.00 44.83 5.69
2388 7571 1.312371 TTGGTGCGGATTTGGCTAGC 61.312 55.000 6.04 6.04 0.00 3.42
2390 7573 1.846007 ATTTGGTGCGGATTTGGCTA 58.154 45.000 0.00 0.00 0.00 3.93
2391 7574 0.975887 AATTTGGTGCGGATTTGGCT 59.024 45.000 0.00 0.00 0.00 4.75
2421 7604 1.298859 GAAAGTGAATCGGCGGCTGT 61.299 55.000 7.21 0.00 0.00 4.40
2423 7606 2.100631 CGAAAGTGAATCGGCGGCT 61.101 57.895 7.21 0.00 36.68 5.52
2424 7607 2.399611 CGAAAGTGAATCGGCGGC 59.600 61.111 7.21 0.00 36.68 6.53
2429 7612 1.425428 GGCAGCCGAAAGTGAATCG 59.575 57.895 0.00 0.00 39.92 3.34
2444 7627 4.980805 AAGCTTCGTTCGGCGGCA 62.981 61.111 10.53 0.00 41.72 5.69
2445 7628 4.148645 GAAGCTTCGTTCGGCGGC 62.149 66.667 11.40 0.00 41.72 6.53
2446 7629 2.432628 AGAAGCTTCGTTCGGCGG 60.433 61.111 20.43 0.00 41.72 6.13
2447 7630 2.445438 GGAGAAGCTTCGTTCGGCG 61.445 63.158 20.43 0.00 43.01 6.46
2448 7631 2.445438 CGGAGAAGCTTCGTTCGGC 61.445 63.158 20.43 7.25 0.00 5.54
2449 7632 1.805945 CCGGAGAAGCTTCGTTCGG 60.806 63.158 29.08 29.08 34.63 4.30
2450 7633 2.445438 GCCGGAGAAGCTTCGTTCG 61.445 63.158 20.43 21.82 29.14 3.95
2451 7634 1.079750 AGCCGGAGAAGCTTCGTTC 60.080 57.895 20.43 13.33 37.24 3.95
2452 7635 1.374758 CAGCCGGAGAAGCTTCGTT 60.375 57.895 20.43 4.20 38.95 3.85
2453 7636 1.608717 ATCAGCCGGAGAAGCTTCGT 61.609 55.000 20.43 9.29 38.95 3.85
2454 7637 1.142748 ATCAGCCGGAGAAGCTTCG 59.857 57.895 20.43 9.83 38.95 3.79
2455 7638 1.435408 GCATCAGCCGGAGAAGCTTC 61.435 60.000 19.11 19.11 38.95 3.86
2469 7895 4.032452 TTCAGGCCAGCCGCATCA 62.032 61.111 5.01 0.00 41.95 3.07
2518 8091 2.040939 GGTCTAGGGTAGGAAGAAGCC 58.959 57.143 0.00 0.00 34.62 4.35
2540 8113 2.036098 TCCACTAACTCCGGCGGA 59.964 61.111 29.14 29.14 0.00 5.54
2602 8175 1.675641 GGCTTCACACGGCCAGAAT 60.676 57.895 2.24 0.00 46.84 2.40
2669 8242 2.961424 TGCACGACAGAGGAGATGA 58.039 52.632 0.00 0.00 0.00 2.92
2733 8306 2.105528 GACGAAATCGGCCGGCTA 59.894 61.111 28.56 15.89 42.67 3.93
2742 8315 1.165270 CTTGTGGGGTGGACGAAATC 58.835 55.000 0.00 0.00 0.00 2.17


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

AutoCloner maintained by Alex Coulton.