Multiple sequence alignment - TraesCS2A01G334000

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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 TraesCS2A01G334000 chr2A 100.000 2839 0 0 1 2839 567734201 567737039 0.000000e+00 5243.0
1 TraesCS2A01G334000 chr2A 95.205 292 10 2 1338 1629 546771202 546770915 2.580000e-125 459.0
2 TraesCS2A01G334000 chr2A 93.985 266 16 0 2236 2501 546743003 546742738 1.220000e-108 403.0
3 TraesCS2A01G334000 chr2A 95.455 154 7 0 157 310 546771352 546771199 2.180000e-61 246.0
4 TraesCS2A01G334000 chr2A 95.833 120 5 0 1 120 546773819 546773700 8.030000e-46 195.0
5 TraesCS2A01G334000 chr2A 97.938 97 2 0 1 97 568283400 568283496 4.860000e-38 169.0
6 TraesCS2A01G334000 chr2A 96.341 82 3 0 2758 2839 546742739 546742658 4.930000e-28 135.0
7 TraesCS2A01G334000 chr2B 90.665 2346 109 32 522 2839 493987200 493989463 0.000000e+00 3018.0
8 TraesCS2A01G334000 chr2B 95.745 94 3 1 1 93 494260736 494260829 1.760000e-32 150.0
9 TraesCS2A01G334000 chr2B 93.878 98 5 1 1 97 493986467 493986564 2.280000e-31 147.0
10 TraesCS2A01G334000 chr2B 96.053 76 2 1 157 231 493986862 493986937 3.840000e-24 122.0
11 TraesCS2A01G334000 chr2B 85.965 114 5 4 306 416 493987045 493987150 8.310000e-21 111.0
12 TraesCS2A01G334000 chr2B 95.455 66 3 0 94 159 494260889 494260954 3.870000e-19 106.0
13 TraesCS2A01G334000 chr2B 90.909 66 3 2 94 157 493986631 493986695 5.040000e-13 86.1
14 TraesCS2A01G334000 chr2D 90.102 1475 78 28 522 1982 421479951 421481371 0.000000e+00 1853.0
15 TraesCS2A01G334000 chr2D 91.171 521 36 3 1981 2499 421481418 421481930 0.000000e+00 699.0
16 TraesCS2A01G334000 chr2D 95.633 229 10 0 2611 2839 421481985 421482213 4.470000e-98 368.0
17 TraesCS2A01G334000 chr2D 90.728 151 5 8 162 305 421477402 421477550 2.890000e-45 193.0
18 TraesCS2A01G334000 chr2D 88.961 154 6 6 306 456 421477609 421477754 2.250000e-41 180.0
19 TraesCS2A01G334000 chr2D 95.876 97 4 0 1 97 421477044 421477140 1.050000e-34 158.0
20 TraesCS2A01G334000 chr2D 93.814 97 6 0 1 97 421792296 421792392 2.280000e-31 147.0
21 TraesCS2A01G334000 chr2D 97.059 68 2 0 2524 2591 421481925 421481992 6.430000e-22 115.0
22 TraesCS2A01G334000 chr2D 92.208 77 4 2 94 168 421792461 421792537 1.080000e-19 108.0
23 TraesCS2A01G334000 chr3B 88.030 944 57 10 1838 2780 9687474 9688362 0.000000e+00 1066.0
24 TraesCS2A01G334000 chr4D 84.146 164 17 7 1 157 323927632 323927793 1.760000e-32 150.0
25 TraesCS2A01G334000 chr4A 93.814 97 6 0 1 97 147567102 147567006 2.280000e-31 147.0
26 TraesCS2A01G334000 chr4A 87.931 58 7 0 100 157 147566933 147566876 5.080000e-08 69.4
27 TraesCS2A01G334000 chr4B 95.000 60 3 0 1 60 404512696 404512755 8.370000e-16 95.3
28 TraesCS2A01G334000 chr1D 94.737 38 1 1 114 151 376281604 376281568 1.100000e-04 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 TraesCS2A01G334000 chr2A 567734201 567737039 2838 False 5243.000000 5243 100.000000 1 2839 1 chr2A.!!$F1 2838
1 TraesCS2A01G334000 chr2A 546770915 546773819 2904 True 300.000000 459 95.497667 1 1629 3 chr2A.!!$R2 1628
2 TraesCS2A01G334000 chr2B 493986467 493989463 2996 False 696.820000 3018 91.494000 1 2839 5 chr2B.!!$F1 2838
3 TraesCS2A01G334000 chr2D 421477044 421482213 5169 False 509.428571 1853 92.790000 1 2839 7 chr2D.!!$F1 2838
4 TraesCS2A01G334000 chr3B 9687474 9688362 888 False 1066.000000 1066 88.030000 1838 2780 1 chr3B.!!$F1 942

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
506 5154 0.036306 GAGGTGCTCCCTTTTTCGGA 59.964 55.0 0.0 0.0 46.51 4.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2209 6943 0.03759 TTGTTTGTCATCCCCTCCGG 59.962 55.0 0.0 0.0 0.0 5.14 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
35 36 4.100808 GCTGAAGATCAAGGAGTCCAGTAT 59.899 45.833 12.86 0.56 0.00 2.12
278 2690 7.719193 TGAAGATGTTGGTTCAAAGATCTGTTA 59.281 33.333 0.00 0.00 30.29 2.41
279 2691 8.463930 AAGATGTTGGTTCAAAGATCTGTTAA 57.536 30.769 0.00 0.00 30.29 2.01
344 2818 1.616725 GCTTGGGGATGATGTGGTGAA 60.617 52.381 0.00 0.00 0.00 3.18
345 2819 2.094675 CTTGGGGATGATGTGGTGAAC 58.905 52.381 0.00 0.00 0.00 3.18
346 2820 1.371467 TGGGGATGATGTGGTGAACT 58.629 50.000 0.00 0.00 0.00 3.01
347 2821 1.004628 TGGGGATGATGTGGTGAACTG 59.995 52.381 0.00 0.00 0.00 3.16
348 2822 1.683011 GGGGATGATGTGGTGAACTGG 60.683 57.143 0.00 0.00 0.00 4.00
349 2823 1.004745 GGGATGATGTGGTGAACTGGT 59.995 52.381 0.00 0.00 0.00 4.00
350 2824 2.086869 GGATGATGTGGTGAACTGGTG 58.913 52.381 0.00 0.00 0.00 4.17
351 2825 2.290260 GGATGATGTGGTGAACTGGTGA 60.290 50.000 0.00 0.00 0.00 4.02
352 2826 3.614092 GATGATGTGGTGAACTGGTGAT 58.386 45.455 0.00 0.00 0.00 3.06
353 2827 2.781923 TGATGTGGTGAACTGGTGATG 58.218 47.619 0.00 0.00 0.00 3.07
354 2828 1.470098 GATGTGGTGAACTGGTGATGC 59.530 52.381 0.00 0.00 0.00 3.91
355 2829 0.182299 TGTGGTGAACTGGTGATGCA 59.818 50.000 0.00 0.00 0.00 3.96
356 2830 1.202915 TGTGGTGAACTGGTGATGCAT 60.203 47.619 0.00 0.00 0.00 3.96
359 2833 1.098050 GTGAACTGGTGATGCATCCC 58.902 55.000 23.67 22.16 0.00 3.85
411 2887 4.338964 TCTCTTTGCAAGCTGATTTGTTCA 59.661 37.500 0.00 0.00 0.00 3.18
480 5128 3.778619 CCGTGGGCATCACTTGATA 57.221 52.632 7.64 0.00 43.94 2.15
481 5129 1.586422 CCGTGGGCATCACTTGATAG 58.414 55.000 7.64 0.00 43.94 2.08
482 5130 1.138859 CCGTGGGCATCACTTGATAGA 59.861 52.381 7.64 0.00 43.94 1.98
483 5131 2.477825 CGTGGGCATCACTTGATAGAG 58.522 52.381 7.64 0.00 43.94 2.43
484 5132 2.804572 CGTGGGCATCACTTGATAGAGG 60.805 54.545 7.64 0.00 43.94 3.69
485 5133 1.141657 TGGGCATCACTTGATAGAGGC 59.858 52.381 0.00 0.00 40.52 4.70
486 5134 1.419387 GGGCATCACTTGATAGAGGCT 59.581 52.381 0.00 0.00 40.98 4.58
487 5135 2.492012 GGCATCACTTGATAGAGGCTG 58.508 52.381 0.00 0.00 40.98 4.85
488 5136 2.103771 GGCATCACTTGATAGAGGCTGA 59.896 50.000 0.00 0.00 40.98 4.26
489 5137 3.391965 GCATCACTTGATAGAGGCTGAG 58.608 50.000 0.00 0.00 38.42 3.35
490 5138 3.803021 GCATCACTTGATAGAGGCTGAGG 60.803 52.174 0.00 0.00 38.42 3.86
491 5139 3.107402 TCACTTGATAGAGGCTGAGGT 57.893 47.619 0.00 0.00 0.00 3.85
492 5140 2.762887 TCACTTGATAGAGGCTGAGGTG 59.237 50.000 0.00 0.00 0.00 4.00
493 5141 1.484240 ACTTGATAGAGGCTGAGGTGC 59.516 52.381 0.00 0.00 0.00 5.01
494 5142 1.761784 CTTGATAGAGGCTGAGGTGCT 59.238 52.381 0.00 0.00 0.00 4.40
495 5143 1.407936 TGATAGAGGCTGAGGTGCTC 58.592 55.000 0.00 0.00 0.00 4.26
496 5144 0.678950 GATAGAGGCTGAGGTGCTCC 59.321 60.000 0.00 0.00 0.00 4.70
497 5145 0.762461 ATAGAGGCTGAGGTGCTCCC 60.762 60.000 0.00 0.00 0.00 4.30
499 5147 2.204059 AGGCTGAGGTGCTCCCTT 60.204 61.111 0.00 0.00 46.51 3.95
500 5148 1.846712 GAGGCTGAGGTGCTCCCTTT 61.847 60.000 0.00 0.00 46.51 3.11
501 5149 1.075659 GGCTGAGGTGCTCCCTTTT 59.924 57.895 0.00 0.00 46.51 2.27
502 5150 0.540597 GGCTGAGGTGCTCCCTTTTT 60.541 55.000 0.00 0.00 46.51 1.94
503 5151 0.884514 GCTGAGGTGCTCCCTTTTTC 59.115 55.000 0.00 0.00 46.51 2.29
504 5152 1.160137 CTGAGGTGCTCCCTTTTTCG 58.840 55.000 0.00 0.00 46.51 3.46
505 5153 0.250727 TGAGGTGCTCCCTTTTTCGG 60.251 55.000 0.00 0.00 46.51 4.30
506 5154 0.036306 GAGGTGCTCCCTTTTTCGGA 59.964 55.000 0.00 0.00 46.51 4.55
507 5155 0.476771 AGGTGCTCCCTTTTTCGGAA 59.523 50.000 0.00 0.00 42.73 4.30
508 5156 1.133606 AGGTGCTCCCTTTTTCGGAAA 60.134 47.619 0.00 0.00 42.73 3.13
509 5157 1.684450 GGTGCTCCCTTTTTCGGAAAA 59.316 47.619 11.68 11.68 33.86 2.29
510 5158 2.101750 GGTGCTCCCTTTTTCGGAAAAA 59.898 45.455 23.04 23.04 37.99 1.94
607 5260 2.492090 CTACTCTCGCCGCTGCTT 59.508 61.111 0.00 0.00 34.43 3.91
645 5301 3.855255 TTTGTGGGAAGATCACTGACA 57.145 42.857 0.00 0.00 36.21 3.58
680 5337 9.739276 AGTCCATCAAACATTTCAGACTTTATA 57.261 29.630 0.00 0.00 29.31 0.98
810 5467 3.126858 GCGTTTGCTCTGAATTATCACCA 59.873 43.478 0.00 0.00 38.39 4.17
832 5489 7.449395 CACCACCATGAATATACATTGATCCTT 59.551 37.037 0.00 0.00 0.00 3.36
833 5490 7.449395 ACCACCATGAATATACATTGATCCTTG 59.551 37.037 0.00 0.00 0.00 3.61
930 5587 4.061699 CCCACAGGTACTACCCCC 57.938 66.667 1.19 0.00 39.75 5.40
931 5588 1.394963 CCCACAGGTACTACCCCCT 59.605 63.158 1.19 0.00 39.75 4.79
932 5589 0.690077 CCCACAGGTACTACCCCCTC 60.690 65.000 1.19 0.00 39.75 4.30
951 5608 1.196012 CCCCCTCTGGAGAACACTAC 58.804 60.000 0.00 0.00 35.39 2.73
952 5609 1.273324 CCCCCTCTGGAGAACACTACT 60.273 57.143 0.00 0.00 35.39 2.57
963 5620 4.517453 GGAGAACACTACTAGCTCGATCAT 59.483 45.833 0.00 0.00 0.00 2.45
976 5633 8.268605 ACTAGCTCGATCATCTATATAAGGTCA 58.731 37.037 0.00 0.00 0.00 4.02
993 5650 1.078918 CACAAGCTCTCGCCATGGA 60.079 57.895 18.40 0.00 36.60 3.41
1024 5681 0.940126 CACCACAGTCACTTCACTGC 59.060 55.000 0.42 0.00 46.81 4.40
1074 5731 3.590824 CAACCTTGCATCCCGGTC 58.409 61.111 0.00 0.00 0.00 4.79
1075 5732 2.046314 AACCTTGCATCCCGGTCG 60.046 61.111 0.00 0.00 0.00 4.79
1076 5733 2.589157 AACCTTGCATCCCGGTCGA 61.589 57.895 0.00 0.00 0.00 4.20
1299 5960 3.243737 TGAAACGATCCACATATCCGGAG 60.244 47.826 11.34 0.00 33.97 4.63
1300 5961 0.603569 ACGATCCACATATCCGGAGC 59.396 55.000 11.34 0.00 33.97 4.70
1301 5962 0.891373 CGATCCACATATCCGGAGCT 59.109 55.000 11.34 0.00 35.50 4.09
1302 5963 1.273606 CGATCCACATATCCGGAGCTT 59.726 52.381 11.34 0.00 35.50 3.74
1303 5964 2.693069 GATCCACATATCCGGAGCTTG 58.307 52.381 11.34 9.89 34.80 4.01
1304 5965 1.496060 TCCACATATCCGGAGCTTGT 58.504 50.000 11.34 10.58 0.00 3.16
1305 5966 2.673258 TCCACATATCCGGAGCTTGTA 58.327 47.619 11.34 0.00 0.00 2.41
1306 5967 3.239449 TCCACATATCCGGAGCTTGTAT 58.761 45.455 11.34 0.00 0.00 2.29
1307 5968 3.258372 TCCACATATCCGGAGCTTGTATC 59.742 47.826 11.34 0.00 0.00 2.24
1309 5970 4.240888 CACATATCCGGAGCTTGTATCAG 58.759 47.826 11.34 0.00 0.00 2.90
1310 5971 3.898123 ACATATCCGGAGCTTGTATCAGT 59.102 43.478 11.34 0.00 0.00 3.41
1312 5973 5.717178 ACATATCCGGAGCTTGTATCAGTAT 59.283 40.000 11.34 0.00 0.00 2.12
1313 5974 6.890268 ACATATCCGGAGCTTGTATCAGTATA 59.110 38.462 11.34 0.00 0.00 1.47
1674 6355 3.838271 GCTGCGGACGATCCTCCA 61.838 66.667 10.83 0.00 33.30 3.86
1677 6358 2.340443 GCGGACGATCCTCCATCC 59.660 66.667 10.83 0.00 33.30 3.51
1716 6397 4.753516 TCCATCCATGAATACTGTCGTT 57.246 40.909 0.00 0.00 0.00 3.85
1838 6519 5.045215 CCGCGTGAGTAGTGGAATAATAAA 58.955 41.667 4.92 0.00 41.54 1.40
1839 6520 5.694910 CCGCGTGAGTAGTGGAATAATAAAT 59.305 40.000 4.92 0.00 41.54 1.40
1840 6521 6.864685 CCGCGTGAGTAGTGGAATAATAAATA 59.135 38.462 4.92 0.00 41.54 1.40
1841 6522 7.544566 CCGCGTGAGTAGTGGAATAATAAATAT 59.455 37.037 4.92 0.00 41.54 1.28
1879 6560 4.679654 CGCAGCTTTATGATCACGTATACA 59.320 41.667 0.00 0.00 0.00 2.29
1954 6635 5.902613 ATTCAGTATGTTGTGGTGGAATG 57.097 39.130 0.00 0.00 37.40 2.67
1959 6643 5.920273 CAGTATGTTGTGGTGGAATGTTTTC 59.080 40.000 0.00 0.00 0.00 2.29
1960 6644 9.081200 TCAGTATGTTGTGGTGGAATGTTTTCC 62.081 40.741 0.00 0.00 44.24 3.13
2002 6734 4.033009 TCAAGAGAGAGATAACATGGGCA 58.967 43.478 0.00 0.00 0.00 5.36
2003 6735 4.100653 TCAAGAGAGAGATAACATGGGCAG 59.899 45.833 0.00 0.00 0.00 4.85
2004 6736 2.971330 AGAGAGAGATAACATGGGCAGG 59.029 50.000 0.00 0.00 0.00 4.85
2005 6737 2.038295 GAGAGAGATAACATGGGCAGGG 59.962 54.545 0.00 0.00 0.00 4.45
2006 6738 0.475906 AGAGATAACATGGGCAGGGC 59.524 55.000 0.00 0.00 0.00 5.19
2026 6758 1.165270 CGCGGGGAAGAGAAAACAAT 58.835 50.000 0.00 0.00 0.00 2.71
2116 6850 6.157297 ACCTATTAAGCAGTACCAACCACATA 59.843 38.462 0.00 0.00 0.00 2.29
2127 6861 9.710979 CAGTACCAACCACATAAAAATATTACG 57.289 33.333 0.00 0.00 0.00 3.18
2194 6928 6.866248 CCCAAAAGCACAACGAAAATACTAAT 59.134 34.615 0.00 0.00 0.00 1.73
2209 6943 2.786777 ACTAATTGGTGAACGTTCCCC 58.213 47.619 24.78 23.06 0.00 4.81
2210 6944 2.089201 CTAATTGGTGAACGTTCCCCC 58.911 52.381 24.46 22.69 0.00 5.40
2237 6971 3.453424 GGATGACAAACAAACGCCTTTT 58.547 40.909 0.00 0.00 0.00 2.27
2256 6990 3.608316 TTGATGGCATTTTTAGGTGGC 57.392 42.857 0.00 0.00 40.89 5.01
2262 6996 2.446435 GCATTTTTAGGTGGCAGGAGA 58.554 47.619 0.00 0.00 0.00 3.71
2365 7099 4.818546 TCTCTGAAGAAACTGCCAGAAAAG 59.181 41.667 0.00 0.00 35.52 2.27
2367 7101 4.576463 TCTGAAGAAACTGCCAGAAAAGAC 59.424 41.667 0.00 0.00 33.26 3.01
2403 7137 2.662527 TCCCGACAAACGTTCGCC 60.663 61.111 0.00 0.00 40.78 5.54
2405 7139 3.031457 CCGACAAACGTTCGCCGA 61.031 61.111 0.00 0.00 40.70 5.54
2495 7229 8.494347 CATCTATGTAGCAATCTCTTTTAGCAC 58.506 37.037 0.00 0.00 0.00 4.40
2503 7237 5.183140 GCAATCTCTTTTAGCACCTTACCAA 59.817 40.000 0.00 0.00 0.00 3.67
2586 7320 6.157211 AGAACAAGGTGTAAACACTATCTCG 58.843 40.000 12.65 0.00 45.73 4.04
2604 7338 3.055819 TCTCGAAAGGAATTCTGGTCCAG 60.056 47.826 13.21 13.21 37.65 3.86
2671 7405 7.070571 AGGAAAGGAAAAATCCACACATAACAA 59.929 33.333 0.00 0.00 35.62 2.83
2711 7445 0.692476 CAGATCAGTCCCCAACACCA 59.308 55.000 0.00 0.00 0.00 4.17
2740 7474 2.737252 GGTTTTTCAGACCACTCTAGCG 59.263 50.000 0.00 0.00 37.14 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
202 2608 2.423538 CCCTGATTAAGCCGGAAAGTTG 59.576 50.000 5.05 0.00 0.00 3.16
235 2647 2.917701 TCAATAAGTAACGACGCGGA 57.082 45.000 12.47 0.00 0.00 5.54
278 2690 5.063880 GTCAGACCAAAGGTATCACACTTT 58.936 41.667 0.00 0.00 35.25 2.66
279 2691 4.102524 TGTCAGACCAAAGGTATCACACTT 59.897 41.667 0.00 0.00 35.25 3.16
346 2820 1.303948 CACCTGGGATGCATCACCA 59.696 57.895 25.88 25.89 0.00 4.17
347 2821 1.454479 CCACCTGGGATGCATCACC 60.454 63.158 25.88 23.09 40.01 4.02
348 2822 1.033746 CACCACCTGGGATGCATCAC 61.034 60.000 27.25 25.01 41.15 3.06
349 2823 1.303948 CACCACCTGGGATGCATCA 59.696 57.895 27.25 8.45 41.15 3.07
350 2824 1.454479 CCACCACCTGGGATGCATC 60.454 63.158 18.81 18.81 41.15 3.91
351 2825 1.291459 ATCCACCACCTGGGATGCAT 61.291 55.000 0.00 0.00 42.24 3.96
352 2826 1.930133 ATCCACCACCTGGGATGCA 60.930 57.895 0.00 0.00 42.24 3.96
353 2827 3.010144 ATCCACCACCTGGGATGC 58.990 61.111 0.00 0.00 42.24 3.91
355 2829 2.693871 GCCATCCACCACCTGGGAT 61.694 63.158 0.00 0.00 44.65 3.85
356 2830 3.338250 GCCATCCACCACCTGGGA 61.338 66.667 0.00 0.00 41.06 4.37
359 2833 2.273449 GAGGCCATCCACCACCTG 59.727 66.667 5.01 0.00 30.95 4.00
386 2860 7.630458 TGAACAAATCAGCTTGCAAAGAGAGA 61.630 38.462 0.00 0.00 38.88 3.10
388 2862 4.338964 TGAACAAATCAGCTTGCAAAGAGA 59.661 37.500 0.00 0.00 38.88 3.10
448 2924 3.418047 GCCCACGGCCATAGTATTTTAT 58.582 45.455 2.24 0.00 44.06 1.40
480 5128 2.686835 GGGAGCACCTCAGCCTCT 60.687 66.667 0.00 0.00 35.85 3.69
489 5137 1.324383 TTTCCGAAAAAGGGAGCACC 58.676 50.000 0.00 0.00 40.67 5.01
490 5138 3.446310 TTTTTCCGAAAAAGGGAGCAC 57.554 42.857 13.84 0.00 35.84 4.40
517 5165 9.362539 GTAGAAACAACAGGAGTCGATTATTTA 57.637 33.333 0.00 0.00 0.00 1.40
518 5166 7.876068 TGTAGAAACAACAGGAGTCGATTATTT 59.124 33.333 0.00 0.00 30.91 1.40
519 5167 7.383687 TGTAGAAACAACAGGAGTCGATTATT 58.616 34.615 0.00 0.00 30.91 1.40
520 5168 6.931838 TGTAGAAACAACAGGAGTCGATTAT 58.068 36.000 0.00 0.00 30.91 1.28
525 5173 5.924475 ATTTGTAGAAACAACAGGAGTCG 57.076 39.130 0.00 0.00 45.18 4.18
527 5175 9.185680 ACTAAAATTTGTAGAAACAACAGGAGT 57.814 29.630 0.46 0.00 45.18 3.85
567 5219 4.192317 GTGATTAGTTAGCCCCTGAACAG 58.808 47.826 0.00 0.00 0.00 3.16
607 5260 6.377996 CCCACAAATCAAATCAAGGTGATAGA 59.622 38.462 0.00 0.00 35.76 1.98
645 5301 9.192642 TGAAATGTTTGATGGACTGATCAATAT 57.807 29.630 0.00 0.00 41.03 1.28
680 5337 0.264657 GAACCAGGGCCCCCATAAAT 59.735 55.000 21.43 0.00 38.92 1.40
681 5338 1.700985 GAACCAGGGCCCCCATAAA 59.299 57.895 21.43 0.00 38.92 1.40
810 5467 6.435277 GCCAAGGATCAATGTATATTCATGGT 59.565 38.462 0.00 0.00 0.00 3.55
924 5581 3.373846 CCAGAGGGGGAGGGGGTA 61.374 72.222 0.00 0.00 0.00 3.69
931 5588 1.089978 TAGTGTTCTCCAGAGGGGGA 58.910 55.000 0.00 0.00 43.90 4.81
932 5589 1.196012 GTAGTGTTCTCCAGAGGGGG 58.804 60.000 0.00 0.00 37.22 5.40
951 5608 8.556194 GTGACCTTATATAGATGATCGAGCTAG 58.444 40.741 0.90 0.00 0.00 3.42
952 5609 8.047310 TGTGACCTTATATAGATGATCGAGCTA 58.953 37.037 0.90 0.00 0.00 3.32
963 5620 6.561737 CGAGAGCTTGTGACCTTATATAGA 57.438 41.667 0.00 0.00 0.00 1.98
993 5650 0.817013 CTGTGGTGCTTGTGGTTTGT 59.183 50.000 0.00 0.00 0.00 2.83
1024 5681 1.367659 GCTCTTGCCAGCTACTTGAG 58.632 55.000 0.00 0.00 36.38 3.02
1075 5732 0.318699 TTGGACGCCATCGATCGATC 60.319 55.000 27.20 16.50 39.41 3.69
1076 5733 0.319040 CTTGGACGCCATCGATCGAT 60.319 55.000 24.60 24.60 39.41 3.59
1292 5953 9.815306 ATATATATACTGATACAAGCTCCGGAT 57.185 33.333 3.57 0.00 0.00 4.18
1309 5970 9.031360 CCCAATGCTCACGTTACATATATATAC 57.969 37.037 0.00 0.00 0.00 1.47
1310 5971 8.755028 ACCCAATGCTCACGTTACATATATATA 58.245 33.333 0.00 0.00 0.00 0.86
1312 5973 6.871492 CACCCAATGCTCACGTTACATATATA 59.129 38.462 0.00 0.00 0.00 0.86
1313 5974 5.700832 CACCCAATGCTCACGTTACATATAT 59.299 40.000 0.00 0.00 0.00 0.86
1343 6014 0.392998 CACCATCGGAACCCCTGAAG 60.393 60.000 0.00 0.00 0.00 3.02
1659 6340 2.498941 GGATGGAGGATCGTCCGCA 61.499 63.158 25.30 12.49 42.75 5.69
1668 6349 2.441532 GGACGGACGGATGGAGGA 60.442 66.667 0.00 0.00 0.00 3.71
1674 6355 2.441532 ATGGACGGACGGACGGAT 60.442 61.111 6.00 0.00 38.39 4.18
1677 6358 2.679132 GATGGATGGACGGACGGACG 62.679 65.000 0.00 0.00 40.31 4.79
1716 6397 2.186160 CCGCAGACAACAGGCAACA 61.186 57.895 0.00 0.00 41.41 3.33
1841 6522 9.929722 CATAAAGCTGCGACTTTATTATTGTTA 57.070 29.630 16.84 0.00 45.98 2.41
1845 6526 9.056005 TGATCATAAAGCTGCGACTTTATTATT 57.944 29.630 16.84 8.24 45.98 1.40
1879 6560 4.273480 GCACAAATCTAGCACCATTCGTAT 59.727 41.667 0.00 0.00 0.00 3.06
1891 6572 5.698832 TCAAACCAAATCGCACAAATCTAG 58.301 37.500 0.00 0.00 0.00 2.43
1954 6635 1.611977 CCGGTTTGAAGGGAGGAAAAC 59.388 52.381 0.00 0.00 32.89 2.43
2004 6736 3.912745 TTTTCTCTTCCCCGCGGCC 62.913 63.158 22.85 0.00 0.00 6.13
2005 6737 2.359478 TTTTCTCTTCCCCGCGGC 60.359 61.111 22.85 0.00 0.00 6.53
2006 6738 0.887387 TTGTTTTCTCTTCCCCGCGG 60.887 55.000 21.04 21.04 0.00 6.46
2007 6739 1.135689 CATTGTTTTCTCTTCCCCGCG 60.136 52.381 0.00 0.00 0.00 6.46
2008 6740 2.159382 TCATTGTTTTCTCTTCCCCGC 58.841 47.619 0.00 0.00 0.00 6.13
2009 6741 3.412386 ACTCATTGTTTTCTCTTCCCCG 58.588 45.455 0.00 0.00 0.00 5.73
2026 6758 1.035385 TCTCATAGCGCCCGAACTCA 61.035 55.000 2.29 0.00 0.00 3.41
2076 6808 9.959721 TGCTTAATAGGTCTAGTTTTTCTTGAT 57.040 29.630 0.00 0.00 31.49 2.57
2077 6809 9.436957 CTGCTTAATAGGTCTAGTTTTTCTTGA 57.563 33.333 0.00 0.00 0.00 3.02
2078 6810 9.220767 ACTGCTTAATAGGTCTAGTTTTTCTTG 57.779 33.333 0.00 0.00 0.00 3.02
2081 6813 9.096160 GGTACTGCTTAATAGGTCTAGTTTTTC 57.904 37.037 0.00 0.00 0.00 2.29
2127 6861 5.419239 TGGATGGGAAATCATTTTTGTCC 57.581 39.130 0.00 0.00 0.00 4.02
2134 6868 5.046376 GTCTTGGTTTGGATGGGAAATCATT 60.046 40.000 0.00 0.00 0.00 2.57
2209 6943 0.037590 TTGTTTGTCATCCCCTCCGG 59.962 55.000 0.00 0.00 0.00 5.14
2210 6944 1.539827 GTTTGTTTGTCATCCCCTCCG 59.460 52.381 0.00 0.00 0.00 4.63
2237 6971 2.496871 CTGCCACCTAAAAATGCCATCA 59.503 45.455 0.00 0.00 0.00 3.07
2365 7099 0.445043 GGGTGGCATTTACGAACGTC 59.555 55.000 2.45 0.00 0.00 4.34
2367 7101 0.675522 AGGGGTGGCATTTACGAACG 60.676 55.000 0.00 0.00 0.00 3.95
2393 7127 1.073177 CCAATAGTCGGCGAACGTTT 58.927 50.000 12.92 0.00 44.69 3.60
2403 7137 2.773487 TGTGTTTGGACCCAATAGTCG 58.227 47.619 1.88 0.00 37.66 4.18
2405 7139 4.898861 ACATTTGTGTTTGGACCCAATAGT 59.101 37.500 1.88 0.00 35.70 2.12
2495 7229 3.317711 TGTTGTGAAGCATGTTGGTAAGG 59.682 43.478 0.00 0.00 0.00 2.69
2503 7237 2.957680 TGGTTGATGTTGTGAAGCATGT 59.042 40.909 0.00 0.00 0.00 3.21
2586 7320 4.145052 ACAACTGGACCAGAATTCCTTTC 58.855 43.478 28.56 0.00 35.18 2.62
2604 7338 2.610374 TCGTGCCACTTTTGAGTACAAC 59.390 45.455 0.00 0.00 35.63 3.32
2652 7386 5.931146 TGGCATTGTTATGTGTGGATTTTTC 59.069 36.000 0.00 0.00 34.12 2.29
2657 7391 3.429492 TGTGGCATTGTTATGTGTGGAT 58.571 40.909 0.00 0.00 34.12 3.41
2671 7405 1.346395 TGTCCTAACTCGTTGTGGCAT 59.654 47.619 0.00 0.00 0.00 4.40
2711 7445 1.153127 TCTGAAAAACCGCGGGTGT 60.153 52.632 31.76 17.67 35.34 4.16
2719 7453 2.737252 CGCTAGAGTGGTCTGAAAAACC 59.263 50.000 0.00 0.00 37.31 3.27
2740 7474 3.997021 ACATGTTCTTCTTGTGTCCGATC 59.003 43.478 0.00 0.00 33.98 3.69
2800 7534 2.885113 GCATTGGCCTCGAAACCC 59.115 61.111 3.32 0.00 0.00 4.11


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

AutoCloner maintained by Alex Coulton.