Multiple sequence alignment - TraesCS5A01G111000

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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 TraesCS5A01G111000 chr5A 100.000 5261 0 0 1 5261 212222978 212217718 0.000000e+00 9716.0
1 TraesCS5A01G111000 chr5A 98.113 53 1 0 5115 5167 212217794 212217742 5.610000e-15 93.5
2 TraesCS5A01G111000 chr5A 98.113 53 1 0 5185 5237 212217864 212217812 5.610000e-15 93.5
3 TraesCS5A01G111000 chr5D 97.584 4760 71 15 11 4763 179943279 179948001 0.000000e+00 8113.0
4 TraesCS5A01G111000 chr5D 93.466 352 9 7 4858 5206 179948016 179948356 1.310000e-140 510.0
5 TraesCS5A01G111000 chr5D 93.651 63 2 2 5175 5237 179948257 179948317 5.610000e-15 93.5
6 TraesCS5A01G111000 chr5B 96.141 2462 50 18 2440 4900 157385432 157383015 0.000000e+00 3978.0
7 TraesCS5A01G111000 chr5B 95.745 1880 42 14 296 2147 157394845 157392976 0.000000e+00 2994.0
8 TraesCS5A01G111000 chr5B 96.129 310 12 0 2143 2452 157390786 157390477 1.690000e-139 507.0
9 TraesCS5A01G111000 chr5B 93.158 190 4 4 98 285 157395004 157394822 2.410000e-68 270.0


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 TraesCS5A01G111000 chr5A 212217718 212222978 5260 True 9716.0 9716 100.000000 1 5261 1 chr5A.!!$R1 5260
1 TraesCS5A01G111000 chr5D 179943279 179948356 5077 False 2905.5 8113 94.900333 11 5237 3 chr5D.!!$F1 5226
2 TraesCS5A01G111000 chr5B 157383015 157385432 2417 True 3978.0 3978 96.141000 2440 4900 1 chr5B.!!$R1 2460
3 TraesCS5A01G111000 chr5B 157390477 157395004 4527 True 1257.0 2994 95.010667 98 2452 3 chr5B.!!$R2 2354

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
376 379 0.036010 CGGCAGATCTTCCACCTTGT 60.036 55.000 12.14 0.0 0.00 3.16 F
383 386 0.104672 TCTTCCACCTTGTCCCCTCA 60.105 55.000 0.00 0.0 0.00 3.86 F
552 570 1.892862 ATCCCTCGTCGCTACCTCG 60.893 63.158 0.00 0.0 0.00 4.63 F
1213 1246 2.247699 TAGCAGTGGAAGGAGCCTTA 57.752 50.000 0.94 0.0 36.26 2.69 F
2089 2124 2.869233 TCTGTGTTTTGCTTTCCTGC 57.131 45.000 0.00 0.0 0.00 4.85 F
2953 5182 3.072915 TCAGCTTCCAATGAGGTTGAAGA 59.927 43.478 0.00 0.0 40.37 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2068 2103 3.888323 TGCAGGAAAGCAAAACACAGATA 59.112 39.130 0.00 0.0 42.46 1.98 R
2121 2156 6.984474 GGTGAGAAACGACTATTCAATATGGA 59.016 38.462 0.00 0.0 0.00 3.41 R
2577 4806 2.244695 TCTACCGTTCCAGTGACACAT 58.755 47.619 8.59 0.0 0.00 3.21 R
2739 4968 0.668535 GTGCCACAAAGACCTTCACC 59.331 55.000 0.00 0.0 0.00 4.02 R
3393 5622 2.429971 CTGCAGAGGAAGATCAGCTACA 59.570 50.000 8.42 0.0 33.26 2.74 R
4791 7021 0.312416 TCGTGCCAATTTTCAACGGG 59.688 50.000 0.00 0.0 0.00 5.28 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
53 54 3.021695 TGTCTACGATTACTCCCCACTG 58.978 50.000 0.00 0.00 0.00 3.66
179 180 4.524318 CGGTTGATACGGCGCCCT 62.524 66.667 23.46 12.81 0.00 5.19
180 181 2.588034 GGTTGATACGGCGCCCTC 60.588 66.667 23.46 15.86 0.00 4.30
181 182 2.960129 GTTGATACGGCGCCCTCG 60.960 66.667 23.46 12.44 39.07 4.63
283 286 3.834056 CCGCTCCCCTCTCCCCTA 61.834 72.222 0.00 0.00 0.00 3.53
284 287 2.522193 CGCTCCCCTCTCCCCTAC 60.522 72.222 0.00 0.00 0.00 3.18
285 288 2.122769 GCTCCCCTCTCCCCTACC 60.123 72.222 0.00 0.00 0.00 3.18
286 289 2.615773 CTCCCCTCTCCCCTACCC 59.384 72.222 0.00 0.00 0.00 3.69
287 290 2.021652 CTCCCCTCTCCCCTACCCT 61.022 68.421 0.00 0.00 0.00 4.34
288 291 1.551964 TCCCCTCTCCCCTACCCTT 60.552 63.158 0.00 0.00 0.00 3.95
289 292 1.074395 CCCCTCTCCCCTACCCTTC 60.074 68.421 0.00 0.00 0.00 3.46
290 293 1.074395 CCCTCTCCCCTACCCTTCC 60.074 68.421 0.00 0.00 0.00 3.46
291 294 1.074395 CCTCTCCCCTACCCTTCCC 60.074 68.421 0.00 0.00 0.00 3.97
292 295 1.074395 CTCTCCCCTACCCTTCCCC 60.074 68.421 0.00 0.00 0.00 4.81
373 376 2.370445 CCCGGCAGATCTTCCACCT 61.370 63.158 12.14 0.00 0.00 4.00
374 377 1.604378 CCGGCAGATCTTCCACCTT 59.396 57.895 12.14 0.00 0.00 3.50
376 379 0.036010 CGGCAGATCTTCCACCTTGT 60.036 55.000 12.14 0.00 0.00 3.16
383 386 0.104672 TCTTCCACCTTGTCCCCTCA 60.105 55.000 0.00 0.00 0.00 3.86
401 404 3.556633 CCTCAGCCATATCGATCTGCTTT 60.557 47.826 0.00 0.00 0.00 3.51
517 535 2.047560 GGTACGCGCCCTGTCTTT 60.048 61.111 5.73 0.00 0.00 2.52
552 570 1.892862 ATCCCTCGTCGCTACCTCG 60.893 63.158 0.00 0.00 0.00 4.63
666 684 3.343941 TTGAGGTAAAATCCGTCCCAG 57.656 47.619 0.00 0.00 0.00 4.45
698 716 2.439409 TGTGATGGAAGTGATGCCAAG 58.561 47.619 0.00 0.00 37.78 3.61
864 882 4.944962 TTTGAGTATGTCTGGCATTTCG 57.055 40.909 0.00 0.00 38.94 3.46
1183 1216 3.554960 GGAAGCCATTTTGAAGTGGTTCC 60.555 47.826 16.13 16.13 37.91 3.62
1213 1246 2.247699 TAGCAGTGGAAGGAGCCTTA 57.752 50.000 0.94 0.00 36.26 2.69
1501 1534 4.496840 GCAGTACAAAAGTACGGCAAAAGT 60.497 41.667 20.46 0.00 45.63 2.66
2068 2103 8.078596 GGCGATATTCTCATTAATTTGCTTCTT 58.921 33.333 0.00 0.00 0.00 2.52
2089 2124 2.869233 TCTGTGTTTTGCTTTCCTGC 57.131 45.000 0.00 0.00 0.00 4.85
2121 2156 9.023962 TGTTTTATTGCTCTTTTATCTCACCAT 57.976 29.630 0.00 0.00 0.00 3.55
2218 4447 9.561069 AGCAGAAAATTATAACATACGAGGAAT 57.439 29.630 0.00 0.00 0.00 3.01
2715 4944 7.503566 ACACAATTATCTATGGCTGCTTATGTT 59.496 33.333 0.00 0.00 0.00 2.71
2739 4968 3.304458 GGGAGCTTGTTTTAACCAACGAG 60.304 47.826 0.00 3.71 40.11 4.18
2953 5182 3.072915 TCAGCTTCCAATGAGGTTGAAGA 59.927 43.478 0.00 0.00 40.37 2.87
3211 5440 7.389607 GGGCTACTGTCAGTTTAATTCAGTTTA 59.610 37.037 11.54 0.00 39.54 2.01
3348 5577 3.626670 GCAGCTTGATTAGAGTCATTGCT 59.373 43.478 0.00 0.00 38.16 3.91
3746 5975 2.484287 ATTCTGCCACCTCCCAACGG 62.484 60.000 0.00 0.00 0.00 4.44
4023 6252 4.083003 GGCGTCAAACCAATTCTTGATGTA 60.083 41.667 12.13 0.00 39.65 2.29
4071 6300 4.007644 CAGAGAGCGGTGTGGGCA 62.008 66.667 0.00 0.00 0.00 5.36
4251 6480 4.587262 TCTGGGATATTTTCGAAGATCGGA 59.413 41.667 4.19 0.00 40.88 4.55
4417 6647 1.103803 TAGTACTGCCGCTCTCCAAG 58.896 55.000 5.39 0.00 0.00 3.61
4476 6706 5.938125 ACTGAAGGTATTGTTGGTGTGTATC 59.062 40.000 0.00 0.00 0.00 2.24
4502 6732 8.746530 CGTATAGTGTATATTTCCACCCTGTAT 58.253 37.037 0.00 0.00 31.88 2.29
4596 6826 1.326328 CTGAGCCCATCTGATCTCGA 58.674 55.000 0.00 0.00 0.00 4.04
4679 6909 4.030134 TGTACCAATTTTCAACGCGTTT 57.970 36.364 24.21 4.14 0.00 3.60
4716 6946 9.965824 GAGAAAGAAAAATATTGGTCTGAACAA 57.034 29.630 11.02 11.02 0.00 2.83
4756 6986 6.097554 ACTGTTTCACATACCACCAATTTTGA 59.902 34.615 0.00 0.00 0.00 2.69
4757 6987 7.060383 TGTTTCACATACCACCAATTTTGAT 57.940 32.000 0.00 0.00 0.00 2.57
4758 6988 7.504403 TGTTTCACATACCACCAATTTTGATT 58.496 30.769 0.00 0.00 0.00 2.57
4759 6989 7.989741 TGTTTCACATACCACCAATTTTGATTT 59.010 29.630 0.00 0.00 0.00 2.17
4791 7021 5.171476 TGAGAGCTACTTAGATGTGCAAAC 58.829 41.667 0.00 0.00 0.00 2.93
4792 7022 4.508662 AGAGCTACTTAGATGTGCAAACC 58.491 43.478 0.00 0.00 0.00 3.27
4793 7023 3.610911 AGCTACTTAGATGTGCAAACCC 58.389 45.455 0.00 0.00 0.00 4.11
4794 7024 2.351726 GCTACTTAGATGTGCAAACCCG 59.648 50.000 0.00 0.00 0.00 5.28
4795 7025 2.561478 ACTTAGATGTGCAAACCCGT 57.439 45.000 0.00 0.00 0.00 5.28
4796 7026 2.858745 ACTTAGATGTGCAAACCCGTT 58.141 42.857 0.00 0.00 0.00 4.44
4799 7029 1.686355 AGATGTGCAAACCCGTTGAA 58.314 45.000 0.00 0.00 39.87 2.69
4800 7030 2.028130 AGATGTGCAAACCCGTTGAAA 58.972 42.857 0.00 0.00 39.87 2.69
4801 7031 2.428890 AGATGTGCAAACCCGTTGAAAA 59.571 40.909 0.00 0.00 39.87 2.29
4802 7032 2.969628 TGTGCAAACCCGTTGAAAAT 57.030 40.000 0.00 0.00 39.87 1.82
4803 7033 3.252974 TGTGCAAACCCGTTGAAAATT 57.747 38.095 0.00 0.00 39.87 1.82
4804 7034 2.932614 TGTGCAAACCCGTTGAAAATTG 59.067 40.909 0.00 0.00 39.87 2.32
4805 7035 2.286563 GTGCAAACCCGTTGAAAATTGG 59.713 45.455 0.00 0.00 39.87 3.16
4806 7036 1.262950 GCAAACCCGTTGAAAATTGGC 59.737 47.619 0.00 0.00 39.87 4.52
4807 7037 2.555199 CAAACCCGTTGAAAATTGGCA 58.445 42.857 0.00 0.00 39.87 4.92
4808 7038 2.232756 AACCCGTTGAAAATTGGCAC 57.767 45.000 0.00 0.00 0.00 5.01
4809 7039 0.031449 ACCCGTTGAAAATTGGCACG 59.969 50.000 0.00 0.00 0.00 5.34
4810 7040 0.312416 CCCGTTGAAAATTGGCACGA 59.688 50.000 0.00 0.00 0.00 4.35
4811 7041 1.269309 CCCGTTGAAAATTGGCACGAA 60.269 47.619 0.00 0.00 0.00 3.85
4900 7130 2.568696 TGCTGTTCATAGTCGAGAGC 57.431 50.000 0.00 0.00 0.00 4.09
4901 7131 1.135139 TGCTGTTCATAGTCGAGAGCC 59.865 52.381 0.00 0.00 0.00 4.70
4902 7132 1.135139 GCTGTTCATAGTCGAGAGCCA 59.865 52.381 0.00 0.00 0.00 4.75
4903 7133 2.223923 GCTGTTCATAGTCGAGAGCCAT 60.224 50.000 0.00 0.00 0.00 4.40
4904 7134 3.739519 GCTGTTCATAGTCGAGAGCCATT 60.740 47.826 0.00 0.00 0.00 3.16
4905 7135 4.437239 CTGTTCATAGTCGAGAGCCATTT 58.563 43.478 0.00 0.00 0.00 2.32
4906 7136 5.592054 CTGTTCATAGTCGAGAGCCATTTA 58.408 41.667 0.00 0.00 0.00 1.40
4907 7137 5.592054 TGTTCATAGTCGAGAGCCATTTAG 58.408 41.667 0.00 0.00 0.00 1.85
4908 7138 4.244425 TCATAGTCGAGAGCCATTTAGC 57.756 45.455 0.00 0.00 0.00 3.09
4909 7139 2.776312 TAGTCGAGAGCCATTTAGCG 57.224 50.000 0.00 0.00 38.01 4.26
4910 7140 0.103208 AGTCGAGAGCCATTTAGCGG 59.897 55.000 0.00 0.00 38.01 5.52
4920 7150 2.099756 GCCATTTAGCGGCTCTCATTTT 59.900 45.455 5.39 0.00 46.56 1.82
4928 7158 2.287547 GCGGCTCTCATTTTTGTGTTCA 60.288 45.455 0.00 0.00 0.00 3.18
4930 7160 3.916172 CGGCTCTCATTTTTGTGTTCATG 59.084 43.478 0.00 0.00 0.00 3.07
4975 7205 6.975197 GGTTGAAACCTGAAAGAGAAAGAAAG 59.025 38.462 4.92 0.00 45.75 2.62
4981 7213 6.125719 ACCTGAAAGAGAAAGAAAGAGCTTT 58.874 36.000 0.00 0.00 37.11 3.51
5052 7284 2.467566 ACGGGAGTGTGTTATGGTTC 57.532 50.000 0.00 0.00 44.82 3.62
5207 7439 9.014297 AGCTTGTGCAATCTTTAATTAAGTAGT 57.986 29.630 0.00 0.00 42.74 2.73
5208 7440 9.626045 GCTTGTGCAATCTTTAATTAAGTAGTT 57.374 29.630 0.00 0.00 39.41 2.24
5235 7467 9.624373 AATTGCTCTGAGAATACATATTTCAGT 57.376 29.630 9.28 0.00 35.19 3.41
5237 7469 9.755804 TTGCTCTGAGAATACATATTTCAGTAG 57.244 33.333 9.28 13.60 35.19 2.57
5238 7470 8.918116 TGCTCTGAGAATACATATTTCAGTAGT 58.082 33.333 9.28 0.00 35.19 2.73
5239 7471 9.757227 GCTCTGAGAATACATATTTCAGTAGTT 57.243 33.333 9.28 0.00 35.19 2.24
5241 7473 9.952188 TCTGAGAATACATATTTCAGTAGTTCG 57.048 33.333 15.60 0.00 35.19 3.95
5242 7474 9.952188 CTGAGAATACATATTTCAGTAGTTCGA 57.048 33.333 11.61 0.00 32.49 3.71
5243 7475 9.731819 TGAGAATACATATTTCAGTAGTTCGAC 57.268 33.333 0.00 0.00 0.00 4.20
5244 7476 8.783999 AGAATACATATTTCAGTAGTTCGACG 57.216 34.615 0.00 0.00 0.00 5.12
5245 7477 8.404000 AGAATACATATTTCAGTAGTTCGACGT 58.596 33.333 0.00 0.00 0.00 4.34
5246 7478 8.557869 AATACATATTTCAGTAGTTCGACGTC 57.442 34.615 5.18 5.18 0.00 4.34
5247 7479 6.192234 ACATATTTCAGTAGTTCGACGTCT 57.808 37.500 14.70 0.00 0.00 4.18
5248 7480 6.028368 ACATATTTCAGTAGTTCGACGTCTG 58.972 40.000 14.70 7.51 0.00 3.51
5249 7481 4.761235 ATTTCAGTAGTTCGACGTCTGA 57.239 40.909 14.70 9.87 33.61 3.27
5250 7482 4.761235 TTTCAGTAGTTCGACGTCTGAT 57.239 40.909 14.70 1.88 34.68 2.90
5251 7483 5.868043 TTTCAGTAGTTCGACGTCTGATA 57.132 39.130 14.70 1.12 34.68 2.15
5252 7484 6.432607 TTTCAGTAGTTCGACGTCTGATAT 57.567 37.500 14.70 6.97 34.68 1.63
5253 7485 7.543947 TTTCAGTAGTTCGACGTCTGATATA 57.456 36.000 14.70 6.11 34.68 0.86
5254 7486 7.725818 TTCAGTAGTTCGACGTCTGATATAT 57.274 36.000 14.70 0.00 34.68 0.86
5255 7487 7.725818 TCAGTAGTTCGACGTCTGATATATT 57.274 36.000 14.70 3.60 31.78 1.28
5256 7488 8.151141 TCAGTAGTTCGACGTCTGATATATTT 57.849 34.615 14.70 0.86 31.78 1.40
5257 7489 8.281194 TCAGTAGTTCGACGTCTGATATATTTC 58.719 37.037 14.70 0.00 31.78 2.17
5258 7490 8.068380 CAGTAGTTCGACGTCTGATATATTTCA 58.932 37.037 14.70 0.00 0.00 2.69
5259 7491 8.283992 AGTAGTTCGACGTCTGATATATTTCAG 58.716 37.037 14.70 14.95 43.70 3.02
5260 7492 7.028926 AGTTCGACGTCTGATATATTTCAGT 57.971 36.000 18.91 5.03 43.02 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 4.826183 AGTGGGGAGTAATCGTAGACATAC 59.174 45.833 0.00 0.00 42.51 2.39
30 31 4.825634 CAGTGGGGAGTAATCGTAGACATA 59.174 45.833 0.00 0.00 42.51 2.29
31 32 3.637229 CAGTGGGGAGTAATCGTAGACAT 59.363 47.826 0.00 0.00 42.51 3.06
32 33 3.021695 CAGTGGGGAGTAATCGTAGACA 58.978 50.000 0.00 0.00 42.51 3.41
33 34 3.285484 TCAGTGGGGAGTAATCGTAGAC 58.715 50.000 0.00 0.00 42.51 2.59
34 35 3.657398 TCAGTGGGGAGTAATCGTAGA 57.343 47.619 0.00 0.00 45.75 2.59
35 36 5.071370 AGTATCAGTGGGGAGTAATCGTAG 58.929 45.833 0.00 0.00 0.00 3.51
36 37 5.057843 AGTATCAGTGGGGAGTAATCGTA 57.942 43.478 0.00 0.00 0.00 3.43
37 38 3.912248 AGTATCAGTGGGGAGTAATCGT 58.088 45.455 0.00 0.00 0.00 3.73
38 39 5.071370 ACTAGTATCAGTGGGGAGTAATCG 58.929 45.833 0.00 0.00 0.00 3.34
39 40 6.308566 AGACTAGTATCAGTGGGGAGTAATC 58.691 44.000 0.00 0.00 0.00 1.75
40 41 6.282568 AGACTAGTATCAGTGGGGAGTAAT 57.717 41.667 0.00 0.00 0.00 1.89
53 54 7.754625 GGATTCAGACCGATAAGACTAGTATC 58.245 42.308 0.00 0.00 0.00 2.24
282 285 0.344435 GGAAGGGTAGGGGAAGGGTA 59.656 60.000 0.00 0.00 0.00 3.69
283 286 1.084273 GGAAGGGTAGGGGAAGGGT 59.916 63.158 0.00 0.00 0.00 4.34
284 287 2.070650 CGGAAGGGTAGGGGAAGGG 61.071 68.421 0.00 0.00 0.00 3.95
285 288 3.643398 CGGAAGGGTAGGGGAAGG 58.357 66.667 0.00 0.00 0.00 3.46
373 376 0.758734 CGATATGGCTGAGGGGACAA 59.241 55.000 0.00 0.00 0.00 3.18
374 377 0.105709 TCGATATGGCTGAGGGGACA 60.106 55.000 0.00 0.00 0.00 4.02
376 379 1.077828 AGATCGATATGGCTGAGGGGA 59.922 52.381 0.00 0.00 0.00 4.81
383 386 3.072184 AGGAAAAGCAGATCGATATGGCT 59.928 43.478 20.77 15.58 36.13 4.75
401 404 3.727258 CATGGCGGTGGGGAGGAA 61.727 66.667 0.00 0.00 0.00 3.36
517 535 0.320374 GATGTTCACAGGACCACCGA 59.680 55.000 0.00 0.00 41.83 4.69
552 570 2.361789 TGTTAAAGCGGGGATTAGCAC 58.638 47.619 0.00 0.00 35.48 4.40
606 624 0.966179 TGAAGCGCACTTAGTGGAGA 59.034 50.000 14.63 0.00 35.82 3.71
666 684 6.707608 TCACTTCCATCACATATCAATGCTAC 59.292 38.462 0.00 0.00 36.50 3.58
834 852 4.756642 CCAGACATACTCAAAAGTTGCTGA 59.243 41.667 0.00 0.00 36.92 4.26
864 882 1.207329 AGATCGTCACCCTAAAGCCAC 59.793 52.381 0.00 0.00 0.00 5.01
1183 1216 4.378774 CTTCCACTGCTATCAGATTCCTG 58.621 47.826 0.00 0.00 42.95 3.86
1213 1246 5.337788 CTCCTTCCTAGTAATAGGGCAGAT 58.662 45.833 15.97 0.00 37.81 2.90
1501 1534 5.596836 ACAAAGCAAAGACTTTCCAATGA 57.403 34.783 0.00 0.00 37.78 2.57
2068 2103 3.888323 TGCAGGAAAGCAAAACACAGATA 59.112 39.130 0.00 0.00 42.46 1.98
2121 2156 6.984474 GGTGAGAAACGACTATTCAATATGGA 59.016 38.462 0.00 0.00 0.00 3.41
2577 4806 2.244695 TCTACCGTTCCAGTGACACAT 58.755 47.619 8.59 0.00 0.00 3.21
2715 4944 2.696187 GTTGGTTAAAACAAGCTCCCCA 59.304 45.455 0.00 0.00 0.00 4.96
2739 4968 0.668535 GTGCCACAAAGACCTTCACC 59.331 55.000 0.00 0.00 0.00 4.02
3348 5577 6.072508 GCTCTTCAGAAATACCATTGTTGTCA 60.073 38.462 0.00 0.00 0.00 3.58
3393 5622 2.429971 CTGCAGAGGAAGATCAGCTACA 59.570 50.000 8.42 0.00 33.26 2.74
3746 5975 7.164803 TGGAAATATTGAAAAACACAATCCCC 58.835 34.615 0.00 0.00 38.61 4.81
3958 6187 3.678289 TCACACCTTGATCAATGTCCAG 58.322 45.455 12.80 5.91 0.00 3.86
4023 6252 3.368843 CCTCAGTCCGATTCTCACACAAT 60.369 47.826 0.00 0.00 0.00 2.71
4071 6300 4.079327 TCCGTCCTAAGGATCCTTTCTACT 60.079 45.833 31.45 9.54 37.47 2.57
4251 6480 2.086869 GCATAACATGGTCACTGTGCT 58.913 47.619 2.12 0.00 0.00 4.40
4357 6587 4.910195 AGCAACTGATTGGTGTGAGATTA 58.090 39.130 0.00 0.00 44.79 1.75
4417 6647 7.605410 TCAATTCGATTAGTTTGGGAACTAC 57.395 36.000 0.00 0.00 45.51 2.73
4476 6706 6.989659 ACAGGGTGGAAATATACACTATACG 58.010 40.000 0.00 0.00 37.72 3.06
4558 6788 5.114764 TCAGGCACAGAAATGGATATTCA 57.885 39.130 0.00 0.00 0.00 2.57
4574 6804 0.693430 AGATCAGATGGGCTCAGGCA 60.693 55.000 0.00 0.00 40.87 4.75
4635 6865 8.891671 ACAGACATGCAAAAATAATCAGTTTT 57.108 26.923 0.00 0.00 32.42 2.43
4636 6866 9.410556 GTACAGACATGCAAAAATAATCAGTTT 57.589 29.630 0.00 0.00 0.00 2.66
4637 6867 8.028938 GGTACAGACATGCAAAAATAATCAGTT 58.971 33.333 0.00 0.00 0.00 3.16
4638 6868 7.176515 TGGTACAGACATGCAAAAATAATCAGT 59.823 33.333 0.00 0.00 0.00 3.41
4643 6873 9.553064 AAAATTGGTACAGACATGCAAAAATAA 57.447 25.926 0.00 0.00 42.39 1.40
4645 6875 7.714377 TGAAAATTGGTACAGACATGCAAAAAT 59.286 29.630 0.00 0.00 42.39 1.82
4766 6996 4.019858 TGCACATCTAAGTAGCTCTCAGT 58.980 43.478 0.00 0.00 0.00 3.41
4768 6998 5.171476 GTTTGCACATCTAAGTAGCTCTCA 58.829 41.667 0.00 0.00 0.00 3.27
4791 7021 0.312416 TCGTGCCAATTTTCAACGGG 59.688 50.000 0.00 0.00 0.00 5.28
4792 7022 1.784283 GTTCGTGCCAATTTTCAACGG 59.216 47.619 0.00 0.00 0.00 4.44
4793 7023 1.784283 GGTTCGTGCCAATTTTCAACG 59.216 47.619 0.00 0.00 0.00 4.10
4794 7024 3.049912 GAGGTTCGTGCCAATTTTCAAC 58.950 45.455 1.38 0.00 0.00 3.18
4795 7025 2.690497 TGAGGTTCGTGCCAATTTTCAA 59.310 40.909 1.38 0.00 0.00 2.69
4796 7026 2.034053 GTGAGGTTCGTGCCAATTTTCA 59.966 45.455 1.38 0.00 0.00 2.69
4799 7029 0.591170 CGTGAGGTTCGTGCCAATTT 59.409 50.000 1.38 0.00 0.00 1.82
4800 7030 1.852067 GCGTGAGGTTCGTGCCAATT 61.852 55.000 1.38 0.00 0.00 2.32
4801 7031 2.325082 GCGTGAGGTTCGTGCCAAT 61.325 57.895 1.38 0.00 0.00 3.16
4802 7032 2.970324 GCGTGAGGTTCGTGCCAA 60.970 61.111 1.38 0.00 0.00 4.52
4803 7033 4.228567 TGCGTGAGGTTCGTGCCA 62.229 61.111 1.38 0.00 0.00 4.92
4804 7034 3.712881 GTGCGTGAGGTTCGTGCC 61.713 66.667 0.00 0.00 0.00 5.01
4805 7035 3.712881 GGTGCGTGAGGTTCGTGC 61.713 66.667 0.00 0.00 0.00 5.34
4806 7036 1.433053 TTTGGTGCGTGAGGTTCGTG 61.433 55.000 0.00 0.00 0.00 4.35
4807 7037 0.745128 TTTTGGTGCGTGAGGTTCGT 60.745 50.000 0.00 0.00 0.00 3.85
4808 7038 0.316689 GTTTTGGTGCGTGAGGTTCG 60.317 55.000 0.00 0.00 0.00 3.95
4809 7039 0.736053 TGTTTTGGTGCGTGAGGTTC 59.264 50.000 0.00 0.00 0.00 3.62
4810 7040 1.398692 ATGTTTTGGTGCGTGAGGTT 58.601 45.000 0.00 0.00 0.00 3.50
4811 7041 1.398692 AATGTTTTGGTGCGTGAGGT 58.601 45.000 0.00 0.00 0.00 3.85
4900 7130 4.107622 CAAAAATGAGAGCCGCTAAATGG 58.892 43.478 0.00 0.00 0.00 3.16
4901 7131 4.560035 CACAAAAATGAGAGCCGCTAAATG 59.440 41.667 0.00 0.00 0.00 2.32
4902 7132 4.218417 ACACAAAAATGAGAGCCGCTAAAT 59.782 37.500 0.00 0.00 0.00 1.40
4903 7133 3.568007 ACACAAAAATGAGAGCCGCTAAA 59.432 39.130 0.00 0.00 0.00 1.85
4904 7134 3.146066 ACACAAAAATGAGAGCCGCTAA 58.854 40.909 0.00 0.00 0.00 3.09
4905 7135 2.778299 ACACAAAAATGAGAGCCGCTA 58.222 42.857 0.00 0.00 0.00 4.26
4906 7136 1.609208 ACACAAAAATGAGAGCCGCT 58.391 45.000 0.00 0.00 0.00 5.52
4907 7137 2.287547 TGAACACAAAAATGAGAGCCGC 60.288 45.455 0.00 0.00 0.00 6.53
4908 7138 3.624326 TGAACACAAAAATGAGAGCCG 57.376 42.857 0.00 0.00 0.00 5.52
4909 7139 3.676646 GCATGAACACAAAAATGAGAGCC 59.323 43.478 0.00 0.00 0.00 4.70
4910 7140 4.384846 CAGCATGAACACAAAAATGAGAGC 59.615 41.667 0.00 0.00 39.69 4.09
4920 7150 7.628769 ATGTATGATTACAGCATGAACACAA 57.371 32.000 0.00 0.00 41.49 3.33
4928 7158 8.623903 CAACCAACTTATGTATGATTACAGCAT 58.376 33.333 0.00 0.00 41.49 3.79
4930 7160 8.208718 TCAACCAACTTATGTATGATTACAGC 57.791 34.615 0.00 0.00 41.49 4.40
4960 7190 6.127647 TGCAAAAGCTCTTTCTTTCTCTTTCA 60.128 34.615 0.00 0.00 35.41 2.69
4975 7205 7.408910 ACAAAATTTATTGTGTGCAAAAGCTC 58.591 30.769 0.00 0.00 41.78 4.09
5052 7284 0.930310 CTGGAACACGCATCATACGG 59.070 55.000 0.00 0.00 34.00 4.02
5209 7441 9.624373 ACTGAAATATGTATTCTCAGAGCAATT 57.376 29.630 19.78 5.62 37.53 2.32
5211 7443 9.755804 CTACTGAAATATGTATTCTCAGAGCAA 57.244 33.333 19.78 0.00 37.53 3.91
5212 7444 8.918116 ACTACTGAAATATGTATTCTCAGAGCA 58.082 33.333 19.78 0.00 37.53 4.26
5213 7445 9.757227 AACTACTGAAATATGTATTCTCAGAGC 57.243 33.333 19.78 0.00 37.53 4.09
5215 7447 9.952188 CGAACTACTGAAATATGTATTCTCAGA 57.048 33.333 19.78 10.50 37.53 3.27
5216 7448 9.952188 TCGAACTACTGAAATATGTATTCTCAG 57.048 33.333 15.49 15.49 39.53 3.35
5217 7449 9.731819 GTCGAACTACTGAAATATGTATTCTCA 57.268 33.333 0.00 0.00 0.00 3.27
5218 7450 8.893884 CGTCGAACTACTGAAATATGTATTCTC 58.106 37.037 0.00 0.00 0.00 2.87
5219 7451 8.404000 ACGTCGAACTACTGAAATATGTATTCT 58.596 33.333 0.00 0.00 0.00 2.40
5220 7452 8.557869 ACGTCGAACTACTGAAATATGTATTC 57.442 34.615 0.00 0.00 0.00 1.75
5221 7453 8.404000 AGACGTCGAACTACTGAAATATGTATT 58.596 33.333 10.46 0.00 0.00 1.89
5222 7454 7.856398 CAGACGTCGAACTACTGAAATATGTAT 59.144 37.037 10.46 0.00 0.00 2.29
5223 7455 7.064966 TCAGACGTCGAACTACTGAAATATGTA 59.935 37.037 10.46 0.00 35.20 2.29
5224 7456 6.028368 CAGACGTCGAACTACTGAAATATGT 58.972 40.000 10.46 0.00 0.00 2.29
5225 7457 6.255950 TCAGACGTCGAACTACTGAAATATG 58.744 40.000 10.46 0.00 35.20 1.78
5226 7458 6.432607 TCAGACGTCGAACTACTGAAATAT 57.567 37.500 10.46 0.00 35.20 1.28
5227 7459 5.868043 TCAGACGTCGAACTACTGAAATA 57.132 39.130 10.46 0.00 35.20 1.40
5228 7460 4.761235 TCAGACGTCGAACTACTGAAAT 57.239 40.909 10.46 0.00 35.20 2.17
5229 7461 4.761235 ATCAGACGTCGAACTACTGAAA 57.239 40.909 10.46 0.00 40.21 2.69
5230 7462 7.725818 ATATATCAGACGTCGAACTACTGAA 57.274 36.000 10.46 0.00 40.21 3.02
5231 7463 7.725818 AATATATCAGACGTCGAACTACTGA 57.274 36.000 10.46 6.89 40.88 3.41
5232 7464 8.068380 TGAAATATATCAGACGTCGAACTACTG 58.932 37.037 10.46 0.80 0.00 2.74
5233 7465 8.151141 TGAAATATATCAGACGTCGAACTACT 57.849 34.615 10.46 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.