Multiple sequence alignment - TraesCS4A01G229000

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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 TraesCS4A01G229000 chr4A 100.000 5860 0 0 1 5860 537529140 537534999 0.000000e+00 10822
1 TraesCS4A01G229000 chr4A 86.087 345 23 12 5256 5591 537538399 537538727 1.210000e-91 348
2 TraesCS4A01G229000 chr4A 84.452 283 30 9 5585 5860 537538797 537539072 3.480000e-67 267
3 TraesCS4A01G229000 chr4A 94.048 84 4 1 2088 2170 537531145 537531228 6.160000e-25 126
4 TraesCS4A01G229000 chr4A 94.048 84 4 1 2006 2089 537531227 537531309 6.160000e-25 126
5 TraesCS4A01G229000 chr4A 94.595 74 4 0 5183 5256 537538294 537538367 1.330000e-21 115
6 TraesCS4A01G229000 chr4D 96.849 5426 115 27 459 5860 58280794 58275401 0.000000e+00 9022
7 TraesCS4A01G229000 chr4D 87.000 400 44 5 15 414 58281281 58280890 1.500000e-120 444
8 TraesCS4A01G229000 chr4D 83.165 297 17 13 5256 5551 58273118 58272854 2.110000e-59 241
9 TraesCS4A01G229000 chr4D 80.282 284 20 26 5601 5855 58272852 58272576 1.300000e-41 182
10 TraesCS4A01G229000 chr4D 96.429 84 2 1 2006 2089 58279166 58279084 2.850000e-28 137
11 TraesCS4A01G229000 chr4D 94.048 84 4 1 2088 2170 58279248 58279165 6.160000e-25 126
12 TraesCS4A01G229000 chr4D 94.366 71 4 0 5183 5253 58273217 58273147 6.210000e-20 110
13 TraesCS4A01G229000 chr4B 93.033 5311 201 71 631 5860 87693778 87688556 0.000000e+00 7601
14 TraesCS4A01G229000 chr4B 90.870 230 11 4 423 650 87694028 87693807 3.430000e-77 300
15 TraesCS4A01G229000 chr4B 87.817 197 24 0 15 211 87694366 87694170 1.270000e-56 231
16 TraesCS4A01G229000 chr4B 94.048 84 4 1 2006 2089 87692346 87692264 6.160000e-25 126
17 TraesCS4A01G229000 chr4B 94.048 84 4 1 2088 2170 87692428 87692345 6.160000e-25 126
18 TraesCS4A01G229000 chr2D 93.777 1398 79 3 1473 2870 360699078 360700467 0.000000e+00 2093
19 TraesCS4A01G229000 chr2D 92.709 1111 67 8 3150 4256 360700463 360701563 0.000000e+00 1591


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 TraesCS4A01G229000 chr4A 537529140 537534999 5859 False 3691.333333 10822 96.032000 1 5860 3 chr4A.!!$F1 5859
1 TraesCS4A01G229000 chr4A 537538294 537539072 778 False 243.333333 348 88.378000 5183 5860 3 chr4A.!!$F2 677
2 TraesCS4A01G229000 chr4D 58272576 58281281 8705 True 1466.000000 9022 90.305571 15 5860 7 chr4D.!!$R1 5845
3 TraesCS4A01G229000 chr4B 87688556 87694366 5810 True 1676.800000 7601 91.963200 15 5860 5 chr4B.!!$R1 5845
4 TraesCS4A01G229000 chr2D 360699078 360701563 2485 False 1842.000000 2093 93.243000 1473 4256 2 chr2D.!!$F1 2783

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
453 520 0.036199 AATTACCCCGTGCAAGCGTA 60.036 50.000 0.00 0.0 0.00 4.42 F
454 521 0.461339 ATTACCCCGTGCAAGCGTAG 60.461 55.000 0.00 0.0 0.00 3.51 F
1076 1204 0.737715 GGTTGATTCTGCGAGCGTCT 60.738 55.000 0.00 0.0 0.00 4.18 F
2319 2451 2.507058 AGAATGGGCTCTGAAGTGCATA 59.493 45.455 6.69 0.0 36.36 3.14 F
2957 3109 2.264813 TGTATTCGGCGTAAACTGCTC 58.735 47.619 6.85 0.0 0.00 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2191 2320 1.686355 ATTCAAAGGCGTCACAACCA 58.314 45.000 0.0 0.0 0.00 3.67 R
2192 2321 3.907894 TTATTCAAAGGCGTCACAACC 57.092 42.857 0.0 0.0 0.00 3.77 R
2957 3109 2.273370 GCATTGTGCATGAAGACTGG 57.727 50.000 0.0 0.0 44.26 4.00 R
3513 3674 2.503356 AGGAAACTGAGGGAGTATGCAG 59.497 50.000 0.0 0.0 41.13 4.41 R
4897 5070 1.018752 CGATGACAATGACGGTGCCA 61.019 55.000 0.0 0.0 0.00 4.92 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
54 55 7.120923 AGACATAATTTCACCGGTACATACT 57.879 36.000 6.87 0.00 0.00 2.12
101 102 3.804873 GGTGTAAATGCGAATCTCTCCTC 59.195 47.826 0.00 0.00 0.00 3.71
112 113 6.183360 TGCGAATCTCTCCTCTCATTTATTCA 60.183 38.462 0.00 0.00 0.00 2.57
119 120 9.224267 TCTCTCCTCTCATTTATTCAAACAAAG 57.776 33.333 0.00 0.00 0.00 2.77
121 122 9.745018 TCTCCTCTCATTTATTCAAACAAAGAT 57.255 29.630 0.00 0.00 0.00 2.40
123 124 8.668353 TCCTCTCATTTATTCAAACAAAGATCG 58.332 33.333 0.00 0.00 0.00 3.69
128 129 9.787532 TCATTTATTCAAACAAAGATCGAATCC 57.212 29.630 0.00 0.00 0.00 3.01
129 130 8.736742 CATTTATTCAAACAAAGATCGAATCCG 58.263 33.333 0.00 0.00 37.07 4.18
130 131 4.678509 TTCAAACAAAGATCGAATCCGG 57.321 40.909 0.00 0.00 36.24 5.14
134 135 2.618053 ACAAAGATCGAATCCGGACAC 58.382 47.619 6.12 2.40 36.24 3.67
162 163 3.066380 TGTGCAAATATCCATCGATCCG 58.934 45.455 0.00 0.00 0.00 4.18
164 165 3.123621 GTGCAAATATCCATCGATCCGAC 59.876 47.826 0.00 0.00 39.18 4.79
165 166 3.244044 TGCAAATATCCATCGATCCGACA 60.244 43.478 0.00 0.00 39.18 4.35
166 167 3.745975 GCAAATATCCATCGATCCGACAA 59.254 43.478 0.00 0.00 39.18 3.18
168 169 4.873746 AATATCCATCGATCCGACAACT 57.126 40.909 0.00 0.00 39.18 3.16
178 179 0.901580 TCCGACAACTACCCCCTCAC 60.902 60.000 0.00 0.00 0.00 3.51
179 180 1.595357 CGACAACTACCCCCTCACC 59.405 63.158 0.00 0.00 0.00 4.02
186 187 1.009552 ACTACCCCCTCACCATCATCA 59.990 52.381 0.00 0.00 0.00 3.07
214 215 3.715628 ATGGCTCAAACCGATTAATGC 57.284 42.857 0.00 0.00 0.00 3.56
226 227 4.202264 ACCGATTAATGCGAATCTCTCCTT 60.202 41.667 0.00 0.00 34.26 3.36
227 228 4.752101 CCGATTAATGCGAATCTCTCCTTT 59.248 41.667 0.00 0.00 34.26 3.11
235 236 6.851222 TGCGAATCTCTCCTTTCATTTATC 57.149 37.500 0.00 0.00 0.00 1.75
245 246 7.816640 TCTCCTTTCATTTATCCGAACAAAAG 58.183 34.615 0.00 0.00 0.00 2.27
304 305 0.469331 CCGACAGCTACCCCCTCATA 60.469 60.000 0.00 0.00 0.00 2.15
393 394 6.424509 CACAATAAACACATGCCTTTCAACAT 59.575 34.615 0.00 0.00 0.00 2.71
394 395 6.646240 ACAATAAACACATGCCTTTCAACATC 59.354 34.615 0.00 0.00 0.00 3.06
395 396 4.942761 AAACACATGCCTTTCAACATCT 57.057 36.364 0.00 0.00 0.00 2.90
414 415 2.073816 CTAAAACCATCCGCAACGAGT 58.926 47.619 0.00 0.00 0.00 4.18
415 416 0.591170 AAAACCATCCGCAACGAGTG 59.409 50.000 0.00 0.00 0.00 3.51
416 417 0.534203 AAACCATCCGCAACGAGTGT 60.534 50.000 0.00 0.00 0.00 3.55
421 422 2.418628 CCATCCGCAACGAGTGTAAAAT 59.581 45.455 0.00 0.00 0.00 1.82
447 514 0.600557 CAGCAAAATTACCCCGTGCA 59.399 50.000 0.00 0.00 37.68 4.57
448 515 1.000283 CAGCAAAATTACCCCGTGCAA 60.000 47.619 0.00 0.00 37.68 4.08
449 516 1.272212 AGCAAAATTACCCCGTGCAAG 59.728 47.619 0.00 0.00 37.68 4.01
450 517 1.708822 CAAAATTACCCCGTGCAAGC 58.291 50.000 0.00 0.00 0.00 4.01
451 518 0.242555 AAAATTACCCCGTGCAAGCG 59.757 50.000 0.00 0.00 0.00 4.68
452 519 0.891904 AAATTACCCCGTGCAAGCGT 60.892 50.000 0.00 0.00 0.00 5.07
453 520 0.036199 AATTACCCCGTGCAAGCGTA 60.036 50.000 0.00 0.00 0.00 4.42
454 521 0.461339 ATTACCCCGTGCAAGCGTAG 60.461 55.000 0.00 0.00 0.00 3.51
498 565 0.895559 CAGTGGCTTTGTTCCCCTCC 60.896 60.000 0.00 0.00 0.00 4.30
719 836 4.521062 CAGGGGCTTCTCGCGAGG 62.521 72.222 33.98 20.83 40.44 4.63
767 884 4.335647 CCCCGTTCACCAGCAGCT 62.336 66.667 0.00 0.00 0.00 4.24
768 885 2.743928 CCCGTTCACCAGCAGCTC 60.744 66.667 0.00 0.00 0.00 4.09
769 886 3.114616 CCGTTCACCAGCAGCTCG 61.115 66.667 0.00 0.00 0.00 5.03
773 890 1.300931 TTCACCAGCAGCTCGTCAC 60.301 57.895 0.00 0.00 0.00 3.67
952 1076 2.517450 CGCCCGCTCTCGATTTGTC 61.517 63.158 0.00 0.00 38.10 3.18
1076 1204 0.737715 GGTTGATTCTGCGAGCGTCT 60.738 55.000 0.00 0.00 0.00 4.18
1154 1283 3.585862 GTGAGTTGGATTCGCTCTGTTA 58.414 45.455 0.00 0.00 0.00 2.41
1181 1310 3.750652 CAGCTGTTTCTTTCTTCTCTCCC 59.249 47.826 5.25 0.00 0.00 4.30
2000 2129 5.063204 TCATGGGTCAAAAGTAAGTCTGTG 58.937 41.667 0.00 0.00 0.00 3.66
2004 2133 4.261197 GGGTCAAAAGTAAGTCTGTGCAAG 60.261 45.833 0.00 0.00 0.00 4.01
2319 2451 2.507058 AGAATGGGCTCTGAAGTGCATA 59.493 45.455 6.69 0.00 36.36 3.14
2637 2769 2.550830 ATGGAAGCACTGAACTCGTT 57.449 45.000 0.00 0.00 0.00 3.85
2669 2801 5.316167 ACTTCAGGTAATGACAAAGCATCA 58.684 37.500 0.00 0.00 37.77 3.07
2957 3109 2.264813 TGTATTCGGCGTAAACTGCTC 58.735 47.619 6.85 0.00 0.00 4.26
3618 3779 5.068234 TCAATGGTACTTACGACAAGGAG 57.932 43.478 0.00 0.00 0.00 3.69
3678 3843 6.348478 TCCATTCCCCACCTAAAATATGAA 57.652 37.500 0.00 0.00 0.00 2.57
3816 3986 6.039616 GGCGCTTGTGGATTTAAATCATTTA 58.960 36.000 25.55 9.32 37.15 1.40
3835 4005 9.822727 ATCATTTACTTCCTTCCCTTTTCTAAA 57.177 29.630 0.00 0.00 0.00 1.85
3989 4162 9.630098 TTTGCTTTCTGACATATGAGAAATTTC 57.370 29.630 15.99 10.33 37.52 2.17
4319 4492 1.283793 CCAGGTTGAAGTTGCTGCG 59.716 57.895 0.00 0.00 0.00 5.18
4355 4528 0.260230 TCCCCCAACTTGTTCTTGCA 59.740 50.000 0.00 0.00 0.00 4.08
4376 4549 2.027745 ACCACTCAGCATCGAGATTGTT 60.028 45.455 4.98 0.00 36.47 2.83
4622 4795 2.110578 ACAAGGATAATGCAAAGGGGC 58.889 47.619 0.00 0.00 0.00 5.80
4795 4968 2.036256 GCAACTGGACAGGGGCAT 59.964 61.111 4.14 0.00 33.61 4.40
4796 4969 2.345760 GCAACTGGACAGGGGCATG 61.346 63.158 4.14 0.00 33.61 4.06
4909 5082 2.699768 CGGCATTGGCACCGTCATT 61.700 57.895 11.10 0.00 44.46 2.57
4962 5135 1.995066 TCGCACCCACCATCCATCT 60.995 57.895 0.00 0.00 0.00 2.90
5085 5259 2.750712 GGTACAAGGTGTTGTGTTGTGT 59.249 45.455 0.98 0.00 46.75 3.72
5086 5260 3.181504 GGTACAAGGTGTTGTGTTGTGTC 60.182 47.826 0.98 0.00 46.75 3.67
5087 5261 1.466950 ACAAGGTGTTGTGTTGTGTCG 59.533 47.619 0.00 0.00 45.58 4.35
5088 5262 1.466950 CAAGGTGTTGTGTTGTGTCGT 59.533 47.619 0.00 0.00 0.00 4.34
5089 5263 1.083489 AGGTGTTGTGTTGTGTCGTG 58.917 50.000 0.00 0.00 0.00 4.35
5090 5264 0.800012 GGTGTTGTGTTGTGTCGTGT 59.200 50.000 0.00 0.00 0.00 4.49
5091 5265 1.201987 GGTGTTGTGTTGTGTCGTGTC 60.202 52.381 0.00 0.00 0.00 3.67
5243 5434 2.223479 CCGTACATATGGCCTTGTTTGC 60.223 50.000 3.32 0.00 0.00 3.68
5244 5435 2.682856 CGTACATATGGCCTTGTTTGCT 59.317 45.455 3.32 0.00 0.00 3.91
5245 5436 3.487376 CGTACATATGGCCTTGTTTGCTG 60.487 47.826 3.32 0.00 0.00 4.41
5246 5437 1.205417 ACATATGGCCTTGTTTGCTGC 59.795 47.619 3.32 0.00 0.00 5.25
5435 5662 1.675116 CCTGAGACATGACACAGCCTG 60.675 57.143 15.00 0.00 0.00 4.85
5517 5753 3.952628 GAACGCCTTCAGACGGGGG 62.953 68.421 13.88 9.03 38.67 5.40
5562 5799 3.519510 TCTTTAGATGTCCTGTCCCTTGG 59.480 47.826 0.00 0.00 0.00 3.61
5570 5807 1.152777 CTGTCCCTTGGTGCCAACA 60.153 57.895 0.00 0.00 0.00 3.33
5594 5899 1.554160 ACCCTGCAATGAGTGAGAGAG 59.446 52.381 0.00 0.00 0.00 3.20
5595 5900 1.829849 CCCTGCAATGAGTGAGAGAGA 59.170 52.381 0.00 0.00 0.00 3.10
5596 5901 2.159071 CCCTGCAATGAGTGAGAGAGAG 60.159 54.545 0.00 0.00 0.00 3.20
5597 5902 2.759535 CCTGCAATGAGTGAGAGAGAGA 59.240 50.000 0.00 0.00 0.00 3.10
5598 5903 3.181484 CCTGCAATGAGTGAGAGAGAGAG 60.181 52.174 0.00 0.00 0.00 3.20
5639 5959 1.001706 GTTGAAAAGTCCCAAGTCGCC 60.002 52.381 0.00 0.00 0.00 5.54
5728 6061 5.650703 TCTGGCGTCGAAGGAATATATATCA 59.349 40.000 0.00 0.00 0.00 2.15
5769 6107 6.426328 TGAAAAGAGAACAAAAGCAAGCAAAA 59.574 30.769 0.00 0.00 0.00 2.44
5800 6138 3.938963 GAGGAAAAATGATAGGTGTCGCA 59.061 43.478 0.00 0.00 0.00 5.10
5825 6165 1.066858 TCGCGCTTCAGAGATTCCTTT 60.067 47.619 5.56 0.00 0.00 3.11
5855 6195 0.320374 CTTGCGAGTTGGGGTCAGTA 59.680 55.000 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 9.537192 TGTACCGGTGAAATTATGTCTTTATAG 57.463 33.333 19.93 0.00 0.00 1.31
41 42 6.092944 TCTGCAAATTTTAGTATGTACCGGTG 59.907 38.462 19.93 0.00 0.00 4.94
44 45 8.002107 CGTATCTGCAAATTTTAGTATGTACCG 58.998 37.037 0.00 0.00 0.00 4.02
112 113 3.435671 GTGTCCGGATTCGATCTTTGTTT 59.564 43.478 7.81 0.00 39.00 2.83
119 120 0.099968 TCGTGTGTCCGGATTCGATC 59.900 55.000 7.81 0.00 39.00 3.69
121 122 0.528924 AATCGTGTGTCCGGATTCGA 59.471 50.000 7.81 15.72 39.00 3.71
123 124 2.073816 ACAAATCGTGTGTCCGGATTC 58.926 47.619 7.81 4.48 39.72 2.52
134 135 8.505052 GATCGATGGATATTTGCACAAATCGTG 61.505 40.741 11.69 0.00 40.99 4.35
145 146 4.991056 AGTTGTCGGATCGATGGATATTTG 59.009 41.667 0.54 0.00 38.42 2.32
147 148 4.873746 AGTTGTCGGATCGATGGATATT 57.126 40.909 0.54 0.00 38.42 1.28
150 151 2.296471 GGTAGTTGTCGGATCGATGGAT 59.704 50.000 0.54 0.00 38.42 3.41
153 154 1.269621 GGGGTAGTTGTCGGATCGATG 60.270 57.143 0.54 0.00 38.42 3.84
162 163 1.209747 GATGGTGAGGGGGTAGTTGTC 59.790 57.143 0.00 0.00 0.00 3.18
164 165 1.285280 TGATGGTGAGGGGGTAGTTG 58.715 55.000 0.00 0.00 0.00 3.16
165 166 2.127708 GATGATGGTGAGGGGGTAGTT 58.872 52.381 0.00 0.00 0.00 2.24
166 167 1.009552 TGATGATGGTGAGGGGGTAGT 59.990 52.381 0.00 0.00 0.00 2.73
168 169 1.507140 GTGATGATGGTGAGGGGGTA 58.493 55.000 0.00 0.00 0.00 3.69
178 179 2.428171 AGCCATTTTTCGGTGATGATGG 59.572 45.455 0.00 0.00 37.64 3.51
179 180 3.129113 TGAGCCATTTTTCGGTGATGATG 59.871 43.478 0.00 0.00 0.00 3.07
186 187 1.000717 CGGTTTGAGCCATTTTTCGGT 60.001 47.619 0.00 0.00 0.00 4.69
214 215 6.216569 TCGGATAAATGAAAGGAGAGATTCG 58.783 40.000 0.00 0.00 0.00 3.34
226 227 6.788684 TCGACTTTTGTTCGGATAAATGAA 57.211 33.333 5.92 0.00 0.00 2.57
227 228 6.788684 TTCGACTTTTGTTCGGATAAATGA 57.211 33.333 5.92 0.00 0.00 2.57
235 236 2.063266 TCGGATTCGACTTTTGTTCGG 58.937 47.619 0.00 0.00 40.88 4.30
245 246 4.266976 ACAAATCGTATGTTCGGATTCGAC 59.733 41.667 0.00 0.00 45.92 4.20
304 305 7.308435 GTTTGAGACATTTTTCGGAGATGATT 58.692 34.615 5.47 0.00 35.04 2.57
379 380 5.782047 TGGTTTTAGATGTTGAAAGGCATG 58.218 37.500 0.00 0.00 0.00 4.06
380 381 6.351286 GGATGGTTTTAGATGTTGAAAGGCAT 60.351 38.462 0.00 0.00 0.00 4.40
393 394 2.289195 ACTCGTTGCGGATGGTTTTAGA 60.289 45.455 0.00 0.00 0.00 2.10
394 395 2.073816 ACTCGTTGCGGATGGTTTTAG 58.926 47.619 0.00 0.00 0.00 1.85
395 396 1.801771 CACTCGTTGCGGATGGTTTTA 59.198 47.619 0.00 0.00 0.00 1.52
414 415 8.821894 GGTAATTTTGCTGTTTCACATTTTACA 58.178 29.630 0.00 0.00 0.00 2.41
415 416 8.279800 GGGTAATTTTGCTGTTTCACATTTTAC 58.720 33.333 0.00 0.00 0.00 2.01
416 417 7.442666 GGGGTAATTTTGCTGTTTCACATTTTA 59.557 33.333 0.00 0.00 0.00 1.52
421 422 3.243569 CGGGGTAATTTTGCTGTTTCACA 60.244 43.478 0.00 0.00 0.00 3.58
447 514 4.260172 GCAAAATTTGTTGTTGCTACGCTT 60.260 37.500 7.60 0.00 43.40 4.68
448 515 3.245048 GCAAAATTTGTTGTTGCTACGCT 59.755 39.130 7.60 0.00 43.40 5.07
449 516 3.000724 TGCAAAATTTGTTGTTGCTACGC 59.999 39.130 7.60 0.00 46.19 4.42
450 517 4.267452 AGTGCAAAATTTGTTGTTGCTACG 59.733 37.500 7.60 0.00 46.19 3.51
451 518 5.491973 CAGTGCAAAATTTGTTGTTGCTAC 58.508 37.500 7.60 8.80 46.19 3.58
452 519 4.033817 GCAGTGCAAAATTTGTTGTTGCTA 59.966 37.500 11.09 0.00 46.19 3.49
453 520 3.181508 GCAGTGCAAAATTTGTTGTTGCT 60.182 39.130 11.09 0.00 46.19 3.91
454 521 3.100089 GCAGTGCAAAATTTGTTGTTGC 58.900 40.909 11.09 8.71 46.21 4.17
455 522 3.126514 TGGCAGTGCAAAATTTGTTGTTG 59.873 39.130 18.61 3.13 0.00 3.33
456 523 3.341823 TGGCAGTGCAAAATTTGTTGTT 58.658 36.364 18.61 0.00 0.00 2.83
457 524 2.937799 CTGGCAGTGCAAAATTTGTTGT 59.062 40.909 18.61 0.00 0.00 3.32
498 565 8.655092 ACGCATTATTGAAACATGGTTTTATTG 58.345 29.630 0.00 0.00 0.00 1.90
624 693 3.033184 CCTCTCTTCTCTCTCTGGCAAT 58.967 50.000 0.00 0.00 0.00 3.56
952 1076 4.033932 CCGGAAAGCAAGAAAACCAAAAAG 59.966 41.667 0.00 0.00 0.00 2.27
980 1104 3.593794 GATCCCCGGACGGACGAG 61.594 72.222 13.13 0.00 37.50 4.18
1181 1310 1.672854 TACGCAGACGAATCAGGGGG 61.673 60.000 0.00 0.00 43.93 5.40
1324 1453 6.391227 TCCAATTGGAACTCAAAGAGAAAC 57.609 37.500 25.13 0.00 42.18 2.78
2000 2129 3.559238 AACGATCACAAACCATCTTGC 57.441 42.857 0.00 0.00 0.00 4.01
2004 2133 5.607119 AACTGTAACGATCACAAACCATC 57.393 39.130 0.00 0.00 0.00 3.51
2191 2320 1.686355 ATTCAAAGGCGTCACAACCA 58.314 45.000 0.00 0.00 0.00 3.67
2192 2321 3.907894 TTATTCAAAGGCGTCACAACC 57.092 42.857 0.00 0.00 0.00 3.77
2520 2652 4.166888 GCTGCCGAGATCCCTGCA 62.167 66.667 0.00 0.00 0.00 4.41
2637 2769 5.105513 TGTCATTACCTGAAGTAAGATGCGA 60.106 40.000 0.00 0.00 44.07 5.10
2669 2801 7.743749 AGTAAGAATAAGATGCACATGAGGAT 58.256 34.615 0.00 0.00 0.00 3.24
2957 3109 2.273370 GCATTGTGCATGAAGACTGG 57.727 50.000 0.00 0.00 44.26 4.00
3246 3405 3.947612 AGATTGGCCATCAAGATGACT 57.052 42.857 6.09 0.00 41.20 3.41
3513 3674 2.503356 AGGAAACTGAGGGAGTATGCAG 59.497 50.000 0.00 0.00 41.13 4.41
3660 3825 8.285891 ACATACAATTCATATTTTAGGTGGGGA 58.714 33.333 0.00 0.00 0.00 4.81
3678 3843 9.693739 TTACTACCATCATTCCAAACATACAAT 57.306 29.630 0.00 0.00 0.00 2.71
3775 3940 4.315803 AGCGCCGCTAAATTAATATCACT 58.684 39.130 11.29 0.00 36.99 3.41
3964 4136 8.246180 GGAAATTTCTCATATGTCAGAAAGCAA 58.754 33.333 17.42 3.46 40.96 3.91
3989 4162 4.696455 ACATTTGTGCCAAGAGAAAAAGG 58.304 39.130 0.00 0.00 0.00 3.11
4015 4188 4.501559 CGTTAAATGCTGCCAATGATTGAG 59.498 41.667 6.76 0.00 0.00 3.02
4319 4492 2.521126 GGGACTAGAGGCAGGAGATAC 58.479 57.143 0.00 0.00 0.00 2.24
4355 4528 1.552337 ACAATCTCGATGCTGAGTGGT 59.448 47.619 5.09 0.00 37.28 4.16
4376 4549 2.725312 CCTCTCGCCAGCAGCCTTA 61.725 63.158 0.00 0.00 38.78 2.69
4897 5070 1.018752 CGATGACAATGACGGTGCCA 61.019 55.000 0.00 0.00 0.00 4.92
4909 5082 1.083806 GCTTGCGATGACCGATGACA 61.084 55.000 0.00 0.00 41.76 3.58
4962 5135 1.403647 CGACAAGCAGGGTACGATGAA 60.404 52.381 0.00 0.00 0.00 2.57
5085 5259 0.524604 CACACACACACGAGACACGA 60.525 55.000 0.00 0.00 45.77 4.35
5087 5261 0.645355 CACACACACACACGAGACAC 59.355 55.000 0.00 0.00 0.00 3.67
5088 5262 0.245266 ACACACACACACACGAGACA 59.755 50.000 0.00 0.00 0.00 3.41
5089 5263 0.645355 CACACACACACACACGAGAC 59.355 55.000 0.00 0.00 0.00 3.36
5090 5264 0.245266 ACACACACACACACACGAGA 59.755 50.000 0.00 0.00 0.00 4.04
5091 5265 0.645355 GACACACACACACACACGAG 59.355 55.000 0.00 0.00 0.00 4.18
5243 5434 2.291741 GGAAGGAAGACAACAACAGCAG 59.708 50.000 0.00 0.00 0.00 4.24
5244 5435 2.297701 GGAAGGAAGACAACAACAGCA 58.702 47.619 0.00 0.00 0.00 4.41
5245 5436 1.609072 GGGAAGGAAGACAACAACAGC 59.391 52.381 0.00 0.00 0.00 4.40
5246 5437 2.930950 TGGGAAGGAAGACAACAACAG 58.069 47.619 0.00 0.00 0.00 3.16
5435 5662 7.780008 TCCAAATGAATGAATGAATGAATGC 57.220 32.000 0.00 0.00 0.00 3.56
5483 5718 2.444421 CGTTCCAGTACTACCCTGACT 58.556 52.381 0.00 0.00 31.38 3.41
5562 5799 1.363807 GCAGGGTTTCTGTTGGCAC 59.636 57.895 0.00 0.00 45.08 5.01
5570 5807 2.373169 TCTCACTCATTGCAGGGTTTCT 59.627 45.455 0.00 0.00 0.00 2.52
5594 5899 5.711976 TGACCAAATTTCTGAATTCCCTCTC 59.288 40.000 2.27 0.00 34.44 3.20
5595 5900 5.644188 TGACCAAATTTCTGAATTCCCTCT 58.356 37.500 2.27 0.00 34.44 3.69
5596 5901 5.478332 ACTGACCAAATTTCTGAATTCCCTC 59.522 40.000 2.27 0.00 34.44 4.30
5597 5902 5.397360 ACTGACCAAATTTCTGAATTCCCT 58.603 37.500 2.27 0.00 34.44 4.20
5598 5903 5.728637 ACTGACCAAATTTCTGAATTCCC 57.271 39.130 2.27 0.00 34.44 3.97
5639 5959 5.926542 TCCTAAAGAACATTTCTCTGTCACG 59.073 40.000 0.00 0.00 39.61 4.35
5728 6061 6.155221 TCTCTTTTCAGCTCCACTACATACAT 59.845 38.462 0.00 0.00 0.00 2.29
5769 6107 6.678857 ACCTATCATTTTTCCTCTCCTAACCT 59.321 38.462 0.00 0.00 0.00 3.50
5800 6138 1.649390 ATCTCTGAAGCGCGACGACT 61.649 55.000 12.10 0.00 0.00 4.18
5825 6165 3.058293 CCAACTCGCAAGCAAAATACTCA 60.058 43.478 0.00 0.00 37.18 3.41


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

AutoCloner maintained by Alex Coulton.