Multiple sequence alignment - TraesCS2A01G255700

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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 TraesCS2A01G255700 chr2A 100.000 5647 0 0 1 5647 391869356 391875002 0.000000e+00 10429.0
1 TraesCS2A01G255700 chr2A 96.552 116 4 0 4948 5063 468295293 468295408 5.770000e-45 193.0
2 TraesCS2A01G255700 chr2A 92.969 128 5 3 4936 5063 96153235 96153112 3.470000e-42 183.0
3 TraesCS2A01G255700 chr2A 96.610 59 2 0 3177 3235 391872475 391872533 1.290000e-16 99.0
4 TraesCS2A01G255700 chr2A 96.610 59 2 0 3120 3178 391872532 391872590 1.290000e-16 99.0
5 TraesCS2A01G255700 chr2B 96.318 4997 128 17 1 4958 395545935 395540956 0.000000e+00 8157.0
6 TraesCS2A01G255700 chr2B 89.907 535 37 10 5062 5595 395540957 395540439 0.000000e+00 673.0
7 TraesCS2A01G255700 chr2B 96.610 59 2 0 3120 3178 395542728 395542670 1.290000e-16 99.0
8 TraesCS2A01G255700 chr2D 95.257 4069 117 28 1 4029 326221615 326217583 0.000000e+00 6375.0
9 TraesCS2A01G255700 chr2D 95.886 875 31 4 4024 4897 326217481 326216611 0.000000e+00 1411.0
10 TraesCS2A01G255700 chr2D 90.678 590 38 7 5074 5647 326215863 326215275 0.000000e+00 769.0
11 TraesCS2A01G255700 chr2D 86.519 586 59 15 4081 4658 643176748 643176175 1.340000e-175 627.0
12 TraesCS2A01G255700 chr2D 99.074 108 1 0 4956 5063 107719708 107719601 1.610000e-45 195.0
13 TraesCS2A01G255700 chr2D 95.000 60 3 0 3119 3178 326218409 326218350 1.670000e-15 95.3
14 TraesCS2A01G255700 chr2D 94.915 59 3 0 3177 3235 326218465 326218407 6.020000e-15 93.5
15 TraesCS2A01G255700 chr3B 96.581 117 4 0 4954 5070 134998290 134998174 1.610000e-45 195.0
16 TraesCS2A01G255700 chr6D 95.726 117 5 0 4950 5066 200871788 200871672 7.470000e-44 189.0
17 TraesCS2A01G255700 chr6D 90.977 133 10 2 4933 5063 38346459 38346327 1.620000e-40 178.0
18 TraesCS2A01G255700 chr5B 94.355 124 5 2 4957 5079 603798362 603798240 7.470000e-44 189.0
19 TraesCS2A01G255700 chr1A 95.000 120 6 0 4957 5076 376756341 376756222 7.470000e-44 189.0
20 TraesCS2A01G255700 chr5A 96.429 112 4 0 4956 5067 574780152 574780263 9.660000e-43 185.0


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 TraesCS2A01G255700 chr2A 391869356 391875002 5646 False 3542.333333 10429 97.740000 1 5647 3 chr2A.!!$F2 5646
1 TraesCS2A01G255700 chr2B 395540439 395545935 5496 True 2976.333333 8157 94.278333 1 5595 3 chr2B.!!$R1 5594
2 TraesCS2A01G255700 chr2D 326215275 326221615 6340 True 1748.760000 6375 94.347200 1 5647 5 chr2D.!!$R3 5646
3 TraesCS2A01G255700 chr2D 643176175 643176748 573 True 627.000000 627 86.519000 4081 4658 1 chr2D.!!$R2 577

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
113 118 0.251165 GCTGGTGGCTGAAAGGGTTA 60.251 55.000 0.00 0.00 38.06 2.85 F
224 229 3.311322 TGTTTGTCGTTTGCTTACTCCTG 59.689 43.478 0.00 0.00 0.00 3.86 F
1042 1055 0.723981 GCGAGGCTTGTGTTCTGATC 59.276 55.000 3.19 0.00 0.00 2.92 F
1361 1374 1.000163 CACGAGAGATCATTACGGGGG 60.000 57.143 0.00 0.00 0.00 5.40 F
2688 2726 1.304630 TGGTCGACCCGGAGATGAA 60.305 57.895 31.19 6.76 35.15 2.57 F
2843 2881 2.035421 CACACATGTGGCAGCACTT 58.965 52.632 28.64 3.06 42.10 3.16 F
3934 3973 0.248565 GAGTGGAACCCGTTAGGACC 59.751 60.000 0.00 0.00 41.02 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1008 1021 1.126846 CCTCGCAACGATTCTGTGTTC 59.873 52.381 0.00 0.0 34.61 3.18 R
1089 1102 4.657039 AGAACAAACAGTAGGACTTACCCA 59.343 41.667 0.00 0.0 40.05 4.51 R
2435 2455 0.911769 AGAACATCTGCGGGATCCAA 59.088 50.000 15.23 0.0 31.27 3.53 R
2930 2968 2.502142 TGCCACATGAAGCTCTCAAT 57.498 45.000 0.00 0.0 37.67 2.57 R
3839 3878 0.909623 TGGCCTTAGCTGGGAAGTAC 59.090 55.000 3.32 0.0 39.73 2.73 R
4115 4265 0.981183 TTCGGCCACCACACTATCTT 59.019 50.000 2.24 0.0 0.00 2.40 R
5394 6236 0.324614 TGAATCCGTGCCATCACTGT 59.675 50.000 0.00 0.0 40.99 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
113 118 0.251165 GCTGGTGGCTGAAAGGGTTA 60.251 55.000 0.00 0.00 38.06 2.85
221 226 4.789095 TCTGTTTGTCGTTTGCTTACTC 57.211 40.909 0.00 0.00 0.00 2.59
224 229 3.311322 TGTTTGTCGTTTGCTTACTCCTG 59.689 43.478 0.00 0.00 0.00 3.86
419 424 4.097892 GGGACATGCCAATTAACTGTAAGG 59.902 45.833 8.20 0.00 36.79 2.69
767 772 7.086685 TCTTGTGGGTCCTACTTTTAATCTT 57.913 36.000 6.95 0.00 0.00 2.40
1008 1021 1.870055 GCTGTGAGCACATGGGGTTG 61.870 60.000 0.00 0.00 41.89 3.77
1042 1055 0.723981 GCGAGGCTTGTGTTCTGATC 59.276 55.000 3.19 0.00 0.00 2.92
1089 1102 8.399304 TTTGGTCAATCAAAAGCGAGAAGCAT 62.399 38.462 0.00 0.00 38.78 3.79
1186 1199 7.865385 TGCATCAAATGTAACAGGACTAAAAAC 59.135 33.333 0.00 0.00 0.00 2.43
1275 1288 6.935167 TCACTATCACTCTTTCAGTTGCATA 58.065 36.000 0.00 0.00 30.26 3.14
1361 1374 1.000163 CACGAGAGATCATTACGGGGG 60.000 57.143 0.00 0.00 0.00 5.40
1473 1489 2.094026 ACTGCGCATGTCTAGTCATTCA 60.094 45.455 12.24 0.00 0.00 2.57
1854 1870 2.163412 TGTCTGTGTTCAACCAGCAAAC 59.837 45.455 2.09 0.00 0.00 2.93
2085 2105 5.488919 TCCAGTTCCAGTTCCATTTCTAGAT 59.511 40.000 0.00 0.00 0.00 1.98
2435 2455 3.556999 AGACCTACTGCAGATGTATCGT 58.443 45.455 23.35 5.90 0.00 3.73
2688 2726 1.304630 TGGTCGACCCGGAGATGAA 60.305 57.895 31.19 6.76 35.15 2.57
2843 2881 2.035421 CACACATGTGGCAGCACTT 58.965 52.632 28.64 3.06 42.10 3.16
2930 2968 2.443255 GAGGCAATTCCCAGGGAAGATA 59.557 50.000 25.76 3.24 45.48 1.98
3279 3317 3.485463 TGGTGGTCGAGAATTTTCACT 57.515 42.857 0.00 0.00 0.00 3.41
3290 3328 5.061064 CGAGAATTTTCACTTACCTCAGTCG 59.939 44.000 0.00 0.00 0.00 4.18
3369 3407 2.079158 CATGACTGAAGAATGCGTGGT 58.921 47.619 0.00 0.00 0.00 4.16
3664 3703 6.292811 CCTGGACAAAACAATAACACAAATGC 60.293 38.462 0.00 0.00 0.00 3.56
3684 3723 2.673368 GCTGTTCCTCCAAAGTGTATCG 59.327 50.000 0.00 0.00 0.00 2.92
3838 3877 7.055667 GTGAATTCTCACCATAGGACTATGA 57.944 40.000 18.40 1.72 45.41 2.15
3839 3878 7.151308 GTGAATTCTCACCATAGGACTATGAG 58.849 42.308 18.40 10.45 45.41 2.90
3857 3896 1.139256 GAGTACTTCCCAGCTAAGGCC 59.861 57.143 0.00 0.00 39.73 5.19
3934 3973 0.248565 GAGTGGAACCCGTTAGGACC 59.751 60.000 0.00 0.00 41.02 4.46
4079 4229 3.884693 CCATGATGTGCTATTGCCTGTTA 59.115 43.478 0.00 0.00 38.71 2.41
4105 4255 2.890945 GCACCATACTTTTCCACAGGTT 59.109 45.455 0.00 0.00 0.00 3.50
4295 4445 6.364568 TGAGGTCACTATATAATGCTGCAT 57.635 37.500 9.81 9.81 0.00 3.96
4631 4782 0.895100 TTTGCCCACTGATGCACCTC 60.895 55.000 0.00 0.00 37.18 3.85
4696 4853 1.884067 GCCTTGCAGCTAGTCCAGTTT 60.884 52.381 3.04 0.00 0.00 2.66
4699 4856 0.037326 TGCAGCTAGTCCAGTTTCCG 60.037 55.000 0.00 0.00 0.00 4.30
4720 4877 4.024048 CCGTTTCAATAAGAGTGTGCAGTT 60.024 41.667 0.00 0.00 0.00 3.16
4721 4878 5.178623 CCGTTTCAATAAGAGTGTGCAGTTA 59.821 40.000 0.00 0.00 0.00 2.24
4722 4879 6.071463 CGTTTCAATAAGAGTGTGCAGTTAC 58.929 40.000 0.00 0.00 0.00 2.50
4724 4881 6.785488 TTCAATAAGAGTGTGCAGTTACAG 57.215 37.500 0.00 0.00 0.00 2.74
4727 4884 7.161404 TCAATAAGAGTGTGCAGTTACAGAAT 58.839 34.615 0.00 0.00 0.00 2.40
4731 4888 9.751542 ATAAGAGTGTGCAGTTACAGAATATAC 57.248 33.333 0.00 0.00 0.00 1.47
4732 4889 7.411486 AGAGTGTGCAGTTACAGAATATACT 57.589 36.000 0.00 0.00 0.00 2.12
4733 4890 7.261325 AGAGTGTGCAGTTACAGAATATACTG 58.739 38.462 0.00 0.00 42.78 2.74
4767 4924 5.047377 AGACATCTGTTTCCTTCTCTGAGAC 60.047 44.000 6.92 0.00 0.00 3.36
4768 4925 4.590647 ACATCTGTTTCCTTCTCTGAGACA 59.409 41.667 6.92 0.72 0.00 3.41
4863 5020 4.586421 TGAAAGGAATGCATTGTGTACCAA 59.414 37.500 18.59 0.00 37.49 3.67
4958 5175 7.835634 TTCAATTTCAAAACAACCAACCTAC 57.164 32.000 0.00 0.00 0.00 3.18
4959 5176 7.176589 TCAATTTCAAAACAACCAACCTACT 57.823 32.000 0.00 0.00 0.00 2.57
4960 5177 7.262048 TCAATTTCAAAACAACCAACCTACTC 58.738 34.615 0.00 0.00 0.00 2.59
4961 5178 5.585820 TTTCAAAACAACCAACCTACTCC 57.414 39.130 0.00 0.00 0.00 3.85
4962 5179 3.558033 TCAAAACAACCAACCTACTCCC 58.442 45.455 0.00 0.00 0.00 4.30
4963 5180 3.203487 TCAAAACAACCAACCTACTCCCT 59.797 43.478 0.00 0.00 0.00 4.20
4964 5181 3.503800 AAACAACCAACCTACTCCCTC 57.496 47.619 0.00 0.00 0.00 4.30
4965 5182 1.359168 ACAACCAACCTACTCCCTCC 58.641 55.000 0.00 0.00 0.00 4.30
4966 5183 0.249398 CAACCAACCTACTCCCTCCG 59.751 60.000 0.00 0.00 0.00 4.63
4967 5184 0.178912 AACCAACCTACTCCCTCCGT 60.179 55.000 0.00 0.00 0.00 4.69
4968 5185 0.178912 ACCAACCTACTCCCTCCGTT 60.179 55.000 0.00 0.00 0.00 4.44
4969 5186 0.535797 CCAACCTACTCCCTCCGTTC 59.464 60.000 0.00 0.00 0.00 3.95
4970 5187 0.535797 CAACCTACTCCCTCCGTTCC 59.464 60.000 0.00 0.00 0.00 3.62
4971 5188 0.115745 AACCTACTCCCTCCGTTCCA 59.884 55.000 0.00 0.00 0.00 3.53
4972 5189 0.115745 ACCTACTCCCTCCGTTCCAA 59.884 55.000 0.00 0.00 0.00 3.53
4973 5190 1.272807 CCTACTCCCTCCGTTCCAAA 58.727 55.000 0.00 0.00 0.00 3.28
4974 5191 1.838077 CCTACTCCCTCCGTTCCAAAT 59.162 52.381 0.00 0.00 0.00 2.32
4975 5192 2.238898 CCTACTCCCTCCGTTCCAAATT 59.761 50.000 0.00 0.00 0.00 1.82
4976 5193 3.453353 CCTACTCCCTCCGTTCCAAATTA 59.547 47.826 0.00 0.00 0.00 1.40
4977 5194 3.345508 ACTCCCTCCGTTCCAAATTAC 57.654 47.619 0.00 0.00 0.00 1.89
4978 5195 2.910977 ACTCCCTCCGTTCCAAATTACT 59.089 45.455 0.00 0.00 0.00 2.24
4979 5196 3.055312 ACTCCCTCCGTTCCAAATTACTC 60.055 47.826 0.00 0.00 0.00 2.59
4980 5197 2.093869 TCCCTCCGTTCCAAATTACTCG 60.094 50.000 0.00 0.00 0.00 4.18
4981 5198 2.354403 CCCTCCGTTCCAAATTACTCGT 60.354 50.000 0.00 0.00 0.00 4.18
4982 5199 2.928116 CCTCCGTTCCAAATTACTCGTC 59.072 50.000 0.00 0.00 0.00 4.20
4983 5200 2.597305 CTCCGTTCCAAATTACTCGTCG 59.403 50.000 0.00 0.00 0.00 5.12
4984 5201 2.030007 TCCGTTCCAAATTACTCGTCGT 60.030 45.455 0.00 0.00 0.00 4.34
4985 5202 3.190327 TCCGTTCCAAATTACTCGTCGTA 59.810 43.478 0.00 0.00 0.00 3.43
4986 5203 3.545078 CCGTTCCAAATTACTCGTCGTAG 59.455 47.826 0.00 0.00 0.00 3.51
4987 5204 4.406069 CGTTCCAAATTACTCGTCGTAGA 58.594 43.478 0.00 0.00 0.00 2.59
4988 5205 4.853196 CGTTCCAAATTACTCGTCGTAGAA 59.147 41.667 0.00 0.00 39.69 2.10
4989 5206 5.343058 CGTTCCAAATTACTCGTCGTAGAAA 59.657 40.000 0.00 0.00 39.69 2.52
4990 5207 6.034256 CGTTCCAAATTACTCGTCGTAGAAAT 59.966 38.462 0.00 0.00 39.69 2.17
4991 5208 6.880822 TCCAAATTACTCGTCGTAGAAATG 57.119 37.500 0.00 0.00 39.69 2.32
4992 5209 5.808540 TCCAAATTACTCGTCGTAGAAATGG 59.191 40.000 0.00 0.00 39.69 3.16
4993 5210 5.808540 CCAAATTACTCGTCGTAGAAATGGA 59.191 40.000 0.00 0.00 39.69 3.41
4994 5211 6.479001 CCAAATTACTCGTCGTAGAAATGGAT 59.521 38.462 0.00 0.00 39.69 3.41
4995 5212 7.650504 CCAAATTACTCGTCGTAGAAATGGATA 59.349 37.037 0.00 0.00 39.69 2.59
4996 5213 9.193133 CAAATTACTCGTCGTAGAAATGGATAT 57.807 33.333 0.00 0.00 39.69 1.63
5000 5217 7.925043 ACTCGTCGTAGAAATGGATATATCT 57.075 36.000 12.42 0.00 39.69 1.98
5002 5219 9.100554 ACTCGTCGTAGAAATGGATATATCTAG 57.899 37.037 12.42 0.00 39.69 2.43
5003 5220 9.315525 CTCGTCGTAGAAATGGATATATCTAGA 57.684 37.037 12.42 0.00 39.69 2.43
5004 5221 9.662947 TCGTCGTAGAAATGGATATATCTAGAA 57.337 33.333 12.42 0.00 39.69 2.10
5005 5222 9.705471 CGTCGTAGAAATGGATATATCTAGAAC 57.295 37.037 12.42 2.68 39.69 3.01
5035 5252 9.775539 AATACATCTAGATACATCCATACCTGT 57.224 33.333 4.54 0.00 0.00 4.00
5036 5253 7.473735 ACATCTAGATACATCCATACCTGTG 57.526 40.000 4.54 0.00 0.00 3.66
5037 5254 7.241628 ACATCTAGATACATCCATACCTGTGA 58.758 38.462 4.54 0.00 0.00 3.58
5038 5255 7.177568 ACATCTAGATACATCCATACCTGTGAC 59.822 40.741 4.54 0.00 0.00 3.67
5039 5256 6.610830 TCTAGATACATCCATACCTGTGACA 58.389 40.000 0.00 0.00 0.00 3.58
5040 5257 7.066781 TCTAGATACATCCATACCTGTGACAA 58.933 38.462 0.00 0.00 0.00 3.18
5041 5258 6.166984 AGATACATCCATACCTGTGACAAG 57.833 41.667 0.00 0.00 0.00 3.16
5042 5259 5.663106 AGATACATCCATACCTGTGACAAGT 59.337 40.000 0.00 0.00 0.00 3.16
5043 5260 6.839134 AGATACATCCATACCTGTGACAAGTA 59.161 38.462 0.00 0.00 0.00 2.24
5044 5261 5.755409 ACATCCATACCTGTGACAAGTAA 57.245 39.130 0.00 0.00 0.00 2.24
5045 5262 6.313519 ACATCCATACCTGTGACAAGTAAT 57.686 37.500 0.00 0.00 0.00 1.89
5046 5263 6.721318 ACATCCATACCTGTGACAAGTAATT 58.279 36.000 0.00 0.00 0.00 1.40
5047 5264 6.823689 ACATCCATACCTGTGACAAGTAATTC 59.176 38.462 0.00 0.00 0.00 2.17
5048 5265 5.416083 TCCATACCTGTGACAAGTAATTCG 58.584 41.667 0.00 0.00 0.00 3.34
5049 5266 4.570772 CCATACCTGTGACAAGTAATTCGG 59.429 45.833 0.00 0.00 0.00 4.30
5050 5267 5.416083 CATACCTGTGACAAGTAATTCGGA 58.584 41.667 0.00 0.00 0.00 4.55
5051 5268 4.345859 ACCTGTGACAAGTAATTCGGAA 57.654 40.909 0.00 0.00 0.00 4.30
5052 5269 4.062991 ACCTGTGACAAGTAATTCGGAAC 58.937 43.478 0.00 0.00 0.00 3.62
5082 5299 7.659390 GGGAGTAGAAACTATTCATTCATGGAG 59.341 40.741 0.00 0.00 38.06 3.86
5159 5994 4.142093 GGAAAGTACCAGGCGTCTATAACA 60.142 45.833 0.00 0.00 0.00 2.41
5197 6032 6.127479 TGGTTTCCAAATCCGAAATTATCTGG 60.127 38.462 0.00 0.00 32.19 3.86
5246 6088 4.778958 AGAAAAATGATTCCATTGCCCTCA 59.221 37.500 0.00 0.00 41.84 3.86
5298 6140 6.275335 ACACATATTAGGAAATTGCATGCAC 58.725 36.000 22.58 8.87 0.00 4.57
5307 6149 4.624882 GGAAATTGCATGCACAAAACGATA 59.375 37.500 22.58 1.96 32.27 2.92
5342 6184 9.476761 GCAAATGATTCGGTTTTGAATATTTTC 57.523 29.630 9.44 0.00 38.65 2.29
5373 6215 4.512571 GCTGTGGCTTTTGAATTGAACATT 59.487 37.500 0.00 0.00 35.22 2.71
5394 6236 6.153680 ACATTGGAATTAAAATAAGGACGGCA 59.846 34.615 0.00 0.00 0.00 5.69
5428 6270 4.399934 ACGGATTCACCTAGAGTCTTTCTC 59.600 45.833 0.00 0.00 38.78 2.87
5512 6354 1.570347 ATAACGCGCGGTTTTCAGCA 61.570 50.000 35.22 11.38 40.88 4.41
5522 6364 2.535574 CGGTTTTCAGCAAGTTTTCAGC 59.464 45.455 0.00 0.00 0.00 4.26
5524 6366 2.866156 GTTTTCAGCAAGTTTTCAGCCC 59.134 45.455 0.00 0.00 0.00 5.19
5525 6367 1.774110 TTCAGCAAGTTTTCAGCCCA 58.226 45.000 0.00 0.00 0.00 5.36
5562 6405 2.948979 CAAGTGTTCCTACAAAGCCACA 59.051 45.455 0.00 0.00 35.69 4.17
5564 6407 3.412386 AGTGTTCCTACAAAGCCACATC 58.588 45.455 0.00 0.00 35.69 3.06
5568 6411 2.551270 TCCTACAAAGCCACATCCTCT 58.449 47.619 0.00 0.00 0.00 3.69
5585 6428 2.619177 CCTCTCATCACTACCGATCGTT 59.381 50.000 15.09 1.36 0.00 3.85
5632 6483 2.094182 ACACGAAGCATACTACACCCTG 60.094 50.000 0.00 0.00 0.00 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
224 229 5.934625 ACTTACTGGAATATGATGAATCCGC 59.065 40.000 0.00 0.00 34.60 5.54
395 400 3.456380 ACAGTTAATTGGCATGTCCCT 57.544 42.857 2.81 0.00 0.00 4.20
419 424 3.925299 GGAAGCTAACCAAGTTCGTACTC 59.075 47.826 0.00 0.00 31.99 2.59
767 772 1.682854 CTTCCCTTTGAAGCACTTGCA 59.317 47.619 3.62 0.00 43.79 4.08
1008 1021 1.126846 CCTCGCAACGATTCTGTGTTC 59.873 52.381 0.00 0.00 34.61 3.18
1042 1055 7.307396 CCAAAATACTGCATACTTCCATAGACG 60.307 40.741 0.00 0.00 0.00 4.18
1089 1102 4.657039 AGAACAAACAGTAGGACTTACCCA 59.343 41.667 0.00 0.00 40.05 4.51
1223 1236 5.756347 ACGACAAATAAGACTAACAGTTGCA 59.244 36.000 0.00 0.00 0.00 4.08
1372 1385 5.497474 AGGTGTTATTATCTGGTTGTCACC 58.503 41.667 0.00 0.00 44.56 4.02
2356 2376 5.671735 TGAAGGATTATGAGGAATTGAGGGA 59.328 40.000 0.00 0.00 0.00 4.20
2415 2435 3.992260 ACGATACATCTGCAGTAGGTC 57.008 47.619 14.67 9.08 0.00 3.85
2435 2455 0.911769 AGAACATCTGCGGGATCCAA 59.088 50.000 15.23 0.00 31.27 3.53
2688 2726 9.753674 TCAACTTATCCATAAATGAGAGGTTTT 57.246 29.630 0.00 0.00 0.00 2.43
2794 2832 4.436113 TTCTTGTGCCATATATGCCAGA 57.564 40.909 7.24 0.00 0.00 3.86
2873 2911 7.272948 GTGCATCTTTGAGTGAATTGAAGAATC 59.727 37.037 0.00 0.00 30.96 2.52
2930 2968 2.502142 TGCCACATGAAGCTCTCAAT 57.498 45.000 0.00 0.00 37.67 2.57
3279 3317 2.526432 AGCCTTCTTCGACTGAGGTAA 58.474 47.619 8.45 0.00 0.00 2.85
3290 3328 3.679389 TGGAAGTCATGAAGCCTTCTTC 58.321 45.455 18.70 15.13 46.85 2.87
3369 3407 6.349528 CCTGTGCATGTCTTGAATTGTATGAA 60.350 38.462 0.00 0.00 0.00 2.57
3664 3703 3.056107 TCCGATACACTTTGGAGGAACAG 60.056 47.826 0.00 0.00 0.00 3.16
3684 3723 1.339535 CCCACCTTCTCAGCTTTCTCC 60.340 57.143 0.00 0.00 0.00 3.71
3735 3774 3.820467 TCTGCAAATCGTTGGTTTCTGAT 59.180 39.130 0.00 0.00 35.10 2.90
3825 3864 5.394738 TGGGAAGTACTCATAGTCCTATGG 58.605 45.833 13.00 7.53 42.32 2.74
3838 3877 1.205055 GGCCTTAGCTGGGAAGTACT 58.795 55.000 11.11 0.00 39.73 2.73
3839 3878 0.909623 TGGCCTTAGCTGGGAAGTAC 59.090 55.000 3.32 0.00 39.73 2.73
3857 3896 6.428385 GACAAATGGTCAGATCTTTAGGTG 57.572 41.667 0.00 0.00 46.19 4.00
3906 3945 5.700722 AACGGGTTCCACTCTAATTTTTC 57.299 39.130 0.00 0.00 0.00 2.29
4060 4210 4.220693 ACTAACAGGCAATAGCACATCA 57.779 40.909 0.00 0.00 44.61 3.07
4061 4211 5.335127 CAAACTAACAGGCAATAGCACATC 58.665 41.667 0.00 0.00 44.61 3.06
4079 4229 3.957497 TGTGGAAAAGTATGGTGCAAACT 59.043 39.130 0.00 0.00 0.00 2.66
4105 4255 7.040271 GGCCACCACACTATCTTTTAAAAACTA 60.040 37.037 0.00 0.00 0.00 2.24
4115 4265 0.981183 TTCGGCCACCACACTATCTT 59.019 50.000 2.24 0.00 0.00 2.40
4295 4445 5.648178 ATGCAATGATGAAAACTAGTGCA 57.352 34.783 0.00 0.00 44.10 4.57
4631 4782 3.555527 TGGAATCATCTCCTCTGCAAG 57.444 47.619 0.00 0.00 36.35 4.01
4696 4853 3.734463 TGCACACTCTTATTGAAACGGA 58.266 40.909 0.00 0.00 0.00 4.69
4699 4856 6.954944 TGTAACTGCACACTCTTATTGAAAC 58.045 36.000 0.00 0.00 0.00 2.78
4720 4877 9.098355 GTCTGCAATGAAACAGTATATTCTGTA 57.902 33.333 14.54 1.21 46.25 2.74
4722 4879 7.977904 TGTCTGCAATGAAACAGTATATTCTG 58.022 34.615 7.73 7.73 40.80 3.02
4724 4881 8.834465 AGATGTCTGCAATGAAACAGTATATTC 58.166 33.333 0.00 0.00 35.37 1.75
4727 4884 7.543947 CAGATGTCTGCAATGAAACAGTATA 57.456 36.000 0.00 0.00 37.15 1.47
4730 4887 4.761235 CAGATGTCTGCAATGAAACAGT 57.239 40.909 0.00 0.00 37.15 3.55
4927 5144 4.703379 TGTTTTGAAATTGAATGCCCCT 57.297 36.364 0.00 0.00 0.00 4.79
4958 5175 3.532542 GAGTAATTTGGAACGGAGGGAG 58.467 50.000 0.00 0.00 0.00 4.30
4959 5176 2.093869 CGAGTAATTTGGAACGGAGGGA 60.094 50.000 0.00 0.00 0.00 4.20
4960 5177 2.277084 CGAGTAATTTGGAACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
4961 5178 2.928116 GACGAGTAATTTGGAACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
4962 5179 2.597305 CGACGAGTAATTTGGAACGGAG 59.403 50.000 0.00 0.00 0.00 4.63
4963 5180 2.030007 ACGACGAGTAATTTGGAACGGA 60.030 45.455 0.00 0.00 0.00 4.69
4964 5181 2.331194 ACGACGAGTAATTTGGAACGG 58.669 47.619 0.00 0.00 0.00 4.44
4965 5182 4.406069 TCTACGACGAGTAATTTGGAACG 58.594 43.478 0.00 0.00 34.45 3.95
4966 5183 6.695292 TTTCTACGACGAGTAATTTGGAAC 57.305 37.500 0.00 0.00 34.45 3.62
4967 5184 6.311935 CCATTTCTACGACGAGTAATTTGGAA 59.688 38.462 0.00 0.00 34.45 3.53
4968 5185 5.808540 CCATTTCTACGACGAGTAATTTGGA 59.191 40.000 0.00 0.00 34.45 3.53
4969 5186 5.808540 TCCATTTCTACGACGAGTAATTTGG 59.191 40.000 0.00 0.59 34.45 3.28
4970 5187 6.880822 TCCATTTCTACGACGAGTAATTTG 57.119 37.500 0.00 0.00 34.45 2.32
4974 5191 9.445878 AGATATATCCATTTCTACGACGAGTAA 57.554 33.333 9.18 0.00 34.45 2.24
4976 5193 7.925043 AGATATATCCATTTCTACGACGAGT 57.075 36.000 9.18 0.00 0.00 4.18
4977 5194 9.315525 TCTAGATATATCCATTTCTACGACGAG 57.684 37.037 9.18 0.00 0.00 4.18
4978 5195 9.662947 TTCTAGATATATCCATTTCTACGACGA 57.337 33.333 9.18 0.00 0.00 4.20
4979 5196 9.705471 GTTCTAGATATATCCATTTCTACGACG 57.295 37.037 9.18 0.00 0.00 5.12
5009 5226 9.775539 ACAGGTATGGATGTATCTAGATGTATT 57.224 33.333 15.79 0.00 0.00 1.89
5010 5227 9.194972 CACAGGTATGGATGTATCTAGATGTAT 57.805 37.037 15.79 9.11 0.00 2.29
5011 5228 8.390921 TCACAGGTATGGATGTATCTAGATGTA 58.609 37.037 15.79 4.44 0.00 2.29
5012 5229 7.177568 GTCACAGGTATGGATGTATCTAGATGT 59.822 40.741 15.79 1.25 0.00 3.06
5013 5230 7.177392 TGTCACAGGTATGGATGTATCTAGATG 59.823 40.741 15.79 0.00 0.00 2.90
5014 5231 7.241628 TGTCACAGGTATGGATGTATCTAGAT 58.758 38.462 10.73 10.73 0.00 1.98
5015 5232 6.610830 TGTCACAGGTATGGATGTATCTAGA 58.389 40.000 0.00 0.00 0.00 2.43
5016 5233 6.901081 TGTCACAGGTATGGATGTATCTAG 57.099 41.667 0.00 0.00 0.00 2.43
5017 5234 6.839134 ACTTGTCACAGGTATGGATGTATCTA 59.161 38.462 0.00 0.00 0.00 1.98
5018 5235 5.663106 ACTTGTCACAGGTATGGATGTATCT 59.337 40.000 0.00 0.00 0.00 1.98
5019 5236 5.918608 ACTTGTCACAGGTATGGATGTATC 58.081 41.667 0.00 0.00 0.00 2.24
5020 5237 5.957771 ACTTGTCACAGGTATGGATGTAT 57.042 39.130 0.00 0.00 0.00 2.29
5021 5238 6.860790 TTACTTGTCACAGGTATGGATGTA 57.139 37.500 0.00 0.00 0.00 2.29
5022 5239 5.755409 TTACTTGTCACAGGTATGGATGT 57.245 39.130 0.00 0.00 0.00 3.06
5023 5240 6.018751 CGAATTACTTGTCACAGGTATGGATG 60.019 42.308 0.00 0.00 0.00 3.51
5024 5241 6.049149 CGAATTACTTGTCACAGGTATGGAT 58.951 40.000 0.00 0.00 0.00 3.41
5025 5242 5.416083 CGAATTACTTGTCACAGGTATGGA 58.584 41.667 0.00 0.00 0.00 3.41
5026 5243 4.570772 CCGAATTACTTGTCACAGGTATGG 59.429 45.833 0.00 0.00 0.00 2.74
5027 5244 5.416083 TCCGAATTACTTGTCACAGGTATG 58.584 41.667 0.00 0.00 0.00 2.39
5028 5245 5.670792 TCCGAATTACTTGTCACAGGTAT 57.329 39.130 0.00 0.00 0.00 2.73
5029 5246 5.232463 GTTCCGAATTACTTGTCACAGGTA 58.768 41.667 0.00 0.00 0.00 3.08
5030 5247 4.062991 GTTCCGAATTACTTGTCACAGGT 58.937 43.478 0.00 0.00 0.00 4.00
5031 5248 3.122948 CGTTCCGAATTACTTGTCACAGG 59.877 47.826 0.00 0.00 0.00 4.00
5032 5249 3.122948 CCGTTCCGAATTACTTGTCACAG 59.877 47.826 0.00 0.00 0.00 3.66
5033 5250 3.061322 CCGTTCCGAATTACTTGTCACA 58.939 45.455 0.00 0.00 0.00 3.58
5034 5251 3.319755 TCCGTTCCGAATTACTTGTCAC 58.680 45.455 0.00 0.00 0.00 3.67
5035 5252 3.581755 CTCCGTTCCGAATTACTTGTCA 58.418 45.455 0.00 0.00 0.00 3.58
5036 5253 2.928116 CCTCCGTTCCGAATTACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
5037 5254 2.354403 CCCTCCGTTCCGAATTACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
5038 5255 2.093869 TCCCTCCGTTCCGAATTACTTG 60.094 50.000 0.00 0.00 0.00 3.16
5039 5256 2.167900 CTCCCTCCGTTCCGAATTACTT 59.832 50.000 0.00 0.00 0.00 2.24
5040 5257 1.755380 CTCCCTCCGTTCCGAATTACT 59.245 52.381 0.00 0.00 0.00 2.24
5041 5258 1.479730 ACTCCCTCCGTTCCGAATTAC 59.520 52.381 0.00 0.00 0.00 1.89
5042 5259 1.856629 ACTCCCTCCGTTCCGAATTA 58.143 50.000 0.00 0.00 0.00 1.40
5043 5260 1.755380 CTACTCCCTCCGTTCCGAATT 59.245 52.381 0.00 0.00 0.00 2.17
5044 5261 1.064166 TCTACTCCCTCCGTTCCGAAT 60.064 52.381 0.00 0.00 0.00 3.34
5045 5262 0.329261 TCTACTCCCTCCGTTCCGAA 59.671 55.000 0.00 0.00 0.00 4.30
5046 5263 0.329261 TTCTACTCCCTCCGTTCCGA 59.671 55.000 0.00 0.00 0.00 4.55
5047 5264 1.135170 GTTTCTACTCCCTCCGTTCCG 60.135 57.143 0.00 0.00 0.00 4.30
5048 5265 2.177734 AGTTTCTACTCCCTCCGTTCC 58.822 52.381 0.00 0.00 0.00 3.62
5049 5266 5.126707 TGAATAGTTTCTACTCCCTCCGTTC 59.873 44.000 0.00 0.00 35.78 3.95
5050 5267 5.021458 TGAATAGTTTCTACTCCCTCCGTT 58.979 41.667 0.00 0.00 35.78 4.44
5051 5268 4.607239 TGAATAGTTTCTACTCCCTCCGT 58.393 43.478 0.00 0.00 35.78 4.69
5052 5269 5.793030 ATGAATAGTTTCTACTCCCTCCG 57.207 43.478 0.00 0.00 35.78 4.63
5053 5270 7.125792 TGAATGAATAGTTTCTACTCCCTCC 57.874 40.000 0.00 0.00 35.78 4.30
5054 5271 7.659390 CCATGAATGAATAGTTTCTACTCCCTC 59.341 40.741 0.00 0.00 35.78 4.30
5055 5272 7.348274 TCCATGAATGAATAGTTTCTACTCCCT 59.652 37.037 0.00 0.00 35.78 4.20
5056 5273 7.509546 TCCATGAATGAATAGTTTCTACTCCC 58.490 38.462 0.00 0.00 35.78 4.30
5057 5274 7.659390 CCTCCATGAATGAATAGTTTCTACTCC 59.341 40.741 0.00 0.00 35.78 3.85
5058 5275 8.207545 ACCTCCATGAATGAATAGTTTCTACTC 58.792 37.037 0.00 0.00 35.78 2.59
5059 5276 7.989741 CACCTCCATGAATGAATAGTTTCTACT 59.010 37.037 0.00 0.00 38.44 2.57
5060 5277 7.987458 TCACCTCCATGAATGAATAGTTTCTAC 59.013 37.037 0.00 0.00 32.78 2.59
5061 5278 7.987458 GTCACCTCCATGAATGAATAGTTTCTA 59.013 37.037 0.00 0.00 32.78 2.10
5062 5279 6.825721 GTCACCTCCATGAATGAATAGTTTCT 59.174 38.462 0.00 0.00 32.78 2.52
5082 5299 1.230635 AACATGCACTCGCTGTCACC 61.231 55.000 0.00 0.00 39.64 4.02
5159 5994 0.872388 GAAACCACGCGAGGACAAAT 59.128 50.000 29.67 9.55 0.00 2.32
5197 6032 2.183858 GACGCTCGAAAACAAGGGGC 62.184 60.000 0.00 0.00 0.00 5.80
5246 6088 7.336931 ACACAAAGAAATCACACAAACTAGACT 59.663 33.333 0.00 0.00 0.00 3.24
5298 6140 3.447752 TGCACGTCATGTATCGTTTTG 57.552 42.857 9.63 3.05 38.23 2.44
5307 6149 2.159531 CCGAATCATTTGCACGTCATGT 60.160 45.455 0.00 0.00 0.00 3.21
5373 6215 5.010933 TGTGCCGTCCTTATTTTAATTCCA 58.989 37.500 0.00 0.00 0.00 3.53
5394 6236 0.324614 TGAATCCGTGCCATCACTGT 59.675 50.000 0.00 0.00 40.99 3.55
5475 6317 4.563184 CGTTATCAGCCAGTTAGAGTCAAC 59.437 45.833 0.00 0.00 0.00 3.18
5482 6324 0.577269 GCGCGTTATCAGCCAGTTAG 59.423 55.000 8.43 0.00 0.00 2.34
5483 6325 1.143373 CGCGCGTTATCAGCCAGTTA 61.143 55.000 24.19 0.00 0.00 2.24
5485 6327 2.885644 CGCGCGTTATCAGCCAGT 60.886 61.111 24.19 0.00 0.00 4.00
5512 6354 3.404899 CAAATGCATGGGCTGAAAACTT 58.595 40.909 0.00 0.00 41.91 2.66
5522 6364 1.002201 TGTTGAAGCCAAATGCATGGG 59.998 47.619 12.25 12.25 44.83 4.00
5524 6366 3.185594 CACTTGTTGAAGCCAAATGCATG 59.814 43.478 0.00 0.00 44.83 4.06
5525 6367 3.181463 ACACTTGTTGAAGCCAAATGCAT 60.181 39.130 0.00 0.00 44.83 3.96
5562 6405 3.078097 CGATCGGTAGTGATGAGAGGAT 58.922 50.000 7.38 0.00 0.00 3.24
5564 6407 2.222886 ACGATCGGTAGTGATGAGAGG 58.777 52.381 20.98 0.00 0.00 3.69
5568 6411 4.439700 GGAGAAAACGATCGGTAGTGATGA 60.440 45.833 20.98 0.00 0.00 2.92
5585 6428 5.427481 AGAATAGGGATAAACGGTGGAGAAA 59.573 40.000 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.