Multiple sequence alignment - TraesCS3A01G176500

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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 TraesCS3A01G176500 chr3A 100.000 5132 0 0 1 5132 197849122 197854253 0.000000e+00 9478.0
1 TraesCS3A01G176500 chr3A 94.737 38 2 0 4659 4696 197853742 197853779 5.550000e-05 60.2
2 TraesCS3A01G176500 chr3A 94.737 38 2 0 4621 4658 197853780 197853817 5.550000e-05 60.2
3 TraesCS3A01G176500 chr3D 95.845 4886 138 30 6 4865 169451991 169447145 0.000000e+00 7838.0
4 TraesCS3A01G176500 chr3D 81.672 311 12 12 4865 5132 169447204 169446896 3.110000e-52 217.0
5 TraesCS3A01G176500 chr3D 100.000 31 0 0 4666 4696 169447382 169447352 2.000000e-04 58.4
6 TraesCS3A01G176500 chr3B 95.857 2872 87 15 1831 4696 244385849 244383004 0.000000e+00 4615.0
7 TraesCS3A01G176500 chr3B 91.062 1544 86 25 6 1539 244387388 244385887 0.000000e+00 2039.0
8 TraesCS3A01G176500 chr3B 92.771 249 14 1 4621 4865 244383041 244382793 1.760000e-94 357.0
9 TraesCS3A01G176500 chr3B 86.842 266 27 7 1544 1804 821290091 821289829 1.810000e-74 291.0
10 TraesCS3A01G176500 chr3B 86.256 211 8 2 4943 5132 244382753 244382543 5.210000e-50 209.0
11 TraesCS3A01G176500 chr3B 94.737 38 2 0 4621 4658 244383003 244382966 5.550000e-05 60.2
12 TraesCS3A01G176500 chr3B 94.737 38 2 0 4659 4696 244383079 244383042 5.550000e-05 60.2
13 TraesCS3A01G176500 chr2D 88.848 269 25 3 1544 1809 120561227 120561493 4.960000e-85 326.0
14 TraesCS3A01G176500 chr2B 88.148 270 29 1 1544 1810 801215314 801215583 8.290000e-83 318.0
15 TraesCS3A01G176500 chr4B 87.687 268 29 4 1544 1808 42938154 42938420 4.990000e-80 309.0
16 TraesCS3A01G176500 chr5D 87.365 277 21 8 1544 1808 8801776 8802050 6.460000e-79 305.0
17 TraesCS3A01G176500 chr7D 86.891 267 31 4 1544 1807 37000918 37000653 3.890000e-76 296.0
18 TraesCS3A01G176500 chrUn 86.617 269 32 3 1544 1808 87230968 87230700 1.400000e-75 294.0
19 TraesCS3A01G176500 chr7B 87.072 263 30 3 1548 1806 41043237 41043499 1.400000e-75 294.0


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 TraesCS3A01G176500 chr3A 197849122 197854253 5131 False 3199.466667 9478 96.491333 1 5132 3 chr3A.!!$F1 5131
1 TraesCS3A01G176500 chr3D 169446896 169451991 5095 True 4027.500000 7838 88.758500 6 5132 2 chr3D.!!$R2 5126
2 TraesCS3A01G176500 chr3B 244382543 244387388 4845 True 1223.400000 4615 92.570000 6 5132 6 chr3B.!!$R2 5126

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
280 283 0.321122 CTTCTTGGCAGCTTCCTCGT 60.321 55.000 3.45 0.00 0.0 4.18 F
773 779 0.611714 TGGTTTAGGGCTCGAGGTTC 59.388 55.000 15.58 0.00 0.0 3.62 F
1044 1054 0.691413 GTAAGGGGAGAGAGGGGGTG 60.691 65.000 0.00 0.00 0.0 4.61 F
2657 2689 1.662629 CTTCCAAGTGATGCTGCTACG 59.337 52.381 0.00 0.00 0.0 3.51 F
3783 3830 2.440980 GGGGGAACATCTGCAGCC 60.441 66.667 9.47 3.51 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2251 2283 0.609957 CAGGGCAGGCTTGACATTCA 60.610 55.000 3.21 0.0 32.23 2.57 R
2657 2689 1.069358 GTGTGAGCAGGGATAGCTACC 59.931 57.143 0.00 0.0 43.58 3.18 R
2769 2801 2.613977 CCGGAGACAGTTGAGCAGAAAT 60.614 50.000 0.00 0.0 0.00 2.17 R
3788 3835 0.824109 TCGAGCCTTGTATGGTGGAG 59.176 55.000 0.00 0.0 0.00 3.86 R
4794 4880 0.606401 ACAAGTGCCCGAATCACAGG 60.606 55.000 4.89 0.0 36.93 4.00 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
57 58 4.435436 TAGCAGCACGCCACTCCG 62.435 66.667 0.00 0.00 44.04 4.63
110 113 2.741092 GAGGACCAACGTGGCTGA 59.259 61.111 0.00 0.00 42.67 4.26
203 206 3.506096 GCCCGCGTTAAGGAAGCC 61.506 66.667 4.92 0.00 0.00 4.35
205 208 1.673009 CCCGCGTTAAGGAAGCCAA 60.673 57.895 4.92 0.00 0.00 4.52
206 209 1.238625 CCCGCGTTAAGGAAGCCAAA 61.239 55.000 4.92 0.00 0.00 3.28
280 283 0.321122 CTTCTTGGCAGCTTCCTCGT 60.321 55.000 3.45 0.00 0.00 4.18
295 298 3.775654 CGTGCAGTCCCTCCCTCC 61.776 72.222 0.00 0.00 0.00 4.30
296 299 3.403558 GTGCAGTCCCTCCCTCCC 61.404 72.222 0.00 0.00 0.00 4.30
297 300 3.615811 TGCAGTCCCTCCCTCCCT 61.616 66.667 0.00 0.00 0.00 4.20
298 301 2.766229 GCAGTCCCTCCCTCCCTC 60.766 72.222 0.00 0.00 0.00 4.30
322 325 2.352032 CCTCTCACCCCACGTCTCC 61.352 68.421 0.00 0.00 0.00 3.71
773 779 0.611714 TGGTTTAGGGCTCGAGGTTC 59.388 55.000 15.58 0.00 0.00 3.62
791 797 3.274288 GTTCTGGTGCTCCTGGATTTAG 58.726 50.000 11.25 0.00 34.13 1.85
896 906 4.564110 GATTCGGGGCCCCTTCCG 62.564 72.222 38.17 24.74 46.89 4.30
955 965 1.134220 GGGGATTCGAGTTGCACCATA 60.134 52.381 0.00 0.00 0.00 2.74
967 977 1.298340 CACCATAGTGCGTGGGGAA 59.702 57.895 0.00 0.00 43.00 3.97
1004 1014 2.603560 GTCTCGTTGCAGTACTAATGGC 59.396 50.000 0.00 0.00 0.00 4.40
1005 1015 1.933853 CTCGTTGCAGTACTAATGGCC 59.066 52.381 0.00 0.00 0.00 5.36
1044 1054 0.691413 GTAAGGGGAGAGAGGGGGTG 60.691 65.000 0.00 0.00 0.00 4.61
1058 1068 3.190439 AGGGGGTGCTGTAAGATTACTT 58.810 45.455 4.50 0.00 39.81 2.24
1059 1069 3.054361 AGGGGGTGCTGTAAGATTACTTG 60.054 47.826 4.50 0.00 37.53 3.16
1065 1080 5.932303 GGTGCTGTAAGATTACTTGAAGTGA 59.068 40.000 8.33 0.00 37.53 3.41
1118 1133 8.821147 TCACAGTACTAATCGTATTTGTGTTT 57.179 30.769 0.00 0.00 41.83 2.83
1131 1146 7.380065 TCGTATTTGTGTTTTGTTATTCTTGCC 59.620 33.333 0.00 0.00 0.00 4.52
1252 1267 9.678941 AAAAAGAAAATACTCGGTCAGAAAATC 57.321 29.630 0.00 0.00 0.00 2.17
1328 1343 4.074970 ACCTGGTAAGTTGAAGATGCTTG 58.925 43.478 0.00 0.00 0.00 4.01
1351 1366 7.744087 TGTATATGGTTGCCTGTGATTATTC 57.256 36.000 0.00 0.00 0.00 1.75
1387 1402 7.486407 AAAATGCAGTATGGAGGAGAAAAAT 57.514 32.000 0.00 0.00 42.42 1.82
1457 1473 3.525537 AGCCTTCTCGTGTCACATAATG 58.474 45.455 3.42 0.00 0.00 1.90
1501 1518 7.782049 TCATAACTAGACATTTGGTAGGAGTG 58.218 38.462 0.00 0.00 0.00 3.51
1717 1737 9.995003 AGTTATTGAAGATAAGGCTAAGAGATG 57.005 33.333 0.00 0.00 0.00 2.90
2345 2377 4.325028 AACAGCATGAGAGAGCTAGATG 57.675 45.455 0.00 0.00 39.50 2.90
2452 2484 9.502091 AACTTGAAATCTAGTGTGCTAATGTTA 57.498 29.630 0.00 0.00 32.55 2.41
2657 2689 1.662629 CTTCCAAGTGATGCTGCTACG 59.337 52.381 0.00 0.00 0.00 3.51
2824 2856 5.237815 TGCTGAATCATCGGTATGTTATCC 58.762 41.667 0.00 0.00 34.20 2.59
3045 3078 6.072452 GCCAGAAAATACTGTAGAACTTTGCT 60.072 38.462 0.00 0.00 36.30 3.91
3061 3094 5.945310 ACTTTGCTGATATGTGGATACCAT 58.055 37.500 0.00 0.00 35.28 3.55
3078 3111 4.617253 ACCATAGACAACAGTGCACTAA 57.383 40.909 21.20 0.00 0.00 2.24
3163 3196 6.239120 CCAAGAAACTCTGAATTGTCCAATGT 60.239 38.462 0.00 0.00 0.00 2.71
3294 3327 2.810852 CTCCTTTGTCCTGTCTCTTTGC 59.189 50.000 0.00 0.00 0.00 3.68
3669 3716 4.818546 AGTCTGTCAAACAACTTCATGGAG 59.181 41.667 0.00 0.00 0.00 3.86
3783 3830 2.440980 GGGGGAACATCTGCAGCC 60.441 66.667 9.47 3.51 0.00 4.85
3979 4026 3.188048 GTCTGATGCAAAGAAGTGTGGAG 59.812 47.826 4.17 0.00 0.00 3.86
4009 4056 0.332632 CCAAGGATTTCTCAGGGGCA 59.667 55.000 0.00 0.00 0.00 5.36
4202 4249 4.366586 CATCTACGCACTGTGATCTTGAT 58.633 43.478 12.86 5.14 0.00 2.57
4203 4250 4.033990 TCTACGCACTGTGATCTTGATC 57.966 45.455 12.86 3.82 0.00 2.92
4204 4251 3.696548 TCTACGCACTGTGATCTTGATCT 59.303 43.478 12.86 0.00 0.00 2.75
4205 4252 3.325293 ACGCACTGTGATCTTGATCTT 57.675 42.857 12.86 0.00 0.00 2.40
4206 4253 2.998670 ACGCACTGTGATCTTGATCTTG 59.001 45.455 12.86 5.40 0.00 3.02
4207 4254 3.256558 CGCACTGTGATCTTGATCTTGA 58.743 45.455 12.86 0.00 0.00 3.02
4233 4280 1.537202 GGCACTGTGATTGAAGTGGAC 59.463 52.381 12.86 0.00 43.29 4.02
4284 4331 1.204941 CCTTCTGGAGGTACTTGGTCG 59.795 57.143 0.00 0.00 41.55 4.79
4285 4332 1.893801 CTTCTGGAGGTACTTGGTCGT 59.106 52.381 0.00 0.00 41.55 4.34
4286 4333 2.005370 TCTGGAGGTACTTGGTCGTT 57.995 50.000 0.00 0.00 41.55 3.85
4287 4334 3.159213 TCTGGAGGTACTTGGTCGTTA 57.841 47.619 0.00 0.00 41.55 3.18
4288 4335 3.087031 TCTGGAGGTACTTGGTCGTTAG 58.913 50.000 0.00 0.00 41.55 2.34
4347 4394 9.359653 CATTGATTCCCTTATATCTGGTTTCTT 57.640 33.333 0.00 0.00 0.00 2.52
4400 4447 4.737855 TTTGATCAGTCTGGCTAGGTAC 57.262 45.455 0.00 0.00 0.00 3.34
4555 4603 2.778299 TCATTCGAGTTGAACCAAGGG 58.222 47.619 0.00 0.00 40.00 3.95
4595 4643 7.665690 AGCGAGTAATAATCATCATCTCACTT 58.334 34.615 0.00 0.00 0.00 3.16
4704 4790 2.035066 ACCTGTTTGCTTGCTGACATTC 59.965 45.455 0.00 0.00 0.00 2.67
4748 4834 3.501828 TGACGCATGACAGCTAAAACAAT 59.498 39.130 0.00 0.00 0.00 2.71
4794 4880 4.337555 AGCACATCTGTCTATTGATTTGCC 59.662 41.667 9.52 0.00 43.40 4.52
4796 4882 4.885907 CACATCTGTCTATTGATTTGCCCT 59.114 41.667 0.00 0.00 0.00 5.19
4803 4889 5.357878 TGTCTATTGATTTGCCCTGTGATTC 59.642 40.000 0.00 0.00 0.00 2.52
4824 4910 1.535226 GGGCACTTGTTTTGACGGAAC 60.535 52.381 0.00 0.00 0.00 3.62
4865 4951 6.780457 AAAATCTCAACCCTGTCAATATGG 57.220 37.500 0.00 0.00 0.00 2.74
4866 4952 3.281727 TCTCAACCCTGTCAATATGGC 57.718 47.619 0.00 0.00 0.00 4.40
4867 4953 2.846206 TCTCAACCCTGTCAATATGGCT 59.154 45.455 0.00 0.00 0.00 4.75
4868 4954 4.037222 TCTCAACCCTGTCAATATGGCTA 58.963 43.478 0.00 0.00 0.00 3.93
4869 4955 4.130118 CTCAACCCTGTCAATATGGCTAC 58.870 47.826 0.00 0.00 0.00 3.58
4870 4956 3.780294 TCAACCCTGTCAATATGGCTACT 59.220 43.478 0.00 0.00 0.00 2.57
4871 4957 4.227300 TCAACCCTGTCAATATGGCTACTT 59.773 41.667 0.00 0.00 0.00 2.24
4872 4958 4.156455 ACCCTGTCAATATGGCTACTTG 57.844 45.455 0.00 0.00 0.00 3.16
4873 4959 3.523564 ACCCTGTCAATATGGCTACTTGT 59.476 43.478 0.00 0.00 0.00 3.16
4874 4960 4.018415 ACCCTGTCAATATGGCTACTTGTT 60.018 41.667 0.00 0.00 0.00 2.83
4875 4961 4.949856 CCCTGTCAATATGGCTACTTGTTT 59.050 41.667 0.00 0.00 0.00 2.83
4876 4962 5.418840 CCCTGTCAATATGGCTACTTGTTTT 59.581 40.000 0.00 0.00 0.00 2.43
4877 4963 6.324819 CCTGTCAATATGGCTACTTGTTTTG 58.675 40.000 0.00 0.00 0.00 2.44
4878 4964 6.150976 CCTGTCAATATGGCTACTTGTTTTGA 59.849 38.462 0.00 0.00 0.00 2.69
4879 4965 6.908825 TGTCAATATGGCTACTTGTTTTGAC 58.091 36.000 0.00 0.00 41.11 3.18
4880 4966 6.021596 GTCAATATGGCTACTTGTTTTGACG 58.978 40.000 0.00 0.00 34.40 4.35
4881 4967 5.123186 TCAATATGGCTACTTGTTTTGACGG 59.877 40.000 0.00 0.00 0.00 4.79
4882 4968 2.623878 TGGCTACTTGTTTTGACGGA 57.376 45.000 0.00 0.00 0.00 4.69
4883 4969 2.920524 TGGCTACTTGTTTTGACGGAA 58.079 42.857 0.00 0.00 0.00 4.30
4884 4970 3.280295 TGGCTACTTGTTTTGACGGAAA 58.720 40.909 0.00 0.00 0.00 3.13
4885 4971 3.886505 TGGCTACTTGTTTTGACGGAAAT 59.113 39.130 0.00 0.00 0.00 2.17
4886 4972 4.339814 TGGCTACTTGTTTTGACGGAAATT 59.660 37.500 0.00 0.00 0.00 1.82
4887 4973 4.679654 GGCTACTTGTTTTGACGGAAATTG 59.320 41.667 0.00 0.00 0.00 2.32
4888 4974 4.148174 GCTACTTGTTTTGACGGAAATTGC 59.852 41.667 0.00 0.00 0.00 3.56
4889 4975 4.385358 ACTTGTTTTGACGGAAATTGCT 57.615 36.364 0.00 0.00 0.00 3.91
4890 4976 4.754322 ACTTGTTTTGACGGAAATTGCTT 58.246 34.783 0.00 0.00 0.00 3.91
4891 4977 4.566360 ACTTGTTTTGACGGAAATTGCTTG 59.434 37.500 0.00 0.00 0.00 4.01
4892 4978 4.377839 TGTTTTGACGGAAATTGCTTGA 57.622 36.364 0.00 0.00 0.00 3.02
4893 4979 4.748892 TGTTTTGACGGAAATTGCTTGAA 58.251 34.783 0.00 0.00 0.00 2.69
4894 4980 5.171476 TGTTTTGACGGAAATTGCTTGAAA 58.829 33.333 0.00 0.00 0.00 2.69
4895 4981 5.639506 TGTTTTGACGGAAATTGCTTGAAAA 59.360 32.000 0.00 0.00 0.00 2.29
4925 5011 6.125029 AGAATTCTCAACCCTGTCAATATGG 58.875 40.000 0.88 0.00 0.00 2.74
4952 5063 7.009815 CACAATATACGTACATCAACCGTTCTT 59.990 37.037 0.00 0.00 36.12 2.52
4955 5066 2.798283 ACGTACATCAACCGTTCTTGTG 59.202 45.455 0.00 0.00 0.00 3.33
4960 5071 1.960417 TCAACCGTTCTTGTGCATCA 58.040 45.000 0.00 0.00 0.00 3.07
5022 5134 4.813750 TCCCTCTTTACTCTTAAACCGG 57.186 45.455 0.00 0.00 0.00 5.28
5024 5136 4.594491 TCCCTCTTTACTCTTAAACCGGTT 59.406 41.667 15.86 15.86 0.00 4.44
5025 5137 4.934001 CCCTCTTTACTCTTAAACCGGTTC 59.066 45.833 22.53 0.00 0.00 3.62
5027 5139 6.228995 CCTCTTTACTCTTAAACCGGTTCTT 58.771 40.000 22.53 8.74 0.00 2.52
5030 5142 8.146479 TCTTTACTCTTAAACCGGTTCTTTTC 57.854 34.615 22.53 0.00 0.00 2.29
5111 5243 5.990120 TTACCTTCTTACTCTGTACACCC 57.010 43.478 0.00 0.00 0.00 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.134250 TGAAGCCTTGGCATACGCATA 60.134 47.619 14.54 0.00 41.24 3.14
1 2 0.394216 TGAAGCCTTGGCATACGCAT 60.394 50.000 14.54 0.00 41.24 4.73
2 3 0.607762 TTGAAGCCTTGGCATACGCA 60.608 50.000 14.54 1.67 41.24 5.24
3 4 0.525761 TTTGAAGCCTTGGCATACGC 59.474 50.000 14.54 0.00 37.44 4.42
4 5 1.465689 CGTTTGAAGCCTTGGCATACG 60.466 52.381 14.54 10.95 32.56 3.06
57 58 3.719173 AGTCTAGCTATCGTGGCTTTC 57.281 47.619 0.00 0.00 40.74 2.62
258 261 2.083002 GAGGAAGCTGCCAAGAAGAAG 58.917 52.381 15.05 0.00 0.00 2.85
259 262 1.609061 CGAGGAAGCTGCCAAGAAGAA 60.609 52.381 15.05 0.00 0.00 2.52
260 263 0.036952 CGAGGAAGCTGCCAAGAAGA 60.037 55.000 15.05 0.00 0.00 2.87
295 298 0.762461 GGGGTGAGAGGATGAGGAGG 60.762 65.000 0.00 0.00 0.00 4.30
296 299 0.031716 TGGGGTGAGAGGATGAGGAG 60.032 60.000 0.00 0.00 0.00 3.69
297 300 0.325671 GTGGGGTGAGAGGATGAGGA 60.326 60.000 0.00 0.00 0.00 3.71
298 301 1.680522 CGTGGGGTGAGAGGATGAGG 61.681 65.000 0.00 0.00 0.00 3.86
339 342 0.977627 GGCTGGAAAAGGGAATGGGG 60.978 60.000 0.00 0.00 0.00 4.96
368 371 3.354645 AGACGCAGACGCAGACGA 61.355 61.111 0.00 0.00 45.53 4.20
388 391 0.941463 CGTGGTGCTGTGTCTCAGAC 60.941 60.000 6.09 0.00 46.27 3.51
389 392 1.363807 CGTGGTGCTGTGTCTCAGA 59.636 57.895 6.09 0.00 46.27 3.27
390 393 2.313172 GCGTGGTGCTGTGTCTCAG 61.313 63.158 0.00 0.00 46.12 3.35
391 394 2.280119 GCGTGGTGCTGTGTCTCA 60.280 61.111 0.00 0.00 41.73 3.27
773 779 1.748591 GCCTAAATCCAGGAGCACCAG 60.749 57.143 2.07 0.00 38.00 4.00
791 797 3.264845 TCCCTGTCCCCAAAGGCC 61.265 66.667 0.00 0.00 34.51 5.19
918 928 1.153901 CCGCTATGTGGTCGTTCGT 60.154 57.895 0.00 0.00 0.00 3.85
922 932 1.335132 AATCCCCGCTATGTGGTCGT 61.335 55.000 0.00 0.00 0.00 4.34
955 965 3.953775 CCCAGTTCCCCACGCACT 61.954 66.667 0.00 0.00 0.00 4.40
1005 1015 1.901464 CCACACGACCAAAAGGGGG 60.901 63.158 0.00 0.00 42.91 5.40
1044 1054 8.485976 AGAATCACTTCAAGTAATCTTACAGC 57.514 34.615 0.00 0.00 33.57 4.40
1082 1097 8.737175 ACGATTAGTACTGTGATTCTGAAACTA 58.263 33.333 5.39 0.00 0.00 2.24
1090 1105 9.084164 ACACAAATACGATTAGTACTGTGATTC 57.916 33.333 19.18 0.00 45.78 2.52
1118 1133 8.217111 TGTATATGATCTGGGCAAGAATAACAA 58.783 33.333 0.00 0.00 38.79 2.83
1131 1146 9.429359 GTAGAGTTTCCATTGTATATGATCTGG 57.571 37.037 0.00 0.00 0.00 3.86
1252 1267 6.813649 CCACCTCTGGTATAATGTCATATTCG 59.186 42.308 0.00 0.00 32.11 3.34
1328 1343 7.094634 CCAGAATAATCACAGGCAACCATATAC 60.095 40.741 0.00 0.00 37.17 1.47
1351 1366 7.498900 TCCATACTGCATTTTACTATGAACCAG 59.501 37.037 0.00 0.00 0.00 4.00
1368 1383 5.904362 AACATTTTTCTCCTCCATACTGC 57.096 39.130 0.00 0.00 0.00 4.40
1396 1411 8.540388 AGAACAAAGTACAAATATAGGAGCAGA 58.460 33.333 0.00 0.00 0.00 4.26
1501 1518 4.748600 GGGTATATGCCACGTTCTTTAGTC 59.251 45.833 12.29 0.00 0.00 2.59
1650 1667 7.769507 ACGTAGTGAGACATGTTCTAAGAGATA 59.230 37.037 0.00 0.00 42.51 1.98
1717 1737 6.699575 ATAAAAGCATGTCTACAATGGGTC 57.300 37.500 0.00 0.00 0.00 4.46
1760 1780 7.784470 AAGACAGTCTTATCTTAAGTCCTGT 57.216 36.000 14.58 15.50 34.42 4.00
2251 2283 0.609957 CAGGGCAGGCTTGACATTCA 60.610 55.000 3.21 0.00 32.23 2.57
2345 2377 5.345741 ACATGTAAAAGATGCAACGAAATGC 59.654 36.000 0.00 0.00 46.58 3.56
2452 2484 5.578073 AGGCATCCTGAAGAAGAAAGAAAT 58.422 37.500 0.00 0.00 29.57 2.17
2657 2689 1.069358 GTGTGAGCAGGGATAGCTACC 59.931 57.143 0.00 0.00 43.58 3.18
2769 2801 2.613977 CCGGAGACAGTTGAGCAGAAAT 60.614 50.000 0.00 0.00 0.00 2.17
2824 2856 3.533606 ATACTAAGCACTGCTGTGAGG 57.466 47.619 25.94 13.87 46.55 3.86
3045 3078 7.290014 ACTGTTGTCTATGGTATCCACATATCA 59.710 37.037 0.00 0.00 35.80 2.15
3061 3094 6.765989 ACTCATTTTTAGTGCACTGTTGTCTA 59.234 34.615 29.57 4.12 0.00 2.59
3100 3133 8.337532 AGCACTGCAATTTAGATTTTGTTTTTC 58.662 29.630 3.30 0.00 0.00 2.29
3138 3171 5.772825 TTGGACAATTCAGAGTTTCTTGG 57.227 39.130 0.00 0.00 0.00 3.61
3294 3327 3.814842 TGAGGTACACACAAATTCAGCAG 59.185 43.478 0.00 0.00 0.00 4.24
3352 3399 6.977213 TGCACTATGATACGCTCATAACTTA 58.023 36.000 8.97 0.00 44.36 2.24
3364 3411 9.552114 GATTGCTCATAATTTGCACTATGATAC 57.448 33.333 11.02 8.34 34.77 2.24
3436 3483 6.198966 GGGAAAATAAATGCAATGAGTAAGCG 59.801 38.462 0.00 0.00 0.00 4.68
3669 3716 6.597280 ACTGTAGCTCTTTCATCTGAAATTCC 59.403 38.462 5.86 0.00 42.44 3.01
3783 3830 1.091771 CCTTGTATGGTGGAGCGCTG 61.092 60.000 18.48 0.00 0.00 5.18
3788 3835 0.824109 TCGAGCCTTGTATGGTGGAG 59.176 55.000 0.00 0.00 0.00 3.86
3979 4026 3.636764 AGAAATCCTTGGTTGTTGTGACC 59.363 43.478 0.00 0.00 37.69 4.02
4009 4056 2.245806 AGCCTCTAAATGCCCTTTGGAT 59.754 45.455 0.00 0.00 34.29 3.41
4233 4280 1.640069 CCACATGCTCAATCGCTCG 59.360 57.895 0.00 0.00 0.00 5.03
4347 4394 6.179756 AGCTTCATATGTACAAACACCATGA 58.820 36.000 0.00 0.06 38.78 3.07
4400 4447 2.105306 TGGCACTCATCCATCACCATAG 59.895 50.000 0.00 0.00 0.00 2.23
4595 4643 8.759481 TGTAATCCAATAATGCTGTAATCCAA 57.241 30.769 0.00 0.00 0.00 3.53
4748 4834 1.578926 CGTGCCCTGCGAATTTTCA 59.421 52.632 0.00 0.00 0.00 2.69
4794 4880 0.606401 ACAAGTGCCCGAATCACAGG 60.606 55.000 4.89 0.00 36.93 4.00
4796 4882 1.686355 AAACAAGTGCCCGAATCACA 58.314 45.000 4.89 0.00 36.93 3.58
4803 4889 1.008995 CCGTCAAAACAAGTGCCCG 60.009 57.895 0.00 0.00 0.00 6.13
4844 4930 4.079558 AGCCATATTGACAGGGTTGAGATT 60.080 41.667 0.00 0.00 0.00 2.40
4845 4931 3.461085 AGCCATATTGACAGGGTTGAGAT 59.539 43.478 0.00 0.00 0.00 2.75
4846 4932 2.846206 AGCCATATTGACAGGGTTGAGA 59.154 45.455 0.00 0.00 0.00 3.27
4847 4933 3.287867 AGCCATATTGACAGGGTTGAG 57.712 47.619 0.00 0.00 0.00 3.02
4848 4934 3.780294 AGTAGCCATATTGACAGGGTTGA 59.220 43.478 0.00 0.00 34.52 3.18
4849 4935 4.156455 AGTAGCCATATTGACAGGGTTG 57.844 45.455 0.00 0.00 34.52 3.77
4850 4936 4.018415 ACAAGTAGCCATATTGACAGGGTT 60.018 41.667 0.00 0.00 34.52 4.11
4851 4937 3.523564 ACAAGTAGCCATATTGACAGGGT 59.476 43.478 0.00 0.00 36.95 4.34
4852 4938 4.156455 ACAAGTAGCCATATTGACAGGG 57.844 45.455 0.00 0.00 0.00 4.45
4853 4939 6.150976 TCAAAACAAGTAGCCATATTGACAGG 59.849 38.462 0.00 0.00 0.00 4.00
4854 4940 7.023575 GTCAAAACAAGTAGCCATATTGACAG 58.976 38.462 9.66 0.00 42.87 3.51
4855 4941 6.348132 CGTCAAAACAAGTAGCCATATTGACA 60.348 38.462 13.62 0.00 43.28 3.58
4856 4942 6.021596 CGTCAAAACAAGTAGCCATATTGAC 58.978 40.000 0.00 0.00 41.02 3.18
4857 4943 5.123186 CCGTCAAAACAAGTAGCCATATTGA 59.877 40.000 0.00 0.00 0.00 2.57
4858 4944 5.123186 TCCGTCAAAACAAGTAGCCATATTG 59.877 40.000 0.00 0.00 0.00 1.90
4859 4945 5.250200 TCCGTCAAAACAAGTAGCCATATT 58.750 37.500 0.00 0.00 0.00 1.28
4860 4946 4.839121 TCCGTCAAAACAAGTAGCCATAT 58.161 39.130 0.00 0.00 0.00 1.78
4861 4947 4.274602 TCCGTCAAAACAAGTAGCCATA 57.725 40.909 0.00 0.00 0.00 2.74
4862 4948 3.134574 TCCGTCAAAACAAGTAGCCAT 57.865 42.857 0.00 0.00 0.00 4.40
4863 4949 2.623878 TCCGTCAAAACAAGTAGCCA 57.376 45.000 0.00 0.00 0.00 4.75
4864 4950 3.974871 TTTCCGTCAAAACAAGTAGCC 57.025 42.857 0.00 0.00 0.00 3.93
4865 4951 4.148174 GCAATTTCCGTCAAAACAAGTAGC 59.852 41.667 0.00 0.00 0.00 3.58
4866 4952 5.519722 AGCAATTTCCGTCAAAACAAGTAG 58.480 37.500 0.00 0.00 0.00 2.57
4867 4953 5.508200 AGCAATTTCCGTCAAAACAAGTA 57.492 34.783 0.00 0.00 0.00 2.24
4868 4954 4.385358 AGCAATTTCCGTCAAAACAAGT 57.615 36.364 0.00 0.00 0.00 3.16
4869 4955 4.803088 TCAAGCAATTTCCGTCAAAACAAG 59.197 37.500 0.00 0.00 0.00 3.16
4870 4956 4.748892 TCAAGCAATTTCCGTCAAAACAA 58.251 34.783 0.00 0.00 0.00 2.83
4871 4957 4.377839 TCAAGCAATTTCCGTCAAAACA 57.622 36.364 0.00 0.00 0.00 2.83
4872 4958 5.710613 TTTCAAGCAATTTCCGTCAAAAC 57.289 34.783 0.00 0.00 0.00 2.43
4873 4959 5.293079 CCTTTTCAAGCAATTTCCGTCAAAA 59.707 36.000 0.00 0.00 0.00 2.44
4874 4960 4.808364 CCTTTTCAAGCAATTTCCGTCAAA 59.192 37.500 0.00 0.00 0.00 2.69
4875 4961 4.098654 TCCTTTTCAAGCAATTTCCGTCAA 59.901 37.500 0.00 0.00 0.00 3.18
4876 4962 3.634448 TCCTTTTCAAGCAATTTCCGTCA 59.366 39.130 0.00 0.00 0.00 4.35
4877 4963 4.023193 TCTCCTTTTCAAGCAATTTCCGTC 60.023 41.667 0.00 0.00 0.00 4.79
4878 4964 3.888930 TCTCCTTTTCAAGCAATTTCCGT 59.111 39.130 0.00 0.00 0.00 4.69
4879 4965 4.503741 TCTCCTTTTCAAGCAATTTCCG 57.496 40.909 0.00 0.00 0.00 4.30
4880 4966 6.089249 TCTTCTCCTTTTCAAGCAATTTCC 57.911 37.500 0.00 0.00 0.00 3.13
4881 4967 8.599055 AATTCTTCTCCTTTTCAAGCAATTTC 57.401 30.769 0.00 0.00 0.00 2.17
4882 4968 8.427276 AGAATTCTTCTCCTTTTCAAGCAATTT 58.573 29.630 0.88 0.00 34.07 1.82
4883 4969 7.960262 AGAATTCTTCTCCTTTTCAAGCAATT 58.040 30.769 0.88 0.00 34.07 2.32
4884 4970 7.536159 AGAATTCTTCTCCTTTTCAAGCAAT 57.464 32.000 0.88 0.00 34.07 3.56
4885 4971 6.966534 AGAATTCTTCTCCTTTTCAAGCAA 57.033 33.333 0.88 0.00 34.07 3.91
4902 4988 5.221126 GCCATATTGACAGGGTTGAGAATTC 60.221 44.000 0.00 0.00 0.00 2.17
4925 5011 4.505191 ACGGTTGATGTACGTATATTGTGC 59.495 41.667 6.26 0.00 39.30 4.57
4940 5028 2.226437 GTGATGCACAAGAACGGTTGAT 59.774 45.455 0.00 0.00 34.08 2.57
4952 5063 3.701205 ACACAGGAATAGTGATGCACA 57.299 42.857 0.00 0.00 40.16 4.57
5024 5136 8.349983 CGGTTTAAGAAAGAAGGATTGAAAAGA 58.650 33.333 0.00 0.00 0.00 2.52
5025 5137 8.349983 TCGGTTTAAGAAAGAAGGATTGAAAAG 58.650 33.333 0.00 0.00 0.00 2.27
5027 5139 7.811117 TCGGTTTAAGAAAGAAGGATTGAAA 57.189 32.000 0.00 0.00 0.00 2.69
5030 5142 8.045176 AGAATCGGTTTAAGAAAGAAGGATTG 57.955 34.615 0.00 0.00 0.00 2.67


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

AutoCloner maintained by Alex Coulton.