Multiple sequence alignment - TraesCS3A01G433200

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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 TraesCS3A01G433200 chr3A 100.000 5634 0 0 576 6209 674744559 674750192 0.000000e+00 10405.0
1 TraesCS3A01G433200 chr3A 100.000 146 0 0 1 146 674743984 674744129 2.850000e-68 270.0
2 TraesCS3A01G433200 chr3D 94.259 5748 181 60 576 6209 539897245 539902957 0.000000e+00 8648.0
3 TraesCS3A01G433200 chr3D 88.679 106 6 5 1 106 539896562 539896661 2.350000e-24 124.0
4 TraesCS3A01G433200 chr3B 88.668 4430 328 86 1873 6209 715881106 715885454 0.000000e+00 5240.0
5 TraesCS3A01G433200 chr3B 88.708 983 66 17 882 1831 715880125 715881095 0.000000e+00 1158.0
6 TraesCS3A01G433200 chr3B 95.745 47 2 0 1 47 715879516 715879562 6.670000e-10 76.8
7 TraesCS3A01G433200 chrUn 100.000 398 0 0 4112 4509 479027681 479028078 0.000000e+00 736.0
8 TraesCS3A01G433200 chr6A 82.451 661 82 21 1177 1831 21546550 21545918 1.180000e-151 547.0
9 TraesCS3A01G433200 chr2A 87.316 339 34 4 4794 5132 688580207 688580536 4.540000e-101 379.0
10 TraesCS3A01G433200 chr2B 84.940 166 18 5 4768 4927 651601809 651601645 1.790000e-35 161.0


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 TraesCS3A01G433200 chr3A 674743984 674750192 6208 False 5337.500000 10405 100.000000 1 6209 2 chr3A.!!$F1 6208
1 TraesCS3A01G433200 chr3D 539896562 539902957 6395 False 4386.000000 8648 91.469000 1 6209 2 chr3D.!!$F1 6208
2 TraesCS3A01G433200 chr3B 715879516 715885454 5938 False 2158.266667 5240 91.040333 1 6209 3 chr3B.!!$F1 6208
3 TraesCS3A01G433200 chr6A 21545918 21546550 632 True 547.000000 547 82.451000 1177 1831 1 chr6A.!!$R1 654

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
144 216 0.112412 TTTGCTTTCTCCCACCCTCC 59.888 55.000 0.00 0.0 0.00 4.30 F
738 876 1.044231 GTCGGGGGTTTGGTTTGGTT 61.044 55.000 0.00 0.0 0.00 3.67 F
1918 2154 0.612174 TCCCAAGTCTCACGCTAGCT 60.612 55.000 13.93 0.0 0.00 3.32 F
2267 2531 1.002868 TGCTCCTTTCCAGCTGCTC 60.003 57.895 8.66 0.0 37.79 4.26 F
2689 2959 1.999735 TGTCGCTCTTGCCTTTTATCG 59.000 47.619 0.00 0.0 35.36 2.92 F
4509 4805 0.174617 CAGACCCTCCGAAGCTCTTC 59.825 60.000 0.00 0.0 36.29 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1844 2080 1.354031 TGTGGGATAGGAAAGCAAGCA 59.646 47.619 0.00 0.00 0.00 3.91 R
2179 2443 0.386478 GTCCTGCAGAAAAGCAAGCG 60.386 55.000 17.39 0.00 45.13 4.68 R
3243 3529 0.798776 ACATAGTCTTGCTGCGTTGC 59.201 50.000 0.00 0.00 0.00 4.17 R
3955 4251 0.685458 GGCATGATGGGAGCAAAGGT 60.685 55.000 0.00 0.00 0.00 3.50 R
4614 4910 0.608035 CCAAAGCCCGCCTTAGTGAA 60.608 55.000 0.00 0.00 32.20 3.18 R
5392 5693 0.108329 TTGCCTACCAGCGCTAGTTC 60.108 55.000 15.04 4.81 34.65 3.01 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
51 52 2.166664 GTGCCACCTTCTACCACTCTAG 59.833 54.545 0.00 0.00 0.00 2.43
52 53 1.137282 GCCACCTTCTACCACTCTAGC 59.863 57.143 0.00 0.00 0.00 3.42
61 62 2.445682 ACCACTCTAGCAGTAGGAGG 57.554 55.000 12.85 0.00 32.21 4.30
64 65 2.092103 CCACTCTAGCAGTAGGAGGAGT 60.092 54.545 0.00 0.00 32.21 3.85
65 66 3.136809 CCACTCTAGCAGTAGGAGGAGTA 59.863 52.174 0.00 0.00 32.21 2.59
66 67 4.385825 CACTCTAGCAGTAGGAGGAGTAG 58.614 52.174 0.00 0.00 32.21 2.57
67 68 4.042174 ACTCTAGCAGTAGGAGGAGTAGT 58.958 47.826 0.00 0.00 33.13 2.73
68 69 4.102054 ACTCTAGCAGTAGGAGGAGTAGTC 59.898 50.000 0.00 0.00 33.13 2.59
69 70 4.300345 TCTAGCAGTAGGAGGAGTAGTCT 58.700 47.826 0.00 0.00 0.00 3.24
70 71 5.465901 TCTAGCAGTAGGAGGAGTAGTCTA 58.534 45.833 0.00 0.00 0.00 2.59
71 72 4.426736 AGCAGTAGGAGGAGTAGTCTAC 57.573 50.000 1.39 1.39 34.08 2.59
72 73 4.042174 AGCAGTAGGAGGAGTAGTCTACT 58.958 47.826 12.50 12.50 41.93 2.57
91 95 0.553819 TCTCTACTGCCTCCTCCTCC 59.446 60.000 0.00 0.00 0.00 4.30
97 101 3.160748 GCCTCCTCCTCCCTGCTC 61.161 72.222 0.00 0.00 0.00 4.26
138 210 2.268076 GCCGCTTTGCTTTCTCCCA 61.268 57.895 0.00 0.00 0.00 4.37
141 213 1.866853 CGCTTTGCTTTCTCCCACCC 61.867 60.000 0.00 0.00 0.00 4.61
142 214 0.540597 GCTTTGCTTTCTCCCACCCT 60.541 55.000 0.00 0.00 0.00 4.34
144 216 0.112412 TTTGCTTTCTCCCACCCTCC 59.888 55.000 0.00 0.00 0.00 4.30
145 217 1.789576 TTGCTTTCTCCCACCCTCCC 61.790 60.000 0.00 0.00 0.00 4.30
629 751 3.182590 TTGGCGTTGGAGCTGCTCT 62.183 57.895 27.09 0.00 37.29 4.09
633 755 1.743252 CGTTGGAGCTGCTCTTCCC 60.743 63.158 27.09 13.35 0.00 3.97
675 811 5.358160 CCTTCTCTTCTCTTCTCTTCTCTCC 59.642 48.000 0.00 0.00 0.00 3.71
678 814 1.757682 TCTCTTCTCTTCTCTCCGGC 58.242 55.000 0.00 0.00 0.00 6.13
738 876 1.044231 GTCGGGGGTTTGGTTTGGTT 61.044 55.000 0.00 0.00 0.00 3.67
787 947 4.794439 GGCGGCGAAATTGTGGGC 62.794 66.667 12.98 0.00 0.00 5.36
794 954 1.883021 GAAATTGTGGGCGACAGGG 59.117 57.895 1.81 0.00 35.44 4.45
864 1029 2.348104 GGTTTGGTTCCGGGGCATC 61.348 63.158 0.00 0.00 0.00 3.91
884 1049 3.774599 AATCCTCCAATCCGGGCGC 62.775 63.158 0.00 0.00 34.36 6.53
914 1116 2.430921 CTCGACCACGCTGTGTCC 60.431 66.667 7.68 0.00 39.58 4.02
1445 1671 2.665089 CCATCACCCAGGTACGGCA 61.665 63.158 0.00 0.00 0.00 5.69
1504 1735 2.941210 GGTGATGCCGGAAAGTGAA 58.059 52.632 5.05 0.00 0.00 3.18
1536 1768 4.886496 AGTAACTAACCCTGTTCTGTCC 57.114 45.455 0.00 0.00 0.00 4.02
1844 2080 5.619086 GCTGTGCGTGACCATTAATTTACTT 60.619 40.000 0.00 0.00 0.00 2.24
1911 2147 1.679898 CCCCACTCCCAAGTCTCAC 59.320 63.158 0.00 0.00 31.71 3.51
1918 2154 0.612174 TCCCAAGTCTCACGCTAGCT 60.612 55.000 13.93 0.00 0.00 3.32
1919 2155 1.103803 CCCAAGTCTCACGCTAGCTA 58.896 55.000 13.93 0.00 0.00 3.32
1920 2156 1.476891 CCCAAGTCTCACGCTAGCTAA 59.523 52.381 13.93 0.00 0.00 3.09
1921 2157 2.480416 CCCAAGTCTCACGCTAGCTAAG 60.480 54.545 13.93 7.31 0.00 2.18
2035 2293 2.105930 AGCGCTGCTGCTACTAGC 59.894 61.111 10.39 8.96 45.14 3.42
2104 2365 5.408604 GGTGTGGTCACTTGTTAGTATCTTG 59.591 44.000 2.66 0.00 43.41 3.02
2129 2393 6.269769 GGGATTCTTCTACTCTGATGAGGAAT 59.730 42.308 10.29 10.29 44.29 3.01
2138 2402 5.605534 ACTCTGATGAGGAATAATCGTTGG 58.394 41.667 0.00 0.00 44.29 3.77
2145 2409 5.419542 TGAGGAATAATCGTTGGTTCTGAG 58.580 41.667 0.00 0.00 0.00 3.35
2179 2443 5.300969 TGATGCTAACAGAAGTGCATTTC 57.699 39.130 13.69 13.69 44.80 2.17
2181 2445 2.095768 TGCTAACAGAAGTGCATTTCGC 60.096 45.455 15.34 12.64 42.89 4.70
2190 2454 2.397549 AGTGCATTTCGCTTGCTTTTC 58.602 42.857 0.00 0.00 43.06 2.29
2267 2531 1.002868 TGCTCCTTTCCAGCTGCTC 60.003 57.895 8.66 0.00 37.79 4.26
2482 2752 4.377841 GGCATATTTGACATAGAAGCGCTC 60.378 45.833 12.06 4.30 0.00 5.03
2608 2878 3.056080 AGGCAGTGGGATGTACCATAAT 58.944 45.455 0.00 0.00 43.59 1.28
2638 2908 2.874701 CAACTTTGGCGATCCATCTAGG 59.125 50.000 0.00 0.00 43.05 3.02
2679 2949 3.438087 AGGTGATTGATTTGTCGCTCTTG 59.562 43.478 0.00 0.00 0.00 3.02
2689 2959 1.999735 TGTCGCTCTTGCCTTTTATCG 59.000 47.619 0.00 0.00 35.36 2.92
2692 2962 2.094182 TCGCTCTTGCCTTTTATCGACT 60.094 45.455 0.00 0.00 35.36 4.18
2774 3044 6.837992 TCTCTGTAAAACACAACAACTGTTC 58.162 36.000 0.00 0.00 35.47 3.18
3027 3301 6.311445 CACAACCTATACTGCTTGTCTAACTG 59.689 42.308 0.00 0.00 0.00 3.16
3029 3303 7.093289 ACAACCTATACTGCTTGTCTAACTGAT 60.093 37.037 0.00 0.00 0.00 2.90
3030 3304 7.425224 ACCTATACTGCTTGTCTAACTGATT 57.575 36.000 0.00 0.00 0.00 2.57
3031 3305 7.852263 ACCTATACTGCTTGTCTAACTGATTT 58.148 34.615 0.00 0.00 0.00 2.17
3032 3306 8.322091 ACCTATACTGCTTGTCTAACTGATTTT 58.678 33.333 0.00 0.00 0.00 1.82
3033 3307 9.167311 CCTATACTGCTTGTCTAACTGATTTTT 57.833 33.333 0.00 0.00 0.00 1.94
3055 3334 4.806640 TTTTTCTCATTCCATGCCCTTC 57.193 40.909 0.00 0.00 0.00 3.46
3134 3413 3.822940 TGGGGTTTTAGGTAAGTGTGTG 58.177 45.455 0.00 0.00 0.00 3.82
3194 3480 4.635765 TGACTGAAGGGATTTAAGCAATCG 59.364 41.667 0.00 0.00 42.27 3.34
3243 3529 3.613671 GCTCATGGATACTGATCTGGACG 60.614 52.174 4.49 0.00 37.61 4.79
3336 3622 5.193663 TCTTGATCAGGCGAAGATAGAAG 57.806 43.478 0.00 0.00 0.00 2.85
3690 3982 9.740239 ATAGTGCAAATAGAAATACAAAGCATG 57.260 29.630 0.00 0.00 0.00 4.06
3750 4045 6.749923 ACTTGTTGGCTGAAGATTTCTATC 57.250 37.500 0.00 0.00 0.00 2.08
3777 4073 6.693315 TTTTCACAGTTTACAGAAAGAGGG 57.307 37.500 0.00 0.00 32.29 4.30
3903 4199 2.419297 CCAGGTAGCTAACAGAAGGCAG 60.419 54.545 12.26 0.00 0.00 4.85
3944 4240 8.079809 CCAACTTTTCAATACGGATTTACACTT 58.920 33.333 0.00 0.00 0.00 3.16
3955 4251 5.047306 ACGGATTTACACTTGTCTGAGATGA 60.047 40.000 0.00 0.00 0.00 2.92
4509 4805 0.174617 CAGACCCTCCGAAGCTCTTC 59.825 60.000 0.00 0.00 36.29 2.87
4543 4839 6.334102 ACCCTACTAATTCTATCAAGAGCG 57.666 41.667 0.00 0.00 31.96 5.03
4651 4947 1.063492 TGGGCGGAGTAGATAAGGTGA 60.063 52.381 0.00 0.00 0.00 4.02
4656 4952 3.321111 GCGGAGTAGATAAGGTGAATGGA 59.679 47.826 0.00 0.00 0.00 3.41
4776 5072 2.906389 TGGTGCTCTCAAGAAGTATGGT 59.094 45.455 0.00 0.00 0.00 3.55
4931 5228 6.483640 ACCATTTCCTTCGAGTATTAATCTGC 59.516 38.462 0.00 0.00 0.00 4.26
5120 5418 3.243301 GCAGATGTTATCCAGGCAACATG 60.243 47.826 18.96 11.30 43.58 3.21
5207 5505 9.403110 GTTGTACAGAGAAGTAACTCGATTTTA 57.597 33.333 0.00 0.00 41.25 1.52
5208 5506 9.970395 TTGTACAGAGAAGTAACTCGATTTTAA 57.030 29.630 0.00 0.00 41.25 1.52
5292 5590 1.141019 CACAGCTCATGGCATTGGC 59.859 57.895 11.94 11.94 44.79 4.52
5334 5632 1.002544 GCAGTGCTCCCAAGAGTAAGT 59.997 52.381 8.18 0.00 42.59 2.24
5348 5646 7.119846 CCCAAGAGTAAGTTCCTCTGTAATTTG 59.880 40.741 0.00 0.00 39.22 2.32
5431 5733 7.784037 AGGCAAAAGAAAATGTGATATGCATA 58.216 30.769 9.27 9.27 33.14 3.14
5433 5735 9.048446 GGCAAAAGAAAATGTGATATGCATATT 57.952 29.630 20.00 3.24 39.64 1.28
5503 5817 3.292460 TGTGGTGGTTTGGTTCTAAAGG 58.708 45.455 0.00 0.00 0.00 3.11
5553 5867 4.202101 GCTCTGATTTTGAGATCTCCGAGA 60.202 45.833 20.03 0.00 33.68 4.04
5571 5885 8.837389 TCTCCGAGATCATTATATTATACACCG 58.163 37.037 0.00 0.00 0.00 4.94
5581 5897 3.764237 ATTATACACCGCGGAATCCTT 57.236 42.857 35.90 13.46 0.00 3.36
5584 5900 0.828022 TACACCGCGGAATCCTTCAT 59.172 50.000 35.90 1.64 0.00 2.57
5788 6107 3.884318 AAAAAGGCCGCCAACCAT 58.116 50.000 13.15 0.00 0.00 3.55
5888 6210 2.579410 TTCCTTCCTTTTTCCTCCCG 57.421 50.000 0.00 0.00 0.00 5.14
5943 6265 2.102252 GTGGTTTGTGCAGGAATTTCCA 59.898 45.455 17.57 0.00 39.61 3.53
6032 6355 3.319122 GCTGAAGCCTTCCTTTTCTTGAA 59.681 43.478 1.21 0.00 32.78 2.69
6052 6375 1.415659 ACTCTCAGCTGCTGTGTTCTT 59.584 47.619 27.24 9.65 32.61 2.52
6055 6378 2.067766 CTCAGCTGCTGTGTTCTTCTC 58.932 52.381 27.24 0.00 32.61 2.87
6093 6422 0.980423 AGTCCTCAACCTCCTGAAGC 59.020 55.000 0.00 0.00 0.00 3.86
6135 6472 6.184789 GGGTTCTCTTCTCTTCTCTTCTCTA 58.815 44.000 0.00 0.00 0.00 2.43
6144 6481 4.787551 TCTTCTCTTCTCTACCCAGCTAG 58.212 47.826 0.00 0.00 0.00 3.42
6145 6482 4.228666 TCTTCTCTTCTCTACCCAGCTAGT 59.771 45.833 0.00 0.00 0.00 2.57
6146 6483 5.429109 TCTTCTCTTCTCTACCCAGCTAGTA 59.571 44.000 0.00 0.00 0.00 1.82
6150 6487 7.813331 TCTCTTCTCTACCCAGCTAGTAATAA 58.187 38.462 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 52 4.426736 AGTAGACTACTCCTCCTACTGC 57.573 50.000 9.45 0.00 39.97 4.40
64 65 4.300345 AGGAGGCAGTAGAGAGTAGACTA 58.700 47.826 0.00 0.00 0.00 2.59
65 66 3.120108 AGGAGGCAGTAGAGAGTAGACT 58.880 50.000 0.00 0.00 0.00 3.24
66 67 3.473625 GAGGAGGCAGTAGAGAGTAGAC 58.526 54.545 0.00 0.00 0.00 2.59
67 68 2.440253 GGAGGAGGCAGTAGAGAGTAGA 59.560 54.545 0.00 0.00 0.00 2.59
68 69 2.441750 AGGAGGAGGCAGTAGAGAGTAG 59.558 54.545 0.00 0.00 0.00 2.57
69 70 2.440253 GAGGAGGAGGCAGTAGAGAGTA 59.560 54.545 0.00 0.00 0.00 2.59
70 71 1.214424 GAGGAGGAGGCAGTAGAGAGT 59.786 57.143 0.00 0.00 0.00 3.24
71 72 1.478654 GGAGGAGGAGGCAGTAGAGAG 60.479 61.905 0.00 0.00 0.00 3.20
72 73 0.553819 GGAGGAGGAGGCAGTAGAGA 59.446 60.000 0.00 0.00 0.00 3.10
73 74 0.469144 GGGAGGAGGAGGCAGTAGAG 60.469 65.000 0.00 0.00 0.00 2.43
114 118 2.205243 GAAAGCAAAGCGGCCAGGAG 62.205 60.000 2.24 0.00 0.00 3.69
115 119 2.203480 AAAGCAAAGCGGCCAGGA 60.203 55.556 2.24 0.00 0.00 3.86
116 120 2.205243 GAGAAAGCAAAGCGGCCAGG 62.205 60.000 2.24 0.00 0.00 4.45
119 123 2.568612 GGAGAAAGCAAAGCGGCC 59.431 61.111 0.00 0.00 0.00 6.13
121 125 1.581447 GTGGGAGAAAGCAAAGCGG 59.419 57.895 0.00 0.00 0.00 5.52
646 768 3.769300 AGAGAAGAGAAGAGAAGGAAGGC 59.231 47.826 0.00 0.00 0.00 4.35
719 857 1.044231 AACCAAACCAAACCCCCGAC 61.044 55.000 0.00 0.00 0.00 4.79
738 876 2.063015 AATCGCCACCACCAGACCAA 62.063 55.000 0.00 0.00 0.00 3.67
864 1029 1.529244 GCCCGGATTGGAGGATTGG 60.529 63.158 0.73 0.00 42.00 3.16
890 1055 2.811317 GCGTGGTCGAGGAAGCTG 60.811 66.667 0.00 0.00 39.71 4.24
891 1056 2.992114 AGCGTGGTCGAGGAAGCT 60.992 61.111 0.00 0.00 39.71 3.74
1445 1671 2.239150 AGAGCAGAGCAAGATTGATGGT 59.761 45.455 0.00 0.00 0.00 3.55
1448 1674 2.483363 CGGAGAGCAGAGCAAGATTGAT 60.483 50.000 0.00 0.00 0.00 2.57
1456 1687 3.071206 GGGACGGAGAGCAGAGCA 61.071 66.667 0.00 0.00 0.00 4.26
1498 1729 6.527057 AGTTACTACTAATCGGCTTCACTT 57.473 37.500 0.00 0.00 31.21 3.16
1500 1731 6.694844 GGTTAGTTACTACTAATCGGCTTCAC 59.305 42.308 0.00 0.00 45.80 3.18
1504 1735 5.301298 CAGGGTTAGTTACTACTAATCGGCT 59.699 44.000 0.00 0.00 45.16 5.52
1516 1748 3.582780 CGGACAGAACAGGGTTAGTTAC 58.417 50.000 0.00 0.00 0.00 2.50
1844 2080 1.354031 TGTGGGATAGGAAAGCAAGCA 59.646 47.619 0.00 0.00 0.00 3.91
1901 2137 2.803451 CTTAGCTAGCGTGAGACTTGG 58.197 52.381 9.55 0.00 0.00 3.61
1919 2155 9.785982 CTAGGCTAAAAAGGATAAATCTAGCTT 57.214 33.333 0.00 4.21 32.70 3.74
1920 2156 8.379331 CCTAGGCTAAAAAGGATAAATCTAGCT 58.621 37.037 0.00 0.00 32.70 3.32
1921 2157 7.119992 GCCTAGGCTAAAAAGGATAAATCTAGC 59.880 40.741 27.17 0.00 38.26 3.42
1922 2158 7.608376 GGCCTAGGCTAAAAAGGATAAATCTAG 59.392 40.741 32.18 0.00 41.60 2.43
2034 2292 4.994852 TCACTGTCAGTGGTAAAATACTGC 59.005 41.667 28.47 0.00 45.94 4.40
2035 2293 7.387673 TCATTCACTGTCAGTGGTAAAATACTG 59.612 37.037 28.47 14.02 45.94 2.74
2036 2294 7.450074 TCATTCACTGTCAGTGGTAAAATACT 58.550 34.615 28.47 3.35 45.94 2.12
2080 2341 5.148651 AGATACTAACAAGTGACCACACC 57.851 43.478 2.78 0.00 46.99 4.16
2104 2365 5.144100 TCCTCATCAGAGTAGAAGAATCCC 58.856 45.833 0.00 0.00 40.40 3.85
2129 2393 7.442969 ACAATGTTAACTCAGAACCAACGATTA 59.557 33.333 7.22 0.00 0.00 1.75
2133 2397 5.418310 ACAATGTTAACTCAGAACCAACG 57.582 39.130 7.22 0.00 0.00 4.10
2138 2402 7.141363 AGCATCAAACAATGTTAACTCAGAAC 58.859 34.615 7.22 0.00 0.00 3.01
2145 2409 8.795786 TTCTGTTAGCATCAAACAATGTTAAC 57.204 30.769 13.40 13.40 45.75 2.01
2179 2443 0.386478 GTCCTGCAGAAAAGCAAGCG 60.386 55.000 17.39 0.00 45.13 4.68
2181 2445 1.229428 TCGTCCTGCAGAAAAGCAAG 58.771 50.000 17.39 0.00 45.13 4.01
2190 2454 2.598619 TTCTCGCGATCGTCCTGCAG 62.599 60.000 17.81 6.78 36.96 4.41
2482 2752 1.792367 TGATGAAGCAACTTGTCGACG 59.208 47.619 11.62 0.00 0.00 5.12
2608 2878 1.565156 CGCCAAAGTTGAGCGTGCTA 61.565 55.000 14.69 0.00 40.47 3.49
2679 2949 2.622436 ACTGCAGAGTCGATAAAAGGC 58.378 47.619 23.35 0.00 0.00 4.35
2689 2959 4.920340 CGAATGTATCCATACTGCAGAGTC 59.080 45.833 23.35 1.96 34.41 3.36
2692 2962 4.556699 CGTCGAATGTATCCATACTGCAGA 60.557 45.833 23.35 4.31 34.41 4.26
2712 2982 1.203994 ACACATGGGCAGTACTACGTC 59.796 52.381 0.00 0.00 0.00 4.34
2774 3044 6.037940 CCTGTTGAAGAGGAATATGTCACATG 59.962 42.308 1.45 0.00 31.48 3.21
3055 3334 3.524541 AGGAACTGCAAACAAGCAAAAG 58.475 40.909 0.00 0.00 45.13 2.27
3126 3405 9.857656 ATTATGGATTAGATCAATCACACACTT 57.142 29.630 15.30 4.12 44.27 3.16
3243 3529 0.798776 ACATAGTCTTGCTGCGTTGC 59.201 50.000 0.00 0.00 0.00 4.17
3336 3622 1.208614 CAAGCTCGAGTTTGCCAGC 59.791 57.895 25.85 5.00 29.96 4.85
3554 3845 3.303881 TGTGGAACTTGATCAGAGACG 57.696 47.619 10.61 0.00 38.04 4.18
3668 3959 7.871973 ACAACATGCTTTGTATTTCTATTTGCA 59.128 29.630 0.08 0.00 37.96 4.08
3883 4179 2.497675 TCTGCCTTCTGTTAGCTACCTG 59.502 50.000 0.00 0.00 0.00 4.00
3903 4199 3.329300 TTGGAAGCTCTGCCAACTC 57.671 52.632 5.22 0.00 39.14 3.01
3944 4240 2.027745 GGAGCAAAGGTCATCTCAGACA 60.028 50.000 0.00 0.00 40.29 3.41
3955 4251 0.685458 GGCATGATGGGAGCAAAGGT 60.685 55.000 0.00 0.00 0.00 3.50
4110 4406 1.815003 AGGCACTTGCTGATGCTTAAC 59.185 47.619 0.38 0.00 41.74 2.01
4509 4805 6.722328 AGAATTAGTAGGGTTCTCCAAAAGG 58.278 40.000 0.00 0.00 38.24 3.11
4527 4823 9.778741 ATATTTGAACCGCTCTTGATAGAATTA 57.221 29.630 0.00 0.00 0.00 1.40
4543 4839 4.894784 TGCTCCCTCGATATATTTGAACC 58.105 43.478 0.00 0.00 0.00 3.62
4614 4910 0.608035 CCAAAGCCCGCCTTAGTGAA 60.608 55.000 0.00 0.00 32.20 3.18
4651 4947 3.758554 CCAACGACTCCATTCTTTCCATT 59.241 43.478 0.00 0.00 0.00 3.16
4656 4952 2.270352 TGCCAACGACTCCATTCTTT 57.730 45.000 0.00 0.00 0.00 2.52
4776 5072 3.882288 TGTCTGCACAAATTACTTCTGCA 59.118 39.130 0.00 0.00 36.46 4.41
5120 5418 2.291465 TCACATTTCAAGCACTGCTCAC 59.709 45.455 3.40 0.00 38.25 3.51
5207 5505 4.889409 ACTGAACATGGTCATGACTTTGTT 59.111 37.500 29.98 29.98 41.20 2.83
5208 5506 4.464008 ACTGAACATGGTCATGACTTTGT 58.536 39.130 24.50 22.50 41.20 2.83
5255 5553 0.103208 GTGGCGACATCCTCCACTAG 59.897 60.000 0.00 0.00 45.04 2.57
5292 5590 0.512952 CTTCAACAAACTCCTCCGCG 59.487 55.000 0.00 0.00 0.00 6.46
5334 5632 4.601857 AGGAGGGAACAAATTACAGAGGAA 59.398 41.667 0.00 0.00 0.00 3.36
5348 5646 2.050144 TGGATGCAGATAGGAGGGAAC 58.950 52.381 0.00 0.00 0.00 3.62
5392 5693 0.108329 TTGCCTACCAGCGCTAGTTC 60.108 55.000 15.04 4.81 34.65 3.01
5553 5867 7.656137 GGATTCCGCGGTGTATAATATAATGAT 59.344 37.037 27.15 0.00 0.00 2.45
5567 5881 0.744414 ACATGAAGGATTCCGCGGTG 60.744 55.000 27.15 15.08 46.93 4.94
5571 5885 4.130118 ACATTAGACATGAAGGATTCCGC 58.870 43.478 0.00 0.00 46.93 5.54
5728 6047 0.938637 TTGCTGAACAAAATGCCGCG 60.939 50.000 0.00 0.00 34.56 6.46
5888 6210 3.655615 TGTACACCCATACAATTCCCC 57.344 47.619 0.00 0.00 32.07 4.81
5974 6297 1.488812 ACTTACAGCTTGGGACACACA 59.511 47.619 0.00 0.00 39.29 3.72
6032 6355 1.047002 AGAACACAGCAGCTGAGAGT 58.953 50.000 29.70 19.57 35.18 3.24
6052 6375 3.272285 TCTGATAGGGACAGGAAAGGAGA 59.728 47.826 0.00 0.00 36.22 3.71
6055 6378 3.379452 ACTCTGATAGGGACAGGAAAGG 58.621 50.000 0.00 0.00 36.22 3.11
6093 6422 0.607489 CCAACCAACAGCAGGAGAGG 60.607 60.000 0.00 0.00 0.00 3.69
6135 6472 5.110814 TGCATGTTTATTACTAGCTGGGT 57.889 39.130 0.85 0.46 0.00 4.51
6145 6482 9.241919 CCACCATTAGGATATGCATGTTTATTA 57.758 33.333 10.16 0.00 38.69 0.98
6146 6483 7.729881 ACCACCATTAGGATATGCATGTTTATT 59.270 33.333 10.16 0.00 38.69 1.40
6150 6487 4.828939 CACCACCATTAGGATATGCATGTT 59.171 41.667 10.16 0.00 38.69 2.71
6165 6502 0.752054 CACAAAAGCCACACCACCAT 59.248 50.000 0.00 0.00 0.00 3.55


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

AutoCloner maintained by Alex Coulton.