Multiple sequence alignment - TraesCS5B01G156000

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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 TraesCS5B01G156000 chr5B 100.000 4203 0 0 1 4203 288179327 288175125 0.000000e+00 7762.0
1 TraesCS5B01G156000 chr5D 95.976 3504 77 26 721 4203 254586185 254589645 0.000000e+00 5631.0
2 TraesCS5B01G156000 chr5D 91.994 637 16 14 79 702 254585582 254586196 0.000000e+00 861.0
3 TraesCS5B01G156000 chr5A 91.517 3678 167 76 210 3822 337940320 337943917 0.000000e+00 4929.0
4 TraesCS5B01G156000 chr5A 94.595 37 2 0 1 37 501420259 501420295 1.630000e-04 58.4
5 TraesCS5B01G156000 chr4D 78.026 537 92 23 1041 1556 119806273 119805742 8.770000e-82 315.0
6 TraesCS5B01G156000 chr4D 79.048 210 44 0 2897 3106 119805511 119805302 1.220000e-30 145.0
7 TraesCS5B01G156000 chr4A 77.574 544 91 25 1034 1556 450765569 450765036 2.460000e-77 300.0
8 TraesCS5B01G156000 chr4A 80.000 210 42 0 2897 3106 450764805 450764596 5.630000e-34 156.0
9 TraesCS5B01G156000 chr4A 94.737 38 1 1 2343 2380 163871684 163871720 1.630000e-04 58.4
10 TraesCS5B01G156000 chr4B 82.716 324 53 3 1234 1556 182260766 182260445 6.880000e-73 285.0
11 TraesCS5B01G156000 chrUn 80.838 167 28 3 3469 3633 21384229 21384393 1.230000e-25 128.0
12 TraesCS5B01G156000 chr2B 87.500 96 12 0 1456 1551 560459351 560459256 1.240000e-20 111.0
13 TraesCS5B01G156000 chr2D 86.458 96 13 0 1456 1551 478119049 478118954 5.750000e-19 106.0
14 TraesCS5B01G156000 chr2A 86.458 96 13 0 1456 1551 621268652 621268557 5.750000e-19 106.0
15 TraesCS5B01G156000 chr7A 89.583 48 3 1 1 46 406061858 406061905 4.540000e-05 60.2
16 TraesCS5B01G156000 chr6A 89.583 48 3 1 1 46 593553364 593553411 4.540000e-05 60.2
17 TraesCS5B01G156000 chr3A 94.737 38 2 0 1 38 483924974 483924937 4.540000e-05 60.2


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 TraesCS5B01G156000 chr5B 288175125 288179327 4202 True 7762 7762 100.000 1 4203 1 chr5B.!!$R1 4202
1 TraesCS5B01G156000 chr5D 254585582 254589645 4063 False 3246 5631 93.985 79 4203 2 chr5D.!!$F1 4124
2 TraesCS5B01G156000 chr5A 337940320 337943917 3597 False 4929 4929 91.517 210 3822 1 chr5A.!!$F1 3612
3 TraesCS5B01G156000 chr4D 119805302 119806273 971 True 230 315 78.537 1041 3106 2 chr4D.!!$R1 2065
4 TraesCS5B01G156000 chr4A 450764596 450765569 973 True 228 300 78.787 1034 3106 2 chr4A.!!$R1 2072

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
55 56 0.033642 GGCTAGGAGCGTGGGAATAC 59.966 60.0 0.0 0.0 43.62 1.89 F
1205 1242 0.617935 TGGCGAATGATCCAAGACCA 59.382 50.0 0.0 0.0 0.00 4.02 F
1869 1941 0.317103 CTCTCGCCCGATAACGACAG 60.317 60.0 0.0 0.0 42.66 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1850 1922 0.317103 CTGTCGTTATCGGGCGAGAG 60.317 60.000 0.00 0.0 40.92 3.20 R
2890 3007 1.133025 GGCAATGACACCTGCATACAC 59.867 52.381 12.18 0.0 40.46 2.90 R
3678 3797 0.929244 CCCACTCCATCCCAATCCTT 59.071 55.000 0.00 0.0 0.00 3.36 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
52 53 3.081409 GGGCTAGGAGCGTGGGAA 61.081 66.667 0.00 0.00 43.62 3.97
53 54 2.444256 GGGCTAGGAGCGTGGGAAT 61.444 63.158 0.00 0.00 43.62 3.01
54 55 1.119574 GGGCTAGGAGCGTGGGAATA 61.120 60.000 0.00 0.00 43.62 1.75
55 56 0.033642 GGCTAGGAGCGTGGGAATAC 59.966 60.000 0.00 0.00 43.62 1.89
56 57 1.041437 GCTAGGAGCGTGGGAATACT 58.959 55.000 0.00 0.00 0.00 2.12
57 58 1.000052 GCTAGGAGCGTGGGAATACTC 60.000 57.143 0.00 0.00 0.00 2.59
58 59 2.307768 CTAGGAGCGTGGGAATACTCA 58.692 52.381 0.00 0.00 0.00 3.41
59 60 1.568504 AGGAGCGTGGGAATACTCAA 58.431 50.000 0.00 0.00 0.00 3.02
60 61 1.906574 AGGAGCGTGGGAATACTCAAA 59.093 47.619 0.00 0.00 0.00 2.69
61 62 2.093447 AGGAGCGTGGGAATACTCAAAG 60.093 50.000 0.00 0.00 0.00 2.77
62 63 2.280628 GAGCGTGGGAATACTCAAAGG 58.719 52.381 0.00 0.00 0.00 3.11
63 64 1.906574 AGCGTGGGAATACTCAAAGGA 59.093 47.619 0.00 0.00 0.00 3.36
64 65 2.304761 AGCGTGGGAATACTCAAAGGAA 59.695 45.455 0.00 0.00 0.00 3.36
65 66 3.054361 AGCGTGGGAATACTCAAAGGAAT 60.054 43.478 0.00 0.00 0.00 3.01
66 67 3.694566 GCGTGGGAATACTCAAAGGAATT 59.305 43.478 0.00 0.00 0.00 2.17
67 68 4.157840 GCGTGGGAATACTCAAAGGAATTT 59.842 41.667 0.00 0.00 0.00 1.82
68 69 5.336451 GCGTGGGAATACTCAAAGGAATTTT 60.336 40.000 0.00 0.00 0.00 1.82
69 70 6.322491 CGTGGGAATACTCAAAGGAATTTTC 58.678 40.000 0.00 0.00 0.00 2.29
70 71 6.072175 CGTGGGAATACTCAAAGGAATTTTCA 60.072 38.462 0.00 0.00 0.00 2.69
71 72 7.523052 CGTGGGAATACTCAAAGGAATTTTCAA 60.523 37.037 0.00 0.00 0.00 2.69
72 73 7.598869 GTGGGAATACTCAAAGGAATTTTCAAC 59.401 37.037 0.00 0.00 0.00 3.18
73 74 7.097192 GGGAATACTCAAAGGAATTTTCAACC 58.903 38.462 0.00 0.00 0.00 3.77
74 75 7.039011 GGGAATACTCAAAGGAATTTTCAACCT 60.039 37.037 0.00 0.00 35.36 3.50
75 76 8.367911 GGAATACTCAAAGGAATTTTCAACCTT 58.632 33.333 0.00 0.00 44.53 3.50
96 97 8.570068 ACCTTATTGGATTAATTGTTACACGT 57.430 30.769 0.00 0.00 39.71 4.49
146 147 2.029838 ATTTCCATGGAGCTCGTGTC 57.970 50.000 15.53 0.00 0.00 3.67
164 165 4.619973 GTGTCATCCAAACAAAATGCAGA 58.380 39.130 0.00 0.00 0.00 4.26
179 180 3.842732 TGCAGATTCATGTTGCAAGAG 57.157 42.857 0.00 0.00 44.13 2.85
180 181 3.414269 TGCAGATTCATGTTGCAAGAGA 58.586 40.909 0.00 0.00 44.13 3.10
181 182 3.439129 TGCAGATTCATGTTGCAAGAGAG 59.561 43.478 0.00 0.00 44.13 3.20
182 183 3.688185 GCAGATTCATGTTGCAAGAGAGA 59.312 43.478 0.00 0.00 37.75 3.10
183 184 4.201832 GCAGATTCATGTTGCAAGAGAGAG 60.202 45.833 0.00 0.00 37.75 3.20
184 185 5.176592 CAGATTCATGTTGCAAGAGAGAGA 58.823 41.667 0.00 0.00 0.00 3.10
185 186 5.292345 CAGATTCATGTTGCAAGAGAGAGAG 59.708 44.000 0.00 0.00 0.00 3.20
186 187 4.879197 TTCATGTTGCAAGAGAGAGAGA 57.121 40.909 0.00 0.00 0.00 3.10
187 188 4.453177 TCATGTTGCAAGAGAGAGAGAG 57.547 45.455 0.00 0.00 0.00 3.20
188 189 4.085009 TCATGTTGCAAGAGAGAGAGAGA 58.915 43.478 0.00 0.00 0.00 3.10
189 190 4.158209 TCATGTTGCAAGAGAGAGAGAGAG 59.842 45.833 0.00 0.00 0.00 3.20
190 191 3.760738 TGTTGCAAGAGAGAGAGAGAGA 58.239 45.455 0.00 0.00 0.00 3.10
191 192 3.758023 TGTTGCAAGAGAGAGAGAGAGAG 59.242 47.826 0.00 0.00 0.00 3.20
192 193 3.998913 TGCAAGAGAGAGAGAGAGAGA 57.001 47.619 0.00 0.00 0.00 3.10
193 194 3.877559 TGCAAGAGAGAGAGAGAGAGAG 58.122 50.000 0.00 0.00 0.00 3.20
194 195 3.519107 TGCAAGAGAGAGAGAGAGAGAGA 59.481 47.826 0.00 0.00 0.00 3.10
195 196 4.125703 GCAAGAGAGAGAGAGAGAGAGAG 58.874 52.174 0.00 0.00 0.00 3.20
199 200 6.232581 AGAGAGAGAGAGAGAGAGAGAAAG 57.767 45.833 0.00 0.00 0.00 2.62
203 204 7.108847 AGAGAGAGAGAGAGAGAGAAAGAAAG 58.891 42.308 0.00 0.00 0.00 2.62
205 206 7.108847 AGAGAGAGAGAGAGAGAAAGAAAGAG 58.891 42.308 0.00 0.00 0.00 2.85
208 209 6.183347 AGAGAGAGAGAGAAAGAAAGAGAGG 58.817 44.000 0.00 0.00 0.00 3.69
356 363 5.721232 ACACACTTAAATCCTCGGAAGTAG 58.279 41.667 0.00 0.00 31.05 2.57
357 364 5.109903 CACACTTAAATCCTCGGAAGTAGG 58.890 45.833 0.00 0.00 31.05 3.18
358 365 5.021458 ACACTTAAATCCTCGGAAGTAGGA 58.979 41.667 0.00 0.00 46.96 2.94
359 366 5.127356 ACACTTAAATCCTCGGAAGTAGGAG 59.873 44.000 0.00 0.00 46.14 3.69
360 367 4.099727 ACTTAAATCCTCGGAAGTAGGAGC 59.900 45.833 0.00 0.00 46.14 4.70
448 459 2.115343 AGCTTTTGGGTAGCTGTAGC 57.885 50.000 0.00 0.00 46.71 3.58
637 649 2.730672 GACGTTTCAGCGCTCGCAT 61.731 57.895 7.13 0.00 44.88 4.73
690 715 5.419788 TGATTCAAGATTTAGCAGCCATTGT 59.580 36.000 0.00 0.00 0.00 2.71
697 722 5.767168 AGATTTAGCAGCCATTGTATTCTCC 59.233 40.000 0.00 0.00 0.00 3.71
699 724 1.210478 AGCAGCCATTGTATTCTCCGT 59.790 47.619 0.00 0.00 0.00 4.69
700 725 2.434336 AGCAGCCATTGTATTCTCCGTA 59.566 45.455 0.00 0.00 0.00 4.02
701 726 3.118408 AGCAGCCATTGTATTCTCCGTAA 60.118 43.478 0.00 0.00 0.00 3.18
702 727 3.815401 GCAGCCATTGTATTCTCCGTAAT 59.185 43.478 0.00 0.00 0.00 1.89
703 728 4.994852 GCAGCCATTGTATTCTCCGTAATA 59.005 41.667 0.00 0.00 0.00 0.98
704 729 5.107065 GCAGCCATTGTATTCTCCGTAATAC 60.107 44.000 0.00 0.00 40.98 1.89
707 732 7.328737 CAGCCATTGTATTCTCCGTAATACTAC 59.671 40.741 11.50 0.00 41.12 2.73
871 900 1.826054 CTGATCCTCCTCGCCTCGT 60.826 63.158 0.00 0.00 0.00 4.18
887 916 4.491328 GTTCGCTCGCTCGCTTGC 62.491 66.667 0.00 0.00 0.00 4.01
921 950 5.624900 TCGCAAAAATTCAACATTTCTCTCG 59.375 36.000 0.00 0.00 0.00 4.04
934 963 7.454260 ACATTTCTCTCGGCTCTTTAATTTT 57.546 32.000 0.00 0.00 0.00 1.82
935 964 7.530863 ACATTTCTCTCGGCTCTTTAATTTTC 58.469 34.615 0.00 0.00 0.00 2.29
936 965 6.496338 TTTCTCTCGGCTCTTTAATTTTCC 57.504 37.500 0.00 0.00 0.00 3.13
969 998 1.469335 TTCCTTCCTGCGACCGAGTT 61.469 55.000 0.00 0.00 0.00 3.01
1201 1238 3.188048 GCTCTAATGGCGAATGATCCAAG 59.812 47.826 0.00 0.00 35.75 3.61
1203 1240 4.380531 TCTAATGGCGAATGATCCAAGAC 58.619 43.478 0.00 0.00 35.75 3.01
1204 1241 1.972872 ATGGCGAATGATCCAAGACC 58.027 50.000 0.00 0.00 35.75 3.85
1205 1242 0.617935 TGGCGAATGATCCAAGACCA 59.382 50.000 0.00 0.00 0.00 4.02
1206 1243 1.004161 TGGCGAATGATCCAAGACCAA 59.996 47.619 0.00 0.00 0.00 3.67
1207 1244 1.401905 GGCGAATGATCCAAGACCAAC 59.598 52.381 0.00 0.00 0.00 3.77
1208 1245 1.401905 GCGAATGATCCAAGACCAACC 59.598 52.381 0.00 0.00 0.00 3.77
1212 1249 2.286365 TGATCCAAGACCAACCAACC 57.714 50.000 0.00 0.00 0.00 3.77
1380 1437 0.922738 TCCCCTCCTTCGACCTCCTA 60.923 60.000 0.00 0.00 0.00 2.94
1651 1714 2.009108 CTACTAGTACGCGGCGACA 58.991 57.895 30.94 13.44 0.00 4.35
1678 1741 3.611433 GGAAACGAGATGCATGCAC 57.389 52.632 25.37 16.77 0.00 4.57
1869 1941 0.317103 CTCTCGCCCGATAACGACAG 60.317 60.000 0.00 0.00 42.66 3.51
1870 1942 1.028330 TCTCGCCCGATAACGACAGT 61.028 55.000 0.00 0.00 42.66 3.55
1871 1943 0.659427 CTCGCCCGATAACGACAGTA 59.341 55.000 0.00 0.00 42.66 2.74
1872 1944 0.659427 TCGCCCGATAACGACAGTAG 59.341 55.000 0.00 0.00 42.66 2.57
1874 1946 1.599071 CGCCCGATAACGACAGTAGTA 59.401 52.381 0.00 0.00 42.66 1.82
1875 1947 2.225019 CGCCCGATAACGACAGTAGTAT 59.775 50.000 0.00 0.00 42.66 2.12
1876 1948 3.433274 CGCCCGATAACGACAGTAGTATA 59.567 47.826 0.00 0.00 42.66 1.47
1877 1949 4.093998 CGCCCGATAACGACAGTAGTATAT 59.906 45.833 0.00 0.00 42.66 0.86
1878 1950 5.391310 CGCCCGATAACGACAGTAGTATATT 60.391 44.000 0.00 0.00 42.66 1.28
1879 1951 6.026513 GCCCGATAACGACAGTAGTATATTC 58.973 44.000 0.00 0.00 42.66 1.75
1880 1952 6.128063 GCCCGATAACGACAGTAGTATATTCT 60.128 42.308 0.00 0.00 42.66 2.40
1881 1953 7.065085 GCCCGATAACGACAGTAGTATATTCTA 59.935 40.741 0.00 0.00 42.66 2.10
1882 1954 8.602328 CCCGATAACGACAGTAGTATATTCTAG 58.398 40.741 0.00 0.00 42.66 2.43
1883 1955 9.149225 CCGATAACGACAGTAGTATATTCTAGT 57.851 37.037 0.00 0.00 42.66 2.57
1922 1994 9.469807 AGTATCTATCTTTGTTGATCGATGAAC 57.530 33.333 19.29 19.29 33.10 3.18
2227 2326 3.814005 ACAACGTACTCTCAAAGGTGT 57.186 42.857 0.00 0.00 0.00 4.16
2442 2541 3.808728 CCGCATATAGTATTCCATGGGG 58.191 50.000 13.02 11.18 42.70 4.96
2443 2542 3.199946 CCGCATATAGTATTCCATGGGGT 59.800 47.826 13.02 3.29 43.10 4.95
2444 2543 4.407621 CCGCATATAGTATTCCATGGGGTA 59.592 45.833 13.02 2.21 43.10 3.69
2445 2544 5.071788 CCGCATATAGTATTCCATGGGGTAT 59.928 44.000 13.02 6.05 43.10 2.73
2466 2565 9.696572 GGGTATGTATATATCAACTGGAGTAGA 57.303 37.037 0.00 0.00 0.00 2.59
2563 2666 3.062763 CCGCATCTACACATCTCAATCC 58.937 50.000 0.00 0.00 0.00 3.01
2569 2672 5.798125 TCTACACATCTCAATCCATCTCC 57.202 43.478 0.00 0.00 0.00 3.71
2748 2865 5.574443 GGAGCTTGATGACTTATTTTGTTGC 59.426 40.000 0.00 0.00 0.00 4.17
2890 3007 1.804748 CTGATGGATGGATCGTGCATG 59.195 52.381 8.16 0.00 31.82 4.06
2911 3028 1.271817 TGTATGCAGGTGTCATTGCCA 60.272 47.619 9.10 0.00 39.54 4.92
3123 3240 5.252586 AGATCATCCCCGAAATCATCATT 57.747 39.130 0.00 0.00 0.00 2.57
3299 3416 1.856265 GCTGGCTACAAGTGTGGTGC 61.856 60.000 0.00 0.00 0.00 5.01
3481 3600 2.588877 CCCCTGCGTTGCTATCGG 60.589 66.667 0.00 0.00 0.00 4.18
3565 3684 1.339055 TGTGGGGAAGAAGCTCAATCG 60.339 52.381 0.00 0.00 0.00 3.34
3678 3797 7.836685 AGTCTACCAGTTTCAAGATAGATGAGA 59.163 37.037 0.00 0.00 0.00 3.27
3699 3818 1.538666 GATTGGGATGGAGTGGGGG 59.461 63.158 0.00 0.00 0.00 5.40
3700 3819 1.230616 ATTGGGATGGAGTGGGGGT 60.231 57.895 0.00 0.00 0.00 4.95
3701 3820 0.047176 ATTGGGATGGAGTGGGGGTA 59.953 55.000 0.00 0.00 0.00 3.69
3702 3821 0.917333 TTGGGATGGAGTGGGGGTAC 60.917 60.000 0.00 0.00 0.00 3.34
3797 3916 0.175760 GGCGTTGAGGAGCAGTCATA 59.824 55.000 0.00 0.00 34.54 2.15
3925 4044 4.012374 CCCAAACTATATATGCAGCCTGG 58.988 47.826 0.00 0.00 0.00 4.45
3948 4067 4.370917 CACAAACAGTTCCAAAATCCCAG 58.629 43.478 0.00 0.00 0.00 4.45
3969 4088 5.648092 CCAGTAGGGATTTGACTACTTTTGG 59.352 44.000 0.00 0.00 45.57 3.28
3983 4102 8.836413 TGACTACTTTTGGTTTTCATCAACTAG 58.164 33.333 0.00 0.00 0.00 2.57
4046 4165 2.055633 TCGTCCTTGCATCCCGCTA 61.056 57.895 0.00 0.00 43.06 4.26
4058 4177 3.257393 CATCCCGCTAATGCTATGTCTC 58.743 50.000 0.00 0.00 36.97 3.36
4068 4187 1.202417 TGCTATGTCTCGCTTACTGCC 60.202 52.381 0.00 0.00 38.78 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 1.119574 TATTCCCACGCTCCTAGCCC 61.120 60.000 0.00 0.00 38.18 5.19
36 37 0.033642 GTATTCCCACGCTCCTAGCC 59.966 60.000 0.00 0.00 38.18 3.93
37 38 1.000052 GAGTATTCCCACGCTCCTAGC 60.000 57.143 0.00 0.00 38.02 3.42
38 39 2.307768 TGAGTATTCCCACGCTCCTAG 58.692 52.381 0.00 0.00 0.00 3.02
39 40 2.447408 TGAGTATTCCCACGCTCCTA 57.553 50.000 0.00 0.00 0.00 2.94
40 41 1.568504 TTGAGTATTCCCACGCTCCT 58.431 50.000 0.00 0.00 0.00 3.69
41 42 2.280628 CTTTGAGTATTCCCACGCTCC 58.719 52.381 0.00 0.00 0.00 4.70
42 43 2.093658 TCCTTTGAGTATTCCCACGCTC 60.094 50.000 0.00 0.00 0.00 5.03
43 44 1.906574 TCCTTTGAGTATTCCCACGCT 59.093 47.619 0.00 0.00 0.00 5.07
44 45 2.396590 TCCTTTGAGTATTCCCACGC 57.603 50.000 0.00 0.00 0.00 5.34
45 46 5.897377 AAATTCCTTTGAGTATTCCCACG 57.103 39.130 0.00 0.00 0.00 4.94
46 47 7.227049 TGAAAATTCCTTTGAGTATTCCCAC 57.773 36.000 0.00 0.00 0.00 4.61
47 48 7.256154 GGTTGAAAATTCCTTTGAGTATTCCCA 60.256 37.037 0.00 0.00 0.00 4.37
48 49 7.039011 AGGTTGAAAATTCCTTTGAGTATTCCC 60.039 37.037 0.00 0.00 0.00 3.97
49 50 7.896811 AGGTTGAAAATTCCTTTGAGTATTCC 58.103 34.615 0.00 0.00 0.00 3.01
54 55 8.150296 CCAATAAGGTTGAAAATTCCTTTGAGT 58.850 33.333 1.09 0.00 41.17 3.41
55 56 8.367156 TCCAATAAGGTTGAAAATTCCTTTGAG 58.633 33.333 1.09 0.00 41.17 3.02
56 57 8.256356 TCCAATAAGGTTGAAAATTCCTTTGA 57.744 30.769 1.09 0.00 41.17 2.69
57 58 9.506018 AATCCAATAAGGTTGAAAATTCCTTTG 57.494 29.630 1.09 0.00 41.17 2.77
69 70 9.284594 CGTGTAACAATTAATCCAATAAGGTTG 57.715 33.333 0.00 0.00 35.76 3.77
70 71 9.016438 ACGTGTAACAATTAATCCAATAAGGTT 57.984 29.630 0.00 0.00 35.76 3.50
71 72 8.570068 ACGTGTAACAATTAATCCAATAAGGT 57.430 30.769 0.00 0.00 35.76 3.50
72 73 9.849166 AAACGTGTAACAATTAATCCAATAAGG 57.151 29.630 0.00 0.00 35.74 2.69
119 120 1.672441 GCTCCATGGAAATTTGCGCAA 60.672 47.619 21.02 21.02 0.00 4.85
146 147 6.370442 ACATGAATCTGCATTTTGTTTGGATG 59.630 34.615 0.00 0.00 0.00 3.51
164 165 5.187381 TCTCTCTCTCTCTTGCAACATGAAT 59.813 40.000 0.00 0.00 0.00 2.57
178 179 6.627087 TTCTTTCTCTCTCTCTCTCTCTCT 57.373 41.667 0.00 0.00 0.00 3.10
179 180 7.106239 TCTTTCTTTCTCTCTCTCTCTCTCTC 58.894 42.308 0.00 0.00 0.00 3.20
180 181 7.020827 TCTTTCTTTCTCTCTCTCTCTCTCT 57.979 40.000 0.00 0.00 0.00 3.10
181 182 7.106239 TCTCTTTCTTTCTCTCTCTCTCTCTC 58.894 42.308 0.00 0.00 0.00 3.20
182 183 7.020827 TCTCTTTCTTTCTCTCTCTCTCTCT 57.979 40.000 0.00 0.00 0.00 3.10
183 184 6.317391 CCTCTCTTTCTTTCTCTCTCTCTCTC 59.683 46.154 0.00 0.00 0.00 3.20
184 185 6.183347 CCTCTCTTTCTTTCTCTCTCTCTCT 58.817 44.000 0.00 0.00 0.00 3.10
185 186 5.358160 CCCTCTCTTTCTTTCTCTCTCTCTC 59.642 48.000 0.00 0.00 0.00 3.20
186 187 5.015178 TCCCTCTCTTTCTTTCTCTCTCTCT 59.985 44.000 0.00 0.00 0.00 3.10
187 188 5.261216 TCCCTCTCTTTCTTTCTCTCTCTC 58.739 45.833 0.00 0.00 0.00 3.20
188 189 5.269554 TCCCTCTCTTTCTTTCTCTCTCT 57.730 43.478 0.00 0.00 0.00 3.10
189 190 5.337250 GGTTCCCTCTCTTTCTTTCTCTCTC 60.337 48.000 0.00 0.00 0.00 3.20
190 191 4.530553 GGTTCCCTCTCTTTCTTTCTCTCT 59.469 45.833 0.00 0.00 0.00 3.10
191 192 4.323180 GGGTTCCCTCTCTTTCTTTCTCTC 60.323 50.000 0.00 0.00 0.00 3.20
192 193 3.585289 GGGTTCCCTCTCTTTCTTTCTCT 59.415 47.826 0.00 0.00 0.00 3.10
193 194 3.328050 TGGGTTCCCTCTCTTTCTTTCTC 59.672 47.826 9.43 0.00 0.00 2.87
194 195 3.327439 TGGGTTCCCTCTCTTTCTTTCT 58.673 45.455 9.43 0.00 0.00 2.52
195 196 3.790089 TGGGTTCCCTCTCTTTCTTTC 57.210 47.619 9.43 0.00 0.00 2.62
199 200 3.223674 TGTTTGGGTTCCCTCTCTTTC 57.776 47.619 9.43 0.00 0.00 2.62
203 204 4.955811 AATTTTGTTTGGGTTCCCTCTC 57.044 40.909 9.43 0.60 0.00 3.20
205 206 7.601130 GTGTATAAATTTTGTTTGGGTTCCCTC 59.399 37.037 9.43 1.25 0.00 4.30
208 209 8.664211 TTGTGTATAAATTTTGTTTGGGTTCC 57.336 30.769 0.00 0.00 0.00 3.62
356 363 1.956477 ACAGTCACAACCAAATGCTCC 59.044 47.619 0.00 0.00 0.00 4.70
357 364 4.829064 TTACAGTCACAACCAAATGCTC 57.171 40.909 0.00 0.00 0.00 4.26
358 365 5.789643 ATTTACAGTCACAACCAAATGCT 57.210 34.783 0.00 0.00 0.00 3.79
359 366 7.145323 ACTAATTTACAGTCACAACCAAATGC 58.855 34.615 0.00 0.00 0.00 3.56
360 367 9.528018 AAACTAATTTACAGTCACAACCAAATG 57.472 29.630 0.00 0.00 0.00 2.32
637 649 9.093970 CAATCACTACTCCGTAATGTTAATTGA 57.906 33.333 0.00 0.00 0.00 2.57
771 799 9.375974 AGTATTACTCCACCAGTATTATAGCAA 57.624 33.333 0.00 0.00 37.44 3.91
772 800 8.951614 AGTATTACTCCACCAGTATTATAGCA 57.048 34.615 0.00 0.00 37.44 3.49
815 844 2.233922 ACAGCTATATATGTGGACGCCC 59.766 50.000 0.00 0.00 0.00 6.13
887 916 2.969443 ATTTTTGCGAGACAGGAACG 57.031 45.000 0.00 0.00 0.00 3.95
893 922 6.272318 AGAAATGTTGAATTTTTGCGAGACA 58.728 32.000 0.00 0.00 0.00 3.41
921 950 2.416836 GCCACGGGAAAATTAAAGAGCC 60.417 50.000 0.00 0.00 0.00 4.70
969 998 1.166129 CTTCTTCTCCGACGACTGGA 58.834 55.000 0.00 0.00 0.00 3.86
1201 1238 2.657143 TGGTTAGTTGGTTGGTTGGTC 58.343 47.619 0.00 0.00 0.00 4.02
1203 1240 2.101750 GGTTGGTTAGTTGGTTGGTTGG 59.898 50.000 0.00 0.00 0.00 3.77
1204 1241 2.761208 TGGTTGGTTAGTTGGTTGGTTG 59.239 45.455 0.00 0.00 0.00 3.77
1205 1242 3.103080 TGGTTGGTTAGTTGGTTGGTT 57.897 42.857 0.00 0.00 0.00 3.67
1206 1243 2.761767 GTTGGTTGGTTAGTTGGTTGGT 59.238 45.455 0.00 0.00 0.00 3.67
1207 1244 2.761208 TGTTGGTTGGTTAGTTGGTTGG 59.239 45.455 0.00 0.00 0.00 3.77
1208 1245 4.367450 CATGTTGGTTGGTTAGTTGGTTG 58.633 43.478 0.00 0.00 0.00 3.77
1212 1249 2.034053 ACGCATGTTGGTTGGTTAGTTG 59.966 45.455 0.00 0.00 0.00 3.16
1305 1362 1.893062 GTAGTCCACCCCGTACACC 59.107 63.158 0.00 0.00 0.00 4.16
1591 1651 4.782156 AGTCTGGACTCTGGAAGATGATTT 59.218 41.667 0.00 0.00 45.62 2.17
1651 1714 2.798680 CATCTCGTTTCCGTCTCGATT 58.201 47.619 0.00 0.00 33.26 3.34
1675 1738 3.367051 ATTGATCGTGCGTGCGTGC 62.367 57.895 1.25 0.00 0.00 5.34
1676 1739 1.296145 GATTGATCGTGCGTGCGTG 60.296 57.895 1.25 0.00 0.00 5.34
1677 1740 2.452813 GGATTGATCGTGCGTGCGT 61.453 57.895 1.25 0.00 0.00 5.24
1678 1741 2.321060 GGATTGATCGTGCGTGCG 59.679 61.111 0.00 0.00 0.00 5.34
1782 1853 8.728088 ATTAAACTAAACAAGTGCGAAATCAG 57.272 30.769 0.00 0.00 38.88 2.90
1850 1922 0.317103 CTGTCGTTATCGGGCGAGAG 60.317 60.000 0.00 0.00 40.92 3.20
1922 1994 7.670009 TGGTCCAAATTAATGAAAGCAAATG 57.330 32.000 0.00 0.00 0.00 2.32
1954 2026 3.327464 ACCCCAGCCTTAGTTTTACGTTA 59.673 43.478 0.00 0.00 0.00 3.18
1955 2027 2.107031 ACCCCAGCCTTAGTTTTACGTT 59.893 45.455 0.00 0.00 0.00 3.99
2249 2348 5.990408 AGAAGTTAGAACATGTTCGCAAAG 58.010 37.500 28.18 0.00 43.97 2.77
2354 2453 9.077885 GCTCCCTCCATTCACAAATATAAAATA 57.922 33.333 0.00 0.00 0.00 1.40
2445 2544 9.975218 TGCTATCTACTCCAGTTGATATATACA 57.025 33.333 10.17 5.74 40.22 2.29
2563 2666 8.743085 TGATCTTAATTGGAGAAAAGGAGATG 57.257 34.615 0.00 0.00 0.00 2.90
2748 2865 6.677781 ACAACAATTATTATGAGACCACGG 57.322 37.500 0.00 0.00 0.00 4.94
2890 3007 1.133025 GGCAATGACACCTGCATACAC 59.867 52.381 12.18 0.00 40.46 2.90
2911 3028 1.137086 CCTCCGTGAACGATCAGGAAT 59.863 52.381 15.87 0.00 42.66 3.01
3403 3520 8.816640 ATTTTGTAAAACTGAAATAGCACTGG 57.183 30.769 0.00 0.00 0.00 4.00
3565 3684 1.102978 AAGTGTGGTGTTGGTTGCTC 58.897 50.000 0.00 0.00 0.00 4.26
3678 3797 0.929244 CCCACTCCATCCCAATCCTT 59.071 55.000 0.00 0.00 0.00 3.36
3699 3818 4.694037 GGTGGTGATTGGTGAGTTTAGTAC 59.306 45.833 0.00 0.00 0.00 2.73
3700 3819 4.348461 TGGTGGTGATTGGTGAGTTTAGTA 59.652 41.667 0.00 0.00 0.00 1.82
3701 3820 3.137544 TGGTGGTGATTGGTGAGTTTAGT 59.862 43.478 0.00 0.00 0.00 2.24
3702 3821 3.750371 TGGTGGTGATTGGTGAGTTTAG 58.250 45.455 0.00 0.00 0.00 1.85
3925 4044 3.130633 GGGATTTTGGAACTGTTTGTGC 58.869 45.455 0.00 0.00 0.00 4.57
3948 4067 7.520451 AAACCAAAAGTAGTCAAATCCCTAC 57.480 36.000 0.00 0.00 34.96 3.18
3957 4076 7.639113 AGTTGATGAAAACCAAAAGTAGTCA 57.361 32.000 0.00 0.00 0.00 3.41
3969 4088 1.743394 CCCGGGCTAGTTGATGAAAAC 59.257 52.381 8.08 0.00 0.00 2.43
3983 4102 0.461870 GGATGCAAAATTTCCCGGGC 60.462 55.000 18.49 0.93 0.00 6.13
4046 4165 3.126831 GCAGTAAGCGAGACATAGCATT 58.873 45.455 0.00 0.00 35.48 3.56
4068 4187 1.078918 TGACGCTGCCTTCCATCTG 60.079 57.895 0.00 0.00 0.00 2.90
4163 4282 5.411669 AGAAAACTGCGTGGAAGGTTATAAG 59.588 40.000 0.00 0.00 0.00 1.73


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

AutoCloner maintained by Alex Coulton.