Multiple sequence alignment - TraesCS3B01G568800

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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 TraesCS3B01G568800 chr3B 100.000 2801 0 0 1 2801 800932130 800934930 0.000000e+00 5173
1 TraesCS3B01G568800 chr3B 81.151 1199 178 28 679 1857 800952979 800954149 0.000000e+00 918
2 TraesCS3B01G568800 chr3D 92.186 1702 111 15 247 1947 596160568 596162248 0.000000e+00 2386
3 TraesCS3B01G568800 chr3D 91.286 1446 90 15 483 1928 596279076 596280485 0.000000e+00 1940
4 TraesCS3B01G568800 chr3D 82.822 1205 179 20 679 1871 596287327 596288515 0.000000e+00 1053
5 TraesCS3B01G568800 chr3D 82.256 975 153 15 870 1835 596177387 596178350 0.000000e+00 824
6 TraesCS3B01G568800 chr3D 82.256 975 153 15 870 1835 596192938 596193901 0.000000e+00 824
7 TraesCS3B01G568800 chr3D 92.460 504 38 0 1 504 596272856 596273359 0.000000e+00 721
8 TraesCS3B01G568800 chr3D 90.341 176 15 2 1 174 596160398 596160573 2.170000e-56 230
9 TraesCS3B01G568800 chr6A 88.684 866 75 9 1948 2797 84049932 84049074 0.000000e+00 1035
10 TraesCS3B01G568800 chr1D 88.046 870 80 10 1948 2799 370322424 370321561 0.000000e+00 1009
11 TraesCS3B01G568800 chr1D 86.039 881 81 13 1935 2797 10775147 10776003 0.000000e+00 907
12 TraesCS3B01G568800 chr5D 86.406 868 78 12 1948 2797 400283549 400282704 0.000000e+00 913
13 TraesCS3B01G568800 chr2D 86.406 868 78 12 1948 2797 81970997 81971842 0.000000e+00 913
14 TraesCS3B01G568800 chr4D 86.290 868 78 13 1948 2797 455762675 455761831 0.000000e+00 905
15 TraesCS3B01G568800 chrUn 82.256 975 153 15 870 1835 278019353 278020316 0.000000e+00 824
16 TraesCS3B01G568800 chrUn 82.256 975 153 15 870 1835 302270927 302269964 0.000000e+00 824
17 TraesCS3B01G568800 chr3A 91.064 235 20 1 2563 2797 682753399 682753632 1.620000e-82 316
18 TraesCS3B01G568800 chr2A 89.787 235 23 1 2563 2797 602689777 602689544 1.630000e-77 300
19 TraesCS3B01G568800 chr2A 85.522 297 29 3 1948 2230 602690519 602690223 5.870000e-77 298
20 TraesCS3B01G568800 chr2A 85.882 170 24 0 1948 2117 68861045 68860876 6.160000e-42 182
21 TraesCS3B01G568800 chr2A 85.119 168 25 0 1950 2117 18291706 18291873 3.710000e-39 172
22 TraesCS3B01G568800 chr5A 84.416 231 32 3 2567 2797 337647739 337647965 1.010000e-54 224


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 TraesCS3B01G568800 chr3B 800932130 800934930 2800 False 5173 5173 100.0000 1 2801 1 chr3B.!!$F1 2800
1 TraesCS3B01G568800 chr3B 800952979 800954149 1170 False 918 918 81.1510 679 1857 1 chr3B.!!$F2 1178
2 TraesCS3B01G568800 chr3D 596279076 596280485 1409 False 1940 1940 91.2860 483 1928 1 chr3D.!!$F4 1445
3 TraesCS3B01G568800 chr3D 596160398 596162248 1850 False 1308 2386 91.2635 1 1947 2 chr3D.!!$F6 1946
4 TraesCS3B01G568800 chr3D 596287327 596288515 1188 False 1053 1053 82.8220 679 1871 1 chr3D.!!$F5 1192
5 TraesCS3B01G568800 chr3D 596177387 596178350 963 False 824 824 82.2560 870 1835 1 chr3D.!!$F1 965
6 TraesCS3B01G568800 chr3D 596192938 596193901 963 False 824 824 82.2560 870 1835 1 chr3D.!!$F2 965
7 TraesCS3B01G568800 chr3D 596272856 596273359 503 False 721 721 92.4600 1 504 1 chr3D.!!$F3 503
8 TraesCS3B01G568800 chr6A 84049074 84049932 858 True 1035 1035 88.6840 1948 2797 1 chr6A.!!$R1 849
9 TraesCS3B01G568800 chr1D 370321561 370322424 863 True 1009 1009 88.0460 1948 2799 1 chr1D.!!$R1 851
10 TraesCS3B01G568800 chr1D 10775147 10776003 856 False 907 907 86.0390 1935 2797 1 chr1D.!!$F1 862
11 TraesCS3B01G568800 chr5D 400282704 400283549 845 True 913 913 86.4060 1948 2797 1 chr5D.!!$R1 849
12 TraesCS3B01G568800 chr2D 81970997 81971842 845 False 913 913 86.4060 1948 2797 1 chr2D.!!$F1 849
13 TraesCS3B01G568800 chr4D 455761831 455762675 844 True 905 905 86.2900 1948 2797 1 chr4D.!!$R1 849
14 TraesCS3B01G568800 chrUn 278019353 278020316 963 False 824 824 82.2560 870 1835 1 chrUn.!!$F1 965
15 TraesCS3B01G568800 chrUn 302269964 302270927 963 True 824 824 82.2560 870 1835 1 chrUn.!!$R1 965
16 TraesCS3B01G568800 chr2A 602689544 602690519 975 True 299 300 87.6545 1948 2797 2 chr2A.!!$R2 849

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
793 798 2.027561 TCCCTACCTATGCACACACAAC 60.028 50.0 0.0 0.0 0.0 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2297 2455 0.030807 TGGCATGGAGGAGGAGATGA 60.031 55.0 0.0 0.0 0.0 2.92 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
84 86 3.260884 TCCACCTGGTCACATAGTTCTTC 59.739 47.826 0.00 0.00 36.34 2.87
157 160 4.199310 TGCAGGATTGTATTTCCAGCTAC 58.801 43.478 8.30 0.00 43.87 3.58
171 174 4.740902 TCCAGCTACCTATCTGCAGAATA 58.259 43.478 22.50 12.36 0.00 1.75
172 175 5.147767 TCCAGCTACCTATCTGCAGAATAA 58.852 41.667 22.50 8.53 0.00 1.40
173 176 5.602561 TCCAGCTACCTATCTGCAGAATAAA 59.397 40.000 22.50 5.90 0.00 1.40
174 177 5.698545 CCAGCTACCTATCTGCAGAATAAAC 59.301 44.000 22.50 7.42 0.00 2.01
175 178 6.283694 CAGCTACCTATCTGCAGAATAAACA 58.716 40.000 22.50 3.88 0.00 2.83
176 179 6.201806 CAGCTACCTATCTGCAGAATAAACAC 59.798 42.308 22.50 8.87 0.00 3.32
177 180 6.049149 GCTACCTATCTGCAGAATAAACACA 58.951 40.000 22.50 0.00 0.00 3.72
178 181 6.538742 GCTACCTATCTGCAGAATAAACACAA 59.461 38.462 22.50 0.00 0.00 3.33
179 182 7.065803 GCTACCTATCTGCAGAATAAACACAAA 59.934 37.037 22.50 0.00 0.00 2.83
180 183 7.759489 ACCTATCTGCAGAATAAACACAAAA 57.241 32.000 22.50 0.00 0.00 2.44
181 184 7.820648 ACCTATCTGCAGAATAAACACAAAAG 58.179 34.615 22.50 4.01 0.00 2.27
182 185 7.665559 ACCTATCTGCAGAATAAACACAAAAGA 59.334 33.333 22.50 0.00 0.00 2.52
183 186 8.680903 CCTATCTGCAGAATAAACACAAAAGAT 58.319 33.333 22.50 0.08 0.00 2.40
186 189 9.768662 ATCTGCAGAATAAACACAAAAGATTTT 57.231 25.926 22.50 0.00 0.00 1.82
206 209 9.101655 AGATTTTGTTAATAAATGGAGCATTGC 57.898 29.630 0.00 0.00 34.04 3.56
207 210 8.789825 ATTTTGTTAATAAATGGAGCATTGCA 57.210 26.923 11.91 0.00 34.04 4.08
208 211 8.789825 TTTTGTTAATAAATGGAGCATTGCAT 57.210 26.923 11.91 0.00 36.89 3.96
209 212 9.881649 TTTTGTTAATAAATGGAGCATTGCATA 57.118 25.926 11.91 0.00 33.86 3.14
237 240 8.523915 TGCCCTCCTATGCATATAATAAATTG 57.476 34.615 6.92 0.00 31.31 2.32
238 241 8.335484 TGCCCTCCTATGCATATAATAAATTGA 58.665 33.333 6.92 0.00 31.31 2.57
239 242 9.359653 GCCCTCCTATGCATATAATAAATTGAT 57.640 33.333 6.92 0.00 0.00 2.57
282 285 6.791867 ACACTAATGAGGCTTATCTACACA 57.208 37.500 0.00 0.00 0.00 3.72
286 289 9.113838 CACTAATGAGGCTTATCTACACAAAAT 57.886 33.333 0.00 0.00 0.00 1.82
326 329 8.879427 AGCCAAACCTATAACTTTAAATGAGT 57.121 30.769 0.00 0.00 0.00 3.41
328 331 9.353999 GCCAAACCTATAACTTTAAATGAGTTG 57.646 33.333 1.99 0.00 37.84 3.16
547 550 8.768957 ATCTATGTCACCAATGAATCTTATCG 57.231 34.615 0.00 0.00 36.31 2.92
699 702 8.416329 ACTTGTCATTAATAAATGGAGGATTGC 58.584 33.333 0.00 0.00 42.40 3.56
793 798 2.027561 TCCCTACCTATGCACACACAAC 60.028 50.000 0.00 0.00 0.00 3.32
841 847 7.212976 ACTATGACACTAATGAGGCTTGTATG 58.787 38.462 0.00 0.00 0.00 2.39
923 932 9.363763 ACAATCTCGAAATACTATGCATATCTG 57.636 33.333 6.92 0.00 0.00 2.90
938 947 6.572519 TGCATATCTGTCCTTTTTAAATGCC 58.427 36.000 0.00 0.00 37.09 4.40
1030 1046 9.103048 CAACACAATCAACTTAATTACGAGTTC 57.897 33.333 0.44 0.00 34.04 3.01
1109 1125 1.397390 GCCATGGCCTTGCAGCTAAT 61.397 55.000 27.24 0.00 34.56 1.73
1177 1193 2.025981 ACAGATGGCCATGAGCTAACAA 60.026 45.455 26.56 0.00 43.05 2.83
1294 1310 2.333926 CGATTCTAACACCGTGCAAGA 58.666 47.619 0.00 0.00 0.00 3.02
1303 1319 1.034838 ACCGTGCAAGAAGTTTGGCA 61.035 50.000 0.00 0.00 0.00 4.92
1343 1359 2.203126 GATCAAGCTGGCGGAGGG 60.203 66.667 0.00 0.00 0.00 4.30
1482 1500 0.884259 CCAACCAGACGCATGTGACA 60.884 55.000 14.43 0.00 0.00 3.58
1487 1505 0.387239 CAGACGCATGTGACAGTCGA 60.387 55.000 14.43 0.00 38.53 4.20
1513 1531 3.406595 GAAGGGATGGAGGGGTGCG 62.407 68.421 0.00 0.00 0.00 5.34
1586 1608 1.078426 GCACCGGGTACAAGCTGAT 60.078 57.895 6.32 0.00 0.00 2.90
1835 1858 3.853671 GCATGAAACAGTCCTATTTTGCG 59.146 43.478 0.00 0.00 0.00 4.85
1836 1859 4.615912 GCATGAAACAGTCCTATTTTGCGT 60.616 41.667 0.00 0.00 0.00 5.24
1837 1860 4.742438 TGAAACAGTCCTATTTTGCGTC 57.258 40.909 0.00 0.00 0.00 5.19
1882 1907 1.739067 GGGTCATTCTAGTGCACCAC 58.261 55.000 14.63 0.00 34.10 4.16
1951 1976 1.337260 GCTGTCCACATGAGTCGAGTT 60.337 52.381 0.00 0.00 0.00 3.01
1956 1981 6.275494 TGTCCACATGAGTCGAGTTAATTA 57.725 37.500 0.00 0.00 0.00 1.40
1975 2000 9.968870 GTTAATTACAAGAAACCACCACATTTA 57.031 29.630 0.00 0.00 0.00 1.40
1978 2003 7.825331 TTACAAGAAACCACCACATTTATGA 57.175 32.000 0.00 0.00 0.00 2.15
1989 2014 4.394920 ACCACATTTATGACTAGGTTTGCG 59.605 41.667 0.00 0.00 0.00 4.85
2011 2036 4.841443 GGAAACCACCAACTCGTTAATT 57.159 40.909 0.00 0.00 0.00 1.40
2012 2037 5.190992 GGAAACCACCAACTCGTTAATTT 57.809 39.130 0.00 0.00 0.00 1.82
2013 2038 6.316440 GGAAACCACCAACTCGTTAATTTA 57.684 37.500 0.00 0.00 0.00 1.40
2021 2046 7.148820 CCACCAACTCGTTAATTTATTGCAAAG 60.149 37.037 1.71 0.00 0.00 2.77
2042 2068 5.941948 AGAACACCGGAAAATCTGTTAAG 57.058 39.130 9.46 0.00 0.00 1.85
2053 2079 6.075046 GGAAAATCTGTTAAGTCGTTGCAAAC 60.075 38.462 0.00 0.00 45.31 2.93
2087 2113 5.847817 AGGATGATTTGGCCCATTTAATCAT 59.152 36.000 17.90 17.90 45.47 2.45
2117 2143 4.079958 ACAGGTAGGGCTAATTTGTAAGGG 60.080 45.833 0.00 0.00 0.00 3.95
2123 2162 4.016944 AGGGCTAATTTGTAAGGGGCTAAA 60.017 41.667 0.00 0.00 0.00 1.85
2136 2175 3.135994 GGGGCTAAATACATACACACCG 58.864 50.000 0.00 0.00 0.00 4.94
2137 2176 3.135994 GGGCTAAATACATACACACCGG 58.864 50.000 0.00 0.00 0.00 5.28
2155 2194 5.247337 ACACCGGTGGATCCAAAAATAAAAT 59.753 36.000 36.47 8.06 35.57 1.82
2166 2207 7.446001 TCCAAAAATAAAATGCAATCAACCC 57.554 32.000 0.00 0.00 0.00 4.11
2180 2221 1.306141 AACCCCCTGCTCTCGATCA 60.306 57.895 0.00 0.00 0.00 2.92
2199 2240 1.950216 CACCTTCTCTCGATCCGATCA 59.050 52.381 9.07 0.00 34.61 2.92
2298 2456 4.468689 CCGTCCCCGCCTTTCCTC 62.469 72.222 0.00 0.00 0.00 3.71
2299 2457 3.702048 CGTCCCCGCCTTTCCTCA 61.702 66.667 0.00 0.00 0.00 3.86
2312 2470 3.316501 CTTTCCTCATCTCCTCCTCCAT 58.683 50.000 0.00 0.00 0.00 3.41
2322 2480 1.452651 CTCCTCCATGCCATGCGTT 60.453 57.895 0.00 0.00 0.00 4.84
2338 2496 4.015406 TTGTCCACGATGCCGGCT 62.015 61.111 29.70 13.55 40.78 5.52
2401 2559 2.415608 CGTCCCTAAGCCAGCGAGA 61.416 63.158 0.00 0.00 0.00 4.04
2416 2574 2.705154 GCGAGATTTTTACCGCATCAC 58.295 47.619 0.00 0.00 46.04 3.06
2418 2576 3.544244 GCGAGATTTTTACCGCATCACTC 60.544 47.826 0.00 0.00 46.04 3.51
2431 2589 0.689080 ATCACTCCCTCCTCATGCGT 60.689 55.000 0.00 0.00 0.00 5.24
2449 2607 1.683025 TGATGAACCGGACGCCCTA 60.683 57.895 9.46 0.00 0.00 3.53
2582 2864 1.963338 GACAAGAAGCAGCACGCCT 60.963 57.895 0.00 0.00 44.04 5.52
2583 2865 1.510480 GACAAGAAGCAGCACGCCTT 61.510 55.000 0.00 0.00 44.04 4.35
2599 2881 0.597637 CCTTGTGAGCTCGTCGTTGT 60.598 55.000 9.64 0.00 0.00 3.32
2604 2886 0.889638 TGAGCTCGTCGTTGTCCTCT 60.890 55.000 9.64 0.00 0.00 3.69
2672 2954 2.439837 CCATGGTGGTTGGCAAACT 58.560 52.632 17.39 0.00 36.48 2.66
2676 2958 1.456705 GGTGGTTGGCAAACTGGGA 60.457 57.895 17.39 0.00 36.48 4.37
2684 2966 0.251341 GGCAAACTGGGATGTGGTCT 60.251 55.000 0.00 0.00 0.00 3.85
2704 2986 1.452953 TATAGGACGGCGGCTGTCTG 61.453 60.000 33.69 8.24 39.49 3.51
2719 3001 1.987855 TCTGGAGGTAAGTGGCGGG 60.988 63.158 0.00 0.00 0.00 6.13
2720 3002 1.987855 CTGGAGGTAAGTGGCGGGA 60.988 63.158 0.00 0.00 0.00 5.14
2722 3004 1.684734 GGAGGTAAGTGGCGGGAGA 60.685 63.158 0.00 0.00 0.00 3.71
2727 3009 0.252197 GTAAGTGGCGGGAGATGGTT 59.748 55.000 0.00 0.00 0.00 3.67
2799 3081 4.683334 GGCGACAAACTGCGGTGC 62.683 66.667 0.00 0.00 0.00 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 50 5.440610 ACCAGGTGGATCTCATTTAATGAC 58.559 41.667 3.20 0.00 38.94 3.06
157 160 8.044060 TCTTTTGTGTTTATTCTGCAGATAGG 57.956 34.615 19.04 0.00 0.00 2.57
180 183 9.101655 GCAATGCTCCATTTATTAACAAAATCT 57.898 29.630 0.00 0.00 31.05 2.40
181 184 8.881743 TGCAATGCTCCATTTATTAACAAAATC 58.118 29.630 6.82 0.00 31.05 2.17
182 185 8.789825 TGCAATGCTCCATTTATTAACAAAAT 57.210 26.923 6.82 0.00 31.05 1.82
183 186 8.789825 ATGCAATGCTCCATTTATTAACAAAA 57.210 26.923 6.82 0.00 31.05 2.44
212 215 8.335484 TCAATTTATTATATGCATAGGAGGGCA 58.665 33.333 12.79 0.00 45.23 5.36
213 216 8.752005 TCAATTTATTATATGCATAGGAGGGC 57.248 34.615 12.79 0.00 0.00 5.19
281 284 5.357878 TGGCTCTTCCTGCAATACTATTTTG 59.642 40.000 0.00 0.00 35.26 2.44
282 285 5.509498 TGGCTCTTCCTGCAATACTATTTT 58.491 37.500 0.00 0.00 35.26 1.82
286 289 4.261801 GTTTGGCTCTTCCTGCAATACTA 58.738 43.478 0.00 0.00 35.26 1.82
290 293 1.203100 AGGTTTGGCTCTTCCTGCAAT 60.203 47.619 0.00 0.00 35.26 3.56
297 300 9.788960 CATTTAAAGTTATAGGTTTGGCTCTTC 57.211 33.333 0.00 0.00 0.00 2.87
298 301 9.528489 TCATTTAAAGTTATAGGTTTGGCTCTT 57.472 29.630 0.00 0.00 0.00 2.85
328 331 4.644103 AGAAATATGTGATTGCAGGTGC 57.356 40.909 0.00 0.00 42.50 5.01
468 471 6.377429 GTGCATAGGTAGGCAGATATACACTA 59.623 42.308 0.00 0.00 44.15 2.74
470 473 5.047306 TGTGCATAGGTAGGCAGATATACAC 60.047 44.000 0.00 0.00 44.15 2.90
528 531 4.811024 TCTGCGATAAGATTCATTGGTGAC 59.189 41.667 0.00 0.00 33.11 3.67
529 532 5.022282 TCTGCGATAAGATTCATTGGTGA 57.978 39.130 0.00 0.00 0.00 4.02
539 542 6.262944 TGCCACAATATTTTCTGCGATAAGAT 59.737 34.615 0.00 0.00 0.00 2.40
547 550 5.713025 TCTTTCTGCCACAATATTTTCTGC 58.287 37.500 0.00 0.00 0.00 4.26
675 678 8.196771 GTGCAATCCTCCATTTATTAATGACAA 58.803 33.333 6.01 0.00 43.12 3.18
677 680 7.864379 CAGTGCAATCCTCCATTTATTAATGAC 59.136 37.037 6.01 0.00 43.12 3.06
699 702 8.507524 TCGGATAGATAGTTGGATATACAGTG 57.492 38.462 0.00 0.00 0.00 3.66
841 847 4.153475 TCTTTCTGCCGCAACAATTACTAC 59.847 41.667 0.00 0.00 0.00 2.73
872 878 5.059833 GGTGGATCTCATTCAATGTCCTAC 58.940 45.833 6.98 4.30 0.00 3.18
923 932 8.825667 TGTAATTTCTGGCATTTAAAAAGGAC 57.174 30.769 0.00 0.00 0.00 3.85
938 947 3.689161 TGGCGAGGAACATGTAATTTCTG 59.311 43.478 0.00 0.00 0.00 3.02
1030 1046 4.576463 GTGTTCCATGGCTATGAAAGTAGG 59.424 45.833 12.26 0.00 36.36 3.18
1057 1073 1.550524 TGAGAGGATGACCAGGAAACG 59.449 52.381 0.00 0.00 38.94 3.60
1144 1160 1.759994 CCATCTGTGTCGTAGATCGC 58.240 55.000 0.00 0.00 40.67 4.58
1177 1193 3.485394 TGATGTTGTACATGTTGTGGCT 58.515 40.909 2.30 0.00 39.27 4.75
1294 1310 2.519013 GTCTGGATTCCTGCCAAACTT 58.481 47.619 3.95 0.00 34.44 2.66
1303 1319 2.176247 ACATACCCGTCTGGATTCCT 57.824 50.000 3.95 0.00 37.49 3.36
1452 1470 1.221840 CTGGTTGGTGATCCCTCCG 59.778 63.158 0.00 0.00 32.88 4.63
1464 1482 0.514255 CTGTCACATGCGTCTGGTTG 59.486 55.000 0.00 0.00 0.00 3.77
1496 1514 3.411517 CGCACCCCTCCATCCCTT 61.412 66.667 0.00 0.00 0.00 3.95
1586 1608 3.422303 GCGCATGGAAGCACGACA 61.422 61.111 0.30 0.00 0.00 4.35
1835 1858 1.925185 GAAAGCAATACCGGACGAGAC 59.075 52.381 9.46 0.00 0.00 3.36
1836 1859 1.822990 AGAAAGCAATACCGGACGAGA 59.177 47.619 9.46 0.00 0.00 4.04
1837 1860 2.295253 AGAAAGCAATACCGGACGAG 57.705 50.000 9.46 0.00 0.00 4.18
1932 1957 2.732412 AACTCGACTCATGTGGACAG 57.268 50.000 0.00 0.00 0.00 3.51
1956 1981 5.833131 AGTCATAAATGTGGTGGTTTCTTGT 59.167 36.000 0.00 0.00 0.00 3.16
1975 2000 2.433436 GTTTCCCGCAAACCTAGTCAT 58.567 47.619 0.00 0.00 38.86 3.06
1976 2001 1.886886 GTTTCCCGCAAACCTAGTCA 58.113 50.000 0.00 0.00 38.86 3.41
1989 2014 2.259266 TAACGAGTTGGTGGTTTCCC 57.741 50.000 0.00 0.00 0.00 3.97
2006 2031 6.982852 TCCGGTGTTCTTTGCAATAAATTAA 58.017 32.000 0.00 0.00 0.00 1.40
2011 2036 4.920640 TTTCCGGTGTTCTTTGCAATAA 57.079 36.364 0.00 0.00 0.00 1.40
2012 2037 4.920640 TTTTCCGGTGTTCTTTGCAATA 57.079 36.364 0.00 0.00 0.00 1.90
2013 2038 3.810310 TTTTCCGGTGTTCTTTGCAAT 57.190 38.095 0.00 0.00 0.00 3.56
2021 2046 5.614013 CGACTTAACAGATTTTCCGGTGTTC 60.614 44.000 8.94 0.00 34.92 3.18
2053 2079 2.947652 CCAAATCATCCTACCAGTGCTG 59.052 50.000 0.00 0.00 0.00 4.41
2061 2087 6.267471 TGATTAAATGGGCCAAATCATCCTAC 59.733 38.462 22.29 2.66 34.34 3.18
2063 2089 5.218179 TGATTAAATGGGCCAAATCATCCT 58.782 37.500 22.29 0.00 34.34 3.24
2117 2143 3.558418 CACCGGTGTGTATGTATTTAGCC 59.442 47.826 26.95 0.00 37.72 3.93
2123 2162 2.367567 GGATCCACCGGTGTGTATGTAT 59.632 50.000 31.80 13.45 41.09 2.29
2136 2175 7.336427 TGATTGCATTTTATTTTTGGATCCACC 59.664 33.333 15.91 0.00 39.54 4.61
2137 2176 8.266392 TGATTGCATTTTATTTTTGGATCCAC 57.734 30.769 15.91 0.00 0.00 4.02
2155 2194 1.304381 GAGCAGGGGGTTGATTGCA 60.304 57.895 0.00 0.00 38.97 4.08
2166 2207 0.103937 GAAGGTGATCGAGAGCAGGG 59.896 60.000 0.00 0.00 0.00 4.45
2283 2441 1.153147 GATGAGGAAAGGCGGGGAC 60.153 63.158 0.00 0.00 0.00 4.46
2284 2442 1.306997 AGATGAGGAAAGGCGGGGA 60.307 57.895 0.00 0.00 0.00 4.81
2287 2445 0.105778 GAGGAGATGAGGAAAGGCGG 59.894 60.000 0.00 0.00 0.00 6.13
2295 2453 0.686224 GCATGGAGGAGGAGATGAGG 59.314 60.000 0.00 0.00 0.00 3.86
2296 2454 0.686224 GGCATGGAGGAGGAGATGAG 59.314 60.000 0.00 0.00 0.00 2.90
2297 2455 0.030807 TGGCATGGAGGAGGAGATGA 60.031 55.000 0.00 0.00 0.00 2.92
2298 2456 1.065647 ATGGCATGGAGGAGGAGATG 58.934 55.000 0.00 0.00 0.00 2.90
2299 2457 1.065647 CATGGCATGGAGGAGGAGAT 58.934 55.000 19.80 0.00 0.00 2.75
2312 2470 3.353029 CGTGGACAACGCATGGCA 61.353 61.111 0.00 0.00 46.99 4.92
2322 2480 3.071837 TAGCCGGCATCGTGGACA 61.072 61.111 31.54 0.00 33.95 4.02
2373 2531 1.303888 TTAGGGACGACACCTCGCT 60.304 57.895 0.00 0.00 44.33 4.93
2390 2548 1.737793 CGGTAAAAATCTCGCTGGCTT 59.262 47.619 0.00 0.00 0.00 4.35
2401 2559 3.279434 GAGGGAGTGATGCGGTAAAAAT 58.721 45.455 0.00 0.00 0.00 1.82
2413 2571 1.305297 ACGCATGAGGAGGGAGTGA 60.305 57.895 0.00 0.00 0.00 3.41
2416 2574 0.249784 CATCACGCATGAGGAGGGAG 60.250 60.000 0.00 0.00 39.01 4.30
2418 2576 0.178767 TTCATCACGCATGAGGAGGG 59.821 55.000 0.00 0.00 45.78 4.30
2431 2589 1.259142 TTAGGGCGTCCGGTTCATCA 61.259 55.000 0.00 0.00 38.33 3.07
2449 2607 3.553095 GAGAAGGGCACGGTGGCTT 62.553 63.158 30.05 22.63 43.20 4.35
2454 2612 1.988406 GGTAGGAGAAGGGCACGGT 60.988 63.158 0.00 0.00 0.00 4.83
2489 2648 4.601042 GAGGCCACTCGGATCCTA 57.399 61.111 10.75 0.00 33.35 2.94
2567 2849 1.526917 ACAAGGCGTGCTGCTTCTT 60.527 52.632 0.00 0.00 45.43 2.52
2582 2864 0.596600 GGACAACGACGAGCTCACAA 60.597 55.000 15.40 0.00 0.00 3.33
2583 2865 1.007734 GGACAACGACGAGCTCACA 60.008 57.895 15.40 0.00 0.00 3.58
2591 2873 0.247735 CTCGCTAGAGGACAACGACG 60.248 60.000 0.00 0.00 40.75 5.12
2672 2954 2.963101 CGTCCTATAAGACCACATCCCA 59.037 50.000 0.00 0.00 32.91 4.37
2676 2958 1.340248 CGCCGTCCTATAAGACCACAT 59.660 52.381 0.00 0.00 32.91 3.21
2684 2966 0.754217 AGACAGCCGCCGTCCTATAA 60.754 55.000 3.01 0.00 33.70 0.98
2704 2986 1.049289 ATCTCCCGCCACTTACCTCC 61.049 60.000 0.00 0.00 0.00 4.30
2709 2991 0.251916 CAACCATCTCCCGCCACTTA 59.748 55.000 0.00 0.00 0.00 2.24
2719 3001 0.179045 CCCCATCGGACAACCATCTC 60.179 60.000 0.00 0.00 35.59 2.75
2720 3002 1.915228 CCCCATCGGACAACCATCT 59.085 57.895 0.00 0.00 35.59 2.90
2722 3004 2.275418 GCCCCATCGGACAACCAT 59.725 61.111 0.00 0.00 35.59 3.55
2727 3009 3.626996 CTTGCAGCCCCATCGGACA 62.627 63.158 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.