Multiple sequence alignment - TraesCS3D01G130200

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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 TraesCS3D01G130200 chr3D 100.000 2746 0 0 1 2746 90370919 90373664 0.000000e+00 5072
1 TraesCS3D01G130200 chr3D 81.947 493 77 7 1977 2466 90379476 90379959 9.160000e-110 407
2 TraesCS3D01G130200 chr3D 89.024 164 15 1 2534 2694 90380072 90380235 1.670000e-47 200
3 TraesCS3D01G130200 chr3B 90.367 1962 102 38 831 2746 139777065 139778985 0.000000e+00 2495
4 TraesCS3D01G130200 chr3B 87.035 833 57 21 1 820 139776137 139776931 0.000000e+00 893
5 TraesCS3D01G130200 chr3B 79.705 882 121 30 1847 2684 139832097 139832964 3.940000e-163 584
6 TraesCS3D01G130200 chr3A 88.184 1718 118 50 157 1843 106659165 106660828 0.000000e+00 1969
7 TraesCS3D01G130200 chr3A 92.323 1029 41 11 1720 2745 106660825 106661818 0.000000e+00 1428
8 TraesCS3D01G130200 chr3A 82.692 260 40 5 1866 2123 106674424 106674680 2.750000e-55 226
9 TraesCS3D01G130200 chr3A 86.875 160 21 0 2534 2693 106677202 106677361 2.170000e-41 180
10 TraesCS3D01G130200 chr3A 92.105 114 9 0 1 114 106658944 106659057 7.870000e-36 161
11 TraesCS3D01G130200 chr4B 75.330 454 74 20 2011 2441 20317404 20317842 1.680000e-42 183
12 TraesCS3D01G130200 chr4B 72.410 830 137 64 1646 2442 20365192 20365962 2.170000e-41 180
13 TraesCS3D01G130200 chr4B 87.786 131 14 2 2554 2682 20361228 20361098 4.740000e-33 152
14 TraesCS3D01G130200 chr4D 73.658 596 102 44 1651 2235 10863122 10863673 2.170000e-41 180
15 TraesCS3D01G130200 chr4D 87.023 131 15 2 2554 2682 10835265 10835135 2.200000e-31 147


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 TraesCS3D01G130200 chr3D 90370919 90373664 2745 False 5072.0 5072 100.000000 1 2746 1 chr3D.!!$F1 2745
1 TraesCS3D01G130200 chr3D 90379476 90380235 759 False 303.5 407 85.485500 1977 2694 2 chr3D.!!$F2 717
2 TraesCS3D01G130200 chr3B 139776137 139778985 2848 False 1694.0 2495 88.701000 1 2746 2 chr3B.!!$F2 2745
3 TraesCS3D01G130200 chr3B 139832097 139832964 867 False 584.0 584 79.705000 1847 2684 1 chr3B.!!$F1 837
4 TraesCS3D01G130200 chr3A 106658944 106661818 2874 False 1186.0 1969 90.870667 1 2745 3 chr3A.!!$F1 2744
5 TraesCS3D01G130200 chr3A 106674424 106677361 2937 False 203.0 226 84.783500 1866 2693 2 chr3A.!!$F2 827

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
730 809 0.034337 GTGTGCTCCGTTTGGTCCTA 59.966 55.0 0.0 0.0 36.3 2.94 F
986 1201 0.109086 CACAGCAGGTACACGAGAGG 60.109 60.0 0.0 0.0 0.0 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1631 1877 0.317269 CCATGGCATCGCAACGAATC 60.317 55.0 0.0 0.0 39.99 2.52 R
2535 5039 1.002366 CACTGAAGCCGCATCTACAC 58.998 55.0 0.0 0.0 0.00 2.90 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
132 133 5.070847 TGATCATATATATCGTGGGCAGCAT 59.929 40.000 0.00 0.00 0.00 3.79
159 225 4.178540 GCCATGAACATTCTCCACATTTG 58.821 43.478 0.00 0.00 0.00 2.32
167 233 8.805175 TGAACATTCTCCACATTTGTCATTATT 58.195 29.630 0.00 0.00 0.00 1.40
196 262 7.116736 TCTGAACTTTCCTCTTTTAACCTTGT 58.883 34.615 0.00 0.00 0.00 3.16
197 263 7.282450 TCTGAACTTTCCTCTTTTAACCTTGTC 59.718 37.037 0.00 0.00 0.00 3.18
213 279 5.008331 ACCTTGTCGTGTGTAGAGATTAGA 58.992 41.667 0.00 0.00 0.00 2.10
275 341 3.306710 CCATTCCAAAAGGCCAAGGTAAC 60.307 47.826 5.01 0.00 0.00 2.50
280 346 3.486383 CAAAAGGCCAAGGTAACAGAGA 58.514 45.455 5.01 0.00 41.41 3.10
281 347 3.876309 AAAGGCCAAGGTAACAGAGAA 57.124 42.857 5.01 0.00 41.41 2.87
282 348 3.425162 AAGGCCAAGGTAACAGAGAAG 57.575 47.619 5.01 0.00 41.41 2.85
283 349 2.621070 AGGCCAAGGTAACAGAGAAGA 58.379 47.619 5.01 0.00 41.41 2.87
284 350 2.979678 AGGCCAAGGTAACAGAGAAGAA 59.020 45.455 5.01 0.00 41.41 2.52
285 351 3.008485 AGGCCAAGGTAACAGAGAAGAAG 59.992 47.826 5.01 0.00 41.41 2.85
286 352 3.008049 GGCCAAGGTAACAGAGAAGAAGA 59.992 47.826 0.00 0.00 41.41 2.87
287 353 4.505039 GGCCAAGGTAACAGAGAAGAAGAA 60.505 45.833 0.00 0.00 41.41 2.52
288 354 5.063880 GCCAAGGTAACAGAGAAGAAGAAA 58.936 41.667 0.00 0.00 41.41 2.52
289 355 5.049336 GCCAAGGTAACAGAGAAGAAGAAAC 60.049 44.000 0.00 0.00 41.41 2.78
290 356 5.177696 CCAAGGTAACAGAGAAGAAGAAACG 59.822 44.000 0.00 0.00 41.41 3.60
291 357 5.786264 AGGTAACAGAGAAGAAGAAACGA 57.214 39.130 0.00 0.00 41.41 3.85
292 358 6.347859 AGGTAACAGAGAAGAAGAAACGAT 57.652 37.500 0.00 0.00 41.41 3.73
293 359 6.159988 AGGTAACAGAGAAGAAGAAACGATG 58.840 40.000 0.00 0.00 41.41 3.84
294 360 5.927115 GGTAACAGAGAAGAAGAAACGATGT 59.073 40.000 0.00 0.00 0.00 3.06
295 361 6.424207 GGTAACAGAGAAGAAGAAACGATGTT 59.576 38.462 0.00 0.00 33.36 2.71
296 362 6.927294 AACAGAGAAGAAGAAACGATGTTT 57.073 33.333 0.00 0.00 0.00 2.83
299 365 8.608844 ACAGAGAAGAAGAAACGATGTTTTAT 57.391 30.769 0.00 0.00 0.00 1.40
302 368 8.930760 AGAGAAGAAGAAACGATGTTTTATCAG 58.069 33.333 0.00 0.00 0.00 2.90
307 373 5.931532 AGAAACGATGTTTTATCAGCAGTG 58.068 37.500 0.00 0.00 0.00 3.66
310 376 3.120199 ACGATGTTTTATCAGCAGTGTGC 60.120 43.478 0.00 0.00 45.46 4.57
316 382 5.476599 TGTTTTATCAGCAGTGTGCCTTATT 59.523 36.000 0.00 0.00 46.52 1.40
332 398 8.417106 TGTGCCTTATTTCTTTGTTTGTCAATA 58.583 29.630 0.00 0.00 35.84 1.90
333 399 9.423061 GTGCCTTATTTCTTTGTTTGTCAATAT 57.577 29.630 0.00 0.00 35.84 1.28
340 406 8.984891 TTTCTTTGTTTGTCAATATATGCCAG 57.015 30.769 0.00 0.00 35.84 4.85
359 425 6.108687 TGCCAGTTCTCTTATGTATGAAGTG 58.891 40.000 0.00 0.00 38.72 3.16
360 426 6.109359 GCCAGTTCTCTTATGTATGAAGTGT 58.891 40.000 0.00 0.00 37.86 3.55
361 427 6.595716 GCCAGTTCTCTTATGTATGAAGTGTT 59.404 38.462 0.00 0.00 37.86 3.32
364 430 9.088512 CAGTTCTCTTATGTATGAAGTGTTACC 57.911 37.037 0.00 0.00 36.00 2.85
365 431 7.974501 AGTTCTCTTATGTATGAAGTGTTACCG 59.025 37.037 0.00 0.00 0.00 4.02
367 444 7.704271 TCTCTTATGTATGAAGTGTTACCGAG 58.296 38.462 0.00 0.00 0.00 4.63
376 453 4.823442 TGAAGTGTTACCGAGACTGACTTA 59.177 41.667 0.00 0.00 31.22 2.24
377 454 4.762956 AGTGTTACCGAGACTGACTTAC 57.237 45.455 0.00 0.00 29.32 2.34
382 459 5.356190 TGTTACCGAGACTGACTTACCTATG 59.644 44.000 0.00 0.00 0.00 2.23
390 467 5.958380 AGACTGACTTACCTATGGATTCACA 59.042 40.000 0.00 0.00 0.00 3.58
508 585 0.865769 CAAACAAAGCCGTAGCGACT 59.134 50.000 0.00 0.00 46.67 4.18
550 627 7.971722 ACTTTGTTATCGCTGTTGTTTAAAACT 59.028 29.630 0.00 0.00 0.00 2.66
631 708 4.759693 TGTCAGTGTTTGTGAACTCTTTGT 59.240 37.500 0.00 0.00 37.47 2.83
633 710 5.122396 GTCAGTGTTTGTGAACTCTTTGTCT 59.878 40.000 0.00 0.00 37.47 3.41
663 742 1.710249 CTGTTTCGCGTGCATTTCTTG 59.290 47.619 5.77 0.00 0.00 3.02
677 756 1.691196 TTCTTGCTCCAAACCACTGG 58.309 50.000 0.00 0.00 37.87 4.00
678 757 0.823356 TCTTGCTCCAAACCACTGGC 60.823 55.000 0.00 0.00 36.32 4.85
679 758 0.825010 CTTGCTCCAAACCACTGGCT 60.825 55.000 0.00 0.00 36.32 4.75
680 759 1.108727 TTGCTCCAAACCACTGGCTG 61.109 55.000 0.00 0.00 36.32 4.85
689 768 3.551259 CCACTGGCTGGTTCGTATT 57.449 52.632 0.00 0.00 34.90 1.89
730 809 0.034337 GTGTGCTCCGTTTGGTCCTA 59.966 55.000 0.00 0.00 36.30 2.94
731 810 0.981183 TGTGCTCCGTTTGGTCCTAT 59.019 50.000 0.00 0.00 36.30 2.57
757 838 5.839621 TCTGGTGGCTCTACGTTTATAATC 58.160 41.667 0.00 0.00 0.00 1.75
788 869 7.877612 TGATTGATATTACTATGGTGCGAATGT 59.122 33.333 0.00 0.00 0.00 2.71
790 871 8.528917 TTGATATTACTATGGTGCGAATGTAC 57.471 34.615 0.00 0.00 0.00 2.90
791 872 7.662897 TGATATTACTATGGTGCGAATGTACA 58.337 34.615 0.00 0.00 31.53 2.90
792 873 7.812669 TGATATTACTATGGTGCGAATGTACAG 59.187 37.037 0.33 0.00 31.53 2.74
815 896 5.945784 AGGCTGTGCTTCTCATGTAATTTTA 59.054 36.000 0.00 0.00 0.00 1.52
821 902 9.638239 TGTGCTTCTCATGTAATTTTATTTTCC 57.362 29.630 0.00 0.00 0.00 3.13
822 903 8.798153 GTGCTTCTCATGTAATTTTATTTTCCG 58.202 33.333 0.00 0.00 0.00 4.30
823 904 8.519526 TGCTTCTCATGTAATTTTATTTTCCGT 58.480 29.630 0.00 0.00 0.00 4.69
824 905 9.353999 GCTTCTCATGTAATTTTATTTTCCGTT 57.646 29.630 0.00 0.00 0.00 4.44
827 908 9.632807 TCTCATGTAATTTTATTTTCCGTTTGG 57.367 29.630 0.00 0.00 0.00 3.28
829 910 9.413048 TCATGTAATTTTATTTTCCGTTTGGAC 57.587 29.630 0.00 0.00 46.45 4.02
862 1076 5.236911 GTGAAATTCTGGAAGCAAATGCAAA 59.763 36.000 8.28 0.00 45.16 3.68
888 1103 2.131776 TTACCCTGGCCAAATTACCG 57.868 50.000 7.01 0.00 0.00 4.02
915 1130 2.184322 CGTGCCACGTAGCCTGAT 59.816 61.111 9.53 0.00 36.74 2.90
951 1166 1.367659 GCTGCGAAGAGAATGAAGCT 58.632 50.000 0.00 0.00 0.00 3.74
955 1170 3.402110 TGCGAAGAGAATGAAGCTTCAA 58.598 40.909 31.55 16.04 41.13 2.69
965 1180 1.408702 TGAAGCTTCAAACAAGCCACC 59.591 47.619 26.61 0.00 44.01 4.61
986 1201 0.109086 CACAGCAGGTACACGAGAGG 60.109 60.000 0.00 0.00 0.00 3.69
993 1208 2.561419 CAGGTACACGAGAGGAAGGAAA 59.439 50.000 0.00 0.00 0.00 3.13
1036 1251 1.140589 CGCTACTGCTGCAGCTACT 59.859 57.895 36.61 21.57 42.66 2.57
1037 1252 0.382158 CGCTACTGCTGCAGCTACTA 59.618 55.000 36.61 21.53 42.66 1.82
1038 1253 1.846541 GCTACTGCTGCAGCTACTAC 58.153 55.000 36.61 20.65 42.66 2.73
1248 1469 4.012895 GACGGCGTGTGCAACCTG 62.013 66.667 21.19 0.00 45.35 4.00
1471 1701 4.277476 TGGACCAAGTGTGAGAAATGTTT 58.723 39.130 0.00 0.00 0.00 2.83
1503 1733 4.162888 TGCAGGTCATACATCAAGTCTGAT 59.837 41.667 0.00 0.00 43.40 2.90
1575 1805 0.246360 CGTTCCTCAAAATTGCCCCC 59.754 55.000 0.00 0.00 0.00 5.40
1600 1846 6.583806 CCTGTAAGCTCAATTCACATTTCAAC 59.416 38.462 0.00 0.00 0.00 3.18
1615 1861 5.301551 ACATTTCAACTGAACCACTGCAATA 59.698 36.000 0.00 0.00 33.13 1.90
1616 1862 6.015180 ACATTTCAACTGAACCACTGCAATAT 60.015 34.615 0.00 0.00 33.13 1.28
1617 1863 7.176515 ACATTTCAACTGAACCACTGCAATATA 59.823 33.333 0.00 0.00 33.13 0.86
1619 1865 6.741992 TCAACTGAACCACTGCAATATAAG 57.258 37.500 0.00 0.00 0.00 1.73
1620 1866 6.237901 TCAACTGAACCACTGCAATATAAGT 58.762 36.000 0.00 0.00 0.00 2.24
1621 1867 7.390823 TCAACTGAACCACTGCAATATAAGTA 58.609 34.615 0.00 0.00 0.00 2.24
1622 1868 7.549134 TCAACTGAACCACTGCAATATAAGTAG 59.451 37.037 0.00 0.00 0.00 2.57
1623 1869 5.817816 ACTGAACCACTGCAATATAAGTAGC 59.182 40.000 0.00 0.00 0.00 3.58
1624 1870 5.739959 TGAACCACTGCAATATAAGTAGCA 58.260 37.500 0.00 0.00 35.43 3.49
1625 1871 6.176896 TGAACCACTGCAATATAAGTAGCAA 58.823 36.000 0.00 0.00 36.44 3.91
1626 1872 6.828273 TGAACCACTGCAATATAAGTAGCAAT 59.172 34.615 0.00 0.00 36.44 3.56
1631 1877 8.285394 CCACTGCAATATAAGTAGCAATTACTG 58.715 37.037 0.00 0.00 41.80 2.74
1861 2230 2.464796 ATGGCATGAACCACCATCAT 57.535 45.000 0.00 0.00 44.17 2.45
1906 2276 2.943978 GCTACCCTGCCTCACGTGT 61.944 63.158 16.51 0.00 0.00 4.49
1948 2318 0.321021 CTGCACTTGCTCCTCTGTCT 59.679 55.000 2.33 0.00 42.66 3.41
2043 2413 4.735132 CCCGCGACGCTTCCTTGA 62.735 66.667 19.02 0.00 0.00 3.02
2244 4694 3.429272 CCTGCAAACGCAACCAATATGAT 60.429 43.478 0.00 0.00 39.39 2.45
2252 4702 6.024552 ACGCAACCAATATGATTTTCAGTT 57.975 33.333 0.00 0.00 0.00 3.16
2257 4707 8.938906 GCAACCAATATGATTTTCAGTTTCAAT 58.061 29.630 0.00 0.00 0.00 2.57
2259 4710 8.915871 ACCAATATGATTTTCAGTTTCAATCG 57.084 30.769 0.00 0.00 30.69 3.34
2263 4714 9.912634 AATATGATTTTCAGTTTCAATCGTTGT 57.087 25.926 0.00 0.00 30.47 3.32
2265 4716 7.026631 TGATTTTCAGTTTCAATCGTTGTCT 57.973 32.000 0.00 0.00 30.69 3.41
2267 4718 7.973388 TGATTTTCAGTTTCAATCGTTGTCTTT 59.027 29.630 0.00 0.00 30.69 2.52
2268 4719 7.734538 TTTTCAGTTTCAATCGTTGTCTTTC 57.265 32.000 0.00 0.00 0.00 2.62
2271 4722 5.007626 TCAGTTTCAATCGTTGTCTTTCAGG 59.992 40.000 0.00 0.00 0.00 3.86
2272 4723 5.007626 CAGTTTCAATCGTTGTCTTTCAGGA 59.992 40.000 0.00 0.00 0.00 3.86
2273 4724 5.765182 AGTTTCAATCGTTGTCTTTCAGGAT 59.235 36.000 0.00 0.00 0.00 3.24
2275 4726 3.436704 TCAATCGTTGTCTTTCAGGATGC 59.563 43.478 0.00 0.00 34.76 3.91
2276 4727 2.542020 TCGTTGTCTTTCAGGATGCA 57.458 45.000 0.00 0.00 34.76 3.96
2277 4728 3.057969 TCGTTGTCTTTCAGGATGCAT 57.942 42.857 0.00 0.00 34.76 3.96
2278 4729 3.002791 TCGTTGTCTTTCAGGATGCATC 58.997 45.455 18.81 18.81 34.76 3.91
2282 4733 4.498894 TGTCTTTCAGGATGCATCTGAT 57.501 40.909 25.28 9.90 40.46 2.90
2310 4763 4.892345 TGGTGGTGACTGAATTCAATTGAA 59.108 37.500 22.52 22.52 38.56 2.69
2329 4782 2.375014 ATTGGTTTCCTCACCCGTTT 57.625 45.000 0.00 0.00 35.73 3.60
2386 4839 5.624344 ATGTCGATAGGATACCGTACTTG 57.376 43.478 0.00 0.00 37.17 3.16
2648 5152 2.032981 CCAGCGCTGGTTTTTCACT 58.967 52.632 42.09 0.00 45.53 3.41
2734 5242 4.909696 TGCTACTCACTAGAGAATGCTC 57.090 45.455 0.00 0.00 44.98 4.26
2738 5246 4.566545 ACTCACTAGAGAATGCTCATCG 57.433 45.455 2.79 0.00 44.98 3.84
2742 5250 4.586421 TCACTAGAGAATGCTCATCGGAAT 59.414 41.667 2.79 0.00 43.81 3.01
2743 5251 5.770162 TCACTAGAGAATGCTCATCGGAATA 59.230 40.000 2.79 0.00 43.81 1.75
2744 5252 6.435591 TCACTAGAGAATGCTCATCGGAATAT 59.564 38.462 2.79 0.00 43.81 1.28
2745 5253 7.611855 TCACTAGAGAATGCTCATCGGAATATA 59.388 37.037 2.79 0.00 43.81 0.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
132 133 1.820519 GGAGAATGTTCATGGCAGCAA 59.179 47.619 0.00 0.00 0.00 3.91
159 225 9.660180 AGAGGAAAGTTCAGAGTAAATAATGAC 57.340 33.333 0.00 0.00 0.00 3.06
167 233 8.491958 AGGTTAAAAGAGGAAAGTTCAGAGTAA 58.508 33.333 0.00 0.00 0.00 2.24
196 262 5.650703 TGGATGTTCTAATCTCTACACACGA 59.349 40.000 0.00 0.00 0.00 4.35
197 263 5.744345 GTGGATGTTCTAATCTCTACACACG 59.256 44.000 0.00 0.00 0.00 4.49
275 341 8.712363 TGATAAAACATCGTTTCTTCTTCTCTG 58.288 33.333 0.00 0.00 0.00 3.35
280 346 7.041098 ACTGCTGATAAAACATCGTTTCTTCTT 60.041 33.333 0.00 0.00 0.00 2.52
281 347 6.428159 ACTGCTGATAAAACATCGTTTCTTCT 59.572 34.615 0.00 0.00 0.00 2.85
282 348 6.521133 CACTGCTGATAAAACATCGTTTCTTC 59.479 38.462 0.00 0.00 0.00 2.87
283 349 6.017109 ACACTGCTGATAAAACATCGTTTCTT 60.017 34.615 0.00 0.00 0.00 2.52
284 350 5.470098 ACACTGCTGATAAAACATCGTTTCT 59.530 36.000 0.00 0.00 0.00 2.52
285 351 5.565259 CACACTGCTGATAAAACATCGTTTC 59.435 40.000 0.00 0.00 0.00 2.78
286 352 5.451908 CACACTGCTGATAAAACATCGTTT 58.548 37.500 0.00 0.00 0.00 3.60
287 353 4.613622 GCACACTGCTGATAAAACATCGTT 60.614 41.667 0.00 0.00 40.96 3.85
288 354 3.120199 GCACACTGCTGATAAAACATCGT 60.120 43.478 0.00 0.00 40.96 3.73
289 355 3.419915 GCACACTGCTGATAAAACATCG 58.580 45.455 0.00 0.00 40.96 3.84
290 356 3.441572 AGGCACACTGCTGATAAAACATC 59.558 43.478 0.00 0.00 44.28 3.06
291 357 3.424703 AGGCACACTGCTGATAAAACAT 58.575 40.909 0.00 0.00 44.28 2.71
292 358 2.862541 AGGCACACTGCTGATAAAACA 58.137 42.857 0.00 0.00 44.28 2.83
293 359 3.923017 AAGGCACACTGCTGATAAAAC 57.077 42.857 0.00 0.00 44.28 2.43
294 360 6.434028 AGAAATAAGGCACACTGCTGATAAAA 59.566 34.615 0.00 0.00 44.28 1.52
295 361 5.945784 AGAAATAAGGCACACTGCTGATAAA 59.054 36.000 0.00 0.00 44.28 1.40
296 362 5.500234 AGAAATAAGGCACACTGCTGATAA 58.500 37.500 0.00 0.00 44.28 1.75
299 365 3.423539 AGAAATAAGGCACACTGCTGA 57.576 42.857 0.00 0.00 44.28 4.26
302 368 4.243007 ACAAAGAAATAAGGCACACTGC 57.757 40.909 0.00 0.00 44.08 4.40
307 373 7.713764 ATTGACAAACAAAGAAATAAGGCAC 57.286 32.000 0.00 0.00 42.03 5.01
316 382 8.121305 ACTGGCATATATTGACAAACAAAGAA 57.879 30.769 0.00 0.00 44.83 2.52
332 398 8.654997 ACTTCATACATAAGAGAACTGGCATAT 58.345 33.333 0.00 0.00 0.00 1.78
333 399 7.928167 CACTTCATACATAAGAGAACTGGCATA 59.072 37.037 0.00 0.00 0.00 3.14
334 400 6.765036 CACTTCATACATAAGAGAACTGGCAT 59.235 38.462 0.00 0.00 0.00 4.40
340 406 7.972277 TCGGTAACACTTCATACATAAGAGAAC 59.028 37.037 0.00 0.00 0.00 3.01
359 425 5.221009 CCATAGGTAAGTCAGTCTCGGTAAC 60.221 48.000 0.00 0.00 0.00 2.50
360 426 4.885907 CCATAGGTAAGTCAGTCTCGGTAA 59.114 45.833 0.00 0.00 0.00 2.85
361 427 4.164796 TCCATAGGTAAGTCAGTCTCGGTA 59.835 45.833 0.00 0.00 0.00 4.02
364 430 5.299531 TGAATCCATAGGTAAGTCAGTCTCG 59.700 44.000 0.00 0.00 0.00 4.04
365 431 6.096987 TGTGAATCCATAGGTAAGTCAGTCTC 59.903 42.308 0.00 0.00 0.00 3.36
367 444 6.043411 GTGTGAATCCATAGGTAAGTCAGTC 58.957 44.000 0.00 0.00 0.00 3.51
376 453 5.426509 TCTCAATCTGTGTGAATCCATAGGT 59.573 40.000 0.00 0.00 0.00 3.08
377 454 5.922053 TCTCAATCTGTGTGAATCCATAGG 58.078 41.667 0.00 0.00 0.00 2.57
382 459 6.815089 ACTCTATCTCAATCTGTGTGAATCC 58.185 40.000 0.00 0.00 33.62 3.01
390 467 6.441924 TCTTTCCCAACTCTATCTCAATCTGT 59.558 38.462 0.00 0.00 0.00 3.41
550 627 3.129462 TGTCTCGTGCATTGGTTTTGAAA 59.871 39.130 0.00 0.00 0.00 2.69
631 708 4.504097 CACGCGAAACAGATTATCATCAGA 59.496 41.667 15.93 0.00 0.00 3.27
633 710 3.001228 GCACGCGAAACAGATTATCATCA 59.999 43.478 15.93 0.00 0.00 3.07
663 742 2.270986 CCAGCCAGTGGTTTGGAGC 61.271 63.158 23.20 3.43 42.17 4.70
673 752 0.324943 AGCAATACGAACCAGCCAGT 59.675 50.000 0.00 0.00 0.00 4.00
677 756 1.448985 TTCCAGCAATACGAACCAGC 58.551 50.000 0.00 0.00 0.00 4.85
678 757 5.811399 TTATTTCCAGCAATACGAACCAG 57.189 39.130 0.00 0.00 0.00 4.00
679 758 6.119536 AGATTATTTCCAGCAATACGAACCA 58.880 36.000 0.00 0.00 0.00 3.67
680 759 6.619801 AGATTATTTCCAGCAATACGAACC 57.380 37.500 0.00 0.00 0.00 3.62
681 760 8.911247 AAAAGATTATTTCCAGCAATACGAAC 57.089 30.769 0.00 0.00 0.00 3.95
682 761 9.567848 GAAAAAGATTATTTCCAGCAATACGAA 57.432 29.630 0.00 0.00 31.98 3.85
683 762 7.908082 CGAAAAAGATTATTTCCAGCAATACGA 59.092 33.333 0.00 0.00 34.10 3.43
684 763 7.305418 GCGAAAAAGATTATTTCCAGCAATACG 60.305 37.037 0.00 0.00 34.10 3.06
685 764 7.305418 CGCGAAAAAGATTATTTCCAGCAATAC 60.305 37.037 0.00 0.00 34.10 1.89
686 765 6.690957 CGCGAAAAAGATTATTTCCAGCAATA 59.309 34.615 0.00 0.00 34.10 1.90
687 766 5.516339 CGCGAAAAAGATTATTTCCAGCAAT 59.484 36.000 0.00 0.00 34.10 3.56
688 767 4.856487 CGCGAAAAAGATTATTTCCAGCAA 59.144 37.500 0.00 0.00 34.10 3.91
689 768 4.083003 ACGCGAAAAAGATTATTTCCAGCA 60.083 37.500 15.93 0.00 34.10 4.41
730 809 4.755266 AAACGTAGAGCCACCAGATTAT 57.245 40.909 0.00 0.00 0.00 1.28
731 810 5.864418 ATAAACGTAGAGCCACCAGATTA 57.136 39.130 0.00 0.00 0.00 1.75
757 838 8.011673 CGCACCATAGTAATATCAATCAACAAG 58.988 37.037 0.00 0.00 0.00 3.16
771 852 4.689071 CCTGTACATTCGCACCATAGTAA 58.311 43.478 0.00 0.00 0.00 2.24
772 853 3.491964 GCCTGTACATTCGCACCATAGTA 60.492 47.826 0.00 0.00 0.00 1.82
788 869 1.625315 ACATGAGAAGCACAGCCTGTA 59.375 47.619 0.00 0.00 0.00 2.74
790 871 2.391616 TACATGAGAAGCACAGCCTG 57.608 50.000 0.00 0.00 0.00 4.85
791 872 3.641434 ATTACATGAGAAGCACAGCCT 57.359 42.857 0.00 0.00 0.00 4.58
792 873 4.708726 AAATTACATGAGAAGCACAGCC 57.291 40.909 0.00 0.00 0.00 4.85
815 896 5.163353 ACATTCCAAAGTCCAAACGGAAAAT 60.163 36.000 0.00 0.00 39.11 1.82
820 901 2.621055 TCACATTCCAAAGTCCAAACGG 59.379 45.455 0.00 0.00 0.00 4.44
821 902 3.980646 TCACATTCCAAAGTCCAAACG 57.019 42.857 0.00 0.00 0.00 3.60
822 903 6.986231 AGAATTTCACATTCCAAAGTCCAAAC 59.014 34.615 0.00 0.00 28.88 2.93
823 904 6.985645 CAGAATTTCACATTCCAAAGTCCAAA 59.014 34.615 0.00 0.00 28.88 3.28
824 905 6.462768 CCAGAATTTCACATTCCAAAGTCCAA 60.463 38.462 0.00 0.00 28.88 3.53
825 906 5.010922 CCAGAATTTCACATTCCAAAGTCCA 59.989 40.000 0.00 0.00 28.88 4.02
826 907 5.243730 TCCAGAATTTCACATTCCAAAGTCC 59.756 40.000 0.00 0.00 28.88 3.85
827 908 6.331369 TCCAGAATTTCACATTCCAAAGTC 57.669 37.500 0.00 0.00 0.00 3.01
829 910 5.636543 GCTTCCAGAATTTCACATTCCAAAG 59.363 40.000 0.00 0.00 0.00 2.77
862 1076 2.009208 TTGGCCAGGGTAAAACGGGT 62.009 55.000 5.11 0.00 0.00 5.28
930 1145 1.012841 CTTCATTCTCTTCGCAGCCC 58.987 55.000 0.00 0.00 0.00 5.19
935 1150 4.154717 GTTTGAAGCTTCATTCTCTTCGC 58.845 43.478 28.89 8.49 39.12 4.70
951 1166 1.315981 TGTGCGGTGGCTTGTTTGAA 61.316 50.000 0.00 0.00 40.82 2.69
955 1170 3.595758 GCTGTGCGGTGGCTTGTT 61.596 61.111 0.00 0.00 40.82 2.83
965 1180 2.049526 TCGTGTACCTGCTGTGCG 60.050 61.111 0.00 0.00 31.26 5.34
975 1190 3.119424 CCTCTTTCCTTCCTCTCGTGTAC 60.119 52.174 0.00 0.00 0.00 2.90
986 1201 1.432270 CGCCATCGCCTCTTTCCTTC 61.432 60.000 0.00 0.00 0.00 3.46
993 1208 3.157252 ATGGTCGCCATCGCCTCT 61.157 61.111 5.65 0.00 40.74 3.69
1218 1439 0.317854 CGCCGTCGAAGAGCATGATA 60.318 55.000 0.00 0.00 36.95 2.15
1306 1527 3.462678 GTCGCTCTGGAGGGGGAC 61.463 72.222 7.87 7.87 41.19 4.46
1471 1701 3.826524 TGTATGACCTGCACTTCCAAAA 58.173 40.909 0.00 0.00 0.00 2.44
1476 1706 4.256920 ACTTGATGTATGACCTGCACTTC 58.743 43.478 0.00 0.00 0.00 3.01
1477 1707 4.019860 AGACTTGATGTATGACCTGCACTT 60.020 41.667 0.00 0.00 0.00 3.16
1478 1708 3.517100 AGACTTGATGTATGACCTGCACT 59.483 43.478 0.00 0.00 0.00 4.40
1503 1733 0.179048 CCATTATCCTCAGCACGGCA 60.179 55.000 0.00 0.00 0.00 5.69
1575 1805 6.258230 TGAAATGTGAATTGAGCTTACAGG 57.742 37.500 0.00 0.00 0.00 4.00
1600 1846 5.817296 TGCTACTTATATTGCAGTGGTTCAG 59.183 40.000 0.00 0.00 0.00 3.02
1615 1861 7.516785 CGCAACGAATCAGTAATTGCTACTTAT 60.517 37.037 0.00 0.00 42.73 1.73
1616 1862 6.237728 CGCAACGAATCAGTAATTGCTACTTA 60.238 38.462 0.00 0.00 42.73 2.24
1617 1863 5.445939 CGCAACGAATCAGTAATTGCTACTT 60.446 40.000 0.00 0.00 42.73 2.24
1619 1865 4.032445 TCGCAACGAATCAGTAATTGCTAC 59.968 41.667 0.00 0.00 42.73 3.58
1620 1866 4.177783 TCGCAACGAATCAGTAATTGCTA 58.822 39.130 0.00 0.00 42.73 3.49
1621 1867 3.000041 TCGCAACGAATCAGTAATTGCT 59.000 40.909 5.80 0.00 42.73 3.91
1622 1868 3.383546 TCGCAACGAATCAGTAATTGC 57.616 42.857 0.00 0.00 41.74 3.56
1623 1869 3.720818 GCATCGCAACGAATCAGTAATTG 59.279 43.478 0.00 0.00 39.99 2.32
1624 1870 3.242739 GGCATCGCAACGAATCAGTAATT 60.243 43.478 0.00 0.00 39.99 1.40
1625 1871 2.287915 GGCATCGCAACGAATCAGTAAT 59.712 45.455 0.00 0.00 39.99 1.89
1626 1872 1.663643 GGCATCGCAACGAATCAGTAA 59.336 47.619 0.00 0.00 39.99 2.24
1631 1877 0.317269 CCATGGCATCGCAACGAATC 60.317 55.000 0.00 0.00 39.99 2.52
1638 1884 2.111669 CCTAGCCATGGCATCGCA 59.888 61.111 37.18 15.87 44.88 5.10
1860 2229 9.816354 GTGCTAAAATTGGATTGGTTGTAATAT 57.184 29.630 0.00 0.00 0.00 1.28
1861 2230 9.030452 AGTGCTAAAATTGGATTGGTTGTAATA 57.970 29.630 0.00 0.00 0.00 0.98
1948 2318 5.555966 TGTGAACATAGTGCTTGGACATAA 58.444 37.500 0.00 0.00 0.00 1.90
2043 2413 5.868454 ACAAAAGCCAAAATCCTAAATGCT 58.132 33.333 0.00 0.00 0.00 3.79
2244 4694 7.309177 TGAAAGACAACGATTGAAACTGAAAA 58.691 30.769 0.00 0.00 0.00 2.29
2252 4702 4.083324 GCATCCTGAAAGACAACGATTGAA 60.083 41.667 0.00 0.00 34.07 2.69
2257 4707 2.542020 TGCATCCTGAAAGACAACGA 57.458 45.000 0.00 0.00 34.07 3.85
2259 4710 4.005650 TCAGATGCATCCTGAAAGACAAC 58.994 43.478 23.06 0.00 37.68 3.32
2263 4714 4.498894 ACATCAGATGCATCCTGAAAGA 57.501 40.909 23.06 11.62 43.07 2.52
2265 4716 5.121105 CACTACATCAGATGCATCCTGAAA 58.879 41.667 23.06 13.28 43.07 2.69
2267 4718 3.070590 CCACTACATCAGATGCATCCTGA 59.929 47.826 23.06 22.78 43.84 3.86
2268 4719 3.181457 ACCACTACATCAGATGCATCCTG 60.181 47.826 23.06 18.92 0.00 3.86
2271 4722 3.136763 CCACCACTACATCAGATGCATC 58.863 50.000 19.37 19.37 0.00 3.91
2272 4723 2.507058 ACCACCACTACATCAGATGCAT 59.493 45.455 10.59 0.00 0.00 3.96
2273 4724 1.908619 ACCACCACTACATCAGATGCA 59.091 47.619 10.59 0.00 0.00 3.96
2275 4726 3.196469 AGTCACCACCACTACATCAGATG 59.804 47.826 9.03 9.03 0.00 2.90
2276 4727 3.196469 CAGTCACCACCACTACATCAGAT 59.804 47.826 0.00 0.00 0.00 2.90
2277 4728 2.562738 CAGTCACCACCACTACATCAGA 59.437 50.000 0.00 0.00 0.00 3.27
2278 4729 2.562738 TCAGTCACCACCACTACATCAG 59.437 50.000 0.00 0.00 0.00 2.90
2282 4733 3.389656 TGAATTCAGTCACCACCACTACA 59.610 43.478 3.38 0.00 0.00 2.74
2310 4763 2.364002 CAAAACGGGTGAGGAAACCAAT 59.636 45.455 0.00 0.00 42.47 3.16
2312 4765 1.394618 CAAAACGGGTGAGGAAACCA 58.605 50.000 0.00 0.00 42.47 3.67
2386 4839 1.902508 TCAGGGACCTCAACATGACTC 59.097 52.381 0.00 0.00 0.00 3.36
2513 4997 1.881324 CATGTGTGTGCCATCAGTTCA 59.119 47.619 0.00 0.00 0.00 3.18
2535 5039 1.002366 CACTGAAGCCGCATCTACAC 58.998 55.000 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.