Multiple sequence alignment - TraesCS6D01G343900

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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 TraesCS6D01G343900 chr6D 100.000 2348 0 0 1 2348 443843588 443845935 0.000000e+00 4337.0
1 TraesCS6D01G343900 chr6A 89.840 2382 156 43 1 2347 591427014 591429344 0.000000e+00 2979.0
2 TraesCS6D01G343900 chr6B 92.323 1003 50 19 809 1801 668245075 668246060 0.000000e+00 1400.0
3 TraesCS6D01G343900 chr6B 88.472 373 23 4 1912 2283 668246077 668246430 1.290000e-117 433.0
4 TraesCS6D01G343900 chr7A 88.924 316 29 5 1974 2287 559261584 559261895 3.660000e-103 385.0
5 TraesCS6D01G343900 chr7A 81.369 263 33 15 1099 1354 97251558 97251305 1.420000e-47 200.0
6 TraesCS6D01G343900 chrUn 92.814 167 11 1 2128 2293 478737642 478737476 8.380000e-60 241.0
7 TraesCS6D01G343900 chr7B 92.814 167 11 1 2128 2293 620326626 620326460 8.380000e-60 241.0
8 TraesCS6D01G343900 chr7B 95.161 124 6 0 1099 1222 47620197 47620074 1.840000e-46 196.0
9 TraesCS6D01G343900 chr7B 95.000 60 2 1 1295 1354 47619975 47619917 2.480000e-15 93.5
10 TraesCS6D01G343900 chr7B 83.673 98 14 2 145 242 57174505 57174600 8.940000e-15 91.6
11 TraesCS6D01G343900 chr5B 92.814 167 11 1 2128 2293 633625864 633625698 8.380000e-60 241.0
12 TraesCS6D01G343900 chr7D 90.972 144 11 2 1099 1240 93938186 93938043 2.380000e-45 193.0
13 TraesCS6D01G343900 chr7D 93.333 60 3 1 1288 1347 93937966 93937908 1.160000e-13 87.9
14 TraesCS6D01G343900 chr3D 78.846 104 20 2 132 233 536017188 536017291 4.190000e-08 69.4


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 TraesCS6D01G343900 chr6D 443843588 443845935 2347 False 4337.0 4337 100.0000 1 2348 1 chr6D.!!$F1 2347
1 TraesCS6D01G343900 chr6A 591427014 591429344 2330 False 2979.0 2979 89.8400 1 2347 1 chr6A.!!$F1 2346
2 TraesCS6D01G343900 chr6B 668245075 668246430 1355 False 916.5 1400 90.3975 809 2283 2 chr6B.!!$F1 1474

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
177 191 0.169672 GTGTGTGATGTCAGCATGGC 59.83 55.0 0.0 0.0 44.49 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1640 1670 0.391793 TGGCACGACACAAACAGACA 60.392 50.0 0.0 0.0 0.0 3.41 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
157 171 9.705290 AAACATGAATAACAAAGGATAAACCAC 57.295 29.630 0.00 0.00 42.04 4.16
176 190 0.445043 CGTGTGTGATGTCAGCATGG 59.555 55.000 0.00 0.00 35.07 3.66
177 191 0.169672 GTGTGTGATGTCAGCATGGC 59.830 55.000 0.00 0.00 44.49 4.40
240 254 2.278271 GCGAGCCGAGCTACTGTC 60.278 66.667 0.00 0.00 39.88 3.51
278 293 4.954092 AAGCTACTGTCTTGCATAAAGC 57.046 40.909 0.00 0.00 45.96 3.51
291 306 2.351835 GCATAAAGCGAGAGATAGCCGA 60.352 50.000 0.00 0.00 0.00 5.54
314 329 1.021390 CCCGATGAATCCGCCTATGC 61.021 60.000 0.00 0.00 0.00 3.14
318 333 1.802960 GATGAATCCGCCTATGCTGTG 59.197 52.381 0.00 0.00 34.43 3.66
329 344 3.474600 CCTATGCTGTGAAGATTGGAGG 58.525 50.000 0.00 0.00 0.00 4.30
332 347 0.807496 GCTGTGAAGATTGGAGGCAC 59.193 55.000 0.00 0.00 0.00 5.01
337 352 1.002134 AAGATTGGAGGCACGGTGG 60.002 57.895 10.60 0.00 0.00 4.61
345 360 1.310904 GAGGCACGGTGGTTTAAACA 58.689 50.000 19.57 3.79 0.00 2.83
350 366 3.243602 GGCACGGTGGTTTAAACAGAAAT 60.244 43.478 19.57 0.00 0.00 2.17
405 422 6.431198 TTTTATGTATGCGGAGTTCTTTCC 57.569 37.500 0.00 0.00 0.00 3.13
419 436 6.301169 AGTTCTTTCCTCCGATGTAAAGAT 57.699 37.500 0.00 0.00 37.68 2.40
424 441 7.338710 TCTTTCCTCCGATGTAAAGATCATTT 58.661 34.615 0.00 0.00 34.05 2.32
432 449 8.739039 TCCGATGTAAAGATCATTTTTGAACAT 58.261 29.630 0.00 0.00 0.00 2.71
436 453 8.309163 TGTAAAGATCATTTTTGAACATTGCC 57.691 30.769 0.00 0.00 0.00 4.52
443 460 5.884792 TCATTTTTGAACATTGCCAAAAGGT 59.115 32.000 13.58 7.65 41.45 3.50
525 542 2.727429 TTTACAGTGTCCCCCTACCT 57.273 50.000 0.00 0.00 0.00 3.08
543 560 6.603201 CCCTACCTTTTCATTTGCTGATTCTA 59.397 38.462 0.00 0.00 32.72 2.10
591 608 6.660949 CCAATTAATATAGCTCTCCCAAAGGG 59.339 42.308 0.00 0.00 46.11 3.95
593 610 6.841781 TTAATATAGCTCTCCCAAAGGGTT 57.158 37.500 1.36 0.00 44.74 4.11
598 615 2.177888 AGCTCTCCCAAAGGGTTTTCTT 59.822 45.455 1.36 0.00 44.74 2.52
672 690 8.168058 AGCTTATTCAACTTAAACTTAAGGGGA 58.832 33.333 7.53 7.33 43.38 4.81
692 710 3.118811 GGACATAGCAAAGAGAGCTGTCT 60.119 47.826 7.74 7.74 43.33 3.41
695 713 6.232581 ACATAGCAAAGAGAGCTGTCTAAT 57.767 37.500 14.66 3.48 43.33 1.73
696 714 6.279882 ACATAGCAAAGAGAGCTGTCTAATC 58.720 40.000 14.66 5.99 43.33 1.75
728 746 0.740737 GTGAACATATGGGCCACAGC 59.259 55.000 9.28 0.00 38.76 4.40
729 747 0.625316 TGAACATATGGGCCACAGCT 59.375 50.000 9.28 0.00 39.73 4.24
733 751 0.820891 CATATGGGCCACAGCTGGAC 60.821 60.000 19.93 3.45 46.67 4.02
735 753 1.626356 TATGGGCCACAGCTGGACTC 61.626 60.000 19.93 7.26 46.57 3.36
769 788 3.963428 ACTGTGATTGTACCACTCTCC 57.037 47.619 0.00 0.00 35.66 3.71
781 800 3.093172 CTCTCCCCAAGAGCCCCC 61.093 72.222 0.00 0.00 44.95 5.40
801 820 6.062258 CCCCCTTTGTTTCTCTAACATAGA 57.938 41.667 8.89 0.00 45.72 1.98
812 831 4.081087 TCTCTAACATAGACCAAGCCCAAC 60.081 45.833 0.00 0.00 0.00 3.77
824 844 4.227300 ACCAAGCCCAACAAGACTATATCA 59.773 41.667 0.00 0.00 0.00 2.15
832 852 7.702348 GCCCAACAAGACTATATCAATCAAAAC 59.298 37.037 0.00 0.00 0.00 2.43
841 861 8.409358 ACTATATCAATCAAAACATAAGGCCC 57.591 34.615 0.00 0.00 0.00 5.80
877 897 1.313812 CCTTGGTCGCTACTCGTCCT 61.314 60.000 2.78 0.00 44.79 3.85
1060 1080 0.955919 CTCCTCCAGCGTTTCAACCC 60.956 60.000 0.00 0.00 0.00 4.11
1237 1258 2.764547 CCGTCCCTCCTCCTTCCC 60.765 72.222 0.00 0.00 0.00 3.97
1256 1279 3.878667 CCCCTTCGATCCAGCCCC 61.879 72.222 0.00 0.00 0.00 5.80
1358 1383 2.029221 GTTCTAGATCCGGCCCGC 59.971 66.667 0.00 0.00 0.00 6.13
1457 1483 3.121929 AGCTAGGAAGTGATTCCAGGA 57.878 47.619 9.55 0.00 43.54 3.86
1458 1484 3.663198 AGCTAGGAAGTGATTCCAGGAT 58.337 45.455 9.55 0.00 43.54 3.24
1623 1653 5.419542 GAATGGTCTACTGTATTGTGCTGA 58.580 41.667 0.00 0.00 0.00 4.26
1626 1656 4.122776 GGTCTACTGTATTGTGCTGATGG 58.877 47.826 0.00 0.00 0.00 3.51
1640 1670 6.179756 TGTGCTGATGGTTATTTCTGTGTAT 58.820 36.000 0.00 0.00 0.00 2.29
1653 1683 5.984233 TTCTGTGTATGTCTGTTTGTGTC 57.016 39.130 0.00 0.00 0.00 3.67
1664 1694 1.474478 TGTTTGTGTCGTGCCATTGTT 59.526 42.857 0.00 0.00 0.00 2.83
1667 1697 4.202060 TGTTTGTGTCGTGCCATTGTTATT 60.202 37.500 0.00 0.00 0.00 1.40
1707 1737 2.231478 TGTAGTGAACTGGCTGCTAGTC 59.769 50.000 19.20 12.66 0.00 2.59
1721 1751 5.510520 GGCTGCTAGTCATGCTATCTAGTTT 60.511 44.000 0.00 0.00 35.14 2.66
1775 1808 1.946768 TGTTGTTGCAGACCACTTAGC 59.053 47.619 0.00 0.00 0.00 3.09
1804 1839 5.070714 AGAGAGAGAGGGATGTGATTTGATG 59.929 44.000 0.00 0.00 0.00 3.07
1805 1840 4.967442 AGAGAGAGGGATGTGATTTGATGA 59.033 41.667 0.00 0.00 0.00 2.92
1823 1858 8.434733 TTTGATGATTGTTTTCTTGATTTGCA 57.565 26.923 0.00 0.00 0.00 4.08
1824 1859 7.410800 TGATGATTGTTTTCTTGATTTGCAC 57.589 32.000 0.00 0.00 0.00 4.57
1849 1888 8.702819 ACTAACTACTAAGGTATTTCATGTCCC 58.297 37.037 0.00 0.00 0.00 4.46
1850 1889 7.750947 AACTACTAAGGTATTTCATGTCCCT 57.249 36.000 0.00 0.00 0.00 4.20
1851 1890 7.125792 ACTACTAAGGTATTTCATGTCCCTG 57.874 40.000 0.00 0.00 0.00 4.45
1858 1897 6.415573 AGGTATTTCATGTCCCTGTAAGTTC 58.584 40.000 0.00 0.00 0.00 3.01
1862 1901 4.537135 TCATGTCCCTGTAAGTTCTGAC 57.463 45.455 0.00 0.00 0.00 3.51
1863 1902 3.901222 TCATGTCCCTGTAAGTTCTGACA 59.099 43.478 0.00 0.00 37.17 3.58
1864 1903 4.532126 TCATGTCCCTGTAAGTTCTGACAT 59.468 41.667 0.00 0.00 42.44 3.06
1866 1905 3.901222 TGTCCCTGTAAGTTCTGACATGA 59.099 43.478 0.00 0.00 0.00 3.07
1868 1907 3.515502 TCCCTGTAAGTTCTGACATGAGG 59.484 47.826 0.00 0.00 0.00 3.86
1869 1908 3.261897 CCCTGTAAGTTCTGACATGAGGT 59.738 47.826 0.00 0.00 0.00 3.85
1870 1909 4.263068 CCCTGTAAGTTCTGACATGAGGTT 60.263 45.833 0.00 0.00 0.00 3.50
1871 1910 5.308825 CCTGTAAGTTCTGACATGAGGTTT 58.691 41.667 0.00 0.00 0.00 3.27
1872 1911 5.765182 CCTGTAAGTTCTGACATGAGGTTTT 59.235 40.000 0.00 0.00 0.00 2.43
1896 1935 5.699097 TTTCCTACCAGCATGTGTTTAAC 57.301 39.130 0.00 0.00 0.00 2.01
1929 1968 6.693315 TTATATTTTGTAAGCAGGGTCAGC 57.307 37.500 0.00 0.00 0.00 4.26
2020 2059 3.064207 ACATGGCGTGTAGTACAGTTTG 58.936 45.455 11.37 0.77 39.91 2.93
2101 2148 8.936864 AGTTTTGAGTACTGTATTATGACTTGC 58.063 33.333 0.00 0.00 0.00 4.01
2102 2149 8.936864 GTTTTGAGTACTGTATTATGACTTGCT 58.063 33.333 0.00 0.00 0.00 3.91
2103 2150 8.479313 TTTGAGTACTGTATTATGACTTGCTG 57.521 34.615 0.00 0.00 0.00 4.41
2104 2151 7.170393 TGAGTACTGTATTATGACTTGCTGT 57.830 36.000 0.00 0.00 0.00 4.40
2105 2152 7.611770 TGAGTACTGTATTATGACTTGCTGTT 58.388 34.615 0.00 0.00 0.00 3.16
2106 2153 8.094548 TGAGTACTGTATTATGACTTGCTGTTT 58.905 33.333 0.00 0.00 0.00 2.83
2107 2154 8.256611 AGTACTGTATTATGACTTGCTGTTTG 57.743 34.615 0.00 0.00 0.00 2.93
2108 2155 8.094548 AGTACTGTATTATGACTTGCTGTTTGA 58.905 33.333 0.00 0.00 0.00 2.69
2109 2156 7.369803 ACTGTATTATGACTTGCTGTTTGAG 57.630 36.000 0.00 0.00 0.00 3.02
2135 2182 9.490663 GTTGTACAAATTGACATACTGATTAGC 57.509 33.333 10.51 0.00 0.00 3.09
2212 2259 5.589452 CCTCTGTCTAGTCGGTACAAACTAT 59.411 44.000 6.96 0.00 0.00 2.12
2224 2271 8.806146 GTCGGTACAAACTATATTTCCCCTATA 58.194 37.037 0.00 0.00 0.00 1.31
2225 2272 9.028284 TCGGTACAAACTATATTTCCCCTATAG 57.972 37.037 0.00 0.00 35.95 1.31
2305 2353 9.693739 ATGAGCTATAGTATTATGAGCTAGTGT 57.306 33.333 5.34 0.00 43.39 3.55
2327 2375 6.472808 GTGTCTTAAATACAGTCTTCCTAGCG 59.527 42.308 0.00 0.00 0.00 4.26
2347 2395 0.976641 TCAGAGAATCGCCACAGGTT 59.023 50.000 0.00 0.00 42.67 3.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
139 153 5.766174 ACACACGTGGTTTATCCTTTGTTAT 59.234 36.000 21.57 0.00 37.07 1.89
141 155 3.949113 ACACACGTGGTTTATCCTTTGTT 59.051 39.130 21.57 0.00 37.07 2.83
148 162 3.743911 TGACATCACACACGTGGTTTATC 59.256 43.478 21.57 8.79 43.79 1.75
150 164 3.127589 CTGACATCACACACGTGGTTTA 58.872 45.455 21.57 2.77 43.79 2.01
157 171 0.445043 CCATGCTGACATCACACACG 59.555 55.000 0.00 0.00 32.87 4.49
166 180 4.408821 GGGTCCGCCATGCTGACA 62.409 66.667 11.75 0.00 42.92 3.58
176 190 1.000955 CTAGTATCCATGTGGGTCCGC 59.999 57.143 0.00 0.00 38.11 5.54
177 191 1.618837 CCTAGTATCCATGTGGGTCCG 59.381 57.143 0.00 0.00 38.11 4.79
263 278 3.515630 TCTCTCGCTTTATGCAAGACAG 58.484 45.455 0.00 0.00 43.06 3.51
264 279 3.592898 TCTCTCGCTTTATGCAAGACA 57.407 42.857 0.00 0.00 43.06 3.41
278 293 2.252855 GGCGTCGGCTATCTCTCG 59.747 66.667 12.17 0.00 39.81 4.04
291 306 4.910585 GCGGATTCATCGGGGCGT 62.911 66.667 0.00 0.00 0.00 5.68
314 329 1.081892 CGTGCCTCCAATCTTCACAG 58.918 55.000 0.00 0.00 0.00 3.66
318 333 1.026718 CCACCGTGCCTCCAATCTTC 61.027 60.000 0.00 0.00 0.00 2.87
329 344 3.423996 TTTCTGTTTAAACCACCGTGC 57.576 42.857 15.59 0.00 0.00 5.34
332 347 6.496571 TGTTACATTTCTGTTTAAACCACCG 58.503 36.000 15.59 2.37 36.79 4.94
405 422 8.236586 TGTTCAAAAATGATCTTTACATCGGAG 58.763 33.333 0.00 0.00 0.00 4.63
409 426 9.962759 GCAATGTTCAAAAATGATCTTTACATC 57.037 29.630 6.98 0.00 0.00 3.06
419 436 5.884792 ACCTTTTGGCAATGTTCAAAAATGA 59.115 32.000 0.00 0.00 45.59 2.57
424 441 5.983540 AGTTACCTTTTGGCAATGTTCAAA 58.016 33.333 0.00 0.00 45.59 2.69
432 449 4.282195 CACCCATTAGTTACCTTTTGGCAA 59.718 41.667 0.00 0.00 45.59 4.52
436 453 5.533154 TGTGTCACCCATTAGTTACCTTTTG 59.467 40.000 0.00 0.00 0.00 2.44
443 460 3.615592 GCTCGTGTGTCACCCATTAGTTA 60.616 47.826 0.00 0.00 0.00 2.24
456 473 5.651387 ATATGCATAGATAGCTCGTGTGT 57.349 39.130 12.79 0.00 0.00 3.72
458 475 7.969536 AAAAATATGCATAGATAGCTCGTGT 57.030 32.000 12.79 0.00 0.00 4.49
505 522 2.994355 AGGTAGGGGGACACTGTAAAA 58.006 47.619 0.00 0.00 0.00 1.52
506 523 2.727429 AGGTAGGGGGACACTGTAAA 57.273 50.000 0.00 0.00 0.00 2.01
507 524 2.727429 AAGGTAGGGGGACACTGTAA 57.273 50.000 0.00 0.00 0.00 2.41
508 525 2.727429 AAAGGTAGGGGGACACTGTA 57.273 50.000 0.00 0.00 0.00 2.74
514 531 2.496070 GCAAATGAAAAGGTAGGGGGAC 59.504 50.000 0.00 0.00 0.00 4.46
561 578 8.917414 TGGGAGAGCTATATTAATTGGATAGT 57.083 34.615 0.00 0.00 0.00 2.12
580 597 6.549736 CTTTTCTAAGAAAACCCTTTGGGAGA 59.450 38.462 9.94 0.00 38.18 3.71
672 690 5.667539 TTAGACAGCTCTCTTTGCTATGT 57.332 39.130 0.00 0.00 38.92 2.29
696 714 7.148018 GCCCATATGTTCACTATATCCAAATGG 60.148 40.741 1.24 0.00 0.00 3.16
709 727 0.740737 GCTGTGGCCCATATGTTCAC 59.259 55.000 0.00 7.51 0.00 3.18
728 746 0.549950 AGGGCCATGAATGAGTCCAG 59.450 55.000 6.18 0.00 0.00 3.86
729 747 1.891933 TAGGGCCATGAATGAGTCCA 58.108 50.000 6.18 0.00 0.00 4.02
733 751 2.947652 CACAGTTAGGGCCATGAATGAG 59.052 50.000 16.75 4.57 0.00 2.90
735 753 3.003394 TCACAGTTAGGGCCATGAATG 57.997 47.619 8.15 8.15 0.00 2.67
797 816 2.644798 AGTCTTGTTGGGCTTGGTCTAT 59.355 45.455 0.00 0.00 0.00 1.98
799 818 0.846693 AGTCTTGTTGGGCTTGGTCT 59.153 50.000 0.00 0.00 0.00 3.85
801 820 4.227300 TGATATAGTCTTGTTGGGCTTGGT 59.773 41.667 0.00 0.00 0.00 3.67
824 844 2.501316 GGCTGGGCCTTATGTTTTGATT 59.499 45.455 4.53 0.00 46.69 2.57
841 861 2.825836 GATGGGCTCGTTGGGCTG 60.826 66.667 0.00 0.00 0.00 4.85
877 897 3.844211 GGGCAGTGGGGAATATATAGTCA 59.156 47.826 11.96 0.00 0.00 3.41
1011 1031 1.767681 CTCCATGGAAAGAGAGGAGGG 59.232 57.143 17.00 0.00 41.65 4.30
1060 1080 1.525306 GGAAATCGGGTTAGCGGGG 60.525 63.158 0.00 0.00 0.00 5.73
1067 1087 2.036571 GCGAACGGGAAATCGGGTT 61.037 57.895 0.00 0.00 39.38 4.11
1267 1290 1.369692 AACGATTGGTCGGTCAGCA 59.630 52.632 2.76 0.00 46.84 4.41
1457 1483 7.921214 ACGACGAAATTGATAACAGAGACATAT 59.079 33.333 0.00 0.00 0.00 1.78
1458 1484 7.220108 CACGACGAAATTGATAACAGAGACATA 59.780 37.037 0.00 0.00 0.00 2.29
1623 1653 8.514594 CAAACAGACATACACAGAAATAACCAT 58.485 33.333 0.00 0.00 0.00 3.55
1626 1656 8.342634 ACACAAACAGACATACACAGAAATAAC 58.657 33.333 0.00 0.00 0.00 1.89
1640 1670 0.391793 TGGCACGACACAAACAGACA 60.392 50.000 0.00 0.00 0.00 3.41
1775 1808 3.117926 TCACATCCCTCTCTCTCTCTCTG 60.118 52.174 0.00 0.00 0.00 3.35
1804 1839 8.579682 AGTTAGTGCAAATCAAGAAAACAATC 57.420 30.769 0.00 0.00 0.00 2.67
1805 1840 9.463443 GTAGTTAGTGCAAATCAAGAAAACAAT 57.537 29.630 0.00 0.00 0.00 2.71
1823 1858 8.702819 GGGACATGAAATACCTTAGTAGTTAGT 58.297 37.037 0.00 0.00 36.92 2.24
1824 1859 8.925338 AGGGACATGAAATACCTTAGTAGTTAG 58.075 37.037 0.00 0.00 36.92 2.34
1849 1888 6.867662 AAAACCTCATGTCAGAACTTACAG 57.132 37.500 0.00 0.00 0.00 2.74
1872 1911 6.508777 GTTAAACACATGCTGGTAGGAAAAA 58.491 36.000 0.00 0.00 0.00 1.94
1877 1916 3.071479 ACGTTAAACACATGCTGGTAGG 58.929 45.455 0.00 0.00 0.00 3.18
1878 1917 4.927425 ACTACGTTAAACACATGCTGGTAG 59.073 41.667 0.00 0.00 0.00 3.18
1894 1933 9.830294 GCTTACAAAATATAAACCAACTACGTT 57.170 29.630 0.00 0.00 0.00 3.99
1896 1935 9.485591 CTGCTTACAAAATATAAACCAACTACG 57.514 33.333 0.00 0.00 0.00 3.51
1910 1949 3.160679 AGCTGACCCTGCTTACAAAAT 57.839 42.857 0.00 0.00 35.17 1.82
1915 1954 2.230660 ACAAAAGCTGACCCTGCTTAC 58.769 47.619 10.64 0.00 45.29 2.34
1929 1968 8.385898 TCTACATGTAAACAGGGTTACAAAAG 57.614 34.615 13.35 10.79 44.80 2.27
2020 2059 4.457466 TGGTTAAACCAGAAGTGAACTCC 58.543 43.478 0.00 0.00 44.79 3.85
2050 2089 1.604604 TGAGTTGGTAACTGGCAAGC 58.395 50.000 0.00 0.00 43.03 4.01
2086 2133 7.369803 ACTCAAACAGCAAGTCATAATACAG 57.630 36.000 0.00 0.00 0.00 2.74
2087 2134 7.228507 ACAACTCAAACAGCAAGTCATAATACA 59.771 33.333 0.00 0.00 0.00 2.29
2088 2135 7.584987 ACAACTCAAACAGCAAGTCATAATAC 58.415 34.615 0.00 0.00 0.00 1.89
2089 2136 7.744087 ACAACTCAAACAGCAAGTCATAATA 57.256 32.000 0.00 0.00 0.00 0.98
2090 2137 6.639632 ACAACTCAAACAGCAAGTCATAAT 57.360 33.333 0.00 0.00 0.00 1.28
2091 2138 6.540551 TGTACAACTCAAACAGCAAGTCATAA 59.459 34.615 0.00 0.00 0.00 1.90
2092 2139 6.052360 TGTACAACTCAAACAGCAAGTCATA 58.948 36.000 0.00 0.00 0.00 2.15
2093 2140 4.881273 TGTACAACTCAAACAGCAAGTCAT 59.119 37.500 0.00 0.00 0.00 3.06
2094 2141 4.257731 TGTACAACTCAAACAGCAAGTCA 58.742 39.130 0.00 0.00 0.00 3.41
2095 2142 4.875544 TGTACAACTCAAACAGCAAGTC 57.124 40.909 0.00 0.00 0.00 3.01
2096 2143 5.637006 TTTGTACAACTCAAACAGCAAGT 57.363 34.783 8.07 0.00 31.17 3.16
2097 2144 6.751425 TCAATTTGTACAACTCAAACAGCAAG 59.249 34.615 8.07 0.00 37.56 4.01
2098 2145 6.529829 GTCAATTTGTACAACTCAAACAGCAA 59.470 34.615 8.07 0.00 37.56 3.91
2099 2146 6.033341 GTCAATTTGTACAACTCAAACAGCA 58.967 36.000 8.07 0.00 37.56 4.41
2100 2147 6.033341 TGTCAATTTGTACAACTCAAACAGC 58.967 36.000 8.07 0.00 37.56 4.40
2101 2148 9.169468 GTATGTCAATTTGTACAACTCAAACAG 57.831 33.333 8.07 0.00 37.56 3.16
2102 2149 8.898761 AGTATGTCAATTTGTACAACTCAAACA 58.101 29.630 8.07 9.68 37.56 2.83
2103 2150 9.169468 CAGTATGTCAATTTGTACAACTCAAAC 57.831 33.333 8.07 4.32 37.56 2.93
2104 2151 9.114952 TCAGTATGTCAATTTGTACAACTCAAA 57.885 29.630 8.07 0.00 36.98 2.69
2105 2152 8.669946 TCAGTATGTCAATTTGTACAACTCAA 57.330 30.769 8.07 0.00 37.40 3.02
2106 2153 8.846943 ATCAGTATGTCAATTTGTACAACTCA 57.153 30.769 8.07 4.09 37.40 3.41
2109 2156 9.490663 GCTAATCAGTATGTCAATTTGTACAAC 57.509 33.333 8.07 0.00 37.40 3.32
2174 2221 2.203181 GAGGCATGGCTCTGAGGC 60.203 66.667 35.12 22.95 41.77 4.70
2224 2271 5.441718 TTGAAAATACATCAGCTCCTCCT 57.558 39.130 0.00 0.00 0.00 3.69
2225 2272 6.705863 ATTTGAAAATACATCAGCTCCTCC 57.294 37.500 0.00 0.00 0.00 4.30
2263 2310 2.223340 GCTCATATTTTGGTCACAGCCG 60.223 50.000 0.00 0.00 0.00 5.52
2300 2348 8.684520 GCTAGGAAGACTGTATTTAAGACACTA 58.315 37.037 0.00 0.00 0.00 2.74
2304 2352 6.562518 ACGCTAGGAAGACTGTATTTAAGAC 58.437 40.000 0.00 0.00 0.00 3.01
2305 2353 6.376299 TGACGCTAGGAAGACTGTATTTAAGA 59.624 38.462 0.00 0.00 0.00 2.10
2314 2362 2.360844 TCTCTGACGCTAGGAAGACTG 58.639 52.381 0.00 0.00 0.00 3.51
2315 2363 2.791347 TCTCTGACGCTAGGAAGACT 57.209 50.000 0.00 0.00 0.00 3.24
2318 2366 2.993545 CGATTCTCTGACGCTAGGAAG 58.006 52.381 0.00 0.00 0.00 3.46
2327 2375 0.247736 ACCTGTGGCGATTCTCTGAC 59.752 55.000 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.