Multiple sequence alignment - TraesCS5A01G497800

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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 TraesCS5A01G497800 chr5A 100.000 5516 0 0 1 5516 664813925 664808410 0 10187
1 TraesCS5A01G497800 chr4D 92.961 5626 221 65 1 5516 484407165 484401605 0 8034
2 TraesCS5A01G497800 chr4B 91.501 3424 159 45 1 3332 616310629 616307246 0 4590
3 TraesCS5A01G497800 chr4B 90.778 1247 90 17 3336 4573 616307183 616305953 0 1642
4 TraesCS5A01G497800 chr4B 85.104 913 58 38 4637 5516 616305872 616305005 0 861


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 TraesCS5A01G497800 chr5A 664808410 664813925 5515 True 10187.000000 10187 100.000000 1 5516 1 chr5A.!!$R1 5515
1 TraesCS5A01G497800 chr4D 484401605 484407165 5560 True 8034.000000 8034 92.961000 1 5516 1 chr4D.!!$R1 5515
2 TraesCS5A01G497800 chr4B 616305005 616310629 5624 True 2364.333333 4590 89.127667 1 5516 3 chr4B.!!$R1 5515

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
478 577 0.618968 AGGAGTTGGAGGGGCACTAG 60.619 60.0 0.00 0.0 0.00 2.57 F
1746 1872 0.108804 ACGCCGAGATCGACAACATT 60.109 50.0 3.31 0.0 43.02 2.71 F
2428 2564 0.040058 ATGAGCCATGTTTCTGCCCA 59.960 50.0 0.00 0.0 0.00 5.36 F
3109 3248 1.294659 CGGTGAGCCTGCAAGAACTC 61.295 60.0 0.00 0.0 37.43 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1787 1913 0.035439 GGAGAATGGAAAGGGCGACA 60.035 55.0 0.00 0.00 0.00 4.35 R
3082 3221 0.884704 GCAGGCTCACCGTTTTCTCA 60.885 55.0 0.00 0.00 42.76 3.27 R
3374 3577 1.053048 CGTAGCATCGAGGCAATACG 58.947 55.0 25.38 24.01 33.60 3.06 R
5017 5268 0.716108 CTTACACAAGCGAGAAGGCG 59.284 55.0 0.00 0.00 38.18 5.52 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
28 29 2.124693 CCGAGGAGGAGAGGCAGAC 61.125 68.421 0.00 0.00 45.00 3.51
252 309 3.838271 TGATCCGGAGCCGCTCAC 61.838 66.667 18.75 10.25 38.24 3.51
381 472 3.936902 TTCCTTGTCGTTTTCTTCGTG 57.063 42.857 0.00 0.00 0.00 4.35
382 473 3.167921 TCCTTGTCGTTTTCTTCGTGA 57.832 42.857 0.00 0.00 0.00 4.35
386 477 1.591158 TGTCGTTTTCTTCGTGAGCAC 59.409 47.619 0.00 0.00 0.00 4.40
387 478 1.859080 GTCGTTTTCTTCGTGAGCACT 59.141 47.619 0.00 0.00 0.00 4.40
412 511 3.213402 CTCCTCCTCCGTCTCCGC 61.213 72.222 0.00 0.00 0.00 5.54
421 520 4.493747 CGTCTCCGCGGGGAAGAC 62.494 72.222 33.94 30.07 43.27 3.01
437 536 1.109920 AGACGAGACGCCATGGCTAT 61.110 55.000 33.07 21.79 39.32 2.97
438 537 0.941463 GACGAGACGCCATGGCTATG 60.941 60.000 33.07 20.69 39.32 2.23
465 564 5.836358 GCCTATGGCTATATAGCTAGGAGTT 59.164 44.000 33.78 19.24 44.09 3.01
478 577 0.618968 AGGAGTTGGAGGGGCACTAG 60.619 60.000 0.00 0.00 0.00 2.57
479 578 1.222113 GAGTTGGAGGGGCACTAGC 59.778 63.158 0.00 0.00 41.10 3.42
517 617 3.127533 GGCCAGCTAGTTGCACGG 61.128 66.667 0.00 0.04 45.94 4.94
584 689 2.101783 TCTACCGTCTCGTCTCTCTCT 58.898 52.381 0.00 0.00 0.00 3.10
585 690 2.496871 TCTACCGTCTCGTCTCTCTCTT 59.503 50.000 0.00 0.00 0.00 2.85
586 691 1.729284 ACCGTCTCGTCTCTCTCTTC 58.271 55.000 0.00 0.00 0.00 2.87
587 692 1.276989 ACCGTCTCGTCTCTCTCTTCT 59.723 52.381 0.00 0.00 0.00 2.85
598 703 5.619086 CGTCTCTCTCTTCTCTTCACTTTCC 60.619 48.000 0.00 0.00 0.00 3.13
709 819 1.939785 CGCTACCGCTACTTGCTCG 60.940 63.158 0.00 0.00 40.11 5.03
718 828 3.932580 TACTTGCTCGTGCCTGCCG 62.933 63.158 7.05 0.00 38.71 5.69
860 971 7.148490 CGAGATTTTTCCTCTCCTCTCTTTTTC 60.148 40.741 0.00 0.00 36.59 2.29
1173 1284 2.301738 CCCCTTCTCCCCGCTCTTT 61.302 63.158 0.00 0.00 0.00 2.52
1746 1872 0.108804 ACGCCGAGATCGACAACATT 60.109 50.000 3.31 0.00 43.02 2.71
1767 1893 1.550524 TGCAACGCTCTCAAGGTAGAT 59.449 47.619 0.00 0.00 0.00 1.98
1768 1894 2.028112 TGCAACGCTCTCAAGGTAGATT 60.028 45.455 0.00 0.00 0.00 2.40
1769 1895 3.194755 TGCAACGCTCTCAAGGTAGATTA 59.805 43.478 0.00 0.00 0.00 1.75
1773 1899 5.189659 ACGCTCTCAAGGTAGATTACATC 57.810 43.478 0.00 0.00 0.00 3.06
1774 1900 4.890581 ACGCTCTCAAGGTAGATTACATCT 59.109 41.667 0.00 0.00 43.33 2.90
1775 1901 5.361285 ACGCTCTCAAGGTAGATTACATCTT 59.639 40.000 0.00 0.00 40.76 2.40
1776 1902 6.546403 ACGCTCTCAAGGTAGATTACATCTTA 59.454 38.462 0.00 0.00 40.76 2.10
1777 1903 7.081349 CGCTCTCAAGGTAGATTACATCTTAG 58.919 42.308 0.00 0.00 40.76 2.18
1778 1904 6.866248 GCTCTCAAGGTAGATTACATCTTAGC 59.134 42.308 0.00 0.00 40.76 3.09
1779 1905 6.971602 TCTCAAGGTAGATTACATCTTAGCG 58.028 40.000 0.00 0.00 40.76 4.26
1780 1906 5.529791 TCAAGGTAGATTACATCTTAGCGC 58.470 41.667 0.00 0.00 40.76 5.92
1781 1907 5.068591 TCAAGGTAGATTACATCTTAGCGCA 59.931 40.000 11.47 0.00 40.76 6.09
1782 1908 5.730296 AGGTAGATTACATCTTAGCGCAT 57.270 39.130 11.47 0.00 40.76 4.73
1783 1909 6.102897 AGGTAGATTACATCTTAGCGCATT 57.897 37.500 11.47 0.00 40.76 3.56
1784 1910 5.928839 AGGTAGATTACATCTTAGCGCATTG 59.071 40.000 11.47 1.55 40.76 2.82
1785 1911 4.739046 AGATTACATCTTAGCGCATTGC 57.261 40.909 11.47 0.00 39.54 3.56
1787 1913 4.818546 AGATTACATCTTAGCGCATTGCTT 59.181 37.500 11.47 0.00 45.01 3.91
1788 1914 5.277683 AGATTACATCTTAGCGCATTGCTTG 60.278 40.000 11.47 2.18 45.01 4.01
1789 1915 7.623963 AGATTACATCTTAGCGCATTGCTTGT 61.624 38.462 11.47 8.61 45.01 3.16
1790 1916 9.313314 AGATTACATCTTAGCGCATTGCTTGTC 62.313 40.741 11.47 0.00 45.01 3.18
1808 1939 0.253044 TCGCCCTTTCCATTCTCCAG 59.747 55.000 0.00 0.00 0.00 3.86
1813 1944 1.064389 CCTTTCCATTCTCCAGACCCC 60.064 57.143 0.00 0.00 0.00 4.95
1817 1948 0.254178 CCATTCTCCAGACCCCTGTG 59.746 60.000 0.00 0.00 38.74 3.66
1820 1951 1.768684 TTCTCCAGACCCCTGTGTGC 61.769 60.000 0.00 0.00 38.74 4.57
1962 2093 7.362401 CCTTGATGATTCCCTTGTGTTCTAAAG 60.362 40.741 0.00 0.00 0.00 1.85
2044 2176 2.620112 CGCACAGGTGGGCTGAAAG 61.620 63.158 2.12 0.00 43.67 2.62
2054 2186 0.875059 GGGCTGAAAGAAAGACACCG 59.125 55.000 0.00 0.00 34.07 4.94
2060 2192 3.463944 TGAAAGAAAGACACCGAGTTCC 58.536 45.455 0.00 0.00 0.00 3.62
2305 2441 1.829096 TGTCTCCACCGTGGACGAA 60.829 57.895 16.73 2.45 42.67 3.85
2318 2454 0.638746 GGACGAAGCGTGTTATGTCG 59.361 55.000 0.00 0.00 41.37 4.35
2324 2460 0.870307 AGCGTGTTATGTCGGCGATC 60.870 55.000 14.79 7.74 0.00 3.69
2356 2492 1.871126 GCTTTCACCAGGCTTGCTCC 61.871 60.000 0.00 0.00 0.00 4.70
2377 2513 1.211457 GAGCATCATCTGTTCAGGGGT 59.789 52.381 0.00 0.00 35.34 4.95
2416 2552 1.377202 GCTCGGGACAAATGAGCCA 60.377 57.895 2.12 0.00 0.00 4.75
2428 2564 0.040058 ATGAGCCATGTTTCTGCCCA 59.960 50.000 0.00 0.00 0.00 5.36
2434 2570 2.173519 CCATGTTTCTGCCCAGACATT 58.826 47.619 0.00 0.00 37.14 2.71
2479 2615 4.521146 ACCCTCTCTCACATTATGCAAAG 58.479 43.478 0.00 0.00 0.00 2.77
2489 2625 2.362169 TTATGCAAAGCTTTTCGGCC 57.638 45.000 9.53 0.00 0.00 6.13
2752 2888 3.693807 TGCTGAAATCTTGGATGAGCTT 58.306 40.909 0.00 0.00 0.00 3.74
2753 2889 3.442625 TGCTGAAATCTTGGATGAGCTTG 59.557 43.478 0.00 0.00 0.00 4.01
2850 2989 5.585390 CCTTGTGGATGTTCAGAATAATGC 58.415 41.667 0.00 0.00 34.57 3.56
3076 3215 1.927895 CAATAGAGAAGCGGCGAACT 58.072 50.000 12.98 5.77 0.00 3.01
3082 3221 3.335579 AGAGAAGCGGCGAACTAAAATT 58.664 40.909 12.98 0.00 0.00 1.82
3091 3230 4.317291 CGGCGAACTAAAATTGAGAAAACG 59.683 41.667 0.00 0.00 0.00 3.60
3109 3248 1.294659 CGGTGAGCCTGCAAGAACTC 61.295 60.000 0.00 0.00 37.43 3.01
3121 3260 2.414691 GCAAGAACTCCGGAAGCATTTC 60.415 50.000 5.23 3.56 0.00 2.17
3183 3322 8.508883 GGTAACTTATGACTCTCTCAACTCTA 57.491 38.462 0.00 0.00 30.60 2.43
3196 3340 6.372103 TCTCTCAACTCTACTCTTCTTTACCG 59.628 42.308 0.00 0.00 0.00 4.02
3209 3353 7.094506 ACTCTTCTTTACCGTTCTTTTTGTTGT 60.095 33.333 0.00 0.00 0.00 3.32
3212 3356 7.800015 TCTTTACCGTTCTTTTTGTTGTTTC 57.200 32.000 0.00 0.00 0.00 2.78
3227 3371 5.964758 TGTTGTTTCACTTGCATTTTCTCT 58.035 33.333 0.00 0.00 0.00 3.10
3228 3372 6.035843 TGTTGTTTCACTTGCATTTTCTCTC 58.964 36.000 0.00 0.00 0.00 3.20
3237 3381 4.445452 TGCATTTTCTCTCTTTGGATGC 57.555 40.909 0.00 0.00 38.97 3.91
3299 3443 5.368523 CACCACTATTCCTTCCTAATACCCA 59.631 44.000 0.00 0.00 0.00 4.51
3312 3456 9.726438 CTTCCTAATACCCATATCTTTACTTGG 57.274 37.037 0.00 0.00 0.00 3.61
3331 3519 1.383523 GGTGGCTCAAATAGGAGTGC 58.616 55.000 0.00 0.00 37.24 4.40
3374 3577 5.392380 CCCAGATTTTGTACTCATTGCAGTC 60.392 44.000 0.00 0.00 0.00 3.51
3390 3593 0.747255 AGTCGTATTGCCTCGATGCT 59.253 50.000 13.93 0.00 38.32 3.79
3443 3646 6.663523 CCAAAAAGGGGAGTGTATAATCACTT 59.336 38.462 0.98 0.00 46.81 3.16
3444 3647 7.832187 CCAAAAAGGGGAGTGTATAATCACTTA 59.168 37.037 0.98 0.00 46.81 2.24
3475 3678 4.715713 ACAGGGACTCTTAAAAACAGACC 58.284 43.478 0.00 0.00 34.60 3.85
3567 3770 5.047660 AGACACACTGGTCTAGATTCTTCAC 60.048 44.000 0.00 0.00 45.95 3.18
3596 3800 5.459536 TTTGCATACATACAAACTGGCAA 57.540 34.783 0.00 0.00 38.13 4.52
3837 4041 6.459066 CAAGACTACATGGTCAGAAAGAGAA 58.541 40.000 0.00 0.00 38.57 2.87
3843 4047 4.217118 ACATGGTCAGAAAGAGAATTGCAC 59.783 41.667 0.00 0.00 0.00 4.57
3930 4134 3.657956 CGAGAGCAGATTCAGTCCC 57.342 57.895 0.00 0.00 0.00 4.46
3939 4143 3.312890 CAGATTCAGTCCCCATACCTCT 58.687 50.000 0.00 0.00 0.00 3.69
3957 4161 3.303938 CTCTGGCTCTAATTCCCTCTCA 58.696 50.000 0.00 0.00 0.00 3.27
3990 4194 3.204526 CCAGAGCTCAAATTCTAGCCTG 58.795 50.000 17.77 15.76 39.64 4.85
4351 4555 1.161843 GTTCGGCATTTCTCGGGAAA 58.838 50.000 13.89 13.89 44.26 3.13
4434 4638 3.131223 ACCTTCTGGAGTGTATCGATGTG 59.869 47.826 8.54 0.00 37.04 3.21
4476 4680 7.148557 GCTAAAACAGTTAGGATCTCTGTGAAC 60.149 40.741 11.63 2.50 41.37 3.18
4480 4684 4.956700 CAGTTAGGATCTCTGTGAACCCTA 59.043 45.833 2.84 5.21 38.27 3.53
4493 4697 0.250597 AACCCTACAGTTCAACCGGC 60.251 55.000 0.00 0.00 0.00 6.13
4929 5176 2.209064 CTTGCTTGAAGGCATGCGCT 62.209 55.000 12.44 7.25 45.31 5.92
4954 5204 7.050377 TGTGGAATTGAGAGAATTATGTCTCC 58.950 38.462 0.00 0.00 43.55 3.71
4982 5232 1.617755 CGCGTCAGTTTGAGCGTCAT 61.618 55.000 0.00 0.00 46.48 3.06
4983 5233 0.179240 GCGTCAGTTTGAGCGTCATG 60.179 55.000 0.00 0.00 0.00 3.07
4984 5234 1.418373 CGTCAGTTTGAGCGTCATGA 58.582 50.000 0.00 0.00 0.00 3.07
4985 5235 1.792367 CGTCAGTTTGAGCGTCATGAA 59.208 47.619 0.00 0.00 0.00 2.57
4986 5236 2.159920 CGTCAGTTTGAGCGTCATGAAG 60.160 50.000 4.06 4.06 0.00 3.02
4987 5237 3.059884 GTCAGTTTGAGCGTCATGAAGA 58.940 45.455 13.18 0.00 0.00 2.87
4988 5238 3.122613 GTCAGTTTGAGCGTCATGAAGAG 59.877 47.826 13.18 1.31 0.00 2.85
4989 5239 3.062763 CAGTTTGAGCGTCATGAAGAGT 58.937 45.455 13.18 0.00 0.00 3.24
5017 5268 1.130561 GCATCCTTACGGTGCTGAAAC 59.869 52.381 5.83 0.00 35.66 2.78
5026 5277 1.493311 GTGCTGAAACGCCTTCTCG 59.507 57.895 0.19 0.00 34.86 4.04
5135 5386 7.776969 ACTGATCTTACTTGCATCCACATATTT 59.223 33.333 0.00 0.00 0.00 1.40
5136 5387 7.933396 TGATCTTACTTGCATCCACATATTTG 58.067 34.615 0.00 0.00 0.00 2.32
5137 5388 6.135290 TCTTACTTGCATCCACATATTTGC 57.865 37.500 0.00 0.00 35.67 3.68
5138 5389 5.651576 TCTTACTTGCATCCACATATTTGCA 59.348 36.000 0.00 0.00 42.90 4.08
5142 5401 4.577834 TGCATCCACATATTTGCAGATG 57.422 40.909 0.00 2.12 39.98 2.90
5143 5402 4.208746 TGCATCCACATATTTGCAGATGA 58.791 39.130 15.60 0.00 39.98 2.92
5145 5404 4.277672 GCATCCACATATTTGCAGATGAGT 59.722 41.667 15.60 2.34 37.65 3.41
5161 5420 2.571212 TGAGTGCACTCGGATTGTTTT 58.429 42.857 35.00 4.40 45.72 2.43
5165 5424 1.266718 TGCACTCGGATTGTTTTGCTC 59.733 47.619 0.00 0.00 0.00 4.26
5166 5425 1.725931 GCACTCGGATTGTTTTGCTCG 60.726 52.381 0.00 0.00 0.00 5.03
5168 5427 0.798776 CTCGGATTGTTTTGCTCGCT 59.201 50.000 0.00 0.00 0.00 4.93
5177 5436 5.933187 TTGTTTTGCTCGCTGTAAGAATA 57.067 34.783 0.00 0.00 34.07 1.75
5181 5440 5.469373 TTTGCTCGCTGTAAGAATACATG 57.531 39.130 0.00 0.00 41.09 3.21
5186 5445 2.218759 CGCTGTAAGAATACATGCGTCC 59.781 50.000 16.96 0.00 44.83 4.79
5192 5451 6.054941 TGTAAGAATACATGCGTCCATCAAT 58.945 36.000 0.00 0.00 37.11 2.57
5202 5461 3.058450 GCGTCCATCAATCTCATCTCTG 58.942 50.000 0.00 0.00 0.00 3.35
5203 5462 3.651206 CGTCCATCAATCTCATCTCTGG 58.349 50.000 0.00 0.00 0.00 3.86
5205 5464 4.630111 GTCCATCAATCTCATCTCTGGTC 58.370 47.826 0.00 0.00 0.00 4.02
5209 5468 3.891049 TCAATCTCATCTCTGGTCTCGA 58.109 45.455 0.00 0.00 0.00 4.04
5241 5500 2.355132 CCTGCTGATTCAAGATCAGTGC 59.645 50.000 15.20 5.82 45.38 4.40
5244 5520 2.223294 GCTGATTCAAGATCAGTGCTGC 60.223 50.000 15.20 0.00 45.38 5.25
5253 5529 1.397343 GATCAGTGCTGCTCATGTGTG 59.603 52.381 0.00 0.00 0.00 3.82
5265 5542 1.922369 ATGTGTGAGGCAGGGAGCT 60.922 57.895 0.00 0.00 44.79 4.09
5288 5567 4.139859 TCTAGACTCCTAGACAACCTCG 57.860 50.000 0.00 0.00 44.69 4.63
5306 5585 3.576356 GGCCGACGATGGTGCATG 61.576 66.667 0.00 0.00 0.00 4.06
5322 5601 6.117488 TGGTGCATGCATAATAGGATGATAG 58.883 40.000 25.64 0.00 39.40 2.08
5343 5622 7.998964 TGATAGGAGATGTTTTATTTTCCTCCC 59.001 37.037 0.00 0.00 39.48 4.30
5428 5710 4.989279 TTACTCGGGATTACACCTGTAC 57.011 45.455 0.00 0.00 37.55 2.90
5452 5734 5.183713 CACCTTGCTTCAGAAATCCATAACA 59.816 40.000 0.00 0.00 0.00 2.41
5502 5785 9.877178 TTATAGACTGATGTTTCTTCTCCTTTC 57.123 33.333 0.00 0.00 0.00 2.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
87 105 1.000896 GAGGATGTGGGTTGGTGGG 60.001 63.158 0.00 0.00 0.00 4.61
137 171 1.208776 AGGAATAAAGTTAGCCGCGGT 59.791 47.619 28.70 16.08 0.00 5.68
176 210 3.126528 CGGTACCAGACGGATCCC 58.873 66.667 13.54 0.00 35.59 3.85
177 211 2.416260 GCGGTACCAGACGGATCC 59.584 66.667 13.54 0.00 35.59 3.36
178 212 1.226888 GTGCGGTACCAGACGGATC 60.227 63.158 13.54 0.00 35.59 3.36
381 472 3.791586 GGAGGAGGGGCAGTGCTC 61.792 72.222 16.11 11.67 0.00 4.26
382 473 4.345286 AGGAGGAGGGGCAGTGCT 62.345 66.667 16.11 0.00 0.00 4.40
386 477 2.445654 GAGGAGGAGGAGGGGCAG 60.446 72.222 0.00 0.00 0.00 4.85
387 478 4.095400 GGAGGAGGAGGAGGGGCA 62.095 72.222 0.00 0.00 0.00 5.36
412 511 4.493747 GGCGTCTCGTCTTCCCCG 62.494 72.222 0.00 0.00 0.00 5.73
421 520 1.665916 CCATAGCCATGGCGTCTCG 60.666 63.158 30.50 17.64 45.29 4.04
584 689 2.639839 CCTGGGAGGAAAGTGAAGAGAA 59.360 50.000 0.00 0.00 37.67 2.87
585 690 2.260822 CCTGGGAGGAAAGTGAAGAGA 58.739 52.381 0.00 0.00 37.67 3.10
586 691 1.280421 CCCTGGGAGGAAAGTGAAGAG 59.720 57.143 7.01 0.00 37.67 2.85
587 692 1.362224 CCCTGGGAGGAAAGTGAAGA 58.638 55.000 7.01 0.00 37.67 2.87
646 756 2.122783 TGATGGAAACTAAAGCGGGG 57.877 50.000 0.00 0.00 0.00 5.73
709 819 2.821366 CACTCCATCGGCAGGCAC 60.821 66.667 0.00 0.00 0.00 5.01
941 1052 1.134487 CGCATACGCACCAACCAAG 59.866 57.895 0.00 0.00 38.40 3.61
942 1053 2.328856 CCGCATACGCACCAACCAA 61.329 57.895 0.00 0.00 38.40 3.67
943 1054 2.744318 CCGCATACGCACCAACCA 60.744 61.111 0.00 0.00 38.40 3.67
1061 1172 0.599728 GAGATCCAGCTCGTCCATGC 60.600 60.000 0.00 0.00 0.00 4.06
1113 1224 1.545706 GCAGGAACTCGGGGAAGTCT 61.546 60.000 0.00 0.00 34.60 3.24
1170 1281 2.328099 GGTGCTGCCGAGGTCAAAG 61.328 63.158 0.00 0.00 0.00 2.77
1173 1284 3.315142 GATGGTGCTGCCGAGGTCA 62.315 63.158 0.00 0.00 41.21 4.02
1287 1413 4.070552 AGCCGCTCCTTCACCGAC 62.071 66.667 0.00 0.00 0.00 4.79
1746 1872 1.343142 TCTACCTTGAGAGCGTTGCAA 59.657 47.619 0.00 0.00 0.00 4.08
1785 1911 1.740025 GAGAATGGAAAGGGCGACAAG 59.260 52.381 0.00 0.00 0.00 3.16
1787 1913 0.035439 GGAGAATGGAAAGGGCGACA 60.035 55.000 0.00 0.00 0.00 4.35
1788 1914 0.035439 TGGAGAATGGAAAGGGCGAC 60.035 55.000 0.00 0.00 0.00 5.19
1789 1915 0.253044 CTGGAGAATGGAAAGGGCGA 59.747 55.000 0.00 0.00 0.00 5.54
1790 1916 0.253044 TCTGGAGAATGGAAAGGGCG 59.747 55.000 0.00 0.00 0.00 6.13
1791 1917 1.683319 GGTCTGGAGAATGGAAAGGGC 60.683 57.143 0.00 0.00 0.00 5.19
1808 1939 4.250305 ACGGTGCACACAGGGGTC 62.250 66.667 20.43 0.00 0.00 4.46
1813 1944 1.955529 GATACGCACGGTGCACACAG 61.956 60.000 30.23 17.04 45.36 3.66
1817 1948 1.348250 CATGATACGCACGGTGCAC 59.652 57.895 30.23 18.43 45.36 4.57
1820 1951 2.348498 GCATAACATGATACGCACGGTG 60.348 50.000 3.15 3.15 0.00 4.94
1962 2093 4.860907 CCTGCAAATTTTCACAGATGTAGC 59.139 41.667 12.16 0.00 31.67 3.58
2044 2176 1.070289 ACCAGGAACTCGGTGTCTTTC 59.930 52.381 0.00 0.00 38.17 2.62
2054 2186 1.269051 CCGCAAAACAACCAGGAACTC 60.269 52.381 0.00 0.00 34.60 3.01
2060 2192 3.564511 CATTCTACCGCAAAACAACCAG 58.435 45.455 0.00 0.00 0.00 4.00
2094 2226 1.453524 GCAGAGCATATGTTAGCGACG 59.546 52.381 4.29 0.00 35.48 5.12
2095 2227 2.748605 AGCAGAGCATATGTTAGCGAC 58.251 47.619 4.29 0.00 35.48 5.19
2107 2239 2.551032 CTGACAACAATGAAGCAGAGCA 59.449 45.455 0.00 0.00 0.00 4.26
2305 2441 0.870307 GATCGCCGACATAACACGCT 60.870 55.000 0.00 0.00 0.00 5.07
2356 2492 1.579698 CCCTGAACAGATGATGCTCG 58.420 55.000 3.19 0.00 0.00 5.03
2377 2513 2.110213 GTGCCGACAACACCCTCA 59.890 61.111 0.00 0.00 31.67 3.86
2416 2552 4.012374 CAGTAATGTCTGGGCAGAAACAT 58.988 43.478 0.00 0.00 39.48 2.71
2753 2889 3.190118 GCAGGAATATCAATGCCACTAGC 59.810 47.826 0.00 0.00 44.14 3.42
2800 2939 4.564041 CAATCCATGAAGATACCTCCTCG 58.436 47.826 0.00 0.00 0.00 4.63
2850 2989 4.093952 CTGTTTCTGCCTGCGCCG 62.094 66.667 4.18 0.00 0.00 6.46
2859 2998 1.068055 GCAGGCCACAATCTGTTTCTG 60.068 52.381 5.01 0.00 33.81 3.02
2887 3026 4.457257 CCTTCATCCTCTTGTTTCCTGAAC 59.543 45.833 0.00 0.00 38.78 3.18
3076 3215 4.825085 AGGCTCACCGTTTTCTCAATTTTA 59.175 37.500 0.00 0.00 42.76 1.52
3082 3221 0.884704 GCAGGCTCACCGTTTTCTCA 60.885 55.000 0.00 0.00 42.76 3.27
3091 3230 0.957888 GGAGTTCTTGCAGGCTCACC 60.958 60.000 5.95 0.00 0.00 4.02
3121 3260 2.808543 AGCTTCTTTCAAACTACCAGCG 59.191 45.455 0.00 0.00 0.00 5.18
3179 3318 8.488764 CAAAAAGAACGGTAAAGAAGAGTAGAG 58.511 37.037 0.00 0.00 0.00 2.43
3180 3319 7.983484 ACAAAAAGAACGGTAAAGAAGAGTAGA 59.017 33.333 0.00 0.00 0.00 2.59
3181 3320 8.139521 ACAAAAAGAACGGTAAAGAAGAGTAG 57.860 34.615 0.00 0.00 0.00 2.57
3183 3322 6.997239 ACAAAAAGAACGGTAAAGAAGAGT 57.003 33.333 0.00 0.00 0.00 3.24
3196 3340 6.221858 TGCAAGTGAAACAACAAAAAGAAC 57.778 33.333 0.00 0.00 41.43 3.01
3209 3353 6.096705 TCCAAAGAGAGAAAATGCAAGTGAAA 59.903 34.615 0.00 0.00 0.00 2.69
3212 3356 5.443185 TCCAAAGAGAGAAAATGCAAGTG 57.557 39.130 0.00 0.00 0.00 3.16
3227 3371 4.014406 TCTACTGACTACGCATCCAAAGA 58.986 43.478 0.00 0.00 0.00 2.52
3228 3372 4.371855 TCTACTGACTACGCATCCAAAG 57.628 45.455 0.00 0.00 0.00 2.77
3237 3381 7.008447 GCAAGTTGTCTAAATCTACTGACTACG 59.992 40.741 4.48 0.00 39.09 3.51
3299 3443 5.450818 TTGAGCCACCCAAGTAAAGATAT 57.549 39.130 0.00 0.00 0.00 1.63
3312 3456 1.383523 GCACTCCTATTTGAGCCACC 58.616 55.000 0.00 0.00 35.72 4.61
3374 3577 1.053048 CGTAGCATCGAGGCAATACG 58.947 55.000 25.38 24.01 33.60 3.06
3453 3656 4.412528 AGGTCTGTTTTTAAGAGTCCCTGT 59.587 41.667 0.00 0.00 31.82 4.00
3837 4041 4.502259 GGATAACTCAGATCTCCGTGCAAT 60.502 45.833 0.00 0.00 0.00 3.56
3843 4047 2.625314 TGCTGGATAACTCAGATCTCCG 59.375 50.000 0.00 0.00 34.36 4.63
3930 4134 3.008485 GGGAATTAGAGCCAGAGGTATGG 59.992 52.174 0.00 0.00 43.72 2.74
3939 4143 2.119495 GGTGAGAGGGAATTAGAGCCA 58.881 52.381 0.00 0.00 0.00 4.75
3957 4161 2.294078 GCTCTGGCTGTAGGTGGGT 61.294 63.158 0.00 0.00 35.22 4.51
4224 4428 7.621428 TTTTATCTTGAGAGAATCAGGCTTG 57.379 36.000 0.00 0.00 39.68 4.01
4351 4555 7.861629 TCATCCAAGTACTTGAGGTCATAAAT 58.138 34.615 32.50 10.47 42.93 1.40
4434 4638 6.954944 TGTTTTAGCACTTGATGACTTGTAC 58.045 36.000 0.00 0.00 0.00 2.90
4476 4680 0.953960 GTGCCGGTTGAACTGTAGGG 60.954 60.000 1.90 0.00 0.00 3.53
4480 4684 1.227853 GGAGTGCCGGTTGAACTGT 60.228 57.895 1.90 0.00 0.00 3.55
4898 5145 3.542712 TCAAGCAAGCTTTCGAATGTC 57.457 42.857 4.24 5.41 33.42 3.06
4929 5176 7.050377 GGAGACATAATTCTCTCAATTCCACA 58.950 38.462 8.99 0.00 41.69 4.17
4954 5204 1.498865 AAACTGACGCGTGAAGGCAG 61.499 55.000 20.70 20.05 0.00 4.85
4979 5229 3.874392 TGCATCTTCGACTCTTCATGA 57.126 42.857 0.00 0.00 0.00 3.07
4982 5232 2.762887 AGGATGCATCTTCGACTCTTCA 59.237 45.455 25.28 0.00 0.00 3.02
4983 5233 3.451141 AGGATGCATCTTCGACTCTTC 57.549 47.619 25.28 5.48 0.00 2.87
4984 5234 3.902881 AAGGATGCATCTTCGACTCTT 57.097 42.857 25.28 14.99 0.00 2.85
4985 5235 3.243234 CGTAAGGATGCATCTTCGACTCT 60.243 47.826 25.28 9.85 0.00 3.24
4986 5236 3.046390 CGTAAGGATGCATCTTCGACTC 58.954 50.000 25.28 7.64 0.00 3.36
4987 5237 3.085443 CGTAAGGATGCATCTTCGACT 57.915 47.619 25.28 11.28 0.00 4.18
5017 5268 0.716108 CTTACACAAGCGAGAAGGCG 59.284 55.000 0.00 0.00 38.18 5.52
5026 5277 4.003648 AGTCCAGCAATACTTACACAAGC 58.996 43.478 0.00 0.00 34.94 4.01
5135 5386 1.079612 CCGAGTGCACTCATCTGCA 60.080 57.895 38.31 0.00 45.06 4.41
5136 5387 0.179089 ATCCGAGTGCACTCATCTGC 60.179 55.000 38.31 17.64 43.00 4.26
5137 5388 1.931841 CAATCCGAGTGCACTCATCTG 59.068 52.381 38.31 26.56 43.00 2.90
5138 5389 1.552337 ACAATCCGAGTGCACTCATCT 59.448 47.619 38.31 22.75 43.00 2.90
5142 5401 2.918131 GCAAAACAATCCGAGTGCACTC 60.918 50.000 32.73 32.73 39.55 3.51
5143 5402 1.001378 GCAAAACAATCCGAGTGCACT 60.001 47.619 21.88 21.88 32.29 4.40
5145 5404 1.266718 GAGCAAAACAATCCGAGTGCA 59.733 47.619 0.00 0.00 34.44 4.57
5161 5420 2.866156 GCATGTATTCTTACAGCGAGCA 59.134 45.455 0.00 0.00 41.49 4.26
5166 5425 3.194861 TGGACGCATGTATTCTTACAGC 58.805 45.455 0.00 0.00 41.49 4.40
5168 5427 5.017294 TGATGGACGCATGTATTCTTACA 57.983 39.130 0.00 0.00 42.35 2.41
5177 5436 2.696989 TGAGATTGATGGACGCATGT 57.303 45.000 0.00 0.00 0.00 3.21
5181 5440 3.058450 CAGAGATGAGATTGATGGACGC 58.942 50.000 0.00 0.00 0.00 5.19
5183 5442 4.344679 AGACCAGAGATGAGATTGATGGAC 59.655 45.833 0.00 0.00 0.00 4.02
5186 5445 4.277921 TCGAGACCAGAGATGAGATTGATG 59.722 45.833 0.00 0.00 0.00 3.07
5192 5451 5.414360 CATTTTTCGAGACCAGAGATGAGA 58.586 41.667 0.00 0.00 0.00 3.27
5202 5461 3.762779 CAGGATTGCATTTTTCGAGACC 58.237 45.455 0.00 0.00 0.00 3.85
5226 5485 3.268330 TGAGCAGCACTGATCTTGAATC 58.732 45.455 16.11 0.00 45.45 2.52
5227 5486 3.345508 TGAGCAGCACTGATCTTGAAT 57.654 42.857 16.11 0.00 45.45 2.57
5231 5490 2.290134 ACACATGAGCAGCACTGATCTT 60.290 45.455 16.11 7.84 45.45 2.40
5253 5529 0.396417 TCTAGACAGCTCCCTGCCTC 60.396 60.000 0.00 0.00 43.02 4.70
5259 5535 2.440253 TCTAGGAGTCTAGACAGCTCCC 59.560 54.545 24.44 15.52 44.99 4.30
5288 5567 4.856801 ATGCACCATCGTCGGCCC 62.857 66.667 0.00 0.00 0.00 5.80
5306 5585 9.678260 AAAACATCTCCTATCATCCTATTATGC 57.322 33.333 0.00 0.00 0.00 3.14
5322 5601 7.482169 AAAGGGAGGAAAATAAAACATCTCC 57.518 36.000 0.00 0.00 38.74 3.71
5405 5686 5.422970 TGTACAGGTGTAATCCCGAGTAATT 59.577 40.000 0.00 0.00 31.52 1.40
5408 5689 3.696051 GTGTACAGGTGTAATCCCGAGTA 59.304 47.826 0.00 0.00 31.52 2.59
5409 5690 2.494870 GTGTACAGGTGTAATCCCGAGT 59.505 50.000 0.00 0.00 31.52 4.18
5410 5691 2.159142 GGTGTACAGGTGTAATCCCGAG 60.159 54.545 0.00 0.00 31.52 4.63
5411 5692 1.826720 GGTGTACAGGTGTAATCCCGA 59.173 52.381 0.00 0.00 31.52 5.14
5413 5694 3.606687 CAAGGTGTACAGGTGTAATCCC 58.393 50.000 0.00 0.00 31.52 3.85
5428 5710 5.183713 TGTTATGGATTTCTGAAGCAAGGTG 59.816 40.000 0.00 0.00 0.00 4.00
5452 5734 4.142534 GCAATCACAGACTGTTGCATACAT 60.143 41.667 20.73 0.24 44.63 2.29


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

AutoCloner maintained by Alex Coulton.