Multiple sequence alignment - TraesCS6A01G265700

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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 TraesCS6A01G265700 chr6A 100.000 2446 0 0 1 2446 490492676 490495121 0.000000e+00 4518
1 TraesCS6A01G265700 chr6A 85.055 542 70 10 1876 2411 490836351 490836887 2.140000e-150 542
2 TraesCS6A01G265700 chr6D 90.990 2353 126 32 127 2446 352358295 352355996 0.000000e+00 3092
3 TraesCS6A01G265700 chr6D 84.686 542 72 10 1876 2411 352154081 352153545 4.630000e-147 531
4 TraesCS6A01G265700 chr6D 90.099 101 6 1 1 97 352358397 352358297 7.100000e-26 128
5 TraesCS6A01G265700 chr6B 93.788 1658 60 18 803 2446 526718526 526720154 0.000000e+00 2451
6 TraesCS6A01G265700 chr6B 83.824 680 85 15 127 799 526717828 526718489 7.430000e-175 623
7 TraesCS6A01G265700 chr6B 85.553 533 69 7 1883 2411 526736600 526737128 3.550000e-153 551
8 TraesCS6A01G265700 chr6B 92.079 101 4 1 1 97 526717726 526717826 3.280000e-29 139
9 TraesCS6A01G265700 chr2A 91.568 676 49 3 1778 2446 763369462 763368788 0.000000e+00 926
10 TraesCS6A01G265700 chr2B 89.838 679 58 4 1778 2446 797627495 797626818 0.000000e+00 861
11 TraesCS6A01G265700 chrUn 86.801 644 73 9 1813 2446 84014925 84015566 0.000000e+00 708
12 TraesCS6A01G265700 chr7D 87.196 617 69 7 1839 2446 59732239 59732854 0.000000e+00 693


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 TraesCS6A01G265700 chr6A 490492676 490495121 2445 False 4518 4518 100.0000 1 2446 1 chr6A.!!$F1 2445
1 TraesCS6A01G265700 chr6A 490836351 490836887 536 False 542 542 85.0550 1876 2411 1 chr6A.!!$F2 535
2 TraesCS6A01G265700 chr6D 352355996 352358397 2401 True 1610 3092 90.5445 1 2446 2 chr6D.!!$R2 2445
3 TraesCS6A01G265700 chr6D 352153545 352154081 536 True 531 531 84.6860 1876 2411 1 chr6D.!!$R1 535
4 TraesCS6A01G265700 chr6B 526717726 526720154 2428 False 1071 2451 89.8970 1 2446 3 chr6B.!!$F2 2445
5 TraesCS6A01G265700 chr6B 526736600 526737128 528 False 551 551 85.5530 1883 2411 1 chr6B.!!$F1 528
6 TraesCS6A01G265700 chr2A 763368788 763369462 674 True 926 926 91.5680 1778 2446 1 chr2A.!!$R1 668
7 TraesCS6A01G265700 chr2B 797626818 797627495 677 True 861 861 89.8380 1778 2446 1 chr2B.!!$R1 668
8 TraesCS6A01G265700 chrUn 84014925 84015566 641 False 708 708 86.8010 1813 2446 1 chrUn.!!$F1 633
9 TraesCS6A01G265700 chr7D 59732239 59732854 615 False 693 693 87.1960 1839 2446 1 chr7D.!!$F1 607

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
285 291 0.172803 GAAGCATGCAAGCCCAGAAG 59.827 55.0 21.98 0.0 34.23 2.85 F
964 1046 0.179121 TTCGTTCCAGCGCGATACAT 60.179 50.0 12.10 0.0 36.97 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1283 1371 0.105401 GAGGAGGTTAGGGCTAGGCT 60.105 60.000 16.8 4.94 0.0 4.58 R
1765 1863 4.085733 CCACCAAAAGAGAGAGAGAGAGA 58.914 47.826 0.0 0.00 0.0 3.10 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
34 35 6.981379 GCATATGCTTGAATGTTACACATC 57.019 37.500 20.64 0.00 36.51 3.06
110 115 7.931015 TCCTGATAAGTACTATTTCCATGGT 57.069 36.000 12.58 0.00 0.00 3.55
111 116 8.331931 TCCTGATAAGTACTATTTCCATGGTT 57.668 34.615 12.58 0.58 0.00 3.67
112 117 8.429641 TCCTGATAAGTACTATTTCCATGGTTC 58.570 37.037 12.58 0.00 0.00 3.62
113 118 7.385205 CCTGATAAGTACTATTTCCATGGTTCG 59.615 40.741 12.58 0.00 0.00 3.95
114 119 8.014070 TGATAAGTACTATTTCCATGGTTCGA 57.986 34.615 12.58 0.00 0.00 3.71
115 120 8.647796 TGATAAGTACTATTTCCATGGTTCGAT 58.352 33.333 12.58 4.57 0.00 3.59
116 121 9.141400 GATAAGTACTATTTCCATGGTTCGATC 57.859 37.037 12.58 0.00 0.00 3.69
117 122 6.479972 AGTACTATTTCCATGGTTCGATCA 57.520 37.500 12.58 0.00 0.00 2.92
118 123 6.281405 AGTACTATTTCCATGGTTCGATCAC 58.719 40.000 12.58 4.29 0.00 3.06
119 124 4.451900 ACTATTTCCATGGTTCGATCACC 58.548 43.478 12.58 0.00 37.34 4.02
125 130 3.641017 TGGTTCGATCACCAATGCA 57.359 47.368 6.50 0.00 44.30 3.96
142 147 2.300433 TGCAAAAGATCCGGATCCATG 58.700 47.619 35.53 30.02 38.58 3.66
145 150 3.499918 GCAAAAGATCCGGATCCATGTAG 59.500 47.826 35.53 22.72 38.58 2.74
146 151 4.708177 CAAAAGATCCGGATCCATGTAGT 58.292 43.478 35.53 16.52 38.58 2.73
147 152 5.741964 GCAAAAGATCCGGATCCATGTAGTA 60.742 44.000 35.53 0.00 38.58 1.82
148 153 5.470047 AAAGATCCGGATCCATGTAGTAC 57.530 43.478 35.53 12.10 38.58 2.73
149 154 3.432378 AGATCCGGATCCATGTAGTACC 58.568 50.000 35.53 11.59 38.58 3.34
155 160 5.603395 TCCGGATCCATGTAGTACCAAAATA 59.397 40.000 13.41 0.00 0.00 1.40
163 168 9.535170 TCCATGTAGTACCAAAATAATTCCAAA 57.465 29.630 0.00 0.00 0.00 3.28
165 170 9.801873 CATGTAGTACCAAAATAATTCCAAAGG 57.198 33.333 0.00 0.00 0.00 3.11
206 211 8.882415 AAGAACTTTCATTAGACTACGAAACA 57.118 30.769 0.00 0.00 0.00 2.83
209 214 7.870588 ACTTTCATTAGACTACGAAACAGTC 57.129 36.000 0.00 0.00 42.30 3.51
234 239 6.018832 CGATGCCCAAATGGATCAAAATTAAC 60.019 38.462 0.00 0.00 37.39 2.01
251 257 8.917655 CAAAATTAACGAAATGTAAACCGGAAT 58.082 29.630 9.46 0.00 0.00 3.01
270 276 5.050702 CGGAATAATTCTTCCTCTTCGAAGC 60.051 44.000 20.56 0.90 42.19 3.86
284 290 1.588824 CGAAGCATGCAAGCCCAGAA 61.589 55.000 21.98 0.00 34.23 3.02
285 291 0.172803 GAAGCATGCAAGCCCAGAAG 59.827 55.000 21.98 0.00 34.23 2.85
289 295 1.250328 CATGCAAGCCCAGAAGAACA 58.750 50.000 0.00 0.00 0.00 3.18
295 301 4.640201 TGCAAGCCCAGAAGAACATATAAC 59.360 41.667 0.00 0.00 0.00 1.89
299 305 6.759497 AGCCCAGAAGAACATATAACAAAC 57.241 37.500 0.00 0.00 0.00 2.93
316 322 5.613358 ACAAACTACACATTCTTAGCAGC 57.387 39.130 0.00 0.00 0.00 5.25
325 331 1.813513 TTCTTAGCAGCTCAAGCCAC 58.186 50.000 0.00 0.00 43.38 5.01
347 353 2.287188 GGTGCATCATGTTTATCGGCAG 60.287 50.000 0.00 0.00 0.00 4.85
364 370 3.303329 CGGCAGAAATACACATTGATCCG 60.303 47.826 0.00 0.00 0.00 4.18
432 451 1.352352 CTCCCATGGCCTCCGAAATAT 59.648 52.381 6.09 0.00 0.00 1.28
445 464 6.058183 CCTCCGAAATATTCAGACAAATCCT 58.942 40.000 0.00 0.00 0.00 3.24
449 468 6.017605 CCGAAATATTCAGACAAATCCTCCAG 60.018 42.308 0.00 0.00 0.00 3.86
451 470 7.710907 CGAAATATTCAGACAAATCCTCCAGTA 59.289 37.037 0.00 0.00 0.00 2.74
465 484 1.992557 TCCAGTAACCCCAGAAGCATT 59.007 47.619 0.00 0.00 0.00 3.56
467 486 2.555227 CCAGTAACCCCAGAAGCATTGT 60.555 50.000 0.00 0.00 0.00 2.71
506 528 1.904412 GTGTAATGCAATCACGCAACG 59.096 47.619 0.00 0.00 46.87 4.10
514 536 3.911365 TGCAATCACGCAACGAAATAAAG 59.089 39.130 0.00 0.00 39.45 1.85
539 561 9.905713 AGCAAGACTTTCTAAATACCAATATGA 57.094 29.630 0.00 0.00 0.00 2.15
565 590 9.745018 AATTTTGAGAGAAGGAACATTATGAGA 57.255 29.630 0.00 0.00 0.00 3.27
567 592 8.954950 TTTGAGAGAAGGAACATTATGAGATC 57.045 34.615 0.00 0.00 0.00 2.75
572 597 9.339850 AGAGAAGGAACATTATGAGATCAAATG 57.660 33.333 0.00 12.28 36.80 2.32
646 671 0.670854 GAACTGGTTCTCACCTCCGC 60.671 60.000 6.26 0.00 44.61 5.54
683 708 3.425713 CCCGACTCCGACGACGAA 61.426 66.667 9.28 0.00 42.66 3.85
697 722 1.453762 GACGAACTCGGATCGGGGAT 61.454 60.000 7.22 0.00 44.32 3.85
699 724 1.452953 CGAACTCGGATCGGGGATGA 61.453 60.000 7.22 0.00 36.68 2.92
704 729 1.000283 CTCGGATCGGGGATGAGAAAG 60.000 57.143 0.00 0.00 0.00 2.62
705 730 0.601311 CGGATCGGGGATGAGAAAGC 60.601 60.000 0.00 0.00 0.00 3.51
896 956 1.083242 GCCTTTCTCTCTCGCTGCTG 61.083 60.000 0.00 0.00 0.00 4.41
954 1036 4.424430 CGCGGCGTTTCGTTCCAG 62.424 66.667 15.36 0.00 0.00 3.86
955 1037 4.736631 GCGGCGTTTCGTTCCAGC 62.737 66.667 9.37 0.00 0.00 4.85
956 1038 4.424430 CGGCGTTTCGTTCCAGCG 62.424 66.667 0.00 0.00 0.00 5.18
957 1039 4.736631 GGCGTTTCGTTCCAGCGC 62.737 66.667 0.00 0.00 46.24 5.92
964 1046 0.179121 TTCGTTCCAGCGCGATACAT 60.179 50.000 12.10 0.00 36.97 2.29
1220 1308 1.617947 AACATCCAGGACCTCCTCGC 61.618 60.000 0.00 0.00 46.65 5.03
1281 1369 1.483004 GTCCCCTAGAGAGCAAGGAAC 59.517 57.143 0.00 0.00 34.58 3.62
1283 1371 1.475403 CCCTAGAGAGCAAGGAACGA 58.525 55.000 0.00 0.00 34.58 3.85
1324 1412 2.502633 GGTACCTCGTCTCTTCCCC 58.497 63.158 4.06 0.00 0.00 4.81
1365 1453 5.846994 GCTCGAGTCGATTGTAATGTAGTAG 59.153 44.000 16.94 0.00 34.61 2.57
1408 1496 6.857451 GCCATTTTGTTCAATTGAAACAATCC 59.143 34.615 22.07 9.53 35.58 3.01
1411 1499 4.313277 TGTTCAATTGAAACAATCCGCA 57.687 36.364 22.07 10.58 35.58 5.69
1415 1503 0.532115 ATTGAAACAATCCGCAGCCC 59.468 50.000 0.00 0.00 0.00 5.19
1465 1553 4.466567 TCATAAATATGTTGCGAAGCCG 57.533 40.909 0.68 0.00 43.48 5.52
1492 1580 3.634568 AACGAAAATTGTCGCCATGAA 57.365 38.095 17.96 0.00 45.00 2.57
1493 1581 3.848272 ACGAAAATTGTCGCCATGAAT 57.152 38.095 17.96 0.00 45.00 2.57
1494 1582 3.758300 ACGAAAATTGTCGCCATGAATC 58.242 40.909 17.96 0.00 45.00 2.52
1509 1597 5.167121 CCATGAATCCAAATTGTGCGTTTA 58.833 37.500 0.00 0.00 0.00 2.01
1511 1599 6.313411 CCATGAATCCAAATTGTGCGTTTAAT 59.687 34.615 0.00 0.00 0.00 1.40
1517 1605 5.294306 TCCAAATTGTGCGTTTAATTTTGCA 59.706 32.000 0.00 0.00 35.07 4.08
1595 1685 4.446994 TGAGATGAACAGTACTGCTCTG 57.553 45.455 22.90 0.00 38.68 3.35
1613 1704 4.686091 GCTCTGAAAGGTATTTTTGCAACC 59.314 41.667 0.00 0.00 0.00 3.77
1630 1721 6.892658 TGCAACCAGTGTCAAAGTTTATAT 57.107 33.333 0.00 0.00 0.00 0.86
1764 1862 4.981806 TCTAGAAGCTTTGCTCTCTCTC 57.018 45.455 0.00 0.00 38.25 3.20
1765 1863 4.599041 TCTAGAAGCTTTGCTCTCTCTCT 58.401 43.478 0.00 0.00 38.25 3.10
1766 1864 3.874392 AGAAGCTTTGCTCTCTCTCTC 57.126 47.619 0.00 0.00 38.25 3.20
1767 1865 3.434309 AGAAGCTTTGCTCTCTCTCTCT 58.566 45.455 0.00 0.00 38.25 3.10
1768 1866 3.445096 AGAAGCTTTGCTCTCTCTCTCTC 59.555 47.826 0.00 0.00 38.25 3.20
1804 1903 7.921786 TTTGGTGGAGAGTACAATAGAAATG 57.078 36.000 0.00 0.00 0.00 2.32
1835 1934 7.544622 TCATACTATTACACTCACACAACTCC 58.455 38.462 0.00 0.00 0.00 3.85
1872 1980 6.663953 ACTAATCTTGTAGCTGTACCTTGAGA 59.336 38.462 0.00 0.00 0.00 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 6.411376 TGACCTACTTCAAACTTCAAAGTGA 58.589 36.000 0.00 0.00 39.66 3.41
34 35 6.677781 TGACCTACTTCAAACTTCAAAGTG 57.322 37.500 0.00 0.00 39.66 3.16
97 102 4.080582 TGGTGATCGAACCATGGAAATAGT 60.081 41.667 21.47 0.00 45.43 2.12
98 103 4.450976 TGGTGATCGAACCATGGAAATAG 58.549 43.478 21.47 4.77 45.43 1.73
99 104 4.495690 TGGTGATCGAACCATGGAAATA 57.504 40.909 21.47 0.97 45.43 1.40
100 105 3.364460 TGGTGATCGAACCATGGAAAT 57.636 42.857 21.47 3.64 45.43 2.17
101 106 2.869101 TGGTGATCGAACCATGGAAA 57.131 45.000 21.47 0.20 45.43 3.13
108 113 3.057596 TCTTTTGCATTGGTGATCGAACC 60.058 43.478 0.00 0.00 40.94 3.62
109 114 4.159377 TCTTTTGCATTGGTGATCGAAC 57.841 40.909 0.00 0.00 0.00 3.95
110 115 4.142403 GGATCTTTTGCATTGGTGATCGAA 60.142 41.667 0.00 0.00 33.30 3.71
111 116 3.378112 GGATCTTTTGCATTGGTGATCGA 59.622 43.478 0.00 0.00 33.30 3.59
112 117 3.699067 GGATCTTTTGCATTGGTGATCG 58.301 45.455 0.00 0.00 33.30 3.69
113 118 3.489738 CCGGATCTTTTGCATTGGTGATC 60.490 47.826 0.00 0.00 0.00 2.92
114 119 2.428171 CCGGATCTTTTGCATTGGTGAT 59.572 45.455 0.00 0.00 0.00 3.06
115 120 1.818060 CCGGATCTTTTGCATTGGTGA 59.182 47.619 0.00 0.00 0.00 4.02
116 121 1.818060 TCCGGATCTTTTGCATTGGTG 59.182 47.619 0.00 0.00 0.00 4.17
117 122 2.214376 TCCGGATCTTTTGCATTGGT 57.786 45.000 0.00 0.00 0.00 3.67
118 123 2.035066 GGATCCGGATCTTTTGCATTGG 59.965 50.000 36.72 0.00 37.92 3.16
119 124 2.689471 TGGATCCGGATCTTTTGCATTG 59.311 45.455 36.72 0.00 37.92 2.82
120 125 3.017048 TGGATCCGGATCTTTTGCATT 57.983 42.857 36.72 5.42 37.92 3.56
121 126 2.734755 TGGATCCGGATCTTTTGCAT 57.265 45.000 36.72 6.24 37.92 3.96
122 127 2.300433 CATGGATCCGGATCTTTTGCA 58.700 47.619 36.72 27.45 37.92 4.08
123 128 2.301346 ACATGGATCCGGATCTTTTGC 58.699 47.619 36.72 23.34 37.92 3.68
124 129 4.708177 ACTACATGGATCCGGATCTTTTG 58.292 43.478 36.72 30.67 37.92 2.44
125 130 5.221661 GGTACTACATGGATCCGGATCTTTT 60.222 44.000 36.72 23.12 37.92 2.27
142 147 7.093684 TGGCCTTTGGAATTATTTTGGTACTAC 60.094 37.037 3.32 0.00 0.00 2.73
145 150 6.043854 TGGCCTTTGGAATTATTTTGGTAC 57.956 37.500 3.32 0.00 0.00 3.34
146 151 6.882768 ATGGCCTTTGGAATTATTTTGGTA 57.117 33.333 3.32 0.00 0.00 3.25
147 152 5.777526 ATGGCCTTTGGAATTATTTTGGT 57.222 34.783 3.32 0.00 0.00 3.67
148 153 6.625520 GCAAATGGCCTTTGGAATTATTTTGG 60.626 38.462 21.58 2.63 43.73 3.28
149 154 6.324042 GCAAATGGCCTTTGGAATTATTTTG 58.676 36.000 21.58 8.27 43.73 2.44
165 170 5.077134 AGTTCTTTATTCTGGCAAATGGC 57.923 39.130 0.00 0.00 43.74 4.40
206 211 1.212688 TGATCCATTTGGGCATCGACT 59.787 47.619 0.00 0.00 36.21 4.18
209 214 3.523606 TTTTGATCCATTTGGGCATCG 57.476 42.857 0.00 0.00 36.21 3.84
210 215 6.018832 CGTTAATTTTGATCCATTTGGGCATC 60.019 38.462 0.00 0.00 36.21 3.91
234 239 7.642586 GGAAGAATTATTCCGGTTTACATTTCG 59.357 37.037 15.72 0.00 39.47 3.46
251 257 4.572389 GCATGCTTCGAAGAGGAAGAATTA 59.428 41.667 28.95 1.68 44.93 1.40
270 276 1.250328 TGTTCTTCTGGGCTTGCATG 58.750 50.000 0.00 0.00 0.00 4.06
295 301 5.409520 TGAGCTGCTAAGAATGTGTAGTTTG 59.590 40.000 0.15 0.00 0.00 2.93
299 305 4.033817 GCTTGAGCTGCTAAGAATGTGTAG 59.966 45.833 17.33 0.00 38.21 2.74
316 322 1.028330 ATGATGCACCGTGGCTTGAG 61.028 55.000 0.00 0.00 34.04 3.02
325 331 1.334059 GCCGATAAACATGATGCACCG 60.334 52.381 0.00 0.00 0.00 4.94
347 353 3.548818 GCCAGCGGATCAATGTGTATTTC 60.549 47.826 0.00 0.00 0.00 2.17
432 451 4.263331 GGGTTACTGGAGGATTTGTCTGAA 60.263 45.833 0.00 0.00 0.00 3.02
445 464 1.668826 ATGCTTCTGGGGTTACTGGA 58.331 50.000 0.00 0.00 0.00 3.86
449 468 1.818674 CCACAATGCTTCTGGGGTTAC 59.181 52.381 0.00 0.00 32.22 2.50
451 470 0.482446 TCCACAATGCTTCTGGGGTT 59.518 50.000 2.14 0.00 38.60 4.11
465 484 3.279116 GTGCTTGCTGCGTCCACA 61.279 61.111 10.22 0.00 46.63 4.17
495 514 4.153958 TGCTTTATTTCGTTGCGTGATT 57.846 36.364 0.00 0.00 0.00 2.57
500 519 3.810373 AGTCTTGCTTTATTTCGTTGCG 58.190 40.909 0.00 0.00 0.00 4.85
537 559 9.519191 TCATAATGTTCCTTCTCTCAAAATTCA 57.481 29.630 0.00 0.00 0.00 2.57
539 561 9.745018 TCTCATAATGTTCCTTCTCTCAAAATT 57.255 29.630 0.00 0.00 0.00 1.82
541 563 9.388506 GATCTCATAATGTTCCTTCTCTCAAAA 57.611 33.333 0.00 0.00 0.00 2.44
542 564 8.542926 TGATCTCATAATGTTCCTTCTCTCAAA 58.457 33.333 0.00 0.00 0.00 2.69
543 565 8.082672 TGATCTCATAATGTTCCTTCTCTCAA 57.917 34.615 0.00 0.00 0.00 3.02
544 566 7.666063 TGATCTCATAATGTTCCTTCTCTCA 57.334 36.000 0.00 0.00 0.00 3.27
545 567 8.954950 TTTGATCTCATAATGTTCCTTCTCTC 57.045 34.615 0.00 0.00 0.00 3.20
549 574 7.938715 AGCATTTGATCTCATAATGTTCCTTC 58.061 34.615 0.00 0.00 32.33 3.46
560 585 6.485984 GGAGTAATGTGAGCATTTGATCTCAT 59.514 38.462 7.37 7.37 43.63 2.90
561 586 5.819379 GGAGTAATGTGAGCATTTGATCTCA 59.181 40.000 3.43 3.43 42.19 3.27
564 589 5.008415 CCTGGAGTAATGTGAGCATTTGATC 59.992 44.000 0.00 0.00 42.19 2.92
565 590 4.885907 CCTGGAGTAATGTGAGCATTTGAT 59.114 41.667 0.00 0.00 42.19 2.57
567 592 3.181493 GCCTGGAGTAATGTGAGCATTTG 60.181 47.826 0.00 0.00 42.19 2.32
572 597 0.464554 GGGCCTGGAGTAATGTGAGC 60.465 60.000 0.84 0.00 0.00 4.26
683 708 0.106167 TTCTCATCCCCGATCCGAGT 60.106 55.000 0.00 0.00 0.00 4.18
688 713 0.601311 CCGCTTTCTCATCCCCGATC 60.601 60.000 0.00 0.00 0.00 3.69
691 716 2.203070 CCCGCTTTCTCATCCCCG 60.203 66.667 0.00 0.00 0.00 5.73
697 722 1.983224 CCTCTTCCCCGCTTTCTCA 59.017 57.895 0.00 0.00 0.00 3.27
699 724 2.671682 GCCTCTTCCCCGCTTTCT 59.328 61.111 0.00 0.00 0.00 2.52
748 773 4.736896 GCTCCGACGAAACCGGCT 62.737 66.667 0.00 0.00 46.10 5.52
858 918 2.614734 GGCTAACTAACTGGGCTTCGTT 60.615 50.000 0.00 0.00 0.00 3.85
859 919 1.066358 GGCTAACTAACTGGGCTTCGT 60.066 52.381 0.00 0.00 0.00 3.85
896 956 3.468326 GATGGAGGCGGAAGGGAGC 62.468 68.421 0.00 0.00 0.00 4.70
937 1019 4.424430 CTGGAACGAAACGCCGCG 62.424 66.667 12.14 12.14 0.00 6.46
938 1020 4.736631 GCTGGAACGAAACGCCGC 62.737 66.667 0.00 0.00 0.00 6.53
939 1021 4.424430 CGCTGGAACGAAACGCCG 62.424 66.667 0.00 0.00 34.06 6.46
940 1022 4.736631 GCGCTGGAACGAAACGCC 62.737 66.667 0.00 0.00 43.58 5.68
942 1024 1.407721 TATCGCGCTGGAACGAAACG 61.408 55.000 5.56 0.00 42.31 3.60
943 1025 0.024619 GTATCGCGCTGGAACGAAAC 59.975 55.000 5.56 0.00 42.31 2.78
944 1026 0.388778 TGTATCGCGCTGGAACGAAA 60.389 50.000 5.56 0.00 42.31 3.46
945 1027 0.179121 ATGTATCGCGCTGGAACGAA 60.179 50.000 5.56 0.00 42.31 3.85
946 1028 0.594028 GATGTATCGCGCTGGAACGA 60.594 55.000 5.56 0.00 43.33 3.85
947 1029 1.846648 GATGTATCGCGCTGGAACG 59.153 57.895 5.56 0.00 0.00 3.95
948 1030 1.846648 CGATGTATCGCGCTGGAAC 59.153 57.895 5.56 0.00 43.84 3.62
949 1031 4.319249 CGATGTATCGCGCTGGAA 57.681 55.556 5.56 0.00 43.84 3.53
958 1040 1.366366 CGACCACCCCCGATGTATC 59.634 63.158 0.00 0.00 0.00 2.24
991 1073 4.856801 CTTCGCCATCCCCCACCG 62.857 72.222 0.00 0.00 0.00 4.94
1261 1349 1.483004 GTTCCTTGCTCTCTAGGGGAC 59.517 57.143 0.00 0.00 36.14 4.46
1281 1369 1.465200 GGAGGTTAGGGCTAGGCTCG 61.465 65.000 16.80 0.00 32.17 5.03
1283 1371 0.105401 GAGGAGGTTAGGGCTAGGCT 60.105 60.000 16.80 4.94 0.00 4.58
1408 1496 4.379243 AGGAACGACTGGGCTGCG 62.379 66.667 0.00 0.00 0.00 5.18
1411 1499 1.115467 CATAGAGGAACGACTGGGCT 58.885 55.000 0.00 0.00 0.00 5.19
1415 1503 4.045104 GTGCATACATAGAGGAACGACTG 58.955 47.826 0.00 0.00 0.00 3.51
1465 1553 5.387279 TGGCGACAATTTTCGTTTCTTATC 58.613 37.500 14.89 0.00 41.26 1.75
1492 1580 6.017605 TGCAAAATTAAACGCACAATTTGGAT 60.018 30.769 0.78 0.00 35.19 3.41
1493 1581 5.294306 TGCAAAATTAAACGCACAATTTGGA 59.706 32.000 0.78 0.00 35.19 3.53
1494 1582 5.505286 TGCAAAATTAAACGCACAATTTGG 58.495 33.333 0.78 2.06 35.19 3.28
1509 1597 5.302360 ACAGCATTCAGTGATTGCAAAATT 58.698 33.333 31.11 14.90 40.15 1.82
1511 1599 4.325028 ACAGCATTCAGTGATTGCAAAA 57.675 36.364 31.11 2.11 40.15 2.44
1517 1605 5.970317 TTCATCAACAGCATTCAGTGATT 57.030 34.783 0.00 0.00 0.00 2.57
1581 1669 5.746990 ATACCTTTCAGAGCAGTACTGTT 57.253 39.130 23.44 18.44 36.81 3.16
1595 1685 5.356426 ACACTGGTTGCAAAAATACCTTTC 58.644 37.500 0.00 0.00 33.05 2.62
1613 1704 8.935844 TGCTAGTTCATATAAACTTTGACACTG 58.064 33.333 0.00 0.00 40.01 3.66
1630 1721 4.548494 CAACACAAATGCATGCTAGTTCA 58.452 39.130 20.33 0.00 0.00 3.18
1723 1821 4.890088 AGATGCGTGTAAACTGTAAAGGA 58.110 39.130 0.00 0.00 0.00 3.36
1764 1862 4.158394 CCACCAAAAGAGAGAGAGAGAGAG 59.842 50.000 0.00 0.00 0.00 3.20
1765 1863 4.085733 CCACCAAAAGAGAGAGAGAGAGA 58.914 47.826 0.00 0.00 0.00 3.10
1766 1864 4.085733 TCCACCAAAAGAGAGAGAGAGAG 58.914 47.826 0.00 0.00 0.00 3.20
1767 1865 4.085733 CTCCACCAAAAGAGAGAGAGAGA 58.914 47.826 0.00 0.00 31.43 3.10
1768 1866 4.085733 TCTCCACCAAAAGAGAGAGAGAG 58.914 47.826 0.00 0.00 34.23 3.20
1835 1934 7.660617 AGCTACAAGATTAGTCATGATCCATTG 59.339 37.037 0.00 3.02 0.00 2.82
1872 1980 8.150945 TGTGTTCTAAGCTAAATCTCTTTCACT 58.849 33.333 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.