Multiple sequence alignment - TraesCS4B01G179200

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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 TraesCS4B01G179200 chr4B 100.000 4536 0 0 1 4536 392370624 392366089 0.000000e+00 8377.0
1 TraesCS4B01G179200 chr4B 100.000 78 0 0 4877 4954 392365748 392365671 1.440000e-30 145.0
2 TraesCS4B01G179200 chr4D 97.125 2087 35 10 2138 4201 314583755 314581671 0.000000e+00 3498.0
3 TraesCS4B01G179200 chr4D 94.460 1408 52 6 760 2142 314585442 314584036 0.000000e+00 2145.0
4 TraesCS4B01G179200 chr4D 89.960 249 9 4 4288 4536 314581657 314581425 1.730000e-79 307.0
5 TraesCS4B01G179200 chr4A 95.886 1653 40 7 2718 4347 161429517 161431164 0.000000e+00 2651.0
6 TraesCS4B01G179200 chr4A 92.602 1203 42 12 743 1919 161427695 161428876 0.000000e+00 1685.0
7 TraesCS4B01G179200 chr4A 94.419 645 30 4 1964 2603 161428875 161429518 0.000000e+00 987.0
8 TraesCS4B01G179200 chr5A 90.405 740 69 2 1 739 227120767 227121505 0.000000e+00 972.0
9 TraesCS4B01G179200 chr5D 88.259 741 82 4 1 740 339756438 339755702 0.000000e+00 881.0
10 TraesCS4B01G179200 chr5D 97.479 119 3 0 2602 2720 118840568 118840450 2.340000e-48 204.0
11 TraesCS4B01G179200 chr6B 86.043 738 101 2 4 740 673858280 673857544 0.000000e+00 791.0
12 TraesCS4B01G179200 chr6B 84.741 734 108 4 8 740 84673251 84673981 0.000000e+00 732.0
13 TraesCS4B01G179200 chr6B 93.077 130 7 2 2602 2729 231349958 231349829 6.550000e-44 189.0
14 TraesCS4B01G179200 chr1A 85.598 736 103 3 4 737 545876728 545875994 0.000000e+00 769.0
15 TraesCS4B01G179200 chr1B 84.688 738 111 2 4 740 11866329 11865593 0.000000e+00 736.0
16 TraesCS4B01G179200 chr1B 80.297 741 142 4 1 740 192283440 192282703 1.560000e-154 556.0
17 TraesCS4B01G179200 chr7B 84.553 738 111 3 4 740 242669772 242669037 0.000000e+00 728.0
18 TraesCS4B01G179200 chr6A 81.452 744 130 6 1 740 386901389 386902128 1.970000e-168 603.0
19 TraesCS4B01G179200 chr6A 95.312 128 6 0 2600 2727 147303658 147303785 2.340000e-48 204.0
20 TraesCS4B01G179200 chr2B 94.444 126 6 1 2595 2720 659534375 659534499 5.060000e-45 193.0
21 TraesCS4B01G179200 chr3D 93.750 128 7 1 2602 2729 609106310 609106184 1.820000e-44 191.0
22 TraesCS4B01G179200 chr3D 85.714 77 6 5 4879 4953 548863096 548863169 5.320000e-10 76.8
23 TraesCS4B01G179200 chr1D 94.400 125 6 1 2596 2720 116548335 116548458 1.820000e-44 191.0
24 TraesCS4B01G179200 chr6D 93.077 130 7 2 2596 2724 17054998 17055126 6.550000e-44 189.0
25 TraesCS4B01G179200 chr3A 92.969 128 9 0 2602 2729 607108182 607108055 2.350000e-43 187.0


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 TraesCS4B01G179200 chr4B 392365671 392370624 4953 True 4261.000000 8377 100.000000 1 4954 2 chr4B.!!$R1 4953
1 TraesCS4B01G179200 chr4D 314581425 314585442 4017 True 1983.333333 3498 93.848333 760 4536 3 chr4D.!!$R1 3776
2 TraesCS4B01G179200 chr4A 161427695 161431164 3469 False 1774.333333 2651 94.302333 743 4347 3 chr4A.!!$F1 3604
3 TraesCS4B01G179200 chr5A 227120767 227121505 738 False 972.000000 972 90.405000 1 739 1 chr5A.!!$F1 738
4 TraesCS4B01G179200 chr5D 339755702 339756438 736 True 881.000000 881 88.259000 1 740 1 chr5D.!!$R2 739
5 TraesCS4B01G179200 chr6B 673857544 673858280 736 True 791.000000 791 86.043000 4 740 1 chr6B.!!$R2 736
6 TraesCS4B01G179200 chr6B 84673251 84673981 730 False 732.000000 732 84.741000 8 740 1 chr6B.!!$F1 732
7 TraesCS4B01G179200 chr1A 545875994 545876728 734 True 769.000000 769 85.598000 4 737 1 chr1A.!!$R1 733
8 TraesCS4B01G179200 chr1B 11865593 11866329 736 True 736.000000 736 84.688000 4 740 1 chr1B.!!$R1 736
9 TraesCS4B01G179200 chr1B 192282703 192283440 737 True 556.000000 556 80.297000 1 740 1 chr1B.!!$R2 739
10 TraesCS4B01G179200 chr7B 242669037 242669772 735 True 728.000000 728 84.553000 4 740 1 chr7B.!!$R1 736
11 TraesCS4B01G179200 chr6A 386901389 386902128 739 False 603.000000 603 81.452000 1 740 1 chr6A.!!$F2 739

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
702 704 0.392998 CTAGACCTTTGCCGCCACAT 60.393 55.0 0.0 0.0 0.00 3.21 F
1219 1245 0.388907 CCTGTTTGCGGGCTTTGATG 60.389 55.0 0.0 0.0 33.82 3.07 F
2618 2938 0.107312 TCTACTCCCTCCGTCCGAAG 60.107 60.0 0.0 0.0 0.00 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1829 1858 0.106217 ACATAATCCGGCAAAGGGGG 60.106 55.0 0.00 0.00 0.00 5.40 R
2694 3014 0.517316 CCTCCGTCCGAAAAAGCTTG 59.483 55.0 0.00 0.00 0.00 4.01 R
4421 4768 0.108615 GACAGACCGATGTGGGACTG 60.109 60.0 10.79 10.79 45.46 3.51 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
27 28 2.159653 CCTTTTGATCTGGAGCGTTTCG 60.160 50.000 0.00 0.00 0.00 3.46
41 42 2.298300 CGTTTCGTGAAATGCAGACAC 58.702 47.619 9.61 9.61 31.50 3.67
53 54 1.901833 TGCAGACACTCATAAGAGGCA 59.098 47.619 0.00 0.00 46.44 4.75
103 104 4.892934 TGGTACAAAAGCAGATTGTTCCTT 59.107 37.500 18.60 0.00 44.15 3.36
113 114 6.115446 AGCAGATTGTTCCTTCGAAATGATA 58.885 36.000 0.00 0.00 0.00 2.15
143 144 6.405176 GCAAGATTACTTTCAGCCTATTTGCT 60.405 38.462 0.00 0.00 36.73 3.91
200 201 3.181465 ACAAACTGATCGGCCTATACTGG 60.181 47.826 0.00 0.00 0.00 4.00
215 216 6.010219 CCTATACTGGGATAAATTTGTGGGG 58.990 44.000 0.00 0.00 0.00 4.96
279 280 0.914417 TTCGGCATTCTCCTCCCCTT 60.914 55.000 0.00 0.00 0.00 3.95
287 288 4.711846 GCATTCTCCTCCCCTTTTACAATT 59.288 41.667 0.00 0.00 0.00 2.32
301 302 9.892130 CCCTTTTACAATTCTCAGTACTATCTT 57.108 33.333 0.00 0.00 0.00 2.40
402 403 5.273674 TGGAAACATCTGAAACAATGCAA 57.726 34.783 0.00 0.00 33.40 4.08
541 543 8.814038 ATAAATTCTGGTAGAAAGCATTCACT 57.186 30.769 4.27 0.00 37.82 3.41
565 567 1.414550 GCCTTTAGCTCTTCCGGATCT 59.585 52.381 4.15 3.00 38.99 2.75
582 584 1.123077 TCTGTTATCTCAGCGCCCAT 58.877 50.000 2.29 0.00 35.63 4.00
678 680 3.391665 CTCCCGCCGAGAGCCATTT 62.392 63.158 0.00 0.00 41.63 2.32
702 704 0.392998 CTAGACCTTTGCCGCCACAT 60.393 55.000 0.00 0.00 0.00 3.21
919 921 3.173167 AACACGTTGGCCCGCTACT 62.173 57.895 0.00 0.00 0.00 2.57
1198 1224 0.733223 GGCTCGTCTCGTTTCTGTCC 60.733 60.000 0.00 0.00 0.00 4.02
1219 1245 0.388907 CCTGTTTGCGGGCTTTGATG 60.389 55.000 0.00 0.00 33.82 3.07
1265 1291 7.644551 GGTAAGACAACGATACTGAAGATACTG 59.355 40.741 0.00 0.00 0.00 2.74
1299 1325 1.097547 GGTGGATCCGAGCATGGTTG 61.098 60.000 7.39 5.08 0.00 3.77
1433 1459 6.606768 GTTGTGCAATTGTTTTCCTTTTTCA 58.393 32.000 7.40 0.00 0.00 2.69
1439 1465 7.064490 TGCAATTGTTTTCCTTTTTCAAGACTC 59.936 33.333 7.40 0.00 30.57 3.36
1449 1475 5.450965 CCTTTTTCAAGACTCTGTTGTGCAT 60.451 40.000 0.00 0.00 30.57 3.96
1461 1487 2.954989 TGTTGTGCATTTGTGAGGCTAA 59.045 40.909 0.00 0.00 0.00 3.09
1485 1511 3.788766 GTCAAGGCGTGCGCGAAT 61.789 61.111 26.19 7.64 43.06 3.34
1493 1519 2.706123 CGTGCGCGAATTTTGCCAC 61.706 57.895 16.08 15.06 41.33 5.01
1499 1525 1.613270 GCGAATTTTGCCACTAACCG 58.387 50.000 0.00 0.00 0.00 4.44
1567 1595 2.504681 CGCGATGTTGCCTTTGCC 60.505 61.111 0.00 0.00 36.33 4.52
1609 1637 2.559698 TGGACATTTCGGCAGAGAAA 57.440 45.000 4.20 4.20 43.28 2.52
1696 1724 8.097662 TCACCCCAAAATTACCAATACAAATTC 58.902 33.333 0.00 0.00 0.00 2.17
1700 1728 8.816144 CCCAAAATTACCAATACAAATTCATCG 58.184 33.333 0.00 0.00 0.00 3.84
1701 1729 9.364989 CCAAAATTACCAATACAAATTCATCGT 57.635 29.630 0.00 0.00 0.00 3.73
1717 1745 5.635417 TCATCGTTAAATCACATTTGCCA 57.365 34.783 0.00 0.00 33.82 4.92
1724 1752 1.784358 ATCACATTTGCCATGGGGAG 58.216 50.000 15.13 0.00 35.59 4.30
1729 1757 1.684983 CATTTGCCATGGGGAGCTTAG 59.315 52.381 15.13 0.00 35.59 2.18
1732 1760 0.704076 TGCCATGGGGAGCTTAGTTT 59.296 50.000 15.13 0.00 35.59 2.66
1736 1764 3.019564 CCATGGGGAGCTTAGTTTTCAG 58.980 50.000 2.85 0.00 35.59 3.02
1758 1787 9.460019 TTCAGATTAATGATACCATGTTCACAA 57.540 29.630 0.00 0.00 32.36 3.33
1777 1806 8.655970 GTTCACAAAACTGAAGTTTGCTATTTT 58.344 29.630 9.11 0.00 46.47 1.82
1784 1813 7.867909 AAACTGAAGTTTGCTATTTTAGCTTCC 59.132 33.333 7.62 0.00 45.55 3.46
1833 1862 4.014406 CTGGTTACTTATTTGTCACCCCC 58.986 47.826 0.00 0.00 34.31 5.40
1851 1880 1.032014 CCTTTGCCGGATTATGTGGG 58.968 55.000 5.05 0.00 0.00 4.61
1859 1888 2.424234 CCGGATTATGTGGGAATGGGTT 60.424 50.000 0.00 0.00 0.00 4.11
1860 1889 2.622942 CGGATTATGTGGGAATGGGTTG 59.377 50.000 0.00 0.00 0.00 3.77
1864 1893 1.631405 ATGTGGGAATGGGTTGTGTG 58.369 50.000 0.00 0.00 0.00 3.82
1925 1955 4.511617 TGCTTCCGCAACAATCAAATTA 57.488 36.364 0.00 0.00 44.62 1.40
1949 1979 2.637872 TCCAGAAATCTCCCGTTTGTCT 59.362 45.455 0.00 0.00 0.00 3.41
1966 1996 6.183360 CGTTTGTCTTGGTCATACTTGCATAT 60.183 38.462 0.00 0.00 0.00 1.78
1971 2001 8.264347 TGTCTTGGTCATACTTGCATATTCTAA 58.736 33.333 0.00 0.00 0.00 2.10
1975 2005 6.992123 TGGTCATACTTGCATATTCTAACCAG 59.008 38.462 0.00 0.00 0.00 4.00
2302 2617 4.762289 ATAAGCTAACCAGGACTTCCAG 57.238 45.455 0.00 0.00 38.89 3.86
2331 2646 4.799715 ATAAATCCAATCCACCCGGTTA 57.200 40.909 0.00 0.00 0.00 2.85
2376 2691 4.816385 CCTTGTGTAATGGTATGCTGGTAG 59.184 45.833 0.00 0.00 0.00 3.18
2384 2700 7.509318 TGTAATGGTATGCTGGTAGAGAATACT 59.491 37.037 0.00 0.00 41.57 2.12
2398 2717 5.238583 AGAGAATACTTTTGAGGAACACCG 58.761 41.667 0.00 0.00 0.00 4.94
2438 2757 6.347725 CCTTTCGAGATGTAAAAGAACAGGTG 60.348 42.308 0.00 0.00 32.89 4.00
2508 2828 7.807977 ATCAAGTCTGTGTGTTATGTTTCTT 57.192 32.000 0.00 0.00 0.00 2.52
2529 2849 4.089408 TGGGGAAAGTACTTGTGTTACC 57.911 45.455 9.34 3.12 0.00 2.85
2581 2901 8.910351 AATTAGGAACTAGGACATAGCATTTC 57.090 34.615 0.00 0.00 44.25 2.17
2618 2938 0.107312 TCTACTCCCTCCGTCCGAAG 60.107 60.000 0.00 0.00 0.00 3.79
2631 2951 2.567985 GTCCGAAGAAACTTGTCCCAA 58.432 47.619 0.00 0.00 0.00 4.12
2694 3014 7.233389 TGCTAGATACATCTATTTGAGGGAC 57.767 40.000 0.00 0.00 38.60 4.46
2802 3126 0.539986 ATATGTCCGGGCGAACAGTT 59.460 50.000 0.00 0.00 0.00 3.16
3581 3928 1.525995 ACCTATTGGCGCCATTCGG 60.526 57.895 33.25 31.26 38.94 4.30
3917 4264 1.524863 CGACGATAGCCGGGGAAGAT 61.525 60.000 2.18 0.00 43.93 2.40
4062 4409 4.637483 TTCTTGCACAAAAGGAACAGAG 57.363 40.909 0.00 0.00 0.00 3.35
4074 4421 7.545615 ACAAAAGGAACAGAGAATTTGACAAAC 59.454 33.333 1.94 0.00 33.30 2.93
4082 4429 3.989817 GAGAATTTGACAAACCATGCACC 59.010 43.478 1.94 0.00 0.00 5.01
4121 4468 7.334844 ACGACAATGTACTCTGAATCTATGA 57.665 36.000 0.00 0.00 0.00 2.15
4250 4597 4.775780 TCTCGGTGAAATAGGAAAGGAAGA 59.224 41.667 0.00 0.00 0.00 2.87
4262 4609 5.406163 AGGAAAGGAAGAACCATTGGAAAT 58.594 37.500 10.37 0.00 42.04 2.17
4405 4752 1.728971 GGACTGAGTTGTCTGCATTCG 59.271 52.381 0.00 0.00 37.16 3.34
4422 4769 3.587933 GGTTTGCCGTCCAACGCA 61.588 61.111 0.00 0.00 40.91 5.24
4423 4770 2.051345 GTTTGCCGTCCAACGCAG 60.051 61.111 0.00 0.00 40.91 5.18
4472 4819 1.193874 CTGTCCGTTTACTCGCAAACC 59.806 52.381 0.00 0.00 35.42 3.27
4503 4850 1.299468 GCGGCAGTCCAGATAGTCG 60.299 63.158 0.00 0.00 0.00 4.18
4515 4862 5.004448 TCCAGATAGTCGACATGTAGGATC 58.996 45.833 19.50 8.21 0.00 3.36
4517 4864 5.007034 CAGATAGTCGACATGTAGGATCCT 58.993 45.833 20.48 20.48 0.00 3.24
4518 4865 5.123186 CAGATAGTCGACATGTAGGATCCTC 59.877 48.000 20.22 10.81 0.00 3.71
4525 4872 1.417890 CATGTAGGATCCTCACACCCC 59.582 57.143 20.22 0.00 0.00 4.95
4905 5252 0.533951 CCCCCTTTGCTTTCATCTGC 59.466 55.000 0.00 0.00 0.00 4.26
4906 5253 1.259609 CCCCTTTGCTTTCATCTGCA 58.740 50.000 0.00 0.00 37.42 4.41
4907 5254 1.067354 CCCCTTTGCTTTCATCTGCAC 60.067 52.381 0.00 0.00 39.05 4.57
4908 5255 1.067354 CCCTTTGCTTTCATCTGCACC 60.067 52.381 0.00 0.00 39.05 5.01
4909 5256 1.067354 CCTTTGCTTTCATCTGCACCC 60.067 52.381 0.00 0.00 39.05 4.61
4910 5257 1.891150 CTTTGCTTTCATCTGCACCCT 59.109 47.619 0.00 0.00 39.05 4.34
4911 5258 1.538047 TTGCTTTCATCTGCACCCTC 58.462 50.000 0.00 0.00 39.05 4.30
4912 5259 0.322816 TGCTTTCATCTGCACCCTCC 60.323 55.000 0.00 0.00 33.94 4.30
4913 5260 0.034670 GCTTTCATCTGCACCCTCCT 60.035 55.000 0.00 0.00 0.00 3.69
4914 5261 2.016096 GCTTTCATCTGCACCCTCCTC 61.016 57.143 0.00 0.00 0.00 3.71
4915 5262 0.250234 TTTCATCTGCACCCTCCTCG 59.750 55.000 0.00 0.00 0.00 4.63
4916 5263 0.904865 TTCATCTGCACCCTCCTCGT 60.905 55.000 0.00 0.00 0.00 4.18
4917 5264 1.142748 CATCTGCACCCTCCTCGTC 59.857 63.158 0.00 0.00 0.00 4.20
4918 5265 2.060980 ATCTGCACCCTCCTCGTCC 61.061 63.158 0.00 0.00 0.00 4.79
4919 5266 4.135153 CTGCACCCTCCTCGTCCG 62.135 72.222 0.00 0.00 0.00 4.79
4920 5267 4.671590 TGCACCCTCCTCGTCCGA 62.672 66.667 0.00 0.00 0.00 4.55
4921 5268 4.131088 GCACCCTCCTCGTCCGAC 62.131 72.222 0.00 0.00 0.00 4.79
4922 5269 2.675423 CACCCTCCTCGTCCGACA 60.675 66.667 0.00 0.00 0.00 4.35
4923 5270 2.675772 ACCCTCCTCGTCCGACAC 60.676 66.667 0.00 0.00 0.00 3.67
4924 5271 3.450115 CCCTCCTCGTCCGACACC 61.450 72.222 0.00 0.00 0.00 4.16
4925 5272 3.812019 CCTCCTCGTCCGACACCG 61.812 72.222 0.00 0.00 0.00 4.94
4926 5273 3.054503 CTCCTCGTCCGACACCGT 61.055 66.667 0.00 0.00 0.00 4.83
4927 5274 3.036783 CTCCTCGTCCGACACCGTC 62.037 68.421 0.00 0.00 0.00 4.79
4937 5284 3.098032 GACACCGTCGTTGTACCTC 57.902 57.895 0.00 0.00 0.00 3.85
4938 5285 0.595095 GACACCGTCGTTGTACCTCT 59.405 55.000 0.00 0.00 0.00 3.69
4939 5286 0.595095 ACACCGTCGTTGTACCTCTC 59.405 55.000 0.00 0.00 0.00 3.20
4940 5287 0.453950 CACCGTCGTTGTACCTCTCG 60.454 60.000 0.00 0.00 0.00 4.04
4941 5288 1.136147 CCGTCGTTGTACCTCTCGG 59.864 63.158 0.00 0.00 0.00 4.63
4942 5289 1.513586 CGTCGTTGTACCTCTCGGC 60.514 63.158 0.00 0.00 0.00 5.54
4943 5290 1.153881 GTCGTTGTACCTCTCGGCC 60.154 63.158 0.00 0.00 0.00 6.13
4944 5291 2.202570 CGTTGTACCTCTCGGCCG 60.203 66.667 22.12 22.12 0.00 6.13
4945 5292 2.508663 GTTGTACCTCTCGGCCGC 60.509 66.667 23.51 4.74 0.00 6.53
4946 5293 3.766691 TTGTACCTCTCGGCCGCC 61.767 66.667 23.51 0.00 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 1.318251 GTCTGCATTTCACGAAACGC 58.682 50.000 3.74 3.74 39.63 4.84
27 28 5.064452 CCTCTTATGAGTGTCTGCATTTCAC 59.936 44.000 5.03 7.63 38.61 3.18
41 42 9.823647 ACGGATAATATTATTGCCTCTTATGAG 57.176 33.333 9.33 0.00 39.92 2.90
53 54 7.766278 GGCAGACTGATCACGGATAATATTATT 59.234 37.037 6.65 0.00 0.00 1.40
98 99 5.034852 TGCCTGATATCATTTCGAAGGAA 57.965 39.130 5.72 0.00 0.00 3.36
103 104 7.445121 AGTAATCTTGCCTGATATCATTTCGA 58.555 34.615 5.72 0.60 0.00 3.71
113 114 3.950395 GGCTGAAAGTAATCTTGCCTGAT 59.050 43.478 0.00 0.00 36.99 2.90
200 201 4.794278 AACGAACCCCACAAATTTATCC 57.206 40.909 0.00 0.00 0.00 2.59
215 216 5.237779 TGTTCTCATTCCAAAGGTAACGAAC 59.762 40.000 0.00 0.00 46.39 3.95
267 268 5.312178 TGAGAATTGTAAAAGGGGAGGAGAA 59.688 40.000 0.00 0.00 0.00 2.87
287 288 8.880991 AGGAAGTTACAAAGATAGTACTGAGA 57.119 34.615 5.39 0.00 0.00 3.27
301 302 6.657541 GGATATTTGTGGTGAGGAAGTTACAA 59.342 38.462 0.00 0.00 0.00 2.41
377 378 4.448732 GCATTGTTTCAGATGTTTCCAACC 59.551 41.667 0.00 0.00 0.00 3.77
398 399 4.202567 ACCAGAGAGGAGGTAAAAATTGCA 60.203 41.667 0.00 0.00 41.22 4.08
402 403 7.474936 GCCATATACCAGAGAGGAGGTAAAAAT 60.475 40.741 0.00 0.00 43.14 1.82
557 559 1.609072 CGCTGAGATAACAGATCCGGA 59.391 52.381 6.61 6.61 39.94 5.14
565 567 2.316108 TCTATGGGCGCTGAGATAACA 58.684 47.619 7.64 0.00 0.00 2.41
647 649 0.234884 GCGGGAGACAAAAACACGAG 59.765 55.000 0.00 0.00 0.00 4.18
678 680 0.321298 GCGGCAAAGGTCTAGGTTGA 60.321 55.000 0.00 0.00 0.00 3.18
702 704 6.244654 AGATGTATCATCGAGAGGAGATCAA 58.755 40.000 0.00 0.00 0.00 2.57
919 921 1.633774 GTGGACAGGACAGGAGAAGA 58.366 55.000 0.00 0.00 0.00 2.87
1177 1203 1.801913 CAGAAACGAGACGAGCCGG 60.802 63.158 0.00 0.00 0.00 6.13
1181 1207 1.135632 GGAGGACAGAAACGAGACGAG 60.136 57.143 0.00 0.00 0.00 4.18
1198 1224 1.172180 TCAAAGCCCGCAAACAGGAG 61.172 55.000 0.00 0.00 0.00 3.69
1265 1291 4.740822 ACCATGTGCTTCCCGCCC 62.741 66.667 0.00 0.00 38.05 6.13
1299 1325 3.400054 CGACCTTCCCAGGACCCC 61.400 72.222 0.00 0.00 44.19 4.95
1433 1459 3.947196 TCACAAATGCACAACAGAGTCTT 59.053 39.130 0.00 0.00 0.00 3.01
1439 1465 1.338973 AGCCTCACAAATGCACAACAG 59.661 47.619 0.00 0.00 0.00 3.16
1449 1475 4.211125 TGACCAATGTTTAGCCTCACAAA 58.789 39.130 0.00 0.00 0.00 2.83
1461 1487 1.659794 GCACGCCTTGACCAATGTT 59.340 52.632 0.00 0.00 0.00 2.71
1485 1511 2.223745 GGAAGACGGTTAGTGGCAAAA 58.776 47.619 0.00 0.00 0.00 2.44
1493 1519 6.897259 TTAAATTCATCGGAAGACGGTTAG 57.103 37.500 0.00 0.00 46.97 2.34
1567 1595 3.572682 TCTGTATATTCACCTGGTAGCCG 59.427 47.826 0.00 0.00 0.00 5.52
1609 1637 2.493278 GCCAGTGACACCAAATAGCATT 59.507 45.455 0.84 0.00 0.00 3.56
1696 1724 5.232626 CCATGGCAAATGTGATTTAACGATG 59.767 40.000 0.00 0.00 0.00 3.84
1700 1728 4.081198 TCCCCATGGCAAATGTGATTTAAC 60.081 41.667 6.09 0.00 0.00 2.01
1701 1729 4.099633 TCCCCATGGCAAATGTGATTTAA 58.900 39.130 6.09 0.00 0.00 1.52
1714 1742 1.751351 GAAAACTAAGCTCCCCATGGC 59.249 52.381 6.09 0.00 0.00 4.40
1717 1745 4.870021 ATCTGAAAACTAAGCTCCCCAT 57.130 40.909 0.00 0.00 0.00 4.00
1732 1760 9.460019 TTGTGAACATGGTATCATTAATCTGAA 57.540 29.630 0.00 0.00 0.00 3.02
1753 1782 9.515020 CTAAAATAGCAAACTTCAGTTTTGTGA 57.485 29.630 2.01 0.00 45.07 3.58
1777 1806 2.794103 TGCATGAAAGCAAGGAAGCTA 58.206 42.857 0.00 0.00 45.89 3.32
1829 1858 0.106217 ACATAATCCGGCAAAGGGGG 60.106 55.000 0.00 0.00 0.00 5.40
1833 1862 2.051334 TCCCACATAATCCGGCAAAG 57.949 50.000 0.00 0.00 0.00 2.77
1864 1893 6.939163 AGATAATTCAAGTCCTCATGTATGGC 59.061 38.462 0.00 0.00 0.00 4.40
1925 1955 5.131142 AGACAAACGGGAGATTTCTGGATAT 59.869 40.000 0.00 0.00 0.00 1.63
1949 1979 7.342581 TGGTTAGAATATGCAAGTATGACCAA 58.657 34.615 0.00 0.00 30.10 3.67
1966 1996 4.331968 CCATTGGCTGTAACTGGTTAGAA 58.668 43.478 0.00 0.00 0.00 2.10
1971 2001 2.961424 GCCATTGGCTGTAACTGGT 58.039 52.632 20.66 0.00 46.69 4.00
2331 2646 3.480133 GGGGCGCCACATAGTCCT 61.480 66.667 30.85 0.00 31.66 3.85
2376 2691 5.235516 TCGGTGTTCCTCAAAAGTATTCTC 58.764 41.667 0.00 0.00 0.00 2.87
2398 2717 5.643777 TCTCGAAAGGATCTTCCAAACAATC 59.356 40.000 0.00 0.00 39.61 2.67
2508 2828 3.181441 GGGTAACACAAGTACTTTCCCCA 60.181 47.826 5.07 0.00 39.74 4.96
2581 2901 5.998553 AGTAGATCATACGACCAACATACG 58.001 41.667 0.00 0.00 0.00 3.06
2631 2951 3.771216 ACATCCATTTGAAGGACAAGCT 58.229 40.909 0.00 0.00 39.77 3.74
2694 3014 0.517316 CCTCCGTCCGAAAAAGCTTG 59.483 55.000 0.00 0.00 0.00 4.01
2802 3126 1.816863 GAGGGTGCTTCTGTGTCCGA 61.817 60.000 0.00 0.00 0.00 4.55
2937 3261 1.598130 GGACATATGCGTCTGGGGC 60.598 63.158 1.58 0.00 36.12 5.80
2976 3300 1.270465 CGGACTTTAACGGTGTTCCCT 60.270 52.381 0.00 0.00 0.00 4.20
2999 3341 0.958091 CCCATTTGTCCGCAGAAACA 59.042 50.000 0.00 0.00 0.00 2.83
3547 3894 6.934645 GCCAATAGGTGTTAATAGTCTGCATA 59.065 38.462 0.00 0.00 37.19 3.14
3581 3928 4.095483 CCATGAGCAACATAGACCTGAAAC 59.905 45.833 0.00 0.00 37.46 2.78
3917 4264 6.745450 CGCTGTTTGAACTGAAAGAAAAGTTA 59.255 34.615 5.13 0.00 36.77 2.24
4062 4409 3.066380 GGGTGCATGGTTTGTCAAATTC 58.934 45.455 0.40 0.00 0.00 2.17
4082 4429 1.202521 TGTCGTATACATGCAGCAGGG 60.203 52.381 12.54 3.52 31.43 4.45
4121 4468 5.790593 ACAATAATAATCGACGCCCAGTAT 58.209 37.500 0.00 0.00 0.00 2.12
4250 4597 2.028561 ACTGGGCATTTCCAATGGTT 57.971 45.000 0.00 0.00 36.21 3.67
4354 4701 1.141053 AGGTCAGCGTTGGAGTTTTCT 59.859 47.619 0.00 0.00 0.00 2.52
4355 4702 1.531578 GAGGTCAGCGTTGGAGTTTTC 59.468 52.381 0.00 0.00 0.00 2.29
4356 4703 1.134220 TGAGGTCAGCGTTGGAGTTTT 60.134 47.619 0.00 0.00 0.00 2.43
4357 4704 0.468226 TGAGGTCAGCGTTGGAGTTT 59.532 50.000 0.00 0.00 0.00 2.66
4358 4705 0.468226 TTGAGGTCAGCGTTGGAGTT 59.532 50.000 0.00 0.00 0.00 3.01
4359 4706 0.468226 TTTGAGGTCAGCGTTGGAGT 59.532 50.000 0.00 0.00 0.00 3.85
4405 4752 3.536498 CTGCGTTGGACGGCAAACC 62.536 63.158 2.01 0.00 42.82 3.27
4413 4760 1.298859 GATGTGGGACTGCGTTGGAC 61.299 60.000 0.00 0.00 0.00 4.02
4414 4761 1.003839 GATGTGGGACTGCGTTGGA 60.004 57.895 0.00 0.00 0.00 3.53
4415 4762 2.390599 CGATGTGGGACTGCGTTGG 61.391 63.158 0.00 0.00 0.00 3.77
4416 4763 2.390599 CCGATGTGGGACTGCGTTG 61.391 63.158 0.00 0.00 0.00 4.10
4417 4764 2.047274 CCGATGTGGGACTGCGTT 60.047 61.111 0.00 0.00 0.00 4.84
4418 4765 3.296709 GACCGATGTGGGACTGCGT 62.297 63.158 0.00 0.00 44.64 5.24
4419 4766 2.509336 GACCGATGTGGGACTGCG 60.509 66.667 0.00 0.00 44.64 5.18
4420 4767 1.448540 CAGACCGATGTGGGACTGC 60.449 63.158 1.35 0.00 44.64 4.40
4421 4768 0.108615 GACAGACCGATGTGGGACTG 60.109 60.000 10.79 10.79 45.46 3.51
4422 4769 1.595993 CGACAGACCGATGTGGGACT 61.596 60.000 0.00 0.00 44.64 3.85
4423 4770 1.153823 CGACAGACCGATGTGGGAC 60.154 63.158 0.00 0.00 44.64 4.46
4448 4795 0.171903 GCGAGTAAACGGACAGGCTA 59.828 55.000 0.00 0.00 0.00 3.93
4472 4819 3.488090 GCCGCGAGTTTCCTTCCG 61.488 66.667 8.23 0.00 0.00 4.30
4503 4850 2.103263 GGGTGTGAGGATCCTACATGTC 59.897 54.545 16.16 12.02 0.00 3.06
4515 4862 3.782443 GTAGGCCGGGGTGTGAGG 61.782 72.222 2.18 0.00 0.00 3.86
4517 4864 2.682494 GAGTAGGCCGGGGTGTGA 60.682 66.667 2.18 0.00 0.00 3.58
4518 4865 3.000819 TGAGTAGGCCGGGGTGTG 61.001 66.667 2.18 0.00 0.00 3.82
4886 5233 0.533951 GCAGATGAAAGCAAAGGGGG 59.466 55.000 0.00 0.00 0.00 5.40
4887 5234 1.067354 GTGCAGATGAAAGCAAAGGGG 60.067 52.381 0.00 0.00 43.20 4.79
4888 5235 1.067354 GGTGCAGATGAAAGCAAAGGG 60.067 52.381 0.00 0.00 43.20 3.95
4889 5236 1.067354 GGGTGCAGATGAAAGCAAAGG 60.067 52.381 0.00 0.00 43.20 3.11
4890 5237 1.891150 AGGGTGCAGATGAAAGCAAAG 59.109 47.619 0.00 0.00 43.20 2.77
4891 5238 1.888512 GAGGGTGCAGATGAAAGCAAA 59.111 47.619 0.00 0.00 43.20 3.68
4892 5239 1.538047 GAGGGTGCAGATGAAAGCAA 58.462 50.000 0.00 0.00 43.20 3.91
4893 5240 0.322816 GGAGGGTGCAGATGAAAGCA 60.323 55.000 0.00 0.00 38.65 3.91
4894 5241 0.034670 AGGAGGGTGCAGATGAAAGC 60.035 55.000 0.00 0.00 0.00 3.51
4895 5242 1.741732 CGAGGAGGGTGCAGATGAAAG 60.742 57.143 0.00 0.00 0.00 2.62
4896 5243 0.250234 CGAGGAGGGTGCAGATGAAA 59.750 55.000 0.00 0.00 0.00 2.69
4897 5244 0.904865 ACGAGGAGGGTGCAGATGAA 60.905 55.000 0.00 0.00 0.00 2.57
4898 5245 1.305297 ACGAGGAGGGTGCAGATGA 60.305 57.895 0.00 0.00 0.00 2.92
4899 5246 1.142748 GACGAGGAGGGTGCAGATG 59.857 63.158 0.00 0.00 0.00 2.90
4900 5247 2.060980 GGACGAGGAGGGTGCAGAT 61.061 63.158 0.00 0.00 0.00 2.90
4901 5248 2.680352 GGACGAGGAGGGTGCAGA 60.680 66.667 0.00 0.00 0.00 4.26
4902 5249 4.135153 CGGACGAGGAGGGTGCAG 62.135 72.222 0.00 0.00 0.00 4.41
4903 5250 4.671590 TCGGACGAGGAGGGTGCA 62.672 66.667 0.00 0.00 0.00 4.57
4904 5251 4.131088 GTCGGACGAGGAGGGTGC 62.131 72.222 0.00 0.00 0.00 5.01
4905 5252 2.675423 TGTCGGACGAGGAGGGTG 60.675 66.667 3.34 0.00 0.00 4.61
4906 5253 2.675772 GTGTCGGACGAGGAGGGT 60.676 66.667 3.34 0.00 0.00 4.34
4907 5254 3.450115 GGTGTCGGACGAGGAGGG 61.450 72.222 3.34 0.00 0.00 4.30
4908 5255 3.812019 CGGTGTCGGACGAGGAGG 61.812 72.222 3.34 0.00 0.00 4.30
4909 5256 3.036783 GACGGTGTCGGACGAGGAG 62.037 68.421 3.34 0.00 41.39 3.69
4910 5257 3.052082 GACGGTGTCGGACGAGGA 61.052 66.667 3.34 0.00 41.39 3.71
4919 5266 0.595095 AGAGGTACAACGACGGTGTC 59.405 55.000 23.97 13.79 0.00 3.67
4920 5267 0.595095 GAGAGGTACAACGACGGTGT 59.405 55.000 23.74 23.74 0.00 4.16
4921 5268 0.453950 CGAGAGGTACAACGACGGTG 60.454 60.000 12.24 12.24 0.00 4.94
4922 5269 1.871772 CGAGAGGTACAACGACGGT 59.128 57.895 0.00 0.00 0.00 4.83
4923 5270 4.759564 CGAGAGGTACAACGACGG 57.240 61.111 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.