Multiple sequence alignment - TraesCS4A01G295400

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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 TraesCS4A01G295400 chr4A 100.000 2676 0 0 1 2676 596167559 596164884 0.000000e+00 4942.0
1 TraesCS4A01G295400 chr4A 77.564 156 30 5 673 825 508357913 508357760 3.670000e-14 89.8
2 TraesCS4A01G295400 chr4A 83.333 96 14 2 731 825 508494185 508494091 1.320000e-13 87.9
3 TraesCS4A01G295400 chr4D 89.742 1862 105 33 41 1849 7419579 7421407 0.000000e+00 2302.0
4 TraesCS4A01G295400 chr2A 98.842 777 5 4 1902 2676 2331836 2332610 0.000000e+00 1382.0
5 TraesCS4A01G295400 chr2A 98.711 776 8 2 1902 2676 751613135 751612361 0.000000e+00 1376.0
6 TraesCS4A01G295400 chr2A 97.938 776 11 4 1903 2676 751196691 751195919 0.000000e+00 1339.0
7 TraesCS4A01G295400 chr2A 98.387 62 1 0 1844 1905 751613259 751613198 2.820000e-20 110.0
8 TraesCS4A01G295400 chr2A 96.774 62 2 0 1844 1905 2331711 2331772 1.310000e-18 104.0
9 TraesCS4A01G295400 chr2A 95.161 62 3 0 1844 1905 751196818 751196757 6.100000e-17 99.0
10 TraesCS4A01G295400 chr2A 93.548 62 4 0 1844 1905 116175060 116175121 2.840000e-15 93.5
11 TraesCS4A01G295400 chr6A 98.582 776 7 4 1902 2676 11070349 11071121 0.000000e+00 1369.0
12 TraesCS4A01G295400 chr7A 98.452 775 10 2 1902 2676 715784014 715783242 0.000000e+00 1363.0
13 TraesCS4A01G295400 chr7A 96.774 62 1 1 1844 1905 715784137 715784077 4.710000e-18 102.0
14 TraesCS4A01G295400 chr1A 96.392 776 8 7 1902 2676 554931305 554930549 0.000000e+00 1260.0
15 TraesCS4A01G295400 chr1A 97.993 598 11 1 1902 2499 544743094 544742498 0.000000e+00 1037.0
16 TraesCS4A01G295400 chr1A 98.387 62 1 0 1844 1905 544743220 544743159 2.820000e-20 110.0
17 TraesCS4A01G295400 chr1A 98.387 62 1 0 1844 1905 554931429 554931368 2.820000e-20 110.0
18 TraesCS4A01G295400 chr4B 87.746 1069 62 35 42 1088 13297182 13298203 0.000000e+00 1184.0
19 TraesCS4A01G295400 chr4B 89.116 441 30 11 1326 1748 13298201 13298641 1.410000e-147 532.0
20 TraesCS4A01G295400 chr4B 78.443 167 32 4 668 832 109222761 109222925 3.640000e-19 106.0
21 TraesCS4A01G295400 chr4B 93.548 62 4 0 1844 1905 540315447 540315508 2.840000e-15 93.5
22 TraesCS4A01G295400 chr3A 96.429 532 15 4 2147 2676 574971378 574970849 0.000000e+00 874.0
23 TraesCS4A01G295400 chr3A 95.677 532 16 5 2147 2676 41247410 41247936 0.000000e+00 848.0
24 TraesCS4A01G295400 chr5A 96.422 531 16 3 2147 2676 41875311 41875839 0.000000e+00 872.0
25 TraesCS4A01G295400 chr5A 89.928 278 13 4 1902 2166 41874994 41875269 7.090000e-91 344.0
26 TraesCS4A01G295400 chr1B 87.879 66 0 3 1844 1905 86748587 86748526 1.330000e-08 71.3


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 TraesCS4A01G295400 chr4A 596164884 596167559 2675 True 4942.0 4942 100.0000 1 2676 1 chr4A.!!$R3 2675
1 TraesCS4A01G295400 chr4D 7419579 7421407 1828 False 2302.0 2302 89.7420 41 1849 1 chr4D.!!$F1 1808
2 TraesCS4A01G295400 chr2A 2331711 2332610 899 False 743.0 1382 97.8080 1844 2676 2 chr2A.!!$F2 832
3 TraesCS4A01G295400 chr2A 751612361 751613259 898 True 743.0 1376 98.5490 1844 2676 2 chr2A.!!$R2 832
4 TraesCS4A01G295400 chr2A 751195919 751196818 899 True 719.0 1339 96.5495 1844 2676 2 chr2A.!!$R1 832
5 TraesCS4A01G295400 chr6A 11070349 11071121 772 False 1369.0 1369 98.5820 1902 2676 1 chr6A.!!$F1 774
6 TraesCS4A01G295400 chr7A 715783242 715784137 895 True 732.5 1363 97.6130 1844 2676 2 chr7A.!!$R1 832
7 TraesCS4A01G295400 chr1A 554930549 554931429 880 True 685.0 1260 97.3895 1844 2676 2 chr1A.!!$R2 832
8 TraesCS4A01G295400 chr1A 544742498 544743220 722 True 573.5 1037 98.1900 1844 2499 2 chr1A.!!$R1 655
9 TraesCS4A01G295400 chr4B 13297182 13298641 1459 False 858.0 1184 88.4310 42 1748 2 chr4B.!!$F3 1706
10 TraesCS4A01G295400 chr3A 574970849 574971378 529 True 874.0 874 96.4290 2147 2676 1 chr3A.!!$R1 529
11 TraesCS4A01G295400 chr3A 41247410 41247936 526 False 848.0 848 95.6770 2147 2676 1 chr3A.!!$F1 529
12 TraesCS4A01G295400 chr5A 41874994 41875839 845 False 608.0 872 93.1750 1902 2676 2 chr5A.!!$F1 774

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
27 28 0.038166 TGCAAAAATCCTCGAGGCCT 59.962 50.0 27.39 3.86 34.44 5.19 F
318 326 0.107945 AAGCGAGAGGAAGCATGGAC 60.108 55.0 0.00 0.00 35.48 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1418 1486 1.135046 CACAGCAAGTCAGTCACTCG 58.865 55.000 0.00 0.00 32.30 4.18 R
1785 1869 2.025605 TCTGCTGCTGATGGAATTCCTT 60.026 45.455 24.73 18.79 36.82 3.36 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
22 23 5.059404 GAAATTCCTGCAAAAATCCTCGA 57.941 39.130 0.00 0.00 0.00 4.04
23 24 4.708726 AATTCCTGCAAAAATCCTCGAG 57.291 40.909 5.13 5.13 0.00 4.04
24 25 2.113860 TCCTGCAAAAATCCTCGAGG 57.886 50.000 26.32 26.32 0.00 4.63
25 26 0.453390 CCTGCAAAAATCCTCGAGGC 59.547 55.000 27.39 13.37 34.44 4.70
26 27 0.453390 CTGCAAAAATCCTCGAGGCC 59.547 55.000 27.39 0.00 34.44 5.19
27 28 0.038166 TGCAAAAATCCTCGAGGCCT 59.962 50.000 27.39 3.86 34.44 5.19
28 29 1.177401 GCAAAAATCCTCGAGGCCTT 58.823 50.000 27.39 18.66 34.44 4.35
29 30 2.290641 TGCAAAAATCCTCGAGGCCTTA 60.291 45.455 27.39 10.08 34.44 2.69
30 31 2.952310 GCAAAAATCCTCGAGGCCTTAT 59.048 45.455 27.39 12.18 34.44 1.73
31 32 4.134563 GCAAAAATCCTCGAGGCCTTATA 58.865 43.478 27.39 8.83 34.44 0.98
32 33 4.023963 GCAAAAATCCTCGAGGCCTTATAC 60.024 45.833 27.39 10.07 34.44 1.47
33 34 5.123227 CAAAAATCCTCGAGGCCTTATACA 58.877 41.667 27.39 7.18 34.44 2.29
34 35 4.608948 AAATCCTCGAGGCCTTATACAG 57.391 45.455 27.39 0.00 34.44 2.74
35 36 3.527507 ATCCTCGAGGCCTTATACAGA 57.472 47.619 27.39 5.55 34.44 3.41
36 37 3.308035 TCCTCGAGGCCTTATACAGAA 57.692 47.619 27.39 1.30 34.44 3.02
37 38 3.223435 TCCTCGAGGCCTTATACAGAAG 58.777 50.000 27.39 0.00 34.44 2.85
38 39 3.117625 TCCTCGAGGCCTTATACAGAAGA 60.118 47.826 27.39 0.58 34.44 2.87
39 40 3.254657 CCTCGAGGCCTTATACAGAAGAG 59.745 52.174 20.67 5.10 0.00 2.85
40 41 3.223435 TCGAGGCCTTATACAGAAGAGG 58.777 50.000 6.77 0.00 0.00 3.69
41 42 3.117625 TCGAGGCCTTATACAGAAGAGGA 60.118 47.826 6.77 0.00 0.00 3.71
42 43 3.637229 CGAGGCCTTATACAGAAGAGGAA 59.363 47.826 6.77 0.00 0.00 3.36
43 44 4.261825 CGAGGCCTTATACAGAAGAGGAAG 60.262 50.000 6.77 0.00 0.00 3.46
44 45 3.970640 AGGCCTTATACAGAAGAGGAAGG 59.029 47.826 0.00 0.00 37.17 3.46
45 46 3.967987 GGCCTTATACAGAAGAGGAAGGA 59.032 47.826 0.00 0.00 36.37 3.36
57 58 1.828595 GAGGAAGGAGAGGAACCACTC 59.171 57.143 9.25 9.25 37.77 3.51
67 68 0.534203 GGAACCACTCGAAACCAGCA 60.534 55.000 0.00 0.00 0.00 4.41
97 99 1.349688 TGTCAGTGTACCATTGGACCC 59.650 52.381 10.37 0.00 0.00 4.46
102 104 2.106857 AGTGTACCATTGGACCCGAAAA 59.893 45.455 10.37 0.00 0.00 2.29
103 105 3.086282 GTGTACCATTGGACCCGAAAAT 58.914 45.455 10.37 0.00 0.00 1.82
104 106 3.508402 GTGTACCATTGGACCCGAAAATT 59.492 43.478 10.37 0.00 0.00 1.82
105 107 3.759618 TGTACCATTGGACCCGAAAATTC 59.240 43.478 10.37 0.00 0.00 2.17
107 109 3.235200 ACCATTGGACCCGAAAATTCAA 58.765 40.909 10.37 0.00 0.00 2.69
109 111 3.584834 CATTGGACCCGAAAATTCAACC 58.415 45.455 0.00 0.00 0.00 3.77
110 112 1.240256 TGGACCCGAAAATTCAACCG 58.760 50.000 0.00 0.00 0.00 4.44
200 205 2.034878 TGTCTGTGAGTCTGAAGCACT 58.965 47.619 11.03 0.00 33.83 4.40
201 206 2.035193 TGTCTGTGAGTCTGAAGCACTC 59.965 50.000 11.03 0.00 40.75 3.51
202 207 2.295909 GTCTGTGAGTCTGAAGCACTCT 59.704 50.000 11.03 0.00 40.93 3.24
203 208 2.295629 TCTGTGAGTCTGAAGCACTCTG 59.704 50.000 11.03 0.00 40.93 3.35
204 209 1.342496 TGTGAGTCTGAAGCACTCTGG 59.658 52.381 11.03 0.00 40.93 3.86
205 210 1.615883 GTGAGTCTGAAGCACTCTGGA 59.384 52.381 3.17 0.00 40.93 3.86
206 211 2.036475 GTGAGTCTGAAGCACTCTGGAA 59.964 50.000 3.17 0.00 40.93 3.53
207 212 2.298446 TGAGTCTGAAGCACTCTGGAAG 59.702 50.000 3.17 0.00 40.93 3.46
271 276 1.068753 CAAGATCGCCGGCTCATCT 59.931 57.895 26.68 25.63 0.00 2.90
302 310 1.073177 ATACGTACACGCCACAAAGC 58.927 50.000 0.00 0.00 44.43 3.51
318 326 0.107945 AAGCGAGAGGAAGCATGGAC 60.108 55.000 0.00 0.00 35.48 4.02
381 389 2.893398 GAGTTCACCGAGGCCGAT 59.107 61.111 0.00 0.00 38.22 4.18
498 506 3.771160 GACCACGTCCTCCCGCAT 61.771 66.667 0.00 0.00 0.00 4.73
549 557 2.187946 GTGGTGGGCTCCATCTCG 59.812 66.667 6.12 0.00 39.81 4.04
841 861 0.109086 CATGTTCAGCCTCTCGTCGT 60.109 55.000 0.00 0.00 0.00 4.34
910 937 8.937634 AGAACCATTTGAATTGAATAATGAGC 57.062 30.769 1.72 0.00 31.29 4.26
915 942 8.415553 CCATTTGAATTGAATAATGAGCAGGTA 58.584 33.333 1.72 0.00 31.29 3.08
919 946 7.216494 TGAATTGAATAATGAGCAGGTATCGA 58.784 34.615 0.00 0.00 0.00 3.59
921 948 8.450578 AATTGAATAATGAGCAGGTATCGAAA 57.549 30.769 0.00 0.00 0.00 3.46
923 950 7.482654 TGAATAATGAGCAGGTATCGAAAAG 57.517 36.000 0.00 0.00 0.00 2.27
924 951 5.931441 ATAATGAGCAGGTATCGAAAAGC 57.069 39.130 0.00 0.00 0.00 3.51
925 952 2.760634 TGAGCAGGTATCGAAAAGCA 57.239 45.000 0.00 0.00 0.00 3.91
926 953 3.052455 TGAGCAGGTATCGAAAAGCAA 57.948 42.857 0.00 0.00 0.00 3.91
927 954 3.002791 TGAGCAGGTATCGAAAAGCAAG 58.997 45.455 0.00 0.00 0.00 4.01
928 955 3.262420 GAGCAGGTATCGAAAAGCAAGA 58.738 45.455 0.00 0.00 0.00 3.02
929 956 3.003480 AGCAGGTATCGAAAAGCAAGAC 58.997 45.455 0.00 0.00 0.00 3.01
930 957 2.222819 GCAGGTATCGAAAAGCAAGACG 60.223 50.000 0.00 0.00 0.00 4.18
931 958 3.250744 CAGGTATCGAAAAGCAAGACGA 58.749 45.455 0.00 0.00 39.01 4.20
932 959 3.865745 CAGGTATCGAAAAGCAAGACGAT 59.134 43.478 0.00 0.00 45.21 3.73
933 960 5.041287 CAGGTATCGAAAAGCAAGACGATA 58.959 41.667 0.00 0.00 43.47 2.92
934 961 5.518847 CAGGTATCGAAAAGCAAGACGATAA 59.481 40.000 14.10 1.94 44.91 1.75
935 962 6.035650 CAGGTATCGAAAAGCAAGACGATAAA 59.964 38.462 14.10 0.00 44.91 1.40
936 963 6.592607 AGGTATCGAAAAGCAAGACGATAAAA 59.407 34.615 14.10 0.00 44.91 1.52
937 964 6.681599 GGTATCGAAAAGCAAGACGATAAAAC 59.318 38.462 14.10 7.81 44.91 2.43
938 965 4.694177 TCGAAAAGCAAGACGATAAAACG 58.306 39.130 0.00 0.00 39.31 3.60
940 967 4.901881 CGAAAAGCAAGACGATAAAACGTT 59.098 37.500 0.00 0.00 46.52 3.99
941 968 5.164415 CGAAAAGCAAGACGATAAAACGTTG 60.164 40.000 0.00 0.00 46.52 4.10
944 987 4.769215 AGCAAGACGATAAAACGTTGAAC 58.231 39.130 0.00 0.00 46.52 3.18
957 1000 1.798223 CGTTGAACTCTCAATCGCCAA 59.202 47.619 0.00 0.00 43.39 4.52
958 1001 2.223144 CGTTGAACTCTCAATCGCCAAA 59.777 45.455 0.00 0.00 43.39 3.28
959 1002 3.665323 CGTTGAACTCTCAATCGCCAAAG 60.665 47.826 0.00 0.00 43.39 2.77
960 1003 3.401033 TGAACTCTCAATCGCCAAAGA 57.599 42.857 0.00 0.00 0.00 2.52
961 1004 3.067106 TGAACTCTCAATCGCCAAAGAC 58.933 45.455 0.00 0.00 0.00 3.01
962 1005 3.244215 TGAACTCTCAATCGCCAAAGACT 60.244 43.478 0.00 0.00 0.00 3.24
963 1006 4.021456 TGAACTCTCAATCGCCAAAGACTA 60.021 41.667 0.00 0.00 0.00 2.59
964 1007 3.851098 ACTCTCAATCGCCAAAGACTAC 58.149 45.455 0.00 0.00 0.00 2.73
965 1008 3.258372 ACTCTCAATCGCCAAAGACTACA 59.742 43.478 0.00 0.00 0.00 2.74
966 1009 4.245660 CTCTCAATCGCCAAAGACTACAA 58.754 43.478 0.00 0.00 0.00 2.41
967 1010 4.832248 TCTCAATCGCCAAAGACTACAAT 58.168 39.130 0.00 0.00 0.00 2.71
968 1011 4.870426 TCTCAATCGCCAAAGACTACAATC 59.130 41.667 0.00 0.00 0.00 2.67
1387 1450 2.756840 AACTCCGTTAGCTGGTAACC 57.243 50.000 20.41 6.64 38.27 2.85
1389 1452 0.179119 CTCCGTTAGCTGGTAACCCG 60.179 60.000 20.41 11.93 38.27 5.28
1648 1729 1.429463 CGGTGTACAGCTTCTTGTCC 58.571 55.000 21.80 3.56 32.56 4.02
1742 1826 7.891498 AACCTCCACTGTTAATAACAAGTTT 57.109 32.000 7.30 0.00 41.61 2.66
1777 1861 4.753610 CCTGATGATTGCCAGTATGTAGTG 59.246 45.833 0.00 0.00 0.00 2.74
1779 1863 5.744171 TGATGATTGCCAGTATGTAGTGTT 58.256 37.500 0.00 0.00 0.00 3.32
1780 1864 6.179756 TGATGATTGCCAGTATGTAGTGTTT 58.820 36.000 0.00 0.00 0.00 2.83
1781 1865 5.878332 TGATTGCCAGTATGTAGTGTTTG 57.122 39.130 0.00 0.00 0.00 2.93
1783 1867 3.417069 TGCCAGTATGTAGTGTTTGCT 57.583 42.857 0.00 0.00 0.00 3.91
1784 1868 3.073678 TGCCAGTATGTAGTGTTTGCTG 58.926 45.455 0.00 0.00 0.00 4.41
1785 1869 3.244387 TGCCAGTATGTAGTGTTTGCTGA 60.244 43.478 0.00 0.00 0.00 4.26
1809 1898 3.276857 GAATTCCATCAGCAGCAGAGAA 58.723 45.455 0.00 0.00 0.00 2.87
1810 1899 2.398252 TTCCATCAGCAGCAGAGAAG 57.602 50.000 0.00 0.00 0.00 2.85
1811 1900 1.565067 TCCATCAGCAGCAGAGAAGA 58.435 50.000 0.00 0.00 0.00 2.87
1812 1901 2.117051 TCCATCAGCAGCAGAGAAGAT 58.883 47.619 0.00 0.00 0.00 2.40
1821 1919 3.752222 GCAGCAGAGAAGATATTCCCATG 59.248 47.826 0.00 0.00 0.00 3.66
1823 1921 3.080319 GCAGAGAAGATATTCCCATGGC 58.920 50.000 6.09 0.00 0.00 4.40
2113 2301 8.770438 ACTTTTTCTTTTGAATGTGCAAACTA 57.230 26.923 0.00 0.00 37.48 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 3.019564 CCTCGAGGATTTTTGCAGGAAT 58.980 45.455 28.21 0.00 37.39 3.01
4 5 2.436417 CCTCGAGGATTTTTGCAGGAA 58.564 47.619 28.21 0.00 37.39 3.36
5 6 1.950484 GCCTCGAGGATTTTTGCAGGA 60.950 52.381 35.69 0.00 37.39 3.86
6 7 0.453390 GCCTCGAGGATTTTTGCAGG 59.547 55.000 35.69 4.98 37.39 4.85
7 8 0.453390 GGCCTCGAGGATTTTTGCAG 59.547 55.000 35.69 4.55 37.39 4.41
8 9 0.038166 AGGCCTCGAGGATTTTTGCA 59.962 50.000 35.69 0.00 37.39 4.08
9 10 1.177401 AAGGCCTCGAGGATTTTTGC 58.823 50.000 35.69 16.91 37.39 3.68
10 11 5.123227 TGTATAAGGCCTCGAGGATTTTTG 58.877 41.667 35.69 6.96 37.39 2.44
11 12 5.130477 TCTGTATAAGGCCTCGAGGATTTTT 59.870 40.000 35.69 22.01 37.39 1.94
12 13 4.654262 TCTGTATAAGGCCTCGAGGATTTT 59.346 41.667 35.69 24.31 37.39 1.82
13 14 4.223953 TCTGTATAAGGCCTCGAGGATTT 58.776 43.478 35.69 26.65 37.39 2.17
14 15 3.845860 TCTGTATAAGGCCTCGAGGATT 58.154 45.455 35.69 27.49 37.39 3.01
15 16 3.527507 TCTGTATAAGGCCTCGAGGAT 57.472 47.619 35.69 20.92 37.39 3.24
16 17 3.117625 TCTTCTGTATAAGGCCTCGAGGA 60.118 47.826 35.69 14.81 37.39 3.71
17 18 3.223435 TCTTCTGTATAAGGCCTCGAGG 58.777 50.000 27.83 27.83 38.53 4.63
18 19 3.254657 CCTCTTCTGTATAAGGCCTCGAG 59.745 52.174 5.23 5.13 0.00 4.04
19 20 3.117625 TCCTCTTCTGTATAAGGCCTCGA 60.118 47.826 5.23 0.00 0.00 4.04
20 21 3.223435 TCCTCTTCTGTATAAGGCCTCG 58.777 50.000 5.23 0.00 0.00 4.63
21 22 4.039852 CCTTCCTCTTCTGTATAAGGCCTC 59.960 50.000 5.23 0.00 0.00 4.70
22 23 3.970640 CCTTCCTCTTCTGTATAAGGCCT 59.029 47.826 0.00 0.00 0.00 5.19
23 24 3.967987 TCCTTCCTCTTCTGTATAAGGCC 59.032 47.826 0.00 0.00 34.72 5.19
24 25 4.896482 TCTCCTTCCTCTTCTGTATAAGGC 59.104 45.833 0.00 0.00 34.72 4.35
25 26 5.538433 CCTCTCCTTCCTCTTCTGTATAAGG 59.462 48.000 0.00 0.00 35.80 2.69
26 27 6.369629 TCCTCTCCTTCCTCTTCTGTATAAG 58.630 44.000 0.00 0.00 0.00 1.73
27 28 6.342819 TCCTCTCCTTCCTCTTCTGTATAA 57.657 41.667 0.00 0.00 0.00 0.98
28 29 5.996271 TCCTCTCCTTCCTCTTCTGTATA 57.004 43.478 0.00 0.00 0.00 1.47
29 30 4.890499 TCCTCTCCTTCCTCTTCTGTAT 57.110 45.455 0.00 0.00 0.00 2.29
30 31 4.345854 GTTCCTCTCCTTCCTCTTCTGTA 58.654 47.826 0.00 0.00 0.00 2.74
31 32 3.169908 GTTCCTCTCCTTCCTCTTCTGT 58.830 50.000 0.00 0.00 0.00 3.41
32 33 2.499693 GGTTCCTCTCCTTCCTCTTCTG 59.500 54.545 0.00 0.00 0.00 3.02
33 34 2.112691 TGGTTCCTCTCCTTCCTCTTCT 59.887 50.000 0.00 0.00 0.00 2.85
34 35 2.235155 GTGGTTCCTCTCCTTCCTCTTC 59.765 54.545 0.00 0.00 0.00 2.87
35 36 2.158081 AGTGGTTCCTCTCCTTCCTCTT 60.158 50.000 0.00 0.00 0.00 2.85
36 37 1.435168 AGTGGTTCCTCTCCTTCCTCT 59.565 52.381 0.00 0.00 0.00 3.69
37 38 1.828595 GAGTGGTTCCTCTCCTTCCTC 59.171 57.143 9.08 0.00 0.00 3.71
38 39 1.893210 CGAGTGGTTCCTCTCCTTCCT 60.893 57.143 13.15 0.00 0.00 3.36
39 40 0.533032 CGAGTGGTTCCTCTCCTTCC 59.467 60.000 13.15 0.00 0.00 3.46
40 41 1.546961 TCGAGTGGTTCCTCTCCTTC 58.453 55.000 13.15 0.00 0.00 3.46
41 42 2.011122 TTCGAGTGGTTCCTCTCCTT 57.989 50.000 13.15 0.00 0.00 3.36
42 43 1.619332 GTTTCGAGTGGTTCCTCTCCT 59.381 52.381 13.15 0.00 0.00 3.69
43 44 1.337917 GGTTTCGAGTGGTTCCTCTCC 60.338 57.143 13.15 2.33 0.00 3.71
44 45 1.343465 TGGTTTCGAGTGGTTCCTCTC 59.657 52.381 9.94 9.94 0.00 3.20
45 46 1.344763 CTGGTTTCGAGTGGTTCCTCT 59.655 52.381 0.00 0.00 0.00 3.69
57 58 1.831389 CGTGTGAGGTGCTGGTTTCG 61.831 60.000 0.00 0.00 0.00 3.46
67 68 1.066605 GTACACTGACACGTGTGAGGT 59.933 52.381 33.36 28.12 46.77 3.85
97 99 3.889196 TTGGTCTCGGTTGAATTTTCG 57.111 42.857 0.00 0.00 0.00 3.46
102 104 5.782893 TTTTCATTTGGTCTCGGTTGAAT 57.217 34.783 0.00 0.00 0.00 2.57
103 105 5.584253 TTTTTCATTTGGTCTCGGTTGAA 57.416 34.783 0.00 0.00 0.00 2.69
104 106 5.300539 TGATTTTTCATTTGGTCTCGGTTGA 59.699 36.000 0.00 0.00 0.00 3.18
105 107 5.527951 TGATTTTTCATTTGGTCTCGGTTG 58.472 37.500 0.00 0.00 0.00 3.77
107 109 4.827284 ACTGATTTTTCATTTGGTCTCGGT 59.173 37.500 0.00 0.00 0.00 4.69
109 111 6.000891 TGACTGATTTTTCATTTGGTCTCG 57.999 37.500 0.00 0.00 0.00 4.04
110 112 7.040823 AGTCTGACTGATTTTTCATTTGGTCTC 60.041 37.037 10.00 0.00 0.00 3.36
148 150 1.394266 AATGCATGCCCCGGTGAATC 61.394 55.000 16.68 0.00 0.00 2.52
200 205 2.516227 ATCGACTCCAGACTTCCAGA 57.484 50.000 0.00 0.00 0.00 3.86
201 206 2.493675 TGAATCGACTCCAGACTTCCAG 59.506 50.000 0.00 0.00 0.00 3.86
202 207 2.525368 TGAATCGACTCCAGACTTCCA 58.475 47.619 0.00 0.00 0.00 3.53
203 208 3.594603 TTGAATCGACTCCAGACTTCC 57.405 47.619 0.00 0.00 0.00 3.46
204 209 4.152580 GGTTTTGAATCGACTCCAGACTTC 59.847 45.833 0.00 0.00 0.00 3.01
205 210 4.065789 GGTTTTGAATCGACTCCAGACTT 58.934 43.478 0.00 0.00 0.00 3.01
206 211 3.665190 GGTTTTGAATCGACTCCAGACT 58.335 45.455 0.00 0.00 0.00 3.24
207 212 2.412089 CGGTTTTGAATCGACTCCAGAC 59.588 50.000 0.00 0.00 0.00 3.51
271 276 7.167302 GTGGCGTGTACGTATTATTTATGTGTA 59.833 37.037 0.00 0.00 42.22 2.90
302 310 0.250234 TTGGTCCATGCTTCCTCTCG 59.750 55.000 0.00 0.00 0.00 4.04
533 541 3.083349 CCGAGATGGAGCCCACCA 61.083 66.667 0.00 0.00 44.41 4.17
832 852 2.800581 CGGTCCGAGACGACGAGAG 61.801 68.421 4.91 0.00 33.30 3.20
833 853 2.812609 CGGTCCGAGACGACGAGA 60.813 66.667 4.91 0.00 33.30 4.04
865 885 6.536941 GGTTCTTTCACTTGTAAATTTTGGCA 59.463 34.615 0.00 0.00 0.00 4.92
906 933 2.760634 TGCTTTTCGATACCTGCTCA 57.239 45.000 0.00 0.00 0.00 4.26
910 937 3.250744 TCGTCTTGCTTTTCGATACCTG 58.749 45.455 0.00 0.00 0.00 4.00
915 942 5.107220 ACGTTTTATCGTCTTGCTTTTCGAT 60.107 36.000 10.75 10.75 43.66 3.59
919 946 5.812652 TCAACGTTTTATCGTCTTGCTTTT 58.187 33.333 0.00 0.00 43.38 2.27
921 948 5.007332 AGTTCAACGTTTTATCGTCTTGCTT 59.993 36.000 0.00 0.00 43.38 3.91
923 950 4.769215 AGTTCAACGTTTTATCGTCTTGC 58.231 39.130 0.00 0.00 43.38 4.01
924 951 6.074516 TGAGAGTTCAACGTTTTATCGTCTTG 60.075 38.462 0.00 0.00 43.38 3.02
925 952 5.981315 TGAGAGTTCAACGTTTTATCGTCTT 59.019 36.000 0.00 0.00 43.38 3.01
926 953 5.526115 TGAGAGTTCAACGTTTTATCGTCT 58.474 37.500 0.00 0.00 43.38 4.18
927 954 5.817616 TGAGAGTTCAACGTTTTATCGTC 57.182 39.130 0.00 0.00 43.38 4.20
928 955 6.399669 CGATTGAGAGTTCAACGTTTTATCGT 60.400 38.462 0.00 0.00 45.54 3.73
929 956 5.946389 CGATTGAGAGTTCAACGTTTTATCG 59.054 40.000 0.00 0.00 45.54 2.92
930 957 5.728507 GCGATTGAGAGTTCAACGTTTTATC 59.271 40.000 0.00 0.00 45.54 1.75
931 958 5.390567 GGCGATTGAGAGTTCAACGTTTTAT 60.391 40.000 0.00 0.00 45.54 1.40
932 959 4.084223 GGCGATTGAGAGTTCAACGTTTTA 60.084 41.667 0.00 0.00 45.54 1.52
933 960 3.303791 GGCGATTGAGAGTTCAACGTTTT 60.304 43.478 0.00 0.00 45.54 2.43
934 961 2.223377 GGCGATTGAGAGTTCAACGTTT 59.777 45.455 0.00 0.00 45.54 3.60
935 962 1.798813 GGCGATTGAGAGTTCAACGTT 59.201 47.619 0.00 0.00 45.54 3.99
936 963 1.270094 TGGCGATTGAGAGTTCAACGT 60.270 47.619 0.00 0.00 45.54 3.99
937 964 1.428448 TGGCGATTGAGAGTTCAACG 58.572 50.000 0.00 0.00 45.54 4.10
938 965 3.498397 TCTTTGGCGATTGAGAGTTCAAC 59.502 43.478 0.00 0.00 45.54 3.18
940 967 3.067106 GTCTTTGGCGATTGAGAGTTCA 58.933 45.455 0.00 0.00 0.00 3.18
941 968 3.330267 AGTCTTTGGCGATTGAGAGTTC 58.670 45.455 0.00 0.00 0.00 3.01
944 987 3.849911 TGTAGTCTTTGGCGATTGAGAG 58.150 45.455 0.00 0.00 0.00 3.20
957 1000 5.634020 GCTCGTGTAGTTTGATTGTAGTCTT 59.366 40.000 0.00 0.00 0.00 3.01
958 1001 5.162075 GCTCGTGTAGTTTGATTGTAGTCT 58.838 41.667 0.00 0.00 0.00 3.24
959 1002 4.921515 TGCTCGTGTAGTTTGATTGTAGTC 59.078 41.667 0.00 0.00 0.00 2.59
960 1003 4.878439 TGCTCGTGTAGTTTGATTGTAGT 58.122 39.130 0.00 0.00 0.00 2.73
961 1004 5.161358 TCTGCTCGTGTAGTTTGATTGTAG 58.839 41.667 2.54 0.00 0.00 2.74
962 1005 5.128992 TCTGCTCGTGTAGTTTGATTGTA 57.871 39.130 2.54 0.00 0.00 2.41
963 1006 3.990092 TCTGCTCGTGTAGTTTGATTGT 58.010 40.909 2.54 0.00 0.00 2.71
964 1007 3.369147 CCTCTGCTCGTGTAGTTTGATTG 59.631 47.826 2.54 0.00 0.00 2.67
965 1008 3.589988 CCTCTGCTCGTGTAGTTTGATT 58.410 45.455 2.54 0.00 0.00 2.57
966 1009 2.675317 GCCTCTGCTCGTGTAGTTTGAT 60.675 50.000 2.54 0.00 33.53 2.57
967 1010 1.336887 GCCTCTGCTCGTGTAGTTTGA 60.337 52.381 2.54 0.00 33.53 2.69
968 1011 1.071605 GCCTCTGCTCGTGTAGTTTG 58.928 55.000 2.54 0.00 33.53 2.93
1260 1318 4.091939 GGGTAGGGCCACACGGAC 62.092 72.222 6.18 0.00 41.20 4.79
1371 1429 1.606885 CCGGGTTACCAGCTAACGGA 61.607 60.000 8.47 0.00 42.19 4.69
1418 1486 1.135046 CACAGCAAGTCAGTCACTCG 58.865 55.000 0.00 0.00 32.30 4.18
1420 1488 2.169352 AGAACACAGCAAGTCAGTCACT 59.831 45.455 0.00 0.00 36.64 3.41
1648 1729 2.829458 GGAGGACGAGGGTCGGAG 60.829 72.222 0.86 0.00 45.59 4.63
1711 1795 2.249844 AACAGTGGAGGTTTACACGG 57.750 50.000 0.00 0.00 42.25 4.94
1742 1826 4.581824 GCAATCATCAGGGCTTCAGATTTA 59.418 41.667 0.00 0.00 0.00 1.40
1755 1839 5.363101 ACACTACATACTGGCAATCATCAG 58.637 41.667 0.00 0.00 37.07 2.90
1777 1861 4.789012 TGATGGAATTCCTTCAGCAAAC 57.211 40.909 29.85 11.11 42.89 2.93
1783 1867 2.291089 TGCTGCTGATGGAATTCCTTCA 60.291 45.455 30.76 30.76 44.74 3.02
1784 1868 2.358267 CTGCTGCTGATGGAATTCCTTC 59.642 50.000 26.18 26.18 39.77 3.46
1785 1869 2.025605 TCTGCTGCTGATGGAATTCCTT 60.026 45.455 24.73 18.79 36.82 3.36
1809 1898 3.607490 AGCAAAGCCATGGGAATATCT 57.393 42.857 15.13 0.00 0.00 1.98
1810 1899 3.638160 TGAAGCAAAGCCATGGGAATATC 59.362 43.478 15.13 0.00 0.00 1.63
1811 1900 3.640029 CTGAAGCAAAGCCATGGGAATAT 59.360 43.478 15.13 0.00 0.00 1.28
1812 1901 3.025978 CTGAAGCAAAGCCATGGGAATA 58.974 45.455 15.13 0.00 0.00 1.75
1821 1919 2.620585 AGTTGAAGACTGAAGCAAAGCC 59.379 45.455 0.00 0.00 37.17 4.35
1823 1921 7.251704 TCTAAAGTTGAAGACTGAAGCAAAG 57.748 36.000 0.00 0.00 39.00 2.77
1860 1958 6.403746 CCAGCTCACTATACATCGTATACAGG 60.404 46.154 3.32 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.