Multiple sequence alignment - TraesCS6A01G247200

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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 TraesCS6A01G247200 chr6A 100.000 3552 0 0 628 4179 459077453 459073902 0.000000e+00 6560.0
1 TraesCS6A01G247200 chr6A 100.000 256 0 0 1 256 459078080 459077825 1.360000e-129 473.0
2 TraesCS6A01G247200 chr6A 88.073 109 11 2 3782 3889 446308962 446309069 1.220000e-25 128.0
3 TraesCS6A01G247200 chr6D 95.618 3286 84 22 628 3889 321776873 321773624 0.000000e+00 5216.0
4 TraesCS6A01G247200 chr6D 90.272 257 18 6 3926 4179 321773447 321773195 3.110000e-86 329.0
5 TraesCS6A01G247200 chr6D 95.652 115 5 0 84 198 321777255 321777141 7.130000e-43 185.0
6 TraesCS6A01G247200 chr6B 95.185 3302 93 34 628 3889 501770620 501773895 0.000000e+00 5156.0
7 TraesCS6A01G247200 chr6B 93.701 254 14 2 3926 4179 501774068 501774319 3.050000e-101 379.0
8 TraesCS6A01G247200 chr6B 88.166 169 7 5 90 255 501770436 501770594 5.520000e-44 189.0
9 TraesCS6A01G247200 chr6B 89.916 119 10 2 3773 3889 487136363 487136245 7.240000e-33 152.0
10 TraesCS6A01G247200 chr6B 98.750 80 1 0 1 80 2609882 2609961 4.360000e-30 143.0
11 TraesCS6A01G247200 chr7B 98.750 80 1 0 1 80 99221053 99221132 4.360000e-30 143.0
12 TraesCS6A01G247200 chr5B 98.750 80 1 0 1 80 362955721 362955800 4.360000e-30 143.0
13 TraesCS6A01G247200 chr2A 98.750 80 1 0 1 80 771492603 771492524 4.360000e-30 143.0
14 TraesCS6A01G247200 chr1D 98.750 80 1 0 1 80 59878446 59878525 4.360000e-30 143.0
15 TraesCS6A01G247200 chr1D 93.182 44 3 0 3782 3825 64215265 64215308 9.700000e-07 65.8
16 TraesCS6A01G247200 chrUn 98.734 79 1 0 1 79 2002197 2002119 1.570000e-29 141.0
17 TraesCS6A01G247200 chr4A 90.000 110 10 1 3781 3889 547297030 547297139 1.570000e-29 141.0
18 TraesCS6A01G247200 chr2D 97.590 83 1 1 1 83 32523230 32523149 1.570000e-29 141.0
19 TraesCS6A01G247200 chr2D 84.874 119 13 4 3926 4041 553760031 553759915 9.490000e-22 115.0
20 TraesCS6A01G247200 chr1B 97.590 83 1 1 1 83 250983970 250984051 1.570000e-29 141.0
21 TraesCS6A01G247200 chr1B 97.531 81 2 0 1 81 14516379 14516459 5.630000e-29 139.0
22 TraesCS6A01G247200 chr1B 84.762 105 13 3 3784 3886 265298122 265298225 7.390000e-18 102.0
23 TraesCS6A01G247200 chr3B 88.182 110 12 1 3781 3889 405949299 405949190 3.390000e-26 130.0
24 TraesCS6A01G247200 chr3B 80.952 147 20 7 3889 4030 397674500 397674357 4.420000e-20 110.0
25 TraesCS6A01G247200 chr4B 87.619 105 11 1 3926 4030 471308041 471308143 2.040000e-23 121.0
26 TraesCS6A01G247200 chr7A 87.379 103 11 2 3926 4028 230301202 230301302 2.640000e-22 117.0
27 TraesCS6A01G247200 chr7A 86.364 110 12 3 3926 4035 649424998 649425104 2.640000e-22 117.0
28 TraesCS6A01G247200 chr7A 86.792 106 10 4 3926 4030 113489677 113489779 9.490000e-22 115.0
29 TraesCS6A01G247200 chr5D 87.379 103 11 1 3926 4028 99307242 99307142 2.640000e-22 117.0
30 TraesCS6A01G247200 chr1A 87.379 103 11 2 3926 4028 293712571 293712671 2.640000e-22 117.0
31 TraesCS6A01G247200 chr1A 95.556 45 1 1 2082 2126 569372540 569372497 2.080000e-08 71.3
32 TraesCS6A01G247200 chr4D 97.368 38 1 0 3818 3855 506730837 506730800 9.700000e-07 65.8
33 TraesCS6A01G247200 chr7D 79.570 93 14 4 3781 3870 518637756 518637666 1.250000e-05 62.1


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 TraesCS6A01G247200 chr6A 459073902 459078080 4178 True 3516.5 6560 100.000000 1 4179 2 chr6A.!!$R1 4178
1 TraesCS6A01G247200 chr6D 321773195 321777255 4060 True 1910.0 5216 93.847333 84 4179 3 chr6D.!!$R1 4095
2 TraesCS6A01G247200 chr6B 501770436 501774319 3883 False 1908.0 5156 92.350667 90 4179 3 chr6B.!!$F2 4089

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
211 215 0.032217 AGAAGGCAGAGAGAGAGGGG 60.032 60.000 0.00 0.0 0.0 4.79 F
217 221 0.185901 CAGAGAGAGAGGGGGAGAGG 59.814 65.000 0.00 0.0 0.0 3.69 F
728 753 1.412710 GCGAGGAGAGAGAGAGAGAGA 59.587 57.143 0.00 0.0 0.0 3.10 F
1767 1821 0.182537 AGTACCAGCAACAGCACCAA 59.817 50.000 0.00 0.0 0.0 3.67 F
2611 2671 0.615331 TCCGGCTGAGCTCATTTCTT 59.385 50.000 18.63 0.0 0.0 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1626 1680 1.292223 CGGTGAGAAGAGGCCGAAA 59.708 57.895 0.00 0.0 46.33 3.46 R
1680 1734 2.933495 CGATACCTTCGTGGAACAGA 57.067 50.000 4.38 0.0 41.80 3.41 R
2646 2706 0.882042 CACGAGCAGAGCAACCAACT 60.882 55.000 0.00 0.0 0.00 3.16 R
3090 3150 1.050988 ACCGCCAGGCTGATACTGAT 61.051 55.000 17.94 0.0 42.76 2.90 R
3454 3516 1.427368 TGCACCAGGAATAACCAAGGT 59.573 47.619 0.00 0.0 45.68 3.50 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
21 22 4.868314 GCCGGGTGATACTCTTAATACT 57.132 45.455 2.18 0.00 0.00 2.12
22 23 5.211174 GCCGGGTGATACTCTTAATACTT 57.789 43.478 2.18 0.00 0.00 2.24
23 24 5.608449 GCCGGGTGATACTCTTAATACTTT 58.392 41.667 2.18 0.00 0.00 2.66
24 25 5.465724 GCCGGGTGATACTCTTAATACTTTG 59.534 44.000 2.18 0.00 0.00 2.77
25 26 6.579865 CCGGGTGATACTCTTAATACTTTGT 58.420 40.000 0.00 0.00 0.00 2.83
26 27 7.685155 GCCGGGTGATACTCTTAATACTTTGTA 60.685 40.741 2.18 0.00 0.00 2.41
27 28 8.365647 CCGGGTGATACTCTTAATACTTTGTAT 58.634 37.037 0.00 0.00 0.00 2.29
28 29 9.408069 CGGGTGATACTCTTAATACTTTGTATC 57.592 37.037 0.00 0.00 37.69 2.24
42 43 9.448438 AATACTTTGTATCACTTTGATGCTACA 57.552 29.630 5.94 0.00 39.71 2.74
43 44 7.928307 ACTTTGTATCACTTTGATGCTACAT 57.072 32.000 5.94 0.00 39.71 2.29
44 45 8.340618 ACTTTGTATCACTTTGATGCTACATT 57.659 30.769 5.94 0.00 39.71 2.71
45 46 8.796475 ACTTTGTATCACTTTGATGCTACATTT 58.204 29.630 5.94 0.00 39.71 2.32
46 47 9.630098 CTTTGTATCACTTTGATGCTACATTTT 57.370 29.630 5.94 0.00 39.71 1.82
47 48 8.969121 TTGTATCACTTTGATGCTACATTTTG 57.031 30.769 5.94 0.00 39.71 2.44
48 49 8.334263 TGTATCACTTTGATGCTACATTTTGA 57.666 30.769 5.94 0.00 39.71 2.69
49 50 8.453320 TGTATCACTTTGATGCTACATTTTGAG 58.547 33.333 5.94 0.00 39.71 3.02
50 51 7.692460 ATCACTTTGATGCTACATTTTGAGA 57.308 32.000 0.00 0.00 35.43 3.27
51 52 7.692460 TCACTTTGATGCTACATTTTGAGAT 57.308 32.000 0.00 0.00 0.00 2.75
52 53 8.791327 TCACTTTGATGCTACATTTTGAGATA 57.209 30.769 0.00 0.00 0.00 1.98
53 54 9.230122 TCACTTTGATGCTACATTTTGAGATAA 57.770 29.630 0.00 0.00 0.00 1.75
61 62 9.669353 ATGCTACATTTTGAGATAATAAAAGCG 57.331 29.630 0.00 0.00 0.00 4.68
62 63 7.643764 TGCTACATTTTGAGATAATAAAAGCGC 59.356 33.333 0.00 0.00 0.00 5.92
63 64 7.113544 GCTACATTTTGAGATAATAAAAGCGCC 59.886 37.037 2.29 0.00 0.00 6.53
64 65 6.273071 ACATTTTGAGATAATAAAAGCGCCC 58.727 36.000 2.29 0.00 0.00 6.13
65 66 6.096846 ACATTTTGAGATAATAAAAGCGCCCT 59.903 34.615 2.29 0.00 0.00 5.19
66 67 6.524101 TTTTGAGATAATAAAAGCGCCCTT 57.476 33.333 2.29 0.00 0.00 3.95
67 68 6.524101 TTTGAGATAATAAAAGCGCCCTTT 57.476 33.333 2.29 7.08 42.93 3.11
68 69 7.633193 TTTGAGATAATAAAAGCGCCCTTTA 57.367 32.000 2.29 9.36 40.30 1.85
69 70 7.817418 TTGAGATAATAAAAGCGCCCTTTAT 57.183 32.000 15.73 15.73 40.30 1.40
70 71 7.435068 TGAGATAATAAAAGCGCCCTTTATC 57.565 36.000 19.70 16.57 40.30 1.75
71 72 6.147164 TGAGATAATAAAAGCGCCCTTTATCG 59.853 38.462 19.70 0.00 40.30 2.92
72 73 6.228258 AGATAATAAAAGCGCCCTTTATCGA 58.772 36.000 19.70 13.69 40.30 3.59
73 74 6.708949 AGATAATAAAAGCGCCCTTTATCGAA 59.291 34.615 19.70 12.05 40.30 3.71
74 75 5.570234 AATAAAAGCGCCCTTTATCGAAA 57.430 34.783 19.70 0.75 40.30 3.46
75 76 3.926821 AAAAGCGCCCTTTATCGAAAA 57.073 38.095 2.29 0.00 40.30 2.29
76 77 3.926821 AAAGCGCCCTTTATCGAAAAA 57.073 38.095 2.29 0.00 39.44 1.94
107 108 2.783135 AGGCATACAGTCCACACAAAG 58.217 47.619 0.00 0.00 0.00 2.77
158 160 6.494893 AGCAAAATACGAGCAGATAAAACA 57.505 33.333 0.00 0.00 0.00 2.83
160 162 6.968904 AGCAAAATACGAGCAGATAAAACATG 59.031 34.615 0.00 0.00 0.00 3.21
209 213 1.756538 GGAAGAAGGCAGAGAGAGAGG 59.243 57.143 0.00 0.00 0.00 3.69
210 214 1.756538 GAAGAAGGCAGAGAGAGAGGG 59.243 57.143 0.00 0.00 0.00 4.30
211 215 0.032217 AGAAGGCAGAGAGAGAGGGG 60.032 60.000 0.00 0.00 0.00 4.79
212 216 1.002792 AAGGCAGAGAGAGAGGGGG 59.997 63.158 0.00 0.00 0.00 5.40
213 217 1.522917 AAGGCAGAGAGAGAGGGGGA 61.523 60.000 0.00 0.00 0.00 4.81
214 218 1.457455 GGCAGAGAGAGAGGGGGAG 60.457 68.421 0.00 0.00 0.00 4.30
217 221 0.185901 CAGAGAGAGAGGGGGAGAGG 59.814 65.000 0.00 0.00 0.00 3.69
245 249 1.453155 CAGACTGAAAACGATGGGGG 58.547 55.000 0.00 0.00 0.00 5.40
698 709 2.716017 GGGAGAGACGAGGCCACAG 61.716 68.421 5.01 0.00 0.00 3.66
715 726 2.740055 GCACCACACAGCGAGGAG 60.740 66.667 0.00 0.00 0.00 3.69
728 753 1.412710 GCGAGGAGAGAGAGAGAGAGA 59.587 57.143 0.00 0.00 0.00 3.10
741 766 3.312890 AGAGAGAGAGGAGAGAGAGAGG 58.687 54.545 0.00 0.00 0.00 3.69
847 888 3.317430 CCGTACCCTGTTGTATACTCTCC 59.683 52.174 4.17 0.00 0.00 3.71
889 934 4.144727 GAGCGAGGGAGGGAGGGA 62.145 72.222 0.00 0.00 0.00 4.20
890 935 4.150454 AGCGAGGGAGGGAGGGAG 62.150 72.222 0.00 0.00 0.00 4.30
891 936 4.144727 GCGAGGGAGGGAGGGAGA 62.145 72.222 0.00 0.00 0.00 3.71
892 937 2.197324 CGAGGGAGGGAGGGAGAG 59.803 72.222 0.00 0.00 0.00 3.20
918 963 2.499520 CATCCAAACGCACGCACG 60.500 61.111 0.00 0.00 39.50 5.34
919 964 4.383602 ATCCAAACGCACGCACGC 62.384 61.111 0.00 0.00 36.19 5.34
928 973 4.249020 CACGCACGCACCAGCAAA 62.249 61.111 0.00 0.00 42.27 3.68
929 974 3.952675 ACGCACGCACCAGCAAAG 61.953 61.111 0.00 0.00 42.27 2.77
930 975 4.688419 CGCACGCACCAGCAAAGG 62.688 66.667 0.00 0.00 42.27 3.11
931 976 3.286751 GCACGCACCAGCAAAGGA 61.287 61.111 0.00 0.00 42.27 3.36
985 1030 2.124570 CGGCCTGCCTGTTATGCT 60.125 61.111 6.60 0.00 0.00 3.79
991 1036 3.211963 GCCTGTTATGCTGCGGGG 61.212 66.667 0.00 0.00 0.00 5.73
1284 1338 3.966543 GGTGGAGGTGGTGGTGGG 61.967 72.222 0.00 0.00 0.00 4.61
1758 1812 2.224523 CCTCTTCAACCAGTACCAGCAA 60.225 50.000 0.00 0.00 0.00 3.91
1767 1821 0.182537 AGTACCAGCAACAGCACCAA 59.817 50.000 0.00 0.00 0.00 3.67
1833 1893 2.792290 CGATCACAACCAGCGCTCG 61.792 63.158 7.13 2.49 0.00 5.03
1905 1965 1.302511 CCTCACCCGAAACCACCTG 60.303 63.158 0.00 0.00 0.00 4.00
2127 2187 1.139498 TCAATCACCAGCTTCCCCCA 61.139 55.000 0.00 0.00 0.00 4.96
2160 2220 1.833049 CCTCCGGTCGGCTTCCTAT 60.833 63.158 0.00 0.00 34.68 2.57
2586 2646 0.745845 ATGCCGTCAGTCTTGATGCC 60.746 55.000 0.00 0.00 38.72 4.40
2598 2658 1.841302 TTGATGCCTTCAGTCCGGCT 61.841 55.000 0.00 0.00 46.42 5.52
2611 2671 0.615331 TCCGGCTGAGCTCATTTCTT 59.385 50.000 18.63 0.00 0.00 2.52
2646 2706 0.835971 TTGTAGCTGTGAGCCTCCCA 60.836 55.000 0.00 0.00 43.77 4.37
2856 2916 2.139118 GCCGATTCTGCCTGTAAGATC 58.861 52.381 0.00 0.00 34.07 2.75
2925 2985 0.663153 GCAAGACCGACAAAGCAGTT 59.337 50.000 0.00 0.00 0.00 3.16
3090 3150 2.432456 CAGCGTGGCGAGCTTGTA 60.432 61.111 2.14 0.00 44.06 2.41
3102 3162 3.312828 CGAGCTTGTATCAGTATCAGCC 58.687 50.000 0.00 0.00 0.00 4.85
3197 3257 5.837586 GCAATTAAAATGTTGCGAAGGAA 57.162 34.783 0.00 0.00 40.95 3.36
3279 3339 6.485171 AGGACTAGTGGATTTAGCAACATTT 58.515 36.000 0.00 0.00 0.00 2.32
3288 3348 5.106475 GGATTTAGCAACATTTGTGTCGGTA 60.106 40.000 0.00 0.00 0.00 4.02
3294 3354 4.449743 GCAACATTTGTGTCGGTAACTCTA 59.550 41.667 0.00 0.00 0.00 2.43
3338 3400 3.395639 GGTTCTTACCACGATGTTCACA 58.604 45.455 0.00 0.00 44.36 3.58
3454 3516 9.123902 AGTATTGATATTTGCTCATGTTGCTTA 57.876 29.630 12.86 3.85 0.00 3.09
3455 3517 9.173939 GTATTGATATTTGCTCATGTTGCTTAC 57.826 33.333 12.86 0.00 0.00 2.34
3456 3518 6.135290 TGATATTTGCTCATGTTGCTTACC 57.865 37.500 12.86 1.90 0.00 2.85
3457 3519 5.887598 TGATATTTGCTCATGTTGCTTACCT 59.112 36.000 12.86 0.00 0.00 3.08
3458 3520 6.377996 TGATATTTGCTCATGTTGCTTACCTT 59.622 34.615 12.86 0.00 0.00 3.50
3459 3521 3.921119 TTGCTCATGTTGCTTACCTTG 57.079 42.857 12.86 0.00 0.00 3.61
3480 3542 4.730966 TGGTTATTCCTGGTGCAACTTAA 58.269 39.130 2.04 0.00 35.16 1.85
3502 3564 8.572828 TTAATTGTGCACTTTATGTTGTTGAG 57.427 30.769 19.41 0.00 0.00 3.02
3617 3679 2.171448 GGGACAGATCTTGCCATAGTGT 59.829 50.000 11.65 0.00 0.00 3.55
3728 3795 2.579873 GGTCCCATTGATGTCCATCTG 58.420 52.381 8.61 0.18 38.60 2.90
3795 3863 6.273260 TGCTATAGAATAGGGCCTCTTTGATT 59.727 38.462 10.74 3.12 0.00 2.57
3823 3891 5.648092 AGGATTCTGAAAACGTTGGAATAGG 59.352 40.000 0.00 0.00 0.00 2.57
3855 3923 6.645790 AGGATTAAAATGTCATGCTCATCC 57.354 37.500 4.24 6.36 0.00 3.51
3865 3934 4.063689 GTCATGCTCATCCAATCCTACAG 58.936 47.826 0.00 0.00 0.00 2.74
3891 3994 5.987777 TTTTGACTGTTTGATTGCATTGG 57.012 34.783 0.00 0.00 0.00 3.16
3902 4005 2.497770 GCATTGGGTGGATGCTGC 59.502 61.111 2.07 0.00 44.92 5.25
3906 4009 1.208535 CATTGGGTGGATGCTGCAAAT 59.791 47.619 6.36 0.00 0.00 2.32
3920 4023 3.817647 GCTGCAAATCCTATGGGAAGTAG 59.182 47.826 0.22 5.68 45.78 2.57
3922 4025 5.454755 GCTGCAAATCCTATGGGAAGTAGTA 60.455 44.000 0.22 0.00 45.78 1.82
3924 4027 5.427157 TGCAAATCCTATGGGAAGTAGTACA 59.573 40.000 0.22 0.00 45.78 2.90
3961 4173 8.906867 CCTATGAATCAAACAACCAACATAGAT 58.093 33.333 0.00 0.00 38.53 1.98
3965 4177 9.829507 TGAATCAAACAACCAACATAGATTTTT 57.170 25.926 0.00 0.00 0.00 1.94
4037 4249 3.007940 TCAATGGAGCCCTAATATGGTCG 59.992 47.826 0.00 0.00 0.00 4.79
4058 4270 0.538584 CAGAGGCACCAGCACAGATA 59.461 55.000 0.00 0.00 44.61 1.98
4154 4367 4.160626 AGTCTGTTTATGTCTGCTACTCCC 59.839 45.833 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.868314 AGTATTAAGAGTATCACCCGGC 57.132 45.455 0.00 0.00 37.82 6.13
1 2 6.579865 ACAAAGTATTAAGAGTATCACCCGG 58.420 40.000 0.00 0.00 37.82 5.73
2 3 9.408069 GATACAAAGTATTAAGAGTATCACCCG 57.592 37.037 0.00 0.00 38.30 5.28
16 17 9.448438 TGTAGCATCAAAGTGATACAAAGTATT 57.552 29.630 2.88 0.00 44.98 1.89
24 25 8.668353 TCTCAAAATGTAGCATCAAAGTGATAC 58.332 33.333 0.00 0.00 40.43 2.24
25 26 8.791327 TCTCAAAATGTAGCATCAAAGTGATA 57.209 30.769 0.00 0.00 34.28 2.15
26 27 7.692460 TCTCAAAATGTAGCATCAAAGTGAT 57.308 32.000 0.00 0.00 37.65 3.06
27 28 7.692460 ATCTCAAAATGTAGCATCAAAGTGA 57.308 32.000 0.00 0.00 0.00 3.41
35 36 9.669353 CGCTTTTATTATCTCAAAATGTAGCAT 57.331 29.630 0.00 0.00 0.00 3.79
36 37 7.643764 GCGCTTTTATTATCTCAAAATGTAGCA 59.356 33.333 0.00 0.00 0.00 3.49
37 38 7.113544 GGCGCTTTTATTATCTCAAAATGTAGC 59.886 37.037 7.64 0.00 0.00 3.58
38 39 7.591426 GGGCGCTTTTATTATCTCAAAATGTAG 59.409 37.037 7.64 0.00 0.00 2.74
39 40 7.284489 AGGGCGCTTTTATTATCTCAAAATGTA 59.716 33.333 7.64 0.00 0.00 2.29
40 41 6.096846 AGGGCGCTTTTATTATCTCAAAATGT 59.903 34.615 7.64 0.00 0.00 2.71
41 42 6.507023 AGGGCGCTTTTATTATCTCAAAATG 58.493 36.000 7.64 0.00 0.00 2.32
42 43 6.715347 AGGGCGCTTTTATTATCTCAAAAT 57.285 33.333 7.64 0.00 0.00 1.82
43 44 6.524101 AAGGGCGCTTTTATTATCTCAAAA 57.476 33.333 10.73 0.00 0.00 2.44
44 45 6.524101 AAAGGGCGCTTTTATTATCTCAAA 57.476 33.333 21.93 0.00 0.00 2.69
45 46 7.307751 CGATAAAGGGCGCTTTTATTATCTCAA 60.308 37.037 30.56 11.58 32.42 3.02
46 47 6.147164 CGATAAAGGGCGCTTTTATTATCTCA 59.853 38.462 30.56 12.27 32.42 3.27
47 48 6.367969 TCGATAAAGGGCGCTTTTATTATCTC 59.632 38.462 30.56 15.50 32.42 2.75
48 49 6.228258 TCGATAAAGGGCGCTTTTATTATCT 58.772 36.000 30.56 9.43 32.42 1.98
49 50 6.476243 TCGATAAAGGGCGCTTTTATTATC 57.524 37.500 30.56 24.08 32.42 1.75
50 51 6.870971 TTCGATAAAGGGCGCTTTTATTAT 57.129 33.333 30.56 19.13 32.42 1.28
51 52 6.680874 TTTCGATAAAGGGCGCTTTTATTA 57.319 33.333 30.56 15.38 32.42 0.98
52 53 5.570234 TTTCGATAAAGGGCGCTTTTATT 57.430 34.783 30.56 17.35 32.42 1.40
53 54 5.570234 TTTTCGATAAAGGGCGCTTTTAT 57.430 34.783 30.56 20.97 34.36 1.40
54 55 5.373981 TTTTTCGATAAAGGGCGCTTTTA 57.626 34.783 30.56 17.78 0.00 1.52
55 56 3.926821 TTTTCGATAAAGGGCGCTTTT 57.073 38.095 30.56 19.07 0.00 2.27
56 57 3.926821 TTTTTCGATAAAGGGCGCTTT 57.073 38.095 28.79 28.79 0.00 3.51
75 76 5.156608 ACTGTATGCCTACGTAGGTTTTT 57.843 39.130 35.78 22.37 45.42 1.94
76 77 4.382362 GGACTGTATGCCTACGTAGGTTTT 60.382 45.833 35.78 24.45 45.42 2.43
77 78 3.131755 GGACTGTATGCCTACGTAGGTTT 59.868 47.826 35.78 26.55 45.42 3.27
78 79 2.692041 GGACTGTATGCCTACGTAGGTT 59.308 50.000 35.78 26.85 45.42 3.50
79 80 2.305009 GGACTGTATGCCTACGTAGGT 58.695 52.381 35.78 23.13 45.42 3.08
80 81 2.034305 GTGGACTGTATGCCTACGTAGG 59.966 54.545 33.18 33.18 46.42 3.18
81 82 2.686405 TGTGGACTGTATGCCTACGTAG 59.314 50.000 15.92 15.92 0.00 3.51
82 83 2.424601 GTGTGGACTGTATGCCTACGTA 59.575 50.000 0.00 0.00 0.00 3.57
88 89 2.778299 TCTTTGTGTGGACTGTATGCC 58.222 47.619 0.00 0.00 0.00 4.40
107 108 2.486918 GGCAATGCATGGGCTTATTTC 58.513 47.619 20.07 0.64 41.91 2.17
158 160 5.789574 TTTCACCCTAGGTTGTATTCCAT 57.210 39.130 8.29 0.00 31.02 3.41
160 162 8.584063 TTTATTTTCACCCTAGGTTGTATTCC 57.416 34.615 8.29 0.00 31.02 3.01
209 213 2.273776 GCTTCAAGCCCTCTCCCC 59.726 66.667 0.00 0.00 34.48 4.81
210 214 1.077858 CTGCTTCAAGCCCTCTCCC 60.078 63.158 7.01 0.00 41.51 4.30
211 215 0.392327 GTCTGCTTCAAGCCCTCTCC 60.392 60.000 7.01 0.00 41.51 3.71
212 216 0.612744 AGTCTGCTTCAAGCCCTCTC 59.387 55.000 7.01 0.00 41.51 3.20
213 217 0.324285 CAGTCTGCTTCAAGCCCTCT 59.676 55.000 7.01 0.00 41.51 3.69
214 218 0.322975 TCAGTCTGCTTCAAGCCCTC 59.677 55.000 7.01 0.00 41.51 4.30
217 221 2.603173 CGTTTTCAGTCTGCTTCAAGCC 60.603 50.000 7.01 0.00 41.51 4.35
698 709 2.740055 CTCCTCGCTGTGTGGTGC 60.740 66.667 8.95 0.00 32.86 5.01
715 726 4.219115 TCTCTCTCCTCTCTCTCTCTCTC 58.781 52.174 0.00 0.00 0.00 3.20
888 933 1.198713 TTGGATGTGGCTCTCCTCTC 58.801 55.000 6.61 0.00 32.47 3.20
889 934 1.280421 GTTTGGATGTGGCTCTCCTCT 59.720 52.381 6.61 0.00 32.47 3.69
890 935 1.743996 GTTTGGATGTGGCTCTCCTC 58.256 55.000 6.61 0.00 32.47 3.71
891 936 0.036010 CGTTTGGATGTGGCTCTCCT 60.036 55.000 6.61 0.00 32.47 3.69
892 937 1.648467 GCGTTTGGATGTGGCTCTCC 61.648 60.000 0.00 0.00 0.00 3.71
918 963 2.818130 TGATTTTCCTTTGCTGGTGC 57.182 45.000 0.00 0.00 40.20 5.01
919 964 4.248058 GGATTGATTTTCCTTTGCTGGTG 58.752 43.478 0.00 0.00 0.00 4.17
920 965 3.261643 GGGATTGATTTTCCTTTGCTGGT 59.738 43.478 0.00 0.00 33.53 4.00
922 967 3.369787 GGGGGATTGATTTTCCTTTGCTG 60.370 47.826 0.00 0.00 33.53 4.41
924 969 2.418609 CGGGGGATTGATTTTCCTTTGC 60.419 50.000 0.00 0.00 33.53 3.68
925 970 2.418609 GCGGGGGATTGATTTTCCTTTG 60.419 50.000 0.00 0.00 33.53 2.77
926 971 1.831106 GCGGGGGATTGATTTTCCTTT 59.169 47.619 0.00 0.00 33.53 3.11
927 972 1.485124 GCGGGGGATTGATTTTCCTT 58.515 50.000 0.00 0.00 33.53 3.36
928 973 0.751643 CGCGGGGGATTGATTTTCCT 60.752 55.000 0.00 0.00 33.53 3.36
929 974 1.733526 CGCGGGGGATTGATTTTCC 59.266 57.895 0.00 0.00 0.00 3.13
930 975 1.065764 GCGCGGGGGATTGATTTTC 59.934 57.895 8.83 0.00 0.00 2.29
931 976 2.770589 CGCGCGGGGGATTGATTTT 61.771 57.895 24.84 0.00 0.00 1.82
985 1030 0.827925 CTCATCTACCTAGCCCCGCA 60.828 60.000 0.00 0.00 0.00 5.69
991 1036 1.968310 CCGCCCTCATCTACCTAGC 59.032 63.158 0.00 0.00 0.00 3.42
1269 1323 3.174987 CACCCACCACCACCTCCA 61.175 66.667 0.00 0.00 0.00 3.86
1272 1326 2.367648 TCACACCCACCACCACCT 60.368 61.111 0.00 0.00 0.00 4.00
1273 1327 2.113139 CTCACACCCACCACCACC 59.887 66.667 0.00 0.00 0.00 4.61
1274 1328 2.594592 GCTCACACCCACCACCAC 60.595 66.667 0.00 0.00 0.00 4.16
1275 1329 2.772191 AGCTCACACCCACCACCA 60.772 61.111 0.00 0.00 0.00 4.17
1276 1330 2.281761 CAGCTCACACCCACCACC 60.282 66.667 0.00 0.00 0.00 4.61
1277 1331 2.980233 GCAGCTCACACCCACCAC 60.980 66.667 0.00 0.00 0.00 4.16
1278 1332 4.269523 GGCAGCTCACACCCACCA 62.270 66.667 0.00 0.00 0.00 4.17
1626 1680 1.292223 CGGTGAGAAGAGGCCGAAA 59.708 57.895 0.00 0.00 46.33 3.46
1680 1734 2.933495 CGATACCTTCGTGGAACAGA 57.067 50.000 4.38 0.00 41.80 3.41
1704 1758 3.474570 CCGAGGAGAGGGGGCTTG 61.475 72.222 0.00 0.00 0.00 4.01
1833 1893 2.985847 GGTGGCTGGTGGAGTTGC 60.986 66.667 0.00 0.00 0.00 4.17
2598 2658 3.677148 CGCCAGTAGAAGAAATGAGCTCA 60.677 47.826 20.79 20.79 0.00 4.26
2611 2671 2.736144 ACAATTTCGTCGCCAGTAGA 57.264 45.000 0.00 0.00 0.00 2.59
2646 2706 0.882042 CACGAGCAGAGCAACCAACT 60.882 55.000 0.00 0.00 0.00 3.16
2856 2916 3.664107 TGGTTGGATCAGAAACTTCTCG 58.336 45.455 0.00 0.00 34.74 4.04
2925 2985 1.336702 GCAAACACATTCCGCCATGAA 60.337 47.619 0.00 0.00 0.00 2.57
3087 3147 1.341209 CGCCAGGCTGATACTGATACA 59.659 52.381 17.94 0.00 38.20 2.29
3090 3150 1.050988 ACCGCCAGGCTGATACTGAT 61.051 55.000 17.94 0.00 42.76 2.90
3102 3162 2.887568 GACGATCAGCACCGCCAG 60.888 66.667 0.00 0.00 0.00 4.85
3197 3257 5.995897 GTGTCCAACAACCAAGATAGTAGTT 59.004 40.000 0.00 0.00 0.00 2.24
3279 3339 7.686438 TTACACTATTAGAGTTACCGACACA 57.314 36.000 0.00 0.00 35.64 3.72
3288 3348 9.319143 GAGCAACATCATTACACTATTAGAGTT 57.681 33.333 0.00 0.00 35.64 3.01
3294 3354 7.796054 ACCTAGAGCAACATCATTACACTATT 58.204 34.615 0.00 0.00 0.00 1.73
3387 3449 5.527582 CCACTGGTTAAAATTATCCTCTCGG 59.472 44.000 2.83 0.00 0.00 4.63
3439 3501 2.557924 CCAAGGTAAGCAACATGAGCAA 59.442 45.455 15.23 2.79 0.00 3.91
3454 3516 1.427368 TGCACCAGGAATAACCAAGGT 59.573 47.619 0.00 0.00 45.68 3.50
3455 3517 2.214376 TGCACCAGGAATAACCAAGG 57.786 50.000 0.00 0.00 42.04 3.61
3456 3518 3.157087 AGTTGCACCAGGAATAACCAAG 58.843 45.455 0.00 0.00 42.04 3.61
3457 3519 3.237268 AGTTGCACCAGGAATAACCAA 57.763 42.857 0.00 0.00 42.04 3.67
3458 3520 2.969821 AGTTGCACCAGGAATAACCA 57.030 45.000 0.00 0.00 42.04 3.67
3459 3521 5.914898 ATTAAGTTGCACCAGGAATAACC 57.085 39.130 0.00 0.00 39.35 2.85
3480 3542 6.147864 ACTCAACAACATAAAGTGCACAAT 57.852 33.333 21.04 9.70 0.00 2.71
3492 3554 9.651913 AAAATAAACAGTTCAACTCAACAACAT 57.348 25.926 0.00 0.00 0.00 2.71
3617 3679 9.162764 GTTGTCTCTAAACATCTAGGCAAAATA 57.837 33.333 0.00 0.00 0.00 1.40
3682 3744 4.546674 AGTCCCCAAATTTCAGTTCAGTT 58.453 39.130 0.00 0.00 0.00 3.16
3683 3745 4.184649 AGTCCCCAAATTTCAGTTCAGT 57.815 40.909 0.00 0.00 0.00 3.41
3684 3746 4.702131 CCTAGTCCCCAAATTTCAGTTCAG 59.298 45.833 0.00 0.00 0.00 3.02
3685 3747 4.508405 CCCTAGTCCCCAAATTTCAGTTCA 60.508 45.833 0.00 0.00 0.00 3.18
3716 3783 9.498176 CTAATGTGAATTATCAGATGGACATCA 57.502 33.333 14.16 0.00 38.52 3.07
3795 3863 2.163818 ACGTTTTCAGAATCCTGCGA 57.836 45.000 0.00 0.00 40.20 5.10
3865 3934 6.790285 ATGCAATCAAACAGTCAAAAATCC 57.210 33.333 0.00 0.00 0.00 3.01
3874 3943 2.037511 CCACCCAATGCAATCAAACAGT 59.962 45.455 0.00 0.00 0.00 3.55
3875 3944 2.299582 TCCACCCAATGCAATCAAACAG 59.700 45.455 0.00 0.00 0.00 3.16
3891 3994 2.057137 TAGGATTTGCAGCATCCACC 57.943 50.000 22.72 8.61 42.63 4.61
3901 4004 5.925509 TGTACTACTTCCCATAGGATTTGC 58.074 41.667 0.00 0.00 43.54 3.68
3902 4005 6.992715 CCTTGTACTACTTCCCATAGGATTTG 59.007 42.308 0.00 0.00 43.54 2.32
3906 4009 5.476950 TCCTTGTACTACTTCCCATAGGA 57.523 43.478 0.00 0.00 41.88 2.94
4006 4218 4.051661 AGGGCTCCATTGATTCAAAGAA 57.948 40.909 2.68 0.00 0.00 2.52
4037 4249 4.648626 TGTGCTGGTGCCTCTGCC 62.649 66.667 3.58 0.00 38.71 4.85
4058 4270 6.801718 ATCCATTGTTGACATGAAATCCAT 57.198 33.333 0.00 0.00 35.44 3.41


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

AutoCloner maintained by Alex Coulton.