Multiple sequence alignment - TraesCS7D01G028700

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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 TraesCS7D01G028700 chr7D 100.000 2719 0 0 1 2719 13902422 13905140 0.000000e+00 5022
1 TraesCS7D01G028700 chr7D 91.054 1006 83 3 642 1646 520555968 520554969 0.000000e+00 1352
2 TraesCS7D01G028700 chr7D 86.650 824 93 12 1643 2462 520554924 520554114 0.000000e+00 896
3 TraesCS7D01G028700 chr3D 98.702 1464 13 1 189 1646 585178103 585176640 0.000000e+00 2593
4 TraesCS7D01G028700 chr3D 98.246 1083 13 3 1643 2719 585176595 585175513 0.000000e+00 1890
5 TraesCS7D01G028700 chr3D 98.469 196 3 0 1 196 585217912 585217717 2.000000e-91 346
6 TraesCS7D01G028700 chr4D 97.413 1005 24 1 642 1646 359889303 359888301 0.000000e+00 1711
7 TraesCS7D01G028700 chr4D 96.825 819 25 1 1643 2460 359888256 359887438 0.000000e+00 1367
8 TraesCS7D01G028700 chr7B 96.418 1005 36 0 642 1646 381385989 381384985 0.000000e+00 1657
9 TraesCS7D01G028700 chr7B 93.051 921 63 1 727 1646 723054416 723055336 0.000000e+00 1345
10 TraesCS7D01G028700 chr7B 92.609 920 68 0 727 1646 723079089 723080008 0.000000e+00 1323
11 TraesCS7D01G028700 chr7B 95.849 819 29 5 1643 2459 381384940 381384125 0.000000e+00 1319
12 TraesCS7D01G028700 chr7B 91.076 818 69 4 1643 2458 723080053 723080868 0.000000e+00 1103
13 TraesCS7D01G028700 chr7B 89.889 811 79 3 1643 2452 723055381 723056189 0.000000e+00 1040
14 TraesCS7D01G028700 chr7B 87.942 821 90 7 1643 2459 620566402 620565587 0.000000e+00 959
15 TraesCS7D01G028700 chr4A 91.054 1006 86 4 642 1646 728816666 728815664 0.000000e+00 1356
16 TraesCS7D01G028700 chr4A 87.956 822 89 8 1643 2459 728815619 728814803 0.000000e+00 961
17 TraesCS7D01G028700 chr1B 87.575 1006 116 5 642 1646 520973664 520974661 0.000000e+00 1157
18 TraesCS7D01G028700 chr1B 86.602 821 87 17 1643 2455 520974706 520975511 0.000000e+00 885
19 TraesCS7D01G028700 chr2D 85.700 1014 132 10 642 1646 291874757 291873748 0.000000e+00 1057
20 TraesCS7D01G028700 chr5B 95.288 191 8 1 2269 2459 573096273 573096462 4.400000e-78 302
21 TraesCS7D01G028700 chr2A 92.593 162 11 1 2298 2459 78587721 78587881 5.860000e-57 231


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 TraesCS7D01G028700 chr7D 13902422 13905140 2718 False 5022.0 5022 100.0000 1 2719 1 chr7D.!!$F1 2718
1 TraesCS7D01G028700 chr7D 520554114 520555968 1854 True 1124.0 1352 88.8520 642 2462 2 chr7D.!!$R1 1820
2 TraesCS7D01G028700 chr3D 585175513 585178103 2590 True 2241.5 2593 98.4740 189 2719 2 chr3D.!!$R2 2530
3 TraesCS7D01G028700 chr4D 359887438 359889303 1865 True 1539.0 1711 97.1190 642 2460 2 chr4D.!!$R1 1818
4 TraesCS7D01G028700 chr7B 381384125 381385989 1864 True 1488.0 1657 96.1335 642 2459 2 chr7B.!!$R2 1817
5 TraesCS7D01G028700 chr7B 723079089 723080868 1779 False 1213.0 1323 91.8425 727 2458 2 chr7B.!!$F2 1731
6 TraesCS7D01G028700 chr7B 723054416 723056189 1773 False 1192.5 1345 91.4700 727 2452 2 chr7B.!!$F1 1725
7 TraesCS7D01G028700 chr7B 620565587 620566402 815 True 959.0 959 87.9420 1643 2459 1 chr7B.!!$R1 816
8 TraesCS7D01G028700 chr4A 728814803 728816666 1863 True 1158.5 1356 89.5050 642 2459 2 chr4A.!!$R1 1817
9 TraesCS7D01G028700 chr1B 520973664 520975511 1847 False 1021.0 1157 87.0885 642 2455 2 chr1B.!!$F1 1813
10 TraesCS7D01G028700 chr2D 291873748 291874757 1009 True 1057.0 1057 85.7000 642 1646 1 chr2D.!!$R1 1004

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
503 504 0.100682 TCGCTGACAAGATACGCTCC 59.899 55.0 0.0 0.0 0.0 4.7 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2174 2253 1.745087 AGTGCTATTGTGGCCAAATCG 59.255 47.619 7.24 7.36 33.44 3.34 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
19 20 2.584835 TGTTCTTGCCAGGCAGTAAT 57.415 45.000 15.50 0.00 40.61 1.89
20 21 2.436417 TGTTCTTGCCAGGCAGTAATC 58.564 47.619 15.50 6.51 40.61 1.75
21 22 2.224744 TGTTCTTGCCAGGCAGTAATCA 60.225 45.455 15.50 9.03 40.61 2.57
22 23 2.819608 GTTCTTGCCAGGCAGTAATCAA 59.180 45.455 15.50 0.00 40.61 2.57
23 24 3.153369 TCTTGCCAGGCAGTAATCAAA 57.847 42.857 15.50 0.00 40.61 2.69
24 25 2.819608 TCTTGCCAGGCAGTAATCAAAC 59.180 45.455 15.50 0.00 40.61 2.93
25 26 2.284754 TGCCAGGCAGTAATCAAACA 57.715 45.000 11.22 0.00 33.32 2.83
26 27 2.806434 TGCCAGGCAGTAATCAAACAT 58.194 42.857 11.22 0.00 33.32 2.71
27 28 2.754552 TGCCAGGCAGTAATCAAACATC 59.245 45.455 11.22 0.00 33.32 3.06
28 29 2.754552 GCCAGGCAGTAATCAAACATCA 59.245 45.455 6.55 0.00 0.00 3.07
29 30 3.193267 GCCAGGCAGTAATCAAACATCAA 59.807 43.478 6.55 0.00 0.00 2.57
30 31 4.142093 GCCAGGCAGTAATCAAACATCAAT 60.142 41.667 6.55 0.00 0.00 2.57
31 32 5.625197 GCCAGGCAGTAATCAAACATCAATT 60.625 40.000 6.55 0.00 0.00 2.32
32 33 6.400568 CCAGGCAGTAATCAAACATCAATTT 58.599 36.000 0.00 0.00 0.00 1.82
33 34 6.875195 CCAGGCAGTAATCAAACATCAATTTT 59.125 34.615 0.00 0.00 0.00 1.82
34 35 7.388500 CCAGGCAGTAATCAAACATCAATTTTT 59.612 33.333 0.00 0.00 0.00 1.94
35 36 9.421806 CAGGCAGTAATCAAACATCAATTTTTA 57.578 29.630 0.00 0.00 0.00 1.52
36 37 9.423061 AGGCAGTAATCAAACATCAATTTTTAC 57.577 29.630 0.00 0.00 0.00 2.01
37 38 9.202273 GGCAGTAATCAAACATCAATTTTTACA 57.798 29.630 0.00 0.00 0.00 2.41
45 46 9.766277 TCAAACATCAATTTTTACACTTTTTGC 57.234 25.926 0.00 0.00 0.00 3.68
46 47 9.771915 CAAACATCAATTTTTACACTTTTTGCT 57.228 25.926 0.00 0.00 0.00 3.91
47 48 9.771915 AAACATCAATTTTTACACTTTTTGCTG 57.228 25.926 0.00 0.00 0.00 4.41
48 49 8.715191 ACATCAATTTTTACACTTTTTGCTGA 57.285 26.923 0.00 0.00 0.00 4.26
49 50 9.160496 ACATCAATTTTTACACTTTTTGCTGAA 57.840 25.926 0.00 0.00 0.00 3.02
54 55 8.839947 ATTTTTACACTTTTTGCTGAATTTGC 57.160 26.923 0.00 0.00 0.00 3.68
55 56 5.982465 TTACACTTTTTGCTGAATTTGCC 57.018 34.783 2.64 0.00 0.00 4.52
56 57 3.871485 ACACTTTTTGCTGAATTTGCCA 58.129 36.364 2.64 0.00 0.00 4.92
57 58 4.260170 ACACTTTTTGCTGAATTTGCCAA 58.740 34.783 2.64 0.00 0.00 4.52
58 59 4.699257 ACACTTTTTGCTGAATTTGCCAAA 59.301 33.333 0.00 0.00 0.00 3.28
59 60 5.029654 CACTTTTTGCTGAATTTGCCAAAC 58.970 37.500 0.00 0.00 0.00 2.93
60 61 4.096231 ACTTTTTGCTGAATTTGCCAAACC 59.904 37.500 0.00 0.00 0.00 3.27
61 62 2.996249 TTGCTGAATTTGCCAAACCA 57.004 40.000 0.00 0.00 0.00 3.67
62 63 2.237393 TGCTGAATTTGCCAAACCAC 57.763 45.000 0.00 0.00 0.00 4.16
63 64 1.761784 TGCTGAATTTGCCAAACCACT 59.238 42.857 0.00 0.00 0.00 4.00
64 65 2.961741 TGCTGAATTTGCCAAACCACTA 59.038 40.909 0.00 0.00 0.00 2.74
65 66 3.577848 TGCTGAATTTGCCAAACCACTAT 59.422 39.130 0.00 0.00 0.00 2.12
66 67 4.040217 TGCTGAATTTGCCAAACCACTATT 59.960 37.500 0.00 0.00 0.00 1.73
67 68 4.627035 GCTGAATTTGCCAAACCACTATTC 59.373 41.667 0.00 0.00 0.00 1.75
68 69 4.804108 TGAATTTGCCAAACCACTATTCG 58.196 39.130 0.00 0.00 0.00 3.34
69 70 4.279671 TGAATTTGCCAAACCACTATTCGT 59.720 37.500 0.00 0.00 0.00 3.85
70 71 5.473846 TGAATTTGCCAAACCACTATTCGTA 59.526 36.000 0.00 0.00 0.00 3.43
71 72 6.151985 TGAATTTGCCAAACCACTATTCGTAT 59.848 34.615 0.00 0.00 0.00 3.06
72 73 7.337184 TGAATTTGCCAAACCACTATTCGTATA 59.663 33.333 0.00 0.00 0.00 1.47
73 74 6.671614 TTTGCCAAACCACTATTCGTATAG 57.328 37.500 7.45 7.45 39.75 1.31
74 75 4.124238 TGCCAAACCACTATTCGTATAGC 58.876 43.478 8.80 0.00 37.80 2.97
75 76 4.124238 GCCAAACCACTATTCGTATAGCA 58.876 43.478 8.80 0.00 37.80 3.49
76 77 4.211374 GCCAAACCACTATTCGTATAGCAG 59.789 45.833 8.80 3.72 37.80 4.24
77 78 5.597806 CCAAACCACTATTCGTATAGCAGA 58.402 41.667 8.80 0.00 37.80 4.26
78 79 6.223852 CCAAACCACTATTCGTATAGCAGAT 58.776 40.000 8.80 0.00 37.80 2.90
79 80 7.375834 CCAAACCACTATTCGTATAGCAGATA 58.624 38.462 8.80 0.00 37.80 1.98
80 81 7.870954 CCAAACCACTATTCGTATAGCAGATAA 59.129 37.037 8.80 0.00 37.80 1.75
81 82 9.424319 CAAACCACTATTCGTATAGCAGATAAT 57.576 33.333 8.80 0.00 37.80 1.28
82 83 9.998106 AAACCACTATTCGTATAGCAGATAATT 57.002 29.630 8.80 0.00 37.80 1.40
83 84 9.998106 AACCACTATTCGTATAGCAGATAATTT 57.002 29.630 8.80 0.00 37.80 1.82
84 85 9.424319 ACCACTATTCGTATAGCAGATAATTTG 57.576 33.333 8.80 0.00 37.80 2.32
85 86 9.424319 CCACTATTCGTATAGCAGATAATTTGT 57.576 33.333 8.80 0.00 37.80 2.83
106 107 8.556213 TTTGTATATAAATAGATTGGACGGCC 57.444 34.615 0.00 0.00 0.00 6.13
107 108 6.334989 TGTATATAAATAGATTGGACGGCCG 58.665 40.000 26.86 26.86 36.79 6.13
108 109 1.873698 TAAATAGATTGGACGGCCGC 58.126 50.000 28.58 18.35 36.79 6.53
109 110 0.818040 AAATAGATTGGACGGCCGCC 60.818 55.000 28.58 26.88 36.79 6.13
124 125 4.241555 GCCGCCACCGATGAGGAT 62.242 66.667 0.00 0.00 45.00 3.24
125 126 2.280389 CCGCCACCGATGAGGATG 60.280 66.667 0.00 0.00 45.00 3.51
126 127 2.969238 CGCCACCGATGAGGATGC 60.969 66.667 0.00 0.00 45.00 3.91
127 128 2.592861 GCCACCGATGAGGATGCC 60.593 66.667 0.00 0.00 45.00 4.40
128 129 2.280389 CCACCGATGAGGATGCCG 60.280 66.667 0.00 0.00 45.00 5.69
129 130 2.796193 CCACCGATGAGGATGCCGA 61.796 63.158 0.00 0.00 45.00 5.54
130 131 1.300465 CACCGATGAGGATGCCGAG 60.300 63.158 0.00 0.00 45.00 4.63
131 132 1.758514 ACCGATGAGGATGCCGAGT 60.759 57.895 0.00 0.00 45.00 4.18
132 133 1.300465 CCGATGAGGATGCCGAGTG 60.300 63.158 0.00 0.00 45.00 3.51
133 134 1.735973 CGATGAGGATGCCGAGTGA 59.264 57.895 0.00 0.00 0.00 3.41
134 135 0.103026 CGATGAGGATGCCGAGTGAA 59.897 55.000 0.00 0.00 0.00 3.18
135 136 1.471501 CGATGAGGATGCCGAGTGAAA 60.472 52.381 0.00 0.00 0.00 2.69
136 137 2.208431 GATGAGGATGCCGAGTGAAAG 58.792 52.381 0.00 0.00 0.00 2.62
137 138 1.266178 TGAGGATGCCGAGTGAAAGA 58.734 50.000 0.00 0.00 0.00 2.52
138 139 1.623311 TGAGGATGCCGAGTGAAAGAA 59.377 47.619 0.00 0.00 0.00 2.52
139 140 2.003301 GAGGATGCCGAGTGAAAGAAC 58.997 52.381 0.00 0.00 0.00 3.01
140 141 1.347707 AGGATGCCGAGTGAAAGAACA 59.652 47.619 0.00 0.00 0.00 3.18
141 142 1.734465 GGATGCCGAGTGAAAGAACAG 59.266 52.381 0.00 0.00 0.00 3.16
142 143 2.417719 GATGCCGAGTGAAAGAACAGT 58.582 47.619 0.00 0.00 0.00 3.55
143 144 1.581934 TGCCGAGTGAAAGAACAGTG 58.418 50.000 0.00 0.00 0.00 3.66
144 145 0.868406 GCCGAGTGAAAGAACAGTGG 59.132 55.000 0.00 0.00 0.00 4.00
145 146 1.810412 GCCGAGTGAAAGAACAGTGGT 60.810 52.381 0.00 0.00 0.00 4.16
146 147 1.867233 CCGAGTGAAAGAACAGTGGTG 59.133 52.381 0.00 0.00 0.00 4.17
147 148 1.867233 CGAGTGAAAGAACAGTGGTGG 59.133 52.381 0.00 0.00 0.00 4.61
148 149 2.483013 CGAGTGAAAGAACAGTGGTGGA 60.483 50.000 0.00 0.00 0.00 4.02
149 150 2.872858 GAGTGAAAGAACAGTGGTGGAC 59.127 50.000 0.00 0.00 0.00 4.02
150 151 2.505819 AGTGAAAGAACAGTGGTGGACT 59.494 45.455 0.00 0.00 34.02 3.85
151 152 3.054361 AGTGAAAGAACAGTGGTGGACTT 60.054 43.478 0.00 0.00 29.75 3.01
152 153 3.065371 GTGAAAGAACAGTGGTGGACTTG 59.935 47.826 0.00 0.00 29.75 3.16
153 154 3.279434 GAAAGAACAGTGGTGGACTTGT 58.721 45.455 0.00 0.00 29.75 3.16
154 155 2.332063 AGAACAGTGGTGGACTTGTG 57.668 50.000 0.00 0.00 29.75 3.33
155 156 1.134098 AGAACAGTGGTGGACTTGTGG 60.134 52.381 0.00 0.00 29.75 4.17
156 157 0.751643 AACAGTGGTGGACTTGTGGC 60.752 55.000 0.00 0.00 29.75 5.01
157 158 1.152984 CAGTGGTGGACTTGTGGCA 60.153 57.895 0.00 0.00 29.75 4.92
158 159 1.149174 AGTGGTGGACTTGTGGCAG 59.851 57.895 0.00 0.00 0.00 4.85
159 160 1.148273 GTGGTGGACTTGTGGCAGA 59.852 57.895 0.00 0.00 0.00 4.26
160 161 0.886490 GTGGTGGACTTGTGGCAGAG 60.886 60.000 0.00 0.00 0.00 3.35
161 162 1.302832 GGTGGACTTGTGGCAGAGG 60.303 63.158 0.00 0.00 0.00 3.69
162 163 1.451936 GTGGACTTGTGGCAGAGGT 59.548 57.895 0.00 0.00 0.00 3.85
163 164 0.886490 GTGGACTTGTGGCAGAGGTG 60.886 60.000 3.57 0.00 0.00 4.00
176 177 2.771089 CAGAGGTGCTTACTTGCTTGA 58.229 47.619 0.00 0.00 0.00 3.02
177 178 2.481952 CAGAGGTGCTTACTTGCTTGAC 59.518 50.000 0.00 0.00 0.00 3.18
178 179 2.104792 AGAGGTGCTTACTTGCTTGACA 59.895 45.455 0.00 0.00 0.00 3.58
179 180 2.222027 AGGTGCTTACTTGCTTGACAC 58.778 47.619 0.00 0.00 0.00 3.67
180 181 2.158755 AGGTGCTTACTTGCTTGACACT 60.159 45.455 0.00 0.00 0.00 3.55
181 182 2.224314 GGTGCTTACTTGCTTGACACTC 59.776 50.000 0.00 0.00 0.00 3.51
182 183 3.134458 GTGCTTACTTGCTTGACACTCT 58.866 45.455 0.00 0.00 0.00 3.24
183 184 3.561725 GTGCTTACTTGCTTGACACTCTT 59.438 43.478 0.00 0.00 0.00 2.85
184 185 4.750098 GTGCTTACTTGCTTGACACTCTTA 59.250 41.667 0.00 0.00 0.00 2.10
185 186 5.409826 GTGCTTACTTGCTTGACACTCTTAT 59.590 40.000 0.00 0.00 0.00 1.73
186 187 6.590292 GTGCTTACTTGCTTGACACTCTTATA 59.410 38.462 0.00 0.00 0.00 0.98
187 188 7.278868 GTGCTTACTTGCTTGACACTCTTATAT 59.721 37.037 0.00 0.00 0.00 0.86
270 271 3.871006 GTGAGTGCGTCATATCCATTTCA 59.129 43.478 0.00 0.00 37.56 2.69
419 420 1.808945 CAGGTCAGCTGCTCGATTTTT 59.191 47.619 9.47 0.00 0.00 1.94
503 504 0.100682 TCGCTGACAAGATACGCTCC 59.899 55.000 0.00 0.00 0.00 4.70
805 806 2.025037 ACCCCAGATGCAAGCTATCAAA 60.025 45.455 0.00 0.00 0.00 2.69
1287 1296 5.862323 TGACAGTGTTAAAGCTATTCGACTC 59.138 40.000 0.00 0.00 0.00 3.36
1861 1931 5.320549 ACCTCTGAAACATTGCAATCATC 57.679 39.130 9.53 8.65 0.00 2.92
2174 2253 0.467290 TGACCCAACAAAGGCTCACC 60.467 55.000 0.00 0.00 0.00 4.02
2509 2596 1.672145 GCCAGACACCCTCGAGTAAAC 60.672 57.143 12.31 0.00 0.00 2.01
2524 2611 6.524734 TCGAGTAAACGGGTAGTATAGATCA 58.475 40.000 0.00 0.00 0.00 2.92
2548 2635 1.351017 GGGGCCATAAGATCGATGGAA 59.649 52.381 25.61 0.00 45.89 3.53
2563 2650 2.435372 TGGAAGTTGATGCCCCATAC 57.565 50.000 0.00 0.00 0.00 2.39
2584 2671 3.056107 ACTCATGCGGGCGTAATGTATAT 60.056 43.478 0.00 0.00 0.00 0.86
2683 2770 2.989909 ACATCGTCTGCATCATTTCCA 58.010 42.857 0.00 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.224744 TGATTACTGCCTGGCAAGAACA 60.225 45.455 23.51 15.36 38.41 3.18
1 2 2.436417 TGATTACTGCCTGGCAAGAAC 58.564 47.619 23.51 13.09 38.41 3.01
2 3 2.877097 TGATTACTGCCTGGCAAGAA 57.123 45.000 23.51 18.68 38.41 2.52
3 4 2.819608 GTTTGATTACTGCCTGGCAAGA 59.180 45.455 23.51 10.50 38.41 3.02
4 5 2.557924 TGTTTGATTACTGCCTGGCAAG 59.442 45.455 23.51 18.02 38.41 4.01
5 6 2.591923 TGTTTGATTACTGCCTGGCAA 58.408 42.857 23.51 8.58 38.41 4.52
6 7 2.284754 TGTTTGATTACTGCCTGGCA 57.715 45.000 21.96 21.96 36.92 4.92
7 8 2.754552 TGATGTTTGATTACTGCCTGGC 59.245 45.455 12.87 12.87 0.00 4.85
8 9 5.587388 ATTGATGTTTGATTACTGCCTGG 57.413 39.130 0.00 0.00 0.00 4.45
9 10 7.894376 AAAATTGATGTTTGATTACTGCCTG 57.106 32.000 0.00 0.00 0.00 4.85
10 11 9.423061 GTAAAAATTGATGTTTGATTACTGCCT 57.577 29.630 0.00 0.00 0.00 4.75
11 12 9.202273 TGTAAAAATTGATGTTTGATTACTGCC 57.798 29.630 0.00 0.00 0.00 4.85
19 20 9.766277 GCAAAAAGTGTAAAAATTGATGTTTGA 57.234 25.926 0.00 0.00 0.00 2.69
20 21 9.771915 AGCAAAAAGTGTAAAAATTGATGTTTG 57.228 25.926 0.00 0.00 0.00 2.93
21 22 9.771915 CAGCAAAAAGTGTAAAAATTGATGTTT 57.228 25.926 0.00 0.00 31.60 2.83
22 23 9.160496 TCAGCAAAAAGTGTAAAAATTGATGTT 57.840 25.926 0.00 0.00 36.08 2.71
23 24 8.715191 TCAGCAAAAAGTGTAAAAATTGATGT 57.285 26.923 0.00 0.00 36.08 3.06
28 29 9.288124 GCAAATTCAGCAAAAAGTGTAAAAATT 57.712 25.926 0.00 0.00 0.00 1.82
29 30 7.914871 GGCAAATTCAGCAAAAAGTGTAAAAAT 59.085 29.630 5.36 0.00 0.00 1.82
30 31 7.094634 TGGCAAATTCAGCAAAAAGTGTAAAAA 60.095 29.630 5.36 0.00 0.00 1.94
31 32 6.372659 TGGCAAATTCAGCAAAAAGTGTAAAA 59.627 30.769 5.36 0.00 0.00 1.52
32 33 5.877012 TGGCAAATTCAGCAAAAAGTGTAAA 59.123 32.000 5.36 0.00 0.00 2.01
33 34 5.423015 TGGCAAATTCAGCAAAAAGTGTAA 58.577 33.333 5.36 0.00 0.00 2.41
34 35 5.016051 TGGCAAATTCAGCAAAAAGTGTA 57.984 34.783 5.36 0.00 0.00 2.90
35 36 3.871485 TGGCAAATTCAGCAAAAAGTGT 58.129 36.364 5.36 0.00 0.00 3.55
36 37 4.879104 TTGGCAAATTCAGCAAAAAGTG 57.121 36.364 0.00 0.00 0.00 3.16
37 38 4.096231 GGTTTGGCAAATTCAGCAAAAAGT 59.904 37.500 16.74 0.00 36.72 2.66
38 39 4.096081 TGGTTTGGCAAATTCAGCAAAAAG 59.904 37.500 16.74 0.00 36.72 2.27
39 40 4.012374 TGGTTTGGCAAATTCAGCAAAAA 58.988 34.783 16.74 3.90 36.72 1.94
40 41 3.376546 GTGGTTTGGCAAATTCAGCAAAA 59.623 39.130 16.74 3.76 32.74 2.44
41 42 2.941720 GTGGTTTGGCAAATTCAGCAAA 59.058 40.909 16.74 0.00 0.00 3.68
42 43 2.170187 AGTGGTTTGGCAAATTCAGCAA 59.830 40.909 16.74 0.00 0.00 3.91
43 44 1.761784 AGTGGTTTGGCAAATTCAGCA 59.238 42.857 16.74 6.69 0.00 4.41
44 45 2.531522 AGTGGTTTGGCAAATTCAGC 57.468 45.000 16.74 3.83 0.00 4.26
45 46 4.858692 CGAATAGTGGTTTGGCAAATTCAG 59.141 41.667 16.74 7.36 0.00 3.02
46 47 4.279671 ACGAATAGTGGTTTGGCAAATTCA 59.720 37.500 16.74 14.34 0.00 2.57
47 48 4.805219 ACGAATAGTGGTTTGGCAAATTC 58.195 39.130 16.74 12.88 0.00 2.17
48 49 4.864704 ACGAATAGTGGTTTGGCAAATT 57.135 36.364 16.74 4.90 0.00 1.82
49 50 6.238648 GCTATACGAATAGTGGTTTGGCAAAT 60.239 38.462 16.74 2.29 37.90 2.32
50 51 5.065474 GCTATACGAATAGTGGTTTGGCAAA 59.935 40.000 8.93 8.93 37.90 3.68
51 52 4.573201 GCTATACGAATAGTGGTTTGGCAA 59.427 41.667 0.00 0.00 37.90 4.52
52 53 4.124238 GCTATACGAATAGTGGTTTGGCA 58.876 43.478 0.00 0.00 37.90 4.92
53 54 4.124238 TGCTATACGAATAGTGGTTTGGC 58.876 43.478 0.00 0.00 37.90 4.52
54 55 5.597806 TCTGCTATACGAATAGTGGTTTGG 58.402 41.667 0.00 0.00 37.90 3.28
55 56 8.812147 TTATCTGCTATACGAATAGTGGTTTG 57.188 34.615 0.00 0.00 37.90 2.93
56 57 9.998106 AATTATCTGCTATACGAATAGTGGTTT 57.002 29.630 0.00 0.00 37.90 3.27
57 58 9.998106 AAATTATCTGCTATACGAATAGTGGTT 57.002 29.630 0.00 0.00 37.90 3.67
58 59 9.424319 CAAATTATCTGCTATACGAATAGTGGT 57.576 33.333 0.00 0.00 37.90 4.16
59 60 9.424319 ACAAATTATCTGCTATACGAATAGTGG 57.576 33.333 0.00 0.00 37.90 4.00
80 81 9.174166 GGCCGTCCAATCTATTTATATACAAAT 57.826 33.333 0.00 0.00 32.91 2.32
81 82 7.332430 CGGCCGTCCAATCTATTTATATACAAA 59.668 37.037 19.50 0.00 0.00 2.83
82 83 6.814644 CGGCCGTCCAATCTATTTATATACAA 59.185 38.462 19.50 0.00 0.00 2.41
83 84 6.334989 CGGCCGTCCAATCTATTTATATACA 58.665 40.000 19.50 0.00 0.00 2.29
84 85 5.233689 GCGGCCGTCCAATCTATTTATATAC 59.766 44.000 28.70 0.00 0.00 1.47
85 86 5.353938 GCGGCCGTCCAATCTATTTATATA 58.646 41.667 28.70 0.00 0.00 0.86
86 87 4.189231 GCGGCCGTCCAATCTATTTATAT 58.811 43.478 28.70 0.00 0.00 0.86
87 88 3.592059 GCGGCCGTCCAATCTATTTATA 58.408 45.455 28.70 0.00 0.00 0.98
88 89 2.423577 GCGGCCGTCCAATCTATTTAT 58.576 47.619 28.70 0.00 0.00 1.40
89 90 1.541670 GGCGGCCGTCCAATCTATTTA 60.542 52.381 28.70 0.00 0.00 1.40
90 91 0.818040 GGCGGCCGTCCAATCTATTT 60.818 55.000 28.70 0.00 0.00 1.40
91 92 1.227853 GGCGGCCGTCCAATCTATT 60.228 57.895 28.70 0.00 0.00 1.73
92 93 2.426023 GGCGGCCGTCCAATCTAT 59.574 61.111 28.70 0.00 0.00 1.98
93 94 4.215742 CGGCGGCCGTCCAATCTA 62.216 66.667 32.14 0.00 42.73 1.98
107 108 4.241555 ATCCTCATCGGTGGCGGC 62.242 66.667 0.00 0.00 0.00 6.53
108 109 2.280389 CATCCTCATCGGTGGCGG 60.280 66.667 0.00 0.00 0.00 6.13
109 110 2.969238 GCATCCTCATCGGTGGCG 60.969 66.667 0.00 0.00 0.00 5.69
110 111 2.592861 GGCATCCTCATCGGTGGC 60.593 66.667 0.00 0.00 34.25 5.01
111 112 2.280389 CGGCATCCTCATCGGTGG 60.280 66.667 0.00 0.00 0.00 4.61
112 113 1.300465 CTCGGCATCCTCATCGGTG 60.300 63.158 0.00 0.00 0.00 4.94
113 114 1.758514 ACTCGGCATCCTCATCGGT 60.759 57.895 0.00 0.00 0.00 4.69
114 115 1.300465 CACTCGGCATCCTCATCGG 60.300 63.158 0.00 0.00 0.00 4.18
115 116 0.103026 TTCACTCGGCATCCTCATCG 59.897 55.000 0.00 0.00 0.00 3.84
116 117 2.159043 TCTTTCACTCGGCATCCTCATC 60.159 50.000 0.00 0.00 0.00 2.92
117 118 1.833630 TCTTTCACTCGGCATCCTCAT 59.166 47.619 0.00 0.00 0.00 2.90
118 119 1.266178 TCTTTCACTCGGCATCCTCA 58.734 50.000 0.00 0.00 0.00 3.86
119 120 2.003301 GTTCTTTCACTCGGCATCCTC 58.997 52.381 0.00 0.00 0.00 3.71
120 121 1.347707 TGTTCTTTCACTCGGCATCCT 59.652 47.619 0.00 0.00 0.00 3.24
121 122 1.734465 CTGTTCTTTCACTCGGCATCC 59.266 52.381 0.00 0.00 0.00 3.51
122 123 2.158449 CACTGTTCTTTCACTCGGCATC 59.842 50.000 0.00 0.00 0.00 3.91
123 124 2.146342 CACTGTTCTTTCACTCGGCAT 58.854 47.619 0.00 0.00 0.00 4.40
124 125 1.581934 CACTGTTCTTTCACTCGGCA 58.418 50.000 0.00 0.00 0.00 5.69
125 126 0.868406 CCACTGTTCTTTCACTCGGC 59.132 55.000 0.00 0.00 0.00 5.54
126 127 1.867233 CACCACTGTTCTTTCACTCGG 59.133 52.381 0.00 0.00 0.00 4.63
127 128 1.867233 CCACCACTGTTCTTTCACTCG 59.133 52.381 0.00 0.00 0.00 4.18
128 129 2.872858 GTCCACCACTGTTCTTTCACTC 59.127 50.000 0.00 0.00 0.00 3.51
129 130 2.505819 AGTCCACCACTGTTCTTTCACT 59.494 45.455 0.00 0.00 32.26 3.41
130 131 2.919228 AGTCCACCACTGTTCTTTCAC 58.081 47.619 0.00 0.00 32.26 3.18
131 132 3.278574 CAAGTCCACCACTGTTCTTTCA 58.721 45.455 0.00 0.00 34.56 2.69
132 133 3.065371 CACAAGTCCACCACTGTTCTTTC 59.935 47.826 0.00 0.00 34.56 2.62
133 134 3.016736 CACAAGTCCACCACTGTTCTTT 58.983 45.455 0.00 0.00 34.56 2.52
134 135 2.643551 CACAAGTCCACCACTGTTCTT 58.356 47.619 0.00 0.00 34.56 2.52
135 136 1.134098 CCACAAGTCCACCACTGTTCT 60.134 52.381 0.00 0.00 34.56 3.01
136 137 1.308998 CCACAAGTCCACCACTGTTC 58.691 55.000 0.00 0.00 34.56 3.18
137 138 0.751643 GCCACAAGTCCACCACTGTT 60.752 55.000 0.00 0.00 34.56 3.16
138 139 1.152963 GCCACAAGTCCACCACTGT 60.153 57.895 0.00 0.00 34.56 3.55
139 140 1.152984 TGCCACAAGTCCACCACTG 60.153 57.895 0.00 0.00 34.56 3.66
140 141 1.149174 CTGCCACAAGTCCACCACT 59.851 57.895 0.00 0.00 36.64 4.00
141 142 0.886490 CTCTGCCACAAGTCCACCAC 60.886 60.000 0.00 0.00 0.00 4.16
142 143 1.451504 CTCTGCCACAAGTCCACCA 59.548 57.895 0.00 0.00 0.00 4.17
143 144 1.302832 CCTCTGCCACAAGTCCACC 60.303 63.158 0.00 0.00 0.00 4.61
144 145 0.886490 CACCTCTGCCACAAGTCCAC 60.886 60.000 0.00 0.00 0.00 4.02
145 146 1.451504 CACCTCTGCCACAAGTCCA 59.548 57.895 0.00 0.00 0.00 4.02
146 147 1.968540 GCACCTCTGCCACAAGTCC 60.969 63.158 0.00 0.00 37.45 3.85
147 148 0.536006 AAGCACCTCTGCCACAAGTC 60.536 55.000 0.00 0.00 45.53 3.01
148 149 0.764890 TAAGCACCTCTGCCACAAGT 59.235 50.000 0.00 0.00 45.53 3.16
149 150 1.160137 GTAAGCACCTCTGCCACAAG 58.840 55.000 0.00 0.00 45.53 3.16
150 151 0.764890 AGTAAGCACCTCTGCCACAA 59.235 50.000 0.00 0.00 45.53 3.33
151 152 0.764890 AAGTAAGCACCTCTGCCACA 59.235 50.000 0.00 0.00 45.53 4.17
152 153 1.160137 CAAGTAAGCACCTCTGCCAC 58.840 55.000 0.00 0.00 45.53 5.01
153 154 0.606401 GCAAGTAAGCACCTCTGCCA 60.606 55.000 0.00 0.00 45.53 4.92
154 155 0.322008 AGCAAGTAAGCACCTCTGCC 60.322 55.000 0.00 0.00 45.53 4.85
155 156 1.198637 CAAGCAAGTAAGCACCTCTGC 59.801 52.381 0.00 0.00 44.63 4.26
156 157 2.481952 GTCAAGCAAGTAAGCACCTCTG 59.518 50.000 0.00 0.00 36.85 3.35
157 158 2.104792 TGTCAAGCAAGTAAGCACCTCT 59.895 45.455 0.00 0.00 36.85 3.69
158 159 2.224314 GTGTCAAGCAAGTAAGCACCTC 59.776 50.000 0.00 0.00 36.85 3.85
159 160 2.158755 AGTGTCAAGCAAGTAAGCACCT 60.159 45.455 0.00 0.00 36.85 4.00
160 161 2.222027 AGTGTCAAGCAAGTAAGCACC 58.778 47.619 0.00 0.00 36.85 5.01
161 162 3.134458 AGAGTGTCAAGCAAGTAAGCAC 58.866 45.455 0.00 0.00 36.85 4.40
162 163 3.475566 AGAGTGTCAAGCAAGTAAGCA 57.524 42.857 0.00 0.00 36.85 3.91
163 164 7.778470 ATATAAGAGTGTCAAGCAAGTAAGC 57.222 36.000 0.00 0.00 0.00 3.09
165 166 9.297586 CGTTATATAAGAGTGTCAAGCAAGTAA 57.702 33.333 0.00 0.00 0.00 2.24
166 167 8.680001 TCGTTATATAAGAGTGTCAAGCAAGTA 58.320 33.333 0.00 0.00 0.00 2.24
167 168 7.488471 GTCGTTATATAAGAGTGTCAAGCAAGT 59.512 37.037 0.00 0.00 0.00 3.16
168 169 7.702772 AGTCGTTATATAAGAGTGTCAAGCAAG 59.297 37.037 0.00 0.00 0.00 4.01
169 170 7.544622 AGTCGTTATATAAGAGTGTCAAGCAA 58.455 34.615 0.00 0.00 0.00 3.91
170 171 7.096884 AGTCGTTATATAAGAGTGTCAAGCA 57.903 36.000 0.00 0.00 0.00 3.91
171 172 9.171701 CTTAGTCGTTATATAAGAGTGTCAAGC 57.828 37.037 0.00 0.00 0.00 4.01
174 175 9.610705 AGTCTTAGTCGTTATATAAGAGTGTCA 57.389 33.333 0.00 0.00 37.64 3.58
185 186 8.582437 CCCATGGATTTAGTCTTAGTCGTTATA 58.418 37.037 15.22 0.00 0.00 0.98
186 187 7.442656 CCCATGGATTTAGTCTTAGTCGTTAT 58.557 38.462 15.22 0.00 0.00 1.89
187 188 6.183360 CCCCATGGATTTAGTCTTAGTCGTTA 60.183 42.308 15.22 0.00 0.00 3.18
419 420 1.227823 CTCCAAGGTGGTTCGTGCA 60.228 57.895 0.00 0.00 39.03 4.57
1755 1824 7.391275 TGAGAGAATTGCTTGATCAACAATACA 59.609 33.333 24.07 18.35 37.88 2.29
1861 1931 8.202745 AGAAGTTTTCAAGCTATTCTTATCCG 57.797 34.615 0.00 0.00 32.74 4.18
2174 2253 1.745087 AGTGCTATTGTGGCCAAATCG 59.255 47.619 7.24 7.36 33.44 3.34
2509 2596 3.510360 CCCCAGTTGATCTATACTACCCG 59.490 52.174 0.00 0.00 0.00 5.28
2524 2611 1.507140 TCGATCTTATGGCCCCAGTT 58.493 50.000 0.00 0.00 0.00 3.16
2548 2635 2.750807 GCATGAGTATGGGGCATCAACT 60.751 50.000 0.00 0.00 34.79 3.16
2563 2650 1.795768 ATACATTACGCCCGCATGAG 58.204 50.000 0.00 0.00 0.00 2.90
2683 2770 5.711506 TGTCTGTGCAGTTCAAATGGAATAT 59.288 36.000 0.00 0.00 37.93 1.28


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

AutoCloner maintained by Alex Coulton.