Multiple sequence alignment - TraesCS6D01G360700

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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 TraesCS6D01G360700 chr6D 100.000 4291 0 0 1 4291 452128825 452124535 0.000000e+00 7925.0
1 TraesCS6D01G360700 chr5B 91.845 2894 176 29 706 3593 507803125 507800286 0.000000e+00 3982.0
2 TraesCS6D01G360700 chr5B 87.042 355 43 3 3936 4288 507798003 507797650 8.650000e-107 398.0
3 TraesCS6D01G360700 chr5B 82.609 299 15 13 323 613 507803416 507803147 3.340000e-56 230.0
4 TraesCS6D01G360700 chr5B 84.774 243 20 9 92 320 314274733 314274494 1.200000e-55 228.0
5 TraesCS6D01G360700 chr5B 95.238 105 4 1 3641 3744 507798276 507798172 9.550000e-37 165.0
6 TraesCS6D01G360700 chr5B 98.113 53 1 0 3590 3642 507798462 507798410 4.570000e-15 93.5
7 TraesCS6D01G360700 chr5B 92.063 63 5 0 3531 3593 507800430 507800368 5.910000e-14 89.8
8 TraesCS6D01G360700 chr3B 92.213 2748 173 24 622 3355 172170324 172173044 0.000000e+00 3851.0
9 TraesCS6D01G360700 chr3B 92.262 2675 171 22 700 3355 172052028 172054685 0.000000e+00 3760.0
10 TraesCS6D01G360700 chr3B 92.302 2650 173 20 716 3355 146982563 146979935 0.000000e+00 3735.0
11 TraesCS6D01G360700 chr3B 77.005 187 16 6 3585 3744 172095084 172095270 9.890000e-12 82.4
12 TraesCS6D01G360700 chr3B 77.005 187 16 6 3585 3744 172214528 172214714 9.890000e-12 82.4
13 TraesCS6D01G360700 chr3D 90.675 2874 204 39 622 3476 120142304 120145132 0.000000e+00 3764.0
14 TraesCS6D01G360700 chr3D 91.119 2680 208 18 751 3420 121342036 121339377 0.000000e+00 3603.0
15 TraesCS6D01G360700 chr3D 86.131 411 41 6 3884 4291 120145433 120145830 3.070000e-116 429.0
16 TraesCS6D01G360700 chr3D 79.771 262 13 18 92 320 540131479 540131733 2.070000e-33 154.0
17 TraesCS6D01G360700 chr3D 95.714 70 3 0 700 769 120124735 120124804 3.510000e-21 113.0
18 TraesCS6D01G360700 chr3D 75.373 268 29 20 3584 3824 120134316 120134573 1.270000e-15 95.3
19 TraesCS6D01G360700 chr1D 91.881 2685 179 19 751 3420 465903205 465900545 0.000000e+00 3714.0
20 TraesCS6D01G360700 chr1D 91.701 2675 176 28 843 3513 341029943 341027311 0.000000e+00 3668.0
21 TraesCS6D01G360700 chr1D 84.397 141 8 8 3586 3712 430229272 430229412 4.500000e-25 126.0
22 TraesCS6D01G360700 chr1D 95.082 61 1 2 711 769 430113575 430113635 1.270000e-15 95.3
23 TraesCS6D01G360700 chr1D 93.443 61 4 0 3533 3593 341027373 341027313 1.640000e-14 91.6
24 TraesCS6D01G360700 chr1B 91.704 2688 178 21 751 3420 642701544 642698884 0.000000e+00 3687.0
25 TraesCS6D01G360700 chr1B 91.701 2675 176 25 843 3513 456714230 456711598 0.000000e+00 3668.0
26 TraesCS6D01G360700 chr1B 83.957 187 17 6 92 267 26602462 26602646 2.650000e-37 167.0
27 TraesCS6D01G360700 chr3A 91.673 2678 186 18 751 3412 127858988 127856332 0.000000e+00 3675.0
28 TraesCS6D01G360700 chr3A 92.778 2520 176 6 1072 3587 127071266 127073783 0.000000e+00 3640.0
29 TraesCS6D01G360700 chr3A 88.976 381 23 8 3738 4115 127074147 127074511 1.820000e-123 453.0
30 TraesCS6D01G360700 chr3A 84.127 189 27 3 4101 4288 127074532 127074718 3.410000e-41 180.0
31 TraesCS6D01G360700 chr3A 96.190 105 4 0 3640 3744 127074017 127074121 5.700000e-39 172.0
32 TraesCS6D01G360700 chr3A 98.305 59 1 0 3584 3642 127073825 127073883 2.110000e-18 104.0
33 TraesCS6D01G360700 chr3A 94.737 57 3 0 3531 3587 127073645 127073701 5.910000e-14 89.8
34 TraesCS6D01G360700 chr4D 85.311 354 18 13 1 323 43672991 43672641 6.880000e-88 335.0
35 TraesCS6D01G360700 chr6B 80.075 266 16 16 92 325 72375535 72375795 3.430000e-36 163.0
36 TraesCS6D01G360700 chr4B 79.310 261 17 18 92 320 664091479 664091734 9.610000e-32 148.0
37 TraesCS6D01G360700 chr2A 79.087 263 15 19 92 320 550705478 550705734 1.240000e-30 145.0
38 TraesCS6D01G360700 chr1A 91.803 61 5 0 3533 3593 440712173 440712113 7.650000e-13 86.1


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 TraesCS6D01G360700 chr6D 452124535 452128825 4290 True 7925.000000 7925 100.000000 1 4291 1 chr6D.!!$R1 4290
1 TraesCS6D01G360700 chr5B 507797650 507803416 5766 True 826.383333 3982 91.151667 323 4288 6 chr5B.!!$R2 3965
2 TraesCS6D01G360700 chr3B 172170324 172173044 2720 False 3851.000000 3851 92.213000 622 3355 1 chr3B.!!$F3 2733
3 TraesCS6D01G360700 chr3B 172052028 172054685 2657 False 3760.000000 3760 92.262000 700 3355 1 chr3B.!!$F1 2655
4 TraesCS6D01G360700 chr3B 146979935 146982563 2628 True 3735.000000 3735 92.302000 716 3355 1 chr3B.!!$R1 2639
5 TraesCS6D01G360700 chr3D 121339377 121342036 2659 True 3603.000000 3603 91.119000 751 3420 1 chr3D.!!$R1 2669
6 TraesCS6D01G360700 chr3D 120142304 120145830 3526 False 2096.500000 3764 88.403000 622 4291 2 chr3D.!!$F4 3669
7 TraesCS6D01G360700 chr1D 465900545 465903205 2660 True 3714.000000 3714 91.881000 751 3420 1 chr1D.!!$R1 2669
8 TraesCS6D01G360700 chr1D 341027311 341029943 2632 True 1879.800000 3668 92.572000 843 3593 2 chr1D.!!$R2 2750
9 TraesCS6D01G360700 chr1B 642698884 642701544 2660 True 3687.000000 3687 91.704000 751 3420 1 chr1B.!!$R2 2669
10 TraesCS6D01G360700 chr1B 456711598 456714230 2632 True 3668.000000 3668 91.701000 843 3513 1 chr1B.!!$R1 2670
11 TraesCS6D01G360700 chr3A 127856332 127858988 2656 True 3675.000000 3675 91.673000 751 3412 1 chr3A.!!$R1 2661
12 TraesCS6D01G360700 chr3A 127071266 127074718 3452 False 773.133333 3640 92.518833 1072 4288 6 chr3A.!!$F1 3216

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
139 140 0.107214 CGAGGGGGAAAGCTATGCAA 60.107 55.0 0.0 0.0 0.00 4.08 F
802 823 0.248012 TCAATAAAGGGTGCGAGCGA 59.752 50.0 0.0 0.0 0.00 4.93 F
2107 2149 0.179121 CAAGGATACGCACGGCTACA 60.179 55.0 0.0 0.0 46.39 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1051 1093 0.957395 CCCTTGAGCAGCACGATGTT 60.957 55.0 0.00 0.0 0.00 2.71 R
2739 2782 0.179032 TGGTGGCGCCGATAATGAAT 60.179 50.0 23.90 0.0 41.21 2.57 R
3922 6035 0.039256 AACCGTAAGACGTAAGCGCA 60.039 50.0 11.47 0.0 40.58 6.09 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
51 52 9.988815 TGCATACAATACATATATACACACACA 57.011 29.630 0.00 0.00 0.00 3.72
79 80 8.492673 AATGTCATTGTATATTGAACGTCAGT 57.507 30.769 0.00 0.00 0.00 3.41
80 81 7.289587 TGTCATTGTATATTGAACGTCAGTG 57.710 36.000 0.00 0.00 0.00 3.66
81 82 6.312672 TGTCATTGTATATTGAACGTCAGTGG 59.687 38.462 0.00 0.00 0.00 4.00
82 83 6.533723 GTCATTGTATATTGAACGTCAGTGGA 59.466 38.462 0.00 0.00 0.00 4.02
83 84 7.224753 GTCATTGTATATTGAACGTCAGTGGAT 59.775 37.037 0.00 0.00 0.00 3.41
84 85 7.438160 TCATTGTATATTGAACGTCAGTGGATC 59.562 37.037 0.00 0.00 0.00 3.36
85 86 6.215495 TGTATATTGAACGTCAGTGGATCA 57.785 37.500 0.00 0.00 0.00 2.92
86 87 6.635755 TGTATATTGAACGTCAGTGGATCAA 58.364 36.000 0.00 0.00 34.80 2.57
87 88 7.272244 TGTATATTGAACGTCAGTGGATCAAT 58.728 34.615 12.51 12.51 41.92 2.57
88 89 8.417884 TGTATATTGAACGTCAGTGGATCAATA 58.582 33.333 15.27 15.27 43.29 1.90
89 90 9.424319 GTATATTGAACGTCAGTGGATCAATAT 57.576 33.333 22.90 22.90 46.91 1.28
91 92 7.715265 ATTGAACGTCAGTGGATCAATATAC 57.285 36.000 7.43 0.00 38.55 1.47
92 93 6.465439 TGAACGTCAGTGGATCAATATACT 57.535 37.500 0.00 0.00 0.00 2.12
93 94 7.576861 TGAACGTCAGTGGATCAATATACTA 57.423 36.000 0.00 0.00 0.00 1.82
94 95 8.178313 TGAACGTCAGTGGATCAATATACTAT 57.822 34.615 0.00 0.00 0.00 2.12
95 96 9.292195 TGAACGTCAGTGGATCAATATACTATA 57.708 33.333 0.00 0.00 0.00 1.31
96 97 9.776158 GAACGTCAGTGGATCAATATACTATAG 57.224 37.037 0.00 0.00 0.00 1.31
97 98 7.763356 ACGTCAGTGGATCAATATACTATAGC 58.237 38.462 0.00 0.00 0.00 2.97
98 99 7.148052 ACGTCAGTGGATCAATATACTATAGCC 60.148 40.741 0.00 0.00 0.00 3.93
99 100 7.148069 CGTCAGTGGATCAATATACTATAGCCA 60.148 40.741 0.00 0.00 0.00 4.75
100 101 7.976734 GTCAGTGGATCAATATACTATAGCCAC 59.023 40.741 10.64 10.64 42.58 5.01
104 105 8.138712 GTGGATCAATATACTATAGCCACTAGC 58.861 40.741 11.11 0.00 39.96 3.42
105 106 7.287927 TGGATCAATATACTATAGCCACTAGCC 59.712 40.741 0.00 0.00 45.47 3.93
106 107 6.694877 TCAATATACTATAGCCACTAGCCG 57.305 41.667 0.00 0.00 45.47 5.52
107 108 6.185511 TCAATATACTATAGCCACTAGCCGT 58.814 40.000 0.00 0.00 45.47 5.68
108 109 6.662234 TCAATATACTATAGCCACTAGCCGTT 59.338 38.462 0.00 0.00 45.47 4.44
109 110 4.785511 ATACTATAGCCACTAGCCGTTG 57.214 45.455 0.00 0.00 45.47 4.10
110 111 2.385803 ACTATAGCCACTAGCCGTTGT 58.614 47.619 0.00 0.00 45.47 3.32
111 112 3.559069 ACTATAGCCACTAGCCGTTGTA 58.441 45.455 0.00 0.00 45.47 2.41
112 113 3.956199 ACTATAGCCACTAGCCGTTGTAA 59.044 43.478 0.00 0.00 45.47 2.41
113 114 4.587684 ACTATAGCCACTAGCCGTTGTAAT 59.412 41.667 0.00 0.00 45.47 1.89
114 115 2.781681 AGCCACTAGCCGTTGTAATT 57.218 45.000 0.00 0.00 45.47 1.40
115 116 3.067684 AGCCACTAGCCGTTGTAATTT 57.932 42.857 0.00 0.00 45.47 1.82
116 117 3.418047 AGCCACTAGCCGTTGTAATTTT 58.582 40.909 0.00 0.00 45.47 1.82
117 118 3.824443 AGCCACTAGCCGTTGTAATTTTT 59.176 39.130 0.00 0.00 45.47 1.94
135 136 3.732048 TTTTTCGAGGGGGAAAGCTAT 57.268 42.857 0.00 0.00 37.24 2.97
136 137 2.710096 TTTCGAGGGGGAAAGCTATG 57.290 50.000 0.00 0.00 32.45 2.23
137 138 0.180406 TTCGAGGGGGAAAGCTATGC 59.820 55.000 0.00 0.00 0.00 3.14
138 139 0.980754 TCGAGGGGGAAAGCTATGCA 60.981 55.000 0.00 0.00 0.00 3.96
139 140 0.107214 CGAGGGGGAAAGCTATGCAA 60.107 55.000 0.00 0.00 0.00 4.08
140 141 1.681780 CGAGGGGGAAAGCTATGCAAA 60.682 52.381 0.00 0.00 0.00 3.68
141 142 1.751351 GAGGGGGAAAGCTATGCAAAC 59.249 52.381 0.00 0.00 0.00 2.93
142 143 1.077005 AGGGGGAAAGCTATGCAAACA 59.923 47.619 0.00 0.00 0.00 2.83
143 144 1.204704 GGGGGAAAGCTATGCAAACAC 59.795 52.381 0.00 0.00 0.00 3.32
144 145 2.171003 GGGGAAAGCTATGCAAACACT 58.829 47.619 0.00 0.00 0.00 3.55
145 146 3.352648 GGGGAAAGCTATGCAAACACTA 58.647 45.455 0.00 0.00 0.00 2.74
146 147 3.954258 GGGGAAAGCTATGCAAACACTAT 59.046 43.478 0.00 0.00 0.00 2.12
147 148 5.130350 GGGGAAAGCTATGCAAACACTATA 58.870 41.667 0.00 0.00 0.00 1.31
148 149 5.008712 GGGGAAAGCTATGCAAACACTATAC 59.991 44.000 0.00 0.00 0.00 1.47
149 150 5.823045 GGGAAAGCTATGCAAACACTATACT 59.177 40.000 0.00 0.00 0.00 2.12
150 151 6.990349 GGGAAAGCTATGCAAACACTATACTA 59.010 38.462 0.00 0.00 0.00 1.82
151 152 7.171678 GGGAAAGCTATGCAAACACTATACTAG 59.828 40.741 0.00 0.00 0.00 2.57
152 153 7.926555 GGAAAGCTATGCAAACACTATACTAGA 59.073 37.037 0.00 0.00 0.00 2.43
153 154 8.879342 AAAGCTATGCAAACACTATACTAGAG 57.121 34.615 0.00 0.00 0.00 2.43
154 155 6.451393 AGCTATGCAAACACTATACTAGAGC 58.549 40.000 0.00 0.00 0.00 4.09
155 156 6.040955 AGCTATGCAAACACTATACTAGAGCA 59.959 38.462 0.00 0.00 0.00 4.26
156 157 6.364706 GCTATGCAAACACTATACTAGAGCAG 59.635 42.308 0.00 0.00 32.59 4.24
157 158 5.661056 TGCAAACACTATACTAGAGCAGT 57.339 39.130 0.00 0.00 41.62 4.40
158 159 5.651530 TGCAAACACTATACTAGAGCAGTC 58.348 41.667 0.00 0.00 38.80 3.51
159 160 5.419155 TGCAAACACTATACTAGAGCAGTCT 59.581 40.000 0.00 0.00 38.80 3.24
160 161 6.602009 TGCAAACACTATACTAGAGCAGTCTA 59.398 38.462 0.00 0.00 38.80 2.59
161 162 7.285629 TGCAAACACTATACTAGAGCAGTCTAT 59.714 37.037 0.00 0.00 38.80 1.98
162 163 8.784994 GCAAACACTATACTAGAGCAGTCTATA 58.215 37.037 0.00 0.00 38.80 1.31
173 174 9.558396 ACTAGAGCAGTCTATATTTAACGTAGT 57.442 33.333 0.00 0.00 37.13 2.73
194 195 4.300814 AAAAAGGCTGGCTTGGCT 57.699 50.000 17.73 0.00 45.04 4.75
195 196 1.750297 AAAAAGGCTGGCTTGGCTG 59.250 52.632 17.73 0.00 42.20 4.85
196 197 0.760189 AAAAAGGCTGGCTTGGCTGA 60.760 50.000 17.73 0.00 42.20 4.26
197 198 0.760189 AAAAGGCTGGCTTGGCTGAA 60.760 50.000 17.73 0.00 42.20 3.02
198 199 1.466851 AAAGGCTGGCTTGGCTGAAC 61.467 55.000 17.73 0.00 42.20 3.18
199 200 2.282745 GGCTGGCTTGGCTGAACT 60.283 61.111 5.34 0.00 0.00 3.01
200 201 2.633509 GGCTGGCTTGGCTGAACTG 61.634 63.158 5.34 0.00 0.00 3.16
201 202 2.633509 GCTGGCTTGGCTGAACTGG 61.634 63.158 5.34 0.00 0.00 4.00
202 203 1.073722 CTGGCTTGGCTGAACTGGA 59.926 57.895 0.00 0.00 0.00 3.86
203 204 0.959372 CTGGCTTGGCTGAACTGGAG 60.959 60.000 0.00 0.00 0.00 3.86
204 205 2.338785 GGCTTGGCTGAACTGGAGC 61.339 63.158 0.00 0.00 35.57 4.70
205 206 2.684843 GCTTGGCTGAACTGGAGCG 61.685 63.158 0.00 0.00 37.32 5.03
206 207 2.032528 TTGGCTGAACTGGAGCGG 59.967 61.111 0.00 0.00 37.32 5.52
207 208 2.738213 CTTGGCTGAACTGGAGCGGT 62.738 60.000 0.00 0.00 37.32 5.68
208 209 2.435059 GGCTGAACTGGAGCGGTC 60.435 66.667 5.93 5.93 37.32 4.79
209 210 2.435059 GCTGAACTGGAGCGGTCC 60.435 66.667 26.70 26.70 44.24 4.46
217 218 2.990479 GGAGCGGTCCATCCACTT 59.010 61.111 28.27 0.00 43.31 3.16
218 219 1.450312 GGAGCGGTCCATCCACTTG 60.450 63.158 28.27 0.00 43.31 3.16
219 220 1.296715 GAGCGGTCCATCCACTTGT 59.703 57.895 2.39 0.00 35.57 3.16
220 221 1.003355 AGCGGTCCATCCACTTGTG 60.003 57.895 0.00 0.00 35.57 3.33
221 222 1.302511 GCGGTCCATCCACTTGTGT 60.303 57.895 0.00 0.00 35.57 3.72
222 223 1.577328 GCGGTCCATCCACTTGTGTG 61.577 60.000 0.00 0.00 43.45 3.82
230 231 4.957266 CACTTGTGTGGCTGCATG 57.043 55.556 0.50 0.00 40.33 4.06
231 232 1.372499 CACTTGTGTGGCTGCATGC 60.372 57.895 11.82 11.82 40.33 4.06
232 233 2.126618 CTTGTGTGGCTGCATGCG 60.127 61.111 14.09 9.16 44.05 4.73
233 234 4.345962 TTGTGTGGCTGCATGCGC 62.346 61.111 21.20 21.20 44.05 6.09
240 241 4.899687 GCTGCATGCGCCGATGTG 62.900 66.667 19.44 1.95 37.32 3.21
247 248 2.560861 GCGCCGATGTGCTTCAAA 59.439 55.556 0.00 0.00 44.66 2.69
248 249 1.137404 GCGCCGATGTGCTTCAAAT 59.863 52.632 0.00 0.00 44.66 2.32
249 250 0.863119 GCGCCGATGTGCTTCAAATC 60.863 55.000 0.00 0.00 44.66 2.17
256 257 3.996032 GATGTGCTTCAAATCGACTGAC 58.004 45.455 0.00 0.00 0.00 3.51
257 258 3.111853 TGTGCTTCAAATCGACTGACT 57.888 42.857 0.00 0.00 0.00 3.41
258 259 4.251543 TGTGCTTCAAATCGACTGACTA 57.748 40.909 0.00 0.00 0.00 2.59
259 260 4.627058 TGTGCTTCAAATCGACTGACTAA 58.373 39.130 0.00 0.00 0.00 2.24
260 261 5.053811 TGTGCTTCAAATCGACTGACTAAA 58.946 37.500 0.00 0.00 0.00 1.85
261 262 5.700832 TGTGCTTCAAATCGACTGACTAAAT 59.299 36.000 0.00 0.00 0.00 1.40
262 263 6.204688 TGTGCTTCAAATCGACTGACTAAATT 59.795 34.615 0.00 0.00 0.00 1.82
263 264 7.078228 GTGCTTCAAATCGACTGACTAAATTT 58.922 34.615 0.00 0.00 0.00 1.82
264 265 7.591426 GTGCTTCAAATCGACTGACTAAATTTT 59.409 33.333 0.00 0.00 0.00 1.82
265 266 7.591057 TGCTTCAAATCGACTGACTAAATTTTG 59.409 33.333 0.00 0.00 0.00 2.44
266 267 7.591426 GCTTCAAATCGACTGACTAAATTTTGT 59.409 33.333 4.91 4.91 0.00 2.83
267 268 8.781067 TTCAAATCGACTGACTAAATTTTGTG 57.219 30.769 10.05 0.00 0.00 3.33
268 269 7.359595 TCAAATCGACTGACTAAATTTTGTGG 58.640 34.615 10.05 5.61 0.00 4.17
269 270 6.877611 AATCGACTGACTAAATTTTGTGGT 57.122 33.333 10.05 8.45 0.00 4.16
270 271 5.917541 TCGACTGACTAAATTTTGTGGTC 57.082 39.130 10.05 14.64 0.00 4.02
271 272 5.361427 TCGACTGACTAAATTTTGTGGTCA 58.639 37.500 22.11 17.47 35.90 4.02
275 276 5.666969 TGACTAAATTTTGTGGTCAGTCG 57.333 39.130 10.05 0.00 34.94 4.18
276 277 5.361427 TGACTAAATTTTGTGGTCAGTCGA 58.639 37.500 10.05 0.00 34.94 4.20
277 278 5.235616 TGACTAAATTTTGTGGTCAGTCGAC 59.764 40.000 7.70 7.70 41.80 4.20
278 279 5.365619 ACTAAATTTTGTGGTCAGTCGACT 58.634 37.500 13.58 13.58 42.21 4.18
279 280 4.552166 AAATTTTGTGGTCAGTCGACTG 57.448 40.909 34.76 34.76 45.08 3.51
289 290 2.417339 CAGTCGACTGACCGAAAAGA 57.583 50.000 36.73 0.00 46.74 2.52
290 291 2.739292 CAGTCGACTGACCGAAAAGAA 58.261 47.619 36.73 0.00 46.74 2.52
291 292 3.120792 CAGTCGACTGACCGAAAAGAAA 58.879 45.455 36.73 0.00 46.74 2.52
292 293 3.554324 CAGTCGACTGACCGAAAAGAAAA 59.446 43.478 36.73 0.00 46.74 2.29
293 294 4.033587 CAGTCGACTGACCGAAAAGAAAAA 59.966 41.667 36.73 0.00 46.74 1.94
313 314 5.526506 AAAACAGTCGACTTGTACCTAGT 57.473 39.130 17.26 5.13 0.00 2.57
314 315 4.762956 AACAGTCGACTTGTACCTAGTC 57.237 45.455 17.26 12.79 38.88 2.59
315 316 3.748083 ACAGTCGACTTGTACCTAGTCA 58.252 45.455 17.26 8.61 41.64 3.41
316 317 4.333690 ACAGTCGACTTGTACCTAGTCAT 58.666 43.478 17.26 7.15 41.64 3.06
317 318 4.765856 ACAGTCGACTTGTACCTAGTCATT 59.234 41.667 17.26 6.65 41.64 2.57
318 319 5.106237 ACAGTCGACTTGTACCTAGTCATTC 60.106 44.000 17.26 11.55 41.64 2.67
319 320 4.398673 AGTCGACTTGTACCTAGTCATTCC 59.601 45.833 13.58 8.25 41.64 3.01
320 321 4.157289 GTCGACTTGTACCTAGTCATTCCA 59.843 45.833 19.37 2.08 41.64 3.53
321 322 4.768448 TCGACTTGTACCTAGTCATTCCAA 59.232 41.667 19.37 0.00 41.64 3.53
397 401 1.550976 GTACCTGGACTGGACCTCTTG 59.449 57.143 0.00 0.00 0.00 3.02
407 411 2.847234 ACCTCTTGGGCGTGGACA 60.847 61.111 0.00 0.00 39.10 4.02
431 435 1.079503 CCTAGTTCGCTGGAAAGTGC 58.920 55.000 0.00 0.00 33.05 4.40
432 436 1.338200 CCTAGTTCGCTGGAAAGTGCT 60.338 52.381 0.00 0.00 33.05 4.40
483 487 2.744768 CGCTGCGCCTTCTTCTTCC 61.745 63.158 9.88 0.00 0.00 3.46
503 507 3.711190 TCCACTGCTTCTTGCTGGATATA 59.289 43.478 0.00 0.00 39.95 0.86
504 508 4.164030 TCCACTGCTTCTTGCTGGATATAA 59.836 41.667 0.00 0.00 39.95 0.98
510 514 4.687219 GCTTCTTGCTGGATATAACAGGGT 60.687 45.833 8.50 0.00 38.95 4.34
517 521 1.067776 GGATATAACAGGGTCGGAGCG 60.068 57.143 0.53 0.00 0.00 5.03
529 533 1.521681 CGGAGCGGGTTGAATCTCC 60.522 63.158 0.00 0.00 41.20 3.71
620 629 0.911769 ATCCGATCAAGCAGGACCAA 59.088 50.000 0.00 0.00 36.81 3.67
634 643 3.771160 CCAAGCGGGCGTAGGACT 61.771 66.667 0.00 0.00 0.00 3.85
647 656 3.060866 GGACTCAGTGGCCGTCTT 58.939 61.111 0.00 0.00 31.76 3.01
648 657 1.374758 GGACTCAGTGGCCGTCTTG 60.375 63.158 0.00 0.00 31.76 3.02
649 658 2.029844 GACTCAGTGGCCGTCTTGC 61.030 63.158 0.00 0.00 0.00 4.01
651 660 1.597854 CTCAGTGGCCGTCTTGCAA 60.598 57.895 0.00 0.00 0.00 4.08
687 696 2.186160 CAGCCGGTCTGCACACAAA 61.186 57.895 12.01 0.00 35.78 2.83
800 821 2.832672 CTTCAATAAAGGGTGCGAGC 57.167 50.000 0.00 0.00 0.00 5.03
801 822 1.062587 CTTCAATAAAGGGTGCGAGCG 59.937 52.381 0.00 0.00 0.00 5.03
802 823 0.248012 TCAATAAAGGGTGCGAGCGA 59.752 50.000 0.00 0.00 0.00 4.93
845 871 0.743688 AACACCAACGCAAATCAGCA 59.256 45.000 0.00 0.00 0.00 4.41
885 923 1.584175 ATACACGATCGAGAGACGCT 58.416 50.000 24.34 0.00 46.97 5.07
888 926 2.109739 ACGATCGAGAGACGCTGCT 61.110 57.895 24.34 0.00 46.97 4.24
889 927 1.368731 CGATCGAGAGACGCTGCTC 60.369 63.158 10.26 0.00 46.97 4.26
900 942 4.427661 GCTGCTCGTCGACCAGCT 62.428 66.667 30.65 0.00 46.28 4.24
907 949 2.277969 CTCGTCGACCAGCTAGAGTTA 58.722 52.381 10.58 0.00 0.00 2.24
908 950 2.873472 CTCGTCGACCAGCTAGAGTTAT 59.127 50.000 10.58 0.00 0.00 1.89
909 951 3.276857 TCGTCGACCAGCTAGAGTTATT 58.723 45.455 10.58 0.00 0.00 1.40
910 952 3.064958 TCGTCGACCAGCTAGAGTTATTG 59.935 47.826 10.58 0.00 0.00 1.90
911 953 3.064958 CGTCGACCAGCTAGAGTTATTGA 59.935 47.826 10.58 0.00 0.00 2.57
918 960 4.391830 CCAGCTAGAGTTATTGAAAACGCA 59.608 41.667 0.00 0.00 34.46 5.24
1000 1042 1.001048 CCACCAACGACGACAACTCTA 60.001 52.381 0.00 0.00 0.00 2.43
1051 1093 3.939740 AGCTCTCCATATTCAAAGGCA 57.060 42.857 0.00 0.00 0.00 4.75
1136 1178 2.032528 CGAGGGGCACAAGCTCAA 59.967 61.111 0.00 0.00 45.55 3.02
1198 1240 4.196108 ACGTCGTGTCCGTGCACA 62.196 61.111 18.64 0.00 39.19 4.57
1404 1446 2.415608 GGAGATCGACCCTGCGACA 61.416 63.158 0.00 0.00 43.79 4.35
1944 1986 1.227438 CACGAACCGTCCCAACAGT 60.227 57.895 0.00 0.00 38.32 3.55
2107 2149 0.179121 CAAGGATACGCACGGCTACA 60.179 55.000 0.00 0.00 46.39 2.74
2226 2269 2.158986 CGAGATCTTGAACTCCATGGCT 60.159 50.000 6.96 0.00 0.00 4.75
2296 2339 1.572941 CTTCGTGAGACCGTCGTCA 59.427 57.895 0.00 0.00 41.87 4.35
2353 2396 2.600769 ACGGCGTCAAGAGGGAGT 60.601 61.111 6.77 0.00 0.00 3.85
2385 2428 2.423898 CCAGTACCCGGTCGAGCAT 61.424 63.158 15.89 1.78 0.00 3.79
2514 2557 1.822990 CAGGCCAACTTCATCAGCATT 59.177 47.619 5.01 0.00 0.00 3.56
2596 2639 1.211969 GACAAGGCGCGTCAGTCTA 59.788 57.895 23.37 0.00 33.43 2.59
2739 2782 4.944962 CATGAATGCAAAGAAGACGGTA 57.055 40.909 0.00 0.00 0.00 4.02
2745 2788 6.150976 TGAATGCAAAGAAGACGGTATTCATT 59.849 34.615 16.87 8.97 30.84 2.57
3021 3065 4.479993 ACATGGAGCGGCAGAGGC 62.480 66.667 1.45 0.00 40.13 4.70
3099 3144 1.816863 AAAGGCGGCTCACTTCGAGA 61.817 55.000 13.70 0.00 45.45 4.04
3254 3299 4.736896 GCCGTCCACACCTCGACC 62.737 72.222 0.00 0.00 0.00 4.79
3294 3339 4.174009 AGACGATTTGTACAAGTGATCCG 58.826 43.478 8.51 8.16 0.00 4.18
3321 3366 9.836076 GTAACCATTGTTAGAAAATGAAGTACC 57.164 33.333 0.00 0.00 37.62 3.34
3378 3437 6.218746 TGTTTCCTCTCATCGATCATGTATG 58.781 40.000 0.00 0.00 33.66 2.39
3476 3566 2.877043 AAGCTCCTTGTTGTGCTTTG 57.123 45.000 0.00 0.00 42.22 2.77
3477 3567 1.767759 AGCTCCTTGTTGTGCTTTGT 58.232 45.000 0.00 0.00 30.96 2.83
3490 3600 5.991328 TGTGCTTTGTTAGACTCTGAAAG 57.009 39.130 0.00 0.00 0.00 2.62
3535 3645 3.985279 TGTCGATTACACGGAACTGAAAG 59.015 43.478 0.00 0.00 34.03 2.62
3687 5765 2.464157 ACTTGTAAGAGAGCACCTGC 57.536 50.000 0.00 0.00 42.49 4.85
3740 5819 8.150945 TCTTAGTTGCAGAGAGTTCTTTGTTAT 58.849 33.333 2.20 0.00 31.41 1.89
3744 5823 5.240891 TGCAGAGAGTTCTTTGTTATCCAG 58.759 41.667 2.20 0.00 31.41 3.86
3745 5824 4.633565 GCAGAGAGTTCTTTGTTATCCAGG 59.366 45.833 2.20 0.00 31.41 4.45
3746 5825 4.633565 CAGAGAGTTCTTTGTTATCCAGGC 59.366 45.833 0.00 0.00 0.00 4.85
3747 5826 3.942115 GAGAGTTCTTTGTTATCCAGGCC 59.058 47.826 0.00 0.00 0.00 5.19
3748 5827 3.330701 AGAGTTCTTTGTTATCCAGGCCA 59.669 43.478 5.01 0.00 0.00 5.36
3749 5828 4.079253 GAGTTCTTTGTTATCCAGGCCAA 58.921 43.478 5.01 0.00 0.00 4.52
3750 5829 4.677182 AGTTCTTTGTTATCCAGGCCAAT 58.323 39.130 5.01 0.00 0.00 3.16
3778 5890 7.653647 GTTGTACCCAACTGAATGTTATTCAA 58.346 34.615 5.82 0.00 46.07 2.69
3794 5906 2.597510 AACCCGGCCTTTCACAGC 60.598 61.111 0.00 0.00 0.00 4.40
3810 5922 0.170561 CAGCATGCTCTTCCTGTTGC 59.829 55.000 19.68 0.00 0.00 4.17
3847 5959 0.170561 GCTTGCTTGGTGCTCATGAG 59.829 55.000 18.84 18.84 43.37 2.90
3848 5960 1.531423 CTTGCTTGGTGCTCATGAGT 58.469 50.000 23.38 0.00 43.37 3.41
3849 5961 1.467734 CTTGCTTGGTGCTCATGAGTC 59.532 52.381 23.38 15.78 43.37 3.36
3850 5962 0.397564 TGCTTGGTGCTCATGAGTCA 59.602 50.000 23.38 18.03 43.37 3.41
3851 5963 1.003928 TGCTTGGTGCTCATGAGTCAT 59.996 47.619 23.38 0.00 43.37 3.06
3852 5964 1.400846 GCTTGGTGCTCATGAGTCATG 59.599 52.381 24.60 24.60 42.60 3.07
3853 5965 2.938314 GCTTGGTGCTCATGAGTCATGA 60.938 50.000 29.39 29.39 46.84 3.07
3854 5966 2.391616 TGGTGCTCATGAGTCATGAC 57.608 50.000 28.18 23.43 44.60 3.06
3921 6034 5.005094 TGCTCATGATCACATTCACAGAAA 58.995 37.500 0.00 0.00 34.15 2.52
3922 6035 5.650703 TGCTCATGATCACATTCACAGAAAT 59.349 36.000 0.00 0.00 34.15 2.17
3923 6036 5.971792 GCTCATGATCACATTCACAGAAATG 59.028 40.000 0.00 0.00 41.46 2.32
3924 6037 5.886992 TCATGATCACATTCACAGAAATGC 58.113 37.500 0.00 0.00 39.72 3.56
3925 6038 4.345271 TGATCACATTCACAGAAATGCG 57.655 40.909 0.00 0.00 39.72 4.73
3926 6039 2.617250 TCACATTCACAGAAATGCGC 57.383 45.000 0.00 0.00 39.72 6.09
3927 6040 2.153645 TCACATTCACAGAAATGCGCT 58.846 42.857 9.73 0.00 39.72 5.92
3928 6041 2.553602 TCACATTCACAGAAATGCGCTT 59.446 40.909 9.73 0.00 39.72 4.68
3929 6042 3.750652 TCACATTCACAGAAATGCGCTTA 59.249 39.130 9.73 0.00 39.72 3.09
3930 6043 3.848019 CACATTCACAGAAATGCGCTTAC 59.152 43.478 9.73 0.38 39.72 2.34
3931 6044 2.873170 TTCACAGAAATGCGCTTACG 57.127 45.000 9.73 0.00 44.07 3.18
3932 6045 1.790755 TCACAGAAATGCGCTTACGT 58.209 45.000 9.73 0.00 42.83 3.57
4014 6130 9.757227 CTCATAAGTTACTCTAGGAATTGAAGG 57.243 37.037 0.00 0.00 0.00 3.46
4039 6156 8.954350 GGGTTAAATTACTTTCTAAGTTCCTCC 58.046 37.037 0.00 0.00 42.81 4.30
4047 6164 7.006865 ACTTTCTAAGTTCCTCCTTAAGGTC 57.993 40.000 21.04 8.03 39.04 3.85
4049 6166 6.607004 TTCTAAGTTCCTCCTTAAGGTCTG 57.393 41.667 21.04 12.09 46.32 3.51
4052 6169 5.491323 AAGTTCCTCCTTAAGGTCTGAAG 57.509 43.478 21.04 10.46 46.32 3.02
4090 6207 0.606401 CGGAGTGGCCACTGTCATTT 60.606 55.000 42.40 17.89 42.66 2.32
4091 6208 1.620822 GGAGTGGCCACTGTCATTTT 58.379 50.000 42.40 17.04 42.66 1.82
4131 6283 4.704833 TCCCGCTGCCAGCTCAAC 62.705 66.667 15.80 0.00 39.60 3.18
4138 6290 1.809651 GCTGCCAGCTCAACTAGATCC 60.810 57.143 10.04 0.00 38.45 3.36
4139 6291 0.833287 TGCCAGCTCAACTAGATCCC 59.167 55.000 0.00 0.00 0.00 3.85
4183 6336 3.005554 AGATTGAATTCCAGTGCACTCG 58.994 45.455 18.64 11.51 0.00 4.18
4202 6355 1.451651 CGTGCAGCGGAAAATTTTGTC 59.548 47.619 8.47 0.00 36.85 3.18
4236 6389 4.207165 ACACTTGTGTTCTATGTGGCTTT 58.793 39.130 0.00 0.00 33.44 3.51
4243 6396 4.927425 GTGTTCTATGTGGCTTTCGAGTTA 59.073 41.667 0.00 0.00 0.00 2.24
4246 6399 4.119862 TCTATGTGGCTTTCGAGTTATGC 58.880 43.478 0.00 0.00 0.00 3.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 9.988815 TGTGTGTGTATATATGTATTGTATGCA 57.011 29.630 0.00 0.00 0.00 3.96
53 54 8.946085 ACTGACGTTCAATATACAATGACATTT 58.054 29.630 0.00 0.00 0.00 2.32
54 55 8.390354 CACTGACGTTCAATATACAATGACATT 58.610 33.333 0.00 0.00 0.00 2.71
55 56 7.011389 CCACTGACGTTCAATATACAATGACAT 59.989 37.037 0.00 0.00 0.00 3.06
56 57 6.312672 CCACTGACGTTCAATATACAATGACA 59.687 38.462 0.00 0.00 0.00 3.58
57 58 6.533723 TCCACTGACGTTCAATATACAATGAC 59.466 38.462 0.00 0.00 0.00 3.06
58 59 6.635755 TCCACTGACGTTCAATATACAATGA 58.364 36.000 0.00 0.00 0.00 2.57
59 60 6.902224 TCCACTGACGTTCAATATACAATG 57.098 37.500 0.00 0.00 0.00 2.82
60 61 7.272244 TGATCCACTGACGTTCAATATACAAT 58.728 34.615 0.00 0.00 0.00 2.71
61 62 6.635755 TGATCCACTGACGTTCAATATACAA 58.364 36.000 0.00 0.00 0.00 2.41
62 63 6.215495 TGATCCACTGACGTTCAATATACA 57.785 37.500 0.00 0.00 0.00 2.29
63 64 7.715265 ATTGATCCACTGACGTTCAATATAC 57.285 36.000 7.43 0.00 35.77 1.47
65 66 9.424319 GTATATTGATCCACTGACGTTCAATAT 57.576 33.333 22.90 22.90 45.21 1.28
66 67 8.638873 AGTATATTGATCCACTGACGTTCAATA 58.361 33.333 15.27 15.27 41.14 1.90
67 68 7.500992 AGTATATTGATCCACTGACGTTCAAT 58.499 34.615 12.51 12.51 39.58 2.57
68 69 6.873997 AGTATATTGATCCACTGACGTTCAA 58.126 36.000 0.00 0.00 0.00 2.69
69 70 6.465439 AGTATATTGATCCACTGACGTTCA 57.535 37.500 0.00 0.00 0.00 3.18
70 71 9.776158 CTATAGTATATTGATCCACTGACGTTC 57.224 37.037 0.00 0.00 0.00 3.95
71 72 8.244802 GCTATAGTATATTGATCCACTGACGTT 58.755 37.037 0.84 0.00 0.00 3.99
72 73 7.148052 GGCTATAGTATATTGATCCACTGACGT 60.148 40.741 0.84 0.00 0.00 4.34
73 74 7.148069 TGGCTATAGTATATTGATCCACTGACG 60.148 40.741 0.84 0.00 0.00 4.35
74 75 7.976734 GTGGCTATAGTATATTGATCCACTGAC 59.023 40.741 11.11 0.00 38.61 3.51
75 76 7.895962 AGTGGCTATAGTATATTGATCCACTGA 59.104 37.037 17.10 0.00 46.83 3.41
76 77 8.072321 AGTGGCTATAGTATATTGATCCACTG 57.928 38.462 17.10 0.00 46.83 3.66
78 79 8.138712 GCTAGTGGCTATAGTATATTGATCCAC 58.861 40.741 10.64 10.64 41.11 4.02
79 80 7.287927 GGCTAGTGGCTATAGTATATTGATCCA 59.712 40.741 0.84 0.00 41.46 3.41
80 81 7.522399 CGGCTAGTGGCTATAGTATATTGATCC 60.522 44.444 0.84 0.00 41.46 3.36
81 82 7.013464 ACGGCTAGTGGCTATAGTATATTGATC 59.987 40.741 0.84 0.00 41.46 2.92
82 83 6.834451 ACGGCTAGTGGCTATAGTATATTGAT 59.166 38.462 0.84 0.00 41.46 2.57
83 84 6.185511 ACGGCTAGTGGCTATAGTATATTGA 58.814 40.000 0.84 0.00 41.46 2.57
84 85 6.452494 ACGGCTAGTGGCTATAGTATATTG 57.548 41.667 0.84 0.00 41.46 1.90
85 86 6.436532 ACAACGGCTAGTGGCTATAGTATATT 59.563 38.462 0.84 0.00 41.46 1.28
86 87 5.950549 ACAACGGCTAGTGGCTATAGTATAT 59.049 40.000 0.84 0.00 41.46 0.86
87 88 5.319453 ACAACGGCTAGTGGCTATAGTATA 58.681 41.667 0.84 0.00 41.46 1.47
88 89 4.150359 ACAACGGCTAGTGGCTATAGTAT 58.850 43.478 0.84 0.00 41.46 2.12
89 90 3.559069 ACAACGGCTAGTGGCTATAGTA 58.441 45.455 0.84 0.00 41.46 1.82
90 91 2.385803 ACAACGGCTAGTGGCTATAGT 58.614 47.619 0.84 0.00 41.46 2.12
91 92 4.579454 TTACAACGGCTAGTGGCTATAG 57.421 45.455 0.00 0.00 41.46 1.31
92 93 5.540400 AATTACAACGGCTAGTGGCTATA 57.460 39.130 0.00 0.00 41.46 1.31
93 94 4.417426 AATTACAACGGCTAGTGGCTAT 57.583 40.909 0.00 0.00 41.46 2.97
94 95 3.899052 AATTACAACGGCTAGTGGCTA 57.101 42.857 0.00 0.00 41.46 3.93
95 96 2.781681 AATTACAACGGCTAGTGGCT 57.218 45.000 0.00 0.00 41.46 4.75
96 97 3.842732 AAAATTACAACGGCTAGTGGC 57.157 42.857 0.00 0.00 40.90 5.01
115 116 3.352648 CATAGCTTTCCCCCTCGAAAAA 58.647 45.455 0.00 0.00 31.56 1.94
116 117 2.944094 GCATAGCTTTCCCCCTCGAAAA 60.944 50.000 0.00 0.00 31.56 2.29
117 118 1.408266 GCATAGCTTTCCCCCTCGAAA 60.408 52.381 0.00 0.00 0.00 3.46
118 119 0.180406 GCATAGCTTTCCCCCTCGAA 59.820 55.000 0.00 0.00 0.00 3.71
119 120 0.980754 TGCATAGCTTTCCCCCTCGA 60.981 55.000 0.00 0.00 0.00 4.04
120 121 0.107214 TTGCATAGCTTTCCCCCTCG 60.107 55.000 0.00 0.00 0.00 4.63
121 122 1.751351 GTTTGCATAGCTTTCCCCCTC 59.249 52.381 0.00 0.00 0.00 4.30
122 123 1.077005 TGTTTGCATAGCTTTCCCCCT 59.923 47.619 0.00 0.00 0.00 4.79
123 124 1.204704 GTGTTTGCATAGCTTTCCCCC 59.795 52.381 0.00 0.00 0.00 5.40
124 125 2.171003 AGTGTTTGCATAGCTTTCCCC 58.829 47.619 0.00 0.00 0.00 4.81
125 126 5.823045 AGTATAGTGTTTGCATAGCTTTCCC 59.177 40.000 0.00 0.00 0.00 3.97
126 127 6.927294 AGTATAGTGTTTGCATAGCTTTCC 57.073 37.500 0.00 0.00 0.00 3.13
127 128 8.873215 TCTAGTATAGTGTTTGCATAGCTTTC 57.127 34.615 0.00 0.00 40.38 2.62
128 129 7.439655 GCTCTAGTATAGTGTTTGCATAGCTTT 59.560 37.037 0.00 0.00 40.38 3.51
129 130 6.926272 GCTCTAGTATAGTGTTTGCATAGCTT 59.074 38.462 0.00 0.00 40.38 3.74
130 131 6.040955 TGCTCTAGTATAGTGTTTGCATAGCT 59.959 38.462 0.00 0.00 40.38 3.32
131 132 6.216569 TGCTCTAGTATAGTGTTTGCATAGC 58.783 40.000 0.00 0.00 40.38 2.97
132 133 7.429633 ACTGCTCTAGTATAGTGTTTGCATAG 58.570 38.462 0.00 0.00 40.38 2.23
133 134 7.285629 AGACTGCTCTAGTATAGTGTTTGCATA 59.714 37.037 0.00 0.00 40.53 3.14
134 135 6.097554 AGACTGCTCTAGTATAGTGTTTGCAT 59.902 38.462 0.00 0.00 40.53 3.96
135 136 5.419155 AGACTGCTCTAGTATAGTGTTTGCA 59.581 40.000 0.00 0.00 40.53 4.08
136 137 5.897050 AGACTGCTCTAGTATAGTGTTTGC 58.103 41.667 0.00 0.00 40.53 3.68
147 148 9.558396 ACTACGTTAAATATAGACTGCTCTAGT 57.442 33.333 0.00 0.00 44.02 2.57
177 178 0.760189 TCAGCCAAGCCAGCCTTTTT 60.760 50.000 0.00 0.00 0.00 1.94
178 179 0.760189 TTCAGCCAAGCCAGCCTTTT 60.760 50.000 0.00 0.00 0.00 2.27
179 180 1.152483 TTCAGCCAAGCCAGCCTTT 60.152 52.632 0.00 0.00 0.00 3.11
180 181 1.905354 GTTCAGCCAAGCCAGCCTT 60.905 57.895 0.00 0.00 0.00 4.35
181 182 2.282745 GTTCAGCCAAGCCAGCCT 60.283 61.111 0.00 0.00 0.00 4.58
182 183 2.282745 AGTTCAGCCAAGCCAGCC 60.283 61.111 0.00 0.00 0.00 4.85
183 184 2.633509 CCAGTTCAGCCAAGCCAGC 61.634 63.158 0.00 0.00 0.00 4.85
184 185 0.959372 CTCCAGTTCAGCCAAGCCAG 60.959 60.000 0.00 0.00 0.00 4.85
185 186 1.073722 CTCCAGTTCAGCCAAGCCA 59.926 57.895 0.00 0.00 0.00 4.75
186 187 2.338785 GCTCCAGTTCAGCCAAGCC 61.339 63.158 0.00 0.00 0.00 4.35
187 188 2.684843 CGCTCCAGTTCAGCCAAGC 61.685 63.158 0.00 0.00 32.83 4.01
188 189 2.037136 CCGCTCCAGTTCAGCCAAG 61.037 63.158 0.00 0.00 32.83 3.61
189 190 2.032528 CCGCTCCAGTTCAGCCAA 59.967 61.111 0.00 0.00 32.83 4.52
190 191 3.240134 GACCGCTCCAGTTCAGCCA 62.240 63.158 0.00 0.00 32.83 4.75
191 192 2.435059 GACCGCTCCAGTTCAGCC 60.435 66.667 0.00 0.00 32.83 4.85
192 193 2.435059 GGACCGCTCCAGTTCAGC 60.435 66.667 0.00 0.00 36.42 4.26
193 194 3.059982 TGGACCGCTCCAGTTCAG 58.940 61.111 0.00 0.00 42.15 3.02
204 205 2.543578 CACACAAGTGGATGGACCG 58.456 57.895 5.08 0.00 42.13 4.79
213 214 1.372499 GCATGCAGCCACACAAGTG 60.372 57.895 14.21 0.00 45.47 3.16
214 215 2.911484 CGCATGCAGCCACACAAGT 61.911 57.895 19.57 0.00 41.38 3.16
215 216 2.126618 CGCATGCAGCCACACAAG 60.127 61.111 19.57 0.00 41.38 3.16
216 217 4.345962 GCGCATGCAGCCACACAA 62.346 61.111 19.57 0.00 42.15 3.33
223 224 4.899687 CACATCGGCGCATGCAGC 62.900 66.667 19.57 20.53 45.35 5.25
224 225 4.899687 GCACATCGGCGCATGCAG 62.900 66.667 19.57 11.69 45.35 4.41
226 227 4.183686 AAGCACATCGGCGCATGC 62.184 61.111 10.83 18.12 39.27 4.06
227 228 2.023741 GAAGCACATCGGCGCATG 59.976 61.111 10.83 8.11 39.27 4.06
228 229 1.585267 TTTGAAGCACATCGGCGCAT 61.585 50.000 10.83 0.00 39.27 4.73
229 230 1.585267 ATTTGAAGCACATCGGCGCA 61.585 50.000 10.83 0.00 39.27 6.09
230 231 0.863119 GATTTGAAGCACATCGGCGC 60.863 55.000 0.00 0.00 39.27 6.53
231 232 0.587242 CGATTTGAAGCACATCGGCG 60.587 55.000 0.00 0.00 39.43 6.46
232 233 0.726827 TCGATTTGAAGCACATCGGC 59.273 50.000 13.78 0.00 42.14 5.54
233 234 2.002586 AGTCGATTTGAAGCACATCGG 58.997 47.619 13.78 0.00 42.14 4.18
234 235 2.667969 TCAGTCGATTTGAAGCACATCG 59.332 45.455 9.06 9.06 42.89 3.84
235 236 3.681897 AGTCAGTCGATTTGAAGCACATC 59.318 43.478 4.41 0.00 0.00 3.06
236 237 3.668447 AGTCAGTCGATTTGAAGCACAT 58.332 40.909 4.41 0.00 0.00 3.21
237 238 3.111853 AGTCAGTCGATTTGAAGCACA 57.888 42.857 4.41 0.00 0.00 4.57
238 239 5.591643 TTTAGTCAGTCGATTTGAAGCAC 57.408 39.130 4.41 0.00 0.00 4.40
239 240 6.801539 AATTTAGTCAGTCGATTTGAAGCA 57.198 33.333 4.41 0.00 0.00 3.91
240 241 7.591426 ACAAAATTTAGTCAGTCGATTTGAAGC 59.409 33.333 7.56 0.00 32.45 3.86
241 242 8.895845 CACAAAATTTAGTCAGTCGATTTGAAG 58.104 33.333 7.56 0.00 32.45 3.02
242 243 7.860373 CCACAAAATTTAGTCAGTCGATTTGAA 59.140 33.333 7.56 0.00 32.45 2.69
243 244 7.012894 ACCACAAAATTTAGTCAGTCGATTTGA 59.987 33.333 7.56 3.64 32.45 2.69
244 245 7.138736 ACCACAAAATTTAGTCAGTCGATTTG 58.861 34.615 0.00 0.00 33.85 2.32
245 246 7.012894 TGACCACAAAATTTAGTCAGTCGATTT 59.987 33.333 8.41 0.00 32.75 2.17
246 247 6.485313 TGACCACAAAATTTAGTCAGTCGATT 59.515 34.615 8.41 0.00 32.75 3.34
247 248 5.995282 TGACCACAAAATTTAGTCAGTCGAT 59.005 36.000 8.41 0.00 32.75 3.59
248 249 5.361427 TGACCACAAAATTTAGTCAGTCGA 58.639 37.500 8.41 0.00 32.75 4.20
249 250 5.666969 TGACCACAAAATTTAGTCAGTCG 57.333 39.130 8.41 0.00 32.75 4.18
253 254 5.235616 GTCGACTGACCACAAAATTTAGTCA 59.764 40.000 8.70 11.85 39.30 3.41
254 255 5.465724 AGTCGACTGACCACAAAATTTAGTC 59.534 40.000 19.30 5.35 46.74 2.59
255 256 5.236478 CAGTCGACTGACCACAAAATTTAGT 59.764 40.000 36.73 0.00 46.74 2.24
256 257 5.679906 CAGTCGACTGACCACAAAATTTAG 58.320 41.667 36.73 6.86 46.74 1.85
257 258 5.666969 CAGTCGACTGACCACAAAATTTA 57.333 39.130 36.73 0.00 46.74 1.40
258 259 4.552166 CAGTCGACTGACCACAAAATTT 57.448 40.909 36.73 0.00 46.74 1.82
271 272 3.447918 TTTCTTTTCGGTCAGTCGACT 57.552 42.857 13.58 13.58 42.21 4.18
272 273 4.525411 TTTTTCTTTTCGGTCAGTCGAC 57.475 40.909 7.70 7.70 39.01 4.20
290 291 5.910614 ACTAGGTACAAGTCGACTGTTTTT 58.089 37.500 20.85 0.00 0.00 1.94
291 292 5.068198 TGACTAGGTACAAGTCGACTGTTTT 59.932 40.000 20.85 0.00 45.19 2.43
292 293 4.581824 TGACTAGGTACAAGTCGACTGTTT 59.418 41.667 20.85 8.92 45.19 2.83
293 294 4.139786 TGACTAGGTACAAGTCGACTGTT 58.860 43.478 20.85 11.61 45.19 3.16
294 295 3.748083 TGACTAGGTACAAGTCGACTGT 58.252 45.455 20.85 20.07 45.19 3.55
295 296 4.966965 ATGACTAGGTACAAGTCGACTG 57.033 45.455 20.85 15.37 45.19 3.51
296 297 4.398673 GGAATGACTAGGTACAAGTCGACT 59.601 45.833 13.58 13.58 45.19 4.18
297 298 4.157289 TGGAATGACTAGGTACAAGTCGAC 59.843 45.833 7.70 7.70 45.19 4.20
298 299 4.338012 TGGAATGACTAGGTACAAGTCGA 58.662 43.478 17.77 10.56 45.19 4.20
299 300 4.713824 TGGAATGACTAGGTACAAGTCG 57.286 45.455 17.77 0.00 45.19 4.18
300 301 7.739498 TTTTTGGAATGACTAGGTACAAGTC 57.261 36.000 16.71 16.71 43.04 3.01
334 335 9.449719 CTGTAAGGTCTGATTTTGGTATTAACT 57.550 33.333 0.00 0.00 0.00 2.24
357 361 1.331756 CGTCTTCAGTTTTGCTGCTGT 59.668 47.619 0.00 0.00 44.66 4.40
373 377 0.611340 GGTCCAGTCCAGGTACGTCT 60.611 60.000 0.00 0.00 0.00 4.18
374 378 0.611340 AGGTCCAGTCCAGGTACGTC 60.611 60.000 0.00 0.00 0.00 4.34
381 385 1.986413 CCCAAGAGGTCCAGTCCAG 59.014 63.158 0.00 0.00 0.00 3.86
407 411 1.327690 TTCCAGCGAACTAGGGCGAT 61.328 55.000 10.20 1.32 0.00 4.58
467 471 0.321122 AGTGGAAGAAGAAGGCGCAG 60.321 55.000 10.83 0.00 0.00 5.18
468 472 0.603707 CAGTGGAAGAAGAAGGCGCA 60.604 55.000 10.83 0.00 0.00 6.09
469 473 1.916697 GCAGTGGAAGAAGAAGGCGC 61.917 60.000 0.00 0.00 0.00 6.53
470 474 0.321122 AGCAGTGGAAGAAGAAGGCG 60.321 55.000 0.00 0.00 0.00 5.52
471 475 1.809547 GAAGCAGTGGAAGAAGAAGGC 59.190 52.381 0.00 0.00 0.00 4.35
472 476 3.415457 AGAAGCAGTGGAAGAAGAAGG 57.585 47.619 0.00 0.00 0.00 3.46
473 477 3.058363 GCAAGAAGCAGTGGAAGAAGAAG 60.058 47.826 0.00 0.00 44.79 2.85
474 478 2.880890 GCAAGAAGCAGTGGAAGAAGAA 59.119 45.455 0.00 0.00 44.79 2.52
475 479 2.498167 GCAAGAAGCAGTGGAAGAAGA 58.502 47.619 0.00 0.00 44.79 2.87
510 514 1.515954 GAGATTCAACCCGCTCCGA 59.484 57.895 0.00 0.00 0.00 4.55
517 521 0.608035 TGTTGCCGGAGATTCAACCC 60.608 55.000 5.05 0.00 39.30 4.11
529 533 2.404789 GCCACGATGATGTTGCCG 59.595 61.111 0.00 0.00 0.00 5.69
613 622 3.771160 CTACGCCCGCTTGGTCCT 61.771 66.667 0.00 0.00 36.04 3.85
615 624 3.766691 TCCTACGCCCGCTTGGTC 61.767 66.667 0.00 0.00 36.04 4.02
616 625 4.078516 GTCCTACGCCCGCTTGGT 62.079 66.667 0.00 0.00 36.04 3.67
620 629 3.141488 CTGAGTCCTACGCCCGCT 61.141 66.667 0.00 0.00 0.00 5.52
634 643 1.597854 CTTGCAAGACGGCCACTGA 60.598 57.895 22.31 0.00 0.00 3.41
647 656 1.412079 AACCAAATCCTGTGCTTGCA 58.588 45.000 0.00 0.00 0.00 4.08
648 657 2.137523 CAAACCAAATCCTGTGCTTGC 58.862 47.619 0.00 0.00 0.00 4.01
649 658 2.137523 GCAAACCAAATCCTGTGCTTG 58.862 47.619 0.00 0.00 0.00 4.01
651 660 1.342174 CTGCAAACCAAATCCTGTGCT 59.658 47.619 0.00 0.00 33.19 4.40
799 820 3.998672 TGGAGACGTGGGGTTCGC 61.999 66.667 0.00 0.00 0.00 4.70
800 821 2.048503 GTGGAGACGTGGGGTTCG 60.049 66.667 0.00 0.00 0.00 3.95
801 822 2.168666 GAGGTGGAGACGTGGGGTTC 62.169 65.000 0.00 0.00 0.00 3.62
802 823 2.122547 AGGTGGAGACGTGGGGTT 60.123 61.111 0.00 0.00 0.00 4.11
845 871 1.633774 ACTCTCGTTGGATGTGGAGT 58.366 50.000 0.00 0.00 0.00 3.85
888 926 2.391616 TAACTCTAGCTGGTCGACGA 57.608 50.000 9.92 4.47 0.00 4.20
889 927 3.064958 TCAATAACTCTAGCTGGTCGACG 59.935 47.826 9.92 0.00 0.00 5.12
900 942 5.636837 GCCATTGCGTTTTCAATAACTCTA 58.363 37.500 0.00 0.00 35.12 2.43
1000 1042 4.033776 CGGGTGGAGGGTGCACAT 62.034 66.667 20.43 6.31 40.73 3.21
1051 1093 0.957395 CCCTTGAGCAGCACGATGTT 60.957 55.000 0.00 0.00 0.00 2.71
1136 1178 1.002134 CGGGCCACCTTGTTGATCT 60.002 57.895 4.39 0.00 33.28 2.75
1339 1381 2.357034 GCCACGCACGAGGAAGAA 60.357 61.111 10.80 0.00 0.00 2.52
1404 1446 1.139734 CGCCACGATGCAGTACTCT 59.860 57.895 0.00 0.00 0.00 3.24
1497 1539 3.621805 ATGCCACCCACGTCGTCA 61.622 61.111 0.00 0.00 0.00 4.35
1944 1986 2.516448 CCTCAAGGCAGGGTCGATA 58.484 57.895 0.00 0.00 0.00 2.92
2353 2396 1.000506 GTACTGGACGGTCTCTTGCAA 59.999 52.381 8.23 0.00 0.00 4.08
2514 2557 2.285668 AGCAGCTCTGGCCCCTTA 60.286 61.111 0.00 0.00 39.73 2.69
2559 2602 0.860203 CGAAGATCTCGCGCACGTTA 60.860 55.000 8.75 0.00 41.49 3.18
2727 2770 5.465724 GCCGATAATGAATACCGTCTTCTTT 59.534 40.000 0.00 1.87 0.00 2.52
2739 2782 0.179032 TGGTGGCGCCGATAATGAAT 60.179 50.000 23.90 0.00 41.21 2.57
2745 2788 1.369692 CCTATTGGTGGCGCCGATA 59.630 57.895 23.90 22.64 41.57 2.92
3021 3065 0.698238 TCCATGGTGTCTTTCCCCAG 59.302 55.000 12.58 0.00 0.00 4.45
3053 3098 0.252467 CCACCTCCTCCTCTTCCTGT 60.252 60.000 0.00 0.00 0.00 4.00
3099 3144 1.202154 CCTCGCGTACTTCATCGACTT 60.202 52.381 5.77 0.00 0.00 3.01
3251 3296 0.879400 CATCCTCATCAGCTGCGGTC 60.879 60.000 9.47 0.00 31.27 4.79
3254 3299 1.202498 TCTTCATCCTCATCAGCTGCG 60.202 52.381 9.47 2.31 0.00 5.18
3294 3339 9.836076 GTACTTCATTTTCTAACAATGGTTACC 57.164 33.333 0.00 0.00 38.45 2.85
3476 3566 4.729227 AGGCTAGCTTTCAGAGTCTAAC 57.271 45.455 15.72 0.00 0.00 2.34
3477 3567 5.163499 GCTTAGGCTAGCTTTCAGAGTCTAA 60.163 44.000 15.72 9.05 35.56 2.10
3490 3600 3.160777 TCAGTTAACGCTTAGGCTAGC 57.839 47.619 6.04 6.04 37.80 3.42
3535 3645 5.631096 GGAAAGCACAACAAGAAGCTTATTC 59.369 40.000 2.67 0.00 45.73 1.75
3687 5765 4.825422 TGAGAGCCATAAGTTTCAGACAG 58.175 43.478 0.00 0.00 0.00 3.51
3740 5819 1.549037 GGTACAACCAATTGGCCTGGA 60.549 52.381 24.79 15.65 40.42 3.86
3744 5823 1.343069 TTGGGTACAACCAATTGGCC 58.657 50.000 24.79 16.14 45.19 5.36
3778 5890 3.210012 ATGCTGTGAAAGGCCGGGT 62.210 57.895 2.18 0.00 0.00 5.28
3794 5906 0.725686 CTCGCAACAGGAAGAGCATG 59.274 55.000 0.00 0.00 0.00 4.06
3810 5922 1.296715 CTCCCCCAACCAGAACTCG 59.703 63.158 0.00 0.00 0.00 4.18
3847 5959 2.299013 TGGTAGACACTGTGGTCATGAC 59.701 50.000 17.91 17.91 40.29 3.06
3848 5960 2.604139 TGGTAGACACTGTGGTCATGA 58.396 47.619 13.09 0.00 40.29 3.07
3849 5961 3.055891 TGATGGTAGACACTGTGGTCATG 60.056 47.826 13.09 0.00 40.29 3.07
3850 5962 3.173151 TGATGGTAGACACTGTGGTCAT 58.827 45.455 13.09 7.80 40.29 3.06
3851 5963 2.604139 TGATGGTAGACACTGTGGTCA 58.396 47.619 13.09 3.40 40.29 4.02
3852 5964 3.326747 GTTGATGGTAGACACTGTGGTC 58.673 50.000 13.09 7.41 38.08 4.02
3853 5965 2.288825 CGTTGATGGTAGACACTGTGGT 60.289 50.000 13.09 1.40 0.00 4.16
3854 5966 2.337583 CGTTGATGGTAGACACTGTGG 58.662 52.381 13.09 0.00 0.00 4.17
3897 6009 4.777463 TCTGTGAATGTGATCATGAGCAT 58.223 39.130 17.94 10.30 34.19 3.79
3921 6034 0.171903 ACCGTAAGACGTAAGCGCAT 59.828 50.000 11.47 0.00 40.58 4.73
3922 6035 0.039256 AACCGTAAGACGTAAGCGCA 60.039 50.000 11.47 0.00 40.58 6.09
3923 6036 1.063031 AAACCGTAAGACGTAAGCGC 58.937 50.000 0.00 0.00 40.58 5.92
3924 6037 1.201736 GCAAACCGTAAGACGTAAGCG 60.202 52.381 0.00 0.00 40.58 4.68
3925 6038 1.794116 TGCAAACCGTAAGACGTAAGC 59.206 47.619 0.00 0.00 40.58 3.09
3926 6039 4.657075 ATTGCAAACCGTAAGACGTAAG 57.343 40.909 1.71 0.00 40.58 2.34
3927 6040 5.925397 TCTTATTGCAAACCGTAAGACGTAA 59.075 36.000 13.67 0.00 40.58 3.18
3928 6041 5.468592 TCTTATTGCAAACCGTAAGACGTA 58.531 37.500 13.67 0.00 40.58 3.57
3929 6042 4.309099 TCTTATTGCAAACCGTAAGACGT 58.691 39.130 13.67 0.00 40.58 4.34
3930 6043 4.624024 TCTCTTATTGCAAACCGTAAGACG 59.376 41.667 13.67 10.93 42.11 4.18
3931 6044 6.476243 TTCTCTTATTGCAAACCGTAAGAC 57.524 37.500 13.67 0.00 43.02 3.01
3932 6045 6.932400 TCTTTCTCTTATTGCAAACCGTAAGA 59.068 34.615 15.82 15.82 43.02 2.10
4014 6130 9.736414 AGGAGGAACTTAGAAAGTAATTTAACC 57.264 33.333 0.00 0.00 41.55 2.85
4047 6164 7.254252 CCGATCAGCAACTTATAAGTTCTTCAG 60.254 40.741 24.77 15.62 45.65 3.02
4049 6166 6.757010 TCCGATCAGCAACTTATAAGTTCTTC 59.243 38.462 24.77 17.03 45.65 2.87
4052 6169 6.019479 CACTCCGATCAGCAACTTATAAGTTC 60.019 42.308 24.77 18.98 45.65 3.01
4071 6188 0.606401 AAATGACAGTGGCCACTCCG 60.606 55.000 35.79 26.62 40.20 4.63
4090 6207 7.498570 GGAATTCCATAGCCATTTAATTGCAAA 59.501 33.333 20.04 0.00 35.64 3.68
4091 6208 6.991531 GGAATTCCATAGCCATTTAATTGCAA 59.008 34.615 20.04 0.00 35.64 4.08
4131 6283 3.010200 AGCAGCCAAAAAGGGATCTAG 57.990 47.619 0.00 0.00 38.09 2.43
4183 6336 2.742774 AGACAAAATTTTCCGCTGCAC 58.257 42.857 0.00 0.00 0.00 4.57
4202 6355 5.928839 AGAACACAAGTGTAGTCTGCAATAG 59.071 40.000 6.24 0.00 44.13 1.73
4236 6389 5.957842 AAATCCTTGTTTGCATAACTCGA 57.042 34.783 11.34 0.00 0.00 4.04
4263 6418 7.652909 CCTGTGCAAATTCACATTAGAAAAGAA 59.347 33.333 0.85 0.00 44.88 2.52
4264 6419 7.147312 CCTGTGCAAATTCACATTAGAAAAGA 58.853 34.615 0.85 0.00 44.88 2.52
4265 6420 6.128742 GCCTGTGCAAATTCACATTAGAAAAG 60.129 38.462 0.85 0.00 44.88 2.27


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

AutoCloner maintained by Alex Coulton.