Multiple sequence alignment - TraesCS5B01G288900

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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 TraesCS5B01G288900 chr5B 100.000 2641 0 0 1 2641 474057462 474054822 0.000000e+00 4878.0
1 TraesCS5B01G288900 chr5B 79.233 626 56 22 1133 1723 474279003 474278417 4.150000e-98 368.0
2 TraesCS5B01G288900 chr5B 81.297 401 40 18 1115 1511 474453455 474453086 2.570000e-75 292.0
3 TraesCS5B01G288900 chr5B 75.732 239 28 18 845 1069 474279253 474279031 2.800000e-15 93.5
4 TraesCS5B01G288900 chr5D 85.127 2091 101 71 664 2641 394190952 394188959 0.000000e+00 1945.0
5 TraesCS5B01G288900 chr5D 78.317 618 66 33 1133 1735 394548797 394548233 1.170000e-88 337.0
6 TraesCS5B01G288900 chr5D 78.317 618 66 33 1133 1735 394550810 394550246 1.170000e-88 337.0
7 TraesCS5B01G288900 chr5D 97.794 136 3 0 476 611 394191170 394191035 4.390000e-58 235.0
8 TraesCS5B01G288900 chr5D 81.928 249 15 15 1133 1354 394280858 394280613 1.610000e-42 183.0
9 TraesCS5B01G288900 chr5D 96.667 60 2 0 294 353 394191295 394191236 1.670000e-17 100.0
10 TraesCS5B01G288900 chr5D 83.654 104 7 8 867 970 394559713 394559620 3.620000e-14 89.8
11 TraesCS5B01G288900 chr5D 83.654 104 7 8 867 970 394563128 394563035 3.620000e-14 89.8
12 TraesCS5B01G288900 chr5D 81.897 116 8 9 846 960 394281123 394281020 4.680000e-13 86.1
13 TraesCS5B01G288900 chr5D 86.792 53 5 1 2511 2561 394279345 394279293 1.020000e-04 58.4
14 TraesCS5B01G288900 chr5A 86.350 1348 91 35 1084 2375 496536510 496535200 0.000000e+00 1384.0
15 TraesCS5B01G288900 chr5A 88.008 984 59 25 752 1721 496175850 496174912 0.000000e+00 1109.0
16 TraesCS5B01G288900 chr5A 91.084 415 22 9 620 1028 496536929 496536524 4.970000e-152 547.0
17 TraesCS5B01G288900 chr5A 79.969 639 68 31 1116 1737 496204816 496204221 1.460000e-112 416.0
18 TraesCS5B01G288900 chr5A 92.462 199 10 2 2421 2616 496533661 496533465 2.000000e-71 279.0
19 TraesCS5B01G288900 chr5A 95.620 137 6 0 475 611 496176721 496176585 1.230000e-53 220.0
20 TraesCS5B01G288900 chr5A 84.388 237 22 6 2415 2641 496174182 496173951 4.430000e-53 219.0
21 TraesCS5B01G288900 chr5A 86.893 206 14 9 2068 2270 496174503 496174308 4.430000e-53 219.0
22 TraesCS5B01G288900 chr5A 87.000 200 13 8 409 605 496537168 496536979 2.060000e-51 213.0
23 TraesCS5B01G288900 chr5A 86.923 130 14 2 1918 2047 496174780 496174654 2.740000e-30 143.0
24 TraesCS5B01G288900 chr5A 85.606 132 12 2 283 407 496177143 496177012 5.930000e-27 132.0
25 TraesCS5B01G288900 chr5A 85.714 91 5 6 867 957 496566638 496566556 3.620000e-14 89.8
26 TraesCS5B01G288900 chr5A 90.625 64 2 1 948 1011 496135332 496135273 6.060000e-12 82.4
27 TraesCS5B01G288900 chrUn 78.317 618 66 33 1133 1735 332176339 332175775 1.170000e-88 337.0
28 TraesCS5B01G288900 chrUn 79.221 154 15 12 867 1013 332176560 332176417 1.010000e-14 91.6
29 TraesCS5B01G288900 chrUn 83.654 104 7 8 867 970 211147308 211147215 3.620000e-14 89.8
30 TraesCS5B01G288900 chr4A 87.500 56 7 0 1581 1636 30287262 30287317 6.100000e-07 65.8
31 TraesCS5B01G288900 chr4D 88.000 50 6 0 1587 1636 437818480 437818431 2.840000e-05 60.2
32 TraesCS5B01G288900 chr4B 88.000 50 6 0 1587 1636 540726071 540726022 2.840000e-05 60.2


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 TraesCS5B01G288900 chr5B 474054822 474057462 2640 True 4878.000000 4878 100.000000 1 2641 1 chr5B.!!$R1 2640
1 TraesCS5B01G288900 chr5B 474278417 474279253 836 True 230.750000 368 77.482500 845 1723 2 chr5B.!!$R3 878
2 TraesCS5B01G288900 chr5D 394188959 394191295 2336 True 760.000000 1945 93.196000 294 2641 3 chr5D.!!$R1 2347
3 TraesCS5B01G288900 chr5D 394548233 394550810 2577 True 337.000000 337 78.317000 1133 1735 2 chr5D.!!$R3 602
4 TraesCS5B01G288900 chr5A 496533465 496537168 3703 True 605.750000 1384 89.224000 409 2616 4 chr5A.!!$R5 2207
5 TraesCS5B01G288900 chr5A 496204221 496204816 595 True 416.000000 416 79.969000 1116 1737 1 chr5A.!!$R2 621
6 TraesCS5B01G288900 chr5A 496173951 496177143 3192 True 340.333333 1109 87.906333 283 2641 6 chr5A.!!$R4 2358
7 TraesCS5B01G288900 chrUn 332175775 332176560 785 True 214.300000 337 78.769000 867 1735 2 chrUn.!!$R2 868

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
215 216 0.035458 CCCAGACCCTGAGTGTGAAC 59.965 60.0 0.0 0.0 42.34 3.18 F
273 274 0.178995 TGCTTGCAATGAGGACACCA 60.179 50.0 0.0 0.0 0.00 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1044 1943 0.662619 TCTTGGCGAAGTTTGTGCTG 59.337 50.0 8.41 0.0 0.00 4.41 R
2258 3445 1.156736 GGCTGCGACAGTGTTTGTAT 58.843 50.0 0.00 0.0 41.05 2.29 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
26 27 6.467723 ACACTGAGTATTTCTGCTAAAACG 57.532 37.500 0.00 0.00 0.00 3.60
27 28 6.220930 ACACTGAGTATTTCTGCTAAAACGA 58.779 36.000 0.00 0.00 0.00 3.85
28 29 6.874134 ACACTGAGTATTTCTGCTAAAACGAT 59.126 34.615 0.00 0.00 0.00 3.73
29 30 7.148573 ACACTGAGTATTTCTGCTAAAACGATG 60.149 37.037 0.00 0.00 0.00 3.84
30 31 6.106877 TGAGTATTTCTGCTAAAACGATGC 57.893 37.500 0.00 0.00 0.00 3.91
31 32 5.641636 TGAGTATTTCTGCTAAAACGATGCA 59.358 36.000 0.00 0.00 35.30 3.96
33 34 7.088589 AGTATTTCTGCTAAAACGATGCATT 57.911 32.000 0.00 0.00 36.07 3.56
34 35 8.208718 AGTATTTCTGCTAAAACGATGCATTA 57.791 30.769 0.00 0.00 36.07 1.90
40 41 5.610908 GCTAAAACGATGCATTAGCTTTG 57.389 39.130 17.72 5.93 45.02 2.77
41 42 5.095490 GCTAAAACGATGCATTAGCTTTGT 58.905 37.500 17.72 0.00 45.02 2.83
42 43 6.255215 GCTAAAACGATGCATTAGCTTTGTA 58.745 36.000 17.72 0.00 45.02 2.41
43 44 6.912591 GCTAAAACGATGCATTAGCTTTGTAT 59.087 34.615 17.72 0.00 45.02 2.29
44 45 7.432252 GCTAAAACGATGCATTAGCTTTGTATT 59.568 33.333 17.72 0.69 45.02 1.89
46 47 5.424121 ACGATGCATTAGCTTTGTATTCC 57.576 39.130 0.00 0.00 39.86 3.01
48 49 5.532406 ACGATGCATTAGCTTTGTATTCCAT 59.468 36.000 0.00 0.00 39.86 3.41
49 50 6.039717 ACGATGCATTAGCTTTGTATTCCATT 59.960 34.615 0.00 0.00 39.86 3.16
50 51 6.361481 CGATGCATTAGCTTTGTATTCCATTG 59.639 38.462 0.00 0.00 42.74 2.82
51 52 5.904941 TGCATTAGCTTTGTATTCCATTGG 58.095 37.500 0.00 0.00 42.74 3.16
52 53 5.163426 TGCATTAGCTTTGTATTCCATTGGG 60.163 40.000 2.09 0.00 42.74 4.12
53 54 5.163416 GCATTAGCTTTGTATTCCATTGGGT 60.163 40.000 2.09 0.00 37.91 4.51
54 55 6.630188 GCATTAGCTTTGTATTCCATTGGGTT 60.630 38.462 2.09 0.00 37.91 4.11
55 56 4.806640 AGCTTTGTATTCCATTGGGTTG 57.193 40.909 2.09 0.00 34.93 3.77
56 57 3.515104 AGCTTTGTATTCCATTGGGTTGG 59.485 43.478 2.09 0.00 38.18 3.77
69 70 2.759795 GTTGGCCCTCCTCAAGCT 59.240 61.111 0.00 0.00 0.00 3.74
70 71 1.075659 GTTGGCCCTCCTCAAGCTT 59.924 57.895 0.00 0.00 0.00 3.74
71 72 1.075482 TTGGCCCTCCTCAAGCTTG 59.925 57.895 20.81 20.81 0.00 4.01
73 74 1.075659 GGCCCTCCTCAAGCTTGTT 59.924 57.895 25.19 0.00 0.00 2.83
74 75 0.540597 GGCCCTCCTCAAGCTTGTTT 60.541 55.000 25.19 0.00 0.00 2.83
75 76 1.271926 GGCCCTCCTCAAGCTTGTTTA 60.272 52.381 25.19 11.04 0.00 2.01
88 89 1.200948 CTTGTTTAGCAGCTCTTGGCC 59.799 52.381 0.00 0.00 43.05 5.36
90 91 0.322906 GTTTAGCAGCTCTTGGCCCT 60.323 55.000 0.00 0.00 43.05 5.19
91 92 0.322816 TTTAGCAGCTCTTGGCCCTG 60.323 55.000 0.00 0.00 43.05 4.45
102 103 2.037847 GGCCCTGCCCATTCAGTT 59.962 61.111 0.00 0.00 44.06 3.16
103 104 1.610379 GGCCCTGCCCATTCAGTTT 60.610 57.895 0.00 0.00 44.06 2.66
104 105 1.194121 GGCCCTGCCCATTCAGTTTT 61.194 55.000 0.00 0.00 44.06 2.43
105 106 0.686789 GCCCTGCCCATTCAGTTTTT 59.313 50.000 0.00 0.00 32.32 1.94
106 107 1.338105 GCCCTGCCCATTCAGTTTTTC 60.338 52.381 0.00 0.00 32.32 2.29
107 108 2.250924 CCCTGCCCATTCAGTTTTTCT 58.749 47.619 0.00 0.00 32.32 2.52
108 109 3.430453 CCCTGCCCATTCAGTTTTTCTA 58.570 45.455 0.00 0.00 32.32 2.10
109 110 3.445096 CCCTGCCCATTCAGTTTTTCTAG 59.555 47.826 0.00 0.00 32.32 2.43
111 112 3.760684 CTGCCCATTCAGTTTTTCTAGCT 59.239 43.478 0.00 0.00 0.00 3.32
112 113 3.758554 TGCCCATTCAGTTTTTCTAGCTC 59.241 43.478 0.00 0.00 0.00 4.09
113 114 3.129462 GCCCATTCAGTTTTTCTAGCTCC 59.871 47.826 0.00 0.00 0.00 4.70
114 115 4.335416 CCCATTCAGTTTTTCTAGCTCCA 58.665 43.478 0.00 0.00 0.00 3.86
115 116 4.952335 CCCATTCAGTTTTTCTAGCTCCAT 59.048 41.667 0.00 0.00 0.00 3.41
117 118 5.649395 CCATTCAGTTTTTCTAGCTCCATCA 59.351 40.000 0.00 0.00 0.00 3.07
118 119 6.404074 CCATTCAGTTTTTCTAGCTCCATCAC 60.404 42.308 0.00 0.00 0.00 3.06
119 120 5.489792 TCAGTTTTTCTAGCTCCATCACT 57.510 39.130 0.00 0.00 0.00 3.41
120 121 5.240891 TCAGTTTTTCTAGCTCCATCACTG 58.759 41.667 0.00 0.00 0.00 3.66
121 122 4.999950 CAGTTTTTCTAGCTCCATCACTGT 59.000 41.667 0.00 0.00 0.00 3.55
122 123 6.014584 TCAGTTTTTCTAGCTCCATCACTGTA 60.015 38.462 0.00 0.00 32.63 2.74
123 124 6.650807 CAGTTTTTCTAGCTCCATCACTGTAA 59.349 38.462 0.00 0.00 0.00 2.41
124 125 7.335422 CAGTTTTTCTAGCTCCATCACTGTAAT 59.665 37.037 0.00 0.00 0.00 1.89
126 127 9.162764 GTTTTTCTAGCTCCATCACTGTAATAA 57.837 33.333 0.00 0.00 0.00 1.40
127 128 9.733556 TTTTTCTAGCTCCATCACTGTAATAAA 57.266 29.630 0.00 0.00 0.00 1.40
128 129 8.718102 TTTCTAGCTCCATCACTGTAATAAAC 57.282 34.615 0.00 0.00 0.00 2.01
129 130 7.418337 TCTAGCTCCATCACTGTAATAAACA 57.582 36.000 0.00 0.00 36.42 2.83
130 131 7.265673 TCTAGCTCCATCACTGTAATAAACAC 58.734 38.462 0.00 0.00 33.45 3.32
131 132 5.804639 AGCTCCATCACTGTAATAAACACA 58.195 37.500 0.00 0.00 33.45 3.72
132 133 5.643777 AGCTCCATCACTGTAATAAACACAC 59.356 40.000 0.00 0.00 33.45 3.82
133 134 5.163754 GCTCCATCACTGTAATAAACACACC 60.164 44.000 0.00 0.00 33.45 4.16
134 135 5.250200 TCCATCACTGTAATAAACACACCC 58.750 41.667 0.00 0.00 33.45 4.61
135 136 4.094294 CCATCACTGTAATAAACACACCCG 59.906 45.833 0.00 0.00 33.45 5.28
136 137 4.339872 TCACTGTAATAAACACACCCGT 57.660 40.909 0.00 0.00 33.45 5.28
147 148 2.428187 CACCCGTGGTTGTAGCCA 59.572 61.111 0.00 0.00 31.02 4.75
148 149 1.002624 CACCCGTGGTTGTAGCCAT 60.003 57.895 0.00 0.00 41.08 4.40
149 150 1.002624 ACCCGTGGTTGTAGCCATG 60.003 57.895 0.45 0.45 43.37 3.66
150 151 1.002624 CCCGTGGTTGTAGCCATGT 60.003 57.895 6.28 0.00 42.47 3.21
151 152 1.305219 CCCGTGGTTGTAGCCATGTG 61.305 60.000 6.28 0.00 42.47 3.21
152 153 1.305219 CCGTGGTTGTAGCCATGTGG 61.305 60.000 6.28 0.00 42.47 4.17
153 154 0.321210 CGTGGTTGTAGCCATGTGGA 60.321 55.000 2.55 0.00 41.08 4.02
154 155 1.880221 CGTGGTTGTAGCCATGTGGAA 60.880 52.381 2.55 0.00 41.08 3.53
156 157 1.423541 TGGTTGTAGCCATGTGGAAGT 59.576 47.619 2.55 0.00 37.39 3.01
157 158 1.812571 GGTTGTAGCCATGTGGAAGTG 59.187 52.381 2.55 0.00 37.39 3.16
158 159 2.504367 GTTGTAGCCATGTGGAAGTGT 58.496 47.619 2.55 0.00 37.39 3.55
159 160 2.472695 TGTAGCCATGTGGAAGTGTC 57.527 50.000 2.55 0.00 37.39 3.67
160 161 1.696884 TGTAGCCATGTGGAAGTGTCA 59.303 47.619 2.55 0.00 37.39 3.58
161 162 2.105649 TGTAGCCATGTGGAAGTGTCAA 59.894 45.455 2.55 0.00 37.39 3.18
162 163 1.901591 AGCCATGTGGAAGTGTCAAG 58.098 50.000 2.55 0.00 37.39 3.02
163 164 0.242017 GCCATGTGGAAGTGTCAAGC 59.758 55.000 2.55 0.00 37.39 4.01
164 165 1.901591 CCATGTGGAAGTGTCAAGCT 58.098 50.000 0.00 0.00 37.39 3.74
166 167 2.224606 CATGTGGAAGTGTCAAGCTGT 58.775 47.619 0.00 0.00 0.00 4.40
167 168 2.418368 TGTGGAAGTGTCAAGCTGTT 57.582 45.000 0.00 0.00 0.00 3.16
168 169 2.722094 TGTGGAAGTGTCAAGCTGTTT 58.278 42.857 0.00 0.00 0.00 2.83
169 170 2.682856 TGTGGAAGTGTCAAGCTGTTTC 59.317 45.455 0.00 0.00 0.00 2.78
172 173 2.945668 GGAAGTGTCAAGCTGTTTCAGT 59.054 45.455 0.00 0.00 33.43 3.41
173 174 3.378427 GGAAGTGTCAAGCTGTTTCAGTT 59.622 43.478 0.00 0.00 33.43 3.16
175 176 3.347216 AGTGTCAAGCTGTTTCAGTTGT 58.653 40.909 0.00 0.00 33.43 3.32
178 179 3.312421 TGTCAAGCTGTTTCAGTTGTAGC 59.688 43.478 0.00 0.00 33.43 3.58
180 181 2.618241 CAAGCTGTTTCAGTTGTAGCCA 59.382 45.455 0.00 0.00 35.05 4.75
183 184 2.605580 GCTGTTTCAGTTGTAGCCAAGC 60.606 50.000 0.00 0.00 33.43 4.01
184 185 1.953686 TGTTTCAGTTGTAGCCAAGCC 59.046 47.619 0.00 0.00 0.00 4.35
185 186 2.230660 GTTTCAGTTGTAGCCAAGCCT 58.769 47.619 0.00 0.00 0.00 4.58
186 187 2.623416 GTTTCAGTTGTAGCCAAGCCTT 59.377 45.455 0.00 0.00 0.00 4.35
187 188 1.896220 TCAGTTGTAGCCAAGCCTTG 58.104 50.000 0.00 0.00 0.00 3.61
188 189 1.419762 TCAGTTGTAGCCAAGCCTTGA 59.580 47.619 5.89 0.00 0.00 3.02
189 190 2.040278 TCAGTTGTAGCCAAGCCTTGAT 59.960 45.455 5.89 0.00 0.00 2.57
191 192 1.398390 GTTGTAGCCAAGCCTTGATCG 59.602 52.381 5.89 0.00 0.00 3.69
192 193 0.613260 TGTAGCCAAGCCTTGATCGT 59.387 50.000 5.89 0.00 0.00 3.73
194 195 0.744414 TAGCCAAGCCTTGATCGTGC 60.744 55.000 5.89 0.00 0.00 5.34
195 196 3.056313 GCCAAGCCTTGATCGTGCC 62.056 63.158 5.89 0.00 0.00 5.01
196 197 2.409870 CCAAGCCTTGATCGTGCCC 61.410 63.158 5.89 0.00 0.00 5.36
197 198 2.044946 AAGCCTTGATCGTGCCCC 60.045 61.111 0.00 0.00 0.00 5.80
199 200 4.424711 GCCTTGATCGTGCCCCCA 62.425 66.667 0.00 0.00 0.00 4.96
200 201 2.124570 CCTTGATCGTGCCCCCAG 60.125 66.667 0.00 0.00 0.00 4.45
201 202 2.669133 CCTTGATCGTGCCCCCAGA 61.669 63.158 0.00 0.00 0.00 3.86
202 203 1.450312 CTTGATCGTGCCCCCAGAC 60.450 63.158 0.00 0.00 0.00 3.51
203 204 2.876368 CTTGATCGTGCCCCCAGACC 62.876 65.000 0.00 0.00 0.00 3.85
204 205 4.176752 GATCGTGCCCCCAGACCC 62.177 72.222 0.00 0.00 0.00 4.46
208 209 3.721706 GTGCCCCCAGACCCTGAG 61.722 72.222 0.00 0.00 32.44 3.35
209 210 4.270153 TGCCCCCAGACCCTGAGT 62.270 66.667 0.00 0.00 32.44 3.41
211 212 2.203998 CCCCCAGACCCTGAGTGT 60.204 66.667 0.00 0.00 32.44 3.55
212 213 2.596851 CCCCCAGACCCTGAGTGTG 61.597 68.421 0.00 0.00 39.46 3.82
213 214 1.536418 CCCCAGACCCTGAGTGTGA 60.536 63.158 0.00 0.00 42.34 3.58
214 215 1.127567 CCCCAGACCCTGAGTGTGAA 61.128 60.000 0.00 0.00 42.34 3.18
215 216 0.035458 CCCAGACCCTGAGTGTGAAC 59.965 60.000 0.00 0.00 42.34 3.18
218 219 1.051812 AGACCCTGAGTGTGAACCTG 58.948 55.000 0.00 0.00 0.00 4.00
219 220 0.603975 GACCCTGAGTGTGAACCTGC 60.604 60.000 0.00 0.00 0.00 4.85
223 224 1.344438 CCTGAGTGTGAACCTGCACTA 59.656 52.381 0.00 0.00 44.89 2.74
224 225 2.611473 CCTGAGTGTGAACCTGCACTAG 60.611 54.545 0.00 0.00 44.89 2.57
225 226 2.297315 CTGAGTGTGAACCTGCACTAGA 59.703 50.000 0.00 0.00 44.89 2.43
227 228 3.324846 TGAGTGTGAACCTGCACTAGAAT 59.675 43.478 0.00 0.00 44.89 2.40
229 230 4.822026 AGTGTGAACCTGCACTAGAATAC 58.178 43.478 0.00 0.00 43.30 1.89
230 231 4.283467 AGTGTGAACCTGCACTAGAATACA 59.717 41.667 0.00 0.00 43.30 2.29
231 232 4.994852 GTGTGAACCTGCACTAGAATACAA 59.005 41.667 0.00 0.00 39.49 2.41
233 234 5.011635 TGTGAACCTGCACTAGAATACAAGA 59.988 40.000 0.00 0.00 39.49 3.02
234 235 6.109359 GTGAACCTGCACTAGAATACAAGAT 58.891 40.000 0.00 0.00 35.91 2.40
237 238 6.491714 ACCTGCACTAGAATACAAGATGAT 57.508 37.500 0.00 0.00 0.00 2.45
238 239 6.520272 ACCTGCACTAGAATACAAGATGATC 58.480 40.000 0.00 0.00 0.00 2.92
240 241 6.463472 CCTGCACTAGAATACAAGATGATCCA 60.463 42.308 0.00 0.00 0.00 3.41
241 242 6.283694 TGCACTAGAATACAAGATGATCCAC 58.716 40.000 0.00 0.00 0.00 4.02
242 243 6.127083 TGCACTAGAATACAAGATGATCCACA 60.127 38.462 0.00 0.00 0.00 4.17
243 244 6.763135 GCACTAGAATACAAGATGATCCACAA 59.237 38.462 0.00 0.00 0.00 3.33
244 245 7.443575 GCACTAGAATACAAGATGATCCACAAT 59.556 37.037 0.00 0.00 0.00 2.71
245 246 9.334947 CACTAGAATACAAGATGATCCACAATT 57.665 33.333 0.00 0.00 0.00 2.32
246 247 9.553064 ACTAGAATACAAGATGATCCACAATTC 57.447 33.333 0.00 0.00 0.00 2.17
247 248 7.814264 AGAATACAAGATGATCCACAATTCC 57.186 36.000 0.00 0.00 0.00 3.01
250 251 3.698040 ACAAGATGATCCACAATTCCTGC 59.302 43.478 0.00 0.00 0.00 4.85
251 252 3.657398 AGATGATCCACAATTCCTGCA 57.343 42.857 0.00 0.00 0.00 4.41
252 253 3.285484 AGATGATCCACAATTCCTGCAC 58.715 45.455 0.00 0.00 0.00 4.57
253 254 2.885135 TGATCCACAATTCCTGCACT 57.115 45.000 0.00 0.00 0.00 4.40
254 255 3.159213 TGATCCACAATTCCTGCACTT 57.841 42.857 0.00 0.00 0.00 3.16
257 258 0.963962 CCACAATTCCTGCACTTGCT 59.036 50.000 2.33 0.00 42.66 3.91
258 259 1.342174 CCACAATTCCTGCACTTGCTT 59.658 47.619 2.33 0.00 42.66 3.91
260 261 1.269936 ACAATTCCTGCACTTGCTTGC 60.270 47.619 2.33 0.00 43.31 4.01
268 269 0.599558 GCACTTGCTTGCAATGAGGA 59.400 50.000 8.55 0.00 42.49 3.71
269 270 1.668047 GCACTTGCTTGCAATGAGGAC 60.668 52.381 8.55 0.00 42.49 3.85
270 271 1.610038 CACTTGCTTGCAATGAGGACA 59.390 47.619 8.55 0.00 0.00 4.02
272 273 0.961019 TTGCTTGCAATGAGGACACC 59.039 50.000 0.00 0.00 0.00 4.16
273 274 0.178995 TGCTTGCAATGAGGACACCA 60.179 50.000 0.00 0.00 0.00 4.17
274 275 0.961019 GCTTGCAATGAGGACACCAA 59.039 50.000 0.00 0.00 0.00 3.67
275 276 1.547372 GCTTGCAATGAGGACACCAAT 59.453 47.619 0.00 0.00 0.00 3.16
276 277 2.028748 GCTTGCAATGAGGACACCAATT 60.029 45.455 0.00 0.00 0.00 2.32
277 278 3.555586 GCTTGCAATGAGGACACCAATTT 60.556 43.478 0.00 0.00 0.00 1.82
279 280 5.782047 CTTGCAATGAGGACACCAATTTAA 58.218 37.500 0.00 0.00 0.00 1.52
281 282 4.176271 GCAATGAGGACACCAATTTAAGC 58.824 43.478 0.00 0.00 0.00 3.09
285 286 2.084546 AGGACACCAATTTAAGCGAGC 58.915 47.619 0.00 0.00 0.00 5.03
340 341 8.611654 TGTACATTTTGAGAGTAAACTTACCC 57.388 34.615 0.00 0.00 34.19 3.69
342 343 7.981102 ACATTTTGAGAGTAAACTTACCCTC 57.019 36.000 4.63 4.63 38.52 4.30
380 388 4.778842 ACGTTATGATCGTTGATGCTTC 57.221 40.909 0.00 0.00 38.38 3.86
394 402 0.657312 TGCTTCGTGCTGTCTTGTTG 59.343 50.000 5.00 0.00 43.37 3.33
445 683 1.948834 TCTTGTCAACGTGTCGGTAGA 59.051 47.619 0.00 0.00 0.00 2.59
447 685 2.867287 TGTCAACGTGTCGGTAGAAA 57.133 45.000 0.00 0.00 0.00 2.52
448 686 2.462889 TGTCAACGTGTCGGTAGAAAC 58.537 47.619 0.00 0.00 0.00 2.78
449 687 1.788886 GTCAACGTGTCGGTAGAAACC 59.211 52.381 0.00 0.00 42.95 3.27
612 854 3.507924 GCCCGATGCATGCGTCAA 61.508 61.111 33.12 9.31 40.77 3.18
614 856 1.226379 CCCGATGCATGCGTCAAAC 60.226 57.895 33.12 12.66 32.55 2.93
615 857 1.580893 CCGATGCATGCGTCAAACG 60.581 57.895 33.12 22.21 45.88 3.60
617 859 0.584785 CGATGCATGCGTCAAACGAG 60.585 55.000 33.12 16.20 46.05 4.18
618 860 0.247814 GATGCATGCGTCAAACGAGG 60.248 55.000 30.58 0.00 46.05 4.63
678 969 1.174783 GAGGGAGCGTACTGACAAGA 58.825 55.000 0.00 0.00 0.00 3.02
905 1765 2.764010 TCCATTCCGTTCTGCTTAGCTA 59.236 45.455 5.60 0.00 0.00 3.32
965 1845 3.283751 TCCCTTCTTCTTCTCTAGCTCG 58.716 50.000 0.00 0.00 0.00 5.03
1044 1943 0.825010 CCAGGCAAGCCATCCATACC 60.825 60.000 14.40 0.00 38.92 2.73
1057 1956 2.422597 TCCATACCAGCACAAACTTCG 58.577 47.619 0.00 0.00 0.00 3.79
1103 2002 4.471904 TCAGTGATCACCATGAACTACC 57.528 45.455 22.21 0.00 0.00 3.18
1129 2028 4.109050 GTGGTTTCTTATCTCTCGCTCTG 58.891 47.826 0.00 0.00 0.00 3.35
1312 2238 1.172180 CCACGCCCAAGAAGAAGCAA 61.172 55.000 0.00 0.00 0.00 3.91
1540 2471 4.526650 ACTGCCGGAATTGGTTTCTTTAAT 59.473 37.500 5.05 0.00 34.56 1.40
1603 2546 1.883638 GCAGAAGTGGAGCATGTGGAA 60.884 52.381 0.00 0.00 0.00 3.53
1645 2588 4.452733 CGTCGCCTCCTGAACCCC 62.453 72.222 0.00 0.00 0.00 4.95
1646 2589 4.452733 GTCGCCTCCTGAACCCCG 62.453 72.222 0.00 0.00 0.00 5.73
1647 2590 4.689549 TCGCCTCCTGAACCCCGA 62.690 66.667 0.00 0.00 0.00 5.14
1648 2591 3.702048 CGCCTCCTGAACCCCGAA 61.702 66.667 0.00 0.00 0.00 4.30
1649 2592 2.754375 GCCTCCTGAACCCCGAAA 59.246 61.111 0.00 0.00 0.00 3.46
1651 2594 1.002502 CCTCCTGAACCCCGAAACC 60.003 63.158 0.00 0.00 0.00 3.27
1652 2595 1.489560 CCTCCTGAACCCCGAAACCT 61.490 60.000 0.00 0.00 0.00 3.50
1653 2596 0.321653 CTCCTGAACCCCGAAACCTG 60.322 60.000 0.00 0.00 0.00 4.00
1657 2600 2.203437 AACCCCGAAACCTGTGGC 60.203 61.111 0.00 0.00 0.00 5.01
1658 2601 4.636435 ACCCCGAAACCTGTGGCG 62.636 66.667 0.00 0.00 0.00 5.69
1702 2673 1.783284 TCGTGTTCATCAGCAGTGTC 58.217 50.000 0.00 0.00 0.00 3.67
1725 2696 6.261158 GTCTATTTGCCCTTTCTCTTGGATAC 59.739 42.308 0.00 0.00 0.00 2.24
1769 2751 2.032377 CCGAGTGTTTTGTGCGTATGTT 60.032 45.455 0.00 0.00 0.00 2.71
1804 2787 6.093633 GGCAAAATGGTTAGTACTCCAGTAAG 59.906 42.308 0.00 0.00 37.14 2.34
1873 2858 8.204836 GTGTGATGTTGGTAAAGATATCTAGGT 58.795 37.037 5.46 0.00 0.00 3.08
1991 3008 6.665680 AGTCTGTTACTATCTGTCAACCTGAT 59.334 38.462 0.00 0.00 36.36 2.90
2047 3087 5.529060 AGTTTGTCACCAGAGATTCAGAAAC 59.471 40.000 0.00 0.00 0.00 2.78
2164 3337 0.537653 TGGTACCCGCATTGATTCGA 59.462 50.000 10.07 0.00 0.00 3.71
2167 3340 0.176910 TACCCGCATTGATTCGAGCA 59.823 50.000 0.00 0.00 0.00 4.26
2179 3352 6.844696 TTGATTCGAGCAGTTGGATAATAC 57.155 37.500 0.00 0.00 0.00 1.89
2181 3354 7.284919 TGATTCGAGCAGTTGGATAATACTA 57.715 36.000 0.00 0.00 0.00 1.82
2182 3355 7.371159 TGATTCGAGCAGTTGGATAATACTAG 58.629 38.462 0.00 0.00 0.00 2.57
2183 3356 6.710597 TTCGAGCAGTTGGATAATACTAGT 57.289 37.500 0.00 0.00 0.00 2.57
2184 3357 7.812690 TTCGAGCAGTTGGATAATACTAGTA 57.187 36.000 4.77 4.77 0.00 1.82
2258 3445 1.301637 CGATCGCCCATGCCATACA 60.302 57.895 0.26 0.00 0.00 2.29
2259 3446 0.674581 CGATCGCCCATGCCATACAT 60.675 55.000 0.26 0.00 40.66 2.29
2263 3466 1.141858 TCGCCCATGCCATACATACAA 59.858 47.619 0.00 0.00 36.64 2.41
2290 3493 3.862124 CAGCCGTGTGTCTGCTAC 58.138 61.111 0.00 0.00 34.96 3.58
2291 3494 1.006220 CAGCCGTGTGTCTGCTACA 60.006 57.895 0.00 0.00 34.96 2.74
2292 3495 0.390340 CAGCCGTGTGTCTGCTACAT 60.390 55.000 0.00 0.00 41.10 2.29
2307 3516 8.406297 TGTCTGCTACATACAAACACTATCTAG 58.594 37.037 0.00 0.00 31.43 2.43
2364 3574 3.177228 AGAAGAGAACTGGCATGGTAGT 58.823 45.455 0.00 0.00 0.00 2.73
2366 3576 4.404073 AGAAGAGAACTGGCATGGTAGTAG 59.596 45.833 0.00 0.00 0.00 2.57
2368 3578 3.957497 AGAGAACTGGCATGGTAGTAGAG 59.043 47.826 0.00 0.00 0.00 2.43
2370 3580 4.353777 AGAACTGGCATGGTAGTAGAGAA 58.646 43.478 0.00 0.00 0.00 2.87
2371 3581 4.777896 AGAACTGGCATGGTAGTAGAGAAA 59.222 41.667 0.00 0.00 0.00 2.52
2372 3582 5.248477 AGAACTGGCATGGTAGTAGAGAAAA 59.752 40.000 0.00 0.00 0.00 2.29
2378 3608 5.755861 GGCATGGTAGTAGAGAAAATGACTC 59.244 44.000 0.00 0.00 34.95 3.36
2387 3617 4.087182 AGAGAAAATGACTCGGACCTACA 58.913 43.478 0.00 0.00 39.12 2.74
2460 5180 0.172803 CCGGAGAAACGAGTAGTGGG 59.827 60.000 0.00 0.00 35.47 4.61
2506 5231 1.722011 TTTTGGATCGAACGGAGCTC 58.278 50.000 4.71 4.71 0.00 4.09
2518 5243 1.869690 GGAGCTCCAGTTTTCACGC 59.130 57.895 28.43 0.00 35.64 5.34
2579 5309 1.412710 GATAGGCATTCCGAGGACACA 59.587 52.381 0.00 0.00 37.47 3.72
2580 5310 1.271856 TAGGCATTCCGAGGACACAA 58.728 50.000 0.00 0.00 37.47 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.095607 CGTTTTAGCAGAAATACTCAGTGTTCT 60.096 37.037 0.70 0.70 0.00 3.01
1 2 7.010023 CGTTTTAGCAGAAATACTCAGTGTTC 58.990 38.462 0.00 0.00 0.00 3.18
3 4 6.220930 TCGTTTTAGCAGAAATACTCAGTGT 58.779 36.000 0.00 0.00 0.00 3.55
4 5 6.706055 TCGTTTTAGCAGAAATACTCAGTG 57.294 37.500 0.00 0.00 0.00 3.66
6 7 6.183360 TGCATCGTTTTAGCAGAAATACTCAG 60.183 38.462 0.00 0.00 33.75 3.35
7 8 5.641636 TGCATCGTTTTAGCAGAAATACTCA 59.358 36.000 0.00 0.00 33.75 3.41
8 9 6.106877 TGCATCGTTTTAGCAGAAATACTC 57.893 37.500 0.00 0.00 33.75 2.59
9 10 6.683974 ATGCATCGTTTTAGCAGAAATACT 57.316 33.333 0.00 0.00 42.14 2.12
10 11 7.112148 GCTAATGCATCGTTTTAGCAGAAATAC 59.888 37.037 19.34 0.00 44.53 1.89
11 12 7.012327 AGCTAATGCATCGTTTTAGCAGAAATA 59.988 33.333 23.84 0.00 46.49 1.40
12 13 5.973565 GCTAATGCATCGTTTTAGCAGAAAT 59.026 36.000 19.34 0.00 44.53 2.17
13 14 5.123820 AGCTAATGCATCGTTTTAGCAGAAA 59.876 36.000 23.84 0.00 46.49 2.52
14 15 4.635765 AGCTAATGCATCGTTTTAGCAGAA 59.364 37.500 23.84 0.00 46.49 3.02
15 16 4.191544 AGCTAATGCATCGTTTTAGCAGA 58.808 39.130 23.84 0.00 46.49 4.26
17 18 4.963276 AAGCTAATGCATCGTTTTAGCA 57.037 36.364 23.84 0.00 46.49 3.49
18 19 5.095490 ACAAAGCTAATGCATCGTTTTAGC 58.905 37.500 17.42 17.42 45.15 3.09
20 21 7.913297 GGAATACAAAGCTAATGCATCGTTTTA 59.087 33.333 0.00 0.00 42.74 1.52
21 22 6.751888 GGAATACAAAGCTAATGCATCGTTTT 59.248 34.615 0.00 2.31 42.74 2.43
22 23 6.127758 TGGAATACAAAGCTAATGCATCGTTT 60.128 34.615 0.00 0.00 42.74 3.60
23 24 5.356751 TGGAATACAAAGCTAATGCATCGTT 59.643 36.000 0.00 0.00 42.74 3.85
24 25 4.881273 TGGAATACAAAGCTAATGCATCGT 59.119 37.500 0.00 0.00 42.74 3.73
26 27 6.643770 CCAATGGAATACAAAGCTAATGCATC 59.356 38.462 0.00 0.00 42.74 3.91
27 28 6.463331 CCCAATGGAATACAAAGCTAATGCAT 60.463 38.462 0.00 0.00 42.74 3.96
28 29 5.163426 CCCAATGGAATACAAAGCTAATGCA 60.163 40.000 0.00 0.00 42.74 3.96
29 30 5.163416 ACCCAATGGAATACAAAGCTAATGC 60.163 40.000 0.00 0.00 35.79 3.56
30 31 6.469782 ACCCAATGGAATACAAAGCTAATG 57.530 37.500 0.00 0.00 34.81 1.90
31 32 6.127083 CCAACCCAATGGAATACAAAGCTAAT 60.127 38.462 0.00 0.00 43.54 1.73
33 34 4.709397 CCAACCCAATGGAATACAAAGCTA 59.291 41.667 0.00 0.00 43.54 3.32
34 35 3.515104 CCAACCCAATGGAATACAAAGCT 59.485 43.478 0.00 0.00 43.54 3.74
36 37 3.369366 GGCCAACCCAATGGAATACAAAG 60.369 47.826 0.00 0.00 43.54 2.77
37 38 2.569404 GGCCAACCCAATGGAATACAAA 59.431 45.455 0.00 0.00 43.54 2.83
38 39 2.183679 GGCCAACCCAATGGAATACAA 58.816 47.619 0.00 0.00 43.54 2.41
39 40 1.859302 GGCCAACCCAATGGAATACA 58.141 50.000 0.00 0.00 43.54 2.29
51 52 2.361737 GCTTGAGGAGGGCCAACC 60.362 66.667 6.18 9.19 40.67 3.77
52 53 1.075659 AAGCTTGAGGAGGGCCAAC 59.924 57.895 6.18 0.00 36.29 3.77
53 54 1.075482 CAAGCTTGAGGAGGGCCAA 59.925 57.895 22.31 0.00 36.29 4.52
54 55 1.719063 AACAAGCTTGAGGAGGGCCA 61.719 55.000 32.50 0.00 36.29 5.36
55 56 0.540597 AAACAAGCTTGAGGAGGGCC 60.541 55.000 32.50 0.00 0.00 5.80
56 57 2.087646 CTAAACAAGCTTGAGGAGGGC 58.912 52.381 32.50 0.00 0.00 5.19
67 68 4.590968 GGCCAAGAGCTGCTAAACAAGC 62.591 54.545 0.15 1.10 45.12 4.01
69 70 1.247567 GGCCAAGAGCTGCTAAACAA 58.752 50.000 0.15 0.00 43.05 2.83
70 71 0.609131 GGGCCAAGAGCTGCTAAACA 60.609 55.000 4.39 0.00 43.05 2.83
71 72 0.322906 AGGGCCAAGAGCTGCTAAAC 60.323 55.000 6.18 0.00 43.05 2.01
73 74 1.300963 CAGGGCCAAGAGCTGCTAA 59.699 57.895 6.18 0.00 43.05 3.09
74 75 2.993008 CAGGGCCAAGAGCTGCTA 59.007 61.111 6.18 0.00 43.05 3.49
75 76 4.737177 GCAGGGCCAAGAGCTGCT 62.737 66.667 20.01 0.00 39.08 4.24
86 87 0.686789 AAAAACTGAATGGGCAGGGC 59.313 50.000 0.00 0.00 40.20 5.19
88 89 3.119352 GCTAGAAAAACTGAATGGGCAGG 60.119 47.826 0.00 0.00 40.20 4.85
90 91 3.758554 GAGCTAGAAAAACTGAATGGGCA 59.241 43.478 0.00 0.00 0.00 5.36
91 92 3.129462 GGAGCTAGAAAAACTGAATGGGC 59.871 47.826 0.00 0.00 0.00 5.36
92 93 4.335416 TGGAGCTAGAAAAACTGAATGGG 58.665 43.478 0.00 0.00 0.00 4.00
94 95 6.373774 AGTGATGGAGCTAGAAAAACTGAATG 59.626 38.462 0.00 0.00 0.00 2.67
96 97 5.702670 CAGTGATGGAGCTAGAAAAACTGAA 59.297 40.000 8.49 0.00 35.63 3.02
97 98 5.221722 ACAGTGATGGAGCTAGAAAAACTGA 60.222 40.000 17.08 0.00 36.78 3.41
99 100 5.234466 ACAGTGATGGAGCTAGAAAAACT 57.766 39.130 0.00 0.00 0.00 2.66
100 101 7.617041 ATTACAGTGATGGAGCTAGAAAAAC 57.383 36.000 0.00 0.00 0.00 2.43
101 102 9.733556 TTTATTACAGTGATGGAGCTAGAAAAA 57.266 29.630 0.00 0.00 0.00 1.94
102 103 9.162764 GTTTATTACAGTGATGGAGCTAGAAAA 57.837 33.333 0.00 0.00 0.00 2.29
103 104 8.318412 TGTTTATTACAGTGATGGAGCTAGAAA 58.682 33.333 0.00 0.00 31.68 2.52
104 105 7.764443 GTGTTTATTACAGTGATGGAGCTAGAA 59.236 37.037 0.00 0.00 37.45 2.10
105 106 7.093509 TGTGTTTATTACAGTGATGGAGCTAGA 60.094 37.037 0.00 0.00 37.45 2.43
106 107 7.010552 GTGTGTTTATTACAGTGATGGAGCTAG 59.989 40.741 0.00 0.00 37.45 3.42
107 108 6.816640 GTGTGTTTATTACAGTGATGGAGCTA 59.183 38.462 0.00 0.00 37.45 3.32
108 109 5.643777 GTGTGTTTATTACAGTGATGGAGCT 59.356 40.000 0.00 0.00 37.45 4.09
109 110 5.163754 GGTGTGTTTATTACAGTGATGGAGC 60.164 44.000 0.00 0.00 37.45 4.70
111 112 5.250200 GGGTGTGTTTATTACAGTGATGGA 58.750 41.667 0.00 0.00 37.45 3.41
112 113 4.094294 CGGGTGTGTTTATTACAGTGATGG 59.906 45.833 0.00 0.00 37.45 3.51
113 114 4.693566 ACGGGTGTGTTTATTACAGTGATG 59.306 41.667 0.00 0.00 37.45 3.07
114 115 4.693566 CACGGGTGTGTTTATTACAGTGAT 59.306 41.667 0.00 0.00 41.34 3.06
115 116 4.059511 CACGGGTGTGTTTATTACAGTGA 58.940 43.478 0.00 0.00 41.34 3.41
117 118 3.181452 ACCACGGGTGTGTTTATTACAGT 60.181 43.478 0.00 0.00 44.92 3.55
118 119 3.404899 ACCACGGGTGTGTTTATTACAG 58.595 45.455 0.00 0.00 44.92 2.74
119 120 3.488778 ACCACGGGTGTGTTTATTACA 57.511 42.857 0.00 0.00 44.92 2.41
120 121 3.565063 ACAACCACGGGTGTGTTTATTAC 59.435 43.478 5.82 0.00 44.92 1.89
121 122 3.818180 ACAACCACGGGTGTGTTTATTA 58.182 40.909 5.82 0.00 44.92 0.98
122 123 2.657143 ACAACCACGGGTGTGTTTATT 58.343 42.857 5.82 0.00 44.92 1.40
123 124 2.351706 ACAACCACGGGTGTGTTTAT 57.648 45.000 5.82 0.00 44.92 1.40
124 125 2.836262 CTACAACCACGGGTGTGTTTA 58.164 47.619 17.16 0.00 44.92 2.01
126 127 0.816421 GCTACAACCACGGGTGTGTT 60.816 55.000 17.16 1.52 44.92 3.32
127 128 1.227734 GCTACAACCACGGGTGTGT 60.228 57.895 17.16 10.61 44.92 3.72
128 129 1.964373 GGCTACAACCACGGGTGTG 60.964 63.158 17.16 8.00 46.00 3.82
129 130 1.774894 ATGGCTACAACCACGGGTGT 61.775 55.000 12.24 12.24 44.17 4.16
130 131 1.002624 ATGGCTACAACCACGGGTG 60.003 57.895 0.00 0.00 44.17 4.61
131 132 1.002624 CATGGCTACAACCACGGGT 60.003 57.895 0.00 0.00 44.17 5.28
132 133 1.002624 ACATGGCTACAACCACGGG 60.003 57.895 0.00 0.00 44.17 5.28
133 134 1.305219 CCACATGGCTACAACCACGG 61.305 60.000 0.00 0.00 44.17 4.94
134 135 0.321210 TCCACATGGCTACAACCACG 60.321 55.000 0.00 0.00 44.17 4.94
135 136 1.812571 CTTCCACATGGCTACAACCAC 59.187 52.381 0.00 0.00 44.17 4.16
136 137 1.423541 ACTTCCACATGGCTACAACCA 59.576 47.619 0.00 0.00 45.82 3.67
140 141 1.696884 TGACACTTCCACATGGCTACA 59.303 47.619 0.00 0.00 34.44 2.74
141 142 2.472695 TGACACTTCCACATGGCTAC 57.527 50.000 0.00 0.00 34.44 3.58
143 144 1.901591 CTTGACACTTCCACATGGCT 58.098 50.000 0.00 0.00 34.44 4.75
147 148 2.645838 ACAGCTTGACACTTCCACAT 57.354 45.000 0.00 0.00 0.00 3.21
148 149 2.418368 AACAGCTTGACACTTCCACA 57.582 45.000 0.00 0.00 0.00 4.17
149 150 2.682856 TGAAACAGCTTGACACTTCCAC 59.317 45.455 0.00 0.00 0.00 4.02
150 151 2.945008 CTGAAACAGCTTGACACTTCCA 59.055 45.455 0.00 0.00 0.00 3.53
151 152 2.945668 ACTGAAACAGCTTGACACTTCC 59.054 45.455 0.00 0.00 34.37 3.46
152 153 4.142600 ACAACTGAAACAGCTTGACACTTC 60.143 41.667 15.19 0.00 34.37 3.01
153 154 3.758554 ACAACTGAAACAGCTTGACACTT 59.241 39.130 15.19 0.00 34.37 3.16
154 155 3.347216 ACAACTGAAACAGCTTGACACT 58.653 40.909 15.19 0.00 34.37 3.55
156 157 3.312421 GCTACAACTGAAACAGCTTGACA 59.688 43.478 15.19 0.00 34.37 3.58
157 158 3.304057 GGCTACAACTGAAACAGCTTGAC 60.304 47.826 15.19 8.20 34.37 3.18
158 159 2.878406 GGCTACAACTGAAACAGCTTGA 59.122 45.455 15.19 4.89 34.37 3.02
159 160 2.618241 TGGCTACAACTGAAACAGCTTG 59.382 45.455 0.00 0.00 34.37 4.01
160 161 2.930950 TGGCTACAACTGAAACAGCTT 58.069 42.857 0.00 0.00 34.37 3.74
161 162 2.638480 TGGCTACAACTGAAACAGCT 57.362 45.000 0.00 0.00 34.37 4.24
162 163 2.605580 GCTTGGCTACAACTGAAACAGC 60.606 50.000 0.00 0.00 34.37 4.40
163 164 2.030805 GGCTTGGCTACAACTGAAACAG 60.031 50.000 0.00 0.00 37.52 3.16
164 165 1.953686 GGCTTGGCTACAACTGAAACA 59.046 47.619 0.00 0.00 32.14 2.83
166 167 2.622942 CAAGGCTTGGCTACAACTGAAA 59.377 45.455 19.55 0.00 32.14 2.69
167 168 2.158682 TCAAGGCTTGGCTACAACTGAA 60.159 45.455 25.92 0.00 32.14 3.02
168 169 1.419762 TCAAGGCTTGGCTACAACTGA 59.580 47.619 25.92 0.49 32.14 3.41
169 170 1.896220 TCAAGGCTTGGCTACAACTG 58.104 50.000 25.92 0.00 32.14 3.16
172 173 1.003118 ACGATCAAGGCTTGGCTACAA 59.997 47.619 25.92 6.96 34.87 2.41
173 174 0.613260 ACGATCAAGGCTTGGCTACA 59.387 50.000 25.92 7.71 0.00 2.74
175 176 0.744414 GCACGATCAAGGCTTGGCTA 60.744 55.000 25.92 8.48 0.00 3.93
178 179 2.409870 GGGCACGATCAAGGCTTGG 61.410 63.158 25.92 13.25 0.00 3.61
180 181 2.044946 GGGGCACGATCAAGGCTT 60.045 61.111 0.00 0.00 0.00 4.35
183 184 2.124570 CTGGGGGCACGATCAAGG 60.125 66.667 0.00 0.00 0.00 3.61
184 185 1.450312 GTCTGGGGGCACGATCAAG 60.450 63.158 0.00 0.00 0.00 3.02
185 186 2.668632 GTCTGGGGGCACGATCAA 59.331 61.111 0.00 0.00 0.00 2.57
186 187 3.399181 GGTCTGGGGGCACGATCA 61.399 66.667 0.00 0.00 0.00 2.92
187 188 4.176752 GGGTCTGGGGGCACGATC 62.177 72.222 0.00 0.00 0.00 3.69
188 189 4.741239 AGGGTCTGGGGGCACGAT 62.741 66.667 0.00 0.00 0.00 3.73
191 192 3.721706 CTCAGGGTCTGGGGGCAC 61.722 72.222 0.00 0.00 31.51 5.01
192 193 4.270153 ACTCAGGGTCTGGGGGCA 62.270 66.667 0.00 0.00 36.05 5.36
194 195 2.203998 ACACTCAGGGTCTGGGGG 60.204 66.667 0.00 0.00 41.92 5.40
195 196 1.127567 TTCACACTCAGGGTCTGGGG 61.128 60.000 0.00 0.00 36.05 4.96
196 197 0.035458 GTTCACACTCAGGGTCTGGG 59.965 60.000 0.00 0.00 38.07 4.45
197 198 0.035458 GGTTCACACTCAGGGTCTGG 59.965 60.000 0.00 0.00 31.51 3.86
199 200 1.051812 CAGGTTCACACTCAGGGTCT 58.948 55.000 0.00 0.00 0.00 3.85
200 201 0.603975 GCAGGTTCACACTCAGGGTC 60.604 60.000 0.00 0.00 0.00 4.46
201 202 1.344953 TGCAGGTTCACACTCAGGGT 61.345 55.000 0.00 0.00 0.00 4.34
202 203 0.886490 GTGCAGGTTCACACTCAGGG 60.886 60.000 0.00 0.00 36.97 4.45
203 204 0.107456 AGTGCAGGTTCACACTCAGG 59.893 55.000 0.00 0.00 43.55 3.86
204 205 2.297315 TCTAGTGCAGGTTCACACTCAG 59.703 50.000 0.00 0.00 43.55 3.35
206 207 3.386768 TTCTAGTGCAGGTTCACACTC 57.613 47.619 0.00 0.00 43.55 3.51
208 209 4.566004 TGTATTCTAGTGCAGGTTCACAC 58.434 43.478 0.00 0.00 39.35 3.82
209 210 4.882842 TGTATTCTAGTGCAGGTTCACA 57.117 40.909 0.00 0.00 39.35 3.58
211 212 5.738619 TCTTGTATTCTAGTGCAGGTTCA 57.261 39.130 0.00 0.00 0.00 3.18
212 213 6.341316 TCATCTTGTATTCTAGTGCAGGTTC 58.659 40.000 0.00 0.00 0.00 3.62
213 214 6.299805 TCATCTTGTATTCTAGTGCAGGTT 57.700 37.500 0.00 0.00 0.00 3.50
214 215 5.939764 TCATCTTGTATTCTAGTGCAGGT 57.060 39.130 0.00 0.00 0.00 4.00
215 216 5.931146 GGATCATCTTGTATTCTAGTGCAGG 59.069 44.000 0.00 0.00 0.00 4.85
218 219 6.283694 TGTGGATCATCTTGTATTCTAGTGC 58.716 40.000 0.00 0.00 0.00 4.40
219 220 8.899427 ATTGTGGATCATCTTGTATTCTAGTG 57.101 34.615 0.00 0.00 0.00 2.74
222 223 8.717717 AGGAATTGTGGATCATCTTGTATTCTA 58.282 33.333 0.00 0.00 0.00 2.10
223 224 7.501559 CAGGAATTGTGGATCATCTTGTATTCT 59.498 37.037 0.00 0.00 0.00 2.40
224 225 7.646314 CAGGAATTGTGGATCATCTTGTATTC 58.354 38.462 0.00 0.00 0.00 1.75
225 226 6.040166 GCAGGAATTGTGGATCATCTTGTATT 59.960 38.462 0.00 0.00 0.00 1.89
227 228 4.883585 GCAGGAATTGTGGATCATCTTGTA 59.116 41.667 0.00 0.00 0.00 2.41
229 230 3.697542 TGCAGGAATTGTGGATCATCTTG 59.302 43.478 0.00 0.00 0.00 3.02
230 231 3.698040 GTGCAGGAATTGTGGATCATCTT 59.302 43.478 0.00 0.00 0.00 2.40
231 232 3.053842 AGTGCAGGAATTGTGGATCATCT 60.054 43.478 0.00 0.00 0.00 2.90
233 234 3.377253 AGTGCAGGAATTGTGGATCAT 57.623 42.857 0.00 0.00 0.00 2.45
234 235 2.821378 CAAGTGCAGGAATTGTGGATCA 59.179 45.455 0.00 0.00 0.00 2.92
237 238 0.961019 GCAAGTGCAGGAATTGTGGA 59.039 50.000 3.95 0.00 41.59 4.02
238 239 0.963962 AGCAAGTGCAGGAATTGTGG 59.036 50.000 6.00 0.00 45.16 4.17
240 241 1.269936 GCAAGCAAGTGCAGGAATTGT 60.270 47.619 6.00 0.00 44.29 2.71
241 242 1.425412 GCAAGCAAGTGCAGGAATTG 58.575 50.000 6.00 0.00 44.29 2.32
242 243 3.900446 GCAAGCAAGTGCAGGAATT 57.100 47.368 6.00 0.00 44.29 2.17
250 251 1.610038 TGTCCTCATTGCAAGCAAGTG 59.390 47.619 13.35 11.05 39.47 3.16
251 252 1.610522 GTGTCCTCATTGCAAGCAAGT 59.389 47.619 13.35 0.00 39.47 3.16
252 253 1.068055 GGTGTCCTCATTGCAAGCAAG 60.068 52.381 13.35 1.89 39.47 4.01
253 254 0.961019 GGTGTCCTCATTGCAAGCAA 59.039 50.000 10.19 10.19 40.47 3.91
254 255 0.178995 TGGTGTCCTCATTGCAAGCA 60.179 50.000 4.94 0.00 0.00 3.91
257 258 5.782047 CTTAAATTGGTGTCCTCATTGCAA 58.218 37.500 0.00 0.00 0.00 4.08
258 259 4.321899 GCTTAAATTGGTGTCCTCATTGCA 60.322 41.667 0.00 0.00 0.00 4.08
260 261 4.155826 TCGCTTAAATTGGTGTCCTCATTG 59.844 41.667 0.00 0.00 0.00 2.82
261 262 4.331968 TCGCTTAAATTGGTGTCCTCATT 58.668 39.130 0.00 0.00 0.00 2.57
262 263 3.941483 CTCGCTTAAATTGGTGTCCTCAT 59.059 43.478 0.00 0.00 0.00 2.90
263 264 3.334691 CTCGCTTAAATTGGTGTCCTCA 58.665 45.455 0.00 0.00 0.00 3.86
264 265 2.096013 GCTCGCTTAAATTGGTGTCCTC 59.904 50.000 0.00 0.00 0.00 3.71
265 266 2.084546 GCTCGCTTAAATTGGTGTCCT 58.915 47.619 0.00 0.00 0.00 3.85
268 269 4.314740 TTTTGCTCGCTTAAATTGGTGT 57.685 36.364 0.00 0.00 0.00 4.16
269 270 5.443170 CGATTTTTGCTCGCTTAAATTGGTG 60.443 40.000 0.00 0.00 0.00 4.17
270 271 4.621034 CGATTTTTGCTCGCTTAAATTGGT 59.379 37.500 0.00 0.00 0.00 3.67
272 273 5.745653 ACGATTTTTGCTCGCTTAAATTG 57.254 34.783 0.00 11.49 39.71 2.32
273 274 6.375377 TGTACGATTTTTGCTCGCTTAAATT 58.625 32.000 0.00 0.00 39.71 1.82
274 275 5.933790 TGTACGATTTTTGCTCGCTTAAAT 58.066 33.333 0.00 0.00 39.71 1.40
275 276 5.345609 TGTACGATTTTTGCTCGCTTAAA 57.654 34.783 0.00 0.00 39.71 1.52
276 277 4.994220 TGTACGATTTTTGCTCGCTTAA 57.006 36.364 0.00 0.00 39.71 1.85
277 278 4.994220 TTGTACGATTTTTGCTCGCTTA 57.006 36.364 0.00 0.00 39.71 3.09
279 280 4.630069 AGTATTGTACGATTTTTGCTCGCT 59.370 37.500 0.00 0.00 39.71 4.93
281 282 7.218145 AGTAGTATTGTACGATTTTTGCTCG 57.782 36.000 0.00 0.00 41.77 5.03
285 286 9.355215 AGTGAGAGTAGTATTGTACGATTTTTG 57.645 33.333 0.00 0.00 0.00 2.44
340 341 5.747951 ACGTTAGGTCCTCTATAAACGAG 57.252 43.478 24.05 3.72 34.87 4.18
342 343 7.642669 TCATAACGTTAGGTCCTCTATAAACG 58.357 38.462 18.46 18.18 36.39 3.60
360 367 3.242944 ACGAAGCATCAACGATCATAACG 59.757 43.478 0.00 0.00 0.00 3.18
376 384 0.657840 ACAACAAGACAGCACGAAGC 59.342 50.000 0.00 0.00 46.19 3.86
380 388 1.139989 ATCGACAACAAGACAGCACG 58.860 50.000 0.00 0.00 0.00 5.34
394 402 5.532664 ACCCCAAGTCTATTTCTATCGAC 57.467 43.478 0.00 0.00 0.00 4.20
404 412 5.289510 AGATGGTTTCTACCCCAAGTCTAT 58.710 41.667 0.00 0.00 44.35 1.98
413 651 3.435671 CGTTGACAAGATGGTTTCTACCC 59.564 47.826 0.00 0.00 44.35 3.69
468 706 4.455190 AGAAAATCTGACTGAGCAAGAAGC 59.545 41.667 0.00 0.00 46.19 3.86
469 707 7.664082 TTAGAAAATCTGACTGAGCAAGAAG 57.336 36.000 0.00 0.00 0.00 2.85
471 709 7.389232 TGATTAGAAAATCTGACTGAGCAAGA 58.611 34.615 0.35 0.00 41.83 3.02
472 710 7.606858 TGATTAGAAAATCTGACTGAGCAAG 57.393 36.000 0.35 0.00 41.83 4.01
473 711 6.093219 GCTGATTAGAAAATCTGACTGAGCAA 59.907 38.462 8.60 0.00 41.26 3.91
713 1004 3.403057 GACAAAGAGCACGCGCGA 61.403 61.111 39.36 0.00 45.49 5.87
715 1006 1.722507 GTTGACAAAGAGCACGCGC 60.723 57.895 5.73 0.00 38.99 6.86
720 1011 0.874390 GGCGATGTTGACAAAGAGCA 59.126 50.000 0.00 0.00 0.00 4.26
747 1039 0.591659 GTTGAAGTGAAGAACCGGCC 59.408 55.000 0.00 0.00 0.00 6.13
875 1735 1.208293 GAACGGAATGGAAGCTCCTCT 59.792 52.381 0.00 0.00 37.46 3.69
905 1765 3.391382 GAGTGGGGCTACGTGGCT 61.391 66.667 23.68 2.68 41.48 4.75
908 1768 1.215647 GAGTGAGTGGGGCTACGTG 59.784 63.158 0.00 0.00 0.00 4.49
965 1845 1.001406 CACAGACAGGGGAGACAGAAC 59.999 57.143 0.00 0.00 0.00 3.01
1044 1943 0.662619 TCTTGGCGAAGTTTGTGCTG 59.337 50.000 8.41 0.00 0.00 4.41
1070 1969 2.498885 TGATCACTGATCAGACCACCAG 59.501 50.000 29.27 9.25 43.11 4.00
1103 2002 3.619038 GCGAGAGATAAGAAACCACAAGG 59.381 47.826 0.00 0.00 42.21 3.61
1646 2589 2.746277 ATCGGCGCCACAGGTTTC 60.746 61.111 28.98 0.00 0.00 2.78
1647 2590 3.055719 CATCGGCGCCACAGGTTT 61.056 61.111 28.98 0.00 0.00 3.27
1651 2594 4.552365 ATCCCATCGGCGCCACAG 62.552 66.667 28.98 14.72 0.00 3.66
1652 2595 4.854924 CATCCCATCGGCGCCACA 62.855 66.667 28.98 13.13 0.00 4.17
1702 2673 6.038714 GTGTATCCAAGAGAAAGGGCAAATAG 59.961 42.308 0.00 0.00 0.00 1.73
1725 2696 6.515531 CGGAGAGAGTACTAGGAGTAGTAGTG 60.516 50.000 0.00 0.00 42.98 2.74
1769 2751 1.211457 ACCATTTTGCCACAAGCCAAA 59.789 42.857 0.00 0.00 40.11 3.28
1888 2873 5.986004 ACACAAAAGAAGTAGAAACTCGG 57.014 39.130 0.00 0.00 33.75 4.63
1991 3008 6.974048 CACATCAAAATTGATCCAAAGCGATA 59.026 34.615 5.68 0.00 45.62 2.92
2032 3072 3.349927 TGCCATGTTTCTGAATCTCTGG 58.650 45.455 12.44 12.44 0.00 3.86
2047 3087 2.741517 TGTTCGTGTATCTGTTGCCATG 59.258 45.455 0.00 0.00 0.00 3.66
2061 3115 2.052237 GGCTTGTGCGTGTTCGTG 60.052 61.111 0.00 0.00 40.82 4.35
2066 3120 4.988598 CTCCGGGCTTGTGCGTGT 62.989 66.667 0.00 0.00 40.82 4.49
2164 3337 6.771749 ACGACTACTAGTATTATCCAACTGCT 59.228 38.462 2.33 0.00 0.00 4.24
2167 3340 8.404000 CACAACGACTACTAGTATTATCCAACT 58.596 37.037 2.33 0.00 0.00 3.16
2179 3352 4.500603 ACCAGTTCACAACGACTACTAG 57.499 45.455 0.00 0.00 36.23 2.57
2181 3354 3.814005 AACCAGTTCACAACGACTACT 57.186 42.857 0.00 0.00 36.23 2.57
2182 3355 4.117685 AGAAACCAGTTCACAACGACTAC 58.882 43.478 0.00 0.00 38.86 2.73
2183 3356 4.395959 AGAAACCAGTTCACAACGACTA 57.604 40.909 0.00 0.00 38.86 2.59
2184 3357 3.261981 AGAAACCAGTTCACAACGACT 57.738 42.857 0.00 0.00 38.86 4.18
2222 3409 4.689079 GATCGAGTCGAGTTGAAACAAAC 58.311 43.478 21.36 0.00 39.91 2.93
2258 3445 1.156736 GGCTGCGACAGTGTTTGTAT 58.843 50.000 0.00 0.00 41.05 2.29
2259 3446 1.218875 CGGCTGCGACAGTGTTTGTA 61.219 55.000 0.00 0.00 41.05 2.41
2263 3466 2.967076 CACGGCTGCGACAGTGTT 60.967 61.111 0.00 0.00 33.43 3.32
2289 3492 9.122779 GAGGTAGACTAGATAGTGTTTGTATGT 57.877 37.037 0.00 0.00 36.50 2.29
2290 3493 8.283992 CGAGGTAGACTAGATAGTGTTTGTATG 58.716 40.741 0.00 0.00 36.50 2.39
2291 3494 7.992033 ACGAGGTAGACTAGATAGTGTTTGTAT 59.008 37.037 0.00 0.00 36.50 2.29
2292 3495 7.279536 CACGAGGTAGACTAGATAGTGTTTGTA 59.720 40.741 0.00 0.00 36.50 2.41
2296 3499 5.743117 ACACGAGGTAGACTAGATAGTGTT 58.257 41.667 0.00 0.00 37.03 3.32
2298 3501 5.603596 AGACACGAGGTAGACTAGATAGTG 58.396 45.833 0.00 5.89 36.50 2.74
2307 3516 3.988517 CCAAGAAAAGACACGAGGTAGAC 59.011 47.826 0.00 0.00 0.00 2.59
2364 3574 5.258841 TGTAGGTCCGAGTCATTTTCTCTA 58.741 41.667 0.00 0.00 0.00 2.43
2366 3576 4.425520 CTGTAGGTCCGAGTCATTTTCTC 58.574 47.826 0.00 0.00 0.00 2.87
2368 3578 2.930682 GCTGTAGGTCCGAGTCATTTTC 59.069 50.000 0.00 0.00 0.00 2.29
2370 3580 2.166664 GAGCTGTAGGTCCGAGTCATTT 59.833 50.000 0.00 0.00 36.62 2.32
2371 3581 1.751924 GAGCTGTAGGTCCGAGTCATT 59.248 52.381 0.00 0.00 36.62 2.57
2372 3582 1.394618 GAGCTGTAGGTCCGAGTCAT 58.605 55.000 0.00 0.00 36.62 3.06
2387 3617 0.260230 TAGCTAGCCAGACTGGAGCT 59.740 55.000 30.26 30.26 45.92 4.09
2460 5180 3.441922 GGCACTCTTCAAGAAGGGAAATC 59.558 47.826 16.18 2.63 41.39 2.17
2506 5231 0.591170 ACATTCCGCGTGAAAACTGG 59.409 50.000 4.92 1.10 36.33 4.00
2518 5243 1.883021 GGAGGGCAACAACATTCCG 59.117 57.895 0.00 0.00 39.74 4.30


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

AutoCloner maintained by Alex Coulton.