Multiple sequence alignment - TraesCS4D01G181100

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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 TraesCS4D01G181100 chr4D 100.000 3459 0 0 1 3459 315595668 315599126 0.000000e+00 6388.0
1 TraesCS4D01G181100 chr4A 91.264 2255 71 50 604 2808 159295872 159293694 0.000000e+00 2957.0
2 TraesCS4D01G181100 chr4A 89.145 304 7 8 331 608 159296427 159296124 4.250000e-94 355.0
3 TraesCS4D01G181100 chr4B 93.253 1912 53 23 931 2803 393405537 393407411 0.000000e+00 2747.0
4 TraesCS4D01G181100 chr4B 87.702 618 24 22 329 900 393404926 393405537 0.000000e+00 673.0
5 TraesCS4D01G181100 chr6D 94.082 659 30 8 2804 3458 55897011 55896358 0.000000e+00 992.0
6 TraesCS4D01G181100 chr6D 87.736 106 11 2 2 106 82668079 82668183 4.690000e-24 122.0
7 TraesCS4D01G181100 chr2D 93.274 669 35 10 2796 3458 589592849 589592185 0.000000e+00 977.0
8 TraesCS4D01G181100 chr2D 91.914 606 34 11 2803 3397 518802486 518803087 0.000000e+00 833.0
9 TraesCS4D01G181100 chr2D 88.961 308 34 0 1656 1963 48133243 48133550 7.010000e-102 381.0
10 TraesCS4D01G181100 chr5D 93.083 665 39 7 2797 3458 461906459 461905799 0.000000e+00 966.0
11 TraesCS4D01G181100 chr5D 85.714 91 10 2 3368 3458 404187463 404187550 3.680000e-15 93.5
12 TraesCS4D01G181100 chr1D 93.333 660 35 8 2806 3458 243704117 243703460 0.000000e+00 966.0
13 TraesCS4D01G181100 chr1D 85.714 308 44 0 1655 1962 60317505 60317812 3.330000e-85 326.0
14 TraesCS4D01G181100 chr1D 88.571 105 10 2 2 106 331198389 331198287 3.620000e-25 126.0
15 TraesCS4D01G181100 chr7D 93.098 652 39 6 2801 3448 458944294 458943645 0.000000e+00 950.0
16 TraesCS4D01G181100 chr3D 93.130 655 34 8 2808 3458 551244752 551244105 0.000000e+00 950.0
17 TraesCS4D01G181100 chr3D 87.342 316 40 0 1659 1974 525917682 525917367 2.540000e-96 363.0
18 TraesCS4D01G181100 chr3D 92.793 111 6 2 2 112 613075356 613075464 3.570000e-35 159.0
19 TraesCS4D01G181100 chr3D 90.291 103 10 0 2 104 40740533 40740431 6.020000e-28 135.0
20 TraesCS4D01G181100 chr2A 92.401 658 43 7 2806 3458 719093634 719094289 0.000000e+00 931.0
21 TraesCS4D01G181100 chr2A 89.216 306 33 0 1659 1964 51008492 51008187 1.950000e-102 383.0
22 TraesCS4D01G181100 chr2A 90.476 105 8 2 2 106 562688585 562688483 1.670000e-28 137.0
23 TraesCS4D01G181100 chr3A 91.806 659 40 12 2806 3458 738058774 738059424 0.000000e+00 905.0
24 TraesCS4D01G181100 chr3A 87.616 323 39 1 1656 1978 660196052 660196373 1.170000e-99 374.0
25 TraesCS4D01G181100 chr3A 85.938 128 9 4 2 120 84689671 84689798 1.010000e-25 128.0
26 TraesCS4D01G181100 chr2B 89.137 313 34 0 1656 1968 75847560 75847872 1.160000e-104 390.0
27 TraesCS4D01G181100 chr2B 89.655 116 10 2 2 115 779132086 779131971 2.780000e-31 147.0
28 TraesCS4D01G181100 chr3B 86.774 310 39 2 1656 1964 694263570 694263878 9.190000e-91 344.0
29 TraesCS4D01G181100 chr1B 89.565 115 11 1 2 115 4475430 4475316 1.000000e-30 145.0
30 TraesCS4D01G181100 chr1B 90.090 111 8 3 2 109 656092968 656093078 1.290000e-29 141.0


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 TraesCS4D01G181100 chr4D 315595668 315599126 3458 False 6388 6388 100.0000 1 3459 1 chr4D.!!$F1 3458
1 TraesCS4D01G181100 chr4A 159293694 159296427 2733 True 1656 2957 90.2045 331 2808 2 chr4A.!!$R1 2477
2 TraesCS4D01G181100 chr4B 393404926 393407411 2485 False 1710 2747 90.4775 329 2803 2 chr4B.!!$F1 2474
3 TraesCS4D01G181100 chr6D 55896358 55897011 653 True 992 992 94.0820 2804 3458 1 chr6D.!!$R1 654
4 TraesCS4D01G181100 chr2D 589592185 589592849 664 True 977 977 93.2740 2796 3458 1 chr2D.!!$R1 662
5 TraesCS4D01G181100 chr2D 518802486 518803087 601 False 833 833 91.9140 2803 3397 1 chr2D.!!$F2 594
6 TraesCS4D01G181100 chr5D 461905799 461906459 660 True 966 966 93.0830 2797 3458 1 chr5D.!!$R1 661
7 TraesCS4D01G181100 chr1D 243703460 243704117 657 True 966 966 93.3330 2806 3458 1 chr1D.!!$R1 652
8 TraesCS4D01G181100 chr7D 458943645 458944294 649 True 950 950 93.0980 2801 3448 1 chr7D.!!$R1 647
9 TraesCS4D01G181100 chr3D 551244105 551244752 647 True 950 950 93.1300 2808 3458 1 chr3D.!!$R3 650
10 TraesCS4D01G181100 chr2A 719093634 719094289 655 False 931 931 92.4010 2806 3458 1 chr2A.!!$F1 652
11 TraesCS4D01G181100 chr3A 738058774 738059424 650 False 905 905 91.8060 2806 3458 1 chr3A.!!$F3 652

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 0.109132 CCCGTGAAAATTGCAGAGGC 60.109 55.0 0.00 0.00 41.68 4.70 F
914 1229 0.109272 TTGTCCTCTACGCGAGCAAG 60.109 55.0 15.93 4.52 38.49 4.01 F
916 1231 0.798771 GTCCTCTACGCGAGCAAGTG 60.799 60.0 15.93 5.43 38.49 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1400 1744 1.066605 TCGTTCACTATAGCTTCCGGC 59.933 52.381 0.00 0.0 42.19 6.13 R
2389 2757 0.892358 TGTCCACGTCGAAGCTACCT 60.892 55.000 0.00 0.0 0.00 3.08 R
2851 3239 0.948623 CAAACAGACGCGGATCCACA 60.949 55.000 12.47 0.0 0.00 4.17 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
23 24 6.567769 CGCACTTAAAACTTTTGTCAATGT 57.432 33.333 0.00 0.00 0.00 2.71
24 25 6.988329 CGCACTTAAAACTTTTGTCAATGTT 58.012 32.000 0.00 0.00 32.90 2.71
25 26 7.452231 CGCACTTAAAACTTTTGTCAATGTTT 58.548 30.769 9.87 9.87 40.32 2.83
26 27 7.630606 CGCACTTAAAACTTTTGTCAATGTTTC 59.369 33.333 13.86 4.48 38.61 2.78
27 28 8.655970 GCACTTAAAACTTTTGTCAATGTTTCT 58.344 29.630 13.86 9.23 38.61 2.52
29 30 9.366216 ACTTAAAACTTTTGTCAATGTTTCTCC 57.634 29.630 13.86 0.00 38.61 3.71
30 31 9.586435 CTTAAAACTTTTGTCAATGTTTCTCCT 57.414 29.630 13.86 5.43 38.61 3.69
33 34 9.936759 AAAACTTTTGTCAATGTTTCTCCTAAA 57.063 25.926 13.86 0.00 38.61 1.85
34 35 9.936759 AAACTTTTGTCAATGTTTCTCCTAAAA 57.063 25.926 9.87 0.00 36.13 1.52
35 36 9.936759 AACTTTTGTCAATGTTTCTCCTAAAAA 57.063 25.926 0.00 0.00 28.24 1.94
79 80 8.804688 TTTATTTTGATTTTACTGTTCACCCG 57.195 30.769 0.00 0.00 0.00 5.28
80 81 6.642707 ATTTTGATTTTACTGTTCACCCGA 57.357 33.333 0.00 0.00 0.00 5.14
81 82 5.682943 TTTGATTTTACTGTTCACCCGAG 57.317 39.130 0.00 0.00 0.00 4.63
82 83 3.071479 TGATTTTACTGTTCACCCGAGC 58.929 45.455 0.00 0.00 0.00 5.03
83 84 2.922740 TTTTACTGTTCACCCGAGCT 57.077 45.000 0.00 0.00 0.00 4.09
84 85 2.450609 TTTACTGTTCACCCGAGCTC 57.549 50.000 2.73 2.73 0.00 4.09
85 86 1.334160 TTACTGTTCACCCGAGCTCA 58.666 50.000 15.40 0.00 0.00 4.26
86 87 1.557099 TACTGTTCACCCGAGCTCAT 58.443 50.000 15.40 0.00 0.00 2.90
87 88 0.687354 ACTGTTCACCCGAGCTCATT 59.313 50.000 15.40 0.00 0.00 2.57
88 89 1.072331 ACTGTTCACCCGAGCTCATTT 59.928 47.619 15.40 0.00 0.00 2.32
89 90 2.301870 ACTGTTCACCCGAGCTCATTTA 59.698 45.455 15.40 0.00 0.00 1.40
90 91 3.244422 ACTGTTCACCCGAGCTCATTTAA 60.244 43.478 15.40 0.00 0.00 1.52
91 92 3.334691 TGTTCACCCGAGCTCATTTAAG 58.665 45.455 15.40 0.00 0.00 1.85
92 93 2.024176 TCACCCGAGCTCATTTAAGC 57.976 50.000 15.40 0.00 42.82 3.09
100 101 2.840296 GCTCATTTAAGCTCAGGTGC 57.160 50.000 0.00 0.00 39.27 5.01
101 102 2.086869 GCTCATTTAAGCTCAGGTGCA 58.913 47.619 0.00 0.00 39.27 4.57
102 103 2.097142 GCTCATTTAAGCTCAGGTGCAG 59.903 50.000 0.00 0.00 39.27 4.41
103 104 3.603532 CTCATTTAAGCTCAGGTGCAGA 58.396 45.455 0.00 0.00 34.99 4.26
104 105 4.005650 CTCATTTAAGCTCAGGTGCAGAA 58.994 43.478 0.00 0.00 34.99 3.02
105 106 4.397420 TCATTTAAGCTCAGGTGCAGAAA 58.603 39.130 0.00 0.00 34.99 2.52
106 107 4.216257 TCATTTAAGCTCAGGTGCAGAAAC 59.784 41.667 0.00 0.00 34.99 2.78
107 108 3.492102 TTAAGCTCAGGTGCAGAAACT 57.508 42.857 0.00 0.00 34.99 2.66
108 109 1.889545 AAGCTCAGGTGCAGAAACTC 58.110 50.000 0.00 0.00 34.99 3.01
109 110 1.055040 AGCTCAGGTGCAGAAACTCT 58.945 50.000 0.00 0.00 34.99 3.24
110 111 1.155042 GCTCAGGTGCAGAAACTCTG 58.845 55.000 0.00 0.00 46.90 3.35
119 120 2.447244 CAGAAACTCTGCGTCTTCCT 57.553 50.000 0.00 0.00 37.72 3.36
120 121 3.577649 CAGAAACTCTGCGTCTTCCTA 57.422 47.619 0.00 0.00 37.72 2.94
121 122 3.506810 CAGAAACTCTGCGTCTTCCTAG 58.493 50.000 0.00 0.00 37.72 3.02
122 123 3.191581 CAGAAACTCTGCGTCTTCCTAGA 59.808 47.826 0.00 0.00 37.72 2.43
123 124 3.442273 AGAAACTCTGCGTCTTCCTAGAG 59.558 47.826 0.00 0.00 41.78 2.43
124 125 2.500392 ACTCTGCGTCTTCCTAGAGT 57.500 50.000 0.00 0.00 43.59 3.24
125 126 2.797786 ACTCTGCGTCTTCCTAGAGTT 58.202 47.619 0.00 0.00 45.48 3.01
126 127 3.158676 ACTCTGCGTCTTCCTAGAGTTT 58.841 45.455 0.00 0.00 45.48 2.66
127 128 3.057174 ACTCTGCGTCTTCCTAGAGTTTG 60.057 47.826 0.00 0.00 45.48 2.93
128 129 2.891580 TCTGCGTCTTCCTAGAGTTTGT 59.108 45.455 0.00 0.00 0.00 2.83
129 130 2.989840 CTGCGTCTTCCTAGAGTTTGTG 59.010 50.000 0.00 0.00 0.00 3.33
130 131 2.364324 TGCGTCTTCCTAGAGTTTGTGT 59.636 45.455 0.00 0.00 0.00 3.72
131 132 3.570975 TGCGTCTTCCTAGAGTTTGTGTA 59.429 43.478 0.00 0.00 0.00 2.90
132 133 4.167268 GCGTCTTCCTAGAGTTTGTGTAG 58.833 47.826 0.00 0.00 0.00 2.74
133 134 4.734917 CGTCTTCCTAGAGTTTGTGTAGG 58.265 47.826 0.00 0.00 42.63 3.18
134 135 4.496360 GTCTTCCTAGAGTTTGTGTAGGC 58.504 47.826 0.00 0.00 41.27 3.93
135 136 4.221041 GTCTTCCTAGAGTTTGTGTAGGCT 59.779 45.833 0.00 0.00 41.27 4.58
136 137 4.463186 TCTTCCTAGAGTTTGTGTAGGCTC 59.537 45.833 0.00 0.00 41.27 4.70
137 138 2.753452 TCCTAGAGTTTGTGTAGGCTCG 59.247 50.000 0.00 0.00 41.27 5.03
138 139 2.753452 CCTAGAGTTTGTGTAGGCTCGA 59.247 50.000 0.00 0.00 35.45 4.04
139 140 3.381908 CCTAGAGTTTGTGTAGGCTCGAT 59.618 47.826 0.00 0.00 35.45 3.59
140 141 4.579340 CCTAGAGTTTGTGTAGGCTCGATA 59.421 45.833 0.00 0.00 35.45 2.92
141 142 4.373348 AGAGTTTGTGTAGGCTCGATAC 57.627 45.455 0.00 0.00 33.57 2.24
142 143 4.017808 AGAGTTTGTGTAGGCTCGATACT 58.982 43.478 0.00 0.00 33.57 2.12
143 144 4.463186 AGAGTTTGTGTAGGCTCGATACTT 59.537 41.667 0.00 0.00 33.57 2.24
144 145 5.047235 AGAGTTTGTGTAGGCTCGATACTTT 60.047 40.000 0.00 0.00 33.57 2.66
145 146 5.548406 AGTTTGTGTAGGCTCGATACTTTT 58.452 37.500 0.00 0.00 0.00 2.27
146 147 5.995897 AGTTTGTGTAGGCTCGATACTTTTT 59.004 36.000 0.00 0.00 0.00 1.94
147 148 6.147328 AGTTTGTGTAGGCTCGATACTTTTTC 59.853 38.462 0.00 0.00 0.00 2.29
148 149 4.501071 TGTGTAGGCTCGATACTTTTTCC 58.499 43.478 0.00 0.00 0.00 3.13
149 150 3.869832 GTGTAGGCTCGATACTTTTTCCC 59.130 47.826 0.00 0.00 0.00 3.97
150 151 3.516300 TGTAGGCTCGATACTTTTTCCCA 59.484 43.478 0.00 0.00 0.00 4.37
151 152 2.987232 AGGCTCGATACTTTTTCCCAC 58.013 47.619 0.00 0.00 0.00 4.61
152 153 2.304761 AGGCTCGATACTTTTTCCCACA 59.695 45.455 0.00 0.00 0.00 4.17
153 154 3.078837 GGCTCGATACTTTTTCCCACAA 58.921 45.455 0.00 0.00 0.00 3.33
154 155 3.694566 GGCTCGATACTTTTTCCCACAAT 59.305 43.478 0.00 0.00 0.00 2.71
155 156 4.157840 GGCTCGATACTTTTTCCCACAATT 59.842 41.667 0.00 0.00 0.00 2.32
156 157 5.095490 GCTCGATACTTTTTCCCACAATTG 58.905 41.667 3.24 3.24 0.00 2.32
157 158 5.637006 TCGATACTTTTTCCCACAATTGG 57.363 39.130 10.83 0.00 43.50 3.16
158 159 5.074115 TCGATACTTTTTCCCACAATTGGT 58.926 37.500 10.83 0.00 42.10 3.67
159 160 6.239396 TCGATACTTTTTCCCACAATTGGTA 58.761 36.000 10.83 0.00 42.10 3.25
160 161 6.149807 TCGATACTTTTTCCCACAATTGGTAC 59.850 38.462 10.83 0.00 42.10 3.34
161 162 6.072397 CGATACTTTTTCCCACAATTGGTACA 60.072 38.462 10.83 0.00 42.10 2.90
162 163 5.270893 ACTTTTTCCCACAATTGGTACAC 57.729 39.130 10.83 0.00 42.10 2.90
163 164 4.712337 ACTTTTTCCCACAATTGGTACACA 59.288 37.500 10.83 0.00 42.10 3.72
164 165 4.927978 TTTTCCCACAATTGGTACACAG 57.072 40.909 10.83 0.00 42.10 3.66
165 166 3.866703 TTCCCACAATTGGTACACAGA 57.133 42.857 10.83 0.00 42.10 3.41
166 167 3.134574 TCCCACAATTGGTACACAGAC 57.865 47.619 10.83 0.00 42.10 3.51
167 168 2.439880 TCCCACAATTGGTACACAGACA 59.560 45.455 10.83 0.00 42.10 3.41
168 169 3.117851 TCCCACAATTGGTACACAGACAA 60.118 43.478 10.83 0.00 42.10 3.18
169 170 3.004315 CCCACAATTGGTACACAGACAAC 59.996 47.826 10.83 0.00 42.10 3.32
170 171 3.882888 CCACAATTGGTACACAGACAACT 59.117 43.478 10.83 0.00 39.29 3.16
171 172 4.338118 CCACAATTGGTACACAGACAACTT 59.662 41.667 10.83 0.00 39.29 2.66
172 173 5.529430 CCACAATTGGTACACAGACAACTTA 59.471 40.000 10.83 0.00 39.29 2.24
173 174 6.038825 CCACAATTGGTACACAGACAACTTAA 59.961 38.462 10.83 0.00 39.29 1.85
174 175 7.255451 CCACAATTGGTACACAGACAACTTAAT 60.255 37.037 10.83 0.00 39.29 1.40
175 176 8.134895 CACAATTGGTACACAGACAACTTAATT 58.865 33.333 10.83 0.00 39.29 1.40
176 177 9.344772 ACAATTGGTACACAGACAACTTAATTA 57.655 29.630 10.83 0.00 39.29 1.40
179 180 8.911918 TTGGTACACAGACAACTTAATTATGT 57.088 30.769 0.00 0.00 39.29 2.29
180 181 8.911918 TGGTACACAGACAACTTAATTATGTT 57.088 30.769 10.18 10.18 0.00 2.71
181 182 9.344772 TGGTACACAGACAACTTAATTATGTTT 57.655 29.630 12.68 6.40 0.00 2.83
182 183 9.821662 GGTACACAGACAACTTAATTATGTTTC 57.178 33.333 12.68 12.84 0.00 2.78
187 188 9.744468 ACAGACAACTTAATTATGTTTCAAACC 57.256 29.630 12.68 2.06 0.00 3.27
188 189 9.965824 CAGACAACTTAATTATGTTTCAAACCT 57.034 29.630 12.68 0.00 0.00 3.50
198 199 8.846943 ATTATGTTTCAAACCTTCAAAATCCC 57.153 30.769 0.00 0.00 0.00 3.85
199 200 4.688021 TGTTTCAAACCTTCAAAATCCCG 58.312 39.130 0.00 0.00 0.00 5.14
200 201 4.160626 TGTTTCAAACCTTCAAAATCCCGT 59.839 37.500 0.00 0.00 0.00 5.28
201 202 4.314740 TTCAAACCTTCAAAATCCCGTG 57.685 40.909 0.00 0.00 0.00 4.94
202 203 3.556999 TCAAACCTTCAAAATCCCGTGA 58.443 40.909 0.00 0.00 0.00 4.35
203 204 3.954904 TCAAACCTTCAAAATCCCGTGAA 59.045 39.130 0.00 0.00 32.91 3.18
204 205 4.402793 TCAAACCTTCAAAATCCCGTGAAA 59.597 37.500 0.00 0.00 33.52 2.69
205 206 5.105310 TCAAACCTTCAAAATCCCGTGAAAA 60.105 36.000 0.00 0.00 33.52 2.29
206 207 5.545063 AACCTTCAAAATCCCGTGAAAAT 57.455 34.783 0.00 0.00 33.52 1.82
207 208 5.545063 ACCTTCAAAATCCCGTGAAAATT 57.455 34.783 0.00 0.00 33.52 1.82
208 209 5.296748 ACCTTCAAAATCCCGTGAAAATTG 58.703 37.500 0.00 0.00 33.52 2.32
209 210 4.152223 CCTTCAAAATCCCGTGAAAATTGC 59.848 41.667 0.00 0.00 33.52 3.56
210 211 4.327982 TCAAAATCCCGTGAAAATTGCA 57.672 36.364 0.00 0.00 0.00 4.08
211 212 4.305769 TCAAAATCCCGTGAAAATTGCAG 58.694 39.130 0.00 0.00 0.00 4.41
212 213 4.038522 TCAAAATCCCGTGAAAATTGCAGA 59.961 37.500 0.00 0.00 0.00 4.26
213 214 3.855689 AATCCCGTGAAAATTGCAGAG 57.144 42.857 0.00 0.00 0.00 3.35
214 215 1.533625 TCCCGTGAAAATTGCAGAGG 58.466 50.000 0.00 0.00 0.00 3.69
215 216 0.109132 CCCGTGAAAATTGCAGAGGC 60.109 55.000 0.00 0.00 41.68 4.70
227 228 2.627515 GCAGAGGCAGTGGATATTCA 57.372 50.000 0.00 0.00 40.72 2.57
228 229 2.216898 GCAGAGGCAGTGGATATTCAC 58.783 52.381 5.96 5.96 40.72 3.18
229 230 2.843701 CAGAGGCAGTGGATATTCACC 58.156 52.381 10.72 0.00 38.34 4.02
230 231 1.771255 AGAGGCAGTGGATATTCACCC 59.229 52.381 10.72 5.96 38.34 4.61
231 232 1.771255 GAGGCAGTGGATATTCACCCT 59.229 52.381 10.72 10.77 38.34 4.34
232 233 1.771255 AGGCAGTGGATATTCACCCTC 59.229 52.381 10.72 0.76 38.34 4.30
233 234 1.771255 GGCAGTGGATATTCACCCTCT 59.229 52.381 10.72 0.00 38.34 3.69
234 235 2.173569 GGCAGTGGATATTCACCCTCTT 59.826 50.000 10.72 0.00 38.34 2.85
235 236 3.372025 GGCAGTGGATATTCACCCTCTTT 60.372 47.826 10.72 0.00 38.34 2.52
236 237 4.273318 GCAGTGGATATTCACCCTCTTTT 58.727 43.478 10.72 0.00 38.34 2.27
237 238 4.706962 GCAGTGGATATTCACCCTCTTTTT 59.293 41.667 10.72 0.00 38.34 1.94
238 239 5.393461 GCAGTGGATATTCACCCTCTTTTTG 60.393 44.000 10.72 1.29 38.34 2.44
239 240 5.126061 CAGTGGATATTCACCCTCTTTTTGG 59.874 44.000 10.72 0.00 38.34 3.28
240 241 5.015178 AGTGGATATTCACCCTCTTTTTGGA 59.985 40.000 10.72 0.00 38.34 3.53
241 242 5.358160 GTGGATATTCACCCTCTTTTTGGAG 59.642 44.000 2.30 0.00 0.00 3.86
242 243 5.252863 TGGATATTCACCCTCTTTTTGGAGA 59.747 40.000 0.00 0.00 35.52 3.71
243 244 6.187682 GGATATTCACCCTCTTTTTGGAGAA 58.812 40.000 0.00 0.00 35.52 2.87
244 245 6.319911 GGATATTCACCCTCTTTTTGGAGAAG 59.680 42.308 0.00 0.00 35.52 2.85
245 246 4.788925 TTCACCCTCTTTTTGGAGAAGA 57.211 40.909 0.00 0.00 35.52 2.87
246 247 4.788925 TCACCCTCTTTTTGGAGAAGAA 57.211 40.909 0.00 0.00 35.52 2.52
247 248 5.124036 TCACCCTCTTTTTGGAGAAGAAA 57.876 39.130 0.00 0.00 35.52 2.52
248 249 5.515106 TCACCCTCTTTTTGGAGAAGAAAA 58.485 37.500 0.00 0.00 35.52 2.29
249 250 5.955355 TCACCCTCTTTTTGGAGAAGAAAAA 59.045 36.000 0.00 0.00 35.52 1.94
270 271 3.503827 AAAATCCCGCGAAAATTCTCC 57.496 42.857 8.23 0.00 0.00 3.71
271 272 1.014352 AATCCCGCGAAAATTCTCCG 58.986 50.000 8.23 0.00 0.00 4.63
272 273 0.177141 ATCCCGCGAAAATTCTCCGA 59.823 50.000 8.23 0.00 0.00 4.55
273 274 0.738412 TCCCGCGAAAATTCTCCGAC 60.738 55.000 8.23 0.00 0.00 4.79
274 275 1.702491 CCCGCGAAAATTCTCCGACC 61.702 60.000 8.23 0.00 0.00 4.79
275 276 1.343821 CGCGAAAATTCTCCGACCG 59.656 57.895 0.00 0.00 0.00 4.79
276 277 1.074319 CGCGAAAATTCTCCGACCGA 61.074 55.000 0.00 0.00 0.00 4.69
277 278 1.073177 GCGAAAATTCTCCGACCGAA 58.927 50.000 0.00 0.00 0.00 4.30
278 279 1.664151 GCGAAAATTCTCCGACCGAAT 59.336 47.619 0.00 0.00 32.75 3.34
279 280 2.861935 GCGAAAATTCTCCGACCGAATA 59.138 45.455 0.00 0.00 31.27 1.75
280 281 3.307782 GCGAAAATTCTCCGACCGAATAA 59.692 43.478 0.00 0.00 31.27 1.40
281 282 4.550255 GCGAAAATTCTCCGACCGAATAAG 60.550 45.833 0.00 0.00 31.27 1.73
282 283 4.550255 CGAAAATTCTCCGACCGAATAAGC 60.550 45.833 0.00 0.00 31.27 3.09
283 284 3.536956 AATTCTCCGACCGAATAAGCA 57.463 42.857 0.00 0.00 31.27 3.91
284 285 3.536956 ATTCTCCGACCGAATAAGCAA 57.463 42.857 0.00 0.00 29.78 3.91
285 286 3.536956 TTCTCCGACCGAATAAGCAAT 57.463 42.857 0.00 0.00 0.00 3.56
286 287 4.659111 TTCTCCGACCGAATAAGCAATA 57.341 40.909 0.00 0.00 0.00 1.90
287 288 4.238761 TCTCCGACCGAATAAGCAATAG 57.761 45.455 0.00 0.00 0.00 1.73
288 289 3.635373 TCTCCGACCGAATAAGCAATAGT 59.365 43.478 0.00 0.00 0.00 2.12
289 290 4.823442 TCTCCGACCGAATAAGCAATAGTA 59.177 41.667 0.00 0.00 0.00 1.82
290 291 5.048921 TCTCCGACCGAATAAGCAATAGTAG 60.049 44.000 0.00 0.00 0.00 2.57
291 292 4.581824 TCCGACCGAATAAGCAATAGTAGT 59.418 41.667 0.00 0.00 0.00 2.73
292 293 4.680110 CCGACCGAATAAGCAATAGTAGTG 59.320 45.833 0.00 0.00 0.00 2.74
293 294 5.506815 CCGACCGAATAAGCAATAGTAGTGA 60.507 44.000 0.88 0.00 0.00 3.41
294 295 6.150318 CGACCGAATAAGCAATAGTAGTGAT 58.850 40.000 0.88 0.00 0.00 3.06
295 296 6.305877 CGACCGAATAAGCAATAGTAGTGATC 59.694 42.308 0.88 0.00 0.00 2.92
296 297 7.291411 ACCGAATAAGCAATAGTAGTGATCT 57.709 36.000 0.88 0.00 0.00 2.75
297 298 8.405418 ACCGAATAAGCAATAGTAGTGATCTA 57.595 34.615 0.88 0.00 0.00 1.98
298 299 8.857098 ACCGAATAAGCAATAGTAGTGATCTAA 58.143 33.333 0.88 0.00 0.00 2.10
299 300 9.130312 CCGAATAAGCAATAGTAGTGATCTAAC 57.870 37.037 0.88 0.00 0.00 2.34
300 301 8.841822 CGAATAAGCAATAGTAGTGATCTAACG 58.158 37.037 0.88 0.00 0.00 3.18
301 302 8.522178 AATAAGCAATAGTAGTGATCTAACGC 57.478 34.615 0.88 0.00 0.00 4.84
302 303 5.776173 AGCAATAGTAGTGATCTAACGCT 57.224 39.130 0.88 0.00 34.85 5.07
303 304 5.764131 AGCAATAGTAGTGATCTAACGCTC 58.236 41.667 0.88 0.00 29.32 5.03
304 305 5.533154 AGCAATAGTAGTGATCTAACGCTCT 59.467 40.000 0.88 0.00 29.32 4.09
305 306 6.039941 AGCAATAGTAGTGATCTAACGCTCTT 59.960 38.462 0.88 0.00 29.32 2.85
306 307 7.228906 AGCAATAGTAGTGATCTAACGCTCTTA 59.771 37.037 0.88 0.00 29.32 2.10
307 308 8.024285 GCAATAGTAGTGATCTAACGCTCTTAT 58.976 37.037 0.88 0.00 32.69 1.73
395 396 1.181098 CCTGGCTGTCACCCAAAAGG 61.181 60.000 0.00 0.00 43.78 3.11
405 406 2.108250 TCACCCAAAAGGGAAGAGAAGG 59.892 50.000 7.71 0.00 41.63 3.46
827 1142 5.163561 CCGCATACTCTTCTCTTCTCTTCTT 60.164 44.000 0.00 0.00 0.00 2.52
836 1151 7.666623 TCTTCTCTTCTCTTCTTTTCTCTTCC 58.333 38.462 0.00 0.00 0.00 3.46
862 1177 2.125753 CAGCACTGCCTCGGTCTC 60.126 66.667 0.00 0.00 0.00 3.36
863 1178 3.753434 AGCACTGCCTCGGTCTCG 61.753 66.667 0.00 0.00 37.82 4.04
864 1179 3.749064 GCACTGCCTCGGTCTCGA 61.749 66.667 0.00 0.00 43.86 4.04
900 1215 3.756117 ACCAAAATCTCCTGAGTTGTCC 58.244 45.455 0.00 0.00 30.40 4.02
901 1216 3.395941 ACCAAAATCTCCTGAGTTGTCCT 59.604 43.478 0.00 0.00 30.40 3.85
902 1217 4.006319 CCAAAATCTCCTGAGTTGTCCTC 58.994 47.826 0.00 0.00 40.89 3.71
903 1218 4.263243 CCAAAATCTCCTGAGTTGTCCTCT 60.263 45.833 0.00 0.00 41.11 3.69
904 1219 5.046304 CCAAAATCTCCTGAGTTGTCCTCTA 60.046 44.000 0.00 0.00 41.11 2.43
905 1220 5.669164 AAATCTCCTGAGTTGTCCTCTAC 57.331 43.478 0.00 0.00 41.11 2.59
906 1221 2.712709 TCTCCTGAGTTGTCCTCTACG 58.287 52.381 0.00 0.00 41.11 3.51
907 1222 1.133407 CTCCTGAGTTGTCCTCTACGC 59.867 57.143 0.00 0.00 41.11 4.42
908 1223 0.179161 CCTGAGTTGTCCTCTACGCG 60.179 60.000 3.53 3.53 41.11 6.01
909 1224 0.803117 CTGAGTTGTCCTCTACGCGA 59.197 55.000 15.93 0.00 41.11 5.87
910 1225 0.803117 TGAGTTGTCCTCTACGCGAG 59.197 55.000 15.93 6.12 41.11 5.03
911 1226 0.523757 GAGTTGTCCTCTACGCGAGC 60.524 60.000 15.93 0.00 38.49 5.03
912 1227 1.211969 GTTGTCCTCTACGCGAGCA 59.788 57.895 15.93 0.00 38.49 4.26
913 1228 0.388134 GTTGTCCTCTACGCGAGCAA 60.388 55.000 15.93 3.94 38.49 3.91
914 1229 0.109272 TTGTCCTCTACGCGAGCAAG 60.109 55.000 15.93 4.52 38.49 4.01
915 1230 1.241990 TGTCCTCTACGCGAGCAAGT 61.242 55.000 15.93 0.00 38.49 3.16
916 1231 0.798771 GTCCTCTACGCGAGCAAGTG 60.799 60.000 15.93 5.43 38.49 3.16
917 1232 1.213013 CCTCTACGCGAGCAAGTGT 59.787 57.895 15.93 3.29 38.49 3.55
918 1233 1.073216 CCTCTACGCGAGCAAGTGTG 61.073 60.000 15.93 0.55 38.49 3.82
929 1244 1.098050 GCAAGTGTGCCAATCCTAGG 58.902 55.000 0.82 0.82 45.68 3.02
952 1267 1.224965 GCTCGCCTGATCAATCCTTC 58.775 55.000 0.00 0.00 0.00 3.46
971 1286 2.520904 GCGTCGCCAGCTTCATCTC 61.521 63.158 5.75 0.00 0.00 2.75
1220 1549 5.040635 GCTACTCTTTCAACTGCTAGCTAG 58.959 45.833 16.84 16.84 0.00 3.42
1221 1550 5.393678 GCTACTCTTTCAACTGCTAGCTAGT 60.394 44.000 21.62 14.35 0.00 2.57
1222 1551 6.183360 GCTACTCTTTCAACTGCTAGCTAGTA 60.183 42.308 21.62 16.60 0.00 1.82
1263 1592 2.077413 TGCATCATTTTGTTTCCGCC 57.923 45.000 0.00 0.00 0.00 6.13
1396 1740 2.803155 TTTGTCTAGCAGCCGCCCAG 62.803 60.000 0.00 0.00 39.83 4.45
1399 1743 3.540751 CTAGCAGCCGCCCAGCTA 61.541 66.667 8.84 8.84 42.61 3.32
1400 1744 3.540751 TAGCAGCCGCCCAGCTAG 61.541 66.667 5.87 0.00 42.61 3.42
1427 1771 5.049680 GGAAGCTATAGTGAACGAGAGAGAG 60.050 48.000 0.84 0.00 0.00 3.20
1431 1775 5.932303 GCTATAGTGAACGAGAGAGAGAGAT 59.068 44.000 0.84 0.00 0.00 2.75
1433 1777 3.950397 AGTGAACGAGAGAGAGAGATGT 58.050 45.455 0.00 0.00 0.00 3.06
1458 1808 5.715279 GGGGAAGAATTTTTAGTGGTTAGCT 59.285 40.000 0.00 0.00 0.00 3.32
1467 1817 6.746745 TTTTAGTGGTTAGCTTTATTCCCG 57.253 37.500 0.00 0.00 0.00 5.14
1563 1916 2.157668 CCGCATCCGCATAAGTAATCAC 59.842 50.000 0.00 0.00 38.40 3.06
1581 1934 5.659440 ATCACCAAGTTGGCGAATTTATT 57.341 34.783 22.25 0.00 42.67 1.40
1582 1935 6.767524 ATCACCAAGTTGGCGAATTTATTA 57.232 33.333 22.25 0.00 42.67 0.98
1583 1936 5.945155 TCACCAAGTTGGCGAATTTATTAC 58.055 37.500 22.25 0.00 42.67 1.89
1585 1938 6.027749 CACCAAGTTGGCGAATTTATTACTC 58.972 40.000 22.25 0.00 42.67 2.59
1586 1939 5.124936 ACCAAGTTGGCGAATTTATTACTCC 59.875 40.000 22.25 0.00 42.67 3.85
1627 1986 4.403113 TGATGTTCCATTCATTCCATGTGG 59.597 41.667 0.00 0.00 0.00 4.17
1643 2002 1.892474 TGTGGTTAATCTTGCCTTGCC 59.108 47.619 0.00 0.00 0.00 4.52
2392 2760 0.463295 TCGCGGACTTCGAGATAGGT 60.463 55.000 6.13 0.00 42.44 3.08
2635 3012 4.752661 TTAATTTACCCTGCACGTGAAC 57.247 40.909 22.23 2.42 0.00 3.18
2672 3049 1.374758 CTCCAGTTCTGTGCCGTCC 60.375 63.158 0.00 0.00 0.00 4.79
2819 3207 7.360361 TCATTCTTTTTCGAAAAGTCTAAGCC 58.640 34.615 21.53 0.00 0.00 4.35
2822 3210 5.591067 TCTTTTTCGAAAAGTCTAAGCCCAA 59.409 36.000 21.53 3.63 0.00 4.12
2851 3239 3.529341 TTGCATCTCGCCCACACGT 62.529 57.895 0.00 0.00 41.33 4.49
2966 3354 1.078072 ACAGCCGTTTCACCACACA 60.078 52.632 0.00 0.00 0.00 3.72
2968 3356 0.813610 CAGCCGTTTCACCACACAGA 60.814 55.000 0.00 0.00 0.00 3.41
3008 3396 4.988598 AGCAGTTCGCCCACACGG 62.989 66.667 0.00 0.00 44.04 4.94
3027 3415 2.159585 CGGCATTTTTCACTCACGCATA 60.160 45.455 0.00 0.00 0.00 3.14
3036 3424 0.613260 ACTCACGCATAAAGGGCTGA 59.387 50.000 0.00 0.00 0.00 4.26
3051 3439 0.604578 GCTGATGTGTGGGCATTTGT 59.395 50.000 0.00 0.00 0.00 2.83
3374 3780 6.582636 TCATGGCAACTATAGTAAACCAGAG 58.417 40.000 20.08 16.22 31.05 3.35
3401 3807 4.057224 CAACAGCCGTAGTTGCCA 57.943 55.556 0.00 0.00 39.76 4.92
3458 3864 0.956633 CTGCAGTTGAGCAACCATGT 59.043 50.000 5.25 0.00 45.13 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 8.655970 AGAAACATTGACAAAAGTTTTAAGTGC 58.344 29.630 17.76 8.51 37.33 4.40
3 4 9.366216 GGAGAAACATTGACAAAAGTTTTAAGT 57.634 29.630 17.76 0.00 37.33 2.24
4 5 9.586435 AGGAGAAACATTGACAAAAGTTTTAAG 57.414 29.630 17.76 0.00 37.33 1.85
7 8 9.936759 TTTAGGAGAAACATTGACAAAAGTTTT 57.063 25.926 17.76 0.00 37.33 2.43
8 9 9.936759 TTTTAGGAGAAACATTGACAAAAGTTT 57.063 25.926 17.09 17.09 39.28 2.66
9 10 9.936759 TTTTTAGGAGAAACATTGACAAAAGTT 57.063 25.926 0.00 0.00 0.00 2.66
53 54 9.250624 CGGGTGAACAGTAAAATCAAAATAAAA 57.749 29.630 0.00 0.00 0.00 1.52
54 55 8.630917 TCGGGTGAACAGTAAAATCAAAATAAA 58.369 29.630 0.00 0.00 0.00 1.40
55 56 8.167605 TCGGGTGAACAGTAAAATCAAAATAA 57.832 30.769 0.00 0.00 0.00 1.40
56 57 7.574217 GCTCGGGTGAACAGTAAAATCAAAATA 60.574 37.037 0.00 0.00 0.00 1.40
57 58 6.642707 TCGGGTGAACAGTAAAATCAAAAT 57.357 33.333 0.00 0.00 0.00 1.82
58 59 5.506649 GCTCGGGTGAACAGTAAAATCAAAA 60.507 40.000 0.00 0.00 0.00 2.44
59 60 4.023536 GCTCGGGTGAACAGTAAAATCAAA 60.024 41.667 0.00 0.00 0.00 2.69
60 61 3.500680 GCTCGGGTGAACAGTAAAATCAA 59.499 43.478 0.00 0.00 0.00 2.57
61 62 3.071479 GCTCGGGTGAACAGTAAAATCA 58.929 45.455 0.00 0.00 0.00 2.57
62 63 3.335579 AGCTCGGGTGAACAGTAAAATC 58.664 45.455 0.00 0.00 0.00 2.17
63 64 3.244422 TGAGCTCGGGTGAACAGTAAAAT 60.244 43.478 9.64 0.00 0.00 1.82
64 65 2.103432 TGAGCTCGGGTGAACAGTAAAA 59.897 45.455 9.64 0.00 0.00 1.52
65 66 1.689813 TGAGCTCGGGTGAACAGTAAA 59.310 47.619 9.64 0.00 0.00 2.01
66 67 1.334160 TGAGCTCGGGTGAACAGTAA 58.666 50.000 9.64 0.00 0.00 2.24
67 68 1.557099 ATGAGCTCGGGTGAACAGTA 58.443 50.000 9.64 0.00 0.00 2.74
68 69 0.687354 AATGAGCTCGGGTGAACAGT 59.313 50.000 9.64 0.00 0.00 3.55
69 70 1.813513 AAATGAGCTCGGGTGAACAG 58.186 50.000 9.64 0.00 0.00 3.16
70 71 3.334691 CTTAAATGAGCTCGGGTGAACA 58.665 45.455 9.64 0.00 0.00 3.18
71 72 2.096013 GCTTAAATGAGCTCGGGTGAAC 59.904 50.000 9.64 0.00 39.57 3.18
72 73 2.356135 GCTTAAATGAGCTCGGGTGAA 58.644 47.619 9.64 0.00 39.57 3.18
73 74 2.024176 GCTTAAATGAGCTCGGGTGA 57.976 50.000 9.64 0.00 39.57 4.02
81 82 2.086869 TGCACCTGAGCTTAAATGAGC 58.913 47.619 0.00 0.00 43.02 4.26
82 83 3.603532 TCTGCACCTGAGCTTAAATGAG 58.396 45.455 0.00 0.00 34.99 2.90
83 84 3.701205 TCTGCACCTGAGCTTAAATGA 57.299 42.857 0.00 0.00 34.99 2.57
84 85 4.217118 AGTTTCTGCACCTGAGCTTAAATG 59.783 41.667 0.00 0.00 34.99 2.32
85 86 4.401925 AGTTTCTGCACCTGAGCTTAAAT 58.598 39.130 0.00 0.00 34.99 1.40
86 87 3.815401 GAGTTTCTGCACCTGAGCTTAAA 59.185 43.478 0.00 0.00 34.99 1.52
87 88 3.071602 AGAGTTTCTGCACCTGAGCTTAA 59.928 43.478 0.00 0.00 34.99 1.85
88 89 2.634940 AGAGTTTCTGCACCTGAGCTTA 59.365 45.455 0.00 0.00 34.99 3.09
89 90 1.419387 AGAGTTTCTGCACCTGAGCTT 59.581 47.619 0.00 0.00 34.99 3.74
90 91 1.055040 AGAGTTTCTGCACCTGAGCT 58.945 50.000 0.00 0.00 34.99 4.09
91 92 1.155042 CAGAGTTTCTGCACCTGAGC 58.845 55.000 0.00 0.00 37.72 4.26
100 101 2.447244 AGGAAGACGCAGAGTTTCTG 57.553 50.000 1.75 1.75 46.90 3.02
101 102 3.422796 TCTAGGAAGACGCAGAGTTTCT 58.577 45.455 0.00 0.00 0.00 2.52
102 103 3.191791 ACTCTAGGAAGACGCAGAGTTTC 59.808 47.826 0.00 0.00 44.03 2.78
103 104 3.158676 ACTCTAGGAAGACGCAGAGTTT 58.841 45.455 0.00 0.00 44.03 2.66
104 105 2.797786 ACTCTAGGAAGACGCAGAGTT 58.202 47.619 0.00 0.00 44.03 3.01
105 106 2.500392 ACTCTAGGAAGACGCAGAGT 57.500 50.000 0.00 0.00 42.20 3.24
106 107 3.057174 ACAAACTCTAGGAAGACGCAGAG 60.057 47.826 0.00 0.00 40.31 3.35
107 108 2.891580 ACAAACTCTAGGAAGACGCAGA 59.108 45.455 0.00 0.00 0.00 4.26
108 109 2.989840 CACAAACTCTAGGAAGACGCAG 59.010 50.000 0.00 0.00 0.00 5.18
109 110 2.364324 ACACAAACTCTAGGAAGACGCA 59.636 45.455 0.00 0.00 0.00 5.24
110 111 3.027974 ACACAAACTCTAGGAAGACGC 57.972 47.619 0.00 0.00 0.00 5.19
111 112 4.734917 CCTACACAAACTCTAGGAAGACG 58.265 47.826 0.00 0.00 30.11 4.18
112 113 4.221041 AGCCTACACAAACTCTAGGAAGAC 59.779 45.833 0.00 0.00 30.11 3.01
113 114 4.417437 AGCCTACACAAACTCTAGGAAGA 58.583 43.478 0.00 0.00 30.11 2.87
114 115 4.675671 CGAGCCTACACAAACTCTAGGAAG 60.676 50.000 0.00 0.00 30.11 3.46
115 116 3.192844 CGAGCCTACACAAACTCTAGGAA 59.807 47.826 0.00 0.00 30.11 3.36
116 117 2.753452 CGAGCCTACACAAACTCTAGGA 59.247 50.000 0.00 0.00 30.11 2.94
117 118 2.753452 TCGAGCCTACACAAACTCTAGG 59.247 50.000 0.00 0.00 0.00 3.02
118 119 4.640789 ATCGAGCCTACACAAACTCTAG 57.359 45.455 0.00 0.00 0.00 2.43
119 120 5.191426 AGTATCGAGCCTACACAAACTCTA 58.809 41.667 0.00 0.00 0.00 2.43
120 121 4.017808 AGTATCGAGCCTACACAAACTCT 58.982 43.478 0.00 0.00 0.00 3.24
121 122 4.373348 AGTATCGAGCCTACACAAACTC 57.627 45.455 0.00 0.00 0.00 3.01
122 123 4.803098 AAGTATCGAGCCTACACAAACT 57.197 40.909 0.00 0.00 0.00 2.66
123 124 5.857822 AAAAGTATCGAGCCTACACAAAC 57.142 39.130 0.00 0.00 0.00 2.93
124 125 5.410439 GGAAAAAGTATCGAGCCTACACAAA 59.590 40.000 0.00 0.00 0.00 2.83
125 126 4.933400 GGAAAAAGTATCGAGCCTACACAA 59.067 41.667 0.00 0.00 0.00 3.33
126 127 4.501071 GGAAAAAGTATCGAGCCTACACA 58.499 43.478 0.00 0.00 0.00 3.72
127 128 3.869832 GGGAAAAAGTATCGAGCCTACAC 59.130 47.826 0.00 0.00 0.00 2.90
128 129 3.516300 TGGGAAAAAGTATCGAGCCTACA 59.484 43.478 0.00 0.00 0.00 2.74
129 130 3.869832 GTGGGAAAAAGTATCGAGCCTAC 59.130 47.826 0.00 0.00 0.00 3.18
130 131 3.516300 TGTGGGAAAAAGTATCGAGCCTA 59.484 43.478 0.00 0.00 0.00 3.93
131 132 2.304761 TGTGGGAAAAAGTATCGAGCCT 59.695 45.455 0.00 0.00 0.00 4.58
132 133 2.706890 TGTGGGAAAAAGTATCGAGCC 58.293 47.619 0.00 0.00 0.00 4.70
133 134 4.965119 ATTGTGGGAAAAAGTATCGAGC 57.035 40.909 0.00 0.00 0.00 5.03
134 135 5.640732 CCAATTGTGGGAAAAAGTATCGAG 58.359 41.667 4.43 0.00 41.77 4.04
135 136 5.637006 CCAATTGTGGGAAAAAGTATCGA 57.363 39.130 4.43 0.00 41.77 3.59
149 150 5.499139 AAGTTGTCTGTGTACCAATTGTG 57.501 39.130 4.43 0.00 0.00 3.33
150 151 7.817418 ATTAAGTTGTCTGTGTACCAATTGT 57.183 32.000 4.43 0.00 0.00 2.71
153 154 9.515226 ACATAATTAAGTTGTCTGTGTACCAAT 57.485 29.630 0.00 0.00 0.00 3.16
154 155 8.911918 ACATAATTAAGTTGTCTGTGTACCAA 57.088 30.769 0.00 0.00 0.00 3.67
155 156 8.911918 AACATAATTAAGTTGTCTGTGTACCA 57.088 30.769 5.33 0.00 0.00 3.25
156 157 9.821662 GAAACATAATTAAGTTGTCTGTGTACC 57.178 33.333 6.84 0.00 0.00 3.34
161 162 9.744468 GGTTTGAAACATAATTAAGTTGTCTGT 57.256 29.630 10.53 0.00 0.00 3.41
162 163 9.965824 AGGTTTGAAACATAATTAAGTTGTCTG 57.034 29.630 10.53 0.00 0.00 3.51
172 173 9.283768 GGGATTTTGAAGGTTTGAAACATAATT 57.716 29.630 10.53 0.00 0.00 1.40
173 174 7.602265 CGGGATTTTGAAGGTTTGAAACATAAT 59.398 33.333 10.53 0.00 0.00 1.28
174 175 6.926272 CGGGATTTTGAAGGTTTGAAACATAA 59.074 34.615 10.53 0.00 0.00 1.90
175 176 6.041069 ACGGGATTTTGAAGGTTTGAAACATA 59.959 34.615 10.53 0.00 0.00 2.29
176 177 5.163353 ACGGGATTTTGAAGGTTTGAAACAT 60.163 36.000 10.53 0.00 0.00 2.71
177 178 4.160626 ACGGGATTTTGAAGGTTTGAAACA 59.839 37.500 10.53 0.00 0.00 2.83
178 179 4.506288 CACGGGATTTTGAAGGTTTGAAAC 59.494 41.667 0.00 0.00 0.00 2.78
179 180 4.402793 TCACGGGATTTTGAAGGTTTGAAA 59.597 37.500 0.00 0.00 0.00 2.69
180 181 3.954904 TCACGGGATTTTGAAGGTTTGAA 59.045 39.130 0.00 0.00 0.00 2.69
181 182 3.556999 TCACGGGATTTTGAAGGTTTGA 58.443 40.909 0.00 0.00 0.00 2.69
182 183 4.314740 TTCACGGGATTTTGAAGGTTTG 57.685 40.909 0.00 0.00 0.00 2.93
183 184 5.346181 TTTTCACGGGATTTTGAAGGTTT 57.654 34.783 0.00 0.00 33.36 3.27
184 185 5.545063 ATTTTCACGGGATTTTGAAGGTT 57.455 34.783 0.00 0.00 33.36 3.50
185 186 5.296748 CAATTTTCACGGGATTTTGAAGGT 58.703 37.500 0.00 0.00 33.36 3.50
186 187 4.152223 GCAATTTTCACGGGATTTTGAAGG 59.848 41.667 8.45 0.00 33.36 3.46
187 188 4.749099 TGCAATTTTCACGGGATTTTGAAG 59.251 37.500 8.45 0.00 33.36 3.02
188 189 4.697514 TGCAATTTTCACGGGATTTTGAA 58.302 34.783 8.45 0.00 0.00 2.69
189 190 4.038522 TCTGCAATTTTCACGGGATTTTGA 59.961 37.500 8.45 0.00 0.00 2.69
190 191 4.305769 TCTGCAATTTTCACGGGATTTTG 58.694 39.130 0.00 0.00 0.00 2.44
191 192 4.559153 CTCTGCAATTTTCACGGGATTTT 58.441 39.130 0.00 0.00 0.00 1.82
192 193 3.056607 CCTCTGCAATTTTCACGGGATTT 60.057 43.478 0.00 0.00 0.00 2.17
193 194 2.493278 CCTCTGCAATTTTCACGGGATT 59.507 45.455 0.00 0.00 0.00 3.01
194 195 2.094675 CCTCTGCAATTTTCACGGGAT 58.905 47.619 0.00 0.00 0.00 3.85
195 196 1.533625 CCTCTGCAATTTTCACGGGA 58.466 50.000 0.00 0.00 0.00 5.14
196 197 0.109132 GCCTCTGCAATTTTCACGGG 60.109 55.000 0.00 0.00 37.47 5.28
197 198 0.597568 TGCCTCTGCAATTTTCACGG 59.402 50.000 0.00 0.00 46.66 4.94
207 208 5.570483 GGTGAATATCCACTGCCTCTGCA 62.570 52.174 0.00 0.00 46.76 4.41
208 209 2.216898 GTGAATATCCACTGCCTCTGC 58.783 52.381 0.00 0.00 34.38 4.26
209 210 2.486191 GGGTGAATATCCACTGCCTCTG 60.486 54.545 0.00 0.00 37.24 3.35
210 211 1.771255 GGGTGAATATCCACTGCCTCT 59.229 52.381 0.00 0.00 37.24 3.69
211 212 1.771255 AGGGTGAATATCCACTGCCTC 59.229 52.381 0.00 0.00 37.24 4.70
212 213 1.771255 GAGGGTGAATATCCACTGCCT 59.229 52.381 0.00 0.00 37.24 4.75
213 214 1.771255 AGAGGGTGAATATCCACTGCC 59.229 52.381 0.00 0.00 37.24 4.85
214 215 3.567478 AAGAGGGTGAATATCCACTGC 57.433 47.619 0.00 0.00 37.24 4.40
215 216 5.126061 CCAAAAAGAGGGTGAATATCCACTG 59.874 44.000 0.00 0.00 37.24 3.66
216 217 5.015178 TCCAAAAAGAGGGTGAATATCCACT 59.985 40.000 0.00 0.00 37.24 4.00
217 218 5.261216 TCCAAAAAGAGGGTGAATATCCAC 58.739 41.667 0.00 0.00 36.37 4.02
218 219 5.252863 TCTCCAAAAAGAGGGTGAATATCCA 59.747 40.000 0.00 0.00 34.46 3.41
219 220 5.755849 TCTCCAAAAAGAGGGTGAATATCC 58.244 41.667 0.00 0.00 34.46 2.59
220 221 7.112779 TCTTCTCCAAAAAGAGGGTGAATATC 58.887 38.462 0.00 0.00 36.44 1.63
221 222 7.032598 TCTTCTCCAAAAAGAGGGTGAATAT 57.967 36.000 0.00 0.00 36.44 1.28
222 223 6.448369 TCTTCTCCAAAAAGAGGGTGAATA 57.552 37.500 0.00 0.00 36.44 1.75
223 224 5.324832 TCTTCTCCAAAAAGAGGGTGAAT 57.675 39.130 0.00 0.00 36.44 2.57
224 225 4.788925 TCTTCTCCAAAAAGAGGGTGAA 57.211 40.909 0.00 0.00 35.87 3.18
225 226 4.788925 TTCTTCTCCAAAAAGAGGGTGA 57.211 40.909 0.00 0.00 34.42 4.02
226 227 5.852282 TTTTCTTCTCCAAAAAGAGGGTG 57.148 39.130 0.00 0.00 34.42 4.61
249 250 3.672241 CGGAGAATTTTCGCGGGATTTTT 60.672 43.478 6.13 0.00 0.00 1.94
250 251 2.159435 CGGAGAATTTTCGCGGGATTTT 60.159 45.455 6.13 0.00 0.00 1.82
251 252 1.400494 CGGAGAATTTTCGCGGGATTT 59.600 47.619 6.13 0.00 0.00 2.17
252 253 1.014352 CGGAGAATTTTCGCGGGATT 58.986 50.000 6.13 4.11 0.00 3.01
253 254 0.177141 TCGGAGAATTTTCGCGGGAT 59.823 50.000 6.13 0.00 0.00 3.85
254 255 0.738412 GTCGGAGAATTTTCGCGGGA 60.738 55.000 6.13 0.00 39.69 5.14
255 256 1.702491 GGTCGGAGAATTTTCGCGGG 61.702 60.000 6.13 0.00 39.69 6.13
256 257 1.713830 GGTCGGAGAATTTTCGCGG 59.286 57.895 6.13 0.00 39.69 6.46
257 258 1.074319 TCGGTCGGAGAATTTTCGCG 61.074 55.000 0.00 0.00 39.69 5.87
258 259 1.073177 TTCGGTCGGAGAATTTTCGC 58.927 50.000 0.00 0.00 39.69 4.70
259 260 4.550255 GCTTATTCGGTCGGAGAATTTTCG 60.550 45.833 6.32 0.00 39.69 3.46
260 261 4.331717 TGCTTATTCGGTCGGAGAATTTTC 59.668 41.667 6.32 0.00 39.69 2.29
261 262 4.258543 TGCTTATTCGGTCGGAGAATTTT 58.741 39.130 6.32 0.00 39.69 1.82
262 263 3.869065 TGCTTATTCGGTCGGAGAATTT 58.131 40.909 6.32 0.00 39.69 1.82
263 264 3.536956 TGCTTATTCGGTCGGAGAATT 57.463 42.857 6.32 0.00 39.69 2.17
264 265 3.536956 TTGCTTATTCGGTCGGAGAAT 57.463 42.857 6.28 6.28 39.69 2.40
265 266 3.536956 ATTGCTTATTCGGTCGGAGAA 57.463 42.857 0.00 0.00 39.69 2.87
266 267 3.635373 ACTATTGCTTATTCGGTCGGAGA 59.365 43.478 0.00 0.00 0.00 3.71
267 268 3.978687 ACTATTGCTTATTCGGTCGGAG 58.021 45.455 0.00 0.00 0.00 4.63
268 269 4.581824 ACTACTATTGCTTATTCGGTCGGA 59.418 41.667 0.00 0.00 0.00 4.55
269 270 4.680110 CACTACTATTGCTTATTCGGTCGG 59.320 45.833 0.00 0.00 0.00 4.79
270 271 5.516996 TCACTACTATTGCTTATTCGGTCG 58.483 41.667 0.00 0.00 0.00 4.79
271 272 7.371936 AGATCACTACTATTGCTTATTCGGTC 58.628 38.462 0.00 0.00 0.00 4.79
272 273 7.291411 AGATCACTACTATTGCTTATTCGGT 57.709 36.000 0.00 0.00 0.00 4.69
273 274 9.130312 GTTAGATCACTACTATTGCTTATTCGG 57.870 37.037 0.00 0.00 0.00 4.30
274 275 8.841822 CGTTAGATCACTACTATTGCTTATTCG 58.158 37.037 0.00 0.00 0.00 3.34
275 276 8.640291 GCGTTAGATCACTACTATTGCTTATTC 58.360 37.037 0.00 0.00 0.00 1.75
276 277 8.361139 AGCGTTAGATCACTACTATTGCTTATT 58.639 33.333 0.00 0.00 31.52 1.40
277 278 7.887381 AGCGTTAGATCACTACTATTGCTTAT 58.113 34.615 0.00 0.00 31.52 1.73
278 279 7.228906 AGAGCGTTAGATCACTACTATTGCTTA 59.771 37.037 0.00 0.00 34.73 3.09
279 280 6.039941 AGAGCGTTAGATCACTACTATTGCTT 59.960 38.462 0.00 0.00 34.73 3.91
280 281 5.533154 AGAGCGTTAGATCACTACTATTGCT 59.467 40.000 0.00 0.00 34.73 3.91
281 282 5.764131 AGAGCGTTAGATCACTACTATTGC 58.236 41.667 0.00 0.00 34.73 3.56
312 313 4.136051 CGTGTTTACACCCTCCCTAAAAA 58.864 43.478 7.39 0.00 43.66 1.94
313 314 3.390639 TCGTGTTTACACCCTCCCTAAAA 59.609 43.478 7.39 0.00 43.66 1.52
314 315 2.971330 TCGTGTTTACACCCTCCCTAAA 59.029 45.455 7.39 0.00 43.66 1.85
315 316 2.607499 TCGTGTTTACACCCTCCCTAA 58.393 47.619 7.39 0.00 43.66 2.69
316 317 2.307496 TCGTGTTTACACCCTCCCTA 57.693 50.000 7.39 0.00 43.66 3.53
317 318 1.346722 CTTCGTGTTTACACCCTCCCT 59.653 52.381 7.39 0.00 43.66 4.20
318 319 1.071228 ACTTCGTGTTTACACCCTCCC 59.929 52.381 7.39 0.00 43.66 4.30
319 320 2.538512 ACTTCGTGTTTACACCCTCC 57.461 50.000 7.39 0.00 43.66 4.30
320 321 4.483311 CTCTACTTCGTGTTTACACCCTC 58.517 47.826 7.39 0.00 43.66 4.30
321 322 3.305881 GCTCTACTTCGTGTTTACACCCT 60.306 47.826 7.39 0.00 43.66 4.34
322 323 2.991866 GCTCTACTTCGTGTTTACACCC 59.008 50.000 7.39 0.00 43.66 4.61
323 324 3.673809 CAGCTCTACTTCGTGTTTACACC 59.326 47.826 7.39 0.00 43.66 4.16
324 325 4.296690 ACAGCTCTACTTCGTGTTTACAC 58.703 43.478 2.92 2.92 43.15 2.90
325 326 4.277672 AGACAGCTCTACTTCGTGTTTACA 59.722 41.667 0.00 0.00 0.00 2.41
326 327 4.796369 AGACAGCTCTACTTCGTGTTTAC 58.204 43.478 0.00 0.00 0.00 2.01
327 328 5.936054 GTAGACAGCTCTACTTCGTGTTTA 58.064 41.667 6.00 0.00 44.02 2.01
338 339 1.566703 AGCCAGGAGTAGACAGCTCTA 59.433 52.381 0.00 0.00 33.73 2.43
395 396 1.834896 GGACCTCTTCCCTTCTCTTCC 59.165 57.143 0.00 0.00 38.70 3.46
405 406 2.435059 GCGCTGTGGACCTCTTCC 60.435 66.667 0.00 0.00 46.13 3.46
442 455 1.581402 CTCACTCGCACTCGCTACG 60.581 63.158 0.00 0.00 35.30 3.51
444 457 0.743345 TAGCTCACTCGCACTCGCTA 60.743 55.000 0.00 0.00 35.30 4.26
445 458 1.987704 CTAGCTCACTCGCACTCGCT 61.988 60.000 0.00 0.00 35.30 4.93
506 537 3.657537 CACGGATTTGAAGTCGTGC 57.342 52.632 0.00 0.00 44.56 5.34
662 962 2.698797 CGGAGATTAGTTTAGGCCTGGA 59.301 50.000 17.99 0.00 0.00 3.86
827 1142 1.302511 GCTGTGCGGGGAAGAGAAA 60.303 57.895 0.00 0.00 0.00 2.52
857 1172 0.591659 GGTTTGGTTTGCTCGAGACC 59.408 55.000 18.75 15.65 0.00 3.85
859 1174 2.045561 TTGGTTTGGTTTGCTCGAGA 57.954 45.000 18.75 0.00 0.00 4.04
861 1176 1.135333 GGTTTGGTTTGGTTTGCTCGA 59.865 47.619 0.00 0.00 0.00 4.04
862 1177 1.134965 TGGTTTGGTTTGGTTTGCTCG 60.135 47.619 0.00 0.00 0.00 5.03
863 1178 2.682155 TGGTTTGGTTTGGTTTGCTC 57.318 45.000 0.00 0.00 0.00 4.26
864 1179 3.425162 TTTGGTTTGGTTTGGTTTGCT 57.575 38.095 0.00 0.00 0.00 3.91
865 1180 4.397730 AGATTTTGGTTTGGTTTGGTTTGC 59.602 37.500 0.00 0.00 0.00 3.68
867 1182 5.045213 AGGAGATTTTGGTTTGGTTTGGTTT 60.045 36.000 0.00 0.00 0.00 3.27
870 1185 4.100808 TCAGGAGATTTTGGTTTGGTTTGG 59.899 41.667 0.00 0.00 0.00 3.28
901 1216 1.733041 GCACACTTGCTCGCGTAGA 60.733 57.895 5.77 0.00 46.17 2.59
902 1217 2.772189 GCACACTTGCTCGCGTAG 59.228 61.111 5.77 3.35 46.17 3.51
919 1234 1.006805 CGAGCGAGCCTAGGATTGG 60.007 63.158 14.75 3.55 0.00 3.16
920 1235 1.663074 GCGAGCGAGCCTAGGATTG 60.663 63.158 14.75 12.25 0.00 2.67
921 1236 2.731374 GCGAGCGAGCCTAGGATT 59.269 61.111 14.75 0.00 0.00 3.01
929 1244 1.555741 GATTGATCAGGCGAGCGAGC 61.556 60.000 0.00 0.00 0.00 5.03
930 1245 0.943359 GGATTGATCAGGCGAGCGAG 60.943 60.000 0.00 0.00 0.00 5.03
952 1267 3.918220 GATGAAGCTGGCGACGCG 61.918 66.667 14.61 3.53 35.50 6.01
1200 1523 5.712917 AGTACTAGCTAGCAGTTGAAAGAGT 59.287 40.000 20.91 7.77 0.00 3.24
1201 1524 6.202516 AGTACTAGCTAGCAGTTGAAAGAG 57.797 41.667 20.91 2.26 0.00 2.85
1210 1539 3.731089 ACTACGGAGTACTAGCTAGCAG 58.269 50.000 20.91 14.32 45.11 4.24
1220 1549 4.097589 AGCAACCAATCTACTACGGAGTAC 59.902 45.833 2.48 0.00 45.11 2.73
1221 1550 4.275810 AGCAACCAATCTACTACGGAGTA 58.724 43.478 7.43 7.43 45.11 2.59
1263 1592 5.837437 AGAAATATCTAAGCCTCACGTCTG 58.163 41.667 0.00 0.00 32.88 3.51
1400 1744 1.066605 TCGTTCACTATAGCTTCCGGC 59.933 52.381 0.00 0.00 42.19 6.13
1401 1745 2.617308 TCTCGTTCACTATAGCTTCCGG 59.383 50.000 0.00 0.00 0.00 5.14
1402 1746 3.560481 TCTCTCGTTCACTATAGCTTCCG 59.440 47.826 0.00 0.00 0.00 4.30
1403 1747 4.817464 TCTCTCTCGTTCACTATAGCTTCC 59.183 45.833 0.00 0.00 0.00 3.46
1404 1748 5.756347 TCTCTCTCTCGTTCACTATAGCTTC 59.244 44.000 0.00 0.00 0.00 3.86
1405 1749 5.676552 TCTCTCTCTCGTTCACTATAGCTT 58.323 41.667 0.00 0.00 0.00 3.74
1418 1762 1.133945 TCCCCACATCTCTCTCTCTCG 60.134 57.143 0.00 0.00 0.00 4.04
1427 1771 6.127619 CCACTAAAAATTCTTCCCCACATCTC 60.128 42.308 0.00 0.00 0.00 2.75
1431 1775 4.810345 ACCACTAAAAATTCTTCCCCACA 58.190 39.130 0.00 0.00 0.00 4.17
1433 1777 5.479027 GCTAACCACTAAAAATTCTTCCCCA 59.521 40.000 0.00 0.00 0.00 4.96
1563 1916 5.124776 TGGAGTAATAAATTCGCCAACTTGG 59.875 40.000 3.10 3.10 41.55 3.61
1581 1934 3.646736 TCAGTGCTAGCTACTGGAGTA 57.353 47.619 30.12 17.81 44.33 2.59
1582 1935 2.516227 TCAGTGCTAGCTACTGGAGT 57.484 50.000 30.12 9.05 44.33 3.85
1583 1936 2.692557 ACATCAGTGCTAGCTACTGGAG 59.307 50.000 30.12 25.91 44.33 3.86
1585 1938 2.428530 TCACATCAGTGCTAGCTACTGG 59.571 50.000 30.12 22.60 45.49 4.00
1586 1939 3.790152 TCACATCAGTGCTAGCTACTG 57.210 47.619 27.52 27.52 45.49 2.74
1627 1986 2.995939 GCAAAGGCAAGGCAAGATTAAC 59.004 45.455 0.00 0.00 40.72 2.01
1643 2002 2.069273 CTTCAGACCTGGTACGCAAAG 58.931 52.381 0.00 0.00 0.00 2.77
2389 2757 0.892358 TGTCCACGTCGAAGCTACCT 60.892 55.000 0.00 0.00 0.00 3.08
2392 2760 1.211969 GCTGTCCACGTCGAAGCTA 59.788 57.895 0.00 0.00 0.00 3.32
2635 3012 1.153289 CAGAACAGGCCGGGAGATG 60.153 63.158 8.08 0.00 0.00 2.90
2672 3049 9.798994 ACGTAGTAATAAATTAACACAGGAGAG 57.201 33.333 0.00 0.00 41.94 3.20
2819 3207 4.347453 GCAAGCGCCCACACTTGG 62.347 66.667 2.29 0.00 42.82 3.61
2822 3210 3.058160 GATGCAAGCGCCCACACT 61.058 61.111 2.29 0.00 37.32 3.55
2851 3239 0.948623 CAAACAGACGCGGATCCACA 60.949 55.000 12.47 0.00 0.00 4.17
2966 3354 2.833913 CCACACACCAGCCCCTTCT 61.834 63.158 0.00 0.00 0.00 2.85
2968 3356 3.902112 CCCACACACCAGCCCCTT 61.902 66.667 0.00 0.00 0.00 3.95
3008 3396 4.324402 CCTTTATGCGTGAGTGAAAAATGC 59.676 41.667 0.00 0.00 0.00 3.56
3015 3403 0.613260 AGCCCTTTATGCGTGAGTGA 59.387 50.000 0.00 0.00 0.00 3.41
3027 3415 1.607467 GCCCACACATCAGCCCTTT 60.607 57.895 0.00 0.00 0.00 3.11
3036 3424 2.756760 GAGATGACAAATGCCCACACAT 59.243 45.455 0.00 0.00 0.00 3.21
3051 3439 4.451150 GGCGTGTGGGCGAGATGA 62.451 66.667 0.00 0.00 0.00 2.92
3271 3677 5.466393 GCTACAAAAAGACATGGCAAAACAT 59.534 36.000 0.00 0.00 0.00 2.71
3374 3780 1.086696 ACGGCTGTTGTCATGTATGC 58.913 50.000 0.00 0.00 0.00 3.14


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

AutoCloner maintained by Alex Coulton.