Multiple sequence alignment - TraesCS2D01G172700

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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 TraesCS2D01G172700 chr2D 100.000 2759 0 0 1 2759 116598208 116595450 0.000000e+00 5096.0
1 TraesCS2D01G172700 chr2D 84.966 592 74 12 1060 1643 116620279 116619695 1.100000e-163 586.0
2 TraesCS2D01G172700 chr2D 84.157 587 75 13 1066 1643 116776868 116776291 1.120000e-153 553.0
3 TraesCS2D01G172700 chr2D 98.649 296 4 0 1 296 116617729 116617434 2.430000e-145 525.0
4 TraesCS2D01G172700 chr2D 78.609 575 98 16 1081 1643 116800645 116800084 9.400000e-95 357.0
5 TraesCS2D01G172700 chr2B 94.328 1816 67 13 973 2756 166813368 166815179 0.000000e+00 2750.0
6 TraesCS2D01G172700 chr2B 91.667 360 27 2 2397 2756 166830364 166830720 1.910000e-136 496.0
7 TraesCS2D01G172700 chr2A 92.322 547 20 8 1377 1913 117850118 117849584 0.000000e+00 758.0
8 TraesCS2D01G172700 chr2A 96.377 414 15 0 971 1384 117850698 117850285 0.000000e+00 682.0
9 TraesCS2D01G172700 chr2A 93.000 400 11 6 802 1194 117851434 117851045 3.990000e-158 568.0
10 TraesCS2D01G172700 chr2A 84.710 569 72 10 1081 1643 118222048 118221489 3.100000e-154 555.0
11 TraesCS2D01G172700 chr2A 88.453 459 47 5 2304 2759 117848413 117847958 1.440000e-152 549.0
12 TraesCS2D01G172700 chr2A 85.496 524 63 9 1125 1643 118213891 118213376 4.040000e-148 534.0
13 TraesCS2D01G172700 chr2A 80.866 716 77 32 297 962 117908940 117908235 2.450000e-140 508.0
14 TraesCS2D01G172700 chr2A 95.726 234 9 1 2057 2290 117848624 117848392 2.590000e-100 375.0
15 TraesCS2D01G172700 chr2A 78.392 597 101 23 1060 1636 118228498 118227910 2.020000e-96 363.0
16 TraesCS2D01G172700 chr2A 100.000 31 0 0 1195 1225 117850727 117850697 1.070000e-04 58.4
17 TraesCS2D01G172700 chr3D 98.649 296 4 0 1 296 85658066 85658361 2.430000e-145 525.0
18 TraesCS2D01G172700 chr3D 98.649 296 4 0 1 296 541811779 541811484 2.430000e-145 525.0
19 TraesCS2D01G172700 chr3D 97.973 296 6 0 1 296 85645532 85645827 5.270000e-142 514.0
20 TraesCS2D01G172700 chr7D 98.311 296 5 0 1 296 418350585 418350290 1.130000e-143 520.0
21 TraesCS2D01G172700 chr7D 97.667 300 7 0 1 300 418338082 418337783 1.460000e-142 516.0
22 TraesCS2D01G172700 chr1D 98.311 296 5 0 1 296 316561366 316561071 1.130000e-143 520.0
23 TraesCS2D01G172700 chr1D 97.980 297 6 0 1 297 316548857 316548561 1.460000e-142 516.0
24 TraesCS2D01G172700 chr4D 97.980 297 6 0 1 297 137481678 137481974 1.460000e-142 516.0
25 TraesCS2D01G172700 chrUn 85.010 487 63 7 1081 1563 460200235 460200715 1.150000e-133 486.0
26 TraesCS2D01G172700 chrUn 78.231 588 97 22 1066 1636 17426554 17427127 5.660000e-92 348.0


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 TraesCS2D01G172700 chr2D 116595450 116598208 2758 True 5096.0 5096 100.0000 1 2759 1 chr2D.!!$R1 2758
1 TraesCS2D01G172700 chr2D 116617434 116620279 2845 True 555.5 586 91.8075 1 1643 2 chr2D.!!$R4 1642
2 TraesCS2D01G172700 chr2D 116776291 116776868 577 True 553.0 553 84.1570 1066 1643 1 chr2D.!!$R2 577
3 TraesCS2D01G172700 chr2D 116800084 116800645 561 True 357.0 357 78.6090 1081 1643 1 chr2D.!!$R3 562
4 TraesCS2D01G172700 chr2B 166813368 166815179 1811 False 2750.0 2750 94.3280 973 2756 1 chr2B.!!$F1 1783
5 TraesCS2D01G172700 chr2A 118221489 118222048 559 True 555.0 555 84.7100 1081 1643 1 chr2A.!!$R3 562
6 TraesCS2D01G172700 chr2A 118213376 118213891 515 True 534.0 534 85.4960 1125 1643 1 chr2A.!!$R2 518
7 TraesCS2D01G172700 chr2A 117908235 117908940 705 True 508.0 508 80.8660 297 962 1 chr2A.!!$R1 665
8 TraesCS2D01G172700 chr2A 117847958 117851434 3476 True 498.4 758 94.3130 802 2759 6 chr2A.!!$R5 1957
9 TraesCS2D01G172700 chr2A 118227910 118228498 588 True 363.0 363 78.3920 1060 1636 1 chr2A.!!$R4 576
10 TraesCS2D01G172700 chrUn 17426554 17427127 573 False 348.0 348 78.2310 1066 1636 1 chrUn.!!$F1 570

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
260 261 0.030399 ATTAGAGTAACCCGGCCCCT 60.03 55.0 0.0 0.0 0.0 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1884 2747 0.391597 AGTACCAACACGTCCACTGG 59.608 55.0 0.0 0.0 34.95 4.0 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
20 21 3.537793 GTTCTTGTTCCTAAACCGCTG 57.462 47.619 0.00 0.00 34.28 5.18
21 22 1.519408 TCTTGTTCCTAAACCGCTGC 58.481 50.000 0.00 0.00 34.28 5.25
22 23 0.521735 CTTGTTCCTAAACCGCTGCC 59.478 55.000 0.00 0.00 34.28 4.85
23 24 1.231958 TTGTTCCTAAACCGCTGCCG 61.232 55.000 0.00 0.00 34.28 5.69
52 53 4.457834 CCTTTATATAGGGAGGCTGACG 57.542 50.000 0.00 0.00 0.00 4.35
53 54 3.368531 CCTTTATATAGGGAGGCTGACGC 60.369 52.174 0.00 0.00 0.00 5.19
69 70 4.486503 GCCCAGCAGCCCTCAGAG 62.487 72.222 0.00 0.00 0.00 3.35
70 71 3.007920 CCCAGCAGCCCTCAGAGT 61.008 66.667 0.00 0.00 0.00 3.24
71 72 2.583520 CCAGCAGCCCTCAGAGTC 59.416 66.667 0.00 0.00 0.00 3.36
72 73 2.583520 CAGCAGCCCTCAGAGTCC 59.416 66.667 0.00 0.00 0.00 3.85
73 74 2.686835 AGCAGCCCTCAGAGTCCC 60.687 66.667 0.00 0.00 0.00 4.46
74 75 4.154347 GCAGCCCTCAGAGTCCCG 62.154 72.222 0.00 0.00 0.00 5.14
75 76 3.465403 CAGCCCTCAGAGTCCCGG 61.465 72.222 0.00 0.00 0.00 5.73
85 86 4.853142 AGTCCCGGCCGGCTCATA 62.853 66.667 39.46 17.51 0.00 2.15
86 87 3.857038 GTCCCGGCCGGCTCATAA 61.857 66.667 39.46 15.60 0.00 1.90
87 88 3.084646 TCCCGGCCGGCTCATAAA 61.085 61.111 39.46 13.75 0.00 1.40
88 89 2.124487 CCCGGCCGGCTCATAAAA 60.124 61.111 39.46 0.00 0.00 1.52
89 90 2.186826 CCCGGCCGGCTCATAAAAG 61.187 63.158 39.46 18.00 0.00 2.27
90 91 2.715624 CGGCCGGCTCATAAAAGC 59.284 61.111 28.56 4.75 41.73 3.51
91 92 2.715624 GGCCGGCTCATAAAAGCG 59.284 61.111 28.56 0.00 43.45 4.68
92 93 2.112815 GGCCGGCTCATAAAAGCGT 61.113 57.895 28.56 0.00 43.45 5.07
93 94 1.352056 GCCGGCTCATAAAAGCGTC 59.648 57.895 22.15 0.00 43.45 5.19
94 95 2.014594 CCGGCTCATAAAAGCGTCC 58.985 57.895 0.00 0.00 43.45 4.79
95 96 1.636340 CGGCTCATAAAAGCGTCCG 59.364 57.895 0.00 0.00 43.45 4.79
96 97 1.762222 CGGCTCATAAAAGCGTCCGG 61.762 60.000 0.00 0.00 43.45 5.14
97 98 1.352056 GCTCATAAAAGCGTCCGGC 59.648 57.895 0.00 0.00 44.05 6.13
111 112 4.719997 CGGCTCGGACTCTCAATC 57.280 61.111 0.00 0.00 0.00 2.67
112 113 1.809869 CGGCTCGGACTCTCAATCA 59.190 57.895 0.00 0.00 0.00 2.57
113 114 0.387202 CGGCTCGGACTCTCAATCAT 59.613 55.000 0.00 0.00 0.00 2.45
114 115 1.609072 CGGCTCGGACTCTCAATCATA 59.391 52.381 0.00 0.00 0.00 2.15
115 116 2.605823 CGGCTCGGACTCTCAATCATAC 60.606 54.545 0.00 0.00 0.00 2.39
116 117 2.625790 GGCTCGGACTCTCAATCATACT 59.374 50.000 0.00 0.00 0.00 2.12
117 118 3.068873 GGCTCGGACTCTCAATCATACTT 59.931 47.826 0.00 0.00 0.00 2.24
118 119 4.047822 GCTCGGACTCTCAATCATACTTG 58.952 47.826 0.00 0.00 0.00 3.16
119 120 4.046938 TCGGACTCTCAATCATACTTGC 57.953 45.455 0.00 0.00 0.00 4.01
120 121 3.126831 CGGACTCTCAATCATACTTGCC 58.873 50.000 0.00 0.00 0.00 4.52
121 122 3.181471 CGGACTCTCAATCATACTTGCCT 60.181 47.826 0.00 0.00 0.00 4.75
122 123 4.681781 CGGACTCTCAATCATACTTGCCTT 60.682 45.833 0.00 0.00 0.00 4.35
123 124 4.574013 GGACTCTCAATCATACTTGCCTTG 59.426 45.833 0.00 0.00 0.00 3.61
124 125 3.944015 ACTCTCAATCATACTTGCCTTGC 59.056 43.478 0.00 0.00 0.00 4.01
125 126 3.943381 CTCTCAATCATACTTGCCTTGCA 59.057 43.478 0.00 0.00 36.47 4.08
126 127 3.691118 TCTCAATCATACTTGCCTTGCAC 59.309 43.478 0.00 0.00 38.71 4.57
127 128 3.689347 TCAATCATACTTGCCTTGCACT 58.311 40.909 0.00 0.00 38.71 4.40
128 129 4.842574 TCAATCATACTTGCCTTGCACTA 58.157 39.130 0.00 0.00 38.71 2.74
129 130 4.635765 TCAATCATACTTGCCTTGCACTAC 59.364 41.667 0.00 0.00 38.71 2.73
130 131 3.694043 TCATACTTGCCTTGCACTACA 57.306 42.857 0.00 0.00 38.71 2.74
131 132 4.014569 TCATACTTGCCTTGCACTACAA 57.985 40.909 0.00 0.00 38.71 2.41
147 148 8.712285 TGCACTACAAGTTCTACCATAATAAC 57.288 34.615 0.00 0.00 0.00 1.89
148 149 7.490079 TGCACTACAAGTTCTACCATAATAACG 59.510 37.037 0.00 0.00 0.00 3.18
149 150 7.703621 GCACTACAAGTTCTACCATAATAACGA 59.296 37.037 0.00 0.00 0.00 3.85
150 151 9.745880 CACTACAAGTTCTACCATAATAACGAT 57.254 33.333 0.00 0.00 0.00 3.73
160 161 9.882996 TCTACCATAATAACGATTGTAACTACG 57.117 33.333 0.00 0.00 0.00 3.51
161 162 7.935338 ACCATAATAACGATTGTAACTACGG 57.065 36.000 0.00 0.00 0.00 4.02
162 163 6.925165 ACCATAATAACGATTGTAACTACGGG 59.075 38.462 0.00 0.00 0.00 5.28
163 164 6.128742 CCATAATAACGATTGTAACTACGGGC 60.129 42.308 0.00 0.00 0.00 6.13
164 165 2.014335 AACGATTGTAACTACGGGCC 57.986 50.000 0.00 0.00 0.00 5.80
165 166 1.188863 ACGATTGTAACTACGGGCCT 58.811 50.000 0.84 0.00 0.00 5.19
166 167 1.551883 ACGATTGTAACTACGGGCCTT 59.448 47.619 0.84 0.00 0.00 4.35
167 168 2.760092 ACGATTGTAACTACGGGCCTTA 59.240 45.455 0.84 0.00 0.00 2.69
168 169 3.195396 ACGATTGTAACTACGGGCCTTAA 59.805 43.478 0.84 0.00 0.00 1.85
169 170 3.800506 CGATTGTAACTACGGGCCTTAAG 59.199 47.826 0.84 0.00 0.00 1.85
170 171 2.678471 TGTAACTACGGGCCTTAAGC 57.322 50.000 0.84 0.00 42.60 3.09
180 181 3.249687 GCCTTAAGCCATATCCGGG 57.750 57.895 0.00 0.00 34.35 5.73
181 182 0.400594 GCCTTAAGCCATATCCGGGT 59.599 55.000 0.00 0.00 38.81 5.28
182 183 1.610886 GCCTTAAGCCATATCCGGGTC 60.611 57.143 0.00 0.00 35.11 4.46
183 184 1.978580 CCTTAAGCCATATCCGGGTCT 59.021 52.381 0.00 0.00 35.11 3.85
184 185 2.372172 CCTTAAGCCATATCCGGGTCTT 59.628 50.000 0.00 0.00 35.11 3.01
185 186 3.581332 CCTTAAGCCATATCCGGGTCTTA 59.419 47.826 0.00 0.00 35.11 2.10
186 187 4.041198 CCTTAAGCCATATCCGGGTCTTAA 59.959 45.833 0.00 3.83 35.11 1.85
187 188 3.771577 AAGCCATATCCGGGTCTTAAG 57.228 47.619 0.00 0.00 35.11 1.85
188 189 1.348036 AGCCATATCCGGGTCTTAAGC 59.652 52.381 0.00 0.00 27.85 3.09
189 190 1.610886 GCCATATCCGGGTCTTAAGCC 60.611 57.143 0.00 2.49 39.82 4.35
190 191 1.003233 CCATATCCGGGTCTTAAGCCC 59.997 57.143 19.51 19.51 40.10 5.19
191 192 1.697432 CATATCCGGGTCTTAAGCCCA 59.303 52.381 25.33 13.50 46.40 5.36
192 193 2.112279 TATCCGGGTCTTAAGCCCAT 57.888 50.000 25.33 17.76 46.40 4.00
193 194 0.765510 ATCCGGGTCTTAAGCCCATC 59.234 55.000 25.33 3.00 46.40 3.51
194 195 0.326238 TCCGGGTCTTAAGCCCATCT 60.326 55.000 25.33 0.00 46.40 2.90
195 196 0.106894 CCGGGTCTTAAGCCCATCTC 59.893 60.000 25.33 2.08 46.40 2.75
196 197 1.123928 CGGGTCTTAAGCCCATCTCT 58.876 55.000 25.33 0.00 46.40 3.10
197 198 1.202580 CGGGTCTTAAGCCCATCTCTG 60.203 57.143 25.33 11.13 46.40 3.35
198 199 1.141858 GGGTCTTAAGCCCATCTCTGG 59.858 57.143 22.72 0.00 45.40 3.86
204 205 4.512914 GCCCATCTCTGGCCCACC 62.513 72.222 0.00 0.00 43.33 4.61
205 206 4.181010 CCCATCTCTGGCCCACCG 62.181 72.222 0.00 0.00 41.64 4.94
206 207 3.402681 CCATCTCTGGCCCACCGT 61.403 66.667 0.00 0.00 39.70 4.83
207 208 2.187946 CATCTCTGGCCCACCGTC 59.812 66.667 0.00 0.00 39.70 4.79
208 209 2.039624 ATCTCTGGCCCACCGTCT 59.960 61.111 0.00 0.00 39.70 4.18
209 210 1.613630 ATCTCTGGCCCACCGTCTT 60.614 57.895 0.00 0.00 39.70 3.01
210 211 1.617947 ATCTCTGGCCCACCGTCTTC 61.618 60.000 0.00 0.00 39.70 2.87
211 212 3.649277 CTCTGGCCCACCGTCTTCG 62.649 68.421 0.00 0.00 39.70 3.79
212 213 3.691342 CTGGCCCACCGTCTTCGA 61.691 66.667 0.00 0.00 39.70 3.71
213 214 3.649277 CTGGCCCACCGTCTTCGAG 62.649 68.421 0.00 0.00 39.70 4.04
215 216 4.070552 GCCCACCGTCTTCGAGCT 62.071 66.667 0.00 0.00 39.71 4.09
216 217 2.657237 CCCACCGTCTTCGAGCTT 59.343 61.111 0.00 0.00 39.71 3.74
217 218 1.738099 CCCACCGTCTTCGAGCTTG 60.738 63.158 0.00 0.00 39.71 4.01
218 219 1.738099 CCACCGTCTTCGAGCTTGG 60.738 63.158 0.00 0.00 39.71 3.61
219 220 2.048127 ACCGTCTTCGAGCTTGGC 60.048 61.111 0.00 0.00 39.71 4.52
220 221 2.262915 CCGTCTTCGAGCTTGGCT 59.737 61.111 0.00 0.00 43.88 4.75
229 230 4.416738 AGCTTGGCTCCGGGCTTC 62.417 66.667 13.58 0.61 41.46 3.86
230 231 4.416738 GCTTGGCTCCGGGCTTCT 62.417 66.667 13.58 0.00 41.46 2.85
231 232 2.437359 CTTGGCTCCGGGCTTCTG 60.437 66.667 13.58 0.83 41.46 3.02
232 233 3.984193 CTTGGCTCCGGGCTTCTGG 62.984 68.421 13.58 0.00 41.46 3.86
234 235 3.081409 GGCTCCGGGCTTCTGGTA 61.081 66.667 13.58 0.00 41.46 3.25
235 236 2.501610 GCTCCGGGCTTCTGGTAG 59.498 66.667 0.00 0.00 38.12 3.18
236 237 2.359967 GCTCCGGGCTTCTGGTAGT 61.360 63.158 0.00 0.00 38.12 2.73
237 238 1.517832 CTCCGGGCTTCTGGTAGTG 59.482 63.158 0.00 0.00 38.12 2.74
238 239 0.970937 CTCCGGGCTTCTGGTAGTGA 60.971 60.000 0.00 0.00 38.12 3.41
239 240 1.218316 CCGGGCTTCTGGTAGTGAC 59.782 63.158 0.00 0.00 32.23 3.67
253 254 5.273674 GGTAGTGACCATTAGAGTAACCC 57.726 47.826 0.00 0.00 46.12 4.11
254 255 4.202090 GGTAGTGACCATTAGAGTAACCCG 60.202 50.000 0.00 0.00 46.12 5.28
255 256 2.764572 AGTGACCATTAGAGTAACCCGG 59.235 50.000 0.00 0.00 0.00 5.73
256 257 1.483415 TGACCATTAGAGTAACCCGGC 59.517 52.381 0.00 0.00 0.00 6.13
257 258 0.835276 ACCATTAGAGTAACCCGGCC 59.165 55.000 0.00 0.00 0.00 6.13
258 259 0.108019 CCATTAGAGTAACCCGGCCC 59.892 60.000 0.00 0.00 0.00 5.80
259 260 0.108019 CATTAGAGTAACCCGGCCCC 59.892 60.000 0.00 0.00 0.00 5.80
260 261 0.030399 ATTAGAGTAACCCGGCCCCT 60.030 55.000 0.00 0.00 0.00 4.79
261 262 0.688749 TTAGAGTAACCCGGCCCCTC 60.689 60.000 0.00 0.00 0.00 4.30
262 263 2.594365 TAGAGTAACCCGGCCCCTCC 62.594 65.000 0.00 0.00 0.00 4.30
263 264 3.997756 GAGTAACCCGGCCCCTCCT 62.998 68.421 0.00 0.00 0.00 3.69
264 265 3.793888 GTAACCCGGCCCCTCCTG 61.794 72.222 0.00 0.00 0.00 3.86
275 276 3.775654 CCTCCTGGCGGGTGACTC 61.776 72.222 15.89 0.00 36.25 3.36
276 277 2.681778 CTCCTGGCGGGTGACTCT 60.682 66.667 13.14 0.00 36.25 3.24
277 278 1.379977 CTCCTGGCGGGTGACTCTA 60.380 63.158 13.14 0.00 36.25 2.43
278 279 0.970937 CTCCTGGCGGGTGACTCTAA 60.971 60.000 13.14 0.00 36.25 2.10
279 280 0.970937 TCCTGGCGGGTGACTCTAAG 60.971 60.000 13.14 0.00 36.25 2.18
280 281 1.517832 CTGGCGGGTGACTCTAAGG 59.482 63.158 0.00 0.00 0.00 2.69
281 282 1.229082 TGGCGGGTGACTCTAAGGT 60.229 57.895 0.00 0.00 0.00 3.50
282 283 1.255667 TGGCGGGTGACTCTAAGGTC 61.256 60.000 0.00 0.00 36.81 3.85
283 284 0.971447 GGCGGGTGACTCTAAGGTCT 60.971 60.000 0.00 0.00 37.16 3.85
284 285 1.684248 GGCGGGTGACTCTAAGGTCTA 60.684 57.143 0.00 0.00 37.16 2.59
285 286 2.308690 GCGGGTGACTCTAAGGTCTAT 58.691 52.381 0.00 0.00 37.16 1.98
286 287 3.484407 GCGGGTGACTCTAAGGTCTATA 58.516 50.000 0.00 0.00 37.16 1.31
287 288 4.080687 GCGGGTGACTCTAAGGTCTATAT 58.919 47.826 0.00 0.00 37.16 0.86
288 289 4.156373 GCGGGTGACTCTAAGGTCTATATC 59.844 50.000 0.00 0.00 37.16 1.63
289 290 4.701171 CGGGTGACTCTAAGGTCTATATCC 59.299 50.000 0.00 0.00 37.16 2.59
290 291 5.515184 CGGGTGACTCTAAGGTCTATATCCT 60.515 48.000 0.00 0.00 37.16 3.24
291 292 5.947566 GGGTGACTCTAAGGTCTATATCCTC 59.052 48.000 0.00 0.00 37.16 3.71
292 293 6.467484 GGGTGACTCTAAGGTCTATATCCTCA 60.467 46.154 0.00 0.00 37.16 3.86
293 294 7.005296 GGTGACTCTAAGGTCTATATCCTCAA 58.995 42.308 0.00 0.00 37.16 3.02
294 295 7.040271 GGTGACTCTAAGGTCTATATCCTCAAC 60.040 44.444 0.00 0.00 37.16 3.18
295 296 7.502895 GTGACTCTAAGGTCTATATCCTCAACA 59.497 40.741 0.00 0.00 37.16 3.33
307 308 1.704628 TCCTCAACAGGCATGGAGAAA 59.295 47.619 2.31 0.00 40.12 2.52
356 357 4.442192 CCTGATTAGTTCCACTGGCTAGTC 60.442 50.000 0.00 0.00 34.07 2.59
375 376 4.380531 AGTCCAGCCGATTGTGTATATTG 58.619 43.478 0.00 0.00 0.00 1.90
377 378 4.024893 GTCCAGCCGATTGTGTATATTGTG 60.025 45.833 0.00 0.00 0.00 3.33
410 411 3.022406 AGTAGTACACCGGATCAAGGTC 58.978 50.000 9.46 0.07 40.59 3.85
419 420 1.467920 GGATCAAGGTCAGCAAAGGG 58.532 55.000 0.00 0.00 0.00 3.95
420 421 1.004745 GGATCAAGGTCAGCAAAGGGA 59.995 52.381 0.00 0.00 0.00 4.20
423 424 0.954452 CAAGGTCAGCAAAGGGACAC 59.046 55.000 0.00 0.00 35.74 3.67
424 425 0.535102 AAGGTCAGCAAAGGGACACG 60.535 55.000 0.00 0.00 35.74 4.49
425 426 1.966451 GGTCAGCAAAGGGACACGG 60.966 63.158 0.00 0.00 35.74 4.94
426 427 2.281484 TCAGCAAAGGGACACGGC 60.281 61.111 0.00 0.00 0.00 5.68
427 428 2.594303 CAGCAAAGGGACACGGCA 60.594 61.111 0.00 0.00 0.00 5.69
429 430 1.973281 AGCAAAGGGACACGGCATG 60.973 57.895 0.00 0.00 0.00 4.06
430 431 1.971167 GCAAAGGGACACGGCATGA 60.971 57.895 0.00 0.00 0.00 3.07
432 433 0.958091 CAAAGGGACACGGCATGAAA 59.042 50.000 0.00 0.00 0.00 2.69
436 437 0.039527 GGGACACGGCATGAAAACAC 60.040 55.000 0.00 0.00 0.00 3.32
437 438 0.039527 GGACACGGCATGAAAACACC 60.040 55.000 0.00 0.00 0.00 4.16
438 439 0.039527 GACACGGCATGAAAACACCC 60.040 55.000 0.00 0.00 0.00 4.61
439 440 0.753479 ACACGGCATGAAAACACCCA 60.753 50.000 0.00 0.00 0.00 4.51
440 441 0.039256 CACGGCATGAAAACACCCAG 60.039 55.000 0.00 0.00 0.00 4.45
441 442 1.178534 ACGGCATGAAAACACCCAGG 61.179 55.000 0.00 0.00 0.00 4.45
442 443 0.893270 CGGCATGAAAACACCCAGGA 60.893 55.000 0.00 0.00 0.00 3.86
443 444 1.560505 GGCATGAAAACACCCAGGAT 58.439 50.000 0.00 0.00 0.00 3.24
481 482 0.039617 CGGCAGCCACGAAATTTCAA 60.040 50.000 17.99 0.00 0.00 2.69
485 486 2.856720 GCAGCCACGAAATTTCAACGAA 60.857 45.455 17.99 0.00 0.00 3.85
486 487 2.973224 CAGCCACGAAATTTCAACGAAG 59.027 45.455 17.99 3.28 0.00 3.79
487 488 2.875933 AGCCACGAAATTTCAACGAAGA 59.124 40.909 17.99 0.00 0.00 2.87
488 489 2.971261 GCCACGAAATTTCAACGAAGAC 59.029 45.455 17.99 0.00 0.00 3.01
489 490 3.547214 GCCACGAAATTTCAACGAAGACA 60.547 43.478 17.99 0.00 0.00 3.41
490 491 4.593157 CCACGAAATTTCAACGAAGACAA 58.407 39.130 17.99 0.00 0.00 3.18
491 492 5.031578 CCACGAAATTTCAACGAAGACAAA 58.968 37.500 17.99 0.00 0.00 2.83
492 493 5.171337 CCACGAAATTTCAACGAAGACAAAG 59.829 40.000 17.99 0.00 0.00 2.77
493 494 5.171337 CACGAAATTTCAACGAAGACAAAGG 59.829 40.000 17.99 0.00 0.00 3.11
494 495 4.675114 CGAAATTTCAACGAAGACAAAGGG 59.325 41.667 17.99 0.00 0.00 3.95
495 496 4.584327 AATTTCAACGAAGACAAAGGGG 57.416 40.909 0.00 0.00 0.00 4.79
496 497 1.975660 TTCAACGAAGACAAAGGGGG 58.024 50.000 0.00 0.00 0.00 5.40
497 498 0.536460 TCAACGAAGACAAAGGGGGC 60.536 55.000 0.00 0.00 0.00 5.80
498 499 1.599797 AACGAAGACAAAGGGGGCG 60.600 57.895 0.00 0.00 0.00 6.13
499 500 2.032071 CGAAGACAAAGGGGGCGT 59.968 61.111 0.00 0.00 0.00 5.68
500 501 2.033194 CGAAGACAAAGGGGGCGTC 61.033 63.158 0.00 0.00 0.00 5.19
501 502 1.072505 GAAGACAAAGGGGGCGTCA 59.927 57.895 0.00 0.00 31.92 4.35
502 503 0.322546 GAAGACAAAGGGGGCGTCAT 60.323 55.000 0.00 0.00 31.92 3.06
538 539 1.079127 AAGACCTCAACGCGGGATG 60.079 57.895 12.47 4.61 0.00 3.51
539 540 3.195698 GACCTCAACGCGGGATGC 61.196 66.667 12.47 0.00 41.47 3.91
541 542 2.745884 CCTCAACGCGGGATGCAA 60.746 61.111 12.47 0.00 46.97 4.08
542 543 2.114670 CCTCAACGCGGGATGCAAT 61.115 57.895 12.47 0.00 46.97 3.56
543 544 1.063006 CTCAACGCGGGATGCAATG 59.937 57.895 12.47 0.00 46.97 2.82
588 621 2.841160 GCAACCGCGAAACACCCTT 61.841 57.895 8.23 0.00 0.00 3.95
594 627 0.721718 CGCGAAACACCCTTCTCATC 59.278 55.000 0.00 0.00 0.00 2.92
595 628 1.087501 GCGAAACACCCTTCTCATCC 58.912 55.000 0.00 0.00 0.00 3.51
613 646 2.127232 CCCCGGGACATTGCATTCC 61.127 63.158 26.32 0.00 0.00 3.01
668 710 8.833231 AATTATTTTCGATGTATGATCCTCGT 57.167 30.769 0.00 0.00 33.10 4.18
674 716 4.035909 TCGATGTATGATCCTCGTTCGAAA 59.964 41.667 0.00 0.00 33.10 3.46
691 733 8.081633 TCGTTCGAAAATTAGAACTAACCACTA 58.918 33.333 14.38 0.00 43.15 2.74
744 786 2.482721 CCCCTGACAAACACGTTGATAC 59.517 50.000 0.00 0.00 39.87 2.24
752 794 1.710013 ACACGTTGATACTCCTTGCG 58.290 50.000 0.00 0.00 0.00 4.85
753 795 1.000506 ACACGTTGATACTCCTTGCGT 59.999 47.619 0.00 0.00 0.00 5.24
756 798 3.676172 CACGTTGATACTCCTTGCGTTTA 59.324 43.478 0.00 0.00 0.00 2.01
764 806 1.810755 CTCCTTGCGTTTACCCCTTTC 59.189 52.381 0.00 0.00 0.00 2.62
766 808 2.158579 TCCTTGCGTTTACCCCTTTCTT 60.159 45.455 0.00 0.00 0.00 2.52
771 813 1.074244 CGTTTACCCCTTTCTTCCCCA 59.926 52.381 0.00 0.00 0.00 4.96
778 820 2.621668 CCCCTTTCTTCCCCAATCACTC 60.622 54.545 0.00 0.00 0.00 3.51
780 822 2.310052 CCTTTCTTCCCCAATCACTCCT 59.690 50.000 0.00 0.00 0.00 3.69
781 823 3.615155 CTTTCTTCCCCAATCACTCCTC 58.385 50.000 0.00 0.00 0.00 3.71
782 824 2.649742 TCTTCCCCAATCACTCCTCT 57.350 50.000 0.00 0.00 0.00 3.69
783 825 2.472029 TCTTCCCCAATCACTCCTCTC 58.528 52.381 0.00 0.00 0.00 3.20
820 885 1.275291 CCAACCTCGCAGTTCCTCTAA 59.725 52.381 0.00 0.00 0.00 2.10
899 969 1.204467 CCTCTCTCTCACTGAACTGCC 59.796 57.143 0.00 0.00 0.00 4.85
905 975 2.297315 CTCTCACTGAACTGCCACTACA 59.703 50.000 0.00 0.00 0.00 2.74
932 1004 2.282040 AGCAGCCACTCAGCAACC 60.282 61.111 0.00 0.00 34.23 3.77
946 1018 2.684881 CAGCAACCTCTCTCTCTCTCTC 59.315 54.545 0.00 0.00 0.00 3.20
947 1019 2.578021 AGCAACCTCTCTCTCTCTCTCT 59.422 50.000 0.00 0.00 0.00 3.10
948 1020 2.945668 GCAACCTCTCTCTCTCTCTCTC 59.054 54.545 0.00 0.00 0.00 3.20
949 1021 3.370953 GCAACCTCTCTCTCTCTCTCTCT 60.371 52.174 0.00 0.00 0.00 3.10
950 1022 4.446371 CAACCTCTCTCTCTCTCTCTCTC 58.554 52.174 0.00 0.00 0.00 3.20
951 1023 4.000928 ACCTCTCTCTCTCTCTCTCTCT 57.999 50.000 0.00 0.00 0.00 3.10
952 1024 3.964031 ACCTCTCTCTCTCTCTCTCTCTC 59.036 52.174 0.00 0.00 0.00 3.20
953 1025 4.222336 CCTCTCTCTCTCTCTCTCTCTCT 58.778 52.174 0.00 0.00 0.00 3.10
954 1026 4.280677 CCTCTCTCTCTCTCTCTCTCTCTC 59.719 54.167 0.00 0.00 0.00 3.20
955 1027 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
976 1048 2.236146 TCTCTCTCTCTCTCACGCTCTT 59.764 50.000 0.00 0.00 0.00 2.85
1120 1765 0.099082 CGTCGTCTACTCTGGCCTTC 59.901 60.000 3.32 0.00 0.00 3.46
1156 1801 4.821589 CGGAGGAGCTGGCGTTCC 62.822 72.222 0.00 4.56 40.53 3.62
1877 2740 3.676291 AATTATGGGTGTGTGTTTGCC 57.324 42.857 0.00 0.00 0.00 4.52
1884 2747 0.318955 GTGTGTGTTTGCCCATGAGC 60.319 55.000 0.00 0.00 0.00 4.26
1904 2767 1.202604 CCAGTGGACGTGTTGGTACTT 60.203 52.381 1.68 0.00 0.00 2.24
1998 4047 2.043664 TGAATGTATGGGGGCCAGAAAA 59.956 45.455 4.39 0.00 36.75 2.29
2026 4075 3.951663 ACCACTGCAATAAACTACTCCC 58.048 45.455 0.00 0.00 0.00 4.30
2044 4102 4.202588 ACTCCCTCTTGACACTACACTAGT 60.203 45.833 0.00 0.00 40.28 2.57
2203 4261 9.248291 GAAATGAATGTGTAGTGTGTTTGAAAT 57.752 29.630 0.00 0.00 0.00 2.17
2228 4286 6.664515 TGTGGAATAGTTTTAGAAAGCAACG 58.335 36.000 0.00 0.00 0.00 4.10
2412 4470 3.136345 CTGTTGCAAGGGCGCACAA 62.136 57.895 14.57 3.48 42.87 3.33
2492 4550 0.464452 AGGATAACCCTTCGGCTTCG 59.536 55.000 0.00 0.00 44.85 3.79
2529 4587 3.059188 CACGCAACCAACTTTATTCGACT 60.059 43.478 0.00 0.00 0.00 4.18
2589 4661 2.548057 TGTGTCTGCCTTCTAAAAAGCG 59.452 45.455 0.00 0.00 0.00 4.68
2591 4663 2.806244 TGTCTGCCTTCTAAAAAGCGTC 59.194 45.455 0.00 0.00 0.00 5.19
2634 4707 1.007154 GCGGTAGATCCTCGCTTCC 60.007 63.158 14.84 0.00 45.16 3.46
2636 4709 1.660917 GGTAGATCCTCGCTTCCCG 59.339 63.158 0.00 0.00 38.61 5.14
2689 5345 2.774439 GTGAATGCACAGAAAACCGT 57.226 45.000 0.00 0.00 44.51 4.83
2692 5348 3.002862 GTGAATGCACAGAAAACCGTGTA 59.997 43.478 0.00 0.00 44.51 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.350484 GCAGCGGTTTAGGAACAAGAAC 60.350 50.000 0.00 0.00 37.51 3.01
1 2 1.877443 GCAGCGGTTTAGGAACAAGAA 59.123 47.619 0.00 0.00 37.51 2.52
2 3 1.519408 GCAGCGGTTTAGGAACAAGA 58.481 50.000 0.00 0.00 37.51 3.02
3 4 0.521735 GGCAGCGGTTTAGGAACAAG 59.478 55.000 0.00 0.00 37.51 3.16
4 5 1.231958 CGGCAGCGGTTTAGGAACAA 61.232 55.000 0.00 0.00 37.51 2.83
5 6 1.669760 CGGCAGCGGTTTAGGAACA 60.670 57.895 0.00 0.00 37.51 3.18
6 7 2.396157 CCGGCAGCGGTTTAGGAAC 61.396 63.158 0.00 0.00 34.96 3.62
7 8 2.046700 CCGGCAGCGGTTTAGGAA 60.047 61.111 0.00 0.00 0.00 3.36
8 9 4.090588 CCCGGCAGCGGTTTAGGA 62.091 66.667 0.00 0.00 0.00 2.94
9 10 4.404098 ACCCGGCAGCGGTTTAGG 62.404 66.667 0.00 0.00 0.00 2.69
10 11 2.818274 GACCCGGCAGCGGTTTAG 60.818 66.667 0.00 0.00 32.27 1.85
11 12 4.745751 CGACCCGGCAGCGGTTTA 62.746 66.667 0.00 0.00 32.27 2.01
30 31 6.423712 GCGTCAGCCTCCCTATATAAAGGG 62.424 54.167 4.33 4.33 46.97 3.95
31 32 3.368531 GCGTCAGCCTCCCTATATAAAGG 60.369 52.174 2.47 2.47 37.42 3.11
32 33 3.851098 GCGTCAGCCTCCCTATATAAAG 58.149 50.000 0.00 0.00 37.42 1.85
33 34 3.955650 GCGTCAGCCTCCCTATATAAA 57.044 47.619 0.00 0.00 37.42 1.40
52 53 4.486503 CTCTGAGGGCTGCTGGGC 62.487 72.222 0.00 0.00 40.05 5.36
53 54 3.007920 ACTCTGAGGGCTGCTGGG 61.008 66.667 9.85 0.00 0.00 4.45
54 55 2.583520 GACTCTGAGGGCTGCTGG 59.416 66.667 9.85 0.00 0.00 4.85
55 56 2.583520 GGACTCTGAGGGCTGCTG 59.416 66.667 9.85 0.00 0.00 4.41
56 57 2.686835 GGGACTCTGAGGGCTGCT 60.687 66.667 9.85 0.00 0.00 4.24
57 58 4.154347 CGGGACTCTGAGGGCTGC 62.154 72.222 9.85 0.00 0.00 5.25
58 59 3.465403 CCGGGACTCTGAGGGCTG 61.465 72.222 9.85 0.00 0.00 4.85
68 69 4.853142 TATGAGCCGGCCGGGACT 62.853 66.667 43.31 32.89 38.47 3.85
69 70 2.879813 TTTTATGAGCCGGCCGGGAC 62.880 60.000 43.31 28.68 38.47 4.46
70 71 2.602746 CTTTTATGAGCCGGCCGGGA 62.603 60.000 43.31 10.93 38.47 5.14
71 72 2.124487 TTTTATGAGCCGGCCGGG 60.124 61.111 43.31 26.06 39.58 5.73
72 73 2.834618 GCTTTTATGAGCCGGCCGG 61.835 63.158 40.26 40.26 36.66 6.13
73 74 2.715624 GCTTTTATGAGCCGGCCG 59.284 61.111 26.15 21.04 36.66 6.13
74 75 2.048312 GACGCTTTTATGAGCCGGCC 62.048 60.000 26.15 15.80 39.51 6.13
75 76 1.352056 GACGCTTTTATGAGCCGGC 59.648 57.895 21.89 21.89 39.51 6.13
76 77 1.762222 CGGACGCTTTTATGAGCCGG 61.762 60.000 0.00 0.00 39.51 6.13
77 78 1.636340 CGGACGCTTTTATGAGCCG 59.364 57.895 0.00 0.00 39.51 5.52
78 79 2.014594 CCGGACGCTTTTATGAGCC 58.985 57.895 0.00 0.00 39.51 4.70
79 80 1.352056 GCCGGACGCTTTTATGAGC 59.648 57.895 5.05 0.00 39.29 4.26
94 95 0.387202 ATGATTGAGAGTCCGAGCCG 59.613 55.000 0.00 0.00 0.00 5.52
95 96 2.625790 AGTATGATTGAGAGTCCGAGCC 59.374 50.000 0.00 0.00 0.00 4.70
96 97 4.047822 CAAGTATGATTGAGAGTCCGAGC 58.952 47.826 0.00 0.00 31.55 5.03
97 98 4.047822 GCAAGTATGATTGAGAGTCCGAG 58.952 47.826 0.00 0.00 31.55 4.63
98 99 3.181475 GGCAAGTATGATTGAGAGTCCGA 60.181 47.826 0.00 0.00 31.55 4.55
99 100 3.126831 GGCAAGTATGATTGAGAGTCCG 58.873 50.000 0.00 0.00 31.55 4.79
100 101 4.414337 AGGCAAGTATGATTGAGAGTCC 57.586 45.455 0.00 0.00 31.55 3.85
101 102 4.034975 GCAAGGCAAGTATGATTGAGAGTC 59.965 45.833 0.00 0.00 31.55 3.36
102 103 3.944015 GCAAGGCAAGTATGATTGAGAGT 59.056 43.478 0.00 0.00 31.55 3.24
103 104 3.943381 TGCAAGGCAAGTATGATTGAGAG 59.057 43.478 0.00 0.00 34.76 3.20
104 105 3.691118 GTGCAAGGCAAGTATGATTGAGA 59.309 43.478 0.00 0.00 41.47 3.27
105 106 3.693085 AGTGCAAGGCAAGTATGATTGAG 59.307 43.478 0.00 0.00 41.47 3.02
106 107 3.689347 AGTGCAAGGCAAGTATGATTGA 58.311 40.909 0.00 0.00 41.47 2.57
107 108 4.395854 TGTAGTGCAAGGCAAGTATGATTG 59.604 41.667 0.00 0.00 41.47 2.67
108 109 4.588899 TGTAGTGCAAGGCAAGTATGATT 58.411 39.130 0.00 0.00 41.47 2.57
109 110 4.220693 TGTAGTGCAAGGCAAGTATGAT 57.779 40.909 0.00 0.00 41.47 2.45
110 111 3.694043 TGTAGTGCAAGGCAAGTATGA 57.306 42.857 0.00 0.00 41.47 2.15
121 122 9.158233 GTTATTATGGTAGAACTTGTAGTGCAA 57.842 33.333 0.00 0.00 35.50 4.08
122 123 7.490079 CGTTATTATGGTAGAACTTGTAGTGCA 59.510 37.037 0.00 0.00 0.00 4.57
123 124 7.703621 TCGTTATTATGGTAGAACTTGTAGTGC 59.296 37.037 0.00 0.00 0.00 4.40
124 125 9.745880 ATCGTTATTATGGTAGAACTTGTAGTG 57.254 33.333 0.00 0.00 0.00 2.74
134 135 9.882996 CGTAGTTACAATCGTTATTATGGTAGA 57.117 33.333 0.00 0.00 0.00 2.59
135 136 9.121517 CCGTAGTTACAATCGTTATTATGGTAG 57.878 37.037 0.00 0.00 0.00 3.18
136 137 8.081633 CCCGTAGTTACAATCGTTATTATGGTA 58.918 37.037 0.00 0.00 0.00 3.25
137 138 6.925165 CCCGTAGTTACAATCGTTATTATGGT 59.075 38.462 0.00 0.00 0.00 3.55
138 139 6.128742 GCCCGTAGTTACAATCGTTATTATGG 60.129 42.308 0.00 0.00 0.00 2.74
139 140 6.128742 GGCCCGTAGTTACAATCGTTATTATG 60.129 42.308 0.00 0.00 0.00 1.90
140 141 5.928264 GGCCCGTAGTTACAATCGTTATTAT 59.072 40.000 0.00 0.00 0.00 1.28
141 142 5.068987 AGGCCCGTAGTTACAATCGTTATTA 59.931 40.000 0.00 0.00 0.00 0.98
142 143 4.122046 GGCCCGTAGTTACAATCGTTATT 58.878 43.478 0.00 0.00 0.00 1.40
143 144 3.385755 AGGCCCGTAGTTACAATCGTTAT 59.614 43.478 0.00 0.00 0.00 1.89
144 145 2.760092 AGGCCCGTAGTTACAATCGTTA 59.240 45.455 0.00 0.00 0.00 3.18
145 146 1.551883 AGGCCCGTAGTTACAATCGTT 59.448 47.619 0.00 0.00 0.00 3.85
146 147 1.188863 AGGCCCGTAGTTACAATCGT 58.811 50.000 0.00 0.00 0.00 3.73
147 148 2.304751 AAGGCCCGTAGTTACAATCG 57.695 50.000 0.00 0.00 0.00 3.34
148 149 3.558829 GCTTAAGGCCCGTAGTTACAATC 59.441 47.826 0.00 0.00 34.27 2.67
149 150 3.538591 GCTTAAGGCCCGTAGTTACAAT 58.461 45.455 0.00 0.00 34.27 2.71
150 151 2.976589 GCTTAAGGCCCGTAGTTACAA 58.023 47.619 0.00 0.00 34.27 2.41
151 152 2.678471 GCTTAAGGCCCGTAGTTACA 57.322 50.000 0.00 0.00 34.27 2.41
162 163 0.400594 ACCCGGATATGGCTTAAGGC 59.599 55.000 21.52 21.52 41.50 4.35
163 164 1.978580 AGACCCGGATATGGCTTAAGG 59.021 52.381 0.73 0.00 0.00 2.69
164 165 3.771577 AAGACCCGGATATGGCTTAAG 57.228 47.619 0.73 0.00 0.00 1.85
165 166 4.504340 GCTTAAGACCCGGATATGGCTTAA 60.504 45.833 13.75 13.75 33.96 1.85
166 167 3.007614 GCTTAAGACCCGGATATGGCTTA 59.992 47.826 0.73 0.28 0.00 3.09
167 168 2.224548 GCTTAAGACCCGGATATGGCTT 60.225 50.000 0.73 1.50 0.00 4.35
168 169 1.348036 GCTTAAGACCCGGATATGGCT 59.652 52.381 0.73 0.00 0.00 4.75
169 170 1.610886 GGCTTAAGACCCGGATATGGC 60.611 57.143 0.73 1.85 0.00 4.40
170 171 1.003233 GGGCTTAAGACCCGGATATGG 59.997 57.143 17.49 0.00 37.19 2.74
171 172 2.474410 GGGCTTAAGACCCGGATATG 57.526 55.000 17.49 0.00 37.19 1.78
178 179 1.141858 CCAGAGATGGGCTTAAGACCC 59.858 57.143 25.11 22.99 44.80 4.46
179 180 2.629336 CCAGAGATGGGCTTAAGACC 57.371 55.000 21.52 21.52 45.93 3.85
188 189 4.181010 CGGTGGGCCAGAGATGGG 62.181 72.222 6.40 0.00 34.09 4.00
189 190 3.391665 GACGGTGGGCCAGAGATGG 62.392 68.421 6.40 0.00 34.09 3.51
190 191 1.903877 AAGACGGTGGGCCAGAGATG 61.904 60.000 6.40 0.00 34.09 2.90
191 192 1.613630 AAGACGGTGGGCCAGAGAT 60.614 57.895 6.40 0.00 34.09 2.75
192 193 2.203788 AAGACGGTGGGCCAGAGA 60.204 61.111 6.40 0.00 34.09 3.10
193 194 2.266055 GAAGACGGTGGGCCAGAG 59.734 66.667 6.40 6.54 34.09 3.35
194 195 3.691342 CGAAGACGGTGGGCCAGA 61.691 66.667 6.40 0.00 35.72 3.86
195 196 3.649277 CTCGAAGACGGTGGGCCAG 62.649 68.421 6.40 0.00 40.21 4.85
196 197 3.691342 CTCGAAGACGGTGGGCCA 61.691 66.667 0.00 0.00 40.21 5.36
198 199 3.591254 AAGCTCGAAGACGGTGGGC 62.591 63.158 0.00 0.00 40.21 5.36
199 200 1.738099 CAAGCTCGAAGACGGTGGG 60.738 63.158 0.00 0.00 40.21 4.61
200 201 1.738099 CCAAGCTCGAAGACGGTGG 60.738 63.158 0.00 0.00 40.21 4.61
201 202 2.383527 GCCAAGCTCGAAGACGGTG 61.384 63.158 0.00 0.00 40.21 4.94
202 203 2.048127 GCCAAGCTCGAAGACGGT 60.048 61.111 0.00 0.00 40.21 4.83
203 204 1.807573 GAGCCAAGCTCGAAGACGG 60.808 63.158 0.06 0.00 45.85 4.79
204 205 3.773974 GAGCCAAGCTCGAAGACG 58.226 61.111 0.06 0.00 45.85 4.18
212 213 4.416738 GAAGCCCGGAGCCAAGCT 62.417 66.667 0.73 0.00 45.47 3.74
213 214 4.416738 AGAAGCCCGGAGCCAAGC 62.417 66.667 0.73 0.00 45.47 4.01
214 215 2.437359 CAGAAGCCCGGAGCCAAG 60.437 66.667 0.73 0.00 45.47 3.61
215 216 4.033776 CCAGAAGCCCGGAGCCAA 62.034 66.667 0.73 0.00 45.47 4.52
216 217 3.916438 TACCAGAAGCCCGGAGCCA 62.916 63.158 0.73 0.00 45.47 4.75
217 218 3.081409 TACCAGAAGCCCGGAGCC 61.081 66.667 0.73 0.00 45.47 4.70
218 219 2.359967 ACTACCAGAAGCCCGGAGC 61.360 63.158 0.73 4.57 44.25 4.70
219 220 0.970937 TCACTACCAGAAGCCCGGAG 60.971 60.000 0.73 0.00 0.00 4.63
220 221 1.077805 TCACTACCAGAAGCCCGGA 59.922 57.895 0.73 0.00 0.00 5.14
221 222 1.218316 GTCACTACCAGAAGCCCGG 59.782 63.158 0.00 0.00 0.00 5.73
222 223 1.218316 GGTCACTACCAGAAGCCCG 59.782 63.158 0.00 0.00 45.98 6.13
231 232 4.202090 CGGGTTACTCTAATGGTCACTACC 60.202 50.000 0.00 0.00 46.98 3.18
232 233 4.202090 CCGGGTTACTCTAATGGTCACTAC 60.202 50.000 0.00 0.00 0.00 2.73
233 234 3.956199 CCGGGTTACTCTAATGGTCACTA 59.044 47.826 0.00 0.00 0.00 2.74
234 235 2.764572 CCGGGTTACTCTAATGGTCACT 59.235 50.000 0.00 0.00 0.00 3.41
235 236 2.740904 GCCGGGTTACTCTAATGGTCAC 60.741 54.545 2.18 0.00 0.00 3.67
236 237 1.483415 GCCGGGTTACTCTAATGGTCA 59.517 52.381 2.18 0.00 0.00 4.02
237 238 1.202615 GGCCGGGTTACTCTAATGGTC 60.203 57.143 2.18 0.00 0.00 4.02
238 239 0.835276 GGCCGGGTTACTCTAATGGT 59.165 55.000 2.18 0.00 0.00 3.55
239 240 0.108019 GGGCCGGGTTACTCTAATGG 59.892 60.000 2.18 0.00 0.00 3.16
240 241 0.108019 GGGGCCGGGTTACTCTAATG 59.892 60.000 2.18 0.00 0.00 1.90
241 242 0.030399 AGGGGCCGGGTTACTCTAAT 60.030 55.000 2.18 0.00 0.00 1.73
242 243 0.688749 GAGGGGCCGGGTTACTCTAA 60.689 60.000 2.18 0.00 0.00 2.10
243 244 1.075748 GAGGGGCCGGGTTACTCTA 60.076 63.158 2.18 0.00 0.00 2.43
244 245 2.365237 GAGGGGCCGGGTTACTCT 60.365 66.667 2.18 0.00 0.00 3.24
245 246 3.477346 GGAGGGGCCGGGTTACTC 61.477 72.222 2.18 0.00 0.00 2.59
246 247 4.020878 AGGAGGGGCCGGGTTACT 62.021 66.667 2.18 0.00 43.43 2.24
247 248 3.793888 CAGGAGGGGCCGGGTTAC 61.794 72.222 2.18 0.00 43.43 2.50
258 259 2.856039 TAGAGTCACCCGCCAGGAGG 62.856 65.000 1.14 1.14 41.02 4.30
259 260 0.970937 TTAGAGTCACCCGCCAGGAG 60.971 60.000 0.00 0.00 41.02 3.69
260 261 0.970937 CTTAGAGTCACCCGCCAGGA 60.971 60.000 0.00 0.00 41.02 3.86
261 262 1.517832 CTTAGAGTCACCCGCCAGG 59.482 63.158 0.00 0.00 43.78 4.45
262 263 1.258445 ACCTTAGAGTCACCCGCCAG 61.258 60.000 0.00 0.00 0.00 4.85
263 264 1.229082 ACCTTAGAGTCACCCGCCA 60.229 57.895 0.00 0.00 0.00 5.69
264 265 0.971447 AGACCTTAGAGTCACCCGCC 60.971 60.000 0.00 0.00 39.34 6.13
265 266 1.760192 TAGACCTTAGAGTCACCCGC 58.240 55.000 0.00 0.00 39.34 6.13
266 267 4.701171 GGATATAGACCTTAGAGTCACCCG 59.299 50.000 0.00 0.00 39.34 5.28
267 268 5.894653 AGGATATAGACCTTAGAGTCACCC 58.105 45.833 0.00 0.00 39.34 4.61
268 269 6.544650 TGAGGATATAGACCTTAGAGTCACC 58.455 44.000 0.00 0.00 39.34 4.02
269 270 7.502895 TGTTGAGGATATAGACCTTAGAGTCAC 59.497 40.741 0.00 0.00 39.34 3.67
270 271 7.583625 TGTTGAGGATATAGACCTTAGAGTCA 58.416 38.462 0.00 0.00 39.34 3.41
271 272 7.175990 CCTGTTGAGGATATAGACCTTAGAGTC 59.824 44.444 3.30 0.00 42.93 3.36
272 273 7.007723 CCTGTTGAGGATATAGACCTTAGAGT 58.992 42.308 3.30 0.00 42.93 3.24
273 274 6.071616 GCCTGTTGAGGATATAGACCTTAGAG 60.072 46.154 0.00 3.71 42.93 2.43
274 275 5.775701 GCCTGTTGAGGATATAGACCTTAGA 59.224 44.000 0.00 0.00 42.93 2.10
275 276 5.540337 TGCCTGTTGAGGATATAGACCTTAG 59.460 44.000 0.00 1.76 42.93 2.18
276 277 5.464069 TGCCTGTTGAGGATATAGACCTTA 58.536 41.667 0.00 0.00 42.93 2.69
277 278 4.298626 TGCCTGTTGAGGATATAGACCTT 58.701 43.478 0.00 0.00 42.93 3.50
278 279 3.928754 TGCCTGTTGAGGATATAGACCT 58.071 45.455 0.00 1.52 42.93 3.85
279 280 4.564406 CCATGCCTGTTGAGGATATAGACC 60.564 50.000 0.00 0.00 42.93 3.85
280 281 4.284490 TCCATGCCTGTTGAGGATATAGAC 59.716 45.833 0.00 0.00 42.93 2.59
281 282 4.492646 TCCATGCCTGTTGAGGATATAGA 58.507 43.478 0.00 0.00 42.93 1.98
282 283 4.529769 TCTCCATGCCTGTTGAGGATATAG 59.470 45.833 0.00 0.00 42.93 1.31
283 284 4.492646 TCTCCATGCCTGTTGAGGATATA 58.507 43.478 0.00 0.00 42.93 0.86
284 285 3.321039 TCTCCATGCCTGTTGAGGATAT 58.679 45.455 0.00 0.00 42.93 1.63
285 286 2.763039 TCTCCATGCCTGTTGAGGATA 58.237 47.619 0.00 0.00 42.93 2.59
286 287 1.588239 TCTCCATGCCTGTTGAGGAT 58.412 50.000 0.00 0.00 42.93 3.24
287 288 1.361204 TTCTCCATGCCTGTTGAGGA 58.639 50.000 0.00 0.00 42.93 3.71
288 289 2.205022 TTTCTCCATGCCTGTTGAGG 57.795 50.000 0.00 0.00 43.19 3.86
307 308 6.590234 ATGACCCTTTAATTTCGCTCTTTT 57.410 33.333 0.00 0.00 0.00 2.27
310 311 4.816925 GCTATGACCCTTTAATTTCGCTCT 59.183 41.667 0.00 0.00 0.00 4.09
356 357 4.126437 TCACAATATACACAATCGGCTGG 58.874 43.478 0.00 0.00 0.00 4.85
375 376 6.549952 GGTGTACTACTGTACTGTACATCAC 58.450 44.000 19.99 18.32 46.70 3.06
377 378 5.220739 CCGGTGTACTACTGTACTGTACATC 60.221 48.000 19.99 16.49 46.70 3.06
410 411 1.973281 ATGCCGTGTCCCTTTGCTG 60.973 57.895 0.00 0.00 0.00 4.41
419 420 0.039527 GGGTGTTTTCATGCCGTGTC 60.040 55.000 0.00 0.00 0.00 3.67
420 421 0.753479 TGGGTGTTTTCATGCCGTGT 60.753 50.000 0.00 0.00 0.00 4.49
423 424 0.893270 TCCTGGGTGTTTTCATGCCG 60.893 55.000 0.00 0.00 0.00 5.69
424 425 1.478105 GATCCTGGGTGTTTTCATGCC 59.522 52.381 0.00 0.00 0.00 4.40
425 426 1.478105 GGATCCTGGGTGTTTTCATGC 59.522 52.381 3.84 0.00 0.00 4.06
426 427 2.806434 TGGATCCTGGGTGTTTTCATG 58.194 47.619 14.23 0.00 0.00 3.07
427 428 3.075882 TCTTGGATCCTGGGTGTTTTCAT 59.924 43.478 14.23 0.00 0.00 2.57
429 430 3.154827 TCTTGGATCCTGGGTGTTTTC 57.845 47.619 14.23 0.00 0.00 2.29
430 431 3.611025 TTCTTGGATCCTGGGTGTTTT 57.389 42.857 14.23 0.00 0.00 2.43
432 433 2.225117 CCTTTCTTGGATCCTGGGTGTT 60.225 50.000 14.23 0.00 0.00 3.32
436 437 3.456380 TTTCCTTTCTTGGATCCTGGG 57.544 47.619 14.23 6.15 35.83 4.45
437 438 5.760131 AGTATTTCCTTTCTTGGATCCTGG 58.240 41.667 14.23 5.76 35.83 4.45
438 439 5.825151 GGAGTATTTCCTTTCTTGGATCCTG 59.175 44.000 14.23 6.15 43.16 3.86
439 440 5.396884 CGGAGTATTTCCTTTCTTGGATCCT 60.397 44.000 14.23 0.00 44.41 3.24
440 441 4.816925 CGGAGTATTTCCTTTCTTGGATCC 59.183 45.833 4.20 4.20 44.41 3.36
441 442 4.816925 CCGGAGTATTTCCTTTCTTGGATC 59.183 45.833 0.00 0.00 44.41 3.36
442 443 4.781934 CCGGAGTATTTCCTTTCTTGGAT 58.218 43.478 0.00 0.00 44.41 3.41
443 444 3.621461 GCCGGAGTATTTCCTTTCTTGGA 60.621 47.826 5.05 0.00 44.41 3.53
481 482 2.032071 CGCCCCCTTTGTCTTCGT 59.968 61.111 0.00 0.00 0.00 3.85
485 486 0.252197 GTATGACGCCCCCTTTGTCT 59.748 55.000 0.00 0.00 33.81 3.41
486 487 0.035820 TGTATGACGCCCCCTTTGTC 60.036 55.000 0.00 0.00 0.00 3.18
487 488 0.322187 GTGTATGACGCCCCCTTTGT 60.322 55.000 0.00 0.00 0.00 2.83
488 489 1.029947 GGTGTATGACGCCCCCTTTG 61.030 60.000 0.00 0.00 42.80 2.77
489 490 1.301954 GGTGTATGACGCCCCCTTT 59.698 57.895 0.00 0.00 42.80 3.11
490 491 2.995547 GGTGTATGACGCCCCCTT 59.004 61.111 0.00 0.00 42.80 3.95
496 497 1.521681 GCTCTGGGGTGTATGACGC 60.522 63.158 0.00 0.00 36.78 5.19
497 498 0.249120 TTGCTCTGGGGTGTATGACG 59.751 55.000 0.00 0.00 0.00 4.35
498 499 1.555075 TCTTGCTCTGGGGTGTATGAC 59.445 52.381 0.00 0.00 0.00 3.06
499 500 1.555075 GTCTTGCTCTGGGGTGTATGA 59.445 52.381 0.00 0.00 0.00 2.15
500 501 1.278985 TGTCTTGCTCTGGGGTGTATG 59.721 52.381 0.00 0.00 0.00 2.39
501 502 1.656587 TGTCTTGCTCTGGGGTGTAT 58.343 50.000 0.00 0.00 0.00 2.29
502 503 1.347707 CTTGTCTTGCTCTGGGGTGTA 59.652 52.381 0.00 0.00 0.00 2.90
553 586 2.492088 GTTGCCCTGGTCACCTTTATTC 59.508 50.000 0.00 0.00 0.00 1.75
594 627 2.043046 AATGCAATGTCCCGGGGG 60.043 61.111 23.50 6.65 0.00 5.40
595 628 2.127232 GGAATGCAATGTCCCGGGG 61.127 63.158 23.50 6.77 0.00 5.73
652 694 3.537793 TCGAACGAGGATCATACATCG 57.462 47.619 0.00 0.00 46.82 3.84
665 707 6.925165 AGTGGTTAGTTCTAATTTTCGAACGA 59.075 34.615 0.00 0.00 43.15 3.85
667 709 9.201127 AGTAGTGGTTAGTTCTAATTTTCGAAC 57.799 33.333 0.00 6.78 39.74 3.95
668 710 9.768662 AAGTAGTGGTTAGTTCTAATTTTCGAA 57.231 29.630 0.00 0.00 0.00 3.71
691 733 9.091220 ACATGGTAGTAAGAACTTCTTAGAAGT 57.909 33.333 20.62 20.62 39.41 3.01
744 786 1.810755 GAAAGGGGTAAACGCAAGGAG 59.189 52.381 0.00 0.00 46.39 3.69
752 794 2.984435 TGGGGAAGAAAGGGGTAAAC 57.016 50.000 0.00 0.00 0.00 2.01
753 795 3.403051 TGATTGGGGAAGAAAGGGGTAAA 59.597 43.478 0.00 0.00 0.00 2.01
756 798 1.077169 GTGATTGGGGAAGAAAGGGGT 59.923 52.381 0.00 0.00 0.00 4.95
764 806 1.488393 GGAGAGGAGTGATTGGGGAAG 59.512 57.143 0.00 0.00 0.00 3.46
766 808 0.719015 AGGAGAGGAGTGATTGGGGA 59.281 55.000 0.00 0.00 0.00 4.81
771 813 4.338795 TTGGTAGAGGAGAGGAGTGATT 57.661 45.455 0.00 0.00 0.00 2.57
782 824 1.008327 TGGAGCTCCATTGGTAGAGGA 59.992 52.381 32.00 3.89 42.01 3.71
783 825 1.500474 TGGAGCTCCATTGGTAGAGG 58.500 55.000 32.00 0.00 42.01 3.69
820 885 0.456221 CGCTGACGGAGGTTATCAGT 59.544 55.000 2.72 0.00 41.62 3.41
899 969 1.871772 GCTGGCAAGCTGTGTAGTG 59.128 57.895 5.60 0.00 46.60 2.74
932 1004 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
946 1018 4.892345 TGAGAGAGAGAGAGAGAGAGAGAG 59.108 50.000 0.00 0.00 0.00 3.20
947 1019 4.646945 GTGAGAGAGAGAGAGAGAGAGAGA 59.353 50.000 0.00 0.00 0.00 3.10
948 1020 4.498850 CGTGAGAGAGAGAGAGAGAGAGAG 60.499 54.167 0.00 0.00 0.00 3.20
949 1021 3.381590 CGTGAGAGAGAGAGAGAGAGAGA 59.618 52.174 0.00 0.00 0.00 3.10
950 1022 3.711086 CGTGAGAGAGAGAGAGAGAGAG 58.289 54.545 0.00 0.00 0.00 3.20
951 1023 2.159099 GCGTGAGAGAGAGAGAGAGAGA 60.159 54.545 0.00 0.00 0.00 3.10
952 1024 2.159043 AGCGTGAGAGAGAGAGAGAGAG 60.159 54.545 0.00 0.00 0.00 3.20
953 1025 1.831106 AGCGTGAGAGAGAGAGAGAGA 59.169 52.381 0.00 0.00 0.00 3.10
954 1026 2.159043 AGAGCGTGAGAGAGAGAGAGAG 60.159 54.545 0.00 0.00 0.00 3.20
955 1027 1.831106 AGAGCGTGAGAGAGAGAGAGA 59.169 52.381 0.00 0.00 0.00 3.10
976 1048 3.324170 GCGACACGAGCTAGCTAAA 57.676 52.632 19.38 0.00 0.00 1.85
1156 1801 2.278206 CGCGGAGATGACGTCCAG 60.278 66.667 14.12 0.00 33.14 3.86
1877 2740 1.742880 CACGTCCACTGGCTCATGG 60.743 63.158 0.00 0.00 37.32 3.66
1884 2747 0.391597 AGTACCAACACGTCCACTGG 59.608 55.000 0.00 0.00 34.95 4.00
1904 2767 6.512253 CGAGCTAAACATATCGTGTACTACCA 60.512 42.308 0.00 0.00 41.14 3.25
1998 4047 9.908152 GAGTAGTTTATTGCAGTGGTTAAAAAT 57.092 29.630 0.00 0.00 0.00 1.82
2067 4125 6.738114 TCAGGAAGAAAACATAAAAGCACAG 58.262 36.000 0.00 0.00 0.00 3.66
2129 4187 2.955660 TCAAAGGCAAGTGTTAACCAGG 59.044 45.455 2.48 0.00 0.00 4.45
2203 4261 7.136119 CGTTGCTTTCTAAAACTATTCCACAA 58.864 34.615 0.00 0.00 0.00 3.33
2412 4470 4.175337 CGATGTGATGGGCCGGGT 62.175 66.667 2.18 0.00 0.00 5.28
2503 4561 2.697431 TAAAGTTGGTTGCGTGCATC 57.303 45.000 0.00 0.00 0.00 3.91
2555 4627 3.008330 GCAGACACAAGAAGCATCTGAT 58.992 45.455 3.80 0.00 39.33 2.90
2566 4638 4.540824 GCTTTTTAGAAGGCAGACACAAG 58.459 43.478 0.00 0.00 37.75 3.16
2589 4661 5.321516 GCATGTACACCAAGAAATTACGAC 58.678 41.667 0.00 0.00 0.00 4.34
2591 4663 4.155099 TGGCATGTACACCAAGAAATTACG 59.845 41.667 0.00 0.00 31.46 3.18
2617 4690 1.660917 GGGAAGCGAGGATCTACCG 59.339 63.158 0.00 0.00 44.74 4.02
2634 4707 3.887621 TGTTGTATCTTTCTCCTCCGG 57.112 47.619 0.00 0.00 0.00 5.14
2636 4709 5.420409 ACGATTGTTGTATCTTTCTCCTCC 58.580 41.667 0.00 0.00 0.00 4.30
2679 4752 3.181495 TGCACCTTTTACACGGTTTTCTG 60.181 43.478 0.00 0.00 0.00 3.02
2688 4762 3.364565 CGTGTACCATGCACCTTTTACAC 60.365 47.826 12.55 12.55 37.18 2.90
2689 5345 2.809119 CGTGTACCATGCACCTTTTACA 59.191 45.455 0.00 0.00 33.61 2.41
2692 5348 2.264005 TCGTGTACCATGCACCTTTT 57.736 45.000 0.00 0.00 33.61 2.27


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

AutoCloner maintained by Alex Coulton.