Multiple sequence alignment - TraesCS2A01G309400

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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 TraesCS2A01G309400 chr2A 100.000 4622 0 0 1 4622 532848120 532852741 0.000000e+00 8536.0
1 TraesCS2A01G309400 chr2D 95.446 4150 144 18 490 4622 394780736 394784857 0.000000e+00 6575.0
2 TraesCS2A01G309400 chr2D 89.744 156 3 1 337 492 394780498 394780640 2.200000e-43 187.0
3 TraesCS2A01G309400 chr2D 80.992 121 19 4 630 748 453696126 453696244 4.920000e-15 93.5
4 TraesCS2A01G309400 chr2B 94.738 3820 171 13 820 4622 467785277 467789083 0.000000e+00 5914.0
5 TraesCS2A01G309400 chr2B 78.571 280 33 9 547 804 467781254 467781528 4.790000e-35 159.0
6 TraesCS2A01G309400 chr7D 95.588 340 15 0 1 340 461941965 461941626 3.140000e-151 545.0
7 TraesCS2A01G309400 chr7D 95.549 337 14 1 1 336 567924567 567924903 5.260000e-149 538.0
8 TraesCS2A01G309400 chr5D 95.833 336 14 0 1 336 423365897 423366232 1.130000e-150 544.0
9 TraesCS2A01G309400 chr5D 95.536 336 15 0 1 336 179940648 179940983 5.260000e-149 538.0
10 TraesCS2A01G309400 chr5D 81.522 92 14 3 558 646 111954767 111954858 6.410000e-09 73.1
11 TraesCS2A01G309400 chr4D 95.833 336 14 0 1 336 294426983 294427318 1.130000e-150 544.0
12 TraesCS2A01G309400 chr4D 95.808 334 14 0 1 334 294418029 294418362 1.460000e-149 540.0
13 TraesCS2A01G309400 chr4D 95.562 338 14 1 1 337 461002462 461002125 1.460000e-149 540.0
14 TraesCS2A01G309400 chr3D 95.536 336 15 0 1 336 508217568 508217903 5.260000e-149 538.0
15 TraesCS2A01G309400 chr1D 95.280 339 16 0 1 339 50284450 50284788 5.260000e-149 538.0
16 TraesCS2A01G309400 chr1D 88.000 50 5 1 560 608 233902713 233902762 1.800000e-04 58.4


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 TraesCS2A01G309400 chr2A 532848120 532852741 4621 False 8536.0 8536 100.0000 1 4622 1 chr2A.!!$F1 4621
1 TraesCS2A01G309400 chr2D 394780498 394784857 4359 False 3381.0 6575 92.5950 337 4622 2 chr2D.!!$F2 4285
2 TraesCS2A01G309400 chr2B 467781254 467789083 7829 False 3036.5 5914 86.6545 547 4622 2 chr2B.!!$F1 4075

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
875 4729 0.178978 GCCCCATCATTTCCTCCCTC 60.179 60.000 0.00 0.00 0.00 4.30 F
1164 5033 0.107017 ACAGGCAGTGCAGTGAACTT 60.107 50.000 25.76 9.74 0.00 2.66 F
1480 5349 1.133976 GGAACATCCTGATCACTGGGG 60.134 57.143 0.00 0.00 36.08 4.96 F
3430 7299 0.176680 CAAGGTCCATGGAGAGGTCG 59.823 60.000 16.81 0.00 0.00 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2115 5984 0.391263 CCCTAGAGTTGCACCCGTTC 60.391 60.0 0.00 0.0 0.0 3.95 R
3049 6918 0.613777 AGGTCTTTGTTAGGGCCGAG 59.386 55.0 0.00 0.0 0.0 4.63 R
3441 7310 0.319728 ACAAGTGATCAGCTGCGAGT 59.680 50.0 9.47 0.0 0.0 4.18 R
4564 8450 0.536006 GTGCCAGACAGCCAGAAAGT 60.536 55.0 0.00 0.0 0.0 2.66 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
63 64 8.525290 AAACTTAATGACCATTATGCTAAGCT 57.475 30.769 12.66 0.00 33.96 3.74
64 65 9.627123 AAACTTAATGACCATTATGCTAAGCTA 57.373 29.630 12.66 0.00 33.96 3.32
65 66 9.627123 AACTTAATGACCATTATGCTAAGCTAA 57.373 29.630 12.66 0.00 33.96 3.09
66 67 9.057089 ACTTAATGACCATTATGCTAAGCTAAC 57.943 33.333 12.66 0.00 33.96 2.34
67 68 6.545504 AATGACCATTATGCTAAGCTAACG 57.454 37.500 0.00 0.00 0.00 3.18
68 69 4.377021 TGACCATTATGCTAAGCTAACGG 58.623 43.478 0.00 0.00 0.00 4.44
69 70 4.100344 TGACCATTATGCTAAGCTAACGGA 59.900 41.667 0.00 0.00 0.00 4.69
70 71 5.221641 TGACCATTATGCTAAGCTAACGGAT 60.222 40.000 0.00 0.00 0.00 4.18
71 72 4.997395 ACCATTATGCTAAGCTAACGGATG 59.003 41.667 0.00 0.00 0.00 3.51
72 73 4.393062 CCATTATGCTAAGCTAACGGATGG 59.607 45.833 0.00 0.00 0.00 3.51
73 74 2.550830 ATGCTAAGCTAACGGATGGG 57.449 50.000 0.00 0.00 0.00 4.00
74 75 1.200519 TGCTAAGCTAACGGATGGGT 58.799 50.000 0.00 0.00 0.00 4.51
75 76 1.138266 TGCTAAGCTAACGGATGGGTC 59.862 52.381 0.00 0.00 0.00 4.46
76 77 1.413077 GCTAAGCTAACGGATGGGTCT 59.587 52.381 0.00 0.00 0.00 3.85
77 78 2.158943 GCTAAGCTAACGGATGGGTCTT 60.159 50.000 0.00 0.00 0.00 3.01
78 79 2.403252 AAGCTAACGGATGGGTCTTG 57.597 50.000 0.00 0.00 0.00 3.02
79 80 1.276622 AGCTAACGGATGGGTCTTGT 58.723 50.000 0.00 0.00 0.00 3.16
80 81 1.207329 AGCTAACGGATGGGTCTTGTC 59.793 52.381 0.00 0.00 0.00 3.18
81 82 1.742750 GCTAACGGATGGGTCTTGTCC 60.743 57.143 0.00 0.00 0.00 4.02
82 83 1.553248 CTAACGGATGGGTCTTGTCCA 59.447 52.381 0.00 0.00 38.82 4.02
83 84 0.991920 AACGGATGGGTCTTGTCCAT 59.008 50.000 0.00 0.00 46.73 3.41
89 90 2.787473 TGGGTCTTGTCCATCACATC 57.213 50.000 0.00 0.00 33.90 3.06
90 91 1.984424 TGGGTCTTGTCCATCACATCA 59.016 47.619 0.00 0.00 33.90 3.07
91 92 2.577563 TGGGTCTTGTCCATCACATCAT 59.422 45.455 0.00 0.00 33.90 2.45
92 93 3.010472 TGGGTCTTGTCCATCACATCATT 59.990 43.478 0.00 0.00 33.90 2.57
93 94 3.629398 GGGTCTTGTCCATCACATCATTC 59.371 47.826 0.00 0.00 33.90 2.67
94 95 4.521146 GGTCTTGTCCATCACATCATTCT 58.479 43.478 0.00 0.00 33.90 2.40
95 96 4.574013 GGTCTTGTCCATCACATCATTCTC 59.426 45.833 0.00 0.00 33.90 2.87
96 97 5.426504 GTCTTGTCCATCACATCATTCTCT 58.573 41.667 0.00 0.00 33.90 3.10
97 98 6.407412 GGTCTTGTCCATCACATCATTCTCTA 60.407 42.308 0.00 0.00 33.90 2.43
98 99 7.044181 GTCTTGTCCATCACATCATTCTCTAA 58.956 38.462 0.00 0.00 33.90 2.10
99 100 7.714377 GTCTTGTCCATCACATCATTCTCTAAT 59.286 37.037 0.00 0.00 33.90 1.73
100 101 7.713942 TCTTGTCCATCACATCATTCTCTAATG 59.286 37.037 0.00 0.00 43.32 1.90
112 113 7.757941 TCATTCTCTAATGATGAGATCTCGT 57.242 36.000 17.50 17.50 45.17 4.18
113 114 8.175925 TCATTCTCTAATGATGAGATCTCGTT 57.824 34.615 18.45 8.24 45.17 3.85
114 115 8.296000 TCATTCTCTAATGATGAGATCTCGTTC 58.704 37.037 18.45 16.62 45.17 3.95
115 116 7.573968 TTCTCTAATGATGAGATCTCGTTCA 57.426 36.000 22.98 22.98 39.87 3.18
116 117 7.757941 TCTCTAATGATGAGATCTCGTTCAT 57.242 36.000 24.65 24.65 36.94 2.57
117 118 7.815641 TCTCTAATGATGAGATCTCGTTCATC 58.184 38.462 27.83 21.18 46.26 2.92
124 125 6.841443 ATGAGATCTCGTTCATCAAATGAC 57.159 37.500 17.76 0.00 39.39 3.06
125 126 5.723295 TGAGATCTCGTTCATCAAATGACA 58.277 37.500 17.76 0.00 39.39 3.58
126 127 6.165577 TGAGATCTCGTTCATCAAATGACAA 58.834 36.000 17.76 0.00 39.39 3.18
127 128 6.091305 TGAGATCTCGTTCATCAAATGACAAC 59.909 38.462 17.76 0.00 39.39 3.32
128 129 5.934043 AGATCTCGTTCATCAAATGACAACA 59.066 36.000 0.00 0.00 39.39 3.33
129 130 5.342806 TCTCGTTCATCAAATGACAACAC 57.657 39.130 7.48 0.00 39.39 3.32
130 131 4.813697 TCTCGTTCATCAAATGACAACACA 59.186 37.500 7.48 0.00 39.39 3.72
131 132 5.469760 TCTCGTTCATCAAATGACAACACAT 59.530 36.000 7.48 0.00 39.39 3.21
132 133 5.451039 TCGTTCATCAAATGACAACACATG 58.549 37.500 0.00 0.00 39.39 3.21
149 150 9.507329 ACAACACATGTCTATGATTAGAAAACT 57.493 29.630 0.00 0.00 37.96 2.66
168 169 8.237267 AGAAAACTTAACCATCTTTGATTAGCG 58.763 33.333 0.00 0.00 0.00 4.26
169 170 7.681939 AAACTTAACCATCTTTGATTAGCGA 57.318 32.000 0.00 0.00 0.00 4.93
170 171 6.910536 ACTTAACCATCTTTGATTAGCGAG 57.089 37.500 0.00 0.00 0.00 5.03
171 172 6.407202 ACTTAACCATCTTTGATTAGCGAGT 58.593 36.000 0.00 0.00 0.00 4.18
172 173 6.879458 ACTTAACCATCTTTGATTAGCGAGTT 59.121 34.615 0.00 0.00 0.00 3.01
173 174 8.038944 ACTTAACCATCTTTGATTAGCGAGTTA 58.961 33.333 0.00 0.00 0.00 2.24
174 175 6.910536 AACCATCTTTGATTAGCGAGTTAG 57.089 37.500 0.00 0.00 0.00 2.34
175 176 5.978814 ACCATCTTTGATTAGCGAGTTAGT 58.021 37.500 0.00 0.00 0.00 2.24
176 177 6.043411 ACCATCTTTGATTAGCGAGTTAGTC 58.957 40.000 0.00 0.00 0.00 2.59
177 178 6.042777 CCATCTTTGATTAGCGAGTTAGTCA 58.957 40.000 0.00 0.00 0.00 3.41
178 179 6.535150 CCATCTTTGATTAGCGAGTTAGTCAA 59.465 38.462 1.95 1.95 30.41 3.18
179 180 7.254252 CCATCTTTGATTAGCGAGTTAGTCAAG 60.254 40.741 5.43 2.38 32.93 3.02
180 181 6.688578 TCTTTGATTAGCGAGTTAGTCAAGT 58.311 36.000 5.43 0.00 32.93 3.16
181 182 7.823665 TCTTTGATTAGCGAGTTAGTCAAGTA 58.176 34.615 5.43 0.00 32.93 2.24
182 183 7.968956 TCTTTGATTAGCGAGTTAGTCAAGTAG 59.031 37.037 5.43 2.95 32.93 2.57
183 184 6.997239 TGATTAGCGAGTTAGTCAAGTAGA 57.003 37.500 0.00 0.00 0.00 2.59
184 185 7.017498 TGATTAGCGAGTTAGTCAAGTAGAG 57.983 40.000 0.00 0.00 0.00 2.43
185 186 5.814764 TTAGCGAGTTAGTCAAGTAGAGG 57.185 43.478 0.00 0.00 0.00 3.69
186 187 2.424246 AGCGAGTTAGTCAAGTAGAGGC 59.576 50.000 0.00 0.00 0.00 4.70
187 188 2.163815 GCGAGTTAGTCAAGTAGAGGCA 59.836 50.000 0.00 0.00 0.00 4.75
188 189 3.181485 GCGAGTTAGTCAAGTAGAGGCAT 60.181 47.826 0.00 0.00 0.00 4.40
189 190 4.036498 GCGAGTTAGTCAAGTAGAGGCATA 59.964 45.833 0.00 0.00 0.00 3.14
190 191 5.512473 CGAGTTAGTCAAGTAGAGGCATAC 58.488 45.833 0.00 0.00 0.00 2.39
191 192 5.297278 CGAGTTAGTCAAGTAGAGGCATACT 59.703 44.000 0.00 0.00 37.61 2.12
192 193 6.482641 CGAGTTAGTCAAGTAGAGGCATACTA 59.517 42.308 3.23 0.00 34.90 1.82
193 194 7.307514 CGAGTTAGTCAAGTAGAGGCATACTAG 60.308 44.444 3.23 0.00 34.90 2.57
194 195 6.773685 AGTTAGTCAAGTAGAGGCATACTAGG 59.226 42.308 3.23 0.67 34.90 3.02
195 196 4.475345 AGTCAAGTAGAGGCATACTAGGG 58.525 47.826 3.23 0.00 34.90 3.53
196 197 4.168283 AGTCAAGTAGAGGCATACTAGGGA 59.832 45.833 3.23 0.66 34.90 4.20
197 198 4.278919 GTCAAGTAGAGGCATACTAGGGAC 59.721 50.000 3.23 7.70 34.90 4.46
198 199 4.079385 TCAAGTAGAGGCATACTAGGGACA 60.079 45.833 3.23 0.00 34.90 4.02
199 200 3.834938 AGTAGAGGCATACTAGGGACAC 58.165 50.000 0.00 0.00 34.21 3.67
200 201 3.464080 AGTAGAGGCATACTAGGGACACT 59.536 47.826 0.00 0.00 34.21 3.55
201 202 4.664064 AGTAGAGGCATACTAGGGACACTA 59.336 45.833 0.00 0.00 34.21 2.74
202 203 4.750833 AGAGGCATACTAGGGACACTAT 57.249 45.455 0.00 0.00 0.00 2.12
203 204 4.411927 AGAGGCATACTAGGGACACTATG 58.588 47.826 0.00 0.00 0.00 2.23
204 205 4.140900 AGAGGCATACTAGGGACACTATGT 60.141 45.833 0.00 0.00 0.00 2.29
205 206 4.557705 AGGCATACTAGGGACACTATGTT 58.442 43.478 0.00 0.00 0.00 2.71
206 207 4.969359 AGGCATACTAGGGACACTATGTTT 59.031 41.667 0.00 0.00 0.00 2.83
207 208 5.428783 AGGCATACTAGGGACACTATGTTTT 59.571 40.000 0.00 0.00 0.00 2.43
208 209 5.527582 GGCATACTAGGGACACTATGTTTTG 59.472 44.000 0.00 0.00 0.00 2.44
209 210 6.113411 GCATACTAGGGACACTATGTTTTGT 58.887 40.000 0.00 0.00 0.00 2.83
210 211 6.258068 GCATACTAGGGACACTATGTTTTGTC 59.742 42.308 0.00 0.00 41.28 3.18
211 212 7.556844 CATACTAGGGACACTATGTTTTGTCT 58.443 38.462 0.00 0.00 41.65 3.41
212 213 8.692710 CATACTAGGGACACTATGTTTTGTCTA 58.307 37.037 0.00 0.00 41.65 2.59
213 214 7.735326 ACTAGGGACACTATGTTTTGTCTAT 57.265 36.000 0.00 0.00 41.65 1.98
214 215 7.556844 ACTAGGGACACTATGTTTTGTCTATG 58.443 38.462 0.00 0.00 41.65 2.23
215 216 6.374417 AGGGACACTATGTTTTGTCTATGT 57.626 37.500 2.04 0.00 41.65 2.29
216 217 7.490657 AGGGACACTATGTTTTGTCTATGTA 57.509 36.000 2.04 0.00 41.65 2.29
217 218 8.090788 AGGGACACTATGTTTTGTCTATGTAT 57.909 34.615 2.04 0.00 41.65 2.29
218 219 8.548877 AGGGACACTATGTTTTGTCTATGTATT 58.451 33.333 2.04 0.00 41.65 1.89
219 220 8.612619 GGGACACTATGTTTTGTCTATGTATTG 58.387 37.037 2.04 0.00 41.65 1.90
220 221 9.378551 GGACACTATGTTTTGTCTATGTATTGA 57.621 33.333 2.04 0.00 41.65 2.57
222 223 9.719355 ACACTATGTTTTGTCTATGTATTGACA 57.281 29.630 5.28 5.28 39.95 3.58
223 224 9.973246 CACTATGTTTTGTCTATGTATTGACAC 57.027 33.333 8.32 0.41 41.04 3.67
224 225 9.719355 ACTATGTTTTGTCTATGTATTGACACA 57.281 29.630 8.32 5.15 41.04 3.72
227 228 8.389779 TGTTTTGTCTATGTATTGACACATGT 57.610 30.769 8.32 0.00 41.04 3.21
228 229 9.495572 TGTTTTGTCTATGTATTGACACATGTA 57.504 29.630 0.00 0.00 41.04 2.29
239 240 8.661257 TGTATTGACACATGTATTAAGTTTCCG 58.339 33.333 0.00 0.00 0.00 4.30
240 241 6.489127 TTGACACATGTATTAAGTTTCCGG 57.511 37.500 0.00 0.00 0.00 5.14
241 242 5.553123 TGACACATGTATTAAGTTTCCGGT 58.447 37.500 0.00 0.00 0.00 5.28
242 243 5.998981 TGACACATGTATTAAGTTTCCGGTT 59.001 36.000 0.00 0.00 0.00 4.44
243 244 7.160049 TGACACATGTATTAAGTTTCCGGTTA 58.840 34.615 0.00 0.00 0.00 2.85
244 245 7.660617 TGACACATGTATTAAGTTTCCGGTTAA 59.339 33.333 0.00 0.00 0.00 2.01
245 246 8.570068 ACACATGTATTAAGTTTCCGGTTAAT 57.430 30.769 0.00 7.17 34.13 1.40
246 247 9.669887 ACACATGTATTAAGTTTCCGGTTAATA 57.330 29.630 0.00 6.13 32.39 0.98
247 248 9.925268 CACATGTATTAAGTTTCCGGTTAATAC 57.075 33.333 24.77 24.77 44.86 1.89
257 258 8.851541 AGTTTCCGGTTAATACAATTCTAACA 57.148 30.769 0.00 0.00 0.00 2.41
258 259 9.457436 AGTTTCCGGTTAATACAATTCTAACAT 57.543 29.630 0.00 0.00 0.00 2.71
259 260 9.498307 GTTTCCGGTTAATACAATTCTAACATG 57.502 33.333 0.00 0.00 0.00 3.21
260 261 9.451002 TTTCCGGTTAATACAATTCTAACATGA 57.549 29.630 0.00 0.00 0.00 3.07
261 262 9.451002 TTCCGGTTAATACAATTCTAACATGAA 57.549 29.630 0.00 0.00 0.00 2.57
262 263 9.621629 TCCGGTTAATACAATTCTAACATGAAT 57.378 29.630 0.00 0.00 38.19 2.57
323 324 8.637196 AATAACTTTATTATTGCCTCTAGGGC 57.363 34.615 13.60 13.60 44.71 5.19
335 336 4.982241 CCTCTAGGGCATATTTCCTTCA 57.018 45.455 0.00 0.00 34.75 3.02
343 344 9.793259 CTAGGGCATATTTCCTTCAAAACTATA 57.207 33.333 0.00 0.00 34.75 1.31
445 446 8.841444 ATTTGAATAGTTAAATGATCACGTGC 57.159 30.769 11.67 0.00 0.00 5.34
446 447 6.976636 TGAATAGTTAAATGATCACGTGCA 57.023 33.333 11.67 4.24 0.00 4.57
447 448 6.771076 TGAATAGTTAAATGATCACGTGCAC 58.229 36.000 11.67 6.82 0.00 4.57
448 449 3.722555 AGTTAAATGATCACGTGCACG 57.277 42.857 35.99 35.99 46.33 5.34
463 464 1.912110 TGCACGTGTTTGCGTAAAAAC 59.088 42.857 18.38 9.06 46.20 2.43
473 474 0.940519 GCGTAAAAACGGGGGTTTGC 60.941 55.000 0.00 0.00 0.00 3.68
492 493 6.239036 GGTTTGCAAATGGAGAGAAAGTAAGT 60.239 38.462 16.21 0.00 0.00 2.24
493 494 6.959639 TTGCAAATGGAGAGAAAGTAAGTT 57.040 33.333 0.00 0.00 0.00 2.66
494 495 6.959639 TGCAAATGGAGAGAAAGTAAGTTT 57.040 33.333 0.00 0.00 0.00 2.66
495 496 8.458573 TTGCAAATGGAGAGAAAGTAAGTTTA 57.541 30.769 0.00 0.00 0.00 2.01
496 497 7.871853 TGCAAATGGAGAGAAAGTAAGTTTAC 58.128 34.615 0.00 0.00 0.00 2.01
497 498 7.015877 GCAAATGGAGAGAAAGTAAGTTTACG 58.984 38.462 0.00 0.00 38.65 3.18
498 499 7.307811 GCAAATGGAGAGAAAGTAAGTTTACGT 60.308 37.037 0.00 0.00 38.65 3.57
499 500 7.653767 AATGGAGAGAAAGTAAGTTTACGTG 57.346 36.000 0.00 0.00 38.65 4.49
500 501 6.152932 TGGAGAGAAAGTAAGTTTACGTGT 57.847 37.500 0.00 0.00 38.65 4.49
517 616 4.542735 ACGTGTAATTTTTGTAGCTTGCC 58.457 39.130 0.00 0.00 0.00 4.52
539 638 3.068024 CCGGGATTATTTTGACCACCATG 59.932 47.826 0.00 0.00 0.00 3.66
669 769 5.700402 AGTAAGCATACCAAATCCTGACT 57.300 39.130 0.00 0.00 32.08 3.41
808 925 3.436577 TTGGGTCAAAATAGCCCGTTA 57.563 42.857 0.00 0.00 45.19 3.18
809 926 3.655615 TGGGTCAAAATAGCCCGTTAT 57.344 42.857 0.00 0.00 45.19 1.89
875 4729 0.178978 GCCCCATCATTTCCTCCCTC 60.179 60.000 0.00 0.00 0.00 4.30
876 4730 1.527457 CCCCATCATTTCCTCCCTCT 58.473 55.000 0.00 0.00 0.00 3.69
880 4734 3.294214 CCATCATTTCCTCCCTCTTTGG 58.706 50.000 0.00 0.00 0.00 3.28
1161 5030 4.146058 CACAGGCAGTGCAGTGAA 57.854 55.556 26.66 0.00 42.15 3.18
1164 5033 0.107017 ACAGGCAGTGCAGTGAACTT 60.107 50.000 25.76 9.74 0.00 2.66
1171 5040 1.765314 AGTGCAGTGAACTTCTCAGGT 59.235 47.619 0.00 0.00 33.60 4.00
1445 5314 1.551883 GTTTGATGAAATGGGCTGCCT 59.448 47.619 19.68 0.00 0.00 4.75
1480 5349 1.133976 GGAACATCCTGATCACTGGGG 60.134 57.143 0.00 0.00 36.08 4.96
1603 5472 2.747446 GTCATTCCGGTATGTGCAAAGT 59.253 45.455 19.20 0.00 0.00 2.66
1884 5753 6.192360 GGAATGTCTTCCGAATTATTCAACG 58.808 40.000 5.76 0.00 41.60 4.10
1929 5798 2.695666 CTCGTTCATGGAGTATGGGAGT 59.304 50.000 0.00 0.00 37.39 3.85
1947 5816 5.222048 TGGGAGTAACTATGGCAAAGAAGTT 60.222 40.000 11.09 11.09 36.26 2.66
2007 5876 6.705825 ACATATCTGTTTGTAATGCGCTGATA 59.294 34.615 9.73 0.00 28.70 2.15
2115 5984 7.654568 ACACAATAATTGCTGGATATGTGATG 58.345 34.615 14.13 0.00 0.00 3.07
2281 6150 9.216117 GTTATATTTATCGGCATCCAGTACTTT 57.784 33.333 0.00 0.00 0.00 2.66
2293 6162 4.448210 TCCAGTACTTTGTCAGGAAACAC 58.552 43.478 0.00 0.00 0.00 3.32
2547 6416 1.267121 TCTGTGGTGCTAAGAGGGTC 58.733 55.000 0.00 0.00 0.00 4.46
2566 6435 2.832129 GTCCGGGAAGCTCATGGATATA 59.168 50.000 0.00 0.00 0.00 0.86
2679 6548 1.468914 CTTTTCAGAAACCTAGCCGGC 59.531 52.381 21.89 21.89 35.61 6.13
2844 6713 6.374565 AATATGTCTGATCAAGCTTTCTGC 57.625 37.500 0.00 0.00 43.29 4.26
3049 6918 5.065988 ACCAATGCATACAACCTATTTCGAC 59.934 40.000 0.00 0.00 0.00 4.20
3052 6921 4.109766 TGCATACAACCTATTTCGACTCG 58.890 43.478 0.00 0.00 0.00 4.18
3248 7117 4.202141 TGCAGGAATCAAGGTTTTCAAGTG 60.202 41.667 0.00 0.00 0.00 3.16
3319 7188 1.896660 GTTGACCTTCTTGCCCGCA 60.897 57.895 0.00 0.00 0.00 5.69
3391 7260 2.464782 TGGCCAATGCAAATGTATGGA 58.535 42.857 0.61 0.00 40.13 3.41
3430 7299 0.176680 CAAGGTCCATGGAGAGGTCG 59.823 60.000 16.81 0.00 0.00 4.79
3635 7504 2.295909 GCCAGTGATGTTAAGCACCAAA 59.704 45.455 0.00 0.00 43.96 3.28
3728 7597 7.186804 AGAACATTCAGTTACAAGTTTCAACG 58.813 34.615 0.00 0.00 41.51 4.10
3818 7688 1.419012 TGCTAGCTCTTCCCATCCATG 59.581 52.381 17.23 0.00 0.00 3.66
3878 7756 4.709397 CCTAAGCCCATTACATTTTGGTCA 59.291 41.667 0.00 0.00 0.00 4.02
3940 7818 2.248248 ACCAGACATGTCCGAGAAAGA 58.752 47.619 22.21 0.00 0.00 2.52
3950 7828 4.868067 TGTCCGAGAAAGAGTTACTTGAC 58.132 43.478 0.00 0.00 38.98 3.18
4100 7979 3.377172 ACAAATAAGTAACATGGCTCCGC 59.623 43.478 0.00 0.00 0.00 5.54
4206 8085 1.202891 AGTACCAACCAAGGTTCAGCC 60.203 52.381 0.51 0.00 43.08 4.85
4230 8110 6.350361 CCACATCTCATTTTGTTCATGCCTTA 60.350 38.462 0.00 0.00 0.00 2.69
4263 8143 6.974622 ACAATGTTGTTTGTTTCTGACATCTC 59.025 34.615 0.00 0.00 38.47 2.75
4333 8214 6.183360 GGGTGCCTGCTGATTAATTTTATCTT 60.183 38.462 0.00 0.00 0.00 2.40
4362 8243 7.433680 AGGGAAACTTATTGTGTGTTTTGATC 58.566 34.615 0.00 0.00 34.55 2.92
4392 8273 4.252878 TGACTTGCAAGATCGCATTCTTA 58.747 39.130 32.50 0.76 42.62 2.10
4393 8274 4.877823 TGACTTGCAAGATCGCATTCTTAT 59.122 37.500 32.50 5.21 42.62 1.73
4394 8275 5.355071 TGACTTGCAAGATCGCATTCTTATT 59.645 36.000 32.50 4.73 42.62 1.40
4395 8276 5.814783 ACTTGCAAGATCGCATTCTTATTC 58.185 37.500 32.50 0.00 42.62 1.75
4416 8301 3.141398 CGTTCATATGGGCTGCTGTAAT 58.859 45.455 2.13 0.00 0.00 1.89
4418 8303 4.136796 GTTCATATGGGCTGCTGTAATCA 58.863 43.478 2.13 0.00 0.00 2.57
4421 8306 6.317663 TCATATGGGCTGCTGTAATCATAT 57.682 37.500 2.13 2.36 0.00 1.78
4430 8315 7.995488 GGGCTGCTGTAATCATATCCTTAATAT 59.005 37.037 0.00 0.00 0.00 1.28
4431 8316 9.050601 GGCTGCTGTAATCATATCCTTAATATC 57.949 37.037 0.00 0.00 0.00 1.63
4564 8450 7.337938 TCTTCATAAAGTTGTATCAGCATGGA 58.662 34.615 0.00 0.00 33.11 3.41
4584 8470 1.572085 CTTTCTGGCTGTCTGGCACG 61.572 60.000 1.56 0.16 46.76 5.34
4616 8502 4.768130 TTAGAACAAGAGTCCGAGACTG 57.232 45.455 10.72 1.89 43.53 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 8.971073 AGCTTAGCATAATGGTCATTAAGTTTT 58.029 29.630 7.07 0.00 36.90 2.43
38 39 8.525290 AGCTTAGCATAATGGTCATTAAGTTT 57.475 30.769 7.07 0.92 36.90 2.66
39 40 9.627123 TTAGCTTAGCATAATGGTCATTAAGTT 57.373 29.630 7.07 4.53 36.90 2.66
40 41 9.057089 GTTAGCTTAGCATAATGGTCATTAAGT 57.943 33.333 7.07 0.00 36.90 2.24
41 42 8.223769 CGTTAGCTTAGCATAATGGTCATTAAG 58.776 37.037 7.07 4.88 36.90 1.85
42 43 7.172532 CCGTTAGCTTAGCATAATGGTCATTAA 59.827 37.037 18.17 0.44 36.90 1.40
43 44 6.649141 CCGTTAGCTTAGCATAATGGTCATTA 59.351 38.462 18.17 5.95 37.64 1.90
44 45 5.470098 CCGTTAGCTTAGCATAATGGTCATT 59.530 40.000 18.17 1.65 34.61 2.57
45 46 4.997395 CCGTTAGCTTAGCATAATGGTCAT 59.003 41.667 18.17 0.00 34.61 3.06
46 47 4.100344 TCCGTTAGCTTAGCATAATGGTCA 59.900 41.667 22.02 10.54 38.61 4.02
47 48 4.628074 TCCGTTAGCTTAGCATAATGGTC 58.372 43.478 22.02 4.44 38.61 4.02
48 49 4.682778 TCCGTTAGCTTAGCATAATGGT 57.317 40.909 22.02 0.00 38.61 3.55
49 50 4.393062 CCATCCGTTAGCTTAGCATAATGG 59.607 45.833 19.37 19.37 38.77 3.16
50 51 4.393062 CCCATCCGTTAGCTTAGCATAATG 59.607 45.833 7.07 7.64 0.00 1.90
51 52 4.041691 ACCCATCCGTTAGCTTAGCATAAT 59.958 41.667 7.07 0.00 0.00 1.28
52 53 3.389983 ACCCATCCGTTAGCTTAGCATAA 59.610 43.478 7.07 0.00 0.00 1.90
53 54 2.969950 ACCCATCCGTTAGCTTAGCATA 59.030 45.455 7.07 0.00 0.00 3.14
54 55 1.768870 ACCCATCCGTTAGCTTAGCAT 59.231 47.619 7.07 0.00 0.00 3.79
55 56 1.138266 GACCCATCCGTTAGCTTAGCA 59.862 52.381 7.07 0.00 0.00 3.49
56 57 1.413077 AGACCCATCCGTTAGCTTAGC 59.587 52.381 0.00 0.00 0.00 3.09
57 58 3.118738 ACAAGACCCATCCGTTAGCTTAG 60.119 47.826 0.00 0.00 0.00 2.18
58 59 2.835764 ACAAGACCCATCCGTTAGCTTA 59.164 45.455 0.00 0.00 0.00 3.09
59 60 1.628846 ACAAGACCCATCCGTTAGCTT 59.371 47.619 0.00 0.00 0.00 3.74
60 61 1.207329 GACAAGACCCATCCGTTAGCT 59.793 52.381 0.00 0.00 0.00 3.32
61 62 1.653151 GACAAGACCCATCCGTTAGC 58.347 55.000 0.00 0.00 0.00 3.09
62 63 1.553248 TGGACAAGACCCATCCGTTAG 59.447 52.381 0.00 0.00 35.06 2.34
63 64 1.646912 TGGACAAGACCCATCCGTTA 58.353 50.000 0.00 0.00 35.06 3.18
64 65 0.991920 ATGGACAAGACCCATCCGTT 59.008 50.000 0.00 0.00 40.16 4.44
65 66 2.696864 ATGGACAAGACCCATCCGT 58.303 52.632 0.00 0.00 40.16 4.69
69 70 2.577563 TGATGTGATGGACAAGACCCAT 59.422 45.455 0.00 0.00 46.40 4.00
70 71 1.984424 TGATGTGATGGACAAGACCCA 59.016 47.619 0.00 0.00 38.36 4.51
71 72 2.787473 TGATGTGATGGACAAGACCC 57.213 50.000 0.00 0.00 38.36 4.46
72 73 4.521146 AGAATGATGTGATGGACAAGACC 58.479 43.478 0.00 0.00 38.36 3.85
73 74 5.426504 AGAGAATGATGTGATGGACAAGAC 58.573 41.667 0.00 0.00 38.36 3.01
74 75 5.688814 AGAGAATGATGTGATGGACAAGA 57.311 39.130 0.00 0.00 38.36 3.02
75 76 7.713942 TCATTAGAGAATGATGTGATGGACAAG 59.286 37.037 0.00 0.00 45.26 3.16
76 77 7.567458 TCATTAGAGAATGATGTGATGGACAA 58.433 34.615 0.00 0.00 45.26 3.18
77 78 7.128234 TCATTAGAGAATGATGTGATGGACA 57.872 36.000 0.00 0.00 45.26 4.02
89 90 8.081025 TGAACGAGATCTCATCATTAGAGAATG 58.919 37.037 22.31 3.54 44.56 2.67
90 91 8.175925 TGAACGAGATCTCATCATTAGAGAAT 57.824 34.615 22.31 0.00 44.56 2.40
91 92 7.573968 TGAACGAGATCTCATCATTAGAGAA 57.426 36.000 22.31 0.00 44.56 2.87
92 93 7.757941 ATGAACGAGATCTCATCATTAGAGA 57.242 36.000 24.85 7.96 45.38 3.10
100 101 6.478016 TGTCATTTGATGAACGAGATCTCATC 59.522 38.462 22.31 18.43 45.44 2.92
101 102 6.343703 TGTCATTTGATGAACGAGATCTCAT 58.656 36.000 22.31 10.46 41.69 2.90
102 103 5.723295 TGTCATTTGATGAACGAGATCTCA 58.277 37.500 22.31 4.15 41.69 3.27
103 104 6.091305 TGTTGTCATTTGATGAACGAGATCTC 59.909 38.462 13.05 13.05 41.69 2.75
104 105 5.934043 TGTTGTCATTTGATGAACGAGATCT 59.066 36.000 0.00 0.00 41.69 2.75
105 106 6.017933 GTGTTGTCATTTGATGAACGAGATC 58.982 40.000 0.00 0.00 41.69 2.75
106 107 5.469760 TGTGTTGTCATTTGATGAACGAGAT 59.530 36.000 0.00 0.00 41.69 2.75
107 108 4.813697 TGTGTTGTCATTTGATGAACGAGA 59.186 37.500 0.00 0.00 41.69 4.04
108 109 5.094429 TGTGTTGTCATTTGATGAACGAG 57.906 39.130 0.00 0.00 41.69 4.18
109 110 5.008514 ACATGTGTTGTCATTTGATGAACGA 59.991 36.000 0.00 0.00 41.69 3.85
110 111 5.214417 ACATGTGTTGTCATTTGATGAACG 58.786 37.500 0.00 0.00 41.69 3.95
123 124 9.507329 AGTTTTCTAATCATAGACATGTGTTGT 57.493 29.630 1.15 0.00 42.79 3.32
142 143 8.237267 CGCTAATCAAAGATGGTTAAGTTTTCT 58.763 33.333 0.00 0.00 31.88 2.52
143 144 8.234546 TCGCTAATCAAAGATGGTTAAGTTTTC 58.765 33.333 0.00 0.00 31.88 2.29
144 145 8.106247 TCGCTAATCAAAGATGGTTAAGTTTT 57.894 30.769 0.00 0.00 31.88 2.43
145 146 7.390718 ACTCGCTAATCAAAGATGGTTAAGTTT 59.609 33.333 0.00 0.00 31.88 2.66
146 147 6.879458 ACTCGCTAATCAAAGATGGTTAAGTT 59.121 34.615 0.00 0.00 31.88 2.66
147 148 6.407202 ACTCGCTAATCAAAGATGGTTAAGT 58.593 36.000 0.00 0.00 31.88 2.24
148 149 6.910536 ACTCGCTAATCAAAGATGGTTAAG 57.089 37.500 0.00 0.00 31.88 1.85
149 150 8.038944 ACTAACTCGCTAATCAAAGATGGTTAA 58.961 33.333 0.00 0.00 31.88 2.01
150 151 7.553334 ACTAACTCGCTAATCAAAGATGGTTA 58.447 34.615 0.00 0.00 30.84 2.85
151 152 6.407202 ACTAACTCGCTAATCAAAGATGGTT 58.593 36.000 0.00 0.00 33.49 3.67
152 153 5.978814 ACTAACTCGCTAATCAAAGATGGT 58.021 37.500 0.00 0.00 0.00 3.55
153 154 6.042777 TGACTAACTCGCTAATCAAAGATGG 58.957 40.000 0.00 0.00 0.00 3.51
154 155 7.276658 ACTTGACTAACTCGCTAATCAAAGATG 59.723 37.037 0.00 0.00 0.00 2.90
155 156 7.324178 ACTTGACTAACTCGCTAATCAAAGAT 58.676 34.615 0.00 0.00 0.00 2.40
156 157 6.688578 ACTTGACTAACTCGCTAATCAAAGA 58.311 36.000 0.00 0.00 0.00 2.52
157 158 6.952935 ACTTGACTAACTCGCTAATCAAAG 57.047 37.500 0.00 0.00 0.00 2.77
158 159 7.823665 TCTACTTGACTAACTCGCTAATCAAA 58.176 34.615 0.00 0.00 0.00 2.69
159 160 7.387119 TCTACTTGACTAACTCGCTAATCAA 57.613 36.000 0.00 0.00 0.00 2.57
160 161 6.038382 CCTCTACTTGACTAACTCGCTAATCA 59.962 42.308 0.00 0.00 0.00 2.57
161 162 6.432107 CCTCTACTTGACTAACTCGCTAATC 58.568 44.000 0.00 0.00 0.00 1.75
162 163 5.221087 GCCTCTACTTGACTAACTCGCTAAT 60.221 44.000 0.00 0.00 0.00 1.73
163 164 4.096081 GCCTCTACTTGACTAACTCGCTAA 59.904 45.833 0.00 0.00 0.00 3.09
164 165 3.626670 GCCTCTACTTGACTAACTCGCTA 59.373 47.826 0.00 0.00 0.00 4.26
165 166 2.424246 GCCTCTACTTGACTAACTCGCT 59.576 50.000 0.00 0.00 0.00 4.93
166 167 2.163815 TGCCTCTACTTGACTAACTCGC 59.836 50.000 0.00 0.00 0.00 5.03
167 168 4.640789 ATGCCTCTACTTGACTAACTCG 57.359 45.455 0.00 0.00 0.00 4.18
168 169 6.702716 AGTATGCCTCTACTTGACTAACTC 57.297 41.667 0.00 0.00 0.00 3.01
169 170 6.773685 CCTAGTATGCCTCTACTTGACTAACT 59.226 42.308 0.00 0.00 33.96 2.24
170 171 6.016108 CCCTAGTATGCCTCTACTTGACTAAC 60.016 46.154 0.00 0.00 33.96 2.34
171 172 6.069331 CCCTAGTATGCCTCTACTTGACTAA 58.931 44.000 0.00 0.00 33.96 2.24
172 173 5.371769 TCCCTAGTATGCCTCTACTTGACTA 59.628 44.000 0.00 0.00 33.96 2.59
173 174 4.168283 TCCCTAGTATGCCTCTACTTGACT 59.832 45.833 0.00 0.00 33.96 3.41
174 175 4.278919 GTCCCTAGTATGCCTCTACTTGAC 59.721 50.000 0.00 0.00 33.96 3.18
175 176 4.079385 TGTCCCTAGTATGCCTCTACTTGA 60.079 45.833 0.00 0.00 33.96 3.02
176 177 4.038162 GTGTCCCTAGTATGCCTCTACTTG 59.962 50.000 0.00 0.00 33.96 3.16
177 178 4.079096 AGTGTCCCTAGTATGCCTCTACTT 60.079 45.833 0.00 0.00 33.96 2.24
178 179 3.464080 AGTGTCCCTAGTATGCCTCTACT 59.536 47.826 0.00 0.00 36.04 2.57
179 180 3.834938 AGTGTCCCTAGTATGCCTCTAC 58.165 50.000 0.00 0.00 0.00 2.59
180 181 5.074652 ACATAGTGTCCCTAGTATGCCTCTA 59.925 44.000 0.00 0.00 37.44 2.43
181 182 4.140900 ACATAGTGTCCCTAGTATGCCTCT 60.141 45.833 0.00 0.00 37.44 3.69
182 183 4.153411 ACATAGTGTCCCTAGTATGCCTC 58.847 47.826 0.00 0.00 37.44 4.70
183 184 4.200447 ACATAGTGTCCCTAGTATGCCT 57.800 45.455 0.00 0.00 37.44 4.75
184 185 4.957684 AACATAGTGTCCCTAGTATGCC 57.042 45.455 0.00 0.00 37.44 4.40
185 186 6.113411 ACAAAACATAGTGTCCCTAGTATGC 58.887 40.000 0.00 0.00 37.44 3.14
186 187 7.556844 AGACAAAACATAGTGTCCCTAGTATG 58.443 38.462 0.36 0.00 44.30 2.39
187 188 7.735326 AGACAAAACATAGTGTCCCTAGTAT 57.265 36.000 0.36 0.00 44.30 2.12
188 189 8.692710 CATAGACAAAACATAGTGTCCCTAGTA 58.307 37.037 0.36 0.00 44.30 1.82
189 190 7.180408 ACATAGACAAAACATAGTGTCCCTAGT 59.820 37.037 0.36 0.00 44.30 2.57
190 191 7.556844 ACATAGACAAAACATAGTGTCCCTAG 58.443 38.462 0.36 0.00 44.30 3.02
191 192 7.490657 ACATAGACAAAACATAGTGTCCCTA 57.509 36.000 0.36 0.00 44.30 3.53
192 193 6.374417 ACATAGACAAAACATAGTGTCCCT 57.626 37.500 0.36 0.00 44.30 4.20
193 194 8.612619 CAATACATAGACAAAACATAGTGTCCC 58.387 37.037 0.36 0.00 44.30 4.46
194 195 9.378551 TCAATACATAGACAAAACATAGTGTCC 57.621 33.333 0.36 0.00 44.30 4.02
196 197 9.719355 TGTCAATACATAGACAAAACATAGTGT 57.281 29.630 0.00 0.00 41.42 3.55
197 198 9.973246 GTGTCAATACATAGACAAAACATAGTG 57.027 33.333 0.00 0.00 45.38 2.74
198 199 9.719355 TGTGTCAATACATAGACAAAACATAGT 57.281 29.630 0.00 0.00 45.38 2.12
201 202 9.013229 ACATGTGTCAATACATAGACAAAACAT 57.987 29.630 0.00 0.00 45.38 2.71
202 203 8.389779 ACATGTGTCAATACATAGACAAAACA 57.610 30.769 0.00 0.00 45.38 2.83
213 214 8.661257 CGGAAACTTAATACATGTGTCAATACA 58.339 33.333 9.11 0.00 34.63 2.29
214 215 8.120465 CCGGAAACTTAATACATGTGTCAATAC 58.880 37.037 9.11 0.00 0.00 1.89
215 216 7.825270 ACCGGAAACTTAATACATGTGTCAATA 59.175 33.333 9.46 0.00 0.00 1.90
216 217 6.657541 ACCGGAAACTTAATACATGTGTCAAT 59.342 34.615 9.46 0.00 0.00 2.57
217 218 5.998981 ACCGGAAACTTAATACATGTGTCAA 59.001 36.000 9.46 0.00 0.00 3.18
218 219 5.553123 ACCGGAAACTTAATACATGTGTCA 58.447 37.500 9.46 0.00 0.00 3.58
219 220 6.490566 AACCGGAAACTTAATACATGTGTC 57.509 37.500 9.46 0.00 0.00 3.67
220 221 7.982761 TTAACCGGAAACTTAATACATGTGT 57.017 32.000 9.46 0.00 0.00 3.72
221 222 9.925268 GTATTAACCGGAAACTTAATACATGTG 57.075 33.333 25.71 0.00 40.33 3.21
222 223 9.669887 TGTATTAACCGGAAACTTAATACATGT 57.330 29.630 27.66 2.69 42.66 3.21
231 232 9.287373 TGTTAGAATTGTATTAACCGGAAACTT 57.713 29.630 9.46 0.00 0.00 2.66
232 233 8.851541 TGTTAGAATTGTATTAACCGGAAACT 57.148 30.769 9.46 0.00 0.00 2.66
233 234 9.498307 CATGTTAGAATTGTATTAACCGGAAAC 57.502 33.333 9.46 0.00 0.00 2.78
234 235 9.451002 TCATGTTAGAATTGTATTAACCGGAAA 57.549 29.630 9.46 1.61 0.00 3.13
235 236 9.451002 TTCATGTTAGAATTGTATTAACCGGAA 57.549 29.630 9.46 0.00 0.00 4.30
236 237 9.621629 ATTCATGTTAGAATTGTATTAACCGGA 57.378 29.630 9.46 0.00 34.70 5.14
314 315 4.982241 TGAAGGAAATATGCCCTAGAGG 57.018 45.455 0.00 0.00 39.47 3.69
315 316 6.830838 AGTTTTGAAGGAAATATGCCCTAGAG 59.169 38.462 0.00 0.00 31.36 2.43
316 317 6.731467 AGTTTTGAAGGAAATATGCCCTAGA 58.269 36.000 0.00 0.00 31.36 2.43
317 318 8.697507 ATAGTTTTGAAGGAAATATGCCCTAG 57.302 34.615 0.00 0.00 31.36 3.02
447 448 1.114047 CCCGTTTTTACGCAAACACG 58.886 50.000 11.84 11.84 43.87 4.49
448 449 1.479170 CCCCGTTTTTACGCAAACAC 58.521 50.000 6.35 0.00 36.58 3.32
449 450 0.384669 CCCCCGTTTTTACGCAAACA 59.615 50.000 6.35 0.00 36.58 2.83
450 451 0.385029 ACCCCCGTTTTTACGCAAAC 59.615 50.000 0.00 0.00 33.90 2.93
451 452 1.109609 AACCCCCGTTTTTACGCAAA 58.890 45.000 0.00 0.00 0.00 3.68
463 464 0.897863 TCTCCATTTGCAAACCCCCG 60.898 55.000 15.41 2.65 0.00 5.73
473 474 8.009974 CACGTAAACTTACTTTCTCTCCATTTG 58.990 37.037 0.00 0.00 0.00 2.32
492 493 6.637658 GGCAAGCTACAAAAATTACACGTAAA 59.362 34.615 0.00 0.00 0.00 2.01
493 494 6.144175 GGCAAGCTACAAAAATTACACGTAA 58.856 36.000 0.00 0.00 0.00 3.18
494 495 5.335035 GGGCAAGCTACAAAAATTACACGTA 60.335 40.000 0.00 0.00 0.00 3.57
495 496 4.542735 GGCAAGCTACAAAAATTACACGT 58.457 39.130 0.00 0.00 0.00 4.49
496 497 3.917985 GGGCAAGCTACAAAAATTACACG 59.082 43.478 0.00 0.00 0.00 4.49
497 498 3.917985 CGGGCAAGCTACAAAAATTACAC 59.082 43.478 0.00 0.00 0.00 2.90
498 499 3.057174 CCGGGCAAGCTACAAAAATTACA 60.057 43.478 0.00 0.00 0.00 2.41
499 500 3.507786 CCGGGCAAGCTACAAAAATTAC 58.492 45.455 0.00 0.00 0.00 1.89
500 501 2.494073 CCCGGGCAAGCTACAAAAATTA 59.506 45.455 8.08 0.00 0.00 1.40
517 616 2.729194 TGGTGGTCAAAATAATCCCGG 58.271 47.619 0.00 0.00 0.00 5.73
539 638 6.613755 AACATTACAGTAATTACCGCATCC 57.386 37.500 12.05 0.00 0.00 3.51
808 925 3.118702 GGAGCATCTCCGATCATCATCAT 60.119 47.826 0.00 0.00 41.08 2.45
809 926 2.233186 GGAGCATCTCCGATCATCATCA 59.767 50.000 0.00 0.00 41.08 3.07
850 4703 0.536006 GGAAATGATGGGGCCGAGAG 60.536 60.000 0.00 0.00 0.00 3.20
929 4783 1.183676 AGGCCTTGAAAGCTTGCTGG 61.184 55.000 0.00 9.15 0.00 4.85
1089 4952 1.375523 GTCGCCGGTGTGGAAGAAT 60.376 57.895 16.01 0.00 42.00 2.40
1161 5030 2.049063 GTGCGCGACCTGAGAAGT 60.049 61.111 12.10 0.00 0.00 3.01
1445 5314 1.149987 GTTCCAACATACCGCGTCAA 58.850 50.000 4.92 0.00 0.00 3.18
1603 5472 2.569853 TCCCAGCCGTTAAATCTCTCAA 59.430 45.455 0.00 0.00 0.00 3.02
1884 5753 7.616313 AGCATACAGGAAGAATATTAGCTACC 58.384 38.462 0.00 0.00 0.00 3.18
1929 5798 6.245408 ACCATGAACTTCTTTGCCATAGTTA 58.755 36.000 0.00 0.00 31.41 2.24
2007 5876 5.630121 TCACACACCTTGGAATAATGAGTT 58.370 37.500 0.00 0.00 0.00 3.01
2085 5954 7.288389 ACATATCCAGCAATTATTGTGTTCCAT 59.712 33.333 6.81 0.00 0.00 3.41
2115 5984 0.391263 CCCTAGAGTTGCACCCGTTC 60.391 60.000 0.00 0.00 0.00 3.95
2281 6150 4.715534 TCATTAAGGGTGTTTCCTGACA 57.284 40.909 0.00 0.00 37.20 3.58
2505 6374 6.483640 AGAAGGTACTCATGCGGATAAAATTC 59.516 38.462 0.00 0.00 38.49 2.17
2547 6416 2.093447 GGTATATCCATGAGCTTCCCGG 60.093 54.545 0.00 0.00 35.97 5.73
2566 6435 3.945285 CCAATATAACCAACTCGCAAGGT 59.055 43.478 0.00 0.00 37.20 3.50
2679 6548 1.529226 TGCCTGTTACAATGTTCCGG 58.471 50.000 0.00 0.00 0.00 5.14
2844 6713 2.620115 ACACTGCAACTGATGAAACAGG 59.380 45.455 0.00 0.00 41.59 4.00
3049 6918 0.613777 AGGTCTTTGTTAGGGCCGAG 59.386 55.000 0.00 0.00 0.00 4.63
3074 6943 3.008375 GCCTCCTATCATGGCAGTGAATA 59.992 47.826 0.00 0.00 45.46 1.75
3248 7117 3.983741 ACTCTGTAAATATCTCTGGCGC 58.016 45.455 0.00 0.00 0.00 6.53
3319 7188 4.070552 GTCTTGGAGACGCCCGCT 62.071 66.667 0.00 0.00 35.28 5.52
3430 7299 2.435938 TGCGAGTTGGCCGATTCC 60.436 61.111 9.81 3.88 0.00 3.01
3441 7310 0.319728 ACAAGTGATCAGCTGCGAGT 59.680 50.000 9.47 0.00 0.00 4.18
3493 7362 5.941733 TGCATAGATGTTTGACACAATGAC 58.058 37.500 0.00 0.00 39.50 3.06
3635 7504 9.886132 AACCATGTCGTAGATAAAAGAACTATT 57.114 29.630 0.00 0.00 40.67 1.73
3728 7597 4.455533 TGTGACCAGATCAATTGCACTAAC 59.544 41.667 0.00 1.33 39.72 2.34
3818 7688 8.677148 TTGCATACCTCAGAAAGATAAATACC 57.323 34.615 0.00 0.00 0.00 2.73
3908 7786 1.812235 TGTCTGGTAGCATGCTGTTG 58.188 50.000 30.42 16.38 0.00 3.33
3940 7818 6.449635 TGCACAAAATTCAGTCAAGTAACT 57.550 33.333 0.00 0.00 0.00 2.24
3950 7828 5.005586 ACAAACGTGAATGCACAAAATTCAG 59.994 36.000 4.29 0.00 42.98 3.02
4100 7979 1.226575 CAAGATGCATGCTGTGGCG 60.227 57.895 20.33 0.00 42.25 5.69
4206 8085 5.068234 AGGCATGAACAAAATGAGATGTG 57.932 39.130 0.00 0.00 0.00 3.21
4333 8214 5.304686 ACACACAATAAGTTTCCCTCTGA 57.695 39.130 0.00 0.00 0.00 3.27
4382 8263 5.408299 CCCATATGAACGAATAAGAATGCGA 59.592 40.000 3.65 0.00 36.08 5.10
4392 8273 2.224606 CAGCAGCCCATATGAACGAAT 58.775 47.619 3.65 0.00 0.00 3.34
4393 8274 1.065491 ACAGCAGCCCATATGAACGAA 60.065 47.619 3.65 0.00 0.00 3.85
4394 8275 0.541392 ACAGCAGCCCATATGAACGA 59.459 50.000 3.65 0.00 0.00 3.85
4395 8276 2.238942 TACAGCAGCCCATATGAACG 57.761 50.000 3.65 0.00 0.00 3.95
4421 8306 8.594550 GCAGGATTTAGGTACAGATATTAAGGA 58.405 37.037 0.00 0.00 0.00 3.36
4430 8315 6.524734 CATACATGCAGGATTTAGGTACAGA 58.475 40.000 4.84 0.00 0.00 3.41
4431 8316 6.791887 CATACATGCAGGATTTAGGTACAG 57.208 41.667 4.84 0.00 0.00 2.74
4564 8450 0.536006 GTGCCAGACAGCCAGAAAGT 60.536 55.000 0.00 0.00 0.00 2.66
4582 8468 3.746045 TGTTCTAAAGGCAAGAGTCGT 57.254 42.857 0.00 0.00 0.00 4.34
4596 8482 4.017177 TCAGTCTCGGACTCTTGTTCTA 57.983 45.455 3.87 0.00 41.37 2.10


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

AutoCloner maintained by Alex Coulton.