Multiple sequence alignment - TraesCS4B01G111000

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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 TraesCS4B01G111000 chr4B 100.000 3492 0 0 1 3492 124564621 124561130 0.000000e+00 6449.0
1 TraesCS4B01G111000 chr4B 96.014 276 10 1 1 275 625103140 625103415 6.880000e-122 448.0
2 TraesCS4B01G111000 chr4B 94.286 280 14 2 1 278 523933307 523933028 8.960000e-116 427.0
3 TraesCS4B01G111000 chr4D 94.057 3214 140 21 316 3492 87965464 87962265 0.000000e+00 4830.0
4 TraesCS4B01G111000 chr4A 93.340 3213 155 23 316 3492 500660735 500657546 0.000000e+00 4693.0
5 TraesCS4B01G111000 chr2B 96.739 276 8 1 1 275 572584098 572583823 3.180000e-125 459.0
6 TraesCS4B01G111000 chr2B 96.014 276 8 3 1 275 459766754 459767027 2.470000e-121 446.0
7 TraesCS4B01G111000 chr6B 96.377 276 9 1 1 275 121014454 121014179 1.480000e-123 453.0
8 TraesCS4B01G111000 chr6B 94.928 276 13 1 1 275 3648562 3648287 6.920000e-117 431.0
9 TraesCS4B01G111000 chr5B 96.029 277 10 1 1 276 622698194 622698470 1.910000e-122 449.0
10 TraesCS4B01G111000 chr1B 95.652 276 11 1 1 275 489572650 489572925 3.200000e-120 442.0
11 TraesCS4B01G111000 chr3B 95.290 276 11 2 1 275 505734534 505734260 1.490000e-118 436.0
12 TraesCS4B01G111000 chr7A 100.000 30 0 0 2270 2299 722953184 722953213 4.870000e-04 56.5
13 TraesCS4B01G111000 chr7A 100.000 30 0 0 2270 2299 723043871 723043900 4.870000e-04 56.5


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 TraesCS4B01G111000 chr4B 124561130 124564621 3491 True 6449 6449 100.000 1 3492 1 chr4B.!!$R1 3491
1 TraesCS4B01G111000 chr4D 87962265 87965464 3199 True 4830 4830 94.057 316 3492 1 chr4D.!!$R1 3176
2 TraesCS4B01G111000 chr4A 500657546 500660735 3189 True 4693 4693 93.340 316 3492 1 chr4A.!!$R1 3176

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
304 305 0.035343 ACGTCTCCATCTCTCCACGA 60.035 55.0 0.0 0.0 0.00 4.35 F
308 309 0.103937 CTCCATCTCTCCACGAAGGC 59.896 60.0 0.0 0.0 37.29 4.35 F
1333 1354 0.107703 GGCTCCGGACAATGACATCA 60.108 55.0 0.0 0.0 0.00 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1269 1284 0.040958 CATTGCGGCCGCTATTCTTC 60.041 55.0 45.79 19.46 42.51 2.87 R
2152 2176 0.700564 TCAAGCTGAAGGCCCTGAAT 59.299 50.0 0.00 0.00 43.05 2.57 R
2766 2814 0.039256 GAAGCTGGCGCATGAAACAA 60.039 50.0 10.83 0.00 39.10 2.83 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 9.238368 CAATTAAAGGTCTTAATTAGTGGTCCA 57.762 33.333 2.95 0.00 34.04 4.02
27 28 9.990868 AATTAAAGGTCTTAATTAGTGGTCCAT 57.009 29.630 0.00 0.00 34.04 3.41
28 29 8.801882 TTAAAGGTCTTAATTAGTGGTCCATG 57.198 34.615 0.00 0.00 0.00 3.66
29 30 5.373812 AGGTCTTAATTAGTGGTCCATGG 57.626 43.478 4.97 4.97 0.00 3.66
30 31 4.166144 AGGTCTTAATTAGTGGTCCATGGG 59.834 45.833 13.02 0.00 0.00 4.00
31 32 3.883489 GTCTTAATTAGTGGTCCATGGGC 59.117 47.826 13.02 10.72 0.00 5.36
32 33 3.785887 TCTTAATTAGTGGTCCATGGGCT 59.214 43.478 17.62 9.92 0.00 5.19
33 34 4.972568 TCTTAATTAGTGGTCCATGGGCTA 59.027 41.667 17.62 7.50 0.00 3.93
34 35 3.864789 AATTAGTGGTCCATGGGCTAG 57.135 47.619 17.62 0.00 0.00 3.42
35 36 2.263895 TTAGTGGTCCATGGGCTAGT 57.736 50.000 17.62 16.24 0.00 2.57
36 37 2.263895 TAGTGGTCCATGGGCTAGTT 57.736 50.000 15.94 3.61 0.00 2.24
37 38 2.263895 AGTGGTCCATGGGCTAGTTA 57.736 50.000 17.62 0.00 0.00 2.24
38 39 2.557869 AGTGGTCCATGGGCTAGTTAA 58.442 47.619 17.62 0.00 0.00 2.01
39 40 2.505819 AGTGGTCCATGGGCTAGTTAAG 59.494 50.000 17.62 0.00 0.00 1.85
40 41 2.504175 GTGGTCCATGGGCTAGTTAAGA 59.496 50.000 17.62 0.00 0.00 2.10
41 42 3.054655 GTGGTCCATGGGCTAGTTAAGAA 60.055 47.826 17.62 0.00 0.00 2.52
42 43 3.054655 TGGTCCATGGGCTAGTTAAGAAC 60.055 47.826 17.62 0.00 0.00 3.01
43 44 3.200165 GGTCCATGGGCTAGTTAAGAACT 59.800 47.826 17.62 0.00 45.40 3.01
44 45 4.324331 GGTCCATGGGCTAGTTAAGAACTT 60.324 45.833 17.62 0.00 42.81 2.66
45 46 5.104652 GGTCCATGGGCTAGTTAAGAACTTA 60.105 44.000 17.62 0.00 42.81 2.24
46 47 6.412214 GTCCATGGGCTAGTTAAGAACTTAA 58.588 40.000 9.76 3.31 42.81 1.85
47 48 6.539103 GTCCATGGGCTAGTTAAGAACTTAAG 59.461 42.308 9.76 0.00 42.81 1.85
48 49 6.442564 TCCATGGGCTAGTTAAGAACTTAAGA 59.557 38.462 13.02 0.00 42.81 2.10
49 50 7.127339 TCCATGGGCTAGTTAAGAACTTAAGAT 59.873 37.037 13.02 0.00 42.81 2.40
50 51 8.429641 CCATGGGCTAGTTAAGAACTTAAGATA 58.570 37.037 10.09 4.06 42.81 1.98
51 52 9.832445 CATGGGCTAGTTAAGAACTTAAGATAA 57.168 33.333 10.09 0.65 42.81 1.75
111 112 7.616528 ATTTATTTTCTGGGTATCCATTGGG 57.383 36.000 0.00 0.00 43.11 4.12
112 113 4.625225 ATTTTCTGGGTATCCATTGGGT 57.375 40.909 0.00 0.00 43.11 4.51
113 114 4.412060 TTTTCTGGGTATCCATTGGGTT 57.588 40.909 0.00 0.00 43.11 4.11
114 115 5.538082 TTTTCTGGGTATCCATTGGGTTA 57.462 39.130 0.00 0.00 43.11 2.85
115 116 4.513406 TTCTGGGTATCCATTGGGTTAC 57.487 45.455 0.00 5.63 43.11 2.50
134 135 8.344446 GGGTTACCCATGGTATAATTTCATAC 57.656 38.462 16.81 0.00 44.65 2.39
135 136 7.395206 GGGTTACCCATGGTATAATTTCATACC 59.605 40.741 16.81 9.62 45.19 2.73
136 137 7.395206 GGTTACCCATGGTATAATTTCATACCC 59.605 40.741 11.73 0.98 46.81 3.69
137 138 6.538209 ACCCATGGTATAATTTCATACCCA 57.462 37.500 11.73 4.38 46.81 4.51
138 139 7.114849 ACCCATGGTATAATTTCATACCCAT 57.885 36.000 11.73 6.01 46.81 4.00
139 140 8.238365 ACCCATGGTATAATTTCATACCCATA 57.762 34.615 11.73 0.00 46.81 2.74
140 141 8.113462 ACCCATGGTATAATTTCATACCCATAC 58.887 37.037 11.73 0.05 46.81 2.39
141 142 7.559897 CCCATGGTATAATTTCATACCCATACC 59.440 40.741 11.73 8.33 46.81 2.73
142 143 8.336235 CCATGGTATAATTTCATACCCATACCT 58.664 37.037 12.82 0.00 46.81 3.08
143 144 9.753674 CATGGTATAATTTCATACCCATACCTT 57.246 33.333 12.82 4.42 46.81 3.50
146 147 9.676861 GGTATAATTTCATACCCATACCTTACC 57.323 37.037 6.23 0.00 43.19 2.85
147 148 9.676861 GTATAATTTCATACCCATACCTTACCC 57.323 37.037 0.00 0.00 0.00 3.69
148 149 6.599986 AATTTCATACCCATACCTTACCCA 57.400 37.500 0.00 0.00 0.00 4.51
149 150 6.796867 ATTTCATACCCATACCTTACCCAT 57.203 37.500 0.00 0.00 0.00 4.00
150 151 5.576563 TTCATACCCATACCTTACCCATG 57.423 43.478 0.00 0.00 0.00 3.66
151 152 3.329520 TCATACCCATACCTTACCCATGC 59.670 47.826 0.00 0.00 0.00 4.06
152 153 1.602440 ACCCATACCTTACCCATGCA 58.398 50.000 0.00 0.00 0.00 3.96
153 154 2.143602 ACCCATACCTTACCCATGCAT 58.856 47.619 0.00 0.00 0.00 3.96
154 155 2.517980 ACCCATACCTTACCCATGCATT 59.482 45.455 0.00 0.00 0.00 3.56
155 156 3.052186 ACCCATACCTTACCCATGCATTT 60.052 43.478 0.00 0.00 0.00 2.32
156 157 3.966665 CCCATACCTTACCCATGCATTTT 59.033 43.478 0.00 0.00 0.00 1.82
157 158 4.202243 CCCATACCTTACCCATGCATTTTG 60.202 45.833 0.00 0.00 0.00 2.44
158 159 4.405358 CCATACCTTACCCATGCATTTTGT 59.595 41.667 0.00 0.00 0.00 2.83
159 160 3.959535 ACCTTACCCATGCATTTTGTG 57.040 42.857 0.00 0.00 0.00 3.33
160 161 2.566724 ACCTTACCCATGCATTTTGTGG 59.433 45.455 0.00 0.00 0.00 4.17
165 166 3.182341 CCCATGCATTTTGTGGGTATG 57.818 47.619 13.36 0.00 46.07 2.39
166 167 2.158928 CCCATGCATTTTGTGGGTATGG 60.159 50.000 13.36 1.11 46.07 2.74
167 168 2.765135 CCATGCATTTTGTGGGTATGGA 59.235 45.455 0.00 0.00 36.56 3.41
168 169 3.388676 CCATGCATTTTGTGGGTATGGAT 59.611 43.478 0.00 0.00 36.56 3.41
169 170 4.588106 CCATGCATTTTGTGGGTATGGATA 59.412 41.667 0.00 0.00 36.56 2.59
170 171 5.509501 CCATGCATTTTGTGGGTATGGATAC 60.510 44.000 0.00 0.00 36.56 2.24
196 197 3.943671 CCCATGGGTATGAAGTGGTAA 57.056 47.619 23.93 0.00 36.36 2.85
197 198 4.243793 CCCATGGGTATGAAGTGGTAAA 57.756 45.455 23.93 0.00 36.36 2.01
198 199 4.605183 CCCATGGGTATGAAGTGGTAAAA 58.395 43.478 23.93 0.00 36.36 1.52
199 200 5.020132 CCCATGGGTATGAAGTGGTAAAAA 58.980 41.667 23.93 0.00 36.36 1.94
200 201 5.127031 CCCATGGGTATGAAGTGGTAAAAAG 59.873 44.000 23.93 0.00 36.36 2.27
201 202 5.714806 CCATGGGTATGAAGTGGTAAAAAGT 59.285 40.000 2.85 0.00 36.36 2.66
202 203 6.127730 CCATGGGTATGAAGTGGTAAAAAGTC 60.128 42.308 2.85 0.00 36.36 3.01
203 204 6.195600 TGGGTATGAAGTGGTAAAAAGTCT 57.804 37.500 0.00 0.00 0.00 3.24
204 205 6.235664 TGGGTATGAAGTGGTAAAAAGTCTC 58.764 40.000 0.00 0.00 0.00 3.36
205 206 6.183361 TGGGTATGAAGTGGTAAAAAGTCTCA 60.183 38.462 0.00 0.00 0.00 3.27
206 207 6.884836 GGGTATGAAGTGGTAAAAAGTCTCAT 59.115 38.462 0.00 0.00 0.00 2.90
207 208 7.065923 GGGTATGAAGTGGTAAAAAGTCTCATC 59.934 40.741 0.00 0.00 0.00 2.92
208 209 7.065923 GGTATGAAGTGGTAAAAAGTCTCATCC 59.934 40.741 0.00 0.00 0.00 3.51
209 210 5.935945 TGAAGTGGTAAAAAGTCTCATCCA 58.064 37.500 0.00 0.00 0.00 3.41
210 211 6.542821 TGAAGTGGTAAAAAGTCTCATCCAT 58.457 36.000 0.00 0.00 0.00 3.41
211 212 7.685481 TGAAGTGGTAAAAAGTCTCATCCATA 58.315 34.615 0.00 0.00 0.00 2.74
212 213 7.606456 TGAAGTGGTAAAAAGTCTCATCCATAC 59.394 37.037 0.00 0.00 0.00 2.39
213 214 6.415573 AGTGGTAAAAAGTCTCATCCATACC 58.584 40.000 0.00 0.00 33.73 2.73
214 215 5.589050 GTGGTAAAAAGTCTCATCCATACCC 59.411 44.000 0.00 0.00 32.46 3.69
215 216 5.251932 TGGTAAAAAGTCTCATCCATACCCA 59.748 40.000 0.00 0.00 32.46 4.51
216 217 5.823045 GGTAAAAAGTCTCATCCATACCCAG 59.177 44.000 0.00 0.00 0.00 4.45
217 218 5.520748 AAAAAGTCTCATCCATACCCAGT 57.479 39.130 0.00 0.00 0.00 4.00
218 219 6.636454 AAAAAGTCTCATCCATACCCAGTA 57.364 37.500 0.00 0.00 0.00 2.74
219 220 6.831664 AAAAGTCTCATCCATACCCAGTAT 57.168 37.500 0.00 0.00 0.00 2.12
220 221 6.831664 AAAGTCTCATCCATACCCAGTATT 57.168 37.500 0.00 0.00 0.00 1.89
221 222 6.831664 AAGTCTCATCCATACCCAGTATTT 57.168 37.500 0.00 0.00 0.00 1.40
222 223 6.831664 AGTCTCATCCATACCCAGTATTTT 57.168 37.500 0.00 0.00 0.00 1.82
223 224 6.831976 AGTCTCATCCATACCCAGTATTTTC 58.168 40.000 0.00 0.00 0.00 2.29
224 225 5.696724 GTCTCATCCATACCCAGTATTTTCG 59.303 44.000 0.00 0.00 0.00 3.46
225 226 4.968259 TCATCCATACCCAGTATTTTCGG 58.032 43.478 0.00 0.00 0.00 4.30
226 227 3.849563 TCCATACCCAGTATTTTCGGG 57.150 47.619 0.00 0.00 46.22 5.14
231 232 2.632987 CCCAGTATTTTCGGGTAGGG 57.367 55.000 0.00 0.00 35.03 3.53
232 233 1.841919 CCCAGTATTTTCGGGTAGGGT 59.158 52.381 0.00 0.00 35.03 4.34
233 234 3.040477 CCCAGTATTTTCGGGTAGGGTA 58.960 50.000 0.00 0.00 35.03 3.69
234 235 3.181462 CCCAGTATTTTCGGGTAGGGTAC 60.181 52.174 0.00 0.00 35.03 3.34
265 266 2.965572 CATACCCATGGGCAAAACTG 57.034 50.000 31.73 14.56 39.32 3.16
266 267 1.134729 CATACCCATGGGCAAAACTGC 60.135 52.381 31.73 0.00 39.32 4.40
276 277 1.839424 GCAAAACTGCCATCCCTACT 58.161 50.000 0.00 0.00 0.00 2.57
277 278 1.745653 GCAAAACTGCCATCCCTACTC 59.254 52.381 0.00 0.00 0.00 2.59
278 279 2.009774 CAAAACTGCCATCCCTACTCG 58.990 52.381 0.00 0.00 0.00 4.18
279 280 0.107654 AAACTGCCATCCCTACTCGC 60.108 55.000 0.00 0.00 0.00 5.03
280 281 0.978146 AACTGCCATCCCTACTCGCT 60.978 55.000 0.00 0.00 0.00 4.93
281 282 1.068753 CTGCCATCCCTACTCGCTG 59.931 63.158 0.00 0.00 0.00 5.18
282 283 2.280457 GCCATCCCTACTCGCTGC 60.280 66.667 0.00 0.00 0.00 5.25
283 284 2.801631 GCCATCCCTACTCGCTGCT 61.802 63.158 0.00 0.00 0.00 4.24
284 285 1.365633 CCATCCCTACTCGCTGCTC 59.634 63.158 0.00 0.00 0.00 4.26
285 286 1.395045 CCATCCCTACTCGCTGCTCA 61.395 60.000 0.00 0.00 0.00 4.26
286 287 0.249238 CATCCCTACTCGCTGCTCAC 60.249 60.000 0.00 0.00 0.00 3.51
287 288 1.729470 ATCCCTACTCGCTGCTCACG 61.729 60.000 0.00 0.00 0.00 4.35
288 289 2.701780 CCCTACTCGCTGCTCACGT 61.702 63.158 0.00 0.00 0.00 4.49
289 290 1.226435 CCTACTCGCTGCTCACGTC 60.226 63.158 0.00 0.00 0.00 4.34
290 291 1.649390 CCTACTCGCTGCTCACGTCT 61.649 60.000 0.00 0.00 0.00 4.18
291 292 0.247894 CTACTCGCTGCTCACGTCTC 60.248 60.000 0.00 0.00 0.00 3.36
292 293 1.645704 TACTCGCTGCTCACGTCTCC 61.646 60.000 0.00 0.00 0.00 3.71
293 294 2.982744 CTCGCTGCTCACGTCTCCA 61.983 63.158 0.00 0.00 0.00 3.86
294 295 2.182791 CGCTGCTCACGTCTCCAT 59.817 61.111 0.00 0.00 0.00 3.41
295 296 1.875813 CGCTGCTCACGTCTCCATC 60.876 63.158 0.00 0.00 0.00 3.51
296 297 1.515020 GCTGCTCACGTCTCCATCT 59.485 57.895 0.00 0.00 0.00 2.90
297 298 0.527385 GCTGCTCACGTCTCCATCTC 60.527 60.000 0.00 0.00 0.00 2.75
298 299 1.102154 CTGCTCACGTCTCCATCTCT 58.898 55.000 0.00 0.00 0.00 3.10
299 300 1.065401 CTGCTCACGTCTCCATCTCTC 59.935 57.143 0.00 0.00 0.00 3.20
300 301 0.383949 GCTCACGTCTCCATCTCTCC 59.616 60.000 0.00 0.00 0.00 3.71
301 302 1.756430 CTCACGTCTCCATCTCTCCA 58.244 55.000 0.00 0.00 0.00 3.86
302 303 1.403679 CTCACGTCTCCATCTCTCCAC 59.596 57.143 0.00 0.00 0.00 4.02
303 304 0.099613 CACGTCTCCATCTCTCCACG 59.900 60.000 0.00 0.00 0.00 4.94
304 305 0.035343 ACGTCTCCATCTCTCCACGA 60.035 55.000 0.00 0.00 0.00 4.35
305 306 1.095600 CGTCTCCATCTCTCCACGAA 58.904 55.000 0.00 0.00 0.00 3.85
306 307 1.064803 CGTCTCCATCTCTCCACGAAG 59.935 57.143 0.00 0.00 0.00 3.79
307 308 1.407258 GTCTCCATCTCTCCACGAAGG 59.593 57.143 0.00 0.00 39.47 3.46
308 309 0.103937 CTCCATCTCTCCACGAAGGC 59.896 60.000 0.00 0.00 37.29 4.35
309 310 0.614697 TCCATCTCTCCACGAAGGCA 60.615 55.000 0.00 0.00 37.29 4.75
310 311 0.467384 CCATCTCTCCACGAAGGCAT 59.533 55.000 0.00 0.00 37.29 4.40
311 312 1.688735 CCATCTCTCCACGAAGGCATA 59.311 52.381 0.00 0.00 37.29 3.14
312 313 2.288702 CCATCTCTCCACGAAGGCATAG 60.289 54.545 0.00 0.00 37.29 2.23
313 314 0.747255 TCTCTCCACGAAGGCATAGC 59.253 55.000 0.00 0.00 37.29 2.97
314 315 0.596083 CTCTCCACGAAGGCATAGCG 60.596 60.000 0.00 0.00 37.29 4.26
340 341 1.455822 AAAGGGGGACATTCTGACCA 58.544 50.000 0.00 0.00 33.85 4.02
380 381 2.472414 TAACGGCACACCATCACCCC 62.472 60.000 0.00 0.00 34.57 4.95
382 383 2.665089 CGGCACACCATCACCCCTA 61.665 63.158 0.00 0.00 34.57 3.53
386 387 0.830648 CACACCATCACCCCTATCGT 59.169 55.000 0.00 0.00 0.00 3.73
408 409 1.865788 CGTGAGGGGTTTGCCATGTG 61.866 60.000 0.00 0.00 36.17 3.21
416 417 0.310543 GTTTGCCATGTGAGAACGCA 59.689 50.000 0.00 0.00 40.86 5.24
419 422 0.950555 TGCCATGTGAGAACGCACTC 60.951 55.000 9.68 3.02 39.38 3.51
424 427 3.058016 CCATGTGAGAACGCACTCAAAAT 60.058 43.478 12.51 7.91 46.34 1.82
435 438 8.730680 AGAACGCACTCAAAATAATACTCAATT 58.269 29.630 0.00 0.00 0.00 2.32
436 439 9.341899 GAACGCACTCAAAATAATACTCAATTT 57.658 29.630 0.00 0.00 0.00 1.82
466 469 3.270027 CCATAGTCAATTCTTCCGTGCA 58.730 45.455 0.00 0.00 0.00 4.57
474 477 5.000591 TCAATTCTTCCGTGCAGTGATTTA 58.999 37.500 0.00 0.00 0.00 1.40
513 516 2.642311 TGGTGGTTTCCTGCTAATGAGA 59.358 45.455 0.00 0.00 0.00 3.27
530 533 2.205074 GAGACCGCTATTGTGATGGTG 58.795 52.381 0.00 0.00 31.86 4.17
633 636 2.241176 TCCCTCTGGTTTATTCGCCATT 59.759 45.455 0.00 0.00 33.84 3.16
664 667 1.301716 CACGAACACACAGAGGGGG 60.302 63.158 0.00 0.00 0.00 5.40
909 917 0.663153 GCAAAGCTTCAGACACCGTT 59.337 50.000 0.00 0.00 0.00 4.44
971 986 4.164413 AGGTTTAAGATAGGTCTGCCTTCC 59.836 45.833 0.00 0.00 44.18 3.46
1009 1024 1.616091 CCCAACCCCAATGGATGCAC 61.616 60.000 0.00 0.00 40.56 4.57
1081 1096 4.263506 GGAAATCAGGTTCTTCCTTCTGGA 60.264 45.833 0.00 0.00 45.67 3.86
1157 1172 1.893786 GCAGGAGCGAGAGGAAGAA 59.106 57.895 0.00 0.00 0.00 2.52
1264 1279 2.359107 TGCTGAGCAGGGAAAGCG 60.359 61.111 1.40 0.00 38.53 4.68
1265 1280 2.046892 GCTGAGCAGGGAAAGCGA 60.047 61.111 0.00 0.00 37.01 4.93
1266 1281 2.105466 GCTGAGCAGGGAAAGCGAG 61.105 63.158 0.00 0.00 37.01 5.03
1267 1282 1.593787 CTGAGCAGGGAAAGCGAGA 59.406 57.895 0.00 0.00 37.01 4.04
1269 1284 1.153469 GAGCAGGGAAAGCGAGAGG 60.153 63.158 0.00 0.00 37.01 3.69
1270 1285 1.608717 GAGCAGGGAAAGCGAGAGGA 61.609 60.000 0.00 0.00 37.01 3.71
1271 1286 1.194781 AGCAGGGAAAGCGAGAGGAA 61.195 55.000 0.00 0.00 37.01 3.36
1333 1354 0.107703 GGCTCCGGACAATGACATCA 60.108 55.000 0.00 0.00 0.00 3.07
1449 1470 3.767230 TCGTCGTCGTCGTCGTCC 61.767 66.667 18.44 3.60 45.27 4.79
1464 1485 4.779966 TCCGCTCTCTCGTCGCCT 62.780 66.667 0.00 0.00 0.00 5.52
1617 1638 1.456165 GAGTTCTTCGTCAAAGCCGAC 59.544 52.381 0.00 0.00 34.76 4.79
1656 1677 1.075836 AACCCGCCATGCAGGTAAA 59.924 52.632 0.00 0.00 38.51 2.01
1735 1756 8.085909 TGTAAATCCATTGATGCATGAATGATC 58.914 33.333 32.35 18.06 33.97 2.92
1810 1831 3.288484 CAGTCCAGCTGGCTCGTA 58.712 61.111 28.91 7.54 41.42 3.43
1900 1921 1.751924 GTGGAGAGGTTCGAGCAGTAT 59.248 52.381 0.53 0.00 0.00 2.12
2149 2173 7.642669 CAAATGTTCAGAGTTCAGAGCTAAAA 58.357 34.615 0.00 0.00 0.00 1.52
2150 2174 7.807977 AATGTTCAGAGTTCAGAGCTAAAAA 57.192 32.000 0.00 0.00 0.00 1.94
2175 2199 0.251077 AGGGCCTTCAGCTTGACAAG 60.251 55.000 11.02 11.02 43.05 3.16
2260 2284 1.661509 TGCTCACGACAAGACGCAG 60.662 57.895 0.00 0.00 36.70 5.18
2375 2408 4.382470 GCAGCAATTCTTCAGAGGAGTCTA 60.382 45.833 0.00 0.00 0.00 2.59
2378 2411 4.358851 CAATTCTTCAGAGGAGTCTAGCG 58.641 47.826 0.00 0.00 0.00 4.26
2395 2428 2.365068 CGGTGACAGCGTCAGTTCG 61.365 63.158 18.54 11.10 43.57 3.95
2633 2676 5.473066 AATCCTTTCAAGTCATGTTTGGG 57.527 39.130 11.09 6.54 0.00 4.12
2636 2679 4.340950 TCCTTTCAAGTCATGTTTGGGAAC 59.659 41.667 11.09 0.00 36.29 3.62
2766 2814 2.381911 CCATGCAATAGGCTCCAAACT 58.618 47.619 0.00 0.00 45.15 2.66
2770 2818 3.230134 TGCAATAGGCTCCAAACTTGTT 58.770 40.909 0.00 0.00 45.15 2.83
2771 2819 3.640967 TGCAATAGGCTCCAAACTTGTTT 59.359 39.130 0.00 0.00 45.15 2.83
2806 2854 8.055181 AGCTTCCAAGATCTACCAAAATCAATA 58.945 33.333 0.00 0.00 0.00 1.90
2815 2863 9.970395 GATCTACCAAAATCAATATCAATGCAA 57.030 29.630 0.00 0.00 0.00 4.08
2852 2900 0.461548 CTGGGCAGATCAGACGCTTA 59.538 55.000 0.00 0.00 34.36 3.09
2901 2949 1.781025 CGCGGAACAGCCAGACAAAA 61.781 55.000 0.00 0.00 35.94 2.44
2971 3024 9.039870 CCACTGATTACTCAATCTCTTGTAATC 57.960 37.037 14.21 14.21 45.31 1.75
2987 3040 3.648067 TGTAATCCCCCTTGAGATGCTAG 59.352 47.826 0.00 0.00 0.00 3.42
3344 3402 4.655963 TGGCACAGCTTAGAAAGAAGATT 58.344 39.130 0.00 0.00 0.00 2.40
3372 3430 6.096141 TGTCCTCAAGTTGCTTGTTTTATTGA 59.904 34.615 8.48 0.00 41.66 2.57
3401 3459 4.537135 TTCTTCAGGCTACGTTCTTCAT 57.463 40.909 0.00 0.00 0.00 2.57
3405 3463 3.011818 TCAGGCTACGTTCTTCATACGA 58.988 45.455 0.00 0.00 41.33 3.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.238368 TGGACCACTAATTAAGACCTTTAATTG 57.762 33.333 12.67 7.31 35.89 2.32
1 2 9.990868 ATGGACCACTAATTAAGACCTTTAATT 57.009 29.630 0.00 9.16 37.99 1.40
2 3 9.408648 CATGGACCACTAATTAAGACCTTTAAT 57.591 33.333 0.00 0.00 0.00 1.40
3 4 7.832187 CCATGGACCACTAATTAAGACCTTTAA 59.168 37.037 5.56 0.00 0.00 1.52
4 5 7.343357 CCATGGACCACTAATTAAGACCTTTA 58.657 38.462 5.56 0.00 0.00 1.85
5 6 6.187682 CCATGGACCACTAATTAAGACCTTT 58.812 40.000 5.56 0.00 0.00 3.11
6 7 5.340027 CCCATGGACCACTAATTAAGACCTT 60.340 44.000 15.22 0.00 0.00 3.50
7 8 4.166144 CCCATGGACCACTAATTAAGACCT 59.834 45.833 15.22 0.00 0.00 3.85
8 9 4.461198 CCCATGGACCACTAATTAAGACC 58.539 47.826 15.22 0.00 0.00 3.85
9 10 3.883489 GCCCATGGACCACTAATTAAGAC 59.117 47.826 15.22 0.00 0.00 3.01
10 11 3.785887 AGCCCATGGACCACTAATTAAGA 59.214 43.478 15.22 0.00 0.00 2.10
11 12 4.170468 AGCCCATGGACCACTAATTAAG 57.830 45.455 15.22 0.00 0.00 1.85
12 13 4.724798 ACTAGCCCATGGACCACTAATTAA 59.275 41.667 15.22 0.00 0.00 1.40
13 14 4.303794 ACTAGCCCATGGACCACTAATTA 58.696 43.478 15.22 0.00 0.00 1.40
14 15 3.123273 ACTAGCCCATGGACCACTAATT 58.877 45.455 15.22 0.00 0.00 1.40
15 16 2.776665 ACTAGCCCATGGACCACTAAT 58.223 47.619 15.22 0.00 0.00 1.73
16 17 2.263895 ACTAGCCCATGGACCACTAA 57.736 50.000 15.22 0.00 0.00 2.24
17 18 2.263895 AACTAGCCCATGGACCACTA 57.736 50.000 15.22 8.32 0.00 2.74
18 19 2.263895 TAACTAGCCCATGGACCACT 57.736 50.000 15.22 7.54 0.00 4.00
19 20 2.504175 TCTTAACTAGCCCATGGACCAC 59.496 50.000 15.22 0.00 0.00 4.16
20 21 2.840511 TCTTAACTAGCCCATGGACCA 58.159 47.619 15.22 0.00 0.00 4.02
21 22 3.200165 AGTTCTTAACTAGCCCATGGACC 59.800 47.826 15.22 3.49 40.69 4.46
22 23 4.489306 AGTTCTTAACTAGCCCATGGAC 57.511 45.455 15.22 0.00 40.69 4.02
23 24 6.442564 TCTTAAGTTCTTAACTAGCCCATGGA 59.557 38.462 15.22 0.00 41.91 3.41
24 25 6.650120 TCTTAAGTTCTTAACTAGCCCATGG 58.350 40.000 4.14 4.14 41.91 3.66
25 26 9.832445 TTATCTTAAGTTCTTAACTAGCCCATG 57.168 33.333 1.63 0.00 41.91 3.66
121 122 9.676861 GGGTAAGGTATGGGTATGAAATTATAC 57.323 37.037 0.00 0.00 33.71 1.47
122 123 9.407957 TGGGTAAGGTATGGGTATGAAATTATA 57.592 33.333 0.00 0.00 0.00 0.98
123 124 8.295597 TGGGTAAGGTATGGGTATGAAATTAT 57.704 34.615 0.00 0.00 0.00 1.28
124 125 7.709024 TGGGTAAGGTATGGGTATGAAATTA 57.291 36.000 0.00 0.00 0.00 1.40
125 126 6.599986 TGGGTAAGGTATGGGTATGAAATT 57.400 37.500 0.00 0.00 0.00 1.82
126 127 6.552008 CATGGGTAAGGTATGGGTATGAAAT 58.448 40.000 0.00 0.00 0.00 2.17
127 128 5.691704 GCATGGGTAAGGTATGGGTATGAAA 60.692 44.000 0.00 0.00 0.00 2.69
128 129 4.202524 GCATGGGTAAGGTATGGGTATGAA 60.203 45.833 0.00 0.00 0.00 2.57
129 130 3.329520 GCATGGGTAAGGTATGGGTATGA 59.670 47.826 0.00 0.00 0.00 2.15
130 131 3.073798 TGCATGGGTAAGGTATGGGTATG 59.926 47.826 0.00 0.00 0.00 2.39
131 132 3.332044 TGCATGGGTAAGGTATGGGTAT 58.668 45.455 0.00 0.00 0.00 2.73
132 133 2.777913 TGCATGGGTAAGGTATGGGTA 58.222 47.619 0.00 0.00 0.00 3.69
133 134 1.602440 TGCATGGGTAAGGTATGGGT 58.398 50.000 0.00 0.00 0.00 4.51
134 135 2.978156 ATGCATGGGTAAGGTATGGG 57.022 50.000 0.00 0.00 0.00 4.00
135 136 4.405358 ACAAAATGCATGGGTAAGGTATGG 59.595 41.667 0.00 0.00 0.00 2.74
136 137 5.350633 CACAAAATGCATGGGTAAGGTATG 58.649 41.667 0.00 0.00 0.00 2.39
137 138 4.405358 CCACAAAATGCATGGGTAAGGTAT 59.595 41.667 0.00 0.00 0.00 2.73
138 139 3.766591 CCACAAAATGCATGGGTAAGGTA 59.233 43.478 0.00 0.00 0.00 3.08
139 140 2.566724 CCACAAAATGCATGGGTAAGGT 59.433 45.455 0.00 0.00 0.00 3.50
140 141 2.093553 CCCACAAAATGCATGGGTAAGG 60.094 50.000 13.36 5.88 46.99 2.69
141 142 3.249986 CCCACAAAATGCATGGGTAAG 57.750 47.619 13.36 2.20 46.99 2.34
146 147 2.765135 TCCATACCCACAAAATGCATGG 59.235 45.455 0.00 0.00 34.36 3.66
147 148 4.675976 ATCCATACCCACAAAATGCATG 57.324 40.909 0.00 0.00 0.00 4.06
148 149 4.588528 GGTATCCATACCCACAAAATGCAT 59.411 41.667 4.57 0.00 45.62 3.96
149 150 3.957497 GGTATCCATACCCACAAAATGCA 59.043 43.478 4.57 0.00 45.62 3.96
150 151 4.584327 GGTATCCATACCCACAAAATGC 57.416 45.455 4.57 0.00 45.62 3.56
176 177 3.943671 TTACCACTTCATACCCATGGG 57.056 47.619 30.23 30.23 42.03 4.00
177 178 5.714806 ACTTTTTACCACTTCATACCCATGG 59.285 40.000 4.14 4.14 36.46 3.66
178 179 6.659242 AGACTTTTTACCACTTCATACCCATG 59.341 38.462 0.00 0.00 0.00 3.66
179 180 6.790319 AGACTTTTTACCACTTCATACCCAT 58.210 36.000 0.00 0.00 0.00 4.00
180 181 6.183361 TGAGACTTTTTACCACTTCATACCCA 60.183 38.462 0.00 0.00 0.00 4.51
181 182 6.235664 TGAGACTTTTTACCACTTCATACCC 58.764 40.000 0.00 0.00 0.00 3.69
182 183 7.065923 GGATGAGACTTTTTACCACTTCATACC 59.934 40.741 0.00 0.00 0.00 2.73
183 184 7.606456 TGGATGAGACTTTTTACCACTTCATAC 59.394 37.037 0.00 0.00 0.00 2.39
184 185 7.685481 TGGATGAGACTTTTTACCACTTCATA 58.315 34.615 0.00 0.00 0.00 2.15
185 186 6.542821 TGGATGAGACTTTTTACCACTTCAT 58.457 36.000 0.00 0.00 0.00 2.57
186 187 5.935945 TGGATGAGACTTTTTACCACTTCA 58.064 37.500 0.00 0.00 0.00 3.02
187 188 7.065923 GGTATGGATGAGACTTTTTACCACTTC 59.934 40.741 0.00 0.00 0.00 3.01
188 189 6.884836 GGTATGGATGAGACTTTTTACCACTT 59.115 38.462 0.00 0.00 0.00 3.16
189 190 6.415573 GGTATGGATGAGACTTTTTACCACT 58.584 40.000 0.00 0.00 0.00 4.00
190 191 5.589050 GGGTATGGATGAGACTTTTTACCAC 59.411 44.000 0.00 0.00 31.53 4.16
191 192 5.251932 TGGGTATGGATGAGACTTTTTACCA 59.748 40.000 0.00 0.00 31.53 3.25
192 193 5.751586 TGGGTATGGATGAGACTTTTTACC 58.248 41.667 0.00 0.00 0.00 2.85
193 194 6.415573 ACTGGGTATGGATGAGACTTTTTAC 58.584 40.000 0.00 0.00 0.00 2.01
194 195 6.636454 ACTGGGTATGGATGAGACTTTTTA 57.364 37.500 0.00 0.00 0.00 1.52
195 196 5.520748 ACTGGGTATGGATGAGACTTTTT 57.479 39.130 0.00 0.00 0.00 1.94
196 197 6.831664 ATACTGGGTATGGATGAGACTTTT 57.168 37.500 0.00 0.00 0.00 2.27
197 198 6.831664 AATACTGGGTATGGATGAGACTTT 57.168 37.500 0.00 0.00 0.00 2.66
198 199 6.831664 AAATACTGGGTATGGATGAGACTT 57.168 37.500 0.00 0.00 0.00 3.01
199 200 6.463049 CGAAAATACTGGGTATGGATGAGACT 60.463 42.308 0.00 0.00 0.00 3.24
200 201 5.696724 CGAAAATACTGGGTATGGATGAGAC 59.303 44.000 0.00 0.00 0.00 3.36
201 202 5.221641 CCGAAAATACTGGGTATGGATGAGA 60.222 44.000 0.00 0.00 0.00 3.27
202 203 4.997395 CCGAAAATACTGGGTATGGATGAG 59.003 45.833 0.00 0.00 0.00 2.90
203 204 4.202419 CCCGAAAATACTGGGTATGGATGA 60.202 45.833 0.00 0.00 38.18 2.92
204 205 4.072131 CCCGAAAATACTGGGTATGGATG 58.928 47.826 0.00 0.00 38.18 3.51
205 206 4.367039 CCCGAAAATACTGGGTATGGAT 57.633 45.455 0.00 0.00 38.18 3.41
206 207 3.849563 CCCGAAAATACTGGGTATGGA 57.150 47.619 0.00 0.00 38.18 3.41
213 214 3.181462 GGTACCCTACCCGAAAATACTGG 60.181 52.174 0.00 0.00 43.18 4.00
214 215 4.063998 GGTACCCTACCCGAAAATACTG 57.936 50.000 0.00 0.00 43.18 2.74
246 247 1.134729 GCAGTTTTGCCCATGGGTATG 60.135 52.381 31.58 22.12 44.74 2.39
247 248 1.194218 GCAGTTTTGCCCATGGGTAT 58.806 50.000 31.58 9.93 44.74 2.73
248 249 2.664825 GCAGTTTTGCCCATGGGTA 58.335 52.632 31.58 25.81 44.74 3.69
249 250 3.470433 GCAGTTTTGCCCATGGGT 58.530 55.556 31.58 8.20 44.74 4.51
258 259 2.009774 CGAGTAGGGATGGCAGTTTTG 58.990 52.381 0.00 0.00 0.00 2.44
259 260 1.679032 GCGAGTAGGGATGGCAGTTTT 60.679 52.381 0.00 0.00 0.00 2.43
260 261 0.107654 GCGAGTAGGGATGGCAGTTT 60.108 55.000 0.00 0.00 0.00 2.66
261 262 0.978146 AGCGAGTAGGGATGGCAGTT 60.978 55.000 0.00 0.00 0.00 3.16
262 263 1.381872 AGCGAGTAGGGATGGCAGT 60.382 57.895 0.00 0.00 0.00 4.40
263 264 1.068753 CAGCGAGTAGGGATGGCAG 59.931 63.158 0.00 0.00 0.00 4.85
264 265 3.094062 GCAGCGAGTAGGGATGGCA 62.094 63.158 0.00 0.00 0.00 4.92
265 266 2.280457 GCAGCGAGTAGGGATGGC 60.280 66.667 0.00 0.00 0.00 4.40
266 267 1.365633 GAGCAGCGAGTAGGGATGG 59.634 63.158 0.00 0.00 0.00 3.51
267 268 0.249238 GTGAGCAGCGAGTAGGGATG 60.249 60.000 0.00 0.00 0.00 3.51
268 269 1.729470 CGTGAGCAGCGAGTAGGGAT 61.729 60.000 0.00 0.00 0.00 3.85
269 270 2.407428 CGTGAGCAGCGAGTAGGGA 61.407 63.158 0.00 0.00 0.00 4.20
270 271 2.103143 CGTGAGCAGCGAGTAGGG 59.897 66.667 0.00 0.00 0.00 3.53
271 272 1.226435 GACGTGAGCAGCGAGTAGG 60.226 63.158 0.00 0.00 0.00 3.18
272 273 0.247894 GAGACGTGAGCAGCGAGTAG 60.248 60.000 0.00 0.00 0.00 2.57
273 274 1.645704 GGAGACGTGAGCAGCGAGTA 61.646 60.000 0.00 0.00 0.00 2.59
274 275 2.563942 GAGACGTGAGCAGCGAGT 59.436 61.111 0.00 0.00 0.00 4.18
275 276 2.202544 GGAGACGTGAGCAGCGAG 60.203 66.667 0.00 0.00 0.00 5.03
276 277 2.271607 GATGGAGACGTGAGCAGCGA 62.272 60.000 0.00 0.00 0.00 4.93
277 278 1.875813 GATGGAGACGTGAGCAGCG 60.876 63.158 0.00 0.00 0.00 5.18
278 279 0.527385 GAGATGGAGACGTGAGCAGC 60.527 60.000 0.00 0.00 0.00 5.25
279 280 1.065401 GAGAGATGGAGACGTGAGCAG 59.935 57.143 0.00 0.00 0.00 4.24
280 281 1.098869 GAGAGATGGAGACGTGAGCA 58.901 55.000 0.00 0.00 0.00 4.26
281 282 0.383949 GGAGAGATGGAGACGTGAGC 59.616 60.000 0.00 0.00 0.00 4.26
282 283 1.403679 GTGGAGAGATGGAGACGTGAG 59.596 57.143 0.00 0.00 0.00 3.51
283 284 1.464734 GTGGAGAGATGGAGACGTGA 58.535 55.000 0.00 0.00 0.00 4.35
284 285 0.099613 CGTGGAGAGATGGAGACGTG 59.900 60.000 0.00 0.00 0.00 4.49
285 286 0.035343 TCGTGGAGAGATGGAGACGT 60.035 55.000 0.00 0.00 0.00 4.34
286 287 1.064803 CTTCGTGGAGAGATGGAGACG 59.935 57.143 0.00 0.00 0.00 4.18
287 288 1.407258 CCTTCGTGGAGAGATGGAGAC 59.593 57.143 0.00 0.00 38.35 3.36
288 289 1.769026 CCTTCGTGGAGAGATGGAGA 58.231 55.000 0.00 0.00 38.35 3.71
289 290 0.103937 GCCTTCGTGGAGAGATGGAG 59.896 60.000 1.63 0.00 38.35 3.86
290 291 0.614697 TGCCTTCGTGGAGAGATGGA 60.615 55.000 1.63 0.00 38.35 3.41
291 292 0.467384 ATGCCTTCGTGGAGAGATGG 59.533 55.000 1.63 0.00 38.35 3.51
292 293 2.865670 GCTATGCCTTCGTGGAGAGATG 60.866 54.545 1.63 0.00 38.35 2.90
293 294 1.342819 GCTATGCCTTCGTGGAGAGAT 59.657 52.381 1.63 0.00 38.35 2.75
294 295 0.747255 GCTATGCCTTCGTGGAGAGA 59.253 55.000 1.63 0.00 38.35 3.10
295 296 0.596083 CGCTATGCCTTCGTGGAGAG 60.596 60.000 1.63 0.00 38.35 3.20
296 297 1.320344 ACGCTATGCCTTCGTGGAGA 61.320 55.000 1.63 0.00 38.35 3.71
297 298 0.460284 AACGCTATGCCTTCGTGGAG 60.460 55.000 1.63 0.00 38.35 3.86
298 299 0.459585 GAACGCTATGCCTTCGTGGA 60.460 55.000 1.63 0.00 38.35 4.02
299 300 1.429148 GGAACGCTATGCCTTCGTGG 61.429 60.000 0.00 0.00 36.49 4.94
300 301 1.429148 GGGAACGCTATGCCTTCGTG 61.429 60.000 0.00 0.00 36.49 4.35
301 302 1.153429 GGGAACGCTATGCCTTCGT 60.153 57.895 0.00 0.00 38.15 3.85
302 303 0.387929 TAGGGAACGCTATGCCTTCG 59.612 55.000 4.07 0.00 41.86 3.79
303 304 2.614829 TTAGGGAACGCTATGCCTTC 57.385 50.000 4.07 0.00 41.86 3.46
304 305 2.421529 CCTTTAGGGAACGCTATGCCTT 60.422 50.000 4.07 0.00 41.86 4.35
305 306 1.141053 CCTTTAGGGAACGCTATGCCT 59.859 52.381 4.19 4.19 44.23 4.75
306 307 1.594331 CCTTTAGGGAACGCTATGCC 58.406 55.000 0.00 0.00 37.23 4.40
330 331 2.409870 GGCCGGCTTGGTCAGAATG 61.410 63.158 28.56 0.00 44.04 2.67
370 371 1.120530 GTGACGATAGGGGTGATGGT 58.879 55.000 0.00 0.00 43.77 3.55
380 381 0.815734 AACCCCTCACGTGACGATAG 59.184 55.000 15.76 8.19 46.19 2.08
382 383 0.320421 CAAACCCCTCACGTGACGAT 60.320 55.000 15.76 0.00 0.00 3.73
386 387 2.063015 ATGGCAAACCCCTCACGTGA 62.063 55.000 18.88 18.88 33.59 4.35
408 409 7.290857 TGAGTATTATTTTGAGTGCGTTCTC 57.709 36.000 2.84 2.84 35.28 2.87
435 438 9.651913 GGAAGAATTGACTATGGCAAAAATAAA 57.348 29.630 0.00 0.00 0.00 1.40
436 439 7.973388 CGGAAGAATTGACTATGGCAAAAATAA 59.027 33.333 0.00 0.00 0.00 1.40
438 441 6.071391 ACGGAAGAATTGACTATGGCAAAAAT 60.071 34.615 0.00 0.00 0.00 1.82
445 448 3.270027 TGCACGGAAGAATTGACTATGG 58.730 45.455 0.00 0.00 0.00 2.74
466 469 6.832520 TTACAATGTGTGCCATAAATCACT 57.167 33.333 0.00 0.00 34.49 3.41
474 477 3.005684 CACCACTTTACAATGTGTGCCAT 59.994 43.478 0.00 0.00 33.60 4.40
481 484 4.340950 CAGGAAACCACCACTTTACAATGT 59.659 41.667 0.00 0.00 0.00 2.71
482 485 4.795962 GCAGGAAACCACCACTTTACAATG 60.796 45.833 0.00 0.00 0.00 2.82
513 516 2.489938 AACACCATCACAATAGCGGT 57.510 45.000 0.00 0.00 0.00 5.68
530 533 5.920840 GGTTTAGGAGAGTGAAATGCAAAAC 59.079 40.000 0.00 0.00 0.00 2.43
706 709 3.467226 GCATGGCATGGGCAGCTT 61.467 61.111 27.48 0.00 42.43 3.74
909 917 0.343372 AGGGGTGCTGAGATTAGGGA 59.657 55.000 0.00 0.00 0.00 4.20
971 986 1.760029 GGGAGGAAGGAGAAGTAGCTG 59.240 57.143 0.00 0.00 0.00 4.24
1081 1096 0.392193 CTCTTCAACGCCATGGCTCT 60.392 55.000 33.07 17.83 39.32 4.09
1157 1172 0.101040 TTTCGTTGTGGTCGTCGTCT 59.899 50.000 0.00 0.00 0.00 4.18
1264 1279 0.319125 CGGCCGCTATTCTTCCTCTC 60.319 60.000 14.67 0.00 0.00 3.20
1265 1280 1.742768 CGGCCGCTATTCTTCCTCT 59.257 57.895 14.67 0.00 0.00 3.69
1266 1281 1.956678 GCGGCCGCTATTCTTCCTC 60.957 63.158 41.71 9.25 38.26 3.71
1267 1282 2.109181 GCGGCCGCTATTCTTCCT 59.891 61.111 41.71 0.00 38.26 3.36
1269 1284 0.040958 CATTGCGGCCGCTATTCTTC 60.041 55.000 45.79 19.46 42.51 2.87
1270 1285 0.748005 ACATTGCGGCCGCTATTCTT 60.748 50.000 45.79 27.93 42.51 2.52
1271 1286 1.153168 ACATTGCGGCCGCTATTCT 60.153 52.632 45.79 28.76 42.51 2.40
1333 1354 4.697756 CACCACGGGCACGGACAT 62.698 66.667 15.46 0.00 46.48 3.06
1449 1470 2.259875 AAAGAGGCGACGAGAGAGCG 62.260 60.000 0.00 0.00 38.65 5.03
1464 1485 2.835605 GGCAACGATGGACGAAAGA 58.164 52.632 0.00 0.00 45.77 2.52
1617 1638 3.522731 CGGTGGAGCTCGAGGGAG 61.523 72.222 15.58 0.00 43.46 4.30
1656 1677 3.735746 GCTTTAATCAGCTGCGTTTTTGT 59.264 39.130 9.47 0.00 36.79 2.83
1735 1756 3.181967 CCGAGCTCCGAAACTGCG 61.182 66.667 8.47 0.00 41.76 5.18
1900 1921 4.143333 GCCTTGACGCGCTCCCTA 62.143 66.667 5.73 0.00 0.00 3.53
2149 2173 2.301009 CAAGCTGAAGGCCCTGAATTTT 59.699 45.455 0.00 0.00 43.05 1.82
2150 2174 1.897802 CAAGCTGAAGGCCCTGAATTT 59.102 47.619 0.00 0.00 43.05 1.82
2151 2175 1.076024 TCAAGCTGAAGGCCCTGAATT 59.924 47.619 0.00 0.00 43.05 2.17
2152 2176 0.700564 TCAAGCTGAAGGCCCTGAAT 59.299 50.000 0.00 0.00 43.05 2.57
2175 2199 3.223157 CTGGCGATAACGAACACAAAAC 58.777 45.455 0.00 0.00 42.66 2.43
2242 2266 1.661509 CTGCGTCTTGTCGTGAGCA 60.662 57.895 0.00 0.00 0.00 4.26
2375 2408 3.151958 AACTGACGCTGTCACCGCT 62.152 57.895 7.20 0.00 37.67 5.52
2378 2411 1.299926 ACGAACTGACGCTGTCACC 60.300 57.895 7.20 1.08 37.67 4.02
2395 2428 4.260170 AGAGTTCATCCAAATCTGAGCAC 58.740 43.478 0.00 0.00 38.03 4.40
2633 2676 4.008074 TGGTCTGAATCCTGTGAAGTTC 57.992 45.455 0.00 0.00 0.00 3.01
2636 2679 4.277515 TCTTGGTCTGAATCCTGTGAAG 57.722 45.455 0.00 0.00 0.00 3.02
2766 2814 0.039256 GAAGCTGGCGCATGAAACAA 60.039 50.000 10.83 0.00 39.10 2.83
2770 2818 1.588824 CTTGGAAGCTGGCGCATGAA 61.589 55.000 10.83 0.00 39.10 2.57
2771 2819 2.033911 TTGGAAGCTGGCGCATGA 59.966 55.556 10.83 0.00 39.10 3.07
2806 2854 4.246712 AGGGACAGAGAATTGCATTGAT 57.753 40.909 0.00 0.00 0.00 2.57
2815 2863 2.553904 CCAGCACAAAGGGACAGAGAAT 60.554 50.000 0.00 0.00 0.00 2.40
2816 2864 1.202806 CCAGCACAAAGGGACAGAGAA 60.203 52.381 0.00 0.00 0.00 2.87
2852 2900 4.405358 CCCAAAACATATGCTTATGGGTGT 59.595 41.667 20.24 4.14 40.89 4.16
2901 2949 7.201821 CCCAAAGTGACTGTTTGTTCTTAATCT 60.202 37.037 0.00 0.00 33.75 2.40
2971 3024 0.179034 GTGCTAGCATCTCAAGGGGG 60.179 60.000 22.51 0.00 0.00 5.40
2987 3040 3.138798 CTGGATGCAGCTGGGTGC 61.139 66.667 17.12 16.49 44.27 5.01
3117 3170 9.106070 CAAGTGGTAACCATTAAATACCTCTAC 57.894 37.037 6.29 0.00 40.68 2.59
3344 3402 1.064758 ACAAGCAACTTGAGGACACCA 60.065 47.619 13.94 0.00 43.42 4.17
3372 3430 3.008049 ACGTAGCCTGAAGAATCCAAACT 59.992 43.478 0.00 0.00 0.00 2.66
3401 3459 2.500714 AACCCCACACAGCGTCGTA 61.501 57.895 0.00 0.00 0.00 3.43
3405 3463 2.748058 GATCCAACCCCACACAGCGT 62.748 60.000 0.00 0.00 0.00 5.07


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

AutoCloner maintained by Alex Coulton.