Multiple sequence alignment - TraesCS1D01G387500

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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 TraesCS1D01G387500 chr1D 100.000 3246 0 0 1 3246 460142162 460145407 0.000000e+00 5995.0
1 TraesCS1D01G387500 chr1D 79.490 980 81 50 2359 3246 459889818 459890769 1.300000e-163 586.0
2 TraesCS1D01G387500 chr1D 84.142 536 45 23 2553 3051 262325340 262324808 1.750000e-132 483.0
3 TraesCS1D01G387500 chr1D 87.671 73 8 1 1708 1779 41980581 41980509 2.080000e-12 84.2
4 TraesCS1D01G387500 chr1D 95.122 41 2 0 600 640 371664939 371664979 7.520000e-07 65.8
5 TraesCS1D01G387500 chr1D 95.122 41 2 0 600 640 420675300 420675260 7.520000e-07 65.8
6 TraesCS1D01G387500 chr1D 95.122 41 2 0 600 640 464631695 464631735 7.520000e-07 65.8
7 TraesCS1D01G387500 chr1B 94.893 2467 79 14 422 2873 632009398 632011832 0.000000e+00 3814.0
8 TraesCS1D01G387500 chr1B 97.802 364 7 1 2883 3246 632011891 632012253 7.650000e-176 627.0
9 TraesCS1D01G387500 chr1B 79.783 737 67 28 2553 3246 632001563 632002260 8.210000e-126 460.0
10 TraesCS1D01G387500 chr1B 89.041 73 7 1 1708 1779 62389848 62389776 4.460000e-14 89.8
11 TraesCS1D01G387500 chr1B 98.039 51 1 0 602 652 632011837 632011887 4.460000e-14 89.8
12 TraesCS1D01G387500 chr1B 87.838 74 8 1 1705 1777 569427093 569427166 5.770000e-13 86.1
13 TraesCS1D01G387500 chr2D 84.544 537 43 23 2553 3052 581827299 581827832 2.250000e-136 496.0
14 TraesCS1D01G387500 chr1A 80.529 719 62 29 2359 3006 551604563 551605274 6.300000e-132 481.0
15 TraesCS1D01G387500 chr7A 88.095 84 8 2 1697 1779 691632762 691632680 7.410000e-17 99.0
16 TraesCS1D01G387500 chr5A 88.158 76 8 1 1705 1779 260411095 260411020 4.460000e-14 89.8
17 TraesCS1D01G387500 chr5A 88.000 75 8 1 1705 1778 552773922 552773996 1.600000e-13 87.9
18 TraesCS1D01G387500 chr3B 87.838 74 8 1 1705 1777 804973922 804973995 5.770000e-13 86.1
19 TraesCS1D01G387500 chr2B 87.838 74 8 1 1705 1777 634206415 634206342 5.770000e-13 86.1
20 TraesCS1D01G387500 chr6D 95.122 41 2 0 600 640 28652692 28652652 7.520000e-07 65.8
21 TraesCS1D01G387500 chr6D 95.122 41 2 0 600 640 48155497 48155457 7.520000e-07 65.8
22 TraesCS1D01G387500 chr6D 95.122 41 2 0 600 640 289616406 289616446 7.520000e-07 65.8
23 TraesCS1D01G387500 chr4D 95.122 41 2 0 600 640 57032432 57032392 7.520000e-07 65.8


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 TraesCS1D01G387500 chr1D 460142162 460145407 3245 False 5995.000000 5995 100.000000 1 3246 1 chr1D.!!$F3 3245
1 TraesCS1D01G387500 chr1D 459889818 459890769 951 False 586.000000 586 79.490000 2359 3246 1 chr1D.!!$F2 887
2 TraesCS1D01G387500 chr1D 262324808 262325340 532 True 483.000000 483 84.142000 2553 3051 1 chr1D.!!$R2 498
3 TraesCS1D01G387500 chr1B 632009398 632012253 2855 False 1510.266667 3814 96.911333 422 3246 3 chr1B.!!$F3 2824
4 TraesCS1D01G387500 chr1B 632001563 632002260 697 False 460.000000 460 79.783000 2553 3246 1 chr1B.!!$F2 693
5 TraesCS1D01G387500 chr2D 581827299 581827832 533 False 496.000000 496 84.544000 2553 3052 1 chr2D.!!$F1 499
6 TraesCS1D01G387500 chr1A 551604563 551605274 711 False 481.000000 481 80.529000 2359 3006 1 chr1A.!!$F1 647

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
715 716 0.038310 TCTCTCTCTCGCTCACCCAA 59.962 55.0 0.00 0.0 0.00 4.12 F
1305 1312 0.179179 GATTCAACAAGCTCAGCGCC 60.179 55.0 2.29 0.0 40.39 6.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1926 1938 0.892755 AATCAGTTGGCAGCATGTGG 59.107 50.0 3.63 0.0 39.31 4.17 R
2881 3031 0.178932 AAAGAAAGGCCCCAGGGAAC 60.179 55.0 7.25 0.0 37.50 3.62 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
25 26 3.098555 CGGCGCGCCTTCTTTATT 58.901 55.556 43.60 0.00 0.00 1.40
26 27 2.303452 CGGCGCGCCTTCTTTATTA 58.697 52.632 43.60 0.00 0.00 0.98
27 28 0.653636 CGGCGCGCCTTCTTTATTAA 59.346 50.000 43.60 0.00 0.00 1.40
28 29 1.332904 CGGCGCGCCTTCTTTATTAAG 60.333 52.381 43.60 22.38 0.00 1.85
29 30 1.597199 GGCGCGCCTTCTTTATTAAGC 60.597 52.381 41.71 10.89 0.00 3.09
30 31 1.597199 GCGCGCCTTCTTTATTAAGCC 60.597 52.381 23.24 0.00 0.00 4.35
31 32 1.002792 CGCGCCTTCTTTATTAAGCCC 60.003 52.381 0.00 0.00 0.00 5.19
32 33 2.298610 GCGCCTTCTTTATTAAGCCCT 58.701 47.619 0.00 0.00 0.00 5.19
33 34 2.290916 GCGCCTTCTTTATTAAGCCCTC 59.709 50.000 0.00 0.00 0.00 4.30
34 35 2.544267 CGCCTTCTTTATTAAGCCCTCG 59.456 50.000 0.00 0.00 0.00 4.63
35 36 2.879026 GCCTTCTTTATTAAGCCCTCGG 59.121 50.000 0.00 0.00 0.00 4.63
36 37 3.477530 CCTTCTTTATTAAGCCCTCGGG 58.522 50.000 0.00 0.00 38.57 5.14
37 38 3.118000 CCTTCTTTATTAAGCCCTCGGGT 60.118 47.826 3.54 0.00 37.65 5.28
38 39 4.524053 CTTCTTTATTAAGCCCTCGGGTT 58.476 43.478 3.54 0.62 45.82 4.11
39 40 4.146745 TCTTTATTAAGCCCTCGGGTTC 57.853 45.455 3.54 0.00 42.80 3.62
40 41 2.607631 TTATTAAGCCCTCGGGTTCG 57.392 50.000 3.54 0.00 42.80 3.95
41 42 0.105408 TATTAAGCCCTCGGGTTCGC 59.895 55.000 3.54 0.00 42.80 4.70
42 43 2.604299 ATTAAGCCCTCGGGTTCGCC 62.604 60.000 3.54 0.00 42.80 5.54
97 98 3.435186 GCCCTGACCGCTTGCTTC 61.435 66.667 0.00 0.00 0.00 3.86
98 99 2.747855 CCCTGACCGCTTGCTTCC 60.748 66.667 0.00 0.00 0.00 3.46
99 100 2.747855 CCTGACCGCTTGCTTCCC 60.748 66.667 0.00 0.00 0.00 3.97
100 101 2.032528 CTGACCGCTTGCTTCCCA 59.967 61.111 0.00 0.00 0.00 4.37
101 102 1.377725 CTGACCGCTTGCTTCCCAT 60.378 57.895 0.00 0.00 0.00 4.00
102 103 0.107703 CTGACCGCTTGCTTCCCATA 60.108 55.000 0.00 0.00 0.00 2.74
103 104 0.392461 TGACCGCTTGCTTCCCATAC 60.392 55.000 0.00 0.00 0.00 2.39
104 105 1.429148 GACCGCTTGCTTCCCATACG 61.429 60.000 0.00 0.00 0.00 3.06
105 106 2.180204 CCGCTTGCTTCCCATACGG 61.180 63.158 0.00 0.00 36.40 4.02
106 107 2.823829 CGCTTGCTTCCCATACGGC 61.824 63.158 0.00 0.00 0.00 5.68
107 108 2.481471 GCTTGCTTCCCATACGGCC 61.481 63.158 0.00 0.00 0.00 6.13
108 109 2.124901 TTGCTTCCCATACGGCCG 60.125 61.111 26.86 26.86 0.00 6.13
109 110 4.849310 TGCTTCCCATACGGCCGC 62.849 66.667 28.58 5.67 0.00 6.53
159 160 3.108521 CGTCCTCCGTCTTGTGAAG 57.891 57.895 0.00 0.00 0.00 3.02
160 161 1.009389 CGTCCTCCGTCTTGTGAAGC 61.009 60.000 0.00 0.00 0.00 3.86
161 162 0.670854 GTCCTCCGTCTTGTGAAGCC 60.671 60.000 0.00 0.00 0.00 4.35
162 163 1.738099 CCTCCGTCTTGTGAAGCCG 60.738 63.158 0.00 0.00 0.00 5.52
163 164 2.357034 TCCGTCTTGTGAAGCCGC 60.357 61.111 0.00 0.00 0.00 6.53
164 165 3.423154 CCGTCTTGTGAAGCCGCC 61.423 66.667 0.00 0.00 0.00 6.13
165 166 2.664851 CGTCTTGTGAAGCCGCCA 60.665 61.111 0.00 0.00 0.00 5.69
166 167 2.946762 GTCTTGTGAAGCCGCCAC 59.053 61.111 0.00 0.00 35.23 5.01
167 168 1.891919 GTCTTGTGAAGCCGCCACA 60.892 57.895 0.00 0.00 42.16 4.17
168 169 1.597854 TCTTGTGAAGCCGCCACAG 60.598 57.895 3.20 0.03 44.22 3.66
169 170 3.259425 CTTGTGAAGCCGCCACAGC 62.259 63.158 3.20 0.00 44.22 4.40
206 207 3.499737 GCCATGTCCGCCGTCTTG 61.500 66.667 0.00 0.00 0.00 3.02
207 208 2.047274 CCATGTCCGCCGTCTTGT 60.047 61.111 0.00 0.00 0.00 3.16
208 209 2.390599 CCATGTCCGCCGTCTTGTG 61.391 63.158 0.00 0.00 0.00 3.33
209 210 1.374125 CATGTCCGCCGTCTTGTGA 60.374 57.895 0.00 0.00 0.00 3.58
210 211 0.948623 CATGTCCGCCGTCTTGTGAA 60.949 55.000 0.00 0.00 0.00 3.18
211 212 0.670546 ATGTCCGCCGTCTTGTGAAG 60.671 55.000 0.00 0.00 0.00 3.02
212 213 1.006571 GTCCGCCGTCTTGTGAAGA 60.007 57.895 0.00 0.00 34.51 2.87
222 223 3.079960 TCTTGTGAAGACGAGTGACAC 57.920 47.619 0.00 0.00 35.32 3.67
223 224 2.128035 CTTGTGAAGACGAGTGACACC 58.872 52.381 0.84 0.00 0.00 4.16
224 225 1.107945 TGTGAAGACGAGTGACACCA 58.892 50.000 0.84 0.00 0.00 4.17
225 226 1.686587 TGTGAAGACGAGTGACACCAT 59.313 47.619 0.84 0.00 0.00 3.55
226 227 2.888414 TGTGAAGACGAGTGACACCATA 59.112 45.455 0.84 0.00 0.00 2.74
227 228 3.243336 GTGAAGACGAGTGACACCATAC 58.757 50.000 0.84 0.00 0.00 2.39
228 229 3.057456 GTGAAGACGAGTGACACCATACT 60.057 47.826 0.84 0.00 0.00 2.12
229 230 3.057526 TGAAGACGAGTGACACCATACTG 60.058 47.826 0.84 0.00 0.00 2.74
230 231 1.202582 AGACGAGTGACACCATACTGC 59.797 52.381 0.84 0.00 0.00 4.40
231 232 0.246635 ACGAGTGACACCATACTGCC 59.753 55.000 0.84 0.00 0.00 4.85
232 233 0.246360 CGAGTGACACCATACTGCCA 59.754 55.000 0.84 0.00 0.00 4.92
233 234 1.337728 CGAGTGACACCATACTGCCAA 60.338 52.381 0.84 0.00 0.00 4.52
234 235 2.350522 GAGTGACACCATACTGCCAAG 58.649 52.381 0.84 0.00 0.00 3.61
235 236 1.003580 AGTGACACCATACTGCCAAGG 59.996 52.381 0.84 0.00 0.00 3.61
236 237 1.064003 TGACACCATACTGCCAAGGT 58.936 50.000 0.00 0.00 33.91 3.50
237 238 1.003118 TGACACCATACTGCCAAGGTC 59.997 52.381 0.00 0.00 30.44 3.85
238 239 1.279271 GACACCATACTGCCAAGGTCT 59.721 52.381 0.00 0.00 30.44 3.85
239 240 1.705186 ACACCATACTGCCAAGGTCTT 59.295 47.619 0.00 0.00 30.44 3.01
240 241 2.290323 ACACCATACTGCCAAGGTCTTC 60.290 50.000 0.00 0.00 30.44 2.87
241 242 1.066143 ACCATACTGCCAAGGTCTTCG 60.066 52.381 0.00 0.00 0.00 3.79
242 243 1.207089 CCATACTGCCAAGGTCTTCGA 59.793 52.381 0.00 0.00 0.00 3.71
243 244 2.158900 CCATACTGCCAAGGTCTTCGAT 60.159 50.000 0.00 0.00 0.00 3.59
244 245 2.961526 TACTGCCAAGGTCTTCGATC 57.038 50.000 0.00 0.00 0.00 3.69
245 246 0.108615 ACTGCCAAGGTCTTCGATCG 60.109 55.000 9.36 9.36 0.00 3.69
246 247 1.424493 CTGCCAAGGTCTTCGATCGC 61.424 60.000 11.09 0.00 0.00 4.58
247 248 2.174319 GCCAAGGTCTTCGATCGCC 61.174 63.158 11.09 5.75 0.00 5.54
248 249 1.878522 CCAAGGTCTTCGATCGCCG 60.879 63.158 11.09 3.55 40.25 6.46
249 250 2.202756 AAGGTCTTCGATCGCCGC 60.203 61.111 11.09 0.21 38.37 6.53
250 251 3.718210 AAGGTCTTCGATCGCCGCC 62.718 63.158 11.09 9.74 38.37 6.13
251 252 4.208686 GGTCTTCGATCGCCGCCT 62.209 66.667 11.09 0.00 38.37 5.52
252 253 2.956964 GTCTTCGATCGCCGCCTG 60.957 66.667 11.09 0.00 38.37 4.85
253 254 4.873129 TCTTCGATCGCCGCCTGC 62.873 66.667 11.09 0.00 38.37 4.85
254 255 4.880537 CTTCGATCGCCGCCTGCT 62.881 66.667 11.09 0.00 38.05 4.24
258 259 3.267860 GATCGCCGCCTGCTGAAG 61.268 66.667 0.00 0.00 38.05 3.02
259 260 3.723235 GATCGCCGCCTGCTGAAGA 62.723 63.158 0.00 0.00 38.05 2.87
260 261 3.315142 ATCGCCGCCTGCTGAAGAA 62.315 57.895 0.00 0.00 38.05 2.52
261 262 2.803155 ATCGCCGCCTGCTGAAGAAA 62.803 55.000 0.00 0.00 38.05 2.52
262 263 2.873288 GCCGCCTGCTGAAGAAAG 59.127 61.111 0.00 0.00 36.87 2.62
263 264 2.694760 GCCGCCTGCTGAAGAAAGG 61.695 63.158 0.00 0.00 36.87 3.11
265 266 2.873288 GCCTGCTGAAGAAAGGCG 59.127 61.111 8.26 0.00 46.50 5.52
266 267 1.672356 GCCTGCTGAAGAAAGGCGA 60.672 57.895 8.26 0.00 46.50 5.54
267 268 1.028868 GCCTGCTGAAGAAAGGCGAT 61.029 55.000 8.26 0.00 46.50 4.58
268 269 1.012841 CCTGCTGAAGAAAGGCGATC 58.987 55.000 0.00 0.00 0.00 3.69
269 270 1.676916 CCTGCTGAAGAAAGGCGATCA 60.677 52.381 0.00 0.00 0.00 2.92
270 271 1.396301 CTGCTGAAGAAAGGCGATCAC 59.604 52.381 0.00 0.00 0.00 3.06
271 272 1.002430 TGCTGAAGAAAGGCGATCACT 59.998 47.619 0.00 0.00 0.00 3.41
272 273 1.663135 GCTGAAGAAAGGCGATCACTC 59.337 52.381 0.00 0.00 0.00 3.51
273 274 2.932622 GCTGAAGAAAGGCGATCACTCA 60.933 50.000 0.00 0.00 0.00 3.41
274 275 3.329386 CTGAAGAAAGGCGATCACTCAA 58.671 45.455 0.00 0.00 0.00 3.02
275 276 3.067106 TGAAGAAAGGCGATCACTCAAC 58.933 45.455 0.00 0.00 0.00 3.18
276 277 3.244215 TGAAGAAAGGCGATCACTCAACT 60.244 43.478 0.00 0.00 0.00 3.16
277 278 2.966050 AGAAAGGCGATCACTCAACTC 58.034 47.619 0.00 0.00 0.00 3.01
278 279 2.003301 GAAAGGCGATCACTCAACTCC 58.997 52.381 0.00 0.00 0.00 3.85
279 280 0.976641 AAGGCGATCACTCAACTCCA 59.023 50.000 0.00 0.00 0.00 3.86
280 281 0.976641 AGGCGATCACTCAACTCCAA 59.023 50.000 0.00 0.00 0.00 3.53
281 282 1.066573 AGGCGATCACTCAACTCCAAG 60.067 52.381 0.00 0.00 0.00 3.61
282 283 1.338200 GGCGATCACTCAACTCCAAGT 60.338 52.381 0.00 0.00 0.00 3.16
283 284 1.996191 GCGATCACTCAACTCCAAGTC 59.004 52.381 0.00 0.00 0.00 3.01
284 285 2.611518 CGATCACTCAACTCCAAGTCC 58.388 52.381 0.00 0.00 0.00 3.85
285 286 2.611518 GATCACTCAACTCCAAGTCCG 58.388 52.381 0.00 0.00 0.00 4.79
286 287 0.679505 TCACTCAACTCCAAGTCCGG 59.320 55.000 0.00 0.00 0.00 5.14
287 288 0.393077 CACTCAACTCCAAGTCCGGT 59.607 55.000 0.00 0.00 0.00 5.28
288 289 0.393077 ACTCAACTCCAAGTCCGGTG 59.607 55.000 0.00 0.00 0.00 4.94
289 290 0.320771 CTCAACTCCAAGTCCGGTGG 60.321 60.000 0.00 1.35 37.51 4.61
290 291 1.052124 TCAACTCCAAGTCCGGTGGT 61.052 55.000 9.27 0.00 37.43 4.16
291 292 0.602905 CAACTCCAAGTCCGGTGGTC 60.603 60.000 9.27 0.00 37.43 4.02
292 293 2.095978 AACTCCAAGTCCGGTGGTCG 62.096 60.000 9.27 5.13 37.43 4.79
293 294 2.203523 TCCAAGTCCGGTGGTCGA 60.204 61.111 9.27 0.00 42.43 4.20
294 295 2.048503 CCAAGTCCGGTGGTCGAC 60.049 66.667 7.13 7.13 42.43 4.20
295 296 2.732016 CAAGTCCGGTGGTCGACA 59.268 61.111 18.91 0.27 42.43 4.35
296 297 1.292223 CAAGTCCGGTGGTCGACAT 59.708 57.895 18.91 0.00 42.43 3.06
297 298 1.014044 CAAGTCCGGTGGTCGACATG 61.014 60.000 18.91 3.26 42.43 3.21
298 299 2.125673 GTCCGGTGGTCGACATGG 60.126 66.667 18.91 12.58 42.43 3.66
299 300 3.387091 TCCGGTGGTCGACATGGG 61.387 66.667 18.91 12.38 42.43 4.00
300 301 3.387091 CCGGTGGTCGACATGGGA 61.387 66.667 18.91 0.00 42.43 4.37
301 302 2.184322 CGGTGGTCGACATGGGAG 59.816 66.667 18.91 0.00 42.43 4.30
302 303 2.584608 GGTGGTCGACATGGGAGG 59.415 66.667 18.91 0.00 0.00 4.30
303 304 1.987855 GGTGGTCGACATGGGAGGA 60.988 63.158 18.91 0.00 0.00 3.71
304 305 1.218316 GTGGTCGACATGGGAGGAC 59.782 63.158 18.91 0.00 0.00 3.85
305 306 1.078528 TGGTCGACATGGGAGGACT 59.921 57.895 18.91 0.00 0.00 3.85
306 307 0.333652 TGGTCGACATGGGAGGACTA 59.666 55.000 18.91 0.00 0.00 2.59
307 308 0.745468 GGTCGACATGGGAGGACTAC 59.255 60.000 18.91 0.00 0.00 2.73
308 309 0.381089 GTCGACATGGGAGGACTACG 59.619 60.000 11.55 0.00 0.00 3.51
309 310 0.253894 TCGACATGGGAGGACTACGA 59.746 55.000 0.00 0.00 0.00 3.43
310 311 0.663688 CGACATGGGAGGACTACGAG 59.336 60.000 0.00 0.00 0.00 4.18
311 312 1.033574 GACATGGGAGGACTACGAGG 58.966 60.000 0.00 0.00 0.00 4.63
312 313 0.335361 ACATGGGAGGACTACGAGGT 59.665 55.000 0.00 0.00 0.00 3.85
313 314 0.747255 CATGGGAGGACTACGAGGTG 59.253 60.000 0.00 0.00 0.00 4.00
314 315 1.043673 ATGGGAGGACTACGAGGTGC 61.044 60.000 0.00 0.00 0.00 5.01
315 316 1.380112 GGGAGGACTACGAGGTGCT 60.380 63.158 6.31 6.31 40.47 4.40
316 317 1.668101 GGGAGGACTACGAGGTGCTG 61.668 65.000 10.43 0.00 37.98 4.41
317 318 0.966370 GGAGGACTACGAGGTGCTGT 60.966 60.000 10.43 0.00 37.98 4.40
318 319 0.171455 GAGGACTACGAGGTGCTGTG 59.829 60.000 10.43 0.00 37.98 3.66
319 320 1.446272 GGACTACGAGGTGCTGTGC 60.446 63.158 0.00 0.00 0.00 4.57
320 321 1.446272 GACTACGAGGTGCTGTGCC 60.446 63.158 0.00 0.00 0.00 5.01
321 322 2.154798 GACTACGAGGTGCTGTGCCA 62.155 60.000 0.00 0.00 0.00 4.92
322 323 1.738099 CTACGAGGTGCTGTGCCAC 60.738 63.158 0.00 0.00 35.00 5.01
327 328 3.964875 GGTGCTGTGCCACCGTTG 61.965 66.667 0.00 0.00 45.13 4.10
328 329 4.629115 GTGCTGTGCCACCGTTGC 62.629 66.667 0.00 0.00 0.00 4.17
341 342 4.651008 GTTGCCCCGACGACGACA 62.651 66.667 9.28 1.14 42.66 4.35
342 343 3.687102 TTGCCCCGACGACGACAT 61.687 61.111 9.28 0.00 42.66 3.06
343 344 3.229156 TTGCCCCGACGACGACATT 62.229 57.895 9.28 0.00 42.66 2.71
344 345 2.433664 GCCCCGACGACGACATTT 60.434 61.111 9.28 0.00 42.66 2.32
345 346 2.736682 GCCCCGACGACGACATTTG 61.737 63.158 9.28 0.00 42.66 2.32
346 347 2.098233 CCCCGACGACGACATTTGG 61.098 63.158 9.28 0.00 42.66 3.28
347 348 2.098233 CCCGACGACGACATTTGGG 61.098 63.158 9.28 0.00 42.66 4.12
348 349 2.098233 CCGACGACGACATTTGGGG 61.098 63.158 9.28 0.00 42.66 4.96
349 350 2.736682 CGACGACGACATTTGGGGC 61.737 63.158 0.00 0.00 42.66 5.80
350 351 2.736682 GACGACGACATTTGGGGCG 61.737 63.158 0.00 0.00 0.00 6.13
351 352 2.433491 CGACGACATTTGGGGCGA 60.433 61.111 0.00 0.00 0.00 5.54
352 353 2.030401 CGACGACATTTGGGGCGAA 61.030 57.895 0.00 0.00 0.00 4.70
353 354 1.794222 GACGACATTTGGGGCGAAG 59.206 57.895 0.00 0.00 0.00 3.79
382 383 2.480555 GCAAGGGCGAATGTCACG 59.519 61.111 0.00 0.00 0.00 4.35
390 391 2.827604 CGAATGTCACGCCTGAAGT 58.172 52.632 0.00 0.00 0.00 3.01
391 392 1.148310 CGAATGTCACGCCTGAAGTT 58.852 50.000 0.00 0.00 0.00 2.66
392 393 1.126846 CGAATGTCACGCCTGAAGTTC 59.873 52.381 0.00 0.00 0.00 3.01
393 394 2.143122 GAATGTCACGCCTGAAGTTCA 58.857 47.619 5.25 5.25 0.00 3.18
394 395 1.800805 ATGTCACGCCTGAAGTTCAG 58.199 50.000 23.58 23.58 43.91 3.02
453 454 1.597742 TCTGAACCTGAACTTGCAGC 58.402 50.000 0.00 0.00 34.56 5.25
499 500 1.819632 GCCTCAGGCCATGTAACCG 60.820 63.158 3.37 0.00 44.06 4.44
500 501 1.153168 CCTCAGGCCATGTAACCGG 60.153 63.158 5.01 0.00 0.00 5.28
563 564 3.459232 TCGGCATCGATGAGAAGAATT 57.541 42.857 29.20 0.00 40.88 2.17
622 623 3.470888 CTCCCAGCGATTCCCCGT 61.471 66.667 0.00 0.00 0.00 5.28
694 695 1.755008 GCGGCTAGGTCAGTCCTCT 60.755 63.158 0.00 0.00 44.42 3.69
695 696 2.010582 GCGGCTAGGTCAGTCCTCTG 62.011 65.000 0.00 0.00 44.42 3.35
715 716 0.038310 TCTCTCTCTCGCTCACCCAA 59.962 55.000 0.00 0.00 0.00 4.12
852 853 2.124983 TCATGCCGCTGCTTCTCC 60.125 61.111 0.70 0.00 38.71 3.71
868 869 4.090588 CCTTCTTGCCGGCCCGTA 62.091 66.667 26.77 0.59 0.00 4.02
890 891 0.319813 GCTGCTTTTCGTGGCCATTT 60.320 50.000 9.72 0.00 0.00 2.32
900 901 0.319813 GTGGCCATTTTGTGTGCTCC 60.320 55.000 9.72 0.00 0.00 4.70
919 920 0.528684 CTGCTACGGCTGCTTACTCC 60.529 60.000 0.00 0.00 39.59 3.85
923 924 1.601419 TACGGCTGCTTACTCCGCTT 61.601 55.000 0.00 0.00 46.49 4.68
1041 1048 1.448540 CATCGCCGTCCTCTTGCTT 60.449 57.895 0.00 0.00 0.00 3.91
1043 1050 2.172483 ATCGCCGTCCTCTTGCTTGT 62.172 55.000 0.00 0.00 0.00 3.16
1054 1061 2.981914 CTTGCTTGTCCCCTGTGCCA 62.982 60.000 0.00 0.00 0.00 4.92
1185 1192 4.597507 TCCTTTTTAGAGAAGGAGGCTGAA 59.402 41.667 0.00 0.00 45.81 3.02
1254 1261 0.899717 GGCTCACCATTTTCTGCCCA 60.900 55.000 0.00 0.00 34.81 5.36
1257 1264 1.815003 CTCACCATTTTCTGCCCAGAC 59.185 52.381 0.00 0.00 37.14 3.51
1263 1270 0.319555 TTTTCTGCCCAGACGACGAG 60.320 55.000 0.00 0.00 37.14 4.18
1293 1300 2.352960 GGCATTCACTCCGAGATTCAAC 59.647 50.000 1.33 0.00 0.00 3.18
1305 1312 0.179179 GATTCAACAAGCTCAGCGCC 60.179 55.000 2.29 0.00 40.39 6.53
1306 1313 0.607489 ATTCAACAAGCTCAGCGCCT 60.607 50.000 2.29 0.00 40.39 5.52
1332 1339 0.896226 AGGTCGCCCTTCTTCTGTAC 59.104 55.000 0.00 0.00 38.13 2.90
1410 1417 1.887707 GCCGACGCTTGATAAGGGG 60.888 63.158 9.87 0.00 44.93 4.79
1452 1459 2.871182 TGCTCACCATCGATGTCTAC 57.129 50.000 23.27 9.67 0.00 2.59
1552 1559 1.871408 GCCTGGCTGTCTACATCATCG 60.871 57.143 12.43 0.00 0.00 3.84
1643 1655 3.862642 GCGTTGTGAGTCTTCATCTCCTT 60.863 47.826 0.00 0.00 35.39 3.36
1749 1761 4.580580 ACTCATCCAAAAGTCCAAACTGAC 59.419 41.667 0.00 0.00 35.36 3.51
1812 1824 3.378427 GTCTGAATTTATCTGTGGGTGGC 59.622 47.826 0.00 0.00 0.00 5.01
1813 1825 3.266772 TCTGAATTTATCTGTGGGTGGCT 59.733 43.478 0.00 0.00 0.00 4.75
1960 1972 5.222007 CCAACTGATTATTAGGGAGATGCCT 60.222 44.000 0.00 0.00 36.66 4.75
2021 2033 6.390721 AGCAGGTGTAAATATATAGCGACAG 58.609 40.000 0.00 0.00 0.00 3.51
2033 2045 4.839668 ATAGCGACAGTGATTCCTAGTC 57.160 45.455 0.00 0.00 0.00 2.59
2285 2299 5.593095 TCAAGATCGCTACTACCTATGTTGT 59.407 40.000 0.00 0.00 34.75 3.32
2286 2300 5.440234 AGATCGCTACTACCTATGTTGTG 57.560 43.478 0.00 0.00 32.62 3.33
2287 2301 4.278669 AGATCGCTACTACCTATGTTGTGG 59.721 45.833 0.00 0.00 32.62 4.17
2288 2302 2.100252 TCGCTACTACCTATGTTGTGGC 59.900 50.000 9.96 9.96 45.98 5.01
2289 2303 2.100916 CGCTACTACCTATGTTGTGGCT 59.899 50.000 15.58 0.00 46.77 4.75
2290 2304 3.718815 GCTACTACCTATGTTGTGGCTC 58.281 50.000 12.01 0.00 45.96 4.70
2291 2305 3.492829 GCTACTACCTATGTTGTGGCTCC 60.493 52.174 12.01 0.00 45.96 4.70
2292 2306 2.546899 ACTACCTATGTTGTGGCTCCA 58.453 47.619 0.00 0.00 0.00 3.86
2293 2307 3.115390 ACTACCTATGTTGTGGCTCCAT 58.885 45.455 0.00 0.00 0.00 3.41
2294 2308 4.295201 ACTACCTATGTTGTGGCTCCATA 58.705 43.478 0.00 0.00 0.00 2.74
2295 2309 4.907875 ACTACCTATGTTGTGGCTCCATAT 59.092 41.667 0.00 0.00 0.00 1.78
2296 2310 6.082031 ACTACCTATGTTGTGGCTCCATATA 58.918 40.000 0.00 0.00 0.00 0.86
2297 2311 6.730977 ACTACCTATGTTGTGGCTCCATATAT 59.269 38.462 0.00 0.00 0.00 0.86
2298 2312 7.899172 ACTACCTATGTTGTGGCTCCATATATA 59.101 37.037 0.00 0.00 0.00 0.86
2299 2313 7.568128 ACCTATGTTGTGGCTCCATATATAA 57.432 36.000 0.00 0.00 0.00 0.98
2323 2337 4.759782 CGACAAGGACCTTAGTTCATGAT 58.240 43.478 6.38 0.00 0.00 2.45
2345 2359 4.439305 TGTTTCATTTACATCAGCTGGC 57.561 40.909 15.13 0.00 0.00 4.85
2357 2371 4.202441 CATCAGCTGGCCTAATGTTAACT 58.798 43.478 15.13 0.00 0.00 2.24
2366 2380 5.183228 GGCCTAATGTTAACTACTTCTGCA 58.817 41.667 7.22 0.00 0.00 4.41
2386 2400 2.515926 TCGACATTATCCTGCTCTGC 57.484 50.000 0.00 0.00 0.00 4.26
2387 2401 1.135046 CGACATTATCCTGCTCTGCG 58.865 55.000 0.00 0.00 0.00 5.18
2401 2415 3.118775 TGCTCTGCGTCATACTTGGTATT 60.119 43.478 0.00 0.00 0.00 1.89
2420 2434 1.821216 TGCTGCCTACCTTTACAAGC 58.179 50.000 0.00 0.00 0.00 4.01
2558 2622 7.934457 ACCACATTCATAGTGCAAATCTAATC 58.066 34.615 0.00 0.00 35.69 1.75
2662 2729 4.276926 GGTAGTGATCTTGCATTGGATTCC 59.723 45.833 0.00 0.00 0.00 3.01
2857 2944 8.070171 AGAGTACAAACATCATTCTTTTGTTCG 58.930 33.333 4.42 0.00 39.82 3.95
2876 3026 3.738982 TCGAAACCTGGCCATGTATATG 58.261 45.455 14.55 5.34 0.00 1.78
2881 3031 1.536766 CCTGGCCATGTATATGTTGCG 59.463 52.381 5.51 0.00 32.21 4.85
3226 3406 0.405585 AGTATGGGCAGCTTTGGTGT 59.594 50.000 0.00 0.00 33.19 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 0.653636 TTAATAAAGAAGGCGCGCCG 59.346 50.000 41.70 0.00 41.95 6.46
9 10 1.597199 GCTTAATAAAGAAGGCGCGCC 60.597 52.381 42.34 42.34 34.37 6.53
10 11 1.597199 GGCTTAATAAAGAAGGCGCGC 60.597 52.381 25.94 25.94 39.36 6.86
11 12 2.384899 GGCTTAATAAAGAAGGCGCG 57.615 50.000 0.00 0.00 39.36 6.86
14 15 2.879026 CCGAGGGCTTAATAAAGAAGGC 59.121 50.000 0.62 0.62 46.03 4.35
15 16 3.118000 ACCCGAGGGCTTAATAAAGAAGG 60.118 47.826 8.33 0.00 39.32 3.46
16 17 4.152284 ACCCGAGGGCTTAATAAAGAAG 57.848 45.455 8.33 0.00 39.32 2.85
17 18 4.520179 GAACCCGAGGGCTTAATAAAGAA 58.480 43.478 8.33 0.00 39.32 2.52
18 19 3.431207 CGAACCCGAGGGCTTAATAAAGA 60.431 47.826 8.33 0.00 39.32 2.52
19 20 2.870411 CGAACCCGAGGGCTTAATAAAG 59.130 50.000 8.33 0.00 39.32 1.85
20 21 2.908916 CGAACCCGAGGGCTTAATAAA 58.091 47.619 8.33 0.00 39.32 1.40
21 22 1.473788 GCGAACCCGAGGGCTTAATAA 60.474 52.381 8.33 0.00 39.32 1.40
22 23 0.105408 GCGAACCCGAGGGCTTAATA 59.895 55.000 8.33 0.00 39.32 0.98
23 24 1.153229 GCGAACCCGAGGGCTTAAT 60.153 57.895 8.33 0.00 39.32 1.40
24 25 2.266689 GCGAACCCGAGGGCTTAA 59.733 61.111 8.33 0.00 39.32 1.85
25 26 3.777910 GGCGAACCCGAGGGCTTA 61.778 66.667 8.33 0.00 39.32 3.09
80 81 3.435186 GAAGCAAGCGGTCAGGGC 61.435 66.667 0.00 0.00 0.00 5.19
81 82 2.747855 GGAAGCAAGCGGTCAGGG 60.748 66.667 0.00 0.00 0.00 4.45
82 83 2.747855 GGGAAGCAAGCGGTCAGG 60.748 66.667 0.00 0.00 0.00 3.86
83 84 0.107703 TATGGGAAGCAAGCGGTCAG 60.108 55.000 0.00 0.00 0.00 3.51
84 85 0.392461 GTATGGGAAGCAAGCGGTCA 60.392 55.000 0.00 0.00 0.00 4.02
85 86 1.429148 CGTATGGGAAGCAAGCGGTC 61.429 60.000 0.00 0.00 0.00 4.79
86 87 1.449601 CGTATGGGAAGCAAGCGGT 60.450 57.895 0.00 0.00 0.00 5.68
87 88 2.180204 CCGTATGGGAAGCAAGCGG 61.180 63.158 0.00 0.00 38.47 5.52
88 89 2.823829 GCCGTATGGGAAGCAAGCG 61.824 63.158 2.41 0.00 38.47 4.68
89 90 2.481471 GGCCGTATGGGAAGCAAGC 61.481 63.158 2.41 0.00 38.47 4.01
90 91 2.180204 CGGCCGTATGGGAAGCAAG 61.180 63.158 19.50 0.00 38.47 4.01
91 92 2.124901 CGGCCGTATGGGAAGCAA 60.125 61.111 19.50 0.00 38.47 3.91
92 93 4.849310 GCGGCCGTATGGGAAGCA 62.849 66.667 28.70 0.00 38.89 3.91
142 143 0.670854 GGCTTCACAAGACGGAGGAC 60.671 60.000 0.00 0.00 0.00 3.85
143 144 1.671742 GGCTTCACAAGACGGAGGA 59.328 57.895 0.00 0.00 0.00 3.71
144 145 4.285851 GGCTTCACAAGACGGAGG 57.714 61.111 0.00 0.00 0.00 4.30
149 150 1.845809 CTGTGGCGGCTTCACAAGAC 61.846 60.000 11.43 0.00 43.45 3.01
150 151 1.597854 CTGTGGCGGCTTCACAAGA 60.598 57.895 11.43 0.00 43.45 3.02
151 152 2.949106 CTGTGGCGGCTTCACAAG 59.051 61.111 11.43 4.70 43.45 3.16
152 153 3.286751 GCTGTGGCGGCTTCACAA 61.287 61.111 11.43 0.00 43.45 3.33
189 190 3.499737 CAAGACGGCGGACATGGC 61.500 66.667 13.24 0.00 0.00 4.40
190 191 2.047274 ACAAGACGGCGGACATGG 60.047 61.111 13.24 0.00 0.00 3.66
191 192 0.948623 TTCACAAGACGGCGGACATG 60.949 55.000 13.24 10.74 0.00 3.21
192 193 0.670546 CTTCACAAGACGGCGGACAT 60.671 55.000 13.24 0.00 0.00 3.06
193 194 1.300620 CTTCACAAGACGGCGGACA 60.301 57.895 13.24 0.00 0.00 4.02
194 195 1.006571 TCTTCACAAGACGGCGGAC 60.007 57.895 13.24 4.88 31.20 4.79
195 196 3.450507 TCTTCACAAGACGGCGGA 58.549 55.556 13.24 0.00 31.20 5.54
202 203 2.223735 GGTGTCACTCGTCTTCACAAGA 60.224 50.000 2.35 0.00 34.51 3.02
203 204 2.128035 GGTGTCACTCGTCTTCACAAG 58.872 52.381 2.35 0.00 0.00 3.16
204 205 1.478916 TGGTGTCACTCGTCTTCACAA 59.521 47.619 2.35 0.00 0.00 3.33
205 206 1.107945 TGGTGTCACTCGTCTTCACA 58.892 50.000 2.35 0.00 0.00 3.58
206 207 2.440539 ATGGTGTCACTCGTCTTCAC 57.559 50.000 2.35 0.00 0.00 3.18
207 208 3.057526 CAGTATGGTGTCACTCGTCTTCA 60.058 47.826 2.35 0.00 0.00 3.02
208 209 3.502920 CAGTATGGTGTCACTCGTCTTC 58.497 50.000 2.35 0.00 0.00 2.87
209 210 2.352814 GCAGTATGGTGTCACTCGTCTT 60.353 50.000 2.35 0.00 35.86 3.01
210 211 1.202582 GCAGTATGGTGTCACTCGTCT 59.797 52.381 2.35 0.00 35.86 4.18
211 212 1.630148 GCAGTATGGTGTCACTCGTC 58.370 55.000 2.35 0.00 35.86 4.20
212 213 0.246635 GGCAGTATGGTGTCACTCGT 59.753 55.000 2.35 0.00 35.86 4.18
213 214 0.246360 TGGCAGTATGGTGTCACTCG 59.754 55.000 2.35 0.00 35.86 4.18
214 215 2.350522 CTTGGCAGTATGGTGTCACTC 58.649 52.381 2.35 0.00 35.86 3.51
215 216 1.003580 CCTTGGCAGTATGGTGTCACT 59.996 52.381 2.35 0.00 35.86 3.41
216 217 1.271379 ACCTTGGCAGTATGGTGTCAC 60.271 52.381 0.00 0.00 35.86 3.67
217 218 1.003118 GACCTTGGCAGTATGGTGTCA 59.997 52.381 7.98 0.00 35.86 3.58
218 219 1.279271 AGACCTTGGCAGTATGGTGTC 59.721 52.381 7.98 0.00 35.86 3.67
219 220 1.362224 AGACCTTGGCAGTATGGTGT 58.638 50.000 7.98 2.52 35.86 4.16
220 221 2.359900 GAAGACCTTGGCAGTATGGTG 58.640 52.381 7.98 0.00 35.86 4.17
221 222 1.066143 CGAAGACCTTGGCAGTATGGT 60.066 52.381 3.80 3.80 35.86 3.55
222 223 1.207089 TCGAAGACCTTGGCAGTATGG 59.793 52.381 0.00 0.00 35.86 2.74
223 224 2.672961 TCGAAGACCTTGGCAGTATG 57.327 50.000 0.00 0.00 40.87 2.39
224 225 2.223829 CGATCGAAGACCTTGGCAGTAT 60.224 50.000 10.26 0.00 42.51 2.12
225 226 1.134367 CGATCGAAGACCTTGGCAGTA 59.866 52.381 10.26 0.00 42.51 2.74
226 227 0.108615 CGATCGAAGACCTTGGCAGT 60.109 55.000 10.26 0.00 42.51 4.40
227 228 1.424493 GCGATCGAAGACCTTGGCAG 61.424 60.000 21.57 0.00 42.51 4.85
228 229 1.447838 GCGATCGAAGACCTTGGCA 60.448 57.895 21.57 0.00 42.51 4.92
229 230 2.174319 GGCGATCGAAGACCTTGGC 61.174 63.158 21.57 0.00 42.51 4.52
230 231 1.878522 CGGCGATCGAAGACCTTGG 60.879 63.158 21.57 0.00 42.51 3.61
231 232 2.517450 GCGGCGATCGAAGACCTTG 61.517 63.158 21.57 0.00 42.51 3.61
232 233 2.202756 GCGGCGATCGAAGACCTT 60.203 61.111 21.57 0.00 42.51 3.50
233 234 4.208686 GGCGGCGATCGAAGACCT 62.209 66.667 21.57 0.00 42.51 3.85
234 235 4.208686 AGGCGGCGATCGAAGACC 62.209 66.667 21.57 13.70 42.51 3.85
235 236 2.956964 CAGGCGGCGATCGAAGAC 60.957 66.667 21.57 13.84 42.51 3.01
236 237 4.873129 GCAGGCGGCGATCGAAGA 62.873 66.667 21.57 0.00 42.43 2.87
245 246 2.694760 CCTTTCTTCAGCAGGCGGC 61.695 63.158 0.00 0.00 45.30 6.53
246 247 2.694760 GCCTTTCTTCAGCAGGCGG 61.695 63.158 0.00 0.00 43.73 6.13
247 248 2.873288 GCCTTTCTTCAGCAGGCG 59.127 61.111 0.00 0.00 43.73 5.52
249 250 1.012841 GATCGCCTTTCTTCAGCAGG 58.987 55.000 0.00 0.00 0.00 4.85
250 251 1.396301 GTGATCGCCTTTCTTCAGCAG 59.604 52.381 0.00 0.00 0.00 4.24
251 252 1.002430 AGTGATCGCCTTTCTTCAGCA 59.998 47.619 1.76 0.00 0.00 4.41
252 253 1.663135 GAGTGATCGCCTTTCTTCAGC 59.337 52.381 1.76 0.00 0.00 4.26
253 254 2.964740 TGAGTGATCGCCTTTCTTCAG 58.035 47.619 1.76 0.00 0.00 3.02
254 255 3.067106 GTTGAGTGATCGCCTTTCTTCA 58.933 45.455 1.76 0.00 0.00 3.02
255 256 3.330267 AGTTGAGTGATCGCCTTTCTTC 58.670 45.455 1.76 0.00 0.00 2.87
256 257 3.330267 GAGTTGAGTGATCGCCTTTCTT 58.670 45.455 1.76 0.00 0.00 2.52
257 258 2.354203 GGAGTTGAGTGATCGCCTTTCT 60.354 50.000 1.76 0.00 0.00 2.52
258 259 2.003301 GGAGTTGAGTGATCGCCTTTC 58.997 52.381 1.76 0.00 0.00 2.62
259 260 1.347707 TGGAGTTGAGTGATCGCCTTT 59.652 47.619 1.76 0.00 0.00 3.11
260 261 0.976641 TGGAGTTGAGTGATCGCCTT 59.023 50.000 1.76 0.00 0.00 4.35
261 262 0.976641 TTGGAGTTGAGTGATCGCCT 59.023 50.000 1.76 0.00 0.00 5.52
262 263 1.338200 ACTTGGAGTTGAGTGATCGCC 60.338 52.381 1.76 0.00 0.00 5.54
263 264 1.996191 GACTTGGAGTTGAGTGATCGC 59.004 52.381 0.00 0.00 0.00 4.58
264 265 2.611518 GGACTTGGAGTTGAGTGATCG 58.388 52.381 0.00 0.00 0.00 3.69
265 266 2.611518 CGGACTTGGAGTTGAGTGATC 58.388 52.381 0.00 0.00 0.00 2.92
266 267 1.276421 CCGGACTTGGAGTTGAGTGAT 59.724 52.381 0.00 0.00 0.00 3.06
267 268 0.679505 CCGGACTTGGAGTTGAGTGA 59.320 55.000 0.00 0.00 0.00 3.41
268 269 0.393077 ACCGGACTTGGAGTTGAGTG 59.607 55.000 9.46 0.00 0.00 3.51
269 270 0.393077 CACCGGACTTGGAGTTGAGT 59.607 55.000 9.46 0.00 0.00 3.41
270 271 0.320771 CCACCGGACTTGGAGTTGAG 60.321 60.000 9.46 0.00 36.02 3.02
271 272 1.052124 ACCACCGGACTTGGAGTTGA 61.052 55.000 16.09 0.00 37.58 3.18
272 273 0.602905 GACCACCGGACTTGGAGTTG 60.603 60.000 16.09 0.00 37.58 3.16
273 274 1.752833 GACCACCGGACTTGGAGTT 59.247 57.895 16.09 0.00 37.58 3.01
274 275 2.571216 CGACCACCGGACTTGGAGT 61.571 63.158 16.09 0.00 37.58 3.85
275 276 2.261671 CGACCACCGGACTTGGAG 59.738 66.667 16.09 6.09 37.58 3.86
276 277 2.203523 TCGACCACCGGACTTGGA 60.204 61.111 16.09 1.07 37.58 3.53
277 278 2.048503 GTCGACCACCGGACTTGG 60.049 66.667 9.46 8.57 40.32 3.61
278 279 1.014044 CATGTCGACCACCGGACTTG 61.014 60.000 9.46 0.00 39.14 3.16
279 280 1.292223 CATGTCGACCACCGGACTT 59.708 57.895 9.46 0.00 39.14 3.01
280 281 2.646175 CCATGTCGACCACCGGACT 61.646 63.158 9.46 0.00 39.14 3.85
281 282 2.125673 CCATGTCGACCACCGGAC 60.126 66.667 9.46 0.00 39.14 4.79
282 283 3.387091 CCCATGTCGACCACCGGA 61.387 66.667 9.46 0.00 39.14 5.14
283 284 3.371097 CTCCCATGTCGACCACCGG 62.371 68.421 14.12 0.00 39.14 5.28
284 285 2.184322 CTCCCATGTCGACCACCG 59.816 66.667 14.12 0.00 40.25 4.94
285 286 1.987855 TCCTCCCATGTCGACCACC 60.988 63.158 14.12 0.00 0.00 4.61
286 287 1.218316 GTCCTCCCATGTCGACCAC 59.782 63.158 14.12 0.00 0.00 4.16
287 288 0.333652 TAGTCCTCCCATGTCGACCA 59.666 55.000 14.12 1.26 0.00 4.02
288 289 0.745468 GTAGTCCTCCCATGTCGACC 59.255 60.000 14.12 0.00 0.00 4.79
289 290 0.381089 CGTAGTCCTCCCATGTCGAC 59.619 60.000 9.11 9.11 0.00 4.20
290 291 0.253894 TCGTAGTCCTCCCATGTCGA 59.746 55.000 0.00 0.00 0.00 4.20
291 292 0.663688 CTCGTAGTCCTCCCATGTCG 59.336 60.000 0.00 0.00 0.00 4.35
292 293 1.033574 CCTCGTAGTCCTCCCATGTC 58.966 60.000 0.00 0.00 0.00 3.06
293 294 0.335361 ACCTCGTAGTCCTCCCATGT 59.665 55.000 0.00 0.00 0.00 3.21
294 295 0.747255 CACCTCGTAGTCCTCCCATG 59.253 60.000 0.00 0.00 0.00 3.66
295 296 1.043673 GCACCTCGTAGTCCTCCCAT 61.044 60.000 0.00 0.00 0.00 4.00
296 297 1.681327 GCACCTCGTAGTCCTCCCA 60.681 63.158 0.00 0.00 0.00 4.37
297 298 1.380112 AGCACCTCGTAGTCCTCCC 60.380 63.158 0.00 0.00 0.00 4.30
298 299 0.966370 ACAGCACCTCGTAGTCCTCC 60.966 60.000 0.00 0.00 0.00 4.30
299 300 0.171455 CACAGCACCTCGTAGTCCTC 59.829 60.000 0.00 0.00 0.00 3.71
300 301 1.878656 GCACAGCACCTCGTAGTCCT 61.879 60.000 0.00 0.00 0.00 3.85
301 302 1.446272 GCACAGCACCTCGTAGTCC 60.446 63.158 0.00 0.00 0.00 3.85
302 303 1.446272 GGCACAGCACCTCGTAGTC 60.446 63.158 0.00 0.00 0.00 2.59
303 304 2.207229 TGGCACAGCACCTCGTAGT 61.207 57.895 0.00 0.00 0.00 2.73
304 305 1.738099 GTGGCACAGCACCTCGTAG 60.738 63.158 13.86 0.00 41.80 3.51
305 306 2.342279 GTGGCACAGCACCTCGTA 59.658 61.111 13.86 0.00 41.80 3.43
324 325 3.927163 ATGTCGTCGTCGGGGCAAC 62.927 63.158 1.55 0.00 37.69 4.17
325 326 2.718747 AAATGTCGTCGTCGGGGCAA 62.719 55.000 1.55 0.00 37.69 4.52
326 327 3.229156 AAATGTCGTCGTCGGGGCA 62.229 57.895 1.55 0.24 37.69 5.36
327 328 2.433664 AAATGTCGTCGTCGGGGC 60.434 61.111 1.55 0.00 37.69 5.80
328 329 2.098233 CCAAATGTCGTCGTCGGGG 61.098 63.158 1.55 0.00 37.69 5.73
329 330 2.098233 CCCAAATGTCGTCGTCGGG 61.098 63.158 1.55 0.00 37.69 5.14
330 331 2.098233 CCCCAAATGTCGTCGTCGG 61.098 63.158 1.55 0.00 37.69 4.79
331 332 2.736682 GCCCCAAATGTCGTCGTCG 61.737 63.158 0.00 0.00 38.55 5.12
332 333 2.736682 CGCCCCAAATGTCGTCGTC 61.737 63.158 0.00 0.00 0.00 4.20
333 334 2.718747 TTCGCCCCAAATGTCGTCGT 62.719 55.000 0.00 0.00 0.00 4.34
334 335 1.966493 CTTCGCCCCAAATGTCGTCG 61.966 60.000 0.00 0.00 0.00 5.12
335 336 1.794222 CTTCGCCCCAAATGTCGTC 59.206 57.895 0.00 0.00 0.00 4.20
336 337 2.332654 GCTTCGCCCCAAATGTCGT 61.333 57.895 0.00 0.00 0.00 4.34
337 338 2.257286 CTGCTTCGCCCCAAATGTCG 62.257 60.000 0.00 0.00 0.00 4.35
338 339 1.508088 CTGCTTCGCCCCAAATGTC 59.492 57.895 0.00 0.00 0.00 3.06
339 340 2.639327 GCTGCTTCGCCCCAAATGT 61.639 57.895 0.00 0.00 0.00 2.71
340 341 2.182537 GCTGCTTCGCCCCAAATG 59.817 61.111 0.00 0.00 0.00 2.32
341 342 2.036256 AGCTGCTTCGCCCCAAAT 59.964 55.556 0.00 0.00 0.00 2.32
342 343 2.985282 CAGCTGCTTCGCCCCAAA 60.985 61.111 0.00 0.00 0.00 3.28
359 360 1.138247 CATTCGCCCTTGCTTGAGC 59.862 57.895 0.00 0.00 42.50 4.26
360 361 0.449388 GACATTCGCCCTTGCTTGAG 59.551 55.000 0.00 0.00 34.43 3.02
361 362 0.250684 TGACATTCGCCCTTGCTTGA 60.251 50.000 0.00 0.00 34.43 3.02
362 363 0.109597 GTGACATTCGCCCTTGCTTG 60.110 55.000 0.00 0.00 34.43 4.01
363 364 1.577328 CGTGACATTCGCCCTTGCTT 61.577 55.000 0.00 0.00 34.43 3.91
364 365 2.034879 CGTGACATTCGCCCTTGCT 61.035 57.895 0.00 0.00 34.43 3.91
365 366 2.480555 CGTGACATTCGCCCTTGC 59.519 61.111 0.00 0.00 0.00 4.01
366 367 2.480555 GCGTGACATTCGCCCTTG 59.519 61.111 0.00 0.00 46.61 3.61
372 373 1.126846 GAACTTCAGGCGTGACATTCG 59.873 52.381 8.96 0.00 30.10 3.34
373 374 2.143122 TGAACTTCAGGCGTGACATTC 58.857 47.619 18.42 18.42 30.10 2.67
374 375 2.146342 CTGAACTTCAGGCGTGACATT 58.854 47.619 8.96 6.32 40.71 2.71
375 376 1.344438 TCTGAACTTCAGGCGTGACAT 59.656 47.619 17.12 0.00 44.39 3.06
376 377 0.750249 TCTGAACTTCAGGCGTGACA 59.250 50.000 17.12 2.97 44.39 3.58
377 378 2.086054 ATCTGAACTTCAGGCGTGAC 57.914 50.000 17.12 0.00 44.39 3.67
378 379 2.094182 GGTATCTGAACTTCAGGCGTGA 60.094 50.000 17.12 4.68 44.39 4.35
379 380 2.093973 AGGTATCTGAACTTCAGGCGTG 60.094 50.000 17.12 0.00 44.39 5.34
380 381 2.180276 AGGTATCTGAACTTCAGGCGT 58.820 47.619 17.12 7.84 44.39 5.68
381 382 2.969628 AGGTATCTGAACTTCAGGCG 57.030 50.000 17.12 0.00 44.39 5.52
382 383 5.966742 AAAAAGGTATCTGAACTTCAGGC 57.033 39.130 17.12 8.92 44.39 4.85
410 411 9.730705 AGATATCTGAACTTCATTGTCTCAAAA 57.269 29.630 3.89 0.00 0.00 2.44
411 412 9.159364 CAGATATCTGAACTTCATTGTCTCAAA 57.841 33.333 25.78 0.00 46.59 2.69
412 413 8.713737 CAGATATCTGAACTTCATTGTCTCAA 57.286 34.615 25.78 0.00 46.59 3.02
428 429 5.181009 TGCAAGTTCAGGTTCAGATATCTG 58.819 41.667 24.32 24.32 45.08 2.90
445 446 2.621763 CTTTCAGTCCGCTGCAAGT 58.378 52.632 0.00 0.00 39.83 3.16
447 448 1.785041 GCACTTTCAGTCCGCTGCAA 61.785 55.000 0.00 0.00 42.29 4.08
453 454 1.864862 CTGCTGCACTTTCAGTCCG 59.135 57.895 0.00 0.00 36.49 4.79
491 492 2.728435 GGCCCTCGACCGGTTACAT 61.728 63.158 9.42 0.00 0.00 2.29
499 500 4.410400 CCACTTGGGCCCTCGACC 62.410 72.222 25.70 0.00 0.00 4.79
563 564 0.537188 GATGGCGAGGGAGTTTCTCA 59.463 55.000 0.00 0.00 31.08 3.27
586 587 1.435515 GAGCCGAGCAGACTAGTGG 59.564 63.158 0.00 0.00 0.00 4.00
592 593 3.844090 GGGAGGAGCCGAGCAGAC 61.844 72.222 0.00 0.00 37.63 3.51
653 654 3.058160 TCGAGGACGACGGGGAAC 61.058 66.667 0.00 0.00 43.81 3.62
694 695 0.678366 GGGTGAGCGAGAGAGAGACA 60.678 60.000 0.00 0.00 0.00 3.41
695 696 0.678366 TGGGTGAGCGAGAGAGAGAC 60.678 60.000 0.00 0.00 0.00 3.36
728 729 1.421480 AACCCTAACCCTAGATCGCC 58.579 55.000 0.00 0.00 0.00 5.54
852 853 2.818274 GTACGGGCCGGCAAGAAG 60.818 66.667 31.78 16.02 0.00 2.85
868 869 3.660111 GCCACGAAAAGCAGCGGT 61.660 61.111 0.00 0.00 0.00 5.68
890 891 1.005037 CCGTAGCAGGAGCACACAA 60.005 57.895 0.00 0.00 45.49 3.33
900 901 0.528684 GGAGTAAGCAGCCGTAGCAG 60.529 60.000 0.00 0.00 43.56 4.24
919 920 2.661566 CCTGCACGACACAGAAGCG 61.662 63.158 0.00 0.00 37.32 4.68
923 924 1.832608 AGTCCCTGCACGACACAGA 60.833 57.895 10.90 0.00 37.32 3.41
949 956 2.383527 GGCAGAAGGAACGACGCAG 61.384 63.158 0.00 0.00 0.00 5.18
983 990 2.948979 GGCATGTGGTTAATTCGATCCA 59.051 45.455 0.00 0.00 0.00 3.41
1030 1037 0.322008 CAGGGGACAAGCAAGAGGAC 60.322 60.000 0.00 0.00 0.00 3.85
1095 1102 2.194597 GCACCACACCCCTTGTCA 59.805 61.111 0.00 0.00 35.67 3.58
1181 1188 1.226030 GAACACGTCGGGGGTTTCAG 61.226 60.000 0.00 0.00 0.00 3.02
1274 1281 4.436584 GCTTGTTGAATCTCGGAGTGAATG 60.437 45.833 4.69 0.00 32.30 2.67
1275 1282 3.686726 GCTTGTTGAATCTCGGAGTGAAT 59.313 43.478 4.69 0.00 32.30 2.57
1552 1559 1.063616 TCTCGGAATCATCACGTCGTC 59.936 52.381 0.00 0.00 0.00 4.20
1643 1655 7.719871 AGAGGTAACAAACTAAGCATAGAGA 57.280 36.000 2.38 0.00 41.41 3.10
1749 1761 7.364522 TGAAATTATTGTTTGTCTCTCTCCG 57.635 36.000 0.00 0.00 0.00 4.63
1812 1824 2.560542 AGTATGATCTAAGCAGCCCGAG 59.439 50.000 0.00 0.00 0.00 4.63
1813 1825 2.598565 AGTATGATCTAAGCAGCCCGA 58.401 47.619 0.00 0.00 0.00 5.14
1846 1858 2.299867 GCACATCCCCAAGTCACAAAAT 59.700 45.455 0.00 0.00 0.00 1.82
1926 1938 0.892755 AATCAGTTGGCAGCATGTGG 59.107 50.000 3.63 0.00 39.31 4.17
1960 1972 7.517614 TGGTTATGTTGCAGAATAAACTCAA 57.482 32.000 15.52 0.00 29.13 3.02
2021 2033 5.967088 TCAAGCAGTAAGACTAGGAATCAC 58.033 41.667 0.00 0.00 0.00 3.06
2033 2045 5.061808 GGTACGTGTGTAATCAAGCAGTAAG 59.938 44.000 0.00 0.00 30.94 2.34
2096 2108 1.134640 CATCACCCATCCCGACGTTTA 60.135 52.381 0.00 0.00 0.00 2.01
2170 2182 5.417580 GCAGGGGAGAGATAGATACAGTTAG 59.582 48.000 0.00 0.00 0.00 2.34
2285 2299 4.322725 CCTTGTCGCTTATATATGGAGCCA 60.323 45.833 13.94 0.00 32.90 4.75
2286 2300 4.081642 TCCTTGTCGCTTATATATGGAGCC 60.082 45.833 13.94 5.38 32.90 4.70
2287 2301 4.865365 GTCCTTGTCGCTTATATATGGAGC 59.135 45.833 11.06 11.06 0.00 4.70
2288 2302 5.186021 AGGTCCTTGTCGCTTATATATGGAG 59.814 44.000 0.00 0.00 0.00 3.86
2289 2303 5.084519 AGGTCCTTGTCGCTTATATATGGA 58.915 41.667 0.00 0.00 0.00 3.41
2290 2304 5.407407 AGGTCCTTGTCGCTTATATATGG 57.593 43.478 0.00 0.00 0.00 2.74
2291 2305 7.603651 ACTAAGGTCCTTGTCGCTTATATATG 58.396 38.462 14.84 0.00 0.00 1.78
2292 2306 7.778185 ACTAAGGTCCTTGTCGCTTATATAT 57.222 36.000 14.84 0.00 0.00 0.86
2293 2307 7.286087 TGAACTAAGGTCCTTGTCGCTTATATA 59.714 37.037 14.84 0.00 0.00 0.86
2294 2308 6.097839 TGAACTAAGGTCCTTGTCGCTTATAT 59.902 38.462 14.84 0.00 0.00 0.86
2295 2309 5.419788 TGAACTAAGGTCCTTGTCGCTTATA 59.580 40.000 14.84 0.00 0.00 0.98
2296 2310 4.222145 TGAACTAAGGTCCTTGTCGCTTAT 59.778 41.667 14.84 0.00 0.00 1.73
2297 2311 3.575256 TGAACTAAGGTCCTTGTCGCTTA 59.425 43.478 14.84 0.00 0.00 3.09
2298 2312 2.367567 TGAACTAAGGTCCTTGTCGCTT 59.632 45.455 14.84 0.00 0.00 4.68
2299 2313 1.968493 TGAACTAAGGTCCTTGTCGCT 59.032 47.619 14.84 0.00 0.00 4.93
2323 2337 4.321899 GGCCAGCTGATGTAAATGAAACAA 60.322 41.667 17.39 0.00 0.00 2.83
2339 2353 5.189934 AGAAGTAGTTAACATTAGGCCAGCT 59.810 40.000 5.01 0.00 0.00 4.24
2345 2359 6.978659 TCGATGCAGAAGTAGTTAACATTAGG 59.021 38.462 8.61 0.00 0.00 2.69
2357 2371 5.532557 CAGGATAATGTCGATGCAGAAGTA 58.467 41.667 0.00 0.00 0.00 2.24
2366 2380 2.608998 CGCAGAGCAGGATAATGTCGAT 60.609 50.000 0.00 0.00 0.00 3.59
2386 2400 2.287915 GGCAGCAATACCAAGTATGACG 59.712 50.000 0.00 0.00 0.00 4.35
2387 2401 3.545703 AGGCAGCAATACCAAGTATGAC 58.454 45.455 0.00 0.00 0.00 3.06
2401 2415 1.073125 TGCTTGTAAAGGTAGGCAGCA 59.927 47.619 0.00 0.00 46.35 4.41
2420 2434 6.974965 AGTTTCTTGGCAGAGAAATTACTTG 58.025 36.000 20.05 0.00 44.73 3.16
2516 2556 1.165270 GGTAACAATCAAGCAGGCGT 58.835 50.000 0.00 0.00 0.00 5.68
2662 2729 2.027745 ACAGCAGGACATGACAAGTAGG 60.028 50.000 0.00 0.00 0.00 3.18
2857 2944 4.499696 GCAACATATACATGGCCAGGTTTC 60.500 45.833 30.28 3.81 36.39 2.78
2881 3031 0.178932 AAAGAAAGGCCCCAGGGAAC 60.179 55.000 7.25 0.00 37.50 3.62
2908 3058 2.917933 TGTGACCTGTGAGTTCTTTGG 58.082 47.619 0.00 0.00 0.00 3.28
2967 3125 3.129287 CGCATGACTAGCCTTTGGATTTT 59.871 43.478 0.00 0.00 0.00 1.82
3176 3355 8.915871 AATTGGTCATAGAAAACATTTGATCG 57.084 30.769 0.00 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.