Multiple sequence alignment - TraesCS4B01G385700

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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 TraesCS4B01G385700 chr4B 100.000 3548 0 0 1 3548 664676686 664680233 0.000000e+00 6553
1 TraesCS4B01G385700 chr4B 95.996 2672 89 8 539 3199 663901516 663904180 0.000000e+00 4325
2 TraesCS4B01G385700 chr4B 92.515 334 20 4 1 332 499727230 499726900 1.150000e-129 473
3 TraesCS4B01G385700 chr4B 92.492 333 22 2 1 332 535411515 535411845 1.150000e-129 473
4 TraesCS4B01G385700 chr4B 92.308 221 8 2 332 543 663901074 663901294 4.450000e-79 305
5 TraesCS4B01G385700 chr4B 88.785 214 14 3 3290 3494 663904471 663904683 1.630000e-63 254
6 TraesCS4B01G385700 chr5A 87.950 1444 172 2 1037 2479 703471105 703472547 0.000000e+00 1701
7 TraesCS4B01G385700 chr5A 80.551 617 87 19 2957 3548 703472721 703473329 9.040000e-121 444
8 TraesCS4B01G385700 chr5A 80.796 427 56 16 2527 2948 703472546 703472951 9.560000e-81 311
9 TraesCS4B01G385700 chr1B 80.575 1462 281 3 1046 2505 50950622 50952082 0.000000e+00 1123
10 TraesCS4B01G385700 chr4D 84.559 1101 146 15 1853 2948 507001772 507002853 0.000000e+00 1070
11 TraesCS4B01G385700 chr4D 91.813 342 24 3 1 341 219676677 219676339 1.150000e-129 473
12 TraesCS4B01G385700 chr4D 79.276 608 85 23 2957 3541 507002621 507003210 1.540000e-103 387
13 TraesCS4B01G385700 chr4D 90.795 239 21 1 1037 1275 507001540 507001777 5.720000e-83 318
14 TraesCS4B01G385700 chr7D 80.041 1458 275 12 1062 2511 497320654 497319205 0.000000e+00 1066
15 TraesCS4B01G385700 chr4A 79.932 1460 281 11 1058 2511 702327744 702326291 0.000000e+00 1062
16 TraesCS4B01G385700 chr7A 79.589 1460 286 12 1058 2511 29009191 29007738 0.000000e+00 1035
17 TraesCS4B01G385700 chr7A 78.919 1461 295 13 1058 2511 28808875 28807421 0.000000e+00 979
18 TraesCS4B01G385700 chr7A 78.850 1461 296 13 1058 2511 28845676 28844222 0.000000e+00 974
19 TraesCS4B01G385700 chr3B 77.603 1460 290 27 1057 2508 6963217 6961787 0.000000e+00 850
20 TraesCS4B01G385700 chr3B 92.447 331 21 3 3 332 222858320 222858647 1.490000e-128 470
21 TraesCS4B01G385700 chr2B 93.072 332 20 2 1 331 461652026 461651697 1.920000e-132 483
22 TraesCS4B01G385700 chr2B 91.354 347 26 3 1 345 302700977 302700633 4.150000e-129 472
23 TraesCS4B01G385700 chrUn 91.643 347 24 3 1 344 288620896 288621240 3.210000e-130 475
24 TraesCS4B01G385700 chrUn 91.643 347 24 3 1 344 341867919 341868263 3.210000e-130 475
25 TraesCS4B01G385700 chr3D 92.192 333 23 2 1 332 180494095 180493765 5.360000e-128 468


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 TraesCS4B01G385700 chr4B 664676686 664680233 3547 False 6553.000000 6553 100.000000 1 3548 1 chr4B.!!$F2 3547
1 TraesCS4B01G385700 chr4B 663901074 663904683 3609 False 1628.000000 4325 92.363000 332 3494 3 chr4B.!!$F3 3162
2 TraesCS4B01G385700 chr5A 703471105 703473329 2224 False 818.666667 1701 83.099000 1037 3548 3 chr5A.!!$F1 2511
3 TraesCS4B01G385700 chr1B 50950622 50952082 1460 False 1123.000000 1123 80.575000 1046 2505 1 chr1B.!!$F1 1459
4 TraesCS4B01G385700 chr4D 507001540 507003210 1670 False 591.666667 1070 84.876667 1037 3541 3 chr4D.!!$F1 2504
5 TraesCS4B01G385700 chr7D 497319205 497320654 1449 True 1066.000000 1066 80.041000 1062 2511 1 chr7D.!!$R1 1449
6 TraesCS4B01G385700 chr4A 702326291 702327744 1453 True 1062.000000 1062 79.932000 1058 2511 1 chr4A.!!$R1 1453
7 TraesCS4B01G385700 chr7A 29007738 29009191 1453 True 1035.000000 1035 79.589000 1058 2511 1 chr7A.!!$R3 1453
8 TraesCS4B01G385700 chr7A 28807421 28808875 1454 True 979.000000 979 78.919000 1058 2511 1 chr7A.!!$R1 1453
9 TraesCS4B01G385700 chr7A 28844222 28845676 1454 True 974.000000 974 78.850000 1058 2511 1 chr7A.!!$R2 1453
10 TraesCS4B01G385700 chr3B 6961787 6963217 1430 True 850.000000 850 77.603000 1057 2508 1 chr3B.!!$R1 1451

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
299 300 0.035439 AGGGATAAACCTGCCGTGTG 60.035 55.0 0.00 0.0 40.04 3.82 F
535 545 0.038159 AGGCGTCTGTTGTAGTGCTC 60.038 55.0 0.00 0.0 0.00 4.26 F
618 857 0.039165 GCAAAAGGGAAGAAGGCGTG 60.039 55.0 0.00 0.0 0.00 5.34 F
1118 1362 0.254178 AAGGCTGCCGACTTCATCAT 59.746 50.0 13.96 0.0 30.96 2.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1849 2093 0.320858 TTAAACATGGCCGCGACAGA 60.321 50.0 8.23 0.00 0.00 3.41 R
2389 2634 0.042731 TGTGCTAGGTAGGCCTTCCT 59.957 55.0 31.25 31.25 44.18 3.36 R
2515 2760 2.158249 TCTCCTCCCCATCGATGATCTT 60.158 50.0 26.86 0.00 0.00 2.40 R
2624 2869 0.246360 AACGACTGCACGGATCATGA 59.754 50.0 0.00 0.00 37.61 3.07 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
61 62 8.890124 ACTATTCATGCTATGATGATATGAGC 57.110 34.615 0.00 0.00 39.39 4.26
62 63 8.706521 ACTATTCATGCTATGATGATATGAGCT 58.293 33.333 0.00 0.00 39.39 4.09
65 66 9.901172 ATTCATGCTATGATGATATGAGCTAAA 57.099 29.630 0.00 0.00 39.39 1.85
66 67 9.729281 TTCATGCTATGATGATATGAGCTAAAA 57.271 29.630 0.00 0.00 39.39 1.52
67 68 9.901172 TCATGCTATGATGATATGAGCTAAAAT 57.099 29.630 0.00 0.00 33.59 1.82
70 71 9.729281 TGCTATGATGATATGAGCTAAAATTGA 57.271 29.630 0.00 0.00 34.19 2.57
76 77 9.635520 GATGATATGAGCTAAAATTGAAATGGG 57.364 33.333 0.00 0.00 0.00 4.00
77 78 7.954835 TGATATGAGCTAAAATTGAAATGGGG 58.045 34.615 0.00 0.00 0.00 4.96
78 79 7.784073 TGATATGAGCTAAAATTGAAATGGGGA 59.216 33.333 0.00 0.00 0.00 4.81
79 80 5.659440 TGAGCTAAAATTGAAATGGGGAC 57.341 39.130 0.00 0.00 0.00 4.46
80 81 5.332743 TGAGCTAAAATTGAAATGGGGACT 58.667 37.500 0.00 0.00 0.00 3.85
81 82 5.185635 TGAGCTAAAATTGAAATGGGGACTG 59.814 40.000 0.00 0.00 0.00 3.51
82 83 4.467438 AGCTAAAATTGAAATGGGGACTGG 59.533 41.667 0.00 0.00 0.00 4.00
83 84 3.701205 AAAATTGAAATGGGGACTGGC 57.299 42.857 0.00 0.00 0.00 4.85
84 85 2.629017 AATTGAAATGGGGACTGGCT 57.371 45.000 0.00 0.00 0.00 4.75
85 86 3.756082 AATTGAAATGGGGACTGGCTA 57.244 42.857 0.00 0.00 0.00 3.93
86 87 3.756082 ATTGAAATGGGGACTGGCTAA 57.244 42.857 0.00 0.00 0.00 3.09
87 88 2.507407 TGAAATGGGGACTGGCTAAC 57.493 50.000 0.00 0.00 0.00 2.34
88 89 1.707989 TGAAATGGGGACTGGCTAACA 59.292 47.619 0.00 0.00 0.00 2.41
89 90 2.092323 GAAATGGGGACTGGCTAACAC 58.908 52.381 0.00 0.00 0.00 3.32
90 91 1.372501 AATGGGGACTGGCTAACACT 58.627 50.000 0.00 0.00 0.00 3.55
91 92 1.372501 ATGGGGACTGGCTAACACTT 58.627 50.000 0.00 0.00 0.00 3.16
92 93 1.145571 TGGGGACTGGCTAACACTTT 58.854 50.000 0.00 0.00 0.00 2.66
93 94 1.497286 TGGGGACTGGCTAACACTTTT 59.503 47.619 0.00 0.00 0.00 2.27
94 95 2.091555 TGGGGACTGGCTAACACTTTTT 60.092 45.455 0.00 0.00 0.00 1.94
126 127 6.969366 GCAAATAACATGCACATATAGGTGA 58.031 36.000 21.10 6.89 43.29 4.02
127 128 7.596494 GCAAATAACATGCACATATAGGTGAT 58.404 34.615 21.10 8.79 43.29 3.06
128 129 7.539710 GCAAATAACATGCACATATAGGTGATG 59.460 37.037 21.10 19.99 43.29 3.07
129 130 6.748333 ATAACATGCACATATAGGTGATGC 57.252 37.500 21.10 6.61 41.32 3.91
130 131 4.362470 ACATGCACATATAGGTGATGCT 57.638 40.909 21.10 9.31 41.32 3.79
131 132 4.722220 ACATGCACATATAGGTGATGCTT 58.278 39.130 21.10 1.75 41.32 3.91
132 133 5.135383 ACATGCACATATAGGTGATGCTTT 58.865 37.500 21.10 4.38 41.32 3.51
133 134 5.595542 ACATGCACATATAGGTGATGCTTTT 59.404 36.000 21.10 4.09 41.32 2.27
134 135 5.756195 TGCACATATAGGTGATGCTTTTC 57.244 39.130 21.10 1.55 41.32 2.29
135 136 5.439721 TGCACATATAGGTGATGCTTTTCT 58.560 37.500 21.10 0.00 41.32 2.52
136 137 5.297527 TGCACATATAGGTGATGCTTTTCTG 59.702 40.000 21.10 0.00 41.32 3.02
137 138 5.528690 GCACATATAGGTGATGCTTTTCTGA 59.471 40.000 21.10 0.00 41.32 3.27
138 139 6.038603 GCACATATAGGTGATGCTTTTCTGAA 59.961 38.462 21.10 0.00 41.32 3.02
139 140 7.412853 CACATATAGGTGATGCTTTTCTGAAC 58.587 38.462 12.10 0.00 41.32 3.18
140 141 7.066163 CACATATAGGTGATGCTTTTCTGAACA 59.934 37.037 12.10 0.00 41.32 3.18
141 142 7.776969 ACATATAGGTGATGCTTTTCTGAACAT 59.223 33.333 0.00 0.00 0.00 2.71
142 143 8.627403 CATATAGGTGATGCTTTTCTGAACATT 58.373 33.333 0.00 0.00 0.00 2.71
143 144 5.796424 AGGTGATGCTTTTCTGAACATTT 57.204 34.783 0.00 0.00 0.00 2.32
144 145 6.165700 AGGTGATGCTTTTCTGAACATTTT 57.834 33.333 0.00 0.00 0.00 1.82
145 146 5.987347 AGGTGATGCTTTTCTGAACATTTTG 59.013 36.000 0.00 0.00 0.00 2.44
146 147 5.984926 GGTGATGCTTTTCTGAACATTTTGA 59.015 36.000 0.00 0.00 0.00 2.69
147 148 6.647895 GGTGATGCTTTTCTGAACATTTTGAT 59.352 34.615 0.00 0.00 0.00 2.57
148 149 7.814107 GGTGATGCTTTTCTGAACATTTTGATA 59.186 33.333 0.00 0.00 0.00 2.15
149 150 9.362539 GTGATGCTTTTCTGAACATTTTGATAT 57.637 29.630 0.00 0.00 0.00 1.63
150 151 9.577110 TGATGCTTTTCTGAACATTTTGATATC 57.423 29.630 0.00 0.00 0.00 1.63
151 152 9.798994 GATGCTTTTCTGAACATTTTGATATCT 57.201 29.630 3.98 0.00 0.00 1.98
208 209 9.912634 TTTTATGAAGTTTTCCAAGTGATGATC 57.087 29.630 0.00 0.00 0.00 2.92
209 210 8.634335 TTATGAAGTTTTCCAAGTGATGATCA 57.366 30.769 0.00 0.00 0.00 2.92
210 211 6.957920 TGAAGTTTTCCAAGTGATGATCAA 57.042 33.333 0.00 0.00 0.00 2.57
211 212 7.345422 TGAAGTTTTCCAAGTGATGATCAAA 57.655 32.000 0.00 0.00 0.00 2.69
212 213 7.202526 TGAAGTTTTCCAAGTGATGATCAAAC 58.797 34.615 0.00 1.18 0.00 2.93
213 214 5.762045 AGTTTTCCAAGTGATGATCAAACG 58.238 37.500 0.00 0.00 32.07 3.60
214 215 4.764679 TTTCCAAGTGATGATCAAACGG 57.235 40.909 0.00 0.00 0.00 4.44
215 216 3.417069 TCCAAGTGATGATCAAACGGT 57.583 42.857 0.00 0.00 0.00 4.83
216 217 3.334691 TCCAAGTGATGATCAAACGGTC 58.665 45.455 0.00 0.00 0.00 4.79
217 218 3.073678 CCAAGTGATGATCAAACGGTCA 58.926 45.455 0.00 0.00 0.00 4.02
218 219 3.501828 CCAAGTGATGATCAAACGGTCAA 59.498 43.478 0.00 0.00 0.00 3.18
219 220 4.023279 CCAAGTGATGATCAAACGGTCAAA 60.023 41.667 0.00 0.00 0.00 2.69
220 221 5.149273 CAAGTGATGATCAAACGGTCAAAG 58.851 41.667 0.00 0.00 0.00 2.77
221 222 3.753272 AGTGATGATCAAACGGTCAAAGG 59.247 43.478 0.00 0.00 0.00 3.11
222 223 3.081061 TGATGATCAAACGGTCAAAGGG 58.919 45.455 0.00 0.00 0.00 3.95
223 224 1.243902 TGATCAAACGGTCAAAGGGC 58.756 50.000 0.00 0.00 0.00 5.19
224 225 1.243902 GATCAAACGGTCAAAGGGCA 58.756 50.000 0.00 0.00 0.00 5.36
225 226 1.611491 GATCAAACGGTCAAAGGGCAA 59.389 47.619 0.00 0.00 0.00 4.52
226 227 1.698506 TCAAACGGTCAAAGGGCAAT 58.301 45.000 0.00 0.00 0.00 3.56
227 228 2.865079 TCAAACGGTCAAAGGGCAATA 58.135 42.857 0.00 0.00 0.00 1.90
228 229 2.817258 TCAAACGGTCAAAGGGCAATAG 59.183 45.455 0.00 0.00 0.00 1.73
229 230 1.173913 AACGGTCAAAGGGCAATAGC 58.826 50.000 0.00 0.00 41.10 2.97
230 231 0.037590 ACGGTCAAAGGGCAATAGCA 59.962 50.000 0.00 0.00 44.61 3.49
231 232 1.340991 ACGGTCAAAGGGCAATAGCAT 60.341 47.619 0.00 0.00 44.61 3.79
232 233 2.092646 ACGGTCAAAGGGCAATAGCATA 60.093 45.455 0.00 0.00 44.61 3.14
233 234 2.948979 CGGTCAAAGGGCAATAGCATAA 59.051 45.455 0.00 0.00 44.61 1.90
234 235 3.003689 CGGTCAAAGGGCAATAGCATAAG 59.996 47.826 0.00 0.00 44.61 1.73
235 236 4.207165 GGTCAAAGGGCAATAGCATAAGA 58.793 43.478 0.00 0.00 44.61 2.10
236 237 4.276926 GGTCAAAGGGCAATAGCATAAGAG 59.723 45.833 0.00 0.00 44.61 2.85
237 238 4.276926 GTCAAAGGGCAATAGCATAAGAGG 59.723 45.833 0.00 0.00 44.61 3.69
238 239 4.165950 TCAAAGGGCAATAGCATAAGAGGA 59.834 41.667 0.00 0.00 44.61 3.71
239 240 4.363991 AAGGGCAATAGCATAAGAGGAG 57.636 45.455 0.00 0.00 44.61 3.69
240 241 2.039613 AGGGCAATAGCATAAGAGGAGC 59.960 50.000 0.00 0.00 44.61 4.70
241 242 2.224621 GGGCAATAGCATAAGAGGAGCA 60.225 50.000 0.00 0.00 44.61 4.26
242 243 3.480470 GGCAATAGCATAAGAGGAGCAA 58.520 45.455 0.00 0.00 44.61 3.91
243 244 3.885297 GGCAATAGCATAAGAGGAGCAAA 59.115 43.478 0.00 0.00 44.61 3.68
244 245 4.339247 GGCAATAGCATAAGAGGAGCAAAA 59.661 41.667 0.00 0.00 44.61 2.44
245 246 5.010415 GGCAATAGCATAAGAGGAGCAAAAT 59.990 40.000 0.00 0.00 44.61 1.82
246 247 5.919141 GCAATAGCATAAGAGGAGCAAAATG 59.081 40.000 0.00 0.00 41.58 2.32
247 248 6.238842 GCAATAGCATAAGAGGAGCAAAATGA 60.239 38.462 0.00 0.00 41.58 2.57
248 249 7.523380 GCAATAGCATAAGAGGAGCAAAATGAT 60.523 37.037 0.00 0.00 41.58 2.45
249 250 8.358148 CAATAGCATAAGAGGAGCAAAATGATT 58.642 33.333 0.00 0.00 0.00 2.57
250 251 6.786967 AGCATAAGAGGAGCAAAATGATTT 57.213 33.333 0.00 0.00 0.00 2.17
252 253 5.751990 GCATAAGAGGAGCAAAATGATTTGG 59.248 40.000 0.00 0.00 44.93 3.28
261 262 4.630111 GCAAAATGATTTGGTCAGGAACA 58.370 39.130 0.00 0.00 44.93 3.18
262 263 5.055812 GCAAAATGATTTGGTCAGGAACAA 58.944 37.500 0.00 0.00 44.93 2.83
263 264 5.178067 GCAAAATGATTTGGTCAGGAACAAG 59.822 40.000 0.00 0.00 44.93 3.16
264 265 6.282930 CAAAATGATTTGGTCAGGAACAAGT 58.717 36.000 0.00 0.00 41.81 3.16
265 266 5.458041 AATGATTTGGTCAGGAACAAGTG 57.542 39.130 0.00 0.00 39.45 3.16
266 267 3.897239 TGATTTGGTCAGGAACAAGTGT 58.103 40.909 0.00 0.00 39.45 3.55
267 268 4.277476 TGATTTGGTCAGGAACAAGTGTT 58.723 39.130 0.00 0.00 39.45 3.32
268 269 4.709397 TGATTTGGTCAGGAACAAGTGTTT 59.291 37.500 0.00 0.00 39.45 2.83
269 270 4.712122 TTTGGTCAGGAACAAGTGTTTC 57.288 40.909 0.00 0.00 39.45 2.78
270 271 2.650322 TGGTCAGGAACAAGTGTTTCC 58.350 47.619 0.00 2.02 38.56 3.13
271 272 1.602377 GGTCAGGAACAAGTGTTTCCG 59.398 52.381 0.00 0.00 38.56 4.30
272 273 1.602377 GTCAGGAACAAGTGTTTCCGG 59.398 52.381 0.00 0.00 38.56 5.14
273 274 1.487142 TCAGGAACAAGTGTTTCCGGA 59.513 47.619 0.00 0.00 38.56 5.14
274 275 2.092861 TCAGGAACAAGTGTTTCCGGAA 60.093 45.455 14.35 14.35 38.56 4.30
275 276 2.685897 CAGGAACAAGTGTTTCCGGAAA 59.314 45.455 25.67 25.67 38.56 3.13
276 277 3.129638 CAGGAACAAGTGTTTCCGGAAAA 59.870 43.478 30.49 17.66 38.56 2.29
277 278 3.764972 AGGAACAAGTGTTTCCGGAAAAA 59.235 39.130 30.49 23.58 38.56 1.94
278 279 4.109766 GGAACAAGTGTTTCCGGAAAAAG 58.890 43.478 30.49 16.19 38.56 2.27
279 280 4.381185 GGAACAAGTGTTTCCGGAAAAAGT 60.381 41.667 30.49 25.02 38.56 2.66
280 281 5.163632 GGAACAAGTGTTTCCGGAAAAAGTA 60.164 40.000 30.49 14.62 38.56 2.24
281 282 5.494632 ACAAGTGTTTCCGGAAAAAGTAG 57.505 39.130 30.49 21.20 31.33 2.57
282 283 4.337274 ACAAGTGTTTCCGGAAAAAGTAGG 59.663 41.667 30.49 23.19 31.33 3.18
283 284 3.483421 AGTGTTTCCGGAAAAAGTAGGG 58.517 45.455 30.49 0.00 31.33 3.53
284 285 3.136992 AGTGTTTCCGGAAAAAGTAGGGA 59.863 43.478 30.49 2.95 31.33 4.20
285 286 4.077108 GTGTTTCCGGAAAAAGTAGGGAT 58.923 43.478 30.49 0.00 31.33 3.85
286 287 5.013391 AGTGTTTCCGGAAAAAGTAGGGATA 59.987 40.000 30.49 1.54 31.33 2.59
287 288 5.706833 GTGTTTCCGGAAAAAGTAGGGATAA 59.293 40.000 30.49 1.31 31.33 1.75
288 289 6.207221 GTGTTTCCGGAAAAAGTAGGGATAAA 59.793 38.462 30.49 0.82 31.33 1.40
289 290 6.207221 TGTTTCCGGAAAAAGTAGGGATAAAC 59.793 38.462 30.49 14.25 31.33 2.01
290 291 4.847198 TCCGGAAAAAGTAGGGATAAACC 58.153 43.478 0.00 0.00 38.08 3.27
291 292 4.537288 TCCGGAAAAAGTAGGGATAAACCT 59.463 41.667 0.00 0.00 44.75 3.50
292 293 4.638865 CCGGAAAAAGTAGGGATAAACCTG 59.361 45.833 0.00 0.00 42.02 4.00
293 294 4.095932 CGGAAAAAGTAGGGATAAACCTGC 59.904 45.833 0.00 0.00 42.02 4.85
294 295 4.401519 GGAAAAAGTAGGGATAAACCTGCC 59.598 45.833 0.00 0.00 43.41 4.85
295 296 3.277142 AAAGTAGGGATAAACCTGCCG 57.723 47.619 0.00 0.00 43.41 5.69
296 297 1.875488 AGTAGGGATAAACCTGCCGT 58.125 50.000 0.00 0.00 43.41 5.68
297 298 1.485066 AGTAGGGATAAACCTGCCGTG 59.515 52.381 0.00 0.00 43.41 4.94
298 299 1.208776 GTAGGGATAAACCTGCCGTGT 59.791 52.381 0.00 0.00 42.02 4.49
299 300 0.035439 AGGGATAAACCTGCCGTGTG 60.035 55.000 0.00 0.00 40.04 3.82
300 301 0.322187 GGGATAAACCTGCCGTGTGT 60.322 55.000 0.00 0.00 38.98 3.72
301 302 0.802494 GGATAAACCTGCCGTGTGTG 59.198 55.000 0.00 0.00 35.41 3.82
302 303 1.609580 GGATAAACCTGCCGTGTGTGA 60.610 52.381 0.00 0.00 35.41 3.58
303 304 1.463444 GATAAACCTGCCGTGTGTGAC 59.537 52.381 0.00 0.00 0.00 3.67
304 305 0.533308 TAAACCTGCCGTGTGTGACC 60.533 55.000 0.00 0.00 0.00 4.02
305 306 3.767630 AACCTGCCGTGTGTGACCC 62.768 63.158 0.00 0.00 0.00 4.46
306 307 4.248842 CCTGCCGTGTGTGACCCA 62.249 66.667 0.00 0.00 0.00 4.51
307 308 2.203139 CTGCCGTGTGTGACCCAA 60.203 61.111 0.00 0.00 0.00 4.12
308 309 2.515057 TGCCGTGTGTGACCCAAC 60.515 61.111 0.00 0.00 0.00 3.77
309 310 2.203153 GCCGTGTGTGACCCAACT 60.203 61.111 0.00 0.00 0.00 3.16
310 311 1.070105 GCCGTGTGTGACCCAACTA 59.930 57.895 0.00 0.00 0.00 2.24
311 312 0.949105 GCCGTGTGTGACCCAACTAG 60.949 60.000 0.00 0.00 0.00 2.57
312 313 0.320421 CCGTGTGTGACCCAACTAGG 60.320 60.000 0.00 0.00 37.03 3.02
327 328 6.484364 CCAACTAGGGGCATAAAATCAATT 57.516 37.500 0.00 0.00 0.00 2.32
328 329 7.595819 CCAACTAGGGGCATAAAATCAATTA 57.404 36.000 0.00 0.00 0.00 1.40
329 330 8.193953 CCAACTAGGGGCATAAAATCAATTAT 57.806 34.615 0.00 0.00 0.00 1.28
330 331 8.306761 CCAACTAGGGGCATAAAATCAATTATC 58.693 37.037 0.00 0.00 0.00 1.75
361 362 5.435686 TTGCAGGTGAAGTTATAGGTCAT 57.564 39.130 0.00 0.00 0.00 3.06
370 371 8.237267 GGTGAAGTTATAGGTCATTTGTTGAAG 58.763 37.037 0.00 0.00 35.70 3.02
376 379 9.255304 GTTATAGGTCATTTGTTGAAGCAAAAA 57.745 29.630 0.00 0.00 41.03 1.94
411 414 4.193334 TGCGCGAGGACCTGATCG 62.193 66.667 12.10 0.00 41.79 3.69
413 416 2.831366 GCGCGAGGACCTGATCGTA 61.831 63.158 12.10 0.00 40.97 3.43
472 475 0.650512 CATGTACGCCGCACCTTTAG 59.349 55.000 0.00 0.00 0.00 1.85
533 543 0.790814 GAAGGCGTCTGTTGTAGTGC 59.209 55.000 0.00 0.00 0.00 4.40
535 545 0.038159 AGGCGTCTGTTGTAGTGCTC 60.038 55.000 0.00 0.00 0.00 4.26
543 553 2.164422 CTGTTGTAGTGCTCGGATCTCA 59.836 50.000 0.00 0.00 0.00 3.27
544 554 2.094700 TGTTGTAGTGCTCGGATCTCAC 60.095 50.000 0.00 0.00 0.00 3.51
545 555 0.733150 TGTAGTGCTCGGATCTCACG 59.267 55.000 0.00 0.00 35.97 4.35
547 557 1.029947 TAGTGCTCGGATCTCACGCA 61.030 55.000 0.00 0.00 35.97 5.24
548 558 2.161486 GTGCTCGGATCTCACGCAC 61.161 63.158 11.83 11.83 43.22 5.34
549 559 2.951745 GCTCGGATCTCACGCACG 60.952 66.667 0.00 0.00 0.00 5.34
550 560 2.485582 CTCGGATCTCACGCACGT 59.514 61.111 0.00 0.00 0.00 4.49
551 561 1.583967 CTCGGATCTCACGCACGTC 60.584 63.158 0.00 0.00 0.00 4.34
553 563 1.443702 CGGATCTCACGCACGTCAA 60.444 57.895 0.00 0.00 0.00 3.18
554 564 1.674611 CGGATCTCACGCACGTCAAC 61.675 60.000 0.00 0.00 0.00 3.18
618 857 0.039165 GCAAAAGGGAAGAAGGCGTG 60.039 55.000 0.00 0.00 0.00 5.34
685 927 5.363005 AGGTTGCACGTATATTTCTACCTCT 59.637 40.000 0.00 0.00 29.33 3.69
707 949 1.001048 GGAACCAGCCGTTACAAAACC 60.001 52.381 0.00 0.00 35.11 3.27
714 956 3.810941 CAGCCGTTACAAAACCTTACTGA 59.189 43.478 0.00 0.00 31.46 3.41
798 1040 0.885196 GCAACAGATTTTACCCGGCA 59.115 50.000 0.00 0.00 0.00 5.69
991 1234 8.137437 CACAAGTCAACAACTTAATTTGATCCT 58.863 33.333 12.06 0.78 46.69 3.24
1039 1282 4.065281 CCCCTTCGTTCGACGCCT 62.065 66.667 0.00 0.00 42.21 5.52
1118 1362 0.254178 AAGGCTGCCGACTTCATCAT 59.746 50.000 13.96 0.00 30.96 2.45
1137 1381 3.196901 TCATGGATTACTACACCAGCGTT 59.803 43.478 0.00 0.00 37.12 4.84
1254 1498 0.820226 TGAAGGAGCTGAGGACATCG 59.180 55.000 0.00 0.00 0.00 3.84
1509 1753 2.187946 GGAGGCGGTGTCATCCTG 59.812 66.667 0.00 0.00 0.00 3.86
1641 1885 2.828868 GGCCAGACACACTCCACA 59.171 61.111 0.00 0.00 0.00 4.17
1703 1947 1.382009 TCCGATCCATTCCCACCGA 60.382 57.895 0.00 0.00 0.00 4.69
1803 2047 1.413767 CGTACATCTGCGCCACTGTC 61.414 60.000 4.18 0.00 0.00 3.51
1849 2093 2.429058 CAGTGAGCACAGTGGCCT 59.571 61.111 10.80 0.00 42.00 5.19
1893 2137 1.153289 GGTCCATGTCGATGCTGCT 60.153 57.895 0.00 0.00 0.00 4.24
2043 2287 3.103911 GACACGAACCGCCTCACG 61.104 66.667 0.00 0.00 43.15 4.35
2385 2630 2.032178 GCTGATTAACCGGCTCAACATC 59.968 50.000 0.00 0.00 35.61 3.06
2389 2634 1.271856 TAACCGGCTCAACATCTCCA 58.728 50.000 0.00 0.00 0.00 3.86
2515 2760 3.305064 GCTCATAAAGAAAACAACCGCCA 60.305 43.478 0.00 0.00 0.00 5.69
2564 2809 7.205297 GTGCAATAAGAGCATTGGTCAATTAT 58.795 34.615 17.46 10.56 44.79 1.28
2565 2810 8.352201 GTGCAATAAGAGCATTGGTCAATTATA 58.648 33.333 17.46 6.83 44.79 0.98
2613 2858 8.919145 TGTTTGTGTGGAGTAATAAAATCCTTT 58.081 29.630 0.00 0.00 34.04 3.11
2622 2867 7.706607 GGAGTAATAAAATCCTTTCAATGGTGC 59.293 37.037 0.00 0.00 0.00 5.01
2624 2869 8.815912 AGTAATAAAATCCTTTCAATGGTGCTT 58.184 29.630 0.00 0.00 0.00 3.91
2634 2879 2.019249 CAATGGTGCTTCATGATCCGT 58.981 47.619 0.00 0.00 0.00 4.69
2658 2903 2.087501 TCGTTGGTTGCACGATGTAT 57.912 45.000 0.00 0.00 41.66 2.29
2738 2986 7.918033 AGAGAGATGTGTAAATTAGTGTCGATG 59.082 37.037 0.00 0.00 0.00 3.84
2752 3000 9.778741 ATTAGTGTCGATGGTAATTTATGTCAT 57.221 29.630 0.00 0.00 0.00 3.06
2953 3202 4.950050 AGAGACCTATTGCTTATGGTTCG 58.050 43.478 0.00 0.00 32.30 3.95
3152 3403 5.568685 TGACTTACTATCAGAGTGCACTC 57.431 43.478 34.82 34.82 39.39 3.51
3200 3451 5.738118 TGTTTACGGTTCAGTGGTAAAAG 57.262 39.130 4.61 0.00 37.73 2.27
3210 3461 5.836024 TCAGTGGTAAAAGTAGGTTCCAT 57.164 39.130 0.00 0.00 0.00 3.41
3215 3466 7.176690 CAGTGGTAAAAGTAGGTTCCATCAAAT 59.823 37.037 0.00 0.00 0.00 2.32
3223 3474 5.652452 AGTAGGTTCCATCAAATTAACAGCC 59.348 40.000 0.00 0.00 0.00 4.85
3228 3479 3.066621 TCCATCAAATTAACAGCCGATGC 59.933 43.478 0.00 0.00 37.95 3.91
3233 3484 1.932156 ATTAACAGCCGATGCCCCCA 61.932 55.000 0.00 0.00 38.69 4.96
3240 3492 2.597340 CGATGCCCCCACCAGAAT 59.403 61.111 0.00 0.00 0.00 2.40
3245 3497 3.497763 CGATGCCCCCACCAGAATAAATA 60.498 47.826 0.00 0.00 0.00 1.40
3248 3500 4.889780 TGCCCCCACCAGAATAAATAAAT 58.110 39.130 0.00 0.00 0.00 1.40
3252 3504 6.074648 CCCCCACCAGAATAAATAAATAGCA 58.925 40.000 0.00 0.00 0.00 3.49
3254 3506 6.209391 CCCCACCAGAATAAATAAATAGCAGG 59.791 42.308 0.00 0.00 0.00 4.85
3258 3510 8.131100 CACCAGAATAAATAAATAGCAGGTGTG 58.869 37.037 0.00 0.00 37.45 3.82
3270 3522 8.816640 AAATAGCAGGTGTGTTTCTTTTAATG 57.183 30.769 0.00 0.00 0.00 1.90
3272 3524 6.463995 AGCAGGTGTGTTTCTTTTAATGAA 57.536 33.333 0.00 0.00 0.00 2.57
3333 3785 6.619801 ACCTTGTTTCTTGTTGACTATCAC 57.380 37.500 0.00 0.00 0.00 3.06
3372 3824 9.563748 AATGCAATTTTATTGGGAAATATCCTG 57.436 29.630 0.00 0.00 38.66 3.86
3410 3862 8.528044 TTTACAAGAACACCAATTTAAGGACT 57.472 30.769 0.00 0.00 0.00 3.85
3451 3915 4.813161 AGATCTGTCAATACTTGGCGATTG 59.187 41.667 0.00 0.00 38.34 2.67
3467 3931 5.182950 TGGCGATTGTTGAGTGATGTTAAAT 59.817 36.000 0.00 0.00 0.00 1.40
3503 3971 5.755409 TTGTGTGCCTCCTTCTAAGATTA 57.245 39.130 0.00 0.00 0.00 1.75
3504 3972 5.344743 TGTGTGCCTCCTTCTAAGATTAG 57.655 43.478 0.00 0.00 0.00 1.73
3508 3976 5.104360 TGTGCCTCCTTCTAAGATTAGCATT 60.104 40.000 0.00 0.00 0.00 3.56
3513 3981 6.489361 CCTCCTTCTAAGATTAGCATTTGCAT 59.511 38.462 5.20 0.00 45.16 3.96
3533 4001 0.104855 GAGACATCATGGCGTGCCTA 59.895 55.000 12.84 0.00 36.94 3.93
3536 4004 0.462581 ACATCATGGCGTGCCTAGTG 60.463 55.000 12.84 8.54 36.94 2.74
3541 4009 1.686325 ATGGCGTGCCTAGTGTAGGG 61.686 60.000 12.84 0.00 46.32 3.53
3542 4010 2.356780 GGCGTGCCTAGTGTAGGGT 61.357 63.158 2.98 0.00 46.32 4.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 9.978044 GCTCATATCATCATAGCATGAATAGTA 57.022 33.333 0.00 0.00 43.50 1.82
36 37 8.706521 AGCTCATATCATCATAGCATGAATAGT 58.293 33.333 0.00 0.00 43.50 2.12
39 40 9.901172 TTTAGCTCATATCATCATAGCATGAAT 57.099 29.630 0.00 0.00 43.50 2.57
40 41 9.729281 TTTTAGCTCATATCATCATAGCATGAA 57.271 29.630 0.00 0.00 43.50 2.57
41 42 9.901172 ATTTTAGCTCATATCATCATAGCATGA 57.099 29.630 0.00 2.05 44.55 3.07
44 45 9.729281 TCAATTTTAGCTCATATCATCATAGCA 57.271 29.630 0.00 0.00 35.63 3.49
50 51 9.635520 CCCATTTCAATTTTAGCTCATATCATC 57.364 33.333 0.00 0.00 0.00 2.92
51 52 8.591072 CCCCATTTCAATTTTAGCTCATATCAT 58.409 33.333 0.00 0.00 0.00 2.45
52 53 7.784073 TCCCCATTTCAATTTTAGCTCATATCA 59.216 33.333 0.00 0.00 0.00 2.15
53 54 8.084684 GTCCCCATTTCAATTTTAGCTCATATC 58.915 37.037 0.00 0.00 0.00 1.63
54 55 7.786464 AGTCCCCATTTCAATTTTAGCTCATAT 59.214 33.333 0.00 0.00 0.00 1.78
55 56 7.068593 CAGTCCCCATTTCAATTTTAGCTCATA 59.931 37.037 0.00 0.00 0.00 2.15
56 57 5.960202 AGTCCCCATTTCAATTTTAGCTCAT 59.040 36.000 0.00 0.00 0.00 2.90
57 58 5.185635 CAGTCCCCATTTCAATTTTAGCTCA 59.814 40.000 0.00 0.00 0.00 4.26
58 59 5.394553 CCAGTCCCCATTTCAATTTTAGCTC 60.395 44.000 0.00 0.00 0.00 4.09
59 60 4.467438 CCAGTCCCCATTTCAATTTTAGCT 59.533 41.667 0.00 0.00 0.00 3.32
60 61 4.758688 CCAGTCCCCATTTCAATTTTAGC 58.241 43.478 0.00 0.00 0.00 3.09
61 62 4.467438 AGCCAGTCCCCATTTCAATTTTAG 59.533 41.667 0.00 0.00 0.00 1.85
62 63 4.424842 AGCCAGTCCCCATTTCAATTTTA 58.575 39.130 0.00 0.00 0.00 1.52
63 64 3.250617 AGCCAGTCCCCATTTCAATTTT 58.749 40.909 0.00 0.00 0.00 1.82
64 65 2.906568 AGCCAGTCCCCATTTCAATTT 58.093 42.857 0.00 0.00 0.00 1.82
65 66 2.629017 AGCCAGTCCCCATTTCAATT 57.371 45.000 0.00 0.00 0.00 2.32
66 67 3.245586 TGTTAGCCAGTCCCCATTTCAAT 60.246 43.478 0.00 0.00 0.00 2.57
67 68 2.109128 TGTTAGCCAGTCCCCATTTCAA 59.891 45.455 0.00 0.00 0.00 2.69
68 69 1.707989 TGTTAGCCAGTCCCCATTTCA 59.292 47.619 0.00 0.00 0.00 2.69
69 70 2.092323 GTGTTAGCCAGTCCCCATTTC 58.908 52.381 0.00 0.00 0.00 2.17
70 71 1.710809 AGTGTTAGCCAGTCCCCATTT 59.289 47.619 0.00 0.00 0.00 2.32
71 72 1.372501 AGTGTTAGCCAGTCCCCATT 58.627 50.000 0.00 0.00 0.00 3.16
72 73 1.372501 AAGTGTTAGCCAGTCCCCAT 58.627 50.000 0.00 0.00 0.00 4.00
73 74 1.145571 AAAGTGTTAGCCAGTCCCCA 58.854 50.000 0.00 0.00 0.00 4.96
74 75 2.287977 AAAAGTGTTAGCCAGTCCCC 57.712 50.000 0.00 0.00 0.00 4.81
102 103 6.969366 TCACCTATATGTGCATGTTATTTGC 58.031 36.000 3.46 0.00 40.55 3.68
103 104 7.539710 GCATCACCTATATGTGCATGTTATTTG 59.460 37.037 15.16 0.00 36.17 2.32
104 105 7.449395 AGCATCACCTATATGTGCATGTTATTT 59.551 33.333 15.16 0.00 38.23 1.40
105 106 6.944290 AGCATCACCTATATGTGCATGTTATT 59.056 34.615 15.16 4.60 38.23 1.40
106 107 6.479006 AGCATCACCTATATGTGCATGTTAT 58.521 36.000 15.16 0.00 38.23 1.89
107 108 5.868454 AGCATCACCTATATGTGCATGTTA 58.132 37.500 15.16 0.00 38.23 2.41
108 109 4.722220 AGCATCACCTATATGTGCATGTT 58.278 39.130 15.16 10.40 38.23 2.71
109 110 4.362470 AGCATCACCTATATGTGCATGT 57.638 40.909 15.16 0.00 38.23 3.21
110 111 5.700722 AAAGCATCACCTATATGTGCATG 57.299 39.130 3.46 8.85 38.23 4.06
111 112 6.016527 CAGAAAAGCATCACCTATATGTGCAT 60.017 38.462 3.46 0.00 38.23 3.96
112 113 5.297527 CAGAAAAGCATCACCTATATGTGCA 59.702 40.000 3.46 0.00 38.23 4.57
113 114 5.528690 TCAGAAAAGCATCACCTATATGTGC 59.471 40.000 3.46 0.00 36.17 4.57
114 115 7.066163 TGTTCAGAAAAGCATCACCTATATGTG 59.934 37.037 1.97 1.97 37.59 3.21
115 116 7.112122 TGTTCAGAAAAGCATCACCTATATGT 58.888 34.615 0.00 0.00 0.00 2.29
116 117 7.558161 TGTTCAGAAAAGCATCACCTATATG 57.442 36.000 0.00 0.00 0.00 1.78
117 118 8.757982 AATGTTCAGAAAAGCATCACCTATAT 57.242 30.769 0.00 0.00 0.00 0.86
118 119 8.579850 AAATGTTCAGAAAAGCATCACCTATA 57.420 30.769 0.00 0.00 0.00 1.31
119 120 7.472334 AAATGTTCAGAAAAGCATCACCTAT 57.528 32.000 0.00 0.00 0.00 2.57
120 121 6.899393 AAATGTTCAGAAAAGCATCACCTA 57.101 33.333 0.00 0.00 0.00 3.08
121 122 5.796424 AAATGTTCAGAAAAGCATCACCT 57.204 34.783 0.00 0.00 0.00 4.00
122 123 5.984926 TCAAAATGTTCAGAAAAGCATCACC 59.015 36.000 0.00 0.00 0.00 4.02
123 124 7.647907 ATCAAAATGTTCAGAAAAGCATCAC 57.352 32.000 0.00 0.00 0.00 3.06
124 125 9.577110 GATATCAAAATGTTCAGAAAAGCATCA 57.423 29.630 0.00 0.00 0.00 3.07
125 126 9.798994 AGATATCAAAATGTTCAGAAAAGCATC 57.201 29.630 5.32 0.00 0.00 3.91
182 183 9.912634 GATCATCACTTGGAAAACTTCATAAAA 57.087 29.630 0.00 0.00 0.00 1.52
183 184 9.076781 TGATCATCACTTGGAAAACTTCATAAA 57.923 29.630 0.00 0.00 0.00 1.40
184 185 8.634335 TGATCATCACTTGGAAAACTTCATAA 57.366 30.769 0.00 0.00 0.00 1.90
185 186 8.634335 TTGATCATCACTTGGAAAACTTCATA 57.366 30.769 0.00 0.00 0.00 2.15
186 187 7.528996 TTGATCATCACTTGGAAAACTTCAT 57.471 32.000 0.00 0.00 0.00 2.57
187 188 6.957920 TTGATCATCACTTGGAAAACTTCA 57.042 33.333 0.00 0.00 0.00 3.02
188 189 6.360681 CGTTTGATCATCACTTGGAAAACTTC 59.639 38.462 0.00 0.00 0.00 3.01
189 190 6.208644 CGTTTGATCATCACTTGGAAAACTT 58.791 36.000 0.00 0.00 0.00 2.66
190 191 5.278463 CCGTTTGATCATCACTTGGAAAACT 60.278 40.000 0.00 0.00 0.00 2.66
191 192 4.917415 CCGTTTGATCATCACTTGGAAAAC 59.083 41.667 0.00 0.00 0.00 2.43
192 193 4.582656 ACCGTTTGATCATCACTTGGAAAA 59.417 37.500 0.00 0.00 0.00 2.29
193 194 4.141287 ACCGTTTGATCATCACTTGGAAA 58.859 39.130 0.00 0.00 0.00 3.13
194 195 3.750371 ACCGTTTGATCATCACTTGGAA 58.250 40.909 0.00 0.00 0.00 3.53
195 196 3.244387 TGACCGTTTGATCATCACTTGGA 60.244 43.478 0.00 0.00 0.00 3.53
196 197 3.073678 TGACCGTTTGATCATCACTTGG 58.926 45.455 0.00 0.00 0.00 3.61
197 198 4.747540 TTGACCGTTTGATCATCACTTG 57.252 40.909 0.00 0.00 0.00 3.16
198 199 4.216257 CCTTTGACCGTTTGATCATCACTT 59.784 41.667 0.00 0.00 0.00 3.16
199 200 3.753272 CCTTTGACCGTTTGATCATCACT 59.247 43.478 0.00 0.00 0.00 3.41
200 201 3.119849 CCCTTTGACCGTTTGATCATCAC 60.120 47.826 0.00 0.00 0.00 3.06
201 202 3.081061 CCCTTTGACCGTTTGATCATCA 58.919 45.455 0.00 0.00 0.00 3.07
202 203 2.159379 GCCCTTTGACCGTTTGATCATC 60.159 50.000 0.00 0.00 0.00 2.92
203 204 1.818674 GCCCTTTGACCGTTTGATCAT 59.181 47.619 0.00 0.00 0.00 2.45
204 205 1.243902 GCCCTTTGACCGTTTGATCA 58.756 50.000 0.00 0.00 0.00 2.92
205 206 1.243902 TGCCCTTTGACCGTTTGATC 58.756 50.000 0.00 0.00 0.00 2.92
206 207 1.698506 TTGCCCTTTGACCGTTTGAT 58.301 45.000 0.00 0.00 0.00 2.57
207 208 1.698506 ATTGCCCTTTGACCGTTTGA 58.301 45.000 0.00 0.00 0.00 2.69
208 209 2.671070 GCTATTGCCCTTTGACCGTTTG 60.671 50.000 0.00 0.00 0.00 2.93
209 210 1.544246 GCTATTGCCCTTTGACCGTTT 59.456 47.619 0.00 0.00 0.00 3.60
210 211 1.173913 GCTATTGCCCTTTGACCGTT 58.826 50.000 0.00 0.00 0.00 4.44
211 212 0.037590 TGCTATTGCCCTTTGACCGT 59.962 50.000 0.00 0.00 38.71 4.83
212 213 1.392589 ATGCTATTGCCCTTTGACCG 58.607 50.000 0.00 0.00 38.71 4.79
213 214 4.207165 TCTTATGCTATTGCCCTTTGACC 58.793 43.478 0.00 0.00 38.71 4.02
214 215 4.276926 CCTCTTATGCTATTGCCCTTTGAC 59.723 45.833 0.00 0.00 38.71 3.18
215 216 4.165950 TCCTCTTATGCTATTGCCCTTTGA 59.834 41.667 0.00 0.00 38.71 2.69
216 217 4.464008 TCCTCTTATGCTATTGCCCTTTG 58.536 43.478 0.00 0.00 38.71 2.77
217 218 4.723309 CTCCTCTTATGCTATTGCCCTTT 58.277 43.478 0.00 0.00 38.71 3.11
218 219 3.497584 GCTCCTCTTATGCTATTGCCCTT 60.498 47.826 0.00 0.00 38.71 3.95
219 220 2.039613 GCTCCTCTTATGCTATTGCCCT 59.960 50.000 0.00 0.00 38.71 5.19
220 221 2.224621 TGCTCCTCTTATGCTATTGCCC 60.225 50.000 0.00 0.00 38.71 5.36
221 222 3.131709 TGCTCCTCTTATGCTATTGCC 57.868 47.619 0.00 0.00 38.71 4.52
222 223 5.505173 TTTTGCTCCTCTTATGCTATTGC 57.495 39.130 0.00 0.00 40.20 3.56
223 224 7.268199 TCATTTTGCTCCTCTTATGCTATTG 57.732 36.000 0.00 0.00 0.00 1.90
224 225 8.474710 AATCATTTTGCTCCTCTTATGCTATT 57.525 30.769 0.00 0.00 0.00 1.73
225 226 8.358148 CAAATCATTTTGCTCCTCTTATGCTAT 58.642 33.333 0.00 0.00 36.13 2.97
226 227 7.201848 CCAAATCATTTTGCTCCTCTTATGCTA 60.202 37.037 0.00 0.00 40.77 3.49
227 228 6.406624 CCAAATCATTTTGCTCCTCTTATGCT 60.407 38.462 0.00 0.00 40.77 3.79
228 229 5.751990 CCAAATCATTTTGCTCCTCTTATGC 59.248 40.000 0.00 0.00 40.77 3.14
229 230 6.870769 ACCAAATCATTTTGCTCCTCTTATG 58.129 36.000 0.00 0.00 40.77 1.90
230 231 6.664816 TGACCAAATCATTTTGCTCCTCTTAT 59.335 34.615 0.00 0.00 40.77 1.73
231 232 6.009589 TGACCAAATCATTTTGCTCCTCTTA 58.990 36.000 0.00 0.00 40.77 2.10
232 233 4.834496 TGACCAAATCATTTTGCTCCTCTT 59.166 37.500 0.00 0.00 40.77 2.85
233 234 4.410099 TGACCAAATCATTTTGCTCCTCT 58.590 39.130 0.00 0.00 40.77 3.69
234 235 4.381292 CCTGACCAAATCATTTTGCTCCTC 60.381 45.833 0.00 0.00 40.77 3.71
235 236 3.512724 CCTGACCAAATCATTTTGCTCCT 59.487 43.478 0.00 0.00 40.77 3.69
236 237 3.511146 TCCTGACCAAATCATTTTGCTCC 59.489 43.478 0.00 0.00 40.77 4.70
237 238 4.789012 TCCTGACCAAATCATTTTGCTC 57.211 40.909 0.00 0.00 40.77 4.26
238 239 4.344679 TGTTCCTGACCAAATCATTTTGCT 59.655 37.500 0.00 0.00 40.77 3.91
239 240 4.630111 TGTTCCTGACCAAATCATTTTGC 58.370 39.130 0.00 0.00 40.77 3.68
240 241 6.201425 CACTTGTTCCTGACCAAATCATTTTG 59.799 38.462 0.00 0.00 41.59 2.44
241 242 6.127083 ACACTTGTTCCTGACCAAATCATTTT 60.127 34.615 0.00 0.00 36.48 1.82
242 243 5.363580 ACACTTGTTCCTGACCAAATCATTT 59.636 36.000 0.00 0.00 36.48 2.32
243 244 4.895297 ACACTTGTTCCTGACCAAATCATT 59.105 37.500 0.00 0.00 36.48 2.57
244 245 4.473444 ACACTTGTTCCTGACCAAATCAT 58.527 39.130 0.00 0.00 36.48 2.45
245 246 3.897239 ACACTTGTTCCTGACCAAATCA 58.103 40.909 0.00 0.00 35.45 2.57
246 247 4.918810 AACACTTGTTCCTGACCAAATC 57.081 40.909 0.00 0.00 31.64 2.17
247 248 4.099419 GGAAACACTTGTTCCTGACCAAAT 59.901 41.667 0.00 0.00 37.25 2.32
248 249 3.445805 GGAAACACTTGTTCCTGACCAAA 59.554 43.478 0.00 0.00 37.25 3.28
249 250 3.020984 GGAAACACTTGTTCCTGACCAA 58.979 45.455 0.00 0.00 37.25 3.67
250 251 2.650322 GGAAACACTTGTTCCTGACCA 58.350 47.619 0.00 0.00 37.25 4.02
251 252 1.602377 CGGAAACACTTGTTCCTGACC 59.398 52.381 0.00 0.00 37.25 4.02
252 253 1.602377 CCGGAAACACTTGTTCCTGAC 59.398 52.381 0.00 0.00 37.25 3.51
253 254 1.487142 TCCGGAAACACTTGTTCCTGA 59.513 47.619 0.00 0.00 37.25 3.86
254 255 1.961793 TCCGGAAACACTTGTTCCTG 58.038 50.000 0.00 0.00 37.25 3.86
255 256 2.721425 TTCCGGAAACACTTGTTCCT 57.279 45.000 16.28 0.00 37.25 3.36
256 257 3.786516 TTTTCCGGAAACACTTGTTCC 57.213 42.857 28.97 0.00 37.25 3.62
257 258 4.740268 ACTTTTTCCGGAAACACTTGTTC 58.260 39.130 28.97 0.00 37.25 3.18
258 259 4.794278 ACTTTTTCCGGAAACACTTGTT 57.206 36.364 28.97 6.81 40.50 2.83
259 260 4.337274 CCTACTTTTTCCGGAAACACTTGT 59.663 41.667 28.97 21.77 0.00 3.16
260 261 4.261447 CCCTACTTTTTCCGGAAACACTTG 60.261 45.833 28.97 17.72 0.00 3.16
261 262 3.887110 CCCTACTTTTTCCGGAAACACTT 59.113 43.478 28.97 15.45 0.00 3.16
262 263 3.136992 TCCCTACTTTTTCCGGAAACACT 59.863 43.478 28.97 15.50 0.00 3.55
263 264 3.479489 TCCCTACTTTTTCCGGAAACAC 58.521 45.455 28.97 0.00 0.00 3.32
264 265 3.860968 TCCCTACTTTTTCCGGAAACA 57.139 42.857 28.97 21.56 0.00 2.83
265 266 6.349611 GGTTTATCCCTACTTTTTCCGGAAAC 60.350 42.308 28.97 12.72 0.00 2.78
266 267 5.711506 GGTTTATCCCTACTTTTTCCGGAAA 59.288 40.000 25.67 25.67 0.00 3.13
267 268 5.014438 AGGTTTATCCCTACTTTTTCCGGAA 59.986 40.000 14.35 14.35 36.75 4.30
268 269 4.537288 AGGTTTATCCCTACTTTTTCCGGA 59.463 41.667 0.00 0.00 36.75 5.14
269 270 4.638865 CAGGTTTATCCCTACTTTTTCCGG 59.361 45.833 0.00 0.00 36.75 5.14
270 271 4.095932 GCAGGTTTATCCCTACTTTTTCCG 59.904 45.833 0.00 0.00 36.75 4.30
271 272 4.401519 GGCAGGTTTATCCCTACTTTTTCC 59.598 45.833 0.00 0.00 36.75 3.13
272 273 4.095932 CGGCAGGTTTATCCCTACTTTTTC 59.904 45.833 0.00 0.00 36.75 2.29
273 274 4.014406 CGGCAGGTTTATCCCTACTTTTT 58.986 43.478 0.00 0.00 36.75 1.94
274 275 3.009805 ACGGCAGGTTTATCCCTACTTTT 59.990 43.478 0.00 0.00 36.75 2.27
275 276 2.574824 ACGGCAGGTTTATCCCTACTTT 59.425 45.455 0.00 0.00 36.75 2.66
276 277 2.093128 CACGGCAGGTTTATCCCTACTT 60.093 50.000 0.00 0.00 36.75 2.24
277 278 1.485066 CACGGCAGGTTTATCCCTACT 59.515 52.381 0.00 0.00 36.75 2.57
278 279 1.208776 ACACGGCAGGTTTATCCCTAC 59.791 52.381 0.00 0.00 36.75 3.18
279 280 1.208535 CACACGGCAGGTTTATCCCTA 59.791 52.381 0.00 0.00 36.75 3.53
280 281 0.035439 CACACGGCAGGTTTATCCCT 60.035 55.000 0.00 0.00 36.75 4.20
281 282 0.322187 ACACACGGCAGGTTTATCCC 60.322 55.000 0.00 0.00 36.75 3.85
282 283 0.802494 CACACACGGCAGGTTTATCC 59.198 55.000 0.00 0.00 0.00 2.59
283 284 1.463444 GTCACACACGGCAGGTTTATC 59.537 52.381 0.00 0.00 0.00 1.75
284 285 1.519408 GTCACACACGGCAGGTTTAT 58.481 50.000 0.00 0.00 0.00 1.40
285 286 0.533308 GGTCACACACGGCAGGTTTA 60.533 55.000 0.00 0.00 0.00 2.01
286 287 1.822186 GGTCACACACGGCAGGTTT 60.822 57.895 0.00 0.00 0.00 3.27
287 288 2.203153 GGTCACACACGGCAGGTT 60.203 61.111 0.00 0.00 0.00 3.50
288 289 4.250305 GGGTCACACACGGCAGGT 62.250 66.667 0.00 0.00 0.00 4.00
289 290 3.765894 TTGGGTCACACACGGCAGG 62.766 63.158 0.00 0.00 0.00 4.85
290 291 2.203139 TTGGGTCACACACGGCAG 60.203 61.111 0.00 0.00 0.00 4.85
291 292 1.687297 TAGTTGGGTCACACACGGCA 61.687 55.000 0.00 0.00 0.00 5.69
292 293 0.949105 CTAGTTGGGTCACACACGGC 60.949 60.000 0.00 0.00 0.00 5.68
293 294 0.320421 CCTAGTTGGGTCACACACGG 60.320 60.000 0.00 0.00 0.00 4.94
294 295 3.210857 CCTAGTTGGGTCACACACG 57.789 57.895 0.00 0.00 0.00 4.49
304 305 6.484364 AATTGATTTTATGCCCCTAGTTGG 57.516 37.500 0.00 0.00 0.00 3.77
305 306 8.306761 GGATAATTGATTTTATGCCCCTAGTTG 58.693 37.037 0.00 0.00 0.00 3.16
306 307 8.234525 AGGATAATTGATTTTATGCCCCTAGTT 58.765 33.333 0.00 0.00 32.17 2.24
307 308 7.769652 AGGATAATTGATTTTATGCCCCTAGT 58.230 34.615 0.00 0.00 32.17 2.57
308 309 8.655935 AAGGATAATTGATTTTATGCCCCTAG 57.344 34.615 0.00 0.00 32.17 3.02
309 310 9.445973 AAAAGGATAATTGATTTTATGCCCCTA 57.554 29.630 0.00 0.00 32.17 3.53
310 311 7.936026 AAAGGATAATTGATTTTATGCCCCT 57.064 32.000 0.00 0.00 32.17 4.79
311 312 8.978874 AAAAAGGATAATTGATTTTATGCCCC 57.021 30.769 0.00 0.00 32.17 5.80
343 344 7.458397 TCAACAAATGACCTATAACTTCACCT 58.542 34.615 0.00 0.00 31.50 4.00
411 414 1.480219 CGTCAATCCGAGCGGCTTAC 61.480 60.000 2.97 0.00 34.68 2.34
413 416 2.509336 CGTCAATCCGAGCGGCTT 60.509 61.111 2.97 0.00 34.68 4.35
533 543 1.583967 GACGTGCGTGAGATCCGAG 60.584 63.158 0.67 0.00 0.00 4.63
535 545 1.443702 TTGACGTGCGTGAGATCCG 60.444 57.895 0.67 0.00 0.00 4.18
543 553 1.661821 GAGCTGAGTTGACGTGCGT 60.662 57.895 0.00 0.00 0.00 5.24
544 554 2.710971 CGAGCTGAGTTGACGTGCG 61.711 63.158 0.00 0.00 0.00 5.34
545 555 0.734253 ATCGAGCTGAGTTGACGTGC 60.734 55.000 0.00 0.00 0.00 5.34
547 557 0.179187 CGATCGAGCTGAGTTGACGT 60.179 55.000 10.26 0.00 0.00 4.34
548 558 0.863538 CCGATCGAGCTGAGTTGACG 60.864 60.000 18.66 0.00 0.00 4.35
549 559 0.452184 TCCGATCGAGCTGAGTTGAC 59.548 55.000 18.66 0.00 0.00 3.18
550 560 1.335182 GATCCGATCGAGCTGAGTTGA 59.665 52.381 18.66 1.66 0.00 3.18
551 561 1.066152 TGATCCGATCGAGCTGAGTTG 59.934 52.381 18.66 0.00 0.00 3.16
553 563 1.393603 TTGATCCGATCGAGCTGAGT 58.606 50.000 18.66 0.00 0.00 3.41
554 564 2.721274 ATTGATCCGATCGAGCTGAG 57.279 50.000 18.66 0.00 0.00 3.35
618 857 2.746269 TCCAAGCAGTACGTACAACAC 58.254 47.619 26.55 12.77 0.00 3.32
685 927 3.140623 GTTTTGTAACGGCTGGTTCCTA 58.859 45.455 0.00 0.00 40.09 2.94
707 949 5.244785 TGTAACTATCACCGCTCAGTAAG 57.755 43.478 0.00 0.00 0.00 2.34
714 956 2.490903 ACGACTTGTAACTATCACCGCT 59.509 45.455 0.00 0.00 0.00 5.52
991 1234 1.689233 CGGGGTCCATCTCAGGGAA 60.689 63.158 0.00 0.00 35.88 3.97
1016 1259 2.260434 CGAACGAAGGGGAAGCGA 59.740 61.111 0.00 0.00 0.00 4.93
1118 1362 2.563620 TCAACGCTGGTGTAGTAATCCA 59.436 45.455 0.00 0.00 0.00 3.41
1137 1381 1.596934 GAGAACCGGCATGGACTCA 59.403 57.895 0.00 0.00 42.00 3.41
1254 1498 4.867599 GTCATCCCGCGGACGACC 62.868 72.222 30.73 7.60 38.77 4.79
1494 1738 3.402681 CCCAGGATGACACCGCCT 61.403 66.667 0.00 0.00 39.69 5.52
1509 1753 2.187163 GCTTCGCTAGTGGTCCCC 59.813 66.667 2.90 0.00 0.00 4.81
1625 1869 1.160137 GAATGTGGAGTGTGTCTGGC 58.840 55.000 0.00 0.00 0.00 4.85
1641 1885 1.811860 GCGGCATGCCTTGAAGAAT 59.188 52.632 33.07 0.00 37.76 2.40
1703 1947 1.749638 CCGTAGTCTGTCTCCGGCT 60.750 63.158 0.00 0.00 38.71 5.52
1803 2047 1.802636 GTTGGATGATGTGGTGCCG 59.197 57.895 0.00 0.00 0.00 5.69
1849 2093 0.320858 TTAAACATGGCCGCGACAGA 60.321 50.000 8.23 0.00 0.00 3.41
2385 2630 1.710816 CTAGGTAGGCCTTCCTGGAG 58.289 60.000 34.72 23.52 44.18 3.86
2389 2634 0.042731 TGTGCTAGGTAGGCCTTCCT 59.957 55.000 31.25 31.25 44.18 3.36
2515 2760 2.158249 TCTCCTCCCCATCGATGATCTT 60.158 50.000 26.86 0.00 0.00 2.40
2586 2831 8.650143 AGGATTTTATTACTCCACACAAACAT 57.350 30.769 0.00 0.00 0.00 2.71
2613 2858 2.291365 CGGATCATGAAGCACCATTGA 58.709 47.619 0.00 0.00 0.00 2.57
2622 2867 0.926155 CGACTGCACGGATCATGAAG 59.074 55.000 0.00 3.18 0.00 3.02
2624 2869 0.246360 AACGACTGCACGGATCATGA 59.754 50.000 0.00 0.00 37.61 3.07
2634 2879 2.818487 CGTGCAACCAACGACTGCA 61.818 57.895 0.00 0.00 43.54 4.41
2658 2903 0.323302 TGCATAAAGGCAGTCACCGA 59.677 50.000 0.00 0.00 39.25 4.69
2890 3139 9.935241 CAGTGCACTCCTATAATAAGTTATGAT 57.065 33.333 18.64 0.00 32.84 2.45
2931 3180 4.740934 GCGAACCATAAGCAATAGGTCTCT 60.741 45.833 0.00 0.00 32.05 3.10
2942 3191 6.787085 ATTTACTATCAGCGAACCATAAGC 57.213 37.500 0.00 0.00 0.00 3.09
2953 3202 7.048512 ACTGGGAACACTAATTTACTATCAGC 58.951 38.462 0.00 0.00 35.60 4.26
3152 3403 6.083098 AGATCTCCATAACAATGTCGAGAG 57.917 41.667 0.00 3.61 30.44 3.20
3200 3451 5.448632 CGGCTGTTAATTTGATGGAACCTAC 60.449 44.000 0.00 0.00 0.00 3.18
3210 3461 1.748493 GGGCATCGGCTGTTAATTTGA 59.252 47.619 0.00 0.00 40.87 2.69
3215 3466 2.274104 GGGGGCATCGGCTGTTAA 59.726 61.111 0.00 0.00 40.87 2.01
3223 3474 0.182537 TTATTCTGGTGGGGGCATCG 59.817 55.000 0.00 0.00 0.00 3.84
3228 3479 6.074648 TGCTATTTATTTATTCTGGTGGGGG 58.925 40.000 0.00 0.00 0.00 5.40
3233 3484 7.834181 ACACACCTGCTATTTATTTATTCTGGT 59.166 33.333 0.00 0.00 0.00 4.00
3245 3497 8.637986 TCATTAAAAGAAACACACCTGCTATTT 58.362 29.630 0.00 0.00 0.00 1.40
3248 3500 7.575414 TTCATTAAAAGAAACACACCTGCTA 57.425 32.000 0.00 0.00 0.00 3.49
3267 3519 8.658609 CACAAATCACAGACAAAAAGTTTCATT 58.341 29.630 0.00 0.00 0.00 2.57
3268 3520 7.818930 ACACAAATCACAGACAAAAAGTTTCAT 59.181 29.630 0.00 0.00 0.00 2.57
3270 3522 7.328249 TCACACAAATCACAGACAAAAAGTTTC 59.672 33.333 0.00 0.00 0.00 2.78
3272 3524 6.686630 TCACACAAATCACAGACAAAAAGTT 58.313 32.000 0.00 0.00 0.00 2.66
3349 3801 8.424133 ACTCAGGATATTTCCCAATAAAATTGC 58.576 33.333 0.00 0.00 43.76 3.56
3513 3981 1.450134 GGCACGCCATGATGTCTCA 60.450 57.895 2.36 0.00 35.81 3.27


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

AutoCloner maintained by Alex Coulton.