Multiple sequence alignment - TraesCS1B01G142700

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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 TraesCS1B01G142700 chr1B 100.000 3922 0 0 1 3922 192277238 192273317 0.000000e+00 7243.0
1 TraesCS1B01G142700 chr1B 99.614 259 1 0 146 404 192282230 192281972 1.280000e-129 473.0
2 TraesCS1B01G142700 chr1B 93.750 64 3 1 768 830 470588418 470588481 1.160000e-15 95.3
3 TraesCS1B01G142700 chr1A 97.232 2746 61 4 405 3140 146944105 146946845 0.000000e+00 4636.0
4 TraesCS1B01G142700 chr1A 94.192 792 25 5 3143 3922 146946908 146947690 0.000000e+00 1188.0
5 TraesCS1B01G142700 chr1D 97.115 1664 38 3 1387 3049 143258445 143256791 0.000000e+00 2798.0
6 TraesCS1B01G142700 chr1D 97.368 988 25 1 405 1391 143264015 143263028 0.000000e+00 1679.0
7 TraesCS1B01G142700 chr1D 94.304 790 29 3 3143 3922 143256665 143255882 0.000000e+00 1195.0
8 TraesCS1B01G142700 chr1D 99.259 405 2 1 1 404 207159247 207159651 0.000000e+00 730.0
9 TraesCS1B01G142700 chr1D 97.674 215 3 2 191 404 207149174 207149387 6.190000e-98 368.0
10 TraesCS1B01G142700 chr1D 93.069 101 6 1 3054 3154 143256814 143256715 3.160000e-31 147.0
11 TraesCS1B01G142700 chr7D 88.825 2085 178 21 547 2592 113448692 113446624 0.000000e+00 2508.0
12 TraesCS1B01G142700 chr7D 86.534 453 41 11 2653 3101 113446630 113446194 7.620000e-132 481.0
13 TraesCS1B01G142700 chr7D 92.793 111 6 2 408 516 113448801 113448691 4.060000e-35 159.0
14 TraesCS1B01G142700 chr7B 88.506 2088 169 31 547 2592 73137267 73135209 0.000000e+00 2460.0
15 TraesCS1B01G142700 chr7A 90.263 1253 102 10 1355 2592 118464060 118462813 0.000000e+00 1620.0
16 TraesCS1B01G142700 chr7A 85.669 956 82 20 408 1317 118465011 118464065 0.000000e+00 955.0
17 TraesCS1B01G142700 chr7A 85.055 455 46 10 2653 3101 118462819 118462381 1.000000e-120 444.0
18 TraesCS1B01G142700 chr7A 80.110 181 34 2 1 180 540902540 540902361 2.460000e-27 134.0
19 TraesCS1B01G142700 chr6A 85.126 874 82 18 475 1318 588864300 588863445 0.000000e+00 850.0
20 TraesCS1B01G142700 chr6A 99.257 404 3 0 1 404 574487146 574487549 0.000000e+00 730.0
21 TraesCS1B01G142700 chr6A 99.225 258 2 0 147 404 574482090 574482347 2.130000e-127 466.0
22 TraesCS1B01G142700 chr6B 98.515 404 6 0 1 404 144806584 144806181 0.000000e+00 713.0
23 TraesCS1B01G142700 chr6B 98.456 259 4 0 146 404 144811638 144811380 1.280000e-124 457.0
24 TraesCS1B01G142700 chr6B 91.791 268 18 3 141 405 32568942 32568676 1.720000e-98 370.0
25 TraesCS1B01G142700 chr6B 97.386 153 4 0 4 156 32569107 32568955 1.080000e-65 261.0
26 TraesCS1B01G142700 chr6B 93.750 64 3 1 768 830 22744494 22744557 1.160000e-15 95.3
27 TraesCS1B01G142700 chr6B 86.170 94 3 3 768 860 71751603 71751687 4.170000e-15 93.5
28 TraesCS1B01G142700 chr5A 88.070 285 15 6 144 409 653369938 653370222 1.760000e-83 320.0
29 TraesCS1B01G142700 chr5A 92.308 156 12 0 1 156 653369411 653369566 5.100000e-54 222.0
30 TraesCS1B01G142700 chr5A 86.170 188 8 6 147 320 653302386 653302569 1.860000e-43 187.0
31 TraesCS1B01G142700 chr4B 81.868 182 29 3 1 180 42918036 42918215 2.440000e-32 150.0
32 TraesCS1B01G142700 chr5D 81.356 177 33 0 4 180 33699804 33699628 1.140000e-30 145.0
33 TraesCS1B01G142700 chr3B 82.530 166 27 2 16 180 152486423 152486259 1.140000e-30 145.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1B01G142700 chr1B 192273317 192277238 3921 True 7243.000000 7243 100.000000 1 3922 1 chr1B.!!$R1 3921
1 TraesCS1B01G142700 chr1A 146944105 146947690 3585 False 2912.000000 4636 95.712000 405 3922 2 chr1A.!!$F1 3517
2 TraesCS1B01G142700 chr1D 143263028 143264015 987 True 1679.000000 1679 97.368000 405 1391 1 chr1D.!!$R1 986
3 TraesCS1B01G142700 chr1D 143255882 143258445 2563 True 1380.000000 2798 94.829333 1387 3922 3 chr1D.!!$R2 2535
4 TraesCS1B01G142700 chr7D 113446194 113448801 2607 True 1049.333333 2508 89.384000 408 3101 3 chr7D.!!$R1 2693
5 TraesCS1B01G142700 chr7B 73135209 73137267 2058 True 2460.000000 2460 88.506000 547 2592 1 chr7B.!!$R1 2045
6 TraesCS1B01G142700 chr7A 118462381 118465011 2630 True 1006.333333 1620 86.995667 408 3101 3 chr7A.!!$R2 2693
7 TraesCS1B01G142700 chr6A 588863445 588864300 855 True 850.000000 850 85.126000 475 1318 1 chr6A.!!$R1 843
8 TraesCS1B01G142700 chr5A 653369411 653370222 811 False 271.000000 320 90.189000 1 409 2 chr5A.!!$F2 408

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
371 372 0.033405 TCCTCGTCCCTTACCTCTGG 60.033 60.0 0.00 0.0 0.0 3.86 F
377 378 0.044092 TCCCTTACCTCTGGCCATGA 59.956 55.0 5.51 5.2 0.0 3.07 F
392 393 0.471617 CATGAAGCCGATCCCCTCTT 59.528 55.0 0.00 0.0 0.0 2.85 F
1156 1201 1.055849 GGCCCCTTTGACAAATTGGT 58.944 50.0 14.13 0.0 0.0 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1331 1386 2.331893 TGGATGCGCAAGAAACCCG 61.332 57.895 17.11 0.0 43.02 5.28 R
1953 2027 3.003480 GGCTACTCGATTGGAATATGCC 58.997 50.000 0.00 0.0 0.00 4.40 R
1954 2028 3.931578 AGGCTACTCGATTGGAATATGC 58.068 45.455 0.00 0.0 0.00 3.14 R
2956 3039 0.036671 AACTACAACTAGGCACGCCC 60.037 55.000 3.95 0.0 36.58 6.13 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
32 33 3.996150 ATTGTGCAGGTCAAAGTTCAG 57.004 42.857 0.00 0.00 0.00 3.02
35 36 1.334869 GTGCAGGTCAAAGTTCAGTGG 59.665 52.381 0.00 0.00 0.00 4.00
41 42 2.544267 GGTCAAAGTTCAGTGGTCTTCG 59.456 50.000 0.00 0.00 0.00 3.79
49 50 1.544691 TCAGTGGTCTTCGTTAGCTCC 59.455 52.381 0.00 0.00 0.00 4.70
57 58 2.431057 TCTTCGTTAGCTCCTGAATCCC 59.569 50.000 0.00 0.00 0.00 3.85
64 65 1.826024 CTCCTGAATCCCCGACCTG 59.174 63.158 0.00 0.00 0.00 4.00
77 78 2.330216 CCGACCTGGGAGGATTATTCT 58.670 52.381 0.00 0.00 37.67 2.40
125 126 0.674895 GCTGTTGGGATGAAGACGCT 60.675 55.000 0.00 0.00 0.00 5.07
156 157 0.883833 GGAGGCAAATGTCACACCTG 59.116 55.000 0.00 0.00 0.00 4.00
157 158 1.545428 GGAGGCAAATGTCACACCTGA 60.545 52.381 0.00 0.00 0.00 3.86
159 160 3.609853 GAGGCAAATGTCACACCTGATA 58.390 45.455 0.00 0.00 0.00 2.15
160 161 3.347216 AGGCAAATGTCACACCTGATAC 58.653 45.455 0.00 0.00 0.00 2.24
161 162 3.081061 GGCAAATGTCACACCTGATACA 58.919 45.455 0.00 0.00 0.00 2.29
162 163 3.696051 GGCAAATGTCACACCTGATACAT 59.304 43.478 0.00 0.00 34.11 2.29
163 164 4.439153 GGCAAATGTCACACCTGATACATG 60.439 45.833 0.00 0.00 33.04 3.21
164 165 4.395854 GCAAATGTCACACCTGATACATGA 59.604 41.667 0.00 0.00 33.04 3.07
165 166 5.448225 GCAAATGTCACACCTGATACATGAG 60.448 44.000 0.00 0.00 33.04 2.90
166 167 5.426689 AATGTCACACCTGATACATGAGT 57.573 39.130 0.00 0.00 33.04 3.41
167 168 6.544928 AATGTCACACCTGATACATGAGTA 57.455 37.500 0.00 0.00 33.04 2.59
168 169 6.737720 ATGTCACACCTGATACATGAGTAT 57.262 37.500 0.00 0.00 43.49 2.12
177 178 4.175787 GATACATGAGTATCGGTGGACC 57.824 50.000 0.00 0.00 45.03 4.46
178 179 2.160721 ACATGAGTATCGGTGGACCT 57.839 50.000 0.00 0.00 38.61 3.85
179 180 1.757118 ACATGAGTATCGGTGGACCTG 59.243 52.381 0.00 0.00 38.61 4.00
180 181 1.069204 CATGAGTATCGGTGGACCTGG 59.931 57.143 0.00 0.00 38.61 4.45
181 182 0.333652 TGAGTATCGGTGGACCTGGA 59.666 55.000 0.00 0.00 38.61 3.86
182 183 1.272816 TGAGTATCGGTGGACCTGGAA 60.273 52.381 0.00 0.00 38.61 3.53
183 184 1.409427 GAGTATCGGTGGACCTGGAAG 59.591 57.143 0.00 0.00 0.00 3.46
202 203 6.900194 TGGAAGGTGAAATAGATAGAAAGGG 58.100 40.000 0.00 0.00 0.00 3.95
203 204 6.126478 TGGAAGGTGAAATAGATAGAAAGGGG 60.126 42.308 0.00 0.00 0.00 4.79
204 205 6.126449 GGAAGGTGAAATAGATAGAAAGGGGT 60.126 42.308 0.00 0.00 0.00 4.95
205 206 6.253946 AGGTGAAATAGATAGAAAGGGGTG 57.746 41.667 0.00 0.00 0.00 4.61
206 207 5.970640 AGGTGAAATAGATAGAAAGGGGTGA 59.029 40.000 0.00 0.00 0.00 4.02
207 208 6.100424 AGGTGAAATAGATAGAAAGGGGTGAG 59.900 42.308 0.00 0.00 0.00 3.51
208 209 5.760743 GTGAAATAGATAGAAAGGGGTGAGC 59.239 44.000 0.00 0.00 0.00 4.26
209 210 4.608948 AATAGATAGAAAGGGGTGAGCG 57.391 45.455 0.00 0.00 0.00 5.03
210 211 1.867363 AGATAGAAAGGGGTGAGCGT 58.133 50.000 0.00 0.00 0.00 5.07
211 212 1.482593 AGATAGAAAGGGGTGAGCGTG 59.517 52.381 0.00 0.00 0.00 5.34
212 213 1.207329 GATAGAAAGGGGTGAGCGTGT 59.793 52.381 0.00 0.00 0.00 4.49
213 214 0.320374 TAGAAAGGGGTGAGCGTGTG 59.680 55.000 0.00 0.00 0.00 3.82
214 215 1.227853 GAAAGGGGTGAGCGTGTGT 60.228 57.895 0.00 0.00 0.00 3.72
215 216 1.507141 GAAAGGGGTGAGCGTGTGTG 61.507 60.000 0.00 0.00 0.00 3.82
216 217 2.265467 AAAGGGGTGAGCGTGTGTGT 62.265 55.000 0.00 0.00 0.00 3.72
217 218 2.940890 AAGGGGTGAGCGTGTGTGTG 62.941 60.000 0.00 0.00 0.00 3.82
218 219 3.649986 GGGTGAGCGTGTGTGTGC 61.650 66.667 0.00 0.00 0.00 4.57
219 220 3.649986 GGTGAGCGTGTGTGTGCC 61.650 66.667 0.00 0.00 0.00 5.01
220 221 2.894879 GTGAGCGTGTGTGTGCCA 60.895 61.111 0.00 0.00 0.00 4.92
221 222 2.588596 TGAGCGTGTGTGTGCCAG 60.589 61.111 0.00 0.00 0.00 4.85
222 223 2.588877 GAGCGTGTGTGTGCCAGT 60.589 61.111 0.00 0.00 0.00 4.00
223 224 2.885676 GAGCGTGTGTGTGCCAGTG 61.886 63.158 0.00 0.00 0.00 3.66
224 225 3.952675 GCGTGTGTGTGCCAGTGG 61.953 66.667 4.20 4.20 0.00 4.00
225 226 3.279116 CGTGTGTGTGCCAGTGGG 61.279 66.667 12.15 0.00 37.18 4.61
244 245 3.740397 CACATGTGGCCAGGCGTG 61.740 66.667 18.51 10.18 0.00 5.34
245 246 4.269523 ACATGTGGCCAGGCGTGT 62.270 61.111 5.11 10.95 0.00 4.49
246 247 3.740397 CATGTGGCCAGGCGTGTG 61.740 66.667 5.11 0.00 0.00 3.82
247 248 4.269523 ATGTGGCCAGGCGTGTGT 62.270 61.111 5.11 0.00 0.00 3.72
253 254 3.208383 CCAGGCGTGTGTGTGCAA 61.208 61.111 5.57 0.00 0.00 4.08
254 255 2.328989 CAGGCGTGTGTGTGCAAG 59.671 61.111 0.00 0.00 0.00 4.01
255 256 2.124736 AGGCGTGTGTGTGCAAGT 60.125 55.556 0.00 0.00 0.00 3.16
256 257 1.145156 AGGCGTGTGTGTGCAAGTA 59.855 52.632 0.00 0.00 0.00 2.24
257 258 0.250295 AGGCGTGTGTGTGCAAGTAT 60.250 50.000 0.00 0.00 0.00 2.12
258 259 1.001520 AGGCGTGTGTGTGCAAGTATA 59.998 47.619 0.00 0.00 0.00 1.47
259 260 1.801771 GGCGTGTGTGTGCAAGTATAA 59.198 47.619 0.00 0.00 0.00 0.98
260 261 2.159707 GGCGTGTGTGTGCAAGTATAAG 60.160 50.000 0.00 0.00 0.00 1.73
261 262 2.734606 GCGTGTGTGTGCAAGTATAAGA 59.265 45.455 0.00 0.00 0.00 2.10
262 263 3.181530 GCGTGTGTGTGCAAGTATAAGAG 60.182 47.826 0.00 0.00 0.00 2.85
263 264 4.234574 CGTGTGTGTGCAAGTATAAGAGA 58.765 43.478 0.00 0.00 0.00 3.10
264 265 4.090066 CGTGTGTGTGCAAGTATAAGAGAC 59.910 45.833 0.00 0.00 0.00 3.36
265 266 4.389077 GTGTGTGTGCAAGTATAAGAGACC 59.611 45.833 0.00 0.00 0.00 3.85
266 267 4.283467 TGTGTGTGCAAGTATAAGAGACCT 59.717 41.667 0.00 0.00 0.00 3.85
267 268 5.479027 TGTGTGTGCAAGTATAAGAGACCTA 59.521 40.000 0.00 0.00 0.00 3.08
268 269 5.805994 GTGTGTGCAAGTATAAGAGACCTAC 59.194 44.000 0.00 0.00 0.00 3.18
269 270 5.105473 TGTGTGCAAGTATAAGAGACCTACC 60.105 44.000 0.00 0.00 0.00 3.18
270 271 4.404715 TGTGCAAGTATAAGAGACCTACCC 59.595 45.833 0.00 0.00 0.00 3.69
271 272 4.650131 GTGCAAGTATAAGAGACCTACCCT 59.350 45.833 0.00 0.00 0.00 4.34
272 273 4.649674 TGCAAGTATAAGAGACCTACCCTG 59.350 45.833 0.00 0.00 0.00 4.45
273 274 4.650131 GCAAGTATAAGAGACCTACCCTGT 59.350 45.833 0.00 0.00 0.00 4.00
274 275 5.832060 GCAAGTATAAGAGACCTACCCTGTA 59.168 44.000 0.00 0.00 0.00 2.74
275 276 6.238981 GCAAGTATAAGAGACCTACCCTGTAC 60.239 46.154 0.00 0.00 0.00 2.90
276 277 6.845168 AGTATAAGAGACCTACCCTGTACT 57.155 41.667 0.00 0.00 0.00 2.73
277 278 6.840527 AGTATAAGAGACCTACCCTGTACTC 58.159 44.000 0.00 0.00 0.00 2.59
278 279 3.385314 AAGAGACCTACCCTGTACTCC 57.615 52.381 0.00 0.00 0.00 3.85
279 280 1.212441 AGAGACCTACCCTGTACTCCG 59.788 57.143 0.00 0.00 0.00 4.63
280 281 0.998145 AGACCTACCCTGTACTCCGT 59.002 55.000 0.00 0.00 0.00 4.69
281 282 1.101331 GACCTACCCTGTACTCCGTG 58.899 60.000 0.00 0.00 0.00 4.94
282 283 0.324091 ACCTACCCTGTACTCCGTGG 60.324 60.000 0.00 0.00 0.00 4.94
283 284 0.033796 CCTACCCTGTACTCCGTGGA 60.034 60.000 0.00 0.00 0.00 4.02
284 285 1.390565 CTACCCTGTACTCCGTGGAG 58.609 60.000 14.35 14.35 46.91 3.86
285 286 0.033796 TACCCTGTACTCCGTGGAGG 60.034 60.000 19.60 4.60 45.88 4.30
299 300 6.740944 TCCGTGGAGGATATGAAATAAGAA 57.259 37.500 0.00 0.00 45.98 2.52
300 301 7.131907 TCCGTGGAGGATATGAAATAAGAAA 57.868 36.000 0.00 0.00 45.98 2.52
301 302 7.570132 TCCGTGGAGGATATGAAATAAGAAAA 58.430 34.615 0.00 0.00 45.98 2.29
302 303 7.715249 TCCGTGGAGGATATGAAATAAGAAAAG 59.285 37.037 0.00 0.00 45.98 2.27
303 304 7.499232 CCGTGGAGGATATGAAATAAGAAAAGT 59.501 37.037 0.00 0.00 45.00 2.66
304 305 8.552034 CGTGGAGGATATGAAATAAGAAAAGTC 58.448 37.037 0.00 0.00 29.06 3.01
305 306 9.620259 GTGGAGGATATGAAATAAGAAAAGTCT 57.380 33.333 0.00 0.00 34.72 3.24
313 314 7.448748 TGAAATAAGAAAAGTCTAGTTGCCC 57.551 36.000 0.00 0.00 32.16 5.36
314 315 7.231467 TGAAATAAGAAAAGTCTAGTTGCCCT 58.769 34.615 0.00 0.00 32.16 5.19
315 316 7.390718 TGAAATAAGAAAAGTCTAGTTGCCCTC 59.609 37.037 0.00 0.00 32.16 4.30
316 317 4.706842 AAGAAAAGTCTAGTTGCCCTCA 57.293 40.909 0.00 0.00 32.16 3.86
317 318 4.917906 AGAAAAGTCTAGTTGCCCTCAT 57.082 40.909 0.00 0.00 29.93 2.90
318 319 4.837972 AGAAAAGTCTAGTTGCCCTCATC 58.162 43.478 0.00 0.00 29.93 2.92
319 320 3.636153 AAAGTCTAGTTGCCCTCATCC 57.364 47.619 0.00 0.00 0.00 3.51
320 321 1.501582 AGTCTAGTTGCCCTCATCCC 58.498 55.000 0.00 0.00 0.00 3.85
321 322 0.470341 GTCTAGTTGCCCTCATCCCC 59.530 60.000 0.00 0.00 0.00 4.81
322 323 0.343372 TCTAGTTGCCCTCATCCCCT 59.657 55.000 0.00 0.00 0.00 4.79
323 324 1.216990 CTAGTTGCCCTCATCCCCTT 58.783 55.000 0.00 0.00 0.00 3.95
324 325 1.566231 CTAGTTGCCCTCATCCCCTTT 59.434 52.381 0.00 0.00 0.00 3.11
325 326 0.332972 AGTTGCCCTCATCCCCTTTC 59.667 55.000 0.00 0.00 0.00 2.62
326 327 0.332972 GTTGCCCTCATCCCCTTTCT 59.667 55.000 0.00 0.00 0.00 2.52
327 328 0.625849 TTGCCCTCATCCCCTTTCTC 59.374 55.000 0.00 0.00 0.00 2.87
328 329 0.253347 TGCCCTCATCCCCTTTCTCT 60.253 55.000 0.00 0.00 0.00 3.10
329 330 0.472044 GCCCTCATCCCCTTTCTCTC 59.528 60.000 0.00 0.00 0.00 3.20
330 331 1.135960 CCCTCATCCCCTTTCTCTCC 58.864 60.000 0.00 0.00 0.00 3.71
331 332 1.344906 CCCTCATCCCCTTTCTCTCCT 60.345 57.143 0.00 0.00 0.00 3.69
332 333 2.486716 CCTCATCCCCTTTCTCTCCTT 58.513 52.381 0.00 0.00 0.00 3.36
333 334 2.437651 CCTCATCCCCTTTCTCTCCTTC 59.562 54.545 0.00 0.00 0.00 3.46
334 335 3.383223 CTCATCCCCTTTCTCTCCTTCT 58.617 50.000 0.00 0.00 0.00 2.85
335 336 3.379452 TCATCCCCTTTCTCTCCTTCTC 58.621 50.000 0.00 0.00 0.00 2.87
336 337 3.110705 CATCCCCTTTCTCTCCTTCTCA 58.889 50.000 0.00 0.00 0.00 3.27
337 338 2.541466 TCCCCTTTCTCTCCTTCTCAC 58.459 52.381 0.00 0.00 0.00 3.51
338 339 1.557371 CCCCTTTCTCTCCTTCTCACC 59.443 57.143 0.00 0.00 0.00 4.02
339 340 2.545810 CCCTTTCTCTCCTTCTCACCT 58.454 52.381 0.00 0.00 0.00 4.00
340 341 3.566775 CCCCTTTCTCTCCTTCTCACCTA 60.567 52.174 0.00 0.00 0.00 3.08
341 342 4.294347 CCCTTTCTCTCCTTCTCACCTAT 58.706 47.826 0.00 0.00 0.00 2.57
342 343 4.343814 CCCTTTCTCTCCTTCTCACCTATC 59.656 50.000 0.00 0.00 0.00 2.08
343 344 4.343814 CCTTTCTCTCCTTCTCACCTATCC 59.656 50.000 0.00 0.00 0.00 2.59
344 345 4.890499 TTCTCTCCTTCTCACCTATCCT 57.110 45.455 0.00 0.00 0.00 3.24
345 346 4.177537 TCTCTCCTTCTCACCTATCCTG 57.822 50.000 0.00 0.00 0.00 3.86
346 347 2.627699 CTCTCCTTCTCACCTATCCTGC 59.372 54.545 0.00 0.00 0.00 4.85
347 348 2.246067 TCTCCTTCTCACCTATCCTGCT 59.754 50.000 0.00 0.00 0.00 4.24
348 349 2.627699 CTCCTTCTCACCTATCCTGCTC 59.372 54.545 0.00 0.00 0.00 4.26
349 350 1.691434 CCTTCTCACCTATCCTGCTCC 59.309 57.143 0.00 0.00 0.00 4.70
350 351 2.676748 CTTCTCACCTATCCTGCTCCT 58.323 52.381 0.00 0.00 0.00 3.69
351 352 2.373335 TCTCACCTATCCTGCTCCTC 57.627 55.000 0.00 0.00 0.00 3.71
352 353 1.856259 TCTCACCTATCCTGCTCCTCT 59.144 52.381 0.00 0.00 0.00 3.69
353 354 2.158534 TCTCACCTATCCTGCTCCTCTC 60.159 54.545 0.00 0.00 0.00 3.20
354 355 1.133325 TCACCTATCCTGCTCCTCTCC 60.133 57.143 0.00 0.00 0.00 3.71
355 356 1.133199 CACCTATCCTGCTCCTCTCCT 60.133 57.143 0.00 0.00 0.00 3.69
356 357 1.146982 ACCTATCCTGCTCCTCTCCTC 59.853 57.143 0.00 0.00 0.00 3.71
357 358 1.533625 CTATCCTGCTCCTCTCCTCG 58.466 60.000 0.00 0.00 0.00 4.63
358 359 0.847373 TATCCTGCTCCTCTCCTCGT 59.153 55.000 0.00 0.00 0.00 4.18
359 360 0.467290 ATCCTGCTCCTCTCCTCGTC 60.467 60.000 0.00 0.00 0.00 4.20
360 361 2.124693 CCTGCTCCTCTCCTCGTCC 61.125 68.421 0.00 0.00 0.00 4.79
361 362 2.043852 TGCTCCTCTCCTCGTCCC 60.044 66.667 0.00 0.00 0.00 4.46
362 363 2.277404 GCTCCTCTCCTCGTCCCT 59.723 66.667 0.00 0.00 0.00 4.20
363 364 1.380650 GCTCCTCTCCTCGTCCCTT 60.381 63.158 0.00 0.00 0.00 3.95
364 365 0.106619 GCTCCTCTCCTCGTCCCTTA 60.107 60.000 0.00 0.00 0.00 2.69
365 366 1.682740 CTCCTCTCCTCGTCCCTTAC 58.317 60.000 0.00 0.00 0.00 2.34
366 367 0.258194 TCCTCTCCTCGTCCCTTACC 59.742 60.000 0.00 0.00 0.00 2.85
367 368 0.259356 CCTCTCCTCGTCCCTTACCT 59.741 60.000 0.00 0.00 0.00 3.08
368 369 1.682740 CTCTCCTCGTCCCTTACCTC 58.317 60.000 0.00 0.00 0.00 3.85
369 370 1.213430 CTCTCCTCGTCCCTTACCTCT 59.787 57.143 0.00 0.00 0.00 3.69
370 371 1.064611 TCTCCTCGTCCCTTACCTCTG 60.065 57.143 0.00 0.00 0.00 3.35
371 372 0.033405 TCCTCGTCCCTTACCTCTGG 60.033 60.000 0.00 0.00 0.00 3.86
372 373 1.677637 CCTCGTCCCTTACCTCTGGC 61.678 65.000 0.00 0.00 0.00 4.85
373 374 1.677637 CTCGTCCCTTACCTCTGGCC 61.678 65.000 0.00 0.00 0.00 5.36
374 375 1.987855 CGTCCCTTACCTCTGGCCA 60.988 63.158 4.71 4.71 0.00 5.36
375 376 1.338136 CGTCCCTTACCTCTGGCCAT 61.338 60.000 5.51 0.00 0.00 4.40
376 377 0.181350 GTCCCTTACCTCTGGCCATG 59.819 60.000 5.51 1.69 0.00 3.66
377 378 0.044092 TCCCTTACCTCTGGCCATGA 59.956 55.000 5.51 5.20 0.00 3.07
378 379 0.918983 CCCTTACCTCTGGCCATGAA 59.081 55.000 5.51 0.00 0.00 2.57
379 380 1.133976 CCCTTACCTCTGGCCATGAAG 60.134 57.143 5.51 4.22 0.00 3.02
380 381 1.673168 CTTACCTCTGGCCATGAAGC 58.327 55.000 5.51 0.00 0.00 3.86
387 388 2.595754 GGCCATGAAGCCGATCCC 60.596 66.667 0.00 0.00 44.57 3.85
388 389 2.595754 GCCATGAAGCCGATCCCC 60.596 66.667 0.00 0.00 0.00 4.81
389 390 3.125376 GCCATGAAGCCGATCCCCT 62.125 63.158 0.00 0.00 0.00 4.79
390 391 1.072159 CCATGAAGCCGATCCCCTC 59.928 63.158 0.00 0.00 0.00 4.30
391 392 1.414061 CCATGAAGCCGATCCCCTCT 61.414 60.000 0.00 0.00 0.00 3.69
392 393 0.471617 CATGAAGCCGATCCCCTCTT 59.528 55.000 0.00 0.00 0.00 2.85
393 394 0.471617 ATGAAGCCGATCCCCTCTTG 59.528 55.000 0.00 0.00 0.00 3.02
394 395 1.147153 GAAGCCGATCCCCTCTTGG 59.853 63.158 0.00 0.00 0.00 3.61
911 935 2.863740 TGTTGCTACGCTCCAAATATCG 59.136 45.455 0.00 0.00 0.00 2.92
1156 1201 1.055849 GGCCCCTTTGACAAATTGGT 58.944 50.000 14.13 0.00 0.00 3.67
1259 1309 4.440103 CGACGACACAAAGGTATGTATAGC 59.560 45.833 0.00 0.00 30.84 2.97
1260 1310 5.333299 ACGACACAAAGGTATGTATAGCA 57.667 39.130 0.00 0.00 33.40 3.49
1331 1386 2.702261 TGCATACGGAAGGTTTACCAC 58.298 47.619 1.13 0.00 38.89 4.16
1950 2024 4.265073 AGTGCACCTTCCAATCATCTTAC 58.735 43.478 14.63 0.00 0.00 2.34
1951 2025 4.018960 AGTGCACCTTCCAATCATCTTACT 60.019 41.667 14.63 0.00 0.00 2.24
1952 2026 4.702131 GTGCACCTTCCAATCATCTTACTT 59.298 41.667 5.22 0.00 0.00 2.24
1953 2027 4.701651 TGCACCTTCCAATCATCTTACTTG 59.298 41.667 0.00 0.00 0.00 3.16
1954 2028 4.096984 GCACCTTCCAATCATCTTACTTGG 59.903 45.833 0.00 0.00 40.66 3.61
2393 2471 2.353030 CGACTGCACGACACGACA 60.353 61.111 0.00 0.00 35.09 4.35
2510 2588 6.716934 ATCATTATCGACCAGAACTACTGT 57.283 37.500 0.00 0.00 44.40 3.55
2735 2818 6.366340 TGTGTTGTTTAAGAACATTAGGGGA 58.634 36.000 10.74 0.00 44.71 4.81
2815 2898 1.804151 GATAGCCTTGCACAACGTCAA 59.196 47.619 0.00 0.00 0.00 3.18
2956 3039 2.477863 GGATTTGAAACGGAATCGCTGG 60.478 50.000 0.00 0.00 40.63 4.85
3017 3104 2.194271 GTTTCGATACGCTTCCTCTGG 58.806 52.381 0.00 0.00 0.00 3.86
3043 3130 2.094390 CCAAGTGAAGTCATGCAATGGG 60.094 50.000 0.00 0.00 46.73 4.00
3112 3207 8.554528 CATTGAAATGTATAGAAGTAGGCACAG 58.445 37.037 0.00 0.00 0.00 3.66
3121 3216 2.320681 AGTAGGCACAGTAGTTGGGA 57.679 50.000 0.00 0.00 28.76 4.37
3140 3235 2.584608 CCTGGGGCTTACGGTGAG 59.415 66.667 0.00 0.00 0.00 3.51
3141 3236 2.291043 CCTGGGGCTTACGGTGAGT 61.291 63.158 1.71 0.00 0.00 3.41
3279 3434 6.499106 AATTTTGAAAAGGACCTTGGATGT 57.501 33.333 7.72 0.00 0.00 3.06
3306 3461 0.102120 CGAAGAGAAGAGATGCGGCT 59.898 55.000 0.00 0.00 0.00 5.52
3442 3597 3.142951 TGAACAATAACCACACGGGAAG 58.857 45.455 0.00 0.00 41.15 3.46
3503 3659 2.439701 CAGCTGGATGCCCACCTG 60.440 66.667 5.57 0.00 44.23 4.00
3542 3701 7.663905 AGCCTTCAAATTGTACAACACAGTATA 59.336 33.333 11.22 0.00 38.72 1.47
3571 3730 7.894376 AATTGTATTCCAAAAGAGCACAATG 57.106 32.000 0.00 0.00 39.12 2.82
3604 3763 1.337703 TGCTGCGATTTTTGCTCTGTT 59.662 42.857 0.00 0.00 0.00 3.16
3663 3822 5.946486 TGGCTCAGAGAGATCACTAAGATA 58.054 41.667 0.00 0.00 37.00 1.98
3695 3854 9.783256 AAATCAGTGTAATTAGAAATAAACGGC 57.217 29.630 0.00 0.00 0.00 5.68
3698 3857 4.965762 GTGTAATTAGAAATAAACGGCCGC 59.034 41.667 28.58 6.84 0.00 6.53
3700 3859 4.976224 AATTAGAAATAAACGGCCGCTT 57.024 36.364 28.58 23.41 0.00 4.68
3722 3882 6.462067 GCTTCTTTATTCGTTACCTAGGCCTA 60.462 42.308 13.09 13.09 0.00 3.93
3773 3950 2.032681 GTGTGACAGCCCCAGGAC 59.967 66.667 0.00 0.00 0.00 3.85
3847 4024 0.104671 TGCCAAGCACAAGGAAAAGC 59.895 50.000 0.00 0.00 31.71 3.51
3871 4048 6.470556 GCTGACACGCTATATATGATACACAG 59.529 42.308 0.00 0.00 0.00 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 3.290710 ACTTTGACCTGCACAATTGAGT 58.709 40.909 13.59 0.00 0.00 3.41
14 15 2.016318 CACTGAACTTTGACCTGCACA 58.984 47.619 0.00 0.00 0.00 4.57
32 33 1.544691 TCAGGAGCTAACGAAGACCAC 59.455 52.381 0.00 0.00 0.00 4.16
35 36 3.449632 GGATTCAGGAGCTAACGAAGAC 58.550 50.000 0.00 0.00 0.00 3.01
41 42 1.120530 TCGGGGATTCAGGAGCTAAC 58.879 55.000 0.00 0.00 0.00 2.34
57 58 2.037772 CAGAATAATCCTCCCAGGTCGG 59.962 54.545 0.00 0.00 36.53 4.79
64 65 2.548920 CGGAGCACAGAATAATCCTCCC 60.549 54.545 0.00 0.00 36.39 4.30
94 95 3.570212 AACAGCTTGCCTCCGGGT 61.570 61.111 0.00 0.00 34.45 5.28
137 138 0.883833 CAGGTGTGACATTTGCCTCC 59.116 55.000 0.00 0.00 0.00 4.30
157 158 3.574396 CAGGTCCACCGATACTCATGTAT 59.426 47.826 0.00 0.00 41.65 2.29
159 160 1.757118 CAGGTCCACCGATACTCATGT 59.243 52.381 0.00 0.00 42.08 3.21
160 161 1.069204 CCAGGTCCACCGATACTCATG 59.931 57.143 0.00 0.00 42.08 3.07
161 162 1.063190 TCCAGGTCCACCGATACTCAT 60.063 52.381 0.00 0.00 42.08 2.90
162 163 0.333652 TCCAGGTCCACCGATACTCA 59.666 55.000 0.00 0.00 42.08 3.41
163 164 1.409427 CTTCCAGGTCCACCGATACTC 59.591 57.143 0.00 0.00 42.08 2.59
164 165 1.486211 CTTCCAGGTCCACCGATACT 58.514 55.000 0.00 0.00 42.08 2.12
165 166 0.464452 CCTTCCAGGTCCACCGATAC 59.536 60.000 0.00 0.00 42.08 2.24
166 167 2.910579 CCTTCCAGGTCCACCGATA 58.089 57.895 0.00 0.00 42.08 2.92
167 168 3.727387 CCTTCCAGGTCCACCGAT 58.273 61.111 0.00 0.00 42.08 4.18
176 177 6.995091 CCTTTCTATCTATTTCACCTTCCAGG 59.005 42.308 0.00 0.00 42.49 4.45
177 178 6.995091 CCCTTTCTATCTATTTCACCTTCCAG 59.005 42.308 0.00 0.00 0.00 3.86
178 179 6.126478 CCCCTTTCTATCTATTTCACCTTCCA 60.126 42.308 0.00 0.00 0.00 3.53
179 180 6.126449 ACCCCTTTCTATCTATTTCACCTTCC 60.126 42.308 0.00 0.00 0.00 3.46
180 181 6.768381 CACCCCTTTCTATCTATTTCACCTTC 59.232 42.308 0.00 0.00 0.00 3.46
181 182 6.447084 TCACCCCTTTCTATCTATTTCACCTT 59.553 38.462 0.00 0.00 0.00 3.50
182 183 5.970640 TCACCCCTTTCTATCTATTTCACCT 59.029 40.000 0.00 0.00 0.00 4.00
183 184 6.248569 TCACCCCTTTCTATCTATTTCACC 57.751 41.667 0.00 0.00 0.00 4.02
184 185 5.760743 GCTCACCCCTTTCTATCTATTTCAC 59.239 44.000 0.00 0.00 0.00 3.18
185 186 5.453339 CGCTCACCCCTTTCTATCTATTTCA 60.453 44.000 0.00 0.00 0.00 2.69
186 187 4.991687 CGCTCACCCCTTTCTATCTATTTC 59.008 45.833 0.00 0.00 0.00 2.17
187 188 4.409247 ACGCTCACCCCTTTCTATCTATTT 59.591 41.667 0.00 0.00 0.00 1.40
188 189 3.967987 ACGCTCACCCCTTTCTATCTATT 59.032 43.478 0.00 0.00 0.00 1.73
189 190 3.322254 CACGCTCACCCCTTTCTATCTAT 59.678 47.826 0.00 0.00 0.00 1.98
190 191 2.693591 CACGCTCACCCCTTTCTATCTA 59.306 50.000 0.00 0.00 0.00 1.98
191 192 1.482593 CACGCTCACCCCTTTCTATCT 59.517 52.381 0.00 0.00 0.00 1.98
192 193 1.207329 ACACGCTCACCCCTTTCTATC 59.793 52.381 0.00 0.00 0.00 2.08
193 194 1.066143 CACACGCTCACCCCTTTCTAT 60.066 52.381 0.00 0.00 0.00 1.98
194 195 0.320374 CACACGCTCACCCCTTTCTA 59.680 55.000 0.00 0.00 0.00 2.10
195 196 1.071471 CACACGCTCACCCCTTTCT 59.929 57.895 0.00 0.00 0.00 2.52
196 197 1.227853 ACACACGCTCACCCCTTTC 60.228 57.895 0.00 0.00 0.00 2.62
197 198 1.525995 CACACACGCTCACCCCTTT 60.526 57.895 0.00 0.00 0.00 3.11
198 199 2.111043 CACACACGCTCACCCCTT 59.889 61.111 0.00 0.00 0.00 3.95
199 200 3.161450 ACACACACGCTCACCCCT 61.161 61.111 0.00 0.00 0.00 4.79
200 201 2.972505 CACACACACGCTCACCCC 60.973 66.667 0.00 0.00 0.00 4.95
201 202 3.649986 GCACACACACGCTCACCC 61.650 66.667 0.00 0.00 0.00 4.61
202 203 3.649986 GGCACACACACGCTCACC 61.650 66.667 0.00 0.00 0.00 4.02
203 204 2.885676 CTGGCACACACACGCTCAC 61.886 63.158 0.00 0.00 0.00 3.51
204 205 2.588596 CTGGCACACACACGCTCA 60.589 61.111 0.00 0.00 0.00 4.26
205 206 2.588877 ACTGGCACACACACGCTC 60.589 61.111 0.00 0.00 0.00 5.03
206 207 2.896854 CACTGGCACACACACGCT 60.897 61.111 0.00 0.00 0.00 5.07
207 208 3.952675 CCACTGGCACACACACGC 61.953 66.667 0.00 0.00 0.00 5.34
208 209 3.279116 CCCACTGGCACACACACG 61.279 66.667 0.00 0.00 0.00 4.49
218 219 2.677524 CCACATGTGGCCCACTGG 60.678 66.667 31.13 10.85 44.73 4.00
227 228 3.740397 CACGCCTGGCCACATGTG 61.740 66.667 19.31 19.31 0.00 3.21
228 229 4.269523 ACACGCCTGGCCACATGT 62.270 61.111 14.12 9.73 0.00 3.21
229 230 3.740397 CACACGCCTGGCCACATG 61.740 66.667 14.12 9.07 0.00 3.21
230 231 4.269523 ACACACGCCTGGCCACAT 62.270 61.111 14.12 0.00 0.00 3.21
236 237 3.185082 CTTGCACACACACGCCTGG 62.185 63.158 0.00 0.00 0.00 4.45
237 238 1.157257 TACTTGCACACACACGCCTG 61.157 55.000 0.00 0.00 0.00 4.85
238 239 0.250295 ATACTTGCACACACACGCCT 60.250 50.000 0.00 0.00 0.00 5.52
239 240 1.434555 TATACTTGCACACACACGCC 58.565 50.000 0.00 0.00 0.00 5.68
240 241 2.734606 TCTTATACTTGCACACACACGC 59.265 45.455 0.00 0.00 0.00 5.34
241 242 4.090066 GTCTCTTATACTTGCACACACACG 59.910 45.833 0.00 0.00 0.00 4.49
242 243 4.389077 GGTCTCTTATACTTGCACACACAC 59.611 45.833 0.00 0.00 0.00 3.82
243 244 4.283467 AGGTCTCTTATACTTGCACACACA 59.717 41.667 0.00 0.00 0.00 3.72
244 245 4.822026 AGGTCTCTTATACTTGCACACAC 58.178 43.478 0.00 0.00 0.00 3.82
245 246 5.105473 GGTAGGTCTCTTATACTTGCACACA 60.105 44.000 0.00 0.00 0.00 3.72
246 247 5.349809 GGTAGGTCTCTTATACTTGCACAC 58.650 45.833 0.00 0.00 0.00 3.82
247 248 4.404715 GGGTAGGTCTCTTATACTTGCACA 59.595 45.833 0.00 0.00 0.00 4.57
248 249 4.650131 AGGGTAGGTCTCTTATACTTGCAC 59.350 45.833 0.00 0.00 0.00 4.57
249 250 4.649674 CAGGGTAGGTCTCTTATACTTGCA 59.350 45.833 0.00 0.00 0.00 4.08
250 251 4.650131 ACAGGGTAGGTCTCTTATACTTGC 59.350 45.833 0.00 0.00 0.00 4.01
251 252 7.061688 AGTACAGGGTAGGTCTCTTATACTTG 58.938 42.308 0.00 0.00 27.41 3.16
252 253 7.223472 AGTACAGGGTAGGTCTCTTATACTT 57.777 40.000 0.00 0.00 27.41 2.24
253 254 6.183361 GGAGTACAGGGTAGGTCTCTTATACT 60.183 46.154 0.00 0.00 32.00 2.12
254 255 6.003326 GGAGTACAGGGTAGGTCTCTTATAC 58.997 48.000 0.00 0.00 0.00 1.47
255 256 5.221803 CGGAGTACAGGGTAGGTCTCTTATA 60.222 48.000 0.00 0.00 0.00 0.98
256 257 4.446023 CGGAGTACAGGGTAGGTCTCTTAT 60.446 50.000 0.00 0.00 0.00 1.73
257 258 3.118112 CGGAGTACAGGGTAGGTCTCTTA 60.118 52.174 0.00 0.00 0.00 2.10
258 259 2.356947 CGGAGTACAGGGTAGGTCTCTT 60.357 54.545 0.00 0.00 0.00 2.85
259 260 1.212441 CGGAGTACAGGGTAGGTCTCT 59.788 57.143 0.00 0.00 0.00 3.10
260 261 1.064832 ACGGAGTACAGGGTAGGTCTC 60.065 57.143 0.00 0.00 41.94 3.36
261 262 0.998145 ACGGAGTACAGGGTAGGTCT 59.002 55.000 0.00 0.00 41.94 3.85
262 263 1.101331 CACGGAGTACAGGGTAGGTC 58.899 60.000 0.00 0.00 41.61 3.85
263 264 0.324091 CCACGGAGTACAGGGTAGGT 60.324 60.000 0.00 0.00 41.61 3.08
264 265 0.033796 TCCACGGAGTACAGGGTAGG 60.034 60.000 0.00 0.00 41.61 3.18
265 266 1.390565 CTCCACGGAGTACAGGGTAG 58.609 60.000 4.83 0.00 41.61 3.18
266 267 0.033796 CCTCCACGGAGTACAGGGTA 60.034 60.000 12.08 0.00 41.61 3.69
267 268 1.305046 CCTCCACGGAGTACAGGGT 60.305 63.158 12.08 0.00 41.61 4.34
268 269 1.000019 TCCTCCACGGAGTACAGGG 60.000 63.158 12.08 0.00 41.61 4.45
269 270 4.757773 TCCTCCACGGAGTACAGG 57.242 61.111 12.08 0.00 41.61 4.00
277 278 7.499232 ACTTTTCTTATTTCATATCCTCCACGG 59.501 37.037 0.00 0.00 0.00 4.94
278 279 8.438676 ACTTTTCTTATTTCATATCCTCCACG 57.561 34.615 0.00 0.00 0.00 4.94
279 280 9.620259 AGACTTTTCTTATTTCATATCCTCCAC 57.380 33.333 0.00 0.00 0.00 4.02
287 288 9.174166 GGGCAACTAGACTTTTCTTATTTCATA 57.826 33.333 0.00 0.00 32.75 2.15
288 289 7.890655 AGGGCAACTAGACTTTTCTTATTTCAT 59.109 33.333 0.00 0.00 32.75 2.57
289 290 7.231467 AGGGCAACTAGACTTTTCTTATTTCA 58.769 34.615 0.00 0.00 32.75 2.69
290 291 7.390718 TGAGGGCAACTAGACTTTTCTTATTTC 59.609 37.037 0.00 0.00 32.75 2.17
291 292 7.231467 TGAGGGCAACTAGACTTTTCTTATTT 58.769 34.615 0.00 0.00 32.75 1.40
292 293 6.779860 TGAGGGCAACTAGACTTTTCTTATT 58.220 36.000 0.00 0.00 32.75 1.40
293 294 6.374417 TGAGGGCAACTAGACTTTTCTTAT 57.626 37.500 0.00 0.00 32.75 1.73
294 295 5.818678 TGAGGGCAACTAGACTTTTCTTA 57.181 39.130 0.00 0.00 32.75 2.10
295 296 4.706842 TGAGGGCAACTAGACTTTTCTT 57.293 40.909 0.00 0.00 32.75 2.52
296 297 4.323868 GGATGAGGGCAACTAGACTTTTCT 60.324 45.833 0.00 0.00 35.66 2.52
297 298 3.942115 GGATGAGGGCAACTAGACTTTTC 59.058 47.826 0.00 0.00 0.00 2.29
298 299 3.308473 GGGATGAGGGCAACTAGACTTTT 60.308 47.826 0.00 0.00 0.00 2.27
299 300 2.239907 GGGATGAGGGCAACTAGACTTT 59.760 50.000 0.00 0.00 0.00 2.66
300 301 1.840635 GGGATGAGGGCAACTAGACTT 59.159 52.381 0.00 0.00 0.00 3.01
301 302 1.501582 GGGATGAGGGCAACTAGACT 58.498 55.000 0.00 0.00 0.00 3.24
302 303 0.470341 GGGGATGAGGGCAACTAGAC 59.530 60.000 0.00 0.00 0.00 2.59
303 304 0.343372 AGGGGATGAGGGCAACTAGA 59.657 55.000 0.00 0.00 0.00 2.43
304 305 1.216990 AAGGGGATGAGGGCAACTAG 58.783 55.000 0.00 0.00 0.00 2.57
305 306 1.564348 GAAAGGGGATGAGGGCAACTA 59.436 52.381 0.00 0.00 0.00 2.24
306 307 0.332972 GAAAGGGGATGAGGGCAACT 59.667 55.000 0.00 0.00 0.00 3.16
307 308 0.332972 AGAAAGGGGATGAGGGCAAC 59.667 55.000 0.00 0.00 0.00 4.17
308 309 0.625849 GAGAAAGGGGATGAGGGCAA 59.374 55.000 0.00 0.00 0.00 4.52
309 310 0.253347 AGAGAAAGGGGATGAGGGCA 60.253 55.000 0.00 0.00 0.00 5.36
310 311 0.472044 GAGAGAAAGGGGATGAGGGC 59.528 60.000 0.00 0.00 0.00 5.19
311 312 1.135960 GGAGAGAAAGGGGATGAGGG 58.864 60.000 0.00 0.00 0.00 4.30
312 313 2.188818 AGGAGAGAAAGGGGATGAGG 57.811 55.000 0.00 0.00 0.00 3.86
313 314 3.383223 AGAAGGAGAGAAAGGGGATGAG 58.617 50.000 0.00 0.00 0.00 2.90
314 315 3.246130 TGAGAAGGAGAGAAAGGGGATGA 60.246 47.826 0.00 0.00 0.00 2.92
315 316 3.110705 TGAGAAGGAGAGAAAGGGGATG 58.889 50.000 0.00 0.00 0.00 3.51
316 317 3.111484 GTGAGAAGGAGAGAAAGGGGAT 58.889 50.000 0.00 0.00 0.00 3.85
317 318 2.541466 GTGAGAAGGAGAGAAAGGGGA 58.459 52.381 0.00 0.00 0.00 4.81
318 319 1.557371 GGTGAGAAGGAGAGAAAGGGG 59.443 57.143 0.00 0.00 0.00 4.79
319 320 2.545810 AGGTGAGAAGGAGAGAAAGGG 58.454 52.381 0.00 0.00 0.00 3.95
320 321 4.343814 GGATAGGTGAGAAGGAGAGAAAGG 59.656 50.000 0.00 0.00 0.00 3.11
321 322 5.068987 CAGGATAGGTGAGAAGGAGAGAAAG 59.931 48.000 0.00 0.00 0.00 2.62
322 323 4.959210 CAGGATAGGTGAGAAGGAGAGAAA 59.041 45.833 0.00 0.00 0.00 2.52
323 324 4.541705 CAGGATAGGTGAGAAGGAGAGAA 58.458 47.826 0.00 0.00 0.00 2.87
324 325 3.689858 GCAGGATAGGTGAGAAGGAGAGA 60.690 52.174 0.00 0.00 0.00 3.10
325 326 2.627699 GCAGGATAGGTGAGAAGGAGAG 59.372 54.545 0.00 0.00 0.00 3.20
326 327 2.246067 AGCAGGATAGGTGAGAAGGAGA 59.754 50.000 0.00 0.00 0.00 3.71
327 328 2.627699 GAGCAGGATAGGTGAGAAGGAG 59.372 54.545 0.00 0.00 0.00 3.69
328 329 2.672098 GAGCAGGATAGGTGAGAAGGA 58.328 52.381 0.00 0.00 0.00 3.36
329 330 1.691434 GGAGCAGGATAGGTGAGAAGG 59.309 57.143 0.00 0.00 0.00 3.46
330 331 2.627699 GAGGAGCAGGATAGGTGAGAAG 59.372 54.545 0.00 0.00 0.00 2.85
331 332 2.246067 AGAGGAGCAGGATAGGTGAGAA 59.754 50.000 0.00 0.00 0.00 2.87
332 333 1.856259 AGAGGAGCAGGATAGGTGAGA 59.144 52.381 0.00 0.00 0.00 3.27
333 334 2.238521 GAGAGGAGCAGGATAGGTGAG 58.761 57.143 0.00 0.00 0.00 3.51
334 335 1.133325 GGAGAGGAGCAGGATAGGTGA 60.133 57.143 0.00 0.00 0.00 4.02
335 336 1.133199 AGGAGAGGAGCAGGATAGGTG 60.133 57.143 0.00 0.00 0.00 4.00
336 337 1.146982 GAGGAGAGGAGCAGGATAGGT 59.853 57.143 0.00 0.00 0.00 3.08
337 338 1.886222 CGAGGAGAGGAGCAGGATAGG 60.886 61.905 0.00 0.00 0.00 2.57
338 339 1.202879 ACGAGGAGAGGAGCAGGATAG 60.203 57.143 0.00 0.00 0.00 2.08
339 340 0.847373 ACGAGGAGAGGAGCAGGATA 59.153 55.000 0.00 0.00 0.00 2.59
340 341 0.467290 GACGAGGAGAGGAGCAGGAT 60.467 60.000 0.00 0.00 0.00 3.24
341 342 1.077357 GACGAGGAGAGGAGCAGGA 60.077 63.158 0.00 0.00 0.00 3.86
342 343 2.124693 GGACGAGGAGAGGAGCAGG 61.125 68.421 0.00 0.00 0.00 4.85
343 344 2.124693 GGGACGAGGAGAGGAGCAG 61.125 68.421 0.00 0.00 0.00 4.24
344 345 2.043852 GGGACGAGGAGAGGAGCA 60.044 66.667 0.00 0.00 0.00 4.26
345 346 0.106619 TAAGGGACGAGGAGAGGAGC 60.107 60.000 0.00 0.00 0.00 4.70
346 347 1.682740 GTAAGGGACGAGGAGAGGAG 58.317 60.000 0.00 0.00 0.00 3.69
347 348 0.258194 GGTAAGGGACGAGGAGAGGA 59.742 60.000 0.00 0.00 0.00 3.71
348 349 0.259356 AGGTAAGGGACGAGGAGAGG 59.741 60.000 0.00 0.00 0.00 3.69
349 350 1.213430 AGAGGTAAGGGACGAGGAGAG 59.787 57.143 0.00 0.00 0.00 3.20
350 351 1.064611 CAGAGGTAAGGGACGAGGAGA 60.065 57.143 0.00 0.00 0.00 3.71
351 352 1.394618 CAGAGGTAAGGGACGAGGAG 58.605 60.000 0.00 0.00 0.00 3.69
352 353 0.033405 CCAGAGGTAAGGGACGAGGA 60.033 60.000 0.00 0.00 0.00 3.71
353 354 1.677637 GCCAGAGGTAAGGGACGAGG 61.678 65.000 0.00 0.00 0.00 4.63
354 355 1.677637 GGCCAGAGGTAAGGGACGAG 61.678 65.000 0.00 0.00 0.00 4.18
355 356 1.684734 GGCCAGAGGTAAGGGACGA 60.685 63.158 0.00 0.00 0.00 4.20
356 357 1.338136 ATGGCCAGAGGTAAGGGACG 61.338 60.000 13.05 0.00 29.93 4.79
357 358 0.181350 CATGGCCAGAGGTAAGGGAC 59.819 60.000 13.05 0.00 0.00 4.46
358 359 0.044092 TCATGGCCAGAGGTAAGGGA 59.956 55.000 13.05 0.00 0.00 4.20
359 360 0.918983 TTCATGGCCAGAGGTAAGGG 59.081 55.000 13.05 0.00 0.00 3.95
360 361 1.748591 GCTTCATGGCCAGAGGTAAGG 60.749 57.143 13.05 0.00 0.00 2.69
361 362 1.673168 GCTTCATGGCCAGAGGTAAG 58.327 55.000 13.05 10.88 0.00 2.34
362 363 3.882131 GCTTCATGGCCAGAGGTAA 57.118 52.632 13.05 0.00 0.00 2.85
371 372 2.595754 GGGGATCGGCTTCATGGC 60.596 66.667 0.00 0.00 37.94 4.40
372 373 1.072159 GAGGGGATCGGCTTCATGG 59.928 63.158 0.00 0.00 0.00 3.66
373 374 0.471617 AAGAGGGGATCGGCTTCATG 59.528 55.000 0.00 0.00 0.00 3.07
374 375 0.471617 CAAGAGGGGATCGGCTTCAT 59.528 55.000 0.00 0.00 0.00 2.57
375 376 1.626356 CCAAGAGGGGATCGGCTTCA 61.626 60.000 0.00 0.00 0.00 3.02
376 377 1.147153 CCAAGAGGGGATCGGCTTC 59.853 63.158 0.00 0.00 0.00 3.86
377 378 3.324713 CCAAGAGGGGATCGGCTT 58.675 61.111 0.00 0.00 0.00 4.35
387 388 1.806542 CATTTGTGACGACCCAAGAGG 59.193 52.381 0.00 0.00 43.78 3.69
388 389 2.480419 GTCATTTGTGACGACCCAAGAG 59.520 50.000 0.00 0.00 0.00 2.85
389 390 2.489971 GTCATTTGTGACGACCCAAGA 58.510 47.619 0.00 0.00 0.00 3.02
390 391 1.535462 GGTCATTTGTGACGACCCAAG 59.465 52.381 0.00 0.00 42.87 3.61
391 392 1.600023 GGTCATTTGTGACGACCCAA 58.400 50.000 0.00 0.00 42.87 4.12
392 393 3.315765 GGTCATTTGTGACGACCCA 57.684 52.632 0.00 0.00 42.87 4.51
395 396 0.438830 GCGAGGTCATTTGTGACGAC 59.561 55.000 0.00 0.00 39.57 4.34
396 397 0.317160 AGCGAGGTCATTTGTGACGA 59.683 50.000 0.00 0.00 39.57 4.20
397 398 1.990799 TAGCGAGGTCATTTGTGACG 58.009 50.000 2.83 0.00 39.57 4.35
398 399 3.585862 TCTTAGCGAGGTCATTTGTGAC 58.414 45.455 0.05 0.05 38.04 3.67
399 400 3.953712 TCTTAGCGAGGTCATTTGTGA 57.046 42.857 0.00 0.00 0.00 3.58
400 401 3.242543 GCATCTTAGCGAGGTCATTTGTG 60.243 47.826 0.00 0.00 0.00 3.33
401 402 2.939103 GCATCTTAGCGAGGTCATTTGT 59.061 45.455 0.00 0.00 0.00 2.83
402 403 2.938451 TGCATCTTAGCGAGGTCATTTG 59.062 45.455 0.00 0.00 37.31 2.32
403 404 3.201290 CTGCATCTTAGCGAGGTCATTT 58.799 45.455 0.00 0.00 37.31 2.32
418 420 1.268437 GGAGATTTCTTGCGCTGCATC 60.268 52.381 9.73 3.28 38.76 3.91
636 639 7.039882 ACGTTTGAACCCTTACAGATGTATAG 58.960 38.462 0.00 0.00 0.00 1.31
911 935 4.640201 TGGTTGATTAGCTAAGTTGGCATC 59.360 41.667 14.14 8.99 0.00 3.91
1259 1309 9.409312 TGCTATGTATTTTGAGTTGATTTTGTG 57.591 29.630 0.00 0.00 0.00 3.33
1331 1386 2.331893 TGGATGCGCAAGAAACCCG 61.332 57.895 17.11 0.00 43.02 5.28
1807 1866 7.790861 ACTTTTTAAAGTTGACAGTGAAACG 57.209 32.000 0.00 0.00 46.52 3.60
1952 2026 3.557054 GGCTACTCGATTGGAATATGCCA 60.557 47.826 0.00 0.00 36.91 4.92
1953 2027 3.003480 GGCTACTCGATTGGAATATGCC 58.997 50.000 0.00 0.00 0.00 4.40
1954 2028 3.931578 AGGCTACTCGATTGGAATATGC 58.068 45.455 0.00 0.00 0.00 3.14
2174 2252 5.030147 TCCTTACTATGGGCGATATGGATT 58.970 41.667 0.00 0.00 0.00 3.01
2393 2471 4.471904 TGTCTTGATACGAGCTCCATTT 57.528 40.909 8.47 0.00 0.00 2.32
2510 2588 1.842052 TACATGGTGTAGCCGAGTCA 58.158 50.000 0.00 0.00 41.21 3.41
2815 2898 2.500504 CCCCCTCGTTTTAGAGTAAGCT 59.499 50.000 0.00 0.00 36.56 3.74
2956 3039 0.036671 AACTACAACTAGGCACGCCC 60.037 55.000 3.95 0.00 36.58 6.13
2960 3043 3.619038 GCTCATCAACTACAACTAGGCAC 59.381 47.826 0.00 0.00 0.00 5.01
3017 3104 3.141398 TGCATGACTTCACTTGGAGAAC 58.859 45.455 0.00 0.00 0.00 3.01
3043 3130 4.874396 TGCATGACTTCACTCAGAATCATC 59.126 41.667 0.00 0.00 34.84 2.92
3112 3207 2.998949 CCCCAGGCTCCCAACTAC 59.001 66.667 0.00 0.00 0.00 2.73
3268 3423 1.379044 CCCTGGCACATCCAAGGTC 60.379 63.158 0.00 0.00 46.01 3.85
3279 3434 1.892819 CTCTTCTCTTCGCCCTGGCA 61.893 60.000 9.17 0.00 42.06 4.92
3442 3597 7.967303 CAGCTGATTTCATTAACTCTTCCTTTC 59.033 37.037 8.42 0.00 0.00 2.62
3503 3659 5.643379 TTTGAAGGCTATGTTCAACCATC 57.357 39.130 0.00 0.00 42.27 3.51
3677 3836 5.413969 AGCGGCCGTTTATTTCTAATTAC 57.586 39.130 28.70 3.31 0.00 1.89
3695 3854 4.743644 CCTAGGTAACGAATAAAGAAGCGG 59.256 45.833 0.00 0.00 46.39 5.52
3698 3857 5.915175 AGGCCTAGGTAACGAATAAAGAAG 58.085 41.667 1.29 0.00 46.39 2.85
3700 3859 5.010415 GCTAGGCCTAGGTAACGAATAAAGA 59.990 44.000 35.44 0.65 46.39 2.52
3722 3882 0.532862 CAAGGACGTGTGGTGAAGCT 60.533 55.000 0.00 0.00 0.00 3.74
3773 3950 3.435671 GGTGGTAAAAGTCATGAACTCCG 59.564 47.826 0.00 0.00 37.17 4.63
3847 4024 7.530863 ACTGTGTATCATATATAGCGTGTCAG 58.469 38.462 0.00 0.00 0.00 3.51
3871 4048 5.374071 TGTTTTACTCTCAGGGAAGGAAAC 58.626 41.667 0.00 0.00 0.00 2.78


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

AutoCloner maintained by Alex Coulton.