Multiple sequence alignment - TraesCS1B01G122800

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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 TraesCS1B01G122800 chr1B 100.000 4127 0 0 1 4127 148417285 148413159 0.000000e+00 7622.0
1 TraesCS1B01G122800 chr1B 92.464 345 23 3 46 387 416353954 416353610 1.330000e-134 490.0
2 TraesCS1B01G122800 chr1B 94.515 237 13 0 116 352 533609390 533609154 2.340000e-97 366.0
3 TraesCS1B01G122800 chr1D 95.596 3724 115 26 450 4127 93105751 93102031 0.000000e+00 5923.0
4 TraesCS1B01G122800 chr1D 91.071 56 3 2 383 437 93105838 93105784 1.590000e-09 75.0
5 TraesCS1B01G122800 chr1A 95.553 3508 113 22 630 4124 90163848 90160371 0.000000e+00 5574.0
6 TraesCS1B01G122800 chr1A 89.080 174 10 3 465 630 90170804 90170632 1.500000e-49 207.0
7 TraesCS1B01G122800 chr2B 90.596 2733 199 28 651 3349 214280766 214283474 0.000000e+00 3570.0
8 TraesCS1B01G122800 chr2B 89.255 2764 217 40 554 3252 214312467 214315215 0.000000e+00 3386.0
9 TraesCS1B01G122800 chr2D 89.935 2762 196 44 554 3252 156707004 156709746 0.000000e+00 3485.0
10 TraesCS1B01G122800 chr2D 92.311 2354 173 6 1010 3360 156592469 156594817 0.000000e+00 3338.0
11 TraesCS1B01G122800 chr2D 90.066 2577 206 33 622 3170 182576300 182573746 0.000000e+00 3295.0
12 TraesCS1B01G122800 chr2A 90.143 2587 191 38 633 3170 197566577 197564006 0.000000e+00 3306.0
13 TraesCS1B01G122800 chr2A 91.497 2411 177 11 578 2977 166254147 166256540 0.000000e+00 3291.0
14 TraesCS1B01G122800 chr2A 92.269 2212 164 5 960 3169 166628058 166630264 0.000000e+00 3131.0
15 TraesCS1B01G122800 chr2A 86.471 1020 106 20 730 1723 197344832 197343819 0.000000e+00 1090.0
16 TraesCS1B01G122800 chr2A 87.833 263 26 4 3100 3360 166256549 166256807 1.860000e-78 303.0
17 TraesCS1B01G122800 chr2A 81.915 94 6 5 3170 3252 166630281 166630374 7.400000e-08 69.4
18 TraesCS1B01G122800 chr7A 93.455 382 24 1 1 381 622376038 622376419 2.150000e-157 566.0
19 TraesCS1B01G122800 chr3A 88.798 366 40 1 17 381 720597787 720597422 8.140000e-122 448.0
20 TraesCS1B01G122800 chr7D 91.534 189 15 1 199 386 403271959 403272147 4.090000e-65 259.0


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 TraesCS1B01G122800 chr1B 148413159 148417285 4126 True 7622.0 7622 100.0000 1 4127 1 chr1B.!!$R1 4126
1 TraesCS1B01G122800 chr1D 93102031 93105838 3807 True 2999.0 5923 93.3335 383 4127 2 chr1D.!!$R1 3744
2 TraesCS1B01G122800 chr1A 90160371 90163848 3477 True 5574.0 5574 95.5530 630 4124 1 chr1A.!!$R1 3494
3 TraesCS1B01G122800 chr2B 214280766 214283474 2708 False 3570.0 3570 90.5960 651 3349 1 chr2B.!!$F1 2698
4 TraesCS1B01G122800 chr2B 214312467 214315215 2748 False 3386.0 3386 89.2550 554 3252 1 chr2B.!!$F2 2698
5 TraesCS1B01G122800 chr2D 156707004 156709746 2742 False 3485.0 3485 89.9350 554 3252 1 chr2D.!!$F2 2698
6 TraesCS1B01G122800 chr2D 156592469 156594817 2348 False 3338.0 3338 92.3110 1010 3360 1 chr2D.!!$F1 2350
7 TraesCS1B01G122800 chr2D 182573746 182576300 2554 True 3295.0 3295 90.0660 622 3170 1 chr2D.!!$R1 2548
8 TraesCS1B01G122800 chr2A 197564006 197566577 2571 True 3306.0 3306 90.1430 633 3170 1 chr2A.!!$R2 2537
9 TraesCS1B01G122800 chr2A 166254147 166256807 2660 False 1797.0 3291 89.6650 578 3360 2 chr2A.!!$F1 2782
10 TraesCS1B01G122800 chr2A 166628058 166630374 2316 False 1600.2 3131 87.0920 960 3252 2 chr2A.!!$F2 2292
11 TraesCS1B01G122800 chr2A 197343819 197344832 1013 True 1090.0 1090 86.4710 730 1723 1 chr2A.!!$R1 993

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
243 244 0.030908 GGGAGACGCGTGGATAGAAG 59.969 60.0 20.7 0.0 0.00 2.85 F
244 245 0.030908 GGAGACGCGTGGATAGAAGG 59.969 60.0 20.7 0.0 0.00 3.46 F
249 250 0.038159 CGCGTGGATAGAAGGGGATC 60.038 60.0 0.0 0.0 0.00 3.36 F
258 259 0.123266 AGAAGGGGATCAAAGGGGGA 59.877 55.0 0.0 0.0 0.00 4.81 F
267 268 0.178816 TCAAAGGGGGATGGAAGGGA 60.179 55.0 0.0 0.0 0.00 4.20 F
278 279 0.185901 TGGAAGGGATTGGGCTATGC 59.814 55.0 0.0 0.0 0.00 3.14 F
859 951 0.253347 TCCAAGAAGAGCATCCCCCT 60.253 55.0 0.0 0.0 33.66 4.79 F
1614 1784 0.259065 TCCCACTCTCCTACATCGCT 59.741 55.0 0.0 0.0 0.00 4.93 F
2276 2447 0.607217 TCGGAGCTGGTGAACGACTA 60.607 55.0 0.0 0.0 0.00 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1950 2121 0.031716 TCATGTAGGAGCTGCCCTCT 60.032 55.000 12.11 3.09 40.57 3.69 R
2199 2370 1.238439 CAAGCCTCGTGTTGTCCATT 58.762 50.000 0.00 0.00 0.00 3.16 R
2253 2424 0.108615 CGTTCACCAGCTCCGAGAAT 60.109 55.000 0.00 0.00 0.00 2.40 R
2265 2436 4.387862 CCATTGTTGTAGTAGTCGTTCACC 59.612 45.833 0.00 0.00 0.00 4.02 R
2276 2447 1.203050 AGGGCAAGCCATTGTTGTAGT 60.203 47.619 13.87 0.00 38.76 2.73 R
2326 2497 1.992557 ACCCTTGAAGCCATAGTCCAA 59.007 47.619 0.00 0.00 0.00 3.53 R
2694 2865 2.867472 GCGTATGCAAACACCGCT 59.133 55.556 0.89 0.00 42.87 5.52 R
3081 3252 0.178921 TCCACTCCTTCAGGCACTCT 60.179 55.000 0.00 0.00 34.60 3.24 R
3733 3955 0.107312 ACTGTGCATCTGAGCCATCC 60.107 55.000 0.00 0.00 0.00 3.51 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
73 74 4.379243 CGTGGTCCCGCAGAAGCT 62.379 66.667 0.00 0.00 39.10 3.74
74 75 2.435059 GTGGTCCCGCAGAAGCTC 60.435 66.667 0.00 0.00 39.10 4.09
75 76 3.706373 TGGTCCCGCAGAAGCTCC 61.706 66.667 0.00 0.00 39.10 4.70
76 77 4.821589 GGTCCCGCAGAAGCTCCG 62.822 72.222 0.00 0.00 39.10 4.63
122 123 4.851214 GGCGGAGGAGAGGGAGCT 62.851 72.222 0.00 0.00 0.00 4.09
123 124 3.223589 GCGGAGGAGAGGGAGCTC 61.224 72.222 4.71 4.71 0.00 4.09
124 125 2.904866 CGGAGGAGAGGGAGCTCG 60.905 72.222 7.83 0.00 35.74 5.03
125 126 3.223589 GGAGGAGAGGGAGCTCGC 61.224 72.222 22.44 22.44 35.74 5.03
126 127 3.591835 GAGGAGAGGGAGCTCGCG 61.592 72.222 23.41 0.00 35.74 5.87
184 185 3.453988 GGAGGCCGAGATGGAGAG 58.546 66.667 0.00 0.00 42.00 3.20
185 186 2.206536 GGAGGCCGAGATGGAGAGG 61.207 68.421 0.00 0.00 42.00 3.69
188 189 4.292178 GCCGAGATGGAGAGGCGG 62.292 72.222 0.00 0.00 44.47 6.13
189 190 3.610669 CCGAGATGGAGAGGCGGG 61.611 72.222 0.00 0.00 42.00 6.13
190 191 4.292178 CGAGATGGAGAGGCGGGC 62.292 72.222 0.00 0.00 0.00 6.13
191 192 4.292178 GAGATGGAGAGGCGGGCG 62.292 72.222 0.00 0.00 0.00 6.13
211 212 4.012895 GCGTGTTCCCTGCGTGTG 62.013 66.667 0.00 0.00 0.00 3.82
212 213 4.012895 CGTGTTCCCTGCGTGTGC 62.013 66.667 0.00 0.00 43.20 4.57
213 214 3.660111 GTGTTCCCTGCGTGTGCC 61.660 66.667 0.00 0.00 41.78 5.01
214 215 4.947147 TGTTCCCTGCGTGTGCCC 62.947 66.667 0.00 0.00 41.78 5.36
215 216 4.643387 GTTCCCTGCGTGTGCCCT 62.643 66.667 0.00 0.00 41.78 5.19
216 217 4.329545 TTCCCTGCGTGTGCCCTC 62.330 66.667 0.00 0.00 41.78 4.30
230 231 3.787001 CCTCGGGGCTTGGGAGAC 61.787 72.222 0.00 0.00 0.00 3.36
231 232 4.148825 CTCGGGGCTTGGGAGACG 62.149 72.222 0.00 0.00 0.00 4.18
237 238 4.373116 GCTTGGGAGACGCGTGGA 62.373 66.667 20.70 0.00 0.00 4.02
238 239 2.579201 CTTGGGAGACGCGTGGAT 59.421 61.111 20.70 0.97 0.00 3.41
239 240 1.813859 CTTGGGAGACGCGTGGATA 59.186 57.895 20.70 0.00 0.00 2.59
240 241 0.249073 CTTGGGAGACGCGTGGATAG 60.249 60.000 20.70 2.05 0.00 2.08
241 242 0.681887 TTGGGAGACGCGTGGATAGA 60.682 55.000 20.70 0.00 0.00 1.98
242 243 0.681887 TGGGAGACGCGTGGATAGAA 60.682 55.000 20.70 0.00 0.00 2.10
243 244 0.030908 GGGAGACGCGTGGATAGAAG 59.969 60.000 20.70 0.00 0.00 2.85
244 245 0.030908 GGAGACGCGTGGATAGAAGG 59.969 60.000 20.70 0.00 0.00 3.46
245 246 0.030908 GAGACGCGTGGATAGAAGGG 59.969 60.000 20.70 0.00 0.00 3.95
246 247 1.067582 GACGCGTGGATAGAAGGGG 59.932 63.158 20.70 0.00 0.00 4.79
247 248 1.380785 ACGCGTGGATAGAAGGGGA 60.381 57.895 12.93 0.00 0.00 4.81
248 249 0.759436 ACGCGTGGATAGAAGGGGAT 60.759 55.000 12.93 0.00 0.00 3.85
249 250 0.038159 CGCGTGGATAGAAGGGGATC 60.038 60.000 0.00 0.00 0.00 3.36
250 251 1.048601 GCGTGGATAGAAGGGGATCA 58.951 55.000 0.00 0.00 0.00 2.92
251 252 1.416401 GCGTGGATAGAAGGGGATCAA 59.584 52.381 0.00 0.00 0.00 2.57
252 253 2.158813 GCGTGGATAGAAGGGGATCAAA 60.159 50.000 0.00 0.00 0.00 2.69
253 254 3.733337 CGTGGATAGAAGGGGATCAAAG 58.267 50.000 0.00 0.00 0.00 2.77
254 255 3.495100 CGTGGATAGAAGGGGATCAAAGG 60.495 52.174 0.00 0.00 0.00 3.11
255 256 3.056080 TGGATAGAAGGGGATCAAAGGG 58.944 50.000 0.00 0.00 0.00 3.95
256 257 2.376855 GGATAGAAGGGGATCAAAGGGG 59.623 54.545 0.00 0.00 0.00 4.79
257 258 1.907240 TAGAAGGGGATCAAAGGGGG 58.093 55.000 0.00 0.00 0.00 5.40
258 259 0.123266 AGAAGGGGATCAAAGGGGGA 59.877 55.000 0.00 0.00 0.00 4.81
259 260 1.235756 GAAGGGGATCAAAGGGGGAT 58.764 55.000 0.00 0.00 0.00 3.85
260 261 0.936691 AAGGGGATCAAAGGGGGATG 59.063 55.000 0.00 0.00 0.00 3.51
261 262 1.001140 AGGGGATCAAAGGGGGATGG 61.001 60.000 0.00 0.00 0.00 3.51
262 263 0.998945 GGGGATCAAAGGGGGATGGA 60.999 60.000 0.00 0.00 0.00 3.41
263 264 0.933700 GGGATCAAAGGGGGATGGAA 59.066 55.000 0.00 0.00 0.00 3.53
264 265 1.133356 GGGATCAAAGGGGGATGGAAG 60.133 57.143 0.00 0.00 0.00 3.46
265 266 1.133356 GGATCAAAGGGGGATGGAAGG 60.133 57.143 0.00 0.00 0.00 3.46
266 267 0.936691 ATCAAAGGGGGATGGAAGGG 59.063 55.000 0.00 0.00 0.00 3.95
267 268 0.178816 TCAAAGGGGGATGGAAGGGA 60.179 55.000 0.00 0.00 0.00 4.20
268 269 0.936691 CAAAGGGGGATGGAAGGGAT 59.063 55.000 0.00 0.00 0.00 3.85
269 270 1.291939 CAAAGGGGGATGGAAGGGATT 59.708 52.381 0.00 0.00 0.00 3.01
270 271 0.936691 AAGGGGGATGGAAGGGATTG 59.063 55.000 0.00 0.00 0.00 2.67
271 272 1.001140 AGGGGGATGGAAGGGATTGG 61.001 60.000 0.00 0.00 0.00 3.16
272 273 1.543690 GGGGATGGAAGGGATTGGG 59.456 63.158 0.00 0.00 0.00 4.12
273 274 1.152461 GGGATGGAAGGGATTGGGC 60.152 63.158 0.00 0.00 0.00 5.36
274 275 1.659035 GGGATGGAAGGGATTGGGCT 61.659 60.000 0.00 0.00 0.00 5.19
275 276 1.149101 GGATGGAAGGGATTGGGCTA 58.851 55.000 0.00 0.00 0.00 3.93
276 277 1.713078 GGATGGAAGGGATTGGGCTAT 59.287 52.381 0.00 0.00 0.00 2.97
277 278 2.556114 GGATGGAAGGGATTGGGCTATG 60.556 54.545 0.00 0.00 0.00 2.23
278 279 0.185901 TGGAAGGGATTGGGCTATGC 59.814 55.000 0.00 0.00 0.00 3.14
279 280 0.185901 GGAAGGGATTGGGCTATGCA 59.814 55.000 0.00 0.00 0.00 3.96
280 281 1.411501 GGAAGGGATTGGGCTATGCAA 60.412 52.381 0.00 0.00 0.00 4.08
281 282 2.387757 GAAGGGATTGGGCTATGCAAA 58.612 47.619 0.00 0.00 0.00 3.68
282 283 1.780503 AGGGATTGGGCTATGCAAAC 58.219 50.000 0.00 0.00 0.00 2.93
283 284 0.752658 GGGATTGGGCTATGCAAACC 59.247 55.000 0.00 0.00 0.00 3.27
284 285 1.484038 GGATTGGGCTATGCAAACCA 58.516 50.000 0.00 0.00 0.00 3.67
285 286 2.041701 GGATTGGGCTATGCAAACCAT 58.958 47.619 0.00 0.00 37.97 3.55
286 287 2.224113 GGATTGGGCTATGCAAACCATG 60.224 50.000 0.00 0.00 35.34 3.66
287 288 1.935799 TTGGGCTATGCAAACCATGT 58.064 45.000 0.00 0.00 35.34 3.21
288 289 1.184431 TGGGCTATGCAAACCATGTG 58.816 50.000 0.00 0.00 35.34 3.21
289 290 1.272369 TGGGCTATGCAAACCATGTGA 60.272 47.619 0.00 0.00 35.34 3.58
290 291 1.824230 GGGCTATGCAAACCATGTGAA 59.176 47.619 0.00 0.00 35.34 3.18
291 292 2.233431 GGGCTATGCAAACCATGTGAAA 59.767 45.455 0.00 0.00 35.34 2.69
292 293 3.253230 GGCTATGCAAACCATGTGAAAC 58.747 45.455 0.00 0.00 35.34 2.78
303 304 3.112842 GTGAAACAAACGGGCCGT 58.887 55.556 28.83 28.83 38.33 5.68
304 305 1.009335 GTGAAACAAACGGGCCGTC 60.009 57.895 34.23 19.14 36.20 4.79
305 306 2.250190 GAAACAAACGGGCCGTCG 59.750 61.111 34.23 27.43 39.99 5.12
306 307 3.244610 GAAACAAACGGGCCGTCGG 62.245 63.158 34.23 27.78 39.99 4.79
307 308 4.550697 AACAAACGGGCCGTCGGT 62.551 61.111 34.23 28.47 39.99 4.69
315 316 3.423154 GGCCGTCGGTGCTTTCAG 61.423 66.667 13.94 0.00 0.00 3.02
316 317 2.357034 GCCGTCGGTGCTTTCAGA 60.357 61.111 13.94 0.00 0.00 3.27
317 318 2.383527 GCCGTCGGTGCTTTCAGAG 61.384 63.158 13.94 0.00 0.00 3.35
318 319 1.738099 CCGTCGGTGCTTTCAGAGG 60.738 63.158 2.08 0.00 0.00 3.69
319 320 1.006102 CGTCGGTGCTTTCAGAGGT 60.006 57.895 0.00 0.00 0.00 3.85
320 321 0.600255 CGTCGGTGCTTTCAGAGGTT 60.600 55.000 0.00 0.00 0.00 3.50
321 322 1.594331 GTCGGTGCTTTCAGAGGTTT 58.406 50.000 0.00 0.00 0.00 3.27
322 323 1.947456 GTCGGTGCTTTCAGAGGTTTT 59.053 47.619 0.00 0.00 0.00 2.43
323 324 2.357952 GTCGGTGCTTTCAGAGGTTTTT 59.642 45.455 0.00 0.00 0.00 1.94
324 325 2.357637 TCGGTGCTTTCAGAGGTTTTTG 59.642 45.455 0.00 0.00 0.00 2.44
325 326 2.543653 CGGTGCTTTCAGAGGTTTTTGG 60.544 50.000 0.00 0.00 0.00 3.28
326 327 2.224042 GGTGCTTTCAGAGGTTTTTGGG 60.224 50.000 0.00 0.00 0.00 4.12
327 328 1.412343 TGCTTTCAGAGGTTTTTGGGC 59.588 47.619 0.00 0.00 0.00 5.36
328 329 1.270305 GCTTTCAGAGGTTTTTGGGCC 60.270 52.381 0.00 0.00 0.00 5.80
329 330 1.344438 CTTTCAGAGGTTTTTGGGCCC 59.656 52.381 17.59 17.59 0.00 5.80
330 331 0.471022 TTCAGAGGTTTTTGGGCCCC 60.471 55.000 22.27 2.04 0.00 5.80
331 332 2.117423 AGAGGTTTTTGGGCCCCG 59.883 61.111 22.27 0.00 0.00 5.73
332 333 3.691342 GAGGTTTTTGGGCCCCGC 61.691 66.667 22.27 0.00 0.00 6.13
345 346 4.547367 CCCGCGGGGTTGATCCTC 62.547 72.222 37.42 0.00 38.25 3.71
346 347 3.470888 CCGCGGGGTTGATCCTCT 61.471 66.667 20.10 0.00 33.68 3.69
347 348 2.202932 CGCGGGGTTGATCCTCTG 60.203 66.667 0.00 0.00 33.68 3.35
348 349 2.190578 GCGGGGTTGATCCTCTGG 59.809 66.667 0.00 0.00 33.68 3.86
349 350 2.367202 GCGGGGTTGATCCTCTGGA 61.367 63.158 0.00 0.00 33.68 3.86
350 351 1.910580 GCGGGGTTGATCCTCTGGAA 61.911 60.000 0.00 0.00 34.34 3.53
351 352 0.618458 CGGGGTTGATCCTCTGGAAA 59.382 55.000 0.00 0.00 34.34 3.13
352 353 1.679032 CGGGGTTGATCCTCTGGAAAC 60.679 57.143 0.00 0.00 34.34 2.78
353 354 1.341089 GGGGTTGATCCTCTGGAAACC 60.341 57.143 10.28 10.28 40.19 3.27
354 355 2.130272 GGTTGATCCTCTGGAAACCC 57.870 55.000 8.34 0.00 36.89 4.11
355 356 1.341089 GGTTGATCCTCTGGAAACCCC 60.341 57.143 8.34 0.00 36.89 4.95
356 357 1.636003 GTTGATCCTCTGGAAACCCCT 59.364 52.381 0.00 0.00 34.34 4.79
357 358 1.584724 TGATCCTCTGGAAACCCCTC 58.415 55.000 0.00 0.00 34.34 4.30
358 359 1.203428 TGATCCTCTGGAAACCCCTCA 60.203 52.381 0.00 0.00 34.34 3.86
359 360 1.916181 GATCCTCTGGAAACCCCTCAA 59.084 52.381 0.00 0.00 34.34 3.02
360 361 1.362224 TCCTCTGGAAACCCCTCAAG 58.638 55.000 0.00 0.00 35.38 3.02
361 362 0.322906 CCTCTGGAAACCCCTCAAGC 60.323 60.000 0.00 0.00 35.38 4.01
362 363 0.322906 CTCTGGAAACCCCTCAAGCC 60.323 60.000 0.00 0.00 35.38 4.35
363 364 1.304464 CTGGAAACCCCTCAAGCCC 60.304 63.158 0.00 0.00 35.38 5.19
364 365 2.037367 GGAAACCCCTCAAGCCCC 59.963 66.667 0.00 0.00 0.00 5.80
365 366 2.548547 GGAAACCCCTCAAGCCCCT 61.549 63.158 0.00 0.00 0.00 4.79
366 367 1.465172 GAAACCCCTCAAGCCCCTT 59.535 57.895 0.00 0.00 0.00 3.95
367 368 0.900182 GAAACCCCTCAAGCCCCTTG 60.900 60.000 0.00 0.00 42.25 3.61
368 369 1.664956 AAACCCCTCAAGCCCCTTGT 61.665 55.000 5.03 0.00 41.66 3.16
369 370 0.774491 AACCCCTCAAGCCCCTTGTA 60.774 55.000 5.03 0.00 41.66 2.41
370 371 1.303282 CCCCTCAAGCCCCTTGTAC 59.697 63.158 5.03 0.00 41.66 2.90
371 372 1.303282 CCCTCAAGCCCCTTGTACC 59.697 63.158 5.03 0.00 41.66 3.34
372 373 1.497309 CCCTCAAGCCCCTTGTACCA 61.497 60.000 5.03 0.00 41.66 3.25
373 374 0.404040 CCTCAAGCCCCTTGTACCAA 59.596 55.000 5.03 0.00 41.66 3.67
374 375 1.203001 CCTCAAGCCCCTTGTACCAAA 60.203 52.381 5.03 0.00 41.66 3.28
375 376 2.557452 CCTCAAGCCCCTTGTACCAAAT 60.557 50.000 5.03 0.00 41.66 2.32
376 377 2.493278 CTCAAGCCCCTTGTACCAAATG 59.507 50.000 5.03 0.00 41.66 2.32
377 378 2.109128 TCAAGCCCCTTGTACCAAATGA 59.891 45.455 5.03 0.00 41.66 2.57
378 379 2.493278 CAAGCCCCTTGTACCAAATGAG 59.507 50.000 0.00 0.00 36.79 2.90
379 380 1.005924 AGCCCCTTGTACCAAATGAGG 59.994 52.381 0.00 0.00 0.00 3.86
380 381 1.474330 CCCCTTGTACCAAATGAGGC 58.526 55.000 0.00 0.00 0.00 4.70
381 382 1.094785 CCCTTGTACCAAATGAGGCG 58.905 55.000 0.00 0.00 0.00 5.52
382 383 1.613255 CCCTTGTACCAAATGAGGCGT 60.613 52.381 0.00 0.00 0.00 5.68
383 384 2.159382 CCTTGTACCAAATGAGGCGTT 58.841 47.619 0.00 0.00 0.00 4.84
384 385 3.340034 CCTTGTACCAAATGAGGCGTTA 58.660 45.455 0.00 0.00 0.00 3.18
385 386 3.374058 CCTTGTACCAAATGAGGCGTTAG 59.626 47.826 0.00 0.00 0.00 2.34
386 387 2.980568 TGTACCAAATGAGGCGTTAGG 58.019 47.619 0.00 0.00 0.00 2.69
387 388 2.568062 TGTACCAAATGAGGCGTTAGGA 59.432 45.455 0.00 0.00 0.00 2.94
394 395 2.467566 TGAGGCGTTAGGAAAAGTCC 57.532 50.000 0.00 0.00 45.35 3.85
471 493 8.793592 GGTGTAAACTTAAATCTGGAAATCACT 58.206 33.333 0.00 0.00 0.00 3.41
472 494 9.612620 GTGTAAACTTAAATCTGGAAATCACTG 57.387 33.333 0.00 0.00 0.00 3.66
473 495 8.792633 TGTAAACTTAAATCTGGAAATCACTGG 58.207 33.333 0.00 0.00 0.00 4.00
501 523 1.024271 TGGACAAGTTTGCTGCTGAC 58.976 50.000 0.00 0.00 0.00 3.51
503 525 2.158827 TGGACAAGTTTGCTGCTGACTA 60.159 45.455 0.00 0.00 0.00 2.59
518 540 2.234908 CTGACTAGCTGGTTTGTAGGCT 59.765 50.000 3.47 0.00 38.62 4.58
519 541 2.028112 TGACTAGCTGGTTTGTAGGCTG 60.028 50.000 3.47 0.00 36.40 4.85
820 912 2.344025 CGGCGCTACCTATTTAATCCC 58.656 52.381 7.64 0.00 35.61 3.85
821 913 2.344025 GGCGCTACCTATTTAATCCCG 58.656 52.381 7.64 0.00 34.51 5.14
859 951 0.253347 TCCAAGAAGAGCATCCCCCT 60.253 55.000 0.00 0.00 33.66 4.79
908 1008 0.983467 TCAAGGCTGCTCCACACATA 59.017 50.000 0.00 0.00 37.29 2.29
1080 1242 3.580319 AACTGGGGGAAAGCGGCT 61.580 61.111 0.00 0.00 0.00 5.52
1102 1264 3.746949 GAGCTGTCGGGGAGCCATG 62.747 68.421 0.00 0.00 37.12 3.66
1599 1769 4.807631 TCCGGCGATCTCGTCCCA 62.808 66.667 9.30 0.00 41.58 4.37
1614 1784 0.259065 TCCCACTCTCCTACATCGCT 59.741 55.000 0.00 0.00 0.00 4.93
1977 2148 0.950116 GCTCCTACATGATGCTTGCC 59.050 55.000 0.00 0.00 0.00 4.52
2001 2172 1.129058 AACTTGGTGAACTCGACCCT 58.871 50.000 0.00 0.00 31.84 4.34
2166 2337 1.976474 TGGAAAGGCAATCCACGGC 60.976 57.895 7.14 0.00 41.98 5.68
2265 2436 0.677731 TTGCCCAATTCTCGGAGCTG 60.678 55.000 0.00 0.00 0.00 4.24
2276 2447 0.607217 TCGGAGCTGGTGAACGACTA 60.607 55.000 0.00 0.00 0.00 2.59
2694 2865 0.970640 TTCAGACAATCGACCGGGAA 59.029 50.000 6.32 0.00 0.00 3.97
2787 2958 3.064324 GAGCACGCCTTGGCCAAT 61.064 61.111 20.85 0.88 0.00 3.16
3081 3252 1.226688 GCACATCGACGCTCTGCTA 60.227 57.895 0.00 0.00 0.00 3.49
3421 3633 2.509964 AGAGAAACAACACCAGGTTCCT 59.490 45.455 0.00 0.00 37.72 3.36
3422 3634 2.879026 GAGAAACAACACCAGGTTCCTC 59.121 50.000 0.00 0.00 37.72 3.71
3593 3806 8.306038 TGCTAAATCATTTTACTGCAAACATCT 58.694 29.630 0.00 0.00 30.15 2.90
3670 3883 4.795308 GCCCTCAAATATCTCATTGCAAGC 60.795 45.833 4.94 0.00 0.00 4.01
3788 4010 4.810790 AGTGAAGAACAACTATCCTGACG 58.189 43.478 0.00 0.00 0.00 4.35
3805 4027 6.234920 TCCTGACGGAAGAAATTTCAATGTA 58.765 36.000 19.99 0.19 36.03 2.29
3806 4028 6.884295 TCCTGACGGAAGAAATTTCAATGTAT 59.116 34.615 19.99 1.17 36.03 2.29
4038 4260 6.483307 AGATTTTCCTTAAAACAAAAGGCAGC 59.517 34.615 0.00 0.00 42.79 5.25
4039 4261 5.351948 TTTCCTTAAAACAAAAGGCAGCT 57.648 34.783 0.00 0.00 42.79 4.24
4063 4285 4.457257 GGAAAAACAGAGATCAGTCCCTTG 59.543 45.833 0.00 0.00 0.00 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
56 57 4.379243 AGCTTCTGCGGGACCACG 62.379 66.667 0.00 0.00 45.42 4.94
57 58 2.435059 GAGCTTCTGCGGGACCAC 60.435 66.667 0.00 0.00 45.42 4.16
58 59 3.706373 GGAGCTTCTGCGGGACCA 61.706 66.667 0.00 0.00 45.42 4.02
59 60 4.821589 CGGAGCTTCTGCGGGACC 62.822 72.222 0.00 0.00 41.42 4.46
105 106 4.851214 AGCTCCCTCTCCTCCGCC 62.851 72.222 0.00 0.00 0.00 6.13
106 107 3.223589 GAGCTCCCTCTCCTCCGC 61.224 72.222 0.87 0.00 35.16 5.54
107 108 2.904866 CGAGCTCCCTCTCCTCCG 60.905 72.222 8.47 0.00 35.90 4.63
108 109 3.223589 GCGAGCTCCCTCTCCTCC 61.224 72.222 8.47 0.00 35.90 4.30
109 110 3.591835 CGCGAGCTCCCTCTCCTC 61.592 72.222 8.47 0.00 35.90 3.71
167 168 2.206536 CCTCTCCATCTCGGCCTCC 61.207 68.421 0.00 0.00 33.14 4.30
168 169 2.866726 GCCTCTCCATCTCGGCCTC 61.867 68.421 0.00 0.00 36.56 4.70
169 170 2.841988 GCCTCTCCATCTCGGCCT 60.842 66.667 0.00 0.00 36.56 5.19
170 171 4.292178 CGCCTCTCCATCTCGGCC 62.292 72.222 0.00 0.00 39.34 6.13
171 172 4.292178 CCGCCTCTCCATCTCGGC 62.292 72.222 0.00 0.00 39.14 5.54
172 173 3.610669 CCCGCCTCTCCATCTCGG 61.611 72.222 0.00 0.00 39.79 4.63
173 174 4.292178 GCCCGCCTCTCCATCTCG 62.292 72.222 0.00 0.00 0.00 4.04
174 175 4.292178 CGCCCGCCTCTCCATCTC 62.292 72.222 0.00 0.00 0.00 2.75
194 195 4.012895 CACACGCAGGGAACACGC 62.013 66.667 0.00 0.00 35.81 5.34
195 196 4.012895 GCACACGCAGGGAACACG 62.013 66.667 0.00 0.00 38.36 4.49
196 197 3.660111 GGCACACGCAGGGAACAC 61.660 66.667 0.00 0.00 41.24 3.32
197 198 4.947147 GGGCACACGCAGGGAACA 62.947 66.667 0.00 0.00 41.24 3.18
198 199 4.643387 AGGGCACACGCAGGGAAC 62.643 66.667 0.00 0.00 41.24 3.62
199 200 4.329545 GAGGGCACACGCAGGGAA 62.330 66.667 0.00 0.00 41.24 3.97
213 214 3.787001 GTCTCCCAAGCCCCGAGG 61.787 72.222 0.00 0.00 0.00 4.63
214 215 4.148825 CGTCTCCCAAGCCCCGAG 62.149 72.222 0.00 0.00 0.00 4.63
220 221 2.292794 TATCCACGCGTCTCCCAAGC 62.293 60.000 9.86 0.00 0.00 4.01
221 222 0.249073 CTATCCACGCGTCTCCCAAG 60.249 60.000 9.86 0.00 0.00 3.61
222 223 0.681887 TCTATCCACGCGTCTCCCAA 60.682 55.000 9.86 0.00 0.00 4.12
223 224 0.681887 TTCTATCCACGCGTCTCCCA 60.682 55.000 9.86 0.00 0.00 4.37
224 225 0.030908 CTTCTATCCACGCGTCTCCC 59.969 60.000 9.86 0.00 0.00 4.30
225 226 0.030908 CCTTCTATCCACGCGTCTCC 59.969 60.000 9.86 0.00 0.00 3.71
226 227 0.030908 CCCTTCTATCCACGCGTCTC 59.969 60.000 9.86 0.00 0.00 3.36
227 228 1.392710 CCCCTTCTATCCACGCGTCT 61.393 60.000 9.86 0.00 0.00 4.18
228 229 1.067582 CCCCTTCTATCCACGCGTC 59.932 63.158 9.86 0.00 0.00 5.19
229 230 0.759436 ATCCCCTTCTATCCACGCGT 60.759 55.000 5.58 5.58 0.00 6.01
230 231 0.038159 GATCCCCTTCTATCCACGCG 60.038 60.000 3.53 3.53 0.00 6.01
231 232 1.048601 TGATCCCCTTCTATCCACGC 58.951 55.000 0.00 0.00 0.00 5.34
232 233 3.495100 CCTTTGATCCCCTTCTATCCACG 60.495 52.174 0.00 0.00 0.00 4.94
233 234 3.181439 CCCTTTGATCCCCTTCTATCCAC 60.181 52.174 0.00 0.00 0.00 4.02
234 235 3.056080 CCCTTTGATCCCCTTCTATCCA 58.944 50.000 0.00 0.00 0.00 3.41
235 236 2.376855 CCCCTTTGATCCCCTTCTATCC 59.623 54.545 0.00 0.00 0.00 2.59
236 237 2.376855 CCCCCTTTGATCCCCTTCTATC 59.623 54.545 0.00 0.00 0.00 2.08
237 238 2.020037 TCCCCCTTTGATCCCCTTCTAT 60.020 50.000 0.00 0.00 0.00 1.98
238 239 1.371774 TCCCCCTTTGATCCCCTTCTA 59.628 52.381 0.00 0.00 0.00 2.10
239 240 0.123266 TCCCCCTTTGATCCCCTTCT 59.877 55.000 0.00 0.00 0.00 2.85
240 241 1.133356 CATCCCCCTTTGATCCCCTTC 60.133 57.143 0.00 0.00 0.00 3.46
241 242 0.936691 CATCCCCCTTTGATCCCCTT 59.063 55.000 0.00 0.00 0.00 3.95
242 243 1.001140 CCATCCCCCTTTGATCCCCT 61.001 60.000 0.00 0.00 0.00 4.79
243 244 0.998945 TCCATCCCCCTTTGATCCCC 60.999 60.000 0.00 0.00 0.00 4.81
244 245 0.933700 TTCCATCCCCCTTTGATCCC 59.066 55.000 0.00 0.00 0.00 3.85
245 246 1.133356 CCTTCCATCCCCCTTTGATCC 60.133 57.143 0.00 0.00 0.00 3.36
246 247 1.133356 CCCTTCCATCCCCCTTTGATC 60.133 57.143 0.00 0.00 0.00 2.92
247 248 0.936691 CCCTTCCATCCCCCTTTGAT 59.063 55.000 0.00 0.00 0.00 2.57
248 249 0.178816 TCCCTTCCATCCCCCTTTGA 60.179 55.000 0.00 0.00 0.00 2.69
249 250 0.936691 ATCCCTTCCATCCCCCTTTG 59.063 55.000 0.00 0.00 0.00 2.77
250 251 1.291939 CAATCCCTTCCATCCCCCTTT 59.708 52.381 0.00 0.00 0.00 3.11
251 252 0.936691 CAATCCCTTCCATCCCCCTT 59.063 55.000 0.00 0.00 0.00 3.95
252 253 1.001140 CCAATCCCTTCCATCCCCCT 61.001 60.000 0.00 0.00 0.00 4.79
253 254 1.543690 CCAATCCCTTCCATCCCCC 59.456 63.158 0.00 0.00 0.00 5.40
254 255 1.543690 CCCAATCCCTTCCATCCCC 59.456 63.158 0.00 0.00 0.00 4.81
255 256 1.152461 GCCCAATCCCTTCCATCCC 60.152 63.158 0.00 0.00 0.00 3.85
256 257 1.149101 TAGCCCAATCCCTTCCATCC 58.851 55.000 0.00 0.00 0.00 3.51
257 258 2.800250 CATAGCCCAATCCCTTCCATC 58.200 52.381 0.00 0.00 0.00 3.51
258 259 1.203100 GCATAGCCCAATCCCTTCCAT 60.203 52.381 0.00 0.00 0.00 3.41
259 260 0.185901 GCATAGCCCAATCCCTTCCA 59.814 55.000 0.00 0.00 0.00 3.53
260 261 0.185901 TGCATAGCCCAATCCCTTCC 59.814 55.000 0.00 0.00 0.00 3.46
261 262 2.071778 TTGCATAGCCCAATCCCTTC 57.928 50.000 0.00 0.00 0.00 3.46
262 263 2.110578 GTTTGCATAGCCCAATCCCTT 58.889 47.619 0.00 0.00 0.00 3.95
263 264 1.689258 GGTTTGCATAGCCCAATCCCT 60.689 52.381 0.00 0.00 0.00 4.20
264 265 0.752658 GGTTTGCATAGCCCAATCCC 59.247 55.000 0.00 0.00 0.00 3.85
265 266 1.484038 TGGTTTGCATAGCCCAATCC 58.516 50.000 3.87 0.00 34.26 3.01
266 267 2.431782 ACATGGTTTGCATAGCCCAATC 59.568 45.455 3.87 0.00 0.00 2.67
267 268 2.168936 CACATGGTTTGCATAGCCCAAT 59.831 45.455 3.87 0.00 0.00 3.16
268 269 1.549620 CACATGGTTTGCATAGCCCAA 59.450 47.619 3.87 0.00 0.00 4.12
269 270 1.184431 CACATGGTTTGCATAGCCCA 58.816 50.000 3.87 0.60 0.00 5.36
270 271 1.473258 TCACATGGTTTGCATAGCCC 58.527 50.000 3.87 0.00 0.00 5.19
271 272 3.253230 GTTTCACATGGTTTGCATAGCC 58.747 45.455 3.87 0.00 0.00 3.93
272 273 3.911868 TGTTTCACATGGTTTGCATAGC 58.088 40.909 0.00 0.00 0.00 2.97
273 274 5.107913 CGTTTGTTTCACATGGTTTGCATAG 60.108 40.000 0.00 0.00 0.00 2.23
274 275 4.742167 CGTTTGTTTCACATGGTTTGCATA 59.258 37.500 0.00 0.00 0.00 3.14
275 276 3.555139 CGTTTGTTTCACATGGTTTGCAT 59.445 39.130 0.00 0.00 0.00 3.96
276 277 2.926200 CGTTTGTTTCACATGGTTTGCA 59.074 40.909 0.00 0.00 0.00 4.08
277 278 2.283884 CCGTTTGTTTCACATGGTTTGC 59.716 45.455 0.00 0.00 0.00 3.68
278 279 2.863137 CCCGTTTGTTTCACATGGTTTG 59.137 45.455 0.00 0.00 0.00 2.93
279 280 2.740256 GCCCGTTTGTTTCACATGGTTT 60.740 45.455 0.00 0.00 0.00 3.27
280 281 1.202475 GCCCGTTTGTTTCACATGGTT 60.202 47.619 0.00 0.00 0.00 3.67
281 282 0.387565 GCCCGTTTGTTTCACATGGT 59.612 50.000 0.00 0.00 0.00 3.55
282 283 0.319469 GGCCCGTTTGTTTCACATGG 60.319 55.000 0.00 0.00 0.00 3.66
283 284 0.662970 CGGCCCGTTTGTTTCACATG 60.663 55.000 0.00 0.00 0.00 3.21
284 285 1.104577 ACGGCCCGTTTGTTTCACAT 61.105 50.000 1.02 0.00 36.35 3.21
285 286 1.716826 GACGGCCCGTTTGTTTCACA 61.717 55.000 11.54 0.00 41.37 3.58
286 287 1.009335 GACGGCCCGTTTGTTTCAC 60.009 57.895 11.54 0.00 41.37 3.18
287 288 2.535788 CGACGGCCCGTTTGTTTCA 61.536 57.895 11.54 0.00 41.37 2.69
288 289 2.250190 CGACGGCCCGTTTGTTTC 59.750 61.111 11.54 0.00 41.37 2.78
289 290 3.281395 CCGACGGCCCGTTTGTTT 61.281 61.111 11.54 0.00 41.37 2.83
290 291 4.550697 ACCGACGGCCCGTTTGTT 62.551 61.111 11.54 0.00 41.37 2.83
298 299 3.423154 CTGAAAGCACCGACGGCC 61.423 66.667 15.39 5.31 0.00 6.13
299 300 2.357034 TCTGAAAGCACCGACGGC 60.357 61.111 15.39 0.00 0.00 5.68
300 301 1.738099 CCTCTGAAAGCACCGACGG 60.738 63.158 13.61 13.61 0.00 4.79
301 302 0.600255 AACCTCTGAAAGCACCGACG 60.600 55.000 0.00 0.00 0.00 5.12
302 303 1.594331 AAACCTCTGAAAGCACCGAC 58.406 50.000 0.00 0.00 0.00 4.79
303 304 2.341846 AAAACCTCTGAAAGCACCGA 57.658 45.000 0.00 0.00 0.00 4.69
304 305 2.543653 CCAAAAACCTCTGAAAGCACCG 60.544 50.000 0.00 0.00 0.00 4.94
305 306 2.224042 CCCAAAAACCTCTGAAAGCACC 60.224 50.000 0.00 0.00 0.00 5.01
306 307 2.803133 GCCCAAAAACCTCTGAAAGCAC 60.803 50.000 0.00 0.00 0.00 4.40
307 308 1.412343 GCCCAAAAACCTCTGAAAGCA 59.588 47.619 0.00 0.00 0.00 3.91
308 309 1.270305 GGCCCAAAAACCTCTGAAAGC 60.270 52.381 0.00 0.00 0.00 3.51
309 310 1.344438 GGGCCCAAAAACCTCTGAAAG 59.656 52.381 19.95 0.00 0.00 2.62
310 311 1.419381 GGGCCCAAAAACCTCTGAAA 58.581 50.000 19.95 0.00 0.00 2.69
311 312 0.471022 GGGGCCCAAAAACCTCTGAA 60.471 55.000 26.86 0.00 0.00 3.02
312 313 1.155155 GGGGCCCAAAAACCTCTGA 59.845 57.895 26.86 0.00 0.00 3.27
313 314 2.275380 CGGGGCCCAAAAACCTCTG 61.275 63.158 26.86 0.00 0.00 3.35
314 315 2.117423 CGGGGCCCAAAAACCTCT 59.883 61.111 26.86 0.00 0.00 3.69
315 316 3.691342 GCGGGGCCCAAAAACCTC 61.691 66.667 26.86 1.48 0.00 3.85
328 329 4.547367 GAGGATCAACCCCGCGGG 62.547 72.222 37.99 37.99 42.06 6.13
329 330 3.470888 AGAGGATCAACCCCGCGG 61.471 66.667 21.04 21.04 40.05 6.46
330 331 2.202932 CAGAGGATCAACCCCGCG 60.203 66.667 0.00 0.00 40.05 6.46
331 332 1.910580 TTCCAGAGGATCAACCCCGC 61.911 60.000 0.00 0.00 40.05 6.13
332 333 0.618458 TTTCCAGAGGATCAACCCCG 59.382 55.000 0.00 0.00 40.05 5.73
333 334 1.341089 GGTTTCCAGAGGATCAACCCC 60.341 57.143 7.98 0.00 36.89 4.95
334 335 2.130272 GGTTTCCAGAGGATCAACCC 57.870 55.000 7.98 0.00 36.89 4.11
335 336 1.341089 GGGGTTTCCAGAGGATCAACC 60.341 57.143 10.01 10.01 40.19 3.77
336 337 1.636003 AGGGGTTTCCAGAGGATCAAC 59.364 52.381 0.00 0.00 37.82 3.18
337 338 1.916181 GAGGGGTTTCCAGAGGATCAA 59.084 52.381 0.00 0.00 37.82 2.57
338 339 1.203428 TGAGGGGTTTCCAGAGGATCA 60.203 52.381 0.00 0.00 37.82 2.92
339 340 1.584724 TGAGGGGTTTCCAGAGGATC 58.415 55.000 0.00 0.00 38.24 3.36
340 341 1.918957 CTTGAGGGGTTTCCAGAGGAT 59.081 52.381 0.00 0.00 38.24 3.24
341 342 1.362224 CTTGAGGGGTTTCCAGAGGA 58.638 55.000 0.00 0.00 38.24 3.71
342 343 0.322906 GCTTGAGGGGTTTCCAGAGG 60.323 60.000 0.00 0.00 38.24 3.69
343 344 0.322906 GGCTTGAGGGGTTTCCAGAG 60.323 60.000 0.00 0.00 38.24 3.35
344 345 1.767692 GGCTTGAGGGGTTTCCAGA 59.232 57.895 0.00 0.00 38.24 3.86
345 346 1.304464 GGGCTTGAGGGGTTTCCAG 60.304 63.158 0.00 0.00 38.24 3.86
346 347 2.851045 GGGCTTGAGGGGTTTCCA 59.149 61.111 0.00 0.00 38.24 3.53
347 348 2.037367 GGGGCTTGAGGGGTTTCC 59.963 66.667 0.00 0.00 0.00 3.13
348 349 0.900182 CAAGGGGCTTGAGGGGTTTC 60.900 60.000 0.00 0.00 43.42 2.78
349 350 1.156095 CAAGGGGCTTGAGGGGTTT 59.844 57.895 0.00 0.00 43.42 3.27
350 351 0.774491 TACAAGGGGCTTGAGGGGTT 60.774 55.000 0.00 0.00 43.42 4.11
351 352 1.151677 TACAAGGGGCTTGAGGGGT 60.152 57.895 0.00 0.00 43.42 4.95
352 353 1.303282 GTACAAGGGGCTTGAGGGG 59.697 63.158 0.00 0.00 43.42 4.79
353 354 1.303282 GGTACAAGGGGCTTGAGGG 59.697 63.158 0.00 0.00 43.42 4.30
354 355 2.074967 TGGTACAAGGGGCTTGAGG 58.925 57.895 0.00 0.00 43.42 3.86
366 367 2.568062 TCCTAACGCCTCATTTGGTACA 59.432 45.455 0.00 0.00 0.00 2.90
367 368 3.255969 TCCTAACGCCTCATTTGGTAC 57.744 47.619 0.00 0.00 0.00 3.34
368 369 3.985019 TTCCTAACGCCTCATTTGGTA 57.015 42.857 0.00 0.00 0.00 3.25
369 370 2.871096 TTCCTAACGCCTCATTTGGT 57.129 45.000 0.00 0.00 0.00 3.67
370 371 3.506067 ACTTTTCCTAACGCCTCATTTGG 59.494 43.478 0.00 0.00 0.00 3.28
371 372 4.379499 GGACTTTTCCTAACGCCTCATTTG 60.379 45.833 0.00 0.00 39.13 2.32
372 373 3.756963 GGACTTTTCCTAACGCCTCATTT 59.243 43.478 0.00 0.00 39.13 2.32
373 374 3.344515 GGACTTTTCCTAACGCCTCATT 58.655 45.455 0.00 0.00 39.13 2.57
374 375 2.677037 CGGACTTTTCCTAACGCCTCAT 60.677 50.000 0.00 0.00 40.23 2.90
375 376 1.337447 CGGACTTTTCCTAACGCCTCA 60.337 52.381 0.00 0.00 40.23 3.86
376 377 1.356938 CGGACTTTTCCTAACGCCTC 58.643 55.000 0.00 0.00 40.23 4.70
377 378 0.672711 GCGGACTTTTCCTAACGCCT 60.673 55.000 0.00 0.00 40.23 5.52
378 379 0.952010 TGCGGACTTTTCCTAACGCC 60.952 55.000 0.00 0.00 45.67 5.68
379 380 0.869730 TTGCGGACTTTTCCTAACGC 59.130 50.000 0.00 0.00 46.34 4.84
380 381 1.136446 CGTTGCGGACTTTTCCTAACG 60.136 52.381 12.53 12.53 45.45 3.18
381 382 2.137523 TCGTTGCGGACTTTTCCTAAC 58.862 47.619 0.00 0.00 40.23 2.34
382 383 2.529780 TCGTTGCGGACTTTTCCTAA 57.470 45.000 0.00 0.00 40.23 2.69
383 384 2.529780 TTCGTTGCGGACTTTTCCTA 57.470 45.000 0.00 0.00 40.23 2.94
384 385 1.670791 TTTCGTTGCGGACTTTTCCT 58.329 45.000 0.00 0.00 40.23 3.36
385 386 2.478547 TTTTCGTTGCGGACTTTTCC 57.521 45.000 0.00 0.00 38.77 3.13
386 387 4.030195 GCATATTTTCGTTGCGGACTTTTC 59.970 41.667 0.00 0.00 0.00 2.29
387 388 3.917985 GCATATTTTCGTTGCGGACTTTT 59.082 39.130 0.00 0.00 0.00 2.27
394 395 5.685195 AATTTCTGCATATTTTCGTTGCG 57.315 34.783 0.00 0.00 39.23 4.85
438 440 9.747898 TCCAGATTTAAGTTTACACCACATTAT 57.252 29.630 0.00 0.00 0.00 1.28
439 441 9.575868 TTCCAGATTTAAGTTTACACCACATTA 57.424 29.630 0.00 0.00 0.00 1.90
440 442 8.472007 TTCCAGATTTAAGTTTACACCACATT 57.528 30.769 0.00 0.00 0.00 2.71
441 443 8.472007 TTTCCAGATTTAAGTTTACACCACAT 57.528 30.769 0.00 0.00 0.00 3.21
443 445 8.573035 TGATTTCCAGATTTAAGTTTACACCAC 58.427 33.333 0.00 0.00 0.00 4.16
444 446 8.573035 GTGATTTCCAGATTTAAGTTTACACCA 58.427 33.333 0.00 0.00 0.00 4.17
445 447 8.793592 AGTGATTTCCAGATTTAAGTTTACACC 58.206 33.333 0.00 0.00 0.00 4.16
448 470 8.244113 CCCAGTGATTTCCAGATTTAAGTTTAC 58.756 37.037 0.00 0.00 0.00 2.01
453 475 5.065218 CGTCCCAGTGATTTCCAGATTTAAG 59.935 44.000 0.00 0.00 0.00 1.85
462 484 3.815401 CCATTATCGTCCCAGTGATTTCC 59.185 47.826 0.00 0.00 0.00 3.13
471 493 3.992943 AACTTGTCCATTATCGTCCCA 57.007 42.857 0.00 0.00 0.00 4.37
472 494 3.181500 GCAAACTTGTCCATTATCGTCCC 60.181 47.826 0.00 0.00 0.00 4.46
473 495 3.689649 AGCAAACTTGTCCATTATCGTCC 59.310 43.478 0.00 0.00 0.00 4.79
501 523 2.014068 GCCAGCCTACAAACCAGCTAG 61.014 57.143 0.00 0.00 33.33 3.42
503 525 1.303643 GCCAGCCTACAAACCAGCT 60.304 57.895 0.00 0.00 35.52 4.24
589 630 3.474034 GCACGAGTCTGACGCTGC 61.474 66.667 15.49 15.49 33.70 5.25
590 631 3.168604 CGCACGAGTCTGACGCTG 61.169 66.667 9.79 7.96 0.00 5.18
591 632 3.195591 AACGCACGAGTCTGACGCT 62.196 57.895 9.79 0.00 0.00 5.07
593 634 2.081212 GGAACGCACGAGTCTGACG 61.081 63.158 1.52 0.00 0.00 4.35
595 636 2.649034 GGGAACGCACGAGTCTGA 59.351 61.111 0.00 0.00 0.00 3.27
596 637 2.432628 GGGGAACGCACGAGTCTG 60.433 66.667 0.00 0.00 42.57 3.51
597 638 2.600769 AGGGGAACGCACGAGTCT 60.601 61.111 0.00 0.00 46.88 3.24
820 912 1.147153 GGAAATGGAGGAGAGGGCG 59.853 63.158 0.00 0.00 0.00 6.13
821 913 0.849417 ATGGAAATGGAGGAGAGGGC 59.151 55.000 0.00 0.00 0.00 5.19
859 951 1.682394 GCTCGTTGGAGTAGGAGAGGA 60.682 57.143 0.00 0.00 42.53 3.71
1599 1769 1.064314 AGTCCAGCGATGTAGGAGAGT 60.064 52.381 0.00 0.00 30.78 3.24
1614 1784 4.308458 CGGCCGGTGACAAGTCCA 62.308 66.667 20.10 0.00 0.00 4.02
1764 1935 4.537433 GCTAGCCCAGAGCCCACG 62.537 72.222 2.29 0.00 45.47 4.94
1779 1950 3.026630 TCAAAGAGAACAATCGACGCT 57.973 42.857 0.00 0.00 0.00 5.07
1950 2121 0.031716 TCATGTAGGAGCTGCCCTCT 60.032 55.000 12.11 3.09 40.57 3.69
1977 2148 3.002348 GGTCGAGTTCACCAAGTTTCTTG 59.998 47.826 2.90 2.90 33.63 3.02
2001 2172 4.877378 ATCTTGCTTTGGCTTCATCAAA 57.123 36.364 0.00 0.00 39.59 2.69
2166 2337 3.365265 GTGCCCTGGAAGTTGCCG 61.365 66.667 0.00 0.00 0.00 5.69
2199 2370 1.238439 CAAGCCTCGTGTTGTCCATT 58.762 50.000 0.00 0.00 0.00 3.16
2253 2424 0.108615 CGTTCACCAGCTCCGAGAAT 60.109 55.000 0.00 0.00 0.00 2.40
2265 2436 4.387862 CCATTGTTGTAGTAGTCGTTCACC 59.612 45.833 0.00 0.00 0.00 4.02
2276 2447 1.203050 AGGGCAAGCCATTGTTGTAGT 60.203 47.619 13.87 0.00 38.76 2.73
2326 2497 1.992557 ACCCTTGAAGCCATAGTCCAA 59.007 47.619 0.00 0.00 0.00 3.53
2694 2865 2.867472 GCGTATGCAAACACCGCT 59.133 55.556 0.89 0.00 42.87 5.52
3081 3252 0.178921 TCCACTCCTTCAGGCACTCT 60.179 55.000 0.00 0.00 34.60 3.24
3329 3541 2.359981 ATACAGCAGTAGACCGCCTA 57.640 50.000 0.00 0.00 32.86 3.93
3421 3633 9.474313 GGGTAATATAAATATTTGATGCCAGGA 57.526 33.333 11.05 0.00 34.91 3.86
3422 3634 8.695456 GGGGTAATATAAATATTTGATGCCAGG 58.305 37.037 11.05 0.00 34.91 4.45
3593 3806 2.039418 AGCATATAGTTCCTGTCGCCA 58.961 47.619 0.00 0.00 0.00 5.69
3627 3840 1.197721 CGGATGTTTGCTGAGACCAAC 59.802 52.381 0.00 0.00 0.00 3.77
3670 3883 3.482156 ACTAGAACCATAGCAGCCATG 57.518 47.619 0.00 0.00 0.00 3.66
3733 3955 0.107312 ACTGTGCATCTGAGCCATCC 60.107 55.000 0.00 0.00 0.00 3.51
3738 3960 3.828657 TCAGACTGTGCATCTGAGC 57.171 52.632 13.30 0.00 46.01 4.26
3788 4010 7.542025 AGTGCTGATACATTGAAATTTCTTCC 58.458 34.615 18.64 2.94 0.00 3.46
3805 4027 8.131847 ACACATATGAGATACATAGTGCTGAT 57.868 34.615 10.38 0.00 43.48 2.90
3806 4028 7.530426 ACACATATGAGATACATAGTGCTGA 57.470 36.000 10.38 0.00 43.48 4.26
4038 4260 4.006319 GGGACTGATCTCTGTTTTTCCAG 58.994 47.826 0.00 0.00 0.00 3.86
4039 4261 3.652869 AGGGACTGATCTCTGTTTTTCCA 59.347 43.478 0.00 0.00 32.84 3.53
4063 4285 1.202687 TGGCTATGGCTGTATGACTGC 60.203 52.381 0.00 0.27 41.55 4.40


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

AutoCloner maintained by Alex Coulton.