Multiple sequence alignment - TraesCS4D01G197500

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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 TraesCS4D01G197500 chr4D 100.000 4006 0 0 1 4006 342788976 342792981 0.000000e+00 7398
1 TraesCS4D01G197500 chr4B 93.039 2284 88 21 1047 3279 424748573 424750836 0.000000e+00 3271
2 TraesCS4D01G197500 chr4B 95.208 626 22 5 418 1039 424747839 424748460 0.000000e+00 983
3 TraesCS4D01G197500 chr4B 91.325 634 32 18 3268 3894 424750851 424751468 0.000000e+00 845
4 TraesCS4D01G197500 chr4B 91.358 243 16 3 8 250 424747561 424747798 1.070000e-85 327
5 TraesCS4D01G197500 chr4A 90.756 1720 107 25 1590 3282 123075917 123074223 0.000000e+00 2248
6 TraesCS4D01G197500 chr4A 94.822 1178 52 8 417 1589 123077130 123075957 0.000000e+00 1829
7 TraesCS4D01G197500 chr4A 88.125 640 64 10 3271 3902 123074199 123073564 0.000000e+00 750
8 TraesCS4D01G197500 chr4A 93.574 249 11 1 1 249 123077425 123077182 2.270000e-97 366
9 TraesCS4D01G197500 chr4A 85.294 136 18 2 2127 2261 655650225 655650359 5.400000e-29 139
10 TraesCS4D01G197500 chr7D 98.182 110 2 0 3897 4006 602827073 602827182 4.090000e-45 193
11 TraesCS4D01G197500 chr3D 97.273 110 3 0 3897 4006 68474652 68474761 1.900000e-43 187
12 TraesCS4D01G197500 chr7B 96.364 110 4 0 3897 4006 399247483 399247374 8.840000e-42 182
13 TraesCS4D01G197500 chr7B 92.727 110 8 0 3897 4006 578109695 578109804 4.140000e-35 159
14 TraesCS4D01G197500 chr5A 95.455 110 5 0 3897 4006 578949523 578949414 4.110000e-40 176
15 TraesCS4D01G197500 chr5A 94.949 99 5 0 3908 4006 32406280 32406182 5.360000e-34 156
16 TraesCS4D01G197500 chr1A 93.636 110 7 0 3897 4006 427704667 427704558 8.910000e-37 165
17 TraesCS4D01G197500 chr1A 87.407 135 15 2 2127 2260 92563421 92563554 1.930000e-33 154
18 TraesCS4D01G197500 chr6D 92.661 109 8 0 3897 4005 446626346 446626238 1.490000e-34 158
19 TraesCS4D01G197500 chr3A 90.000 110 11 0 3897 4006 501141820 501141711 4.170000e-30 143
20 TraesCS4D01G197500 chr1B 83.824 136 20 2 2127 2261 64515505 64515639 1.170000e-25 128
21 TraesCS4D01G197500 chr6B 86.364 110 13 2 2153 2261 130900886 130900994 7.030000e-23 119


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 TraesCS4D01G197500 chr4D 342788976 342792981 4005 False 7398.00 7398 100.00000 1 4006 1 chr4D.!!$F1 4005
1 TraesCS4D01G197500 chr4B 424747561 424751468 3907 False 1356.50 3271 92.73250 8 3894 4 chr4B.!!$F1 3886
2 TraesCS4D01G197500 chr4A 123073564 123077425 3861 True 1298.25 2248 91.81925 1 3902 4 chr4A.!!$R1 3901

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
397 403 0.029035 GGCTGCGCTGAGATTTCATG 59.971 55.0 19.32 0.0 31.68 3.07 F
1959 2150 0.916809 AACTTTGTATCCCCCTCCCG 59.083 55.0 0.00 0.0 0.00 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2247 2449 0.881118 CGCCTGGTTGTAGTGCAATT 59.119 50.0 0.0 0.0 39.55 2.32 R
3902 4169 0.251608 TTTGCCTTGCTTACTCCCCC 60.252 55.0 0.0 0.0 0.00 5.40 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
140 141 2.242965 TGATCTGAACCATTGGAGCCAT 59.757 45.455 10.37 0.00 0.00 4.40
173 174 3.184683 CGCGCTCTCAGAGGCAAC 61.185 66.667 5.56 2.70 0.00 4.17
186 192 3.670377 GCAACCGGGACAACAGGC 61.670 66.667 6.32 0.00 0.00 4.85
187 193 2.203280 CAACCGGGACAACAGGCA 60.203 61.111 6.32 0.00 0.00 4.75
188 194 1.826054 CAACCGGGACAACAGGCAA 60.826 57.895 6.32 0.00 0.00 4.52
189 195 1.528309 AACCGGGACAACAGGCAAG 60.528 57.895 6.32 0.00 0.00 4.01
190 196 1.990160 AACCGGGACAACAGGCAAGA 61.990 55.000 6.32 0.00 0.00 3.02
200 206 5.009610 GGACAACAGGCAAGATACTTTTTCA 59.990 40.000 0.00 0.00 0.00 2.69
250 256 4.785346 ATGAATAGGTGAGGTGATTGCT 57.215 40.909 0.00 0.00 0.00 3.91
251 257 4.142609 TGAATAGGTGAGGTGATTGCTC 57.857 45.455 0.00 0.00 0.00 4.26
252 258 3.519107 TGAATAGGTGAGGTGATTGCTCA 59.481 43.478 0.00 0.00 0.00 4.26
253 259 3.834489 ATAGGTGAGGTGATTGCTCAG 57.166 47.619 0.00 0.00 30.18 3.35
254 260 1.356124 AGGTGAGGTGATTGCTCAGT 58.644 50.000 0.00 0.00 30.18 3.41
255 261 2.540383 AGGTGAGGTGATTGCTCAGTA 58.460 47.619 0.00 0.00 30.18 2.74
256 262 2.499289 AGGTGAGGTGATTGCTCAGTAG 59.501 50.000 0.00 0.00 30.18 2.57
257 263 2.419297 GGTGAGGTGATTGCTCAGTAGG 60.419 54.545 0.00 0.00 30.18 3.18
258 264 1.208052 TGAGGTGATTGCTCAGTAGGC 59.792 52.381 0.00 0.00 30.18 3.93
259 265 1.208052 GAGGTGATTGCTCAGTAGGCA 59.792 52.381 0.00 0.00 37.97 4.75
260 266 1.842562 AGGTGATTGCTCAGTAGGCAT 59.157 47.619 0.00 0.00 39.54 4.40
261 267 1.945394 GGTGATTGCTCAGTAGGCATG 59.055 52.381 0.00 0.00 39.54 4.06
262 268 1.332997 GTGATTGCTCAGTAGGCATGC 59.667 52.381 9.90 9.90 39.54 4.06
263 269 1.065272 TGATTGCTCAGTAGGCATGCA 60.065 47.619 21.36 0.00 39.54 3.96
264 270 2.019249 GATTGCTCAGTAGGCATGCAA 58.981 47.619 21.36 3.60 45.62 4.08
265 271 1.456296 TTGCTCAGTAGGCATGCAAG 58.544 50.000 21.36 7.46 38.49 4.01
266 272 1.028330 TGCTCAGTAGGCATGCAAGC 61.028 55.000 21.36 16.68 34.56 4.01
267 273 1.028330 GCTCAGTAGGCATGCAAGCA 61.028 55.000 21.36 0.00 35.83 3.91
297 303 4.353437 GAGTCCGCCAACGTCCGT 62.353 66.667 0.00 0.00 37.70 4.69
306 312 1.790755 CCAACGTCCGTGAGATGAAA 58.209 50.000 0.00 0.00 35.30 2.69
307 313 2.139917 CCAACGTCCGTGAGATGAAAA 58.860 47.619 0.00 0.00 35.30 2.29
310 316 4.390603 CCAACGTCCGTGAGATGAAAATTA 59.609 41.667 0.00 0.00 35.30 1.40
311 317 5.106869 CCAACGTCCGTGAGATGAAAATTAA 60.107 40.000 0.00 0.00 35.30 1.40
313 319 4.092968 ACGTCCGTGAGATGAAAATTAAGC 59.907 41.667 0.00 0.00 35.30 3.09
314 320 4.494199 CGTCCGTGAGATGAAAATTAAGCC 60.494 45.833 0.00 0.00 32.76 4.35
315 321 3.945285 TCCGTGAGATGAAAATTAAGCCC 59.055 43.478 0.00 0.00 0.00 5.19
317 323 4.157656 CCGTGAGATGAAAATTAAGCCCAA 59.842 41.667 0.00 0.00 0.00 4.12
318 324 5.095490 CGTGAGATGAAAATTAAGCCCAAC 58.905 41.667 0.00 0.00 0.00 3.77
319 325 5.335583 CGTGAGATGAAAATTAAGCCCAACA 60.336 40.000 0.00 0.00 0.00 3.33
320 326 6.625740 CGTGAGATGAAAATTAAGCCCAACAT 60.626 38.462 0.00 0.00 0.00 2.71
321 327 6.532657 GTGAGATGAAAATTAAGCCCAACATG 59.467 38.462 0.00 0.00 0.00 3.21
322 328 5.981174 AGATGAAAATTAAGCCCAACATGG 58.019 37.500 0.00 0.00 37.25 3.66
323 329 5.484998 AGATGAAAATTAAGCCCAACATGGT 59.515 36.000 0.00 0.00 35.17 3.55
324 330 5.559148 TGAAAATTAAGCCCAACATGGTT 57.441 34.783 0.00 0.00 35.17 3.67
325 331 6.672266 TGAAAATTAAGCCCAACATGGTTA 57.328 33.333 0.00 0.00 35.17 2.85
326 332 7.251321 TGAAAATTAAGCCCAACATGGTTAT 57.749 32.000 0.00 0.00 35.17 1.89
327 333 7.684529 TGAAAATTAAGCCCAACATGGTTATT 58.315 30.769 0.00 0.00 35.17 1.40
328 334 8.816894 TGAAAATTAAGCCCAACATGGTTATTA 58.183 29.630 0.00 0.00 35.17 0.98
329 335 9.660180 GAAAATTAAGCCCAACATGGTTATTAA 57.340 29.630 0.00 0.00 35.17 1.40
331 337 9.665719 AAATTAAGCCCAACATGGTTATTAAAG 57.334 29.630 0.00 0.00 35.17 1.85
332 338 7.784470 TTAAGCCCAACATGGTTATTAAAGT 57.216 32.000 0.00 0.00 35.17 2.66
333 339 8.880991 TTAAGCCCAACATGGTTATTAAAGTA 57.119 30.769 0.00 0.00 35.17 2.24
334 340 7.784470 AAGCCCAACATGGTTATTAAAGTAA 57.216 32.000 0.00 0.00 35.17 2.24
335 341 7.165460 AGCCCAACATGGTTATTAAAGTAAC 57.835 36.000 0.00 0.00 35.17 2.50
336 342 6.722129 AGCCCAACATGGTTATTAAAGTAACA 59.278 34.615 0.00 0.00 36.51 2.41
337 343 7.233757 AGCCCAACATGGTTATTAAAGTAACAA 59.766 33.333 0.00 0.00 36.51 2.83
338 344 7.873505 GCCCAACATGGTTATTAAAGTAACAAA 59.126 33.333 0.00 0.00 36.51 2.83
339 345 9.418045 CCCAACATGGTTATTAAAGTAACAAAG 57.582 33.333 0.00 0.00 36.51 2.77
340 346 9.974980 CCAACATGGTTATTAAAGTAACAAAGT 57.025 29.630 0.00 0.00 36.51 2.66
361 367 9.309796 CAAAGTTTAGTTTATTTTCGGTAGACG 57.690 33.333 0.00 0.00 46.11 4.18
362 368 8.593492 AAGTTTAGTTTATTTTCGGTAGACGT 57.407 30.769 0.00 0.00 44.69 4.34
363 369 8.593492 AGTTTAGTTTATTTTCGGTAGACGTT 57.407 30.769 0.00 0.00 44.69 3.99
364 370 8.703336 AGTTTAGTTTATTTTCGGTAGACGTTC 58.297 33.333 0.00 0.00 44.69 3.95
365 371 8.487176 GTTTAGTTTATTTTCGGTAGACGTTCA 58.513 33.333 0.00 0.00 44.69 3.18
366 372 8.761575 TTAGTTTATTTTCGGTAGACGTTCAT 57.238 30.769 0.00 0.00 44.69 2.57
367 373 7.057149 AGTTTATTTTCGGTAGACGTTCATG 57.943 36.000 0.00 0.00 44.69 3.07
368 374 6.091713 AGTTTATTTTCGGTAGACGTTCATGG 59.908 38.462 0.00 0.00 44.69 3.66
369 375 3.663995 TTTTCGGTAGACGTTCATGGA 57.336 42.857 0.00 0.00 44.69 3.41
370 376 2.642139 TTCGGTAGACGTTCATGGAC 57.358 50.000 0.00 0.00 44.69 4.02
372 378 1.138047 CGGTAGACGTTCATGGACGC 61.138 60.000 26.36 18.10 46.47 5.19
373 379 0.804933 GGTAGACGTTCATGGACGCC 60.805 60.000 26.36 16.24 46.47 5.68
374 380 0.108992 GTAGACGTTCATGGACGCCA 60.109 55.000 26.36 8.79 46.47 5.69
375 381 0.821517 TAGACGTTCATGGACGCCAT 59.178 50.000 26.36 14.40 46.37 4.40
376 382 0.460284 AGACGTTCATGGACGCCATC 60.460 55.000 26.36 16.16 43.15 3.51
377 383 1.429148 GACGTTCATGGACGCCATCC 61.429 60.000 26.36 7.04 43.15 3.51
390 396 4.519437 CATCCGGCTGCGCTGAGA 62.519 66.667 19.32 11.11 37.02 3.27
391 397 3.544607 ATCCGGCTGCGCTGAGAT 61.545 61.111 19.32 12.86 37.02 2.75
392 398 3.099211 ATCCGGCTGCGCTGAGATT 62.099 57.895 19.32 0.00 37.02 2.40
393 399 2.599645 ATCCGGCTGCGCTGAGATTT 62.600 55.000 19.32 0.00 37.02 2.17
394 400 2.705826 CGGCTGCGCTGAGATTTC 59.294 61.111 19.32 0.00 37.02 2.17
395 401 2.102438 CGGCTGCGCTGAGATTTCA 61.102 57.895 19.32 0.00 37.02 2.69
396 402 1.434622 CGGCTGCGCTGAGATTTCAT 61.435 55.000 19.32 0.00 37.02 2.57
397 403 0.029035 GGCTGCGCTGAGATTTCATG 59.971 55.000 19.32 0.00 31.68 3.07
398 404 1.012086 GCTGCGCTGAGATTTCATGA 58.988 50.000 19.32 0.00 31.68 3.07
399 405 1.602851 GCTGCGCTGAGATTTCATGAT 59.397 47.619 19.32 0.00 31.68 2.45
400 406 2.349627 GCTGCGCTGAGATTTCATGATC 60.350 50.000 19.32 0.00 31.68 2.92
401 407 2.216046 TGCGCTGAGATTTCATGATCC 58.784 47.619 9.73 0.00 31.68 3.36
402 408 2.216046 GCGCTGAGATTTCATGATCCA 58.784 47.619 0.00 0.00 31.68 3.41
403 409 2.032204 GCGCTGAGATTTCATGATCCAC 60.032 50.000 0.00 0.00 31.68 4.02
404 410 3.200483 CGCTGAGATTTCATGATCCACA 58.800 45.455 0.00 0.00 31.68 4.17
405 411 3.002042 CGCTGAGATTTCATGATCCACAC 59.998 47.826 0.00 0.00 31.68 3.82
406 412 4.197750 GCTGAGATTTCATGATCCACACT 58.802 43.478 0.00 0.00 31.68 3.55
407 413 5.363101 GCTGAGATTTCATGATCCACACTA 58.637 41.667 0.00 0.00 31.68 2.74
408 414 5.466058 GCTGAGATTTCATGATCCACACTAG 59.534 44.000 0.00 0.00 31.68 2.57
409 415 6.684865 GCTGAGATTTCATGATCCACACTAGA 60.685 42.308 0.00 0.00 31.68 2.43
410 416 6.814043 TGAGATTTCATGATCCACACTAGAG 58.186 40.000 0.00 0.00 0.00 2.43
411 417 6.172136 AGATTTCATGATCCACACTAGAGG 57.828 41.667 0.00 0.00 0.00 3.69
412 418 5.664908 AGATTTCATGATCCACACTAGAGGT 59.335 40.000 0.00 0.00 0.00 3.85
723 729 2.892305 CGAGGATCCTTCGCACATC 58.108 57.895 17.42 0.00 0.00 3.06
751 757 2.350522 CTCAAACCTCAGATTCCCACG 58.649 52.381 0.00 0.00 0.00 4.94
763 769 2.243602 TTCCCACGGTAAGTTGACAC 57.756 50.000 0.00 0.00 0.00 3.67
784 790 7.064016 TGACACAAATTTCCAGTTTTAAGTTGC 59.936 33.333 0.00 0.00 32.01 4.17
806 812 4.129380 CGCTGTCCCATTATCAGATTTCA 58.871 43.478 0.00 0.00 0.00 2.69
950 957 2.094417 CGAAAAAGGGCTCATCTTCGTC 59.906 50.000 5.96 0.00 32.98 4.20
963 970 2.781595 CTTCGTCCCTCCCAACACCG 62.782 65.000 0.00 0.00 0.00 4.94
1039 1049 8.917415 GGAATTGTATCCTTTTGTCAAAGATC 57.083 34.615 3.92 0.00 41.97 2.75
1040 1155 7.976175 GGAATTGTATCCTTTTGTCAAAGATCC 59.024 37.037 3.92 0.00 41.97 3.36
1043 1158 7.687941 TGTATCCTTTTGTCAAAGATCCTTC 57.312 36.000 3.92 0.00 41.97 3.46
1045 1160 8.602424 TGTATCCTTTTGTCAAAGATCCTTCTA 58.398 33.333 3.92 0.00 41.97 2.10
1053 1168 7.325660 TGTCAAAGATCCTTCTATTCATTGC 57.674 36.000 0.00 0.00 0.00 3.56
1055 1170 7.394077 TGTCAAAGATCCTTCTATTCATTGCAA 59.606 33.333 0.00 0.00 0.00 4.08
1092 1207 8.897752 GTGCATGATCTCCTACTTTTATTTTCT 58.102 33.333 0.00 0.00 0.00 2.52
1093 1208 8.896744 TGCATGATCTCCTACTTTTATTTTCTG 58.103 33.333 0.00 0.00 0.00 3.02
1114 1229 2.823196 TTGTCAACTCACGTGCTTTG 57.177 45.000 11.67 15.70 0.00 2.77
1315 1430 1.590932 GGCTCAGCTACACCATCATG 58.409 55.000 0.00 0.00 0.00 3.07
1399 1514 0.984230 AGGATGAGAAACTGGGCGAA 59.016 50.000 0.00 0.00 0.00 4.70
1604 1788 7.243824 AGGCCATTACTGGATAATCATGAAAT 58.756 34.615 5.01 0.00 46.37 2.17
1854 2045 5.474876 CCAAAGAGCAGAACAGGTTAGAAAT 59.525 40.000 0.00 0.00 0.00 2.17
1959 2150 0.916809 AACTTTGTATCCCCCTCCCG 59.083 55.000 0.00 0.00 0.00 5.14
2010 2202 2.695666 CCCTCGTCAGTGATCAAGGTAT 59.304 50.000 14.03 0.00 0.00 2.73
2187 2389 2.076863 ACGGCTGCTCTGAAAATGTAC 58.923 47.619 0.00 0.00 0.00 2.90
2191 2393 2.096496 GCTGCTCTGAAAATGTACGCAT 59.904 45.455 0.00 0.00 36.80 4.73
2224 2426 5.423886 CCTCCTAGTCATTTTCAGTCCTTC 58.576 45.833 0.00 0.00 0.00 3.46
2225 2427 5.046304 CCTCCTAGTCATTTTCAGTCCTTCA 60.046 44.000 0.00 0.00 0.00 3.02
2245 2447 2.155732 CAGACGAATGGAAACGACACTG 59.844 50.000 0.00 0.00 0.00 3.66
2247 2449 2.798283 GACGAATGGAAACGACACTGAA 59.202 45.455 0.00 0.00 0.00 3.02
2248 2450 3.199677 ACGAATGGAAACGACACTGAAA 58.800 40.909 0.00 0.00 0.00 2.69
2473 2675 7.736893 TCAGAGATCTATGTGTACTGCTACTA 58.263 38.462 16.60 0.00 0.00 1.82
2485 2687 6.866770 GTGTACTGCTACTATCAAGTTTGACA 59.133 38.462 0.00 0.00 40.49 3.58
2486 2688 7.545965 GTGTACTGCTACTATCAAGTTTGACAT 59.454 37.037 0.00 0.00 40.49 3.06
2487 2689 8.094548 TGTACTGCTACTATCAAGTTTGACATT 58.905 33.333 0.00 0.00 40.49 2.71
2488 2690 7.986085 ACTGCTACTATCAAGTTTGACATTT 57.014 32.000 0.00 0.00 40.49 2.32
2489 2691 8.396272 ACTGCTACTATCAAGTTTGACATTTT 57.604 30.769 0.00 0.00 40.49 1.82
2490 2692 8.850156 ACTGCTACTATCAAGTTTGACATTTTT 58.150 29.630 0.00 0.00 40.49 1.94
2491 2693 9.334693 CTGCTACTATCAAGTTTGACATTTTTC 57.665 33.333 0.00 0.00 40.49 2.29
2492 2694 8.845227 TGCTACTATCAAGTTTGACATTTTTCA 58.155 29.630 0.00 0.00 40.49 2.69
2493 2695 9.118236 GCTACTATCAAGTTTGACATTTTTCAC 57.882 33.333 0.00 0.00 40.49 3.18
2496 2698 9.467258 ACTATCAAGTTTGACATTTTTCACATG 57.533 29.630 0.00 0.00 40.49 3.21
2497 2699 6.586868 TCAAGTTTGACATTTTTCACATGC 57.413 33.333 0.00 0.00 31.01 4.06
2498 2700 6.339730 TCAAGTTTGACATTTTTCACATGCT 58.660 32.000 0.00 0.00 31.01 3.79
2499 2701 6.817641 TCAAGTTTGACATTTTTCACATGCTT 59.182 30.769 0.00 0.00 31.01 3.91
2500 2702 7.333921 TCAAGTTTGACATTTTTCACATGCTTT 59.666 29.630 0.00 0.00 31.01 3.51
2501 2703 8.602328 CAAGTTTGACATTTTTCACATGCTTTA 58.398 29.630 0.00 0.00 0.00 1.85
2502 2704 8.891671 AGTTTGACATTTTTCACATGCTTTAT 57.108 26.923 0.00 0.00 0.00 1.40
2503 2705 8.981647 AGTTTGACATTTTTCACATGCTTTATC 58.018 29.630 0.00 0.00 0.00 1.75
2517 2722 3.694072 TGCTTTATCTACATGGGTTGCAC 59.306 43.478 0.00 0.00 0.00 4.57
2521 2726 0.391130 TCTACATGGGTTGCACTCGC 60.391 55.000 0.00 0.00 39.24 5.03
2532 2737 0.610174 TGCACTCGCTTCAGGATTCT 59.390 50.000 0.00 0.00 39.64 2.40
2562 2767 4.380531 CCGTGATGACCATATACAAGCTT 58.619 43.478 0.00 0.00 0.00 3.74
2566 2771 5.817296 GTGATGACCATATACAAGCTTGTGA 59.183 40.000 36.50 25.76 42.31 3.58
2651 2861 3.488047 GCATATCTTGTCAAACTGCGCAT 60.488 43.478 12.24 0.00 0.00 4.73
3076 3294 1.455822 TCCCAAACCAGGAGGACATT 58.544 50.000 0.00 0.00 38.69 2.71
3189 3407 1.292223 GGGCTGTAAGTGCGTCTGA 59.708 57.895 0.00 0.00 35.30 3.27
3220 3441 5.796424 AAAGTATTGGATGATGGAATGCC 57.204 39.130 0.00 0.00 0.00 4.40
3260 3482 2.627221 GAGGGTTTATACTCGGACCTCC 59.373 54.545 0.00 0.00 37.62 4.30
3386 3646 3.120025 GCTCTCTTTGCAGGCTAGTTTTC 60.120 47.826 0.00 0.00 0.00 2.29
3444 3705 4.906747 ACCCGGCCGGTTTATTAATATA 57.093 40.909 40.52 0.00 45.36 0.86
3596 3860 9.857957 ACTTTGCAAAATTGAAAACATTTCATT 57.142 22.222 13.84 1.19 32.44 2.57
3739 4005 6.693978 ACGGATTTTTAAGAAAAACTTCACGG 59.306 34.615 0.00 0.00 42.57 4.94
3853 4119 4.010349 CCATAGAAAACCCAGAGTGTTCC 58.990 47.826 0.00 0.00 42.93 3.62
3896 4163 4.616802 CGCGCAACAAGAATAGAAAAACAT 59.383 37.500 8.75 0.00 0.00 2.71
3898 4165 6.345723 CGCGCAACAAGAATAGAAAAACATTT 60.346 34.615 8.75 0.00 0.00 2.32
3902 4169 8.063630 GCAACAAGAATAGAAAAACATTTGGTG 58.936 33.333 0.00 0.00 35.65 4.17
3903 4170 8.550376 CAACAAGAATAGAAAAACATTTGGTGG 58.450 33.333 0.00 0.00 30.53 4.61
3904 4171 7.216494 ACAAGAATAGAAAAACATTTGGTGGG 58.784 34.615 0.00 0.00 0.00 4.61
3905 4172 6.358974 AGAATAGAAAAACATTTGGTGGGG 57.641 37.500 0.00 0.00 0.00 4.96
3906 4173 5.248248 AGAATAGAAAAACATTTGGTGGGGG 59.752 40.000 0.00 0.00 0.00 5.40
3907 4174 3.053359 AGAAAAACATTTGGTGGGGGA 57.947 42.857 0.00 0.00 0.00 4.81
3908 4175 2.972021 AGAAAAACATTTGGTGGGGGAG 59.028 45.455 0.00 0.00 0.00 4.30
3909 4176 2.487746 AAAACATTTGGTGGGGGAGT 57.512 45.000 0.00 0.00 0.00 3.85
3910 4177 3.621682 AAAACATTTGGTGGGGGAGTA 57.378 42.857 0.00 0.00 0.00 2.59
3911 4178 3.621682 AAACATTTGGTGGGGGAGTAA 57.378 42.857 0.00 0.00 0.00 2.24
3912 4179 2.899303 ACATTTGGTGGGGGAGTAAG 57.101 50.000 0.00 0.00 0.00 2.34
3913 4180 1.272480 ACATTTGGTGGGGGAGTAAGC 60.272 52.381 0.00 0.00 0.00 3.09
3914 4181 1.080638 ATTTGGTGGGGGAGTAAGCA 58.919 50.000 0.00 0.00 0.00 3.91
3915 4182 0.854218 TTTGGTGGGGGAGTAAGCAA 59.146 50.000 0.00 0.00 0.00 3.91
3916 4183 0.404040 TTGGTGGGGGAGTAAGCAAG 59.596 55.000 0.00 0.00 0.00 4.01
3917 4184 1.303282 GGTGGGGGAGTAAGCAAGG 59.697 63.158 0.00 0.00 0.00 3.61
3918 4185 1.378646 GTGGGGGAGTAAGCAAGGC 60.379 63.158 0.00 0.00 0.00 4.35
3919 4186 1.850289 TGGGGGAGTAAGCAAGGCA 60.850 57.895 0.00 0.00 0.00 4.75
3920 4187 1.382629 GGGGGAGTAAGCAAGGCAA 59.617 57.895 0.00 0.00 0.00 4.52
3921 4188 0.251608 GGGGGAGTAAGCAAGGCAAA 60.252 55.000 0.00 0.00 0.00 3.68
3922 4189 0.888619 GGGGAGTAAGCAAGGCAAAC 59.111 55.000 0.00 0.00 0.00 2.93
3923 4190 0.521735 GGGAGTAAGCAAGGCAAACG 59.478 55.000 0.00 0.00 0.00 3.60
3924 4191 1.519408 GGAGTAAGCAAGGCAAACGA 58.481 50.000 0.00 0.00 0.00 3.85
3925 4192 1.877443 GGAGTAAGCAAGGCAAACGAA 59.123 47.619 0.00 0.00 0.00 3.85
3926 4193 2.292292 GGAGTAAGCAAGGCAAACGAAA 59.708 45.455 0.00 0.00 0.00 3.46
3927 4194 3.243267 GGAGTAAGCAAGGCAAACGAAAA 60.243 43.478 0.00 0.00 0.00 2.29
3928 4195 3.702330 AGTAAGCAAGGCAAACGAAAAC 58.298 40.909 0.00 0.00 0.00 2.43
3929 4196 1.934589 AAGCAAGGCAAACGAAAACC 58.065 45.000 0.00 0.00 0.00 3.27
3930 4197 0.820871 AGCAAGGCAAACGAAAACCA 59.179 45.000 0.00 0.00 0.00 3.67
3931 4198 1.205893 AGCAAGGCAAACGAAAACCAA 59.794 42.857 0.00 0.00 0.00 3.67
3932 4199 2.003301 GCAAGGCAAACGAAAACCAAA 58.997 42.857 0.00 0.00 0.00 3.28
3933 4200 2.222931 GCAAGGCAAACGAAAACCAAAC 60.223 45.455 0.00 0.00 0.00 2.93
3934 4201 3.258228 CAAGGCAAACGAAAACCAAACT 58.742 40.909 0.00 0.00 0.00 2.66
3935 4202 2.887337 AGGCAAACGAAAACCAAACTG 58.113 42.857 0.00 0.00 0.00 3.16
3936 4203 1.930503 GGCAAACGAAAACCAAACTGG 59.069 47.619 0.00 0.00 45.02 4.00
3937 4204 1.930503 GCAAACGAAAACCAAACTGGG 59.069 47.619 0.00 0.00 43.37 4.45
3938 4205 2.675603 GCAAACGAAAACCAAACTGGGT 60.676 45.455 0.00 0.00 40.89 4.51
3944 4211 4.275781 ACCAAACTGGGTTGCCTG 57.724 55.556 0.00 0.00 43.37 4.85
3945 4212 1.457455 ACCAAACTGGGTTGCCTGG 60.457 57.895 0.00 0.00 43.37 4.45
3946 4213 2.209315 CCAAACTGGGTTGCCTGGG 61.209 63.158 0.00 0.00 32.67 4.45
3947 4214 1.152567 CAAACTGGGTTGCCTGGGA 60.153 57.895 0.00 0.00 0.00 4.37
3948 4215 1.152546 AAACTGGGTTGCCTGGGAC 60.153 57.895 0.00 0.00 0.00 4.46
3949 4216 1.943730 AAACTGGGTTGCCTGGGACA 61.944 55.000 0.00 0.00 0.00 4.02
3950 4217 2.282462 CTGGGTTGCCTGGGACAC 60.282 66.667 0.00 0.00 0.00 3.67
3951 4218 2.776526 TGGGTTGCCTGGGACACT 60.777 61.111 0.00 0.00 0.00 3.55
3952 4219 1.462432 TGGGTTGCCTGGGACACTA 60.462 57.895 0.00 0.00 0.00 2.74
3953 4220 0.844661 TGGGTTGCCTGGGACACTAT 60.845 55.000 0.00 0.00 0.00 2.12
3954 4221 0.394352 GGGTTGCCTGGGACACTATG 60.394 60.000 0.00 0.00 0.00 2.23
3955 4222 0.618458 GGTTGCCTGGGACACTATGA 59.382 55.000 0.00 0.00 0.00 2.15
3956 4223 1.212935 GGTTGCCTGGGACACTATGAT 59.787 52.381 0.00 0.00 0.00 2.45
3957 4224 2.438021 GGTTGCCTGGGACACTATGATA 59.562 50.000 0.00 0.00 0.00 2.15
3958 4225 3.467803 GTTGCCTGGGACACTATGATAC 58.532 50.000 0.00 0.00 0.00 2.24
3959 4226 2.758130 TGCCTGGGACACTATGATACA 58.242 47.619 0.00 0.00 0.00 2.29
3960 4227 3.111484 TGCCTGGGACACTATGATACAA 58.889 45.455 0.00 0.00 0.00 2.41
3961 4228 3.118408 TGCCTGGGACACTATGATACAAC 60.118 47.826 0.00 0.00 0.00 3.32
3962 4229 3.744530 GCCTGGGACACTATGATACAACC 60.745 52.174 0.00 0.00 0.00 3.77
3963 4230 3.454447 CCTGGGACACTATGATACAACCA 59.546 47.826 0.00 0.00 0.00 3.67
3964 4231 4.080582 CCTGGGACACTATGATACAACCAA 60.081 45.833 0.00 0.00 0.00 3.67
3965 4232 5.496556 CTGGGACACTATGATACAACCAAA 58.503 41.667 0.00 0.00 0.00 3.28
3966 4233 5.882040 TGGGACACTATGATACAACCAAAA 58.118 37.500 0.00 0.00 0.00 2.44
3967 4234 5.708230 TGGGACACTATGATACAACCAAAAC 59.292 40.000 0.00 0.00 0.00 2.43
3968 4235 5.708230 GGGACACTATGATACAACCAAAACA 59.292 40.000 0.00 0.00 0.00 2.83
3969 4236 6.128007 GGGACACTATGATACAACCAAAACAG 60.128 42.308 0.00 0.00 0.00 3.16
3970 4237 6.430000 GGACACTATGATACAACCAAAACAGT 59.570 38.462 0.00 0.00 0.00 3.55
3971 4238 7.040686 GGACACTATGATACAACCAAAACAGTT 60.041 37.037 0.00 0.00 0.00 3.16
3978 4245 2.239681 AACCAAAACAGTTGGGTGGA 57.760 45.000 14.92 0.00 40.52 4.02
3979 4246 1.480789 ACCAAAACAGTTGGGTGGAC 58.519 50.000 14.92 0.00 39.84 4.02
3980 4247 1.006639 ACCAAAACAGTTGGGTGGACT 59.993 47.619 14.92 0.00 39.84 3.85
3981 4248 2.107366 CCAAAACAGTTGGGTGGACTT 58.893 47.619 5.35 0.00 35.96 3.01
3982 4249 2.159114 CCAAAACAGTTGGGTGGACTTG 60.159 50.000 5.35 0.00 35.96 3.16
3983 4250 1.775385 AAACAGTTGGGTGGACTTGG 58.225 50.000 0.00 0.00 0.00 3.61
3984 4251 0.923358 AACAGTTGGGTGGACTTGGA 59.077 50.000 0.00 0.00 0.00 3.53
3985 4252 1.149101 ACAGTTGGGTGGACTTGGAT 58.851 50.000 0.00 0.00 0.00 3.41
3986 4253 1.499007 ACAGTTGGGTGGACTTGGATT 59.501 47.619 0.00 0.00 0.00 3.01
3987 4254 2.162681 CAGTTGGGTGGACTTGGATTC 58.837 52.381 0.00 0.00 0.00 2.52
3988 4255 1.075536 AGTTGGGTGGACTTGGATTCC 59.924 52.381 0.00 0.00 0.00 3.01
3989 4256 0.037590 TTGGGTGGACTTGGATTCCG 59.962 55.000 0.00 0.00 35.70 4.30
3990 4257 1.131303 TGGGTGGACTTGGATTCCGT 61.131 55.000 0.00 0.00 35.70 4.69
3991 4258 0.676782 GGGTGGACTTGGATTCCGTG 60.677 60.000 0.00 0.00 35.70 4.94
3992 4259 0.323629 GGTGGACTTGGATTCCGTGA 59.676 55.000 0.00 0.00 35.70 4.35
3993 4260 1.065418 GGTGGACTTGGATTCCGTGAT 60.065 52.381 0.00 0.00 35.70 3.06
3994 4261 2.618045 GGTGGACTTGGATTCCGTGATT 60.618 50.000 0.00 0.00 35.70 2.57
3995 4262 3.081804 GTGGACTTGGATTCCGTGATTT 58.918 45.455 0.00 0.00 35.70 2.17
3996 4263 3.081061 TGGACTTGGATTCCGTGATTTG 58.919 45.455 0.00 0.00 35.70 2.32
3997 4264 2.423538 GGACTTGGATTCCGTGATTTGG 59.576 50.000 0.00 0.00 0.00 3.28
3998 4265 3.343617 GACTTGGATTCCGTGATTTGGA 58.656 45.455 0.00 0.00 0.00 3.53
3999 4266 3.347216 ACTTGGATTCCGTGATTTGGAG 58.653 45.455 0.00 0.00 36.72 3.86
4000 4267 3.009033 ACTTGGATTCCGTGATTTGGAGA 59.991 43.478 0.00 0.00 36.72 3.71
4001 4268 3.931907 TGGATTCCGTGATTTGGAGAT 57.068 42.857 0.00 0.00 36.72 2.75
4002 4269 3.544684 TGGATTCCGTGATTTGGAGATG 58.455 45.455 0.00 0.00 36.72 2.90
4003 4270 3.054434 TGGATTCCGTGATTTGGAGATGT 60.054 43.478 0.00 0.00 36.72 3.06
4004 4271 3.947834 GGATTCCGTGATTTGGAGATGTT 59.052 43.478 0.00 0.00 36.72 2.71
4005 4272 4.035675 GGATTCCGTGATTTGGAGATGTTC 59.964 45.833 0.00 0.00 36.72 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
157 158 2.817396 GGTTGCCTCTGAGAGCGC 60.817 66.667 13.69 13.69 0.00 5.92
166 167 1.966451 CTGTTGTCCCGGTTGCCTC 60.966 63.158 0.00 0.00 0.00 4.70
173 174 0.251916 TATCTTGCCTGTTGTCCCGG 59.748 55.000 0.00 0.00 0.00 5.73
186 192 7.488322 TCTTTGTGGGTTGAAAAAGTATCTTG 58.512 34.615 0.00 0.00 32.64 3.02
187 193 7.654022 TCTTTGTGGGTTGAAAAAGTATCTT 57.346 32.000 0.00 0.00 32.64 2.40
188 194 7.654022 TTCTTTGTGGGTTGAAAAAGTATCT 57.346 32.000 0.00 0.00 32.64 1.98
189 195 7.223971 GGTTTCTTTGTGGGTTGAAAAAGTATC 59.776 37.037 0.00 0.00 32.64 2.24
190 196 7.045416 GGTTTCTTTGTGGGTTGAAAAAGTAT 58.955 34.615 0.00 0.00 32.64 2.12
200 206 4.030216 ACTTCATGGTTTCTTTGTGGGTT 58.970 39.130 0.00 0.00 0.00 4.11
235 241 1.356124 ACTGAGCAATCACCTCACCT 58.644 50.000 0.00 0.00 35.60 4.00
236 242 2.419297 CCTACTGAGCAATCACCTCACC 60.419 54.545 0.00 0.00 35.60 4.02
250 256 0.614812 TCTGCTTGCATGCCTACTGA 59.385 50.000 20.65 10.45 0.00 3.41
251 257 0.731417 GTCTGCTTGCATGCCTACTG 59.269 55.000 20.65 8.23 0.00 2.74
252 258 0.617413 AGTCTGCTTGCATGCCTACT 59.383 50.000 20.65 19.03 0.00 2.57
253 259 0.731417 CAGTCTGCTTGCATGCCTAC 59.269 55.000 20.65 17.34 0.00 3.18
254 260 0.325933 ACAGTCTGCTTGCATGCCTA 59.674 50.000 20.65 6.96 0.00 3.93
255 261 1.074423 ACAGTCTGCTTGCATGCCT 59.926 52.632 20.65 8.80 0.00 4.75
256 262 1.211969 CACAGTCTGCTTGCATGCC 59.788 57.895 20.65 6.66 0.00 4.40
257 263 0.109873 GACACAGTCTGCTTGCATGC 60.110 55.000 17.19 17.19 0.00 4.06
258 264 0.520404 GGACACAGTCTGCTTGCATG 59.480 55.000 0.00 0.00 32.47 4.06
259 265 0.952497 CGGACACAGTCTGCTTGCAT 60.952 55.000 0.00 0.00 31.96 3.96
260 266 1.595109 CGGACACAGTCTGCTTGCA 60.595 57.895 0.00 0.00 31.96 4.08
261 267 3.248029 CGGACACAGTCTGCTTGC 58.752 61.111 0.00 0.00 31.96 4.01
266 272 1.442857 GACTCGCGGACACAGTCTG 60.443 63.158 15.39 0.00 41.44 3.51
267 273 2.627737 GGACTCGCGGACACAGTCT 61.628 63.158 20.13 0.00 37.34 3.24
288 294 4.404507 AATTTTCATCTCACGGACGTTG 57.595 40.909 0.00 0.00 0.00 4.10
294 300 3.694072 TGGGCTTAATTTTCATCTCACGG 59.306 43.478 0.00 0.00 0.00 4.94
295 301 4.963276 TGGGCTTAATTTTCATCTCACG 57.037 40.909 0.00 0.00 0.00 4.35
297 303 6.351202 CCATGTTGGGCTTAATTTTCATCTCA 60.351 38.462 0.00 0.00 32.67 3.27
306 312 8.821817 ACTTTAATAACCATGTTGGGCTTAATT 58.178 29.630 0.00 0.00 43.37 1.40
307 313 8.374184 ACTTTAATAACCATGTTGGGCTTAAT 57.626 30.769 0.00 0.00 43.37 1.40
310 316 7.233757 TGTTACTTTAATAACCATGTTGGGCTT 59.766 33.333 0.00 0.00 43.37 4.35
311 317 6.722129 TGTTACTTTAATAACCATGTTGGGCT 59.278 34.615 0.00 0.00 43.37 5.19
313 319 9.418045 CTTTGTTACTTTAATAACCATGTTGGG 57.582 33.333 0.00 0.00 43.37 4.12
314 320 9.974980 ACTTTGTTACTTTAATAACCATGTTGG 57.025 29.630 0.00 0.00 45.02 3.77
335 341 9.309796 CGTCTACCGAAAATAAACTAAACTTTG 57.690 33.333 0.00 0.00 39.56 2.77
336 342 9.045223 ACGTCTACCGAAAATAAACTAAACTTT 57.955 29.630 0.00 0.00 40.70 2.66
337 343 8.593492 ACGTCTACCGAAAATAAACTAAACTT 57.407 30.769 0.00 0.00 40.70 2.66
338 344 8.593492 AACGTCTACCGAAAATAAACTAAACT 57.407 30.769 0.00 0.00 40.70 2.66
339 345 8.487176 TGAACGTCTACCGAAAATAAACTAAAC 58.513 33.333 0.00 0.00 40.70 2.01
340 346 8.586570 TGAACGTCTACCGAAAATAAACTAAA 57.413 30.769 0.00 0.00 40.70 1.85
341 347 8.649841 CATGAACGTCTACCGAAAATAAACTAA 58.350 33.333 0.00 0.00 40.70 2.24
342 348 7.276218 CCATGAACGTCTACCGAAAATAAACTA 59.724 37.037 0.00 0.00 40.70 2.24
343 349 6.091713 CCATGAACGTCTACCGAAAATAAACT 59.908 38.462 0.00 0.00 40.70 2.66
344 350 6.091169 TCCATGAACGTCTACCGAAAATAAAC 59.909 38.462 0.00 0.00 40.70 2.01
345 351 6.091169 GTCCATGAACGTCTACCGAAAATAAA 59.909 38.462 0.00 0.00 40.70 1.40
346 352 5.577945 GTCCATGAACGTCTACCGAAAATAA 59.422 40.000 0.00 0.00 40.70 1.40
347 353 5.104374 GTCCATGAACGTCTACCGAAAATA 58.896 41.667 0.00 0.00 40.70 1.40
348 354 3.930848 GTCCATGAACGTCTACCGAAAAT 59.069 43.478 0.00 0.00 40.70 1.82
349 355 3.319755 GTCCATGAACGTCTACCGAAAA 58.680 45.455 0.00 0.00 40.70 2.29
350 356 2.669113 CGTCCATGAACGTCTACCGAAA 60.669 50.000 0.00 0.00 40.70 3.46
351 357 1.135603 CGTCCATGAACGTCTACCGAA 60.136 52.381 0.00 0.00 40.70 4.30
352 358 0.448990 CGTCCATGAACGTCTACCGA 59.551 55.000 0.00 0.00 40.70 4.69
353 359 1.138047 GCGTCCATGAACGTCTACCG 61.138 60.000 6.29 0.00 44.38 4.02
354 360 0.804933 GGCGTCCATGAACGTCTACC 60.805 60.000 6.29 0.00 43.64 3.18
355 361 0.108992 TGGCGTCCATGAACGTCTAC 60.109 55.000 11.20 0.00 46.94 2.59
356 362 0.821517 ATGGCGTCCATGAACGTCTA 59.178 50.000 11.20 0.00 46.94 2.59
357 363 0.460284 GATGGCGTCCATGAACGTCT 60.460 55.000 11.20 0.00 45.26 4.18
358 364 1.429148 GGATGGCGTCCATGAACGTC 61.429 60.000 20.92 0.63 45.26 4.34
359 365 1.449601 GGATGGCGTCCATGAACGT 60.450 57.895 20.92 0.00 45.26 3.99
360 366 3.409856 GGATGGCGTCCATGAACG 58.590 61.111 20.92 0.00 45.26 3.95
380 386 2.223611 GGATCATGAAATCTCAGCGCAG 59.776 50.000 11.47 0.00 34.23 5.18
381 387 2.216046 GGATCATGAAATCTCAGCGCA 58.784 47.619 11.47 0.00 34.23 6.09
382 388 2.032204 GTGGATCATGAAATCTCAGCGC 60.032 50.000 0.00 0.00 34.23 5.92
383 389 3.002042 GTGTGGATCATGAAATCTCAGCG 59.998 47.826 0.00 0.00 34.23 5.18
384 390 4.197750 AGTGTGGATCATGAAATCTCAGC 58.802 43.478 0.00 0.00 34.23 4.26
385 391 6.814043 TCTAGTGTGGATCATGAAATCTCAG 58.186 40.000 0.00 0.00 34.23 3.35
386 392 6.183360 CCTCTAGTGTGGATCATGAAATCTCA 60.183 42.308 0.00 0.00 35.56 3.27
387 393 6.183360 ACCTCTAGTGTGGATCATGAAATCTC 60.183 42.308 0.00 0.00 0.00 2.75
388 394 5.664908 ACCTCTAGTGTGGATCATGAAATCT 59.335 40.000 0.00 0.00 0.00 2.40
389 395 5.757320 CACCTCTAGTGTGGATCATGAAATC 59.243 44.000 0.00 0.00 41.93 2.17
390 396 5.678583 CACCTCTAGTGTGGATCATGAAAT 58.321 41.667 0.00 0.00 41.93 2.17
391 397 5.089970 CACCTCTAGTGTGGATCATGAAA 57.910 43.478 0.00 0.00 41.93 2.69
392 398 4.743057 CACCTCTAGTGTGGATCATGAA 57.257 45.455 0.00 0.00 41.93 2.57
751 757 6.144078 ACTGGAAATTTGTGTCAACTTACC 57.856 37.500 0.00 0.00 0.00 2.85
763 769 5.234116 AGCGCAACTTAAAACTGGAAATTTG 59.766 36.000 11.47 0.00 0.00 2.32
806 812 4.323792 CCACTTATGACCTCCAACAGATGT 60.324 45.833 0.00 0.00 0.00 3.06
950 957 2.033602 GGTTCGGTGTTGGGAGGG 59.966 66.667 0.00 0.00 0.00 4.30
1030 1039 7.325660 TGCAATGAATAGAAGGATCTTTGAC 57.674 36.000 0.00 0.00 37.10 3.18
1052 1167 1.125384 CATGCACACAAAGCGATTTGC 59.875 47.619 24.95 13.17 46.98 3.68
1053 1168 2.663808 TCATGCACACAAAGCGATTTG 58.336 42.857 23.59 23.59 37.89 2.32
1055 1170 2.751259 AGATCATGCACACAAAGCGATT 59.249 40.909 0.00 0.00 33.85 3.34
1092 1207 1.732941 AGCACGTGAGTTGACAAACA 58.267 45.000 22.23 0.00 46.40 2.83
1093 1208 2.825086 AAGCACGTGAGTTGACAAAC 57.175 45.000 22.23 0.00 46.40 2.93
1099 1214 0.042188 CGACCAAAGCACGTGAGTTG 60.042 55.000 22.23 20.39 46.40 3.16
1114 1229 1.376812 AAGGTCCGGCAAATCGACC 60.377 57.895 0.00 0.00 36.25 4.79
1315 1430 3.801698 TGTATTCTGCTGCTCCATCTTC 58.198 45.455 0.00 0.00 0.00 2.87
1399 1514 1.073923 ACTTTCGAGGTGAATTGGCCT 59.926 47.619 3.32 0.00 36.22 5.19
1604 1788 3.003275 CGCTTCCAGTGCTTTTTCTTACA 59.997 43.478 0.00 0.00 0.00 2.41
1698 1883 6.323996 TCCGAGTTCATCCAGTAATCTGTTAT 59.676 38.462 0.00 0.00 39.82 1.89
1720 1911 7.275560 CAGTTTTTAAGGGAAATAATTGCTCCG 59.724 37.037 0.00 0.00 0.00 4.63
2010 2202 7.395489 AGACATAAGGGTTTCTCTACTTCGTAA 59.605 37.037 0.00 0.00 0.00 3.18
2224 2426 2.155732 CAGTGTCGTTTCCATTCGTCTG 59.844 50.000 0.00 0.00 0.00 3.51
2225 2427 2.035449 TCAGTGTCGTTTCCATTCGTCT 59.965 45.455 0.00 0.00 0.00 4.18
2232 2434 2.685388 TGCAATTTCAGTGTCGTTTCCA 59.315 40.909 0.00 0.00 0.00 3.53
2245 2447 2.668279 CGCCTGGTTGTAGTGCAATTTC 60.668 50.000 0.00 0.00 39.55 2.17
2247 2449 0.881118 CGCCTGGTTGTAGTGCAATT 59.119 50.000 0.00 0.00 39.55 2.32
2248 2450 1.586154 GCGCCTGGTTGTAGTGCAAT 61.586 55.000 0.00 0.00 39.55 3.56
2295 2497 1.746220 CGACGATCTCCACCTCTCTTT 59.254 52.381 0.00 0.00 0.00 2.52
2473 2675 6.987992 AGCATGTGAAAAATGTCAAACTTGAT 59.012 30.769 0.00 0.00 39.73 2.57
2485 2687 8.199449 CCCATGTAGATAAAGCATGTGAAAAAT 58.801 33.333 0.00 0.00 38.53 1.82
2486 2688 7.178274 ACCCATGTAGATAAAGCATGTGAAAAA 59.822 33.333 0.00 0.00 38.53 1.94
2487 2689 6.663093 ACCCATGTAGATAAAGCATGTGAAAA 59.337 34.615 0.00 0.00 38.53 2.29
2488 2690 6.186957 ACCCATGTAGATAAAGCATGTGAAA 58.813 36.000 0.00 0.00 38.53 2.69
2489 2691 5.754782 ACCCATGTAGATAAAGCATGTGAA 58.245 37.500 0.00 0.00 38.53 3.18
2490 2692 5.372343 ACCCATGTAGATAAAGCATGTGA 57.628 39.130 0.00 0.00 38.53 3.58
2491 2693 5.734220 GCAACCCATGTAGATAAAGCATGTG 60.734 44.000 0.00 0.00 38.53 3.21
2492 2694 4.339247 GCAACCCATGTAGATAAAGCATGT 59.661 41.667 0.00 0.00 38.53 3.21
2493 2695 4.338964 TGCAACCCATGTAGATAAAGCATG 59.661 41.667 0.00 0.00 39.54 4.06
2494 2696 4.339247 GTGCAACCCATGTAGATAAAGCAT 59.661 41.667 0.00 0.00 0.00 3.79
2495 2697 3.694072 GTGCAACCCATGTAGATAAAGCA 59.306 43.478 0.00 0.00 0.00 3.91
2496 2698 3.947834 AGTGCAACCCATGTAGATAAAGC 59.052 43.478 0.00 0.00 37.80 3.51
2497 2699 4.271049 CGAGTGCAACCCATGTAGATAAAG 59.729 45.833 0.00 0.00 37.80 1.85
2498 2700 4.188462 CGAGTGCAACCCATGTAGATAAA 58.812 43.478 0.00 0.00 37.80 1.40
2499 2701 3.792401 CGAGTGCAACCCATGTAGATAA 58.208 45.455 0.00 0.00 37.80 1.75
2500 2702 2.483013 GCGAGTGCAACCCATGTAGATA 60.483 50.000 0.00 0.00 42.15 1.98
2501 2703 1.743772 GCGAGTGCAACCCATGTAGAT 60.744 52.381 0.00 0.00 42.15 1.98
2502 2704 0.391130 GCGAGTGCAACCCATGTAGA 60.391 55.000 0.00 0.00 42.15 2.59
2503 2705 0.391661 AGCGAGTGCAACCCATGTAG 60.392 55.000 0.00 0.00 46.23 2.74
2517 2722 1.012841 GGCAAGAATCCTGAAGCGAG 58.987 55.000 0.00 0.00 0.00 5.03
2521 2726 1.373570 GGACGGCAAGAATCCTGAAG 58.626 55.000 0.00 0.00 0.00 3.02
2610 2815 2.185867 GGTACCGCGATGAGGCAA 59.814 61.111 8.23 0.00 0.00 4.52
2651 2861 1.207811 TGCCAGATTCAGATCAAGCGA 59.792 47.619 0.00 0.00 36.12 4.93
3076 3294 3.394674 TGGACGCACACTTAATCTGAA 57.605 42.857 0.00 0.00 0.00 3.02
3260 3482 3.432592 CAGCTCTCCATTCTATTGATGCG 59.567 47.826 0.00 0.00 0.00 4.73
3424 3685 6.762702 AAATATATTAATAAACCGGCCGGG 57.237 37.500 44.99 28.13 43.62 5.73
3853 4119 3.303791 GCGTCAACTTGTAACCCTGAAAG 60.304 47.826 0.00 0.00 0.00 2.62
3896 4163 0.854218 TTGCTTACTCCCCCACCAAA 59.146 50.000 0.00 0.00 0.00 3.28
3898 4165 1.497309 CCTTGCTTACTCCCCCACCA 61.497 60.000 0.00 0.00 0.00 4.17
3902 4169 0.251608 TTTGCCTTGCTTACTCCCCC 60.252 55.000 0.00 0.00 0.00 5.40
3903 4170 0.888619 GTTTGCCTTGCTTACTCCCC 59.111 55.000 0.00 0.00 0.00 4.81
3904 4171 0.521735 CGTTTGCCTTGCTTACTCCC 59.478 55.000 0.00 0.00 0.00 4.30
3905 4172 1.519408 TCGTTTGCCTTGCTTACTCC 58.481 50.000 0.00 0.00 0.00 3.85
3906 4173 3.619233 TTTCGTTTGCCTTGCTTACTC 57.381 42.857 0.00 0.00 0.00 2.59
3907 4174 3.490249 GGTTTTCGTTTGCCTTGCTTACT 60.490 43.478 0.00 0.00 0.00 2.24
3908 4175 2.792674 GGTTTTCGTTTGCCTTGCTTAC 59.207 45.455 0.00 0.00 0.00 2.34
3909 4176 2.427453 TGGTTTTCGTTTGCCTTGCTTA 59.573 40.909 0.00 0.00 0.00 3.09
3910 4177 1.205893 TGGTTTTCGTTTGCCTTGCTT 59.794 42.857 0.00 0.00 0.00 3.91
3911 4178 0.820871 TGGTTTTCGTTTGCCTTGCT 59.179 45.000 0.00 0.00 0.00 3.91
3912 4179 1.646189 TTGGTTTTCGTTTGCCTTGC 58.354 45.000 0.00 0.00 0.00 4.01
3913 4180 3.061965 CAGTTTGGTTTTCGTTTGCCTTG 59.938 43.478 0.00 0.00 0.00 3.61
3914 4181 3.258228 CAGTTTGGTTTTCGTTTGCCTT 58.742 40.909 0.00 0.00 0.00 4.35
3915 4182 2.418060 CCAGTTTGGTTTTCGTTTGCCT 60.418 45.455 0.00 0.00 31.35 4.75
3916 4183 1.930503 CCAGTTTGGTTTTCGTTTGCC 59.069 47.619 0.00 0.00 31.35 4.52
3917 4184 1.930503 CCCAGTTTGGTTTTCGTTTGC 59.069 47.619 0.00 0.00 35.17 3.68
3918 4185 3.239587 ACCCAGTTTGGTTTTCGTTTG 57.760 42.857 0.00 0.00 33.91 2.93
3919 4186 3.591023 CAACCCAGTTTGGTTTTCGTTT 58.409 40.909 0.00 0.00 46.45 3.60
3920 4187 2.675603 GCAACCCAGTTTGGTTTTCGTT 60.676 45.455 0.00 0.00 46.45 3.85
3921 4188 1.134936 GCAACCCAGTTTGGTTTTCGT 60.135 47.619 0.00 0.00 46.45 3.85
3922 4189 1.566404 GCAACCCAGTTTGGTTTTCG 58.434 50.000 0.00 0.00 46.45 3.46
3923 4190 1.484653 AGGCAACCCAGTTTGGTTTTC 59.515 47.619 0.00 0.00 46.45 2.29
3924 4191 1.209261 CAGGCAACCCAGTTTGGTTTT 59.791 47.619 0.00 0.00 46.45 2.43
3925 4192 0.829990 CAGGCAACCCAGTTTGGTTT 59.170 50.000 0.00 0.00 46.45 3.27
3927 4194 1.457455 CCAGGCAACCCAGTTTGGT 60.457 57.895 0.00 0.00 41.55 3.67
3928 4195 2.209315 CCCAGGCAACCCAGTTTGG 61.209 63.158 0.00 0.00 37.25 3.28
3929 4196 1.152567 TCCCAGGCAACCCAGTTTG 60.153 57.895 0.00 0.00 37.17 2.93
3930 4197 1.152546 GTCCCAGGCAACCCAGTTT 60.153 57.895 0.00 0.00 37.17 2.66
3931 4198 2.391130 TGTCCCAGGCAACCCAGTT 61.391 57.895 0.00 0.00 37.17 3.16
3932 4199 2.776526 TGTCCCAGGCAACCCAGT 60.777 61.111 0.00 0.00 37.17 4.00
3933 4200 1.488705 TAGTGTCCCAGGCAACCCAG 61.489 60.000 0.00 0.00 37.17 4.45
3934 4201 0.844661 ATAGTGTCCCAGGCAACCCA 60.845 55.000 0.00 0.00 37.17 4.51
3935 4202 0.394352 CATAGTGTCCCAGGCAACCC 60.394 60.000 0.00 0.00 37.17 4.11
3936 4203 0.618458 TCATAGTGTCCCAGGCAACC 59.382 55.000 0.00 0.00 37.17 3.77
3937 4204 2.717639 ATCATAGTGTCCCAGGCAAC 57.282 50.000 0.00 0.00 0.00 4.17
3938 4205 3.111484 TGTATCATAGTGTCCCAGGCAA 58.889 45.455 0.00 0.00 0.00 4.52
3939 4206 2.758130 TGTATCATAGTGTCCCAGGCA 58.242 47.619 0.00 0.00 0.00 4.75
3940 4207 3.467803 GTTGTATCATAGTGTCCCAGGC 58.532 50.000 0.00 0.00 0.00 4.85
3941 4208 3.454447 TGGTTGTATCATAGTGTCCCAGG 59.546 47.826 0.00 0.00 0.00 4.45
3942 4209 4.753516 TGGTTGTATCATAGTGTCCCAG 57.246 45.455 0.00 0.00 0.00 4.45
3943 4210 5.506730 TTTGGTTGTATCATAGTGTCCCA 57.493 39.130 0.00 0.00 0.00 4.37
3944 4211 5.708230 TGTTTTGGTTGTATCATAGTGTCCC 59.292 40.000 0.00 0.00 0.00 4.46
3945 4212 6.430000 ACTGTTTTGGTTGTATCATAGTGTCC 59.570 38.462 0.00 0.00 0.00 4.02
3946 4213 7.435068 ACTGTTTTGGTTGTATCATAGTGTC 57.565 36.000 0.00 0.00 0.00 3.67
3947 4214 7.255451 CCAACTGTTTTGGTTGTATCATAGTGT 60.255 37.037 0.00 0.00 41.47 3.55
3948 4215 7.083858 CCAACTGTTTTGGTTGTATCATAGTG 58.916 38.462 0.00 0.00 41.47 2.74
3949 4216 6.208599 CCCAACTGTTTTGGTTGTATCATAGT 59.791 38.462 2.48 0.00 41.47 2.12
3950 4217 6.208599 ACCCAACTGTTTTGGTTGTATCATAG 59.791 38.462 5.83 0.00 41.47 2.23
3951 4218 6.015856 CACCCAACTGTTTTGGTTGTATCATA 60.016 38.462 8.40 0.00 41.47 2.15
3952 4219 4.898861 ACCCAACTGTTTTGGTTGTATCAT 59.101 37.500 5.83 0.00 41.47 2.45
3953 4220 4.098654 CACCCAACTGTTTTGGTTGTATCA 59.901 41.667 8.40 0.00 41.47 2.15
3954 4221 4.500716 CCACCCAACTGTTTTGGTTGTATC 60.501 45.833 8.40 0.00 41.47 2.24
3955 4222 3.386402 CCACCCAACTGTTTTGGTTGTAT 59.614 43.478 8.40 0.00 41.47 2.29
3956 4223 2.761208 CCACCCAACTGTTTTGGTTGTA 59.239 45.455 8.40 0.00 41.47 2.41
3957 4224 1.552792 CCACCCAACTGTTTTGGTTGT 59.447 47.619 8.40 0.00 41.47 3.32
3958 4225 1.827969 TCCACCCAACTGTTTTGGTTG 59.172 47.619 8.40 6.33 42.35 3.77
3959 4226 1.828595 GTCCACCCAACTGTTTTGGTT 59.171 47.619 8.40 0.00 37.88 3.67
3960 4227 1.006639 AGTCCACCCAACTGTTTTGGT 59.993 47.619 5.83 5.83 37.88 3.67
3961 4228 1.775385 AGTCCACCCAACTGTTTTGG 58.225 50.000 6.34 6.34 39.25 3.28
3962 4229 2.159114 CCAAGTCCACCCAACTGTTTTG 60.159 50.000 0.00 0.00 0.00 2.44
3963 4230 2.107366 CCAAGTCCACCCAACTGTTTT 58.893 47.619 0.00 0.00 0.00 2.43
3964 4231 1.286553 TCCAAGTCCACCCAACTGTTT 59.713 47.619 0.00 0.00 0.00 2.83
3965 4232 0.923358 TCCAAGTCCACCCAACTGTT 59.077 50.000 0.00 0.00 0.00 3.16
3966 4233 1.149101 ATCCAAGTCCACCCAACTGT 58.851 50.000 0.00 0.00 0.00 3.55
3967 4234 2.162681 GAATCCAAGTCCACCCAACTG 58.837 52.381 0.00 0.00 0.00 3.16
3968 4235 1.075536 GGAATCCAAGTCCACCCAACT 59.924 52.381 0.00 0.00 35.05 3.16
3969 4236 1.545841 GGAATCCAAGTCCACCCAAC 58.454 55.000 0.00 0.00 35.05 3.77
3970 4237 0.037590 CGGAATCCAAGTCCACCCAA 59.962 55.000 0.00 0.00 34.56 4.12
3971 4238 1.131303 ACGGAATCCAAGTCCACCCA 61.131 55.000 0.00 0.00 34.56 4.51
3972 4239 0.676782 CACGGAATCCAAGTCCACCC 60.677 60.000 0.00 0.00 34.56 4.61
3973 4240 0.323629 TCACGGAATCCAAGTCCACC 59.676 55.000 0.00 0.00 34.56 4.61
3974 4241 2.403252 ATCACGGAATCCAAGTCCAC 57.597 50.000 0.00 0.00 34.56 4.02
3975 4242 3.081061 CAAATCACGGAATCCAAGTCCA 58.919 45.455 0.00 0.00 34.56 4.02
3976 4243 2.423538 CCAAATCACGGAATCCAAGTCC 59.576 50.000 0.00 0.00 0.00 3.85
3977 4244 3.343617 TCCAAATCACGGAATCCAAGTC 58.656 45.455 0.00 0.00 0.00 3.01
3978 4245 3.009033 TCTCCAAATCACGGAATCCAAGT 59.991 43.478 0.00 0.00 30.33 3.16
3979 4246 3.609853 TCTCCAAATCACGGAATCCAAG 58.390 45.455 0.00 0.00 30.33 3.61
3980 4247 3.712016 TCTCCAAATCACGGAATCCAA 57.288 42.857 0.00 0.00 30.33 3.53
3981 4248 3.054434 ACATCTCCAAATCACGGAATCCA 60.054 43.478 0.00 0.00 30.33 3.41
3982 4249 3.545703 ACATCTCCAAATCACGGAATCC 58.454 45.455 0.00 0.00 30.33 3.01
3983 4250 5.162000 GAACATCTCCAAATCACGGAATC 57.838 43.478 0.00 0.00 30.33 2.52


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

AutoCloner maintained by Alex Coulton.