Multiple sequence alignment - TraesCS7B01G252200

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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 TraesCS7B01G252200 chr7B 100.000 3874 0 0 1 3874 465119594 465115721 0.000000e+00 7155.0
1 TraesCS7B01G252200 chr7B 92.969 128 9 0 3616 3743 465115877 465115750 1.840000e-43 187.0
2 TraesCS7B01G252200 chr7B 92.969 128 9 0 3718 3845 465115979 465115852 1.840000e-43 187.0
3 TraesCS7B01G252200 chr7B 94.872 117 4 1 228 344 465119284 465119170 8.550000e-42 182.0
4 TraesCS7B01G252200 chr7B 94.872 117 4 1 311 425 465119367 465119251 8.550000e-42 182.0
5 TraesCS7B01G252200 chr7D 93.522 1451 61 16 895 2328 447762587 447761153 0.000000e+00 2128.0
6 TraesCS7B01G252200 chr7D 94.138 870 35 1 3005 3874 447760431 447759578 0.000000e+00 1310.0
7 TraesCS7B01G252200 chr7D 95.223 649 23 4 2360 3002 447761153 447760507 0.000000e+00 1020.0
8 TraesCS7B01G252200 chr7D 92.654 422 14 6 411 818 447763440 447763022 3.330000e-165 592.0
9 TraesCS7B01G252200 chr7D 95.327 214 9 1 4 216 447763655 447763442 4.790000e-89 339.0
10 TraesCS7B01G252200 chr7D 83.846 260 35 7 3543 3797 447759861 447759604 1.390000e-59 241.0
11 TraesCS7B01G252200 chr7D 83.784 259 33 8 3590 3845 447759910 447759658 1.800000e-58 237.0
12 TraesCS7B01G252200 chr7D 91.241 137 10 2 3612 3746 447759740 447759604 6.610000e-43 185.0
13 TraesCS7B01G252200 chr7D 89.844 128 13 0 3718 3845 447759836 447759709 8.610000e-37 165.0
14 TraesCS7B01G252200 chr7D 85.217 115 16 1 492 606 531603011 531603124 2.450000e-22 117.0
15 TraesCS7B01G252200 chr7A 83.898 1329 126 45 2377 3689 547955514 547956770 0.000000e+00 1188.0
16 TraesCS7B01G252200 chr7A 90.829 567 39 9 1807 2372 547953581 547954135 0.000000e+00 747.0
17 TraesCS7B01G252200 chr7A 84.728 681 53 21 1159 1815 547950481 547951134 5.460000e-178 634.0
18 TraesCS7B01G252200 chr7A 87.805 164 18 2 443 605 593374981 593375143 1.420000e-44 191.0
19 TraesCS7B01G252200 chr6B 88.211 246 26 3 362 605 678355602 678355846 1.360000e-74 291.0
20 TraesCS7B01G252200 chr6B 92.982 57 3 1 281 336 678355602 678355658 8.920000e-12 82.4
21 TraesCS7B01G252200 chr5B 87.552 241 28 2 365 604 662735118 662734879 1.060000e-70 278.0
22 TraesCS7B01G252200 chr5B 96.226 53 2 0 284 336 662735118 662735066 1.920000e-13 87.9
23 TraesCS7B01G252200 chr1B 89.571 163 15 2 443 604 25431174 25431335 5.070000e-49 206.0
24 TraesCS7B01G252200 chr3D 80.087 231 30 8 390 608 383552409 383552635 1.440000e-34 158.0
25 TraesCS7B01G252200 chr1A 91.589 107 9 0 498 604 94116149 94116043 8.670000e-32 148.0
26 TraesCS7B01G252200 chr2D 86.087 115 15 1 492 606 619160864 619160751 5.260000e-24 122.0


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 TraesCS7B01G252200 chr7B 465115721 465119594 3873 True 1578.600000 7155 95.136400 1 3874 5 chr7B.!!$R1 3873
1 TraesCS7B01G252200 chr7D 447759578 447763655 4077 True 690.777778 2128 91.064333 4 3874 9 chr7D.!!$R1 3870
2 TraesCS7B01G252200 chr7A 547950481 547956770 6289 False 856.333333 1188 86.485000 1159 3689 3 chr7A.!!$F2 2530

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
911 1285 0.037697 CGTCCAATCCGTCCTGTTGA 60.038 55.0 0.00 0.00 0.00 3.18 F
1492 1890 0.255890 GGCCACCTCCATGTACATGT 59.744 55.0 29.25 12.21 37.11 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1966 4834 0.110056 GTGCACAATCAAGCCTGACG 60.110 55.0 13.17 0.0 33.3 4.35 R
3396 7734 0.548031 TGATGGCCAAGGATCAGGTC 59.452 55.0 10.96 0.0 0.0 3.85 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
182 184 2.810274 GTGGCTGTTGCATCGATCATAT 59.190 45.455 0.00 0.00 41.91 1.78
183 185 2.809696 TGGCTGTTGCATCGATCATATG 59.190 45.455 0.00 0.00 41.91 1.78
186 188 2.809696 CTGTTGCATCGATCATATGGCA 59.190 45.455 2.13 0.00 0.00 4.92
203 205 1.360551 CATAGAGCACGGGTCTCGG 59.639 63.158 8.57 0.86 44.45 4.63
217 219 3.285371 TCGGGTTCGAGCCTCTTC 58.715 61.111 18.44 0.06 40.88 2.87
218 220 2.202623 CGGGTTCGAGCCTCTTCG 60.203 66.667 18.44 9.17 41.79 3.79
219 221 2.971452 GGGTTCGAGCCTCTTCGT 59.029 61.111 18.44 0.00 41.22 3.85
220 222 1.446272 GGGTTCGAGCCTCTTCGTG 60.446 63.158 18.44 0.00 41.22 4.35
221 223 2.095252 GGTTCGAGCCTCTTCGTGC 61.095 63.158 11.59 0.00 41.22 5.34
222 224 1.372997 GTTCGAGCCTCTTCGTGCA 60.373 57.895 0.00 0.00 41.22 4.57
223 225 1.372997 TTCGAGCCTCTTCGTGCAC 60.373 57.895 6.82 6.82 41.22 4.57
224 226 1.806461 TTCGAGCCTCTTCGTGCACT 61.806 55.000 16.19 0.00 41.22 4.40
225 227 2.091112 CGAGCCTCTTCGTGCACTG 61.091 63.158 16.19 8.79 35.91 3.66
226 228 2.358003 AGCCTCTTCGTGCACTGC 60.358 61.111 16.19 7.65 0.00 4.40
227 229 2.358003 GCCTCTTCGTGCACTGCT 60.358 61.111 16.19 0.00 0.00 4.24
228 230 1.963338 GCCTCTTCGTGCACTGCTT 60.963 57.895 16.19 0.00 0.00 3.91
229 231 1.510480 GCCTCTTCGTGCACTGCTTT 61.510 55.000 16.19 0.00 0.00 3.51
230 232 0.947244 CCTCTTCGTGCACTGCTTTT 59.053 50.000 16.19 0.00 0.00 2.27
231 233 1.334869 CCTCTTCGTGCACTGCTTTTT 59.665 47.619 16.19 0.00 0.00 1.94
232 234 2.378806 CTCTTCGTGCACTGCTTTTTG 58.621 47.619 16.19 0.00 0.00 2.44
233 235 1.742831 TCTTCGTGCACTGCTTTTTGT 59.257 42.857 16.19 0.00 0.00 2.83
234 236 2.163412 TCTTCGTGCACTGCTTTTTGTT 59.837 40.909 16.19 0.00 0.00 2.83
235 237 2.645730 TCGTGCACTGCTTTTTGTTT 57.354 40.000 16.19 0.00 0.00 2.83
236 238 2.953020 TCGTGCACTGCTTTTTGTTTT 58.047 38.095 16.19 0.00 0.00 2.43
237 239 3.321497 TCGTGCACTGCTTTTTGTTTTT 58.679 36.364 16.19 0.00 0.00 1.94
264 266 2.741759 AAAAATAAAGCGGGCTGGTG 57.258 45.000 0.00 0.00 0.00 4.17
265 267 0.246360 AAAATAAAGCGGGCTGGTGC 59.754 50.000 0.00 0.00 38.76 5.01
266 268 0.897863 AAATAAAGCGGGCTGGTGCA 60.898 50.000 0.00 0.00 41.91 4.57
267 269 1.595093 AATAAAGCGGGCTGGTGCAC 61.595 55.000 8.80 8.80 41.91 4.57
268 270 2.484287 ATAAAGCGGGCTGGTGCACT 62.484 55.000 17.98 0.00 41.26 4.40
269 271 1.832719 TAAAGCGGGCTGGTGCACTA 61.833 55.000 17.98 10.29 41.26 2.74
270 272 2.484287 AAAGCGGGCTGGTGCACTAT 62.484 55.000 17.98 0.00 41.26 2.12
271 273 1.622607 AAGCGGGCTGGTGCACTATA 61.623 55.000 17.98 2.80 41.26 1.31
272 274 1.071471 GCGGGCTGGTGCACTATAT 59.929 57.895 17.98 0.00 41.26 0.86
273 275 0.535102 GCGGGCTGGTGCACTATATT 60.535 55.000 17.98 0.00 41.26 1.28
274 276 1.967319 CGGGCTGGTGCACTATATTT 58.033 50.000 17.98 0.00 41.26 1.40
275 277 1.603802 CGGGCTGGTGCACTATATTTG 59.396 52.381 17.98 0.00 41.26 2.32
276 278 2.654863 GGGCTGGTGCACTATATTTGT 58.345 47.619 17.98 0.00 40.03 2.83
277 279 3.023832 GGGCTGGTGCACTATATTTGTT 58.976 45.455 17.98 0.00 40.03 2.83
278 280 3.447229 GGGCTGGTGCACTATATTTGTTT 59.553 43.478 17.98 0.00 40.03 2.83
279 281 4.081697 GGGCTGGTGCACTATATTTGTTTT 60.082 41.667 17.98 0.00 40.03 2.43
280 282 5.126384 GGGCTGGTGCACTATATTTGTTTTA 59.874 40.000 17.98 0.00 40.03 1.52
281 283 6.350612 GGGCTGGTGCACTATATTTGTTTTAA 60.351 38.462 17.98 0.00 40.03 1.52
282 284 6.530181 GGCTGGTGCACTATATTTGTTTTAAC 59.470 38.462 17.98 0.00 41.91 2.01
283 285 7.087639 GCTGGTGCACTATATTTGTTTTAACA 58.912 34.615 17.98 0.00 39.41 2.41
284 286 7.596995 GCTGGTGCACTATATTTGTTTTAACAA 59.403 33.333 17.98 4.02 41.93 2.83
304 306 2.741759 AAAATTAAAGCGGGCCAGTG 57.258 45.000 4.39 0.00 0.00 3.66
305 307 1.627864 AAATTAAAGCGGGCCAGTGT 58.372 45.000 4.39 0.00 0.00 3.55
306 308 2.500392 AATTAAAGCGGGCCAGTGTA 57.500 45.000 4.39 0.00 0.00 2.90
307 309 1.746470 ATTAAAGCGGGCCAGTGTAC 58.254 50.000 4.39 0.00 0.00 2.90
308 310 0.688487 TTAAAGCGGGCCAGTGTACT 59.312 50.000 4.39 0.00 0.00 2.73
309 311 1.559368 TAAAGCGGGCCAGTGTACTA 58.441 50.000 4.39 0.00 0.00 1.82
310 312 0.909623 AAAGCGGGCCAGTGTACTAT 59.090 50.000 4.39 0.00 0.00 2.12
311 313 0.909623 AAGCGGGCCAGTGTACTATT 59.090 50.000 4.39 0.00 0.00 1.73
312 314 0.909623 AGCGGGCCAGTGTACTATTT 59.090 50.000 4.39 0.00 0.00 1.40
313 315 1.280998 AGCGGGCCAGTGTACTATTTT 59.719 47.619 4.39 0.00 0.00 1.82
314 316 2.089201 GCGGGCCAGTGTACTATTTTT 58.911 47.619 4.39 0.00 0.00 1.94
315 317 2.159435 GCGGGCCAGTGTACTATTTTTG 60.159 50.000 4.39 0.00 0.00 2.44
316 318 3.078837 CGGGCCAGTGTACTATTTTTGT 58.921 45.455 4.39 0.00 0.00 2.83
317 319 3.504520 CGGGCCAGTGTACTATTTTTGTT 59.495 43.478 4.39 0.00 0.00 2.83
318 320 4.022676 CGGGCCAGTGTACTATTTTTGTTT 60.023 41.667 4.39 0.00 0.00 2.83
319 321 5.508320 CGGGCCAGTGTACTATTTTTGTTTT 60.508 40.000 4.39 0.00 0.00 2.43
320 322 6.294065 CGGGCCAGTGTACTATTTTTGTTTTA 60.294 38.462 4.39 0.00 0.00 1.52
321 323 7.435305 GGGCCAGTGTACTATTTTTGTTTTAA 58.565 34.615 4.39 0.00 0.00 1.52
322 324 7.383029 GGGCCAGTGTACTATTTTTGTTTTAAC 59.617 37.037 4.39 0.00 0.00 2.01
323 325 7.113825 GGCCAGTGTACTATTTTTGTTTTAACG 59.886 37.037 0.00 0.00 0.00 3.18
324 326 7.856894 GCCAGTGTACTATTTTTGTTTTAACGA 59.143 33.333 0.00 0.00 0.00 3.85
325 327 9.719279 CCAGTGTACTATTTTTGTTTTAACGAA 57.281 29.630 0.00 0.00 0.00 3.85
346 348 2.749280 AAAATAAAGCAGGCTGGTGC 57.251 45.000 21.35 4.23 44.35 5.01
347 349 1.631405 AAATAAAGCAGGCTGGTGCA 58.369 45.000 21.35 11.39 46.60 4.57
348 350 0.890683 AATAAAGCAGGCTGGTGCAC 59.109 50.000 21.35 8.80 46.60 4.57
349 351 0.038744 ATAAAGCAGGCTGGTGCACT 59.961 50.000 21.35 7.93 46.60 4.40
350 352 0.690192 TAAAGCAGGCTGGTGCACTA 59.310 50.000 21.35 10.29 46.60 2.74
351 353 0.038744 AAAGCAGGCTGGTGCACTAT 59.961 50.000 21.35 0.00 46.60 2.12
352 354 0.911769 AAGCAGGCTGGTGCACTATA 59.088 50.000 21.35 2.80 46.60 1.31
353 355 1.135094 AGCAGGCTGGTGCACTATAT 58.865 50.000 19.90 0.00 46.60 0.86
354 356 1.492176 AGCAGGCTGGTGCACTATATT 59.508 47.619 19.90 0.00 46.60 1.28
355 357 2.092212 AGCAGGCTGGTGCACTATATTT 60.092 45.455 19.90 0.00 46.60 1.40
356 358 2.033801 GCAGGCTGGTGCACTATATTTG 59.966 50.000 17.98 9.69 43.41 2.32
357 359 3.282021 CAGGCTGGTGCACTATATTTGT 58.718 45.455 17.98 0.00 41.91 2.83
358 360 3.696051 CAGGCTGGTGCACTATATTTGTT 59.304 43.478 17.98 0.00 41.91 2.83
359 361 4.158394 CAGGCTGGTGCACTATATTTGTTT 59.842 41.667 17.98 0.00 41.91 2.83
360 362 4.772100 AGGCTGGTGCACTATATTTGTTTT 59.228 37.500 17.98 0.00 41.91 2.43
361 363 5.949354 AGGCTGGTGCACTATATTTGTTTTA 59.051 36.000 17.98 0.00 41.91 1.52
362 364 6.435904 AGGCTGGTGCACTATATTTGTTTTAA 59.564 34.615 17.98 0.00 41.91 1.52
363 365 6.530181 GGCTGGTGCACTATATTTGTTTTAAC 59.470 38.462 17.98 0.00 41.91 2.01
364 366 7.087639 GCTGGTGCACTATATTTGTTTTAACA 58.912 34.615 17.98 0.00 39.41 2.41
365 367 7.596995 GCTGGTGCACTATATTTGTTTTAACAA 59.403 33.333 17.98 4.02 41.93 2.83
385 387 2.741759 AAAATTAAAGCGGGCCAGTG 57.258 45.000 4.39 0.00 0.00 3.66
386 388 1.627864 AAATTAAAGCGGGCCAGTGT 58.372 45.000 4.39 0.00 0.00 3.55
387 389 2.500392 AATTAAAGCGGGCCAGTGTA 57.500 45.000 4.39 0.00 0.00 2.90
388 390 1.746470 ATTAAAGCGGGCCAGTGTAC 58.254 50.000 4.39 0.00 0.00 2.90
389 391 0.688487 TTAAAGCGGGCCAGTGTACT 59.312 50.000 4.39 0.00 0.00 2.73
390 392 1.559368 TAAAGCGGGCCAGTGTACTA 58.441 50.000 4.39 0.00 0.00 1.82
391 393 0.909623 AAAGCGGGCCAGTGTACTAT 59.090 50.000 4.39 0.00 0.00 2.12
392 394 0.909623 AAGCGGGCCAGTGTACTATT 59.090 50.000 4.39 0.00 0.00 1.73
393 395 0.909623 AGCGGGCCAGTGTACTATTT 59.090 50.000 4.39 0.00 0.00 1.40
394 396 1.280998 AGCGGGCCAGTGTACTATTTT 59.719 47.619 4.39 0.00 0.00 1.82
395 397 2.089201 GCGGGCCAGTGTACTATTTTT 58.911 47.619 4.39 0.00 0.00 1.94
396 398 2.159435 GCGGGCCAGTGTACTATTTTTG 60.159 50.000 4.39 0.00 0.00 2.44
397 399 3.078837 CGGGCCAGTGTACTATTTTTGT 58.921 45.455 4.39 0.00 0.00 2.83
398 400 3.504520 CGGGCCAGTGTACTATTTTTGTT 59.495 43.478 4.39 0.00 0.00 2.83
399 401 4.022676 CGGGCCAGTGTACTATTTTTGTTT 60.023 41.667 4.39 0.00 0.00 2.83
400 402 5.508320 CGGGCCAGTGTACTATTTTTGTTTT 60.508 40.000 4.39 0.00 0.00 2.43
401 403 6.294065 CGGGCCAGTGTACTATTTTTGTTTTA 60.294 38.462 4.39 0.00 0.00 1.52
402 404 7.088272 GGGCCAGTGTACTATTTTTGTTTTAG 58.912 38.462 4.39 0.00 0.00 1.85
403 405 6.584942 GGCCAGTGTACTATTTTTGTTTTAGC 59.415 38.462 0.00 0.00 0.00 3.09
404 406 6.304683 GCCAGTGTACTATTTTTGTTTTAGCG 59.695 38.462 0.00 0.00 0.00 4.26
405 407 7.577979 CCAGTGTACTATTTTTGTTTTAGCGA 58.422 34.615 0.00 0.00 0.00 4.93
406 408 8.071368 CCAGTGTACTATTTTTGTTTTAGCGAA 58.929 33.333 0.00 0.00 0.00 4.70
407 409 9.440784 CAGTGTACTATTTTTGTTTTAGCGAAA 57.559 29.630 0.00 0.00 0.00 3.46
464 474 2.194868 CCCCTGCGAAATACCCCC 59.805 66.667 0.00 0.00 0.00 5.40
472 482 0.470766 CGAAATACCCCCAATCCCGA 59.529 55.000 0.00 0.00 0.00 5.14
474 484 0.554305 AAATACCCCCAATCCCGACC 59.446 55.000 0.00 0.00 0.00 4.79
482 492 1.102978 CCAATCCCGACCATCCAAAC 58.897 55.000 0.00 0.00 0.00 2.93
491 501 0.321298 ACCATCCAAACGACCCGAAG 60.321 55.000 0.00 0.00 0.00 3.79
534 544 3.873361 CCATAGTTCAGTGTGCAATCGAT 59.127 43.478 0.00 0.00 0.00 3.59
546 556 3.003689 GTGCAATCGATCGGGATTTTGAT 59.996 43.478 16.41 0.00 34.50 2.57
551 561 6.441274 CAATCGATCGGGATTTTGATTTGAT 58.559 36.000 16.41 0.00 34.50 2.57
553 563 4.275689 TCGATCGGGATTTTGATTTGATGG 59.724 41.667 16.41 0.00 0.00 3.51
571 581 3.676091 GTTCATTTCGCCGAACCTG 57.324 52.632 0.00 0.24 36.36 4.00
583 593 2.093783 GCCGAACCTGTACGAATTCAAG 59.906 50.000 6.22 0.00 0.00 3.02
669 679 8.243289 ACAAACTTTGAAATCTGACTTTTGTG 57.757 30.769 8.55 0.00 34.31 3.33
670 680 8.087750 ACAAACTTTGAAATCTGACTTTTGTGA 58.912 29.630 8.55 0.00 34.31 3.58
785 801 2.120718 AGCCCTCGTCCTCTTGGT 59.879 61.111 0.00 0.00 34.23 3.67
806 822 2.432874 TCGGATCTTCTCTCTCGAGTCT 59.567 50.000 13.13 0.00 38.45 3.24
848 878 1.658114 CACGCCGCCTAGTGCTATA 59.342 57.895 2.39 0.00 38.05 1.31
849 879 0.387367 CACGCCGCCTAGTGCTATAG 60.387 60.000 0.00 0.00 38.05 1.31
850 880 0.822532 ACGCCGCCTAGTGCTATAGT 60.823 55.000 0.84 0.00 38.05 2.12
851 881 0.314302 CGCCGCCTAGTGCTATAGTT 59.686 55.000 0.84 0.00 38.05 2.24
852 882 1.666311 CGCCGCCTAGTGCTATAGTTC 60.666 57.143 0.84 0.00 38.05 3.01
853 883 1.614413 GCCGCCTAGTGCTATAGTTCT 59.386 52.381 0.84 3.20 38.05 3.01
854 884 2.036089 GCCGCCTAGTGCTATAGTTCTT 59.964 50.000 0.84 0.00 38.05 2.52
855 885 3.857756 GCCGCCTAGTGCTATAGTTCTTC 60.858 52.174 0.84 0.00 38.05 2.87
856 886 3.305471 CCGCCTAGTGCTATAGTTCTTCC 60.305 52.174 0.84 0.00 38.05 3.46
857 887 3.305471 CGCCTAGTGCTATAGTTCTTCCC 60.305 52.174 0.84 0.00 38.05 3.97
858 888 3.898741 GCCTAGTGCTATAGTTCTTCCCT 59.101 47.826 0.84 0.00 36.87 4.20
859 889 4.021807 GCCTAGTGCTATAGTTCTTCCCTC 60.022 50.000 0.84 0.00 36.87 4.30
860 890 4.525100 CCTAGTGCTATAGTTCTTCCCTCC 59.475 50.000 0.84 0.00 0.00 4.30
861 891 3.310193 AGTGCTATAGTTCTTCCCTCCC 58.690 50.000 0.84 0.00 0.00 4.30
862 892 2.369203 GTGCTATAGTTCTTCCCTCCCC 59.631 54.545 0.84 0.00 0.00 4.81
863 893 2.250273 TGCTATAGTTCTTCCCTCCCCT 59.750 50.000 0.84 0.00 0.00 4.79
864 894 2.901192 GCTATAGTTCTTCCCTCCCCTC 59.099 54.545 0.84 0.00 0.00 4.30
865 895 2.498473 ATAGTTCTTCCCTCCCCTCC 57.502 55.000 0.00 0.00 0.00 4.30
866 896 0.342313 TAGTTCTTCCCTCCCCTCCC 59.658 60.000 0.00 0.00 0.00 4.30
867 897 2.001838 GTTCTTCCCTCCCCTCCCC 61.002 68.421 0.00 0.00 0.00 4.81
868 898 2.191846 TTCTTCCCTCCCCTCCCCT 61.192 63.158 0.00 0.00 0.00 4.79
869 899 2.040359 CTTCCCTCCCCTCCCCTC 60.040 72.222 0.00 0.00 0.00 4.30
870 900 3.707189 TTCCCTCCCCTCCCCTCC 61.707 72.222 0.00 0.00 0.00 4.30
873 903 4.179599 CCTCCCCTCCCCTCCCTC 62.180 77.778 0.00 0.00 0.00 4.30
874 904 4.179599 CTCCCCTCCCCTCCCTCC 62.180 77.778 0.00 0.00 0.00 4.30
876 906 3.795924 CCCCTCCCCTCCCTCCAT 61.796 72.222 0.00 0.00 0.00 3.41
877 907 2.122189 CCCTCCCCTCCCTCCATC 60.122 72.222 0.00 0.00 0.00 3.51
878 908 2.122189 CCTCCCCTCCCTCCATCC 60.122 72.222 0.00 0.00 0.00 3.51
879 909 2.122189 CTCCCCTCCCTCCATCCC 60.122 72.222 0.00 0.00 0.00 3.85
880 910 2.964039 TCCCCTCCCTCCATCCCA 60.964 66.667 0.00 0.00 0.00 4.37
881 911 2.774351 CCCCTCCCTCCATCCCAC 60.774 72.222 0.00 0.00 0.00 4.61
882 912 2.774351 CCCTCCCTCCATCCCACC 60.774 72.222 0.00 0.00 0.00 4.61
883 913 3.164269 CCTCCCTCCATCCCACCG 61.164 72.222 0.00 0.00 0.00 4.94
884 914 3.164269 CTCCCTCCATCCCACCGG 61.164 72.222 0.00 0.00 0.00 5.28
911 1285 0.037697 CGTCCAATCCGTCCTGTTGA 60.038 55.000 0.00 0.00 0.00 3.18
912 1286 1.405526 CGTCCAATCCGTCCTGTTGAT 60.406 52.381 0.00 0.00 0.00 2.57
935 1309 9.357652 TGATTCCGAATTTTCAATCAATCTTTC 57.642 29.630 0.00 0.00 33.34 2.62
954 1328 6.525629 TCTTTCTAACAACAGCTAGCTTCTT 58.474 36.000 16.46 6.54 0.00 2.52
959 1333 2.027653 ACAACAGCTAGCTTCTTCTCCC 60.028 50.000 16.46 0.00 0.00 4.30
966 1340 1.450360 AGCTTCTTCTCCCCCTTTGT 58.550 50.000 0.00 0.00 0.00 2.83
978 1352 2.051345 CTTTGTGCACGCGGTTCC 60.051 61.111 12.47 0.00 0.00 3.62
980 1354 2.058829 CTTTGTGCACGCGGTTCCTT 62.059 55.000 12.47 0.00 0.00 3.36
994 1368 1.468914 GTTCCTTGATCCGCTTGGTTC 59.531 52.381 0.00 0.00 32.92 3.62
1017 1391 2.764128 ATGGAGATGCCGACGGGT 60.764 61.111 17.22 0.00 40.66 5.28
1021 1395 1.218316 GAGATGCCGACGGGTTCTT 59.782 57.895 17.22 0.00 34.97 2.52
1175 1549 3.857052 TGCGAGTATAACTTGGTTCTGG 58.143 45.455 0.00 0.00 30.15 3.86
1252 1630 0.389817 TCTGGTGAGTTGCGGATTCG 60.390 55.000 0.00 0.00 39.81 3.34
1254 1632 0.669318 TGGTGAGTTGCGGATTCGTC 60.669 55.000 0.00 0.00 38.89 4.20
1312 1700 3.965539 ATGCTCAGCTGTCCACCGC 62.966 63.158 14.67 8.48 0.00 5.68
1492 1890 0.255890 GGCCACCTCCATGTACATGT 59.744 55.000 29.25 12.21 37.11 3.21
1493 1891 1.340991 GGCCACCTCCATGTACATGTT 60.341 52.381 29.25 11.72 37.11 2.71
1494 1892 1.745087 GCCACCTCCATGTACATGTTG 59.255 52.381 29.25 21.41 37.11 3.33
1545 1943 6.801539 TCTTTAGTGCTAGGACACAAATTG 57.198 37.500 17.34 5.94 43.23 2.32
1546 1944 5.705441 TCTTTAGTGCTAGGACACAAATTGG 59.295 40.000 17.34 5.33 43.23 3.16
1572 1970 7.710907 GCTGTTCATGTGGTTAATCATCTAGTA 59.289 37.037 0.00 0.00 0.00 1.82
1577 1981 8.544622 TCATGTGGTTAATCATCTAGTACCAAA 58.455 33.333 0.00 0.00 0.00 3.28
1588 1992 4.569943 TCTAGTACCAAAGAAAGCTGCAG 58.430 43.478 10.11 10.11 0.00 4.41
1596 2000 4.456911 CCAAAGAAAGCTGCAGAACTATCA 59.543 41.667 20.43 0.00 0.00 2.15
1609 2013 5.000012 AGAACTATCAAGCCGTTCTGTAG 58.000 43.478 3.38 0.00 43.96 2.74
1715 2127 7.035840 AGATGATTGGTTCTTGCATATTGTC 57.964 36.000 0.00 0.00 0.00 3.18
1717 2129 5.263599 TGATTGGTTCTTGCATATTGTCCT 58.736 37.500 0.00 0.00 0.00 3.85
1727 2139 8.800370 TCTTGCATATTGTCCTGTGTTAAATA 57.200 30.769 0.00 0.00 0.00 1.40
1755 2167 5.921429 GTCAACTAAGAGATGACAAAGCAC 58.079 41.667 10.88 0.00 44.41 4.40
1760 2172 6.159988 ACTAAGAGATGACAAAGCACTGTAC 58.840 40.000 0.00 0.00 0.00 2.90
1761 2173 4.881019 AGAGATGACAAAGCACTGTACT 57.119 40.909 0.00 0.00 0.00 2.73
1762 2174 4.564041 AGAGATGACAAAGCACTGTACTG 58.436 43.478 0.00 0.00 0.00 2.74
1763 2175 3.668447 AGATGACAAAGCACTGTACTGG 58.332 45.455 4.66 0.00 0.00 4.00
1764 2176 3.324846 AGATGACAAAGCACTGTACTGGA 59.675 43.478 4.66 0.00 0.00 3.86
1765 2177 3.769739 TGACAAAGCACTGTACTGGAT 57.230 42.857 4.66 0.00 0.00 3.41
1805 2217 6.548321 TGGTAACAGTTGATGGAATTAAGGT 58.452 36.000 0.00 0.00 46.17 3.50
1835 4703 7.383300 CCATTGTCATTTCTTTTCTTGAACTCC 59.617 37.037 0.00 0.00 0.00 3.85
1966 4834 8.538701 AGGTAATCTCATCTGAACATCCATATC 58.461 37.037 0.00 0.00 0.00 1.63
2068 4936 6.872020 GCCAACTTATCGAGCATATAAGGTTA 59.128 38.462 13.83 0.00 39.97 2.85
2071 4939 6.323266 ACTTATCGAGCATATAAGGTTAGCG 58.677 40.000 13.83 0.00 39.97 4.26
2087 4955 0.877071 AGCGTTCTTAACCGTCTCGA 59.123 50.000 0.00 0.00 0.00 4.04
2108 4976 0.107654 GTGCTATCCGCTGTTTCCCT 60.108 55.000 0.00 0.00 40.11 4.20
2157 5026 0.534877 CTGTGTACCTGGCAAGCACA 60.535 55.000 10.99 10.99 38.23 4.57
2242 5111 3.610821 GCCCATCAGTTGTTCCGTTTAAC 60.611 47.826 0.00 0.00 0.00 2.01
2358 5231 2.586648 ATTCTCCAACACCCCTTCAC 57.413 50.000 0.00 0.00 0.00 3.18
2442 6689 3.650942 AGTACCCAATCTGTTCAGGTTCA 59.349 43.478 0.00 0.00 31.89 3.18
2449 6696 5.939883 CCAATCTGTTCAGGTTCACTCATAA 59.060 40.000 0.00 0.00 0.00 1.90
2531 6780 3.293337 GGGTTGGTTAACTTTGTCACCT 58.707 45.455 5.42 0.00 36.99 4.00
2545 6794 7.532571 ACTTTGTCACCTTTTTGTACTTACAC 58.467 34.615 0.00 0.00 35.64 2.90
2550 6799 7.175293 TGTCACCTTTTTGTACTTACACTGTTT 59.825 33.333 0.00 0.00 35.64 2.83
2704 6953 6.980397 ACATTTGATCTTTGCTTTTCGAAACT 59.020 30.769 10.79 0.00 0.00 2.66
2707 6956 3.602390 TCTTTGCTTTTCGAAACTCCG 57.398 42.857 10.79 0.90 0.00 4.63
2744 6993 8.871686 TGTACTATTACTGTTGTGCATATCAG 57.128 34.615 17.17 17.17 0.00 2.90
2901 7150 1.278537 CAAAGGTTGGGATGGGCATT 58.721 50.000 0.00 0.00 0.00 3.56
2906 7155 1.756538 GGTTGGGATGGGCATTTACAG 59.243 52.381 0.00 0.00 0.00 2.74
2907 7156 2.456577 GTTGGGATGGGCATTTACAGT 58.543 47.619 0.00 0.00 0.00 3.55
2971 7220 1.272490 GCAAAACCAGCCCTTCCTTAC 59.728 52.381 0.00 0.00 0.00 2.34
2992 7246 7.041508 CCTTACCATGCATGAATCTCTAGAAAC 60.042 40.741 28.31 0.00 0.00 2.78
3042 7370 5.191522 TCAGTTATCATGAGGTGATTTCCCA 59.808 40.000 0.09 0.00 45.25 4.37
3142 7471 9.597170 TTAAAAACCTGTTTAATGGTAACCAAC 57.403 29.630 0.00 0.00 35.17 3.77
3143 7472 6.584488 AAAACCTGTTTAATGGTAACCAACC 58.416 36.000 0.00 0.00 39.34 3.77
3144 7473 6.384595 AAAACCTGTTTAATGGTAACCAACCT 59.615 34.615 0.00 0.00 39.50 3.50
3155 7484 4.850680 GGTAACCAACCTAATCATGTCCA 58.149 43.478 0.00 0.00 45.75 4.02
3156 7485 4.881850 GGTAACCAACCTAATCATGTCCAG 59.118 45.833 0.00 0.00 45.75 3.86
3251 7584 5.185454 TGAACACTATGCTAAATGTGAGGG 58.815 41.667 0.00 0.00 34.81 4.30
3278 7611 6.150307 ACACCATAAAATATGAACACTGCGAA 59.850 34.615 0.00 0.00 0.00 4.70
3310 7645 1.536766 TCGATTGCTTCTTGCTGGTTG 59.463 47.619 0.00 0.00 43.37 3.77
3320 7655 1.198637 CTTGCTGGTTGCTGCTAACTC 59.801 52.381 0.00 0.00 43.37 3.01
3396 7734 8.777865 TTGTTTTGAGATATCTGTTACTCTGG 57.222 34.615 10.74 0.00 0.00 3.86
3424 7762 3.545124 TTGGCCATCAACGTCGGCT 62.545 57.895 6.09 0.00 45.50 5.52
3539 7904 2.353208 GGTATATCCTCGAGCAAGCCAG 60.353 54.545 6.99 0.00 0.00 4.85
3589 7954 2.997899 GACATCTTCGAGCATGGGG 58.002 57.895 9.71 0.00 0.00 4.96
3656 8021 0.997226 CGAATCTATGTCGTCGGGCG 60.997 60.000 0.00 0.00 43.01 6.13
3699 8064 2.283298 CACCTGCTGCGAATCTATGTT 58.717 47.619 0.00 0.00 0.00 2.71
3702 8067 2.286294 CCTGCTGCGAATCTATGTTGTC 59.714 50.000 0.00 0.00 0.00 3.18
3710 8075 2.260844 ATCTATGTTGTCGGGCATGG 57.739 50.000 0.00 0.00 0.00 3.66
3720 8085 3.825623 GGGCATGGGGGAAGAGGG 61.826 72.222 0.00 0.00 0.00 4.30
3734 8099 3.161557 AGGGACTCACAGCAACCC 58.838 61.111 0.00 0.00 40.71 4.11
3758 8123 0.030235 TGAATCTATGTCGTCGGGCG 59.970 55.000 0.00 0.00 43.01 6.13
3761 8126 2.071844 ATCTATGTCGTCGGGCGTGG 62.072 60.000 0.49 0.00 42.13 4.94
3801 8166 2.756760 CCACCTGCTGCAAATCTATGTT 59.243 45.455 3.02 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.311690 TGTTTGAAATTGACGAACTTTTTCCC 59.688 34.615 13.53 0.00 34.05 3.97
1 2 7.284518 TGTTTGAAATTGACGAACTTTTTCC 57.715 32.000 13.53 0.00 34.05 3.13
2 3 9.587461 TTTTGTTTGAAATTGACGAACTTTTTC 57.413 25.926 13.53 0.00 34.05 2.29
155 157 0.749454 GATGCAACAGCCACTAGGGG 60.749 60.000 6.68 6.68 37.04 4.79
165 167 2.809696 TGCCATATGATCGATGCAACAG 59.190 45.455 0.54 0.00 0.00 3.16
182 184 1.676678 GAGACCCGTGCTCTATGCCA 61.677 60.000 0.00 0.00 42.00 4.92
183 185 1.068250 GAGACCCGTGCTCTATGCC 59.932 63.158 0.00 0.00 42.00 4.40
186 188 1.828660 CCCGAGACCCGTGCTCTAT 60.829 63.158 0.00 0.00 36.31 1.98
203 205 2.095252 GCACGAAGAGGCTCGAACC 61.095 63.158 9.22 0.00 41.44 3.62
216 218 2.645730 AAACAAAAAGCAGTGCACGA 57.354 40.000 19.20 0.00 0.00 4.35
217 219 3.720818 AAAAACAAAAAGCAGTGCACG 57.279 38.095 19.20 7.77 0.00 5.34
245 247 1.337728 GCACCAGCCCGCTTTATTTTT 60.338 47.619 0.00 0.00 33.58 1.94
246 248 0.246360 GCACCAGCCCGCTTTATTTT 59.754 50.000 0.00 0.00 33.58 1.82
247 249 0.897863 TGCACCAGCCCGCTTTATTT 60.898 50.000 0.00 0.00 41.13 1.40
248 250 1.304052 TGCACCAGCCCGCTTTATT 60.304 52.632 0.00 0.00 41.13 1.40
249 251 2.046285 GTGCACCAGCCCGCTTTAT 61.046 57.895 5.22 0.00 41.13 1.40
250 252 1.832719 TAGTGCACCAGCCCGCTTTA 61.833 55.000 14.63 0.00 41.13 1.85
251 253 2.484287 ATAGTGCACCAGCCCGCTTT 62.484 55.000 14.63 0.00 41.13 3.51
252 254 1.622607 TATAGTGCACCAGCCCGCTT 61.623 55.000 14.63 0.00 41.13 4.68
253 255 1.410850 ATATAGTGCACCAGCCCGCT 61.411 55.000 14.63 0.00 41.13 5.52
254 256 0.535102 AATATAGTGCACCAGCCCGC 60.535 55.000 14.63 0.00 41.13 6.13
255 257 1.603802 CAAATATAGTGCACCAGCCCG 59.396 52.381 14.63 0.00 41.13 6.13
256 258 2.654863 ACAAATATAGTGCACCAGCCC 58.345 47.619 14.63 0.00 41.13 5.19
257 259 4.718940 AAACAAATATAGTGCACCAGCC 57.281 40.909 14.63 0.00 41.13 4.85
258 260 7.087639 TGTTAAAACAAATATAGTGCACCAGC 58.912 34.615 14.63 0.00 37.33 4.85
284 286 2.367241 ACACTGGCCCGCTTTAATTTTT 59.633 40.909 0.00 0.00 0.00 1.94
285 287 1.967779 ACACTGGCCCGCTTTAATTTT 59.032 42.857 0.00 0.00 0.00 1.82
286 288 1.627864 ACACTGGCCCGCTTTAATTT 58.372 45.000 0.00 0.00 0.00 1.82
287 289 2.089201 GTACACTGGCCCGCTTTAATT 58.911 47.619 0.00 0.00 0.00 1.40
288 290 1.280998 AGTACACTGGCCCGCTTTAAT 59.719 47.619 0.00 0.00 0.00 1.40
289 291 0.688487 AGTACACTGGCCCGCTTTAA 59.312 50.000 0.00 0.00 0.00 1.52
290 292 1.559368 TAGTACACTGGCCCGCTTTA 58.441 50.000 0.00 0.00 0.00 1.85
291 293 0.909623 ATAGTACACTGGCCCGCTTT 59.090 50.000 0.00 0.00 0.00 3.51
292 294 0.909623 AATAGTACACTGGCCCGCTT 59.090 50.000 0.00 0.00 0.00 4.68
293 295 0.909623 AAATAGTACACTGGCCCGCT 59.090 50.000 0.00 0.00 0.00 5.52
294 296 1.746470 AAAATAGTACACTGGCCCGC 58.254 50.000 0.00 0.00 0.00 6.13
295 297 3.078837 ACAAAAATAGTACACTGGCCCG 58.921 45.455 0.00 0.00 0.00 6.13
296 298 5.462530 AAACAAAAATAGTACACTGGCCC 57.537 39.130 0.00 0.00 0.00 5.80
297 299 7.113825 CGTTAAAACAAAAATAGTACACTGGCC 59.886 37.037 0.00 0.00 0.00 5.36
298 300 7.856894 TCGTTAAAACAAAAATAGTACACTGGC 59.143 33.333 0.00 0.00 0.00 4.85
299 301 9.719279 TTCGTTAAAACAAAAATAGTACACTGG 57.281 29.630 0.00 0.00 0.00 4.00
326 328 2.368221 TGCACCAGCCTGCTTTATTTTT 59.632 40.909 0.00 0.00 41.13 1.94
327 329 1.969923 TGCACCAGCCTGCTTTATTTT 59.030 42.857 0.00 0.00 41.13 1.82
328 330 1.273327 GTGCACCAGCCTGCTTTATTT 59.727 47.619 5.22 0.00 41.13 1.40
329 331 0.890683 GTGCACCAGCCTGCTTTATT 59.109 50.000 5.22 0.00 41.13 1.40
330 332 0.038744 AGTGCACCAGCCTGCTTTAT 59.961 50.000 14.63 0.00 41.13 1.40
331 333 0.690192 TAGTGCACCAGCCTGCTTTA 59.310 50.000 14.63 0.00 41.13 1.85
332 334 0.038744 ATAGTGCACCAGCCTGCTTT 59.961 50.000 14.63 0.00 41.13 3.51
333 335 0.911769 TATAGTGCACCAGCCTGCTT 59.088 50.000 14.63 0.00 41.13 3.91
334 336 1.135094 ATATAGTGCACCAGCCTGCT 58.865 50.000 14.63 0.00 41.13 4.24
335 337 1.972872 AATATAGTGCACCAGCCTGC 58.027 50.000 14.63 0.00 41.13 4.85
336 338 3.282021 ACAAATATAGTGCACCAGCCTG 58.718 45.455 14.63 7.04 41.13 4.85
337 339 3.652057 ACAAATATAGTGCACCAGCCT 57.348 42.857 14.63 0.00 41.13 4.58
338 340 4.718940 AAACAAATATAGTGCACCAGCC 57.281 40.909 14.63 0.00 41.13 4.85
339 341 7.087639 TGTTAAAACAAATATAGTGCACCAGC 58.912 34.615 14.63 0.00 37.33 4.85
365 367 2.367241 ACACTGGCCCGCTTTAATTTTT 59.633 40.909 0.00 0.00 0.00 1.94
366 368 1.967779 ACACTGGCCCGCTTTAATTTT 59.032 42.857 0.00 0.00 0.00 1.82
367 369 1.627864 ACACTGGCCCGCTTTAATTT 58.372 45.000 0.00 0.00 0.00 1.82
368 370 2.089201 GTACACTGGCCCGCTTTAATT 58.911 47.619 0.00 0.00 0.00 1.40
369 371 1.280998 AGTACACTGGCCCGCTTTAAT 59.719 47.619 0.00 0.00 0.00 1.40
370 372 0.688487 AGTACACTGGCCCGCTTTAA 59.312 50.000 0.00 0.00 0.00 1.52
371 373 1.559368 TAGTACACTGGCCCGCTTTA 58.441 50.000 0.00 0.00 0.00 1.85
372 374 0.909623 ATAGTACACTGGCCCGCTTT 59.090 50.000 0.00 0.00 0.00 3.51
373 375 0.909623 AATAGTACACTGGCCCGCTT 59.090 50.000 0.00 0.00 0.00 4.68
374 376 0.909623 AAATAGTACACTGGCCCGCT 59.090 50.000 0.00 0.00 0.00 5.52
375 377 1.746470 AAAATAGTACACTGGCCCGC 58.254 50.000 0.00 0.00 0.00 6.13
376 378 3.078837 ACAAAAATAGTACACTGGCCCG 58.921 45.455 0.00 0.00 0.00 6.13
377 379 5.462530 AAACAAAAATAGTACACTGGCCC 57.537 39.130 0.00 0.00 0.00 5.80
378 380 6.584942 GCTAAAACAAAAATAGTACACTGGCC 59.415 38.462 0.00 0.00 0.00 5.36
379 381 6.304683 CGCTAAAACAAAAATAGTACACTGGC 59.695 38.462 0.00 0.00 0.00 4.85
380 382 7.577979 TCGCTAAAACAAAAATAGTACACTGG 58.422 34.615 0.00 0.00 0.00 4.00
381 383 8.996988 TTCGCTAAAACAAAAATAGTACACTG 57.003 30.769 0.00 0.00 0.00 3.66
407 409 1.216977 GCCGGCCCGCTTTATTTTT 59.783 52.632 18.11 0.00 0.00 1.94
408 410 2.717044 GGCCGGCCCGCTTTATTTT 61.717 57.895 36.64 0.00 0.00 1.82
409 411 3.144871 GGCCGGCCCGCTTTATTT 61.145 61.111 36.64 0.00 0.00 1.40
464 474 0.732571 CGTTTGGATGGTCGGGATTG 59.267 55.000 0.00 0.00 0.00 2.67
472 482 0.321298 CTTCGGGTCGTTTGGATGGT 60.321 55.000 0.00 0.00 0.00 3.55
474 484 2.466867 CCTTCGGGTCGTTTGGATG 58.533 57.895 0.00 0.00 0.00 3.51
491 501 4.703093 TGGAATTCCGGTCTAAATTGAACC 59.297 41.667 19.57 0.00 39.43 3.62
496 506 7.343357 TGAACTATGGAATTCCGGTCTAAATT 58.657 34.615 19.57 0.00 39.43 1.82
534 544 4.769488 TGAACCATCAAATCAAAATCCCGA 59.231 37.500 0.00 0.00 30.99 5.14
546 556 2.155279 TCGGCGAAATGAACCATCAAA 58.845 42.857 7.35 0.00 39.49 2.69
553 563 0.872388 ACAGGTTCGGCGAAATGAAC 59.128 50.000 30.91 18.55 42.87 3.18
777 788 2.360801 GAGAGAAGATCCGACCAAGAGG 59.639 54.545 0.00 0.00 42.21 3.69
842 872 2.250273 AGGGGAGGGAAGAACTATAGCA 59.750 50.000 0.00 0.00 0.00 3.49
843 873 2.901192 GAGGGGAGGGAAGAACTATAGC 59.099 54.545 0.00 0.00 0.00 2.97
848 878 1.083141 GGGAGGGGAGGGAAGAACT 59.917 63.158 0.00 0.00 0.00 3.01
849 879 2.001838 GGGGAGGGGAGGGAAGAAC 61.002 68.421 0.00 0.00 0.00 3.01
850 880 2.191846 AGGGGAGGGGAGGGAAGAA 61.192 63.158 0.00 0.00 0.00 2.52
851 881 2.543637 AGGGGAGGGGAGGGAAGA 60.544 66.667 0.00 0.00 0.00 2.87
852 882 2.040359 GAGGGGAGGGGAGGGAAG 60.040 72.222 0.00 0.00 0.00 3.46
853 883 3.707189 GGAGGGGAGGGGAGGGAA 61.707 72.222 0.00 0.00 0.00 3.97
856 886 4.179599 GAGGGAGGGGAGGGGAGG 62.180 77.778 0.00 0.00 0.00 4.30
857 887 4.179599 GGAGGGAGGGGAGGGGAG 62.180 77.778 0.00 0.00 0.00 4.30
859 889 3.795924 ATGGAGGGAGGGGAGGGG 61.796 72.222 0.00 0.00 0.00 4.79
860 890 2.122189 GATGGAGGGAGGGGAGGG 60.122 72.222 0.00 0.00 0.00 4.30
861 891 2.122189 GGATGGAGGGAGGGGAGG 60.122 72.222 0.00 0.00 0.00 4.30
862 892 2.122189 GGGATGGAGGGAGGGGAG 60.122 72.222 0.00 0.00 0.00 4.30
863 893 2.964039 TGGGATGGAGGGAGGGGA 60.964 66.667 0.00 0.00 0.00 4.81
864 894 2.774351 GTGGGATGGAGGGAGGGG 60.774 72.222 0.00 0.00 0.00 4.79
865 895 2.774351 GGTGGGATGGAGGGAGGG 60.774 72.222 0.00 0.00 0.00 4.30
866 896 3.164269 CGGTGGGATGGAGGGAGG 61.164 72.222 0.00 0.00 0.00 4.30
867 897 3.164269 CCGGTGGGATGGAGGGAG 61.164 72.222 0.00 0.00 34.06 4.30
887 917 3.195698 GACGGATTGGACGCAGGC 61.196 66.667 0.00 0.00 34.00 4.85
888 918 2.511600 GGACGGATTGGACGCAGG 60.512 66.667 0.00 0.00 34.00 4.85
889 919 1.811266 CAGGACGGATTGGACGCAG 60.811 63.158 0.00 0.00 34.00 5.18
890 920 2.107041 AACAGGACGGATTGGACGCA 62.107 55.000 0.00 0.00 34.00 5.24
891 921 1.375523 AACAGGACGGATTGGACGC 60.376 57.895 0.00 0.00 34.00 5.19
892 922 0.037697 TCAACAGGACGGATTGGACG 60.038 55.000 0.00 0.00 37.36 4.79
893 923 2.403252 ATCAACAGGACGGATTGGAC 57.597 50.000 0.00 0.00 0.00 4.02
935 1309 4.867608 GGAGAAGAAGCTAGCTGTTGTTAG 59.132 45.833 20.16 0.00 0.00 2.34
954 1328 2.429930 CGTGCACAAAGGGGGAGA 59.570 61.111 18.64 0.00 0.00 3.71
959 1333 3.536498 GAACCGCGTGCACAAAGGG 62.536 63.158 18.64 13.63 0.00 3.95
966 1340 2.031919 ATCAAGGAACCGCGTGCA 59.968 55.556 4.92 0.00 0.00 4.57
978 1352 1.982073 GCGGAACCAAGCGGATCAAG 61.982 60.000 0.00 0.00 35.80 3.02
980 1354 2.435938 GCGGAACCAAGCGGATCA 60.436 61.111 0.00 0.00 35.80 2.92
987 1361 0.250234 TCTCCATCTGCGGAACCAAG 59.750 55.000 0.00 0.00 33.65 3.61
994 1368 2.664185 CGGCATCTCCATCTGCGG 60.664 66.667 0.00 0.00 39.30 5.69
1017 1391 2.032528 CCACCTGCCTGCGAAGAA 59.967 61.111 0.00 0.00 0.00 2.52
1119 1493 5.958380 ACTCCCACTATGACAGATTGTTCTA 59.042 40.000 0.00 0.00 0.00 2.10
1137 1511 1.202568 CGCAATCAGATAGCACTCCCA 60.203 52.381 0.00 0.00 0.00 4.37
1252 1630 3.361724 GCATTCGATCAAATACGACCGAC 60.362 47.826 0.00 0.00 38.24 4.79
1254 1632 2.794910 AGCATTCGATCAAATACGACCG 59.205 45.455 0.00 0.00 38.24 4.79
1312 1700 1.887854 TGTCACAATGACCTGCCAATG 59.112 47.619 6.51 0.00 46.40 2.82
1439 1834 7.774134 TGCAGAACTGATAATGCAAATAACAT 58.226 30.769 5.97 0.00 45.09 2.71
1448 1843 5.240183 ACCACATATGCAGAACTGATAATGC 59.760 40.000 1.58 0.00 39.14 3.56
1449 1844 6.293790 CCACCACATATGCAGAACTGATAATG 60.294 42.308 1.58 7.37 0.00 1.90
1450 1845 5.766670 CCACCACATATGCAGAACTGATAAT 59.233 40.000 1.58 0.00 0.00 1.28
1451 1846 5.125356 CCACCACATATGCAGAACTGATAA 58.875 41.667 1.58 0.00 0.00 1.75
1452 1847 4.707105 CCACCACATATGCAGAACTGATA 58.293 43.478 1.58 2.17 0.00 2.15
1492 1890 7.921786 CAGACCTGGAACTTACAAATATCAA 57.078 36.000 0.00 0.00 0.00 2.57
1545 1943 4.641989 AGATGATTAACCACATGAACAGCC 59.358 41.667 0.00 0.00 0.00 4.85
1546 1944 5.824904 AGATGATTAACCACATGAACAGC 57.175 39.130 0.00 0.00 0.00 4.40
1572 1970 2.659428 AGTTCTGCAGCTTTCTTTGGT 58.341 42.857 9.47 0.00 0.00 3.67
1577 1981 3.688673 GCTTGATAGTTCTGCAGCTTTCT 59.311 43.478 9.47 6.90 0.00 2.52
1588 1992 4.995124 TCTACAGAACGGCTTGATAGTTC 58.005 43.478 0.00 0.00 43.13 3.01
1596 2000 2.610727 GCAAGACTCTACAGAACGGCTT 60.611 50.000 0.00 0.00 0.00 4.35
1715 2127 9.825972 CTTAGTTGACACATTATTTAACACAGG 57.174 33.333 0.00 0.00 0.00 4.00
1755 2167 5.248640 ACAAAACATCCAGATCCAGTACAG 58.751 41.667 0.00 0.00 0.00 2.74
1760 2172 4.637534 CCAGTACAAAACATCCAGATCCAG 59.362 45.833 0.00 0.00 0.00 3.86
1761 2173 4.042809 ACCAGTACAAAACATCCAGATCCA 59.957 41.667 0.00 0.00 0.00 3.41
1762 2174 4.589908 ACCAGTACAAAACATCCAGATCC 58.410 43.478 0.00 0.00 0.00 3.36
1763 2175 6.653320 TGTTACCAGTACAAAACATCCAGATC 59.347 38.462 0.00 0.00 0.00 2.75
1764 2176 6.539173 TGTTACCAGTACAAAACATCCAGAT 58.461 36.000 0.00 0.00 0.00 2.90
1765 2177 5.931294 TGTTACCAGTACAAAACATCCAGA 58.069 37.500 0.00 0.00 0.00 3.86
1835 4703 4.142600 GGGTTAGTAAAGAATGCAGCACAG 60.143 45.833 0.00 0.00 0.00 3.66
1966 4834 0.110056 GTGCACAATCAAGCCTGACG 60.110 55.000 13.17 0.00 33.30 4.35
2068 4936 0.877071 TCGAGACGGTTAAGAACGCT 59.123 50.000 0.00 0.00 0.00 5.07
2157 5026 9.632638 ATCCAAACTTACATGCAGTTATTATCT 57.367 29.630 10.51 0.00 33.12 1.98
2242 5111 4.081752 TGCCAATACTGCTTAACCAAATGG 60.082 41.667 0.00 0.00 42.17 3.16
2329 5202 6.792473 AGGGGTGTTGGAGAATATATGTATGA 59.208 38.462 0.00 0.00 0.00 2.15
2331 5204 7.294720 TGAAGGGGTGTTGGAGAATATATGTAT 59.705 37.037 0.00 0.00 0.00 2.29
2333 5206 5.431731 TGAAGGGGTGTTGGAGAATATATGT 59.568 40.000 0.00 0.00 0.00 2.29
2336 5209 5.036916 AGTGAAGGGGTGTTGGAGAATATA 58.963 41.667 0.00 0.00 0.00 0.86
2339 5212 2.065799 AGTGAAGGGGTGTTGGAGAAT 58.934 47.619 0.00 0.00 0.00 2.40
2348 5221 1.880027 GCTTACAACAGTGAAGGGGTG 59.120 52.381 0.00 0.00 0.00 4.61
2350 5223 2.270352 TGCTTACAACAGTGAAGGGG 57.730 50.000 0.00 0.00 0.00 4.79
2358 5231 6.740002 CGAAGAAAGATCAATGCTTACAACAG 59.260 38.462 0.00 0.00 0.00 3.16
2442 6689 6.705302 CATGTGGTATATCAGCCTTATGAGT 58.295 40.000 0.00 0.00 31.44 3.41
2449 6696 2.057140 TGGCATGTGGTATATCAGCCT 58.943 47.619 14.06 0.00 41.12 4.58
2509 6756 2.363038 GGTGACAAAGTTAACCAACCCC 59.637 50.000 0.88 0.00 35.05 4.95
2545 6794 7.064490 ACCACTTCAAAACAAGCATAAAAACAG 59.936 33.333 0.00 0.00 0.00 3.16
2550 6799 7.199766 CACTACCACTTCAAAACAAGCATAAA 58.800 34.615 0.00 0.00 0.00 1.40
2555 6804 3.795488 GCCACTACCACTTCAAAACAAGC 60.795 47.826 0.00 0.00 0.00 4.01
2704 6953 9.132923 AGTAATAGTACATGAGAATTTCTCGGA 57.867 33.333 18.95 5.58 38.26 4.55
2744 6993 3.383761 CAAAATGGCAAACTGTCCTCAC 58.616 45.455 0.00 0.00 0.00 3.51
2901 7150 6.208007 TCTCTGTAGATGAACCGAAACTGTAA 59.792 38.462 0.00 0.00 0.00 2.41
2906 7155 7.921214 TCAATATCTCTGTAGATGAACCGAAAC 59.079 37.037 0.00 0.00 42.60 2.78
2907 7156 7.921214 GTCAATATCTCTGTAGATGAACCGAAA 59.079 37.037 0.00 0.00 42.60 3.46
2957 7206 0.753111 GCATGGTAAGGAAGGGCTGG 60.753 60.000 0.00 0.00 0.00 4.85
2971 7220 7.660617 ACATAGTTTCTAGAGATTCATGCATGG 59.339 37.037 25.97 7.85 0.00 3.66
3078 7406 4.037927 TCAAGTAGCAACCCCTAAGCTAT 58.962 43.478 0.00 0.00 42.21 2.97
3142 7471 7.478322 CAATTTCTTCACTGGACATGATTAGG 58.522 38.462 0.00 0.00 0.00 2.69
3143 7472 6.971184 GCAATTTCTTCACTGGACATGATTAG 59.029 38.462 0.00 0.00 0.00 1.73
3144 7473 6.660521 AGCAATTTCTTCACTGGACATGATTA 59.339 34.615 0.00 0.00 0.00 1.75
3155 7484 3.505293 GCCTGAGAAGCAATTTCTTCACT 59.495 43.478 18.18 0.50 46.12 3.41
3156 7485 3.254166 TGCCTGAGAAGCAATTTCTTCAC 59.746 43.478 18.18 13.06 46.12 3.18
3251 7584 6.468956 CGCAGTGTTCATATTTTATGGTGTTC 59.531 38.462 0.00 0.00 0.00 3.18
3278 7611 7.171678 GCAAGAAGCAATCGATAGTACCTTAAT 59.828 37.037 0.00 0.00 44.79 1.40
3396 7734 0.548031 TGATGGCCAAGGATCAGGTC 59.452 55.000 10.96 0.00 0.00 3.85
3424 7762 4.367023 GACGCACCACCACCGCTA 62.367 66.667 0.00 0.00 0.00 4.26
3539 7904 4.715520 TGCTCGAAGATATTGATTTCGC 57.284 40.909 1.35 0.00 42.36 4.70
3580 7945 5.106396 CGAAGATATTGATTTCCCCATGCTC 60.106 44.000 0.00 0.00 0.00 4.26
3589 7954 5.049129 CCCCAAGCTCGAAGATATTGATTTC 60.049 44.000 0.00 0.00 34.92 2.17
3637 8002 2.797515 GCCCGACGACATAGATTCG 58.202 57.895 0.00 0.00 42.36 3.34
3656 8021 1.597461 CGAGTTCCTCTTCCCCCAC 59.403 63.158 0.00 0.00 0.00 4.61
3690 8055 2.575532 CCATGCCCGACAACATAGATT 58.424 47.619 0.00 0.00 0.00 2.40
3699 8064 3.727258 CTTCCCCCATGCCCGACA 61.727 66.667 0.00 0.00 0.00 4.35
3702 8067 4.195334 CCTCTTCCCCCATGCCCG 62.195 72.222 0.00 0.00 0.00 6.13
3710 8075 1.904990 GCTGTGAGTCCCTCTTCCCC 61.905 65.000 0.00 0.00 0.00 4.81
3730 8095 2.738643 CGACATAGATTCACAGCGGGTT 60.739 50.000 0.00 0.00 0.00 4.11
3734 8099 1.775770 CGACGACATAGATTCACAGCG 59.224 52.381 0.00 0.00 0.00 5.18
3739 8104 3.959478 GCCCGACGACATAGATTCA 57.041 52.632 0.00 0.00 0.00 2.57
3758 8123 1.597461 CGAGTTCCTCTTCCCCCAC 59.403 63.158 0.00 0.00 0.00 4.61
3761 8126 1.219393 CTGCGAGTTCCTCTTCCCC 59.781 63.158 0.00 0.00 0.00 4.81
3770 8135 3.426568 GCAGGTGGCTGCGAGTTC 61.427 66.667 0.00 0.00 40.72 3.01
3791 8156 2.951642 CCATGCCCGACAACATAGATTT 59.048 45.455 0.00 0.00 0.00 2.17
3801 8166 3.727258 CTTCCCCCATGCCCGACA 61.727 66.667 0.00 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.