Multiple sequence alignment - TraesCS2A01G015500

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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 TraesCS2A01G015500 chr2A 100.000 2549 0 0 1 2549 6303297 6300749 0.000000e+00 4708
1 TraesCS2A01G015500 chr2A 96.165 1982 57 3 587 2549 764220190 764222171 0.000000e+00 3221
2 TraesCS2A01G015500 chr2A 97.695 1128 25 1 585 1711 775967964 775966837 0.000000e+00 1938
3 TraesCS2A01G015500 chr2A 95.326 1134 38 6 579 1710 233255253 233256373 0.000000e+00 1786
4 TraesCS2A01G015500 chr2A 95.075 1137 43 5 577 1711 611725146 611724021 0.000000e+00 1777
5 TraesCS2A01G015500 chr3A 96.376 1987 51 5 583 2549 719846455 719848440 0.000000e+00 3251
6 TraesCS2A01G015500 chr3A 96.908 841 23 2 1712 2549 683236507 683235667 0.000000e+00 1406
7 TraesCS2A01G015500 chr3A 83.092 414 62 6 2 410 247243999 247244409 1.110000e-98 370
8 TraesCS2A01G015500 chr7A 95.619 1986 64 6 586 2549 18189929 18191913 0.000000e+00 3164
9 TraesCS2A01G015500 chr7A 97.852 838 18 0 1712 2549 49209387 49210224 0.000000e+00 1448
10 TraesCS2A01G015500 chr7A 97.020 839 24 1 1712 2549 14471904 14471066 0.000000e+00 1410
11 TraesCS2A01G015500 chr7A 96.908 841 23 2 1712 2549 689995208 689994368 0.000000e+00 1406
12 TraesCS2A01G015500 chr7A 84.058 414 59 5 2 410 669664503 669664914 2.380000e-105 392
13 TraesCS2A01G015500 chr6A 96.014 1129 30 5 587 1711 203520912 203519795 0.000000e+00 1821
14 TraesCS2A01G015500 chr6A 95.752 1130 32 6 585 1711 57901157 57902273 0.000000e+00 1807
15 TraesCS2A01G015500 chr6A 96.602 883 26 2 1668 2549 14689817 14688938 0.000000e+00 1461
16 TraesCS2A01G015500 chr5A 95.026 1146 41 7 568 1711 357171129 357169998 0.000000e+00 1786
17 TraesCS2A01G015500 chr5A 97.500 840 18 2 1712 2549 563445102 563445940 0.000000e+00 1432
18 TraesCS2A01G015500 chr5B 94.498 1145 33 5 584 1711 121670948 121669817 0.000000e+00 1738
19 TraesCS2A01G015500 chrUn 94.396 1142 34 6 587 1711 43129528 43128400 0.000000e+00 1727
20 TraesCS2A01G015500 chrUn 94.391 1141 34 6 588 1711 231572793 231573920 0.000000e+00 1725
21 TraesCS2A01G015500 chr5D 89.841 1132 75 21 586 1711 514514291 514513194 0.000000e+00 1417
22 TraesCS2A01G015500 chr1B 91.362 602 34 6 2 586 41158088 41158688 0.000000e+00 808
23 TraesCS2A01G015500 chr1B 90.365 602 40 6 2 586 41196194 41196794 0.000000e+00 774
24 TraesCS2A01G015500 chr4A 91.030 602 36 6 2 586 710923535 710922935 0.000000e+00 797
25 TraesCS2A01G015500 chr7D 91.193 545 30 3 2 528 14670673 14670129 0.000000e+00 725
26 TraesCS2A01G015500 chr7D 88.342 609 26 7 2 584 48497740 48498329 0.000000e+00 689
27 TraesCS2A01G015500 chr3D 89.924 397 23 5 207 586 73923980 73924376 1.760000e-136 496
28 TraesCS2A01G015500 chr6B 84.652 417 52 10 5 410 61636972 61636557 3.050000e-109 405


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 TraesCS2A01G015500 chr2A 6300749 6303297 2548 True 4708 4708 100.000 1 2549 1 chr2A.!!$R1 2548
1 TraesCS2A01G015500 chr2A 764220190 764222171 1981 False 3221 3221 96.165 587 2549 1 chr2A.!!$F2 1962
2 TraesCS2A01G015500 chr2A 775966837 775967964 1127 True 1938 1938 97.695 585 1711 1 chr2A.!!$R3 1126
3 TraesCS2A01G015500 chr2A 233255253 233256373 1120 False 1786 1786 95.326 579 1710 1 chr2A.!!$F1 1131
4 TraesCS2A01G015500 chr2A 611724021 611725146 1125 True 1777 1777 95.075 577 1711 1 chr2A.!!$R2 1134
5 TraesCS2A01G015500 chr3A 719846455 719848440 1985 False 3251 3251 96.376 583 2549 1 chr3A.!!$F2 1966
6 TraesCS2A01G015500 chr3A 683235667 683236507 840 True 1406 1406 96.908 1712 2549 1 chr3A.!!$R1 837
7 TraesCS2A01G015500 chr7A 18189929 18191913 1984 False 3164 3164 95.619 586 2549 1 chr7A.!!$F1 1963
8 TraesCS2A01G015500 chr7A 49209387 49210224 837 False 1448 1448 97.852 1712 2549 1 chr7A.!!$F2 837
9 TraesCS2A01G015500 chr7A 14471066 14471904 838 True 1410 1410 97.020 1712 2549 1 chr7A.!!$R1 837
10 TraesCS2A01G015500 chr7A 689994368 689995208 840 True 1406 1406 96.908 1712 2549 1 chr7A.!!$R2 837
11 TraesCS2A01G015500 chr6A 203519795 203520912 1117 True 1821 1821 96.014 587 1711 1 chr6A.!!$R2 1124
12 TraesCS2A01G015500 chr6A 57901157 57902273 1116 False 1807 1807 95.752 585 1711 1 chr6A.!!$F1 1126
13 TraesCS2A01G015500 chr6A 14688938 14689817 879 True 1461 1461 96.602 1668 2549 1 chr6A.!!$R1 881
14 TraesCS2A01G015500 chr5A 357169998 357171129 1131 True 1786 1786 95.026 568 1711 1 chr5A.!!$R1 1143
15 TraesCS2A01G015500 chr5A 563445102 563445940 838 False 1432 1432 97.500 1712 2549 1 chr5A.!!$F1 837
16 TraesCS2A01G015500 chr5B 121669817 121670948 1131 True 1738 1738 94.498 584 1711 1 chr5B.!!$R1 1127
17 TraesCS2A01G015500 chrUn 43128400 43129528 1128 True 1727 1727 94.396 587 1711 1 chrUn.!!$R1 1124
18 TraesCS2A01G015500 chrUn 231572793 231573920 1127 False 1725 1725 94.391 588 1711 1 chrUn.!!$F1 1123
19 TraesCS2A01G015500 chr5D 514513194 514514291 1097 True 1417 1417 89.841 586 1711 1 chr5D.!!$R1 1125
20 TraesCS2A01G015500 chr1B 41158088 41158688 600 False 808 808 91.362 2 586 1 chr1B.!!$F1 584
21 TraesCS2A01G015500 chr1B 41196194 41196794 600 False 774 774 90.365 2 586 1 chr1B.!!$F2 584
22 TraesCS2A01G015500 chr4A 710922935 710923535 600 True 797 797 91.030 2 586 1 chr4A.!!$R1 584
23 TraesCS2A01G015500 chr7D 14670129 14670673 544 True 725 725 91.193 2 528 1 chr7D.!!$R1 526
24 TraesCS2A01G015500 chr7D 48497740 48498329 589 False 689 689 88.342 2 584 1 chr7D.!!$F1 582

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
534 538 0.036022 AGAAGTCACCTCTGCCTTGC 59.964 55.0 0.0 0.0 0.0 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2021 2226 0.179119 CCTGGCGTAAACCTCTACCG 60.179 60.0 0.0 0.0 0.0 4.02 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
153 154 6.755542 TGGTCCTCCAAATAAAACCAATTT 57.244 33.333 0.00 0.00 41.25 1.82
274 278 4.416516 TGAGAGTTACAGGAAGGATGACA 58.583 43.478 0.00 0.00 0.00 3.58
275 279 4.464244 TGAGAGTTACAGGAAGGATGACAG 59.536 45.833 0.00 0.00 0.00 3.51
276 280 3.772025 AGAGTTACAGGAAGGATGACAGG 59.228 47.826 0.00 0.00 0.00 4.00
277 281 3.769844 GAGTTACAGGAAGGATGACAGGA 59.230 47.826 0.00 0.00 0.00 3.86
278 282 4.366267 AGTTACAGGAAGGATGACAGGAT 58.634 43.478 0.00 0.00 0.00 3.24
279 283 4.163078 AGTTACAGGAAGGATGACAGGATG 59.837 45.833 0.00 0.00 46.00 3.51
293 297 2.625737 CAGGATGTGAGTAAGCCTGTG 58.374 52.381 0.00 0.00 40.88 3.66
294 298 2.234661 CAGGATGTGAGTAAGCCTGTGA 59.765 50.000 0.00 0.00 40.88 3.58
295 299 3.110705 AGGATGTGAGTAAGCCTGTGAT 58.889 45.455 0.00 0.00 0.00 3.06
296 300 3.118482 AGGATGTGAGTAAGCCTGTGATG 60.118 47.826 0.00 0.00 0.00 3.07
297 301 2.099141 TGTGAGTAAGCCTGTGATGC 57.901 50.000 0.00 0.00 0.00 3.91
298 302 1.002366 GTGAGTAAGCCTGTGATGCG 58.998 55.000 0.00 0.00 0.00 4.73
299 303 0.608130 TGAGTAAGCCTGTGATGCGT 59.392 50.000 0.00 0.00 0.00 5.24
300 304 1.002366 GAGTAAGCCTGTGATGCGTG 58.998 55.000 0.00 0.00 0.00 5.34
301 305 0.608130 AGTAAGCCTGTGATGCGTGA 59.392 50.000 0.00 0.00 0.00 4.35
302 306 1.208052 AGTAAGCCTGTGATGCGTGAT 59.792 47.619 0.00 0.00 0.00 3.06
303 307 1.328680 GTAAGCCTGTGATGCGTGATG 59.671 52.381 0.00 0.00 0.00 3.07
304 308 0.321919 AAGCCTGTGATGCGTGATGT 60.322 50.000 0.00 0.00 0.00 3.06
305 309 0.321919 AGCCTGTGATGCGTGATGTT 60.322 50.000 0.00 0.00 0.00 2.71
306 310 0.179181 GCCTGTGATGCGTGATGTTG 60.179 55.000 0.00 0.00 0.00 3.33
307 311 0.179181 CCTGTGATGCGTGATGTTGC 60.179 55.000 0.00 0.00 0.00 4.17
308 312 0.800631 CTGTGATGCGTGATGTTGCT 59.199 50.000 0.00 0.00 0.00 3.91
309 313 0.518195 TGTGATGCGTGATGTTGCTG 59.482 50.000 0.00 0.00 0.00 4.41
310 314 0.798159 GTGATGCGTGATGTTGCTGA 59.202 50.000 0.00 0.00 0.00 4.26
311 315 0.798159 TGATGCGTGATGTTGCTGAC 59.202 50.000 0.00 0.00 0.00 3.51
312 316 0.798159 GATGCGTGATGTTGCTGACA 59.202 50.000 0.00 0.00 43.71 3.58
313 317 1.197492 GATGCGTGATGTTGCTGACAA 59.803 47.619 0.00 0.00 42.62 3.18
322 326 2.584166 GTTGCTGACAACGACATCAG 57.416 50.000 9.30 9.30 46.20 2.90
323 327 2.135139 GTTGCTGACAACGACATCAGA 58.865 47.619 15.47 2.43 46.20 3.27
324 328 2.524569 TGCTGACAACGACATCAGAA 57.475 45.000 15.47 5.27 44.32 3.02
325 329 2.407090 TGCTGACAACGACATCAGAAG 58.593 47.619 15.47 0.00 44.32 2.85
326 330 1.728971 GCTGACAACGACATCAGAAGG 59.271 52.381 15.47 0.00 44.32 3.46
327 331 1.728971 CTGACAACGACATCAGAAGGC 59.271 52.381 8.30 0.00 44.32 4.35
328 332 1.344438 TGACAACGACATCAGAAGGCT 59.656 47.619 0.00 0.00 0.00 4.58
329 333 2.224281 TGACAACGACATCAGAAGGCTT 60.224 45.455 0.00 0.00 0.00 4.35
330 334 2.808543 GACAACGACATCAGAAGGCTTT 59.191 45.455 0.00 0.00 0.00 3.51
331 335 2.808543 ACAACGACATCAGAAGGCTTTC 59.191 45.455 0.00 0.00 0.00 2.62
332 336 1.714794 ACGACATCAGAAGGCTTTCG 58.285 50.000 13.49 13.49 38.38 3.46
333 337 1.000955 ACGACATCAGAAGGCTTTCGT 59.999 47.619 14.63 14.63 38.38 3.85
334 338 1.656095 CGACATCAGAAGGCTTTCGTC 59.344 52.381 0.00 3.90 38.38 4.20
335 339 2.688507 GACATCAGAAGGCTTTCGTCA 58.311 47.619 0.00 0.00 38.38 4.35
336 340 2.670414 GACATCAGAAGGCTTTCGTCAG 59.330 50.000 0.00 0.00 38.38 3.51
337 341 1.396301 CATCAGAAGGCTTTCGTCAGC 59.604 52.381 0.00 0.52 38.38 4.26
338 342 0.667487 TCAGAAGGCTTTCGTCAGCG 60.667 55.000 0.00 0.00 41.12 5.18
339 343 1.374758 AGAAGGCTTTCGTCAGCGG 60.375 57.895 0.00 0.00 41.12 5.52
340 344 3.028366 GAAGGCTTTCGTCAGCGGC 62.028 63.158 0.00 0.00 41.12 6.53
343 347 3.353836 GCTTTCGTCAGCGGCCAA 61.354 61.111 2.24 0.00 38.89 4.52
344 348 2.690778 GCTTTCGTCAGCGGCCAAT 61.691 57.895 2.24 0.00 38.89 3.16
345 349 1.135315 CTTTCGTCAGCGGCCAATG 59.865 57.895 2.24 0.00 38.89 2.82
346 350 2.257286 CTTTCGTCAGCGGCCAATGG 62.257 60.000 2.24 0.00 38.89 3.16
347 351 3.545124 TTCGTCAGCGGCCAATGGT 62.545 57.895 2.24 0.00 38.89 3.55
348 352 2.125310 CGTCAGCGGCCAATGGTA 60.125 61.111 2.24 0.00 0.00 3.25
349 353 2.461110 CGTCAGCGGCCAATGGTAC 61.461 63.158 2.24 0.00 0.00 3.34
369 373 7.732025 TGGTACAGGTTATATGATTCGATTGT 58.268 34.615 0.00 0.00 0.00 2.71
370 374 8.208224 TGGTACAGGTTATATGATTCGATTGTT 58.792 33.333 0.00 0.00 0.00 2.83
371 375 8.495949 GGTACAGGTTATATGATTCGATTGTTG 58.504 37.037 0.00 0.00 0.00 3.33
372 376 6.959361 ACAGGTTATATGATTCGATTGTTGC 58.041 36.000 0.00 0.00 0.00 4.17
373 377 6.767902 ACAGGTTATATGATTCGATTGTTGCT 59.232 34.615 0.00 0.00 0.00 3.91
374 378 7.073883 CAGGTTATATGATTCGATTGTTGCTG 58.926 38.462 0.00 0.00 0.00 4.41
375 379 5.853282 GGTTATATGATTCGATTGTTGCTGC 59.147 40.000 0.00 0.00 0.00 5.25
376 380 6.429624 GTTATATGATTCGATTGTTGCTGCA 58.570 36.000 0.00 0.00 0.00 4.41
377 381 5.700722 ATATGATTCGATTGTTGCTGCAT 57.299 34.783 1.84 0.00 0.00 3.96
378 382 3.853831 TGATTCGATTGTTGCTGCATT 57.146 38.095 1.84 0.00 0.00 3.56
379 383 4.177165 TGATTCGATTGTTGCTGCATTT 57.823 36.364 1.84 0.00 0.00 2.32
380 384 4.558178 TGATTCGATTGTTGCTGCATTTT 58.442 34.783 1.84 0.00 0.00 1.82
381 385 5.707931 TGATTCGATTGTTGCTGCATTTTA 58.292 33.333 1.84 0.00 0.00 1.52
382 386 6.331845 TGATTCGATTGTTGCTGCATTTTAT 58.668 32.000 1.84 0.00 0.00 1.40
383 387 6.812656 TGATTCGATTGTTGCTGCATTTTATT 59.187 30.769 1.84 0.00 0.00 1.40
384 388 6.630676 TTCGATTGTTGCTGCATTTTATTC 57.369 33.333 1.84 0.00 0.00 1.75
385 389 5.953183 TCGATTGTTGCTGCATTTTATTCT 58.047 33.333 1.84 0.00 0.00 2.40
386 390 6.389091 TCGATTGTTGCTGCATTTTATTCTT 58.611 32.000 1.84 0.00 0.00 2.52
387 391 6.867816 TCGATTGTTGCTGCATTTTATTCTTT 59.132 30.769 1.84 0.00 0.00 2.52
388 392 6.951530 CGATTGTTGCTGCATTTTATTCTTTG 59.048 34.615 1.84 0.00 0.00 2.77
389 393 7.359431 CGATTGTTGCTGCATTTTATTCTTTGT 60.359 33.333 1.84 0.00 0.00 2.83
390 394 8.830201 ATTGTTGCTGCATTTTATTCTTTGTA 57.170 26.923 1.84 0.00 0.00 2.41
391 395 8.830201 TTGTTGCTGCATTTTATTCTTTGTAT 57.170 26.923 1.84 0.00 0.00 2.29
392 396 8.464770 TGTTGCTGCATTTTATTCTTTGTATC 57.535 30.769 1.84 0.00 0.00 2.24
393 397 8.306038 TGTTGCTGCATTTTATTCTTTGTATCT 58.694 29.630 1.84 0.00 0.00 1.98
394 398 9.143631 GTTGCTGCATTTTATTCTTTGTATCTT 57.856 29.630 1.84 0.00 0.00 2.40
437 441 9.833917 AAAAAGAAGTAGCTAAGTTACTCAAGT 57.166 29.630 0.00 0.00 28.67 3.16
438 442 8.819643 AAAGAAGTAGCTAAGTTACTCAAGTG 57.180 34.615 0.00 0.00 28.67 3.16
439 443 6.391537 AGAAGTAGCTAAGTTACTCAAGTGC 58.608 40.000 0.00 0.00 28.67 4.40
440 444 5.986501 AGTAGCTAAGTTACTCAAGTGCT 57.013 39.130 0.00 0.00 0.00 4.40
441 445 5.956642 AGTAGCTAAGTTACTCAAGTGCTC 58.043 41.667 0.00 0.00 0.00 4.26
442 446 4.195225 AGCTAAGTTACTCAAGTGCTCC 57.805 45.455 0.00 0.00 0.00 4.70
443 447 3.835395 AGCTAAGTTACTCAAGTGCTCCT 59.165 43.478 0.00 0.00 0.00 3.69
444 448 4.284746 AGCTAAGTTACTCAAGTGCTCCTT 59.715 41.667 0.00 0.00 0.00 3.36
445 449 4.998033 GCTAAGTTACTCAAGTGCTCCTTT 59.002 41.667 0.00 0.00 0.00 3.11
446 450 6.014499 AGCTAAGTTACTCAAGTGCTCCTTTA 60.014 38.462 0.00 0.00 0.00 1.85
447 451 6.819146 GCTAAGTTACTCAAGTGCTCCTTTAT 59.181 38.462 0.00 0.00 0.00 1.40
448 452 7.201565 GCTAAGTTACTCAAGTGCTCCTTTATG 60.202 40.741 0.00 0.00 0.00 1.90
449 453 5.491982 AGTTACTCAAGTGCTCCTTTATGG 58.508 41.667 0.00 0.00 37.10 2.74
450 454 5.013183 AGTTACTCAAGTGCTCCTTTATGGT 59.987 40.000 0.00 0.00 37.07 3.55
451 455 4.373156 ACTCAAGTGCTCCTTTATGGTT 57.627 40.909 0.00 0.00 37.07 3.67
452 456 4.729868 ACTCAAGTGCTCCTTTATGGTTT 58.270 39.130 0.00 0.00 37.07 3.27
453 457 4.520492 ACTCAAGTGCTCCTTTATGGTTTG 59.480 41.667 0.00 0.00 37.07 2.93
454 458 4.469657 TCAAGTGCTCCTTTATGGTTTGT 58.530 39.130 0.00 0.00 37.07 2.83
455 459 4.518970 TCAAGTGCTCCTTTATGGTTTGTC 59.481 41.667 0.00 0.00 37.07 3.18
456 460 4.373156 AGTGCTCCTTTATGGTTTGTCT 57.627 40.909 0.00 0.00 37.07 3.41
457 461 4.729868 AGTGCTCCTTTATGGTTTGTCTT 58.270 39.130 0.00 0.00 37.07 3.01
458 462 4.520492 AGTGCTCCTTTATGGTTTGTCTTG 59.480 41.667 0.00 0.00 37.07 3.02
459 463 4.518970 GTGCTCCTTTATGGTTTGTCTTGA 59.481 41.667 0.00 0.00 37.07 3.02
460 464 5.009610 GTGCTCCTTTATGGTTTGTCTTGAA 59.990 40.000 0.00 0.00 37.07 2.69
461 465 5.596361 TGCTCCTTTATGGTTTGTCTTGAAA 59.404 36.000 0.00 0.00 37.07 2.69
462 466 6.152379 GCTCCTTTATGGTTTGTCTTGAAAG 58.848 40.000 0.00 0.00 37.07 2.62
463 467 6.084326 TCCTTTATGGTTTGTCTTGAAAGC 57.916 37.500 0.00 0.00 37.07 3.51
464 468 5.596361 TCCTTTATGGTTTGTCTTGAAAGCA 59.404 36.000 0.00 0.00 44.86 3.91
465 469 6.097554 TCCTTTATGGTTTGTCTTGAAAGCAA 59.902 34.615 0.00 0.00 44.19 3.91
466 470 7.684187 TCCTTTATGGTTTGTCTTGAAAGCAAG 60.684 37.037 0.00 0.00 44.19 4.01
477 481 4.998671 TTGAAAGCAAGATTGGTTGTCA 57.001 36.364 10.48 12.27 46.98 3.58
478 482 5.534207 TTGAAAGCAAGATTGGTTGTCAT 57.466 34.783 10.48 0.00 46.98 3.06
479 483 4.873817 TGAAAGCAAGATTGGTTGTCATG 58.126 39.130 10.48 0.00 46.98 3.07
480 484 3.308438 AAGCAAGATTGGTTGTCATGC 57.692 42.857 9.07 0.00 46.03 4.06
481 485 2.522185 AGCAAGATTGGTTGTCATGCT 58.478 42.857 0.57 0.57 43.43 3.79
482 486 2.895404 AGCAAGATTGGTTGTCATGCTT 59.105 40.909 0.57 0.00 45.22 3.91
483 487 3.057033 AGCAAGATTGGTTGTCATGCTTC 60.057 43.478 0.57 0.00 45.22 3.86
484 488 3.305539 GCAAGATTGGTTGTCATGCTTCA 60.306 43.478 0.00 0.00 37.34 3.02
485 489 4.619863 GCAAGATTGGTTGTCATGCTTCAT 60.620 41.667 0.00 0.00 37.34 2.57
486 490 5.393352 GCAAGATTGGTTGTCATGCTTCATA 60.393 40.000 0.00 0.00 37.34 2.15
487 491 6.623486 CAAGATTGGTTGTCATGCTTCATAA 58.377 36.000 0.00 0.00 0.00 1.90
488 492 7.262772 CAAGATTGGTTGTCATGCTTCATAAT 58.737 34.615 0.00 0.00 0.00 1.28
489 493 8.407832 CAAGATTGGTTGTCATGCTTCATAATA 58.592 33.333 0.00 0.00 0.00 0.98
490 494 8.701908 AGATTGGTTGTCATGCTTCATAATAT 57.298 30.769 0.00 0.00 0.00 1.28
491 495 9.139734 AGATTGGTTGTCATGCTTCATAATATT 57.860 29.630 0.00 0.00 0.00 1.28
492 496 9.754382 GATTGGTTGTCATGCTTCATAATATTT 57.246 29.630 0.00 0.00 0.00 1.40
494 498 8.929827 TGGTTGTCATGCTTCATAATATTTTG 57.070 30.769 0.00 0.00 0.00 2.44
495 499 8.747471 TGGTTGTCATGCTTCATAATATTTTGA 58.253 29.630 4.67 4.67 0.00 2.69
496 500 9.023967 GGTTGTCATGCTTCATAATATTTTGAC 57.976 33.333 7.96 0.09 33.37 3.18
497 501 9.571810 GTTGTCATGCTTCATAATATTTTGACA 57.428 29.630 7.96 5.21 39.16 3.58
498 502 9.571810 TTGTCATGCTTCATAATATTTTGACAC 57.428 29.630 7.96 4.75 40.22 3.67
499 503 8.738106 TGTCATGCTTCATAATATTTTGACACA 58.262 29.630 7.96 9.42 36.85 3.72
500 504 9.229784 GTCATGCTTCATAATATTTTGACACAG 57.770 33.333 7.96 5.26 33.08 3.66
501 505 7.916977 TCATGCTTCATAATATTTTGACACAGC 59.083 33.333 17.35 17.35 0.00 4.40
502 506 6.563422 TGCTTCATAATATTTTGACACAGCC 58.437 36.000 19.60 9.22 0.00 4.85
503 507 6.152492 TGCTTCATAATATTTTGACACAGCCA 59.848 34.615 19.60 10.80 0.00 4.75
504 508 6.694411 GCTTCATAATATTTTGACACAGCCAG 59.306 38.462 14.98 7.84 0.00 4.85
505 509 7.629222 GCTTCATAATATTTTGACACAGCCAGT 60.629 37.037 14.98 0.00 0.00 4.00
506 510 7.320443 TCATAATATTTTGACACAGCCAGTC 57.680 36.000 4.67 0.00 36.55 3.51
507 511 6.883756 TCATAATATTTTGACACAGCCAGTCA 59.116 34.615 4.67 0.00 43.72 3.41
511 515 3.871701 TGACACAGCCAGTCAAACA 57.128 47.368 1.46 0.00 42.57 2.83
512 516 2.346766 TGACACAGCCAGTCAAACAT 57.653 45.000 1.46 0.00 42.57 2.71
513 517 3.483808 TGACACAGCCAGTCAAACATA 57.516 42.857 1.46 0.00 42.57 2.29
514 518 3.402110 TGACACAGCCAGTCAAACATAG 58.598 45.455 1.46 0.00 42.57 2.23
515 519 3.070878 TGACACAGCCAGTCAAACATAGA 59.929 43.478 1.46 0.00 42.57 1.98
516 520 3.668447 ACACAGCCAGTCAAACATAGAG 58.332 45.455 0.00 0.00 0.00 2.43
517 521 3.324846 ACACAGCCAGTCAAACATAGAGA 59.675 43.478 0.00 0.00 0.00 3.10
518 522 4.202357 ACACAGCCAGTCAAACATAGAGAA 60.202 41.667 0.00 0.00 0.00 2.87
519 523 4.391216 CACAGCCAGTCAAACATAGAGAAG 59.609 45.833 0.00 0.00 0.00 2.85
520 524 4.040952 ACAGCCAGTCAAACATAGAGAAGT 59.959 41.667 0.00 0.00 0.00 3.01
521 525 4.629200 CAGCCAGTCAAACATAGAGAAGTC 59.371 45.833 0.00 0.00 0.00 3.01
522 526 4.284490 AGCCAGTCAAACATAGAGAAGTCA 59.716 41.667 0.00 0.00 0.00 3.41
523 527 4.390297 GCCAGTCAAACATAGAGAAGTCAC 59.610 45.833 0.00 0.00 0.00 3.67
524 528 4.932200 CCAGTCAAACATAGAGAAGTCACC 59.068 45.833 0.00 0.00 0.00 4.02
525 529 5.279708 CCAGTCAAACATAGAGAAGTCACCT 60.280 44.000 0.00 0.00 0.00 4.00
526 530 5.866633 CAGTCAAACATAGAGAAGTCACCTC 59.133 44.000 0.00 0.00 0.00 3.85
527 531 5.777732 AGTCAAACATAGAGAAGTCACCTCT 59.222 40.000 0.00 0.00 42.97 3.69
528 532 5.866633 GTCAAACATAGAGAAGTCACCTCTG 59.133 44.000 0.00 0.00 40.84 3.35
529 533 4.464069 AACATAGAGAAGTCACCTCTGC 57.536 45.455 0.00 0.00 40.84 4.26
530 534 2.763448 ACATAGAGAAGTCACCTCTGCC 59.237 50.000 0.00 0.00 40.84 4.85
531 535 2.909504 TAGAGAAGTCACCTCTGCCT 57.090 50.000 0.00 0.00 40.84 4.75
532 536 2.022718 AGAGAAGTCACCTCTGCCTT 57.977 50.000 0.00 0.00 39.36 4.35
533 537 1.622811 AGAGAAGTCACCTCTGCCTTG 59.377 52.381 0.00 0.00 39.36 3.61
534 538 0.036022 AGAAGTCACCTCTGCCTTGC 59.964 55.000 0.00 0.00 0.00 4.01
535 539 0.957888 GAAGTCACCTCTGCCTTGCC 60.958 60.000 0.00 0.00 0.00 4.52
536 540 2.738213 AAGTCACCTCTGCCTTGCCG 62.738 60.000 0.00 0.00 0.00 5.69
537 541 3.241530 TCACCTCTGCCTTGCCGT 61.242 61.111 0.00 0.00 0.00 5.68
538 542 1.911269 TCACCTCTGCCTTGCCGTA 60.911 57.895 0.00 0.00 0.00 4.02
539 543 1.448540 CACCTCTGCCTTGCCGTAG 60.449 63.158 0.00 0.00 0.00 3.51
540 544 2.512515 CCTCTGCCTTGCCGTAGC 60.513 66.667 0.00 0.00 40.48 3.58
551 555 3.975992 GCCGTAGCAACAACTGATG 57.024 52.632 0.00 0.00 39.53 3.07
552 556 1.438651 GCCGTAGCAACAACTGATGA 58.561 50.000 0.00 0.00 39.53 2.92
553 557 1.804151 GCCGTAGCAACAACTGATGAA 59.196 47.619 0.00 0.00 39.53 2.57
554 558 2.159653 GCCGTAGCAACAACTGATGAAG 60.160 50.000 0.00 0.00 39.53 3.02
555 559 3.067106 CCGTAGCAACAACTGATGAAGT 58.933 45.455 0.00 0.00 42.60 3.01
556 560 6.091875 GCCGTAGCAACAACTGATGAAGTT 62.092 45.833 0.00 0.00 44.15 2.66
557 561 7.491161 GCCGTAGCAACAACTGATGAAGTTT 62.491 44.000 0.00 0.00 42.56 2.66
571 575 8.078596 ACTGATGAAGTTTGTCTTTTTAGATGC 58.921 33.333 0.00 0.00 34.57 3.91
572 576 7.370383 TGATGAAGTTTGTCTTTTTAGATGCC 58.630 34.615 0.00 0.00 36.40 4.40
573 577 6.084326 TGAAGTTTGTCTTTTTAGATGCCC 57.916 37.500 0.00 0.00 36.40 5.36
574 578 5.010617 TGAAGTTTGTCTTTTTAGATGCCCC 59.989 40.000 0.00 0.00 36.40 5.80
575 579 4.479158 AGTTTGTCTTTTTAGATGCCCCA 58.521 39.130 0.00 0.00 0.00 4.96
576 580 4.898861 AGTTTGTCTTTTTAGATGCCCCAA 59.101 37.500 0.00 0.00 0.00 4.12
577 581 5.365314 AGTTTGTCTTTTTAGATGCCCCAAA 59.635 36.000 0.00 0.00 0.00 3.28
578 582 5.878406 TTGTCTTTTTAGATGCCCCAAAA 57.122 34.783 0.00 0.00 0.00 2.44
579 583 5.878406 TGTCTTTTTAGATGCCCCAAAAA 57.122 34.783 0.00 0.00 32.06 1.94
580 584 6.432403 TGTCTTTTTAGATGCCCCAAAAAT 57.568 33.333 0.00 0.00 32.43 1.82
581 585 6.229733 TGTCTTTTTAGATGCCCCAAAAATG 58.770 36.000 0.00 0.00 32.43 2.32
908 947 1.165907 CGGCGAGAGAGAGAGAGCAT 61.166 60.000 0.00 0.00 0.00 3.79
936 975 1.115467 GAAGCTAGCTGTAGAGGGCA 58.885 55.000 20.16 0.00 0.00 5.36
1076 1116 1.067283 CATGCCTGTCTTCGTCTGTCT 60.067 52.381 0.00 0.00 0.00 3.41
1078 1118 0.315568 GCCTGTCTTCGTCTGTCTGT 59.684 55.000 0.00 0.00 0.00 3.41
1133 1173 1.275291 GACACCGAGGAACCAGAATCA 59.725 52.381 0.00 0.00 0.00 2.57
1153 1193 1.663388 CCGTTCTACGTGTGCAGCA 60.663 57.895 0.00 0.00 40.58 4.41
1337 1424 4.183686 GCGCATGCTGCCACGAAT 62.184 61.111 17.13 0.00 41.12 3.34
1629 1824 8.148999 TGTTGGTTAAAGTTGTTTAAAGGTTGT 58.851 29.630 0.00 0.00 39.34 3.32
1630 1825 8.991026 GTTGGTTAAAGTTGTTTAAAGGTTGTT 58.009 29.630 0.00 0.00 39.34 2.83
1631 1826 9.557061 TTGGTTAAAGTTGTTTAAAGGTTGTTT 57.443 25.926 0.00 0.00 39.34 2.83
1980 2185 6.987386 TCCAATTCAAATACACCGTGATTTT 58.013 32.000 5.28 1.87 0.00 1.82
2021 2226 0.813821 GGAAAATGTGCCTCAGCTCC 59.186 55.000 0.00 0.00 40.80 4.70
2152 2358 2.747855 GCGGCTGGGGACTTGAAG 60.748 66.667 0.00 0.00 0.00 3.02
2163 2369 2.032528 CTTGAAGCCAGGACCGCA 59.967 61.111 0.00 0.00 0.00 5.69
2188 2394 3.215975 GTTTGTGGTGTTTAGGGCTACA 58.784 45.455 0.00 0.00 0.00 2.74
2189 2395 3.799432 TTGTGGTGTTTAGGGCTACAT 57.201 42.857 0.00 0.00 0.00 2.29
2223 2429 5.033589 AGGATAGATGGCAAGACTTTGAG 57.966 43.478 0.00 0.00 36.36 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.363038 GCAGCAATATTGGGAGCATTGA 59.637 45.455 17.02 0.00 32.54 2.57
50 51 1.094785 GCACCACAATCTACCGCAAT 58.905 50.000 0.00 0.00 0.00 3.56
147 148 9.672086 TCGTAAGTTTGAAAACAGATAAATTGG 57.328 29.630 8.53 0.00 41.30 3.16
153 154 7.278203 TGTGTGTCGTAAGTTTGAAAACAGATA 59.722 33.333 8.53 0.00 41.30 1.98
165 168 6.531594 CACATGAGATATGTGTGTCGTAAGTT 59.468 38.462 0.00 0.00 43.11 2.66
167 170 6.502195 CACATGAGATATGTGTGTCGTAAG 57.498 41.667 0.00 0.00 43.11 2.34
199 202 5.186797 TCGTTAATTTGCCATCCTTCCATTT 59.813 36.000 0.00 0.00 0.00 2.32
274 278 2.540383 TCACAGGCTTACTCACATCCT 58.460 47.619 0.00 0.00 0.00 3.24
275 279 3.201290 CATCACAGGCTTACTCACATCC 58.799 50.000 0.00 0.00 0.00 3.51
276 280 2.611292 GCATCACAGGCTTACTCACATC 59.389 50.000 0.00 0.00 0.00 3.06
277 281 2.636830 GCATCACAGGCTTACTCACAT 58.363 47.619 0.00 0.00 0.00 3.21
278 282 1.672737 CGCATCACAGGCTTACTCACA 60.673 52.381 0.00 0.00 0.00 3.58
279 283 1.002366 CGCATCACAGGCTTACTCAC 58.998 55.000 0.00 0.00 0.00 3.51
280 284 0.608130 ACGCATCACAGGCTTACTCA 59.392 50.000 0.00 0.00 0.00 3.41
281 285 1.002366 CACGCATCACAGGCTTACTC 58.998 55.000 0.00 0.00 0.00 2.59
282 286 0.608130 TCACGCATCACAGGCTTACT 59.392 50.000 0.00 0.00 0.00 2.24
283 287 1.328680 CATCACGCATCACAGGCTTAC 59.671 52.381 0.00 0.00 0.00 2.34
284 288 1.066215 ACATCACGCATCACAGGCTTA 60.066 47.619 0.00 0.00 0.00 3.09
285 289 0.321919 ACATCACGCATCACAGGCTT 60.322 50.000 0.00 0.00 0.00 4.35
286 290 0.321919 AACATCACGCATCACAGGCT 60.322 50.000 0.00 0.00 0.00 4.58
287 291 0.179181 CAACATCACGCATCACAGGC 60.179 55.000 0.00 0.00 0.00 4.85
288 292 0.179181 GCAACATCACGCATCACAGG 60.179 55.000 0.00 0.00 0.00 4.00
289 293 0.800631 AGCAACATCACGCATCACAG 59.199 50.000 0.00 0.00 0.00 3.66
290 294 0.518195 CAGCAACATCACGCATCACA 59.482 50.000 0.00 0.00 0.00 3.58
291 295 0.798159 TCAGCAACATCACGCATCAC 59.202 50.000 0.00 0.00 0.00 3.06
292 296 0.798159 GTCAGCAACATCACGCATCA 59.202 50.000 0.00 0.00 0.00 3.07
293 297 0.798159 TGTCAGCAACATCACGCATC 59.202 50.000 0.00 0.00 31.20 3.91
294 298 1.237533 TTGTCAGCAACATCACGCAT 58.762 45.000 0.00 0.00 37.82 4.73
295 299 2.700329 TTGTCAGCAACATCACGCA 58.300 47.368 0.00 0.00 37.82 5.24
304 308 2.524569 TCTGATGTCGTTGTCAGCAA 57.475 45.000 8.22 0.00 41.21 3.91
305 309 2.407090 CTTCTGATGTCGTTGTCAGCA 58.593 47.619 8.22 0.00 41.21 4.41
306 310 1.728971 CCTTCTGATGTCGTTGTCAGC 59.271 52.381 8.22 0.00 41.21 4.26
307 311 1.728971 GCCTTCTGATGTCGTTGTCAG 59.271 52.381 7.17 7.17 42.46 3.51
308 312 1.344438 AGCCTTCTGATGTCGTTGTCA 59.656 47.619 0.00 0.00 0.00 3.58
309 313 2.086054 AGCCTTCTGATGTCGTTGTC 57.914 50.000 0.00 0.00 0.00 3.18
310 314 2.550830 AAGCCTTCTGATGTCGTTGT 57.449 45.000 0.00 0.00 0.00 3.32
311 315 2.159787 CGAAAGCCTTCTGATGTCGTTG 60.160 50.000 0.00 0.00 0.00 4.10
312 316 2.069273 CGAAAGCCTTCTGATGTCGTT 58.931 47.619 0.00 0.00 0.00 3.85
313 317 1.000955 ACGAAAGCCTTCTGATGTCGT 59.999 47.619 0.00 0.00 35.58 4.34
314 318 1.656095 GACGAAAGCCTTCTGATGTCG 59.344 52.381 0.00 0.00 0.00 4.35
315 319 2.670414 CTGACGAAAGCCTTCTGATGTC 59.330 50.000 0.00 0.00 0.00 3.06
316 320 2.693069 CTGACGAAAGCCTTCTGATGT 58.307 47.619 0.00 0.00 0.00 3.06
317 321 1.396301 GCTGACGAAAGCCTTCTGATG 59.604 52.381 0.00 0.00 37.20 3.07
318 322 1.731720 GCTGACGAAAGCCTTCTGAT 58.268 50.000 0.00 0.00 37.20 2.90
319 323 0.667487 CGCTGACGAAAGCCTTCTGA 60.667 55.000 8.20 0.00 43.93 3.27
320 324 1.630244 CCGCTGACGAAAGCCTTCTG 61.630 60.000 8.20 0.00 43.93 3.02
321 325 1.374758 CCGCTGACGAAAGCCTTCT 60.375 57.895 8.20 0.00 43.93 2.85
322 326 3.028366 GCCGCTGACGAAAGCCTTC 62.028 63.158 8.20 0.00 43.93 3.46
323 327 3.050275 GCCGCTGACGAAAGCCTT 61.050 61.111 8.20 0.00 43.93 4.35
326 330 2.690778 ATTGGCCGCTGACGAAAGC 61.691 57.895 0.00 0.00 43.93 3.51
327 331 1.135315 CATTGGCCGCTGACGAAAG 59.865 57.895 0.00 0.00 43.93 2.62
328 332 2.331893 CCATTGGCCGCTGACGAAA 61.332 57.895 5.95 0.00 43.93 3.46
329 333 2.173758 TACCATTGGCCGCTGACGAA 62.174 55.000 1.54 0.00 43.93 3.85
330 334 2.651105 TACCATTGGCCGCTGACGA 61.651 57.895 1.54 0.00 43.93 4.20
331 335 2.125310 TACCATTGGCCGCTGACG 60.125 61.111 1.54 0.00 39.67 4.35
332 336 1.369091 CTGTACCATTGGCCGCTGAC 61.369 60.000 1.54 0.00 0.00 3.51
333 337 1.078497 CTGTACCATTGGCCGCTGA 60.078 57.895 1.54 0.00 0.00 4.26
334 338 2.114670 CCTGTACCATTGGCCGCTG 61.115 63.158 1.54 0.00 0.00 5.18
335 339 2.137177 AACCTGTACCATTGGCCGCT 62.137 55.000 1.54 0.00 0.00 5.52
336 340 0.393267 TAACCTGTACCATTGGCCGC 60.393 55.000 1.54 0.00 0.00 6.53
337 341 2.341846 ATAACCTGTACCATTGGCCG 57.658 50.000 1.54 0.00 0.00 6.13
338 342 4.980573 TCATATAACCTGTACCATTGGCC 58.019 43.478 1.54 0.00 0.00 5.36
339 343 6.128282 CGAATCATATAACCTGTACCATTGGC 60.128 42.308 1.54 0.00 0.00 4.52
340 344 7.158697 TCGAATCATATAACCTGTACCATTGG 58.841 38.462 0.00 0.00 0.00 3.16
341 345 8.777865 ATCGAATCATATAACCTGTACCATTG 57.222 34.615 0.00 0.00 0.00 2.82
342 346 9.219603 CAATCGAATCATATAACCTGTACCATT 57.780 33.333 0.00 0.00 0.00 3.16
343 347 8.375506 ACAATCGAATCATATAACCTGTACCAT 58.624 33.333 0.00 0.00 0.00 3.55
344 348 7.732025 ACAATCGAATCATATAACCTGTACCA 58.268 34.615 0.00 0.00 0.00 3.25
345 349 8.495949 CAACAATCGAATCATATAACCTGTACC 58.504 37.037 0.00 0.00 0.00 3.34
346 350 8.009974 GCAACAATCGAATCATATAACCTGTAC 58.990 37.037 0.00 0.00 0.00 2.90
347 351 7.931407 AGCAACAATCGAATCATATAACCTGTA 59.069 33.333 0.00 0.00 0.00 2.74
348 352 6.767902 AGCAACAATCGAATCATATAACCTGT 59.232 34.615 0.00 0.00 0.00 4.00
349 353 7.073883 CAGCAACAATCGAATCATATAACCTG 58.926 38.462 0.00 0.00 0.00 4.00
350 354 6.293626 GCAGCAACAATCGAATCATATAACCT 60.294 38.462 0.00 0.00 0.00 3.50
351 355 5.853282 GCAGCAACAATCGAATCATATAACC 59.147 40.000 0.00 0.00 0.00 2.85
352 356 6.429624 TGCAGCAACAATCGAATCATATAAC 58.570 36.000 0.00 0.00 0.00 1.89
353 357 6.616774 TGCAGCAACAATCGAATCATATAA 57.383 33.333 0.00 0.00 0.00 0.98
354 358 6.806388 ATGCAGCAACAATCGAATCATATA 57.194 33.333 0.00 0.00 0.00 0.86
355 359 5.700722 ATGCAGCAACAATCGAATCATAT 57.299 34.783 0.00 0.00 0.00 1.78
356 360 5.503662 AATGCAGCAACAATCGAATCATA 57.496 34.783 0.00 0.00 0.00 2.15
357 361 4.380841 AATGCAGCAACAATCGAATCAT 57.619 36.364 0.00 0.00 0.00 2.45
358 362 3.853831 AATGCAGCAACAATCGAATCA 57.146 38.095 0.00 0.00 0.00 2.57
359 363 6.817270 ATAAAATGCAGCAACAATCGAATC 57.183 33.333 0.00 0.00 0.00 2.52
360 364 7.037438 AGAATAAAATGCAGCAACAATCGAAT 58.963 30.769 0.00 0.00 0.00 3.34
361 365 6.389091 AGAATAAAATGCAGCAACAATCGAA 58.611 32.000 0.00 0.00 0.00 3.71
362 366 5.953183 AGAATAAAATGCAGCAACAATCGA 58.047 33.333 0.00 0.00 0.00 3.59
363 367 6.636666 AAGAATAAAATGCAGCAACAATCG 57.363 33.333 0.00 0.00 0.00 3.34
364 368 7.799784 ACAAAGAATAAAATGCAGCAACAATC 58.200 30.769 0.00 0.00 0.00 2.67
365 369 7.733402 ACAAAGAATAAAATGCAGCAACAAT 57.267 28.000 0.00 0.00 0.00 2.71
366 370 8.830201 ATACAAAGAATAAAATGCAGCAACAA 57.170 26.923 0.00 0.00 0.00 2.83
367 371 8.306038 AGATACAAAGAATAAAATGCAGCAACA 58.694 29.630 0.00 0.00 0.00 3.33
368 372 8.693542 AGATACAAAGAATAAAATGCAGCAAC 57.306 30.769 0.00 0.00 0.00 4.17
411 415 9.833917 ACTTGAGTAACTTAGCTACTTCTTTTT 57.166 29.630 0.00 0.00 29.62 1.94
412 416 9.262358 CACTTGAGTAACTTAGCTACTTCTTTT 57.738 33.333 0.00 0.00 29.62 2.27
413 417 7.385478 GCACTTGAGTAACTTAGCTACTTCTTT 59.615 37.037 0.00 0.00 29.62 2.52
414 418 6.869388 GCACTTGAGTAACTTAGCTACTTCTT 59.131 38.462 0.00 0.00 29.62 2.52
415 419 6.209788 AGCACTTGAGTAACTTAGCTACTTCT 59.790 38.462 0.00 0.00 29.62 2.85
416 420 6.391537 AGCACTTGAGTAACTTAGCTACTTC 58.608 40.000 0.00 0.00 29.62 3.01
417 421 6.347859 AGCACTTGAGTAACTTAGCTACTT 57.652 37.500 0.00 0.00 29.62 2.24
418 422 5.105675 GGAGCACTTGAGTAACTTAGCTACT 60.106 44.000 0.00 0.00 32.20 2.57
419 423 5.103687 GGAGCACTTGAGTAACTTAGCTAC 58.896 45.833 0.00 0.00 0.00 3.58
420 424 5.017490 AGGAGCACTTGAGTAACTTAGCTA 58.983 41.667 0.00 0.00 0.00 3.32
421 425 3.835395 AGGAGCACTTGAGTAACTTAGCT 59.165 43.478 0.00 0.00 0.00 3.32
422 426 4.195225 AGGAGCACTTGAGTAACTTAGC 57.805 45.455 0.00 0.00 0.00 3.09
423 427 7.278868 CCATAAAGGAGCACTTGAGTAACTTAG 59.721 40.741 0.00 0.00 39.96 2.18
424 428 7.103641 CCATAAAGGAGCACTTGAGTAACTTA 58.896 38.462 0.00 0.00 39.96 2.24
425 429 5.940470 CCATAAAGGAGCACTTGAGTAACTT 59.060 40.000 0.00 0.00 39.96 2.66
426 430 5.013183 ACCATAAAGGAGCACTTGAGTAACT 59.987 40.000 0.00 0.00 39.96 2.24
427 431 5.246307 ACCATAAAGGAGCACTTGAGTAAC 58.754 41.667 0.00 0.00 39.96 2.50
428 432 5.499004 ACCATAAAGGAGCACTTGAGTAA 57.501 39.130 0.00 0.00 39.96 2.24
429 433 5.499004 AACCATAAAGGAGCACTTGAGTA 57.501 39.130 0.00 0.00 39.96 2.59
430 434 4.373156 AACCATAAAGGAGCACTTGAGT 57.627 40.909 0.00 0.00 39.96 3.41
431 435 4.520492 ACAAACCATAAAGGAGCACTTGAG 59.480 41.667 0.00 0.00 39.96 3.02
432 436 4.469657 ACAAACCATAAAGGAGCACTTGA 58.530 39.130 0.00 0.00 39.96 3.02
433 437 4.520492 AGACAAACCATAAAGGAGCACTTG 59.480 41.667 0.00 0.00 39.96 3.16
434 438 4.729868 AGACAAACCATAAAGGAGCACTT 58.270 39.130 0.00 0.00 42.52 3.16
435 439 4.373156 AGACAAACCATAAAGGAGCACT 57.627 40.909 0.00 0.00 41.22 4.40
436 440 4.518970 TCAAGACAAACCATAAAGGAGCAC 59.481 41.667 0.00 0.00 41.22 4.40
437 441 4.724399 TCAAGACAAACCATAAAGGAGCA 58.276 39.130 0.00 0.00 41.22 4.26
438 442 5.705609 TTCAAGACAAACCATAAAGGAGC 57.294 39.130 0.00 0.00 41.22 4.70
439 443 6.152379 GCTTTCAAGACAAACCATAAAGGAG 58.848 40.000 0.00 0.00 41.22 3.69
440 444 5.596361 TGCTTTCAAGACAAACCATAAAGGA 59.404 36.000 0.00 0.00 41.22 3.36
441 445 5.841810 TGCTTTCAAGACAAACCATAAAGG 58.158 37.500 0.00 0.00 45.67 3.11
456 460 4.998671 TGACAACCAATCTTGCTTTCAA 57.001 36.364 0.00 0.00 0.00 2.69
457 461 4.796946 GCATGACAACCAATCTTGCTTTCA 60.797 41.667 0.00 0.00 41.59 2.69
458 462 3.676646 GCATGACAACCAATCTTGCTTTC 59.323 43.478 0.00 0.00 41.59 2.62
459 463 3.656559 GCATGACAACCAATCTTGCTTT 58.343 40.909 0.00 0.00 41.59 3.51
460 464 3.308438 GCATGACAACCAATCTTGCTT 57.692 42.857 0.00 0.00 41.59 3.91
461 465 2.522185 AGCATGACAACCAATCTTGCT 58.478 42.857 8.98 8.98 46.84 3.91
462 466 3.248266 GAAGCATGACAACCAATCTTGC 58.752 45.455 0.00 5.07 43.85 4.01
463 467 4.508461 TGAAGCATGACAACCAATCTTG 57.492 40.909 0.00 0.00 0.00 3.02
464 468 6.839124 TTATGAAGCATGACAACCAATCTT 57.161 33.333 0.00 0.00 0.00 2.40
465 469 8.701908 ATATTATGAAGCATGACAACCAATCT 57.298 30.769 0.00 0.00 0.00 2.40
466 470 9.754382 AAATATTATGAAGCATGACAACCAATC 57.246 29.630 0.00 0.00 0.00 2.67
468 472 9.368674 CAAAATATTATGAAGCATGACAACCAA 57.631 29.630 0.00 0.00 0.00 3.67
469 473 8.747471 TCAAAATATTATGAAGCATGACAACCA 58.253 29.630 0.00 0.00 0.00 3.67
470 474 9.023967 GTCAAAATATTATGAAGCATGACAACC 57.976 33.333 0.00 0.00 35.82 3.77
471 475 9.571810 TGTCAAAATATTATGAAGCATGACAAC 57.428 29.630 0.00 0.00 40.94 3.32
472 476 9.571810 GTGTCAAAATATTATGAAGCATGACAA 57.428 29.630 0.00 0.00 44.11 3.18
473 477 8.738106 TGTGTCAAAATATTATGAAGCATGACA 58.262 29.630 0.00 0.00 41.44 3.58
474 478 9.229784 CTGTGTCAAAATATTATGAAGCATGAC 57.770 33.333 0.00 0.00 36.19 3.06
475 479 7.916977 GCTGTGTCAAAATATTATGAAGCATGA 59.083 33.333 0.00 0.00 30.81 3.07
476 480 7.168637 GGCTGTGTCAAAATATTATGAAGCATG 59.831 37.037 0.00 0.00 31.61 4.06
477 481 7.147863 TGGCTGTGTCAAAATATTATGAAGCAT 60.148 33.333 0.00 0.00 31.61 3.79
478 482 6.152492 TGGCTGTGTCAAAATATTATGAAGCA 59.848 34.615 0.00 0.00 31.61 3.91
479 483 6.563422 TGGCTGTGTCAAAATATTATGAAGC 58.437 36.000 0.00 0.00 0.00 3.86
480 484 7.765307 ACTGGCTGTGTCAAAATATTATGAAG 58.235 34.615 0.00 0.00 0.00 3.02
481 485 7.392953 TGACTGGCTGTGTCAAAATATTATGAA 59.607 33.333 0.29 0.00 40.89 2.57
482 486 6.883756 TGACTGGCTGTGTCAAAATATTATGA 59.116 34.615 0.29 0.00 40.89 2.15
483 487 7.087409 TGACTGGCTGTGTCAAAATATTATG 57.913 36.000 0.29 0.00 40.89 1.90
493 497 2.346766 ATGTTTGACTGGCTGTGTCA 57.653 45.000 0.29 3.14 41.94 3.58
494 498 3.664107 TCTATGTTTGACTGGCTGTGTC 58.336 45.455 0.29 0.32 35.21 3.67
495 499 3.324846 TCTCTATGTTTGACTGGCTGTGT 59.675 43.478 0.29 0.00 0.00 3.72
496 500 3.930336 TCTCTATGTTTGACTGGCTGTG 58.070 45.455 0.29 0.00 0.00 3.66
497 501 4.040952 ACTTCTCTATGTTTGACTGGCTGT 59.959 41.667 0.00 0.00 0.00 4.40
498 502 4.573900 ACTTCTCTATGTTTGACTGGCTG 58.426 43.478 0.00 0.00 0.00 4.85
499 503 4.284490 TGACTTCTCTATGTTTGACTGGCT 59.716 41.667 0.00 0.00 0.00 4.75
500 504 4.390297 GTGACTTCTCTATGTTTGACTGGC 59.610 45.833 0.00 0.00 0.00 4.85
501 505 4.932200 GGTGACTTCTCTATGTTTGACTGG 59.068 45.833 0.00 0.00 0.00 4.00
502 506 5.788450 AGGTGACTTCTCTATGTTTGACTG 58.212 41.667 0.00 0.00 37.44 3.51
503 507 5.777732 AGAGGTGACTTCTCTATGTTTGACT 59.222 40.000 0.00 0.00 44.43 3.41
504 508 5.866633 CAGAGGTGACTTCTCTATGTTTGAC 59.133 44.000 0.00 0.00 44.43 3.18
505 509 5.567623 GCAGAGGTGACTTCTCTATGTTTGA 60.568 44.000 0.00 0.00 44.43 2.69
506 510 4.629200 GCAGAGGTGACTTCTCTATGTTTG 59.371 45.833 0.00 0.00 44.43 2.93
507 511 4.323104 GGCAGAGGTGACTTCTCTATGTTT 60.323 45.833 0.00 0.00 44.43 2.83
508 512 3.196685 GGCAGAGGTGACTTCTCTATGTT 59.803 47.826 0.00 0.00 44.43 2.71
509 513 2.763448 GGCAGAGGTGACTTCTCTATGT 59.237 50.000 0.00 0.00 44.43 2.29
510 514 3.030291 AGGCAGAGGTGACTTCTCTATG 58.970 50.000 0.00 0.00 40.16 2.23
511 515 3.396685 AGGCAGAGGTGACTTCTCTAT 57.603 47.619 0.00 0.00 40.16 1.98
512 516 2.909504 AGGCAGAGGTGACTTCTCTA 57.090 50.000 0.00 0.00 40.16 2.43
513 517 3.784429 AGGCAGAGGTGACTTCTCT 57.216 52.632 0.00 0.00 40.16 3.10
519 523 2.167398 TACGGCAAGGCAGAGGTGAC 62.167 60.000 0.00 0.00 0.00 3.67
520 524 1.888436 CTACGGCAAGGCAGAGGTGA 61.888 60.000 0.00 0.00 0.00 4.02
521 525 1.448540 CTACGGCAAGGCAGAGGTG 60.449 63.158 0.00 0.00 0.00 4.00
522 526 2.982130 CTACGGCAAGGCAGAGGT 59.018 61.111 0.00 0.00 0.00 3.85
523 527 2.512515 GCTACGGCAAGGCAGAGG 60.513 66.667 0.00 0.00 38.54 3.69
524 528 2.265739 TGCTACGGCAAGGCAGAG 59.734 61.111 0.00 0.00 46.36 3.35
533 537 1.438651 TCATCAGTTGTTGCTACGGC 58.561 50.000 0.00 0.00 39.26 5.68
534 538 3.067106 ACTTCATCAGTTGTTGCTACGG 58.933 45.455 0.00 0.00 27.32 4.02
535 539 4.732285 AACTTCATCAGTTGTTGCTACG 57.268 40.909 0.00 0.00 44.70 3.51
536 540 5.821204 ACAAACTTCATCAGTTGTTGCTAC 58.179 37.500 0.00 0.00 45.77 3.58
537 541 5.822519 AGACAAACTTCATCAGTTGTTGCTA 59.177 36.000 0.00 0.00 45.77 3.49
538 542 4.641989 AGACAAACTTCATCAGTTGTTGCT 59.358 37.500 0.00 0.00 45.77 3.91
539 543 4.925068 AGACAAACTTCATCAGTTGTTGC 58.075 39.130 0.00 0.00 45.77 4.17
540 544 7.816945 AAAAGACAAACTTCATCAGTTGTTG 57.183 32.000 0.00 0.00 45.77 3.33
541 545 9.573133 CTAAAAAGACAAACTTCATCAGTTGTT 57.427 29.630 0.00 0.00 45.77 2.83
542 546 8.956426 TCTAAAAAGACAAACTTCATCAGTTGT 58.044 29.630 0.00 0.00 45.77 3.32
543 547 9.956720 ATCTAAAAAGACAAACTTCATCAGTTG 57.043 29.630 0.00 0.00 45.77 3.16
545 549 8.078596 GCATCTAAAAAGACAAACTTCATCAGT 58.921 33.333 0.00 0.00 37.93 3.41
546 550 7.540055 GGCATCTAAAAAGACAAACTTCATCAG 59.460 37.037 0.00 0.00 37.93 2.90
547 551 7.370383 GGCATCTAAAAAGACAAACTTCATCA 58.630 34.615 0.00 0.00 37.93 3.07
548 552 6.808704 GGGCATCTAAAAAGACAAACTTCATC 59.191 38.462 0.00 0.00 37.93 2.92
549 553 6.295292 GGGGCATCTAAAAAGACAAACTTCAT 60.295 38.462 0.00 0.00 37.93 2.57
550 554 5.010617 GGGGCATCTAAAAAGACAAACTTCA 59.989 40.000 0.00 0.00 37.93 3.02
551 555 5.010617 TGGGGCATCTAAAAAGACAAACTTC 59.989 40.000 0.00 0.00 37.93 3.01
552 556 4.898861 TGGGGCATCTAAAAAGACAAACTT 59.101 37.500 0.00 0.00 40.98 2.66
553 557 4.479158 TGGGGCATCTAAAAAGACAAACT 58.521 39.130 0.00 0.00 0.00 2.66
554 558 4.864704 TGGGGCATCTAAAAAGACAAAC 57.135 40.909 0.00 0.00 0.00 2.93
555 559 5.878406 TTTGGGGCATCTAAAAAGACAAA 57.122 34.783 0.00 0.00 0.00 2.83
556 560 5.878406 TTTTGGGGCATCTAAAAAGACAA 57.122 34.783 0.00 0.00 0.00 3.18
557 561 5.878406 TTTTTGGGGCATCTAAAAAGACA 57.122 34.783 8.46 0.00 31.75 3.41
558 562 5.122239 GCATTTTTGGGGCATCTAAAAAGAC 59.878 40.000 14.73 8.49 36.91 3.01
559 563 5.012975 AGCATTTTTGGGGCATCTAAAAAGA 59.987 36.000 14.73 0.00 36.91 2.52
560 564 5.247862 AGCATTTTTGGGGCATCTAAAAAG 58.752 37.500 14.73 7.35 36.91 2.27
561 565 5.240013 AGCATTTTTGGGGCATCTAAAAA 57.760 34.783 12.84 12.84 37.59 1.94
562 566 4.906747 AGCATTTTTGGGGCATCTAAAA 57.093 36.364 0.00 0.00 0.00 1.52
563 567 4.906747 AAGCATTTTTGGGGCATCTAAA 57.093 36.364 0.00 0.00 0.00 1.85
564 568 4.405358 CCTAAGCATTTTTGGGGCATCTAA 59.595 41.667 0.00 0.00 0.00 2.10
565 569 3.960102 CCTAAGCATTTTTGGGGCATCTA 59.040 43.478 0.00 0.00 0.00 1.98
566 570 2.767960 CCTAAGCATTTTTGGGGCATCT 59.232 45.455 0.00 0.00 0.00 2.90
567 571 2.158914 CCCTAAGCATTTTTGGGGCATC 60.159 50.000 0.00 0.00 41.26 3.91
568 572 1.839354 CCCTAAGCATTTTTGGGGCAT 59.161 47.619 0.00 0.00 41.26 4.40
569 573 1.274712 CCCTAAGCATTTTTGGGGCA 58.725 50.000 0.00 0.00 41.26 5.36
572 576 7.931407 GGATAATTAACCCTAAGCATTTTTGGG 59.069 37.037 0.24 5.11 43.26 4.12
573 577 8.704668 AGGATAATTAACCCTAAGCATTTTTGG 58.295 33.333 8.09 0.00 0.00 3.28
578 582 8.204160 GCAAAAGGATAATTAACCCTAAGCATT 58.796 33.333 8.09 0.00 0.00 3.56
579 583 7.202001 GGCAAAAGGATAATTAACCCTAAGCAT 60.202 37.037 8.09 0.00 0.00 3.79
580 584 6.097696 GGCAAAAGGATAATTAACCCTAAGCA 59.902 38.462 8.09 0.00 0.00 3.91
581 585 6.462487 GGGCAAAAGGATAATTAACCCTAAGC 60.462 42.308 8.09 11.74 31.84 3.09
886 923 2.047151 CTCTCTCTCTCTCGCCGTGC 62.047 65.000 0.00 0.00 0.00 5.34
936 975 3.771160 CTAGCTTCCCACCGCCGT 61.771 66.667 0.00 0.00 0.00 5.68
1153 1193 2.174854 CCCCGATTCTTACCCCATTCTT 59.825 50.000 0.00 0.00 0.00 2.52
1453 1560 4.081697 GCAAATGGGTATTGGTAGTGCTTT 60.082 41.667 0.00 0.00 0.00 3.51
1636 1831 7.976175 GGTCACTTCTTCTCTTTTTGTTTCAAT 59.024 33.333 0.00 0.00 0.00 2.57
1637 1832 7.040062 TGGTCACTTCTTCTCTTTTTGTTTCAA 60.040 33.333 0.00 0.00 0.00 2.69
1638 1833 6.432783 TGGTCACTTCTTCTCTTTTTGTTTCA 59.567 34.615 0.00 0.00 0.00 2.69
1639 1834 6.852664 TGGTCACTTCTTCTCTTTTTGTTTC 58.147 36.000 0.00 0.00 0.00 2.78
1980 2185 7.773489 TCCATGACATTTTGGTCTTTGATTA 57.227 32.000 0.00 0.00 38.61 1.75
2021 2226 0.179119 CCTGGCGTAAACCTCTACCG 60.179 60.000 0.00 0.00 0.00 4.02
2163 2369 2.604139 CCCTAAACACCACAAACCCAT 58.396 47.619 0.00 0.00 0.00 4.00
2188 2394 4.223032 CCATCTATCCTAGCGGTTACCAAT 59.777 45.833 1.13 0.00 0.00 3.16
2189 2395 3.576982 CCATCTATCCTAGCGGTTACCAA 59.423 47.826 1.13 0.00 0.00 3.67
2223 2429 6.023603 TGTATACCTTCCTTCCCTATCCATC 58.976 44.000 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.