Multiple sequence alignment - TraesCS2A01G527900

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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 TraesCS2A01G527900 chr2A 100.000 2300 0 0 1 2300 747146491 747144192 0.000000e+00 4248
1 TraesCS2A01G527900 chr2A 87.112 1094 107 20 520 1592 746978955 746977875 0.000000e+00 1208
2 TraesCS2A01G527900 chr2A 84.919 557 74 3 1708 2257 746977660 746977107 2.580000e-154 555
3 TraesCS2A01G527900 chr2A 98.214 224 4 0 296 519 29804976 29804753 2.140000e-105 392
4 TraesCS2A01G527900 chr2A 89.967 299 26 3 1 296 746979243 746978946 1.290000e-102 383
5 TraesCS2A01G527900 chr2D 94.880 1797 80 7 511 2300 617075098 617073307 0.000000e+00 2798
6 TraesCS2A01G527900 chr2B 93.805 1808 87 13 511 2300 752832115 752830315 0.000000e+00 2695
7 TraesCS2A01G527900 chr5B 81.455 1100 149 32 508 1561 570933375 570934465 0.000000e+00 850
8 TraesCS2A01G527900 chr5B 78.394 884 133 29 774 1602 571121725 571122605 2.620000e-144 521
9 TraesCS2A01G527900 chr5B 77.458 590 98 21 1726 2300 570934758 570935327 1.030000e-83 320
10 TraesCS2A01G527900 chr5A 80.996 1084 145 31 508 1540 584490681 584491754 0.000000e+00 804
11 TraesCS2A01G527900 chr5A 79.443 574 88 19 1726 2288 584507059 584507613 1.670000e-101 379
12 TraesCS2A01G527900 chr5D 81.582 771 101 25 872 1602 464076392 464077161 1.180000e-167 599
13 TraesCS2A01G527900 chr5D 79.417 549 88 13 1726 2267 464077315 464077845 4.670000e-97 364
14 TraesCS2A01G527900 chr5D 86.136 339 41 5 517 849 464075995 464076333 6.040000e-96 361
15 TraesCS2A01G527900 chr3B 84.615 572 78 4 1731 2300 671747470 671746907 5.550000e-156 560
16 TraesCS2A01G527900 chr7A 98.206 223 3 1 297 519 67668964 67669185 2.770000e-104 388
17 TraesCS2A01G527900 chr7A 96.930 228 7 0 294 521 68336992 68337219 1.290000e-102 383
18 TraesCS2A01G527900 chr7A 96.861 223 7 0 297 519 621019192 621019414 7.760000e-100 374
19 TraesCS2A01G527900 chr4A 96.861 223 7 0 297 519 576597313 576597535 7.760000e-100 374
20 TraesCS2A01G527900 chr3A 96.413 223 8 0 297 519 21312796 21313018 3.610000e-98 368
21 TraesCS2A01G527900 chr1A 96.413 223 8 0 297 519 4557627 4557849 3.610000e-98 368
22 TraesCS2A01G527900 chr1A 96.413 223 8 0 297 519 549561593 549561371 3.610000e-98 368
23 TraesCS2A01G527900 chr1A 95.982 224 9 0 296 519 133152297 133152074 4.670000e-97 364


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 TraesCS2A01G527900 chr2A 747144192 747146491 2299 True 4248.000000 4248 100.000000 1 2300 1 chr2A.!!$R2 2299
1 TraesCS2A01G527900 chr2A 746977107 746979243 2136 True 715.333333 1208 87.332667 1 2257 3 chr2A.!!$R3 2256
2 TraesCS2A01G527900 chr2D 617073307 617075098 1791 True 2798.000000 2798 94.880000 511 2300 1 chr2D.!!$R1 1789
3 TraesCS2A01G527900 chr2B 752830315 752832115 1800 True 2695.000000 2695 93.805000 511 2300 1 chr2B.!!$R1 1789
4 TraesCS2A01G527900 chr5B 570933375 570935327 1952 False 585.000000 850 79.456500 508 2300 2 chr5B.!!$F2 1792
5 TraesCS2A01G527900 chr5B 571121725 571122605 880 False 521.000000 521 78.394000 774 1602 1 chr5B.!!$F1 828
6 TraesCS2A01G527900 chr5A 584490681 584491754 1073 False 804.000000 804 80.996000 508 1540 1 chr5A.!!$F1 1032
7 TraesCS2A01G527900 chr5A 584507059 584507613 554 False 379.000000 379 79.443000 1726 2288 1 chr5A.!!$F2 562
8 TraesCS2A01G527900 chr5D 464075995 464077845 1850 False 441.333333 599 82.378333 517 2267 3 chr5D.!!$F1 1750
9 TraesCS2A01G527900 chr3B 671746907 671747470 563 True 560.000000 560 84.615000 1731 2300 1 chr3B.!!$R1 569

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
507 511 0.038166 GGCTGAACCATGGTCCAGAA 59.962 55.0 33.14 9.67 38.86 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1936 2285 0.4546 GCTCGTATGACGGAGAACCA 59.545 55.0 0.0 0.0 42.81 3.67 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
50 51 9.829507 AATTTGACAACAAAACTCATGGAAATA 57.170 25.926 0.00 0.00 46.77 1.40
58 59 6.127647 ACAAAACTCATGGAAATATCGCACAT 60.128 34.615 0.00 0.00 0.00 3.21
59 60 5.679734 AACTCATGGAAATATCGCACATC 57.320 39.130 0.00 0.00 0.00 3.06
148 151 6.220400 AGGATAATATAGGATGGCATGGGTTT 59.780 38.462 3.81 0.00 0.00 3.27
149 152 6.897413 GGATAATATAGGATGGCATGGGTTTT 59.103 38.462 3.81 0.00 0.00 2.43
150 153 7.068716 GGATAATATAGGATGGCATGGGTTTTC 59.931 40.741 3.81 0.00 0.00 2.29
152 155 2.149973 AGGATGGCATGGGTTTTCTC 57.850 50.000 3.81 0.00 0.00 2.87
153 156 0.740737 GGATGGCATGGGTTTTCTCG 59.259 55.000 3.81 0.00 0.00 4.04
155 158 2.301346 GATGGCATGGGTTTTCTCGAT 58.699 47.619 3.81 0.00 0.00 3.59
204 207 4.540824 GGTTGAGACAAGCAGAATGTTTC 58.459 43.478 8.47 0.00 37.46 2.78
261 265 2.053627 CTGTTCGCATTTTTGGCACTC 58.946 47.619 0.00 0.00 0.00 3.51
265 269 1.536766 TCGCATTTTTGGCACTCAGAG 59.463 47.619 0.00 0.00 0.00 3.35
275 279 2.050144 GGCACTCAGAGGGAATGGATA 58.950 52.381 2.91 0.00 0.00 2.59
283 287 0.765510 AGGGAATGGATAACGGCTCC 59.234 55.000 0.00 0.00 0.00 4.70
284 288 0.765510 GGGAATGGATAACGGCTCCT 59.234 55.000 2.48 0.00 33.69 3.69
285 289 1.543429 GGGAATGGATAACGGCTCCTG 60.543 57.143 2.48 0.00 33.69 3.86
286 290 1.141053 GGAATGGATAACGGCTCCTGT 59.859 52.381 2.48 0.00 33.69 4.00
287 291 2.421529 GGAATGGATAACGGCTCCTGTT 60.422 50.000 2.48 0.00 33.69 3.16
288 292 2.622064 ATGGATAACGGCTCCTGTTC 57.378 50.000 0.00 0.00 33.69 3.18
289 293 1.271856 TGGATAACGGCTCCTGTTCA 58.728 50.000 0.00 0.00 33.69 3.18
290 294 1.066430 TGGATAACGGCTCCTGTTCAC 60.066 52.381 0.00 0.00 33.69 3.18
291 295 1.207329 GGATAACGGCTCCTGTTCACT 59.793 52.381 0.00 0.00 0.00 3.41
292 296 2.541556 GATAACGGCTCCTGTTCACTC 58.458 52.381 0.00 0.00 0.00 3.51
293 297 0.606604 TAACGGCTCCTGTTCACTCC 59.393 55.000 0.00 0.00 0.00 3.85
294 298 1.407656 AACGGCTCCTGTTCACTCCA 61.408 55.000 0.00 0.00 0.00 3.86
295 299 1.079543 CGGCTCCTGTTCACTCCAG 60.080 63.158 0.00 0.00 0.00 3.86
296 300 1.376553 GGCTCCTGTTCACTCCAGC 60.377 63.158 0.00 0.00 0.00 4.85
297 301 1.739562 GCTCCTGTTCACTCCAGCG 60.740 63.158 0.00 0.00 0.00 5.18
298 302 1.967535 CTCCTGTTCACTCCAGCGA 59.032 57.895 0.00 0.00 0.00 4.93
299 303 0.318441 CTCCTGTTCACTCCAGCGAA 59.682 55.000 0.00 0.00 0.00 4.70
300 304 0.756294 TCCTGTTCACTCCAGCGAAA 59.244 50.000 0.00 0.00 0.00 3.46
301 305 1.140052 TCCTGTTCACTCCAGCGAAAA 59.860 47.619 0.00 0.00 0.00 2.29
302 306 2.154462 CCTGTTCACTCCAGCGAAAAT 58.846 47.619 0.00 0.00 0.00 1.82
303 307 2.095567 CCTGTTCACTCCAGCGAAAATG 60.096 50.000 0.00 0.00 0.00 2.32
304 308 2.549754 CTGTTCACTCCAGCGAAAATGT 59.450 45.455 0.00 0.00 0.00 2.71
305 309 2.948979 TGTTCACTCCAGCGAAAATGTT 59.051 40.909 0.00 0.00 0.00 2.71
306 310 4.130857 TGTTCACTCCAGCGAAAATGTTA 58.869 39.130 0.00 0.00 0.00 2.41
307 311 4.759693 TGTTCACTCCAGCGAAAATGTTAT 59.240 37.500 0.00 0.00 0.00 1.89
308 312 5.935206 TGTTCACTCCAGCGAAAATGTTATA 59.065 36.000 0.00 0.00 0.00 0.98
309 313 6.128391 TGTTCACTCCAGCGAAAATGTTATAC 60.128 38.462 0.00 0.00 0.00 1.47
310 314 4.565166 TCACTCCAGCGAAAATGTTATACG 59.435 41.667 0.00 0.00 0.00 3.06
311 315 3.869246 ACTCCAGCGAAAATGTTATACGG 59.131 43.478 0.00 0.00 0.00 4.02
312 316 4.116961 CTCCAGCGAAAATGTTATACGGA 58.883 43.478 0.00 0.00 0.00 4.69
313 317 4.505808 TCCAGCGAAAATGTTATACGGAA 58.494 39.130 0.00 0.00 0.00 4.30
314 318 4.330620 TCCAGCGAAAATGTTATACGGAAC 59.669 41.667 0.00 0.00 0.00 3.62
315 319 4.495184 CCAGCGAAAATGTTATACGGAACC 60.495 45.833 0.00 0.00 0.00 3.62
316 320 4.093703 CAGCGAAAATGTTATACGGAACCA 59.906 41.667 0.00 0.00 0.00 3.67
317 321 4.879545 AGCGAAAATGTTATACGGAACCAT 59.120 37.500 0.00 0.00 0.00 3.55
318 322 4.967575 GCGAAAATGTTATACGGAACCATG 59.032 41.667 0.00 0.00 0.00 3.66
319 323 5.507077 CGAAAATGTTATACGGAACCATGG 58.493 41.667 11.19 11.19 0.00 3.66
320 324 5.065474 CGAAAATGTTATACGGAACCATGGT 59.935 40.000 13.00 13.00 0.00 3.55
321 325 6.403855 CGAAAATGTTATACGGAACCATGGTT 60.404 38.462 30.23 30.23 41.54 3.67
330 334 2.641197 AACCATGGTTCTGCCGAAC 58.359 52.632 24.86 12.16 46.93 3.95
336 340 3.471399 GTTCTGCCGAACCTACGC 58.529 61.111 9.67 0.00 42.93 4.42
337 341 1.080025 GTTCTGCCGAACCTACGCT 60.080 57.895 9.67 0.00 42.93 5.07
338 342 1.077089 GTTCTGCCGAACCTACGCTC 61.077 60.000 9.67 0.00 42.93 5.03
339 343 2.537792 TTCTGCCGAACCTACGCTCG 62.538 60.000 0.00 0.00 34.83 5.03
340 344 3.047718 CTGCCGAACCTACGCTCGA 62.048 63.158 0.00 0.00 37.23 4.04
341 345 2.578981 GCCGAACCTACGCTCGAC 60.579 66.667 0.00 0.00 37.23 4.20
342 346 2.872557 CCGAACCTACGCTCGACA 59.127 61.111 0.00 0.00 37.23 4.35
343 347 1.513586 CCGAACCTACGCTCGACAC 60.514 63.158 0.00 0.00 37.23 3.67
344 348 1.513586 CGAACCTACGCTCGACACC 60.514 63.158 0.00 0.00 37.23 4.16
345 349 1.582968 GAACCTACGCTCGACACCA 59.417 57.895 0.00 0.00 0.00 4.17
346 350 0.172803 GAACCTACGCTCGACACCAT 59.827 55.000 0.00 0.00 0.00 3.55
347 351 0.606604 AACCTACGCTCGACACCATT 59.393 50.000 0.00 0.00 0.00 3.16
348 352 1.466856 ACCTACGCTCGACACCATTA 58.533 50.000 0.00 0.00 0.00 1.90
349 353 1.820519 ACCTACGCTCGACACCATTAA 59.179 47.619 0.00 0.00 0.00 1.40
350 354 2.429610 ACCTACGCTCGACACCATTAAT 59.570 45.455 0.00 0.00 0.00 1.40
351 355 3.050619 CCTACGCTCGACACCATTAATC 58.949 50.000 0.00 0.00 0.00 1.75
352 356 2.961526 ACGCTCGACACCATTAATCT 57.038 45.000 0.00 0.00 0.00 2.40
353 357 2.810650 ACGCTCGACACCATTAATCTC 58.189 47.619 0.00 0.00 0.00 2.75
354 358 2.427453 ACGCTCGACACCATTAATCTCT 59.573 45.455 0.00 0.00 0.00 3.10
355 359 2.791560 CGCTCGACACCATTAATCTCTG 59.208 50.000 0.00 0.00 0.00 3.35
356 360 3.126831 GCTCGACACCATTAATCTCTGG 58.873 50.000 0.00 0.00 38.55 3.86
357 361 3.181475 GCTCGACACCATTAATCTCTGGA 60.181 47.826 0.00 0.00 36.35 3.86
358 362 4.363999 CTCGACACCATTAATCTCTGGAC 58.636 47.826 0.00 0.00 36.35 4.02
359 363 3.767131 TCGACACCATTAATCTCTGGACA 59.233 43.478 0.00 0.00 36.35 4.02
360 364 3.865745 CGACACCATTAATCTCTGGACAC 59.134 47.826 0.00 0.00 36.35 3.67
361 365 4.382040 CGACACCATTAATCTCTGGACACT 60.382 45.833 0.00 0.00 36.35 3.55
362 366 5.491982 GACACCATTAATCTCTGGACACTT 58.508 41.667 0.00 0.00 36.35 3.16
363 367 5.880901 ACACCATTAATCTCTGGACACTTT 58.119 37.500 0.00 0.00 36.35 2.66
364 368 6.306987 ACACCATTAATCTCTGGACACTTTT 58.693 36.000 0.00 0.00 36.35 2.27
365 369 6.431234 ACACCATTAATCTCTGGACACTTTTC 59.569 38.462 0.00 0.00 36.35 2.29
366 370 6.430925 CACCATTAATCTCTGGACACTTTTCA 59.569 38.462 0.00 0.00 36.35 2.69
367 371 7.121759 CACCATTAATCTCTGGACACTTTTCAT 59.878 37.037 0.00 0.00 36.35 2.57
368 372 8.328758 ACCATTAATCTCTGGACACTTTTCATA 58.671 33.333 0.00 0.00 36.35 2.15
369 373 9.177608 CCATTAATCTCTGGACACTTTTCATAA 57.822 33.333 0.00 0.00 34.24 1.90
371 375 8.792830 TTAATCTCTGGACACTTTTCATAAGG 57.207 34.615 0.00 0.00 0.00 2.69
372 376 6.627087 ATCTCTGGACACTTTTCATAAGGA 57.373 37.500 0.00 0.00 0.00 3.36
373 377 6.627087 TCTCTGGACACTTTTCATAAGGAT 57.373 37.500 0.00 0.00 0.00 3.24
374 378 6.644347 TCTCTGGACACTTTTCATAAGGATC 58.356 40.000 0.00 0.00 0.00 3.36
375 379 5.745227 TCTGGACACTTTTCATAAGGATCC 58.255 41.667 2.48 2.48 0.00 3.36
376 380 4.513442 TGGACACTTTTCATAAGGATCCG 58.487 43.478 5.98 0.00 0.00 4.18
377 381 4.019681 TGGACACTTTTCATAAGGATCCGT 60.020 41.667 5.98 5.61 0.00 4.69
378 382 4.332819 GGACACTTTTCATAAGGATCCGTG 59.667 45.833 10.81 9.47 0.00 4.94
379 383 3.689649 ACACTTTTCATAAGGATCCGTGC 59.310 43.478 10.81 0.00 0.00 5.34
380 384 3.689161 CACTTTTCATAAGGATCCGTGCA 59.311 43.478 10.81 0.00 0.00 4.57
381 385 4.336433 CACTTTTCATAAGGATCCGTGCAT 59.664 41.667 10.81 0.00 0.00 3.96
382 386 4.336433 ACTTTTCATAAGGATCCGTGCATG 59.664 41.667 10.81 7.24 0.00 4.06
383 387 3.836365 TTCATAAGGATCCGTGCATGA 57.164 42.857 10.81 9.51 0.00 3.07
384 388 4.356405 TTCATAAGGATCCGTGCATGAT 57.644 40.909 10.81 4.27 0.00 2.45
385 389 4.356405 TCATAAGGATCCGTGCATGATT 57.644 40.909 10.81 0.00 0.00 2.57
386 390 4.067192 TCATAAGGATCCGTGCATGATTG 58.933 43.478 10.81 0.04 0.00 2.67
387 391 2.715749 AAGGATCCGTGCATGATTGA 57.284 45.000 7.72 0.00 0.00 2.57
388 392 2.945080 AGGATCCGTGCATGATTGAT 57.055 45.000 7.72 1.33 0.00 2.57
389 393 3.219176 AGGATCCGTGCATGATTGATT 57.781 42.857 7.72 0.00 0.00 2.57
390 394 4.356405 AGGATCCGTGCATGATTGATTA 57.644 40.909 7.72 0.00 0.00 1.75
391 395 4.717877 AGGATCCGTGCATGATTGATTAA 58.282 39.130 7.72 0.00 0.00 1.40
392 396 5.132502 AGGATCCGTGCATGATTGATTAAA 58.867 37.500 7.72 0.00 0.00 1.52
393 397 5.593909 AGGATCCGTGCATGATTGATTAAAA 59.406 36.000 7.72 0.00 0.00 1.52
394 398 6.096705 AGGATCCGTGCATGATTGATTAAAAA 59.903 34.615 7.72 0.00 0.00 1.94
411 415 3.536956 AAAAATGCATGATGGGAGCTG 57.463 42.857 0.00 0.00 0.00 4.24
412 416 2.154567 AAATGCATGATGGGAGCTGT 57.845 45.000 0.00 0.00 0.00 4.40
413 417 2.154567 AATGCATGATGGGAGCTGTT 57.845 45.000 0.00 0.00 0.00 3.16
414 418 2.154567 ATGCATGATGGGAGCTGTTT 57.845 45.000 0.00 0.00 0.00 2.83
415 419 1.179152 TGCATGATGGGAGCTGTTTG 58.821 50.000 0.00 0.00 0.00 2.93
416 420 0.179119 GCATGATGGGAGCTGTTTGC 60.179 55.000 0.00 0.00 43.29 3.68
417 421 1.179152 CATGATGGGAGCTGTTTGCA 58.821 50.000 0.00 0.00 45.94 4.08
418 422 1.754803 CATGATGGGAGCTGTTTGCAT 59.245 47.619 0.00 0.00 45.94 3.96
419 423 2.804986 TGATGGGAGCTGTTTGCATA 57.195 45.000 0.00 0.00 45.94 3.14
420 424 3.301794 TGATGGGAGCTGTTTGCATAT 57.698 42.857 0.00 0.00 45.94 1.78
421 425 3.634504 TGATGGGAGCTGTTTGCATATT 58.365 40.909 0.00 0.00 45.94 1.28
422 426 4.790937 TGATGGGAGCTGTTTGCATATTA 58.209 39.130 0.00 0.00 45.94 0.98
423 427 5.199723 TGATGGGAGCTGTTTGCATATTAA 58.800 37.500 0.00 0.00 45.94 1.40
424 428 5.655974 TGATGGGAGCTGTTTGCATATTAAA 59.344 36.000 0.00 0.00 45.94 1.52
425 429 5.323371 TGGGAGCTGTTTGCATATTAAAC 57.677 39.130 0.00 5.71 45.94 2.01
426 430 4.769488 TGGGAGCTGTTTGCATATTAAACA 59.231 37.500 12.18 12.18 43.50 2.83
427 431 5.244851 TGGGAGCTGTTTGCATATTAAACAA 59.755 36.000 13.24 0.00 44.58 2.83
428 432 6.070881 TGGGAGCTGTTTGCATATTAAACAAT 60.071 34.615 13.24 7.49 44.58 2.71
429 433 6.256321 GGGAGCTGTTTGCATATTAAACAATG 59.744 38.462 13.24 6.77 44.58 2.82
430 434 6.237915 GGAGCTGTTTGCATATTAAACAATGC 60.238 38.462 13.24 13.31 44.58 3.56
436 440 4.911754 GCATATTAAACAATGCGTGACG 57.088 40.909 0.00 0.00 39.15 4.35
437 441 4.339429 GCATATTAAACAATGCGTGACGT 58.661 39.130 6.91 0.00 39.15 4.34
438 442 4.202158 GCATATTAAACAATGCGTGACGTG 59.798 41.667 6.91 0.00 39.15 4.49
439 443 2.672188 TTAAACAATGCGTGACGTGG 57.328 45.000 6.91 0.00 0.00 4.94
440 444 1.867166 TAAACAATGCGTGACGTGGA 58.133 45.000 6.91 0.00 0.00 4.02
441 445 1.234821 AAACAATGCGTGACGTGGAT 58.765 45.000 6.91 0.00 0.00 3.41
442 446 0.796312 AACAATGCGTGACGTGGATC 59.204 50.000 6.91 0.00 0.00 3.36
443 447 1.019278 ACAATGCGTGACGTGGATCC 61.019 55.000 6.91 4.20 0.00 3.36
444 448 1.018752 CAATGCGTGACGTGGATCCA 61.019 55.000 11.44 11.44 0.00 3.41
445 449 1.019278 AATGCGTGACGTGGATCCAC 61.019 55.000 31.59 31.59 43.01 4.02
446 450 2.048597 GCGTGACGTGGATCCACA 60.049 61.111 37.42 20.65 46.47 4.17
447 451 1.447838 GCGTGACGTGGATCCACAT 60.448 57.895 37.42 28.32 46.47 3.21
448 452 1.695893 GCGTGACGTGGATCCACATG 61.696 60.000 37.42 26.68 46.47 3.21
449 453 0.389817 CGTGACGTGGATCCACATGT 60.390 55.000 37.42 29.36 46.47 3.21
450 454 1.135228 CGTGACGTGGATCCACATGTA 60.135 52.381 37.42 21.11 46.47 2.29
451 455 2.540515 GTGACGTGGATCCACATGTAG 58.459 52.381 37.42 25.39 46.47 2.74
452 456 1.134818 TGACGTGGATCCACATGTAGC 60.135 52.381 37.42 21.70 46.47 3.58
453 457 0.901827 ACGTGGATCCACATGTAGCA 59.098 50.000 37.42 1.89 46.47 3.49
454 458 1.134699 ACGTGGATCCACATGTAGCAG 60.135 52.381 37.42 23.48 46.47 4.24
455 459 1.807755 CGTGGATCCACATGTAGCAGG 60.808 57.143 37.42 18.50 46.47 4.85
456 460 1.486310 GTGGATCCACATGTAGCAGGA 59.514 52.381 35.21 0.75 45.53 3.86
457 461 2.105477 GTGGATCCACATGTAGCAGGAT 59.895 50.000 35.21 13.74 45.53 3.24
458 462 2.105306 TGGATCCACATGTAGCAGGATG 59.895 50.000 17.66 0.00 40.80 3.51
459 463 2.105477 GGATCCACATGTAGCAGGATGT 59.895 50.000 17.66 0.00 40.80 3.06
460 464 3.434167 GGATCCACATGTAGCAGGATGTT 60.434 47.826 17.66 0.00 40.80 2.71
461 465 2.989909 TCCACATGTAGCAGGATGTTG 58.010 47.619 0.00 0.00 39.31 3.33
462 466 2.571202 TCCACATGTAGCAGGATGTTGA 59.429 45.455 0.00 0.00 39.31 3.18
463 467 3.008923 TCCACATGTAGCAGGATGTTGAA 59.991 43.478 0.00 0.00 39.31 2.69
464 468 3.949754 CCACATGTAGCAGGATGTTGAAT 59.050 43.478 0.00 0.00 39.31 2.57
465 469 4.036027 CCACATGTAGCAGGATGTTGAATC 59.964 45.833 0.00 0.00 39.31 2.52
466 470 3.873361 ACATGTAGCAGGATGTTGAATCG 59.127 43.478 0.00 0.00 39.31 3.34
467 471 3.610040 TGTAGCAGGATGTTGAATCGT 57.390 42.857 0.00 0.00 39.31 3.73
468 472 4.729227 TGTAGCAGGATGTTGAATCGTA 57.271 40.909 0.00 0.00 39.31 3.43
469 473 4.430007 TGTAGCAGGATGTTGAATCGTAC 58.570 43.478 0.00 0.00 39.31 3.67
470 474 2.540515 AGCAGGATGTTGAATCGTACG 58.459 47.619 9.53 9.53 39.31 3.67
471 475 1.593006 GCAGGATGTTGAATCGTACGG 59.407 52.381 16.52 0.00 39.31 4.02
472 476 1.593006 CAGGATGTTGAATCGTACGGC 59.407 52.381 16.52 6.10 0.00 5.68
473 477 0.575390 GGATGTTGAATCGTACGGCG 59.425 55.000 16.52 4.80 43.01 6.46
474 478 1.274596 GATGTTGAATCGTACGGCGT 58.725 50.000 19.64 19.64 42.13 5.68
475 479 1.254570 GATGTTGAATCGTACGGCGTC 59.745 52.381 19.21 7.68 42.13 5.19
476 480 1.066656 TGTTGAATCGTACGGCGTCG 61.067 55.000 19.21 19.96 42.13 5.12
477 481 0.794229 GTTGAATCGTACGGCGTCGA 60.794 55.000 27.11 27.11 42.13 4.20
478 482 0.794229 TTGAATCGTACGGCGTCGAC 60.794 55.000 27.35 17.32 42.13 4.20
479 483 1.936398 GAATCGTACGGCGTCGACC 60.936 63.158 27.35 20.40 42.13 4.79
480 484 2.582202 GAATCGTACGGCGTCGACCA 62.582 60.000 27.35 9.32 42.13 4.02
481 485 1.996786 AATCGTACGGCGTCGACCAT 61.997 55.000 27.35 17.72 42.13 3.55
482 486 1.159713 ATCGTACGGCGTCGACCATA 61.160 55.000 27.35 12.43 42.13 2.74
483 487 1.368493 CGTACGGCGTCGACCATAG 60.368 63.158 20.03 1.68 40.11 2.23
484 488 1.009222 GTACGGCGTCGACCATAGG 60.009 63.158 20.03 0.00 40.11 2.57
485 489 1.451927 TACGGCGTCGACCATAGGT 60.452 57.895 20.03 3.95 39.44 3.08
486 490 1.031571 TACGGCGTCGACCATAGGTT 61.032 55.000 20.03 0.00 35.25 3.50
487 491 1.588139 CGGCGTCGACCATAGGTTC 60.588 63.158 1.44 0.00 35.25 3.62
488 492 1.588139 GGCGTCGACCATAGGTTCG 60.588 63.158 10.58 0.00 35.25 3.95
489 493 1.588139 GCGTCGACCATAGGTTCGG 60.588 63.158 10.58 0.00 35.25 4.30
490 494 1.588139 CGTCGACCATAGGTTCGGC 60.588 63.158 10.58 0.00 35.25 5.54
491 495 1.814527 GTCGACCATAGGTTCGGCT 59.185 57.895 3.51 0.00 35.25 5.52
492 496 0.527817 GTCGACCATAGGTTCGGCTG 60.528 60.000 3.51 0.00 35.25 4.85
493 497 0.681887 TCGACCATAGGTTCGGCTGA 60.682 55.000 0.00 0.00 35.25 4.26
494 498 0.174845 CGACCATAGGTTCGGCTGAA 59.825 55.000 3.13 3.13 35.25 3.02
502 506 4.713946 TTCGGCTGAACCATGGTC 57.286 55.556 20.07 12.36 39.03 4.02
503 507 1.002624 TTCGGCTGAACCATGGTCC 60.003 57.895 20.07 14.14 39.03 4.46
504 508 1.773856 TTCGGCTGAACCATGGTCCA 61.774 55.000 20.07 11.67 39.03 4.02
505 509 1.746615 CGGCTGAACCATGGTCCAG 60.747 63.158 25.82 25.82 39.03 3.86
506 510 1.685224 GGCTGAACCATGGTCCAGA 59.315 57.895 33.14 9.80 38.86 3.86
507 511 0.038166 GGCTGAACCATGGTCCAGAA 59.962 55.000 33.14 9.67 38.86 3.02
508 512 1.341383 GGCTGAACCATGGTCCAGAAT 60.341 52.381 33.14 10.00 38.86 2.40
509 513 2.019984 GCTGAACCATGGTCCAGAATC 58.980 52.381 33.14 18.88 0.00 2.52
510 514 2.618816 GCTGAACCATGGTCCAGAATCA 60.619 50.000 33.14 22.23 0.00 2.57
511 515 3.012518 CTGAACCATGGTCCAGAATCAC 58.987 50.000 25.99 5.81 0.00 3.06
512 516 2.009774 GAACCATGGTCCAGAATCACG 58.990 52.381 20.07 0.00 0.00 4.35
513 517 0.392998 ACCATGGTCCAGAATCACGC 60.393 55.000 13.00 0.00 0.00 5.34
514 518 1.097547 CCATGGTCCAGAATCACGCC 61.098 60.000 2.57 0.00 0.00 5.68
515 519 0.107508 CATGGTCCAGAATCACGCCT 60.108 55.000 0.00 0.00 0.00 5.52
518 522 0.179097 GGTCCAGAATCACGCCTCTC 60.179 60.000 0.00 0.00 0.00 3.20
532 536 1.827681 CCTCTCTTCACTCCAGTCGA 58.172 55.000 0.00 0.00 0.00 4.20
549 553 5.755375 CCAGTCGACTGCTATGTCATAAAAT 59.245 40.000 35.09 0.00 42.47 1.82
571 578 1.283321 GGAGGGCTCCTTCTTCAACAT 59.717 52.381 0.00 0.00 46.16 2.71
685 698 2.151202 CAGTTGCCACCAAATACGAGT 58.849 47.619 0.00 0.00 31.68 4.18
732 745 1.419381 TTGGGCCAGCGATAGTATCA 58.581 50.000 6.23 0.00 39.35 2.15
817 830 1.118965 TGGCGTGAACTCCCTTGAGA 61.119 55.000 0.00 0.00 41.42 3.27
851 864 2.316108 TCCAGTTCTGCTGTAGTGTGA 58.684 47.619 4.73 0.29 43.55 3.58
886 935 1.302192 GCAGCCGGTGGTGAACTTA 60.302 57.895 1.90 0.00 42.66 2.24
888 937 1.821216 CAGCCGGTGGTGAACTTATT 58.179 50.000 1.90 0.00 42.66 1.40
965 1015 2.645802 GGCACCGGTGTAATTTATGGA 58.354 47.619 33.92 0.00 0.00 3.41
1030 1080 2.191375 GGCCTGAGCATGCTAGCA 59.809 61.111 28.09 21.85 42.56 3.49
1122 1202 1.033746 CATCTTTGCTGCACCGGGAT 61.034 55.000 6.32 1.01 0.00 3.85
1164 1244 3.499406 TGGTCATCCCAAGCTGCT 58.501 55.556 0.00 0.00 41.50 4.24
1349 1451 3.258622 CCTGAGTAAGAACTTCCTCCGTT 59.741 47.826 5.06 0.00 35.56 4.44
1388 1492 5.937111 ACCTCCTGTATGTTGTTTTGTAGT 58.063 37.500 0.00 0.00 0.00 2.73
1389 1493 7.069877 ACCTCCTGTATGTTGTTTTGTAGTA 57.930 36.000 0.00 0.00 0.00 1.82
1390 1494 7.159372 ACCTCCTGTATGTTGTTTTGTAGTAG 58.841 38.462 0.00 0.00 0.00 2.57
1391 1495 6.092259 CCTCCTGTATGTTGTTTTGTAGTAGC 59.908 42.308 0.00 0.00 0.00 3.58
1477 1601 4.323028 CCTGACACTGACATGTATCAACCT 60.323 45.833 0.00 0.00 31.24 3.50
1514 1638 3.262915 AGAAGCATATACCAGCATCCCTC 59.737 47.826 0.00 0.00 0.00 4.30
1637 1877 2.100197 CTGACCGGGTCATTCTACAGA 58.900 52.381 28.85 4.17 41.94 3.41
1671 1923 7.547697 TCCATCATCCCTTGTATATTTCGTA 57.452 36.000 0.00 0.00 0.00 3.43
1695 1952 6.607004 TTTGTTTTCACCCTTGTTTCCTTA 57.393 33.333 0.00 0.00 0.00 2.69
1762 2096 9.424319 GAACAAGAGATAAACAGTTGACTATCA 57.576 33.333 6.34 0.00 0.00 2.15
1848 2197 5.483937 AGGGGCGACATGATATTACTGATAA 59.516 40.000 0.00 0.00 0.00 1.75
1852 2201 7.169982 GGGCGACATGATATTACTGATAATAGC 59.830 40.741 0.00 0.00 39.24 2.97
1875 2224 5.405063 AGGTATACCTGCTCTCCTTTCTA 57.595 43.478 24.01 0.00 46.55 2.10
1882 2231 1.555075 TGCTCTCCTTTCTATTGCGGT 59.445 47.619 0.00 0.00 0.00 5.68
1936 2285 1.852157 AAGGCGATCCATGGTGGTGT 61.852 55.000 12.58 0.00 39.03 4.16
1957 2306 1.134560 GGTTCTCCGTCATACGAGCTT 59.865 52.381 0.15 0.00 46.05 3.74
1960 2309 1.945394 TCTCCGTCATACGAGCTTACC 59.055 52.381 0.15 0.00 46.05 2.85
2074 2423 1.901591 CCAACTTGGACATGAGCAGT 58.098 50.000 0.92 0.00 40.96 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 9.237187 TGTCAAATTATTTTGCATACCAGTAGA 57.763 29.630 5.41 0.00 41.66 2.59
7 8 9.853555 TTGTCAAATTATTTTGCATACCAGTAG 57.146 29.630 5.41 0.00 41.66 2.57
36 37 5.589855 TGATGTGCGATATTTCCATGAGTTT 59.410 36.000 0.00 0.00 0.00 2.66
42 43 8.260114 TCATATACTGATGTGCGATATTTCCAT 58.740 33.333 0.00 0.00 0.00 3.41
50 51 6.207614 AGTGTACTCATATACTGATGTGCGAT 59.792 38.462 0.00 0.00 31.98 4.58
102 105 5.131475 TCCTGTTAACTCCCAGTTTTGTAGT 59.869 40.000 7.22 0.00 39.51 2.73
112 115 9.046846 CATCCTATATTATCCTGTTAACTCCCA 57.953 37.037 7.22 0.00 0.00 4.37
181 184 2.508526 ACATTCTGCTTGTCTCAACCC 58.491 47.619 0.00 0.00 0.00 4.11
204 207 2.666619 GCATTCAGCTCACAAAGGAACG 60.667 50.000 0.00 0.00 41.15 3.95
237 240 2.159184 TGCCAAAAATGCGAACAGAACA 60.159 40.909 0.00 0.00 0.00 3.18
243 247 2.053627 CTGAGTGCCAAAAATGCGAAC 58.946 47.619 0.00 0.00 0.00 3.95
261 265 1.417890 AGCCGTTATCCATTCCCTCTG 59.582 52.381 0.00 0.00 0.00 3.35
265 269 0.765510 AGGAGCCGTTATCCATTCCC 59.234 55.000 1.25 0.00 39.47 3.97
275 279 1.371558 GGAGTGAACAGGAGCCGTT 59.628 57.895 0.00 0.00 0.00 4.44
283 287 2.549754 ACATTTTCGCTGGAGTGAACAG 59.450 45.455 2.09 0.00 43.34 3.16
284 288 2.571212 ACATTTTCGCTGGAGTGAACA 58.429 42.857 2.09 0.00 43.34 3.18
285 289 3.626028 AACATTTTCGCTGGAGTGAAC 57.374 42.857 2.09 0.00 43.34 3.18
286 290 5.062934 CGTATAACATTTTCGCTGGAGTGAA 59.937 40.000 0.00 0.00 42.14 3.18
287 291 4.565166 CGTATAACATTTTCGCTGGAGTGA 59.435 41.667 0.00 0.00 0.00 3.41
288 292 4.260212 CCGTATAACATTTTCGCTGGAGTG 60.260 45.833 0.00 0.00 0.00 3.51
289 293 3.869246 CCGTATAACATTTTCGCTGGAGT 59.131 43.478 0.00 0.00 0.00 3.85
290 294 4.116961 TCCGTATAACATTTTCGCTGGAG 58.883 43.478 0.00 0.00 0.00 3.86
291 295 4.126208 TCCGTATAACATTTTCGCTGGA 57.874 40.909 0.00 0.00 0.00 3.86
292 296 4.495184 GGTTCCGTATAACATTTTCGCTGG 60.495 45.833 0.00 0.00 0.00 4.85
293 297 4.093703 TGGTTCCGTATAACATTTTCGCTG 59.906 41.667 0.00 0.00 0.00 5.18
294 298 4.255301 TGGTTCCGTATAACATTTTCGCT 58.745 39.130 0.00 0.00 0.00 4.93
295 299 4.603231 TGGTTCCGTATAACATTTTCGC 57.397 40.909 0.00 0.00 0.00 4.70
296 300 5.065474 ACCATGGTTCCGTATAACATTTTCG 59.935 40.000 13.00 0.00 0.00 3.46
297 301 6.445357 ACCATGGTTCCGTATAACATTTTC 57.555 37.500 13.00 0.00 0.00 2.29
298 302 6.844097 AACCATGGTTCCGTATAACATTTT 57.156 33.333 24.86 0.00 32.09 1.82
299 303 6.445357 GAACCATGGTTCCGTATAACATTT 57.555 37.500 37.55 10.82 46.21 2.32
320 324 1.214589 GAGCGTAGGTTCGGCAGAA 59.785 57.895 0.00 0.00 39.88 3.02
321 325 2.882876 GAGCGTAGGTTCGGCAGA 59.117 61.111 0.00 0.00 39.88 4.26
322 326 2.579787 CGAGCGTAGGTTCGGCAG 60.580 66.667 13.05 0.00 42.33 4.85
323 327 3.057548 TCGAGCGTAGGTTCGGCA 61.058 61.111 19.24 0.95 45.52 5.69
324 328 2.578981 GTCGAGCGTAGGTTCGGC 60.579 66.667 19.24 15.13 45.52 5.54
325 329 1.513586 GTGTCGAGCGTAGGTTCGG 60.514 63.158 19.24 3.89 45.52 4.30
326 330 1.513586 GGTGTCGAGCGTAGGTTCG 60.514 63.158 14.47 14.47 46.64 3.95
327 331 0.172803 ATGGTGTCGAGCGTAGGTTC 59.827 55.000 0.00 0.00 39.88 3.62
328 332 0.606604 AATGGTGTCGAGCGTAGGTT 59.393 50.000 0.00 0.00 39.88 3.50
329 333 1.466856 TAATGGTGTCGAGCGTAGGT 58.533 50.000 0.00 0.00 46.54 3.08
330 334 2.572191 TTAATGGTGTCGAGCGTAGG 57.428 50.000 0.00 0.00 0.00 3.18
331 335 3.966154 AGATTAATGGTGTCGAGCGTAG 58.034 45.455 0.00 0.00 0.00 3.51
332 336 3.630769 AGAGATTAATGGTGTCGAGCGTA 59.369 43.478 0.00 0.00 0.00 4.42
333 337 2.427453 AGAGATTAATGGTGTCGAGCGT 59.573 45.455 0.00 0.00 0.00 5.07
334 338 2.791560 CAGAGATTAATGGTGTCGAGCG 59.208 50.000 0.00 0.00 0.00 5.03
335 339 3.126831 CCAGAGATTAATGGTGTCGAGC 58.873 50.000 0.00 0.00 0.00 5.03
336 340 4.142160 TGTCCAGAGATTAATGGTGTCGAG 60.142 45.833 0.00 0.00 37.84 4.04
337 341 3.767131 TGTCCAGAGATTAATGGTGTCGA 59.233 43.478 0.00 0.00 37.84 4.20
338 342 3.865745 GTGTCCAGAGATTAATGGTGTCG 59.134 47.826 0.00 0.00 37.84 4.35
339 343 5.091261 AGTGTCCAGAGATTAATGGTGTC 57.909 43.478 0.00 0.00 37.84 3.67
340 344 5.505181 AAGTGTCCAGAGATTAATGGTGT 57.495 39.130 0.00 0.00 37.84 4.16
341 345 6.430925 TGAAAAGTGTCCAGAGATTAATGGTG 59.569 38.462 0.00 0.00 37.84 4.17
342 346 6.542821 TGAAAAGTGTCCAGAGATTAATGGT 58.457 36.000 0.00 0.00 37.84 3.55
343 347 7.636150 ATGAAAAGTGTCCAGAGATTAATGG 57.364 36.000 0.00 0.00 37.97 3.16
345 349 9.401058 CCTTATGAAAAGTGTCCAGAGATTAAT 57.599 33.333 0.00 0.00 0.00 1.40
346 350 8.602424 TCCTTATGAAAAGTGTCCAGAGATTAA 58.398 33.333 0.00 0.00 0.00 1.40
347 351 8.146053 TCCTTATGAAAAGTGTCCAGAGATTA 57.854 34.615 0.00 0.00 0.00 1.75
348 352 7.020827 TCCTTATGAAAAGTGTCCAGAGATT 57.979 36.000 0.00 0.00 0.00 2.40
349 353 6.627087 TCCTTATGAAAAGTGTCCAGAGAT 57.373 37.500 0.00 0.00 0.00 2.75
350 354 6.352222 GGATCCTTATGAAAAGTGTCCAGAGA 60.352 42.308 3.84 0.00 0.00 3.10
351 355 5.819901 GGATCCTTATGAAAAGTGTCCAGAG 59.180 44.000 3.84 0.00 0.00 3.35
352 356 5.626809 CGGATCCTTATGAAAAGTGTCCAGA 60.627 44.000 10.75 0.00 0.00 3.86
353 357 4.572389 CGGATCCTTATGAAAAGTGTCCAG 59.428 45.833 10.75 0.00 0.00 3.86
354 358 4.019681 ACGGATCCTTATGAAAAGTGTCCA 60.020 41.667 10.75 0.00 0.00 4.02
355 359 4.332819 CACGGATCCTTATGAAAAGTGTCC 59.667 45.833 10.75 0.00 0.00 4.02
356 360 4.201822 GCACGGATCCTTATGAAAAGTGTC 60.202 45.833 10.75 0.71 31.39 3.67
357 361 3.689649 GCACGGATCCTTATGAAAAGTGT 59.310 43.478 10.75 0.00 31.39 3.55
358 362 3.689161 TGCACGGATCCTTATGAAAAGTG 59.311 43.478 10.75 8.13 0.00 3.16
359 363 3.950397 TGCACGGATCCTTATGAAAAGT 58.050 40.909 10.75 0.00 0.00 2.66
360 364 4.576053 TCATGCACGGATCCTTATGAAAAG 59.424 41.667 10.75 0.00 0.00 2.27
361 365 4.522114 TCATGCACGGATCCTTATGAAAA 58.478 39.130 10.75 0.00 0.00 2.29
362 366 4.149511 TCATGCACGGATCCTTATGAAA 57.850 40.909 10.75 0.00 0.00 2.69
363 367 3.836365 TCATGCACGGATCCTTATGAA 57.164 42.857 10.75 0.08 0.00 2.57
364 368 4.067192 CAATCATGCACGGATCCTTATGA 58.933 43.478 10.75 13.51 0.00 2.15
365 369 4.067192 TCAATCATGCACGGATCCTTATG 58.933 43.478 10.75 6.67 0.00 1.90
366 370 4.356405 TCAATCATGCACGGATCCTTAT 57.644 40.909 10.75 0.00 0.00 1.73
367 371 3.836365 TCAATCATGCACGGATCCTTA 57.164 42.857 10.75 0.00 0.00 2.69
368 372 2.715749 TCAATCATGCACGGATCCTT 57.284 45.000 10.75 0.00 0.00 3.36
369 373 2.945080 ATCAATCATGCACGGATCCT 57.055 45.000 10.75 0.00 0.00 3.24
370 374 5.437289 TTTAATCAATCATGCACGGATCC 57.563 39.130 0.00 0.00 0.00 3.36
391 395 2.835764 ACAGCTCCCATCATGCATTTTT 59.164 40.909 0.00 0.00 0.00 1.94
392 396 2.463752 ACAGCTCCCATCATGCATTTT 58.536 42.857 0.00 0.00 0.00 1.82
393 397 2.154567 ACAGCTCCCATCATGCATTT 57.845 45.000 0.00 0.00 0.00 2.32
394 398 2.154567 AACAGCTCCCATCATGCATT 57.845 45.000 0.00 0.00 0.00 3.56
395 399 1.754803 CAAACAGCTCCCATCATGCAT 59.245 47.619 0.00 0.00 0.00 3.96
396 400 1.179152 CAAACAGCTCCCATCATGCA 58.821 50.000 0.00 0.00 0.00 3.96
397 401 0.179119 GCAAACAGCTCCCATCATGC 60.179 55.000 0.00 0.00 41.15 4.06
398 402 1.179152 TGCAAACAGCTCCCATCATG 58.821 50.000 0.00 0.00 45.94 3.07
399 403 2.154567 ATGCAAACAGCTCCCATCAT 57.845 45.000 0.00 0.00 45.94 2.45
400 404 2.804986 TATGCAAACAGCTCCCATCA 57.195 45.000 0.00 0.00 45.94 3.07
401 405 5.772825 TTAATATGCAAACAGCTCCCATC 57.227 39.130 0.00 0.00 45.94 3.51
402 406 5.421693 TGTTTAATATGCAAACAGCTCCCAT 59.578 36.000 10.38 0.00 45.94 4.00
403 407 4.769488 TGTTTAATATGCAAACAGCTCCCA 59.231 37.500 10.38 0.00 45.94 4.37
404 408 5.323371 TGTTTAATATGCAAACAGCTCCC 57.677 39.130 10.38 0.00 45.94 4.30
405 409 6.237915 GCATTGTTTAATATGCAAACAGCTCC 60.238 38.462 12.91 4.19 44.30 4.70
406 410 6.506827 CGCATTGTTTAATATGCAAACAGCTC 60.507 38.462 16.76 10.14 45.73 4.09
407 411 5.289193 CGCATTGTTTAATATGCAAACAGCT 59.711 36.000 16.76 8.66 45.73 4.24
408 412 5.062058 ACGCATTGTTTAATATGCAAACAGC 59.938 36.000 12.91 12.79 45.73 4.40
409 413 6.307558 TCACGCATTGTTTAATATGCAAACAG 59.692 34.615 12.91 6.88 45.73 3.16
410 414 6.088749 GTCACGCATTGTTTAATATGCAAACA 59.911 34.615 10.38 10.38 45.73 2.83
411 415 6.457676 GTCACGCATTGTTTAATATGCAAAC 58.542 36.000 14.32 6.34 45.73 2.93
412 416 5.284897 CGTCACGCATTGTTTAATATGCAAA 59.715 36.000 14.32 0.00 45.73 3.68
413 417 4.790651 CGTCACGCATTGTTTAATATGCAA 59.209 37.500 14.32 2.97 45.73 4.08
414 418 4.142795 ACGTCACGCATTGTTTAATATGCA 60.143 37.500 0.00 0.00 45.73 3.96
415 419 4.202158 CACGTCACGCATTGTTTAATATGC 59.798 41.667 0.00 0.00 42.82 3.14
416 420 4.728131 CCACGTCACGCATTGTTTAATATG 59.272 41.667 0.00 0.00 0.00 1.78
417 421 4.632251 TCCACGTCACGCATTGTTTAATAT 59.368 37.500 0.00 0.00 0.00 1.28
418 422 3.995048 TCCACGTCACGCATTGTTTAATA 59.005 39.130 0.00 0.00 0.00 0.98
419 423 2.809119 TCCACGTCACGCATTGTTTAAT 59.191 40.909 0.00 0.00 0.00 1.40
420 424 2.210961 TCCACGTCACGCATTGTTTAA 58.789 42.857 0.00 0.00 0.00 1.52
421 425 1.867166 TCCACGTCACGCATTGTTTA 58.133 45.000 0.00 0.00 0.00 2.01
422 426 1.196808 GATCCACGTCACGCATTGTTT 59.803 47.619 0.00 0.00 0.00 2.83
423 427 0.796312 GATCCACGTCACGCATTGTT 59.204 50.000 0.00 0.00 0.00 2.83
424 428 1.019278 GGATCCACGTCACGCATTGT 61.019 55.000 6.95 0.00 0.00 2.71
425 429 1.018752 TGGATCCACGTCACGCATTG 61.019 55.000 11.44 0.00 0.00 2.82
426 430 1.019278 GTGGATCCACGTCACGCATT 61.019 55.000 28.52 0.00 37.19 3.56
427 431 1.447838 GTGGATCCACGTCACGCAT 60.448 57.895 28.52 0.00 37.19 4.73
428 432 2.048597 GTGGATCCACGTCACGCA 60.049 61.111 28.52 0.00 37.19 5.24
436 440 1.486310 TCCTGCTACATGTGGATCCAC 59.514 52.381 33.97 33.97 46.33 4.02
437 441 1.878211 TCCTGCTACATGTGGATCCA 58.122 50.000 11.44 11.44 0.00 3.41
438 442 2.105477 ACATCCTGCTACATGTGGATCC 59.895 50.000 14.15 4.20 37.22 3.36
439 443 3.482156 ACATCCTGCTACATGTGGATC 57.518 47.619 14.15 0.00 37.22 3.36
440 444 3.200605 TCAACATCCTGCTACATGTGGAT 59.799 43.478 14.15 11.31 39.64 3.41
441 445 2.571202 TCAACATCCTGCTACATGTGGA 59.429 45.455 14.15 9.29 33.38 4.02
442 446 2.989909 TCAACATCCTGCTACATGTGG 58.010 47.619 9.11 6.75 33.38 4.17
443 447 4.260497 CGATTCAACATCCTGCTACATGTG 60.260 45.833 9.11 0.00 33.38 3.21
444 448 3.873361 CGATTCAACATCCTGCTACATGT 59.127 43.478 2.69 2.69 34.58 3.21
445 449 3.873361 ACGATTCAACATCCTGCTACATG 59.127 43.478 0.00 0.00 0.00 3.21
446 450 4.142609 ACGATTCAACATCCTGCTACAT 57.857 40.909 0.00 0.00 0.00 2.29
447 451 3.610040 ACGATTCAACATCCTGCTACA 57.390 42.857 0.00 0.00 0.00 2.74
448 452 3.486108 CGTACGATTCAACATCCTGCTAC 59.514 47.826 10.44 0.00 0.00 3.58
449 453 3.490249 CCGTACGATTCAACATCCTGCTA 60.490 47.826 18.76 0.00 0.00 3.49
450 454 2.540515 CGTACGATTCAACATCCTGCT 58.459 47.619 10.44 0.00 0.00 4.24
451 455 1.593006 CCGTACGATTCAACATCCTGC 59.407 52.381 18.76 0.00 0.00 4.85
452 456 1.593006 GCCGTACGATTCAACATCCTG 59.407 52.381 18.76 0.00 0.00 3.86
453 457 1.935933 GCCGTACGATTCAACATCCT 58.064 50.000 18.76 0.00 0.00 3.24
466 470 1.009222 CCTATGGTCGACGCCGTAC 60.009 63.158 9.92 0.00 37.05 3.67
467 471 1.031571 AACCTATGGTCGACGCCGTA 61.032 55.000 9.92 1.57 33.12 4.02
468 472 2.275547 GAACCTATGGTCGACGCCGT 62.276 60.000 9.92 0.24 33.12 5.68
469 473 1.588139 GAACCTATGGTCGACGCCG 60.588 63.158 9.92 0.00 33.12 6.46
470 474 1.588139 CGAACCTATGGTCGACGCC 60.588 63.158 9.92 0.00 33.12 5.68
471 475 1.588139 CCGAACCTATGGTCGACGC 60.588 63.158 9.92 3.20 33.12 5.19
472 476 1.588139 GCCGAACCTATGGTCGACG 60.588 63.158 9.92 0.00 33.12 5.12
473 477 0.527817 CAGCCGAACCTATGGTCGAC 60.528 60.000 7.13 7.13 33.12 4.20
474 478 0.681887 TCAGCCGAACCTATGGTCGA 60.682 55.000 7.05 0.00 33.12 4.20
475 479 0.174845 TTCAGCCGAACCTATGGTCG 59.825 55.000 0.00 0.00 33.12 4.79
476 480 1.653151 GTTCAGCCGAACCTATGGTC 58.347 55.000 1.04 0.00 44.92 4.02
477 481 3.855159 GTTCAGCCGAACCTATGGT 57.145 52.632 1.04 0.00 44.92 3.55
485 489 1.002624 GGACCATGGTTCAGCCGAA 60.003 57.895 20.85 0.00 41.21 4.30
486 490 2.184020 CTGGACCATGGTTCAGCCGA 62.184 60.000 35.13 12.08 43.78 5.54
487 491 1.746615 CTGGACCATGGTTCAGCCG 60.747 63.158 35.13 17.28 43.78 5.52
488 492 4.326255 CTGGACCATGGTTCAGCC 57.674 61.111 35.13 23.89 43.78 4.85
491 495 2.615240 CGTGATTCTGGACCATGGTTCA 60.615 50.000 24.84 24.84 31.93 3.18
492 496 2.009774 CGTGATTCTGGACCATGGTTC 58.990 52.381 20.85 18.93 0.00 3.62
493 497 1.950484 GCGTGATTCTGGACCATGGTT 60.950 52.381 20.85 0.38 0.00 3.67
494 498 0.392998 GCGTGATTCTGGACCATGGT 60.393 55.000 19.89 19.89 0.00 3.55
495 499 1.097547 GGCGTGATTCTGGACCATGG 61.098 60.000 11.19 11.19 0.00 3.66
496 500 0.107508 AGGCGTGATTCTGGACCATG 60.108 55.000 0.00 0.00 0.00 3.66
497 501 0.179000 GAGGCGTGATTCTGGACCAT 59.821 55.000 0.00 0.00 0.00 3.55
498 502 0.904865 AGAGGCGTGATTCTGGACCA 60.905 55.000 0.00 0.00 0.00 4.02
499 503 0.179097 GAGAGGCGTGATTCTGGACC 60.179 60.000 0.00 0.00 0.00 4.46
500 504 0.820871 AGAGAGGCGTGATTCTGGAC 59.179 55.000 0.00 0.00 0.00 4.02
501 505 1.478510 GAAGAGAGGCGTGATTCTGGA 59.521 52.381 0.00 0.00 0.00 3.86
502 506 1.205655 TGAAGAGAGGCGTGATTCTGG 59.794 52.381 0.00 0.00 0.00 3.86
503 507 2.094286 AGTGAAGAGAGGCGTGATTCTG 60.094 50.000 0.00 0.00 0.00 3.02
504 508 2.165437 GAGTGAAGAGAGGCGTGATTCT 59.835 50.000 0.00 0.00 0.00 2.40
505 509 2.535331 GAGTGAAGAGAGGCGTGATTC 58.465 52.381 0.00 0.00 0.00 2.52
506 510 1.205893 GGAGTGAAGAGAGGCGTGATT 59.794 52.381 0.00 0.00 0.00 2.57
507 511 0.820871 GGAGTGAAGAGAGGCGTGAT 59.179 55.000 0.00 0.00 0.00 3.06
508 512 0.539669 TGGAGTGAAGAGAGGCGTGA 60.540 55.000 0.00 0.00 0.00 4.35
509 513 0.108898 CTGGAGTGAAGAGAGGCGTG 60.109 60.000 0.00 0.00 0.00 5.34
510 514 0.540830 ACTGGAGTGAAGAGAGGCGT 60.541 55.000 0.00 0.00 0.00 5.68
511 515 0.172352 GACTGGAGTGAAGAGAGGCG 59.828 60.000 0.00 0.00 0.00 5.52
512 516 0.172352 CGACTGGAGTGAAGAGAGGC 59.828 60.000 0.00 0.00 0.00 4.70
513 517 1.470890 GTCGACTGGAGTGAAGAGAGG 59.529 57.143 8.70 0.00 0.00 3.69
514 518 2.432444 AGTCGACTGGAGTGAAGAGAG 58.568 52.381 19.30 0.00 0.00 3.20
515 519 2.570415 AGTCGACTGGAGTGAAGAGA 57.430 50.000 19.30 0.00 0.00 3.10
532 536 5.829924 CCCTCCAATTTTATGACATAGCAGT 59.170 40.000 0.00 0.00 0.00 4.40
571 578 3.557054 GGATATTATGGCTCCAAGCACGA 60.557 47.826 0.86 0.00 44.75 4.35
685 698 2.888414 GCCTTAGCAACAAAACCCACTA 59.112 45.455 0.00 0.00 39.53 2.74
732 745 2.046120 GCTTCTGCCTCAGCTGCT 60.046 61.111 9.47 0.00 40.80 4.24
817 830 2.887151 ACTGGAATGCTTGTAGGCTT 57.113 45.000 0.00 0.00 0.00 4.35
851 864 1.070758 CTGCTGACCACCACTGTACTT 59.929 52.381 0.00 0.00 0.00 2.24
886 935 8.841300 CACAATGATTCAGAATCTCATCTCAAT 58.159 33.333 21.44 4.08 38.72 2.57
888 937 6.260271 GCACAATGATTCAGAATCTCATCTCA 59.740 38.462 21.44 4.03 38.72 3.27
965 1015 0.542467 TGGCCCATGCAATGTCAACT 60.542 50.000 0.00 0.00 44.81 3.16
1058 1135 2.223340 CGGCTTGATTCCAGCAATACAC 60.223 50.000 11.44 0.00 0.00 2.90
1122 1202 0.756294 TCTTCAGAAACTGTCCGCCA 59.244 50.000 0.00 0.00 32.61 5.69
1164 1244 0.320683 CCGACATGACCACAGCTTCA 60.321 55.000 0.00 0.00 0.00 3.02
1349 1451 1.669760 GGTTTGCACCGATCCACGA 60.670 57.895 0.00 0.00 45.77 4.35
1388 1492 1.763968 ACGATGCAGTCACCTAGCTA 58.236 50.000 0.00 0.00 0.00 3.32
1389 1493 0.898320 AACGATGCAGTCACCTAGCT 59.102 50.000 0.00 0.00 0.00 3.32
1390 1494 1.002366 CAACGATGCAGTCACCTAGC 58.998 55.000 0.00 0.00 0.00 3.42
1391 1495 2.370281 ACAACGATGCAGTCACCTAG 57.630 50.000 0.00 0.00 0.00 3.02
1477 1601 1.815408 GCTTCTGTGACTTGGCAAGGA 60.815 52.381 29.26 14.62 0.00 3.36
1514 1638 5.403512 TCCTCCTGGTTAGTATAATCAGGG 58.596 45.833 22.59 15.30 43.66 4.45
1561 1691 4.571984 TGTCATCATAAAGAGGATGTTGCG 59.428 41.667 0.00 0.00 43.04 4.85
1637 1877 9.887862 ATACAAGGGATGATGGAATAAAAGAAT 57.112 29.630 0.00 0.00 0.00 2.40
1671 1923 5.692115 AGGAAACAAGGGTGAAAACAAAT 57.308 34.783 0.00 0.00 0.00 2.32
1762 2096 1.348008 ACCACCATGGAGGCATCGAT 61.348 55.000 26.47 4.54 40.96 3.59
1854 2203 6.459923 CAATAGAAAGGAGAGCAGGTATACC 58.540 44.000 14.54 14.54 0.00 2.73
1859 2208 2.419297 CGCAATAGAAAGGAGAGCAGGT 60.419 50.000 0.00 0.00 0.00 4.00
1865 2214 3.706594 AGATGACCGCAATAGAAAGGAGA 59.293 43.478 0.00 0.00 0.00 3.71
1875 2224 1.740380 CGTCTTGGAGATGACCGCAAT 60.740 52.381 0.00 0.00 33.07 3.56
1882 2231 1.924731 ACTGGACGTCTTGGAGATGA 58.075 50.000 16.46 0.00 34.89 2.92
1936 2285 0.454600 GCTCGTATGACGGAGAACCA 59.545 55.000 0.00 0.00 42.81 3.67
1957 2306 1.810031 GCATTGCTATCGGTGCAGGTA 60.810 52.381 0.16 0.00 41.71 3.08
1960 2309 1.528586 GTAGCATTGCTATCGGTGCAG 59.471 52.381 20.63 0.00 43.30 4.41
2074 2423 2.427245 GCGAGGAAGAGGGCAGCTA 61.427 63.158 0.00 0.00 0.00 3.32
2171 2523 3.492313 GCGAACAATTCACAAAGCTAGG 58.508 45.455 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.