Multiple sequence alignment - TraesCS2A01G576100

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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 TraesCS2A01G576100 chr2A 100.000 2387 0 0 1 2387 770291855 770289469 0.000000e+00 4409.0
1 TraesCS2A01G576100 chr2A 86.011 1058 128 17 1079 2127 770343037 770341991 0.000000e+00 1116.0
2 TraesCS2A01G576100 chr2A 100.000 393 0 0 1 393 770273085 770272693 0.000000e+00 726.0
3 TraesCS2A01G576100 chr2A 96.063 381 14 1 1 380 770308176 770307796 9.370000e-174 619.0
4 TraesCS2A01G576100 chr2A 89.399 283 28 2 697 978 770343315 770343034 2.920000e-94 355.0
5 TraesCS2A01G576100 chr2B 97.333 1800 38 6 590 2387 790623332 790625123 0.000000e+00 3049.0
6 TraesCS2A01G576100 chr2B 87.014 1440 167 17 697 2127 790612615 790614043 0.000000e+00 1605.0
7 TraesCS2A01G576100 chr2D 96.921 1689 35 7 590 2276 644924754 644923081 0.000000e+00 2815.0
8 TraesCS2A01G576100 chr2D 87.664 1524 167 18 613 2127 644976041 644974530 0.000000e+00 1753.0
9 TraesCS2A01G576100 chr2D 93.069 1111 66 9 613 1720 644981534 644980432 0.000000e+00 1615.0
10 TraesCS2A01G576100 chr2D 81.202 782 129 7 765 1538 644733796 644733025 4.360000e-172 614.0
11 TraesCS2A01G576100 chr2D 85.691 608 52 23 3 589 640776823 640777416 2.030000e-170 608.0
12 TraesCS2A01G576100 chr2D 88.114 387 38 8 207 589 158295006 158295388 1.010000e-123 453.0
13 TraesCS2A01G576100 chr2D 86.684 383 34 11 211 591 137488944 137489311 2.210000e-110 409.0
14 TraesCS2A01G576100 chr2D 92.405 237 13 5 373 606 209074288 209074054 1.370000e-87 333.0
15 TraesCS2A01G576100 chr2D 92.308 234 13 5 373 604 545906475 545906245 6.360000e-86 327.0
16 TraesCS2A01G576100 chr2D 74.356 776 146 34 814 1546 579511275 579510510 5.020000e-72 281.0
17 TraesCS2A01G576100 chr2D 96.491 114 1 1 2274 2387 644922654 644922544 4.050000e-43 185.0
18 TraesCS2A01G576100 chr3B 88.912 1443 144 15 610 2044 48668842 48667408 0.000000e+00 1764.0
19 TraesCS2A01G576100 chr3B 86.682 428 45 9 172 589 758296576 758297001 4.650000e-127 464.0
20 TraesCS2A01G576100 chr6B 88.945 597 53 12 1 590 448313374 448312784 0.000000e+00 725.0
21 TraesCS2A01G576100 chr7A 96.597 382 11 2 1 380 217415143 217415524 1.200000e-177 632.0
22 TraesCS2A01G576100 chr7A 95.812 382 13 3 1 380 217408314 217408694 4.360000e-172 614.0
23 TraesCS2A01G576100 chr7A 84.665 463 47 20 164 611 247034999 247034546 7.830000e-120 440.0
24 TraesCS2A01G576100 chr3A 96.533 375 11 2 7 380 411418837 411418464 9.370000e-174 619.0
25 TraesCS2A01G576100 chr3A 88.060 67 7 1 2271 2337 720856501 720856566 7.070000e-11 78.7
26 TraesCS2A01G576100 chr3A 87.500 64 7 1 2271 2334 549912962 549913024 3.290000e-09 73.1
27 TraesCS2A01G576100 chr4A 96.063 381 12 3 1 380 500718260 500718638 3.370000e-173 617.0
28 TraesCS2A01G576100 chr5A 95.801 381 14 2 1 380 325772963 325773342 4.360000e-172 614.0
29 TraesCS2A01G576100 chr7D 82.871 613 61 26 3 593 464351994 464352584 5.890000e-141 510.0
30 TraesCS2A01G576100 chr7B 81.260 619 68 35 11 602 632698870 632698273 7.780000e-125 457.0
31 TraesCS2A01G576100 chr6A 80.293 614 77 29 3 598 173144322 173143735 7.890000e-115 424.0
32 TraesCS2A01G576100 chr1D 91.983 237 15 4 373 609 479857109 479857341 1.770000e-86 329.0
33 TraesCS2A01G576100 chr1D 94.009 217 11 2 373 589 205013030 205013244 6.360000e-86 327.0
34 TraesCS2A01G576100 chr3D 90.323 248 17 7 370 614 173899763 173900006 3.830000e-83 318.0


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 TraesCS2A01G576100 chr2A 770289469 770291855 2386 True 4409.0 4409 100.000 1 2387 1 chr2A.!!$R2 2386
1 TraesCS2A01G576100 chr2A 770341991 770343315 1324 True 735.5 1116 87.705 697 2127 2 chr2A.!!$R4 1430
2 TraesCS2A01G576100 chr2B 790623332 790625123 1791 False 3049.0 3049 97.333 590 2387 1 chr2B.!!$F2 1797
3 TraesCS2A01G576100 chr2B 790612615 790614043 1428 False 1605.0 1605 87.014 697 2127 1 chr2B.!!$F1 1430
4 TraesCS2A01G576100 chr2D 644974530 644976041 1511 True 1753.0 1753 87.664 613 2127 1 chr2D.!!$R5 1514
5 TraesCS2A01G576100 chr2D 644980432 644981534 1102 True 1615.0 1615 93.069 613 1720 1 chr2D.!!$R6 1107
6 TraesCS2A01G576100 chr2D 644922544 644924754 2210 True 1500.0 2815 96.706 590 2387 2 chr2D.!!$R7 1797
7 TraesCS2A01G576100 chr2D 644733025 644733796 771 True 614.0 614 81.202 765 1538 1 chr2D.!!$R4 773
8 TraesCS2A01G576100 chr2D 640776823 640777416 593 False 608.0 608 85.691 3 589 1 chr2D.!!$F3 586
9 TraesCS2A01G576100 chr2D 579510510 579511275 765 True 281.0 281 74.356 814 1546 1 chr2D.!!$R3 732
10 TraesCS2A01G576100 chr3B 48667408 48668842 1434 True 1764.0 1764 88.912 610 2044 1 chr3B.!!$R1 1434
11 TraesCS2A01G576100 chr6B 448312784 448313374 590 True 725.0 725 88.945 1 590 1 chr6B.!!$R1 589
12 TraesCS2A01G576100 chr7D 464351994 464352584 590 False 510.0 510 82.871 3 593 1 chr7D.!!$F1 590
13 TraesCS2A01G576100 chr7B 632698273 632698870 597 True 457.0 457 81.260 11 602 1 chr7B.!!$R1 591
14 TraesCS2A01G576100 chr6A 173143735 173144322 587 True 424.0 424 80.293 3 598 1 chr6A.!!$R1 595

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
398 412 0.101579 TGAACGTGTGCTGAACTCGA 59.898 50.0 16.41 0.0 46.19 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1924 2166 1.149627 ACCCAGCCTAACACGCAAA 59.85 52.632 0.0 0.0 0.0 3.68 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
153 164 3.168528 ACTCCCCACACTTGGCGT 61.169 61.111 0.00 0.00 42.35 5.68
170 182 4.860881 TGCCTCCTCTAGGGCCGG 62.861 72.222 0.00 0.00 46.65 6.13
194 206 5.581054 GCCTCTCCCTCCCTCCTTTATATAT 60.581 48.000 0.00 0.00 0.00 0.86
205 218 2.358195 CCTTTATATATGGGGGCAGGGC 60.358 54.545 0.00 0.00 0.00 5.19
222 235 1.446272 GCGGCACCTCTAGACACAC 60.446 63.158 0.00 0.00 0.00 3.82
223 236 1.964448 CGGCACCTCTAGACACACA 59.036 57.895 0.00 0.00 0.00 3.72
225 238 1.670087 CGGCACCTCTAGACACACAAG 60.670 57.143 0.00 0.00 0.00 3.16
230 243 4.800914 GCACCTCTAGACACACAAGTTGAT 60.801 45.833 10.54 0.00 0.00 2.57
233 246 5.167121 CCTCTAGACACACAAGTTGATCTG 58.833 45.833 10.54 0.00 0.00 2.90
243 256 5.931146 ACACAAGTTGATCTGTTGATCTCTC 59.069 40.000 10.54 0.00 46.84 3.20
244 257 5.350914 CACAAGTTGATCTGTTGATCTCTCC 59.649 44.000 10.54 0.00 46.84 3.71
245 258 4.751767 AGTTGATCTGTTGATCTCTCCC 57.248 45.455 7.42 0.00 46.84 4.30
274 288 3.422204 GTGCCCCCTCCACCATAA 58.578 61.111 0.00 0.00 0.00 1.90
283 297 2.126882 CCTCCACCATAATCCACCTCA 58.873 52.381 0.00 0.00 0.00 3.86
284 298 2.509548 CCTCCACCATAATCCACCTCAA 59.490 50.000 0.00 0.00 0.00 3.02
286 300 4.392940 CTCCACCATAATCCACCTCAATC 58.607 47.826 0.00 0.00 0.00 2.67
308 322 2.679132 ATCGTAGCGGTGCTTAGGCG 62.679 60.000 0.00 0.00 40.44 5.52
333 347 0.249031 CTGCGTCGGTAGCATCATCA 60.249 55.000 0.00 0.00 44.26 3.07
334 348 0.389025 TGCGTCGGTAGCATCATCAT 59.611 50.000 0.00 0.00 40.01 2.45
335 349 1.063806 GCGTCGGTAGCATCATCATC 58.936 55.000 0.00 0.00 34.19 2.92
336 350 1.602920 GCGTCGGTAGCATCATCATCA 60.603 52.381 0.00 0.00 34.19 3.07
337 351 2.054363 CGTCGGTAGCATCATCATCAC 58.946 52.381 0.00 0.00 0.00 3.06
338 352 2.408050 GTCGGTAGCATCATCATCACC 58.592 52.381 0.00 0.00 0.00 4.02
339 353 1.422388 CGGTAGCATCATCATCACCG 58.578 55.000 0.00 0.00 42.41 4.94
340 354 1.269778 CGGTAGCATCATCATCACCGT 60.270 52.381 2.91 0.00 42.93 4.83
341 355 2.408050 GGTAGCATCATCATCACCGTC 58.592 52.381 0.00 0.00 0.00 4.79
342 356 2.224042 GGTAGCATCATCATCACCGTCA 60.224 50.000 0.00 0.00 0.00 4.35
343 357 2.924757 AGCATCATCATCACCGTCAT 57.075 45.000 0.00 0.00 0.00 3.06
344 358 2.763933 AGCATCATCATCACCGTCATC 58.236 47.619 0.00 0.00 0.00 2.92
345 359 2.103601 AGCATCATCATCACCGTCATCA 59.896 45.455 0.00 0.00 0.00 3.07
346 360 2.222678 GCATCATCATCACCGTCATCAC 59.777 50.000 0.00 0.00 0.00 3.06
347 361 3.460103 CATCATCATCACCGTCATCACA 58.540 45.455 0.00 0.00 0.00 3.58
348 362 2.892374 TCATCATCACCGTCATCACAC 58.108 47.619 0.00 0.00 0.00 3.82
349 363 1.935873 CATCATCACCGTCATCACACC 59.064 52.381 0.00 0.00 0.00 4.16
350 364 0.108851 TCATCACCGTCATCACACCG 60.109 55.000 0.00 0.00 0.00 4.94
351 365 0.389817 CATCACCGTCATCACACCGT 60.390 55.000 0.00 0.00 0.00 4.83
352 366 0.108804 ATCACCGTCATCACACCGTC 60.109 55.000 0.00 0.00 0.00 4.79
353 367 2.086426 CACCGTCATCACACCGTCG 61.086 63.158 0.00 0.00 0.00 5.12
354 368 2.257371 CCGTCATCACACCGTCGT 59.743 61.111 0.00 0.00 0.00 4.34
355 369 2.086426 CCGTCATCACACCGTCGTG 61.086 63.158 0.00 0.00 46.11 4.35
356 370 2.716828 CGTCATCACACCGTCGTGC 61.717 63.158 0.00 0.00 44.40 5.34
357 371 1.372997 GTCATCACACCGTCGTGCT 60.373 57.895 0.00 0.00 44.40 4.40
358 372 1.372872 TCATCACACCGTCGTGCTG 60.373 57.895 0.00 0.29 44.40 4.41
359 373 1.372872 CATCACACCGTCGTGCTGA 60.373 57.895 0.40 1.20 44.40 4.26
360 374 0.737367 CATCACACCGTCGTGCTGAT 60.737 55.000 0.40 3.07 44.40 2.90
361 375 0.737367 ATCACACCGTCGTGCTGATG 60.737 55.000 8.14 0.00 44.40 3.07
366 380 4.578913 CGTCGTGCTGATGGAACT 57.421 55.556 0.00 0.00 0.00 3.01
367 381 2.363807 CGTCGTGCTGATGGAACTC 58.636 57.895 0.00 0.00 0.00 3.01
368 382 0.109086 CGTCGTGCTGATGGAACTCT 60.109 55.000 0.00 0.00 0.00 3.24
369 383 1.634702 GTCGTGCTGATGGAACTCTC 58.365 55.000 0.00 0.00 0.00 3.20
370 384 0.532573 TCGTGCTGATGGAACTCTCC 59.467 55.000 0.00 0.00 42.81 3.71
371 385 0.460987 CGTGCTGATGGAACTCTCCC 60.461 60.000 0.00 0.00 41.64 4.30
372 386 0.908198 GTGCTGATGGAACTCTCCCT 59.092 55.000 0.00 0.00 41.64 4.20
373 387 1.134551 GTGCTGATGGAACTCTCCCTC 60.135 57.143 0.00 0.00 41.64 4.30
374 388 0.103937 GCTGATGGAACTCTCCCTCG 59.896 60.000 0.00 0.00 41.64 4.63
375 389 1.769026 CTGATGGAACTCTCCCTCGA 58.231 55.000 0.00 0.00 41.64 4.04
376 390 2.103373 CTGATGGAACTCTCCCTCGAA 58.897 52.381 0.00 0.00 41.64 3.71
377 391 2.100584 CTGATGGAACTCTCCCTCGAAG 59.899 54.545 0.00 0.00 41.64 3.79
378 392 0.827368 ATGGAACTCTCCCTCGAAGC 59.173 55.000 0.00 0.00 41.64 3.86
379 393 0.251832 TGGAACTCTCCCTCGAAGCT 60.252 55.000 0.00 0.00 41.64 3.74
380 394 0.174617 GGAACTCTCCCTCGAAGCTG 59.825 60.000 0.00 0.00 35.42 4.24
381 395 1.178276 GAACTCTCCCTCGAAGCTGA 58.822 55.000 0.00 0.00 0.00 4.26
382 396 1.546476 GAACTCTCCCTCGAAGCTGAA 59.454 52.381 0.00 0.00 0.00 3.02
383 397 0.892063 ACTCTCCCTCGAAGCTGAAC 59.108 55.000 0.00 0.00 0.00 3.18
384 398 0.179150 CTCTCCCTCGAAGCTGAACG 60.179 60.000 0.00 0.00 0.00 3.95
385 399 0.894184 TCTCCCTCGAAGCTGAACGT 60.894 55.000 7.80 0.00 0.00 3.99
386 400 0.734253 CTCCCTCGAAGCTGAACGTG 60.734 60.000 0.00 5.93 0.00 4.49
387 401 1.006102 CCCTCGAAGCTGAACGTGT 60.006 57.895 0.00 0.00 0.00 4.49
388 402 1.284982 CCCTCGAAGCTGAACGTGTG 61.285 60.000 0.00 0.00 0.00 3.82
389 403 1.488957 CTCGAAGCTGAACGTGTGC 59.511 57.895 0.00 0.00 0.00 4.57
390 404 0.941463 CTCGAAGCTGAACGTGTGCT 60.941 55.000 4.66 4.66 38.87 4.40
391 405 1.202568 CGAAGCTGAACGTGTGCTG 59.797 57.895 10.26 0.00 37.11 4.41
392 406 1.215014 CGAAGCTGAACGTGTGCTGA 61.215 55.000 10.26 0.00 37.11 4.26
393 407 0.937304 GAAGCTGAACGTGTGCTGAA 59.063 50.000 10.26 0.00 37.11 3.02
394 408 0.657840 AAGCTGAACGTGTGCTGAAC 59.342 50.000 10.26 0.00 37.11 3.18
395 409 0.179073 AGCTGAACGTGTGCTGAACT 60.179 50.000 8.99 0.00 35.54 3.01
396 410 0.233332 GCTGAACGTGTGCTGAACTC 59.767 55.000 0.00 0.00 0.00 3.01
398 412 0.101579 TGAACGTGTGCTGAACTCGA 59.898 50.000 16.41 0.00 46.19 4.04
399 413 1.205657 GAACGTGTGCTGAACTCGAA 58.794 50.000 16.41 0.00 46.19 3.71
400 414 1.190323 GAACGTGTGCTGAACTCGAAG 59.810 52.381 16.41 0.00 46.19 3.79
401 415 0.597637 ACGTGTGCTGAACTCGAAGG 60.598 55.000 16.41 0.00 46.19 3.46
402 416 0.597637 CGTGTGCTGAACTCGAAGGT 60.598 55.000 4.26 0.00 46.19 3.50
403 417 0.861837 GTGTGCTGAACTCGAAGGTG 59.138 55.000 0.00 0.00 0.00 4.00
404 418 0.880278 TGTGCTGAACTCGAAGGTGC 60.880 55.000 0.00 0.00 0.00 5.01
405 419 1.301716 TGCTGAACTCGAAGGTGCC 60.302 57.895 0.00 0.00 0.00 5.01
406 420 2.383527 GCTGAACTCGAAGGTGCCG 61.384 63.158 0.00 0.00 0.00 5.69
407 421 1.006102 CTGAACTCGAAGGTGCCGT 60.006 57.895 0.00 0.00 0.00 5.68
408 422 1.284982 CTGAACTCGAAGGTGCCGTG 61.285 60.000 0.00 0.00 0.00 4.94
409 423 2.665185 AACTCGAAGGTGCCGTGC 60.665 61.111 0.00 0.00 0.00 5.34
410 424 3.454587 AACTCGAAGGTGCCGTGCA 62.455 57.895 0.00 0.00 35.60 4.57
411 425 2.434884 CTCGAAGGTGCCGTGCAT 60.435 61.111 1.90 0.00 41.91 3.96
412 426 2.031919 TCGAAGGTGCCGTGCATT 59.968 55.556 1.90 0.00 41.91 3.56
413 427 1.970917 CTCGAAGGTGCCGTGCATTC 61.971 60.000 1.90 2.86 41.91 2.67
414 428 2.480555 GAAGGTGCCGTGCATTCG 59.519 61.111 1.90 0.00 41.91 3.34
422 436 2.086510 CCGTGCATTCGGTACTTGG 58.913 57.895 7.56 0.00 44.77 3.61
423 437 0.390603 CCGTGCATTCGGTACTTGGA 60.391 55.000 7.56 0.00 44.77 3.53
424 438 1.651987 CGTGCATTCGGTACTTGGAT 58.348 50.000 0.00 0.00 0.00 3.41
425 439 1.593006 CGTGCATTCGGTACTTGGATC 59.407 52.381 0.00 0.00 0.00 3.36
426 440 1.593006 GTGCATTCGGTACTTGGATCG 59.407 52.381 0.00 0.00 0.00 3.69
427 441 1.217882 GCATTCGGTACTTGGATCGG 58.782 55.000 0.00 0.00 0.00 4.18
428 442 1.472728 GCATTCGGTACTTGGATCGGT 60.473 52.381 0.00 0.00 0.00 4.69
429 443 2.470821 CATTCGGTACTTGGATCGGTC 58.529 52.381 0.00 0.00 0.00 4.79
430 444 0.452987 TTCGGTACTTGGATCGGTCG 59.547 55.000 0.00 0.00 0.00 4.79
431 445 1.065273 CGGTACTTGGATCGGTCGG 59.935 63.158 0.00 0.00 0.00 4.79
432 446 1.378882 CGGTACTTGGATCGGTCGGA 61.379 60.000 0.00 0.00 0.00 4.55
433 447 1.038280 GGTACTTGGATCGGTCGGAT 58.962 55.000 0.00 0.00 38.35 4.18
440 454 3.165559 GATCGGTCGGATCGTGAAG 57.834 57.895 10.85 0.00 42.02 3.02
441 455 0.661552 GATCGGTCGGATCGTGAAGA 59.338 55.000 10.85 0.00 42.02 2.87
442 456 0.381089 ATCGGTCGGATCGTGAAGAC 59.619 55.000 10.85 0.00 0.00 3.01
444 458 1.505353 GGTCGGATCGTGAAGACGT 59.495 57.895 0.00 0.00 46.20 4.34
445 459 0.729116 GGTCGGATCGTGAAGACGTA 59.271 55.000 0.00 0.00 46.20 3.57
446 460 1.530646 GGTCGGATCGTGAAGACGTAC 60.531 57.143 0.00 0.00 46.20 3.67
447 461 1.129251 GTCGGATCGTGAAGACGTACA 59.871 52.381 0.00 0.00 46.20 2.90
448 462 1.805943 TCGGATCGTGAAGACGTACAA 59.194 47.619 0.00 0.00 46.20 2.41
449 463 1.909532 CGGATCGTGAAGACGTACAAC 59.090 52.381 0.00 0.00 46.20 3.32
450 464 2.413765 CGGATCGTGAAGACGTACAACT 60.414 50.000 0.00 0.00 46.20 3.16
451 465 3.181517 CGGATCGTGAAGACGTACAACTA 60.182 47.826 0.00 0.00 46.20 2.24
452 466 4.094212 GGATCGTGAAGACGTACAACTAC 58.906 47.826 0.00 0.00 46.20 2.73
453 467 4.378770 GGATCGTGAAGACGTACAACTACA 60.379 45.833 0.00 0.00 46.20 2.74
454 468 4.754372 TCGTGAAGACGTACAACTACAT 57.246 40.909 0.00 0.00 46.20 2.29
455 469 4.715896 TCGTGAAGACGTACAACTACATC 58.284 43.478 0.00 0.00 46.20 3.06
456 470 4.213906 TCGTGAAGACGTACAACTACATCA 59.786 41.667 0.00 0.00 46.20 3.07
457 471 4.913345 CGTGAAGACGTACAACTACATCAA 59.087 41.667 0.00 0.00 40.91 2.57
458 472 5.164215 CGTGAAGACGTACAACTACATCAAC 60.164 44.000 0.00 0.00 40.91 3.18
459 473 5.118203 GTGAAGACGTACAACTACATCAACC 59.882 44.000 0.00 0.00 0.00 3.77
460 474 4.859304 AGACGTACAACTACATCAACCA 57.141 40.909 0.00 0.00 0.00 3.67
461 475 4.553323 AGACGTACAACTACATCAACCAC 58.447 43.478 0.00 0.00 0.00 4.16
462 476 3.311106 ACGTACAACTACATCAACCACG 58.689 45.455 0.00 0.00 0.00 4.94
463 477 3.243501 ACGTACAACTACATCAACCACGT 60.244 43.478 0.00 0.00 35.49 4.49
464 478 3.737266 CGTACAACTACATCAACCACGTT 59.263 43.478 0.00 0.00 0.00 3.99
465 479 4.375606 CGTACAACTACATCAACCACGTTG 60.376 45.833 0.00 0.00 43.99 4.10
466 480 3.537580 ACAACTACATCAACCACGTTGT 58.462 40.909 4.56 0.00 43.23 3.32
467 481 3.311322 ACAACTACATCAACCACGTTGTG 59.689 43.478 0.00 5.35 43.23 3.33
468 482 1.871039 ACTACATCAACCACGTTGTGC 59.129 47.619 4.56 0.00 43.23 4.57
469 483 2.143122 CTACATCAACCACGTTGTGCT 58.857 47.619 4.56 0.00 43.23 4.40
470 484 2.248280 ACATCAACCACGTTGTGCTA 57.752 45.000 4.56 0.00 43.23 3.49
471 485 2.566913 ACATCAACCACGTTGTGCTAA 58.433 42.857 4.56 0.00 43.23 3.09
472 486 2.289547 ACATCAACCACGTTGTGCTAAC 59.710 45.455 4.56 0.00 43.23 2.34
473 487 2.319136 TCAACCACGTTGTGCTAACT 57.681 45.000 4.56 0.00 43.23 2.24
474 488 2.206750 TCAACCACGTTGTGCTAACTC 58.793 47.619 4.56 0.00 43.23 3.01
475 489 2.159014 TCAACCACGTTGTGCTAACTCT 60.159 45.455 4.56 0.00 43.23 3.24
476 490 2.612212 CAACCACGTTGTGCTAACTCTT 59.388 45.455 0.00 0.00 38.56 2.85
477 491 2.480845 ACCACGTTGTGCTAACTCTTC 58.519 47.619 0.00 0.00 31.34 2.87
478 492 1.798813 CCACGTTGTGCTAACTCTTCC 59.201 52.381 0.00 0.00 31.34 3.46
479 493 1.455786 CACGTTGTGCTAACTCTTCCG 59.544 52.381 0.00 0.00 0.00 4.30
480 494 0.438830 CGTTGTGCTAACTCTTCCGC 59.561 55.000 3.56 0.00 0.00 5.54
481 495 1.797025 GTTGTGCTAACTCTTCCGCT 58.203 50.000 0.00 0.00 0.00 5.52
482 496 2.143925 GTTGTGCTAACTCTTCCGCTT 58.856 47.619 0.00 0.00 0.00 4.68
483 497 2.543777 TGTGCTAACTCTTCCGCTTT 57.456 45.000 0.00 0.00 0.00 3.51
484 498 2.413837 TGTGCTAACTCTTCCGCTTTC 58.586 47.619 0.00 0.00 0.00 2.62
485 499 1.390463 GTGCTAACTCTTCCGCTTTCG 59.610 52.381 0.00 0.00 0.00 3.46
503 517 2.101700 GGTCTACGAGGGTACGTGG 58.898 63.158 0.00 0.00 46.02 4.94
505 519 3.159298 TCTACGAGGGTACGTGGAC 57.841 57.895 0.00 0.00 45.53 4.02
506 520 0.324614 TCTACGAGGGTACGTGGACA 59.675 55.000 0.00 0.00 45.53 4.02
507 521 1.167851 CTACGAGGGTACGTGGACAA 58.832 55.000 0.00 0.00 44.98 3.18
508 522 0.881118 TACGAGGGTACGTGGACAAC 59.119 55.000 0.00 0.00 46.02 3.32
509 523 1.108727 ACGAGGGTACGTGGACAACA 61.109 55.000 0.00 0.00 44.84 3.33
510 524 0.665369 CGAGGGTACGTGGACAACAC 60.665 60.000 0.00 0.00 46.78 3.32
519 533 2.156343 GTGGACAACACTCTCCTCAC 57.844 55.000 0.00 0.00 46.72 3.51
520 534 1.689273 GTGGACAACACTCTCCTCACT 59.311 52.381 0.00 0.00 46.72 3.41
521 535 1.964223 TGGACAACACTCTCCTCACTC 59.036 52.381 0.00 0.00 0.00 3.51
522 536 1.068194 GGACAACACTCTCCTCACTCG 60.068 57.143 0.00 0.00 0.00 4.18
523 537 1.609555 GACAACACTCTCCTCACTCGT 59.390 52.381 0.00 0.00 0.00 4.18
524 538 2.032620 ACAACACTCTCCTCACTCGTT 58.967 47.619 0.00 0.00 0.00 3.85
525 539 2.223829 ACAACACTCTCCTCACTCGTTG 60.224 50.000 0.00 0.00 38.51 4.10
526 540 0.315568 ACACTCTCCTCACTCGTTGC 59.684 55.000 0.00 0.00 0.00 4.17
527 541 0.600557 CACTCTCCTCACTCGTTGCT 59.399 55.000 0.00 0.00 0.00 3.91
528 542 1.813178 CACTCTCCTCACTCGTTGCTA 59.187 52.381 0.00 0.00 0.00 3.49
529 543 2.425312 CACTCTCCTCACTCGTTGCTAT 59.575 50.000 0.00 0.00 0.00 2.97
530 544 2.425312 ACTCTCCTCACTCGTTGCTATG 59.575 50.000 0.00 0.00 0.00 2.23
531 545 1.135139 TCTCCTCACTCGTTGCTATGC 59.865 52.381 0.00 0.00 0.00 3.14
532 546 0.894835 TCCTCACTCGTTGCTATGCA 59.105 50.000 0.00 0.00 36.47 3.96
533 547 1.482182 TCCTCACTCGTTGCTATGCAT 59.518 47.619 3.79 3.79 38.76 3.96
534 548 1.863454 CCTCACTCGTTGCTATGCATC 59.137 52.381 0.19 0.00 38.76 3.91
535 549 2.543641 CTCACTCGTTGCTATGCATCA 58.456 47.619 0.19 0.00 38.76 3.07
536 550 2.270923 TCACTCGTTGCTATGCATCAC 58.729 47.619 0.19 0.00 38.76 3.06
537 551 1.328680 CACTCGTTGCTATGCATCACC 59.671 52.381 0.19 0.00 38.76 4.02
538 552 1.066215 ACTCGTTGCTATGCATCACCA 60.066 47.619 0.19 0.00 38.76 4.17
539 553 2.216046 CTCGTTGCTATGCATCACCAT 58.784 47.619 0.19 0.00 38.76 3.55
540 554 1.941975 TCGTTGCTATGCATCACCATG 59.058 47.619 0.19 0.00 38.76 3.66
541 555 1.941975 CGTTGCTATGCATCACCATGA 59.058 47.619 0.19 0.00 38.76 3.07
542 556 2.551032 CGTTGCTATGCATCACCATGAT 59.449 45.455 0.19 0.00 38.76 2.45
543 557 3.364664 CGTTGCTATGCATCACCATGATC 60.365 47.826 0.19 0.00 38.76 2.92
544 558 2.786777 TGCTATGCATCACCATGATCC 58.213 47.619 0.19 0.00 34.28 3.36
545 559 2.374170 TGCTATGCATCACCATGATCCT 59.626 45.455 0.19 0.00 34.28 3.24
546 560 2.747989 GCTATGCATCACCATGATCCTG 59.252 50.000 0.19 0.00 34.28 3.86
547 561 3.809678 GCTATGCATCACCATGATCCTGT 60.810 47.826 0.19 0.00 34.28 4.00
548 562 2.047002 TGCATCACCATGATCCTGTG 57.953 50.000 0.00 0.00 34.28 3.66
549 563 1.282738 TGCATCACCATGATCCTGTGT 59.717 47.619 0.00 0.00 34.28 3.72
550 564 1.674441 GCATCACCATGATCCTGTGTG 59.326 52.381 0.00 10.98 34.28 3.82
551 565 2.942752 GCATCACCATGATCCTGTGTGT 60.943 50.000 14.49 0.00 34.28 3.72
552 566 2.477845 TCACCATGATCCTGTGTGTG 57.522 50.000 14.49 8.57 0.00 3.82
553 567 0.806868 CACCATGATCCTGTGTGTGC 59.193 55.000 0.00 0.00 0.00 4.57
554 568 0.674581 ACCATGATCCTGTGTGTGCG 60.675 55.000 0.00 0.00 0.00 5.34
555 569 0.674581 CCATGATCCTGTGTGTGCGT 60.675 55.000 0.00 0.00 0.00 5.24
556 570 1.405391 CCATGATCCTGTGTGTGCGTA 60.405 52.381 0.00 0.00 0.00 4.42
557 571 1.929169 CATGATCCTGTGTGTGCGTAG 59.071 52.381 0.00 0.00 0.00 3.51
558 572 0.246360 TGATCCTGTGTGTGCGTAGG 59.754 55.000 0.00 0.00 0.00 3.18
559 573 0.530744 GATCCTGTGTGTGCGTAGGA 59.469 55.000 0.00 0.00 43.01 2.94
560 574 0.973632 ATCCTGTGTGTGCGTAGGAA 59.026 50.000 0.00 0.00 42.20 3.36
561 575 0.753867 TCCTGTGTGTGCGTAGGAAA 59.246 50.000 0.00 0.00 36.44 3.13
562 576 1.139256 TCCTGTGTGTGCGTAGGAAAA 59.861 47.619 0.00 0.00 36.44 2.29
563 577 2.151202 CCTGTGTGTGCGTAGGAAAAT 58.849 47.619 0.00 0.00 31.91 1.82
564 578 2.552315 CCTGTGTGTGCGTAGGAAAATT 59.448 45.455 0.00 0.00 31.91 1.82
565 579 3.004315 CCTGTGTGTGCGTAGGAAAATTT 59.996 43.478 0.00 0.00 31.91 1.82
566 580 4.499019 CCTGTGTGTGCGTAGGAAAATTTT 60.499 41.667 2.28 2.28 31.91 1.82
567 581 4.355437 TGTGTGTGCGTAGGAAAATTTTG 58.645 39.130 8.47 0.00 0.00 2.44
568 582 4.096532 TGTGTGTGCGTAGGAAAATTTTGA 59.903 37.500 8.47 0.00 0.00 2.69
569 583 5.038033 GTGTGTGCGTAGGAAAATTTTGAA 58.962 37.500 8.47 0.00 0.00 2.69
570 584 5.517054 GTGTGTGCGTAGGAAAATTTTGAAA 59.483 36.000 8.47 0.00 0.00 2.69
571 585 6.200097 GTGTGTGCGTAGGAAAATTTTGAAAT 59.800 34.615 8.47 0.00 0.00 2.17
572 586 6.758886 TGTGTGCGTAGGAAAATTTTGAAATT 59.241 30.769 8.47 0.00 40.15 1.82
573 587 7.921214 TGTGTGCGTAGGAAAATTTTGAAATTA 59.079 29.630 8.47 0.00 37.62 1.40
574 588 8.211838 GTGTGCGTAGGAAAATTTTGAAATTAC 58.788 33.333 8.47 3.20 37.62 1.89
575 589 8.138712 TGTGCGTAGGAAAATTTTGAAATTACT 58.861 29.630 8.47 0.00 37.62 2.24
576 590 9.615295 GTGCGTAGGAAAATTTTGAAATTACTA 57.385 29.630 8.47 0.00 37.62 1.82
577 591 9.615295 TGCGTAGGAAAATTTTGAAATTACTAC 57.385 29.630 8.47 17.54 37.62 2.73
579 593 9.815936 CGTAGGAAAATTTTGAAATTACTACGT 57.184 29.630 27.13 0.00 44.84 3.57
587 601 9.673454 AATTTTGAAATTACTACGTTCTCCAAC 57.327 29.630 0.00 0.00 36.88 3.77
588 602 7.789273 TTTGAAATTACTACGTTCTCCAACA 57.211 32.000 0.00 0.00 32.14 3.33
695 709 4.020839 TGGGTGCACTAGTTACTACCTTTC 60.021 45.833 17.98 0.00 0.00 2.62
807 821 5.887214 ACTTTTGAATAAAGTTTGCCCCT 57.113 34.783 0.00 0.00 37.18 4.79
1413 1637 5.173664 AGTGGCAATAACTTCGGTAGTAAC 58.826 41.667 0.00 0.00 35.54 2.50
1436 1660 6.680810 ACAATTGTGATGTACCAGATTTGTG 58.319 36.000 11.07 0.00 34.68 3.33
1647 1885 5.593010 AGGTTTTAGCACTAGATCGATCAC 58.407 41.667 26.47 11.66 0.00 3.06
1682 1920 1.287425 GGGATAGTTTCCGCAAGACG 58.713 55.000 0.00 0.00 46.52 4.18
1875 2117 0.943835 CTCATGTGACGGCGACAACA 60.944 55.000 16.62 15.04 0.00 3.33
1924 2166 0.178873 TGAGGCTTGGGGTTAGAGGT 60.179 55.000 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
170 182 0.031010 TAAAGGAGGGAGGGAGAGGC 60.031 60.000 0.00 0.00 0.00 4.70
182 194 3.203040 CCCTGCCCCCATATATAAAGGAG 59.797 52.174 6.24 0.00 0.00 3.69
205 218 0.317160 TTGTGTGTCTAGAGGTGCCG 59.683 55.000 0.00 0.00 0.00 5.69
222 235 4.874966 GGGAGAGATCAACAGATCAACTTG 59.125 45.833 8.06 0.00 40.49 3.16
223 236 4.533707 TGGGAGAGATCAACAGATCAACTT 59.466 41.667 8.06 0.00 40.49 2.66
225 238 4.440880 CTGGGAGAGATCAACAGATCAAC 58.559 47.826 8.06 2.45 40.49 3.18
230 243 1.198713 GGCTGGGAGAGATCAACAGA 58.801 55.000 0.00 0.00 0.00 3.41
233 246 0.460987 CACGGCTGGGAGAGATCAAC 60.461 60.000 0.00 0.00 0.00 3.18
272 286 6.625081 CGCTACGATATGATTGAGGTGGATTA 60.625 42.308 0.00 0.00 0.00 1.75
274 288 4.380973 CGCTACGATATGATTGAGGTGGAT 60.381 45.833 0.00 0.00 0.00 3.41
283 297 3.386768 AAGCACCGCTACGATATGATT 57.613 42.857 0.00 0.00 38.25 2.57
284 298 3.119459 CCTAAGCACCGCTACGATATGAT 60.119 47.826 0.00 0.00 38.25 2.45
286 300 2.596452 CCTAAGCACCGCTACGATATG 58.404 52.381 0.00 0.00 38.25 1.78
308 322 2.202756 CTACCGACGCAGGGCTTC 60.203 66.667 1.73 0.00 35.02 3.86
318 332 2.408050 GGTGATGATGATGCTACCGAC 58.592 52.381 0.00 0.00 0.00 4.79
320 334 1.422388 CGGTGATGATGATGCTACCG 58.578 55.000 0.00 0.00 43.93 4.02
333 347 0.108804 GACGGTGTGATGACGGTGAT 60.109 55.000 0.00 0.00 30.20 3.06
334 348 1.287815 GACGGTGTGATGACGGTGA 59.712 57.895 0.00 0.00 30.20 4.02
335 349 2.086426 CGACGGTGTGATGACGGTG 61.086 63.158 0.00 0.00 30.20 4.94
336 350 2.257371 CGACGGTGTGATGACGGT 59.743 61.111 0.00 0.00 32.52 4.83
337 351 2.086426 CACGACGGTGTGATGACGG 61.086 63.158 0.00 0.00 42.55 4.79
338 352 2.716828 GCACGACGGTGTGATGACG 61.717 63.158 12.76 0.00 46.13 4.35
339 353 1.372997 AGCACGACGGTGTGATGAC 60.373 57.895 12.76 0.00 46.13 3.06
340 354 3.047735 AGCACGACGGTGTGATGA 58.952 55.556 12.76 0.00 46.13 2.92
342 356 0.737367 CATCAGCACGACGGTGTGAT 60.737 55.000 12.76 3.93 46.13 3.06
343 357 1.372872 CATCAGCACGACGGTGTGA 60.373 57.895 12.76 6.53 46.13 3.58
344 358 2.382746 CCATCAGCACGACGGTGTG 61.383 63.158 0.00 5.06 46.13 3.82
345 359 2.048222 CCATCAGCACGACGGTGT 60.048 61.111 0.00 0.00 46.13 4.16
347 361 1.374252 GTTCCATCAGCACGACGGT 60.374 57.895 0.00 0.00 0.00 4.83
348 362 1.078759 GAGTTCCATCAGCACGACGG 61.079 60.000 0.00 0.00 0.00 4.79
349 363 0.109086 AGAGTTCCATCAGCACGACG 60.109 55.000 0.00 0.00 0.00 5.12
350 364 1.634702 GAGAGTTCCATCAGCACGAC 58.365 55.000 0.00 0.00 0.00 4.34
351 365 0.532573 GGAGAGTTCCATCAGCACGA 59.467 55.000 0.00 0.00 43.45 4.35
352 366 0.460987 GGGAGAGTTCCATCAGCACG 60.461 60.000 0.00 0.00 45.98 5.34
353 367 0.908198 AGGGAGAGTTCCATCAGCAC 59.092 55.000 0.00 0.00 45.98 4.40
354 368 3.406442 AGGGAGAGTTCCATCAGCA 57.594 52.632 0.00 0.00 45.98 4.41
359 373 0.827368 GCTTCGAGGGAGAGTTCCAT 59.173 55.000 0.00 0.00 45.98 3.41
360 374 0.251832 AGCTTCGAGGGAGAGTTCCA 60.252 55.000 0.00 0.00 45.98 3.53
361 375 0.174617 CAGCTTCGAGGGAGAGTTCC 59.825 60.000 0.00 0.00 43.23 3.62
362 376 1.178276 TCAGCTTCGAGGGAGAGTTC 58.822 55.000 0.00 0.00 0.00 3.01
363 377 1.273886 GTTCAGCTTCGAGGGAGAGTT 59.726 52.381 0.00 0.00 0.00 3.01
364 378 0.892063 GTTCAGCTTCGAGGGAGAGT 59.108 55.000 0.00 0.00 0.00 3.24
365 379 0.179150 CGTTCAGCTTCGAGGGAGAG 60.179 60.000 0.00 0.00 0.00 3.20
366 380 0.894184 ACGTTCAGCTTCGAGGGAGA 60.894 55.000 9.22 0.00 0.00 3.71
367 381 0.734253 CACGTTCAGCTTCGAGGGAG 60.734 60.000 9.22 0.00 0.00 4.30
368 382 1.289066 CACGTTCAGCTTCGAGGGA 59.711 57.895 9.22 0.00 0.00 4.20
369 383 1.006102 ACACGTTCAGCTTCGAGGG 60.006 57.895 9.22 0.00 0.00 4.30
370 384 1.891060 GCACACGTTCAGCTTCGAGG 61.891 60.000 9.22 0.00 0.00 4.63
371 385 0.941463 AGCACACGTTCAGCTTCGAG 60.941 55.000 9.22 4.63 34.37 4.04
372 386 1.067416 AGCACACGTTCAGCTTCGA 59.933 52.632 9.22 0.00 34.37 3.71
373 387 1.202568 CAGCACACGTTCAGCTTCG 59.797 57.895 3.60 0.00 36.26 3.79
374 388 0.937304 TTCAGCACACGTTCAGCTTC 59.063 50.000 3.60 0.00 36.26 3.86
375 389 0.657840 GTTCAGCACACGTTCAGCTT 59.342 50.000 3.60 0.00 36.26 3.74
376 390 0.179073 AGTTCAGCACACGTTCAGCT 60.179 50.000 0.64 0.64 39.63 4.24
377 391 0.233332 GAGTTCAGCACACGTTCAGC 59.767 55.000 0.00 0.00 0.00 4.26
378 392 0.504384 CGAGTTCAGCACACGTTCAG 59.496 55.000 0.00 0.00 35.01 3.02
379 393 0.101579 TCGAGTTCAGCACACGTTCA 59.898 50.000 0.00 0.00 40.12 3.18
380 394 1.190323 CTTCGAGTTCAGCACACGTTC 59.810 52.381 0.00 0.00 40.12 3.95
381 395 1.209128 CTTCGAGTTCAGCACACGTT 58.791 50.000 0.00 0.00 40.12 3.99
382 396 0.597637 CCTTCGAGTTCAGCACACGT 60.598 55.000 0.00 0.00 40.12 4.49
383 397 0.597637 ACCTTCGAGTTCAGCACACG 60.598 55.000 0.00 0.00 40.52 4.49
384 398 0.861837 CACCTTCGAGTTCAGCACAC 59.138 55.000 0.00 0.00 0.00 3.82
385 399 0.880278 GCACCTTCGAGTTCAGCACA 60.880 55.000 0.00 0.00 0.00 4.57
386 400 1.569479 GGCACCTTCGAGTTCAGCAC 61.569 60.000 0.00 0.00 0.00 4.40
387 401 1.301716 GGCACCTTCGAGTTCAGCA 60.302 57.895 0.00 0.00 0.00 4.41
388 402 2.383527 CGGCACCTTCGAGTTCAGC 61.384 63.158 0.00 0.00 0.00 4.26
389 403 1.006102 ACGGCACCTTCGAGTTCAG 60.006 57.895 0.00 0.00 0.00 3.02
390 404 1.300620 CACGGCACCTTCGAGTTCA 60.301 57.895 0.00 0.00 0.00 3.18
391 405 2.668280 GCACGGCACCTTCGAGTTC 61.668 63.158 0.00 0.00 0.00 3.01
392 406 2.665185 GCACGGCACCTTCGAGTT 60.665 61.111 0.00 0.00 0.00 3.01
393 407 2.731691 AATGCACGGCACCTTCGAGT 62.732 55.000 0.50 0.00 43.04 4.18
394 408 1.970917 GAATGCACGGCACCTTCGAG 61.971 60.000 0.50 0.00 43.04 4.04
395 409 2.031919 AATGCACGGCACCTTCGA 59.968 55.556 0.50 0.00 43.04 3.71
396 410 2.480555 GAATGCACGGCACCTTCG 59.519 61.111 0.50 0.00 43.04 3.79
397 411 2.480555 CGAATGCACGGCACCTTC 59.519 61.111 0.50 2.31 43.04 3.46
398 412 3.055719 CCGAATGCACGGCACCTT 61.056 61.111 2.49 0.00 46.20 3.50
405 419 1.593006 GATCCAAGTACCGAATGCACG 59.407 52.381 0.00 0.00 0.00 5.34
406 420 1.593006 CGATCCAAGTACCGAATGCAC 59.407 52.381 0.00 0.00 0.00 4.57
407 421 1.472552 CCGATCCAAGTACCGAATGCA 60.473 52.381 0.00 0.00 0.00 3.96
408 422 1.217882 CCGATCCAAGTACCGAATGC 58.782 55.000 0.00 0.00 0.00 3.56
409 423 2.470821 GACCGATCCAAGTACCGAATG 58.529 52.381 0.00 0.00 0.00 2.67
410 424 1.066605 CGACCGATCCAAGTACCGAAT 59.933 52.381 0.00 0.00 0.00 3.34
411 425 0.452987 CGACCGATCCAAGTACCGAA 59.547 55.000 0.00 0.00 0.00 4.30
412 426 1.378882 CCGACCGATCCAAGTACCGA 61.379 60.000 0.00 0.00 0.00 4.69
413 427 1.065273 CCGACCGATCCAAGTACCG 59.935 63.158 0.00 0.00 0.00 4.02
414 428 1.000496 GATCCGACCGATCCAAGTACC 60.000 57.143 0.00 0.00 41.51 3.34
415 429 1.334779 CGATCCGACCGATCCAAGTAC 60.335 57.143 0.00 0.00 44.07 2.73
416 430 0.949397 CGATCCGACCGATCCAAGTA 59.051 55.000 0.00 0.00 44.07 2.24
417 431 1.035932 ACGATCCGACCGATCCAAGT 61.036 55.000 0.00 0.00 44.07 3.16
418 432 0.595053 CACGATCCGACCGATCCAAG 60.595 60.000 0.00 0.00 44.07 3.61
419 433 1.033202 TCACGATCCGACCGATCCAA 61.033 55.000 0.00 0.00 44.07 3.53
420 434 1.033202 TTCACGATCCGACCGATCCA 61.033 55.000 0.00 0.00 44.07 3.41
421 435 0.317938 CTTCACGATCCGACCGATCC 60.318 60.000 0.00 0.00 44.07 3.36
422 436 0.661552 TCTTCACGATCCGACCGATC 59.338 55.000 0.00 0.00 43.58 3.69
423 437 0.381089 GTCTTCACGATCCGACCGAT 59.619 55.000 0.00 0.00 0.00 4.18
424 438 1.798735 GTCTTCACGATCCGACCGA 59.201 57.895 0.00 0.00 0.00 4.69
425 439 4.379221 GTCTTCACGATCCGACCG 57.621 61.111 0.00 0.00 0.00 4.79
435 449 5.118203 GGTTGATGTAGTTGTACGTCTTCAC 59.882 44.000 0.00 0.00 43.23 3.18
436 450 5.221283 TGGTTGATGTAGTTGTACGTCTTCA 60.221 40.000 0.00 0.00 43.23 3.02
437 451 5.118203 GTGGTTGATGTAGTTGTACGTCTTC 59.882 44.000 0.00 0.00 43.23 2.87
438 452 4.986659 GTGGTTGATGTAGTTGTACGTCTT 59.013 41.667 0.00 0.00 43.23 3.01
439 453 4.553323 GTGGTTGATGTAGTTGTACGTCT 58.447 43.478 0.00 0.00 43.23 4.18
440 454 3.362831 CGTGGTTGATGTAGTTGTACGTC 59.637 47.826 0.00 0.00 43.16 4.34
441 455 3.243501 ACGTGGTTGATGTAGTTGTACGT 60.244 43.478 0.00 0.00 37.41 3.57
442 456 3.311106 ACGTGGTTGATGTAGTTGTACG 58.689 45.455 0.00 0.00 35.40 3.67
443 457 4.508861 ACAACGTGGTTGATGTAGTTGTAC 59.491 41.667 14.79 0.00 46.66 2.90
444 458 4.508492 CACAACGTGGTTGATGTAGTTGTA 59.492 41.667 14.79 0.00 46.76 2.41
445 459 3.537580 ACAACGTGGTTGATGTAGTTGT 58.462 40.909 14.79 6.02 45.28 3.32
446 460 3.848191 GCACAACGTGGTTGATGTAGTTG 60.848 47.826 14.79 4.81 45.28 3.16
447 461 2.289547 GCACAACGTGGTTGATGTAGTT 59.710 45.455 14.79 0.00 45.28 2.24
448 462 1.871039 GCACAACGTGGTTGATGTAGT 59.129 47.619 14.79 0.00 45.28 2.73
449 463 2.143122 AGCACAACGTGGTTGATGTAG 58.857 47.619 14.79 1.74 45.28 2.74
450 464 2.248280 AGCACAACGTGGTTGATGTA 57.752 45.000 14.79 0.00 45.28 2.29
451 465 2.248280 TAGCACAACGTGGTTGATGT 57.752 45.000 14.79 0.00 45.28 3.06
452 466 2.548057 AGTTAGCACAACGTGGTTGATG 59.452 45.455 14.79 10.04 45.28 3.07
453 467 2.806244 GAGTTAGCACAACGTGGTTGAT 59.194 45.455 14.79 0.00 45.28 2.57
454 468 2.159014 AGAGTTAGCACAACGTGGTTGA 60.159 45.455 14.79 0.00 45.28 3.18
456 470 2.614829 AGAGTTAGCACAACGTGGTT 57.385 45.000 3.94 0.00 41.72 3.67
457 471 2.480845 GAAGAGTTAGCACAACGTGGT 58.519 47.619 4.09 4.09 46.27 4.16
458 472 1.798813 GGAAGAGTTAGCACAACGTGG 59.201 52.381 0.00 0.00 33.64 4.94
459 473 1.455786 CGGAAGAGTTAGCACAACGTG 59.544 52.381 0.00 0.00 36.51 4.49
460 474 1.779569 CGGAAGAGTTAGCACAACGT 58.220 50.000 0.00 0.00 0.00 3.99
461 475 0.438830 GCGGAAGAGTTAGCACAACG 59.561 55.000 0.00 0.00 0.00 4.10
462 476 1.797025 AGCGGAAGAGTTAGCACAAC 58.203 50.000 0.00 0.00 0.00 3.32
463 477 2.543777 AAGCGGAAGAGTTAGCACAA 57.456 45.000 0.00 0.00 0.00 3.33
464 478 2.413837 GAAAGCGGAAGAGTTAGCACA 58.586 47.619 0.00 0.00 0.00 4.57
465 479 1.390463 CGAAAGCGGAAGAGTTAGCAC 59.610 52.381 0.00 0.00 0.00 4.40
466 480 1.710013 CGAAAGCGGAAGAGTTAGCA 58.290 50.000 0.00 0.00 0.00 3.49
478 492 1.226603 CCCTCGTAGACCGAAAGCG 60.227 63.158 0.00 0.00 46.75 4.68
479 493 1.098050 TACCCTCGTAGACCGAAAGC 58.902 55.000 0.00 0.00 46.75 3.51
480 494 1.063174 CGTACCCTCGTAGACCGAAAG 59.937 57.143 0.00 0.00 46.75 2.62
481 495 1.086696 CGTACCCTCGTAGACCGAAA 58.913 55.000 0.00 0.00 46.75 3.46
482 496 0.036388 ACGTACCCTCGTAGACCGAA 60.036 55.000 0.00 0.00 46.75 4.30
483 497 0.740868 CACGTACCCTCGTAGACCGA 60.741 60.000 0.00 0.00 45.00 4.69
484 498 1.709147 CCACGTACCCTCGTAGACCG 61.709 65.000 0.00 0.00 42.27 4.79
485 499 0.392998 TCCACGTACCCTCGTAGACC 60.393 60.000 0.00 0.00 42.27 3.85
486 500 0.729690 GTCCACGTACCCTCGTAGAC 59.270 60.000 0.00 2.79 42.50 2.59
487 501 0.324614 TGTCCACGTACCCTCGTAGA 59.675 55.000 0.00 0.00 42.27 2.59
488 502 1.135575 GTTGTCCACGTACCCTCGTAG 60.136 57.143 0.00 0.00 42.27 3.51
489 503 0.881118 GTTGTCCACGTACCCTCGTA 59.119 55.000 0.00 0.00 42.27 3.43
490 504 1.108727 TGTTGTCCACGTACCCTCGT 61.109 55.000 0.00 0.00 45.10 4.18
491 505 0.665369 GTGTTGTCCACGTACCCTCG 60.665 60.000 0.00 0.00 33.61 4.63
492 506 3.206090 GTGTTGTCCACGTACCCTC 57.794 57.895 0.00 0.00 33.61 4.30
500 514 1.689273 AGTGAGGAGAGTGTTGTCCAC 59.311 52.381 0.00 0.00 44.89 4.02
501 515 1.964223 GAGTGAGGAGAGTGTTGTCCA 59.036 52.381 0.00 0.00 39.21 4.02
502 516 1.068194 CGAGTGAGGAGAGTGTTGTCC 60.068 57.143 0.00 0.00 37.02 4.02
503 517 1.609555 ACGAGTGAGGAGAGTGTTGTC 59.390 52.381 0.00 0.00 0.00 3.18
504 518 1.693627 ACGAGTGAGGAGAGTGTTGT 58.306 50.000 0.00 0.00 0.00 3.32
505 519 2.398498 CAACGAGTGAGGAGAGTGTTG 58.602 52.381 0.00 0.00 0.00 3.33
506 520 1.269831 GCAACGAGTGAGGAGAGTGTT 60.270 52.381 0.00 0.00 0.00 3.32
507 521 0.315568 GCAACGAGTGAGGAGAGTGT 59.684 55.000 0.00 0.00 0.00 3.55
508 522 0.600557 AGCAACGAGTGAGGAGAGTG 59.399 55.000 0.00 0.00 0.00 3.51
509 523 2.201921 TAGCAACGAGTGAGGAGAGT 57.798 50.000 0.00 0.00 0.00 3.24
510 524 2.797792 GCATAGCAACGAGTGAGGAGAG 60.798 54.545 0.00 0.00 0.00 3.20
511 525 1.135139 GCATAGCAACGAGTGAGGAGA 59.865 52.381 0.00 0.00 0.00 3.71
512 526 1.134995 TGCATAGCAACGAGTGAGGAG 60.135 52.381 0.00 0.00 34.76 3.69
513 527 0.894835 TGCATAGCAACGAGTGAGGA 59.105 50.000 0.00 0.00 34.76 3.71
514 528 1.863454 GATGCATAGCAACGAGTGAGG 59.137 52.381 0.00 0.00 43.62 3.86
515 529 2.283617 GTGATGCATAGCAACGAGTGAG 59.716 50.000 0.00 0.00 43.62 3.51
516 530 2.270923 GTGATGCATAGCAACGAGTGA 58.729 47.619 0.00 0.00 43.62 3.41
517 531 1.328680 GGTGATGCATAGCAACGAGTG 59.671 52.381 0.00 0.00 43.62 3.51
518 532 1.066215 TGGTGATGCATAGCAACGAGT 60.066 47.619 0.00 0.00 43.62 4.18
519 533 1.655484 TGGTGATGCATAGCAACGAG 58.345 50.000 0.00 0.00 43.62 4.18
520 534 1.941975 CATGGTGATGCATAGCAACGA 59.058 47.619 0.00 0.00 43.62 3.85
521 535 1.941975 TCATGGTGATGCATAGCAACG 59.058 47.619 0.00 1.35 43.62 4.10
522 536 3.057736 GGATCATGGTGATGCATAGCAAC 60.058 47.826 0.00 0.00 43.55 4.17
523 537 3.151554 GGATCATGGTGATGCATAGCAA 58.848 45.455 0.00 0.00 43.55 3.91
524 538 2.374170 AGGATCATGGTGATGCATAGCA 59.626 45.455 12.83 4.86 46.03 3.49
525 539 2.747989 CAGGATCATGGTGATGCATAGC 59.252 50.000 12.83 0.00 46.03 2.97
526 540 3.751698 CACAGGATCATGGTGATGCATAG 59.248 47.826 12.66 5.87 46.03 2.23
527 541 3.136992 ACACAGGATCATGGTGATGCATA 59.863 43.478 12.66 0.00 46.03 3.14
528 542 2.092049 ACACAGGATCATGGTGATGCAT 60.092 45.455 12.66 0.00 46.03 3.96
529 543 1.282738 ACACAGGATCATGGTGATGCA 59.717 47.619 12.66 0.00 46.03 3.96
530 544 1.674441 CACACAGGATCATGGTGATGC 59.326 52.381 18.31 3.59 44.29 3.91
531 545 2.681344 CACACACAGGATCATGGTGATG 59.319 50.000 25.47 18.22 37.20 3.07
532 546 2.942752 GCACACACAGGATCATGGTGAT 60.943 50.000 25.47 13.21 40.34 3.06
533 547 1.611410 GCACACACAGGATCATGGTGA 60.611 52.381 25.47 0.00 36.42 4.02
534 548 0.806868 GCACACACAGGATCATGGTG 59.193 55.000 20.27 20.27 38.47 4.17
535 549 0.674581 CGCACACACAGGATCATGGT 60.675 55.000 12.66 4.08 0.00 3.55
536 550 0.674581 ACGCACACACAGGATCATGG 60.675 55.000 12.66 3.43 0.00 3.66
537 551 1.929169 CTACGCACACACAGGATCATG 59.071 52.381 5.68 5.68 0.00 3.07
538 552 1.134699 CCTACGCACACACAGGATCAT 60.135 52.381 0.00 0.00 0.00 2.45
539 553 0.246360 CCTACGCACACACAGGATCA 59.754 55.000 0.00 0.00 0.00 2.92
540 554 0.530744 TCCTACGCACACACAGGATC 59.469 55.000 0.00 0.00 32.20 3.36
541 555 0.973632 TTCCTACGCACACACAGGAT 59.026 50.000 0.00 0.00 37.06 3.24
542 556 0.753867 TTTCCTACGCACACACAGGA 59.246 50.000 0.00 0.00 35.38 3.86
543 557 1.588674 TTTTCCTACGCACACACAGG 58.411 50.000 0.00 0.00 0.00 4.00
544 558 3.896648 AATTTTCCTACGCACACACAG 57.103 42.857 0.00 0.00 0.00 3.66
545 559 4.096532 TCAAAATTTTCCTACGCACACACA 59.903 37.500 0.00 0.00 0.00 3.72
546 560 4.602995 TCAAAATTTTCCTACGCACACAC 58.397 39.130 0.00 0.00 0.00 3.82
547 561 4.902443 TCAAAATTTTCCTACGCACACA 57.098 36.364 0.00 0.00 0.00 3.72
548 562 6.763303 ATTTCAAAATTTTCCTACGCACAC 57.237 33.333 0.00 0.00 0.00 3.82
549 563 8.138712 AGTAATTTCAAAATTTTCCTACGCACA 58.861 29.630 0.00 0.00 39.24 4.57
550 564 8.515473 AGTAATTTCAAAATTTTCCTACGCAC 57.485 30.769 0.00 0.00 39.24 5.34
551 565 9.615295 GTAGTAATTTCAAAATTTTCCTACGCA 57.385 29.630 0.00 0.00 39.24 5.24
552 566 8.782327 CGTAGTAATTTCAAAATTTTCCTACGC 58.218 33.333 23.29 10.35 41.85 4.42
553 567 9.815936 ACGTAGTAATTTCAAAATTTTCCTACG 57.184 29.630 27.28 27.28 45.94 3.51
561 575 9.673454 GTTGGAGAACGTAGTAATTTCAAAATT 57.327 29.630 6.04 6.04 45.00 1.82
562 576 8.842280 TGTTGGAGAACGTAGTAATTTCAAAAT 58.158 29.630 0.00 0.00 45.00 1.82
563 577 8.211116 TGTTGGAGAACGTAGTAATTTCAAAA 57.789 30.769 0.00 0.00 45.00 2.44
564 578 7.789273 TGTTGGAGAACGTAGTAATTTCAAA 57.211 32.000 0.00 0.00 45.00 2.69
565 579 7.789273 TTGTTGGAGAACGTAGTAATTTCAA 57.211 32.000 0.00 0.00 45.00 2.69
566 580 7.972832 ATTGTTGGAGAACGTAGTAATTTCA 57.027 32.000 0.00 0.00 45.00 2.69
569 583 8.395633 GCATTATTGTTGGAGAACGTAGTAATT 58.604 33.333 0.00 0.00 45.00 1.40
570 584 7.012044 GGCATTATTGTTGGAGAACGTAGTAAT 59.988 37.037 0.00 0.00 45.00 1.89
571 585 6.314400 GGCATTATTGTTGGAGAACGTAGTAA 59.686 38.462 0.00 0.00 45.00 2.24
572 586 5.813672 GGCATTATTGTTGGAGAACGTAGTA 59.186 40.000 0.00 0.00 45.00 1.82
574 588 4.876107 AGGCATTATTGTTGGAGAACGTAG 59.124 41.667 0.00 0.00 34.49 3.51
575 589 4.839121 AGGCATTATTGTTGGAGAACGTA 58.161 39.130 0.00 0.00 34.49 3.57
576 590 3.686016 AGGCATTATTGTTGGAGAACGT 58.314 40.909 0.00 0.00 34.49 3.99
577 591 5.760253 AGATAGGCATTATTGTTGGAGAACG 59.240 40.000 0.00 0.00 34.49 3.95
578 592 7.500559 AGAAGATAGGCATTATTGTTGGAGAAC 59.499 37.037 0.00 0.00 0.00 3.01
579 593 7.577303 AGAAGATAGGCATTATTGTTGGAGAA 58.423 34.615 0.00 0.00 0.00 2.87
580 594 7.141758 AGAAGATAGGCATTATTGTTGGAGA 57.858 36.000 0.00 0.00 0.00 3.71
581 595 7.814264 AAGAAGATAGGCATTATTGTTGGAG 57.186 36.000 0.00 0.00 0.00 3.86
582 596 9.866655 ATAAAGAAGATAGGCATTATTGTTGGA 57.133 29.630 0.00 0.00 0.00 3.53
695 709 7.223387 GCTTTTTAGATGGTTGCATTTCATAGG 59.777 37.037 0.00 0.00 0.00 2.57
705 719 7.832503 AAATACATGCTTTTTAGATGGTTGC 57.167 32.000 0.00 0.00 0.00 4.17
807 821 8.354711 TGGCATTTATGACAACCTTTTATACA 57.645 30.769 0.00 0.00 44.23 2.29
1413 1637 6.912082 TCACAAATCTGGTACATCACAATTG 58.088 36.000 3.24 3.24 38.20 2.32
1436 1660 4.365723 TCGTCGATAAATAAACCCAGCTC 58.634 43.478 0.00 0.00 0.00 4.09
1772 2012 7.148722 GGAGATATATTCAAGCAGAGTTAACGC 60.149 40.741 0.43 0.43 0.00 4.84
1779 2019 9.545105 GGATATTGGAGATATATTCAAGCAGAG 57.455 37.037 0.00 0.00 0.00 3.35
1816 2058 3.744426 ACCTTCGAAATTTCACCAGTACG 59.256 43.478 17.99 2.42 0.00 3.67
1924 2166 1.149627 ACCCAGCCTAACACGCAAA 59.850 52.632 0.00 0.00 0.00 3.68
2098 2342 6.466885 ACTACCTACTATTTGCTCGTCAAT 57.533 37.500 0.00 0.00 34.12 2.57
2136 2380 5.209659 CAGATGAACTAACTACCTACCCCT 58.790 45.833 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.