Multiple sequence alignment - TraesCS6D01G314100

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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 TraesCS6D01G314100 chr6D 100.000 2564 0 0 1 2564 422605032 422602469 0.000000e+00 4735.0
1 TraesCS6D01G314100 chr6D 88.360 945 91 11 1197 2127 422217928 422216989 0.000000e+00 1118.0
2 TraesCS6D01G314100 chr6D 89.703 573 45 5 994 1552 421697028 421696456 0.000000e+00 719.0
3 TraesCS6D01G314100 chr6D 87.884 619 58 6 994 1596 421664590 421663973 0.000000e+00 712.0
4 TraesCS6D01G314100 chr6D 87.765 613 59 7 994 1590 421463348 421463960 0.000000e+00 702.0
5 TraesCS6D01G314100 chr6D 82.700 763 92 26 1836 2564 421466051 421466807 2.150000e-180 641.0
6 TraesCS6D01G314100 chr6D 81.987 755 97 28 1842 2564 421681709 421680962 2.820000e-169 604.0
7 TraesCS6D01G314100 chr6D 81.722 755 98 28 1842 2564 421663735 421662989 6.110000e-166 593.0
8 TraesCS6D01G314100 chr6D 85.941 505 41 12 994 1479 420966380 420966873 1.760000e-141 512.0
9 TraesCS6D01G314100 chr6D 88.084 428 20 14 2121 2544 422216965 422216565 1.780000e-131 479.0
10 TraesCS6D01G314100 chr6B 88.569 1216 118 13 467 1664 636768215 636767003 0.000000e+00 1456.0
11 TraesCS6D01G314100 chr6B 89.044 931 83 9 1646 2564 636748219 636747296 0.000000e+00 1136.0
12 TraesCS6D01G314100 chr6B 88.058 762 71 8 994 1737 634501631 634502390 0.000000e+00 885.0
13 TraesCS6D01G314100 chr6B 80.579 242 28 11 2286 2514 634502445 634502680 4.390000e-38 169.0
14 TraesCS6D01G314100 chr6B 84.211 133 10 9 1 123 636795513 636795382 4.480000e-23 119.0
15 TraesCS6D01G314100 chr6A 88.508 1166 103 11 1415 2564 565342683 565341533 0.000000e+00 1382.0
16 TraesCS6D01G314100 chr6A 90.226 399 27 3 994 1383 564276192 564276587 6.330000e-141 510.0
17 TraesCS6D01G314100 chr6A 89.646 367 20 6 1 364 565343427 565343076 3.890000e-123 451.0
18 TraesCS6D01G314100 chr6A 86.068 323 36 7 2250 2564 564277359 564277680 3.160000e-89 339.0
19 TraesCS6D01G314100 chr6A 86.047 86 12 0 2290 2375 490473256 490473341 2.720000e-15 93.5
20 TraesCS6D01G314100 chr4B 83.871 124 20 0 2159 2282 535426818 535426941 4.480000e-23 119.0
21 TraesCS6D01G314100 chr1A 72.160 449 102 17 997 1437 300116712 300116279 5.800000e-22 115.0
22 TraesCS6D01G314100 chr7B 86.047 86 12 0 2291 2376 721311667 721311582 2.720000e-15 93.5
23 TraesCS6D01G314100 chr7A 87.302 63 7 1 2159 2221 272531126 272531187 1.270000e-08 71.3


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 TraesCS6D01G314100 chr6D 422602469 422605032 2563 True 4735.0 4735 100.0000 1 2564 1 chr6D.!!$R3 2563
1 TraesCS6D01G314100 chr6D 422216565 422217928 1363 True 798.5 1118 88.2220 1197 2544 2 chr6D.!!$R5 1347
2 TraesCS6D01G314100 chr6D 421696456 421697028 572 True 719.0 719 89.7030 994 1552 1 chr6D.!!$R2 558
3 TraesCS6D01G314100 chr6D 421463348 421466807 3459 False 671.5 702 85.2325 994 2564 2 chr6D.!!$F2 1570
4 TraesCS6D01G314100 chr6D 421662989 421664590 1601 True 652.5 712 84.8030 994 2564 2 chr6D.!!$R4 1570
5 TraesCS6D01G314100 chr6D 421680962 421681709 747 True 604.0 604 81.9870 1842 2564 1 chr6D.!!$R1 722
6 TraesCS6D01G314100 chr6B 636767003 636768215 1212 True 1456.0 1456 88.5690 467 1664 1 chr6B.!!$R2 1197
7 TraesCS6D01G314100 chr6B 636747296 636748219 923 True 1136.0 1136 89.0440 1646 2564 1 chr6B.!!$R1 918
8 TraesCS6D01G314100 chr6B 634501631 634502680 1049 False 527.0 885 84.3185 994 2514 2 chr6B.!!$F1 1520
9 TraesCS6D01G314100 chr6A 565341533 565343427 1894 True 916.5 1382 89.0770 1 2564 2 chr6A.!!$R1 2563
10 TraesCS6D01G314100 chr6A 564276192 564277680 1488 False 424.5 510 88.1470 994 2564 2 chr6A.!!$F2 1570

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
447 450 0.030638 CGTGGCCACAAAAGAAGGTG 59.969 55.0 34.16 11.04 34.82 4.00 F
1257 1284 0.464036 TCACAGTCAACGGCTTCAGT 59.536 50.0 0.00 0.00 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1449 2286 1.336887 GCTCCTTGTACTTGTGCTCGA 60.337 52.381 0.0 0.0 0.0 4.04 R
2460 5325 1.214367 TCGAGAACACGCAAAAGTCC 58.786 50.000 0.0 0.0 0.0 3.85 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 1.136891 GGTTCAGCCATGCCCATTAAC 59.863 52.381 0.00 0.00 37.17 2.01
38 39 1.102154 TTCAGCCATGCCCATTAACG 58.898 50.000 0.00 0.00 0.00 3.18
39 40 1.066257 CAGCCATGCCCATTAACGC 59.934 57.895 0.00 0.00 0.00 4.84
40 41 2.127232 AGCCATGCCCATTAACGCC 61.127 57.895 0.00 0.00 0.00 5.68
41 42 3.128375 CCATGCCCATTAACGCCC 58.872 61.111 0.00 0.00 0.00 6.13
42 43 2.498056 CCATGCCCATTAACGCCCC 61.498 63.158 0.00 0.00 0.00 5.80
43 44 1.756172 CATGCCCATTAACGCCCCA 60.756 57.895 0.00 0.00 0.00 4.96
44 45 1.114722 CATGCCCATTAACGCCCCAT 61.115 55.000 0.00 0.00 0.00 4.00
45 46 0.398381 ATGCCCATTAACGCCCCATT 60.398 50.000 0.00 0.00 0.00 3.16
46 47 0.259065 TGCCCATTAACGCCCCATTA 59.741 50.000 0.00 0.00 0.00 1.90
47 48 1.342076 TGCCCATTAACGCCCCATTAA 60.342 47.619 0.00 0.00 0.00 1.40
275 278 4.021368 TCCTAACTTTGAGACGAAGGGAAG 60.021 45.833 0.00 0.00 0.00 3.46
277 280 4.417426 AACTTTGAGACGAAGGGAAGAA 57.583 40.909 0.00 0.00 0.00 2.52
314 317 1.077357 AAGGAACCCACGCACACAA 60.077 52.632 0.00 0.00 0.00 3.33
331 334 2.670414 CACAACTTCCTCTCAAGCGATC 59.330 50.000 0.00 0.00 0.00 3.69
332 335 2.564947 ACAACTTCCTCTCAAGCGATCT 59.435 45.455 0.00 0.00 0.00 2.75
344 347 3.957535 CGATCTGCAATGGCGGCC 61.958 66.667 13.32 13.32 46.35 6.13
364 367 4.466726 GGCCTCCAACCACTAGTATATAGG 59.533 50.000 0.00 0.00 0.00 2.57
365 368 4.466726 GCCTCCAACCACTAGTATATAGGG 59.533 50.000 0.00 0.00 0.00 3.53
366 369 5.024118 CCTCCAACCACTAGTATATAGGGG 58.976 50.000 0.00 1.56 43.66 4.79
367 370 4.422984 TCCAACCACTAGTATATAGGGGC 58.577 47.826 3.05 0.00 41.80 5.80
369 372 4.223032 CCAACCACTAGTATATAGGGGCTG 59.777 50.000 3.05 1.67 41.80 4.85
371 374 3.181410 ACCACTAGTATATAGGGGCTGCA 60.181 47.826 0.50 0.00 41.80 4.41
372 375 3.195825 CCACTAGTATATAGGGGCTGCAC 59.804 52.174 0.50 0.00 30.41 4.57
374 377 4.528596 CACTAGTATATAGGGGCTGCACTT 59.471 45.833 0.21 0.00 0.00 3.16
375 378 5.715279 CACTAGTATATAGGGGCTGCACTTA 59.285 44.000 0.21 0.00 0.00 2.24
376 379 6.381420 CACTAGTATATAGGGGCTGCACTTAT 59.619 42.308 11.45 11.45 0.00 1.73
377 380 7.560262 CACTAGTATATAGGGGCTGCACTTATA 59.440 40.741 14.98 14.98 0.00 0.98
380 383 8.214721 AGTATATAGGGGCTGCACTTATAAAA 57.785 34.615 16.32 6.60 0.00 1.52
381 384 8.101419 AGTATATAGGGGCTGCACTTATAAAAC 58.899 37.037 16.32 16.05 0.00 2.43
382 385 2.735151 AGGGGCTGCACTTATAAAACC 58.265 47.619 0.21 0.00 0.00 3.27
383 386 2.311841 AGGGGCTGCACTTATAAAACCT 59.688 45.455 0.21 0.00 0.00 3.50
384 387 3.526019 AGGGGCTGCACTTATAAAACCTA 59.474 43.478 0.21 0.00 0.00 3.08
385 388 3.630769 GGGGCTGCACTTATAAAACCTAC 59.369 47.826 0.21 0.00 0.00 3.18
386 389 4.266714 GGGCTGCACTTATAAAACCTACA 58.733 43.478 0.50 0.00 0.00 2.74
387 390 4.887655 GGGCTGCACTTATAAAACCTACAT 59.112 41.667 0.50 0.00 0.00 2.29
388 391 5.008712 GGGCTGCACTTATAAAACCTACATC 59.991 44.000 0.50 0.00 0.00 3.06
389 392 5.823045 GGCTGCACTTATAAAACCTACATCT 59.177 40.000 0.50 0.00 0.00 2.90
390 393 6.990349 GGCTGCACTTATAAAACCTACATCTA 59.010 38.462 0.50 0.00 0.00 1.98
391 394 7.171678 GGCTGCACTTATAAAACCTACATCTAG 59.828 40.741 0.50 0.00 0.00 2.43
392 395 7.171678 GCTGCACTTATAAAACCTACATCTAGG 59.828 40.741 0.00 0.00 44.99 3.02
393 396 6.990349 TGCACTTATAAAACCTACATCTAGGC 59.010 38.462 0.00 0.00 43.42 3.93
394 397 7.147549 TGCACTTATAAAACCTACATCTAGGCT 60.148 37.037 0.00 0.00 43.42 4.58
395 398 7.715686 GCACTTATAAAACCTACATCTAGGCTT 59.284 37.037 0.00 0.00 43.42 4.35
401 404 5.827326 AACCTACATCTAGGCTTATTCCC 57.173 43.478 0.00 0.00 43.42 3.97
402 405 4.168883 ACCTACATCTAGGCTTATTCCCC 58.831 47.826 0.00 0.00 43.42 4.81
403 406 4.140423 ACCTACATCTAGGCTTATTCCCCT 60.140 45.833 0.00 0.00 43.42 4.79
404 407 4.846940 CCTACATCTAGGCTTATTCCCCTT 59.153 45.833 0.00 0.00 33.12 3.95
405 408 4.713792 ACATCTAGGCTTATTCCCCTTG 57.286 45.455 0.00 0.00 32.65 3.61
406 409 4.047883 ACATCTAGGCTTATTCCCCTTGT 58.952 43.478 0.00 0.00 32.65 3.16
407 410 4.141390 ACATCTAGGCTTATTCCCCTTGTG 60.141 45.833 0.00 0.00 32.65 3.33
408 411 2.777692 TCTAGGCTTATTCCCCTTGTGG 59.222 50.000 0.00 0.00 32.65 4.17
409 412 0.033109 AGGCTTATTCCCCTTGTGGC 60.033 55.000 0.00 0.00 0.00 5.01
410 413 1.043116 GGCTTATTCCCCTTGTGGCC 61.043 60.000 0.00 0.00 0.00 5.36
411 414 0.033109 GCTTATTCCCCTTGTGGCCT 60.033 55.000 3.32 0.00 0.00 5.19
412 415 1.214424 GCTTATTCCCCTTGTGGCCTA 59.786 52.381 3.32 0.00 0.00 3.93
413 416 2.158460 GCTTATTCCCCTTGTGGCCTAT 60.158 50.000 3.32 0.00 0.00 2.57
414 417 3.756117 CTTATTCCCCTTGTGGCCTATC 58.244 50.000 3.32 0.00 0.00 2.08
415 418 1.607225 ATTCCCCTTGTGGCCTATCA 58.393 50.000 3.32 0.00 0.00 2.15
416 419 1.607225 TTCCCCTTGTGGCCTATCAT 58.393 50.000 3.32 0.00 0.00 2.45
417 420 1.607225 TCCCCTTGTGGCCTATCATT 58.393 50.000 3.32 0.00 0.00 2.57
418 421 2.782922 TCCCCTTGTGGCCTATCATTA 58.217 47.619 3.32 0.00 0.00 1.90
419 422 3.335748 TCCCCTTGTGGCCTATCATTAT 58.664 45.455 3.32 0.00 0.00 1.28
420 423 3.330701 TCCCCTTGTGGCCTATCATTATC 59.669 47.826 3.32 0.00 0.00 1.75
421 424 3.074390 CCCCTTGTGGCCTATCATTATCA 59.926 47.826 3.32 0.00 0.00 2.15
422 425 4.074970 CCCTTGTGGCCTATCATTATCAC 58.925 47.826 3.32 0.00 0.00 3.06
423 426 4.074970 CCTTGTGGCCTATCATTATCACC 58.925 47.826 3.32 0.00 0.00 4.02
424 427 4.446167 CCTTGTGGCCTATCATTATCACCA 60.446 45.833 3.32 0.00 0.00 4.17
425 428 4.356405 TGTGGCCTATCATTATCACCAG 57.644 45.455 3.32 0.00 0.00 4.00
426 429 3.077359 GTGGCCTATCATTATCACCAGC 58.923 50.000 3.32 0.00 0.00 4.85
427 430 2.981784 TGGCCTATCATTATCACCAGCT 59.018 45.455 3.32 0.00 0.00 4.24
428 431 3.008375 TGGCCTATCATTATCACCAGCTC 59.992 47.826 3.32 0.00 0.00 4.09
429 432 3.257393 GCCTATCATTATCACCAGCTCG 58.743 50.000 0.00 0.00 0.00 5.03
430 433 3.306364 GCCTATCATTATCACCAGCTCGT 60.306 47.826 0.00 0.00 0.00 4.18
431 434 4.240888 CCTATCATTATCACCAGCTCGTG 58.759 47.826 4.93 4.93 34.93 4.35
439 442 2.594303 CCAGCTCGTGGCCACAAA 60.594 61.111 34.16 20.78 40.39 2.83
440 443 2.192861 CCAGCTCGTGGCCACAAAA 61.193 57.895 34.16 18.25 40.39 2.44
441 444 1.283793 CAGCTCGTGGCCACAAAAG 59.716 57.895 34.16 26.42 43.05 2.27
442 445 1.148273 AGCTCGTGGCCACAAAAGA 59.852 52.632 34.16 21.73 43.05 2.52
443 446 0.465460 AGCTCGTGGCCACAAAAGAA 60.465 50.000 34.16 11.60 43.05 2.52
444 447 0.040067 GCTCGTGGCCACAAAAGAAG 60.040 55.000 34.16 20.26 34.27 2.85
445 448 0.593128 CTCGTGGCCACAAAAGAAGG 59.407 55.000 34.16 16.05 0.00 3.46
446 449 0.106918 TCGTGGCCACAAAAGAAGGT 60.107 50.000 34.16 0.00 0.00 3.50
447 450 0.030638 CGTGGCCACAAAAGAAGGTG 59.969 55.000 34.16 11.04 34.82 4.00
448 451 1.398692 GTGGCCACAAAAGAAGGTGA 58.601 50.000 31.23 0.00 37.18 4.02
449 452 1.067060 GTGGCCACAAAAGAAGGTGAC 59.933 52.381 31.23 0.00 37.18 3.67
451 454 2.173782 TGGCCACAAAAGAAGGTGACTA 59.826 45.455 0.00 0.00 42.68 2.59
452 455 2.814336 GGCCACAAAAGAAGGTGACTAG 59.186 50.000 0.00 0.00 42.68 2.57
453 456 2.814336 GCCACAAAAGAAGGTGACTAGG 59.186 50.000 0.00 0.00 42.68 3.02
454 457 3.496160 GCCACAAAAGAAGGTGACTAGGA 60.496 47.826 0.00 0.00 42.68 2.94
455 458 4.714632 CCACAAAAGAAGGTGACTAGGAA 58.285 43.478 0.00 0.00 42.68 3.36
456 459 4.757149 CCACAAAAGAAGGTGACTAGGAAG 59.243 45.833 0.00 0.00 42.68 3.46
457 460 4.757149 CACAAAAGAAGGTGACTAGGAAGG 59.243 45.833 0.00 0.00 42.68 3.46
458 461 4.202472 ACAAAAGAAGGTGACTAGGAAGGG 60.202 45.833 0.00 0.00 42.68 3.95
459 462 2.255770 AGAAGGTGACTAGGAAGGGG 57.744 55.000 0.00 0.00 42.68 4.79
460 463 1.722851 AGAAGGTGACTAGGAAGGGGA 59.277 52.381 0.00 0.00 42.68 4.81
461 464 2.319438 AGAAGGTGACTAGGAAGGGGAT 59.681 50.000 0.00 0.00 42.68 3.85
462 465 2.182516 AGGTGACTAGGAAGGGGATG 57.817 55.000 0.00 0.00 40.61 3.51
463 466 1.132500 GGTGACTAGGAAGGGGATGG 58.868 60.000 0.00 0.00 0.00 3.51
464 467 1.344087 GGTGACTAGGAAGGGGATGGA 60.344 57.143 0.00 0.00 0.00 3.41
465 468 2.695585 GTGACTAGGAAGGGGATGGAT 58.304 52.381 0.00 0.00 0.00 3.41
485 488 2.461695 TGAGGGAGAAGATGAGGACAC 58.538 52.381 0.00 0.00 0.00 3.67
486 489 1.760029 GAGGGAGAAGATGAGGACACC 59.240 57.143 0.00 0.00 0.00 4.16
507 510 0.627451 TGATGATGCAAAGGGGCTCT 59.373 50.000 0.00 0.00 34.04 4.09
510 513 1.379576 GATGCAAAGGGGCTCTGCT 60.380 57.895 0.03 0.00 37.00 4.24
515 518 1.203287 GCAAAGGGGCTCTGCTTTTAG 59.797 52.381 0.00 0.00 33.20 1.85
518 521 1.754621 GGGGCTCTGCTTTTAGGGC 60.755 63.158 0.00 0.00 43.56 5.19
521 524 1.661498 GGCTCTGCTTTTAGGGCTGC 61.661 60.000 0.00 0.00 43.77 5.25
522 525 0.962356 GCTCTGCTTTTAGGGCTGCA 60.962 55.000 0.50 0.00 41.05 4.41
538 541 0.521291 TGCAACATTGTAGCGAAGGC 59.479 50.000 0.00 0.00 40.37 4.35
570 573 2.189521 GACTACACCCGGGCCATG 59.810 66.667 24.08 15.03 0.00 3.66
587 590 5.009110 GGGCCATGCTAAATTTCTAGTTCTC 59.991 44.000 4.39 0.00 0.00 2.87
607 610 0.935366 GCTACACGAGATGCGCCTAC 60.935 60.000 4.18 0.00 46.04 3.18
622 625 3.192466 CGCCTACCGCTTTTAATGTAGT 58.808 45.455 0.00 0.00 34.21 2.73
666 669 3.284617 TGCTACACTTCGGCTATGACTA 58.715 45.455 0.00 0.00 0.00 2.59
668 671 4.202020 TGCTACACTTCGGCTATGACTAAG 60.202 45.833 0.00 0.00 0.00 2.18
671 674 4.745649 ACACTTCGGCTATGACTAAGAAC 58.254 43.478 0.00 0.00 0.00 3.01
672 675 3.791887 CACTTCGGCTATGACTAAGAACG 59.208 47.826 0.00 0.00 0.00 3.95
674 677 1.121240 CGGCTATGACTAAGAACGCG 58.879 55.000 3.53 3.53 0.00 6.01
675 678 1.533338 CGGCTATGACTAAGAACGCGT 60.533 52.381 5.58 5.58 0.00 6.01
676 679 1.852895 GGCTATGACTAAGAACGCGTG 59.147 52.381 14.98 1.17 0.00 5.34
677 680 1.852895 GCTATGACTAAGAACGCGTGG 59.147 52.381 14.98 3.60 0.00 4.94
678 681 2.479049 GCTATGACTAAGAACGCGTGGA 60.479 50.000 14.98 0.00 0.00 4.02
679 682 2.961526 ATGACTAAGAACGCGTGGAT 57.038 45.000 14.98 4.05 0.00 3.41
681 684 2.602878 TGACTAAGAACGCGTGGATTC 58.397 47.619 14.98 6.52 0.00 2.52
682 685 2.029739 TGACTAAGAACGCGTGGATTCA 60.030 45.455 14.98 8.50 0.00 2.57
713 726 3.243873 TGGACGATGTTGATATCAGGAGC 60.244 47.826 5.39 0.00 0.00 4.70
721 734 1.969208 TGATATCAGGAGCAGCTGAGG 59.031 52.381 20.43 0.76 32.74 3.86
722 735 0.686224 ATATCAGGAGCAGCTGAGGC 59.314 55.000 20.43 1.09 39.06 4.70
724 737 3.714001 CAGGAGCAGCTGAGGCCA 61.714 66.667 20.43 0.00 39.73 5.36
740 753 1.004628 GGCCAGGCCCAAAATCAAATT 59.995 47.619 21.62 0.00 44.06 1.82
744 757 4.396522 CCAGGCCCAAAATCAAATTTTCA 58.603 39.130 0.00 0.00 40.27 2.69
746 759 5.477637 CCAGGCCCAAAATCAAATTTTCATT 59.522 36.000 0.00 0.00 40.27 2.57
777 790 7.560991 TGTACTCAAATGGGAATAATGAGCATT 59.439 33.333 0.97 0.97 40.86 3.56
797 810 9.507329 GAGCATTAGGTGGAATAGATCAAAATA 57.493 33.333 0.00 0.00 0.00 1.40
908 923 7.964604 AAGGATAGTAGTTTGACACTTTGAC 57.035 36.000 0.00 0.00 36.88 3.18
909 924 7.304497 AGGATAGTAGTTTGACACTTTGACT 57.696 36.000 0.00 0.00 36.88 3.41
910 925 8.418597 AGGATAGTAGTTTGACACTTTGACTA 57.581 34.615 0.00 0.00 36.88 2.59
911 926 9.036980 AGGATAGTAGTTTGACACTTTGACTAT 57.963 33.333 0.00 0.00 37.45 2.12
946 961 1.078143 CTACCCTGAGTTGCCCAGC 60.078 63.158 0.00 0.00 0.00 4.85
951 966 1.114722 CCTGAGTTGCCCAGCCAAAA 61.115 55.000 0.00 0.00 0.00 2.44
989 1004 1.202290 GCATTGGTATCCGTTTGGCTG 60.202 52.381 0.00 0.00 34.14 4.85
1050 1071 2.362503 ATCGTCCTCCTCGCCACA 60.363 61.111 0.00 0.00 0.00 4.17
1148 1175 2.722201 GGTCCGGGAACTGCGAGAT 61.722 63.158 4.39 0.00 0.00 2.75
1149 1176 1.218316 GTCCGGGAACTGCGAGATT 59.782 57.895 0.00 0.00 0.00 2.40
1157 1184 2.742053 GGAACTGCGAGATTAGCAACAA 59.258 45.455 0.00 0.00 44.67 2.83
1190 1217 2.813908 CGACGGCAAGCAGTACCC 60.814 66.667 0.00 0.00 0.00 3.69
1257 1284 0.464036 TCACAGTCAACGGCTTCAGT 59.536 50.000 0.00 0.00 0.00 3.41
1308 1335 2.202570 GACAGCGCGTACCACGAT 60.203 61.111 8.43 0.00 46.05 3.73
1360 1387 2.045926 GGTTCAGCGGCATGTCCT 60.046 61.111 1.45 0.00 0.00 3.85
1449 2286 4.353437 GACTCCCGGTTGCGACGT 62.353 66.667 0.00 0.00 0.00 4.34
1459 2296 2.300066 TTGCGACGTCGAGCACAAG 61.300 57.895 39.74 10.32 43.69 3.16
1463 2300 0.385098 CGACGTCGAGCACAAGTACA 60.385 55.000 33.35 0.00 43.02 2.90
1487 2325 2.461110 CCATGCGCCTACAACGTCC 61.461 63.158 4.18 0.00 0.00 4.79
1491 2329 2.125673 CGCCTACAACGTCCTGGG 60.126 66.667 0.00 0.00 0.00 4.45
1497 2335 4.077184 CAACGTCCTGGGCGCCTA 62.077 66.667 28.56 21.41 0.00 3.93
1539 2377 0.103208 GGCCTCGATCAGAACATCGT 59.897 55.000 0.00 0.00 44.99 3.73
1558 2396 2.811431 CGTTTTGCAGGATGTTACCTCA 59.189 45.455 0.00 0.00 38.32 3.86
1562 2400 5.692115 TTTGCAGGATGTTACCTCATCTA 57.308 39.130 6.63 0.00 42.45 1.98
1605 2483 3.840666 ACCATATGGATATTCGTGCTCCT 59.159 43.478 28.77 0.00 38.94 3.69
1728 2613 5.201713 AGAGTGAGATTCTCGTGTTTCAA 57.798 39.130 9.07 0.00 37.07 2.69
1749 2657 7.263100 TCAATAAATTCATCTTGGATCCACG 57.737 36.000 15.91 13.74 0.00 4.94
1751 2659 7.555914 TCAATAAATTCATCTTGGATCCACGAA 59.444 33.333 23.39 18.22 0.00 3.85
1756 2664 3.260632 TCATCTTGGATCCACGAACTCAA 59.739 43.478 23.39 1.62 0.00 3.02
1758 2666 4.079980 TCTTGGATCCACGAACTCAAAA 57.920 40.909 18.09 0.00 0.00 2.44
1858 4648 5.109210 CAAGACTGATTTGATGTAGGCGTA 58.891 41.667 0.00 0.00 0.00 4.42
1872 4662 5.549347 TGTAGGCGTATTTAAAGTGGACAA 58.451 37.500 0.00 0.00 0.00 3.18
1919 4709 8.611654 AAAGTCGACCTTAGCAAGTTTTATAA 57.388 30.769 13.01 0.00 31.48 0.98
1923 4716 9.836076 GTCGACCTTAGCAAGTTTTATAAATTT 57.164 29.630 3.51 0.00 0.00 1.82
1997 4797 2.472816 ACAATTGCTTTTGTTCCGCTG 58.527 42.857 5.05 0.00 36.43 5.18
2045 4860 2.115266 CAAACTGCCTCCCGGGTT 59.885 61.111 22.86 2.48 37.43 4.11
2111 4930 4.698625 ACCGCTTCCCTCCCTCGT 62.699 66.667 0.00 0.00 0.00 4.18
2131 4978 2.887152 GTCATTGTTGAAGGAGGCTGTT 59.113 45.455 0.00 0.00 32.48 3.16
2228 5077 2.972505 CAACGTCCCGCAACTGCT 60.973 61.111 0.00 0.00 39.32 4.24
2230 5079 1.374252 AACGTCCCGCAACTGCTAG 60.374 57.895 0.00 0.00 39.32 3.42
2282 5131 1.472878 GATGGCTACTCACACTCGTCA 59.527 52.381 0.00 0.00 0.00 4.35
2319 5168 3.983344 GCCAGATGTGTGTTCATTGTTTC 59.017 43.478 0.00 0.00 0.00 2.78
2450 5315 2.467838 AGAATCATGTCGATCGTGCAG 58.532 47.619 15.94 4.62 31.11 4.41
2460 5325 3.483922 GTCGATCGTGCAGAGAAATGTAG 59.516 47.826 15.94 0.00 0.00 2.74
2540 5408 0.526524 CAAGACGGATGGAGCTCGAC 60.527 60.000 7.83 1.23 0.00 4.20
2544 5413 0.393944 ACGGATGGAGCTCGACTACA 60.394 55.000 7.83 0.00 45.80 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 2.024414 CTTCTTTCGGCCTTAATGGGG 58.976 52.381 0.00 0.00 36.00 4.96
40 41 2.024414 CCTTCTTTCGGCCTTAATGGG 58.976 52.381 0.00 0.00 36.00 4.00
41 42 2.024414 CCCTTCTTTCGGCCTTAATGG 58.976 52.381 0.00 0.00 39.35 3.16
42 43 2.024414 CCCCTTCTTTCGGCCTTAATG 58.976 52.381 0.00 0.00 0.00 1.90
43 44 1.685180 GCCCCTTCTTTCGGCCTTAAT 60.685 52.381 0.00 0.00 36.63 1.40
44 45 0.323087 GCCCCTTCTTTCGGCCTTAA 60.323 55.000 0.00 0.00 36.63 1.85
45 46 1.301954 GCCCCTTCTTTCGGCCTTA 59.698 57.895 0.00 0.00 36.63 2.69
46 47 2.035783 GCCCCTTCTTTCGGCCTT 59.964 61.111 0.00 0.00 36.63 4.35
217 220 6.014584 TCACATCAACCAACTAGCTTAAGAGA 60.015 38.462 6.67 0.00 0.00 3.10
251 254 3.899360 TCCCTTCGTCTCAAAGTTAGGAA 59.101 43.478 0.00 0.00 0.00 3.36
253 256 3.955650 TCCCTTCGTCTCAAAGTTAGG 57.044 47.619 0.00 0.00 0.00 2.69
258 261 5.948992 AAATTCTTCCCTTCGTCTCAAAG 57.051 39.130 0.00 0.00 0.00 2.77
299 302 0.028902 GAAGTTGTGTGCGTGGGTTC 59.971 55.000 0.00 0.00 0.00 3.62
303 306 0.532862 AGAGGAAGTTGTGTGCGTGG 60.533 55.000 0.00 0.00 0.00 4.94
304 307 0.861837 GAGAGGAAGTTGTGTGCGTG 59.138 55.000 0.00 0.00 0.00 5.34
305 308 0.464036 TGAGAGGAAGTTGTGTGCGT 59.536 50.000 0.00 0.00 0.00 5.24
314 317 1.134848 GCAGATCGCTTGAGAGGAAGT 60.135 52.381 2.84 0.00 37.77 3.01
332 335 4.675161 TTGGAGGCCGCCATTGCA 62.675 61.111 30.16 11.73 37.86 4.08
344 347 4.466726 GCCCCTATATACTAGTGGTTGGAG 59.533 50.000 5.39 0.00 0.00 3.86
364 367 4.266714 TGTAGGTTTTATAAGTGCAGCCC 58.733 43.478 0.00 0.00 0.00 5.19
365 368 5.823045 AGATGTAGGTTTTATAAGTGCAGCC 59.177 40.000 0.00 0.00 0.00 4.85
366 369 6.927294 AGATGTAGGTTTTATAAGTGCAGC 57.073 37.500 0.00 0.00 0.00 5.25
367 370 8.594881 CCTAGATGTAGGTTTTATAAGTGCAG 57.405 38.462 7.79 0.00 41.15 4.41
369 372 7.715686 AAGCCTAGATGTAGGTTTTATAAGTGC 59.284 37.037 16.81 0.00 45.10 4.40
375 378 8.383947 GGGAATAAGCCTAGATGTAGGTTTTAT 58.616 37.037 20.72 17.83 45.10 1.40
376 379 7.202158 GGGGAATAAGCCTAGATGTAGGTTTTA 60.202 40.741 20.72 16.65 45.10 1.52
377 380 6.410504 GGGGAATAAGCCTAGATGTAGGTTTT 60.411 42.308 20.72 15.29 45.10 2.43
382 385 5.308237 ACAAGGGGAATAAGCCTAGATGTAG 59.692 44.000 0.00 0.00 0.00 2.74
383 386 5.071788 CACAAGGGGAATAAGCCTAGATGTA 59.928 44.000 0.00 0.00 0.00 2.29
384 387 4.047883 ACAAGGGGAATAAGCCTAGATGT 58.952 43.478 0.00 0.00 0.00 3.06
385 388 4.392940 CACAAGGGGAATAAGCCTAGATG 58.607 47.826 0.00 0.00 0.00 2.90
386 389 3.395941 CCACAAGGGGAATAAGCCTAGAT 59.604 47.826 0.00 0.00 0.00 1.98
387 390 2.777692 CCACAAGGGGAATAAGCCTAGA 59.222 50.000 0.00 0.00 0.00 2.43
388 391 2.749800 GCCACAAGGGGAATAAGCCTAG 60.750 54.545 0.00 0.00 37.04 3.02
389 392 1.214424 GCCACAAGGGGAATAAGCCTA 59.786 52.381 0.00 0.00 37.04 3.93
390 393 0.033109 GCCACAAGGGGAATAAGCCT 60.033 55.000 0.00 0.00 37.04 4.58
391 394 1.043116 GGCCACAAGGGGAATAAGCC 61.043 60.000 0.00 0.00 37.04 4.35
392 395 0.033109 AGGCCACAAGGGGAATAAGC 60.033 55.000 5.01 0.00 37.04 3.09
393 396 3.138283 TGATAGGCCACAAGGGGAATAAG 59.862 47.826 5.01 0.00 37.04 1.73
394 397 3.127250 TGATAGGCCACAAGGGGAATAA 58.873 45.455 5.01 0.00 37.04 1.40
395 398 2.782922 TGATAGGCCACAAGGGGAATA 58.217 47.619 5.01 0.00 37.04 1.75
396 399 1.607225 TGATAGGCCACAAGGGGAAT 58.393 50.000 5.01 0.00 37.04 3.01
397 400 1.607225 ATGATAGGCCACAAGGGGAA 58.393 50.000 5.01 0.00 37.04 3.97
398 401 1.607225 AATGATAGGCCACAAGGGGA 58.393 50.000 5.01 0.00 37.04 4.81
399 402 3.074390 TGATAATGATAGGCCACAAGGGG 59.926 47.826 5.01 0.00 37.04 4.79
400 403 4.074970 GTGATAATGATAGGCCACAAGGG 58.925 47.826 5.01 0.00 40.85 3.95
401 404 4.074970 GGTGATAATGATAGGCCACAAGG 58.925 47.826 5.01 0.00 38.23 3.61
402 405 4.717877 TGGTGATAATGATAGGCCACAAG 58.282 43.478 5.01 0.00 0.00 3.16
403 406 4.717877 CTGGTGATAATGATAGGCCACAA 58.282 43.478 5.01 0.00 0.00 3.33
404 407 3.496692 GCTGGTGATAATGATAGGCCACA 60.497 47.826 5.01 2.06 0.00 4.17
405 408 3.077359 GCTGGTGATAATGATAGGCCAC 58.923 50.000 5.01 0.00 0.00 5.01
406 409 2.981784 AGCTGGTGATAATGATAGGCCA 59.018 45.455 5.01 0.00 0.00 5.36
407 410 3.604582 GAGCTGGTGATAATGATAGGCC 58.395 50.000 0.00 0.00 0.00 5.19
408 411 3.257393 CGAGCTGGTGATAATGATAGGC 58.743 50.000 0.00 0.00 0.00 3.93
409 412 4.240888 CACGAGCTGGTGATAATGATAGG 58.759 47.826 23.05 0.00 40.38 2.57
410 413 4.240888 CCACGAGCTGGTGATAATGATAG 58.759 47.826 28.17 6.06 40.38 2.08
411 414 3.554960 GCCACGAGCTGGTGATAATGATA 60.555 47.826 28.17 0.00 42.99 2.15
412 415 2.808202 GCCACGAGCTGGTGATAATGAT 60.808 50.000 28.17 0.00 42.99 2.45
413 416 1.473257 GCCACGAGCTGGTGATAATGA 60.473 52.381 28.17 0.00 42.99 2.57
414 417 0.940126 GCCACGAGCTGGTGATAATG 59.060 55.000 28.17 13.14 42.99 1.90
415 418 0.179045 GGCCACGAGCTGGTGATAAT 60.179 55.000 28.17 0.00 42.99 1.28
416 419 1.220749 GGCCACGAGCTGGTGATAA 59.779 57.895 28.17 0.00 42.99 1.75
417 420 1.987306 TGGCCACGAGCTGGTGATA 60.987 57.895 28.17 12.07 42.99 2.15
418 421 3.321648 TGGCCACGAGCTGGTGAT 61.322 61.111 28.17 0.00 42.99 3.06
419 422 4.314440 GTGGCCACGAGCTGGTGA 62.314 66.667 28.17 7.52 42.99 4.02
420 423 4.624364 TGTGGCCACGAGCTGGTG 62.624 66.667 30.07 20.86 42.99 4.17
421 424 2.902423 TTTTGTGGCCACGAGCTGGT 62.902 55.000 30.07 0.00 42.99 4.00
422 425 2.133742 CTTTTGTGGCCACGAGCTGG 62.134 60.000 30.07 15.04 44.08 4.85
423 426 1.165907 TCTTTTGTGGCCACGAGCTG 61.166 55.000 30.07 20.24 43.05 4.24
424 427 0.465460 TTCTTTTGTGGCCACGAGCT 60.465 50.000 30.07 0.00 43.05 4.09
425 428 0.040067 CTTCTTTTGTGGCCACGAGC 60.040 55.000 30.07 7.85 42.60 5.03
426 429 0.593128 CCTTCTTTTGTGGCCACGAG 59.407 55.000 30.07 25.11 0.00 4.18
427 430 0.106918 ACCTTCTTTTGTGGCCACGA 60.107 50.000 30.07 26.57 0.00 4.35
428 431 0.030638 CACCTTCTTTTGTGGCCACG 59.969 55.000 30.07 16.33 0.00 4.94
429 432 1.067060 GTCACCTTCTTTTGTGGCCAC 59.933 52.381 29.67 29.67 30.98 5.01
430 433 1.064017 AGTCACCTTCTTTTGTGGCCA 60.064 47.619 0.00 0.00 37.82 5.36
431 434 1.692411 AGTCACCTTCTTTTGTGGCC 58.308 50.000 0.00 0.00 37.82 5.36
432 435 2.814336 CCTAGTCACCTTCTTTTGTGGC 59.186 50.000 0.00 0.00 37.36 5.01
433 436 4.351874 TCCTAGTCACCTTCTTTTGTGG 57.648 45.455 0.00 0.00 33.29 4.17
434 437 4.757149 CCTTCCTAGTCACCTTCTTTTGTG 59.243 45.833 0.00 0.00 0.00 3.33
435 438 4.202472 CCCTTCCTAGTCACCTTCTTTTGT 60.202 45.833 0.00 0.00 0.00 2.83
436 439 4.327680 CCCTTCCTAGTCACCTTCTTTTG 58.672 47.826 0.00 0.00 0.00 2.44
437 440 3.330998 CCCCTTCCTAGTCACCTTCTTTT 59.669 47.826 0.00 0.00 0.00 2.27
438 441 2.913617 CCCCTTCCTAGTCACCTTCTTT 59.086 50.000 0.00 0.00 0.00 2.52
439 442 2.113777 TCCCCTTCCTAGTCACCTTCTT 59.886 50.000 0.00 0.00 0.00 2.52
440 443 1.722851 TCCCCTTCCTAGTCACCTTCT 59.277 52.381 0.00 0.00 0.00 2.85
441 444 2.249309 TCCCCTTCCTAGTCACCTTC 57.751 55.000 0.00 0.00 0.00 3.46
442 445 2.482494 CATCCCCTTCCTAGTCACCTT 58.518 52.381 0.00 0.00 0.00 3.50
443 446 1.344496 CCATCCCCTTCCTAGTCACCT 60.344 57.143 0.00 0.00 0.00 4.00
444 447 1.132500 CCATCCCCTTCCTAGTCACC 58.868 60.000 0.00 0.00 0.00 4.02
445 448 2.176247 TCCATCCCCTTCCTAGTCAC 57.824 55.000 0.00 0.00 0.00 3.67
446 449 2.250008 TCATCCATCCCCTTCCTAGTCA 59.750 50.000 0.00 0.00 0.00 3.41
447 450 2.903135 CTCATCCATCCCCTTCCTAGTC 59.097 54.545 0.00 0.00 0.00 2.59
448 451 2.428484 CCTCATCCATCCCCTTCCTAGT 60.428 54.545 0.00 0.00 0.00 2.57
449 452 2.264455 CCTCATCCATCCCCTTCCTAG 58.736 57.143 0.00 0.00 0.00 3.02
450 453 1.132397 CCCTCATCCATCCCCTTCCTA 60.132 57.143 0.00 0.00 0.00 2.94
451 454 0.402566 CCCTCATCCATCCCCTTCCT 60.403 60.000 0.00 0.00 0.00 3.36
452 455 0.401979 TCCCTCATCCATCCCCTTCC 60.402 60.000 0.00 0.00 0.00 3.46
453 456 1.063183 CTCCCTCATCCATCCCCTTC 58.937 60.000 0.00 0.00 0.00 3.46
454 457 0.649992 TCTCCCTCATCCATCCCCTT 59.350 55.000 0.00 0.00 0.00 3.95
455 458 0.649992 TTCTCCCTCATCCATCCCCT 59.350 55.000 0.00 0.00 0.00 4.79
456 459 1.063183 CTTCTCCCTCATCCATCCCC 58.937 60.000 0.00 0.00 0.00 4.81
457 460 2.109229 TCTTCTCCCTCATCCATCCC 57.891 55.000 0.00 0.00 0.00 3.85
458 461 3.246301 TCATCTTCTCCCTCATCCATCC 58.754 50.000 0.00 0.00 0.00 3.51
459 462 3.261390 CCTCATCTTCTCCCTCATCCATC 59.739 52.174 0.00 0.00 0.00 3.51
460 463 3.116434 TCCTCATCTTCTCCCTCATCCAT 60.116 47.826 0.00 0.00 0.00 3.41
461 464 2.248423 TCCTCATCTTCTCCCTCATCCA 59.752 50.000 0.00 0.00 0.00 3.41
462 465 2.632512 GTCCTCATCTTCTCCCTCATCC 59.367 54.545 0.00 0.00 0.00 3.51
463 466 3.069443 GTGTCCTCATCTTCTCCCTCATC 59.931 52.174 0.00 0.00 0.00 2.92
464 467 3.037549 GTGTCCTCATCTTCTCCCTCAT 58.962 50.000 0.00 0.00 0.00 2.90
465 468 2.461695 GTGTCCTCATCTTCTCCCTCA 58.538 52.381 0.00 0.00 0.00 3.86
485 488 2.008268 GCCCCTTTGCATCATCACGG 62.008 60.000 0.00 0.00 0.00 4.94
486 489 1.033746 AGCCCCTTTGCATCATCACG 61.034 55.000 0.00 0.00 0.00 4.35
507 510 1.631405 ATGTTGCAGCCCTAAAAGCA 58.369 45.000 0.00 0.00 34.79 3.91
510 513 3.056891 GCTACAATGTTGCAGCCCTAAAA 60.057 43.478 14.44 0.00 40.80 1.52
515 518 1.137404 CGCTACAATGTTGCAGCCC 59.863 57.895 18.64 0.00 43.10 5.19
518 521 1.466360 GCCTTCGCTACAATGTTGCAG 60.466 52.381 18.64 9.76 34.26 4.41
538 541 4.106925 GTCCTGGGCCTGCCTGAG 62.107 72.222 4.53 4.61 36.10 3.35
552 555 3.087906 ATGGCCCGGGTGTAGTCC 61.088 66.667 24.63 14.34 0.00 3.85
570 573 6.291164 CGTGTAGCGAGAACTAGAAATTTAGC 60.291 42.308 0.00 0.00 44.77 3.09
607 610 3.498082 GCCAACACTACATTAAAAGCGG 58.502 45.455 0.00 0.00 0.00 5.52
651 654 3.734293 GCGTTCTTAGTCATAGCCGAAGT 60.734 47.826 0.00 0.00 0.00 3.01
658 661 3.416119 TCCACGCGTTCTTAGTCATAG 57.584 47.619 10.22 0.00 0.00 2.23
660 663 2.961526 ATCCACGCGTTCTTAGTCAT 57.038 45.000 10.22 0.00 0.00 3.06
661 664 2.029739 TGAATCCACGCGTTCTTAGTCA 60.030 45.455 10.22 7.49 0.00 3.41
666 669 1.464608 CATGTGAATCCACGCGTTCTT 59.535 47.619 10.22 2.66 46.06 2.52
668 671 1.061131 CTCATGTGAATCCACGCGTTC 59.939 52.381 10.22 5.12 46.06 3.95
671 674 2.009108 CCTCATGTGAATCCACGCG 58.991 57.895 3.53 3.53 46.06 6.01
672 675 0.745845 AGCCTCATGTGAATCCACGC 60.746 55.000 0.00 0.00 46.06 5.34
674 677 1.065199 TCCAGCCTCATGTGAATCCAC 60.065 52.381 0.00 0.00 43.46 4.02
675 678 1.065199 GTCCAGCCTCATGTGAATCCA 60.065 52.381 0.00 0.00 0.00 3.41
676 679 1.673168 GTCCAGCCTCATGTGAATCC 58.327 55.000 0.00 0.00 0.00 3.01
677 680 1.134699 TCGTCCAGCCTCATGTGAATC 60.135 52.381 0.00 0.00 0.00 2.52
678 681 0.904649 TCGTCCAGCCTCATGTGAAT 59.095 50.000 0.00 0.00 0.00 2.57
679 682 0.904649 ATCGTCCAGCCTCATGTGAA 59.095 50.000 0.00 0.00 0.00 3.18
681 684 0.107993 ACATCGTCCAGCCTCATGTG 60.108 55.000 0.00 0.00 0.00 3.21
682 685 0.615331 AACATCGTCCAGCCTCATGT 59.385 50.000 0.00 0.00 0.00 3.21
721 734 2.495155 AATTTGATTTTGGGCCTGGC 57.505 45.000 11.05 11.05 0.00 4.85
722 735 4.396522 TGAAAATTTGATTTTGGGCCTGG 58.603 39.130 4.53 0.00 42.15 4.45
724 737 8.882557 ATAAATGAAAATTTGATTTTGGGCCT 57.117 26.923 8.31 0.00 42.15 5.19
757 770 7.149973 CACCTAATGCTCATTATTCCCATTTG 58.850 38.462 3.11 0.00 33.29 2.32
760 773 5.074929 TCCACCTAATGCTCATTATTCCCAT 59.925 40.000 3.11 0.00 33.29 4.00
905 920 3.069586 CGATCCAAACAGCCCTATAGTCA 59.930 47.826 0.00 0.00 0.00 3.41
908 923 2.037772 AGCGATCCAAACAGCCCTATAG 59.962 50.000 0.00 0.00 0.00 1.31
909 924 2.047061 AGCGATCCAAACAGCCCTATA 58.953 47.619 0.00 0.00 0.00 1.31
910 925 0.839946 AGCGATCCAAACAGCCCTAT 59.160 50.000 0.00 0.00 0.00 2.57
911 926 1.138266 GTAGCGATCCAAACAGCCCTA 59.862 52.381 0.00 0.00 0.00 3.53
912 927 0.107654 GTAGCGATCCAAACAGCCCT 60.108 55.000 0.00 0.00 0.00 5.19
913 928 1.095807 GGTAGCGATCCAAACAGCCC 61.096 60.000 0.00 0.00 0.00 5.19
914 929 1.095807 GGGTAGCGATCCAAACAGCC 61.096 60.000 0.00 0.00 0.00 4.85
951 966 5.180271 CAATGCTATGGTCAAAGCCAAAAT 58.820 37.500 0.00 0.00 42.48 1.82
981 996 1.555967 TCTTATTGCCCCAGCCAAAC 58.444 50.000 0.00 0.00 38.69 2.93
984 999 0.106066 CCATCTTATTGCCCCAGCCA 60.106 55.000 0.00 0.00 38.69 4.75
989 1004 0.179018 AGTCGCCATCTTATTGCCCC 60.179 55.000 0.00 0.00 0.00 5.80
1050 1071 2.997897 GTGTGGGAGGCCGAGAGT 60.998 66.667 0.00 0.00 0.00 3.24
1148 1175 0.470766 ACAGTCCGGGTTGTTGCTAA 59.529 50.000 0.00 0.00 0.00 3.09
1149 1176 0.470766 AACAGTCCGGGTTGTTGCTA 59.529 50.000 19.35 0.00 36.26 3.49
1157 1184 4.657824 CGACGCAACAGTCCGGGT 62.658 66.667 0.00 0.00 37.85 5.28
1257 1284 4.090588 CCGCCGTCCTTGCCCTTA 62.091 66.667 0.00 0.00 0.00 2.69
1308 1335 1.366854 CGACGACCATCTCCGAGTCA 61.367 60.000 0.00 0.00 0.00 3.41
1367 1394 2.349590 CAGTGATCTTGATGTTGCGGA 58.650 47.619 0.00 0.00 0.00 5.54
1373 1400 2.625737 CCTTCGCAGTGATCTTGATGT 58.374 47.619 0.00 0.00 0.00 3.06
1426 2258 2.030562 CAACCGGGAGTCGCACTT 59.969 61.111 6.32 0.00 37.59 3.16
1449 2286 1.336887 GCTCCTTGTACTTGTGCTCGA 60.337 52.381 0.00 0.00 0.00 4.04
1459 2296 2.472909 GGCGCATGGCTCCTTGTAC 61.473 63.158 10.83 0.00 42.94 2.90
1528 2366 2.844946 TCCTGCAAAACGATGTTCTGA 58.155 42.857 0.00 0.00 0.00 3.27
1539 2377 4.922206 AGATGAGGTAACATCCTGCAAAA 58.078 39.130 0.00 0.00 45.20 2.44
1558 2396 6.377429 TCCAACTAACTGATCACTCGTTAGAT 59.623 38.462 27.35 18.72 38.88 1.98
1562 2400 4.557205 GTCCAACTAACTGATCACTCGTT 58.443 43.478 4.47 4.47 0.00 3.85
1690 2572 4.641396 TCACTCTTGAACAACCATCGATT 58.359 39.130 0.00 0.00 0.00 3.34
1728 2613 7.056635 AGTTCGTGGATCCAAGATGAATTTAT 58.943 34.615 27.82 8.03 34.70 1.40
1790 2698 8.865244 TTTTAATATAGGACACCCTTACCTCT 57.135 34.615 0.00 0.00 40.78 3.69
1799 2707 8.682710 TGTGAGCAAATTTTAATATAGGACACC 58.317 33.333 0.00 0.00 0.00 4.16
1829 2737 5.886960 ACATCAAATCAGTCTTGCTTACC 57.113 39.130 0.00 0.00 0.00 2.85
1831 2739 5.586243 GCCTACATCAAATCAGTCTTGCTTA 59.414 40.000 0.00 0.00 0.00 3.09
1832 2740 4.397417 GCCTACATCAAATCAGTCTTGCTT 59.603 41.667 0.00 0.00 0.00 3.91
1833 2741 3.944015 GCCTACATCAAATCAGTCTTGCT 59.056 43.478 0.00 0.00 0.00 3.91
1872 4662 9.355916 ACTTTAGAAGCCTTAAGACAAATCTTT 57.644 29.630 3.36 0.00 42.91 2.52
1987 4787 2.535012 TCACATGTACAGCGGAACAA 57.465 45.000 0.00 0.00 0.00 2.83
1989 4789 3.747193 CAATTCACATGTACAGCGGAAC 58.253 45.455 0.00 0.00 0.00 3.62
1997 4797 2.722094 TGGGAGGCAATTCACATGTAC 58.278 47.619 0.00 0.00 0.00 2.90
2067 4884 2.829003 CTCTAGGAGTGGCGGCGA 60.829 66.667 12.98 0.00 0.00 5.54
2111 4930 2.886523 CAACAGCCTCCTTCAACAATGA 59.113 45.455 0.00 0.00 0.00 2.57
2200 5049 1.522569 GGACGTTGGATCTGAGGGG 59.477 63.158 0.00 0.00 0.00 4.79
2228 5077 2.062777 CCTGGCCAGAGAGCAGCTA 61.063 63.158 34.91 0.00 0.00 3.32
2230 5079 4.486503 CCCTGGCCAGAGAGCAGC 62.487 72.222 34.91 0.00 0.00 5.25
2383 5238 7.197071 TGGTGAAACATGTTGTTAGATGTAC 57.803 36.000 12.82 1.65 40.14 2.90
2450 5315 4.213482 ACACGCAAAAGTCCTACATTTCTC 59.787 41.667 0.00 0.00 0.00 2.87
2460 5325 1.214367 TCGAGAACACGCAAAAGTCC 58.786 50.000 0.00 0.00 0.00 3.85
2540 5408 4.682787 TCATAGTCTCCGCAACATTGTAG 58.317 43.478 0.00 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.