Multiple sequence alignment - TraesCS7D01G172000

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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 TraesCS7D01G172000 chr7D 100.000 4481 0 0 1 4481 124297565 124302045 0.000000e+00 8275.0
1 TraesCS7D01G172000 chr7D 88.859 736 63 7 3759 4481 397758644 397757915 0.000000e+00 887.0
2 TraesCS7D01G172000 chr7D 88.056 720 80 6 3760 4479 342217617 342216904 0.000000e+00 848.0
3 TraesCS7D01G172000 chr7A 95.492 3438 124 11 581 4006 126864635 126868053 0.000000e+00 5461.0
4 TraesCS7D01G172000 chr7A 88.456 719 73 8 3760 4475 503629017 503629728 0.000000e+00 859.0
5 TraesCS7D01G172000 chr7B 92.568 2072 95 26 581 2619 86138909 86140954 0.000000e+00 2918.0
6 TraesCS7D01G172000 chr7B 95.793 1141 46 2 2616 3756 86141032 86142170 0.000000e+00 1840.0
7 TraesCS7D01G172000 chr7B 89.097 587 44 12 3 579 539866287 539865711 0.000000e+00 712.0
8 TraesCS7D01G172000 chr7B 90.037 271 26 1 3756 4026 27203018 27203287 2.560000e-92 350.0
9 TraesCS7D01G172000 chr5D 98.448 580 6 3 1 579 489087916 489087339 0.000000e+00 1018.0
10 TraesCS7D01G172000 chr5D 88.920 722 76 4 3760 4481 162727247 162727964 0.000000e+00 887.0
11 TraesCS7D01G172000 chr3D 89.039 739 56 12 3760 4481 284325387 284326117 0.000000e+00 893.0
12 TraesCS7D01G172000 chr3D 88.071 679 66 4 3816 4481 125957242 125956566 0.000000e+00 791.0
13 TraesCS7D01G172000 chr2B 88.980 735 62 5 3760 4481 256919682 256918954 0.000000e+00 891.0
14 TraesCS7D01G172000 chr2B 86.434 258 25 6 332 579 683380023 683379766 1.590000e-69 274.0
15 TraesCS7D01G172000 chr1D 90.149 670 56 6 3760 4426 256070024 256069362 0.000000e+00 863.0
16 TraesCS7D01G172000 chr4D 87.758 678 65 10 3750 4425 365959491 365960152 0.000000e+00 776.0
17 TraesCS7D01G172000 chr4D 79.327 1040 193 14 2656 3675 52468959 52469996 0.000000e+00 710.0
18 TraesCS7D01G172000 chr4D 80.000 505 81 15 953 1450 52467476 52467967 5.510000e-94 355.0
19 TraesCS7D01G172000 chr4B 80.246 977 176 13 2656 3617 76814889 76815863 0.000000e+00 719.0
20 TraesCS7D01G172000 chr4B 80.198 505 80 15 953 1450 76813401 76813892 1.180000e-95 361.0
21 TraesCS7D01G172000 chr4A 79.195 1019 189 18 2685 3682 544202764 544201748 0.000000e+00 686.0
22 TraesCS7D01G172000 chr2D 81.831 732 62 33 3760 4481 136738914 136738244 2.360000e-152 549.0
23 TraesCS7D01G172000 chr2D 83.738 535 40 21 3760 4284 568421745 568422242 3.160000e-126 462.0
24 TraesCS7D01G172000 chr5A 80.544 478 82 7 960 1436 606060638 606060171 1.530000e-94 357.0
25 TraesCS7D01G172000 chr2A 95.122 41 2 0 3359 3399 761176660 761176700 1.040000e-06 65.8
26 TraesCS7D01G172000 chr5B 97.143 35 1 0 596 630 595642454 595642420 4.840000e-05 60.2


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 TraesCS7D01G172000 chr7D 124297565 124302045 4480 False 8275.0 8275 100.0000 1 4481 1 chr7D.!!$F1 4480
1 TraesCS7D01G172000 chr7D 397757915 397758644 729 True 887.0 887 88.8590 3759 4481 1 chr7D.!!$R2 722
2 TraesCS7D01G172000 chr7D 342216904 342217617 713 True 848.0 848 88.0560 3760 4479 1 chr7D.!!$R1 719
3 TraesCS7D01G172000 chr7A 126864635 126868053 3418 False 5461.0 5461 95.4920 581 4006 1 chr7A.!!$F1 3425
4 TraesCS7D01G172000 chr7A 503629017 503629728 711 False 859.0 859 88.4560 3760 4475 1 chr7A.!!$F2 715
5 TraesCS7D01G172000 chr7B 86138909 86142170 3261 False 2379.0 2918 94.1805 581 3756 2 chr7B.!!$F2 3175
6 TraesCS7D01G172000 chr7B 539865711 539866287 576 True 712.0 712 89.0970 3 579 1 chr7B.!!$R1 576
7 TraesCS7D01G172000 chr5D 489087339 489087916 577 True 1018.0 1018 98.4480 1 579 1 chr5D.!!$R1 578
8 TraesCS7D01G172000 chr5D 162727247 162727964 717 False 887.0 887 88.9200 3760 4481 1 chr5D.!!$F1 721
9 TraesCS7D01G172000 chr3D 284325387 284326117 730 False 893.0 893 89.0390 3760 4481 1 chr3D.!!$F1 721
10 TraesCS7D01G172000 chr3D 125956566 125957242 676 True 791.0 791 88.0710 3816 4481 1 chr3D.!!$R1 665
11 TraesCS7D01G172000 chr2B 256918954 256919682 728 True 891.0 891 88.9800 3760 4481 1 chr2B.!!$R1 721
12 TraesCS7D01G172000 chr1D 256069362 256070024 662 True 863.0 863 90.1490 3760 4426 1 chr1D.!!$R1 666
13 TraesCS7D01G172000 chr4D 365959491 365960152 661 False 776.0 776 87.7580 3750 4425 1 chr4D.!!$F1 675
14 TraesCS7D01G172000 chr4D 52467476 52469996 2520 False 532.5 710 79.6635 953 3675 2 chr4D.!!$F2 2722
15 TraesCS7D01G172000 chr4B 76813401 76815863 2462 False 540.0 719 80.2220 953 3617 2 chr4B.!!$F1 2664
16 TraesCS7D01G172000 chr4A 544201748 544202764 1016 True 686.0 686 79.1950 2685 3682 1 chr4A.!!$R1 997
17 TraesCS7D01G172000 chr2D 136738244 136738914 670 True 549.0 549 81.8310 3760 4481 1 chr2D.!!$R1 721

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
410 418 0.030504 TGCATTTGTCAGGTTGTGCG 59.969 50.0 0.00 0.00 35.46 5.34 F
547 555 0.251121 TAATGGGTGCAGTGTGGGTG 60.251 55.0 0.00 0.00 0.00 4.61 F
766 774 0.321298 GGAACGCTTGGCTTCAGGTA 60.321 55.0 0.00 0.00 0.00 3.08 F
2242 2542 0.615331 GCCAGACTCCTCATGGTGAA 59.385 55.0 0.00 0.00 36.43 3.18 F
2716 3110 0.329261 CATGGTCCAGGCTCCTGAAA 59.671 55.0 17.08 2.51 46.30 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2211 2511 1.279271 GAGTCTGGCAACACACCCTAT 59.721 52.381 0.00 0.0 46.17 2.57 R
2231 2531 2.288395 GGCACAACTTTTCACCATGAGG 60.288 50.000 0.00 0.0 42.21 3.86 R
2405 2716 2.942376 ACGCAGTTGATGACAGAAACAA 59.058 40.909 5.98 0.0 37.78 2.83 R
3224 3618 0.322008 CTCTGACAGGTTTGCCTCCC 60.322 60.000 1.81 0.0 44.97 4.30 R
4440 4914 0.336048 CCTGTTCATCCACCCCCAAT 59.664 55.000 0.00 0.0 0.00 3.16 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
367 375 3.909776 ACATGCATGTGACAGAAAGTG 57.090 42.857 30.92 2.24 40.03 3.16
369 377 0.953727 TGCATGTGACAGAAAGTGGC 59.046 50.000 0.00 0.00 32.89 5.01
370 378 0.110056 GCATGTGACAGAAAGTGGCG 60.110 55.000 0.00 0.00 36.69 5.69
371 379 1.229428 CATGTGACAGAAAGTGGCGT 58.771 50.000 0.00 0.00 36.69 5.68
372 380 1.069703 CATGTGACAGAAAGTGGCGTG 60.070 52.381 0.00 0.00 36.69 5.34
373 381 0.176910 TGTGACAGAAAGTGGCGTGA 59.823 50.000 0.00 0.00 36.69 4.35
374 382 0.861837 GTGACAGAAAGTGGCGTGAG 59.138 55.000 0.00 0.00 36.69 3.51
375 383 0.249868 TGACAGAAAGTGGCGTGAGG 60.250 55.000 0.00 0.00 36.69 3.86
376 384 0.951040 GACAGAAAGTGGCGTGAGGG 60.951 60.000 0.00 0.00 0.00 4.30
377 385 1.672356 CAGAAAGTGGCGTGAGGGG 60.672 63.158 0.00 0.00 0.00 4.79
378 386 1.841556 AGAAAGTGGCGTGAGGGGA 60.842 57.895 0.00 0.00 0.00 4.81
379 387 1.376037 GAAAGTGGCGTGAGGGGAG 60.376 63.158 0.00 0.00 0.00 4.30
380 388 1.827399 GAAAGTGGCGTGAGGGGAGA 61.827 60.000 0.00 0.00 0.00 3.71
381 389 1.831652 AAAGTGGCGTGAGGGGAGAG 61.832 60.000 0.00 0.00 0.00 3.20
382 390 2.680352 GTGGCGTGAGGGGAGAGA 60.680 66.667 0.00 0.00 0.00 3.10
383 391 2.363018 TGGCGTGAGGGGAGAGAG 60.363 66.667 0.00 0.00 0.00 3.20
384 392 2.043852 GGCGTGAGGGGAGAGAGA 60.044 66.667 0.00 0.00 0.00 3.10
385 393 1.456705 GGCGTGAGGGGAGAGAGAT 60.457 63.158 0.00 0.00 0.00 2.75
386 394 1.739049 GCGTGAGGGGAGAGAGATG 59.261 63.158 0.00 0.00 0.00 2.90
387 395 1.040339 GCGTGAGGGGAGAGAGATGT 61.040 60.000 0.00 0.00 0.00 3.06
388 396 0.743688 CGTGAGGGGAGAGAGATGTG 59.256 60.000 0.00 0.00 0.00 3.21
389 397 0.463620 GTGAGGGGAGAGAGATGTGC 59.536 60.000 0.00 0.00 0.00 4.57
390 398 0.041684 TGAGGGGAGAGAGATGTGCA 59.958 55.000 0.00 0.00 0.00 4.57
391 399 1.343782 TGAGGGGAGAGAGATGTGCAT 60.344 52.381 0.00 0.00 0.00 3.96
392 400 1.070445 GAGGGGAGAGAGATGTGCATG 59.930 57.143 0.00 0.00 0.00 4.06
393 401 0.534652 GGGGAGAGAGATGTGCATGC 60.535 60.000 11.82 11.82 0.00 4.06
394 402 0.179702 GGGAGAGAGATGTGCATGCA 59.820 55.000 18.46 18.46 0.00 3.96
395 403 1.202782 GGGAGAGAGATGTGCATGCAT 60.203 52.381 25.64 8.94 0.00 3.96
396 404 2.573369 GGAGAGAGATGTGCATGCATT 58.427 47.619 25.64 14.89 0.00 3.56
397 405 2.950309 GGAGAGAGATGTGCATGCATTT 59.050 45.455 25.64 14.49 0.00 2.32
398 406 3.243101 GGAGAGAGATGTGCATGCATTTG 60.243 47.826 25.64 0.00 0.00 2.32
399 407 3.353557 AGAGAGATGTGCATGCATTTGT 58.646 40.909 25.64 12.86 0.00 2.83
400 408 3.377485 AGAGAGATGTGCATGCATTTGTC 59.623 43.478 25.64 20.39 0.00 3.18
401 409 3.086282 AGAGATGTGCATGCATTTGTCA 58.914 40.909 25.64 16.96 0.00 3.58
402 410 3.128764 AGAGATGTGCATGCATTTGTCAG 59.871 43.478 25.64 0.00 0.00 3.51
403 411 2.165641 AGATGTGCATGCATTTGTCAGG 59.834 45.455 25.64 0.00 0.00 3.86
404 412 1.330234 TGTGCATGCATTTGTCAGGT 58.670 45.000 25.64 0.00 0.00 4.00
405 413 1.687660 TGTGCATGCATTTGTCAGGTT 59.312 42.857 25.64 0.00 0.00 3.50
406 414 2.063266 GTGCATGCATTTGTCAGGTTG 58.937 47.619 25.64 0.00 0.00 3.77
407 415 1.687660 TGCATGCATTTGTCAGGTTGT 59.312 42.857 18.46 0.00 0.00 3.32
408 416 2.063266 GCATGCATTTGTCAGGTTGTG 58.937 47.619 14.21 0.00 0.00 3.33
409 417 2.063266 CATGCATTTGTCAGGTTGTGC 58.937 47.619 0.00 0.00 0.00 4.57
410 418 0.030504 TGCATTTGTCAGGTTGTGCG 59.969 50.000 0.00 0.00 35.46 5.34
411 419 0.664166 GCATTTGTCAGGTTGTGCGG 60.664 55.000 0.00 0.00 0.00 5.69
412 420 0.667993 CATTTGTCAGGTTGTGCGGT 59.332 50.000 0.00 0.00 0.00 5.68
413 421 0.667993 ATTTGTCAGGTTGTGCGGTG 59.332 50.000 0.00 0.00 0.00 4.94
414 422 0.393132 TTTGTCAGGTTGTGCGGTGA 60.393 50.000 0.00 0.00 0.00 4.02
415 423 0.393132 TTGTCAGGTTGTGCGGTGAA 60.393 50.000 0.00 0.00 0.00 3.18
416 424 1.092921 TGTCAGGTTGTGCGGTGAAC 61.093 55.000 0.00 0.00 0.00 3.18
417 425 1.092921 GTCAGGTTGTGCGGTGAACA 61.093 55.000 0.00 0.00 0.00 3.18
418 426 0.813610 TCAGGTTGTGCGGTGAACAG 60.814 55.000 0.00 0.00 0.00 3.16
419 427 1.095228 CAGGTTGTGCGGTGAACAGT 61.095 55.000 0.00 0.00 0.00 3.55
420 428 0.466543 AGGTTGTGCGGTGAACAGTA 59.533 50.000 0.00 0.00 0.00 2.74
421 429 0.584876 GGTTGTGCGGTGAACAGTAC 59.415 55.000 0.00 0.00 0.00 2.73
422 430 0.584876 GTTGTGCGGTGAACAGTACC 59.415 55.000 0.08 0.00 34.81 3.34
423 431 0.533308 TTGTGCGGTGAACAGTACCC 60.533 55.000 0.08 0.00 34.66 3.69
424 432 1.370064 GTGCGGTGAACAGTACCCT 59.630 57.895 0.00 0.00 34.66 4.34
425 433 0.604578 GTGCGGTGAACAGTACCCTA 59.395 55.000 0.00 0.00 34.66 3.53
426 434 1.206371 GTGCGGTGAACAGTACCCTAT 59.794 52.381 0.00 0.00 34.66 2.57
427 435 1.903860 TGCGGTGAACAGTACCCTATT 59.096 47.619 0.00 0.00 34.66 1.73
428 436 2.093869 TGCGGTGAACAGTACCCTATTC 60.094 50.000 0.00 0.00 34.66 1.75
429 437 2.167900 GCGGTGAACAGTACCCTATTCT 59.832 50.000 0.00 0.00 34.66 2.40
430 438 3.782046 CGGTGAACAGTACCCTATTCTG 58.218 50.000 0.00 0.00 34.66 3.02
431 439 3.194968 CGGTGAACAGTACCCTATTCTGT 59.805 47.826 0.00 0.00 43.04 3.41
438 446 6.732896 ACAGTACCCTATTCTGTTCCTATG 57.267 41.667 0.00 0.00 39.00 2.23
439 447 6.203072 ACAGTACCCTATTCTGTTCCTATGT 58.797 40.000 0.00 0.00 39.00 2.29
440 448 6.324254 ACAGTACCCTATTCTGTTCCTATGTC 59.676 42.308 0.00 0.00 39.00 3.06
441 449 6.551601 CAGTACCCTATTCTGTTCCTATGTCT 59.448 42.308 0.00 0.00 0.00 3.41
442 450 6.778559 AGTACCCTATTCTGTTCCTATGTCTC 59.221 42.308 0.00 0.00 0.00 3.36
443 451 4.902448 ACCCTATTCTGTTCCTATGTCTCC 59.098 45.833 0.00 0.00 0.00 3.71
444 452 5.151454 CCCTATTCTGTTCCTATGTCTCCT 58.849 45.833 0.00 0.00 0.00 3.69
445 453 5.011533 CCCTATTCTGTTCCTATGTCTCCTG 59.988 48.000 0.00 0.00 0.00 3.86
446 454 3.895232 TTCTGTTCCTATGTCTCCTGC 57.105 47.619 0.00 0.00 0.00 4.85
447 455 2.111384 TCTGTTCCTATGTCTCCTGCC 58.889 52.381 0.00 0.00 0.00 4.85
448 456 2.114616 CTGTTCCTATGTCTCCTGCCT 58.885 52.381 0.00 0.00 0.00 4.75
449 457 3.052869 TCTGTTCCTATGTCTCCTGCCTA 60.053 47.826 0.00 0.00 0.00 3.93
450 458 3.706594 CTGTTCCTATGTCTCCTGCCTAA 59.293 47.826 0.00 0.00 0.00 2.69
451 459 4.101114 TGTTCCTATGTCTCCTGCCTAAA 58.899 43.478 0.00 0.00 0.00 1.85
452 460 4.721776 TGTTCCTATGTCTCCTGCCTAAAT 59.278 41.667 0.00 0.00 0.00 1.40
453 461 5.191722 TGTTCCTATGTCTCCTGCCTAAATT 59.808 40.000 0.00 0.00 0.00 1.82
454 462 6.385759 TGTTCCTATGTCTCCTGCCTAAATTA 59.614 38.462 0.00 0.00 0.00 1.40
455 463 6.420913 TCCTATGTCTCCTGCCTAAATTAC 57.579 41.667 0.00 0.00 0.00 1.89
456 464 6.143915 TCCTATGTCTCCTGCCTAAATTACT 58.856 40.000 0.00 0.00 0.00 2.24
457 465 7.302948 TCCTATGTCTCCTGCCTAAATTACTA 58.697 38.462 0.00 0.00 0.00 1.82
458 466 7.956315 TCCTATGTCTCCTGCCTAAATTACTAT 59.044 37.037 0.00 0.00 0.00 2.12
459 467 8.598041 CCTATGTCTCCTGCCTAAATTACTATT 58.402 37.037 0.00 0.00 0.00 1.73
460 468 9.646427 CTATGTCTCCTGCCTAAATTACTATTC 57.354 37.037 0.00 0.00 0.00 1.75
461 469 7.432148 TGTCTCCTGCCTAAATTACTATTCA 57.568 36.000 0.00 0.00 0.00 2.57
462 470 7.272978 TGTCTCCTGCCTAAATTACTATTCAC 58.727 38.462 0.00 0.00 0.00 3.18
463 471 6.421202 GTCTCCTGCCTAAATTACTATTCACG 59.579 42.308 0.00 0.00 0.00 4.35
464 472 5.054477 TCCTGCCTAAATTACTATTCACGC 58.946 41.667 0.00 0.00 0.00 5.34
465 473 4.814234 CCTGCCTAAATTACTATTCACGCA 59.186 41.667 0.00 0.00 0.00 5.24
466 474 5.277345 CCTGCCTAAATTACTATTCACGCAC 60.277 44.000 0.00 0.00 0.00 5.34
467 475 5.424757 TGCCTAAATTACTATTCACGCACT 58.575 37.500 0.00 0.00 0.00 4.40
468 476 5.293324 TGCCTAAATTACTATTCACGCACTG 59.707 40.000 0.00 0.00 0.00 3.66
469 477 5.738370 CCTAAATTACTATTCACGCACTGC 58.262 41.667 0.00 0.00 0.00 4.40
470 478 5.523916 CCTAAATTACTATTCACGCACTGCT 59.476 40.000 0.00 0.00 0.00 4.24
471 479 5.880054 AAATTACTATTCACGCACTGCTT 57.120 34.783 0.00 0.00 0.00 3.91
472 480 5.880054 AATTACTATTCACGCACTGCTTT 57.120 34.783 0.00 0.00 0.00 3.51
473 481 6.978343 AATTACTATTCACGCACTGCTTTA 57.022 33.333 0.00 0.00 0.00 1.85
474 482 6.978343 ATTACTATTCACGCACTGCTTTAA 57.022 33.333 0.00 0.00 0.00 1.52
475 483 6.978343 TTACTATTCACGCACTGCTTTAAT 57.022 33.333 0.00 0.00 0.00 1.40
476 484 5.470845 ACTATTCACGCACTGCTTTAATC 57.529 39.130 0.00 0.00 0.00 1.75
477 485 5.178797 ACTATTCACGCACTGCTTTAATCT 58.821 37.500 0.00 0.00 0.00 2.40
478 486 4.606457 ATTCACGCACTGCTTTAATCTC 57.394 40.909 0.00 0.00 0.00 2.75
479 487 3.038788 TCACGCACTGCTTTAATCTCA 57.961 42.857 0.00 0.00 0.00 3.27
480 488 2.995939 TCACGCACTGCTTTAATCTCAG 59.004 45.455 0.00 0.00 0.00 3.35
481 489 2.738846 CACGCACTGCTTTAATCTCAGT 59.261 45.455 0.00 0.00 41.29 3.41
482 490 3.187227 CACGCACTGCTTTAATCTCAGTT 59.813 43.478 0.00 0.00 38.85 3.16
483 491 3.433615 ACGCACTGCTTTAATCTCAGTTC 59.566 43.478 0.00 0.00 38.85 3.01
484 492 3.681897 CGCACTGCTTTAATCTCAGTTCT 59.318 43.478 0.00 0.00 38.85 3.01
485 493 4.153117 CGCACTGCTTTAATCTCAGTTCTT 59.847 41.667 0.00 0.00 38.85 2.52
486 494 5.388944 GCACTGCTTTAATCTCAGTTCTTG 58.611 41.667 0.00 0.00 38.85 3.02
487 495 5.180117 GCACTGCTTTAATCTCAGTTCTTGA 59.820 40.000 0.00 0.00 38.85 3.02
488 496 6.293626 GCACTGCTTTAATCTCAGTTCTTGAA 60.294 38.462 0.00 0.00 38.85 2.69
489 497 7.642669 CACTGCTTTAATCTCAGTTCTTGAAA 58.357 34.615 0.00 0.00 38.85 2.69
490 498 8.295288 CACTGCTTTAATCTCAGTTCTTGAAAT 58.705 33.333 0.00 0.00 38.85 2.17
491 499 8.295288 ACTGCTTTAATCTCAGTTCTTGAAATG 58.705 33.333 4.66 4.66 37.78 2.32
492 500 8.169977 TGCTTTAATCTCAGTTCTTGAAATGT 57.830 30.769 10.00 0.00 34.81 2.71
493 501 9.283768 TGCTTTAATCTCAGTTCTTGAAATGTA 57.716 29.630 10.00 2.12 34.81 2.29
498 506 8.417780 AATCTCAGTTCTTGAAATGTATCTCG 57.582 34.615 10.00 0.00 34.81 4.04
499 507 7.158099 TCTCAGTTCTTGAAATGTATCTCGA 57.842 36.000 10.00 0.00 34.81 4.04
500 508 7.254137 TCTCAGTTCTTGAAATGTATCTCGAG 58.746 38.462 5.93 5.93 34.81 4.04
501 509 6.333416 TCAGTTCTTGAAATGTATCTCGAGG 58.667 40.000 13.56 0.00 31.34 4.63
502 510 6.152831 TCAGTTCTTGAAATGTATCTCGAGGA 59.847 38.462 13.56 0.00 31.34 3.71
503 511 6.813649 CAGTTCTTGAAATGTATCTCGAGGAA 59.186 38.462 13.56 0.38 0.00 3.36
504 512 7.331934 CAGTTCTTGAAATGTATCTCGAGGAAA 59.668 37.037 13.56 0.00 0.00 3.13
505 513 7.547370 AGTTCTTGAAATGTATCTCGAGGAAAG 59.453 37.037 13.56 4.08 0.00 2.62
506 514 5.812642 TCTTGAAATGTATCTCGAGGAAAGC 59.187 40.000 13.56 0.00 0.00 3.51
507 515 5.084818 TGAAATGTATCTCGAGGAAAGCA 57.915 39.130 13.56 5.64 0.00 3.91
508 516 5.111989 TGAAATGTATCTCGAGGAAAGCAG 58.888 41.667 13.56 0.00 0.00 4.24
509 517 2.586258 TGTATCTCGAGGAAAGCAGC 57.414 50.000 13.56 0.00 0.00 5.25
510 518 1.824852 TGTATCTCGAGGAAAGCAGCA 59.175 47.619 13.56 0.00 0.00 4.41
511 519 2.233676 TGTATCTCGAGGAAAGCAGCAA 59.766 45.455 13.56 0.00 0.00 3.91
512 520 2.479566 ATCTCGAGGAAAGCAGCAAA 57.520 45.000 13.56 0.00 0.00 3.68
513 521 1.512926 TCTCGAGGAAAGCAGCAAAC 58.487 50.000 13.56 0.00 0.00 2.93
514 522 1.202639 TCTCGAGGAAAGCAGCAAACA 60.203 47.619 13.56 0.00 0.00 2.83
515 523 1.808945 CTCGAGGAAAGCAGCAAACAT 59.191 47.619 3.91 0.00 0.00 2.71
516 524 1.536766 TCGAGGAAAGCAGCAAACATG 59.463 47.619 0.00 0.00 0.00 3.21
517 525 1.401931 CGAGGAAAGCAGCAAACATGG 60.402 52.381 0.00 0.00 0.00 3.66
518 526 1.888512 GAGGAAAGCAGCAAACATGGA 59.111 47.619 0.00 0.00 0.00 3.41
519 527 2.494870 GAGGAAAGCAGCAAACATGGAT 59.505 45.455 0.00 0.00 0.00 3.41
520 528 2.232941 AGGAAAGCAGCAAACATGGATG 59.767 45.455 0.00 0.00 0.00 3.51
521 529 2.613691 GAAAGCAGCAAACATGGATGG 58.386 47.619 0.00 0.00 0.00 3.51
522 530 0.899720 AAGCAGCAAACATGGATGGG 59.100 50.000 0.00 0.00 0.00 4.00
523 531 1.153509 GCAGCAAACATGGATGGGC 60.154 57.895 0.00 0.00 0.00 5.36
524 532 1.610554 GCAGCAAACATGGATGGGCT 61.611 55.000 0.00 0.00 35.29 5.19
525 533 1.766494 CAGCAAACATGGATGGGCTA 58.234 50.000 0.00 0.00 33.92 3.93
526 534 1.679680 CAGCAAACATGGATGGGCTAG 59.320 52.381 0.00 0.00 33.92 3.42
527 535 1.565759 AGCAAACATGGATGGGCTAGA 59.434 47.619 0.00 0.00 33.92 2.43
528 536 2.176364 AGCAAACATGGATGGGCTAGAT 59.824 45.455 0.00 0.00 33.92 1.98
529 537 3.395607 AGCAAACATGGATGGGCTAGATA 59.604 43.478 0.00 0.00 33.92 1.98
530 538 4.141181 AGCAAACATGGATGGGCTAGATAA 60.141 41.667 0.00 0.00 33.92 1.75
531 539 4.768968 GCAAACATGGATGGGCTAGATAAT 59.231 41.667 0.00 0.00 0.00 1.28
532 540 5.336213 GCAAACATGGATGGGCTAGATAATG 60.336 44.000 0.00 0.00 0.00 1.90
533 541 4.581309 ACATGGATGGGCTAGATAATGG 57.419 45.455 0.00 0.00 0.00 3.16
534 542 3.267812 ACATGGATGGGCTAGATAATGGG 59.732 47.826 0.00 0.00 0.00 4.00
535 543 3.004126 TGGATGGGCTAGATAATGGGT 57.996 47.619 0.00 0.00 0.00 4.51
536 544 2.644299 TGGATGGGCTAGATAATGGGTG 59.356 50.000 0.00 0.00 0.00 4.61
537 545 2.619074 GGATGGGCTAGATAATGGGTGC 60.619 54.545 0.00 0.00 0.00 5.01
538 546 1.517238 TGGGCTAGATAATGGGTGCA 58.483 50.000 0.00 0.00 0.00 4.57
539 547 1.421268 TGGGCTAGATAATGGGTGCAG 59.579 52.381 0.00 0.00 0.00 4.41
540 548 1.421646 GGGCTAGATAATGGGTGCAGT 59.578 52.381 0.00 0.00 0.00 4.40
541 549 2.498167 GGCTAGATAATGGGTGCAGTG 58.502 52.381 0.00 0.00 0.00 3.66
542 550 2.158755 GGCTAGATAATGGGTGCAGTGT 60.159 50.000 0.00 0.00 0.00 3.55
543 551 2.874701 GCTAGATAATGGGTGCAGTGTG 59.125 50.000 0.00 0.00 0.00 3.82
544 552 2.425143 AGATAATGGGTGCAGTGTGG 57.575 50.000 0.00 0.00 0.00 4.17
545 553 1.064463 AGATAATGGGTGCAGTGTGGG 60.064 52.381 0.00 0.00 0.00 4.61
546 554 0.704076 ATAATGGGTGCAGTGTGGGT 59.296 50.000 0.00 0.00 0.00 4.51
547 555 0.251121 TAATGGGTGCAGTGTGGGTG 60.251 55.000 0.00 0.00 0.00 4.61
548 556 4.892965 TGGGTGCAGTGTGGGTGC 62.893 66.667 0.00 0.00 41.59 5.01
572 580 4.021229 CCAACCCTGGGTATAGAAAAACC 58.979 47.826 20.91 0.00 39.30 3.27
573 581 4.509482 CCAACCCTGGGTATAGAAAAACCA 60.509 45.833 20.91 0.00 39.30 3.67
574 582 4.311520 ACCCTGGGTATAGAAAAACCAC 57.688 45.455 18.99 0.00 37.51 4.16
575 583 3.920841 ACCCTGGGTATAGAAAAACCACT 59.079 43.478 18.99 0.00 37.51 4.00
576 584 4.018688 ACCCTGGGTATAGAAAAACCACTC 60.019 45.833 18.99 0.00 37.51 3.51
577 585 4.227527 CCCTGGGTATAGAAAAACCACTCT 59.772 45.833 3.97 0.00 37.51 3.24
578 586 5.429130 CCTGGGTATAGAAAAACCACTCTC 58.571 45.833 0.00 0.00 37.51 3.20
579 587 5.429130 CTGGGTATAGAAAAACCACTCTCC 58.571 45.833 0.00 0.00 37.51 3.71
580 588 4.847512 TGGGTATAGAAAAACCACTCTCCA 59.152 41.667 0.00 0.00 37.51 3.86
581 589 5.491078 TGGGTATAGAAAAACCACTCTCCAT 59.509 40.000 0.00 0.00 37.51 3.41
582 590 6.056236 GGGTATAGAAAAACCACTCTCCATC 58.944 44.000 0.00 0.00 37.51 3.51
583 591 6.126739 GGGTATAGAAAAACCACTCTCCATCT 60.127 42.308 0.00 0.00 37.51 2.90
584 592 7.339482 GGTATAGAAAAACCACTCTCCATCTT 58.661 38.462 0.00 0.00 35.73 2.40
585 593 7.496263 GGTATAGAAAAACCACTCTCCATCTTC 59.504 40.741 0.00 0.00 35.73 2.87
586 594 5.574970 AGAAAAACCACTCTCCATCTTCT 57.425 39.130 0.00 0.00 0.00 2.85
747 755 2.736721 CGGATATATCACACCCAAAGCG 59.263 50.000 14.60 1.32 0.00 4.68
766 774 0.321298 GGAACGCTTGGCTTCAGGTA 60.321 55.000 0.00 0.00 0.00 3.08
771 779 2.434336 ACGCTTGGCTTCAGGTATGATA 59.566 45.455 0.00 0.00 34.73 2.15
787 795 6.046593 GGTATGATAGAACCAAATGACACGA 58.953 40.000 0.00 0.00 35.73 4.35
906 914 6.640518 TCTTCAGGCACCTGTTAAATAGTAG 58.359 40.000 16.12 2.64 43.96 2.57
908 916 5.730550 TCAGGCACCTGTTAAATAGTAGTG 58.269 41.667 16.12 0.00 43.96 2.74
1027 1035 2.224159 ACCCTTGCCACCGATGTCT 61.224 57.895 0.00 0.00 0.00 3.41
1389 1411 2.618053 GCCGTGTGCAACTATAAGTCT 58.382 47.619 0.00 0.00 40.77 3.24
1495 1597 8.347771 TCTACATGTCTATATGTCGTTGTTACC 58.652 37.037 0.00 0.00 41.31 2.85
1503 1609 2.215196 TGTCGTTGTTACCCTGAAAGC 58.785 47.619 0.00 0.00 0.00 3.51
1615 1724 4.275443 TGGTTTCCATGCAAATGCTTTTTC 59.725 37.500 6.97 0.00 42.66 2.29
1794 1912 7.254795 GGCGGTGATATATTTAGGCATAATCAC 60.255 40.741 11.48 11.48 36.22 3.06
1795 1913 7.516785 GCGGTGATATATTTAGGCATAATCACG 60.517 40.741 12.87 10.30 37.38 4.35
1796 1914 7.704899 CGGTGATATATTTAGGCATAATCACGA 59.295 37.037 12.87 0.00 37.38 4.35
2091 2387 8.593945 ATTGATATTTTACCTGTTGTCCACAT 57.406 30.769 0.00 0.00 33.76 3.21
2092 2388 8.415950 TTGATATTTTACCTGTTGTCCACATT 57.584 30.769 0.00 0.00 33.76 2.71
2211 2511 8.688747 ATTTGAATATGCAACCCTTTTTCAAA 57.311 26.923 14.00 14.00 39.89 2.69
2225 2525 4.329462 TTTTCAAATAGGGTGTGTTGCC 57.671 40.909 0.00 0.00 0.00 4.52
2231 2531 0.685097 TAGGGTGTGTTGCCAGACTC 59.315 55.000 0.00 0.00 35.60 3.36
2242 2542 0.615331 GCCAGACTCCTCATGGTGAA 59.385 55.000 0.00 0.00 36.43 3.18
2405 2716 8.197592 TGTTATGACCATCTACCCGTTAATAT 57.802 34.615 0.00 0.00 0.00 1.28
2420 2731 7.392113 ACCCGTTAATATTGTTTCTGTCATCAA 59.608 33.333 0.00 0.00 0.00 2.57
2421 2732 7.696453 CCCGTTAATATTGTTTCTGTCATCAAC 59.304 37.037 0.00 0.00 0.00 3.18
2424 2735 9.065871 GTTAATATTGTTTCTGTCATCAACTGC 57.934 33.333 0.00 0.00 0.00 4.40
2716 3110 0.329261 CATGGTCCAGGCTCCTGAAA 59.671 55.000 17.08 2.51 46.30 2.69
2751 3145 4.872691 GTGAACTCATGGGTAGAGAATGTG 59.127 45.833 0.00 0.00 36.91 3.21
3053 3447 4.280929 TCTTCTTCCTGAAAGACGTGATGA 59.719 41.667 0.00 0.00 43.75 2.92
3135 3529 4.755123 CCAACGGAGAAAGTTGTAGTTGAT 59.245 41.667 6.95 0.00 45.31 2.57
3224 3618 3.119708 GGTCTTCAGTTGCCATTTAGCAG 60.120 47.826 0.00 0.00 45.13 4.24
3225 3619 3.084039 TCTTCAGTTGCCATTTAGCAGG 58.916 45.455 0.00 0.00 45.13 4.85
3263 3657 3.184628 AGATGGTGAATTCTCAGGTGGA 58.815 45.455 7.05 0.00 30.14 4.02
3715 4129 5.762825 GCATCCTGATGAAATGCTTCTTA 57.237 39.130 11.23 0.00 41.95 2.10
3843 4257 8.194769 TGCTTATGACACTTCTATGACGATAAA 58.805 33.333 0.00 0.00 0.00 1.40
3892 4306 0.984995 GTGGTGGGCTCCTACTTCTT 59.015 55.000 2.46 0.00 0.00 2.52
4123 4579 1.183549 GGCTCTAACTGAACCCGAGA 58.816 55.000 0.00 0.00 0.00 4.04
4148 4604 1.719780 CGTTCGCTTACTGAACCTGAC 59.280 52.381 0.72 0.00 42.08 3.51
4185 4646 1.135199 GTTACTGAACCCGAGCGATCA 60.135 52.381 0.00 0.00 0.00 2.92
4266 4728 2.375174 TGAAGCCAATGGAACCTACTGT 59.625 45.455 2.05 0.00 0.00 3.55
4271 4739 3.866651 CCAATGGAACCTACTGTCTCTG 58.133 50.000 0.00 0.00 0.00 3.35
4296 4764 1.147376 CAGTGAACGTGGGGGTTGA 59.853 57.895 0.00 0.00 0.00 3.18
4345 4813 3.309556 GGGGTTGGATGAATAGTTCCCAA 60.310 47.826 0.00 0.00 35.77 4.12
4349 4818 5.200483 GTTGGATGAATAGTTCCCAATGGA 58.800 41.667 0.00 0.00 38.88 3.41
4412 4881 0.904865 TCGCTGGATGAACAGGACCT 60.905 55.000 0.00 0.00 38.90 3.85
4440 4914 4.680237 CCGCCACAGCCGAGTTGA 62.680 66.667 0.00 0.00 34.57 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
367 375 1.456705 ATCTCTCTCCCCTCACGCC 60.457 63.158 0.00 0.00 0.00 5.68
369 377 0.743688 CACATCTCTCTCCCCTCACG 59.256 60.000 0.00 0.00 0.00 4.35
370 378 0.463620 GCACATCTCTCTCCCCTCAC 59.536 60.000 0.00 0.00 0.00 3.51
371 379 0.041684 TGCACATCTCTCTCCCCTCA 59.958 55.000 0.00 0.00 0.00 3.86
372 380 1.070445 CATGCACATCTCTCTCCCCTC 59.930 57.143 0.00 0.00 0.00 4.30
373 381 1.129917 CATGCACATCTCTCTCCCCT 58.870 55.000 0.00 0.00 0.00 4.79
374 382 0.534652 GCATGCACATCTCTCTCCCC 60.535 60.000 14.21 0.00 0.00 4.81
375 383 0.179702 TGCATGCACATCTCTCTCCC 59.820 55.000 18.46 0.00 0.00 4.30
376 384 2.257691 ATGCATGCACATCTCTCTCC 57.742 50.000 25.37 0.00 0.00 3.71
377 385 3.377485 ACAAATGCATGCACATCTCTCTC 59.623 43.478 25.37 0.00 0.00 3.20
378 386 3.353557 ACAAATGCATGCACATCTCTCT 58.646 40.909 25.37 0.38 0.00 3.10
379 387 3.128068 TGACAAATGCATGCACATCTCTC 59.872 43.478 25.37 13.02 0.00 3.20
380 388 3.086282 TGACAAATGCATGCACATCTCT 58.914 40.909 25.37 2.19 0.00 3.10
381 389 3.435566 CTGACAAATGCATGCACATCTC 58.564 45.455 25.37 15.50 0.00 2.75
382 390 2.165641 CCTGACAAATGCATGCACATCT 59.834 45.455 25.37 3.57 0.00 2.90
383 391 2.094390 ACCTGACAAATGCATGCACATC 60.094 45.455 25.37 17.62 0.00 3.06
384 392 1.897133 ACCTGACAAATGCATGCACAT 59.103 42.857 25.37 12.68 0.00 3.21
385 393 1.330234 ACCTGACAAATGCATGCACA 58.670 45.000 25.37 15.10 0.00 4.57
386 394 2.063266 CAACCTGACAAATGCATGCAC 58.937 47.619 25.37 10.66 0.00 4.57
387 395 1.687660 ACAACCTGACAAATGCATGCA 59.312 42.857 25.04 25.04 0.00 3.96
388 396 2.063266 CACAACCTGACAAATGCATGC 58.937 47.619 11.82 11.82 0.00 4.06
389 397 2.063266 GCACAACCTGACAAATGCATG 58.937 47.619 0.00 0.00 33.27 4.06
390 398 1.336148 CGCACAACCTGACAAATGCAT 60.336 47.619 0.00 0.00 33.27 3.96
391 399 0.030504 CGCACAACCTGACAAATGCA 59.969 50.000 0.00 0.00 33.27 3.96
392 400 0.664166 CCGCACAACCTGACAAATGC 60.664 55.000 0.00 0.00 0.00 3.56
393 401 0.667993 ACCGCACAACCTGACAAATG 59.332 50.000 0.00 0.00 0.00 2.32
394 402 0.667993 CACCGCACAACCTGACAAAT 59.332 50.000 0.00 0.00 0.00 2.32
395 403 0.393132 TCACCGCACAACCTGACAAA 60.393 50.000 0.00 0.00 0.00 2.83
396 404 0.393132 TTCACCGCACAACCTGACAA 60.393 50.000 0.00 0.00 0.00 3.18
397 405 1.092921 GTTCACCGCACAACCTGACA 61.093 55.000 0.00 0.00 0.00 3.58
398 406 1.092921 TGTTCACCGCACAACCTGAC 61.093 55.000 0.00 0.00 0.00 3.51
399 407 0.813610 CTGTTCACCGCACAACCTGA 60.814 55.000 0.00 0.00 0.00 3.86
400 408 1.095228 ACTGTTCACCGCACAACCTG 61.095 55.000 0.00 0.00 0.00 4.00
401 409 0.466543 TACTGTTCACCGCACAACCT 59.533 50.000 0.00 0.00 0.00 3.50
402 410 0.584876 GTACTGTTCACCGCACAACC 59.415 55.000 0.00 0.00 0.00 3.77
403 411 0.584876 GGTACTGTTCACCGCACAAC 59.415 55.000 0.00 0.00 0.00 3.32
404 412 0.533308 GGGTACTGTTCACCGCACAA 60.533 55.000 0.00 0.00 36.89 3.33
405 413 1.070105 GGGTACTGTTCACCGCACA 59.930 57.895 0.00 0.00 36.89 4.57
406 414 0.604578 TAGGGTACTGTTCACCGCAC 59.395 55.000 0.00 0.00 36.89 5.34
407 415 1.563924 ATAGGGTACTGTTCACCGCA 58.436 50.000 0.00 0.00 36.89 5.69
408 416 2.167900 AGAATAGGGTACTGTTCACCGC 59.832 50.000 6.92 0.00 44.50 5.68
409 417 3.194968 ACAGAATAGGGTACTGTTCACCG 59.805 47.826 6.92 0.00 44.50 4.94
410 418 4.820894 ACAGAATAGGGTACTGTTCACC 57.179 45.455 6.92 0.00 44.50 4.02
415 423 6.203072 ACATAGGAACAGAATAGGGTACTGT 58.797 40.000 0.00 0.00 45.02 3.55
416 424 6.551601 AGACATAGGAACAGAATAGGGTACTG 59.448 42.308 0.00 0.00 37.62 2.74
417 425 6.684538 AGACATAGGAACAGAATAGGGTACT 58.315 40.000 0.00 0.00 0.00 2.73
418 426 6.015265 GGAGACATAGGAACAGAATAGGGTAC 60.015 46.154 0.00 0.00 0.00 3.34
419 427 6.075984 GGAGACATAGGAACAGAATAGGGTA 58.924 44.000 0.00 0.00 0.00 3.69
420 428 4.902448 GGAGACATAGGAACAGAATAGGGT 59.098 45.833 0.00 0.00 0.00 4.34
421 429 5.011533 CAGGAGACATAGGAACAGAATAGGG 59.988 48.000 0.00 0.00 0.00 3.53
422 430 5.510520 GCAGGAGACATAGGAACAGAATAGG 60.511 48.000 0.00 0.00 0.00 2.57
423 431 5.510520 GGCAGGAGACATAGGAACAGAATAG 60.511 48.000 0.00 0.00 0.00 1.73
424 432 4.345257 GGCAGGAGACATAGGAACAGAATA 59.655 45.833 0.00 0.00 0.00 1.75
425 433 3.135530 GGCAGGAGACATAGGAACAGAAT 59.864 47.826 0.00 0.00 0.00 2.40
426 434 2.501723 GGCAGGAGACATAGGAACAGAA 59.498 50.000 0.00 0.00 0.00 3.02
427 435 2.111384 GGCAGGAGACATAGGAACAGA 58.889 52.381 0.00 0.00 0.00 3.41
428 436 2.114616 AGGCAGGAGACATAGGAACAG 58.885 52.381 0.00 0.00 0.00 3.16
429 437 2.254152 AGGCAGGAGACATAGGAACA 57.746 50.000 0.00 0.00 0.00 3.18
430 438 4.755266 TTTAGGCAGGAGACATAGGAAC 57.245 45.455 0.00 0.00 0.00 3.62
431 439 5.975988 AATTTAGGCAGGAGACATAGGAA 57.024 39.130 0.00 0.00 0.00 3.36
432 440 6.143915 AGTAATTTAGGCAGGAGACATAGGA 58.856 40.000 0.00 0.00 0.00 2.94
433 441 6.426646 AGTAATTTAGGCAGGAGACATAGG 57.573 41.667 0.00 0.00 0.00 2.57
434 442 9.646427 GAATAGTAATTTAGGCAGGAGACATAG 57.354 37.037 0.00 0.00 0.00 2.23
435 443 9.154632 TGAATAGTAATTTAGGCAGGAGACATA 57.845 33.333 0.00 0.00 0.00 2.29
436 444 7.934120 GTGAATAGTAATTTAGGCAGGAGACAT 59.066 37.037 0.00 0.00 0.00 3.06
437 445 7.272978 GTGAATAGTAATTTAGGCAGGAGACA 58.727 38.462 0.00 0.00 0.00 3.41
438 446 6.421202 CGTGAATAGTAATTTAGGCAGGAGAC 59.579 42.308 0.00 0.00 0.00 3.36
439 447 6.513180 CGTGAATAGTAATTTAGGCAGGAGA 58.487 40.000 0.00 0.00 0.00 3.71
440 448 5.177696 GCGTGAATAGTAATTTAGGCAGGAG 59.822 44.000 3.60 0.00 40.34 3.69
441 449 5.054477 GCGTGAATAGTAATTTAGGCAGGA 58.946 41.667 3.60 0.00 40.34 3.86
442 450 4.814234 TGCGTGAATAGTAATTTAGGCAGG 59.186 41.667 6.27 0.00 43.36 4.85
443 451 5.523916 AGTGCGTGAATAGTAATTTAGGCAG 59.476 40.000 9.56 0.00 46.51 4.85
444 452 5.293324 CAGTGCGTGAATAGTAATTTAGGCA 59.707 40.000 6.27 6.27 44.91 4.75
445 453 5.738370 CAGTGCGTGAATAGTAATTTAGGC 58.262 41.667 1.93 1.93 40.76 3.93
446 454 5.523916 AGCAGTGCGTGAATAGTAATTTAGG 59.476 40.000 10.00 0.00 0.00 2.69
447 455 6.589830 AGCAGTGCGTGAATAGTAATTTAG 57.410 37.500 10.00 0.00 0.00 1.85
448 456 6.978343 AAGCAGTGCGTGAATAGTAATTTA 57.022 33.333 10.00 0.00 0.00 1.40
449 457 5.880054 AAGCAGTGCGTGAATAGTAATTT 57.120 34.783 10.00 0.00 0.00 1.82
450 458 5.880054 AAAGCAGTGCGTGAATAGTAATT 57.120 34.783 10.00 0.00 0.00 1.40
451 459 6.978343 TTAAAGCAGTGCGTGAATAGTAAT 57.022 33.333 10.00 0.00 0.00 1.89
452 460 6.816640 AGATTAAAGCAGTGCGTGAATAGTAA 59.183 34.615 12.99 3.74 0.00 2.24
453 461 6.338146 AGATTAAAGCAGTGCGTGAATAGTA 58.662 36.000 12.99 0.00 0.00 1.82
454 462 5.178797 AGATTAAAGCAGTGCGTGAATAGT 58.821 37.500 12.99 2.31 0.00 2.12
455 463 5.291858 TGAGATTAAAGCAGTGCGTGAATAG 59.708 40.000 12.99 0.00 0.00 1.73
456 464 5.175127 TGAGATTAAAGCAGTGCGTGAATA 58.825 37.500 12.99 0.00 0.00 1.75
457 465 4.002982 TGAGATTAAAGCAGTGCGTGAAT 58.997 39.130 12.89 12.89 0.00 2.57
458 466 3.398406 TGAGATTAAAGCAGTGCGTGAA 58.602 40.909 10.00 6.36 0.00 3.18
459 467 2.995939 CTGAGATTAAAGCAGTGCGTGA 59.004 45.455 10.00 0.00 0.00 4.35
460 468 2.738846 ACTGAGATTAAAGCAGTGCGTG 59.261 45.455 10.00 0.00 41.02 5.34
461 469 3.045601 ACTGAGATTAAAGCAGTGCGT 57.954 42.857 10.00 2.83 41.02 5.24
462 470 3.681897 AGAACTGAGATTAAAGCAGTGCG 59.318 43.478 10.00 0.00 41.94 5.34
463 471 5.180117 TCAAGAACTGAGATTAAAGCAGTGC 59.820 40.000 7.13 7.13 41.65 4.40
464 472 6.791887 TCAAGAACTGAGATTAAAGCAGTG 57.208 37.500 8.42 0.00 41.65 3.66
465 473 7.807977 TTTCAAGAACTGAGATTAAAGCAGT 57.192 32.000 0.00 0.00 44.15 4.40
466 474 8.295288 ACATTTCAAGAACTGAGATTAAAGCAG 58.705 33.333 7.09 0.00 34.81 4.24
467 475 8.169977 ACATTTCAAGAACTGAGATTAAAGCA 57.830 30.769 7.09 0.00 34.81 3.91
472 480 9.521503 CGAGATACATTTCAAGAACTGAGATTA 57.478 33.333 7.09 0.00 34.81 1.75
473 481 8.253810 TCGAGATACATTTCAAGAACTGAGATT 58.746 33.333 7.09 0.00 34.81 2.40
474 482 7.776107 TCGAGATACATTTCAAGAACTGAGAT 58.224 34.615 7.09 1.14 34.81 2.75
475 483 7.158099 TCGAGATACATTTCAAGAACTGAGA 57.842 36.000 7.09 0.00 34.81 3.27
476 484 6.475076 CCTCGAGATACATTTCAAGAACTGAG 59.525 42.308 15.71 0.00 34.81 3.35
477 485 6.152831 TCCTCGAGATACATTTCAAGAACTGA 59.847 38.462 15.71 0.00 0.00 3.41
478 486 6.333416 TCCTCGAGATACATTTCAAGAACTG 58.667 40.000 15.71 0.00 0.00 3.16
479 487 6.531503 TCCTCGAGATACATTTCAAGAACT 57.468 37.500 15.71 0.00 0.00 3.01
480 488 7.596749 TTTCCTCGAGATACATTTCAAGAAC 57.403 36.000 15.71 0.00 0.00 3.01
481 489 6.313905 GCTTTCCTCGAGATACATTTCAAGAA 59.686 38.462 15.71 0.96 0.00 2.52
482 490 5.812642 GCTTTCCTCGAGATACATTTCAAGA 59.187 40.000 15.71 0.00 0.00 3.02
483 491 5.582269 TGCTTTCCTCGAGATACATTTCAAG 59.418 40.000 15.71 2.60 0.00 3.02
484 492 5.487433 TGCTTTCCTCGAGATACATTTCAA 58.513 37.500 15.71 0.00 0.00 2.69
485 493 5.084818 TGCTTTCCTCGAGATACATTTCA 57.915 39.130 15.71 0.00 0.00 2.69
486 494 4.025313 GCTGCTTTCCTCGAGATACATTTC 60.025 45.833 15.71 0.00 0.00 2.17
487 495 3.873952 GCTGCTTTCCTCGAGATACATTT 59.126 43.478 15.71 0.00 0.00 2.32
488 496 3.118629 TGCTGCTTTCCTCGAGATACATT 60.119 43.478 15.71 0.00 0.00 2.71
489 497 2.432146 TGCTGCTTTCCTCGAGATACAT 59.568 45.455 15.71 0.00 0.00 2.29
490 498 1.824852 TGCTGCTTTCCTCGAGATACA 59.175 47.619 15.71 3.80 0.00 2.29
491 499 2.586258 TGCTGCTTTCCTCGAGATAC 57.414 50.000 15.71 0.00 0.00 2.24
492 500 3.262420 GTTTGCTGCTTTCCTCGAGATA 58.738 45.455 15.71 0.00 0.00 1.98
493 501 2.079925 GTTTGCTGCTTTCCTCGAGAT 58.920 47.619 15.71 0.00 0.00 2.75
494 502 1.202639 TGTTTGCTGCTTTCCTCGAGA 60.203 47.619 15.71 0.00 0.00 4.04
495 503 1.229428 TGTTTGCTGCTTTCCTCGAG 58.771 50.000 5.13 5.13 0.00 4.04
496 504 1.536766 CATGTTTGCTGCTTTCCTCGA 59.463 47.619 0.00 0.00 0.00 4.04
497 505 1.401931 CCATGTTTGCTGCTTTCCTCG 60.402 52.381 0.00 0.00 0.00 4.63
498 506 1.888512 TCCATGTTTGCTGCTTTCCTC 59.111 47.619 0.00 0.00 0.00 3.71
499 507 1.999648 TCCATGTTTGCTGCTTTCCT 58.000 45.000 0.00 0.00 0.00 3.36
500 508 2.613691 CATCCATGTTTGCTGCTTTCC 58.386 47.619 0.00 0.00 0.00 3.13
501 509 2.613691 CCATCCATGTTTGCTGCTTTC 58.386 47.619 0.00 0.00 0.00 2.62
502 510 1.276989 CCCATCCATGTTTGCTGCTTT 59.723 47.619 0.00 0.00 0.00 3.51
503 511 0.899720 CCCATCCATGTTTGCTGCTT 59.100 50.000 0.00 0.00 0.00 3.91
504 512 1.610554 GCCCATCCATGTTTGCTGCT 61.611 55.000 0.00 0.00 0.00 4.24
505 513 1.153509 GCCCATCCATGTTTGCTGC 60.154 57.895 0.00 0.00 0.00 5.25
506 514 1.679680 CTAGCCCATCCATGTTTGCTG 59.320 52.381 0.00 0.00 31.03 4.41
507 515 1.565759 TCTAGCCCATCCATGTTTGCT 59.434 47.619 0.00 0.00 32.50 3.91
508 516 2.057137 TCTAGCCCATCCATGTTTGC 57.943 50.000 0.00 0.00 0.00 3.68
509 517 5.184479 CCATTATCTAGCCCATCCATGTTTG 59.816 44.000 0.00 0.00 0.00 2.93
510 518 5.327732 CCATTATCTAGCCCATCCATGTTT 58.672 41.667 0.00 0.00 0.00 2.83
511 519 4.264083 CCCATTATCTAGCCCATCCATGTT 60.264 45.833 0.00 0.00 0.00 2.71
512 520 3.267812 CCCATTATCTAGCCCATCCATGT 59.732 47.826 0.00 0.00 0.00 3.21
513 521 3.267812 ACCCATTATCTAGCCCATCCATG 59.732 47.826 0.00 0.00 0.00 3.66
514 522 3.267812 CACCCATTATCTAGCCCATCCAT 59.732 47.826 0.00 0.00 0.00 3.41
515 523 2.644299 CACCCATTATCTAGCCCATCCA 59.356 50.000 0.00 0.00 0.00 3.41
516 524 2.619074 GCACCCATTATCTAGCCCATCC 60.619 54.545 0.00 0.00 0.00 3.51
517 525 2.040278 TGCACCCATTATCTAGCCCATC 59.960 50.000 0.00 0.00 0.00 3.51
518 526 2.040813 CTGCACCCATTATCTAGCCCAT 59.959 50.000 0.00 0.00 0.00 4.00
519 527 1.421268 CTGCACCCATTATCTAGCCCA 59.579 52.381 0.00 0.00 0.00 5.36
520 528 1.421646 ACTGCACCCATTATCTAGCCC 59.578 52.381 0.00 0.00 0.00 5.19
521 529 2.158755 ACACTGCACCCATTATCTAGCC 60.159 50.000 0.00 0.00 0.00 3.93
522 530 2.874701 CACACTGCACCCATTATCTAGC 59.125 50.000 0.00 0.00 0.00 3.42
523 531 3.470709 CCACACTGCACCCATTATCTAG 58.529 50.000 0.00 0.00 0.00 2.43
524 532 2.172505 CCCACACTGCACCCATTATCTA 59.827 50.000 0.00 0.00 0.00 1.98
525 533 1.064463 CCCACACTGCACCCATTATCT 60.064 52.381 0.00 0.00 0.00 1.98
526 534 1.340991 ACCCACACTGCACCCATTATC 60.341 52.381 0.00 0.00 0.00 1.75
527 535 0.704076 ACCCACACTGCACCCATTAT 59.296 50.000 0.00 0.00 0.00 1.28
528 536 0.251121 CACCCACACTGCACCCATTA 60.251 55.000 0.00 0.00 0.00 1.90
529 537 1.531365 CACCCACACTGCACCCATT 60.531 57.895 0.00 0.00 0.00 3.16
530 538 2.115910 CACCCACACTGCACCCAT 59.884 61.111 0.00 0.00 0.00 4.00
531 539 4.892965 GCACCCACACTGCACCCA 62.893 66.667 0.00 0.00 34.56 4.51
532 540 4.892965 TGCACCCACACTGCACCC 62.893 66.667 0.00 0.00 39.76 4.61
535 543 3.651980 TTGGTGCACCCACACTGCA 62.652 57.895 32.62 8.94 45.19 4.41
536 544 2.832661 TTGGTGCACCCACACTGC 60.833 61.111 32.62 5.95 45.19 4.40
537 545 2.489275 GGTTGGTGCACCCACACTG 61.489 63.158 33.82 0.00 45.19 3.66
538 546 2.123897 GGTTGGTGCACCCACACT 60.124 61.111 33.82 0.00 45.19 3.55
544 552 2.150014 ATACCCAGGGTTGGTGCACC 62.150 60.000 29.67 29.67 43.40 5.01
545 553 0.621609 TATACCCAGGGTTGGTGCAC 59.378 55.000 19.18 8.80 43.40 4.57
546 554 0.916086 CTATACCCAGGGTTGGTGCA 59.084 55.000 19.18 0.00 43.40 4.57
547 555 1.209621 TCTATACCCAGGGTTGGTGC 58.790 55.000 19.18 0.00 43.40 5.01
548 556 4.310022 TTTTCTATACCCAGGGTTGGTG 57.690 45.455 19.18 5.35 43.40 4.17
549 557 4.509663 GGTTTTTCTATACCCAGGGTTGGT 60.510 45.833 19.18 6.26 43.40 3.67
550 558 4.021229 GGTTTTTCTATACCCAGGGTTGG 58.979 47.826 19.18 7.65 44.60 3.77
551 559 4.461431 GTGGTTTTTCTATACCCAGGGTTG 59.539 45.833 19.18 8.06 37.09 3.77
552 560 4.355889 AGTGGTTTTTCTATACCCAGGGTT 59.644 41.667 19.18 7.52 37.09 4.11
553 561 3.920841 AGTGGTTTTTCTATACCCAGGGT 59.079 43.478 17.82 17.82 40.16 4.34
554 562 4.227527 AGAGTGGTTTTTCTATACCCAGGG 59.772 45.833 2.85 2.85 33.34 4.45
555 563 5.429130 GAGAGTGGTTTTTCTATACCCAGG 58.571 45.833 0.00 0.00 33.34 4.45
556 564 5.045869 TGGAGAGTGGTTTTTCTATACCCAG 60.046 44.000 0.00 0.00 33.34 4.45
557 565 4.847512 TGGAGAGTGGTTTTTCTATACCCA 59.152 41.667 0.00 0.00 33.34 4.51
558 566 5.431179 TGGAGAGTGGTTTTTCTATACCC 57.569 43.478 0.00 0.00 33.34 3.69
559 567 6.890293 AGATGGAGAGTGGTTTTTCTATACC 58.110 40.000 0.00 0.00 34.93 2.73
560 568 8.261522 AGAAGATGGAGAGTGGTTTTTCTATAC 58.738 37.037 0.00 0.00 0.00 1.47
561 569 8.380742 AGAAGATGGAGAGTGGTTTTTCTATA 57.619 34.615 0.00 0.00 0.00 1.31
562 570 7.264294 AGAAGATGGAGAGTGGTTTTTCTAT 57.736 36.000 0.00 0.00 0.00 1.98
563 571 6.688073 AGAAGATGGAGAGTGGTTTTTCTA 57.312 37.500 0.00 0.00 0.00 2.10
564 572 5.574970 AGAAGATGGAGAGTGGTTTTTCT 57.425 39.130 0.00 0.00 0.00 2.52
565 573 6.540551 GGATAGAAGATGGAGAGTGGTTTTTC 59.459 42.308 0.00 0.00 0.00 2.29
566 574 6.216456 AGGATAGAAGATGGAGAGTGGTTTTT 59.784 38.462 0.00 0.00 0.00 1.94
567 575 5.728741 AGGATAGAAGATGGAGAGTGGTTTT 59.271 40.000 0.00 0.00 0.00 2.43
568 576 5.284582 AGGATAGAAGATGGAGAGTGGTTT 58.715 41.667 0.00 0.00 0.00 3.27
569 577 4.889780 AGGATAGAAGATGGAGAGTGGTT 58.110 43.478 0.00 0.00 0.00 3.67
570 578 4.551215 AGGATAGAAGATGGAGAGTGGT 57.449 45.455 0.00 0.00 0.00 4.16
571 579 5.640147 AGTAGGATAGAAGATGGAGAGTGG 58.360 45.833 0.00 0.00 0.00 4.00
572 580 7.595819 AAAGTAGGATAGAAGATGGAGAGTG 57.404 40.000 0.00 0.00 0.00 3.51
573 581 9.716556 TTTAAAGTAGGATAGAAGATGGAGAGT 57.283 33.333 0.00 0.00 0.00 3.24
574 582 9.974980 GTTTAAAGTAGGATAGAAGATGGAGAG 57.025 37.037 0.00 0.00 0.00 3.20
575 583 9.716556 AGTTTAAAGTAGGATAGAAGATGGAGA 57.283 33.333 0.00 0.00 0.00 3.71
747 755 0.321298 TACCTGAAGCCAAGCGTTCC 60.321 55.000 0.00 0.00 0.00 3.62
766 774 5.487433 TGTCGTGTCATTTGGTTCTATCAT 58.513 37.500 0.00 0.00 0.00 2.45
771 779 3.304659 GCATTGTCGTGTCATTTGGTTCT 60.305 43.478 0.00 0.00 0.00 3.01
787 795 6.588719 TTGCTTAGTTCAATTAGGCATTGT 57.411 33.333 0.00 0.00 42.79 2.71
906 914 4.035208 GCATGGGTGTTATGTAGTTAGCAC 59.965 45.833 0.00 0.00 33.88 4.40
908 916 4.196193 TGCATGGGTGTTATGTAGTTAGC 58.804 43.478 0.00 0.00 0.00 3.09
1437 1459 8.535690 AGTATCACTTTTTGAACTAGCAGTAC 57.464 34.615 0.00 0.00 37.92 2.73
1495 1597 3.564225 AGAACAAAACTACCGCTTTCAGG 59.436 43.478 0.00 0.00 0.00 3.86
1794 1912 4.454161 AGATCACGACCTTAGATCATCTCG 59.546 45.833 0.00 0.00 40.39 4.04
1795 1913 5.240623 ACAGATCACGACCTTAGATCATCTC 59.759 44.000 0.00 0.00 40.39 2.75
1796 1914 5.009510 CACAGATCACGACCTTAGATCATCT 59.990 44.000 0.00 0.00 40.39 2.90
2211 2511 1.279271 GAGTCTGGCAACACACCCTAT 59.721 52.381 0.00 0.00 46.17 2.57
2225 2525 4.013267 ACTTTTCACCATGAGGAGTCTG 57.987 45.455 0.00 0.00 38.69 3.51
2231 2531 2.288395 GGCACAACTTTTCACCATGAGG 60.288 50.000 0.00 0.00 42.21 3.86
2242 2542 4.097286 ACGTAAGAAACATGGCACAACTTT 59.903 37.500 0.00 0.00 42.74 2.66
2383 2694 8.197592 ACAATATTAACGGGTAGATGGTCATA 57.802 34.615 0.00 0.00 0.00 2.15
2395 2706 7.315247 TGATGACAGAAACAATATTAACGGG 57.685 36.000 0.00 0.00 0.00 5.28
2405 2716 2.942376 ACGCAGTTGATGACAGAAACAA 59.058 40.909 5.98 0.00 37.78 2.83
2421 2732 5.545658 ATGTAAAAAGGTCACATACGCAG 57.454 39.130 0.00 0.00 31.26 5.18
2716 3110 4.940046 CCATGAGTTCACTTGACTAGCAAT 59.060 41.667 0.00 0.00 35.59 3.56
2751 3145 3.761218 TCTCTCTGATGAGACCTGTTGTC 59.239 47.826 3.66 0.00 43.73 3.18
3053 3447 1.075601 TTTGGCCAAGGTCCAGAGAT 58.924 50.000 19.48 0.00 34.66 2.75
3135 3529 4.206375 TGAACTTTGGAAGCATGAACTGA 58.794 39.130 0.00 0.00 0.00 3.41
3224 3618 0.322008 CTCTGACAGGTTTGCCTCCC 60.322 60.000 1.81 0.00 44.97 4.30
3225 3619 0.687354 TCTCTGACAGGTTTGCCTCC 59.313 55.000 1.81 0.00 44.97 4.30
3237 3631 4.081198 ACCTGAGAATTCACCATCTCTGAC 60.081 45.833 8.44 0.00 41.49 3.51
3263 3657 5.488919 TGGAAAACAGATGAGAGGAATAGGT 59.511 40.000 0.00 0.00 0.00 3.08
3843 4257 7.943079 TGATGATACCAGATTTTGTCACAAT 57.057 32.000 0.00 0.00 0.00 2.71
3892 4306 5.096443 ACAAAAAGCCCATTTTCTGTCAA 57.904 34.783 0.00 0.00 40.27 3.18
3929 4381 3.939837 ATGTCCTGCAGGTGCGTCG 62.940 63.158 31.58 5.02 45.83 5.12
3942 4394 1.313091 GGACGGCCCAAAGAATGTCC 61.313 60.000 0.00 6.45 39.10 4.02
3978 4432 3.140225 CTCGCCCTCGCTTCTACCC 62.140 68.421 0.00 0.00 35.26 3.69
4123 4579 0.601558 TTCAGTAAGCGAACGCCTCT 59.398 50.000 15.44 8.69 43.17 3.69
4148 4604 1.922570 AACGTAGCTAGTGCAATCGG 58.077 50.000 0.00 0.00 42.74 4.18
4185 4646 3.941483 CAGTTAACAGCCAAGGATCGATT 59.059 43.478 8.61 0.00 0.00 3.34
4266 4728 2.628178 ACGTTCACTGTTCATCCAGAGA 59.372 45.455 0.00 0.00 36.30 3.10
4271 4739 1.156736 CCCACGTTCACTGTTCATCC 58.843 55.000 0.00 0.00 0.00 3.51
4296 4764 6.096987 ACCATGTATGTCTCTACTCGTTCAAT 59.903 38.462 0.00 0.00 0.00 2.57
4345 4813 2.025887 GTCCTGTTCATCCAACCTCCAT 60.026 50.000 0.00 0.00 33.51 3.41
4349 4818 0.698818 GGGTCCTGTTCATCCAACCT 59.301 55.000 0.00 0.00 33.51 3.50
4437 4911 1.430853 TGTTCATCCACCCCCAATCAA 59.569 47.619 0.00 0.00 0.00 2.57
4440 4914 0.336048 CCTGTTCATCCACCCCCAAT 59.664 55.000 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.