Multiple sequence alignment - TraesCS4A01G217000

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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 TraesCS4A01G217000 chr4A 100.000 2681 0 0 1 2681 516342042 516344722 0.000000e+00 4951.0
1 TraesCS4A01G217000 chr4A 92.348 1738 88 20 712 2428 515750539 515748826 0.000000e+00 2431.0
2 TraesCS4A01G217000 chr4A 91.843 331 24 2 15 342 515752358 515752028 2.430000e-125 459.0
3 TraesCS4A01G217000 chr4A 91.275 149 13 0 573 721 515751992 515751844 1.260000e-48 204.0
4 TraesCS4A01G217000 chr4A 86.842 152 20 0 2530 2681 515748736 515748585 1.280000e-38 171.0
5 TraesCS4A01G217000 chr4D 91.150 1209 74 14 573 1754 66935769 66934567 0.000000e+00 1609.0
6 TraesCS4A01G217000 chr4D 92.062 1096 54 13 674 1757 67238585 67239659 0.000000e+00 1511.0
7 TraesCS4A01G217000 chr4D 86.900 229 20 5 362 582 96715853 96715627 5.730000e-62 248.0
8 TraesCS4A01G217000 chr4B 88.108 1337 94 27 770 2067 99048680 99049990 0.000000e+00 1528.0
9 TraesCS4A01G217000 chr4B 90.968 1085 81 13 612 1686 99040238 99041315 0.000000e+00 1445.0
10 TraesCS4A01G217000 chr4B 89.755 937 67 17 851 1766 99077967 99078895 0.000000e+00 1171.0
11 TraesCS4A01G217000 chr4B 87.963 324 25 6 1455 1766 99051859 99052180 1.170000e-98 370.0
12 TraesCS4A01G217000 chr4B 85.816 282 26 6 1787 2067 99041560 99041828 1.210000e-73 287.0
13 TraesCS4A01G217000 chr4B 87.168 226 19 6 362 579 516975456 516975679 5.730000e-62 248.0
14 TraesCS4A01G217000 chr4B 90.000 90 8 1 584 673 99051404 99051492 6.070000e-22 115.0
15 TraesCS4A01G217000 chr1D 90.256 195 17 1 361 555 64887444 64887636 1.230000e-63 254.0
16 TraesCS4A01G217000 chr2D 87.330 221 20 4 360 574 347449508 347449726 2.060000e-61 246.0
17 TraesCS4A01G217000 chr3D 87.215 219 20 4 362 574 2719882 2720098 2.670000e-60 243.0
18 TraesCS4A01G217000 chr2A 86.937 222 21 5 360 575 333742409 333742190 2.670000e-60 243.0
19 TraesCS4A01G217000 chr6D 86.878 221 21 4 360 574 3325790 3326008 9.590000e-60 241.0
20 TraesCS4A01G217000 chr6D 86.878 221 21 4 360 574 3331666 3331884 9.590000e-60 241.0
21 TraesCS4A01G217000 chr6D 86.878 221 21 4 360 574 3337546 3337764 9.590000e-60 241.0
22 TraesCS4A01G217000 chr3B 90.541 74 7 0 280 353 785357217 785357290 6.110000e-17 99.0
23 TraesCS4A01G217000 chr7D 94.737 57 1 2 280 336 593933627 593933681 1.320000e-13 87.9


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 TraesCS4A01G217000 chr4A 516342042 516344722 2680 False 4951.00 4951 100.000000 1 2681 1 chr4A.!!$F1 2680
1 TraesCS4A01G217000 chr4A 515748585 515752358 3773 True 816.25 2431 90.577000 15 2681 4 chr4A.!!$R1 2666
2 TraesCS4A01G217000 chr4D 66934567 66935769 1202 True 1609.00 1609 91.150000 573 1754 1 chr4D.!!$R1 1181
3 TraesCS4A01G217000 chr4D 67238585 67239659 1074 False 1511.00 1511 92.062000 674 1757 1 chr4D.!!$F1 1083
4 TraesCS4A01G217000 chr4B 99077967 99078895 928 False 1171.00 1171 89.755000 851 1766 1 chr4B.!!$F1 915
5 TraesCS4A01G217000 chr4B 99040238 99041828 1590 False 866.00 1445 88.392000 612 2067 2 chr4B.!!$F3 1455
6 TraesCS4A01G217000 chr4B 99048680 99052180 3500 False 671.00 1528 88.690333 584 2067 3 chr4B.!!$F4 1483


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
564 568 0.099968 GTACGCGCACACCTATGAGA 59.9 55.0 5.73 0.0 0.0 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2169 6243 0.179 GGAGACCGTGGATCAAGCAT 59.821 55.0 0.0 0.0 0.0 3.79 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
68 69 7.307337 CCACAAATAAAGAAAACACAAGGATGC 60.307 37.037 0.00 0.00 0.00 3.91
129 130 1.209504 ACAGGTGGGACCATAATCACG 59.790 52.381 0.00 0.00 41.95 4.35
135 136 3.739300 GTGGGACCATAATCACGAATACG 59.261 47.826 0.00 0.00 45.75 3.06
167 168 5.411361 ACGTATTTTGTGACTGTATGTGCAT 59.589 36.000 0.00 0.00 0.00 3.96
186 187 4.142838 TGCATGCTTGAATCGAGTTAAGTG 60.143 41.667 20.33 10.44 0.00 3.16
191 192 5.862323 TGCTTGAATCGAGTTAAGTGACTAC 59.138 40.000 17.10 2.24 0.00 2.73
192 193 5.862323 GCTTGAATCGAGTTAAGTGACTACA 59.138 40.000 17.10 0.00 0.00 2.74
196 197 9.917129 TTGAATCGAGTTAAGTGACTACAAATA 57.083 29.630 0.00 0.00 0.00 1.40
249 250 3.741344 ACATTGAGCACAAGTTCTACGAC 59.259 43.478 2.37 0.00 39.46 4.34
251 252 3.728076 TGAGCACAAGTTCTACGACTT 57.272 42.857 0.00 0.00 40.37 3.01
260 261 3.705051 AGTTCTACGACTTGGGGTGATA 58.295 45.455 0.00 0.00 0.00 2.15
306 308 2.145397 GGTTTCCCCCTCTGATTTCC 57.855 55.000 0.00 0.00 0.00 3.13
342 346 1.961793 AAACGAGCTACAAGCACCAA 58.038 45.000 1.22 0.00 45.56 3.67
344 348 2.185004 ACGAGCTACAAGCACCAATT 57.815 45.000 1.22 0.00 45.56 2.32
345 349 2.076863 ACGAGCTACAAGCACCAATTC 58.923 47.619 1.22 0.00 45.56 2.17
346 350 2.289694 ACGAGCTACAAGCACCAATTCT 60.290 45.455 1.22 0.00 45.56 2.40
348 352 3.932710 CGAGCTACAAGCACCAATTCTTA 59.067 43.478 1.22 0.00 45.56 2.10
349 353 4.201724 CGAGCTACAAGCACCAATTCTTAC 60.202 45.833 1.22 0.00 45.56 2.34
350 354 3.684788 AGCTACAAGCACCAATTCTTACG 59.315 43.478 1.22 0.00 45.56 3.18
351 355 3.682858 GCTACAAGCACCAATTCTTACGA 59.317 43.478 0.00 0.00 41.89 3.43
352 356 4.435651 GCTACAAGCACCAATTCTTACGAC 60.436 45.833 0.00 0.00 41.89 4.34
353 357 3.740115 ACAAGCACCAATTCTTACGACT 58.260 40.909 0.00 0.00 0.00 4.18
354 358 3.746492 ACAAGCACCAATTCTTACGACTC 59.254 43.478 0.00 0.00 0.00 3.36
355 359 3.678056 AGCACCAATTCTTACGACTCA 57.322 42.857 0.00 0.00 0.00 3.41
356 360 3.589988 AGCACCAATTCTTACGACTCAG 58.410 45.455 0.00 0.00 0.00 3.35
357 361 2.094417 GCACCAATTCTTACGACTCAGC 59.906 50.000 0.00 0.00 0.00 4.26
358 362 3.589988 CACCAATTCTTACGACTCAGCT 58.410 45.455 0.00 0.00 0.00 4.24
360 364 4.563184 CACCAATTCTTACGACTCAGCTAC 59.437 45.833 0.00 0.00 0.00 3.58
361 365 4.463186 ACCAATTCTTACGACTCAGCTACT 59.537 41.667 0.00 0.00 0.00 2.57
363 367 5.972382 CCAATTCTTACGACTCAGCTACTAC 59.028 44.000 0.00 0.00 0.00 2.73
364 368 6.183360 CCAATTCTTACGACTCAGCTACTACT 60.183 42.308 0.00 0.00 0.00 2.57
365 369 7.251994 CAATTCTTACGACTCAGCTACTACTT 58.748 38.462 0.00 0.00 0.00 2.24
367 371 4.874966 TCTTACGACTCAGCTACTACTTCC 59.125 45.833 0.00 0.00 0.00 3.46
368 372 3.353370 ACGACTCAGCTACTACTTCCT 57.647 47.619 0.00 0.00 0.00 3.36
371 375 3.622630 GACTCAGCTACTACTTCCTCCA 58.377 50.000 0.00 0.00 0.00 3.86
372 376 4.211920 GACTCAGCTACTACTTCCTCCAT 58.788 47.826 0.00 0.00 0.00 3.41
373 377 4.615513 ACTCAGCTACTACTTCCTCCATT 58.384 43.478 0.00 0.00 0.00 3.16
374 378 5.026790 ACTCAGCTACTACTTCCTCCATTT 58.973 41.667 0.00 0.00 0.00 2.32
375 379 5.128008 ACTCAGCTACTACTTCCTCCATTTC 59.872 44.000 0.00 0.00 0.00 2.17
376 380 5.023452 TCAGCTACTACTTCCTCCATTTCA 58.977 41.667 0.00 0.00 0.00 2.69
377 381 5.483937 TCAGCTACTACTTCCTCCATTTCAA 59.516 40.000 0.00 0.00 0.00 2.69
378 382 6.156949 TCAGCTACTACTTCCTCCATTTCAAT 59.843 38.462 0.00 0.00 0.00 2.57
379 383 6.825721 CAGCTACTACTTCCTCCATTTCAATT 59.174 38.462 0.00 0.00 0.00 2.32
380 384 7.337942 CAGCTACTACTTCCTCCATTTCAATTT 59.662 37.037 0.00 0.00 0.00 1.82
381 385 8.548877 AGCTACTACTTCCTCCATTTCAATTTA 58.451 33.333 0.00 0.00 0.00 1.40
382 386 8.613482 GCTACTACTTCCTCCATTTCAATTTAC 58.387 37.037 0.00 0.00 0.00 2.01
383 387 9.667107 CTACTACTTCCTCCATTTCAATTTACA 57.333 33.333 0.00 0.00 0.00 2.41
384 388 8.934023 ACTACTTCCTCCATTTCAATTTACAA 57.066 30.769 0.00 0.00 0.00 2.41
385 389 9.362151 ACTACTTCCTCCATTTCAATTTACAAA 57.638 29.630 0.00 0.00 0.00 2.83
388 392 8.314021 ACTTCCTCCATTTCAATTTACAAATCC 58.686 33.333 0.00 0.00 0.00 3.01
389 393 8.434589 TTCCTCCATTTCAATTTACAAATCCT 57.565 30.769 0.00 0.00 0.00 3.24
390 394 9.540538 TTCCTCCATTTCAATTTACAAATCCTA 57.459 29.630 0.00 0.00 0.00 2.94
391 395 8.966868 TCCTCCATTTCAATTTACAAATCCTAC 58.033 33.333 0.00 0.00 0.00 3.18
392 396 7.915397 CCTCCATTTCAATTTACAAATCCTACG 59.085 37.037 0.00 0.00 0.00 3.51
393 397 7.254852 TCCATTTCAATTTACAAATCCTACGC 58.745 34.615 0.00 0.00 0.00 4.42
394 398 6.196353 CCATTTCAATTTACAAATCCTACGCG 59.804 38.462 3.53 3.53 0.00 6.01
395 399 5.866335 TTCAATTTACAAATCCTACGCGT 57.134 34.783 19.17 19.17 0.00 6.01
396 400 6.964741 TTCAATTTACAAATCCTACGCGTA 57.035 33.333 19.40 19.40 0.00 4.42
397 401 7.542534 TTCAATTTACAAATCCTACGCGTAT 57.457 32.000 20.91 2.73 0.00 3.06
398 402 8.645730 TTCAATTTACAAATCCTACGCGTATA 57.354 30.769 20.91 11.64 0.00 1.47
399 403 8.821147 TCAATTTACAAATCCTACGCGTATAT 57.179 30.769 20.91 13.50 0.00 0.86
400 404 8.918658 TCAATTTACAAATCCTACGCGTATATC 58.081 33.333 20.91 0.00 0.00 1.63
401 405 8.922676 CAATTTACAAATCCTACGCGTATATCT 58.077 33.333 20.91 0.34 0.00 1.98
403 407 9.784680 ATTTACAAATCCTACGCGTATATCTAG 57.215 33.333 20.91 8.56 0.00 2.43
404 408 6.192234 ACAAATCCTACGCGTATATCTAGG 57.808 41.667 20.91 18.03 0.00 3.02
405 409 5.709164 ACAAATCCTACGCGTATATCTAGGT 59.291 40.000 20.91 10.15 0.00 3.08
406 410 6.208204 ACAAATCCTACGCGTATATCTAGGTT 59.792 38.462 20.91 10.22 0.00 3.50
407 411 5.814764 ATCCTACGCGTATATCTAGGTTG 57.185 43.478 20.91 3.59 0.00 3.77
408 412 4.645535 TCCTACGCGTATATCTAGGTTGT 58.354 43.478 20.91 0.00 0.00 3.32
409 413 4.692625 TCCTACGCGTATATCTAGGTTGTC 59.307 45.833 20.91 0.00 0.00 3.18
410 414 4.453478 CCTACGCGTATATCTAGGTTGTCA 59.547 45.833 20.91 0.00 0.00 3.58
411 415 4.906065 ACGCGTATATCTAGGTTGTCAA 57.094 40.909 11.67 0.00 0.00 3.18
412 416 5.449107 ACGCGTATATCTAGGTTGTCAAT 57.551 39.130 11.67 0.00 0.00 2.57
413 417 5.839621 ACGCGTATATCTAGGTTGTCAATT 58.160 37.500 11.67 0.00 0.00 2.32
414 418 6.278363 ACGCGTATATCTAGGTTGTCAATTT 58.722 36.000 11.67 0.00 0.00 1.82
415 419 6.759827 ACGCGTATATCTAGGTTGTCAATTTT 59.240 34.615 11.67 0.00 0.00 1.82
416 420 7.922278 ACGCGTATATCTAGGTTGTCAATTTTA 59.078 33.333 11.67 0.00 0.00 1.52
417 421 8.212495 CGCGTATATCTAGGTTGTCAATTTTAC 58.788 37.037 0.00 0.00 0.00 2.01
418 422 8.493547 GCGTATATCTAGGTTGTCAATTTTACC 58.506 37.037 0.00 0.00 0.00 2.85
419 423 9.537192 CGTATATCTAGGTTGTCAATTTTACCA 57.463 33.333 0.00 0.00 33.02 3.25
422 426 7.923414 ATCTAGGTTGTCAATTTTACCACTC 57.077 36.000 0.00 0.00 33.02 3.51
423 427 7.074653 TCTAGGTTGTCAATTTTACCACTCT 57.925 36.000 0.00 0.00 33.02 3.24
424 428 8.197592 TCTAGGTTGTCAATTTTACCACTCTA 57.802 34.615 0.00 0.00 33.02 2.43
425 429 8.653191 TCTAGGTTGTCAATTTTACCACTCTAA 58.347 33.333 0.00 0.00 33.02 2.10
426 430 9.449719 CTAGGTTGTCAATTTTACCACTCTAAT 57.550 33.333 0.00 0.00 33.02 1.73
428 432 9.975218 AGGTTGTCAATTTTACCACTCTAATAT 57.025 29.630 0.00 0.00 33.02 1.28
463 467 8.853469 AACACAAAAATTATACGGTTCGAAAA 57.147 26.923 0.00 0.00 0.00 2.29
464 468 9.465985 AACACAAAAATTATACGGTTCGAAAAT 57.534 25.926 0.00 0.00 0.00 1.82
550 554 7.920908 ATAAATTAACGACTTAGAGGTACGC 57.079 36.000 0.00 0.00 0.00 4.42
551 555 3.389687 TTAACGACTTAGAGGTACGCG 57.610 47.619 3.53 3.53 0.00 6.01
552 556 0.179179 AACGACTTAGAGGTACGCGC 60.179 55.000 5.73 0.00 0.00 6.86
553 557 1.300971 ACGACTTAGAGGTACGCGCA 61.301 55.000 5.73 0.00 0.00 6.09
554 558 0.860618 CGACTTAGAGGTACGCGCAC 60.861 60.000 5.73 2.26 0.00 5.34
555 559 0.169672 GACTTAGAGGTACGCGCACA 59.830 55.000 12.27 0.00 0.00 4.57
556 560 0.109412 ACTTAGAGGTACGCGCACAC 60.109 55.000 12.27 3.64 0.00 3.82
557 561 0.801067 CTTAGAGGTACGCGCACACC 60.801 60.000 17.49 17.49 34.86 4.16
559 563 0.392863 TAGAGGTACGCGCACACCTA 60.393 55.000 25.30 14.50 45.32 3.08
560 564 1.035932 AGAGGTACGCGCACACCTAT 61.036 55.000 25.30 20.94 45.32 2.57
561 565 0.870307 GAGGTACGCGCACACCTATG 60.870 60.000 25.30 1.54 45.32 2.23
562 566 1.140161 GGTACGCGCACACCTATGA 59.860 57.895 17.82 0.00 0.00 2.15
563 567 0.870307 GGTACGCGCACACCTATGAG 60.870 60.000 17.82 0.00 0.00 2.90
564 568 0.099968 GTACGCGCACACCTATGAGA 59.900 55.000 5.73 0.00 0.00 3.27
565 569 0.380733 TACGCGCACACCTATGAGAG 59.619 55.000 5.73 0.00 0.00 3.20
568 572 0.249238 GCGCACACCTATGAGAGAGG 60.249 60.000 0.30 0.00 40.22 3.69
569 573 0.387202 CGCACACCTATGAGAGAGGG 59.613 60.000 0.00 0.00 38.52 4.30
571 575 1.686052 GCACACCTATGAGAGAGGGAG 59.314 57.143 0.00 0.00 38.52 4.30
577 581 5.613544 ACACCTATGAGAGAGGGAGTACTAT 59.386 44.000 0.00 0.00 38.52 2.12
588 592 4.808042 AGGGAGTACTATTAAACCGCCTA 58.192 43.478 0.00 0.00 0.00 3.93
651 655 2.903855 CGCTGGCCATGATCACCC 60.904 66.667 5.51 0.00 0.00 4.61
748 2100 4.560035 CCTAAACCGTCAACTGTATGTACG 59.440 45.833 0.00 0.00 0.00 3.67
750 2102 4.764679 AACCGTCAACTGTATGTACGTA 57.235 40.909 0.00 0.00 31.87 3.57
966 2356 3.175324 CGTCGTTTTAGACATCGATCGAC 59.825 47.826 22.06 17.20 40.98 4.20
971 2361 2.750301 TAGACATCGATCGACAACGG 57.250 50.000 22.06 10.18 40.21 4.44
1012 2402 3.224324 CATGCATGGCAGCCCTCC 61.224 66.667 19.40 0.00 43.65 4.30
1024 2414 2.584608 CCCTCCACACGATCCACC 59.415 66.667 0.00 0.00 0.00 4.61
1319 2730 4.675029 CGAGAACCCCAACCGCGT 62.675 66.667 4.92 0.00 0.00 6.01
1688 5558 2.169769 TGAAGTTATGGTGATCCGGACC 59.830 50.000 6.12 4.73 36.30 4.46
1715 5601 2.126467 TGCCGTTAAACGACACACTAC 58.874 47.619 0.00 0.00 46.05 2.73
1722 5772 6.362686 CGTTAAACGACACACTACTACTGTA 58.637 40.000 0.00 0.00 46.05 2.74
1723 5773 7.017645 CGTTAAACGACACACTACTACTGTAT 58.982 38.462 0.00 0.00 46.05 2.29
1972 6034 3.386402 GTCAATCGATTCTTCCTCCTCCT 59.614 47.826 7.92 0.00 0.00 3.69
2001 6063 6.264970 TCAACAGTCAAATGTCAATCCAATGA 59.735 34.615 0.00 0.00 31.50 2.57
2086 6148 1.557371 CCACCTTCTTCCTTCTCCCTC 59.443 57.143 0.00 0.00 0.00 4.30
2126 6188 2.790791 CCCTGCGTTGGCCAAACAA 61.791 57.895 22.47 7.43 38.84 2.83
2132 6194 1.496934 CGTTGGCCAAACAATTGTCC 58.503 50.000 22.47 9.28 38.84 4.02
2134 6196 1.115467 TTGGCCAAACAATTGTCCGT 58.885 45.000 17.98 0.00 37.38 4.69
2141 6203 1.398692 AACAATTGTCCGTTGCCACT 58.601 45.000 12.39 0.00 0.00 4.00
2146 6208 0.393132 TTGTCCGTTGCCACTCACAA 60.393 50.000 0.00 0.00 0.00 3.33
2148 6210 1.525077 TCCGTTGCCACTCACAACC 60.525 57.895 0.00 0.00 43.57 3.77
2151 6213 1.525077 GTTGCCACTCACAACCGGA 60.525 57.895 9.46 0.00 41.22 5.14
2154 6216 2.738521 CCACTCACAACCGGAGCG 60.739 66.667 9.46 0.00 35.79 5.03
2155 6217 3.414700 CACTCACAACCGGAGCGC 61.415 66.667 9.46 0.00 35.79 5.92
2174 6248 2.203669 TGCCACCTTGCCATGCTT 60.204 55.556 0.00 0.00 0.00 3.91
2181 6255 0.458669 CCTTGCCATGCTTGATCCAC 59.541 55.000 0.22 0.00 0.00 4.02
2182 6256 0.099968 CTTGCCATGCTTGATCCACG 59.900 55.000 0.22 0.00 0.00 4.94
2184 6258 1.750399 GCCATGCTTGATCCACGGT 60.750 57.895 0.22 0.00 0.00 4.83
2199 6273 2.501610 GGTCTCCGTCATGCCTCC 59.498 66.667 0.00 0.00 0.00 4.30
2219 6293 1.377725 CCGCACTCAGCCATCCTTT 60.378 57.895 0.00 0.00 41.38 3.11
2230 6304 2.831526 AGCCATCCTTTTAAAACCGCAT 59.168 40.909 0.00 0.00 0.00 4.73
2232 6306 3.367910 GCCATCCTTTTAAAACCGCATGA 60.368 43.478 0.00 0.00 0.00 3.07
2258 6332 2.832733 ACTAGAGGGACAAGCAACCTAC 59.167 50.000 0.00 0.00 34.02 3.18
2261 6335 0.693049 AGGGACAAGCAACCTACCAG 59.307 55.000 0.00 0.00 31.53 4.00
2262 6336 0.400594 GGGACAAGCAACCTACCAGT 59.599 55.000 0.00 0.00 0.00 4.00
2264 6338 1.071699 GGACAAGCAACCTACCAGTGA 59.928 52.381 0.00 0.00 0.00 3.41
2305 6383 0.393808 GATAGAAGGGGGCGCAACAA 60.394 55.000 10.83 0.00 0.00 2.83
2307 6385 4.056125 GAAGGGGGCGCAACAAGC 62.056 66.667 10.83 0.00 40.87 4.01
2325 6403 2.680352 GGGGAGAGTGCTCGACCA 60.680 66.667 15.64 0.00 42.25 4.02
2332 6410 3.311110 GTGCTCGACCAGGTGGGA 61.311 66.667 0.00 0.00 41.15 4.37
2333 6411 2.525629 TGCTCGACCAGGTGGGAA 60.526 61.111 0.00 0.00 41.15 3.97
2334 6412 2.144078 TGCTCGACCAGGTGGGAAA 61.144 57.895 0.00 0.00 41.15 3.13
2340 6418 0.036875 GACCAGGTGGGAAAGGTCTG 59.963 60.000 0.00 0.00 45.46 3.51
2347 6425 2.355818 GGTGGGAAAGGTCTGTGTATCC 60.356 54.545 0.00 0.00 0.00 2.59
2352 6430 3.118592 GGAAAGGTCTGTGTATCCTCCTG 60.119 52.174 0.00 0.00 0.00 3.86
2353 6431 1.490574 AGGTCTGTGTATCCTCCTGC 58.509 55.000 0.00 0.00 0.00 4.85
2358 6436 2.012673 CTGTGTATCCTCCTGCTTTGC 58.987 52.381 0.00 0.00 0.00 3.68
2413 6491 4.326255 CCTGCTAGGGTTGCCTTG 57.674 61.111 0.00 0.00 0.00 3.61
2435 6513 2.672996 CCAAACAGGGGGCTCGTG 60.673 66.667 5.34 5.34 37.29 4.35
2436 6514 3.365265 CAAACAGGGGGCTCGTGC 61.365 66.667 7.04 0.00 34.84 5.34
2446 6524 3.300013 GCTCGTGCCCCTAGAGTT 58.700 61.111 0.00 0.00 34.69 3.01
2447 6525 1.153549 GCTCGTGCCCCTAGAGTTG 60.154 63.158 0.00 0.00 34.69 3.16
2448 6526 1.153549 CTCGTGCCCCTAGAGTTGC 60.154 63.158 0.00 0.00 0.00 4.17
2449 6527 2.125106 CGTGCCCCTAGAGTTGCC 60.125 66.667 0.00 0.00 0.00 4.52
2450 6528 2.660064 CGTGCCCCTAGAGTTGCCT 61.660 63.158 0.00 0.00 0.00 4.75
2451 6529 1.685820 GTGCCCCTAGAGTTGCCTT 59.314 57.895 0.00 0.00 0.00 4.35
2452 6530 0.678048 GTGCCCCTAGAGTTGCCTTG 60.678 60.000 0.00 0.00 0.00 3.61
2453 6531 1.750780 GCCCCTAGAGTTGCCTTGC 60.751 63.158 0.00 0.00 0.00 4.01
2454 6532 1.077429 CCCCTAGAGTTGCCTTGCC 60.077 63.158 0.00 0.00 0.00 4.52
2455 6533 1.077429 CCCTAGAGTTGCCTTGCCC 60.077 63.158 0.00 0.00 0.00 5.36
2456 6534 1.685224 CCTAGAGTTGCCTTGCCCA 59.315 57.895 0.00 0.00 0.00 5.36
2457 6535 0.257039 CCTAGAGTTGCCTTGCCCAT 59.743 55.000 0.00 0.00 0.00 4.00
2458 6536 1.490490 CCTAGAGTTGCCTTGCCCATA 59.510 52.381 0.00 0.00 0.00 2.74
2459 6537 2.107204 CCTAGAGTTGCCTTGCCCATAT 59.893 50.000 0.00 0.00 0.00 1.78
2460 6538 2.062971 AGAGTTGCCTTGCCCATATG 57.937 50.000 0.00 0.00 0.00 1.78
2461 6539 0.386838 GAGTTGCCTTGCCCATATGC 59.613 55.000 0.00 0.00 0.00 3.14
2462 6540 0.324552 AGTTGCCTTGCCCATATGCA 60.325 50.000 0.00 0.00 40.07 3.96
2463 6541 0.754472 GTTGCCTTGCCCATATGCAT 59.246 50.000 3.79 3.79 41.70 3.96
2464 6542 0.753867 TTGCCTTGCCCATATGCATG 59.246 50.000 10.16 0.00 41.70 4.06
2465 6543 0.397394 TGCCTTGCCCATATGCATGT 60.397 50.000 10.16 0.00 41.70 3.21
2466 6544 0.032952 GCCTTGCCCATATGCATGTG 59.967 55.000 15.95 15.95 41.70 3.21
2467 6545 0.677288 CCTTGCCCATATGCATGTGG 59.323 55.000 30.11 30.11 41.70 4.17
2468 6546 1.405872 CTTGCCCATATGCATGTGGT 58.594 50.000 32.81 1.64 41.70 4.16
2469 6547 1.067974 CTTGCCCATATGCATGTGGTG 59.932 52.381 32.81 25.84 41.70 4.17
2484 6562 4.218686 GTGCACCCCACCCCAACT 62.219 66.667 5.22 0.00 38.55 3.16
2485 6563 3.897122 TGCACCCCACCCCAACTC 61.897 66.667 0.00 0.00 0.00 3.01
2486 6564 3.897122 GCACCCCACCCCAACTCA 61.897 66.667 0.00 0.00 0.00 3.41
2487 6565 2.931107 CACCCCACCCCAACTCAA 59.069 61.111 0.00 0.00 0.00 3.02
2490 6568 1.378514 CCCCACCCCAACTCAATCG 60.379 63.158 0.00 0.00 0.00 3.34
2495 6573 0.988832 ACCCCAACTCAATCGCCTTA 59.011 50.000 0.00 0.00 0.00 2.69
2508 6586 1.682344 GCCTTACCCCCAAGCAAGG 60.682 63.158 0.00 0.00 40.48 3.61
2517 6595 2.132996 CCAAGCAAGGTTGGGTGCA 61.133 57.895 20.37 0.00 43.02 4.57
2521 6599 1.607467 GCAAGGTTGGGTGCATCCT 60.607 57.895 18.94 4.63 40.58 3.24
2522 6600 1.598701 GCAAGGTTGGGTGCATCCTC 61.599 60.000 18.94 10.30 40.58 3.71
2523 6601 1.002134 AAGGTTGGGTGCATCCTCG 60.002 57.895 18.94 0.00 36.25 4.63
2524 6602 1.488705 AAGGTTGGGTGCATCCTCGA 61.489 55.000 18.94 0.00 36.25 4.04
2525 6603 1.224592 GGTTGGGTGCATCCTCGAT 59.775 57.895 18.94 0.00 36.25 3.59
2528 6654 0.982852 TTGGGTGCATCCTCGATCCT 60.983 55.000 18.94 0.00 36.25 3.24
2536 6662 3.258372 TGCATCCTCGATCCTTACATACC 59.742 47.826 0.00 0.00 0.00 2.73
2537 6663 3.258372 GCATCCTCGATCCTTACATACCA 59.742 47.826 0.00 0.00 0.00 3.25
2538 6664 4.262463 GCATCCTCGATCCTTACATACCAA 60.262 45.833 0.00 0.00 0.00 3.67
2560 6686 7.037873 ACCAAAACACTCCATGGTATAACTAGA 60.038 37.037 12.58 0.00 44.11 2.43
2567 6693 3.838903 CCATGGTATAACTAGACCCTCCC 59.161 52.174 2.57 0.00 36.76 4.30
2569 6695 4.845530 TGGTATAACTAGACCCTCCCAT 57.154 45.455 0.00 0.00 36.76 4.00
2578 6704 6.997942 ACTAGACCCTCCCATAATACTTTC 57.002 41.667 0.00 0.00 0.00 2.62
2609 6735 3.336138 GAAAGACATTCGGAACCCTCT 57.664 47.619 0.00 0.00 0.00 3.69
2613 6739 2.104170 GACATTCGGAACCCTCTCTCT 58.896 52.381 0.00 0.00 0.00 3.10
2619 6745 1.410882 CGGAACCCTCTCTCTCATTCC 59.589 57.143 0.00 0.00 33.67 3.01
2622 6748 0.719015 ACCCTCTCTCTCATTCCCCA 59.281 55.000 0.00 0.00 0.00 4.96
2640 6766 6.078456 TCCCCATTATCTCATGTTTCAAGT 57.922 37.500 0.00 0.00 0.00 3.16
2642 6768 6.603201 TCCCCATTATCTCATGTTTCAAGTTC 59.397 38.462 0.00 0.00 0.00 3.01
2644 6770 6.458751 CCCATTATCTCATGTTTCAAGTTCGG 60.459 42.308 0.00 0.00 0.00 4.30
2645 6771 5.545658 TTATCTCATGTTTCAAGTTCGGC 57.454 39.130 0.00 0.00 0.00 5.54
2674 6800 1.975680 ACCATGTACGGAACACCTTCT 59.024 47.619 0.00 0.00 42.09 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 2.014128 CAGACCACCGTCACACTTTTT 58.986 47.619 0.00 0.00 41.87 1.94
16 17 1.663695 CAGACCACCGTCACACTTTT 58.336 50.000 0.00 0.00 41.87 2.27
17 18 0.814010 GCAGACCACCGTCACACTTT 60.814 55.000 0.00 0.00 41.87 2.66
18 19 1.227556 GCAGACCACCGTCACACTT 60.228 57.895 0.00 0.00 41.87 3.16
19 20 1.686325 AAGCAGACCACCGTCACACT 61.686 55.000 0.00 0.00 41.87 3.55
25 26 0.106918 TGGAAAAAGCAGACCACCGT 60.107 50.000 0.00 0.00 0.00 4.83
68 69 2.533942 GCCGGCGTATTTTTGCATAAAG 59.466 45.455 12.58 0.00 0.00 1.85
73 74 1.131504 CTTAGCCGGCGTATTTTTGCA 59.868 47.619 23.20 0.00 0.00 4.08
100 101 1.629043 GTCCCACCTGTCAGTGACTA 58.371 55.000 23.29 9.59 40.34 2.59
135 136 5.924825 ACAGTCACAAAATACGTAAGAGGAC 59.075 40.000 0.00 3.58 43.62 3.85
143 144 4.752604 TGCACATACAGTCACAAAATACGT 59.247 37.500 0.00 0.00 0.00 3.57
154 155 4.595116 GATTCAAGCATGCACATACAGTC 58.405 43.478 21.98 3.68 0.00 3.51
167 168 4.883083 AGTCACTTAACTCGATTCAAGCA 58.117 39.130 0.00 0.00 0.00 3.91
209 210 7.798982 GCTCAATGTTCAGTTTAGTGTTAGAAC 59.201 37.037 0.00 0.00 36.73 3.01
216 217 5.422666 TGTGCTCAATGTTCAGTTTAGTG 57.577 39.130 0.00 0.00 0.00 2.74
223 224 4.825546 AGAACTTGTGCTCAATGTTCAG 57.174 40.909 26.75 11.54 40.19 3.02
306 308 6.033966 GCTCGTTTATTGGTTTCCCTTAATG 58.966 40.000 0.00 0.00 0.00 1.90
325 327 2.076863 GAATTGGTGCTTGTAGCTCGT 58.923 47.619 0.00 0.00 42.97 4.18
345 349 4.877251 AGGAAGTAGTAGCTGAGTCGTAAG 59.123 45.833 0.00 0.00 0.00 2.34
346 350 4.841422 AGGAAGTAGTAGCTGAGTCGTAA 58.159 43.478 0.00 0.00 0.00 3.18
348 352 3.272581 GAGGAAGTAGTAGCTGAGTCGT 58.727 50.000 0.00 0.00 0.00 4.34
349 353 2.614983 GGAGGAAGTAGTAGCTGAGTCG 59.385 54.545 0.00 0.00 0.00 4.18
350 354 3.622630 TGGAGGAAGTAGTAGCTGAGTC 58.377 50.000 0.00 0.00 0.00 3.36
351 355 3.741245 TGGAGGAAGTAGTAGCTGAGT 57.259 47.619 0.00 0.00 0.00 3.41
352 356 5.127845 TGAAATGGAGGAAGTAGTAGCTGAG 59.872 44.000 0.00 0.00 0.00 3.35
353 357 5.023452 TGAAATGGAGGAAGTAGTAGCTGA 58.977 41.667 0.00 0.00 0.00 4.26
354 358 5.344743 TGAAATGGAGGAAGTAGTAGCTG 57.655 43.478 0.00 0.00 0.00 4.24
355 359 6.567602 ATTGAAATGGAGGAAGTAGTAGCT 57.432 37.500 0.00 0.00 0.00 3.32
356 360 7.631717 AAATTGAAATGGAGGAAGTAGTAGC 57.368 36.000 0.00 0.00 0.00 3.58
357 361 9.667107 TGTAAATTGAAATGGAGGAAGTAGTAG 57.333 33.333 0.00 0.00 0.00 2.57
363 367 8.534496 AGGATTTGTAAATTGAAATGGAGGAAG 58.466 33.333 0.00 0.00 0.00 3.46
364 368 8.434589 AGGATTTGTAAATTGAAATGGAGGAA 57.565 30.769 0.00 0.00 0.00 3.36
365 369 8.966868 GTAGGATTTGTAAATTGAAATGGAGGA 58.033 33.333 0.00 0.00 0.00 3.71
367 371 7.432252 GCGTAGGATTTGTAAATTGAAATGGAG 59.568 37.037 0.00 0.00 0.00 3.86
368 372 7.254852 GCGTAGGATTTGTAAATTGAAATGGA 58.745 34.615 0.00 0.00 0.00 3.41
371 375 6.848451 ACGCGTAGGATTTGTAAATTGAAAT 58.152 32.000 11.67 0.00 0.00 2.17
372 376 6.243811 ACGCGTAGGATTTGTAAATTGAAA 57.756 33.333 11.67 0.00 0.00 2.69
373 377 5.866335 ACGCGTAGGATTTGTAAATTGAA 57.134 34.783 11.67 0.00 0.00 2.69
374 378 8.821147 ATATACGCGTAGGATTTGTAAATTGA 57.179 30.769 24.78 0.00 0.00 2.57
375 379 8.922676 AGATATACGCGTAGGATTTGTAAATTG 58.077 33.333 24.78 0.00 0.00 2.32
377 381 9.784680 CTAGATATACGCGTAGGATTTGTAAAT 57.215 33.333 24.78 6.54 0.00 1.40
378 382 8.239314 CCTAGATATACGCGTAGGATTTGTAAA 58.761 37.037 24.78 0.00 34.99 2.01
379 383 7.391554 ACCTAGATATACGCGTAGGATTTGTAA 59.608 37.037 25.95 1.90 36.34 2.41
380 384 6.881065 ACCTAGATATACGCGTAGGATTTGTA 59.119 38.462 25.95 12.32 36.34 2.41
381 385 5.709164 ACCTAGATATACGCGTAGGATTTGT 59.291 40.000 25.95 14.24 36.34 2.83
382 386 6.192234 ACCTAGATATACGCGTAGGATTTG 57.808 41.667 25.95 14.10 36.34 2.32
383 387 6.208204 ACAACCTAGATATACGCGTAGGATTT 59.792 38.462 25.95 17.70 36.34 2.17
384 388 5.709164 ACAACCTAGATATACGCGTAGGATT 59.291 40.000 25.95 12.28 36.34 3.01
385 389 5.251764 ACAACCTAGATATACGCGTAGGAT 58.748 41.667 25.95 20.20 36.34 3.24
386 390 4.645535 ACAACCTAGATATACGCGTAGGA 58.354 43.478 25.95 16.64 36.34 2.94
387 391 4.453478 TGACAACCTAGATATACGCGTAGG 59.547 45.833 24.78 21.85 38.45 3.18
388 392 5.602458 TGACAACCTAGATATACGCGTAG 57.398 43.478 24.78 11.28 0.00 3.51
389 393 6.564709 ATTGACAACCTAGATATACGCGTA 57.435 37.500 22.94 22.94 0.00 4.42
390 394 4.906065 TTGACAACCTAGATATACGCGT 57.094 40.909 19.17 19.17 0.00 6.01
391 395 6.764877 AAATTGACAACCTAGATATACGCG 57.235 37.500 3.53 3.53 0.00 6.01
392 396 8.493547 GGTAAAATTGACAACCTAGATATACGC 58.506 37.037 0.00 0.00 0.00 4.42
393 397 9.537192 TGGTAAAATTGACAACCTAGATATACG 57.463 33.333 0.00 0.00 32.99 3.06
396 400 9.614792 GAGTGGTAAAATTGACAACCTAGATAT 57.385 33.333 0.00 0.00 32.99 1.63
397 401 8.822805 AGAGTGGTAAAATTGACAACCTAGATA 58.177 33.333 0.00 0.00 32.99 1.98
398 402 7.690256 AGAGTGGTAAAATTGACAACCTAGAT 58.310 34.615 0.00 0.00 32.99 1.98
399 403 7.074653 AGAGTGGTAAAATTGACAACCTAGA 57.925 36.000 0.00 0.00 32.99 2.43
400 404 8.842358 TTAGAGTGGTAAAATTGACAACCTAG 57.158 34.615 0.00 0.00 32.99 3.02
402 406 9.975218 ATATTAGAGTGGTAAAATTGACAACCT 57.025 29.630 0.00 0.00 32.99 3.50
437 441 9.941664 TTTTCGAACCGTATAATTTTTGTGTTA 57.058 25.926 0.00 0.00 0.00 2.41
438 442 8.853469 TTTTCGAACCGTATAATTTTTGTGTT 57.147 26.923 0.00 0.00 0.00 3.32
448 452 9.976255 CAAATGTTCTATTTTCGAACCGTATAA 57.024 29.630 0.00 0.00 39.92 0.98
449 453 9.368674 TCAAATGTTCTATTTTCGAACCGTATA 57.631 29.630 0.00 0.00 39.92 1.47
450 454 8.259049 TCAAATGTTCTATTTTCGAACCGTAT 57.741 30.769 0.00 0.00 39.92 3.06
451 455 7.655236 TCAAATGTTCTATTTTCGAACCGTA 57.345 32.000 0.00 0.00 39.92 4.02
452 456 6.548441 TCAAATGTTCTATTTTCGAACCGT 57.452 33.333 0.00 0.00 39.92 4.83
453 457 7.075741 ACTTCAAATGTTCTATTTTCGAACCG 58.924 34.615 0.00 0.00 39.92 4.44
454 458 8.797266 AACTTCAAATGTTCTATTTTCGAACC 57.203 30.769 0.00 0.00 39.92 3.62
524 528 9.450807 GCGTACCTCTAAGTCGTTAATTTATAA 57.549 33.333 0.00 0.00 0.00 0.98
525 529 7.798516 CGCGTACCTCTAAGTCGTTAATTTATA 59.201 37.037 0.00 0.00 0.00 0.98
526 530 6.634436 CGCGTACCTCTAAGTCGTTAATTTAT 59.366 38.462 0.00 0.00 0.00 1.40
527 531 5.965334 CGCGTACCTCTAAGTCGTTAATTTA 59.035 40.000 0.00 0.00 0.00 1.40
528 532 4.795278 CGCGTACCTCTAAGTCGTTAATTT 59.205 41.667 0.00 0.00 0.00 1.82
529 533 4.346129 CGCGTACCTCTAAGTCGTTAATT 58.654 43.478 0.00 0.00 0.00 1.40
530 534 3.790123 GCGCGTACCTCTAAGTCGTTAAT 60.790 47.826 8.43 0.00 0.00 1.40
531 535 2.476185 GCGCGTACCTCTAAGTCGTTAA 60.476 50.000 8.43 0.00 0.00 2.01
532 536 1.062587 GCGCGTACCTCTAAGTCGTTA 59.937 52.381 8.43 0.00 0.00 3.18
533 537 0.179179 GCGCGTACCTCTAAGTCGTT 60.179 55.000 8.43 0.00 0.00 3.85
534 538 1.300971 TGCGCGTACCTCTAAGTCGT 61.301 55.000 8.43 0.00 0.00 4.34
535 539 0.860618 GTGCGCGTACCTCTAAGTCG 60.861 60.000 17.10 0.00 0.00 4.18
536 540 0.169672 TGTGCGCGTACCTCTAAGTC 59.830 55.000 24.54 0.00 0.00 3.01
537 541 0.109412 GTGTGCGCGTACCTCTAAGT 60.109 55.000 24.54 0.00 0.00 2.24
538 542 0.801067 GGTGTGCGCGTACCTCTAAG 60.801 60.000 24.54 0.00 34.11 2.18
539 543 1.213537 GGTGTGCGCGTACCTCTAA 59.786 57.895 24.54 2.18 34.11 2.10
540 544 0.392863 TAGGTGTGCGCGTACCTCTA 60.393 55.000 30.99 22.18 43.69 2.43
541 545 1.035932 ATAGGTGTGCGCGTACCTCT 61.036 55.000 30.99 21.92 43.69 3.69
542 546 0.870307 CATAGGTGTGCGCGTACCTC 60.870 60.000 30.99 18.90 43.69 3.85
544 548 0.870307 CTCATAGGTGTGCGCGTACC 60.870 60.000 24.54 21.36 37.23 3.34
545 549 0.099968 TCTCATAGGTGTGCGCGTAC 59.900 55.000 21.02 21.02 0.00 3.67
546 550 0.380733 CTCTCATAGGTGTGCGCGTA 59.619 55.000 8.43 0.00 0.00 4.42
547 551 1.139734 CTCTCATAGGTGTGCGCGT 59.860 57.895 8.43 0.00 0.00 6.01
548 552 0.593518 CTCTCTCATAGGTGTGCGCG 60.594 60.000 0.00 0.00 0.00 6.86
549 553 0.249238 CCTCTCTCATAGGTGTGCGC 60.249 60.000 0.00 0.00 0.00 6.09
550 554 0.387202 CCCTCTCTCATAGGTGTGCG 59.613 60.000 0.00 0.00 31.70 5.34
551 555 1.686052 CTCCCTCTCTCATAGGTGTGC 59.314 57.143 0.00 0.00 31.70 4.57
552 556 3.025322 ACTCCCTCTCTCATAGGTGTG 57.975 52.381 0.00 0.00 31.70 3.82
553 557 3.789274 AGTACTCCCTCTCTCATAGGTGT 59.211 47.826 0.00 0.00 31.70 4.16
554 558 4.447138 AGTACTCCCTCTCTCATAGGTG 57.553 50.000 0.00 0.00 31.70 4.00
555 559 6.790177 AATAGTACTCCCTCTCTCATAGGT 57.210 41.667 0.00 0.00 31.70 3.08
556 560 9.016438 GTTTAATAGTACTCCCTCTCTCATAGG 57.984 40.741 0.00 0.00 0.00 2.57
557 561 9.016438 GGTTTAATAGTACTCCCTCTCTCATAG 57.984 40.741 0.00 0.00 0.00 2.23
558 562 7.664731 CGGTTTAATAGTACTCCCTCTCTCATA 59.335 40.741 0.00 0.00 0.00 2.15
559 563 6.490721 CGGTTTAATAGTACTCCCTCTCTCAT 59.509 42.308 0.00 0.00 0.00 2.90
560 564 5.826737 CGGTTTAATAGTACTCCCTCTCTCA 59.173 44.000 0.00 0.00 0.00 3.27
561 565 5.278414 GCGGTTTAATAGTACTCCCTCTCTC 60.278 48.000 0.00 0.00 0.00 3.20
562 566 4.583907 GCGGTTTAATAGTACTCCCTCTCT 59.416 45.833 0.00 0.00 0.00 3.10
563 567 4.261952 GGCGGTTTAATAGTACTCCCTCTC 60.262 50.000 0.00 0.00 0.00 3.20
564 568 3.640498 GGCGGTTTAATAGTACTCCCTCT 59.360 47.826 0.00 0.00 0.00 3.69
565 569 3.640498 AGGCGGTTTAATAGTACTCCCTC 59.360 47.826 0.00 0.00 0.00 4.30
568 572 5.781210 ACTAGGCGGTTTAATAGTACTCC 57.219 43.478 0.00 0.00 0.00 3.85
569 573 6.699204 GGAAACTAGGCGGTTTAATAGTACTC 59.301 42.308 0.00 0.00 39.20 2.59
571 575 5.755375 GGGAAACTAGGCGGTTTAATAGTAC 59.245 44.000 10.55 0.00 39.20 2.73
577 581 3.505480 TTGGGAAACTAGGCGGTTTAA 57.495 42.857 10.55 1.78 39.20 1.52
651 655 3.600388 GTGCAAGATATCCCCGGATTAG 58.400 50.000 0.73 0.00 36.17 1.73
748 2100 1.409427 AGCGAACCATGCTAGGAGTAC 59.591 52.381 1.88 0.00 41.87 2.73
750 2102 0.176680 CAGCGAACCATGCTAGGAGT 59.823 55.000 1.88 0.00 41.72 3.85
971 2361 3.672255 TACACAGCGCGCGGTACTC 62.672 63.158 34.97 15.77 0.00 2.59
1012 2402 0.884259 TTGTGCTGGTGGATCGTGTG 60.884 55.000 0.00 0.00 0.00 3.82
1024 2414 0.952497 AGGTCACGCTCATTGTGCTG 60.952 55.000 8.87 6.51 37.26 4.41
1169 2580 2.718073 TAAAGAGCCCCGAGGACGC 61.718 63.158 0.00 0.00 38.29 5.19
1319 2730 0.586802 CTCGTACGAGATGCCGATGA 59.413 55.000 36.12 1.92 44.53 2.92
1401 2812 2.584608 CGGTGGCCCTGGTAGAAG 59.415 66.667 0.00 0.00 0.00 2.85
1638 5508 2.670479 CTCATCGTCTTGATCCGGATG 58.330 52.381 24.82 7.94 34.13 3.51
1645 5515 2.005451 GTTGCAGCTCATCGTCTTGAT 58.995 47.619 0.00 0.00 38.01 2.57
1688 5558 3.943858 GTCGTTTAACGGCAAAGCCCG 62.944 57.143 17.44 0.00 46.84 6.13
1715 5601 7.860872 TCATTGTACGCTTCACATATACAGTAG 59.139 37.037 0.00 0.00 0.00 2.57
1722 5772 7.710907 ACATAACTCATTGTACGCTTCACATAT 59.289 33.333 0.00 0.00 0.00 1.78
1723 5773 7.039270 ACATAACTCATTGTACGCTTCACATA 58.961 34.615 0.00 0.00 0.00 2.29
1850 5912 7.731882 TGAACTATCGATACAAACAAACCAA 57.268 32.000 0.00 0.00 0.00 3.67
1972 6034 5.241506 GGATTGACATTTGACTGTTGAGGAA 59.758 40.000 0.00 0.00 0.00 3.36
2009 6071 7.657354 GGAGAAAGAAAATAAACAATGCACCTT 59.343 33.333 0.00 0.00 0.00 3.50
2106 6168 3.222855 TTTGGCCAACGCAGGGTG 61.223 61.111 20.35 0.00 36.38 4.61
2107 6169 3.223589 GTTTGGCCAACGCAGGGT 61.224 61.111 20.35 0.00 36.38 4.34
2126 6188 0.179032 TGTGAGTGGCAACGGACAAT 60.179 50.000 0.00 0.00 42.51 2.71
2132 6194 2.631428 CGGTTGTGAGTGGCAACG 59.369 61.111 0.00 0.00 45.01 4.10
2134 6196 1.227823 CTCCGGTTGTGAGTGGCAA 60.228 57.895 0.00 0.00 0.00 4.52
2141 6203 4.680237 CAGGCGCTCCGGTTGTGA 62.680 66.667 7.64 0.00 37.47 3.58
2164 6238 1.314534 CCGTGGATCAAGCATGGCAA 61.315 55.000 0.00 0.00 0.00 4.52
2165 6239 1.750018 CCGTGGATCAAGCATGGCA 60.750 57.895 0.00 0.00 0.00 4.92
2169 6243 0.179000 GGAGACCGTGGATCAAGCAT 59.821 55.000 0.00 0.00 0.00 3.79
2182 6256 2.501610 GGAGGCATGACGGAGACC 59.498 66.667 0.00 0.00 0.00 3.85
2184 6258 3.838271 GCGGAGGCATGACGGAGA 61.838 66.667 0.00 0.00 39.62 3.71
2241 6315 0.690762 TGGTAGGTTGCTTGTCCCTC 59.309 55.000 0.00 0.00 0.00 4.30
2247 6321 3.340814 AGATCACTGGTAGGTTGCTTG 57.659 47.619 0.00 0.00 0.00 4.01
2253 6327 5.654901 TCTCATCTAGATCACTGGTAGGT 57.345 43.478 1.03 0.00 0.00 3.08
2280 6358 1.400530 CGCCCCCTTCTATCTCGGTT 61.401 60.000 0.00 0.00 0.00 4.44
2305 6383 4.742649 TCGAGCACTCTCCCCGCT 62.743 66.667 0.00 0.00 39.12 5.52
2307 6385 3.827898 GGTCGAGCACTCTCCCCG 61.828 72.222 10.30 0.00 35.94 5.73
2308 6386 2.680352 TGGTCGAGCACTCTCCCC 60.680 66.667 14.39 0.00 35.94 4.81
2325 6403 2.112279 TACACAGACCTTTCCCACCT 57.888 50.000 0.00 0.00 0.00 4.00
2332 6410 2.237392 GCAGGAGGATACACAGACCTTT 59.763 50.000 0.00 0.00 41.41 3.11
2333 6411 1.834263 GCAGGAGGATACACAGACCTT 59.166 52.381 0.00 0.00 41.41 3.50
2334 6412 1.007721 AGCAGGAGGATACACAGACCT 59.992 52.381 0.00 0.00 41.41 3.85
2340 6418 1.383523 GGCAAAGCAGGAGGATACAC 58.616 55.000 0.00 0.00 41.41 2.90
2372 6450 4.527427 GTCAACCCTCCTCCACCTATATAC 59.473 50.000 0.00 0.00 0.00 1.47
2429 6507 1.153549 CAACTCTAGGGGCACGAGC 60.154 63.158 0.00 0.00 41.10 5.03
2430 6508 1.153549 GCAACTCTAGGGGCACGAG 60.154 63.158 0.00 0.00 0.00 4.18
2431 6509 2.656069 GGCAACTCTAGGGGCACGA 61.656 63.158 0.00 0.00 0.00 4.35
2432 6510 2.125106 GGCAACTCTAGGGGCACG 60.125 66.667 0.00 0.00 0.00 5.34
2444 6522 2.200989 TGCATATGGGCAAGGCAAC 58.799 52.632 4.56 0.00 41.65 4.17
2445 6523 4.781264 TGCATATGGGCAAGGCAA 57.219 50.000 4.56 0.00 41.65 4.52
2467 6545 4.218686 AGTTGGGGTGGGGTGCAC 62.219 66.667 8.80 8.80 0.00 4.57
2468 6546 3.897122 GAGTTGGGGTGGGGTGCA 61.897 66.667 0.00 0.00 0.00 4.57
2469 6547 2.730129 ATTGAGTTGGGGTGGGGTGC 62.730 60.000 0.00 0.00 0.00 5.01
2470 6548 0.611896 GATTGAGTTGGGGTGGGGTG 60.612 60.000 0.00 0.00 0.00 4.61
2471 6549 1.774300 GATTGAGTTGGGGTGGGGT 59.226 57.895 0.00 0.00 0.00 4.95
2472 6550 1.378514 CGATTGAGTTGGGGTGGGG 60.379 63.158 0.00 0.00 0.00 4.96
2473 6551 2.046285 GCGATTGAGTTGGGGTGGG 61.046 63.158 0.00 0.00 0.00 4.61
2474 6552 2.046285 GGCGATTGAGTTGGGGTGG 61.046 63.158 0.00 0.00 0.00 4.61
2475 6553 0.609131 AAGGCGATTGAGTTGGGGTG 60.609 55.000 0.00 0.00 0.00 4.61
2476 6554 0.988832 TAAGGCGATTGAGTTGGGGT 59.011 50.000 0.00 0.00 0.00 4.95
2477 6555 1.379527 GTAAGGCGATTGAGTTGGGG 58.620 55.000 0.00 0.00 0.00 4.96
2478 6556 1.379527 GGTAAGGCGATTGAGTTGGG 58.620 55.000 0.00 0.00 0.00 4.12
2479 6557 1.379527 GGGTAAGGCGATTGAGTTGG 58.620 55.000 0.00 0.00 0.00 3.77
2480 6558 1.379527 GGGGTAAGGCGATTGAGTTG 58.620 55.000 0.00 0.00 0.00 3.16
2481 6559 0.255033 GGGGGTAAGGCGATTGAGTT 59.745 55.000 0.00 0.00 0.00 3.01
2482 6560 0.912487 TGGGGGTAAGGCGATTGAGT 60.912 55.000 0.00 0.00 0.00 3.41
2483 6561 0.254747 TTGGGGGTAAGGCGATTGAG 59.745 55.000 0.00 0.00 0.00 3.02
2484 6562 0.254747 CTTGGGGGTAAGGCGATTGA 59.745 55.000 0.00 0.00 0.00 2.57
2485 6563 1.384222 GCTTGGGGGTAAGGCGATTG 61.384 60.000 0.00 0.00 0.00 2.67
2486 6564 1.076995 GCTTGGGGGTAAGGCGATT 60.077 57.895 0.00 0.00 0.00 3.34
2487 6565 1.858739 TTGCTTGGGGGTAAGGCGAT 61.859 55.000 0.00 0.00 0.00 4.58
2490 6568 1.682344 CCTTGCTTGGGGGTAAGGC 60.682 63.158 0.00 0.00 40.88 4.35
2495 6573 2.201210 CCAACCTTGCTTGGGGGT 59.799 61.111 0.00 0.00 37.62 4.95
2508 6586 0.815615 GGATCGAGGATGCACCCAAC 60.816 60.000 0.00 0.00 40.05 3.77
2513 6591 2.890808 TGTAAGGATCGAGGATGCAC 57.109 50.000 0.00 0.00 32.78 4.57
2517 6595 6.126883 TGTTTTGGTATGTAAGGATCGAGGAT 60.127 38.462 0.00 0.00 0.00 3.24
2521 6599 6.045072 AGTGTTTTGGTATGTAAGGATCGA 57.955 37.500 0.00 0.00 0.00 3.59
2522 6600 5.293569 GGAGTGTTTTGGTATGTAAGGATCG 59.706 44.000 0.00 0.00 0.00 3.69
2523 6601 6.177610 TGGAGTGTTTTGGTATGTAAGGATC 58.822 40.000 0.00 0.00 0.00 3.36
2524 6602 6.134535 TGGAGTGTTTTGGTATGTAAGGAT 57.865 37.500 0.00 0.00 0.00 3.24
2525 6603 5.570205 TGGAGTGTTTTGGTATGTAAGGA 57.430 39.130 0.00 0.00 0.00 3.36
2528 6654 5.636123 ACCATGGAGTGTTTTGGTATGTAA 58.364 37.500 21.47 0.00 40.62 2.41
2536 6662 7.280205 GGTCTAGTTATACCATGGAGTGTTTTG 59.720 40.741 21.47 3.01 35.73 2.44
2537 6663 7.336396 GGTCTAGTTATACCATGGAGTGTTTT 58.664 38.462 21.47 0.00 35.73 2.43
2538 6664 6.126854 GGGTCTAGTTATACCATGGAGTGTTT 60.127 42.308 21.47 0.00 37.51 2.83
2554 6680 6.041751 CGAAAGTATTATGGGAGGGTCTAGTT 59.958 42.308 0.00 0.00 0.00 2.24
2560 6686 2.709397 CCCGAAAGTATTATGGGAGGGT 59.291 50.000 0.00 0.00 42.77 4.34
2589 6715 3.055747 AGAGAGGGTTCCGAATGTCTTTC 60.056 47.826 0.00 0.00 0.00 2.62
2593 6719 2.100087 GAGAGAGAGGGTTCCGAATGTC 59.900 54.545 0.00 0.00 0.00 3.06
2601 6727 1.765904 GGGGAATGAGAGAGAGGGTTC 59.234 57.143 0.00 0.00 0.00 3.62
2609 6735 5.848369 ACATGAGATAATGGGGAATGAGAGA 59.152 40.000 0.00 0.00 31.46 3.10
2613 6739 6.671605 TGAAACATGAGATAATGGGGAATGA 58.328 36.000 0.00 0.00 31.46 2.57
2619 6745 6.458751 CCGAACTTGAAACATGAGATAATGGG 60.459 42.308 0.00 0.00 31.46 4.00
2622 6748 5.647658 TGCCGAACTTGAAACATGAGATAAT 59.352 36.000 0.00 0.00 0.00 1.28
2640 6766 2.098614 ACATGGTTGCATATTGCCGAA 58.901 42.857 0.00 0.00 44.23 4.30
2642 6768 2.601979 CGTACATGGTTGCATATTGCCG 60.602 50.000 0.00 0.00 44.23 5.69
2644 6770 2.616376 TCCGTACATGGTTGCATATTGC 59.384 45.455 0.00 0.00 45.29 3.56
2645 6771 4.095632 TGTTCCGTACATGGTTGCATATTG 59.904 41.667 0.00 0.00 0.00 1.90



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

AutoCloner maintained by Alex Coulton.