Multiple sequence alignment - TraesCS1B01G411800

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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 TraesCS1B01G411800 chr1B 100.000 4567 0 0 1 4567 637916482 637911916 0.000000e+00 8434.0
1 TraesCS1B01G411800 chr1B 97.059 34 1 0 3919 3952 565340907 565340940 1.770000e-04 58.4
2 TraesCS1B01G411800 chr1D 94.822 3167 125 16 641 3785 462968450 462965301 0.000000e+00 4903.0
3 TraesCS1B01G411800 chr1D 94.137 2132 102 12 888 3004 462927770 462925647 0.000000e+00 3223.0
4 TraesCS1B01G411800 chr1D 93.794 2143 102 16 887 3004 462890821 462888685 0.000000e+00 3192.0
5 TraesCS1B01G411800 chr1D 93.770 2135 108 12 887 3004 462934939 462932813 0.000000e+00 3182.0
6 TraesCS1B01G411800 chr1D 93.645 2140 110 10 887 3004 462888253 462886118 0.000000e+00 3175.0
7 TraesCS1B01G411800 chr1D 93.648 2141 107 13 887 3004 462913894 462911760 0.000000e+00 3173.0
8 TraesCS1B01G411800 chr1D 93.604 2142 110 10 887 3004 462893392 462891254 0.000000e+00 3171.0
9 TraesCS1B01G411800 chr1D 93.601 2141 107 14 887 3004 462921121 462918988 0.000000e+00 3168.0
10 TraesCS1B01G411800 chr1D 93.231 2142 119 10 887 3004 462898507 462896368 0.000000e+00 3129.0
11 TraesCS1B01G411800 chr1D 93.781 1833 89 14 1194 3004 462910972 462909143 0.000000e+00 2730.0
12 TraesCS1B01G411800 chr1D 93.781 1833 89 14 1194 3004 462918200 462916371 0.000000e+00 2730.0
13 TraesCS1B01G411800 chr1D 93.338 1396 76 9 1621 3004 462929593 462928203 0.000000e+00 2047.0
14 TraesCS1B01G411800 chr1D 93.030 1406 72 13 1621 3004 462915727 462914326 0.000000e+00 2030.0
15 TraesCS1B01G411800 chr1D 93.503 1293 60 14 1734 3004 462905350 462904060 0.000000e+00 1901.0
16 TraesCS1B01G411800 chr1D 92.664 1295 71 10 1734 3004 462907893 462906599 0.000000e+00 1844.0
17 TraesCS1B01G411800 chr1D 97.478 793 15 1 3775 4567 462947671 462946884 0.000000e+00 1349.0
18 TraesCS1B01G411800 chr2D 94.529 3016 131 17 897 3885 634645040 634648048 0.000000e+00 4625.0
19 TraesCS1B01G411800 chr2D 97.118 694 11 5 3873 4565 634649448 634650133 0.000000e+00 1162.0
20 TraesCS1B01G411800 chr2D 74.620 461 82 22 11 444 625300943 625300491 2.180000e-38 171.0
21 TraesCS1B01G411800 chr3B 94.176 2009 70 21 2589 4567 397678494 397676503 0.000000e+00 3018.0
22 TraesCS1B01G411800 chr3B 90.312 640 33 12 1 638 726625213 726625825 0.000000e+00 811.0
23 TraesCS1B01G411800 chr3B 86.739 641 56 16 1955 2589 427160588 427161205 0.000000e+00 686.0
24 TraesCS1B01G411800 chr3B 74.316 475 80 29 1 444 766375614 766375151 3.660000e-36 163.0
25 TraesCS1B01G411800 chr3D 94.673 995 36 10 3579 4567 321873079 321874062 0.000000e+00 1528.0
26 TraesCS1B01G411800 chr3D 77.907 344 53 13 8 335 30384555 30384219 4.660000e-45 193.0
27 TraesCS1B01G411800 chr3D 83.799 179 18 4 4215 4384 508466470 508466646 4.730000e-35 159.0
28 TraesCS1B01G411800 chr3D 85.417 144 18 3 4077 4217 508465557 508465700 3.680000e-31 147.0
29 TraesCS1B01G411800 chr3D 84.536 97 5 2 3919 4015 606777996 606777910 2.260000e-13 87.9
30 TraesCS1B01G411800 chr3A 94.311 1002 36 12 3581 4567 402135057 402134062 0.000000e+00 1515.0
31 TraesCS1B01G411800 chr3A 86.318 899 75 23 2597 3474 402135967 402135096 0.000000e+00 935.0
32 TraesCS1B01G411800 chr2B 87.171 951 72 17 1657 2588 8622521 8623440 0.000000e+00 1035.0
33 TraesCS1B01G411800 chr2B 86.603 948 84 20 1659 2588 669496258 669497180 0.000000e+00 1007.0
34 TraesCS1B01G411800 chr2B 84.868 945 82 35 1663 2589 582311985 582311084 0.000000e+00 896.0
35 TraesCS1B01G411800 chr5D 85.121 867 86 27 1648 2495 456753083 456753925 0.000000e+00 846.0
36 TraesCS1B01G411800 chr7B 89.862 651 48 6 1 641 470479263 470478621 0.000000e+00 821.0
37 TraesCS1B01G411800 chr1A 82.595 655 81 20 1 633 418085052 418084409 8.640000e-152 547.0
38 TraesCS1B01G411800 chr6A 83.230 483 54 14 4054 4522 508249112 508249581 7.070000e-113 418.0
39 TraesCS1B01G411800 chr6D 84.593 344 29 12 4236 4567 367749521 367749852 2.050000e-83 320.0
40 TraesCS1B01G411800 chr7D 84.962 266 28 4 4128 4384 41303797 41303535 4.530000e-65 259.0
41 TraesCS1B01G411800 chr7D 85.185 216 16 8 3919 4130 41306360 41306157 1.670000e-49 207.0
42 TraesCS1B01G411800 chrUn 77.119 354 53 22 1 335 24330376 24330032 3.630000e-41 180.0
43 TraesCS1B01G411800 chr7A 81.731 104 15 2 224 327 540882 540981 2.930000e-12 84.2


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 TraesCS1B01G411800 chr1B 637911916 637916482 4566 True 8434.000000 8434 100.000000 1 4567 1 chr1B.!!$R1 4566
1 TraesCS1B01G411800 chr1D 462965301 462968450 3149 True 4903.000000 4903 94.822000 641 3785 1 chr1D.!!$R2 3144
2 TraesCS1B01G411800 chr1D 462886118 462898507 12389 True 3166.750000 3192 93.568500 887 3004 4 chr1D.!!$R3 2117
3 TraesCS1B01G411800 chr1D 462925647 462934939 9292 True 2817.333333 3223 93.748333 887 3004 3 chr1D.!!$R5 2117
4 TraesCS1B01G411800 chr1D 462904060 462921121 17061 True 2510.857143 3173 93.429714 887 3004 7 chr1D.!!$R4 2117
5 TraesCS1B01G411800 chr1D 462946884 462947671 787 True 1349.000000 1349 97.478000 3775 4567 1 chr1D.!!$R1 792
6 TraesCS1B01G411800 chr2D 634645040 634650133 5093 False 2893.500000 4625 95.823500 897 4565 2 chr2D.!!$F1 3668
7 TraesCS1B01G411800 chr3B 397676503 397678494 1991 True 3018.000000 3018 94.176000 2589 4567 1 chr3B.!!$R1 1978
8 TraesCS1B01G411800 chr3B 726625213 726625825 612 False 811.000000 811 90.312000 1 638 1 chr3B.!!$F2 637
9 TraesCS1B01G411800 chr3B 427160588 427161205 617 False 686.000000 686 86.739000 1955 2589 1 chr3B.!!$F1 634
10 TraesCS1B01G411800 chr3D 321873079 321874062 983 False 1528.000000 1528 94.673000 3579 4567 1 chr3D.!!$F1 988
11 TraesCS1B01G411800 chr3A 402134062 402135967 1905 True 1225.000000 1515 90.314500 2597 4567 2 chr3A.!!$R1 1970
12 TraesCS1B01G411800 chr2B 8622521 8623440 919 False 1035.000000 1035 87.171000 1657 2588 1 chr2B.!!$F1 931
13 TraesCS1B01G411800 chr2B 669496258 669497180 922 False 1007.000000 1007 86.603000 1659 2588 1 chr2B.!!$F2 929
14 TraesCS1B01G411800 chr2B 582311084 582311985 901 True 896.000000 896 84.868000 1663 2589 1 chr2B.!!$R1 926
15 TraesCS1B01G411800 chr5D 456753083 456753925 842 False 846.000000 846 85.121000 1648 2495 1 chr5D.!!$F1 847
16 TraesCS1B01G411800 chr7B 470478621 470479263 642 True 821.000000 821 89.862000 1 641 1 chr7B.!!$R1 640
17 TraesCS1B01G411800 chr1A 418084409 418085052 643 True 547.000000 547 82.595000 1 633 1 chr1A.!!$R1 632
18 TraesCS1B01G411800 chr7D 41303535 41306360 2825 True 233.000000 259 85.073500 3919 4384 2 chr7D.!!$R1 465

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
634 649 0.098200 GCCCCGAGTTTTATGTTCGC 59.902 55.0 0.0 0.0 33.25 4.70 F
710 726 0.321387 TACAGTGGACTCTCGCTCGT 60.321 55.0 0.0 0.0 0.00 4.18 F
1888 7155 0.748005 ACTTTGGTGCGCAAGACACT 60.748 50.0 14.0 0.0 41.79 3.55 F
2802 23548 0.766288 TGATATCCACATCCCCGGCA 60.766 55.0 0.0 0.0 0.00 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2297 17941 0.035317 ACATTCAAGCAGCTCGTGGA 59.965 50.000 0.00 0.00 0.00 4.02 R
2326 20513 0.596082 AGACCCGTGCAAAATTTCGG 59.404 50.000 8.64 8.64 42.22 4.30 R
3123 23878 0.034896 ACCGTGGAGCAGGTGTAAAG 59.965 55.000 0.00 0.00 39.66 1.85 R
4180 28738 2.125633 GAGGTCGGCCGAGTTTCC 60.126 66.667 31.97 25.98 40.50 3.13 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
34 36 1.904865 AGTACGCCGACCAACTCCA 60.905 57.895 0.00 0.00 0.00 3.86
54 56 2.298446 CACTCAGCTCTCTGGTCTTCAA 59.702 50.000 0.00 0.00 40.69 2.69
126 128 5.235616 ACAAAAATCCATATCGCGTTATCGT 59.764 36.000 5.77 0.00 39.49 3.73
127 129 5.917541 AAAATCCATATCGCGTTATCGTT 57.082 34.783 5.77 0.00 39.49 3.85
128 130 4.903638 AATCCATATCGCGTTATCGTTG 57.096 40.909 5.77 0.00 39.49 4.10
226 228 2.029073 CGGTCGCTGGTCTGTTGT 59.971 61.111 0.00 0.00 0.00 3.32
263 270 2.678580 TCCGCCACCTGATCGTGA 60.679 61.111 2.63 0.00 35.68 4.35
264 271 2.021068 CTCCGCCACCTGATCGTGAT 62.021 60.000 2.63 0.00 35.68 3.06
265 272 0.753848 TCCGCCACCTGATCGTGATA 60.754 55.000 2.63 0.00 35.68 2.15
266 273 0.597637 CCGCCACCTGATCGTGATAC 60.598 60.000 2.63 0.00 35.68 2.24
332 347 0.318955 ATTCTTGCACTGGCGTTTGC 60.319 50.000 0.00 0.00 45.35 3.68
342 357 3.059386 GCGTTTGCCCCCGATTCA 61.059 61.111 0.00 0.00 33.98 2.57
343 358 2.414785 GCGTTTGCCCCCGATTCAT 61.415 57.895 0.00 0.00 33.98 2.57
344 359 1.433064 CGTTTGCCCCCGATTCATG 59.567 57.895 0.00 0.00 0.00 3.07
345 360 1.141665 GTTTGCCCCCGATTCATGC 59.858 57.895 0.00 0.00 0.00 4.06
346 361 1.304796 TTTGCCCCCGATTCATGCA 60.305 52.632 0.00 0.00 0.00 3.96
347 362 0.687098 TTTGCCCCCGATTCATGCAT 60.687 50.000 0.00 0.00 0.00 3.96
348 363 1.393487 TTGCCCCCGATTCATGCATG 61.393 55.000 21.07 21.07 0.00 4.06
349 364 1.829533 GCCCCCGATTCATGCATGT 60.830 57.895 25.43 8.12 0.00 3.21
350 365 0.537143 GCCCCCGATTCATGCATGTA 60.537 55.000 25.43 17.45 0.00 2.29
351 366 1.527034 CCCCCGATTCATGCATGTAG 58.473 55.000 25.43 14.61 0.00 2.74
352 367 0.877071 CCCCGATTCATGCATGTAGC 59.123 55.000 25.43 18.21 45.96 3.58
361 376 3.585990 GCATGTAGCGCCGGCAAT 61.586 61.111 28.98 16.84 43.41 3.56
362 377 3.110139 CATGTAGCGCCGGCAATT 58.890 55.556 28.98 13.53 43.41 2.32
363 378 1.298563 CATGTAGCGCCGGCAATTG 60.299 57.895 28.98 11.41 43.41 2.32
364 379 1.748879 ATGTAGCGCCGGCAATTGT 60.749 52.632 28.98 7.77 43.41 2.71
365 380 1.714899 ATGTAGCGCCGGCAATTGTC 61.715 55.000 28.98 11.55 43.41 3.18
366 381 2.822255 TAGCGCCGGCAATTGTCC 60.822 61.111 28.98 6.65 43.41 4.02
367 382 3.323758 TAGCGCCGGCAATTGTCCT 62.324 57.895 28.98 12.08 43.41 3.85
368 383 1.962321 TAGCGCCGGCAATTGTCCTA 61.962 55.000 28.98 11.09 43.41 2.94
369 384 2.186826 GCGCCGGCAATTGTCCTAT 61.187 57.895 28.98 0.00 39.62 2.57
370 385 0.882927 GCGCCGGCAATTGTCCTATA 60.883 55.000 28.98 0.00 39.62 1.31
371 386 1.808411 CGCCGGCAATTGTCCTATAT 58.192 50.000 28.98 0.00 0.00 0.86
372 387 2.151202 CGCCGGCAATTGTCCTATATT 58.849 47.619 28.98 0.00 0.00 1.28
373 388 3.331150 CGCCGGCAATTGTCCTATATTA 58.669 45.455 28.98 0.00 0.00 0.98
374 389 3.370978 CGCCGGCAATTGTCCTATATTAG 59.629 47.826 28.98 0.00 0.00 1.73
375 390 3.127030 GCCGGCAATTGTCCTATATTAGC 59.873 47.826 24.80 0.00 0.00 3.09
376 391 4.323417 CCGGCAATTGTCCTATATTAGCA 58.677 43.478 4.07 0.00 0.00 3.49
377 392 4.943705 CCGGCAATTGTCCTATATTAGCAT 59.056 41.667 4.07 0.00 0.00 3.79
378 393 5.415701 CCGGCAATTGTCCTATATTAGCATT 59.584 40.000 4.07 0.00 0.00 3.56
379 394 6.403636 CCGGCAATTGTCCTATATTAGCATTC 60.404 42.308 4.07 0.00 0.00 2.67
380 395 6.372659 CGGCAATTGTCCTATATTAGCATTCT 59.627 38.462 4.07 0.00 0.00 2.40
381 396 7.549134 CGGCAATTGTCCTATATTAGCATTCTA 59.451 37.037 4.07 0.00 0.00 2.10
382 397 9.231297 GGCAATTGTCCTATATTAGCATTCTAA 57.769 33.333 7.40 0.00 38.97 2.10
391 406 9.360093 CCTATATTAGCATTCTAAGTGTACTGC 57.640 37.037 0.00 0.00 38.11 4.40
392 407 7.875316 ATATTAGCATTCTAAGTGTACTGCG 57.125 36.000 0.00 0.00 38.11 5.18
393 408 3.868757 AGCATTCTAAGTGTACTGCGA 57.131 42.857 0.00 0.00 34.89 5.10
394 409 3.775202 AGCATTCTAAGTGTACTGCGAG 58.225 45.455 0.00 0.00 34.89 5.03
395 410 2.860735 GCATTCTAAGTGTACTGCGAGG 59.139 50.000 0.00 0.00 0.00 4.63
396 411 3.428999 GCATTCTAAGTGTACTGCGAGGA 60.429 47.826 0.00 0.00 0.00 3.71
397 412 4.737946 GCATTCTAAGTGTACTGCGAGGAT 60.738 45.833 0.00 0.00 0.00 3.24
398 413 5.352284 CATTCTAAGTGTACTGCGAGGATT 58.648 41.667 0.00 0.00 0.00 3.01
399 414 5.401531 TTCTAAGTGTACTGCGAGGATTT 57.598 39.130 0.00 0.00 0.00 2.17
400 415 5.401531 TCTAAGTGTACTGCGAGGATTTT 57.598 39.130 0.00 0.00 0.00 1.82
401 416 6.519679 TCTAAGTGTACTGCGAGGATTTTA 57.480 37.500 0.00 0.00 0.00 1.52
402 417 6.561614 TCTAAGTGTACTGCGAGGATTTTAG 58.438 40.000 0.00 0.00 0.00 1.85
403 418 5.401531 AAGTGTACTGCGAGGATTTTAGA 57.598 39.130 0.00 0.00 0.00 2.10
404 419 5.401531 AGTGTACTGCGAGGATTTTAGAA 57.598 39.130 0.00 0.00 0.00 2.10
405 420 5.790593 AGTGTACTGCGAGGATTTTAGAAA 58.209 37.500 0.00 0.00 0.00 2.52
406 421 5.638234 AGTGTACTGCGAGGATTTTAGAAAC 59.362 40.000 0.00 0.00 0.00 2.78
407 422 4.933400 TGTACTGCGAGGATTTTAGAAACC 59.067 41.667 0.00 0.00 0.00 3.27
408 423 4.287766 ACTGCGAGGATTTTAGAAACCT 57.712 40.909 0.00 0.00 40.41 3.50
409 424 4.003648 ACTGCGAGGATTTTAGAAACCTG 58.996 43.478 0.00 0.00 38.09 4.00
410 425 4.253685 CTGCGAGGATTTTAGAAACCTGA 58.746 43.478 0.00 0.00 38.09 3.86
411 426 4.647611 TGCGAGGATTTTAGAAACCTGAA 58.352 39.130 0.00 0.00 38.09 3.02
412 427 5.253330 TGCGAGGATTTTAGAAACCTGAAT 58.747 37.500 0.00 0.00 38.09 2.57
413 428 5.710099 TGCGAGGATTTTAGAAACCTGAATT 59.290 36.000 0.00 0.00 38.09 2.17
414 429 6.208599 TGCGAGGATTTTAGAAACCTGAATTT 59.791 34.615 0.00 0.00 38.09 1.82
415 430 7.392113 TGCGAGGATTTTAGAAACCTGAATTTA 59.608 33.333 0.00 0.00 38.09 1.40
416 431 7.696872 GCGAGGATTTTAGAAACCTGAATTTAC 59.303 37.037 0.00 0.00 38.09 2.01
417 432 8.182227 CGAGGATTTTAGAAACCTGAATTTACC 58.818 37.037 0.00 0.00 38.09 2.85
418 433 8.950007 AGGATTTTAGAAACCTGAATTTACCA 57.050 30.769 0.00 0.00 36.75 3.25
419 434 9.547279 AGGATTTTAGAAACCTGAATTTACCAT 57.453 29.630 0.00 0.00 36.75 3.55
457 472 7.812690 ATCTTCATATAGCTTGCATTGTTCA 57.187 32.000 0.00 0.00 0.00 3.18
458 473 7.628769 TCTTCATATAGCTTGCATTGTTCAA 57.371 32.000 0.00 0.00 0.00 2.69
459 474 7.700505 TCTTCATATAGCTTGCATTGTTCAAG 58.299 34.615 0.00 0.00 42.72 3.02
470 485 8.692110 CTTGCATTGTTCAAGCTTTAATATGA 57.308 30.769 16.42 1.99 35.15 2.15
471 486 9.142515 CTTGCATTGTTCAAGCTTTAATATGAA 57.857 29.630 16.42 7.21 35.15 2.57
472 487 9.486497 TTGCATTGTTCAAGCTTTAATATGAAA 57.514 25.926 16.42 11.97 33.93 2.69
473 488 9.486497 TGCATTGTTCAAGCTTTAATATGAAAA 57.514 25.926 16.42 3.40 33.93 2.29
474 489 9.962759 GCATTGTTCAAGCTTTAATATGAAAAG 57.037 29.630 16.42 6.49 37.08 2.27
481 496 9.959721 TCAAGCTTTAATATGAAAAGTACTCCT 57.040 29.630 0.00 0.00 36.52 3.69
493 508 7.782049 TGAAAAGTACTCCTATATGTGTCTGG 58.218 38.462 0.00 0.00 0.00 3.86
494 509 7.399191 TGAAAAGTACTCCTATATGTGTCTGGT 59.601 37.037 0.00 0.00 0.00 4.00
495 510 8.834004 AAAAGTACTCCTATATGTGTCTGGTA 57.166 34.615 0.00 0.00 0.00 3.25
496 511 8.466617 AAAGTACTCCTATATGTGTCTGGTAG 57.533 38.462 0.00 0.00 0.00 3.18
497 512 7.151694 AGTACTCCTATATGTGTCTGGTAGT 57.848 40.000 0.00 0.00 0.00 2.73
498 513 6.999272 AGTACTCCTATATGTGTCTGGTAGTG 59.001 42.308 0.00 0.00 0.00 2.74
499 514 6.014771 ACTCCTATATGTGTCTGGTAGTGA 57.985 41.667 0.00 0.00 0.00 3.41
500 515 6.432581 ACTCCTATATGTGTCTGGTAGTGAA 58.567 40.000 0.00 0.00 0.00 3.18
501 516 6.895756 ACTCCTATATGTGTCTGGTAGTGAAA 59.104 38.462 0.00 0.00 0.00 2.69
502 517 7.399191 ACTCCTATATGTGTCTGGTAGTGAAAA 59.601 37.037 0.00 0.00 0.00 2.29
503 518 8.141298 TCCTATATGTGTCTGGTAGTGAAAAA 57.859 34.615 0.00 0.00 0.00 1.94
566 581 9.860650 AGATGCATGTATAGGTTTATTGGTAAA 57.139 29.630 2.46 0.00 0.00 2.01
575 590 8.920509 ATAGGTTTATTGGTAAAATTTCACGC 57.079 30.769 0.00 0.00 31.94 5.34
576 591 5.859648 AGGTTTATTGGTAAAATTTCACGCG 59.140 36.000 3.53 3.53 31.94 6.01
577 592 5.630264 GGTTTATTGGTAAAATTTCACGCGT 59.370 36.000 5.58 5.58 31.94 6.01
578 593 6.800892 GGTTTATTGGTAAAATTTCACGCGTA 59.199 34.615 13.44 0.00 31.94 4.42
579 594 7.485595 GGTTTATTGGTAAAATTTCACGCGTAT 59.514 33.333 13.44 0.00 31.94 3.06
580 595 9.488124 GTTTATTGGTAAAATTTCACGCGTATA 57.512 29.630 13.44 0.00 31.94 1.47
582 597 9.866936 TTATTGGTAAAATTTCACGCGTATATC 57.133 29.630 13.44 0.00 0.00 1.63
583 598 6.905544 TGGTAAAATTTCACGCGTATATCA 57.094 33.333 13.44 0.53 0.00 2.15
584 599 7.304919 TGGTAAAATTTCACGCGTATATCAA 57.695 32.000 13.44 0.31 0.00 2.57
585 600 7.921787 TGGTAAAATTTCACGCGTATATCAAT 58.078 30.769 13.44 2.99 0.00 2.57
586 601 8.399425 TGGTAAAATTTCACGCGTATATCAATT 58.601 29.630 13.44 9.25 0.00 2.32
587 602 9.866936 GGTAAAATTTCACGCGTATATCAATTA 57.133 29.630 13.44 3.92 0.00 1.40
620 635 9.675464 TTATACTATTTTATATGAAAGGCCCCG 57.325 33.333 0.00 0.00 0.00 5.73
621 636 6.195600 ACTATTTTATATGAAAGGCCCCGA 57.804 37.500 0.00 0.00 0.00 5.14
622 637 6.238648 ACTATTTTATATGAAAGGCCCCGAG 58.761 40.000 0.00 0.00 0.00 4.63
623 638 4.513406 TTTTATATGAAAGGCCCCGAGT 57.487 40.909 0.00 0.00 0.00 4.18
624 639 4.513406 TTTATATGAAAGGCCCCGAGTT 57.487 40.909 0.00 0.00 0.00 3.01
625 640 4.513406 TTATATGAAAGGCCCCGAGTTT 57.487 40.909 0.00 0.00 0.00 2.66
626 641 2.891191 TATGAAAGGCCCCGAGTTTT 57.109 45.000 0.00 0.00 0.00 2.43
627 642 2.891191 ATGAAAGGCCCCGAGTTTTA 57.109 45.000 0.00 0.00 0.00 1.52
628 643 2.891191 TGAAAGGCCCCGAGTTTTAT 57.109 45.000 0.00 0.00 0.00 1.40
629 644 2.442413 TGAAAGGCCCCGAGTTTTATG 58.558 47.619 0.00 0.00 0.00 1.90
630 645 2.224917 TGAAAGGCCCCGAGTTTTATGT 60.225 45.455 0.00 0.00 0.00 2.29
631 646 2.597578 AAGGCCCCGAGTTTTATGTT 57.402 45.000 0.00 0.00 0.00 2.71
632 647 2.124277 AGGCCCCGAGTTTTATGTTC 57.876 50.000 0.00 0.00 0.00 3.18
633 648 0.730840 GGCCCCGAGTTTTATGTTCG 59.269 55.000 0.00 0.00 0.00 3.95
634 649 0.098200 GCCCCGAGTTTTATGTTCGC 59.902 55.000 0.00 0.00 33.25 4.70
635 650 0.730840 CCCCGAGTTTTATGTTCGCC 59.269 55.000 0.00 0.00 33.25 5.54
636 651 0.730840 CCCGAGTTTTATGTTCGCCC 59.269 55.000 0.00 0.00 33.25 6.13
637 652 0.730840 CCGAGTTTTATGTTCGCCCC 59.269 55.000 0.00 0.00 33.25 5.80
638 653 1.677820 CCGAGTTTTATGTTCGCCCCT 60.678 52.381 0.00 0.00 33.25 4.79
639 654 1.396996 CGAGTTTTATGTTCGCCCCTG 59.603 52.381 0.00 0.00 0.00 4.45
661 676 4.124351 TGATCCACGCGGACGGAC 62.124 66.667 12.47 8.73 46.79 4.79
697 712 3.119919 GGTTGACGTAGAGAGGTACAGTG 60.120 52.174 0.00 0.00 0.00 3.66
710 726 0.321387 TACAGTGGACTCTCGCTCGT 60.321 55.000 0.00 0.00 0.00 4.18
802 818 8.073355 AGTTATTTATAAGCACGACTACATGC 57.927 34.615 0.00 0.00 42.39 4.06
803 819 7.709182 AGTTATTTATAAGCACGACTACATGCA 59.291 33.333 0.00 0.00 44.59 3.96
808 824 1.416049 CACGACTACATGCACGCAC 59.584 57.895 0.00 0.00 0.00 5.34
872 888 3.701241 CGAGGATCTTTCTTTCTCTCGG 58.299 50.000 0.00 0.00 38.93 4.63
880 896 1.299468 CTTTCTCTCGGCGGGATCG 60.299 63.158 11.19 0.00 39.81 3.69
885 901 1.721664 CTCTCGGCGGGATCGTTACA 61.722 60.000 11.19 0.00 38.89 2.41
966 982 2.189594 TGTTCCTCGAAGACTCCGTA 57.810 50.000 0.00 0.00 0.00 4.02
967 983 2.507484 TGTTCCTCGAAGACTCCGTAA 58.493 47.619 0.00 0.00 0.00 3.18
995 1011 2.890311 CTCGAACAGATCTGCCTCCTAT 59.110 50.000 22.83 0.00 0.00 2.57
1009 1025 0.931468 TCCTATCCCGTCTTCTCCCA 59.069 55.000 0.00 0.00 0.00 4.37
1412 1429 4.020751 TCTGAATGCAAGAAGCTCTACTGT 60.021 41.667 0.00 0.00 45.94 3.55
1429 1446 2.224305 ACTGTGAGTGCTTCAAGGTACC 60.224 50.000 2.73 2.73 37.61 3.34
1441 1458 5.105473 GCTTCAAGGTACCTACATACTCACA 60.105 44.000 16.67 0.00 0.00 3.58
1467 4105 4.981674 TCCTCTGCTTTTATTTGTTTTGCG 59.018 37.500 0.00 0.00 0.00 4.85
1681 4322 5.070047 GGGAGAAGTATATTTTCCGTCCTCA 59.930 44.000 0.00 0.00 0.00 3.86
1802 7043 2.664398 GCGGTTTTAGTCCGGGGA 59.336 61.111 0.00 0.00 46.90 4.81
1888 7155 0.748005 ACTTTGGTGCGCAAGACACT 60.748 50.000 14.00 0.00 41.79 3.55
1896 7163 0.848305 GCGCAAGACACTTGCAAAAG 59.152 50.000 27.63 16.58 45.14 2.27
1915 7182 7.981789 TGCAAAAGTTTGTGGTGTTTTGATATA 59.018 29.630 9.89 0.00 40.70 0.86
2033 7304 8.722480 AATTATTTTGGCATAAAAGAGGCTTC 57.278 30.769 0.00 0.00 34.44 3.86
2174 12598 4.614993 GCTAGAGCTCCTCGTATGTCATTC 60.615 50.000 10.93 0.00 38.21 2.67
2326 20513 1.606668 TGCTTGAATGTCGAAACACCC 59.393 47.619 0.00 0.00 38.48 4.61
2355 20543 4.555709 ACGGGTCTTGCGCACCAA 62.556 61.111 11.12 0.00 35.35 3.67
2500 23241 6.092533 GGACGAAAACTATCCGGTTTTGATAA 59.907 38.462 0.00 0.00 45.62 1.75
2501 23242 6.834876 ACGAAAACTATCCGGTTTTGATAAC 58.165 36.000 0.00 0.00 45.62 1.89
2537 23278 2.500098 TCTCCGGTTTAGAGTTGATGGG 59.500 50.000 0.00 0.00 32.93 4.00
2554 23295 3.973206 TGGGCGATTTCTAAACTCTCA 57.027 42.857 0.00 0.00 0.00 3.27
2556 23297 3.260884 TGGGCGATTTCTAAACTCTCAGT 59.739 43.478 0.00 0.00 0.00 3.41
2745 23487 1.359848 GTCCGCAATCATCAACGACT 58.640 50.000 0.00 0.00 0.00 4.18
2770 23512 4.090761 TGGCTTCTCAGTTGACAGAAAT 57.909 40.909 0.00 0.00 0.00 2.17
2774 23519 5.934625 GGCTTCTCAGTTGACAGAAATAAGA 59.065 40.000 0.00 0.00 0.00 2.10
2802 23548 0.766288 TGATATCCACATCCCCGGCA 60.766 55.000 0.00 0.00 0.00 5.69
2894 23640 4.019411 TCCTTGTCAAATGCCATCTACTCA 60.019 41.667 0.00 0.00 0.00 3.41
2982 23733 6.432162 TGGCAATAATATGAAGAGGAGCAATC 59.568 38.462 0.00 0.00 0.00 2.67
3053 23804 3.857157 TCCAGTTTACCAGACTTTGCT 57.143 42.857 0.00 0.00 0.00 3.91
3123 23878 6.034044 GTCGTGATAGTCTTCTTTGTGATGTC 59.966 42.308 0.00 0.00 0.00 3.06
3184 23949 6.651643 TGCAAGTGACAGTTTACGGTAAATAT 59.348 34.615 15.70 6.13 0.00 1.28
3195 23960 9.880157 AGTTTACGGTAAATATGATGTGTTAGT 57.120 29.630 15.70 0.00 0.00 2.24
3268 24036 7.040494 TCATCTTCTATTCAGACTTTCAGCAG 58.960 38.462 0.00 0.00 0.00 4.24
3270 24038 7.180322 TCTTCTATTCAGACTTTCAGCAGAT 57.820 36.000 0.00 0.00 0.00 2.90
3332 24100 0.674269 TGCATCGCTGAGCAATGACA 60.674 50.000 9.96 4.05 37.90 3.58
3492 24260 8.370182 TGAGTATTGTGATGCTGATACATACAT 58.630 33.333 0.00 0.00 0.00 2.29
3657 24426 3.678289 TCTCTGGTGTGTTTGATGATGG 58.322 45.455 0.00 0.00 0.00 3.51
4180 28738 3.023591 GAAAAGCCCGAGTTCCGCG 62.024 63.158 0.00 0.00 36.84 6.46
4269 28827 9.588096 AGAAGGAAATGAACCATTTTTAGTAGT 57.412 29.630 6.40 0.00 43.05 2.73
4272 28830 9.802039 AGGAAATGAACCATTTTTAGTAGTACA 57.198 29.630 2.52 0.00 43.05 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 36 2.300956 TGAAGACCAGAGAGCTGAGT 57.699 50.000 0.00 0.00 45.17 3.41
126 128 2.504920 ATCGGTCAGATCTCGGCAA 58.495 52.632 0.00 0.00 33.45 4.52
127 129 4.259952 ATCGGTCAGATCTCGGCA 57.740 55.556 0.00 0.00 33.45 5.69
264 271 9.297586 GTTTGTGAATCTTACGAGATGTATGTA 57.702 33.333 0.00 0.00 41.78 2.29
265 272 7.817478 TGTTTGTGAATCTTACGAGATGTATGT 59.183 33.333 0.00 0.00 41.78 2.29
266 273 8.185003 TGTTTGTGAATCTTACGAGATGTATG 57.815 34.615 0.00 0.00 41.78 2.39
332 347 1.527034 CTACATGCATGAATCGGGGG 58.473 55.000 32.75 3.35 0.00 5.40
333 348 0.877071 GCTACATGCATGAATCGGGG 59.123 55.000 32.75 13.84 42.31 5.73
334 349 0.514255 CGCTACATGCATGAATCGGG 59.486 55.000 32.75 19.15 43.06 5.14
335 350 0.110509 GCGCTACATGCATGAATCGG 60.111 55.000 32.75 17.15 43.06 4.18
336 351 0.110509 GGCGCTACATGCATGAATCG 60.111 55.000 32.75 27.26 43.06 3.34
337 352 0.110509 CGGCGCTACATGCATGAATC 60.111 55.000 32.75 17.84 43.06 2.52
338 353 1.509644 CCGGCGCTACATGCATGAAT 61.510 55.000 32.75 14.25 43.06 2.57
339 354 2.179547 CCGGCGCTACATGCATGAA 61.180 57.895 32.75 0.00 43.06 2.57
340 355 2.588596 CCGGCGCTACATGCATGA 60.589 61.111 32.75 15.12 43.06 3.07
341 356 4.318021 GCCGGCGCTACATGCATG 62.318 66.667 25.09 25.09 43.06 4.06
342 357 4.854924 TGCCGGCGCTACATGCAT 62.855 61.111 23.90 0.00 43.06 3.96
344 359 3.124798 AATTGCCGGCGCTACATGC 62.125 57.895 23.90 3.71 35.36 4.06
345 360 1.298563 CAATTGCCGGCGCTACATG 60.299 57.895 23.90 10.86 35.36 3.21
346 361 1.714899 GACAATTGCCGGCGCTACAT 61.715 55.000 23.90 5.12 35.36 2.29
347 362 2.359354 ACAATTGCCGGCGCTACA 60.359 55.556 23.90 0.00 35.36 2.74
348 363 2.403586 GACAATTGCCGGCGCTAC 59.596 61.111 23.90 7.18 35.36 3.58
349 364 1.962321 TAGGACAATTGCCGGCGCTA 61.962 55.000 23.90 10.35 35.36 4.26
350 365 2.608970 ATAGGACAATTGCCGGCGCT 62.609 55.000 23.90 8.60 35.36 5.92
351 366 0.882927 TATAGGACAATTGCCGGCGC 60.883 55.000 23.90 0.00 0.00 6.53
352 367 1.808411 ATATAGGACAATTGCCGGCG 58.192 50.000 23.90 10.06 0.00 6.46
353 368 3.127030 GCTAATATAGGACAATTGCCGGC 59.873 47.826 22.73 22.73 0.00 6.13
354 369 4.323417 TGCTAATATAGGACAATTGCCGG 58.677 43.478 5.05 0.00 0.00 6.13
355 370 6.372659 AGAATGCTAATATAGGACAATTGCCG 59.627 38.462 5.05 0.00 0.00 5.69
356 371 7.693969 AGAATGCTAATATAGGACAATTGCC 57.306 36.000 5.05 8.05 0.00 4.52
365 380 9.360093 GCAGTACACTTAGAATGCTAATATAGG 57.640 37.037 0.00 0.00 36.10 2.57
366 381 9.066939 CGCAGTACACTTAGAATGCTAATATAG 57.933 37.037 0.00 0.00 36.10 1.31
367 382 8.789762 TCGCAGTACACTTAGAATGCTAATATA 58.210 33.333 0.00 0.00 36.10 0.86
368 383 7.658261 TCGCAGTACACTTAGAATGCTAATAT 58.342 34.615 0.00 0.00 36.10 1.28
369 384 7.034685 TCGCAGTACACTTAGAATGCTAATA 57.965 36.000 0.00 0.00 36.10 0.98
370 385 5.902681 TCGCAGTACACTTAGAATGCTAAT 58.097 37.500 0.00 0.00 36.10 1.73
371 386 5.319140 TCGCAGTACACTTAGAATGCTAA 57.681 39.130 0.00 0.00 35.40 3.09
372 387 4.202020 CCTCGCAGTACACTTAGAATGCTA 60.202 45.833 0.00 0.00 0.00 3.49
373 388 3.429547 CCTCGCAGTACACTTAGAATGCT 60.430 47.826 0.00 0.00 0.00 3.79
374 389 2.860735 CCTCGCAGTACACTTAGAATGC 59.139 50.000 0.00 0.00 0.00 3.56
375 390 4.371855 TCCTCGCAGTACACTTAGAATG 57.628 45.455 0.00 0.00 0.00 2.67
376 391 5.599999 AATCCTCGCAGTACACTTAGAAT 57.400 39.130 0.00 0.00 0.00 2.40
377 392 5.401531 AAATCCTCGCAGTACACTTAGAA 57.598 39.130 0.00 0.00 0.00 2.10
378 393 5.401531 AAAATCCTCGCAGTACACTTAGA 57.598 39.130 0.00 0.00 0.00 2.10
379 394 6.561614 TCTAAAATCCTCGCAGTACACTTAG 58.438 40.000 0.00 0.00 0.00 2.18
380 395 6.519679 TCTAAAATCCTCGCAGTACACTTA 57.480 37.500 0.00 0.00 0.00 2.24
381 396 5.401531 TCTAAAATCCTCGCAGTACACTT 57.598 39.130 0.00 0.00 0.00 3.16
382 397 5.401531 TTCTAAAATCCTCGCAGTACACT 57.598 39.130 0.00 0.00 0.00 3.55
383 398 5.163884 GGTTTCTAAAATCCTCGCAGTACAC 60.164 44.000 0.00 0.00 0.00 2.90
384 399 4.933400 GGTTTCTAAAATCCTCGCAGTACA 59.067 41.667 0.00 0.00 0.00 2.90
385 400 5.063564 CAGGTTTCTAAAATCCTCGCAGTAC 59.936 44.000 0.00 0.00 33.16 2.73
386 401 5.046878 TCAGGTTTCTAAAATCCTCGCAGTA 60.047 40.000 0.00 0.00 33.16 2.74
387 402 4.003648 CAGGTTTCTAAAATCCTCGCAGT 58.996 43.478 0.00 0.00 33.16 4.40
388 403 4.253685 TCAGGTTTCTAAAATCCTCGCAG 58.746 43.478 0.00 0.00 33.16 5.18
389 404 4.280436 TCAGGTTTCTAAAATCCTCGCA 57.720 40.909 0.00 0.00 33.16 5.10
390 405 5.819825 ATTCAGGTTTCTAAAATCCTCGC 57.180 39.130 0.00 0.00 33.16 5.03
391 406 8.182227 GGTAAATTCAGGTTTCTAAAATCCTCG 58.818 37.037 0.00 0.00 33.16 4.63
392 407 9.020731 TGGTAAATTCAGGTTTCTAAAATCCTC 57.979 33.333 0.00 0.00 33.16 3.71
393 408 8.950007 TGGTAAATTCAGGTTTCTAAAATCCT 57.050 30.769 0.00 0.00 35.37 3.24
431 446 9.341078 TGAACAATGCAAGCTATATGAAGATAA 57.659 29.630 0.00 0.00 0.00 1.75
432 447 8.907222 TGAACAATGCAAGCTATATGAAGATA 57.093 30.769 0.00 0.00 0.00 1.98
433 448 7.812690 TGAACAATGCAAGCTATATGAAGAT 57.187 32.000 0.00 0.00 0.00 2.40
434 449 7.628769 TTGAACAATGCAAGCTATATGAAGA 57.371 32.000 0.00 0.00 0.00 2.87
435 450 7.909777 CTTGAACAATGCAAGCTATATGAAG 57.090 36.000 0.00 0.00 36.66 3.02
445 460 8.692110 TCATATTAAAGCTTGAACAATGCAAG 57.308 30.769 12.89 0.00 44.22 4.01
446 461 9.486497 TTTCATATTAAAGCTTGAACAATGCAA 57.514 25.926 12.89 8.09 0.00 4.08
447 462 9.486497 TTTTCATATTAAAGCTTGAACAATGCA 57.514 25.926 12.89 0.00 0.00 3.96
448 463 9.962759 CTTTTCATATTAAAGCTTGAACAATGC 57.037 29.630 12.89 0.00 0.00 3.56
455 470 9.959721 AGGAGTACTTTTCATATTAAAGCTTGA 57.040 29.630 0.00 0.00 36.33 3.02
467 482 8.424918 CCAGACACATATAGGAGTACTTTTCAT 58.575 37.037 0.00 0.00 0.00 2.57
468 483 7.399191 ACCAGACACATATAGGAGTACTTTTCA 59.601 37.037 0.00 0.00 0.00 2.69
469 484 7.783042 ACCAGACACATATAGGAGTACTTTTC 58.217 38.462 0.00 0.00 0.00 2.29
470 485 7.735326 ACCAGACACATATAGGAGTACTTTT 57.265 36.000 0.00 0.00 0.00 2.27
471 486 8.060075 ACTACCAGACACATATAGGAGTACTTT 58.940 37.037 0.00 0.00 0.00 2.66
472 487 7.502895 CACTACCAGACACATATAGGAGTACTT 59.497 40.741 0.00 0.00 0.00 2.24
473 488 6.999272 CACTACCAGACACATATAGGAGTACT 59.001 42.308 0.00 0.00 0.00 2.73
474 489 6.996879 TCACTACCAGACACATATAGGAGTAC 59.003 42.308 0.00 0.00 0.00 2.73
475 490 7.145474 TCACTACCAGACACATATAGGAGTA 57.855 40.000 0.00 0.00 0.00 2.59
476 491 6.014771 TCACTACCAGACACATATAGGAGT 57.985 41.667 0.00 0.00 0.00 3.85
477 492 6.961360 TTCACTACCAGACACATATAGGAG 57.039 41.667 0.00 0.00 0.00 3.69
478 493 7.727578 TTTTCACTACCAGACACATATAGGA 57.272 36.000 0.00 0.00 0.00 2.94
540 555 9.860650 TTTACCAATAAACCTATACATGCATCT 57.139 29.630 0.00 0.00 0.00 2.90
550 565 7.698970 CGCGTGAAATTTTACCAATAAACCTAT 59.301 33.333 7.45 0.00 29.77 2.57
551 566 7.022384 CGCGTGAAATTTTACCAATAAACCTA 58.978 34.615 7.45 0.00 29.77 3.08
552 567 5.859648 CGCGTGAAATTTTACCAATAAACCT 59.140 36.000 7.45 0.00 29.77 3.50
553 568 5.630264 ACGCGTGAAATTTTACCAATAAACC 59.370 36.000 12.93 0.00 29.77 3.27
554 569 6.678540 ACGCGTGAAATTTTACCAATAAAC 57.321 33.333 12.93 0.00 29.77 2.01
556 571 9.866936 GATATACGCGTGAAATTTTACCAATAA 57.133 29.630 24.59 0.00 0.00 1.40
557 572 9.043079 TGATATACGCGTGAAATTTTACCAATA 57.957 29.630 24.59 7.00 0.00 1.90
558 573 7.921787 TGATATACGCGTGAAATTTTACCAAT 58.078 30.769 24.59 4.65 0.00 3.16
559 574 7.304919 TGATATACGCGTGAAATTTTACCAA 57.695 32.000 24.59 0.00 0.00 3.67
560 575 6.905544 TGATATACGCGTGAAATTTTACCA 57.094 33.333 24.59 0.00 0.00 3.25
561 576 8.776680 AATTGATATACGCGTGAAATTTTACC 57.223 30.769 24.59 0.98 0.00 2.85
594 609 9.675464 CGGGGCCTTTCATATAAAATAGTATAA 57.325 33.333 0.84 0.00 0.00 0.98
595 610 9.049050 TCGGGGCCTTTCATATAAAATAGTATA 57.951 33.333 0.84 0.00 0.00 1.47
596 611 7.924541 TCGGGGCCTTTCATATAAAATAGTAT 58.075 34.615 0.84 0.00 0.00 2.12
597 612 7.016858 ACTCGGGGCCTTTCATATAAAATAGTA 59.983 37.037 0.84 0.00 0.00 1.82
598 613 6.183361 ACTCGGGGCCTTTCATATAAAATAGT 60.183 38.462 0.84 0.00 0.00 2.12
599 614 6.238648 ACTCGGGGCCTTTCATATAAAATAG 58.761 40.000 0.84 0.00 0.00 1.73
600 615 6.195600 ACTCGGGGCCTTTCATATAAAATA 57.804 37.500 0.84 0.00 0.00 1.40
601 616 5.061721 ACTCGGGGCCTTTCATATAAAAT 57.938 39.130 0.84 0.00 0.00 1.82
602 617 4.513406 ACTCGGGGCCTTTCATATAAAA 57.487 40.909 0.84 0.00 0.00 1.52
603 618 4.513406 AACTCGGGGCCTTTCATATAAA 57.487 40.909 0.84 0.00 0.00 1.40
604 619 4.513406 AAACTCGGGGCCTTTCATATAA 57.487 40.909 0.84 0.00 0.00 0.98
605 620 4.513406 AAAACTCGGGGCCTTTCATATA 57.487 40.909 0.84 0.00 0.00 0.86
606 621 3.382083 AAAACTCGGGGCCTTTCATAT 57.618 42.857 0.84 0.00 0.00 1.78
607 622 2.891191 AAAACTCGGGGCCTTTCATA 57.109 45.000 0.84 0.00 0.00 2.15
608 623 2.891191 TAAAACTCGGGGCCTTTCAT 57.109 45.000 0.84 0.00 0.00 2.57
609 624 2.224917 ACATAAAACTCGGGGCCTTTCA 60.225 45.455 0.84 0.00 0.00 2.69
610 625 2.443416 ACATAAAACTCGGGGCCTTTC 58.557 47.619 0.84 0.00 0.00 2.62
611 626 2.597578 ACATAAAACTCGGGGCCTTT 57.402 45.000 0.84 0.00 0.00 3.11
612 627 2.443416 GAACATAAAACTCGGGGCCTT 58.557 47.619 0.84 0.00 0.00 4.35
613 628 1.677820 CGAACATAAAACTCGGGGCCT 60.678 52.381 0.84 0.00 0.00 5.19
614 629 0.730840 CGAACATAAAACTCGGGGCC 59.269 55.000 0.00 0.00 0.00 5.80
615 630 0.098200 GCGAACATAAAACTCGGGGC 59.902 55.000 0.00 0.00 33.23 5.80
616 631 0.730840 GGCGAACATAAAACTCGGGG 59.269 55.000 0.00 0.00 33.23 5.73
617 632 0.730840 GGGCGAACATAAAACTCGGG 59.269 55.000 0.00 0.00 33.23 5.14
618 633 0.730840 GGGGCGAACATAAAACTCGG 59.269 55.000 0.00 0.00 33.23 4.63
619 634 1.396996 CAGGGGCGAACATAAAACTCG 59.603 52.381 0.00 0.00 35.70 4.18
620 635 1.743394 CCAGGGGCGAACATAAAACTC 59.257 52.381 0.00 0.00 0.00 3.01
621 636 1.353022 TCCAGGGGCGAACATAAAACT 59.647 47.619 0.00 0.00 0.00 2.66
622 637 1.828979 TCCAGGGGCGAACATAAAAC 58.171 50.000 0.00 0.00 0.00 2.43
623 638 2.241176 AGATCCAGGGGCGAACATAAAA 59.759 45.455 0.00 0.00 0.00 1.52
624 639 1.843851 AGATCCAGGGGCGAACATAAA 59.156 47.619 0.00 0.00 0.00 1.40
625 640 1.140852 CAGATCCAGGGGCGAACATAA 59.859 52.381 0.00 0.00 0.00 1.90
626 641 0.758734 CAGATCCAGGGGCGAACATA 59.241 55.000 0.00 0.00 0.00 2.29
627 642 0.982852 TCAGATCCAGGGGCGAACAT 60.983 55.000 0.00 0.00 0.00 2.71
628 643 0.982852 ATCAGATCCAGGGGCGAACA 60.983 55.000 0.00 0.00 0.00 3.18
629 644 0.250081 GATCAGATCCAGGGGCGAAC 60.250 60.000 0.00 0.00 0.00 3.95
630 645 2.136791 GATCAGATCCAGGGGCGAA 58.863 57.895 0.00 0.00 0.00 4.70
631 646 3.876873 GATCAGATCCAGGGGCGA 58.123 61.111 0.00 0.00 0.00 5.54
661 676 2.508439 AACCGTAGATGCACGCCG 60.508 61.111 0.00 0.00 40.59 6.46
697 712 0.375803 GAGAGAACGAGCGAGAGTCC 59.624 60.000 0.00 0.00 0.00 3.85
731 747 3.315972 AAAAACAGTCGCGCGTTTT 57.684 42.105 30.98 24.18 44.90 2.43
872 888 1.326548 GTTGATGTGTAACGATCCCGC 59.673 52.381 0.00 0.00 42.39 6.13
880 896 7.746475 GCAATTCTAGTCAAGTTGATGTGTAAC 59.254 37.037 9.18 0.00 37.35 2.50
885 901 6.127814 CCATGCAATTCTAGTCAAGTTGATGT 60.128 38.462 9.18 2.44 0.00 3.06
966 982 4.180057 GCAGATCTGTTCGAGTCTGATTT 58.820 43.478 23.38 7.14 40.30 2.17
967 983 3.430098 GGCAGATCTGTTCGAGTCTGATT 60.430 47.826 23.38 4.54 40.30 2.57
995 1011 0.335019 TCAGATGGGAGAAGACGGGA 59.665 55.000 0.00 0.00 0.00 5.14
1009 1025 1.283321 GCCAAGGAAGAAGGGTCAGAT 59.717 52.381 0.00 0.00 0.00 2.90
1128 1144 1.644786 GAATGCGGTTTCGGTGAGGG 61.645 60.000 0.00 0.00 36.79 4.30
1217 1234 1.891919 GTCCTCTGTGTTGCGGCAA 60.892 57.895 12.11 12.11 0.00 4.52
1244 1261 4.819761 GCGCGCTCATCCACCTCA 62.820 66.667 26.67 0.00 0.00 3.86
1412 1429 3.236047 TGTAGGTACCTTGAAGCACTCA 58.764 45.455 22.11 0.00 0.00 3.41
1429 1446 4.826733 AGCAGAGGAGATGTGAGTATGTAG 59.173 45.833 0.00 0.00 0.00 2.74
1441 1458 6.870439 GCAAAACAAATAAAAGCAGAGGAGAT 59.130 34.615 0.00 0.00 0.00 2.75
1661 4300 7.764901 AGAGTTTGAGGACGGAAAATATACTTC 59.235 37.037 0.00 0.00 0.00 3.01
1888 7155 4.816385 TCAAAACACCACAAACTTTTGCAA 59.184 33.333 0.00 0.00 41.79 4.08
1896 7163 5.793457 GCTCGTATATCAAAACACCACAAAC 59.207 40.000 0.00 0.00 0.00 2.93
1993 7263 7.064016 GCCAAAATAATTCATACCGCTTTGAAA 59.936 33.333 0.00 0.00 35.63 2.69
2012 7283 4.381932 CCGAAGCCTCTTTTATGCCAAAAT 60.382 41.667 0.00 0.00 0.00 1.82
2174 12598 4.648917 TGCATGCAAAATTTTGTGATCG 57.351 36.364 27.13 14.94 40.24 3.69
2297 17941 0.035317 ACATTCAAGCAGCTCGTGGA 59.965 50.000 0.00 0.00 0.00 4.02
2326 20513 0.596082 AGACCCGTGCAAAATTTCGG 59.404 50.000 8.64 8.64 42.22 4.30
2422 23162 6.074302 CGGGATGAATAGTAAATCAGTGAACG 60.074 42.308 0.00 0.00 0.00 3.95
2500 23241 1.619332 GGAGAGTTTTCGTCCCTCAGT 59.381 52.381 0.00 0.00 0.00 3.41
2501 23242 1.402984 CGGAGAGTTTTCGTCCCTCAG 60.403 57.143 0.00 0.00 0.00 3.35
2537 23278 6.094061 ACTGTACTGAGAGTTTAGAAATCGC 58.906 40.000 6.77 0.00 0.00 4.58
2607 23349 5.063438 GCAAGAACACGACTGAGCATAAATA 59.937 40.000 0.00 0.00 0.00 1.40
2745 23487 3.578282 TCTGTCAACTGAGAAGCCATGTA 59.422 43.478 0.00 0.00 0.00 2.29
2802 23548 6.662234 AGATCAACATCCATGTGACTCAATTT 59.338 34.615 0.00 0.00 41.61 1.82
2845 23591 3.655777 TGAAAATAGAACTCACCCCAGGT 59.344 43.478 0.00 0.00 35.62 4.00
3053 23804 4.520078 GACGTTCATAAAAGTTTGTCGCA 58.480 39.130 0.00 0.00 0.00 5.10
3123 23878 0.034896 ACCGTGGAGCAGGTGTAAAG 59.965 55.000 0.00 0.00 39.66 1.85
3195 23960 8.862325 ACACAAAGGAACACATGATTAGAATA 57.138 30.769 0.00 0.00 0.00 1.75
3268 24036 4.828939 TGATGTGCTTGGGGATCAATAATC 59.171 41.667 0.00 0.00 34.45 1.75
3270 24038 4.209538 CTGATGTGCTTGGGGATCAATAA 58.790 43.478 0.00 0.00 34.45 1.40
3310 24078 0.661020 CATTGCTCAGCGATGCATCA 59.339 50.000 25.70 5.90 42.45 3.07
3332 24100 3.100671 CCTGCTCTAGTAGGGAGTTTGT 58.899 50.000 0.00 0.00 43.16 2.83
3492 24260 3.055819 AGCAAATCTCAAACTAGGCGAGA 60.056 43.478 0.28 9.59 39.95 4.04
3657 24426 3.181556 CGACTTTTCACGTCACGTCATAC 60.182 47.826 0.00 0.00 38.32 2.39
3679 24448 8.347035 GTTCTACTTCTATATCAGTCCAGTGTC 58.653 40.741 0.00 0.00 0.00 3.67
4180 28738 2.125633 GAGGTCGGCCGAGTTTCC 60.126 66.667 31.97 25.98 40.50 3.13
4268 28826 9.431887 TCTGAATTGTGGAATTTACTACTGTAC 57.568 33.333 0.00 0.00 31.58 2.90
4270 28828 8.918202 TTCTGAATTGTGGAATTTACTACTGT 57.082 30.769 0.00 0.00 31.58 3.55
4271 28829 9.219603 TCTTCTGAATTGTGGAATTTACTACTG 57.780 33.333 0.00 0.00 31.58 2.74
4272 28830 9.442047 CTCTTCTGAATTGTGGAATTTACTACT 57.558 33.333 0.00 0.00 31.58 2.57


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

AutoCloner maintained by Alex Coulton.