Multiple sequence alignment - TraesCS2D01G188400

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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 TraesCS2D01G188400 chr2D 100.000 4578 0 0 950 5527 131469439 131464862 0.000000e+00 8455.0
1 TraesCS2D01G188400 chr2D 100.000 730 0 0 1 730 131470388 131469659 0.000000e+00 1349.0
2 TraesCS2D01G188400 chr2D 85.961 463 45 5 5084 5527 534402686 534403147 1.390000e-130 477.0
3 TraesCS2D01G188400 chr2B 95.789 3325 107 18 1586 4894 185809008 185805701 0.000000e+00 5334.0
4 TraesCS2D01G188400 chr2B 98.174 493 6 2 981 1473 185809493 185809004 0.000000e+00 857.0
5 TraesCS2D01G188400 chr2B 94.194 155 4 4 552 704 185810147 185809996 1.200000e-56 231.0
6 TraesCS2D01G188400 chr2B 98.876 89 1 0 5000 5088 201234349 201234261 5.730000e-35 159.0
7 TraesCS2D01G188400 chr2A 96.573 2772 49 9 995 3755 138187146 138184410 0.000000e+00 4551.0
8 TraesCS2D01G188400 chr2A 96.070 1145 42 3 3754 4897 138184306 138183164 0.000000e+00 1862.0
9 TraesCS2D01G188400 chr2A 86.207 261 19 9 3 246 138188163 138187903 3.280000e-67 267.0
10 TraesCS2D01G188400 chr2A 93.750 144 5 4 556 698 138187628 138187488 4.340000e-51 213.0
11 TraesCS2D01G188400 chr2A 86.905 84 11 0 410 493 138187720 138187637 1.640000e-15 95.3
12 TraesCS2D01G188400 chr7D 93.612 454 19 5 5084 5527 141927213 141927666 0.000000e+00 669.0
13 TraesCS2D01G188400 chr7D 91.630 454 21 8 5084 5527 279748822 279748376 3.660000e-171 612.0
14 TraesCS2D01G188400 chr7D 98.198 111 2 0 4893 5003 279748930 279748820 1.570000e-45 195.0
15 TraesCS2D01G188400 chr7D 94.783 115 6 0 4889 5003 141927101 141927215 4.400000e-41 180.0
16 TraesCS2D01G188400 chr1D 91.921 458 23 8 5084 5527 486741203 486740746 3.630000e-176 628.0
17 TraesCS2D01G188400 chr1D 98.230 113 0 1 4893 5003 486741313 486741201 4.370000e-46 196.0
18 TraesCS2D01G188400 chr1D 100.000 87 0 0 5001 5087 485967767 485967853 1.590000e-35 161.0
19 TraesCS2D01G188400 chr7B 91.126 462 24 7 5083 5527 24411422 24410961 1.320000e-170 610.0
20 TraesCS2D01G188400 chr7B 96.396 111 4 0 4893 5003 24411529 24411419 3.400000e-42 183.0
21 TraesCS2D01G188400 chr3B 91.126 462 24 7 5083 5527 790995932 790996393 1.320000e-170 610.0
22 TraesCS2D01G188400 chr3B 94.737 114 6 0 4890 5003 790995822 790995935 1.580000e-40 178.0
23 TraesCS2D01G188400 chr3B 97.727 88 2 0 5001 5088 550785695 550785782 9.590000e-33 152.0
24 TraesCS2D01G188400 chr1A 90.889 461 25 7 5084 5527 522241445 522240985 2.200000e-168 603.0
25 TraesCS2D01G188400 chr1A 83.974 468 51 10 5083 5527 477981608 477982074 1.420000e-115 427.0
26 TraesCS2D01G188400 chr1A 95.495 111 5 0 4893 5003 522241553 522241443 1.580000e-40 178.0
27 TraesCS2D01G188400 chr1A 91.129 124 10 1 4880 5003 408484722 408484600 3.420000e-37 167.0
28 TraesCS2D01G188400 chr3D 89.648 454 29 8 5084 5527 38047778 38048223 3.740000e-156 562.0
29 TraesCS2D01G188400 chr3D 86.404 456 48 8 5084 5527 135725735 135725282 2.310000e-133 486.0
30 TraesCS2D01G188400 chr3D 99.099 111 1 0 4893 5003 38047670 38047780 3.380000e-47 200.0
31 TraesCS2D01G188400 chr3D 95.614 114 5 0 4890 5003 588020892 588021005 3.400000e-42 183.0
32 TraesCS2D01G188400 chr5D 96.809 94 3 0 4992 5085 15905595 15905688 2.060000e-34 158.0
33 TraesCS2D01G188400 chr5B 97.753 89 2 0 4999 5087 14288928 14289016 2.670000e-33 154.0
34 TraesCS2D01G188400 chr3A 94.949 99 3 2 5001 5097 443203672 443203574 2.670000e-33 154.0
35 TraesCS2D01G188400 chr7A 94.000 100 6 0 2615 2714 642744448 642744349 9.590000e-33 152.0
36 TraesCS2D01G188400 chr5A 91.150 113 9 1 4974 5086 688672104 688671993 9.590000e-33 152.0
37 TraesCS2D01G188400 chr4D 94.059 101 4 2 4991 5090 99160663 99160564 9.590000e-33 152.0
38 TraesCS2D01G188400 chr4A 92.381 105 6 1 4990 5094 112585033 112585135 1.240000e-31 148.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G188400 chr2D 131464862 131470388 5526 True 4902.000000 8455 100.000000 1 5527 2 chr2D.!!$R1 5526
1 TraesCS2D01G188400 chr2B 185805701 185810147 4446 True 2140.666667 5334 96.052333 552 4894 3 chr2B.!!$R2 4342
2 TraesCS2D01G188400 chr2A 138183164 138188163 4999 True 1397.660000 4551 91.901000 3 4897 5 chr2A.!!$R1 4894
3 TraesCS2D01G188400 chr7D 141927101 141927666 565 False 424.500000 669 94.197500 4889 5527 2 chr7D.!!$F1 638
4 TraesCS2D01G188400 chr7D 279748376 279748930 554 True 403.500000 612 94.914000 4893 5527 2 chr7D.!!$R1 634
5 TraesCS2D01G188400 chr1D 486740746 486741313 567 True 412.000000 628 95.075500 4893 5527 2 chr1D.!!$R1 634
6 TraesCS2D01G188400 chr7B 24410961 24411529 568 True 396.500000 610 93.761000 4893 5527 2 chr7B.!!$R1 634
7 TraesCS2D01G188400 chr3B 790995822 790996393 571 False 394.000000 610 92.931500 4890 5527 2 chr3B.!!$F2 637
8 TraesCS2D01G188400 chr1A 522240985 522241553 568 True 390.500000 603 93.192000 4893 5527 2 chr1A.!!$R2 634
9 TraesCS2D01G188400 chr3D 38047670 38048223 553 False 381.000000 562 94.373500 4893 5527 2 chr3D.!!$F2 634

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
273 290 0.109597 GAAATGCGAGCACCAAGTGG 60.110 55.000 0.0 0.0 42.17 4.00 F
597 671 0.600255 AGAAGGGCAGTGACGAAACG 60.600 55.000 0.0 0.0 0.00 3.60 F
648 723 0.608640 TCGGGGCTTCTCTTCTGTTC 59.391 55.000 0.0 0.0 0.00 3.18 F
1683 1993 0.694771 TGTGCTCAAGCCCATTCTCT 59.305 50.000 0.0 0.0 41.18 3.10 F
2630 2954 0.105964 CCCTGTTCACCGTTCAGTCA 59.894 55.000 0.0 0.0 0.00 3.41 F
3795 4225 1.135257 TGTGTTGCCCTTTGTGTTTCG 60.135 47.619 0.0 0.0 0.00 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1416 1717 3.011119 GTCGTAGAGAGGCAGAAAGAGA 58.989 50.000 0.00 0.00 36.95 3.10 R
2551 2875 2.857186 ATTCCAAACCAAACATGGCC 57.143 45.000 0.00 0.00 34.13 5.36 R
2615 2939 3.058914 CCTTCATTGACTGAACGGTGAAC 60.059 47.826 0.00 0.00 38.97 3.18 R
3251 3576 3.680458 TCGCAGTTATGTACGAATGCAAA 59.320 39.130 13.78 2.25 33.33 3.68 R
4146 4576 0.464452 ATACAGCAACTCCCTACGGC 59.536 55.000 0.00 0.00 0.00 5.68 R
5342 5785 1.043116 TGCCCCCTGTCTAGTCATCG 61.043 60.000 0.00 0.00 0.00 3.84 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
24 25 4.864806 TGAGCAATTTCGAGCTTACACTAG 59.135 41.667 0.00 0.00 42.04 2.57
46 51 2.261671 CTGCCGCGTAGGTGAACT 59.738 61.111 4.92 0.00 43.70 3.01
77 82 7.406104 AGGATGATAATCCCAGGCTTATAAAC 58.594 38.462 5.34 0.00 41.65 2.01
164 172 6.387041 TTGGGTCGTAGAATATACAGTGAG 57.613 41.667 0.00 0.00 39.69 3.51
168 176 5.008811 GGTCGTAGAATATACAGTGAGCACT 59.991 44.000 0.00 0.00 40.03 4.40
170 178 7.070798 GTCGTAGAATATACAGTGAGCACTAC 58.929 42.308 2.36 0.00 37.82 2.73
196 211 7.358830 GTGAGTACGTAGAGTTCACTTTTACT 58.641 38.462 16.22 1.14 36.21 2.24
235 252 8.445275 AACACAACGAGCATTATAAATATCCA 57.555 30.769 0.00 0.00 0.00 3.41
236 253 8.621532 ACACAACGAGCATTATAAATATCCAT 57.378 30.769 0.00 0.00 0.00 3.41
266 283 5.230726 CCATAGATTTTTGAAATGCGAGCAC 59.769 40.000 0.00 0.00 0.00 4.40
267 284 3.578688 AGATTTTTGAAATGCGAGCACC 58.421 40.909 0.00 0.00 0.00 5.01
268 285 2.879002 TTTTTGAAATGCGAGCACCA 57.121 40.000 0.00 0.00 0.00 4.17
269 286 2.879002 TTTTGAAATGCGAGCACCAA 57.121 40.000 0.00 2.83 0.00 3.67
270 287 2.420628 TTTGAAATGCGAGCACCAAG 57.579 45.000 0.00 0.00 0.00 3.61
271 288 1.317613 TTGAAATGCGAGCACCAAGT 58.682 45.000 0.00 0.00 0.00 3.16
272 289 0.592637 TGAAATGCGAGCACCAAGTG 59.407 50.000 0.00 0.00 36.51 3.16
273 290 0.109597 GAAATGCGAGCACCAAGTGG 60.110 55.000 0.00 0.00 42.17 4.00
316 334 6.939132 ATAATCCATCTGAACTCAAAGCAG 57.061 37.500 0.00 0.00 0.00 4.24
322 340 1.471684 CTGAACTCAAAGCAGGCCATC 59.528 52.381 5.01 0.00 0.00 3.51
332 350 1.353694 AGCAGGCCATCTCTGAAACTT 59.646 47.619 5.01 0.00 34.36 2.66
333 351 2.165998 GCAGGCCATCTCTGAAACTTT 58.834 47.619 5.01 0.00 34.36 2.66
334 352 2.094854 GCAGGCCATCTCTGAAACTTTG 60.095 50.000 5.01 0.00 34.36 2.77
337 355 5.188434 CAGGCCATCTCTGAAACTTTGATA 58.812 41.667 5.01 0.00 34.36 2.15
338 356 5.065731 CAGGCCATCTCTGAAACTTTGATAC 59.934 44.000 5.01 0.00 34.36 2.24
339 357 4.034510 GGCCATCTCTGAAACTTTGATACG 59.965 45.833 0.00 0.00 0.00 3.06
341 359 4.631377 CCATCTCTGAAACTTTGATACGCA 59.369 41.667 0.00 0.00 0.00 5.24
342 360 5.295292 CCATCTCTGAAACTTTGATACGCAT 59.705 40.000 0.00 0.00 0.00 4.73
343 361 6.479990 CCATCTCTGAAACTTTGATACGCATA 59.520 38.462 0.00 0.00 0.00 3.14
344 362 6.887376 TCTCTGAAACTTTGATACGCATAC 57.113 37.500 0.00 0.00 0.00 2.39
345 363 6.631016 TCTCTGAAACTTTGATACGCATACT 58.369 36.000 0.00 0.00 0.00 2.12
346 364 7.768240 TCTCTGAAACTTTGATACGCATACTA 58.232 34.615 0.00 0.00 0.00 1.82
348 366 7.544622 TCTGAAACTTTGATACGCATACTACT 58.455 34.615 0.00 0.00 0.00 2.57
349 367 8.033038 TCTGAAACTTTGATACGCATACTACTT 58.967 33.333 0.00 0.00 0.00 2.24
350 368 8.181487 TGAAACTTTGATACGCATACTACTTC 57.819 34.615 0.00 0.00 0.00 3.01
351 369 8.033038 TGAAACTTTGATACGCATACTACTTCT 58.967 33.333 0.00 0.00 0.00 2.85
352 370 7.757097 AACTTTGATACGCATACTACTTCTG 57.243 36.000 0.00 0.00 0.00 3.02
356 428 6.694877 TGATACGCATACTACTTCTGTTCT 57.305 37.500 0.00 0.00 0.00 3.01
365 437 8.596380 GCATACTACTTCTGTTCTGTATCAAAC 58.404 37.037 0.00 0.00 0.00 2.93
366 438 9.862371 CATACTACTTCTGTTCTGTATCAAACT 57.138 33.333 0.00 0.00 0.00 2.66
373 445 7.540474 TCTGTTCTGTATCAAACTTACTCCT 57.460 36.000 0.00 0.00 0.00 3.69
376 448 7.963532 TGTTCTGTATCAAACTTACTCCTTCT 58.036 34.615 0.00 0.00 0.00 2.85
384 456 4.559862 AACTTACTCCTTCTGTCCCATG 57.440 45.455 0.00 0.00 0.00 3.66
386 458 4.366267 ACTTACTCCTTCTGTCCCATGAT 58.634 43.478 0.00 0.00 0.00 2.45
387 459 4.163078 ACTTACTCCTTCTGTCCCATGATG 59.837 45.833 0.00 0.00 0.00 3.07
388 460 2.555664 ACTCCTTCTGTCCCATGATGT 58.444 47.619 0.00 0.00 0.00 3.06
389 461 3.724478 ACTCCTTCTGTCCCATGATGTA 58.276 45.455 0.00 0.00 0.00 2.29
391 463 4.163078 ACTCCTTCTGTCCCATGATGTAAG 59.837 45.833 0.00 0.00 0.00 2.34
392 464 4.361783 TCCTTCTGTCCCATGATGTAAGA 58.638 43.478 0.00 0.00 0.00 2.10
393 465 4.162320 TCCTTCTGTCCCATGATGTAAGAC 59.838 45.833 0.00 0.00 0.00 3.01
394 466 4.163078 CCTTCTGTCCCATGATGTAAGACT 59.837 45.833 0.00 0.00 0.00 3.24
396 468 5.762179 TCTGTCCCATGATGTAAGACTTT 57.238 39.130 0.00 0.00 0.00 2.66
397 469 6.126863 TCTGTCCCATGATGTAAGACTTTT 57.873 37.500 0.00 0.00 0.00 2.27
398 470 6.542821 TCTGTCCCATGATGTAAGACTTTTT 58.457 36.000 0.00 0.00 0.00 1.94
431 503 9.550406 CCAGTAGGTTACATAAATAATTTCCGA 57.450 33.333 0.00 0.00 0.00 4.55
438 510 8.617809 GTTACATAAATAATTTCCGAGGCTTCA 58.382 33.333 0.00 0.00 0.00 3.02
468 540 2.742053 ACAACTTCACGATTTCATCCCG 59.258 45.455 0.00 0.00 0.00 5.14
473 545 1.488812 TCACGATTTCATCCCGGGATT 59.511 47.619 34.13 19.73 30.06 3.01
476 548 2.436542 ACGATTTCATCCCGGGATTACA 59.563 45.455 34.13 19.73 31.62 2.41
483 555 1.946984 TCCCGGGATTACAAGTGTCT 58.053 50.000 22.63 0.00 0.00 3.41
493 565 4.873746 TTACAAGTGTCTCAGAAGGAGG 57.126 45.455 0.00 0.00 44.19 4.30
494 566 2.964209 ACAAGTGTCTCAGAAGGAGGA 58.036 47.619 0.00 0.00 44.19 3.71
495 567 2.630580 ACAAGTGTCTCAGAAGGAGGAC 59.369 50.000 0.00 0.00 44.19 3.85
496 568 2.896685 CAAGTGTCTCAGAAGGAGGACT 59.103 50.000 0.00 0.00 44.19 3.85
497 569 2.524306 AGTGTCTCAGAAGGAGGACTG 58.476 52.381 0.00 0.00 44.19 3.51
499 571 2.230266 GTGTCTCAGAAGGAGGACTGTC 59.770 54.545 0.00 0.00 44.19 3.51
500 572 2.158460 TGTCTCAGAAGGAGGACTGTCA 60.158 50.000 10.38 0.00 44.19 3.58
501 573 2.894126 GTCTCAGAAGGAGGACTGTCAA 59.106 50.000 10.38 0.00 44.19 3.18
502 574 3.513515 GTCTCAGAAGGAGGACTGTCAAT 59.486 47.826 10.38 0.00 44.19 2.57
503 575 3.513119 TCTCAGAAGGAGGACTGTCAATG 59.487 47.826 10.38 0.00 44.19 2.82
504 576 2.568956 TCAGAAGGAGGACTGTCAATGG 59.431 50.000 10.38 0.00 35.84 3.16
505 577 2.304180 CAGAAGGAGGACTGTCAATGGT 59.696 50.000 10.38 0.00 0.00 3.55
506 578 2.569404 AGAAGGAGGACTGTCAATGGTC 59.431 50.000 10.38 1.48 0.00 4.02
507 579 2.334006 AGGAGGACTGTCAATGGTCT 57.666 50.000 10.38 0.00 33.46 3.85
508 580 1.905215 AGGAGGACTGTCAATGGTCTG 59.095 52.381 10.38 0.00 33.46 3.51
509 581 1.065854 GGAGGACTGTCAATGGTCTGG 60.066 57.143 10.38 0.00 33.46 3.86
510 582 0.987294 AGGACTGTCAATGGTCTGGG 59.013 55.000 10.38 0.00 33.46 4.45
511 583 0.678048 GGACTGTCAATGGTCTGGGC 60.678 60.000 10.38 0.00 33.46 5.36
512 584 1.003355 ACTGTCAATGGTCTGGGCG 60.003 57.895 0.00 0.00 0.00 6.13
513 585 1.003355 CTGTCAATGGTCTGGGCGT 60.003 57.895 0.00 0.00 0.00 5.68
514 586 1.003839 TGTCAATGGTCTGGGCGTC 60.004 57.895 0.00 0.00 0.00 5.19
515 587 1.745489 GTCAATGGTCTGGGCGTCC 60.745 63.158 0.00 0.00 0.00 4.79
516 588 2.819595 CAATGGTCTGGGCGTCCG 60.820 66.667 0.00 0.00 35.24 4.79
517 589 4.096003 AATGGTCTGGGCGTCCGG 62.096 66.667 9.17 9.17 40.84 5.14
548 620 2.109425 GGCACCTTGGTAAGTGGTAG 57.891 55.000 0.00 0.00 32.13 3.18
549 621 1.350019 GGCACCTTGGTAAGTGGTAGT 59.650 52.381 0.00 0.00 32.13 2.73
550 622 2.568509 GGCACCTTGGTAAGTGGTAGTA 59.431 50.000 0.00 0.00 32.13 1.82
551 623 3.008266 GGCACCTTGGTAAGTGGTAGTAA 59.992 47.826 0.00 0.00 32.13 2.24
552 624 3.999001 GCACCTTGGTAAGTGGTAGTAAC 59.001 47.826 0.00 0.00 32.13 2.50
553 625 4.240096 CACCTTGGTAAGTGGTAGTAACG 58.760 47.826 0.00 0.00 32.13 3.18
554 626 4.022068 CACCTTGGTAAGTGGTAGTAACGA 60.022 45.833 0.00 0.00 32.13 3.85
555 627 4.774200 ACCTTGGTAAGTGGTAGTAACGAT 59.226 41.667 0.00 0.00 31.50 3.73
597 671 0.600255 AGAAGGGCAGTGACGAAACG 60.600 55.000 0.00 0.00 0.00 3.60
648 723 0.608640 TCGGGGCTTCTCTTCTGTTC 59.391 55.000 0.00 0.00 0.00 3.18
728 803 4.726304 CCCGCGCCCCCACTAAAA 62.726 66.667 0.00 0.00 0.00 1.52
729 804 3.436924 CCGCGCCCCCACTAAAAC 61.437 66.667 0.00 0.00 0.00 2.43
974 1049 4.404098 GAACCCCACCGTCGGCAT 62.404 66.667 12.28 0.00 0.00 4.40
975 1050 4.404098 AACCCCACCGTCGGCATC 62.404 66.667 12.28 0.00 0.00 3.91
1459 1760 4.457603 ACTCAACTGCTCTAGTGTACTCTG 59.542 45.833 7.70 0.00 40.26 3.35
1482 1783 4.386954 GGGTAGTTTACAAACTCGTAGCAC 59.613 45.833 10.51 3.22 45.65 4.40
1491 1792 2.873133 ACTCGTAGCACATCCTAAGC 57.127 50.000 0.00 0.00 0.00 3.09
1523 1824 9.276590 TCAACATATGGATTGCTTAGTTATCTG 57.723 33.333 7.80 0.00 0.00 2.90
1549 1850 8.517862 GTTGTTACACAAGAATACGTTTGTTTC 58.482 33.333 0.00 0.00 39.00 2.78
1577 1881 2.292828 ATTGTGGAACCTCAACCCAG 57.707 50.000 9.92 0.00 34.36 4.45
1615 1919 4.697514 TCTTCTGTCTGGTATTAGCATGC 58.302 43.478 10.51 10.51 0.00 4.06
1662 1966 5.522460 GCTAGTTGCAAAGGTCGTATATTCA 59.478 40.000 0.00 0.00 42.31 2.57
1683 1993 0.694771 TGTGCTCAAGCCCATTCTCT 59.305 50.000 0.00 0.00 41.18 3.10
2138 2462 6.071952 TGACTCAGCCTTCAAATATTTGGAAC 60.072 38.462 24.40 13.09 38.66 3.62
2321 2645 7.881775 AGGAATTTGATATTACAGTTGACCC 57.118 36.000 0.00 0.00 0.00 4.46
2630 2954 0.105964 CCCTGTTCACCGTTCAGTCA 59.894 55.000 0.00 0.00 0.00 3.41
3018 3342 8.691661 AAAAGCATCTACCATATAATTCCGTT 57.308 30.769 0.00 0.00 0.00 4.44
3795 4225 1.135257 TGTGTTGCCCTTTGTGTTTCG 60.135 47.619 0.00 0.00 0.00 3.46
4121 4551 1.574702 GCAGTCCCTGTGTAAACGGC 61.575 60.000 0.00 0.00 33.43 5.68
4130 4560 2.612212 CTGTGTAAACGGCTGAACTTGT 59.388 45.455 0.00 0.00 0.00 3.16
4146 4576 2.184020 TTGTGGATGGGCGGTGAGAG 62.184 60.000 0.00 0.00 0.00 3.20
4171 4601 5.357257 CGTAGGGAGTTGCTGTATAACATT 58.643 41.667 0.00 0.00 0.00 2.71
4204 4634 3.378742 CCGAGTACTGAAGCAGTGAGTAT 59.621 47.826 0.00 0.00 45.01 2.12
4268 4698 2.414559 CCTCAGCCGCAGTACATTTTTG 60.415 50.000 0.00 0.00 0.00 2.44
4470 4900 0.603569 TTTCGCTGGAGAGACAGGAC 59.396 55.000 0.00 0.00 38.90 3.85
4483 4913 7.123697 TGGAGAGACAGGACGAGATTTTATTTA 59.876 37.037 0.00 0.00 0.00 1.40
4772 5203 5.666969 TTGATCGTCAAACTTTCGATTGT 57.333 34.783 0.00 0.00 42.91 2.71
4792 5223 8.611757 CGATTGTTGAACATAATGGAGTCATTA 58.388 33.333 0.00 1.95 46.23 1.90
4799 5230 4.997395 ACATAATGGAGTCATTACCGATGC 59.003 41.667 1.53 0.00 45.35 3.91
4837 5268 4.948341 TGGGTATGTCAGCGTATATTGT 57.052 40.909 0.00 0.00 0.00 2.71
4863 5294 1.478510 CTACTGAGCAGACCGAACCAT 59.521 52.381 4.21 0.00 0.00 3.55
4874 5305 5.934625 GCAGACCGAACCATATTATGAGAAT 59.065 40.000 5.21 0.00 0.00 2.40
5003 5436 9.379791 GTTATTCTGTTAAGGTAAGCACATACT 57.620 33.333 0.00 0.00 0.00 2.12
5004 5437 9.595823 TTATTCTGTTAAGGTAAGCACATACTC 57.404 33.333 0.00 0.00 0.00 2.59
5005 5438 5.974108 TCTGTTAAGGTAAGCACATACTCC 58.026 41.667 0.00 0.00 0.00 3.85
5006 5439 5.093849 TGTTAAGGTAAGCACATACTCCC 57.906 43.478 0.00 0.00 0.00 4.30
5007 5440 4.781087 TGTTAAGGTAAGCACATACTCCCT 59.219 41.667 0.00 0.00 0.00 4.20
5008 5441 5.105064 TGTTAAGGTAAGCACATACTCCCTC 60.105 44.000 0.00 0.00 0.00 4.30
5009 5442 2.399580 AGGTAAGCACATACTCCCTCC 58.600 52.381 0.00 0.00 0.00 4.30
5010 5443 1.068741 GGTAAGCACATACTCCCTCCG 59.931 57.143 0.00 0.00 0.00 4.63
5011 5444 1.755380 GTAAGCACATACTCCCTCCGT 59.245 52.381 0.00 0.00 0.00 4.69
5012 5445 2.154567 AAGCACATACTCCCTCCGTA 57.845 50.000 0.00 0.00 0.00 4.02
5013 5446 2.154567 AGCACATACTCCCTCCGTAA 57.845 50.000 0.00 0.00 0.00 3.18
5014 5447 2.463752 AGCACATACTCCCTCCGTAAA 58.536 47.619 0.00 0.00 0.00 2.01
5015 5448 2.167900 AGCACATACTCCCTCCGTAAAC 59.832 50.000 0.00 0.00 0.00 2.01
5016 5449 2.167900 GCACATACTCCCTCCGTAAACT 59.832 50.000 0.00 0.00 0.00 2.66
5017 5450 3.382546 GCACATACTCCCTCCGTAAACTA 59.617 47.826 0.00 0.00 0.00 2.24
5018 5451 4.142093 GCACATACTCCCTCCGTAAACTAA 60.142 45.833 0.00 0.00 0.00 2.24
5019 5452 5.452917 GCACATACTCCCTCCGTAAACTAAT 60.453 44.000 0.00 0.00 0.00 1.73
5020 5453 6.239120 GCACATACTCCCTCCGTAAACTAATA 60.239 42.308 0.00 0.00 0.00 0.98
5021 5454 7.525029 GCACATACTCCCTCCGTAAACTAATAT 60.525 40.741 0.00 0.00 0.00 1.28
5022 5455 9.017509 CACATACTCCCTCCGTAAACTAATATA 57.982 37.037 0.00 0.00 0.00 0.86
5023 5456 9.592196 ACATACTCCCTCCGTAAACTAATATAA 57.408 33.333 0.00 0.00 0.00 0.98
5026 5459 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
5027 5460 8.003629 ACTCCCTCCGTAAACTAATATAAGAGT 58.996 37.037 0.00 0.00 0.00 3.24
5028 5461 8.174733 TCCCTCCGTAAACTAATATAAGAGTG 57.825 38.462 0.00 0.00 0.00 3.51
5029 5462 7.781693 TCCCTCCGTAAACTAATATAAGAGTGT 59.218 37.037 0.00 0.00 0.00 3.55
5030 5463 8.419442 CCCTCCGTAAACTAATATAAGAGTGTT 58.581 37.037 0.00 0.00 0.00 3.32
5031 5464 9.813446 CCTCCGTAAACTAATATAAGAGTGTTT 57.187 33.333 0.00 0.00 0.00 2.83
5058 5491 9.733219 AGATCACTACTTTAGTTATCTAAACGC 57.267 33.333 7.85 0.00 43.99 4.84
5059 5492 9.733219 GATCACTACTTTAGTTATCTAAACGCT 57.267 33.333 2.47 0.00 40.05 5.07
5060 5493 9.733219 ATCACTACTTTAGTTATCTAAACGCTC 57.267 33.333 2.47 0.00 40.05 5.03
5061 5494 8.954350 TCACTACTTTAGTTATCTAAACGCTCT 58.046 33.333 2.47 0.00 40.05 4.09
5062 5495 9.570488 CACTACTTTAGTTATCTAAACGCTCTT 57.430 33.333 2.47 0.00 40.05 2.85
5079 5512 9.530633 AAACGCTCTTATATTAGTTTACAGAGG 57.469 33.333 0.00 0.00 31.14 3.69
5080 5513 7.659186 ACGCTCTTATATTAGTTTACAGAGGG 58.341 38.462 8.36 8.36 42.53 4.30
5081 5514 7.504911 ACGCTCTTATATTAGTTTACAGAGGGA 59.495 37.037 14.96 0.00 40.49 4.20
5082 5515 8.024285 CGCTCTTATATTAGTTTACAGAGGGAG 58.976 40.741 4.76 0.00 40.49 4.30
5083 5516 8.862085 GCTCTTATATTAGTTTACAGAGGGAGT 58.138 37.037 0.00 0.00 0.00 3.85
5136 5569 0.815213 GCATGGATACGCAGCTCCAA 60.815 55.000 5.98 0.00 44.14 3.53
5279 5712 2.932234 CGGCGACAGAGACAAGGGT 61.932 63.158 0.00 0.00 0.00 4.34
5294 5727 4.760047 GGTGCTGTCGGTGGCGAT 62.760 66.667 0.00 0.00 0.00 4.58
5352 5799 0.741326 GTCCTGCTGCGATGACTAGA 59.259 55.000 0.00 0.00 0.00 2.43
5369 5816 0.916358 AGACAGGGGGCAGTGCTTAT 60.916 55.000 16.11 0.00 0.00 1.73
5386 5833 3.310774 GCTTATGATGTGATGCTGTTCGT 59.689 43.478 0.00 0.00 0.00 3.85
5388 5835 2.453983 TGATGTGATGCTGTTCGTCA 57.546 45.000 0.00 0.00 38.33 4.35
5392 5839 2.765122 TGTGATGCTGTTCGTCATTCA 58.235 42.857 0.00 0.00 42.23 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.681897 AGTGTAAGCTCGAAATTGCTCAG 59.318 43.478 0.00 0.00 38.75 3.35
1 2 3.664107 AGTGTAAGCTCGAAATTGCTCA 58.336 40.909 0.00 0.00 38.75 4.26
26 27 3.523087 TTCACCTACGCGGCAGCAA 62.523 57.895 12.47 0.00 45.49 3.91
210 225 8.445275 TGGATATTTATAATGCTCGTTGTGTT 57.555 30.769 0.00 0.00 0.00 3.32
241 258 5.125257 TGCTCGCATTTCAAAAATCTATGGA 59.875 36.000 0.00 0.00 0.00 3.41
242 259 5.230726 GTGCTCGCATTTCAAAAATCTATGG 59.769 40.000 0.00 0.00 0.00 2.74
244 261 5.105797 TGGTGCTCGCATTTCAAAAATCTAT 60.106 36.000 0.00 0.00 0.00 1.98
245 262 4.217334 TGGTGCTCGCATTTCAAAAATCTA 59.783 37.500 0.00 0.00 0.00 1.98
246 263 3.005684 TGGTGCTCGCATTTCAAAAATCT 59.994 39.130 0.00 0.00 0.00 2.40
247 264 3.316283 TGGTGCTCGCATTTCAAAAATC 58.684 40.909 0.00 0.00 0.00 2.17
248 265 3.383620 TGGTGCTCGCATTTCAAAAAT 57.616 38.095 0.00 0.00 0.00 1.82
250 267 2.100584 ACTTGGTGCTCGCATTTCAAAA 59.899 40.909 0.00 0.00 0.00 2.44
251 268 1.680735 ACTTGGTGCTCGCATTTCAAA 59.319 42.857 0.00 0.00 0.00 2.69
252 269 1.001487 CACTTGGTGCTCGCATTTCAA 60.001 47.619 0.00 0.75 0.00 2.69
254 271 0.109597 CCACTTGGTGCTCGCATTTC 60.110 55.000 0.00 0.00 31.34 2.17
290 307 8.985315 TGCTTTGAGTTCAGATGGATTATATT 57.015 30.769 0.00 0.00 0.00 1.28
293 310 5.826737 CCTGCTTTGAGTTCAGATGGATTAT 59.173 40.000 0.00 0.00 0.00 1.28
304 321 1.742268 GAGATGGCCTGCTTTGAGTTC 59.258 52.381 3.32 0.00 0.00 3.01
316 334 4.034510 CGTATCAAAGTTTCAGAGATGGCC 59.965 45.833 0.00 0.00 0.00 5.36
322 340 6.893958 AGTATGCGTATCAAAGTTTCAGAG 57.106 37.500 0.00 0.00 0.00 3.35
332 350 6.972901 CAGAACAGAAGTAGTATGCGTATCAA 59.027 38.462 0.00 0.00 0.00 2.57
333 351 6.095021 ACAGAACAGAAGTAGTATGCGTATCA 59.905 38.462 0.00 0.00 0.00 2.15
334 352 6.496571 ACAGAACAGAAGTAGTATGCGTATC 58.503 40.000 0.00 0.00 0.00 2.24
337 355 4.785511 ACAGAACAGAAGTAGTATGCGT 57.214 40.909 0.00 0.00 0.00 5.24
338 356 6.495706 TGATACAGAACAGAAGTAGTATGCG 58.504 40.000 0.00 0.00 0.00 4.73
339 357 8.596380 GTTTGATACAGAACAGAAGTAGTATGC 58.404 37.037 0.00 0.00 0.00 3.14
343 361 9.694137 GTAAGTTTGATACAGAACAGAAGTAGT 57.306 33.333 0.00 0.00 0.00 2.73
344 362 9.915629 AGTAAGTTTGATACAGAACAGAAGTAG 57.084 33.333 0.00 0.00 0.00 2.57
345 363 9.909644 GAGTAAGTTTGATACAGAACAGAAGTA 57.090 33.333 0.00 0.00 0.00 2.24
346 364 7.873505 GGAGTAAGTTTGATACAGAACAGAAGT 59.126 37.037 0.00 0.00 0.00 3.01
348 366 7.963532 AGGAGTAAGTTTGATACAGAACAGAA 58.036 34.615 0.00 0.00 0.00 3.02
349 367 7.540474 AGGAGTAAGTTTGATACAGAACAGA 57.460 36.000 0.00 0.00 0.00 3.41
350 368 8.091449 AGAAGGAGTAAGTTTGATACAGAACAG 58.909 37.037 0.00 0.00 0.00 3.16
351 369 7.872993 CAGAAGGAGTAAGTTTGATACAGAACA 59.127 37.037 0.00 0.00 0.00 3.18
352 370 7.873505 ACAGAAGGAGTAAGTTTGATACAGAAC 59.126 37.037 0.00 0.00 0.00 3.01
356 428 6.295688 GGGACAGAAGGAGTAAGTTTGATACA 60.296 42.308 0.00 0.00 0.00 2.29
405 477 9.550406 TCGGAAATTATTTATGTAACCTACTGG 57.450 33.333 0.00 0.00 39.83 4.00
407 479 9.774413 CCTCGGAAATTATTTATGTAACCTACT 57.226 33.333 0.00 0.00 0.00 2.57
408 480 8.501580 GCCTCGGAAATTATTTATGTAACCTAC 58.498 37.037 0.00 0.00 0.00 3.18
409 481 8.434392 AGCCTCGGAAATTATTTATGTAACCTA 58.566 33.333 0.00 0.00 0.00 3.08
410 482 7.287810 AGCCTCGGAAATTATTTATGTAACCT 58.712 34.615 0.00 0.00 0.00 3.50
411 483 7.506328 AGCCTCGGAAATTATTTATGTAACC 57.494 36.000 0.00 0.00 0.00 2.85
412 484 8.617809 TGAAGCCTCGGAAATTATTTATGTAAC 58.382 33.333 0.00 0.00 0.00 2.50
418 490 4.272504 CGCTGAAGCCTCGGAAATTATTTA 59.727 41.667 0.00 0.00 37.91 1.40
426 498 3.315142 ATGCGCTGAAGCCTCGGAA 62.315 57.895 9.73 0.00 37.91 4.30
428 500 2.355445 TAGATGCGCTGAAGCCTCGG 62.355 60.000 9.73 0.00 36.97 4.63
429 501 1.066422 TAGATGCGCTGAAGCCTCG 59.934 57.895 9.73 0.00 36.97 4.63
431 503 0.250234 TTGTAGATGCGCTGAAGCCT 59.750 50.000 9.73 0.00 37.91 4.58
438 510 1.067846 TCGTGAAGTTGTAGATGCGCT 60.068 47.619 9.73 0.00 0.00 5.92
468 540 4.223032 TCCTTCTGAGACACTTGTAATCCC 59.777 45.833 0.00 0.00 0.00 3.85
473 545 3.827302 GTCCTCCTTCTGAGACACTTGTA 59.173 47.826 0.00 0.00 44.42 2.41
476 548 2.896685 CAGTCCTCCTTCTGAGACACTT 59.103 50.000 0.00 0.00 44.42 3.16
483 555 2.568956 CCATTGACAGTCCTCCTTCTGA 59.431 50.000 0.00 0.00 35.84 3.27
493 565 1.021390 CGCCCAGACCATTGACAGTC 61.021 60.000 0.00 0.00 0.00 3.51
494 566 1.003355 CGCCCAGACCATTGACAGT 60.003 57.895 0.00 0.00 0.00 3.55
495 567 1.003355 ACGCCCAGACCATTGACAG 60.003 57.895 0.00 0.00 0.00 3.51
496 568 1.003839 GACGCCCAGACCATTGACA 60.004 57.895 0.00 0.00 0.00 3.58
497 569 1.745489 GGACGCCCAGACCATTGAC 60.745 63.158 0.00 0.00 34.74 3.18
499 571 2.819595 CGGACGCCCAGACCATTG 60.820 66.667 0.00 0.00 34.24 2.82
500 572 4.096003 CCGGACGCCCAGACCATT 62.096 66.667 0.00 0.00 34.24 3.16
516 588 2.516225 GTGCCCTACGGAATGGCC 60.516 66.667 5.44 0.00 44.72 5.36
517 589 2.516225 GGTGCCCTACGGAATGGC 60.516 66.667 0.75 0.75 45.56 4.40
518 590 0.748005 CAAGGTGCCCTACGGAATGG 60.748 60.000 0.00 0.00 31.13 3.16
519 591 0.748005 CCAAGGTGCCCTACGGAATG 60.748 60.000 4.49 0.00 31.13 2.67
520 592 1.205460 ACCAAGGTGCCCTACGGAAT 61.205 55.000 13.37 0.00 32.52 3.01
521 593 0.544833 TACCAAGGTGCCCTACGGAA 60.545 55.000 13.37 0.00 32.52 4.30
522 594 0.544833 TTACCAAGGTGCCCTACGGA 60.545 55.000 13.37 0.00 32.52 4.69
523 595 0.107848 CTTACCAAGGTGCCCTACGG 60.108 60.000 1.07 7.62 33.86 4.02
524 596 0.611714 ACTTACCAAGGTGCCCTACG 59.388 55.000 1.07 0.00 31.13 3.51
525 597 1.339727 CCACTTACCAAGGTGCCCTAC 60.340 57.143 1.07 0.00 31.13 3.18
526 598 0.988832 CCACTTACCAAGGTGCCCTA 59.011 55.000 1.07 0.00 31.13 3.53
527 599 1.065997 ACCACTTACCAAGGTGCCCT 61.066 55.000 1.07 0.00 33.57 5.19
528 600 0.694196 TACCACTTACCAAGGTGCCC 59.306 55.000 1.07 0.00 36.87 5.36
529 601 1.350019 ACTACCACTTACCAAGGTGCC 59.650 52.381 1.07 0.00 36.87 5.01
530 602 2.853235 ACTACCACTTACCAAGGTGC 57.147 50.000 1.07 0.00 36.87 5.01
531 603 4.022068 TCGTTACTACCACTTACCAAGGTG 60.022 45.833 1.07 0.00 36.87 4.00
532 604 4.151883 TCGTTACTACCACTTACCAAGGT 58.848 43.478 0.00 0.00 39.41 3.50
533 605 4.789012 TCGTTACTACCACTTACCAAGG 57.211 45.455 0.00 0.00 0.00 3.61
534 606 7.662604 AAAATCGTTACTACCACTTACCAAG 57.337 36.000 0.00 0.00 0.00 3.61
568 640 4.279420 GTCACTGCCCTTCTTCTTTTTCAT 59.721 41.667 0.00 0.00 0.00 2.57
569 641 3.632145 GTCACTGCCCTTCTTCTTTTTCA 59.368 43.478 0.00 0.00 0.00 2.69
570 642 3.304057 CGTCACTGCCCTTCTTCTTTTTC 60.304 47.826 0.00 0.00 0.00 2.29
648 723 2.819284 GGGAGTAGGCGGAATGGGG 61.819 68.421 0.00 0.00 0.00 4.96
711 786 4.726304 TTTTAGTGGGGGCGCGGG 62.726 66.667 8.83 0.00 0.00 6.13
712 787 3.436924 GTTTTAGTGGGGGCGCGG 61.437 66.667 8.83 0.00 0.00 6.46
957 1032 4.404098 ATGCCGACGGTGGGGTTC 62.404 66.667 16.73 0.00 0.00 3.62
958 1033 4.404098 GATGCCGACGGTGGGGTT 62.404 66.667 16.73 0.00 0.00 4.11
963 1038 4.096003 AAGGGGATGCCGACGGTG 62.096 66.667 16.73 0.00 0.00 4.94
964 1039 2.866523 TAGAAGGGGATGCCGACGGT 62.867 60.000 16.73 0.00 0.00 4.83
965 1040 2.131709 TAGAAGGGGATGCCGACGG 61.132 63.158 10.29 10.29 0.00 4.79
966 1041 1.067582 GTAGAAGGGGATGCCGACG 59.932 63.158 0.00 0.00 0.00 5.12
967 1042 1.067582 CGTAGAAGGGGATGCCGAC 59.932 63.158 0.00 0.00 0.00 4.79
968 1043 2.131709 CCGTAGAAGGGGATGCCGA 61.132 63.158 0.00 0.00 0.00 5.54
969 1044 2.421739 CCGTAGAAGGGGATGCCG 59.578 66.667 0.00 0.00 0.00 5.69
970 1045 2.111251 GCCGTAGAAGGGGATGCC 59.889 66.667 0.00 0.00 0.00 4.40
971 1046 2.280186 CGCCGTAGAAGGGGATGC 60.280 66.667 0.00 0.00 45.92 3.91
972 1047 3.533720 TCGCCGTAGAAGGGGATG 58.466 61.111 0.00 0.00 46.44 3.51
975 1050 1.447314 GTTGTCGCCGTAGAAGGGG 60.447 63.158 0.00 0.00 44.59 4.79
976 1051 0.736325 CAGTTGTCGCCGTAGAAGGG 60.736 60.000 0.00 0.00 0.00 3.95
977 1052 0.736325 CCAGTTGTCGCCGTAGAAGG 60.736 60.000 0.00 0.00 0.00 3.46
978 1053 1.352156 GCCAGTTGTCGCCGTAGAAG 61.352 60.000 0.00 0.00 0.00 2.85
979 1054 1.373748 GCCAGTTGTCGCCGTAGAA 60.374 57.895 0.00 0.00 0.00 2.10
1416 1717 3.011119 GTCGTAGAGAGGCAGAAAGAGA 58.989 50.000 0.00 0.00 36.95 3.10
1482 1783 7.879677 TCCATATGTTGACAATAGCTTAGGATG 59.120 37.037 1.24 0.00 0.00 3.51
1491 1792 9.060347 ACTAAGCAATCCATATGTTGACAATAG 57.940 33.333 9.60 7.68 0.00 1.73
1549 1850 6.423604 GGTTGAGGTTCCACAATACAATTTTG 59.576 38.462 5.16 0.00 0.00 2.44
1577 1881 6.931840 AGACAGAAGAGGATTTGTTTGTAGAC 59.068 38.462 0.00 0.00 0.00 2.59
1615 1919 5.722263 CATCAGATCAAGCTATCACCCTAG 58.278 45.833 0.00 0.00 0.00 3.02
1654 1958 5.113502 GGGCTTGAGCACAATGAATATAC 57.886 43.478 5.24 0.00 45.57 1.47
1683 1993 7.015098 TCAGCACATCCATAGAAAAAGGAAAAA 59.985 33.333 0.00 0.00 34.62 1.94
2138 2462 4.722203 CGTAGCCTGATTTAAGCATCAG 57.278 45.455 9.37 9.37 46.89 2.90
2266 2590 6.034256 GCATACAAGCAATGAATGAACTGTTC 59.966 38.462 13.49 13.49 0.00 3.18
2321 2645 6.824305 AACTCACAAACATCTAAGGAATGG 57.176 37.500 0.00 0.00 0.00 3.16
2551 2875 2.857186 ATTCCAAACCAAACATGGCC 57.143 45.000 0.00 0.00 34.13 5.36
2615 2939 3.058914 CCTTCATTGACTGAACGGTGAAC 60.059 47.826 0.00 0.00 38.97 3.18
2630 2954 6.613153 AGCTGAGAGTACTAAACCTTCATT 57.387 37.500 0.00 0.00 0.00 2.57
3103 3427 7.506114 TGACCAAGTGAAAATAACAGTAGAGT 58.494 34.615 0.00 0.00 0.00 3.24
3251 3576 3.680458 TCGCAGTTATGTACGAATGCAAA 59.320 39.130 13.78 2.25 33.33 3.68
3431 3756 9.378551 AGAGCATTCAATCATACGTACTTAAAA 57.621 29.630 0.00 0.00 0.00 1.52
3435 3760 7.438459 GGTTAGAGCATTCAATCATACGTACTT 59.562 37.037 0.00 0.00 0.00 2.24
3436 3761 6.924060 GGTTAGAGCATTCAATCATACGTACT 59.076 38.462 0.00 0.00 0.00 2.73
3438 3763 7.050970 AGGTTAGAGCATTCAATCATACGTA 57.949 36.000 0.00 0.00 0.00 3.57
3440 3765 9.295214 CTATAGGTTAGAGCATTCAATCATACG 57.705 37.037 0.00 0.00 0.00 3.06
3795 4225 4.142049 ACATTACTAGCTTCCTCTGTCTGC 60.142 45.833 0.00 0.00 0.00 4.26
4121 4551 1.308069 CCGCCCATCCACAAGTTCAG 61.308 60.000 0.00 0.00 0.00 3.02
4130 4560 3.785859 GCTCTCACCGCCCATCCA 61.786 66.667 0.00 0.00 0.00 3.41
4146 4576 0.464452 ATACAGCAACTCCCTACGGC 59.536 55.000 0.00 0.00 0.00 5.68
4171 4601 3.086282 TCAGTACTCGGCACTGTATTCA 58.914 45.455 0.00 0.00 43.21 2.57
4268 4698 3.119388 TCAGCAAACAAGGCATAATCAGC 60.119 43.478 0.00 0.00 0.00 4.26
4377 4807 3.594603 TTTACAGACTACAGCCTCTGC 57.405 47.619 0.00 0.00 37.96 4.26
4772 5203 6.645306 TCGGTAATGACTCCATTATGTTCAA 58.355 36.000 0.00 0.00 44.37 2.69
4792 5223 1.910722 ATGCTCTTGAGGCATCGGT 59.089 52.632 0.00 0.00 45.85 4.69
4799 5230 2.025887 ACCCAAGGTAATGCTCTTGAGG 60.026 50.000 4.83 6.78 41.94 3.86
4852 5283 8.980481 AAAATTCTCATAATATGGTTCGGTCT 57.020 30.769 0.00 0.00 0.00 3.85
4874 5305 6.800072 ACCACTTAGTCATTTTCCCAAAAA 57.200 33.333 0.00 0.00 38.66 1.94
5003 5436 7.781693 ACACTCTTATATTAGTTTACGGAGGGA 59.218 37.037 0.00 0.00 0.00 4.20
5004 5437 7.949434 ACACTCTTATATTAGTTTACGGAGGG 58.051 38.462 0.00 0.00 0.00 4.30
5005 5438 9.813446 AAACACTCTTATATTAGTTTACGGAGG 57.187 33.333 0.00 0.00 0.00 4.30
5033 5466 9.733219 AGCGTTTAGATAACTAAAGTAGTGATC 57.267 33.333 5.51 5.03 45.42 2.92
5034 5467 9.733219 GAGCGTTTAGATAACTAAAGTAGTGAT 57.267 33.333 5.51 0.00 45.42 3.06
5035 5468 8.954350 AGAGCGTTTAGATAACTAAAGTAGTGA 58.046 33.333 5.51 0.00 45.42 3.41
5036 5469 9.570488 AAGAGCGTTTAGATAACTAAAGTAGTG 57.430 33.333 5.51 0.00 45.42 2.74
5053 5486 9.530633 CCTCTGTAAACTAATATAAGAGCGTTT 57.469 33.333 0.00 0.00 0.00 3.60
5054 5487 8.142551 CCCTCTGTAAACTAATATAAGAGCGTT 58.857 37.037 0.00 0.00 0.00 4.84
5055 5488 7.504911 TCCCTCTGTAAACTAATATAAGAGCGT 59.495 37.037 0.00 0.00 0.00 5.07
5056 5489 7.883217 TCCCTCTGTAAACTAATATAAGAGCG 58.117 38.462 0.00 0.00 0.00 5.03
5057 5490 8.862085 ACTCCCTCTGTAAACTAATATAAGAGC 58.138 37.037 0.00 0.00 0.00 4.09
5065 5498 9.490083 AGTATTGTACTCCCTCTGTAAACTAAT 57.510 33.333 0.00 0.00 32.47 1.73
5066 5499 8.890410 AGTATTGTACTCCCTCTGTAAACTAA 57.110 34.615 0.00 0.00 32.47 2.24
5067 5500 8.890410 AAGTATTGTACTCCCTCTGTAAACTA 57.110 34.615 0.00 0.00 38.26 2.24
5068 5501 7.793948 AAGTATTGTACTCCCTCTGTAAACT 57.206 36.000 0.00 0.00 38.26 2.66
5069 5502 8.252964 CAAAGTATTGTACTCCCTCTGTAAAC 57.747 38.462 0.00 0.00 38.26 2.01
5136 5569 2.882927 TTGACTAAGTCGCTGTGTGT 57.117 45.000 0.00 0.00 34.95 3.72
5294 5727 1.680735 GCCTGTTTGTTGTCATCACCA 59.319 47.619 0.00 0.00 0.00 4.17
5342 5785 1.043116 TGCCCCCTGTCTAGTCATCG 61.043 60.000 0.00 0.00 0.00 3.84
5352 5799 1.207488 TCATAAGCACTGCCCCCTGT 61.207 55.000 0.00 0.00 0.00 4.00
5369 5816 2.453983 TGACGAACAGCATCACATCA 57.546 45.000 0.00 0.00 0.00 3.07
5386 5833 1.375396 CCCCAGCGAACGTGAATGA 60.375 57.895 0.00 0.00 0.00 2.57
5388 5835 1.079127 CTCCCCAGCGAACGTGAAT 60.079 57.895 0.00 0.00 0.00 2.57
5392 5839 1.949847 CTGATCTCCCCAGCGAACGT 61.950 60.000 0.00 0.00 0.00 3.99


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

AutoCloner maintained by Alex Coulton.