Multiple sequence alignment - TraesCS7D01G099700

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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 TraesCS7D01G099700 chr7D 100.000 2288 0 0 1 2288 59901336 59903623 0.000000e+00 4226.0
1 TraesCS7D01G099700 chr7D 84.884 774 61 18 1528 2287 59945219 59945950 0.000000e+00 730.0
2 TraesCS7D01G099700 chr7D 87.698 569 41 10 454 995 14172007 14171441 8.920000e-179 636.0
3 TraesCS7D01G099700 chr7D 87.522 569 42 10 454 995 8079798 8080364 4.150000e-177 630.0
4 TraesCS7D01G099700 chr7D 83.684 380 48 6 1805 2172 63945424 63945801 1.680000e-91 346.0
5 TraesCS7D01G099700 chr2D 96.918 584 4 2 425 995 355481231 355481813 0.000000e+00 966.0
6 TraesCS7D01G099700 chr2D 98.155 542 9 1 986 1527 355483245 355483785 0.000000e+00 944.0
7 TraesCS7D01G099700 chr2D 98.125 320 6 0 1 320 355480914 355481233 1.990000e-155 558.0
8 TraesCS7D01G099700 chr2D 96.000 50 2 0 260 309 193993403 193993452 5.240000e-12 82.4
9 TraesCS7D01G099700 chr2A 97.422 543 13 1 986 1528 377109379 377109920 0.000000e+00 924.0
10 TraesCS7D01G099700 chr2A 93.578 545 32 2 986 1528 755356966 755356423 0.000000e+00 809.0
11 TraesCS7D01G099700 chr2A 94.688 320 16 1 1 320 755361045 755360727 1.580000e-136 496.0
12 TraesCS7D01G099700 chr2A 93.134 335 10 2 674 995 755358734 755358400 1.590000e-131 479.0
13 TraesCS7D01G099700 chr5A 95.205 584 15 1 425 995 315534464 315535047 0.000000e+00 911.0
14 TraesCS7D01G099700 chr5A 95.387 542 23 1 986 1527 315536482 315537021 0.000000e+00 861.0
15 TraesCS7D01G099700 chr5A 87.478 567 46 7 454 995 685196901 685196335 4.150000e-177 630.0
16 TraesCS7D01G099700 chr5A 94.410 322 16 1 1 320 315534145 315534466 5.680000e-136 494.0
17 TraesCS7D01G099700 chr3B 94.521 584 19 1 425 995 782021526 782022109 0.000000e+00 889.0
18 TraesCS7D01G099700 chr3B 94.343 548 29 2 986 1533 782023544 782024089 0.000000e+00 839.0
19 TraesCS7D01G099700 chr3B 85.859 594 61 4 425 995 16673537 16672944 5.400000e-171 610.0
20 TraesCS7D01G099700 chr3B 93.750 320 20 0 1 320 782021209 782021528 4.420000e-132 481.0
21 TraesCS7D01G099700 chr3A 94.465 542 29 1 986 1527 27685798 27685258 0.000000e+00 833.0
22 TraesCS7D01G099700 chr3A 94.150 547 30 2 986 1532 27686182 27686726 0.000000e+00 832.0
23 TraesCS7D01G099700 chr5D 93.002 543 26 5 986 1528 7892400 7891870 0.000000e+00 782.0
24 TraesCS7D01G099700 chr5D 92.066 542 31 5 986 1527 7883962 7884491 0.000000e+00 752.0
25 TraesCS7D01G099700 chr5D 87.522 569 42 10 454 995 460676995 460677561 4.150000e-177 630.0
26 TraesCS7D01G099700 chr5D 93.125 320 22 0 1 320 7908951 7908632 9.570000e-129 470.0
27 TraesCS7D01G099700 chr5D 90.938 320 29 0 1 320 7882718 7883037 4.520000e-117 431.0
28 TraesCS7D01G099700 chr5D 89.062 320 24 2 1 309 450668137 450667818 9.910000e-104 387.0
29 TraesCS7D01G099700 chr5D 100.000 54 0 0 321 374 79998096 79998043 1.450000e-17 100.0
30 TraesCS7D01G099700 chr5D 100.000 54 0 0 321 374 301057054 301057107 1.450000e-17 100.0
31 TraesCS7D01G099700 chr2B 86.847 593 53 14 425 995 35304860 35305449 6.890000e-180 640.0
32 TraesCS7D01G099700 chr7A 87.522 569 42 10 454 995 736404528 736403962 4.150000e-177 630.0
33 TraesCS7D01G099700 chr6A 89.084 513 40 4 499 995 108918821 108918309 6.940000e-175 623.0
34 TraesCS7D01G099700 chr6A 100.000 54 0 0 321 374 597224552 597224605 1.450000e-17 100.0
35 TraesCS7D01G099700 chrUn 87.170 569 44 10 454 995 95717716 95718282 8.980000e-174 619.0
36 TraesCS7D01G099700 chrUn 93.151 73 1 3 356 424 189423307 189423235 1.120000e-18 104.0
37 TraesCS7D01G099700 chrUn 93.151 73 1 3 356 424 396572325 396572397 1.120000e-18 104.0
38 TraesCS7D01G099700 chrUn 93.151 73 1 3 356 424 396598362 396598290 1.120000e-18 104.0
39 TraesCS7D01G099700 chrUn 93.151 73 1 3 356 424 408583350 408583422 1.120000e-18 104.0
40 TraesCS7D01G099700 chrUn 93.151 73 1 3 356 424 408825124 408825196 1.120000e-18 104.0
41 TraesCS7D01G099700 chrUn 100.000 54 0 0 321 374 403405275 403405328 1.450000e-17 100.0
42 TraesCS7D01G099700 chr4D 88.750 320 25 2 1 309 483639488 483639169 4.610000e-102 381.0
43 TraesCS7D01G099700 chr4D 93.151 73 1 3 356 424 450886701 450886773 1.120000e-18 104.0
44 TraesCS7D01G099700 chr4D 100.000 54 0 0 321 374 123352778 123352831 1.450000e-17 100.0
45 TraesCS7D01G099700 chr4D 100.000 54 0 0 321 374 123563717 123563770 1.450000e-17 100.0
46 TraesCS7D01G099700 chr4D 100.000 54 0 0 321 374 471890493 471890440 1.450000e-17 100.0
47 TraesCS7D01G099700 chr1B 92.135 89 6 1 71 159 9590762 9590849 8.580000e-25 124.0
48 TraesCS7D01G099700 chr4A 93.151 73 1 3 356 424 275496077 275496005 1.120000e-18 104.0
49 TraesCS7D01G099700 chr4A 93.151 73 1 3 356 424 350243053 350242981 1.120000e-18 104.0
50 TraesCS7D01G099700 chr3D 93.151 73 1 2 356 424 399840121 399840193 1.120000e-18 104.0
51 TraesCS7D01G099700 chr6D 100.000 54 0 0 321 374 370025161 370025214 1.450000e-17 100.0
52 TraesCS7D01G099700 chr1D 100.000 54 0 0 321 374 351019103 351019156 1.450000e-17 100.0


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 TraesCS7D01G099700 chr7D 59901336 59903623 2287 False 4226.000000 4226 100.000000 1 2288 1 chr7D.!!$F2 2287
1 TraesCS7D01G099700 chr7D 59945219 59945950 731 False 730.000000 730 84.884000 1528 2287 1 chr7D.!!$F3 759
2 TraesCS7D01G099700 chr7D 14171441 14172007 566 True 636.000000 636 87.698000 454 995 1 chr7D.!!$R1 541
3 TraesCS7D01G099700 chr7D 8079798 8080364 566 False 630.000000 630 87.522000 454 995 1 chr7D.!!$F1 541
4 TraesCS7D01G099700 chr2D 355480914 355483785 2871 False 822.666667 966 97.732667 1 1527 3 chr2D.!!$F2 1526
5 TraesCS7D01G099700 chr2A 377109379 377109920 541 False 924.000000 924 97.422000 986 1528 1 chr2A.!!$F1 542
6 TraesCS7D01G099700 chr2A 755356423 755361045 4622 True 594.666667 809 93.800000 1 1528 3 chr2A.!!$R1 1527
7 TraesCS7D01G099700 chr5A 315534145 315537021 2876 False 755.333333 911 95.000667 1 1527 3 chr5A.!!$F1 1526
8 TraesCS7D01G099700 chr5A 685196335 685196901 566 True 630.000000 630 87.478000 454 995 1 chr5A.!!$R1 541
9 TraesCS7D01G099700 chr3B 782021209 782024089 2880 False 736.333333 889 94.204667 1 1533 3 chr3B.!!$F1 1532
10 TraesCS7D01G099700 chr3B 16672944 16673537 593 True 610.000000 610 85.859000 425 995 1 chr3B.!!$R1 570
11 TraesCS7D01G099700 chr3A 27685258 27685798 540 True 833.000000 833 94.465000 986 1527 1 chr3A.!!$R1 541
12 TraesCS7D01G099700 chr3A 27686182 27686726 544 False 832.000000 832 94.150000 986 1532 1 chr3A.!!$F1 546
13 TraesCS7D01G099700 chr5D 7891870 7892400 530 True 782.000000 782 93.002000 986 1528 1 chr5D.!!$R1 542
14 TraesCS7D01G099700 chr5D 460676995 460677561 566 False 630.000000 630 87.522000 454 995 1 chr5D.!!$F2 541
15 TraesCS7D01G099700 chr5D 7882718 7884491 1773 False 591.500000 752 91.502000 1 1527 2 chr5D.!!$F3 1526
16 TraesCS7D01G099700 chr2B 35304860 35305449 589 False 640.000000 640 86.847000 425 995 1 chr2B.!!$F1 570
17 TraesCS7D01G099700 chr7A 736403962 736404528 566 True 630.000000 630 87.522000 454 995 1 chr7A.!!$R1 541
18 TraesCS7D01G099700 chr6A 108918309 108918821 512 True 623.000000 623 89.084000 499 995 1 chr6A.!!$R1 496
19 TraesCS7D01G099700 chrUn 95717716 95718282 566 False 619.000000 619 87.170000 454 995 1 chrUn.!!$F1 541

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
355 358 0.102481 GTCGCTTTCTCTATGCCCGA 59.898 55.0 0.0 0.0 0.0 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1589 5224 0.109132 GCTCAAAATTGCCGTCAGGG 60.109 55.0 0.0 0.0 38.2 4.45 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
105 106 5.048504 GGTGTCTGATTCTTTCTTTGCATCA 60.049 40.000 0.00 0.00 0.00 3.07
165 166 7.775093 AGTCATGTTGCCTAAAAAGCATCTATA 59.225 33.333 0.00 0.00 40.59 1.31
318 321 4.559502 CGAACAACCAGATCAGACTGAGAA 60.560 45.833 11.52 0.00 39.94 2.87
319 322 5.486526 GAACAACCAGATCAGACTGAGAAT 58.513 41.667 11.52 0.00 39.94 2.40
320 323 5.083533 ACAACCAGATCAGACTGAGAATC 57.916 43.478 11.52 3.93 39.94 2.52
321 324 4.081198 ACAACCAGATCAGACTGAGAATCC 60.081 45.833 11.52 0.00 39.94 3.01
322 325 3.037549 ACCAGATCAGACTGAGAATCCC 58.962 50.000 11.52 0.00 39.94 3.85
323 326 2.368221 CCAGATCAGACTGAGAATCCCC 59.632 54.545 11.52 0.00 39.94 4.81
324 327 3.307506 CAGATCAGACTGAGAATCCCCT 58.692 50.000 11.52 0.00 39.94 4.79
325 328 3.321682 CAGATCAGACTGAGAATCCCCTC 59.678 52.174 11.52 1.00 39.94 4.30
326 329 2.928036 TCAGACTGAGAATCCCCTCA 57.072 50.000 0.00 0.00 40.57 3.86
327 330 3.190383 TCAGACTGAGAATCCCCTCAA 57.810 47.619 0.00 0.00 42.05 3.02
328 331 3.729108 TCAGACTGAGAATCCCCTCAAT 58.271 45.455 0.00 0.00 42.05 2.57
329 332 3.708631 TCAGACTGAGAATCCCCTCAATC 59.291 47.826 0.00 0.00 42.05 2.67
330 333 3.710677 CAGACTGAGAATCCCCTCAATCT 59.289 47.826 0.00 0.00 46.76 2.40
331 334 3.966665 AGACTGAGAATCCCCTCAATCTC 59.033 47.826 0.00 0.00 43.70 2.75
332 335 3.708631 GACTGAGAATCCCCTCAATCTCA 59.291 47.826 4.47 4.47 44.35 3.27
334 337 3.044156 TGAGAATCCCCTCAATCTCAGG 58.956 50.000 0.46 0.00 42.36 3.86
335 338 3.310879 TGAGAATCCCCTCAATCTCAGGA 60.311 47.826 0.46 0.00 42.36 3.86
336 339 3.316501 AGAATCCCCTCAATCTCAGGAG 58.683 50.000 0.00 0.00 31.91 3.69
337 340 2.885388 ATCCCCTCAATCTCAGGAGT 57.115 50.000 0.00 0.00 31.91 3.85
338 341 2.166907 TCCCCTCAATCTCAGGAGTC 57.833 55.000 0.00 0.00 31.91 3.36
339 342 0.749649 CCCCTCAATCTCAGGAGTCG 59.250 60.000 0.00 0.00 31.91 4.18
340 343 0.103937 CCCTCAATCTCAGGAGTCGC 59.896 60.000 0.00 0.00 31.91 5.19
341 344 1.110442 CCTCAATCTCAGGAGTCGCT 58.890 55.000 0.00 0.00 31.91 4.93
342 345 1.480137 CCTCAATCTCAGGAGTCGCTT 59.520 52.381 0.00 0.00 31.91 4.68
343 346 2.093764 CCTCAATCTCAGGAGTCGCTTT 60.094 50.000 0.00 0.00 31.91 3.51
344 347 3.186119 CTCAATCTCAGGAGTCGCTTTC 58.814 50.000 0.00 0.00 0.00 2.62
345 348 2.828520 TCAATCTCAGGAGTCGCTTTCT 59.171 45.455 0.00 0.00 0.00 2.52
346 349 3.119316 TCAATCTCAGGAGTCGCTTTCTC 60.119 47.826 0.00 0.00 0.00 2.87
347 350 2.208132 TCTCAGGAGTCGCTTTCTCT 57.792 50.000 0.00 0.00 33.06 3.10
348 351 3.351794 TCTCAGGAGTCGCTTTCTCTA 57.648 47.619 0.00 0.00 33.06 2.43
349 352 3.892284 TCTCAGGAGTCGCTTTCTCTAT 58.108 45.455 0.00 0.00 33.06 1.98
350 353 3.629855 TCTCAGGAGTCGCTTTCTCTATG 59.370 47.826 0.00 0.00 33.06 2.23
351 354 2.099921 TCAGGAGTCGCTTTCTCTATGC 59.900 50.000 0.00 0.00 33.06 3.14
352 355 1.410882 AGGAGTCGCTTTCTCTATGCC 59.589 52.381 0.00 0.00 33.06 4.40
353 356 1.539280 GGAGTCGCTTTCTCTATGCCC 60.539 57.143 0.00 0.00 33.06 5.36
354 357 0.103208 AGTCGCTTTCTCTATGCCCG 59.897 55.000 0.00 0.00 0.00 6.13
355 358 0.102481 GTCGCTTTCTCTATGCCCGA 59.898 55.000 0.00 0.00 0.00 5.14
356 359 0.102481 TCGCTTTCTCTATGCCCGAC 59.898 55.000 0.00 0.00 0.00 4.79
357 360 0.103208 CGCTTTCTCTATGCCCGACT 59.897 55.000 0.00 0.00 0.00 4.18
358 361 1.471676 CGCTTTCTCTATGCCCGACTT 60.472 52.381 0.00 0.00 0.00 3.01
359 362 2.223735 CGCTTTCTCTATGCCCGACTTA 60.224 50.000 0.00 0.00 0.00 2.24
360 363 3.124560 GCTTTCTCTATGCCCGACTTAC 58.875 50.000 0.00 0.00 0.00 2.34
361 364 3.372954 CTTTCTCTATGCCCGACTTACG 58.627 50.000 0.00 0.00 42.18 3.18
362 365 2.336945 TCTCTATGCCCGACTTACGA 57.663 50.000 0.00 0.00 45.77 3.43
363 366 2.219458 TCTCTATGCCCGACTTACGAG 58.781 52.381 0.00 0.00 45.77 4.18
364 367 0.666913 TCTATGCCCGACTTACGAGC 59.333 55.000 0.00 0.00 45.61 5.03
365 368 0.669077 CTATGCCCGACTTACGAGCT 59.331 55.000 0.00 0.00 45.61 4.09
366 369 0.666913 TATGCCCGACTTACGAGCTC 59.333 55.000 2.73 2.73 45.61 4.09
367 370 1.038130 ATGCCCGACTTACGAGCTCT 61.038 55.000 12.85 1.42 45.61 4.09
368 371 1.248785 TGCCCGACTTACGAGCTCTT 61.249 55.000 12.85 4.80 45.61 2.85
369 372 0.108756 GCCCGACTTACGAGCTCTTT 60.109 55.000 12.85 0.65 42.27 2.52
370 373 1.630148 CCCGACTTACGAGCTCTTTG 58.370 55.000 12.85 0.00 45.77 2.77
371 374 0.992802 CCGACTTACGAGCTCTTTGC 59.007 55.000 12.85 0.00 45.77 3.68
391 394 3.118542 GCTTGAGCAACTTCTTTTGTGG 58.881 45.455 0.00 0.00 41.59 4.17
392 395 3.181487 GCTTGAGCAACTTCTTTTGTGGA 60.181 43.478 0.00 0.00 41.59 4.02
393 396 4.354587 CTTGAGCAACTTCTTTTGTGGAC 58.645 43.478 0.00 0.00 0.00 4.02
394 397 3.351740 TGAGCAACTTCTTTTGTGGACA 58.648 40.909 0.00 0.00 0.00 4.02
395 398 3.378112 TGAGCAACTTCTTTTGTGGACAG 59.622 43.478 0.00 0.00 0.00 3.51
396 399 2.099756 AGCAACTTCTTTTGTGGACAGC 59.900 45.455 0.00 0.00 0.00 4.40
397 400 2.799562 GCAACTTCTTTTGTGGACAGCC 60.800 50.000 0.00 0.00 0.00 4.85
398 401 2.689983 CAACTTCTTTTGTGGACAGCCT 59.310 45.455 0.00 0.00 34.31 4.58
399 402 3.018423 ACTTCTTTTGTGGACAGCCTT 57.982 42.857 0.00 0.00 34.31 4.35
400 403 3.365472 ACTTCTTTTGTGGACAGCCTTT 58.635 40.909 0.00 0.00 34.31 3.11
401 404 3.381590 ACTTCTTTTGTGGACAGCCTTTC 59.618 43.478 0.00 0.00 34.31 2.62
402 405 3.297134 TCTTTTGTGGACAGCCTTTCT 57.703 42.857 0.00 0.00 34.31 2.52
403 406 3.631250 TCTTTTGTGGACAGCCTTTCTT 58.369 40.909 0.00 0.00 34.31 2.52
404 407 4.787551 TCTTTTGTGGACAGCCTTTCTTA 58.212 39.130 0.00 0.00 34.31 2.10
405 408 5.197451 TCTTTTGTGGACAGCCTTTCTTAA 58.803 37.500 0.00 0.00 34.31 1.85
406 409 5.654650 TCTTTTGTGGACAGCCTTTCTTAAA 59.345 36.000 0.00 0.00 34.31 1.52
407 410 5.514274 TTTGTGGACAGCCTTTCTTAAAG 57.486 39.130 0.00 0.00 38.24 1.85
408 411 4.164843 TGTGGACAGCCTTTCTTAAAGT 57.835 40.909 0.00 0.00 36.77 2.66
409 412 3.882888 TGTGGACAGCCTTTCTTAAAGTG 59.117 43.478 0.00 0.00 36.77 3.16
410 413 3.253432 GTGGACAGCCTTTCTTAAAGTGG 59.747 47.826 0.00 0.00 36.77 4.00
411 414 3.117663 TGGACAGCCTTTCTTAAAGTGGT 60.118 43.478 0.00 0.00 36.77 4.16
412 415 3.502595 GGACAGCCTTTCTTAAAGTGGTC 59.497 47.826 0.00 0.00 36.77 4.02
413 416 4.390264 GACAGCCTTTCTTAAAGTGGTCT 58.610 43.478 0.00 0.00 36.77 3.85
414 417 4.390264 ACAGCCTTTCTTAAAGTGGTCTC 58.610 43.478 0.00 0.00 36.77 3.36
415 418 4.103311 ACAGCCTTTCTTAAAGTGGTCTCT 59.897 41.667 0.00 0.00 36.77 3.10
416 419 4.693095 CAGCCTTTCTTAAAGTGGTCTCTC 59.307 45.833 0.00 0.00 36.77 3.20
417 420 4.595350 AGCCTTTCTTAAAGTGGTCTCTCT 59.405 41.667 0.00 0.00 36.77 3.10
418 421 5.072464 AGCCTTTCTTAAAGTGGTCTCTCTT 59.928 40.000 0.00 0.00 36.77 2.85
419 422 5.410132 GCCTTTCTTAAAGTGGTCTCTCTTC 59.590 44.000 0.00 0.00 36.77 2.87
420 423 6.742926 GCCTTTCTTAAAGTGGTCTCTCTTCT 60.743 42.308 0.00 0.00 36.77 2.85
421 424 7.220740 CCTTTCTTAAAGTGGTCTCTCTTCTT 58.779 38.462 0.00 0.00 36.77 2.52
422 425 7.717436 CCTTTCTTAAAGTGGTCTCTCTTCTTT 59.283 37.037 0.00 0.00 36.77 2.52
423 426 9.114952 CTTTCTTAAAGTGGTCTCTCTTCTTTT 57.885 33.333 0.00 0.00 33.80 2.27
1043 4670 3.412386 AGTTTGTTAGAGCTGCGGATTT 58.588 40.909 0.00 0.00 0.00 2.17
1229 4858 7.953158 AGAATATGTTGGACAGTATTGATCG 57.047 36.000 0.00 0.00 0.00 3.69
1536 5168 2.703798 CCGGCCCTGCATTCAAGTG 61.704 63.158 0.00 0.00 0.00 3.16
1537 5169 1.675310 CGGCCCTGCATTCAAGTGA 60.675 57.895 0.00 0.00 0.00 3.41
1546 5178 5.404946 CCTGCATTCAAGTGATTTTGGTAG 58.595 41.667 0.00 0.00 0.00 3.18
1562 5197 1.619160 GGTAGTCCCCTTCTTCGGTCT 60.619 57.143 0.00 0.00 0.00 3.85
1567 5202 0.820871 CCCCTTCTTCGGTCTGAGAG 59.179 60.000 0.00 0.00 0.00 3.20
1569 5204 2.383855 CCCTTCTTCGGTCTGAGAGAT 58.616 52.381 0.00 0.00 0.00 2.75
1573 5208 3.636153 TCTTCGGTCTGAGAGATCAGA 57.364 47.619 3.88 3.88 43.68 3.27
1589 5224 4.576463 AGATCAGACACACAAAAACTGGAC 59.424 41.667 0.00 0.00 0.00 4.02
1598 5233 0.822121 AAAAACTGGACCCTGACGGC 60.822 55.000 0.00 0.00 33.26 5.68
1624 5259 2.281484 GCCACAGGCTCGGTCAAA 60.281 61.111 0.00 0.00 46.69 2.69
1625 5260 1.896660 GCCACAGGCTCGGTCAAAA 60.897 57.895 0.00 0.00 46.69 2.44
1689 5324 4.314740 TTTGGACTGGAAATTTGGAACG 57.685 40.909 0.00 0.00 0.00 3.95
1692 5327 2.488153 GGACTGGAAATTTGGAACGGAG 59.512 50.000 0.00 0.00 0.00 4.63
1693 5328 3.408634 GACTGGAAATTTGGAACGGAGA 58.591 45.455 0.00 0.00 0.00 3.71
1702 5337 6.442513 AATTTGGAACGGAGAGAATTCATC 57.557 37.500 8.44 5.22 0.00 2.92
1705 5340 3.515502 TGGAACGGAGAGAATTCATCAGT 59.484 43.478 8.44 9.13 0.00 3.41
1707 5342 4.568760 GGAACGGAGAGAATTCATCAGTTC 59.431 45.833 28.45 28.45 35.92 3.01
1718 5353 4.871933 TTCATCAGTTCTGCACTAGTCA 57.128 40.909 0.00 0.00 32.76 3.41
1722 5357 3.982475 TCAGTTCTGCACTAGTCAACAG 58.018 45.455 9.75 9.75 32.76 3.16
1729 5364 6.208988 TCTGCACTAGTCAACAGGTATAAG 57.791 41.667 14.15 0.00 0.00 1.73
1740 5375 8.147058 AGTCAACAGGTATAAGCTTGAGATATG 58.853 37.037 9.86 3.67 0.00 1.78
1751 5386 3.243569 GCTTGAGATATGTGAGCGGTACT 60.244 47.826 0.00 0.00 0.00 2.73
1816 5456 2.749621 GTGGTATCCTTGCTTCCAACAG 59.250 50.000 0.00 0.00 0.00 3.16
1842 5482 4.516323 TCGAGGCAATCATCTGAATGAAA 58.484 39.130 0.00 0.00 44.85 2.69
1849 5489 8.080417 AGGCAATCATCTGAATGAAAAATATCG 58.920 33.333 0.00 0.00 44.85 2.92
1853 5493 8.915057 ATCATCTGAATGAAAAATATCGTCCT 57.085 30.769 0.00 0.00 44.85 3.85
1854 5494 8.146479 TCATCTGAATGAAAAATATCGTCCTG 57.854 34.615 0.00 0.00 38.97 3.86
1857 5497 7.974675 TCTGAATGAAAAATATCGTCCTGTTC 58.025 34.615 0.00 0.00 0.00 3.18
1858 5498 7.824289 TCTGAATGAAAAATATCGTCCTGTTCT 59.176 33.333 0.00 0.00 0.00 3.01
1859 5499 7.974675 TGAATGAAAAATATCGTCCTGTTCTC 58.025 34.615 0.00 0.00 0.00 2.87
1862 5502 6.472887 TGAAAAATATCGTCCTGTTCTCCTT 58.527 36.000 0.00 0.00 0.00 3.36
1894 5534 1.599797 AGTTTGTGCCGGTACCTGC 60.600 57.895 20.66 20.46 0.00 4.85
1895 5535 2.281900 TTTGTGCCGGTACCTGCC 60.282 61.111 23.67 15.68 0.00 4.85
1897 5537 2.741486 TTTGTGCCGGTACCTGCCTC 62.741 60.000 23.67 16.95 0.00 4.70
1898 5538 3.391382 GTGCCGGTACCTGCCTCT 61.391 66.667 23.67 0.00 0.00 3.69
1899 5539 2.056223 GTGCCGGTACCTGCCTCTA 61.056 63.158 23.67 3.98 0.00 2.43
1900 5540 2.056223 TGCCGGTACCTGCCTCTAC 61.056 63.158 23.67 0.00 0.00 2.59
1901 5541 2.056223 GCCGGTACCTGCCTCTACA 61.056 63.158 16.93 0.00 0.00 2.74
1902 5542 1.400530 GCCGGTACCTGCCTCTACAT 61.401 60.000 16.93 0.00 0.00 2.29
1903 5543 0.674534 CCGGTACCTGCCTCTACATC 59.325 60.000 10.90 0.00 0.00 3.06
1904 5544 1.693627 CGGTACCTGCCTCTACATCT 58.306 55.000 10.90 0.00 0.00 2.90
1905 5545 1.338337 CGGTACCTGCCTCTACATCTG 59.662 57.143 10.90 0.00 0.00 2.90
1906 5546 2.667470 GGTACCTGCCTCTACATCTGA 58.333 52.381 4.06 0.00 0.00 3.27
1907 5547 3.235200 GGTACCTGCCTCTACATCTGAT 58.765 50.000 4.06 0.00 0.00 2.90
1908 5548 3.257127 GGTACCTGCCTCTACATCTGATC 59.743 52.174 4.06 0.00 0.00 2.92
1933 5573 3.303461 CGAACCGTCTGCAACAAAATGTA 60.303 43.478 0.00 0.00 0.00 2.29
1966 5606 5.061853 CCTGTAGATCTGCAGCACAAATAT 58.938 41.667 29.43 0.00 41.15 1.28
1976 5616 6.538381 TCTGCAGCACAAATATATTTCTTCGA 59.462 34.615 9.47 0.00 0.00 3.71
1981 5621 8.272176 CAGCACAAATATATTTCTTCGAGAGAC 58.728 37.037 7.76 0.00 41.84 3.36
2040 5680 7.038154 TGACAAGCAGTTAAACTTTAGCAAT 57.962 32.000 0.00 0.00 0.00 3.56
2041 5681 8.160521 TGACAAGCAGTTAAACTTTAGCAATA 57.839 30.769 0.00 0.00 0.00 1.90
2044 5684 9.981114 ACAAGCAGTTAAACTTTAGCAATAAAT 57.019 25.926 0.00 0.00 0.00 1.40
2075 5715 6.128526 GCTTACTGTATCTTCGAATATTGGCC 60.129 42.308 0.00 0.00 0.00 5.36
2087 5727 4.560513 CGAATATTGGCCAAACCTTTGTGT 60.561 41.667 24.71 4.81 40.22 3.72
2102 5742 3.726291 TTGTGTTGCTTAGGAAAAGCC 57.274 42.857 7.23 0.00 42.36 4.35
2135 5775 7.648908 CACAAGTTGCTCAAAATTTCACTGATA 59.351 33.333 1.81 0.00 0.00 2.15
2136 5776 8.196771 ACAAGTTGCTCAAAATTTCACTGATAA 58.803 29.630 1.81 0.00 0.00 1.75
2139 5779 8.416329 AGTTGCTCAAAATTTCACTGATAAAGT 58.584 29.630 0.00 0.00 40.93 2.66
2180 5820 4.070716 CAGCATCCCAAGTGATATTCCTC 58.929 47.826 0.00 0.00 0.00 3.71
2181 5821 3.718434 AGCATCCCAAGTGATATTCCTCA 59.282 43.478 0.00 0.00 0.00 3.86
2182 5822 4.070716 GCATCCCAAGTGATATTCCTCAG 58.929 47.826 0.00 0.00 0.00 3.35
2183 5823 4.445448 GCATCCCAAGTGATATTCCTCAGT 60.445 45.833 0.00 0.00 0.00 3.41
2184 5824 5.221722 GCATCCCAAGTGATATTCCTCAGTA 60.222 44.000 0.00 0.00 0.00 2.74
2185 5825 6.521427 GCATCCCAAGTGATATTCCTCAGTAT 60.521 42.308 0.00 0.00 0.00 2.12
2186 5826 7.310671 GCATCCCAAGTGATATTCCTCAGTATA 60.311 40.741 0.00 0.00 0.00 1.47
2187 5827 7.782897 TCCCAAGTGATATTCCTCAGTATAG 57.217 40.000 0.00 0.00 0.00 1.31
2188 5828 6.211584 TCCCAAGTGATATTCCTCAGTATAGC 59.788 42.308 0.00 0.00 0.00 2.97
2189 5829 6.212388 CCCAAGTGATATTCCTCAGTATAGCT 59.788 42.308 0.00 0.00 0.00 3.32
2197 5837 5.961396 TTCCTCAGTATAGCTCGGTATTC 57.039 43.478 0.00 0.00 0.00 1.75
2200 5840 4.156922 CCTCAGTATAGCTCGGTATTCCTG 59.843 50.000 0.00 2.64 0.00 3.86
2212 5852 2.106684 GGTATTCCTGACATTCCCCTCC 59.893 54.545 0.00 0.00 0.00 4.30
2213 5853 2.293598 ATTCCTGACATTCCCCTCCT 57.706 50.000 0.00 0.00 0.00 3.69
2214 5854 1.289160 TTCCTGACATTCCCCTCCTG 58.711 55.000 0.00 0.00 0.00 3.86
2215 5855 0.621571 TCCTGACATTCCCCTCCTGG 60.622 60.000 0.00 0.00 0.00 4.45
2216 5856 0.621571 CCTGACATTCCCCTCCTGGA 60.622 60.000 0.00 0.00 35.39 3.86
2219 5859 1.354368 TGACATTCCCCTCCTGGAAAC 59.646 52.381 0.00 0.00 46.99 2.78
2220 5860 1.636003 GACATTCCCCTCCTGGAAACT 59.364 52.381 0.00 0.00 46.99 2.66
2222 5862 0.912486 ATTCCCCTCCTGGAAACTCG 59.088 55.000 0.00 0.00 46.99 4.18
2223 5863 1.198759 TTCCCCTCCTGGAAACTCGG 61.199 60.000 0.00 0.00 41.40 4.63
2224 5864 2.269241 CCCTCCTGGAAACTCGGC 59.731 66.667 0.00 0.00 35.39 5.54
2227 5872 0.036875 CCTCCTGGAAACTCGGCTTT 59.963 55.000 0.00 0.00 34.57 3.51
2233 5878 1.202830 TGGAAACTCGGCTTTAAGGCA 60.203 47.619 18.35 5.12 41.44 4.75
2241 5886 1.676014 CGGCTTTAAGGCAGCTACAGT 60.676 52.381 18.35 0.00 41.44 3.55
2254 5899 2.297597 AGCTACAGTTGCGATATCCCTC 59.702 50.000 1.05 0.00 35.28 4.30
2287 5932 0.668401 GCTTGTGGCCATTGCTTGTC 60.668 55.000 9.72 0.00 37.74 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
105 106 2.552802 GCAGCTGCAAGTGATGAGT 58.447 52.632 33.36 0.00 41.59 3.41
165 166 7.939039 TCTTGTTAGTTCTTTTCTGATGACCAT 59.061 33.333 0.00 0.00 0.00 3.55
318 321 2.688477 GACTCCTGAGATTGAGGGGAT 58.312 52.381 0.22 0.00 34.28 3.85
319 322 1.686428 CGACTCCTGAGATTGAGGGGA 60.686 57.143 0.22 0.00 34.28 4.81
320 323 0.749649 CGACTCCTGAGATTGAGGGG 59.250 60.000 0.22 0.00 37.08 4.79
321 324 0.103937 GCGACTCCTGAGATTGAGGG 59.896 60.000 0.22 0.00 32.80 4.30
322 325 1.110442 AGCGACTCCTGAGATTGAGG 58.890 55.000 0.22 0.00 32.80 3.86
323 326 2.957491 AAGCGACTCCTGAGATTGAG 57.043 50.000 0.22 0.00 34.73 3.02
324 327 2.828520 AGAAAGCGACTCCTGAGATTGA 59.171 45.455 0.22 0.00 0.00 2.57
325 328 3.119173 AGAGAAAGCGACTCCTGAGATTG 60.119 47.826 0.22 0.00 35.27 2.67
326 329 3.096092 AGAGAAAGCGACTCCTGAGATT 58.904 45.455 0.22 0.00 35.27 2.40
327 330 2.733956 AGAGAAAGCGACTCCTGAGAT 58.266 47.619 0.22 0.00 35.27 2.75
328 331 2.208132 AGAGAAAGCGACTCCTGAGA 57.792 50.000 0.22 0.00 35.27 3.27
329 332 3.795150 GCATAGAGAAAGCGACTCCTGAG 60.795 52.174 0.00 0.00 35.27 3.35
330 333 2.099921 GCATAGAGAAAGCGACTCCTGA 59.900 50.000 0.00 0.00 35.27 3.86
331 334 2.468831 GCATAGAGAAAGCGACTCCTG 58.531 52.381 0.00 0.00 35.27 3.86
332 335 1.410882 GGCATAGAGAAAGCGACTCCT 59.589 52.381 0.00 0.00 35.27 3.69
333 336 1.539280 GGGCATAGAGAAAGCGACTCC 60.539 57.143 0.00 0.00 35.27 3.85
334 337 1.859383 GGGCATAGAGAAAGCGACTC 58.141 55.000 0.00 0.00 34.95 3.36
335 338 0.103208 CGGGCATAGAGAAAGCGACT 59.897 55.000 0.00 0.00 0.00 4.18
336 339 0.102481 TCGGGCATAGAGAAAGCGAC 59.898 55.000 0.00 0.00 0.00 5.19
337 340 0.102481 GTCGGGCATAGAGAAAGCGA 59.898 55.000 0.00 0.00 0.00 4.93
338 341 0.103208 AGTCGGGCATAGAGAAAGCG 59.897 55.000 0.00 0.00 0.00 4.68
339 342 2.317530 AAGTCGGGCATAGAGAAAGC 57.682 50.000 0.00 0.00 0.00 3.51
340 343 3.066342 TCGTAAGTCGGGCATAGAGAAAG 59.934 47.826 0.00 0.00 40.32 2.62
341 344 3.018856 TCGTAAGTCGGGCATAGAGAAA 58.981 45.455 0.00 0.00 40.32 2.52
342 345 2.617308 CTCGTAAGTCGGGCATAGAGAA 59.383 50.000 0.00 0.00 40.32 2.87
343 346 2.219458 CTCGTAAGTCGGGCATAGAGA 58.781 52.381 0.00 0.00 40.32 3.10
344 347 2.690173 CTCGTAAGTCGGGCATAGAG 57.310 55.000 0.00 0.00 40.32 2.43
351 354 1.630148 CAAAGAGCTCGTAAGTCGGG 58.370 55.000 8.37 0.00 43.80 5.14
352 355 0.992802 GCAAAGAGCTCGTAAGTCGG 59.007 55.000 8.37 0.00 41.15 4.79
370 373 3.118542 CCACAAAAGAAGTTGCTCAAGC 58.881 45.455 0.00 0.00 42.50 4.01
371 374 4.142403 TGTCCACAAAAGAAGTTGCTCAAG 60.142 41.667 0.00 0.00 31.29 3.02
372 375 3.761218 TGTCCACAAAAGAAGTTGCTCAA 59.239 39.130 0.00 0.00 31.29 3.02
373 376 3.351740 TGTCCACAAAAGAAGTTGCTCA 58.648 40.909 0.00 0.00 31.29 4.26
374 377 3.793465 GCTGTCCACAAAAGAAGTTGCTC 60.793 47.826 0.00 0.00 31.29 4.26
375 378 2.099756 GCTGTCCACAAAAGAAGTTGCT 59.900 45.455 0.00 0.00 31.29 3.91
376 379 2.463876 GCTGTCCACAAAAGAAGTTGC 58.536 47.619 0.00 0.00 31.29 4.17
377 380 2.689983 AGGCTGTCCACAAAAGAAGTTG 59.310 45.455 0.00 0.00 33.74 3.16
378 381 3.018423 AGGCTGTCCACAAAAGAAGTT 57.982 42.857 0.00 0.00 33.74 2.66
379 382 2.736670 AGGCTGTCCACAAAAGAAGT 57.263 45.000 0.00 0.00 33.74 3.01
380 383 3.633986 AGAAAGGCTGTCCACAAAAGAAG 59.366 43.478 0.00 0.00 33.74 2.85
381 384 3.631250 AGAAAGGCTGTCCACAAAAGAA 58.369 40.909 0.00 0.00 33.74 2.52
382 385 3.297134 AGAAAGGCTGTCCACAAAAGA 57.703 42.857 0.00 0.00 33.74 2.52
383 386 5.514274 TTAAGAAAGGCTGTCCACAAAAG 57.486 39.130 0.00 0.00 33.74 2.27
384 387 5.420739 ACTTTAAGAAAGGCTGTCCACAAAA 59.579 36.000 0.00 0.00 42.82 2.44
385 388 4.953579 ACTTTAAGAAAGGCTGTCCACAAA 59.046 37.500 0.00 0.00 42.82 2.83
386 389 4.338118 CACTTTAAGAAAGGCTGTCCACAA 59.662 41.667 0.00 0.00 42.82 3.33
387 390 3.882888 CACTTTAAGAAAGGCTGTCCACA 59.117 43.478 0.00 0.00 42.82 4.17
388 391 3.253432 CCACTTTAAGAAAGGCTGTCCAC 59.747 47.826 0.00 0.00 42.82 4.02
389 392 3.117663 ACCACTTTAAGAAAGGCTGTCCA 60.118 43.478 0.00 0.00 42.82 4.02
390 393 3.487372 ACCACTTTAAGAAAGGCTGTCC 58.513 45.455 0.00 0.00 42.82 4.02
391 394 4.390264 AGACCACTTTAAGAAAGGCTGTC 58.610 43.478 0.00 0.00 42.82 3.51
392 395 4.103311 AGAGACCACTTTAAGAAAGGCTGT 59.897 41.667 0.00 0.00 42.82 4.40
393 396 4.646572 AGAGACCACTTTAAGAAAGGCTG 58.353 43.478 0.00 0.00 42.82 4.85
394 397 4.595350 AGAGAGACCACTTTAAGAAAGGCT 59.405 41.667 0.00 0.00 42.82 4.58
395 398 4.900684 AGAGAGACCACTTTAAGAAAGGC 58.099 43.478 0.00 0.00 42.82 4.35
396 399 6.764379 AGAAGAGAGACCACTTTAAGAAAGG 58.236 40.000 0.00 0.27 42.82 3.11
397 400 8.669946 AAAGAAGAGAGACCACTTTAAGAAAG 57.330 34.615 0.00 0.00 44.10 2.62
402 405 8.784043 GCATTAAAAGAAGAGAGACCACTTTAA 58.216 33.333 0.00 0.00 31.86 1.52
403 406 7.936847 TGCATTAAAAGAAGAGAGACCACTTTA 59.063 33.333 0.00 0.00 31.86 1.85
404 407 6.772716 TGCATTAAAAGAAGAGAGACCACTTT 59.227 34.615 0.00 0.00 33.18 2.66
405 408 6.299141 TGCATTAAAAGAAGAGAGACCACTT 58.701 36.000 0.00 0.00 0.00 3.16
406 409 5.869579 TGCATTAAAAGAAGAGAGACCACT 58.130 37.500 0.00 0.00 0.00 4.00
407 410 5.703130 ACTGCATTAAAAGAAGAGAGACCAC 59.297 40.000 0.00 0.00 0.00 4.16
408 411 5.869579 ACTGCATTAAAAGAAGAGAGACCA 58.130 37.500 0.00 0.00 0.00 4.02
409 412 6.428159 TCAACTGCATTAAAAGAAGAGAGACC 59.572 38.462 0.00 0.00 0.00 3.85
410 413 7.360776 CCTCAACTGCATTAAAAGAAGAGAGAC 60.361 40.741 0.00 0.00 0.00 3.36
411 414 6.652481 CCTCAACTGCATTAAAAGAAGAGAGA 59.348 38.462 0.00 0.00 0.00 3.10
412 415 6.652481 TCCTCAACTGCATTAAAAGAAGAGAG 59.348 38.462 0.00 0.00 0.00 3.20
413 416 6.533730 TCCTCAACTGCATTAAAAGAAGAGA 58.466 36.000 0.00 0.00 0.00 3.10
414 417 6.808008 TCCTCAACTGCATTAAAAGAAGAG 57.192 37.500 0.00 0.00 0.00 2.85
415 418 7.581213 TTTCCTCAACTGCATTAAAAGAAGA 57.419 32.000 0.00 0.00 0.00 2.87
416 419 8.822652 ATTTTCCTCAACTGCATTAAAAGAAG 57.177 30.769 0.00 0.00 0.00 2.85
417 420 9.044150 CAATTTTCCTCAACTGCATTAAAAGAA 57.956 29.630 0.00 0.00 0.00 2.52
418 421 8.203485 ACAATTTTCCTCAACTGCATTAAAAGA 58.797 29.630 0.00 0.00 0.00 2.52
419 422 8.277713 CACAATTTTCCTCAACTGCATTAAAAG 58.722 33.333 0.00 0.00 0.00 2.27
420 423 7.254727 GCACAATTTTCCTCAACTGCATTAAAA 60.255 33.333 0.00 0.00 0.00 1.52
421 424 6.202570 GCACAATTTTCCTCAACTGCATTAAA 59.797 34.615 0.00 0.00 0.00 1.52
422 425 5.695816 GCACAATTTTCCTCAACTGCATTAA 59.304 36.000 0.00 0.00 0.00 1.40
423 426 5.229423 GCACAATTTTCCTCAACTGCATTA 58.771 37.500 0.00 0.00 0.00 1.90
1229 4858 6.453265 CGCAAAATCATCAATGACAATGTCAC 60.453 38.462 19.17 0.12 45.65 3.67
1269 4898 6.183360 CCAGAATTCATGAGAAGCGAGATTTT 60.183 38.462 8.44 0.00 37.14 1.82
1536 5168 3.939592 CGAAGAAGGGGACTACCAAAATC 59.060 47.826 0.00 0.00 42.68 2.17
1537 5169 3.308188 CCGAAGAAGGGGACTACCAAAAT 60.308 47.826 0.00 0.00 42.68 1.82
1546 5178 0.533032 CTCAGACCGAAGAAGGGGAC 59.467 60.000 0.00 0.00 35.02 4.46
1562 5197 5.525012 CAGTTTTTGTGTGTCTGATCTCTCA 59.475 40.000 0.00 0.00 0.00 3.27
1567 5202 4.261197 GGTCCAGTTTTTGTGTGTCTGATC 60.261 45.833 0.00 0.00 0.00 2.92
1569 5204 3.013921 GGTCCAGTTTTTGTGTGTCTGA 58.986 45.455 0.00 0.00 0.00 3.27
1573 5208 2.099405 CAGGGTCCAGTTTTTGTGTGT 58.901 47.619 0.00 0.00 0.00 3.72
1589 5224 0.109132 GCTCAAAATTGCCGTCAGGG 60.109 55.000 0.00 0.00 38.20 4.45
1612 5247 5.070685 ACTTCTTTAATTTTGACCGAGCCT 58.929 37.500 0.00 0.00 0.00 4.58
1613 5248 5.372547 ACTTCTTTAATTTTGACCGAGCC 57.627 39.130 0.00 0.00 0.00 4.70
1614 5249 6.915843 TCAAACTTCTTTAATTTTGACCGAGC 59.084 34.615 0.00 0.00 38.56 5.03
1615 5250 8.850454 TTCAAACTTCTTTAATTTTGACCGAG 57.150 30.769 3.91 0.00 41.32 4.63
1616 5251 9.810545 ATTTCAAACTTCTTTAATTTTGACCGA 57.189 25.926 3.91 0.00 41.32 4.69
1653 5288 9.581289 TTCCAGTCCAAATTAATCAAACTTCTA 57.419 29.630 0.00 0.00 0.00 2.10
1659 5294 9.282569 CCAAATTTCCAGTCCAAATTAATCAAA 57.717 29.630 0.00 0.00 33.24 2.69
1661 5296 8.200024 TCCAAATTTCCAGTCCAAATTAATCA 57.800 30.769 0.00 0.00 33.24 2.57
1674 5309 3.674997 TCTCTCCGTTCCAAATTTCCAG 58.325 45.455 0.00 0.00 0.00 3.86
1689 5324 4.332268 GTGCAGAACTGATGAATTCTCTCC 59.668 45.833 7.05 0.00 32.77 3.71
1692 5327 6.105333 ACTAGTGCAGAACTGATGAATTCTC 58.895 40.000 7.05 2.78 40.26 2.87
1693 5328 6.047511 ACTAGTGCAGAACTGATGAATTCT 57.952 37.500 7.05 0.00 40.26 2.40
1702 5337 3.062763 CCTGTTGACTAGTGCAGAACTG 58.937 50.000 16.02 10.09 40.26 3.16
1705 5340 6.599356 TTATACCTGTTGACTAGTGCAGAA 57.401 37.500 16.02 7.67 0.00 3.02
1707 5342 4.806247 GCTTATACCTGTTGACTAGTGCAG 59.194 45.833 0.00 5.93 0.00 4.41
1718 5353 8.023021 TCACATATCTCAAGCTTATACCTGTT 57.977 34.615 0.00 0.00 0.00 3.16
1722 5357 5.574830 CGCTCACATATCTCAAGCTTATACC 59.425 44.000 0.00 0.00 0.00 2.73
1729 5364 2.231215 ACCGCTCACATATCTCAAGC 57.769 50.000 0.00 0.00 0.00 4.01
1740 5375 0.796927 GCTGGAAAAGTACCGCTCAC 59.203 55.000 0.00 0.00 0.00 3.51
1751 5386 0.773644 AGAGAAGCCCTGCTGGAAAA 59.226 50.000 11.88 0.00 39.62 2.29
1816 5456 5.237996 TCATTCAGATGATTGCCTCGATTTC 59.762 40.000 0.00 0.00 37.37 2.17
1868 5508 2.028130 ACCGGCACAAACTGAAAATGA 58.972 42.857 0.00 0.00 0.00 2.57
1894 5534 3.551863 GGTTCGCAGATCAGATGTAGAGG 60.552 52.174 0.00 0.00 35.04 3.69
1895 5535 3.637432 GGTTCGCAGATCAGATGTAGAG 58.363 50.000 0.00 0.00 35.04 2.43
1897 5537 2.223595 ACGGTTCGCAGATCAGATGTAG 60.224 50.000 0.00 0.00 35.04 2.74
1898 5538 1.749063 ACGGTTCGCAGATCAGATGTA 59.251 47.619 0.00 0.00 35.04 2.29
1899 5539 0.532573 ACGGTTCGCAGATCAGATGT 59.467 50.000 0.00 0.00 35.04 3.06
1900 5540 1.202348 AGACGGTTCGCAGATCAGATG 60.202 52.381 0.00 0.00 35.04 2.90
1901 5541 1.107114 AGACGGTTCGCAGATCAGAT 58.893 50.000 0.00 0.00 35.04 2.90
1902 5542 0.171231 CAGACGGTTCGCAGATCAGA 59.829 55.000 0.00 0.00 35.04 3.27
1903 5543 1.416813 GCAGACGGTTCGCAGATCAG 61.417 60.000 0.00 0.00 35.04 2.90
1904 5544 1.446099 GCAGACGGTTCGCAGATCA 60.446 57.895 0.00 0.00 35.04 2.92
1905 5545 1.014044 TTGCAGACGGTTCGCAGATC 61.014 55.000 5.70 0.00 35.04 2.75
1906 5546 1.005037 TTGCAGACGGTTCGCAGAT 60.005 52.632 5.70 0.00 35.04 2.90
1907 5547 1.954146 GTTGCAGACGGTTCGCAGA 60.954 57.895 5.70 0.00 34.34 4.26
1908 5548 1.771073 TTGTTGCAGACGGTTCGCAG 61.771 55.000 5.70 0.00 34.34 5.18
1933 5573 4.652881 TGCAGATCTACAGGAATCAGTGAT 59.347 41.667 0.00 0.00 0.00 3.06
1976 5616 6.098838 TGCCTGTATATGTTCTTCATGTCTCT 59.901 38.462 0.00 0.00 37.91 3.10
1981 5621 5.999600 TCCATGCCTGTATATGTTCTTCATG 59.000 40.000 0.00 0.00 37.91 3.07
2041 5681 8.958119 TCGAAGATACAGTAAGCCATAAATTT 57.042 30.769 0.00 0.00 0.00 1.82
2064 5704 3.925913 CACAAAGGTTTGGCCAATATTCG 59.074 43.478 21.26 9.26 42.34 3.34
2075 5715 4.647424 TCCTAAGCAACACAAAGGTTTG 57.353 40.909 0.77 0.77 43.62 2.93
2087 5727 0.538516 TGCCGGCTTTTCCTAAGCAA 60.539 50.000 29.70 0.00 44.71 3.91
2125 5765 7.318141 CCTCGGTTAGTACTTTATCAGTGAAA 58.682 38.462 0.00 0.00 35.97 2.69
2128 5768 5.041940 GCCTCGGTTAGTACTTTATCAGTG 58.958 45.833 0.00 0.00 35.97 3.66
2135 5775 3.518590 CATTCGCCTCGGTTAGTACTTT 58.481 45.455 0.00 0.00 0.00 2.66
2136 5776 2.737679 GCATTCGCCTCGGTTAGTACTT 60.738 50.000 0.00 0.00 0.00 2.24
2139 5779 3.654178 GCATTCGCCTCGGTTAGTA 57.346 52.632 0.00 0.00 0.00 1.82
2180 5820 4.519350 TGTCAGGAATACCGAGCTATACTG 59.481 45.833 0.00 0.00 41.83 2.74
2181 5821 4.726583 TGTCAGGAATACCGAGCTATACT 58.273 43.478 0.00 0.00 41.83 2.12
2182 5822 5.646577 ATGTCAGGAATACCGAGCTATAC 57.353 43.478 0.00 0.00 41.83 1.47
2183 5823 5.185249 GGAATGTCAGGAATACCGAGCTATA 59.815 44.000 0.00 0.00 41.83 1.31
2184 5824 4.021016 GGAATGTCAGGAATACCGAGCTAT 60.021 45.833 0.00 0.00 41.83 2.97
2185 5825 3.321111 GGAATGTCAGGAATACCGAGCTA 59.679 47.826 0.00 0.00 41.83 3.32
2186 5826 2.103263 GGAATGTCAGGAATACCGAGCT 59.897 50.000 0.00 0.00 41.83 4.09
2187 5827 2.484889 GGAATGTCAGGAATACCGAGC 58.515 52.381 0.00 0.00 41.83 5.03
2188 5828 2.224305 GGGGAATGTCAGGAATACCGAG 60.224 54.545 0.00 0.00 41.83 4.63
2189 5829 1.766496 GGGGAATGTCAGGAATACCGA 59.234 52.381 0.00 0.00 41.83 4.69
2197 5837 0.621571 TCCAGGAGGGGAATGTCAGG 60.622 60.000 0.00 0.00 37.22 3.86
2200 5840 1.636003 AGTTTCCAGGAGGGGAATGTC 59.364 52.381 0.00 0.00 45.90 3.06
2212 5852 1.468914 GCCTTAAAGCCGAGTTTCCAG 59.531 52.381 0.00 0.00 0.00 3.86
2213 5853 1.202830 TGCCTTAAAGCCGAGTTTCCA 60.203 47.619 0.00 0.00 0.00 3.53
2214 5854 1.468914 CTGCCTTAAAGCCGAGTTTCC 59.531 52.381 0.00 0.00 0.00 3.13
2215 5855 1.135660 GCTGCCTTAAAGCCGAGTTTC 60.136 52.381 0.00 0.00 34.45 2.78
2216 5856 0.881796 GCTGCCTTAAAGCCGAGTTT 59.118 50.000 0.00 0.00 34.45 2.66
2219 5859 1.291132 GTAGCTGCCTTAAAGCCGAG 58.709 55.000 0.00 0.00 41.82 4.63
2220 5860 0.611200 TGTAGCTGCCTTAAAGCCGA 59.389 50.000 0.00 0.00 41.82 5.54
2222 5862 2.115343 ACTGTAGCTGCCTTAAAGCC 57.885 50.000 0.00 0.00 41.82 4.35
2223 5863 2.414691 GCAACTGTAGCTGCCTTAAAGC 60.415 50.000 0.00 0.00 41.15 3.51
2224 5864 2.159653 CGCAACTGTAGCTGCCTTAAAG 60.160 50.000 0.00 0.00 33.87 1.85
2227 5872 0.606096 TCGCAACTGTAGCTGCCTTA 59.394 50.000 0.00 0.00 33.87 2.69
2233 5878 2.297597 GAGGGATATCGCAACTGTAGCT 59.702 50.000 20.64 0.00 0.00 3.32
2241 5886 1.616865 CCTTACCGAGGGATATCGCAA 59.383 52.381 20.64 6.03 42.26 4.85
2254 5899 1.539827 CACAAGCCTTTTCCCTTACCG 59.460 52.381 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.