Multiple sequence alignment - TraesCS1B01G018300

Loading Multiple Alignment...

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 TraesCS1B01G018300 chr1B 100.000 4542 0 0 1 4542 8820921 8816380 0.000000e+00 8388.0
1 TraesCS1B01G018300 chr1B 83.518 2706 352 49 1000 3671 548193684 548191039 0.000000e+00 2440.0
2 TraesCS1B01G018300 chr1B 84.298 242 23 9 498 737 548193667 548193439 5.910000e-54 222.0
3 TraesCS1B01G018300 chr1B 95.745 47 1 1 577 622 548198257 548198303 1.750000e-09 75.0
4 TraesCS1B01G018300 chr1D 95.955 3609 129 11 948 4542 6913108 6916713 0.000000e+00 5840.0
5 TraesCS1B01G018300 chr1D 84.312 2709 342 53 1000 3671 407672543 407669881 0.000000e+00 2571.0
6 TraesCS1B01G018300 chr1D 82.116 2807 393 65 960 3708 6714654 6711899 0.000000e+00 2302.0
7 TraesCS1B01G018300 chr1D 85.000 240 25 4 498 737 407672526 407672298 2.730000e-57 233.0
8 TraesCS1B01G018300 chr1D 90.066 151 14 1 345 494 463381915 463382065 1.290000e-45 195.0
9 TraesCS1B01G018300 chr1D 93.617 47 2 1 577 622 6900092 6900046 8.150000e-08 69.4
10 TraesCS1B01G018300 chr1A 91.770 2734 214 5 820 3542 8341863 8344596 0.000000e+00 3792.0
11 TraesCS1B01G018300 chr1A 91.262 2701 221 9 853 3541 8331799 8334496 0.000000e+00 3666.0
12 TraesCS1B01G018300 chr1A 81.927 2750 420 50 995 3708 7834679 7837387 0.000000e+00 2254.0
13 TraesCS1B01G018300 chr1A 86.885 305 21 10 498 797 8340222 8340512 1.580000e-84 324.0
14 TraesCS1B01G018300 chr1A 82.008 239 26 9 498 733 7834701 7834925 2.160000e-43 187.0
15 TraesCS1B01G018300 chr1A 83.077 195 21 5 109 302 8339155 8339338 2.810000e-37 167.0
16 TraesCS1B01G018300 chr1A 78.455 246 33 11 498 737 9375631 9375400 4.740000e-30 143.0
17 TraesCS1B01G018300 chr1A 85.393 89 9 4 3781 3868 8141675 8141590 6.260000e-14 89.8
18 TraesCS1B01G018300 chr1A 91.489 47 3 1 577 622 7189841 7189887 3.790000e-06 63.9
19 TraesCS1B01G018300 chr2A 84.880 2672 359 32 907 3546 611302729 611305387 0.000000e+00 2654.0
20 TraesCS1B01G018300 chr2B 84.833 2657 350 35 924 3546 548623904 548626541 0.000000e+00 2625.0
21 TraesCS1B01G018300 chr2B 93.617 47 2 1 577 622 729768229 729768183 8.150000e-08 69.4
22 TraesCS1B01G018300 chr2D 84.618 2659 361 33 924 3546 469990501 469993147 0.000000e+00 2601.0
23 TraesCS1B01G018300 chr2D 81.595 2809 405 66 912 3664 469983939 469986691 0.000000e+00 2220.0
24 TraesCS1B01G018300 chr2D 90.000 150 15 0 345 494 419068135 419068284 1.290000e-45 195.0
25 TraesCS1B01G018300 chr5A 83.221 2813 387 50 1000 3776 12194215 12191452 0.000000e+00 2501.0
26 TraesCS1B01G018300 chr5A 94.737 114 6 0 624 737 12194083 12193970 1.300000e-40 178.0
27 TraesCS1B01G018300 chr5A 89.583 48 4 1 577 623 12192585 12192632 4.910000e-05 60.2
28 TraesCS1B01G018300 chr5B 82.868 2831 396 54 993 3785 13776139 13773360 0.000000e+00 2459.0
29 TraesCS1B01G018300 chr5B 80.591 237 33 9 498 733 13776115 13775891 2.170000e-38 171.0
30 TraesCS1B01G018300 chr5B 87.719 114 14 0 624 737 546145768 546145655 2.850000e-27 134.0
31 TraesCS1B01G018300 chr5B 93.617 47 2 1 577 622 549549608 549549562 8.150000e-08 69.4
32 TraesCS1B01G018300 chr7B 92.361 144 11 0 351 494 618428269 618428126 5.960000e-49 206.0
33 TraesCS1B01G018300 chr5D 92.361 144 11 0 351 494 383645468 383645325 5.960000e-49 206.0
34 TraesCS1B01G018300 chr5D 91.837 147 9 2 351 494 558575637 558575783 7.700000e-48 202.0
35 TraesCS1B01G018300 chr5D 79.512 205 25 8 498 699 18083694 18083884 3.690000e-26 130.0
36 TraesCS1B01G018300 chr5D 91.489 47 3 1 577 622 447107380 447107334 3.790000e-06 63.9
37 TraesCS1B01G018300 chr7D 90.667 150 14 0 345 494 530857985 530858134 2.770000e-47 200.0
38 TraesCS1B01G018300 chr3D 90.667 150 14 0 345 494 137981490 137981639 2.770000e-47 200.0
39 TraesCS1B01G018300 chr3D 90.667 150 14 0 345 494 200383828 200383977 2.770000e-47 200.0
40 TraesCS1B01G018300 chr3D 91.034 145 12 1 351 494 537154847 537154703 1.290000e-45 195.0


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 TraesCS1B01G018300 chr1B 8816380 8820921 4541 True 8388.000000 8388 100.0000 1 4542 1 chr1B.!!$R1 4541
1 TraesCS1B01G018300 chr1B 548191039 548193684 2645 True 1331.000000 2440 83.9080 498 3671 2 chr1B.!!$R2 3173
2 TraesCS1B01G018300 chr1D 6913108 6916713 3605 False 5840.000000 5840 95.9550 948 4542 1 chr1D.!!$F1 3594
3 TraesCS1B01G018300 chr1D 6711899 6714654 2755 True 2302.000000 2302 82.1160 960 3708 1 chr1D.!!$R1 2748
4 TraesCS1B01G018300 chr1D 407669881 407672543 2662 True 1402.000000 2571 84.6560 498 3671 2 chr1D.!!$R3 3173
5 TraesCS1B01G018300 chr1A 8331799 8334496 2697 False 3666.000000 3666 91.2620 853 3541 1 chr1A.!!$F2 2688
6 TraesCS1B01G018300 chr1A 8339155 8344596 5441 False 1427.666667 3792 87.2440 109 3542 3 chr1A.!!$F4 3433
7 TraesCS1B01G018300 chr1A 7834679 7837387 2708 False 1220.500000 2254 81.9675 498 3708 2 chr1A.!!$F3 3210
8 TraesCS1B01G018300 chr2A 611302729 611305387 2658 False 2654.000000 2654 84.8800 907 3546 1 chr2A.!!$F1 2639
9 TraesCS1B01G018300 chr2B 548623904 548626541 2637 False 2625.000000 2625 84.8330 924 3546 1 chr2B.!!$F1 2622
10 TraesCS1B01G018300 chr2D 469983939 469993147 9208 False 2410.500000 2601 83.1065 912 3664 2 chr2D.!!$F2 2752
11 TraesCS1B01G018300 chr5A 12191452 12194215 2763 True 1339.500000 2501 88.9790 624 3776 2 chr5A.!!$R1 3152
12 TraesCS1B01G018300 chr5B 13773360 13776139 2779 True 1315.000000 2459 81.7295 498 3785 2 chr5B.!!$R3 3287

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
525 564 0.036022 GGCTTCTCCTCTTGCACACT 59.964 55.0 0.00 0.00 0.00 3.55 F
573 612 0.179076 ATGATGACATTCTCGCGGCA 60.179 50.0 6.13 0.00 32.21 5.69 F
1492 7155 0.030101 CGGAAACCTTGCGCTCAAAA 59.970 50.0 9.73 0.00 37.76 2.44 F
1581 7250 0.461961 CAAAGTTTGGCCGGGACAAA 59.538 50.0 23.98 23.98 38.31 2.83 F
3127 8827 0.625849 CTGTGGGTTATCTTGCCCCT 59.374 55.0 0.00 0.00 44.20 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1492 7155 0.692419 AGGTCGGATGATGGGCTCTT 60.692 55.000 0.0 0.0 0.00 2.85 R
2230 7920 1.336240 ACAAGCTTCTTCGCATTTGCC 60.336 47.619 0.0 0.0 37.91 4.52 R
3167 8867 0.393808 ACCATGCCGAAGCCGTAAAT 60.394 50.000 0.0 0.0 38.69 1.40 R
3244 8944 1.972872 AGTTACTGTTGCTGCTGCTT 58.027 45.000 17.0 0.0 40.48 3.91 R
4502 10234 1.277273 CCTCAGCACATGACCTCTTGA 59.723 52.381 0.0 0.0 33.22 3.02 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 7.778470 AGGCGAAATAGAATCAACTAAGAAG 57.222 36.000 0.00 0.00 0.00 2.85
27 28 8.451748 GGCGAAATAGAATCAACTAAGAAGTTT 58.548 33.333 0.00 0.00 43.60 2.66
28 29 9.827411 GCGAAATAGAATCAACTAAGAAGTTTT 57.173 29.630 0.00 0.00 43.60 2.43
38 39 8.810990 TCAACTAAGAAGTTTTAAACAAGGGA 57.189 30.769 10.60 0.66 43.60 4.20
39 40 8.680001 TCAACTAAGAAGTTTTAAACAAGGGAC 58.320 33.333 10.60 0.00 43.60 4.46
40 41 8.683615 CAACTAAGAAGTTTTAAACAAGGGACT 58.316 33.333 10.60 0.00 43.60 3.85
41 42 9.910267 AACTAAGAAGTTTTAAACAAGGGACTA 57.090 29.630 10.60 0.00 43.60 2.59
55 56 8.533569 AACAAGGGACTAAAAAGAAAAGATGA 57.466 30.769 0.00 0.00 38.49 2.92
56 57 8.533569 ACAAGGGACTAAAAAGAAAAGATGAA 57.466 30.769 0.00 0.00 38.49 2.57
58 59 9.987272 CAAGGGACTAAAAAGAAAAGATGAATT 57.013 29.630 0.00 0.00 38.49 2.17
74 75 8.970859 AAGATGAATTAATCAGTCTAACAGGG 57.029 34.615 5.56 0.00 42.53 4.45
76 77 6.636454 TGAATTAATCAGTCTAACAGGGGT 57.364 37.500 0.00 0.00 33.04 4.95
77 78 7.027874 TGAATTAATCAGTCTAACAGGGGTT 57.972 36.000 0.00 0.00 35.90 4.11
80 81 4.993705 AATCAGTCTAACAGGGGTTGAA 57.006 40.909 0.00 0.00 37.88 2.69
82 83 3.314693 TCAGTCTAACAGGGGTTGAACT 58.685 45.455 0.00 0.00 37.88 3.01
84 85 5.091552 TCAGTCTAACAGGGGTTGAACTAT 58.908 41.667 0.00 0.00 37.88 2.12
85 86 5.187186 TCAGTCTAACAGGGGTTGAACTATC 59.813 44.000 0.00 0.00 37.88 2.08
86 87 4.470304 AGTCTAACAGGGGTTGAACTATCC 59.530 45.833 0.00 0.00 37.88 2.59
87 88 3.778629 TCTAACAGGGGTTGAACTATCCC 59.221 47.826 0.41 0.41 37.88 3.85
92 93 0.913924 GGGTTGAACTATCCCCGGAA 59.086 55.000 0.73 0.00 35.52 4.30
93 94 1.282738 GGGTTGAACTATCCCCGGAAA 59.717 52.381 0.73 0.00 35.52 3.13
95 96 3.423749 GGTTGAACTATCCCCGGAAAAA 58.576 45.455 0.73 0.00 0.00 1.94
124 125 3.008049 GGGTTGAACTAGAGAAGGCTTCA 59.992 47.826 27.70 7.76 0.00 3.02
130 131 3.422796 ACTAGAGAAGGCTTCACTCGAA 58.577 45.455 26.87 11.92 36.03 3.71
131 132 3.827302 ACTAGAGAAGGCTTCACTCGAAA 59.173 43.478 26.87 11.60 36.03 3.46
133 134 3.855858 AGAGAAGGCTTCACTCGAAATC 58.144 45.455 27.70 14.15 36.03 2.17
134 135 2.600867 GAGAAGGCTTCACTCGAAATCG 59.399 50.000 27.70 0.00 41.45 3.34
135 136 1.061276 GAAGGCTTCACTCGAAATCGC 59.939 52.381 21.99 0.00 39.60 4.58
140 141 2.222685 GCTTCACTCGAAATCGCTGAAG 60.223 50.000 24.12 24.12 45.82 3.02
155 156 3.313803 CGCTGAAGCTGTAGATCACTCTA 59.686 47.826 0.10 0.00 39.32 2.43
222 224 4.106029 ACAGCGTATGTCGTATTTCTGT 57.894 40.909 0.00 0.00 37.75 3.41
224 226 5.271625 ACAGCGTATGTCGTATTTCTGTAG 58.728 41.667 0.00 0.00 37.75 2.74
225 227 5.163683 ACAGCGTATGTCGTATTTCTGTAGT 60.164 40.000 0.00 0.00 37.75 2.73
227 229 5.065602 AGCGTATGTCGTATTTCTGTAGTCA 59.934 40.000 0.00 0.00 42.13 3.41
228 230 5.913514 GCGTATGTCGTATTTCTGTAGTCAT 59.086 40.000 0.00 0.00 42.13 3.06
229 231 7.041576 AGCGTATGTCGTATTTCTGTAGTCATA 60.042 37.037 0.00 0.00 42.13 2.15
230 232 7.059260 GCGTATGTCGTATTTCTGTAGTCATAC 59.941 40.741 0.00 0.00 42.13 2.39
258 260 3.944055 TGTCTTTCTAGCGAGCTTCTT 57.056 42.857 1.86 0.00 0.00 2.52
261 263 5.779922 TGTCTTTCTAGCGAGCTTCTTTTA 58.220 37.500 1.86 0.00 0.00 1.52
263 265 7.544622 TGTCTTTCTAGCGAGCTTCTTTTATA 58.455 34.615 1.86 0.00 0.00 0.98
265 267 9.680315 GTCTTTCTAGCGAGCTTCTTTTATATA 57.320 33.333 1.86 0.00 0.00 0.86
323 362 2.146920 TGATCATTCAGGCCATTGCA 57.853 45.000 5.01 0.00 40.13 4.08
335 374 2.459060 CCATTGCATTGTTGGCTGAA 57.541 45.000 7.75 0.00 0.00 3.02
340 379 2.580962 TGCATTGTTGGCTGAACACTA 58.419 42.857 1.86 0.00 44.53 2.74
345 384 3.275617 TGTTGGCTGAACACTAACTGT 57.724 42.857 0.00 0.00 39.78 3.55
347 386 2.543777 TGGCTGAACACTAACTGTCC 57.456 50.000 0.00 0.00 30.29 4.02
350 389 1.071699 GCTGAACACTAACTGTCCCCA 59.928 52.381 0.00 0.00 30.29 4.96
353 392 4.398319 CTGAACACTAACTGTCCCCAAAT 58.602 43.478 0.00 0.00 30.29 2.32
357 396 7.691213 TGAACACTAACTGTCCCCAAATATAA 58.309 34.615 0.00 0.00 30.29 0.98
361 400 7.182206 ACACTAACTGTCCCCAAATATAAGTCT 59.818 37.037 0.00 0.00 0.00 3.24
364 403 9.462606 CTAACTGTCCCCAAATATAAGTCTTTT 57.537 33.333 0.00 0.00 0.00 2.27
365 404 8.721133 AACTGTCCCCAAATATAAGTCTTTTT 57.279 30.769 0.00 0.00 0.00 1.94
367 406 9.239551 ACTGTCCCCAAATATAAGTCTTTTTAC 57.760 33.333 0.00 0.00 0.00 2.01
368 407 9.238368 CTGTCCCCAAATATAAGTCTTTTTACA 57.762 33.333 0.00 0.00 0.00 2.41
369 408 9.238368 TGTCCCCAAATATAAGTCTTTTTACAG 57.762 33.333 0.00 0.00 0.00 2.74
381 420 6.164176 AGTCTTTTTACAGATTCCACTACGG 58.836 40.000 0.00 0.00 0.00 4.02
382 421 5.350640 GTCTTTTTACAGATTCCACTACGGG 59.649 44.000 0.00 0.00 34.36 5.28
384 423 2.154567 TACAGATTCCACTACGGGCT 57.845 50.000 0.00 0.00 34.36 5.19
386 425 1.755380 ACAGATTCCACTACGGGCTAC 59.245 52.381 0.00 0.00 34.36 3.58
390 429 3.573110 AGATTCCACTACGGGCTACATAC 59.427 47.826 0.00 0.00 34.36 2.39
391 430 2.440517 TCCACTACGGGCTACATACA 57.559 50.000 0.00 0.00 34.36 2.29
398 437 1.553248 ACGGGCTACATACAGAGCAAA 59.447 47.619 0.00 0.00 40.64 3.68
399 438 2.027561 ACGGGCTACATACAGAGCAAAA 60.028 45.455 0.00 0.00 40.64 2.44
403 442 5.050091 CGGGCTACATACAGAGCAAAATAAG 60.050 44.000 0.00 0.00 40.64 1.73
405 444 6.238484 GGGCTACATACAGAGCAAAATAAGTG 60.238 42.308 0.00 0.00 40.64 3.16
406 445 6.538742 GGCTACATACAGAGCAAAATAAGTGA 59.461 38.462 0.00 0.00 40.64 3.41
407 446 7.065803 GGCTACATACAGAGCAAAATAAGTGAA 59.934 37.037 0.00 0.00 40.64 3.18
410 449 8.798859 ACATACAGAGCAAAATAAGTGAATCT 57.201 30.769 0.00 0.00 0.00 2.40
413 452 9.890629 ATACAGAGCAAAATAAGTGAATCTACA 57.109 29.630 0.00 0.00 0.00 2.74
414 453 8.034058 ACAGAGCAAAATAAGTGAATCTACAC 57.966 34.615 0.00 0.00 40.60 2.90
462 501 9.661563 TTCGTATGTAGTTTGTATTGAAATCCT 57.338 29.630 0.00 0.00 0.00 3.24
471 510 9.965902 AGTTTGTATTGAAATCCTAGAATGACT 57.034 29.630 0.00 0.00 0.00 3.41
494 533 9.535878 GACTTATATTTAGAAACAGAGGGAGTG 57.464 37.037 0.00 0.00 0.00 3.51
495 534 7.988028 ACTTATATTTAGAAACAGAGGGAGTGC 59.012 37.037 0.00 0.00 0.00 4.40
496 535 2.743636 TTAGAAACAGAGGGAGTGCG 57.256 50.000 0.00 0.00 0.00 5.34
498 537 1.629043 AGAAACAGAGGGAGTGCGTA 58.371 50.000 0.00 0.00 0.00 4.42
500 539 1.272769 GAAACAGAGGGAGTGCGTACT 59.727 52.381 5.62 5.62 40.66 2.73
501 540 2.211250 AACAGAGGGAGTGCGTACTA 57.789 50.000 6.01 0.00 37.25 1.82
504 543 2.093106 CAGAGGGAGTGCGTACTACTT 58.907 52.381 15.92 8.19 37.91 2.24
505 544 2.093106 AGAGGGAGTGCGTACTACTTG 58.907 52.381 15.92 0.00 37.91 3.16
506 545 1.134560 GAGGGAGTGCGTACTACTTGG 59.865 57.143 15.92 0.00 37.91 3.61
507 546 0.175073 GGGAGTGCGTACTACTTGGG 59.825 60.000 15.92 0.00 37.91 4.12
509 548 0.531200 GAGTGCGTACTACTTGGGCT 59.469 55.000 6.01 0.00 37.25 5.19
510 549 0.974383 AGTGCGTACTACTTGGGCTT 59.026 50.000 3.62 0.00 34.74 4.35
511 550 1.067071 AGTGCGTACTACTTGGGCTTC 60.067 52.381 3.62 0.00 34.74 3.86
512 551 1.067071 GTGCGTACTACTTGGGCTTCT 60.067 52.381 0.00 0.00 0.00 2.85
514 553 1.471153 GCGTACTACTTGGGCTTCTCC 60.471 57.143 0.00 0.00 0.00 3.71
516 555 2.099427 CGTACTACTTGGGCTTCTCCTC 59.901 54.545 0.00 0.00 34.39 3.71
517 556 2.632763 ACTACTTGGGCTTCTCCTCT 57.367 50.000 0.00 0.00 34.39 3.69
518 557 2.909217 ACTACTTGGGCTTCTCCTCTT 58.091 47.619 0.00 0.00 34.39 2.85
519 558 2.569404 ACTACTTGGGCTTCTCCTCTTG 59.431 50.000 0.00 0.00 34.39 3.02
520 559 0.037447 ACTTGGGCTTCTCCTCTTGC 59.963 55.000 0.00 0.00 34.39 4.01
521 560 0.037303 CTTGGGCTTCTCCTCTTGCA 59.963 55.000 0.00 0.00 34.39 4.08
523 562 1.376466 GGGCTTCTCCTCTTGCACA 59.624 57.895 0.00 0.00 34.39 4.57
524 563 0.957888 GGGCTTCTCCTCTTGCACAC 60.958 60.000 0.00 0.00 34.39 3.82
525 564 0.036022 GGCTTCTCCTCTTGCACACT 59.964 55.000 0.00 0.00 0.00 3.55
526 565 1.155042 GCTTCTCCTCTTGCACACTG 58.845 55.000 0.00 0.00 0.00 3.66
527 566 1.270518 GCTTCTCCTCTTGCACACTGA 60.271 52.381 0.00 0.00 0.00 3.41
529 568 3.260740 CTTCTCCTCTTGCACACTGATC 58.739 50.000 0.00 0.00 0.00 2.92
530 569 1.552337 TCTCCTCTTGCACACTGATCC 59.448 52.381 0.00 0.00 0.00 3.36
532 571 1.980765 TCCTCTTGCACACTGATCCTT 59.019 47.619 0.00 0.00 0.00 3.36
533 572 2.082231 CCTCTTGCACACTGATCCTTG 58.918 52.381 0.00 0.00 0.00 3.61
536 575 1.538512 CTTGCACACTGATCCTTGGTG 59.461 52.381 0.00 0.00 37.05 4.17
537 576 1.878775 GCACACTGATCCTTGGTGC 59.121 57.895 11.42 11.42 46.53 5.01
538 577 1.915614 GCACACTGATCCTTGGTGCG 61.916 60.000 11.42 2.45 44.32 5.34
541 580 2.270205 CTGATCCTTGGTGCGCCT 59.730 61.111 18.96 0.00 35.27 5.52
563 602 2.579207 GCAGCTGCAAATGATGACAT 57.421 45.000 33.36 0.00 41.59 3.06
566 605 3.428999 GCAGCTGCAAATGATGACATTCT 60.429 43.478 33.36 0.00 44.67 2.40
567 606 4.352039 CAGCTGCAAATGATGACATTCTC 58.648 43.478 0.00 0.00 44.67 2.87
568 607 3.064958 AGCTGCAAATGATGACATTCTCG 59.935 43.478 1.02 0.00 44.67 4.04
569 608 3.360533 CTGCAAATGATGACATTCTCGC 58.639 45.455 0.00 0.00 44.67 5.03
570 609 2.223089 TGCAAATGATGACATTCTCGCG 60.223 45.455 0.00 0.00 44.67 5.87
572 611 0.940126 AATGATGACATTCTCGCGGC 59.060 50.000 6.13 0.00 42.20 6.53
573 612 0.179076 ATGATGACATTCTCGCGGCA 60.179 50.000 6.13 0.00 32.21 5.69
574 613 0.807275 TGATGACATTCTCGCGGCAG 60.807 55.000 6.13 0.00 0.00 4.85
576 615 3.567797 GACATTCTCGCGGCAGGC 61.568 66.667 6.13 0.00 38.69 4.85
593 632 2.854076 CCACCTCCCCCAGCTTTT 59.146 61.111 0.00 0.00 0.00 2.27
594 633 1.304464 CCACCTCCCCCAGCTTTTC 60.304 63.158 0.00 0.00 0.00 2.29
595 634 1.770324 CACCTCCCCCAGCTTTTCT 59.230 57.895 0.00 0.00 0.00 2.52
596 635 0.610232 CACCTCCCCCAGCTTTTCTG 60.610 60.000 0.00 0.00 42.49 3.02
599 638 0.987294 CTCCCCCAGCTTTTCTGAGA 59.013 55.000 0.00 0.00 45.72 3.27
601 640 1.352352 TCCCCCAGCTTTTCTGAGAAG 59.648 52.381 3.71 3.71 45.72 2.85
606 645 4.100035 CCCCAGCTTTTCTGAGAAGTTTTT 59.900 41.667 9.37 0.00 45.72 1.94
607 646 5.301805 CCCCAGCTTTTCTGAGAAGTTTTTA 59.698 40.000 9.37 0.00 45.72 1.52
608 647 6.442112 CCCAGCTTTTCTGAGAAGTTTTTAG 58.558 40.000 9.37 0.00 45.72 1.85
609 648 6.039829 CCCAGCTTTTCTGAGAAGTTTTTAGT 59.960 38.462 9.37 0.00 45.72 2.24
610 649 7.228706 CCCAGCTTTTCTGAGAAGTTTTTAGTA 59.771 37.037 9.37 0.00 45.72 1.82
611 650 8.286097 CCAGCTTTTCTGAGAAGTTTTTAGTAG 58.714 37.037 9.37 0.00 45.72 2.57
613 652 7.499232 AGCTTTTCTGAGAAGTTTTTAGTAGCA 59.501 33.333 9.37 0.00 0.00 3.49
616 655 7.478520 TTCTGAGAAGTTTTTAGTAGCACAC 57.521 36.000 0.00 0.00 0.00 3.82
618 657 6.479001 TCTGAGAAGTTTTTAGTAGCACACAC 59.521 38.462 0.00 0.00 0.00 3.82
621 660 7.982919 TGAGAAGTTTTTAGTAGCACACACTAA 59.017 33.333 0.00 0.00 36.85 2.24
622 661 8.904099 AGAAGTTTTTAGTAGCACACACTAAT 57.096 30.769 0.00 0.00 38.08 1.73
623 662 9.991906 AGAAGTTTTTAGTAGCACACACTAATA 57.008 29.630 0.00 0.00 38.08 0.98
627 666 9.309796 GTTTTTAGTAGCACACACTAATAAACG 57.690 33.333 4.29 0.00 40.43 3.60
628 667 7.585286 TTTAGTAGCACACACTAATAAACGG 57.415 36.000 0.00 0.00 37.61 4.44
756 1458 8.933653 TCAGTAATCATGAGGTTATTACATCCA 58.066 33.333 15.18 0.00 38.15 3.41
759 1461 9.209175 GTAATCATGAGGTTATTACATCCAGAC 57.791 37.037 0.09 0.00 36.52 3.51
811 1559 6.096423 ACGATAAGTGCATTCTCCTACTGTAA 59.904 38.462 0.00 0.00 0.00 2.41
815 1563 4.938226 AGTGCATTCTCCTACTGTAAAAGC 59.062 41.667 0.00 0.00 0.00 3.51
816 1564 4.695455 GTGCATTCTCCTACTGTAAAAGCA 59.305 41.667 0.00 0.00 0.00 3.91
821 2851 5.755409 TCTCCTACTGTAAAAGCAATCCA 57.245 39.130 0.00 0.00 0.00 3.41
837 2867 2.024176 TCCACCTGGTAGAAGCTTCA 57.976 50.000 27.57 11.42 36.34 3.02
930 6570 4.732285 AACATACTTGTTCAGCTCAACG 57.268 40.909 0.00 0.00 42.43 4.10
1093 6744 3.620374 AGCTGCAAACAATGATACTCTCG 59.380 43.478 1.02 0.00 0.00 4.04
1211 6862 1.315690 AAGTCGTCTCAGAACACCGA 58.684 50.000 0.00 0.00 0.00 4.69
1360 7011 8.212995 TCAAGATATCAAGTGATGGCAATCTTA 58.787 33.333 13.11 4.55 33.89 2.10
1492 7155 0.030101 CGGAAACCTTGCGCTCAAAA 59.970 50.000 9.73 0.00 37.76 2.44
1581 7250 0.461961 CAAAGTTTGGCCGGGACAAA 59.538 50.000 23.98 23.98 38.31 2.83
1693 7368 0.862283 GCTCGTCCTTAAGCGTCTCG 60.862 60.000 0.00 0.00 0.00 4.04
1795 7470 2.498644 TATGGATCCACGCACCAAAA 57.501 45.000 18.99 0.00 37.24 2.44
2144 7834 1.581934 TGCACTAGTGACAGCAACAC 58.418 50.000 27.08 5.76 38.38 3.32
2255 7945 2.238942 TGCGAAGAAGCTTGTCTCAA 57.761 45.000 2.10 0.00 38.13 3.02
2279 7969 2.420547 CCTGCTCCTGCACTGCTTATTA 60.421 50.000 1.98 0.00 45.31 0.98
2487 8178 5.311121 TGGGTTTGGGTTACTCATTCTTCTA 59.689 40.000 0.00 0.00 0.00 2.10
2529 8225 2.293122 ACAAATTCATGTGGTGTGGTCG 59.707 45.455 0.00 0.00 30.82 4.79
2548 8244 4.256920 GTCGGCTGCCATTATTCTATGAT 58.743 43.478 20.29 0.00 0.00 2.45
2608 8304 9.538508 AAATATACTGATTTAGTTCGTGGTACC 57.461 33.333 4.43 4.43 40.89 3.34
2625 8321 6.263344 GTGGTACCAAAAACTTCTCTGAAAC 58.737 40.000 18.31 0.00 0.00 2.78
2848 8544 8.744568 TTGTGTATGAGCATATGTTAAATGGA 57.255 30.769 4.29 0.00 0.00 3.41
3004 8703 3.458189 ACACTGCGATATTAAGCCAGAC 58.542 45.455 0.00 0.00 0.00 3.51
3026 8725 4.637534 ACAACATACTTCTGGATGCATCAC 59.362 41.667 27.25 16.88 0.00 3.06
3127 8827 0.625849 CTGTGGGTTATCTTGCCCCT 59.374 55.000 0.00 0.00 44.20 4.79
3140 8840 2.604118 GCCCCTGAGTGGCTTACTA 58.396 57.895 0.00 0.00 45.70 1.82
3167 8867 3.064207 GCTATCACACCGAAAGTTGACA 58.936 45.455 0.00 0.00 0.00 3.58
3244 8944 5.372373 TCACCTGAAACATCATACAACACA 58.628 37.500 0.00 0.00 0.00 3.72
3263 8972 1.605710 CAAGCAGCAGCAACAGTAACT 59.394 47.619 3.17 0.00 45.49 2.24
3536 9248 2.211250 ATCTGGTGCTGCAACTTCAT 57.789 45.000 19.68 5.07 0.00 2.57
3542 9254 3.004629 TGGTGCTGCAACTTCATTGTAAG 59.995 43.478 19.68 0.00 40.77 2.34
3546 9258 5.922544 GTGCTGCAACTTCATTGTAAGAATT 59.077 36.000 2.77 0.00 40.77 2.17
3719 9445 6.384224 CAATCATTGTAGCGAAATATGGCAT 58.616 36.000 4.88 4.88 31.86 4.40
3820 9546 9.862371 TTTTTCAAACTGCTCACAATAAAACTA 57.138 25.926 0.00 0.00 0.00 2.24
3826 9552 7.328277 ACTGCTCACAATAAAACTACAACAA 57.672 32.000 0.00 0.00 0.00 2.83
3829 9555 8.572828 TGCTCACAATAAAACTACAACAATTG 57.427 30.769 3.24 3.24 0.00 2.32
3856 9582 4.629200 CAGTTCTGCAAGTAGGAAGATGTC 59.371 45.833 0.00 0.00 33.76 3.06
3900 9626 7.634671 TGATATGATCAAGCAAAACATCAGT 57.365 32.000 0.00 0.00 36.11 3.41
3951 9677 5.423886 TCCGTGTGATTTGTATAATGCTGA 58.576 37.500 0.00 0.00 0.00 4.26
4044 9770 2.027192 TCCGAAGTGCATTCTAGGCTTT 60.027 45.455 0.00 0.00 35.61 3.51
4083 9809 5.675684 ACTGTTTTTCTTTTCCACACCAT 57.324 34.783 0.00 0.00 0.00 3.55
4090 9816 7.473735 TTTTCTTTTCCACACCATGCATATA 57.526 32.000 0.00 0.00 0.00 0.86
4093 9819 7.473735 TCTTTTCCACACCATGCATATAAAA 57.526 32.000 0.00 0.00 0.00 1.52
4095 9821 8.538701 TCTTTTCCACACCATGCATATAAAAAT 58.461 29.630 0.00 0.00 0.00 1.82
4102 9828 8.533965 CACACCATGCATATAAAAATTTTCTCG 58.466 33.333 3.41 0.00 0.00 4.04
4128 9854 3.193479 GGAAAATGTGGAACTGATCACCC 59.807 47.826 0.00 0.00 38.04 4.61
4203 9929 7.766738 TCAACTTGGAAGGTTATTTGTTTTTCC 59.233 33.333 0.00 0.00 35.72 3.13
4271 9998 6.365247 CGGTTTTCGCTATATAGTTACATGCT 59.635 38.462 11.38 0.00 0.00 3.79
4279 10006 7.220108 CGCTATATAGTTACATGCTTGCGAATA 59.780 37.037 11.38 0.00 40.75 1.75
4351 10082 1.134401 ACTCTGGCCATGATACCAACG 60.134 52.381 5.51 0.00 34.96 4.10
4421 10153 6.826668 TCTGTTTGGTTGTTATCTCTTCAGA 58.173 36.000 0.00 0.00 0.00 3.27
4443 10175 7.066645 TCAGATTCATTTTTCTGCGATTCTCAT 59.933 33.333 0.00 0.00 39.36 2.90
4494 10226 2.770164 GAAGCTGCTTCCTTGGACTA 57.230 50.000 27.74 0.00 34.71 2.59
4499 10231 1.902508 CTGCTTCCTTGGACTAGACCA 59.097 52.381 10.05 10.05 38.24 4.02
4509 10241 3.165875 TGGACTAGACCAAGTCAAGAGG 58.834 50.000 11.73 0.00 46.40 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.331791 ACTTCTTAGTTGATTCTATTTCGCCT 58.668 34.615 0.00 0.00 0.00 5.52
2 3 9.827411 AAAACTTCTTAGTTGATTCTATTTCGC 57.173 29.630 0.00 0.00 43.74 4.70
12 13 9.416284 TCCCTTGTTTAAAACTTCTTAGTTGAT 57.584 29.630 0.00 0.00 43.74 2.57
13 14 8.680001 GTCCCTTGTTTAAAACTTCTTAGTTGA 58.320 33.333 0.00 0.00 43.74 3.18
15 16 8.818622 AGTCCCTTGTTTAAAACTTCTTAGTT 57.181 30.769 0.00 0.00 46.44 2.24
16 17 9.910267 TTAGTCCCTTGTTTAAAACTTCTTAGT 57.090 29.630 0.00 0.00 35.68 2.24
30 31 8.533569 TCATCTTTTCTTTTTAGTCCCTTGTT 57.466 30.769 0.00 0.00 0.00 2.83
31 32 8.533569 TTCATCTTTTCTTTTTAGTCCCTTGT 57.466 30.769 0.00 0.00 0.00 3.16
32 33 9.987272 AATTCATCTTTTCTTTTTAGTCCCTTG 57.013 29.630 0.00 0.00 0.00 3.61
48 49 9.401058 CCCTGTTAGACTGATTAATTCATCTTT 57.599 33.333 1.53 0.00 32.72 2.52
49 50 7.995488 CCCCTGTTAGACTGATTAATTCATCTT 59.005 37.037 1.53 0.00 32.72 2.40
50 51 7.127955 ACCCCTGTTAGACTGATTAATTCATCT 59.872 37.037 1.53 0.00 32.72 2.90
51 52 7.283329 ACCCCTGTTAGACTGATTAATTCATC 58.717 38.462 0.00 0.00 32.72 2.92
52 53 7.213178 ACCCCTGTTAGACTGATTAATTCAT 57.787 36.000 0.00 0.00 32.72 2.57
54 55 7.110155 TCAACCCCTGTTAGACTGATTAATTC 58.890 38.462 0.00 0.00 32.09 2.17
55 56 7.027874 TCAACCCCTGTTAGACTGATTAATT 57.972 36.000 0.00 0.00 32.09 1.40
56 57 6.636454 TCAACCCCTGTTAGACTGATTAAT 57.364 37.500 0.00 0.00 32.09 1.40
58 59 5.546499 AGTTCAACCCCTGTTAGACTGATTA 59.454 40.000 0.00 0.00 31.44 1.75
59 60 4.351111 AGTTCAACCCCTGTTAGACTGATT 59.649 41.667 0.00 0.00 31.44 2.57
60 61 3.910627 AGTTCAACCCCTGTTAGACTGAT 59.089 43.478 0.00 0.00 31.44 2.90
61 62 3.314693 AGTTCAACCCCTGTTAGACTGA 58.685 45.455 0.00 0.00 31.44 3.41
62 63 3.771577 AGTTCAACCCCTGTTAGACTG 57.228 47.619 0.00 0.00 31.44 3.51
63 64 4.470304 GGATAGTTCAACCCCTGTTAGACT 59.530 45.833 0.00 0.00 34.81 3.24
64 65 4.383880 GGGATAGTTCAACCCCTGTTAGAC 60.384 50.000 0.00 0.00 37.85 2.59
65 66 3.778629 GGGATAGTTCAACCCCTGTTAGA 59.221 47.826 0.00 0.00 37.85 2.10
66 67 4.152284 GGGATAGTTCAACCCCTGTTAG 57.848 50.000 0.00 0.00 37.85 2.34
74 75 2.793288 TTTCCGGGGATAGTTCAACC 57.207 50.000 0.00 0.00 0.00 3.77
95 96 5.377478 CTTCTCTAGTTCAACCCCTGTTTT 58.623 41.667 0.00 0.00 30.42 2.43
96 97 4.202472 CCTTCTCTAGTTCAACCCCTGTTT 60.202 45.833 0.00 0.00 30.42 2.83
97 98 3.328050 CCTTCTCTAGTTCAACCCCTGTT 59.672 47.826 0.00 0.00 34.14 3.16
98 99 2.907042 CCTTCTCTAGTTCAACCCCTGT 59.093 50.000 0.00 0.00 0.00 4.00
100 101 1.909986 GCCTTCTCTAGTTCAACCCCT 59.090 52.381 0.00 0.00 0.00 4.79
101 102 1.909986 AGCCTTCTCTAGTTCAACCCC 59.090 52.381 0.00 0.00 0.00 4.95
102 103 3.008049 TGAAGCCTTCTCTAGTTCAACCC 59.992 47.826 5.96 0.00 0.00 4.11
104 105 4.888917 AGTGAAGCCTTCTCTAGTTCAAC 58.111 43.478 7.23 0.00 32.21 3.18
105 106 4.321304 CGAGTGAAGCCTTCTCTAGTTCAA 60.321 45.833 8.90 0.00 33.98 2.69
107 108 3.440872 TCGAGTGAAGCCTTCTCTAGTTC 59.559 47.826 8.90 0.00 33.98 3.01
134 135 3.799281 AGAGTGATCTACAGCTTCAGC 57.201 47.619 0.00 0.00 42.49 4.26
135 136 7.715657 AGATTTAGAGTGATCTACAGCTTCAG 58.284 38.462 0.00 0.00 31.09 3.02
140 141 7.488322 ACAGAAGATTTAGAGTGATCTACAGC 58.512 38.462 0.00 0.00 32.52 4.40
204 206 5.268544 TGACTACAGAAATACGACATACGC 58.731 41.667 0.00 0.00 46.94 4.42
206 208 9.947669 AAGTATGACTACAGAAATACGACATAC 57.052 33.333 0.00 0.00 38.29 2.39
208 210 9.871238 AAAAGTATGACTACAGAAATACGACAT 57.129 29.630 0.00 0.00 32.05 3.06
210 212 9.136952 ACAAAAGTATGACTACAGAAATACGAC 57.863 33.333 0.00 0.00 32.05 4.34
224 226 7.530861 CGCTAGAAAGACAAACAAAAGTATGAC 59.469 37.037 0.00 0.00 0.00 3.06
225 227 7.439955 TCGCTAGAAAGACAAACAAAAGTATGA 59.560 33.333 0.00 0.00 0.00 2.15
227 229 7.571428 GCTCGCTAGAAAGACAAACAAAAGTAT 60.571 37.037 0.00 0.00 0.00 2.12
228 230 6.292703 GCTCGCTAGAAAGACAAACAAAAGTA 60.293 38.462 0.00 0.00 0.00 2.24
229 231 5.504173 GCTCGCTAGAAAGACAAACAAAAGT 60.504 40.000 0.00 0.00 0.00 2.66
230 232 4.906437 GCTCGCTAGAAAGACAAACAAAAG 59.094 41.667 0.00 0.00 0.00 2.27
302 304 3.834938 TGCAATGGCCTGAATGATCATA 58.165 40.909 9.04 0.00 40.13 2.15
304 306 2.146920 TGCAATGGCCTGAATGATCA 57.853 45.000 3.32 0.00 40.13 2.92
305 307 3.181469 ACAATGCAATGGCCTGAATGATC 60.181 43.478 6.73 0.00 40.13 2.92
306 308 2.769663 ACAATGCAATGGCCTGAATGAT 59.230 40.909 6.73 0.00 40.13 2.45
323 362 4.207165 ACAGTTAGTGTTCAGCCAACAAT 58.793 39.130 4.69 4.69 46.90 2.71
335 374 7.182206 AGACTTATATTTGGGGACAGTTAGTGT 59.818 37.037 0.00 0.00 44.54 3.55
340 379 8.721133 AAAAAGACTTATATTTGGGGACAGTT 57.279 30.769 0.00 0.00 44.54 3.16
357 396 6.164176 CCGTAGTGGAATCTGTAAAAAGACT 58.836 40.000 0.00 0.00 42.00 3.24
361 400 4.004982 GCCCGTAGTGGAATCTGTAAAAA 58.995 43.478 0.00 0.00 42.00 1.94
364 403 2.463752 AGCCCGTAGTGGAATCTGTAA 58.536 47.619 0.00 0.00 42.00 2.41
365 404 2.154567 AGCCCGTAGTGGAATCTGTA 57.845 50.000 0.00 0.00 42.00 2.74
367 406 1.754803 TGTAGCCCGTAGTGGAATCTG 59.245 52.381 0.00 0.00 42.00 2.90
368 407 2.154567 TGTAGCCCGTAGTGGAATCT 57.845 50.000 0.00 0.00 42.00 2.40
369 408 3.319972 TGTATGTAGCCCGTAGTGGAATC 59.680 47.826 0.00 0.00 42.00 2.52
372 411 2.092267 TCTGTATGTAGCCCGTAGTGGA 60.092 50.000 0.00 0.00 42.00 4.02
373 412 2.293677 CTCTGTATGTAGCCCGTAGTGG 59.706 54.545 0.00 0.00 37.55 4.00
377 416 2.061509 TGCTCTGTATGTAGCCCGTA 57.938 50.000 0.00 0.00 37.97 4.02
378 417 1.191535 TTGCTCTGTATGTAGCCCGT 58.808 50.000 0.00 0.00 37.97 5.28
379 418 2.309528 TTTGCTCTGTATGTAGCCCG 57.690 50.000 0.00 0.00 37.97 6.13
381 420 6.538742 TCACTTATTTTGCTCTGTATGTAGCC 59.461 38.462 0.00 0.00 37.97 3.93
382 421 7.539712 TCACTTATTTTGCTCTGTATGTAGC 57.460 36.000 0.00 0.00 39.25 3.58
384 423 9.890629 AGATTCACTTATTTTGCTCTGTATGTA 57.109 29.630 0.00 0.00 0.00 2.29
390 429 8.261492 AGTGTAGATTCACTTATTTTGCTCTG 57.739 34.615 0.00 0.00 44.92 3.35
391 430 8.317679 AGAGTGTAGATTCACTTATTTTGCTCT 58.682 33.333 0.98 0.00 46.81 4.09
436 475 9.661563 AGGATTTCAATACAAACTACATACGAA 57.338 29.630 0.00 0.00 0.00 3.85
468 507 9.535878 CACTCCCTCTGTTTCTAAATATAAGTC 57.464 37.037 0.00 0.00 0.00 3.01
471 510 6.984474 CGCACTCCCTCTGTTTCTAAATATAA 59.016 38.462 0.00 0.00 0.00 0.98
473 512 5.104900 ACGCACTCCCTCTGTTTCTAAATAT 60.105 40.000 0.00 0.00 0.00 1.28
476 515 2.367567 ACGCACTCCCTCTGTTTCTAAA 59.632 45.455 0.00 0.00 0.00 1.85
477 516 1.968493 ACGCACTCCCTCTGTTTCTAA 59.032 47.619 0.00 0.00 0.00 2.10
480 519 1.272769 AGTACGCACTCCCTCTGTTTC 59.727 52.381 0.00 0.00 0.00 2.78
482 521 1.817447 GTAGTACGCACTCCCTCTGTT 59.183 52.381 0.00 0.00 36.14 3.16
485 524 2.093106 CAAGTAGTACGCACTCCCTCT 58.907 52.381 0.00 0.00 36.14 3.69
488 527 0.175073 CCCAAGTAGTACGCACTCCC 59.825 60.000 0.00 0.00 36.14 4.30
490 529 0.531200 AGCCCAAGTAGTACGCACTC 59.469 55.000 0.00 0.00 36.14 3.51
491 530 0.974383 AAGCCCAAGTAGTACGCACT 59.026 50.000 0.00 0.00 38.91 4.40
494 533 1.471153 GGAGAAGCCCAAGTAGTACGC 60.471 57.143 0.00 0.00 0.00 4.42
495 534 2.099427 GAGGAGAAGCCCAAGTAGTACG 59.901 54.545 0.00 0.00 37.37 3.67
496 535 3.367321 AGAGGAGAAGCCCAAGTAGTAC 58.633 50.000 0.00 0.00 37.37 2.73
498 537 2.569404 CAAGAGGAGAAGCCCAAGTAGT 59.431 50.000 0.00 0.00 37.37 2.73
500 539 1.279271 GCAAGAGGAGAAGCCCAAGTA 59.721 52.381 0.00 0.00 37.37 2.24
501 540 0.037447 GCAAGAGGAGAAGCCCAAGT 59.963 55.000 0.00 0.00 37.37 3.16
504 543 1.376466 GTGCAAGAGGAGAAGCCCA 59.624 57.895 0.00 0.00 37.37 5.36
505 544 0.957888 GTGTGCAAGAGGAGAAGCCC 60.958 60.000 0.00 0.00 37.37 5.19
506 545 0.036022 AGTGTGCAAGAGGAGAAGCC 59.964 55.000 0.00 0.00 0.00 4.35
507 546 1.155042 CAGTGTGCAAGAGGAGAAGC 58.845 55.000 0.00 0.00 0.00 3.86
509 548 2.027745 GGATCAGTGTGCAAGAGGAGAA 60.028 50.000 0.00 0.00 0.00 2.87
510 549 1.552337 GGATCAGTGTGCAAGAGGAGA 59.448 52.381 0.00 0.00 0.00 3.71
511 550 1.554160 AGGATCAGTGTGCAAGAGGAG 59.446 52.381 0.00 0.00 0.00 3.69
512 551 1.649321 AGGATCAGTGTGCAAGAGGA 58.351 50.000 0.00 0.00 0.00 3.71
514 553 2.082231 CCAAGGATCAGTGTGCAAGAG 58.918 52.381 0.00 0.00 0.00 2.85
516 555 1.538512 CACCAAGGATCAGTGTGCAAG 59.461 52.381 0.00 0.00 0.00 4.01
517 556 1.608055 CACCAAGGATCAGTGTGCAA 58.392 50.000 0.00 0.00 0.00 4.08
518 557 3.327600 CACCAAGGATCAGTGTGCA 57.672 52.632 0.00 0.00 0.00 4.57
519 558 1.878775 GCACCAAGGATCAGTGTGC 59.121 57.895 11.42 11.42 44.53 4.57
520 559 1.915614 GCGCACCAAGGATCAGTGTG 61.916 60.000 0.30 11.42 43.25 3.82
521 560 1.672356 GCGCACCAAGGATCAGTGT 60.672 57.895 0.30 0.00 33.96 3.55
523 562 2.045926 GGCGCACCAAGGATCAGT 60.046 61.111 10.83 0.00 35.26 3.41
524 563 1.817099 GAGGCGCACCAAGGATCAG 60.817 63.158 10.83 0.00 39.06 2.90
525 564 2.268920 GAGGCGCACCAAGGATCA 59.731 61.111 10.83 0.00 39.06 2.92
526 565 1.817099 CAGAGGCGCACCAAGGATC 60.817 63.158 10.83 0.00 39.06 3.36
527 566 2.270205 CAGAGGCGCACCAAGGAT 59.730 61.111 10.83 0.00 39.06 3.24
530 569 3.429141 CTGCAGAGGCGCACCAAG 61.429 66.667 8.42 0.00 45.35 3.61
541 580 5.883336 AATGTCATCATTTGCAGCTGCAGA 61.883 41.667 37.42 34.38 41.94 4.26
546 585 3.064958 CGAGAATGTCATCATTTGCAGCT 59.935 43.478 0.00 0.00 43.33 4.24
547 586 3.360533 CGAGAATGTCATCATTTGCAGC 58.639 45.455 0.00 0.00 43.33 5.25
548 587 3.360533 GCGAGAATGTCATCATTTGCAG 58.639 45.455 0.00 0.00 43.33 4.41
550 589 2.369600 CGCGAGAATGTCATCATTTGC 58.630 47.619 0.00 0.00 43.33 3.68
553 592 0.940126 GCCGCGAGAATGTCATCATT 59.060 50.000 8.23 0.00 45.57 2.57
556 595 1.493950 CCTGCCGCGAGAATGTCATC 61.494 60.000 8.23 0.00 0.00 2.92
557 596 1.522355 CCTGCCGCGAGAATGTCAT 60.522 57.895 8.23 0.00 0.00 3.06
558 597 2.125552 CCTGCCGCGAGAATGTCA 60.126 61.111 8.23 0.00 0.00 3.58
559 598 3.567797 GCCTGCCGCGAGAATGTC 61.568 66.667 8.23 0.00 0.00 3.06
576 615 1.304464 GAAAAGCTGGGGGAGGTGG 60.304 63.158 0.00 0.00 30.84 4.61
577 616 0.610232 CAGAAAAGCTGGGGGAGGTG 60.610 60.000 0.00 0.00 41.07 4.00
578 617 0.772124 TCAGAAAAGCTGGGGGAGGT 60.772 55.000 0.00 0.00 44.98 3.85
582 621 1.074566 ACTTCTCAGAAAAGCTGGGGG 59.925 52.381 0.00 0.00 45.62 5.40
583 622 2.575805 ACTTCTCAGAAAAGCTGGGG 57.424 50.000 0.00 0.00 45.62 4.96
585 624 7.032377 ACTAAAAACTTCTCAGAAAAGCTGG 57.968 36.000 0.00 0.00 44.98 4.85
586 625 7.800847 GCTACTAAAAACTTCTCAGAAAAGCTG 59.199 37.037 0.00 0.00 46.31 4.24
587 626 7.499232 TGCTACTAAAAACTTCTCAGAAAAGCT 59.501 33.333 0.00 0.00 0.00 3.74
588 627 7.588123 GTGCTACTAAAAACTTCTCAGAAAAGC 59.412 37.037 0.00 0.00 0.00 3.51
590 629 8.395633 GTGTGCTACTAAAAACTTCTCAGAAAA 58.604 33.333 0.00 0.00 0.00 2.29
591 630 7.551262 TGTGTGCTACTAAAAACTTCTCAGAAA 59.449 33.333 0.00 0.00 0.00 2.52
593 632 6.479001 GTGTGTGCTACTAAAAACTTCTCAGA 59.521 38.462 0.00 0.00 0.00 3.27
594 633 6.480320 AGTGTGTGCTACTAAAAACTTCTCAG 59.520 38.462 0.00 0.00 0.00 3.35
595 634 6.346096 AGTGTGTGCTACTAAAAACTTCTCA 58.654 36.000 0.00 0.00 0.00 3.27
596 635 6.846325 AGTGTGTGCTACTAAAAACTTCTC 57.154 37.500 0.00 0.00 0.00 2.87
601 640 9.309796 CGTTTATTAGTGTGTGCTACTAAAAAC 57.690 33.333 4.65 4.65 42.13 2.43
606 645 5.418524 TCCCGTTTATTAGTGTGTGCTACTA 59.581 40.000 0.00 0.00 0.00 1.82
607 646 4.221262 TCCCGTTTATTAGTGTGTGCTACT 59.779 41.667 0.00 0.00 0.00 2.57
608 647 4.497300 TCCCGTTTATTAGTGTGTGCTAC 58.503 43.478 0.00 0.00 0.00 3.58
609 648 4.804868 TCCCGTTTATTAGTGTGTGCTA 57.195 40.909 0.00 0.00 0.00 3.49
610 649 3.688694 TCCCGTTTATTAGTGTGTGCT 57.311 42.857 0.00 0.00 0.00 4.40
611 650 3.749609 ACTTCCCGTTTATTAGTGTGTGC 59.250 43.478 0.00 0.00 0.00 4.57
613 652 4.687483 CGAACTTCCCGTTTATTAGTGTGT 59.313 41.667 0.00 0.00 35.56 3.72
616 655 3.063045 GGCGAACTTCCCGTTTATTAGTG 59.937 47.826 0.00 0.00 35.56 2.74
618 657 2.610833 GGGCGAACTTCCCGTTTATTAG 59.389 50.000 0.00 0.00 35.56 1.73
621 660 3.164026 GGGCGAACTTCCCGTTTAT 57.836 52.632 0.00 0.00 35.56 1.40
622 661 4.699626 GGGCGAACTTCCCGTTTA 57.300 55.556 0.00 0.00 35.56 2.01
756 1458 2.170817 GGCTATTTTCTTCGAGGGGTCT 59.829 50.000 0.00 0.00 0.00 3.85
759 1461 2.710096 TGGCTATTTTCTTCGAGGGG 57.290 50.000 0.00 0.00 0.00 4.79
811 1559 3.690460 CTTCTACCAGGTGGATTGCTTT 58.310 45.455 6.46 0.00 38.94 3.51
815 1563 3.274288 GAAGCTTCTACCAGGTGGATTG 58.726 50.000 19.44 4.46 38.94 2.67
816 1564 2.912956 TGAAGCTTCTACCAGGTGGATT 59.087 45.455 26.09 0.00 38.94 3.01
821 2851 2.711547 ACCTTTGAAGCTTCTACCAGGT 59.288 45.455 26.09 23.45 0.00 4.00
837 2867 2.243736 TCAAACTGGGAAGTGGACCTTT 59.756 45.455 0.00 0.00 32.03 3.11
958 6599 7.935755 TCTGCTATGATATTTGGAGAAAGAAGG 59.064 37.037 0.00 0.00 0.00 3.46
963 6609 6.484643 GTGCTCTGCTATGATATTTGGAGAAA 59.515 38.462 0.00 0.00 0.00 2.52
1360 7011 3.098377 TGGCAGCATGGTTTACAATGAT 58.902 40.909 0.00 0.00 35.86 2.45
1434 7097 3.673809 CGGTACTAGTGTTGTTTCTGCTC 59.326 47.826 5.39 0.00 0.00 4.26
1492 7155 0.692419 AGGTCGGATGATGGGCTCTT 60.692 55.000 0.00 0.00 0.00 2.85
1581 7250 1.837439 TGGTGACTGAAACCAGTGACT 59.163 47.619 13.17 0.00 44.59 3.41
1693 7368 5.248380 AGCCAATATTCTACCAAGGGATC 57.752 43.478 0.00 0.00 0.00 3.36
1795 7470 4.603131 ACATATGTTGGGTTCATCAAGCT 58.397 39.130 1.41 0.00 0.00 3.74
2144 7834 4.142687 GGAACATGTCCGTTGAACTTATGG 60.143 45.833 0.00 0.00 36.40 2.74
2230 7920 1.336240 ACAAGCTTCTTCGCATTTGCC 60.336 47.619 0.00 0.00 37.91 4.52
2487 8178 4.019681 TGTTCCTCCGATTCTAACAACCAT 60.020 41.667 0.00 0.00 0.00 3.55
2529 8225 7.870509 TGATTATCATAGAATAATGGCAGCC 57.129 36.000 3.66 3.66 33.10 4.85
2548 8244 2.432444 CCGCCAACACTTCCTTGATTA 58.568 47.619 0.00 0.00 0.00 1.75
2604 8300 6.115450 ACGTTTCAGAGAAGTTTTTGGTAC 57.885 37.500 0.00 0.00 0.00 3.34
2608 8304 6.687105 CACCTAACGTTTCAGAGAAGTTTTTG 59.313 38.462 5.91 0.00 0.00 2.44
2625 8321 3.379057 ACCAAAACTTCCAACACCTAACG 59.621 43.478 0.00 0.00 0.00 3.18
2882 8578 4.229096 CAATTCAGGACGACAACATTTGG 58.771 43.478 0.00 0.00 34.12 3.28
3004 8703 4.880120 AGTGATGCATCCAGAAGTATGTTG 59.120 41.667 23.67 0.00 0.00 3.33
3041 8740 0.823356 GCTGCCAACCCAAAGTCTGA 60.823 55.000 0.00 0.00 0.00 3.27
3127 8827 1.825474 GCCACTCTAGTAAGCCACTCA 59.175 52.381 0.00 0.00 38.80 3.41
3140 8840 1.557099 TTCGGTGTGATAGCCACTCT 58.443 50.000 0.00 0.00 45.86 3.24
3167 8867 0.393808 ACCATGCCGAAGCCGTAAAT 60.394 50.000 0.00 0.00 38.69 1.40
3244 8944 1.972872 AGTTACTGTTGCTGCTGCTT 58.027 45.000 17.00 0.00 40.48 3.91
3263 8972 6.382859 TGCACAGGGAAGTACTCAATATTCTA 59.617 38.462 0.00 0.00 0.00 2.10
3363 9075 2.440409 TGCAAATCCTTTCAGCCTCTC 58.560 47.619 0.00 0.00 0.00 3.20
3588 9305 8.258007 TCCTGTCCACATTACAACTTATAAGAG 58.742 37.037 19.38 12.70 0.00 2.85
3594 9311 5.308497 TCCTTCCTGTCCACATTACAACTTA 59.692 40.000 0.00 0.00 0.00 2.24
3610 9327 3.968265 TGCCTTCCTTTATTCCTTCCTG 58.032 45.455 0.00 0.00 0.00 3.86
3751 9477 2.196595 CAAGTTCCCATCCCAGGTCTA 58.803 52.381 0.00 0.00 0.00 2.59
3800 9526 7.767261 TGTTGTAGTTTTATTGTGAGCAGTTT 58.233 30.769 0.00 0.00 0.00 2.66
3820 9546 3.088194 CAGAACTGCAGCAATTGTTGT 57.912 42.857 21.37 3.69 0.00 3.32
3856 9582 5.102953 TCAACCCATATCTTTCAGACCTG 57.897 43.478 0.00 0.00 0.00 4.00
3898 9624 6.266558 TGAAAATACCTGGCAATTGTACAACT 59.733 34.615 11.22 0.00 0.00 3.16
3900 9626 6.656632 TGAAAATACCTGGCAATTGTACAA 57.343 33.333 11.41 11.41 0.00 2.41
3974 9700 6.762187 TGTCATTTCAGCACAACATTGAAATT 59.238 30.769 8.49 0.00 44.69 1.82
4064 9790 4.187694 TGCATGGTGTGGAAAAGAAAAAC 58.812 39.130 0.00 0.00 0.00 2.43
4083 9809 9.698309 TTCCAAACGAGAAAATTTTTATATGCA 57.302 25.926 4.63 0.00 0.00 3.96
4090 9816 8.180920 CCACATTTTCCAAACGAGAAAATTTTT 58.819 29.630 4.63 0.00 46.62 1.94
4093 9819 6.578023 TCCACATTTTCCAAACGAGAAAATT 58.422 32.000 8.37 0.47 46.62 1.82
4095 9821 5.584253 TCCACATTTTCCAAACGAGAAAA 57.416 34.783 1.57 1.57 44.76 2.29
4102 9828 5.691754 GTGATCAGTTCCACATTTTCCAAAC 59.308 40.000 0.00 0.00 33.72 2.93
4156 9882 9.628500 AGTTGACCAAGTAGAAGAAATTTACTT 57.372 29.630 0.00 0.00 37.95 2.24
4167 9893 4.165372 ACCTTCCAAGTTGACCAAGTAGAA 59.835 41.667 3.87 0.00 0.00 2.10
4203 9929 8.044060 TCTGCACAAGAAATTTCTACCTTATG 57.956 34.615 20.76 15.70 36.28 1.90
4421 10153 7.092137 TCATGAGAATCGCAGAAAAATGAAT 57.908 32.000 0.00 0.00 43.58 2.57
4459 10191 3.441572 CAGCTTCCTCATTCAACCGAATT 59.558 43.478 0.00 0.00 39.96 2.17
4464 10196 1.831580 AGCAGCTTCCTCATTCAACC 58.168 50.000 0.00 0.00 0.00 3.77
4499 10231 2.369860 TCAGCACATGACCTCTTGACTT 59.630 45.455 0.00 0.00 31.12 3.01
4502 10234 1.277273 CCTCAGCACATGACCTCTTGA 59.723 52.381 0.00 0.00 33.22 3.02
4509 10241 1.748122 CTGCCCCTCAGCACATGAC 60.748 63.158 0.00 0.00 38.00 3.06


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

AutoCloner maintained by Alex Coulton.