Multiple sequence alignment - TraesCS6A01G289000

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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 TraesCS6A01G289000 chr6A 100.000 3533 0 0 1 3533 520873444 520869912 0.000000e+00 6525.0
1 TraesCS6A01G289000 chr6A 86.011 1780 188 32 614 2366 90032316 90034061 0.000000e+00 1851.0
2 TraesCS6A01G289000 chr6A 84.890 867 101 7 983 1822 83362151 83363014 0.000000e+00 848.0
3 TraesCS6A01G289000 chr6B 92.179 2506 130 29 6 2485 566538881 566536416 0.000000e+00 3482.0
4 TraesCS6A01G289000 chr6B 85.620 1815 189 39 583 2366 147961088 147962861 0.000000e+00 1840.0
5 TraesCS6A01G289000 chr6B 84.642 853 107 8 983 1814 140451435 140450586 0.000000e+00 828.0
6 TraesCS6A01G289000 chr6B 92.396 434 18 9 3100 3533 566535930 566535512 3.900000e-169 604.0
7 TraesCS6A01G289000 chr6B 80.890 382 45 11 1456 1814 140413214 140412838 3.470000e-70 276.0
8 TraesCS6A01G289000 chr6B 93.878 49 3 0 3481 3529 204333952 204334000 1.360000e-09 75.0
9 TraesCS6A01G289000 chr6D 93.148 2160 115 22 351 2485 379720811 379722962 0.000000e+00 3138.0
10 TraesCS6A01G289000 chr6D 86.157 1806 190 28 584 2366 73587594 73589362 0.000000e+00 1895.0
11 TraesCS6A01G289000 chr6D 84.544 867 107 5 983 1822 65390056 65389190 0.000000e+00 833.0
12 TraesCS6A01G289000 chr6D 86.923 520 24 14 3014 3533 379723524 379723999 8.630000e-151 544.0
13 TraesCS6A01G289000 chr6D 85.236 508 40 21 2486 2965 379722915 379723415 1.140000e-134 490.0
14 TraesCS6A01G289000 chr6D 93.878 49 3 0 3481 3529 115021106 115021154 1.360000e-09 75.0
15 TraesCS6A01G289000 chr7B 89.540 239 18 4 276 507 651359170 651359408 2.670000e-76 296.0
16 TraesCS6A01G289000 chr7B 89.121 239 19 4 276 507 442800895 442801133 1.240000e-74 291.0
17 TraesCS6A01G289000 chr7B 88.745 231 22 3 6 235 651358933 651359160 2.690000e-71 279.0
18 TraesCS6A01G289000 chr7B 91.192 193 13 3 45 235 442800695 442800885 3.500000e-65 259.0
19 TraesCS6A01G289000 chr7B 81.982 222 32 6 3316 3533 99130563 99130780 7.790000e-42 182.0
20 TraesCS6A01G289000 chr5B 89.076 238 20 3 276 507 524924750 524924987 1.240000e-74 291.0
21 TraesCS6A01G289000 chr5B 88.745 231 22 3 6 235 141600779 141600552 2.690000e-71 279.0
22 TraesCS6A01G289000 chr5B 87.603 242 23 4 276 510 141600542 141600301 1.250000e-69 274.0
23 TraesCS6A01G289000 chr5B 86.713 143 17 2 6 147 524914514 524914655 1.310000e-34 158.0
24 TraesCS6A01G289000 chr5B 84.524 84 11 2 3441 3523 123760693 123760775 8.130000e-12 82.4
25 TraesCS6A01G289000 chr3B 89.121 239 19 4 276 507 278404504 278404742 1.240000e-74 291.0
26 TraesCS6A01G289000 chr3B 89.177 231 21 3 6 235 278404267 278404494 5.770000e-73 285.0
27 TraesCS6A01G289000 chr7D 82.432 222 31 6 3316 3533 136253117 136253334 1.670000e-43 187.0
28 TraesCS6A01G289000 chr2A 85.124 121 15 2 985 1104 22184892 22184774 1.720000e-23 121.0
29 TraesCS6A01G289000 chr5A 84.524 84 11 2 3441 3523 118670734 118670816 8.130000e-12 82.4
30 TraesCS6A01G289000 chr5D 84.810 79 10 2 3446 3523 113391514 113391591 1.050000e-10 78.7


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 TraesCS6A01G289000 chr6A 520869912 520873444 3532 True 6525.000000 6525 100.000000 1 3533 1 chr6A.!!$R1 3532
1 TraesCS6A01G289000 chr6A 90032316 90034061 1745 False 1851.000000 1851 86.011000 614 2366 1 chr6A.!!$F2 1752
2 TraesCS6A01G289000 chr6A 83362151 83363014 863 False 848.000000 848 84.890000 983 1822 1 chr6A.!!$F1 839
3 TraesCS6A01G289000 chr6B 566535512 566538881 3369 True 2043.000000 3482 92.287500 6 3533 2 chr6B.!!$R3 3527
4 TraesCS6A01G289000 chr6B 147961088 147962861 1773 False 1840.000000 1840 85.620000 583 2366 1 chr6B.!!$F1 1783
5 TraesCS6A01G289000 chr6B 140450586 140451435 849 True 828.000000 828 84.642000 983 1814 1 chr6B.!!$R2 831
6 TraesCS6A01G289000 chr6D 73587594 73589362 1768 False 1895.000000 1895 86.157000 584 2366 1 chr6D.!!$F1 1782
7 TraesCS6A01G289000 chr6D 379720811 379723999 3188 False 1390.666667 3138 88.435667 351 3533 3 chr6D.!!$F3 3182
8 TraesCS6A01G289000 chr6D 65389190 65390056 866 True 833.000000 833 84.544000 983 1822 1 chr6D.!!$R1 839

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
904 916 0.17902 ACTTGCTACAGCCAGTGCAA 60.179 50.0 7.12 12.53 44.11 4.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2559 2618 1.133823 ACAGGCACACCAGATGAAACA 60.134 47.619 0.0 0.0 39.06 2.83 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
20 21 2.610438 ATGCTTTTGGTCCATGTCCT 57.390 45.000 0.00 0.00 0.00 3.85
21 22 2.380064 TGCTTTTGGTCCATGTCCTT 57.620 45.000 0.00 0.00 0.00 3.36
22 23 3.517296 TGCTTTTGGTCCATGTCCTTA 57.483 42.857 0.00 0.00 0.00 2.69
23 24 3.838565 TGCTTTTGGTCCATGTCCTTAA 58.161 40.909 0.00 0.00 0.00 1.85
29 30 7.628580 GCTTTTGGTCCATGTCCTTAAAGATAC 60.629 40.741 21.36 10.62 33.52 2.24
33 34 5.696724 GGTCCATGTCCTTAAAGATACGATG 59.303 44.000 0.00 0.00 0.00 3.84
40 41 8.058667 TGTCCTTAAAGATACGATGTTCAGTA 57.941 34.615 0.00 0.00 0.00 2.74
53 54 7.364878 CGATGTTCAGTATCGTTAGTTGTAG 57.635 40.000 0.00 0.00 41.71 2.74
56 57 9.219497 GATGTTCAGTATCGTTAGTTGTAGTAC 57.781 37.037 0.00 0.00 0.00 2.73
87 88 4.202357 TGAGTTTGTCAGTATGCCTTGACT 60.202 41.667 6.24 0.00 43.15 3.41
104 105 5.064452 CCTTGACTTAGCATGTGATCAAGAC 59.936 44.000 19.76 8.22 43.65 3.01
137 138 5.541101 TGTGTGCCCTAAAACTAGAGTAGAA 59.459 40.000 0.00 0.00 0.00 2.10
155 156 2.107204 AGAACTCTGCTGTGGTTTGGAT 59.893 45.455 0.00 0.00 0.00 3.41
185 186 3.578282 CAGGAGTTGCCCCAAAAGTTTAT 59.422 43.478 0.00 0.00 37.37 1.40
186 187 4.770010 CAGGAGTTGCCCCAAAAGTTTATA 59.230 41.667 0.00 0.00 37.37 0.98
187 188 5.016831 AGGAGTTGCCCCAAAAGTTTATAG 58.983 41.667 0.00 0.00 37.37 1.31
189 190 5.105877 GGAGTTGCCCCAAAAGTTTATAGTC 60.106 44.000 0.00 0.00 0.00 2.59
190 191 4.770531 AGTTGCCCCAAAAGTTTATAGTCC 59.229 41.667 0.00 0.00 0.00 3.85
212 213 2.295885 CTCATCTTCACCATCCCTTGC 58.704 52.381 0.00 0.00 0.00 4.01
231 232 1.587946 GCGAACTTGCTGGTTGTTTTG 59.412 47.619 0.00 0.00 0.00 2.44
232 233 2.874849 CGAACTTGCTGGTTGTTTTGT 58.125 42.857 0.02 0.00 0.00 2.83
233 234 2.598192 CGAACTTGCTGGTTGTTTTGTG 59.402 45.455 0.02 0.00 0.00 3.33
234 235 3.584834 GAACTTGCTGGTTGTTTTGTGT 58.415 40.909 0.02 0.00 0.00 3.72
235 236 3.676291 ACTTGCTGGTTGTTTTGTGTT 57.324 38.095 0.00 0.00 0.00 3.32
236 237 3.324993 ACTTGCTGGTTGTTTTGTGTTG 58.675 40.909 0.00 0.00 0.00 3.33
237 238 2.376808 TGCTGGTTGTTTTGTGTTGG 57.623 45.000 0.00 0.00 0.00 3.77
238 239 1.895798 TGCTGGTTGTTTTGTGTTGGA 59.104 42.857 0.00 0.00 0.00 3.53
239 240 2.499289 TGCTGGTTGTTTTGTGTTGGAT 59.501 40.909 0.00 0.00 0.00 3.41
240 241 2.865551 GCTGGTTGTTTTGTGTTGGATG 59.134 45.455 0.00 0.00 0.00 3.51
241 242 3.678529 GCTGGTTGTTTTGTGTTGGATGT 60.679 43.478 0.00 0.00 0.00 3.06
242 243 4.440802 GCTGGTTGTTTTGTGTTGGATGTA 60.441 41.667 0.00 0.00 0.00 2.29
243 244 5.000012 TGGTTGTTTTGTGTTGGATGTAC 58.000 39.130 0.00 0.00 0.00 2.90
244 245 4.039032 GGTTGTTTTGTGTTGGATGTACG 58.961 43.478 0.00 0.00 0.00 3.67
245 246 4.439016 GGTTGTTTTGTGTTGGATGTACGT 60.439 41.667 0.00 0.00 0.00 3.57
246 247 4.539509 TGTTTTGTGTTGGATGTACGTC 57.460 40.909 6.53 6.53 0.00 4.34
259 260 5.064579 TGGATGTACGTCTGTAATTTGCATG 59.935 40.000 14.61 0.00 30.94 4.06
264 265 4.072131 ACGTCTGTAATTTGCATGGAACT 58.928 39.130 0.00 0.00 0.00 3.01
265 266 5.242434 ACGTCTGTAATTTGCATGGAACTA 58.758 37.500 0.00 0.00 0.00 2.24
266 267 5.880332 ACGTCTGTAATTTGCATGGAACTAT 59.120 36.000 0.00 0.00 0.00 2.12
267 268 6.183360 ACGTCTGTAATTTGCATGGAACTATG 60.183 38.462 0.00 0.00 0.00 2.23
268 269 6.037062 CGTCTGTAATTTGCATGGAACTATGA 59.963 38.462 0.00 0.00 0.00 2.15
269 270 7.189512 GTCTGTAATTTGCATGGAACTATGAC 58.810 38.462 0.00 0.00 0.00 3.06
270 271 6.883756 TCTGTAATTTGCATGGAACTATGACA 59.116 34.615 0.00 0.45 0.00 3.58
271 272 7.392953 TCTGTAATTTGCATGGAACTATGACAA 59.607 33.333 0.00 3.91 0.00 3.18
272 273 8.065473 TGTAATTTGCATGGAACTATGACAAT 57.935 30.769 0.00 0.00 30.26 2.71
273 274 8.530311 TGTAATTTGCATGGAACTATGACAATT 58.470 29.630 0.00 0.00 31.60 2.32
274 275 7.837202 AATTTGCATGGAACTATGACAATTG 57.163 32.000 3.24 3.24 30.26 2.32
348 349 2.064762 CTGTGCTGTCTAGACTGTTGC 58.935 52.381 25.19 20.94 33.50 4.17
367 372 3.661944 TGCCAACATGCTGGTTATTTTG 58.338 40.909 16.37 0.00 38.86 2.44
369 374 3.432933 GCCAACATGCTGGTTATTTTGTG 59.567 43.478 16.37 0.00 38.86 3.33
370 375 4.630111 CCAACATGCTGGTTATTTTGTGT 58.370 39.130 7.00 0.00 0.00 3.72
374 379 5.911752 ACATGCTGGTTATTTTGTGTTTGA 58.088 33.333 0.00 0.00 0.00 2.69
375 380 6.523840 ACATGCTGGTTATTTTGTGTTTGAT 58.476 32.000 0.00 0.00 0.00 2.57
376 381 6.424509 ACATGCTGGTTATTTTGTGTTTGATG 59.575 34.615 0.00 0.00 0.00 3.07
382 387 8.864069 TGGTTATTTTGTGTTTGATGTACTTG 57.136 30.769 0.00 0.00 0.00 3.16
416 421 3.181462 TGGAGCTATGCCAGTTGATACAG 60.181 47.826 0.00 0.00 0.00 2.74
432 437 8.584157 AGTTGATACAGATATCTTAGCCTCTTG 58.416 37.037 1.33 0.00 38.47 3.02
457 462 7.688629 GGGACAACCTGACATTGTTGATGTTA 61.689 42.308 19.30 0.00 43.50 2.41
463 468 3.829886 ACATTGTTGATGTTAGCCACG 57.170 42.857 0.00 0.00 46.80 4.94
472 477 0.888736 TGTTAGCCACGCATGTGCTT 60.889 50.000 6.08 0.00 45.04 3.91
474 479 0.521291 TTAGCCACGCATGTGCTTTC 59.479 50.000 6.08 0.00 45.04 2.62
477 482 0.734889 GCCACGCATGTGCTTTCTAT 59.265 50.000 6.08 0.00 45.04 1.98
487 492 6.847792 CGCATGTGCTTTCTATACTGTTTATG 59.152 38.462 3.25 0.00 39.32 1.90
495 502 7.115095 GCTTTCTATACTGTTTATGTAGCTCCG 59.885 40.741 0.00 0.00 0.00 4.63
529 539 9.196139 TCATTAAATTTGGTAGTCCCCTTTATG 57.804 33.333 0.00 0.00 0.00 1.90
549 559 1.615392 GCAATTCTGCCTTCAACTGGT 59.385 47.619 0.00 0.00 43.26 4.00
550 560 2.036346 GCAATTCTGCCTTCAACTGGTT 59.964 45.455 0.00 0.00 43.26 3.67
551 561 3.645884 CAATTCTGCCTTCAACTGGTTG 58.354 45.455 7.10 7.10 41.71 3.77
552 562 2.435372 TTCTGCCTTCAACTGGTTGT 57.565 45.000 12.34 0.00 41.16 3.32
553 563 3.569194 TTCTGCCTTCAACTGGTTGTA 57.431 42.857 12.34 3.45 41.16 2.41
554 564 3.788227 TCTGCCTTCAACTGGTTGTAT 57.212 42.857 12.34 0.00 41.16 2.29
555 565 3.411446 TCTGCCTTCAACTGGTTGTATG 58.589 45.455 12.34 3.01 41.16 2.39
556 566 3.149196 CTGCCTTCAACTGGTTGTATGT 58.851 45.455 12.34 0.00 41.16 2.29
557 567 2.884012 TGCCTTCAACTGGTTGTATGTG 59.116 45.455 12.34 1.75 41.16 3.21
558 568 3.146066 GCCTTCAACTGGTTGTATGTGA 58.854 45.455 12.34 0.00 41.16 3.58
559 569 3.568007 GCCTTCAACTGGTTGTATGTGAA 59.432 43.478 12.34 0.00 41.16 3.18
560 570 4.556699 GCCTTCAACTGGTTGTATGTGAAC 60.557 45.833 12.34 0.00 41.16 3.18
562 572 5.277974 CCTTCAACTGGTTGTATGTGAACTG 60.278 44.000 12.34 0.00 41.16 3.16
563 573 5.029807 TCAACTGGTTGTATGTGAACTGA 57.970 39.130 12.34 0.00 41.16 3.41
565 575 6.764379 TCAACTGGTTGTATGTGAACTGATA 58.236 36.000 12.34 0.00 41.16 2.15
566 576 6.649141 TCAACTGGTTGTATGTGAACTGATAC 59.351 38.462 12.34 0.00 41.16 2.24
573 583 7.334421 GGTTGTATGTGAACTGATACTGTGATT 59.666 37.037 0.00 0.00 0.00 2.57
600 610 7.776107 TCTAGTCTCCTTTCTGTAATGTGATG 58.224 38.462 0.00 0.00 0.00 3.07
606 616 8.988060 TCTCCTTTCTGTAATGTGATGGTATAA 58.012 33.333 0.00 0.00 0.00 0.98
697 709 2.478872 AATCCAGGTAGCAGCCTCTA 57.521 50.000 0.00 0.00 36.58 2.43
829 841 1.946768 TGACGAGAAAAAGGCACAAGG 59.053 47.619 0.00 0.00 0.00 3.61
863 875 2.288030 GCATGCATCAAGAGCCCATTAC 60.288 50.000 14.21 0.00 0.00 1.89
869 881 3.695830 TCAAGAGCCCATTACGTTCTT 57.304 42.857 0.00 0.00 0.00 2.52
891 903 2.435805 TGGTTCTGAGAGTTCACTTGCT 59.564 45.455 0.00 0.00 0.00 3.91
894 906 4.501571 GGTTCTGAGAGTTCACTTGCTACA 60.502 45.833 0.00 0.00 0.00 2.74
903 915 1.451504 ACTTGCTACAGCCAGTGCA 59.548 52.632 7.12 0.00 44.11 4.57
904 916 0.179020 ACTTGCTACAGCCAGTGCAA 60.179 50.000 7.12 12.53 44.11 4.08
933 945 1.889170 CTCAGTTTTCTTCAAGGGCCC 59.111 52.381 16.46 16.46 0.00 5.80
943 955 4.101448 AAGGGCCCGCAGCTACTG 62.101 66.667 18.44 0.00 43.05 2.74
994 1006 1.971481 TCTGCTGCAGAAAGCTTGAA 58.029 45.000 28.72 3.78 45.94 2.69
1062 1074 3.197766 CCTTCTACAGGTACAAGATGCCA 59.802 47.826 0.00 0.00 37.99 4.92
1089 1101 4.138290 TGTTGACAAAAATAGAAGGCCGA 58.862 39.130 0.00 0.00 0.00 5.54
1608 1644 4.785453 GCTGCTGGGGGAGGTTCG 62.785 72.222 0.00 0.00 0.00 3.95
1654 1690 0.829990 TCACAGTCAAGGTGCTGACA 59.170 50.000 6.59 0.00 46.81 3.58
1865 1910 0.895559 GGGACACCAAAGGCTGAAGG 60.896 60.000 0.00 0.00 36.50 3.46
2289 2337 1.672356 CGGCAAGAACTCCCAGGTG 60.672 63.158 0.00 0.00 0.00 4.00
2387 2435 3.436180 CGATTCCCTACCACCCTACTACT 60.436 52.174 0.00 0.00 0.00 2.57
2388 2436 4.202503 CGATTCCCTACCACCCTACTACTA 60.203 50.000 0.00 0.00 0.00 1.82
2391 2439 3.117360 TCCCTACCACCCTACTACTAAGC 60.117 52.174 0.00 0.00 0.00 3.09
2405 2464 7.856894 CCTACTACTAAGCGTCTTTGATAAGTC 59.143 40.741 7.69 0.00 32.98 3.01
2408 2467 6.518208 ACTAAGCGTCTTTGATAAGTCTCT 57.482 37.500 7.69 0.00 32.98 3.10
2417 2476 6.421202 GTCTTTGATAAGTCTCTGTCGTTGTT 59.579 38.462 0.00 0.00 32.98 2.83
2423 2482 5.470845 AAGTCTCTGTCGTTGTTTTTCAG 57.529 39.130 0.00 0.00 0.00 3.02
2437 2496 7.462200 CGTTGTTTTTCAGCTTTTCGTATTTGT 60.462 33.333 0.00 0.00 0.00 2.83
2438 2497 7.215696 TGTTTTTCAGCTTTTCGTATTTGTG 57.784 32.000 0.00 0.00 0.00 3.33
2439 2498 6.254589 TGTTTTTCAGCTTTTCGTATTTGTGG 59.745 34.615 0.00 0.00 0.00 4.17
2440 2499 5.508200 TTTCAGCTTTTCGTATTTGTGGT 57.492 34.783 0.00 0.00 0.00 4.16
2441 2500 4.481930 TCAGCTTTTCGTATTTGTGGTG 57.518 40.909 0.00 0.00 0.00 4.17
2443 2502 4.336993 TCAGCTTTTCGTATTTGTGGTGTT 59.663 37.500 0.00 0.00 0.00 3.32
2445 2504 6.038382 TCAGCTTTTCGTATTTGTGGTGTTTA 59.962 34.615 0.00 0.00 0.00 2.01
2446 2505 6.693545 CAGCTTTTCGTATTTGTGGTGTTTAA 59.306 34.615 0.00 0.00 0.00 1.52
2449 2508 7.221259 GCTTTTCGTATTTGTGGTGTTTAAACT 59.779 33.333 18.72 0.00 0.00 2.66
2450 2509 8.983307 TTTTCGTATTTGTGGTGTTTAAACTT 57.017 26.923 18.72 0.00 0.00 2.66
2451 2510 8.983307 TTTCGTATTTGTGGTGTTTAAACTTT 57.017 26.923 18.72 0.00 0.00 2.66
2452 2511 7.972623 TCGTATTTGTGGTGTTTAAACTTTG 57.027 32.000 18.72 0.00 0.00 2.77
2453 2512 7.759465 TCGTATTTGTGGTGTTTAAACTTTGA 58.241 30.769 18.72 0.00 0.00 2.69
2454 2513 7.911205 TCGTATTTGTGGTGTTTAAACTTTGAG 59.089 33.333 18.72 0.64 0.00 3.02
2455 2514 7.698970 CGTATTTGTGGTGTTTAAACTTTGAGT 59.301 33.333 18.72 2.37 0.00 3.41
2456 2515 9.361315 GTATTTGTGGTGTTTAAACTTTGAGTT 57.639 29.630 18.72 1.93 40.80 3.01
2459 2518 9.930693 TTTGTGGTGTTTAAACTTTGAGTTATT 57.069 25.926 18.72 0.00 37.47 1.40
2460 2519 8.918961 TGTGGTGTTTAAACTTTGAGTTATTG 57.081 30.769 18.72 0.00 37.47 1.90
2461 2520 7.976734 TGTGGTGTTTAAACTTTGAGTTATTGG 59.023 33.333 18.72 0.00 37.47 3.16
2462 2521 7.977293 GTGGTGTTTAAACTTTGAGTTATTGGT 59.023 33.333 18.72 0.00 37.47 3.67
2463 2522 8.532819 TGGTGTTTAAACTTTGAGTTATTGGTT 58.467 29.630 18.72 0.00 37.47 3.67
2482 2541 8.954950 ATTGGTTATTTCAGTATCTGAGTCAG 57.045 34.615 14.36 14.36 41.75 3.51
2483 2542 7.482169 TGGTTATTTCAGTATCTGAGTCAGT 57.518 36.000 19.53 9.79 41.75 3.41
2484 2543 7.907389 TGGTTATTTCAGTATCTGAGTCAGTT 58.093 34.615 19.53 13.93 41.75 3.16
2485 2544 8.375506 TGGTTATTTCAGTATCTGAGTCAGTTT 58.624 33.333 19.53 11.09 41.75 2.66
2486 2545 8.660373 GGTTATTTCAGTATCTGAGTCAGTTTG 58.340 37.037 19.53 13.02 41.75 2.93
2487 2546 8.660373 GTTATTTCAGTATCTGAGTCAGTTTGG 58.340 37.037 19.53 7.48 41.75 3.28
2488 2547 5.808366 TTCAGTATCTGAGTCAGTTTGGT 57.192 39.130 19.53 5.28 41.75 3.67
2489 2548 5.139435 TCAGTATCTGAGTCAGTTTGGTG 57.861 43.478 19.53 11.69 35.39 4.17
2490 2549 4.588951 TCAGTATCTGAGTCAGTTTGGTGT 59.411 41.667 19.53 2.15 35.39 4.16
2491 2550 5.070446 TCAGTATCTGAGTCAGTTTGGTGTT 59.930 40.000 19.53 0.00 35.39 3.32
2492 2551 5.760253 CAGTATCTGAGTCAGTTTGGTGTTT 59.240 40.000 19.53 0.00 32.44 2.83
2493 2552 6.929049 CAGTATCTGAGTCAGTTTGGTGTTTA 59.071 38.462 19.53 0.00 32.44 2.01
2494 2553 7.441157 CAGTATCTGAGTCAGTTTGGTGTTTAA 59.559 37.037 19.53 0.00 32.44 1.52
2495 2554 7.990886 AGTATCTGAGTCAGTTTGGTGTTTAAA 59.009 33.333 19.53 0.00 32.61 1.52
2496 2555 6.431198 TCTGAGTCAGTTTGGTGTTTAAAC 57.569 37.500 19.53 11.54 38.09 2.01
2497 2556 5.355910 TCTGAGTCAGTTTGGTGTTTAAACC 59.644 40.000 19.53 2.53 38.47 3.27
2505 2564 7.393796 TCAGTTTGGTGTTTAAACCTTGAGTTA 59.606 33.333 15.59 0.00 41.16 2.24
2533 2592 8.692710 TGGTTATTTCTGTATCGAGTCAGTTAT 58.307 33.333 15.79 12.98 33.89 1.89
2534 2593 9.530633 GGTTATTTCTGTATCGAGTCAGTTATT 57.469 33.333 15.79 7.67 33.89 1.40
2542 2601 8.969121 TGTATCGAGTCAGTTATTAAACGAAA 57.031 30.769 0.00 0.00 40.73 3.46
2552 2611 9.982291 TCAGTTATTAAACGAAAGACAATATGC 57.018 29.630 0.00 0.00 40.73 3.14
2559 2618 3.055094 ACGAAAGACAATATGCCTGGTCT 60.055 43.478 0.00 0.00 42.08 3.85
2563 2622 4.307032 AGACAATATGCCTGGTCTGTTT 57.693 40.909 0.00 0.00 39.04 2.83
2587 2646 2.094286 TCTGGTGTGCCTGTTTGTTTTG 60.094 45.455 0.00 0.00 35.49 2.44
2599 2658 5.447548 CCTGTTTGTTTTGTTGCCATCTTTG 60.448 40.000 0.00 0.00 0.00 2.77
2695 2765 4.446857 TTTATGCTATACGCGTTTGCTC 57.553 40.909 20.78 4.04 43.27 4.26
2725 2795 7.147949 CCTTTTGCTTATCCAGAAATCTCATGT 60.148 37.037 0.00 0.00 0.00 3.21
2730 2802 7.828717 TGCTTATCCAGAAATCTCATGTTACAA 59.171 33.333 0.00 0.00 0.00 2.41
2737 2809 7.551974 CCAGAAATCTCATGTTACAAGAGACAT 59.448 37.037 20.28 12.97 40.24 3.06
2774 2846 4.290093 ACAGTTACATAGCTCCCTGATGA 58.710 43.478 0.00 0.00 0.00 2.92
2783 2855 3.443052 AGCTCCCTGATGAGGATCTATG 58.557 50.000 0.00 0.00 42.93 2.23
2786 2858 3.581770 CTCCCTGATGAGGATCTATGCAA 59.418 47.826 0.00 0.00 42.93 4.08
2800 2872 5.263968 TCTATGCAACCTAGTCAAGTAGC 57.736 43.478 0.00 0.00 0.00 3.58
2801 2873 4.956700 TCTATGCAACCTAGTCAAGTAGCT 59.043 41.667 0.00 0.00 0.00 3.32
2803 2875 2.003301 GCAACCTAGTCAAGTAGCTGC 58.997 52.381 0.00 0.00 0.00 5.25
2804 2876 2.354203 GCAACCTAGTCAAGTAGCTGCT 60.354 50.000 7.57 7.57 30.36 4.24
2806 2878 2.808919 ACCTAGTCAAGTAGCTGCTGA 58.191 47.619 13.43 2.44 0.00 4.26
2809 2881 2.021355 AGTCAAGTAGCTGCTGATGC 57.979 50.000 13.43 5.25 40.20 3.91
2810 2882 1.012841 GTCAAGTAGCTGCTGATGCC 58.987 55.000 13.43 0.00 38.71 4.40
2811 2883 0.614812 TCAAGTAGCTGCTGATGCCA 59.385 50.000 13.43 0.00 38.71 4.92
2812 2884 1.015109 CAAGTAGCTGCTGATGCCAG 58.985 55.000 13.43 0.00 43.22 4.85
2856 2937 1.747355 GCTGTCATGAAATCACCTGGG 59.253 52.381 0.00 0.00 0.00 4.45
2871 2952 6.636454 TCACCTGGGTAGATTATCTTTGTT 57.364 37.500 0.00 0.00 0.00 2.83
2878 2959 7.826690 TGGGTAGATTATCTTTGTTTTTCTGC 58.173 34.615 0.00 0.00 0.00 4.26
2940 3027 6.254589 GTGATTTGCGGAGATATATAGCACTC 59.745 42.308 0.07 3.80 37.57 3.51
2942 3029 2.097629 TGCGGAGATATATAGCACTCGC 59.902 50.000 18.66 18.66 38.99 5.03
2965 3052 1.776975 TTTTTGCCATGGCCCTTGGG 61.777 55.000 33.44 8.97 41.09 4.12
2967 3054 2.686246 TTTGCCATGGCCCTTGGGAA 62.686 55.000 33.44 20.52 42.06 3.97
2968 3055 2.284552 GCCATGGCCCTTGGGAAA 60.285 61.111 27.24 0.00 34.66 3.13
2969 3056 1.917787 GCCATGGCCCTTGGGAAAA 60.918 57.895 27.24 0.00 34.66 2.29
2970 3057 1.487850 GCCATGGCCCTTGGGAAAAA 61.488 55.000 27.24 0.00 34.66 1.94
2971 3058 1.288188 CCATGGCCCTTGGGAAAAAT 58.712 50.000 10.36 0.00 0.00 1.82
2972 3059 2.476199 CCATGGCCCTTGGGAAAAATA 58.524 47.619 10.36 0.00 0.00 1.40
2973 3060 2.843113 CCATGGCCCTTGGGAAAAATAA 59.157 45.455 10.36 0.00 0.00 1.40
2974 3061 3.265479 CCATGGCCCTTGGGAAAAATAAA 59.735 43.478 10.36 0.00 0.00 1.40
2975 3062 4.263683 CCATGGCCCTTGGGAAAAATAAAA 60.264 41.667 10.36 0.00 0.00 1.52
2976 3063 5.320277 CATGGCCCTTGGGAAAAATAAAAA 58.680 37.500 10.36 0.00 0.00 1.94
3006 3093 5.248477 AGCATGAAGTTCCTCCTTTGTACTA 59.752 40.000 0.00 0.00 0.00 1.82
3008 3095 6.464222 CATGAAGTTCCTCCTTTGTACTACA 58.536 40.000 0.00 0.00 0.00 2.74
3011 3098 6.269077 TGAAGTTCCTCCTTTGTACTACATGA 59.731 38.462 0.00 0.00 0.00 3.07
3012 3099 6.038997 AGTTCCTCCTTTGTACTACATGAC 57.961 41.667 0.00 0.00 0.00 3.06
3042 3207 8.924511 ACAGAAGATTATGAAAGAAACTGGAA 57.075 30.769 0.00 0.00 0.00 3.53
3044 3209 9.837525 CAGAAGATTATGAAAGAAACTGGAAAG 57.162 33.333 0.00 0.00 0.00 2.62
3045 3210 9.018582 AGAAGATTATGAAAGAAACTGGAAAGG 57.981 33.333 0.00 0.00 0.00 3.11
3049 3214 5.774498 ATGAAAGAAACTGGAAAGGTCAC 57.226 39.130 0.00 0.00 0.00 3.67
3062 3227 0.615331 AGGTCACCACTACATGCCAG 59.385 55.000 0.00 0.00 0.00 4.85
3081 3246 4.631377 GCCAGCATTTTCTTATTTGGAACC 59.369 41.667 0.00 0.00 0.00 3.62
3084 3249 6.458210 CAGCATTTTCTTATTTGGAACCACT 58.542 36.000 0.00 0.00 0.00 4.00
3085 3250 7.309744 CCAGCATTTTCTTATTTGGAACCACTA 60.310 37.037 0.00 0.00 0.00 2.74
3086 3251 7.756722 CAGCATTTTCTTATTTGGAACCACTAG 59.243 37.037 0.00 0.00 0.00 2.57
3087 3252 7.451566 AGCATTTTCTTATTTGGAACCACTAGT 59.548 33.333 0.00 0.00 0.00 2.57
3088 3253 8.736244 GCATTTTCTTATTTGGAACCACTAGTA 58.264 33.333 0.00 0.00 0.00 1.82
3093 3258 8.890410 TCTTATTTGGAACCACTAGTACTAGT 57.110 34.615 26.61 26.61 46.52 2.57
3094 3259 9.979897 TCTTATTTGGAACCACTAGTACTAGTA 57.020 33.333 30.34 15.84 43.98 1.82
3096 3261 9.759473 TTATTTGGAACCACTAGTACTAGTAGT 57.241 33.333 30.34 26.73 43.98 2.73
3098 3263 8.798859 TTTGGAACCACTAGTACTAGTAGTAG 57.201 38.462 30.75 30.75 43.98 2.57
3159 3333 1.670811 CTAACAATGGCGTCCCACATC 59.329 52.381 0.00 0.00 45.77 3.06
3165 3339 2.887568 GCGTCCCACATCGAGCAG 60.888 66.667 0.00 0.00 0.00 4.24
3166 3340 2.887568 CGTCCCACATCGAGCAGC 60.888 66.667 0.00 0.00 0.00 5.25
3167 3341 2.887568 GTCCCACATCGAGCAGCG 60.888 66.667 0.00 0.00 42.69 5.18
3239 3413 6.116680 TCGATCATCATCTAGTCGATCATG 57.883 41.667 0.00 0.00 36.52 3.07
3255 3429 2.619446 ATGTCACCCTGGGCAGCAT 61.619 57.895 14.08 11.40 0.00 3.79
3276 3450 3.491652 GCTCAACTTCTCCCGCGC 61.492 66.667 0.00 0.00 0.00 6.86
3340 3514 2.359230 GAGCCGCTCCTGCAGTTT 60.359 61.111 13.81 0.00 39.64 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.893424 AGGACATGGACCAAAAGCATT 58.107 42.857 0.00 0.00 0.00 3.56
1 2 2.610438 AGGACATGGACCAAAAGCAT 57.390 45.000 0.00 0.00 0.00 3.79
3 4 4.522789 TCTTTAAGGACATGGACCAAAAGC 59.477 41.667 20.69 0.00 35.06 3.51
4 5 6.840780 ATCTTTAAGGACATGGACCAAAAG 57.159 37.500 20.09 20.09 35.71 2.27
5 6 6.373216 CGTATCTTTAAGGACATGGACCAAAA 59.627 38.462 0.00 10.77 0.00 2.44
6 7 5.878116 CGTATCTTTAAGGACATGGACCAAA 59.122 40.000 0.00 5.62 0.00 3.28
8 9 4.712829 TCGTATCTTTAAGGACATGGACCA 59.287 41.667 12.49 0.00 0.00 4.02
9 10 5.272283 TCGTATCTTTAAGGACATGGACC 57.728 43.478 0.00 0.00 0.00 4.46
10 11 6.281405 ACATCGTATCTTTAAGGACATGGAC 58.719 40.000 0.00 0.00 0.00 4.02
13 14 7.492669 ACTGAACATCGTATCTTTAAGGACATG 59.507 37.037 0.00 0.00 0.00 3.21
14 15 7.556844 ACTGAACATCGTATCTTTAAGGACAT 58.443 34.615 0.00 0.00 0.00 3.06
15 16 6.931838 ACTGAACATCGTATCTTTAAGGACA 58.068 36.000 0.00 0.00 0.00 4.02
16 17 9.182933 GATACTGAACATCGTATCTTTAAGGAC 57.817 37.037 0.00 0.00 39.10 3.85
18 19 8.217077 CGATACTGAACATCGTATCTTTAAGG 57.783 38.462 14.37 0.00 39.70 2.69
33 34 8.446273 TGAGTACTACAACTAACGATACTGAAC 58.554 37.037 0.00 0.00 0.00 3.18
75 76 4.191544 TCACATGCTAAGTCAAGGCATAC 58.808 43.478 0.00 0.00 43.62 2.39
87 88 6.038603 GCCATTTAGTCTTGATCACATGCTAA 59.961 38.462 0.00 0.00 0.00 3.09
93 94 4.696877 CACAGCCATTTAGTCTTGATCACA 59.303 41.667 0.00 0.00 0.00 3.58
137 138 2.290323 GGTATCCAAACCACAGCAGAGT 60.290 50.000 0.00 0.00 39.50 3.24
147 148 3.009143 ACTCCTGTTCAGGTATCCAAACC 59.991 47.826 17.00 0.00 40.06 3.27
155 156 0.690762 GGGCAACTCCTGTTCAGGTA 59.309 55.000 17.00 5.14 33.52 3.08
185 186 3.706594 GGATGGTGAAGATGAGTGGACTA 59.293 47.826 0.00 0.00 0.00 2.59
186 187 2.503356 GGATGGTGAAGATGAGTGGACT 59.497 50.000 0.00 0.00 0.00 3.85
187 188 2.420687 GGGATGGTGAAGATGAGTGGAC 60.421 54.545 0.00 0.00 0.00 4.02
189 190 1.842562 AGGGATGGTGAAGATGAGTGG 59.157 52.381 0.00 0.00 0.00 4.00
190 191 3.276857 CAAGGGATGGTGAAGATGAGTG 58.723 50.000 0.00 0.00 0.00 3.51
212 213 2.598192 CACAAAACAACCAGCAAGTTCG 59.402 45.455 0.00 0.00 0.00 3.95
231 232 6.304126 CAAATTACAGACGTACATCCAACAC 58.696 40.000 0.00 0.00 0.00 3.32
232 233 5.106869 GCAAATTACAGACGTACATCCAACA 60.107 40.000 0.00 0.00 0.00 3.33
233 234 5.106869 TGCAAATTACAGACGTACATCCAAC 60.107 40.000 0.00 0.00 0.00 3.77
234 235 4.998033 TGCAAATTACAGACGTACATCCAA 59.002 37.500 0.00 0.00 0.00 3.53
235 236 4.570930 TGCAAATTACAGACGTACATCCA 58.429 39.130 0.00 0.00 0.00 3.41
236 237 5.501715 CATGCAAATTACAGACGTACATCC 58.498 41.667 0.00 0.00 0.00 3.51
237 238 5.293324 TCCATGCAAATTACAGACGTACATC 59.707 40.000 0.00 0.00 0.00 3.06
238 239 5.182487 TCCATGCAAATTACAGACGTACAT 58.818 37.500 0.00 0.00 0.00 2.29
239 240 4.570930 TCCATGCAAATTACAGACGTACA 58.429 39.130 0.00 0.00 0.00 2.90
240 241 5.121768 AGTTCCATGCAAATTACAGACGTAC 59.878 40.000 0.00 0.00 0.00 3.67
241 242 5.242434 AGTTCCATGCAAATTACAGACGTA 58.758 37.500 0.00 0.00 0.00 3.57
242 243 4.072131 AGTTCCATGCAAATTACAGACGT 58.928 39.130 0.00 0.00 0.00 4.34
243 244 4.685169 AGTTCCATGCAAATTACAGACG 57.315 40.909 0.00 0.00 0.00 4.18
244 245 7.148255 TGTCATAGTTCCATGCAAATTACAGAC 60.148 37.037 0.00 0.00 0.00 3.51
245 246 6.883756 TGTCATAGTTCCATGCAAATTACAGA 59.116 34.615 0.00 0.00 0.00 3.41
246 247 7.087409 TGTCATAGTTCCATGCAAATTACAG 57.913 36.000 0.00 0.00 0.00 2.74
266 267 9.412460 AGGCTAAGATATTTGAATCAATTGTCA 57.588 29.630 14.06 0.00 0.00 3.58
267 268 9.890352 GAGGCTAAGATATTTGAATCAATTGTC 57.110 33.333 5.13 1.65 0.00 3.18
268 269 9.638176 AGAGGCTAAGATATTTGAATCAATTGT 57.362 29.630 5.13 0.00 0.00 2.71
272 273 9.784531 CCTAAGAGGCTAAGATATTTGAATCAA 57.215 33.333 0.00 0.00 0.00 2.57
273 274 9.159254 TCCTAAGAGGCTAAGATATTTGAATCA 57.841 33.333 0.00 0.00 34.61 2.57
274 275 9.430623 GTCCTAAGAGGCTAAGATATTTGAATC 57.569 37.037 0.00 0.00 34.61 2.52
289 290 3.686916 AGTCAAGTTGTCCTAAGAGGC 57.313 47.619 2.11 0.00 34.61 4.70
296 297 3.443681 CACCAACAAAGTCAAGTTGTCCT 59.556 43.478 2.11 0.00 42.62 3.85
348 349 4.630111 ACACAAAATAACCAGCATGTTGG 58.370 39.130 25.46 25.46 44.09 3.77
367 372 7.433719 TGCAAATTACACAAGTACATCAAACAC 59.566 33.333 0.00 0.00 0.00 3.32
369 374 7.922505 TGCAAATTACACAAGTACATCAAAC 57.077 32.000 0.00 0.00 0.00 2.93
370 375 7.598118 CCATGCAAATTACACAAGTACATCAAA 59.402 33.333 0.00 0.00 0.00 2.69
374 379 6.625740 GCTCCATGCAAATTACACAAGTACAT 60.626 38.462 0.00 0.00 42.31 2.29
375 380 5.335583 GCTCCATGCAAATTACACAAGTACA 60.336 40.000 0.00 0.00 42.31 2.90
376 381 5.095490 GCTCCATGCAAATTACACAAGTAC 58.905 41.667 0.00 0.00 42.31 2.73
416 421 5.301555 GTTGTCCCAAGAGGCTAAGATATC 58.698 45.833 0.00 0.00 34.51 1.63
432 437 2.582052 TCAACAATGTCAGGTTGTCCC 58.418 47.619 15.74 0.00 43.64 4.46
445 450 2.158559 TGCGTGGCTAACATCAACAAT 58.841 42.857 0.00 0.00 0.00 2.71
463 468 7.697691 ACATAAACAGTATAGAAAGCACATGC 58.302 34.615 0.00 0.00 42.49 4.06
472 477 6.774170 TCCGGAGCTACATAAACAGTATAGAA 59.226 38.462 0.00 0.00 0.00 2.10
474 479 6.570672 TCCGGAGCTACATAAACAGTATAG 57.429 41.667 0.00 0.00 0.00 1.31
477 482 5.864418 AATCCGGAGCTACATAAACAGTA 57.136 39.130 11.34 0.00 0.00 2.74
514 524 4.580580 CAGAATTGCATAAAGGGGACTACC 59.419 45.833 0.00 0.00 42.68 3.18
529 539 4.103836 CAACCAGTTGAAGGCAGAATTGC 61.104 47.826 4.47 0.00 45.04 3.56
540 550 5.432645 TCAGTTCACATACAACCAGTTGAA 58.567 37.500 17.06 0.00 42.93 2.69
541 551 5.029807 TCAGTTCACATACAACCAGTTGA 57.970 39.130 17.06 1.85 42.93 3.18
549 559 8.314021 AGAATCACAGTATCAGTTCACATACAA 58.686 33.333 0.00 0.00 0.00 2.41
550 560 7.840931 AGAATCACAGTATCAGTTCACATACA 58.159 34.615 0.00 0.00 0.00 2.29
551 561 8.194104 AGAGAATCACAGTATCAGTTCACATAC 58.806 37.037 0.00 0.00 37.82 2.39
552 562 8.298729 AGAGAATCACAGTATCAGTTCACATA 57.701 34.615 0.00 0.00 37.82 2.29
553 563 7.180322 AGAGAATCACAGTATCAGTTCACAT 57.820 36.000 0.00 0.00 37.82 3.21
554 564 6.596309 AGAGAATCACAGTATCAGTTCACA 57.404 37.500 0.00 0.00 37.82 3.58
555 565 7.767261 ACTAGAGAATCACAGTATCAGTTCAC 58.233 38.462 0.00 0.00 37.82 3.18
556 566 7.831690 AGACTAGAGAATCACAGTATCAGTTCA 59.168 37.037 0.00 0.00 37.82 3.18
557 567 8.220755 AGACTAGAGAATCACAGTATCAGTTC 57.779 38.462 0.00 0.00 37.82 3.01
558 568 7.284489 GGAGACTAGAGAATCACAGTATCAGTT 59.716 40.741 0.00 0.00 40.34 3.16
559 569 6.770785 GGAGACTAGAGAATCACAGTATCAGT 59.229 42.308 0.00 0.00 40.34 3.41
560 570 6.998074 AGGAGACTAGAGAATCACAGTATCAG 59.002 42.308 0.00 0.00 40.34 2.90
562 572 7.817418 AAGGAGACTAGAGAATCACAGTATC 57.183 40.000 0.00 0.00 42.68 2.24
563 573 8.058847 AGAAAGGAGACTAGAGAATCACAGTAT 58.941 37.037 0.00 0.00 42.68 2.12
565 575 6.152661 CAGAAAGGAGACTAGAGAATCACAGT 59.847 42.308 0.00 0.00 42.68 3.55
566 576 6.152661 ACAGAAAGGAGACTAGAGAATCACAG 59.847 42.308 0.00 0.00 42.68 3.66
573 583 7.175797 TCACATTACAGAAAGGAGACTAGAGA 58.824 38.462 0.00 0.00 42.68 3.10
697 709 4.034858 CACTTTGTCAGATTGCAGCGATAT 59.965 41.667 0.00 0.00 0.00 1.63
807 819 3.548818 CCTTGTGCCTTTTTCTCGTCAAG 60.549 47.826 0.00 0.00 0.00 3.02
809 821 1.946768 CCTTGTGCCTTTTTCTCGTCA 59.053 47.619 0.00 0.00 0.00 4.35
810 822 1.947456 ACCTTGTGCCTTTTTCTCGTC 59.053 47.619 0.00 0.00 0.00 4.20
829 841 0.966875 TGCATGCAGGGGATCACAAC 60.967 55.000 18.46 0.00 0.00 3.32
835 847 0.554305 TCTTGATGCATGCAGGGGAT 59.446 50.000 26.69 8.70 0.00 3.85
863 875 4.025647 GTGAACTCTCAGAACCAAAGAACG 60.026 45.833 0.00 0.00 30.14 3.95
869 881 3.118261 AGCAAGTGAACTCTCAGAACCAA 60.118 43.478 0.00 0.00 30.14 3.67
891 903 2.618241 CTGACTTTTTGCACTGGCTGTA 59.382 45.455 0.00 0.00 41.91 2.74
894 906 0.386838 GCTGACTTTTTGCACTGGCT 59.613 50.000 0.00 0.00 41.91 4.75
903 915 6.515272 TGAAGAAAACTGAGCTGACTTTTT 57.485 33.333 0.00 0.00 0.00 1.94
904 916 6.405176 CCTTGAAGAAAACTGAGCTGACTTTT 60.405 38.462 0.00 0.00 0.00 2.27
943 955 3.712187 TGTGGAAAATTTCAGAAACGGC 58.288 40.909 8.09 0.00 0.00 5.68
944 956 5.630680 CAGATGTGGAAAATTTCAGAAACGG 59.369 40.000 8.09 0.00 0.00 4.44
994 1006 0.889994 TTTTGCAGCGCCATCTTGAT 59.110 45.000 2.29 0.00 0.00 2.57
1062 1074 7.154656 GGCCTTCTATTTTTGTCAACATTCTT 58.845 34.615 0.00 0.00 0.00 2.52
1089 1101 7.342799 ACAATATTTGTCTTGATGCCATTACCT 59.657 33.333 0.00 0.00 40.56 3.08
1215 1227 2.380064 TGACCAAGGCAATTCCTGTT 57.620 45.000 0.00 0.00 46.94 3.16
1608 1644 3.084039 TGAGGTTGCATGTTCTTCATCC 58.916 45.455 0.00 0.00 34.09 3.51
1654 1690 0.255033 TCATCTCCAGCAGCTGCAAT 59.745 50.000 38.24 18.36 45.16 3.56
1865 1910 3.763897 AGTCTGGTTGCCATTGGAATTAC 59.236 43.478 6.95 0.00 30.82 1.89
2061 2109 4.855340 TCTTGTTCTTCACCACTTCCTTT 58.145 39.130 0.00 0.00 0.00 3.11
2289 2337 2.954611 GGCTTGGCGTTCTTCACC 59.045 61.111 0.00 0.00 0.00 4.02
2387 2435 6.268825 ACAGAGACTTATCAAAGACGCTTA 57.731 37.500 0.00 0.00 35.93 3.09
2388 2436 5.140747 ACAGAGACTTATCAAAGACGCTT 57.859 39.130 0.00 0.00 35.93 4.68
2391 2439 4.724303 ACGACAGAGACTTATCAAAGACG 58.276 43.478 0.00 0.00 36.50 4.18
2405 2464 3.951979 AGCTGAAAAACAACGACAGAG 57.048 42.857 0.00 0.00 0.00 3.35
2408 2467 3.849145 CGAAAAGCTGAAAAACAACGACA 59.151 39.130 0.00 0.00 0.00 4.35
2417 2476 5.746245 CACCACAAATACGAAAAGCTGAAAA 59.254 36.000 0.00 0.00 0.00 2.29
2423 2482 7.221259 AGTTTAAACACCACAAATACGAAAAGC 59.779 33.333 20.06 0.00 0.00 3.51
2437 2496 8.068892 ACCAATAACTCAAAGTTTAAACACCA 57.931 30.769 20.06 0.77 39.51 4.17
2438 2497 8.936070 AACCAATAACTCAAAGTTTAAACACC 57.064 30.769 20.06 0.00 39.51 4.16
2457 2516 8.543774 ACTGACTCAGATACTGAAATAACCAAT 58.456 33.333 13.25 0.00 40.18 3.16
2458 2517 7.907389 ACTGACTCAGATACTGAAATAACCAA 58.093 34.615 13.25 0.00 40.18 3.67
2459 2518 7.482169 ACTGACTCAGATACTGAAATAACCA 57.518 36.000 13.25 0.00 40.18 3.67
2460 2519 8.660373 CAAACTGACTCAGATACTGAAATAACC 58.340 37.037 13.25 0.00 40.18 2.85
2461 2520 8.660373 CCAAACTGACTCAGATACTGAAATAAC 58.340 37.037 13.25 0.00 40.18 1.89
2462 2521 8.375506 ACCAAACTGACTCAGATACTGAAATAA 58.624 33.333 13.25 0.00 40.18 1.40
2463 2522 7.819415 CACCAAACTGACTCAGATACTGAAATA 59.181 37.037 13.25 0.00 40.18 1.40
2464 2523 6.652481 CACCAAACTGACTCAGATACTGAAAT 59.348 38.462 13.25 0.00 40.18 2.17
2465 2524 5.991606 CACCAAACTGACTCAGATACTGAAA 59.008 40.000 13.25 0.00 40.18 2.69
2466 2525 5.070446 ACACCAAACTGACTCAGATACTGAA 59.930 40.000 13.25 0.00 40.18 3.02
2467 2526 4.588951 ACACCAAACTGACTCAGATACTGA 59.411 41.667 13.25 0.00 38.25 3.41
2468 2527 4.887748 ACACCAAACTGACTCAGATACTG 58.112 43.478 13.25 4.26 35.18 2.74
2469 2528 5.552870 AACACCAAACTGACTCAGATACT 57.447 39.130 13.25 0.00 35.18 2.12
2470 2529 7.724305 TTAAACACCAAACTGACTCAGATAC 57.276 36.000 13.25 0.00 35.18 2.24
2471 2530 7.227910 GGTTTAAACACCAAACTGACTCAGATA 59.772 37.037 19.57 0.00 36.73 1.98
2472 2531 6.039382 GGTTTAAACACCAAACTGACTCAGAT 59.961 38.462 19.57 0.00 36.73 2.90
2473 2532 5.355910 GGTTTAAACACCAAACTGACTCAGA 59.644 40.000 19.57 0.00 36.73 3.27
2474 2533 5.357032 AGGTTTAAACACCAAACTGACTCAG 59.643 40.000 19.57 4.36 39.62 3.35
2475 2534 5.258051 AGGTTTAAACACCAAACTGACTCA 58.742 37.500 19.57 0.00 39.62 3.41
2476 2535 5.830000 AGGTTTAAACACCAAACTGACTC 57.170 39.130 19.57 0.00 39.62 3.36
2477 2536 5.712917 TCAAGGTTTAAACACCAAACTGACT 59.287 36.000 19.57 1.15 39.62 3.41
2478 2537 5.956642 TCAAGGTTTAAACACCAAACTGAC 58.043 37.500 19.57 0.00 39.62 3.51
2479 2538 5.712917 ACTCAAGGTTTAAACACCAAACTGA 59.287 36.000 19.57 9.40 39.62 3.41
2480 2539 5.961272 ACTCAAGGTTTAAACACCAAACTG 58.039 37.500 19.57 6.06 39.62 3.16
2481 2540 6.599356 AACTCAAGGTTTAAACACCAAACT 57.401 33.333 19.57 3.92 39.62 2.66
2482 2541 8.813282 CAATAACTCAAGGTTTAAACACCAAAC 58.187 33.333 19.57 1.61 39.62 2.93
2483 2542 7.982354 CCAATAACTCAAGGTTTAAACACCAAA 59.018 33.333 19.57 0.88 39.62 3.28
2484 2543 7.124448 ACCAATAACTCAAGGTTTAAACACCAA 59.876 33.333 19.57 2.20 39.62 3.67
2485 2544 6.608002 ACCAATAACTCAAGGTTTAAACACCA 59.392 34.615 19.57 0.22 39.62 4.17
2486 2545 7.046292 ACCAATAACTCAAGGTTTAAACACC 57.954 36.000 19.57 4.42 39.17 4.16
2493 2552 9.143155 ACAGAAATAACCAATAACTCAAGGTTT 57.857 29.630 0.00 0.00 41.33 3.27
2494 2553 8.706322 ACAGAAATAACCAATAACTCAAGGTT 57.294 30.769 0.00 0.00 45.63 3.50
2495 2554 9.975218 ATACAGAAATAACCAATAACTCAAGGT 57.025 29.630 0.00 0.00 35.47 3.50
2505 2564 7.556844 ACTGACTCGATACAGAAATAACCAAT 58.443 34.615 20.49 0.00 37.54 3.16
2533 2592 5.708230 ACCAGGCATATTGTCTTTCGTTTAA 59.292 36.000 0.00 0.00 23.66 1.52
2534 2593 5.250200 ACCAGGCATATTGTCTTTCGTTTA 58.750 37.500 0.00 0.00 23.66 2.01
2535 2594 4.079253 ACCAGGCATATTGTCTTTCGTTT 58.921 39.130 0.00 0.00 23.66 3.60
2542 2601 4.263462 TGAAACAGACCAGGCATATTGTCT 60.263 41.667 0.00 0.00 38.56 3.41
2552 2611 2.224621 ACACCAGATGAAACAGACCAGG 60.225 50.000 0.00 0.00 0.00 4.45
2559 2618 1.133823 ACAGGCACACCAGATGAAACA 60.134 47.619 0.00 0.00 39.06 2.83
2563 2622 1.133823 ACAAACAGGCACACCAGATGA 60.134 47.619 0.00 0.00 39.06 2.92
2587 2646 8.221928 ACGTAGTTTCATCCAAAGATGGCAAC 62.222 42.308 0.00 6.96 44.99 4.17
2636 2695 6.038050 TCTGCGCAAACATCATCATATAACAA 59.962 34.615 13.05 0.00 0.00 2.83
2643 2702 4.109766 CAAATCTGCGCAAACATCATCAT 58.890 39.130 13.05 0.00 0.00 2.45
2644 2703 3.503891 CAAATCTGCGCAAACATCATCA 58.496 40.909 13.05 0.00 0.00 3.07
2645 2704 2.280708 GCAAATCTGCGCAAACATCATC 59.719 45.455 13.05 0.00 39.20 2.92
2680 2739 1.254570 GGTTCGAGCAAACGCGTATAG 59.745 52.381 14.46 6.66 40.29 1.31
2695 2765 5.371115 TTTCTGGATAAGCAAAAGGTTCG 57.629 39.130 0.00 0.00 0.00 3.95
2730 2802 9.507329 ACTGTAAAATCAATGTTACATGTCTCT 57.493 29.630 0.00 0.00 39.00 3.10
2742 2814 8.345565 GGGAGCTATGTAACTGTAAAATCAATG 58.654 37.037 0.00 0.00 0.00 2.82
2743 2815 8.275040 AGGGAGCTATGTAACTGTAAAATCAAT 58.725 33.333 0.00 0.00 0.00 2.57
2752 2824 4.290093 TCATCAGGGAGCTATGTAACTGT 58.710 43.478 0.00 0.00 0.00 3.55
2766 2838 3.558746 GGTTGCATAGATCCTCATCAGGG 60.559 52.174 0.00 0.00 40.80 4.45
2774 2846 4.965532 ACTTGACTAGGTTGCATAGATCCT 59.034 41.667 0.00 0.96 0.00 3.24
2783 2855 2.003301 GCAGCTACTTGACTAGGTTGC 58.997 52.381 0.00 0.00 35.21 4.17
2786 2858 2.808919 TCAGCAGCTACTTGACTAGGT 58.191 47.619 0.00 0.00 0.00 3.08
2803 2875 3.005472 CCCAATCAATTAGCTGGCATCAG 59.995 47.826 0.00 0.00 43.64 2.90
2804 2876 2.960384 CCCAATCAATTAGCTGGCATCA 59.040 45.455 0.00 0.00 0.00 3.07
2806 2878 1.690352 GCCCAATCAATTAGCTGGCAT 59.310 47.619 0.00 0.00 37.36 4.40
2809 2881 4.411256 AATTGCCCAATCAATTAGCTGG 57.589 40.909 0.00 0.00 42.82 4.85
2810 2882 5.904941 TGTAATTGCCCAATCAATTAGCTG 58.095 37.500 0.00 0.00 44.68 4.24
2811 2883 6.515531 CGATGTAATTGCCCAATCAATTAGCT 60.516 38.462 8.63 0.00 44.68 3.32
2812 2884 5.630680 CGATGTAATTGCCCAATCAATTAGC 59.369 40.000 8.63 5.89 44.68 3.09
2856 2937 8.656849 TCTCGCAGAAAAACAAAGATAATCTAC 58.343 33.333 0.00 0.00 34.09 2.59
2871 2952 6.317893 AGTTTAAAAACCTCTCTCGCAGAAAA 59.682 34.615 2.02 0.00 39.71 2.29
2923 3010 4.357018 TTGCGAGTGCTATATATCTCCG 57.643 45.455 0.00 0.00 43.34 4.63
2942 3029 2.203470 AGGGCCATGGCAAAAATTTG 57.797 45.000 36.56 1.52 44.11 2.32
2973 3060 4.734266 AGGAACTTCATGCTCTCCTTTTT 58.266 39.130 0.00 0.00 32.42 1.94
2974 3061 4.331108 GAGGAACTTCATGCTCTCCTTTT 58.669 43.478 6.84 0.00 41.55 2.27
2975 3062 3.308046 GGAGGAACTTCATGCTCTCCTTT 60.308 47.826 0.00 0.00 41.55 3.11
2976 3063 2.238395 GGAGGAACTTCATGCTCTCCTT 59.762 50.000 0.00 0.00 41.55 3.36
2977 3064 1.836802 GGAGGAACTTCATGCTCTCCT 59.163 52.381 5.47 5.47 41.55 3.69
2978 3065 1.836802 AGGAGGAACTTCATGCTCTCC 59.163 52.381 0.00 0.00 41.55 3.71
2979 3066 3.625649 AAGGAGGAACTTCATGCTCTC 57.374 47.619 0.00 0.00 41.55 3.20
2980 3067 3.073650 ACAAAGGAGGAACTTCATGCTCT 59.926 43.478 0.00 0.00 41.55 4.09
2981 3068 3.416156 ACAAAGGAGGAACTTCATGCTC 58.584 45.455 0.00 0.00 41.55 4.26
2982 3069 3.515602 ACAAAGGAGGAACTTCATGCT 57.484 42.857 0.00 0.00 41.55 3.79
2983 3070 4.327680 AGTACAAAGGAGGAACTTCATGC 58.672 43.478 0.00 0.00 41.55 4.06
2984 3071 6.464222 TGTAGTACAAAGGAGGAACTTCATG 58.536 40.000 0.00 0.00 41.55 3.07
2985 3072 6.681729 TGTAGTACAAAGGAGGAACTTCAT 57.318 37.500 0.00 0.00 41.55 2.57
2986 3073 6.269077 TCATGTAGTACAAAGGAGGAACTTCA 59.731 38.462 7.16 0.00 41.55 3.02
2987 3074 6.590677 GTCATGTAGTACAAAGGAGGAACTTC 59.409 42.308 7.16 0.00 41.55 3.01
2988 3075 6.465084 GTCATGTAGTACAAAGGAGGAACTT 58.535 40.000 7.16 0.00 41.55 2.66
2990 3077 4.863131 CGTCATGTAGTACAAAGGAGGAAC 59.137 45.833 7.16 0.00 0.00 3.62
2991 3078 4.768448 TCGTCATGTAGTACAAAGGAGGAA 59.232 41.667 7.16 0.72 0.00 3.36
2992 3079 4.338012 TCGTCATGTAGTACAAAGGAGGA 58.662 43.478 7.16 12.64 0.00 3.71
2993 3080 4.713824 TCGTCATGTAGTACAAAGGAGG 57.286 45.455 7.16 10.74 0.00 4.30
3006 3093 6.809869 TCATAATCTTCTGTCATCGTCATGT 58.190 36.000 0.00 0.00 0.00 3.21
3008 3095 8.200120 TCTTTCATAATCTTCTGTCATCGTCAT 58.800 33.333 0.00 0.00 0.00 3.06
3011 3098 8.660373 GTTTCTTTCATAATCTTCTGTCATCGT 58.340 33.333 0.00 0.00 0.00 3.73
3012 3099 8.877779 AGTTTCTTTCATAATCTTCTGTCATCG 58.122 33.333 0.00 0.00 0.00 3.84
3042 3207 1.003580 CTGGCATGTAGTGGTGACCTT 59.996 52.381 2.11 0.00 0.00 3.50
3044 3209 1.026718 GCTGGCATGTAGTGGTGACC 61.027 60.000 0.00 0.00 0.00 4.02
3045 3210 0.321564 TGCTGGCATGTAGTGGTGAC 60.322 55.000 0.00 0.00 0.00 3.67
3049 3214 2.756760 AGAAAATGCTGGCATGTAGTGG 59.243 45.455 8.91 0.00 36.68 4.00
3062 3227 7.602753 ACTAGTGGTTCCAAATAAGAAAATGC 58.397 34.615 0.00 0.00 0.00 3.56
3087 3252 7.066645 CAGTGTTGGCATGTACTACTACTAGTA 59.933 40.741 1.89 1.89 34.79 1.82
3088 3253 5.950549 AGTGTTGGCATGTACTACTACTAGT 59.049 40.000 0.00 0.00 37.04 2.57
3089 3254 6.266323 CAGTGTTGGCATGTACTACTACTAG 58.734 44.000 0.00 0.00 0.00 2.57
3090 3255 5.126545 CCAGTGTTGGCATGTACTACTACTA 59.873 44.000 0.00 0.00 37.73 1.82
3091 3256 4.081642 CCAGTGTTGGCATGTACTACTACT 60.082 45.833 0.00 0.43 37.73 2.57
3092 3257 4.181578 CCAGTGTTGGCATGTACTACTAC 58.818 47.826 0.00 0.00 37.73 2.73
3093 3258 4.465632 CCAGTGTTGGCATGTACTACTA 57.534 45.455 0.00 0.00 37.73 1.82
3094 3259 3.334583 CCAGTGTTGGCATGTACTACT 57.665 47.619 0.00 0.00 37.73 2.57
3159 3333 4.869440 CCTCTGCTCCGCTGCTCG 62.869 72.222 0.00 0.00 38.08 5.03
3165 3339 1.519408 TTTTTGTACCTCTGCTCCGC 58.481 50.000 0.00 0.00 0.00 5.54
3166 3340 2.420022 CCATTTTTGTACCTCTGCTCCG 59.580 50.000 0.00 0.00 0.00 4.63
3167 3341 3.421844 ACCATTTTTGTACCTCTGCTCC 58.578 45.455 0.00 0.00 0.00 4.70
3207 3381 9.432077 CGACTAGATGATGATCGATGTTATTAG 57.568 37.037 0.54 0.00 34.77 1.73
3239 3413 2.439156 GATGCTGCCCAGGGTGAC 60.439 66.667 7.55 0.00 0.00 3.67
3255 3429 0.320771 GCGGGAGAAGTTGAGCTTGA 60.321 55.000 0.00 0.00 37.59 3.02
3384 3558 4.873129 CGTCATCCGGGACTGCGG 62.873 72.222 0.00 0.00 35.63 5.69
3394 3568 2.125512 AGCTCAACCGCGTCATCC 60.126 61.111 4.92 0.00 34.40 3.51


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

AutoCloner maintained by Alex Coulton.