Multiple sequence alignment - TraesCS5D01G287000

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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 TraesCS5D01G287000 chr5D 100.000 3879 0 0 1 3879 386982211 386986089 0.000000e+00 7164.0
1 TraesCS5D01G287000 chr5D 94.845 97 4 1 1746 1841 322375745 322375841 2.410000e-32 150.0
2 TraesCS5D01G287000 chr5A 92.884 1321 69 11 1842 3147 489790586 489791896 0.000000e+00 1895.0
3 TraesCS5D01G287000 chr5A 89.024 1312 73 39 483 1751 489789300 489790583 0.000000e+00 1559.0
4 TraesCS5D01G287000 chr5A 83.361 613 81 8 3247 3846 458281429 458282033 7.330000e-152 547.0
5 TraesCS5D01G287000 chr5B 91.228 969 48 10 2232 3185 465231879 465232825 0.000000e+00 1284.0
6 TraesCS5D01G287000 chr5B 93.774 530 25 4 1207 1731 465230936 465231462 0.000000e+00 789.0
7 TraesCS5D01G287000 chr5B 91.242 491 36 4 693 1180 465230451 465230937 0.000000e+00 662.0
8 TraesCS5D01G287000 chr5B 91.877 357 22 4 1851 2201 465231525 465231880 3.480000e-135 492.0
9 TraesCS5D01G287000 chr5B 93.069 101 6 1 1741 1841 3917878 3917779 3.120000e-31 147.0
10 TraesCS5D01G287000 chr1D 84.043 658 88 11 3222 3867 204985852 204986504 5.510000e-173 617.0
11 TraesCS5D01G287000 chr1D 82.710 642 88 10 3233 3872 392947008 392947628 2.040000e-152 549.0
12 TraesCS5D01G287000 chr7A 83.553 608 82 10 3243 3838 166480463 166481064 1.570000e-153 553.0
13 TraesCS5D01G287000 chr7A 78.355 462 75 16 3432 3872 534145683 534146140 3.820000e-70 276.0
14 TraesCS5D01G287000 chr4B 82.663 646 73 19 3242 3879 482643556 482642942 1.590000e-148 536.0
15 TraesCS5D01G287000 chr3D 82.028 651 97 14 3222 3861 347447602 347448243 1.590000e-148 536.0
16 TraesCS5D01G287000 chr3D 80.110 543 80 18 3221 3745 283615081 283615613 2.830000e-101 379.0
17 TraesCS5D01G287000 chr3D 76.190 567 72 38 2303 2854 38278181 38278699 1.390000e-59 241.0
18 TraesCS5D01G287000 chr6D 80.800 625 97 14 3243 3851 115645049 115644432 5.870000e-128 468.0
19 TraesCS5D01G287000 chr6D 79.125 594 98 10 3261 3836 111626200 111625615 1.690000e-103 387.0
20 TraesCS5D01G287000 chr6D 78.764 518 80 17 3369 3872 313886417 313886918 1.740000e-83 320.0
21 TraesCS5D01G287000 chr6D 78.049 451 78 14 3448 3877 379363431 379362981 8.260000e-67 265.0
22 TraesCS5D01G287000 chr6D 80.000 340 51 9 3498 3836 386334332 386334655 6.480000e-58 235.0
23 TraesCS5D01G287000 chr6D 94.059 101 4 2 1749 1849 104147595 104147693 6.710000e-33 152.0
24 TraesCS5D01G287000 chr2B 81.975 405 68 4 3232 3634 772151713 772152114 4.800000e-89 339.0
25 TraesCS5D01G287000 chr2B 95.789 95 3 1 1750 1843 31741715 31741621 6.710000e-33 152.0
26 TraesCS5D01G287000 chr3B 88.535 157 18 0 2698 2854 60868087 60868243 1.420000e-44 191.0
27 TraesCS5D01G287000 chr3B 94.792 96 3 2 1749 1844 18673033 18672940 8.680000e-32 148.0
28 TraesCS5D01G287000 chr3B 92.381 105 4 3 1744 1846 719780243 719780141 3.120000e-31 147.0
29 TraesCS5D01G287000 chr2D 98.864 88 1 0 1747 1834 534934506 534934593 1.440000e-34 158.0
30 TraesCS5D01G287000 chr6A 94.898 98 3 2 1746 1843 540320442 540320347 6.710000e-33 152.0
31 TraesCS5D01G287000 chr6A 82.105 95 15 2 230 324 21434965 21435057 3.210000e-11 80.5
32 TraesCS5D01G287000 chr3A 95.789 95 3 1 1745 1839 221948899 221948992 6.710000e-33 152.0


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 TraesCS5D01G287000 chr5D 386982211 386986089 3878 False 7164.00 7164 100.00000 1 3879 1 chr5D.!!$F2 3878
1 TraesCS5D01G287000 chr5A 489789300 489791896 2596 False 1727.00 1895 90.95400 483 3147 2 chr5A.!!$F2 2664
2 TraesCS5D01G287000 chr5A 458281429 458282033 604 False 547.00 547 83.36100 3247 3846 1 chr5A.!!$F1 599
3 TraesCS5D01G287000 chr5B 465230451 465232825 2374 False 806.75 1284 92.03025 693 3185 4 chr5B.!!$F1 2492
4 TraesCS5D01G287000 chr1D 204985852 204986504 652 False 617.00 617 84.04300 3222 3867 1 chr1D.!!$F1 645
5 TraesCS5D01G287000 chr1D 392947008 392947628 620 False 549.00 549 82.71000 3233 3872 1 chr1D.!!$F2 639
6 TraesCS5D01G287000 chr7A 166480463 166481064 601 False 553.00 553 83.55300 3243 3838 1 chr7A.!!$F1 595
7 TraesCS5D01G287000 chr4B 482642942 482643556 614 True 536.00 536 82.66300 3242 3879 1 chr4B.!!$R1 637
8 TraesCS5D01G287000 chr3D 347447602 347448243 641 False 536.00 536 82.02800 3222 3861 1 chr3D.!!$F3 639
9 TraesCS5D01G287000 chr3D 283615081 283615613 532 False 379.00 379 80.11000 3221 3745 1 chr3D.!!$F2 524
10 TraesCS5D01G287000 chr3D 38278181 38278699 518 False 241.00 241 76.19000 2303 2854 1 chr3D.!!$F1 551
11 TraesCS5D01G287000 chr6D 115644432 115645049 617 True 468.00 468 80.80000 3243 3851 1 chr6D.!!$R2 608
12 TraesCS5D01G287000 chr6D 111625615 111626200 585 True 387.00 387 79.12500 3261 3836 1 chr6D.!!$R1 575
13 TraesCS5D01G287000 chr6D 313886417 313886918 501 False 320.00 320 78.76400 3369 3872 1 chr6D.!!$F2 503

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
738 787 0.038166 GGCATTTCTCCAGGTGGTGA 59.962 55.0 0.00 0.0 36.07 4.02 F
1261 1313 0.471617 CGAAGGATCCATTCAGGGCT 59.528 55.0 15.82 0.0 38.24 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1539 1599 0.181350 ATCGAGATGAAGGGGTTGGC 59.819 55.0 0.0 0.0 0.0 4.52 R
3193 3299 0.250513 GGTGCTCTCAGTCCCGAAAT 59.749 55.0 0.0 0.0 0.0 2.17 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
249 250 8.732413 TTCAGAAAATGTTCATCAAATTCGAG 57.268 30.769 0.00 0.00 36.09 4.04
250 251 7.874940 TCAGAAAATGTTCATCAAATTCGAGT 58.125 30.769 0.00 0.00 36.09 4.18
251 252 8.352201 TCAGAAAATGTTCATCAAATTCGAGTT 58.648 29.630 0.00 0.00 36.09 3.01
252 253 8.971321 CAGAAAATGTTCATCAAATTCGAGTTT 58.029 29.630 0.00 0.00 36.09 2.66
253 254 9.533253 AGAAAATGTTCATCAAATTCGAGTTTT 57.467 25.926 2.77 0.00 36.09 2.43
299 300 9.597170 TGTTCATCAAATTCAAGAAAATGTTCA 57.403 25.926 0.00 0.00 36.09 3.18
305 306 9.820725 TCAAATTCAAGAAAATGTTCATTGAGT 57.179 25.926 0.00 0.29 34.89 3.41
320 321 9.360093 TGTTCATTGAGTTTAAATTTTGTTCGT 57.640 25.926 0.00 0.00 0.00 3.85
321 322 9.829637 GTTCATTGAGTTTAAATTTTGTTCGTC 57.170 29.630 0.00 0.00 0.00 4.20
322 323 9.574458 TTCATTGAGTTTAAATTTTGTTCGTCA 57.426 25.926 0.00 0.00 0.00 4.35
323 324 9.574458 TCATTGAGTTTAAATTTTGTTCGTCAA 57.426 25.926 0.00 0.00 0.00 3.18
324 325 9.618410 CATTGAGTTTAAATTTTGTTCGTCAAC 57.382 29.630 0.00 0.00 35.61 3.18
325 326 8.744008 TTGAGTTTAAATTTTGTTCGTCAACA 57.256 26.923 0.00 0.00 40.97 3.33
326 327 8.918961 TGAGTTTAAATTTTGTTCGTCAACAT 57.081 26.923 0.00 0.00 42.28 2.71
327 328 8.802856 TGAGTTTAAATTTTGTTCGTCAACATG 58.197 29.630 0.00 0.00 42.28 3.21
328 329 7.617557 AGTTTAAATTTTGTTCGTCAACATGC 58.382 30.769 0.00 0.00 42.28 4.06
329 330 7.276658 AGTTTAAATTTTGTTCGTCAACATGCA 59.723 29.630 0.00 0.00 42.28 3.96
330 331 5.640218 AAATTTTGTTCGTCAACATGCAG 57.360 34.783 0.00 0.00 42.28 4.41
331 332 3.773860 TTTTGTTCGTCAACATGCAGT 57.226 38.095 0.00 0.00 42.28 4.40
332 333 3.773860 TTTGTTCGTCAACATGCAGTT 57.226 38.095 0.00 0.00 42.28 3.16
333 334 3.773860 TTGTTCGTCAACATGCAGTTT 57.226 38.095 0.00 0.00 42.28 2.66
334 335 3.773860 TGTTCGTCAACATGCAGTTTT 57.226 38.095 0.00 0.00 38.74 2.43
335 336 4.103365 TGTTCGTCAACATGCAGTTTTT 57.897 36.364 0.00 0.00 38.74 1.94
336 337 4.101942 TGTTCGTCAACATGCAGTTTTTC 58.898 39.130 0.00 0.00 38.74 2.29
337 338 2.980586 TCGTCAACATGCAGTTTTTCG 58.019 42.857 0.00 2.56 38.74 3.46
338 339 2.609916 TCGTCAACATGCAGTTTTTCGA 59.390 40.909 0.00 4.65 38.74 3.71
339 340 3.064134 TCGTCAACATGCAGTTTTTCGAA 59.936 39.130 0.00 0.00 38.74 3.71
340 341 3.788694 CGTCAACATGCAGTTTTTCGAAA 59.211 39.130 6.47 6.47 38.74 3.46
341 342 4.440758 CGTCAACATGCAGTTTTTCGAAAT 59.559 37.500 12.12 0.00 38.74 2.17
342 343 5.607994 CGTCAACATGCAGTTTTTCGAAATG 60.608 40.000 12.12 8.48 38.74 2.32
343 344 5.458452 GTCAACATGCAGTTTTTCGAAATGA 59.542 36.000 12.12 5.46 38.74 2.57
344 345 6.144402 GTCAACATGCAGTTTTTCGAAATGAT 59.856 34.615 12.12 0.00 38.74 2.45
345 346 6.144241 TCAACATGCAGTTTTTCGAAATGATG 59.856 34.615 12.12 9.88 38.74 3.07
346 347 5.771469 ACATGCAGTTTTTCGAAATGATGA 58.229 33.333 12.12 0.00 0.00 2.92
347 348 6.215121 ACATGCAGTTTTTCGAAATGATGAA 58.785 32.000 12.12 5.71 0.00 2.57
348 349 6.869913 ACATGCAGTTTTTCGAAATGATGAAT 59.130 30.769 12.12 7.76 0.00 2.57
349 350 8.028354 ACATGCAGTTTTTCGAAATGATGAATA 58.972 29.630 12.12 0.00 0.00 1.75
350 351 9.027129 CATGCAGTTTTTCGAAATGATGAATAT 57.973 29.630 12.12 4.29 0.00 1.28
351 352 8.984891 TGCAGTTTTTCGAAATGATGAATATT 57.015 26.923 12.12 0.00 0.00 1.28
352 353 9.421806 TGCAGTTTTTCGAAATGATGAATATTT 57.578 25.926 12.12 0.00 0.00 1.40
395 396 8.539770 TTTTTAAGCAATGAGTGTTTTTGTGA 57.460 26.923 0.00 0.00 32.27 3.58
396 397 7.754069 TTTAAGCAATGAGTGTTTTTGTGAG 57.246 32.000 0.00 0.00 32.27 3.51
397 398 5.581126 AAGCAATGAGTGTTTTTGTGAGA 57.419 34.783 0.00 0.00 0.00 3.27
398 399 5.779529 AGCAATGAGTGTTTTTGTGAGAT 57.220 34.783 0.00 0.00 0.00 2.75
399 400 6.152932 AGCAATGAGTGTTTTTGTGAGATT 57.847 33.333 0.00 0.00 0.00 2.40
400 401 6.211515 AGCAATGAGTGTTTTTGTGAGATTC 58.788 36.000 0.00 0.00 0.00 2.52
401 402 5.978919 GCAATGAGTGTTTTTGTGAGATTCA 59.021 36.000 0.00 0.00 0.00 2.57
402 403 6.643770 GCAATGAGTGTTTTTGTGAGATTCAT 59.356 34.615 0.00 0.00 0.00 2.57
403 404 7.358931 GCAATGAGTGTTTTTGTGAGATTCATG 60.359 37.037 0.00 0.00 0.00 3.07
404 405 6.940831 TGAGTGTTTTTGTGAGATTCATGA 57.059 33.333 0.00 0.00 0.00 3.07
405 406 7.332213 TGAGTGTTTTTGTGAGATTCATGAA 57.668 32.000 11.26 11.26 0.00 2.57
406 407 7.944061 TGAGTGTTTTTGTGAGATTCATGAAT 58.056 30.769 20.85 20.85 0.00 2.57
407 408 7.863877 TGAGTGTTTTTGTGAGATTCATGAATG 59.136 33.333 25.37 0.00 0.00 2.67
408 409 7.719483 AGTGTTTTTGTGAGATTCATGAATGT 58.281 30.769 25.37 21.31 0.00 2.71
409 410 8.199449 AGTGTTTTTGTGAGATTCATGAATGTT 58.801 29.630 25.37 13.06 0.00 2.71
410 411 8.819974 GTGTTTTTGTGAGATTCATGAATGTTT 58.180 29.630 25.37 10.60 0.00 2.83
411 412 9.381033 TGTTTTTGTGAGATTCATGAATGTTTT 57.619 25.926 25.37 8.17 0.00 2.43
503 504 7.121759 CCACAAACATCTTATGATTTCTGGAGT 59.878 37.037 0.00 0.00 29.70 3.85
524 526 9.898152 TGGAGTATTTTTGGAAAATTCACTTTT 57.102 25.926 4.21 0.00 39.78 2.27
629 639 2.584418 CGTCCAGCTCCGCTCATG 60.584 66.667 0.00 0.00 36.40 3.07
656 666 2.222227 CCAAAAGGGGAGGAAAGGAG 57.778 55.000 0.00 0.00 0.00 3.69
657 667 1.272704 CCAAAAGGGGAGGAAAGGAGG 60.273 57.143 0.00 0.00 0.00 4.30
658 668 1.429299 CAAAAGGGGAGGAAAGGAGGT 59.571 52.381 0.00 0.00 0.00 3.85
659 669 1.076438 AAAGGGGAGGAAAGGAGGTG 58.924 55.000 0.00 0.00 0.00 4.00
660 670 1.501654 AAGGGGAGGAAAGGAGGTGC 61.502 60.000 0.00 0.00 0.00 5.01
661 671 2.269241 GGGAGGAAAGGAGGTGCG 59.731 66.667 0.00 0.00 0.00 5.34
662 672 2.436824 GGAGGAAAGGAGGTGCGC 60.437 66.667 0.00 0.00 0.00 6.09
663 673 2.815647 GAGGAAAGGAGGTGCGCG 60.816 66.667 0.00 0.00 0.00 6.86
666 676 3.793144 GAAAGGAGGTGCGCGCTG 61.793 66.667 33.29 0.00 0.00 5.18
715 764 7.201661 GCCAAATGGTATAAACTAACACGATCA 60.202 37.037 0.71 0.00 37.57 2.92
722 771 0.885879 ACTAACACGATCAGACGGCA 59.114 50.000 0.00 0.00 37.61 5.69
736 785 1.002134 CGGCATTTCTCCAGGTGGT 60.002 57.895 0.00 0.00 36.34 4.16
737 786 1.308069 CGGCATTTCTCCAGGTGGTG 61.308 60.000 0.00 0.00 36.34 4.17
738 787 0.038166 GGCATTTCTCCAGGTGGTGA 59.962 55.000 0.00 0.00 36.07 4.02
739 788 1.168714 GCATTTCTCCAGGTGGTGAC 58.831 55.000 0.14 0.00 37.43 3.67
740 789 1.826385 CATTTCTCCAGGTGGTGACC 58.174 55.000 0.00 0.00 43.52 4.02
778 827 1.535462 CCGCGGACAAAAGTGATCTTT 59.465 47.619 24.07 0.00 44.59 2.52
807 856 2.311688 AATCCGTCGGGTGGATGAGC 62.312 60.000 12.29 0.00 45.46 4.26
854 903 4.218635 TCATCGACTAGCTCTTGTTCTTGT 59.781 41.667 0.00 0.00 0.00 3.16
894 943 8.837389 GTTTTTGTCTCCTTGTTCTGTTATAGT 58.163 33.333 0.00 0.00 0.00 2.12
908 957 9.048446 GTTCTGTTATAGTAGTGTTTTTGACCA 57.952 33.333 0.00 0.00 0.00 4.02
914 963 5.112129 AGTAGTGTTTTTGACCAGTTCCT 57.888 39.130 0.00 0.00 0.00 3.36
915 964 4.881850 AGTAGTGTTTTTGACCAGTTCCTG 59.118 41.667 0.00 0.00 0.00 3.86
972 1021 1.204704 TCCTACCACATCACGAGCTTG 59.795 52.381 0.00 0.00 0.00 4.01
975 1024 0.952497 ACCACATCACGAGCTTGCTG 60.952 55.000 0.00 0.00 0.00 4.41
993 1045 1.004044 CTGGTGTTGGGAGCTGAGAAT 59.996 52.381 0.00 0.00 0.00 2.40
1142 1194 2.024588 CACACAACACACCGCTGC 59.975 61.111 0.00 0.00 0.00 5.25
1261 1313 0.471617 CGAAGGATCCATTCAGGGCT 59.528 55.000 15.82 0.00 38.24 5.19
1283 1339 3.718815 AGGAAACTCTGAAACTCGTGTC 58.281 45.455 0.00 0.00 32.90 3.67
1304 1364 3.041946 CTCATTTACAGGAGGGCCTAGT 58.958 50.000 5.73 8.63 44.80 2.57
1521 1581 1.909302 TGAACCTCCCTCTCAACATCC 59.091 52.381 0.00 0.00 0.00 3.51
1539 1599 5.314923 CATCCTGATGTAACCAAAACCAG 57.685 43.478 0.00 0.00 34.23 4.00
1540 1600 3.153919 TCCTGATGTAACCAAAACCAGC 58.846 45.455 0.00 0.00 0.00 4.85
1591 1652 7.440523 ACTCCATTTTCTTCTTCATGTGTAC 57.559 36.000 0.00 0.00 0.00 2.90
1673 1734 2.024176 TGTTCTGTCCCTTCCAGCTA 57.976 50.000 0.00 0.00 0.00 3.32
1742 1803 1.884075 ATTGTCTCGGCACAGCGGTA 61.884 55.000 0.00 0.00 0.00 4.02
1751 1812 2.740452 GGCACAGCGGTAGTTATCTAC 58.260 52.381 2.79 2.79 44.00 2.59
1765 1826 7.998580 GTAGTTATCTACTGCCTCTGTAAACT 58.001 38.462 4.05 0.00 42.15 2.66
1766 1827 9.118300 GTAGTTATCTACTGCCTCTGTAAACTA 57.882 37.037 4.05 0.00 42.15 2.24
1767 1828 8.591114 AGTTATCTACTGCCTCTGTAAACTAA 57.409 34.615 0.00 0.00 35.19 2.24
1776 1837 8.145122 ACTGCCTCTGTAAACTAATATAAGAGC 58.855 37.037 0.00 0.00 0.00 4.09
1778 1839 7.146648 GCCTCTGTAAACTAATATAAGAGCGT 58.853 38.462 0.00 0.00 0.00 5.07
1779 1840 7.652507 GCCTCTGTAAACTAATATAAGAGCGTT 59.347 37.037 0.00 0.00 0.00 4.84
1780 1841 9.530633 CCTCTGTAAACTAATATAAGAGCGTTT 57.469 33.333 0.00 0.00 0.00 3.60
1795 1856 9.953697 ATAAGAGCGTTTAGATCACTACTTTAG 57.046 33.333 0.00 0.00 37.82 1.85
1796 1857 7.393841 AGAGCGTTTAGATCACTACTTTAGT 57.606 36.000 0.00 0.00 37.82 2.24
1810 1871 7.393841 ACTACTTTAGTGATCTAAACGCTCT 57.606 36.000 0.00 0.00 40.05 4.09
1811 1872 7.828712 ACTACTTTAGTGATCTAAACGCTCTT 58.171 34.615 0.00 0.00 40.05 2.85
1812 1873 8.954350 ACTACTTTAGTGATCTAAACGCTCTTA 58.046 33.333 0.00 0.00 40.05 2.10
1813 1874 9.953697 CTACTTTAGTGATCTAAACGCTCTTAT 57.046 33.333 0.00 0.00 40.05 1.73
1825 1886 9.669353 TCTAAACGCTCTTATATTAGTTTACGG 57.331 33.333 0.00 0.00 34.29 4.02
1826 1887 9.669353 CTAAACGCTCTTATATTAGTTTACGGA 57.331 33.333 0.00 0.00 34.29 4.69
1827 1888 8.571461 AAACGCTCTTATATTAGTTTACGGAG 57.429 34.615 0.00 0.00 31.14 4.63
1828 1889 6.675987 ACGCTCTTATATTAGTTTACGGAGG 58.324 40.000 0.00 0.00 0.00 4.30
1829 1890 6.091437 CGCTCTTATATTAGTTTACGGAGGG 58.909 44.000 0.00 0.00 0.00 4.30
1830 1891 6.072286 CGCTCTTATATTAGTTTACGGAGGGA 60.072 42.308 0.00 0.00 34.63 4.20
1831 1892 7.314393 GCTCTTATATTAGTTTACGGAGGGAG 58.686 42.308 0.00 0.00 0.00 4.30
1832 1893 7.039853 GCTCTTATATTAGTTTACGGAGGGAGT 60.040 40.741 0.00 0.00 0.00 3.85
1833 1894 9.512588 CTCTTATATTAGTTTACGGAGGGAGTA 57.487 37.037 0.00 0.00 0.00 2.59
1838 1899 7.757941 ATTAGTTTACGGAGGGAGTATCTAC 57.242 40.000 0.00 0.00 33.73 2.59
1839 1900 5.121380 AGTTTACGGAGGGAGTATCTACA 57.879 43.478 0.00 0.00 33.73 2.74
1840 1901 5.131784 AGTTTACGGAGGGAGTATCTACAG 58.868 45.833 0.00 0.00 33.73 2.74
1919 1980 0.819259 TGACCAACCTGCTGCTTGAC 60.819 55.000 0.00 0.00 0.00 3.18
2153 2220 3.435846 TGGACAATCCAAGCTTGCA 57.564 47.368 21.43 6.76 45.00 4.08
2162 2229 3.921119 TCCAAGCTTGCAAACATACTG 57.079 42.857 21.43 3.37 0.00 2.74
2209 2280 6.357367 GGCTCAAGGTATTATTTCTCTCCAA 58.643 40.000 0.00 0.00 0.00 3.53
2219 2290 3.934457 TTTCTCTCCAAATTTTCGCCC 57.066 42.857 0.00 0.00 0.00 6.13
2220 2291 2.879103 TCTCTCCAAATTTTCGCCCT 57.121 45.000 0.00 0.00 0.00 5.19
2222 2293 3.081804 TCTCTCCAAATTTTCGCCCTTC 58.918 45.455 0.00 0.00 0.00 3.46
2223 2294 3.084786 CTCTCCAAATTTTCGCCCTTCT 58.915 45.455 0.00 0.00 0.00 2.85
2224 2295 4.019681 TCTCTCCAAATTTTCGCCCTTCTA 60.020 41.667 0.00 0.00 0.00 2.10
2226 2297 3.086282 TCCAAATTTTCGCCCTTCTACC 58.914 45.455 0.00 0.00 0.00 3.18
2228 2299 3.128764 CCAAATTTTCGCCCTTCTACCTC 59.871 47.826 0.00 0.00 0.00 3.85
2273 2344 7.986553 ATGCTAAATAGAGGGCTCATACTAT 57.013 36.000 0.00 0.00 0.00 2.12
2323 2394 4.037208 CCATTCTGACCCATCATAAACTGC 59.963 45.833 0.00 0.00 33.22 4.40
2497 2577 6.030228 GTCAAGTTTTAGCTATGCACCATTC 58.970 40.000 0.00 0.00 0.00 2.67
2532 2612 2.502213 TATGTCTCCACGGCGTTATG 57.498 50.000 11.19 1.54 0.00 1.90
2545 2631 6.288419 CACGGCGTTATGAATTTTCTTTTTG 58.712 36.000 11.19 0.00 0.00 2.44
2636 2722 8.983307 ACTCTTTACCTTCGAGTAACAAATAG 57.017 34.615 0.00 0.00 36.33 1.73
2646 2732 6.827641 TCGAGTAACAAATAGTTCATTGTGC 58.172 36.000 0.00 0.00 41.64 4.57
2652 2738 9.030301 GTAACAAATAGTTCATTGTGCACTTTT 57.970 29.630 19.41 0.00 41.64 2.27
2978 3066 1.336440 TGCTTGTTGTTTGGATCGTGG 59.664 47.619 0.00 0.00 0.00 4.94
3017 3113 6.723977 TGCACCCTGGTTAAATTTCTCTAATT 59.276 34.615 0.00 0.00 38.08 1.40
3018 3114 7.891183 TGCACCCTGGTTAAATTTCTCTAATTA 59.109 33.333 0.00 0.00 35.39 1.40
3019 3115 8.745590 GCACCCTGGTTAAATTTCTCTAATTAA 58.254 33.333 0.00 0.00 35.39 1.40
3069 3173 5.235516 GGTTAATGGGACTGGTATATGTCG 58.764 45.833 0.00 0.00 34.31 4.35
3084 3188 7.040617 TGGTATATGTCGTCCTAGTTTCAGATC 60.041 40.741 0.00 0.00 0.00 2.75
3109 3215 4.155709 TGTTGCCTGAAATATCACCCAAA 58.844 39.130 0.00 0.00 0.00 3.28
3129 3235 6.536224 CCCAAATTTCAGAGATATTTTGGTGC 59.464 38.462 10.37 0.00 28.75 5.01
3155 3261 5.873164 GCCTGAAACTTTTTCGGTATAGAGA 59.127 40.000 6.71 0.00 0.00 3.10
3166 3272 4.418392 TCGGTATAGAGAGAAAAACACGC 58.582 43.478 0.00 0.00 0.00 5.34
3169 3275 3.695830 ATAGAGAGAAAAACACGCCCA 57.304 42.857 0.00 0.00 0.00 5.36
3185 3291 0.875728 CCCAGCTATCGTCGTAGAGG 59.124 60.000 0.00 6.48 44.69 3.69
3186 3292 1.595466 CCAGCTATCGTCGTAGAGGT 58.405 55.000 0.00 0.00 43.64 3.85
3187 3293 2.549563 CCCAGCTATCGTCGTAGAGGTA 60.550 54.545 0.00 0.00 43.64 3.08
3188 3294 2.737783 CCAGCTATCGTCGTAGAGGTAG 59.262 54.545 0.00 0.00 43.64 3.18
3189 3295 3.554544 CCAGCTATCGTCGTAGAGGTAGA 60.555 52.174 0.00 0.00 43.64 2.59
3190 3296 4.056740 CAGCTATCGTCGTAGAGGTAGAA 58.943 47.826 0.00 0.00 43.64 2.10
3191 3297 4.691685 CAGCTATCGTCGTAGAGGTAGAAT 59.308 45.833 0.00 0.00 43.64 2.40
3192 3298 4.691685 AGCTATCGTCGTAGAGGTAGAATG 59.308 45.833 0.00 0.00 43.64 2.67
3193 3299 4.689812 GCTATCGTCGTAGAGGTAGAATGA 59.310 45.833 6.18 0.00 43.64 2.57
3194 3300 5.352016 GCTATCGTCGTAGAGGTAGAATGAT 59.648 44.000 6.18 0.00 43.64 2.45
3195 3301 6.128227 GCTATCGTCGTAGAGGTAGAATGATT 60.128 42.308 6.18 0.00 43.64 2.57
3196 3302 6.636562 ATCGTCGTAGAGGTAGAATGATTT 57.363 37.500 0.00 0.00 43.64 2.17
3197 3303 6.057627 TCGTCGTAGAGGTAGAATGATTTC 57.942 41.667 0.00 0.00 43.64 2.17
3198 3304 4.904724 CGTCGTAGAGGTAGAATGATTTCG 59.095 45.833 0.00 0.00 36.95 3.46
3199 3305 5.213675 GTCGTAGAGGTAGAATGATTTCGG 58.786 45.833 0.00 0.00 36.95 4.30
3200 3306 4.277672 TCGTAGAGGTAGAATGATTTCGGG 59.722 45.833 0.00 0.00 36.93 5.14
3201 3307 4.277672 CGTAGAGGTAGAATGATTTCGGGA 59.722 45.833 0.00 0.00 36.93 5.14
3202 3308 4.674281 AGAGGTAGAATGATTTCGGGAC 57.326 45.455 0.00 0.00 36.93 4.46
3203 3309 4.290942 AGAGGTAGAATGATTTCGGGACT 58.709 43.478 0.00 0.00 36.93 3.85
3204 3310 4.100189 AGAGGTAGAATGATTTCGGGACTG 59.900 45.833 0.00 0.00 36.93 3.51
3205 3311 4.030913 AGGTAGAATGATTTCGGGACTGA 58.969 43.478 0.00 0.00 36.93 3.41
3206 3312 4.100189 AGGTAGAATGATTTCGGGACTGAG 59.900 45.833 0.00 0.00 36.93 3.35
3207 3313 4.099573 GGTAGAATGATTTCGGGACTGAGA 59.900 45.833 0.00 0.00 36.93 3.27
3208 3314 4.399004 AGAATGATTTCGGGACTGAGAG 57.601 45.455 0.00 0.00 36.93 3.20
3209 3315 2.611225 ATGATTTCGGGACTGAGAGC 57.389 50.000 0.00 0.00 0.00 4.09
3210 3316 1.266178 TGATTTCGGGACTGAGAGCA 58.734 50.000 0.00 0.00 0.00 4.26
3211 3317 1.066858 TGATTTCGGGACTGAGAGCAC 60.067 52.381 0.00 0.00 0.00 4.40
3212 3318 0.250513 ATTTCGGGACTGAGAGCACC 59.749 55.000 0.00 0.00 0.00 5.01
3213 3319 1.827399 TTTCGGGACTGAGAGCACCC 61.827 60.000 0.00 0.00 39.02 4.61
3214 3320 2.681778 CGGGACTGAGAGCACCCT 60.682 66.667 0.00 0.00 40.12 4.34
3215 3321 1.379977 CGGGACTGAGAGCACCCTA 60.380 63.158 0.00 0.00 40.12 3.53
3216 3322 0.757188 CGGGACTGAGAGCACCCTAT 60.757 60.000 0.00 0.00 40.12 2.57
3217 3323 0.755686 GGGACTGAGAGCACCCTATG 59.244 60.000 0.00 0.00 39.28 2.23
3230 3336 2.890474 CTATGCACCCGCGGACAC 60.890 66.667 30.73 15.75 42.97 3.67
3231 3337 4.805231 TATGCACCCGCGGACACG 62.805 66.667 30.73 12.89 42.97 4.49
3252 3358 2.496470 GTGACCGACTGTCCCTAAATCT 59.504 50.000 1.55 0.00 43.78 2.40
3256 3362 1.135083 CGACTGTCCCTAAATCTGCGT 60.135 52.381 1.55 0.00 0.00 5.24
3288 3398 2.093500 GCATATCTCATATCCGGCACCA 60.093 50.000 0.00 0.00 0.00 4.17
3292 3402 6.528321 CATATCTCATATCCGGCACCATATT 58.472 40.000 0.00 0.00 0.00 1.28
3294 3404 5.241403 TCTCATATCCGGCACCATATTTT 57.759 39.130 0.00 0.00 0.00 1.82
3306 3416 6.420604 CGGCACCATATTTTCATACAAATTCC 59.579 38.462 0.00 0.00 0.00 3.01
3402 3515 5.914635 GGCATAATTCACATAAACATCACCG 59.085 40.000 0.00 0.00 0.00 4.94
3423 3537 0.402504 AAGGTGGTCAAACGGGCATA 59.597 50.000 0.00 0.00 0.00 3.14
3424 3538 0.322187 AGGTGGTCAAACGGGCATAC 60.322 55.000 0.00 0.00 0.00 2.39
3446 3561 1.282817 TTCACACAGTTCAACGACCG 58.717 50.000 0.00 0.00 0.00 4.79
3468 3583 5.462405 CGGGCACATTCTAACTAGATACTC 58.538 45.833 0.00 0.00 31.40 2.59
3478 3593 8.991243 TTCTAACTAGATACTCGAGCTAGATC 57.009 38.462 23.99 16.55 45.48 2.75
3526 3643 3.004354 TTCCTCGCCGGCCCTTTA 61.004 61.111 23.46 0.10 0.00 1.85
3541 3658 2.175035 CTTTACCCTTCCGGTCGCCA 62.175 60.000 0.00 0.00 43.58 5.69
3583 3709 2.987547 GGAGGTGGGTCGACGTCA 60.988 66.667 17.16 7.80 33.31 4.35
3619 3760 3.735514 CGAAGAAGGAGAAACCGGAGATC 60.736 52.174 9.46 2.68 44.74 2.75
3748 3925 2.031919 TGCGTGGCGTTGATCCTT 59.968 55.556 0.00 0.00 0.00 3.36
3760 3937 0.972471 TGATCCTTCAGAGCTGCCGA 60.972 55.000 0.00 0.00 0.00 5.54
3804 3982 1.202915 TGACCGACAGTACACCCACTA 60.203 52.381 0.00 0.00 0.00 2.74
3818 3996 2.104170 CCCACTAGAAGAGACACTCCC 58.896 57.143 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
223 224 9.350357 CTCGAATTTGATGAACATTTTCTGAAT 57.650 29.630 0.00 0.00 32.36 2.57
224 225 8.352201 ACTCGAATTTGATGAACATTTTCTGAA 58.648 29.630 0.00 0.00 32.36 3.02
225 226 7.874940 ACTCGAATTTGATGAACATTTTCTGA 58.125 30.769 0.00 0.00 32.36 3.27
226 227 8.511465 AACTCGAATTTGATGAACATTTTCTG 57.489 30.769 0.00 0.00 32.36 3.02
227 228 9.533253 AAAACTCGAATTTGATGAACATTTTCT 57.467 25.926 0.00 0.00 32.36 2.52
273 274 9.597170 TGAACATTTTCTTGAATTTGATGAACA 57.403 25.926 0.00 0.00 32.36 3.18
279 280 9.820725 ACTCAATGAACATTTTCTTGAATTTGA 57.179 25.926 0.00 0.00 32.88 2.69
294 295 9.360093 ACGAACAAAATTTAAACTCAATGAACA 57.640 25.926 0.00 0.00 0.00 3.18
295 296 9.829637 GACGAACAAAATTTAAACTCAATGAAC 57.170 29.630 0.00 0.00 0.00 3.18
296 297 9.574458 TGACGAACAAAATTTAAACTCAATGAA 57.426 25.926 0.00 0.00 0.00 2.57
297 298 9.574458 TTGACGAACAAAATTTAAACTCAATGA 57.426 25.926 0.00 0.00 35.39 2.57
298 299 9.618410 GTTGACGAACAAAATTTAAACTCAATG 57.382 29.630 0.00 0.00 40.36 2.82
299 300 9.360093 TGTTGACGAACAAAATTTAAACTCAAT 57.640 25.926 0.00 0.00 39.20 2.57
300 301 8.744008 TGTTGACGAACAAAATTTAAACTCAA 57.256 26.923 0.00 0.00 39.20 3.02
301 302 8.802856 CATGTTGACGAACAAAATTTAAACTCA 58.197 29.630 0.00 0.00 45.23 3.41
302 303 7.787480 GCATGTTGACGAACAAAATTTAAACTC 59.213 33.333 0.00 0.00 45.23 3.01
303 304 7.276658 TGCATGTTGACGAACAAAATTTAAACT 59.723 29.630 0.00 0.00 45.23 2.66
304 305 7.394872 TGCATGTTGACGAACAAAATTTAAAC 58.605 30.769 0.00 0.00 45.23 2.01
305 306 7.276658 ACTGCATGTTGACGAACAAAATTTAAA 59.723 29.630 0.00 0.00 45.23 1.52
306 307 6.754209 ACTGCATGTTGACGAACAAAATTTAA 59.246 30.769 0.00 0.00 45.23 1.52
307 308 6.269315 ACTGCATGTTGACGAACAAAATTTA 58.731 32.000 0.00 0.00 45.23 1.40
308 309 5.108517 ACTGCATGTTGACGAACAAAATTT 58.891 33.333 0.00 0.00 45.23 1.82
309 310 4.681744 ACTGCATGTTGACGAACAAAATT 58.318 34.783 0.00 0.00 45.23 1.82
310 311 4.305989 ACTGCATGTTGACGAACAAAAT 57.694 36.364 0.00 0.00 45.23 1.82
311 312 3.773860 ACTGCATGTTGACGAACAAAA 57.226 38.095 0.00 0.00 45.23 2.44
312 313 3.773860 AACTGCATGTTGACGAACAAA 57.226 38.095 0.00 0.00 45.23 2.83
313 314 3.773860 AAACTGCATGTTGACGAACAA 57.226 38.095 0.00 0.00 45.23 2.83
314 315 3.773860 AAAACTGCATGTTGACGAACA 57.226 38.095 0.00 0.00 46.13 3.18
315 316 3.177643 CGAAAAACTGCATGTTGACGAAC 59.822 43.478 0.00 0.00 39.13 3.95
316 317 3.064134 TCGAAAAACTGCATGTTGACGAA 59.936 39.130 15.20 6.76 39.13 3.85
317 318 2.609916 TCGAAAAACTGCATGTTGACGA 59.390 40.909 14.39 14.39 39.13 4.20
318 319 2.980586 TCGAAAAACTGCATGTTGACG 58.019 42.857 0.00 8.44 39.13 4.35
319 320 5.458452 TCATTTCGAAAAACTGCATGTTGAC 59.542 36.000 15.66 0.00 39.13 3.18
320 321 5.586339 TCATTTCGAAAAACTGCATGTTGA 58.414 33.333 15.66 7.02 39.13 3.18
321 322 5.886715 TCATTTCGAAAAACTGCATGTTG 57.113 34.783 15.66 4.64 39.13 3.33
322 323 6.215121 TCATCATTTCGAAAAACTGCATGTT 58.785 32.000 15.66 0.00 41.29 2.71
323 324 5.771469 TCATCATTTCGAAAAACTGCATGT 58.229 33.333 15.66 0.00 0.00 3.21
324 325 6.693761 TTCATCATTTCGAAAAACTGCATG 57.306 33.333 15.66 13.07 0.00 4.06
325 326 9.590451 AATATTCATCATTTCGAAAAACTGCAT 57.410 25.926 15.66 10.18 0.00 3.96
326 327 8.984891 AATATTCATCATTTCGAAAAACTGCA 57.015 26.923 15.66 3.48 0.00 4.41
370 371 8.539770 TCACAAAAACACTCATTGCTTAAAAA 57.460 26.923 0.00 0.00 0.00 1.94
371 372 8.031864 TCTCACAAAAACACTCATTGCTTAAAA 58.968 29.630 0.00 0.00 0.00 1.52
372 373 7.542890 TCTCACAAAAACACTCATTGCTTAAA 58.457 30.769 0.00 0.00 0.00 1.52
373 374 7.094508 TCTCACAAAAACACTCATTGCTTAA 57.905 32.000 0.00 0.00 0.00 1.85
374 375 6.691754 TCTCACAAAAACACTCATTGCTTA 57.308 33.333 0.00 0.00 0.00 3.09
375 376 5.581126 TCTCACAAAAACACTCATTGCTT 57.419 34.783 0.00 0.00 0.00 3.91
376 377 5.779529 ATCTCACAAAAACACTCATTGCT 57.220 34.783 0.00 0.00 0.00 3.91
377 378 5.978919 TGAATCTCACAAAAACACTCATTGC 59.021 36.000 0.00 0.00 0.00 3.56
378 379 7.863877 TCATGAATCTCACAAAAACACTCATTG 59.136 33.333 0.00 0.00 0.00 2.82
379 380 7.944061 TCATGAATCTCACAAAAACACTCATT 58.056 30.769 0.00 0.00 0.00 2.57
380 381 7.514784 TCATGAATCTCACAAAAACACTCAT 57.485 32.000 0.00 0.00 0.00 2.90
381 382 6.940831 TCATGAATCTCACAAAAACACTCA 57.059 33.333 0.00 0.00 0.00 3.41
382 383 7.864379 ACATTCATGAATCTCACAAAAACACTC 59.136 33.333 18.16 0.00 0.00 3.51
383 384 7.719483 ACATTCATGAATCTCACAAAAACACT 58.281 30.769 18.16 0.00 0.00 3.55
384 385 7.935338 ACATTCATGAATCTCACAAAAACAC 57.065 32.000 18.16 0.00 0.00 3.32
385 386 8.945481 AAACATTCATGAATCTCACAAAAACA 57.055 26.923 18.16 0.00 0.00 2.83
474 475 8.090214 CCAGAAATCATAAGATGTTTGTGGTTT 58.910 33.333 15.04 0.46 38.43 3.27
475 476 7.451255 TCCAGAAATCATAAGATGTTTGTGGTT 59.549 33.333 18.72 0.00 40.80 3.67
476 477 6.947733 TCCAGAAATCATAAGATGTTTGTGGT 59.052 34.615 18.72 0.00 40.80 4.16
477 478 7.121759 ACTCCAGAAATCATAAGATGTTTGTGG 59.878 37.037 16.10 16.10 41.02 4.17
478 479 8.048534 ACTCCAGAAATCATAAGATGTTTGTG 57.951 34.615 0.00 0.00 33.90 3.33
479 480 9.911788 ATACTCCAGAAATCATAAGATGTTTGT 57.088 29.630 0.00 0.00 33.90 2.83
598 608 2.296073 TGGACGCCCCAGTTTATTTT 57.704 45.000 0.00 0.00 40.82 1.82
641 651 1.501654 GCACCTCCTTTCCTCCCCTT 61.502 60.000 0.00 0.00 0.00 3.95
643 653 2.677848 GCACCTCCTTTCCTCCCC 59.322 66.667 0.00 0.00 0.00 4.81
696 706 5.684626 CCGTCTGATCGTGTTAGTTTATACC 59.315 44.000 0.00 0.00 0.00 2.73
715 764 0.036010 CACCTGGAGAAATGCCGTCT 60.036 55.000 0.00 0.00 0.00 4.18
722 771 0.324943 CGGTCACCACCTGGAGAAAT 59.675 55.000 0.00 0.00 41.17 2.17
736 785 1.758936 TCGCTAATCCTTCTCGGTCA 58.241 50.000 0.00 0.00 0.00 4.02
737 786 2.865343 TTCGCTAATCCTTCTCGGTC 57.135 50.000 0.00 0.00 0.00 4.79
738 787 3.372660 GATTCGCTAATCCTTCTCGGT 57.627 47.619 0.00 0.00 36.30 4.69
762 811 4.695455 TCGATGGAAAGATCACTTTTGTCC 59.305 41.667 0.00 0.00 44.97 4.02
778 827 0.313987 CCGACGGATTGATCGATGGA 59.686 55.000 8.64 0.00 40.86 3.41
807 856 0.877649 CGTTCTGGGCATCATCGAGG 60.878 60.000 0.00 0.00 0.00 4.63
841 890 0.877743 GAGCCCACAAGAACAAGAGC 59.122 55.000 0.00 0.00 0.00 4.09
854 903 5.495640 AGACAAAAACAAAATTTGAGCCCA 58.504 33.333 13.19 0.00 39.56 5.36
949 998 1.469940 GCTCGTGATGTGGTAGGAGTG 60.470 57.143 0.00 0.00 32.85 3.51
972 1021 1.673665 CTCAGCTCCCAACACCAGC 60.674 63.158 0.00 0.00 0.00 4.85
975 1024 1.003580 TGATTCTCAGCTCCCAACACC 59.996 52.381 0.00 0.00 0.00 4.16
993 1045 2.392662 GACAGGAGACCCATCTGATGA 58.607 52.381 18.92 0.00 34.34 2.92
1261 1313 4.583489 AGACACGAGTTTCAGAGTTTCCTA 59.417 41.667 0.00 0.00 0.00 2.94
1283 1339 3.041946 ACTAGGCCCTCCTGTAAATGAG 58.958 50.000 0.00 0.00 44.08 2.90
1343 1403 0.604780 CGATGATGACATGGGCTCCC 60.605 60.000 0.00 0.00 36.82 4.30
1521 1581 2.890311 TGGCTGGTTTTGGTTACATCAG 59.110 45.455 0.00 0.00 0.00 2.90
1534 1594 0.251787 GATGAAGGGGTTGGCTGGTT 60.252 55.000 0.00 0.00 0.00 3.67
1535 1595 1.142688 AGATGAAGGGGTTGGCTGGT 61.143 55.000 0.00 0.00 0.00 4.00
1536 1596 0.394899 GAGATGAAGGGGTTGGCTGG 60.395 60.000 0.00 0.00 0.00 4.85
1537 1597 0.745845 CGAGATGAAGGGGTTGGCTG 60.746 60.000 0.00 0.00 0.00 4.85
1538 1598 0.909610 TCGAGATGAAGGGGTTGGCT 60.910 55.000 0.00 0.00 0.00 4.75
1539 1599 0.181350 ATCGAGATGAAGGGGTTGGC 59.819 55.000 0.00 0.00 0.00 4.52
1540 1600 1.765314 AGATCGAGATGAAGGGGTTGG 59.235 52.381 0.00 0.00 0.00 3.77
1584 1644 2.680312 ATTCAGAGCAGCGTACACAT 57.320 45.000 0.00 0.00 0.00 3.21
1585 1645 3.250744 GTTATTCAGAGCAGCGTACACA 58.749 45.455 0.00 0.00 0.00 3.72
1586 1646 2.603560 GGTTATTCAGAGCAGCGTACAC 59.396 50.000 0.00 0.00 0.00 2.90
1591 1652 1.063174 GCTTGGTTATTCAGAGCAGCG 59.937 52.381 0.00 0.00 33.68 5.18
1673 1734 2.518587 TCGACGCCATCCTCGGAT 60.519 61.111 0.00 0.00 34.81 4.18
1742 1803 8.591114 TTAGTTTACAGAGGCAGTAGATAACT 57.409 34.615 0.00 0.00 39.81 2.24
1751 1812 7.327275 CGCTCTTATATTAGTTTACAGAGGCAG 59.673 40.741 0.00 0.00 0.00 4.85
1753 1814 7.146648 ACGCTCTTATATTAGTTTACAGAGGC 58.853 38.462 0.00 0.00 0.00 4.70
1754 1815 9.530633 AAACGCTCTTATATTAGTTTACAGAGG 57.469 33.333 0.00 0.00 31.14 3.69
1770 1831 8.954350 ACTAAAGTAGTGATCTAAACGCTCTTA 58.046 33.333 0.00 0.00 37.69 2.10
1772 1833 7.393841 ACTAAAGTAGTGATCTAAACGCTCT 57.606 36.000 0.00 0.00 37.69 4.09
1787 1848 9.953697 ATAAGAGCGTTTAGATCACTAAAGTAG 57.046 33.333 0.00 0.00 45.42 2.57
1799 1860 9.669353 CCGTAAACTAATATAAGAGCGTTTAGA 57.331 33.333 0.00 0.00 30.36 2.10
1800 1861 9.669353 TCCGTAAACTAATATAAGAGCGTTTAG 57.331 33.333 0.00 0.00 30.36 1.85
1801 1862 9.669353 CTCCGTAAACTAATATAAGAGCGTTTA 57.331 33.333 0.00 0.00 0.00 2.01
1802 1863 7.650903 CCTCCGTAAACTAATATAAGAGCGTTT 59.349 37.037 0.00 0.00 0.00 3.60
1803 1864 7.144000 CCTCCGTAAACTAATATAAGAGCGTT 58.856 38.462 0.00 0.00 0.00 4.84
1804 1865 6.294397 CCCTCCGTAAACTAATATAAGAGCGT 60.294 42.308 0.00 0.00 0.00 5.07
1805 1866 6.072286 TCCCTCCGTAAACTAATATAAGAGCG 60.072 42.308 0.00 0.00 0.00 5.03
1806 1867 7.039853 ACTCCCTCCGTAAACTAATATAAGAGC 60.040 40.741 0.00 0.00 0.00 4.09
1807 1868 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
1812 1873 9.460019 GTAGATACTCCCTCCGTAAACTAATAT 57.540 37.037 0.00 0.00 0.00 1.28
1813 1874 8.439971 TGTAGATACTCCCTCCGTAAACTAATA 58.560 37.037 0.00 0.00 0.00 0.98
1814 1875 7.293073 TGTAGATACTCCCTCCGTAAACTAAT 58.707 38.462 0.00 0.00 0.00 1.73
1815 1876 6.662755 TGTAGATACTCCCTCCGTAAACTAA 58.337 40.000 0.00 0.00 0.00 2.24
1816 1877 6.126652 ACTGTAGATACTCCCTCCGTAAACTA 60.127 42.308 0.00 0.00 0.00 2.24
1817 1878 5.121380 TGTAGATACTCCCTCCGTAAACT 57.879 43.478 0.00 0.00 0.00 2.66
1818 1879 4.886489 ACTGTAGATACTCCCTCCGTAAAC 59.114 45.833 0.00 0.00 0.00 2.01
1819 1880 5.121380 ACTGTAGATACTCCCTCCGTAAA 57.879 43.478 0.00 0.00 0.00 2.01
1820 1881 4.785346 ACTGTAGATACTCCCTCCGTAA 57.215 45.455 0.00 0.00 0.00 3.18
1821 1882 5.784390 AGATACTGTAGATACTCCCTCCGTA 59.216 44.000 0.00 0.00 0.00 4.02
1822 1883 4.598373 AGATACTGTAGATACTCCCTCCGT 59.402 45.833 0.00 0.00 0.00 4.69
1823 1884 5.168647 AGATACTGTAGATACTCCCTCCG 57.831 47.826 0.00 0.00 0.00 4.63
1824 1885 7.842887 AAAAGATACTGTAGATACTCCCTCC 57.157 40.000 0.00 0.00 0.00 4.30
2153 2220 3.125316 GCTCTTTAGCGTGCAGTATGTTT 59.875 43.478 0.00 0.00 39.39 2.83
2180 2247 5.360591 AGAAATAATACCTTGAGCCGTCTG 58.639 41.667 0.00 0.00 0.00 3.51
2209 2280 3.713826 TGAGGTAGAAGGGCGAAAATT 57.286 42.857 0.00 0.00 0.00 1.82
2219 2290 8.700051 TCTTCCTCTGAATAAATGAGGTAGAAG 58.300 37.037 12.82 7.94 45.11 2.85
2220 2291 8.609617 TCTTCCTCTGAATAAATGAGGTAGAA 57.390 34.615 12.82 0.00 45.11 2.10
2222 2293 8.646004 TGATCTTCCTCTGAATAAATGAGGTAG 58.354 37.037 7.94 8.02 45.46 3.18
2223 2294 8.553085 TGATCTTCCTCTGAATAAATGAGGTA 57.447 34.615 7.94 0.00 45.46 3.08
2224 2295 7.443302 TGATCTTCCTCTGAATAAATGAGGT 57.557 36.000 7.94 0.00 45.46 3.85
2226 2297 8.291032 GCATTGATCTTCCTCTGAATAAATGAG 58.709 37.037 0.00 0.00 0.00 2.90
2228 2299 8.167605 AGCATTGATCTTCCTCTGAATAAATG 57.832 34.615 0.00 0.00 0.00 2.32
2292 2363 5.085920 TGATGGGTCAGAATGGTTTGAAAT 58.914 37.500 0.00 0.00 36.16 2.17
2301 2372 4.641541 TGCAGTTTATGATGGGTCAGAATG 59.358 41.667 0.00 0.00 35.66 2.67
2323 2394 4.697352 CCTTCCTCCTGTTTCAGTAACATG 59.303 45.833 0.00 0.00 45.31 3.21
2532 2612 6.292542 GCCTCTGCAAGTCAAAAAGAAAATTC 60.293 38.462 0.00 0.00 37.47 2.17
2670 2756 4.199432 CGCAAGGCATCCTCTATTAGAT 57.801 45.455 0.00 0.00 30.89 1.98
2744 2832 3.586470 TTTGCCTGTAACTCCCTTCAA 57.414 42.857 0.00 0.00 0.00 2.69
2915 3003 0.528924 CTGGTTCACCATGCATGTGG 59.471 55.000 24.58 15.19 46.46 4.17
2916 3004 1.068125 CACTGGTTCACCATGCATGTG 60.068 52.381 24.58 20.71 46.46 3.21
2917 3005 1.250328 CACTGGTTCACCATGCATGT 58.750 50.000 24.58 10.59 46.46 3.21
2978 3066 3.755378 CAGGGTGCATATTGATCTTAGGC 59.245 47.826 0.00 0.19 0.00 3.93
3017 3113 4.699637 AGAACCGATCGGCAAATACATTA 58.300 39.130 33.62 0.00 39.32 1.90
3018 3114 3.541632 AGAACCGATCGGCAAATACATT 58.458 40.909 33.62 17.58 39.32 2.71
3019 3115 3.131396 GAGAACCGATCGGCAAATACAT 58.869 45.455 33.62 9.08 39.32 2.29
3020 3116 2.546778 GAGAACCGATCGGCAAATACA 58.453 47.619 33.62 0.00 39.32 2.29
3069 3173 4.867608 GCAACAGAGATCTGAAACTAGGAC 59.132 45.833 16.52 0.00 46.59 3.85
3084 3188 3.629398 GGGTGATATTTCAGGCAACAGAG 59.371 47.826 0.00 0.00 41.41 3.35
3109 3215 5.163478 GGCAGCACCAAAATATCTCTGAAAT 60.163 40.000 0.00 0.00 38.86 2.17
3129 3235 4.766404 ATACCGAAAAAGTTTCAGGCAG 57.234 40.909 9.83 0.00 0.00 4.85
3155 3261 2.084546 GATAGCTGGGCGTGTTTTTCT 58.915 47.619 0.00 0.00 0.00 2.52
3161 3267 2.494918 GACGATAGCTGGGCGTGT 59.505 61.111 13.72 0.00 38.51 4.49
3166 3272 0.875728 CCTCTACGACGATAGCTGGG 59.124 60.000 0.00 0.49 42.67 4.45
3169 3275 4.333913 TTCTACCTCTACGACGATAGCT 57.666 45.455 0.00 0.00 42.67 3.32
3185 3291 5.263968 TCTCAGTCCCGAAATCATTCTAC 57.736 43.478 0.00 0.00 33.17 2.59
3186 3292 4.202161 GCTCTCAGTCCCGAAATCATTCTA 60.202 45.833 0.00 0.00 33.17 2.10
3187 3293 3.431486 GCTCTCAGTCCCGAAATCATTCT 60.431 47.826 0.00 0.00 33.17 2.40
3188 3294 2.869192 GCTCTCAGTCCCGAAATCATTC 59.131 50.000 0.00 0.00 0.00 2.67
3189 3295 2.237143 TGCTCTCAGTCCCGAAATCATT 59.763 45.455 0.00 0.00 0.00 2.57
3190 3296 1.833630 TGCTCTCAGTCCCGAAATCAT 59.166 47.619 0.00 0.00 0.00 2.45
3191 3297 1.066858 GTGCTCTCAGTCCCGAAATCA 60.067 52.381 0.00 0.00 0.00 2.57
3192 3298 1.646189 GTGCTCTCAGTCCCGAAATC 58.354 55.000 0.00 0.00 0.00 2.17
3193 3299 0.250513 GGTGCTCTCAGTCCCGAAAT 59.749 55.000 0.00 0.00 0.00 2.17
3194 3300 1.671742 GGTGCTCTCAGTCCCGAAA 59.328 57.895 0.00 0.00 0.00 3.46
3195 3301 2.283529 GGGTGCTCTCAGTCCCGAA 61.284 63.158 0.00 0.00 0.00 4.30
3196 3302 1.859841 TAGGGTGCTCTCAGTCCCGA 61.860 60.000 0.00 0.00 44.13 5.14
3197 3303 0.757188 ATAGGGTGCTCTCAGTCCCG 60.757 60.000 0.00 0.00 44.13 5.14
3198 3304 0.755686 CATAGGGTGCTCTCAGTCCC 59.244 60.000 0.00 0.00 40.16 4.46
3211 3317 4.910585 GTCCGCGGGTGCATAGGG 62.911 72.222 27.83 0.00 42.97 3.53
3212 3318 4.155733 TGTCCGCGGGTGCATAGG 62.156 66.667 27.83 0.00 42.97 2.57
3213 3319 2.890474 GTGTCCGCGGGTGCATAG 60.890 66.667 27.83 0.00 42.97 2.23
3214 3320 4.805231 CGTGTCCGCGGGTGCATA 62.805 66.667 27.83 0.17 42.97 3.14
3233 3339 2.738964 GCAGATTTAGGGACAGTCGGTC 60.739 54.545 0.00 0.00 46.20 4.79
3234 3340 1.207329 GCAGATTTAGGGACAGTCGGT 59.793 52.381 0.00 0.00 0.00 4.69
3236 3342 1.135083 ACGCAGATTTAGGGACAGTCG 60.135 52.381 0.00 0.00 0.00 4.18
3238 3344 2.166664 GAGACGCAGATTTAGGGACAGT 59.833 50.000 0.00 0.00 0.00 3.55
3240 3346 1.480954 GGAGACGCAGATTTAGGGACA 59.519 52.381 0.00 0.00 0.00 4.02
3256 3362 0.676184 GAGATATGCGGCTGTGGAGA 59.324 55.000 0.00 0.00 0.00 3.71
3313 3423 8.178313 TGATCGTTTGGTGATCTACATACTAT 57.822 34.615 4.78 0.00 42.18 2.12
3402 3515 1.104577 TGCCCGTTTGACCACCTTTC 61.105 55.000 0.00 0.00 0.00 2.62
3409 3523 2.490115 TGAATTGTATGCCCGTTTGACC 59.510 45.455 0.00 0.00 0.00 4.02
3410 3524 3.057876 TGTGAATTGTATGCCCGTTTGAC 60.058 43.478 0.00 0.00 0.00 3.18
3423 3537 3.064820 GGTCGTTGAACTGTGTGAATTGT 59.935 43.478 0.00 0.00 0.00 2.71
3424 3538 3.617669 GGTCGTTGAACTGTGTGAATTG 58.382 45.455 0.00 0.00 0.00 2.32
3446 3561 5.241064 TCGAGTATCTAGTTAGAATGTGCCC 59.759 44.000 0.00 0.00 35.69 5.36
3468 3583 7.416213 CCCTCTCCTTTTATATGATCTAGCTCG 60.416 44.444 0.00 0.00 0.00 5.03
3478 3593 3.823304 GCTTGGCCCTCTCCTTTTATATG 59.177 47.826 0.00 0.00 0.00 1.78
3565 3682 3.756727 GACGTCGACCCACCTCCC 61.757 72.222 10.58 0.00 0.00 4.30
3583 3709 2.033141 TTCGACGGGTCCGACTCT 59.967 61.111 16.90 0.00 42.83 3.24
3608 3749 2.481449 GCTACATCGTGATCTCCGGTTT 60.481 50.000 0.00 0.00 0.00 3.27
3619 3760 0.097674 GCTTGCAAGGCTACATCGTG 59.902 55.000 27.10 0.00 0.00 4.35
3663 3810 2.677875 GGGTGGCCAAGCTCAAGG 60.678 66.667 7.24 0.00 0.00 3.61
3734 3911 1.363744 CTCTGAAGGATCAACGCCAC 58.636 55.000 0.00 0.00 34.49 5.01
3748 3925 4.121669 GACGCTCGGCAGCTCTGA 62.122 66.667 0.29 0.00 44.40 3.27
3804 3982 0.323908 CGAGGGGGAGTGTCTCTTCT 60.324 60.000 0.00 0.00 0.00 2.85


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

AutoCloner maintained by Alex Coulton.