Multiple sequence alignment - TraesCS5B01G439000

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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 TraesCS5B01G439000 chr5B 100.000 3810 0 0 1 3810 611389847 611386038 0.000000e+00 7036.0
1 TraesCS5B01G439000 chr5D 92.113 2802 119 48 615 3371 494818072 494815328 0.000000e+00 3856.0
2 TraesCS5B01G439000 chr5D 89.846 325 21 7 3481 3801 494815276 494814960 1.270000e-109 407.0
3 TraesCS5B01G439000 chr5D 80.470 553 33 42 76 608 494818618 494818121 1.680000e-93 353.0
4 TraesCS5B01G439000 chr5A 89.567 1572 57 45 609 2115 618968424 618966895 0.000000e+00 1895.0
5 TraesCS5B01G439000 chr5A 92.691 1204 51 17 2189 3376 618966788 618965606 0.000000e+00 1701.0
6 TraesCS5B01G439000 chr5A 87.204 422 38 9 3382 3800 618965504 618965096 2.070000e-127 466.0
7 TraesCS5B01G439000 chr5A 81.535 482 30 35 138 608 618968903 618968470 3.640000e-90 342.0
8 TraesCS5B01G439000 chr5A 100.000 30 0 0 3410 3439 585407067 585407038 5.320000e-04 56.5
9 TraesCS5B01G439000 chr6B 79.339 121 16 6 3324 3439 13965242 13965358 4.080000e-10 76.8
10 TraesCS5B01G439000 chr6B 100.000 30 0 0 3410 3439 365708207 365708236 5.320000e-04 56.5
11 TraesCS5B01G439000 chrUn 100.000 30 0 0 3410 3439 69192840 69192811 5.320000e-04 56.5
12 TraesCS5B01G439000 chr6D 100.000 30 0 0 3410 3439 221214290 221214261 5.320000e-04 56.5
13 TraesCS5B01G439000 chr6A 100.000 30 0 0 3410 3439 53932075 53932104 5.320000e-04 56.5
14 TraesCS5B01G439000 chr6A 100.000 30 0 0 3410 3439 262044753 262044724 5.320000e-04 56.5
15 TraesCS5B01G439000 chr4B 86.792 53 4 2 3391 3442 394640776 394640726 5.320000e-04 56.5


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 TraesCS5B01G439000 chr5B 611386038 611389847 3809 True 7036.000000 7036 100.000000 1 3810 1 chr5B.!!$R1 3809
1 TraesCS5B01G439000 chr5D 494814960 494818618 3658 True 1538.666667 3856 87.476333 76 3801 3 chr5D.!!$R1 3725
2 TraesCS5B01G439000 chr5A 618965096 618968903 3807 True 1101.000000 1895 87.749250 138 3800 4 chr5A.!!$R2 3662

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
304 312 0.037447 GGAGAGAAAAGGCAGGCAGT 59.963 55.0 0.00 0.00 0.00 4.40 F
552 576 0.179161 CATCAAGAAGCAGCAGCAGC 60.179 55.0 3.17 0.46 45.49 5.25 F
1390 1531 0.398696 TACACACCACACCACCATCC 59.601 55.0 0.00 0.00 0.00 3.51 F
1616 1757 0.179200 ATGCGCGAACGAAACCATTC 60.179 50.0 12.10 0.00 43.93 2.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1245 1380 0.250901 TCTTGAGGTTGCTCTTGGGC 60.251 55.0 0.00 0.00 0.0 5.36 R
1532 1673 0.889186 ATCGGGTCTTTGGTGCACAC 60.889 55.0 20.43 7.48 0.0 3.82 R
2597 2810 0.968901 ACGCCAAGGTCCGTCTATCA 60.969 55.0 0.00 0.00 31.0 2.15 R
3469 3788 0.323451 ACCCTCCTTCCAATTTCGCC 60.323 55.0 0.00 0.00 0.0 5.54 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
18 19 3.845625 GACACGCAGAAGGGTTTTG 57.154 52.632 0.00 0.00 39.11 2.44
19 20 1.305201 GACACGCAGAAGGGTTTTGA 58.695 50.000 0.00 0.00 39.11 2.69
20 21 1.264288 GACACGCAGAAGGGTTTTGAG 59.736 52.381 0.00 0.00 39.11 3.02
21 22 1.308998 CACGCAGAAGGGTTTTGAGT 58.691 50.000 0.00 0.00 39.11 3.41
22 23 1.676006 CACGCAGAAGGGTTTTGAGTT 59.324 47.619 0.00 0.00 39.11 3.01
23 24 1.676006 ACGCAGAAGGGTTTTGAGTTG 59.324 47.619 0.00 0.00 37.72 3.16
24 25 1.676006 CGCAGAAGGGTTTTGAGTTGT 59.324 47.619 0.00 0.00 0.00 3.32
25 26 2.875933 CGCAGAAGGGTTTTGAGTTGTA 59.124 45.455 0.00 0.00 0.00 2.41
26 27 3.303791 CGCAGAAGGGTTTTGAGTTGTAC 60.304 47.826 0.00 0.00 0.00 2.90
27 28 3.303791 GCAGAAGGGTTTTGAGTTGTACG 60.304 47.826 0.00 0.00 0.00 3.67
28 29 3.875134 CAGAAGGGTTTTGAGTTGTACGT 59.125 43.478 0.00 0.00 0.00 3.57
29 30 4.025145 CAGAAGGGTTTTGAGTTGTACGTC 60.025 45.833 0.00 0.00 0.00 4.34
30 31 3.832615 AGGGTTTTGAGTTGTACGTCT 57.167 42.857 0.00 0.00 0.00 4.18
31 32 3.725490 AGGGTTTTGAGTTGTACGTCTC 58.275 45.455 0.00 9.31 0.00 3.36
32 33 3.387050 AGGGTTTTGAGTTGTACGTCTCT 59.613 43.478 14.95 0.11 0.00 3.10
33 34 3.739810 GGGTTTTGAGTTGTACGTCTCTC 59.260 47.826 14.95 8.36 0.00 3.20
34 35 3.424529 GGTTTTGAGTTGTACGTCTCTCG 59.575 47.826 14.95 0.00 46.00 4.04
35 36 2.327081 TTGAGTTGTACGTCTCTCGC 57.673 50.000 14.95 0.00 44.19 5.03
36 37 1.232119 TGAGTTGTACGTCTCTCGCA 58.768 50.000 14.95 0.00 44.19 5.10
37 38 1.605232 TGAGTTGTACGTCTCTCGCAA 59.395 47.619 14.95 0.00 44.19 4.85
38 39 2.243407 GAGTTGTACGTCTCTCGCAAG 58.757 52.381 0.00 0.00 44.19 4.01
57 58 7.703328 TCGCAAGATATAACCTTCAAAATTCC 58.297 34.615 0.00 0.00 45.01 3.01
58 59 7.338196 TCGCAAGATATAACCTTCAAAATTCCA 59.662 33.333 0.00 0.00 45.01 3.53
59 60 7.973388 CGCAAGATATAACCTTCAAAATTCCAA 59.027 33.333 0.00 0.00 43.02 3.53
60 61 9.651913 GCAAGATATAACCTTCAAAATTCCAAA 57.348 29.630 0.00 0.00 0.00 3.28
68 69 8.750515 AACCTTCAAAATTCCAAACATGATTT 57.249 26.923 0.00 0.00 0.00 2.17
69 70 8.750515 ACCTTCAAAATTCCAAACATGATTTT 57.249 26.923 0.00 0.00 0.00 1.82
70 71 9.187996 ACCTTCAAAATTCCAAACATGATTTTT 57.812 25.926 0.00 0.00 0.00 1.94
95 96 9.619316 TTTGTTCGAACATAAATTTGTGGATAG 57.381 29.630 30.10 7.93 38.95 2.08
107 108 8.538409 AAATTTGTGGATAGAAAAAGATGCAC 57.462 30.769 0.00 0.17 42.76 4.57
109 110 5.627499 TGTGGATAGAAAAAGATGCACAC 57.373 39.130 5.27 0.00 45.77 3.82
111 112 6.472016 TGTGGATAGAAAAAGATGCACACTA 58.528 36.000 5.27 0.00 45.77 2.74
112 113 7.112122 TGTGGATAGAAAAAGATGCACACTAT 58.888 34.615 5.27 0.00 45.77 2.12
113 114 8.264347 TGTGGATAGAAAAAGATGCACACTATA 58.736 33.333 5.27 0.00 45.77 1.31
114 115 9.109393 GTGGATAGAAAAAGATGCACACTATAA 57.891 33.333 0.00 0.00 42.21 0.98
115 116 9.851686 TGGATAGAAAAAGATGCACACTATAAT 57.148 29.630 0.00 0.00 0.00 1.28
121 122 9.282247 GAAAAAGATGCACACTATAATTCTGTG 57.718 33.333 0.00 0.00 38.68 3.66
125 129 5.159273 TGCACACTATAATTCTGTGGACA 57.841 39.130 9.25 5.15 36.58 4.02
127 131 4.034510 GCACACTATAATTCTGTGGACAGC 59.965 45.833 1.63 5.25 43.46 4.40
139 143 4.397103 TCTGTGGACAGCAATCATCAAATC 59.603 41.667 1.63 0.00 43.46 2.17
140 144 4.080687 TGTGGACAGCAATCATCAAATCA 58.919 39.130 0.00 0.00 0.00 2.57
142 146 5.010820 TGTGGACAGCAATCATCAAATCAAA 59.989 36.000 0.00 0.00 0.00 2.69
143 147 5.346822 GTGGACAGCAATCATCAAATCAAAC 59.653 40.000 0.00 0.00 0.00 2.93
189 193 0.385974 GCGTGGCTGTCATCAACAAC 60.386 55.000 0.00 0.00 37.45 3.32
219 223 5.668471 ACTCTAAAATAAGTAGAACCCGGC 58.332 41.667 0.00 0.00 0.00 6.13
220 224 4.685924 TCTAAAATAAGTAGAACCCGGCG 58.314 43.478 0.00 0.00 0.00 6.46
258 263 0.826256 ACAGCGACTCCAGTGTGGTA 60.826 55.000 0.00 0.00 39.03 3.25
272 277 6.326323 TCCAGTGTGGTAGCAATAGATTATCA 59.674 38.462 0.00 0.00 39.03 2.15
274 279 6.425114 CAGTGTGGTAGCAATAGATTATCACC 59.575 42.308 0.00 0.00 0.00 4.02
278 283 6.014156 GTGGTAGCAATAGATTATCACCCTCT 60.014 42.308 0.00 0.00 0.00 3.69
279 284 6.558775 TGGTAGCAATAGATTATCACCCTCTT 59.441 38.462 0.00 0.00 0.00 2.85
280 285 7.100409 GGTAGCAATAGATTATCACCCTCTTC 58.900 42.308 0.00 0.00 0.00 2.87
281 286 6.120507 AGCAATAGATTATCACCCTCTTCC 57.879 41.667 0.00 0.00 0.00 3.46
282 287 5.848921 AGCAATAGATTATCACCCTCTTCCT 59.151 40.000 0.00 0.00 0.00 3.36
302 310 1.003355 CGGAGAGAAAAGGCAGGCA 60.003 57.895 0.00 0.00 0.00 4.75
303 311 1.023513 CGGAGAGAAAAGGCAGGCAG 61.024 60.000 0.00 0.00 0.00 4.85
304 312 0.037447 GGAGAGAAAAGGCAGGCAGT 59.963 55.000 0.00 0.00 0.00 4.40
305 313 1.163554 GAGAGAAAAGGCAGGCAGTG 58.836 55.000 0.00 0.00 0.00 3.66
317 325 3.513225 GCAGTGCGCCACCATAAT 58.487 55.556 4.18 0.00 34.49 1.28
318 326 2.701587 GCAGTGCGCCACCATAATA 58.298 52.632 4.18 0.00 34.49 0.98
319 327 1.021202 GCAGTGCGCCACCATAATAA 58.979 50.000 4.18 0.00 34.49 1.40
320 328 1.403679 GCAGTGCGCCACCATAATAAA 59.596 47.619 4.18 0.00 34.49 1.40
321 329 2.034558 GCAGTGCGCCACCATAATAAAT 59.965 45.455 4.18 0.00 34.49 1.40
332 340 3.007614 ACCATAATAAATCCCCGTCTCCG 59.992 47.826 0.00 0.00 0.00 4.63
345 353 3.374402 CTCCGCAGACCAGTCCGT 61.374 66.667 0.00 0.00 0.00 4.69
347 355 4.436998 CCGCAGACCAGTCCGTCC 62.437 72.222 0.00 0.00 32.91 4.79
348 356 4.778415 CGCAGACCAGTCCGTCCG 62.778 72.222 0.00 0.00 32.91 4.79
350 358 3.374402 CAGACCAGTCCGTCCGCT 61.374 66.667 0.00 0.00 32.91 5.52
351 359 3.063084 AGACCAGTCCGTCCGCTC 61.063 66.667 0.00 0.00 32.91 5.03
409 433 2.813908 ACTCGCCGTGCCGAATTC 60.814 61.111 0.00 0.00 36.72 2.17
410 434 3.564027 CTCGCCGTGCCGAATTCC 61.564 66.667 0.00 0.00 36.72 3.01
417 441 2.360600 TGCCGAATTCCCCCGTTG 60.361 61.111 0.00 0.00 0.00 4.10
428 452 0.806241 CCCCCGTTGTTTTATCCACG 59.194 55.000 0.00 0.00 0.00 4.94
429 453 1.525941 CCCCGTTGTTTTATCCACGT 58.474 50.000 0.00 0.00 0.00 4.49
430 454 2.614987 CCCCCGTTGTTTTATCCACGTA 60.615 50.000 0.00 0.00 0.00 3.57
465 489 1.470996 ATCTCCCTCTCATGCGCCTC 61.471 60.000 4.18 0.00 0.00 4.70
477 501 2.256461 CGCCTCTTGCCTTGCAAC 59.744 61.111 0.00 0.00 43.99 4.17
502 526 3.644738 GGATGCATTTGATTTGATCCCCT 59.355 43.478 0.00 0.00 0.00 4.79
504 528 3.033184 TGCATTTGATTTGATCCCCTCC 58.967 45.455 0.00 0.00 0.00 4.30
505 529 2.366590 GCATTTGATTTGATCCCCTCCC 59.633 50.000 0.00 0.00 0.00 4.30
535 559 3.120086 GCGGCCTGTGGGGTATCAT 62.120 63.158 0.00 0.00 37.43 2.45
536 560 1.071471 CGGCCTGTGGGGTATCATC 59.929 63.158 0.00 0.00 37.43 2.92
543 567 3.209410 CTGTGGGGTATCATCAAGAAGC 58.791 50.000 0.00 0.00 0.00 3.86
546 570 2.225467 GGGGTATCATCAAGAAGCAGC 58.775 52.381 0.00 0.00 0.00 5.25
549 573 2.290093 GGTATCATCAAGAAGCAGCAGC 59.710 50.000 0.00 0.00 42.56 5.25
552 576 0.179161 CATCAAGAAGCAGCAGCAGC 60.179 55.000 3.17 0.46 45.49 5.25
559 583 0.536687 AAGCAGCAGCAGCAGAAGAA 60.537 50.000 12.92 0.00 45.49 2.52
560 584 0.956410 AGCAGCAGCAGCAGAAGAAG 60.956 55.000 12.92 0.00 45.49 2.85
562 586 1.520494 CAGCAGCAGCAGAAGAAGAA 58.480 50.000 3.17 0.00 45.49 2.52
563 587 1.465387 CAGCAGCAGCAGAAGAAGAAG 59.535 52.381 3.17 0.00 45.49 2.85
564 588 1.347050 AGCAGCAGCAGAAGAAGAAGA 59.653 47.619 3.17 0.00 45.49 2.87
565 589 1.733360 GCAGCAGCAGAAGAAGAAGAG 59.267 52.381 0.00 0.00 41.58 2.85
566 590 2.612471 GCAGCAGCAGAAGAAGAAGAGA 60.612 50.000 0.00 0.00 41.58 3.10
567 591 3.661944 CAGCAGCAGAAGAAGAAGAGAA 58.338 45.455 0.00 0.00 0.00 2.87
570 594 3.679502 GCAGCAGAAGAAGAAGAGAAGAC 59.320 47.826 0.00 0.00 0.00 3.01
595 619 2.879907 CCGCTGCCACCATCTTTG 59.120 61.111 0.00 0.00 0.00 2.77
630 703 2.363147 AGAGAGACCCACCTCGCC 60.363 66.667 0.00 0.00 38.19 5.54
636 709 3.966930 GACCCACCTCGCCTCCTCT 62.967 68.421 0.00 0.00 0.00 3.69
710 792 4.527583 GCTCCTGCTCCGCTCCTG 62.528 72.222 0.00 0.00 36.03 3.86
711 793 4.527583 CTCCTGCTCCGCTCCTGC 62.528 72.222 0.00 0.00 0.00 4.85
836 949 2.571216 CCAAAGGCTGCTGCTTGCT 61.571 57.895 15.64 1.20 43.37 3.91
837 950 1.366366 CAAAGGCTGCTGCTTGCTT 59.634 52.632 15.64 7.56 43.37 3.91
838 951 0.944311 CAAAGGCTGCTGCTTGCTTG 60.944 55.000 15.64 6.63 43.37 4.01
839 952 2.710724 AAAGGCTGCTGCTTGCTTGC 62.711 55.000 15.64 7.68 43.37 4.01
1033 1150 2.202623 GTGAGACCTACTGCGCCG 60.203 66.667 4.18 0.00 0.00 6.46
1320 1455 0.610232 AGGGCAATGTGAAGTGGCTC 60.610 55.000 0.00 0.00 40.05 4.70
1390 1531 0.398696 TACACACCACACCACCATCC 59.601 55.000 0.00 0.00 0.00 3.51
1402 1543 0.855598 CACCATCCCCCTCCATGAAT 59.144 55.000 0.00 0.00 0.00 2.57
1532 1673 4.196971 CTCCGATTTTAGTAACCCAAGGG 58.803 47.826 2.91 2.91 42.03 3.95
1574 1715 6.555463 TCCTCCCGGGATATTAAATCATAC 57.445 41.667 27.07 0.00 39.58 2.39
1606 1747 2.865151 GCGTTGACATGCGCGAAC 60.865 61.111 12.10 2.61 44.13 3.95
1616 1757 0.179200 ATGCGCGAACGAAACCATTC 60.179 50.000 12.10 0.00 43.93 2.67
1619 1760 1.570347 CGCGAACGAAACCATTCCCA 61.570 55.000 0.00 0.00 43.93 4.37
1708 1849 6.402222 TGTTCTTCCTAGAAATCTGCTTCTC 58.598 40.000 0.00 0.00 41.86 2.87
1760 1905 3.981211 TGTACTACAACTTGGAACGACC 58.019 45.455 0.00 0.00 39.54 4.79
1768 1913 1.004320 TTGGAACGACCCGGTCATG 60.004 57.895 17.87 4.72 46.28 3.07
1783 1928 5.479306 CCGGTCATGATATTTACTTCGGAT 58.521 41.667 0.00 0.00 36.30 4.18
1784 1929 5.348724 CCGGTCATGATATTTACTTCGGATG 59.651 44.000 0.00 0.00 36.30 3.51
1787 1932 4.929211 TCATGATATTTACTTCGGATGCGG 59.071 41.667 6.82 0.00 0.00 5.69
1884 2033 2.335681 TGGTGGGGAGTAGATGACAA 57.664 50.000 0.00 0.00 0.00 3.18
1885 2034 1.906574 TGGTGGGGAGTAGATGACAAC 59.093 52.381 0.00 0.00 0.00 3.32
1887 2036 2.304761 GGTGGGGAGTAGATGACAACAA 59.695 50.000 0.00 0.00 0.00 2.83
1888 2037 3.600388 GTGGGGAGTAGATGACAACAAG 58.400 50.000 0.00 0.00 0.00 3.16
1890 2039 4.080863 GTGGGGAGTAGATGACAACAAGAT 60.081 45.833 0.00 0.00 0.00 2.40
1892 2041 4.162320 GGGGAGTAGATGACAACAAGATCA 59.838 45.833 0.00 0.00 0.00 2.92
1893 2042 5.338381 GGGGAGTAGATGACAACAAGATCAA 60.338 44.000 0.00 0.00 0.00 2.57
1894 2043 5.582665 GGGAGTAGATGACAACAAGATCAAC 59.417 44.000 0.00 0.00 0.00 3.18
1895 2044 6.402222 GGAGTAGATGACAACAAGATCAACT 58.598 40.000 0.00 0.00 33.15 3.16
1896 2045 6.876257 GGAGTAGATGACAACAAGATCAACTT 59.124 38.462 0.00 0.00 39.70 2.66
1897 2046 7.064016 GGAGTAGATGACAACAAGATCAACTTC 59.936 40.741 0.00 0.00 36.61 3.01
1898 2047 7.445121 AGTAGATGACAACAAGATCAACTTCA 58.555 34.615 0.00 0.00 36.61 3.02
1922 2071 7.931407 TCATATACATGTGTTGGACTTGGTATC 59.069 37.037 9.11 0.00 34.66 2.24
1949 2099 5.684184 AGCGAGTTTTGTTTATTCCGAAAAC 59.316 36.000 0.00 0.00 38.17 2.43
1974 2124 7.335422 ACTTAGCTATGACTTCTGAAATGTTGG 59.665 37.037 13.22 0.00 0.00 3.77
1979 2129 1.615392 ACTTCTGAAATGTTGGCAGCC 59.385 47.619 3.66 3.66 0.00 4.85
2073 2223 0.609957 CTCAGGGCATGCTTTCCACA 60.610 55.000 18.92 0.23 0.00 4.17
2096 2247 9.368921 CACATGTGTATAATAGCGTAAATTGTG 57.631 33.333 18.03 0.00 0.00 3.33
2130 2334 2.537143 TGGAGTCTCCCCTACAGTTTC 58.463 52.381 16.60 0.00 35.03 2.78
2136 2340 3.519913 GTCTCCCCTACAGTTTCCTGATT 59.480 47.826 0.00 0.00 41.50 2.57
2138 2342 4.962995 TCTCCCCTACAGTTTCCTGATTAG 59.037 45.833 0.00 0.00 41.50 1.73
2234 2438 4.223700 TGAGCCACATGATTTCAGTAGTCT 59.776 41.667 0.00 0.00 0.00 3.24
2275 2479 1.627329 TGAAATGACAGCAGCTCTCCT 59.373 47.619 0.00 0.00 0.00 3.69
2282 2486 1.696336 ACAGCAGCTCTCCTCAGAAAA 59.304 47.619 0.00 0.00 0.00 2.29
2295 2499 5.488341 TCCTCAGAAAATTGTAGTGTAGCC 58.512 41.667 0.00 0.00 0.00 3.93
2381 2593 5.651139 TCACTGGTCATCACTACTAACTACC 59.349 44.000 0.00 0.00 0.00 3.18
2533 2746 4.858850 TGAGTGGCATGTTCCTATTTCAT 58.141 39.130 0.00 0.00 0.00 2.57
2576 2789 5.645497 AGCAATAAAACAACAAAGCAAACCA 59.355 32.000 0.00 0.00 0.00 3.67
2578 2791 6.403092 GCAATAAAACAACAAAGCAAACCACT 60.403 34.615 0.00 0.00 0.00 4.00
2597 2810 4.023193 CCACTTTTTGTGCTCCTTTATCGT 60.023 41.667 0.00 0.00 44.92 3.73
2601 2814 6.653320 ACTTTTTGTGCTCCTTTATCGTGATA 59.347 34.615 0.00 0.00 0.00 2.15
2642 2855 3.125146 CGGAAATGAATTCTTGAGCGACA 59.875 43.478 7.05 0.00 38.18 4.35
2645 2858 6.095377 GGAAATGAATTCTTGAGCGACATTT 58.905 36.000 7.05 0.00 38.55 2.32
2646 2859 7.250569 GGAAATGAATTCTTGAGCGACATTTA 58.749 34.615 7.05 0.00 36.87 1.40
2648 2861 5.545658 TGAATTCTTGAGCGACATTTACC 57.454 39.130 7.05 0.00 0.00 2.85
2650 2863 5.705441 TGAATTCTTGAGCGACATTTACCTT 59.295 36.000 7.05 0.00 0.00 3.50
2651 2864 5.551760 ATTCTTGAGCGACATTTACCTTG 57.448 39.130 0.00 0.00 0.00 3.61
2681 2894 6.654161 AGATATTATGCTTGTTCTCATGGCTC 59.346 38.462 0.00 0.00 0.00 4.70
2688 2901 1.216122 GTTCTCATGGCTCGCTGATC 58.784 55.000 0.00 0.00 0.00 2.92
2727 2941 6.202954 ACTGCTTATTAAACTCACAGTGTGTC 59.797 38.462 22.29 0.00 35.68 3.67
2894 3108 2.290008 TGTACCAGTTTCATCGGTGCAT 60.290 45.455 0.00 0.00 40.00 3.96
2904 3118 3.653009 CGGTGCATGCCGCCATAG 61.653 66.667 22.78 7.88 45.47 2.23
2905 3119 3.969802 GGTGCATGCCGCCATAGC 61.970 66.667 16.68 0.43 43.83 2.97
2906 3120 2.903855 GTGCATGCCGCCATAGCT 60.904 61.111 16.68 0.00 41.33 3.32
2950 3167 1.908299 GGTGGGGGTTTTCTGCTGG 60.908 63.158 0.00 0.00 0.00 4.85
2969 3186 4.505922 GCTGGTTTTATCAGTCTCAGATCG 59.494 45.833 0.00 0.00 34.89 3.69
3011 3228 1.903404 GTGGGGGTGGAGCTTTGTG 60.903 63.158 0.00 0.00 0.00 3.33
3121 3339 7.891561 TGTAAAGTTCCCAATACAAAAGATGG 58.108 34.615 0.00 0.00 0.00 3.51
3177 3395 0.179020 TGCTGTGCTGCTGGTTACTT 60.179 50.000 0.00 0.00 0.00 2.24
3178 3396 0.239347 GCTGTGCTGCTGGTTACTTG 59.761 55.000 0.00 0.00 0.00 3.16
3179 3397 0.877071 CTGTGCTGCTGGTTACTTGG 59.123 55.000 0.00 0.00 0.00 3.61
3180 3398 0.472044 TGTGCTGCTGGTTACTTGGA 59.528 50.000 0.00 0.00 0.00 3.53
3239 3457 3.045634 CTGGGAACATGGGGATGTAGTA 58.954 50.000 0.00 0.00 41.51 1.82
3240 3458 3.045634 TGGGAACATGGGGATGTAGTAG 58.954 50.000 0.00 0.00 33.81 2.57
3241 3459 3.046374 GGGAACATGGGGATGTAGTAGT 58.954 50.000 0.00 0.00 33.81 2.73
3343 3565 4.815533 ATCATACTTCCTCCGATCCATG 57.184 45.455 0.00 0.00 0.00 3.66
3357 3579 4.695455 CCGATCCATGTTACTTGTTTCAGT 59.305 41.667 0.00 0.00 0.00 3.41
3361 3583 7.647715 CGATCCATGTTACTTGTTTCAGTTTTT 59.352 33.333 0.00 0.00 0.00 1.94
3383 3605 8.473358 TTTTTCTAGATACTGATGGATACGGA 57.527 34.615 0.00 0.00 42.51 4.69
3384 3606 8.651589 TTTTCTAGATACTGATGGATACGGAT 57.348 34.615 0.00 0.00 42.51 4.18
3410 3729 7.914427 ATCTAAATGTGTCTAGGTACATCCA 57.086 36.000 11.51 4.46 36.56 3.41
3411 3730 7.727578 TCTAAATGTGTCTAGGTACATCCAA 57.272 36.000 11.51 2.94 36.56 3.53
3417 3736 7.727578 TGTGTCTAGGTACATCCAAATCTAA 57.272 36.000 0.00 0.00 39.02 2.10
3418 3737 7.782049 TGTGTCTAGGTACATCCAAATCTAAG 58.218 38.462 0.00 0.00 39.02 2.18
3420 3739 7.921745 GTGTCTAGGTACATCCAAATCTAAGAC 59.078 40.741 0.00 0.00 39.02 3.01
3423 3742 8.696374 TCTAGGTACATCCAAATCTAAGACAAG 58.304 37.037 0.00 0.00 39.02 3.16
3424 3743 7.259088 AGGTACATCCAAATCTAAGACAAGT 57.741 36.000 0.00 0.00 39.02 3.16
3425 3744 8.375493 AGGTACATCCAAATCTAAGACAAGTA 57.625 34.615 0.00 0.00 39.02 2.24
3427 3746 9.614792 GGTACATCCAAATCTAAGACAAGTAAT 57.385 33.333 0.00 0.00 35.97 1.89
3438 3757 8.112016 TCTAAGACAAGTAATATGGATCGGAG 57.888 38.462 0.00 0.00 0.00 4.63
3439 3758 6.732896 AAGACAAGTAATATGGATCGGAGT 57.267 37.500 0.00 0.00 0.00 3.85
3442 3761 6.098409 AGACAAGTAATATGGATCGGAGTGTT 59.902 38.462 0.00 0.00 0.00 3.32
3444 3763 7.110155 ACAAGTAATATGGATCGGAGTGTTTT 58.890 34.615 0.00 0.00 0.00 2.43
3445 3764 7.610305 ACAAGTAATATGGATCGGAGTGTTTTT 59.390 33.333 0.00 0.00 0.00 1.94
3467 3786 1.470051 TTTTTGATAAGAGGGGCCGC 58.530 50.000 12.88 12.88 0.00 6.53
3469 3788 2.602746 TTTGATAAGAGGGGCCGCCG 62.603 60.000 17.56 0.00 0.00 6.46
3527 3846 6.200854 GTCCAAAAGCAACCTTGACAATTTAG 59.799 38.462 0.00 0.00 0.00 1.85
3533 3852 7.112452 AGCAACCTTGACAATTTAGAAGTTT 57.888 32.000 0.00 0.00 0.00 2.66
3551 3870 7.154656 AGAAGTTTCATTTTGTATGGAAAGGC 58.845 34.615 0.00 0.00 30.61 4.35
3552 3871 5.469479 AGTTTCATTTTGTATGGAAAGGCG 58.531 37.500 0.00 0.00 30.61 5.52
3568 3887 0.245266 GGCGGGGTTATGTTTGGTTG 59.755 55.000 0.00 0.00 0.00 3.77
3571 3890 2.232696 GCGGGGTTATGTTTGGTTGATT 59.767 45.455 0.00 0.00 0.00 2.57
3573 3892 3.508012 CGGGGTTATGTTTGGTTGATTGA 59.492 43.478 0.00 0.00 0.00 2.57
3579 3898 7.281100 GGGTTATGTTTGGTTGATTGACAAAAA 59.719 33.333 0.00 0.00 40.36 1.94
3595 3918 8.558973 TTGACAAAAATTTCTTGTTTGGATGT 57.441 26.923 15.27 0.00 37.14 3.06
3606 3929 5.296283 TCTTGTTTGGATGTTTGGCAAAATG 59.704 36.000 15.29 0.00 0.00 2.32
3639 3962 5.248640 CCAACCTTGCTCTCTCTAATTCAA 58.751 41.667 0.00 0.00 0.00 2.69
3730 4053 1.008538 GTGGTGCGAACTTTGGCTG 60.009 57.895 0.00 0.00 32.75 4.85
3770 4093 1.202687 CCACTCACGCCACCATATCAT 60.203 52.381 0.00 0.00 0.00 2.45
3771 4094 2.037121 CCACTCACGCCACCATATCATA 59.963 50.000 0.00 0.00 0.00 2.15
3772 4095 3.306989 CCACTCACGCCACCATATCATAT 60.307 47.826 0.00 0.00 0.00 1.78
3777 4100 2.283298 CGCCACCATATCATATCAGGC 58.717 52.381 0.00 0.00 37.54 4.85
3778 4101 2.648059 GCCACCATATCATATCAGGCC 58.352 52.381 0.00 0.00 34.94 5.19
3779 4102 2.025981 GCCACCATATCATATCAGGCCA 60.026 50.000 5.01 0.00 34.94 5.36
3780 4103 3.882444 CCACCATATCATATCAGGCCAG 58.118 50.000 5.01 0.00 0.00 4.85
3781 4104 3.371273 CCACCATATCATATCAGGCCAGG 60.371 52.174 5.01 0.00 0.00 4.45
3782 4105 3.265221 CACCATATCATATCAGGCCAGGT 59.735 47.826 5.01 0.00 0.00 4.00
3783 4106 4.471025 CACCATATCATATCAGGCCAGGTA 59.529 45.833 5.01 0.00 0.00 3.08
3784 4107 4.471386 ACCATATCATATCAGGCCAGGTAC 59.529 45.833 5.01 0.00 0.00 3.34
3785 4108 4.471025 CCATATCATATCAGGCCAGGTACA 59.529 45.833 5.01 0.00 0.00 2.90
3801 4124 2.303175 GTACAAAGAGCAACCACCCAA 58.697 47.619 0.00 0.00 0.00 4.12
3802 4125 1.859302 ACAAAGAGCAACCACCCAAA 58.141 45.000 0.00 0.00 0.00 3.28
3803 4126 2.397597 ACAAAGAGCAACCACCCAAAT 58.602 42.857 0.00 0.00 0.00 2.32
3804 4127 3.571590 ACAAAGAGCAACCACCCAAATA 58.428 40.909 0.00 0.00 0.00 1.40
3805 4128 3.320826 ACAAAGAGCAACCACCCAAATAC 59.679 43.478 0.00 0.00 0.00 1.89
3806 4129 2.215942 AGAGCAACCACCCAAATACC 57.784 50.000 0.00 0.00 0.00 2.73
3807 4130 0.808755 GAGCAACCACCCAAATACCG 59.191 55.000 0.00 0.00 0.00 4.02
3808 4131 0.402504 AGCAACCACCCAAATACCGA 59.597 50.000 0.00 0.00 0.00 4.69
3809 4132 1.202952 AGCAACCACCCAAATACCGAA 60.203 47.619 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.264288 CTCAAAACCCTTCTGCGTGTC 59.736 52.381 0.00 0.00 0.00 3.67
1 2 1.308998 CTCAAAACCCTTCTGCGTGT 58.691 50.000 0.00 0.00 0.00 4.49
3 4 1.676006 CAACTCAAAACCCTTCTGCGT 59.324 47.619 0.00 0.00 0.00 5.24
4 5 1.676006 ACAACTCAAAACCCTTCTGCG 59.324 47.619 0.00 0.00 0.00 5.18
5 6 3.303791 CGTACAACTCAAAACCCTTCTGC 60.304 47.826 0.00 0.00 0.00 4.26
6 7 3.875134 ACGTACAACTCAAAACCCTTCTG 59.125 43.478 0.00 0.00 0.00 3.02
7 8 4.124970 GACGTACAACTCAAAACCCTTCT 58.875 43.478 0.00 0.00 0.00 2.85
8 9 4.124970 AGACGTACAACTCAAAACCCTTC 58.875 43.478 0.00 0.00 0.00 3.46
9 10 4.124970 GAGACGTACAACTCAAAACCCTT 58.875 43.478 10.24 0.00 33.86 3.95
10 11 3.387050 AGAGACGTACAACTCAAAACCCT 59.613 43.478 15.43 0.00 35.83 4.34
11 12 3.725490 AGAGACGTACAACTCAAAACCC 58.275 45.455 15.43 0.00 35.83 4.11
12 13 3.424529 CGAGAGACGTACAACTCAAAACC 59.575 47.826 15.43 2.84 35.83 3.27
13 14 3.121429 GCGAGAGACGTACAACTCAAAAC 60.121 47.826 15.43 6.16 44.60 2.43
14 15 3.047796 GCGAGAGACGTACAACTCAAAA 58.952 45.455 15.43 0.00 44.60 2.44
15 16 2.033675 TGCGAGAGACGTACAACTCAAA 59.966 45.455 15.43 0.23 44.60 2.69
16 17 1.605232 TGCGAGAGACGTACAACTCAA 59.395 47.619 15.43 0.50 44.60 3.02
17 18 1.232119 TGCGAGAGACGTACAACTCA 58.768 50.000 15.43 0.00 44.60 3.41
18 19 2.095869 TCTTGCGAGAGACGTACAACTC 60.096 50.000 0.00 7.85 44.60 3.01
19 20 1.878088 TCTTGCGAGAGACGTACAACT 59.122 47.619 0.00 0.00 44.60 3.16
20 21 2.327081 TCTTGCGAGAGACGTACAAC 57.673 50.000 0.00 0.00 44.60 3.32
21 22 4.895224 ATATCTTGCGAGAGACGTACAA 57.105 40.909 10.06 0.00 44.60 2.41
22 23 5.277683 GGTTATATCTTGCGAGAGACGTACA 60.278 44.000 10.06 0.00 44.60 2.90
23 24 5.049543 AGGTTATATCTTGCGAGAGACGTAC 60.050 44.000 10.06 4.24 44.60 3.67
24 25 5.061853 AGGTTATATCTTGCGAGAGACGTA 58.938 41.667 10.06 0.00 44.60 3.57
25 26 3.884091 AGGTTATATCTTGCGAGAGACGT 59.116 43.478 10.06 4.72 44.60 4.34
26 27 4.491234 AGGTTATATCTTGCGAGAGACG 57.509 45.455 10.06 0.00 45.66 4.18
27 28 5.833082 TGAAGGTTATATCTTGCGAGAGAC 58.167 41.667 10.06 5.56 34.85 3.36
28 29 6.465439 TTGAAGGTTATATCTTGCGAGAGA 57.535 37.500 10.06 5.10 34.85 3.10
29 30 7.539712 TTTTGAAGGTTATATCTTGCGAGAG 57.460 36.000 10.06 0.00 34.85 3.20
30 31 8.506168 AATTTTGAAGGTTATATCTTGCGAGA 57.494 30.769 6.01 6.01 36.09 4.04
31 32 7.857885 GGAATTTTGAAGGTTATATCTTGCGAG 59.142 37.037 0.00 0.00 0.00 5.03
32 33 7.338196 TGGAATTTTGAAGGTTATATCTTGCGA 59.662 33.333 0.00 0.00 0.00 5.10
33 34 7.479980 TGGAATTTTGAAGGTTATATCTTGCG 58.520 34.615 0.00 0.00 0.00 4.85
34 35 9.651913 TTTGGAATTTTGAAGGTTATATCTTGC 57.348 29.630 0.00 0.00 0.00 4.01
42 43 9.844257 AAATCATGTTTGGAATTTTGAAGGTTA 57.156 25.926 0.00 0.00 0.00 2.85
43 44 8.750515 AAATCATGTTTGGAATTTTGAAGGTT 57.249 26.923 0.00 0.00 0.00 3.50
44 45 8.750515 AAAATCATGTTTGGAATTTTGAAGGT 57.249 26.923 0.00 0.00 0.00 3.50
67 68 8.703604 TCCACAAATTTATGTTCGAACAAAAA 57.296 26.923 32.69 25.31 43.03 1.94
68 69 8.879342 ATCCACAAATTTATGTTCGAACAAAA 57.121 26.923 32.69 28.59 43.03 2.44
69 70 9.619316 CTATCCACAAATTTATGTTCGAACAAA 57.381 29.630 32.69 23.62 43.03 2.83
70 71 9.004717 TCTATCCACAAATTTATGTTCGAACAA 57.995 29.630 32.69 18.47 43.03 2.83
71 72 8.554835 TCTATCCACAAATTTATGTTCGAACA 57.445 30.769 31.41 31.41 44.06 3.18
72 73 9.834628 TTTCTATCCACAAATTTATGTTCGAAC 57.165 29.630 21.42 21.42 0.00 3.95
84 85 7.039504 AGTGTGCATCTTTTTCTATCCACAAAT 60.040 33.333 0.00 0.00 34.26 2.32
95 96 9.282247 CACAGAATTATAGTGTGCATCTTTTTC 57.718 33.333 0.00 0.00 35.53 2.29
100 101 6.051717 GTCCACAGAATTATAGTGTGCATCT 58.948 40.000 0.00 0.00 40.26 2.90
101 102 5.817296 TGTCCACAGAATTATAGTGTGCATC 59.183 40.000 0.00 0.00 40.26 3.91
102 103 5.744171 TGTCCACAGAATTATAGTGTGCAT 58.256 37.500 0.00 0.00 40.26 3.96
103 104 5.159273 TGTCCACAGAATTATAGTGTGCA 57.841 39.130 0.00 0.00 40.26 4.57
104 105 4.034510 GCTGTCCACAGAATTATAGTGTGC 59.965 45.833 11.04 0.00 46.59 4.57
105 106 5.178061 TGCTGTCCACAGAATTATAGTGTG 58.822 41.667 11.04 0.00 46.59 3.82
106 107 5.420725 TGCTGTCCACAGAATTATAGTGT 57.579 39.130 11.04 0.00 46.59 3.55
107 108 6.539826 TGATTGCTGTCCACAGAATTATAGTG 59.460 38.462 11.04 0.00 46.59 2.74
108 109 6.653020 TGATTGCTGTCCACAGAATTATAGT 58.347 36.000 11.04 0.00 46.59 2.12
109 110 7.443272 TGATGATTGCTGTCCACAGAATTATAG 59.557 37.037 11.04 0.00 46.59 1.31
111 112 6.124340 TGATGATTGCTGTCCACAGAATTAT 58.876 36.000 11.04 9.07 46.59 1.28
112 113 5.499313 TGATGATTGCTGTCCACAGAATTA 58.501 37.500 11.04 5.23 46.59 1.40
113 114 4.338012 TGATGATTGCTGTCCACAGAATT 58.662 39.130 11.04 0.00 46.59 2.17
114 115 3.959293 TGATGATTGCTGTCCACAGAAT 58.041 40.909 11.04 7.35 46.59 2.40
115 116 3.421919 TGATGATTGCTGTCCACAGAA 57.578 42.857 11.04 0.00 46.59 3.02
117 118 4.157105 TGATTTGATGATTGCTGTCCACAG 59.843 41.667 2.06 2.06 46.40 3.66
118 119 4.080687 TGATTTGATGATTGCTGTCCACA 58.919 39.130 0.00 0.00 0.00 4.17
119 120 4.707030 TGATTTGATGATTGCTGTCCAC 57.293 40.909 0.00 0.00 0.00 4.02
121 122 5.346822 GTGTTTGATTTGATGATTGCTGTCC 59.653 40.000 0.00 0.00 0.00 4.02
125 129 5.924254 CAGTGTGTTTGATTTGATGATTGCT 59.076 36.000 0.00 0.00 0.00 3.91
127 131 7.435784 TCAACAGTGTGTTTGATTTGATGATTG 59.564 33.333 0.00 0.00 38.77 2.67
139 143 4.717991 TCTCGTTTTCAACAGTGTGTTTG 58.282 39.130 0.00 0.00 38.77 2.93
140 144 5.123186 TCATCTCGTTTTCAACAGTGTGTTT 59.877 36.000 0.00 0.00 38.77 2.83
142 146 4.034048 GTCATCTCGTTTTCAACAGTGTGT 59.966 41.667 0.00 0.00 0.00 3.72
143 147 4.033932 TGTCATCTCGTTTTCAACAGTGTG 59.966 41.667 0.00 0.00 0.00 3.82
160 164 0.523072 ACAGCCACGCAATTGTCATC 59.477 50.000 7.40 0.00 0.00 2.92
195 199 6.111382 GCCGGGTTCTACTTATTTTAGAGTT 58.889 40.000 2.18 0.00 0.00 3.01
208 212 1.518792 GCTTCTCGCCGGGTTCTAC 60.519 63.158 2.18 0.00 0.00 2.59
209 213 2.890371 GCTTCTCGCCGGGTTCTA 59.110 61.111 2.18 0.00 0.00 2.10
258 263 5.848921 AGGAAGAGGGTGATAATCTATTGCT 59.151 40.000 0.00 0.00 0.00 3.91
281 286 0.107945 CCTGCCTTTTCTCTCCGGAG 60.108 60.000 26.32 26.32 40.73 4.63
282 287 1.983224 CCTGCCTTTTCTCTCCGGA 59.017 57.895 2.93 2.93 0.00 5.14
302 310 2.884639 GGATTTATTATGGTGGCGCACT 59.115 45.455 10.83 0.00 34.40 4.40
303 311 2.030274 GGGATTTATTATGGTGGCGCAC 60.030 50.000 10.83 5.50 0.00 5.34
304 312 2.235016 GGGATTTATTATGGTGGCGCA 58.765 47.619 10.83 0.00 0.00 6.09
305 313 1.544246 GGGGATTTATTATGGTGGCGC 59.456 52.381 0.00 0.00 0.00 6.53
306 314 1.810151 CGGGGATTTATTATGGTGGCG 59.190 52.381 0.00 0.00 0.00 5.69
347 355 0.321671 ATGGATGGATTACCGGAGCG 59.678 55.000 9.46 0.00 39.42 5.03
348 356 1.347707 TGATGGATGGATTACCGGAGC 59.652 52.381 9.46 0.00 39.42 4.70
350 358 4.019792 CAATGATGGATGGATTACCGGA 57.980 45.455 9.46 0.00 39.42 5.14
409 433 0.806241 CGTGGATAAAACAACGGGGG 59.194 55.000 0.00 0.00 0.00 5.40
410 434 1.525941 ACGTGGATAAAACAACGGGG 58.474 50.000 0.00 0.00 0.00 5.73
411 435 3.328505 ACTACGTGGATAAAACAACGGG 58.671 45.455 5.70 0.00 0.00 5.28
414 438 6.238022 GGCATCTACTACGTGGATAAAACAAC 60.238 42.308 5.70 0.00 32.15 3.32
417 441 4.443394 CGGCATCTACTACGTGGATAAAAC 59.557 45.833 5.70 0.00 32.15 2.43
428 452 4.865365 GGAGATAATTGCGGCATCTACTAC 59.135 45.833 2.28 0.00 28.60 2.73
429 453 4.081642 GGGAGATAATTGCGGCATCTACTA 60.082 45.833 12.05 0.00 31.40 1.82
430 454 3.307059 GGGAGATAATTGCGGCATCTACT 60.307 47.826 12.05 5.50 31.40 2.57
477 501 5.054477 GGGATCAAATCAAATGCATCCAAG 58.946 41.667 0.00 0.00 32.80 3.61
509 533 4.814294 CACAGGCCGCGTAGGGAC 62.814 72.222 4.92 0.00 46.37 4.46
516 540 4.910585 GATACCCCACAGGCCGCG 62.911 72.222 0.00 0.00 40.58 6.46
517 541 3.120086 ATGATACCCCACAGGCCGC 62.120 63.158 0.00 0.00 40.58 6.53
518 542 1.071471 GATGATACCCCACAGGCCG 59.929 63.158 0.00 0.00 40.58 6.13
519 543 0.550914 TTGATGATACCCCACAGGCC 59.449 55.000 0.00 0.00 40.58 5.19
532 556 1.450025 CTGCTGCTGCTTCTTGATGA 58.550 50.000 17.00 0.00 40.48 2.92
535 559 1.228033 TGCTGCTGCTGCTTCTTGA 60.228 52.632 27.67 7.82 40.48 3.02
536 560 1.210413 CTGCTGCTGCTGCTTCTTG 59.790 57.895 27.67 11.95 40.48 3.02
543 567 1.465387 CTTCTTCTTCTGCTGCTGCTG 59.535 52.381 17.00 15.94 40.48 4.41
546 570 3.316071 TCTCTTCTTCTTCTGCTGCTG 57.684 47.619 0.00 0.00 0.00 4.41
549 573 3.919804 CGTCTTCTCTTCTTCTTCTGCTG 59.080 47.826 0.00 0.00 0.00 4.41
552 576 4.732784 CCTCGTCTTCTCTTCTTCTTCTG 58.267 47.826 0.00 0.00 0.00 3.02
559 583 0.530288 GCAGCCTCGTCTTCTCTTCT 59.470 55.000 0.00 0.00 0.00 2.85
560 584 0.459411 GGCAGCCTCGTCTTCTCTTC 60.459 60.000 3.29 0.00 0.00 2.87
562 586 2.705821 CGGCAGCCTCGTCTTCTCT 61.706 63.158 10.54 0.00 0.00 3.10
563 587 2.202676 CGGCAGCCTCGTCTTCTC 60.203 66.667 10.54 0.00 0.00 2.87
564 588 4.443266 GCGGCAGCCTCGTCTTCT 62.443 66.667 10.54 0.00 37.42 2.85
565 589 4.443266 AGCGGCAGCCTCGTCTTC 62.443 66.667 10.54 0.00 46.67 2.87
566 590 4.749310 CAGCGGCAGCCTCGTCTT 62.749 66.667 10.54 0.00 46.67 3.01
630 703 0.338120 ACCAGAGGGAGGAAGAGGAG 59.662 60.000 0.00 0.00 38.05 3.69
668 750 5.420104 AGATTGAATCTTGCACTAAAAGGGG 59.580 40.000 0.97 0.00 35.76 4.79
709 791 3.011635 GCGAGGAGGAGCAAGAGCA 62.012 63.158 0.00 0.00 45.49 4.26
710 792 2.202864 GCGAGGAGGAGCAAGAGC 60.203 66.667 0.00 0.00 42.56 4.09
711 793 2.498726 GGCGAGGAGGAGCAAGAG 59.501 66.667 0.00 0.00 34.54 2.85
712 794 3.077556 GGGCGAGGAGGAGCAAGA 61.078 66.667 0.00 0.00 34.54 3.02
972 1089 3.830192 GAATTGGGGCAGCGGCAG 61.830 66.667 11.88 0.00 43.71 4.85
1245 1380 0.250901 TCTTGAGGTTGCTCTTGGGC 60.251 55.000 0.00 0.00 0.00 5.36
1320 1455 1.133976 AGATCCTTCCCCAGCAAATCG 60.134 52.381 0.00 0.00 0.00 3.34
1390 1531 3.840078 AGTTGGAAAAATTCATGGAGGGG 59.160 43.478 0.00 0.00 0.00 4.79
1420 1561 1.370900 CAACAGCGGCAAAGACAGC 60.371 57.895 1.45 0.00 0.00 4.40
1421 1562 1.370900 GCAACAGCGGCAAAGACAG 60.371 57.895 1.45 0.00 0.00 3.51
1426 1567 2.433231 GAATGGGCAACAGCGGCAAA 62.433 55.000 1.45 0.00 39.74 3.68
1431 1572 2.203972 CTGGTGAATGGGCAACAGCG 62.204 60.000 0.00 0.00 45.54 5.18
1532 1673 0.889186 ATCGGGTCTTTGGTGCACAC 60.889 55.000 20.43 7.48 0.00 3.82
1606 1747 1.873165 CACCGTGGGAATGGTTTCG 59.127 57.895 0.00 0.00 35.96 3.46
1708 1849 2.123597 TGTCCCCTCCCCGTATCG 60.124 66.667 0.00 0.00 0.00 2.92
1760 1905 4.878439 TCCGAAGTAAATATCATGACCGG 58.122 43.478 0.00 0.00 35.07 5.28
1768 1913 6.561614 TCTATCCGCATCCGAAGTAAATATC 58.438 40.000 0.00 0.00 36.29 1.63
1783 1928 6.824196 CAGTAAGACCTATCTATCTATCCGCA 59.176 42.308 0.00 0.00 33.57 5.69
1784 1929 6.238538 GCAGTAAGACCTATCTATCTATCCGC 60.239 46.154 0.00 0.00 33.57 5.54
1787 1932 7.576861 GGGCAGTAAGACCTATCTATCTATC 57.423 44.000 0.00 0.00 44.70 2.08
1884 2033 9.453572 AACACATGTATATGAAGTTGATCTTGT 57.546 29.630 6.45 0.00 35.97 3.16
1885 2034 9.712359 CAACACATGTATATGAAGTTGATCTTG 57.288 33.333 23.90 7.06 45.46 3.02
1887 2036 8.267183 TCCAACACATGTATATGAAGTTGATCT 58.733 33.333 26.92 5.32 45.46 2.75
1888 2037 8.338259 GTCCAACACATGTATATGAAGTTGATC 58.662 37.037 26.92 19.78 45.46 2.92
1890 2039 7.394016 AGTCCAACACATGTATATGAAGTTGA 58.606 34.615 26.92 17.53 45.46 3.18
1892 2041 7.121168 CCAAGTCCAACACATGTATATGAAGTT 59.879 37.037 6.45 7.66 37.73 2.66
1893 2042 6.599244 CCAAGTCCAACACATGTATATGAAGT 59.401 38.462 6.45 1.89 37.73 3.01
1894 2043 6.599244 ACCAAGTCCAACACATGTATATGAAG 59.401 38.462 6.45 1.28 37.73 3.02
1895 2044 6.480763 ACCAAGTCCAACACATGTATATGAA 58.519 36.000 6.45 0.00 37.73 2.57
1896 2045 6.061022 ACCAAGTCCAACACATGTATATGA 57.939 37.500 6.45 0.00 37.73 2.15
1897 2046 7.933577 AGATACCAAGTCCAACACATGTATATG 59.066 37.037 0.00 0.00 40.24 1.78
1898 2047 8.034313 AGATACCAAGTCCAACACATGTATAT 57.966 34.615 0.00 0.00 0.00 0.86
1922 2071 6.160664 TCGGAATAAACAAAACTCGCTTAG 57.839 37.500 0.00 0.00 0.00 2.18
1949 2099 7.678218 GCCAACATTTCAGAAGTCATAGCTAAG 60.678 40.741 0.00 0.00 0.00 2.18
1974 2124 3.941483 ACACAATCTACATAACTGGCTGC 59.059 43.478 0.00 0.00 0.00 5.25
1979 2129 5.878332 TGCCAACACAATCTACATAACTG 57.122 39.130 0.00 0.00 0.00 3.16
2073 2223 8.556194 CCACACAATTTACGCTATTATACACAT 58.444 33.333 0.00 0.00 0.00 3.21
2096 2247 5.125578 GGGAGACTCCAAAATTATTGACCAC 59.874 44.000 23.06 0.00 38.64 4.16
2130 2334 5.532779 GCCCCAGAATTACTTTCTAATCAGG 59.467 44.000 0.00 0.00 42.98 3.86
2136 2340 5.163131 GGTATGGCCCCAGAATTACTTTCTA 60.163 44.000 0.00 0.00 42.98 2.10
2138 2342 3.889538 GGTATGGCCCCAGAATTACTTTC 59.110 47.826 0.00 0.00 34.31 2.62
2177 2381 8.995027 ATATCATGAACATGGCCTAAAACTAA 57.005 30.769 3.32 0.00 39.24 2.24
2180 2384 7.715657 TCAATATCATGAACATGGCCTAAAAC 58.284 34.615 3.32 0.00 39.24 2.43
2211 2415 4.223700 AGACTACTGAAATCATGTGGCTCA 59.776 41.667 0.00 0.00 0.00 4.26
2251 2455 2.676839 AGAGCTGCTGTCATTTCAATCG 59.323 45.455 7.01 0.00 0.00 3.34
2275 2479 6.296026 ACAAGGCTACACTACAATTTTCTGA 58.704 36.000 0.00 0.00 0.00 3.27
2282 2486 6.381420 AGACTATGACAAGGCTACACTACAAT 59.619 38.462 0.00 0.00 31.11 2.71
2346 2550 6.772716 AGTGATGACCAGTGATTTTACAGTTT 59.227 34.615 0.00 0.00 0.00 2.66
2347 2551 6.299141 AGTGATGACCAGTGATTTTACAGTT 58.701 36.000 0.00 0.00 0.00 3.16
2348 2552 5.869579 AGTGATGACCAGTGATTTTACAGT 58.130 37.500 0.00 0.00 0.00 3.55
2349 2553 7.099764 AGTAGTGATGACCAGTGATTTTACAG 58.900 38.462 0.00 0.00 0.00 2.74
2350 2554 7.004555 AGTAGTGATGACCAGTGATTTTACA 57.995 36.000 0.00 0.00 0.00 2.41
2381 2593 4.610945 AGGAATTTTCTTGTTGCGAAGTG 58.389 39.130 0.00 0.00 0.00 3.16
2472 2684 9.622004 CATGATATAGTTCCATGAAGCATTTTC 57.378 33.333 0.00 0.00 39.86 2.29
2533 2746 3.262420 GCTTGCTTCAAGATAAGACCGA 58.738 45.455 10.44 0.00 43.42 4.69
2576 2789 4.819630 TCACGATAAAGGAGCACAAAAAGT 59.180 37.500 0.00 0.00 0.00 2.66
2578 2791 5.957842 ATCACGATAAAGGAGCACAAAAA 57.042 34.783 0.00 0.00 0.00 1.94
2597 2810 0.968901 ACGCCAAGGTCCGTCTATCA 60.969 55.000 0.00 0.00 31.00 2.15
2601 2814 1.904865 TACACGCCAAGGTCCGTCT 60.905 57.895 0.00 0.00 35.17 4.18
2645 2858 8.492415 ACAAGCATAATATCTCTACCAAGGTA 57.508 34.615 0.00 0.00 0.00 3.08
2646 2859 7.380423 ACAAGCATAATATCTCTACCAAGGT 57.620 36.000 0.00 0.00 0.00 3.50
2648 2861 9.202273 GAGAACAAGCATAATATCTCTACCAAG 57.798 37.037 0.00 0.00 32.54 3.61
2650 2863 8.250143 TGAGAACAAGCATAATATCTCTACCA 57.750 34.615 0.00 0.00 35.49 3.25
2651 2864 9.149225 CATGAGAACAAGCATAATATCTCTACC 57.851 37.037 0.00 0.00 35.49 3.18
2688 2901 1.871080 AGCAGTCAAGGAAGTCAACG 58.129 50.000 0.00 0.00 0.00 4.10
2727 2941 3.622163 GCTGAAATCATCACAGGAGACAG 59.378 47.826 0.00 0.00 33.47 3.51
2729 2943 2.606725 CGCTGAAATCATCACAGGAGAC 59.393 50.000 0.00 0.00 33.47 3.36
2736 2950 2.032549 CCGGATTCGCTGAAATCATCAC 60.033 50.000 0.00 0.00 37.38 3.06
2872 3086 1.463444 GCACCGATGAAACTGGTACAC 59.537 52.381 0.00 0.00 33.82 2.90
2904 3118 4.314740 ACTACATCTACTAAGCAGCAGC 57.685 45.455 0.00 0.00 42.56 5.25
2905 3119 6.072728 CCTCTACTACATCTACTAAGCAGCAG 60.073 46.154 0.00 0.00 0.00 4.24
2906 3120 5.765677 CCTCTACTACATCTACTAAGCAGCA 59.234 44.000 0.00 0.00 0.00 4.41
2950 3167 4.735822 CGACCGATCTGAGACTGATAAAAC 59.264 45.833 0.00 0.00 0.00 2.43
2969 3186 3.343421 GAACACGCACCCACGACC 61.343 66.667 0.00 0.00 36.70 4.79
3011 3228 1.734465 GCACTGTATCAACTCCAGCAC 59.266 52.381 0.00 0.00 0.00 4.40
3121 3339 3.066342 TGTCTTCCGACTCCGATGAATAC 59.934 47.826 0.00 0.00 40.86 1.89
3177 3395 4.104738 ACCTTTGTTCTCTTCTTCCATCCA 59.895 41.667 0.00 0.00 0.00 3.41
3178 3396 4.457257 CACCTTTGTTCTCTTCTTCCATCC 59.543 45.833 0.00 0.00 0.00 3.51
3179 3397 4.083057 GCACCTTTGTTCTCTTCTTCCATC 60.083 45.833 0.00 0.00 0.00 3.51
3180 3398 3.823304 GCACCTTTGTTCTCTTCTTCCAT 59.177 43.478 0.00 0.00 0.00 3.41
3239 3457 1.331214 CCCATGTGCAAAAGGTCACT 58.669 50.000 0.00 0.00 34.49 3.41
3240 3458 1.039856 ACCCATGTGCAAAAGGTCAC 58.960 50.000 0.00 0.00 0.00 3.67
3241 3459 1.039068 CACCCATGTGCAAAAGGTCA 58.961 50.000 0.00 0.00 35.31 4.02
3287 3507 8.854614 AATGTGCAGAGTATTCTTTTAGAACT 57.145 30.769 0.00 0.00 37.00 3.01
3324 3546 4.342862 AACATGGATCGGAGGAAGTATG 57.657 45.455 0.00 0.00 0.00 2.39
3330 3552 3.104512 ACAAGTAACATGGATCGGAGGA 58.895 45.455 0.00 0.00 0.00 3.71
3361 3583 9.922477 ATAATCCGTATCCATCAGTATCTAGAA 57.078 33.333 0.00 0.00 0.00 2.10
3362 3584 9.562408 GATAATCCGTATCCATCAGTATCTAGA 57.438 37.037 0.00 0.00 33.63 2.43
3371 3593 8.593679 ACACATTTAGATAATCCGTATCCATCA 58.406 33.333 0.00 0.00 39.72 3.07
3376 3598 9.790389 CCTAGACACATTTAGATAATCCGTATC 57.210 37.037 0.00 0.00 39.24 2.24
3378 3600 8.701908 ACCTAGACACATTTAGATAATCCGTA 57.298 34.615 0.00 0.00 0.00 4.02
3379 3601 7.598759 ACCTAGACACATTTAGATAATCCGT 57.401 36.000 0.00 0.00 0.00 4.69
3384 3606 9.429109 TGGATGTACCTAGACACATTTAGATAA 57.571 33.333 9.65 0.00 35.55 1.75
3410 3729 9.712305 CCGATCCATATTACTTGTCTTAGATTT 57.288 33.333 0.00 0.00 0.00 2.17
3411 3730 9.090103 TCCGATCCATATTACTTGTCTTAGATT 57.910 33.333 0.00 0.00 0.00 2.40
3417 3736 5.598830 ACACTCCGATCCATATTACTTGTCT 59.401 40.000 0.00 0.00 0.00 3.41
3418 3737 5.844004 ACACTCCGATCCATATTACTTGTC 58.156 41.667 0.00 0.00 0.00 3.18
3420 3739 7.553881 AAAACACTCCGATCCATATTACTTG 57.446 36.000 0.00 0.00 0.00 3.16
3464 3783 3.395470 CTTCCAATTTCGCCGGCGG 62.395 63.158 44.95 29.44 40.25 6.13
3467 3786 1.376609 CCTCCTTCCAATTTCGCCGG 61.377 60.000 0.00 0.00 0.00 6.13
3469 3788 0.323451 ACCCTCCTTCCAATTTCGCC 60.323 55.000 0.00 0.00 0.00 5.54
3472 3791 5.105351 CCAAACATACCCTCCTTCCAATTTC 60.105 44.000 0.00 0.00 0.00 2.17
3510 3829 6.978080 TGAAACTTCTAAATTGTCAAGGTTGC 59.022 34.615 0.00 0.00 0.00 4.17
3527 3846 6.089417 CGCCTTTCCATACAAAATGAAACTTC 59.911 38.462 0.00 0.00 0.00 3.01
3533 3852 2.757868 CCCGCCTTTCCATACAAAATGA 59.242 45.455 0.00 0.00 0.00 2.57
3546 3865 1.262417 CCAAACATAACCCCGCCTTT 58.738 50.000 0.00 0.00 0.00 3.11
3551 3870 3.508012 TCAATCAACCAAACATAACCCCG 59.492 43.478 0.00 0.00 0.00 5.73
3552 3871 4.282195 TGTCAATCAACCAAACATAACCCC 59.718 41.667 0.00 0.00 0.00 4.95
3568 3887 9.654417 CATCCAAACAAGAAATTTTTGTCAATC 57.346 29.630 14.76 0.00 37.77 2.67
3571 3890 8.558973 AACATCCAAACAAGAAATTTTTGTCA 57.441 26.923 14.76 5.27 37.77 3.58
3573 3892 8.242739 CCAAACATCCAAACAAGAAATTTTTGT 58.757 29.630 10.86 10.86 40.30 2.83
3579 3898 5.033589 TGCCAAACATCCAAACAAGAAAT 57.966 34.783 0.00 0.00 0.00 2.17
3606 3929 1.229975 GCAAGGTTGGCATGGCAAAC 61.230 55.000 35.74 35.74 41.35 2.93
3639 3962 1.551883 GGCCAATGTCTGCAGGAAAAT 59.448 47.619 15.13 0.00 0.00 1.82
3730 4053 1.666023 GGCGTGGCTACTTTTGCTTTC 60.666 52.381 0.00 0.00 0.00 2.62
3770 4093 2.170607 GCTCTTTGTACCTGGCCTGATA 59.829 50.000 11.88 0.00 0.00 2.15
3771 4094 1.065126 GCTCTTTGTACCTGGCCTGAT 60.065 52.381 11.88 0.00 0.00 2.90
3772 4095 0.324943 GCTCTTTGTACCTGGCCTGA 59.675 55.000 11.88 0.00 0.00 3.86
3777 4100 1.880027 GTGGTTGCTCTTTGTACCTGG 59.120 52.381 0.00 0.00 0.00 4.45
3778 4101 1.880027 GGTGGTTGCTCTTTGTACCTG 59.120 52.381 0.00 0.00 0.00 4.00
3779 4102 1.202891 GGGTGGTTGCTCTTTGTACCT 60.203 52.381 0.00 0.00 0.00 3.08
3780 4103 1.244816 GGGTGGTTGCTCTTTGTACC 58.755 55.000 0.00 0.00 0.00 3.34
3781 4104 1.975660 TGGGTGGTTGCTCTTTGTAC 58.024 50.000 0.00 0.00 0.00 2.90
3782 4105 2.738587 TTGGGTGGTTGCTCTTTGTA 57.261 45.000 0.00 0.00 0.00 2.41
3783 4106 1.859302 TTTGGGTGGTTGCTCTTTGT 58.141 45.000 0.00 0.00 0.00 2.83
3784 4107 3.306019 GGTATTTGGGTGGTTGCTCTTTG 60.306 47.826 0.00 0.00 0.00 2.77
3785 4108 2.897326 GGTATTTGGGTGGTTGCTCTTT 59.103 45.455 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.