Multiple sequence alignment - TraesCS1A01G043000

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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 TraesCS1A01G043000 chr1A 100.000 2483 0 0 1 2483 23827429 23829911 0.000000e+00 4586
1 TraesCS1A01G043000 chr1D 88.262 1099 41 34 770 1808 22736019 22737089 0.000000e+00 1234
2 TraesCS1A01G043000 chr1D 88.439 692 61 9 1793 2483 22737107 22737780 0.000000e+00 817
3 TraesCS1A01G043000 chr1D 90.947 243 18 1 420 662 22734806 22735044 8.570000e-85 324
4 TraesCS1A01G043000 chr1B 92.000 775 29 11 748 1495 39235079 39234311 0.000000e+00 1057
5 TraesCS1A01G043000 chr1B 87.798 377 24 11 1793 2166 39233387 39233030 2.950000e-114 422
6 TraesCS1A01G043000 chr1B 87.702 309 37 1 2173 2481 39232872 39232565 2.350000e-95 359
7 TraesCS1A01G043000 chr1B 88.498 313 15 2 1488 1781 39234287 39233977 2.350000e-95 359
8 TraesCS1A01G043000 chr1B 88.333 300 27 2 373 671 39235904 39235612 1.090000e-93 353


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 TraesCS1A01G043000 chr1A 23827429 23829911 2482 False 4586.000000 4586 100.0000 1 2483 1 chr1A.!!$F1 2482
1 TraesCS1A01G043000 chr1D 22734806 22737780 2974 False 791.666667 1234 89.2160 420 2483 3 chr1D.!!$F1 2063
2 TraesCS1A01G043000 chr1B 39232565 39235904 3339 True 510.000000 1057 88.8662 373 2481 5 chr1B.!!$R1 2108

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
398 399 0.103937 CAAAATGGCCCGTGTTGTGT 59.896 50.0 0.0 0.0 0.0 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2150 4035 0.184451 GGATGTCATGATGTGGGCCT 59.816 55.0 4.53 0.0 0.0 5.19 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 4.838152 ATTCGCGCGTGCCCTGAT 62.838 61.111 30.98 10.32 38.08 2.90
23 24 2.511373 CGCGTGCCCTGATGCTTA 60.511 61.111 0.00 0.00 0.00 3.09
24 25 1.889105 CGCGTGCCCTGATGCTTAT 60.889 57.895 0.00 0.00 0.00 1.73
25 26 1.439353 CGCGTGCCCTGATGCTTATT 61.439 55.000 0.00 0.00 0.00 1.40
26 27 0.740737 GCGTGCCCTGATGCTTATTT 59.259 50.000 0.00 0.00 0.00 1.40
27 28 1.946768 GCGTGCCCTGATGCTTATTTA 59.053 47.619 0.00 0.00 0.00 1.40
28 29 2.554032 GCGTGCCCTGATGCTTATTTAT 59.446 45.455 0.00 0.00 0.00 1.40
29 30 3.610114 GCGTGCCCTGATGCTTATTTATG 60.610 47.826 0.00 0.00 0.00 1.90
30 31 3.565482 CGTGCCCTGATGCTTATTTATGT 59.435 43.478 0.00 0.00 0.00 2.29
31 32 4.319766 CGTGCCCTGATGCTTATTTATGTC 60.320 45.833 0.00 0.00 0.00 3.06
32 33 4.580167 GTGCCCTGATGCTTATTTATGTCA 59.420 41.667 0.00 0.00 0.00 3.58
33 34 5.067674 GTGCCCTGATGCTTATTTATGTCAA 59.932 40.000 0.00 0.00 0.00 3.18
34 35 5.655974 TGCCCTGATGCTTATTTATGTCAAA 59.344 36.000 0.00 0.00 0.00 2.69
35 36 6.183360 TGCCCTGATGCTTATTTATGTCAAAG 60.183 38.462 0.00 0.00 0.00 2.77
36 37 6.039717 GCCCTGATGCTTATTTATGTCAAAGA 59.960 38.462 0.00 0.00 0.00 2.52
37 38 7.646314 CCCTGATGCTTATTTATGTCAAAGAG 58.354 38.462 0.00 0.00 0.00 2.85
38 39 7.500227 CCCTGATGCTTATTTATGTCAAAGAGA 59.500 37.037 0.00 0.00 0.00 3.10
46 47 2.654877 GTCAAAGAGACGGCCGGA 59.345 61.111 31.76 12.38 37.53 5.14
47 48 1.737008 GTCAAAGAGACGGCCGGAC 60.737 63.158 31.76 22.49 37.53 4.79
48 49 2.204461 TCAAAGAGACGGCCGGACA 61.204 57.895 31.76 3.03 0.00 4.02
49 50 1.301401 CAAAGAGACGGCCGGACAA 60.301 57.895 31.76 0.00 0.00 3.18
50 51 0.882927 CAAAGAGACGGCCGGACAAA 60.883 55.000 31.76 0.00 0.00 2.83
51 52 0.883370 AAAGAGACGGCCGGACAAAC 60.883 55.000 31.76 16.69 0.00 2.93
52 53 2.029964 GAGACGGCCGGACAAACA 59.970 61.111 31.76 0.00 0.00 2.83
53 54 1.375523 GAGACGGCCGGACAAACAT 60.376 57.895 31.76 4.91 0.00 2.71
54 55 1.635663 GAGACGGCCGGACAAACATG 61.636 60.000 31.76 0.00 0.00 3.21
55 56 3.322706 GACGGCCGGACAAACATGC 62.323 63.158 31.76 1.18 0.00 4.06
56 57 3.361158 CGGCCGGACAAACATGCA 61.361 61.111 20.10 0.00 0.00 3.96
57 58 2.699768 CGGCCGGACAAACATGCAT 61.700 57.895 20.10 0.00 0.00 3.96
58 59 1.139520 GGCCGGACAAACATGCATC 59.860 57.895 5.05 0.00 0.00 3.91
59 60 1.139520 GCCGGACAAACATGCATCC 59.860 57.895 5.05 0.00 0.00 3.51
60 61 1.315257 GCCGGACAAACATGCATCCT 61.315 55.000 5.05 0.00 0.00 3.24
61 62 0.734889 CCGGACAAACATGCATCCTC 59.265 55.000 0.00 0.00 0.00 3.71
62 63 0.734889 CGGACAAACATGCATCCTCC 59.265 55.000 0.00 0.00 0.00 4.30
63 64 0.734889 GGACAAACATGCATCCTCCG 59.265 55.000 0.00 0.00 0.00 4.63
64 65 1.678728 GGACAAACATGCATCCTCCGA 60.679 52.381 0.00 0.00 0.00 4.55
65 66 1.398390 GACAAACATGCATCCTCCGAC 59.602 52.381 0.00 0.00 0.00 4.79
66 67 1.003580 ACAAACATGCATCCTCCGACT 59.996 47.619 0.00 0.00 0.00 4.18
67 68 1.399440 CAAACATGCATCCTCCGACTG 59.601 52.381 0.00 0.00 0.00 3.51
68 69 0.107508 AACATGCATCCTCCGACTGG 60.108 55.000 0.00 0.00 0.00 4.00
69 70 1.227764 CATGCATCCTCCGACTGGG 60.228 63.158 0.00 0.00 35.24 4.45
70 71 3.112205 ATGCATCCTCCGACTGGGC 62.112 63.158 0.00 0.00 35.24 5.36
71 72 4.554036 GCATCCTCCGACTGGGCC 62.554 72.222 0.00 0.00 35.24 5.80
72 73 3.083349 CATCCTCCGACTGGGCCA 61.083 66.667 5.85 5.85 35.24 5.36
73 74 2.765807 ATCCTCCGACTGGGCCAG 60.766 66.667 31.62 31.62 37.52 4.85
77 78 4.392166 TCCGACTGGGCCAGCCTA 62.392 66.667 33.04 13.63 34.37 3.93
78 79 3.164269 CCGACTGGGCCAGCCTAT 61.164 66.667 33.04 14.25 34.37 2.57
79 80 2.423446 CGACTGGGCCAGCCTATC 59.577 66.667 33.04 21.08 34.37 2.08
80 81 2.136878 CGACTGGGCCAGCCTATCT 61.137 63.158 33.04 12.99 34.37 1.98
81 82 1.690219 CGACTGGGCCAGCCTATCTT 61.690 60.000 33.04 12.17 34.37 2.40
82 83 0.179034 GACTGGGCCAGCCTATCTTG 60.179 60.000 33.04 7.82 34.37 3.02
83 84 1.527844 CTGGGCCAGCCTATCTTGC 60.528 63.158 22.68 0.00 36.10 4.01
84 85 2.592861 GGGCCAGCCTATCTTGCG 60.593 66.667 4.39 0.00 34.50 4.85
85 86 2.190578 GGCCAGCCTATCTTGCGT 59.809 61.111 0.00 0.00 34.50 5.24
86 87 1.889573 GGCCAGCCTATCTTGCGTC 60.890 63.158 0.00 0.00 34.50 5.19
87 88 1.144936 GCCAGCCTATCTTGCGTCT 59.855 57.895 0.00 0.00 0.00 4.18
88 89 0.389391 GCCAGCCTATCTTGCGTCTA 59.611 55.000 0.00 0.00 0.00 2.59
89 90 1.604185 GCCAGCCTATCTTGCGTCTAG 60.604 57.143 0.00 0.00 0.00 2.43
99 100 3.507009 GCGTCTAGCGACCCGAGT 61.507 66.667 10.17 0.00 44.77 4.18
100 101 2.708255 CGTCTAGCGACCCGAGTC 59.292 66.667 0.98 0.00 44.77 3.36
101 102 2.821688 CGTCTAGCGACCCGAGTCC 61.822 68.421 0.00 0.00 44.77 3.85
102 103 1.748122 GTCTAGCGACCCGAGTCCA 60.748 63.158 0.00 0.00 40.12 4.02
103 104 1.451567 TCTAGCGACCCGAGTCCAG 60.452 63.158 0.00 0.00 40.12 3.86
104 105 1.749638 CTAGCGACCCGAGTCCAGT 60.750 63.158 0.00 0.00 40.12 4.00
105 106 0.463295 CTAGCGACCCGAGTCCAGTA 60.463 60.000 0.00 0.00 40.12 2.74
106 107 0.463295 TAGCGACCCGAGTCCAGTAG 60.463 60.000 0.00 0.00 40.12 2.57
107 108 2.799371 CGACCCGAGTCCAGTAGC 59.201 66.667 0.00 0.00 40.12 3.58
108 109 2.772691 CGACCCGAGTCCAGTAGCC 61.773 68.421 0.00 0.00 40.12 3.93
109 110 1.681327 GACCCGAGTCCAGTAGCCA 60.681 63.158 0.00 0.00 37.00 4.75
110 111 1.668101 GACCCGAGTCCAGTAGCCAG 61.668 65.000 0.00 0.00 37.00 4.85
111 112 1.682684 CCCGAGTCCAGTAGCCAGT 60.683 63.158 0.00 0.00 0.00 4.00
112 113 1.258445 CCCGAGTCCAGTAGCCAGTT 61.258 60.000 0.00 0.00 0.00 3.16
113 114 0.108615 CCGAGTCCAGTAGCCAGTTG 60.109 60.000 0.00 0.00 0.00 3.16
114 115 0.603569 CGAGTCCAGTAGCCAGTTGT 59.396 55.000 0.00 0.00 0.00 3.32
115 116 1.402984 CGAGTCCAGTAGCCAGTTGTC 60.403 57.143 0.00 0.00 0.00 3.18
116 117 1.896465 GAGTCCAGTAGCCAGTTGTCT 59.104 52.381 0.00 0.00 0.00 3.41
117 118 3.090037 GAGTCCAGTAGCCAGTTGTCTA 58.910 50.000 0.00 0.00 0.00 2.59
118 119 3.702045 GAGTCCAGTAGCCAGTTGTCTAT 59.298 47.826 0.00 0.00 0.00 1.98
119 120 4.868268 AGTCCAGTAGCCAGTTGTCTATA 58.132 43.478 0.00 0.00 0.00 1.31
120 121 4.890581 AGTCCAGTAGCCAGTTGTCTATAG 59.109 45.833 0.00 0.00 0.00 1.31
121 122 4.888239 GTCCAGTAGCCAGTTGTCTATAGA 59.112 45.833 0.00 0.00 0.00 1.98
122 123 5.009210 GTCCAGTAGCCAGTTGTCTATAGAG 59.991 48.000 1.64 0.00 0.00 2.43
123 124 4.279671 CCAGTAGCCAGTTGTCTATAGAGG 59.720 50.000 1.64 1.52 0.00 3.69
124 125 5.133941 CAGTAGCCAGTTGTCTATAGAGGA 58.866 45.833 1.64 0.00 0.00 3.71
125 126 5.772672 CAGTAGCCAGTTGTCTATAGAGGAT 59.227 44.000 1.64 1.77 0.00 3.24
126 127 6.007703 AGTAGCCAGTTGTCTATAGAGGATC 58.992 44.000 1.64 0.00 0.00 3.36
127 128 4.156477 AGCCAGTTGTCTATAGAGGATCC 58.844 47.826 2.48 2.48 33.66 3.36
128 129 4.140805 AGCCAGTTGTCTATAGAGGATCCT 60.141 45.833 16.13 16.13 33.66 3.24
129 130 4.591072 GCCAGTTGTCTATAGAGGATCCTT 59.409 45.833 17.42 8.62 33.66 3.36
130 131 5.071115 GCCAGTTGTCTATAGAGGATCCTTT 59.929 44.000 17.42 13.51 33.66 3.11
131 132 6.408662 GCCAGTTGTCTATAGAGGATCCTTTT 60.409 42.308 17.42 10.28 33.66 2.27
132 133 7.569240 CCAGTTGTCTATAGAGGATCCTTTTT 58.431 38.462 17.42 8.16 33.66 1.94
261 262 7.869016 TTTTGTAAACGTGAACATGTTTTCA 57.131 28.000 23.65 21.62 45.31 2.69
262 263 6.856494 TTGTAAACGTGAACATGTTTTCAC 57.144 33.333 23.65 17.24 45.31 3.18
271 272 6.698008 TGAACATGTTTTCACAGTTCTGAT 57.302 33.333 13.36 0.00 42.95 2.90
272 273 6.497437 TGAACATGTTTTCACAGTTCTGATG 58.503 36.000 13.36 1.22 42.95 3.07
273 274 6.095300 TGAACATGTTTTCACAGTTCTGATGT 59.905 34.615 13.36 1.79 42.95 3.06
274 275 6.455360 ACATGTTTTCACAGTTCTGATGTT 57.545 33.333 6.83 0.00 35.94 2.71
275 276 6.866480 ACATGTTTTCACAGTTCTGATGTTT 58.134 32.000 6.83 0.00 35.94 2.83
276 277 7.322664 ACATGTTTTCACAGTTCTGATGTTTT 58.677 30.769 6.83 0.00 35.94 2.43
277 278 7.818930 ACATGTTTTCACAGTTCTGATGTTTTT 59.181 29.630 6.83 0.00 35.94 1.94
278 279 9.299963 CATGTTTTCACAGTTCTGATGTTTTTA 57.700 29.630 6.83 0.00 35.94 1.52
279 280 8.682128 TGTTTTCACAGTTCTGATGTTTTTAC 57.318 30.769 6.83 0.00 0.00 2.01
280 281 8.300286 TGTTTTCACAGTTCTGATGTTTTTACA 58.700 29.630 6.83 0.00 0.00 2.41
281 282 8.583765 GTTTTCACAGTTCTGATGTTTTTACAC 58.416 33.333 6.83 0.00 0.00 2.90
282 283 6.993786 TCACAGTTCTGATGTTTTTACACA 57.006 33.333 6.83 0.00 0.00 3.72
283 284 7.015226 TCACAGTTCTGATGTTTTTACACAG 57.985 36.000 6.83 0.00 0.00 3.66
284 285 6.821160 TCACAGTTCTGATGTTTTTACACAGA 59.179 34.615 6.83 0.00 36.11 3.41
285 286 7.335673 TCACAGTTCTGATGTTTTTACACAGAA 59.664 33.333 6.83 0.00 42.59 3.02
286 287 7.641411 CACAGTTCTGATGTTTTTACACAGAAG 59.359 37.037 16.31 11.64 44.42 2.85
287 288 6.634436 CAGTTCTGATGTTTTTACACAGAAGC 59.366 38.462 16.31 13.09 44.42 3.86
288 289 6.318648 AGTTCTGATGTTTTTACACAGAAGCA 59.681 34.615 16.31 0.00 44.42 3.91
289 290 6.882610 TCTGATGTTTTTACACAGAAGCAT 57.117 33.333 0.00 0.00 35.20 3.79
290 291 7.275888 TCTGATGTTTTTACACAGAAGCATT 57.724 32.000 0.00 0.00 35.20 3.56
291 292 7.715657 TCTGATGTTTTTACACAGAAGCATTT 58.284 30.769 0.00 0.00 35.20 2.32
292 293 8.196771 TCTGATGTTTTTACACAGAAGCATTTT 58.803 29.630 0.00 0.00 35.20 1.82
293 294 8.715191 TGATGTTTTTACACAGAAGCATTTTT 57.285 26.923 0.00 0.00 28.72 1.94
294 295 8.816144 TGATGTTTTTACACAGAAGCATTTTTC 58.184 29.630 0.00 0.00 28.72 2.29
295 296 8.715191 ATGTTTTTACACAGAAGCATTTTTCA 57.285 26.923 0.00 0.00 0.00 2.69
296 297 8.539770 TGTTTTTACACAGAAGCATTTTTCAA 57.460 26.923 0.00 0.00 0.00 2.69
297 298 8.993121 TGTTTTTACACAGAAGCATTTTTCAAA 58.007 25.926 0.00 0.00 0.00 2.69
298 299 9.476761 GTTTTTACACAGAAGCATTTTTCAAAG 57.523 29.630 0.00 0.00 0.00 2.77
299 300 8.770438 TTTTACACAGAAGCATTTTTCAAAGT 57.230 26.923 0.00 0.00 0.00 2.66
300 301 8.770438 TTTACACAGAAGCATTTTTCAAAGTT 57.230 26.923 0.00 0.00 0.00 2.66
301 302 8.770438 TTACACAGAAGCATTTTTCAAAGTTT 57.230 26.923 0.00 0.00 0.00 2.66
302 303 7.064060 ACACAGAAGCATTTTTCAAAGTTTG 57.936 32.000 9.44 9.44 0.00 2.93
303 304 5.961263 CACAGAAGCATTTTTCAAAGTTTGC 59.039 36.000 10.90 0.00 0.00 3.68
304 305 5.192496 CAGAAGCATTTTTCAAAGTTTGCG 58.808 37.500 10.90 0.00 0.00 4.85
305 306 5.005586 CAGAAGCATTTTTCAAAGTTTGCGA 59.994 36.000 10.90 0.00 0.00 5.10
306 307 4.777140 AGCATTTTTCAAAGTTTGCGAC 57.223 36.364 10.90 0.00 0.00 5.19
307 308 4.432712 AGCATTTTTCAAAGTTTGCGACT 58.567 34.783 10.90 0.00 41.47 4.18
316 317 3.878160 AAGTTTGCGACTTTTTGGGAA 57.122 38.095 0.00 0.00 46.34 3.97
317 318 3.159353 AGTTTGCGACTTTTTGGGAAC 57.841 42.857 0.00 0.00 33.92 3.62
318 319 1.849829 GTTTGCGACTTTTTGGGAACG 59.150 47.619 0.00 0.00 0.00 3.95
319 320 0.248702 TTGCGACTTTTTGGGAACGC 60.249 50.000 0.00 0.00 44.95 4.84
320 321 1.371267 GCGACTTTTTGGGAACGCC 60.371 57.895 0.00 0.00 40.14 5.68
321 322 2.026522 CGACTTTTTGGGAACGCCA 58.973 52.632 0.00 0.00 35.15 5.69
322 323 0.382515 CGACTTTTTGGGAACGCCAA 59.617 50.000 0.00 0.00 35.15 4.52
323 324 1.202313 CGACTTTTTGGGAACGCCAAA 60.202 47.619 2.02 2.02 35.69 3.28
324 325 2.469826 GACTTTTTGGGAACGCCAAAG 58.530 47.619 5.95 0.00 38.21 2.77
325 326 1.217001 CTTTTTGGGAACGCCAAAGC 58.783 50.000 5.95 0.00 38.21 3.51
326 327 0.537188 TTTTTGGGAACGCCAAAGCA 59.463 45.000 5.95 0.00 38.21 3.91
327 328 0.755686 TTTTGGGAACGCCAAAGCAT 59.244 45.000 5.95 0.00 38.21 3.79
328 329 0.755686 TTTGGGAACGCCAAAGCATT 59.244 45.000 2.02 0.00 39.83 3.56
329 330 0.755686 TTGGGAACGCCAAAGCATTT 59.244 45.000 0.00 0.00 40.26 2.32
330 331 0.755686 TGGGAACGCCAAAGCATTTT 59.244 45.000 0.00 0.00 35.03 1.82
331 332 1.139853 TGGGAACGCCAAAGCATTTTT 59.860 42.857 0.00 0.00 35.03 1.94
332 333 1.798223 GGGAACGCCAAAGCATTTTTC 59.202 47.619 0.00 0.00 35.03 2.29
333 334 2.478831 GGAACGCCAAAGCATTTTTCA 58.521 42.857 0.00 0.00 35.03 2.69
334 335 2.869192 GGAACGCCAAAGCATTTTTCAA 59.131 40.909 0.00 0.00 35.03 2.69
335 336 3.311048 GGAACGCCAAAGCATTTTTCAAA 59.689 39.130 0.00 0.00 35.03 2.69
336 337 4.517287 GAACGCCAAAGCATTTTTCAAAG 58.483 39.130 0.00 0.00 35.03 2.77
337 338 3.530535 ACGCCAAAGCATTTTTCAAAGT 58.469 36.364 0.00 0.00 35.03 2.66
338 339 3.555547 ACGCCAAAGCATTTTTCAAAGTC 59.444 39.130 0.00 0.00 35.03 3.01
339 340 3.803778 CGCCAAAGCATTTTTCAAAGTCT 59.196 39.130 0.00 0.00 35.03 3.24
340 341 4.318263 CGCCAAAGCATTTTTCAAAGTCTG 60.318 41.667 0.00 0.00 35.03 3.51
341 342 4.810491 GCCAAAGCATTTTTCAAAGTCTGA 59.190 37.500 0.00 0.00 35.03 3.27
342 343 5.467735 GCCAAAGCATTTTTCAAAGTCTGAT 59.532 36.000 0.00 0.00 35.03 2.90
343 344 6.347160 GCCAAAGCATTTTTCAAAGTCTGATC 60.347 38.462 0.00 0.00 35.03 2.92
344 345 6.927381 CCAAAGCATTTTTCAAAGTCTGATCT 59.073 34.615 0.00 0.00 35.03 2.75
345 346 8.084073 CCAAAGCATTTTTCAAAGTCTGATCTA 58.916 33.333 0.00 0.00 35.03 1.98
346 347 9.635520 CAAAGCATTTTTCAAAGTCTGATCTAT 57.364 29.630 0.00 0.00 35.03 1.98
347 348 9.852091 AAAGCATTTTTCAAAGTCTGATCTATC 57.148 29.630 0.00 0.00 31.62 2.08
348 349 8.804912 AGCATTTTTCAAAGTCTGATCTATCT 57.195 30.769 0.00 0.00 32.78 1.98
349 350 8.891720 AGCATTTTTCAAAGTCTGATCTATCTC 58.108 33.333 0.00 0.00 32.78 2.75
350 351 8.891720 GCATTTTTCAAAGTCTGATCTATCTCT 58.108 33.333 0.00 0.00 32.78 3.10
358 359 9.814899 CAAAGTCTGATCTATCTCTATGTTTGT 57.185 33.333 0.00 0.00 0.00 2.83
361 362 9.860650 AGTCTGATCTATCTCTATGTTTGTAGT 57.139 33.333 0.00 0.00 0.00 2.73
362 363 9.891828 GTCTGATCTATCTCTATGTTTGTAGTG 57.108 37.037 0.00 0.00 0.00 2.74
363 364 8.572185 TCTGATCTATCTCTATGTTTGTAGTGC 58.428 37.037 0.00 0.00 0.00 4.40
364 365 7.363431 TGATCTATCTCTATGTTTGTAGTGCG 58.637 38.462 0.00 0.00 0.00 5.34
365 366 5.520632 TCTATCTCTATGTTTGTAGTGCGC 58.479 41.667 0.00 0.00 0.00 6.09
366 367 3.586100 TCTCTATGTTTGTAGTGCGCA 57.414 42.857 5.66 5.66 0.00 6.09
367 368 3.250744 TCTCTATGTTTGTAGTGCGCAC 58.749 45.455 32.79 32.79 0.00 5.34
368 369 2.343101 TCTATGTTTGTAGTGCGCACC 58.657 47.619 35.51 22.20 0.00 5.01
369 370 2.073056 CTATGTTTGTAGTGCGCACCA 58.927 47.619 35.51 24.59 0.00 4.17
370 371 1.313772 ATGTTTGTAGTGCGCACCAA 58.686 45.000 35.51 28.49 0.00 3.67
371 372 0.378962 TGTTTGTAGTGCGCACCAAC 59.621 50.000 35.51 31.08 0.00 3.77
378 379 1.299850 GTGCGCACCAACCCTTTTC 60.300 57.895 30.12 0.00 0.00 2.29
380 381 2.494530 GCGCACCAACCCTTTTCCA 61.495 57.895 0.30 0.00 0.00 3.53
388 389 2.503331 CAACCCTTTTCCAAAATGGCC 58.497 47.619 0.00 0.00 37.23 5.36
389 390 1.064003 ACCCTTTTCCAAAATGGCCC 58.936 50.000 0.00 0.00 37.23 5.80
398 399 0.103937 CAAAATGGCCCGTGTTGTGT 59.896 50.000 0.00 0.00 0.00 3.72
413 414 0.746063 TGTGTTCAGGGCTTTGCAAG 59.254 50.000 0.00 0.00 0.00 4.01
432 433 4.072088 CGAACCGTGTTGCGCTCC 62.072 66.667 9.73 0.00 39.71 4.70
471 472 7.744715 CCTAATGTTCATGTAAAACAACGTCTC 59.255 37.037 2.91 0.00 39.84 3.36
474 475 2.477375 TCATGTAAAACAACGTCTCCGC 59.523 45.455 0.00 0.00 37.70 5.54
493 494 2.597305 CGCTACAACGTGGTCTATGTTC 59.403 50.000 0.00 0.00 36.38 3.18
540 542 3.659334 CAGCATGCCTCGTGTTGT 58.341 55.556 15.66 0.00 29.23 3.32
589 591 2.737180 CTGAGCTCCCACACACGT 59.263 61.111 12.15 0.00 0.00 4.49
596 598 1.151777 CTCCCACACACGTGTCACAC 61.152 60.000 20.49 0.00 42.83 3.82
615 617 3.003113 GCCTCACGCTACCCTCGTT 62.003 63.158 0.00 0.00 38.19 3.85
664 666 3.050275 GCTCAACTCCCACACGGC 61.050 66.667 0.00 0.00 0.00 5.68
673 1420 4.602259 CCACACGGCCACACGACT 62.602 66.667 2.24 0.00 37.61 4.18
677 1656 3.224324 ACGGCCACACGACTCAGT 61.224 61.111 2.24 0.00 37.61 3.41
682 1661 1.560860 GCCACACGACTCAGTTGAGC 61.561 60.000 8.99 2.02 45.79 4.26
688 1667 0.169230 CGACTCAGTTGAGCGCTAGT 59.831 55.000 11.50 9.37 45.79 2.57
690 1669 0.528470 ACTCAGTTGAGCGCTAGTCC 59.472 55.000 11.50 0.00 45.79 3.85
739 1965 8.008332 TGGTAGTATTATCATAGTGGAGGAACA 58.992 37.037 0.00 0.00 0.00 3.18
749 1975 9.647918 ATCATAGTGGAGGAACATCGTATATAT 57.352 33.333 0.00 0.00 0.00 0.86
894 2123 3.633525 TGCATGCAGAGGATAAAATGGAC 59.366 43.478 18.46 0.00 0.00 4.02
967 2196 2.923177 CGCGCGTTTCTGTTCGACA 61.923 57.895 24.19 0.00 0.00 4.35
1008 2237 2.031163 CGGGGATCGATGAAGGCC 59.969 66.667 0.54 0.00 42.43 5.19
1033 2262 3.121030 GCAAGAGCATGTCGGCGT 61.121 61.111 6.85 0.00 41.58 5.68
1034 2263 3.084579 CAAGAGCATGTCGGCGTC 58.915 61.111 6.85 0.72 39.27 5.19
1205 2446 2.711311 CATGATGCTGAACGCCGG 59.289 61.111 0.00 0.00 38.05 6.13
1583 2869 1.372087 CCAGGCAGCTTTGATCCGAC 61.372 60.000 0.00 0.00 0.00 4.79
1592 2878 3.664025 TTGATCCGACTGGCCTGCG 62.664 63.158 9.95 13.56 34.14 5.18
1675 2980 5.066246 GGGTAGTGGCTCGAGTATATATGTC 59.934 48.000 15.13 0.00 0.00 3.06
1679 2984 5.712446 AGTGGCTCGAGTATATATGTCATGT 59.288 40.000 15.13 0.00 0.00 3.21
1680 2985 6.884836 AGTGGCTCGAGTATATATGTCATGTA 59.115 38.462 15.13 0.00 0.00 2.29
1781 3086 5.045213 TCCATTCTTCATACCCAACTTGCTA 60.045 40.000 0.00 0.00 0.00 3.49
1784 3089 2.710096 TCATACCCAACTTGCTAGGC 57.290 50.000 0.00 0.00 0.00 3.93
1786 3091 2.509548 TCATACCCAACTTGCTAGGCAT 59.490 45.455 0.00 0.00 38.76 4.40
1808 3691 5.201713 TCAAAGGTTGTTGTTGTTGTTGA 57.798 34.783 0.00 0.00 0.00 3.18
1822 3705 6.486657 TGTTGTTGTTGAAATCCCAAAACAAA 59.513 30.769 0.75 0.00 42.37 2.83
1881 3764 1.201647 CACCAGTATCTCGTTGGACGT 59.798 52.381 0.00 0.00 43.14 4.34
1884 3767 3.698040 ACCAGTATCTCGTTGGACGTTAT 59.302 43.478 0.00 0.00 43.14 1.89
1918 3801 1.369091 CGTCTGGGCCAAGGAATTCG 61.369 60.000 7.48 0.00 0.00 3.34
1933 3816 3.909258 TTCGCCCGAAGTCGACTGC 62.909 63.158 20.85 17.34 43.02 4.40
1955 3840 1.660104 GGTTTGCCAAAATAGCATGCG 59.340 47.619 13.01 0.00 40.59 4.73
1972 3857 0.939106 GCGCTTTGCCGATTGTTTGT 60.939 50.000 0.00 0.00 37.76 2.83
2038 3923 8.742777 ACAATCATCTTTGTGCATATTTGTAGT 58.257 29.630 0.00 0.00 38.37 2.73
2077 3962 4.053983 TGACGCGACGTAGATCTAGTTAT 58.946 43.478 15.93 0.00 41.37 1.89
2086 3971 8.382130 CGACGTAGATCTAGTTATTACCATCTC 58.618 40.741 1.64 0.00 0.00 2.75
2113 3998 3.149196 GAGAACTTGGAGAAACATGCCA 58.851 45.455 0.00 0.00 0.00 4.92
2150 4035 9.146984 GTATAATGTCAACTAGCACAAGTACAA 57.853 33.333 0.00 0.00 0.00 2.41
2151 4036 6.545504 AATGTCAACTAGCACAAGTACAAG 57.454 37.500 0.00 0.00 0.00 3.16
2171 4207 1.410648 GGCCCACATCATGACATCCTT 60.411 52.381 0.00 0.00 0.00 3.36
2228 4264 3.513912 ACTTATCGATGGTGGTGACTGAA 59.486 43.478 8.54 0.00 0.00 3.02
2242 4278 1.285950 CTGAACAGCCGTCGAGACA 59.714 57.895 4.02 0.00 0.00 3.41
2262 4298 6.310149 AGACAAAAGACCAAATGAGAAGGAT 58.690 36.000 0.00 0.00 0.00 3.24
2302 4338 1.612991 CCGACCCACCATGTTCATGAA 60.613 52.381 13.51 3.38 0.00 2.57
2309 4345 3.569277 CCACCATGTTCATGAAGTCACAA 59.431 43.478 8.80 0.00 0.00 3.33
2316 4352 4.142491 TGTTCATGAAGTCACAAACACCAC 60.142 41.667 8.80 0.00 32.26 4.16
2329 4365 2.780924 ACCACCCCCAAGCTCCAA 60.781 61.111 0.00 0.00 0.00 3.53
2341 4377 3.317149 CCAAGCTCCAACATATCACCATG 59.683 47.826 0.00 0.00 0.00 3.66
2353 4389 1.195442 TCACCATGGCACCGTTAGGA 61.195 55.000 13.04 0.00 41.02 2.94
2358 4394 0.328258 ATGGCACCGTTAGGAAAGCT 59.672 50.000 0.00 0.00 41.02 3.74
2359 4395 0.109723 TGGCACCGTTAGGAAAGCTT 59.890 50.000 0.00 0.00 41.02 3.74
2397 4433 6.539173 ACCAAGGATAAACAACATAGTGTGA 58.461 36.000 0.00 0.00 0.00 3.58
2398 4434 7.175104 ACCAAGGATAAACAACATAGTGTGAT 58.825 34.615 0.00 0.00 0.00 3.06
2401 4437 9.161629 CAAGGATAAACAACATAGTGTGATGTA 57.838 33.333 3.25 0.00 42.28 2.29
2402 4438 9.905713 AAGGATAAACAACATAGTGTGATGTAT 57.094 29.630 3.25 0.00 42.28 2.29
2437 4473 6.546772 ACAATTGAAACAAAATGATTGGCCTT 59.453 30.769 13.59 0.00 0.00 4.35
2476 4512 2.350522 CACTTCAGCCTTGATAACGCT 58.649 47.619 0.00 0.00 32.27 5.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.838152 ATCAGGGCACGCGCGAAT 62.838 61.111 39.36 13.15 39.92 3.34
6 7 1.439353 AATAAGCATCAGGGCACGCG 61.439 55.000 3.53 3.53 35.83 6.01
7 8 0.740737 AAATAAGCATCAGGGCACGC 59.259 50.000 0.00 0.00 35.83 5.34
8 9 3.565482 ACATAAATAAGCATCAGGGCACG 59.435 43.478 0.00 0.00 35.83 5.34
9 10 4.580167 TGACATAAATAAGCATCAGGGCAC 59.420 41.667 0.00 0.00 35.83 5.01
10 11 4.790937 TGACATAAATAAGCATCAGGGCA 58.209 39.130 0.00 0.00 35.83 5.36
11 12 5.772825 TTGACATAAATAAGCATCAGGGC 57.227 39.130 0.00 0.00 0.00 5.19
12 13 7.500227 TCTCTTTGACATAAATAAGCATCAGGG 59.500 37.037 0.00 0.00 0.00 4.45
13 14 8.341173 GTCTCTTTGACATAAATAAGCATCAGG 58.659 37.037 0.00 0.00 44.73 3.86
14 15 8.060679 CGTCTCTTTGACATAAATAAGCATCAG 58.939 37.037 0.00 0.00 45.60 2.90
15 16 7.011389 CCGTCTCTTTGACATAAATAAGCATCA 59.989 37.037 0.00 0.00 45.60 3.07
16 17 7.348201 CCGTCTCTTTGACATAAATAAGCATC 58.652 38.462 0.00 0.00 45.60 3.91
17 18 6.238484 GCCGTCTCTTTGACATAAATAAGCAT 60.238 38.462 0.00 0.00 45.60 3.79
18 19 5.064707 GCCGTCTCTTTGACATAAATAAGCA 59.935 40.000 0.00 0.00 45.60 3.91
19 20 5.502606 GCCGTCTCTTTGACATAAATAAGC 58.497 41.667 0.00 0.00 45.60 3.09
20 21 5.276868 CGGCCGTCTCTTTGACATAAATAAG 60.277 44.000 19.50 0.00 45.60 1.73
21 22 4.569162 CGGCCGTCTCTTTGACATAAATAA 59.431 41.667 19.50 0.00 45.60 1.40
22 23 4.116961 CGGCCGTCTCTTTGACATAAATA 58.883 43.478 19.50 0.00 45.60 1.40
23 24 2.936498 CGGCCGTCTCTTTGACATAAAT 59.064 45.455 19.50 0.00 45.60 1.40
24 25 2.343101 CGGCCGTCTCTTTGACATAAA 58.657 47.619 19.50 0.00 45.60 1.40
25 26 1.404986 CCGGCCGTCTCTTTGACATAA 60.405 52.381 26.12 0.00 45.60 1.90
26 27 0.174845 CCGGCCGTCTCTTTGACATA 59.825 55.000 26.12 0.00 45.60 2.29
27 28 1.079127 CCGGCCGTCTCTTTGACAT 60.079 57.895 26.12 0.00 45.60 3.06
28 29 2.204461 TCCGGCCGTCTCTTTGACA 61.204 57.895 26.12 0.00 45.60 3.58
29 30 1.737008 GTCCGGCCGTCTCTTTGAC 60.737 63.158 26.12 17.97 42.06 3.18
30 31 1.750341 TTGTCCGGCCGTCTCTTTGA 61.750 55.000 26.12 9.36 0.00 2.69
31 32 0.882927 TTTGTCCGGCCGTCTCTTTG 60.883 55.000 26.12 6.69 0.00 2.77
32 33 0.883370 GTTTGTCCGGCCGTCTCTTT 60.883 55.000 26.12 0.00 0.00 2.52
33 34 1.301479 GTTTGTCCGGCCGTCTCTT 60.301 57.895 26.12 0.00 0.00 2.85
34 35 1.827399 ATGTTTGTCCGGCCGTCTCT 61.827 55.000 26.12 0.00 0.00 3.10
35 36 1.375523 ATGTTTGTCCGGCCGTCTC 60.376 57.895 26.12 14.11 0.00 3.36
36 37 1.671054 CATGTTTGTCCGGCCGTCT 60.671 57.895 26.12 0.00 0.00 4.18
37 38 2.867472 CATGTTTGTCCGGCCGTC 59.133 61.111 26.12 17.15 0.00 4.79
38 39 3.361977 GCATGTTTGTCCGGCCGT 61.362 61.111 26.12 0.00 0.00 5.68
39 40 2.597117 GATGCATGTTTGTCCGGCCG 62.597 60.000 21.04 21.04 0.00 6.13
40 41 1.139520 GATGCATGTTTGTCCGGCC 59.860 57.895 2.46 0.00 0.00 6.13
41 42 1.139520 GGATGCATGTTTGTCCGGC 59.860 57.895 2.46 0.00 0.00 6.13
42 43 0.734889 GAGGATGCATGTTTGTCCGG 59.265 55.000 2.46 0.00 35.89 5.14
43 44 0.734889 GGAGGATGCATGTTTGTCCG 59.265 55.000 2.46 0.00 35.89 4.79
44 45 0.734889 CGGAGGATGCATGTTTGTCC 59.265 55.000 2.46 0.00 0.00 4.02
45 46 1.398390 GTCGGAGGATGCATGTTTGTC 59.602 52.381 2.46 0.00 0.00 3.18
46 47 1.003580 AGTCGGAGGATGCATGTTTGT 59.996 47.619 2.46 0.00 0.00 2.83
47 48 1.399440 CAGTCGGAGGATGCATGTTTG 59.601 52.381 2.46 0.00 0.00 2.93
48 49 1.679944 CCAGTCGGAGGATGCATGTTT 60.680 52.381 2.46 0.00 0.00 2.83
49 50 0.107508 CCAGTCGGAGGATGCATGTT 60.108 55.000 2.46 0.00 0.00 2.71
50 51 1.524002 CCAGTCGGAGGATGCATGT 59.476 57.895 2.46 0.00 0.00 3.21
51 52 1.227764 CCCAGTCGGAGGATGCATG 60.228 63.158 2.46 0.00 0.00 4.06
52 53 3.112205 GCCCAGTCGGAGGATGCAT 62.112 63.158 0.00 0.00 0.00 3.96
53 54 3.785859 GCCCAGTCGGAGGATGCA 61.786 66.667 0.00 0.00 0.00 3.96
54 55 4.554036 GGCCCAGTCGGAGGATGC 62.554 72.222 0.00 0.00 0.00 3.91
55 56 3.083349 TGGCCCAGTCGGAGGATG 61.083 66.667 0.00 0.00 0.00 3.51
56 57 2.765807 CTGGCCCAGTCGGAGGAT 60.766 66.667 1.39 0.00 0.00 3.24
60 61 3.696518 ATAGGCTGGCCCAGTCGGA 62.697 63.158 13.35 3.83 41.46 4.55
61 62 3.164269 ATAGGCTGGCCCAGTCGG 61.164 66.667 13.35 0.00 41.46 4.79
62 63 1.690219 AAGATAGGCTGGCCCAGTCG 61.690 60.000 13.35 0.00 41.46 4.18
63 64 0.179034 CAAGATAGGCTGGCCCAGTC 60.179 60.000 7.43 7.43 36.18 3.51
64 65 1.918253 CAAGATAGGCTGGCCCAGT 59.082 57.895 13.35 0.00 36.58 4.00
65 66 1.527844 GCAAGATAGGCTGGCCCAG 60.528 63.158 6.32 6.32 37.61 4.45
66 67 2.597340 GCAAGATAGGCTGGCCCA 59.403 61.111 8.11 0.00 37.61 5.36
67 68 2.592861 CGCAAGATAGGCTGGCCC 60.593 66.667 8.11 0.00 40.72 5.80
68 69 1.889573 GACGCAAGATAGGCTGGCC 60.890 63.158 3.00 3.00 40.72 5.36
69 70 0.389391 TAGACGCAAGATAGGCTGGC 59.611 55.000 0.00 0.00 40.38 4.85
70 71 1.604185 GCTAGACGCAAGATAGGCTGG 60.604 57.143 0.00 0.00 43.62 4.85
71 72 1.777101 GCTAGACGCAAGATAGGCTG 58.223 55.000 0.00 0.00 43.62 4.85
72 73 0.312416 CGCTAGACGCAAGATAGGCT 59.688 55.000 0.00 0.00 43.62 4.58
73 74 0.311165 TCGCTAGACGCAAGATAGGC 59.689 55.000 0.00 0.00 43.23 3.93
74 75 2.039327 GTCGCTAGACGCAAGATAGG 57.961 55.000 0.00 0.00 43.23 2.57
84 85 1.716826 CTGGACTCGGGTCGCTAGAC 61.717 65.000 9.83 0.00 46.34 2.59
85 86 1.451567 CTGGACTCGGGTCGCTAGA 60.452 63.158 9.83 0.00 42.97 2.43
86 87 0.463295 TACTGGACTCGGGTCGCTAG 60.463 60.000 9.83 10.14 42.97 3.42
87 88 0.463295 CTACTGGACTCGGGTCGCTA 60.463 60.000 9.83 0.00 42.97 4.26
88 89 1.749638 CTACTGGACTCGGGTCGCT 60.750 63.158 9.83 0.00 42.97 4.93
89 90 2.799371 CTACTGGACTCGGGTCGC 59.201 66.667 9.83 3.01 42.97 5.19
90 91 2.772691 GGCTACTGGACTCGGGTCG 61.773 68.421 9.83 0.00 42.97 4.79
91 92 1.668101 CTGGCTACTGGACTCGGGTC 61.668 65.000 6.97 6.97 41.43 4.46
92 93 1.682684 CTGGCTACTGGACTCGGGT 60.683 63.158 0.00 0.00 0.00 5.28
93 94 1.258445 AACTGGCTACTGGACTCGGG 61.258 60.000 0.00 0.00 0.00 5.14
94 95 0.108615 CAACTGGCTACTGGACTCGG 60.109 60.000 0.00 0.00 0.00 4.63
95 96 0.603569 ACAACTGGCTACTGGACTCG 59.396 55.000 0.00 0.00 0.00 4.18
96 97 1.896465 AGACAACTGGCTACTGGACTC 59.104 52.381 0.00 0.00 0.00 3.36
97 98 2.016905 AGACAACTGGCTACTGGACT 57.983 50.000 0.00 0.00 0.00 3.85
98 99 4.888239 TCTATAGACAACTGGCTACTGGAC 59.112 45.833 0.00 0.00 38.71 4.02
99 100 5.125367 TCTATAGACAACTGGCTACTGGA 57.875 43.478 0.00 0.00 38.71 3.86
100 101 4.279671 CCTCTATAGACAACTGGCTACTGG 59.720 50.000 0.00 0.00 38.71 4.00
101 102 5.133941 TCCTCTATAGACAACTGGCTACTG 58.866 45.833 0.00 0.00 38.71 2.74
102 103 5.390087 TCCTCTATAGACAACTGGCTACT 57.610 43.478 0.00 0.00 38.71 2.57
103 104 5.184287 GGATCCTCTATAGACAACTGGCTAC 59.816 48.000 3.84 0.00 38.71 3.58
104 105 5.075205 AGGATCCTCTATAGACAACTGGCTA 59.925 44.000 9.02 0.00 40.47 3.93
105 106 4.140805 AGGATCCTCTATAGACAACTGGCT 60.141 45.833 9.02 0.00 37.13 4.75
106 107 4.156477 AGGATCCTCTATAGACAACTGGC 58.844 47.826 9.02 0.00 0.00 4.85
107 108 6.739331 AAAGGATCCTCTATAGACAACTGG 57.261 41.667 16.52 0.00 0.00 4.00
236 237 8.215132 GTGAAAACATGTTCACGTTTACAAAAA 58.785 29.630 12.39 0.00 45.71 1.94
237 238 7.721402 GTGAAAACATGTTCACGTTTACAAAA 58.279 30.769 12.39 0.00 45.71 2.44
238 239 7.266939 GTGAAAACATGTTCACGTTTACAAA 57.733 32.000 12.39 0.00 45.71 2.83
239 240 6.856494 GTGAAAACATGTTCACGTTTACAA 57.144 33.333 12.39 0.00 45.71 2.41
248 249 6.095300 ACATCAGAACTGTGAAAACATGTTCA 59.905 34.615 12.39 3.56 39.33 3.18
249 250 6.498304 ACATCAGAACTGTGAAAACATGTTC 58.502 36.000 12.39 0.43 37.76 3.18
250 251 6.455360 ACATCAGAACTGTGAAAACATGTT 57.545 33.333 4.92 4.92 0.00 2.71
251 252 6.455360 AACATCAGAACTGTGAAAACATGT 57.545 33.333 0.00 0.00 0.00 3.21
252 253 7.760131 AAAACATCAGAACTGTGAAAACATG 57.240 32.000 1.73 0.00 0.00 3.21
253 254 9.301153 GTAAAAACATCAGAACTGTGAAAACAT 57.699 29.630 1.73 0.00 0.00 2.71
254 255 8.300286 TGTAAAAACATCAGAACTGTGAAAACA 58.700 29.630 1.73 0.00 0.00 2.83
255 256 8.583765 GTGTAAAAACATCAGAACTGTGAAAAC 58.416 33.333 1.73 0.00 0.00 2.43
256 257 8.300286 TGTGTAAAAACATCAGAACTGTGAAAA 58.700 29.630 1.73 0.00 0.00 2.29
257 258 7.821652 TGTGTAAAAACATCAGAACTGTGAAA 58.178 30.769 1.73 0.00 0.00 2.69
258 259 7.335673 TCTGTGTAAAAACATCAGAACTGTGAA 59.664 33.333 1.73 0.00 33.18 3.18
259 260 6.821160 TCTGTGTAAAAACATCAGAACTGTGA 59.179 34.615 1.73 0.00 33.18 3.58
260 261 7.015226 TCTGTGTAAAAACATCAGAACTGTG 57.985 36.000 1.73 3.08 33.18 3.66
261 262 7.624360 TTCTGTGTAAAAACATCAGAACTGT 57.376 32.000 14.13 0.00 39.27 3.55
262 263 6.634436 GCTTCTGTGTAAAAACATCAGAACTG 59.366 38.462 14.13 0.00 39.27 3.16
263 264 6.318648 TGCTTCTGTGTAAAAACATCAGAACT 59.681 34.615 14.13 0.00 39.27 3.01
264 265 6.494842 TGCTTCTGTGTAAAAACATCAGAAC 58.505 36.000 14.13 12.44 39.27 3.01
265 266 6.691754 TGCTTCTGTGTAAAAACATCAGAA 57.308 33.333 15.83 15.83 41.00 3.02
266 267 6.882610 ATGCTTCTGTGTAAAAACATCAGA 57.117 33.333 6.68 6.68 34.08 3.27
267 268 7.935338 AAATGCTTCTGTGTAAAAACATCAG 57.065 32.000 0.00 0.00 0.00 2.90
268 269 8.715191 AAAAATGCTTCTGTGTAAAAACATCA 57.285 26.923 0.00 0.00 0.00 3.07
269 270 8.816144 TGAAAAATGCTTCTGTGTAAAAACATC 58.184 29.630 0.00 0.00 0.00 3.06
270 271 8.715191 TGAAAAATGCTTCTGTGTAAAAACAT 57.285 26.923 0.00 0.00 0.00 2.71
271 272 8.539770 TTGAAAAATGCTTCTGTGTAAAAACA 57.460 26.923 0.00 0.00 0.00 2.83
272 273 9.476761 CTTTGAAAAATGCTTCTGTGTAAAAAC 57.523 29.630 0.00 0.00 0.00 2.43
273 274 9.213799 ACTTTGAAAAATGCTTCTGTGTAAAAA 57.786 25.926 0.00 0.00 0.00 1.94
274 275 8.770438 ACTTTGAAAAATGCTTCTGTGTAAAA 57.230 26.923 0.00 0.00 0.00 1.52
275 276 8.770438 AACTTTGAAAAATGCTTCTGTGTAAA 57.230 26.923 0.00 0.00 0.00 2.01
276 277 8.655092 CAAACTTTGAAAAATGCTTCTGTGTAA 58.345 29.630 0.00 0.00 0.00 2.41
277 278 7.201513 GCAAACTTTGAAAAATGCTTCTGTGTA 60.202 33.333 5.65 0.00 0.00 2.90
278 279 6.402442 GCAAACTTTGAAAAATGCTTCTGTGT 60.402 34.615 5.65 0.00 0.00 3.72
279 280 5.961263 GCAAACTTTGAAAAATGCTTCTGTG 59.039 36.000 5.65 0.00 0.00 3.66
280 281 5.220453 CGCAAACTTTGAAAAATGCTTCTGT 60.220 36.000 5.65 0.00 0.00 3.41
281 282 5.005586 TCGCAAACTTTGAAAAATGCTTCTG 59.994 36.000 5.65 0.00 0.00 3.02
282 283 5.005682 GTCGCAAACTTTGAAAAATGCTTCT 59.994 36.000 5.65 0.00 0.00 2.85
283 284 5.005682 AGTCGCAAACTTTGAAAAATGCTTC 59.994 36.000 5.65 2.28 33.03 3.86
284 285 4.869861 AGTCGCAAACTTTGAAAAATGCTT 59.130 33.333 5.65 0.00 33.03 3.91
285 286 4.432712 AGTCGCAAACTTTGAAAAATGCT 58.567 34.783 5.65 0.00 33.03 3.79
286 287 4.777140 AGTCGCAAACTTTGAAAAATGC 57.223 36.364 5.65 0.00 33.03 3.56
297 298 2.478879 CGTTCCCAAAAAGTCGCAAACT 60.479 45.455 0.00 0.00 41.10 2.66
298 299 1.849829 CGTTCCCAAAAAGTCGCAAAC 59.150 47.619 0.00 0.00 0.00 2.93
299 300 1.799548 GCGTTCCCAAAAAGTCGCAAA 60.800 47.619 0.00 0.00 42.54 3.68
300 301 0.248702 GCGTTCCCAAAAAGTCGCAA 60.249 50.000 0.00 0.00 42.54 4.85
301 302 1.357334 GCGTTCCCAAAAAGTCGCA 59.643 52.632 0.00 0.00 42.54 5.10
302 303 1.371267 GGCGTTCCCAAAAAGTCGC 60.371 57.895 0.00 0.00 42.32 5.19
303 304 2.026522 TGGCGTTCCCAAAAAGTCG 58.973 52.632 0.00 0.00 41.82 4.18
311 312 0.755686 AAAATGCTTTGGCGTTCCCA 59.244 45.000 0.00 0.00 45.72 4.37
312 313 1.798223 GAAAAATGCTTTGGCGTTCCC 59.202 47.619 0.00 0.00 45.72 3.97
313 314 2.478831 TGAAAAATGCTTTGGCGTTCC 58.521 42.857 0.00 0.00 45.72 3.62
314 315 4.033932 ACTTTGAAAAATGCTTTGGCGTTC 59.966 37.500 0.00 0.00 45.72 3.95
316 317 3.530535 ACTTTGAAAAATGCTTTGGCGT 58.469 36.364 0.00 0.00 42.25 5.68
317 318 3.803778 AGACTTTGAAAAATGCTTTGGCG 59.196 39.130 0.00 0.00 42.25 5.69
318 319 4.810491 TCAGACTTTGAAAAATGCTTTGGC 59.190 37.500 0.00 0.00 33.96 4.52
319 320 6.927381 AGATCAGACTTTGAAAAATGCTTTGG 59.073 34.615 0.00 0.00 39.77 3.28
320 321 7.941795 AGATCAGACTTTGAAAAATGCTTTG 57.058 32.000 0.00 0.00 39.77 2.77
321 322 9.852091 GATAGATCAGACTTTGAAAAATGCTTT 57.148 29.630 0.00 0.00 39.77 3.51
322 323 9.240734 AGATAGATCAGACTTTGAAAAATGCTT 57.759 29.630 0.00 0.00 39.77 3.91
323 324 8.804912 AGATAGATCAGACTTTGAAAAATGCT 57.195 30.769 0.00 0.00 39.77 3.79
324 325 8.891720 AGAGATAGATCAGACTTTGAAAAATGC 58.108 33.333 0.00 0.00 39.77 3.56
332 333 9.814899 ACAAACATAGAGATAGATCAGACTTTG 57.185 33.333 0.00 0.00 0.00 2.77
335 336 9.860650 ACTACAAACATAGAGATAGATCAGACT 57.139 33.333 0.00 0.00 0.00 3.24
336 337 9.891828 CACTACAAACATAGAGATAGATCAGAC 57.108 37.037 0.00 0.00 0.00 3.51
337 338 8.572185 GCACTACAAACATAGAGATAGATCAGA 58.428 37.037 0.00 0.00 0.00 3.27
338 339 7.536964 CGCACTACAAACATAGAGATAGATCAG 59.463 40.741 0.00 0.00 0.00 2.90
339 340 7.363431 CGCACTACAAACATAGAGATAGATCA 58.637 38.462 0.00 0.00 0.00 2.92
340 341 6.306837 GCGCACTACAAACATAGAGATAGATC 59.693 42.308 0.30 0.00 0.00 2.75
341 342 6.153067 GCGCACTACAAACATAGAGATAGAT 58.847 40.000 0.30 0.00 0.00 1.98
342 343 5.067283 TGCGCACTACAAACATAGAGATAGA 59.933 40.000 5.66 0.00 0.00 1.98
343 344 5.174035 GTGCGCACTACAAACATAGAGATAG 59.826 44.000 32.55 0.00 0.00 2.08
344 345 5.041287 GTGCGCACTACAAACATAGAGATA 58.959 41.667 32.55 0.00 0.00 1.98
345 346 3.865745 GTGCGCACTACAAACATAGAGAT 59.134 43.478 32.55 0.00 0.00 2.75
346 347 3.250744 GTGCGCACTACAAACATAGAGA 58.749 45.455 32.55 0.00 0.00 3.10
347 348 2.348666 GGTGCGCACTACAAACATAGAG 59.651 50.000 36.84 0.00 0.00 2.43
348 349 2.289133 TGGTGCGCACTACAAACATAGA 60.289 45.455 36.84 3.35 0.00 1.98
349 350 2.073056 TGGTGCGCACTACAAACATAG 58.927 47.619 36.84 0.00 0.00 2.23
350 351 2.171341 TGGTGCGCACTACAAACATA 57.829 45.000 36.84 11.65 0.00 2.29
351 352 1.001815 GTTGGTGCGCACTACAAACAT 60.002 47.619 36.84 0.00 0.00 2.71
352 353 0.378962 GTTGGTGCGCACTACAAACA 59.621 50.000 36.84 23.44 0.00 2.83
353 354 0.317519 GGTTGGTGCGCACTACAAAC 60.318 55.000 36.84 30.28 0.00 2.93
354 355 1.448922 GGGTTGGTGCGCACTACAAA 61.449 55.000 36.84 23.25 0.00 2.83
355 356 1.894756 GGGTTGGTGCGCACTACAA 60.895 57.895 36.84 29.31 0.00 2.41
356 357 2.281208 GGGTTGGTGCGCACTACA 60.281 61.111 36.84 25.60 0.00 2.74
357 358 1.170290 AAAGGGTTGGTGCGCACTAC 61.170 55.000 36.84 31.21 0.00 2.73
358 359 0.466555 AAAAGGGTTGGTGCGCACTA 60.467 50.000 36.84 30.87 0.00 2.74
359 360 1.734388 GAAAAGGGTTGGTGCGCACT 61.734 55.000 36.84 16.49 0.00 4.40
360 361 1.299850 GAAAAGGGTTGGTGCGCAC 60.300 57.895 32.15 32.15 0.00 5.34
361 362 2.494530 GGAAAAGGGTTGGTGCGCA 61.495 57.895 5.66 5.66 0.00 6.09
362 363 2.022240 TTGGAAAAGGGTTGGTGCGC 62.022 55.000 0.00 0.00 0.00 6.09
363 364 0.461961 TTTGGAAAAGGGTTGGTGCG 59.538 50.000 0.00 0.00 0.00 5.34
364 365 2.700722 TTTTGGAAAAGGGTTGGTGC 57.299 45.000 0.00 0.00 0.00 5.01
365 366 3.475575 CCATTTTGGAAAAGGGTTGGTG 58.524 45.455 7.27 0.00 43.00 4.17
366 367 3.855255 CCATTTTGGAAAAGGGTTGGT 57.145 42.857 7.27 0.00 43.00 3.67
378 379 0.599728 CACAACACGGGCCATTTTGG 60.600 55.000 4.39 0.00 41.55 3.28
380 381 0.827368 AACACAACACGGGCCATTTT 59.173 45.000 4.39 0.00 0.00 1.82
388 389 1.101049 AAGCCCTGAACACAACACGG 61.101 55.000 0.00 0.00 0.00 4.94
389 390 0.738389 AAAGCCCTGAACACAACACG 59.262 50.000 0.00 0.00 0.00 4.49
398 399 0.179032 TCGTCTTGCAAAGCCCTGAA 60.179 50.000 0.00 0.00 45.70 3.02
432 433 2.331194 ACATTAGGAAACGGTTCGACG 58.669 47.619 7.19 0.00 40.31 5.12
471 472 1.135199 ACATAGACCACGTTGTAGCGG 60.135 52.381 0.00 0.00 35.98 5.52
474 475 4.387862 GGTTGAACATAGACCACGTTGTAG 59.612 45.833 0.00 0.00 33.61 2.74
652 654 4.250305 GTGTGGCCGTGTGGGAGT 62.250 66.667 0.00 0.00 38.47 3.85
664 666 1.278172 CGCTCAACTGAGTCGTGTGG 61.278 60.000 8.46 0.00 43.85 4.17
671 1418 0.528470 GGACTAGCGCTCAACTGAGT 59.472 55.000 16.34 11.32 43.85 3.41
672 1419 0.814457 AGGACTAGCGCTCAACTGAG 59.186 55.000 16.34 7.23 44.75 3.35
673 1420 1.257743 AAGGACTAGCGCTCAACTGA 58.742 50.000 16.34 0.00 0.00 3.41
677 1656 4.530710 TTAGAAAAGGACTAGCGCTCAA 57.469 40.909 16.34 0.00 0.00 3.02
712 1691 8.524487 GTTCCTCCACTATGATAATACTACCAG 58.476 40.741 0.00 0.00 0.00 4.00
714 1693 8.418597 TGTTCCTCCACTATGATAATACTACC 57.581 38.462 0.00 0.00 0.00 3.18
716 1695 8.957466 CGATGTTCCTCCACTATGATAATACTA 58.043 37.037 0.00 0.00 0.00 1.82
717 1696 7.451877 ACGATGTTCCTCCACTATGATAATACT 59.548 37.037 0.00 0.00 0.00 2.12
721 1700 7.776618 ATACGATGTTCCTCCACTATGATAA 57.223 36.000 0.00 0.00 0.00 1.75
723 1702 7.962995 ATATACGATGTTCCTCCACTATGAT 57.037 36.000 0.00 0.00 0.00 2.45
753 1979 9.511272 TCAAAGTACACACTTCAGTATAGTAGA 57.489 33.333 0.00 0.00 44.41 2.59
756 1982 9.998106 ATTTCAAAGTACACACTTCAGTATAGT 57.002 29.630 0.00 0.00 44.41 2.12
771 1997 9.953825 CACGTGTCTCTATTTATTTCAAAGTAC 57.046 33.333 7.58 0.00 0.00 2.73
809 2038 2.301346 GTGCACCTAAATCTGGATGGG 58.699 52.381 5.22 0.00 0.00 4.00
1008 2237 1.154093 CATGCTCTTGCTGCCGTTG 60.154 57.895 0.00 0.00 40.48 4.10
1033 2262 1.823169 GCCAGGTTACACGTCAGGGA 61.823 60.000 0.00 0.00 0.00 4.20
1034 2263 1.375523 GCCAGGTTACACGTCAGGG 60.376 63.158 0.00 0.00 0.00 4.45
1205 2446 0.318784 CTCTATAGGGCCGTTGTCGC 60.319 60.000 1.81 0.00 35.54 5.19
1252 2499 4.406173 CTGCTGCTGCTGCTGTGC 62.406 66.667 27.67 18.47 39.81 4.57
1253 2500 2.188849 CTTCTGCTGCTGCTGCTGTG 62.189 60.000 27.67 19.97 39.81 3.66
1254 2501 1.966972 CTTCTGCTGCTGCTGCTGT 60.967 57.895 27.67 0.00 39.81 4.40
1264 2511 3.429141 CGTGGCCTGCTTCTGCTG 61.429 66.667 3.32 0.00 40.48 4.41
1307 2560 1.202143 TGATCATCGTCTTGGTCGTCG 60.202 52.381 0.00 0.00 28.82 5.12
1308 2561 2.561733 TGATCATCGTCTTGGTCGTC 57.438 50.000 0.00 0.00 28.82 4.20
1309 2562 2.492088 TCTTGATCATCGTCTTGGTCGT 59.508 45.455 0.00 0.00 28.82 4.34
1489 2742 2.694628 TGGGATCATGCATGGCTTTTAC 59.305 45.455 25.97 10.86 0.00 2.01
1547 2833 3.349006 GCTGGGCAGTCACACACG 61.349 66.667 0.00 0.00 0.00 4.49
1583 2869 2.749044 AGCATTGACGCAGGCCAG 60.749 61.111 5.01 0.00 0.00 4.85
1603 2889 9.859427 AACCATGATCAAATTTGTTGTATACTG 57.141 29.630 17.47 5.37 0.00 2.74
1679 2984 9.363401 ACAGTTACCTTGCACTATACAGATATA 57.637 33.333 0.00 0.00 0.00 0.86
1680 2985 8.251383 ACAGTTACCTTGCACTATACAGATAT 57.749 34.615 0.00 0.00 0.00 1.63
1781 3086 2.765699 ACAACAACAACCTTTGATGCCT 59.234 40.909 0.00 0.00 36.98 4.75
1784 3089 5.636965 TCAACAACAACAACAACCTTTGATG 59.363 36.000 0.00 0.00 39.12 3.07
1786 3091 5.201713 TCAACAACAACAACAACCTTTGA 57.798 34.783 0.00 0.00 0.00 2.69
1828 3711 5.530543 CCCAAAGGTATGTTTGCATTTTGTT 59.469 36.000 0.00 0.00 36.29 2.83
1829 3712 5.062528 CCCAAAGGTATGTTTGCATTTTGT 58.937 37.500 0.00 0.00 36.29 2.83
1830 3713 4.083377 GCCCAAAGGTATGTTTGCATTTTG 60.083 41.667 0.00 0.00 36.29 2.44
1831 3714 4.071423 GCCCAAAGGTATGTTTGCATTTT 58.929 39.130 0.00 0.00 36.29 1.82
1832 3715 3.558958 GGCCCAAAGGTATGTTTGCATTT 60.559 43.478 0.00 0.00 36.29 2.32
1834 3717 1.554617 GGCCCAAAGGTATGTTTGCAT 59.445 47.619 0.00 0.00 36.29 3.96
1835 3718 0.972883 GGCCCAAAGGTATGTTTGCA 59.027 50.000 0.00 0.00 36.29 4.08
1836 3719 1.266178 AGGCCCAAAGGTATGTTTGC 58.734 50.000 0.00 0.00 36.29 3.68
1837 3720 3.613910 CGAAAGGCCCAAAGGTATGTTTG 60.614 47.826 0.00 0.00 37.20 2.93
1838 3721 2.560981 CGAAAGGCCCAAAGGTATGTTT 59.439 45.455 0.00 0.00 34.57 2.83
1840 3723 1.834188 CGAAAGGCCCAAAGGTATGT 58.166 50.000 0.00 0.00 34.57 2.29
1881 3764 5.105063 CAGACGTCAATGAGAGCAAGATAA 58.895 41.667 19.50 0.00 0.00 1.75
1884 3767 2.353109 CCAGACGTCAATGAGAGCAAGA 60.353 50.000 19.50 0.00 0.00 3.02
1933 3816 2.270047 CATGCTATTTTGGCAAACCGG 58.730 47.619 13.10 0.00 43.14 5.28
1934 3817 1.660104 GCATGCTATTTTGGCAAACCG 59.340 47.619 13.10 5.14 43.14 4.44
1955 3840 4.233789 TCAATACAAACAATCGGCAAAGC 58.766 39.130 0.00 0.00 0.00 3.51
1972 3857 7.319646 GTTGGCTTTAATTGTGGTCATCAATA 58.680 34.615 0.00 0.00 34.92 1.90
2086 3971 1.198759 TTCTCCAAGTTCTCCCGGGG 61.199 60.000 23.50 12.05 0.00 5.73
2150 4035 0.184451 GGATGTCATGATGTGGGCCT 59.816 55.000 4.53 0.00 0.00 5.19
2151 4036 0.184451 AGGATGTCATGATGTGGGCC 59.816 55.000 0.00 0.00 0.00 5.80
2188 4224 6.259608 CGATAAGTGAATGGAATTTCAGCTCT 59.740 38.462 0.00 0.00 36.07 4.09
2228 4264 0.387929 TCTTTTGTCTCGACGGCTGT 59.612 50.000 0.00 0.00 0.00 4.40
2262 4298 1.994779 GCGACGTCTTCCGGAATTAAA 59.005 47.619 19.21 0.70 42.24 1.52
2286 4322 2.489329 GTGACTTCATGAACATGGTGGG 59.511 50.000 3.38 0.00 39.24 4.61
2292 4328 4.644234 TGGTGTTTGTGACTTCATGAACAT 59.356 37.500 3.38 0.00 36.57 2.71
2293 4329 4.013050 TGGTGTTTGTGACTTCATGAACA 58.987 39.130 3.38 0.00 33.92 3.18
2302 4338 1.229076 GGGGGTGGTGTTTGTGACT 59.771 57.895 0.00 0.00 0.00 3.41
2309 4345 2.520968 GAGCTTGGGGGTGGTGTT 59.479 61.111 0.00 0.00 0.00 3.32
2316 4352 1.215173 TGATATGTTGGAGCTTGGGGG 59.785 52.381 0.00 0.00 0.00 5.40
2329 4365 0.546122 ACGGTGCCATGGTGATATGT 59.454 50.000 14.67 2.16 0.00 2.29
2341 4377 1.199327 GAAAGCTTTCCTAACGGTGCC 59.801 52.381 25.80 0.00 0.00 5.01
2358 4394 3.261897 TCCTTGGTTGTTTGGCTTTGAAA 59.738 39.130 0.00 0.00 0.00 2.69
2359 4395 2.834549 TCCTTGGTTGTTTGGCTTTGAA 59.165 40.909 0.00 0.00 0.00 2.69
2397 4433 9.836864 TGTTTCAATTGTAGAGATGCTATACAT 57.163 29.630 5.13 0.00 37.87 2.29
2398 4434 9.665719 TTGTTTCAATTGTAGAGATGCTATACA 57.334 29.630 5.13 0.00 36.56 2.29
2402 4438 9.844790 CATTTTGTTTCAATTGTAGAGATGCTA 57.155 29.630 5.13 0.00 0.00 3.49
2421 4457 4.141528 TGGTTTCAAGGCCAATCATTTTGT 60.142 37.500 5.01 0.00 0.00 2.83
2437 4473 3.201266 AGTGGTCCTACAGTTTGGTTTCA 59.799 43.478 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.