Multiple sequence alignment - TraesCS7A01G346100

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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 TraesCS7A01G346100 chr7A 100.000 5699 0 0 1 5699 509217581 509211883 0.000000e+00 10525.0
1 TraesCS7A01G346100 chr7A 79.869 457 72 8 2497 2943 509214986 509214540 3.310000e-82 316.0
2 TraesCS7A01G346100 chr7A 79.869 457 72 8 2596 3042 509215085 509214639 3.310000e-82 316.0
3 TraesCS7A01G346100 chr7B 91.679 4879 289 53 130 4932 441508067 441512904 0.000000e+00 6652.0
4 TraesCS7A01G346100 chr7B 92.193 538 15 12 5180 5699 441513151 441513679 0.000000e+00 736.0
5 TraesCS7A01G346100 chr7B 82.119 453 69 2 2596 3042 441510462 441510908 1.500000e-100 377.0
6 TraesCS7A01G346100 chr7B 81.058 359 56 5 2497 2849 441510654 441511006 5.620000e-70 276.0
7 TraesCS7A01G346100 chr7B 80.663 362 57 6 2687 3041 441510459 441510814 9.410000e-68 268.0
8 TraesCS7A01G346100 chr7B 95.238 42 1 1 5055 5095 441513069 441513110 1.330000e-06 65.8
9 TraesCS7A01G346100 chr7D 96.607 3419 89 17 2297 5699 424099023 424102430 0.000000e+00 5646.0
10 TraesCS7A01G346100 chr7D 87.246 2462 194 62 564 2943 424097348 424099771 0.000000e+00 2697.0
11 TraesCS7A01G346100 chr7D 83.242 364 44 9 2687 3041 424099223 424099578 9.210000e-83 318.0
12 TraesCS7A01G346100 chr7D 81.918 365 47 11 2494 2849 424099416 424099770 2.010000e-74 291.0
13 TraesCS7A01G346100 chr2B 76.410 195 28 15 1385 1570 717467852 717468037 7.860000e-14 89.8
14 TraesCS7A01G346100 chr3D 75.839 149 31 5 1432 1576 38367296 38367149 2.850000e-08 71.3
15 TraesCS7A01G346100 chr3D 78.000 100 19 3 1483 1579 38382609 38382510 6.170000e-05 60.2
16 TraesCS7A01G346100 chr3A 76.000 150 29 7 1432 1576 49506737 49506590 2.850000e-08 71.3
17 TraesCS7A01G346100 chr3A 80.220 91 15 2 1483 1570 49819542 49819632 1.330000e-06 65.8
18 TraesCS7A01G346100 chr2D 82.927 82 11 2 1430 1511 591947212 591947290 2.850000e-08 71.3


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 TraesCS7A01G346100 chr7A 509211883 509217581 5698 True 3719.0 10525 86.579333 1 5699 3 chr7A.!!$R1 5698
1 TraesCS7A01G346100 chr7B 441508067 441513679 5612 False 1395.8 6652 87.158333 130 5699 6 chr7B.!!$F1 5569
2 TraesCS7A01G346100 chr7D 424097348 424102430 5082 False 2238.0 5646 87.253250 564 5699 4 chr7D.!!$F1 5135

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
295 302 0.041833 TGGCTCACTTCCTCCTAGCT 59.958 55.0 0.0 0.0 33.67 3.32 F
540 552 0.390603 CGATGCAGTGGGACCGTTAA 60.391 55.0 0.0 0.0 0.00 2.01 F
960 993 0.605589 GAAGACCCGTCCAACCCTTG 60.606 60.0 0.0 0.0 0.00 3.61 F
2003 2066 0.678048 GCGGGGAAGCTTGTTCAGAT 60.678 55.0 2.1 0.0 0.00 2.90 F
3236 3299 0.680921 ACATCAAAGGTGGCGGATGG 60.681 55.0 0.0 0.0 41.03 3.51 F
3940 4006 0.914417 GAATGGAGTGGACCTGGGGA 60.914 60.0 0.0 0.0 0.00 4.81 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2157 2220 0.108585 GCCCCGATTCATCCAAGCTA 59.891 55.0 0.00 0.00 0.00 3.32 R
2331 2394 0.689055 AATCCACAGCTGCTGTCTCA 59.311 50.0 30.96 18.04 43.43 3.27 R
2732 2795 0.475475 TGCATCCTCATCCATCACCC 59.525 55.0 0.00 0.00 0.00 4.61 R
3261 3324 0.462789 CATCCCCTGCCTTTGATTGC 59.537 55.0 0.00 0.00 0.00 3.56 R
4263 4329 0.473755 TCTCTTGCTCAAACCTGGCA 59.526 50.0 0.00 0.00 0.00 4.92 R
5444 5634 0.320683 CCCATGTCTCGCTGTTGACA 60.321 55.0 0.00 0.00 45.56 3.58 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 7.865875 TTGACATAATGTTTGTCCGATTTTG 57.134 32.000 1.73 0.00 42.25 2.44
25 26 7.208225 TGACATAATGTTTGTCCGATTTTGA 57.792 32.000 1.73 0.00 42.25 2.69
26 27 7.081349 TGACATAATGTTTGTCCGATTTTGAC 58.919 34.615 1.73 0.00 42.25 3.18
27 28 6.976088 ACATAATGTTTGTCCGATTTTGACA 58.024 32.000 0.00 0.00 40.80 3.58
35 36 6.480524 TTGTCCGATTTTGACAACATAGAG 57.519 37.500 1.94 0.00 45.19 2.43
36 37 5.789521 TGTCCGATTTTGACAACATAGAGA 58.210 37.500 0.00 0.00 39.66 3.10
37 38 6.227522 TGTCCGATTTTGACAACATAGAGAA 58.772 36.000 0.00 0.00 39.66 2.87
38 39 6.878923 TGTCCGATTTTGACAACATAGAGAAT 59.121 34.615 0.00 0.00 39.66 2.40
39 40 7.148423 TGTCCGATTTTGACAACATAGAGAATG 60.148 37.037 0.00 0.00 39.66 2.67
40 41 6.316140 TCCGATTTTGACAACATAGAGAATGG 59.684 38.462 0.00 0.00 40.16 3.16
41 42 6.316140 CCGATTTTGACAACATAGAGAATGGA 59.684 38.462 0.00 0.00 40.16 3.41
42 43 7.404985 CGATTTTGACAACATAGAGAATGGAG 58.595 38.462 0.00 0.00 40.16 3.86
43 44 7.278646 CGATTTTGACAACATAGAGAATGGAGA 59.721 37.037 0.00 0.00 40.16 3.71
44 45 8.868522 ATTTTGACAACATAGAGAATGGAGAA 57.131 30.769 0.00 0.00 40.16 2.87
45 46 8.690203 TTTTGACAACATAGAGAATGGAGAAA 57.310 30.769 0.00 0.00 40.16 2.52
46 47 7.672983 TTGACAACATAGAGAATGGAGAAAC 57.327 36.000 0.00 0.00 40.16 2.78
47 48 6.768483 TGACAACATAGAGAATGGAGAAACA 58.232 36.000 0.00 0.00 40.16 2.83
48 49 7.397221 TGACAACATAGAGAATGGAGAAACAT 58.603 34.615 0.00 0.00 40.16 2.71
49 50 8.539544 TGACAACATAGAGAATGGAGAAACATA 58.460 33.333 0.00 0.00 40.16 2.29
50 51 9.383519 GACAACATAGAGAATGGAGAAACATAA 57.616 33.333 0.00 0.00 40.16 1.90
51 52 9.911788 ACAACATAGAGAATGGAGAAACATAAT 57.088 29.630 0.00 0.00 40.16 1.28
74 75 5.934935 ACTATCTTTTGGTAAACACACCG 57.065 39.130 0.00 0.00 41.88 4.94
75 76 5.613329 ACTATCTTTTGGTAAACACACCGA 58.387 37.500 0.00 0.00 41.88 4.69
76 77 6.056884 ACTATCTTTTGGTAAACACACCGAA 58.943 36.000 0.00 0.00 41.88 4.30
77 78 5.838531 ATCTTTTGGTAAACACACCGAAA 57.161 34.783 7.33 7.33 45.66 3.46
78 79 5.838531 TCTTTTGGTAAACACACCGAAAT 57.161 34.783 7.89 0.00 46.29 2.17
79 80 5.583495 TCTTTTGGTAAACACACCGAAATG 58.417 37.500 7.89 4.12 46.29 2.32
80 81 3.357166 TTGGTAAACACACCGAAATGC 57.643 42.857 0.00 0.00 41.88 3.56
81 82 1.264557 TGGTAAACACACCGAAATGCG 59.735 47.619 0.00 0.00 41.88 4.73
90 91 3.146913 CGAAATGCGGCCCCCAAT 61.147 61.111 0.00 0.00 36.03 3.16
91 92 2.500646 GAAATGCGGCCCCCAATG 59.499 61.111 0.00 0.00 0.00 2.82
92 93 3.082701 AAATGCGGCCCCCAATGG 61.083 61.111 0.00 0.00 0.00 3.16
93 94 3.615480 AAATGCGGCCCCCAATGGA 62.615 57.895 0.00 0.00 35.39 3.41
94 95 2.894885 AAATGCGGCCCCCAATGGAT 62.895 55.000 0.00 0.00 35.39 3.41
95 96 4.837797 TGCGGCCCCCAATGGATG 62.838 66.667 0.00 0.00 35.39 3.51
96 97 4.521292 GCGGCCCCCAATGGATGA 62.521 66.667 0.00 0.00 35.39 2.92
97 98 2.278404 CGGCCCCCAATGGATGAA 59.722 61.111 0.00 0.00 35.39 2.57
98 99 2.127232 CGGCCCCCAATGGATGAAC 61.127 63.158 0.00 0.00 35.39 3.18
99 100 1.762063 GGCCCCCAATGGATGAACC 60.762 63.158 0.00 0.00 35.39 3.62
100 101 1.762063 GCCCCCAATGGATGAACCC 60.762 63.158 0.00 0.00 38.00 4.11
101 102 2.018447 CCCCCAATGGATGAACCCT 58.982 57.895 0.00 0.00 38.00 4.34
102 103 0.397535 CCCCCAATGGATGAACCCTG 60.398 60.000 0.00 0.00 38.00 4.45
103 104 0.630673 CCCCAATGGATGAACCCTGA 59.369 55.000 0.00 0.00 38.00 3.86
104 105 1.686115 CCCCAATGGATGAACCCTGAC 60.686 57.143 0.00 0.00 38.00 3.51
105 106 1.005805 CCCAATGGATGAACCCTGACA 59.994 52.381 0.00 0.00 38.00 3.58
106 107 2.557229 CCCAATGGATGAACCCTGACAA 60.557 50.000 0.00 0.00 38.00 3.18
107 108 3.164268 CCAATGGATGAACCCTGACAAA 58.836 45.455 0.00 0.00 38.00 2.83
108 109 3.577848 CCAATGGATGAACCCTGACAAAA 59.422 43.478 0.00 0.00 38.00 2.44
109 110 4.040217 CCAATGGATGAACCCTGACAAAAA 59.960 41.667 0.00 0.00 38.00 1.94
110 111 5.280113 CCAATGGATGAACCCTGACAAAAAT 60.280 40.000 0.00 0.00 38.00 1.82
111 112 4.870123 TGGATGAACCCTGACAAAAATG 57.130 40.909 0.00 0.00 38.00 2.32
112 113 4.478203 TGGATGAACCCTGACAAAAATGA 58.522 39.130 0.00 0.00 38.00 2.57
113 114 4.898265 TGGATGAACCCTGACAAAAATGAA 59.102 37.500 0.00 0.00 38.00 2.57
114 115 5.221422 TGGATGAACCCTGACAAAAATGAAC 60.221 40.000 0.00 0.00 38.00 3.18
115 116 4.664150 TGAACCCTGACAAAAATGAACC 57.336 40.909 0.00 0.00 0.00 3.62
116 117 4.285863 TGAACCCTGACAAAAATGAACCT 58.714 39.130 0.00 0.00 0.00 3.50
117 118 4.714308 TGAACCCTGACAAAAATGAACCTT 59.286 37.500 0.00 0.00 0.00 3.50
118 119 5.188751 TGAACCCTGACAAAAATGAACCTTT 59.811 36.000 0.00 0.00 0.00 3.11
119 120 6.381420 TGAACCCTGACAAAAATGAACCTTTA 59.619 34.615 0.00 0.00 0.00 1.85
120 121 6.156748 ACCCTGACAAAAATGAACCTTTAC 57.843 37.500 0.00 0.00 0.00 2.01
121 122 5.659079 ACCCTGACAAAAATGAACCTTTACA 59.341 36.000 0.00 0.00 0.00 2.41
122 123 6.155393 ACCCTGACAAAAATGAACCTTTACAA 59.845 34.615 0.00 0.00 0.00 2.41
123 124 7.044798 CCCTGACAAAAATGAACCTTTACAAA 58.955 34.615 0.00 0.00 0.00 2.83
124 125 7.714813 CCCTGACAAAAATGAACCTTTACAAAT 59.285 33.333 0.00 0.00 0.00 2.32
125 126 9.757227 CCTGACAAAAATGAACCTTTACAAATA 57.243 29.630 0.00 0.00 0.00 1.40
166 167 6.757237 TCATTTTGCTTATCTGGCTTGAAAA 58.243 32.000 0.00 0.00 0.00 2.29
168 169 4.519540 TTGCTTATCTGGCTTGAAAACC 57.480 40.909 0.00 0.00 0.00 3.27
171 172 3.057526 GCTTATCTGGCTTGAAAACCGTT 60.058 43.478 0.00 0.00 0.00 4.44
174 175 6.636562 TTATCTGGCTTGAAAACCGTTTAA 57.363 33.333 0.00 0.00 0.00 1.52
183 184 7.361894 GCTTGAAAACCGTTTAACCTACATTA 58.638 34.615 0.00 0.00 0.00 1.90
188 189 9.550811 GAAAACCGTTTAACCTACATTATCAAG 57.449 33.333 0.00 0.00 0.00 3.02
199 200 8.888579 ACCTACATTATCAAGTTCTAATTCCG 57.111 34.615 0.00 0.00 0.00 4.30
202 203 9.197694 CTACATTATCAAGTTCTAATTCCGGAG 57.802 37.037 3.34 0.00 0.00 4.63
205 206 9.712305 CATTATCAAGTTCTAATTCCGGAGTAT 57.288 33.333 3.34 0.00 0.00 2.12
212 213 9.708092 AAGTTCTAATTCCGGAGTATATTAAGC 57.292 33.333 3.34 0.00 0.00 3.09
213 214 8.312564 AGTTCTAATTCCGGAGTATATTAAGCC 58.687 37.037 3.34 0.00 0.00 4.35
214 215 7.179076 TCTAATTCCGGAGTATATTAAGCCC 57.821 40.000 3.34 0.00 0.00 5.19
215 216 4.838904 ATTCCGGAGTATATTAAGCCCC 57.161 45.455 3.34 0.00 0.00 5.80
216 217 3.555117 TCCGGAGTATATTAAGCCCCT 57.445 47.619 0.00 0.00 0.00 4.79
217 218 3.865571 TCCGGAGTATATTAAGCCCCTT 58.134 45.455 0.00 0.00 0.00 3.95
218 219 3.581332 TCCGGAGTATATTAAGCCCCTTG 59.419 47.826 0.00 0.00 0.00 3.61
219 220 3.335579 CGGAGTATATTAAGCCCCTTGC 58.664 50.000 0.00 0.00 41.71 4.01
220 221 3.244422 CGGAGTATATTAAGCCCCTTGCA 60.244 47.826 0.00 0.00 44.83 4.08
222 223 5.338056 CGGAGTATATTAAGCCCCTTGCATA 60.338 44.000 0.00 0.00 44.83 3.14
223 224 6.632672 CGGAGTATATTAAGCCCCTTGCATAT 60.633 42.308 0.00 0.00 44.83 1.78
224 225 6.768381 GGAGTATATTAAGCCCCTTGCATATC 59.232 42.308 0.00 0.00 44.83 1.63
225 226 7.270832 AGTATATTAAGCCCCTTGCATATCA 57.729 36.000 0.00 0.00 44.83 2.15
230 237 1.496001 AGCCCCTTGCATATCATCACA 59.504 47.619 0.00 0.00 44.83 3.58
243 250 7.975058 TGCATATCATCACAACACAAAATAAGG 59.025 33.333 0.00 0.00 0.00 2.69
248 255 7.890515 TCATCACAACACAAAATAAGGCAATA 58.109 30.769 0.00 0.00 0.00 1.90
249 256 8.530311 TCATCACAACACAAAATAAGGCAATAT 58.470 29.630 0.00 0.00 0.00 1.28
254 261 9.200817 ACAACACAAAATAAGGCAATATAGGAT 57.799 29.630 0.00 0.00 0.00 3.24
255 262 9.467258 CAACACAAAATAAGGCAATATAGGATG 57.533 33.333 0.00 0.00 0.00 3.51
261 268 3.882102 AGGCAATATAGGATGTGGCAA 57.118 42.857 0.00 0.00 38.91 4.52
263 270 4.147321 AGGCAATATAGGATGTGGCAAAG 58.853 43.478 0.00 0.00 38.91 2.77
266 273 5.068987 GGCAATATAGGATGTGGCAAAGAAA 59.931 40.000 0.00 0.00 36.61 2.52
267 274 6.406849 GGCAATATAGGATGTGGCAAAGAAAA 60.407 38.462 0.00 0.00 36.61 2.29
268 275 6.698766 GCAATATAGGATGTGGCAAAGAAAAG 59.301 38.462 0.00 0.00 0.00 2.27
270 277 8.902806 CAATATAGGATGTGGCAAAGAAAAGTA 58.097 33.333 0.00 0.00 0.00 2.24
273 280 6.759497 AGGATGTGGCAAAGAAAAGTATAC 57.241 37.500 0.00 0.00 0.00 1.47
280 287 4.459337 GGCAAAGAAAAGTATACTGTGGCT 59.541 41.667 6.06 0.00 39.99 4.75
290 297 1.267121 TACTGTGGCTCACTTCCTCC 58.733 55.000 6.83 0.00 35.11 4.30
291 298 0.472734 ACTGTGGCTCACTTCCTCCT 60.473 55.000 6.83 0.00 35.11 3.69
293 300 1.480137 CTGTGGCTCACTTCCTCCTAG 59.520 57.143 6.83 0.00 35.11 3.02
295 302 0.041833 TGGCTCACTTCCTCCTAGCT 59.958 55.000 0.00 0.00 33.67 3.32
314 321 3.509575 AGCTGTCTAGGAGAAGAAGTGTG 59.490 47.826 0.00 0.00 0.00 3.82
315 322 3.508012 GCTGTCTAGGAGAAGAAGTGTGA 59.492 47.826 0.00 0.00 0.00 3.58
329 336 6.394345 AGAAGTGTGAAAAAGGGGATAGAT 57.606 37.500 0.00 0.00 0.00 1.98
339 346 9.009675 TGAAAAAGGGGATAGATGATTTACCTA 57.990 33.333 0.00 0.00 0.00 3.08
347 354 7.896496 GGGATAGATGATTTACCTAGGAGAGAA 59.104 40.741 17.98 4.61 0.00 2.87
352 359 7.507616 AGATGATTTACCTAGGAGAGAAACGAT 59.492 37.037 17.98 5.83 0.00 3.73
357 364 8.763984 TTTACCTAGGAGAGAAACGATAAGAT 57.236 34.615 17.98 0.00 0.00 2.40
360 367 5.536916 CCTAGGAGAGAAACGATAAGATGGT 59.463 44.000 1.05 0.00 0.00 3.55
361 368 6.715718 CCTAGGAGAGAAACGATAAGATGGTA 59.284 42.308 1.05 0.00 0.00 3.25
362 369 7.230913 CCTAGGAGAGAAACGATAAGATGGTAA 59.769 40.741 1.05 0.00 0.00 2.85
363 370 7.604657 AGGAGAGAAACGATAAGATGGTAAT 57.395 36.000 0.00 0.00 0.00 1.89
364 371 8.707796 AGGAGAGAAACGATAAGATGGTAATA 57.292 34.615 0.00 0.00 0.00 0.98
365 372 8.798402 AGGAGAGAAACGATAAGATGGTAATAG 58.202 37.037 0.00 0.00 0.00 1.73
366 373 8.794553 GGAGAGAAACGATAAGATGGTAATAGA 58.205 37.037 0.00 0.00 0.00 1.98
373 380 8.018677 ACGATAAGATGGTAATAGATTTTGCG 57.981 34.615 0.00 0.00 0.00 4.85
379 386 8.225603 AGATGGTAATAGATTTTGCGTGAAAT 57.774 30.769 0.00 0.00 32.16 2.17
385 392 1.648681 GATTTTGCGTGAAATCCGTGC 59.351 47.619 11.99 0.00 39.16 5.34
404 411 4.235762 CCGCCGAGTGGGGTATGG 62.236 72.222 0.00 0.00 46.46 2.74
405 412 3.467226 CGCCGAGTGGGGTATGGT 61.467 66.667 0.00 0.00 43.03 3.55
410 417 2.043992 CCGAGTGGGGTATGGTGAATA 58.956 52.381 0.00 0.00 0.00 1.75
411 418 2.436542 CCGAGTGGGGTATGGTGAATAA 59.563 50.000 0.00 0.00 0.00 1.40
413 420 3.477530 GAGTGGGGTATGGTGAATAAGC 58.522 50.000 0.00 0.00 0.00 3.09
417 424 3.214328 GGGGTATGGTGAATAAGCTGTG 58.786 50.000 0.00 0.00 0.00 3.66
418 425 3.371595 GGGGTATGGTGAATAAGCTGTGT 60.372 47.826 0.00 0.00 0.00 3.72
419 426 4.270008 GGGTATGGTGAATAAGCTGTGTT 58.730 43.478 0.00 0.00 0.00 3.32
420 427 4.705023 GGGTATGGTGAATAAGCTGTGTTT 59.295 41.667 0.00 0.00 0.00 2.83
421 428 5.393027 GGGTATGGTGAATAAGCTGTGTTTG 60.393 44.000 0.00 0.00 0.00 2.93
422 429 5.183140 GGTATGGTGAATAAGCTGTGTTTGT 59.817 40.000 0.00 0.00 0.00 2.83
423 430 4.566545 TGGTGAATAAGCTGTGTTTGTG 57.433 40.909 0.00 0.00 0.00 3.33
428 435 4.803088 TGAATAAGCTGTGTTTGTGTTTGC 59.197 37.500 0.00 0.00 0.00 3.68
431 438 1.751536 GCTGTGTTTGTGTTTGCCGC 61.752 55.000 0.00 0.00 0.00 6.53
432 439 1.470699 CTGTGTTTGTGTTTGCCGCG 61.471 55.000 0.00 0.00 0.00 6.46
447 454 1.599542 GCCGCGAGATGCTTATCTTTT 59.400 47.619 8.23 0.00 43.27 2.27
448 455 2.032178 GCCGCGAGATGCTTATCTTTTT 59.968 45.455 8.23 0.00 43.27 1.94
449 456 3.611517 CCGCGAGATGCTTATCTTTTTG 58.388 45.455 8.23 0.00 43.27 2.44
457 464 7.062605 CGAGATGCTTATCTTTTTGCATTTTGT 59.937 33.333 0.00 0.00 44.80 2.83
494 505 9.916397 CATTACTTTACTAATTGTGACGAATCC 57.084 33.333 0.00 0.00 0.00 3.01
503 514 8.141268 ACTAATTGTGACGAATCCATTGTTTTT 58.859 29.630 0.00 0.00 0.00 1.94
504 515 7.406799 AATTGTGACGAATCCATTGTTTTTC 57.593 32.000 0.00 0.00 0.00 2.29
505 516 4.532276 TGTGACGAATCCATTGTTTTTCG 58.468 39.130 0.00 9.79 44.73 3.46
514 526 3.567585 TCCATTGTTTTTCGTGAGATGCA 59.432 39.130 0.00 0.00 41.60 3.96
516 528 5.414144 TCCATTGTTTTTCGTGAGATGCATA 59.586 36.000 0.00 0.00 41.60 3.14
522 534 2.492019 TCGTGAGATGCATACCTTCG 57.508 50.000 0.00 3.69 33.31 3.79
532 544 1.586422 CATACCTTCGATGCAGTGGG 58.414 55.000 0.00 0.00 0.00 4.61
540 552 0.390603 CGATGCAGTGGGACCGTTAA 60.391 55.000 0.00 0.00 0.00 2.01
576 588 8.135529 AGCTTGAAAGTCAAAACAAATACTACC 58.864 33.333 0.00 0.00 35.73 3.18
605 617 8.247562 TCTTTATTTATAAAGGCAAACGCACAT 58.752 29.630 17.66 0.00 45.73 3.21
612 624 5.637006 AAAGGCAAACGCACATATAAGAA 57.363 34.783 0.00 0.00 0.00 2.52
617 629 5.036737 GCAAACGCACATATAAGAAGCATT 58.963 37.500 0.00 0.00 0.00 3.56
641 653 9.722056 ATTTCAAGTCAAAGTGCGAAATATATC 57.278 29.630 0.00 0.00 32.77 1.63
645 657 7.303634 AGTCAAAGTGCGAAATATATCGTTT 57.696 32.000 0.00 0.00 44.49 3.60
679 699 7.730364 AAGTGTGAAATATATTAAGCCTCCG 57.270 36.000 0.00 0.00 0.00 4.63
681 701 7.155328 AGTGTGAAATATATTAAGCCTCCGAG 58.845 38.462 0.00 0.00 0.00 4.63
682 702 6.369065 GTGTGAAATATATTAAGCCTCCGAGG 59.631 42.308 10.41 10.41 38.80 4.63
702 722 5.551760 AGGCACAACTCGAAATATTGAAG 57.448 39.130 5.64 0.00 0.00 3.02
705 725 5.122396 GGCACAACTCGAAATATTGAAGTCT 59.878 40.000 5.64 0.00 0.00 3.24
706 726 6.348540 GGCACAACTCGAAATATTGAAGTCTT 60.349 38.462 5.64 0.00 0.00 3.01
707 727 7.078228 GCACAACTCGAAATATTGAAGTCTTT 58.922 34.615 5.64 0.00 0.00 2.52
775 807 8.716646 TTTTCTAGGCCAAAGAAAAAGAAAAG 57.283 30.769 29.53 1.90 45.33 2.27
789 821 4.672587 AAGAAAAGGAAAGAAACCCAGC 57.327 40.909 0.00 0.00 0.00 4.85
820 852 0.825425 TTGAATTTGGTGGCGCTCCA 60.825 50.000 17.84 17.84 40.85 3.86
829 861 4.802051 GGCGCTCCATTGGGCAGA 62.802 66.667 7.64 0.00 45.91 4.26
858 890 0.869880 TTGACGTCATATCTGCGCCG 60.870 55.000 20.80 0.00 0.00 6.46
897 929 1.765230 GATGTAGACCTGGAGGACGT 58.235 55.000 0.00 0.00 38.94 4.34
903 935 1.646624 GACCTGGAGGACGTCGAGAC 61.647 65.000 9.92 0.29 38.94 3.36
904 936 2.408241 CCTGGAGGACGTCGAGACC 61.408 68.421 9.92 10.27 37.39 3.85
907 939 2.408241 GGAGGACGTCGAGACCTGG 61.408 68.421 9.92 0.00 44.84 4.45
909 941 2.675772 GGACGTCGAGACCTGGGT 60.676 66.667 9.92 0.00 0.00 4.51
910 942 2.567049 GACGTCGAGACCTGGGTG 59.433 66.667 0.00 0.00 0.00 4.61
911 943 2.989824 ACGTCGAGACCTGGGTGG 60.990 66.667 0.00 0.00 42.93 4.61
912 944 3.760035 CGTCGAGACCTGGGTGGG 61.760 72.222 0.00 0.00 41.11 4.61
913 945 2.283676 GTCGAGACCTGGGTGGGA 60.284 66.667 0.00 0.00 41.11 4.37
915 947 3.775654 CGAGACCTGGGTGGGAGC 61.776 72.222 0.00 0.00 41.11 4.70
917 949 2.121963 AGACCTGGGTGGGAGCAA 60.122 61.111 0.00 0.00 41.11 3.91
918 950 1.774217 AGACCTGGGTGGGAGCAAA 60.774 57.895 0.00 0.00 41.11 3.68
919 951 1.303643 GACCTGGGTGGGAGCAAAG 60.304 63.158 0.00 0.00 41.11 2.77
920 952 2.036256 CCTGGGTGGGAGCAAAGG 59.964 66.667 0.00 0.00 0.00 3.11
921 953 2.677875 CTGGGTGGGAGCAAAGGC 60.678 66.667 0.00 0.00 41.61 4.35
922 954 3.506743 TGGGTGGGAGCAAAGGCA 61.507 61.111 0.00 0.00 44.61 4.75
923 955 2.037847 GGGTGGGAGCAAAGGCAT 59.962 61.111 0.00 0.00 44.61 4.40
960 993 0.605589 GAAGACCCGTCCAACCCTTG 60.606 60.000 0.00 0.00 0.00 3.61
961 994 2.671963 GACCCGTCCAACCCTTGC 60.672 66.667 0.00 0.00 0.00 4.01
962 995 3.175710 ACCCGTCCAACCCTTGCT 61.176 61.111 0.00 0.00 0.00 3.91
963 996 2.115266 CCCGTCCAACCCTTGCTT 59.885 61.111 0.00 0.00 0.00 3.91
1590 1653 4.863131 GCCTATTACGACCGGATTAATCAG 59.137 45.833 17.07 12.75 0.00 2.90
1666 1729 1.550327 CTTCTCCCTCCCCAAAAAGC 58.450 55.000 0.00 0.00 0.00 3.51
1771 1834 2.398554 CCCTGGTTCACGGATTGCG 61.399 63.158 0.00 0.00 0.00 4.85
1777 1840 1.596752 TTCACGGATTGCGCACTGT 60.597 52.632 11.12 8.39 0.00 3.55
1815 1878 1.784525 CGGAACAGACTGTGAAGGAC 58.215 55.000 9.33 0.00 0.00 3.85
1841 1904 1.064979 ACCGCATAAGGTTAACTGGGG 60.065 52.381 20.47 20.47 43.00 4.96
1863 1926 2.719739 GGCATCATCTGGGGTATCATG 58.280 52.381 0.00 0.00 0.00 3.07
1889 1952 2.184322 GATTCACGAGCTGCCCGA 59.816 61.111 11.37 0.00 0.00 5.14
1986 2049 2.510238 CCGCAGAAAGAGGAGGCG 60.510 66.667 0.00 0.00 46.61 5.52
2003 2066 0.678048 GCGGGGAAGCTTGTTCAGAT 60.678 55.000 2.10 0.00 0.00 2.90
2074 2137 1.228675 AACAAGGGCTTGCAGGAGG 60.229 57.895 0.00 0.00 44.03 4.30
2157 2220 1.271054 GGTGTGAGTCTGACCAGCAAT 60.271 52.381 3.76 0.00 0.00 3.56
2236 2299 1.524482 GAGTCTGGGGATGTGAGGC 59.476 63.158 0.00 0.00 0.00 4.70
2289 2352 3.698040 GTGTGGATTTGAGGAGCAATGAT 59.302 43.478 0.00 0.00 36.15 2.45
2309 2372 4.018141 TGATTTGAATGAGTCTGGGGATGT 60.018 41.667 0.00 0.00 0.00 3.06
2319 2382 2.771943 GTCTGGGGATGTGACCAAGATA 59.228 50.000 0.00 0.00 36.09 1.98
2322 2385 4.139786 CTGGGGATGTGACCAAGATATTG 58.860 47.826 0.00 0.00 36.09 1.90
2331 2394 5.429762 TGTGACCAAGATATTGGAGGAATCT 59.570 40.000 25.55 0.63 44.82 2.40
2352 2415 1.736681 GAGACAGCAGCTGTGGATTTC 59.263 52.381 33.03 16.56 45.44 2.17
2354 2417 1.467734 GACAGCAGCTGTGGATTTCAG 59.532 52.381 33.03 0.00 45.44 3.02
2547 2610 1.487976 CAGGATACATCAGTGGTGGCT 59.512 52.381 8.56 0.00 41.41 4.75
2630 2693 3.322466 AGGGAGCAAGTCACCGGG 61.322 66.667 6.32 0.00 0.00 5.73
2916 2979 4.518970 AGCAATAATTCGCCGGATACATTT 59.481 37.500 5.05 0.00 0.00 2.32
2949 3012 2.306805 TGAGGATGCAAAGGTCATGAGT 59.693 45.455 0.00 0.00 0.00 3.41
2969 3032 4.398319 AGTTTGGATGTCGAATTGGAGTT 58.602 39.130 0.00 0.00 0.00 3.01
3046 3109 4.780554 TGTATGAGGATGTAAAGGTGGACA 59.219 41.667 0.00 0.00 0.00 4.02
3134 3197 1.622607 TTCGGGGGTGTGGATGCTAG 61.623 60.000 0.00 0.00 0.00 3.42
3222 3285 3.444029 TGTGGAGAGATTGGAGACATCA 58.556 45.455 0.00 0.00 42.32 3.07
3236 3299 0.680921 ACATCAAAGGTGGCGGATGG 60.681 55.000 0.00 0.00 41.03 3.51
3261 3324 2.019984 GTAAAGGGCATGAGCTTGGAG 58.980 52.381 0.00 0.00 41.70 3.86
3320 3383 3.619038 GCTGTAGCTCCTACACATGAAAC 59.381 47.826 0.00 0.00 41.33 2.78
3325 3388 3.935203 AGCTCCTACACATGAAACGAATG 59.065 43.478 0.00 0.00 0.00 2.67
3455 3518 3.511934 ACACAGGAGAAAGTGCTAGTAGG 59.488 47.826 0.00 0.00 39.30 3.18
3940 4006 0.914417 GAATGGAGTGGACCTGGGGA 60.914 60.000 0.00 0.00 0.00 4.81
4009 4075 6.533730 GTTGAGGATATTGATGATGGGTACA 58.466 40.000 0.00 0.00 0.00 2.90
4164 4230 3.631686 TGGTCAATGCCAGCATGTTATAC 59.368 43.478 5.78 0.98 36.68 1.47
4263 4329 6.951971 AGCAATTATCCACTCACTAAACTCT 58.048 36.000 0.00 0.00 0.00 3.24
4375 4441 3.584733 AGAGGGCTTTGAAACAGAGTT 57.415 42.857 0.00 0.00 0.00 3.01
4424 4490 3.236896 AGTTCCCTTCTAACGAGTTCCA 58.763 45.455 0.00 0.00 32.00 3.53
4567 4645 4.317488 TGGAAATTTCAAGCTTGAATGGC 58.683 39.130 35.66 25.01 45.65 4.40
4741 4819 9.275572 AGGTACATGGATTACCTACTTTCTTAA 57.724 33.333 10.93 0.00 46.34 1.85
4764 4842 6.721571 AGTCCGTGTACTGTGATTAAATTG 57.278 37.500 0.00 0.00 0.00 2.32
5172 5323 5.613329 ACGGAGTAACATTTCAGGTTAACA 58.387 37.500 8.10 0.00 41.94 2.41
5173 5324 6.235664 ACGGAGTAACATTTCAGGTTAACAT 58.764 36.000 8.10 0.00 41.94 2.71
5333 5500 7.096065 GGTTTTTGTCTTGTTATCAGAACATGC 60.096 37.037 0.00 0.00 0.00 4.06
5355 5522 9.357652 CATGCTTTGTACTTGCTTGTTTATTAT 57.642 29.630 0.00 0.00 0.00 1.28
5444 5634 4.383989 GGAGAGCTCTCTTGGATGTTTGAT 60.384 45.833 36.09 2.07 42.48 2.57
5538 5728 4.516698 AGGCATAATTCCAGCTGTAAATCG 59.483 41.667 13.81 6.00 0.00 3.34
5612 5802 4.864704 TTTAGATGGCCTTTTGGTTGAC 57.135 40.909 3.32 0.00 42.99 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 7.081349 TGTCAAAATCGGACAAACATTATGTC 58.919 34.615 0.00 0.00 41.96 3.06
3 4 6.976088 TGTCAAAATCGGACAAACATTATGT 58.024 32.000 0.00 0.00 41.96 2.29
13 14 5.789521 TCTCTATGTTGTCAAAATCGGACA 58.210 37.500 0.00 0.00 43.12 4.02
14 15 6.721571 TTCTCTATGTTGTCAAAATCGGAC 57.278 37.500 0.00 0.00 35.83 4.79
15 16 6.316140 CCATTCTCTATGTTGTCAAAATCGGA 59.684 38.462 0.00 0.00 31.99 4.55
16 17 6.316140 TCCATTCTCTATGTTGTCAAAATCGG 59.684 38.462 0.00 0.00 31.99 4.18
17 18 7.278646 TCTCCATTCTCTATGTTGTCAAAATCG 59.721 37.037 0.00 0.00 31.99 3.34
18 19 8.498054 TCTCCATTCTCTATGTTGTCAAAATC 57.502 34.615 0.00 0.00 31.99 2.17
19 20 8.868522 TTCTCCATTCTCTATGTTGTCAAAAT 57.131 30.769 0.00 0.00 31.99 1.82
20 21 8.567948 GTTTCTCCATTCTCTATGTTGTCAAAA 58.432 33.333 0.00 0.00 31.99 2.44
21 22 7.719193 TGTTTCTCCATTCTCTATGTTGTCAAA 59.281 33.333 0.00 0.00 31.99 2.69
22 23 7.223584 TGTTTCTCCATTCTCTATGTTGTCAA 58.776 34.615 0.00 0.00 31.99 3.18
23 24 6.768483 TGTTTCTCCATTCTCTATGTTGTCA 58.232 36.000 0.00 0.00 31.99 3.58
24 25 7.856145 ATGTTTCTCCATTCTCTATGTTGTC 57.144 36.000 0.00 0.00 31.99 3.18
25 26 9.911788 ATTATGTTTCTCCATTCTCTATGTTGT 57.088 29.630 0.00 0.00 31.99 3.32
48 49 9.153721 CGGTGTGTTTACCAAAAGATAGTATTA 57.846 33.333 0.00 0.00 40.89 0.98
49 50 7.879160 TCGGTGTGTTTACCAAAAGATAGTATT 59.121 33.333 0.00 0.00 40.89 1.89
50 51 7.388437 TCGGTGTGTTTACCAAAAGATAGTAT 58.612 34.615 0.00 0.00 40.89 2.12
51 52 6.757237 TCGGTGTGTTTACCAAAAGATAGTA 58.243 36.000 0.00 0.00 40.89 1.82
52 53 5.613329 TCGGTGTGTTTACCAAAAGATAGT 58.387 37.500 0.00 0.00 40.89 2.12
53 54 6.548441 TTCGGTGTGTTTACCAAAAGATAG 57.452 37.500 0.00 0.00 40.89 2.08
54 55 6.939132 TTTCGGTGTGTTTACCAAAAGATA 57.061 33.333 0.00 0.00 40.89 1.98
55 56 5.838531 TTTCGGTGTGTTTACCAAAAGAT 57.161 34.783 0.00 0.00 40.89 2.40
56 57 5.583495 CATTTCGGTGTGTTTACCAAAAGA 58.417 37.500 0.00 0.00 40.89 2.52
57 58 4.208253 GCATTTCGGTGTGTTTACCAAAAG 59.792 41.667 0.00 0.00 40.89 2.27
58 59 4.113354 GCATTTCGGTGTGTTTACCAAAA 58.887 39.130 0.00 0.00 40.89 2.44
59 60 3.707793 GCATTTCGGTGTGTTTACCAAA 58.292 40.909 0.00 0.00 40.89 3.28
60 61 2.287069 CGCATTTCGGTGTGTTTACCAA 60.287 45.455 0.00 0.00 40.89 3.67
61 62 1.264557 CGCATTTCGGTGTGTTTACCA 59.735 47.619 0.00 0.00 40.89 3.25
62 63 1.958417 CGCATTTCGGTGTGTTTACC 58.042 50.000 0.00 0.00 37.37 2.85
73 74 3.146913 ATTGGGGGCCGCATTTCG 61.147 61.111 25.00 0.00 38.08 3.46
74 75 2.500646 CATTGGGGGCCGCATTTC 59.499 61.111 25.00 4.37 0.00 2.17
75 76 2.894885 ATCCATTGGGGGCCGCATTT 62.895 55.000 25.00 12.25 37.22 2.32
76 77 3.393743 ATCCATTGGGGGCCGCATT 62.394 57.895 25.00 17.93 37.22 3.56
77 78 3.836481 ATCCATTGGGGGCCGCAT 61.836 61.111 25.00 11.57 37.22 4.73
78 79 4.837797 CATCCATTGGGGGCCGCA 62.838 66.667 20.63 20.63 37.22 5.69
79 80 4.521292 TCATCCATTGGGGGCCGC 62.521 66.667 14.65 14.65 37.22 6.53
80 81 2.127232 GTTCATCCATTGGGGGCCG 61.127 63.158 2.09 0.00 37.22 6.13
81 82 1.762063 GGTTCATCCATTGGGGGCC 60.762 63.158 2.09 0.00 37.22 5.80
82 83 1.762063 GGGTTCATCCATTGGGGGC 60.762 63.158 2.09 0.00 38.11 5.80
83 84 0.397535 CAGGGTTCATCCATTGGGGG 60.398 60.000 2.09 0.00 38.11 5.40
84 85 0.630673 TCAGGGTTCATCCATTGGGG 59.369 55.000 2.09 0.00 38.11 4.96
85 86 1.005805 TGTCAGGGTTCATCCATTGGG 59.994 52.381 2.09 0.00 38.11 4.12
86 87 2.512692 TGTCAGGGTTCATCCATTGG 57.487 50.000 0.00 0.00 38.11 3.16
87 88 4.870123 TTTTGTCAGGGTTCATCCATTG 57.130 40.909 0.00 0.00 38.11 2.82
88 89 5.543405 TCATTTTTGTCAGGGTTCATCCATT 59.457 36.000 0.00 0.00 38.11 3.16
89 90 5.085920 TCATTTTTGTCAGGGTTCATCCAT 58.914 37.500 0.00 0.00 38.11 3.41
90 91 4.478203 TCATTTTTGTCAGGGTTCATCCA 58.522 39.130 0.00 0.00 38.11 3.41
91 92 5.230182 GTTCATTTTTGTCAGGGTTCATCC 58.770 41.667 0.00 0.00 0.00 3.51
92 93 5.011023 AGGTTCATTTTTGTCAGGGTTCATC 59.989 40.000 0.00 0.00 0.00 2.92
93 94 4.901250 AGGTTCATTTTTGTCAGGGTTCAT 59.099 37.500 0.00 0.00 0.00 2.57
94 95 4.285863 AGGTTCATTTTTGTCAGGGTTCA 58.714 39.130 0.00 0.00 0.00 3.18
95 96 4.937201 AGGTTCATTTTTGTCAGGGTTC 57.063 40.909 0.00 0.00 0.00 3.62
96 97 5.692115 AAAGGTTCATTTTTGTCAGGGTT 57.308 34.783 0.00 0.00 0.00 4.11
97 98 5.659079 TGTAAAGGTTCATTTTTGTCAGGGT 59.341 36.000 0.00 0.00 0.00 4.34
98 99 6.155475 TGTAAAGGTTCATTTTTGTCAGGG 57.845 37.500 0.00 0.00 0.00 4.45
99 100 8.661352 ATTTGTAAAGGTTCATTTTTGTCAGG 57.339 30.769 0.00 0.00 0.00 3.86
134 135 8.193438 AGCCAGATAAGCAAAATGAACTATTTC 58.807 33.333 0.00 0.00 38.01 2.17
155 156 3.067601 AGGTTAAACGGTTTTCAAGCCAG 59.932 43.478 11.87 0.00 0.00 4.85
156 157 3.025262 AGGTTAAACGGTTTTCAAGCCA 58.975 40.909 11.87 0.00 0.00 4.75
166 167 8.098912 AGAACTTGATAATGTAGGTTAAACGGT 58.901 33.333 0.00 0.00 0.00 4.83
174 175 7.931948 CCGGAATTAGAACTTGATAATGTAGGT 59.068 37.037 0.00 0.00 0.00 3.08
188 189 7.548427 GGGCTTAATATACTCCGGAATTAGAAC 59.452 40.741 5.23 0.64 0.00 3.01
196 197 3.555117 AGGGGCTTAATATACTCCGGA 57.445 47.619 2.93 2.93 0.00 5.14
199 200 4.367039 TGCAAGGGGCTTAATATACTCC 57.633 45.455 0.00 0.00 45.15 3.85
202 203 7.775093 TGATGATATGCAAGGGGCTTAATATAC 59.225 37.037 0.00 0.00 45.15 1.47
205 206 5.945784 GTGATGATATGCAAGGGGCTTAATA 59.054 40.000 0.00 0.00 45.15 0.98
206 207 4.768968 GTGATGATATGCAAGGGGCTTAAT 59.231 41.667 0.00 0.00 45.15 1.40
207 208 4.144297 GTGATGATATGCAAGGGGCTTAA 58.856 43.478 0.00 0.00 45.15 1.85
208 209 3.138098 TGTGATGATATGCAAGGGGCTTA 59.862 43.478 0.00 0.00 45.15 3.09
209 210 2.091720 TGTGATGATATGCAAGGGGCTT 60.092 45.455 0.00 0.00 45.15 4.35
210 211 1.496001 TGTGATGATATGCAAGGGGCT 59.504 47.619 0.00 0.00 45.15 5.19
211 212 1.985473 TGTGATGATATGCAAGGGGC 58.015 50.000 0.00 0.00 45.13 5.80
212 213 3.067180 GTGTTGTGATGATATGCAAGGGG 59.933 47.826 0.00 0.00 0.00 4.79
213 214 3.695556 TGTGTTGTGATGATATGCAAGGG 59.304 43.478 0.00 0.00 0.00 3.95
214 215 4.968812 TGTGTTGTGATGATATGCAAGG 57.031 40.909 0.00 0.00 0.00 3.61
215 216 7.821595 ATTTTGTGTTGTGATGATATGCAAG 57.178 32.000 0.00 0.00 0.00 4.01
216 217 9.356433 CTTATTTTGTGTTGTGATGATATGCAA 57.644 29.630 0.00 0.00 0.00 4.08
217 218 7.975058 CCTTATTTTGTGTTGTGATGATATGCA 59.025 33.333 0.00 0.00 0.00 3.96
218 219 7.043192 GCCTTATTTTGTGTTGTGATGATATGC 60.043 37.037 0.00 0.00 0.00 3.14
219 220 7.975058 TGCCTTATTTTGTGTTGTGATGATATG 59.025 33.333 0.00 0.00 0.00 1.78
220 221 8.065473 TGCCTTATTTTGTGTTGTGATGATAT 57.935 30.769 0.00 0.00 0.00 1.63
222 223 6.343716 TGCCTTATTTTGTGTTGTGATGAT 57.656 33.333 0.00 0.00 0.00 2.45
223 224 5.781210 TGCCTTATTTTGTGTTGTGATGA 57.219 34.783 0.00 0.00 0.00 2.92
224 225 8.706492 ATATTGCCTTATTTTGTGTTGTGATG 57.294 30.769 0.00 0.00 0.00 3.07
230 237 9.200817 ACATCCTATATTGCCTTATTTTGTGTT 57.799 29.630 0.00 0.00 0.00 3.32
243 250 5.772825 TTCTTTGCCACATCCTATATTGC 57.227 39.130 0.00 0.00 0.00 3.56
248 255 8.275040 AGTATACTTTTCTTTGCCACATCCTAT 58.725 33.333 0.00 0.00 0.00 2.57
249 256 7.552687 CAGTATACTTTTCTTTGCCACATCCTA 59.447 37.037 1.56 0.00 0.00 2.94
254 261 5.240623 CCACAGTATACTTTTCTTTGCCACA 59.759 40.000 1.56 0.00 0.00 4.17
255 262 5.699839 CCACAGTATACTTTTCTTTGCCAC 58.300 41.667 1.56 0.00 0.00 5.01
261 268 6.115448 AGTGAGCCACAGTATACTTTTCTT 57.885 37.500 1.56 0.00 36.74 2.52
263 270 5.351740 GGAAGTGAGCCACAGTATACTTTTC 59.648 44.000 1.56 0.00 36.74 2.29
266 273 4.097418 AGGAAGTGAGCCACAGTATACTT 58.903 43.478 1.56 0.00 36.74 2.24
267 274 3.702045 GAGGAAGTGAGCCACAGTATACT 59.298 47.826 0.00 0.00 36.74 2.12
268 275 3.181474 GGAGGAAGTGAGCCACAGTATAC 60.181 52.174 7.86 0.00 36.74 1.47
270 277 1.834263 GGAGGAAGTGAGCCACAGTAT 59.166 52.381 7.86 0.00 36.74 2.12
272 279 0.472734 AGGAGGAAGTGAGCCACAGT 60.473 55.000 7.86 0.00 36.74 3.55
273 280 1.480137 CTAGGAGGAAGTGAGCCACAG 59.520 57.143 7.86 0.00 36.74 3.66
280 287 2.909504 AGACAGCTAGGAGGAAGTGA 57.090 50.000 0.00 0.00 0.00 3.41
290 297 4.947388 ACACTTCTTCTCCTAGACAGCTAG 59.053 45.833 0.00 0.00 43.08 3.42
291 298 4.702612 CACACTTCTTCTCCTAGACAGCTA 59.297 45.833 0.00 0.00 0.00 3.32
293 300 3.508012 TCACACTTCTTCTCCTAGACAGC 59.492 47.826 0.00 0.00 0.00 4.40
295 302 6.479972 TTTTCACACTTCTTCTCCTAGACA 57.520 37.500 0.00 0.00 0.00 3.41
311 318 7.559897 GGTAAATCATCTATCCCCTTTTTCACA 59.440 37.037 0.00 0.00 0.00 3.58
314 321 9.508642 CTAGGTAAATCATCTATCCCCTTTTTC 57.491 37.037 0.00 0.00 0.00 2.29
315 322 8.448816 CCTAGGTAAATCATCTATCCCCTTTTT 58.551 37.037 0.00 0.00 0.00 1.94
329 336 8.529424 TTATCGTTTCTCTCCTAGGTAAATCA 57.471 34.615 9.08 0.00 0.00 2.57
339 346 7.604657 ATTACCATCTTATCGTTTCTCTCCT 57.395 36.000 0.00 0.00 0.00 3.69
347 354 8.495949 CGCAAAATCTATTACCATCTTATCGTT 58.504 33.333 0.00 0.00 0.00 3.85
349 356 7.952101 CACGCAAAATCTATTACCATCTTATCG 59.048 37.037 0.00 0.00 0.00 2.92
352 359 8.725405 TTCACGCAAAATCTATTACCATCTTA 57.275 30.769 0.00 0.00 0.00 2.10
357 364 6.457663 CGGATTTCACGCAAAATCTATTACCA 60.458 38.462 17.59 0.00 42.63 3.25
360 367 6.482835 CACGGATTTCACGCAAAATCTATTA 58.517 36.000 17.59 0.00 42.63 0.98
361 368 5.331902 CACGGATTTCACGCAAAATCTATT 58.668 37.500 17.59 5.17 42.63 1.73
362 369 4.730613 GCACGGATTTCACGCAAAATCTAT 60.731 41.667 17.59 7.82 42.63 1.98
363 370 3.425625 GCACGGATTTCACGCAAAATCTA 60.426 43.478 17.59 0.00 42.63 1.98
364 371 2.668279 GCACGGATTTCACGCAAAATCT 60.668 45.455 17.59 2.55 42.63 2.40
365 372 1.648681 GCACGGATTTCACGCAAAATC 59.351 47.619 12.40 12.40 42.41 2.17
366 373 1.696988 GCACGGATTTCACGCAAAAT 58.303 45.000 0.00 0.00 34.00 1.82
367 374 0.658829 CGCACGGATTTCACGCAAAA 60.659 50.000 0.00 0.00 34.00 2.44
373 380 4.811761 GCGGCGCACGGATTTCAC 62.812 66.667 29.21 0.00 44.51 3.18
399 406 6.086222 CACAAACACAGCTTATTCACCATAC 58.914 40.000 0.00 0.00 0.00 2.39
404 411 5.276348 GCAAACACAAACACAGCTTATTCAC 60.276 40.000 0.00 0.00 0.00 3.18
405 412 4.803088 GCAAACACAAACACAGCTTATTCA 59.197 37.500 0.00 0.00 0.00 2.57
410 417 1.735369 CGGCAAACACAAACACAGCTT 60.735 47.619 0.00 0.00 0.00 3.74
411 418 0.179140 CGGCAAACACAAACACAGCT 60.179 50.000 0.00 0.00 0.00 4.24
413 420 1.470699 CGCGGCAAACACAAACACAG 61.471 55.000 0.00 0.00 0.00 3.66
417 424 0.040425 ATCTCGCGGCAAACACAAAC 60.040 50.000 6.13 0.00 0.00 2.93
418 425 0.040514 CATCTCGCGGCAAACACAAA 60.041 50.000 6.13 0.00 0.00 2.83
419 426 1.573932 CATCTCGCGGCAAACACAA 59.426 52.632 6.13 0.00 0.00 3.33
420 427 2.965147 GCATCTCGCGGCAAACACA 61.965 57.895 6.13 0.00 0.00 3.72
421 428 2.202349 GCATCTCGCGGCAAACAC 60.202 61.111 6.13 0.00 0.00 3.32
431 438 7.062605 ACAAAATGCAAAAAGATAAGCATCTCG 59.937 33.333 0.00 0.00 46.10 4.04
432 439 8.248117 ACAAAATGCAAAAAGATAAGCATCTC 57.752 30.769 0.00 0.00 46.10 2.75
464 471 9.701098 TCGTCACAATTAGTAAAGTAATGAGTT 57.299 29.630 0.00 0.00 0.00 3.01
465 472 9.701098 TTCGTCACAATTAGTAAAGTAATGAGT 57.299 29.630 0.00 0.00 0.00 3.41
471 478 9.661563 AATGGATTCGTCACAATTAGTAAAGTA 57.338 29.630 0.00 0.00 0.00 2.24
494 505 5.512788 GGTATGCATCTCACGAAAAACAATG 59.487 40.000 0.19 0.00 0.00 2.82
503 514 2.021457 TCGAAGGTATGCATCTCACGA 58.979 47.619 0.19 7.86 0.00 4.35
504 515 2.492019 TCGAAGGTATGCATCTCACG 57.508 50.000 0.19 5.64 0.00 4.35
514 526 1.139058 GTCCCACTGCATCGAAGGTAT 59.861 52.381 0.00 0.00 0.00 2.73
516 528 1.296715 GTCCCACTGCATCGAAGGT 59.703 57.895 0.00 0.00 0.00 3.50
522 534 1.084289 GTTAACGGTCCCACTGCATC 58.916 55.000 0.00 0.00 0.00 3.91
528 540 5.235831 GCTATCTTTATGTTAACGGTCCCAC 59.764 44.000 0.26 0.00 0.00 4.61
531 543 6.759827 TCAAGCTATCTTTATGTTAACGGTCC 59.240 38.462 0.26 0.00 0.00 4.46
532 544 7.766219 TCAAGCTATCTTTATGTTAACGGTC 57.234 36.000 0.26 0.00 0.00 4.79
540 552 9.899226 GTTTTGACTTTCAAGCTATCTTTATGT 57.101 29.630 0.00 0.00 37.70 2.29
576 588 9.081997 TGCGTTTGCCTTTATAAATAAAGATTG 57.918 29.630 19.44 7.92 45.49 2.67
592 604 3.065371 GCTTCTTATATGTGCGTTTGCCT 59.935 43.478 0.00 0.00 41.78 4.75
599 611 6.489675 ACTTGAAATGCTTCTTATATGTGCG 58.510 36.000 0.00 0.00 32.33 5.34
605 617 8.023128 GCACTTTGACTTGAAATGCTTCTTATA 58.977 33.333 0.00 0.00 32.33 0.98
612 624 2.618241 TCGCACTTTGACTTGAAATGCT 59.382 40.909 0.00 0.00 0.00 3.79
617 629 7.064134 ACGATATATTTCGCACTTTGACTTGAA 59.936 33.333 14.43 0.00 42.82 2.69
658 670 6.464222 CCTCGGAGGCTTAATATATTTCACA 58.536 40.000 11.83 0.00 0.00 3.58
679 699 5.122396 ACTTCAATATTTCGAGTTGTGCCTC 59.878 40.000 0.00 0.00 0.00 4.70
681 701 5.122396 AGACTTCAATATTTCGAGTTGTGCC 59.878 40.000 0.00 0.00 0.00 5.01
682 702 6.170675 AGACTTCAATATTTCGAGTTGTGC 57.829 37.500 0.00 0.00 0.00 4.57
764 796 6.037172 GCTGGGTTTCTTTCCTTTTCTTTTTC 59.963 38.462 0.00 0.00 0.00 2.29
766 798 5.045942 TGCTGGGTTTCTTTCCTTTTCTTTT 60.046 36.000 0.00 0.00 0.00 2.27
775 807 5.529060 CAGATATACTGCTGGGTTTCTTTCC 59.471 44.000 0.00 0.00 39.86 3.13
820 852 0.904394 AAACCGCCAATCTGCCCAAT 60.904 50.000 0.00 0.00 0.00 3.16
829 861 1.243902 ATGACGTCAAAACCGCCAAT 58.756 45.000 24.13 0.00 0.00 3.16
858 890 7.101652 ACATCGCCATATATATCGGATATCC 57.898 40.000 13.56 12.14 0.00 2.59
897 929 2.037367 CTCCCACCCAGGTCTCGA 59.963 66.667 0.00 0.00 34.66 4.04
903 935 2.036256 CCTTTGCTCCCACCCAGG 59.964 66.667 0.00 0.00 37.03 4.45
904 936 2.677875 GCCTTTGCTCCCACCCAG 60.678 66.667 0.00 0.00 33.53 4.45
905 937 2.384933 AATGCCTTTGCTCCCACCCA 62.385 55.000 0.00 0.00 38.71 4.51
907 939 0.686789 AAAATGCCTTTGCTCCCACC 59.313 50.000 0.00 0.00 38.71 4.61
933 965 1.893801 TGGACGGGTCTTCTTCTTCTC 59.106 52.381 0.00 0.00 0.00 2.87
960 993 2.456443 GGGGGATGGGGAGAGAAGC 61.456 68.421 0.00 0.00 0.00 3.86
961 994 1.004758 TGGGGGATGGGGAGAGAAG 59.995 63.158 0.00 0.00 0.00 2.85
962 995 1.307866 GTGGGGGATGGGGAGAGAA 60.308 63.158 0.00 0.00 0.00 2.87
963 996 2.372688 GTGGGGGATGGGGAGAGA 59.627 66.667 0.00 0.00 0.00 3.10
1590 1653 4.742201 TCCCAGACGAAGCTGCGC 62.742 66.667 15.86 7.26 34.56 6.09
1618 1681 3.682292 ATTCGGAGCGGTTGAGGCC 62.682 63.158 0.00 0.00 0.00 5.19
1620 1683 1.369091 CCAATTCGGAGCGGTTGAGG 61.369 60.000 0.00 0.00 36.56 3.86
1696 1759 2.635443 CCAAGGCCGCGGTTTTGAT 61.635 57.895 31.76 12.24 0.00 2.57
1727 1790 1.446792 CAGACGCGCATGAACTCCT 60.447 57.895 5.73 0.00 0.00 3.69
1771 1834 2.740055 CACCTCCTGCGACAGTGC 60.740 66.667 6.19 0.00 0.00 4.40
1794 1857 0.951040 CCTTCACAGTCTGTTCCGCC 60.951 60.000 1.67 0.00 0.00 6.13
1841 1904 0.674895 GATACCCCAGATGATGCCGC 60.675 60.000 0.00 0.00 0.00 6.53
1863 1926 1.754226 AGCTCGTGAATCTCCTTCTCC 59.246 52.381 0.00 0.00 34.75 3.71
1889 1952 1.925455 CACACCCCATCACCCCTCT 60.925 63.158 0.00 0.00 0.00 3.69
1895 1958 1.102978 GTATTGGCACACCCCATCAC 58.897 55.000 0.00 0.00 39.29 3.06
1917 1980 2.278857 AGCCGCTGAAGATACGCG 60.279 61.111 3.53 3.53 45.86 6.01
1986 2049 1.272147 ACCATCTGAACAAGCTTCCCC 60.272 52.381 0.00 0.00 0.00 4.81
2003 2066 7.159372 GTCCTTAACTAAATCAGAAGACACCA 58.841 38.462 0.00 0.00 0.00 4.17
2074 2137 1.407936 TCTGCATCTCTAGGCTCCAC 58.592 55.000 0.00 0.00 32.35 4.02
2117 2180 4.467795 CACCCTCTAACTCAGATTCCTTCA 59.532 45.833 0.00 0.00 31.13 3.02
2157 2220 0.108585 GCCCCGATTCATCCAAGCTA 59.891 55.000 0.00 0.00 0.00 3.32
2236 2299 2.353889 CTGATTCCTCCAAGATGTTGCG 59.646 50.000 0.00 0.00 31.64 4.85
2289 2352 3.330405 TCACATCCCCAGACTCATTCAAA 59.670 43.478 0.00 0.00 0.00 2.69
2319 2382 2.842496 TGCTGTCTCAGATTCCTCCAAT 59.158 45.455 0.66 0.00 32.44 3.16
2322 2385 1.473080 GCTGCTGTCTCAGATTCCTCC 60.473 57.143 0.66 0.00 36.19 4.30
2331 2394 0.689055 AATCCACAGCTGCTGTCTCA 59.311 50.000 30.96 18.04 43.43 3.27
2352 2415 4.008330 ACTCATTCAAGTCATTGCTCCTG 58.992 43.478 0.00 0.00 36.30 3.86
2354 2417 4.094590 CAGACTCATTCAAGTCATTGCTCC 59.905 45.833 6.79 0.00 46.65 4.70
2528 2591 1.487976 CAGCCACCACTGATGTATCCT 59.512 52.381 0.00 0.00 40.25 3.24
2547 2610 1.381599 GCCCTTTGCATCCCCATCA 60.382 57.895 0.00 0.00 40.77 3.07
2573 2636 2.482664 CCTGACTCCATCTCAACATCCG 60.483 54.545 0.00 0.00 0.00 4.18
2630 2693 5.540337 TCCTCATCCATCACCTTAGATGTAC 59.460 44.000 0.00 0.00 43.00 2.90
2732 2795 0.475475 TGCATCCTCATCCATCACCC 59.525 55.000 0.00 0.00 0.00 4.61
2813 2876 5.071653 TCATCCATAACCTTCGATGAATCCA 59.928 40.000 0.00 0.00 38.47 3.41
2916 2979 4.853468 TGCATCCTCATTAACCACCTTA 57.147 40.909 0.00 0.00 0.00 2.69
2949 3012 4.941263 CCTAACTCCAATTCGACATCCAAA 59.059 41.667 0.00 0.00 0.00 3.28
2969 3032 2.290514 GCATTAGCATCTGCATCCCCTA 60.291 50.000 4.79 0.00 45.16 3.53
3222 3285 2.316586 ATCCCCATCCGCCACCTTT 61.317 57.895 0.00 0.00 0.00 3.11
3236 3299 1.133668 AGCTCATGCCCTTTACATCCC 60.134 52.381 0.00 0.00 40.80 3.85
3261 3324 0.462789 CATCCCCTGCCTTTGATTGC 59.537 55.000 0.00 0.00 0.00 3.56
3320 3383 1.399440 CCTCACCATTCACAGCATTCG 59.601 52.381 0.00 0.00 0.00 3.34
3325 3388 2.288395 CCAAAACCTCACCATTCACAGC 60.288 50.000 0.00 0.00 0.00 4.40
3455 3518 1.074926 TCCTCATCCTCCTCTGGCC 60.075 63.158 0.00 0.00 0.00 5.36
3705 3771 1.571457 TCAAACTCCACCCCTGGAAAA 59.429 47.619 0.00 0.00 46.63 2.29
3940 4006 4.516321 GCCAAAGAAAAATGAATTGCCAGT 59.484 37.500 0.00 0.00 0.00 4.00
4009 4075 3.384146 TGTTGTGTTTGCATCTGGTCATT 59.616 39.130 0.00 0.00 0.00 2.57
4164 4230 5.948588 TGAATCTCTCTCTCTTTCTGTTCG 58.051 41.667 0.00 0.00 0.00 3.95
4263 4329 0.473755 TCTCTTGCTCAAACCTGGCA 59.526 50.000 0.00 0.00 0.00 4.92
4375 4441 6.946340 TCCTGTACTCATTGAAAGAAGCATA 58.054 36.000 0.00 0.00 0.00 3.14
4424 4490 4.690748 CGCCATTAGGAACATCACGATAAT 59.309 41.667 0.00 0.00 36.89 1.28
4567 4645 3.765511 TCCCAATCATCAGGCTTTGAAAG 59.234 43.478 0.00 0.00 39.77 2.62
4741 4819 6.460781 TCAATTTAATCACAGTACACGGACT 58.539 36.000 0.00 0.00 0.00 3.85
4764 4842 8.751242 AGAAACTAGTTTATCTCCTAACCACTC 58.249 37.037 20.58 3.05 32.11 3.51
4808 4887 5.046520 AGGACAGTCTACTAACCACCATTTC 60.047 44.000 0.00 0.00 0.00 2.17
5024 5105 8.846211 CAAAGAAAATAAGGTGAGTTAAGTGGA 58.154 33.333 0.00 0.00 0.00 4.02
5170 5321 6.931840 TGTGTGTGTGTGTGTGTTATATATGT 59.068 34.615 0.00 0.00 0.00 2.29
5171 5322 7.095439 TGTGTGTGTGTGTGTGTGTTATATATG 60.095 37.037 0.00 0.00 0.00 1.78
5172 5323 6.931840 TGTGTGTGTGTGTGTGTGTTATATAT 59.068 34.615 0.00 0.00 0.00 0.86
5173 5324 6.201234 GTGTGTGTGTGTGTGTGTGTTATATA 59.799 38.462 0.00 0.00 0.00 0.86
5313 5480 6.262944 ACAAAGCATGTTCTGATAACAAGACA 59.737 34.615 0.00 0.00 40.06 3.41
5315 5482 6.882610 ACAAAGCATGTTCTGATAACAAGA 57.117 33.333 0.00 0.00 40.06 3.02
5355 5522 9.511272 AGTACAGACATATATACCGTAACATGA 57.489 33.333 0.00 0.00 0.00 3.07
5444 5634 0.320683 CCCATGTCTCGCTGTTGACA 60.321 55.000 0.00 0.00 45.56 3.58
5538 5728 3.588955 GCCCTTGGATGACAAAACATTC 58.411 45.455 0.00 0.00 38.91 2.67


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

AutoCloner maintained by Alex Coulton.