Multiple sequence alignment - TraesCS1B01G175200

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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 TraesCS1B01G175200 chr1B 100.000 4135 0 0 1 4135 315833434 315837568 0.000000e+00 7637
1 TraesCS1B01G175200 chr1B 99.434 3531 14 4 608 4135 315614976 315618503 0.000000e+00 6405
2 TraesCS1B01G175200 chr1B 96.817 377 12 0 1 377 316036306 316036682 7.540000e-177 630
3 TraesCS1B01G175200 chr1B 89.710 379 15 17 398 776 659968501 659968855 2.910000e-126 462
4 TraesCS1B01G175200 chr1B 97.717 219 5 0 398 616 315614291 315614509 1.090000e-100 377
5 TraesCS1B01G175200 chr1B 92.810 153 10 1 624 776 120492155 120492306 1.940000e-53 220
6 TraesCS1B01G175200 chr1B 88.144 194 11 2 428 609 651903131 651903324 1.940000e-53 220
7 TraesCS1B01G175200 chr1B 90.196 153 14 1 624 776 284063347 284063498 9.070000e-47 198
8 TraesCS1B01G175200 chr1B 92.553 94 7 0 683 776 51564254 51564161 7.210000e-28 135
9 TraesCS1B01G175200 chr2A 96.000 375 15 0 1 375 689738843 689738469 9.830000e-171 610
10 TraesCS1B01G175200 chr2A 89.175 194 9 3 428 609 771859020 771859213 8.940000e-57 231
11 TraesCS1B01G175200 chr3A 95.491 377 17 0 1 377 678670579 678670955 1.640000e-168 603
12 TraesCS1B01G175200 chr3A 88.614 202 11 1 420 609 41525604 41525403 6.910000e-58 235
13 TraesCS1B01G175200 chr3A 93.902 82 4 1 527 608 58039716 58039636 5.610000e-24 122
14 TraesCS1B01G175200 chr3A 79.310 145 26 4 3993 4135 629219509 629219651 9.460000e-17 99
15 TraesCS1B01G175200 chr7A 94.737 380 19 1 1 380 594967458 594967080 1.280000e-164 590
16 TraesCS1B01G175200 chr6D 94.695 377 20 0 1 377 374798532 374798908 1.660000e-163 586
17 TraesCS1B01G175200 chr5A 94.211 380 22 0 1 380 672151810 672151431 7.710000e-162 580
18 TraesCS1B01G175200 chr7D 93.947 380 23 0 1 380 373124488 373124109 3.580000e-160 575
19 TraesCS1B01G175200 chr7D 93.684 380 24 0 1 380 487927117 487926738 1.670000e-158 569
20 TraesCS1B01G175200 chr4D 93.899 377 23 0 1 377 479393535 479393911 1.670000e-158 569
21 TraesCS1B01G175200 chr5B 90.289 381 23 8 398 776 455274636 455274268 1.730000e-133 486
22 TraesCS1B01G175200 chr4B 88.918 379 18 17 398 776 238157730 238157376 2.930000e-121 446
23 TraesCS1B01G175200 chr4B 88.462 104 8 2 675 776 518655559 518655660 5.610000e-24 122
24 TraesCS1B01G175200 chr7B 97.581 124 3 0 653 776 700869266 700869143 3.240000e-51 213
25 TraesCS1B01G175200 chr7B 86.538 104 12 1 675 776 406682407 406682304 3.380000e-21 113
26 TraesCS1B01G175200 chr4A 91.558 154 12 1 624 776 657089277 657089124 1.160000e-50 211
27 TraesCS1B01G175200 chr4A 85.876 177 13 7 2144 2308 467259343 467259519 1.180000e-40 178
28 TraesCS1B01G175200 chr3D 90.090 111 6 3 499 609 604404864 604404969 5.570000e-29 139
29 TraesCS1B01G175200 chr2B 88.235 102 10 1 677 776 758565363 758565262 2.020000e-23 121
30 TraesCS1B01G175200 chr6A 83.929 112 12 2 2523 2628 480803724 480803613 7.310000e-18 102


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 TraesCS1B01G175200 chr1B 315833434 315837568 4134 False 7637 7637 100.0000 1 4135 1 chr1B.!!$F3 4134
1 TraesCS1B01G175200 chr1B 315614291 315618503 4212 False 3391 6405 98.5755 398 4135 2 chr1B.!!$F7 3737

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
245 246 0.033796 AAGATGCCAGGTCCATGTGG 60.034 55.000 0.00 0.0 36.85 4.17 F
333 334 0.034477 CCGAACACTAAATGGCCCCT 60.034 55.000 0.00 0.0 0.00 4.79 F
345 346 0.551377 TGGCCCCTCCAACCAGAATA 60.551 55.000 0.00 0.0 43.21 1.75 F
346 347 0.629058 GGCCCCTCCAACCAGAATAA 59.371 55.000 0.00 0.0 34.01 1.40 F
373 374 0.938168 GTCGTCAAGACCACGGACAC 60.938 60.000 0.00 0.0 43.95 3.67 F
394 395 1.414897 CGAGCGCGTTGTAAGGAAC 59.585 57.895 8.43 0.0 0.00 3.62 F
2518 2997 2.017049 ACAGCTGACAGTTTTGTGTCC 58.983 47.619 23.35 0.0 45.42 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1976 2455 3.315142 GAGCGATCACTGCACCCCA 62.315 63.158 0.00 0.00 33.85 4.96 R
2486 2965 4.145876 TGTCAGCTGTAAAGCAATTTCG 57.854 40.909 14.67 0.00 37.25 3.46 R
2518 2997 0.880278 ACCGGATTGCCAATCGATCG 60.880 55.000 9.46 9.36 38.82 3.69 R
2596 3075 0.392706 ACATGCCACTTCTCACACGA 59.607 50.000 0.00 0.00 0.00 4.35 R
2807 3286 0.780002 GCAAATGTCGCAAGCACAAG 59.220 50.000 0.00 0.00 32.67 3.16 R
2848 3327 5.616270 TGACAATACTTGCCTCACTGTAAA 58.384 37.500 0.00 0.00 0.00 2.01 R
4061 4540 0.033366 GTTCGGGCCACAAAAATGCT 59.967 50.000 4.39 0.00 0.00 3.79 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 7.625828 AAAAATCAGCCACAGTAATACTACC 57.374 36.000 0.00 0.00 0.00 3.18
25 26 6.561519 AAATCAGCCACAGTAATACTACCT 57.438 37.500 0.00 0.00 0.00 3.08
26 27 6.561519 AATCAGCCACAGTAATACTACCTT 57.438 37.500 0.00 0.00 0.00 3.50
27 28 5.593679 TCAGCCACAGTAATACTACCTTC 57.406 43.478 0.00 0.00 0.00 3.46
28 29 5.020795 TCAGCCACAGTAATACTACCTTCA 58.979 41.667 0.00 0.00 0.00 3.02
29 30 5.482526 TCAGCCACAGTAATACTACCTTCAA 59.517 40.000 0.00 0.00 0.00 2.69
30 31 5.812642 CAGCCACAGTAATACTACCTTCAAG 59.187 44.000 0.00 0.00 0.00 3.02
31 32 5.104900 AGCCACAGTAATACTACCTTCAAGG 60.105 44.000 0.22 0.22 42.49 3.61
32 33 5.671493 CCACAGTAATACTACCTTCAAGGG 58.329 45.833 8.75 0.00 40.58 3.95
33 34 5.424252 CCACAGTAATACTACCTTCAAGGGA 59.576 44.000 8.75 0.00 40.58 4.20
43 44 6.163135 CTACCTTCAAGGGAGTAATACCAG 57.837 45.833 7.66 0.00 41.66 4.00
44 45 3.780850 ACCTTCAAGGGAGTAATACCAGG 59.219 47.826 8.75 0.00 40.58 4.45
45 46 3.433740 CCTTCAAGGGAGTAATACCAGGC 60.434 52.174 0.00 0.00 0.00 4.85
46 47 2.124411 TCAAGGGAGTAATACCAGGCC 58.876 52.381 0.00 0.00 0.00 5.19
47 48 1.143073 CAAGGGAGTAATACCAGGCCC 59.857 57.143 0.00 0.00 35.79 5.80
48 49 0.345502 AGGGAGTAATACCAGGCCCA 59.654 55.000 0.00 0.00 38.04 5.36
49 50 0.765510 GGGAGTAATACCAGGCCCAG 59.234 60.000 0.00 0.00 35.63 4.45
50 51 1.694693 GGGAGTAATACCAGGCCCAGA 60.695 57.143 0.00 0.00 35.63 3.86
51 52 1.694696 GGAGTAATACCAGGCCCAGAG 59.305 57.143 0.00 0.00 0.00 3.35
52 53 1.694696 GAGTAATACCAGGCCCAGAGG 59.305 57.143 0.00 0.00 0.00 3.69
72 73 3.826754 CGCTGCACGGGCTCTCTA 61.827 66.667 12.74 0.00 41.91 2.43
73 74 2.818132 GCTGCACGGGCTCTCTAT 59.182 61.111 12.74 0.00 41.91 1.98
74 75 1.144936 GCTGCACGGGCTCTCTATT 59.855 57.895 12.74 0.00 41.91 1.73
75 76 0.389391 GCTGCACGGGCTCTCTATTA 59.611 55.000 12.74 0.00 41.91 0.98
76 77 1.870167 GCTGCACGGGCTCTCTATTAC 60.870 57.143 12.74 0.00 41.91 1.89
77 78 1.683917 CTGCACGGGCTCTCTATTACT 59.316 52.381 12.74 0.00 41.91 2.24
78 79 2.885266 CTGCACGGGCTCTCTATTACTA 59.115 50.000 12.74 0.00 41.91 1.82
79 80 2.885266 TGCACGGGCTCTCTATTACTAG 59.115 50.000 12.74 0.00 41.91 2.57
80 81 3.147629 GCACGGGCTCTCTATTACTAGA 58.852 50.000 0.00 0.00 36.96 2.43
81 82 5.282719 TGCACGGGCTCTCTATTACTAGAG 61.283 50.000 12.74 10.19 43.76 2.43
93 94 8.393671 CTCTATTACTAGAGGTTGTATTCGGT 57.606 38.462 8.85 0.00 44.95 4.69
94 95 8.757982 TCTATTACTAGAGGTTGTATTCGGTT 57.242 34.615 0.00 0.00 30.36 4.44
95 96 8.844244 TCTATTACTAGAGGTTGTATTCGGTTC 58.156 37.037 0.00 0.00 30.36 3.62
96 97 7.657023 ATTACTAGAGGTTGTATTCGGTTCT 57.343 36.000 0.00 0.00 0.00 3.01
97 98 5.997384 ACTAGAGGTTGTATTCGGTTCTT 57.003 39.130 0.00 0.00 0.00 2.52
98 99 5.963594 ACTAGAGGTTGTATTCGGTTCTTC 58.036 41.667 0.00 0.00 0.00 2.87
99 100 4.203654 AGAGGTTGTATTCGGTTCTTCC 57.796 45.455 0.00 0.00 0.00 3.46
110 111 1.145803 GGTTCTTCCGACAACTTCCG 58.854 55.000 0.00 0.00 0.00 4.30
111 112 1.269936 GGTTCTTCCGACAACTTCCGA 60.270 52.381 0.00 0.00 0.00 4.55
112 113 2.476821 GTTCTTCCGACAACTTCCGAA 58.523 47.619 0.00 0.00 0.00 4.30
113 114 2.433868 TCTTCCGACAACTTCCGAAG 57.566 50.000 6.59 6.59 39.59 3.79
114 115 0.790814 CTTCCGACAACTTCCGAAGC 59.209 55.000 8.11 0.00 34.23 3.86
115 116 0.942410 TTCCGACAACTTCCGAAGCG 60.942 55.000 8.11 3.77 0.00 4.68
116 117 1.372499 CCGACAACTTCCGAAGCGA 60.372 57.895 8.11 0.00 0.00 4.93
117 118 0.942410 CCGACAACTTCCGAAGCGAA 60.942 55.000 8.11 0.00 0.00 4.70
118 119 0.856641 CGACAACTTCCGAAGCGAAA 59.143 50.000 8.11 0.00 0.00 3.46
119 120 1.259507 CGACAACTTCCGAAGCGAAAA 59.740 47.619 8.11 0.00 0.00 2.29
120 121 2.659291 CGACAACTTCCGAAGCGAAAAG 60.659 50.000 8.11 0.00 0.00 2.27
121 122 2.285977 ACAACTTCCGAAGCGAAAAGT 58.714 42.857 8.11 0.00 35.44 2.66
122 123 2.681344 ACAACTTCCGAAGCGAAAAGTT 59.319 40.909 8.11 11.67 40.41 2.66
123 124 3.872771 ACAACTTCCGAAGCGAAAAGTTA 59.127 39.130 8.11 0.00 39.04 2.24
124 125 4.333372 ACAACTTCCGAAGCGAAAAGTTAA 59.667 37.500 8.11 0.00 39.04 2.01
125 126 4.463515 ACTTCCGAAGCGAAAAGTTAAC 57.536 40.909 8.11 0.00 32.12 2.01
126 127 3.249320 ACTTCCGAAGCGAAAAGTTAACC 59.751 43.478 8.11 0.00 32.12 2.85
127 128 3.116079 TCCGAAGCGAAAAGTTAACCT 57.884 42.857 0.88 0.00 0.00 3.50
128 129 3.469739 TCCGAAGCGAAAAGTTAACCTT 58.530 40.909 0.88 0.00 33.79 3.50
129 130 3.495753 TCCGAAGCGAAAAGTTAACCTTC 59.504 43.478 0.88 6.04 31.27 3.46
130 131 3.466836 CGAAGCGAAAAGTTAACCTTCG 58.533 45.455 25.17 25.17 43.38 3.79
131 132 4.720530 GAAGCGAAAAGTTAACCTTCGA 57.279 40.909 30.06 0.00 43.53 3.71
132 133 4.452447 GAAGCGAAAAGTTAACCTTCGAC 58.548 43.478 30.06 23.24 43.53 4.20
133 134 3.460103 AGCGAAAAGTTAACCTTCGACA 58.540 40.909 30.06 0.00 43.53 4.35
134 135 4.062991 AGCGAAAAGTTAACCTTCGACAT 58.937 39.130 30.06 18.39 43.53 3.06
135 136 4.151867 AGCGAAAAGTTAACCTTCGACATC 59.848 41.667 30.06 18.57 43.53 3.06
136 137 4.625135 CGAAAAGTTAACCTTCGACATCG 58.375 43.478 25.24 12.08 43.53 3.84
137 138 4.392216 GAAAAGTTAACCTTCGACATCGC 58.608 43.478 0.88 0.00 39.60 4.58
138 139 3.314541 AAGTTAACCTTCGACATCGCT 57.685 42.857 0.88 0.00 39.60 4.93
139 140 2.877335 AGTTAACCTTCGACATCGCTC 58.123 47.619 0.88 0.00 39.60 5.03
140 141 1.925185 GTTAACCTTCGACATCGCTCC 59.075 52.381 0.00 0.00 39.60 4.70
141 142 1.179152 TAACCTTCGACATCGCTCCA 58.821 50.000 0.00 0.00 39.60 3.86
142 143 0.537188 AACCTTCGACATCGCTCCAT 59.463 50.000 0.00 0.00 39.60 3.41
143 144 0.537188 ACCTTCGACATCGCTCCATT 59.463 50.000 0.00 0.00 39.60 3.16
144 145 1.212616 CCTTCGACATCGCTCCATTC 58.787 55.000 0.00 0.00 39.60 2.67
145 146 1.212616 CTTCGACATCGCTCCATTCC 58.787 55.000 0.00 0.00 39.60 3.01
146 147 0.527600 TTCGACATCGCTCCATTCCG 60.528 55.000 0.00 0.00 39.60 4.30
147 148 1.065764 CGACATCGCTCCATTCCGA 59.934 57.895 0.00 0.00 37.91 4.55
148 149 0.527600 CGACATCGCTCCATTCCGAA 60.528 55.000 0.00 0.00 37.00 4.30
149 150 1.212616 GACATCGCTCCATTCCGAAG 58.787 55.000 0.00 0.00 37.00 3.79
150 151 0.537188 ACATCGCTCCATTCCGAAGT 59.463 50.000 0.00 0.00 37.00 3.01
151 152 0.933097 CATCGCTCCATTCCGAAGTG 59.067 55.000 0.00 0.00 37.00 3.16
152 153 0.179073 ATCGCTCCATTCCGAAGTGG 60.179 55.000 0.00 4.18 37.00 4.00
153 154 2.464459 CGCTCCATTCCGAAGTGGC 61.464 63.158 5.26 0.00 37.80 5.01
154 155 1.078143 GCTCCATTCCGAAGTGGCT 60.078 57.895 5.26 0.00 37.80 4.75
155 156 0.178068 GCTCCATTCCGAAGTGGCTA 59.822 55.000 5.26 0.00 37.80 3.93
156 157 1.202698 GCTCCATTCCGAAGTGGCTAT 60.203 52.381 5.26 0.00 37.80 2.97
157 158 2.760374 CTCCATTCCGAAGTGGCTATC 58.240 52.381 5.26 0.00 37.80 2.08
158 159 2.103094 CTCCATTCCGAAGTGGCTATCA 59.897 50.000 5.26 0.00 37.80 2.15
159 160 2.503765 TCCATTCCGAAGTGGCTATCAA 59.496 45.455 5.26 0.00 37.80 2.57
160 161 2.874701 CCATTCCGAAGTGGCTATCAAG 59.125 50.000 0.00 0.00 37.80 3.02
195 196 2.520686 CGGCTTTCGCTCGTTTTAAT 57.479 45.000 0.00 0.00 36.09 1.40
196 197 2.166007 CGGCTTTCGCTCGTTTTAATG 58.834 47.619 0.00 0.00 36.09 1.90
197 198 1.911464 GGCTTTCGCTCGTTTTAATGC 59.089 47.619 0.00 0.00 36.09 3.56
198 199 2.580589 GCTTTCGCTCGTTTTAATGCA 58.419 42.857 0.00 0.00 0.00 3.96
199 200 2.589841 GCTTTCGCTCGTTTTAATGCAG 59.410 45.455 0.00 0.00 0.00 4.41
200 201 3.810373 CTTTCGCTCGTTTTAATGCAGT 58.190 40.909 0.00 0.00 0.00 4.40
201 202 4.668177 GCTTTCGCTCGTTTTAATGCAGTA 60.668 41.667 0.00 0.00 0.00 2.74
202 203 3.984018 TCGCTCGTTTTAATGCAGTAC 57.016 42.857 0.00 0.00 0.00 2.73
203 204 2.669434 TCGCTCGTTTTAATGCAGTACC 59.331 45.455 0.00 0.00 0.00 3.34
204 205 2.534150 CGCTCGTTTTAATGCAGTACCG 60.534 50.000 0.00 0.00 0.00 4.02
205 206 2.786700 GCTCGTTTTAATGCAGTACCGC 60.787 50.000 0.00 0.00 0.00 5.68
213 214 3.778619 TGCAGTACCGCATTATGCT 57.221 47.368 15.54 0.00 42.25 3.79
214 215 2.036958 TGCAGTACCGCATTATGCTT 57.963 45.000 15.54 4.62 42.25 3.91
215 216 1.939934 TGCAGTACCGCATTATGCTTC 59.060 47.619 15.54 3.14 42.25 3.86
216 217 2.213499 GCAGTACCGCATTATGCTTCT 58.787 47.619 15.54 5.27 42.25 2.85
217 218 2.221981 GCAGTACCGCATTATGCTTCTC 59.778 50.000 15.54 3.81 42.25 2.87
218 219 3.722147 CAGTACCGCATTATGCTTCTCT 58.278 45.455 15.54 5.92 42.25 3.10
219 220 3.738282 CAGTACCGCATTATGCTTCTCTC 59.262 47.826 15.54 1.51 42.25 3.20
220 221 2.988010 ACCGCATTATGCTTCTCTCA 57.012 45.000 15.54 0.00 42.25 3.27
221 222 3.266510 ACCGCATTATGCTTCTCTCAA 57.733 42.857 15.54 0.00 42.25 3.02
222 223 3.201290 ACCGCATTATGCTTCTCTCAAG 58.799 45.455 15.54 0.00 42.25 3.02
223 224 2.032204 CCGCATTATGCTTCTCTCAAGC 60.032 50.000 15.54 0.00 42.25 4.01
224 225 2.871022 CGCATTATGCTTCTCTCAAGCT 59.129 45.455 15.54 0.00 42.25 3.74
225 226 3.311871 CGCATTATGCTTCTCTCAAGCTT 59.688 43.478 15.54 0.00 42.25 3.74
226 227 4.509230 CGCATTATGCTTCTCTCAAGCTTA 59.491 41.667 15.54 3.35 42.25 3.09
227 228 5.007039 CGCATTATGCTTCTCTCAAGCTTAA 59.993 40.000 15.54 13.80 42.25 1.85
228 229 6.428799 GCATTATGCTTCTCTCAAGCTTAAG 58.571 40.000 10.27 0.00 42.31 1.85
229 230 6.259608 GCATTATGCTTCTCTCAAGCTTAAGA 59.740 38.462 10.27 4.65 42.31 2.10
230 231 7.041235 GCATTATGCTTCTCTCAAGCTTAAGAT 60.041 37.037 10.27 0.00 42.31 2.40
231 232 7.783090 TTATGCTTCTCTCAAGCTTAAGATG 57.217 36.000 6.67 6.92 43.38 2.90
232 233 3.937706 TGCTTCTCTCAAGCTTAAGATGC 59.062 43.478 23.02 23.02 43.38 3.91
233 234 3.312146 GCTTCTCTCAAGCTTAAGATGCC 59.688 47.826 21.08 11.15 40.01 4.40
234 235 4.511527 CTTCTCTCAAGCTTAAGATGCCA 58.488 43.478 6.67 0.00 0.00 4.92
235 236 4.134379 TCTCTCAAGCTTAAGATGCCAG 57.866 45.455 6.67 4.05 0.00 4.85
236 237 3.118482 TCTCTCAAGCTTAAGATGCCAGG 60.118 47.826 6.67 0.00 0.00 4.45
237 238 2.573462 TCTCAAGCTTAAGATGCCAGGT 59.427 45.455 6.67 0.00 0.00 4.00
238 239 2.941720 CTCAAGCTTAAGATGCCAGGTC 59.058 50.000 6.67 0.00 0.00 3.85
239 240 2.019984 CAAGCTTAAGATGCCAGGTCC 58.980 52.381 6.67 0.00 0.00 4.46
240 241 1.289160 AGCTTAAGATGCCAGGTCCA 58.711 50.000 6.67 0.00 0.00 4.02
241 242 1.849039 AGCTTAAGATGCCAGGTCCAT 59.151 47.619 6.67 0.00 0.00 3.41
242 243 1.952296 GCTTAAGATGCCAGGTCCATG 59.048 52.381 6.67 0.00 0.00 3.66
243 244 2.684927 GCTTAAGATGCCAGGTCCATGT 60.685 50.000 6.67 0.00 0.00 3.21
244 245 2.715749 TAAGATGCCAGGTCCATGTG 57.284 50.000 0.00 0.00 0.00 3.21
245 246 0.033796 AAGATGCCAGGTCCATGTGG 60.034 55.000 0.00 0.00 36.85 4.17
249 250 4.247781 CCAGGTCCATGTGGCATC 57.752 61.111 0.00 0.00 34.44 3.91
250 251 1.303948 CCAGGTCCATGTGGCATCA 59.696 57.895 0.00 0.00 34.44 3.07
251 252 0.106369 CCAGGTCCATGTGGCATCAT 60.106 55.000 0.00 0.00 34.44 2.45
252 253 1.315690 CAGGTCCATGTGGCATCATC 58.684 55.000 0.00 0.00 34.44 2.92
253 254 0.921166 AGGTCCATGTGGCATCATCA 59.079 50.000 0.00 0.00 34.44 3.07
254 255 1.027357 GGTCCATGTGGCATCATCAC 58.973 55.000 0.00 0.00 35.82 3.06
255 256 1.027357 GTCCATGTGGCATCATCACC 58.973 55.000 0.00 0.00 34.46 4.02
256 257 0.624785 TCCATGTGGCATCATCACCA 59.375 50.000 0.00 0.00 34.46 4.17
257 258 1.215924 TCCATGTGGCATCATCACCAT 59.784 47.619 0.00 0.00 38.46 3.55
258 259 2.036387 CCATGTGGCATCATCACCATT 58.964 47.619 0.00 0.00 38.46 3.16
259 260 3.117587 TCCATGTGGCATCATCACCATTA 60.118 43.478 0.00 0.00 38.46 1.90
260 261 3.254903 CCATGTGGCATCATCACCATTAG 59.745 47.826 0.00 0.00 38.46 1.73
261 262 2.300433 TGTGGCATCATCACCATTAGC 58.700 47.619 0.00 0.00 38.46 3.09
262 263 1.265095 GTGGCATCATCACCATTAGCG 59.735 52.381 0.00 0.00 38.46 4.26
263 264 0.877071 GGCATCATCACCATTAGCGG 59.123 55.000 0.00 0.00 0.00 5.52
264 265 1.543208 GGCATCATCACCATTAGCGGA 60.543 52.381 0.00 0.00 0.00 5.54
265 266 2.221169 GCATCATCACCATTAGCGGAA 58.779 47.619 0.00 0.00 0.00 4.30
266 267 2.618241 GCATCATCACCATTAGCGGAAA 59.382 45.455 0.00 0.00 0.00 3.13
267 268 3.548818 GCATCATCACCATTAGCGGAAAC 60.549 47.826 0.00 0.00 0.00 2.78
286 287 2.856091 CGCTGAACGTTCCTTACAAG 57.144 50.000 24.78 15.08 36.87 3.16
287 288 1.136336 CGCTGAACGTTCCTTACAAGC 60.136 52.381 24.78 22.20 36.87 4.01
288 289 1.136336 GCTGAACGTTCCTTACAAGCG 60.136 52.381 24.78 4.09 0.00 4.68
289 290 1.459592 CTGAACGTTCCTTACAAGCGG 59.540 52.381 24.78 0.00 0.00 5.52
290 291 1.068895 TGAACGTTCCTTACAAGCGGA 59.931 47.619 24.78 0.00 0.00 5.54
291 292 2.137523 GAACGTTCCTTACAAGCGGAA 58.862 47.619 17.68 0.00 36.98 4.30
292 293 1.792006 ACGTTCCTTACAAGCGGAAG 58.208 50.000 0.00 0.00 39.80 3.46
293 294 1.342174 ACGTTCCTTACAAGCGGAAGA 59.658 47.619 0.00 0.00 39.80 2.87
294 295 2.224113 ACGTTCCTTACAAGCGGAAGAA 60.224 45.455 0.00 0.00 39.80 2.52
295 296 3.000727 CGTTCCTTACAAGCGGAAGAAT 58.999 45.455 0.00 0.00 39.80 2.40
296 297 3.181520 CGTTCCTTACAAGCGGAAGAATG 60.182 47.826 0.00 0.00 39.80 2.67
297 298 3.695830 TCCTTACAAGCGGAAGAATGT 57.304 42.857 0.00 0.00 35.90 2.71
298 299 3.334691 TCCTTACAAGCGGAAGAATGTG 58.665 45.455 0.00 0.00 34.14 3.21
299 300 2.159517 CCTTACAAGCGGAAGAATGTGC 60.160 50.000 0.00 0.00 34.14 4.57
300 301 1.075542 TACAAGCGGAAGAATGTGCG 58.924 50.000 0.00 0.00 34.14 5.34
301 302 0.602638 ACAAGCGGAAGAATGTGCGA 60.603 50.000 0.00 0.00 33.69 5.10
302 303 0.179215 CAAGCGGAAGAATGTGCGAC 60.179 55.000 0.00 0.00 33.69 5.19
303 304 1.626654 AAGCGGAAGAATGTGCGACG 61.627 55.000 0.00 0.00 33.69 5.12
304 305 2.092291 GCGGAAGAATGTGCGACGA 61.092 57.895 0.00 0.00 33.69 4.20
305 306 1.702299 CGGAAGAATGTGCGACGAC 59.298 57.895 0.00 0.00 33.69 4.34
306 307 0.732880 CGGAAGAATGTGCGACGACT 60.733 55.000 0.00 0.00 33.69 4.18
307 308 1.429463 GGAAGAATGTGCGACGACTT 58.571 50.000 0.00 0.00 0.00 3.01
308 309 1.798813 GGAAGAATGTGCGACGACTTT 59.201 47.619 0.00 0.00 0.00 2.66
309 310 2.991190 GGAAGAATGTGCGACGACTTTA 59.009 45.455 0.00 0.00 0.00 1.85
310 311 3.430895 GGAAGAATGTGCGACGACTTTAA 59.569 43.478 0.00 0.00 0.00 1.52
311 312 4.092968 GGAAGAATGTGCGACGACTTTAAT 59.907 41.667 0.00 0.00 0.00 1.40
312 313 5.290158 GGAAGAATGTGCGACGACTTTAATA 59.710 40.000 0.00 0.00 0.00 0.98
313 314 5.950965 AGAATGTGCGACGACTTTAATAG 57.049 39.130 0.00 0.00 0.00 1.73
314 315 4.267928 AGAATGTGCGACGACTTTAATAGC 59.732 41.667 0.00 0.00 0.00 2.97
315 316 2.264813 TGTGCGACGACTTTAATAGCC 58.735 47.619 0.00 0.00 0.00 3.93
316 317 1.254570 GTGCGACGACTTTAATAGCCG 59.745 52.381 0.00 0.00 35.67 5.52
317 318 1.132834 TGCGACGACTTTAATAGCCGA 59.867 47.619 0.00 0.00 33.56 5.54
318 319 2.187707 GCGACGACTTTAATAGCCGAA 58.812 47.619 0.00 0.00 33.56 4.30
319 320 2.035093 GCGACGACTTTAATAGCCGAAC 60.035 50.000 0.00 0.00 33.56 3.95
320 321 3.173599 CGACGACTTTAATAGCCGAACA 58.826 45.455 0.00 0.00 33.56 3.18
321 322 3.001365 CGACGACTTTAATAGCCGAACAC 60.001 47.826 0.00 0.00 33.56 3.32
322 323 4.171754 GACGACTTTAATAGCCGAACACT 58.828 43.478 0.00 0.00 33.56 3.55
323 324 5.314923 ACGACTTTAATAGCCGAACACTA 57.685 39.130 0.00 0.00 33.56 2.74
324 325 5.713025 ACGACTTTAATAGCCGAACACTAA 58.287 37.500 0.00 0.00 33.56 2.24
325 326 6.158598 ACGACTTTAATAGCCGAACACTAAA 58.841 36.000 0.00 0.00 33.56 1.85
326 327 6.815142 ACGACTTTAATAGCCGAACACTAAAT 59.185 34.615 0.00 0.00 33.56 1.40
327 328 7.117454 CGACTTTAATAGCCGAACACTAAATG 58.883 38.462 0.00 0.00 30.47 2.32
328 329 7.316544 ACTTTAATAGCCGAACACTAAATGG 57.683 36.000 0.00 0.00 0.00 3.16
329 330 5.744666 TTAATAGCCGAACACTAAATGGC 57.255 39.130 0.00 0.00 46.07 4.40
330 331 2.032680 TAGCCGAACACTAAATGGCC 57.967 50.000 0.00 0.00 46.92 5.36
331 332 0.679960 AGCCGAACACTAAATGGCCC 60.680 55.000 0.00 0.00 46.92 5.80
332 333 1.663379 GCCGAACACTAAATGGCCCC 61.663 60.000 0.00 0.00 39.83 5.80
333 334 0.034477 CCGAACACTAAATGGCCCCT 60.034 55.000 0.00 0.00 0.00 4.79
334 335 1.379527 CGAACACTAAATGGCCCCTC 58.620 55.000 0.00 0.00 0.00 4.30
335 336 1.763968 GAACACTAAATGGCCCCTCC 58.236 55.000 0.00 0.00 0.00 4.30
343 344 2.451493 TGGCCCCTCCAACCAGAA 60.451 61.111 0.00 0.00 43.21 3.02
344 345 1.856873 TGGCCCCTCCAACCAGAAT 60.857 57.895 0.00 0.00 43.21 2.40
345 346 0.551377 TGGCCCCTCCAACCAGAATA 60.551 55.000 0.00 0.00 43.21 1.75
346 347 0.629058 GGCCCCTCCAACCAGAATAA 59.371 55.000 0.00 0.00 34.01 1.40
347 348 1.006639 GGCCCCTCCAACCAGAATAAA 59.993 52.381 0.00 0.00 34.01 1.40
348 349 2.379005 GCCCCTCCAACCAGAATAAAG 58.621 52.381 0.00 0.00 0.00 1.85
349 350 2.950418 GCCCCTCCAACCAGAATAAAGG 60.950 54.545 0.00 0.00 0.00 3.11
350 351 2.580783 CCCCTCCAACCAGAATAAAGGA 59.419 50.000 0.00 0.00 0.00 3.36
351 352 3.205282 CCCCTCCAACCAGAATAAAGGAT 59.795 47.826 0.00 0.00 0.00 3.24
352 353 4.464947 CCCTCCAACCAGAATAAAGGATC 58.535 47.826 0.00 0.00 0.00 3.36
353 354 4.130118 CCTCCAACCAGAATAAAGGATCG 58.870 47.826 0.00 0.00 0.00 3.69
354 355 4.130118 CTCCAACCAGAATAAAGGATCGG 58.870 47.826 0.00 0.00 0.00 4.18
355 356 3.521937 TCCAACCAGAATAAAGGATCGGT 59.478 43.478 0.00 0.00 0.00 4.69
356 357 3.877508 CCAACCAGAATAAAGGATCGGTC 59.122 47.826 0.00 0.00 0.00 4.79
357 358 3.454371 ACCAGAATAAAGGATCGGTCG 57.546 47.619 0.00 0.00 0.00 4.79
358 359 2.764572 ACCAGAATAAAGGATCGGTCGT 59.235 45.455 0.00 0.00 0.00 4.34
359 360 3.181478 ACCAGAATAAAGGATCGGTCGTC 60.181 47.826 0.00 0.00 0.00 4.20
360 361 3.181479 CCAGAATAAAGGATCGGTCGTCA 60.181 47.826 0.00 0.00 0.00 4.35
361 362 4.430007 CAGAATAAAGGATCGGTCGTCAA 58.570 43.478 0.00 0.00 0.00 3.18
362 363 4.504461 CAGAATAAAGGATCGGTCGTCAAG 59.496 45.833 0.00 0.00 0.00 3.02
363 364 4.401519 AGAATAAAGGATCGGTCGTCAAGA 59.598 41.667 0.00 0.00 0.00 3.02
371 372 4.240049 GTCGTCAAGACCACGGAC 57.760 61.111 0.00 0.00 43.95 4.79
372 373 1.361271 GTCGTCAAGACCACGGACA 59.639 57.895 0.00 0.00 43.95 4.02
373 374 0.938168 GTCGTCAAGACCACGGACAC 60.938 60.000 0.00 0.00 43.95 3.67
375 376 1.663702 GTCAAGACCACGGACACGG 60.664 63.158 0.00 0.00 46.48 4.94
376 377 3.041940 CAAGACCACGGACACGGC 61.042 66.667 0.00 0.00 46.48 5.68
377 378 4.657824 AAGACCACGGACACGGCG 62.658 66.667 4.80 4.80 46.48 6.46
390 391 4.191485 CGGCGAGCGCGTTGTAAG 62.191 66.667 12.44 0.00 43.06 2.34
391 392 3.849953 GGCGAGCGCGTTGTAAGG 61.850 66.667 12.44 0.00 43.06 2.69
392 393 2.807895 GCGAGCGCGTTGTAAGGA 60.808 61.111 12.44 0.00 40.36 3.36
393 394 2.377310 GCGAGCGCGTTGTAAGGAA 61.377 57.895 12.44 0.00 40.36 3.36
394 395 1.414897 CGAGCGCGTTGTAAGGAAC 59.585 57.895 8.43 0.00 0.00 3.62
559 560 4.101448 GCAGGGATCGGCAGGTGT 62.101 66.667 0.00 0.00 34.23 4.16
2486 2965 3.088532 TGTTCCTGGTCAATTATGTGCC 58.911 45.455 0.00 0.00 0.00 5.01
2518 2997 2.017049 ACAGCTGACAGTTTTGTGTCC 58.983 47.619 23.35 0.00 45.42 4.02
2596 3075 9.193133 GTTAGATATGTAGTGTCGTGCAAATAT 57.807 33.333 0.00 0.00 0.00 1.28
2658 3137 7.155655 TGTGCAGTCAATTTATTTGCATAGA 57.844 32.000 0.53 0.00 45.31 1.98
2807 3286 5.067023 GGACCCTCATCATGAGTTTTTGATC 59.933 44.000 13.82 0.00 42.80 2.92
2848 3327 4.617530 GCTCAAGACATTGCATCACATTGT 60.618 41.667 0.00 0.00 43.69 2.71
2913 3392 4.703575 CACTCATCATGGGTTTCTGACATT 59.296 41.667 0.00 0.00 0.00 2.71
3104 3583 6.182627 TGTGGTTCAGCAGAAATCTAATCAT 58.817 36.000 0.00 0.00 35.08 2.45
3143 3622 4.219507 TCTGTGCAGGAGTAGAAGAGAAAG 59.780 45.833 0.00 0.00 0.00 2.62
3949 4428 4.202223 GGTAGACACAGAACAAGTGAAGGA 60.202 45.833 0.00 0.00 40.16 3.36
4020 4499 6.650120 AGAATCTCTAGCAAATCCCGTAAAA 58.350 36.000 0.00 0.00 0.00 1.52
4061 4540 0.393808 GGGCTGATAAGCGGGTTTGA 60.394 55.000 0.00 0.00 35.24 2.69
4095 4574 0.389391 CGAACAGACCCCGCATATCT 59.611 55.000 0.00 0.00 0.00 1.98
4096 4575 1.611977 CGAACAGACCCCGCATATCTA 59.388 52.381 0.00 0.00 0.00 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.402862 AGGTAGTATTACTGTGGCTGATTTTT 58.597 34.615 6.60 0.00 0.00 1.94
1 2 6.958767 AGGTAGTATTACTGTGGCTGATTTT 58.041 36.000 6.60 0.00 0.00 1.82
2 3 6.561519 AGGTAGTATTACTGTGGCTGATTT 57.438 37.500 6.60 0.00 0.00 2.17
3 4 6.156256 TGAAGGTAGTATTACTGTGGCTGATT 59.844 38.462 6.60 0.00 0.00 2.57
4 5 5.661312 TGAAGGTAGTATTACTGTGGCTGAT 59.339 40.000 6.60 0.00 0.00 2.90
5 6 5.020795 TGAAGGTAGTATTACTGTGGCTGA 58.979 41.667 6.60 0.00 0.00 4.26
6 7 5.339008 TGAAGGTAGTATTACTGTGGCTG 57.661 43.478 6.60 0.00 0.00 4.85
7 8 5.104900 CCTTGAAGGTAGTATTACTGTGGCT 60.105 44.000 2.25 0.00 0.00 4.75
8 9 5.116882 CCTTGAAGGTAGTATTACTGTGGC 58.883 45.833 2.25 0.00 0.00 5.01
9 10 5.424252 TCCCTTGAAGGTAGTATTACTGTGG 59.576 44.000 10.82 0.00 31.93 4.17
10 11 6.154706 ACTCCCTTGAAGGTAGTATTACTGTG 59.845 42.308 7.78 0.00 31.93 3.66
11 12 6.262207 ACTCCCTTGAAGGTAGTATTACTGT 58.738 40.000 7.78 0.00 31.93 3.55
12 13 6.793505 ACTCCCTTGAAGGTAGTATTACTG 57.206 41.667 7.78 0.00 31.93 2.74
15 16 9.372189 GGTATTACTCCCTTGAAGGTAGTATTA 57.628 37.037 16.10 13.79 31.93 0.98
16 17 7.847848 TGGTATTACTCCCTTGAAGGTAGTATT 59.152 37.037 16.10 14.65 31.93 1.89
17 18 7.367828 TGGTATTACTCCCTTGAAGGTAGTAT 58.632 38.462 16.10 9.74 31.93 2.12
18 19 6.744822 TGGTATTACTCCCTTGAAGGTAGTA 58.255 40.000 12.07 12.07 31.93 1.82
19 20 5.596763 TGGTATTACTCCCTTGAAGGTAGT 58.403 41.667 14.12 14.12 31.93 2.73
20 21 5.070580 CCTGGTATTACTCCCTTGAAGGTAG 59.929 48.000 10.82 6.36 31.93 3.18
21 22 4.966805 CCTGGTATTACTCCCTTGAAGGTA 59.033 45.833 10.82 0.00 31.93 3.08
22 23 3.780850 CCTGGTATTACTCCCTTGAAGGT 59.219 47.826 10.82 0.00 31.93 3.50
23 24 3.433740 GCCTGGTATTACTCCCTTGAAGG 60.434 52.174 3.69 3.69 34.30 3.46
24 25 3.433740 GGCCTGGTATTACTCCCTTGAAG 60.434 52.174 0.00 0.00 0.00 3.02
25 26 2.508300 GGCCTGGTATTACTCCCTTGAA 59.492 50.000 0.00 0.00 0.00 2.69
26 27 2.124411 GGCCTGGTATTACTCCCTTGA 58.876 52.381 0.00 0.00 0.00 3.02
27 28 1.143073 GGGCCTGGTATTACTCCCTTG 59.857 57.143 0.84 0.00 0.00 3.61
28 29 1.274767 TGGGCCTGGTATTACTCCCTT 60.275 52.381 4.53 0.00 34.89 3.95
29 30 0.345502 TGGGCCTGGTATTACTCCCT 59.654 55.000 4.53 0.00 34.89 4.20
30 31 0.765510 CTGGGCCTGGTATTACTCCC 59.234 60.000 4.53 0.00 0.00 4.30
31 32 1.694696 CTCTGGGCCTGGTATTACTCC 59.305 57.143 10.79 0.00 0.00 3.85
32 33 1.694696 CCTCTGGGCCTGGTATTACTC 59.305 57.143 10.79 0.00 0.00 2.59
33 34 1.807814 CCTCTGGGCCTGGTATTACT 58.192 55.000 10.79 0.00 0.00 2.24
55 56 2.635229 AATAGAGAGCCCGTGCAGCG 62.635 60.000 0.00 0.00 41.13 5.18
56 57 0.389391 TAATAGAGAGCCCGTGCAGC 59.611 55.000 0.00 0.00 41.13 5.25
57 58 1.683917 AGTAATAGAGAGCCCGTGCAG 59.316 52.381 0.00 0.00 41.13 4.41
58 59 1.776662 AGTAATAGAGAGCCCGTGCA 58.223 50.000 0.00 0.00 41.13 4.57
59 60 3.147629 TCTAGTAATAGAGAGCCCGTGC 58.852 50.000 0.00 0.00 37.95 5.34
60 61 3.754323 CCTCTAGTAATAGAGAGCCCGTG 59.246 52.174 25.07 6.01 44.79 4.94
61 62 3.395273 ACCTCTAGTAATAGAGAGCCCGT 59.605 47.826 25.07 12.95 44.79 5.28
62 63 4.023726 ACCTCTAGTAATAGAGAGCCCG 57.976 50.000 25.07 12.38 44.79 6.13
63 64 5.141910 ACAACCTCTAGTAATAGAGAGCCC 58.858 45.833 25.07 0.00 44.79 5.19
64 65 8.411991 AATACAACCTCTAGTAATAGAGAGCC 57.588 38.462 25.07 0.00 44.79 4.70
65 66 8.231837 CGAATACAACCTCTAGTAATAGAGAGC 58.768 40.741 25.07 7.01 44.79 4.09
66 67 8.723311 CCGAATACAACCTCTAGTAATAGAGAG 58.277 40.741 25.07 17.65 44.79 3.20
67 68 8.216423 ACCGAATACAACCTCTAGTAATAGAGA 58.784 37.037 25.07 8.17 44.79 3.10
68 69 8.393671 ACCGAATACAACCTCTAGTAATAGAG 57.606 38.462 18.28 18.28 42.38 2.43
69 70 8.757982 AACCGAATACAACCTCTAGTAATAGA 57.242 34.615 0.00 0.00 0.00 1.98
70 71 8.848182 AGAACCGAATACAACCTCTAGTAATAG 58.152 37.037 0.00 0.00 0.00 1.73
71 72 8.757982 AGAACCGAATACAACCTCTAGTAATA 57.242 34.615 0.00 0.00 0.00 0.98
72 73 7.657023 AGAACCGAATACAACCTCTAGTAAT 57.343 36.000 0.00 0.00 0.00 1.89
73 74 7.363268 GGAAGAACCGAATACAACCTCTAGTAA 60.363 40.741 0.00 0.00 0.00 2.24
74 75 6.096001 GGAAGAACCGAATACAACCTCTAGTA 59.904 42.308 0.00 0.00 0.00 1.82
75 76 5.105432 GGAAGAACCGAATACAACCTCTAGT 60.105 44.000 0.00 0.00 0.00 2.57
76 77 5.349809 GGAAGAACCGAATACAACCTCTAG 58.650 45.833 0.00 0.00 0.00 2.43
77 78 5.334724 GGAAGAACCGAATACAACCTCTA 57.665 43.478 0.00 0.00 0.00 2.43
78 79 4.203654 GGAAGAACCGAATACAACCTCT 57.796 45.455 0.00 0.00 0.00 3.69
91 92 1.145803 CGGAAGTTGTCGGAAGAACC 58.854 55.000 0.00 0.00 45.01 3.62
92 93 2.144482 TCGGAAGTTGTCGGAAGAAC 57.856 50.000 0.00 0.00 45.01 3.01
93 94 2.894763 TTCGGAAGTTGTCGGAAGAA 57.105 45.000 0.00 0.00 45.01 2.52
96 97 0.942410 CGCTTCGGAAGTTGTCGGAA 60.942 55.000 18.32 0.00 41.75 4.30
97 98 1.372499 CGCTTCGGAAGTTGTCGGA 60.372 57.895 18.32 0.00 34.01 4.55
98 99 0.942410 TTCGCTTCGGAAGTTGTCGG 60.942 55.000 18.32 3.02 0.00 4.79
99 100 0.856641 TTTCGCTTCGGAAGTTGTCG 59.143 50.000 18.32 13.05 0.00 4.35
100 101 2.287103 ACTTTTCGCTTCGGAAGTTGTC 59.713 45.455 18.32 1.77 32.94 3.18
101 102 2.285977 ACTTTTCGCTTCGGAAGTTGT 58.714 42.857 18.32 6.61 32.94 3.32
102 103 3.334272 AACTTTTCGCTTCGGAAGTTG 57.666 42.857 18.32 11.69 39.75 3.16
103 104 4.260907 GGTTAACTTTTCGCTTCGGAAGTT 60.261 41.667 18.32 17.95 41.84 2.66
104 105 3.249320 GGTTAACTTTTCGCTTCGGAAGT 59.751 43.478 18.32 0.00 36.10 3.01
105 106 3.497262 AGGTTAACTTTTCGCTTCGGAAG 59.503 43.478 13.39 13.39 0.00 3.46
106 107 3.469739 AGGTTAACTTTTCGCTTCGGAA 58.530 40.909 5.42 0.00 0.00 4.30
107 108 3.116079 AGGTTAACTTTTCGCTTCGGA 57.884 42.857 5.42 0.00 0.00 4.55
108 109 3.663493 CGAAGGTTAACTTTTCGCTTCGG 60.663 47.826 23.41 12.24 40.21 4.30
109 110 3.182972 TCGAAGGTTAACTTTTCGCTTCG 59.817 43.478 26.43 25.42 42.36 3.79
110 111 4.025480 TGTCGAAGGTTAACTTTTCGCTTC 60.025 41.667 26.43 18.52 42.36 3.86
111 112 3.872771 TGTCGAAGGTTAACTTTTCGCTT 59.127 39.130 26.43 13.67 42.36 4.68
112 113 3.460103 TGTCGAAGGTTAACTTTTCGCT 58.540 40.909 26.43 7.25 42.36 4.93
113 114 3.865224 TGTCGAAGGTTAACTTTTCGC 57.135 42.857 26.43 22.71 42.36 4.70
114 115 4.625135 CGATGTCGAAGGTTAACTTTTCG 58.375 43.478 25.83 25.83 43.58 3.46
115 116 4.151867 AGCGATGTCGAAGGTTAACTTTTC 59.848 41.667 6.60 8.48 40.21 2.29
116 117 4.062991 AGCGATGTCGAAGGTTAACTTTT 58.937 39.130 6.60 0.28 40.21 2.27
117 118 3.660865 AGCGATGTCGAAGGTTAACTTT 58.339 40.909 2.11 2.11 40.21 2.66
118 119 3.251571 GAGCGATGTCGAAGGTTAACTT 58.748 45.455 6.60 0.00 43.65 2.66
119 120 2.416972 GGAGCGATGTCGAAGGTTAACT 60.417 50.000 6.60 0.00 43.02 2.24
120 121 1.925185 GGAGCGATGTCGAAGGTTAAC 59.075 52.381 6.60 0.00 43.02 2.01
121 122 1.546923 TGGAGCGATGTCGAAGGTTAA 59.453 47.619 6.60 0.00 43.02 2.01
122 123 1.179152 TGGAGCGATGTCGAAGGTTA 58.821 50.000 6.60 0.00 43.02 2.85
123 124 0.537188 ATGGAGCGATGTCGAAGGTT 59.463 50.000 6.60 0.00 43.02 3.50
124 125 0.537188 AATGGAGCGATGTCGAAGGT 59.463 50.000 6.60 0.00 43.02 3.50
125 126 1.212616 GAATGGAGCGATGTCGAAGG 58.787 55.000 6.60 0.00 43.02 3.46
126 127 1.212616 GGAATGGAGCGATGTCGAAG 58.787 55.000 6.60 0.00 43.02 3.79
127 128 0.527600 CGGAATGGAGCGATGTCGAA 60.528 55.000 6.60 0.00 43.02 3.71
128 129 1.065764 CGGAATGGAGCGATGTCGA 59.934 57.895 6.60 0.00 43.02 4.20
129 130 0.527600 TTCGGAATGGAGCGATGTCG 60.528 55.000 0.00 0.00 43.27 4.35
130 131 1.212616 CTTCGGAATGGAGCGATGTC 58.787 55.000 0.00 0.00 0.00 3.06
131 132 0.537188 ACTTCGGAATGGAGCGATGT 59.463 50.000 0.00 0.00 0.00 3.06
132 133 0.933097 CACTTCGGAATGGAGCGATG 59.067 55.000 0.00 0.00 0.00 3.84
133 134 0.179073 CCACTTCGGAATGGAGCGAT 60.179 55.000 11.46 0.00 38.34 4.58
134 135 1.218047 CCACTTCGGAATGGAGCGA 59.782 57.895 11.46 0.00 38.34 4.93
135 136 2.464459 GCCACTTCGGAATGGAGCG 61.464 63.158 17.73 0.00 38.34 5.03
136 137 0.178068 TAGCCACTTCGGAATGGAGC 59.822 55.000 17.73 8.15 38.34 4.70
137 138 2.103094 TGATAGCCACTTCGGAATGGAG 59.897 50.000 17.73 0.00 38.34 3.86
138 139 2.115427 TGATAGCCACTTCGGAATGGA 58.885 47.619 17.73 4.27 38.34 3.41
139 140 2.620251 TGATAGCCACTTCGGAATGG 57.380 50.000 12.18 12.18 39.16 3.16
140 141 2.289002 GCTTGATAGCCACTTCGGAATG 59.711 50.000 0.00 0.00 41.74 2.67
141 142 2.565841 GCTTGATAGCCACTTCGGAAT 58.434 47.619 0.00 0.00 41.74 3.01
142 143 2.024176 GCTTGATAGCCACTTCGGAA 57.976 50.000 0.00 0.00 41.74 4.30
143 144 3.760693 GCTTGATAGCCACTTCGGA 57.239 52.632 0.00 0.00 41.74 4.55
150 151 8.553681 CTCTTTCGAGTAGTGCTTGATAGCCA 62.554 46.154 9.98 0.00 38.29 4.75
151 152 6.240569 CTCTTTCGAGTAGTGCTTGATAGCC 61.241 48.000 9.98 0.00 38.29 3.93
152 153 4.737765 CTCTTTCGAGTAGTGCTTGATAGC 59.262 45.833 9.98 0.00 36.91 2.97
153 154 4.737765 GCTCTTTCGAGTAGTGCTTGATAG 59.262 45.833 8.91 8.91 39.53 2.08
154 155 4.673441 GCTCTTTCGAGTAGTGCTTGATA 58.327 43.478 13.27 0.00 39.53 2.15
155 156 3.516615 GCTCTTTCGAGTAGTGCTTGAT 58.483 45.455 13.27 0.00 39.53 2.57
156 157 2.668556 CGCTCTTTCGAGTAGTGCTTGA 60.669 50.000 16.46 0.00 39.53 3.02
157 158 1.651138 CGCTCTTTCGAGTAGTGCTTG 59.349 52.381 16.46 0.00 39.53 4.01
158 159 1.402984 CCGCTCTTTCGAGTAGTGCTT 60.403 52.381 16.46 0.00 39.53 3.91
159 160 0.171455 CCGCTCTTTCGAGTAGTGCT 59.829 55.000 16.46 0.00 39.53 4.40
160 161 1.414527 GCCGCTCTTTCGAGTAGTGC 61.415 60.000 11.44 11.44 39.53 4.40
161 162 0.171455 AGCCGCTCTTTCGAGTAGTG 59.829 55.000 0.00 0.00 39.53 2.74
162 163 0.889306 AAGCCGCTCTTTCGAGTAGT 59.111 50.000 0.00 0.00 39.53 2.73
163 164 1.997669 AAAGCCGCTCTTTCGAGTAG 58.002 50.000 0.00 0.00 40.89 2.57
179 180 3.810373 ACTGCATTAAAACGAGCGAAAG 58.190 40.909 0.00 0.00 0.00 2.62
180 181 3.889196 ACTGCATTAAAACGAGCGAAA 57.111 38.095 0.00 0.00 0.00 3.46
181 182 3.123959 GGTACTGCATTAAAACGAGCGAA 59.876 43.478 0.00 0.00 0.00 4.70
182 183 2.669434 GGTACTGCATTAAAACGAGCGA 59.331 45.455 0.00 0.00 0.00 4.93
183 184 2.534150 CGGTACTGCATTAAAACGAGCG 60.534 50.000 0.00 0.00 0.00 5.03
184 185 2.786700 GCGGTACTGCATTAAAACGAGC 60.787 50.000 21.95 0.00 34.15 5.03
185 186 2.413796 TGCGGTACTGCATTAAAACGAG 59.586 45.455 25.46 0.00 40.62 4.18
186 187 2.414806 TGCGGTACTGCATTAAAACGA 58.585 42.857 25.46 0.00 40.62 3.85
187 188 2.884663 TGCGGTACTGCATTAAAACG 57.115 45.000 25.46 0.68 40.62 3.60
204 205 4.897025 AAGCTTGAGAGAAGCATAATGC 57.103 40.909 0.00 0.00 45.30 3.56
205 206 7.783090 TCTTAAGCTTGAGAGAAGCATAATG 57.217 36.000 16.41 3.13 45.30 1.90
206 207 7.041235 GCATCTTAAGCTTGAGAGAAGCATAAT 60.041 37.037 23.39 3.63 45.30 1.28
207 208 6.259608 GCATCTTAAGCTTGAGAGAAGCATAA 59.740 38.462 23.39 6.56 45.30 1.90
208 209 5.757320 GCATCTTAAGCTTGAGAGAAGCATA 59.243 40.000 23.39 1.28 45.30 3.14
209 210 4.575645 GCATCTTAAGCTTGAGAGAAGCAT 59.424 41.667 23.39 5.64 45.30 3.79
210 211 3.937706 GCATCTTAAGCTTGAGAGAAGCA 59.062 43.478 23.39 2.66 45.30 3.91
211 212 3.312146 GGCATCTTAAGCTTGAGAGAAGC 59.688 47.826 23.39 23.37 43.31 3.86
212 213 4.511527 TGGCATCTTAAGCTTGAGAGAAG 58.488 43.478 23.39 16.83 0.00 2.85
213 214 4.511527 CTGGCATCTTAAGCTTGAGAGAA 58.488 43.478 23.39 9.91 0.00 2.87
214 215 3.118482 CCTGGCATCTTAAGCTTGAGAGA 60.118 47.826 23.39 16.52 0.00 3.10
215 216 3.204526 CCTGGCATCTTAAGCTTGAGAG 58.795 50.000 23.39 16.56 0.00 3.20
216 217 2.573462 ACCTGGCATCTTAAGCTTGAGA 59.427 45.455 21.75 21.75 0.00 3.27
217 218 2.941720 GACCTGGCATCTTAAGCTTGAG 59.058 50.000 11.90 11.90 0.00 3.02
218 219 2.356125 GGACCTGGCATCTTAAGCTTGA 60.356 50.000 9.86 0.00 0.00 3.02
219 220 2.019984 GGACCTGGCATCTTAAGCTTG 58.980 52.381 9.86 0.00 0.00 4.01
220 221 1.635487 TGGACCTGGCATCTTAAGCTT 59.365 47.619 3.48 3.48 0.00 3.74
221 222 1.289160 TGGACCTGGCATCTTAAGCT 58.711 50.000 0.00 0.00 0.00 3.74
222 223 1.952296 CATGGACCTGGCATCTTAAGC 59.048 52.381 0.00 0.00 0.00 3.09
223 224 2.947652 CACATGGACCTGGCATCTTAAG 59.052 50.000 0.00 0.00 0.00 1.85
224 225 2.357050 CCACATGGACCTGGCATCTTAA 60.357 50.000 0.00 0.00 37.39 1.85
225 226 1.212688 CCACATGGACCTGGCATCTTA 59.787 52.381 0.00 0.00 37.39 2.10
226 227 0.033796 CCACATGGACCTGGCATCTT 60.034 55.000 0.00 0.00 37.39 2.40
227 228 1.611419 CCACATGGACCTGGCATCT 59.389 57.895 0.00 0.00 37.39 2.90
228 229 4.247781 CCACATGGACCTGGCATC 57.752 61.111 0.00 0.00 37.39 3.91
232 233 0.106369 ATGATGCCACATGGACCTGG 60.106 55.000 0.87 0.00 37.39 4.45
233 234 1.315690 GATGATGCCACATGGACCTG 58.684 55.000 0.87 0.00 37.39 4.00
234 235 0.921166 TGATGATGCCACATGGACCT 59.079 50.000 0.87 0.00 37.39 3.85
235 236 1.027357 GTGATGATGCCACATGGACC 58.973 55.000 0.87 0.00 37.39 4.46
236 237 1.027357 GGTGATGATGCCACATGGAC 58.973 55.000 0.87 0.00 37.39 4.02
237 238 0.624785 TGGTGATGATGCCACATGGA 59.375 50.000 0.87 0.00 37.39 3.41
238 239 1.699730 ATGGTGATGATGCCACATGG 58.300 50.000 0.00 0.00 37.62 3.66
239 240 3.305131 GCTAATGGTGATGATGCCACATG 60.305 47.826 0.00 0.00 37.62 3.21
240 241 2.889045 GCTAATGGTGATGATGCCACAT 59.111 45.455 0.00 0.00 37.62 3.21
241 242 2.300433 GCTAATGGTGATGATGCCACA 58.700 47.619 0.00 0.00 37.62 4.17
242 243 1.265095 CGCTAATGGTGATGATGCCAC 59.735 52.381 0.00 0.00 37.62 5.01
243 244 1.596603 CGCTAATGGTGATGATGCCA 58.403 50.000 0.00 0.00 39.33 4.92
244 245 0.877071 CCGCTAATGGTGATGATGCC 59.123 55.000 0.00 0.00 0.00 4.40
245 246 1.882912 TCCGCTAATGGTGATGATGC 58.117 50.000 0.00 0.00 0.00 3.91
246 247 3.303329 CGTTTCCGCTAATGGTGATGATG 60.303 47.826 0.00 0.00 0.00 3.07
247 248 2.872245 CGTTTCCGCTAATGGTGATGAT 59.128 45.455 0.00 0.00 0.00 2.45
248 249 2.276201 CGTTTCCGCTAATGGTGATGA 58.724 47.619 0.00 0.00 0.00 2.92
249 250 2.737467 CGTTTCCGCTAATGGTGATG 57.263 50.000 0.00 0.00 0.00 3.07
268 269 1.136336 CGCTTGTAAGGAACGTTCAGC 60.136 52.381 28.24 23.77 0.00 4.26
269 270 1.459592 CCGCTTGTAAGGAACGTTCAG 59.540 52.381 28.24 16.94 0.00 3.02
270 271 1.068895 TCCGCTTGTAAGGAACGTTCA 59.931 47.619 28.24 6.67 32.86 3.18
271 272 1.787012 TCCGCTTGTAAGGAACGTTC 58.213 50.000 20.14 20.14 32.86 3.95
272 273 2.140717 CTTCCGCTTGTAAGGAACGTT 58.859 47.619 0.00 0.00 41.19 3.99
273 274 1.342174 TCTTCCGCTTGTAAGGAACGT 59.658 47.619 0.00 0.00 41.19 3.99
274 275 2.074547 TCTTCCGCTTGTAAGGAACG 57.925 50.000 0.00 0.00 41.19 3.95
275 276 3.751698 ACATTCTTCCGCTTGTAAGGAAC 59.248 43.478 0.00 0.00 41.19 3.62
276 277 3.751175 CACATTCTTCCGCTTGTAAGGAA 59.249 43.478 0.00 0.00 43.57 3.36
277 278 3.334691 CACATTCTTCCGCTTGTAAGGA 58.665 45.455 0.00 0.00 34.19 3.36
278 279 2.159517 GCACATTCTTCCGCTTGTAAGG 60.160 50.000 0.00 0.00 0.00 2.69
279 280 2.474526 CGCACATTCTTCCGCTTGTAAG 60.475 50.000 0.00 0.00 0.00 2.34
280 281 1.463056 CGCACATTCTTCCGCTTGTAA 59.537 47.619 0.00 0.00 0.00 2.41
281 282 1.075542 CGCACATTCTTCCGCTTGTA 58.924 50.000 0.00 0.00 0.00 2.41
282 283 0.602638 TCGCACATTCTTCCGCTTGT 60.603 50.000 0.00 0.00 0.00 3.16
283 284 0.179215 GTCGCACATTCTTCCGCTTG 60.179 55.000 0.00 0.00 0.00 4.01
284 285 1.626654 CGTCGCACATTCTTCCGCTT 61.627 55.000 0.00 0.00 0.00 4.68
285 286 2.094659 CGTCGCACATTCTTCCGCT 61.095 57.895 0.00 0.00 0.00 5.52
286 287 2.092291 TCGTCGCACATTCTTCCGC 61.092 57.895 0.00 0.00 0.00 5.54
287 288 0.732880 AGTCGTCGCACATTCTTCCG 60.733 55.000 0.00 0.00 0.00 4.30
288 289 1.429463 AAGTCGTCGCACATTCTTCC 58.571 50.000 0.00 0.00 0.00 3.46
289 290 4.640805 TTAAAGTCGTCGCACATTCTTC 57.359 40.909 0.00 0.00 0.00 2.87
290 291 5.220416 GCTATTAAAGTCGTCGCACATTCTT 60.220 40.000 0.00 0.00 0.00 2.52
291 292 4.267928 GCTATTAAAGTCGTCGCACATTCT 59.732 41.667 0.00 0.00 0.00 2.40
292 293 4.506217 GCTATTAAAGTCGTCGCACATTC 58.494 43.478 0.00 0.00 0.00 2.67
293 294 3.308866 GGCTATTAAAGTCGTCGCACATT 59.691 43.478 0.00 0.00 0.00 2.71
294 295 2.864343 GGCTATTAAAGTCGTCGCACAT 59.136 45.455 0.00 0.00 0.00 3.21
295 296 2.264813 GGCTATTAAAGTCGTCGCACA 58.735 47.619 0.00 0.00 0.00 4.57
296 297 2.992744 GGCTATTAAAGTCGTCGCAC 57.007 50.000 0.00 0.00 0.00 5.34
303 304 7.407337 CCATTTAGTGTTCGGCTATTAAAGTC 58.593 38.462 0.00 0.00 0.00 3.01
304 305 6.183360 GCCATTTAGTGTTCGGCTATTAAAGT 60.183 38.462 0.00 0.00 39.73 2.66
305 306 6.199393 GCCATTTAGTGTTCGGCTATTAAAG 58.801 40.000 0.00 0.00 39.73 1.85
306 307 5.066764 GGCCATTTAGTGTTCGGCTATTAAA 59.933 40.000 0.00 0.00 42.56 1.52
307 308 4.577283 GGCCATTTAGTGTTCGGCTATTAA 59.423 41.667 0.00 0.00 42.56 1.40
308 309 4.131596 GGCCATTTAGTGTTCGGCTATTA 58.868 43.478 0.00 0.00 42.56 0.98
309 310 2.949644 GGCCATTTAGTGTTCGGCTATT 59.050 45.455 0.00 0.00 42.56 1.73
310 311 2.572290 GGCCATTTAGTGTTCGGCTAT 58.428 47.619 0.00 0.00 42.56 2.97
311 312 1.407712 GGGCCATTTAGTGTTCGGCTA 60.408 52.381 4.39 0.00 42.56 3.93
312 313 0.679960 GGGCCATTTAGTGTTCGGCT 60.680 55.000 4.39 0.00 42.56 5.52
313 314 1.663379 GGGGCCATTTAGTGTTCGGC 61.663 60.000 4.39 0.00 42.21 5.54
314 315 0.034477 AGGGGCCATTTAGTGTTCGG 60.034 55.000 4.39 0.00 0.00 4.30
315 316 1.379527 GAGGGGCCATTTAGTGTTCG 58.620 55.000 4.39 0.00 0.00 3.95
316 317 1.005450 TGGAGGGGCCATTTAGTGTTC 59.995 52.381 4.39 0.00 43.33 3.18
317 318 1.080638 TGGAGGGGCCATTTAGTGTT 58.919 50.000 4.39 0.00 43.33 3.32
318 319 2.799576 TGGAGGGGCCATTTAGTGT 58.200 52.632 4.39 0.00 43.33 3.55
327 328 0.629058 TTATTCTGGTTGGAGGGGCC 59.371 55.000 0.00 0.00 37.10 5.80
328 329 2.379005 CTTTATTCTGGTTGGAGGGGC 58.621 52.381 0.00 0.00 0.00 5.80
329 330 2.580783 TCCTTTATTCTGGTTGGAGGGG 59.419 50.000 0.00 0.00 0.00 4.79
330 331 4.464947 GATCCTTTATTCTGGTTGGAGGG 58.535 47.826 0.00 0.00 0.00 4.30
331 332 4.130118 CGATCCTTTATTCTGGTTGGAGG 58.870 47.826 0.00 0.00 0.00 4.30
332 333 4.130118 CCGATCCTTTATTCTGGTTGGAG 58.870 47.826 0.00 0.00 0.00 3.86
333 334 3.521937 ACCGATCCTTTATTCTGGTTGGA 59.478 43.478 0.00 0.00 0.00 3.53
334 335 3.877508 GACCGATCCTTTATTCTGGTTGG 59.122 47.826 0.00 0.00 0.00 3.77
335 336 3.555956 CGACCGATCCTTTATTCTGGTTG 59.444 47.826 0.00 0.00 0.00 3.77
336 337 3.197116 ACGACCGATCCTTTATTCTGGTT 59.803 43.478 0.00 0.00 0.00 3.67
337 338 2.764572 ACGACCGATCCTTTATTCTGGT 59.235 45.455 0.00 0.00 0.00 4.00
338 339 3.181479 TGACGACCGATCCTTTATTCTGG 60.181 47.826 0.00 0.00 0.00 3.86
339 340 4.041740 TGACGACCGATCCTTTATTCTG 57.958 45.455 0.00 0.00 0.00 3.02
340 341 4.401519 TCTTGACGACCGATCCTTTATTCT 59.598 41.667 0.00 0.00 0.00 2.40
341 342 4.503370 GTCTTGACGACCGATCCTTTATTC 59.497 45.833 0.00 0.00 36.62 1.75
342 343 4.430908 GTCTTGACGACCGATCCTTTATT 58.569 43.478 0.00 0.00 36.62 1.40
343 344 4.043037 GTCTTGACGACCGATCCTTTAT 57.957 45.455 0.00 0.00 36.62 1.40
344 345 3.498927 GTCTTGACGACCGATCCTTTA 57.501 47.619 0.00 0.00 36.62 1.85
345 346 2.365408 GTCTTGACGACCGATCCTTT 57.635 50.000 0.00 0.00 36.62 3.11
354 355 0.938168 GTGTCCGTGGTCTTGACGAC 60.938 60.000 5.95 5.95 39.21 4.34
355 356 1.361271 GTGTCCGTGGTCTTGACGA 59.639 57.895 0.00 0.00 39.21 4.20
356 357 2.014554 CGTGTCCGTGGTCTTGACG 61.015 63.158 0.00 0.00 36.56 4.35
357 358 1.663702 CCGTGTCCGTGGTCTTGAC 60.664 63.158 0.00 0.00 0.00 3.18
358 359 2.732016 CCGTGTCCGTGGTCTTGA 59.268 61.111 0.00 0.00 0.00 3.02
359 360 3.041940 GCCGTGTCCGTGGTCTTG 61.042 66.667 0.00 0.00 0.00 3.02
360 361 4.657824 CGCCGTGTCCGTGGTCTT 62.658 66.667 0.00 0.00 0.00 3.01
373 374 4.191485 CTTACAACGCGCTCGCCG 62.191 66.667 5.73 6.62 39.84 6.46
374 375 3.849953 CCTTACAACGCGCTCGCC 61.850 66.667 5.73 0.00 39.84 5.54
375 376 2.377310 TTCCTTACAACGCGCTCGC 61.377 57.895 5.73 3.90 39.84 5.03
376 377 1.414897 GTTCCTTACAACGCGCTCG 59.585 57.895 5.73 0.00 42.43 5.03
377 378 1.414897 CGTTCCTTACAACGCGCTC 59.585 57.895 5.73 0.00 42.45 5.03
378 379 3.545911 CGTTCCTTACAACGCGCT 58.454 55.556 5.73 0.00 42.45 5.92
391 392 1.082104 CGCAAGGCAAGGAACGTTC 60.082 57.895 20.14 20.14 0.00 3.95
392 393 3.030652 CGCAAGGCAAGGAACGTT 58.969 55.556 0.00 0.00 0.00 3.99
574 575 2.115911 CCTCGTCTCCCGTCTCCAG 61.116 68.421 0.00 0.00 37.94 3.86
1976 2455 3.315142 GAGCGATCACTGCACCCCA 62.315 63.158 0.00 0.00 33.85 4.96
2486 2965 4.145876 TGTCAGCTGTAAAGCAATTTCG 57.854 40.909 14.67 0.00 37.25 3.46
2518 2997 0.880278 ACCGGATTGCCAATCGATCG 60.880 55.000 9.46 9.36 38.82 3.69
2596 3075 0.392706 ACATGCCACTTCTCACACGA 59.607 50.000 0.00 0.00 0.00 4.35
2807 3286 0.780002 GCAAATGTCGCAAGCACAAG 59.220 50.000 0.00 0.00 32.67 3.16
2848 3327 5.616270 TGACAATACTTGCCTCACTGTAAA 58.384 37.500 0.00 0.00 0.00 2.01
3104 3583 3.118992 GCACAGAGACCAGATGTATGTGA 60.119 47.826 6.60 0.00 37.83 3.58
3143 3622 4.516698 CCAATAGCCTCATTCACCATGTAC 59.483 45.833 0.00 0.00 34.06 2.90
3949 4428 9.924650 ATAAGAACTAGTTGTAGATTCGTGTTT 57.075 29.630 14.14 0.00 0.00 2.83
4061 4540 0.033366 GTTCGGGCCACAAAAATGCT 59.967 50.000 4.39 0.00 0.00 3.79


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

AutoCloner maintained by Alex Coulton.