Multiple sequence alignment - TraesCS6D01G017800

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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 TraesCS6D01G017800 chr6D 100.000 3614 0 0 1 3614 7359970 7356357 0.000000e+00 6674.0
1 TraesCS6D01G017800 chr6D 89.151 2203 229 9 465 2662 7345967 7343770 0.000000e+00 2736.0
2 TraesCS6D01G017800 chr6D 81.699 306 47 7 2625 2927 7343738 7343439 2.790000e-61 246.0
3 TraesCS6D01G017800 chr6A 89.893 2998 271 24 466 3445 7079615 7082598 0.000000e+00 3829.0
4 TraesCS6D01G017800 chr6A 88.409 2269 247 13 465 2725 7175964 7173704 0.000000e+00 2719.0
5 TraesCS6D01G017800 chr6A 86.667 855 71 11 2644 3482 7184659 7183832 0.000000e+00 907.0
6 TraesCS6D01G017800 chr6A 85.479 303 29 2 2640 2927 7092339 7092641 5.860000e-78 302.0
7 TraesCS6D01G017800 chr6A 89.535 86 7 1 2714 2799 7184365 7184282 1.370000e-19 108.0
8 TraesCS6D01G017800 chr6A 89.394 66 6 1 2714 2778 7082070 7082135 8.320000e-12 82.4
9 TraesCS6D01G017800 chr6A 83.333 72 11 1 315 386 7079307 7079377 8.380000e-07 65.8
10 TraesCS6D01G017800 chr5B 90.263 2475 213 23 466 2928 432982684 432985142 0.000000e+00 3210.0
11 TraesCS6D01G017800 chr5B 85.484 62 4 4 357 415 432982448 432982507 3.900000e-05 60.2
12 TraesCS6D01G017800 chr7D 90.777 2266 202 7 465 2725 597677135 597674872 0.000000e+00 3020.0
13 TraesCS6D01G017800 chrUn 90.392 2269 206 12 465 2725 80037142 80034878 0.000000e+00 2972.0
14 TraesCS6D01G017800 chrUn 90.216 2269 207 14 465 2725 79937104 79939365 0.000000e+00 2946.0
15 TraesCS6D01G017800 chr6B 88.987 2370 241 18 465 2824 26861803 26864162 0.000000e+00 2913.0
16 TraesCS6D01G017800 chr6B 89.809 2257 217 12 466 2718 12886583 12888830 0.000000e+00 2881.0
17 TraesCS6D01G017800 chr6B 89.346 2187 213 17 465 2639 13653924 13651746 0.000000e+00 2730.0
18 TraesCS6D01G017800 chr6B 80.247 324 33 20 95 397 13441949 13441636 7.860000e-52 215.0
19 TraesCS6D01G017800 chr6B 85.484 62 4 4 357 415 12886332 12886391 3.900000e-05 60.2


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 TraesCS6D01G017800 chr6D 7356357 7359970 3613 True 6674.000000 6674 100.0000 1 3614 1 chr6D.!!$R1 3613
1 TraesCS6D01G017800 chr6D 7343439 7345967 2528 True 1491.000000 2736 85.4250 465 2927 2 chr6D.!!$R2 2462
2 TraesCS6D01G017800 chr6A 7173704 7175964 2260 True 2719.000000 2719 88.4090 465 2725 1 chr6A.!!$R1 2260
3 TraesCS6D01G017800 chr6A 7079307 7082598 3291 False 1325.733333 3829 87.5400 315 3445 3 chr6A.!!$F2 3130
4 TraesCS6D01G017800 chr6A 7183832 7184659 827 True 507.500000 907 88.1010 2644 3482 2 chr6A.!!$R2 838
5 TraesCS6D01G017800 chr5B 432982448 432985142 2694 False 1635.100000 3210 87.8735 357 2928 2 chr5B.!!$F1 2571
6 TraesCS6D01G017800 chr7D 597674872 597677135 2263 True 3020.000000 3020 90.7770 465 2725 1 chr7D.!!$R1 2260
7 TraesCS6D01G017800 chrUn 80034878 80037142 2264 True 2972.000000 2972 90.3920 465 2725 1 chrUn.!!$R1 2260
8 TraesCS6D01G017800 chrUn 79937104 79939365 2261 False 2946.000000 2946 90.2160 465 2725 1 chrUn.!!$F1 2260
9 TraesCS6D01G017800 chr6B 26861803 26864162 2359 False 2913.000000 2913 88.9870 465 2824 1 chr6B.!!$F1 2359
10 TraesCS6D01G017800 chr6B 13651746 13653924 2178 True 2730.000000 2730 89.3460 465 2639 1 chr6B.!!$R2 2174
11 TraesCS6D01G017800 chr6B 12886332 12888830 2498 False 1470.600000 2881 87.6465 357 2718 2 chr6B.!!$F2 2361

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
996 1172 0.175302 AGGCTGTCGAGCTGATTCAG 59.825 55.0 9.40 9.4 45.44 3.02 F
997 1173 0.809241 GGCTGTCGAGCTGATTCAGG 60.809 60.0 15.28 0.0 45.44 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1893 2075 0.033228 TTTTGCAAAGGCGGTCCATG 59.967 50.0 12.41 0.0 45.35 3.66 R
2676 2931 0.257039 CTTGGGGGATGCAAGCTACT 59.743 55.0 0.00 0.0 0.00 2.57 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
44 45 7.946655 TGTTATTCAACACACAAACACAAAA 57.053 28.000 0.00 0.00 39.75 2.44
45 46 8.365399 TGTTATTCAACACACAAACACAAAAA 57.635 26.923 0.00 0.00 39.75 1.94
46 47 8.993121 TGTTATTCAACACACAAACACAAAAAT 58.007 25.926 0.00 0.00 39.75 1.82
51 52 8.818141 TCAACACACAAACACAAAAATAAAGA 57.182 26.923 0.00 0.00 0.00 2.52
52 53 9.261180 TCAACACACAAACACAAAAATAAAGAA 57.739 25.926 0.00 0.00 0.00 2.52
53 54 9.869844 CAACACACAAACACAAAAATAAAGAAA 57.130 25.926 0.00 0.00 0.00 2.52
54 55 9.871299 AACACACAAACACAAAAATAAAGAAAC 57.129 25.926 0.00 0.00 0.00 2.78
55 56 9.046296 ACACACAAACACAAAAATAAAGAAACA 57.954 25.926 0.00 0.00 0.00 2.83
56 57 9.869844 CACACAAACACAAAAATAAAGAAACAA 57.130 25.926 0.00 0.00 0.00 2.83
72 73 7.935338 AAGAAACAAAAATAGCACATGTCTG 57.065 32.000 0.00 0.00 0.00 3.51
73 74 7.275888 AGAAACAAAAATAGCACATGTCTGA 57.724 32.000 0.00 0.00 0.00 3.27
74 75 7.715657 AGAAACAAAAATAGCACATGTCTGAA 58.284 30.769 0.00 0.00 0.00 3.02
75 76 8.196771 AGAAACAAAAATAGCACATGTCTGAAA 58.803 29.630 0.00 0.00 0.00 2.69
76 77 8.891671 AAACAAAAATAGCACATGTCTGAAAT 57.108 26.923 0.00 0.00 0.00 2.17
77 78 7.878477 ACAAAAATAGCACATGTCTGAAATG 57.122 32.000 6.27 6.27 0.00 2.32
78 79 7.660112 ACAAAAATAGCACATGTCTGAAATGA 58.340 30.769 14.63 0.00 0.00 2.57
79 80 7.811236 ACAAAAATAGCACATGTCTGAAATGAG 59.189 33.333 14.63 7.79 0.00 2.90
80 81 5.496133 AATAGCACATGTCTGAAATGAGC 57.504 39.130 18.85 18.85 40.58 4.26
81 82 2.089980 AGCACATGTCTGAAATGAGCC 58.910 47.619 21.65 8.45 41.00 4.70
82 83 2.089980 GCACATGTCTGAAATGAGCCT 58.910 47.619 16.53 0.00 36.13 4.58
83 84 2.159421 GCACATGTCTGAAATGAGCCTG 60.159 50.000 16.53 5.60 36.13 4.85
84 85 3.340928 CACATGTCTGAAATGAGCCTGA 58.659 45.455 14.63 0.00 0.00 3.86
85 86 3.126514 CACATGTCTGAAATGAGCCTGAC 59.873 47.826 14.63 0.00 33.60 3.51
86 87 3.008813 ACATGTCTGAAATGAGCCTGACT 59.991 43.478 14.63 0.00 33.96 3.41
87 88 4.223700 ACATGTCTGAAATGAGCCTGACTA 59.776 41.667 14.63 0.00 33.96 2.59
88 89 4.462508 TGTCTGAAATGAGCCTGACTAG 57.537 45.455 0.00 0.00 33.96 2.57
89 90 3.834813 TGTCTGAAATGAGCCTGACTAGT 59.165 43.478 0.00 0.00 33.96 2.57
90 91 4.284490 TGTCTGAAATGAGCCTGACTAGTT 59.716 41.667 0.00 0.00 33.96 2.24
91 92 4.629200 GTCTGAAATGAGCCTGACTAGTTG 59.371 45.833 0.00 0.00 0.00 3.16
92 93 4.284490 TCTGAAATGAGCCTGACTAGTTGT 59.716 41.667 0.00 0.00 0.00 3.32
93 94 4.973168 TGAAATGAGCCTGACTAGTTGTT 58.027 39.130 0.00 0.00 0.00 2.83
94 95 4.997395 TGAAATGAGCCTGACTAGTTGTTC 59.003 41.667 0.00 0.00 0.00 3.18
95 96 3.618690 ATGAGCCTGACTAGTTGTTCC 57.381 47.619 0.00 0.00 0.00 3.62
96 97 2.609747 TGAGCCTGACTAGTTGTTCCT 58.390 47.619 0.00 0.00 0.00 3.36
97 98 2.563179 TGAGCCTGACTAGTTGTTCCTC 59.437 50.000 0.00 1.08 0.00 3.71
98 99 1.903183 AGCCTGACTAGTTGTTCCTCC 59.097 52.381 0.00 0.00 0.00 4.30
99 100 1.623811 GCCTGACTAGTTGTTCCTCCA 59.376 52.381 0.00 0.00 0.00 3.86
100 101 2.237392 GCCTGACTAGTTGTTCCTCCAT 59.763 50.000 0.00 0.00 0.00 3.41
101 102 3.866651 CCTGACTAGTTGTTCCTCCATG 58.133 50.000 0.00 0.00 0.00 3.66
102 103 3.261897 CCTGACTAGTTGTTCCTCCATGT 59.738 47.826 0.00 0.00 0.00 3.21
103 104 4.499183 CTGACTAGTTGTTCCTCCATGTC 58.501 47.826 0.00 0.00 0.00 3.06
104 105 3.901222 TGACTAGTTGTTCCTCCATGTCA 59.099 43.478 0.00 0.00 0.00 3.58
105 106 4.021104 TGACTAGTTGTTCCTCCATGTCAG 60.021 45.833 0.00 0.00 0.00 3.51
106 107 2.867109 AGTTGTTCCTCCATGTCAGG 57.133 50.000 2.04 2.04 0.00 3.86
107 108 2.057922 AGTTGTTCCTCCATGTCAGGT 58.942 47.619 7.63 0.00 32.20 4.00
108 109 3.248024 AGTTGTTCCTCCATGTCAGGTA 58.752 45.455 7.63 0.00 32.20 3.08
109 110 3.846588 AGTTGTTCCTCCATGTCAGGTAT 59.153 43.478 7.63 0.00 32.20 2.73
110 111 5.030147 AGTTGTTCCTCCATGTCAGGTATA 58.970 41.667 7.63 0.00 32.20 1.47
111 112 5.104900 AGTTGTTCCTCCATGTCAGGTATAC 60.105 44.000 7.63 0.00 32.20 1.47
112 113 4.358214 TGTTCCTCCATGTCAGGTATACA 58.642 43.478 5.01 7.92 32.20 2.29
113 114 4.968719 TGTTCCTCCATGTCAGGTATACAT 59.031 41.667 5.01 0.00 38.08 2.29
114 115 6.140377 TGTTCCTCCATGTCAGGTATACATA 58.860 40.000 5.01 0.00 35.82 2.29
115 116 6.267699 TGTTCCTCCATGTCAGGTATACATAG 59.732 42.308 5.01 0.00 35.82 2.23
116 117 5.965486 TCCTCCATGTCAGGTATACATAGT 58.035 41.667 5.01 0.00 35.82 2.12
117 118 6.382087 TCCTCCATGTCAGGTATACATAGTT 58.618 40.000 5.01 0.00 35.82 2.24
118 119 6.844388 TCCTCCATGTCAGGTATACATAGTTT 59.156 38.462 5.01 0.00 35.82 2.66
119 120 7.347222 TCCTCCATGTCAGGTATACATAGTTTT 59.653 37.037 5.01 0.00 35.82 2.43
120 121 7.993183 CCTCCATGTCAGGTATACATAGTTTTT 59.007 37.037 5.01 0.00 35.82 1.94
125 126 9.847224 ATGTCAGGTATACATAGTTTTTAAGGG 57.153 33.333 5.01 0.00 35.82 3.95
126 127 7.771826 TGTCAGGTATACATAGTTTTTAAGGGC 59.228 37.037 5.01 0.00 0.00 5.19
127 128 7.771826 GTCAGGTATACATAGTTTTTAAGGGCA 59.228 37.037 5.01 0.00 0.00 5.36
128 129 8.330247 TCAGGTATACATAGTTTTTAAGGGCAA 58.670 33.333 5.01 0.00 0.00 4.52
129 130 8.962679 CAGGTATACATAGTTTTTAAGGGCAAA 58.037 33.333 5.01 0.00 0.00 3.68
130 131 9.536510 AGGTATACATAGTTTTTAAGGGCAAAA 57.463 29.630 5.01 0.00 0.00 2.44
131 132 9.577110 GGTATACATAGTTTTTAAGGGCAAAAC 57.423 33.333 5.01 3.46 42.22 2.43
141 142 8.884726 GTTTTTAAGGGCAAAACTGTAAAATCA 58.115 29.630 4.25 0.00 39.86 2.57
142 143 9.620259 TTTTTAAGGGCAAAACTGTAAAATCAT 57.380 25.926 0.00 0.00 0.00 2.45
143 144 9.620259 TTTTAAGGGCAAAACTGTAAAATCATT 57.380 25.926 0.00 0.00 0.00 2.57
144 145 9.620259 TTTAAGGGCAAAACTGTAAAATCATTT 57.380 25.926 0.00 0.00 0.00 2.32
145 146 9.620259 TTAAGGGCAAAACTGTAAAATCATTTT 57.380 25.926 0.02 0.02 36.67 1.82
146 147 8.518430 AAGGGCAAAACTGTAAAATCATTTTT 57.482 26.923 0.00 0.00 38.56 1.94
147 148 9.620259 AAGGGCAAAACTGTAAAATCATTTTTA 57.380 25.926 0.00 0.00 36.47 1.52
148 149 9.620259 AGGGCAAAACTGTAAAATCATTTTTAA 57.380 25.926 0.00 0.00 38.63 1.52
161 162 9.693739 AAAATCATTTTTAAAGGGGAAAACTGT 57.306 25.926 0.00 0.00 33.29 3.55
168 169 8.874744 TTTTAAAGGGGAAAACTGTAAAATCG 57.125 30.769 0.00 0.00 34.40 3.34
169 170 4.514781 AAGGGGAAAACTGTAAAATCGC 57.485 40.909 0.00 0.00 0.00 4.58
170 171 3.492337 AGGGGAAAACTGTAAAATCGCA 58.508 40.909 0.00 0.00 0.00 5.10
171 172 4.086457 AGGGGAAAACTGTAAAATCGCAT 58.914 39.130 0.00 0.00 0.00 4.73
172 173 4.082245 AGGGGAAAACTGTAAAATCGCATG 60.082 41.667 0.00 0.00 0.00 4.06
173 174 4.173256 GGGAAAACTGTAAAATCGCATGG 58.827 43.478 0.00 0.00 0.00 3.66
174 175 4.321675 GGGAAAACTGTAAAATCGCATGGT 60.322 41.667 0.00 0.00 0.00 3.55
175 176 4.621034 GGAAAACTGTAAAATCGCATGGTG 59.379 41.667 0.00 0.00 0.00 4.17
176 177 4.846779 AAACTGTAAAATCGCATGGTGT 57.153 36.364 0.00 0.00 0.00 4.16
177 178 3.829886 ACTGTAAAATCGCATGGTGTG 57.170 42.857 0.00 0.00 0.00 3.82
178 179 2.487762 ACTGTAAAATCGCATGGTGTGG 59.512 45.455 0.00 0.00 0.00 4.17
179 180 2.746904 CTGTAAAATCGCATGGTGTGGA 59.253 45.455 0.00 0.00 0.00 4.02
180 181 2.746904 TGTAAAATCGCATGGTGTGGAG 59.253 45.455 0.00 0.00 0.00 3.86
181 182 2.198827 AAAATCGCATGGTGTGGAGA 57.801 45.000 0.00 0.00 0.00 3.71
182 183 2.425143 AAATCGCATGGTGTGGAGAT 57.575 45.000 0.00 0.00 0.00 2.75
183 184 1.671979 AATCGCATGGTGTGGAGATG 58.328 50.000 0.00 0.00 0.00 2.90
184 185 0.816825 ATCGCATGGTGTGGAGATGC 60.817 55.000 0.00 0.00 39.31 3.91
185 186 2.475466 CGCATGGTGTGGAGATGCC 61.475 63.158 0.00 0.00 39.50 4.40
186 187 1.378911 GCATGGTGTGGAGATGCCA 60.379 57.895 0.00 0.00 46.96 4.92
202 203 2.166821 GCCAAATGCAAATGGTGTGA 57.833 45.000 19.03 0.00 40.77 3.58
203 204 2.492012 GCCAAATGCAAATGGTGTGAA 58.508 42.857 19.03 0.00 40.77 3.18
204 205 2.481185 GCCAAATGCAAATGGTGTGAAG 59.519 45.455 19.03 0.00 40.77 3.02
205 206 3.803021 GCCAAATGCAAATGGTGTGAAGA 60.803 43.478 19.03 0.00 40.77 2.87
206 207 4.571919 CCAAATGCAAATGGTGTGAAGAT 58.428 39.130 11.91 0.00 31.84 2.40
207 208 4.390603 CCAAATGCAAATGGTGTGAAGATG 59.609 41.667 11.91 0.00 31.84 2.90
208 209 2.728690 TGCAAATGGTGTGAAGATGC 57.271 45.000 0.00 0.00 0.00 3.91
209 210 1.273048 TGCAAATGGTGTGAAGATGCC 59.727 47.619 0.00 0.00 0.00 4.40
210 211 1.404583 GCAAATGGTGTGAAGATGCCC 60.405 52.381 0.00 0.00 0.00 5.36
211 212 2.173519 CAAATGGTGTGAAGATGCCCT 58.826 47.619 0.00 0.00 0.00 5.19
212 213 2.564062 CAAATGGTGTGAAGATGCCCTT 59.436 45.455 0.00 0.00 37.93 3.95
213 214 2.610438 ATGGTGTGAAGATGCCCTTT 57.390 45.000 0.00 0.00 34.68 3.11
214 215 1.619654 TGGTGTGAAGATGCCCTTTG 58.380 50.000 0.00 0.00 34.68 2.77
215 216 1.133513 TGGTGTGAAGATGCCCTTTGT 60.134 47.619 0.00 0.00 34.68 2.83
216 217 1.963515 GGTGTGAAGATGCCCTTTGTT 59.036 47.619 0.00 0.00 34.68 2.83
217 218 3.153919 GGTGTGAAGATGCCCTTTGTTA 58.846 45.455 0.00 0.00 34.68 2.41
218 219 3.572255 GGTGTGAAGATGCCCTTTGTTAA 59.428 43.478 0.00 0.00 34.68 2.01
219 220 4.220602 GGTGTGAAGATGCCCTTTGTTAAT 59.779 41.667 0.00 0.00 34.68 1.40
220 221 5.279456 GGTGTGAAGATGCCCTTTGTTAATT 60.279 40.000 0.00 0.00 34.68 1.40
221 222 6.223120 GTGTGAAGATGCCCTTTGTTAATTT 58.777 36.000 0.00 0.00 34.68 1.82
222 223 6.366061 GTGTGAAGATGCCCTTTGTTAATTTC 59.634 38.462 0.00 0.00 34.68 2.17
223 224 6.041409 TGTGAAGATGCCCTTTGTTAATTTCA 59.959 34.615 0.00 0.00 34.68 2.69
224 225 6.366061 GTGAAGATGCCCTTTGTTAATTTCAC 59.634 38.462 0.00 0.00 34.68 3.18
225 226 5.059404 AGATGCCCTTTGTTAATTTCACG 57.941 39.130 0.00 0.00 0.00 4.35
226 227 3.651803 TGCCCTTTGTTAATTTCACGG 57.348 42.857 0.00 0.00 0.00 4.94
227 228 2.959707 TGCCCTTTGTTAATTTCACGGT 59.040 40.909 0.00 0.00 0.00 4.83
228 229 4.142790 TGCCCTTTGTTAATTTCACGGTA 58.857 39.130 0.00 0.00 0.00 4.02
229 230 4.023021 TGCCCTTTGTTAATTTCACGGTAC 60.023 41.667 0.00 0.00 0.00 3.34
230 231 4.023021 GCCCTTTGTTAATTTCACGGTACA 60.023 41.667 0.00 0.00 0.00 2.90
231 232 5.695818 CCCTTTGTTAATTTCACGGTACAG 58.304 41.667 0.00 0.00 0.00 2.74
232 233 5.470777 CCCTTTGTTAATTTCACGGTACAGA 59.529 40.000 0.00 0.00 0.00 3.41
233 234 6.348213 CCCTTTGTTAATTTCACGGTACAGAG 60.348 42.308 0.00 0.00 0.00 3.35
234 235 6.348213 CCTTTGTTAATTTCACGGTACAGAGG 60.348 42.308 0.00 0.00 33.41 3.69
235 236 5.217978 TGTTAATTTCACGGTACAGAGGT 57.782 39.130 0.00 0.00 0.00 3.85
236 237 5.613329 TGTTAATTTCACGGTACAGAGGTT 58.387 37.500 0.00 0.00 0.00 3.50
237 238 5.467399 TGTTAATTTCACGGTACAGAGGTTG 59.533 40.000 0.00 0.00 0.00 3.77
238 239 4.345859 AATTTCACGGTACAGAGGTTGA 57.654 40.909 0.00 0.00 0.00 3.18
239 240 2.806608 TTCACGGTACAGAGGTTGAC 57.193 50.000 0.00 0.00 0.00 3.18
240 241 1.991121 TCACGGTACAGAGGTTGACT 58.009 50.000 0.00 0.00 0.00 3.41
241 242 2.313317 TCACGGTACAGAGGTTGACTT 58.687 47.619 0.00 0.00 0.00 3.01
242 243 2.295349 TCACGGTACAGAGGTTGACTTC 59.705 50.000 0.00 0.00 0.00 3.01
243 244 2.296471 CACGGTACAGAGGTTGACTTCT 59.704 50.000 0.00 0.00 32.03 2.85
244 245 2.963782 ACGGTACAGAGGTTGACTTCTT 59.036 45.455 0.00 0.00 29.11 2.52
245 246 3.243771 ACGGTACAGAGGTTGACTTCTTG 60.244 47.826 0.00 0.00 29.11 3.02
246 247 3.005472 CGGTACAGAGGTTGACTTCTTGA 59.995 47.826 0.00 0.00 29.11 3.02
247 248 4.561105 GGTACAGAGGTTGACTTCTTGAG 58.439 47.826 0.00 0.00 29.11 3.02
248 249 4.281182 GGTACAGAGGTTGACTTCTTGAGA 59.719 45.833 0.00 0.00 29.11 3.27
249 250 4.599047 ACAGAGGTTGACTTCTTGAGAG 57.401 45.455 0.00 0.00 29.11 3.20
250 251 4.219115 ACAGAGGTTGACTTCTTGAGAGA 58.781 43.478 0.00 0.00 29.11 3.10
251 252 4.280677 ACAGAGGTTGACTTCTTGAGAGAG 59.719 45.833 0.00 0.00 32.44 3.20
252 253 3.258123 AGAGGTTGACTTCTTGAGAGAGC 59.742 47.826 0.00 0.00 32.44 4.09
253 254 2.301583 AGGTTGACTTCTTGAGAGAGCC 59.698 50.000 0.00 0.00 32.44 4.70
254 255 2.333014 GTTGACTTCTTGAGAGAGCCG 58.667 52.381 0.00 0.00 32.44 5.52
255 256 1.911057 TGACTTCTTGAGAGAGCCGA 58.089 50.000 0.00 0.00 32.44 5.54
256 257 1.542030 TGACTTCTTGAGAGAGCCGAC 59.458 52.381 0.00 0.00 32.44 4.79
257 258 0.523966 ACTTCTTGAGAGAGCCGACG 59.476 55.000 0.00 0.00 32.44 5.12
258 259 0.179150 CTTCTTGAGAGAGCCGACGG 60.179 60.000 10.29 10.29 32.44 4.79
259 260 1.595993 TTCTTGAGAGAGCCGACGGG 61.596 60.000 17.22 0.00 32.44 5.28
260 261 2.035155 TTGAGAGAGCCGACGGGA 59.965 61.111 17.22 0.00 34.06 5.14
261 262 1.999071 CTTGAGAGAGCCGACGGGAG 61.999 65.000 17.22 0.00 34.06 4.30
262 263 3.894947 GAGAGAGCCGACGGGAGC 61.895 72.222 17.22 0.56 34.06 4.70
333 334 1.079057 GGAGGGCCGTCTTGTCTTC 60.079 63.158 23.90 2.75 0.00 2.87
334 335 1.079057 GAGGGCCGTCTTGTCTTCC 60.079 63.158 18.26 0.00 0.00 3.46
335 336 2.046217 GGGCCGTCTTGTCTTCCC 60.046 66.667 0.00 0.00 0.00 3.97
337 338 2.747686 GCCGTCTTGTCTTCCCCA 59.252 61.111 0.00 0.00 0.00 4.96
340 341 1.738099 CGTCTTGTCTTCCCCAGCG 60.738 63.158 0.00 0.00 0.00 5.18
422 439 2.211353 GGAGATCTCCTGTACGTTGC 57.789 55.000 31.11 3.67 46.16 4.17
423 440 1.476891 GGAGATCTCCTGTACGTTGCA 59.523 52.381 31.11 0.00 46.16 4.08
425 442 2.164624 GAGATCTCCTGTACGTTGCAGT 59.835 50.000 12.00 1.27 32.41 4.40
426 443 2.164624 AGATCTCCTGTACGTTGCAGTC 59.835 50.000 15.49 8.64 32.41 3.51
428 445 2.786777 TCTCCTGTACGTTGCAGTCTA 58.213 47.619 15.49 3.98 32.41 2.59
429 446 2.486982 TCTCCTGTACGTTGCAGTCTAC 59.513 50.000 15.49 0.00 32.41 2.59
430 447 1.542915 TCCTGTACGTTGCAGTCTACC 59.457 52.381 15.49 0.00 32.41 3.18
431 448 1.544691 CCTGTACGTTGCAGTCTACCT 59.455 52.381 15.49 0.00 32.41 3.08
432 449 2.415625 CCTGTACGTTGCAGTCTACCTC 60.416 54.545 15.49 0.00 32.41 3.85
433 450 2.228103 CTGTACGTTGCAGTCTACCTCA 59.772 50.000 0.00 0.00 0.00 3.86
442 460 2.888414 GCAGTCTACCTCATACCTCCTC 59.112 54.545 0.00 0.00 0.00 3.71
449 485 1.076559 TCATACCTCCTCCGGCGAA 60.077 57.895 9.30 0.00 0.00 4.70
455 491 2.602267 TCCTCCGGCGAAGGTGAA 60.602 61.111 13.22 0.00 35.29 3.18
462 498 0.673644 CGGCGAAGGTGAACATCCTT 60.674 55.000 0.00 0.00 46.44 3.36
463 499 1.534729 GGCGAAGGTGAACATCCTTT 58.465 50.000 0.00 0.00 44.19 3.11
533 705 1.985662 ATCAAGGACCGGTACCGCA 60.986 57.895 29.15 5.92 38.24 5.69
535 707 2.918802 AAGGACCGGTACCGCACA 60.919 61.111 29.15 0.00 38.24 4.57
539 711 3.637926 GACCGGTACCGCACAGGAC 62.638 68.421 29.15 11.21 44.66 3.85
593 765 0.449388 CGAATTGCTCCAGGTTGCTC 59.551 55.000 8.30 0.00 0.00 4.26
607 779 1.267574 TTGCTCAGCCCTCCTCGATT 61.268 55.000 0.00 0.00 0.00 3.34
608 780 1.227497 GCTCAGCCCTCCTCGATTG 60.227 63.158 0.00 0.00 0.00 2.67
644 819 3.948086 CTCACTGTCGTCGGCCGTC 62.948 68.421 27.15 19.73 37.94 4.79
702 877 0.538287 GCAAGAACCAAGGTGCCTCT 60.538 55.000 0.00 0.00 0.00 3.69
706 881 0.322008 GAACCAAGGTGCCTCTCCAG 60.322 60.000 0.00 0.00 0.00 3.86
731 906 4.030216 TGTCACCTATGGCATTCTAGTCA 58.970 43.478 4.78 0.00 34.80 3.41
739 914 2.038952 TGGCATTCTAGTCAACTGCTGT 59.961 45.455 0.00 0.00 33.43 4.40
815 990 6.699575 AGATGGGTTTTATGAAAGAATCCG 57.300 37.500 0.00 0.00 0.00 4.18
820 995 6.041069 TGGGTTTTATGAAAGAATCCGTTGTT 59.959 34.615 0.00 0.00 0.00 2.83
821 996 6.364976 GGGTTTTATGAAAGAATCCGTTGTTG 59.635 38.462 0.00 0.00 0.00 3.33
996 1172 0.175302 AGGCTGTCGAGCTGATTCAG 59.825 55.000 9.40 9.40 45.44 3.02
997 1173 0.809241 GGCTGTCGAGCTGATTCAGG 60.809 60.000 15.28 0.00 45.44 3.86
1070 1249 2.414559 CCGTGATTGATGGCTTGTTGAC 60.415 50.000 0.00 0.00 0.00 3.18
1084 1263 1.048601 GTTGACAGAGGGTGAGGTGA 58.951 55.000 0.00 0.00 0.00 4.02
1114 1293 6.389906 GCTTACAGCCTATTTTGTGAAATGT 58.610 36.000 0.00 0.00 34.68 2.71
1197 1376 1.368345 TTCATGCGATGGACAAGGCG 61.368 55.000 0.00 0.00 0.00 5.52
1224 1403 5.049129 GGAGGTTCTTCAACAGATGTTTGAG 60.049 44.000 0.00 0.00 35.83 3.02
1306 1485 2.508526 GACAGTGCAAAGAGGTGGATT 58.491 47.619 0.00 0.00 0.00 3.01
1314 1493 5.047377 GTGCAAAGAGGTGGATTGGATTTTA 60.047 40.000 0.00 0.00 0.00 1.52
1315 1494 5.721000 TGCAAAGAGGTGGATTGGATTTTAT 59.279 36.000 0.00 0.00 0.00 1.40
1316 1495 6.044682 GCAAAGAGGTGGATTGGATTTTATG 58.955 40.000 0.00 0.00 0.00 1.90
1587 1766 5.305386 TGGCTACAACATACTCATATCTGCT 59.695 40.000 0.00 0.00 0.00 4.24
1682 1861 1.136305 TGTAGTGAACTATGGAGCGGC 59.864 52.381 0.00 0.00 0.00 6.53
2231 2413 1.950216 TGGTGCGTTGCTTAAATGTCA 59.050 42.857 0.00 0.00 0.00 3.58
2445 2628 4.936685 AAGCTTACTTCAGAAAGGGGAT 57.063 40.909 0.00 0.00 36.78 3.85
2479 2662 7.280356 GGCTGGGACTTATCTGTCTAAAATTA 58.720 38.462 0.00 0.00 37.16 1.40
2516 2699 2.427506 CCTTGAAGGTTCCACAGCTAC 58.572 52.381 2.25 0.00 30.90 3.58
2642 2825 9.487790 CCTTTTCTAGAGATTTTGCCTAGATAG 57.512 37.037 0.00 0.00 38.75 2.08
2676 2931 1.614903 TCGAGGCCTCAACGTTTCTTA 59.385 47.619 31.67 0.00 0.00 2.10
2784 3039 7.666388 ACTTGTACTAGTAGTGAATGTCTGACT 59.334 37.037 13.29 0.00 0.00 3.41
2785 3040 7.379098 TGTACTAGTAGTGAATGTCTGACTG 57.621 40.000 13.29 0.00 0.00 3.51
2838 3110 1.066002 CTATTTCAATGGGGCTGTGCG 59.934 52.381 0.00 0.00 0.00 5.34
2932 3205 6.156748 ACGCCTTTTTCCTTGTCTAAAATT 57.843 33.333 0.00 0.00 0.00 1.82
2962 3235 7.822822 GCCACTTTTCTTACTAGTAATTCTGGA 59.177 37.037 15.57 6.61 0.00 3.86
2963 3236 9.892130 CCACTTTTCTTACTAGTAATTCTGGAT 57.108 33.333 15.57 0.00 0.00 3.41
2973 3246 7.331791 ACTAGTAATTCTGGATGGAACTTGTC 58.668 38.462 0.00 0.00 0.00 3.18
2995 3268 3.449018 CCTAGTAGTGAATGTCTGGCTGT 59.551 47.826 0.00 0.00 0.00 4.40
2996 3269 3.325293 AGTAGTGAATGTCTGGCTGTG 57.675 47.619 0.00 0.00 0.00 3.66
2997 3270 1.734465 GTAGTGAATGTCTGGCTGTGC 59.266 52.381 0.00 0.00 0.00 4.57
2998 3271 0.952497 AGTGAATGTCTGGCTGTGCG 60.952 55.000 0.00 0.00 0.00 5.34
3106 3389 4.574421 TGATGAACGACTGTGTGTTTCATT 59.426 37.500 0.00 0.00 36.68 2.57
3166 3449 0.745845 CGGCCTGAACTAAGCTGCAT 60.746 55.000 0.00 0.00 0.00 3.96
3363 3647 0.678684 TGATGACCATGCTGTGCCTG 60.679 55.000 0.00 0.00 0.00 4.85
3370 3654 1.679640 CCATGCTGTGCCTGTACATCA 60.680 52.381 0.00 0.00 32.07 3.07
3378 3662 3.758023 TGTGCCTGTACATCAATTGAAGG 59.242 43.478 13.09 14.78 0.00 3.46
3454 3738 7.867403 GGAAACATACAGCTTTCAAAGAATCAA 59.133 33.333 0.00 0.00 0.00 2.57
3461 3745 5.344128 CAGCTTTCAAAGAATCAATGTTCCG 59.656 40.000 0.00 0.00 0.00 4.30
3476 3760 0.034337 TTCCGTCCACCACTTAGCAC 59.966 55.000 0.00 0.00 0.00 4.40
3482 3766 3.119101 CGTCCACCACTTAGCACTCTATT 60.119 47.826 0.00 0.00 0.00 1.73
3483 3767 4.434520 GTCCACCACTTAGCACTCTATTC 58.565 47.826 0.00 0.00 0.00 1.75
3484 3768 4.081642 GTCCACCACTTAGCACTCTATTCA 60.082 45.833 0.00 0.00 0.00 2.57
3485 3769 4.716784 TCCACCACTTAGCACTCTATTCAT 59.283 41.667 0.00 0.00 0.00 2.57
3486 3770 5.189736 TCCACCACTTAGCACTCTATTCATT 59.810 40.000 0.00 0.00 0.00 2.57
3487 3771 6.382859 TCCACCACTTAGCACTCTATTCATTA 59.617 38.462 0.00 0.00 0.00 1.90
3488 3772 7.071196 TCCACCACTTAGCACTCTATTCATTAT 59.929 37.037 0.00 0.00 0.00 1.28
3489 3773 7.172190 CCACCACTTAGCACTCTATTCATTATG 59.828 40.741 0.00 0.00 0.00 1.90
3490 3774 7.928167 CACCACTTAGCACTCTATTCATTATGA 59.072 37.037 0.00 0.00 0.00 2.15
3491 3775 8.486210 ACCACTTAGCACTCTATTCATTATGAA 58.514 33.333 10.23 10.23 41.09 2.57
3492 3776 9.330063 CCACTTAGCACTCTATTCATTATGAAA 57.670 33.333 11.88 1.42 40.12 2.69
3498 3782 8.887717 AGCACTCTATTCATTATGAAAACTGAC 58.112 33.333 11.88 0.31 40.12 3.51
3499 3783 8.668353 GCACTCTATTCATTATGAAAACTGACA 58.332 33.333 11.88 0.00 40.12 3.58
3600 3884 9.528018 TTAGCACTTTTATTGTTTTTCAAGAGG 57.472 29.630 0.00 0.00 39.55 3.69
3601 3885 6.986231 AGCACTTTTATTGTTTTTCAAGAGGG 59.014 34.615 0.00 0.00 39.55 4.30
3602 3886 6.292865 GCACTTTTATTGTTTTTCAAGAGGGC 60.293 38.462 0.00 0.00 39.55 5.19
3603 3887 5.983118 ACTTTTATTGTTTTTCAAGAGGGCG 59.017 36.000 0.00 0.00 39.55 6.13
3604 3888 4.513198 TTATTGTTTTTCAAGAGGGCGG 57.487 40.909 0.00 0.00 39.55 6.13
3605 3889 1.770294 TTGTTTTTCAAGAGGGCGGT 58.230 45.000 0.00 0.00 0.00 5.68
3606 3890 1.770294 TGTTTTTCAAGAGGGCGGTT 58.230 45.000 0.00 0.00 0.00 4.44
3607 3891 2.933573 TGTTTTTCAAGAGGGCGGTTA 58.066 42.857 0.00 0.00 0.00 2.85
3608 3892 3.492337 TGTTTTTCAAGAGGGCGGTTAT 58.508 40.909 0.00 0.00 0.00 1.89
3609 3893 3.254657 TGTTTTTCAAGAGGGCGGTTATG 59.745 43.478 0.00 0.00 0.00 1.90
3610 3894 1.459450 TTTCAAGAGGGCGGTTATGC 58.541 50.000 0.00 0.00 0.00 3.14
3611 3895 0.618458 TTCAAGAGGGCGGTTATGCT 59.382 50.000 0.00 0.00 34.52 3.79
3612 3896 0.618458 TCAAGAGGGCGGTTATGCTT 59.382 50.000 0.00 0.00 34.52 3.91
3613 3897 1.834896 TCAAGAGGGCGGTTATGCTTA 59.165 47.619 0.00 0.00 34.52 3.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 7.946655 TTTTGTGTTTGTGTGTTGAATAACA 57.053 28.000 0.00 0.00 44.17 2.41
25 26 9.261180 TCTTTATTTTTGTGTTTGTGTGTTGAA 57.739 25.926 0.00 0.00 0.00 2.69
26 27 8.818141 TCTTTATTTTTGTGTTTGTGTGTTGA 57.182 26.923 0.00 0.00 0.00 3.18
27 28 9.869844 TTTCTTTATTTTTGTGTTTGTGTGTTG 57.130 25.926 0.00 0.00 0.00 3.33
28 29 9.871299 GTTTCTTTATTTTTGTGTTTGTGTGTT 57.129 25.926 0.00 0.00 0.00 3.32
29 30 9.046296 TGTTTCTTTATTTTTGTGTTTGTGTGT 57.954 25.926 0.00 0.00 0.00 3.72
30 31 9.869844 TTGTTTCTTTATTTTTGTGTTTGTGTG 57.130 25.926 0.00 0.00 0.00 3.82
46 47 9.462174 CAGACATGTGCTATTTTTGTTTCTTTA 57.538 29.630 1.15 0.00 0.00 1.85
47 48 8.196771 TCAGACATGTGCTATTTTTGTTTCTTT 58.803 29.630 1.15 0.00 0.00 2.52
48 49 7.715657 TCAGACATGTGCTATTTTTGTTTCTT 58.284 30.769 1.15 0.00 0.00 2.52
49 50 7.275888 TCAGACATGTGCTATTTTTGTTTCT 57.724 32.000 1.15 0.00 0.00 2.52
50 51 7.928908 TTCAGACATGTGCTATTTTTGTTTC 57.071 32.000 1.15 0.00 0.00 2.78
51 52 8.767085 CATTTCAGACATGTGCTATTTTTGTTT 58.233 29.630 1.15 0.00 0.00 2.83
52 53 8.143193 TCATTTCAGACATGTGCTATTTTTGTT 58.857 29.630 1.15 0.00 0.00 2.83
53 54 7.660112 TCATTTCAGACATGTGCTATTTTTGT 58.340 30.769 1.15 0.00 0.00 2.83
54 55 7.201410 GCTCATTTCAGACATGTGCTATTTTTG 60.201 37.037 1.15 0.00 37.88 2.44
55 56 6.810182 GCTCATTTCAGACATGTGCTATTTTT 59.190 34.615 1.15 0.00 37.88 1.94
56 57 6.327934 GCTCATTTCAGACATGTGCTATTTT 58.672 36.000 1.15 0.00 37.88 1.82
57 58 5.163581 GGCTCATTTCAGACATGTGCTATTT 60.164 40.000 18.49 0.00 39.83 1.40
58 59 4.337555 GGCTCATTTCAGACATGTGCTATT 59.662 41.667 18.49 0.00 39.83 1.73
59 60 3.881688 GGCTCATTTCAGACATGTGCTAT 59.118 43.478 18.49 0.00 39.83 2.97
60 61 3.054875 AGGCTCATTTCAGACATGTGCTA 60.055 43.478 18.49 0.00 39.83 3.49
61 62 2.089980 GGCTCATTTCAGACATGTGCT 58.910 47.619 18.49 0.00 39.83 4.40
62 63 2.089980 AGGCTCATTTCAGACATGTGC 58.910 47.619 1.15 13.11 39.41 4.57
63 64 3.126514 GTCAGGCTCATTTCAGACATGTG 59.873 47.826 1.15 0.00 0.00 3.21
64 65 3.008813 AGTCAGGCTCATTTCAGACATGT 59.991 43.478 0.00 0.00 0.00 3.21
65 66 3.607741 AGTCAGGCTCATTTCAGACATG 58.392 45.455 0.00 0.00 0.00 3.21
66 67 3.996921 AGTCAGGCTCATTTCAGACAT 57.003 42.857 2.34 0.00 0.00 3.06
67 68 3.834813 ACTAGTCAGGCTCATTTCAGACA 59.165 43.478 0.00 0.00 0.00 3.41
68 69 4.464069 ACTAGTCAGGCTCATTTCAGAC 57.536 45.455 0.00 0.00 0.00 3.51
69 70 4.284490 ACAACTAGTCAGGCTCATTTCAGA 59.716 41.667 0.00 0.00 0.00 3.27
70 71 4.573900 ACAACTAGTCAGGCTCATTTCAG 58.426 43.478 0.00 0.00 0.00 3.02
71 72 4.623932 ACAACTAGTCAGGCTCATTTCA 57.376 40.909 0.00 0.00 0.00 2.69
72 73 4.393371 GGAACAACTAGTCAGGCTCATTTC 59.607 45.833 0.00 0.00 0.00 2.17
73 74 4.042187 AGGAACAACTAGTCAGGCTCATTT 59.958 41.667 0.00 0.00 0.00 2.32
74 75 3.584848 AGGAACAACTAGTCAGGCTCATT 59.415 43.478 0.00 0.00 0.00 2.57
75 76 3.177228 AGGAACAACTAGTCAGGCTCAT 58.823 45.455 0.00 0.00 0.00 2.90
76 77 2.563179 GAGGAACAACTAGTCAGGCTCA 59.437 50.000 0.00 0.00 0.00 4.26
77 78 2.093921 GGAGGAACAACTAGTCAGGCTC 60.094 54.545 0.00 0.00 0.00 4.70
78 79 1.903183 GGAGGAACAACTAGTCAGGCT 59.097 52.381 0.00 0.00 0.00 4.58
79 80 1.623811 TGGAGGAACAACTAGTCAGGC 59.376 52.381 0.00 0.00 0.00 4.85
80 81 3.261897 ACATGGAGGAACAACTAGTCAGG 59.738 47.826 0.00 0.00 0.00 3.86
81 82 4.021104 TGACATGGAGGAACAACTAGTCAG 60.021 45.833 0.00 0.00 0.00 3.51
82 83 3.901222 TGACATGGAGGAACAACTAGTCA 59.099 43.478 0.00 0.00 0.00 3.41
83 84 4.499183 CTGACATGGAGGAACAACTAGTC 58.501 47.826 0.00 0.00 0.00 2.59
84 85 3.261897 CCTGACATGGAGGAACAACTAGT 59.738 47.826 7.16 0.00 31.48 2.57
85 86 3.261897 ACCTGACATGGAGGAACAACTAG 59.738 47.826 17.61 0.00 34.37 2.57
86 87 3.248024 ACCTGACATGGAGGAACAACTA 58.752 45.455 17.61 0.00 34.37 2.24
87 88 2.057922 ACCTGACATGGAGGAACAACT 58.942 47.619 17.61 0.00 34.37 3.16
88 89 2.568623 ACCTGACATGGAGGAACAAC 57.431 50.000 17.61 0.00 34.37 3.32
89 90 4.780554 TGTATACCTGACATGGAGGAACAA 59.219 41.667 17.61 3.38 34.37 2.83
90 91 4.358214 TGTATACCTGACATGGAGGAACA 58.642 43.478 17.61 14.49 34.37 3.18
91 92 5.552870 ATGTATACCTGACATGGAGGAAC 57.447 43.478 17.61 12.67 36.18 3.62
92 93 6.382087 ACTATGTATACCTGACATGGAGGAA 58.618 40.000 17.61 2.81 37.84 3.36
93 94 5.965486 ACTATGTATACCTGACATGGAGGA 58.035 41.667 17.61 4.46 37.84 3.71
94 95 6.672266 AACTATGTATACCTGACATGGAGG 57.328 41.667 10.72 10.72 37.84 4.30
95 96 8.964476 AAAAACTATGTATACCTGACATGGAG 57.036 34.615 0.00 0.00 37.84 3.86
99 100 9.847224 CCCTTAAAAACTATGTATACCTGACAT 57.153 33.333 0.00 0.00 40.59 3.06
100 101 7.771826 GCCCTTAAAAACTATGTATACCTGACA 59.228 37.037 0.00 0.00 0.00 3.58
101 102 7.771826 TGCCCTTAAAAACTATGTATACCTGAC 59.228 37.037 0.00 0.00 0.00 3.51
102 103 7.863722 TGCCCTTAAAAACTATGTATACCTGA 58.136 34.615 0.00 0.00 0.00 3.86
103 104 8.514330 TTGCCCTTAAAAACTATGTATACCTG 57.486 34.615 0.00 0.00 0.00 4.00
104 105 9.536510 TTTTGCCCTTAAAAACTATGTATACCT 57.463 29.630 0.00 0.00 0.00 3.08
105 106 9.577110 GTTTTGCCCTTAAAAACTATGTATACC 57.423 33.333 0.00 0.00 41.92 2.73
115 116 8.884726 TGATTTTACAGTTTTGCCCTTAAAAAC 58.115 29.630 4.08 4.08 44.29 2.43
116 117 9.620259 ATGATTTTACAGTTTTGCCCTTAAAAA 57.380 25.926 0.00 0.00 31.92 1.94
117 118 9.620259 AATGATTTTACAGTTTTGCCCTTAAAA 57.380 25.926 0.00 0.00 0.00 1.52
118 119 9.620259 AAATGATTTTACAGTTTTGCCCTTAAA 57.380 25.926 0.00 0.00 0.00 1.52
119 120 9.620259 AAAATGATTTTACAGTTTTGCCCTTAA 57.380 25.926 0.49 0.00 35.12 1.85
120 121 9.620259 AAAAATGATTTTACAGTTTTGCCCTTA 57.380 25.926 3.26 0.00 43.12 2.69
121 122 8.518430 AAAAATGATTTTACAGTTTTGCCCTT 57.482 26.923 3.26 0.00 43.12 3.95
122 123 9.620259 TTAAAAATGATTTTACAGTTTTGCCCT 57.380 25.926 14.07 0.00 43.99 5.19
135 136 9.693739 ACAGTTTTCCCCTTTAAAAATGATTTT 57.306 25.926 13.59 0.00 41.81 1.82
142 143 9.315525 CGATTTTACAGTTTTCCCCTTTAAAAA 57.684 29.630 0.00 0.00 31.54 1.94
143 144 7.438757 GCGATTTTACAGTTTTCCCCTTTAAAA 59.561 33.333 0.00 0.00 32.02 1.52
144 145 6.924612 GCGATTTTACAGTTTTCCCCTTTAAA 59.075 34.615 0.00 0.00 0.00 1.52
145 146 6.040616 TGCGATTTTACAGTTTTCCCCTTTAA 59.959 34.615 0.00 0.00 0.00 1.52
146 147 5.535406 TGCGATTTTACAGTTTTCCCCTTTA 59.465 36.000 0.00 0.00 0.00 1.85
147 148 4.342665 TGCGATTTTACAGTTTTCCCCTTT 59.657 37.500 0.00 0.00 0.00 3.11
148 149 3.892588 TGCGATTTTACAGTTTTCCCCTT 59.107 39.130 0.00 0.00 0.00 3.95
149 150 3.492337 TGCGATTTTACAGTTTTCCCCT 58.508 40.909 0.00 0.00 0.00 4.79
150 151 3.926821 TGCGATTTTACAGTTTTCCCC 57.073 42.857 0.00 0.00 0.00 4.81
151 152 4.173256 CCATGCGATTTTACAGTTTTCCC 58.827 43.478 0.00 0.00 0.00 3.97
152 153 4.621034 CACCATGCGATTTTACAGTTTTCC 59.379 41.667 0.00 0.00 0.00 3.13
153 154 5.116983 CACACCATGCGATTTTACAGTTTTC 59.883 40.000 0.00 0.00 0.00 2.29
154 155 4.981674 CACACCATGCGATTTTACAGTTTT 59.018 37.500 0.00 0.00 0.00 2.43
155 156 4.545610 CACACCATGCGATTTTACAGTTT 58.454 39.130 0.00 0.00 0.00 2.66
156 157 3.057596 CCACACCATGCGATTTTACAGTT 60.058 43.478 0.00 0.00 0.00 3.16
157 158 2.487762 CCACACCATGCGATTTTACAGT 59.512 45.455 0.00 0.00 0.00 3.55
158 159 2.746904 TCCACACCATGCGATTTTACAG 59.253 45.455 0.00 0.00 0.00 2.74
159 160 2.746904 CTCCACACCATGCGATTTTACA 59.253 45.455 0.00 0.00 0.00 2.41
160 161 3.006940 TCTCCACACCATGCGATTTTAC 58.993 45.455 0.00 0.00 0.00 2.01
161 162 3.342377 TCTCCACACCATGCGATTTTA 57.658 42.857 0.00 0.00 0.00 1.52
162 163 2.198827 TCTCCACACCATGCGATTTT 57.801 45.000 0.00 0.00 0.00 1.82
163 164 2.019249 CATCTCCACACCATGCGATTT 58.981 47.619 0.00 0.00 0.00 2.17
164 165 1.671979 CATCTCCACACCATGCGATT 58.328 50.000 0.00 0.00 0.00 3.34
165 166 0.816825 GCATCTCCACACCATGCGAT 60.817 55.000 0.00 0.00 34.01 4.58
166 167 1.450134 GCATCTCCACACCATGCGA 60.450 57.895 0.00 0.00 34.01 5.10
167 168 2.475466 GGCATCTCCACACCATGCG 61.475 63.158 0.00 0.00 43.32 4.73
168 169 0.966875 TTGGCATCTCCACACCATGC 60.967 55.000 0.00 0.00 46.55 4.06
169 170 1.548081 TTTGGCATCTCCACACCATG 58.452 50.000 0.00 0.00 46.55 3.66
170 171 2.104967 CATTTGGCATCTCCACACCAT 58.895 47.619 0.00 0.00 46.55 3.55
171 172 1.548081 CATTTGGCATCTCCACACCA 58.452 50.000 0.00 0.00 46.55 4.17
172 173 0.174162 GCATTTGGCATCTCCACACC 59.826 55.000 0.00 0.00 46.55 4.16
173 174 3.727419 GCATTTGGCATCTCCACAC 57.273 52.632 0.00 0.00 46.55 3.82
183 184 2.166821 TCACACCATTTGCATTTGGC 57.833 45.000 13.81 0.00 45.13 4.52
184 185 3.992643 TCTTCACACCATTTGCATTTGG 58.007 40.909 12.61 12.61 39.02 3.28
185 186 4.142988 GCATCTTCACACCATTTGCATTTG 60.143 41.667 0.00 0.00 0.00 2.32
186 187 3.998341 GCATCTTCACACCATTTGCATTT 59.002 39.130 0.00 0.00 0.00 2.32
187 188 3.592059 GCATCTTCACACCATTTGCATT 58.408 40.909 0.00 0.00 0.00 3.56
188 189 2.093869 GGCATCTTCACACCATTTGCAT 60.094 45.455 0.00 0.00 0.00 3.96
189 190 1.273048 GGCATCTTCACACCATTTGCA 59.727 47.619 0.00 0.00 0.00 4.08
190 191 1.404583 GGGCATCTTCACACCATTTGC 60.405 52.381 0.00 0.00 0.00 3.68
191 192 2.173519 AGGGCATCTTCACACCATTTG 58.826 47.619 0.00 0.00 0.00 2.32
192 193 2.610438 AGGGCATCTTCACACCATTT 57.390 45.000 0.00 0.00 0.00 2.32
193 194 2.564062 CAAAGGGCATCTTCACACCATT 59.436 45.455 0.00 0.00 33.94 3.16
194 195 2.173519 CAAAGGGCATCTTCACACCAT 58.826 47.619 0.00 0.00 33.94 3.55
195 196 1.133513 ACAAAGGGCATCTTCACACCA 60.134 47.619 0.00 0.00 33.94 4.17
196 197 1.620822 ACAAAGGGCATCTTCACACC 58.379 50.000 0.00 0.00 33.94 4.16
197 198 4.846779 TTAACAAAGGGCATCTTCACAC 57.153 40.909 0.00 0.00 33.94 3.82
198 199 6.041409 TGAAATTAACAAAGGGCATCTTCACA 59.959 34.615 0.00 0.00 33.94 3.58
199 200 6.366061 GTGAAATTAACAAAGGGCATCTTCAC 59.634 38.462 0.00 0.00 33.94 3.18
200 201 6.454795 GTGAAATTAACAAAGGGCATCTTCA 58.545 36.000 0.00 0.00 33.94 3.02
201 202 5.572896 CGTGAAATTAACAAAGGGCATCTTC 59.427 40.000 0.00 0.00 33.94 2.87
202 203 5.469479 CGTGAAATTAACAAAGGGCATCTT 58.531 37.500 0.00 0.00 37.28 2.40
203 204 4.082245 CCGTGAAATTAACAAAGGGCATCT 60.082 41.667 0.00 0.00 0.00 2.90
204 205 4.173256 CCGTGAAATTAACAAAGGGCATC 58.827 43.478 0.00 0.00 0.00 3.91
205 206 3.576550 ACCGTGAAATTAACAAAGGGCAT 59.423 39.130 10.56 0.00 0.00 4.40
206 207 2.959707 ACCGTGAAATTAACAAAGGGCA 59.040 40.909 10.56 0.00 0.00 5.36
207 208 3.653539 ACCGTGAAATTAACAAAGGGC 57.346 42.857 10.56 0.00 0.00 5.19
208 209 5.470777 TCTGTACCGTGAAATTAACAAAGGG 59.529 40.000 0.00 0.00 0.00 3.95
209 210 6.348213 CCTCTGTACCGTGAAATTAACAAAGG 60.348 42.308 0.00 0.00 0.00 3.11
210 211 6.204108 ACCTCTGTACCGTGAAATTAACAAAG 59.796 38.462 0.00 0.00 0.00 2.77
211 212 6.056884 ACCTCTGTACCGTGAAATTAACAAA 58.943 36.000 0.00 0.00 0.00 2.83
212 213 5.613329 ACCTCTGTACCGTGAAATTAACAA 58.387 37.500 0.00 0.00 0.00 2.83
213 214 5.217978 ACCTCTGTACCGTGAAATTAACA 57.782 39.130 0.00 0.00 0.00 2.41
214 215 5.697633 TCAACCTCTGTACCGTGAAATTAAC 59.302 40.000 0.00 0.00 0.00 2.01
215 216 5.697633 GTCAACCTCTGTACCGTGAAATTAA 59.302 40.000 0.00 0.00 0.00 1.40
216 217 5.011329 AGTCAACCTCTGTACCGTGAAATTA 59.989 40.000 0.00 0.00 0.00 1.40
217 218 4.062991 GTCAACCTCTGTACCGTGAAATT 58.937 43.478 0.00 0.00 0.00 1.82
218 219 3.323979 AGTCAACCTCTGTACCGTGAAAT 59.676 43.478 0.00 0.00 0.00 2.17
219 220 2.696707 AGTCAACCTCTGTACCGTGAAA 59.303 45.455 0.00 0.00 0.00 2.69
220 221 2.313317 AGTCAACCTCTGTACCGTGAA 58.687 47.619 0.00 0.00 0.00 3.18
221 222 1.991121 AGTCAACCTCTGTACCGTGA 58.009 50.000 0.00 0.00 0.00 4.35
222 223 2.296471 AGAAGTCAACCTCTGTACCGTG 59.704 50.000 0.00 0.00 0.00 4.94
223 224 2.595238 AGAAGTCAACCTCTGTACCGT 58.405 47.619 0.00 0.00 0.00 4.83
224 225 3.005472 TCAAGAAGTCAACCTCTGTACCG 59.995 47.826 0.00 0.00 0.00 4.02
225 226 4.281182 TCTCAAGAAGTCAACCTCTGTACC 59.719 45.833 0.00 0.00 0.00 3.34
226 227 5.241949 TCTCTCAAGAAGTCAACCTCTGTAC 59.758 44.000 0.00 0.00 0.00 2.90
227 228 5.386060 TCTCTCAAGAAGTCAACCTCTGTA 58.614 41.667 0.00 0.00 0.00 2.74
228 229 4.219115 TCTCTCAAGAAGTCAACCTCTGT 58.781 43.478 0.00 0.00 0.00 3.41
229 230 4.808558 CTCTCTCAAGAAGTCAACCTCTG 58.191 47.826 0.00 0.00 0.00 3.35
230 231 3.258123 GCTCTCTCAAGAAGTCAACCTCT 59.742 47.826 0.00 0.00 0.00 3.69
231 232 3.584834 GCTCTCTCAAGAAGTCAACCTC 58.415 50.000 0.00 0.00 0.00 3.85
232 233 2.301583 GGCTCTCTCAAGAAGTCAACCT 59.698 50.000 0.00 0.00 0.00 3.50
233 234 2.694213 GGCTCTCTCAAGAAGTCAACC 58.306 52.381 0.00 0.00 0.00 3.77
234 235 2.029828 TCGGCTCTCTCAAGAAGTCAAC 60.030 50.000 0.00 0.00 0.00 3.18
235 236 2.029828 GTCGGCTCTCTCAAGAAGTCAA 60.030 50.000 0.00 0.00 0.00 3.18
236 237 1.542030 GTCGGCTCTCTCAAGAAGTCA 59.458 52.381 0.00 0.00 0.00 3.41
237 238 1.466697 CGTCGGCTCTCTCAAGAAGTC 60.467 57.143 0.00 0.00 0.00 3.01
238 239 0.523966 CGTCGGCTCTCTCAAGAAGT 59.476 55.000 0.00 0.00 0.00 3.01
239 240 0.179150 CCGTCGGCTCTCTCAAGAAG 60.179 60.000 0.00 0.00 0.00 2.85
240 241 1.595993 CCCGTCGGCTCTCTCAAGAA 61.596 60.000 5.50 0.00 0.00 2.52
241 242 2.046864 CCCGTCGGCTCTCTCAAGA 61.047 63.158 5.50 0.00 0.00 3.02
242 243 1.999071 CTCCCGTCGGCTCTCTCAAG 61.999 65.000 5.50 0.00 0.00 3.02
243 244 2.035155 TCCCGTCGGCTCTCTCAA 59.965 61.111 5.50 0.00 0.00 3.02
244 245 2.438614 CTCCCGTCGGCTCTCTCA 60.439 66.667 5.50 0.00 0.00 3.27
245 246 3.894947 GCTCCCGTCGGCTCTCTC 61.895 72.222 5.50 0.00 0.00 3.20
321 322 1.376037 GCTGGGGAAGACAAGACGG 60.376 63.158 0.00 0.00 0.00 4.79
324 325 1.118965 TGACGCTGGGGAAGACAAGA 61.119 55.000 0.00 0.00 0.00 3.02
327 328 2.583441 CCTGACGCTGGGGAAGACA 61.583 63.158 0.00 0.00 0.00 3.41
355 356 4.632458 GACGAGATCTCCGCCGCC 62.632 72.222 17.13 0.00 0.00 6.13
417 434 2.427453 AGGTATGAGGTAGACTGCAACG 59.573 50.000 0.00 0.00 0.00 4.10
418 435 3.181474 GGAGGTATGAGGTAGACTGCAAC 60.181 52.174 0.00 0.00 0.00 4.17
419 436 3.031736 GGAGGTATGAGGTAGACTGCAA 58.968 50.000 0.00 0.00 0.00 4.08
420 437 2.245028 AGGAGGTATGAGGTAGACTGCA 59.755 50.000 0.00 0.00 0.00 4.41
421 438 2.888414 GAGGAGGTATGAGGTAGACTGC 59.112 54.545 0.00 0.00 0.00 4.40
422 439 3.492337 GGAGGAGGTATGAGGTAGACTG 58.508 54.545 0.00 0.00 0.00 3.51
423 440 2.106857 CGGAGGAGGTATGAGGTAGACT 59.893 54.545 0.00 0.00 0.00 3.24
425 442 2.953284 CGGAGGAGGTATGAGGTAGA 57.047 55.000 0.00 0.00 0.00 2.59
442 460 2.106683 GGATGTTCACCTTCGCCGG 61.107 63.158 0.00 0.00 0.00 6.13
449 485 4.521146 CTCATAGCAAAGGATGTTCACCT 58.479 43.478 0.00 0.00 39.69 4.00
455 491 1.959042 CGGCTCATAGCAAAGGATGT 58.041 50.000 0.78 0.00 44.75 3.06
533 705 1.600636 CGGTGCCAATGTGTCCTGT 60.601 57.895 0.00 0.00 0.00 4.00
535 707 1.003355 CTCGGTGCCAATGTGTCCT 60.003 57.895 0.00 0.00 0.00 3.85
539 711 1.996786 GCATCCTCGGTGCCAATGTG 61.997 60.000 0.00 0.00 36.61 3.21
593 765 1.523258 CAGCAATCGAGGAGGGCTG 60.523 63.158 10.67 10.67 44.91 4.85
702 877 1.195115 GCCATAGGTGACACTCTGGA 58.805 55.000 19.27 0.00 37.00 3.86
706 881 3.550437 AGAATGCCATAGGTGACACTC 57.450 47.619 5.39 0.00 0.00 3.51
799 974 6.744112 AGCAACAACGGATTCTTTCATAAAA 58.256 32.000 0.00 0.00 0.00 1.52
805 980 4.606961 TGAAAGCAACAACGGATTCTTTC 58.393 39.130 0.00 0.00 39.59 2.62
806 981 4.610945 CTGAAAGCAACAACGGATTCTTT 58.389 39.130 0.00 0.00 0.00 2.52
807 982 4.228912 CTGAAAGCAACAACGGATTCTT 57.771 40.909 0.00 0.00 0.00 2.52
982 1158 2.200067 CATCACCTGAATCAGCTCGAC 58.800 52.381 4.40 0.00 0.00 4.20
996 1172 1.386533 CTCCATGCTCAACCATCACC 58.613 55.000 0.00 0.00 0.00 4.02
997 1173 1.340405 ACCTCCATGCTCAACCATCAC 60.340 52.381 0.00 0.00 0.00 3.06
1070 1249 1.271054 CCTTGTTCACCTCACCCTCTG 60.271 57.143 0.00 0.00 0.00 3.35
1114 1293 1.406341 CGGCGAAATTCCCCTCTGTAA 60.406 52.381 0.00 0.00 0.00 2.41
1197 1376 3.008485 ACATCTGTTGAAGAACCTCCTCC 59.992 47.826 0.00 0.00 38.79 4.30
1224 1403 2.898705 ACATCTGGCAGAATTCGTCTC 58.101 47.619 22.84 0.00 32.70 3.36
1306 1485 9.713684 ATTTCTAGACATTTCCCATAAAATCCA 57.286 29.630 0.00 0.00 0.00 3.41
1314 1493 5.831103 ACACCATTTCTAGACATTTCCCAT 58.169 37.500 0.00 0.00 0.00 4.00
1315 1494 5.255397 ACACCATTTCTAGACATTTCCCA 57.745 39.130 0.00 0.00 0.00 4.37
1316 1495 5.710099 TGAACACCATTTCTAGACATTTCCC 59.290 40.000 0.00 0.00 0.00 3.97
1651 1830 4.543590 AGTTCACTACATCAGGGTTCAG 57.456 45.455 0.00 0.00 0.00 3.02
1682 1861 6.998258 CAATCTTGGAAAGCAAGTTTACTG 57.002 37.500 0.00 0.00 45.70 2.74
1893 2075 0.033228 TTTTGCAAAGGCGGTCCATG 59.967 50.000 12.41 0.00 45.35 3.66
2231 2413 4.170468 TCTTTTGCTTCTTCCTTCCTGT 57.830 40.909 0.00 0.00 0.00 4.00
2479 2662 1.963985 AGGGTGAAGCTCCTCTCATT 58.036 50.000 0.00 0.00 0.00 2.57
2504 2687 2.548480 GTCAACAAGGTAGCTGTGGAAC 59.452 50.000 0.00 0.00 28.47 3.62
2516 2699 0.317269 CGCAAGTGCAGTCAACAAGG 60.317 55.000 3.87 0.00 42.21 3.61
2546 2729 4.984146 AACTCCTTATATTCCTGGCCTC 57.016 45.455 3.32 0.00 0.00 4.70
2642 2825 1.666189 GCCTCGATTAGCAGTCCAAAC 59.334 52.381 0.00 0.00 0.00 2.93
2676 2931 0.257039 CTTGGGGGATGCAAGCTACT 59.743 55.000 0.00 0.00 0.00 2.57
2838 3110 1.068264 GCAGCTTAGTTGAGGCCAAAC 60.068 52.381 5.01 9.58 33.49 2.93
2932 3205 9.662947 GAATTACTAGTAAGAAAAGTGGCCTAA 57.337 33.333 19.58 0.00 0.00 2.69
2973 3246 3.449018 ACAGCCAGACATTCACTACTAGG 59.551 47.826 0.00 0.00 0.00 3.02
2995 3268 2.016318 CCTACATTTCAGAATGGCGCA 58.984 47.619 10.83 0.00 45.56 6.09
2996 3269 2.017049 ACCTACATTTCAGAATGGCGC 58.983 47.619 0.00 0.00 45.56 6.53
2997 3270 3.063997 GTGACCTACATTTCAGAATGGCG 59.936 47.826 4.39 0.00 45.56 5.69
2998 3271 4.265073 AGTGACCTACATTTCAGAATGGC 58.735 43.478 4.39 0.00 45.56 4.40
3050 3333 5.185249 CCAGTCAGAAGTTTACTACTAGCCA 59.815 44.000 0.00 0.00 35.54 4.75
3106 3389 8.762481 TGAAGAAGTAGTACTCAGCCATATAA 57.238 34.615 2.58 0.00 0.00 0.98
3147 3430 0.745845 ATGCAGCTTAGTTCAGGCCG 60.746 55.000 0.00 0.00 0.00 6.13
3221 3504 0.102120 CACAGCGCACAAGGGAAAAA 59.898 50.000 11.47 0.00 0.00 1.94
3363 3647 6.149474 ACTGCTAACACCTTCAATTGATGTAC 59.851 38.462 9.40 5.40 0.00 2.90
3370 3654 7.937394 ACTAACTTACTGCTAACACCTTCAATT 59.063 33.333 0.00 0.00 0.00 2.32
3436 3720 6.218746 GGAACATTGATTCTTTGAAAGCTGT 58.781 36.000 0.00 0.00 0.00 4.40
3440 3724 5.858581 GGACGGAACATTGATTCTTTGAAAG 59.141 40.000 0.00 0.00 0.00 2.62
3445 3729 3.506067 GGTGGACGGAACATTGATTCTTT 59.494 43.478 0.00 0.00 0.00 2.52
3454 3738 1.338769 GCTAAGTGGTGGACGGAACAT 60.339 52.381 0.00 0.00 0.00 2.71
3461 3745 4.081642 TGAATAGAGTGCTAAGTGGTGGAC 60.082 45.833 0.00 0.00 0.00 4.02
3574 3858 9.528018 CCTCTTGAAAAACAATAAAAGTGCTAA 57.472 29.630 0.00 0.00 37.88 3.09
3575 3859 8.141268 CCCTCTTGAAAAACAATAAAAGTGCTA 58.859 33.333 0.00 0.00 37.88 3.49
3576 3860 6.986231 CCCTCTTGAAAAACAATAAAAGTGCT 59.014 34.615 0.00 0.00 37.88 4.40
3577 3861 6.292865 GCCCTCTTGAAAAACAATAAAAGTGC 60.293 38.462 0.00 0.00 37.88 4.40
3578 3862 6.074356 CGCCCTCTTGAAAAACAATAAAAGTG 60.074 38.462 0.00 0.00 37.88 3.16
3579 3863 5.983118 CGCCCTCTTGAAAAACAATAAAAGT 59.017 36.000 0.00 0.00 37.88 2.66
3580 3864 5.405269 CCGCCCTCTTGAAAAACAATAAAAG 59.595 40.000 0.00 0.00 37.88 2.27
3581 3865 5.163395 ACCGCCCTCTTGAAAAACAATAAAA 60.163 36.000 0.00 0.00 37.88 1.52
3582 3866 4.342665 ACCGCCCTCTTGAAAAACAATAAA 59.657 37.500 0.00 0.00 37.88 1.40
3583 3867 3.892588 ACCGCCCTCTTGAAAAACAATAA 59.107 39.130 0.00 0.00 37.88 1.40
3584 3868 3.492337 ACCGCCCTCTTGAAAAACAATA 58.508 40.909 0.00 0.00 37.88 1.90
3585 3869 2.316108 ACCGCCCTCTTGAAAAACAAT 58.684 42.857 0.00 0.00 37.88 2.71
3586 3870 1.770294 ACCGCCCTCTTGAAAAACAA 58.230 45.000 0.00 0.00 36.97 2.83
3587 3871 1.770294 AACCGCCCTCTTGAAAAACA 58.230 45.000 0.00 0.00 0.00 2.83
3588 3872 3.833442 CATAACCGCCCTCTTGAAAAAC 58.167 45.455 0.00 0.00 0.00 2.43
3589 3873 2.230266 GCATAACCGCCCTCTTGAAAAA 59.770 45.455 0.00 0.00 0.00 1.94
3590 3874 1.816224 GCATAACCGCCCTCTTGAAAA 59.184 47.619 0.00 0.00 0.00 2.29
3591 3875 1.004277 AGCATAACCGCCCTCTTGAAA 59.996 47.619 0.00 0.00 0.00 2.69
3592 3876 0.618458 AGCATAACCGCCCTCTTGAA 59.382 50.000 0.00 0.00 0.00 2.69
3593 3877 0.618458 AAGCATAACCGCCCTCTTGA 59.382 50.000 0.00 0.00 0.00 3.02
3594 3878 2.325583 TAAGCATAACCGCCCTCTTG 57.674 50.000 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.