Multiple sequence alignment - TraesCS5A01G443500

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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 TraesCS5A01G443500 chr5A 100.000 3412 0 0 1 3412 623557050 623553639 0.000000e+00 6301.0
1 TraesCS5A01G443500 chr5A 97.007 3040 66 6 396 3412 78266799 78263762 0.000000e+00 5086.0
2 TraesCS5A01G443500 chr5A 97.240 2826 55 4 609 3412 78325418 78322594 0.000000e+00 4765.0
3 TraesCS5A01G443500 chr5A 97.287 1364 29 3 396 1751 426932589 426931226 0.000000e+00 2307.0
4 TraesCS5A01G443500 chr1A 97.302 3039 59 4 396 3412 244511207 244508170 0.000000e+00 5136.0
5 TraesCS5A01G443500 chr1A 96.963 3029 70 3 406 3412 587388435 587385407 0.000000e+00 5064.0
6 TraesCS5A01G443500 chr1A 95.570 1964 68 2 396 2340 97647344 97645381 0.000000e+00 3127.0
7 TraesCS5A01G443500 chr1A 98.555 1038 10 3 2378 3412 97645379 97644344 0.000000e+00 1829.0
8 TraesCS5A01G443500 chr1A 90.148 609 35 10 1249 1832 452018765 452019373 0.000000e+00 769.0
9 TraesCS5A01G443500 chr2B 96.631 3057 63 6 396 3412 596913677 596910621 0.000000e+00 5038.0
10 TraesCS5A01G443500 chr2B 91.632 729 53 7 407 1134 103893468 103894189 0.000000e+00 1002.0
11 TraesCS5A01G443500 chr2B 95.498 311 13 1 82 392 798371634 798371943 2.360000e-136 496.0
12 TraesCS5A01G443500 chr3D 92.824 864 54 7 386 1248 281331199 281330343 0.000000e+00 1245.0
13 TraesCS5A01G443500 chr4A 92.740 854 57 4 396 1248 599904992 599904143 0.000000e+00 1229.0
14 TraesCS5A01G443500 chr4A 94.357 319 17 1 81 399 460894359 460894042 3.960000e-134 488.0
15 TraesCS5A01G443500 chr6B 93.672 806 40 6 1858 2656 270876417 270877218 0.000000e+00 1195.0
16 TraesCS5A01G443500 chr6B 91.525 767 40 6 2655 3412 270877251 270878001 0.000000e+00 1033.0
17 TraesCS5A01G443500 chr6B 95.161 310 14 1 81 390 551770223 551769915 3.960000e-134 488.0
18 TraesCS5A01G443500 chr5B 93.641 802 46 4 1858 2656 127701892 127701093 0.000000e+00 1194.0
19 TraesCS5A01G443500 chr1B 89.984 639 37 10 1249 1861 473822496 473823133 0.000000e+00 800.0
20 TraesCS5A01G443500 chr1D 89.117 634 42 12 1249 1855 351245770 351246403 0.000000e+00 763.0
21 TraesCS5A01G443500 chr7A 94.969 318 13 3 87 401 709593943 709594260 2.360000e-136 496.0
22 TraesCS5A01G443500 chr7A 95.177 311 13 2 83 392 727101583 727101274 1.100000e-134 490.0
23 TraesCS5A01G443500 chr7B 95.455 308 13 1 87 393 717329210 717328903 1.100000e-134 490.0
24 TraesCS5A01G443500 chr6A 95.177 311 14 1 83 393 181910154 181909845 1.100000e-134 490.0
25 TraesCS5A01G443500 chr4B 94.855 311 16 0 86 396 132047496 132047186 1.420000e-133 486.0
26 TraesCS5A01G443500 chr3A 93.558 326 20 1 81 405 673603896 673603571 5.120000e-133 484.0
27 TraesCS5A01G443500 chr3A 89.542 306 28 2 3110 3412 670100950 670100646 5.340000e-103 385.0
28 TraesCS5A01G443500 chr5D 84.534 472 41 16 2086 2531 382914210 382913745 4.040000e-119 438.0
29 TraesCS5A01G443500 chr2A 90.523 306 25 2 3110 3412 456212800 456213104 5.300000e-108 401.0
30 TraesCS5A01G443500 chr2A 100.000 28 0 0 2966 2993 2811096 2811069 6.000000e-03 52.8
31 TraesCS5A01G443500 chrUn 90.234 256 23 1 1858 2111 8502817 8503072 1.960000e-87 333.0


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 TraesCS5A01G443500 chr5A 623553639 623557050 3411 True 6301 6301 100.0000 1 3412 1 chr5A.!!$R4 3411
1 TraesCS5A01G443500 chr5A 78263762 78266799 3037 True 5086 5086 97.0070 396 3412 1 chr5A.!!$R1 3016
2 TraesCS5A01G443500 chr5A 78322594 78325418 2824 True 4765 4765 97.2400 609 3412 1 chr5A.!!$R2 2803
3 TraesCS5A01G443500 chr5A 426931226 426932589 1363 True 2307 2307 97.2870 396 1751 1 chr5A.!!$R3 1355
4 TraesCS5A01G443500 chr1A 244508170 244511207 3037 True 5136 5136 97.3020 396 3412 1 chr1A.!!$R1 3016
5 TraesCS5A01G443500 chr1A 587385407 587388435 3028 True 5064 5064 96.9630 406 3412 1 chr1A.!!$R2 3006
6 TraesCS5A01G443500 chr1A 97644344 97647344 3000 True 2478 3127 97.0625 396 3412 2 chr1A.!!$R3 3016
7 TraesCS5A01G443500 chr1A 452018765 452019373 608 False 769 769 90.1480 1249 1832 1 chr1A.!!$F1 583
8 TraesCS5A01G443500 chr2B 596910621 596913677 3056 True 5038 5038 96.6310 396 3412 1 chr2B.!!$R1 3016
9 TraesCS5A01G443500 chr2B 103893468 103894189 721 False 1002 1002 91.6320 407 1134 1 chr2B.!!$F1 727
10 TraesCS5A01G443500 chr3D 281330343 281331199 856 True 1245 1245 92.8240 386 1248 1 chr3D.!!$R1 862
11 TraesCS5A01G443500 chr4A 599904143 599904992 849 True 1229 1229 92.7400 396 1248 1 chr4A.!!$R2 852
12 TraesCS5A01G443500 chr6B 270876417 270878001 1584 False 1114 1195 92.5985 1858 3412 2 chr6B.!!$F1 1554
13 TraesCS5A01G443500 chr5B 127701093 127701892 799 True 1194 1194 93.6410 1858 2656 1 chr5B.!!$R1 798
14 TraesCS5A01G443500 chr1B 473822496 473823133 637 False 800 800 89.9840 1249 1861 1 chr1B.!!$F1 612
15 TraesCS5A01G443500 chr1D 351245770 351246403 633 False 763 763 89.1170 1249 1855 1 chr1D.!!$F1 606

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
142 143 0.033503 GGTATTCCCAACCCACCAGG 60.034 60.0 0.00 0.00 43.78 4.45 F
300 301 0.033601 AGTCTCTCGGAGGTGCTCAT 60.034 55.0 4.96 0.00 31.08 2.90 F
364 365 0.093535 CGTGTGTACATGAGCGCTTG 59.906 55.0 13.26 9.93 34.90 4.01 F
371 372 0.250038 ACATGAGCGCTTGTGTCTGT 60.250 50.0 13.26 6.50 31.88 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1713 1766 2.048222 CACCATGCACTCGTCGGT 60.048 61.111 0.00 0.00 0.0 4.69 R
2363 2439 4.376223 TCCCTGGGACATTAGGTATTCAA 58.624 43.478 12.53 0.00 38.2 2.69 R
2407 2484 2.682856 TGTCAGCAGAAAACAGTTCACC 59.317 45.455 0.00 0.00 0.0 4.02 R
2670 2781 5.900339 TGAAACAGTTAGTCAGCTTAACG 57.100 39.130 2.01 1.05 0.0 3.18 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 3.225235 CCTCCTAGCAGTGAGGGC 58.775 66.667 7.37 0.00 43.69 5.19
19 20 2.790791 CCTCCTAGCAGTGAGGGCG 61.791 68.421 7.37 0.00 43.69 6.13
20 21 2.759973 TCCTAGCAGTGAGGGCGG 60.760 66.667 0.00 0.00 34.56 6.13
21 22 3.854669 CCTAGCAGTGAGGGCGGG 61.855 72.222 0.00 0.00 36.08 6.13
22 23 4.537433 CTAGCAGTGAGGGCGGGC 62.537 72.222 0.00 0.00 36.08 6.13
52 53 2.874751 GACCAAACGGGCGAATGG 59.125 61.111 0.00 0.00 42.05 3.16
53 54 2.114411 ACCAAACGGGCGAATGGT 59.886 55.556 0.00 0.00 42.05 3.55
54 55 0.674269 GACCAAACGGGCGAATGGTA 60.674 55.000 0.00 0.00 45.85 3.25
55 56 0.034863 ACCAAACGGGCGAATGGTAT 60.035 50.000 0.00 0.00 44.11 2.73
56 57 1.209990 ACCAAACGGGCGAATGGTATA 59.790 47.619 0.00 0.00 44.11 1.47
57 58 2.158726 ACCAAACGGGCGAATGGTATAT 60.159 45.455 0.00 0.00 44.11 0.86
58 59 2.482721 CCAAACGGGCGAATGGTATATC 59.517 50.000 0.00 0.00 0.00 1.63
59 60 3.399330 CAAACGGGCGAATGGTATATCT 58.601 45.455 0.00 0.00 0.00 1.98
60 61 3.764237 AACGGGCGAATGGTATATCTT 57.236 42.857 0.00 0.00 0.00 2.40
61 62 3.764237 ACGGGCGAATGGTATATCTTT 57.236 42.857 0.00 0.00 0.00 2.52
62 63 4.877378 ACGGGCGAATGGTATATCTTTA 57.123 40.909 0.00 0.00 0.00 1.85
63 64 4.563061 ACGGGCGAATGGTATATCTTTAC 58.437 43.478 0.00 0.00 0.00 2.01
64 65 3.930848 CGGGCGAATGGTATATCTTTACC 59.069 47.826 0.00 0.00 41.77 2.85
65 66 4.322499 CGGGCGAATGGTATATCTTTACCT 60.322 45.833 2.63 0.00 41.90 3.08
66 67 5.105635 CGGGCGAATGGTATATCTTTACCTA 60.106 44.000 2.63 0.00 41.90 3.08
67 68 6.406624 CGGGCGAATGGTATATCTTTACCTAT 60.407 42.308 2.63 0.00 41.90 2.57
68 69 7.336396 GGGCGAATGGTATATCTTTACCTATT 58.664 38.462 2.63 1.62 41.90 1.73
69 70 8.480501 GGGCGAATGGTATATCTTTACCTATTA 58.519 37.037 2.63 0.00 41.90 0.98
70 71 9.880157 GGCGAATGGTATATCTTTACCTATTAA 57.120 33.333 2.63 0.00 41.90 1.40
114 115 3.551846 ACCTGTTGTTGAGTTGGTTAGG 58.448 45.455 0.00 0.00 0.00 2.69
115 116 3.053917 ACCTGTTGTTGAGTTGGTTAGGT 60.054 43.478 0.00 0.00 0.00 3.08
116 117 3.315191 CCTGTTGTTGAGTTGGTTAGGTG 59.685 47.826 0.00 0.00 0.00 4.00
117 118 3.945285 CTGTTGTTGAGTTGGTTAGGTGT 59.055 43.478 0.00 0.00 0.00 4.16
118 119 5.100344 TGTTGTTGAGTTGGTTAGGTGTA 57.900 39.130 0.00 0.00 0.00 2.90
119 120 4.877251 TGTTGTTGAGTTGGTTAGGTGTAC 59.123 41.667 0.00 0.00 0.00 2.90
120 121 4.757019 TGTTGAGTTGGTTAGGTGTACA 57.243 40.909 0.00 0.00 0.00 2.90
121 122 5.100344 TGTTGAGTTGGTTAGGTGTACAA 57.900 39.130 0.00 0.00 0.00 2.41
122 123 5.686753 TGTTGAGTTGGTTAGGTGTACAAT 58.313 37.500 0.00 0.00 0.00 2.71
123 124 5.529430 TGTTGAGTTGGTTAGGTGTACAATG 59.471 40.000 0.00 0.00 0.00 2.82
124 125 4.647611 TGAGTTGGTTAGGTGTACAATGG 58.352 43.478 0.00 0.00 0.00 3.16
125 126 4.103469 TGAGTTGGTTAGGTGTACAATGGT 59.897 41.667 0.00 0.00 0.00 3.55
126 127 5.307456 TGAGTTGGTTAGGTGTACAATGGTA 59.693 40.000 0.00 0.00 0.00 3.25
127 128 6.013206 TGAGTTGGTTAGGTGTACAATGGTAT 60.013 38.462 0.00 0.00 0.00 2.73
128 129 6.786122 AGTTGGTTAGGTGTACAATGGTATT 58.214 36.000 0.00 0.00 0.00 1.89
129 130 6.882678 AGTTGGTTAGGTGTACAATGGTATTC 59.117 38.462 0.00 0.00 0.00 1.75
130 131 5.747342 TGGTTAGGTGTACAATGGTATTCC 58.253 41.667 0.00 0.00 0.00 3.01
131 132 5.128205 GGTTAGGTGTACAATGGTATTCCC 58.872 45.833 0.00 0.00 0.00 3.97
140 141 2.884412 TGGTATTCCCAACCCACCA 58.116 52.632 0.00 0.00 41.50 4.17
141 142 0.701731 TGGTATTCCCAACCCACCAG 59.298 55.000 0.00 0.00 41.50 4.00
142 143 0.033503 GGTATTCCCAACCCACCAGG 60.034 60.000 0.00 0.00 43.78 4.45
158 159 3.363787 AGGGTTCAAATCCTGGTGC 57.636 52.632 0.00 0.00 38.36 5.01
159 160 0.779997 AGGGTTCAAATCCTGGTGCT 59.220 50.000 0.00 0.00 38.36 4.40
160 161 1.177401 GGGTTCAAATCCTGGTGCTC 58.823 55.000 0.00 0.00 0.00 4.26
161 162 0.804989 GGTTCAAATCCTGGTGCTCG 59.195 55.000 0.00 0.00 0.00 5.03
162 163 0.169009 GTTCAAATCCTGGTGCTCGC 59.831 55.000 0.00 0.00 0.00 5.03
163 164 0.250684 TTCAAATCCTGGTGCTCGCA 60.251 50.000 0.00 0.00 0.00 5.10
164 165 0.035152 TCAAATCCTGGTGCTCGCAT 60.035 50.000 0.00 0.00 0.00 4.73
165 166 0.813184 CAAATCCTGGTGCTCGCATT 59.187 50.000 0.00 0.00 0.00 3.56
166 167 2.016318 CAAATCCTGGTGCTCGCATTA 58.984 47.619 0.00 0.00 0.00 1.90
167 168 2.620115 CAAATCCTGGTGCTCGCATTAT 59.380 45.455 0.00 0.00 0.00 1.28
168 169 2.645838 ATCCTGGTGCTCGCATTATT 57.354 45.000 0.00 0.00 0.00 1.40
169 170 1.953559 TCCTGGTGCTCGCATTATTC 58.046 50.000 0.00 0.00 0.00 1.75
170 171 0.947244 CCTGGTGCTCGCATTATTCC 59.053 55.000 0.00 0.00 0.00 3.01
171 172 1.475751 CCTGGTGCTCGCATTATTCCT 60.476 52.381 0.00 0.00 0.00 3.36
172 173 1.600957 CTGGTGCTCGCATTATTCCTG 59.399 52.381 0.00 0.00 0.00 3.86
173 174 0.947244 GGTGCTCGCATTATTCCTGG 59.053 55.000 0.00 0.00 0.00 4.45
174 175 1.475034 GGTGCTCGCATTATTCCTGGA 60.475 52.381 0.00 0.00 0.00 3.86
175 176 2.498167 GTGCTCGCATTATTCCTGGAT 58.502 47.619 0.00 0.00 0.00 3.41
176 177 2.880890 GTGCTCGCATTATTCCTGGATT 59.119 45.455 0.00 0.00 0.00 3.01
177 178 3.316308 GTGCTCGCATTATTCCTGGATTT 59.684 43.478 0.00 0.00 0.00 2.17
178 179 4.515191 GTGCTCGCATTATTCCTGGATTTA 59.485 41.667 0.00 0.00 0.00 1.40
179 180 5.182001 GTGCTCGCATTATTCCTGGATTTAT 59.818 40.000 0.00 0.00 0.00 1.40
180 181 5.769662 TGCTCGCATTATTCCTGGATTTATT 59.230 36.000 0.00 0.00 0.00 1.40
181 182 6.265196 TGCTCGCATTATTCCTGGATTTATTT 59.735 34.615 0.00 0.00 0.00 1.40
182 183 6.803807 GCTCGCATTATTCCTGGATTTATTTC 59.196 38.462 0.00 0.00 0.00 2.17
183 184 7.522073 GCTCGCATTATTCCTGGATTTATTTCA 60.522 37.037 0.00 0.00 0.00 2.69
184 185 7.874940 TCGCATTATTCCTGGATTTATTTCAG 58.125 34.615 0.00 0.00 0.00 3.02
185 186 7.040478 TCGCATTATTCCTGGATTTATTTCAGG 60.040 37.037 0.00 0.00 46.91 3.86
193 194 6.076981 CTGGATTTATTTCAGGATTTCCGG 57.923 41.667 0.00 0.00 42.08 5.14
194 195 4.340950 TGGATTTATTTCAGGATTTCCGGC 59.659 41.667 0.00 0.00 42.08 6.13
195 196 4.537015 GATTTATTTCAGGATTTCCGGCG 58.463 43.478 0.00 0.00 42.08 6.46
196 197 2.992124 TATTTCAGGATTTCCGGCGA 57.008 45.000 9.30 0.00 42.08 5.54
197 198 2.348411 ATTTCAGGATTTCCGGCGAT 57.652 45.000 9.30 0.00 42.08 4.58
198 199 1.378531 TTTCAGGATTTCCGGCGATG 58.621 50.000 9.30 0.00 42.08 3.84
199 200 1.095228 TTCAGGATTTCCGGCGATGC 61.095 55.000 9.30 0.00 42.08 3.91
200 201 2.588877 AGGATTTCCGGCGATGCG 60.589 61.111 9.30 0.00 42.08 4.73
211 212 2.787249 CGATGCGCTTTCAGTGGG 59.213 61.111 9.73 0.00 0.00 4.61
212 213 1.741401 CGATGCGCTTTCAGTGGGA 60.741 57.895 9.73 0.00 0.00 4.37
213 214 1.699656 CGATGCGCTTTCAGTGGGAG 61.700 60.000 9.73 0.00 0.00 4.30
214 215 1.372087 GATGCGCTTTCAGTGGGAGG 61.372 60.000 9.73 0.00 0.00 4.30
215 216 1.841302 ATGCGCTTTCAGTGGGAGGA 61.841 55.000 9.73 0.00 0.00 3.71
216 217 1.302511 GCGCTTTCAGTGGGAGGAA 60.303 57.895 0.00 0.00 0.00 3.36
217 218 0.889186 GCGCTTTCAGTGGGAGGAAA 60.889 55.000 0.00 0.00 0.00 3.13
218 219 0.875059 CGCTTTCAGTGGGAGGAAAC 59.125 55.000 0.00 0.00 0.00 2.78
219 220 0.875059 GCTTTCAGTGGGAGGAAACG 59.125 55.000 0.00 0.00 0.00 3.60
220 221 1.814248 GCTTTCAGTGGGAGGAAACGT 60.814 52.381 0.00 0.00 0.00 3.99
221 222 2.572290 CTTTCAGTGGGAGGAAACGTT 58.428 47.619 0.00 0.00 0.00 3.99
222 223 2.249844 TTCAGTGGGAGGAAACGTTC 57.750 50.000 0.00 0.00 0.00 3.95
245 246 4.883300 GACGACGAGGCGCCTACG 62.883 72.222 32.91 32.91 44.07 3.51
248 249 4.849329 GACGAGGCGCCTACGGTG 62.849 72.222 34.97 23.88 40.57 4.94
250 251 4.849329 CGAGGCGCCTACGGTGAC 62.849 72.222 32.97 14.51 42.50 3.67
253 254 2.508663 GGCGCCTACGGTGACTTC 60.509 66.667 22.15 0.00 38.38 3.01
254 255 2.879462 GCGCCTACGGTGACTTCG 60.879 66.667 0.00 0.00 40.57 3.79
255 256 2.564975 CGCCTACGGTGACTTCGT 59.435 61.111 0.00 0.00 43.64 3.85
256 257 1.796151 CGCCTACGGTGACTTCGTA 59.204 57.895 0.00 0.00 41.38 3.43
257 258 0.168788 CGCCTACGGTGACTTCGTAA 59.831 55.000 0.00 0.00 41.62 3.18
258 259 1.401409 CGCCTACGGTGACTTCGTAAA 60.401 52.381 0.00 0.00 41.62 2.01
259 260 2.733227 CGCCTACGGTGACTTCGTAAAT 60.733 50.000 0.00 0.00 41.62 1.40
260 261 2.856557 GCCTACGGTGACTTCGTAAATC 59.143 50.000 0.00 0.00 41.62 2.17
261 262 3.428589 GCCTACGGTGACTTCGTAAATCT 60.429 47.826 0.00 0.00 41.62 2.40
262 263 4.349501 CCTACGGTGACTTCGTAAATCTC 58.650 47.826 0.00 0.00 41.62 2.75
263 264 3.928727 ACGGTGACTTCGTAAATCTCA 57.071 42.857 0.00 0.00 39.22 3.27
264 265 4.247267 ACGGTGACTTCGTAAATCTCAA 57.753 40.909 0.00 0.00 39.22 3.02
265 266 4.235360 ACGGTGACTTCGTAAATCTCAAG 58.765 43.478 0.00 0.00 39.22 3.02
266 267 4.022589 ACGGTGACTTCGTAAATCTCAAGA 60.023 41.667 0.00 0.00 39.22 3.02
267 268 5.103000 CGGTGACTTCGTAAATCTCAAGAT 58.897 41.667 0.00 0.00 36.07 2.40
268 269 5.004821 CGGTGACTTCGTAAATCTCAAGATG 59.995 44.000 0.00 0.00 34.49 2.90
269 270 6.100004 GGTGACTTCGTAAATCTCAAGATGA 58.900 40.000 0.00 0.00 34.49 2.92
270 271 6.758886 GGTGACTTCGTAAATCTCAAGATGAT 59.241 38.462 0.00 0.00 34.49 2.45
271 272 7.921214 GGTGACTTCGTAAATCTCAAGATGATA 59.079 37.037 0.00 0.00 34.49 2.15
272 273 9.469807 GTGACTTCGTAAATCTCAAGATGATAT 57.530 33.333 0.00 0.00 34.49 1.63
273 274 9.468532 TGACTTCGTAAATCTCAAGATGATATG 57.531 33.333 0.00 0.00 34.49 1.78
274 275 9.469807 GACTTCGTAAATCTCAAGATGATATGT 57.530 33.333 0.00 0.00 34.49 2.29
275 276 9.469807 ACTTCGTAAATCTCAAGATGATATGTC 57.530 33.333 0.00 0.00 34.49 3.06
276 277 8.507470 TTCGTAAATCTCAAGATGATATGTCG 57.493 34.615 0.00 0.00 34.49 4.35
277 278 7.084486 TCGTAAATCTCAAGATGATATGTCGG 58.916 38.462 0.00 0.00 34.49 4.79
278 279 6.183360 CGTAAATCTCAAGATGATATGTCGGC 60.183 42.308 0.00 0.00 34.49 5.54
279 280 5.480642 AATCTCAAGATGATATGTCGGCT 57.519 39.130 0.00 0.00 34.49 5.52
280 281 4.511617 TCTCAAGATGATATGTCGGCTC 57.488 45.455 0.00 0.00 0.00 4.70
281 282 3.891366 TCTCAAGATGATATGTCGGCTCA 59.109 43.478 0.00 0.00 0.00 4.26
282 283 4.022503 TCTCAAGATGATATGTCGGCTCAG 60.023 45.833 0.00 0.00 0.00 3.35
283 284 3.638627 TCAAGATGATATGTCGGCTCAGT 59.361 43.478 0.00 0.00 0.00 3.41
284 285 3.932545 AGATGATATGTCGGCTCAGTC 57.067 47.619 0.00 0.00 0.00 3.51
285 286 3.495331 AGATGATATGTCGGCTCAGTCT 58.505 45.455 0.00 0.00 0.00 3.24
286 287 3.505680 AGATGATATGTCGGCTCAGTCTC 59.494 47.826 0.00 0.00 0.00 3.36
287 288 2.937519 TGATATGTCGGCTCAGTCTCT 58.062 47.619 0.00 0.00 0.00 3.10
288 289 2.881513 TGATATGTCGGCTCAGTCTCTC 59.118 50.000 0.00 0.00 0.00 3.20
289 290 1.300481 TATGTCGGCTCAGTCTCTCG 58.700 55.000 0.00 0.00 0.00 4.04
290 291 1.380403 ATGTCGGCTCAGTCTCTCGG 61.380 60.000 0.00 0.00 0.00 4.63
291 292 1.745864 GTCGGCTCAGTCTCTCGGA 60.746 63.158 0.00 0.00 0.00 4.55
292 293 1.450491 TCGGCTCAGTCTCTCGGAG 60.450 63.158 0.00 0.00 40.44 4.63
293 294 2.477176 CGGCTCAGTCTCTCGGAGG 61.477 68.421 4.96 0.00 38.48 4.30
294 295 1.379309 GGCTCAGTCTCTCGGAGGT 60.379 63.158 4.96 0.00 38.48 3.85
295 296 1.662438 GGCTCAGTCTCTCGGAGGTG 61.662 65.000 4.96 0.00 38.48 4.00
296 297 1.806568 CTCAGTCTCTCGGAGGTGC 59.193 63.158 4.96 0.00 35.32 5.01
297 298 0.679640 CTCAGTCTCTCGGAGGTGCT 60.680 60.000 4.96 0.00 35.32 4.40
298 299 0.678366 TCAGTCTCTCGGAGGTGCTC 60.678 60.000 4.96 0.00 0.00 4.26
299 300 0.962855 CAGTCTCTCGGAGGTGCTCA 60.963 60.000 4.96 0.00 31.08 4.26
300 301 0.033601 AGTCTCTCGGAGGTGCTCAT 60.034 55.000 4.96 0.00 31.08 2.90
301 302 1.213182 AGTCTCTCGGAGGTGCTCATA 59.787 52.381 4.96 0.00 31.08 2.15
302 303 1.606668 GTCTCTCGGAGGTGCTCATAG 59.393 57.143 4.96 0.00 31.08 2.23
303 304 0.958091 CTCTCGGAGGTGCTCATAGG 59.042 60.000 4.96 0.00 31.08 2.57
304 305 0.468214 TCTCGGAGGTGCTCATAGGG 60.468 60.000 4.96 0.00 31.08 3.53
305 306 1.457643 TCGGAGGTGCTCATAGGGG 60.458 63.158 0.00 0.00 31.08 4.79
306 307 1.762460 CGGAGGTGCTCATAGGGGT 60.762 63.158 0.00 0.00 31.08 4.95
307 308 0.469331 CGGAGGTGCTCATAGGGGTA 60.469 60.000 0.00 0.00 31.08 3.69
308 309 1.343069 GGAGGTGCTCATAGGGGTAG 58.657 60.000 0.00 0.00 31.08 3.18
309 310 1.343069 GAGGTGCTCATAGGGGTAGG 58.657 60.000 0.00 0.00 0.00 3.18
310 311 0.104934 AGGTGCTCATAGGGGTAGGG 60.105 60.000 0.00 0.00 0.00 3.53
311 312 0.400093 GGTGCTCATAGGGGTAGGGT 60.400 60.000 0.00 0.00 0.00 4.34
312 313 0.759346 GTGCTCATAGGGGTAGGGTG 59.241 60.000 0.00 0.00 0.00 4.61
313 314 0.341961 TGCTCATAGGGGTAGGGTGT 59.658 55.000 0.00 0.00 0.00 4.16
314 315 0.759346 GCTCATAGGGGTAGGGTGTG 59.241 60.000 0.00 0.00 0.00 3.82
315 316 0.759346 CTCATAGGGGTAGGGTGTGC 59.241 60.000 0.00 0.00 0.00 4.57
316 317 1.046472 TCATAGGGGTAGGGTGTGCG 61.046 60.000 0.00 0.00 0.00 5.34
317 318 1.002533 ATAGGGGTAGGGTGTGCGT 59.997 57.895 0.00 0.00 0.00 5.24
318 319 1.335132 ATAGGGGTAGGGTGTGCGTG 61.335 60.000 0.00 0.00 0.00 5.34
319 320 2.735151 TAGGGGTAGGGTGTGCGTGT 62.735 60.000 0.00 0.00 0.00 4.49
320 321 2.285024 GGGGTAGGGTGTGCGTGTA 61.285 63.158 0.00 0.00 0.00 2.90
321 322 1.619807 GGGGTAGGGTGTGCGTGTAT 61.620 60.000 0.00 0.00 0.00 2.29
322 323 0.461339 GGGTAGGGTGTGCGTGTATG 60.461 60.000 0.00 0.00 0.00 2.39
323 324 1.087771 GGTAGGGTGTGCGTGTATGC 61.088 60.000 0.00 0.00 0.00 3.14
324 325 1.153726 TAGGGTGTGCGTGTATGCG 60.154 57.895 0.00 0.00 37.81 4.73
325 326 1.879737 TAGGGTGTGCGTGTATGCGT 61.880 55.000 0.00 0.00 37.81 5.24
326 327 2.322081 GGGTGTGCGTGTATGCGTT 61.322 57.895 0.00 0.00 37.81 4.84
327 328 1.131826 GGTGTGCGTGTATGCGTTC 59.868 57.895 0.00 0.00 37.81 3.95
328 329 1.561717 GGTGTGCGTGTATGCGTTCA 61.562 55.000 0.00 0.00 37.81 3.18
329 330 0.442310 GTGTGCGTGTATGCGTTCAT 59.558 50.000 0.00 0.00 37.81 2.57
330 331 1.656594 GTGTGCGTGTATGCGTTCATA 59.343 47.619 0.00 0.00 37.81 2.15
331 332 1.923864 TGTGCGTGTATGCGTTCATAG 59.076 47.619 0.00 0.00 35.96 2.23
332 333 1.257936 GTGCGTGTATGCGTTCATAGG 59.742 52.381 0.00 0.00 35.96 2.57
333 334 0.859232 GCGTGTATGCGTTCATAGGG 59.141 55.000 0.00 0.00 35.96 3.53
334 335 1.497991 CGTGTATGCGTTCATAGGGG 58.502 55.000 0.00 0.00 35.96 4.79
335 336 1.202486 CGTGTATGCGTTCATAGGGGT 60.202 52.381 0.00 0.00 35.96 4.95
336 337 2.210116 GTGTATGCGTTCATAGGGGTG 58.790 52.381 0.00 0.00 35.96 4.61
337 338 2.112190 TGTATGCGTTCATAGGGGTGA 58.888 47.619 0.00 0.00 35.96 4.02
338 339 2.102420 TGTATGCGTTCATAGGGGTGAG 59.898 50.000 0.00 0.00 35.96 3.51
339 340 0.469917 ATGCGTTCATAGGGGTGAGG 59.530 55.000 0.00 0.00 0.00 3.86
340 341 1.146263 GCGTTCATAGGGGTGAGGG 59.854 63.158 0.00 0.00 0.00 4.30
341 342 1.623542 GCGTTCATAGGGGTGAGGGT 61.624 60.000 0.00 0.00 0.00 4.34
342 343 1.784358 CGTTCATAGGGGTGAGGGTA 58.216 55.000 0.00 0.00 0.00 3.69
343 344 2.326428 CGTTCATAGGGGTGAGGGTAT 58.674 52.381 0.00 0.00 0.00 2.73
344 345 2.037251 CGTTCATAGGGGTGAGGGTATG 59.963 54.545 0.00 0.00 0.00 2.39
345 346 1.729586 TCATAGGGGTGAGGGTATGC 58.270 55.000 0.00 0.00 0.00 3.14
346 347 0.321671 CATAGGGGTGAGGGTATGCG 59.678 60.000 0.00 0.00 0.00 4.73
347 348 0.105142 ATAGGGGTGAGGGTATGCGT 60.105 55.000 0.00 0.00 0.00 5.24
348 349 1.046472 TAGGGGTGAGGGTATGCGTG 61.046 60.000 0.00 0.00 0.00 5.34
349 350 2.666098 GGGGTGAGGGTATGCGTGT 61.666 63.158 0.00 0.00 0.00 4.49
350 351 1.449601 GGGTGAGGGTATGCGTGTG 60.450 63.158 0.00 0.00 0.00 3.82
351 352 1.295423 GGTGAGGGTATGCGTGTGT 59.705 57.895 0.00 0.00 0.00 3.72
352 353 0.533491 GGTGAGGGTATGCGTGTGTA 59.467 55.000 0.00 0.00 0.00 2.90
353 354 1.636988 GTGAGGGTATGCGTGTGTAC 58.363 55.000 0.00 0.00 0.00 2.90
354 355 1.067425 GTGAGGGTATGCGTGTGTACA 60.067 52.381 0.00 0.00 0.00 2.90
355 356 1.828595 TGAGGGTATGCGTGTGTACAT 59.171 47.619 0.00 0.00 0.00 2.29
356 357 2.201732 GAGGGTATGCGTGTGTACATG 58.798 52.381 0.00 0.00 36.01 3.21
357 358 1.828595 AGGGTATGCGTGTGTACATGA 59.171 47.619 8.34 0.00 34.90 3.07
358 359 2.159099 AGGGTATGCGTGTGTACATGAG 60.159 50.000 8.34 0.00 34.90 2.90
359 360 1.593006 GGTATGCGTGTGTACATGAGC 59.407 52.381 8.34 5.65 34.90 4.26
360 361 1.255342 GTATGCGTGTGTACATGAGCG 59.745 52.381 8.34 3.01 34.90 5.03
361 362 1.695893 ATGCGTGTGTACATGAGCGC 61.696 55.000 20.94 20.94 44.29 5.92
362 363 2.094659 GCGTGTGTACATGAGCGCT 61.095 57.895 11.27 11.27 41.37 5.92
363 364 1.626654 GCGTGTGTACATGAGCGCTT 61.627 55.000 13.26 0.00 41.37 4.68
364 365 0.093535 CGTGTGTACATGAGCGCTTG 59.906 55.000 13.26 9.93 34.90 4.01
365 366 1.148310 GTGTGTACATGAGCGCTTGT 58.852 50.000 18.09 18.09 36.50 3.16
366 367 1.136252 GTGTGTACATGAGCGCTTGTG 60.136 52.381 22.01 19.92 34.61 3.33
367 368 1.148310 GTGTACATGAGCGCTTGTGT 58.852 50.000 25.24 25.24 34.61 3.72
368 369 1.126846 GTGTACATGAGCGCTTGTGTC 59.873 52.381 25.53 17.38 34.61 3.67
369 370 1.000843 TGTACATGAGCGCTTGTGTCT 59.999 47.619 25.53 10.42 34.61 3.41
370 371 1.391485 GTACATGAGCGCTTGTGTCTG 59.609 52.381 25.53 13.69 34.61 3.51
371 372 0.250038 ACATGAGCGCTTGTGTCTGT 60.250 50.000 13.26 6.50 31.88 3.41
372 373 1.000843 ACATGAGCGCTTGTGTCTGTA 59.999 47.619 13.26 0.00 31.88 2.74
373 374 1.391485 CATGAGCGCTTGTGTCTGTAC 59.609 52.381 13.26 0.00 0.00 2.90
374 375 0.673985 TGAGCGCTTGTGTCTGTACT 59.326 50.000 13.26 0.00 0.00 2.73
375 376 1.063806 GAGCGCTTGTGTCTGTACTG 58.936 55.000 13.26 0.00 0.00 2.74
376 377 0.673985 AGCGCTTGTGTCTGTACTGA 59.326 50.000 2.64 0.00 0.00 3.41
377 378 1.273606 AGCGCTTGTGTCTGTACTGAT 59.726 47.619 2.64 0.00 0.00 2.90
378 379 1.391485 GCGCTTGTGTCTGTACTGATG 59.609 52.381 0.00 0.00 0.00 3.07
379 380 1.391485 CGCTTGTGTCTGTACTGATGC 59.609 52.381 5.69 3.20 0.00 3.91
380 381 2.693069 GCTTGTGTCTGTACTGATGCT 58.307 47.619 5.69 0.00 0.00 3.79
381 382 3.673323 CGCTTGTGTCTGTACTGATGCTA 60.673 47.826 5.69 0.00 0.00 3.49
382 383 4.245660 GCTTGTGTCTGTACTGATGCTAA 58.754 43.478 5.69 0.07 0.00 3.09
383 384 4.690748 GCTTGTGTCTGTACTGATGCTAAA 59.309 41.667 5.69 0.00 0.00 1.85
384 385 5.179368 GCTTGTGTCTGTACTGATGCTAAAA 59.821 40.000 5.69 0.00 0.00 1.52
385 386 6.293407 GCTTGTGTCTGTACTGATGCTAAAAA 60.293 38.462 5.69 0.00 0.00 1.94
552 553 6.064060 CCTATAGGCATTTCAATTCAGTCCA 58.936 40.000 5.67 0.00 0.00 4.02
606 607 2.124860 GGCTACGCCCATTCCGTT 60.125 61.111 0.00 0.00 44.06 4.44
787 805 1.153647 CCATAAGCAGCGACCGTCA 60.154 57.895 0.00 0.00 0.00 4.35
874 901 2.124487 CCTCGACCTCGCCTCTCT 60.124 66.667 0.00 0.00 39.60 3.10
879 906 2.601666 ACCTCGCCTCTCTGTGCA 60.602 61.111 0.00 0.00 0.00 4.57
1050 1078 2.352032 GCCTGCCTCGTCTACCTGT 61.352 63.158 0.00 0.00 0.00 4.00
1266 1294 0.528466 GCGTGCTCATGGATCTCGAA 60.528 55.000 0.00 0.00 0.00 3.71
1571 1600 3.626924 GTGTGCCACTCCCTCGGT 61.627 66.667 0.00 0.00 0.00 4.69
2407 2484 0.401738 TTCAAGGGTGAGGAAGCTGG 59.598 55.000 0.00 0.00 34.49 4.85
2670 2781 4.870991 GTGAAGTATGGCTTTAGTCTGTCC 59.129 45.833 0.00 0.00 37.59 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 2.790791 CCGCCCTCACTGCTAGGAG 61.791 68.421 10.09 10.09 36.08 3.69
3 4 2.759973 CCGCCCTCACTGCTAGGA 60.760 66.667 0.00 0.00 36.08 2.94
4 5 3.854669 CCCGCCCTCACTGCTAGG 61.855 72.222 0.00 0.00 0.00 3.02
5 6 4.537433 GCCCGCCCTCACTGCTAG 62.537 72.222 0.00 0.00 0.00 3.42
33 34 3.428282 ATTCGCCCGTTTGGTCGC 61.428 61.111 0.00 0.00 34.80 5.19
34 35 2.478746 CATTCGCCCGTTTGGTCG 59.521 61.111 0.00 0.00 36.04 4.79
35 36 0.674269 TACCATTCGCCCGTTTGGTC 60.674 55.000 16.26 0.00 41.46 4.02
36 37 0.034863 ATACCATTCGCCCGTTTGGT 60.035 50.000 16.73 16.73 44.43 3.67
37 38 1.956297 TATACCATTCGCCCGTTTGG 58.044 50.000 9.09 9.09 35.31 3.28
38 39 3.399330 AGATATACCATTCGCCCGTTTG 58.601 45.455 0.00 0.00 0.00 2.93
39 40 3.764237 AGATATACCATTCGCCCGTTT 57.236 42.857 0.00 0.00 0.00 3.60
40 41 3.764237 AAGATATACCATTCGCCCGTT 57.236 42.857 0.00 0.00 0.00 4.44
41 42 3.764237 AAAGATATACCATTCGCCCGT 57.236 42.857 0.00 0.00 0.00 5.28
42 43 3.930848 GGTAAAGATATACCATTCGCCCG 59.069 47.826 0.00 0.00 44.01 6.13
43 44 5.161943 AGGTAAAGATATACCATTCGCCC 57.838 43.478 6.30 0.00 46.48 6.13
44 45 9.880157 TTAATAGGTAAAGATATACCATTCGCC 57.120 33.333 6.30 0.00 46.48 5.54
69 70 8.827677 GGTTGATTCGTCAATAGCTAGTTTATT 58.172 33.333 0.00 0.00 31.79 1.40
70 71 8.204836 AGGTTGATTCGTCAATAGCTAGTTTAT 58.795 33.333 0.00 0.00 31.79 1.40
71 72 7.491372 CAGGTTGATTCGTCAATAGCTAGTTTA 59.509 37.037 0.00 0.00 31.79 2.01
72 73 6.313905 CAGGTTGATTCGTCAATAGCTAGTTT 59.686 38.462 0.00 0.00 31.79 2.66
73 74 5.812642 CAGGTTGATTCGTCAATAGCTAGTT 59.187 40.000 0.00 0.00 31.79 2.24
74 75 5.105310 ACAGGTTGATTCGTCAATAGCTAGT 60.105 40.000 0.00 0.00 31.79 2.57
75 76 5.352284 ACAGGTTGATTCGTCAATAGCTAG 58.648 41.667 0.00 0.00 31.79 3.42
76 77 5.339008 ACAGGTTGATTCGTCAATAGCTA 57.661 39.130 0.00 0.00 31.79 3.32
77 78 4.207891 ACAGGTTGATTCGTCAATAGCT 57.792 40.909 0.00 0.00 31.79 3.32
78 79 4.154195 ACAACAGGTTGATTCGTCAATAGC 59.846 41.667 18.28 0.00 42.93 2.97
79 80 5.862924 ACAACAGGTTGATTCGTCAATAG 57.137 39.130 18.28 0.00 42.93 1.73
92 93 3.951680 CCTAACCAACTCAACAACAGGTT 59.048 43.478 0.00 0.00 41.74 3.50
93 94 3.053917 ACCTAACCAACTCAACAACAGGT 60.054 43.478 0.00 0.00 0.00 4.00
94 95 3.315191 CACCTAACCAACTCAACAACAGG 59.685 47.826 0.00 0.00 0.00 4.00
95 96 3.945285 ACACCTAACCAACTCAACAACAG 59.055 43.478 0.00 0.00 0.00 3.16
96 97 3.958018 ACACCTAACCAACTCAACAACA 58.042 40.909 0.00 0.00 0.00 3.33
97 98 4.877251 TGTACACCTAACCAACTCAACAAC 59.123 41.667 0.00 0.00 0.00 3.32
98 99 5.100344 TGTACACCTAACCAACTCAACAA 57.900 39.130 0.00 0.00 0.00 2.83
99 100 4.757019 TGTACACCTAACCAACTCAACA 57.243 40.909 0.00 0.00 0.00 3.33
100 101 5.048991 CCATTGTACACCTAACCAACTCAAC 60.049 44.000 0.00 0.00 0.00 3.18
101 102 5.067273 CCATTGTACACCTAACCAACTCAA 58.933 41.667 0.00 0.00 0.00 3.02
102 103 4.103469 ACCATTGTACACCTAACCAACTCA 59.897 41.667 0.00 0.00 0.00 3.41
103 104 4.648651 ACCATTGTACACCTAACCAACTC 58.351 43.478 0.00 0.00 0.00 3.01
104 105 4.717279 ACCATTGTACACCTAACCAACT 57.283 40.909 0.00 0.00 0.00 3.16
105 106 6.094464 GGAATACCATTGTACACCTAACCAAC 59.906 42.308 0.00 0.00 35.97 3.77
106 107 6.181908 GGAATACCATTGTACACCTAACCAA 58.818 40.000 0.00 0.00 35.97 3.67
107 108 5.339365 GGGAATACCATTGTACACCTAACCA 60.339 44.000 0.00 0.00 39.85 3.67
108 109 5.128205 GGGAATACCATTGTACACCTAACC 58.872 45.833 0.00 0.00 39.85 2.85
109 110 5.747342 TGGGAATACCATTGTACACCTAAC 58.253 41.667 0.00 0.00 46.80 2.34
123 124 0.033503 CCTGGTGGGTTGGGAATACC 60.034 60.000 0.00 0.00 40.81 2.73
124 125 3.588742 CCTGGTGGGTTGGGAATAC 57.411 57.895 0.00 0.00 0.00 1.89
135 136 1.549203 CAGGATTTGAACCCTGGTGG 58.451 55.000 0.00 0.00 44.68 4.61
140 141 0.779997 AGCACCAGGATTTGAACCCT 59.220 50.000 0.00 0.00 0.00 4.34
141 142 1.177401 GAGCACCAGGATTTGAACCC 58.823 55.000 0.00 0.00 0.00 4.11
142 143 0.804989 CGAGCACCAGGATTTGAACC 59.195 55.000 0.00 0.00 0.00 3.62
143 144 0.169009 GCGAGCACCAGGATTTGAAC 59.831 55.000 0.00 0.00 0.00 3.18
144 145 0.250684 TGCGAGCACCAGGATTTGAA 60.251 50.000 0.00 0.00 0.00 2.69
145 146 0.035152 ATGCGAGCACCAGGATTTGA 60.035 50.000 0.00 0.00 0.00 2.69
146 147 0.813184 AATGCGAGCACCAGGATTTG 59.187 50.000 0.00 0.00 0.00 2.32
147 148 2.418368 TAATGCGAGCACCAGGATTT 57.582 45.000 0.00 0.00 31.11 2.17
148 149 2.645838 ATAATGCGAGCACCAGGATT 57.354 45.000 0.00 0.00 33.17 3.01
149 150 2.498167 GAATAATGCGAGCACCAGGAT 58.502 47.619 0.00 0.00 0.00 3.24
150 151 1.475034 GGAATAATGCGAGCACCAGGA 60.475 52.381 0.00 0.00 0.00 3.86
151 152 0.947244 GGAATAATGCGAGCACCAGG 59.053 55.000 0.00 0.00 0.00 4.45
152 153 1.600957 CAGGAATAATGCGAGCACCAG 59.399 52.381 0.00 0.00 0.00 4.00
153 154 1.667236 CAGGAATAATGCGAGCACCA 58.333 50.000 0.00 0.00 0.00 4.17
154 155 0.947244 CCAGGAATAATGCGAGCACC 59.053 55.000 0.00 0.00 0.00 5.01
155 156 1.953559 TCCAGGAATAATGCGAGCAC 58.046 50.000 0.00 0.00 0.00 4.40
156 157 2.936919 ATCCAGGAATAATGCGAGCA 57.063 45.000 0.00 0.00 0.00 4.26
157 158 5.886960 ATAAATCCAGGAATAATGCGAGC 57.113 39.130 0.00 0.00 0.00 5.03
158 159 7.874940 TGAAATAAATCCAGGAATAATGCGAG 58.125 34.615 0.00 0.00 0.00 5.03
159 160 7.815840 TGAAATAAATCCAGGAATAATGCGA 57.184 32.000 0.00 0.00 0.00 5.10
169 170 5.010012 CCGGAAATCCTGAAATAAATCCAGG 59.990 44.000 0.00 0.00 46.64 4.45
170 171 5.507985 GCCGGAAATCCTGAAATAAATCCAG 60.508 44.000 5.05 0.00 0.00 3.86
171 172 4.340950 GCCGGAAATCCTGAAATAAATCCA 59.659 41.667 5.05 0.00 0.00 3.41
172 173 4.556699 CGCCGGAAATCCTGAAATAAATCC 60.557 45.833 5.05 0.00 0.00 3.01
173 174 4.274950 TCGCCGGAAATCCTGAAATAAATC 59.725 41.667 5.05 0.00 0.00 2.17
174 175 4.204012 TCGCCGGAAATCCTGAAATAAAT 58.796 39.130 5.05 0.00 0.00 1.40
175 176 3.611970 TCGCCGGAAATCCTGAAATAAA 58.388 40.909 5.05 0.00 0.00 1.40
176 177 3.269538 TCGCCGGAAATCCTGAAATAA 57.730 42.857 5.05 0.00 0.00 1.40
177 178 2.992124 TCGCCGGAAATCCTGAAATA 57.008 45.000 5.05 0.00 0.00 1.40
178 179 1.949525 CATCGCCGGAAATCCTGAAAT 59.050 47.619 5.05 0.00 0.00 2.17
179 180 1.378531 CATCGCCGGAAATCCTGAAA 58.621 50.000 5.05 0.00 0.00 2.69
180 181 1.095228 GCATCGCCGGAAATCCTGAA 61.095 55.000 5.05 0.00 0.00 3.02
181 182 1.523711 GCATCGCCGGAAATCCTGA 60.524 57.895 5.05 0.00 0.00 3.86
182 183 2.885676 CGCATCGCCGGAAATCCTG 61.886 63.158 5.05 0.00 0.00 3.86
183 184 2.588877 CGCATCGCCGGAAATCCT 60.589 61.111 5.05 0.00 0.00 3.24
194 195 1.699656 CTCCCACTGAAAGCGCATCG 61.700 60.000 11.47 6.82 37.60 3.84
195 196 1.372087 CCTCCCACTGAAAGCGCATC 61.372 60.000 11.47 8.39 37.60 3.91
196 197 1.377725 CCTCCCACTGAAAGCGCAT 60.378 57.895 11.47 0.00 37.60 4.73
197 198 2.032528 CCTCCCACTGAAAGCGCA 59.967 61.111 11.47 0.00 37.60 6.09
198 199 0.889186 TTTCCTCCCACTGAAAGCGC 60.889 55.000 0.00 0.00 37.60 5.92
199 200 0.875059 GTTTCCTCCCACTGAAAGCG 59.125 55.000 0.00 0.00 37.60 4.68
200 201 0.875059 CGTTTCCTCCCACTGAAAGC 59.125 55.000 0.00 0.00 37.60 3.51
201 202 2.256117 ACGTTTCCTCCCACTGAAAG 57.744 50.000 0.00 0.00 42.29 2.62
202 203 2.567985 GAACGTTTCCTCCCACTGAAA 58.432 47.619 0.46 0.00 0.00 2.69
203 204 1.202722 GGAACGTTTCCTCCCACTGAA 60.203 52.381 0.46 0.00 46.57 3.02
204 205 0.395312 GGAACGTTTCCTCCCACTGA 59.605 55.000 0.46 0.00 46.57 3.41
205 206 2.928416 GGAACGTTTCCTCCCACTG 58.072 57.895 0.46 0.00 46.57 3.66
227 228 4.883300 GTAGGCGCCTCGTCGTCG 62.883 72.222 36.73 0.00 39.34 5.12
228 229 4.883300 CGTAGGCGCCTCGTCGTC 62.883 72.222 36.73 15.88 36.23 4.20
241 242 4.978186 TGAGATTTACGAAGTCACCGTAG 58.022 43.478 0.00 0.00 43.93 3.51
242 243 5.181811 TCTTGAGATTTACGAAGTCACCGTA 59.818 40.000 0.00 0.00 43.93 4.02
243 244 3.928727 TGAGATTTACGAAGTCACCGT 57.071 42.857 0.00 0.00 43.93 4.83
244 245 4.482386 TCTTGAGATTTACGAAGTCACCG 58.518 43.478 0.00 0.00 43.93 4.94
245 246 6.100004 TCATCTTGAGATTTACGAAGTCACC 58.900 40.000 0.00 0.00 35.39 4.02
246 247 7.763172 ATCATCTTGAGATTTACGAAGTCAC 57.237 36.000 0.00 0.00 35.39 3.67
247 248 9.468532 CATATCATCTTGAGATTTACGAAGTCA 57.531 33.333 0.00 0.00 35.39 3.41
248 249 9.469807 ACATATCATCTTGAGATTTACGAAGTC 57.530 33.333 0.00 0.00 35.39 3.01
249 250 9.469807 GACATATCATCTTGAGATTTACGAAGT 57.530 33.333 0.00 0.00 37.29 3.01
250 251 8.634265 CGACATATCATCTTGAGATTTACGAAG 58.366 37.037 0.00 0.00 31.21 3.79
251 252 7.595130 CCGACATATCATCTTGAGATTTACGAA 59.405 37.037 0.00 0.00 31.21 3.85
252 253 7.084486 CCGACATATCATCTTGAGATTTACGA 58.916 38.462 0.00 0.00 31.21 3.43
253 254 6.183360 GCCGACATATCATCTTGAGATTTACG 60.183 42.308 0.00 0.00 31.21 3.18
254 255 6.870965 AGCCGACATATCATCTTGAGATTTAC 59.129 38.462 0.00 0.00 31.21 2.01
255 256 6.997655 AGCCGACATATCATCTTGAGATTTA 58.002 36.000 0.00 0.00 31.21 1.40
256 257 5.862845 AGCCGACATATCATCTTGAGATTT 58.137 37.500 0.00 0.00 31.21 2.17
257 258 5.011431 TGAGCCGACATATCATCTTGAGATT 59.989 40.000 0.00 0.00 31.21 2.40
258 259 4.525874 TGAGCCGACATATCATCTTGAGAT 59.474 41.667 0.00 0.00 34.56 2.75
259 260 3.891366 TGAGCCGACATATCATCTTGAGA 59.109 43.478 0.00 0.00 0.00 3.27
260 261 4.236147 CTGAGCCGACATATCATCTTGAG 58.764 47.826 0.00 0.00 0.00 3.02
261 262 3.638627 ACTGAGCCGACATATCATCTTGA 59.361 43.478 0.00 0.00 0.00 3.02
262 263 3.986572 GACTGAGCCGACATATCATCTTG 59.013 47.826 0.00 0.00 0.00 3.02
263 264 3.894427 AGACTGAGCCGACATATCATCTT 59.106 43.478 0.00 0.00 0.00 2.40
264 265 3.495331 AGACTGAGCCGACATATCATCT 58.505 45.455 0.00 0.00 0.00 2.90
265 266 3.505680 AGAGACTGAGCCGACATATCATC 59.494 47.826 0.00 0.00 0.00 2.92
266 267 3.495331 AGAGACTGAGCCGACATATCAT 58.505 45.455 0.00 0.00 0.00 2.45
267 268 2.881513 GAGAGACTGAGCCGACATATCA 59.118 50.000 0.00 0.00 0.00 2.15
268 269 2.095969 CGAGAGACTGAGCCGACATATC 60.096 54.545 0.00 0.00 0.00 1.63
269 270 1.876799 CGAGAGACTGAGCCGACATAT 59.123 52.381 0.00 0.00 0.00 1.78
270 271 1.300481 CGAGAGACTGAGCCGACATA 58.700 55.000 0.00 0.00 0.00 2.29
271 272 1.380403 CCGAGAGACTGAGCCGACAT 61.380 60.000 0.00 0.00 0.00 3.06
272 273 2.041115 CCGAGAGACTGAGCCGACA 61.041 63.158 0.00 0.00 0.00 4.35
273 274 1.711060 CTCCGAGAGACTGAGCCGAC 61.711 65.000 0.00 0.00 0.00 4.79
274 275 1.450491 CTCCGAGAGACTGAGCCGA 60.450 63.158 0.00 0.00 0.00 5.54
275 276 2.477176 CCTCCGAGAGACTGAGCCG 61.477 68.421 0.00 0.00 0.00 5.52
276 277 1.379309 ACCTCCGAGAGACTGAGCC 60.379 63.158 0.00 0.00 0.00 4.70
277 278 1.806568 CACCTCCGAGAGACTGAGC 59.193 63.158 0.00 0.00 0.00 4.26
278 279 0.679640 AGCACCTCCGAGAGACTGAG 60.680 60.000 0.00 0.00 0.00 3.35
279 280 0.678366 GAGCACCTCCGAGAGACTGA 60.678 60.000 0.00 0.00 0.00 3.41
280 281 0.962855 TGAGCACCTCCGAGAGACTG 60.963 60.000 0.00 0.22 0.00 3.51
281 282 0.033601 ATGAGCACCTCCGAGAGACT 60.034 55.000 0.00 0.00 0.00 3.24
282 283 1.606668 CTATGAGCACCTCCGAGAGAC 59.393 57.143 0.00 0.00 0.00 3.36
283 284 1.477740 CCTATGAGCACCTCCGAGAGA 60.478 57.143 0.00 0.00 0.00 3.10
284 285 0.958091 CCTATGAGCACCTCCGAGAG 59.042 60.000 0.00 0.00 0.00 3.20
285 286 0.468214 CCCTATGAGCACCTCCGAGA 60.468 60.000 0.00 0.00 0.00 4.04
286 287 1.467678 CCCCTATGAGCACCTCCGAG 61.468 65.000 0.00 0.00 0.00 4.63
287 288 1.457643 CCCCTATGAGCACCTCCGA 60.458 63.158 0.00 0.00 0.00 4.55
288 289 0.469331 TACCCCTATGAGCACCTCCG 60.469 60.000 0.00 0.00 0.00 4.63
289 290 1.343069 CTACCCCTATGAGCACCTCC 58.657 60.000 0.00 0.00 0.00 4.30
290 291 1.343069 CCTACCCCTATGAGCACCTC 58.657 60.000 0.00 0.00 0.00 3.85
291 292 0.104934 CCCTACCCCTATGAGCACCT 60.105 60.000 0.00 0.00 0.00 4.00
292 293 0.400093 ACCCTACCCCTATGAGCACC 60.400 60.000 0.00 0.00 0.00 5.01
293 294 0.759346 CACCCTACCCCTATGAGCAC 59.241 60.000 0.00 0.00 0.00 4.40
294 295 0.341961 ACACCCTACCCCTATGAGCA 59.658 55.000 0.00 0.00 0.00 4.26
295 296 0.759346 CACACCCTACCCCTATGAGC 59.241 60.000 0.00 0.00 0.00 4.26
296 297 0.759346 GCACACCCTACCCCTATGAG 59.241 60.000 0.00 0.00 0.00 2.90
297 298 1.046472 CGCACACCCTACCCCTATGA 61.046 60.000 0.00 0.00 0.00 2.15
298 299 1.335132 ACGCACACCCTACCCCTATG 61.335 60.000 0.00 0.00 0.00 2.23
299 300 1.002533 ACGCACACCCTACCCCTAT 59.997 57.895 0.00 0.00 0.00 2.57
300 301 1.985662 CACGCACACCCTACCCCTA 60.986 63.158 0.00 0.00 0.00 3.53
301 302 2.735151 TACACGCACACCCTACCCCT 62.735 60.000 0.00 0.00 0.00 4.79
302 303 1.619807 ATACACGCACACCCTACCCC 61.620 60.000 0.00 0.00 0.00 4.95
303 304 0.461339 CATACACGCACACCCTACCC 60.461 60.000 0.00 0.00 0.00 3.69
304 305 1.087771 GCATACACGCACACCCTACC 61.088 60.000 0.00 0.00 0.00 3.18
305 306 1.418342 CGCATACACGCACACCCTAC 61.418 60.000 0.00 0.00 0.00 3.18
306 307 1.153726 CGCATACACGCACACCCTA 60.154 57.895 0.00 0.00 0.00 3.53
307 308 2.434185 CGCATACACGCACACCCT 60.434 61.111 0.00 0.00 0.00 4.34
308 309 2.235536 GAACGCATACACGCACACCC 62.236 60.000 0.00 0.00 36.19 4.61
309 310 1.131826 GAACGCATACACGCACACC 59.868 57.895 0.00 0.00 36.19 4.16
310 311 0.442310 ATGAACGCATACACGCACAC 59.558 50.000 0.00 0.00 36.19 3.82
311 312 1.923864 CTATGAACGCATACACGCACA 59.076 47.619 0.00 0.00 35.94 4.57
312 313 1.257936 CCTATGAACGCATACACGCAC 59.742 52.381 0.00 0.00 35.94 5.34
313 314 1.566404 CCTATGAACGCATACACGCA 58.434 50.000 0.00 0.00 35.94 5.24
314 315 0.859232 CCCTATGAACGCATACACGC 59.141 55.000 0.00 0.00 35.94 5.34
315 316 1.202486 ACCCCTATGAACGCATACACG 60.202 52.381 0.00 0.00 35.94 4.49
316 317 2.159014 TCACCCCTATGAACGCATACAC 60.159 50.000 0.00 0.00 35.94 2.90
317 318 2.102420 CTCACCCCTATGAACGCATACA 59.898 50.000 0.00 0.00 35.94 2.29
318 319 2.548067 CCTCACCCCTATGAACGCATAC 60.548 54.545 0.00 0.00 35.94 2.39
319 320 1.691976 CCTCACCCCTATGAACGCATA 59.308 52.381 0.00 0.00 35.94 3.14
320 321 0.469917 CCTCACCCCTATGAACGCAT 59.530 55.000 0.00 0.00 38.54 4.73
321 322 1.622607 CCCTCACCCCTATGAACGCA 61.623 60.000 0.00 0.00 0.00 5.24
322 323 1.146263 CCCTCACCCCTATGAACGC 59.854 63.158 0.00 0.00 0.00 4.84
323 324 1.784358 TACCCTCACCCCTATGAACG 58.216 55.000 0.00 0.00 0.00 3.95
324 325 2.224548 GCATACCCTCACCCCTATGAAC 60.225 54.545 0.00 0.00 0.00 3.18
325 326 2.054799 GCATACCCTCACCCCTATGAA 58.945 52.381 0.00 0.00 0.00 2.57
326 327 1.729586 GCATACCCTCACCCCTATGA 58.270 55.000 0.00 0.00 0.00 2.15
327 328 0.321671 CGCATACCCTCACCCCTATG 59.678 60.000 0.00 0.00 0.00 2.23
328 329 0.105142 ACGCATACCCTCACCCCTAT 60.105 55.000 0.00 0.00 0.00 2.57
329 330 1.046472 CACGCATACCCTCACCCCTA 61.046 60.000 0.00 0.00 0.00 3.53
330 331 2.040606 ACGCATACCCTCACCCCT 59.959 61.111 0.00 0.00 0.00 4.79
331 332 2.189521 CACGCATACCCTCACCCC 59.810 66.667 0.00 0.00 0.00 4.95
332 333 1.449601 CACACGCATACCCTCACCC 60.450 63.158 0.00 0.00 0.00 4.61
333 334 0.533491 TACACACGCATACCCTCACC 59.467 55.000 0.00 0.00 0.00 4.02
334 335 1.067425 TGTACACACGCATACCCTCAC 60.067 52.381 0.00 0.00 0.00 3.51
335 336 1.258676 TGTACACACGCATACCCTCA 58.741 50.000 0.00 0.00 0.00 3.86
336 337 2.159156 TCATGTACACACGCATACCCTC 60.159 50.000 0.00 0.00 0.00 4.30
337 338 1.828595 TCATGTACACACGCATACCCT 59.171 47.619 0.00 0.00 0.00 4.34
338 339 2.201732 CTCATGTACACACGCATACCC 58.798 52.381 0.00 0.00 0.00 3.69
339 340 1.593006 GCTCATGTACACACGCATACC 59.407 52.381 0.00 0.00 0.00 2.73
340 341 1.255342 CGCTCATGTACACACGCATAC 59.745 52.381 0.00 0.00 0.00 2.39
341 342 1.555477 CGCTCATGTACACACGCATA 58.445 50.000 0.00 0.00 0.00 3.14
342 343 1.695893 GCGCTCATGTACACACGCAT 61.696 55.000 21.51 0.00 45.25 4.73
343 344 2.379634 GCGCTCATGTACACACGCA 61.380 57.895 21.51 0.00 45.25 5.24
344 345 1.626654 AAGCGCTCATGTACACACGC 61.627 55.000 12.06 19.82 46.20 5.34
345 346 0.093535 CAAGCGCTCATGTACACACG 59.906 55.000 12.06 0.67 0.00 4.49
346 347 1.136252 CACAAGCGCTCATGTACACAC 60.136 52.381 12.06 0.00 0.00 3.82
347 348 1.147473 CACAAGCGCTCATGTACACA 58.853 50.000 12.06 0.00 0.00 3.72
348 349 1.126846 GACACAAGCGCTCATGTACAC 59.873 52.381 22.37 9.99 0.00 2.90
349 350 1.000843 AGACACAAGCGCTCATGTACA 59.999 47.619 22.37 0.00 0.00 2.90
350 351 1.391485 CAGACACAAGCGCTCATGTAC 59.609 52.381 22.37 15.28 0.00 2.90
351 352 1.000843 ACAGACACAAGCGCTCATGTA 59.999 47.619 22.37 0.00 0.00 2.29
352 353 0.250038 ACAGACACAAGCGCTCATGT 60.250 50.000 22.48 22.48 0.00 3.21
353 354 1.391485 GTACAGACACAAGCGCTCATG 59.609 52.381 12.06 15.18 0.00 3.07
354 355 1.273606 AGTACAGACACAAGCGCTCAT 59.726 47.619 12.06 0.00 0.00 2.90
355 356 0.673985 AGTACAGACACAAGCGCTCA 59.326 50.000 12.06 0.00 0.00 4.26
356 357 1.063806 CAGTACAGACACAAGCGCTC 58.936 55.000 12.06 0.00 0.00 5.03
357 358 0.673985 TCAGTACAGACACAAGCGCT 59.326 50.000 2.64 2.64 0.00 5.92
358 359 1.391485 CATCAGTACAGACACAAGCGC 59.609 52.381 0.00 0.00 0.00 5.92
359 360 1.391485 GCATCAGTACAGACACAAGCG 59.609 52.381 0.00 0.00 0.00 4.68
360 361 2.693069 AGCATCAGTACAGACACAAGC 58.307 47.619 0.00 0.00 0.00 4.01
361 362 6.785488 TTTTAGCATCAGTACAGACACAAG 57.215 37.500 0.00 0.00 0.00 3.16
414 415 2.784356 AACCACGACGGACGACCAA 61.784 57.895 6.90 0.00 45.77 3.67
552 553 4.471747 GGATAAGAGGAAGGAAAGGACTGT 59.528 45.833 0.00 0.00 0.00 3.55
874 901 0.247340 CGACGTCGTTTGTTTGCACA 60.247 50.000 29.08 0.00 34.11 4.57
1050 1078 2.668632 GGCAACATCCTCGTCCCA 59.331 61.111 0.00 0.00 0.00 4.37
1266 1294 3.717294 GAGCCCATGGTGTCGGGT 61.717 66.667 11.73 0.00 45.07 5.28
1713 1766 2.048222 CACCATGCACTCGTCGGT 60.048 61.111 0.00 0.00 0.00 4.69
2363 2439 4.376223 TCCCTGGGACATTAGGTATTCAA 58.624 43.478 12.53 0.00 38.20 2.69
2407 2484 2.682856 TGTCAGCAGAAAACAGTTCACC 59.317 45.455 0.00 0.00 0.00 4.02
2670 2781 5.900339 TGAAACAGTTAGTCAGCTTAACG 57.100 39.130 2.01 1.05 0.00 3.18


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

AutoCloner maintained by Alex Coulton.