Multiple sequence alignment - TraesCS7A01G452600

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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 TraesCS7A01G452600 chr7A 100.000 4138 0 0 1 4138 645106797 645102660 0.000000e+00 7642.0
1 TraesCS7A01G452600 chr7B 94.118 3366 129 33 373 3693 608916564 608913223 0.000000e+00 5055.0
2 TraesCS7A01G452600 chr7B 83.991 456 52 8 3692 4138 608912485 608912042 6.400000e-113 418.0
3 TraesCS7A01G452600 chr7B 84.615 130 16 4 3692 3817 659264641 659264770 4.340000e-25 126.0
4 TraesCS7A01G452600 chr7D 93.438 3383 134 35 374 3693 561024767 561021410 0.000000e+00 4937.0
5 TraesCS7A01G452600 chr7D 87.692 195 21 3 1 195 71109399 71109208 1.500000e-54 224.0
6 TraesCS7A01G452600 chr7D 89.744 117 5 4 754 870 129513135 129513026 4.310000e-30 143.0
7 TraesCS7A01G452600 chr7D 85.714 119 13 4 3692 3806 587838028 587838146 5.620000e-24 122.0
8 TraesCS7A01G452600 chr7D 92.000 50 3 1 3741 3789 4149914 4149865 7.420000e-08 69.4
9 TraesCS7A01G452600 chr2B 82.107 503 56 13 998 1494 100424534 100425008 2.320000e-107 399.0
10 TraesCS7A01G452600 chr2B 90.090 111 11 0 197 307 31581558 31581448 1.200000e-30 145.0
11 TraesCS7A01G452600 chr2B 84.722 72 7 2 3752 3823 4750287 4750220 7.420000e-08 69.4
12 TraesCS7A01G452600 chr1A 90.476 294 19 4 765 1058 510312453 510312737 3.020000e-101 379.0
13 TraesCS7A01G452600 chr1A 88.983 118 6 2 753 870 138320605 138320495 5.580000e-29 139.0
14 TraesCS7A01G452600 chr5A 89.447 199 17 4 1 199 307706414 307706220 8.880000e-62 248.0
15 TraesCS7A01G452600 chr5A 88.983 118 6 2 753 870 589301950 589302060 5.580000e-29 139.0
16 TraesCS7A01G452600 chr3D 88.945 199 20 2 2 200 335198245 335198441 1.150000e-60 244.0
17 TraesCS7A01G452600 chr3D 87.000 200 21 4 2 200 341843303 341843498 1.940000e-53 220.0
18 TraesCS7A01G452600 chr5D 88.177 203 21 3 1 202 163809127 163809327 5.350000e-59 239.0
19 TraesCS7A01G452600 chr5D 87.000 200 23 3 1 200 446686273 446686077 5.380000e-54 222.0
20 TraesCS7A01G452600 chr5D 93.578 109 7 0 199 307 501424276 501424168 3.310000e-36 163.0
21 TraesCS7A01G452600 chr5D 90.826 109 9 1 200 307 379407728 379407620 1.200000e-30 145.0
22 TraesCS7A01G452600 chr4A 88.000 200 21 2 1 200 120452948 120453144 2.490000e-57 233.0
23 TraesCS7A01G452600 chr3B 87.437 199 22 3 1 199 742632631 742632826 4.160000e-55 226.0
24 TraesCS7A01G452600 chr3A 86.935 199 23 2 1 199 575889877 575889682 1.940000e-53 220.0
25 TraesCS7A01G452600 chr3A 90.826 109 9 1 200 307 134598942 134598834 1.200000e-30 145.0
26 TraesCS7A01G452600 chr1D 92.793 111 6 2 199 307 347050731 347050841 4.280000e-35 159.0
27 TraesCS7A01G452600 chr1D 90.826 109 9 1 200 307 423281885 423281777 1.200000e-30 145.0
28 TraesCS7A01G452600 chr2D 92.035 113 7 2 193 305 70020124 70020014 1.540000e-34 158.0
29 TraesCS7A01G452600 chr2D 90.351 114 10 1 196 309 27620700 27620588 9.270000e-32 148.0
30 TraesCS7A01G452600 chrUn 89.655 116 11 1 193 307 41161093 41160978 3.330000e-31 147.0
31 TraesCS7A01G452600 chr4D 86.486 111 9 6 3692 3797 62728924 62729033 2.610000e-22 117.0
32 TraesCS7A01G452600 chr4D 90.278 72 6 1 3745 3815 449962246 449962175 4.400000e-15 93.5
33 TraesCS7A01G452600 chr2A 79.528 127 21 5 3692 3814 40615021 40614896 7.370000e-13 86.1
34 TraesCS7A01G452600 chr6B 84.091 88 11 2 3695 3781 717856735 717856820 9.530000e-12 82.4


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 TraesCS7A01G452600 chr7A 645102660 645106797 4137 True 7642.0 7642 100.0000 1 4138 1 chr7A.!!$R1 4137
1 TraesCS7A01G452600 chr7B 608912042 608916564 4522 True 2736.5 5055 89.0545 373 4138 2 chr7B.!!$R1 3765
2 TraesCS7A01G452600 chr7D 561021410 561024767 3357 True 4937.0 4937 93.4380 374 3693 1 chr7D.!!$R4 3319

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
291 292 0.034059 CCCGGCCTCTGCATAGTTAG 59.966 60.0 0.0 0.00 40.13 2.34 F
728 734 0.179192 CTCAGCGCGCATTGCTTTAA 60.179 50.0 35.1 6.18 41.72 1.52 F
1596 1648 0.111639 TTGGAGGTGGTGTTTAGGGC 59.888 55.0 0.0 0.00 0.00 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1568 1620 0.544697 ACCACCTCCAAGTGTCGTTT 59.455 50.000 0.00 0.0 35.93 3.60 R
2540 2599 1.202758 TCCCATGTCAGTGTGTGGAAC 60.203 52.381 11.16 0.0 33.53 3.62 R
3230 3289 0.026674 CATTGCGGTGTCATAGCACG 59.973 55.000 4.91 0.0 40.92 5.34 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
61 62 4.881057 TTTTTCTCGCCCCGTCAA 57.119 50.000 0.00 0.00 0.00 3.18
62 63 3.097461 TTTTTCTCGCCCCGTCAAA 57.903 47.368 0.00 0.00 0.00 2.69
63 64 1.390565 TTTTTCTCGCCCCGTCAAAA 58.609 45.000 0.00 0.00 0.00 2.44
64 65 1.390565 TTTTCTCGCCCCGTCAAAAA 58.609 45.000 0.00 0.00 0.00 1.94
65 66 1.611519 TTTCTCGCCCCGTCAAAAAT 58.388 45.000 0.00 0.00 0.00 1.82
66 67 0.878416 TTCTCGCCCCGTCAAAAATG 59.122 50.000 0.00 0.00 0.00 2.32
67 68 0.958382 TCTCGCCCCGTCAAAAATGG 60.958 55.000 0.00 0.00 0.00 3.16
73 74 1.880186 CCGTCAAAAATGGGTCGGG 59.120 57.895 0.00 0.00 35.25 5.14
74 75 1.211709 CGTCAAAAATGGGTCGGGC 59.788 57.895 0.00 0.00 0.00 6.13
75 76 1.589630 GTCAAAAATGGGTCGGGCC 59.410 57.895 0.00 0.00 0.00 5.80
76 77 1.153989 TCAAAAATGGGTCGGGCCA 59.846 52.632 4.39 0.00 39.65 5.36
77 78 0.897863 TCAAAAATGGGTCGGGCCAG 60.898 55.000 4.39 0.00 39.65 4.85
78 79 2.282783 AAAAATGGGTCGGGCCAGC 61.283 57.895 4.39 0.00 39.65 4.85
79 80 3.521765 AAAATGGGTCGGGCCAGCA 62.522 57.895 4.39 0.00 39.65 4.41
80 81 2.803593 AAAATGGGTCGGGCCAGCAT 62.804 55.000 4.39 0.00 39.65 3.79
81 82 2.803593 AAATGGGTCGGGCCAGCATT 62.804 55.000 4.39 3.03 39.65 3.56
82 83 4.738998 TGGGTCGGGCCAGCATTG 62.739 66.667 4.39 0.00 39.65 2.82
103 104 4.776647 GCATGCGCCGACCCAAAC 62.777 66.667 4.18 0.00 0.00 2.93
104 105 4.459331 CATGCGCCGACCCAAACG 62.459 66.667 4.18 0.00 0.00 3.60
122 123 3.147294 CGGAAGCAGACGTTCGTG 58.853 61.111 1.74 0.00 0.00 4.35
123 124 1.660575 CGGAAGCAGACGTTCGTGT 60.661 57.895 1.74 0.00 0.00 4.49
124 125 1.606350 CGGAAGCAGACGTTCGTGTC 61.606 60.000 1.74 0.00 39.21 3.67
125 126 1.282930 GGAAGCAGACGTTCGTGTCC 61.283 60.000 1.74 0.00 39.77 4.02
126 127 1.606350 GAAGCAGACGTTCGTGTCCG 61.606 60.000 1.74 0.00 39.77 4.79
127 128 3.764049 GCAGACGTTCGTGTCCGC 61.764 66.667 1.74 0.00 39.77 5.54
128 129 3.103911 CAGACGTTCGTGTCCGCC 61.104 66.667 1.74 0.00 39.77 6.13
129 130 3.292936 AGACGTTCGTGTCCGCCT 61.293 61.111 1.74 0.00 39.77 5.52
130 131 3.103911 GACGTTCGTGTCCGCCTG 61.104 66.667 1.74 0.00 32.61 4.85
131 132 3.547249 GACGTTCGTGTCCGCCTGA 62.547 63.158 1.74 0.00 32.61 3.86
132 133 3.103911 CGTTCGTGTCCGCCTGAC 61.104 66.667 0.00 0.00 44.72 3.51
142 143 3.047877 CGCCTGACGGACCCAAAC 61.048 66.667 0.00 0.00 38.44 2.93
143 144 3.047877 GCCTGACGGACCCAAACG 61.048 66.667 0.00 0.00 0.00 3.60
144 145 2.358247 CCTGACGGACCCAAACGG 60.358 66.667 0.00 0.00 37.81 4.44
145 146 2.738480 CTGACGGACCCAAACGGA 59.262 61.111 0.00 0.00 34.64 4.69
146 147 1.666872 CTGACGGACCCAAACGGAC 60.667 63.158 0.00 0.00 34.64 4.79
147 148 2.372040 CTGACGGACCCAAACGGACA 62.372 60.000 0.00 0.00 34.64 4.02
148 149 1.227615 GACGGACCCAAACGGACAA 60.228 57.895 0.00 0.00 34.64 3.18
149 150 0.814812 GACGGACCCAAACGGACAAA 60.815 55.000 0.00 0.00 34.64 2.83
150 151 0.394080 ACGGACCCAAACGGACAAAA 60.394 50.000 0.00 0.00 34.64 2.44
151 152 0.955905 CGGACCCAAACGGACAAAAT 59.044 50.000 0.00 0.00 34.64 1.82
152 153 1.335506 CGGACCCAAACGGACAAAATG 60.336 52.381 0.00 0.00 34.64 2.32
153 154 1.604438 GGACCCAAACGGACAAAATGC 60.604 52.381 0.00 0.00 34.64 3.56
160 161 3.855630 CGGACAAAATGCGGACAAA 57.144 47.368 0.00 0.00 38.73 2.83
161 162 2.126914 CGGACAAAATGCGGACAAAA 57.873 45.000 0.00 0.00 38.73 2.44
162 163 2.671596 CGGACAAAATGCGGACAAAAT 58.328 42.857 0.00 0.00 38.73 1.82
163 164 3.056304 CGGACAAAATGCGGACAAAATT 58.944 40.909 0.00 0.00 38.73 1.82
164 165 4.230657 CGGACAAAATGCGGACAAAATTA 58.769 39.130 0.00 0.00 38.73 1.40
165 166 4.862018 CGGACAAAATGCGGACAAAATTAT 59.138 37.500 0.00 0.00 38.73 1.28
166 167 5.004345 CGGACAAAATGCGGACAAAATTATC 59.996 40.000 0.00 0.00 38.73 1.75
167 168 5.004345 GGACAAAATGCGGACAAAATTATCG 59.996 40.000 0.00 0.00 0.00 2.92
168 169 5.465935 ACAAAATGCGGACAAAATTATCGT 58.534 33.333 0.00 0.00 0.00 3.73
169 170 5.571357 ACAAAATGCGGACAAAATTATCGTC 59.429 36.000 0.00 0.00 0.00 4.20
170 171 3.963383 ATGCGGACAAAATTATCGTCC 57.037 42.857 9.70 9.70 44.79 4.79
176 177 4.408694 GGACAAAATTATCGTCCGTTTGG 58.591 43.478 5.40 0.00 39.86 3.28
177 178 4.408694 GACAAAATTATCGTCCGTTTGGG 58.591 43.478 0.00 0.00 34.28 4.12
178 179 3.822167 ACAAAATTATCGTCCGTTTGGGT 59.178 39.130 0.00 0.00 34.28 4.51
179 180 4.083164 ACAAAATTATCGTCCGTTTGGGTC 60.083 41.667 0.00 0.00 34.28 4.46
180 181 1.930567 ATTATCGTCCGTTTGGGTCG 58.069 50.000 0.00 0.00 46.78 4.79
181 182 0.108709 TTATCGTCCGTTTGGGTCGG 60.109 55.000 0.00 0.00 45.67 4.79
182 183 2.561549 TATCGTCCGTTTGGGTCGGC 62.562 60.000 0.00 0.00 45.67 5.54
193 194 4.324991 GGTCGGCCCGTTGGAGTT 62.325 66.667 1.63 0.00 0.00 3.01
194 195 3.047877 GTCGGCCCGTTGGAGTTG 61.048 66.667 1.63 0.00 0.00 3.16
195 196 3.552384 TCGGCCCGTTGGAGTTGT 61.552 61.111 1.63 0.00 0.00 3.32
196 197 2.593436 CGGCCCGTTGGAGTTGTT 60.593 61.111 0.00 0.00 0.00 2.83
197 198 2.613506 CGGCCCGTTGGAGTTGTTC 61.614 63.158 0.00 0.00 0.00 3.18
198 199 1.228154 GGCCCGTTGGAGTTGTTCT 60.228 57.895 0.00 0.00 0.00 3.01
199 200 0.035739 GGCCCGTTGGAGTTGTTCTA 59.964 55.000 0.00 0.00 0.00 2.10
200 201 1.339727 GGCCCGTTGGAGTTGTTCTAT 60.340 52.381 0.00 0.00 0.00 1.98
201 202 2.433436 GCCCGTTGGAGTTGTTCTATT 58.567 47.619 0.00 0.00 0.00 1.73
202 203 2.817844 GCCCGTTGGAGTTGTTCTATTT 59.182 45.455 0.00 0.00 0.00 1.40
203 204 3.254903 GCCCGTTGGAGTTGTTCTATTTT 59.745 43.478 0.00 0.00 0.00 1.82
204 205 4.261867 GCCCGTTGGAGTTGTTCTATTTTT 60.262 41.667 0.00 0.00 0.00 1.94
249 250 9.635520 ATTAACTCAAAATGAAGCATCAAGAAG 57.364 29.630 0.00 0.00 39.49 2.85
250 251 6.889301 ACTCAAAATGAAGCATCAAGAAGA 57.111 33.333 0.00 0.00 39.49 2.87
251 252 7.463961 ACTCAAAATGAAGCATCAAGAAGAT 57.536 32.000 0.00 0.00 39.49 2.40
252 253 8.571461 ACTCAAAATGAAGCATCAAGAAGATA 57.429 30.769 0.00 0.00 39.49 1.98
253 254 8.457261 ACTCAAAATGAAGCATCAAGAAGATAC 58.543 33.333 0.00 0.00 39.49 2.24
254 255 8.339344 TCAAAATGAAGCATCAAGAAGATACA 57.661 30.769 0.00 0.00 39.49 2.29
255 256 8.795513 TCAAAATGAAGCATCAAGAAGATACAA 58.204 29.630 0.00 0.00 39.49 2.41
256 257 9.414295 CAAAATGAAGCATCAAGAAGATACAAA 57.586 29.630 0.00 0.00 39.49 2.83
257 258 8.976986 AAATGAAGCATCAAGAAGATACAAAC 57.023 30.769 0.00 0.00 39.49 2.93
258 259 7.692460 ATGAAGCATCAAGAAGATACAAACA 57.308 32.000 0.00 0.00 39.49 2.83
259 260 6.902341 TGAAGCATCAAGAAGATACAAACAC 58.098 36.000 0.00 0.00 34.43 3.32
260 261 6.486320 TGAAGCATCAAGAAGATACAAACACA 59.514 34.615 0.00 0.00 34.43 3.72
261 262 6.882610 AGCATCAAGAAGATACAAACACAA 57.117 33.333 0.00 0.00 34.43 3.33
262 263 6.672147 AGCATCAAGAAGATACAAACACAAC 58.328 36.000 0.00 0.00 34.43 3.32
263 264 5.565259 GCATCAAGAAGATACAAACACAACG 59.435 40.000 0.00 0.00 34.43 4.10
264 265 6.565811 GCATCAAGAAGATACAAACACAACGA 60.566 38.462 0.00 0.00 34.43 3.85
265 266 6.525121 TCAAGAAGATACAAACACAACGAG 57.475 37.500 0.00 0.00 0.00 4.18
266 267 6.046593 TCAAGAAGATACAAACACAACGAGT 58.953 36.000 0.00 0.00 0.00 4.18
267 268 7.204604 TCAAGAAGATACAAACACAACGAGTA 58.795 34.615 0.00 0.00 0.00 2.59
268 269 7.870954 TCAAGAAGATACAAACACAACGAGTAT 59.129 33.333 0.00 0.00 0.00 2.12
269 270 9.135843 CAAGAAGATACAAACACAACGAGTATA 57.864 33.333 0.00 0.00 0.00 1.47
270 271 8.684973 AGAAGATACAAACACAACGAGTATAC 57.315 34.615 0.00 0.00 0.00 1.47
271 272 8.301720 AGAAGATACAAACACAACGAGTATACA 58.698 33.333 5.50 0.00 0.00 2.29
272 273 7.807687 AGATACAAACACAACGAGTATACAC 57.192 36.000 5.50 0.00 0.00 2.90
273 274 6.810182 AGATACAAACACAACGAGTATACACC 59.190 38.462 5.50 0.00 0.00 4.16
274 275 4.060205 ACAAACACAACGAGTATACACCC 58.940 43.478 5.50 0.00 0.00 4.61
275 276 2.642139 ACACAACGAGTATACACCCG 57.358 50.000 5.50 8.05 0.00 5.28
276 277 1.203052 ACACAACGAGTATACACCCGG 59.797 52.381 5.50 0.00 0.00 5.73
277 278 0.174162 ACAACGAGTATACACCCGGC 59.826 55.000 5.50 0.00 0.00 6.13
278 279 0.529119 CAACGAGTATACACCCGGCC 60.529 60.000 5.50 0.00 0.00 6.13
279 280 0.685458 AACGAGTATACACCCGGCCT 60.685 55.000 5.50 0.00 0.00 5.19
280 281 1.105759 ACGAGTATACACCCGGCCTC 61.106 60.000 5.50 0.00 0.00 4.70
281 282 0.822532 CGAGTATACACCCGGCCTCT 60.823 60.000 5.50 0.00 0.00 3.69
282 283 0.674534 GAGTATACACCCGGCCTCTG 59.325 60.000 5.50 0.00 0.00 3.35
283 284 1.069258 GTATACACCCGGCCTCTGC 59.931 63.158 0.00 0.00 0.00 4.26
284 285 1.382009 TATACACCCGGCCTCTGCA 60.382 57.895 0.00 0.00 40.13 4.41
285 286 0.762842 TATACACCCGGCCTCTGCAT 60.763 55.000 0.00 0.00 40.13 3.96
286 287 0.762842 ATACACCCGGCCTCTGCATA 60.763 55.000 0.00 0.00 40.13 3.14
287 288 1.399744 TACACCCGGCCTCTGCATAG 61.400 60.000 0.00 0.00 40.13 2.23
288 289 2.365635 ACCCGGCCTCTGCATAGT 60.366 61.111 0.00 0.00 40.13 2.12
289 290 1.995626 ACCCGGCCTCTGCATAGTT 60.996 57.895 0.00 0.00 40.13 2.24
290 291 0.689745 ACCCGGCCTCTGCATAGTTA 60.690 55.000 0.00 0.00 40.13 2.24
291 292 0.034059 CCCGGCCTCTGCATAGTTAG 59.966 60.000 0.00 0.00 40.13 2.34
292 293 0.034059 CCGGCCTCTGCATAGTTAGG 59.966 60.000 0.00 0.00 40.13 2.69
293 294 1.040646 CGGCCTCTGCATAGTTAGGA 58.959 55.000 0.00 0.00 40.13 2.94
294 295 1.620819 CGGCCTCTGCATAGTTAGGAT 59.379 52.381 0.00 0.00 40.13 3.24
295 296 2.611473 CGGCCTCTGCATAGTTAGGATG 60.611 54.545 0.00 0.00 40.13 3.51
316 317 7.599630 GATGCACACATCCAATAAAATTGTT 57.400 32.000 0.00 0.00 45.94 2.83
317 318 7.599630 ATGCACACATCCAATAAAATTGTTC 57.400 32.000 0.00 0.00 0.00 3.18
318 319 6.757237 TGCACACATCCAATAAAATTGTTCT 58.243 32.000 0.00 0.00 0.00 3.01
319 320 7.890515 TGCACACATCCAATAAAATTGTTCTA 58.109 30.769 0.00 0.00 0.00 2.10
320 321 8.363390 TGCACACATCCAATAAAATTGTTCTAA 58.637 29.630 0.00 0.00 0.00 2.10
321 322 9.369904 GCACACATCCAATAAAATTGTTCTAAT 57.630 29.630 0.00 0.00 0.00 1.73
348 349 9.073475 ACAGTATAAAAAGAATTAGGCACAACA 57.927 29.630 0.00 0.00 0.00 3.33
351 352 9.516314 GTATAAAAAGAATTAGGCACAACATCC 57.484 33.333 0.00 0.00 0.00 3.51
352 353 5.405935 AAAAGAATTAGGCACAACATCCC 57.594 39.130 0.00 0.00 0.00 3.85
353 354 4.322057 AAGAATTAGGCACAACATCCCT 57.678 40.909 0.00 0.00 0.00 4.20
354 355 3.624777 AGAATTAGGCACAACATCCCTG 58.375 45.455 0.00 0.00 0.00 4.45
355 356 3.010584 AGAATTAGGCACAACATCCCTGT 59.989 43.478 0.00 0.00 37.12 4.00
356 357 2.969821 TTAGGCACAACATCCCTGTT 57.030 45.000 0.00 0.00 46.54 3.16
357 358 4.584638 ATTAGGCACAACATCCCTGTTA 57.415 40.909 0.00 0.00 43.76 2.41
358 359 4.584638 TTAGGCACAACATCCCTGTTAT 57.415 40.909 0.00 0.00 43.76 1.89
359 360 3.456380 AGGCACAACATCCCTGTTATT 57.544 42.857 0.00 0.00 43.76 1.40
360 361 3.778265 AGGCACAACATCCCTGTTATTT 58.222 40.909 0.00 0.00 43.76 1.40
361 362 4.159557 AGGCACAACATCCCTGTTATTTT 58.840 39.130 0.00 0.00 43.76 1.82
362 363 4.592778 AGGCACAACATCCCTGTTATTTTT 59.407 37.500 0.00 0.00 43.76 1.94
399 400 5.105756 GGTTTCTCATCAAAACAATCCGGAT 60.106 40.000 12.38 12.38 38.16 4.18
401 402 3.871006 TCTCATCAAAACAATCCGGATCG 59.129 43.478 19.43 9.69 0.00 3.69
476 482 5.864418 ATAAATACTCGAGTTAGGTGGCA 57.136 39.130 25.44 2.65 0.00 4.92
478 484 2.502142 TACTCGAGTTAGGTGGCAGA 57.498 50.000 25.44 0.00 0.00 4.26
555 561 3.003763 AAGAGACCCGAGGCCACC 61.004 66.667 5.01 0.00 0.00 4.61
595 601 3.834799 GGTACCCCACCGAGCGAG 61.835 72.222 0.00 0.00 37.63 5.03
596 602 2.753043 GTACCCCACCGAGCGAGA 60.753 66.667 0.00 0.00 0.00 4.04
597 603 2.439701 TACCCCACCGAGCGAGAG 60.440 66.667 0.00 0.00 0.00 3.20
712 718 3.003173 CCCCCAACGAGAGCCTCA 61.003 66.667 0.00 0.00 0.00 3.86
728 734 0.179192 CTCAGCGCGCATTGCTTTAA 60.179 50.000 35.10 6.18 41.72 1.52
925 947 1.935327 GAGTCGCGGTAGCTGAAGGT 61.935 60.000 6.13 0.00 42.32 3.50
926 948 0.679002 AGTCGCGGTAGCTGAAGGTA 60.679 55.000 6.13 0.00 42.32 3.08
933 955 1.861982 GTAGCTGAAGGTACAGGGGA 58.138 55.000 13.42 0.00 45.45 4.81
1185 1232 1.207488 AGTAGTTGATGCCCAGCCCA 61.207 55.000 0.00 0.00 0.00 5.36
1207 1254 2.109181 GCTGCGGAGGTATGGGTC 59.891 66.667 5.93 0.00 0.00 4.46
1214 1261 2.104281 GCGGAGGTATGGGTCAGTAATT 59.896 50.000 0.00 0.00 0.00 1.40
1223 1270 1.602377 GGGTCAGTAATTACGCATGGC 59.398 52.381 9.91 4.85 0.00 4.40
1293 1341 2.346244 CGCTTACTGAATTTTCGGCGTA 59.654 45.455 6.85 0.00 37.06 4.42
1368 1416 8.499162 CCTAGGATTTCTATTTCAAGTTATGCG 58.501 37.037 1.05 0.00 0.00 4.73
1455 1507 1.336440 CCACACGGAATTGCTGTTTGA 59.664 47.619 8.72 0.00 35.95 2.69
1478 1530 7.715657 TGAGGTATCATGCCAAATGTTAATTC 58.284 34.615 0.00 0.00 0.00 2.17
1559 1611 1.662044 CAGAAGCAAGTGGGGCAAC 59.338 57.895 0.00 0.00 0.00 4.17
1568 1620 0.994247 AGTGGGGCAACATGATGAGA 59.006 50.000 7.22 0.00 39.74 3.27
1596 1648 0.111639 TTGGAGGTGGTGTTTAGGGC 59.888 55.000 0.00 0.00 0.00 5.19
1637 1689 2.393768 GGGCATATGGATCGCTGCG 61.394 63.158 17.25 17.25 35.47 5.18
1745 1797 0.924090 CCATAGTTGAGTTCGCTCGC 59.076 55.000 0.00 0.00 46.95 5.03
1886 1938 3.640407 GCAGCCTCACCCCTGTCA 61.640 66.667 0.00 0.00 0.00 3.58
2108 2160 7.815068 AGTGATACTAAGAAAAGCTGTACACTG 59.185 37.037 0.00 0.00 31.39 3.66
2125 2177 6.837048 TGTACACTGCTTCCATATTAGTCCTA 59.163 38.462 0.00 0.00 0.00 2.94
2126 2178 7.509318 TGTACACTGCTTCCATATTAGTCCTAT 59.491 37.037 0.00 0.00 0.00 2.57
2127 2179 6.998802 ACACTGCTTCCATATTAGTCCTATC 58.001 40.000 0.00 0.00 0.00 2.08
2157 2209 3.954258 ACTGGCTTACAATATTTCCCTGC 59.046 43.478 0.00 0.00 0.00 4.85
2261 2320 3.079578 CACATGGTTGAAGCTGATCAGT 58.920 45.455 23.38 4.98 0.00 3.41
2297 2356 8.210946 TGCATAGCAGGAACAATTATAGTTAGT 58.789 33.333 0.00 0.00 33.32 2.24
2540 2599 1.880819 ATTTTGCCAAGCTGGAGCCG 61.881 55.000 6.40 0.00 40.96 5.52
2624 2683 8.700722 TTCACACATTTATTCATTTACATGCC 57.299 30.769 0.00 0.00 0.00 4.40
2648 2707 6.127897 CCTGTTGCTATTCTTTAGAAACCTGG 60.128 42.308 0.00 0.00 37.61 4.45
2658 2717 0.329596 AGAAACCTGGGGTGCTCATC 59.670 55.000 0.00 0.00 35.34 2.92
2864 2923 5.480073 TGACTACTTATGGGCAAAAGCAATT 59.520 36.000 0.00 0.00 0.00 2.32
3186 3245 4.980573 TGTCCAAGTGTAATTACCAAGCT 58.019 39.130 13.01 3.69 0.00 3.74
3199 3258 1.660560 CCAAGCTGTGTATGCCTGGC 61.661 60.000 12.87 12.87 35.57 4.85
3230 3289 0.251209 GGTTCAGTCAGGTTTCCCCC 60.251 60.000 0.00 0.00 0.00 5.40
3237 3296 0.912487 TCAGGTTTCCCCCGTGCTAT 60.912 55.000 0.00 0.00 0.00 2.97
3263 3322 2.154462 CGCAATGGAAGGGATGGATAC 58.846 52.381 0.00 0.00 0.00 2.24
3372 3431 9.360093 CTAAATTTTGTTGTACAAGGTGAAACA 57.640 29.630 8.98 0.00 39.53 2.83
3431 3490 9.328845 GGGTTGCATGATTATTACATTGAATTT 57.671 29.630 0.00 0.00 0.00 1.82
3454 3526 2.983229 AGCTCATGATGTTCACCTGAC 58.017 47.619 0.00 0.00 0.00 3.51
3457 3529 3.373439 GCTCATGATGTTCACCTGACTTC 59.627 47.826 0.00 0.00 0.00 3.01
3459 3531 4.971939 TCATGATGTTCACCTGACTTCAA 58.028 39.130 0.00 0.00 0.00 2.69
3461 3533 4.422073 TGATGTTCACCTGACTTCAACT 57.578 40.909 0.00 0.00 0.00 3.16
3530 3602 0.892755 ATGCAGTGCCAATGGACAAG 59.107 50.000 13.72 0.00 0.00 3.16
3558 3631 5.154222 GGAACTTGTTACATTAGCAGCAAC 58.846 41.667 0.00 0.00 0.00 4.17
3574 3648 6.085573 AGCAGCAACAAACATTTTCAAAAAC 58.914 32.000 0.00 0.00 0.00 2.43
3600 3675 9.578439 CAAAGAAAAGATGAAGAGTTGTTCTTT 57.422 29.630 0.00 0.00 46.12 2.52
3607 3682 6.648725 AGATGAAGAGTTGTTCTTTAGCTGAC 59.351 38.462 0.00 0.00 43.81 3.51
3638 3713 4.821805 CGTATGCAAGGATAGGGAATTTGT 59.178 41.667 0.00 0.00 0.00 2.83
3643 3718 5.530915 TGCAAGGATAGGGAATTTGTAATCG 59.469 40.000 0.00 0.00 0.00 3.34
3723 4542 9.959749 ATGAAATACGTTTTGATGTAAGTTGTT 57.040 25.926 0.00 0.00 0.00 2.83
3758 4579 9.920826 TCGTGTACTTTTATAGTGAATAGTACG 57.079 33.333 0.00 0.00 40.30 3.67
3798 4619 8.863049 CATGATTTTGTTATTTTGTGTAGCTCC 58.137 33.333 0.00 0.00 0.00 4.70
3800 4621 5.365403 TTTGTTATTTTGTGTAGCTCCCG 57.635 39.130 0.00 0.00 0.00 5.14
3814 4635 9.048446 TGTGTAGCTCCCGTAAAAATATATTTC 57.952 33.333 11.08 0.00 0.00 2.17
3815 4636 9.048446 GTGTAGCTCCCGTAAAAATATATTTCA 57.952 33.333 11.08 0.36 0.00 2.69
3838 4659 6.072728 TCACCATGAATTTTTACGGAGAAGTG 60.073 38.462 0.00 0.00 0.00 3.16
3839 4660 5.768164 ACCATGAATTTTTACGGAGAAGTGT 59.232 36.000 0.00 0.00 0.00 3.55
3840 4661 6.086222 CCATGAATTTTTACGGAGAAGTGTG 58.914 40.000 0.00 0.00 0.00 3.82
3842 4663 6.055231 TGAATTTTTACGGAGAAGTGTGTG 57.945 37.500 0.00 0.00 0.00 3.82
3843 4664 5.587043 TGAATTTTTACGGAGAAGTGTGTGT 59.413 36.000 0.00 0.00 0.00 3.72
3844 4665 4.868450 TTTTTACGGAGAAGTGTGTGTG 57.132 40.909 0.00 0.00 0.00 3.82
3846 4667 2.502213 TACGGAGAAGTGTGTGTGTG 57.498 50.000 0.00 0.00 0.00 3.82
3848 4669 0.930310 CGGAGAAGTGTGTGTGTGTG 59.070 55.000 0.00 0.00 0.00 3.82
3850 4671 1.665679 GGAGAAGTGTGTGTGTGTGTG 59.334 52.381 0.00 0.00 0.00 3.82
3852 4673 2.076100 AGAAGTGTGTGTGTGTGTGTG 58.924 47.619 0.00 0.00 0.00 3.82
3854 4675 1.155889 AGTGTGTGTGTGTGTGTGTG 58.844 50.000 0.00 0.00 0.00 3.82
3855 4676 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
3856 4677 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
3857 4678 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
3858 4679 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
3859 4680 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
3860 4681 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
3861 4682 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
3862 4683 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
3863 4684 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
3867 4688 2.093625 GTGTGTGTGTGTGTGTGTACAG 59.906 50.000 0.00 0.00 37.52 2.74
3877 4698 3.133183 TGTGTGTGTACAGGTATGTGTGT 59.867 43.478 0.00 0.00 40.79 3.72
3884 4705 8.013378 GTGTGTACAGGTATGTGTGTATTTTTC 58.987 37.037 0.00 0.00 40.79 2.29
3885 4706 7.715686 TGTGTACAGGTATGTGTGTATTTTTCA 59.284 33.333 0.00 0.00 40.79 2.69
3886 4707 8.227791 GTGTACAGGTATGTGTGTATTTTTCAG 58.772 37.037 0.00 0.00 40.79 3.02
3888 4709 8.995220 GTACAGGTATGTGTGTATTTTTCAGAA 58.005 33.333 0.00 0.00 40.79 3.02
3890 4711 9.077885 ACAGGTATGTGTGTATTTTTCAGAAAT 57.922 29.630 0.00 0.00 38.57 2.17
3949 4777 9.715121 ATCAAATGCAATCTCTGTTGTTTTATT 57.285 25.926 0.00 0.00 0.00 1.40
3956 4784 7.624344 GCAATCTCTGTTGTTTTATTAGAGCGT 60.624 37.037 0.00 0.00 35.89 5.07
3959 4787 8.236084 TCTCTGTTGTTTTATTAGAGCGTAAC 57.764 34.615 0.00 0.00 35.89 2.50
3962 4790 8.995220 TCTGTTGTTTTATTAGAGCGTAACATT 58.005 29.630 0.00 0.00 0.00 2.71
4058 4886 2.951458 GGCTAACCCGTGTTGTGC 59.049 61.111 0.00 0.00 35.87 4.57
4060 4888 1.957186 GCTAACCCGTGTTGTGCGA 60.957 57.895 0.00 0.00 35.87 5.10
4075 4903 0.320858 TGCGACAGCCCAATTCGTTA 60.321 50.000 0.00 0.00 44.33 3.18
4094 4922 2.566010 CCCGTCCCATTTTGCACG 59.434 61.111 0.00 0.00 0.00 5.34
4095 4923 2.265182 CCCGTCCCATTTTGCACGT 61.265 57.895 0.00 0.00 0.00 4.49
4105 4933 1.464734 TTTTGCACGTGAGGAAACCA 58.535 45.000 22.23 2.21 0.00 3.67
4122 4950 3.223674 ACCACCAAACCCTAGAAACAG 57.776 47.619 0.00 0.00 0.00 3.16
4124 4952 1.886542 CACCAAACCCTAGAAACAGCC 59.113 52.381 0.00 0.00 0.00 4.85
4134 4962 4.974721 AAACAGCCCCCGCACCTG 62.975 66.667 0.00 0.00 37.52 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 1.390565 TTTTGACGGGGCGAGAAAAA 58.609 45.000 0.00 0.00 0.00 1.94
45 46 1.390565 TTTTTGACGGGGCGAGAAAA 58.609 45.000 0.00 0.00 0.00 2.29
46 47 1.268352 CATTTTTGACGGGGCGAGAAA 59.732 47.619 0.00 0.00 0.00 2.52
47 48 0.878416 CATTTTTGACGGGGCGAGAA 59.122 50.000 0.00 0.00 0.00 2.87
48 49 0.958382 CCATTTTTGACGGGGCGAGA 60.958 55.000 0.00 0.00 0.00 4.04
49 50 1.506262 CCATTTTTGACGGGGCGAG 59.494 57.895 0.00 0.00 0.00 5.03
50 51 1.974343 CCCATTTTTGACGGGGCGA 60.974 57.895 0.00 0.00 36.21 5.54
51 52 2.207788 GACCCATTTTTGACGGGGCG 62.208 60.000 0.00 0.00 44.96 6.13
52 53 1.589630 GACCCATTTTTGACGGGGC 59.410 57.895 0.00 0.00 44.96 5.80
53 54 1.591504 CCGACCCATTTTTGACGGGG 61.592 60.000 0.00 0.00 44.96 5.73
54 55 1.880186 CCGACCCATTTTTGACGGG 59.120 57.895 0.00 0.00 46.22 5.28
55 56 1.880186 CCCGACCCATTTTTGACGG 59.120 57.895 0.00 0.00 40.03 4.79
56 57 1.211709 GCCCGACCCATTTTTGACG 59.788 57.895 0.00 0.00 0.00 4.35
57 58 1.182385 TGGCCCGACCCATTTTTGAC 61.182 55.000 0.00 0.00 37.83 3.18
58 59 0.897863 CTGGCCCGACCCATTTTTGA 60.898 55.000 0.00 0.00 37.83 2.69
59 60 1.591183 CTGGCCCGACCCATTTTTG 59.409 57.895 0.00 0.00 37.83 2.44
60 61 2.282783 GCTGGCCCGACCCATTTTT 61.283 57.895 0.00 0.00 37.83 1.94
61 62 2.679996 GCTGGCCCGACCCATTTT 60.680 61.111 0.00 0.00 37.83 1.82
62 63 2.803593 AATGCTGGCCCGACCCATTT 62.804 55.000 0.00 0.00 37.83 2.32
63 64 3.301222 AATGCTGGCCCGACCCATT 62.301 57.895 0.00 0.00 37.83 3.16
64 65 3.743017 AATGCTGGCCCGACCCAT 61.743 61.111 0.00 0.00 37.83 4.00
65 66 4.738998 CAATGCTGGCCCGACCCA 62.739 66.667 0.00 0.00 37.83 4.51
73 74 4.884257 CATGCGCCCAATGCTGGC 62.884 66.667 4.18 0.00 45.70 4.85
74 75 4.884257 GCATGCGCCCAATGCTGG 62.884 66.667 20.41 0.00 43.10 4.85
86 87 4.776647 GTTTGGGTCGGCGCATGC 62.777 66.667 7.88 7.91 37.40 4.06
87 88 4.459331 CGTTTGGGTCGGCGCATG 62.459 66.667 7.88 0.00 37.40 4.06
93 94 3.419759 CTTCCGCGTTTGGGTCGG 61.420 66.667 4.92 0.00 44.16 4.79
94 95 4.084888 GCTTCCGCGTTTGGGTCG 62.085 66.667 4.92 0.00 0.00 4.79
95 96 2.966309 CTGCTTCCGCGTTTGGGTC 61.966 63.158 4.92 0.00 39.65 4.46
96 97 2.978010 CTGCTTCCGCGTTTGGGT 60.978 61.111 4.92 0.00 39.65 4.51
97 98 2.668212 TCTGCTTCCGCGTTTGGG 60.668 61.111 4.92 0.00 39.65 4.12
98 99 2.556287 GTCTGCTTCCGCGTTTGG 59.444 61.111 4.92 0.00 39.65 3.28
99 100 2.101209 AACGTCTGCTTCCGCGTTTG 62.101 55.000 4.92 0.00 43.69 2.93
100 101 1.828331 GAACGTCTGCTTCCGCGTTT 61.828 55.000 4.92 0.00 45.68 3.60
101 102 2.279918 AACGTCTGCTTCCGCGTT 60.280 55.556 4.92 0.00 41.79 4.84
102 103 2.733593 GAACGTCTGCTTCCGCGT 60.734 61.111 4.92 0.00 39.65 6.01
103 104 3.827784 CGAACGTCTGCTTCCGCG 61.828 66.667 0.00 0.00 39.65 6.46
104 105 2.733593 ACGAACGTCTGCTTCCGC 60.734 61.111 0.00 0.00 0.00 5.54
105 106 1.606350 GACACGAACGTCTGCTTCCG 61.606 60.000 0.00 0.00 32.92 4.30
106 107 1.282930 GGACACGAACGTCTGCTTCC 61.283 60.000 0.00 0.00 36.12 3.46
107 108 1.606350 CGGACACGAACGTCTGCTTC 61.606 60.000 0.00 0.00 44.60 3.86
108 109 1.660575 CGGACACGAACGTCTGCTT 60.661 57.895 0.00 0.00 44.60 3.91
109 110 2.050351 CGGACACGAACGTCTGCT 60.050 61.111 0.00 0.00 44.60 4.24
111 112 3.103911 GGCGGACACGAACGTCTG 61.104 66.667 0.00 8.29 44.60 3.51
112 113 3.292936 AGGCGGACACGAACGTCT 61.293 61.111 0.00 0.00 44.60 4.18
113 114 3.103911 CAGGCGGACACGAACGTC 61.104 66.667 0.00 0.00 44.60 4.34
114 115 3.598715 TCAGGCGGACACGAACGT 61.599 61.111 0.00 0.00 44.60 3.99
115 116 3.103911 GTCAGGCGGACACGAACG 61.104 66.667 13.03 0.00 46.19 3.95
125 126 3.047877 GTTTGGGTCCGTCAGGCG 61.048 66.667 0.00 0.00 40.95 5.52
126 127 3.047877 CGTTTGGGTCCGTCAGGC 61.048 66.667 0.00 0.00 37.47 4.85
127 128 2.358247 CCGTTTGGGTCCGTCAGG 60.358 66.667 0.00 0.00 39.46 3.86
128 129 1.666872 GTCCGTTTGGGTCCGTCAG 60.667 63.158 0.00 0.00 37.00 3.51
129 130 1.969200 TTGTCCGTTTGGGTCCGTCA 61.969 55.000 0.00 0.00 37.00 4.35
130 131 0.814812 TTTGTCCGTTTGGGTCCGTC 60.815 55.000 0.00 0.00 37.00 4.79
131 132 0.394080 TTTTGTCCGTTTGGGTCCGT 60.394 50.000 0.00 0.00 37.00 4.69
132 133 0.955905 ATTTTGTCCGTTTGGGTCCG 59.044 50.000 0.00 0.00 37.00 4.79
133 134 1.604438 GCATTTTGTCCGTTTGGGTCC 60.604 52.381 0.00 0.00 37.00 4.46
134 135 1.778334 GCATTTTGTCCGTTTGGGTC 58.222 50.000 0.00 0.00 37.00 4.46
135 136 0.031449 CGCATTTTGTCCGTTTGGGT 59.969 50.000 0.00 0.00 37.00 4.51
136 137 0.665972 CCGCATTTTGTCCGTTTGGG 60.666 55.000 0.00 0.00 35.24 4.12
137 138 0.312416 TCCGCATTTTGTCCGTTTGG 59.688 50.000 0.00 0.00 0.00 3.28
138 139 1.268794 TGTCCGCATTTTGTCCGTTTG 60.269 47.619 0.00 0.00 0.00 2.93
139 140 1.025812 TGTCCGCATTTTGTCCGTTT 58.974 45.000 0.00 0.00 0.00 3.60
140 141 1.025812 TTGTCCGCATTTTGTCCGTT 58.974 45.000 0.00 0.00 0.00 4.44
141 142 1.025812 TTTGTCCGCATTTTGTCCGT 58.974 45.000 0.00 0.00 0.00 4.69
142 143 2.126914 TTTTGTCCGCATTTTGTCCG 57.873 45.000 0.00 0.00 0.00 4.79
143 144 5.004345 CGATAATTTTGTCCGCATTTTGTCC 59.996 40.000 0.00 0.00 0.00 4.02
144 145 5.571357 ACGATAATTTTGTCCGCATTTTGTC 59.429 36.000 0.00 0.00 0.00 3.18
145 146 5.465935 ACGATAATTTTGTCCGCATTTTGT 58.534 33.333 0.00 0.00 0.00 2.83
146 147 5.004345 GGACGATAATTTTGTCCGCATTTTG 59.996 40.000 7.44 0.00 46.68 2.44
147 148 5.099575 GGACGATAATTTTGTCCGCATTTT 58.900 37.500 7.44 0.00 46.68 1.82
148 149 4.668289 GGACGATAATTTTGTCCGCATTT 58.332 39.130 7.44 0.00 46.68 2.32
149 150 4.287238 GGACGATAATTTTGTCCGCATT 57.713 40.909 7.44 0.00 46.68 3.56
150 151 3.963383 GGACGATAATTTTGTCCGCAT 57.037 42.857 7.44 0.00 46.68 4.73
155 156 4.083164 ACCCAAACGGACGATAATTTTGTC 60.083 41.667 0.00 0.00 37.94 3.18
156 157 3.822167 ACCCAAACGGACGATAATTTTGT 59.178 39.130 0.00 0.00 34.64 2.83
157 158 4.408694 GACCCAAACGGACGATAATTTTG 58.591 43.478 0.00 0.00 34.64 2.44
158 159 4.690184 GACCCAAACGGACGATAATTTT 57.310 40.909 0.00 0.00 34.64 1.82
176 177 4.324991 AACTCCAACGGGCCGACC 62.325 66.667 35.78 0.00 0.00 4.79
177 178 3.047877 CAACTCCAACGGGCCGAC 61.048 66.667 35.78 0.00 0.00 4.79
178 179 2.999739 GAACAACTCCAACGGGCCGA 63.000 60.000 35.78 9.29 0.00 5.54
179 180 2.593436 AACAACTCCAACGGGCCG 60.593 61.111 27.06 27.06 0.00 6.13
180 181 0.035739 TAGAACAACTCCAACGGGCC 59.964 55.000 0.00 0.00 0.00 5.80
181 182 2.109425 ATAGAACAACTCCAACGGGC 57.891 50.000 0.00 0.00 0.00 6.13
182 183 5.447624 AAAAATAGAACAACTCCAACGGG 57.552 39.130 0.00 0.00 0.00 5.28
223 224 9.635520 CTTCTTGATGCTTCATTTTGAGTTAAT 57.364 29.630 2.75 0.00 0.00 1.40
224 225 8.849168 TCTTCTTGATGCTTCATTTTGAGTTAA 58.151 29.630 2.75 0.00 0.00 2.01
225 226 8.394971 TCTTCTTGATGCTTCATTTTGAGTTA 57.605 30.769 2.75 0.00 0.00 2.24
226 227 7.281040 TCTTCTTGATGCTTCATTTTGAGTT 57.719 32.000 2.75 0.00 0.00 3.01
227 228 6.889301 TCTTCTTGATGCTTCATTTTGAGT 57.111 33.333 2.75 0.00 0.00 3.41
228 229 8.456471 TGTATCTTCTTGATGCTTCATTTTGAG 58.544 33.333 2.75 0.00 38.39 3.02
229 230 8.339344 TGTATCTTCTTGATGCTTCATTTTGA 57.661 30.769 2.75 1.59 38.39 2.69
230 231 8.975410 TTGTATCTTCTTGATGCTTCATTTTG 57.025 30.769 2.75 0.00 38.39 2.44
231 232 9.415544 GTTTGTATCTTCTTGATGCTTCATTTT 57.584 29.630 2.75 0.00 38.39 1.82
232 233 8.579006 TGTTTGTATCTTCTTGATGCTTCATTT 58.421 29.630 2.75 0.00 38.39 2.32
233 234 8.025445 GTGTTTGTATCTTCTTGATGCTTCATT 58.975 33.333 2.75 0.00 38.39 2.57
234 235 7.175467 TGTGTTTGTATCTTCTTGATGCTTCAT 59.825 33.333 2.75 0.00 38.39 2.57
235 236 6.486320 TGTGTTTGTATCTTCTTGATGCTTCA 59.514 34.615 0.00 0.00 38.39 3.02
236 237 6.902341 TGTGTTTGTATCTTCTTGATGCTTC 58.098 36.000 0.00 0.00 38.39 3.86
237 238 6.882610 TGTGTTTGTATCTTCTTGATGCTT 57.117 33.333 0.00 0.00 38.39 3.91
238 239 6.566564 CGTTGTGTTTGTATCTTCTTGATGCT 60.567 38.462 0.00 0.00 38.39 3.79
239 240 5.565259 CGTTGTGTTTGTATCTTCTTGATGC 59.435 40.000 0.00 0.00 38.12 3.91
240 241 6.887368 TCGTTGTGTTTGTATCTTCTTGATG 58.113 36.000 0.00 0.00 36.65 3.07
241 242 6.706270 ACTCGTTGTGTTTGTATCTTCTTGAT 59.294 34.615 0.00 0.00 39.11 2.57
242 243 6.046593 ACTCGTTGTGTTTGTATCTTCTTGA 58.953 36.000 0.00 0.00 0.00 3.02
243 244 6.287107 ACTCGTTGTGTTTGTATCTTCTTG 57.713 37.500 0.00 0.00 0.00 3.02
244 245 9.136952 GTATACTCGTTGTGTTTGTATCTTCTT 57.863 33.333 0.00 0.00 0.00 2.52
245 246 8.301720 TGTATACTCGTTGTGTTTGTATCTTCT 58.698 33.333 4.17 0.00 0.00 2.85
246 247 8.371053 GTGTATACTCGTTGTGTTTGTATCTTC 58.629 37.037 4.17 0.00 0.00 2.87
247 248 7.330208 GGTGTATACTCGTTGTGTTTGTATCTT 59.670 37.037 4.17 0.00 0.00 2.40
248 249 6.810182 GGTGTATACTCGTTGTGTTTGTATCT 59.190 38.462 4.17 0.00 0.00 1.98
249 250 6.035327 GGGTGTATACTCGTTGTGTTTGTATC 59.965 42.308 4.17 0.00 0.00 2.24
250 251 5.870978 GGGTGTATACTCGTTGTGTTTGTAT 59.129 40.000 4.17 0.00 0.00 2.29
251 252 5.229423 GGGTGTATACTCGTTGTGTTTGTA 58.771 41.667 4.17 0.00 0.00 2.41
252 253 4.060205 GGGTGTATACTCGTTGTGTTTGT 58.940 43.478 4.17 0.00 0.00 2.83
253 254 3.122278 CGGGTGTATACTCGTTGTGTTTG 59.878 47.826 3.37 0.00 45.61 2.93
254 255 3.319755 CGGGTGTATACTCGTTGTGTTT 58.680 45.455 3.37 0.00 45.61 2.83
255 256 2.950433 CGGGTGTATACTCGTTGTGTT 58.050 47.619 3.37 0.00 45.61 3.32
256 257 2.642139 CGGGTGTATACTCGTTGTGT 57.358 50.000 3.37 0.00 45.61 3.72
263 264 0.674534 CAGAGGCCGGGTGTATACTC 59.325 60.000 2.18 0.00 0.00 2.59
264 265 1.400530 GCAGAGGCCGGGTGTATACT 61.401 60.000 2.18 0.00 0.00 2.12
265 266 1.069258 GCAGAGGCCGGGTGTATAC 59.931 63.158 2.18 0.00 0.00 1.47
266 267 0.762842 ATGCAGAGGCCGGGTGTATA 60.763 55.000 2.18 0.00 40.13 1.47
267 268 0.762842 TATGCAGAGGCCGGGTGTAT 60.763 55.000 2.18 3.94 40.13 2.29
268 269 1.382009 TATGCAGAGGCCGGGTGTA 60.382 57.895 2.18 0.00 40.13 2.90
269 270 2.687200 TATGCAGAGGCCGGGTGT 60.687 61.111 2.18 0.00 40.13 4.16
270 271 2.109799 CTATGCAGAGGCCGGGTG 59.890 66.667 2.18 0.00 40.13 4.61
271 272 0.689745 TAACTATGCAGAGGCCGGGT 60.690 55.000 13.85 0.00 40.13 5.28
272 273 0.034059 CTAACTATGCAGAGGCCGGG 59.966 60.000 13.85 0.00 40.13 5.73
273 274 0.034059 CCTAACTATGCAGAGGCCGG 59.966 60.000 13.85 0.00 40.13 6.13
274 275 1.040646 TCCTAACTATGCAGAGGCCG 58.959 55.000 13.85 0.00 40.13 6.13
275 276 3.051081 CATCCTAACTATGCAGAGGCC 57.949 52.381 13.85 0.00 40.13 5.19
293 294 7.388437 AGAACAATTTTATTGGATGTGTGCAT 58.612 30.769 0.00 0.00 38.18 3.96
294 295 6.757237 AGAACAATTTTATTGGATGTGTGCA 58.243 32.000 4.61 0.00 0.00 4.57
295 296 8.755696 TTAGAACAATTTTATTGGATGTGTGC 57.244 30.769 4.61 0.00 0.00 4.57
322 323 9.073475 TGTTGTGCCTAATTCTTTTTATACTGT 57.927 29.630 0.00 0.00 0.00 3.55
325 326 9.516314 GGATGTTGTGCCTAATTCTTTTTATAC 57.484 33.333 0.00 0.00 0.00 1.47
326 327 8.691797 GGGATGTTGTGCCTAATTCTTTTTATA 58.308 33.333 0.00 0.00 35.01 0.98
327 328 7.555965 GGGATGTTGTGCCTAATTCTTTTTAT 58.444 34.615 0.00 0.00 35.01 1.40
328 329 6.930731 GGGATGTTGTGCCTAATTCTTTTTA 58.069 36.000 0.00 0.00 35.01 1.52
329 330 5.793817 GGGATGTTGTGCCTAATTCTTTTT 58.206 37.500 0.00 0.00 35.01 1.94
330 331 5.405935 GGGATGTTGTGCCTAATTCTTTT 57.594 39.130 0.00 0.00 35.01 2.27
340 341 4.535526 AAAATAACAGGGATGTTGTGCC 57.464 40.909 3.95 0.00 38.92 5.01
359 360 5.363005 TGAGAAACCAAACGGGGAATAAAAA 59.637 36.000 0.00 0.00 42.91 1.94
360 361 4.894114 TGAGAAACCAAACGGGGAATAAAA 59.106 37.500 0.00 0.00 42.91 1.52
361 362 4.471548 TGAGAAACCAAACGGGGAATAAA 58.528 39.130 0.00 0.00 42.91 1.40
362 363 4.101645 TGAGAAACCAAACGGGGAATAA 57.898 40.909 0.00 0.00 42.91 1.40
363 364 3.791953 TGAGAAACCAAACGGGGAATA 57.208 42.857 0.00 0.00 42.91 1.75
364 365 2.668144 TGAGAAACCAAACGGGGAAT 57.332 45.000 0.00 0.00 42.91 3.01
365 366 2.158593 TGATGAGAAACCAAACGGGGAA 60.159 45.455 0.00 0.00 42.91 3.97
366 367 1.422024 TGATGAGAAACCAAACGGGGA 59.578 47.619 0.00 0.00 42.91 4.81
367 368 1.904287 TGATGAGAAACCAAACGGGG 58.096 50.000 0.00 0.00 42.91 5.73
368 369 4.048504 GTTTTGATGAGAAACCAAACGGG 58.951 43.478 0.00 0.00 44.81 5.28
369 370 4.677584 TGTTTTGATGAGAAACCAAACGG 58.322 39.130 0.00 0.00 36.43 4.44
370 371 6.074356 GGATTGTTTTGATGAGAAACCAAACG 60.074 38.462 0.00 0.00 36.43 3.60
371 372 6.074356 CGGATTGTTTTGATGAGAAACCAAAC 60.074 38.462 0.00 0.00 36.43 2.93
399 400 1.666553 GAACACGTGGTGATGGCGA 60.667 57.895 21.57 0.00 36.96 5.54
401 402 1.599518 TGGAACACGTGGTGATGGC 60.600 57.895 21.57 0.00 36.96 4.40
476 482 2.644212 CGCTGTCAGCCTCAGGTCT 61.644 63.158 19.14 0.00 38.18 3.85
478 484 3.699894 CCGCTGTCAGCCTCAGGT 61.700 66.667 19.14 0.00 38.18 4.00
528 534 1.600916 GGGTCTCTTGTGGTGGTGC 60.601 63.158 0.00 0.00 0.00 5.01
530 536 1.458777 TCGGGTCTCTTGTGGTGGT 60.459 57.895 0.00 0.00 0.00 4.16
538 544 3.003763 GGTGGCCTCGGGTCTCTT 61.004 66.667 3.32 0.00 0.00 2.85
580 586 2.439701 CTCTCGCTCGGTGGGGTA 60.440 66.667 0.00 0.00 0.00 3.69
582 588 2.167398 TTTTCTCTCGCTCGGTGGGG 62.167 60.000 0.00 0.00 0.00 4.96
691 697 3.319198 GCTCTCGTTGGGGGTGGA 61.319 66.667 0.00 0.00 0.00 4.02
915 937 1.343075 CCTCCCCTGTACCTTCAGCTA 60.343 57.143 0.00 0.00 34.47 3.32
925 947 0.927767 GTCTCTCTCCCTCCCCTGTA 59.072 60.000 0.00 0.00 0.00 2.74
926 948 1.700985 GTCTCTCTCCCTCCCCTGT 59.299 63.158 0.00 0.00 0.00 4.00
928 950 1.619975 TCGTCTCTCTCCCTCCCCT 60.620 63.158 0.00 0.00 0.00 4.79
931 953 1.826487 GCCTCGTCTCTCTCCCTCC 60.826 68.421 0.00 0.00 0.00 4.30
933 955 2.124487 CGCCTCGTCTCTCTCCCT 60.124 66.667 0.00 0.00 0.00 4.20
1185 1232 2.448542 ATACCTCCGCAGCCCCAT 60.449 61.111 0.00 0.00 0.00 4.00
1207 1254 2.201732 ACGAGCCATGCGTAATTACTG 58.798 47.619 13.56 8.26 40.65 2.74
1214 1261 2.100031 CAGCAACGAGCCATGCGTA 61.100 57.895 0.00 0.00 46.98 4.42
1223 1270 1.061131 CAATCGCCTAACAGCAACGAG 59.939 52.381 0.00 0.00 36.05 4.18
1293 1341 3.157087 ACCAGAATTCATGCCGAGTTTT 58.843 40.909 8.44 0.00 0.00 2.43
1368 1416 1.630244 CTGCAGCAGGTAAGCGACAC 61.630 60.000 15.35 0.00 40.15 3.67
1455 1507 7.902920 AGAATTAACATTTGGCATGATACCT 57.097 32.000 0.00 0.00 0.00 3.08
1559 1611 3.996363 TCCAAGTGTCGTTTCTCATCATG 59.004 43.478 0.00 0.00 0.00 3.07
1568 1620 0.544697 ACCACCTCCAAGTGTCGTTT 59.455 50.000 0.00 0.00 35.93 3.60
1596 1648 4.790854 CGATAGCGACGATGTAAATCAG 57.209 45.455 0.00 0.00 40.82 2.90
1637 1689 3.430931 GACAGACTGAACGATGTAGCTC 58.569 50.000 10.08 0.00 0.00 4.09
2127 2179 9.683069 GGAAATATTGTAAGCCAGTTATTGATG 57.317 33.333 0.00 0.00 0.00 3.07
2157 2209 5.007626 TCAGGATCGTGTTTGACTGAAAAAG 59.992 40.000 14.67 0.00 32.60 2.27
2297 2356 2.302733 TGTACTGCCTGAATCAGCAAGA 59.697 45.455 14.65 2.31 35.04 3.02
2540 2599 1.202758 TCCCATGTCAGTGTGTGGAAC 60.203 52.381 11.16 0.00 33.53 3.62
2624 2683 6.127897 CCCAGGTTTCTAAAGAATAGCAACAG 60.128 42.308 0.00 0.00 33.54 3.16
2648 2707 3.209410 CTGACATAAAGGATGAGCACCC 58.791 50.000 0.00 0.00 39.06 4.61
2714 2773 8.593492 TTCAATGTCATGTATATAGCACTCAC 57.407 34.615 0.00 0.00 0.00 3.51
2748 2807 3.865745 CGGCTCTACAAGTCATTTCGATT 59.134 43.478 0.00 0.00 0.00 3.34
2864 2923 1.208535 ACGGTGGTTGTTGTGAGAAGA 59.791 47.619 0.00 0.00 0.00 2.87
3102 3161 4.800023 TCGGTAGAATTCCTATCACTGGA 58.200 43.478 0.65 0.00 0.00 3.86
3186 3245 2.584064 CGAGGCCAGGCATACACA 59.416 61.111 15.19 0.00 0.00 3.72
3199 3258 3.649277 CTGAACCGGTCTGGCGAGG 62.649 68.421 8.04 0.00 43.94 4.63
3230 3289 0.026674 CATTGCGGTGTCATAGCACG 59.973 55.000 4.91 0.00 40.92 5.34
3237 3296 1.303236 CCCTTCCATTGCGGTGTCA 60.303 57.895 0.00 0.00 35.57 3.58
3263 3322 3.057596 ACAATTTGTTACGTGGATGCCAG 60.058 43.478 0.00 0.00 32.34 4.85
3272 3331 6.635239 GCATGAAACTGTACAATTTGTTACGT 59.365 34.615 7.08 0.00 0.00 3.57
3431 3490 3.008266 TCAGGTGAACATCATGAGCTTGA 59.992 43.478 0.09 0.00 0.00 3.02
3439 3498 4.978099 AGTTGAAGTCAGGTGAACATCAT 58.022 39.130 0.00 0.00 0.00 2.45
3530 3602 6.143919 GCTGCTAATGTAACAAGTTCCAAAAC 59.856 38.462 0.00 0.00 35.50 2.43
3574 3648 9.578439 AAAGAACAACTCTTCATCTTTTCTTTG 57.422 29.630 5.44 0.00 44.00 2.77
3749 4570 8.691727 CATGTATTTCTAGCACACGTACTATTC 58.308 37.037 0.00 0.00 0.00 1.75
3758 4579 8.970691 AACAAAATCATGTATTTCTAGCACAC 57.029 30.769 0.00 0.00 36.76 3.82
3784 4605 6.584185 ATTTTTACGGGAGCTACACAAAAT 57.416 33.333 0.00 0.00 0.00 1.82
3814 4635 6.086222 CACTTCTCCGTAAAAATTCATGGTG 58.914 40.000 0.00 0.00 0.00 4.17
3815 4636 5.768164 ACACTTCTCCGTAAAAATTCATGGT 59.232 36.000 0.00 0.00 0.00 3.55
3823 4644 4.093703 CACACACACACTTCTCCGTAAAAA 59.906 41.667 0.00 0.00 0.00 1.94
3830 4651 1.665679 CACACACACACACACTTCTCC 59.334 52.381 0.00 0.00 0.00 3.71
3833 4654 1.804151 ACACACACACACACACACTTC 59.196 47.619 0.00 0.00 0.00 3.01
3838 4659 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
3839 4660 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
3840 4661 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
3842 4663 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
3843 4664 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
3844 4665 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
3846 4667 2.070028 TGTACACACACACACACACAC 58.930 47.619 0.00 0.00 0.00 3.82
3848 4669 1.663643 CCTGTACACACACACACACAC 59.336 52.381 0.00 0.00 0.00 3.82
3850 4671 2.018542 ACCTGTACACACACACACAC 57.981 50.000 0.00 0.00 0.00 3.82
3852 4673 3.493129 CACATACCTGTACACACACACAC 59.507 47.826 0.00 0.00 33.14 3.82
3854 4675 3.493129 CACACATACCTGTACACACACAC 59.507 47.826 0.00 0.00 33.14 3.82
3855 4676 3.133183 ACACACATACCTGTACACACACA 59.867 43.478 0.00 0.00 33.14 3.72
3856 4677 3.724374 ACACACATACCTGTACACACAC 58.276 45.455 0.00 0.00 33.14 3.82
3857 4678 5.731957 ATACACACATACCTGTACACACA 57.268 39.130 0.00 0.00 33.14 3.72
3858 4679 7.429636 AAAATACACACATACCTGTACACAC 57.570 36.000 0.00 0.00 33.14 3.82
3859 4680 7.715686 TGAAAAATACACACATACCTGTACACA 59.284 33.333 0.00 0.00 33.14 3.72
3860 4681 8.090250 TGAAAAATACACACATACCTGTACAC 57.910 34.615 0.00 0.00 33.14 2.90
3861 4682 8.151596 TCTGAAAAATACACACATACCTGTACA 58.848 33.333 0.00 0.00 33.14 2.90
3862 4683 8.542497 TCTGAAAAATACACACATACCTGTAC 57.458 34.615 0.00 0.00 33.14 2.90
3863 4684 9.562408 TTTCTGAAAAATACACACATACCTGTA 57.438 29.630 0.00 0.00 33.14 2.74
3917 4745 9.715121 ACAACAGAGATTGCATTTGATATTTTT 57.285 25.926 0.00 0.00 32.47 1.94
3930 4758 6.684555 CGCTCTAATAAAACAACAGAGATTGC 59.315 38.462 1.23 0.00 35.77 3.56
3956 4784 6.181908 AGGGTCTAAAAATGGCGTAATGTTA 58.818 36.000 0.00 0.00 0.00 2.41
3959 4787 5.576447 AAGGGTCTAAAAATGGCGTAATG 57.424 39.130 0.00 0.00 0.00 1.90
4044 4872 0.876777 CTGTCGCACAACACGGGTTA 60.877 55.000 0.85 0.00 34.87 2.85
4058 4886 0.373716 GCTAACGAATTGGGCTGTCG 59.626 55.000 0.00 0.00 40.56 4.35
4060 4888 0.679960 GGGCTAACGAATTGGGCTGT 60.680 55.000 0.00 0.00 41.12 4.40
4075 4903 2.117206 TGCAAAATGGGACGGGCT 59.883 55.556 0.00 0.00 0.00 5.19
4094 4922 1.037493 GGGTTTGGTGGTTTCCTCAC 58.963 55.000 0.00 0.00 34.61 3.51
4095 4923 0.930726 AGGGTTTGGTGGTTTCCTCA 59.069 50.000 0.00 0.00 0.00 3.86
4105 4933 1.203013 GGGCTGTTTCTAGGGTTTGGT 60.203 52.381 0.00 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.