Multiple sequence alignment - TraesCS4B01G197300

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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 TraesCS4B01G197300 chr4B 100.000 2263 0 0 1 2263 424861167 424863429 0.000000e+00 4180.0
1 TraesCS4B01G197300 chr4D 91.623 1325 51 28 312 1616 343060772 343062056 0.000000e+00 1777.0
2 TraesCS4B01G197300 chr4D 81.754 707 82 25 755 1430 343088635 343089325 4.250000e-152 547.0
3 TraesCS4B01G197300 chr4D 85.676 370 50 2 1888 2257 381395390 381395024 9.800000e-104 387.0
4 TraesCS4B01G197300 chr4A 95.656 1082 34 10 428 1502 122736763 122735688 0.000000e+00 1725.0
5 TraesCS4B01G197300 chr4A 80.171 701 78 31 778 1439 122627722 122627044 3.400000e-128 468.0
6 TraesCS4B01G197300 chr4A 90.476 147 12 2 1739 1885 310386857 310387001 2.290000e-45 193.0
7 TraesCS4B01G197300 chr4A 92.537 67 4 1 1528 1593 122728536 122728470 6.650000e-16 95.3
8 TraesCS4B01G197300 chr2D 87.772 368 42 3 1896 2263 524047362 524046998 5.780000e-116 427.0
9 TraesCS4B01G197300 chr2D 84.574 376 51 6 1888 2263 37945689 37945321 1.280000e-97 366.0
10 TraesCS4B01G197300 chr2D 84.293 382 48 8 1885 2263 611208673 611208301 1.650000e-96 363.0
11 TraesCS4B01G197300 chr2D 87.162 148 17 2 1743 1890 543287953 543287808 1.390000e-37 167.0
12 TraesCS4B01G197300 chr3D 85.752 379 48 6 1889 2263 572429660 572429284 1.630000e-106 396.0
13 TraesCS4B01G197300 chr3D 84.777 381 52 4 1888 2263 190271230 190271609 5.900000e-101 377.0
14 TraesCS4B01G197300 chr3D 87.500 152 17 2 1739 1890 572430062 572429913 8.310000e-40 174.0
15 TraesCS4B01G197300 chr2B 85.676 370 43 10 1898 2263 534248117 534247754 4.560000e-102 381.0
16 TraesCS4B01G197300 chr5B 84.737 380 49 6 1888 2263 144176941 144177315 2.750000e-99 372.0
17 TraesCS4B01G197300 chr5B 87.586 145 16 2 1743 1887 497381401 497381259 1.390000e-37 167.0
18 TraesCS4B01G197300 chr3B 84.350 377 54 4 1888 2263 637131475 637131103 4.590000e-97 364.0
19 TraesCS4B01G197300 chr7D 87.838 148 17 1 1743 1890 395853488 395853342 2.990000e-39 172.0
20 TraesCS4B01G197300 chr7D 81.013 79 11 3 276 350 124041590 124041668 2.430000e-05 60.2
21 TraesCS4B01G197300 chr2A 89.130 138 13 2 1752 1889 634627383 634627518 1.070000e-38 171.0
22 TraesCS4B01G197300 chr1B 87.162 148 17 2 1743 1890 112413948 112414093 1.390000e-37 167.0
23 TraesCS4B01G197300 chr1B 80.412 97 14 3 276 368 488470980 488470885 4.030000e-08 69.4
24 TraesCS4B01G197300 chr5A 87.500 144 16 2 1739 1882 671619652 671619793 5.000000e-37 165.0
25 TraesCS4B01G197300 chr5D 86.986 146 17 2 1743 1888 112339380 112339237 1.800000e-36 163.0


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 TraesCS4B01G197300 chr4B 424861167 424863429 2262 False 4180 4180 100.000 1 2263 1 chr4B.!!$F1 2262
1 TraesCS4B01G197300 chr4D 343060772 343062056 1284 False 1777 1777 91.623 312 1616 1 chr4D.!!$F1 1304
2 TraesCS4B01G197300 chr4D 343088635 343089325 690 False 547 547 81.754 755 1430 1 chr4D.!!$F2 675
3 TraesCS4B01G197300 chr4A 122735688 122736763 1075 True 1725 1725 95.656 428 1502 1 chr4A.!!$R3 1074
4 TraesCS4B01G197300 chr4A 122627044 122627722 678 True 468 468 80.171 778 1439 1 chr4A.!!$R1 661
5 TraesCS4B01G197300 chr3D 572429284 572430062 778 True 285 396 86.626 1739 2263 2 chr3D.!!$R1 524

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
150 151 0.030504 CGTTGTTGCTTCATGTGGCA 59.969 50.0 10.3 10.3 36.62 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1818 1874 0.108804 ATGTAACTGTCTGCGTCCGG 60.109 55.0 0.0 0.0 0.0 5.14 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
23 24 3.190849 CGATGACCCGCTGTGCTG 61.191 66.667 0.00 0.00 0.00 4.41
24 25 3.503363 GATGACCCGCTGTGCTGC 61.503 66.667 0.00 0.00 0.00 5.25
32 33 3.020627 GCTGTGCTGCGATGGATC 58.979 61.111 0.00 0.00 0.00 3.36
33 34 1.816679 GCTGTGCTGCGATGGATCA 60.817 57.895 0.00 0.00 0.00 2.92
34 35 1.164662 GCTGTGCTGCGATGGATCAT 61.165 55.000 0.00 0.00 0.00 2.45
35 36 0.866427 CTGTGCTGCGATGGATCATC 59.134 55.000 0.00 0.00 37.50 2.92
42 43 3.782244 GATGGATCATCGCCGCGC 61.782 66.667 8.21 0.00 31.01 6.86
43 44 4.305479 ATGGATCATCGCCGCGCT 62.305 61.111 8.21 0.00 0.00 5.92
46 47 3.264897 GATCATCGCCGCGCTGTT 61.265 61.111 15.58 8.10 0.00 3.16
47 48 3.497407 GATCATCGCCGCGCTGTTG 62.497 63.158 15.58 7.36 0.00 3.33
49 50 4.088762 CATCGCCGCGCTGTTGTT 62.089 61.111 8.21 0.00 0.00 2.83
50 51 4.088762 ATCGCCGCGCTGTTGTTG 62.089 61.111 8.21 0.00 0.00 3.33
52 53 4.605967 CGCCGCGCTGTTGTTGTT 62.606 61.111 5.56 0.00 0.00 2.83
53 54 3.024043 GCCGCGCTGTTGTTGTTG 61.024 61.111 5.56 0.00 0.00 3.33
54 55 3.024043 CCGCGCTGTTGTTGTTGC 61.024 61.111 5.56 0.00 0.00 4.17
55 56 3.024043 CGCGCTGTTGTTGTTGCC 61.024 61.111 5.56 0.00 0.00 4.52
56 57 3.024043 GCGCTGTTGTTGTTGCCG 61.024 61.111 0.00 0.00 0.00 5.69
57 58 2.712539 CGCTGTTGTTGTTGCCGA 59.287 55.556 0.00 0.00 0.00 5.54
58 59 1.063327 CGCTGTTGTTGTTGCCGAA 59.937 52.632 0.00 0.00 0.00 4.30
59 60 1.199852 CGCTGTTGTTGTTGCCGAAC 61.200 55.000 0.00 0.00 0.00 3.95
60 61 1.199852 GCTGTTGTTGTTGCCGAACG 61.200 55.000 0.00 0.00 34.49 3.95
61 62 1.199852 CTGTTGTTGTTGCCGAACGC 61.200 55.000 0.00 0.00 34.49 4.84
62 63 1.942223 GTTGTTGTTGCCGAACGCC 60.942 57.895 0.00 0.00 34.49 5.68
63 64 3.127352 TTGTTGTTGCCGAACGCCC 62.127 57.895 0.00 0.00 34.49 6.13
64 65 3.284449 GTTGTTGCCGAACGCCCT 61.284 61.111 0.00 0.00 34.49 5.19
65 66 3.283684 TTGTTGCCGAACGCCCTG 61.284 61.111 0.00 0.00 34.49 4.45
78 79 4.161295 CCCTGCTCCGCCGATGAA 62.161 66.667 0.00 0.00 0.00 2.57
79 80 2.587194 CCTGCTCCGCCGATGAAG 60.587 66.667 0.00 0.00 0.00 3.02
80 81 2.587194 CTGCTCCGCCGATGAAGG 60.587 66.667 0.00 0.00 0.00 3.46
81 82 4.161295 TGCTCCGCCGATGAAGGG 62.161 66.667 0.00 0.00 0.00 3.95
82 83 4.918201 GCTCCGCCGATGAAGGGG 62.918 72.222 0.00 0.00 43.07 4.79
83 84 3.470888 CTCCGCCGATGAAGGGGT 61.471 66.667 0.00 0.00 42.03 4.95
84 85 3.740128 CTCCGCCGATGAAGGGGTG 62.740 68.421 0.00 0.00 42.03 4.61
89 90 4.473520 CGATGAAGGGGTGCGGCT 62.474 66.667 0.00 0.00 0.00 5.52
90 91 2.514824 GATGAAGGGGTGCGGCTC 60.515 66.667 0.00 0.00 0.00 4.70
91 92 4.473520 ATGAAGGGGTGCGGCTCG 62.474 66.667 0.00 0.00 0.00 5.03
101 102 4.748679 GCGGCTCGTGCTTGCAAG 62.749 66.667 22.44 22.44 39.22 4.01
125 126 3.869272 GGTGCTGCTTCCGCGATG 61.869 66.667 8.23 0.00 39.65 3.84
126 127 2.815211 GTGCTGCTTCCGCGATGA 60.815 61.111 8.23 0.00 39.65 2.92
127 128 2.815211 TGCTGCTTCCGCGATGAC 60.815 61.111 8.23 0.00 39.65 3.06
128 129 2.510238 GCTGCTTCCGCGATGACT 60.510 61.111 8.23 0.00 39.65 3.41
129 130 2.520904 GCTGCTTCCGCGATGACTC 61.521 63.158 8.23 0.00 39.65 3.36
139 140 1.225475 CGATGACTCGCGTTGTTGC 60.225 57.895 5.77 0.00 38.20 4.17
140 141 1.617755 CGATGACTCGCGTTGTTGCT 61.618 55.000 5.77 0.00 38.20 3.91
141 142 0.512952 GATGACTCGCGTTGTTGCTT 59.487 50.000 5.77 0.00 0.00 3.91
142 143 0.512952 ATGACTCGCGTTGTTGCTTC 59.487 50.000 5.77 0.00 0.00 3.86
143 144 0.808060 TGACTCGCGTTGTTGCTTCA 60.808 50.000 5.77 0.00 0.00 3.02
144 145 0.512952 GACTCGCGTTGTTGCTTCAT 59.487 50.000 5.77 0.00 0.00 2.57
145 146 0.235665 ACTCGCGTTGTTGCTTCATG 59.764 50.000 5.77 0.00 0.00 3.07
146 147 0.235665 CTCGCGTTGTTGCTTCATGT 59.764 50.000 5.77 0.00 0.00 3.21
147 148 0.041400 TCGCGTTGTTGCTTCATGTG 60.041 50.000 5.77 0.00 0.00 3.21
148 149 0.998226 CGCGTTGTTGCTTCATGTGG 60.998 55.000 0.00 0.00 0.00 4.17
149 150 1.277495 GCGTTGTTGCTTCATGTGGC 61.277 55.000 0.00 0.00 0.00 5.01
150 151 0.030504 CGTTGTTGCTTCATGTGGCA 59.969 50.000 10.30 10.30 36.62 4.92
151 152 1.490621 GTTGTTGCTTCATGTGGCAC 58.509 50.000 11.55 11.55 38.23 5.01
152 153 1.109609 TTGTTGCTTCATGTGGCACA 58.890 45.000 24.36 24.36 38.23 4.57
153 154 1.109609 TGTTGCTTCATGTGGCACAA 58.890 45.000 25.95 6.10 44.16 3.33
154 155 1.687660 TGTTGCTTCATGTGGCACAAT 59.312 42.857 25.95 10.47 44.16 2.71
155 156 2.063266 GTTGCTTCATGTGGCACAATG 58.937 47.619 25.95 21.13 44.16 2.82
156 157 1.330234 TGCTTCATGTGGCACAATGT 58.670 45.000 25.95 5.23 44.16 2.71
157 158 1.000052 TGCTTCATGTGGCACAATGTG 60.000 47.619 25.95 18.36 44.16 3.21
158 159 1.000060 GCTTCATGTGGCACAATGTGT 60.000 47.619 25.95 4.35 44.16 3.72
166 167 4.632037 CACAATGTGTGTTGGCCG 57.368 55.556 5.00 0.00 43.08 6.13
167 168 2.028936 CACAATGTGTGTTGGCCGA 58.971 52.632 5.00 0.00 43.08 5.54
168 169 0.597568 CACAATGTGTGTTGGCCGAT 59.402 50.000 5.00 0.00 43.08 4.18
169 170 0.881118 ACAATGTGTGTTGGCCGATC 59.119 50.000 0.00 0.00 37.01 3.69
170 171 0.171007 CAATGTGTGTTGGCCGATCC 59.829 55.000 0.00 0.00 0.00 3.36
171 172 0.251121 AATGTGTGTTGGCCGATCCA 60.251 50.000 0.00 0.00 44.85 3.41
214 215 4.329545 GGCCTGCAACCCGACTGA 62.330 66.667 0.00 0.00 0.00 3.41
215 216 2.045926 GCCTGCAACCCGACTGAT 60.046 61.111 0.00 0.00 0.00 2.90
216 217 1.675641 GCCTGCAACCCGACTGATT 60.676 57.895 0.00 0.00 0.00 2.57
217 218 1.244019 GCCTGCAACCCGACTGATTT 61.244 55.000 0.00 0.00 0.00 2.17
218 219 0.804989 CCTGCAACCCGACTGATTTC 59.195 55.000 0.00 0.00 0.00 2.17
219 220 1.611673 CCTGCAACCCGACTGATTTCT 60.612 52.381 0.00 0.00 0.00 2.52
220 221 2.154462 CTGCAACCCGACTGATTTCTT 58.846 47.619 0.00 0.00 0.00 2.52
221 222 2.151202 TGCAACCCGACTGATTTCTTC 58.849 47.619 0.00 0.00 0.00 2.87
222 223 2.151202 GCAACCCGACTGATTTCTTCA 58.849 47.619 0.00 0.00 0.00 3.02
223 224 2.095718 GCAACCCGACTGATTTCTTCAC 60.096 50.000 0.00 0.00 0.00 3.18
224 225 2.080286 ACCCGACTGATTTCTTCACG 57.920 50.000 0.00 0.00 0.00 4.35
225 226 1.616865 ACCCGACTGATTTCTTCACGA 59.383 47.619 0.00 0.00 0.00 4.35
226 227 2.036733 ACCCGACTGATTTCTTCACGAA 59.963 45.455 0.00 0.00 0.00 3.85
227 228 3.064207 CCCGACTGATTTCTTCACGAAA 58.936 45.455 0.00 0.00 45.08 3.46
234 235 3.991605 ATTTCTTCACGAAATCGACCG 57.008 42.857 10.16 0.00 46.71 4.79
235 236 1.065358 TTCTTCACGAAATCGACCGC 58.935 50.000 10.16 0.00 43.02 5.68
236 237 0.242825 TCTTCACGAAATCGACCGCT 59.757 50.000 10.16 0.00 43.02 5.52
237 238 0.640768 CTTCACGAAATCGACCGCTC 59.359 55.000 10.16 0.00 43.02 5.03
238 239 1.068832 TTCACGAAATCGACCGCTCG 61.069 55.000 10.16 0.00 43.02 5.03
245 246 4.468007 TCGACCGCTCGATCCATA 57.532 55.556 0.00 0.00 44.14 2.74
246 247 2.244946 TCGACCGCTCGATCCATAG 58.755 57.895 0.00 0.00 44.14 2.23
247 248 1.442857 CGACCGCTCGATCCATAGC 60.443 63.158 0.00 0.38 43.06 2.97
248 249 1.660355 GACCGCTCGATCCATAGCA 59.340 57.895 9.32 0.00 38.70 3.49
249 250 0.387878 GACCGCTCGATCCATAGCAG 60.388 60.000 9.32 1.83 38.70 4.24
250 251 1.735920 CCGCTCGATCCATAGCAGC 60.736 63.158 9.32 0.00 38.70 5.25
251 252 1.735920 CGCTCGATCCATAGCAGCC 60.736 63.158 9.32 0.00 38.70 4.85
252 253 1.735920 GCTCGATCCATAGCAGCCG 60.736 63.158 4.86 0.00 38.63 5.52
253 254 1.662608 CTCGATCCATAGCAGCCGT 59.337 57.895 0.00 0.00 0.00 5.68
254 255 0.387878 CTCGATCCATAGCAGCCGTC 60.388 60.000 0.00 0.00 0.00 4.79
255 256 1.106944 TCGATCCATAGCAGCCGTCA 61.107 55.000 0.00 0.00 0.00 4.35
256 257 0.037882 CGATCCATAGCAGCCGTCAT 60.038 55.000 0.00 0.00 0.00 3.06
257 258 1.606480 CGATCCATAGCAGCCGTCATT 60.606 52.381 0.00 0.00 0.00 2.57
258 259 2.498167 GATCCATAGCAGCCGTCATTT 58.502 47.619 0.00 0.00 0.00 2.32
259 260 1.953559 TCCATAGCAGCCGTCATTTC 58.046 50.000 0.00 0.00 0.00 2.17
260 261 1.209261 TCCATAGCAGCCGTCATTTCA 59.791 47.619 0.00 0.00 0.00 2.69
261 262 2.016318 CCATAGCAGCCGTCATTTCAA 58.984 47.619 0.00 0.00 0.00 2.69
262 263 2.423185 CCATAGCAGCCGTCATTTCAAA 59.577 45.455 0.00 0.00 0.00 2.69
263 264 3.067180 CCATAGCAGCCGTCATTTCAAAT 59.933 43.478 0.00 0.00 0.00 2.32
264 265 4.275689 CCATAGCAGCCGTCATTTCAAATA 59.724 41.667 0.00 0.00 0.00 1.40
265 266 5.446709 CATAGCAGCCGTCATTTCAAATAG 58.553 41.667 0.00 0.00 0.00 1.73
266 267 3.347216 AGCAGCCGTCATTTCAAATAGT 58.653 40.909 0.00 0.00 0.00 2.12
267 268 3.758554 AGCAGCCGTCATTTCAAATAGTT 59.241 39.130 0.00 0.00 0.00 2.24
268 269 4.218417 AGCAGCCGTCATTTCAAATAGTTT 59.782 37.500 0.00 0.00 0.00 2.66
269 270 4.923281 GCAGCCGTCATTTCAAATAGTTTT 59.077 37.500 0.00 0.00 0.00 2.43
270 271 5.164061 GCAGCCGTCATTTCAAATAGTTTTG 60.164 40.000 0.00 0.00 42.98 2.44
283 284 7.584987 TCAAATAGTTTTGAAGCTAGTCTTGC 58.415 34.615 4.45 0.00 46.26 4.01
284 285 7.445402 TCAAATAGTTTTGAAGCTAGTCTTGCT 59.555 33.333 2.68 2.68 46.26 3.91
285 286 8.721478 CAAATAGTTTTGAAGCTAGTCTTGCTA 58.279 33.333 9.28 0.00 44.11 3.49
286 287 8.848474 AATAGTTTTGAAGCTAGTCTTGCTAA 57.152 30.769 9.28 0.00 40.22 3.09
287 288 8.848474 ATAGTTTTGAAGCTAGTCTTGCTAAA 57.152 30.769 9.28 4.90 40.22 1.85
288 289 7.751768 AGTTTTGAAGCTAGTCTTGCTAAAT 57.248 32.000 9.28 0.00 40.22 1.40
289 290 8.171164 AGTTTTGAAGCTAGTCTTGCTAAATT 57.829 30.769 9.28 1.55 40.22 1.82
290 291 8.633561 AGTTTTGAAGCTAGTCTTGCTAAATTT 58.366 29.630 9.28 0.00 40.22 1.82
291 292 8.906693 GTTTTGAAGCTAGTCTTGCTAAATTTC 58.093 33.333 9.28 3.93 40.22 2.17
292 293 7.744087 TTGAAGCTAGTCTTGCTAAATTTCA 57.256 32.000 9.28 6.40 40.22 2.69
293 294 7.369803 TGAAGCTAGTCTTGCTAAATTTCAG 57.630 36.000 9.28 0.00 40.22 3.02
294 295 6.936900 TGAAGCTAGTCTTGCTAAATTTCAGT 59.063 34.615 9.28 0.00 40.22 3.41
295 296 6.976636 AGCTAGTCTTGCTAAATTTCAGTC 57.023 37.500 7.04 0.00 39.21 3.51
296 297 6.467677 AGCTAGTCTTGCTAAATTTCAGTCA 58.532 36.000 7.04 0.00 39.21 3.41
297 298 6.936900 AGCTAGTCTTGCTAAATTTCAGTCAA 59.063 34.615 7.04 0.00 39.21 3.18
298 299 7.018235 GCTAGTCTTGCTAAATTTCAGTCAAC 58.982 38.462 0.00 0.00 0.00 3.18
299 300 7.095017 GCTAGTCTTGCTAAATTTCAGTCAACT 60.095 37.037 0.00 0.00 0.00 3.16
300 301 6.963796 AGTCTTGCTAAATTTCAGTCAACTG 58.036 36.000 3.69 3.69 45.08 3.16
310 311 3.898517 TCAGTCAACTGAGACGTAGTG 57.101 47.619 8.75 0.00 45.26 2.74
327 328 2.847441 AGTGTCTCGGTCGATGCTATA 58.153 47.619 0.00 0.00 0.00 1.31
328 329 3.413327 AGTGTCTCGGTCGATGCTATAT 58.587 45.455 0.00 0.00 0.00 0.86
329 330 3.821600 AGTGTCTCGGTCGATGCTATATT 59.178 43.478 0.00 0.00 0.00 1.28
330 331 4.083217 AGTGTCTCGGTCGATGCTATATTC 60.083 45.833 0.00 0.00 0.00 1.75
331 332 3.818773 TGTCTCGGTCGATGCTATATTCA 59.181 43.478 0.00 0.00 0.00 2.57
332 333 4.459337 TGTCTCGGTCGATGCTATATTCAT 59.541 41.667 0.00 0.00 0.00 2.57
333 334 4.795795 GTCTCGGTCGATGCTATATTCATG 59.204 45.833 0.00 0.00 0.00 3.07
568 569 0.324460 TTGGAAACACCCCAAACGGT 60.324 50.000 0.00 0.00 42.67 4.83
640 642 3.364277 GGATACAACGAGCCAGGTC 57.636 57.895 0.00 0.00 0.00 3.85
759 763 0.600255 CCCATATTCGCACGGTCTCC 60.600 60.000 0.00 0.00 0.00 3.71
795 799 1.607467 GGAGTGCAGGTGGCCAAAT 60.607 57.895 7.24 0.00 43.89 2.32
974 1002 5.512232 GGAAAGCAGAGAGAAAGAAAGGAGA 60.512 44.000 0.00 0.00 0.00 3.71
975 1003 4.806640 AGCAGAGAGAAAGAAAGGAGAG 57.193 45.455 0.00 0.00 0.00 3.20
1163 1201 6.222038 TCTGATCTGGTTATTACTGGTGTC 57.778 41.667 0.00 0.00 0.00 3.67
1168 1206 3.527533 TGGTTATTACTGGTGTCGATGC 58.472 45.455 0.00 0.00 0.00 3.91
1527 1582 1.438651 TTCGGAAGCAATCGAAGTGG 58.561 50.000 0.00 0.00 39.94 4.00
1555 1610 4.332543 TCAGTACTGTTGCAAGTGTTTCAG 59.667 41.667 21.99 5.07 0.00 3.02
1594 1650 3.921119 TGCATGATGGAACAACAACTC 57.079 42.857 0.00 0.00 46.01 3.01
1595 1651 2.557924 TGCATGATGGAACAACAACTCC 59.442 45.455 0.00 0.00 46.01 3.85
1596 1652 2.557924 GCATGATGGAACAACAACTCCA 59.442 45.455 0.00 0.00 46.01 3.86
1601 1657 3.576078 TGGAACAACAACTCCATCTGT 57.424 42.857 0.00 0.00 36.79 3.41
1602 1658 3.476552 TGGAACAACAACTCCATCTGTC 58.523 45.455 0.00 0.00 36.79 3.51
1603 1659 2.814336 GGAACAACAACTCCATCTGTCC 59.186 50.000 0.00 0.00 0.00 4.02
1604 1660 2.568623 ACAACAACTCCATCTGTCCC 57.431 50.000 0.00 0.00 0.00 4.46
1605 1661 1.774254 ACAACAACTCCATCTGTCCCA 59.226 47.619 0.00 0.00 0.00 4.37
1606 1662 2.376518 ACAACAACTCCATCTGTCCCAT 59.623 45.455 0.00 0.00 0.00 4.00
1607 1663 3.587061 ACAACAACTCCATCTGTCCCATA 59.413 43.478 0.00 0.00 0.00 2.74
1608 1664 4.042809 ACAACAACTCCATCTGTCCCATAA 59.957 41.667 0.00 0.00 0.00 1.90
1609 1665 4.494091 ACAACTCCATCTGTCCCATAAG 57.506 45.455 0.00 0.00 0.00 1.73
1610 1666 3.200825 ACAACTCCATCTGTCCCATAAGG 59.799 47.826 0.00 0.00 0.00 2.69
1611 1667 3.136641 ACTCCATCTGTCCCATAAGGT 57.863 47.619 0.00 0.00 36.75 3.50
1612 1668 2.774234 ACTCCATCTGTCCCATAAGGTG 59.226 50.000 0.00 0.00 36.75 4.00
1613 1669 1.490490 TCCATCTGTCCCATAAGGTGC 59.510 52.381 0.00 0.00 36.75 5.01
1614 1670 1.212688 CCATCTGTCCCATAAGGTGCA 59.787 52.381 0.00 0.00 36.75 4.57
1615 1671 2.158564 CCATCTGTCCCATAAGGTGCAT 60.159 50.000 0.00 0.00 36.75 3.96
1616 1672 2.715749 TCTGTCCCATAAGGTGCATG 57.284 50.000 0.00 0.00 36.75 4.06
1617 1673 1.027357 CTGTCCCATAAGGTGCATGC 58.973 55.000 11.82 11.82 36.75 4.06
1618 1674 0.330941 TGTCCCATAAGGTGCATGCA 59.669 50.000 18.46 18.46 36.75 3.96
1619 1675 1.027357 GTCCCATAAGGTGCATGCAG 58.973 55.000 23.41 8.11 36.75 4.41
1620 1676 0.752743 TCCCATAAGGTGCATGCAGC 60.753 55.000 36.42 36.42 43.95 5.25
1630 1686 3.267900 GCATGCAGCATGATGGAAC 57.732 52.632 35.16 15.03 43.81 3.62
1631 1687 0.458260 GCATGCAGCATGATGGAACA 59.542 50.000 35.16 0.12 43.81 3.18
1632 1688 1.801395 GCATGCAGCATGATGGAACAC 60.801 52.381 35.16 13.64 43.81 3.32
1633 1689 1.108776 ATGCAGCATGATGGAACACC 58.891 50.000 9.83 0.00 37.84 4.16
1634 1690 0.251253 TGCAGCATGATGGAACACCA 60.251 50.000 13.73 0.00 37.84 4.17
1652 1708 3.054434 CACCAACTCCATCTGTCCCATAA 60.054 47.826 0.00 0.00 0.00 1.90
1665 1721 3.614399 CCATAAGGGCATCTCCGAC 57.386 57.895 0.00 0.00 34.94 4.79
1666 1722 0.319900 CCATAAGGGCATCTCCGACG 60.320 60.000 0.00 0.00 34.94 5.12
1667 1723 0.319900 CATAAGGGCATCTCCGACGG 60.320 60.000 7.84 7.84 34.94 4.79
1668 1724 2.100879 ATAAGGGCATCTCCGACGGC 62.101 60.000 9.66 0.00 34.94 5.68
1670 1726 4.467084 GGGCATCTCCGACGGCAA 62.467 66.667 9.66 0.00 34.94 4.52
1671 1727 3.195698 GGCATCTCCGACGGCAAC 61.196 66.667 9.66 0.00 0.00 4.17
1672 1728 2.434185 GCATCTCCGACGGCAACA 60.434 61.111 9.66 0.00 0.00 3.33
1673 1729 2.740714 GCATCTCCGACGGCAACAC 61.741 63.158 9.66 0.00 0.00 3.32
1674 1730 2.100631 CATCTCCGACGGCAACACC 61.101 63.158 9.66 0.00 0.00 4.16
1675 1731 3.310860 ATCTCCGACGGCAACACCC 62.311 63.158 9.66 0.00 33.26 4.61
1683 1739 4.678743 GGCAACACCCCCACCCTC 62.679 72.222 0.00 0.00 0.00 4.30
1685 1741 3.246112 CAACACCCCCACCCTCGA 61.246 66.667 0.00 0.00 0.00 4.04
1686 1742 2.928396 AACACCCCCACCCTCGAG 60.928 66.667 5.13 5.13 0.00 4.04
1687 1743 3.477956 AACACCCCCACCCTCGAGA 62.478 63.158 15.71 0.00 0.00 4.04
1688 1744 2.606519 CACCCCCACCCTCGAGAA 60.607 66.667 15.71 0.00 0.00 2.87
1689 1745 2.206036 ACCCCCACCCTCGAGAAA 59.794 61.111 15.71 0.00 0.00 2.52
1690 1746 1.462627 ACCCCCACCCTCGAGAAAA 60.463 57.895 15.71 0.00 0.00 2.29
1691 1747 1.063654 ACCCCCACCCTCGAGAAAAA 61.064 55.000 15.71 0.00 0.00 1.94
1692 1748 0.608308 CCCCCACCCTCGAGAAAAAC 60.608 60.000 15.71 0.00 0.00 2.43
1693 1749 0.608308 CCCCACCCTCGAGAAAAACC 60.608 60.000 15.71 0.00 0.00 3.27
1694 1750 0.400594 CCCACCCTCGAGAAAAACCT 59.599 55.000 15.71 0.00 0.00 3.50
1695 1751 1.610886 CCCACCCTCGAGAAAAACCTC 60.611 57.143 15.71 0.00 0.00 3.85
1696 1752 1.610886 CCACCCTCGAGAAAAACCTCC 60.611 57.143 15.71 0.00 0.00 4.30
1697 1753 1.348036 CACCCTCGAGAAAAACCTCCT 59.652 52.381 15.71 0.00 0.00 3.69
1698 1754 1.348036 ACCCTCGAGAAAAACCTCCTG 59.652 52.381 15.71 0.00 0.00 3.86
1699 1755 1.443802 CCTCGAGAAAAACCTCCTGC 58.556 55.000 15.71 0.00 0.00 4.85
1700 1756 1.002544 CCTCGAGAAAAACCTCCTGCT 59.997 52.381 15.71 0.00 0.00 4.24
1701 1757 2.551071 CCTCGAGAAAAACCTCCTGCTT 60.551 50.000 15.71 0.00 0.00 3.91
1702 1758 2.739379 CTCGAGAAAAACCTCCTGCTTC 59.261 50.000 6.58 0.00 0.00 3.86
1703 1759 1.807142 CGAGAAAAACCTCCTGCTTCC 59.193 52.381 0.00 0.00 0.00 3.46
1704 1760 1.807142 GAGAAAAACCTCCTGCTTCCG 59.193 52.381 0.00 0.00 0.00 4.30
1705 1761 1.143073 AGAAAAACCTCCTGCTTCCGT 59.857 47.619 0.00 0.00 0.00 4.69
1706 1762 1.535896 GAAAAACCTCCTGCTTCCGTC 59.464 52.381 0.00 0.00 0.00 4.79
1707 1763 0.250770 AAAACCTCCTGCTTCCGTCC 60.251 55.000 0.00 0.00 0.00 4.79
1708 1764 2.450479 AAACCTCCTGCTTCCGTCCG 62.450 60.000 0.00 0.00 0.00 4.79
1709 1765 4.821589 CCTCCTGCTTCCGTCCGC 62.822 72.222 0.00 0.00 0.00 5.54
1710 1766 4.821589 CTCCTGCTTCCGTCCGCC 62.822 72.222 0.00 0.00 0.00 6.13
1778 1834 1.066929 GGCCGGATTTCATGCAAACTT 60.067 47.619 5.05 0.00 0.00 2.66
1781 1837 3.676873 GCCGGATTTCATGCAAACTTGAT 60.677 43.478 5.05 0.00 30.75 2.57
1783 1839 3.787634 CGGATTTCATGCAAACTTGATCG 59.212 43.478 0.00 0.00 30.75 3.69
1785 1841 4.380867 GGATTTCATGCAAACTTGATCGGT 60.381 41.667 0.00 0.00 30.75 4.69
1800 1856 8.330466 ACTTGATCGGTTTTCATACAAACATA 57.670 30.769 0.00 0.00 38.25 2.29
1809 1865 9.843334 GGTTTTCATACAAACATAACGGATTTA 57.157 29.630 0.00 0.00 38.25 1.40
1820 1876 8.898983 AACATAACGGATTTAATACAAAACCG 57.101 30.769 14.43 14.43 38.18 4.44
1827 1883 4.407496 TTTAATACAAAACCGGACGCAG 57.593 40.909 9.46 0.00 0.00 5.18
1830 1886 0.104487 TACAAAACCGGACGCAGACA 59.896 50.000 9.46 0.00 0.00 3.41
1842 1898 3.496884 GGACGCAGACAGTTACATTTTGA 59.503 43.478 0.00 0.00 0.00 2.69
1883 1939 5.908106 AGTTAAAAACTATGTGCACGTACG 58.092 37.500 14.85 15.01 40.69 3.67
1948 2261 1.134694 GCCTCGCGTGTTCCATTTC 59.865 57.895 5.77 0.00 0.00 2.17
1954 2267 0.322546 GCGTGTTCCATTTCCCCTCT 60.323 55.000 0.00 0.00 0.00 3.69
1969 2282 0.741221 CCTCTAAGTTGCCAGCGGAC 60.741 60.000 0.00 0.00 0.00 4.79
1970 2283 0.037326 CTCTAAGTTGCCAGCGGACA 60.037 55.000 0.00 0.00 0.00 4.02
1995 2308 4.783621 GGATGCGCTGGCCACTGA 62.784 66.667 9.73 0.00 38.85 3.41
2001 2314 2.433318 GCTGGCCACTGACTCGTC 60.433 66.667 0.00 0.00 0.00 4.20
2045 2359 0.035317 TTTCTCTGTCTGCATGGCGT 59.965 50.000 0.00 0.00 0.00 5.68
2065 2379 3.812019 CTACGCGTGCCCTCGACT 61.812 66.667 24.59 0.00 0.00 4.18
2074 2388 2.660064 GCCCTCGACTGTGGATGGT 61.660 63.158 13.78 0.00 0.00 3.55
2096 2410 2.363795 TCGTAGGCACTGGAGGGG 60.364 66.667 0.00 0.00 41.52 4.79
2097 2411 4.162690 CGTAGGCACTGGAGGGGC 62.163 72.222 0.00 0.00 41.52 5.80
2123 2437 1.355210 CGCAACGTTATCCATGCCC 59.645 57.895 0.00 0.00 35.41 5.36
2129 2443 1.855213 CGTTATCCATGCCCATGCCG 61.855 60.000 2.75 0.00 37.49 5.69
2174 2488 1.882989 GAGCAACTCGCCACTCCTCT 61.883 60.000 0.00 0.00 44.04 3.69
2175 2489 1.739562 GCAACTCGCCACTCCTCTG 60.740 63.158 0.00 0.00 32.94 3.35
2176 2490 1.668294 CAACTCGCCACTCCTCTGT 59.332 57.895 0.00 0.00 0.00 3.41
2188 2502 1.376942 CCTCTGTGAGCTGGCTTGG 60.377 63.158 0.00 0.00 0.00 3.61
2192 2506 3.123620 GTGAGCTGGCTTGGAGCG 61.124 66.667 0.00 0.00 43.62 5.03
2194 2508 4.400961 GAGCTGGCTTGGAGCGGT 62.401 66.667 0.00 0.00 43.62 5.68
2213 2527 2.203015 AGTTGCTGAACCACGCGT 60.203 55.556 5.58 5.58 31.81 6.01
2216 2530 3.776659 TTGCTGAACCACGCGTCGA 62.777 57.895 9.86 0.00 0.00 4.20
2222 2536 1.286354 GAACCACGCGTCGAATTGGA 61.286 55.000 9.86 0.00 33.02 3.53
2223 2537 1.562575 AACCACGCGTCGAATTGGAC 61.563 55.000 9.86 10.32 33.02 4.02
2238 2552 2.281484 GACCGGCAACTTGCTCCA 60.281 61.111 13.43 0.00 44.28 3.86
2239 2553 1.675641 GACCGGCAACTTGCTCCAT 60.676 57.895 13.43 0.00 44.28 3.41
2243 2557 2.486966 GCAACTTGCTCCATCGGC 59.513 61.111 6.50 0.00 40.96 5.54
2244 2558 2.334946 GCAACTTGCTCCATCGGCA 61.335 57.895 6.50 0.00 40.96 5.69
2249 2563 0.604780 CTTGCTCCATCGGCATAGGG 60.605 60.000 0.00 0.00 39.54 3.53
2250 2564 1.053835 TTGCTCCATCGGCATAGGGA 61.054 55.000 0.00 0.00 39.54 4.20
2254 2568 1.127567 TCCATCGGCATAGGGAAGGG 61.128 60.000 0.00 0.00 0.00 3.95
2255 2569 1.127567 CCATCGGCATAGGGAAGGGA 61.128 60.000 0.00 0.00 0.00 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 3.190849 CAGCACAGCGGGTCATCG 61.191 66.667 0.00 0.00 0.00 3.84
7 8 3.503363 GCAGCACAGCGGGTCATC 61.503 66.667 0.00 0.00 0.00 2.92
15 16 1.164662 ATGATCCATCGCAGCACAGC 61.165 55.000 0.00 0.00 0.00 4.40
16 17 0.866427 GATGATCCATCGCAGCACAG 59.134 55.000 0.00 0.00 31.01 3.66
17 18 2.996444 GATGATCCATCGCAGCACA 58.004 52.632 0.00 0.00 31.01 4.57
25 26 3.782244 GCGCGGCGATGATCCATC 61.782 66.667 28.54 0.14 37.50 3.51
26 27 4.305479 AGCGCGGCGATGATCCAT 62.305 61.111 28.54 0.00 0.00 3.41
29 30 3.264897 AACAGCGCGGCGATGATC 61.265 61.111 41.74 17.65 46.56 2.92
30 31 3.566853 CAACAGCGCGGCGATGAT 61.567 61.111 41.74 30.53 46.56 2.45
33 34 4.088762 CAACAACAGCGCGGCGAT 62.089 61.111 28.54 19.18 0.00 4.58
35 36 4.605967 AACAACAACAGCGCGGCG 62.606 61.111 19.62 19.62 0.00 6.46
36 37 3.024043 CAACAACAACAGCGCGGC 61.024 61.111 8.83 0.00 0.00 6.53
37 38 3.024043 GCAACAACAACAGCGCGG 61.024 61.111 8.83 5.83 0.00 6.46
38 39 3.024043 GGCAACAACAACAGCGCG 61.024 61.111 0.00 0.00 0.00 6.86
39 40 2.928313 TTCGGCAACAACAACAGCGC 62.928 55.000 0.00 0.00 0.00 5.92
40 41 1.063327 TTCGGCAACAACAACAGCG 59.937 52.632 0.00 0.00 0.00 5.18
41 42 1.199852 CGTTCGGCAACAACAACAGC 61.200 55.000 0.00 0.00 32.14 4.40
42 43 1.199852 GCGTTCGGCAACAACAACAG 61.200 55.000 0.00 0.00 42.87 3.16
43 44 1.226435 GCGTTCGGCAACAACAACA 60.226 52.632 0.00 0.00 42.87 3.33
44 45 1.942223 GGCGTTCGGCAACAACAAC 60.942 57.895 13.49 0.00 46.16 3.32
45 46 2.409651 GGCGTTCGGCAACAACAA 59.590 55.556 13.49 0.00 46.16 2.83
46 47 3.587933 GGGCGTTCGGCAACAACA 61.588 61.111 19.20 0.00 46.16 3.33
47 48 3.284449 AGGGCGTTCGGCAACAAC 61.284 61.111 19.20 2.94 46.16 3.32
48 49 3.283684 CAGGGCGTTCGGCAACAA 61.284 61.111 19.20 0.00 46.16 2.83
66 67 3.470888 ACCCCTTCATCGGCGGAG 61.471 66.667 7.21 0.00 0.00 4.63
67 68 3.781307 CACCCCTTCATCGGCGGA 61.781 66.667 7.21 0.00 0.00 5.54
72 73 4.473520 AGCCGCACCCCTTCATCG 62.474 66.667 0.00 0.00 0.00 3.84
73 74 2.514824 GAGCCGCACCCCTTCATC 60.515 66.667 0.00 0.00 0.00 2.92
74 75 4.473520 CGAGCCGCACCCCTTCAT 62.474 66.667 0.00 0.00 0.00 2.57
84 85 4.748679 CTTGCAAGCACGAGCCGC 62.749 66.667 14.65 9.44 43.56 6.53
127 128 0.235665 ACATGAAGCAACAACGCGAG 59.764 50.000 15.93 7.57 36.85 5.03
128 129 0.041400 CACATGAAGCAACAACGCGA 60.041 50.000 15.93 0.00 36.85 5.87
129 130 0.998226 CCACATGAAGCAACAACGCG 60.998 55.000 3.53 3.53 36.85 6.01
130 131 1.277495 GCCACATGAAGCAACAACGC 61.277 55.000 0.00 0.00 0.00 4.84
131 132 0.030504 TGCCACATGAAGCAACAACG 59.969 50.000 11.17 0.00 35.69 4.10
132 133 1.202394 TGTGCCACATGAAGCAACAAC 60.202 47.619 14.43 5.00 41.48 3.32
133 134 1.109609 TGTGCCACATGAAGCAACAA 58.890 45.000 14.43 3.37 41.48 2.83
134 135 1.109609 TTGTGCCACATGAAGCAACA 58.890 45.000 14.43 12.08 41.48 3.33
135 136 2.063266 CATTGTGCCACATGAAGCAAC 58.937 47.619 14.43 10.17 41.48 4.17
136 137 1.687660 ACATTGTGCCACATGAAGCAA 59.312 42.857 14.43 5.89 41.48 3.91
137 138 1.000052 CACATTGTGCCACATGAAGCA 60.000 47.619 3.43 9.80 36.44 3.91
138 139 1.000060 ACACATTGTGCCACATGAAGC 60.000 47.619 16.62 1.71 36.98 3.86
139 140 2.668250 CACACATTGTGCCACATGAAG 58.332 47.619 16.62 1.64 41.89 3.02
140 141 2.797074 CACACATTGTGCCACATGAA 57.203 45.000 16.62 0.00 41.89 2.57
149 150 4.584055 GGATCGGCCAACACACATTGTG 62.584 54.545 15.18 15.18 44.67 3.33
150 151 0.881118 GATCGGCCAACACACATTGT 59.119 50.000 2.24 0.00 41.74 2.71
151 152 0.171007 GGATCGGCCAACACACATTG 59.829 55.000 2.24 0.00 36.34 2.82
152 153 0.251121 TGGATCGGCCAACACACATT 60.251 50.000 2.24 0.00 45.87 2.71
153 154 1.378378 TGGATCGGCCAACACACAT 59.622 52.632 2.24 0.00 45.87 3.21
154 155 2.832498 TGGATCGGCCAACACACA 59.168 55.556 2.24 0.00 45.87 3.72
197 198 3.628646 ATCAGTCGGGTTGCAGGCC 62.629 63.158 0.00 0.00 0.00 5.19
198 199 1.244019 AAATCAGTCGGGTTGCAGGC 61.244 55.000 0.00 0.00 0.00 4.85
199 200 0.804989 GAAATCAGTCGGGTTGCAGG 59.195 55.000 0.00 0.00 0.00 4.85
200 201 1.813513 AGAAATCAGTCGGGTTGCAG 58.186 50.000 0.00 0.00 0.00 4.41
201 202 2.151202 GAAGAAATCAGTCGGGTTGCA 58.849 47.619 0.00 0.00 0.00 4.08
202 203 2.095718 GTGAAGAAATCAGTCGGGTTGC 60.096 50.000 0.00 0.00 39.19 4.17
203 204 2.157668 CGTGAAGAAATCAGTCGGGTTG 59.842 50.000 0.00 0.00 39.19 3.77
204 205 2.036733 TCGTGAAGAAATCAGTCGGGTT 59.963 45.455 0.00 0.00 39.19 4.11
205 206 1.616865 TCGTGAAGAAATCAGTCGGGT 59.383 47.619 0.00 0.00 39.19 5.28
206 207 2.363788 TCGTGAAGAAATCAGTCGGG 57.636 50.000 0.00 0.00 39.19 5.14
216 217 1.065358 GCGGTCGATTTCGTGAAGAA 58.935 50.000 0.00 0.00 40.80 2.52
217 218 0.242825 AGCGGTCGATTTCGTGAAGA 59.757 50.000 0.00 0.00 40.80 2.87
218 219 0.640768 GAGCGGTCGATTTCGTGAAG 59.359 55.000 0.00 0.00 40.80 3.02
219 220 2.733127 GAGCGGTCGATTTCGTGAA 58.267 52.632 0.00 0.00 40.80 3.18
220 221 4.470876 GAGCGGTCGATTTCGTGA 57.529 55.556 0.00 0.00 40.80 4.35
230 231 0.387878 CTGCTATGGATCGAGCGGTC 60.388 60.000 4.06 4.06 41.83 4.79
231 232 1.662608 CTGCTATGGATCGAGCGGT 59.337 57.895 11.64 0.00 41.83 5.68
232 233 1.735920 GCTGCTATGGATCGAGCGG 60.736 63.158 14.35 14.35 46.07 5.52
233 234 1.735920 GGCTGCTATGGATCGAGCG 60.736 63.158 0.00 5.06 41.83 5.03
234 235 1.735920 CGGCTGCTATGGATCGAGC 60.736 63.158 0.00 0.00 39.25 5.03
235 236 0.387878 GACGGCTGCTATGGATCGAG 60.388 60.000 0.00 0.00 0.00 4.04
236 237 1.106944 TGACGGCTGCTATGGATCGA 61.107 55.000 0.00 0.00 0.00 3.59
237 238 0.037882 ATGACGGCTGCTATGGATCG 60.038 55.000 0.00 0.00 0.00 3.69
238 239 2.175878 AATGACGGCTGCTATGGATC 57.824 50.000 0.00 0.00 0.00 3.36
239 240 2.158769 TGAAATGACGGCTGCTATGGAT 60.159 45.455 0.00 0.00 0.00 3.41
240 241 1.209261 TGAAATGACGGCTGCTATGGA 59.791 47.619 0.00 0.00 0.00 3.41
241 242 1.667236 TGAAATGACGGCTGCTATGG 58.333 50.000 0.00 0.00 0.00 2.74
242 243 3.763097 TTTGAAATGACGGCTGCTATG 57.237 42.857 0.00 0.00 0.00 2.23
243 244 5.126067 ACTATTTGAAATGACGGCTGCTAT 58.874 37.500 0.00 0.00 0.00 2.97
244 245 4.513442 ACTATTTGAAATGACGGCTGCTA 58.487 39.130 0.00 0.00 0.00 3.49
245 246 3.347216 ACTATTTGAAATGACGGCTGCT 58.653 40.909 0.00 0.00 0.00 4.24
246 247 3.764885 ACTATTTGAAATGACGGCTGC 57.235 42.857 0.00 0.00 0.00 5.25
259 260 7.588512 AGCAAGACTAGCTTCAAAACTATTTG 58.411 34.615 0.00 0.00 39.87 2.32
260 261 7.751768 AGCAAGACTAGCTTCAAAACTATTT 57.248 32.000 0.00 0.00 39.87 1.40
261 262 8.848474 TTAGCAAGACTAGCTTCAAAACTATT 57.152 30.769 0.00 0.00 43.25 1.73
262 263 8.848474 TTTAGCAAGACTAGCTTCAAAACTAT 57.152 30.769 0.00 0.00 43.25 2.12
263 264 8.848474 ATTTAGCAAGACTAGCTTCAAAACTA 57.152 30.769 0.00 0.00 43.25 2.24
264 265 7.751768 ATTTAGCAAGACTAGCTTCAAAACT 57.248 32.000 0.00 0.00 43.25 2.66
265 266 8.803201 AAATTTAGCAAGACTAGCTTCAAAAC 57.197 30.769 0.00 0.00 43.25 2.43
266 267 8.629158 TGAAATTTAGCAAGACTAGCTTCAAAA 58.371 29.630 0.00 0.00 43.25 2.44
267 268 8.165239 TGAAATTTAGCAAGACTAGCTTCAAA 57.835 30.769 0.00 0.00 43.25 2.69
268 269 7.445402 ACTGAAATTTAGCAAGACTAGCTTCAA 59.555 33.333 0.00 0.00 43.25 2.69
269 270 6.936900 ACTGAAATTTAGCAAGACTAGCTTCA 59.063 34.615 0.00 0.00 43.25 3.02
270 271 7.118390 TGACTGAAATTTAGCAAGACTAGCTTC 59.882 37.037 0.00 0.00 43.25 3.86
271 272 6.936900 TGACTGAAATTTAGCAAGACTAGCTT 59.063 34.615 0.00 0.00 43.25 3.74
272 273 6.467677 TGACTGAAATTTAGCAAGACTAGCT 58.532 36.000 0.00 0.00 45.77 3.32
273 274 6.727824 TGACTGAAATTTAGCAAGACTAGC 57.272 37.500 0.00 0.00 30.79 3.42
274 275 8.226448 CAGTTGACTGAAATTTAGCAAGACTAG 58.774 37.037 5.19 0.00 46.59 2.57
275 276 8.087982 CAGTTGACTGAAATTTAGCAAGACTA 57.912 34.615 5.19 0.00 46.59 2.59
276 277 6.963796 CAGTTGACTGAAATTTAGCAAGACT 58.036 36.000 5.19 0.00 46.59 3.24
291 292 3.556513 GACACTACGTCTCAGTTGACTG 58.443 50.000 4.77 4.77 41.81 3.51
292 293 3.900388 GACACTACGTCTCAGTTGACT 57.100 47.619 0.00 0.00 41.81 3.41
302 303 1.005340 ATCGACCGAGACACTACGTC 58.995 55.000 0.00 0.00 45.77 4.34
303 304 0.725686 CATCGACCGAGACACTACGT 59.274 55.000 0.00 0.00 0.00 3.57
304 305 0.589229 GCATCGACCGAGACACTACG 60.589 60.000 0.00 0.00 0.00 3.51
305 306 0.733729 AGCATCGACCGAGACACTAC 59.266 55.000 0.00 0.00 0.00 2.73
306 307 2.320745 TAGCATCGACCGAGACACTA 57.679 50.000 0.00 0.00 0.00 2.74
307 308 1.681538 ATAGCATCGACCGAGACACT 58.318 50.000 0.00 0.00 0.00 3.55
308 309 3.833545 ATATAGCATCGACCGAGACAC 57.166 47.619 0.00 0.00 0.00 3.67
309 310 3.818773 TGAATATAGCATCGACCGAGACA 59.181 43.478 0.00 0.00 0.00 3.41
310 311 4.421033 TGAATATAGCATCGACCGAGAC 57.579 45.455 0.00 0.00 0.00 3.36
403 404 4.617959 GCTGTGGCTACGTCTAATATCAA 58.382 43.478 0.00 0.00 35.22 2.57
541 542 3.445987 TGGGGTGTTTCCAAAGTTTTCT 58.554 40.909 0.00 0.00 38.11 2.52
639 641 1.691196 CTGTGCCTGTCCTTTTTGGA 58.309 50.000 0.00 0.00 43.86 3.53
640 642 0.032540 GCTGTGCCTGTCCTTTTTGG 59.967 55.000 0.00 0.00 37.10 3.28
759 763 3.119316 ACTCCACGTAGCATCTTCTTCTG 60.119 47.826 0.00 0.00 0.00 3.02
974 1002 1.228894 TCACTTCACTCGAGGCCCT 60.229 57.895 18.41 0.00 0.00 5.19
975 1003 1.216710 CTCACTTCACTCGAGGCCC 59.783 63.158 18.41 0.00 0.00 5.80
1168 1206 1.202582 AGAACTCCACCTGAATCGACG 59.797 52.381 0.00 0.00 0.00 5.12
1416 1464 2.094545 CACTCGTGACATCACAGGATCA 60.095 50.000 12.32 0.00 46.75 2.92
1502 1557 3.422417 TCGATTGCTTCCGAAGTAGAG 57.578 47.619 9.87 1.65 0.00 2.43
1503 1558 3.861276 TTCGATTGCTTCCGAAGTAGA 57.139 42.857 9.87 0.00 39.49 2.59
1527 1582 2.224305 ACTTGCAACAGTACTGACCTCC 60.224 50.000 29.30 12.17 0.00 4.30
1600 1656 1.027357 CTGCATGCACCTTATGGGAC 58.973 55.000 18.46 0.00 38.76 4.46
1601 1657 0.752743 GCTGCATGCACCTTATGGGA 60.753 55.000 18.46 0.00 42.31 4.37
1602 1658 1.737816 GCTGCATGCACCTTATGGG 59.262 57.895 18.46 5.54 42.31 4.00
1612 1668 0.458260 TGTTCCATCATGCTGCATGC 59.542 50.000 32.23 19.73 41.18 4.06
1613 1669 1.202371 GGTGTTCCATCATGCTGCATG 60.202 52.381 31.48 31.48 42.60 4.06
1614 1670 1.108776 GGTGTTCCATCATGCTGCAT 58.891 50.000 9.81 9.81 0.00 3.96
1615 1671 0.251253 TGGTGTTCCATCATGCTGCA 60.251 50.000 4.13 4.13 39.03 4.41
1616 1672 0.889994 TTGGTGTTCCATCATGCTGC 59.110 50.000 0.00 0.00 43.91 5.25
1617 1673 2.163010 GAGTTGGTGTTCCATCATGCTG 59.837 50.000 0.00 0.00 43.91 4.41
1618 1674 2.440409 GAGTTGGTGTTCCATCATGCT 58.560 47.619 0.00 0.00 43.91 3.79
1619 1675 1.474077 GGAGTTGGTGTTCCATCATGC 59.526 52.381 0.00 0.00 43.91 4.06
1620 1676 2.794103 TGGAGTTGGTGTTCCATCATG 58.206 47.619 0.00 0.00 43.91 3.07
1625 1681 1.774254 ACAGATGGAGTTGGTGTTCCA 59.226 47.619 0.00 0.00 46.79 3.53
1626 1682 2.427506 GACAGATGGAGTTGGTGTTCC 58.572 52.381 0.00 0.00 0.00 3.62
1627 1683 2.427506 GGACAGATGGAGTTGGTGTTC 58.572 52.381 0.00 0.00 0.00 3.18
1628 1684 1.073923 GGGACAGATGGAGTTGGTGTT 59.926 52.381 0.00 0.00 0.00 3.32
1629 1685 0.693049 GGGACAGATGGAGTTGGTGT 59.307 55.000 0.00 0.00 0.00 4.16
1630 1686 0.692476 TGGGACAGATGGAGTTGGTG 59.308 55.000 0.00 0.00 0.00 4.17
1631 1687 3.180449 TGGGACAGATGGAGTTGGT 57.820 52.632 0.00 0.00 0.00 3.67
1632 1688 3.434167 CCTTATGGGACAGATGGAGTTGG 60.434 52.174 0.00 0.00 46.11 3.77
1633 1689 3.813443 CCTTATGGGACAGATGGAGTTG 58.187 50.000 0.00 0.00 46.11 3.16
1666 1722 4.678743 GAGGGTGGGGGTGTTGCC 62.679 72.222 0.00 0.00 0.00 4.52
1668 1724 3.246112 TCGAGGGTGGGGGTGTTG 61.246 66.667 0.00 0.00 0.00 3.33
1669 1725 2.928396 CTCGAGGGTGGGGGTGTT 60.928 66.667 3.91 0.00 0.00 3.32
1670 1726 2.976284 TTTCTCGAGGGTGGGGGTGT 62.976 60.000 13.56 0.00 0.00 4.16
1671 1727 1.774894 TTTTCTCGAGGGTGGGGGTG 61.775 60.000 13.56 0.00 0.00 4.61
1672 1728 1.063654 TTTTTCTCGAGGGTGGGGGT 61.064 55.000 13.56 0.00 0.00 4.95
1673 1729 0.608308 GTTTTTCTCGAGGGTGGGGG 60.608 60.000 13.56 0.00 0.00 5.40
1674 1730 0.608308 GGTTTTTCTCGAGGGTGGGG 60.608 60.000 13.56 0.00 0.00 4.96
1675 1731 0.400594 AGGTTTTTCTCGAGGGTGGG 59.599 55.000 13.56 0.00 0.00 4.61
1676 1732 1.610886 GGAGGTTTTTCTCGAGGGTGG 60.611 57.143 13.56 0.00 34.74 4.61
1677 1733 1.348036 AGGAGGTTTTTCTCGAGGGTG 59.652 52.381 13.56 0.00 34.74 4.61
1678 1734 1.348036 CAGGAGGTTTTTCTCGAGGGT 59.652 52.381 13.56 0.00 34.74 4.34
1679 1735 1.946283 GCAGGAGGTTTTTCTCGAGGG 60.946 57.143 13.56 0.00 34.74 4.30
1680 1736 1.002544 AGCAGGAGGTTTTTCTCGAGG 59.997 52.381 13.56 0.00 34.74 4.63
1681 1737 2.464157 AGCAGGAGGTTTTTCTCGAG 57.536 50.000 5.93 5.93 34.74 4.04
1682 1738 2.550208 GGAAGCAGGAGGTTTTTCTCGA 60.550 50.000 0.00 0.00 35.19 4.04
1683 1739 1.807142 GGAAGCAGGAGGTTTTTCTCG 59.193 52.381 0.00 0.00 35.19 4.04
1684 1740 1.807142 CGGAAGCAGGAGGTTTTTCTC 59.193 52.381 0.00 0.00 35.19 2.87
1685 1741 1.143073 ACGGAAGCAGGAGGTTTTTCT 59.857 47.619 0.00 0.00 35.19 2.52
1686 1742 1.535896 GACGGAAGCAGGAGGTTTTTC 59.464 52.381 0.00 0.00 35.19 2.29
1687 1743 1.605753 GACGGAAGCAGGAGGTTTTT 58.394 50.000 0.00 0.00 35.19 1.94
1688 1744 0.250770 GGACGGAAGCAGGAGGTTTT 60.251 55.000 0.00 0.00 35.19 2.43
1689 1745 1.375326 GGACGGAAGCAGGAGGTTT 59.625 57.895 0.00 0.00 35.19 3.27
1690 1746 2.943978 CGGACGGAAGCAGGAGGTT 61.944 63.158 0.00 0.00 38.36 3.50
1691 1747 3.382832 CGGACGGAAGCAGGAGGT 61.383 66.667 0.00 0.00 0.00 3.85
1692 1748 4.821589 GCGGACGGAAGCAGGAGG 62.822 72.222 0.00 0.00 0.00 4.30
1693 1749 4.821589 GGCGGACGGAAGCAGGAG 62.822 72.222 0.00 0.00 34.54 3.69
1726 1782 3.181495 TGAATTTTGTCAACCGTGTCCAC 60.181 43.478 0.00 0.00 0.00 4.02
1727 1783 3.017442 TGAATTTTGTCAACCGTGTCCA 58.983 40.909 0.00 0.00 0.00 4.02
1728 1784 3.701532 TGAATTTTGTCAACCGTGTCC 57.298 42.857 0.00 0.00 0.00 4.02
1729 1785 3.425193 GCATGAATTTTGTCAACCGTGTC 59.575 43.478 0.00 0.00 0.00 3.67
1730 1786 3.181482 TGCATGAATTTTGTCAACCGTGT 60.181 39.130 0.00 0.00 0.00 4.49
1731 1787 3.379240 TGCATGAATTTTGTCAACCGTG 58.621 40.909 0.00 0.00 0.00 4.94
1732 1788 3.724508 TGCATGAATTTTGTCAACCGT 57.275 38.095 0.00 0.00 0.00 4.83
1733 1789 4.269603 TGTTTGCATGAATTTTGTCAACCG 59.730 37.500 0.00 0.00 0.00 4.44
1734 1790 5.500825 GTGTTTGCATGAATTTTGTCAACC 58.499 37.500 0.00 0.00 0.00 3.77
1735 1791 5.189625 CGTGTTTGCATGAATTTTGTCAAC 58.810 37.500 0.00 0.00 33.58 3.18
1736 1792 4.269603 CCGTGTTTGCATGAATTTTGTCAA 59.730 37.500 0.00 0.00 33.58 3.18
1737 1793 3.801050 CCGTGTTTGCATGAATTTTGTCA 59.199 39.130 0.00 0.00 33.58 3.58
1741 1797 2.142319 GGCCGTGTTTGCATGAATTTT 58.858 42.857 0.00 0.00 33.58 1.82
1778 1834 7.237871 CGTTATGTTTGTATGAAAACCGATCA 58.762 34.615 0.00 0.00 38.93 2.92
1781 1837 5.699915 TCCGTTATGTTTGTATGAAAACCGA 59.300 36.000 3.47 0.00 38.93 4.69
1783 1839 8.751302 AAATCCGTTATGTTTGTATGAAAACC 57.249 30.769 3.47 0.00 38.93 3.27
1800 1856 5.390779 CGTCCGGTTTTGTATTAAATCCGTT 60.391 40.000 16.17 0.00 33.66 4.44
1809 1865 1.802365 GTCTGCGTCCGGTTTTGTATT 59.198 47.619 0.00 0.00 0.00 1.89
1817 1873 1.288127 GTAACTGTCTGCGTCCGGT 59.712 57.895 0.00 0.00 0.00 5.28
1818 1874 0.108804 ATGTAACTGTCTGCGTCCGG 60.109 55.000 0.00 0.00 0.00 5.14
1819 1875 1.710013 AATGTAACTGTCTGCGTCCG 58.290 50.000 0.00 0.00 0.00 4.79
1820 1876 3.496884 TCAAAATGTAACTGTCTGCGTCC 59.503 43.478 0.00 0.00 0.00 4.79
1854 1910 9.228636 ACGTGCACATAGTTTTTAACTTTTTAG 57.771 29.630 18.64 0.00 42.81 1.85
1856 1912 9.012448 GTACGTGCACATAGTTTTTAACTTTTT 57.988 29.630 18.64 0.00 42.81 1.94
1861 1917 5.074791 CCGTACGTGCACATAGTTTTTAAC 58.925 41.667 18.64 0.85 0.00 2.01
1864 1920 3.132925 ACCGTACGTGCACATAGTTTTT 58.867 40.909 18.64 0.00 0.00 1.94
1907 2220 3.411517 CCGCTTGGGTCCCAGGAT 61.412 66.667 23.95 0.00 31.89 3.24
1943 2256 3.019564 CTGGCAACTTAGAGGGGAAATG 58.980 50.000 0.00 0.00 37.61 2.32
1945 2258 1.271926 GCTGGCAACTTAGAGGGGAAA 60.272 52.381 0.00 0.00 37.61 3.13
1948 2261 1.450312 CGCTGGCAACTTAGAGGGG 60.450 63.158 0.00 0.00 37.61 4.79
1954 2267 0.676466 CCATGTCCGCTGGCAACTTA 60.676 55.000 0.00 0.00 37.61 2.24
1993 2306 0.810426 CGGAGGAGATCGACGAGTCA 60.810 60.000 3.01 0.00 0.00 3.41
1995 2308 2.181521 GCGGAGGAGATCGACGAGT 61.182 63.158 3.01 0.00 0.00 4.18
2001 2314 4.933064 GGTGCGCGGAGGAGATCG 62.933 72.222 8.83 0.00 0.00 3.69
2028 2342 1.079612 CACGCCATGCAGACAGAGA 60.080 57.895 0.00 0.00 0.00 3.10
2054 2368 1.448540 CATCCACAGTCGAGGGCAC 60.449 63.158 0.00 0.00 0.00 5.01
2055 2369 2.659063 CCATCCACAGTCGAGGGCA 61.659 63.158 0.00 0.00 0.00 5.36
2058 2372 1.448540 GCACCATCCACAGTCGAGG 60.449 63.158 0.00 0.00 0.00 4.63
2060 2374 2.261361 CGCACCATCCACAGTCGA 59.739 61.111 0.00 0.00 0.00 4.20
2065 2379 2.220615 CTACGACCGCACCATCCACA 62.221 60.000 0.00 0.00 0.00 4.17
2067 2381 2.717044 CCTACGACCGCACCATCCA 61.717 63.158 0.00 0.00 0.00 3.41
2074 2388 4.063967 CCAGTGCCTACGACCGCA 62.064 66.667 0.00 0.00 0.00 5.69
2097 2411 0.562950 GATAACGTTGCGTCGTACCG 59.437 55.000 11.99 0.00 43.38 4.02
2107 2421 1.269206 GCATGGGCATGGATAACGTTG 60.269 52.381 11.99 0.00 40.72 4.10
2108 2422 1.032014 GCATGGGCATGGATAACGTT 58.968 50.000 5.88 5.88 40.72 3.99
2113 2427 2.282391 GCGGCATGGGCATGGATA 60.282 61.111 0.00 0.00 43.71 2.59
2129 2443 3.423154 CACGAAGGGAAGCACGGC 61.423 66.667 0.00 0.00 0.00 5.68
2137 2451 2.284331 TAGGCTGGCACGAAGGGA 60.284 61.111 3.38 0.00 0.00 4.20
2142 2456 2.282783 TTGCTCTAGGCTGGCACGA 61.283 57.895 3.38 0.00 42.39 4.35
2174 2488 2.033141 GCTCCAAGCCAGCTCACA 59.967 61.111 0.00 0.00 34.48 3.58
2175 2489 3.123620 CGCTCCAAGCCAGCTCAC 61.124 66.667 0.00 0.00 38.18 3.51
2176 2490 4.399395 CCGCTCCAAGCCAGCTCA 62.399 66.667 0.00 0.00 38.18 4.26
2188 2502 1.569479 GGTTCAGCAACTCACCGCTC 61.569 60.000 0.00 0.00 35.96 5.03
2192 2506 1.941812 CGTGGTTCAGCAACTCACC 59.058 57.895 0.00 0.00 33.47 4.02
2194 2508 2.243957 CGCGTGGTTCAGCAACTCA 61.244 57.895 0.00 0.00 32.50 3.41
2213 2527 0.250553 AAGTTGCCGGTCCAATTCGA 60.251 50.000 1.90 0.00 0.00 3.71
2216 2530 0.827507 AGCAAGTTGCCGGTCCAATT 60.828 50.000 24.02 0.00 46.52 2.32
2222 2536 1.675641 GATGGAGCAAGTTGCCGGT 60.676 57.895 24.02 5.97 46.52 5.28
2223 2537 2.753966 CGATGGAGCAAGTTGCCGG 61.754 63.158 24.02 0.00 46.52 6.13
2238 2552 0.838122 CCTCCCTTCCCTATGCCGAT 60.838 60.000 0.00 0.00 0.00 4.18
2239 2553 1.459539 CCTCCCTTCCCTATGCCGA 60.460 63.158 0.00 0.00 0.00 5.54
2243 2557 1.428869 CTCCACCTCCCTTCCCTATG 58.571 60.000 0.00 0.00 0.00 2.23
2244 2558 3.979313 CTCCACCTCCCTTCCCTAT 57.021 57.895 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.