Multiple sequence alignment - TraesCS7A01G421800

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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 TraesCS7A01G421800 chr7A 100.000 3100 0 0 1 3100 612600120 612597021 0.000000e+00 5725
1 TraesCS7A01G421800 chr7A 89.530 745 38 16 2358 3096 612585382 612584672 0.000000e+00 907
2 TraesCS7A01G421800 chr7A 91.724 290 21 2 1570 1857 612585946 612585658 1.730000e-107 399
3 TraesCS7A01G421800 chr7A 89.860 286 17 6 2024 2305 612585662 612585385 1.060000e-94 357
4 TraesCS7A01G421800 chr7D 93.592 2216 85 17 889 3100 532370004 532367842 0.000000e+00 3253
5 TraesCS7A01G421800 chr7D 88.477 755 43 19 2352 3100 532264158 532263442 0.000000e+00 872
6 TraesCS7A01G421800 chr7D 87.762 621 35 12 285 865 532370717 532370098 0.000000e+00 688
7 TraesCS7A01G421800 chr7D 88.520 392 23 9 1928 2305 532264540 532264157 3.640000e-124 455
8 TraesCS7A01G421800 chr7B 92.770 1632 58 19 619 2237 572652288 572650704 0.000000e+00 2305
9 TraesCS7A01G421800 chr7B 89.987 749 43 15 2358 3100 572639281 572638559 0.000000e+00 939
10 TraesCS7A01G421800 chr7B 88.829 743 49 12 1570 2305 572639999 572639284 0.000000e+00 881
11 TraesCS7A01G421800 chr7B 89.158 701 53 12 2397 3093 572650693 572650012 0.000000e+00 852
12 TraesCS7A01G421800 chr7B 88.776 196 15 2 285 474 572652538 572652344 1.860000e-57 233
13 TraesCS7A01G421800 chr6A 97.973 296 4 2 1 295 490914926 490914632 2.130000e-141 512
14 TraesCS7A01G421800 chr6A 98.951 286 2 1 1 285 334694501 334694786 7.670000e-141 510
15 TraesCS7A01G421800 chr6A 98.951 286 2 1 1 285 588959819 588959534 7.670000e-141 510
16 TraesCS7A01G421800 chrUn 98.951 286 2 1 1 285 328877204 328876919 7.670000e-141 510
17 TraesCS7A01G421800 chrUn 98.246 285 4 1 1 284 372911399 372911683 5.970000e-137 497
18 TraesCS7A01G421800 chr2A 98.951 286 2 1 1 285 154622180 154621895 7.670000e-141 510
19 TraesCS7A01G421800 chr2A 97.315 298 4 4 1 296 448704206 448703911 1.280000e-138 503
20 TraesCS7A01G421800 chr1B 98.951 286 2 1 1 285 631586545 631586260 7.670000e-141 510
21 TraesCS7A01G421800 chr1B 98.951 286 2 1 1 285 631596698 631596413 7.670000e-141 510


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 TraesCS7A01G421800 chr7A 612597021 612600120 3099 True 5725.000000 5725 100.000000 1 3100 1 chr7A.!!$R1 3099
1 TraesCS7A01G421800 chr7A 612584672 612585946 1274 True 554.333333 907 90.371333 1570 3096 3 chr7A.!!$R2 1526
2 TraesCS7A01G421800 chr7D 532367842 532370717 2875 True 1970.500000 3253 90.677000 285 3100 2 chr7D.!!$R2 2815
3 TraesCS7A01G421800 chr7D 532263442 532264540 1098 True 663.500000 872 88.498500 1928 3100 2 chr7D.!!$R1 1172
4 TraesCS7A01G421800 chr7B 572650012 572652538 2526 True 1130.000000 2305 90.234667 285 3093 3 chr7B.!!$R2 2808
5 TraesCS7A01G421800 chr7B 572638559 572639999 1440 True 910.000000 939 89.408000 1570 3100 2 chr7B.!!$R1 1530

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
479 486 0.108424 GCTGCAGTACTCTGTGGGAG 60.108 60.0 16.64 0.0 46.87 4.30 F
1050 1161 0.323451 GTGTTCTTCCCCATCCCCAC 60.323 60.0 0.00 0.0 0.00 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1988 2104 0.396435 TCCATCAACGGAAGCACTGT 59.604 50.0 0.00 0.00 40.17 3.55 R
2947 3256 0.899717 ATGTTGGCCAAGCGGTTGAT 60.900 50.0 27.92 9.84 35.46 2.57 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
69 70 8.305046 TGATTTAATTCAAAACCCTAGGATGG 57.695 34.615 11.48 0.00 0.00 3.51
70 71 6.538945 TTTAATTCAAAACCCTAGGATGGC 57.461 37.500 11.48 0.00 0.00 4.40
71 72 2.525105 TTCAAAACCCTAGGATGGCC 57.475 50.000 11.48 0.00 0.00 5.36
73 74 2.853430 TCAAAACCCTAGGATGGCCTA 58.147 47.619 11.48 0.00 44.74 3.93
83 84 3.303351 AGGATGGCCTAGGAAAATGTG 57.697 47.619 14.75 0.00 44.74 3.21
84 85 1.683385 GGATGGCCTAGGAAAATGTGC 59.317 52.381 14.75 0.00 0.00 4.57
85 86 2.378038 GATGGCCTAGGAAAATGTGCA 58.622 47.619 14.75 0.00 0.00 4.57
86 87 1.544724 TGGCCTAGGAAAATGTGCAC 58.455 50.000 14.75 10.75 0.00 4.57
87 88 0.817654 GGCCTAGGAAAATGTGCACC 59.182 55.000 14.75 0.00 0.00 5.01
88 89 1.544724 GCCTAGGAAAATGTGCACCA 58.455 50.000 14.75 2.61 0.00 4.17
89 90 2.102578 GCCTAGGAAAATGTGCACCAT 58.897 47.619 14.75 5.14 34.36 3.55
90 91 2.497273 GCCTAGGAAAATGTGCACCATT 59.503 45.455 14.75 11.19 45.81 3.16
97 98 2.634815 AATGTGCACCATTTTTGGCA 57.365 40.000 15.69 0.00 41.01 4.92
98 99 2.172851 ATGTGCACCATTTTTGGCAG 57.827 45.000 15.69 0.00 36.86 4.85
99 100 1.117994 TGTGCACCATTTTTGGCAGA 58.882 45.000 15.69 0.00 36.86 4.26
100 101 1.068895 TGTGCACCATTTTTGGCAGAG 59.931 47.619 15.69 0.00 36.86 3.35
101 102 0.680618 TGCACCATTTTTGGCAGAGG 59.319 50.000 0.00 0.00 0.00 3.69
102 103 0.681175 GCACCATTTTTGGCAGAGGT 59.319 50.000 0.00 0.00 0.00 3.85
103 104 1.070601 GCACCATTTTTGGCAGAGGTT 59.929 47.619 0.00 0.00 0.00 3.50
104 105 2.867647 GCACCATTTTTGGCAGAGGTTC 60.868 50.000 0.00 0.00 0.00 3.62
105 106 2.629617 CACCATTTTTGGCAGAGGTTCT 59.370 45.455 0.00 0.00 0.00 3.01
106 107 2.629617 ACCATTTTTGGCAGAGGTTCTG 59.370 45.455 1.75 1.75 46.90 3.02
125 126 7.398834 GTTCTGAACCAAGACAAAAATGATG 57.601 36.000 9.38 0.00 0.00 3.07
126 127 6.088016 TCTGAACCAAGACAAAAATGATGG 57.912 37.500 0.00 0.00 0.00 3.51
127 128 5.010922 TCTGAACCAAGACAAAAATGATGGG 59.989 40.000 0.00 0.00 32.21 4.00
128 129 3.683365 ACCAAGACAAAAATGATGGGC 57.317 42.857 0.00 0.00 32.21 5.36
129 130 2.971330 ACCAAGACAAAAATGATGGGCA 59.029 40.909 0.00 0.00 32.21 5.36
130 131 3.583966 ACCAAGACAAAAATGATGGGCAT 59.416 39.130 0.00 0.00 39.43 4.40
141 142 2.387757 TGATGGGCATTTTAGAAGGGC 58.612 47.619 0.00 0.00 40.88 5.19
142 143 2.292126 TGATGGGCATTTTAGAAGGGCA 60.292 45.455 6.55 0.00 43.07 5.36
143 144 2.548464 TGGGCATTTTAGAAGGGCAT 57.452 45.000 6.55 0.00 43.07 4.40
144 145 2.831565 TGGGCATTTTAGAAGGGCATT 58.168 42.857 6.55 0.00 43.07 3.56
145 146 3.180507 TGGGCATTTTAGAAGGGCATTT 58.819 40.909 6.55 0.00 43.07 2.32
146 147 3.197549 TGGGCATTTTAGAAGGGCATTTC 59.802 43.478 6.55 0.00 43.07 2.17
147 148 3.197549 GGGCATTTTAGAAGGGCATTTCA 59.802 43.478 6.55 0.00 43.07 2.69
148 149 4.436332 GGCATTTTAGAAGGGCATTTCAG 58.564 43.478 0.00 0.00 41.21 3.02
149 150 4.436332 GCATTTTAGAAGGGCATTTCAGG 58.564 43.478 4.19 0.00 0.00 3.86
150 151 4.081476 GCATTTTAGAAGGGCATTTCAGGT 60.081 41.667 4.19 0.00 0.00 4.00
151 152 5.569428 GCATTTTAGAAGGGCATTTCAGGTT 60.569 40.000 4.19 0.00 0.00 3.50
152 153 5.722021 TTTTAGAAGGGCATTTCAGGTTC 57.278 39.130 4.19 0.00 0.00 3.62
153 154 2.978156 AGAAGGGCATTTCAGGTTCA 57.022 45.000 4.19 0.00 0.00 3.18
154 155 3.463048 AGAAGGGCATTTCAGGTTCAT 57.537 42.857 4.19 0.00 0.00 2.57
155 156 3.782992 AGAAGGGCATTTCAGGTTCATT 58.217 40.909 4.19 0.00 0.00 2.57
156 157 3.512724 AGAAGGGCATTTCAGGTTCATTG 59.487 43.478 4.19 0.00 0.00 2.82
157 158 3.173953 AGGGCATTTCAGGTTCATTGA 57.826 42.857 0.00 0.00 0.00 2.57
158 159 3.509442 AGGGCATTTCAGGTTCATTGAA 58.491 40.909 0.00 0.00 33.00 2.69
159 160 3.903090 AGGGCATTTCAGGTTCATTGAAA 59.097 39.130 0.00 3.25 45.49 2.69
160 161 4.347583 AGGGCATTTCAGGTTCATTGAAAA 59.652 37.500 0.00 0.00 44.83 2.29
161 162 5.062528 GGGCATTTCAGGTTCATTGAAAAA 58.937 37.500 0.00 0.00 44.83 1.94
162 163 5.706833 GGGCATTTCAGGTTCATTGAAAAAT 59.293 36.000 0.00 1.28 44.83 1.82
163 164 6.207221 GGGCATTTCAGGTTCATTGAAAAATT 59.793 34.615 0.00 0.00 44.83 1.82
164 165 7.390162 GGGCATTTCAGGTTCATTGAAAAATTA 59.610 33.333 0.00 0.00 44.83 1.40
165 166 8.949177 GGCATTTCAGGTTCATTGAAAAATTAT 58.051 29.630 0.00 0.00 44.83 1.28
191 192 9.729281 TTTTAGTAACCCTAGTTGGTTTCATAG 57.271 33.333 8.49 0.00 46.45 2.23
192 193 6.309389 AGTAACCCTAGTTGGTTTCATAGG 57.691 41.667 8.49 0.00 46.45 2.57
197 198 4.770795 CCTAGTTGGTTTCATAGGGACTG 58.229 47.826 0.00 0.00 41.52 3.51
198 199 3.721087 AGTTGGTTTCATAGGGACTGG 57.279 47.619 0.00 0.00 41.52 4.00
199 200 2.308866 AGTTGGTTTCATAGGGACTGGG 59.691 50.000 0.00 0.00 41.52 4.45
200 201 1.295020 TGGTTTCATAGGGACTGGGG 58.705 55.000 0.00 0.00 41.52 4.96
201 202 0.551396 GGTTTCATAGGGACTGGGGG 59.449 60.000 0.00 0.00 41.52 5.40
202 203 1.296002 GTTTCATAGGGACTGGGGGT 58.704 55.000 0.00 0.00 41.52 4.95
203 204 1.639108 GTTTCATAGGGACTGGGGGTT 59.361 52.381 0.00 0.00 41.52 4.11
204 205 1.591768 TTCATAGGGACTGGGGGTTC 58.408 55.000 0.00 0.00 41.52 3.62
205 206 0.722676 TCATAGGGACTGGGGGTTCT 59.277 55.000 0.00 0.00 41.52 3.01
206 207 0.839946 CATAGGGACTGGGGGTTCTG 59.160 60.000 0.00 0.00 41.52 3.02
207 208 0.421904 ATAGGGACTGGGGGTTCTGT 59.578 55.000 0.00 0.00 41.52 3.41
208 209 0.252558 TAGGGACTGGGGGTTCTGTC 60.253 60.000 0.00 0.00 41.52 3.51
209 210 1.846124 GGGACTGGGGGTTCTGTCA 60.846 63.158 0.00 0.00 37.35 3.58
210 211 1.208165 GGGACTGGGGGTTCTGTCAT 61.208 60.000 0.00 0.00 37.35 3.06
211 212 0.253327 GGACTGGGGGTTCTGTCATC 59.747 60.000 0.00 0.00 37.35 2.92
212 213 0.253327 GACTGGGGGTTCTGTCATCC 59.747 60.000 0.00 0.00 36.19 3.51
213 214 1.208165 ACTGGGGGTTCTGTCATCCC 61.208 60.000 0.00 0.00 40.41 3.85
218 219 2.532250 GGGTTCTGTCATCCCCATTT 57.468 50.000 0.00 0.00 37.09 2.32
219 220 2.379005 GGGTTCTGTCATCCCCATTTC 58.621 52.381 0.00 0.00 37.09 2.17
220 221 2.291540 GGGTTCTGTCATCCCCATTTCA 60.292 50.000 0.00 0.00 37.09 2.69
221 222 3.430453 GGTTCTGTCATCCCCATTTCAA 58.570 45.455 0.00 0.00 0.00 2.69
222 223 3.445096 GGTTCTGTCATCCCCATTTCAAG 59.555 47.826 0.00 0.00 0.00 3.02
223 224 4.082125 GTTCTGTCATCCCCATTTCAAGT 58.918 43.478 0.00 0.00 0.00 3.16
224 225 4.387026 TCTGTCATCCCCATTTCAAGTT 57.613 40.909 0.00 0.00 0.00 2.66
225 226 4.739793 TCTGTCATCCCCATTTCAAGTTT 58.260 39.130 0.00 0.00 0.00 2.66
226 227 4.766891 TCTGTCATCCCCATTTCAAGTTTC 59.233 41.667 0.00 0.00 0.00 2.78
227 228 4.739793 TGTCATCCCCATTTCAAGTTTCT 58.260 39.130 0.00 0.00 0.00 2.52
228 229 4.523943 TGTCATCCCCATTTCAAGTTTCTG 59.476 41.667 0.00 0.00 0.00 3.02
229 230 4.766891 GTCATCCCCATTTCAAGTTTCTGA 59.233 41.667 0.00 0.00 0.00 3.27
230 231 5.243730 GTCATCCCCATTTCAAGTTTCTGAA 59.756 40.000 0.00 0.00 33.48 3.02
231 232 5.477984 TCATCCCCATTTCAAGTTTCTGAAG 59.522 40.000 0.00 0.00 36.69 3.02
232 233 5.060427 TCCCCATTTCAAGTTTCTGAAGA 57.940 39.130 0.00 0.00 36.69 2.87
233 234 5.454062 TCCCCATTTCAAGTTTCTGAAGAA 58.546 37.500 0.00 0.00 36.69 2.52
234 235 5.896678 TCCCCATTTCAAGTTTCTGAAGAAA 59.103 36.000 1.31 1.31 41.29 2.52
235 236 6.040842 TCCCCATTTCAAGTTTCTGAAGAAAG 59.959 38.462 5.74 0.00 43.82 2.62
236 237 6.040842 CCCCATTTCAAGTTTCTGAAGAAAGA 59.959 38.462 5.74 0.00 43.82 2.52
237 238 7.144000 CCCATTTCAAGTTTCTGAAGAAAGAG 58.856 38.462 5.74 0.38 43.82 2.85
238 239 7.201857 CCCATTTCAAGTTTCTGAAGAAAGAGT 60.202 37.037 5.74 0.00 43.82 3.24
239 240 8.840321 CCATTTCAAGTTTCTGAAGAAAGAGTA 58.160 33.333 5.74 0.00 43.82 2.59
243 244 8.786826 TCAAGTTTCTGAAGAAAGAGTAAACA 57.213 30.769 5.74 0.00 43.82 2.83
244 245 9.396022 TCAAGTTTCTGAAGAAAGAGTAAACAT 57.604 29.630 5.74 0.00 43.82 2.71
245 246 9.443283 CAAGTTTCTGAAGAAAGAGTAAACATG 57.557 33.333 5.74 0.00 43.82 3.21
246 247 8.964476 AGTTTCTGAAGAAAGAGTAAACATGA 57.036 30.769 5.74 0.00 43.82 3.07
247 248 9.566432 AGTTTCTGAAGAAAGAGTAAACATGAT 57.434 29.630 5.74 0.00 43.82 2.45
248 249 9.604626 GTTTCTGAAGAAAGAGTAAACATGATG 57.395 33.333 5.74 0.00 43.82 3.07
249 250 7.369803 TCTGAAGAAAGAGTAAACATGATGC 57.630 36.000 0.00 0.00 0.00 3.91
250 251 6.936335 TCTGAAGAAAGAGTAAACATGATGCA 59.064 34.615 0.00 0.00 0.00 3.96
251 252 7.445096 TCTGAAGAAAGAGTAAACATGATGCAA 59.555 33.333 0.00 0.00 0.00 4.08
252 253 7.362662 TGAAGAAAGAGTAAACATGATGCAAC 58.637 34.615 0.00 0.00 0.00 4.17
253 254 6.882610 AGAAAGAGTAAACATGATGCAACA 57.117 33.333 0.00 0.00 0.00 3.33
254 255 6.672147 AGAAAGAGTAAACATGATGCAACAC 58.328 36.000 0.00 0.00 0.00 3.32
255 256 6.488006 AGAAAGAGTAAACATGATGCAACACT 59.512 34.615 0.00 0.00 0.00 3.55
256 257 5.618056 AGAGTAAACATGATGCAACACTG 57.382 39.130 0.00 2.08 0.00 3.66
257 258 5.065914 AGAGTAAACATGATGCAACACTGT 58.934 37.500 0.00 2.72 0.00 3.55
258 259 6.230472 AGAGTAAACATGATGCAACACTGTA 58.770 36.000 0.00 0.00 0.00 2.74
259 260 6.710295 AGAGTAAACATGATGCAACACTGTAA 59.290 34.615 0.00 0.00 0.00 2.41
260 261 7.391554 AGAGTAAACATGATGCAACACTGTAAT 59.608 33.333 0.00 2.03 0.00 1.89
261 262 7.307694 AGTAAACATGATGCAACACTGTAATG 58.692 34.615 0.00 0.00 0.00 1.90
262 263 4.100707 ACATGATGCAACACTGTAATGC 57.899 40.909 0.00 9.33 40.45 3.56
267 268 3.557577 TGCAACACTGTAATGCATGAC 57.442 42.857 7.30 7.30 44.52 3.06
268 269 3.148412 TGCAACACTGTAATGCATGACT 58.852 40.909 15.42 0.00 44.52 3.41
269 270 4.322567 TGCAACACTGTAATGCATGACTA 58.677 39.130 15.42 1.43 44.52 2.59
270 271 4.392754 TGCAACACTGTAATGCATGACTAG 59.607 41.667 15.42 12.54 44.52 2.57
271 272 4.728882 GCAACACTGTAATGCATGACTAGC 60.729 45.833 15.42 6.55 39.81 3.42
272 273 4.478206 ACACTGTAATGCATGACTAGCT 57.522 40.909 15.42 0.00 0.00 3.32
273 274 5.598416 ACACTGTAATGCATGACTAGCTA 57.402 39.130 15.42 0.00 0.00 3.32
274 275 5.595885 ACACTGTAATGCATGACTAGCTAG 58.404 41.667 19.44 19.44 0.00 3.42
275 276 4.987285 CACTGTAATGCATGACTAGCTAGG 59.013 45.833 24.35 7.95 0.00 3.02
276 277 4.039730 ACTGTAATGCATGACTAGCTAGGG 59.960 45.833 24.35 11.76 0.00 3.53
277 278 3.967326 TGTAATGCATGACTAGCTAGGGT 59.033 43.478 24.35 5.47 0.00 4.34
278 279 3.482156 AATGCATGACTAGCTAGGGTG 57.518 47.619 24.35 18.63 0.00 4.61
279 280 1.866015 TGCATGACTAGCTAGGGTGT 58.134 50.000 24.35 4.29 0.00 4.16
280 281 1.482182 TGCATGACTAGCTAGGGTGTG 59.518 52.381 24.35 16.75 0.00 3.82
281 282 1.757118 GCATGACTAGCTAGGGTGTGA 59.243 52.381 24.35 0.00 0.00 3.58
282 283 2.482142 GCATGACTAGCTAGGGTGTGAC 60.482 54.545 24.35 9.83 0.00 3.67
283 284 2.597578 TGACTAGCTAGGGTGTGACA 57.402 50.000 24.35 9.62 0.00 3.58
338 339 4.634133 ACGCGCGTTCGTCCTTCA 62.634 61.111 32.73 0.00 38.44 3.02
341 342 1.225745 GCGCGTTCGTCCTTCATTG 60.226 57.895 8.43 0.00 38.14 2.82
386 387 2.162338 TTGTAGGCTTCGTGGGTCCG 62.162 60.000 0.00 0.00 0.00 4.79
427 428 1.014564 GGTAACGCTGTGACTCTGGC 61.015 60.000 0.00 0.00 0.00 4.85
441 448 2.438021 ACTCTGGCCACACTCAAGTTTA 59.562 45.455 0.00 0.00 0.00 2.01
457 464 6.607689 TCAAGTTTATGCCGTCTGTAAATTG 58.392 36.000 0.00 0.00 0.00 2.32
466 473 0.804364 TCTGTAAATTGGCGCTGCAG 59.196 50.000 10.11 10.11 0.00 4.41
474 481 2.099652 TTGGCGCTGCAGTACTCTGT 62.100 55.000 16.64 0.00 43.05 3.41
476 483 2.097038 GCGCTGCAGTACTCTGTGG 61.097 63.158 16.64 0.00 43.05 4.17
478 485 1.877576 CGCTGCAGTACTCTGTGGGA 61.878 60.000 16.64 0.00 43.05 4.37
479 486 0.108424 GCTGCAGTACTCTGTGGGAG 60.108 60.000 16.64 0.00 46.87 4.30
496 528 8.235230 TCTGTGGGAGTAGGAATATAAGATCTT 58.765 37.037 13.56 13.56 0.00 2.40
557 589 8.169268 GTGTAATACAGTACAAGCTTTCATGTC 58.831 37.037 0.00 0.00 35.79 3.06
620 661 3.885484 CAGTGGTGCTTTTGTGTAGAG 57.115 47.619 0.00 0.00 0.00 2.43
632 673 6.675002 GCTTTTGTGTAGAGCTCTGATCATTG 60.675 42.308 26.78 10.81 33.72 2.82
634 675 5.411831 TGTGTAGAGCTCTGATCATTGTT 57.588 39.130 26.78 0.00 0.00 2.83
679 720 2.224499 TGCTGCTGAACTGATGTTGGTA 60.224 45.455 0.00 0.00 36.39 3.25
746 787 1.643868 TTGCACGATTTAGCCCGCTG 61.644 55.000 0.00 0.00 0.00 5.18
764 805 2.213499 CTGCCATTTAGTAGGAAGCCG 58.787 52.381 0.00 0.00 0.00 5.52
765 806 1.834896 TGCCATTTAGTAGGAAGCCGA 59.165 47.619 0.00 0.00 0.00 5.54
985 1096 9.258826 CACCTCAAAAGATACTAATCAGAGATG 57.741 37.037 0.00 0.00 34.28 2.90
1050 1161 0.323451 GTGTTCTTCCCCATCCCCAC 60.323 60.000 0.00 0.00 0.00 4.61
1121 1233 4.230502 AGGGTATTGTTGATCAGGATTGGT 59.769 41.667 0.00 0.00 0.00 3.67
1143 1257 6.183360 TGGTTTTGCTTACAGATTGGAAATGT 60.183 34.615 0.00 0.00 0.00 2.71
1204 1318 5.364157 ACCAGAGGATGTCCATAAGTTCTAC 59.636 44.000 1.30 0.00 38.89 2.59
1211 1325 6.876257 GGATGTCCATAAGTTCTACCATGATC 59.124 42.308 0.00 0.00 35.64 2.92
1268 1382 7.801104 TGGTACATTGACATCTATAACCACAT 58.199 34.615 0.00 0.00 29.85 3.21
1704 1820 1.210478 ACCTCAAGGGATGTTCGATGG 59.790 52.381 0.29 0.00 40.27 3.51
1799 1915 1.224075 CTGATGCCATGAAGCGTAGG 58.776 55.000 0.00 0.00 34.65 3.18
2005 2121 2.159627 GGTTACAGTGCTTCCGTTGATG 59.840 50.000 0.00 0.00 0.00 3.07
2085 2366 2.306805 ACCTCCATCAGCAATGAAGTCA 59.693 45.455 0.96 0.00 37.59 3.41
2197 2487 3.535280 ACAAATGGGTGCGAAAAGTTT 57.465 38.095 0.00 0.00 0.00 2.66
2199 2489 5.012328 ACAAATGGGTGCGAAAAGTTTAA 57.988 34.783 0.00 0.00 0.00 1.52
2208 2498 4.205385 GTGCGAAAAGTTTAACATTTGCGA 59.795 37.500 17.83 8.24 39.34 5.10
2212 2502 5.778345 CGAAAAGTTTAACATTTGCGAATGC 59.222 36.000 23.99 9.39 45.25 3.56
2250 2544 8.966868 ACATACATTATGACTTGTTAAAAGGGG 58.033 33.333 0.00 0.00 39.45 4.79
2261 2555 6.609616 ACTTGTTAAAAGGGGAGAAAACATCA 59.390 34.615 0.00 0.00 0.00 3.07
2270 2564 5.251700 AGGGGAGAAAACATCAGACAAGTAT 59.748 40.000 0.00 0.00 0.00 2.12
2384 2678 7.220108 GTCTAGCGAGTGAAAACACAAAATTTT 59.780 33.333 0.00 0.00 31.96 1.82
2477 2785 0.108992 TCCGAAGAAACATCGACCCG 60.109 55.000 0.00 0.00 42.76 5.28
2506 2814 3.497763 CCTCTGTACAAACATTGACCCCA 60.498 47.826 0.00 0.00 34.37 4.96
2517 2825 1.828979 TTGACCCCAAACGCTATTCC 58.171 50.000 0.00 0.00 0.00 3.01
2771 3080 8.198109 GCGGAATATATCTACATACAGGAACAT 58.802 37.037 0.00 0.00 0.00 2.71
2804 3113 6.390721 TCGAGGAAGAATCAAGTTACTGAAG 58.609 40.000 0.00 0.00 0.00 3.02
2805 3114 6.208797 TCGAGGAAGAATCAAGTTACTGAAGA 59.791 38.462 0.00 0.00 0.00 2.87
2806 3115 6.529829 CGAGGAAGAATCAAGTTACTGAAGAG 59.470 42.308 0.00 0.00 0.00 2.85
2807 3116 7.546250 AGGAAGAATCAAGTTACTGAAGAGA 57.454 36.000 0.00 0.00 0.00 3.10
2808 3117 7.967908 AGGAAGAATCAAGTTACTGAAGAGAA 58.032 34.615 0.00 0.00 0.00 2.87
2947 3256 4.308458 CCCGCTTGACCGACCACA 62.308 66.667 0.00 0.00 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 8.927411 CCATCCTAGGGTTTTGAATTAAATCAT 58.073 33.333 9.46 0.00 0.00 2.45
44 45 7.147742 GCCATCCTAGGGTTTTGAATTAAATCA 60.148 37.037 9.46 0.00 0.00 2.57
45 46 7.210174 GCCATCCTAGGGTTTTGAATTAAATC 58.790 38.462 9.46 0.00 0.00 2.17
46 47 6.099701 GGCCATCCTAGGGTTTTGAATTAAAT 59.900 38.462 9.46 0.00 0.00 1.40
47 48 5.423931 GGCCATCCTAGGGTTTTGAATTAAA 59.576 40.000 9.46 0.00 0.00 1.52
48 49 4.959839 GGCCATCCTAGGGTTTTGAATTAA 59.040 41.667 9.46 0.00 0.00 1.40
49 50 4.231890 AGGCCATCCTAGGGTTTTGAATTA 59.768 41.667 9.46 0.00 42.06 1.40
50 51 3.012844 AGGCCATCCTAGGGTTTTGAATT 59.987 43.478 9.46 0.00 42.06 2.17
51 52 2.587307 AGGCCATCCTAGGGTTTTGAAT 59.413 45.455 9.46 0.00 42.06 2.57
52 53 2.000048 AGGCCATCCTAGGGTTTTGAA 59.000 47.619 9.46 0.00 42.06 2.69
53 54 1.681229 AGGCCATCCTAGGGTTTTGA 58.319 50.000 9.46 0.00 42.06 2.69
62 63 3.435026 GCACATTTTCCTAGGCCATCCTA 60.435 47.826 5.01 0.00 43.91 2.94
63 64 2.687914 GCACATTTTCCTAGGCCATCCT 60.688 50.000 5.01 0.00 46.57 3.24
64 65 1.683385 GCACATTTTCCTAGGCCATCC 59.317 52.381 5.01 0.00 0.00 3.51
65 66 2.099756 GTGCACATTTTCCTAGGCCATC 59.900 50.000 13.17 0.00 0.00 3.51
66 67 2.102578 GTGCACATTTTCCTAGGCCAT 58.897 47.619 13.17 0.00 0.00 4.40
67 68 1.544724 GTGCACATTTTCCTAGGCCA 58.455 50.000 13.17 0.00 0.00 5.36
68 69 0.817654 GGTGCACATTTTCCTAGGCC 59.182 55.000 20.43 0.00 0.00 5.19
69 70 1.544724 TGGTGCACATTTTCCTAGGC 58.455 50.000 20.43 0.00 0.00 3.93
79 80 1.693062 TCTGCCAAAAATGGTGCACAT 59.307 42.857 20.43 7.56 43.07 3.21
80 81 1.068895 CTCTGCCAAAAATGGTGCACA 59.931 47.619 20.43 5.24 0.00 4.57
81 82 1.606224 CCTCTGCCAAAAATGGTGCAC 60.606 52.381 8.80 8.80 0.00 4.57
82 83 0.680618 CCTCTGCCAAAAATGGTGCA 59.319 50.000 0.00 0.00 0.00 4.57
83 84 0.681175 ACCTCTGCCAAAAATGGTGC 59.319 50.000 0.00 0.00 0.00 5.01
84 85 2.629617 AGAACCTCTGCCAAAAATGGTG 59.370 45.455 0.00 0.00 0.00 4.17
85 86 2.629617 CAGAACCTCTGCCAAAAATGGT 59.370 45.455 0.00 0.00 37.72 3.55
86 87 2.892852 TCAGAACCTCTGCCAAAAATGG 59.107 45.455 0.00 0.00 43.95 3.16
87 88 4.301628 GTTCAGAACCTCTGCCAAAAATG 58.698 43.478 1.29 0.00 43.95 2.32
88 89 4.590850 GTTCAGAACCTCTGCCAAAAAT 57.409 40.909 1.29 0.00 43.95 1.82
101 102 6.421801 CCATCATTTTTGTCTTGGTTCAGAAC 59.578 38.462 4.52 4.52 0.00 3.01
102 103 6.462768 CCCATCATTTTTGTCTTGGTTCAGAA 60.463 38.462 0.00 0.00 0.00 3.02
103 104 5.010922 CCCATCATTTTTGTCTTGGTTCAGA 59.989 40.000 0.00 0.00 0.00 3.27
104 105 5.232463 CCCATCATTTTTGTCTTGGTTCAG 58.768 41.667 0.00 0.00 0.00 3.02
105 106 4.502950 GCCCATCATTTTTGTCTTGGTTCA 60.503 41.667 0.00 0.00 0.00 3.18
106 107 3.996363 GCCCATCATTTTTGTCTTGGTTC 59.004 43.478 0.00 0.00 0.00 3.62
107 108 3.390639 TGCCCATCATTTTTGTCTTGGTT 59.609 39.130 0.00 0.00 0.00 3.67
108 109 2.971330 TGCCCATCATTTTTGTCTTGGT 59.029 40.909 0.00 0.00 0.00 3.67
109 110 3.681593 TGCCCATCATTTTTGTCTTGG 57.318 42.857 0.00 0.00 0.00 3.61
119 120 3.389002 GCCCTTCTAAAATGCCCATCATT 59.611 43.478 0.00 0.00 46.82 2.57
120 121 2.967887 GCCCTTCTAAAATGCCCATCAT 59.032 45.455 0.00 0.00 36.87 2.45
121 122 2.292126 TGCCCTTCTAAAATGCCCATCA 60.292 45.455 0.00 0.00 0.00 3.07
122 123 2.387757 TGCCCTTCTAAAATGCCCATC 58.612 47.619 0.00 0.00 0.00 3.51
123 124 2.548464 TGCCCTTCTAAAATGCCCAT 57.452 45.000 0.00 0.00 0.00 4.00
124 125 2.548464 ATGCCCTTCTAAAATGCCCA 57.452 45.000 0.00 0.00 0.00 5.36
125 126 3.197549 TGAAATGCCCTTCTAAAATGCCC 59.802 43.478 0.00 0.00 0.00 5.36
126 127 4.436332 CTGAAATGCCCTTCTAAAATGCC 58.564 43.478 0.00 0.00 0.00 4.40
127 128 4.081476 ACCTGAAATGCCCTTCTAAAATGC 60.081 41.667 0.00 0.00 0.00 3.56
128 129 5.665916 ACCTGAAATGCCCTTCTAAAATG 57.334 39.130 0.00 0.00 0.00 2.32
129 130 5.779771 TGAACCTGAAATGCCCTTCTAAAAT 59.220 36.000 0.00 0.00 0.00 1.82
130 131 5.144100 TGAACCTGAAATGCCCTTCTAAAA 58.856 37.500 0.00 0.00 0.00 1.52
131 132 4.735369 TGAACCTGAAATGCCCTTCTAAA 58.265 39.130 0.00 0.00 0.00 1.85
132 133 4.380843 TGAACCTGAAATGCCCTTCTAA 57.619 40.909 0.00 0.00 0.00 2.10
133 134 4.591321 ATGAACCTGAAATGCCCTTCTA 57.409 40.909 0.00 0.00 0.00 2.10
134 135 2.978156 TGAACCTGAAATGCCCTTCT 57.022 45.000 0.00 0.00 0.00 2.85
135 136 3.511146 TCAATGAACCTGAAATGCCCTTC 59.489 43.478 0.00 0.00 0.00 3.46
136 137 3.509442 TCAATGAACCTGAAATGCCCTT 58.491 40.909 0.00 0.00 0.00 3.95
137 138 3.173953 TCAATGAACCTGAAATGCCCT 57.826 42.857 0.00 0.00 0.00 5.19
138 139 3.959535 TTCAATGAACCTGAAATGCCC 57.040 42.857 0.00 0.00 29.93 5.36
139 140 6.806388 ATTTTTCAATGAACCTGAAATGCC 57.194 33.333 0.00 0.00 41.23 4.40
175 176 4.384208 CCAGTCCCTATGAAACCAACTAGG 60.384 50.000 0.00 0.00 45.67 3.02
176 177 4.384208 CCCAGTCCCTATGAAACCAACTAG 60.384 50.000 0.00 0.00 0.00 2.57
177 178 3.521937 CCCAGTCCCTATGAAACCAACTA 59.478 47.826 0.00 0.00 0.00 2.24
178 179 2.308866 CCCAGTCCCTATGAAACCAACT 59.691 50.000 0.00 0.00 0.00 3.16
179 180 2.620627 CCCCAGTCCCTATGAAACCAAC 60.621 54.545 0.00 0.00 0.00 3.77
180 181 1.638589 CCCCAGTCCCTATGAAACCAA 59.361 52.381 0.00 0.00 0.00 3.67
181 182 1.295020 CCCCAGTCCCTATGAAACCA 58.705 55.000 0.00 0.00 0.00 3.67
182 183 0.551396 CCCCCAGTCCCTATGAAACC 59.449 60.000 0.00 0.00 0.00 3.27
183 184 1.296002 ACCCCCAGTCCCTATGAAAC 58.704 55.000 0.00 0.00 0.00 2.78
184 185 1.920351 GAACCCCCAGTCCCTATGAAA 59.080 52.381 0.00 0.00 0.00 2.69
185 186 1.082194 AGAACCCCCAGTCCCTATGAA 59.918 52.381 0.00 0.00 0.00 2.57
186 187 0.722676 AGAACCCCCAGTCCCTATGA 59.277 55.000 0.00 0.00 0.00 2.15
187 188 0.839946 CAGAACCCCCAGTCCCTATG 59.160 60.000 0.00 0.00 0.00 2.23
188 189 0.421904 ACAGAACCCCCAGTCCCTAT 59.578 55.000 0.00 0.00 0.00 2.57
189 190 0.252558 GACAGAACCCCCAGTCCCTA 60.253 60.000 0.00 0.00 0.00 3.53
190 191 1.539124 GACAGAACCCCCAGTCCCT 60.539 63.158 0.00 0.00 0.00 4.20
191 192 1.208165 ATGACAGAACCCCCAGTCCC 61.208 60.000 0.00 0.00 0.00 4.46
192 193 0.253327 GATGACAGAACCCCCAGTCC 59.747 60.000 0.00 0.00 0.00 3.85
193 194 0.253327 GGATGACAGAACCCCCAGTC 59.747 60.000 0.00 0.00 0.00 3.51
194 195 1.208165 GGGATGACAGAACCCCCAGT 61.208 60.000 0.00 0.00 37.85 4.00
195 196 1.609783 GGGATGACAGAACCCCCAG 59.390 63.158 0.00 0.00 37.85 4.45
196 197 3.835134 GGGATGACAGAACCCCCA 58.165 61.111 0.00 0.00 37.85 4.96
199 200 2.291540 TGAAATGGGGATGACAGAACCC 60.292 50.000 5.21 5.21 43.64 4.11
200 201 3.085952 TGAAATGGGGATGACAGAACC 57.914 47.619 0.00 0.00 0.00 3.62
201 202 4.082125 ACTTGAAATGGGGATGACAGAAC 58.918 43.478 0.00 0.00 0.00 3.01
202 203 4.387026 ACTTGAAATGGGGATGACAGAA 57.613 40.909 0.00 0.00 0.00 3.02
203 204 4.387026 AACTTGAAATGGGGATGACAGA 57.613 40.909 0.00 0.00 0.00 3.41
204 205 4.768968 AGAAACTTGAAATGGGGATGACAG 59.231 41.667 0.00 0.00 0.00 3.51
205 206 4.523943 CAGAAACTTGAAATGGGGATGACA 59.476 41.667 0.00 0.00 0.00 3.58
206 207 4.766891 TCAGAAACTTGAAATGGGGATGAC 59.233 41.667 0.00 0.00 0.00 3.06
207 208 4.996793 TCAGAAACTTGAAATGGGGATGA 58.003 39.130 0.00 0.00 0.00 2.92
208 209 5.477984 TCTTCAGAAACTTGAAATGGGGATG 59.522 40.000 0.00 0.00 36.69 3.51
209 210 5.644188 TCTTCAGAAACTTGAAATGGGGAT 58.356 37.500 0.00 0.00 36.69 3.85
210 211 5.060427 TCTTCAGAAACTTGAAATGGGGA 57.940 39.130 0.00 0.00 36.69 4.81
211 212 5.789643 TTCTTCAGAAACTTGAAATGGGG 57.210 39.130 0.00 0.00 36.69 4.96
212 213 7.042797 TCTTTCTTCAGAAACTTGAAATGGG 57.957 36.000 0.00 0.00 38.94 4.00
213 214 7.710896 ACTCTTTCTTCAGAAACTTGAAATGG 58.289 34.615 0.00 0.00 38.94 3.16
217 218 9.226606 TGTTTACTCTTTCTTCAGAAACTTGAA 57.773 29.630 0.00 0.00 38.94 2.69
218 219 8.786826 TGTTTACTCTTTCTTCAGAAACTTGA 57.213 30.769 0.00 0.00 38.94 3.02
219 220 9.443283 CATGTTTACTCTTTCTTCAGAAACTTG 57.557 33.333 0.00 0.00 38.94 3.16
220 221 9.396022 TCATGTTTACTCTTTCTTCAGAAACTT 57.604 29.630 0.00 0.00 38.94 2.66
221 222 8.964476 TCATGTTTACTCTTTCTTCAGAAACT 57.036 30.769 0.00 0.00 38.94 2.66
222 223 9.604626 CATCATGTTTACTCTTTCTTCAGAAAC 57.395 33.333 0.00 0.00 38.94 2.78
223 224 8.292448 GCATCATGTTTACTCTTTCTTCAGAAA 58.708 33.333 2.07 2.07 41.29 2.52
224 225 7.445096 TGCATCATGTTTACTCTTTCTTCAGAA 59.555 33.333 0.00 0.00 0.00 3.02
225 226 6.936335 TGCATCATGTTTACTCTTTCTTCAGA 59.064 34.615 0.00 0.00 0.00 3.27
226 227 7.137490 TGCATCATGTTTACTCTTTCTTCAG 57.863 36.000 0.00 0.00 0.00 3.02
227 228 7.013178 TGTTGCATCATGTTTACTCTTTCTTCA 59.987 33.333 0.00 0.00 0.00 3.02
228 229 7.324616 GTGTTGCATCATGTTTACTCTTTCTTC 59.675 37.037 0.00 0.00 0.00 2.87
229 230 7.013655 AGTGTTGCATCATGTTTACTCTTTCTT 59.986 33.333 0.00 0.00 0.00 2.52
230 231 6.488006 AGTGTTGCATCATGTTTACTCTTTCT 59.512 34.615 0.00 0.00 0.00 2.52
231 232 6.580041 CAGTGTTGCATCATGTTTACTCTTTC 59.420 38.462 0.00 0.00 0.00 2.62
232 233 6.039717 ACAGTGTTGCATCATGTTTACTCTTT 59.960 34.615 0.00 0.00 0.00 2.52
233 234 5.532406 ACAGTGTTGCATCATGTTTACTCTT 59.468 36.000 0.00 0.00 0.00 2.85
234 235 5.065914 ACAGTGTTGCATCATGTTTACTCT 58.934 37.500 0.00 0.00 0.00 3.24
235 236 5.362556 ACAGTGTTGCATCATGTTTACTC 57.637 39.130 0.00 0.00 0.00 2.59
236 237 6.875948 TTACAGTGTTGCATCATGTTTACT 57.124 33.333 0.00 0.00 0.00 2.24
237 238 6.033831 GCATTACAGTGTTGCATCATGTTTAC 59.966 38.462 13.82 0.00 36.40 2.01
238 239 6.092092 GCATTACAGTGTTGCATCATGTTTA 58.908 36.000 13.82 7.28 36.40 2.01
239 240 4.925054 GCATTACAGTGTTGCATCATGTTT 59.075 37.500 13.82 4.95 36.40 2.83
240 241 4.022155 TGCATTACAGTGTTGCATCATGTT 60.022 37.500 16.78 1.17 41.18 2.71
241 242 3.506844 TGCATTACAGTGTTGCATCATGT 59.493 39.130 16.78 8.84 41.18 3.21
242 243 4.099380 TGCATTACAGTGTTGCATCATG 57.901 40.909 16.78 5.13 41.18 3.07
248 249 3.837213 AGTCATGCATTACAGTGTTGC 57.163 42.857 13.29 12.16 36.91 4.17
249 250 4.633126 AGCTAGTCATGCATTACAGTGTTG 59.367 41.667 13.29 0.00 0.00 3.33
250 251 4.836825 AGCTAGTCATGCATTACAGTGTT 58.163 39.130 13.29 0.00 0.00 3.32
251 252 4.478206 AGCTAGTCATGCATTACAGTGT 57.522 40.909 13.29 0.00 0.00 3.55
252 253 4.987285 CCTAGCTAGTCATGCATTACAGTG 59.013 45.833 19.31 4.16 0.00 3.66
253 254 4.039730 CCCTAGCTAGTCATGCATTACAGT 59.960 45.833 19.31 0.00 0.00 3.55
254 255 4.039730 ACCCTAGCTAGTCATGCATTACAG 59.960 45.833 19.31 9.24 0.00 2.74
255 256 3.967326 ACCCTAGCTAGTCATGCATTACA 59.033 43.478 19.31 0.00 0.00 2.41
256 257 4.202264 ACACCCTAGCTAGTCATGCATTAC 60.202 45.833 19.31 2.65 0.00 1.89
257 258 3.967326 ACACCCTAGCTAGTCATGCATTA 59.033 43.478 19.31 0.00 0.00 1.90
258 259 2.774234 ACACCCTAGCTAGTCATGCATT 59.226 45.455 19.31 0.00 0.00 3.56
259 260 2.103771 CACACCCTAGCTAGTCATGCAT 59.896 50.000 19.31 0.00 0.00 3.96
260 261 1.482182 CACACCCTAGCTAGTCATGCA 59.518 52.381 19.31 0.00 0.00 3.96
261 262 1.757118 TCACACCCTAGCTAGTCATGC 59.243 52.381 19.31 0.00 0.00 4.06
262 263 2.760650 TGTCACACCCTAGCTAGTCATG 59.239 50.000 19.31 15.31 0.00 3.07
263 264 3.101643 TGTCACACCCTAGCTAGTCAT 57.898 47.619 19.31 1.55 0.00 3.06
264 265 2.597578 TGTCACACCCTAGCTAGTCA 57.402 50.000 19.31 4.53 0.00 3.41
265 266 3.195825 ACATTGTCACACCCTAGCTAGTC 59.804 47.826 19.31 2.23 0.00 2.59
266 267 3.173965 ACATTGTCACACCCTAGCTAGT 58.826 45.455 19.31 0.00 0.00 2.57
267 268 3.449018 AGACATTGTCACACCCTAGCTAG 59.551 47.826 18.57 14.20 34.60 3.42
268 269 3.441101 AGACATTGTCACACCCTAGCTA 58.559 45.455 18.57 0.00 34.60 3.32
269 270 2.234908 GAGACATTGTCACACCCTAGCT 59.765 50.000 18.57 0.00 34.60 3.32
270 271 2.622436 GAGACATTGTCACACCCTAGC 58.378 52.381 18.57 0.00 34.60 3.42
271 272 2.834549 AGGAGACATTGTCACACCCTAG 59.165 50.000 18.57 0.00 34.60 3.02
272 273 2.832129 GAGGAGACATTGTCACACCCTA 59.168 50.000 18.57 0.00 34.60 3.53
273 274 1.625818 GAGGAGACATTGTCACACCCT 59.374 52.381 18.57 16.65 34.60 4.34
274 275 1.625818 AGAGGAGACATTGTCACACCC 59.374 52.381 18.57 12.81 34.60 4.61
275 276 3.409026 AAGAGGAGACATTGTCACACC 57.591 47.619 18.57 16.58 34.60 4.16
276 277 6.473397 CTAAAAGAGGAGACATTGTCACAC 57.527 41.667 18.57 9.56 34.60 3.82
278 279 8.944113 TCGCCTAAAAGAGGAGACATTGTCAC 62.944 46.154 18.57 12.19 46.25 3.67
279 280 7.022574 TCGCCTAAAAGAGGAGACATTGTCA 62.023 44.000 18.57 0.00 46.25 3.58
280 281 4.620803 TCGCCTAAAAGAGGAGACATTGTC 60.621 45.833 8.82 8.82 46.25 3.18
281 282 3.260884 TCGCCTAAAAGAGGAGACATTGT 59.739 43.478 0.00 0.00 46.25 2.71
282 283 3.861840 TCGCCTAAAAGAGGAGACATTG 58.138 45.455 0.00 0.00 46.25 2.82
283 284 3.680196 GCTCGCCTAAAAGAGGAGACATT 60.680 47.826 0.00 0.00 46.25 2.71
364 365 0.605589 ACCCACGAAGCCTACAAAGC 60.606 55.000 0.00 0.00 0.00 3.51
386 387 4.622456 CGCACCAAACGCCCACAC 62.622 66.667 0.00 0.00 0.00 3.82
405 406 1.079336 GAGTCACAGCGTTACCCCC 60.079 63.158 0.00 0.00 0.00 5.40
423 424 2.095059 GCATAAACTTGAGTGTGGCCAG 60.095 50.000 5.11 0.00 0.00 4.85
427 428 2.151202 ACGGCATAAACTTGAGTGTGG 58.849 47.619 0.00 0.00 0.00 4.17
441 448 0.732571 CGCCAATTTACAGACGGCAT 59.267 50.000 0.00 0.00 43.13 4.40
457 464 2.097038 CACAGAGTACTGCAGCGCC 61.097 63.158 15.27 1.18 46.95 6.53
474 481 9.535170 CTACAAGATCTTATATTCCTACTCCCA 57.465 37.037 7.86 0.00 0.00 4.37
496 528 8.740906 CCTCTGAAAACTAAGTGATCTACTACA 58.259 37.037 0.00 0.00 39.18 2.74
608 640 6.370994 ACAATGATCAGAGCTCTACACAAAAG 59.629 38.462 17.75 11.88 0.00 2.27
620 661 4.005650 TCCAGACAAACAATGATCAGAGC 58.994 43.478 0.09 0.00 0.00 4.09
632 673 3.600388 ACGAGAATCCATCCAGACAAAC 58.400 45.455 0.00 0.00 0.00 2.93
634 675 2.831526 TGACGAGAATCCATCCAGACAA 59.168 45.455 0.00 0.00 0.00 3.18
679 720 1.073923 CTCCAAAGTACCAGCCCAACT 59.926 52.381 0.00 0.00 0.00 3.16
746 787 2.614829 TCGGCTTCCTACTAAATGGC 57.385 50.000 0.00 0.00 0.00 4.40
764 805 0.538118 TACACAAGGGTACGGGCATC 59.462 55.000 0.00 0.00 0.00 3.91
765 806 0.539986 CTACACAAGGGTACGGGCAT 59.460 55.000 0.00 0.00 0.00 4.40
903 1014 4.343526 TGTTGCCAGAAAGGAAAATGCTTA 59.656 37.500 0.00 0.00 36.38 3.09
906 1017 3.110447 TGTTGCCAGAAAGGAAAATGC 57.890 42.857 0.00 0.00 36.38 3.56
985 1096 2.214387 GCCATTGCTGCATAAGGAAC 57.786 50.000 16.54 0.34 39.28 3.62
1050 1161 7.926555 ACTAATATGGAGAAAATCACTACCACG 59.073 37.037 0.00 0.00 0.00 4.94
1099 1210 4.536765 ACCAATCCTGATCAACAATACCC 58.463 43.478 0.00 0.00 0.00 3.69
1104 1216 4.344679 AGCAAAACCAATCCTGATCAACAA 59.655 37.500 0.00 0.00 0.00 2.83
1121 1233 9.995003 AAATACATTTCCAATCTGTAAGCAAAA 57.005 25.926 0.00 0.00 0.00 2.44
1143 1257 7.768807 ATTTTGTAGTAGTGTTGGGCAAATA 57.231 32.000 0.00 0.00 0.00 1.40
1204 1318 5.008019 CCGACCAAGAATACTTTGATCATGG 59.992 44.000 0.00 0.00 37.81 3.66
1211 1325 3.127030 GGCTTCCGACCAAGAATACTTTG 59.873 47.826 0.00 0.00 33.70 2.77
1268 1382 2.135139 CTGCAGAGAACTTACACGCAA 58.865 47.619 8.42 0.00 0.00 4.85
1300 1414 7.031226 ACCGAAATGGAAAGATCATACAATG 57.969 36.000 0.00 0.00 42.00 2.82
1374 1488 6.224584 TCACATTTCAACACGTATGGTCTAA 58.775 36.000 0.00 0.00 0.00 2.10
1704 1820 7.090173 GGCTGAGAATCTACATTGTCTATCTC 58.910 42.308 11.73 11.73 34.12 2.75
1799 1915 4.084485 GCAAGGAAGAACGACTGAGTAAAC 60.084 45.833 0.00 0.00 0.00 2.01
1910 2026 2.421619 GAGCAACTCTGAGGGTGAAAG 58.578 52.381 9.85 0.00 0.00 2.62
1988 2104 0.396435 TCCATCAACGGAAGCACTGT 59.604 50.000 0.00 0.00 40.17 3.55
2005 2121 9.265901 CGATATCATCATACCCAGAAATAATCC 57.734 37.037 3.12 0.00 0.00 3.01
2197 2487 3.441922 TGCTAAGGCATTCGCAAATGTTA 59.558 39.130 7.92 0.00 44.28 2.41
2199 2489 1.818060 TGCTAAGGCATTCGCAAATGT 59.182 42.857 7.92 0.00 44.28 2.71
2212 2502 9.494271 AGTCATAATGTATGTACAATGCTAAGG 57.506 33.333 0.00 0.00 39.99 2.69
2250 2544 9.209175 AGTTGTATACTTGTCTGATGTTTTCTC 57.791 33.333 4.17 0.00 31.29 2.87
2477 2785 6.092807 GTCAATGTTTGTACAGAGGGAGAATC 59.907 42.308 0.00 0.00 37.77 2.52
2506 2814 2.423577 ACAAAGAGCGGAATAGCGTTT 58.576 42.857 0.00 0.00 43.00 3.60
2517 2825 2.009774 CAGGGGTCAATACAAAGAGCG 58.990 52.381 0.00 0.00 33.28 5.03
2551 2859 5.951747 AGGCTGCAAATATTCCTTCTAACAA 59.048 36.000 0.50 0.00 0.00 2.83
2771 3080 4.017126 TGATTCTTCCTCGAGCTTACTGA 58.983 43.478 6.99 0.00 0.00 3.41
2883 3192 1.289109 GACGCACAACACGCCTGTAT 61.289 55.000 0.00 0.00 0.00 2.29
2947 3256 0.899717 ATGTTGGCCAAGCGGTTGAT 60.900 50.000 27.92 9.84 35.46 2.57


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

AutoCloner maintained by Alex Coulton.