Multiple sequence alignment - TraesCS4A01G183900

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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 TraesCS4A01G183900 chr4A 100.000 2948 0 0 1 2948 462206056 462203109 0.000000e+00 5445.0
1 TraesCS4A01G183900 chr4A 92.143 1260 52 16 1621 2876 611199281 611200497 0.000000e+00 1735.0
2 TraesCS4A01G183900 chr4A 91.026 78 7 0 1506 1583 27665579 27665656 4.020000e-19 106.0
3 TraesCS4A01G183900 chr4D 94.283 1959 71 19 538 2466 115120955 115122902 0.000000e+00 2959.0
4 TraesCS4A01G183900 chr4D 91.017 1258 49 31 1621 2876 447979498 447980693 0.000000e+00 1639.0
5 TraesCS4A01G183900 chr4D 94.200 500 28 1 2450 2948 115123431 115123930 0.000000e+00 761.0
6 TraesCS4A01G183900 chr4D 90.598 117 9 1 1 117 115068246 115068360 1.410000e-33 154.0
7 TraesCS4A01G183900 chr4B 93.773 1606 57 15 381 1965 175560538 175562121 0.000000e+00 2372.0
8 TraesCS4A01G183900 chr4B 94.989 938 35 3 2023 2948 175562146 175563083 0.000000e+00 1461.0
9 TraesCS4A01G183900 chr4B 94.872 117 6 0 1 117 175560417 175560533 1.800000e-42 183.0
10 TraesCS4A01G183900 chr2B 93.243 1258 46 13 1621 2876 654362830 654361610 0.000000e+00 1816.0
11 TraesCS4A01G183900 chr2B 91.398 186 16 0 197 382 655527033 655527218 3.770000e-64 255.0
12 TraesCS4A01G183900 chr2B 90.741 54 5 0 1366 1419 66199483 66199430 4.080000e-09 73.1
13 TraesCS4A01G183900 chr3D 90.547 1407 71 19 1553 2948 554391669 554393024 0.000000e+00 1805.0
14 TraesCS4A01G183900 chr7B 92.613 1259 50 20 1621 2876 686929106 686930324 0.000000e+00 1770.0
15 TraesCS4A01G183900 chr7B 91.712 917 55 10 1553 2456 109172678 109171770 0.000000e+00 1253.0
16 TraesCS4A01G183900 chr7B 91.586 309 20 4 2641 2948 109180132 109180435 3.510000e-114 422.0
17 TraesCS4A01G183900 chr7B 90.659 182 16 1 200 381 487043768 487043588 1.060000e-59 241.0
18 TraesCS4A01G183900 chr5B 91.905 1260 57 13 1621 2876 614981676 614980458 0.000000e+00 1720.0
19 TraesCS4A01G183900 chr5B 82.450 604 73 19 1327 1919 241200559 241199978 5.670000e-137 497.0
20 TraesCS4A01G183900 chr6D 89.635 1341 54 26 1553 2876 163352695 163353967 0.000000e+00 1628.0
21 TraesCS4A01G183900 chr2A 93.472 674 27 10 1621 2293 711070410 711071067 0.000000e+00 985.0
22 TraesCS4A01G183900 chr2A 91.809 586 25 7 2292 2876 711071160 711071723 0.000000e+00 795.0
23 TraesCS4A01G183900 chr2A 89.000 200 20 2 197 396 718829210 718829407 2.270000e-61 246.0
24 TraesCS4A01G183900 chr2A 90.374 187 17 1 197 383 756821928 756822113 8.160000e-61 244.0
25 TraesCS4A01G183900 chr5A 77.938 970 124 51 1001 1910 291605328 291604389 9.360000e-145 523.0
26 TraesCS4A01G183900 chr5A 90.811 185 16 1 197 381 523588717 523588900 2.270000e-61 246.0
27 TraesCS4A01G183900 chr5A 90.659 182 16 1 200 381 83550058 83550238 1.060000e-59 241.0
28 TraesCS4A01G183900 chr6B 92.350 183 13 1 200 382 564063818 564063637 2.910000e-65 259.0
29 TraesCS4A01G183900 chr1D 90.860 186 15 2 197 382 213551096 213551279 6.310000e-62 248.0
30 TraesCS4A01G183900 chr1A 90.811 185 16 1 197 381 583603937 583603754 2.270000e-61 246.0


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 TraesCS4A01G183900 chr4A 462203109 462206056 2947 True 5445.000000 5445 100.000000 1 2948 1 chr4A.!!$R1 2947
1 TraesCS4A01G183900 chr4A 611199281 611200497 1216 False 1735.000000 1735 92.143000 1621 2876 1 chr4A.!!$F2 1255
2 TraesCS4A01G183900 chr4D 115120955 115123930 2975 False 1860.000000 2959 94.241500 538 2948 2 chr4D.!!$F3 2410
3 TraesCS4A01G183900 chr4D 447979498 447980693 1195 False 1639.000000 1639 91.017000 1621 2876 1 chr4D.!!$F2 1255
4 TraesCS4A01G183900 chr4B 175560417 175563083 2666 False 1338.666667 2372 94.544667 1 2948 3 chr4B.!!$F1 2947
5 TraesCS4A01G183900 chr2B 654361610 654362830 1220 True 1816.000000 1816 93.243000 1621 2876 1 chr2B.!!$R2 1255
6 TraesCS4A01G183900 chr3D 554391669 554393024 1355 False 1805.000000 1805 90.547000 1553 2948 1 chr3D.!!$F1 1395
7 TraesCS4A01G183900 chr7B 686929106 686930324 1218 False 1770.000000 1770 92.613000 1621 2876 1 chr7B.!!$F2 1255
8 TraesCS4A01G183900 chr7B 109171770 109172678 908 True 1253.000000 1253 91.712000 1553 2456 1 chr7B.!!$R1 903
9 TraesCS4A01G183900 chr5B 614980458 614981676 1218 True 1720.000000 1720 91.905000 1621 2876 1 chr5B.!!$R2 1255
10 TraesCS4A01G183900 chr5B 241199978 241200559 581 True 497.000000 497 82.450000 1327 1919 1 chr5B.!!$R1 592
11 TraesCS4A01G183900 chr6D 163352695 163353967 1272 False 1628.000000 1628 89.635000 1553 2876 1 chr6D.!!$F1 1323
12 TraesCS4A01G183900 chr2A 711070410 711071723 1313 False 890.000000 985 92.640500 1621 2876 2 chr2A.!!$F3 1255
13 TraesCS4A01G183900 chr5A 291604389 291605328 939 True 523.000000 523 77.938000 1001 1910 1 chr5A.!!$R1 909

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
133 134 0.034960 CTCCTGTCCCACTCTCTCGA 60.035 60.0 0.00 0.0 0.00 4.04 F
453 456 0.109272 CTCTCGAGCCAACGTGCTAA 60.109 55.0 7.81 0.0 42.95 3.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1923 2041 1.303155 GGCAGGGGCAGATGATAGC 60.303 63.158 0.0 0.0 43.71 2.97 R
2323 2583 1.819632 GCAGACACTATTGCCCCCG 60.820 63.158 0.0 0.0 34.28 5.73 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
62 63 0.618968 AAACGCTCCCTCCCTGATCT 60.619 55.000 0.00 0.00 0.00 2.75
84 85 9.877178 GATCTAGAATCACCTTCAAAGAGTAAA 57.123 33.333 0.00 0.00 36.24 2.01
86 87 8.871125 TCTAGAATCACCTTCAAAGAGTAAAGT 58.129 33.333 0.00 0.00 36.24 2.66
94 95 8.713271 CACCTTCAAAGAGTAAAGTTAGATGAC 58.287 37.037 0.00 0.00 0.00 3.06
117 118 2.131183 GATGAGAATAGCACGCACTCC 58.869 52.381 0.00 0.00 0.00 3.85
118 119 1.186200 TGAGAATAGCACGCACTCCT 58.814 50.000 0.00 0.00 0.00 3.69
119 120 1.134995 TGAGAATAGCACGCACTCCTG 60.135 52.381 0.00 0.00 0.00 3.86
120 121 0.898320 AGAATAGCACGCACTCCTGT 59.102 50.000 0.00 0.00 0.00 4.00
121 122 1.134965 AGAATAGCACGCACTCCTGTC 60.135 52.381 0.00 0.00 0.00 3.51
122 123 0.108138 AATAGCACGCACTCCTGTCC 60.108 55.000 0.00 0.00 0.00 4.02
123 124 1.961180 ATAGCACGCACTCCTGTCCC 61.961 60.000 0.00 0.00 0.00 4.46
124 125 4.314440 GCACGCACTCCTGTCCCA 62.314 66.667 0.00 0.00 0.00 4.37
125 126 2.357517 CACGCACTCCTGTCCCAC 60.358 66.667 0.00 0.00 0.00 4.61
126 127 2.524394 ACGCACTCCTGTCCCACT 60.524 61.111 0.00 0.00 0.00 4.00
127 128 2.262915 CGCACTCCTGTCCCACTC 59.737 66.667 0.00 0.00 0.00 3.51
128 129 2.279069 CGCACTCCTGTCCCACTCT 61.279 63.158 0.00 0.00 0.00 3.24
129 130 1.594310 GCACTCCTGTCCCACTCTC 59.406 63.158 0.00 0.00 0.00 3.20
130 131 0.902516 GCACTCCTGTCCCACTCTCT 60.903 60.000 0.00 0.00 0.00 3.10
131 132 1.181786 CACTCCTGTCCCACTCTCTC 58.818 60.000 0.00 0.00 0.00 3.20
132 133 0.322997 ACTCCTGTCCCACTCTCTCG 60.323 60.000 0.00 0.00 0.00 4.04
133 134 0.034960 CTCCTGTCCCACTCTCTCGA 60.035 60.000 0.00 0.00 0.00 4.04
134 135 0.626382 TCCTGTCCCACTCTCTCGAT 59.374 55.000 0.00 0.00 0.00 3.59
135 136 0.743688 CCTGTCCCACTCTCTCGATG 59.256 60.000 0.00 0.00 0.00 3.84
136 137 1.468985 CTGTCCCACTCTCTCGATGT 58.531 55.000 0.00 0.00 0.00 3.06
137 138 2.644676 CTGTCCCACTCTCTCGATGTA 58.355 52.381 0.00 0.00 0.00 2.29
138 139 3.218453 CTGTCCCACTCTCTCGATGTAT 58.782 50.000 0.00 0.00 0.00 2.29
139 140 2.952310 TGTCCCACTCTCTCGATGTATG 59.048 50.000 0.00 0.00 0.00 2.39
140 141 2.952978 GTCCCACTCTCTCGATGTATGT 59.047 50.000 0.00 0.00 0.00 2.29
141 142 3.381908 GTCCCACTCTCTCGATGTATGTT 59.618 47.826 0.00 0.00 0.00 2.71
142 143 4.023980 TCCCACTCTCTCGATGTATGTTT 58.976 43.478 0.00 0.00 0.00 2.83
143 144 4.466370 TCCCACTCTCTCGATGTATGTTTT 59.534 41.667 0.00 0.00 0.00 2.43
144 145 4.568359 CCCACTCTCTCGATGTATGTTTTG 59.432 45.833 0.00 0.00 0.00 2.44
145 146 5.410924 CCACTCTCTCGATGTATGTTTTGA 58.589 41.667 0.00 0.00 0.00 2.69
146 147 5.869344 CCACTCTCTCGATGTATGTTTTGAA 59.131 40.000 0.00 0.00 0.00 2.69
147 148 6.536582 CCACTCTCTCGATGTATGTTTTGAAT 59.463 38.462 0.00 0.00 0.00 2.57
148 149 7.065085 CCACTCTCTCGATGTATGTTTTGAATT 59.935 37.037 0.00 0.00 0.00 2.17
149 150 8.446273 CACTCTCTCGATGTATGTTTTGAATTT 58.554 33.333 0.00 0.00 0.00 1.82
150 151 9.003658 ACTCTCTCGATGTATGTTTTGAATTTT 57.996 29.630 0.00 0.00 0.00 1.82
151 152 9.270576 CTCTCTCGATGTATGTTTTGAATTTTG 57.729 33.333 0.00 0.00 0.00 2.44
152 153 8.998377 TCTCTCGATGTATGTTTTGAATTTTGA 58.002 29.630 0.00 0.00 0.00 2.69
153 154 9.611284 CTCTCGATGTATGTTTTGAATTTTGAA 57.389 29.630 0.00 0.00 0.00 2.69
154 155 9.958234 TCTCGATGTATGTTTTGAATTTTGAAA 57.042 25.926 0.00 0.00 0.00 2.69
157 158 9.288845 CGATGTATGTTTTGAATTTTGAAAACG 57.711 29.630 11.60 0.00 43.90 3.60
176 177 9.716507 TGAAAACGAAAAAGAGAAACTTAGATG 57.283 29.630 0.00 0.00 37.93 2.90
177 178 9.717892 GAAAACGAAAAAGAGAAACTTAGATGT 57.282 29.630 0.00 0.00 37.93 3.06
178 179 9.503427 AAAACGAAAAAGAGAAACTTAGATGTG 57.497 29.630 0.00 0.00 37.93 3.21
179 180 8.433421 AACGAAAAAGAGAAACTTAGATGTGA 57.567 30.769 0.00 0.00 37.93 3.58
180 181 8.433421 ACGAAAAAGAGAAACTTAGATGTGAA 57.567 30.769 0.00 0.00 37.93 3.18
181 182 9.057089 ACGAAAAAGAGAAACTTAGATGTGAAT 57.943 29.630 0.00 0.00 37.93 2.57
186 187 9.660180 AAAGAGAAACTTAGATGTGAATAGTCC 57.340 33.333 0.00 0.00 37.93 3.85
187 188 8.367660 AGAGAAACTTAGATGTGAATAGTCCA 57.632 34.615 0.00 0.00 0.00 4.02
188 189 8.254508 AGAGAAACTTAGATGTGAATAGTCCAC 58.745 37.037 0.00 0.00 35.23 4.02
189 190 7.907389 AGAAACTTAGATGTGAATAGTCCACA 58.093 34.615 0.00 0.00 46.90 4.17
190 191 8.037758 AGAAACTTAGATGTGAATAGTCCACAG 58.962 37.037 0.00 0.00 46.19 3.66
191 192 6.227298 ACTTAGATGTGAATAGTCCACAGG 57.773 41.667 0.00 0.00 46.19 4.00
192 193 5.721960 ACTTAGATGTGAATAGTCCACAGGT 59.278 40.000 0.00 0.00 46.19 4.00
193 194 4.478206 AGATGTGAATAGTCCACAGGTG 57.522 45.455 0.00 0.00 46.19 4.00
194 195 3.840666 AGATGTGAATAGTCCACAGGTGT 59.159 43.478 0.00 0.00 46.19 4.16
195 196 3.678056 TGTGAATAGTCCACAGGTGTC 57.322 47.619 0.00 0.00 39.36 3.67
196 197 2.029380 TGTGAATAGTCCACAGGTGTCG 60.029 50.000 0.00 0.00 39.36 4.35
197 198 2.230508 GTGAATAGTCCACAGGTGTCGA 59.769 50.000 0.00 0.00 34.81 4.20
198 199 2.492088 TGAATAGTCCACAGGTGTCGAG 59.508 50.000 0.00 0.00 0.00 4.04
199 200 2.217510 ATAGTCCACAGGTGTCGAGT 57.782 50.000 0.00 0.00 0.00 4.18
200 201 1.991121 TAGTCCACAGGTGTCGAGTT 58.009 50.000 0.00 0.00 0.00 3.01
201 202 1.120530 AGTCCACAGGTGTCGAGTTT 58.879 50.000 0.00 0.00 0.00 2.66
202 203 1.068741 AGTCCACAGGTGTCGAGTTTC 59.931 52.381 0.00 0.00 0.00 2.78
203 204 1.068741 GTCCACAGGTGTCGAGTTTCT 59.931 52.381 0.00 0.00 0.00 2.52
204 205 1.340248 TCCACAGGTGTCGAGTTTCTC 59.660 52.381 0.00 0.00 0.00 2.87
205 206 1.341531 CCACAGGTGTCGAGTTTCTCT 59.658 52.381 0.00 0.00 0.00 3.10
206 207 2.224066 CCACAGGTGTCGAGTTTCTCTT 60.224 50.000 0.00 0.00 0.00 2.85
207 208 3.458189 CACAGGTGTCGAGTTTCTCTTT 58.542 45.455 0.00 0.00 0.00 2.52
208 209 3.871594 CACAGGTGTCGAGTTTCTCTTTT 59.128 43.478 0.00 0.00 0.00 2.27
209 210 4.332819 CACAGGTGTCGAGTTTCTCTTTTT 59.667 41.667 0.00 0.00 0.00 1.94
230 231 7.830217 TTTTTGTTTCTCGATGTATGTTTCG 57.170 32.000 0.00 0.00 36.72 3.46
231 232 6.772770 TTTGTTTCTCGATGTATGTTTCGA 57.227 33.333 0.00 0.00 41.70 3.71
232 233 6.772770 TTGTTTCTCGATGTATGTTTCGAA 57.227 33.333 0.00 0.00 43.14 3.71
233 234 6.961359 TGTTTCTCGATGTATGTTTCGAAT 57.039 33.333 0.00 0.00 43.14 3.34
234 235 7.359262 TGTTTCTCGATGTATGTTTCGAATT 57.641 32.000 0.00 0.00 43.14 2.17
235 236 7.802738 TGTTTCTCGATGTATGTTTCGAATTT 58.197 30.769 0.00 0.00 43.14 1.82
236 237 8.286800 TGTTTCTCGATGTATGTTTCGAATTTT 58.713 29.630 0.00 0.00 43.14 1.82
237 238 8.567221 GTTTCTCGATGTATGTTTCGAATTTTG 58.433 33.333 0.00 0.00 43.14 2.44
238 239 7.589574 TCTCGATGTATGTTTCGAATTTTGA 57.410 32.000 0.00 0.00 43.14 2.69
239 240 8.196802 TCTCGATGTATGTTTCGAATTTTGAT 57.803 30.769 0.00 0.00 43.14 2.57
240 241 8.328146 TCTCGATGTATGTTTCGAATTTTGATC 58.672 33.333 0.00 0.00 43.14 2.92
241 242 8.196802 TCGATGTATGTTTCGAATTTTGATCT 57.803 30.769 0.00 0.00 41.06 2.75
242 243 8.116136 TCGATGTATGTTTCGAATTTTGATCTG 58.884 33.333 0.00 0.00 41.06 2.90
243 244 8.116136 CGATGTATGTTTCGAATTTTGATCTGA 58.884 33.333 0.00 0.00 37.55 3.27
244 245 9.773328 GATGTATGTTTCGAATTTTGATCTGAA 57.227 29.630 0.00 0.00 0.00 3.02
274 275 9.914834 TTTAAGGGTTATCTTAATATGTGCTGT 57.085 29.630 0.00 0.00 38.52 4.40
275 276 7.807977 AAGGGTTATCTTAATATGTGCTGTG 57.192 36.000 0.00 0.00 0.00 3.66
276 277 7.136822 AGGGTTATCTTAATATGTGCTGTGA 57.863 36.000 0.00 0.00 0.00 3.58
277 278 7.573710 AGGGTTATCTTAATATGTGCTGTGAA 58.426 34.615 0.00 0.00 0.00 3.18
278 279 7.716998 AGGGTTATCTTAATATGTGCTGTGAAG 59.283 37.037 0.00 0.00 0.00 3.02
279 280 7.715249 GGGTTATCTTAATATGTGCTGTGAAGA 59.285 37.037 0.00 0.00 0.00 2.87
280 281 9.277783 GGTTATCTTAATATGTGCTGTGAAGAT 57.722 33.333 0.00 0.00 36.44 2.40
282 283 6.609237 TCTTAATATGTGCTGTGAAGATGC 57.391 37.500 0.00 0.00 0.00 3.91
283 284 6.114767 TCTTAATATGTGCTGTGAAGATGCA 58.885 36.000 0.00 0.00 0.00 3.96
284 285 4.895224 AATATGTGCTGTGAAGATGCAG 57.105 40.909 0.00 0.00 37.39 4.41
285 286 1.460504 ATGTGCTGTGAAGATGCAGG 58.539 50.000 0.00 0.00 37.39 4.85
286 287 0.397564 TGTGCTGTGAAGATGCAGGA 59.602 50.000 0.00 0.00 37.39 3.86
287 288 1.003928 TGTGCTGTGAAGATGCAGGAT 59.996 47.619 0.00 0.00 37.39 3.24
288 289 2.089980 GTGCTGTGAAGATGCAGGATT 58.910 47.619 0.00 0.00 37.39 3.01
289 290 2.097142 GTGCTGTGAAGATGCAGGATTC 59.903 50.000 0.00 0.00 37.39 2.52
290 291 2.026542 TGCTGTGAAGATGCAGGATTCT 60.027 45.455 9.06 0.00 33.62 2.40
291 292 3.015327 GCTGTGAAGATGCAGGATTCTT 58.985 45.455 0.00 0.00 34.95 2.52
292 293 3.442977 GCTGTGAAGATGCAGGATTCTTT 59.557 43.478 1.99 0.00 32.46 2.52
293 294 4.082354 GCTGTGAAGATGCAGGATTCTTTT 60.082 41.667 1.99 0.00 32.46 2.27
294 295 5.566230 GCTGTGAAGATGCAGGATTCTTTTT 60.566 40.000 1.99 0.00 32.46 1.94
295 296 6.017400 TGTGAAGATGCAGGATTCTTTTTC 57.983 37.500 1.99 0.00 32.46 2.29
296 297 5.535783 TGTGAAGATGCAGGATTCTTTTTCA 59.464 36.000 1.99 0.00 32.46 2.69
297 298 6.040729 TGTGAAGATGCAGGATTCTTTTTCAA 59.959 34.615 1.99 0.00 32.46 2.69
298 299 6.925165 GTGAAGATGCAGGATTCTTTTTCAAA 59.075 34.615 1.99 0.00 32.46 2.69
299 300 7.439056 GTGAAGATGCAGGATTCTTTTTCAAAA 59.561 33.333 1.99 0.00 32.46 2.44
300 301 7.986320 TGAAGATGCAGGATTCTTTTTCAAAAA 59.014 29.630 1.99 0.00 32.46 1.94
330 331 8.713271 TCACAATGTTTAAATTTAAATTCCGGC 58.287 29.630 22.66 11.62 35.35 6.13
331 332 7.960195 CACAATGTTTAAATTTAAATTCCGGCC 59.040 33.333 22.66 11.03 35.35 6.13
332 333 6.895607 ATGTTTAAATTTAAATTCCGGCCG 57.104 33.333 22.66 21.04 35.35 6.13
333 334 4.626172 TGTTTAAATTTAAATTCCGGCCGC 59.374 37.500 22.85 9.86 35.35 6.53
334 335 4.451629 TTAAATTTAAATTCCGGCCGCA 57.548 36.364 22.85 0.00 0.00 5.69
335 336 3.320673 AAATTTAAATTCCGGCCGCAA 57.679 38.095 22.85 13.59 0.00 4.85
336 337 2.577449 ATTTAAATTCCGGCCGCAAG 57.423 45.000 22.85 6.58 0.00 4.01
337 338 1.249407 TTTAAATTCCGGCCGCAAGT 58.751 45.000 22.85 8.21 0.00 3.16
338 339 0.806241 TTAAATTCCGGCCGCAAGTC 59.194 50.000 22.85 0.00 0.00 3.01
339 340 0.321741 TAAATTCCGGCCGCAAGTCA 60.322 50.000 22.85 0.00 0.00 3.41
340 341 1.862602 AAATTCCGGCCGCAAGTCAC 61.863 55.000 22.85 0.00 0.00 3.67
341 342 3.545124 ATTCCGGCCGCAAGTCACA 62.545 57.895 22.85 0.00 0.00 3.58
342 343 4.980805 TCCGGCCGCAAGTCACAC 62.981 66.667 22.85 0.00 0.00 3.82
347 348 4.347096 CCGCAAGTCACACGGTAA 57.653 55.556 0.00 0.00 42.01 2.85
348 349 1.857364 CCGCAAGTCACACGGTAAC 59.143 57.895 0.00 0.00 42.01 2.50
349 350 0.876777 CCGCAAGTCACACGGTAACA 60.877 55.000 0.00 0.00 42.01 2.41
350 351 1.144969 CGCAAGTCACACGGTAACAT 58.855 50.000 0.00 0.00 0.00 2.71
351 352 1.136363 CGCAAGTCACACGGTAACATG 60.136 52.381 0.00 0.00 0.00 3.21
352 353 1.399727 GCAAGTCACACGGTAACATGC 60.400 52.381 0.00 3.20 31.57 4.06
353 354 1.870402 CAAGTCACACGGTAACATGCA 59.130 47.619 0.00 0.00 0.00 3.96
354 355 2.248280 AGTCACACGGTAACATGCAA 57.752 45.000 0.00 0.00 0.00 4.08
355 356 2.566913 AGTCACACGGTAACATGCAAA 58.433 42.857 0.00 0.00 0.00 3.68
356 357 2.289547 AGTCACACGGTAACATGCAAAC 59.710 45.455 0.00 0.00 0.00 2.93
357 358 1.261885 TCACACGGTAACATGCAAACG 59.738 47.619 3.95 3.95 0.00 3.60
358 359 1.003331 CACACGGTAACATGCAAACGT 60.003 47.619 5.23 5.23 34.61 3.99
359 360 1.669184 CACGGTAACATGCAAACGTG 58.331 50.000 19.94 19.94 44.20 4.49
370 371 3.460114 CAAACGTGCATGTCACCTG 57.540 52.632 12.96 4.18 42.69 4.00
371 372 0.943673 CAAACGTGCATGTCACCTGA 59.056 50.000 12.96 0.00 42.69 3.86
372 373 1.536766 CAAACGTGCATGTCACCTGAT 59.463 47.619 12.96 0.00 42.69 2.90
373 374 1.442769 AACGTGCATGTCACCTGATC 58.557 50.000 12.96 0.00 42.69 2.92
374 375 0.610174 ACGTGCATGTCACCTGATCT 59.390 50.000 5.51 0.00 42.69 2.75
375 376 1.004595 CGTGCATGTCACCTGATCTG 58.995 55.000 12.62 0.00 42.69 2.90
376 377 1.673923 CGTGCATGTCACCTGATCTGT 60.674 52.381 12.62 0.00 42.69 3.41
377 378 1.736126 GTGCATGTCACCTGATCTGTG 59.264 52.381 9.00 9.00 39.79 3.66
378 379 1.348696 TGCATGTCACCTGATCTGTGT 59.651 47.619 13.35 2.86 35.25 3.72
379 380 2.005451 GCATGTCACCTGATCTGTGTC 58.995 52.381 13.35 9.78 35.25 3.67
394 395 2.750237 GTCCCGTTGGCACCATCC 60.750 66.667 0.00 0.00 0.00 3.51
397 398 2.751436 CCGTTGGCACCATCCTGG 60.751 66.667 0.00 0.00 45.02 4.45
411 412 0.675837 TCCTGGTCGTAGGACTCACG 60.676 60.000 14.75 6.23 41.85 4.35
453 456 0.109272 CTCTCGAGCCAACGTGCTAA 60.109 55.000 7.81 0.00 42.95 3.09
529 538 3.049912 CGCCCAACTTTAAGAACAAAGC 58.950 45.455 0.00 0.00 38.79 3.51
535 544 4.918810 ACTTTAAGAACAAAGCCAGGTG 57.081 40.909 0.00 0.00 38.79 4.00
543 557 2.962859 ACAAAGCCAGGTGATTTCCTT 58.037 42.857 0.00 0.00 35.37 3.36
564 578 4.273148 TGGGCAGTCTACTTCTTTTCTC 57.727 45.455 0.00 0.00 0.00 2.87
566 580 3.254892 GGCAGTCTACTTCTTTTCTCCG 58.745 50.000 0.00 0.00 0.00 4.63
574 588 3.821748 ACTTCTTTTCTCCGCCTTTTCT 58.178 40.909 0.00 0.00 0.00 2.52
575 589 4.969484 ACTTCTTTTCTCCGCCTTTTCTA 58.031 39.130 0.00 0.00 0.00 2.10
576 590 5.561679 ACTTCTTTTCTCCGCCTTTTCTAT 58.438 37.500 0.00 0.00 0.00 1.98
703 726 1.688735 GGATTGCCCTTCCATTTAGCC 59.311 52.381 0.00 0.00 33.21 3.93
716 739 5.431765 TCCATTTAGCCTTTCAGATGACTC 58.568 41.667 0.00 0.00 0.00 3.36
733 757 0.526524 CTCGGCACTTCATCTCGTCC 60.527 60.000 0.00 0.00 0.00 4.79
755 779 4.592192 CGGCCAGTGCGATCGGAT 62.592 66.667 18.30 1.35 38.85 4.18
762 786 0.179100 AGTGCGATCGGATGGTTCAG 60.179 55.000 18.30 0.00 0.00 3.02
768 792 2.418746 CGATCGGATGGTTCAGGTTTCT 60.419 50.000 7.38 0.00 0.00 2.52
775 799 1.202722 TGGTTCAGGTTTCTCCGTTCC 60.203 52.381 0.00 0.00 41.99 3.62
795 819 4.087892 ATCCAACGGCTGAGCGCT 62.088 61.111 11.27 11.27 39.13 5.92
800 824 3.941657 AACGGCTGAGCGCTCTTCC 62.942 63.158 35.27 30.83 39.13 3.46
849 873 2.202623 GTCGAACGCGCCTCTCAT 60.203 61.111 5.73 0.00 37.46 2.90
960 993 3.721706 CTGGCCACCACCTCCTCC 61.722 72.222 0.00 0.00 0.00 4.30
961 994 4.270153 TGGCCACCACCTCCTCCT 62.270 66.667 0.00 0.00 0.00 3.69
962 995 3.721706 GGCCACCACCTCCTCCTG 61.722 72.222 0.00 0.00 0.00 3.86
1921 2039 3.628646 AAGTCCCGCACTGATGGGC 62.629 63.158 2.52 0.00 45.60 5.36
1979 2106 6.577103 TGTAGCTACTCCATTCAAATGAGAG 58.423 40.000 23.84 14.46 38.70 3.20
2026 2153 1.312815 ACTGCCTGTTTCACTGAAGC 58.687 50.000 0.00 0.00 0.00 3.86
2077 2212 6.417258 ACATGATCATGAACATAACAGGTGA 58.583 36.000 36.37 0.00 41.20 4.02
2078 2213 6.885918 ACATGATCATGAACATAACAGGTGAA 59.114 34.615 36.37 0.00 41.20 3.18
2079 2214 7.558807 ACATGATCATGAACATAACAGGTGAAT 59.441 33.333 36.37 9.76 41.20 2.57
2080 2215 9.059260 CATGATCATGAACATAACAGGTGAATA 57.941 33.333 28.37 0.00 41.20 1.75
2081 2216 8.437360 TGATCATGAACATAACAGGTGAATAC 57.563 34.615 0.00 0.00 0.00 1.89
2082 2217 8.046107 TGATCATGAACATAACAGGTGAATACA 58.954 33.333 0.00 0.00 0.00 2.29
2083 2218 8.985315 ATCATGAACATAACAGGTGAATACAT 57.015 30.769 0.00 0.00 0.00 2.29
2084 2219 8.806429 TCATGAACATAACAGGTGAATACATT 57.194 30.769 0.00 0.00 0.00 2.71
2085 2220 8.676401 TCATGAACATAACAGGTGAATACATTG 58.324 33.333 0.00 0.00 0.00 2.82
2086 2221 8.676401 CATGAACATAACAGGTGAATACATTGA 58.324 33.333 0.00 0.00 0.00 2.57
2087 2222 8.806429 TGAACATAACAGGTGAATACATTGAT 57.194 30.769 0.00 0.00 0.00 2.57
2088 2223 8.676401 TGAACATAACAGGTGAATACATTGATG 58.324 33.333 0.00 0.00 0.00 3.07
2089 2224 8.579850 AACATAACAGGTGAATACATTGATGT 57.420 30.769 1.84 1.84 44.48 3.06
2090 2225 7.988737 ACATAACAGGTGAATACATTGATGTG 58.011 34.615 6.87 0.00 41.89 3.21
2235 2401 4.639078 TGGATCCTTCTGTGTTGAATGA 57.361 40.909 14.23 0.00 0.00 2.57
2323 2583 6.997655 TGAATGATGAGGTGGTGTAGATATC 58.002 40.000 0.00 0.00 0.00 1.63
2386 2647 7.275779 ACTGCTGACTGTTCTTATGTAAATACG 59.724 37.037 0.00 0.00 0.00 3.06
2401 2662 7.354025 TGTAAATACGTCAATAACAGTGGTG 57.646 36.000 0.00 0.00 0.00 4.17
2590 3409 3.770263 AAATGGACACATGATGCTTCG 57.230 42.857 0.00 0.00 37.40 3.79
2600 3419 4.385146 CACATGATGCTTCGCTAGACATAG 59.615 45.833 0.00 0.00 0.00 2.23
2609 3428 1.064208 CGCTAGACATAGACTGTGCGT 59.936 52.381 0.00 0.00 38.54 5.24
2680 3499 1.251251 GGGAAGAAACTGTGCATGCT 58.749 50.000 20.33 0.00 0.00 3.79
2733 3552 3.136763 ACTGCTTGAGTGTGATCAACAG 58.863 45.455 0.00 12.95 40.26 3.16
2882 3702 2.551459 CAGACTGCAGGAAAAGGAACTG 59.449 50.000 19.93 8.73 40.86 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
84 85 5.047660 GCTATTCTCATCCGGTCATCTAACT 60.048 44.000 0.00 0.00 0.00 2.24
86 87 4.832823 TGCTATTCTCATCCGGTCATCTAA 59.167 41.667 0.00 0.00 0.00 2.10
94 95 0.249447 TGCGTGCTATTCTCATCCGG 60.249 55.000 0.00 0.00 0.00 5.14
127 128 9.611284 TTCAAAATTCAAAACATACATCGAGAG 57.389 29.630 0.00 0.00 0.00 3.20
128 129 9.958234 TTTCAAAATTCAAAACATACATCGAGA 57.042 25.926 0.00 0.00 0.00 4.04
131 132 9.288845 CGTTTTCAAAATTCAAAACATACATCG 57.711 29.630 15.33 0.00 40.90 3.84
150 151 9.716507 CATCTAAGTTTCTCTTTTTCGTTTTCA 57.283 29.630 0.00 0.00 37.56 2.69
151 152 9.717892 ACATCTAAGTTTCTCTTTTTCGTTTTC 57.282 29.630 0.00 0.00 37.56 2.29
152 153 9.503427 CACATCTAAGTTTCTCTTTTTCGTTTT 57.497 29.630 0.00 0.00 37.56 2.43
153 154 8.889717 TCACATCTAAGTTTCTCTTTTTCGTTT 58.110 29.630 0.00 0.00 37.56 3.60
154 155 8.433421 TCACATCTAAGTTTCTCTTTTTCGTT 57.567 30.769 0.00 0.00 37.56 3.85
155 156 8.433421 TTCACATCTAAGTTTCTCTTTTTCGT 57.567 30.769 0.00 0.00 37.56 3.85
160 161 9.660180 GGACTATTCACATCTAAGTTTCTCTTT 57.340 33.333 0.00 0.00 37.56 2.52
161 162 8.816894 TGGACTATTCACATCTAAGTTTCTCTT 58.183 33.333 0.00 0.00 39.89 2.85
162 163 8.254508 GTGGACTATTCACATCTAAGTTTCTCT 58.745 37.037 0.00 0.00 35.39 3.10
163 164 8.035394 TGTGGACTATTCACATCTAAGTTTCTC 58.965 37.037 0.00 0.00 39.83 2.87
164 165 7.907389 TGTGGACTATTCACATCTAAGTTTCT 58.093 34.615 0.00 0.00 39.83 2.52
165 166 7.278868 CCTGTGGACTATTCACATCTAAGTTTC 59.721 40.741 0.00 0.00 43.16 2.78
166 167 7.106239 CCTGTGGACTATTCACATCTAAGTTT 58.894 38.462 0.00 0.00 43.16 2.66
167 168 6.213600 ACCTGTGGACTATTCACATCTAAGTT 59.786 38.462 0.00 0.00 43.16 2.66
168 169 5.721960 ACCTGTGGACTATTCACATCTAAGT 59.278 40.000 0.00 0.00 43.16 2.24
169 170 6.045318 CACCTGTGGACTATTCACATCTAAG 58.955 44.000 0.00 0.00 43.16 2.18
170 171 5.483937 ACACCTGTGGACTATTCACATCTAA 59.516 40.000 1.91 0.00 43.16 2.10
171 172 5.023452 ACACCTGTGGACTATTCACATCTA 58.977 41.667 1.91 0.00 43.16 1.98
172 173 3.840666 ACACCTGTGGACTATTCACATCT 59.159 43.478 1.91 0.00 43.16 2.90
173 174 4.184629 GACACCTGTGGACTATTCACATC 58.815 47.826 1.91 0.00 43.16 3.06
174 175 3.368427 CGACACCTGTGGACTATTCACAT 60.368 47.826 1.91 0.00 43.16 3.21
175 176 2.029380 CGACACCTGTGGACTATTCACA 60.029 50.000 1.91 0.00 42.11 3.58
176 177 2.230508 TCGACACCTGTGGACTATTCAC 59.769 50.000 1.91 0.00 35.82 3.18
177 178 2.492088 CTCGACACCTGTGGACTATTCA 59.508 50.000 1.91 0.00 34.19 2.57
178 179 2.492484 ACTCGACACCTGTGGACTATTC 59.508 50.000 1.91 0.00 34.19 1.75
179 180 2.526432 ACTCGACACCTGTGGACTATT 58.474 47.619 1.91 0.00 34.19 1.73
180 181 2.217510 ACTCGACACCTGTGGACTAT 57.782 50.000 1.91 0.00 34.19 2.12
181 182 1.991121 AACTCGACACCTGTGGACTA 58.009 50.000 1.91 0.00 34.19 2.59
182 183 1.068741 GAAACTCGACACCTGTGGACT 59.931 52.381 1.91 0.00 34.19 3.85
183 184 1.068741 AGAAACTCGACACCTGTGGAC 59.931 52.381 1.91 0.00 34.19 4.02
184 185 1.340248 GAGAAACTCGACACCTGTGGA 59.660 52.381 1.91 0.00 34.19 4.02
185 186 1.341531 AGAGAAACTCGACACCTGTGG 59.658 52.381 1.91 0.00 35.36 4.17
186 187 2.802787 AGAGAAACTCGACACCTGTG 57.197 50.000 0.00 0.00 35.36 3.66
187 188 3.821421 AAAGAGAAACTCGACACCTGT 57.179 42.857 0.00 0.00 35.36 4.00
206 207 7.631822 TCGAAACATACATCGAGAAACAAAAA 58.368 30.769 0.00 0.00 42.61 1.94
207 208 7.179927 TCGAAACATACATCGAGAAACAAAA 57.820 32.000 0.00 0.00 42.61 2.44
208 209 6.772770 TCGAAACATACATCGAGAAACAAA 57.227 33.333 0.00 0.00 42.61 2.83
216 217 8.116136 CAGATCAAAATTCGAAACATACATCGA 58.884 33.333 0.00 0.00 45.48 3.59
217 218 8.116136 TCAGATCAAAATTCGAAACATACATCG 58.884 33.333 0.00 0.00 40.31 3.84
218 219 9.773328 TTCAGATCAAAATTCGAAACATACATC 57.227 29.630 0.00 0.31 0.00 3.06
248 249 9.914834 ACAGCACATATTAAGATAACCCTTAAA 57.085 29.630 0.00 0.00 40.65 1.52
249 250 9.337396 CACAGCACATATTAAGATAACCCTTAA 57.663 33.333 0.00 0.00 41.27 1.85
250 251 8.710239 TCACAGCACATATTAAGATAACCCTTA 58.290 33.333 0.00 0.00 0.00 2.69
251 252 7.573710 TCACAGCACATATTAAGATAACCCTT 58.426 34.615 0.00 0.00 0.00 3.95
252 253 7.136822 TCACAGCACATATTAAGATAACCCT 57.863 36.000 0.00 0.00 0.00 4.34
253 254 7.715249 TCTTCACAGCACATATTAAGATAACCC 59.285 37.037 0.00 0.00 0.00 4.11
254 255 8.662781 TCTTCACAGCACATATTAAGATAACC 57.337 34.615 0.00 0.00 0.00 2.85
256 257 8.777413 GCATCTTCACAGCACATATTAAGATAA 58.223 33.333 0.00 0.00 32.48 1.75
257 258 7.933033 TGCATCTTCACAGCACATATTAAGATA 59.067 33.333 0.00 0.00 32.48 1.98
258 259 6.769341 TGCATCTTCACAGCACATATTAAGAT 59.231 34.615 0.00 0.00 33.63 2.40
259 260 6.114767 TGCATCTTCACAGCACATATTAAGA 58.885 36.000 0.00 0.00 32.55 2.10
260 261 6.367686 TGCATCTTCACAGCACATATTAAG 57.632 37.500 0.00 0.00 32.55 1.85
261 262 5.297527 CCTGCATCTTCACAGCACATATTAA 59.702 40.000 0.00 0.00 34.13 1.40
262 263 4.818005 CCTGCATCTTCACAGCACATATTA 59.182 41.667 0.00 0.00 34.13 0.98
263 264 3.630769 CCTGCATCTTCACAGCACATATT 59.369 43.478 0.00 0.00 34.13 1.28
264 265 3.118149 TCCTGCATCTTCACAGCACATAT 60.118 43.478 0.00 0.00 34.13 1.78
265 266 2.236893 TCCTGCATCTTCACAGCACATA 59.763 45.455 0.00 0.00 34.13 2.29
266 267 1.003928 TCCTGCATCTTCACAGCACAT 59.996 47.619 0.00 0.00 34.13 3.21
267 268 0.397564 TCCTGCATCTTCACAGCACA 59.602 50.000 0.00 0.00 34.13 4.57
268 269 1.747709 ATCCTGCATCTTCACAGCAC 58.252 50.000 0.00 0.00 34.13 4.40
269 270 2.026542 AGAATCCTGCATCTTCACAGCA 60.027 45.455 0.00 0.00 36.72 4.41
270 271 2.641305 AGAATCCTGCATCTTCACAGC 58.359 47.619 0.00 0.00 32.37 4.40
271 272 5.640189 AAAAGAATCCTGCATCTTCACAG 57.360 39.130 0.92 0.00 34.90 3.66
272 273 5.535783 TGAAAAAGAATCCTGCATCTTCACA 59.464 36.000 0.92 0.75 34.90 3.58
273 274 6.017400 TGAAAAAGAATCCTGCATCTTCAC 57.983 37.500 0.92 0.00 34.90 3.18
274 275 6.653526 TTGAAAAAGAATCCTGCATCTTCA 57.346 33.333 0.92 0.00 34.90 3.02
275 276 7.951530 TTTTGAAAAAGAATCCTGCATCTTC 57.048 32.000 0.92 0.00 34.90 2.87
304 305 8.713271 GCCGGAATTTAAATTTAAACATTGTGA 58.287 29.630 22.35 1.90 35.65 3.58
305 306 7.960195 GGCCGGAATTTAAATTTAAACATTGTG 59.040 33.333 22.35 12.28 35.65 3.33
306 307 7.148557 CGGCCGGAATTTAAATTTAAACATTGT 60.149 33.333 22.35 6.70 35.65 2.71
307 308 7.176741 CGGCCGGAATTTAAATTTAAACATTG 58.823 34.615 22.35 13.85 35.65 2.82
308 309 6.183360 GCGGCCGGAATTTAAATTTAAACATT 60.183 34.615 29.38 15.07 35.65 2.71
309 310 5.292345 GCGGCCGGAATTTAAATTTAAACAT 59.708 36.000 29.38 15.44 35.65 2.71
310 311 4.626172 GCGGCCGGAATTTAAATTTAAACA 59.374 37.500 29.38 5.29 35.65 2.83
311 312 4.626172 TGCGGCCGGAATTTAAATTTAAAC 59.374 37.500 29.38 12.52 35.65 2.01
312 313 4.817517 TGCGGCCGGAATTTAAATTTAAA 58.182 34.783 29.38 22.20 37.08 1.52
313 314 4.451629 TGCGGCCGGAATTTAAATTTAA 57.548 36.364 29.38 6.54 0.00 1.52
314 315 4.082136 ACTTGCGGCCGGAATTTAAATTTA 60.082 37.500 32.76 6.34 0.00 1.40
315 316 3.258228 CTTGCGGCCGGAATTTAAATTT 58.742 40.909 32.76 0.00 0.00 1.82
316 317 2.232696 ACTTGCGGCCGGAATTTAAATT 59.767 40.909 32.76 13.24 0.00 1.82
317 318 1.822371 ACTTGCGGCCGGAATTTAAAT 59.178 42.857 32.76 11.14 0.00 1.40
318 319 1.200484 GACTTGCGGCCGGAATTTAAA 59.800 47.619 32.76 9.68 0.00 1.52
319 320 0.806241 GACTTGCGGCCGGAATTTAA 59.194 50.000 32.76 10.52 0.00 1.52
320 321 0.321741 TGACTTGCGGCCGGAATTTA 60.322 50.000 32.76 20.96 0.00 1.40
321 322 1.602323 TGACTTGCGGCCGGAATTT 60.602 52.632 32.76 22.08 0.00 1.82
322 323 2.033448 TGACTTGCGGCCGGAATT 59.967 55.556 32.76 27.25 0.00 2.17
323 324 2.746277 GTGACTTGCGGCCGGAAT 60.746 61.111 32.76 21.56 0.00 3.01
324 325 4.243008 TGTGACTTGCGGCCGGAA 62.243 61.111 30.75 30.75 0.00 4.30
325 326 4.980805 GTGTGACTTGCGGCCGGA 62.981 66.667 29.38 24.35 0.00 5.14
331 332 1.136363 CATGTTACCGTGTGACTTGCG 60.136 52.381 0.00 0.00 0.00 4.85
332 333 1.399727 GCATGTTACCGTGTGACTTGC 60.400 52.381 17.02 17.02 42.32 4.01
333 334 1.870402 TGCATGTTACCGTGTGACTTG 59.130 47.619 0.00 9.05 32.95 3.16
334 335 2.248280 TGCATGTTACCGTGTGACTT 57.752 45.000 0.00 0.00 0.00 3.01
335 336 2.248280 TTGCATGTTACCGTGTGACT 57.752 45.000 0.00 0.00 0.00 3.41
336 337 2.646250 GTTTGCATGTTACCGTGTGAC 58.354 47.619 0.00 0.00 0.00 3.67
337 338 1.261885 CGTTTGCATGTTACCGTGTGA 59.738 47.619 0.00 0.00 0.00 3.58
338 339 1.003331 ACGTTTGCATGTTACCGTGTG 60.003 47.619 0.00 0.00 0.00 3.82
339 340 1.003331 CACGTTTGCATGTTACCGTGT 60.003 47.619 16.54 0.00 40.37 4.49
340 341 1.669184 CACGTTTGCATGTTACCGTG 58.331 50.000 12.97 12.97 39.51 4.94
357 358 1.736126 CACAGATCAGGTGACATGCAC 59.264 52.381 10.99 10.63 46.98 4.57
358 359 1.348696 ACACAGATCAGGTGACATGCA 59.651 47.619 20.35 0.00 39.53 3.96
359 360 2.005451 GACACAGATCAGGTGACATGC 58.995 52.381 20.35 4.76 39.53 4.06
360 361 2.625737 GGACACAGATCAGGTGACATG 58.374 52.381 20.35 0.00 39.53 3.21
361 362 1.556911 GGGACACAGATCAGGTGACAT 59.443 52.381 20.35 2.54 39.53 3.06
362 363 0.976641 GGGACACAGATCAGGTGACA 59.023 55.000 20.35 0.00 39.53 3.58
363 364 0.108615 CGGGACACAGATCAGGTGAC 60.109 60.000 20.35 15.06 39.53 3.67
364 365 0.541998 ACGGGACACAGATCAGGTGA 60.542 55.000 20.35 0.00 39.53 4.02
365 366 0.321671 AACGGGACACAGATCAGGTG 59.678 55.000 13.98 13.98 41.95 4.00
366 367 0.321671 CAACGGGACACAGATCAGGT 59.678 55.000 0.00 0.00 0.00 4.00
367 368 0.391661 CCAACGGGACACAGATCAGG 60.392 60.000 0.00 0.00 35.59 3.86
368 369 1.021390 GCCAACGGGACACAGATCAG 61.021 60.000 0.00 0.00 35.59 2.90
369 370 1.003839 GCCAACGGGACACAGATCA 60.004 57.895 0.00 0.00 35.59 2.92
370 371 1.003839 TGCCAACGGGACACAGATC 60.004 57.895 0.00 0.00 35.59 2.75
371 372 1.302511 GTGCCAACGGGACACAGAT 60.303 57.895 0.00 0.00 43.66 2.90
372 373 2.110213 GTGCCAACGGGACACAGA 59.890 61.111 0.00 0.00 43.66 3.41
373 374 2.978010 GGTGCCAACGGGACACAG 60.978 66.667 7.00 0.00 46.07 3.66
374 375 3.126703 ATGGTGCCAACGGGACACA 62.127 57.895 7.00 3.10 46.07 3.72
375 376 2.282180 ATGGTGCCAACGGGACAC 60.282 61.111 7.00 2.83 46.07 3.67
376 377 2.033448 GATGGTGCCAACGGGACA 59.967 61.111 7.00 0.00 46.07 4.02
377 378 2.750237 GGATGGTGCCAACGGGAC 60.750 66.667 0.00 0.00 43.47 4.46
378 379 2.933287 AGGATGGTGCCAACGGGA 60.933 61.111 0.00 0.00 35.59 5.14
379 380 2.751436 CAGGATGGTGCCAACGGG 60.751 66.667 0.00 0.00 37.18 5.28
394 395 1.654954 CCCGTGAGTCCTACGACCAG 61.655 65.000 4.68 0.00 43.82 4.00
397 398 1.870055 TTGCCCGTGAGTCCTACGAC 61.870 60.000 4.68 0.00 43.82 4.34
453 456 4.463891 CACTTGGGATTTTGCCTTCACTAT 59.536 41.667 0.00 0.00 0.00 2.12
529 538 0.251742 TGCCCAAGGAAATCACCTGG 60.252 55.000 0.00 0.00 40.49 4.45
535 544 3.636153 AGTAGACTGCCCAAGGAAATC 57.364 47.619 0.00 0.00 0.00 2.17
543 557 3.008049 GGAGAAAAGAAGTAGACTGCCCA 59.992 47.826 0.00 0.00 0.00 5.36
564 578 3.120786 CGCGGTAATAATAGAAAAGGCGG 60.121 47.826 0.00 0.00 36.62 6.13
566 580 4.748600 ACTCGCGGTAATAATAGAAAAGGC 59.251 41.667 6.13 0.00 0.00 4.35
574 588 5.417811 TGGTCAAAACTCGCGGTAATAATA 58.582 37.500 6.13 0.00 0.00 0.98
575 589 4.255301 TGGTCAAAACTCGCGGTAATAAT 58.745 39.130 6.13 0.00 0.00 1.28
576 590 3.661944 TGGTCAAAACTCGCGGTAATAA 58.338 40.909 6.13 0.00 0.00 1.40
703 726 2.376808 AGTGCCGAGTCATCTGAAAG 57.623 50.000 0.00 0.00 0.00 2.62
716 739 0.738975 TAGGACGAGATGAAGTGCCG 59.261 55.000 0.00 0.00 0.00 5.69
733 757 1.299468 GATCGCACTGGCCGAGTAG 60.299 63.158 7.41 0.00 36.38 2.57
755 779 1.202722 GGAACGGAGAAACCTGAACCA 60.203 52.381 0.00 0.00 36.31 3.67
762 786 1.278127 TGGATGAGGAACGGAGAAACC 59.722 52.381 0.00 0.00 0.00 3.27
795 819 0.680618 TTTAAGTGCGTCGGGGAAGA 59.319 50.000 0.00 0.00 0.00 2.87
800 824 2.289547 CCCATTATTTAAGTGCGTCGGG 59.710 50.000 0.00 0.00 0.00 5.14
889 919 2.837291 CTCTCCTCCCGCTCCCAG 60.837 72.222 0.00 0.00 0.00 4.45
924 954 3.820467 CCAGTGGTTTTCAACTCATAGCA 59.180 43.478 0.00 0.00 0.00 3.49
960 993 2.166254 GTCAAGAAGAGAGGAGGAGCAG 59.834 54.545 0.00 0.00 0.00 4.24
961 994 2.175202 GTCAAGAAGAGAGGAGGAGCA 58.825 52.381 0.00 0.00 0.00 4.26
962 995 2.094234 GTGTCAAGAAGAGAGGAGGAGC 60.094 54.545 0.00 0.00 0.00 4.70
1702 1820 4.388499 CACGGTCTGGTTCCCCCG 62.388 72.222 9.16 9.16 45.72 5.73
1923 2041 1.303155 GGCAGGGGCAGATGATAGC 60.303 63.158 0.00 0.00 43.71 2.97
1979 2106 3.110178 CCACGAAGTTCGCCGTCC 61.110 66.667 24.64 0.00 45.12 4.79
2026 2153 2.990066 AAGCTTACTGATCCCTTCGG 57.010 50.000 0.00 0.00 36.72 4.30
2043 2170 6.614160 TGTTCATGATCATGTTGCTTGTAAG 58.386 36.000 30.01 5.39 39.72 2.34
2077 2212 7.161404 ACACTACACACTCACATCAATGTATT 58.839 34.615 0.00 0.00 39.39 1.89
2078 2213 6.701340 ACACTACACACTCACATCAATGTAT 58.299 36.000 0.00 0.00 39.39 2.29
2079 2214 6.096673 ACACTACACACTCACATCAATGTA 57.903 37.500 0.00 0.00 39.39 2.29
2080 2215 4.960938 ACACTACACACTCACATCAATGT 58.039 39.130 0.00 0.00 42.84 2.71
2081 2216 5.578336 CCTACACTACACACTCACATCAATG 59.422 44.000 0.00 0.00 0.00 2.82
2082 2217 5.724328 CCTACACTACACACTCACATCAAT 58.276 41.667 0.00 0.00 0.00 2.57
2083 2218 4.560716 GCCTACACTACACACTCACATCAA 60.561 45.833 0.00 0.00 0.00 2.57
2084 2219 3.056821 GCCTACACTACACACTCACATCA 60.057 47.826 0.00 0.00 0.00 3.07
2085 2220 3.056821 TGCCTACACTACACACTCACATC 60.057 47.826 0.00 0.00 0.00 3.06
2086 2221 2.897326 TGCCTACACTACACACTCACAT 59.103 45.455 0.00 0.00 0.00 3.21
2087 2222 2.312390 TGCCTACACTACACACTCACA 58.688 47.619 0.00 0.00 0.00 3.58
2088 2223 3.380479 TTGCCTACACTACACACTCAC 57.620 47.619 0.00 0.00 0.00 3.51
2089 2224 4.617253 ATTTGCCTACACTACACACTCA 57.383 40.909 0.00 0.00 0.00 3.41
2090 2225 5.468746 TGAAATTTGCCTACACTACACACTC 59.531 40.000 0.00 0.00 0.00 3.51
2285 2451 6.058553 TCATCATTCAACACAGAAGGATCT 57.941 37.500 1.39 0.00 43.23 2.75
2323 2583 1.819632 GCAGACACTATTGCCCCCG 60.820 63.158 0.00 0.00 34.28 5.73
2386 2647 4.513692 TGTAACTGCACCACTGTTATTGAC 59.486 41.667 0.00 0.00 42.46 3.18
2401 2662 3.963665 TGCAACAATCACTTGTAACTGC 58.036 40.909 6.66 6.66 44.83 4.40
2590 3409 2.853731 ACGCACAGTCTATGTCTAGC 57.146 50.000 0.00 0.00 41.41 3.42
2600 3419 3.423645 GCTTAATCAGACAACGCACAGTC 60.424 47.826 0.00 0.00 35.02 3.51
2609 3428 4.202461 ACTGGGAAGTGCTTAATCAGACAA 60.202 41.667 12.26 0.00 0.00 3.18
2680 3499 2.698274 TCACACTCAAGTACTCAGGCAA 59.302 45.455 0.00 0.00 0.00 4.52
2733 3552 7.755373 GGTTTCTTCTTAAAGCACCACATTATC 59.245 37.037 0.00 0.00 36.37 1.75
2927 3747 2.616634 ACATAGAGAGTCCTCGCGTA 57.383 50.000 5.77 0.00 44.08 4.42


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

AutoCloner maintained by Alex Coulton.