Multiple sequence alignment - TraesCS7B01G201600

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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 TraesCS7B01G201600 chr7B 100.000 4703 0 0 1 4703 368620788 368625490 0.000000e+00 8685.0
1 TraesCS7B01G201600 chr7B 82.803 314 46 6 1 311 540778529 540778221 1.670000e-69 274.0
2 TraesCS7B01G201600 chr7D 96.142 4406 127 17 314 4703 373582780 373587158 0.000000e+00 7155.0
3 TraesCS7B01G201600 chr7D 83.333 318 41 10 1 311 603159959 603160271 2.770000e-72 283.0
4 TraesCS7B01G201600 chr7A 96.705 4097 98 9 421 4506 419564559 419568629 0.000000e+00 6783.0
5 TraesCS7B01G201600 chr7A 85.496 131 15 4 315 444 419561788 419561915 2.950000e-27 134.0
6 TraesCS7B01G201600 chr3B 85.304 313 43 3 1 311 564315562 564315251 2.110000e-83 320.0
7 TraesCS7B01G201600 chr3B 84.345 313 44 5 1 311 574710924 574711233 7.650000e-78 302.0
8 TraesCS7B01G201600 chr4A 84.641 306 40 5 13 314 596868696 596868394 9.890000e-77 298.0
9 TraesCS7B01G201600 chr1B 82.857 315 45 5 4 313 12919527 12919217 1.670000e-69 274.0
10 TraesCS7B01G201600 chr3D 82.595 316 45 8 1 311 335198130 335198440 2.160000e-68 270.0
11 TraesCS7B01G201600 chr1D 83.502 297 40 6 17 311 79830082 79829793 7.760000e-68 268.0
12 TraesCS7B01G201600 chr1D 82.019 317 47 9 1 311 481680999 481681311 1.300000e-65 261.0
13 TraesCS7B01G201600 chr5A 96.774 31 1 0 3057 3087 487270265 487270295 9.000000e-03 52.8


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 TraesCS7B01G201600 chr7B 368620788 368625490 4702 False 8685.0 8685 100.0000 1 4703 1 chr7B.!!$F1 4702
1 TraesCS7B01G201600 chr7D 373582780 373587158 4378 False 7155.0 7155 96.1420 314 4703 1 chr7D.!!$F1 4389
2 TraesCS7B01G201600 chr7A 419561788 419568629 6841 False 3458.5 6783 91.1005 315 4506 2 chr7A.!!$F1 4191

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
846 3519 0.036388 CTGTGCCCTTTAGCGGAGAA 60.036 55.000 0.00 0.0 34.65 2.87 F
914 3587 0.326927 GGATCGGGGTCAACCAAGAA 59.673 55.000 0.89 0.0 42.91 2.52 F
1494 4167 0.597637 CCGTGTCGACCATATCAGCC 60.598 60.000 14.12 0.0 0.00 4.85 F
1602 4275 0.721718 CGCCGAGGAATGTCAAGTTC 59.278 55.000 0.00 0.0 0.00 3.01 F
3297 5970 1.003839 AATGCGAGGCAAAGACCGA 60.004 52.632 0.00 0.0 43.62 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2499 5172 1.414181 GAATCCTCCGAGAAGCCATCA 59.586 52.381 0.00 0.0 0.00 3.07 R
2844 5517 4.067896 AGCCATGCAAATACTCTATTCCG 58.932 43.478 0.00 0.0 0.00 4.30 R
2928 5601 2.051435 GCAACACGCGCATTGTGA 60.051 55.556 18.84 0.0 39.73 3.58 R
3519 6192 0.034896 ACGAGGTCACGCTTGGAAAT 59.965 50.000 0.00 0.0 36.70 2.17 R
4179 6862 1.069227 GCAGACAAACCGTGATGTTCC 60.069 52.381 0.00 0.0 0.00 3.62 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
17 18 4.591852 GACGACGATGACGCCTAG 57.408 61.111 0.00 0.00 43.96 3.02
18 19 1.009900 GACGACGATGACGCCTAGG 60.010 63.158 3.67 3.67 43.96 3.02
19 20 2.331805 CGACGATGACGCCTAGGG 59.668 66.667 11.72 3.13 43.96 3.53
20 21 2.027751 GACGATGACGCCTAGGGC 59.972 66.667 11.72 1.76 46.75 5.19
44 45 3.961570 GCCCGTGCGTAGTTTTTAG 57.038 52.632 0.00 0.00 0.00 1.85
45 46 1.150827 GCCCGTGCGTAGTTTTTAGT 58.849 50.000 0.00 0.00 0.00 2.24
46 47 1.532437 GCCCGTGCGTAGTTTTTAGTT 59.468 47.619 0.00 0.00 0.00 2.24
47 48 2.031769 GCCCGTGCGTAGTTTTTAGTTT 60.032 45.455 0.00 0.00 0.00 2.66
48 49 3.186205 GCCCGTGCGTAGTTTTTAGTTTA 59.814 43.478 0.00 0.00 0.00 2.01
49 50 4.142838 GCCCGTGCGTAGTTTTTAGTTTAT 60.143 41.667 0.00 0.00 0.00 1.40
50 51 5.617529 GCCCGTGCGTAGTTTTTAGTTTATT 60.618 40.000 0.00 0.00 0.00 1.40
51 52 6.372981 CCCGTGCGTAGTTTTTAGTTTATTT 58.627 36.000 0.00 0.00 0.00 1.40
52 53 6.857451 CCCGTGCGTAGTTTTTAGTTTATTTT 59.143 34.615 0.00 0.00 0.00 1.82
53 54 7.379262 CCCGTGCGTAGTTTTTAGTTTATTTTT 59.621 33.333 0.00 0.00 0.00 1.94
54 55 9.379811 CCGTGCGTAGTTTTTAGTTTATTTTTA 57.620 29.630 0.00 0.00 0.00 1.52
81 82 8.981370 TTTTATTAAATGCTAATGTAGACGCG 57.019 30.769 3.53 3.53 0.00 6.01
82 83 7.703298 TTATTAAATGCTAATGTAGACGCGT 57.297 32.000 13.85 13.85 0.00 6.01
83 84 3.925688 AAATGCTAATGTAGACGCGTG 57.074 42.857 20.70 0.00 0.00 5.34
84 85 1.852942 ATGCTAATGTAGACGCGTGG 58.147 50.000 20.70 0.00 0.00 4.94
85 86 0.812549 TGCTAATGTAGACGCGTGGA 59.187 50.000 20.70 0.00 0.00 4.02
86 87 1.197910 GCTAATGTAGACGCGTGGAC 58.802 55.000 20.70 15.28 0.00 4.02
87 88 1.202268 GCTAATGTAGACGCGTGGACT 60.202 52.381 20.70 10.88 0.00 3.85
88 89 2.717530 CTAATGTAGACGCGTGGACTC 58.282 52.381 20.70 0.13 0.00 3.36
89 90 0.172803 AATGTAGACGCGTGGACTCC 59.827 55.000 20.70 0.00 0.00 3.85
90 91 1.664321 ATGTAGACGCGTGGACTCCC 61.664 60.000 20.70 0.00 0.00 4.30
91 92 2.753043 TAGACGCGTGGACTCCCC 60.753 66.667 20.70 0.00 0.00 4.81
98 99 2.936032 GTGGACTCCCCCAGCCTT 60.936 66.667 0.00 0.00 36.78 4.35
99 100 2.610859 TGGACTCCCCCAGCCTTC 60.611 66.667 0.00 0.00 0.00 3.46
100 101 3.787001 GGACTCCCCCAGCCTTCG 61.787 72.222 0.00 0.00 0.00 3.79
101 102 3.003763 GACTCCCCCAGCCTTCGT 61.004 66.667 0.00 0.00 0.00 3.85
102 103 3.316573 GACTCCCCCAGCCTTCGTG 62.317 68.421 0.00 0.00 0.00 4.35
103 104 4.101448 CTCCCCCAGCCTTCGTGG 62.101 72.222 0.00 0.00 39.35 4.94
112 113 2.046700 CCTTCGTGGCCGGCTTTA 60.047 61.111 28.56 10.66 33.95 1.85
113 114 1.673009 CCTTCGTGGCCGGCTTTAA 60.673 57.895 28.56 14.43 33.95 1.52
114 115 1.029947 CCTTCGTGGCCGGCTTTAAT 61.030 55.000 28.56 0.00 33.95 1.40
115 116 0.098728 CTTCGTGGCCGGCTTTAATG 59.901 55.000 28.56 14.81 33.95 1.90
116 117 0.606944 TTCGTGGCCGGCTTTAATGT 60.607 50.000 28.56 0.00 33.95 2.71
117 118 0.606944 TCGTGGCCGGCTTTAATGTT 60.607 50.000 28.56 0.00 33.95 2.71
118 119 0.242555 CGTGGCCGGCTTTAATGTTT 59.757 50.000 28.56 0.00 0.00 2.83
119 120 1.469308 CGTGGCCGGCTTTAATGTTTA 59.531 47.619 28.56 0.00 0.00 2.01
120 121 2.095161 CGTGGCCGGCTTTAATGTTTAA 60.095 45.455 28.56 0.00 0.00 1.52
121 122 3.428316 CGTGGCCGGCTTTAATGTTTAAT 60.428 43.478 28.56 0.00 0.00 1.40
122 123 4.500127 GTGGCCGGCTTTAATGTTTAATT 58.500 39.130 28.56 0.00 0.00 1.40
123 124 5.652518 GTGGCCGGCTTTAATGTTTAATTA 58.347 37.500 28.56 0.00 0.00 1.40
124 125 6.100668 GTGGCCGGCTTTAATGTTTAATTAA 58.899 36.000 28.56 0.00 0.00 1.40
125 126 6.759356 GTGGCCGGCTTTAATGTTTAATTAAT 59.241 34.615 28.56 0.00 0.00 1.40
126 127 7.279090 GTGGCCGGCTTTAATGTTTAATTAATT 59.721 33.333 28.56 5.89 0.00 1.40
127 128 7.824779 TGGCCGGCTTTAATGTTTAATTAATTT 59.175 29.630 28.56 0.00 0.00 1.82
128 129 8.670135 GGCCGGCTTTAATGTTTAATTAATTTT 58.330 29.630 28.56 0.00 0.00 1.82
129 130 9.484326 GCCGGCTTTAATGTTTAATTAATTTTG 57.516 29.630 22.15 0.00 0.00 2.44
130 131 9.980780 CCGGCTTTAATGTTTAATTAATTTTGG 57.019 29.630 5.91 0.00 0.00 3.28
152 153 9.440773 TTTGGTTTTATGTTAAATATGCATGCA 57.559 25.926 25.04 25.04 0.00 3.96
153 154 9.610705 TTGGTTTTATGTTAAATATGCATGCAT 57.389 25.926 33.92 33.92 40.19 3.96
154 155 9.610705 TGGTTTTATGTTAAATATGCATGCATT 57.389 25.926 36.23 22.55 37.82 3.56
181 182 3.651803 TTTTTCGCCGTCAAAATGGAT 57.348 38.095 0.00 0.00 32.79 3.41
182 183 2.911819 TTTCGCCGTCAAAATGGATC 57.088 45.000 0.00 0.00 32.79 3.36
183 184 0.724549 TTCGCCGTCAAAATGGATCG 59.275 50.000 0.00 0.00 32.79 3.69
184 185 1.297598 CGCCGTCAAAATGGATCGC 60.298 57.895 0.00 0.00 32.79 4.58
185 186 1.800032 GCCGTCAAAATGGATCGCA 59.200 52.632 0.00 0.00 32.79 5.10
186 187 0.523335 GCCGTCAAAATGGATCGCAC 60.523 55.000 0.00 0.00 32.79 5.34
187 188 0.098728 CCGTCAAAATGGATCGCACC 59.901 55.000 0.00 0.00 32.79 5.01
188 189 0.801872 CGTCAAAATGGATCGCACCA 59.198 50.000 3.15 3.15 44.41 4.17
189 190 1.202065 CGTCAAAATGGATCGCACCAG 60.202 52.381 6.56 0.00 43.49 4.00
190 191 0.810648 TCAAAATGGATCGCACCAGC 59.189 50.000 6.56 0.00 43.49 4.85
207 208 2.279851 CGTTGGACGCACTCACCA 60.280 61.111 0.00 0.00 33.65 4.17
208 209 1.885388 CGTTGGACGCACTCACCAA 60.885 57.895 0.00 0.00 40.68 3.67
209 210 4.134623 TTGGACGCACTCACCAAC 57.865 55.556 0.00 0.00 38.52 3.77
210 211 1.525077 TTGGACGCACTCACCAACC 60.525 57.895 0.00 0.00 38.52 3.77
211 212 2.668550 GGACGCACTCACCAACCC 60.669 66.667 0.00 0.00 0.00 4.11
212 213 2.668550 GACGCACTCACCAACCCC 60.669 66.667 0.00 0.00 0.00 4.95
213 214 3.469863 GACGCACTCACCAACCCCA 62.470 63.158 0.00 0.00 0.00 4.96
214 215 2.203280 CGCACTCACCAACCCCAA 60.203 61.111 0.00 0.00 0.00 4.12
215 216 2.551912 CGCACTCACCAACCCCAAC 61.552 63.158 0.00 0.00 0.00 3.77
216 217 2.551912 GCACTCACCAACCCCAACG 61.552 63.158 0.00 0.00 0.00 4.10
217 218 2.203294 ACTCACCAACCCCAACGC 60.203 61.111 0.00 0.00 0.00 4.84
218 219 3.353836 CTCACCAACCCCAACGCG 61.354 66.667 3.53 3.53 0.00 6.01
219 220 4.939368 TCACCAACCCCAACGCGG 62.939 66.667 12.47 0.00 0.00 6.46
220 221 4.939368 CACCAACCCCAACGCGGA 62.939 66.667 12.47 0.00 36.56 5.54
221 222 4.192453 ACCAACCCCAACGCGGAA 62.192 61.111 12.47 0.00 36.56 4.30
222 223 3.361977 CCAACCCCAACGCGGAAG 61.362 66.667 12.47 0.00 36.56 3.46
234 235 3.467119 CGGAAGCGGACGTTCGTG 61.467 66.667 19.12 0.00 0.00 4.35
235 236 2.355481 GGAAGCGGACGTTCGTGT 60.355 61.111 19.12 5.74 0.00 4.49
236 237 2.370393 GGAAGCGGACGTTCGTGTC 61.370 63.158 19.12 14.73 38.17 3.67
242 243 3.103911 GACGTTCGTGTCCGCCTG 61.104 66.667 1.74 0.00 32.61 4.85
243 244 4.657824 ACGTTCGTGTCCGCCTGG 62.658 66.667 0.00 0.00 0.00 4.45
255 256 3.508840 GCCTGGCGGATCCAAACG 61.509 66.667 13.41 0.00 46.01 3.60
256 257 2.267642 CCTGGCGGATCCAAACGA 59.732 61.111 13.41 0.00 46.01 3.85
257 258 1.376683 CCTGGCGGATCCAAACGAA 60.377 57.895 13.41 0.00 46.01 3.85
258 259 1.644786 CCTGGCGGATCCAAACGAAC 61.645 60.000 13.41 0.00 46.01 3.95
259 260 0.953471 CTGGCGGATCCAAACGAACA 60.953 55.000 13.41 0.30 46.01 3.18
260 261 0.535328 TGGCGGATCCAAACGAACAA 60.535 50.000 13.41 0.00 43.21 2.83
261 262 0.594110 GGCGGATCCAAACGAACAAA 59.406 50.000 13.41 0.00 34.01 2.83
262 263 1.001158 GGCGGATCCAAACGAACAAAA 60.001 47.619 13.41 0.00 34.01 2.44
263 264 2.048498 GCGGATCCAAACGAACAAAAC 58.952 47.619 13.41 0.00 0.00 2.43
264 265 2.541999 GCGGATCCAAACGAACAAAACA 60.542 45.455 13.41 0.00 0.00 2.83
265 266 3.040099 CGGATCCAAACGAACAAAACAC 58.960 45.455 13.41 0.00 0.00 3.32
266 267 3.487711 CGGATCCAAACGAACAAAACACA 60.488 43.478 13.41 0.00 0.00 3.72
267 268 4.041723 GGATCCAAACGAACAAAACACAG 58.958 43.478 6.95 0.00 0.00 3.66
268 269 4.201970 GGATCCAAACGAACAAAACACAGA 60.202 41.667 6.95 0.00 0.00 3.41
269 270 4.086199 TCCAAACGAACAAAACACAGAC 57.914 40.909 0.00 0.00 0.00 3.51
270 271 3.502595 TCCAAACGAACAAAACACAGACA 59.497 39.130 0.00 0.00 0.00 3.41
271 272 4.023107 TCCAAACGAACAAAACACAGACAA 60.023 37.500 0.00 0.00 0.00 3.18
272 273 4.681942 CCAAACGAACAAAACACAGACAAA 59.318 37.500 0.00 0.00 0.00 2.83
273 274 5.175856 CCAAACGAACAAAACACAGACAAAA 59.824 36.000 0.00 0.00 0.00 2.44
274 275 6.128688 CCAAACGAACAAAACACAGACAAAAT 60.129 34.615 0.00 0.00 0.00 1.82
275 276 6.626199 AACGAACAAAACACAGACAAAATC 57.374 33.333 0.00 0.00 0.00 2.17
276 277 5.704888 ACGAACAAAACACAGACAAAATCA 58.295 33.333 0.00 0.00 0.00 2.57
277 278 5.571357 ACGAACAAAACACAGACAAAATCAC 59.429 36.000 0.00 0.00 0.00 3.06
278 279 5.004345 CGAACAAAACACAGACAAAATCACC 59.996 40.000 0.00 0.00 0.00 4.02
279 280 4.420168 ACAAAACACAGACAAAATCACCG 58.580 39.130 0.00 0.00 0.00 4.94
280 281 4.082463 ACAAAACACAGACAAAATCACCGT 60.082 37.500 0.00 0.00 0.00 4.83
281 282 3.691049 AACACAGACAAAATCACCGTG 57.309 42.857 0.00 0.00 33.02 4.94
282 283 1.333619 ACACAGACAAAATCACCGTGC 59.666 47.619 0.00 0.00 31.03 5.34
283 284 1.333308 CACAGACAAAATCACCGTGCA 59.667 47.619 0.00 0.00 0.00 4.57
284 285 2.030893 CACAGACAAAATCACCGTGCAT 60.031 45.455 0.00 0.00 0.00 3.96
285 286 2.622942 ACAGACAAAATCACCGTGCATT 59.377 40.909 0.00 0.00 0.00 3.56
286 287 3.068024 ACAGACAAAATCACCGTGCATTT 59.932 39.130 0.00 0.00 0.00 2.32
287 288 3.426191 CAGACAAAATCACCGTGCATTTG 59.574 43.478 19.16 19.16 37.10 2.32
288 289 2.730928 GACAAAATCACCGTGCATTTGG 59.269 45.455 22.20 15.51 35.77 3.28
289 290 2.067766 CAAAATCACCGTGCATTTGGG 58.932 47.619 15.58 1.70 0.00 4.12
290 291 1.337118 AAATCACCGTGCATTTGGGT 58.663 45.000 7.41 2.28 33.37 4.51
291 292 0.887933 AATCACCGTGCATTTGGGTC 59.112 50.000 7.41 0.00 29.82 4.46
292 293 1.305219 ATCACCGTGCATTTGGGTCG 61.305 55.000 7.41 0.00 29.82 4.79
293 294 1.963855 CACCGTGCATTTGGGTCGA 60.964 57.895 7.41 0.00 29.82 4.20
294 295 1.964373 ACCGTGCATTTGGGTCGAC 60.964 57.895 7.13 7.13 0.00 4.20
295 296 2.686816 CCGTGCATTTGGGTCGACC 61.687 63.158 27.04 27.04 40.81 4.79
307 308 0.514255 GGTCGACCCGTTAAAGTTGC 59.486 55.000 24.75 0.00 0.00 4.17
308 309 1.505425 GTCGACCCGTTAAAGTTGCT 58.495 50.000 3.51 0.00 0.00 3.91
309 310 1.458445 GTCGACCCGTTAAAGTTGCTC 59.542 52.381 3.51 0.00 0.00 4.26
310 311 1.342174 TCGACCCGTTAAAGTTGCTCT 59.658 47.619 0.00 0.00 0.00 4.09
311 312 1.459592 CGACCCGTTAAAGTTGCTCTG 59.540 52.381 0.00 0.00 0.00 3.35
312 313 2.762745 GACCCGTTAAAGTTGCTCTGA 58.237 47.619 0.00 0.00 0.00 3.27
313 314 2.479275 GACCCGTTAAAGTTGCTCTGAC 59.521 50.000 0.00 0.00 0.00 3.51
314 315 1.459592 CCCGTTAAAGTTGCTCTGACG 59.540 52.381 0.00 0.00 0.00 4.35
315 316 1.136336 CCGTTAAAGTTGCTCTGACGC 60.136 52.381 0.00 0.00 31.33 5.19
316 317 1.136336 CGTTAAAGTTGCTCTGACGCC 60.136 52.381 0.00 0.00 0.00 5.68
317 318 2.143925 GTTAAAGTTGCTCTGACGCCT 58.856 47.619 0.00 0.00 0.00 5.52
318 319 2.543777 TAAAGTTGCTCTGACGCCTT 57.456 45.000 0.00 0.00 0.00 4.35
319 320 2.543777 AAAGTTGCTCTGACGCCTTA 57.456 45.000 0.00 0.00 0.00 2.69
320 321 2.770164 AAGTTGCTCTGACGCCTTAT 57.230 45.000 0.00 0.00 0.00 1.73
323 324 3.412386 AGTTGCTCTGACGCCTTATTTT 58.588 40.909 0.00 0.00 0.00 1.82
372 373 2.704572 ACTGGATTTTTCGAGGCTCAG 58.295 47.619 15.95 7.64 0.00 3.35
383 385 2.283460 GGCTCAGCCTTTGCCCTT 60.283 61.111 9.09 0.00 46.69 3.95
387 389 2.048877 CAGCCTTTGCCCTTTGCG 60.049 61.111 0.00 0.00 45.60 4.85
490 3158 5.165676 CACCTTTTCCCGTTAAAAATAGGC 58.834 41.667 0.00 0.00 0.00 3.93
566 3236 1.005332 TCAGTCCTCTCCTCTCCACTG 59.995 57.143 0.00 0.00 33.90 3.66
568 3238 1.379176 TCCTCTCCTCTCCACTGCG 60.379 63.158 0.00 0.00 0.00 5.18
702 3375 1.228894 TCCACTCCTCTCCGCAACT 60.229 57.895 0.00 0.00 0.00 3.16
824 3497 5.536161 AGGTAACCGTTGTACTCTGTTTCTA 59.464 40.000 0.00 0.00 37.17 2.10
846 3519 0.036388 CTGTGCCCTTTAGCGGAGAA 60.036 55.000 0.00 0.00 34.65 2.87
907 3580 3.078836 GGTCGGGATCGGGGTCAA 61.079 66.667 0.00 0.00 36.95 3.18
908 3581 2.186125 GTCGGGATCGGGGTCAAC 59.814 66.667 0.00 0.00 36.95 3.18
909 3582 3.078836 TCGGGATCGGGGTCAACC 61.079 66.667 0.00 0.00 36.95 3.77
910 3583 3.395702 CGGGATCGGGGTCAACCA 61.396 66.667 0.89 0.00 42.91 3.67
911 3584 2.961893 CGGGATCGGGGTCAACCAA 61.962 63.158 0.89 0.00 42.91 3.67
912 3585 1.077716 GGGATCGGGGTCAACCAAG 60.078 63.158 0.89 0.00 42.91 3.61
913 3586 1.559065 GGGATCGGGGTCAACCAAGA 61.559 60.000 0.89 0.11 42.91 3.02
914 3587 0.326927 GGATCGGGGTCAACCAAGAA 59.673 55.000 0.89 0.00 42.91 2.52
915 3588 1.271707 GGATCGGGGTCAACCAAGAAA 60.272 52.381 0.89 0.00 42.91 2.52
916 3589 2.510613 GATCGGGGTCAACCAAGAAAA 58.489 47.619 0.89 0.00 42.91 2.29
917 3590 2.438800 TCGGGGTCAACCAAGAAAAA 57.561 45.000 0.89 0.00 42.91 1.94
918 3591 2.303175 TCGGGGTCAACCAAGAAAAAG 58.697 47.619 0.89 0.00 42.91 2.27
919 3592 1.269569 CGGGGTCAACCAAGAAAAAGC 60.270 52.381 0.89 0.00 42.91 3.51
920 3593 1.070134 GGGGTCAACCAAGAAAAAGCC 59.930 52.381 0.89 0.00 42.91 4.35
921 3594 1.760029 GGGTCAACCAAGAAAAAGCCA 59.240 47.619 0.89 0.00 39.85 4.75
922 3595 2.169561 GGGTCAACCAAGAAAAAGCCAA 59.830 45.455 0.89 0.00 39.85 4.52
923 3596 3.369997 GGGTCAACCAAGAAAAAGCCAAA 60.370 43.478 0.89 0.00 39.85 3.28
924 3597 4.257731 GGTCAACCAAGAAAAAGCCAAAA 58.742 39.130 0.00 0.00 35.64 2.44
925 3598 4.697828 GGTCAACCAAGAAAAAGCCAAAAA 59.302 37.500 0.00 0.00 35.64 1.94
1009 3682 3.368427 CGAGCTTCAAGGAATGGACAGTA 60.368 47.826 0.00 0.00 0.00 2.74
1150 3823 3.934391 GACGGCTCCCACTTGGTCG 62.934 68.421 0.00 0.00 34.77 4.79
1260 3933 2.284190 GGTCTCTTGCTTGATACCAGC 58.716 52.381 8.43 0.00 34.54 4.85
1440 4113 1.141657 TCAGTGATAGATTGCTGGGGC 59.858 52.381 0.00 0.00 39.26 5.80
1467 4140 1.761449 TGACTGCCACACATGTTGTT 58.239 45.000 0.00 0.00 35.67 2.83
1494 4167 0.597637 CCGTGTCGACCATATCAGCC 60.598 60.000 14.12 0.00 0.00 4.85
1533 4206 1.646540 CTTGTTTGCGCGGAACAGA 59.353 52.632 22.65 15.32 38.17 3.41
1602 4275 0.721718 CGCCGAGGAATGTCAAGTTC 59.278 55.000 0.00 0.00 0.00 3.01
1620 4293 1.050988 TCCAGTCCATAGGAGCAGGC 61.051 60.000 0.00 0.00 29.39 4.85
1623 4296 2.041922 TCCATAGGAGCAGGCGGT 60.042 61.111 0.00 0.00 0.00 5.68
1698 4371 1.297689 GGAGATGCAGCAGGTGTCA 59.702 57.895 4.07 0.40 0.00 3.58
1873 4546 3.244911 ACCCAAAGGTCTCAGGTTGTATG 60.245 47.826 0.00 0.00 46.45 2.39
2391 5064 3.365767 GCAAGTTGAGGATGACAAAGAGC 60.366 47.826 7.16 0.00 0.00 4.09
2441 5114 1.903877 AAGATCCAGCCTGACGTGGG 61.904 60.000 0.00 0.00 34.27 4.61
2499 5172 8.925233 CCTATGAGGAGTTGGAACAAGCAACT 62.925 46.154 0.00 0.00 40.63 3.16
2616 5289 4.260579 CGTGCAATAAAAGTATCGGATGCA 60.261 41.667 8.78 1.17 39.95 3.96
2928 5601 8.152898 TCTTCAAACATATTGATCGATGAGGAT 58.847 33.333 0.54 0.00 0.00 3.24
3255 5928 1.932511 GAGGCTCTGAAGAAGATTGCG 59.067 52.381 7.40 0.00 33.29 4.85
3297 5970 1.003839 AATGCGAGGCAAAGACCGA 60.004 52.632 0.00 0.00 43.62 4.69
3693 6366 2.616510 GGAGGACTTGTACTTGCAGCAT 60.617 50.000 0.00 0.00 0.00 3.79
3765 6438 5.270853 CCGTTTTAAGTTCAGACTTTGTGG 58.729 41.667 0.00 0.00 43.48 4.17
3770 6443 0.312102 GTTCAGACTTTGTGGCCTGC 59.688 55.000 3.32 0.00 0.00 4.85
3777 6450 0.961019 CTTTGTGGCCTGCTGCTTTA 59.039 50.000 3.32 0.00 40.92 1.85
3883 6558 7.178983 TGGAGGCATTTCTTTGTAGATTGATTT 59.821 33.333 0.00 0.00 0.00 2.17
3924 6599 5.050490 CACTTCTATTTACGAGTGGATGGG 58.950 45.833 0.00 0.00 36.68 4.00
4023 6701 7.040478 TCGCCTGCAAATTAGCATAATATTCTT 60.040 33.333 0.00 0.00 44.68 2.52
4102 6783 5.514279 GCATAATATTGTGCCAACTGAGAC 58.486 41.667 22.62 0.00 39.09 3.36
4106 6787 2.031258 TTGTGCCAACTGAGACGAAA 57.969 45.000 0.00 0.00 0.00 3.46
4113 6794 2.290641 CCAACTGAGACGAAACTTTGGG 59.709 50.000 0.00 0.00 0.00 4.12
4137 6818 7.201902 GGGGATCAAATTGCATGTCTAACATTA 60.202 37.037 0.00 0.00 36.53 1.90
4212 6895 4.757149 GGTTTGTCTGCTAATCTTCAGTGT 59.243 41.667 0.00 0.00 0.00 3.55
4325 7008 0.674895 AGACAATGAAGGCAGGTCGC 60.675 55.000 0.00 0.00 37.35 5.19
4411 7094 5.231357 GCAAAGGCGGTAATACTTTAAATGC 59.769 40.000 0.00 0.00 33.47 3.56
4442 7125 3.188159 AGAGTAACACTTTCGGTTGCA 57.812 42.857 0.00 0.00 33.93 4.08
4479 7162 4.371855 CTCACGAGCTCAAATACACCTA 57.628 45.455 15.40 0.00 0.00 3.08
4491 7174 8.673711 GCTCAAATACACCTACATGAACATTAA 58.326 33.333 0.00 0.00 0.00 1.40
4572 7259 3.853671 CGACAAATTTCTAACATGCTGCC 59.146 43.478 0.00 0.00 0.00 4.85
4573 7260 3.836949 ACAAATTTCTAACATGCTGCCG 58.163 40.909 0.00 0.00 0.00 5.69
4598 7285 1.230324 GCCCTTAGAATGACATCCGC 58.770 55.000 0.00 0.00 0.00 5.54
4622 7309 5.470368 GGAGGCCTGTACAAAAAGAAAATC 58.530 41.667 12.00 0.00 0.00 2.17
4631 7318 5.514274 ACAAAAAGAAAATCGGAGCTCAA 57.486 34.783 17.19 2.91 0.00 3.02
4636 7323 4.773323 AGAAAATCGGAGCTCAAAAAGG 57.227 40.909 17.19 0.00 0.00 3.11
4638 7325 0.804989 AATCGGAGCTCAAAAAGGCG 59.195 50.000 17.19 8.01 0.00 5.52
4651 7338 2.636768 AAAGGCGCATTTTCTAGCAC 57.363 45.000 15.24 0.00 0.00 4.40
4653 7340 2.691409 AGGCGCATTTTCTAGCACTA 57.309 45.000 10.83 0.00 0.00 2.74
4655 7342 3.545703 AGGCGCATTTTCTAGCACTAAT 58.454 40.909 10.83 0.00 0.00 1.73
4656 7343 3.947834 AGGCGCATTTTCTAGCACTAATT 59.052 39.130 10.83 0.00 0.00 1.40
4658 7345 5.765182 AGGCGCATTTTCTAGCACTAATTAT 59.235 36.000 10.83 0.00 0.00 1.28
4659 7346 6.263168 AGGCGCATTTTCTAGCACTAATTATT 59.737 34.615 10.83 0.00 0.00 1.40
4660 7347 6.360681 GGCGCATTTTCTAGCACTAATTATTG 59.639 38.462 10.83 0.00 0.00 1.90
4661 7348 6.912591 GCGCATTTTCTAGCACTAATTATTGT 59.087 34.615 0.30 0.00 0.00 2.71
4662 7349 7.432252 GCGCATTTTCTAGCACTAATTATTGTT 59.568 33.333 0.30 1.65 0.00 2.83
4663 7350 9.289303 CGCATTTTCTAGCACTAATTATTGTTT 57.711 29.630 4.91 0.00 0.00 2.83
4690 7378 3.130869 GGCACTTGCATCATTGGTGATAA 59.869 43.478 0.00 0.00 43.14 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.009900 CCTAGGCGTCATCGTCGTC 60.010 63.158 0.00 0.00 46.96 4.20
1 2 2.478890 CCCTAGGCGTCATCGTCGT 61.479 63.158 2.05 0.00 46.96 4.34
3 4 2.027751 GCCCTAGGCGTCATCGTC 59.972 66.667 2.05 0.00 39.62 4.20
26 27 1.150827 ACTAAAAACTACGCACGGGC 58.849 50.000 0.00 0.00 0.00 6.13
27 28 3.883631 AAACTAAAAACTACGCACGGG 57.116 42.857 0.00 0.00 0.00 5.28
28 29 7.840981 AAAATAAACTAAAAACTACGCACGG 57.159 32.000 0.00 0.00 0.00 4.94
55 56 9.428363 CGCGTCTACATTAGCATTTAATAAAAA 57.572 29.630 0.00 0.00 0.00 1.94
56 57 8.605746 ACGCGTCTACATTAGCATTTAATAAAA 58.394 29.630 5.58 0.00 0.00 1.52
57 58 8.059502 CACGCGTCTACATTAGCATTTAATAAA 58.940 33.333 9.86 0.00 0.00 1.40
58 59 7.306925 CCACGCGTCTACATTAGCATTTAATAA 60.307 37.037 9.86 0.00 0.00 1.40
59 60 6.144886 CCACGCGTCTACATTAGCATTTAATA 59.855 38.462 9.86 0.00 0.00 0.98
60 61 5.050363 CCACGCGTCTACATTAGCATTTAAT 60.050 40.000 9.86 0.00 0.00 1.40
61 62 4.269123 CCACGCGTCTACATTAGCATTTAA 59.731 41.667 9.86 0.00 0.00 1.52
62 63 3.799963 CCACGCGTCTACATTAGCATTTA 59.200 43.478 9.86 0.00 0.00 1.40
63 64 2.607635 CCACGCGTCTACATTAGCATTT 59.392 45.455 9.86 0.00 0.00 2.32
64 65 2.159156 TCCACGCGTCTACATTAGCATT 60.159 45.455 9.86 0.00 0.00 3.56
65 66 1.407618 TCCACGCGTCTACATTAGCAT 59.592 47.619 9.86 0.00 0.00 3.79
66 67 0.812549 TCCACGCGTCTACATTAGCA 59.187 50.000 9.86 0.00 0.00 3.49
67 68 1.197910 GTCCACGCGTCTACATTAGC 58.802 55.000 9.86 0.00 0.00 3.09
68 69 2.541178 GGAGTCCACGCGTCTACATTAG 60.541 54.545 9.86 0.00 0.00 1.73
69 70 1.402968 GGAGTCCACGCGTCTACATTA 59.597 52.381 9.86 0.00 0.00 1.90
70 71 0.172803 GGAGTCCACGCGTCTACATT 59.827 55.000 9.86 0.00 0.00 2.71
71 72 1.664321 GGGAGTCCACGCGTCTACAT 61.664 60.000 9.86 0.45 0.00 2.29
72 73 2.338015 GGGAGTCCACGCGTCTACA 61.338 63.158 9.86 0.00 0.00 2.74
73 74 2.488820 GGGAGTCCACGCGTCTAC 59.511 66.667 9.86 10.95 0.00 2.59
74 75 2.753043 GGGGAGTCCACGCGTCTA 60.753 66.667 9.86 0.00 35.00 2.59
81 82 2.936032 AAGGCTGGGGGAGTCCAC 60.936 66.667 12.30 7.34 37.22 4.02
82 83 2.610859 GAAGGCTGGGGGAGTCCA 60.611 66.667 12.30 0.00 37.22 4.02
83 84 3.787001 CGAAGGCTGGGGGAGTCC 61.787 72.222 0.00 0.00 0.00 3.85
84 85 3.003763 ACGAAGGCTGGGGGAGTC 61.004 66.667 0.00 0.00 0.00 3.36
85 86 3.322466 CACGAAGGCTGGGGGAGT 61.322 66.667 0.00 0.00 0.00 3.85
86 87 4.101448 CCACGAAGGCTGGGGGAG 62.101 72.222 0.89 0.00 0.00 4.30
95 96 1.029947 ATTAAAGCCGGCCACGAAGG 61.030 55.000 26.15 0.00 44.60 3.46
96 97 0.098728 CATTAAAGCCGGCCACGAAG 59.901 55.000 26.15 5.89 44.60 3.79
97 98 0.606944 ACATTAAAGCCGGCCACGAA 60.607 50.000 26.15 13.16 44.60 3.85
98 99 0.606944 AACATTAAAGCCGGCCACGA 60.607 50.000 26.15 7.86 44.60 4.35
99 100 0.242555 AAACATTAAAGCCGGCCACG 59.757 50.000 26.15 8.66 40.55 4.94
100 101 3.579335 TTAAACATTAAAGCCGGCCAC 57.421 42.857 26.15 0.00 0.00 5.01
101 102 4.810191 AATTAAACATTAAAGCCGGCCA 57.190 36.364 26.15 5.71 0.00 5.36
102 103 7.780008 AATTAATTAAACATTAAAGCCGGCC 57.220 32.000 26.15 5.07 0.00 6.13
103 104 9.484326 CAAAATTAATTAAACATTAAAGCCGGC 57.516 29.630 21.89 21.89 0.00 6.13
104 105 9.980780 CCAAAATTAATTAAACATTAAAGCCGG 57.019 29.630 1.21 0.00 0.00 6.13
126 127 9.440773 TGCATGCATATTTAACATAAAACCAAA 57.559 25.926 18.46 0.00 0.00 3.28
127 128 9.610705 ATGCATGCATATTTAACATAAAACCAA 57.389 25.926 31.35 0.00 34.49 3.67
128 129 9.610705 AATGCATGCATATTTAACATAAAACCA 57.389 25.926 32.36 0.00 35.31 3.67
161 162 3.570559 GATCCATTTTGACGGCGAAAAA 58.429 40.909 16.62 19.48 31.43 1.94
162 163 2.413502 CGATCCATTTTGACGGCGAAAA 60.414 45.455 16.62 11.70 31.43 2.29
163 164 1.129624 CGATCCATTTTGACGGCGAAA 59.870 47.619 16.62 6.03 0.00 3.46
164 165 0.724549 CGATCCATTTTGACGGCGAA 59.275 50.000 16.62 0.00 0.00 4.70
165 166 1.701545 GCGATCCATTTTGACGGCGA 61.702 55.000 16.62 0.00 0.00 5.54
166 167 1.297598 GCGATCCATTTTGACGGCG 60.298 57.895 4.80 4.80 0.00 6.46
167 168 0.523335 GTGCGATCCATTTTGACGGC 60.523 55.000 0.00 0.00 0.00 5.68
168 169 0.098728 GGTGCGATCCATTTTGACGG 59.901 55.000 0.00 0.00 0.00 4.79
169 170 0.801872 TGGTGCGATCCATTTTGACG 59.198 50.000 0.00 0.00 31.96 4.35
170 171 1.468054 GCTGGTGCGATCCATTTTGAC 60.468 52.381 0.00 0.00 36.84 3.18
171 172 0.810648 GCTGGTGCGATCCATTTTGA 59.189 50.000 0.00 0.00 36.84 2.69
172 173 3.334078 GCTGGTGCGATCCATTTTG 57.666 52.632 0.00 0.00 36.84 2.44
190 191 1.885388 TTGGTGAGTGCGTCCAACG 60.885 57.895 0.00 0.00 45.88 4.10
191 192 4.134623 TTGGTGAGTGCGTCCAAC 57.865 55.556 0.00 0.00 36.48 3.77
192 193 1.525077 GGTTGGTGAGTGCGTCCAA 60.525 57.895 0.00 0.00 38.65 3.53
193 194 2.110213 GGTTGGTGAGTGCGTCCA 59.890 61.111 0.00 0.00 0.00 4.02
194 195 2.668550 GGGTTGGTGAGTGCGTCC 60.669 66.667 0.00 0.00 0.00 4.79
195 196 2.668550 GGGGTTGGTGAGTGCGTC 60.669 66.667 0.00 0.00 0.00 5.19
196 197 3.050354 TTGGGGTTGGTGAGTGCGT 62.050 57.895 0.00 0.00 0.00 5.24
197 198 2.203280 TTGGGGTTGGTGAGTGCG 60.203 61.111 0.00 0.00 0.00 5.34
198 199 2.551912 CGTTGGGGTTGGTGAGTGC 61.552 63.158 0.00 0.00 0.00 4.40
199 200 2.551912 GCGTTGGGGTTGGTGAGTG 61.552 63.158 0.00 0.00 0.00 3.51
200 201 2.203294 GCGTTGGGGTTGGTGAGT 60.203 61.111 0.00 0.00 0.00 3.41
201 202 3.353836 CGCGTTGGGGTTGGTGAG 61.354 66.667 0.00 0.00 0.00 3.51
202 203 4.939368 CCGCGTTGGGGTTGGTGA 62.939 66.667 4.92 0.00 0.00 4.02
203 204 4.939368 TCCGCGTTGGGGTTGGTG 62.939 66.667 4.92 0.00 38.76 4.17
204 205 4.192453 TTCCGCGTTGGGGTTGGT 62.192 61.111 4.92 0.00 38.76 3.67
205 206 3.361977 CTTCCGCGTTGGGGTTGG 61.362 66.667 4.92 0.00 38.76 3.77
206 207 4.038080 GCTTCCGCGTTGGGGTTG 62.038 66.667 4.92 0.00 38.76 3.77
217 218 3.467119 CACGAACGTCCGCTTCCG 61.467 66.667 0.00 0.00 0.00 4.30
218 219 2.355481 ACACGAACGTCCGCTTCC 60.355 61.111 0.00 0.00 0.00 3.46
219 220 2.370393 GGACACGAACGTCCGCTTC 61.370 63.158 0.00 0.00 45.77 3.86
220 221 2.355481 GGACACGAACGTCCGCTT 60.355 61.111 0.00 0.00 45.77 4.68
225 226 3.103911 CAGGCGGACACGAACGTC 61.104 66.667 0.00 0.00 44.60 4.34
226 227 4.657824 CCAGGCGGACACGAACGT 62.658 66.667 0.00 0.00 44.60 3.99
242 243 0.594110 TTTGTTCGTTTGGATCCGCC 59.406 50.000 7.39 0.00 37.10 6.13
243 244 2.048498 GTTTTGTTCGTTTGGATCCGC 58.952 47.619 7.39 0.00 0.00 5.54
244 245 3.040099 GTGTTTTGTTCGTTTGGATCCG 58.960 45.455 7.39 0.00 0.00 4.18
245 246 4.035278 TGTGTTTTGTTCGTTTGGATCC 57.965 40.909 4.20 4.20 0.00 3.36
246 247 4.733405 GTCTGTGTTTTGTTCGTTTGGATC 59.267 41.667 0.00 0.00 0.00 3.36
247 248 4.156922 TGTCTGTGTTTTGTTCGTTTGGAT 59.843 37.500 0.00 0.00 0.00 3.41
248 249 3.502595 TGTCTGTGTTTTGTTCGTTTGGA 59.497 39.130 0.00 0.00 0.00 3.53
249 250 3.827625 TGTCTGTGTTTTGTTCGTTTGG 58.172 40.909 0.00 0.00 0.00 3.28
250 251 5.814314 TTTGTCTGTGTTTTGTTCGTTTG 57.186 34.783 0.00 0.00 0.00 2.93
251 252 6.642950 TGATTTTGTCTGTGTTTTGTTCGTTT 59.357 30.769 0.00 0.00 0.00 3.60
252 253 6.088883 GTGATTTTGTCTGTGTTTTGTTCGTT 59.911 34.615 0.00 0.00 0.00 3.85
253 254 5.571357 GTGATTTTGTCTGTGTTTTGTTCGT 59.429 36.000 0.00 0.00 0.00 3.85
254 255 5.004345 GGTGATTTTGTCTGTGTTTTGTTCG 59.996 40.000 0.00 0.00 0.00 3.95
255 256 5.004345 CGGTGATTTTGTCTGTGTTTTGTTC 59.996 40.000 0.00 0.00 0.00 3.18
256 257 4.862018 CGGTGATTTTGTCTGTGTTTTGTT 59.138 37.500 0.00 0.00 0.00 2.83
257 258 4.082463 ACGGTGATTTTGTCTGTGTTTTGT 60.082 37.500 0.00 0.00 0.00 2.83
258 259 4.265085 CACGGTGATTTTGTCTGTGTTTTG 59.735 41.667 0.74 0.00 0.00 2.44
259 260 4.420168 CACGGTGATTTTGTCTGTGTTTT 58.580 39.130 0.74 0.00 0.00 2.43
260 261 3.733684 GCACGGTGATTTTGTCTGTGTTT 60.734 43.478 13.29 0.00 31.93 2.83
261 262 2.223479 GCACGGTGATTTTGTCTGTGTT 60.223 45.455 13.29 0.00 31.93 3.32
262 263 1.333619 GCACGGTGATTTTGTCTGTGT 59.666 47.619 13.29 0.00 31.93 3.72
263 264 1.333308 TGCACGGTGATTTTGTCTGTG 59.667 47.619 13.29 0.00 0.00 3.66
264 265 1.674359 TGCACGGTGATTTTGTCTGT 58.326 45.000 13.29 0.00 0.00 3.41
265 266 2.995466 ATGCACGGTGATTTTGTCTG 57.005 45.000 13.29 0.00 0.00 3.51
266 267 3.552684 CCAAATGCACGGTGATTTTGTCT 60.553 43.478 23.01 3.62 0.00 3.41
267 268 2.730928 CCAAATGCACGGTGATTTTGTC 59.269 45.455 23.01 4.73 0.00 3.18
268 269 2.547642 CCCAAATGCACGGTGATTTTGT 60.548 45.455 23.01 4.12 0.00 2.83
269 270 2.067766 CCCAAATGCACGGTGATTTTG 58.932 47.619 13.29 17.93 0.00 2.44
270 271 1.691434 ACCCAAATGCACGGTGATTTT 59.309 42.857 13.29 7.54 0.00 1.82
271 272 1.272212 GACCCAAATGCACGGTGATTT 59.728 47.619 13.29 11.60 0.00 2.17
272 273 0.887933 GACCCAAATGCACGGTGATT 59.112 50.000 13.29 6.19 0.00 2.57
273 274 1.305219 CGACCCAAATGCACGGTGAT 61.305 55.000 13.29 0.00 0.00 3.06
274 275 1.963855 CGACCCAAATGCACGGTGA 60.964 57.895 13.29 0.00 0.00 4.02
275 276 1.963855 TCGACCCAAATGCACGGTG 60.964 57.895 3.15 3.15 0.00 4.94
276 277 1.964373 GTCGACCCAAATGCACGGT 60.964 57.895 3.51 0.00 0.00 4.83
277 278 2.686816 GGTCGACCCAAATGCACGG 61.687 63.158 24.75 0.00 0.00 4.94
278 279 2.867472 GGTCGACCCAAATGCACG 59.133 61.111 24.75 0.00 0.00 5.34
288 289 0.514255 GCAACTTTAACGGGTCGACC 59.486 55.000 27.04 27.04 0.00 4.79
289 290 1.458445 GAGCAACTTTAACGGGTCGAC 59.542 52.381 7.13 7.13 0.00 4.20
290 291 1.342174 AGAGCAACTTTAACGGGTCGA 59.658 47.619 0.00 0.00 33.29 4.20
291 292 1.459592 CAGAGCAACTTTAACGGGTCG 59.540 52.381 0.00 0.00 33.29 4.79
292 293 2.479275 GTCAGAGCAACTTTAACGGGTC 59.521 50.000 0.00 0.00 0.00 4.46
293 294 2.490991 GTCAGAGCAACTTTAACGGGT 58.509 47.619 0.00 0.00 0.00 5.28
294 295 1.459592 CGTCAGAGCAACTTTAACGGG 59.540 52.381 0.00 0.00 0.00 5.28
295 296 1.136336 GCGTCAGAGCAACTTTAACGG 60.136 52.381 0.00 0.00 37.05 4.44
296 297 1.136336 GGCGTCAGAGCAACTTTAACG 60.136 52.381 0.00 0.00 39.27 3.18
297 298 2.143925 AGGCGTCAGAGCAACTTTAAC 58.856 47.619 0.00 0.00 39.27 2.01
298 299 2.543777 AGGCGTCAGAGCAACTTTAA 57.456 45.000 0.00 0.00 39.27 1.52
299 300 2.543777 AAGGCGTCAGAGCAACTTTA 57.456 45.000 0.00 0.00 39.27 1.85
300 301 2.543777 TAAGGCGTCAGAGCAACTTT 57.456 45.000 0.00 0.00 39.27 2.66
301 302 2.770164 ATAAGGCGTCAGAGCAACTT 57.230 45.000 0.00 0.00 39.27 2.66
302 303 2.770164 AATAAGGCGTCAGAGCAACT 57.230 45.000 0.00 0.00 39.27 3.16
303 304 3.831715 AAAATAAGGCGTCAGAGCAAC 57.168 42.857 0.00 0.00 39.27 4.17
304 305 5.001232 AGTAAAAATAAGGCGTCAGAGCAA 58.999 37.500 0.00 0.00 39.27 3.91
305 306 4.575885 AGTAAAAATAAGGCGTCAGAGCA 58.424 39.130 0.00 0.00 39.27 4.26
306 307 4.870991 AGAGTAAAAATAAGGCGTCAGAGC 59.129 41.667 0.00 0.00 0.00 4.09
307 308 5.230306 CGAGAGTAAAAATAAGGCGTCAGAG 59.770 44.000 0.00 0.00 0.00 3.35
308 309 5.100259 CGAGAGTAAAAATAAGGCGTCAGA 58.900 41.667 0.00 0.00 0.00 3.27
309 310 4.863131 ACGAGAGTAAAAATAAGGCGTCAG 59.137 41.667 0.00 0.00 46.88 3.51
310 311 4.813027 ACGAGAGTAAAAATAAGGCGTCA 58.187 39.130 0.00 0.00 46.88 4.35
372 373 3.994853 AGCGCAAAGGGCAAAGGC 61.995 61.111 11.47 0.00 44.06 4.35
399 401 9.921637 GGTGAAATCAGTTTTGGATGTTTATTA 57.078 29.630 0.00 0.00 0.00 0.98
795 3468 1.615392 AGTACAACGGTTACCTTCGCT 59.385 47.619 0.00 0.00 0.00 4.93
824 3497 0.618458 TCCGCTAAAGGGCACAGAAT 59.382 50.000 0.00 0.00 0.00 2.40
846 3519 0.529337 CGCCTGATTCGCTGTCAGAT 60.529 55.000 3.32 0.00 44.57 2.90
949 3622 4.913784 AGATTCCTGCCAAAATTGCAAAT 58.086 34.783 1.71 0.00 38.46 2.32
1288 3961 1.097547 GGCACCCCGATCTTGACATG 61.098 60.000 0.00 0.00 0.00 3.21
1440 4113 2.493035 TGTGTGGCAGTCATGTTGTAG 58.507 47.619 0.00 0.00 0.00 2.74
1467 4140 4.357947 GTCGACACGGCTCCAGCA 62.358 66.667 11.55 0.00 44.36 4.41
1494 4167 0.110238 CACAATTGAACACCGAGCCG 60.110 55.000 13.59 0.00 0.00 5.52
1533 4206 0.466189 CACCCCAGCAGAACACTGTT 60.466 55.000 0.00 0.00 34.51 3.16
1602 4275 1.449353 GCCTGCTCCTATGGACTGG 59.551 63.158 0.00 0.00 0.00 4.00
1620 4293 0.392461 CCCCACAGACATGGTAACCG 60.392 60.000 0.00 0.00 38.16 4.44
1623 4296 0.037590 GCACCCCACAGACATGGTAA 59.962 55.000 0.00 0.00 38.16 2.85
1873 4546 2.432510 AGTAGTCTCCAGCCACTATTGC 59.567 50.000 0.00 0.00 0.00 3.56
1983 4656 4.299586 TGCAGAAGATACACAAATCCCA 57.700 40.909 0.00 0.00 0.00 4.37
2391 5064 4.151689 TCCTTTCGAAAAGAGTATGTTGCG 59.848 41.667 12.41 0.00 0.00 4.85
2499 5172 1.414181 GAATCCTCCGAGAAGCCATCA 59.586 52.381 0.00 0.00 0.00 3.07
2616 5289 4.956075 TGGAACTCCTTTGAGCTTTTCTTT 59.044 37.500 0.00 0.00 42.74 2.52
2844 5517 4.067896 AGCCATGCAAATACTCTATTCCG 58.932 43.478 0.00 0.00 0.00 4.30
2928 5601 2.051435 GCAACACGCGCATTGTGA 60.051 55.556 18.84 0.00 39.73 3.58
3021 5694 3.952967 GGTAGTACTCAGGGTCAAGGTAG 59.047 52.174 0.00 0.00 0.00 3.18
3075 5748 4.816925 AGAAGAACAACTCCAAAGCTGTAC 59.183 41.667 0.00 0.00 30.58 2.90
3255 5928 2.260434 CACTTGCATGCCACAGCC 59.740 61.111 16.68 0.00 38.69 4.85
3519 6192 0.034896 ACGAGGTCACGCTTGGAAAT 59.965 50.000 0.00 0.00 36.70 2.17
3693 6366 6.885918 TGATCTTGGCATTTCATCAGAAGTTA 59.114 34.615 0.00 0.00 34.71 2.24
3765 6438 4.024218 CAGTTGATCTATAAAGCAGCAGGC 60.024 45.833 0.00 0.00 45.30 4.85
3770 6443 6.423302 CCTGCTACAGTTGATCTATAAAGCAG 59.577 42.308 20.17 20.17 42.84 4.24
3777 6450 3.041211 TGGCCTGCTACAGTTGATCTAT 58.959 45.455 3.32 0.00 0.00 1.98
3883 6558 2.769663 AGTGCCAATTATAGGACGACCA 59.230 45.455 6.71 0.00 38.94 4.02
3924 6599 2.440409 ACAGGATTCATCAAGTGTGGC 58.560 47.619 0.00 0.00 0.00 5.01
4023 6701 6.074195 CGAAAAGATACTTAACACGGTGAACA 60.074 38.462 16.29 0.00 0.00 3.18
4102 6783 3.679502 GCAATTTGATCCCCAAAGTTTCG 59.320 43.478 0.00 0.00 46.72 3.46
4106 6787 3.583966 ACATGCAATTTGATCCCCAAAGT 59.416 39.130 0.00 0.00 46.72 2.66
4113 6794 9.754382 AATAATGTTAGACATGCAATTTGATCC 57.246 29.630 0.00 0.00 37.97 3.36
4179 6862 1.069227 GCAGACAAACCGTGATGTTCC 60.069 52.381 0.00 0.00 0.00 3.62
4212 6895 5.530915 CCACTGAAAATTACACTTCACCTGA 59.469 40.000 0.00 0.00 0.00 3.86
4391 7074 3.562557 CCGCATTTAAAGTATTACCGCCT 59.437 43.478 0.00 0.00 0.00 5.52
4399 7082 7.431249 TCTAATCTCGACCGCATTTAAAGTAT 58.569 34.615 0.00 0.00 0.00 2.12
4411 7094 4.879104 AGTGTTACTCTAATCTCGACCG 57.121 45.455 0.00 0.00 0.00 4.79
4442 7125 3.638627 TCGTGAGCAGATTATCCATGTCT 59.361 43.478 0.00 0.00 0.00 3.41
4542 7228 7.201266 GCATGTTAGAAATTTGTCGATGTTCAC 60.201 37.037 0.00 0.00 0.00 3.18
4551 7237 3.853671 CGGCAGCATGTTAGAAATTTGTC 59.146 43.478 0.00 0.00 39.31 3.18
4572 7259 4.963276 TGTCATTCTAAGGGCAAATTCG 57.037 40.909 0.00 0.00 0.00 3.34
4573 7260 5.506317 CGGATGTCATTCTAAGGGCAAATTC 60.506 44.000 0.00 0.00 0.00 2.17
4598 7285 2.178912 TCTTTTTGTACAGGCCTCCG 57.821 50.000 0.00 0.00 0.00 4.63
4622 7309 1.926511 ATGCGCCTTTTTGAGCTCCG 61.927 55.000 12.15 6.59 0.00 4.63
4631 7318 2.558359 AGTGCTAGAAAATGCGCCTTTT 59.442 40.909 21.07 21.07 40.18 2.27
4636 7323 6.912591 ACAATAATTAGTGCTAGAAAATGCGC 59.087 34.615 12.62 0.00 39.68 6.09
4663 7350 3.139850 CCAATGATGCAAGTGCCAAAAA 58.860 40.909 0.00 0.00 41.18 1.94
4664 7351 2.104451 ACCAATGATGCAAGTGCCAAAA 59.896 40.909 0.00 0.00 41.18 2.44
4665 7352 1.693062 ACCAATGATGCAAGTGCCAAA 59.307 42.857 0.00 0.00 41.18 3.28


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

AutoCloner maintained by Alex Coulton.