Multiple sequence alignment - TraesCS7B01G162700

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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 TraesCS7B01G162700 chr7B 100.000 7511 0 0 1 7511 223359654 223352144 0.000000e+00 13871.0
1 TraesCS7B01G162700 chr7D 95.585 6772 172 58 372 7090 246838382 246831685 0.000000e+00 10732.0
2 TraesCS7B01G162700 chr7D 82.320 181 22 4 1 175 246838771 246838595 1.690000e-31 148.0
3 TraesCS7B01G162700 chr7D 92.308 91 5 2 7298 7387 246831601 246831512 2.200000e-25 128.0
4 TraesCS7B01G162700 chr7A 96.295 6343 146 40 456 6736 264333096 264326781 0.000000e+00 10329.0
5 TraesCS7B01G162700 chr7A 87.192 406 31 10 6732 7125 264324975 264324579 6.920000e-120 442.0
6 TraesCS7B01G162700 chr7A 81.670 491 54 23 6948 7427 264323204 264322739 7.120000e-100 375.0
7 TraesCS7B01G162700 chr7A 86.667 195 23 1 263 454 264336799 264336605 5.900000e-51 213.0
8 TraesCS7B01G162700 chr7A 88.235 153 13 3 7278 7427 264323439 264323289 2.150000e-40 178.0
9 TraesCS7B01G162700 chr7A 93.421 76 4 1 7150 7224 264323858 264323783 2.220000e-20 111.0
10 TraesCS7B01G162700 chr7A 86.667 90 10 2 174 262 534333520 534333608 1.720000e-16 99.0
11 TraesCS7B01G162700 chr7A 97.959 49 1 0 7176 7224 264323520 264323472 1.340000e-12 86.1
12 TraesCS7B01G162700 chr1B 87.900 719 50 18 4794 5503 641627774 641628464 0.000000e+00 811.0
13 TraesCS7B01G162700 chr1B 92.857 98 6 1 4453 4550 641627367 641627463 2.830000e-29 141.0
14 TraesCS7B01G162700 chr1D 92.800 250 11 5 5259 5508 464860673 464860915 9.270000e-94 355.0
15 TraesCS7B01G162700 chr1D 92.063 63 4 1 4453 4515 464860626 464860687 3.730000e-13 87.9
16 TraesCS7B01G162700 chr3A 87.023 131 16 1 315 444 7263184 7263054 6.070000e-31 147.0
17 TraesCS7B01G162700 chr3D 86.719 128 16 1 315 441 1760253 1760380 2.830000e-29 141.0
18 TraesCS7B01G162700 chr3D 86.458 96 11 2 169 263 223683454 223683360 3.710000e-18 104.0
19 TraesCS7B01G162700 chr3D 86.667 90 12 0 173 262 455100574 455100663 4.800000e-17 100.0
20 TraesCS7B01G162700 chr2B 89.773 88 9 0 174 261 74066058 74065971 6.160000e-21 113.0
21 TraesCS7B01G162700 chr2B 85.870 92 13 0 171 262 26955597 26955688 1.720000e-16 99.0
22 TraesCS7B01G162700 chr6D 87.097 93 10 2 174 265 382702952 382702861 3.710000e-18 104.0
23 TraesCS7B01G162700 chr6D 87.356 87 11 0 174 260 464854611 464854697 4.800000e-17 100.0
24 TraesCS7B01G162700 chr5D 87.640 89 9 2 174 262 416973500 416973414 1.330000e-17 102.0
25 TraesCS7B01G162700 chr5D 86.667 90 12 0 174 263 495621793 495621704 4.800000e-17 100.0
26 TraesCS7B01G162700 chr5D 85.965 57 6 2 236 291 530379326 530379271 8.140000e-05 60.2
27 TraesCS7B01G162700 chr2D 78.082 146 26 6 313 454 17826049 17826192 3.730000e-13 87.9
28 TraesCS7B01G162700 chr6B 89.091 55 4 2 7435 7487 347591217 347591271 4.860000e-07 67.6


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 TraesCS7B01G162700 chr7B 223352144 223359654 7510 True 13871.000000 13871 100.000000 1 7511 1 chr7B.!!$R1 7510
1 TraesCS7B01G162700 chr7D 246831512 246838771 7259 True 3669.333333 10732 90.071000 1 7387 3 chr7D.!!$R1 7386
2 TraesCS7B01G162700 chr7A 264322739 264336799 14060 True 1676.300000 10329 90.205571 263 7427 7 chr7A.!!$R1 7164
3 TraesCS7B01G162700 chr1B 641627367 641628464 1097 False 476.000000 811 90.378500 4453 5503 2 chr1B.!!$F1 1050

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
635 4250 0.812811 TGCATCGCAAGCCTCTCATC 60.813 55.000 0.00 0.0 34.76 2.92 F
1181 4820 0.462759 CCCAGTCAATCGCCTTCTCC 60.463 60.000 0.00 0.0 0.00 3.71 F
1480 5124 0.541863 TTCTCGCCCCTTCAGATTCC 59.458 55.000 0.00 0.0 0.00 3.01 F
1595 5247 0.734889 CTGGCGGCTAATTTCTGTGG 59.265 55.000 11.43 0.0 0.00 4.17 F
2097 5774 0.782384 GTGTCCTTTACTGCGTGTCG 59.218 55.000 0.00 0.0 0.00 4.35 F
3968 7648 1.375140 AGTGAGCACAGCCATGACG 60.375 57.895 3.19 0.0 0.00 4.35 F
4034 7714 2.454832 CTTCTGGGGAGTTGCTGCGA 62.455 60.000 0.00 0.0 0.00 5.10 F
5370 9296 2.559668 CAACAGGCACATTGACCAGATT 59.440 45.455 0.00 0.0 0.00 2.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1972 5649 1.069513 ACGGTTTGTGGATGAAGACGA 59.930 47.619 0.00 0.00 0.00 4.20 R
2991 6671 1.134907 GCACAGCCTGCAAGCAATAAT 60.135 47.619 10.50 0.00 46.29 1.28 R
3157 6837 1.342496 CCAATCGATGCAGAGGCTAGA 59.658 52.381 0.00 0.00 41.91 2.43 R
3361 7041 3.915437 TCCGAGCATGGTTTCTTTTTC 57.085 42.857 0.00 0.00 0.00 2.29 R
4034 7714 6.244552 TCCTTATCACATGCAGAGAAGAAT 57.755 37.500 19.12 0.00 36.66 2.40 R
5195 9116 2.165167 GGGCCAAAAAGGGTACAGTAC 58.835 52.381 4.39 1.59 38.09 2.73 R
5609 9535 3.673543 ACAAGGTGAAGTTTTACCCCA 57.326 42.857 2.52 0.00 37.70 4.96 R
6622 10566 1.349026 CACAGAGTGACTCCCCATGTT 59.651 52.381 9.33 0.00 35.23 2.71 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
26 27 5.869649 ATTTTCTTACCTGTTTGGCTGTT 57.130 34.783 0.00 0.00 40.22 3.16
27 28 4.647424 TTTCTTACCTGTTTGGCTGTTG 57.353 40.909 0.00 0.00 40.22 3.33
28 29 1.953686 TCTTACCTGTTTGGCTGTTGC 59.046 47.619 0.00 0.00 40.22 4.17
33 34 1.280066 CTGTTTGGCTGTTGCAACAC 58.720 50.000 27.96 22.19 41.91 3.32
85 92 5.902681 ACGACACAACATATAGTACATGCT 58.097 37.500 0.00 0.00 0.00 3.79
86 93 7.034685 ACGACACAACATATAGTACATGCTA 57.965 36.000 0.00 0.00 0.00 3.49
87 94 6.916387 ACGACACAACATATAGTACATGCTAC 59.084 38.462 0.00 0.00 0.00 3.58
115 122 6.607004 ATTATGTTATACTCCCTCCTTCCG 57.393 41.667 0.00 0.00 0.00 4.30
116 123 2.674420 TGTTATACTCCCTCCTTCCGG 58.326 52.381 0.00 0.00 0.00 5.14
127 134 5.412384 TCCCTCCTTCCGGAAATATAAGAT 58.588 41.667 19.39 0.00 39.29 2.40
129 136 7.020629 TCCCTCCTTCCGGAAATATAAGATAA 58.979 38.462 19.39 0.00 39.29 1.75
130 137 7.180408 TCCCTCCTTCCGGAAATATAAGATAAG 59.820 40.741 19.39 1.04 39.29 1.73
150 157 9.141400 AGATAAGTTTGACTTTACACGATCTTC 57.859 33.333 0.00 0.00 39.51 2.87
153 160 6.157211 AGTTTGACTTTACACGATCTTCGAT 58.843 36.000 3.62 0.00 43.74 3.59
154 161 6.089551 AGTTTGACTTTACACGATCTTCGATG 59.910 38.462 3.62 0.00 43.74 3.84
161 168 2.159184 ACACGATCTTCGATGCATGACT 60.159 45.455 2.46 0.00 43.74 3.41
166 173 4.210746 CGATCTTCGATGCATGACTTTGAT 59.789 41.667 2.46 0.00 43.74 2.57
175 182 8.498358 TCGATGCATGACTTTGATCATTAATAC 58.502 33.333 2.46 0.00 37.20 1.89
177 184 9.823098 GATGCATGACTTTGATCATTAATACTC 57.177 33.333 2.46 0.00 37.20 2.59
179 186 7.229306 TGCATGACTTTGATCATTAATACTCCC 59.771 37.037 0.00 0.00 37.20 4.30
180 187 7.446625 GCATGACTTTGATCATTAATACTCCCT 59.553 37.037 0.00 0.00 37.20 4.20
181 188 9.347240 CATGACTTTGATCATTAATACTCCCTT 57.653 33.333 0.00 0.00 37.20 3.95
182 189 8.964476 TGACTTTGATCATTAATACTCCCTTC 57.036 34.615 0.00 0.00 0.00 3.46
183 190 7.710907 TGACTTTGATCATTAATACTCCCTTCG 59.289 37.037 0.00 0.00 0.00 3.79
184 191 7.565680 ACTTTGATCATTAATACTCCCTTCGT 58.434 34.615 0.00 0.00 0.00 3.85
185 192 7.711339 ACTTTGATCATTAATACTCCCTTCGTC 59.289 37.037 0.00 0.00 0.00 4.20
186 193 6.097915 TGATCATTAATACTCCCTTCGTCC 57.902 41.667 0.00 0.00 0.00 4.79
187 194 4.950205 TCATTAATACTCCCTTCGTCCC 57.050 45.455 0.00 0.00 0.00 4.46
188 195 4.291792 TCATTAATACTCCCTTCGTCCCA 58.708 43.478 0.00 0.00 0.00 4.37
189 196 4.905456 TCATTAATACTCCCTTCGTCCCAT 59.095 41.667 0.00 0.00 0.00 4.00
190 197 6.079336 TCATTAATACTCCCTTCGTCCCATA 58.921 40.000 0.00 0.00 0.00 2.74
191 198 6.555738 TCATTAATACTCCCTTCGTCCCATAA 59.444 38.462 0.00 0.00 0.00 1.90
192 199 7.236847 TCATTAATACTCCCTTCGTCCCATAAT 59.763 37.037 0.00 0.00 0.00 1.28
193 200 5.906772 AATACTCCCTTCGTCCCATAATT 57.093 39.130 0.00 0.00 0.00 1.40
194 201 5.906772 ATACTCCCTTCGTCCCATAATTT 57.093 39.130 0.00 0.00 0.00 1.82
195 202 7.383156 AATACTCCCTTCGTCCCATAATTTA 57.617 36.000 0.00 0.00 0.00 1.40
196 203 5.703730 ACTCCCTTCGTCCCATAATTTAA 57.296 39.130 0.00 0.00 0.00 1.52
197 204 5.681639 ACTCCCTTCGTCCCATAATTTAAG 58.318 41.667 0.00 0.00 0.00 1.85
198 205 5.427481 ACTCCCTTCGTCCCATAATTTAAGA 59.573 40.000 0.00 0.00 0.00 2.10
199 206 6.069847 ACTCCCTTCGTCCCATAATTTAAGAA 60.070 38.462 0.00 0.00 0.00 2.52
200 207 6.117488 TCCCTTCGTCCCATAATTTAAGAAC 58.883 40.000 0.00 0.00 0.00 3.01
201 208 6.069847 TCCCTTCGTCCCATAATTTAAGAACT 60.070 38.462 0.00 0.00 0.00 3.01
202 209 6.602009 CCCTTCGTCCCATAATTTAAGAACTT 59.398 38.462 0.00 0.00 0.00 2.66
203 210 7.122204 CCCTTCGTCCCATAATTTAAGAACTTT 59.878 37.037 0.00 0.00 0.00 2.66
204 211 8.520351 CCTTCGTCCCATAATTTAAGAACTTTT 58.480 33.333 0.00 0.00 0.00 2.27
205 212 9.341899 CTTCGTCCCATAATTTAAGAACTTTTG 57.658 33.333 0.00 0.00 0.00 2.44
206 213 8.398878 TCGTCCCATAATTTAAGAACTTTTGT 57.601 30.769 0.00 0.00 0.00 2.83
207 214 8.508875 TCGTCCCATAATTTAAGAACTTTTGTC 58.491 33.333 0.00 0.00 0.00 3.18
208 215 8.293867 CGTCCCATAATTTAAGAACTTTTGTCA 58.706 33.333 0.00 0.00 0.00 3.58
209 216 9.974980 GTCCCATAATTTAAGAACTTTTGTCAA 57.025 29.630 0.00 0.00 0.00 3.18
220 227 6.786207 AGAACTTTTGTCAAACTGTCTTAGC 58.214 36.000 0.00 0.00 0.00 3.09
221 228 6.599638 AGAACTTTTGTCAAACTGTCTTAGCT 59.400 34.615 0.00 0.00 0.00 3.32
222 229 6.759497 ACTTTTGTCAAACTGTCTTAGCTT 57.241 33.333 0.00 0.00 0.00 3.74
223 230 7.158099 ACTTTTGTCAAACTGTCTTAGCTTT 57.842 32.000 0.00 0.00 0.00 3.51
224 231 8.276252 ACTTTTGTCAAACTGTCTTAGCTTTA 57.724 30.769 0.00 0.00 0.00 1.85
225 232 8.736244 ACTTTTGTCAAACTGTCTTAGCTTTAA 58.264 29.630 0.00 0.00 0.00 1.52
226 233 9.567848 CTTTTGTCAAACTGTCTTAGCTTTAAA 57.432 29.630 0.00 0.00 0.00 1.52
227 234 9.915629 TTTTGTCAAACTGTCTTAGCTTTAAAA 57.084 25.926 0.00 0.00 0.00 1.52
228 235 9.915629 TTTGTCAAACTGTCTTAGCTTTAAAAA 57.084 25.926 0.00 0.00 0.00 1.94
230 237 9.515020 TGTCAAACTGTCTTAGCTTTAAAAATG 57.485 29.630 0.00 0.00 0.00 2.32
231 238 9.516314 GTCAAACTGTCTTAGCTTTAAAAATGT 57.484 29.630 0.00 0.00 0.00 2.71
252 259 7.996098 ATGTTTTTATATTATGGGACGGAGG 57.004 36.000 0.00 0.00 0.00 4.30
253 260 6.300703 TGTTTTTATATTATGGGACGGAGGG 58.699 40.000 0.00 0.00 0.00 4.30
254 261 6.101442 TGTTTTTATATTATGGGACGGAGGGA 59.899 38.462 0.00 0.00 0.00 4.20
255 262 6.368779 TTTTATATTATGGGACGGAGGGAG 57.631 41.667 0.00 0.00 0.00 4.30
256 263 3.562108 ATATTATGGGACGGAGGGAGT 57.438 47.619 0.00 0.00 0.00 3.85
257 264 4.687262 ATATTATGGGACGGAGGGAGTA 57.313 45.455 0.00 0.00 0.00 2.59
258 265 2.376695 TTATGGGACGGAGGGAGTAG 57.623 55.000 0.00 0.00 0.00 2.57
259 266 1.229131 TATGGGACGGAGGGAGTAGT 58.771 55.000 0.00 0.00 0.00 2.73
260 267 1.229131 ATGGGACGGAGGGAGTAGTA 58.771 55.000 0.00 0.00 0.00 1.82
261 268 1.229131 TGGGACGGAGGGAGTAGTAT 58.771 55.000 0.00 0.00 0.00 2.12
265 272 3.825585 GGGACGGAGGGAGTAGTATAAAG 59.174 52.174 0.00 0.00 0.00 1.85
270 277 4.281182 CGGAGGGAGTAGTATAAAGTGCAT 59.719 45.833 0.00 0.00 0.00 3.96
461 566 9.450807 GTGAAGCGCACTTTATATTCATATTTT 57.549 29.630 11.47 0.00 44.27 1.82
462 567 9.449550 TGAAGCGCACTTTATATTCATATTTTG 57.550 29.630 11.47 0.00 35.82 2.44
520 4129 7.164803 AGTTTTTGATGAGAAAGAGGGAGTAG 58.835 38.462 0.00 0.00 0.00 2.57
561 4173 2.649331 CCGTGAAATCGGTACAGAGT 57.351 50.000 1.40 0.00 44.77 3.24
562 4174 2.259618 CCGTGAAATCGGTACAGAGTG 58.740 52.381 1.40 0.00 44.77 3.51
563 4175 2.352421 CCGTGAAATCGGTACAGAGTGT 60.352 50.000 1.40 0.00 44.77 3.55
564 4176 3.119743 CCGTGAAATCGGTACAGAGTGTA 60.120 47.826 1.40 0.00 44.77 2.90
565 4177 4.096311 CGTGAAATCGGTACAGAGTGTAG 58.904 47.826 1.40 0.00 32.84 2.74
566 4178 4.379186 CGTGAAATCGGTACAGAGTGTAGT 60.379 45.833 1.40 0.00 32.84 2.73
567 4179 5.163824 CGTGAAATCGGTACAGAGTGTAGTA 60.164 44.000 1.40 0.00 32.84 1.82
568 4180 6.256686 GTGAAATCGGTACAGAGTGTAGTAG 58.743 44.000 1.40 0.00 32.84 2.57
569 4181 5.942236 TGAAATCGGTACAGAGTGTAGTAGT 59.058 40.000 1.40 0.00 32.84 2.73
570 4182 7.065085 GTGAAATCGGTACAGAGTGTAGTAGTA 59.935 40.741 1.40 0.00 32.84 1.82
610 4225 2.098607 CGAAGGAGCACGGAACTGTATA 59.901 50.000 0.00 0.00 0.00 1.47
634 4249 1.094073 GTGCATCGCAAGCCTCTCAT 61.094 55.000 0.00 0.00 41.47 2.90
635 4250 0.812811 TGCATCGCAAGCCTCTCATC 60.813 55.000 0.00 0.00 34.76 2.92
636 4251 0.812811 GCATCGCAAGCCTCTCATCA 60.813 55.000 0.00 0.00 37.18 3.07
672 4287 2.342648 GAGCCGGACACGTTTCCT 59.657 61.111 18.20 0.00 38.78 3.36
675 4290 2.047560 CCGGACACGTTTCCTCCC 60.048 66.667 18.20 0.00 38.78 4.30
879 4505 3.204467 TTTTCCCCTGCCTCCCACG 62.204 63.158 0.00 0.00 0.00 4.94
962 4588 1.067821 GAGTCCGTAGCCTCCAGATTG 59.932 57.143 0.00 0.00 0.00 2.67
963 4589 1.112113 GTCCGTAGCCTCCAGATTGA 58.888 55.000 0.00 0.00 0.00 2.57
966 4592 2.092049 TCCGTAGCCTCCAGATTGAGTA 60.092 50.000 0.00 0.00 0.00 2.59
971 4597 1.751924 GCCTCCAGATTGAGTACGTCT 59.248 52.381 0.00 0.00 0.00 4.18
1180 4819 0.537188 TCCCAGTCAATCGCCTTCTC 59.463 55.000 0.00 0.00 0.00 2.87
1181 4820 0.462759 CCCAGTCAATCGCCTTCTCC 60.463 60.000 0.00 0.00 0.00 3.71
1304 4948 3.383620 TGCGCCATTCTCAAATTTTGT 57.616 38.095 4.18 0.00 0.00 2.83
1369 5013 4.963276 TCCCGCTTATCTTTTTCATGTG 57.037 40.909 0.00 0.00 0.00 3.21
1424 5068 1.438469 CCCCATGCTCCAGATCCTTA 58.562 55.000 0.00 0.00 0.00 2.69
1480 5124 0.541863 TTCTCGCCCCTTCAGATTCC 59.458 55.000 0.00 0.00 0.00 3.01
1551 5203 0.739462 CGGTGCTGTTATCTTGGCGA 60.739 55.000 0.00 0.00 0.00 5.54
1595 5247 0.734889 CTGGCGGCTAATTTCTGTGG 59.265 55.000 11.43 0.00 0.00 4.17
1609 5261 2.035155 GTGGCCTGTGGTTACCCC 59.965 66.667 3.32 0.00 0.00 4.95
1769 5446 2.846206 TGACCATGATTTAGGGCAGACT 59.154 45.455 0.00 0.00 38.22 3.24
1928 5605 5.620738 TTAAGGAGACCAAGATCATCCTG 57.379 43.478 0.00 0.00 40.28 3.86
1972 5649 2.481449 GCAGTGGATCGGTAAATCTCGT 60.481 50.000 0.00 0.00 0.00 4.18
1991 5668 1.459592 GTCGTCTTCATCCACAAACCG 59.540 52.381 0.00 0.00 0.00 4.44
1994 5671 1.069227 GTCTTCATCCACAAACCGTGC 60.069 52.381 0.00 0.00 44.91 5.34
2003 5680 0.951558 ACAAACCGTGCCATGTTCTC 59.048 50.000 0.00 0.00 0.00 2.87
2012 5689 3.338249 GTGCCATGTTCTCATGTACAGT 58.662 45.455 0.33 0.00 46.99 3.55
2013 5690 3.753272 GTGCCATGTTCTCATGTACAGTT 59.247 43.478 0.33 0.00 46.99 3.16
2097 5774 0.782384 GTGTCCTTTACTGCGTGTCG 59.218 55.000 0.00 0.00 0.00 4.35
2549 6229 5.591099 CATGTAACCTAAAATGCCCACATC 58.409 41.667 0.00 0.00 34.62 3.06
2758 6438 7.699812 CCTGCAAATAATTCTTCAGAGCTAAAC 59.300 37.037 0.00 0.00 0.00 2.01
3098 6778 5.772825 TGATTCCCTCTTTGTTTTGACTG 57.227 39.130 0.00 0.00 0.00 3.51
3529 7209 5.064707 TGTCACAGCTACTTTGTTCTTTGAC 59.935 40.000 0.00 0.00 37.00 3.18
3968 7648 1.375140 AGTGAGCACAGCCATGACG 60.375 57.895 3.19 0.00 0.00 4.35
4034 7714 2.454832 CTTCTGGGGAGTTGCTGCGA 62.455 60.000 0.00 0.00 0.00 5.10
4410 8090 2.939103 ACTGGCATAACAGCTTTCGATC 59.061 45.455 0.00 0.00 42.21 3.69
4735 8415 7.878127 ACCACTAACATATGCCTGTTATATCAC 59.122 37.037 1.58 0.00 40.00 3.06
4738 8418 6.785488 AACATATGCCTGTTATATCACGTG 57.215 37.500 9.94 9.94 37.58 4.49
4890 8807 5.182001 GCATGTACTGAAAGGAGAAATGTGT 59.818 40.000 0.00 0.00 39.30 3.72
4997 8918 7.394641 AGGTTTAACATTTCTTCCTGATTCCTC 59.605 37.037 0.00 0.00 0.00 3.71
5195 9116 3.103738 GCACTAAAATGCTTGCTGATCG 58.896 45.455 0.00 0.00 42.62 3.69
5211 9132 4.092968 GCTGATCGTACTGTACCCTTTTTG 59.907 45.833 12.08 0.00 0.00 2.44
5370 9296 2.559668 CAACAGGCACATTGACCAGATT 59.440 45.455 0.00 0.00 0.00 2.40
5454 9380 3.614092 CTTCAGATAAAGGCCTTGCTCA 58.386 45.455 21.33 5.22 0.00 4.26
5609 9535 2.270205 CCATCAAGGAGCCGCAGT 59.730 61.111 0.00 0.00 41.22 4.40
5688 9615 2.420687 GGCTGGTATTCTGAAGGGAGTG 60.421 54.545 0.00 0.00 0.00 3.51
5706 9633 5.998363 GGGAGTGTCTGATAAACTGTTTTCT 59.002 40.000 11.48 0.00 0.00 2.52
6622 10566 4.323569 AGTCTCTGATCTGTGTTCCCTA 57.676 45.455 0.00 0.00 0.00 3.53
6722 10666 3.788766 CTAACCTGTGCCGCGTGC 61.789 66.667 4.92 9.16 41.77 5.34
6773 12528 5.359860 GCAAGGGGTTTATGCTAATGTTAGT 59.640 40.000 2.11 0.00 37.12 2.24
6804 12559 8.962857 GTAGTAGTACTACCTCTGTTTGTTTC 57.037 38.462 25.97 1.82 43.96 2.78
6805 12560 7.836479 AGTAGTACTACCTCTGTTTGTTTCT 57.164 36.000 25.97 3.03 36.75 2.52
6853 12608 3.004024 TGAACTGTCGAAACGTCCTAC 57.996 47.619 0.00 0.00 0.00 3.18
6866 12632 2.860062 CGTCCTACGTTGGTCTAACAG 58.140 52.381 15.74 0.71 39.30 3.16
7000 12766 5.592054 TGAATGATAGCGTAGAAGACTTGG 58.408 41.667 0.00 0.00 0.00 3.61
7014 12780 7.423844 AGAAGACTTGGTTCCAAATCTTTTT 57.576 32.000 22.97 14.75 40.87 1.94
7027 12793 4.836125 AATCTTTTTCAGCGTGTCATGT 57.164 36.364 0.00 0.00 0.00 3.21
7030 12796 3.183574 TCTTTTTCAGCGTGTCATGTACG 59.816 43.478 16.93 16.93 43.93 3.67
7070 13589 2.917933 TGTTGATAGAAATCCAGGCCG 58.082 47.619 0.00 0.00 0.00 6.13
7094 14401 4.177026 CTGGAGATCTAACACTTTGGTCG 58.823 47.826 0.00 0.00 0.00 4.79
7095 14402 3.576982 TGGAGATCTAACACTTTGGTCGT 59.423 43.478 0.00 0.00 0.00 4.34
7096 14403 4.768448 TGGAGATCTAACACTTTGGTCGTA 59.232 41.667 0.00 0.00 0.00 3.43
7097 14404 5.100943 GGAGATCTAACACTTTGGTCGTAC 58.899 45.833 0.00 0.00 0.00 3.67
7105 14412 8.796475 TCTAACACTTTGGTCGTACTATAAACT 58.204 33.333 0.00 0.00 0.00 2.66
7129 14443 8.955388 ACTGCACATTTATACATACAACATCAA 58.045 29.630 0.00 0.00 0.00 2.57
7130 14444 9.786105 CTGCACATTTATACATACAACATCAAA 57.214 29.630 0.00 0.00 0.00 2.69
7131 14445 9.566530 TGCACATTTATACATACAACATCAAAC 57.433 29.630 0.00 0.00 0.00 2.93
7167 14482 0.036732 TGCAAAATGAGACGGGAGCT 59.963 50.000 0.00 0.00 0.00 4.09
7173 14488 1.813513 ATGAGACGGGAGCTTTGTTG 58.186 50.000 0.00 0.00 0.00 3.33
7179 14494 0.742990 CGGGAGCTTTGTTGGCGATA 60.743 55.000 0.00 0.00 34.52 2.92
7183 14498 2.945668 GGAGCTTTGTTGGCGATAAGAT 59.054 45.455 0.00 0.00 34.52 2.40
7193 14508 4.811555 TGGCGATAAGATGTACAATTGC 57.188 40.909 5.05 4.24 0.00 3.56
7194 14509 3.563808 TGGCGATAAGATGTACAATTGCC 59.436 43.478 22.21 22.21 45.50 4.52
7220 14548 1.655885 TGCTGCTGTGATGCACAAC 59.344 52.632 0.00 0.00 44.08 3.32
7225 14553 2.810274 CTGCTGTGATGCACAACTACTT 59.190 45.455 1.64 0.00 44.08 2.24
7227 14555 2.159787 GCTGTGATGCACAACTACTTCG 60.160 50.000 1.64 0.00 44.08 3.79
7228 14556 3.059884 CTGTGATGCACAACTACTTCGT 58.940 45.455 1.64 0.00 44.08 3.85
7229 14557 4.234574 CTGTGATGCACAACTACTTCGTA 58.765 43.478 1.64 0.00 44.08 3.43
7230 14558 4.234574 TGTGATGCACAACTACTTCGTAG 58.765 43.478 0.00 0.00 41.69 3.51
7232 14560 4.090066 GTGATGCACAACTACTTCGTAGTG 59.910 45.833 4.78 5.19 46.96 2.74
7233 14561 3.720949 TGCACAACTACTTCGTAGTGT 57.279 42.857 4.78 5.71 46.96 3.55
7234 14562 4.834357 TGCACAACTACTTCGTAGTGTA 57.166 40.909 4.78 0.00 46.96 2.90
7235 14563 4.790878 TGCACAACTACTTCGTAGTGTAG 58.209 43.478 4.78 5.38 46.96 2.74
7236 14564 4.276678 TGCACAACTACTTCGTAGTGTAGT 59.723 41.667 4.78 5.95 46.96 2.73
7237 14565 5.469760 TGCACAACTACTTCGTAGTGTAGTA 59.530 40.000 4.78 0.00 46.96 1.82
7238 14566 6.020372 GCACAACTACTTCGTAGTGTAGTAG 58.980 44.000 4.78 0.00 46.96 2.57
7239 14567 6.020372 CACAACTACTTCGTAGTGTAGTAGC 58.980 44.000 4.78 0.00 46.96 3.58
7240 14568 5.702670 ACAACTACTTCGTAGTGTAGTAGCA 59.297 40.000 4.78 0.00 46.96 3.49
7241 14569 6.205464 ACAACTACTTCGTAGTGTAGTAGCAA 59.795 38.462 4.78 0.00 46.96 3.91
7242 14570 6.808008 ACTACTTCGTAGTGTAGTAGCAAA 57.192 37.500 4.78 0.00 46.06 3.68
7243 14571 7.206981 ACTACTTCGTAGTGTAGTAGCAAAA 57.793 36.000 4.78 0.00 46.06 2.44
7244 14572 7.651808 ACTACTTCGTAGTGTAGTAGCAAAAA 58.348 34.615 4.78 0.00 46.06 1.94
7267 14595 7.731556 AAAACGTCTTACATTAGCGTAGTAG 57.268 36.000 0.00 0.00 35.22 2.57
7268 14596 4.842029 ACGTCTTACATTAGCGTAGTAGC 58.158 43.478 0.00 0.00 33.85 3.58
7273 14601 7.513196 CGTCTTACATTAGCGTAGTAGCAAAAG 60.513 40.741 0.00 0.00 40.15 2.27
7275 14603 7.487189 TCTTACATTAGCGTAGTAGCAAAAGAC 59.513 37.037 0.00 0.00 40.15 3.01
7282 14610 4.262510 GCGTAGTAGCAAAAGACGTCTTAG 59.737 45.833 29.91 24.46 35.97 2.18
7295 14623 3.299340 CGTCTTAGATTATGGGACGGG 57.701 52.381 0.00 0.00 43.69 5.28
7298 14626 3.258622 GTCTTAGATTATGGGACGGGGAG 59.741 52.174 0.00 0.00 0.00 4.30
7299 14627 3.116862 TCTTAGATTATGGGACGGGGAGT 60.117 47.826 0.00 0.00 0.00 3.85
7303 14633 2.555732 TTATGGGACGGGGAGTAGTT 57.444 50.000 0.00 0.00 0.00 2.24
7304 14634 1.784358 TATGGGACGGGGAGTAGTTG 58.216 55.000 0.00 0.00 0.00 3.16
7309 14639 1.154197 GACGGGGAGTAGTTGTTTGC 58.846 55.000 0.00 0.00 0.00 3.68
7319 14649 6.092807 GGGAGTAGTTGTTTGCTGAGAAATAG 59.907 42.308 0.00 0.00 0.00 1.73
7321 14651 6.234177 AGTAGTTGTTTGCTGAGAAATAGCT 58.766 36.000 0.00 0.00 41.66 3.32
7416 14746 8.868635 AACACTACTAGTTCAACTTCTAACAC 57.131 34.615 0.00 0.00 0.00 3.32
7427 14757 6.339730 TCAACTTCTAACACGGTGTTTTCTA 58.660 36.000 29.22 12.26 41.45 2.10
7428 14758 6.256321 TCAACTTCTAACACGGTGTTTTCTAC 59.744 38.462 29.22 0.00 41.45 2.59
7429 14759 5.910614 ACTTCTAACACGGTGTTTTCTACT 58.089 37.500 29.22 8.13 41.45 2.57
7430 14760 5.981915 ACTTCTAACACGGTGTTTTCTACTC 59.018 40.000 29.22 0.00 41.45 2.59
7431 14761 4.874970 TCTAACACGGTGTTTTCTACTCC 58.125 43.478 29.22 0.00 41.45 3.85
7432 14762 2.538512 ACACGGTGTTTTCTACTCCC 57.461 50.000 8.21 0.00 37.15 4.30
7433 14763 2.044758 ACACGGTGTTTTCTACTCCCT 58.955 47.619 8.21 0.00 37.15 4.20
7434 14764 2.224209 ACACGGTGTTTTCTACTCCCTG 60.224 50.000 8.21 0.00 37.15 4.45
7435 14765 2.036733 CACGGTGTTTTCTACTCCCTGA 59.963 50.000 0.00 0.00 37.15 3.86
7436 14766 2.036862 ACGGTGTTTTCTACTCCCTGAC 59.963 50.000 0.00 0.00 37.15 3.51
7437 14767 2.685100 GGTGTTTTCTACTCCCTGACG 58.315 52.381 0.00 0.00 34.91 4.35
7438 14768 2.036862 GGTGTTTTCTACTCCCTGACGT 59.963 50.000 0.00 0.00 34.91 4.34
7439 14769 3.493873 GGTGTTTTCTACTCCCTGACGTT 60.494 47.826 0.00 0.00 34.91 3.99
7440 14770 4.124970 GTGTTTTCTACTCCCTGACGTTT 58.875 43.478 0.00 0.00 0.00 3.60
7441 14771 4.573607 GTGTTTTCTACTCCCTGACGTTTT 59.426 41.667 0.00 0.00 0.00 2.43
7442 14772 5.065602 GTGTTTTCTACTCCCTGACGTTTTT 59.934 40.000 0.00 0.00 0.00 1.94
7443 14773 6.258507 GTGTTTTCTACTCCCTGACGTTTTTA 59.741 38.462 0.00 0.00 0.00 1.52
7444 14774 6.993902 TGTTTTCTACTCCCTGACGTTTTTAT 59.006 34.615 0.00 0.00 0.00 1.40
7445 14775 8.149647 TGTTTTCTACTCCCTGACGTTTTTATA 58.850 33.333 0.00 0.00 0.00 0.98
7446 14776 8.438513 GTTTTCTACTCCCTGACGTTTTTATAC 58.561 37.037 0.00 0.00 0.00 1.47
7447 14777 7.472334 TTCTACTCCCTGACGTTTTTATACT 57.528 36.000 0.00 0.00 0.00 2.12
7448 14778 8.579850 TTCTACTCCCTGACGTTTTTATACTA 57.420 34.615 0.00 0.00 0.00 1.82
7449 14779 8.218338 TCTACTCCCTGACGTTTTTATACTAG 57.782 38.462 0.00 0.00 0.00 2.57
7450 14780 6.847421 ACTCCCTGACGTTTTTATACTAGT 57.153 37.500 0.00 0.00 0.00 2.57
7451 14781 7.944729 ACTCCCTGACGTTTTTATACTAGTA 57.055 36.000 4.77 4.77 0.00 1.82
7452 14782 8.530804 ACTCCCTGACGTTTTTATACTAGTAT 57.469 34.615 19.07 19.07 0.00 2.12
7453 14783 9.632638 ACTCCCTGACGTTTTTATACTAGTATA 57.367 33.333 17.03 17.03 0.00 1.47
7480 14810 4.492791 AAAAACCGTCTTACATTTCGGG 57.507 40.909 7.34 0.00 46.06 5.14
7481 14811 3.405823 AAACCGTCTTACATTTCGGGA 57.594 42.857 7.34 0.00 46.06 5.14
7482 14812 2.375173 ACCGTCTTACATTTCGGGAC 57.625 50.000 7.34 0.00 46.06 4.46
7503 14833 7.893658 GGGACGGAGAGACTATAAAATAATGA 58.106 38.462 0.00 0.00 0.00 2.57
7504 14834 8.365647 GGGACGGAGAGACTATAAAATAATGAA 58.634 37.037 0.00 0.00 0.00 2.57
7505 14835 9.760077 GGACGGAGAGACTATAAAATAATGAAA 57.240 33.333 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 1.407258 GTTGCAACAGCCAAACAGGTA 59.593 47.619 24.52 0.00 40.61 3.08
15 16 0.605083 TGTGTTGCAACAGCCAAACA 59.395 45.000 31.81 21.31 40.05 2.83
19 20 0.679321 TGAGTGTGTTGCAACAGCCA 60.679 50.000 31.81 23.44 40.05 4.75
60 67 7.485810 AGCATGTACTATATGTTGTGTCGTTA 58.514 34.615 0.00 0.00 0.00 3.18
90 97 8.130671 CGGAAGGAGGGAGTATAACATAATAA 57.869 38.462 0.00 0.00 0.00 1.40
127 134 7.140705 TCGAAGATCGTGTAAAGTCAAACTTA 58.859 34.615 0.00 0.00 38.11 2.24
129 136 5.526115 TCGAAGATCGTGTAAAGTCAAACT 58.474 37.500 0.00 0.00 41.35 2.66
130 137 5.817616 TCGAAGATCGTGTAAAGTCAAAC 57.182 39.130 0.00 0.00 41.35 2.93
140 147 2.159184 AGTCATGCATCGAAGATCGTGT 60.159 45.455 0.00 0.00 45.12 4.49
141 148 2.467838 AGTCATGCATCGAAGATCGTG 58.532 47.619 0.00 0.00 45.12 4.35
145 152 5.121105 TGATCAAAGTCATGCATCGAAGAT 58.879 37.500 0.00 0.00 45.12 2.40
150 157 8.501580 AGTATTAATGATCAAAGTCATGCATCG 58.498 33.333 0.00 0.00 38.76 3.84
153 160 7.229306 GGGAGTATTAATGATCAAAGTCATGCA 59.771 37.037 0.00 0.00 38.76 3.96
154 161 7.446625 AGGGAGTATTAATGATCAAAGTCATGC 59.553 37.037 0.00 0.00 38.76 4.06
161 168 6.990349 GGACGAAGGGAGTATTAATGATCAAA 59.010 38.462 0.00 0.00 0.00 2.69
166 173 4.291792 TGGGACGAAGGGAGTATTAATGA 58.708 43.478 0.00 0.00 0.00 2.57
175 182 5.925509 TCTTAAATTATGGGACGAAGGGAG 58.074 41.667 0.00 0.00 0.00 4.30
177 184 6.120220 AGTTCTTAAATTATGGGACGAAGGG 58.880 40.000 0.00 0.00 0.00 3.95
179 186 9.341899 CAAAAGTTCTTAAATTATGGGACGAAG 57.658 33.333 0.00 0.00 0.00 3.79
180 187 8.852135 ACAAAAGTTCTTAAATTATGGGACGAA 58.148 29.630 0.00 0.00 0.00 3.85
181 188 8.398878 ACAAAAGTTCTTAAATTATGGGACGA 57.601 30.769 0.00 0.00 0.00 4.20
182 189 8.293867 TGACAAAAGTTCTTAAATTATGGGACG 58.706 33.333 0.00 0.00 0.00 4.79
183 190 9.974980 TTGACAAAAGTTCTTAAATTATGGGAC 57.025 29.630 0.00 0.00 0.00 4.46
194 201 8.395633 GCTAAGACAGTTTGACAAAAGTTCTTA 58.604 33.333 17.29 17.29 33.30 2.10
195 202 7.121315 AGCTAAGACAGTTTGACAAAAGTTCTT 59.879 33.333 17.02 17.02 34.33 2.52
196 203 6.599638 AGCTAAGACAGTTTGACAAAAGTTCT 59.400 34.615 1.27 1.81 0.00 3.01
197 204 6.786207 AGCTAAGACAGTTTGACAAAAGTTC 58.214 36.000 1.27 0.00 0.00 3.01
198 205 6.759497 AGCTAAGACAGTTTGACAAAAGTT 57.241 33.333 1.27 0.00 0.00 2.66
199 206 6.759497 AAGCTAAGACAGTTTGACAAAAGT 57.241 33.333 1.27 4.64 0.00 2.66
200 207 9.567848 TTTAAAGCTAAGACAGTTTGACAAAAG 57.432 29.630 1.27 1.27 0.00 2.27
201 208 9.915629 TTTTAAAGCTAAGACAGTTTGACAAAA 57.084 25.926 1.27 0.00 0.00 2.44
202 209 9.915629 TTTTTAAAGCTAAGACAGTTTGACAAA 57.084 25.926 0.00 0.00 0.00 2.83
204 211 9.515020 CATTTTTAAAGCTAAGACAGTTTGACA 57.485 29.630 0.00 0.00 0.00 3.58
205 212 9.516314 ACATTTTTAAAGCTAAGACAGTTTGAC 57.484 29.630 0.00 0.00 0.00 3.18
226 233 8.856103 CCTCCGTCCCATAATATAAAAACATTT 58.144 33.333 0.00 0.00 0.00 2.32
227 234 7.450323 CCCTCCGTCCCATAATATAAAAACATT 59.550 37.037 0.00 0.00 0.00 2.71
228 235 6.946009 CCCTCCGTCCCATAATATAAAAACAT 59.054 38.462 0.00 0.00 0.00 2.71
229 236 6.101442 TCCCTCCGTCCCATAATATAAAAACA 59.899 38.462 0.00 0.00 0.00 2.83
230 237 6.536447 TCCCTCCGTCCCATAATATAAAAAC 58.464 40.000 0.00 0.00 0.00 2.43
231 238 6.330778 ACTCCCTCCGTCCCATAATATAAAAA 59.669 38.462 0.00 0.00 0.00 1.94
232 239 5.847817 ACTCCCTCCGTCCCATAATATAAAA 59.152 40.000 0.00 0.00 0.00 1.52
233 240 5.408824 ACTCCCTCCGTCCCATAATATAAA 58.591 41.667 0.00 0.00 0.00 1.40
234 241 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
235 242 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
236 243 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
237 244 3.400322 ACTACTCCCTCCGTCCCATAATA 59.600 47.826 0.00 0.00 0.00 0.98
238 245 2.179424 ACTACTCCCTCCGTCCCATAAT 59.821 50.000 0.00 0.00 0.00 1.28
239 246 1.572415 ACTACTCCCTCCGTCCCATAA 59.428 52.381 0.00 0.00 0.00 1.90
240 247 1.229131 ACTACTCCCTCCGTCCCATA 58.771 55.000 0.00 0.00 0.00 2.74
241 248 1.229131 TACTACTCCCTCCGTCCCAT 58.771 55.000 0.00 0.00 0.00 4.00
242 249 1.229131 ATACTACTCCCTCCGTCCCA 58.771 55.000 0.00 0.00 0.00 4.37
243 250 3.515602 TTATACTACTCCCTCCGTCCC 57.484 52.381 0.00 0.00 0.00 4.46
244 251 4.277921 CACTTTATACTACTCCCTCCGTCC 59.722 50.000 0.00 0.00 0.00 4.79
245 252 4.261530 GCACTTTATACTACTCCCTCCGTC 60.262 50.000 0.00 0.00 0.00 4.79
246 253 3.635836 GCACTTTATACTACTCCCTCCGT 59.364 47.826 0.00 0.00 0.00 4.69
247 254 3.635373 TGCACTTTATACTACTCCCTCCG 59.365 47.826 0.00 0.00 0.00 4.63
248 255 5.511545 CCATGCACTTTATACTACTCCCTCC 60.512 48.000 0.00 0.00 0.00 4.30
249 256 5.304614 TCCATGCACTTTATACTACTCCCTC 59.695 44.000 0.00 0.00 0.00 4.30
250 257 5.216622 TCCATGCACTTTATACTACTCCCT 58.783 41.667 0.00 0.00 0.00 4.20
251 258 5.546621 TCCATGCACTTTATACTACTCCC 57.453 43.478 0.00 0.00 0.00 4.30
252 259 7.217200 TCAATCCATGCACTTTATACTACTCC 58.783 38.462 0.00 0.00 0.00 3.85
253 260 8.552034 GTTCAATCCATGCACTTTATACTACTC 58.448 37.037 0.00 0.00 0.00 2.59
254 261 8.046708 TGTTCAATCCATGCACTTTATACTACT 58.953 33.333 0.00 0.00 0.00 2.57
255 262 8.208718 TGTTCAATCCATGCACTTTATACTAC 57.791 34.615 0.00 0.00 0.00 2.73
256 263 8.978874 ATGTTCAATCCATGCACTTTATACTA 57.021 30.769 0.00 0.00 0.00 1.82
257 264 7.776969 AGATGTTCAATCCATGCACTTTATACT 59.223 33.333 0.00 0.00 0.00 2.12
258 265 7.934457 AGATGTTCAATCCATGCACTTTATAC 58.066 34.615 0.00 0.00 0.00 1.47
259 266 7.994911 AGAGATGTTCAATCCATGCACTTTATA 59.005 33.333 0.00 0.00 0.00 0.98
260 267 6.832384 AGAGATGTTCAATCCATGCACTTTAT 59.168 34.615 0.00 0.00 0.00 1.40
261 268 6.182627 AGAGATGTTCAATCCATGCACTTTA 58.817 36.000 0.00 0.00 0.00 1.85
265 272 4.978083 AAGAGATGTTCAATCCATGCAC 57.022 40.909 0.00 0.00 0.00 4.57
270 277 7.449395 AGAATCAACAAAGAGATGTTCAATCCA 59.551 33.333 0.00 0.00 41.44 3.41
308 318 9.932699 CAAATGTGAAGATGCAATTTACAAAAA 57.067 25.926 14.01 0.00 31.06 1.94
309 319 9.107177 ACAAATGTGAAGATGCAATTTACAAAA 57.893 25.926 14.01 0.00 31.06 2.44
328 338 8.407064 AATGAAATTGTTTTGCATGACAAATGT 58.593 25.926 16.32 7.36 40.97 2.71
454 559 8.997323 GTACCTCCTTCTCATCATCAAAATATG 58.003 37.037 0.00 0.00 0.00 1.78
456 561 8.324191 AGTACCTCCTTCTCATCATCAAAATA 57.676 34.615 0.00 0.00 0.00 1.40
457 562 7.205515 AGTACCTCCTTCTCATCATCAAAAT 57.794 36.000 0.00 0.00 0.00 1.82
458 563 6.627087 AGTACCTCCTTCTCATCATCAAAA 57.373 37.500 0.00 0.00 0.00 2.44
459 564 6.627087 AAGTACCTCCTTCTCATCATCAAA 57.373 37.500 0.00 0.00 0.00 2.69
460 565 6.627087 AAAGTACCTCCTTCTCATCATCAA 57.373 37.500 0.00 0.00 0.00 2.57
461 566 7.921041 ATAAAGTACCTCCTTCTCATCATCA 57.079 36.000 0.00 0.00 0.00 3.07
492 4101 8.166726 ACTCCCTCTTTCTCATCAAAAACTAAT 58.833 33.333 0.00 0.00 0.00 1.73
493 4102 7.518188 ACTCCCTCTTTCTCATCAAAAACTAA 58.482 34.615 0.00 0.00 0.00 2.24
496 4105 6.372937 CCTACTCCCTCTTTCTCATCAAAAAC 59.627 42.308 0.00 0.00 0.00 2.43
497 4106 6.044404 ACCTACTCCCTCTTTCTCATCAAAAA 59.956 38.462 0.00 0.00 0.00 1.94
510 4119 7.463054 TGAATTACTAGTACCTACTCCCTCT 57.537 40.000 0.91 0.00 37.73 3.69
520 4129 4.748600 GGATGCCGTTGAATTACTAGTACC 59.251 45.833 0.91 0.00 0.00 3.34
547 4159 7.108847 ACTACTACTACACTCTGTACCGATTT 58.891 38.462 0.00 0.00 0.00 2.17
558 4170 5.297278 AGTGCTGCATACTACTACTACACTC 59.703 44.000 5.27 0.00 29.08 3.51
559 4171 5.066634 CAGTGCTGCATACTACTACTACACT 59.933 44.000 5.27 0.00 35.16 3.55
560 4172 5.066117 TCAGTGCTGCATACTACTACTACAC 59.934 44.000 5.27 0.00 0.00 2.90
561 4173 5.190677 TCAGTGCTGCATACTACTACTACA 58.809 41.667 5.27 0.00 0.00 2.74
562 4174 5.752892 TCAGTGCTGCATACTACTACTAC 57.247 43.478 5.27 0.00 0.00 2.73
563 4175 5.067413 GGTTCAGTGCTGCATACTACTACTA 59.933 44.000 5.27 0.00 0.00 1.82
564 4176 4.142138 GGTTCAGTGCTGCATACTACTACT 60.142 45.833 5.27 0.00 0.00 2.57
565 4177 4.113354 GGTTCAGTGCTGCATACTACTAC 58.887 47.826 5.27 0.00 0.00 2.73
566 4178 3.132289 GGGTTCAGTGCTGCATACTACTA 59.868 47.826 5.27 0.00 0.00 1.82
567 4179 2.093447 GGGTTCAGTGCTGCATACTACT 60.093 50.000 5.27 0.00 0.00 2.57
568 4180 2.280628 GGGTTCAGTGCTGCATACTAC 58.719 52.381 5.27 2.59 0.00 2.73
569 4181 1.209504 GGGGTTCAGTGCTGCATACTA 59.790 52.381 5.27 0.00 0.00 1.82
570 4182 0.035056 GGGGTTCAGTGCTGCATACT 60.035 55.000 5.27 0.00 0.00 2.12
610 4225 1.137404 GGCTTGCGATGCACGATTT 59.863 52.632 11.94 0.00 45.77 2.17
634 4249 0.894184 GTCTCAGTCTGGGACGGTGA 60.894 60.000 17.03 0.00 38.21 4.02
635 4250 1.587054 GTCTCAGTCTGGGACGGTG 59.413 63.158 17.03 0.00 38.21 4.94
636 4251 4.098847 GTCTCAGTCTGGGACGGT 57.901 61.111 17.03 0.00 38.21 4.83
948 4574 2.688958 ACGTACTCAATCTGGAGGCTAC 59.311 50.000 0.00 0.00 39.27 3.58
971 4597 2.687902 CCCAGTAGGACCTCCGGA 59.312 66.667 2.93 2.93 42.08 5.14
1073 4705 4.776322 CGCCGTTCATCCTGCCCA 62.776 66.667 0.00 0.00 0.00 5.36
1181 4820 2.616458 CCCTGGTCCAAGAAGGGGG 61.616 68.421 6.08 1.90 46.05 5.40
1424 5068 1.435515 GACGAGAGCGCAGAATCCT 59.564 57.895 11.47 0.00 42.48 3.24
1480 5124 2.507110 ATCACACCGAACCCGCAGAG 62.507 60.000 0.00 0.00 0.00 3.35
1539 5183 5.095490 CCAAAAAGATGTCGCCAAGATAAC 58.905 41.667 0.00 0.00 0.00 1.89
1551 5203 2.524306 TCATTCGCCCCAAAAAGATGT 58.476 42.857 0.00 0.00 0.00 3.06
1609 5261 7.323420 GGTGAATTTTTCTAAGATTTGGAGGG 58.677 38.462 0.00 0.00 0.00 4.30
1972 5649 1.069513 ACGGTTTGTGGATGAAGACGA 59.930 47.619 0.00 0.00 0.00 4.20
2003 5680 6.642131 ACAAATTTTAGCTGCAACTGTACATG 59.358 34.615 1.02 0.00 0.00 3.21
2012 5689 6.593382 ACAAGAAACACAAATTTTAGCTGCAA 59.407 30.769 1.02 0.00 0.00 4.08
2013 5690 6.035866 CACAAGAAACACAAATTTTAGCTGCA 59.964 34.615 1.02 0.00 0.00 4.41
2097 5774 3.793144 CCTGCGTTGCCGAGCTTC 61.793 66.667 0.00 0.00 35.63 3.86
2549 6229 3.062763 AGATTCAGTGAACAGAGTTGCG 58.937 45.455 7.96 0.00 0.00 4.85
2758 6438 2.693797 ATTCAGAAGCTTGTTGCACG 57.306 45.000 2.10 0.00 45.94 5.34
2991 6671 1.134907 GCACAGCCTGCAAGCAATAAT 60.135 47.619 10.50 0.00 46.29 1.28
3098 6778 3.492011 CCAAACAAGCTGAGCATGAAAAC 59.508 43.478 17.22 0.00 31.38 2.43
3157 6837 1.342496 CCAATCGATGCAGAGGCTAGA 59.658 52.381 0.00 0.00 41.91 2.43
3361 7041 3.915437 TCCGAGCATGGTTTCTTTTTC 57.085 42.857 0.00 0.00 0.00 2.29
3562 7242 7.081526 ACTTGATTTCAATGAATCTTCCTCG 57.918 36.000 0.00 0.00 37.04 4.63
4034 7714 6.244552 TCCTTATCACATGCAGAGAAGAAT 57.755 37.500 19.12 0.00 36.66 2.40
4410 8090 4.389890 AGCTCTCTATGACTTTGCTCAG 57.610 45.455 0.00 0.00 0.00 3.35
4735 8415 0.179240 GCAGCACAGATTCGAACACG 60.179 55.000 0.00 0.00 0.00 4.49
4738 8418 4.093408 TCAATTAGCAGCACAGATTCGAAC 59.907 41.667 0.00 0.00 0.00 3.95
4890 8807 5.705441 GTGATCTAAATGAGTTGTCCACCAA 59.295 40.000 0.00 0.00 0.00 3.67
4997 8918 2.989840 CGCTAACCTGAAGAGTTCACAG 59.010 50.000 0.00 0.00 35.46 3.66
5195 9116 2.165167 GGGCCAAAAAGGGTACAGTAC 58.835 52.381 4.39 1.59 38.09 2.73
5370 9296 6.857437 ACTCCATATATGCAGCACAGTATA 57.143 37.500 7.24 0.00 0.00 1.47
5609 9535 3.673543 ACAAGGTGAAGTTTTACCCCA 57.326 42.857 2.52 0.00 37.70 4.96
5688 9615 8.142994 TCTGTCAAGAAAACAGTTTATCAGAC 57.857 34.615 0.00 10.99 43.68 3.51
5706 9633 4.844085 TGGTCCTCTCCTATTTTCTGTCAA 59.156 41.667 0.00 0.00 0.00 3.18
6117 10056 5.413833 CAGCAACATTGATCAAGGACTAGTT 59.586 40.000 25.68 13.32 0.00 2.24
6622 10566 1.349026 CACAGAGTGACTCCCCATGTT 59.651 52.381 9.33 0.00 35.23 2.71
6722 10666 4.082895 CCAAGAGGCTCAAAAGTCAGAATG 60.083 45.833 18.26 0.00 37.54 2.67
6730 10674 2.101249 TGCAAACCAAGAGGCTCAAAAG 59.899 45.455 18.26 4.82 39.06 2.27
6791 12546 9.003658 ACATCTTACATTAGAAACAAACAGAGG 57.996 33.333 0.00 0.00 0.00 3.69
6802 12557 7.972832 ACCGTCAAAACATCTTACATTAGAA 57.027 32.000 0.00 0.00 0.00 2.10
6803 12558 7.972832 AACCGTCAAAACATCTTACATTAGA 57.027 32.000 0.00 0.00 0.00 2.10
6853 12608 7.411274 TCATTTACAAAACTGTTAGACCAACG 58.589 34.615 0.00 0.00 40.26 4.10
6860 12626 6.798959 GCAGCTCTCATTTACAAAACTGTTAG 59.201 38.462 0.00 0.00 0.00 2.34
6866 12632 4.773323 AGGCAGCTCTCATTTACAAAAC 57.227 40.909 0.00 0.00 0.00 2.43
6973 12739 7.043961 AGTCTTCTACGCTATCATTCATCAA 57.956 36.000 0.00 0.00 0.00 2.57
7000 12766 4.359706 ACACGCTGAAAAAGATTTGGAAC 58.640 39.130 0.00 0.00 0.00 3.62
7014 12780 1.808343 AGTACGTACATGACACGCTGA 59.192 47.619 26.55 7.21 43.10 4.26
7070 13589 5.153950 ACCAAAGTGTTAGATCTCCAGTC 57.846 43.478 0.00 0.00 0.00 3.51
7077 14384 9.793252 TTTATAGTACGACCAAAGTGTTAGATC 57.207 33.333 0.00 0.00 0.00 2.75
7105 14412 9.566530 GTTTGATGTTGTATGTATAAATGTGCA 57.433 29.630 0.00 0.00 0.00 4.57
7137 14451 1.872952 TCATTTTGCAGACAGTGACCG 59.127 47.619 0.00 0.00 0.00 4.79
7143 14457 1.466167 CCCGTCTCATTTTGCAGACAG 59.534 52.381 2.90 0.00 39.29 3.51
7167 14482 6.751514 ATTGTACATCTTATCGCCAACAAA 57.248 33.333 0.00 0.00 0.00 2.83
7173 14488 3.363970 CGGCAATTGTACATCTTATCGCC 60.364 47.826 7.40 0.00 0.00 5.54
7179 14494 3.216147 GCAACGGCAATTGTACATCTT 57.784 42.857 7.40 0.00 40.72 2.40
7204 14532 2.420642 AGTAGTTGTGCATCACAGCAG 58.579 47.619 14.43 0.00 45.60 4.24
7242 14570 7.201384 GCTACTACGCTAATGTAAGACGTTTTT 60.201 37.037 0.00 0.00 38.12 1.94
7243 14571 6.252228 GCTACTACGCTAATGTAAGACGTTTT 59.748 38.462 0.00 0.00 38.12 2.43
7244 14572 5.741040 GCTACTACGCTAATGTAAGACGTTT 59.259 40.000 0.00 0.00 38.12 3.60
7245 14573 5.163723 TGCTACTACGCTAATGTAAGACGTT 60.164 40.000 0.00 0.00 38.12 3.99
7246 14574 4.333649 TGCTACTACGCTAATGTAAGACGT 59.666 41.667 0.00 0.00 40.53 4.34
7247 14575 4.840911 TGCTACTACGCTAATGTAAGACG 58.159 43.478 0.00 0.00 0.00 4.18
7248 14576 7.487189 TCTTTTGCTACTACGCTAATGTAAGAC 59.513 37.037 0.00 0.00 0.00 3.01
7249 14577 7.487189 GTCTTTTGCTACTACGCTAATGTAAGA 59.513 37.037 0.00 0.00 0.00 2.10
7250 14578 7.513196 CGTCTTTTGCTACTACGCTAATGTAAG 60.513 40.741 0.00 0.00 0.00 2.34
7251 14579 6.252015 CGTCTTTTGCTACTACGCTAATGTAA 59.748 38.462 0.00 0.00 0.00 2.41
7252 14580 5.740569 CGTCTTTTGCTACTACGCTAATGTA 59.259 40.000 0.00 0.00 0.00 2.29
7253 14581 4.561606 CGTCTTTTGCTACTACGCTAATGT 59.438 41.667 0.00 0.00 0.00 2.71
7254 14582 4.561606 ACGTCTTTTGCTACTACGCTAATG 59.438 41.667 0.00 0.00 37.07 1.90
7255 14583 4.741342 ACGTCTTTTGCTACTACGCTAAT 58.259 39.130 0.00 0.00 37.07 1.73
7256 14584 4.083110 AGACGTCTTTTGCTACTACGCTAA 60.083 41.667 13.58 0.00 37.07 3.09
7257 14585 3.438087 AGACGTCTTTTGCTACTACGCTA 59.562 43.478 13.58 0.00 37.07 4.26
7258 14586 2.228343 AGACGTCTTTTGCTACTACGCT 59.772 45.455 13.58 0.00 37.07 5.07
7259 14587 2.593257 AGACGTCTTTTGCTACTACGC 58.407 47.619 13.58 0.00 37.07 4.42
7260 14588 5.625251 TCTAAGACGTCTTTTGCTACTACG 58.375 41.667 33.82 5.97 37.40 3.51
7261 14589 9.733219 ATAATCTAAGACGTCTTTTGCTACTAC 57.267 33.333 33.82 0.00 37.40 2.73
7266 14594 5.817816 CCCATAATCTAAGACGTCTTTTGCT 59.182 40.000 33.82 18.91 37.40 3.91
7267 14595 5.815740 TCCCATAATCTAAGACGTCTTTTGC 59.184 40.000 33.82 0.00 37.40 3.68
7268 14596 6.019801 CGTCCCATAATCTAAGACGTCTTTTG 60.020 42.308 33.82 25.20 43.89 2.44
7273 14601 3.305199 CCCGTCCCATAATCTAAGACGTC 60.305 52.174 7.70 7.70 46.62 4.34
7282 14610 2.606378 ACTACTCCCCGTCCCATAATC 58.394 52.381 0.00 0.00 0.00 1.75
7295 14623 5.948992 ATTTCTCAGCAAACAACTACTCC 57.051 39.130 0.00 0.00 0.00 3.85
7298 14626 6.487689 AGCTATTTCTCAGCAAACAACTAC 57.512 37.500 0.00 0.00 41.66 2.73
7299 14627 7.510549 AAAGCTATTTCTCAGCAAACAACTA 57.489 32.000 0.00 0.00 41.66 2.24
7416 14746 2.685100 GTCAGGGAGTAGAAAACACCG 58.315 52.381 0.00 0.00 39.58 4.94
7427 14757 6.847421 ACTAGTATAAAAACGTCAGGGAGT 57.153 37.500 0.00 0.00 0.00 3.85
7429 14759 9.632638 ACTATACTAGTATAAAAACGTCAGGGA 57.367 33.333 20.45 0.00 37.23 4.20
7459 14789 4.023792 GTCCCGAAATGTAAGACGGTTTTT 60.024 41.667 0.00 0.00 43.22 1.94
7460 14790 3.499537 GTCCCGAAATGTAAGACGGTTTT 59.500 43.478 0.00 0.00 43.22 2.43
7461 14791 3.069289 GTCCCGAAATGTAAGACGGTTT 58.931 45.455 0.00 0.00 43.22 3.27
7462 14792 2.691927 GTCCCGAAATGTAAGACGGTT 58.308 47.619 0.00 0.00 43.22 4.44
7463 14793 1.403249 CGTCCCGAAATGTAAGACGGT 60.403 52.381 0.00 0.00 44.86 4.83
7464 14794 1.274596 CGTCCCGAAATGTAAGACGG 58.725 55.000 0.00 0.00 44.86 4.79
7466 14796 2.165030 TCTCCGTCCCGAAATGTAAGAC 59.835 50.000 0.00 0.00 0.00 3.01
7467 14797 2.426024 CTCTCCGTCCCGAAATGTAAGA 59.574 50.000 0.00 0.00 0.00 2.10
7468 14798 2.426024 TCTCTCCGTCCCGAAATGTAAG 59.574 50.000 0.00 0.00 0.00 2.34
7469 14799 2.165030 GTCTCTCCGTCCCGAAATGTAA 59.835 50.000 0.00 0.00 0.00 2.41
7470 14800 1.747355 GTCTCTCCGTCCCGAAATGTA 59.253 52.381 0.00 0.00 0.00 2.29
7471 14801 0.531200 GTCTCTCCGTCCCGAAATGT 59.469 55.000 0.00 0.00 0.00 2.71
7472 14802 0.818296 AGTCTCTCCGTCCCGAAATG 59.182 55.000 0.00 0.00 0.00 2.32
7473 14803 2.431954 TAGTCTCTCCGTCCCGAAAT 57.568 50.000 0.00 0.00 0.00 2.17
7474 14804 2.431954 ATAGTCTCTCCGTCCCGAAA 57.568 50.000 0.00 0.00 0.00 3.46
7475 14805 3.565764 TTATAGTCTCTCCGTCCCGAA 57.434 47.619 0.00 0.00 0.00 4.30
7476 14806 3.565764 TTTATAGTCTCTCCGTCCCGA 57.434 47.619 0.00 0.00 0.00 5.14
7477 14807 4.850347 ATTTTATAGTCTCTCCGTCCCG 57.150 45.455 0.00 0.00 0.00 5.14
7478 14808 7.893658 TCATTATTTTATAGTCTCTCCGTCCC 58.106 38.462 0.00 0.00 0.00 4.46
7479 14809 9.760077 TTTCATTATTTTATAGTCTCTCCGTCC 57.240 33.333 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.