Multiple sequence alignment - TraesCS4B01G374400

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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 TraesCS4B01G374400 chr4B 100.000 3285 0 0 1 3285 658210410 658213694 0.000000e+00 6067.0
1 TraesCS4B01G374400 chr4D 89.588 2401 97 67 264 2632 509058857 509056578 0.000000e+00 2907.0
2 TraesCS4B01G374400 chr4D 88.344 163 11 7 1 159 509059035 509058877 4.330000e-44 189.0
3 TraesCS4B01G374400 chr5A 88.809 2368 108 69 300 2626 696926987 696924736 0.000000e+00 2760.0
4 TraesCS4B01G374400 chr5A 87.256 667 66 10 2636 3285 590240295 590239631 0.000000e+00 743.0
5 TraesCS4B01G374400 chr5A 90.000 160 7 5 1 159 696927183 696927032 7.190000e-47 198.0
6 TraesCS4B01G374400 chr6B 84.178 651 68 19 2660 3285 703390270 703390910 1.690000e-167 599.0
7 TraesCS4B01G374400 chr1D 76.164 730 124 36 1593 2288 310815728 310815015 4.060000e-89 339.0
8 TraesCS4B01G374400 chr1D 89.474 209 22 0 1968 2176 432319760 432319968 6.990000e-67 265.0
9 TraesCS4B01G374400 chr1D 100.000 29 0 0 157 185 206091429 206091401 2.000000e-03 54.7
10 TraesCS4B01G374400 chr1B 77.316 626 94 33 1587 2182 420685268 420685875 3.160000e-85 326.0
11 TraesCS4B01G374400 chr1B 88.995 209 23 0 1968 2176 583760667 583760875 3.250000e-65 259.0
12 TraesCS4B01G374400 chr1A 90.431 209 20 0 1968 2176 530781648 530781856 3.230000e-70 276.0
13 TraesCS4B01G374400 chr3D 89.372 207 21 1 1969 2175 380815056 380815261 3.250000e-65 259.0
14 TraesCS4B01G374400 chr3A 89.372 207 21 1 1969 2175 504024842 504025047 3.250000e-65 259.0
15 TraesCS4B01G374400 chr3A 90.833 120 5 1 3172 3285 649604928 649605047 4.390000e-34 156.0
16 TraesCS4B01G374400 chr3A 100.000 28 0 0 188 215 225475445 225475472 6.000000e-03 52.8
17 TraesCS4B01G374400 chr3B 84.746 236 20 9 2653 2874 825536922 825536689 4.270000e-54 222.0
18 TraesCS4B01G374400 chrUn 83.478 230 22 10 2653 2868 209290108 209290335 2.000000e-47 200.0
19 TraesCS4B01G374400 chr7B 83.478 230 22 10 2653 2868 642250241 642250468 2.000000e-47 200.0


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 TraesCS4B01G374400 chr4B 658210410 658213694 3284 False 6067 6067 100.0000 1 3285 1 chr4B.!!$F1 3284
1 TraesCS4B01G374400 chr4D 509056578 509059035 2457 True 1548 2907 88.9660 1 2632 2 chr4D.!!$R1 2631
2 TraesCS4B01G374400 chr5A 696924736 696927183 2447 True 1479 2760 89.4045 1 2626 2 chr5A.!!$R2 2625
3 TraesCS4B01G374400 chr5A 590239631 590240295 664 True 743 743 87.2560 2636 3285 1 chr5A.!!$R1 649
4 TraesCS4B01G374400 chr6B 703390270 703390910 640 False 599 599 84.1780 2660 3285 1 chr6B.!!$F1 625
5 TraesCS4B01G374400 chr1D 310815015 310815728 713 True 339 339 76.1640 1593 2288 1 chr1D.!!$R2 695
6 TraesCS4B01G374400 chr1B 420685268 420685875 607 False 326 326 77.3160 1587 2182 1 chr1B.!!$F1 595

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
417 443 0.042431 ATGGGTGAGTGAGCCTCTCT 59.958 55.0 0.0 0.0 43.37 3.10 F
694 727 0.179015 CCTCTCACCTCGCCTAGCTA 60.179 60.0 0.0 0.0 0.00 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1429 1496 0.369931 CGCGATCGAGCAACAATTGA 59.630 50.0 21.57 0.0 38.10 2.57 R
2680 2828 0.105964 CCAGGTGTCACTCAACGGAA 59.894 55.0 2.35 0.0 39.03 4.30 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
37 38 1.051812 CTTGTCACTGGAGTGTCCCT 58.948 55.000 6.68 0.00 45.76 4.20
38 39 0.758734 TTGTCACTGGAGTGTCCCTG 59.241 55.000 6.68 0.00 45.76 4.45
45 46 3.640407 GAGTGTCCCTGGGCTGCA 61.640 66.667 8.22 4.05 0.00 4.41
61 62 1.668793 GCATGCAACAAACCAGCCC 60.669 57.895 14.21 0.00 0.00 5.19
65 66 4.341502 CAACAAACCAGCCCGCCG 62.342 66.667 0.00 0.00 0.00 6.46
85 86 3.943691 TGCCCCACCGTGTACACC 61.944 66.667 20.11 4.91 0.00 4.16
110 111 0.396811 GATAAGGTGGGGGTGATCGG 59.603 60.000 0.00 0.00 0.00 4.18
155 161 7.315142 CCAAGTAAATGTATCAACACATGCTT 58.685 34.615 0.00 0.00 39.10 3.91
159 165 5.627499 AATGTATCAACACATGCTTCGTT 57.373 34.783 0.00 0.00 39.10 3.85
161 167 4.314961 TGTATCAACACATGCTTCGTTCT 58.685 39.130 0.00 0.00 0.00 3.01
162 168 5.474825 TGTATCAACACATGCTTCGTTCTA 58.525 37.500 0.00 0.00 0.00 2.10
164 170 5.940192 ATCAACACATGCTTCGTTCTAAA 57.060 34.783 0.00 0.00 0.00 1.85
166 172 6.312399 TCAACACATGCTTCGTTCTAAAAT 57.688 33.333 0.00 0.00 0.00 1.82
169 175 7.386573 TCAACACATGCTTCGTTCTAAAATAGA 59.613 33.333 0.00 0.00 0.00 1.98
170 176 7.849804 ACACATGCTTCGTTCTAAAATAGAT 57.150 32.000 0.00 0.00 34.22 1.98
171 177 7.688372 ACACATGCTTCGTTCTAAAATAGATG 58.312 34.615 0.00 0.00 34.22 2.90
172 178 7.549134 ACACATGCTTCGTTCTAAAATAGATGA 59.451 33.333 0.00 0.00 34.22 2.92
173 179 7.848051 CACATGCTTCGTTCTAAAATAGATGAC 59.152 37.037 0.00 0.00 34.22 3.06
174 180 7.766278 ACATGCTTCGTTCTAAAATAGATGACT 59.234 33.333 0.00 0.00 34.22 3.41
175 181 7.757097 TGCTTCGTTCTAAAATAGATGACTC 57.243 36.000 0.00 0.00 34.22 3.36
176 182 6.757010 TGCTTCGTTCTAAAATAGATGACTCC 59.243 38.462 0.00 0.00 34.22 3.85
177 183 6.757010 GCTTCGTTCTAAAATAGATGACTCCA 59.243 38.462 0.00 0.00 34.22 3.86
178 184 7.254151 GCTTCGTTCTAAAATAGATGACTCCAC 60.254 40.741 0.00 0.00 34.22 4.02
179 185 7.406031 TCGTTCTAAAATAGATGACTCCACT 57.594 36.000 0.00 0.00 34.22 4.00
180 186 7.837863 TCGTTCTAAAATAGATGACTCCACTT 58.162 34.615 0.00 0.00 34.22 3.16
181 187 8.311836 TCGTTCTAAAATAGATGACTCCACTTT 58.688 33.333 0.00 0.00 34.22 2.66
182 188 8.383619 CGTTCTAAAATAGATGACTCCACTTTG 58.616 37.037 0.00 0.00 34.22 2.77
183 189 9.220767 GTTCTAAAATAGATGACTCCACTTTGT 57.779 33.333 0.00 0.00 34.22 2.83
187 193 8.425577 AAAATAGATGACTCCACTTTGTATCG 57.574 34.615 0.00 0.00 0.00 2.92
188 194 6.961360 ATAGATGACTCCACTTTGTATCGA 57.039 37.500 0.00 0.00 0.00 3.59
189 195 5.860941 AGATGACTCCACTTTGTATCGAT 57.139 39.130 2.16 2.16 0.00 3.59
190 196 6.227298 AGATGACTCCACTTTGTATCGATT 57.773 37.500 1.71 0.00 0.00 3.34
191 197 6.276847 AGATGACTCCACTTTGTATCGATTC 58.723 40.000 1.71 0.00 0.00 2.52
192 198 5.400066 TGACTCCACTTTGTATCGATTCA 57.600 39.130 1.71 0.71 0.00 2.57
193 199 5.789521 TGACTCCACTTTGTATCGATTCAA 58.210 37.500 12.80 12.80 0.00 2.69
194 200 5.637810 TGACTCCACTTTGTATCGATTCAAC 59.362 40.000 15.98 3.50 0.00 3.18
195 201 5.794894 ACTCCACTTTGTATCGATTCAACT 58.205 37.500 15.98 3.18 0.00 3.16
196 202 6.231211 ACTCCACTTTGTATCGATTCAACTT 58.769 36.000 15.98 4.56 0.00 2.66
197 203 6.710744 ACTCCACTTTGTATCGATTCAACTTT 59.289 34.615 15.98 2.29 0.00 2.66
198 204 6.898041 TCCACTTTGTATCGATTCAACTTTG 58.102 36.000 15.98 12.59 0.00 2.77
199 205 6.485313 TCCACTTTGTATCGATTCAACTTTGT 59.515 34.615 15.98 10.26 0.00 2.83
200 206 7.658167 TCCACTTTGTATCGATTCAACTTTGTA 59.342 33.333 15.98 1.43 0.00 2.41
201 207 7.744715 CCACTTTGTATCGATTCAACTTTGTAC 59.255 37.037 15.98 0.00 0.00 2.90
202 208 8.495949 CACTTTGTATCGATTCAACTTTGTACT 58.504 33.333 15.98 0.00 0.00 2.73
203 209 9.701098 ACTTTGTATCGATTCAACTTTGTACTA 57.299 29.630 15.98 0.00 0.00 1.82
206 212 9.701098 TTGTATCGATTCAACTTTGTACTAACT 57.299 29.630 12.80 0.00 0.00 2.24
207 213 9.701098 TGTATCGATTCAACTTTGTACTAACTT 57.299 29.630 1.71 0.00 0.00 2.66
248 254 8.982723 ACTACTTACCACATATTTGAGTCATCT 58.017 33.333 0.00 0.00 0.00 2.90
255 261 9.685276 ACCACATATTTGAGTCATCTATTTTGA 57.315 29.630 0.00 0.00 0.00 2.69
262 268 7.928307 TTGAGTCATCTATTTTGAAAGGAGG 57.072 36.000 0.00 0.00 0.00 4.30
263 269 6.418101 TGAGTCATCTATTTTGAAAGGAGGG 58.582 40.000 0.00 0.00 0.00 4.30
264 270 6.012508 TGAGTCATCTATTTTGAAAGGAGGGT 60.013 38.462 0.00 0.00 0.00 4.34
265 271 7.182026 TGAGTCATCTATTTTGAAAGGAGGGTA 59.818 37.037 0.00 0.00 0.00 3.69
266 272 7.339482 AGTCATCTATTTTGAAAGGAGGGTAC 58.661 38.462 0.00 0.00 0.00 3.34
267 273 7.182930 AGTCATCTATTTTGAAAGGAGGGTACT 59.817 37.037 0.00 0.00 0.00 2.73
268 274 8.483758 GTCATCTATTTTGAAAGGAGGGTACTA 58.516 37.037 0.00 0.00 0.00 1.82
269 275 9.225682 TCATCTATTTTGAAAGGAGGGTACTAT 57.774 33.333 0.00 0.00 0.00 2.12
270 276 9.277783 CATCTATTTTGAAAGGAGGGTACTATG 57.722 37.037 0.00 0.00 0.00 2.23
271 277 8.388656 TCTATTTTGAAAGGAGGGTACTATGT 57.611 34.615 0.00 0.00 0.00 2.29
272 278 9.496710 TCTATTTTGAAAGGAGGGTACTATGTA 57.503 33.333 0.00 0.00 0.00 2.29
273 279 9.543783 CTATTTTGAAAGGAGGGTACTATGTAC 57.456 37.037 0.00 0.00 0.00 2.90
274 280 7.563724 TTTTGAAAGGAGGGTACTATGTACT 57.436 36.000 7.64 0.00 0.00 2.73
275 281 8.669055 TTTTGAAAGGAGGGTACTATGTACTA 57.331 34.615 7.64 0.00 0.00 1.82
276 282 8.669055 TTTGAAAGGAGGGTACTATGTACTAA 57.331 34.615 7.64 0.00 0.00 2.24
277 283 8.669055 TTGAAAGGAGGGTACTATGTACTAAA 57.331 34.615 7.64 0.00 0.00 1.85
278 284 8.071177 TGAAAGGAGGGTACTATGTACTAAAC 57.929 38.462 7.64 0.00 0.00 2.01
283 289 6.239515 GGAGGGTACTATGTACTAAACCATGG 60.240 46.154 11.19 11.19 0.00 3.66
285 291 7.080353 AGGGTACTATGTACTAAACCATGGAT 58.920 38.462 21.47 2.68 0.00 3.41
302 308 6.884832 CCATGGATGGTGAAAGTAACTAGTA 58.115 40.000 5.56 0.00 43.05 1.82
330 345 2.548464 AACTGATCCAGAGAGAGGCT 57.452 50.000 0.45 0.00 35.18 4.58
331 346 2.071778 ACTGATCCAGAGAGAGGCTC 57.928 55.000 6.34 6.34 44.29 4.70
332 347 1.287442 ACTGATCCAGAGAGAGGCTCA 59.713 52.381 18.26 0.00 46.45 4.26
333 348 2.292126 ACTGATCCAGAGAGAGGCTCAA 60.292 50.000 18.26 0.00 46.45 3.02
334 349 2.363038 CTGATCCAGAGAGAGGCTCAAG 59.637 54.545 18.26 1.13 46.45 3.02
416 442 1.781786 TATGGGTGAGTGAGCCTCTC 58.218 55.000 0.00 0.00 43.37 3.20
417 443 0.042431 ATGGGTGAGTGAGCCTCTCT 59.958 55.000 0.00 0.00 43.37 3.10
419 445 0.613292 GGGTGAGTGAGCCTCTCTGA 60.613 60.000 0.13 0.00 41.11 3.27
420 446 0.817013 GGTGAGTGAGCCTCTCTGAG 59.183 60.000 0.13 0.00 41.11 3.35
421 447 1.544724 GTGAGTGAGCCTCTCTGAGT 58.455 55.000 0.13 0.00 41.11 3.41
460 493 1.408702 CTGTTCCTTGTGTTGGGTTGG 59.591 52.381 0.00 0.00 0.00 3.77
461 494 0.750249 GTTCCTTGTGTTGGGTTGGG 59.250 55.000 0.00 0.00 0.00 4.12
462 495 1.045911 TTCCTTGTGTTGGGTTGGGC 61.046 55.000 0.00 0.00 0.00 5.36
480 513 1.107114 GCTGCACCTAGCTCACTCTA 58.893 55.000 0.00 0.00 45.94 2.43
481 514 1.202359 GCTGCACCTAGCTCACTCTAC 60.202 57.143 0.00 0.00 45.94 2.59
482 515 2.374184 CTGCACCTAGCTCACTCTACT 58.626 52.381 0.00 0.00 45.94 2.57
483 516 2.357637 CTGCACCTAGCTCACTCTACTC 59.642 54.545 0.00 0.00 45.94 2.59
484 517 1.332375 GCACCTAGCTCACTCTACTCG 59.668 57.143 0.00 0.00 41.15 4.18
485 518 2.634600 CACCTAGCTCACTCTACTCGT 58.365 52.381 0.00 0.00 0.00 4.18
486 519 2.610374 CACCTAGCTCACTCTACTCGTC 59.390 54.545 0.00 0.00 0.00 4.20
487 520 2.502538 ACCTAGCTCACTCTACTCGTCT 59.497 50.000 0.00 0.00 0.00 4.18
488 521 3.705579 ACCTAGCTCACTCTACTCGTCTA 59.294 47.826 0.00 0.00 0.00 2.59
489 522 4.053295 CCTAGCTCACTCTACTCGTCTAC 58.947 52.174 0.00 0.00 0.00 2.59
567 600 1.078567 CTGCTGCTTCCTCACTCCC 60.079 63.158 0.00 0.00 0.00 4.30
568 601 1.537397 TGCTGCTTCCTCACTCCCT 60.537 57.895 0.00 0.00 0.00 4.20
569 602 1.220477 GCTGCTTCCTCACTCCCTC 59.780 63.158 0.00 0.00 0.00 4.30
570 603 1.548357 GCTGCTTCCTCACTCCCTCA 61.548 60.000 0.00 0.00 0.00 3.86
571 604 0.536260 CTGCTTCCTCACTCCCTCAG 59.464 60.000 0.00 0.00 0.00 3.35
615 648 6.072893 GGTAGTAATAATTTACCACCATGGCG 60.073 42.308 13.04 0.90 44.67 5.69
693 726 1.454847 CCTCTCACCTCGCCTAGCT 60.455 63.158 0.00 0.00 0.00 3.32
694 727 0.179015 CCTCTCACCTCGCCTAGCTA 60.179 60.000 0.00 0.00 0.00 3.32
695 728 1.234821 CTCTCACCTCGCCTAGCTAG 58.765 60.000 14.20 14.20 0.00 3.42
696 729 0.179015 TCTCACCTCGCCTAGCTAGG 60.179 60.000 32.12 32.12 45.42 3.02
724 761 1.892819 TTGGCTTGCTCTCCTCCTCG 61.893 60.000 0.00 0.00 0.00 4.63
725 762 2.202864 GCTTGCTCTCCTCCTCGC 60.203 66.667 0.00 0.00 0.00 5.03
726 763 2.720134 GCTTGCTCTCCTCCTCGCT 61.720 63.158 0.00 0.00 0.00 4.93
727 764 1.437160 CTTGCTCTCCTCCTCGCTC 59.563 63.158 0.00 0.00 0.00 5.03
856 893 1.375652 CAGCCACAGCCACTCTCAG 60.376 63.158 0.00 0.00 41.25 3.35
880 917 2.283604 TCCCGCTCACTGCCACTA 60.284 61.111 0.00 0.00 38.78 2.74
885 922 1.376037 GCTCACTGCCACTACCACC 60.376 63.158 0.00 0.00 35.15 4.61
886 923 1.831652 GCTCACTGCCACTACCACCT 61.832 60.000 0.00 0.00 35.15 4.00
888 925 0.471022 TCACTGCCACTACCACCTCA 60.471 55.000 0.00 0.00 0.00 3.86
889 926 0.320771 CACTGCCACTACCACCTCAC 60.321 60.000 0.00 0.00 0.00 3.51
890 927 0.471971 ACTGCCACTACCACCTCACT 60.472 55.000 0.00 0.00 0.00 3.41
891 928 0.247736 CTGCCACTACCACCTCACTC 59.752 60.000 0.00 0.00 0.00 3.51
941 993 2.506472 GCTAGCTAGCCACCCCAC 59.494 66.667 31.67 4.78 43.39 4.61
942 994 2.066999 GCTAGCTAGCCACCCCACT 61.067 63.158 31.67 0.00 43.39 4.00
943 995 2.034048 GCTAGCTAGCCACCCCACTC 62.034 65.000 31.67 3.32 43.39 3.51
944 996 1.382695 TAGCTAGCCACCCCACTCC 60.383 63.158 12.13 0.00 0.00 3.85
945 997 2.176202 TAGCTAGCCACCCCACTCCA 62.176 60.000 12.13 0.00 0.00 3.86
973 1025 1.801913 CTGCACGCTCCTGTACGTC 60.802 63.158 0.00 0.00 41.32 4.34
996 1048 3.924686 CCGGTAGTATAATTAAGCTGGCG 59.075 47.826 0.00 0.00 0.00 5.69
1272 1327 2.431942 TTCTTCTCCGGCGCGAAC 60.432 61.111 12.10 0.00 0.00 3.95
1350 1417 4.974721 CACCAGCACCACCACCCC 62.975 72.222 0.00 0.00 0.00 4.95
1409 1476 2.306512 TGCCTGTCCCGGTAATTACTTT 59.693 45.455 15.05 0.00 0.00 2.66
1414 1481 4.835678 TGTCCCGGTAATTACTTTCTTCC 58.164 43.478 15.05 0.00 0.00 3.46
1415 1482 4.533311 TGTCCCGGTAATTACTTTCTTCCT 59.467 41.667 15.05 0.00 0.00 3.36
1416 1483 5.013391 TGTCCCGGTAATTACTTTCTTCCTT 59.987 40.000 15.05 0.00 0.00 3.36
1417 1484 5.583854 GTCCCGGTAATTACTTTCTTCCTTC 59.416 44.000 15.05 0.00 0.00 3.46
1418 1485 5.248934 TCCCGGTAATTACTTTCTTCCTTCA 59.751 40.000 15.05 0.00 0.00 3.02
1419 1486 5.941647 CCCGGTAATTACTTTCTTCCTTCAA 59.058 40.000 15.05 0.00 0.00 2.69
1420 1487 6.128090 CCCGGTAATTACTTTCTTCCTTCAAC 60.128 42.308 15.05 0.00 0.00 3.18
1421 1488 6.428771 CCGGTAATTACTTTCTTCCTTCAACA 59.571 38.462 15.05 0.00 0.00 3.33
1422 1489 7.120726 CCGGTAATTACTTTCTTCCTTCAACAT 59.879 37.037 15.05 0.00 0.00 2.71
1423 1490 8.175716 CGGTAATTACTTTCTTCCTTCAACATC 58.824 37.037 15.05 0.00 0.00 3.06
1424 1491 8.459635 GGTAATTACTTTCTTCCTTCAACATCC 58.540 37.037 15.05 0.00 0.00 3.51
1425 1492 6.743575 ATTACTTTCTTCCTTCAACATCCG 57.256 37.500 0.00 0.00 0.00 4.18
1426 1493 2.814336 ACTTTCTTCCTTCAACATCCGC 59.186 45.455 0.00 0.00 0.00 5.54
1427 1494 2.559698 TTCTTCCTTCAACATCCGCA 57.440 45.000 0.00 0.00 0.00 5.69
1428 1495 2.099141 TCTTCCTTCAACATCCGCAG 57.901 50.000 0.00 0.00 0.00 5.18
1429 1496 1.347707 TCTTCCTTCAACATCCGCAGT 59.652 47.619 0.00 0.00 0.00 4.40
1430 1497 1.734465 CTTCCTTCAACATCCGCAGTC 59.266 52.381 0.00 0.00 0.00 3.51
1431 1498 0.684535 TCCTTCAACATCCGCAGTCA 59.315 50.000 0.00 0.00 0.00 3.41
1432 1499 1.071542 TCCTTCAACATCCGCAGTCAA 59.928 47.619 0.00 0.00 0.00 3.18
1433 1500 2.086869 CCTTCAACATCCGCAGTCAAT 58.913 47.619 0.00 0.00 0.00 2.57
1434 1501 2.489329 CCTTCAACATCCGCAGTCAATT 59.511 45.455 0.00 0.00 0.00 2.32
1435 1502 3.495193 CTTCAACATCCGCAGTCAATTG 58.505 45.455 0.00 0.00 0.00 2.32
1436 1503 2.503331 TCAACATCCGCAGTCAATTGT 58.497 42.857 5.13 0.00 0.00 2.71
1437 1504 2.884012 TCAACATCCGCAGTCAATTGTT 59.116 40.909 5.13 0.00 0.00 2.83
1438 1505 2.981805 CAACATCCGCAGTCAATTGTTG 59.018 45.455 5.13 6.82 38.32 3.33
1439 1506 1.068333 ACATCCGCAGTCAATTGTTGC 60.068 47.619 20.40 20.40 34.58 4.17
1449 1516 1.060937 AATTGTTGCTCGATCGCGC 59.939 52.632 22.54 22.54 37.46 6.86
1476 1543 5.819379 TCGATCTCAATTCCTGAAGAAATGG 59.181 40.000 0.00 0.00 38.21 3.16
1478 1545 5.519183 TCTCAATTCCTGAAGAAATGGGA 57.481 39.130 0.00 0.00 41.65 4.37
1491 1566 6.600822 TGAAGAAATGGGAGAGAATTAAGCAG 59.399 38.462 0.00 0.00 0.00 4.24
1493 1568 4.516652 AATGGGAGAGAATTAAGCAGCT 57.483 40.909 0.00 0.00 0.00 4.24
1494 1569 3.550437 TGGGAGAGAATTAAGCAGCTC 57.450 47.619 0.00 0.00 0.00 4.09
1495 1570 2.159043 TGGGAGAGAATTAAGCAGCTCG 60.159 50.000 0.00 0.00 32.80 5.03
1497 1572 3.244044 GGGAGAGAATTAAGCAGCTCGAT 60.244 47.826 0.00 0.00 32.80 3.59
1498 1573 3.987220 GGAGAGAATTAAGCAGCTCGATC 59.013 47.826 0.00 0.00 32.80 3.69
1502 1577 5.016051 AGAATTAAGCAGCTCGATCAAGA 57.984 39.130 0.00 0.00 0.00 3.02
1503 1578 5.423015 AGAATTAAGCAGCTCGATCAAGAA 58.577 37.500 0.00 0.00 0.00 2.52
1504 1579 5.293079 AGAATTAAGCAGCTCGATCAAGAAC 59.707 40.000 0.00 0.00 0.00 3.01
1505 1580 2.758736 AAGCAGCTCGATCAAGAACT 57.241 45.000 0.00 0.00 0.00 3.01
1506 1581 2.007360 AGCAGCTCGATCAAGAACTG 57.993 50.000 0.00 0.00 37.39 3.16
1507 1582 1.547820 AGCAGCTCGATCAAGAACTGA 59.452 47.619 5.50 0.00 36.69 3.41
1508 1583 1.925847 GCAGCTCGATCAAGAACTGAG 59.074 52.381 5.50 0.00 36.69 3.35
1509 1584 2.416566 GCAGCTCGATCAAGAACTGAGA 60.417 50.000 5.50 0.00 36.69 3.27
1510 1585 3.437428 CAGCTCGATCAAGAACTGAGAG 58.563 50.000 0.00 0.00 36.69 3.20
1511 1586 3.088532 AGCTCGATCAAGAACTGAGAGT 58.911 45.455 0.00 0.00 37.52 3.24
1512 1587 4.095632 CAGCTCGATCAAGAACTGAGAGTA 59.904 45.833 0.00 0.00 36.69 2.59
1533 1608 9.812347 AGAGTAATGAGATGATTGAGATCTACT 57.188 33.333 0.00 0.00 33.28 2.57
1538 1613 6.614657 TGAGATGATTGAGATCTACTACCCA 58.385 40.000 0.00 0.00 33.28 4.51
1539 1614 7.244558 TGAGATGATTGAGATCTACTACCCAT 58.755 38.462 0.00 0.00 33.28 4.00
1540 1615 8.394040 TGAGATGATTGAGATCTACTACCCATA 58.606 37.037 0.00 0.00 33.28 2.74
1541 1616 9.420118 GAGATGATTGAGATCTACTACCCATAT 57.580 37.037 0.00 0.00 33.28 1.78
1544 1619 8.526667 TGATTGAGATCTACTACCCATATAGC 57.473 38.462 0.00 0.00 33.28 2.97
1547 1622 9.860650 ATTGAGATCTACTACCCATATAGCTAG 57.139 37.037 0.00 0.00 0.00 3.42
1548 1623 7.284074 TGAGATCTACTACCCATATAGCTAGC 58.716 42.308 6.62 6.62 0.00 3.42
1559 1634 8.258850 ACCCATATAGCTAGCTAAACACTTAA 57.741 34.615 27.47 4.43 31.73 1.85
1560 1635 8.148999 ACCCATATAGCTAGCTAAACACTTAAC 58.851 37.037 27.47 0.00 31.73 2.01
1567 1642 8.494016 AGCTAGCTAAACACTTAACTAATTGG 57.506 34.615 17.69 0.00 0.00 3.16
1581 1656 9.142515 CTTAACTAATTGGTTGATGTGTACGTA 57.857 33.333 16.66 0.00 0.00 3.57
1583 1658 4.914312 AATTGGTTGATGTGTACGTACG 57.086 40.909 20.18 15.01 0.00 3.67
2193 2301 4.007644 CGAGCTGGTGCACCTCCA 62.008 66.667 34.75 15.75 42.74 3.86
2351 2481 0.523546 CTTGGAGTCACCGATCGACG 60.524 60.000 18.66 7.07 42.61 5.12
2399 2536 3.320078 CGATTAGCGCCACGACGG 61.320 66.667 2.29 0.00 38.11 4.79
2447 2586 4.937201 TCCTTTTTCCTTGCTTTCTTCC 57.063 40.909 0.00 0.00 0.00 3.46
2448 2587 3.317993 TCCTTTTTCCTTGCTTTCTTCCG 59.682 43.478 0.00 0.00 0.00 4.30
2449 2588 3.068165 CCTTTTTCCTTGCTTTCTTCCGT 59.932 43.478 0.00 0.00 0.00 4.69
2450 2589 4.277423 CCTTTTTCCTTGCTTTCTTCCGTA 59.723 41.667 0.00 0.00 0.00 4.02
2485 2625 3.289076 GCGTTGCTTGTTTCTGTAGTTC 58.711 45.455 0.00 0.00 0.00 3.01
2505 2645 8.976353 GTAGTTCATATATGGGTCTCATCATCT 58.024 37.037 12.78 0.00 37.30 2.90
2506 2646 8.446714 AGTTCATATATGGGTCTCATCATCTT 57.553 34.615 12.78 0.00 37.30 2.40
2507 2647 8.888419 AGTTCATATATGGGTCTCATCATCTTT 58.112 33.333 12.78 0.00 37.30 2.52
2570 2713 5.105106 ACCCGGGAATAAATTGGAAATGTTC 60.105 40.000 32.02 0.00 0.00 3.18
2627 2775 2.350102 CGTTCTGCACGTACACTGTCTA 60.350 50.000 0.00 0.00 44.49 2.59
2632 2780 2.485038 TGCACGTACACTGTCTATCGAA 59.515 45.455 0.00 0.00 0.00 3.71
2633 2781 3.058085 TGCACGTACACTGTCTATCGAAA 60.058 43.478 0.00 0.00 0.00 3.46
2634 2782 3.916172 GCACGTACACTGTCTATCGAAAA 59.084 43.478 0.00 0.00 0.00 2.29
2635 2783 4.383649 GCACGTACACTGTCTATCGAAAAA 59.616 41.667 0.00 0.00 0.00 1.94
2680 2828 6.434652 CGTATACTTCTAATCTGGAGACCCAT 59.565 42.308 0.56 0.00 42.59 4.00
2706 2854 0.969894 GAGTGACACCTGGCAGTACT 59.030 55.000 14.43 9.20 36.71 2.73
2707 2855 2.168496 GAGTGACACCTGGCAGTACTA 58.832 52.381 14.43 0.00 36.71 1.82
2715 2863 4.184629 CACCTGGCAGTACTAATCTCAAC 58.815 47.826 14.43 0.00 0.00 3.18
2746 2899 5.957774 AGGAGCTTCTTCTTAGTCTGAATCT 59.042 40.000 0.00 0.00 0.00 2.40
2767 2920 2.104111 TCAGTTGTGAAATCCCGACTGT 59.896 45.455 11.47 0.00 41.72 3.55
2775 2928 1.480212 AATCCCGACTGTCACTGCCA 61.480 55.000 8.73 0.00 0.00 4.92
2825 2992 3.518068 CGCGGATTTTCCCCTGGC 61.518 66.667 0.00 0.00 31.13 4.85
2842 3009 1.169661 GGCCACAACACGTTGGATGA 61.170 55.000 14.07 0.00 44.45 2.92
2874 3042 2.920645 CGCGGCCATACTCCTCGAT 61.921 63.158 2.24 0.00 34.02 3.59
2881 3049 2.920645 ATACTCCTCGATGCCGGCG 61.921 63.158 23.90 7.87 36.24 6.46
2901 3069 1.024579 CAATTACGACGCTTGCCCCT 61.025 55.000 0.00 0.00 0.00 4.79
2902 3070 1.024579 AATTACGACGCTTGCCCCTG 61.025 55.000 0.00 0.00 0.00 4.45
2903 3071 2.180159 ATTACGACGCTTGCCCCTGT 62.180 55.000 0.00 0.00 0.00 4.00
2986 3154 1.900498 AGCAGCAACTGAACCTGGC 60.900 57.895 0.00 0.00 32.44 4.85
2987 3155 1.900498 GCAGCAACTGAACCTGGCT 60.900 57.895 0.00 0.00 32.44 4.75
2993 3161 0.535102 AACTGAACCTGGCTGGAACG 60.535 55.000 18.12 5.03 39.71 3.95
2998 3166 2.046023 CCTGGCTGGAACGCATGA 60.046 61.111 4.05 0.00 38.35 3.07
3009 3180 0.521291 AACGCATGAATTCACGGTGG 59.479 50.000 19.01 10.35 0.00 4.61
3030 3201 3.512680 GTGTAGAACAAGACCATCTCCG 58.487 50.000 0.00 0.00 0.00 4.63
3065 3245 1.967319 AACACAAACCAGTCAGCGAT 58.033 45.000 0.00 0.00 0.00 4.58
3067 3247 1.202639 ACACAAACCAGTCAGCGATCA 60.203 47.619 0.00 0.00 0.00 2.92
3128 3308 5.185454 TCAAGAGAAACTTTCAGCTTGTCA 58.815 37.500 22.94 11.84 41.25 3.58
3154 3334 3.257561 CGGTGAGATTCGCAGGCG 61.258 66.667 7.46 7.46 41.35 5.52
3170 3350 4.336581 CGGAAGACGCTCACACAA 57.663 55.556 0.00 0.00 34.82 3.33
3178 3358 1.369692 CGCTCACACAACCCACCTA 59.630 57.895 0.00 0.00 0.00 3.08
3211 3391 2.961768 AAAAATCCTGCCGTGCCG 59.038 55.556 0.00 0.00 0.00 5.69
3259 3439 1.308998 AATCGACATGGGGATTTCGC 58.691 50.000 7.46 0.00 28.81 4.70
3265 3445 0.394216 CATGGGGATTTCGCAGTGGA 60.394 55.000 0.00 0.00 41.71 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 1.069427 GTTTGTTGCATGCAGCCCA 59.931 52.632 28.62 19.58 44.83 5.36
38 39 1.668793 GGTTTGTTGCATGCAGCCC 60.669 57.895 28.62 19.71 44.83 5.19
45 46 3.050339 CGGGCTGGTTTGTTGCAT 58.950 55.556 0.00 0.00 0.00 3.96
85 86 0.926293 ACCCCCACCTTATCACCATG 59.074 55.000 0.00 0.00 0.00 3.66
110 111 4.295119 ACGGCCCGGCATATCGAC 62.295 66.667 12.58 0.00 0.00 4.20
131 137 7.216881 CGAAGCATGTGTTGATACATTTACTTG 59.783 37.037 0.00 0.00 39.17 3.16
155 161 7.406031 AGTGGAGTCATCTATTTTAGAACGA 57.594 36.000 0.00 0.00 38.50 3.85
161 167 9.529325 CGATACAAAGTGGAGTCATCTATTTTA 57.471 33.333 0.00 0.00 27.21 1.52
162 168 8.258007 TCGATACAAAGTGGAGTCATCTATTTT 58.742 33.333 0.00 0.00 0.00 1.82
164 170 7.348080 TCGATACAAAGTGGAGTCATCTATT 57.652 36.000 0.00 0.00 0.00 1.73
166 172 6.961360 ATCGATACAAAGTGGAGTCATCTA 57.039 37.500 0.00 0.00 0.00 1.98
169 175 5.977635 TGAATCGATACAAAGTGGAGTCAT 58.022 37.500 0.00 0.00 28.20 3.06
170 176 5.400066 TGAATCGATACAAAGTGGAGTCA 57.600 39.130 0.00 0.00 30.39 3.41
171 177 5.869888 AGTTGAATCGATACAAAGTGGAGTC 59.130 40.000 0.00 0.00 0.00 3.36
172 178 5.794894 AGTTGAATCGATACAAAGTGGAGT 58.205 37.500 0.00 0.00 0.00 3.85
173 179 6.727824 AAGTTGAATCGATACAAAGTGGAG 57.272 37.500 0.00 0.00 0.00 3.86
174 180 6.485313 ACAAAGTTGAATCGATACAAAGTGGA 59.515 34.615 0.00 0.00 0.00 4.02
175 181 6.668323 ACAAAGTTGAATCGATACAAAGTGG 58.332 36.000 0.00 0.00 0.00 4.00
176 182 8.495949 AGTACAAAGTTGAATCGATACAAAGTG 58.504 33.333 0.00 0.00 0.00 3.16
177 183 8.603242 AGTACAAAGTTGAATCGATACAAAGT 57.397 30.769 0.00 0.00 0.00 2.66
180 186 9.701098 AGTTAGTACAAAGTTGAATCGATACAA 57.299 29.630 0.00 0.00 0.00 2.41
181 187 9.701098 AAGTTAGTACAAAGTTGAATCGATACA 57.299 29.630 0.00 0.00 0.00 2.29
237 243 7.394359 CCCTCCTTTCAAAATAGATGACTCAAA 59.606 37.037 0.00 0.00 0.00 2.69
239 245 6.012508 ACCCTCCTTTCAAAATAGATGACTCA 60.013 38.462 0.00 0.00 0.00 3.41
240 246 6.418946 ACCCTCCTTTCAAAATAGATGACTC 58.581 40.000 0.00 0.00 0.00 3.36
242 248 7.339482 AGTACCCTCCTTTCAAAATAGATGAC 58.661 38.462 0.00 0.00 0.00 3.06
243 249 7.510675 AGTACCCTCCTTTCAAAATAGATGA 57.489 36.000 0.00 0.00 0.00 2.92
245 251 9.004231 ACATAGTACCCTCCTTTCAAAATAGAT 57.996 33.333 0.00 0.00 0.00 1.98
246 252 8.388656 ACATAGTACCCTCCTTTCAAAATAGA 57.611 34.615 0.00 0.00 0.00 1.98
247 253 9.543783 GTACATAGTACCCTCCTTTCAAAATAG 57.456 37.037 0.00 0.00 0.00 1.73
248 254 9.275572 AGTACATAGTACCCTCCTTTCAAAATA 57.724 33.333 3.85 0.00 0.00 1.40
249 255 8.159229 AGTACATAGTACCCTCCTTTCAAAAT 57.841 34.615 3.85 0.00 0.00 1.82
250 256 7.563724 AGTACATAGTACCCTCCTTTCAAAA 57.436 36.000 3.85 0.00 0.00 2.44
251 257 8.669055 TTAGTACATAGTACCCTCCTTTCAAA 57.331 34.615 3.85 0.00 0.00 2.69
252 258 8.534496 GTTTAGTACATAGTACCCTCCTTTCAA 58.466 37.037 3.85 0.00 0.00 2.69
253 259 7.124750 GGTTTAGTACATAGTACCCTCCTTTCA 59.875 40.741 3.85 0.00 0.00 2.69
254 260 7.124750 TGGTTTAGTACATAGTACCCTCCTTTC 59.875 40.741 3.85 0.00 0.00 2.62
255 261 6.961721 TGGTTTAGTACATAGTACCCTCCTTT 59.038 38.462 3.85 0.00 0.00 3.11
256 262 6.505754 TGGTTTAGTACATAGTACCCTCCTT 58.494 40.000 3.85 0.00 0.00 3.36
257 263 6.096164 TGGTTTAGTACATAGTACCCTCCT 57.904 41.667 3.85 0.00 0.00 3.69
258 264 6.239515 CCATGGTTTAGTACATAGTACCCTCC 60.240 46.154 2.57 3.54 0.00 4.30
259 265 6.552350 TCCATGGTTTAGTACATAGTACCCTC 59.448 42.308 12.58 0.00 0.00 4.30
260 266 6.446451 TCCATGGTTTAGTACATAGTACCCT 58.554 40.000 12.58 0.00 0.00 4.34
261 267 6.736110 TCCATGGTTTAGTACATAGTACCC 57.264 41.667 12.58 0.00 0.00 3.69
262 268 7.159372 CCATCCATGGTTTAGTACATAGTACC 58.841 42.308 12.58 0.00 43.05 3.34
283 289 9.819267 AATTAGCTACTAGTTACTTTCACCATC 57.181 33.333 0.00 0.00 0.00 3.51
300 306 8.634444 TCTCTCTGGATCAGTTAAATTAGCTAC 58.366 37.037 0.00 0.00 32.61 3.58
302 308 7.201992 CCTCTCTCTGGATCAGTTAAATTAGCT 60.202 40.741 0.00 0.00 32.61 3.32
330 345 4.460034 CCCATCACACAATCATTGACTTGA 59.540 41.667 3.79 3.77 0.00 3.02
331 346 4.740268 CCCATCACACAATCATTGACTTG 58.260 43.478 3.79 0.00 0.00 3.16
332 347 3.194116 GCCCATCACACAATCATTGACTT 59.806 43.478 3.79 0.00 0.00 3.01
333 348 2.756760 GCCCATCACACAATCATTGACT 59.243 45.455 3.79 0.00 0.00 3.41
334 349 2.478370 CGCCCATCACACAATCATTGAC 60.478 50.000 3.79 0.00 0.00 3.18
416 442 1.086067 CATGCACTGCCCGTACTCAG 61.086 60.000 0.00 5.47 36.45 3.35
417 443 1.079197 CATGCACTGCCCGTACTCA 60.079 57.895 0.00 0.00 0.00 3.41
419 445 2.268920 CCATGCACTGCCCGTACT 59.731 61.111 0.00 0.00 0.00 2.73
420 446 2.824041 CCCATGCACTGCCCGTAC 60.824 66.667 0.00 0.00 0.00 3.67
421 447 4.794648 GCCCATGCACTGCCCGTA 62.795 66.667 0.00 0.00 37.47 4.02
460 493 1.153469 GAGTGAGCTAGGTGCAGCC 60.153 63.158 13.29 4.65 45.94 4.85
461 494 1.107114 TAGAGTGAGCTAGGTGCAGC 58.893 55.000 8.11 8.11 45.94 5.25
462 495 2.357637 GAGTAGAGTGAGCTAGGTGCAG 59.642 54.545 0.00 0.00 45.94 4.41
480 513 0.108615 GCTGCATGGTGTAGACGAGT 60.109 55.000 0.00 0.00 31.36 4.18
481 514 0.174389 AGCTGCATGGTGTAGACGAG 59.826 55.000 1.02 0.00 31.36 4.18
482 515 0.108662 CAGCTGCATGGTGTAGACGA 60.109 55.000 0.00 0.00 39.17 4.20
483 516 1.086067 CCAGCTGCATGGTGTAGACG 61.086 60.000 8.66 0.00 42.19 4.18
484 517 1.372087 GCCAGCTGCATGGTGTAGAC 61.372 60.000 8.66 0.00 42.75 2.59
485 518 1.078214 GCCAGCTGCATGGTGTAGA 60.078 57.895 8.66 0.00 42.75 2.59
486 519 2.466982 CGCCAGCTGCATGGTGTAG 61.467 63.158 8.66 0.00 44.30 2.74
487 520 2.436469 CGCCAGCTGCATGGTGTA 60.436 61.111 8.66 0.00 44.30 2.90
571 604 4.434685 CTGGCAGTAGCTAGCAGC 57.565 61.111 18.83 14.49 42.60 5.25
615 648 4.410400 CTTGCCGGGGAGGTCCAC 62.410 72.222 2.18 0.00 43.70 4.02
636 669 3.729274 ATGAGCACATGAAAGGGCAACC 61.729 50.000 0.00 0.00 46.77 3.77
693 726 1.139058 GCAAGCCAAGCTAGCTACCTA 59.861 52.381 19.70 0.00 40.49 3.08
694 727 0.107459 GCAAGCCAAGCTAGCTACCT 60.107 55.000 19.70 11.57 40.49 3.08
695 728 0.107459 AGCAAGCCAAGCTAGCTACC 60.107 55.000 19.70 9.32 40.49 3.18
696 729 1.134551 AGAGCAAGCCAAGCTAGCTAC 60.135 52.381 19.70 10.91 43.58 3.58
724 761 6.348540 CCGAGGCAAAACCATTAATATAGAGC 60.349 42.308 0.00 0.00 43.14 4.09
725 762 6.348540 GCCGAGGCAAAACCATTAATATAGAG 60.349 42.308 9.58 0.00 43.14 2.43
726 763 5.472137 GCCGAGGCAAAACCATTAATATAGA 59.528 40.000 9.58 0.00 43.14 1.98
727 764 5.616866 CGCCGAGGCAAAACCATTAATATAG 60.617 44.000 15.03 0.00 43.14 1.31
848 885 0.808125 CGGGAGTGAGACTGAGAGTG 59.192 60.000 0.00 0.00 0.00 3.51
849 886 0.963355 GCGGGAGTGAGACTGAGAGT 60.963 60.000 0.00 0.00 0.00 3.24
850 887 0.679640 AGCGGGAGTGAGACTGAGAG 60.680 60.000 0.00 0.00 0.00 3.20
851 888 0.678366 GAGCGGGAGTGAGACTGAGA 60.678 60.000 0.00 0.00 0.00 3.27
852 889 0.962855 TGAGCGGGAGTGAGACTGAG 60.963 60.000 0.00 0.00 0.00 3.35
853 890 1.074951 TGAGCGGGAGTGAGACTGA 59.925 57.895 0.00 0.00 0.00 3.41
856 893 1.214062 CAGTGAGCGGGAGTGAGAC 59.786 63.158 0.00 0.00 0.00 3.36
880 917 0.178932 TGGCAGTAGAGTGAGGTGGT 60.179 55.000 0.00 0.00 0.00 4.16
885 922 1.901085 GGGGTGGCAGTAGAGTGAG 59.099 63.158 0.00 0.00 0.00 3.51
886 923 1.982395 CGGGGTGGCAGTAGAGTGA 60.982 63.158 0.00 0.00 0.00 3.41
888 925 3.391382 GCGGGGTGGCAGTAGAGT 61.391 66.667 0.00 0.00 0.00 3.24
889 926 4.162690 GGCGGGGTGGCAGTAGAG 62.163 72.222 0.00 0.00 44.08 2.43
941 993 2.125753 GCAGCGAGTGGAGTGGAG 60.126 66.667 0.00 0.00 0.00 3.86
942 994 2.917227 TGCAGCGAGTGGAGTGGA 60.917 61.111 0.00 0.00 0.00 4.02
943 995 2.740055 GTGCAGCGAGTGGAGTGG 60.740 66.667 0.00 0.00 0.00 4.00
944 996 3.108289 CGTGCAGCGAGTGGAGTG 61.108 66.667 3.04 0.00 44.77 3.51
973 1025 4.251268 GCCAGCTTAATTATACTACCGGG 58.749 47.826 6.32 0.00 0.00 5.73
1149 1201 3.191791 CCCCGTAAAAATTGTACTGGTGG 59.808 47.826 3.60 2.13 0.00 4.61
1159 1211 3.290567 GGCGCCCCCGTAAAAATT 58.709 55.556 18.11 0.00 36.67 1.82
1350 1417 1.551452 AGGAGAGGTTGAAGGACGAG 58.449 55.000 0.00 0.00 0.00 4.18
1409 1476 1.347707 ACTGCGGATGTTGAAGGAAGA 59.652 47.619 0.00 0.00 0.00 2.87
1414 1481 3.058016 ACAATTGACTGCGGATGTTGAAG 60.058 43.478 13.59 0.00 0.00 3.02
1415 1482 2.884012 ACAATTGACTGCGGATGTTGAA 59.116 40.909 13.59 0.00 0.00 2.69
1416 1483 2.503331 ACAATTGACTGCGGATGTTGA 58.497 42.857 13.59 0.00 0.00 3.18
1417 1484 2.981805 CAACAATTGACTGCGGATGTTG 59.018 45.455 13.59 8.72 40.87 3.33
1418 1485 2.607771 GCAACAATTGACTGCGGATGTT 60.608 45.455 13.59 0.00 0.00 2.71
1419 1486 1.068333 GCAACAATTGACTGCGGATGT 60.068 47.619 13.59 0.00 0.00 3.06
1420 1487 1.200716 AGCAACAATTGACTGCGGATG 59.799 47.619 22.57 7.71 41.05 3.51
1421 1488 1.470098 GAGCAACAATTGACTGCGGAT 59.530 47.619 22.57 11.91 41.05 4.18
1422 1489 0.874390 GAGCAACAATTGACTGCGGA 59.126 50.000 22.57 0.00 41.05 5.54
1423 1490 0.453282 CGAGCAACAATTGACTGCGG 60.453 55.000 22.57 17.42 41.05 5.69
1424 1491 0.512518 TCGAGCAACAATTGACTGCG 59.487 50.000 22.57 14.83 41.05 5.18
1425 1492 2.778659 GATCGAGCAACAATTGACTGC 58.221 47.619 21.86 21.86 36.29 4.40
1426 1493 2.785681 GCGATCGAGCAACAATTGACTG 60.786 50.000 21.57 9.96 37.05 3.51
1427 1494 1.394917 GCGATCGAGCAACAATTGACT 59.605 47.619 21.57 6.28 37.05 3.41
1428 1495 1.802839 GCGATCGAGCAACAATTGAC 58.197 50.000 21.57 0.97 37.05 3.18
1429 1496 0.369931 CGCGATCGAGCAACAATTGA 59.630 50.000 21.57 0.00 38.10 2.57
1430 1497 1.189989 GCGCGATCGAGCAACAATTG 61.190 55.000 34.15 3.24 40.60 2.32
1431 1498 1.060937 GCGCGATCGAGCAACAATT 59.939 52.632 34.15 0.00 40.60 2.32
1432 1499 2.703409 GCGCGATCGAGCAACAAT 59.297 55.556 34.15 0.00 40.60 2.71
1433 1500 3.837687 CGCGCGATCGAGCAACAA 61.838 61.111 36.43 0.00 40.94 2.83
1449 1516 2.498807 TCAGGAATTGAGATCGAGCG 57.501 50.000 0.00 0.00 0.00 5.03
1451 1518 6.018098 CCATTTCTTCAGGAATTGAGATCGAG 60.018 42.308 0.00 0.00 37.44 4.04
1459 1526 5.503927 TCTCTCCCATTTCTTCAGGAATTG 58.496 41.667 0.00 0.00 35.96 2.32
1476 1543 3.444703 TCGAGCTGCTTAATTCTCTCC 57.555 47.619 2.53 0.00 0.00 3.71
1478 1545 4.662468 TGATCGAGCTGCTTAATTCTCT 57.338 40.909 2.53 0.00 0.00 3.10
1491 1566 3.502191 ACTCTCAGTTCTTGATCGAGC 57.498 47.619 4.94 0.00 33.54 5.03
1493 1568 6.599638 TCTCATTACTCTCAGTTCTTGATCGA 59.400 38.462 0.00 0.00 34.68 3.59
1494 1569 6.790282 TCTCATTACTCTCAGTTCTTGATCG 58.210 40.000 0.00 0.00 34.68 3.69
1495 1570 8.412456 TCATCTCATTACTCTCAGTTCTTGATC 58.588 37.037 0.00 0.00 34.68 2.92
1497 1572 7.709149 TCATCTCATTACTCTCAGTTCTTGA 57.291 36.000 0.00 0.00 0.00 3.02
1498 1573 8.819015 CAATCATCTCATTACTCTCAGTTCTTG 58.181 37.037 0.00 0.00 0.00 3.02
1502 1577 8.303780 TCTCAATCATCTCATTACTCTCAGTT 57.696 34.615 0.00 0.00 0.00 3.16
1503 1578 7.894753 TCTCAATCATCTCATTACTCTCAGT 57.105 36.000 0.00 0.00 0.00 3.41
1504 1579 8.799367 AGATCTCAATCATCTCATTACTCTCAG 58.201 37.037 0.00 0.00 34.07 3.35
1505 1580 8.709272 AGATCTCAATCATCTCATTACTCTCA 57.291 34.615 0.00 0.00 34.07 3.27
1507 1582 9.812347 AGTAGATCTCAATCATCTCATTACTCT 57.188 33.333 0.00 0.00 34.07 3.24
1511 1586 9.249053 GGGTAGTAGATCTCAATCATCTCATTA 57.751 37.037 0.00 0.00 34.07 1.90
1512 1587 7.732140 TGGGTAGTAGATCTCAATCATCTCATT 59.268 37.037 0.00 0.00 34.07 2.57
1532 1607 7.469537 AGTGTTTAGCTAGCTATATGGGTAG 57.530 40.000 24.69 18.12 39.46 3.18
1533 1608 7.850935 AAGTGTTTAGCTAGCTATATGGGTA 57.149 36.000 24.69 5.62 0.00 3.69
1534 1609 6.749036 AAGTGTTTAGCTAGCTATATGGGT 57.251 37.500 24.69 7.37 0.00 4.51
1535 1610 8.368668 AGTTAAGTGTTTAGCTAGCTATATGGG 58.631 37.037 24.69 0.00 29.74 4.00
1541 1616 9.595823 CCAATTAGTTAAGTGTTTAGCTAGCTA 57.404 33.333 20.67 20.67 35.09 3.32
1542 1617 8.101419 ACCAATTAGTTAAGTGTTTAGCTAGCT 58.899 33.333 23.12 23.12 35.09 3.32
1543 1618 8.265165 ACCAATTAGTTAAGTGTTTAGCTAGC 57.735 34.615 6.62 6.62 35.09 3.42
1547 1622 9.341899 CATCAACCAATTAGTTAAGTGTTTAGC 57.658 33.333 0.00 0.00 30.00 3.09
1559 1634 5.574055 CGTACGTACACATCAACCAATTAGT 59.426 40.000 24.50 0.00 0.00 2.24
1560 1635 5.574055 ACGTACGTACACATCAACCAATTAG 59.426 40.000 21.41 5.67 0.00 1.73
1564 1639 3.051327 CACGTACGTACACATCAACCAA 58.949 45.455 22.34 0.00 0.00 3.67
1567 1642 2.052891 TGCACGTACGTACACATCAAC 58.947 47.619 22.34 7.54 0.00 3.18
1581 1656 1.005630 GCTTCCTCAGTCTGCACGT 60.006 57.895 0.00 0.00 0.00 4.49
1583 1658 1.739562 CGGCTTCCTCAGTCTGCAC 60.740 63.158 0.00 0.00 0.00 4.57
1831 1921 2.123640 GAGGAGGAGGACGGGGAG 60.124 72.222 0.00 0.00 0.00 4.30
1896 2004 1.807573 CTCTTCTTGACGCCTCCGC 60.808 63.158 0.00 0.00 38.22 5.54
1897 2005 1.807573 GCTCTTCTTGACGCCTCCG 60.808 63.158 0.00 0.00 41.14 4.63
1898 2006 1.807573 CGCTCTTCTTGACGCCTCC 60.808 63.158 0.00 0.00 0.00 4.30
1899 2007 1.807573 CCGCTCTTCTTGACGCCTC 60.808 63.158 0.00 0.00 0.00 4.70
1900 2008 2.262915 CCGCTCTTCTTGACGCCT 59.737 61.111 0.00 0.00 0.00 5.52
1901 2009 3.491652 GCCGCTCTTCTTGACGCC 61.492 66.667 0.00 0.00 0.00 5.68
2372 2502 0.388649 GCGCTAATCGGATCGTCCAT 60.389 55.000 0.00 0.00 35.91 3.41
2373 2503 1.007734 GCGCTAATCGGATCGTCCA 60.008 57.895 0.00 0.00 35.91 4.02
2374 2504 1.733399 GGCGCTAATCGGATCGTCC 60.733 63.158 7.64 0.00 38.94 4.79
2375 2505 1.007734 TGGCGCTAATCGGATCGTC 60.008 57.895 7.64 0.00 38.94 4.20
2376 2506 1.299926 GTGGCGCTAATCGGATCGT 60.300 57.895 7.64 0.00 38.94 3.73
2377 2507 2.365068 CGTGGCGCTAATCGGATCG 61.365 63.158 7.64 0.00 38.94 3.69
2447 2586 2.430956 ACGCGAAATAGTACACGTACG 58.569 47.619 15.93 15.01 40.80 3.67
2448 2587 3.538258 GCAACGCGAAATAGTACACGTAC 60.538 47.826 15.93 0.00 36.35 3.67
2449 2588 2.593775 GCAACGCGAAATAGTACACGTA 59.406 45.455 15.93 0.00 32.76 3.57
2450 2589 1.387756 GCAACGCGAAATAGTACACGT 59.612 47.619 15.93 0.00 34.85 4.49
2546 2689 4.358214 ACATTTCCAATTTATTCCCGGGT 58.642 39.130 22.86 4.16 0.00 5.28
2562 2705 9.142515 TCACATAATGCAAAAGATGAACATTTC 57.857 29.630 0.00 0.00 33.31 2.17
2570 2713 5.886992 TCAGCTCACATAATGCAAAAGATG 58.113 37.500 0.00 0.00 0.00 2.90
2634 2782 3.279434 GACCAGGTCGCATAGGATTTTT 58.721 45.455 3.05 0.00 0.00 1.94
2635 2783 2.919228 GACCAGGTCGCATAGGATTTT 58.081 47.619 3.05 0.00 0.00 1.82
2636 2784 2.622064 GACCAGGTCGCATAGGATTT 57.378 50.000 3.05 0.00 0.00 2.17
2651 2799 6.485984 GTCTCCAGATTAGAAGTATACGACCA 59.514 42.308 0.00 0.00 0.00 4.02
2680 2828 0.105964 CCAGGTGTCACTCAACGGAA 59.894 55.000 2.35 0.00 39.03 4.30
2706 2854 2.621338 CTCCTTGCTGCGTTGAGATTA 58.379 47.619 6.33 0.00 0.00 1.75
2707 2855 1.446907 CTCCTTGCTGCGTTGAGATT 58.553 50.000 6.33 0.00 0.00 2.40
2746 2899 2.104111 ACAGTCGGGATTTCACAACTGA 59.896 45.455 7.86 0.00 37.97 3.41
2825 2992 2.921912 GCAATCATCCAACGTGTTGTGG 60.922 50.000 11.45 0.00 38.85 4.17
2842 3009 2.882777 CGCGAGCGACAGAGCAAT 60.883 61.111 12.58 0.00 42.83 3.56
2881 3049 1.226295 GGGCAAGCGTCGTAATTGC 60.226 57.895 17.88 17.88 46.67 3.56
2902 3070 3.711541 ATACTGGCCGCGACCGAAC 62.712 63.158 8.23 0.00 36.29 3.95
2903 3071 3.420214 GATACTGGCCGCGACCGAA 62.420 63.158 8.23 0.00 36.29 4.30
2986 3154 1.202065 CCGTGAATTCATGCGTTCCAG 60.202 52.381 20.29 3.24 0.00 3.86
2987 3155 0.801872 CCGTGAATTCATGCGTTCCA 59.198 50.000 20.29 0.00 0.00 3.53
2993 3161 0.881118 ACACCACCGTGAATTCATGC 59.119 50.000 20.29 4.20 43.14 4.06
2998 3166 3.478857 TGTTCTACACCACCGTGAATT 57.521 42.857 0.00 0.00 43.14 2.17
3009 3180 3.512680 CGGAGATGGTCTTGTTCTACAC 58.487 50.000 0.00 0.00 0.00 2.90
3058 3238 2.741759 TTAGCAACACTGATCGCTGA 57.258 45.000 1.32 0.00 35.93 4.26
3065 3245 1.899814 ACCGGAGATTAGCAACACTGA 59.100 47.619 9.46 0.00 0.00 3.41
3067 3247 1.899814 TCACCGGAGATTAGCAACACT 59.100 47.619 9.46 0.00 0.00 3.55
3154 3334 1.228657 GGGTTGTGTGAGCGTCTTCC 61.229 60.000 0.00 0.00 0.00 3.46
3259 3439 3.099267 ACAACGTCTTCTTCTCCACTG 57.901 47.619 0.00 0.00 0.00 3.66


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

AutoCloner maintained by Alex Coulton.