Multiple sequence alignment - TraesCS7A01G097100

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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 TraesCS7A01G097100 chr7A 100.000 3644 0 0 1 3644 59416191 59419834 0.000000e+00 6730.0
1 TraesCS7A01G097100 chr7D 89.292 2783 156 69 392 3078 55427965 55430701 0.000000e+00 3358.0
2 TraesCS7A01G097100 chr7D 88.516 566 37 13 3094 3640 55430683 55431239 0.000000e+00 660.0
3 TraesCS7A01G097100 chr7D 86.551 461 41 5 2388 2841 55605477 55605923 4.230000e-134 488.0
4 TraesCS7A01G097100 chr7D 85.965 171 13 6 40 204 55427533 55427698 4.840000e-39 172.0
5 TraesCS7A01G097100 chr7D 86.765 68 2 6 3131 3198 55606036 55606096 6.530000e-08 69.4
6 TraesCS7A01G097100 chr4A 88.658 2363 158 60 762 3078 671944769 671947067 0.000000e+00 2778.0
7 TraesCS7A01G097100 chr4A 85.653 467 40 18 3196 3644 671947615 671948072 1.980000e-127 466.0
8 TraesCS7A01G097100 chr4A 84.175 297 20 12 383 662 671944324 671944610 2.790000e-66 263.0
9 TraesCS7A01G097100 chr4A 84.795 171 15 8 40 204 671943902 671944067 1.050000e-35 161.0
10 TraesCS7A01G097100 chrUn 87.982 441 22 10 1 430 311852313 311851893 3.270000e-135 492.0
11 TraesCS7A01G097100 chr5D 87.402 127 9 3 310 430 195151242 195151117 4.910000e-29 139.0


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 TraesCS7A01G097100 chr7A 59416191 59419834 3643 False 6730.000000 6730 100.000000 1 3644 1 chr7A.!!$F1 3643
1 TraesCS7A01G097100 chr7D 55427533 55431239 3706 False 1396.666667 3358 87.924333 40 3640 3 chr7D.!!$F1 3600
2 TraesCS7A01G097100 chr7D 55605477 55606096 619 False 278.700000 488 86.658000 2388 3198 2 chr7D.!!$F2 810
3 TraesCS7A01G097100 chr4A 671943902 671948072 4170 False 917.000000 2778 85.820250 40 3644 4 chr4A.!!$F1 3604

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
229 234 0.036294 AAGAAACCTACCGAGCTGGC 60.036 55.0 0.0 0.0 43.94 4.85 F
887 1048 0.173029 TTTTGTGTGTGTGCAGGCAG 59.827 50.0 0.0 0.0 0.00 4.85 F
2026 2196 0.252330 TCCATCCTTGGTACGGGTCA 60.252 55.0 0.0 0.0 44.06 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1944 2114 0.456824 TGACGAAGATGCTGACGAGC 60.457 55.000 0.0 0.0 46.44 5.03 R
2290 2482 0.172352 GAGAGGTGACGAGGCTGAAG 59.828 60.000 0.0 0.0 0.00 3.02 R
3463 4175 1.329292 TGTTTCTGTTTTCCACGAGCG 59.671 47.619 0.0 0.0 0.00 5.03 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
23 24 5.854010 AATCAGCAATGCATGAGAATCTT 57.146 34.783 8.35 0.00 34.92 2.40
24 25 5.854010 ATCAGCAATGCATGAGAATCTTT 57.146 34.783 8.35 0.00 34.92 2.52
25 26 5.654603 TCAGCAATGCATGAGAATCTTTT 57.345 34.783 8.35 0.00 34.92 2.27
26 27 6.032956 TCAGCAATGCATGAGAATCTTTTT 57.967 33.333 8.35 0.00 34.92 1.94
27 28 6.097356 TCAGCAATGCATGAGAATCTTTTTC 58.903 36.000 8.35 0.00 34.92 2.29
28 29 6.071560 TCAGCAATGCATGAGAATCTTTTTCT 60.072 34.615 8.35 0.00 34.92 2.52
29 30 7.121611 TCAGCAATGCATGAGAATCTTTTTCTA 59.878 33.333 8.35 0.00 34.92 2.10
30 31 7.432545 CAGCAATGCATGAGAATCTTTTTCTAG 59.567 37.037 8.35 0.00 34.92 2.43
31 32 7.338703 AGCAATGCATGAGAATCTTTTTCTAGA 59.661 33.333 8.35 0.00 34.92 2.43
32 33 7.972277 GCAATGCATGAGAATCTTTTTCTAGAA 59.028 33.333 0.00 0.00 34.92 2.10
36 37 8.820933 TGCATGAGAATCTTTTTCTAGAATACG 58.179 33.333 5.89 0.00 34.92 3.06
37 38 7.796197 GCATGAGAATCTTTTTCTAGAATACGC 59.204 37.037 5.89 0.00 34.92 4.42
38 39 8.820933 CATGAGAATCTTTTTCTAGAATACGCA 58.179 33.333 5.89 0.00 34.92 5.24
39 40 8.186178 TGAGAATCTTTTTCTAGAATACGCAC 57.814 34.615 5.89 0.00 34.92 5.34
40 41 7.817478 TGAGAATCTTTTTCTAGAATACGCACA 59.183 33.333 5.89 0.00 34.92 4.57
41 42 8.547967 AGAATCTTTTTCTAGAATACGCACAA 57.452 30.769 5.89 0.00 0.00 3.33
42 43 8.660373 AGAATCTTTTTCTAGAATACGCACAAG 58.340 33.333 5.89 1.48 0.00 3.16
43 44 6.165659 TCTTTTTCTAGAATACGCACAAGC 57.834 37.500 5.89 0.00 37.42 4.01
46 47 7.547722 TCTTTTTCTAGAATACGCACAAGCATA 59.452 33.333 5.89 0.00 42.27 3.14
58 59 7.178712 ACGCACAAGCATAAGAATCTTATAC 57.821 36.000 14.46 9.77 42.27 1.47
60 61 6.593978 GCACAAGCATAAGAATCTTATACGG 58.406 40.000 14.46 9.80 41.58 4.02
71 72 6.049790 AGAATCTTATACGGACTCTTTTGCC 58.950 40.000 0.00 0.00 0.00 4.52
76 77 4.772886 ATACGGACTCTTTTGCCCTAAT 57.227 40.909 0.00 0.00 0.00 1.73
77 78 5.881923 ATACGGACTCTTTTGCCCTAATA 57.118 39.130 0.00 0.00 0.00 0.98
78 79 4.563140 ACGGACTCTTTTGCCCTAATAA 57.437 40.909 0.00 0.00 0.00 1.40
93 94 8.055279 TGCCCTAATAATTCAATAATAGCAGC 57.945 34.615 0.00 0.00 0.00 5.25
94 95 7.669304 TGCCCTAATAATTCAATAATAGCAGCA 59.331 33.333 0.00 0.00 0.00 4.41
113 114 6.380274 AGCAGCATTACTAGTAAACAGGAGTA 59.620 38.462 18.88 0.00 0.00 2.59
176 181 0.172803 CGCCGTAGCTTCCAAGTAGT 59.827 55.000 0.00 0.00 36.60 2.73
177 182 1.402968 CGCCGTAGCTTCCAAGTAGTA 59.597 52.381 0.00 0.00 36.60 1.82
178 183 2.541178 CGCCGTAGCTTCCAAGTAGTAG 60.541 54.545 0.00 0.00 36.60 2.57
179 184 2.426381 GCCGTAGCTTCCAAGTAGTAGT 59.574 50.000 0.00 0.00 35.50 2.73
180 185 3.629398 GCCGTAGCTTCCAAGTAGTAGTA 59.371 47.826 0.00 0.00 35.50 1.82
181 186 4.261114 GCCGTAGCTTCCAAGTAGTAGTAG 60.261 50.000 0.00 0.00 35.50 2.57
184 189 5.066246 CGTAGCTTCCAAGTAGTAGTAGCTT 59.934 44.000 5.52 0.00 38.36 3.74
189 194 6.752815 GCTTCCAAGTAGTAGTAGCTTACTTG 59.247 42.308 20.96 20.96 44.10 3.16
204 209 4.557496 GCTTACTTGAACCAGGCAAGAAAG 60.557 45.833 12.48 1.21 44.16 2.62
205 210 3.297134 ACTTGAACCAGGCAAGAAAGA 57.703 42.857 12.48 0.00 44.16 2.52
206 211 3.631250 ACTTGAACCAGGCAAGAAAGAA 58.369 40.909 12.48 0.00 44.16 2.52
208 213 4.098501 ACTTGAACCAGGCAAGAAAGAAAG 59.901 41.667 12.48 0.00 44.16 2.62
209 214 3.897239 TGAACCAGGCAAGAAAGAAAGA 58.103 40.909 0.00 0.00 0.00 2.52
210 215 4.277476 TGAACCAGGCAAGAAAGAAAGAA 58.723 39.130 0.00 0.00 0.00 2.52
211 216 4.709397 TGAACCAGGCAAGAAAGAAAGAAA 59.291 37.500 0.00 0.00 0.00 2.52
212 217 4.926140 ACCAGGCAAGAAAGAAAGAAAG 57.074 40.909 0.00 0.00 0.00 2.62
213 218 4.536765 ACCAGGCAAGAAAGAAAGAAAGA 58.463 39.130 0.00 0.00 0.00 2.52
214 219 4.956075 ACCAGGCAAGAAAGAAAGAAAGAA 59.044 37.500 0.00 0.00 0.00 2.52
215 220 5.422012 ACCAGGCAAGAAAGAAAGAAAGAAA 59.578 36.000 0.00 0.00 0.00 2.52
216 221 5.750547 CCAGGCAAGAAAGAAAGAAAGAAAC 59.249 40.000 0.00 0.00 0.00 2.78
217 222 5.750547 CAGGCAAGAAAGAAAGAAAGAAACC 59.249 40.000 0.00 0.00 0.00 3.27
219 224 6.833933 AGGCAAGAAAGAAAGAAAGAAACCTA 59.166 34.615 0.00 0.00 0.00 3.08
222 227 6.862711 AGAAAGAAAGAAAGAAACCTACCG 57.137 37.500 0.00 0.00 0.00 4.02
223 228 6.589135 AGAAAGAAAGAAAGAAACCTACCGA 58.411 36.000 0.00 0.00 0.00 4.69
224 229 6.706716 AGAAAGAAAGAAAGAAACCTACCGAG 59.293 38.462 0.00 0.00 0.00 4.63
225 230 4.316645 AGAAAGAAAGAAACCTACCGAGC 58.683 43.478 0.00 0.00 0.00 5.03
226 231 4.040584 AGAAAGAAAGAAACCTACCGAGCT 59.959 41.667 0.00 0.00 0.00 4.09
227 232 3.320673 AGAAAGAAACCTACCGAGCTG 57.679 47.619 0.00 0.00 0.00 4.24
228 233 2.028020 AGAAAGAAACCTACCGAGCTGG 60.028 50.000 0.00 0.00 46.41 4.85
229 234 0.036294 AAGAAACCTACCGAGCTGGC 60.036 55.000 0.00 0.00 43.94 4.85
230 235 1.192146 AGAAACCTACCGAGCTGGCA 61.192 55.000 0.00 0.00 43.94 4.92
232 237 2.781595 AAACCTACCGAGCTGGCACG 62.782 60.000 0.00 5.51 43.94 5.34
244 249 2.048503 GGCACGGCGTTCACTAGT 60.049 61.111 11.19 0.00 0.00 2.57
245 250 2.380410 GGCACGGCGTTCACTAGTG 61.380 63.158 17.17 17.17 36.05 2.74
247 252 1.615107 GCACGGCGTTCACTAGTGTC 61.615 60.000 21.99 14.86 35.46 3.67
248 253 1.081641 ACGGCGTTCACTAGTGTCG 60.082 57.895 26.00 26.00 34.46 4.35
249 254 1.208358 CGGCGTTCACTAGTGTCGA 59.792 57.895 30.67 15.83 33.75 4.20
250 255 0.793478 CGGCGTTCACTAGTGTCGAG 60.793 60.000 30.67 23.13 33.75 4.04
268 314 2.715046 GAGTGGCATTGATGGAAGTCA 58.285 47.619 0.00 0.00 0.00 3.41
284 330 5.183969 GGAAGTCATCCTTACAAACCTACC 58.816 45.833 0.00 0.00 45.56 3.18
285 331 4.467198 AGTCATCCTTACAAACCTACCG 57.533 45.455 0.00 0.00 0.00 4.02
286 332 4.091549 AGTCATCCTTACAAACCTACCGA 58.908 43.478 0.00 0.00 0.00 4.69
287 333 4.159879 AGTCATCCTTACAAACCTACCGAG 59.840 45.833 0.00 0.00 0.00 4.63
289 335 4.960469 TCATCCTTACAAACCTACCGAGAT 59.040 41.667 0.00 0.00 0.00 2.75
290 336 4.730949 TCCTTACAAACCTACCGAGATG 57.269 45.455 0.00 0.00 0.00 2.90
325 374 1.538047 AAGATTTGCACCGCACAGAT 58.462 45.000 0.00 0.00 38.71 2.90
328 377 1.402968 GATTTGCACCGCACAGATCAT 59.597 47.619 0.00 0.00 38.71 2.45
330 379 2.330440 TTGCACCGCACAGATCATAT 57.670 45.000 0.00 0.00 38.71 1.78
344 393 7.147689 GCACAGATCATATCCTCCAGAATCTAT 60.148 40.741 0.00 0.00 0.00 1.98
345 394 8.760735 CACAGATCATATCCTCCAGAATCTATT 58.239 37.037 0.00 0.00 0.00 1.73
346 395 8.760735 ACAGATCATATCCTCCAGAATCTATTG 58.239 37.037 0.00 0.00 0.00 1.90
347 396 7.711772 CAGATCATATCCTCCAGAATCTATTGC 59.288 40.741 0.00 0.00 0.00 3.56
348 397 6.940430 TCATATCCTCCAGAATCTATTGCA 57.060 37.500 0.00 0.00 0.00 4.08
349 398 6.705302 TCATATCCTCCAGAATCTATTGCAC 58.295 40.000 0.00 0.00 0.00 4.57
350 399 3.845781 TCCTCCAGAATCTATTGCACC 57.154 47.619 0.00 0.00 0.00 5.01
351 400 2.439507 TCCTCCAGAATCTATTGCACCC 59.560 50.000 0.00 0.00 0.00 4.61
352 401 2.173356 CCTCCAGAATCTATTGCACCCA 59.827 50.000 0.00 0.00 0.00 4.51
353 402 3.474600 CTCCAGAATCTATTGCACCCAG 58.525 50.000 0.00 0.00 0.00 4.45
354 403 2.173356 TCCAGAATCTATTGCACCCAGG 59.827 50.000 0.00 0.00 0.00 4.45
355 404 2.092212 CCAGAATCTATTGCACCCAGGT 60.092 50.000 0.00 0.00 0.00 4.00
358 407 1.898863 ATCTATTGCACCCAGGTCCT 58.101 50.000 0.00 0.00 0.00 3.85
359 408 0.911769 TCTATTGCACCCAGGTCCTG 59.088 55.000 12.40 12.40 0.00 3.86
363 432 1.640593 TTGCACCCAGGTCCTGTGAA 61.641 55.000 17.85 1.99 31.66 3.18
401 485 3.828451 GGACCCAATGCATATATTGTGCT 59.172 43.478 0.00 0.00 42.92 4.40
402 486 4.082571 GGACCCAATGCATATATTGTGCTC 60.083 45.833 0.00 3.05 42.92 4.26
417 504 1.464608 GTGCTCGTACAACATGTGCAT 59.535 47.619 0.00 0.00 42.77 3.96
425 512 4.083537 CGTACAACATGTGCATTAACTGGT 60.084 41.667 0.00 0.00 32.27 4.00
455 542 4.947147 GCGTGGTGGGCTGTTGGA 62.947 66.667 0.00 0.00 0.00 3.53
466 553 1.538047 GCTGTTGGAGCCTTCATTCA 58.462 50.000 0.00 0.00 42.54 2.57
477 564 4.205587 AGCCTTCATTCATCTCATGTTCC 58.794 43.478 0.00 0.00 0.00 3.62
483 570 2.408271 TCATCTCATGTTCCTGCCAC 57.592 50.000 0.00 0.00 0.00 5.01
498 585 2.756760 CTGCCACTTCTATTGCCAATGT 59.243 45.455 0.00 0.00 0.00 2.71
507 594 5.565592 TCTATTGCCAATGTGTTGTGATC 57.434 39.130 0.00 0.00 33.36 2.92
508 595 2.702898 TTGCCAATGTGTTGTGATCG 57.297 45.000 0.00 0.00 33.36 3.69
509 596 1.889545 TGCCAATGTGTTGTGATCGA 58.110 45.000 0.00 0.00 33.36 3.59
510 597 2.435422 TGCCAATGTGTTGTGATCGAT 58.565 42.857 0.00 0.00 33.36 3.59
511 598 2.162008 TGCCAATGTGTTGTGATCGATG 59.838 45.455 0.54 0.00 33.36 3.84
512 599 2.162208 GCCAATGTGTTGTGATCGATGT 59.838 45.455 0.54 0.00 33.36 3.06
513 600 3.750512 CCAATGTGTTGTGATCGATGTG 58.249 45.455 0.54 0.00 33.36 3.21
514 601 3.165890 CAATGTGTTGTGATCGATGTGC 58.834 45.455 0.54 0.00 0.00 4.57
516 603 1.270785 TGTGTTGTGATCGATGTGCCT 60.271 47.619 0.54 0.00 0.00 4.75
517 604 1.394917 GTGTTGTGATCGATGTGCCTC 59.605 52.381 0.54 0.00 0.00 4.70
518 605 1.001860 TGTTGTGATCGATGTGCCTCA 59.998 47.619 0.54 0.00 0.00 3.86
519 606 2.283298 GTTGTGATCGATGTGCCTCAT 58.717 47.619 0.54 0.00 39.77 2.90
520 607 2.229675 TGTGATCGATGTGCCTCATC 57.770 50.000 0.54 8.38 46.68 2.92
528 615 0.616891 ATGTGCCTCATCAGTCAGCA 59.383 50.000 0.00 0.00 29.76 4.41
530 617 1.023513 GTGCCTCATCAGTCAGCACC 61.024 60.000 2.09 0.00 46.25 5.01
532 619 1.985614 CCTCATCAGTCAGCACCCA 59.014 57.895 0.00 0.00 0.00 4.51
533 620 0.392193 CCTCATCAGTCAGCACCCAC 60.392 60.000 0.00 0.00 0.00 4.61
534 621 0.322648 CTCATCAGTCAGCACCCACA 59.677 55.000 0.00 0.00 0.00 4.17
535 622 0.322648 TCATCAGTCAGCACCCACAG 59.677 55.000 0.00 0.00 0.00 3.66
536 623 1.002868 ATCAGTCAGCACCCACAGC 60.003 57.895 0.00 0.00 0.00 4.40
537 624 1.771783 ATCAGTCAGCACCCACAGCA 61.772 55.000 0.00 0.00 0.00 4.41
538 625 1.303074 CAGTCAGCACCCACAGCAT 60.303 57.895 0.00 0.00 0.00 3.79
539 626 1.002868 AGTCAGCACCCACAGCATC 60.003 57.895 0.00 0.00 0.00 3.91
540 627 2.042831 GTCAGCACCCACAGCATCC 61.043 63.158 0.00 0.00 0.00 3.51
541 628 2.753043 CAGCACCCACAGCATCCC 60.753 66.667 0.00 0.00 0.00 3.85
542 629 4.052518 AGCACCCACAGCATCCCC 62.053 66.667 0.00 0.00 0.00 4.81
570 657 1.526887 CGCCCTGCTTCCCTATCAA 59.473 57.895 0.00 0.00 0.00 2.57
662 762 0.452987 ATGTGATGCGACAACCATGC 59.547 50.000 0.00 0.00 0.00 4.06
663 763 1.226101 GTGATGCGACAACCATGCG 60.226 57.895 0.00 0.00 0.00 4.73
705 830 4.085721 GCGTACTATATTCAGCGTGTTGTC 60.086 45.833 0.00 0.00 0.00 3.18
709 834 5.103000 ACTATATTCAGCGTGTTGTCTGAC 58.897 41.667 0.00 0.00 38.87 3.51
714 839 1.007734 GCGTGTTGTCTGACGGAGA 60.008 57.895 2.98 0.00 36.09 3.71
717 842 1.129326 GTGTTGTCTGACGGAGAACG 58.871 55.000 16.93 0.00 46.98 3.95
718 843 1.026584 TGTTGTCTGACGGAGAACGA 58.973 50.000 16.93 6.20 46.98 3.85
721 846 3.253921 TGTTGTCTGACGGAGAACGAATA 59.746 43.478 16.93 0.00 46.98 1.75
725 851 9.961382 TGTTGTCTGACGGAGAACGAATAAACA 62.961 40.741 16.93 0.95 46.98 2.83
733 859 5.505286 GGAGAACGAATAAACATGATGCAG 58.495 41.667 0.00 0.00 0.00 4.41
735 861 6.183360 GGAGAACGAATAAACATGATGCAGAA 60.183 38.462 0.00 0.00 0.00 3.02
737 863 7.765307 AGAACGAATAAACATGATGCAGAAAT 58.235 30.769 0.00 0.00 0.00 2.17
739 888 9.502145 GAACGAATAAACATGATGCAGAAATTA 57.498 29.630 0.00 0.00 0.00 1.40
749 900 4.577693 TGATGCAGAAATTAGATGACAGCC 59.422 41.667 0.00 0.00 0.00 4.85
757 908 1.043116 TAGATGACAGCCAGGTCCCG 61.043 60.000 0.00 0.00 36.97 5.14
870 1031 5.273170 CAATTGTGTGTGTCATCTCGTTTT 58.727 37.500 0.00 0.00 0.00 2.43
887 1048 0.173029 TTTTGTGTGTGTGCAGGCAG 59.827 50.000 0.00 0.00 0.00 4.85
888 1049 2.282147 TTTGTGTGTGTGCAGGCAGC 62.282 55.000 0.00 0.00 45.96 5.25
891 1052 3.667282 GTGTGTGCAGGCAGCCAG 61.667 66.667 15.80 6.89 44.83 4.85
892 1053 4.960866 TGTGTGCAGGCAGCCAGG 62.961 66.667 15.80 6.47 44.83 4.45
903 1064 4.569180 AGCCAGGCACACGCACTT 62.569 61.111 15.80 0.00 41.24 3.16
904 1065 4.332637 GCCAGGCACACGCACTTG 62.333 66.667 6.55 0.00 41.24 3.16
914 1075 4.271687 GCACACGCACTTGTATATAAAGC 58.728 43.478 5.22 0.00 38.36 3.51
939 1100 3.055819 ACACACGTTCCATTAGAGCAGAT 60.056 43.478 0.00 0.00 0.00 2.90
964 1125 3.118629 TGCGCTTCTCCTCACAAGATAAT 60.119 43.478 9.73 0.00 0.00 1.28
969 1130 5.523188 GCTTCTCCTCACAAGATAATCACAG 59.477 44.000 0.00 0.00 0.00 3.66
975 1136 5.163612 CCTCACAAGATAATCACAGACTCGA 60.164 44.000 0.00 0.00 0.00 4.04
976 1137 6.456795 TCACAAGATAATCACAGACTCGAT 57.543 37.500 0.00 0.00 0.00 3.59
977 1138 6.499172 TCACAAGATAATCACAGACTCGATC 58.501 40.000 0.00 0.00 0.00 3.69
978 1139 5.397828 CACAAGATAATCACAGACTCGATCG 59.602 44.000 9.36 9.36 0.00 3.69
979 1140 5.297029 ACAAGATAATCACAGACTCGATCGA 59.703 40.000 18.32 18.32 0.00 3.59
980 1141 5.605564 AGATAATCACAGACTCGATCGAG 57.394 43.478 36.95 36.95 46.91 4.04
981 1142 5.301555 AGATAATCACAGACTCGATCGAGA 58.698 41.667 42.97 25.00 44.53 4.04
982 1143 3.961477 AATCACAGACTCGATCGAGAG 57.039 47.619 42.97 32.50 44.53 3.20
983 1144 1.010580 TCACAGACTCGATCGAGAGC 58.989 55.000 42.97 32.91 44.53 4.09
984 1145 1.013596 CACAGACTCGATCGAGAGCT 58.986 55.000 42.97 34.23 44.53 4.09
985 1146 1.400142 CACAGACTCGATCGAGAGCTT 59.600 52.381 42.97 25.87 44.53 3.74
986 1147 1.400142 ACAGACTCGATCGAGAGCTTG 59.600 52.381 42.97 32.72 44.53 4.01
1004 1165 1.619654 TGTCTTGGTTCTGCAATGGG 58.380 50.000 0.00 0.00 0.00 4.00
1039 1200 1.988956 CTCCTGGCTGTGCTCCTCT 60.989 63.158 0.00 0.00 0.00 3.69
1044 1205 2.350514 GCTGTGCTCCTCTTGGCT 59.649 61.111 0.00 0.00 0.00 4.75
1049 1210 3.011517 GCTCCTCTTGGCTGGGGA 61.012 66.667 0.20 0.20 0.00 4.81
1247 1408 2.483876 CGACATCACTGGTCAGTTTGT 58.516 47.619 13.17 13.17 40.20 2.83
1250 1411 4.377021 GACATCACTGGTCAGTTTGTACA 58.623 43.478 13.24 0.00 40.20 2.90
1260 1421 4.985409 GGTCAGTTTGTACACTCTCTCTTG 59.015 45.833 0.00 0.00 0.00 3.02
1264 1425 3.944055 TTGTACACTCTCTCTTGCTCC 57.056 47.619 0.00 0.00 0.00 4.70
1265 1426 3.162147 TGTACACTCTCTCTTGCTCCT 57.838 47.619 0.00 0.00 0.00 3.69
1267 1428 3.256879 TGTACACTCTCTCTTGCTCCTTG 59.743 47.826 0.00 0.00 0.00 3.61
1268 1429 2.324541 ACACTCTCTCTTGCTCCTTGT 58.675 47.619 0.00 0.00 0.00 3.16
1269 1430 2.703007 ACACTCTCTCTTGCTCCTTGTT 59.297 45.455 0.00 0.00 0.00 2.83
1270 1431 3.898123 ACACTCTCTCTTGCTCCTTGTTA 59.102 43.478 0.00 0.00 0.00 2.41
1328 1490 4.974275 GCAGTATTATGATTGCACTTGCTG 59.026 41.667 2.33 0.00 42.66 4.41
1331 1493 6.856426 CAGTATTATGATTGCACTTGCTGATG 59.144 38.462 2.33 0.00 42.66 3.07
1336 1503 4.263435 TGATTGCACTTGCTGATGTATCA 58.737 39.130 2.33 0.00 42.66 2.15
1337 1504 4.701171 TGATTGCACTTGCTGATGTATCAA 59.299 37.500 2.33 0.00 42.66 2.57
1340 1507 5.648178 TGCACTTGCTGATGTATCAATTT 57.352 34.783 2.33 0.00 42.66 1.82
1361 1528 2.052237 CGACTTGCGTGGTTGCAC 60.052 61.111 0.00 0.00 46.25 4.57
1369 1536 0.953471 GCGTGGTTGCACCTGATACA 60.953 55.000 6.83 0.00 39.58 2.29
1378 1545 1.679032 GCACCTGATACACTGGGGTTC 60.679 57.143 0.00 0.00 42.06 3.62
1381 1548 1.405526 CCTGATACACTGGGGTTCACG 60.406 57.143 0.00 0.00 34.55 4.35
1462 1629 0.538584 ACTTCGCATCTGCTGGATCA 59.461 50.000 0.09 0.00 39.32 2.92
1480 1647 2.022195 TCAGGCTACTACGATCACACC 58.978 52.381 0.00 0.00 0.00 4.16
1531 1698 1.009449 GTCTCTCGAGGAATCGGCG 60.009 63.158 13.56 0.00 0.00 6.46
1534 1701 4.207281 CTCGAGGAATCGGCGCCA 62.207 66.667 28.98 14.46 0.00 5.69
1553 1720 3.465871 CCATGAAAGGAGAAGCTCTAGC 58.534 50.000 0.00 0.00 42.49 3.42
1656 1825 6.822442 TCTGTCACCGCCTCATTATTATTTA 58.178 36.000 0.00 0.00 0.00 1.40
1657 1826 6.704493 TCTGTCACCGCCTCATTATTATTTAC 59.296 38.462 0.00 0.00 0.00 2.01
1839 2009 1.064906 CAGGCCAAGTCCATCATCAGT 60.065 52.381 5.01 0.00 0.00 3.41
1845 2015 1.576577 AGTCCATCATCAGTGGCTCA 58.423 50.000 0.00 0.00 36.66 4.26
1846 2016 2.125233 AGTCCATCATCAGTGGCTCAT 58.875 47.619 0.00 0.00 36.66 2.90
1878 2048 0.663153 GCTTCGGTGCAAGTGACTTT 59.337 50.000 0.00 0.00 0.00 2.66
1944 2114 2.572284 GACCAGTTCTCGGACCGG 59.428 66.667 15.25 0.00 0.00 5.28
2015 2185 3.694566 GCCTAAACAAACGATCCATCCTT 59.305 43.478 0.00 0.00 0.00 3.36
2018 2188 2.879103 ACAAACGATCCATCCTTGGT 57.121 45.000 0.00 0.00 44.06 3.67
2026 2196 0.252330 TCCATCCTTGGTACGGGTCA 60.252 55.000 0.00 0.00 44.06 4.02
2221 2413 2.509336 AACGGGAAGATGAGCGCG 60.509 61.111 0.00 0.00 44.59 6.86
2272 2464 0.608640 ACCTCAAGATCGCCGTCTTT 59.391 50.000 0.27 0.00 36.33 2.52
2290 2482 0.457853 TTGACATCTACACGCCGCTC 60.458 55.000 0.00 0.00 0.00 5.03
2292 2484 0.179134 GACATCTACACGCCGCTCTT 60.179 55.000 0.00 0.00 0.00 2.85
2671 2893 1.800315 CACTGGTCGGCTAACGTCG 60.800 63.158 0.00 0.00 44.69 5.12
2815 3042 0.530650 CTCACCATATCGCCAGCGTT 60.531 55.000 12.32 6.38 40.74 4.84
2842 3069 0.475632 AGGGACTGGGACACATGGAA 60.476 55.000 0.00 0.00 37.18 3.53
2902 3129 2.414691 GCAAGCACCGGATCTTTTCTTC 60.415 50.000 9.46 0.00 0.00 2.87
2942 3169 9.246670 TCATGTCCTTCAAATTTGATGATAACT 57.753 29.630 27.10 9.28 37.00 2.24
3075 3306 7.639113 TGAACGGGCAAAGAAGATATAATTT 57.361 32.000 0.00 0.00 0.00 1.82
3076 3307 7.479980 TGAACGGGCAAAGAAGATATAATTTG 58.520 34.615 0.00 0.00 36.07 2.32
3077 3308 7.122055 TGAACGGGCAAAGAAGATATAATTTGT 59.878 33.333 0.00 0.00 35.55 2.83
3078 3309 7.404671 ACGGGCAAAGAAGATATAATTTGTT 57.595 32.000 0.00 0.00 35.55 2.83
3079 3310 7.836842 ACGGGCAAAGAAGATATAATTTGTTT 58.163 30.769 0.00 0.00 35.55 2.83
3080 3311 8.311109 ACGGGCAAAGAAGATATAATTTGTTTT 58.689 29.630 0.00 0.00 35.55 2.43
3081 3312 9.150348 CGGGCAAAGAAGATATAATTTGTTTTT 57.850 29.630 0.00 0.00 35.55 1.94
3180 3860 0.998928 AGGGTGCAGAGAGAGAGAGA 59.001 55.000 0.00 0.00 0.00 3.10
3181 3861 1.064463 AGGGTGCAGAGAGAGAGAGAG 60.064 57.143 0.00 0.00 0.00 3.20
3182 3862 1.064758 GGGTGCAGAGAGAGAGAGAGA 60.065 57.143 0.00 0.00 0.00 3.10
3183 3863 2.292267 GGTGCAGAGAGAGAGAGAGAG 58.708 57.143 0.00 0.00 0.00 3.20
3184 3864 1.672881 GTGCAGAGAGAGAGAGAGAGC 59.327 57.143 0.00 0.00 0.00 4.09
3185 3865 1.561076 TGCAGAGAGAGAGAGAGAGCT 59.439 52.381 0.00 0.00 0.00 4.09
3198 3893 4.810191 GAGAGAGCTCTTTCCTGGTTTA 57.190 45.455 20.94 0.00 40.61 2.01
3203 3898 6.657117 AGAGAGCTCTTTCCTGGTTTATTTTC 59.343 38.462 19.36 0.00 36.31 2.29
3226 3921 9.547753 TTTCCATTTTTCGATTTGGTTATTTCA 57.452 25.926 0.00 0.00 0.00 2.69
3228 3923 8.580720 TCCATTTTTCGATTTGGTTATTTCAGA 58.419 29.630 0.00 0.00 0.00 3.27
3318 4024 9.947669 TTTTTCAAAATGCACAATATTTGGAAG 57.052 25.926 0.00 0.00 38.20 3.46
3386 4098 7.658575 ACACTTTAATGTACTCCATACACGTTT 59.341 33.333 0.00 0.00 46.65 3.60
3388 4100 7.874016 ACTTTAATGTACTCCATACACGTTTCA 59.126 33.333 0.00 0.00 46.65 2.69
3417 4129 5.248640 ACATGTTGGATACTGGAACTCAAG 58.751 41.667 0.00 0.00 37.61 3.02
3463 4175 3.414269 TCCGTTTTACCATTCCAGAACC 58.586 45.455 0.00 0.00 0.00 3.62
3487 4199 4.623595 GCTCGTGGAAAACAGAAACAAAAA 59.376 37.500 0.00 0.00 0.00 1.94
3608 4320 5.702209 TCCCGGACTTAATAAAAGTTCACAC 59.298 40.000 0.73 0.00 0.00 3.82
3609 4321 5.470777 CCCGGACTTAATAAAAGTTCACACA 59.529 40.000 0.73 0.00 0.00 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.954487 AAGATTCTCATGCATTGCTGATTA 57.046 33.333 10.49 3.34 0.00 1.75
4 5 6.100004 AGAAAAAGATTCTCATGCATTGCTG 58.900 36.000 10.49 6.03 0.00 4.41
5 6 6.282199 AGAAAAAGATTCTCATGCATTGCT 57.718 33.333 10.49 0.00 0.00 3.91
6 7 7.478322 TCTAGAAAAAGATTCTCATGCATTGC 58.522 34.615 0.00 0.46 0.00 3.56
10 11 8.820933 CGTATTCTAGAAAAAGATTCTCATGCA 58.179 33.333 9.71 0.00 0.00 3.96
11 12 7.796197 GCGTATTCTAGAAAAAGATTCTCATGC 59.204 37.037 9.71 0.00 0.00 4.06
12 13 8.820933 TGCGTATTCTAGAAAAAGATTCTCATG 58.179 33.333 9.71 0.00 0.00 3.07
13 14 8.821894 GTGCGTATTCTAGAAAAAGATTCTCAT 58.178 33.333 9.71 0.00 0.00 2.90
14 15 7.817478 TGTGCGTATTCTAGAAAAAGATTCTCA 59.183 33.333 9.71 0.82 0.00 3.27
15 16 8.186178 TGTGCGTATTCTAGAAAAAGATTCTC 57.814 34.615 9.71 0.00 0.00 2.87
16 17 8.547967 TTGTGCGTATTCTAGAAAAAGATTCT 57.452 30.769 9.71 0.00 0.00 2.40
17 18 7.426743 GCTTGTGCGTATTCTAGAAAAAGATTC 59.573 37.037 9.71 0.00 0.00 2.52
18 19 7.094805 TGCTTGTGCGTATTCTAGAAAAAGATT 60.095 33.333 9.71 0.00 43.34 2.40
19 20 6.371548 TGCTTGTGCGTATTCTAGAAAAAGAT 59.628 34.615 9.71 0.00 43.34 2.40
20 21 5.699001 TGCTTGTGCGTATTCTAGAAAAAGA 59.301 36.000 9.71 0.00 43.34 2.52
21 22 5.927030 TGCTTGTGCGTATTCTAGAAAAAG 58.073 37.500 9.71 4.80 43.34 2.27
22 23 5.933187 TGCTTGTGCGTATTCTAGAAAAA 57.067 34.783 9.71 0.00 43.34 1.94
23 24 7.547722 TCTTATGCTTGTGCGTATTCTAGAAAA 59.452 33.333 9.71 0.00 43.34 2.29
24 25 7.039270 TCTTATGCTTGTGCGTATTCTAGAAA 58.961 34.615 9.71 0.00 43.34 2.52
25 26 6.569780 TCTTATGCTTGTGCGTATTCTAGAA 58.430 36.000 7.82 7.82 43.34 2.10
26 27 6.144078 TCTTATGCTTGTGCGTATTCTAGA 57.856 37.500 0.00 0.00 43.34 2.43
27 28 6.828502 TTCTTATGCTTGTGCGTATTCTAG 57.171 37.500 0.00 0.00 43.34 2.43
28 29 7.210174 AGATTCTTATGCTTGTGCGTATTCTA 58.790 34.615 0.00 0.00 43.34 2.10
29 30 6.051717 AGATTCTTATGCTTGTGCGTATTCT 58.948 36.000 0.00 0.00 43.34 2.40
30 31 6.292389 AGATTCTTATGCTTGTGCGTATTC 57.708 37.500 0.00 0.00 43.34 1.75
31 32 6.683974 AAGATTCTTATGCTTGTGCGTATT 57.316 33.333 0.00 0.00 43.34 1.89
32 33 7.969536 ATAAGATTCTTATGCTTGTGCGTAT 57.030 32.000 16.38 0.00 43.34 3.06
33 34 7.114388 CGTATAAGATTCTTATGCTTGTGCGTA 59.886 37.037 23.35 2.64 43.34 4.42
34 35 6.074302 CGTATAAGATTCTTATGCTTGTGCGT 60.074 38.462 23.35 2.62 43.34 5.24
35 36 6.292129 CGTATAAGATTCTTATGCTTGTGCG 58.708 40.000 23.35 11.95 43.34 5.34
36 37 6.423905 TCCGTATAAGATTCTTATGCTTGTGC 59.576 38.462 23.35 5.24 40.20 4.57
37 38 7.653713 AGTCCGTATAAGATTCTTATGCTTGTG 59.346 37.037 23.35 12.21 0.00 3.33
38 39 7.727181 AGTCCGTATAAGATTCTTATGCTTGT 58.273 34.615 23.35 8.59 0.00 3.16
39 40 8.085296 AGAGTCCGTATAAGATTCTTATGCTTG 58.915 37.037 23.35 16.68 26.71 4.01
40 41 8.184304 AGAGTCCGTATAAGATTCTTATGCTT 57.816 34.615 23.35 11.16 26.71 3.91
41 42 7.768807 AGAGTCCGTATAAGATTCTTATGCT 57.231 36.000 23.35 14.71 26.71 3.79
42 43 8.819643 AAAGAGTCCGTATAAGATTCTTATGC 57.180 34.615 23.35 21.14 38.81 3.14
46 47 6.539103 GGCAAAAGAGTCCGTATAAGATTCTT 59.461 38.462 4.03 4.03 40.73 2.52
58 59 5.588648 TGAATTATTAGGGCAAAAGAGTCCG 59.411 40.000 0.00 0.00 38.64 4.79
100 101 9.878737 ATGGTATACAGTATACTCCTGTTTACT 57.121 33.333 24.10 0.00 42.26 2.24
176 181 3.835978 TGCCTGGTTCAAGTAAGCTACTA 59.164 43.478 0.00 0.00 38.26 1.82
177 182 2.637872 TGCCTGGTTCAAGTAAGCTACT 59.362 45.455 0.00 0.00 41.73 2.57
178 183 3.053831 TGCCTGGTTCAAGTAAGCTAC 57.946 47.619 0.00 0.00 36.51 3.58
179 184 3.326588 TCTTGCCTGGTTCAAGTAAGCTA 59.673 43.478 12.04 0.00 41.13 3.32
180 185 2.106511 TCTTGCCTGGTTCAAGTAAGCT 59.893 45.455 12.04 0.00 41.13 3.74
181 186 2.504367 TCTTGCCTGGTTCAAGTAAGC 58.496 47.619 12.04 0.00 41.13 3.09
184 189 4.431416 TCTTTCTTGCCTGGTTCAAGTA 57.569 40.909 12.04 2.67 41.13 2.24
189 194 4.918810 TTCTTTCTTTCTTGCCTGGTTC 57.081 40.909 0.00 0.00 0.00 3.62
204 209 4.152580 CAGCTCGGTAGGTTTCTTTCTTTC 59.847 45.833 0.00 0.00 0.00 2.62
205 210 4.065789 CAGCTCGGTAGGTTTCTTTCTTT 58.934 43.478 0.00 0.00 0.00 2.52
206 211 3.557264 CCAGCTCGGTAGGTTTCTTTCTT 60.557 47.826 0.00 0.00 0.00 2.52
208 213 2.347731 CCAGCTCGGTAGGTTTCTTTC 58.652 52.381 0.00 0.00 0.00 2.62
209 214 1.610886 GCCAGCTCGGTAGGTTTCTTT 60.611 52.381 4.45 0.00 36.97 2.52
210 215 0.036294 GCCAGCTCGGTAGGTTTCTT 60.036 55.000 4.45 0.00 36.97 2.52
211 216 1.192146 TGCCAGCTCGGTAGGTTTCT 61.192 55.000 4.45 0.00 36.97 2.52
212 217 1.019805 GTGCCAGCTCGGTAGGTTTC 61.020 60.000 4.45 0.00 36.97 2.78
213 218 1.003718 GTGCCAGCTCGGTAGGTTT 60.004 57.895 4.45 0.00 36.97 3.27
214 219 2.663196 GTGCCAGCTCGGTAGGTT 59.337 61.111 4.45 0.00 36.97 3.50
215 220 3.760035 CGTGCCAGCTCGGTAGGT 61.760 66.667 6.22 0.00 36.97 3.08
216 221 4.514577 CCGTGCCAGCTCGGTAGG 62.515 72.222 21.61 5.04 44.86 3.18
225 230 2.048597 TAGTGAACGCCGTGCCAG 60.049 61.111 0.00 0.00 0.00 4.85
226 231 2.048597 CTAGTGAACGCCGTGCCA 60.049 61.111 0.00 0.00 0.00 4.92
227 232 2.048503 ACTAGTGAACGCCGTGCC 60.049 61.111 0.00 0.00 0.00 5.01
228 233 1.615107 GACACTAGTGAACGCCGTGC 61.615 60.000 29.30 0.00 0.00 5.34
229 234 1.334992 CGACACTAGTGAACGCCGTG 61.335 60.000 29.30 0.31 0.00 4.94
230 235 1.081641 CGACACTAGTGAACGCCGT 60.082 57.895 29.30 4.62 0.00 5.68
232 237 0.240411 ACTCGACACTAGTGAACGCC 59.760 55.000 29.30 10.94 35.46 5.68
233 238 1.328439 CACTCGACACTAGTGAACGC 58.672 55.000 29.30 13.44 45.89 4.84
235 240 1.000607 TGCCACTCGACACTAGTGAAC 60.001 52.381 29.30 19.40 45.89 3.18
236 241 1.324383 TGCCACTCGACACTAGTGAA 58.676 50.000 29.30 12.65 45.89 3.18
237 242 1.545841 ATGCCACTCGACACTAGTGA 58.454 50.000 29.30 6.22 45.89 3.41
239 244 1.893137 TCAATGCCACTCGACACTAGT 59.107 47.619 0.00 0.00 0.00 2.57
240 245 2.654749 TCAATGCCACTCGACACTAG 57.345 50.000 0.00 0.00 0.00 2.57
241 246 2.418609 CCATCAATGCCACTCGACACTA 60.419 50.000 0.00 0.00 0.00 2.74
244 249 0.612744 TCCATCAATGCCACTCGACA 59.387 50.000 0.00 0.00 0.00 4.35
245 250 1.667724 CTTCCATCAATGCCACTCGAC 59.332 52.381 0.00 0.00 0.00 4.20
247 252 1.667724 GACTTCCATCAATGCCACTCG 59.332 52.381 0.00 0.00 0.00 4.18
248 253 2.715046 TGACTTCCATCAATGCCACTC 58.285 47.619 0.00 0.00 0.00 3.51
249 254 2.885135 TGACTTCCATCAATGCCACT 57.115 45.000 0.00 0.00 0.00 4.00
268 314 4.101119 CCATCTCGGTAGGTTTGTAAGGAT 59.899 45.833 0.00 0.00 0.00 3.24
273 319 2.093869 GTGCCATCTCGGTAGGTTTGTA 60.094 50.000 0.00 0.00 36.97 2.41
274 320 0.981183 TGCCATCTCGGTAGGTTTGT 59.019 50.000 0.00 0.00 36.97 2.83
275 321 1.338674 TGTGCCATCTCGGTAGGTTTG 60.339 52.381 0.00 0.00 36.97 2.93
276 322 0.981183 TGTGCCATCTCGGTAGGTTT 59.019 50.000 0.00 0.00 36.97 3.27
278 324 1.134401 CAATGTGCCATCTCGGTAGGT 60.134 52.381 0.00 0.00 36.97 3.08
279 325 1.134401 ACAATGTGCCATCTCGGTAGG 60.134 52.381 0.00 0.00 36.97 3.18
280 326 2.315925 ACAATGTGCCATCTCGGTAG 57.684 50.000 0.00 0.00 36.97 3.18
281 327 2.764010 AGTACAATGTGCCATCTCGGTA 59.236 45.455 0.00 0.00 36.97 4.02
282 328 1.555075 AGTACAATGTGCCATCTCGGT 59.445 47.619 0.00 0.00 36.97 4.69
284 330 3.261580 TCAAGTACAATGTGCCATCTCG 58.738 45.455 0.00 0.00 0.00 4.04
285 331 5.412594 TCTTTCAAGTACAATGTGCCATCTC 59.587 40.000 0.00 0.00 0.00 2.75
286 332 5.316167 TCTTTCAAGTACAATGTGCCATCT 58.684 37.500 0.00 0.00 0.00 2.90
287 333 5.627499 TCTTTCAAGTACAATGTGCCATC 57.373 39.130 0.00 0.00 0.00 3.51
289 335 6.215121 CAAATCTTTCAAGTACAATGTGCCA 58.785 36.000 0.00 0.00 0.00 4.92
290 336 5.119125 GCAAATCTTTCAAGTACAATGTGCC 59.881 40.000 0.00 0.00 0.00 5.01
311 360 2.212652 GATATGATCTGTGCGGTGCAA 58.787 47.619 0.00 0.00 41.47 4.08
325 374 6.296087 GGTGCAATAGATTCTGGAGGATATGA 60.296 42.308 0.00 0.00 0.00 2.15
328 377 4.287067 GGGTGCAATAGATTCTGGAGGATA 59.713 45.833 0.00 0.00 0.00 2.59
330 379 2.439507 GGGTGCAATAGATTCTGGAGGA 59.560 50.000 0.00 0.00 0.00 3.71
344 393 1.640593 TTCACAGGACCTGGGTGCAA 61.641 55.000 23.30 7.95 38.98 4.08
345 394 2.075566 TTCACAGGACCTGGGTGCA 61.076 57.895 23.30 6.30 38.98 4.57
346 395 1.600916 GTTCACAGGACCTGGGTGC 60.601 63.158 23.30 13.24 36.13 5.01
347 396 1.301716 CGTTCACAGGACCTGGGTG 60.302 63.158 23.30 14.12 36.13 4.61
348 397 0.836400 ATCGTTCACAGGACCTGGGT 60.836 55.000 23.30 0.22 36.13 4.51
349 398 0.108138 GATCGTTCACAGGACCTGGG 60.108 60.000 25.34 22.17 36.00 4.45
350 399 0.108138 GGATCGTTCACAGGACCTGG 60.108 60.000 25.34 14.09 35.51 4.45
351 400 0.898320 AGGATCGTTCACAGGACCTG 59.102 55.000 20.45 20.45 37.52 4.00
352 401 1.550976 GAAGGATCGTTCACAGGACCT 59.449 52.381 20.46 0.00 0.00 3.85
353 402 1.405661 GGAAGGATCGTTCACAGGACC 60.406 57.143 25.03 7.15 0.00 4.46
354 403 1.275291 TGGAAGGATCGTTCACAGGAC 59.725 52.381 25.03 10.55 0.00 3.85
355 404 1.550524 CTGGAAGGATCGTTCACAGGA 59.449 52.381 25.03 6.66 0.00 3.86
358 407 3.138304 CAAACTGGAAGGATCGTTCACA 58.862 45.455 25.03 19.20 39.30 3.58
359 408 2.484264 CCAAACTGGAAGGATCGTTCAC 59.516 50.000 25.03 16.37 40.96 3.18
401 485 4.153296 CCAGTTAATGCACATGTTGTACGA 59.847 41.667 0.00 0.00 0.00 3.43
402 486 4.083537 ACCAGTTAATGCACATGTTGTACG 60.084 41.667 0.00 0.00 0.00 3.67
417 504 4.320870 GCAACCACTAGCTAACCAGTTAA 58.679 43.478 0.00 0.00 0.00 2.01
425 512 0.682852 ACCACGCAACCACTAGCTAA 59.317 50.000 0.00 0.00 0.00 3.09
455 542 4.079901 AGGAACATGAGATGAATGAAGGCT 60.080 41.667 0.00 0.00 0.00 4.58
466 553 2.575279 AGAAGTGGCAGGAACATGAGAT 59.425 45.455 0.00 0.00 0.00 2.75
483 570 5.375417 TCACAACACATTGGCAATAGAAG 57.625 39.130 13.23 2.96 40.42 2.85
498 585 1.001860 TGAGGCACATCGATCACAACA 59.998 47.619 0.00 0.00 0.00 3.33
509 596 0.616891 TGCTGACTGATGAGGCACAT 59.383 50.000 0.00 0.00 42.47 3.21
510 597 2.060370 TGCTGACTGATGAGGCACA 58.940 52.632 0.00 0.00 31.99 4.57
511 598 2.464682 GTGCTGACTGATGAGGCAC 58.535 57.895 0.00 0.00 44.53 5.01
512 599 1.297689 GGTGCTGACTGATGAGGCA 59.702 57.895 0.00 0.00 35.22 4.75
513 600 1.451028 GGGTGCTGACTGATGAGGC 60.451 63.158 0.00 0.00 0.00 4.70
514 601 0.392193 GTGGGTGCTGACTGATGAGG 60.392 60.000 0.00 0.00 0.00 3.86
516 603 0.322648 CTGTGGGTGCTGACTGATGA 59.677 55.000 0.00 0.00 0.00 2.92
517 604 1.303799 GCTGTGGGTGCTGACTGATG 61.304 60.000 0.00 0.00 0.00 3.07
518 605 1.002868 GCTGTGGGTGCTGACTGAT 60.003 57.895 0.00 0.00 0.00 2.90
519 606 1.771783 ATGCTGTGGGTGCTGACTGA 61.772 55.000 0.00 0.00 0.00 3.41
520 607 1.303074 ATGCTGTGGGTGCTGACTG 60.303 57.895 0.00 0.00 0.00 3.51
521 608 1.002868 GATGCTGTGGGTGCTGACT 60.003 57.895 0.00 0.00 0.00 3.41
522 609 2.042831 GGATGCTGTGGGTGCTGAC 61.043 63.158 0.00 0.00 0.00 3.51
523 610 2.352422 GGATGCTGTGGGTGCTGA 59.648 61.111 0.00 0.00 0.00 4.26
524 611 2.753043 GGGATGCTGTGGGTGCTG 60.753 66.667 0.00 0.00 0.00 4.41
525 612 4.052518 GGGGATGCTGTGGGTGCT 62.053 66.667 0.00 0.00 0.00 4.40
528 615 3.017581 GAGGGGGATGCTGTGGGT 61.018 66.667 0.00 0.00 0.00 4.51
530 617 1.379044 GTTGAGGGGGATGCTGTGG 60.379 63.158 0.00 0.00 0.00 4.17
532 619 1.852157 TGGTTGAGGGGGATGCTGT 60.852 57.895 0.00 0.00 0.00 4.40
533 620 1.379044 GTGGTTGAGGGGGATGCTG 60.379 63.158 0.00 0.00 0.00 4.41
534 621 2.616458 GGTGGTTGAGGGGGATGCT 61.616 63.158 0.00 0.00 0.00 3.79
535 622 2.043953 GGTGGTTGAGGGGGATGC 60.044 66.667 0.00 0.00 0.00 3.91
536 623 2.272146 CGGTGGTTGAGGGGGATG 59.728 66.667 0.00 0.00 0.00 3.51
537 624 3.728373 GCGGTGGTTGAGGGGGAT 61.728 66.667 0.00 0.00 0.00 3.85
541 628 4.722700 CAGGGCGGTGGTTGAGGG 62.723 72.222 0.00 0.00 0.00 4.30
570 657 4.920376 GCAATGGCGACTATTTATTGTGT 58.080 39.130 0.00 0.00 32.75 3.72
682 806 3.795101 ACAACACGCTGAATATAGTACGC 59.205 43.478 0.00 0.00 0.00 4.42
705 830 4.862574 TCATGTTTATTCGTTCTCCGTCAG 59.137 41.667 0.00 0.00 37.94 3.51
709 834 4.033932 TGCATCATGTTTATTCGTTCTCCG 59.966 41.667 0.00 0.00 38.13 4.63
714 839 9.507280 CTAATTTCTGCATCATGTTTATTCGTT 57.493 29.630 0.00 0.00 0.00 3.85
721 846 8.058667 TGTCATCTAATTTCTGCATCATGTTT 57.941 30.769 0.00 0.00 0.00 2.83
725 851 5.241064 GGCTGTCATCTAATTTCTGCATCAT 59.759 40.000 0.00 0.00 0.00 2.45
726 852 4.577693 GGCTGTCATCTAATTTCTGCATCA 59.422 41.667 0.00 0.00 0.00 3.07
728 854 4.529897 TGGCTGTCATCTAATTTCTGCAT 58.470 39.130 0.00 0.00 0.00 3.96
733 859 3.879892 GGACCTGGCTGTCATCTAATTTC 59.120 47.826 9.39 0.00 36.97 2.17
735 861 2.173569 GGGACCTGGCTGTCATCTAATT 59.826 50.000 9.39 0.00 36.97 1.40
737 863 1.204146 GGGACCTGGCTGTCATCTAA 58.796 55.000 9.39 0.00 36.97 2.10
739 888 2.362369 CGGGACCTGGCTGTCATCT 61.362 63.158 9.39 0.00 36.97 2.90
767 927 0.111253 AAAGACCAGGAAGCACCCAG 59.889 55.000 0.00 0.00 40.05 4.45
870 1031 2.773745 GCTGCCTGCACACACACAA 61.774 57.895 0.00 0.00 42.31 3.33
887 1048 4.332637 CAAGTGCGTGTGCCTGGC 62.333 66.667 12.87 12.87 41.78 4.85
888 1049 0.955428 ATACAAGTGCGTGTGCCTGG 60.955 55.000 1.22 0.00 41.78 4.45
891 1052 4.785341 GCTTTATATACAAGTGCGTGTGCC 60.785 45.833 1.22 0.00 41.78 5.01
892 1053 4.034048 AGCTTTATATACAAGTGCGTGTGC 59.966 41.667 1.22 0.00 43.20 4.57
893 1054 5.290885 TGAGCTTTATATACAAGTGCGTGTG 59.709 40.000 1.22 0.00 32.75 3.82
894 1055 5.291128 GTGAGCTTTATATACAAGTGCGTGT 59.709 40.000 0.00 0.00 35.43 4.49
895 1056 5.290885 TGTGAGCTTTATATACAAGTGCGTG 59.709 40.000 0.00 0.00 0.00 5.34
896 1057 5.291128 GTGTGAGCTTTATATACAAGTGCGT 59.709 40.000 0.00 0.00 0.00 5.24
897 1058 5.290885 TGTGTGAGCTTTATATACAAGTGCG 59.709 40.000 0.00 0.00 0.00 5.34
898 1059 6.478588 GTGTGTGAGCTTTATATACAAGTGC 58.521 40.000 0.00 0.00 0.00 4.40
899 1060 6.310467 ACGTGTGTGAGCTTTATATACAAGTG 59.690 38.462 0.00 0.00 30.43 3.16
900 1061 6.395629 ACGTGTGTGAGCTTTATATACAAGT 58.604 36.000 0.00 0.00 0.00 3.16
901 1062 6.887376 ACGTGTGTGAGCTTTATATACAAG 57.113 37.500 0.00 0.00 0.00 3.16
902 1063 6.311935 GGAACGTGTGTGAGCTTTATATACAA 59.688 38.462 0.00 0.00 0.00 2.41
903 1064 5.808540 GGAACGTGTGTGAGCTTTATATACA 59.191 40.000 0.00 0.00 0.00 2.29
904 1065 5.808540 TGGAACGTGTGTGAGCTTTATATAC 59.191 40.000 0.00 0.00 0.00 1.47
914 1075 2.668457 GCTCTAATGGAACGTGTGTGAG 59.332 50.000 0.00 0.00 0.00 3.51
939 1100 2.082629 TTGTGAGGAGAAGCGCACGA 62.083 55.000 11.47 0.00 34.12 4.35
945 1106 5.423015 TGTGATTATCTTGTGAGGAGAAGC 58.577 41.667 0.00 0.00 0.00 3.86
946 1107 6.756074 GTCTGTGATTATCTTGTGAGGAGAAG 59.244 42.308 0.00 0.00 0.00 2.85
964 1125 1.010580 GCTCTCGATCGAGTCTGTGA 58.989 55.000 36.68 20.50 42.49 3.58
969 1130 1.668751 AGACAAGCTCTCGATCGAGTC 59.331 52.381 36.68 29.16 42.49 3.36
975 1136 2.564947 AGAACCAAGACAAGCTCTCGAT 59.435 45.455 0.00 0.00 0.00 3.59
976 1137 1.964223 AGAACCAAGACAAGCTCTCGA 59.036 47.619 0.00 0.00 0.00 4.04
977 1138 2.064762 CAGAACCAAGACAAGCTCTCG 58.935 52.381 0.00 0.00 0.00 4.04
978 1139 1.803555 GCAGAACCAAGACAAGCTCTC 59.196 52.381 0.00 0.00 0.00 3.20
979 1140 1.141657 TGCAGAACCAAGACAAGCTCT 59.858 47.619 0.00 0.00 0.00 4.09
980 1141 1.597742 TGCAGAACCAAGACAAGCTC 58.402 50.000 0.00 0.00 0.00 4.09
981 1142 2.057137 TTGCAGAACCAAGACAAGCT 57.943 45.000 0.00 0.00 0.00 3.74
982 1143 2.608752 CCATTGCAGAACCAAGACAAGC 60.609 50.000 0.00 0.00 0.00 4.01
983 1144 2.029649 CCCATTGCAGAACCAAGACAAG 60.030 50.000 0.00 0.00 0.00 3.16
984 1145 1.962807 CCCATTGCAGAACCAAGACAA 59.037 47.619 0.00 0.00 0.00 3.18
985 1146 1.619654 CCCATTGCAGAACCAAGACA 58.380 50.000 0.00 0.00 0.00 3.41
986 1147 0.890683 CCCCATTGCAGAACCAAGAC 59.109 55.000 0.00 0.00 0.00 3.01
1039 1200 2.279743 GCCATGATCCCCAGCCAA 59.720 61.111 0.00 0.00 0.00 4.52
1044 1205 4.833495 TCCCCGCCATGATCCCCA 62.833 66.667 0.00 0.00 0.00 4.96
1080 1241 2.431942 CCGAACGTGAAGACCCCG 60.432 66.667 0.00 0.00 0.00 5.73
1247 1408 3.501349 ACAAGGAGCAAGAGAGAGTGTA 58.499 45.455 0.00 0.00 0.00 2.90
1250 1411 5.753721 ATTAACAAGGAGCAAGAGAGAGT 57.246 39.130 0.00 0.00 0.00 3.24
1260 1421 7.377766 TGAAGAACACATATTAACAAGGAGC 57.622 36.000 0.00 0.00 0.00 4.70
1264 1425 8.671921 AGATGCTGAAGAACACATATTAACAAG 58.328 33.333 0.00 0.00 0.00 3.16
1265 1426 8.565896 AGATGCTGAAGAACACATATTAACAA 57.434 30.769 0.00 0.00 0.00 2.83
1267 1428 8.269424 CGTAGATGCTGAAGAACACATATTAAC 58.731 37.037 0.00 0.00 0.00 2.01
1268 1429 7.979537 ACGTAGATGCTGAAGAACACATATTAA 59.020 33.333 0.00 0.00 0.00 1.40
1269 1430 7.489160 ACGTAGATGCTGAAGAACACATATTA 58.511 34.615 0.00 0.00 0.00 0.98
1270 1431 6.341316 ACGTAGATGCTGAAGAACACATATT 58.659 36.000 0.00 0.00 0.00 1.28
1328 1490 7.350779 CGCAAGTCGTAAAAATTGATACATC 57.649 36.000 0.00 0.00 0.00 3.06
1361 1528 1.405526 CGTGAACCCCAGTGTATCAGG 60.406 57.143 0.00 0.00 0.00 3.86
1369 1536 1.542187 GGTAGCTCGTGAACCCCAGT 61.542 60.000 0.00 0.00 0.00 4.00
1450 1617 2.100128 AGTAGCCTGATCCAGCAGAT 57.900 50.000 6.81 0.00 38.14 2.90
1462 1629 1.022735 CGGTGTGATCGTAGTAGCCT 58.977 55.000 0.00 0.00 0.00 4.58
1480 1647 7.427318 TCGATAATACTTACATACATAAGCGCG 59.573 37.037 0.00 0.00 35.86 6.86
1531 1698 2.416680 AGAGCTTCTCCTTTCATGGC 57.583 50.000 0.00 0.00 0.00 4.40
1553 1720 1.671328 CATGCAGGCAGAACATCTCAG 59.329 52.381 0.00 0.00 0.00 3.35
1656 1825 1.424638 AAGTGCTACTGGTGTCAGGT 58.575 50.000 0.00 0.00 44.99 4.00
1657 1826 2.146342 CAAAGTGCTACTGGTGTCAGG 58.854 52.381 0.00 0.00 44.99 3.86
1788 1958 1.741770 GAACGCCGTCAGCTTGGAT 60.742 57.895 0.00 0.00 40.39 3.41
1839 2009 2.892374 CTGACGATGTACAATGAGCCA 58.108 47.619 0.00 0.00 0.00 4.75
1845 2015 2.094182 ACCGAAGCTGACGATGTACAAT 60.094 45.455 13.82 0.00 0.00 2.71
1846 2016 1.271379 ACCGAAGCTGACGATGTACAA 59.729 47.619 13.82 0.00 0.00 2.41
1878 2048 4.562757 GGGTTGATGTAGTAGTTCTGCACA 60.563 45.833 0.00 0.00 41.20 4.57
1944 2114 0.456824 TGACGAAGATGCTGACGAGC 60.457 55.000 0.00 0.00 46.44 5.03
1985 2155 1.598407 TTTGTTTAGGCTGGCGCGA 60.598 52.632 12.10 0.00 36.88 5.87
2015 2185 0.470456 ACCTCACTTGACCCGTACCA 60.470 55.000 0.00 0.00 0.00 3.25
2018 2188 1.933021 ATCACCTCACTTGACCCGTA 58.067 50.000 0.00 0.00 0.00 4.02
2026 2196 8.571336 CAGTTTCAGAAATTAATCACCTCACTT 58.429 33.333 0.00 0.00 0.00 3.16
2167 2359 1.954146 GTTGAGCCTCGACACGCAA 60.954 57.895 7.24 0.00 31.07 4.85
2237 2429 2.562912 GTCGTGGTACCGCTTCGA 59.437 61.111 22.65 17.83 0.00 3.71
2272 2464 1.138883 GAGCGGCGTGTAGATGTCA 59.861 57.895 9.37 0.00 0.00 3.58
2290 2482 0.172352 GAGAGGTGACGAGGCTGAAG 59.828 60.000 0.00 0.00 0.00 3.02
2292 2484 1.679305 GGAGAGGTGACGAGGCTGA 60.679 63.158 0.00 0.00 0.00 4.26
2484 2703 0.544697 ACACCGTGAACTCCACCTTT 59.455 50.000 5.28 0.00 42.76 3.11
2545 2764 1.342174 GTCCCAGAACACGTAGGTTGA 59.658 52.381 0.00 0.00 0.00 3.18
2547 2766 0.316204 CGTCCCAGAACACGTAGGTT 59.684 55.000 0.00 0.00 0.00 3.50
2622 2841 1.604147 ATGTGACGAGGTCGATGCCA 61.604 55.000 6.35 0.00 43.02 4.92
2661 2880 2.575262 CGACCGACGACGTTAGCC 60.575 66.667 0.13 0.00 45.77 3.93
2760 2987 2.529643 TAACCCCTCCCGCCACAA 60.530 61.111 0.00 0.00 0.00 3.33
2801 3028 1.070577 GCTACAAACGCTGGCGATATG 60.071 52.381 21.77 16.96 42.83 1.78
2815 3042 1.078159 TGTCCCAGTCCCTAGCTACAA 59.922 52.381 0.00 0.00 0.00 2.41
2842 3069 6.369615 AGCTTTTCGTACGTATAAACCATGTT 59.630 34.615 16.05 0.00 0.00 2.71
3091 3322 9.262358 GGTCCTACAAATTATATCTTCTGTGTC 57.738 37.037 0.00 0.00 0.00 3.67
3092 3323 8.211629 GGGTCCTACAAATTATATCTTCTGTGT 58.788 37.037 0.00 0.00 0.00 3.72
3093 3324 7.661847 GGGGTCCTACAAATTATATCTTCTGTG 59.338 40.741 0.00 0.00 0.00 3.66
3094 3325 7.202195 GGGGGTCCTACAAATTATATCTTCTGT 60.202 40.741 0.00 0.00 0.00 3.41
3095 3326 7.168905 GGGGGTCCTACAAATTATATCTTCTG 58.831 42.308 0.00 0.00 0.00 3.02
3096 3327 7.331089 GGGGGTCCTACAAATTATATCTTCT 57.669 40.000 0.00 0.00 0.00 2.85
3180 3860 5.712446 GGAAAATAAACCAGGAAAGAGCTCT 59.288 40.000 11.45 11.45 0.00 4.09
3181 3861 5.476945 TGGAAAATAAACCAGGAAAGAGCTC 59.523 40.000 5.27 5.27 0.00 4.09
3182 3862 5.393866 TGGAAAATAAACCAGGAAAGAGCT 58.606 37.500 0.00 0.00 0.00 4.09
3183 3863 5.722021 TGGAAAATAAACCAGGAAAGAGC 57.278 39.130 0.00 0.00 0.00 4.09
3184 3864 9.559732 AAAAATGGAAAATAAACCAGGAAAGAG 57.440 29.630 0.00 0.00 39.62 2.85
3185 3865 9.554395 GAAAAATGGAAAATAAACCAGGAAAGA 57.446 29.630 0.00 0.00 39.62 2.52
3188 3868 7.727181 TCGAAAAATGGAAAATAAACCAGGAA 58.273 30.769 0.00 0.00 39.62 3.36
3189 3869 7.291411 TCGAAAAATGGAAAATAAACCAGGA 57.709 32.000 0.00 0.00 39.62 3.86
3190 3870 8.546597 AATCGAAAAATGGAAAATAAACCAGG 57.453 30.769 0.00 0.00 39.62 4.45
3191 3871 9.810231 CAAATCGAAAAATGGAAAATAAACCAG 57.190 29.630 0.00 0.00 39.62 4.00
3193 3873 8.779303 ACCAAATCGAAAAATGGAAAATAAACC 58.221 29.630 13.87 0.00 36.75 3.27
3203 3898 8.755696 TCTGAAATAACCAAATCGAAAAATGG 57.244 30.769 7.38 7.38 38.91 3.16
3386 4098 7.194112 TCCAGTATCCAACATGTTTCTATGA 57.806 36.000 8.77 1.41 0.00 2.15
3388 4100 7.633789 AGTTCCAGTATCCAACATGTTTCTAT 58.366 34.615 8.77 5.41 0.00 1.98
3417 4129 6.166279 TGTGAATCAAGTAATCTCTGTGGAC 58.834 40.000 0.00 0.00 0.00 4.02
3463 4175 1.329292 TGTTTCTGTTTTCCACGAGCG 59.671 47.619 0.00 0.00 0.00 5.03
3561 4273 7.277917 GGAACATTTTTCCAATTTTACGAACG 58.722 34.615 0.00 0.00 38.45 3.95
3566 4278 6.146510 GTCCGGGAACATTTTTCCAATTTTAC 59.853 38.462 0.00 0.00 40.32 2.01
3581 4293 6.205270 GTGAACTTTTATTAAGTCCGGGAACA 59.795 38.462 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.