Multiple sequence alignment - TraesCS5D01G408500

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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 TraesCS5D01G408500 chr5D 100.000 4581 0 0 1 4581 473004580 473000000 0.000000e+00 8460
1 TraesCS5D01G408500 chr5D 81.740 701 95 12 2400 3085 551984531 551985213 5.180000e-154 555
2 TraesCS5D01G408500 chr5D 76.676 343 56 15 1853 2181 551983997 551984329 7.880000e-38 169
3 TraesCS5D01G408500 chr5B 91.821 2910 123 55 1021 3849 580366843 580363968 0.000000e+00 3949
4 TraesCS5D01G408500 chr5B 90.087 343 23 6 3903 4242 580363965 580363631 7.040000e-118 435
5 TraesCS5D01G408500 chr5B 85.424 295 27 9 619 902 580367389 580367100 4.480000e-75 292
6 TraesCS5D01G408500 chr5B 87.283 173 4 2 1 155 580367564 580367392 1.010000e-41 182
7 TraesCS5D01G408500 chr5A 87.550 2265 122 79 143 2324 592639873 592637686 0.000000e+00 2473
8 TraesCS5D01G408500 chr5A 88.752 1298 90 28 3272 4538 592636635 592635363 0.000000e+00 1537
9 TraesCS5D01G408500 chr5A 91.579 950 49 12 2332 3261 592637637 592636699 0.000000e+00 1282
10 TraesCS5D01G408500 chr1A 83.580 676 87 10 2424 3085 564320589 564319924 3.030000e-171 612
11 TraesCS5D01G408500 chrUn 83.707 669 86 10 2431 3085 376497649 376496990 1.090000e-170 610
12 TraesCS5D01G408500 chrUn 83.707 669 86 10 2431 3085 376510424 376509765 1.090000e-170 610
13 TraesCS5D01G408500 chrUn 83.707 669 86 10 2431 3085 456468597 456467938 1.090000e-170 610
14 TraesCS5D01G408500 chrUn 78.586 495 70 23 1823 2298 63569573 63569096 1.250000e-75 294
15 TraesCS5D01G408500 chr7A 82.249 676 94 11 2424 3085 367840865 367841528 1.110000e-155 560
16 TraesCS5D01G408500 chr4A 80.924 498 80 7 2599 3085 616429362 616428869 3.340000e-101 379
17 TraesCS5D01G408500 chr4A 85.246 183 18 5 2400 2582 616444577 616444404 3.640000e-41 180
18 TraesCS5D01G408500 chr4A 82.456 171 26 3 1194 1362 40860255 40860423 3.690000e-31 147
19 TraesCS5D01G408500 chr4B 83.626 171 24 3 1194 1362 519824585 519824417 1.710000e-34 158
20 TraesCS5D01G408500 chr4D 84.615 143 22 0 1194 1336 423429821 423429679 4.780000e-30 143


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 TraesCS5D01G408500 chr5D 473000000 473004580 4580 True 8460.0 8460 100.000000 1 4581 1 chr5D.!!$R1 4580
1 TraesCS5D01G408500 chr5D 551983997 551985213 1216 False 362.0 555 79.208000 1853 3085 2 chr5D.!!$F1 1232
2 TraesCS5D01G408500 chr5B 580363631 580367564 3933 True 1214.5 3949 88.653750 1 4242 4 chr5B.!!$R1 4241
3 TraesCS5D01G408500 chr5A 592635363 592639873 4510 True 1764.0 2473 89.293667 143 4538 3 chr5A.!!$R1 4395
4 TraesCS5D01G408500 chr1A 564319924 564320589 665 True 612.0 612 83.580000 2424 3085 1 chr1A.!!$R1 661
5 TraesCS5D01G408500 chrUn 376496990 376497649 659 True 610.0 610 83.707000 2431 3085 1 chrUn.!!$R2 654
6 TraesCS5D01G408500 chrUn 376509765 376510424 659 True 610.0 610 83.707000 2431 3085 1 chrUn.!!$R3 654
7 TraesCS5D01G408500 chrUn 456467938 456468597 659 True 610.0 610 83.707000 2431 3085 1 chrUn.!!$R4 654
8 TraesCS5D01G408500 chr7A 367840865 367841528 663 False 560.0 560 82.249000 2424 3085 1 chr7A.!!$F1 661

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
278 307 0.037605 CACACTACCCGGGTTCTCAC 60.038 60.000 35.42 0.00 0.00 3.51 F
861 923 0.116940 TAACCACCGTAGACCCCCTT 59.883 55.000 0.00 0.00 0.00 3.95 F
1850 2110 0.188587 AGAGCCCGGTGATGAGGATA 59.811 55.000 0.00 0.00 0.00 2.59 F
2341 2691 1.073763 CACAGTCAACCCTGGATTCCA 59.926 52.381 5.05 5.05 36.75 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1858 2118 2.031683 GCACGAAATTAATCAGACGGGG 59.968 50.0 0.0 0.0 0.0 5.73 R
1895 2158 2.374830 ATCAGCGATCCTTGCCTCCG 62.375 60.0 0.0 0.0 0.0 4.63 R
3338 3785 0.618458 GATCTGCAACCCTACCACCA 59.382 55.0 0.0 0.0 0.0 4.17 R
4274 4732 0.033228 TGGCCATTTTGCAACGAAGG 59.967 50.0 0.0 0.0 0.0 3.46 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
27 28 4.302455 CACTTATCGAAGGCCACTATCAG 58.698 47.826 5.01 0.06 36.95 2.90
87 105 5.625921 TGGTTTGTTTATTAGCCGTAACC 57.374 39.130 0.00 0.00 35.51 2.85
164 183 2.803479 GGGTGTACCTCTACGCGG 59.197 66.667 12.47 0.00 34.62 6.46
167 186 1.436336 GTGTACCTCTACGCGGCAT 59.564 57.895 12.47 0.00 0.00 4.40
193 213 3.570926 TTCCAAGTAGAGTAGTGTGCG 57.429 47.619 0.00 0.00 0.00 5.34
198 218 4.482386 CAAGTAGAGTAGTGTGCGCTTTA 58.518 43.478 9.73 0.00 0.00 1.85
201 221 4.940046 AGTAGAGTAGTGTGCGCTTTACTA 59.060 41.667 9.73 11.62 31.27 1.82
206 226 3.662247 AGTGTGCGCTTTACTAGTTCT 57.338 42.857 9.73 0.00 0.00 3.01
240 269 3.686016 ACAAAGTTATGATTCCCGTGCT 58.314 40.909 0.00 0.00 0.00 4.40
241 270 4.079253 ACAAAGTTATGATTCCCGTGCTT 58.921 39.130 0.00 0.00 0.00 3.91
242 271 4.156008 ACAAAGTTATGATTCCCGTGCTTC 59.844 41.667 0.00 0.00 0.00 3.86
243 272 2.919228 AGTTATGATTCCCGTGCTTCC 58.081 47.619 0.00 0.00 0.00 3.46
244 273 1.597663 GTTATGATTCCCGTGCTTCCG 59.402 52.381 0.00 0.00 0.00 4.30
245 274 0.828022 TATGATTCCCGTGCTTCCGT 59.172 50.000 0.00 0.00 0.00 4.69
246 275 0.744414 ATGATTCCCGTGCTTCCGTG 60.744 55.000 0.00 0.00 0.00 4.94
247 276 2.746277 ATTCCCGTGCTTCCGTGC 60.746 61.111 0.00 0.00 0.00 5.34
266 295 3.793144 GCGCCTGCTGCACACTAC 61.793 66.667 0.00 0.00 41.33 2.73
270 299 2.434884 CTGCTGCACACTACCCGG 60.435 66.667 0.00 0.00 0.00 5.73
271 300 3.958147 CTGCTGCACACTACCCGGG 62.958 68.421 22.25 22.25 0.00 5.73
272 301 4.016706 GCTGCACACTACCCGGGT 62.017 66.667 32.66 32.66 0.00 5.28
273 302 2.747686 CTGCACACTACCCGGGTT 59.252 61.111 35.42 12.96 0.00 4.11
274 303 1.375523 CTGCACACTACCCGGGTTC 60.376 63.158 35.42 14.39 0.00 3.62
275 304 1.827399 CTGCACACTACCCGGGTTCT 61.827 60.000 35.42 14.90 0.00 3.01
276 305 1.079336 GCACACTACCCGGGTTCTC 60.079 63.158 35.42 11.71 0.00 2.87
277 306 1.823169 GCACACTACCCGGGTTCTCA 61.823 60.000 35.42 13.48 0.00 3.27
278 307 0.037605 CACACTACCCGGGTTCTCAC 60.038 60.000 35.42 0.00 0.00 3.51
279 308 0.178941 ACACTACCCGGGTTCTCACT 60.179 55.000 35.42 7.20 0.00 3.41
280 309 0.531200 CACTACCCGGGTTCTCACTC 59.469 60.000 35.42 0.00 0.00 3.51
282 311 2.280823 CTACCCGGGTTCTCACTCGC 62.281 65.000 35.42 0.00 46.45 5.03
283 312 4.452733 CCCGGGTTCTCACTCGCC 62.453 72.222 14.18 0.00 46.45 5.54
284 313 4.796231 CCGGGTTCTCACTCGCCG 62.796 72.222 0.00 0.00 46.45 6.46
286 315 4.070552 GGGTTCTCACTCGCCGCT 62.071 66.667 0.00 0.00 0.00 5.52
287 316 2.507324 GGTTCTCACTCGCCGCTC 60.507 66.667 0.00 0.00 0.00 5.03
288 317 2.876645 GTTCTCACTCGCCGCTCG 60.877 66.667 0.00 0.00 40.15 5.03
289 318 3.362797 TTCTCACTCGCCGCTCGT 61.363 61.111 0.00 0.00 39.67 4.18
290 319 2.916052 TTCTCACTCGCCGCTCGTT 61.916 57.895 0.00 0.00 39.67 3.85
343 376 5.819379 TCATCATCTCTTTACGTACGTAGGT 59.181 40.000 25.56 22.91 31.71 3.08
344 377 6.317140 TCATCATCTCTTTACGTACGTAGGTT 59.683 38.462 25.56 10.17 31.71 3.50
349 382 1.981254 TTACGTACGTAGGTTGCTGC 58.019 50.000 25.56 0.00 31.71 5.25
372 405 1.222936 CCGCTCCCTCTTCAATGCT 59.777 57.895 0.00 0.00 0.00 3.79
391 424 4.016706 CACCGCCTCCCGTTTCCT 62.017 66.667 0.00 0.00 34.38 3.36
395 428 1.599797 CGCCTCCCGTTTCCTTGTT 60.600 57.895 0.00 0.00 0.00 2.83
396 429 0.320946 CGCCTCCCGTTTCCTTGTTA 60.321 55.000 0.00 0.00 0.00 2.41
397 430 1.162698 GCCTCCCGTTTCCTTGTTAC 58.837 55.000 0.00 0.00 0.00 2.50
401 434 4.189231 CCTCCCGTTTCCTTGTTACTATG 58.811 47.826 0.00 0.00 0.00 2.23
412 445 6.289834 TCCTTGTTACTATGTTTTTGACCGA 58.710 36.000 0.00 0.00 0.00 4.69
417 450 8.385898 TGTTACTATGTTTTTGACCGAATCTT 57.614 30.769 0.00 0.00 0.00 2.40
436 469 7.523380 CGAATCTTCCCGTATTCCTGTTATACT 60.523 40.741 0.00 0.00 0.00 2.12
437 470 8.716674 AATCTTCCCGTATTCCTGTTATACTA 57.283 34.615 0.00 0.00 0.00 1.82
438 471 7.516198 TCTTCCCGTATTCCTGTTATACTAC 57.484 40.000 0.00 0.00 0.00 2.73
439 472 6.491403 TCTTCCCGTATTCCTGTTATACTACC 59.509 42.308 0.00 0.00 0.00 3.18
471 505 3.810310 ACCTCGATCCAGTCATTCTTC 57.190 47.619 0.00 0.00 0.00 2.87
472 506 2.432510 ACCTCGATCCAGTCATTCTTCC 59.567 50.000 0.00 0.00 0.00 3.46
481 515 1.079405 TCATTCTTCCCGTCGTGGC 60.079 57.895 0.00 0.00 35.87 5.01
482 516 1.375396 CATTCTTCCCGTCGTGGCA 60.375 57.895 0.00 0.00 35.87 4.92
483 517 0.953471 CATTCTTCCCGTCGTGGCAA 60.953 55.000 0.00 0.00 35.87 4.52
484 518 0.673644 ATTCTTCCCGTCGTGGCAAG 60.674 55.000 0.00 0.00 35.87 4.01
485 519 2.725203 TTCTTCCCGTCGTGGCAAGG 62.725 60.000 0.00 0.00 35.87 3.61
486 520 3.234630 CTTCCCGTCGTGGCAAGGA 62.235 63.158 0.00 0.00 35.87 3.36
487 521 3.524648 TTCCCGTCGTGGCAAGGAC 62.525 63.158 3.72 3.72 37.75 3.85
491 525 3.041940 GTCGTGGCAAGGACGTGG 61.042 66.667 0.00 0.00 38.04 4.94
492 526 4.980805 TCGTGGCAAGGACGTGGC 62.981 66.667 0.00 4.94 44.09 5.01
515 549 2.579787 GATCGCCACCTCGTCACG 60.580 66.667 0.00 0.00 0.00 4.35
516 550 4.129737 ATCGCCACCTCGTCACGG 62.130 66.667 0.00 0.00 0.00 4.94
521 565 2.725641 CACCTCGTCACGGTCACA 59.274 61.111 0.00 0.00 30.82 3.58
523 567 2.049433 CCTCGTCACGGTCACACC 60.049 66.667 0.00 0.00 34.05 4.16
527 571 2.502093 GTCACGGTCACACCCACA 59.498 61.111 0.00 0.00 33.75 4.17
570 614 1.211457 GTCTCCGGACCTACACCTCTA 59.789 57.143 0.00 0.00 36.53 2.43
577 621 3.257624 CGGACCTACACCTCTACAAACTT 59.742 47.826 0.00 0.00 0.00 2.66
593 637 0.674895 ACTTGGAGAGCATCAACGGC 60.675 55.000 0.00 0.00 37.82 5.68
638 682 2.099756 GCAGCCAGGATTGTTTATGACC 59.900 50.000 0.00 0.00 0.00 4.02
645 689 3.118371 AGGATTGTTTATGACCCTCCGTC 60.118 47.826 0.00 0.00 42.33 4.79
748 797 2.358898 CCACCTGTCAGAAACCAACAAG 59.641 50.000 0.00 0.00 0.00 3.16
757 806 5.013547 TCAGAAACCAACAAGTTCCAGAAA 58.986 37.500 0.00 0.00 0.00 2.52
759 808 6.015010 TCAGAAACCAACAAGTTCCAGAAAAA 60.015 34.615 0.00 0.00 0.00 1.94
760 809 6.090763 CAGAAACCAACAAGTTCCAGAAAAAC 59.909 38.462 0.00 0.00 0.00 2.43
761 810 4.104696 ACCAACAAGTTCCAGAAAAACG 57.895 40.909 0.00 0.00 0.00 3.60
762 811 2.857748 CCAACAAGTTCCAGAAAAACGC 59.142 45.455 0.00 0.00 0.00 4.84
763 812 3.506810 CAACAAGTTCCAGAAAAACGCA 58.493 40.909 0.00 0.00 0.00 5.24
765 814 2.159296 ACAAGTTCCAGAAAAACGCACC 60.159 45.455 0.00 0.00 0.00 5.01
768 817 0.464013 TTCCAGAAAAACGCACCGGA 60.464 50.000 9.46 0.00 0.00 5.14
772 821 2.531206 CAGAAAAACGCACCGGAAAAA 58.469 42.857 9.46 0.00 0.00 1.94
774 823 1.855978 GAAAAACGCACCGGAAAAAGG 59.144 47.619 9.46 0.00 0.00 3.11
780 829 0.596577 GCACCGGAAAAAGGAAGGAC 59.403 55.000 9.46 0.00 0.00 3.85
861 923 0.116940 TAACCACCGTAGACCCCCTT 59.883 55.000 0.00 0.00 0.00 3.95
862 924 1.196766 AACCACCGTAGACCCCCTTC 61.197 60.000 0.00 0.00 0.00 3.46
864 926 1.305887 CACCGTAGACCCCCTTCCT 60.306 63.158 0.00 0.00 0.00 3.36
872 934 2.456840 CCCCCTTCCTCCCACTCT 59.543 66.667 0.00 0.00 0.00 3.24
902 964 4.796495 CGCTTTCCCCTTCCCCCG 62.796 72.222 0.00 0.00 0.00 5.73
903 965 4.442454 GCTTTCCCCTTCCCCCGG 62.442 72.222 0.00 0.00 0.00 5.73
904 966 4.442454 CTTTCCCCTTCCCCCGGC 62.442 72.222 0.00 0.00 0.00 6.13
921 983 2.048877 CACGTCCCGCCGTTACTT 60.049 61.111 0.00 0.00 39.45 2.24
922 984 1.212490 CACGTCCCGCCGTTACTTA 59.788 57.895 0.00 0.00 39.45 2.24
923 985 0.388391 CACGTCCCGCCGTTACTTAA 60.388 55.000 0.00 0.00 39.45 1.85
924 986 0.388520 ACGTCCCGCCGTTACTTAAC 60.389 55.000 0.00 0.00 37.96 2.01
927 991 1.810853 CCCGCCGTTACTTAACCCG 60.811 63.158 0.00 0.00 32.69 5.28
935 999 1.208052 GTTACTTAACCCGACCCCTCC 59.792 57.143 0.00 0.00 0.00 4.30
975 1051 2.292455 CCCCATTCCACTTCCATTTCCT 60.292 50.000 0.00 0.00 0.00 3.36
976 1052 3.026694 CCCATTCCACTTCCATTTCCTC 58.973 50.000 0.00 0.00 0.00 3.71
977 1053 3.026694 CCATTCCACTTCCATTTCCTCC 58.973 50.000 0.00 0.00 0.00 4.30
978 1054 2.899303 TTCCACTTCCATTTCCTCCC 57.101 50.000 0.00 0.00 0.00 4.30
979 1055 0.618458 TCCACTTCCATTTCCTCCCG 59.382 55.000 0.00 0.00 0.00 5.14
980 1056 0.328258 CCACTTCCATTTCCTCCCGT 59.672 55.000 0.00 0.00 0.00 5.28
981 1057 1.679032 CCACTTCCATTTCCTCCCGTC 60.679 57.143 0.00 0.00 0.00 4.79
995 1207 3.081409 CGTCCCCGTCCCCATTCT 61.081 66.667 0.00 0.00 0.00 2.40
1007 1219 4.010349 GTCCCCATTCTTTCATTCGTTCT 58.990 43.478 0.00 0.00 0.00 3.01
1021 1233 0.247497 CGTTCTCAGAGAGACGAGCG 60.247 60.000 21.21 9.41 38.51 5.03
1026 1238 3.199190 AGAGAGACGAGCGGCGAG 61.199 66.667 12.98 3.03 44.57 5.03
1043 1255 2.021106 GGCGAGACGACGACTACG 59.979 66.667 0.00 8.18 45.75 3.51
1073 1285 1.068943 AGGGGGAGAGCTCGGATCTA 61.069 60.000 8.37 0.00 0.00 1.98
1116 1335 0.681243 GGTGAAGGATGTTGAGGGCC 60.681 60.000 0.00 0.00 0.00 5.80
1414 1669 0.956633 TCTCGGTATGGTATGGTCGC 59.043 55.000 0.00 0.00 0.00 5.19
1447 1707 2.286950 TGATTTTGCTGCACGTCTTGTC 60.287 45.455 0.00 0.00 0.00 3.18
1448 1708 1.378531 TTTTGCTGCACGTCTTGTCT 58.621 45.000 0.00 0.00 0.00 3.41
1449 1709 1.378531 TTTGCTGCACGTCTTGTCTT 58.621 45.000 0.00 0.00 0.00 3.01
1450 1710 0.657312 TTGCTGCACGTCTTGTCTTG 59.343 50.000 0.00 0.00 0.00 3.02
1451 1711 0.461870 TGCTGCACGTCTTGTCTTGT 60.462 50.000 0.00 0.00 0.00 3.16
1548 1808 3.649277 CTTCCTGCACGAGGTCCGG 62.649 68.421 0.00 0.00 43.37 5.14
1839 2099 0.830648 TAATTCAGGTGAGAGCCCGG 59.169 55.000 0.00 0.00 0.00 5.73
1850 2110 0.188587 AGAGCCCGGTGATGAGGATA 59.811 55.000 0.00 0.00 0.00 2.59
1876 2136 3.498397 CCATCCCCGTCTGATTAATTTCG 59.502 47.826 0.00 0.00 0.00 3.46
2046 2323 4.815308 CACAGATTCAGAGCTCCCTAATTG 59.185 45.833 10.93 5.73 0.00 2.32
2073 2350 6.307776 AGTACTAGTGCAGAGCCATTAGATA 58.692 40.000 13.75 0.00 31.68 1.98
2081 2358 5.484998 TGCAGAGCCATTAGATACCATATCA 59.515 40.000 0.00 0.00 0.00 2.15
2170 2448 6.152379 CCCTTTTGTTCAATCTTCAGCTTAC 58.848 40.000 0.00 0.00 0.00 2.34
2205 2507 2.021936 AGGGGTTAGATGAAGTAGGCCT 60.022 50.000 11.78 11.78 0.00 5.19
2237 2539 7.973944 CAGAAATGGTAACTAGCCCAATTTAAC 59.026 37.037 0.97 0.00 33.66 2.01
2325 2628 2.046313 GCGAACACTGAAATTGCACAG 58.954 47.619 0.75 0.75 39.65 3.66
2330 2680 4.032703 ACACTGAAATTGCACAGTCAAC 57.967 40.909 4.80 0.00 44.07 3.18
2341 2691 1.073763 CACAGTCAACCCTGGATTCCA 59.926 52.381 5.05 5.05 36.75 3.53
2425 2787 3.646162 AGGATTGCTGGGATCATAACGTA 59.354 43.478 0.00 0.00 0.00 3.57
2426 2788 4.287067 AGGATTGCTGGGATCATAACGTAT 59.713 41.667 0.00 0.00 0.00 3.06
2427 2789 4.631813 GGATTGCTGGGATCATAACGTATC 59.368 45.833 0.00 0.00 0.00 2.24
2428 2790 3.678056 TGCTGGGATCATAACGTATCC 57.322 47.619 6.54 6.54 40.89 2.59
2429 2791 3.239449 TGCTGGGATCATAACGTATCCT 58.761 45.455 13.44 0.00 41.29 3.24
2433 2795 5.569630 GCTGGGATCATAACGTATCCTTGAT 60.570 44.000 13.44 6.66 41.29 2.57
2439 2801 6.479972 TCATAACGTATCCTTGATTCCTGT 57.520 37.500 0.00 0.00 0.00 4.00
2440 2802 6.280643 TCATAACGTATCCTTGATTCCTGTG 58.719 40.000 0.00 0.00 0.00 3.66
2441 2803 4.819105 AACGTATCCTTGATTCCTGTGA 57.181 40.909 0.00 0.00 0.00 3.58
2447 2809 3.184628 TCCTTGATTCCTGTGATCCTGT 58.815 45.455 0.00 0.00 0.00 4.00
2955 3327 9.899661 AATGTAACAGTACCATTTGCTATTCTA 57.100 29.630 0.00 0.00 0.00 2.10
2992 3368 3.381045 TCCGCGTATGAATCATCTGTTC 58.619 45.455 4.92 0.00 0.00 3.18
3327 3774 6.094719 GCAGAAGCTCAGACTATATGATCAG 58.905 44.000 0.09 0.00 37.91 2.90
3334 3781 6.214177 TCAGACTATATGATCAGGGTGGTA 57.786 41.667 0.09 0.00 0.00 3.25
3338 3785 8.378565 CAGACTATATGATCAGGGTGGTAAAAT 58.621 37.037 0.09 0.00 0.00 1.82
3498 3945 7.849804 TGTAATTGCAGGATTTAACTCTCTC 57.150 36.000 0.00 0.00 0.00 3.20
3559 4010 2.260481 GTGAACTAGAACGGTAGCAGC 58.740 52.381 0.00 0.00 0.00 5.25
3735 4188 6.481644 CAGGAATCACTTGGCTTTAGTAGATC 59.518 42.308 0.00 0.00 0.00 2.75
3850 4305 2.111077 TCGGGGAAAAGGGGAAATTCTT 59.889 45.455 0.00 0.00 0.00 2.52
3852 4307 3.699538 CGGGGAAAAGGGGAAATTCTTAG 59.300 47.826 0.00 0.00 0.00 2.18
3871 4326 1.269998 AGCTAGTGTCGTCTCGCTTTT 59.730 47.619 0.00 0.00 33.69 2.27
3900 4355 2.514803 TGATCCACTCACTGTCGAAGA 58.485 47.619 0.00 0.00 0.00 2.87
3956 4411 0.182775 ATGACCTAATTCCGGCACCC 59.817 55.000 0.00 0.00 0.00 4.61
4033 4488 5.924475 ACCAAATGTCTTTGTAACGAGAG 57.076 39.130 0.00 0.00 40.15 3.20
4052 4507 0.659123 GCACGTTGCAAAAGGTACCG 60.659 55.000 6.18 0.53 44.26 4.02
4057 4512 2.324860 GTTGCAAAAGGTACCGAATGC 58.675 47.619 23.57 23.57 0.00 3.56
4169 4626 3.827722 AGTTGGAAGTGGAATTCGGAAA 58.172 40.909 0.00 0.00 0.00 3.13
4242 4700 3.118408 TCAAGGGATCTCCATTTGTACCG 60.118 47.826 10.60 0.00 38.04 4.02
4243 4701 2.478292 AGGGATCTCCATTTGTACCGT 58.522 47.619 0.00 0.00 38.24 4.83
4249 4707 0.390603 TCCATTTGTACCGTGGCGAG 60.391 55.000 3.99 0.00 33.01 5.03
4255 4713 4.444838 TACCGTGGCGAGCGCAAT 62.445 61.111 17.16 0.00 44.11 3.56
4256 4714 3.066233 TACCGTGGCGAGCGCAATA 62.066 57.895 17.16 0.00 44.11 1.90
4257 4715 2.358193 TACCGTGGCGAGCGCAATAT 62.358 55.000 17.16 0.00 44.11 1.28
4260 4718 1.949133 GTGGCGAGCGCAATATCGA 60.949 57.895 19.38 0.00 44.11 3.59
4262 4720 1.215014 TGGCGAGCGCAATATCGAAG 61.215 55.000 19.38 0.00 44.11 3.79
4263 4721 1.488957 GCGAGCGCAATATCGAAGG 59.511 57.895 19.38 0.00 41.40 3.46
4264 4722 1.488957 CGAGCGCAATATCGAAGGC 59.511 57.895 11.47 0.00 41.40 4.35
4266 4724 1.221414 GAGCGCAATATCGAAGGCTT 58.779 50.000 11.47 0.00 0.00 4.35
4267 4725 0.940126 AGCGCAATATCGAAGGCTTG 59.060 50.000 11.47 0.00 0.00 4.01
4269 4727 1.299541 CGCAATATCGAAGGCTTGGT 58.700 50.000 3.46 0.00 0.00 3.67
4270 4728 1.261619 CGCAATATCGAAGGCTTGGTC 59.738 52.381 3.46 0.00 0.00 4.02
4272 4730 2.545946 GCAATATCGAAGGCTTGGTCTC 59.454 50.000 3.46 0.00 0.00 3.36
4273 4731 3.134458 CAATATCGAAGGCTTGGTCTCC 58.866 50.000 3.46 0.00 0.00 3.71
4274 4732 1.120530 TATCGAAGGCTTGGTCTCCC 58.879 55.000 3.46 0.00 0.00 4.30
4275 4733 1.627297 ATCGAAGGCTTGGTCTCCCC 61.627 60.000 3.46 0.00 0.00 4.81
4345 4803 3.781770 CTGATCGCCTCGCCAGACC 62.782 68.421 0.00 0.00 32.38 3.85
4348 4806 2.852495 GATCGCCTCGCCAGACCAAA 62.852 60.000 0.00 0.00 0.00 3.28
4352 4810 1.376037 CCTCGCCAGACCAAACCTC 60.376 63.158 0.00 0.00 0.00 3.85
4353 4811 1.376037 CTCGCCAGACCAAACCTCC 60.376 63.158 0.00 0.00 0.00 4.30
4357 4815 1.843421 CCAGACCAAACCTCCCACA 59.157 57.895 0.00 0.00 0.00 4.17
4371 4829 1.621317 TCCCACATAACGAGAACTGCA 59.379 47.619 0.00 0.00 0.00 4.41
4388 4846 0.733909 GCATGCTTTGCGGTTCTTCC 60.734 55.000 11.37 0.00 42.54 3.46
4393 4851 3.853698 TTTGCGGTTCTTCCCCGGG 62.854 63.158 15.80 15.80 45.57 5.73
4408 4866 1.475034 CCCGGGGGATGCATATTATCG 60.475 57.143 14.71 0.46 37.50 2.92
4416 4881 4.393062 GGGATGCATATTATCGTCTTGTGG 59.607 45.833 0.00 0.00 0.00 4.17
4417 4882 4.142816 GGATGCATATTATCGTCTTGTGGC 60.143 45.833 0.00 0.00 0.00 5.01
4418 4883 4.071961 TGCATATTATCGTCTTGTGGCT 57.928 40.909 0.00 0.00 0.00 4.75
4429 4894 3.438360 GTCTTGTGGCTTGTTCAGTTTG 58.562 45.455 0.00 0.00 0.00 2.93
4430 4895 3.128589 GTCTTGTGGCTTGTTCAGTTTGA 59.871 43.478 0.00 0.00 0.00 2.69
4450 4915 4.631131 TGATGCGTTCTATGGAGTTATGG 58.369 43.478 0.00 0.00 0.00 2.74
4451 4916 4.100963 TGATGCGTTCTATGGAGTTATGGT 59.899 41.667 0.00 0.00 0.00 3.55
4452 4917 5.303333 TGATGCGTTCTATGGAGTTATGGTA 59.697 40.000 0.00 0.00 0.00 3.25
4458 4939 0.763035 ATGGAGTTATGGTACCCGGC 59.237 55.000 10.07 0.00 0.00 6.13
4464 4945 0.685785 TTATGGTACCCGGCGGTGTA 60.686 55.000 26.32 22.07 44.40 2.90
4475 4956 4.338327 CGGTGTAGCCCGCTATTC 57.662 61.111 0.00 0.00 41.78 1.75
4476 4957 1.440060 CGGTGTAGCCCGCTATTCA 59.560 57.895 0.00 0.00 41.78 2.57
4505 4986 2.354109 TGAGAGCTGTTGTTCTAGCG 57.646 50.000 0.00 0.00 44.43 4.26
4518 4999 4.181578 TGTTCTAGCGTAAGAAATGGAGC 58.818 43.478 3.58 0.00 37.24 4.70
4527 5008 1.147153 GAAATGGAGCCCCTCTCGG 59.853 63.158 0.00 0.00 42.82 4.63
4535 5016 3.221222 CCCCTCTCGGCAGTTAGG 58.779 66.667 0.00 0.00 0.00 2.69
4544 5025 4.625800 GCAGTTAGGGCCAGTCTG 57.374 61.111 6.18 11.66 0.00 3.51
4545 5026 1.078143 GCAGTTAGGGCCAGTCTGG 60.078 63.158 15.15 15.15 41.55 3.86
4546 5027 1.604378 CAGTTAGGGCCAGTCTGGG 59.396 63.158 20.72 2.60 38.19 4.45
4547 5028 0.909610 CAGTTAGGGCCAGTCTGGGA 60.910 60.000 20.72 0.00 38.19 4.37
4548 5029 0.178873 AGTTAGGGCCAGTCTGGGAA 60.179 55.000 20.72 0.00 38.19 3.97
4549 5030 0.696501 GTTAGGGCCAGTCTGGGAAA 59.303 55.000 20.72 0.00 38.19 3.13
4550 5031 1.285078 GTTAGGGCCAGTCTGGGAAAT 59.715 52.381 20.72 0.00 38.19 2.17
4551 5032 1.681229 TAGGGCCAGTCTGGGAAATT 58.319 50.000 20.72 0.00 38.19 1.82
4552 5033 0.786435 AGGGCCAGTCTGGGAAATTT 59.214 50.000 20.72 0.00 38.19 1.82
4553 5034 2.000048 AGGGCCAGTCTGGGAAATTTA 59.000 47.619 20.72 0.00 38.19 1.40
4554 5035 2.381961 AGGGCCAGTCTGGGAAATTTAA 59.618 45.455 20.72 0.00 38.19 1.52
4555 5036 2.496070 GGGCCAGTCTGGGAAATTTAAC 59.504 50.000 20.72 0.03 38.19 2.01
4556 5037 2.496070 GGCCAGTCTGGGAAATTTAACC 59.504 50.000 20.72 5.87 38.19 2.85
4557 5038 3.431415 GCCAGTCTGGGAAATTTAACCT 58.569 45.455 20.72 0.00 38.19 3.50
4558 5039 3.193479 GCCAGTCTGGGAAATTTAACCTG 59.807 47.826 20.72 10.87 38.19 4.00
4559 5040 4.662278 CCAGTCTGGGAAATTTAACCTGA 58.338 43.478 11.46 13.57 32.67 3.86
4560 5041 5.076873 CCAGTCTGGGAAATTTAACCTGAA 58.923 41.667 11.46 5.21 34.63 3.02
4561 5042 5.538433 CCAGTCTGGGAAATTTAACCTGAAA 59.462 40.000 11.46 1.25 34.63 2.69
4562 5043 6.041523 CCAGTCTGGGAAATTTAACCTGAAAA 59.958 38.462 11.46 0.73 34.63 2.29
4563 5044 7.418483 CCAGTCTGGGAAATTTAACCTGAAAAA 60.418 37.037 11.46 0.47 34.63 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 0.449388 CTTTGATTGCGGGACAGCTC 59.551 55.000 0.00 0.00 38.13 4.09
158 177 0.889638 TGGAAAAACCATGCCGCGTA 60.890 50.000 4.92 0.00 44.64 4.42
188 208 5.381174 TTCTAGAACTAGTAAAGCGCACA 57.619 39.130 11.47 0.00 34.84 4.57
265 294 3.692406 GCGAGTGAGAACCCGGGT 61.692 66.667 24.16 24.16 0.00 5.28
266 295 4.452733 GGCGAGTGAGAACCCGGG 62.453 72.222 22.25 22.25 0.00 5.73
270 299 2.507324 GAGCGGCGAGTGAGAACC 60.507 66.667 12.98 0.00 0.00 3.62
271 300 2.876645 CGAGCGGCGAGTGAGAAC 60.877 66.667 12.98 0.00 44.57 3.01
272 301 1.579964 TAACGAGCGGCGAGTGAGAA 61.580 55.000 12.98 0.00 44.57 2.87
273 302 2.036571 TAACGAGCGGCGAGTGAGA 61.037 57.895 12.98 0.00 44.57 3.27
274 303 1.868251 GTAACGAGCGGCGAGTGAG 60.868 63.158 12.98 0.00 44.57 3.51
275 304 1.859427 AAGTAACGAGCGGCGAGTGA 61.859 55.000 12.98 0.00 44.57 3.41
276 305 1.403972 GAAGTAACGAGCGGCGAGTG 61.404 60.000 12.98 0.12 44.57 3.51
277 306 1.154073 GAAGTAACGAGCGGCGAGT 60.154 57.895 12.98 3.81 44.57 4.18
278 307 0.456312 AAGAAGTAACGAGCGGCGAG 60.456 55.000 12.98 3.03 44.57 5.03
279 308 0.038892 AAAGAAGTAACGAGCGGCGA 60.039 50.000 12.98 0.00 44.57 5.54
281 310 1.796459 TGAAAAGAAGTAACGAGCGGC 59.204 47.619 0.00 0.00 0.00 6.53
282 311 3.660904 CGTTGAAAAGAAGTAACGAGCGG 60.661 47.826 0.00 0.00 46.18 5.52
283 312 3.457596 CGTTGAAAAGAAGTAACGAGCG 58.542 45.455 0.00 0.00 46.18 5.03
284 313 3.492011 TCCGTTGAAAAGAAGTAACGAGC 59.508 43.478 9.59 0.00 46.18 5.03
285 314 4.743644 ACTCCGTTGAAAAGAAGTAACGAG 59.256 41.667 9.59 7.70 46.18 4.18
286 315 4.685924 ACTCCGTTGAAAAGAAGTAACGA 58.314 39.130 9.59 0.00 46.18 3.85
287 316 5.399604 AACTCCGTTGAAAAGAAGTAACG 57.600 39.130 0.00 0.00 43.79 3.18
288 317 5.429615 CGAACTCCGTTGAAAAGAAGTAAC 58.570 41.667 0.00 0.00 0.00 2.50
289 318 5.646467 CGAACTCCGTTGAAAAGAAGTAA 57.354 39.130 0.00 0.00 0.00 2.24
310 339 5.729883 CGTAAAGAGATGATGAAAAGCAACG 59.270 40.000 0.00 0.00 0.00 4.10
319 348 5.819379 ACCTACGTACGTAAAGAGATGATGA 59.181 40.000 26.68 4.17 0.00 2.92
364 397 2.282391 AGGCGGTGCAGCATTGAA 60.282 55.556 17.33 0.00 39.27 2.69
389 422 6.548441 TCGGTCAAAAACATAGTAACAAGG 57.452 37.500 0.00 0.00 0.00 3.61
391 424 8.385898 AGATTCGGTCAAAAACATAGTAACAA 57.614 30.769 0.00 0.00 0.00 2.83
395 428 6.596497 GGGAAGATTCGGTCAAAAACATAGTA 59.404 38.462 0.00 0.00 0.00 1.82
396 429 5.414765 GGGAAGATTCGGTCAAAAACATAGT 59.585 40.000 0.00 0.00 0.00 2.12
397 430 5.447279 CGGGAAGATTCGGTCAAAAACATAG 60.447 44.000 0.00 0.00 0.00 2.23
401 434 2.551032 ACGGGAAGATTCGGTCAAAAAC 59.449 45.455 0.00 0.00 0.00 2.43
412 445 7.613551 AGTATAACAGGAATACGGGAAGATT 57.386 36.000 0.00 0.00 35.42 2.40
417 450 5.704354 TGGTAGTATAACAGGAATACGGGA 58.296 41.667 0.00 0.00 29.83 5.14
436 469 6.043590 TGGATCGAGGTAGATAAGTACTGGTA 59.956 42.308 0.00 0.00 0.00 3.25
437 470 5.163120 TGGATCGAGGTAGATAAGTACTGGT 60.163 44.000 0.00 0.00 0.00 4.00
438 471 5.314529 TGGATCGAGGTAGATAAGTACTGG 58.685 45.833 0.00 0.00 0.00 4.00
439 472 5.998981 ACTGGATCGAGGTAGATAAGTACTG 59.001 44.000 9.72 0.00 30.46 2.74
494 528 4.129737 ACGAGGTGGCGATCACGG 62.130 66.667 3.70 0.00 46.96 4.94
495 529 2.579787 GACGAGGTGGCGATCACG 60.580 66.667 0.00 0.00 46.96 4.35
496 530 1.805945 GTGACGAGGTGGCGATCAC 60.806 63.158 0.00 0.00 45.34 3.06
497 531 2.571757 GTGACGAGGTGGCGATCA 59.428 61.111 0.00 0.00 34.83 2.92
498 532 2.579787 CGTGACGAGGTGGCGATC 60.580 66.667 0.00 0.00 34.83 3.69
499 533 4.129737 CCGTGACGAGGTGGCGAT 62.130 66.667 6.54 0.00 34.83 4.58
515 549 4.280019 GGGGGTGTGGGTGTGACC 62.280 72.222 0.00 0.00 37.60 4.02
516 550 4.636435 CGGGGGTGTGGGTGTGAC 62.636 72.222 0.00 0.00 0.00 3.67
558 602 4.228824 TCCAAGTTTGTAGAGGTGTAGGT 58.771 43.478 0.00 0.00 0.00 3.08
561 605 4.021368 GCTCTCCAAGTTTGTAGAGGTGTA 60.021 45.833 13.98 0.00 40.42 2.90
562 606 3.244249 GCTCTCCAAGTTTGTAGAGGTGT 60.244 47.826 13.98 0.00 40.42 4.16
570 614 2.549754 CGTTGATGCTCTCCAAGTTTGT 59.450 45.455 0.00 0.00 0.00 2.83
577 621 2.123248 TTGGCCGTTGATGCTCTCCA 62.123 55.000 0.00 0.00 0.00 3.86
614 658 3.831333 TCATAAACAATCCTGGCTGCAAA 59.169 39.130 0.50 0.00 0.00 3.68
622 666 3.206150 CGGAGGGTCATAAACAATCCTG 58.794 50.000 0.00 0.00 33.78 3.86
638 682 4.336889 TTGAGCCTAATTATGACGGAGG 57.663 45.455 0.00 0.00 0.00 4.30
748 797 0.317519 CCGGTGCGTTTTTCTGGAAC 60.318 55.000 0.00 0.00 0.00 3.62
757 806 1.066454 CTTCCTTTTTCCGGTGCGTTT 59.934 47.619 0.00 0.00 0.00 3.60
759 808 1.170290 CCTTCCTTTTTCCGGTGCGT 61.170 55.000 0.00 0.00 0.00 5.24
760 809 0.887387 TCCTTCCTTTTTCCGGTGCG 60.887 55.000 0.00 0.00 0.00 5.34
761 810 0.596577 GTCCTTCCTTTTTCCGGTGC 59.403 55.000 0.00 0.00 0.00 5.01
762 811 0.872388 CGTCCTTCCTTTTTCCGGTG 59.128 55.000 0.00 0.00 0.00 4.94
763 812 0.760572 TCGTCCTTCCTTTTTCCGGT 59.239 50.000 0.00 0.00 0.00 5.28
765 814 1.873698 TGTCGTCCTTCCTTTTTCCG 58.126 50.000 0.00 0.00 0.00 4.30
768 817 3.881220 TGACTTGTCGTCCTTCCTTTTT 58.119 40.909 0.00 0.00 42.13 1.94
772 821 2.484947 GGTTTGACTTGTCGTCCTTCCT 60.485 50.000 0.00 0.00 42.13 3.36
774 823 1.871676 GGGTTTGACTTGTCGTCCTTC 59.128 52.381 0.00 0.00 42.13 3.46
780 829 1.890876 TGGATGGGTTTGACTTGTCG 58.109 50.000 0.00 0.00 0.00 4.35
861 923 0.325671 GGTGATGGAGAGTGGGAGGA 60.326 60.000 0.00 0.00 0.00 3.71
862 924 1.341156 GGGTGATGGAGAGTGGGAGG 61.341 65.000 0.00 0.00 0.00 4.30
864 926 0.909610 GTGGGTGATGGAGAGTGGGA 60.910 60.000 0.00 0.00 0.00 4.37
872 934 3.545124 AAAGCGCGTGGGTGATGGA 62.545 57.895 8.43 0.00 0.00 3.41
907 969 0.740868 GGGTTAAGTAACGGCGGGAC 60.741 60.000 13.24 8.74 37.07 4.46
908 970 1.596408 GGGTTAAGTAACGGCGGGA 59.404 57.895 13.24 0.00 37.07 5.14
913 975 0.108186 GGGGTCGGGTTAAGTAACGG 60.108 60.000 0.00 0.00 37.07 4.44
919 981 2.372890 GGGGAGGGGTCGGGTTAAG 61.373 68.421 0.00 0.00 0.00 1.85
921 983 4.419900 GGGGGAGGGGTCGGGTTA 62.420 72.222 0.00 0.00 0.00 2.85
954 1018 2.110578 GGAAATGGAAGTGGAATGGGG 58.889 52.381 0.00 0.00 0.00 4.96
979 1055 0.393944 GAAAGAATGGGGACGGGGAC 60.394 60.000 0.00 0.00 0.00 4.46
980 1056 0.842905 TGAAAGAATGGGGACGGGGA 60.843 55.000 0.00 0.00 0.00 4.81
981 1057 0.258774 ATGAAAGAATGGGGACGGGG 59.741 55.000 0.00 0.00 0.00 5.73
995 1207 4.215613 TCGTCTCTCTGAGAACGAATGAAA 59.784 41.667 27.02 13.89 40.59 2.69
1007 1219 3.500642 CGCCGCTCGTCTCTCTGA 61.501 66.667 0.00 0.00 0.00 3.27
1026 1238 2.021106 CGTAGTCGTCGTCTCGCC 59.979 66.667 0.00 0.00 0.00 5.54
1028 1240 0.799917 TCCTCGTAGTCGTCGTCTCG 60.800 60.000 0.00 0.87 38.33 4.04
1029 1241 0.922717 CTCCTCGTAGTCGTCGTCTC 59.077 60.000 0.00 0.00 38.33 3.36
1030 1242 0.459934 CCTCCTCGTAGTCGTCGTCT 60.460 60.000 0.00 0.00 38.33 4.18
1031 1243 0.459237 TCCTCCTCGTAGTCGTCGTC 60.459 60.000 0.00 0.00 38.33 4.20
1032 1244 0.459934 CTCCTCCTCGTAGTCGTCGT 60.460 60.000 0.00 0.00 38.33 4.34
1033 1245 1.764180 GCTCCTCCTCGTAGTCGTCG 61.764 65.000 0.00 0.00 38.33 5.12
1034 1246 1.764180 CGCTCCTCCTCGTAGTCGTC 61.764 65.000 0.00 0.00 38.33 4.20
1035 1247 1.814586 CGCTCCTCCTCGTAGTCGT 60.815 63.158 0.00 0.00 38.33 4.34
1036 1248 1.492319 CTCGCTCCTCCTCGTAGTCG 61.492 65.000 0.00 0.00 38.55 4.18
1037 1249 1.161563 CCTCGCTCCTCCTCGTAGTC 61.162 65.000 0.00 0.00 0.00 2.59
1038 1250 1.153127 CCTCGCTCCTCCTCGTAGT 60.153 63.158 0.00 0.00 0.00 2.73
1039 1251 1.894756 CCCTCGCTCCTCCTCGTAG 60.895 68.421 0.00 0.00 0.00 3.51
1040 1252 2.192443 CCCTCGCTCCTCCTCGTA 59.808 66.667 0.00 0.00 0.00 3.43
1041 1253 4.824515 CCCCTCGCTCCTCCTCGT 62.825 72.222 0.00 0.00 0.00 4.18
1043 1255 4.144727 TCCCCCTCGCTCCTCCTC 62.145 72.222 0.00 0.00 0.00 3.71
1073 1285 4.202430 ACCAACTAGACAAAAATCTCCGGT 60.202 41.667 0.00 0.00 0.00 5.28
1370 1589 2.115427 GGGGAAGGAGAAGAGAAGAGG 58.885 57.143 0.00 0.00 0.00 3.69
1447 1707 2.097038 CGAAGCCTGCCGAGACAAG 61.097 63.158 0.00 0.00 0.00 3.16
1448 1708 2.048222 CGAAGCCTGCCGAGACAA 60.048 61.111 0.00 0.00 0.00 3.18
1839 2099 3.515901 GGGGATGGTAGTATCCTCATCAC 59.484 52.174 4.92 0.00 45.40 3.06
1850 2110 2.176247 AATCAGACGGGGATGGTAGT 57.824 50.000 0.00 0.00 0.00 2.73
1858 2118 2.031683 GCACGAAATTAATCAGACGGGG 59.968 50.000 0.00 0.00 0.00 5.73
1895 2158 2.374830 ATCAGCGATCCTTGCCTCCG 62.375 60.000 0.00 0.00 0.00 4.63
2046 2323 2.376109 TGGCTCTGCACTAGTACTACC 58.624 52.381 0.00 0.00 0.00 3.18
2081 2358 8.109634 AGGTCAATGACATTAGTTAAGTTCCAT 58.890 33.333 15.86 0.00 33.68 3.41
2170 2448 5.801380 TCTAACCCCTTACACAAAGCTAAG 58.199 41.667 0.00 0.00 33.49 2.18
2205 2507 6.069905 TGGGCTAGTTACCATTTCTGACATAA 60.070 38.462 0.00 0.00 0.00 1.90
2237 2539 8.755018 GTTTCCAAAAACACAGTGAATATCTTG 58.245 33.333 7.81 2.20 43.52 3.02
2346 2696 4.330250 CAGCAATCCTGGATAGGTTATGG 58.670 47.826 10.13 0.00 44.88 2.74
2425 2787 3.784763 ACAGGATCACAGGAATCAAGGAT 59.215 43.478 0.00 0.00 0.00 3.24
2426 2788 3.054875 CACAGGATCACAGGAATCAAGGA 60.055 47.826 0.00 0.00 0.00 3.36
2427 2789 3.054875 TCACAGGATCACAGGAATCAAGG 60.055 47.826 0.00 0.00 0.00 3.61
2428 2790 4.212143 TCACAGGATCACAGGAATCAAG 57.788 45.455 0.00 0.00 0.00 3.02
2429 2791 4.849813 ATCACAGGATCACAGGAATCAA 57.150 40.909 0.00 0.00 0.00 2.57
2955 3327 1.152546 GGAGCAAAACCCCCACACT 60.153 57.895 0.00 0.00 0.00 3.55
2992 3368 4.915085 ACTTGGCGTTATTTCATTTTGTCG 59.085 37.500 0.00 0.00 0.00 4.35
3241 3628 1.687563 GAGCTGGAGGAGGAGTAGAC 58.312 60.000 0.00 0.00 0.00 2.59
3282 3693 2.722201 CCCGTCTGGTCTGGCCTAC 61.722 68.421 3.32 1.65 38.35 3.18
3327 3774 2.622190 CCCTACCACCATTTTACCACCC 60.622 54.545 0.00 0.00 0.00 4.61
3334 3781 2.158385 TCTGCAACCCTACCACCATTTT 60.158 45.455 0.00 0.00 0.00 1.82
3338 3785 0.618458 GATCTGCAACCCTACCACCA 59.382 55.000 0.00 0.00 0.00 4.17
3599 4052 2.863740 GCACGGACGAATTCACATGATA 59.136 45.455 6.22 0.00 0.00 2.15
3601 4054 1.075542 GCACGGACGAATTCACATGA 58.924 50.000 6.22 0.00 0.00 3.07
3613 4066 1.303317 ATTTCCCACCAGCACGGAC 60.303 57.895 0.00 0.00 38.63 4.79
3645 4098 9.666626 GATCGATCGAAAAGTAGATAGAAAAGA 57.333 33.333 23.50 0.00 33.50 2.52
3766 4219 2.778679 GACCGACGATGCAAGTGC 59.221 61.111 2.77 0.00 42.50 4.40
3767 4220 1.733041 ACGACCGACGATGCAAGTG 60.733 57.895 2.77 0.00 45.77 3.16
3768 4221 1.733041 CACGACCGACGATGCAAGT 60.733 57.895 0.00 0.00 45.77 3.16
3769 4222 2.444624 CCACGACCGACGATGCAAG 61.445 63.158 0.00 0.00 45.77 4.01
3777 4230 4.295119 AGCCACACCACGACCGAC 62.295 66.667 0.00 0.00 0.00 4.79
3850 4305 1.735386 AAGCGAGACGACACTAGCTA 58.265 50.000 13.66 0.00 45.17 3.32
3852 4307 1.699343 AAAAGCGAGACGACACTAGC 58.301 50.000 0.00 0.00 38.45 3.42
3900 4355 8.624776 CAGACCTCTCAATAAAGAAACAACTTT 58.375 33.333 0.00 0.00 41.90 2.66
3921 4376 2.622436 GTCATGGTAAGCACTCAGACC 58.378 52.381 0.00 0.00 0.00 3.85
3956 4411 6.561614 AGTGTACACGGATAACTCATAACTG 58.438 40.000 19.93 0.00 36.20 3.16
4033 4488 0.659123 CGGTACCTTTTGCAACGTGC 60.659 55.000 10.90 0.00 45.29 5.34
4047 4502 2.995258 TCGTTACAAAGGCATTCGGTAC 59.005 45.455 0.00 0.00 0.00 3.34
4052 4507 3.732943 CGTTCTCGTTACAAAGGCATTC 58.267 45.455 0.00 0.00 0.00 2.67
4146 4603 3.934068 TCCGAATTCCACTTCCAACTAC 58.066 45.455 0.00 0.00 0.00 2.73
4169 4626 5.590818 TGGGAATCAACTAGGAGTAGAAGT 58.409 41.667 0.00 0.00 0.00 3.01
4214 4671 3.550437 ATGGAGATCCCTTGAAACGAG 57.450 47.619 0.00 0.00 35.38 4.18
4230 4687 0.390603 CTCGCCACGGTACAAATGGA 60.391 55.000 12.20 0.00 35.33 3.41
4242 4700 1.487452 TTCGATATTGCGCTCGCCAC 61.487 55.000 9.73 0.00 41.09 5.01
4243 4701 1.215014 CTTCGATATTGCGCTCGCCA 61.215 55.000 9.73 0.57 41.09 5.69
4249 4707 0.040958 CCAAGCCTTCGATATTGCGC 60.041 55.000 0.00 0.00 0.00 6.09
4269 4727 1.885887 CATTTTGCAACGAAGGGGAGA 59.114 47.619 0.00 0.00 0.00 3.71
4270 4728 1.067635 CCATTTTGCAACGAAGGGGAG 60.068 52.381 0.00 0.00 0.00 4.30
4272 4730 0.670239 GCCATTTTGCAACGAAGGGG 60.670 55.000 14.55 7.93 0.00 4.79
4273 4731 0.670239 GGCCATTTTGCAACGAAGGG 60.670 55.000 9.66 9.66 0.00 3.95
4274 4732 0.033228 TGGCCATTTTGCAACGAAGG 59.967 50.000 0.00 0.00 0.00 3.46
4275 4733 1.994779 GATGGCCATTTTGCAACGAAG 59.005 47.619 21.84 0.00 0.00 3.79
4345 4803 3.328382 TCTCGTTATGTGGGAGGTTTG 57.672 47.619 0.00 0.00 0.00 2.93
4348 4806 2.233922 CAGTTCTCGTTATGTGGGAGGT 59.766 50.000 0.00 0.00 0.00 3.85
4352 4810 2.093306 TGCAGTTCTCGTTATGTGGG 57.907 50.000 0.00 0.00 0.00 4.61
4353 4811 2.223112 GCATGCAGTTCTCGTTATGTGG 60.223 50.000 14.21 0.00 0.00 4.17
4357 4815 4.346734 CAAAGCATGCAGTTCTCGTTAT 57.653 40.909 21.98 0.00 0.00 1.89
4371 4829 2.267045 GGGAAGAACCGCAAAGCAT 58.733 52.632 0.00 0.00 40.11 3.79
4388 4846 1.475034 CGATAATATGCATCCCCCGGG 60.475 57.143 15.80 15.80 0.00 5.73
4393 4851 4.393062 CCACAAGACGATAATATGCATCCC 59.607 45.833 0.19 0.00 0.00 3.85
4399 4857 5.991328 ACAAGCCACAAGACGATAATATG 57.009 39.130 0.00 0.00 0.00 1.78
4404 4862 3.244078 ACTGAACAAGCCACAAGACGATA 60.244 43.478 0.00 0.00 0.00 2.92
4408 4866 3.128589 TCAAACTGAACAAGCCACAAGAC 59.871 43.478 0.00 0.00 0.00 3.01
4416 4881 2.405892 ACGCATCAAACTGAACAAGC 57.594 45.000 0.00 0.00 0.00 4.01
4417 4882 4.214980 AGAACGCATCAAACTGAACAAG 57.785 40.909 0.00 0.00 0.00 3.16
4418 4883 5.334802 CCATAGAACGCATCAAACTGAACAA 60.335 40.000 0.00 0.00 0.00 2.83
4429 4894 4.632153 ACCATAACTCCATAGAACGCATC 58.368 43.478 0.00 0.00 0.00 3.91
4430 4895 4.689612 ACCATAACTCCATAGAACGCAT 57.310 40.909 0.00 0.00 0.00 4.73
4464 4945 1.450312 GTGCTGTGAATAGCGGGCT 60.450 57.895 0.00 0.00 46.61 5.19
4471 4952 3.008375 AGCTCTCAAAGGTGCTGTGAATA 59.992 43.478 0.00 0.00 33.44 1.75
4475 4956 0.873054 CAGCTCTCAAAGGTGCTGTG 59.127 55.000 0.00 0.00 45.77 3.66
4476 4957 3.319135 CAGCTCTCAAAGGTGCTGT 57.681 52.632 0.00 0.00 45.77 4.40
4505 4986 2.483889 CGAGAGGGGCTCCATTTCTTAC 60.484 54.545 4.79 0.00 40.70 2.34
4527 5008 1.078143 CCAGACTGGCCCTAACTGC 60.078 63.158 8.99 0.00 0.00 4.40
4535 5016 2.496070 GGTTAAATTTCCCAGACTGGCC 59.504 50.000 16.72 4.65 35.79 5.36
4538 5019 6.648879 TTTCAGGTTAAATTTCCCAGACTG 57.351 37.500 0.00 0.00 0.00 3.51
4539 5020 7.669089 TTTTTCAGGTTAAATTTCCCAGACT 57.331 32.000 0.00 0.00 0.00 3.24


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

AutoCloner maintained by Alex Coulton.