Multiple sequence alignment - TraesCS5B01G263000

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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 TraesCS5B01G263000 chr5B 100.000 3323 0 0 1 3323 447557418 447560740 0.000000e+00 6137
1 TraesCS5B01G263000 chr5D 93.361 1657 63 21 734 2369 374706620 374708250 0.000000e+00 2407
2 TraesCS5B01G263000 chr5D 94.672 244 8 2 1 244 374706021 374706259 1.130000e-99 374
3 TraesCS5B01G263000 chr5D 88.732 213 16 4 489 694 374706404 374706615 1.530000e-63 254
4 TraesCS5B01G263000 chr5D 89.535 172 17 1 320 491 9947608 9947778 2.010000e-52 217
5 TraesCS5B01G263000 chr5D 89.412 170 17 1 322 490 6083530 6083361 2.600000e-51 213
6 TraesCS5B01G263000 chr5D 94.382 89 3 1 3237 3323 374708236 374708324 5.780000e-28 135
7 TraesCS5B01G263000 chr5D 77.990 209 36 8 1306 1509 44137380 44137177 4.500000e-24 122
8 TraesCS5B01G263000 chr5A 94.511 1494 60 16 876 2368 476413092 476414564 0.000000e+00 2285
9 TraesCS5B01G263000 chr5A 88.938 226 22 3 488 712 476410859 476411082 3.270000e-70 276
10 TraesCS5B01G263000 chr5A 89.247 186 10 4 1 186 476410327 476410502 1.200000e-54 224
11 TraesCS5B01G263000 chr7B 95.529 850 36 2 2370 3218 498599769 498598921 0.000000e+00 1358
12 TraesCS5B01G263000 chr7B 88.525 183 20 1 322 504 428839132 428838951 1.550000e-53 220
13 TraesCS5B01G263000 chr1B 95.529 850 37 1 2370 3218 643024952 643025801 0.000000e+00 1358
14 TraesCS5B01G263000 chr1B 89.474 171 16 2 325 494 639429465 639429634 7.220000e-52 215
15 TraesCS5B01G263000 chr3B 95.294 850 37 3 2370 3218 533445418 533444571 0.000000e+00 1345
16 TraesCS5B01G263000 chr3B 95.182 851 37 2 2370 3219 708392762 708391915 0.000000e+00 1341
17 TraesCS5B01G263000 chr3B 94.749 857 44 1 2363 3218 824305060 824304204 0.000000e+00 1332
18 TraesCS5B01G263000 chr3B 91.463 164 13 1 331 494 23713599 23713437 1.200000e-54 224
19 TraesCS5B01G263000 chr2B 95.176 850 38 3 2370 3218 452910178 452911025 0.000000e+00 1339
20 TraesCS5B01G263000 chr2B 95.272 846 38 2 2370 3214 475124888 475125732 0.000000e+00 1339
21 TraesCS5B01G263000 chr2B 94.941 850 42 1 2370 3218 175454603 175453754 0.000000e+00 1330
22 TraesCS5B01G263000 chr2B 90.419 167 16 0 325 491 799360450 799360616 1.550000e-53 220
23 TraesCS5B01G263000 chr2B 87.978 183 16 6 322 501 659694463 659694642 9.340000e-51 211
24 TraesCS5B01G263000 chr6B 94.737 855 42 3 2365 3218 563975874 563975022 0.000000e+00 1327
25 TraesCS5B01G263000 chr6B 89.881 168 16 1 323 490 29399881 29400047 7.220000e-52 215
26 TraesCS5B01G263000 chr7A 82.105 475 82 2 1819 2290 222638540 222638066 1.440000e-108 403
27 TraesCS5B01G263000 chr7D 82.468 462 78 2 1819 2277 210022305 210021844 5.160000e-108 401
28 TraesCS5B01G263000 chrUn 92.667 150 11 0 340 489 48430252 48430103 2.010000e-52 217


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 TraesCS5B01G263000 chr5B 447557418 447560740 3322 False 6137.000000 6137 100.000000 1 3323 1 chr5B.!!$F1 3322
1 TraesCS5B01G263000 chr5D 374706021 374708324 2303 False 792.500000 2407 92.786750 1 3323 4 chr5D.!!$F2 3322
2 TraesCS5B01G263000 chr5A 476410327 476414564 4237 False 928.333333 2285 90.898667 1 2368 3 chr5A.!!$F1 2367
3 TraesCS5B01G263000 chr7B 498598921 498599769 848 True 1358.000000 1358 95.529000 2370 3218 1 chr7B.!!$R2 848
4 TraesCS5B01G263000 chr1B 643024952 643025801 849 False 1358.000000 1358 95.529000 2370 3218 1 chr1B.!!$F2 848
5 TraesCS5B01G263000 chr3B 533444571 533445418 847 True 1345.000000 1345 95.294000 2370 3218 1 chr3B.!!$R2 848
6 TraesCS5B01G263000 chr3B 708391915 708392762 847 True 1341.000000 1341 95.182000 2370 3219 1 chr3B.!!$R3 849
7 TraesCS5B01G263000 chr3B 824304204 824305060 856 True 1332.000000 1332 94.749000 2363 3218 1 chr3B.!!$R4 855
8 TraesCS5B01G263000 chr2B 452910178 452911025 847 False 1339.000000 1339 95.176000 2370 3218 1 chr2B.!!$F1 848
9 TraesCS5B01G263000 chr2B 475124888 475125732 844 False 1339.000000 1339 95.272000 2370 3214 1 chr2B.!!$F2 844
10 TraesCS5B01G263000 chr2B 175453754 175454603 849 True 1330.000000 1330 94.941000 2370 3218 1 chr2B.!!$R1 848
11 TraesCS5B01G263000 chr6B 563975022 563975874 852 True 1327.000000 1327 94.737000 2365 3218 1 chr6B.!!$R1 853

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
707 1002 0.034574 TTGGCATGGCACGGACTATT 60.035 50.0 23.26 0.00 0.00 1.73 F
1467 3654 0.612174 AGCCTGAGAACGTGCTCCTA 60.612 55.0 21.10 2.01 33.95 2.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2085 4272 1.227380 CCTTCTCGCGGGATCCTTG 60.227 63.158 10.79 5.92 0.00 3.61 R
3227 5416 0.385029 AAACGGTAAAACCCAACGGC 59.615 50.000 0.00 0.00 33.75 5.68 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
142 143 0.096976 GGATGTTCCGTTGCATCACG 59.903 55.000 3.92 3.92 42.22 4.35
164 165 3.428452 GGTCACATGATTGATGCCTTGTG 60.428 47.826 0.00 0.00 38.80 3.33
165 166 2.756207 TCACATGATTGATGCCTTGTGG 59.244 45.455 0.00 0.00 38.32 4.17
166 167 2.494471 CACATGATTGATGCCTTGTGGT 59.506 45.455 0.00 0.00 35.85 4.16
167 168 2.494471 ACATGATTGATGCCTTGTGGTG 59.506 45.455 0.00 0.00 35.15 4.17
247 478 7.223260 TCTGATTCTTGCAGTCAAAATCATT 57.777 32.000 9.97 0.00 36.19 2.57
248 479 7.663827 TCTGATTCTTGCAGTCAAAATCATTT 58.336 30.769 9.97 0.00 36.19 2.32
249 480 7.597369 TCTGATTCTTGCAGTCAAAATCATTTG 59.403 33.333 9.97 0.00 38.57 2.32
278 559 3.056328 GCTCCACGCCCTTGTTCC 61.056 66.667 0.00 0.00 0.00 3.62
298 579 5.925506 TCCAACAATTCATCTGCATCAAT 57.074 34.783 0.00 0.00 0.00 2.57
302 583 6.035650 CCAACAATTCATCTGCATCAATTGTC 59.964 38.462 18.31 0.00 44.76 3.18
305 586 8.058667 ACAATTCATCTGCATCAATTGTCTAA 57.941 30.769 14.79 0.00 42.96 2.10
316 597 8.593842 TGCATCAATTGTCTAAATATTTTTGCG 58.406 29.630 5.91 0.79 0.00 4.85
319 600 7.948137 TCAATTGTCTAAATATTTTTGCGCAC 58.052 30.769 11.12 0.00 0.00 5.34
323 604 6.777101 TGTCTAAATATTTTTGCGCACGTAT 58.223 32.000 11.12 6.03 0.00 3.06
324 605 7.244898 TGTCTAAATATTTTTGCGCACGTATT 58.755 30.769 11.12 9.61 0.00 1.89
326 607 8.667204 GTCTAAATATTTTTGCGCACGTATTAC 58.333 33.333 11.12 4.58 0.00 1.89
327 608 8.605746 TCTAAATATTTTTGCGCACGTATTACT 58.394 29.630 11.12 1.73 0.00 2.24
328 609 7.431215 AAATATTTTTGCGCACGTATTACTG 57.569 32.000 11.12 0.00 0.00 2.74
329 610 2.884663 TTTTGCGCACGTATTACTGG 57.115 45.000 11.12 0.00 0.00 4.00
331 612 0.390603 TTGCGCACGTATTACTGGCT 60.391 50.000 11.12 0.00 0.00 4.75
333 614 1.488261 GCGCACGTATTACTGGCTCC 61.488 60.000 0.30 0.00 0.00 4.70
334 615 1.206745 CGCACGTATTACTGGCTCCG 61.207 60.000 0.00 0.00 0.00 4.63
335 616 0.179119 GCACGTATTACTGGCTCCGT 60.179 55.000 0.00 0.00 0.00 4.69
337 618 2.613691 CACGTATTACTGGCTCCGTTT 58.386 47.619 0.00 0.00 0.00 3.60
338 619 2.997986 CACGTATTACTGGCTCCGTTTT 59.002 45.455 0.00 0.00 0.00 2.43
339 620 3.434299 CACGTATTACTGGCTCCGTTTTT 59.566 43.478 0.00 0.00 0.00 1.94
340 621 4.626604 CACGTATTACTGGCTCCGTTTTTA 59.373 41.667 0.00 0.00 0.00 1.52
341 622 5.120519 CACGTATTACTGGCTCCGTTTTTAA 59.879 40.000 0.00 0.00 0.00 1.52
342 623 5.700373 ACGTATTACTGGCTCCGTTTTTAAA 59.300 36.000 0.00 0.00 0.00 1.52
343 624 6.372381 ACGTATTACTGGCTCCGTTTTTAAAT 59.628 34.615 0.00 0.00 0.00 1.40
344 625 7.548780 ACGTATTACTGGCTCCGTTTTTAAATA 59.451 33.333 0.00 0.00 0.00 1.40
345 626 8.553696 CGTATTACTGGCTCCGTTTTTAAATAT 58.446 33.333 0.00 0.00 0.00 1.28
348 629 8.973835 TTACTGGCTCCGTTTTTAAATATTTG 57.026 30.769 11.05 0.00 0.00 2.32
349 630 6.988522 ACTGGCTCCGTTTTTAAATATTTGT 58.011 32.000 11.05 0.00 0.00 2.83
350 631 7.088272 ACTGGCTCCGTTTTTAAATATTTGTC 58.912 34.615 11.05 0.00 0.00 3.18
351 632 7.039993 ACTGGCTCCGTTTTTAAATATTTGTCT 60.040 33.333 11.05 0.00 0.00 3.41
352 633 7.662897 TGGCTCCGTTTTTAAATATTTGTCTT 58.337 30.769 11.05 0.00 0.00 3.01
353 634 8.145122 TGGCTCCGTTTTTAAATATTTGTCTTT 58.855 29.630 11.05 0.00 0.00 2.52
354 635 8.644619 GGCTCCGTTTTTAAATATTTGTCTTTC 58.355 33.333 11.05 0.00 0.00 2.62
355 636 9.406828 GCTCCGTTTTTAAATATTTGTCTTTCT 57.593 29.630 11.05 0.00 0.00 2.52
371 652 8.964476 TTGTCTTTCTAGAGATTTCAACAAGT 57.036 30.769 0.00 0.00 0.00 3.16
386 667 9.893305 ATTTCAACAAGTAACTACATACAAAGC 57.107 29.630 0.00 0.00 0.00 3.51
387 668 8.439993 TTCAACAAGTAACTACATACAAAGCA 57.560 30.769 0.00 0.00 0.00 3.91
388 669 8.439993 TCAACAAGTAACTACATACAAAGCAA 57.560 30.769 0.00 0.00 0.00 3.91
389 670 8.894731 TCAACAAGTAACTACATACAAAGCAAA 58.105 29.630 0.00 0.00 0.00 3.68
390 671 9.509855 CAACAAGTAACTACATACAAAGCAAAA 57.490 29.630 0.00 0.00 0.00 2.44
392 673 9.677567 ACAAGTAACTACATACAAAGCAAAATG 57.322 29.630 0.00 0.00 0.00 2.32
393 674 9.891828 CAAGTAACTACATACAAAGCAAAATGA 57.108 29.630 0.00 0.00 0.00 2.57
395 676 9.284968 AGTAACTACATACAAAGCAAAATGAGT 57.715 29.630 0.00 0.00 0.00 3.41
406 687 8.850156 ACAAAGCAAAATGAGTAAATCTACACT 58.150 29.630 0.00 0.00 0.00 3.55
407 688 9.683069 CAAAGCAAAATGAGTAAATCTACACTT 57.317 29.630 0.00 0.00 0.00 3.16
481 762 7.533289 AGAAAGAAAAATATTTGGGAACGGA 57.467 32.000 0.39 0.00 0.00 4.69
482 763 7.602753 AGAAAGAAAAATATTTGGGAACGGAG 58.397 34.615 0.39 0.00 0.00 4.63
483 764 5.914898 AGAAAAATATTTGGGAACGGAGG 57.085 39.130 0.39 0.00 0.00 4.30
484 765 4.709886 AGAAAAATATTTGGGAACGGAGGG 59.290 41.667 0.39 0.00 0.00 4.30
485 766 4.325084 AAAATATTTGGGAACGGAGGGA 57.675 40.909 0.39 0.00 0.00 4.20
486 767 3.577805 AATATTTGGGAACGGAGGGAG 57.422 47.619 0.00 0.00 0.00 4.30
494 775 1.477295 GGAACGGAGGGAGTAGAAGTG 59.523 57.143 0.00 0.00 0.00 3.16
502 783 2.110188 AGGGAGTAGAAGTGAGTGGACA 59.890 50.000 0.00 0.00 0.00 4.02
506 787 3.978687 AGTAGAAGTGAGTGGACAAACG 58.021 45.455 0.00 0.00 0.00 3.60
546 828 3.044059 GCATCCGGACTGTTGCTGC 62.044 63.158 18.42 13.52 32.41 5.25
558 841 2.030371 TGTTGCTGCAATCCAAGTGAA 58.970 42.857 19.11 0.00 0.00 3.18
595 884 6.909550 ACTTTGCCACCTATAAACAATTCA 57.090 33.333 0.00 0.00 0.00 2.57
694 989 5.822132 ATTAGATGACTCTAGCTTGGCAT 57.178 39.130 0.00 0.00 35.43 4.40
696 991 2.104451 AGATGACTCTAGCTTGGCATGG 59.896 50.000 7.06 0.00 0.00 3.66
697 992 0.107508 TGACTCTAGCTTGGCATGGC 60.108 55.000 13.29 13.29 0.00 4.40
698 993 0.107508 GACTCTAGCTTGGCATGGCA 60.108 55.000 19.43 19.43 0.00 4.92
699 994 0.393537 ACTCTAGCTTGGCATGGCAC 60.394 55.000 23.26 11.77 0.00 5.01
700 995 1.434622 CTCTAGCTTGGCATGGCACG 61.435 60.000 23.26 21.41 0.00 5.34
702 997 2.874648 CTAGCTTGGCATGGCACGGA 62.875 60.000 23.26 6.71 0.00 4.69
703 998 4.120331 GCTTGGCATGGCACGGAC 62.120 66.667 23.26 7.83 0.00 4.79
704 999 2.360350 CTTGGCATGGCACGGACT 60.360 61.111 23.26 0.00 0.00 3.85
706 1001 0.464373 CTTGGCATGGCACGGACTAT 60.464 55.000 23.26 0.00 0.00 2.12
707 1002 0.034574 TTGGCATGGCACGGACTATT 60.035 50.000 23.26 0.00 0.00 1.73
708 1003 0.833949 TGGCATGGCACGGACTATTA 59.166 50.000 19.43 0.00 0.00 0.98
709 1004 1.226746 GGCATGGCACGGACTATTAC 58.773 55.000 15.47 0.00 0.00 1.89
710 1005 1.474320 GGCATGGCACGGACTATTACA 60.474 52.381 15.47 0.00 0.00 2.41
711 1006 2.285083 GCATGGCACGGACTATTACAA 58.715 47.619 0.00 0.00 0.00 2.41
712 1007 2.680841 GCATGGCACGGACTATTACAAA 59.319 45.455 0.00 0.00 0.00 2.83
713 1008 3.127895 GCATGGCACGGACTATTACAAAA 59.872 43.478 0.00 0.00 0.00 2.44
714 1009 4.202010 GCATGGCACGGACTATTACAAAAT 60.202 41.667 0.00 0.00 0.00 1.82
715 1010 4.955925 TGGCACGGACTATTACAAAATG 57.044 40.909 0.00 0.00 0.00 2.32
716 1011 4.328536 TGGCACGGACTATTACAAAATGT 58.671 39.130 0.00 0.00 0.00 2.71
717 1012 5.489249 TGGCACGGACTATTACAAAATGTA 58.511 37.500 0.00 0.00 0.00 2.29
718 1013 6.116806 TGGCACGGACTATTACAAAATGTAT 58.883 36.000 0.00 0.00 32.20 2.29
719 1014 6.600032 TGGCACGGACTATTACAAAATGTATT 59.400 34.615 0.00 0.00 32.20 1.89
720 1015 7.121463 TGGCACGGACTATTACAAAATGTATTT 59.879 33.333 0.00 0.00 32.20 1.40
721 1016 7.971722 GGCACGGACTATTACAAAATGTATTTT 59.028 33.333 0.00 0.00 40.37 1.82
722 1017 9.349145 GCACGGACTATTACAAAATGTATTTTT 57.651 29.630 0.04 0.00 37.86 1.94
810 1596 3.542676 ACGCCGGAGACACCAACA 61.543 61.111 13.83 0.00 38.90 3.33
813 1599 1.841663 CGCCGGAGACACCAACAAAG 61.842 60.000 5.05 0.00 38.90 2.77
850 1636 3.552132 TGGCCGCTCTGTTTCAATATA 57.448 42.857 0.00 0.00 0.00 0.86
851 1637 3.879998 TGGCCGCTCTGTTTCAATATAA 58.120 40.909 0.00 0.00 0.00 0.98
853 1639 4.702612 TGGCCGCTCTGTTTCAATATAAAA 59.297 37.500 0.00 0.00 0.00 1.52
856 1642 5.687285 GCCGCTCTGTTTCAATATAAAATGG 59.313 40.000 0.00 0.00 0.00 3.16
857 1643 5.687285 CCGCTCTGTTTCAATATAAAATGGC 59.313 40.000 0.00 0.00 0.00 4.40
858 1644 6.264832 CGCTCTGTTTCAATATAAAATGGCA 58.735 36.000 0.00 0.00 0.00 4.92
861 1647 7.170320 GCTCTGTTTCAATATAAAATGGCATGG 59.830 37.037 0.00 0.00 0.00 3.66
862 1648 6.985645 TCTGTTTCAATATAAAATGGCATGGC 59.014 34.615 13.29 13.29 0.00 4.40
872 1658 2.592861 GGCATGGCCGATCAGACC 60.593 66.667 8.35 0.00 39.62 3.85
874 1660 2.501128 CATGGCCGATCAGACCGT 59.499 61.111 0.00 0.00 0.00 4.83
901 3072 3.060611 CCCCTCCCCACCTTTATATGAA 58.939 50.000 0.00 0.00 0.00 2.57
977 3155 4.178255 CGCACGCATCGACACGAC 62.178 66.667 15.07 6.34 39.18 4.34
978 3156 4.178255 GCACGCATCGACACGACG 62.178 66.667 15.07 4.59 39.18 5.12
979 3157 2.799502 CACGCATCGACACGACGT 60.800 61.111 15.07 0.00 38.66 4.34
980 3158 2.799502 ACGCATCGACACGACGTG 60.800 61.111 25.72 25.72 37.25 4.49
981 3159 4.178255 CGCATCGACACGACGTGC 62.178 66.667 27.11 18.09 39.18 5.34
992 3170 4.961511 GACGTGCGTGCCCAGTCA 62.962 66.667 0.67 0.00 32.57 3.41
1149 3336 2.210116 GTGCTCAAGGTCTTCGACAAA 58.790 47.619 0.00 0.00 33.68 2.83
1452 3639 2.678934 TACCGCGACCTCAAGCCT 60.679 61.111 8.23 0.00 0.00 4.58
1467 3654 0.612174 AGCCTGAGAACGTGCTCCTA 60.612 55.000 21.10 2.01 33.95 2.94
1851 4038 1.540707 GAGAGGTCCTTCTCGTTCGTT 59.459 52.381 0.00 0.00 38.71 3.85
2071 4258 0.684805 GGACCTCACCGACCTCATCT 60.685 60.000 0.00 0.00 0.00 2.90
2085 4272 4.521062 ATCTCGCGCCTGCTGGAC 62.521 66.667 14.77 3.37 39.65 4.02
2091 4278 2.270205 CGCCTGCTGGACAAGGAT 59.730 61.111 14.77 0.00 34.57 3.24
2214 4401 4.853142 TACATCCCTCCGCCGGCT 62.853 66.667 26.68 4.30 0.00 5.52
2283 4470 3.160585 CTTCACCAGCCTCCACCA 58.839 61.111 0.00 0.00 0.00 4.17
2343 4531 2.595536 ACGTTCGATCGTTATTTCACCG 59.404 45.455 15.44 0.29 41.37 4.94
2357 4545 2.851263 TCACCGGCTATGTCAGTTTT 57.149 45.000 0.00 0.00 0.00 2.43
2358 4546 3.965379 TCACCGGCTATGTCAGTTTTA 57.035 42.857 0.00 0.00 0.00 1.52
2359 4547 3.592059 TCACCGGCTATGTCAGTTTTAC 58.408 45.455 0.00 0.00 0.00 2.01
2360 4548 2.676342 CACCGGCTATGTCAGTTTTACC 59.324 50.000 0.00 0.00 0.00 2.85
2361 4549 1.931172 CCGGCTATGTCAGTTTTACCG 59.069 52.381 0.00 0.00 39.11 4.02
2362 4550 2.613691 CGGCTATGTCAGTTTTACCGT 58.386 47.619 0.00 0.00 34.83 4.83
2363 4551 2.997986 CGGCTATGTCAGTTTTACCGTT 59.002 45.455 0.00 0.00 34.83 4.44
2364 4552 3.434299 CGGCTATGTCAGTTTTACCGTTT 59.566 43.478 0.00 0.00 34.83 3.60
2365 4553 4.083696 CGGCTATGTCAGTTTTACCGTTTT 60.084 41.667 0.00 0.00 34.83 2.43
2366 4554 5.151389 GGCTATGTCAGTTTTACCGTTTTG 58.849 41.667 0.00 0.00 0.00 2.44
2367 4555 4.615541 GCTATGTCAGTTTTACCGTTTTGC 59.384 41.667 0.00 0.00 0.00 3.68
2368 4556 4.640789 ATGTCAGTTTTACCGTTTTGCA 57.359 36.364 0.00 0.00 0.00 4.08
2586 4774 3.041874 CGGCTCCATCGCTGATATC 57.958 57.895 0.00 0.00 38.57 1.63
2718 4907 2.079158 ACCACGATAAGACGTCGAAGA 58.921 47.619 10.46 0.00 44.76 2.87
2756 4945 1.524165 CCACGAACCACGAACCCAA 60.524 57.895 0.00 0.00 45.77 4.12
2773 4962 1.931172 CCAACACACGTTTCGTCTTCT 59.069 47.619 0.00 0.00 38.32 2.85
2810 4999 0.322816 ACCACAATCTGCATCCGCTT 60.323 50.000 0.00 0.00 39.64 4.68
2834 5023 0.178903 ACTACCTCCCAAGCTCCACA 60.179 55.000 0.00 0.00 0.00 4.17
2835 5024 0.539051 CTACCTCCCAAGCTCCACAG 59.461 60.000 0.00 0.00 0.00 3.66
2949 5138 5.447778 ACAGACTGATTTCCAGATCCATT 57.552 39.130 10.08 0.00 45.78 3.16
2973 5162 2.170607 CAACCATAGGACCGATGACCTT 59.829 50.000 15.57 2.06 37.78 3.50
3219 5408 1.621814 CCAGGTACGAGAGGAAAACCA 59.378 52.381 0.00 0.00 32.43 3.67
3220 5409 2.038033 CCAGGTACGAGAGGAAAACCAA 59.962 50.000 0.00 0.00 32.43 3.67
3221 5410 3.495453 CCAGGTACGAGAGGAAAACCAAA 60.495 47.826 0.00 0.00 32.43 3.28
3222 5411 3.746492 CAGGTACGAGAGGAAAACCAAAG 59.254 47.826 0.00 0.00 32.43 2.77
3223 5412 3.644738 AGGTACGAGAGGAAAACCAAAGA 59.355 43.478 0.00 0.00 32.43 2.52
3224 5413 3.995048 GGTACGAGAGGAAAACCAAAGAG 59.005 47.826 0.00 0.00 0.00 2.85
3225 5414 3.840124 ACGAGAGGAAAACCAAAGAGT 57.160 42.857 0.00 0.00 0.00 3.24
3226 5415 3.729966 ACGAGAGGAAAACCAAAGAGTC 58.270 45.455 0.00 0.00 0.00 3.36
3227 5416 2.731976 CGAGAGGAAAACCAAAGAGTCG 59.268 50.000 0.00 0.00 0.00 4.18
3228 5417 2.480802 GAGAGGAAAACCAAAGAGTCGC 59.519 50.000 0.00 0.00 0.00 5.19
3229 5418 1.535896 GAGGAAAACCAAAGAGTCGCC 59.464 52.381 0.00 0.00 0.00 5.54
3230 5419 0.237498 GGAAAACCAAAGAGTCGCCG 59.763 55.000 0.00 0.00 0.00 6.46
3231 5420 0.942252 GAAAACCAAAGAGTCGCCGT 59.058 50.000 0.00 0.00 0.00 5.68
3232 5421 1.332686 GAAAACCAAAGAGTCGCCGTT 59.667 47.619 0.00 0.00 0.00 4.44
3233 5422 0.661020 AAACCAAAGAGTCGCCGTTG 59.339 50.000 0.00 0.00 0.00 4.10
3234 5423 1.164041 AACCAAAGAGTCGCCGTTGG 61.164 55.000 13.25 13.25 46.47 3.77
3235 5424 2.325082 CCAAAGAGTCGCCGTTGGG 61.325 63.158 9.02 0.00 40.46 4.12
3236 5425 1.597027 CAAAGAGTCGCCGTTGGGT 60.597 57.895 0.00 0.00 34.97 4.51
3237 5426 1.147600 AAAGAGTCGCCGTTGGGTT 59.852 52.632 0.00 0.00 34.97 4.11
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 4.224406 CCTCGATAGGACGTGTCGTACG 62.224 59.091 9.53 9.53 46.41 3.67
29 30 2.642124 CTCGATAGGACGTGTCGTAC 57.358 55.000 12.91 0.00 41.37 3.67
142 143 2.756760 ACAAGGCATCAATCATGTGACC 59.243 45.455 0.00 0.00 34.56 4.02
247 478 0.405198 TGGAGCCCAAGAGCATTCAA 59.595 50.000 0.00 0.00 34.23 2.69
248 479 0.322816 GTGGAGCCCAAGAGCATTCA 60.323 55.000 0.00 0.00 34.18 2.57
249 480 1.372087 CGTGGAGCCCAAGAGCATTC 61.372 60.000 1.83 0.00 35.05 2.67
250 481 1.377725 CGTGGAGCCCAAGAGCATT 60.378 57.895 1.83 0.00 35.05 3.56
274 555 5.063180 TGATGCAGATGAATTGTTGGAAC 57.937 39.130 0.00 0.00 0.00 3.62
298 579 5.453648 ACGTGCGCAAAAATATTTAGACAA 58.546 33.333 14.00 0.00 0.00 3.18
302 583 8.669801 CAGTAATACGTGCGCAAAAATATTTAG 58.330 33.333 14.00 4.27 0.00 1.85
305 586 5.968848 CCAGTAATACGTGCGCAAAAATATT 59.031 36.000 14.00 15.58 0.00 1.28
312 593 0.390603 AGCCAGTAATACGTGCGCAA 60.391 50.000 14.00 0.00 0.00 4.85
316 597 0.179119 ACGGAGCCAGTAATACGTGC 60.179 55.000 0.00 0.00 32.90 5.34
319 600 5.783100 TTAAAAACGGAGCCAGTAATACG 57.217 39.130 0.00 0.00 0.00 3.06
323 604 8.578151 ACAAATATTTAAAAACGGAGCCAGTAA 58.422 29.630 0.00 0.00 0.00 2.24
324 605 8.113173 ACAAATATTTAAAAACGGAGCCAGTA 57.887 30.769 0.00 0.00 0.00 2.74
326 607 7.312899 AGACAAATATTTAAAAACGGAGCCAG 58.687 34.615 0.00 0.00 0.00 4.85
327 608 7.222000 AGACAAATATTTAAAAACGGAGCCA 57.778 32.000 0.00 0.00 0.00 4.75
328 609 8.528917 AAAGACAAATATTTAAAAACGGAGCC 57.471 30.769 0.00 0.00 0.00 4.70
329 610 9.406828 AGAAAGACAAATATTTAAAAACGGAGC 57.593 29.630 0.00 0.00 0.00 4.70
345 626 9.396022 ACTTGTTGAAATCTCTAGAAAGACAAA 57.604 29.630 0.00 0.00 0.00 2.83
346 627 8.964476 ACTTGTTGAAATCTCTAGAAAGACAA 57.036 30.769 0.00 0.00 0.00 3.18
360 641 9.893305 GCTTTGTATGTAGTTACTTGTTGAAAT 57.107 29.630 0.00 0.00 0.00 2.17
361 642 8.894731 TGCTTTGTATGTAGTTACTTGTTGAAA 58.105 29.630 0.00 0.00 0.00 2.69
362 643 8.439993 TGCTTTGTATGTAGTTACTTGTTGAA 57.560 30.769 0.00 0.00 0.00 2.69
363 644 8.439993 TTGCTTTGTATGTAGTTACTTGTTGA 57.560 30.769 0.00 0.00 0.00 3.18
364 645 9.509855 TTTTGCTTTGTATGTAGTTACTTGTTG 57.490 29.630 0.00 0.00 0.00 3.33
366 647 9.677567 CATTTTGCTTTGTATGTAGTTACTTGT 57.322 29.630 0.00 0.00 0.00 3.16
367 648 9.891828 TCATTTTGCTTTGTATGTAGTTACTTG 57.108 29.630 0.00 0.00 0.00 3.16
369 650 9.284968 ACTCATTTTGCTTTGTATGTAGTTACT 57.715 29.630 0.00 0.00 0.00 2.24
380 661 8.850156 AGTGTAGATTTACTCATTTTGCTTTGT 58.150 29.630 0.00 0.00 0.00 2.83
381 662 9.683069 AAGTGTAGATTTACTCATTTTGCTTTG 57.317 29.630 0.00 0.00 0.00 2.77
455 736 9.250246 TCCGTTCCCAAATATTTTTCTTTCTAT 57.750 29.630 0.00 0.00 0.00 1.98
456 737 8.638629 TCCGTTCCCAAATATTTTTCTTTCTA 57.361 30.769 0.00 0.00 0.00 2.10
457 738 7.309805 CCTCCGTTCCCAAATATTTTTCTTTCT 60.310 37.037 0.00 0.00 0.00 2.52
458 739 6.811665 CCTCCGTTCCCAAATATTTTTCTTTC 59.188 38.462 0.00 0.00 0.00 2.62
459 740 6.295632 CCCTCCGTTCCCAAATATTTTTCTTT 60.296 38.462 0.00 0.00 0.00 2.52
460 741 5.186992 CCCTCCGTTCCCAAATATTTTTCTT 59.813 40.000 0.00 0.00 0.00 2.52
461 742 4.709886 CCCTCCGTTCCCAAATATTTTTCT 59.290 41.667 0.00 0.00 0.00 2.52
462 743 4.707934 TCCCTCCGTTCCCAAATATTTTTC 59.292 41.667 0.00 0.00 0.00 2.29
463 744 4.679331 TCCCTCCGTTCCCAAATATTTTT 58.321 39.130 0.00 0.00 0.00 1.94
464 745 4.264217 ACTCCCTCCGTTCCCAAATATTTT 60.264 41.667 0.00 0.00 0.00 1.82
465 746 3.268595 ACTCCCTCCGTTCCCAAATATTT 59.731 43.478 0.00 0.00 0.00 1.40
466 747 2.850568 ACTCCCTCCGTTCCCAAATATT 59.149 45.455 0.00 0.00 0.00 1.28
467 748 2.488836 ACTCCCTCCGTTCCCAAATAT 58.511 47.619 0.00 0.00 0.00 1.28
468 749 1.961133 ACTCCCTCCGTTCCCAAATA 58.039 50.000 0.00 0.00 0.00 1.40
469 750 1.838077 CTACTCCCTCCGTTCCCAAAT 59.162 52.381 0.00 0.00 0.00 2.32
470 751 1.203212 TCTACTCCCTCCGTTCCCAAA 60.203 52.381 0.00 0.00 0.00 3.28
471 752 0.410663 TCTACTCCCTCCGTTCCCAA 59.589 55.000 0.00 0.00 0.00 4.12
472 753 0.410663 TTCTACTCCCTCCGTTCCCA 59.589 55.000 0.00 0.00 0.00 4.37
473 754 1.112950 CTTCTACTCCCTCCGTTCCC 58.887 60.000 0.00 0.00 0.00 3.97
474 755 1.477295 CACTTCTACTCCCTCCGTTCC 59.523 57.143 0.00 0.00 0.00 3.62
475 756 2.424246 CTCACTTCTACTCCCTCCGTTC 59.576 54.545 0.00 0.00 0.00 3.95
476 757 2.225066 ACTCACTTCTACTCCCTCCGTT 60.225 50.000 0.00 0.00 0.00 4.44
477 758 1.355043 ACTCACTTCTACTCCCTCCGT 59.645 52.381 0.00 0.00 0.00 4.69
478 759 1.746220 CACTCACTTCTACTCCCTCCG 59.254 57.143 0.00 0.00 0.00 4.63
479 760 2.104170 CCACTCACTTCTACTCCCTCC 58.896 57.143 0.00 0.00 0.00 4.30
480 761 2.756207 GTCCACTCACTTCTACTCCCTC 59.244 54.545 0.00 0.00 0.00 4.30
481 762 2.110188 TGTCCACTCACTTCTACTCCCT 59.890 50.000 0.00 0.00 0.00 4.20
482 763 2.526432 TGTCCACTCACTTCTACTCCC 58.474 52.381 0.00 0.00 0.00 4.30
483 764 4.308265 GTTTGTCCACTCACTTCTACTCC 58.692 47.826 0.00 0.00 0.00 3.85
484 765 3.982058 CGTTTGTCCACTCACTTCTACTC 59.018 47.826 0.00 0.00 0.00 2.59
485 766 3.243771 CCGTTTGTCCACTCACTTCTACT 60.244 47.826 0.00 0.00 0.00 2.57
486 767 3.057734 CCGTTTGTCCACTCACTTCTAC 58.942 50.000 0.00 0.00 0.00 2.59
494 775 3.723348 GGCGCCGTTTGTCCACTC 61.723 66.667 12.58 0.00 0.00 3.51
502 783 2.835895 AGGGTTTTGGCGCCGTTT 60.836 55.556 23.90 0.00 0.00 3.60
546 828 1.815003 GGCCAGTCTTCACTTGGATTG 59.185 52.381 0.00 0.00 0.00 2.67
558 841 0.963962 CAAAGTTGCATGGCCAGTCT 59.036 50.000 13.05 1.70 0.00 3.24
580 863 8.936864 CGAGAGAAGTTTGAATTGTTTATAGGT 58.063 33.333 0.00 0.00 0.00 3.08
677 966 1.476471 GCCATGCCAAGCTAGAGTCAT 60.476 52.381 0.00 0.00 0.00 3.06
678 967 0.107508 GCCATGCCAAGCTAGAGTCA 60.108 55.000 0.00 0.00 0.00 3.41
694 989 4.328536 ACATTTTGTAATAGTCCGTGCCA 58.671 39.130 0.00 0.00 0.00 4.92
696 991 8.905103 AAAATACATTTTGTAATAGTCCGTGC 57.095 30.769 0.00 0.00 38.46 5.34
728 1023 9.085645 AGTTTTATCCCCGAGAAAGTTATTTTT 57.914 29.630 0.00 0.00 0.00 1.94
729 1024 8.520351 CAGTTTTATCCCCGAGAAAGTTATTTT 58.480 33.333 0.00 0.00 0.00 1.82
730 1025 7.886446 TCAGTTTTATCCCCGAGAAAGTTATTT 59.114 33.333 0.00 0.00 0.00 1.40
731 1026 7.336176 GTCAGTTTTATCCCCGAGAAAGTTATT 59.664 37.037 0.00 0.00 0.00 1.40
732 1027 6.822170 GTCAGTTTTATCCCCGAGAAAGTTAT 59.178 38.462 0.00 0.00 0.00 1.89
753 1048 2.350293 CGTCAGTCAGTCAGTCAGTCAG 60.350 54.545 0.00 0.00 0.00 3.51
810 1596 1.896220 TGCCATTTCGACAGAGCTTT 58.104 45.000 0.00 0.00 0.00 3.51
813 1599 0.379669 CCATGCCATTTCGACAGAGC 59.620 55.000 0.00 0.00 0.00 4.09
856 1642 2.969238 CGGTCTGATCGGCCATGC 60.969 66.667 2.24 0.00 0.00 4.06
857 1643 1.884464 CACGGTCTGATCGGCCATG 60.884 63.158 15.53 0.00 0.00 3.66
858 1644 2.501128 CACGGTCTGATCGGCCAT 59.499 61.111 15.53 0.00 0.00 4.40
901 3072 4.681978 GGGCTTGCGAGGACGTGT 62.682 66.667 2.37 0.00 41.98 4.49
961 3139 4.178255 CGTCGTGTCGATGCGTGC 62.178 66.667 10.51 5.58 38.42 5.34
962 3140 2.799502 ACGTCGTGTCGATGCGTG 60.800 61.111 10.60 7.79 45.42 5.34
963 3141 2.799502 CACGTCGTGTCGATGCGT 60.800 61.111 17.30 6.63 45.42 5.24
964 3142 4.178255 GCACGTCGTGTCGATGCG 62.178 66.667 25.18 5.41 45.42 4.73
975 3153 4.961511 TGACTGGGCACGCACGTC 62.962 66.667 8.63 8.63 0.00 4.34
982 3160 3.188786 GATCGCGTGACTGGGCAC 61.189 66.667 5.77 0.00 35.46 5.01
983 3161 3.017771 ATGATCGCGTGACTGGGCA 62.018 57.895 5.77 0.00 0.00 5.36
984 3162 2.202932 ATGATCGCGTGACTGGGC 60.203 61.111 5.77 0.00 0.00 5.36
985 3163 2.528743 GCATGATCGCGTGACTGGG 61.529 63.158 5.77 0.00 32.63 4.45
986 3164 1.759293 CTGCATGATCGCGTGACTGG 61.759 60.000 5.77 0.00 32.63 4.00
987 3165 1.634753 CTGCATGATCGCGTGACTG 59.365 57.895 5.77 0.40 32.63 3.51
988 3166 2.169789 GCTGCATGATCGCGTGACT 61.170 57.895 5.77 0.00 32.63 3.41
989 3167 2.322422 GCTGCATGATCGCGTGAC 59.678 61.111 5.77 0.00 32.63 3.67
990 3168 2.891936 GGCTGCATGATCGCGTGA 60.892 61.111 5.77 0.00 32.63 4.35
991 3169 3.945434 GGGCTGCATGATCGCGTG 61.945 66.667 5.77 0.00 33.35 5.34
1024 3202 1.000283 GCCGAGGTCTATGTCCATCAG 60.000 57.143 0.00 0.00 0.00 2.90
1124 3311 1.068472 CGAAGACCTTGAGCACGTACT 60.068 52.381 0.00 0.00 0.00 2.73
1434 3621 2.202756 GGCTTGAGGTCGCGGTAG 60.203 66.667 6.13 0.00 0.00 3.18
1452 3639 1.211969 GCGTAGGAGCACGTTCTCA 59.788 57.895 16.98 0.00 43.79 3.27
1611 3798 3.379445 AGGTGGCGGTACTGTCGG 61.379 66.667 1.06 0.00 0.00 4.79
1677 3864 2.450502 AGGTTGTGGGGCTCCTGT 60.451 61.111 3.07 0.00 0.00 4.00
1851 4038 2.282674 ACGTACTCCTCCGTGCCA 60.283 61.111 0.00 0.00 35.69 4.92
2085 4272 1.227380 CCTTCTCGCGGGATCCTTG 60.227 63.158 10.79 5.92 0.00 3.61
2214 4401 1.875262 GCACGCCACAATGTCATCA 59.125 52.632 0.00 0.00 0.00 3.07
2295 4482 2.125350 GGCAAGGACTCTGGCGAG 60.125 66.667 5.08 5.08 40.87 5.03
2343 4531 5.151389 CAAAACGGTAAAACTGACATAGCC 58.849 41.667 0.00 0.00 0.00 3.93
2376 4564 3.173668 TGAGACACGTATTACCATGCC 57.826 47.619 0.00 0.00 0.00 4.40
2479 4667 1.301165 GGTGACGGGCGTTAGTGTT 60.301 57.895 0.00 0.00 0.00 3.32
2586 4774 2.747855 GGAGGTCCGCAAAGCTGG 60.748 66.667 0.00 0.00 0.00 4.85
2633 4821 1.415374 CGGTCTGATTCGTTCAACGT 58.585 50.000 10.31 0.00 43.14 3.99
2712 4901 3.618997 GCAGGTATGGTTTCCTTCTTCGA 60.619 47.826 0.00 0.00 30.91 3.71
2718 4907 2.358195 GGATGGCAGGTATGGTTTCCTT 60.358 50.000 0.00 0.00 30.91 3.36
2756 4945 3.976793 TCTAGAAGACGAAACGTGTGT 57.023 42.857 0.62 0.00 41.37 3.72
2773 4962 1.333931 GGTCTGCATCGACGACATCTA 59.666 52.381 0.00 0.00 34.75 1.98
2834 5023 3.044305 GTTTGCTCCAGCGTCGCT 61.044 61.111 15.47 15.47 45.83 4.93
2835 5024 4.430423 CGTTTGCTCCAGCGTCGC 62.430 66.667 9.80 9.80 45.83 5.19
2881 5070 2.584608 CATCCTCGTGGTGGACCC 59.415 66.667 2.99 0.00 36.30 4.46
2949 5138 1.128200 CATCGGTCCTATGGTTGGGA 58.872 55.000 0.00 0.00 0.00 4.37
2973 5162 5.768980 ATTCTTCAGATCCTTTCCTGACA 57.231 39.130 0.00 0.00 38.95 3.58
3115 5304 2.125673 CCGGCGACTTCGGTCATT 60.126 61.111 9.30 0.00 44.65 2.57
3219 5408 0.464916 AAACCCAACGGCGACTCTTT 60.465 50.000 16.62 1.06 0.00 2.52
3220 5409 0.464916 AAAACCCAACGGCGACTCTT 60.465 50.000 16.62 0.00 0.00 2.85
3221 5410 0.393820 TAAAACCCAACGGCGACTCT 59.606 50.000 16.62 0.00 0.00 3.24
3222 5411 0.514255 GTAAAACCCAACGGCGACTC 59.486 55.000 16.62 0.00 0.00 3.36
3223 5412 0.886043 GGTAAAACCCAACGGCGACT 60.886 55.000 16.62 0.00 30.04 4.18
3224 5413 1.575922 GGTAAAACCCAACGGCGAC 59.424 57.895 16.62 0.00 30.04 5.19
3225 5414 1.960250 CGGTAAAACCCAACGGCGA 60.960 57.895 16.62 0.00 33.75 5.54
3226 5415 1.784036 AACGGTAAAACCCAACGGCG 61.784 55.000 4.80 4.80 33.75 6.46
3227 5416 0.385029 AAACGGTAAAACCCAACGGC 59.615 50.000 0.00 0.00 33.75 5.68
3228 5417 2.461903 CAAAACGGTAAAACCCAACGG 58.538 47.619 0.00 0.00 33.75 4.44
3229 5418 1.853510 GCAAAACGGTAAAACCCAACG 59.146 47.619 0.00 0.00 33.75 4.10
3230 5419 2.604011 GTGCAAAACGGTAAAACCCAAC 59.396 45.455 0.00 0.00 33.75 3.77
3231 5420 2.418334 GGTGCAAAACGGTAAAACCCAA 60.418 45.455 0.00 0.00 33.75 4.12
3232 5421 1.136500 GGTGCAAAACGGTAAAACCCA 59.864 47.619 0.00 0.00 33.75 4.51
3233 5422 1.409790 AGGTGCAAAACGGTAAAACCC 59.590 47.619 0.00 0.00 33.75 4.11
3234 5423 2.875087 AGGTGCAAAACGGTAAAACC 57.125 45.000 0.00 0.00 34.05 3.27
3235 5424 5.007921 TCTCTAAGGTGCAAAACGGTAAAAC 59.992 40.000 0.00 0.00 0.00 2.43
3236 5425 5.124645 TCTCTAAGGTGCAAAACGGTAAAA 58.875 37.500 0.00 0.00 0.00 1.52
3237 5426 4.706035 TCTCTAAGGTGCAAAACGGTAAA 58.294 39.130 0.00 0.00 0.00 2.01
3278 5467 7.255001 CGACAAGAACAATACAAGTAAACCCTT 60.255 37.037 0.00 0.00 0.00 3.95


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

AutoCloner maintained by Alex Coulton.