Multiple sequence alignment - TraesCS2B01G226500

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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 TraesCS2B01G226500 chr2B 100.000 3170 0 0 1 3170 217274682 217271513 0.000000e+00 5854
1 TraesCS2B01G226500 chr1B 91.904 2285 173 8 885 3164 270324035 270326312 0.000000e+00 3184
2 TraesCS2B01G226500 chr6B 91.000 2289 202 4 885 3170 152385471 152383184 0.000000e+00 3083
3 TraesCS2B01G226500 chr7D 89.078 2289 246 4 885 3170 154941713 154939426 0.000000e+00 2839
4 TraesCS2B01G226500 chr7D 83.473 956 150 8 2219 3170 609173506 609174457 0.000000e+00 883
5 TraesCS2B01G226500 chr4D 88.729 2289 246 7 885 3170 486551384 486553663 0.000000e+00 2787
6 TraesCS2B01G226500 chr7A 86.344 2292 300 12 885 3170 580559189 580561473 0.000000e+00 2486
7 TraesCS2B01G226500 chr5D 83.399 2295 365 15 885 3170 7615689 7613402 0.000000e+00 2113
8 TraesCS2B01G226500 chr5A 81.628 2297 403 19 885 3170 608867853 608865565 0.000000e+00 1886
9 TraesCS2B01G226500 chr3A 81.908 1310 230 7 887 2191 21358654 21357347 0.000000e+00 1099
10 TraesCS2B01G226500 chr3A 83.489 963 154 5 2210 3170 21356988 21356029 0.000000e+00 893
11 TraesCS2B01G226500 chr3B 78.484 1464 273 37 887 2325 586751894 586753340 0.000000e+00 920
12 TraesCS2B01G226500 chr3B 74.203 690 153 19 2131 2807 790653372 790652695 6.740000e-67 265
13 TraesCS2B01G226500 chr2A 85.897 546 28 19 1 527 171848972 171848457 1.290000e-148 536
14 TraesCS2B01G226500 chr2A 91.030 301 15 9 554 844 171848461 171848163 2.290000e-106 396
15 TraesCS2B01G226500 chr2D 94.752 343 16 2 532 873 160329279 160328938 1.670000e-147 532
16 TraesCS2B01G226500 chr2D 89.222 334 24 10 7 338 160343185 160342862 1.060000e-109 407
17 TraesCS2B01G226500 chr2D 90.116 172 7 2 373 534 160342864 160342693 6.890000e-52 215


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 TraesCS2B01G226500 chr2B 217271513 217274682 3169 True 5854 5854 100.0000 1 3170 1 chr2B.!!$R1 3169
1 TraesCS2B01G226500 chr1B 270324035 270326312 2277 False 3184 3184 91.9040 885 3164 1 chr1B.!!$F1 2279
2 TraesCS2B01G226500 chr6B 152383184 152385471 2287 True 3083 3083 91.0000 885 3170 1 chr6B.!!$R1 2285
3 TraesCS2B01G226500 chr7D 154939426 154941713 2287 True 2839 2839 89.0780 885 3170 1 chr7D.!!$R1 2285
4 TraesCS2B01G226500 chr7D 609173506 609174457 951 False 883 883 83.4730 2219 3170 1 chr7D.!!$F1 951
5 TraesCS2B01G226500 chr4D 486551384 486553663 2279 False 2787 2787 88.7290 885 3170 1 chr4D.!!$F1 2285
6 TraesCS2B01G226500 chr7A 580559189 580561473 2284 False 2486 2486 86.3440 885 3170 1 chr7A.!!$F1 2285
7 TraesCS2B01G226500 chr5D 7613402 7615689 2287 True 2113 2113 83.3990 885 3170 1 chr5D.!!$R1 2285
8 TraesCS2B01G226500 chr5A 608865565 608867853 2288 True 1886 1886 81.6280 885 3170 1 chr5A.!!$R1 2285
9 TraesCS2B01G226500 chr3A 21356029 21358654 2625 True 996 1099 82.6985 887 3170 2 chr3A.!!$R1 2283
10 TraesCS2B01G226500 chr3B 586751894 586753340 1446 False 920 920 78.4840 887 2325 1 chr3B.!!$F1 1438
11 TraesCS2B01G226500 chr3B 790652695 790653372 677 True 265 265 74.2030 2131 2807 1 chr3B.!!$R1 676
12 TraesCS2B01G226500 chr2A 171848163 171848972 809 True 466 536 88.4635 1 844 2 chr2A.!!$R1 843

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
455 467 0.035056 ACCGGGCCATCTTCTTTCTG 60.035 55.0 6.32 0.00 0.0 3.02 F
1667 1700 0.318120 AAATTGGCCCGTTTCTGCAG 59.682 50.0 7.63 7.63 0.0 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2073 2108 0.040958 GTTTGGAGCTTGACGTGCTG 60.041 55.0 3.28 0.0 41.3 4.41 R
2615 2993 0.167908 GTGATTCCGCACGCATTGAA 59.832 50.0 0.00 0.0 0.0 2.69 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
35 36 2.428890 AGAGAAGCGAAGAACGGATCAT 59.571 45.455 0.00 0.00 42.83 2.45
61 62 2.167487 AGCGGGCAAGAAAAGAAAACAA 59.833 40.909 0.00 0.00 0.00 2.83
62 63 2.539688 GCGGGCAAGAAAAGAAAACAAG 59.460 45.455 0.00 0.00 0.00 3.16
87 88 0.875059 CGAGGACAGAAAAAGGGCAC 59.125 55.000 0.00 0.00 0.00 5.01
271 278 2.654877 GAAACGAGAGCGACCCCA 59.345 61.111 0.00 0.00 41.64 4.96
272 279 1.737008 GAAACGAGAGCGACCCCAC 60.737 63.158 0.00 0.00 41.64 4.61
273 280 2.430382 GAAACGAGAGCGACCCCACA 62.430 60.000 0.00 0.00 41.64 4.17
274 281 2.035237 AAACGAGAGCGACCCCACAA 62.035 55.000 0.00 0.00 41.64 3.33
275 282 2.125912 CGAGAGCGACCCCACAAG 60.126 66.667 0.00 0.00 40.82 3.16
276 283 2.435059 GAGAGCGACCCCACAAGC 60.435 66.667 0.00 0.00 0.00 4.01
277 284 2.925170 AGAGCGACCCCACAAGCT 60.925 61.111 0.00 0.00 43.33 3.74
279 286 3.241530 AGCGACCCCACAAGCTCA 61.242 61.111 0.00 0.00 34.48 4.26
295 302 1.919918 CTCAAGCTCCATGAGACGAC 58.080 55.000 7.99 0.00 45.74 4.34
296 303 1.203287 CTCAAGCTCCATGAGACGACA 59.797 52.381 7.99 0.00 45.74 4.35
297 304 1.618343 TCAAGCTCCATGAGACGACAA 59.382 47.619 0.00 0.00 0.00 3.18
298 305 1.728971 CAAGCTCCATGAGACGACAAC 59.271 52.381 0.00 0.00 0.00 3.32
299 306 0.969149 AGCTCCATGAGACGACAACA 59.031 50.000 0.00 0.00 0.00 3.33
306 313 1.300697 GAGACGACAACACGGGCTT 60.301 57.895 0.00 0.00 37.61 4.35
307 314 1.557443 GAGACGACAACACGGGCTTG 61.557 60.000 0.00 0.00 37.61 4.01
309 316 4.025401 CGACAACACGGGCTTGGC 62.025 66.667 5.25 1.18 0.00 4.52
336 343 1.432270 CGCGCTGGGAAGAAAGGATC 61.432 60.000 5.56 0.00 0.00 3.36
342 349 1.095600 GGGAAGAAAGGATCGTTGCC 58.904 55.000 0.58 1.90 0.00 4.52
354 361 1.594293 CGTTGCCTGGACGTGAACT 60.594 57.895 0.00 0.00 35.88 3.01
365 372 1.200484 GACGTGAACTCTCCTCCTGTC 59.800 57.143 0.00 0.00 0.00 3.51
366 373 0.528470 CGTGAACTCTCCTCCTGTCC 59.472 60.000 0.00 0.00 0.00 4.02
367 374 0.899019 GTGAACTCTCCTCCTGTCCC 59.101 60.000 0.00 0.00 0.00 4.46
368 375 0.612174 TGAACTCTCCTCCTGTCCCG 60.612 60.000 0.00 0.00 0.00 5.14
369 376 0.612453 GAACTCTCCTCCTGTCCCGT 60.612 60.000 0.00 0.00 0.00 5.28
371 378 2.037367 TCTCCTCCTGTCCCGTGG 59.963 66.667 0.00 0.00 0.00 4.94
372 379 2.283966 CTCCTCCTGTCCCGTGGT 60.284 66.667 0.00 0.00 0.00 4.16
373 380 2.283676 TCCTCCTGTCCCGTGGTC 60.284 66.667 0.00 0.00 0.00 4.02
374 381 3.760035 CCTCCTGTCCCGTGGTCG 61.760 72.222 0.00 0.00 0.00 4.79
452 464 1.303282 GGACCGGGCCATCTTCTTT 59.697 57.895 25.88 0.00 0.00 2.52
453 465 0.748367 GGACCGGGCCATCTTCTTTC 60.748 60.000 25.88 0.00 0.00 2.62
454 466 0.253327 GACCGGGCCATCTTCTTTCT 59.747 55.000 6.32 0.00 0.00 2.52
455 467 0.035056 ACCGGGCCATCTTCTTTCTG 60.035 55.000 6.32 0.00 0.00 3.02
479 499 8.277490 TGTTAATTAATTATTACCGTGCCACA 57.723 30.769 8.70 3.87 0.00 4.17
482 502 1.658994 ATTATTACCGTGCCACACCG 58.341 50.000 0.00 0.00 0.00 4.94
527 547 2.306805 TGAGACTGATGGATGGCAACTT 59.693 45.455 0.00 0.00 37.61 2.66
528 548 3.519107 TGAGACTGATGGATGGCAACTTA 59.481 43.478 0.00 0.00 37.61 2.24
530 550 4.458397 AGACTGATGGATGGCAACTTATG 58.542 43.478 0.00 0.00 37.61 1.90
531 551 4.080129 AGACTGATGGATGGCAACTTATGT 60.080 41.667 0.00 0.00 37.61 2.29
532 552 4.603131 ACTGATGGATGGCAACTTATGTT 58.397 39.130 0.00 0.00 36.75 2.71
533 553 5.754782 ACTGATGGATGGCAACTTATGTTA 58.245 37.500 0.00 0.00 34.60 2.41
534 554 5.590259 ACTGATGGATGGCAACTTATGTTAC 59.410 40.000 0.00 0.00 34.60 2.50
535 555 4.574421 TGATGGATGGCAACTTATGTTACG 59.426 41.667 0.00 0.00 34.60 3.18
536 556 3.945346 TGGATGGCAACTTATGTTACGT 58.055 40.909 0.00 0.00 34.60 3.57
537 557 3.936453 TGGATGGCAACTTATGTTACGTC 59.064 43.478 0.00 2.37 34.60 4.34
539 559 2.339418 TGGCAACTTATGTTACGTCGG 58.661 47.619 0.00 0.00 34.60 4.79
540 560 2.288948 TGGCAACTTATGTTACGTCGGT 60.289 45.455 0.00 0.00 34.60 4.69
541 561 2.346545 GGCAACTTATGTTACGTCGGTC 59.653 50.000 0.00 0.00 34.60 4.79
542 562 2.988493 GCAACTTATGTTACGTCGGTCA 59.012 45.455 0.00 0.00 34.60 4.02
544 564 3.221964 ACTTATGTTACGTCGGTCACC 57.778 47.619 0.00 0.00 0.00 4.02
545 565 3.914514 AACTTATGTTACGTCGGTCACCG 60.915 47.826 11.06 11.06 40.65 4.94
546 566 6.101050 AACTTATGTTACGTCGGTCACCGA 62.101 45.833 17.12 17.12 43.51 4.69
547 567 7.818279 AACTTATGTTACGTCGGTCACCGAG 62.818 48.000 22.32 16.28 45.04 4.63
556 576 3.544615 GGTCACCGAGCAAAACAAC 57.455 52.632 0.00 0.00 0.00 3.32
557 577 1.021968 GGTCACCGAGCAAAACAACT 58.978 50.000 0.00 0.00 0.00 3.16
558 578 1.268539 GGTCACCGAGCAAAACAACTG 60.269 52.381 0.00 0.00 0.00 3.16
559 579 0.380378 TCACCGAGCAAAACAACTGC 59.620 50.000 0.00 0.00 40.24 4.40
566 586 1.787012 GCAAAACAACTGCTCCATGG 58.213 50.000 4.97 4.97 36.84 3.66
567 587 1.606224 GCAAAACAACTGCTCCATGGG 60.606 52.381 13.02 3.69 36.84 4.00
568 588 1.962807 CAAAACAACTGCTCCATGGGA 59.037 47.619 13.02 0.00 0.00 4.37
569 589 1.620822 AAACAACTGCTCCATGGGAC 58.379 50.000 13.02 4.83 0.00 4.46
570 590 0.606401 AACAACTGCTCCATGGGACG 60.606 55.000 13.02 1.91 0.00 4.79
571 591 1.746615 CAACTGCTCCATGGGACGG 60.747 63.158 13.02 11.84 0.00 4.79
572 592 1.918293 AACTGCTCCATGGGACGGA 60.918 57.895 13.02 1.19 0.00 4.69
573 593 2.185310 AACTGCTCCATGGGACGGAC 62.185 60.000 13.02 0.00 0.00 4.79
574 594 3.723235 CTGCTCCATGGGACGGACG 62.723 68.421 13.02 0.00 0.00 4.79
575 595 3.771160 GCTCCATGGGACGGACGT 61.771 66.667 13.02 0.00 0.00 4.34
667 688 0.454600 GGAGACCGTGTATCTTCGCA 59.545 55.000 0.00 0.00 0.00 5.10
681 703 2.099921 TCTTCGCAGTATCTTGCCTCTC 59.900 50.000 0.00 0.00 41.01 3.20
688 710 4.431809 CAGTATCTTGCCTCTCTGTCTTG 58.568 47.826 0.00 0.00 0.00 3.02
689 711 4.159321 CAGTATCTTGCCTCTCTGTCTTGA 59.841 45.833 0.00 0.00 0.00 3.02
690 712 4.961730 AGTATCTTGCCTCTCTGTCTTGAT 59.038 41.667 0.00 0.00 0.00 2.57
691 713 3.883830 TCTTGCCTCTCTGTCTTGATC 57.116 47.619 0.00 0.00 0.00 2.92
705 732 3.873952 GTCTTGATCTGCTGATGGTTACC 59.126 47.826 11.21 0.00 32.19 2.85
715 742 1.073763 TGATGGTTACCTTGTGCTGCT 59.926 47.619 2.07 0.00 0.00 4.24
716 743 1.470098 GATGGTTACCTTGTGCTGCTG 59.530 52.381 2.07 0.00 0.00 4.41
761 788 2.095919 GTGGGTGACGCATGTAAAAGTC 60.096 50.000 5.42 0.00 0.00 3.01
768 796 4.383649 TGACGCATGTAAAAGTCGAGTTAC 59.616 41.667 5.80 6.31 36.49 2.50
801 829 0.390472 CCAAGGAAGGAGCTGTCGTC 60.390 60.000 0.00 0.00 0.00 4.20
809 837 0.955919 GGAGCTGTCGTCCTTTTGGG 60.956 60.000 0.00 0.00 40.87 4.12
844 872 2.354203 GCAGTAAGACCTCAGGTGGAAG 60.354 54.545 0.00 0.00 35.25 3.46
845 873 2.234908 CAGTAAGACCTCAGGTGGAAGG 59.765 54.545 0.00 0.00 35.25 3.46
846 874 1.066071 GTAAGACCTCAGGTGGAAGGC 60.066 57.143 0.00 0.00 35.25 4.35
847 875 1.831652 AAGACCTCAGGTGGAAGGCG 61.832 60.000 0.00 0.00 35.25 5.52
848 876 2.526873 ACCTCAGGTGGAAGGCGT 60.527 61.111 0.00 0.00 32.98 5.68
849 877 2.113243 GACCTCAGGTGGAAGGCGTT 62.113 60.000 0.00 0.00 35.25 4.84
850 878 1.073199 CCTCAGGTGGAAGGCGTTT 59.927 57.895 0.00 0.00 0.00 3.60
851 879 0.537371 CCTCAGGTGGAAGGCGTTTT 60.537 55.000 0.00 0.00 0.00 2.43
852 880 1.318576 CTCAGGTGGAAGGCGTTTTT 58.681 50.000 0.00 0.00 0.00 1.94
876 904 7.991084 TTTACTCAAGCAGTAGTAGTAGTCA 57.009 36.000 0.00 0.00 38.90 3.41
877 905 7.991084 TTACTCAAGCAGTAGTAGTAGTCAA 57.009 36.000 0.00 0.00 38.90 3.18
878 906 6.503589 ACTCAAGCAGTAGTAGTAGTCAAG 57.496 41.667 0.00 0.00 31.37 3.02
879 907 6.239396 ACTCAAGCAGTAGTAGTAGTCAAGA 58.761 40.000 0.00 0.00 31.37 3.02
880 908 6.887545 ACTCAAGCAGTAGTAGTAGTCAAGAT 59.112 38.462 0.00 0.00 31.37 2.40
881 909 8.047911 ACTCAAGCAGTAGTAGTAGTCAAGATA 58.952 37.037 0.00 0.00 31.37 1.98
882 910 8.439993 TCAAGCAGTAGTAGTAGTCAAGATAG 57.560 38.462 0.00 0.00 0.00 2.08
883 911 7.499563 TCAAGCAGTAGTAGTAGTCAAGATAGG 59.500 40.741 0.00 0.00 0.00 2.57
917 945 1.004200 GGGTTTTTCTCCTCGGCGA 60.004 57.895 10.14 10.14 0.00 5.54
942 971 2.063979 AATCGCCCCGAGTCCATCA 61.064 57.895 0.00 0.00 39.91 3.07
973 1003 2.968206 GTACCCGCCGACTCTGTT 59.032 61.111 0.00 0.00 0.00 3.16
986 1018 3.123620 CTGTTGAGCGGGCTCTGC 61.124 66.667 20.27 13.34 43.12 4.26
1089 1121 2.480802 GGAAGAGTTTTTCGACCAGCTC 59.519 50.000 0.00 0.00 0.00 4.09
1275 1308 0.613260 TGAGATTCAGACCGGTTGGG 59.387 55.000 9.42 0.89 40.75 4.12
1353 1386 0.687427 AAGGGCCATGGATTTTCCGG 60.687 55.000 18.40 0.00 40.17 5.14
1398 1431 2.898729 ATGATGGGTTCAGTAGAGCG 57.101 50.000 0.00 0.00 37.89 5.03
1480 1513 4.377841 CCTTCTGCAAAGAGAACATCGTTC 60.378 45.833 9.37 0.00 0.00 3.95
1578 1611 6.656693 GGGTGAGGGTAAATCATGATATTCAG 59.343 42.308 9.04 0.00 0.00 3.02
1667 1700 0.318120 AAATTGGCCCGTTTCTGCAG 59.682 50.000 7.63 7.63 0.00 4.41
1737 1772 4.587584 TCATGATGCAACAAAGCTCAAA 57.412 36.364 0.00 0.00 34.99 2.69
1799 1834 2.159226 GGTCCGATCTGAACAGTGGTAG 60.159 54.545 0.00 0.00 0.00 3.18
1802 1837 2.492088 CCGATCTGAACAGTGGTAGTCA 59.508 50.000 0.00 0.00 0.00 3.41
1809 1844 1.121407 ACAGTGGTAGTCAGGCTGCA 61.121 55.000 10.34 0.00 0.00 4.41
1893 1928 2.178106 AGACCCGGAGACCAGAGATATT 59.822 50.000 0.73 0.00 0.00 1.28
2073 2108 1.080995 CAGCGAGCTCACCAACTAGC 61.081 60.000 15.40 6.19 39.08 3.42
2126 2161 4.083696 CGCTAAGGAAAACGTTACCAATGT 60.084 41.667 21.03 9.66 0.00 2.71
2170 2205 4.467084 ACCGCCGGACGCAATGAT 62.467 61.111 11.71 0.00 41.76 2.45
2227 2602 1.342672 ACAGTTCGGGAGGTGTTGGT 61.343 55.000 0.00 0.00 0.00 3.67
2318 2693 0.696501 AATTACGGTGGAGGCTTGGT 59.303 50.000 0.00 0.00 0.00 3.67
2357 2732 1.527311 GTTGACAGTGACGGAAGAAGC 59.473 52.381 0.00 0.00 0.00 3.86
2358 2733 0.750249 TGACAGTGACGGAAGAAGCA 59.250 50.000 0.00 0.00 0.00 3.91
2399 2774 0.667487 ATGAGTCGTTGGCTGTGACG 60.667 55.000 0.00 0.00 40.43 4.35
2416 2791 0.940126 ACGATTCTGGATTCATGCGC 59.060 50.000 0.00 0.00 0.00 6.09
2460 2837 1.147600 GAGGGTGTCACCGGTTTGT 59.852 57.895 15.93 0.00 39.83 2.83
2591 2969 2.673368 CGGTGACTACAATGAAGCCTTC 59.327 50.000 0.00 0.00 0.00 3.46
2609 2987 1.677966 CTGGCAGCATGAGCACCTT 60.678 57.895 0.00 0.00 45.49 3.50
2615 2993 1.675641 GCATGAGCACCTTTCCCGT 60.676 57.895 0.00 0.00 41.58 5.28
2618 2996 0.400213 ATGAGCACCTTTCCCGTTCA 59.600 50.000 0.00 0.00 0.00 3.18
2627 3005 2.450960 TTTCCCGTTCAATGCGTGCG 62.451 55.000 0.00 0.00 0.00 5.34
2636 3014 0.521867 CAATGCGTGCGGAATCACAG 60.522 55.000 0.00 0.00 36.80 3.66
2664 3042 2.306805 TCATTCAGGGATTGTCTGCAGT 59.693 45.455 14.67 0.00 32.63 4.40
2735 3113 1.553690 ATGGCCAAGCACTAGACCGT 61.554 55.000 10.96 0.00 0.00 4.83
2839 3217 1.299850 CGTCGTGCTCTGACCACAA 60.300 57.895 4.18 0.00 32.68 3.33
2847 3225 0.035056 CTCTGACCACAACCCCATCC 60.035 60.000 0.00 0.00 0.00 3.51
2882 3260 2.035442 GGTTCAGGAGAAGCGGCAC 61.035 63.158 1.45 0.00 41.76 5.01
2884 3262 1.301716 TTCAGGAGAAGCGGCACAC 60.302 57.895 1.45 0.00 0.00 3.82
2885 3263 1.758440 TTCAGGAGAAGCGGCACACT 61.758 55.000 1.45 0.00 0.00 3.55
2924 3302 3.430453 TGAAATCATGTGGGAAAGGGAC 58.570 45.455 0.00 0.00 0.00 4.46
2939 3317 3.728373 GACCCCACCTTGCCGGAT 61.728 66.667 5.05 0.00 36.31 4.18
2969 3347 1.442526 GGAGTTGGCATGAGCATCGG 61.443 60.000 0.00 0.00 44.61 4.18
2974 3352 3.643978 GCATGAGCATCGGCCGAC 61.644 66.667 33.75 19.74 42.56 4.79
3059 3437 5.729510 AGCAAAACACACTTTGGTAATGTT 58.270 33.333 0.00 0.00 43.33 2.71
3080 3458 7.853377 TGTTATAAAAGATATCGAGTCGCTG 57.147 36.000 7.92 0.00 0.00 5.18
3083 3461 0.039978 AAGATATCGAGTCGCTGCGG 60.040 55.000 23.03 5.91 0.00 5.69
3098 3476 2.851071 GCGGTCTCAGCTAGCGGAT 61.851 63.158 18.11 0.00 38.24 4.18
3140 3525 1.006391 CGTGCGCTTATACGGTCAAAG 60.006 52.381 9.73 0.00 36.71 2.77
3147 3532 4.804139 CGCTTATACGGTCAAAGATGAACT 59.196 41.667 6.58 0.00 41.34 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 2.028130 TCTTTTCTTGCCCGCTTTTCA 58.972 42.857 0.00 0.00 0.00 2.69
62 63 3.894547 TTTTCTGTCCTCGCCCCGC 62.895 63.158 0.00 0.00 0.00 6.13
190 197 0.729690 GAGAATGAAGCTTCGTGCCC 59.270 55.000 21.64 7.21 44.23 5.36
254 261 1.737008 GTGGGGTCGCTCTCGTTTC 60.737 63.158 0.00 0.00 36.96 2.78
275 282 0.174389 TCGTCTCATGGAGCTTGAGC 59.826 55.000 8.75 0.00 40.35 4.26
276 283 1.203287 TGTCGTCTCATGGAGCTTGAG 59.797 52.381 7.47 7.47 41.61 3.02
277 284 1.256812 TGTCGTCTCATGGAGCTTGA 58.743 50.000 0.00 0.00 0.00 3.02
278 285 1.728971 GTTGTCGTCTCATGGAGCTTG 59.271 52.381 0.00 0.00 0.00 4.01
279 286 1.344438 TGTTGTCGTCTCATGGAGCTT 59.656 47.619 0.00 0.00 0.00 3.74
285 292 1.626654 GCCCGTGTTGTCGTCTCATG 61.627 60.000 0.00 0.00 0.00 3.07
288 295 1.300697 AAGCCCGTGTTGTCGTCTC 60.301 57.895 0.00 0.00 0.00 3.36
289 296 1.594293 CAAGCCCGTGTTGTCGTCT 60.594 57.895 0.00 0.00 0.00 4.18
290 297 2.604174 CCAAGCCCGTGTTGTCGTC 61.604 63.158 0.00 0.00 0.00 4.20
291 298 2.590575 CCAAGCCCGTGTTGTCGT 60.591 61.111 0.00 0.00 0.00 4.34
295 302 3.726517 CGAGCCAAGCCCGTGTTG 61.727 66.667 0.00 0.00 0.00 3.33
296 303 3.883744 CTCGAGCCAAGCCCGTGTT 62.884 63.158 0.00 0.00 0.00 3.32
297 304 4.379243 CTCGAGCCAAGCCCGTGT 62.379 66.667 0.00 0.00 0.00 4.49
315 322 2.103042 CCTTTCTTCCCAGCGCGAG 61.103 63.158 12.10 0.00 0.00 5.03
316 323 1.899437 ATCCTTTCTTCCCAGCGCGA 61.899 55.000 12.10 0.00 0.00 5.87
317 324 1.432270 GATCCTTTCTTCCCAGCGCG 61.432 60.000 0.00 0.00 0.00 6.86
319 326 0.108138 ACGATCCTTTCTTCCCAGCG 60.108 55.000 0.00 0.00 0.00 5.18
320 327 1.740025 CAACGATCCTTTCTTCCCAGC 59.260 52.381 0.00 0.00 0.00 4.85
321 328 1.740025 GCAACGATCCTTTCTTCCCAG 59.260 52.381 0.00 0.00 0.00 4.45
322 329 1.613255 GGCAACGATCCTTTCTTCCCA 60.613 52.381 0.00 0.00 0.00 4.37
325 332 1.740025 CCAGGCAACGATCCTTTCTTC 59.260 52.381 0.00 0.00 46.39 2.87
326 333 1.351017 TCCAGGCAACGATCCTTTCTT 59.649 47.619 0.00 0.00 46.39 2.52
327 334 0.984230 TCCAGGCAACGATCCTTTCT 59.016 50.000 0.00 0.00 46.39 2.52
336 343 1.557443 GAGTTCACGTCCAGGCAACG 61.557 60.000 0.00 0.00 45.37 4.10
342 349 0.528470 GGAGGAGAGTTCACGTCCAG 59.472 60.000 11.68 0.00 39.93 3.86
354 361 2.037367 CCACGGGACAGGAGGAGA 59.963 66.667 0.00 0.00 0.00 3.71
452 464 8.614346 GTGGCACGGTAATAATTAATTAACAGA 58.386 33.333 11.80 0.00 37.58 3.41
453 465 8.399425 TGTGGCACGGTAATAATTAATTAACAG 58.601 33.333 13.77 9.57 37.58 3.16
454 466 8.182881 GTGTGGCACGGTAATAATTAATTAACA 58.817 33.333 13.77 5.25 37.58 2.41
455 467 7.644945 GGTGTGGCACGGTAATAATTAATTAAC 59.355 37.037 13.77 6.73 34.83 2.01
482 502 4.166011 GTTGATGCGAGCGGGTGC 62.166 66.667 0.00 0.00 43.24 5.01
508 528 4.080129 ACATAAGTTGCCATCCATCAGTCT 60.080 41.667 0.00 0.00 0.00 3.24
539 559 1.859998 GCAGTTGTTTTGCTCGGTGAC 60.860 52.381 0.00 0.00 38.51 3.67
540 560 0.380378 GCAGTTGTTTTGCTCGGTGA 59.620 50.000 0.00 0.00 38.51 4.02
541 561 2.872028 GCAGTTGTTTTGCTCGGTG 58.128 52.632 0.00 0.00 38.51 4.94
547 567 1.606224 CCCATGGAGCAGTTGTTTTGC 60.606 52.381 15.22 0.00 41.83 3.68
548 568 1.962807 TCCCATGGAGCAGTTGTTTTG 59.037 47.619 15.22 0.00 0.00 2.44
549 569 1.963515 GTCCCATGGAGCAGTTGTTTT 59.036 47.619 15.22 0.00 29.39 2.43
550 570 1.620822 GTCCCATGGAGCAGTTGTTT 58.379 50.000 15.22 0.00 29.39 2.83
551 571 0.606401 CGTCCCATGGAGCAGTTGTT 60.606 55.000 15.22 0.00 29.39 2.83
552 572 1.003355 CGTCCCATGGAGCAGTTGT 60.003 57.895 15.22 0.00 29.39 3.32
553 573 1.746615 CCGTCCCATGGAGCAGTTG 60.747 63.158 15.22 0.00 29.39 3.16
554 574 1.918293 TCCGTCCCATGGAGCAGTT 60.918 57.895 15.22 0.00 29.39 3.16
555 575 2.284625 TCCGTCCCATGGAGCAGT 60.285 61.111 15.22 0.00 29.39 4.40
556 576 2.187946 GTCCGTCCCATGGAGCAG 59.812 66.667 15.22 1.16 33.08 4.24
557 577 3.770040 CGTCCGTCCCATGGAGCA 61.770 66.667 15.22 0.00 33.08 4.26
558 578 3.718210 GACGTCCGTCCCATGGAGC 62.718 68.421 15.22 4.23 39.08 4.70
559 579 2.284798 CTGACGTCCGTCCCATGGAG 62.285 65.000 15.22 3.25 43.97 3.86
560 580 2.283316 TGACGTCCGTCCCATGGA 60.283 61.111 15.22 0.00 43.97 3.41
561 581 2.184322 CTGACGTCCGTCCCATGG 59.816 66.667 14.12 4.14 43.97 3.66
562 582 2.167398 AACCTGACGTCCGTCCCATG 62.167 60.000 14.12 5.63 43.97 3.66
563 583 1.911766 AACCTGACGTCCGTCCCAT 60.912 57.895 14.12 0.00 43.97 4.00
564 584 2.522436 AACCTGACGTCCGTCCCA 60.522 61.111 14.12 0.00 43.97 4.37
565 585 2.048503 CAACCTGACGTCCGTCCC 60.049 66.667 14.12 0.00 43.97 4.46
566 586 2.048503 CCAACCTGACGTCCGTCC 60.049 66.667 14.12 0.59 43.97 4.79
567 587 1.080705 CTCCAACCTGACGTCCGTC 60.081 63.158 14.12 12.66 44.77 4.79
568 588 3.048602 CTCCAACCTGACGTCCGT 58.951 61.111 14.12 6.32 0.00 4.69
569 589 2.432628 GCTCCAACCTGACGTCCG 60.433 66.667 14.12 6.54 0.00 4.79
570 590 0.535335 TATGCTCCAACCTGACGTCC 59.465 55.000 14.12 0.00 0.00 4.79
571 591 1.067142 TGTATGCTCCAACCTGACGTC 60.067 52.381 9.11 9.11 0.00 4.34
572 592 0.973632 TGTATGCTCCAACCTGACGT 59.026 50.000 0.00 0.00 0.00 4.34
573 593 1.204704 TCTGTATGCTCCAACCTGACG 59.795 52.381 0.00 0.00 0.00 4.35
574 594 3.334583 TTCTGTATGCTCCAACCTGAC 57.665 47.619 0.00 0.00 0.00 3.51
575 595 4.517285 GATTTCTGTATGCTCCAACCTGA 58.483 43.478 0.00 0.00 0.00 3.86
667 688 4.348486 TCAAGACAGAGAGGCAAGATACT 58.652 43.478 0.00 0.00 0.00 2.12
681 703 3.263489 ACCATCAGCAGATCAAGACAG 57.737 47.619 0.00 0.00 30.20 3.51
688 710 3.624861 CACAAGGTAACCATCAGCAGATC 59.375 47.826 0.00 0.00 30.20 2.75
689 711 3.614092 CACAAGGTAACCATCAGCAGAT 58.386 45.455 0.00 0.00 33.87 2.90
690 712 2.875672 GCACAAGGTAACCATCAGCAGA 60.876 50.000 0.00 0.00 37.17 4.26
691 713 1.470098 GCACAAGGTAACCATCAGCAG 59.530 52.381 0.00 0.00 37.17 4.24
705 732 0.535780 TCTTGTCCCAGCAGCACAAG 60.536 55.000 14.45 14.45 45.66 3.16
715 742 1.271163 GGACGGAAACATCTTGTCCCA 60.271 52.381 0.00 0.00 42.57 4.37
716 743 1.271163 TGGACGGAAACATCTTGTCCC 60.271 52.381 7.19 0.24 46.73 4.46
761 788 6.721571 TGGATTAAAGAAGCAAGTAACTCG 57.278 37.500 0.00 0.00 0.00 4.18
768 796 5.711976 TCCTTCCTTGGATTAAAGAAGCAAG 59.288 40.000 0.00 0.00 0.00 4.01
822 850 0.250513 CCACCTGAGGTCTTACTGCC 59.749 60.000 0.00 0.00 31.02 4.85
850 878 8.853126 TGACTACTACTACTGCTTGAGTAAAAA 58.147 33.333 0.00 0.00 36.69 1.94
851 879 8.400184 TGACTACTACTACTGCTTGAGTAAAA 57.600 34.615 0.00 0.00 36.69 1.52
852 880 7.991084 TGACTACTACTACTGCTTGAGTAAA 57.009 36.000 0.00 0.00 36.69 2.01
853 881 7.881751 TCTTGACTACTACTACTGCTTGAGTAA 59.118 37.037 0.00 0.00 36.69 2.24
854 882 7.392418 TCTTGACTACTACTACTGCTTGAGTA 58.608 38.462 0.00 0.00 35.96 2.59
855 883 6.239396 TCTTGACTACTACTACTGCTTGAGT 58.761 40.000 0.00 0.00 38.88 3.41
856 884 6.745159 TCTTGACTACTACTACTGCTTGAG 57.255 41.667 0.00 0.00 0.00 3.02
857 885 7.499563 CCTATCTTGACTACTACTACTGCTTGA 59.500 40.741 0.00 0.00 0.00 3.02
858 886 7.499563 TCCTATCTTGACTACTACTACTGCTTG 59.500 40.741 0.00 0.00 0.00 4.01
859 887 7.575505 TCCTATCTTGACTACTACTACTGCTT 58.424 38.462 0.00 0.00 0.00 3.91
860 888 7.139287 TCCTATCTTGACTACTACTACTGCT 57.861 40.000 0.00 0.00 0.00 4.24
861 889 6.428771 CCTCCTATCTTGACTACTACTACTGC 59.571 46.154 0.00 0.00 0.00 4.40
862 890 6.428771 GCCTCCTATCTTGACTACTACTACTG 59.571 46.154 0.00 0.00 0.00 2.74
863 891 6.330778 AGCCTCCTATCTTGACTACTACTACT 59.669 42.308 0.00 0.00 0.00 2.57
864 892 6.536447 AGCCTCCTATCTTGACTACTACTAC 58.464 44.000 0.00 0.00 0.00 2.73
865 893 6.239944 GGAGCCTCCTATCTTGACTACTACTA 60.240 46.154 2.64 0.00 32.53 1.82
866 894 5.457052 GGAGCCTCCTATCTTGACTACTACT 60.457 48.000 2.64 0.00 32.53 2.57
867 895 4.763279 GGAGCCTCCTATCTTGACTACTAC 59.237 50.000 2.64 0.00 32.53 2.73
868 896 4.202588 GGGAGCCTCCTATCTTGACTACTA 60.203 50.000 11.29 0.00 36.57 1.82
869 897 3.437344 GGGAGCCTCCTATCTTGACTACT 60.437 52.174 11.29 0.00 36.57 2.57
870 898 2.894765 GGGAGCCTCCTATCTTGACTAC 59.105 54.545 11.29 0.00 36.57 2.73
871 899 2.489255 CGGGAGCCTCCTATCTTGACTA 60.489 54.545 11.29 0.00 36.57 2.59
872 900 1.755977 CGGGAGCCTCCTATCTTGACT 60.756 57.143 11.29 0.00 36.57 3.41
873 901 0.676736 CGGGAGCCTCCTATCTTGAC 59.323 60.000 11.29 0.00 36.57 3.18
874 902 3.133437 CGGGAGCCTCCTATCTTGA 57.867 57.895 11.29 0.00 36.57 3.02
942 971 1.047034 GGGTACGTAGGTGGCTGGAT 61.047 60.000 0.00 0.00 0.00 3.41
973 1003 4.074526 GACAGCAGAGCCCGCTCA 62.075 66.667 18.44 0.00 44.99 4.26
986 1018 2.806856 GCCATCGAAGCGCAGACAG 61.807 63.158 11.47 2.40 0.00 3.51
1051 1083 2.464796 TCCAGATTAGGGTTAGCGGA 57.535 50.000 0.00 0.00 0.00 5.54
1089 1121 5.003692 TGAACTCTTCCTCATTGAGATCG 57.996 43.478 15.36 2.95 33.98 3.69
1200 1233 3.198635 CCTTGTAGAAGGCAGATGGAGAA 59.801 47.826 5.60 0.00 42.60 2.87
1275 1308 5.125417 TGCTTGAACCACAAATCTATTAGGC 59.875 40.000 0.00 0.00 38.08 3.93
1353 1386 4.811557 GGACATAGAAGTACTGCCATGTTC 59.188 45.833 15.17 10.26 28.98 3.18
1398 1431 1.201647 TGATCGAACACGACTTCCTCC 59.798 52.381 0.00 0.00 38.85 4.30
1480 1513 2.607771 CCGCACCCTTCAACAATTTCTG 60.608 50.000 0.00 0.00 0.00 3.02
1578 1611 0.875059 CAAACTTCGTCAGGGGCTTC 59.125 55.000 0.00 0.00 0.00 3.86
1667 1700 4.160635 CGATCAAACCGCACGCCC 62.161 66.667 0.00 0.00 0.00 6.13
1737 1772 1.048601 CATACAGCCACTCCCCGTAT 58.951 55.000 0.00 0.00 0.00 3.06
1767 1802 2.093973 CAGATCGGACCTGTAGCTGTTT 60.094 50.000 0.00 0.00 0.00 2.83
1809 1844 2.361357 CTCCCCTGACGACGAGGT 60.361 66.667 0.00 0.00 0.00 3.85
1893 1928 0.539986 CCTTTAAGGGGCTCGTAGCA 59.460 55.000 2.44 0.00 44.75 3.49
1916 1951 1.281867 CCACTTCCATCCTAGCCACAA 59.718 52.381 0.00 0.00 0.00 3.33
1986 2021 0.107459 GAGCACTGGGTTCCCTGATC 60.107 60.000 19.15 9.99 0.00 2.92
1988 2023 2.583441 CGAGCACTGGGTTCCCTGA 61.583 63.158 19.15 0.00 0.00 3.86
2006 2041 3.645268 ATGGCAAGGACCGGCTTCC 62.645 63.158 0.00 0.95 35.66 3.46
2034 2069 2.303022 TGATCCCAACTCTGTTCCACTC 59.697 50.000 0.00 0.00 0.00 3.51
2073 2108 0.040958 GTTTGGAGCTTGACGTGCTG 60.041 55.000 3.28 0.00 41.30 4.41
2126 2161 3.857038 GGGAGGCCGCCGATGTAA 61.857 66.667 20.27 0.00 0.00 2.41
2170 2205 1.410083 GGCAGTTCCATGATAGGGCAA 60.410 52.381 0.00 0.00 34.01 4.52
2204 2248 2.203596 ACCTCCCGAACTGTCCGT 60.204 61.111 0.00 0.00 0.00 4.69
2227 2602 3.563479 GGGGTTATTGGCTTTTGAGAGGA 60.563 47.826 0.00 0.00 0.00 3.71
2318 2693 1.780309 ACACCATGGAAACCCTTGAGA 59.220 47.619 21.47 0.00 32.31 3.27
2399 2774 3.657634 TCTAGCGCATGAATCCAGAATC 58.342 45.455 11.47 0.00 0.00 2.52
2447 2824 0.542333 TCCAAGACAAACCGGTGACA 59.458 50.000 8.52 0.00 0.00 3.58
2449 2826 0.107831 CCTCCAAGACAAACCGGTGA 59.892 55.000 8.52 0.00 0.00 4.02
2570 2948 2.386661 AGGCTTCATTGTAGTCACCG 57.613 50.000 0.00 0.00 0.00 4.94
2591 2969 1.248785 AAAGGTGCTCATGCTGCCAG 61.249 55.000 0.00 0.00 40.48 4.85
2609 2987 2.950673 GCACGCATTGAACGGGAA 59.049 55.556 0.00 0.00 35.45 3.97
2615 2993 0.167908 GTGATTCCGCACGCATTGAA 59.832 50.000 0.00 0.00 0.00 2.69
2618 2996 0.673333 TCTGTGATTCCGCACGCATT 60.673 50.000 0.00 0.00 41.63 3.56
2627 3005 1.959042 ATGACGCCATCTGTGATTCC 58.041 50.000 0.00 0.00 0.00 3.01
2636 3014 1.605710 CAATCCCTGAATGACGCCATC 59.394 52.381 0.00 0.00 31.40 3.51
2664 3042 4.943705 GCCAAGATCCTCTAATTCACACAA 59.056 41.667 0.00 0.00 0.00 3.33
2839 3217 1.285962 CCAACTGAATCAGGATGGGGT 59.714 52.381 22.13 0.00 38.24 4.95
2847 3225 2.887151 ACCCCTTCCAACTGAATCAG 57.113 50.000 8.98 8.98 37.52 2.90
2882 3260 1.280982 AACGCATCATAGTCGCAGTG 58.719 50.000 0.00 0.00 0.00 3.66
2884 3262 3.308530 TCATAACGCATCATAGTCGCAG 58.691 45.455 0.00 0.00 0.00 5.18
2885 3263 3.363341 TCATAACGCATCATAGTCGCA 57.637 42.857 0.00 0.00 0.00 5.10
2924 3302 2.192175 GTATCCGGCAAGGTGGGG 59.808 66.667 0.00 0.00 41.99 4.96
2939 3317 1.373435 CCAACTCCTGGCAACCGTA 59.627 57.895 0.00 0.00 38.76 4.02
2948 3326 1.022735 GATGCTCATGCCAACTCCTG 58.977 55.000 0.00 0.00 38.71 3.86
2974 3352 3.058160 CCGAGCCAAGGTTGCCAG 61.058 66.667 0.00 0.00 0.00 4.85
3059 3437 5.086727 CGCAGCGACTCGATATCTTTTATA 58.913 41.667 9.98 0.00 0.00 0.98
3080 3458 2.356818 AATCCGCTAGCTGAGACCGC 62.357 60.000 13.93 0.00 0.00 5.68
3083 3461 0.933796 GCAAATCCGCTAGCTGAGAC 59.066 55.000 13.93 0.00 0.00 3.36
3092 3470 1.604593 AGCCAGTTGCAAATCCGCT 60.605 52.632 11.20 11.20 44.83 5.52
3098 3476 3.233231 GCCCCAGCCAGTTGCAAA 61.233 61.111 0.00 0.00 44.83 3.68
3125 3503 6.074249 GCTAGTTCATCTTTGACCGTATAAGC 60.074 42.308 0.00 0.00 0.00 3.09
3140 3525 1.846541 GCTCGTCCAGCTAGTTCATC 58.153 55.000 0.00 0.00 45.83 2.92


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

AutoCloner maintained by Alex Coulton.