Multiple sequence alignment - TraesCS3B01G343400

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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 TraesCS3B01G343400 chr3B 100.000 4989 0 0 1 4989 552233972 552228984 0.000000e+00 9214
1 TraesCS3B01G343400 chr3A 93.526 4557 232 20 448 4989 564947027 564942519 0.000000e+00 6722
2 TraesCS3B01G343400 chr3A 86.866 434 29 12 1 425 564947431 564947017 1.270000e-125 460
3 TraesCS3B01G343400 chr3D 93.495 4443 197 23 555 4989 424008557 424012915 0.000000e+00 6519
4 TraesCS3B01G343400 chr3D 82.865 356 31 12 1 344 424008000 424008337 4.890000e-75 292


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 TraesCS3B01G343400 chr3B 552228984 552233972 4988 True 9214.0 9214 100.000 1 4989 1 chr3B.!!$R1 4988
1 TraesCS3B01G343400 chr3A 564942519 564947431 4912 True 3591.0 6722 90.196 1 4989 2 chr3A.!!$R1 4988
2 TraesCS3B01G343400 chr3D 424008000 424012915 4915 False 3405.5 6519 88.180 1 4989 2 chr3D.!!$F1 4988

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
93 100 0.115152 CCCCCTTCCTTTTTGGCTCT 59.885 55.0 0.00 0.0 35.26 4.09 F
126 133 0.179018 TCGCAGATCGGGATCTCTCA 60.179 55.0 8.19 0.0 45.78 3.27 F
1164 1287 0.242825 TACCTTGTCCGTTCTGCTCG 59.757 55.0 0.00 0.0 0.00 5.03 F
2364 2491 0.036010 AGGGGACAGAAATCACTGCG 60.036 55.0 0.00 0.0 41.06 5.18 F
2518 2660 0.817654 TCTCCACTGTAGCATCCACG 59.182 55.0 0.00 0.0 0.00 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1109 1232 0.038166 ACGGGCAAATCTGGTGATGT 59.962 50.000 0.00 0.0 32.44 3.06 R
1188 1311 0.242825 TGTAGAAGCACGGTTCCTCG 59.757 55.000 5.40 0.0 0.00 4.63 R
2938 3081 0.108186 TGTAGGCCTCGTTCATGCTG 60.108 55.000 9.68 0.0 0.00 4.41 R
3291 3434 0.386113 GCAGAGGAGGTGTATCGACC 59.614 60.000 0.00 0.0 36.09 4.79 R
4030 4173 1.780309 ACAAGTTGGGTGGGAATCTGA 59.220 47.619 7.96 0.0 0.00 3.27 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
62 63 2.695314 CTTAGCCTTAAGCCAGCCG 58.305 57.895 0.00 0.00 45.47 5.52
63 64 1.440145 CTTAGCCTTAAGCCAGCCGC 61.440 60.000 0.00 0.00 45.47 6.53
64 65 2.886730 TTAGCCTTAAGCCAGCCGCC 62.887 60.000 0.00 0.00 45.47 6.13
93 100 0.115152 CCCCCTTCCTTTTTGGCTCT 59.885 55.000 0.00 0.00 35.26 4.09
107 114 3.842923 CTCTGCTCCGGCCATCGT 61.843 66.667 2.24 0.00 37.74 3.73
126 133 0.179018 TCGCAGATCGGGATCTCTCA 60.179 55.000 8.19 0.00 45.78 3.27
179 189 5.242838 CAGGCGAGGTTCTAATTCTATCTCT 59.757 44.000 0.00 0.00 0.00 3.10
185 195 6.381250 AGGTTCTAATTCTATCTCTGCTCCT 58.619 40.000 0.00 0.00 0.00 3.69
196 206 2.499289 TCTCTGCTCCTCCTGTGATTTC 59.501 50.000 0.00 0.00 0.00 2.17
197 207 1.556911 TCTGCTCCTCCTGTGATTTCC 59.443 52.381 0.00 0.00 0.00 3.13
241 251 1.705186 AGCTTAGTTTGCTTCCTGGGA 59.295 47.619 0.00 0.00 37.52 4.37
242 252 1.813178 GCTTAGTTTGCTTCCTGGGAC 59.187 52.381 0.00 0.00 0.00 4.46
243 253 2.553247 GCTTAGTTTGCTTCCTGGGACT 60.553 50.000 0.00 0.00 0.00 3.85
244 254 2.859165 TAGTTTGCTTCCTGGGACTG 57.141 50.000 0.00 0.00 0.00 3.51
245 255 0.846693 AGTTTGCTTCCTGGGACTGT 59.153 50.000 0.00 0.00 0.00 3.55
246 256 0.954452 GTTTGCTTCCTGGGACTGTG 59.046 55.000 0.00 0.00 0.00 3.66
348 365 3.570125 TCTGTACGCATCCTAGATTCCTG 59.430 47.826 0.00 0.00 0.00 3.86
349 366 2.628178 TGTACGCATCCTAGATTCCTGG 59.372 50.000 0.00 0.00 0.00 4.45
418 444 2.695147 CCCACAGCTTTGAGGAAAAGTT 59.305 45.455 0.17 0.00 46.05 2.66
424 450 5.966742 AGCTTTGAGGAAAAGTTGGTATC 57.033 39.130 0.30 0.00 46.05 2.24
425 451 5.385198 AGCTTTGAGGAAAAGTTGGTATCA 58.615 37.500 0.30 0.00 46.05 2.15
426 452 5.241728 AGCTTTGAGGAAAAGTTGGTATCAC 59.758 40.000 0.30 0.00 46.05 3.06
427 453 5.241728 GCTTTGAGGAAAAGTTGGTATCACT 59.758 40.000 0.30 0.00 46.05 3.41
428 454 6.633500 TTTGAGGAAAAGTTGGTATCACTG 57.367 37.500 0.00 0.00 0.00 3.66
429 455 5.304686 TGAGGAAAAGTTGGTATCACTGT 57.695 39.130 0.00 0.00 0.00 3.55
430 456 5.690865 TGAGGAAAAGTTGGTATCACTGTT 58.309 37.500 0.00 0.00 0.00 3.16
431 457 6.833041 TGAGGAAAAGTTGGTATCACTGTTA 58.167 36.000 0.00 0.00 0.00 2.41
432 458 6.934645 TGAGGAAAAGTTGGTATCACTGTTAG 59.065 38.462 0.00 0.00 0.00 2.34
433 459 7.074653 AGGAAAAGTTGGTATCACTGTTAGA 57.925 36.000 0.00 0.00 0.00 2.10
434 460 7.514721 AGGAAAAGTTGGTATCACTGTTAGAA 58.485 34.615 0.00 0.00 0.00 2.10
435 461 8.164070 AGGAAAAGTTGGTATCACTGTTAGAAT 58.836 33.333 0.00 0.00 0.00 2.40
436 462 8.451748 GGAAAAGTTGGTATCACTGTTAGAATC 58.548 37.037 0.00 0.00 0.00 2.52
437 463 7.923414 AAAGTTGGTATCACTGTTAGAATCC 57.077 36.000 0.00 0.00 0.00 3.01
438 464 5.990668 AGTTGGTATCACTGTTAGAATCCC 58.009 41.667 0.00 0.00 0.00 3.85
439 465 5.487488 AGTTGGTATCACTGTTAGAATCCCA 59.513 40.000 0.00 0.00 0.00 4.37
440 466 6.158695 AGTTGGTATCACTGTTAGAATCCCAT 59.841 38.462 0.00 0.00 0.00 4.00
441 467 6.575244 TGGTATCACTGTTAGAATCCCATT 57.425 37.500 0.00 0.00 0.00 3.16
442 468 7.684317 TGGTATCACTGTTAGAATCCCATTA 57.316 36.000 0.00 0.00 0.00 1.90
443 469 8.275187 TGGTATCACTGTTAGAATCCCATTAT 57.725 34.615 0.00 0.00 0.00 1.28
444 470 8.156820 TGGTATCACTGTTAGAATCCCATTATG 58.843 37.037 0.00 0.00 0.00 1.90
445 471 7.119846 GGTATCACTGTTAGAATCCCATTATGC 59.880 40.741 0.00 0.00 0.00 3.14
446 472 5.376625 TCACTGTTAGAATCCCATTATGCC 58.623 41.667 0.00 0.00 0.00 4.40
447 473 5.104151 TCACTGTTAGAATCCCATTATGCCA 60.104 40.000 0.00 0.00 0.00 4.92
448 474 5.593909 CACTGTTAGAATCCCATTATGCCAA 59.406 40.000 0.00 0.00 0.00 4.52
449 475 5.829924 ACTGTTAGAATCCCATTATGCCAAG 59.170 40.000 0.00 0.00 0.00 3.61
450 476 5.765510 TGTTAGAATCCCATTATGCCAAGT 58.234 37.500 0.00 0.00 0.00 3.16
453 479 3.205056 AGAATCCCATTATGCCAAGTGGA 59.795 43.478 0.18 0.00 37.39 4.02
467 493 0.673644 AGTGGATTTCGTTGCCGGAG 60.674 55.000 5.05 0.00 33.95 4.63
479 505 1.268066 TGCCGGAGTATGGTGTGTTA 58.732 50.000 5.05 0.00 0.00 2.41
483 509 2.612212 CCGGAGTATGGTGTGTTATTGC 59.388 50.000 0.00 0.00 0.00 3.56
488 514 1.750193 ATGGTGTGTTATTGCCGGAG 58.250 50.000 5.05 0.00 0.00 4.63
508 534 3.924144 AGTTTAGTTGCTCAGCTCTCAG 58.076 45.455 0.00 0.00 0.00 3.35
525 551 3.321968 TCTCAGCAAGTTTCAGCTCACTA 59.678 43.478 0.00 0.00 39.50 2.74
528 554 3.561310 CAGCAAGTTTCAGCTCACTACAA 59.439 43.478 0.00 0.00 39.50 2.41
545 571 1.134580 ACAAGGATCATCTGTCCTGCG 60.135 52.381 0.00 0.00 45.23 5.18
554 580 6.428159 GGATCATCTGTCCTGCGTAATTTATT 59.572 38.462 0.00 0.00 32.85 1.40
599 721 2.159379 GCCAATTAGCCACTGTAGTTGC 60.159 50.000 0.19 0.19 37.00 4.17
600 722 2.423538 CCAATTAGCCACTGTAGTTGCC 59.576 50.000 4.66 0.00 37.40 4.52
601 723 3.347216 CAATTAGCCACTGTAGTTGCCT 58.653 45.455 4.66 0.00 37.40 4.75
602 724 4.513442 CAATTAGCCACTGTAGTTGCCTA 58.487 43.478 4.66 0.00 37.40 3.93
603 725 3.887621 TTAGCCACTGTAGTTGCCTAG 57.112 47.619 4.66 0.00 37.40 3.02
604 726 1.645710 AGCCACTGTAGTTGCCTAGT 58.354 50.000 4.66 0.00 37.40 2.57
605 727 1.276421 AGCCACTGTAGTTGCCTAGTG 59.724 52.381 4.66 0.00 37.40 2.74
694 816 6.067217 AGACTGGCTTTATACTTCACCAAT 57.933 37.500 0.00 0.00 0.00 3.16
698 820 5.192927 TGGCTTTATACTTCACCAATCCTG 58.807 41.667 0.00 0.00 0.00 3.86
729 851 3.379372 GCTGCAATGACACTACCATCATT 59.621 43.478 0.00 0.00 44.52 2.57
736 858 7.649306 GCAATGACACTACCATCATTATTTTCC 59.351 37.037 0.00 0.00 42.35 3.13
759 881 5.468072 CCCGTTCATCTTCTCAATGATAAGG 59.532 44.000 8.25 0.00 33.36 2.69
769 892 5.018809 TCTCAATGATAAGGCAAAGGCTTT 58.981 37.500 6.68 6.68 46.16 3.51
847 970 5.064558 TGTTACTTTTATCACCAAGCGGAA 58.935 37.500 0.00 0.00 35.59 4.30
869 992 8.932791 CGGAATAACTGTAACACTGAAGTAAAT 58.067 33.333 0.00 0.00 0.00 1.40
887 1010 7.158099 AGTAAATTCCCACTTTGCTGATTAC 57.842 36.000 0.00 0.00 29.07 1.89
891 1014 6.759497 ATTCCCACTTTGCTGATTACTAAC 57.241 37.500 0.00 0.00 0.00 2.34
957 1080 2.093973 CCTCTGACCATCTAAACAGCGT 60.094 50.000 0.00 0.00 0.00 5.07
964 1087 2.159627 CCATCTAAACAGCGTGTTGGAC 59.840 50.000 4.51 0.00 40.14 4.02
966 1089 1.139256 TCTAAACAGCGTGTTGGACCA 59.861 47.619 0.00 0.00 40.14 4.02
1164 1287 0.242825 TACCTTGTCCGTTCTGCTCG 59.757 55.000 0.00 0.00 0.00 5.03
1185 1308 1.133325 AGGCTAGATCATGTCCTCGGT 60.133 52.381 0.00 0.00 0.00 4.69
1188 1311 3.305471 GGCTAGATCATGTCCTCGGTAAC 60.305 52.174 0.00 0.00 0.00 2.50
1361 1484 3.864583 CCAAACAACAATGACAACACAGG 59.135 43.478 0.00 0.00 0.00 4.00
1369 1492 1.148273 GACAACACAGGTGAGCCCA 59.852 57.895 6.40 0.00 34.66 5.36
1381 1504 2.927856 AGCCCACCGTGGATGTCA 60.928 61.111 19.81 0.00 40.96 3.58
1573 1696 1.811965 CATGGCAACTGGACGAATCAA 59.188 47.619 0.00 0.00 37.61 2.57
1722 1845 7.614583 CCTCATGAAGCCTATGATATGGAAAAT 59.385 37.037 0.00 0.00 34.33 1.82
1768 1891 4.927267 TTTGAGATACCAGGTGTTCCAT 57.073 40.909 0.76 0.00 35.89 3.41
1769 1892 4.487714 TTGAGATACCAGGTGTTCCATC 57.512 45.455 0.76 0.00 35.89 3.51
1775 1898 1.379044 CAGGTGTTCCATCCCCTGC 60.379 63.158 0.00 0.00 38.19 4.85
1859 1982 1.358877 TGTTCGGCAGATCATGTTCG 58.641 50.000 0.00 0.61 0.00 3.95
1860 1983 0.652592 GTTCGGCAGATCATGTTCGG 59.347 55.000 0.00 0.00 0.00 4.30
1943 2066 0.461516 AGACGAGCATCACAGCATGG 60.462 55.000 0.00 0.00 43.62 3.66
2162 2289 1.203287 TCAGAGGACGAATGACAGCAG 59.797 52.381 0.00 0.00 0.00 4.24
2295 2422 8.236586 TGAAGGACATTTTGTTTCTATTCATCG 58.763 33.333 0.00 0.00 0.00 3.84
2301 2428 7.807907 ACATTTTGTTTCTATTCATCGAACCAC 59.192 33.333 0.00 0.00 0.00 4.16
2311 2438 2.150390 CATCGAACCACCATGACACAA 58.850 47.619 0.00 0.00 0.00 3.33
2350 2477 0.117140 TCCAGAAGAAGCTCAGGGGA 59.883 55.000 0.00 0.00 0.00 4.81
2351 2478 0.251634 CCAGAAGAAGCTCAGGGGAC 59.748 60.000 0.00 0.00 0.00 4.46
2364 2491 0.036010 AGGGGACAGAAATCACTGCG 60.036 55.000 0.00 0.00 41.06 5.18
2375 2502 5.521372 CAGAAATCACTGCGATATCAAGTGA 59.479 40.000 27.66 27.66 42.57 3.41
2377 2504 2.797491 TCACTGCGATATCAAGTGACG 58.203 47.619 24.32 8.66 35.00 4.35
2379 2506 3.375922 TCACTGCGATATCAAGTGACGTA 59.624 43.478 24.32 10.50 35.00 3.57
2407 2534 4.080356 ACCAGAGAAGCACATTGGCTAATA 60.080 41.667 0.00 0.00 45.07 0.98
2445 2572 4.008916 ACCAGTACCCAAGGACTATCAT 57.991 45.455 0.00 0.00 0.00 2.45
2460 2587 7.568349 AGGACTATCATTATGTTGCTTCAGAA 58.432 34.615 0.00 0.00 0.00 3.02
2461 2588 7.714377 AGGACTATCATTATGTTGCTTCAGAAG 59.286 37.037 5.72 5.72 0.00 2.85
2462 2589 7.712639 GGACTATCATTATGTTGCTTCAGAAGA 59.287 37.037 14.86 0.00 0.00 2.87
2463 2590 9.270640 GACTATCATTATGTTGCTTCAGAAGAT 57.729 33.333 14.86 0.97 0.00 2.40
2466 2593 8.969260 ATCATTATGTTGCTTCAGAAGATACA 57.031 30.769 14.86 15.52 0.00 2.29
2467 2594 8.969260 TCATTATGTTGCTTCAGAAGATACAT 57.031 30.769 23.36 23.36 37.60 2.29
2471 2598 7.976135 ATGTTGCTTCAGAAGATACATATCC 57.024 36.000 20.65 1.71 34.45 2.59
2472 2599 5.985530 TGTTGCTTCAGAAGATACATATCCG 59.014 40.000 14.86 0.00 33.17 4.18
2473 2600 6.183360 TGTTGCTTCAGAAGATACATATCCGA 60.183 38.462 14.86 0.00 33.17 4.55
2474 2601 6.405278 TGCTTCAGAAGATACATATCCGAA 57.595 37.500 14.86 0.00 33.17 4.30
2514 2656 4.400884 TCTCTCTTTCTCCACTGTAGCATC 59.599 45.833 0.00 0.00 0.00 3.91
2518 2660 0.817654 TCTCCACTGTAGCATCCACG 59.182 55.000 0.00 0.00 0.00 4.94
2526 2668 5.414765 CCACTGTAGCATCCACGTATCTATA 59.585 44.000 0.00 0.00 0.00 1.31
2579 2721 7.992033 ACTCTCTTTCAGATAATTTCAGGGATG 59.008 37.037 0.00 0.00 0.00 3.51
2720 2862 5.656416 TCCAGTTCAACTTCCAAAGATTTGT 59.344 36.000 4.71 0.00 36.45 2.83
2737 2879 7.770801 AGATTTGTTAGCAAAAGGTTTGTTC 57.229 32.000 8.89 0.04 46.23 3.18
2813 2956 7.114754 ACCATTTTGATCAGATGCTAAAGAGA 58.885 34.615 13.05 0.00 0.00 3.10
2890 3033 2.025863 GCCATTGAGGAACATCCCCAG 61.026 57.143 0.00 0.00 41.22 4.45
2938 3081 4.584325 AGACCATCTCTTAGCACTCAGATC 59.416 45.833 0.00 0.00 0.00 2.75
2962 3105 2.961526 TGAACGAGGCCTACAATCTC 57.038 50.000 4.42 0.00 0.00 2.75
3004 3147 1.000359 CCCATCCCCAACCTTGACC 60.000 63.158 0.00 0.00 0.00 4.02
3031 3174 3.074390 TGATTCTTGGAAAGGGCTCTTCA 59.926 43.478 0.00 0.00 46.24 3.02
3070 3213 2.692557 ACTGAGGCTACTGCTATCACAG 59.307 50.000 0.00 0.00 43.59 3.66
3155 3298 2.290641 GGGCGTGGTGATGATTTGATAC 59.709 50.000 0.00 0.00 0.00 2.24
3175 3318 6.595326 TGATACTGCAGAACATAACAAGAAGG 59.405 38.462 23.35 0.00 0.00 3.46
3291 3434 3.058570 CGACAGATTGATCTAGACCGGAG 60.059 52.174 9.46 0.00 34.85 4.63
3334 3477 2.093711 GGAGCTGGAAGAAGAGAGGAAC 60.094 54.545 0.00 0.00 34.07 3.62
3337 3480 0.608640 TGGAAGAAGAGAGGAACGCC 59.391 55.000 0.00 0.00 0.00 5.68
3503 3646 1.077915 GCTGCTTGCTCAGAGAGAAC 58.922 55.000 0.00 0.00 38.95 3.01
3578 3721 2.525105 TGGAGGGCCAATAAAGGAAC 57.475 50.000 6.18 0.00 42.49 3.62
3583 3726 4.281657 GAGGGCCAATAAAGGAACAAGAT 58.718 43.478 6.18 0.00 0.00 2.40
3584 3727 4.026052 AGGGCCAATAAAGGAACAAGATG 58.974 43.478 6.18 0.00 0.00 2.90
3608 3751 2.958355 CAGCTCCCCTTTGAAGAACAAA 59.042 45.455 0.00 0.00 44.79 2.83
3701 3844 3.303132 GCTTCACTTGTACTCCAACAACG 60.303 47.826 0.00 0.00 35.56 4.10
3799 3942 5.671735 TCAATCTTCTAGAATGGATGGGGAA 59.328 40.000 5.44 0.00 0.00 3.97
3817 3960 3.471680 GGAAGCTGACCTATCCACATTC 58.528 50.000 0.00 0.00 32.08 2.67
4030 4173 2.033299 CACACAAAACCTCTTCGTGCAT 59.967 45.455 0.00 0.00 0.00 3.96
4091 4234 8.257306 TGTGCTCCAAAAGAAAAGAAATAGTTT 58.743 29.630 0.00 0.00 0.00 2.66
4179 4323 4.438744 GGCAAGTATACTGGCATGTGTTTC 60.439 45.833 29.19 9.36 44.72 2.78
4330 4476 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
4332 4478 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
4487 4635 1.969589 GTCGGCGACAAAACCCCAT 60.970 57.895 33.07 0.00 32.09 4.00
4655 4803 6.205101 CCTTTTGGAATGAGAAGGAGAATG 57.795 41.667 0.00 0.00 44.07 2.67
4656 4804 5.948162 CCTTTTGGAATGAGAAGGAGAATGA 59.052 40.000 0.00 0.00 44.07 2.57
4657 4805 6.095160 CCTTTTGGAATGAGAAGGAGAATGAG 59.905 42.308 0.00 0.00 44.07 2.90
4658 4806 6.378661 TTTGGAATGAGAAGGAGAATGAGA 57.621 37.500 0.00 0.00 0.00 3.27
4659 4807 6.378661 TTGGAATGAGAAGGAGAATGAGAA 57.621 37.500 0.00 0.00 0.00 2.87
4660 4808 5.987098 TGGAATGAGAAGGAGAATGAGAAG 58.013 41.667 0.00 0.00 0.00 2.85
4673 4821 3.678056 ATGAGAAGTTACGGTTGAGCA 57.322 42.857 0.00 0.00 0.00 4.26
4674 4822 3.026630 TGAGAAGTTACGGTTGAGCAG 57.973 47.619 0.00 0.00 0.00 4.24
4791 4947 4.923871 GCGATACATGTATTCCTCATTCGT 59.076 41.667 19.19 0.00 30.65 3.85
4906 5062 1.740025 GGCTTGGATGAAAAGGAGTCG 59.260 52.381 0.00 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
126 133 1.591594 CCGATAATCAGCACGCCGT 60.592 57.895 0.00 0.00 0.00 5.68
179 189 1.661463 AGGAAATCACAGGAGGAGCA 58.339 50.000 0.00 0.00 0.00 4.26
185 195 2.553028 GCCACAGAAGGAAATCACAGGA 60.553 50.000 0.00 0.00 0.00 3.86
196 206 2.046892 CGGGTCAGCCACAGAAGG 60.047 66.667 0.00 0.00 36.17 3.46
197 207 1.669115 CACGGGTCAGCCACAGAAG 60.669 63.158 0.00 0.00 36.17 2.85
241 251 1.458639 GCTTCCTTGCAAGGCACAGT 61.459 55.000 36.24 0.00 46.06 3.55
242 252 1.288127 GCTTCCTTGCAAGGCACAG 59.712 57.895 36.24 29.41 46.06 3.66
243 253 1.042003 TTGCTTCCTTGCAAGGCACA 61.042 50.000 36.24 28.85 46.43 4.57
244 254 1.741525 TTGCTTCCTTGCAAGGCAC 59.258 52.632 36.24 26.91 46.43 5.01
245 255 4.274012 TTGCTTCCTTGCAAGGCA 57.726 50.000 36.24 27.91 46.43 4.75
265 281 2.218603 AGGAACAACACGGTAAGCAAG 58.781 47.619 0.00 0.00 0.00 4.01
267 283 2.335316 AAGGAACAACACGGTAAGCA 57.665 45.000 0.00 0.00 0.00 3.91
268 284 3.703286 AAAAGGAACAACACGGTAAGC 57.297 42.857 0.00 0.00 0.00 3.09
269 285 7.198306 AGAATAAAAGGAACAACACGGTAAG 57.802 36.000 0.00 0.00 0.00 2.34
271 287 7.933033 ACTAAGAATAAAAGGAACAACACGGTA 59.067 33.333 0.00 0.00 0.00 4.02
272 288 6.769341 ACTAAGAATAAAAGGAACAACACGGT 59.231 34.615 0.00 0.00 0.00 4.83
320 337 5.592104 TCTAGGATGCGTACAGAATCAAA 57.408 39.130 7.64 0.00 36.57 2.69
348 365 8.638873 CCAAATCCCCAATAGAAAATAACTACC 58.361 37.037 0.00 0.00 0.00 3.18
349 366 8.638873 CCCAAATCCCCAATAGAAAATAACTAC 58.361 37.037 0.00 0.00 0.00 2.73
364 390 0.549902 TCTCAGCTCCCAAATCCCCA 60.550 55.000 0.00 0.00 0.00 4.96
418 444 6.575244 AATGGGATTCTAACAGTGATACCA 57.425 37.500 0.00 0.00 0.00 3.25
419 445 7.119846 GCATAATGGGATTCTAACAGTGATACC 59.880 40.741 0.00 0.00 0.00 2.73
420 446 7.119846 GGCATAATGGGATTCTAACAGTGATAC 59.880 40.741 0.00 0.00 0.00 2.24
421 447 7.168219 GGCATAATGGGATTCTAACAGTGATA 58.832 38.462 0.00 0.00 0.00 2.15
422 448 6.006449 GGCATAATGGGATTCTAACAGTGAT 58.994 40.000 0.00 0.00 0.00 3.06
423 449 5.104151 TGGCATAATGGGATTCTAACAGTGA 60.104 40.000 0.00 0.00 0.00 3.41
424 450 5.132502 TGGCATAATGGGATTCTAACAGTG 58.867 41.667 0.00 0.00 0.00 3.66
425 451 5.387113 TGGCATAATGGGATTCTAACAGT 57.613 39.130 0.00 0.00 0.00 3.55
426 452 5.829924 ACTTGGCATAATGGGATTCTAACAG 59.170 40.000 0.00 0.00 0.00 3.16
427 453 5.593909 CACTTGGCATAATGGGATTCTAACA 59.406 40.000 0.00 0.00 0.00 2.41
428 454 5.010012 CCACTTGGCATAATGGGATTCTAAC 59.990 44.000 4.66 0.00 0.00 2.34
429 455 5.103728 TCCACTTGGCATAATGGGATTCTAA 60.104 40.000 11.08 0.00 32.73 2.10
430 456 4.415179 TCCACTTGGCATAATGGGATTCTA 59.585 41.667 11.08 0.00 32.73 2.10
431 457 3.205056 TCCACTTGGCATAATGGGATTCT 59.795 43.478 11.08 0.00 32.73 2.40
432 458 3.565307 TCCACTTGGCATAATGGGATTC 58.435 45.455 11.08 0.00 32.73 2.52
433 459 3.686227 TCCACTTGGCATAATGGGATT 57.314 42.857 11.08 0.00 32.73 3.01
434 460 3.909427 ATCCACTTGGCATAATGGGAT 57.091 42.857 11.08 6.60 32.73 3.85
435 461 3.686227 AATCCACTTGGCATAATGGGA 57.314 42.857 11.08 4.77 32.73 4.37
436 462 3.243501 CGAAATCCACTTGGCATAATGGG 60.244 47.826 11.08 0.00 32.73 4.00
437 463 3.381272 ACGAAATCCACTTGGCATAATGG 59.619 43.478 5.97 5.97 34.44 3.16
438 464 4.637483 ACGAAATCCACTTGGCATAATG 57.363 40.909 0.00 0.00 34.44 1.90
439 465 4.677779 GCAACGAAATCCACTTGGCATAAT 60.678 41.667 0.00 0.00 34.44 1.28
440 466 3.366883 GCAACGAAATCCACTTGGCATAA 60.367 43.478 0.00 0.00 34.44 1.90
441 467 2.163412 GCAACGAAATCCACTTGGCATA 59.837 45.455 0.00 0.00 34.44 3.14
442 468 1.067635 GCAACGAAATCCACTTGGCAT 60.068 47.619 0.00 0.00 34.44 4.40
443 469 0.313672 GCAACGAAATCCACTTGGCA 59.686 50.000 0.00 0.00 34.44 4.92
444 470 0.388520 GGCAACGAAATCCACTTGGC 60.389 55.000 0.00 0.00 34.44 4.52
445 471 3.792716 GGCAACGAAATCCACTTGG 57.207 52.632 0.00 0.00 0.00 3.61
467 493 2.612212 CTCCGGCAATAACACACCATAC 59.388 50.000 0.00 0.00 0.00 2.39
479 505 2.084546 GAGCAACTAAACTCCGGCAAT 58.915 47.619 0.00 0.00 0.00 3.56
483 509 1.079503 GCTGAGCAACTAAACTCCGG 58.920 55.000 0.00 0.00 31.65 5.14
488 514 2.414825 GCTGAGAGCTGAGCAACTAAAC 59.585 50.000 7.39 0.00 39.66 2.01
508 534 3.058639 CCTTGTAGTGAGCTGAAACTTGC 60.059 47.826 0.00 0.00 0.00 4.01
525 551 1.134580 CGCAGGACAGATGATCCTTGT 60.135 52.381 0.00 0.00 44.64 3.16
554 580 3.617284 TCGCAGATACACTAGACCAAGA 58.383 45.455 0.00 0.00 0.00 3.02
684 806 4.262635 CGATATAGGCAGGATTGGTGAAGT 60.263 45.833 0.00 0.00 0.00 3.01
694 816 1.047801 TTGCAGCGATATAGGCAGGA 58.952 50.000 0.00 0.00 37.59 3.86
698 820 2.158449 GTGTCATTGCAGCGATATAGGC 59.842 50.000 0.00 0.00 0.00 3.93
729 851 7.109501 TCATTGAGAAGATGAACGGGAAAATA 58.890 34.615 0.00 0.00 30.96 1.40
736 858 5.049818 GCCTTATCATTGAGAAGATGAACGG 60.050 44.000 19.95 5.88 37.11 4.44
847 970 9.227777 GGGAATTTACTTCAGTGTTACAGTTAT 57.772 33.333 0.00 0.00 35.41 1.89
869 992 5.007682 GGTTAGTAATCAGCAAAGTGGGAA 58.992 41.667 0.00 0.00 0.00 3.97
872 995 6.381801 CAAAGGTTAGTAATCAGCAAAGTGG 58.618 40.000 0.00 0.00 0.00 4.00
887 1010 6.136541 ACAAGAAGTCAAAGCAAAGGTTAG 57.863 37.500 0.00 0.00 0.00 2.34
891 1014 4.540824 GCTACAAGAAGTCAAAGCAAAGG 58.459 43.478 0.00 0.00 0.00 3.11
957 1080 0.537653 TCACGACAGTTGGTCCAACA 59.462 50.000 31.59 10.58 45.66 3.33
964 1087 2.663602 CTCGAATCTTCACGACAGTTGG 59.336 50.000 0.00 0.00 34.82 3.77
966 1089 3.644884 ACTCGAATCTTCACGACAGTT 57.355 42.857 0.00 0.00 34.82 3.16
1109 1232 0.038166 ACGGGCAAATCTGGTGATGT 59.962 50.000 0.00 0.00 32.44 3.06
1164 1287 1.543802 CCGAGGACATGATCTAGCCTC 59.456 57.143 0.00 11.85 41.29 4.70
1185 1308 0.963962 AGAAGCACGGTTCCTCGTTA 59.036 50.000 5.40 0.00 41.86 3.18
1188 1311 0.242825 TGTAGAAGCACGGTTCCTCG 59.757 55.000 5.40 0.00 0.00 4.63
1197 1320 4.574013 CAGATCAATTCCCTGTAGAAGCAC 59.426 45.833 0.00 0.00 0.00 4.40
1361 1484 2.436646 CATCCACGGTGGGCTCAC 60.437 66.667 26.07 8.68 42.91 3.51
1369 1492 2.565391 TGAGTACATTGACATCCACGGT 59.435 45.455 0.00 0.00 0.00 4.83
1381 1504 3.194968 CCCTGAGTACCGTTGAGTACATT 59.805 47.826 0.00 0.00 44.19 2.71
1518 1641 3.044986 CGTGCAAATCTTTGGTGACTTG 58.955 45.455 4.93 0.00 38.57 3.16
1573 1696 6.098982 TGGTGGTAAATGTCTTTGGTTTCAAT 59.901 34.615 0.00 0.00 32.28 2.57
1613 1736 6.067350 TGTAGAGCACTGTATCTCTCATGAT 58.933 40.000 12.99 0.00 40.00 2.45
1722 1845 6.352016 ACTGCATCTTCTTGAAAGTCTCTA 57.648 37.500 0.00 0.00 0.00 2.43
1734 1857 6.240894 TGGTATCTCAAAAACTGCATCTTCT 58.759 36.000 0.00 0.00 0.00 2.85
1859 1982 3.941483 CACACTGTCAGGGTCATAATTCC 59.059 47.826 4.25 0.00 21.60 3.01
1860 1983 4.832248 TCACACTGTCAGGGTCATAATTC 58.168 43.478 4.25 0.00 21.60 2.17
1943 2066 3.290710 TCTTCAATGGCAATTAGAGGGC 58.709 45.455 0.00 0.00 0.00 5.19
2125 2252 4.999311 CCTCTGACATGATTCAGTTTCACA 59.001 41.667 11.82 0.00 43.19 3.58
2162 2289 7.493645 TGAATTGAGATGTATATGGATCGATGC 59.506 37.037 10.37 10.37 0.00 3.91
2273 2400 7.484959 GGTTCGATGAATAGAAACAAAATGTCC 59.515 37.037 0.00 0.00 34.43 4.02
2282 2409 5.584649 TCATGGTGGTTCGATGAATAGAAAC 59.415 40.000 0.00 0.00 38.10 2.78
2288 2415 3.009723 GTGTCATGGTGGTTCGATGAAT 58.990 45.455 0.00 0.00 41.52 2.57
2289 2416 2.224402 TGTGTCATGGTGGTTCGATGAA 60.224 45.455 0.00 0.00 41.52 2.57
2295 2422 3.791973 TTTGTTGTGTCATGGTGGTTC 57.208 42.857 0.00 0.00 0.00 3.62
2350 2477 5.292834 CACTTGATATCGCAGTGATTTCTGT 59.707 40.000 22.17 10.17 38.57 3.41
2351 2478 5.521372 TCACTTGATATCGCAGTGATTTCTG 59.479 40.000 24.02 9.70 38.57 3.02
2364 2491 6.978659 TCTGGTGAAATACGTCACTTGATATC 59.021 38.462 0.00 0.00 45.98 1.63
2375 2502 3.244078 TGTGCTTCTCTGGTGAAATACGT 60.244 43.478 0.00 0.00 0.00 3.57
2377 2504 5.392380 CCAATGTGCTTCTCTGGTGAAATAC 60.392 44.000 0.00 0.00 0.00 1.89
2379 2506 3.508793 CCAATGTGCTTCTCTGGTGAAAT 59.491 43.478 0.00 0.00 0.00 2.17
2407 2534 5.048846 ACTGGTTCACTTGTAACTGGATT 57.951 39.130 0.00 0.00 0.00 3.01
2445 2572 9.494271 GGATATGTATCTTCTGAAGCAACATAA 57.506 33.333 28.44 19.77 38.32 1.90
2460 2587 8.925338 ACTAAGAAACCTTTCGGATATGTATCT 58.075 33.333 0.51 0.00 41.92 1.98
2461 2588 9.543783 AACTAAGAAACCTTTCGGATATGTATC 57.456 33.333 0.00 0.00 41.92 2.24
2462 2589 9.901172 AAACTAAGAAACCTTTCGGATATGTAT 57.099 29.630 0.00 0.00 41.92 2.29
2463 2590 9.729281 AAAACTAAGAAACCTTTCGGATATGTA 57.271 29.630 0.00 0.00 41.92 2.29
2464 2591 8.512138 CAAAACTAAGAAACCTTTCGGATATGT 58.488 33.333 0.00 0.00 41.92 2.29
2465 2592 8.512138 ACAAAACTAAGAAACCTTTCGGATATG 58.488 33.333 0.00 0.00 41.92 1.78
2466 2593 8.631480 ACAAAACTAAGAAACCTTTCGGATAT 57.369 30.769 0.00 0.00 41.92 1.63
2467 2594 7.935210 AGACAAAACTAAGAAACCTTTCGGATA 59.065 33.333 0.00 0.00 41.92 2.59
2468 2595 6.771267 AGACAAAACTAAGAAACCTTTCGGAT 59.229 34.615 0.00 0.00 41.92 4.18
2469 2596 6.117488 AGACAAAACTAAGAAACCTTTCGGA 58.883 36.000 0.00 0.00 41.92 4.55
2470 2597 6.260271 AGAGACAAAACTAAGAAACCTTTCGG 59.740 38.462 0.00 0.00 41.92 4.30
2471 2598 7.224949 AGAGAGACAAAACTAAGAAACCTTTCG 59.775 37.037 0.00 0.00 41.92 3.46
2472 2599 8.439993 AGAGAGACAAAACTAAGAAACCTTTC 57.560 34.615 0.00 0.00 37.45 2.62
2473 2600 8.809468 AAGAGAGACAAAACTAAGAAACCTTT 57.191 30.769 0.00 0.00 0.00 3.11
2474 2601 8.809468 AAAGAGAGACAAAACTAAGAAACCTT 57.191 30.769 0.00 0.00 0.00 3.50
2514 2656 9.491934 CGAGATTCAGTTAATATAGATACGTGG 57.508 37.037 0.00 0.00 0.00 4.94
2720 2862 5.471257 ACAAACGAACAAACCTTTTGCTAA 58.529 33.333 0.00 0.00 31.61 3.09
2737 2879 1.737793 GCTGGATGGAAGGTACAAACG 59.262 52.381 0.00 0.00 0.00 3.60
2795 2938 6.728089 ATGAGTCTCTTTAGCATCTGATCA 57.272 37.500 0.65 0.00 0.00 2.92
2806 2949 7.331026 CAACTGGTGGAATATGAGTCTCTTTA 58.669 38.462 0.65 0.00 0.00 1.85
2813 2956 3.009473 ACAGCAACTGGTGGAATATGAGT 59.991 43.478 13.08 0.00 46.90 3.41
2890 3033 3.701532 TCACCAACCGTTTCAATTGTC 57.298 42.857 5.13 0.00 0.00 3.18
2938 3081 0.108186 TGTAGGCCTCGTTCATGCTG 60.108 55.000 9.68 0.00 0.00 4.41
2950 3093 0.947244 CAATGGCGAGATTGTAGGCC 59.053 55.000 0.00 0.00 45.76 5.19
3004 3147 2.098117 GCCCTTTCCAAGAATCACATCG 59.902 50.000 0.00 0.00 0.00 3.84
3031 3174 5.105146 CCTCAGTTCTCCATTTACACTAGCT 60.105 44.000 0.00 0.00 0.00 3.32
3073 3216 2.532715 AGCCCCCTGGAAGCTGAA 60.533 61.111 9.29 0.00 34.99 3.02
3076 3219 4.722535 TCGAGCCCCCTGGAAGCT 62.723 66.667 9.78 9.78 40.24 3.74
3127 3270 2.731571 ATCACCACGCCCATACGCT 61.732 57.895 0.00 0.00 36.19 5.07
3155 3298 5.879223 AGATCCTTCTTGTTATGTTCTGCAG 59.121 40.000 7.63 7.63 0.00 4.41
3291 3434 0.386113 GCAGAGGAGGTGTATCGACC 59.614 60.000 0.00 0.00 36.09 4.79
3496 3639 7.554118 TCCAATTCCTGTATTTGATGTTCTCTC 59.446 37.037 0.00 0.00 0.00 3.20
3503 3646 5.594926 GGCTTCCAATTCCTGTATTTGATG 58.405 41.667 0.00 0.00 0.00 3.07
3533 3676 2.480073 CAGGTTGTGTCCTGCACTTTTG 60.480 50.000 0.00 0.00 46.53 2.44
3570 3713 5.431765 GGAGCTGATCATCTTGTTCCTTTA 58.568 41.667 0.00 0.00 0.00 1.85
3572 3715 3.371380 GGGAGCTGATCATCTTGTTCCTT 60.371 47.826 13.06 0.00 0.00 3.36
3575 3718 2.172293 AGGGGAGCTGATCATCTTGTTC 59.828 50.000 0.00 0.00 0.00 3.18
3578 3721 2.950309 CAAAGGGGAGCTGATCATCTTG 59.050 50.000 0.00 0.00 0.00 3.02
3583 3726 2.269023 TCTTCAAAGGGGAGCTGATCA 58.731 47.619 0.00 0.00 0.00 2.92
3584 3727 3.013219 GTTCTTCAAAGGGGAGCTGATC 58.987 50.000 0.00 0.00 0.00 2.92
3735 3878 2.242926 TGGACTCTTGTGTCTCCTCTG 58.757 52.381 3.40 0.00 37.16 3.35
3799 3942 2.481441 TGGAATGTGGATAGGTCAGCT 58.519 47.619 0.00 0.00 0.00 4.24
3817 3960 2.935201 CAAGCTCGAGATTTCCTCTTGG 59.065 50.000 18.75 0.00 39.78 3.61
4030 4173 1.780309 ACAAGTTGGGTGGGAATCTGA 59.220 47.619 7.96 0.00 0.00 3.27
4087 4230 7.253905 TCCTAGATGTAGCAACCTAAAAACT 57.746 36.000 0.00 0.00 0.00 2.66
4091 4234 6.869206 AGTTCCTAGATGTAGCAACCTAAA 57.131 37.500 0.20 0.00 28.13 1.85
4179 4323 6.776094 ACTCGTCTCACAAAGAAAAGAAAAG 58.224 36.000 0.00 0.00 35.21 2.27
4292 4438 3.196901 ACACACACACTTCCTGTTCAGTA 59.803 43.478 0.00 0.00 0.00 2.74
4330 4476 2.769663 AGTCTCAACCAGGTTACACACA 59.230 45.455 3.89 0.00 0.00 3.72
4332 4478 3.199071 ACAAGTCTCAACCAGGTTACACA 59.801 43.478 3.89 0.00 0.00 3.72
4487 4635 1.992667 CTGCAGCTAACGAATCGAACA 59.007 47.619 10.55 0.00 0.00 3.18
4649 4797 4.327627 GCTCAACCGTAACTTCTCATTCTC 59.672 45.833 0.00 0.00 0.00 2.87
4650 4798 4.246458 GCTCAACCGTAACTTCTCATTCT 58.754 43.478 0.00 0.00 0.00 2.40
4651 4799 3.994392 TGCTCAACCGTAACTTCTCATTC 59.006 43.478 0.00 0.00 0.00 2.67
4652 4800 3.997021 CTGCTCAACCGTAACTTCTCATT 59.003 43.478 0.00 0.00 0.00 2.57
4653 4801 3.258372 TCTGCTCAACCGTAACTTCTCAT 59.742 43.478 0.00 0.00 0.00 2.90
4654 4802 2.626266 TCTGCTCAACCGTAACTTCTCA 59.374 45.455 0.00 0.00 0.00 3.27
4655 4803 2.987821 GTCTGCTCAACCGTAACTTCTC 59.012 50.000 0.00 0.00 0.00 2.87
4656 4804 2.288886 GGTCTGCTCAACCGTAACTTCT 60.289 50.000 0.00 0.00 0.00 2.85
4657 4805 2.067013 GGTCTGCTCAACCGTAACTTC 58.933 52.381 0.00 0.00 0.00 3.01
4658 4806 1.692519 AGGTCTGCTCAACCGTAACTT 59.307 47.619 0.00 0.00 41.89 2.66
4659 4807 1.339097 AGGTCTGCTCAACCGTAACT 58.661 50.000 0.00 0.00 41.89 2.24
4660 4808 1.798813 CAAGGTCTGCTCAACCGTAAC 59.201 52.381 0.00 0.00 41.89 2.50
4673 4821 1.136329 ATGGTGCAGGTCCAAGGTCT 61.136 55.000 0.00 0.00 38.52 3.85
4674 4822 0.962356 CATGGTGCAGGTCCAAGGTC 60.962 60.000 0.00 0.00 38.52 3.85
4739 4895 1.541147 CGGTCAATGGTGATGCTTGTT 59.459 47.619 0.00 0.00 35.80 2.83


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

AutoCloner maintained by Alex Coulton.