Multiple sequence alignment - TraesCS3A01G533700

Loading Multiple Alignment...

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 TraesCS3A01G533700 chr3A 100.000 3507 0 0 1 3507 746180200 746176694 0.000000e+00 6477
1 TraesCS3A01G533700 chr3D 90.242 2972 195 30 601 3506 611256770 611253828 0.000000e+00 3794
2 TraesCS3A01G533700 chr3D 92.683 123 5 4 8 127 611257584 611257463 1.290000e-39 174
3 TraesCS3A01G533700 chr3B 85.418 1927 199 40 924 2810 829017757 829015873 0.000000e+00 1927
4 TraesCS3A01G533700 chr3B 88.372 688 44 16 2847 3507 829015876 829015198 0.000000e+00 795
5 TraesCS3A01G533700 chr3B 79.949 394 37 18 12 367 829018855 829018466 5.810000e-63 252


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 TraesCS3A01G533700 chr3A 746176694 746180200 3506 True 6477.000000 6477 100.000000 1 3507 1 chr3A.!!$R1 3506
1 TraesCS3A01G533700 chr3D 611253828 611257584 3756 True 1984.000000 3794 91.462500 8 3506 2 chr3D.!!$R1 3498
2 TraesCS3A01G533700 chr3B 829015198 829018855 3657 True 991.333333 1927 84.579667 12 3507 3 chr3B.!!$R1 3495

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
379 457 0.039074 GTCGGATGTATGAGGCGGAG 60.039 60.0 0.0 0.0 0.0 4.63 F
439 517 0.178873 ACTGGGGAGTTCAAGGGCTA 60.179 55.0 0.0 0.0 0.0 3.93 F
441 519 0.178873 TGGGGAGTTCAAGGGCTAGT 60.179 55.0 0.0 0.0 0.0 2.57 F
716 1056 0.390472 CTCTTCTGCCCGTCCTTGAC 60.390 60.0 0.0 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1572 1963 0.603569 ACACGGCTGAGAGGTTAGTG 59.396 55.000 0.0 0.0 0.00 2.74 R
2297 2748 1.024046 TTCACACGCATGATTCCCGG 61.024 55.000 0.0 0.0 0.00 5.73 R
2299 2750 2.423185 TGATTTCACACGCATGATTCCC 59.577 45.455 0.0 0.0 0.00 3.97 R
2534 2986 0.041238 TACACCTCCTCTGGGGTCTG 59.959 60.000 0.0 0.0 40.16 3.51 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
54 58 1.755008 CACCCTCCTCCTCCTCGTC 60.755 68.421 0.00 0.00 0.00 4.20
86 90 2.121042 TCAAGCCCCCTTCCCCTT 60.121 61.111 0.00 0.00 0.00 3.95
127 131 2.178984 CCATCTCTCCTAACTCCCTCCT 59.821 54.545 0.00 0.00 0.00 3.69
128 132 3.399644 CCATCTCTCCTAACTCCCTCCTA 59.600 52.174 0.00 0.00 0.00 2.94
137 151 2.248742 ACTCCCTCCTATCCCCTACT 57.751 55.000 0.00 0.00 0.00 2.57
142 156 0.612453 CTCCTATCCCCTACTCGCCC 60.612 65.000 0.00 0.00 0.00 6.13
143 157 1.072505 TCCTATCCCCTACTCGCCCT 61.073 60.000 0.00 0.00 0.00 5.19
189 227 1.815421 CCCCGGCATTTCTCGACAG 60.815 63.158 0.00 0.00 0.00 3.51
230 284 1.880819 TTACTCCGTGGGCTCCGTTC 61.881 60.000 0.00 0.00 0.00 3.95
239 293 2.956964 GCTCCGTTCATCGCCGAG 60.957 66.667 0.00 0.00 38.35 4.63
256 310 1.835927 GAGTGCTTCCACCCAGCTCT 61.836 60.000 0.00 0.00 43.09 4.09
257 311 1.376553 GTGCTTCCACCCAGCTCTC 60.377 63.158 0.00 0.00 38.19 3.20
291 345 3.522343 AGGTACTTTACAACCAGGGATCC 59.478 47.826 1.92 1.92 38.30 3.36
362 440 3.195698 GAGCCGGCCACGATTGTC 61.196 66.667 26.15 7.69 44.60 3.18
365 443 4.444838 CCGGCCACGATTGTCGGA 62.445 66.667 2.24 0.00 45.59 4.55
366 444 2.202878 CGGCCACGATTGTCGGAT 60.203 61.111 2.24 0.00 45.59 4.18
367 445 2.525248 CGGCCACGATTGTCGGATG 61.525 63.158 2.24 0.00 45.59 3.51
368 446 1.449601 GGCCACGATTGTCGGATGT 60.450 57.895 0.00 0.00 45.59 3.06
369 447 0.179094 GGCCACGATTGTCGGATGTA 60.179 55.000 0.00 0.00 45.59 2.29
370 448 1.540363 GGCCACGATTGTCGGATGTAT 60.540 52.381 0.00 0.00 45.59 2.29
371 449 1.526887 GCCACGATTGTCGGATGTATG 59.473 52.381 4.28 0.00 45.59 2.39
372 450 2.801699 GCCACGATTGTCGGATGTATGA 60.802 50.000 4.28 0.00 45.59 2.15
373 451 3.052745 CCACGATTGTCGGATGTATGAG 58.947 50.000 4.28 0.00 45.59 2.90
374 452 3.052745 CACGATTGTCGGATGTATGAGG 58.947 50.000 4.28 0.00 45.59 3.86
375 453 2.061773 CGATTGTCGGATGTATGAGGC 58.938 52.381 0.00 0.00 36.00 4.70
376 454 2.061773 GATTGTCGGATGTATGAGGCG 58.938 52.381 0.00 0.00 0.00 5.52
377 455 0.104120 TTGTCGGATGTATGAGGCGG 59.896 55.000 0.00 0.00 0.00 6.13
378 456 0.753848 TGTCGGATGTATGAGGCGGA 60.754 55.000 0.00 0.00 0.00 5.54
379 457 0.039074 GTCGGATGTATGAGGCGGAG 60.039 60.000 0.00 0.00 0.00 4.63
380 458 0.467474 TCGGATGTATGAGGCGGAGT 60.467 55.000 0.00 0.00 0.00 3.85
381 459 0.319040 CGGATGTATGAGGCGGAGTG 60.319 60.000 0.00 0.00 0.00 3.51
400 478 3.006323 AGTGCCAACTAGAGAGTTCACAG 59.994 47.826 0.00 0.00 44.39 3.66
405 483 5.126384 GCCAACTAGAGAGTTCACAGAGTAT 59.874 44.000 0.00 0.00 44.39 2.12
413 491 6.954684 AGAGAGTTCACAGAGTATAAAAGGGA 59.045 38.462 0.00 0.00 0.00 4.20
414 492 7.621683 AGAGAGTTCACAGAGTATAAAAGGGAT 59.378 37.037 0.00 0.00 0.00 3.85
415 493 7.560368 AGAGTTCACAGAGTATAAAAGGGATG 58.440 38.462 0.00 0.00 0.00 3.51
416 494 6.653989 AGTTCACAGAGTATAAAAGGGATGG 58.346 40.000 0.00 0.00 0.00 3.51
417 495 5.630415 TCACAGAGTATAAAAGGGATGGG 57.370 43.478 0.00 0.00 0.00 4.00
418 496 4.412199 TCACAGAGTATAAAAGGGATGGGG 59.588 45.833 0.00 0.00 0.00 4.96
419 497 3.722101 ACAGAGTATAAAAGGGATGGGGG 59.278 47.826 0.00 0.00 0.00 5.40
422 500 3.981375 GAGTATAAAAGGGATGGGGGACT 59.019 47.826 0.00 0.00 0.00 3.85
424 502 1.304891 TAAAAGGGATGGGGGACTGG 58.695 55.000 0.00 0.00 0.00 4.00
425 503 1.518431 AAAAGGGATGGGGGACTGGG 61.518 60.000 0.00 0.00 0.00 4.45
426 504 3.990141 AAGGGATGGGGGACTGGGG 62.990 68.421 0.00 0.00 0.00 4.96
427 505 4.448340 GGGATGGGGGACTGGGGA 62.448 72.222 0.00 0.00 0.00 4.81
428 506 2.774351 GGATGGGGGACTGGGGAG 60.774 72.222 0.00 0.00 0.00 4.30
429 507 2.042930 GATGGGGGACTGGGGAGT 59.957 66.667 0.00 0.00 0.00 3.85
430 508 1.619669 GATGGGGGACTGGGGAGTT 60.620 63.158 0.00 0.00 0.00 3.01
431 509 1.619669 ATGGGGGACTGGGGAGTTC 60.620 63.158 0.00 0.00 0.00 3.01
432 510 2.204090 GGGGGACTGGGGAGTTCA 60.204 66.667 0.00 0.00 0.00 3.18
433 511 1.850755 GGGGGACTGGGGAGTTCAA 60.851 63.158 0.00 0.00 0.00 2.69
434 512 1.685820 GGGGACTGGGGAGTTCAAG 59.314 63.158 0.00 0.00 0.00 3.02
435 513 1.685820 GGGACTGGGGAGTTCAAGG 59.314 63.158 0.00 0.00 0.00 3.61
436 514 1.685820 GGACTGGGGAGTTCAAGGG 59.314 63.158 0.00 0.00 0.00 3.95
437 515 1.002011 GACTGGGGAGTTCAAGGGC 60.002 63.158 0.00 0.00 0.00 5.19
438 516 1.464198 ACTGGGGAGTTCAAGGGCT 60.464 57.895 0.00 0.00 0.00 5.19
439 517 0.178873 ACTGGGGAGTTCAAGGGCTA 60.179 55.000 0.00 0.00 0.00 3.93
440 518 0.543749 CTGGGGAGTTCAAGGGCTAG 59.456 60.000 0.00 0.00 0.00 3.42
441 519 0.178873 TGGGGAGTTCAAGGGCTAGT 60.179 55.000 0.00 0.00 0.00 2.57
442 520 1.079825 TGGGGAGTTCAAGGGCTAGTA 59.920 52.381 0.00 0.00 0.00 1.82
443 521 2.193993 GGGGAGTTCAAGGGCTAGTAA 58.806 52.381 0.00 0.00 0.00 2.24
454 532 2.502130 AGGGCTAGTAAACTCTTCTGCC 59.498 50.000 0.00 0.00 38.49 4.85
477 555 1.607628 GCAGGATGAATCATCACTGGC 59.392 52.381 27.21 19.68 42.13 4.85
486 564 2.957402 TCATCACTGGCCAGAGTTTT 57.043 45.000 39.19 13.98 0.00 2.43
514 596 4.385825 TCTTCCTCGTAATGCAACAAGTT 58.614 39.130 0.00 0.00 0.00 2.66
515 597 4.451096 TCTTCCTCGTAATGCAACAAGTTC 59.549 41.667 0.00 0.00 0.00 3.01
517 599 2.811431 CCTCGTAATGCAACAAGTTCCA 59.189 45.455 0.00 0.00 0.00 3.53
521 603 2.086610 AATGCAACAAGTTCCACCCT 57.913 45.000 0.00 0.00 0.00 4.34
526 608 2.038557 GCAACAAGTTCCACCCTAGAGA 59.961 50.000 0.00 0.00 0.00 3.10
544 626 6.890814 CCTAGAGAAAGAGTAGAGTGGGTTAA 59.109 42.308 0.00 0.00 0.00 2.01
552 649 9.892130 AAAGAGTAGAGTGGGTTAATAGATTTG 57.108 33.333 0.00 0.00 0.00 2.32
553 650 7.501844 AGAGTAGAGTGGGTTAATAGATTTGC 58.498 38.462 0.00 0.00 0.00 3.68
554 651 7.125811 AGAGTAGAGTGGGTTAATAGATTTGCA 59.874 37.037 0.00 0.00 0.00 4.08
555 652 7.275920 AGTAGAGTGGGTTAATAGATTTGCAG 58.724 38.462 0.00 0.00 0.00 4.41
556 653 6.313519 AGAGTGGGTTAATAGATTTGCAGA 57.686 37.500 0.00 0.00 0.00 4.26
561 658 8.664079 AGTGGGTTAATAGATTTGCAGATATCT 58.336 33.333 0.00 0.00 35.41 1.98
563 660 8.439971 TGGGTTAATAGATTTGCAGATATCTGT 58.560 33.333 28.92 13.07 45.45 3.41
571 706 8.798859 AGATTTGCAGATATCTGTTGTTTAGT 57.201 30.769 28.92 11.05 45.45 2.24
575 710 7.977789 TGCAGATATCTGTTGTTTAGTTTGA 57.022 32.000 28.92 0.77 45.45 2.69
618 957 6.951062 TCACATTCACAGATTTGTTAACCA 57.049 33.333 2.48 0.00 34.62 3.67
664 1003 5.289917 AGTTTGCGTTGTTGTTTTTGGTATC 59.710 36.000 0.00 0.00 0.00 2.24
668 1007 5.038033 GCGTTGTTGTTTTTGGTATCTGAA 58.962 37.500 0.00 0.00 0.00 3.02
671 1010 6.915300 CGTTGTTGTTTTTGGTATCTGAATCA 59.085 34.615 0.00 0.00 0.00 2.57
672 1011 7.113404 CGTTGTTGTTTTTGGTATCTGAATCAG 59.887 37.037 3.38 3.38 0.00 2.90
673 1012 7.581213 TGTTGTTTTTGGTATCTGAATCAGT 57.419 32.000 10.36 0.67 32.61 3.41
674 1013 7.424803 TGTTGTTTTTGGTATCTGAATCAGTG 58.575 34.615 10.36 0.00 32.61 3.66
675 1014 6.573664 TGTTTTTGGTATCTGAATCAGTGG 57.426 37.500 10.36 0.00 32.61 4.00
677 1016 6.775142 TGTTTTTGGTATCTGAATCAGTGGAA 59.225 34.615 10.36 0.00 32.61 3.53
678 1017 7.040478 TGTTTTTGGTATCTGAATCAGTGGAAG 60.040 37.037 10.36 0.00 32.61 3.46
679 1018 5.762179 TTGGTATCTGAATCAGTGGAAGT 57.238 39.130 10.36 0.00 32.61 3.01
680 1019 5.762179 TGGTATCTGAATCAGTGGAAGTT 57.238 39.130 10.36 0.00 32.61 2.66
681 1020 5.491070 TGGTATCTGAATCAGTGGAAGTTG 58.509 41.667 10.36 0.00 32.61 3.16
682 1021 5.248248 TGGTATCTGAATCAGTGGAAGTTGA 59.752 40.000 10.36 0.00 32.61 3.18
693 1033 3.073062 AGTGGAAGTTGACTGGTTGCTAT 59.927 43.478 0.00 0.00 0.00 2.97
699 1039 6.258947 GGAAGTTGACTGGTTGCTATTATCTC 59.741 42.308 0.00 0.00 0.00 2.75
705 1045 5.363939 ACTGGTTGCTATTATCTCTTCTGC 58.636 41.667 0.00 0.00 0.00 4.26
707 1047 4.068599 GGTTGCTATTATCTCTTCTGCCC 58.931 47.826 0.00 0.00 0.00 5.36
716 1056 0.390472 CTCTTCTGCCCGTCCTTGAC 60.390 60.000 0.00 0.00 0.00 3.18
734 1074 7.691050 GTCCTTGACGTAATGTAGTTAATTTGC 59.309 37.037 0.00 0.00 0.00 3.68
742 1082 9.051027 CGTAATGTAGTTAATTTGCTCAACAAG 57.949 33.333 0.00 0.00 40.06 3.16
758 1098 6.490566 TCAACAAGTGAGATTCATCATGTG 57.509 37.500 0.00 0.00 0.00 3.21
855 1199 2.009774 CTGGTTGCTTCTTATGACCCG 58.990 52.381 0.00 0.00 0.00 5.28
866 1210 7.602644 TGCTTCTTATGACCCGTTGATTATATC 59.397 37.037 0.00 0.00 0.00 1.63
907 1282 1.006102 CTGTCCACCGTCACACTCC 60.006 63.158 0.00 0.00 0.00 3.85
913 1288 2.430921 CCGTCACACTCCGCTGAC 60.431 66.667 0.00 0.00 34.57 3.51
971 1352 9.890629 TTTCTATGCATTTCCGCTAATATCTAT 57.109 29.630 3.54 0.00 0.00 1.98
983 1364 6.393990 CGCTAATATCTATCTGCCTTCTTGT 58.606 40.000 0.00 0.00 0.00 3.16
1148 1529 0.824759 GTGGAGCTCCGTCATAACCT 59.175 55.000 27.43 0.00 39.43 3.50
1254 1635 0.620556 GAGGCAAAGGAGGTGATGGA 59.379 55.000 0.00 0.00 0.00 3.41
1276 1657 3.393426 ACTCCCATGCAATCTCCAATT 57.607 42.857 0.00 0.00 0.00 2.32
1291 1672 5.690865 TCTCCAATTACAGTGAACCAAAGT 58.309 37.500 0.00 0.00 0.00 2.66
1300 1681 3.561725 CAGTGAACCAAAGTCCTCTTCAC 59.438 47.826 0.00 0.00 32.90 3.18
1336 1717 1.797025 GTCCTTTCCGGTGAGTTCAG 58.203 55.000 0.00 0.00 0.00 3.02
1371 1752 2.283298 CCGTGATTGCTTCAGCTATGT 58.717 47.619 0.16 0.00 42.66 2.29
1385 1769 3.806521 CAGCTATGTCGATGCTTTTAGCT 59.193 43.478 0.00 0.00 42.97 3.32
1417 1806 4.573607 GTGGTATCTTTATGAACGGGGAAC 59.426 45.833 0.00 0.00 0.00 3.62
1437 1826 1.804372 CGGGTGCTTGAGATCTAGTGC 60.804 57.143 0.00 0.50 0.00 4.40
1502 1891 8.424918 AGATGGGTATTCTTGCTATAATATCCG 58.575 37.037 9.78 0.00 40.37 4.18
1505 1894 7.181305 TGGGTATTCTTGCTATAATATCCGGAA 59.819 37.037 9.01 0.00 40.37 4.30
1507 1896 8.880750 GGTATTCTTGCTATAATATCCGGAAAC 58.119 37.037 9.01 0.00 0.00 2.78
1508 1897 7.923414 ATTCTTGCTATAATATCCGGAAACC 57.077 36.000 9.01 0.00 0.00 3.27
1539 1930 6.913673 TCATAGGTGAAAAACGTTTAGCAAAC 59.086 34.615 15.03 11.22 38.02 2.93
1558 1949 5.928264 GCAAACTCAAAAGGCAGTGATAATT 59.072 36.000 0.00 0.00 0.00 1.40
1560 1951 7.359514 GCAAACTCAAAAGGCAGTGATAATTTC 60.360 37.037 0.00 0.00 0.00 2.17
1572 1963 4.154195 AGTGATAATTTCTTGTGGCGTGTC 59.846 41.667 0.00 0.00 0.00 3.67
1626 2018 3.205338 CATGTTCACCTATCCGCATTGA 58.795 45.455 0.00 0.00 0.00 2.57
1631 2023 5.163353 TGTTCACCTATCCGCATTGAGAATA 60.163 40.000 0.00 0.00 0.00 1.75
1676 2068 5.265350 TGATGTGACCATGCCATTTAATG 57.735 39.130 0.00 0.00 0.00 1.90
1709 2101 6.215845 CCAGGCCAATTATACTATTTGTTGC 58.784 40.000 5.01 0.00 0.00 4.17
1725 2117 9.248291 CTATTTGTTGCGCCTAATGAATTATTT 57.752 29.630 4.18 0.00 0.00 1.40
1728 2120 5.809562 TGTTGCGCCTAATGAATTATTTTGG 59.190 36.000 4.18 0.00 0.00 3.28
1733 2125 5.451798 CGCCTAATGAATTATTTTGGCCAGT 60.452 40.000 5.11 0.00 40.76 4.00
1742 2141 3.525800 ATTTTGGCCAGTTGTCTAGGT 57.474 42.857 5.11 0.00 0.00 3.08
1753 2152 6.630413 GCCAGTTGTCTAGGTTCATCAATCTA 60.630 42.308 0.00 0.00 0.00 1.98
1781 2180 6.642131 GTGTGAATTTGAATGAGCTAAGCAAA 59.358 34.615 4.79 4.79 33.59 3.68
1846 2248 4.353777 AGTTCTGTTCCTACCTGCTATGA 58.646 43.478 0.00 0.00 0.00 2.15
1890 2292 0.608035 TTTAAGCTGGGCCTTCACGG 60.608 55.000 4.53 0.00 0.00 4.94
1913 2315 5.233689 GGTAAGTTGATACTGTAATCGTGGC 59.766 44.000 0.00 0.00 34.01 5.01
1916 2318 4.081642 AGTTGATACTGTAATCGTGGCAGT 60.082 41.667 0.00 0.00 44.49 4.40
1927 2329 4.853924 ATCGTGGCAGTTTTTCTGATTT 57.146 36.364 0.00 0.00 46.27 2.17
2033 2449 2.650116 GGAGGCCGTGAGAGAAGCA 61.650 63.158 0.00 0.00 0.00 3.91
2078 2494 2.676471 GCCACGTGAATTGGGCCT 60.676 61.111 19.30 0.00 40.55 5.19
2089 2505 5.564550 GTGAATTGGGCCTCAGATGTATAT 58.435 41.667 4.53 0.00 0.00 0.86
2264 2715 2.125673 CGCCGGGTAAGACCACAG 60.126 66.667 2.18 0.00 41.02 3.66
2297 2748 2.027625 CACCTTCGGTTCCACGCTC 61.028 63.158 0.00 0.00 31.02 5.03
2299 2750 2.809601 CTTCGGTTCCACGCTCCG 60.810 66.667 0.00 0.00 44.76 4.63
2425 2876 2.126071 TACAGCGCCTTCGACAGC 60.126 61.111 2.29 0.00 38.10 4.40
2491 2942 4.675029 CGGACGTGTTTCCCCGCT 62.675 66.667 0.00 0.00 35.29 5.52
2508 2959 4.147449 TGCCGAGGCGTCATGAGG 62.147 66.667 11.07 11.07 45.51 3.86
2601 3053 1.980765 AGAGAAATCCAGGCTGTGTGA 59.019 47.619 14.43 3.94 0.00 3.58
2602 3054 2.027377 AGAGAAATCCAGGCTGTGTGAG 60.027 50.000 14.43 0.00 0.00 3.51
2603 3055 1.701847 AGAAATCCAGGCTGTGTGAGT 59.298 47.619 14.43 0.00 0.00 3.41
2604 3056 1.808945 GAAATCCAGGCTGTGTGAGTG 59.191 52.381 14.43 0.00 0.00 3.51
2671 3125 7.378194 GCGTCCTTTATTAGTAAGTAGTGTAGC 59.622 40.741 0.00 0.00 0.00 3.58
2724 3178 0.463204 AGCCACGGACTGATGAGATG 59.537 55.000 0.00 0.00 0.00 2.90
2727 3181 1.284657 CACGGACTGATGAGATGTGC 58.715 55.000 0.00 0.00 0.00 4.57
2752 3206 6.096846 CGAATAATTGAATCCCCTTTTGAGGT 59.903 38.462 0.00 0.00 0.00 3.85
2753 3207 7.363793 CGAATAATTGAATCCCCTTTTGAGGTT 60.364 37.037 0.00 0.00 0.00 3.50
2791 3245 4.754114 GTGCTAATCTTATCTTGGCTCCAG 59.246 45.833 0.00 0.00 31.99 3.86
2808 3262 2.240414 TCCAGTGTCATCCATTGCTCAT 59.760 45.455 0.00 0.00 29.82 2.90
2814 3268 3.285484 GTCATCCATTGCTCATTGGTCT 58.715 45.455 9.73 0.00 34.40 3.85
3051 3529 3.087253 CACCGGTATGGGGGCTCA 61.087 66.667 6.87 0.00 44.64 4.26
3053 3531 4.235762 CCGGTATGGGGGCTCACG 62.236 72.222 0.00 0.00 0.00 4.35
3056 3534 2.676265 GGTATGGGGGCTCACGGTT 61.676 63.158 0.00 0.00 0.00 4.44
3065 3543 2.281761 CTCACGGTTGCTGCCCTT 60.282 61.111 0.00 0.00 0.00 3.95
3161 3639 2.122167 CGCGCTTACCCTCCTCTCT 61.122 63.158 5.56 0.00 0.00 3.10
3194 3672 4.557705 AGAAGGGTGCAGGTACACTATAT 58.442 43.478 0.00 0.00 40.52 0.86
3195 3673 5.712752 AGAAGGGTGCAGGTACACTATATA 58.287 41.667 0.00 0.00 40.52 0.86
3423 3908 5.879237 TGAGTTAGGCAAATCAAATTAGCG 58.121 37.500 0.00 0.00 35.91 4.26
3434 3919 2.564947 TCAAATTAGCGGCCACCAAAAT 59.435 40.909 2.24 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 3.403558 GAGGAGGAGGGTGTGGCC 61.404 72.222 0.00 0.00 0.00 5.36
35 36 2.360980 CGAGGAGGAGGAGGGTGT 59.639 66.667 0.00 0.00 0.00 4.16
109 113 3.658705 GGATAGGAGGGAGTTAGGAGAGA 59.341 52.174 0.00 0.00 0.00 3.10
127 131 0.404812 GAGAGGGCGAGTAGGGGATA 59.595 60.000 0.00 0.00 0.00 2.59
128 132 1.154221 GAGAGGGCGAGTAGGGGAT 59.846 63.158 0.00 0.00 0.00 3.85
137 151 2.798445 TTAGCTGGGTGAGAGGGCGA 62.798 60.000 0.00 0.00 0.00 5.54
142 156 0.618968 AGGGGTTAGCTGGGTGAGAG 60.619 60.000 0.00 0.00 0.00 3.20
143 157 0.617820 GAGGGGTTAGCTGGGTGAGA 60.618 60.000 0.00 0.00 0.00 3.27
239 293 1.376553 GAGAGCTGGGTGGAAGCAC 60.377 63.158 0.00 0.00 43.37 4.40
256 310 0.040351 AGTACCTGAGCTGCTGAGGA 59.960 55.000 36.48 19.75 37.01 3.71
257 311 0.901124 AAGTACCTGAGCTGCTGAGG 59.099 55.000 29.94 29.94 40.68 3.86
362 440 0.319040 CACTCCGCCTCATACATCCG 60.319 60.000 0.00 0.00 0.00 4.18
363 441 0.601311 GCACTCCGCCTCATACATCC 60.601 60.000 0.00 0.00 32.94 3.51
364 442 2.906047 GCACTCCGCCTCATACATC 58.094 57.895 0.00 0.00 32.94 3.06
374 452 0.179124 CTCTCTAGTTGGCACTCCGC 60.179 60.000 0.00 0.00 41.28 5.54
375 453 1.178276 ACTCTCTAGTTGGCACTCCG 58.822 55.000 0.00 0.00 34.06 4.63
376 454 2.563179 TGAACTCTCTAGTTGGCACTCC 59.437 50.000 0.00 0.00 46.09 3.85
377 455 3.005897 TGTGAACTCTCTAGTTGGCACTC 59.994 47.826 9.90 0.00 46.09 3.51
378 456 2.965831 TGTGAACTCTCTAGTTGGCACT 59.034 45.455 9.90 0.00 46.09 4.40
379 457 3.005897 TCTGTGAACTCTCTAGTTGGCAC 59.994 47.826 0.00 0.18 46.09 5.01
380 458 3.230976 TCTGTGAACTCTCTAGTTGGCA 58.769 45.455 0.00 0.00 46.09 4.92
381 459 3.257127 ACTCTGTGAACTCTCTAGTTGGC 59.743 47.826 0.00 0.00 46.09 4.52
386 464 8.410141 CCCTTTTATACTCTGTGAACTCTCTAG 58.590 40.741 0.00 0.00 0.00 2.43
400 478 3.981375 AGTCCCCCATCCCTTTTATACTC 59.019 47.826 0.00 0.00 0.00 2.59
405 483 1.304891 CCAGTCCCCCATCCCTTTTA 58.695 55.000 0.00 0.00 0.00 1.52
409 487 4.455137 CCCCAGTCCCCCATCCCT 62.455 72.222 0.00 0.00 0.00 4.20
413 491 1.619669 GAACTCCCCAGTCCCCCAT 60.620 63.158 0.00 0.00 29.93 4.00
414 492 2.204090 GAACTCCCCAGTCCCCCA 60.204 66.667 0.00 0.00 29.93 4.96
415 493 1.850755 TTGAACTCCCCAGTCCCCC 60.851 63.158 0.00 0.00 29.93 5.40
416 494 1.685820 CTTGAACTCCCCAGTCCCC 59.314 63.158 0.00 0.00 29.93 4.81
417 495 1.685820 CCTTGAACTCCCCAGTCCC 59.314 63.158 0.00 0.00 29.93 4.46
418 496 1.685820 CCCTTGAACTCCCCAGTCC 59.314 63.158 0.00 0.00 29.93 3.85
419 497 1.002011 GCCCTTGAACTCCCCAGTC 60.002 63.158 0.00 0.00 29.93 3.51
422 500 0.178873 ACTAGCCCTTGAACTCCCCA 60.179 55.000 0.00 0.00 0.00 4.96
424 502 3.263681 AGTTTACTAGCCCTTGAACTCCC 59.736 47.826 0.00 0.00 0.00 4.30
425 503 4.223255 AGAGTTTACTAGCCCTTGAACTCC 59.777 45.833 13.17 1.34 42.25 3.85
426 504 5.408880 AGAGTTTACTAGCCCTTGAACTC 57.591 43.478 10.27 10.27 41.84 3.01
427 505 5.544562 AGAAGAGTTTACTAGCCCTTGAACT 59.455 40.000 0.00 0.00 0.00 3.01
428 506 5.639931 CAGAAGAGTTTACTAGCCCTTGAAC 59.360 44.000 0.00 0.00 0.00 3.18
429 507 5.794894 CAGAAGAGTTTACTAGCCCTTGAA 58.205 41.667 0.00 0.00 0.00 2.69
430 508 4.322801 GCAGAAGAGTTTACTAGCCCTTGA 60.323 45.833 0.00 0.00 0.00 3.02
431 509 3.935828 GCAGAAGAGTTTACTAGCCCTTG 59.064 47.826 0.00 0.00 0.00 3.61
432 510 3.055021 GGCAGAAGAGTTTACTAGCCCTT 60.055 47.826 0.00 0.00 34.94 3.95
433 511 2.502130 GGCAGAAGAGTTTACTAGCCCT 59.498 50.000 0.00 0.00 34.94 5.19
434 512 2.907634 GGCAGAAGAGTTTACTAGCCC 58.092 52.381 0.00 0.00 34.94 5.19
435 513 2.236395 TGGGCAGAAGAGTTTACTAGCC 59.764 50.000 0.00 0.00 40.08 3.93
436 514 3.526534 CTGGGCAGAAGAGTTTACTAGC 58.473 50.000 0.00 0.00 0.00 3.42
437 515 3.055819 TGCTGGGCAGAAGAGTTTACTAG 60.056 47.826 0.00 0.00 33.32 2.57
438 516 2.903784 TGCTGGGCAGAAGAGTTTACTA 59.096 45.455 0.00 0.00 33.32 1.82
439 517 1.699634 TGCTGGGCAGAAGAGTTTACT 59.300 47.619 0.00 0.00 33.32 2.24
440 518 2.185004 TGCTGGGCAGAAGAGTTTAC 57.815 50.000 0.00 0.00 33.32 2.01
454 532 2.879026 CAGTGATGATTCATCCTGCTGG 59.121 50.000 21.08 2.58 39.87 4.85
464 542 2.706339 ACTCTGGCCAGTGATGATTC 57.294 50.000 35.28 0.00 0.00 2.52
465 543 3.446442 AAACTCTGGCCAGTGATGATT 57.554 42.857 35.28 21.80 0.00 2.57
486 564 5.529430 TGTTGCATTACGAGGAAGAAGAAAA 59.471 36.000 0.00 0.00 0.00 2.29
488 566 4.637276 TGTTGCATTACGAGGAAGAAGAA 58.363 39.130 0.00 0.00 0.00 2.52
490 568 4.452455 ACTTGTTGCATTACGAGGAAGAAG 59.548 41.667 10.00 0.00 41.35 2.85
491 569 4.385825 ACTTGTTGCATTACGAGGAAGAA 58.614 39.130 10.00 0.00 34.42 2.52
492 570 4.002906 ACTTGTTGCATTACGAGGAAGA 57.997 40.909 10.00 0.00 34.42 2.87
493 571 4.378459 GGAACTTGTTGCATTACGAGGAAG 60.378 45.833 10.00 0.00 34.42 3.46
495 573 3.071479 GGAACTTGTTGCATTACGAGGA 58.929 45.455 10.00 0.00 34.42 3.71
496 574 2.811431 TGGAACTTGTTGCATTACGAGG 59.189 45.455 10.00 0.00 34.42 4.63
499 577 2.351350 GGGTGGAACTTGTTGCATTACG 60.351 50.000 10.62 0.00 36.74 3.18
500 578 2.890945 AGGGTGGAACTTGTTGCATTAC 59.109 45.455 10.62 5.24 36.74 1.89
501 579 3.237268 AGGGTGGAACTTGTTGCATTA 57.763 42.857 10.62 0.00 36.74 1.90
502 580 2.086610 AGGGTGGAACTTGTTGCATT 57.913 45.000 10.62 0.00 36.74 3.56
503 581 2.375174 TCTAGGGTGGAACTTGTTGCAT 59.625 45.455 10.62 0.00 36.74 3.96
514 596 4.540906 ACTCTACTCTTTCTCTAGGGTGGA 59.459 45.833 0.00 0.00 34.19 4.02
515 597 4.642885 CACTCTACTCTTTCTCTAGGGTGG 59.357 50.000 0.00 0.00 35.94 4.61
517 599 4.325501 CCCACTCTACTCTTTCTCTAGGGT 60.326 50.000 0.00 0.00 32.47 4.34
521 603 9.629878 CTATTAACCCACTCTACTCTTTCTCTA 57.370 37.037 0.00 0.00 0.00 2.43
526 608 9.892130 CAAATCTATTAACCCACTCTACTCTTT 57.108 33.333 0.00 0.00 0.00 2.52
591 726 9.722056 GGTTAACAAATCTGTGAATGTGATATC 57.278 33.333 8.10 0.00 35.37 1.63
592 727 9.241919 TGGTTAACAAATCTGTGAATGTGATAT 57.758 29.630 8.10 0.00 35.37 1.63
593 728 8.511321 GTGGTTAACAAATCTGTGAATGTGATA 58.489 33.333 8.10 0.00 35.37 2.15
595 730 6.545666 AGTGGTTAACAAATCTGTGAATGTGA 59.454 34.615 8.10 0.00 35.37 3.58
597 732 6.545666 TCAGTGGTTAACAAATCTGTGAATGT 59.454 34.615 8.10 0.00 35.37 2.71
598 733 6.969366 TCAGTGGTTAACAAATCTGTGAATG 58.031 36.000 8.10 0.00 35.37 2.67
629 968 7.422399 ACAACAACGCAAACTAAATAACAGAT 58.578 30.769 0.00 0.00 0.00 2.90
630 969 6.787225 ACAACAACGCAAACTAAATAACAGA 58.213 32.000 0.00 0.00 0.00 3.41
664 1003 3.750130 CCAGTCAACTTCCACTGATTCAG 59.250 47.826 12.17 12.17 42.37 3.02
668 1007 3.480470 CAACCAGTCAACTTCCACTGAT 58.520 45.455 0.55 0.00 42.37 2.90
671 1010 1.212935 AGCAACCAGTCAACTTCCACT 59.787 47.619 0.00 0.00 0.00 4.00
672 1011 1.680338 AGCAACCAGTCAACTTCCAC 58.320 50.000 0.00 0.00 0.00 4.02
673 1012 3.788227 ATAGCAACCAGTCAACTTCCA 57.212 42.857 0.00 0.00 0.00 3.53
674 1013 6.116126 AGATAATAGCAACCAGTCAACTTCC 58.884 40.000 0.00 0.00 0.00 3.46
675 1014 7.044798 AGAGATAATAGCAACCAGTCAACTTC 58.955 38.462 0.00 0.00 0.00 3.01
677 1016 6.552445 AGAGATAATAGCAACCAGTCAACT 57.448 37.500 0.00 0.00 0.00 3.16
678 1017 7.010923 CAGAAGAGATAATAGCAACCAGTCAAC 59.989 40.741 0.00 0.00 0.00 3.18
679 1018 7.044181 CAGAAGAGATAATAGCAACCAGTCAA 58.956 38.462 0.00 0.00 0.00 3.18
680 1019 6.577103 CAGAAGAGATAATAGCAACCAGTCA 58.423 40.000 0.00 0.00 0.00 3.41
681 1020 5.465056 GCAGAAGAGATAATAGCAACCAGTC 59.535 44.000 0.00 0.00 0.00 3.51
682 1021 5.363939 GCAGAAGAGATAATAGCAACCAGT 58.636 41.667 0.00 0.00 0.00 4.00
693 1033 2.160721 AGGACGGGCAGAAGAGATAA 57.839 50.000 0.00 0.00 0.00 1.75
699 1039 4.285851 GTCAAGGACGGGCAGAAG 57.714 61.111 0.00 0.00 0.00 2.85
716 1056 8.942669 TTGTTGAGCAAATTAACTACATTACG 57.057 30.769 0.00 0.00 33.53 3.18
734 1074 6.370718 TCACATGATGAATCTCACTTGTTGAG 59.629 38.462 0.00 0.00 43.27 3.02
742 1082 7.375106 AGTTTCTTCACATGATGAATCTCAC 57.625 36.000 0.00 6.53 46.37 3.51
794 1138 6.034898 GTCAAATTTCTGACCAACTTGTTGTG 59.965 38.462 11.82 6.59 39.93 3.33
836 1180 1.349688 ACGGGTCATAAGAAGCAACCA 59.650 47.619 0.00 0.00 0.00 3.67
837 1181 2.109425 ACGGGTCATAAGAAGCAACC 57.891 50.000 0.00 0.00 0.00 3.77
866 1210 4.574013 GGGATCTCTTTGCATGTGTCTAAG 59.426 45.833 0.00 0.00 0.00 2.18
882 1226 0.970937 TGACGGTGGACAGGGATCTC 60.971 60.000 0.00 0.00 0.00 2.75
907 1282 2.572191 TAAAGGTATGGTCGTCAGCG 57.428 50.000 0.00 0.00 39.92 5.18
913 1288 5.348724 CCATCAATCGATAAAGGTATGGTCG 59.651 44.000 0.00 0.00 0.00 4.79
983 1364 1.204704 CCATGGAGTCGCTTGTCACTA 59.795 52.381 5.56 0.00 0.00 2.74
1107 1488 0.768221 AAGAACCTGGAGTCTGCCCA 60.768 55.000 0.00 0.00 0.00 5.36
1134 1515 0.105039 CCTCCAGGTTATGACGGAGC 59.895 60.000 6.17 0.00 43.15 4.70
1148 1529 3.073798 TGCTTGTTTATGAGTTCCCTCCA 59.926 43.478 0.00 0.00 36.86 3.86
1254 1635 2.905415 TGGAGATTGCATGGGAGTTT 57.095 45.000 0.00 0.00 0.00 2.66
1276 1657 4.407621 TGAAGAGGACTTTGGTTCACTGTA 59.592 41.667 0.00 0.00 36.39 2.74
1291 1672 1.137086 GCGCTCATAAGGTGAAGAGGA 59.863 52.381 0.00 0.00 36.14 3.71
1300 1681 1.766143 GACGGCAAGCGCTCATAAGG 61.766 60.000 12.06 0.45 38.60 2.69
1336 1717 5.149273 CAATCACGGCATAATCTAACATGC 58.851 41.667 0.00 0.00 45.47 4.06
1356 1737 2.547211 GCATCGACATAGCTGAAGCAAT 59.453 45.455 4.90 0.00 45.16 3.56
1371 1752 4.864806 CACAGAGTAAGCTAAAAGCATCGA 59.135 41.667 1.22 0.00 45.56 3.59
1385 1769 7.758076 CGTTCATAAAGATACCACACAGAGTAA 59.242 37.037 0.00 0.00 0.00 2.24
1417 1806 1.804372 GCACTAGATCTCAAGCACCCG 60.804 57.143 0.00 0.00 0.00 5.28
1502 1891 5.890424 TTCACCTATGAAAATCGGTTTCC 57.110 39.130 0.00 0.00 44.41 3.13
1516 1905 7.034685 AGTTTGCTAAACGTTTTTCACCTAT 57.965 32.000 20.19 0.00 45.88 2.57
1539 1930 7.327761 CACAAGAAATTATCACTGCCTTTTGAG 59.672 37.037 0.00 0.00 0.00 3.02
1558 1949 2.206750 GTTAGTGACACGCCACAAGAA 58.793 47.619 0.00 0.00 39.42 2.52
1560 1951 0.865769 GGTTAGTGACACGCCACAAG 59.134 55.000 0.00 0.00 39.42 3.16
1572 1963 0.603569 ACACGGCTGAGAGGTTAGTG 59.396 55.000 0.00 0.00 0.00 2.74
1626 2018 6.837471 AGTCAGTTAGAACTTCCGTATTCT 57.163 37.500 0.00 0.00 37.08 2.40
1631 2023 4.667519 ACAAGTCAGTTAGAACTTCCGT 57.332 40.909 0.00 0.00 37.08 4.69
1676 2068 1.632589 AATTGGCCTGGGAACTGAAC 58.367 50.000 3.32 0.00 0.00 3.18
1709 2101 4.942852 TGGCCAAAATAATTCATTAGGCG 58.057 39.130 0.61 0.00 43.71 5.52
1725 2117 1.771854 TGAACCTAGACAACTGGCCAA 59.228 47.619 7.01 0.00 0.00 4.52
1728 2120 3.334583 TGATGAACCTAGACAACTGGC 57.665 47.619 0.00 0.00 0.00 4.85
1733 2125 7.092891 ACACCATAGATTGATGAACCTAGACAA 60.093 37.037 0.00 0.00 0.00 3.18
1742 2141 8.578448 TCAAATTCACACCATAGATTGATGAA 57.422 30.769 0.00 0.00 0.00 2.57
1753 2152 6.626623 GCTTAGCTCATTCAAATTCACACCAT 60.627 38.462 0.00 0.00 0.00 3.55
1846 2248 2.576191 ACCAATACCACTACAGCACCAT 59.424 45.455 0.00 0.00 0.00 3.55
1890 2292 5.808540 TGCCACGATTACAGTATCAACTTAC 59.191 40.000 0.00 0.00 31.97 2.34
1927 2329 9.037737 GTCAGGCAACGATAAAACTGTATTATA 57.962 33.333 0.00 0.00 46.39 0.98
2264 2715 5.385396 CGAAGGTGGTAATACGAAATGTC 57.615 43.478 0.00 0.00 0.00 3.06
2297 2748 1.024046 TTCACACGCATGATTCCCGG 61.024 55.000 0.00 0.00 0.00 5.73
2299 2750 2.423185 TGATTTCACACGCATGATTCCC 59.577 45.455 0.00 0.00 0.00 3.97
2532 2984 3.086600 CCTCCTCTGGGGTCTGGC 61.087 72.222 0.00 0.00 36.25 4.85
2533 2985 1.992277 CACCTCCTCTGGGGTCTGG 60.992 68.421 0.00 0.00 32.95 3.86
2534 2986 0.041238 TACACCTCCTCTGGGGTCTG 59.959 60.000 0.00 0.00 40.16 3.51
2535 2987 0.336737 CTACACCTCCTCTGGGGTCT 59.663 60.000 0.00 0.00 40.16 3.85
2542 2994 4.598373 ACCGTATCTATCTACACCTCCTCT 59.402 45.833 0.00 0.00 0.00 3.69
2601 3053 2.633967 GGGCATCTCATCTCATCTCACT 59.366 50.000 0.00 0.00 0.00 3.41
2602 3054 2.633967 AGGGCATCTCATCTCATCTCAC 59.366 50.000 0.00 0.00 0.00 3.51
2603 3055 2.973710 AGGGCATCTCATCTCATCTCA 58.026 47.619 0.00 0.00 0.00 3.27
2604 3056 4.040706 AGAAAGGGCATCTCATCTCATCTC 59.959 45.833 0.00 0.00 0.00 2.75
2647 3101 8.401709 ACGCTACACTACTTACTAATAAAGGAC 58.598 37.037 0.00 0.00 0.00 3.85
2724 3178 4.918810 AAGGGGATTCAATTATTCGCAC 57.081 40.909 0.00 0.00 0.00 5.34
2727 3181 6.507023 CCTCAAAAGGGGATTCAATTATTCG 58.493 40.000 0.00 0.00 39.21 3.34
2752 3206 0.955428 GCACAAGGACTCGGCATCAA 60.955 55.000 0.00 0.00 0.00 2.57
2753 3207 1.375908 GCACAAGGACTCGGCATCA 60.376 57.895 0.00 0.00 0.00 3.07
2791 3245 2.756760 ACCAATGAGCAATGGATGACAC 59.243 45.455 11.35 0.00 39.12 3.67
2808 3262 0.397564 TGCTGCTGATCACAGACCAA 59.602 50.000 21.90 7.45 46.03 3.67
2814 3268 2.038837 GCTGCTGCTGCTGATCACA 61.039 57.895 23.39 0.00 40.01 3.58
2903 3360 1.471287 CCTTGCCGCTTTAAGTAACCC 59.529 52.381 0.00 0.00 0.00 4.11
3034 3512 3.087253 TGAGCCCCCATACCGGTG 61.087 66.667 19.93 0.00 0.00 4.94
3051 3529 2.281761 CAGAAGGGCAGCAACCGT 60.282 61.111 0.00 0.00 0.00 4.83
3053 3531 2.282745 AGCAGAAGGGCAGCAACC 60.283 61.111 0.00 0.00 35.83 3.77
3056 3534 3.573229 ACCAGCAGAAGGGCAGCA 61.573 61.111 0.00 0.00 35.83 4.41
3065 3543 3.896356 GAGCAGCAGCACCAGCAGA 62.896 63.158 3.17 0.00 45.49 4.26
3149 3627 2.442272 GCGCCAGAGAGGAGGGTA 60.442 66.667 0.00 0.00 41.22 3.69
3161 3639 4.082523 CCCTTCTCCTTCGCGCCA 62.083 66.667 0.00 0.00 0.00 5.69
3194 3672 9.364653 GGAAGGAAGAAACCTAGATATACAGTA 57.635 37.037 0.00 0.00 39.62 2.74
3195 3673 7.844779 TGGAAGGAAGAAACCTAGATATACAGT 59.155 37.037 0.00 0.00 39.62 3.55
3238 3717 4.610945 CACACTGAAACCAGACCAAATTC 58.389 43.478 0.00 0.00 35.67 2.17
3450 3938 7.274250 GTCAAAGCAGATTTTGGTAATGACATC 59.726 37.037 14.80 0.00 44.84 3.06
3453 3941 6.446318 TGTCAAAGCAGATTTTGGTAATGAC 58.554 36.000 13.66 13.66 45.23 3.06
3458 3946 6.003326 TCTCATGTCAAAGCAGATTTTGGTA 58.997 36.000 0.00 0.00 38.33 3.25


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

AutoCloner maintained by Alex Coulton.