Multiple sequence alignment - TraesCS1A01G150600

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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 TraesCS1A01G150600 chr1A 100.000 4056 0 0 1 4056 258737300 258741355 0.000000e+00 7491.0
1 TraesCS1A01G150600 chr1D 93.622 3418 121 40 676 4048 203745276 203748641 0.000000e+00 5014.0
2 TraesCS1A01G150600 chr1D 89.212 584 51 11 65 644 203744630 203745205 0.000000e+00 719.0
3 TraesCS1A01G150600 chr1B 95.340 3004 94 21 1047 4048 297723972 297726931 0.000000e+00 4730.0
4 TraesCS1A01G150600 chr1B 81.675 191 9 12 818 1005 297723544 297723711 7.070000e-28 135.0
5 TraesCS1A01G150600 chr1B 95.238 42 2 0 26 67 487686018 487685977 2.620000e-07 67.6
6 TraesCS1A01G150600 chr4A 91.837 49 4 0 19 67 647110867 647110819 7.270000e-08 69.4


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 TraesCS1A01G150600 chr1A 258737300 258741355 4055 False 7491.0 7491 100.0000 1 4056 1 chr1A.!!$F1 4055
1 TraesCS1A01G150600 chr1D 203744630 203748641 4011 False 2866.5 5014 91.4170 65 4048 2 chr1D.!!$F1 3983
2 TraesCS1A01G150600 chr1B 297723544 297726931 3387 False 2432.5 4730 88.5075 818 4048 2 chr1B.!!$F1 3230

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
20 21 0.095762 GCCGTCCGTAATTTTGTCCG 59.904 55.0 0.00 0.0 0.00 4.79 F
1453 1750 0.036875 GGCCTAGGGGTGTGCATATC 59.963 60.0 11.72 0.0 34.45 1.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1476 1773 0.252479 AGCACAAGAGAGATGCCCAG 59.748 55.0 0.0 0.0 40.33 4.45 R
3212 3509 0.250513 AGCAGCTACAGTACCAAGCC 59.749 55.0 0.0 0.0 36.92 4.35 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
19 20 1.445871 AGCCGTCCGTAATTTTGTCC 58.554 50.000 0.00 0.00 0.00 4.02
20 21 0.095762 GCCGTCCGTAATTTTGTCCG 59.904 55.000 0.00 0.00 0.00 4.79
21 22 1.431496 CCGTCCGTAATTTTGTCCGT 58.569 50.000 0.00 0.00 0.00 4.69
22 23 1.799994 CCGTCCGTAATTTTGTCCGTT 59.200 47.619 0.00 0.00 0.00 4.44
23 24 2.992543 CCGTCCGTAATTTTGTCCGTTA 59.007 45.455 0.00 0.00 0.00 3.18
24 25 3.181531 CCGTCCGTAATTTTGTCCGTTAC 60.182 47.826 0.00 0.00 0.00 2.50
25 26 3.674753 CGTCCGTAATTTTGTCCGTTACT 59.325 43.478 0.00 0.00 0.00 2.24
26 27 4.150451 CGTCCGTAATTTTGTCCGTTACTT 59.850 41.667 0.00 0.00 0.00 2.24
27 28 5.333263 CGTCCGTAATTTTGTCCGTTACTTT 60.333 40.000 0.00 0.00 0.00 2.66
28 29 6.128956 CGTCCGTAATTTTGTCCGTTACTTTA 60.129 38.462 0.00 0.00 0.00 1.85
29 30 7.411804 CGTCCGTAATTTTGTCCGTTACTTTAT 60.412 37.037 0.00 0.00 0.00 1.40
30 31 8.229811 GTCCGTAATTTTGTCCGTTACTTTATT 58.770 33.333 0.00 0.00 0.00 1.40
31 32 8.782144 TCCGTAATTTTGTCCGTTACTTTATTT 58.218 29.630 0.00 0.00 0.00 1.40
32 33 9.396938 CCGTAATTTTGTCCGTTACTTTATTTT 57.603 29.630 0.00 0.00 0.00 1.82
40 41 9.881529 TTGTCCGTTACTTTATTTTGTAATCAC 57.118 29.630 0.00 0.00 32.32 3.06
41 42 9.275398 TGTCCGTTACTTTATTTTGTAATCACT 57.725 29.630 0.00 0.00 32.32 3.41
93 94 7.866393 AGCTGTTTTCAAAGAATGATCAGAAAG 59.134 33.333 0.09 0.00 38.03 2.62
96 97 9.740239 TGTTTTCAAAGAATGATCAGAAAGAAG 57.260 29.630 0.09 0.00 38.03 2.85
97 98 9.741647 GTTTTCAAAGAATGATCAGAAAGAAGT 57.258 29.630 0.09 0.00 38.03 3.01
101 102 9.948964 TCAAAGAATGATCAGAAAGAAGTATGA 57.051 29.630 0.09 0.00 31.50 2.15
122 123 0.396435 ATGTTGGACGAAGCACTCCA 59.604 50.000 0.00 0.00 34.58 3.86
124 125 1.070786 TTGGACGAAGCACTCCACC 59.929 57.895 0.00 0.00 36.24 4.61
148 149 7.751768 CTGGAAGGAAAAGAAACACTATTCT 57.248 36.000 0.00 0.00 41.34 2.40
230 234 4.440839 CTTCTAATGAAGGCAACCCAAC 57.559 45.455 0.00 0.00 44.33 3.77
232 236 3.420893 TCTAATGAAGGCAACCCAACAG 58.579 45.455 0.00 0.00 37.17 3.16
236 240 0.244721 GAAGGCAACCCAACAGATGC 59.755 55.000 0.00 0.00 38.06 3.91
238 242 0.469705 AGGCAACCCAACAGATGCAA 60.470 50.000 0.00 0.00 40.51 4.08
250 254 4.900635 ACAGATGCAAAATACGGGAATC 57.099 40.909 0.00 0.00 0.00 2.52
252 256 3.885297 CAGATGCAAAATACGGGAATCCT 59.115 43.478 0.00 0.00 0.00 3.24
262 266 8.314751 CAAAATACGGGAATCCTATCTCTACAT 58.685 37.037 0.00 0.00 0.00 2.29
312 316 2.704725 AAATGCACACGTCATGAACC 57.295 45.000 0.00 0.00 0.00 3.62
317 321 3.206964 TGCACACGTCATGAACCTTAAA 58.793 40.909 0.00 0.00 0.00 1.52
344 348 1.141019 CGCTGCCCAGTGTATACGT 59.859 57.895 0.00 0.00 34.41 3.57
354 358 2.789339 CAGTGTATACGTGATTGCTCCG 59.211 50.000 0.00 0.00 0.00 4.63
402 407 5.776519 GATCCATCGACAATTCATAGCTC 57.223 43.478 0.00 0.00 0.00 4.09
406 411 4.813161 CCATCGACAATTCATAGCTCAGTT 59.187 41.667 0.00 0.00 0.00 3.16
413 418 7.138692 ACAATTCATAGCTCAGTTTGAGTTC 57.861 36.000 7.80 0.00 45.94 3.01
418 423 6.336566 TCATAGCTCAGTTTGAGTTCATCTC 58.663 40.000 7.80 0.00 45.94 2.75
431 436 2.432510 GTTCATCTCCTCTCGGGTGAAT 59.567 50.000 0.00 0.00 40.44 2.57
437 442 4.350245 TCTCCTCTCGGGTGAATAAGAAA 58.650 43.478 0.00 0.00 35.00 2.52
442 447 4.439057 TCTCGGGTGAATAAGAAATTCGG 58.561 43.478 0.00 0.00 0.00 4.30
461 466 8.846943 AATTCGGAAAAATAGCAAAAGGATTT 57.153 26.923 0.00 0.00 42.41 2.17
495 500 6.303054 TGAATTAGTTTGACACCAAGGATGA 58.697 36.000 0.00 0.00 33.23 2.92
496 501 6.947733 TGAATTAGTTTGACACCAAGGATGAT 59.052 34.615 0.00 0.00 33.23 2.45
525 530 6.601741 TTTTCTAGGTGCTTGCAAAATTTG 57.398 33.333 0.00 0.57 0.00 2.32
527 532 1.596603 AGGTGCTTGCAAAATTTGGC 58.403 45.000 10.83 10.83 0.00 4.52
530 535 1.154617 GCTTGCAAAATTTGGCGCG 60.155 52.632 12.85 0.00 0.00 6.86
531 536 1.830368 GCTTGCAAAATTTGGCGCGT 61.830 50.000 12.85 0.00 0.00 6.01
542 547 1.860676 TTGGCGCGTAGATTACATCC 58.139 50.000 8.43 0.00 0.00 3.51
562 567 2.072298 CGGAGGAGCTCAGTCAAAAAG 58.928 52.381 17.19 0.00 31.08 2.27
567 572 5.067805 GGAGGAGCTCAGTCAAAAAGAAAAA 59.932 40.000 17.19 0.00 31.08 1.94
602 607 2.892852 TCAGAGTTCCAAAATGCCCAAG 59.107 45.455 0.00 0.00 0.00 3.61
607 612 0.396060 TCCAAAATGCCCAAGGTTGC 59.604 50.000 0.00 0.00 0.00 4.17
617 622 2.419990 GCCCAAGGTTGCTTGAGTTTTT 60.420 45.455 0.00 0.00 36.50 1.94
621 626 4.093261 CCAAGGTTGCTTGAGTTTTTGTTG 59.907 41.667 0.00 0.00 36.50 3.33
640 645 5.310451 TGTTGTTTTTACCGAGCTCCTTAT 58.690 37.500 8.47 0.00 0.00 1.73
660 687 7.054124 CCTTATATGGCACCTAGAAACTTTGA 58.946 38.462 0.00 0.00 0.00 2.69
661 688 7.227512 CCTTATATGGCACCTAGAAACTTTGAG 59.772 40.741 0.00 0.00 0.00 3.02
662 689 2.504367 TGGCACCTAGAAACTTTGAGC 58.496 47.619 0.00 0.00 0.00 4.26
663 690 2.158682 TGGCACCTAGAAACTTTGAGCA 60.159 45.455 0.00 0.00 0.00 4.26
664 691 3.084786 GGCACCTAGAAACTTTGAGCAT 58.915 45.455 0.00 0.00 0.00 3.79
665 692 3.127721 GGCACCTAGAAACTTTGAGCATC 59.872 47.826 0.00 0.00 0.00 3.91
666 693 4.006319 GCACCTAGAAACTTTGAGCATCT 58.994 43.478 0.00 0.00 34.92 2.90
667 694 4.457257 GCACCTAGAAACTTTGAGCATCTT 59.543 41.667 0.00 0.00 34.92 2.40
668 695 5.048434 GCACCTAGAAACTTTGAGCATCTTT 60.048 40.000 0.00 0.00 34.92 2.52
669 696 6.376978 CACCTAGAAACTTTGAGCATCTTTG 58.623 40.000 0.00 0.00 34.92 2.77
672 699 5.192327 AGAAACTTTGAGCATCTTTGGTG 57.808 39.130 0.00 0.00 34.92 4.17
674 701 4.574599 AACTTTGAGCATCTTTGGTGTC 57.425 40.909 0.00 0.00 34.92 3.67
809 854 1.605058 AAGAGATCCACCGGTCCACG 61.605 60.000 2.59 0.00 43.80 4.94
810 855 2.283676 AGATCCACCGGTCCACGT 60.284 61.111 2.59 0.00 42.24 4.49
811 856 2.125673 GATCCACCGGTCCACGTG 60.126 66.667 2.59 9.08 42.24 4.49
812 857 3.659089 GATCCACCGGTCCACGTGG 62.659 68.421 29.26 29.26 41.79 4.94
839 916 2.100989 AGTTCGGCCCAAGTAGAGTAG 58.899 52.381 0.00 0.00 0.00 2.57
851 928 5.177696 CCAAGTAGAGTAGCAACAAGAACAC 59.822 44.000 0.00 0.00 0.00 3.32
857 934 4.020543 AGTAGCAACAAGAACACCCAAAA 58.979 39.130 0.00 0.00 0.00 2.44
858 935 3.525268 AGCAACAAGAACACCCAAAAG 57.475 42.857 0.00 0.00 0.00 2.27
861 938 1.119684 ACAAGAACACCCAAAAGCCC 58.880 50.000 0.00 0.00 0.00 5.19
862 939 0.392706 CAAGAACACCCAAAAGCCCC 59.607 55.000 0.00 0.00 0.00 5.80
863 940 0.264657 AAGAACACCCAAAAGCCCCT 59.735 50.000 0.00 0.00 0.00 4.79
864 941 0.264657 AGAACACCCAAAAGCCCCTT 59.735 50.000 0.00 0.00 0.00 3.95
865 942 1.501604 AGAACACCCAAAAGCCCCTTA 59.498 47.619 0.00 0.00 0.00 2.69
866 943 2.111792 AGAACACCCAAAAGCCCCTTAT 59.888 45.455 0.00 0.00 0.00 1.73
867 944 3.335484 AGAACACCCAAAAGCCCCTTATA 59.665 43.478 0.00 0.00 0.00 0.98
868 945 3.095912 ACACCCAAAAGCCCCTTATAC 57.904 47.619 0.00 0.00 0.00 1.47
881 958 4.334759 GCCCCTTATACGAGAAAAAGAACC 59.665 45.833 0.00 0.00 0.00 3.62
885 962 2.460757 TACGAGAAAAAGAACCCCGG 57.539 50.000 0.00 0.00 0.00 5.73
894 971 3.974293 GAACCCCGGAAAGCCCCA 61.974 66.667 0.73 0.00 0.00 4.96
903 980 2.222027 CGGAAAGCCCCAATGAGATAC 58.778 52.381 0.00 0.00 0.00 2.24
906 983 4.263068 CGGAAAGCCCCAATGAGATACTAT 60.263 45.833 0.00 0.00 0.00 2.12
907 984 5.249420 GGAAAGCCCCAATGAGATACTATC 58.751 45.833 0.00 0.00 0.00 2.08
909 986 5.495926 AAGCCCCAATGAGATACTATCAG 57.504 43.478 0.00 0.00 0.00 2.90
911 988 5.158141 AGCCCCAATGAGATACTATCAGAA 58.842 41.667 0.00 0.00 0.00 3.02
912 989 5.608437 AGCCCCAATGAGATACTATCAGAAA 59.392 40.000 0.00 0.00 0.00 2.52
913 990 5.703130 GCCCCAATGAGATACTATCAGAAAC 59.297 44.000 0.00 0.00 0.00 2.78
914 991 6.234177 CCCCAATGAGATACTATCAGAAACC 58.766 44.000 0.00 0.00 0.00 3.27
915 992 6.234177 CCCAATGAGATACTATCAGAAACCC 58.766 44.000 0.00 0.00 0.00 4.11
916 993 6.043706 CCCAATGAGATACTATCAGAAACCCT 59.956 42.308 0.00 0.00 0.00 4.34
917 994 7.235606 CCCAATGAGATACTATCAGAAACCCTA 59.764 40.741 0.00 0.00 0.00 3.53
918 995 8.091449 CCAATGAGATACTATCAGAAACCCTAC 58.909 40.741 0.00 0.00 0.00 3.18
919 996 8.865090 CAATGAGATACTATCAGAAACCCTACT 58.135 37.037 0.00 0.00 0.00 2.57
921 998 8.921353 TGAGATACTATCAGAAACCCTACTAC 57.079 38.462 0.00 0.00 0.00 2.73
922 999 8.500238 TGAGATACTATCAGAAACCCTACTACA 58.500 37.037 0.00 0.00 0.00 2.74
923 1000 8.927675 AGATACTATCAGAAACCCTACTACAG 57.072 38.462 0.00 0.00 0.00 2.74
924 1001 8.504409 AGATACTATCAGAAACCCTACTACAGT 58.496 37.037 0.00 0.00 0.00 3.55
925 1002 9.790344 GATACTATCAGAAACCCTACTACAGTA 57.210 37.037 0.00 0.00 0.00 2.74
926 1003 7.878547 ACTATCAGAAACCCTACTACAGTAC 57.121 40.000 0.00 0.00 0.00 2.73
927 1004 7.641249 ACTATCAGAAACCCTACTACAGTACT 58.359 38.462 0.00 0.00 0.00 2.73
928 1005 6.777213 ATCAGAAACCCTACTACAGTACTG 57.223 41.667 21.44 21.44 0.00 2.74
932 1009 5.887035 AGAAACCCTACTACAGTACTGCTAG 59.113 44.000 22.90 21.84 0.00 3.42
1236 1532 2.047844 ATGCGCGACAAGCTCACT 60.048 55.556 12.10 0.00 44.00 3.41
1338 1634 4.519437 GGCCGCACGGTACCTACC 62.519 72.222 10.90 0.00 42.98 3.18
1451 1748 2.439960 CGGCCTAGGGGTGTGCATA 61.440 63.158 11.72 0.00 34.45 3.14
1453 1750 0.036875 GGCCTAGGGGTGTGCATATC 59.963 60.000 11.72 0.00 34.45 1.63
1456 1753 1.349026 CCTAGGGGTGTGCATATCTGG 59.651 57.143 0.00 0.00 0.00 3.86
1457 1754 1.349026 CTAGGGGTGTGCATATCTGGG 59.651 57.143 0.00 0.00 0.00 4.45
1458 1755 0.327480 AGGGGTGTGCATATCTGGGA 60.327 55.000 0.00 0.00 0.00 4.37
1459 1756 0.179018 GGGGTGTGCATATCTGGGAC 60.179 60.000 0.00 0.00 0.00 4.46
1460 1757 0.532862 GGGTGTGCATATCTGGGACG 60.533 60.000 0.00 0.00 0.00 4.79
1461 1758 0.464036 GGTGTGCATATCTGGGACGA 59.536 55.000 0.00 0.00 0.00 4.20
1462 1759 1.539065 GGTGTGCATATCTGGGACGAG 60.539 57.143 0.00 0.00 0.00 4.18
1464 1761 1.040646 GTGCATATCTGGGACGAGGA 58.959 55.000 0.00 0.00 0.00 3.71
1466 1763 1.333177 GCATATCTGGGACGAGGAGT 58.667 55.000 0.00 0.00 0.00 3.85
1467 1764 2.158519 TGCATATCTGGGACGAGGAGTA 60.159 50.000 0.00 0.00 0.00 2.59
1468 1765 2.891580 GCATATCTGGGACGAGGAGTAA 59.108 50.000 0.00 0.00 0.00 2.24
1469 1766 3.305471 GCATATCTGGGACGAGGAGTAAC 60.305 52.174 0.00 0.00 0.00 2.50
1470 1767 2.830651 ATCTGGGACGAGGAGTAACT 57.169 50.000 0.00 0.00 0.00 2.24
1471 1768 2.125773 TCTGGGACGAGGAGTAACTC 57.874 55.000 0.00 0.00 0.00 3.01
1472 1769 1.353358 TCTGGGACGAGGAGTAACTCA 59.647 52.381 0.00 0.00 37.34 3.41
1473 1770 2.025226 TCTGGGACGAGGAGTAACTCAT 60.025 50.000 0.00 0.00 37.34 2.90
1474 1771 2.099921 CTGGGACGAGGAGTAACTCATG 59.900 54.545 0.00 0.00 37.34 3.07
1475 1772 1.202428 GGGACGAGGAGTAACTCATGC 60.202 57.143 0.00 0.00 37.34 4.06
1476 1773 1.202428 GGACGAGGAGTAACTCATGCC 60.202 57.143 0.00 0.00 37.34 4.40
1477 1774 1.751924 GACGAGGAGTAACTCATGCCT 59.248 52.381 0.00 0.00 37.34 4.75
1478 1775 1.478510 ACGAGGAGTAACTCATGCCTG 59.521 52.381 0.00 0.00 37.34 4.85
1479 1776 1.202463 CGAGGAGTAACTCATGCCTGG 60.202 57.143 0.00 0.00 37.34 4.45
1480 1777 1.139853 GAGGAGTAACTCATGCCTGGG 59.860 57.143 0.00 0.00 37.44 4.45
1481 1778 0.464554 GGAGTAACTCATGCCTGGGC 60.465 60.000 4.43 4.43 35.32 5.36
1494 1791 0.747283 CCTGGGCATCTCTCTTGTGC 60.747 60.000 0.00 0.00 38.12 4.57
1497 1794 1.339438 TGGGCATCTCTCTTGTGCTTC 60.339 52.381 0.00 0.00 38.83 3.86
1508 1805 4.063689 CTCTTGTGCTTCTGTTGTCTCAT 58.936 43.478 0.00 0.00 0.00 2.90
1509 1806 4.060900 TCTTGTGCTTCTGTTGTCTCATC 58.939 43.478 0.00 0.00 0.00 2.92
1510 1807 3.473923 TGTGCTTCTGTTGTCTCATCA 57.526 42.857 0.00 0.00 0.00 3.07
1598 1895 2.113243 GAAGGAACGCTGGAGGTGGT 62.113 60.000 0.00 0.00 0.00 4.16
1601 1898 4.643387 AACGCTGGAGGTGGTGGC 62.643 66.667 0.00 0.00 0.00 5.01
1652 1949 4.327680 GTGGTGCTAGGACAAAGAAGATT 58.672 43.478 16.81 0.00 0.00 2.40
1664 1961 2.286365 AGAAGATTTTTGTGGGCGGA 57.714 45.000 0.00 0.00 0.00 5.54
1763 2060 0.106708 ATGACCAGACAACACAGCGT 59.893 50.000 0.00 0.00 0.00 5.07
1877 2174 3.426568 GTGAAGCGTGCTCTGCCC 61.427 66.667 0.00 0.00 0.00 5.36
2072 2369 2.674380 GGCAGTGCTCCAACTGGG 60.674 66.667 16.11 0.00 46.34 4.45
2137 2434 1.147153 GGTCTGCAGGGTATGGAGC 59.853 63.158 15.13 0.00 46.40 4.70
2441 2738 1.318576 GGTATGGTGCTTATGGTGGC 58.681 55.000 0.00 0.00 0.00 5.01
2717 3014 3.439825 TGGGCAGCATATGTATTATTGCG 59.560 43.478 4.29 0.00 0.00 4.85
2825 3122 6.015180 TCCTTTCGTGGCTTAACTAGAACTTA 60.015 38.462 0.00 0.00 0.00 2.24
3063 3360 4.483950 TGGATACTCTCTCCCTATTGTGG 58.516 47.826 0.00 0.00 37.61 4.17
3080 3377 4.868450 TGTGGTTAAGTCTGAAACGTTG 57.132 40.909 0.00 0.00 0.00 4.10
3089 3386 0.179215 CTGAAACGTTGATCGCTGGC 60.179 55.000 0.00 0.00 44.19 4.85
3109 3406 2.069273 CGGTTGTGTTCATCTCTGGTC 58.931 52.381 0.00 0.00 0.00 4.02
3212 3509 4.038042 TCCCGAAACTATGCACTGATAGAG 59.962 45.833 0.00 0.00 31.36 2.43
3222 3519 2.432510 GCACTGATAGAGGCTTGGTACT 59.567 50.000 0.00 0.00 0.00 2.73
3250 3547 2.746269 CTTCAAACGGACGGTCAAGTA 58.254 47.619 10.76 0.00 0.00 2.24
3256 3553 2.996631 ACGGACGGTCAAGTATAGTCT 58.003 47.619 10.76 0.00 32.86 3.24
3290 3587 6.957631 TGTAACTGGAATGTGACATCCTATT 58.042 36.000 0.00 4.18 36.64 1.73
3292 3589 6.764308 AACTGGAATGTGACATCCTATTTG 57.236 37.500 0.00 0.00 36.64 2.32
3299 3596 8.345565 GGAATGTGACATCCTATTTGTACATTC 58.654 37.037 14.85 14.85 40.92 2.67
3300 3597 9.113838 GAATGTGACATCCTATTTGTACATTCT 57.886 33.333 15.54 0.00 40.06 2.40
3301 3598 9.466497 AATGTGACATCCTATTTGTACATTCTT 57.534 29.630 0.00 0.00 32.34 2.52
3381 3678 6.709397 AGCATCTGATGTTTGGTATGTAGATG 59.291 38.462 18.19 0.00 41.78 2.90
3385 3682 7.805163 TCTGATGTTTGGTATGTAGATGGATT 58.195 34.615 0.00 0.00 0.00 3.01
3516 3814 7.650104 GCATCAACTTCTAAGGTAGTGTAGATC 59.350 40.741 0.00 0.00 0.00 2.75
3641 3940 3.120321 TCGTTTCTGTACAGGTTGCAT 57.880 42.857 22.48 0.00 0.00 3.96
3663 3962 0.096454 GACGCCATTCCGTGTAAAGC 59.904 55.000 0.00 0.00 42.24 3.51
3691 3990 6.378280 GTCCAAGTGAGGGTGAAAATGATATT 59.622 38.462 0.00 0.00 0.00 1.28
3704 4003 8.192774 GTGAAAATGATATTGGAAATCTGCTGA 58.807 33.333 0.00 0.00 0.00 4.26
3832 4131 1.223417 GGTGGTGGTACGTGGAAACG 61.223 60.000 0.00 0.00 39.31 3.60
3844 4143 3.163594 CGTGGAAACGAAGATTCATTGC 58.836 45.455 0.00 0.00 41.27 3.56
3917 4216 2.173569 AGATGATACCTTGGTTCCTGCC 59.826 50.000 0.00 0.00 0.00 4.85
3919 4218 0.463833 GATACCTTGGTTCCTGCCCG 60.464 60.000 0.00 0.00 0.00 6.13
3933 4232 2.635915 CCTGCCCGGTAGATTTGGTATA 59.364 50.000 3.70 0.00 0.00 1.47
3996 4305 6.321181 ACTGAAGTCAAGCCTTGTCAATTTTA 59.679 34.615 4.04 0.00 0.00 1.52
4014 4323 4.415881 TTTAGCCCGCAATATCTTCTCA 57.584 40.909 0.00 0.00 0.00 3.27
4018 4327 4.210331 AGCCCGCAATATCTTCTCAAAAT 58.790 39.130 0.00 0.00 0.00 1.82
4025 4334 7.307632 CCGCAATATCTTCTCAAAATGTCTAGG 60.308 40.741 0.00 0.00 0.00 3.02
4033 4342 8.437575 TCTTCTCAAAATGTCTAGGTTAACCTT 58.562 33.333 31.47 15.87 46.09 3.50
4034 4343 7.979444 TCTCAAAATGTCTAGGTTAACCTTG 57.021 36.000 31.47 27.90 46.09 3.61
4035 4344 7.741785 TCTCAAAATGTCTAGGTTAACCTTGA 58.258 34.615 31.47 29.61 46.09 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.445871 GGACAAAATTACGGACGGCT 58.554 50.000 0.00 0.00 0.00 5.52
1 2 0.095762 CGGACAAAATTACGGACGGC 59.904 55.000 0.00 0.00 0.00 5.68
2 3 1.431496 ACGGACAAAATTACGGACGG 58.569 50.000 0.00 0.00 0.00 4.79
3 4 3.674753 AGTAACGGACAAAATTACGGACG 59.325 43.478 0.00 0.00 34.63 4.79
4 5 5.596268 AAGTAACGGACAAAATTACGGAC 57.404 39.130 0.00 0.00 34.63 4.79
5 6 7.903995 ATAAAGTAACGGACAAAATTACGGA 57.096 32.000 0.00 0.00 34.63 4.69
6 7 8.953507 AAATAAAGTAACGGACAAAATTACGG 57.046 30.769 0.00 0.00 34.63 4.02
14 15 9.881529 GTGATTACAAAATAAAGTAACGGACAA 57.118 29.630 0.00 0.00 33.49 3.18
15 16 9.275398 AGTGATTACAAAATAAAGTAACGGACA 57.725 29.630 0.00 0.00 33.49 4.02
63 64 9.635520 CTGATCATTCTTTGAAAACAGCTTTAT 57.364 29.630 0.00 0.00 38.03 1.40
67 68 6.889301 TCTGATCATTCTTTGAAAACAGCT 57.111 33.333 0.00 0.00 38.03 4.24
93 94 5.106712 TGCTTCGTCCAACATTTCATACTTC 60.107 40.000 0.00 0.00 0.00 3.01
96 97 4.154195 AGTGCTTCGTCCAACATTTCATAC 59.846 41.667 0.00 0.00 0.00 2.39
97 98 4.323417 AGTGCTTCGTCCAACATTTCATA 58.677 39.130 0.00 0.00 0.00 2.15
99 100 2.548057 GAGTGCTTCGTCCAACATTTCA 59.452 45.455 0.00 0.00 0.00 2.69
100 101 2.095718 GGAGTGCTTCGTCCAACATTTC 60.096 50.000 0.00 0.00 32.55 2.17
101 102 1.880027 GGAGTGCTTCGTCCAACATTT 59.120 47.619 0.00 0.00 32.55 2.32
103 104 0.396435 TGGAGTGCTTCGTCCAACAT 59.604 50.000 0.00 0.00 40.01 2.71
104 105 0.531974 GTGGAGTGCTTCGTCCAACA 60.532 55.000 0.00 0.00 44.58 3.33
105 106 1.228657 GGTGGAGTGCTTCGTCCAAC 61.229 60.000 0.00 0.00 44.58 3.77
122 123 4.251103 AGTGTTTCTTTTCCTTCCAGGT 57.749 40.909 0.00 0.00 36.53 4.00
124 125 7.751768 AGAATAGTGTTTCTTTTCCTTCCAG 57.248 36.000 0.00 0.00 35.64 3.86
226 230 2.752354 TCCCGTATTTTGCATCTGTTGG 59.248 45.455 0.00 0.00 0.00 3.77
230 234 3.885297 AGGATTCCCGTATTTTGCATCTG 59.115 43.478 0.00 0.00 37.58 2.90
232 236 5.940470 AGATAGGATTCCCGTATTTTGCATC 59.060 40.000 0.00 0.00 37.58 3.91
236 240 7.667557 TGTAGAGATAGGATTCCCGTATTTTG 58.332 38.462 0.00 0.00 37.58 2.44
238 242 8.437274 AATGTAGAGATAGGATTCCCGTATTT 57.563 34.615 0.00 0.00 37.58 1.40
303 307 2.678336 CGGGCTCTTTAAGGTTCATGAC 59.322 50.000 0.00 0.00 0.00 3.06
387 392 5.784750 TCAAACTGAGCTATGAATTGTCG 57.215 39.130 0.00 0.00 0.00 4.35
402 407 4.172505 CGAGAGGAGATGAACTCAAACTG 58.827 47.826 0.00 0.00 46.54 3.16
431 436 9.418045 CCTTTTGCTATTTTTCCGAATTTCTTA 57.582 29.630 0.00 0.00 0.00 2.10
437 442 8.093927 TCAAATCCTTTTGCTATTTTTCCGAAT 58.906 29.630 0.00 0.00 41.66 3.34
468 473 4.827284 CCTTGGTGTCAAACTAATTCAGGT 59.173 41.667 0.00 0.00 31.77 4.00
478 483 5.452078 TCAAATCATCCTTGGTGTCAAAC 57.548 39.130 0.00 0.00 31.77 2.93
495 500 6.100404 TGCAAGCACCTAGAAAATTCAAAT 57.900 33.333 0.00 0.00 0.00 2.32
496 501 5.528043 TGCAAGCACCTAGAAAATTCAAA 57.472 34.783 0.00 0.00 0.00 2.69
525 530 1.007336 CCGGATGTAATCTACGCGCC 61.007 60.000 5.73 0.00 44.71 6.53
527 532 1.401148 CCTCCGGATGTAATCTACGCG 60.401 57.143 3.57 3.53 44.71 6.01
530 535 3.158676 AGCTCCTCCGGATGTAATCTAC 58.841 50.000 3.57 0.00 44.71 2.59
531 536 3.181433 TGAGCTCCTCCGGATGTAATCTA 60.181 47.826 12.15 0.00 44.71 1.98
542 547 2.072298 CTTTTTGACTGAGCTCCTCCG 58.928 52.381 12.15 0.00 0.00 4.63
575 580 5.279657 GGGCATTTTGGAACTCTGATTTTCT 60.280 40.000 0.00 0.00 0.00 2.52
584 589 1.970640 ACCTTGGGCATTTTGGAACTC 59.029 47.619 0.00 0.00 0.00 3.01
602 607 5.605564 AAACAACAAAAACTCAAGCAACC 57.394 34.783 0.00 0.00 0.00 3.77
607 612 7.569677 TCGGTAAAAACAACAAAAACTCAAG 57.430 32.000 0.00 0.00 0.00 3.02
617 622 3.202829 AGGAGCTCGGTAAAAACAACA 57.797 42.857 7.83 0.00 0.00 3.33
621 626 5.049612 GCCATATAAGGAGCTCGGTAAAAAC 60.050 44.000 7.83 0.00 0.00 2.43
640 645 4.261801 GCTCAAAGTTTCTAGGTGCCATA 58.738 43.478 0.00 0.00 0.00 2.74
660 687 5.343307 AACTTTTTGACACCAAAGATGCT 57.657 34.783 11.62 0.00 42.55 3.79
661 688 7.532682 TTAAACTTTTTGACACCAAAGATGC 57.467 32.000 11.62 0.00 42.55 3.91
766 811 7.230849 TCCCGTACGTGGACAATAATATATT 57.769 36.000 18.02 2.97 0.00 1.28
769 814 5.302568 TCTTCCCGTACGTGGACAATAATAT 59.697 40.000 20.64 0.00 0.00 1.28
779 824 0.384669 GGATCTCTTCCCGTACGTGG 59.615 60.000 15.21 14.78 38.75 4.94
784 829 0.754217 CCGGTGGATCTCTTCCCGTA 60.754 60.000 0.00 0.00 44.77 4.02
809 854 1.092348 GGGCCGAACTTTACATCCAC 58.908 55.000 0.00 0.00 0.00 4.02
810 855 0.693622 TGGGCCGAACTTTACATCCA 59.306 50.000 0.00 0.00 0.00 3.41
811 856 1.743394 CTTGGGCCGAACTTTACATCC 59.257 52.381 0.00 0.00 0.00 3.51
812 857 2.433436 ACTTGGGCCGAACTTTACATC 58.567 47.619 0.00 0.00 0.00 3.06
816 890 2.901839 ACTCTACTTGGGCCGAACTTTA 59.098 45.455 0.00 0.00 0.00 1.85
839 916 1.933181 GCTTTTGGGTGTTCTTGTTGC 59.067 47.619 0.00 0.00 0.00 4.17
851 928 2.171870 TCTCGTATAAGGGGCTTTTGGG 59.828 50.000 0.00 0.00 0.00 4.12
857 934 5.183969 GTTCTTTTTCTCGTATAAGGGGCT 58.816 41.667 0.00 0.00 0.00 5.19
858 935 4.334759 GGTTCTTTTTCTCGTATAAGGGGC 59.665 45.833 0.00 0.00 0.00 5.80
861 938 4.569564 CGGGGTTCTTTTTCTCGTATAAGG 59.430 45.833 0.00 0.00 0.00 2.69
862 939 4.569564 CCGGGGTTCTTTTTCTCGTATAAG 59.430 45.833 0.00 0.00 0.00 1.73
863 940 4.222588 TCCGGGGTTCTTTTTCTCGTATAA 59.777 41.667 0.00 0.00 0.00 0.98
864 941 3.768757 TCCGGGGTTCTTTTTCTCGTATA 59.231 43.478 0.00 0.00 0.00 1.47
865 942 2.568509 TCCGGGGTTCTTTTTCTCGTAT 59.431 45.455 0.00 0.00 0.00 3.06
866 943 1.969923 TCCGGGGTTCTTTTTCTCGTA 59.030 47.619 0.00 0.00 0.00 3.43
867 944 0.760572 TCCGGGGTTCTTTTTCTCGT 59.239 50.000 0.00 0.00 0.00 4.18
868 945 1.886886 TTCCGGGGTTCTTTTTCTCG 58.113 50.000 0.00 0.00 0.00 4.04
881 958 1.754234 CTCATTGGGGCTTTCCGGG 60.754 63.158 0.00 0.00 36.01 5.73
885 962 5.869579 TGATAGTATCTCATTGGGGCTTTC 58.130 41.667 11.40 0.00 0.00 2.62
903 980 7.468906 GCAGTACTGTAGTAGGGTTTCTGATAG 60.469 44.444 23.44 0.00 0.00 2.08
906 983 4.461781 GCAGTACTGTAGTAGGGTTTCTGA 59.538 45.833 23.44 0.00 0.00 3.27
907 984 4.463186 AGCAGTACTGTAGTAGGGTTTCTG 59.537 45.833 23.44 0.00 0.00 3.02
909 986 5.651576 ACTAGCAGTACTGTAGTAGGGTTTC 59.348 44.000 24.46 7.98 30.99 2.78
911 988 5.190357 ACTAGCAGTACTGTAGTAGGGTT 57.810 43.478 24.46 9.15 30.99 4.11
912 989 4.858965 ACTAGCAGTACTGTAGTAGGGT 57.141 45.455 24.46 13.37 30.99 4.34
924 1001 2.292267 GTGGGCGTAGTACTAGCAGTA 58.708 52.381 19.36 7.81 0.00 2.74
925 1002 1.101331 GTGGGCGTAGTACTAGCAGT 58.899 55.000 19.36 0.00 0.00 4.40
926 1003 0.384669 GGTGGGCGTAGTACTAGCAG 59.615 60.000 19.36 9.84 0.00 4.24
927 1004 1.378882 CGGTGGGCGTAGTACTAGCA 61.379 60.000 19.36 4.43 0.00 3.49
928 1005 1.097547 TCGGTGGGCGTAGTACTAGC 61.098 60.000 1.87 9.04 0.00 3.42
932 1009 0.249197 GGAATCGGTGGGCGTAGTAC 60.249 60.000 0.00 0.00 0.00 2.73
935 1012 2.108362 GGGAATCGGTGGGCGTAG 59.892 66.667 0.00 0.00 0.00 3.51
1106 1402 1.402896 GCCCTGATCCGACTCCATCA 61.403 60.000 0.00 0.00 0.00 3.07
1443 1740 1.539065 CCTCGTCCCAGATATGCACAC 60.539 57.143 0.00 0.00 0.00 3.82
1446 1743 1.332195 CTCCTCGTCCCAGATATGCA 58.668 55.000 0.00 0.00 0.00 3.96
1449 1746 4.141228 TGAGTTACTCCTCGTCCCAGATAT 60.141 45.833 10.10 0.00 34.04 1.63
1451 1748 2.025226 TGAGTTACTCCTCGTCCCAGAT 60.025 50.000 10.10 0.00 34.04 2.90
1453 1750 1.835494 TGAGTTACTCCTCGTCCCAG 58.165 55.000 10.10 0.00 34.04 4.45
1456 1753 1.202428 GGCATGAGTTACTCCTCGTCC 60.202 57.143 10.10 0.84 34.04 4.79
1457 1754 1.751924 AGGCATGAGTTACTCCTCGTC 59.248 52.381 10.10 0.00 34.04 4.20
1458 1755 1.478510 CAGGCATGAGTTACTCCTCGT 59.521 52.381 10.10 0.00 34.04 4.18
1459 1756 1.202463 CCAGGCATGAGTTACTCCTCG 60.202 57.143 10.10 0.00 34.04 4.63
1460 1757 1.139853 CCCAGGCATGAGTTACTCCTC 59.860 57.143 10.10 0.00 0.00 3.71
1461 1758 1.207791 CCCAGGCATGAGTTACTCCT 58.792 55.000 10.10 0.00 0.00 3.69
1462 1759 0.464554 GCCCAGGCATGAGTTACTCC 60.465 60.000 10.10 0.00 41.49 3.85
1474 1771 0.747283 CACAAGAGAGATGCCCAGGC 60.747 60.000 0.38 0.38 42.35 4.85
1475 1772 0.747283 GCACAAGAGAGATGCCCAGG 60.747 60.000 0.00 0.00 33.06 4.45
1476 1773 0.252479 AGCACAAGAGAGATGCCCAG 59.748 55.000 0.00 0.00 40.33 4.45
1477 1774 0.694771 AAGCACAAGAGAGATGCCCA 59.305 50.000 0.00 0.00 40.33 5.36
1478 1775 1.065564 AGAAGCACAAGAGAGATGCCC 60.066 52.381 0.00 0.00 40.33 5.36
1479 1776 2.008329 CAGAAGCACAAGAGAGATGCC 58.992 52.381 0.00 0.00 40.33 4.40
1480 1777 2.697654 ACAGAAGCACAAGAGAGATGC 58.302 47.619 0.00 0.00 39.74 3.91
1481 1778 4.063689 ACAACAGAAGCACAAGAGAGATG 58.936 43.478 0.00 0.00 0.00 2.90
1482 1779 4.040217 AGACAACAGAAGCACAAGAGAGAT 59.960 41.667 0.00 0.00 0.00 2.75
1483 1780 3.386078 AGACAACAGAAGCACAAGAGAGA 59.614 43.478 0.00 0.00 0.00 3.10
1484 1781 3.726607 AGACAACAGAAGCACAAGAGAG 58.273 45.455 0.00 0.00 0.00 3.20
1485 1782 3.132824 TGAGACAACAGAAGCACAAGAGA 59.867 43.478 0.00 0.00 0.00 3.10
1486 1783 3.461061 TGAGACAACAGAAGCACAAGAG 58.539 45.455 0.00 0.00 0.00 2.85
1487 1784 3.541996 TGAGACAACAGAAGCACAAGA 57.458 42.857 0.00 0.00 0.00 3.02
1494 1791 3.057245 TCGACCTGATGAGACAACAGAAG 60.057 47.826 9.86 2.78 36.57 2.85
1497 1794 3.516981 ATCGACCTGATGAGACAACAG 57.483 47.619 0.00 0.00 35.45 3.16
1508 1805 1.215382 CCGCTTCACATCGACCTGA 59.785 57.895 0.00 0.00 0.00 3.86
1509 1806 1.811266 CCCGCTTCACATCGACCTG 60.811 63.158 0.00 0.00 0.00 4.00
1510 1807 2.579201 CCCGCTTCACATCGACCT 59.421 61.111 0.00 0.00 0.00 3.85
1664 1961 1.152247 TGTCAGACTGGAGGGCAGT 60.152 57.895 1.81 0.00 35.30 4.40
1877 2174 2.419198 CCAGGATTCGCCTCTCGG 59.581 66.667 0.00 0.00 46.97 4.63
2072 2369 2.949177 TGGTGTGCCCATATCCATAC 57.051 50.000 0.00 0.00 38.72 2.39
2137 2434 0.742281 AGCATACGCAGCAGGAACAG 60.742 55.000 0.00 0.00 42.27 3.16
2441 2738 4.181010 CCAGCACCATCTCCCCGG 62.181 72.222 0.00 0.00 0.00 5.73
2564 2861 0.539438 TGACTGCACCACCAAATCCC 60.539 55.000 0.00 0.00 0.00 3.85
2618 2915 1.409521 GGCTGCATACCACCATAACCA 60.410 52.381 0.50 0.00 0.00 3.67
2717 3014 1.936547 CGAGAGCAAAGCCAGAATACC 59.063 52.381 0.00 0.00 0.00 2.73
2825 3122 9.900710 CTCGACATAATAGCTACTTATTGACTT 57.099 33.333 0.00 0.00 0.00 3.01
2896 3193 1.948834 CACTCATGACAAAGCACACCA 59.051 47.619 0.00 0.00 0.00 4.17
3063 3360 4.150098 AGCGATCAACGTTTCAGACTTAAC 59.850 41.667 0.00 0.00 44.60 2.01
3080 3377 2.240612 GAACACAACCGCCAGCGATC 62.241 60.000 14.67 0.00 42.83 3.69
3089 3386 2.069273 GACCAGAGATGAACACAACCG 58.931 52.381 0.00 0.00 0.00 4.44
3109 3406 1.888512 TGAGCTAAAGCAAAGCAAGGG 59.111 47.619 4.54 0.00 45.16 3.95
3188 3485 2.380084 TCAGTGCATAGTTTCGGGAC 57.620 50.000 0.00 0.00 0.00 4.46
3192 3489 3.738282 GCCTCTATCAGTGCATAGTTTCG 59.262 47.826 0.00 0.00 0.00 3.46
3212 3509 0.250513 AGCAGCTACAGTACCAAGCC 59.749 55.000 0.00 0.00 36.92 4.35
3222 3519 1.508632 GTCCGTTTGAAGCAGCTACA 58.491 50.000 0.00 0.00 0.00 2.74
3250 3547 8.079211 TCCAGTTACATAAAGAAGCAGACTAT 57.921 34.615 0.00 0.00 0.00 2.12
3256 3553 6.939730 TCACATTCCAGTTACATAAAGAAGCA 59.060 34.615 0.00 0.00 0.00 3.91
3301 3598 6.975197 TGCATACGAACAATGTTTCTCAAAAA 59.025 30.769 0.00 0.00 0.00 1.94
3308 3605 6.257423 TCATCATGCATACGAACAATGTTTC 58.743 36.000 0.00 0.00 0.00 2.78
3381 3678 5.307196 TCCCTCTACTATGCCTGTTTAATCC 59.693 44.000 0.00 0.00 0.00 3.01
3385 3682 5.128827 CAGTTCCCTCTACTATGCCTGTTTA 59.871 44.000 0.00 0.00 0.00 2.01
3451 3749 7.816995 GCTAGTAAGCTCTTTATCACTGCATAT 59.183 37.037 0.00 0.00 45.85 1.78
3453 3751 5.988561 GCTAGTAAGCTCTTTATCACTGCAT 59.011 40.000 0.00 0.00 45.85 3.96
3641 3940 0.033642 TTACACGGAATGGCGTCACA 59.966 50.000 0.00 0.00 0.00 3.58
3663 3962 2.566833 TTCACCCTCACTTGGACATG 57.433 50.000 0.00 0.00 0.00 3.21
3767 4066 6.088016 AGAACATGAAGCACATAAAAAGCA 57.912 33.333 0.00 0.00 37.46 3.91
3832 4131 6.703165 ACAAAACTGAAAGGCAATGAATCTTC 59.297 34.615 0.00 0.00 39.30 2.87
3844 4143 6.312672 ACGATTTTCCAAACAAAACTGAAAGG 59.687 34.615 0.00 0.00 39.30 3.11
3906 4205 0.912487 ATCTACCGGGCAGGAACCAA 60.912 55.000 11.67 0.00 45.00 3.67
3917 4216 5.995565 TCAGGATATACCAAATCTACCGG 57.004 43.478 0.00 0.00 42.04 5.28
3969 4278 2.170397 TGACAAGGCTTGACTTCAGTGA 59.830 45.455 32.50 6.88 0.00 3.41
3975 4284 5.509670 GGCTAAAATTGACAAGGCTTGACTT 60.510 40.000 32.50 18.03 0.00 3.01
3996 4305 3.281727 TTTGAGAAGATATTGCGGGCT 57.718 42.857 0.00 0.00 0.00 5.19


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

AutoCloner maintained by Alex Coulton.