Multiple sequence alignment - TraesCS1B01G066200

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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 TraesCS1B01G066200 chr1B 100.000 2498 0 0 1 2498 50301948 50304445 0.000000e+00 4614
1 TraesCS1B01G066200 chr1B 95.604 91 3 1 1 91 301905100 301905189 7.200000e-31 145
2 TraesCS1B01G066200 chr1B 90.000 110 7 4 1 108 396516224 396516331 3.350000e-29 139
3 TraesCS1B01G066200 chr1B 89.908 109 6 4 1 107 483322442 483322337 4.330000e-28 135
4 TraesCS1B01G066200 chr6B 94.118 1751 87 5 750 2498 653199856 653198120 0.000000e+00 2649
5 TraesCS1B01G066200 chr6B 90.015 681 56 3 81 749 706413392 706412712 0.000000e+00 870
6 TraesCS1B01G066200 chr6B 89.912 684 56 4 81 751 122825536 122824853 0.000000e+00 869
7 TraesCS1B01G066200 chr6B 93.000 100 3 2 1 96 688240990 688241089 2.590000e-30 143
8 TraesCS1B01G066200 chr6B 86.508 126 12 5 1 122 614657066 614657190 1.560000e-27 134
9 TraesCS1B01G066200 chr4B 92.453 1749 127 4 750 2498 574292836 574291093 0.000000e+00 2494
10 TraesCS1B01G066200 chr4B 90.323 682 52 5 81 749 120259342 120258662 0.000000e+00 881
11 TraesCS1B01G066200 chr4B 90.162 681 54 8 81 749 222598267 222598946 0.000000e+00 874
12 TraesCS1B01G066200 chr4B 89.605 683 52 9 81 749 40496040 40496717 0.000000e+00 850
13 TraesCS1B01G066200 chr7A 92.846 1286 72 6 750 2035 348726245 348727510 0.000000e+00 1847
14 TraesCS1B01G066200 chr7A 92.007 1101 86 1 936 2036 595398201 595397103 0.000000e+00 1544
15 TraesCS1B01G066200 chr7A 89.157 664 51 13 102 749 492419734 492419076 0.000000e+00 808
16 TraesCS1B01G066200 chr7A 94.872 156 7 1 785 940 595407760 595407606 2.480000e-60 243
17 TraesCS1B01G066200 chr4A 93.516 987 61 3 1050 2036 636128178 636127195 0.000000e+00 1465
18 TraesCS1B01G066200 chr4A 92.341 692 50 3 1808 2498 731998043 731997354 0.000000e+00 981
19 TraesCS1B01G066200 chr4A 96.825 126 4 0 750 875 636128304 636128179 7.000000e-51 211
20 TraesCS1B01G066200 chr5B 91.884 998 78 3 1043 2038 488979308 488980304 0.000000e+00 1391
21 TraesCS1B01G066200 chr5B 90.323 682 53 3 81 749 10415620 10414939 0.000000e+00 881
22 TraesCS1B01G066200 chr5B 90.219 685 50 9 82 749 35771607 35770923 0.000000e+00 878
23 TraesCS1B01G066200 chr5B 89.312 683 56 8 81 750 590999921 591000599 0.000000e+00 841
24 TraesCS1B01G066200 chr5B 96.629 89 2 1 1 89 445758391 445758304 2.000000e-31 147
25 TraesCS1B01G066200 chr5B 90.265 113 6 5 1 109 340942248 340942137 2.590000e-30 143
26 TraesCS1B01G066200 chr2B 86.143 967 115 16 750 1713 593014210 593015160 0.000000e+00 1026
27 TraesCS1B01G066200 chr2B 90.616 682 50 5 81 749 680790697 680790017 0.000000e+00 893
28 TraesCS1B01G066200 chr2B 87.792 557 58 7 1947 2498 680187643 680188194 0.000000e+00 643
29 TraesCS1B01G066200 chr2B 96.629 89 2 1 1 89 217345433 217345346 2.000000e-31 147
30 TraesCS1B01G066200 chr2D 85.385 999 115 24 750 1740 505837882 505838857 0.000000e+00 1007
31 TraesCS1B01G066200 chr2D 92.669 682 35 6 81 749 340328652 340327973 0.000000e+00 968
32 TraesCS1B01G066200 chr2D 87.410 556 54 10 1947 2494 290557789 290557242 2.110000e-175 625
33 TraesCS1B01G066200 chr6D 89.314 758 64 9 1751 2498 46496048 46495298 0.000000e+00 935
34 TraesCS1B01G066200 chr3D 92.812 626 42 2 1413 2038 41146795 41147417 0.000000e+00 904
35 TraesCS1B01G066200 chr3D 88.141 683 67 6 81 752 555154969 555154290 0.000000e+00 800
36 TraesCS1B01G066200 chr3D 94.553 514 28 0 907 1420 41141428 41141941 0.000000e+00 795
37 TraesCS1B01G066200 chr3D 96.341 164 6 0 750 913 41135980 41136143 1.140000e-68 270
38 TraesCS1B01G066200 chr3A 89.443 682 55 5 81 749 91841609 91842286 0.000000e+00 845
39 TraesCS1B01G066200 chr7D 87.261 628 64 7 1885 2498 83949056 83949681 0.000000e+00 702
40 TraesCS1B01G066200 chr7D 87.261 628 64 7 1885 2498 83971695 83972320 0.000000e+00 702
41 TraesCS1B01G066200 chr2A 85.286 700 81 17 1026 1719 650256699 650257382 0.000000e+00 702
42 TraesCS1B01G066200 chr2A 88.321 274 28 2 755 1027 650256324 650256594 2.400000e-85 326
43 TraesCS1B01G066200 chr5D 88.067 595 57 6 1885 2471 481218712 481219300 0.000000e+00 693
44 TraesCS1B01G066200 chr6A 88.991 109 9 3 1 109 508946405 508946510 5.610000e-27 132


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 TraesCS1B01G066200 chr1B 50301948 50304445 2497 False 4614 4614 100.0000 1 2498 1 chr1B.!!$F1 2497
1 TraesCS1B01G066200 chr6B 653198120 653199856 1736 True 2649 2649 94.1180 750 2498 1 chr6B.!!$R2 1748
2 TraesCS1B01G066200 chr6B 706412712 706413392 680 True 870 870 90.0150 81 749 1 chr6B.!!$R3 668
3 TraesCS1B01G066200 chr6B 122824853 122825536 683 True 869 869 89.9120 81 751 1 chr6B.!!$R1 670
4 TraesCS1B01G066200 chr4B 574291093 574292836 1743 True 2494 2494 92.4530 750 2498 1 chr4B.!!$R2 1748
5 TraesCS1B01G066200 chr4B 120258662 120259342 680 True 881 881 90.3230 81 749 1 chr4B.!!$R1 668
6 TraesCS1B01G066200 chr4B 222598267 222598946 679 False 874 874 90.1620 81 749 1 chr4B.!!$F2 668
7 TraesCS1B01G066200 chr4B 40496040 40496717 677 False 850 850 89.6050 81 749 1 chr4B.!!$F1 668
8 TraesCS1B01G066200 chr7A 348726245 348727510 1265 False 1847 1847 92.8460 750 2035 1 chr7A.!!$F1 1285
9 TraesCS1B01G066200 chr7A 595397103 595398201 1098 True 1544 1544 92.0070 936 2036 1 chr7A.!!$R2 1100
10 TraesCS1B01G066200 chr7A 492419076 492419734 658 True 808 808 89.1570 102 749 1 chr7A.!!$R1 647
11 TraesCS1B01G066200 chr4A 731997354 731998043 689 True 981 981 92.3410 1808 2498 1 chr4A.!!$R1 690
12 TraesCS1B01G066200 chr4A 636127195 636128304 1109 True 838 1465 95.1705 750 2036 2 chr4A.!!$R2 1286
13 TraesCS1B01G066200 chr5B 488979308 488980304 996 False 1391 1391 91.8840 1043 2038 1 chr5B.!!$F1 995
14 TraesCS1B01G066200 chr5B 10414939 10415620 681 True 881 881 90.3230 81 749 1 chr5B.!!$R1 668
15 TraesCS1B01G066200 chr5B 35770923 35771607 684 True 878 878 90.2190 82 749 1 chr5B.!!$R2 667
16 TraesCS1B01G066200 chr5B 590999921 591000599 678 False 841 841 89.3120 81 750 1 chr5B.!!$F2 669
17 TraesCS1B01G066200 chr2B 593014210 593015160 950 False 1026 1026 86.1430 750 1713 1 chr2B.!!$F1 963
18 TraesCS1B01G066200 chr2B 680790017 680790697 680 True 893 893 90.6160 81 749 1 chr2B.!!$R2 668
19 TraesCS1B01G066200 chr2B 680187643 680188194 551 False 643 643 87.7920 1947 2498 1 chr2B.!!$F2 551
20 TraesCS1B01G066200 chr2D 505837882 505838857 975 False 1007 1007 85.3850 750 1740 1 chr2D.!!$F1 990
21 TraesCS1B01G066200 chr2D 340327973 340328652 679 True 968 968 92.6690 81 749 1 chr2D.!!$R2 668
22 TraesCS1B01G066200 chr2D 290557242 290557789 547 True 625 625 87.4100 1947 2494 1 chr2D.!!$R1 547
23 TraesCS1B01G066200 chr6D 46495298 46496048 750 True 935 935 89.3140 1751 2498 1 chr6D.!!$R1 747
24 TraesCS1B01G066200 chr3D 41146795 41147417 622 False 904 904 92.8120 1413 2038 1 chr3D.!!$F3 625
25 TraesCS1B01G066200 chr3D 555154290 555154969 679 True 800 800 88.1410 81 752 1 chr3D.!!$R1 671
26 TraesCS1B01G066200 chr3D 41141428 41141941 513 False 795 795 94.5530 907 1420 1 chr3D.!!$F2 513
27 TraesCS1B01G066200 chr3A 91841609 91842286 677 False 845 845 89.4430 81 749 1 chr3A.!!$F1 668
28 TraesCS1B01G066200 chr7D 83949056 83949681 625 False 702 702 87.2610 1885 2498 1 chr7D.!!$F1 613
29 TraesCS1B01G066200 chr7D 83971695 83972320 625 False 702 702 87.2610 1885 2498 1 chr7D.!!$F2 613
30 TraesCS1B01G066200 chr2A 650256324 650257382 1058 False 514 702 86.8035 755 1719 2 chr2A.!!$F1 964
31 TraesCS1B01G066200 chr5D 481218712 481219300 588 False 693 693 88.0670 1885 2471 1 chr5D.!!$F1 586

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
53 54 2.183679 ACAAGGGCAAAAGTGTTTGGA 58.816 42.857 1.72 0.0 43.73 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1717 1865 0.320421 TCCCGAGCAACTGCAACTAC 60.32 55.0 4.22 0.0 45.16 2.73 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
25 26 8.619146 GTTTCATTCGAATCATGCAAATTAGA 57.381 30.769 7.92 0.00 0.00 2.10
26 27 8.740369 GTTTCATTCGAATCATGCAAATTAGAG 58.260 33.333 7.92 0.00 0.00 2.43
27 28 7.558161 TCATTCGAATCATGCAAATTAGAGT 57.442 32.000 7.92 0.00 0.00 3.24
28 29 7.633621 TCATTCGAATCATGCAAATTAGAGTC 58.366 34.615 7.92 0.00 0.00 3.36
29 30 5.991328 TCGAATCATGCAAATTAGAGTCC 57.009 39.130 0.00 0.00 0.00 3.85
30 31 5.427378 TCGAATCATGCAAATTAGAGTCCA 58.573 37.500 0.00 0.00 0.00 4.02
31 32 5.879777 TCGAATCATGCAAATTAGAGTCCAA 59.120 36.000 0.00 0.00 0.00 3.53
32 33 6.374053 TCGAATCATGCAAATTAGAGTCCAAA 59.626 34.615 0.00 0.00 0.00 3.28
33 34 7.028962 CGAATCATGCAAATTAGAGTCCAAAA 58.971 34.615 0.00 0.00 0.00 2.44
34 35 7.008628 CGAATCATGCAAATTAGAGTCCAAAAC 59.991 37.037 0.00 0.00 0.00 2.43
35 36 6.647334 TCATGCAAATTAGAGTCCAAAACA 57.353 33.333 0.00 0.00 0.00 2.83
36 37 7.048629 TCATGCAAATTAGAGTCCAAAACAA 57.951 32.000 0.00 0.00 0.00 2.83
37 38 7.147312 TCATGCAAATTAGAGTCCAAAACAAG 58.853 34.615 0.00 0.00 0.00 3.16
38 39 5.841810 TGCAAATTAGAGTCCAAAACAAGG 58.158 37.500 0.00 0.00 0.00 3.61
39 40 5.221422 TGCAAATTAGAGTCCAAAACAAGGG 60.221 40.000 0.00 0.00 0.00 3.95
40 41 5.230182 CAAATTAGAGTCCAAAACAAGGGC 58.770 41.667 0.00 0.00 0.00 5.19
41 42 3.586470 TTAGAGTCCAAAACAAGGGCA 57.414 42.857 0.00 0.00 31.65 5.36
42 43 2.452600 AGAGTCCAAAACAAGGGCAA 57.547 45.000 0.00 0.00 31.65 4.52
43 44 2.745968 AGAGTCCAAAACAAGGGCAAA 58.254 42.857 0.00 0.00 31.65 3.68
44 45 3.103742 AGAGTCCAAAACAAGGGCAAAA 58.896 40.909 0.00 0.00 31.65 2.44
45 46 3.132824 AGAGTCCAAAACAAGGGCAAAAG 59.867 43.478 0.00 0.00 31.65 2.27
46 47 2.837591 AGTCCAAAACAAGGGCAAAAGT 59.162 40.909 0.00 0.00 31.65 2.66
47 48 2.935849 GTCCAAAACAAGGGCAAAAGTG 59.064 45.455 0.00 0.00 0.00 3.16
48 49 2.569404 TCCAAAACAAGGGCAAAAGTGT 59.431 40.909 0.00 0.00 0.00 3.55
49 50 3.008485 TCCAAAACAAGGGCAAAAGTGTT 59.992 39.130 0.00 0.00 35.77 3.32
50 51 3.755905 CCAAAACAAGGGCAAAAGTGTTT 59.244 39.130 0.00 0.00 44.01 2.83
51 52 4.379290 CCAAAACAAGGGCAAAAGTGTTTG 60.379 41.667 1.73 0.00 41.94 2.93
52 53 2.689553 ACAAGGGCAAAAGTGTTTGG 57.310 45.000 1.72 0.00 43.73 3.28
53 54 2.183679 ACAAGGGCAAAAGTGTTTGGA 58.816 42.857 1.72 0.00 43.73 3.53
54 55 2.569404 ACAAGGGCAAAAGTGTTTGGAA 59.431 40.909 1.72 0.00 43.73 3.53
55 56 3.008485 ACAAGGGCAAAAGTGTTTGGAAA 59.992 39.130 1.72 0.00 43.73 3.13
56 57 3.990959 AGGGCAAAAGTGTTTGGAAAA 57.009 38.095 1.72 0.00 43.73 2.29
57 58 3.872696 AGGGCAAAAGTGTTTGGAAAAG 58.127 40.909 1.72 0.00 43.73 2.27
58 59 3.263170 AGGGCAAAAGTGTTTGGAAAAGT 59.737 39.130 1.72 0.00 43.73 2.66
59 60 4.468153 AGGGCAAAAGTGTTTGGAAAAGTA 59.532 37.500 1.72 0.00 43.73 2.24
60 61 4.808895 GGGCAAAAGTGTTTGGAAAAGTAG 59.191 41.667 1.72 0.00 43.73 2.57
61 62 5.394773 GGGCAAAAGTGTTTGGAAAAGTAGA 60.395 40.000 1.72 0.00 43.73 2.59
62 63 6.280643 GGCAAAAGTGTTTGGAAAAGTAGAT 58.719 36.000 1.72 0.00 43.73 1.98
63 64 7.430441 GGCAAAAGTGTTTGGAAAAGTAGATA 58.570 34.615 1.72 0.00 43.73 1.98
64 65 7.381408 GGCAAAAGTGTTTGGAAAAGTAGATAC 59.619 37.037 1.72 0.00 43.73 2.24
65 66 7.112984 GCAAAAGTGTTTGGAAAAGTAGATACG 59.887 37.037 1.72 0.00 43.73 3.06
66 67 7.797038 AAAGTGTTTGGAAAAGTAGATACGT 57.203 32.000 0.00 0.00 0.00 3.57
67 68 7.797038 AAGTGTTTGGAAAAGTAGATACGTT 57.203 32.000 0.00 0.00 0.00 3.99
68 69 7.186021 AGTGTTTGGAAAAGTAGATACGTTG 57.814 36.000 0.00 0.00 0.00 4.10
69 70 6.204108 AGTGTTTGGAAAAGTAGATACGTTGG 59.796 38.462 0.00 0.00 0.00 3.77
70 71 6.203338 GTGTTTGGAAAAGTAGATACGTTGGA 59.797 38.462 0.00 0.00 0.00 3.53
71 72 6.425721 TGTTTGGAAAAGTAGATACGTTGGAG 59.574 38.462 0.00 0.00 0.00 3.86
72 73 5.988310 TGGAAAAGTAGATACGTTGGAGA 57.012 39.130 0.00 0.00 0.00 3.71
73 74 5.717119 TGGAAAAGTAGATACGTTGGAGAC 58.283 41.667 0.00 0.00 0.00 3.36
151 156 4.924305 ATGTGTTGTGCTTCAGTTTCAT 57.076 36.364 0.00 0.00 0.00 2.57
161 166 8.746922 TGTGCTTCAGTTTCATTATCATTTTC 57.253 30.769 0.00 0.00 0.00 2.29
366 382 8.621286 CAAAATTTGTTACTGGAGTAGTTGACT 58.379 33.333 0.00 0.00 42.90 3.41
424 440 2.831685 ACTAGTTGTGTTCCGATGCA 57.168 45.000 0.00 0.00 0.00 3.96
490 509 2.981859 ACCACCGATGTTCTATGTCC 57.018 50.000 0.00 0.00 0.00 4.02
535 563 4.699257 TGTTACAAAAGTGTGTTACCGGTT 59.301 37.500 15.04 0.00 38.82 4.44
650 680 4.565564 CCACTTAGTAACACGGTCTAATGC 59.434 45.833 0.00 0.00 0.00 3.56
684 715 8.029782 TCAAACTGTGTTACTATATGGCCTAT 57.970 34.615 3.32 1.96 0.00 2.57
718 749 4.098155 TGGGCCTGTAGTAACACAAGATA 58.902 43.478 4.53 0.00 0.00 1.98
848 879 2.352651 GCGCAAATCAGTGAGCTCATTA 59.647 45.455 21.47 8.88 40.70 1.90
902 933 4.956700 TCCTATGAGTTAGACAGGTTCAGG 59.043 45.833 0.00 0.00 0.00 3.86
1005 1036 0.391130 GCAGGTACAACGCCATGAGA 60.391 55.000 0.00 0.00 0.00 3.27
1007 1038 2.632377 CAGGTACAACGCCATGAGAAT 58.368 47.619 0.00 0.00 0.00 2.40
1048 1185 9.243637 CGATAAGAAACCTTTCTAGAGATTCAG 57.756 37.037 0.68 0.00 46.22 3.02
1119 1258 4.808414 TTAGTGAGAGAATCCACACCTG 57.192 45.455 0.00 0.00 41.54 4.00
1289 1430 3.017048 TGCTATTGGATTTGGGTCTGG 57.983 47.619 0.00 0.00 0.00 3.86
1347 1488 4.318332 CTCTTTGCACCTACATCTTCACA 58.682 43.478 0.00 0.00 0.00 3.58
1431 1574 0.106167 AGCTAGTGCCATCCGACCTA 60.106 55.000 0.00 0.00 40.80 3.08
1432 1575 0.969894 GCTAGTGCCATCCGACCTAT 59.030 55.000 0.00 0.00 0.00 2.57
1472 1615 0.683504 GCCCTGGGAGTCTTCTACGA 60.684 60.000 19.27 0.00 0.00 3.43
1565 1708 1.614583 GCTTCCTTCAAGGTTCCCTCC 60.615 57.143 2.50 0.00 36.53 4.30
1574 1717 3.855599 TCAAGGTTCCCTCCCATAAATGA 59.144 43.478 0.00 0.00 30.89 2.57
1599 1746 1.480212 ATTGGGACTGAGCACCGACA 61.480 55.000 0.00 0.00 0.00 4.35
1650 1797 5.833131 AGTCCCAACAAACATCATTTAGTGT 59.167 36.000 0.00 0.00 0.00 3.55
1664 1811 8.960591 CATCATTTAGTGTCCCTCTATTTGTTT 58.039 33.333 0.00 0.00 0.00 2.83
1709 1857 0.108662 TCAGTTGTCGATGCGCTGAT 60.109 50.000 9.73 0.00 32.09 2.90
1710 1858 0.723414 CAGTTGTCGATGCGCTGATT 59.277 50.000 9.73 0.00 0.00 2.57
1711 1859 0.723414 AGTTGTCGATGCGCTGATTG 59.277 50.000 9.73 0.00 0.00 2.67
1712 1860 0.858961 GTTGTCGATGCGCTGATTGC 60.859 55.000 9.73 0.00 38.57 3.56
1714 1862 1.011463 GTCGATGCGCTGATTGCAG 60.011 57.895 9.73 0.00 46.98 4.41
1715 1863 1.448365 TCGATGCGCTGATTGCAGT 60.448 52.632 9.73 0.00 46.98 4.40
1716 1864 1.020861 TCGATGCGCTGATTGCAGTT 61.021 50.000 9.73 0.00 46.98 3.16
1717 1865 0.860203 CGATGCGCTGATTGCAGTTG 60.860 55.000 9.73 0.00 46.98 3.16
1718 1866 0.169672 GATGCGCTGATTGCAGTTGT 59.830 50.000 9.73 0.00 46.98 3.32
1719 1867 1.398041 GATGCGCTGATTGCAGTTGTA 59.602 47.619 9.73 0.00 46.98 2.41
1720 1868 0.798159 TGCGCTGATTGCAGTTGTAG 59.202 50.000 9.73 0.00 44.17 2.74
1740 1900 2.811317 GCAGTTGCTCGGGACTCG 60.811 66.667 0.00 0.00 38.21 4.18
1826 1986 5.221904 TGCTATGCATACACCATAAGGATGT 60.222 40.000 1.16 0.00 33.96 3.06
1906 2066 6.214208 TGAATTAGAGGGTATGCTGATGCTAT 59.786 38.462 0.00 0.00 40.48 2.97
1907 2067 7.400052 TGAATTAGAGGGTATGCTGATGCTATA 59.600 37.037 0.00 0.00 40.48 1.31
2027 2197 5.829924 ACTATCAACCTGGCTCATAAAATGG 59.170 40.000 0.00 0.00 0.00 3.16
2196 2370 4.166919 CTTGGATTCAATAAGGAGGGGACT 59.833 45.833 0.00 0.00 36.17 3.85
2214 2388 2.427453 GACTCGGCCTTCTTCATGTCTA 59.573 50.000 0.00 0.00 0.00 2.59
2227 2402 6.521162 TCTTCATGTCTAGTGCAACAAGTAA 58.479 36.000 0.00 0.00 41.43 2.24
2228 2403 6.989759 TCTTCATGTCTAGTGCAACAAGTAAA 59.010 34.615 0.00 0.00 41.43 2.01
2229 2404 7.497579 TCTTCATGTCTAGTGCAACAAGTAAAA 59.502 33.333 0.00 0.00 41.43 1.52
2270 2445 4.141205 TCCTATTGATTCATGTGCATGGGA 60.141 41.667 11.68 5.62 39.24 4.37
2313 2488 0.034198 TGGATTTGAACGAGGACGCA 59.966 50.000 0.00 0.00 43.96 5.24
2420 2599 1.682684 ACTCGGAGGCGGACTTCAT 60.683 57.895 10.23 0.00 0.00 2.57
2494 2680 1.376942 GAGGTCGTCGAGGTGGAGA 60.377 63.158 4.85 0.00 0.00 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 7.988737 ACTCTAATTTGCATGATTCGAATGAA 58.011 30.769 16.96 3.82 38.76 2.57
3 4 7.254898 GGACTCTAATTTGCATGATTCGAATGA 60.255 37.037 16.96 7.77 0.00 2.57
4 5 6.854892 GGACTCTAATTTGCATGATTCGAATG 59.145 38.462 16.96 3.88 0.00 2.67
5 6 6.543465 TGGACTCTAATTTGCATGATTCGAAT 59.457 34.615 11.20 11.20 0.00 3.34
6 7 5.879777 TGGACTCTAATTTGCATGATTCGAA 59.120 36.000 0.00 0.00 0.00 3.71
7 8 5.427378 TGGACTCTAATTTGCATGATTCGA 58.573 37.500 0.00 0.00 0.00 3.71
8 9 5.739752 TGGACTCTAATTTGCATGATTCG 57.260 39.130 0.00 0.00 0.00 3.34
9 10 7.814107 TGTTTTGGACTCTAATTTGCATGATTC 59.186 33.333 0.00 0.00 0.00 2.52
10 11 7.669427 TGTTTTGGACTCTAATTTGCATGATT 58.331 30.769 0.00 0.00 0.00 2.57
11 12 7.230849 TGTTTTGGACTCTAATTTGCATGAT 57.769 32.000 0.00 0.00 0.00 2.45
12 13 6.647334 TGTTTTGGACTCTAATTTGCATGA 57.353 33.333 0.00 0.00 0.00 3.07
13 14 6.366877 CCTTGTTTTGGACTCTAATTTGCATG 59.633 38.462 0.00 0.00 0.00 4.06
14 15 6.458210 CCTTGTTTTGGACTCTAATTTGCAT 58.542 36.000 0.00 0.00 0.00 3.96
15 16 5.221422 CCCTTGTTTTGGACTCTAATTTGCA 60.221 40.000 0.00 0.00 0.00 4.08
16 17 5.230182 CCCTTGTTTTGGACTCTAATTTGC 58.770 41.667 0.00 0.00 0.00 3.68
17 18 5.221422 TGCCCTTGTTTTGGACTCTAATTTG 60.221 40.000 0.00 0.00 0.00 2.32
18 19 4.898861 TGCCCTTGTTTTGGACTCTAATTT 59.101 37.500 0.00 0.00 0.00 1.82
19 20 4.479158 TGCCCTTGTTTTGGACTCTAATT 58.521 39.130 0.00 0.00 0.00 1.40
20 21 4.112634 TGCCCTTGTTTTGGACTCTAAT 57.887 40.909 0.00 0.00 0.00 1.73
21 22 3.586470 TGCCCTTGTTTTGGACTCTAA 57.414 42.857 0.00 0.00 0.00 2.10
22 23 3.586470 TTGCCCTTGTTTTGGACTCTA 57.414 42.857 0.00 0.00 0.00 2.43
23 24 2.452600 TTGCCCTTGTTTTGGACTCT 57.547 45.000 0.00 0.00 0.00 3.24
24 25 3.118775 ACTTTTGCCCTTGTTTTGGACTC 60.119 43.478 0.00 0.00 0.00 3.36
25 26 2.837591 ACTTTTGCCCTTGTTTTGGACT 59.162 40.909 0.00 0.00 0.00 3.85
26 27 2.935849 CACTTTTGCCCTTGTTTTGGAC 59.064 45.455 0.00 0.00 0.00 4.02
27 28 2.569404 ACACTTTTGCCCTTGTTTTGGA 59.431 40.909 0.00 0.00 0.00 3.53
28 29 2.984562 ACACTTTTGCCCTTGTTTTGG 58.015 42.857 0.00 0.00 0.00 3.28
29 30 4.379290 CCAAACACTTTTGCCCTTGTTTTG 60.379 41.667 0.00 0.00 39.56 2.44
30 31 3.755905 CCAAACACTTTTGCCCTTGTTTT 59.244 39.130 0.00 0.00 39.56 2.43
31 32 3.008485 TCCAAACACTTTTGCCCTTGTTT 59.992 39.130 0.00 0.00 41.69 2.83
32 33 2.569404 TCCAAACACTTTTGCCCTTGTT 59.431 40.909 0.00 0.00 40.84 2.83
33 34 2.183679 TCCAAACACTTTTGCCCTTGT 58.816 42.857 0.00 0.00 40.84 3.16
34 35 2.977772 TCCAAACACTTTTGCCCTTG 57.022 45.000 0.00 0.00 40.84 3.61
35 36 3.990959 TTTCCAAACACTTTTGCCCTT 57.009 38.095 0.00 0.00 40.84 3.95
36 37 3.263170 ACTTTTCCAAACACTTTTGCCCT 59.737 39.130 0.00 0.00 40.84 5.19
37 38 3.605634 ACTTTTCCAAACACTTTTGCCC 58.394 40.909 0.00 0.00 40.84 5.36
38 39 5.656480 TCTACTTTTCCAAACACTTTTGCC 58.344 37.500 0.00 0.00 40.84 4.52
39 40 7.112984 CGTATCTACTTTTCCAAACACTTTTGC 59.887 37.037 0.00 0.00 40.84 3.68
40 41 8.126700 ACGTATCTACTTTTCCAAACACTTTTG 58.873 33.333 0.00 0.00 41.71 2.44
41 42 8.217131 ACGTATCTACTTTTCCAAACACTTTT 57.783 30.769 0.00 0.00 0.00 2.27
42 43 7.797038 ACGTATCTACTTTTCCAAACACTTT 57.203 32.000 0.00 0.00 0.00 2.66
43 44 7.255001 CCAACGTATCTACTTTTCCAAACACTT 60.255 37.037 0.00 0.00 0.00 3.16
44 45 6.204108 CCAACGTATCTACTTTTCCAAACACT 59.796 38.462 0.00 0.00 0.00 3.55
45 46 6.203338 TCCAACGTATCTACTTTTCCAAACAC 59.797 38.462 0.00 0.00 0.00 3.32
46 47 6.289834 TCCAACGTATCTACTTTTCCAAACA 58.710 36.000 0.00 0.00 0.00 2.83
47 48 6.647895 TCTCCAACGTATCTACTTTTCCAAAC 59.352 38.462 0.00 0.00 0.00 2.93
48 49 6.647895 GTCTCCAACGTATCTACTTTTCCAAA 59.352 38.462 0.00 0.00 0.00 3.28
49 50 6.161381 GTCTCCAACGTATCTACTTTTCCAA 58.839 40.000 0.00 0.00 0.00 3.53
50 51 5.620654 CGTCTCCAACGTATCTACTTTTCCA 60.621 44.000 0.00 0.00 46.42 3.53
51 52 4.797349 CGTCTCCAACGTATCTACTTTTCC 59.203 45.833 0.00 0.00 46.42 3.13
52 53 5.928601 CGTCTCCAACGTATCTACTTTTC 57.071 43.478 0.00 0.00 46.42 2.29
65 66 6.273825 AGTGTATGATTGATACGTCTCCAAC 58.726 40.000 0.00 0.00 40.07 3.77
66 67 6.321435 AGAGTGTATGATTGATACGTCTCCAA 59.679 38.462 0.00 0.00 40.07 3.53
67 68 5.828328 AGAGTGTATGATTGATACGTCTCCA 59.172 40.000 0.00 0.00 40.07 3.86
68 69 6.320494 AGAGTGTATGATTGATACGTCTCC 57.680 41.667 0.00 0.00 40.07 3.71
69 70 7.197017 ACAAGAGTGTATGATTGATACGTCTC 58.803 38.462 0.00 0.00 40.07 3.36
70 71 7.101652 ACAAGAGTGTATGATTGATACGTCT 57.898 36.000 0.00 0.00 40.07 4.18
124 125 4.060900 ACTGAAGCACAACACATACAGAG 58.939 43.478 0.00 0.00 0.00 3.35
151 156 6.223351 TGCTTGGCATCATGAAAATGATAA 57.777 33.333 0.00 0.00 39.10 1.75
535 563 3.059733 GTGCGTTATGTGTTACCGAACAA 60.060 43.478 0.00 0.00 46.99 2.83
684 715 2.741145 ACAGGCCCAAAAGTGTGTTAA 58.259 42.857 0.00 0.00 0.00 2.01
718 749 3.487120 GGACAGACCTTTGGTAACACT 57.513 47.619 0.00 0.00 40.78 3.55
848 879 7.622502 TTTACTACTCCAAAAGGTAGGAACT 57.377 36.000 0.00 0.00 38.23 3.01
902 933 5.056894 AGAAAAGACAATGAATCTGCAGC 57.943 39.130 9.47 0.00 0.00 5.25
944 975 7.387673 TCTCTTTAATGCATAATACACCATCCG 59.612 37.037 0.00 0.00 0.00 4.18
1005 1036 7.681939 TCTTATCGTTTTGTTTCTAGCCATT 57.318 32.000 0.00 0.00 0.00 3.16
1007 1038 7.357303 GTTTCTTATCGTTTTGTTTCTAGCCA 58.643 34.615 0.00 0.00 0.00 4.75
1048 1185 5.178996 CCATAGAATCAGCAAGTATGAGCAC 59.821 44.000 0.00 0.00 0.00 4.40
1119 1258 2.419324 CACAGCAGGAAGAAGATTGCTC 59.581 50.000 0.00 0.00 44.49 4.26
1250 1390 0.394565 ATCGCCTAGTGCCTTCATCC 59.605 55.000 0.00 0.00 36.24 3.51
1289 1430 1.678101 ACACAGAGGCAAACAGAAAGC 59.322 47.619 0.00 0.00 0.00 3.51
1347 1488 3.379372 CGGCAATGTCAGATCCTGATTTT 59.621 43.478 0.00 0.00 42.73 1.82
1431 1574 5.083533 CACCTAGAGAGAGTGCTGAAAAT 57.916 43.478 0.00 0.00 0.00 1.82
1432 1575 4.527509 CACCTAGAGAGAGTGCTGAAAA 57.472 45.455 0.00 0.00 0.00 2.29
1599 1746 1.752833 GTTGGGAGGAACACCGACT 59.247 57.895 0.00 0.00 41.07 4.18
1664 1811 1.284491 TGGCCACAGCTTATCATTGGA 59.716 47.619 0.00 0.00 39.73 3.53
1710 1858 1.065401 GCAACTGCAACTACAACTGCA 59.935 47.619 0.00 0.00 46.01 4.41
1711 1859 1.334869 AGCAACTGCAACTACAACTGC 59.665 47.619 4.22 0.00 45.16 4.40
1712 1860 2.348872 CGAGCAACTGCAACTACAACTG 60.349 50.000 4.22 0.00 45.16 3.16
1713 1861 1.867233 CGAGCAACTGCAACTACAACT 59.133 47.619 4.22 0.00 45.16 3.16
1714 1862 1.069906 CCGAGCAACTGCAACTACAAC 60.070 52.381 4.22 0.00 45.16 3.32
1715 1863 1.225855 CCGAGCAACTGCAACTACAA 58.774 50.000 4.22 0.00 45.16 2.41
1716 1864 0.602638 CCCGAGCAACTGCAACTACA 60.603 55.000 4.22 0.00 45.16 2.74
1717 1865 0.320421 TCCCGAGCAACTGCAACTAC 60.320 55.000 4.22 0.00 45.16 2.73
1718 1866 0.320421 GTCCCGAGCAACTGCAACTA 60.320 55.000 4.22 0.00 45.16 2.24
1719 1867 1.598130 GTCCCGAGCAACTGCAACT 60.598 57.895 4.22 0.00 45.16 3.16
1720 1868 1.569479 GAGTCCCGAGCAACTGCAAC 61.569 60.000 4.22 0.00 45.16 4.17
1855 2015 0.600057 GAGTTGCAAGCAAGGGGAAG 59.400 55.000 7.88 0.00 36.52 3.46
1906 2066 7.517614 TTGCTTCACCAACAATGATTAGTTA 57.482 32.000 0.00 0.00 0.00 2.24
1907 2067 6.403866 TTGCTTCACCAACAATGATTAGTT 57.596 33.333 0.00 0.00 0.00 2.24
1986 2156 7.040409 GGTTGATAGTTTTGAGACACAGGAAAT 60.040 37.037 0.00 0.00 0.00 2.17
2196 2370 2.166459 CACTAGACATGAAGAAGGCCGA 59.834 50.000 0.00 0.00 0.00 5.54
2227 2402 3.381590 GGAACAACCAGAGTCTGCTTTTT 59.618 43.478 15.10 6.94 38.79 1.94
2228 2403 2.952310 GGAACAACCAGAGTCTGCTTTT 59.048 45.455 15.10 4.49 38.79 2.27
2229 2404 2.173569 AGGAACAACCAGAGTCTGCTTT 59.826 45.455 15.10 6.99 42.04 3.51
2232 2407 3.618690 ATAGGAACAACCAGAGTCTGC 57.381 47.619 15.10 0.00 42.04 4.26
2236 2411 6.126863 TGAATCAATAGGAACAACCAGAGT 57.873 37.500 0.00 0.00 42.04 3.24
2248 2423 4.146564 TCCCATGCACATGAATCAATAGG 58.853 43.478 12.18 2.57 41.20 2.57
2270 2445 8.314021 CCAGCAGGGTATTTTCTTTCTTTTTAT 58.686 33.333 0.00 0.00 0.00 1.40
2341 2516 2.129146 CAATCACCCATGCGCCCAT 61.129 57.895 4.18 0.00 0.00 4.00
2420 2599 0.811915 GCAGTCTCTAGGCTTCACGA 59.188 55.000 0.00 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.