Multiple sequence alignment - TraesCS2D01G104100

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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 TraesCS2D01G104100 chr2D 100.000 4584 0 0 1 4584 56191988 56196571 0.000000e+00 8466.0
1 TraesCS2D01G104100 chr2D 80.867 392 67 6 375 762 566452724 566453111 7.450000e-78 302.0
2 TraesCS2D01G104100 chr2D 87.429 175 17 5 4 173 209113398 209113224 3.620000e-46 196.0
3 TraesCS2D01G104100 chr2D 85.915 142 18 2 242 382 56201386 56201526 2.860000e-32 150.0
4 TraesCS2D01G104100 chr2D 85.057 87 9 1 3337 3419 629726125 629726039 8.170000e-13 86.1
5 TraesCS2D01G104100 chr2A 93.842 2842 115 18 798 3619 57821473 57824274 0.000000e+00 4224.0
6 TraesCS2D01G104100 chr2A 94.550 422 18 5 3780 4196 57828365 57828786 0.000000e+00 647.0
7 TraesCS2D01G104100 chr2A 89.206 491 45 7 310 798 57719780 57720264 1.410000e-169 606.0
8 TraesCS2D01G104100 chr2A 92.833 293 16 2 4269 4556 57828785 57829077 1.970000e-113 420.0
9 TraesCS2D01G104100 chr2A 79.614 466 75 13 1076 1528 758526616 758526158 2.660000e-82 316.0
10 TraesCS2D01G104100 chr2A 98.204 167 3 0 3616 3782 57828040 57828206 4.490000e-75 292.0
11 TraesCS2D01G104100 chr2A 84.270 89 10 1 3333 3417 776162496 776162408 2.940000e-12 84.2
12 TraesCS2D01G104100 chr2B 90.658 2933 150 36 1 2893 88925264 88928112 0.000000e+00 3784.0
13 TraesCS2D01G104100 chr2B 95.750 847 31 3 3416 4258 88928510 88929355 0.000000e+00 1360.0
14 TraesCS2D01G104100 chr2B 93.765 417 12 4 2921 3337 88928107 88928509 8.430000e-172 614.0
15 TraesCS2D01G104100 chr2B 79.399 466 75 14 1076 1528 771160311 771159854 4.450000e-80 309.0
16 TraesCS2D01G104100 chr2B 84.281 299 40 5 479 776 416184380 416184672 7.510000e-73 285.0
17 TraesCS2D01G104100 chr2B 78.811 387 75 5 380 762 679303493 679303876 2.120000e-63 254.0
18 TraesCS2D01G104100 chr2B 77.551 392 74 8 375 765 719433433 719433055 1.660000e-54 224.0
19 TraesCS2D01G104100 chr2B 87.324 142 16 2 242 382 88931232 88931372 1.320000e-35 161.0
20 TraesCS2D01G104100 chr2B 95.238 84 3 1 4477 4559 88930071 88930154 1.030000e-26 132.0
21 TraesCS2D01G104100 chr2B 95.745 47 2 0 4258 4304 88929570 88929616 4.920000e-10 76.8
22 TraesCS2D01G104100 chr6D 74.732 2426 433 103 1019 3337 19972518 19970166 0.000000e+00 918.0
23 TraesCS2D01G104100 chr6D 75.325 1844 347 65 1079 2866 16865447 16863656 0.000000e+00 785.0
24 TraesCS2D01G104100 chr6D 75.317 1815 330 64 975 2710 20399970 20401745 0.000000e+00 761.0
25 TraesCS2D01G104100 chr6D 77.326 1032 198 21 1019 2035 20648703 20649713 1.110000e-160 577.0
26 TraesCS2D01G104100 chr6A 74.800 1877 339 83 1036 2845 69361747 69359938 0.000000e+00 723.0
27 TraesCS2D01G104100 chr6A 76.013 1259 251 36 1020 2263 19611737 19610515 5.070000e-169 604.0
28 TraesCS2D01G104100 chr6A 85.870 92 8 2 3169 3260 19828016 19827930 4.880000e-15 93.5
29 TraesCS2D01G104100 chr6B 74.986 1751 340 59 1019 2706 33737832 33736117 0.000000e+00 717.0
30 TraesCS2D01G104100 chr6B 76.256 1314 256 34 975 2265 34856709 34857989 0.000000e+00 647.0
31 TraesCS2D01G104100 chr6B 75.255 1273 253 43 1020 2263 33718386 33717147 2.410000e-152 549.0
32 TraesCS2D01G104100 chr6B 78.293 539 86 17 2343 2866 33736112 33735590 7.400000e-83 318.0
33 TraesCS2D01G104100 chr6B 84.100 239 34 4 3522 3756 33732080 33731842 1.280000e-55 228.0
34 TraesCS2D01G104100 chr6B 76.744 387 51 27 3418 3802 124547769 124548118 3.640000e-41 180.0
35 TraesCS2D01G104100 chr6B 89.855 69 7 0 3661 3729 34867233 34867301 6.320000e-14 89.8
36 TraesCS2D01G104100 chrUn 76.115 1457 279 37 1019 2441 76454440 76453019 0.000000e+00 699.0
37 TraesCS2D01G104100 chrUn 86.047 86 8 1 3336 3417 461112369 461112284 6.320000e-14 89.8
38 TraesCS2D01G104100 chr1A 74.800 1873 301 93 1051 2863 557138672 557140433 0.000000e+00 686.0
39 TraesCS2D01G104100 chr1A 88.372 86 5 2 3336 3417 353176264 353176180 1.050000e-16 99.0
40 TraesCS2D01G104100 chr4A 78.316 392 68 10 375 762 25704532 25704154 2.130000e-58 237.0
41 TraesCS2D01G104100 chr4A 84.783 92 8 3 3337 3423 603411288 603411378 2.270000e-13 87.9
42 TraesCS2D01G104100 chr4A 85.542 83 8 1 3336 3414 714743730 714743812 2.940000e-12 84.2
43 TraesCS2D01G104100 chr3A 78.529 340 65 6 428 765 745373235 745372902 2.780000e-52 217.0
44 TraesCS2D01G104100 chr7D 88.000 175 18 3 4 175 595869490 595869664 2.160000e-48 204.0
45 TraesCS2D01G104100 chr7D 86.471 170 21 2 4 171 632121226 632121395 7.830000e-43 185.0
46 TraesCS2D01G104100 chr5A 84.466 206 31 1 380 584 693323919 693324124 7.780000e-48 202.0
47 TraesCS2D01G104100 chr5A 86.207 174 21 3 4 174 608399616 608399443 7.830000e-43 185.0
48 TraesCS2D01G104100 chr4D 81.933 238 37 5 428 661 441746636 441746871 3.620000e-46 196.0
49 TraesCS2D01G104100 chr3D 86.782 174 20 3 4 174 476503726 476503899 1.680000e-44 191.0
50 TraesCS2D01G104100 chr3D 83.871 93 7 5 3334 3420 574507841 574507931 1.060000e-11 82.4
51 TraesCS2D01G104100 chr1D 87.135 171 15 6 10 175 435528995 435528827 2.180000e-43 187.0
52 TraesCS2D01G104100 chr1D 85.795 176 22 3 3 175 10419533 10419708 2.820000e-42 183.0
53 TraesCS2D01G104100 chr1D 86.250 80 8 2 3337 3414 199427782 199427860 2.940000e-12 84.2
54 TraesCS2D01G104100 chr4B 86.207 174 21 3 4 174 37857601 37857774 7.830000e-43 185.0


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 TraesCS2D01G104100 chr2D 56191988 56196571 4583 False 8466.00 8466 100.000000 1 4584 1 chr2D.!!$F1 4583
1 TraesCS2D01G104100 chr2A 57821473 57829077 7604 False 1395.75 4224 94.857250 798 4556 4 chr2A.!!$F2 3758
2 TraesCS2D01G104100 chr2B 88925264 88931372 6108 False 1021.30 3784 93.080000 1 4559 6 chr2B.!!$F3 4558
3 TraesCS2D01G104100 chr6D 19970166 19972518 2352 True 918.00 918 74.732000 1019 3337 1 chr6D.!!$R2 2318
4 TraesCS2D01G104100 chr6D 16863656 16865447 1791 True 785.00 785 75.325000 1079 2866 1 chr6D.!!$R1 1787
5 TraesCS2D01G104100 chr6D 20399970 20401745 1775 False 761.00 761 75.317000 975 2710 1 chr6D.!!$F1 1735
6 TraesCS2D01G104100 chr6D 20648703 20649713 1010 False 577.00 577 77.326000 1019 2035 1 chr6D.!!$F2 1016
7 TraesCS2D01G104100 chr6A 69359938 69361747 1809 True 723.00 723 74.800000 1036 2845 1 chr6A.!!$R3 1809
8 TraesCS2D01G104100 chr6A 19610515 19611737 1222 True 604.00 604 76.013000 1020 2263 1 chr6A.!!$R1 1243
9 TraesCS2D01G104100 chr6B 34856709 34857989 1280 False 647.00 647 76.256000 975 2265 1 chr6B.!!$F1 1290
10 TraesCS2D01G104100 chr6B 33717147 33718386 1239 True 549.00 549 75.255000 1020 2263 1 chr6B.!!$R1 1243
11 TraesCS2D01G104100 chr6B 33731842 33737832 5990 True 421.00 717 79.126333 1019 3756 3 chr6B.!!$R2 2737
12 TraesCS2D01G104100 chrUn 76453019 76454440 1421 True 699.00 699 76.115000 1019 2441 1 chrUn.!!$R1 1422
13 TraesCS2D01G104100 chr1A 557138672 557140433 1761 False 686.00 686 74.800000 1051 2863 1 chr1A.!!$F1 1812

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
220 223 0.378610 GATGCGGCTTGGTTAAGAGC 59.621 55.000 0.0 0.0 38.62 4.09 F
938 957 0.933796 GAGCATGTTTCTAGCCGCTC 59.066 55.000 0.0 0.0 39.10 5.03 F
1630 1720 2.167281 ACGTCATTCAGAGTGATCTGGG 59.833 50.000 0.0 0.0 38.23 4.45 F
2238 5910 1.339055 CCACCATCGTTGTCATCACCT 60.339 52.381 0.0 0.0 0.00 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1944 5579 0.529119 GTGGGCCGTATGTAAGGACG 60.529 60.0 0.00 0.00 36.05 4.79 R
2107 5761 5.346281 GGCATAATTCTTCGTCGAAGGATAG 59.654 44.0 29.52 21.05 36.92 2.08 R
3452 7287 5.600484 TGGAAAATTGCTTAGGAGGAAACAA 59.400 36.0 0.00 0.00 36.76 2.83 R
4206 11984 1.205055 GTAGGGAAAGTCCTCCAGGG 58.795 60.0 0.00 0.00 38.30 4.45 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
31 32 5.311844 ACCTTCTTCCATATTTAGGGAGC 57.688 43.478 0.00 0.00 37.47 4.70
34 35 2.038557 TCTTCCATATTTAGGGAGCCGC 59.961 50.000 0.00 0.00 37.47 6.53
52 53 1.134367 CGCCATTGTCTCGTCTTCCTA 59.866 52.381 0.00 0.00 0.00 2.94
65 67 1.079503 CTTCCTAAGCAGGCACGAAC 58.920 55.000 0.00 0.00 42.30 3.95
82 84 5.390567 GCACGAACCCTAACAAATCACTAAG 60.391 44.000 0.00 0.00 0.00 2.18
83 85 5.929992 CACGAACCCTAACAAATCACTAAGA 59.070 40.000 0.00 0.00 0.00 2.10
87 89 6.182507 ACCCTAACAAATCACTAAGACACA 57.817 37.500 0.00 0.00 0.00 3.72
97 99 9.318041 CAAATCACTAAGACACATCTAAAAACG 57.682 33.333 0.00 0.00 33.57 3.60
105 107 3.081804 CACATCTAAAAACGGAGCCCTT 58.918 45.455 0.00 0.00 0.00 3.95
210 213 0.846693 AATTAGGGAGGATGCGGCTT 59.153 50.000 0.00 0.00 0.00 4.35
220 223 0.378610 GATGCGGCTTGGTTAAGAGC 59.621 55.000 0.00 0.00 38.62 4.09
225 228 1.360820 GGCTTGGTTAAGAGCGTCTC 58.639 55.000 0.00 0.00 39.78 3.36
226 229 1.360820 GCTTGGTTAAGAGCGTCTCC 58.639 55.000 3.66 0.00 35.92 3.71
268 276 2.594303 CGACAAACAGGGGCTGCA 60.594 61.111 0.50 0.00 34.37 4.41
288 296 5.671493 TGCAAAGAGTAGGAACTATAAGCC 58.329 41.667 0.00 0.00 45.60 4.35
363 371 2.284754 TATGCAACTCAACTTGCCCA 57.715 45.000 0.00 0.00 45.13 5.36
380 388 5.534207 TGCCCATTAGCATTTCAAATAGG 57.466 39.130 0.00 0.00 38.00 2.57
395 403 8.633075 TTTCAAATAGGAAAATCGATTGATGC 57.367 30.769 12.25 9.34 34.05 3.91
397 405 6.259829 TCAAATAGGAAAATCGATTGATGCGA 59.740 34.615 12.25 6.23 42.48 5.10
403 411 5.490139 AAAATCGATTGATGCGAAGATGT 57.510 34.783 12.25 0.00 41.52 3.06
422 430 1.136305 GTGCTTATGACCGAGGCACTA 59.864 52.381 8.79 0.00 46.39 2.74
426 434 3.857052 CTTATGACCGAGGCACTAACAA 58.143 45.455 0.00 0.00 41.55 2.83
431 439 1.134907 ACCGAGGCACTAACAATACGG 60.135 52.381 0.00 0.00 41.55 4.02
462 470 8.474831 GTCTTATTTTGGCAACTATAATTGGGT 58.525 33.333 0.00 0.00 37.61 4.51
533 541 5.762179 TGAATAATGGAGATCGCCCTTAT 57.238 39.130 16.63 16.63 32.34 1.73
541 549 3.260884 GGAGATCGCCCTTATGGTTATCA 59.739 47.826 3.71 0.00 36.04 2.15
562 570 5.122519 TCAGCGGCAGTTTTTGATGATATA 58.877 37.500 1.45 0.00 0.00 0.86
565 573 7.607607 TCAGCGGCAGTTTTTGATGATATATAT 59.392 33.333 1.45 0.00 0.00 0.86
566 574 7.907045 CAGCGGCAGTTTTTGATGATATATATC 59.093 37.037 14.77 14.77 0.00 1.63
567 575 7.607607 AGCGGCAGTTTTTGATGATATATATCA 59.392 33.333 24.17 24.17 45.78 2.15
568 576 7.693951 GCGGCAGTTTTTGATGATATATATCAC 59.306 37.037 24.39 18.27 44.66 3.06
569 577 8.939929 CGGCAGTTTTTGATGATATATATCACT 58.060 33.333 24.39 13.76 44.66 3.41
626 634 6.820656 ACATGCTCCTAGAAAGACTAATTGTG 59.179 38.462 0.00 0.00 0.00 3.33
628 636 5.046304 TGCTCCTAGAAAGACTAATTGTGCT 60.046 40.000 0.00 0.00 0.00 4.40
631 639 5.046304 TCCTAGAAAGACTAATTGTGCTGCT 60.046 40.000 0.00 0.00 0.00 4.24
636 644 4.212143 AGACTAATTGTGCTGCTCATGA 57.788 40.909 5.13 0.00 0.00 3.07
638 646 4.815308 AGACTAATTGTGCTGCTCATGATC 59.185 41.667 5.13 0.00 0.00 2.92
676 684 1.279271 AGTAAGATGAGTGTGGGGTGC 59.721 52.381 0.00 0.00 0.00 5.01
679 687 1.583556 AGATGAGTGTGGGGTGCATA 58.416 50.000 0.00 0.00 0.00 3.14
686 694 3.356290 AGTGTGGGGTGCATAAAAGATC 58.644 45.455 0.00 0.00 0.00 2.75
688 696 2.042297 TGTGGGGTGCATAAAAGATCCA 59.958 45.455 0.00 0.00 0.00 3.41
689 697 2.427095 GTGGGGTGCATAAAAGATCCAC 59.573 50.000 0.00 0.00 36.97 4.02
692 700 1.676006 GGTGCATAAAAGATCCACCCG 59.324 52.381 0.00 0.00 39.95 5.28
693 701 2.365582 GTGCATAAAAGATCCACCCGT 58.634 47.619 0.00 0.00 0.00 5.28
709 718 4.334481 CCACCCGTAGAAAATGTTGATACC 59.666 45.833 0.00 0.00 0.00 2.73
799 808 4.569162 CGCCTTTGAAAATCATCATGCATT 59.431 37.500 0.00 0.00 0.00 3.56
802 811 7.042321 CGCCTTTGAAAATCATCATGCATTTAT 60.042 33.333 0.00 0.00 0.00 1.40
839 858 7.144000 AGAAAGAGAGATTTTGCATGTGTTTC 58.856 34.615 0.00 0.00 0.00 2.78
842 861 4.539870 AGAGATTTTGCATGTGTTTCACG 58.460 39.130 0.00 0.00 37.14 4.35
859 878 2.886859 CGGTCATCGTACAGGATGC 58.113 57.895 6.97 3.45 42.78 3.91
912 931 6.295462 CCATCAAAATGTCCAAATTCCAGTCT 60.295 38.462 0.00 0.00 0.00 3.24
913 932 6.729690 TCAAAATGTCCAAATTCCAGTCTT 57.270 33.333 0.00 0.00 0.00 3.01
914 933 7.123355 TCAAAATGTCCAAATTCCAGTCTTT 57.877 32.000 0.00 0.00 0.00 2.52
915 934 7.209475 TCAAAATGTCCAAATTCCAGTCTTTC 58.791 34.615 0.00 0.00 0.00 2.62
916 935 6.983906 AAATGTCCAAATTCCAGTCTTTCT 57.016 33.333 0.00 0.00 0.00 2.52
917 936 8.359642 CAAAATGTCCAAATTCCAGTCTTTCTA 58.640 33.333 0.00 0.00 0.00 2.10
918 937 7.693969 AATGTCCAAATTCCAGTCTTTCTAG 57.306 36.000 0.00 0.00 0.00 2.43
919 938 5.560724 TGTCCAAATTCCAGTCTTTCTAGG 58.439 41.667 0.00 0.00 0.00 3.02
920 939 5.309543 TGTCCAAATTCCAGTCTTTCTAGGA 59.690 40.000 0.00 0.00 0.00 2.94
921 940 5.877564 GTCCAAATTCCAGTCTTTCTAGGAG 59.122 44.000 0.00 0.00 0.00 3.69
922 941 4.637977 CCAAATTCCAGTCTTTCTAGGAGC 59.362 45.833 0.00 0.00 0.00 4.70
923 942 5.248640 CAAATTCCAGTCTTTCTAGGAGCA 58.751 41.667 0.00 0.00 0.00 4.26
924 943 5.707066 AATTCCAGTCTTTCTAGGAGCAT 57.293 39.130 0.00 0.00 0.00 3.79
925 944 4.478206 TTCCAGTCTTTCTAGGAGCATG 57.522 45.455 0.00 0.00 0.00 4.06
926 945 3.445008 TCCAGTCTTTCTAGGAGCATGT 58.555 45.455 0.00 0.00 0.00 3.21
927 946 3.840666 TCCAGTCTTTCTAGGAGCATGTT 59.159 43.478 0.00 0.00 0.00 2.71
928 947 4.287067 TCCAGTCTTTCTAGGAGCATGTTT 59.713 41.667 0.00 0.00 0.00 2.83
929 948 4.633565 CCAGTCTTTCTAGGAGCATGTTTC 59.366 45.833 0.00 0.00 0.00 2.78
932 951 6.756074 CAGTCTTTCTAGGAGCATGTTTCTAG 59.244 42.308 16.77 16.77 0.00 2.43
938 957 0.933796 GAGCATGTTTCTAGCCGCTC 59.066 55.000 0.00 0.00 39.10 5.03
1015 1035 3.134127 GGATGGGCCGCAACTCAC 61.134 66.667 0.00 0.00 0.00 3.51
1104 1127 4.271816 CCGATCCCCGACGAGCTG 62.272 72.222 0.00 0.00 41.76 4.24
1449 1494 4.651778 TGGAAAATTCTCATGGAGTCGTT 58.348 39.130 0.00 0.00 0.00 3.85
1630 1720 2.167281 ACGTCATTCAGAGTGATCTGGG 59.833 50.000 0.00 0.00 38.23 4.45
1674 1765 5.068987 GCTCATCACCTATGTCTTCTCTTCT 59.931 44.000 0.00 0.00 36.89 2.85
1686 1777 4.159506 GTCTTCTCTTCTAGCACCAGACAT 59.840 45.833 0.00 0.00 31.56 3.06
1872 5504 2.290577 GGAGTTCTCCATTGCTGAACCT 60.291 50.000 13.31 4.98 40.42 3.50
2037 5678 3.568430 GGCAAAAGGATAAGGTAATCCCG 59.432 47.826 0.00 0.00 45.74 5.14
2107 5761 2.238521 TGCTTTTGAATCACTGGGGAC 58.761 47.619 0.00 0.00 0.00 4.46
2238 5910 1.339055 CCACCATCGTTGTCATCACCT 60.339 52.381 0.00 0.00 0.00 4.00
2348 6067 9.825972 CACTAATTCTCATTTACACGTTTCATT 57.174 29.630 0.00 0.00 0.00 2.57
2477 6221 4.689071 AGATGTTGAACACGACAAGTACA 58.311 39.130 0.00 0.00 32.59 2.90
2604 6378 4.918810 ATTATTTTCACCTCCGGATTGC 57.081 40.909 3.57 0.00 0.00 3.56
2732 6519 9.903682 CAAATCCATTTATCATATTGACTCCAC 57.096 33.333 0.00 0.00 0.00 4.02
2757 6550 8.826765 ACATAAATATAAGTAGGCATAGCTGGT 58.173 33.333 0.00 0.00 0.00 4.00
3047 6872 6.681729 TTTGATTGTCACTACCTAGACCTT 57.318 37.500 0.00 0.00 33.89 3.50
3346 7181 2.429971 GGTTTAAGACCTACTCCCTCCG 59.570 54.545 0.00 0.00 45.55 4.63
3348 7183 3.463048 TTAAGACCTACTCCCTCCGTT 57.537 47.619 0.00 0.00 0.00 4.44
3366 7201 6.127814 CCTCCGTTCCATAATATAAGAGCGTA 60.128 42.308 7.53 0.00 32.01 4.42
3367 7202 7.218228 TCCGTTCCATAATATAAGAGCGTAA 57.782 36.000 7.53 0.00 32.01 3.18
3368 7203 7.086376 TCCGTTCCATAATATAAGAGCGTAAC 58.914 38.462 7.53 0.00 32.01 2.50
3369 7204 6.864685 CCGTTCCATAATATAAGAGCGTAACA 59.135 38.462 7.53 0.00 32.01 2.41
3370 7205 7.148853 CCGTTCCATAATATAAGAGCGTAACAC 60.149 40.741 7.53 0.00 32.01 3.32
3393 7228 6.631962 ACTACACTAGTGTAAAAGATGCTCC 58.368 40.000 30.31 0.00 44.47 4.70
3414 7249 6.192398 TCCTATATTATGGGATGGAGGGAA 57.808 41.667 4.74 0.00 34.71 3.97
3503 7338 8.119891 ACTTGTTACCCAATATAAAGACCCAAT 58.880 33.333 0.00 0.00 31.20 3.16
3544 7379 7.961827 GCTAACAAGTTTCTGAAGATCTGAATG 59.038 37.037 0.00 0.00 34.93 2.67
3859 11636 7.801547 AATCGATGTTTATTTTCTGTGCAAG 57.198 32.000 0.00 0.00 0.00 4.01
3886 11663 4.826274 TGCTGATTAAGGCTCTGTACTT 57.174 40.909 0.00 0.00 0.00 2.24
4054 11832 0.390866 AGCCAAGCTCGATGACAGTG 60.391 55.000 0.00 0.00 30.62 3.66
4111 11889 7.588497 AAAAGAGATGCCATTTTACCTATCC 57.412 36.000 0.00 0.00 0.00 2.59
4122 11900 8.914011 GCCATTTTACCTATCCTGTTTTAGAAT 58.086 33.333 0.00 0.00 0.00 2.40
4130 11908 4.640771 TCCTGTTTTAGAATGCTCAGGT 57.359 40.909 6.15 0.00 41.88 4.00
4206 11984 4.454728 TTTTGCCTATTCAACATGGCTC 57.545 40.909 0.00 0.00 45.11 4.70
4243 12021 9.703677 TTTCCCTACCCTATTAGGTAATTTTTG 57.296 33.333 8.91 0.00 41.85 2.44
4310 12418 4.713321 AGTTTTCCATGATTCATCCCCTTG 59.287 41.667 0.00 0.00 0.00 3.61
4323 12431 1.455849 CCCTTGTCTTCACCTGCCA 59.544 57.895 0.00 0.00 0.00 4.92
4352 12460 2.949644 GGCCATGTATTCCAACCTGTAC 59.050 50.000 0.00 0.00 0.00 2.90
4355 12463 4.625324 GCCATGTATTCCAACCTGTACTGA 60.625 45.833 0.60 0.00 0.00 3.41
4364 12472 5.441500 TCCAACCTGTACTGAAATTCACAA 58.558 37.500 0.60 0.00 0.00 3.33
4499 12775 3.153369 TGTGCTTTGATTTGAGCCCTA 57.847 42.857 0.00 0.00 38.11 3.53
4529 12805 5.048083 GTCTAAATGCTGTCCAAATGGTTCA 60.048 40.000 0.00 0.40 36.34 3.18
4556 12832 7.201767 GGGAAACTTTTGAGAGATCCATGTATG 60.202 40.741 0.00 0.00 31.94 2.39
4557 12833 7.554118 GGAAACTTTTGAGAGATCCATGTATGA 59.446 37.037 0.00 0.00 0.00 2.15
4558 12834 9.118300 GAAACTTTTGAGAGATCCATGTATGAT 57.882 33.333 0.00 0.00 0.00 2.45
4559 12835 8.447924 AACTTTTGAGAGATCCATGTATGATG 57.552 34.615 0.00 0.00 0.00 3.07
4560 12836 7.571919 ACTTTTGAGAGATCCATGTATGATGT 58.428 34.615 0.00 0.00 0.00 3.06
4561 12837 8.708378 ACTTTTGAGAGATCCATGTATGATGTA 58.292 33.333 0.00 0.00 0.00 2.29
4562 12838 9.722184 CTTTTGAGAGATCCATGTATGATGTAT 57.278 33.333 0.00 0.00 0.00 2.29
4563 12839 9.716531 TTTTGAGAGATCCATGTATGATGTATC 57.283 33.333 0.00 0.00 0.00 2.24
4564 12840 8.426569 TTGAGAGATCCATGTATGATGTATCA 57.573 34.615 0.00 0.00 41.70 2.15
4573 12849 8.753133 TCCATGTATGATGTATCAATAGGACTC 58.247 37.037 0.00 0.00 40.69 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 1.686325 GAGACAATGGCGGCTCCCTA 61.686 60.000 11.43 0.00 0.00 3.53
31 32 1.084370 GGAAGACGAGACAATGGCGG 61.084 60.000 0.00 0.00 0.00 6.13
34 35 3.190874 GCTTAGGAAGACGAGACAATGG 58.809 50.000 0.00 0.00 0.00 3.16
52 53 0.605589 GTTAGGGTTCGTGCCTGCTT 60.606 55.000 0.00 0.00 0.00 3.91
65 67 7.106239 AGATGTGTCTTAGTGATTTGTTAGGG 58.894 38.462 0.00 0.00 0.00 3.53
82 84 2.418976 GGGCTCCGTTTTTAGATGTGTC 59.581 50.000 0.00 0.00 0.00 3.67
83 85 2.039879 AGGGCTCCGTTTTTAGATGTGT 59.960 45.455 0.00 0.00 0.00 3.72
87 89 3.344515 GTGAAGGGCTCCGTTTTTAGAT 58.655 45.455 0.00 0.00 0.00 1.98
105 107 3.691342 CCCGACTCTTGCCGGTGA 61.691 66.667 1.90 0.00 43.93 4.02
140 143 2.687566 CTCCGGTGGCCTTAGGGT 60.688 66.667 3.32 0.00 34.45 4.34
203 206 2.032634 CGCTCTTAACCAAGCCGCA 61.033 57.895 0.00 0.00 35.00 5.69
210 213 1.888018 CGGGAGACGCTCTTAACCA 59.112 57.895 6.78 0.00 34.82 3.67
225 228 2.556622 ACAAAGTTTAGCAATGGACGGG 59.443 45.455 0.00 0.00 0.00 5.28
226 229 3.502211 AGACAAAGTTTAGCAATGGACGG 59.498 43.478 0.00 0.00 0.00 4.79
268 276 5.655532 TCGTGGCTTATAGTTCCTACTCTTT 59.344 40.000 0.00 0.00 35.78 2.52
288 296 6.661982 TTTATTTTATGCAAACGTGTCGTG 57.338 33.333 0.00 0.00 39.99 4.35
380 388 5.394613 CACATCTTCGCATCAATCGATTTTC 59.605 40.000 8.21 0.00 35.75 2.29
394 402 1.258982 CGGTCATAAGCACATCTTCGC 59.741 52.381 0.00 0.00 36.25 4.70
395 403 2.791560 CTCGGTCATAAGCACATCTTCG 59.208 50.000 0.00 0.00 36.25 3.79
397 405 2.743183 GCCTCGGTCATAAGCACATCTT 60.743 50.000 0.00 0.00 38.79 2.40
403 411 1.480789 TAGTGCCTCGGTCATAAGCA 58.519 50.000 0.00 0.00 0.00 3.91
422 430 7.149307 CCAAAATAAGACCAAACCGTATTGTT 58.851 34.615 0.00 0.00 0.00 2.83
426 434 4.767928 TGCCAAAATAAGACCAAACCGTAT 59.232 37.500 0.00 0.00 0.00 3.06
431 439 9.869757 ATTATAGTTGCCAAAATAAGACCAAAC 57.130 29.630 1.49 0.00 0.00 2.93
462 470 6.095300 TCGGAGTTCACCTTTATACGATTACA 59.905 38.462 0.00 0.00 0.00 2.41
523 531 2.612972 CGCTGATAACCATAAGGGCGAT 60.613 50.000 0.00 0.00 43.25 4.58
533 541 1.904287 AAAACTGCCGCTGATAACCA 58.096 45.000 4.02 0.00 0.00 3.67
541 549 7.607607 TGATATATATCATCAAAAACTGCCGCT 59.392 33.333 19.44 0.00 37.76 5.52
572 580 1.685302 ATGTGCGAAAAATCACACGC 58.315 45.000 0.00 0.00 44.74 5.34
589 597 9.859427 TTTCTAGGAGCATGTTCAAAAATAATG 57.141 29.630 11.93 0.00 0.00 1.90
626 634 5.511234 AATTTGGTTAGATCATGAGCAGC 57.489 39.130 14.38 3.60 0.00 5.25
628 636 9.330063 CTAACTAATTTGGTTAGATCATGAGCA 57.670 33.333 21.64 0.00 45.06 4.26
668 676 2.427095 GTGGATCTTTTATGCACCCCAC 59.573 50.000 0.00 0.00 34.83 4.61
676 684 6.995511 TTTTCTACGGGTGGATCTTTTATG 57.004 37.500 0.00 0.00 0.00 1.90
679 687 5.321927 ACATTTTCTACGGGTGGATCTTTT 58.678 37.500 0.00 0.00 0.00 2.27
686 694 4.334481 GGTATCAACATTTTCTACGGGTGG 59.666 45.833 0.00 0.00 0.00 4.61
688 696 4.226620 AGGGTATCAACATTTTCTACGGGT 59.773 41.667 0.00 0.00 0.00 5.28
689 697 4.777463 AGGGTATCAACATTTTCTACGGG 58.223 43.478 0.00 0.00 0.00 5.28
815 834 6.919662 TGAAACACATGCAAAATCTCTCTTTC 59.080 34.615 0.00 0.00 0.00 2.62
842 861 0.597637 CCGCATCCTGTACGATGACC 60.598 60.000 13.15 0.00 41.92 4.02
853 872 0.252197 GTACAAACTCCCCGCATCCT 59.748 55.000 0.00 0.00 0.00 3.24
856 875 2.491693 CAAATGTACAAACTCCCCGCAT 59.508 45.455 0.00 0.00 0.00 4.73
857 876 1.883275 CAAATGTACAAACTCCCCGCA 59.117 47.619 0.00 0.00 0.00 5.69
859 878 1.201414 GGCAAATGTACAAACTCCCCG 59.799 52.381 0.00 0.00 0.00 5.73
912 931 4.680708 CGGCTAGAAACATGCTCCTAGAAA 60.681 45.833 15.73 0.00 32.49 2.52
913 932 3.181475 CGGCTAGAAACATGCTCCTAGAA 60.181 47.826 15.73 0.00 32.49 2.10
914 933 2.362397 CGGCTAGAAACATGCTCCTAGA 59.638 50.000 15.73 0.00 32.49 2.43
915 934 2.748605 CGGCTAGAAACATGCTCCTAG 58.251 52.381 0.00 10.00 33.58 3.02
916 935 1.202533 GCGGCTAGAAACATGCTCCTA 60.203 52.381 0.00 0.00 0.00 2.94
917 936 0.462759 GCGGCTAGAAACATGCTCCT 60.463 55.000 0.00 0.00 0.00 3.69
918 937 0.462759 AGCGGCTAGAAACATGCTCC 60.463 55.000 0.00 0.00 0.00 4.70
919 938 0.933796 GAGCGGCTAGAAACATGCTC 59.066 55.000 0.60 0.00 41.57 4.26
920 939 0.462759 GGAGCGGCTAGAAACATGCT 60.463 55.000 0.60 0.00 34.96 3.79
921 940 1.440145 GGGAGCGGCTAGAAACATGC 61.440 60.000 0.60 0.00 0.00 4.06
922 941 0.179000 AGGGAGCGGCTAGAAACATG 59.821 55.000 0.60 0.00 0.00 3.21
923 942 0.912486 AAGGGAGCGGCTAGAAACAT 59.088 50.000 0.60 0.00 0.00 2.71
924 943 0.249398 GAAGGGAGCGGCTAGAAACA 59.751 55.000 0.60 0.00 0.00 2.83
925 944 0.462225 GGAAGGGAGCGGCTAGAAAC 60.462 60.000 0.60 0.00 0.00 2.78
926 945 0.617820 AGGAAGGGAGCGGCTAGAAA 60.618 55.000 0.60 0.00 0.00 2.52
927 946 1.001760 AGGAAGGGAGCGGCTAGAA 59.998 57.895 0.60 0.00 0.00 2.10
928 947 1.455959 GAGGAAGGGAGCGGCTAGA 60.456 63.158 0.60 0.00 0.00 2.43
929 948 1.045911 AAGAGGAAGGGAGCGGCTAG 61.046 60.000 0.60 0.00 0.00 3.42
932 951 2.188207 GAAGAGGAAGGGAGCGGC 59.812 66.667 0.00 0.00 0.00 6.53
938 957 1.063642 GGATTTGGGGAAGAGGAAGGG 60.064 57.143 0.00 0.00 0.00 3.95
1104 1127 1.266598 CGAACGAAGATTTCAGCGAGC 60.267 52.381 0.00 0.00 0.00 5.03
1375 1414 2.048503 GACGTCCCAGACAACCCG 60.049 66.667 3.51 0.00 32.09 5.28
1449 1494 0.828022 ACACCACCGTCTCTGTGAAA 59.172 50.000 0.00 0.00 35.74 2.69
1630 1720 3.142174 GCTTATCTTCATAGTGCCCCAC 58.858 50.000 0.00 0.00 34.10 4.61
1686 1777 1.037030 GGGATCGAATGGCTTGCCAA 61.037 55.000 18.76 2.12 0.00 4.52
1872 5504 2.031120 CAAACTTTGGGTTCAGCTGGA 58.969 47.619 15.13 0.46 37.12 3.86
1944 5579 0.529119 GTGGGCCGTATGTAAGGACG 60.529 60.000 0.00 0.00 36.05 4.79
2107 5761 5.346281 GGCATAATTCTTCGTCGAAGGATAG 59.654 44.000 29.52 21.05 36.92 2.08
2238 5910 8.812972 ACAGAGAGTTTACCATTTGATACTGTA 58.187 33.333 0.00 0.00 32.05 2.74
2348 6067 7.093354 TCACAAGCACAAAAGAATTAACAACA 58.907 30.769 0.00 0.00 0.00 3.33
2477 6221 6.302535 TGAATTCATGATGCCTCCAAAATT 57.697 33.333 3.38 0.00 0.00 1.82
2604 6378 5.754406 TGCAATGATTGTTTCCAAGTTGAAG 59.246 36.000 3.87 0.00 33.17 3.02
2757 6550 8.768501 TGGGTGTTTATTTGCAACCATATATA 57.231 30.769 0.00 0.00 46.41 0.86
2758 6551 7.667575 TGGGTGTTTATTTGCAACCATATAT 57.332 32.000 0.00 0.00 46.41 0.86
3021 6846 6.935208 AGGTCTAGGTAGTGACAATCAAAAAC 59.065 38.462 0.00 0.00 35.11 2.43
3346 7181 8.813643 AGTGTTACGCTCTTATATTATGGAAC 57.186 34.615 0.00 0.00 0.00 3.62
3348 7183 9.070179 TGTAGTGTTACGCTCTTATATTATGGA 57.930 33.333 0.20 0.00 32.21 3.41
3369 7204 6.437793 AGGAGCATCTTTTACACTAGTGTAGT 59.562 38.462 29.34 12.02 40.33 2.73
3370 7205 6.868622 AGGAGCATCTTTTACACTAGTGTAG 58.131 40.000 29.34 22.34 40.33 2.74
3377 7212 9.950496 CCATAATATAGGAGCATCTTTTACACT 57.050 33.333 0.00 0.00 33.73 3.55
3386 7221 6.239829 CCTCCATCCCATAATATAGGAGCATC 60.240 46.154 0.00 0.00 39.78 3.91
3393 7228 8.805145 ACTATTCCCTCCATCCCATAATATAG 57.195 38.462 0.00 0.00 0.00 1.31
3452 7287 5.600484 TGGAAAATTGCTTAGGAGGAAACAA 59.400 36.000 0.00 0.00 36.76 2.83
3544 7379 6.503616 TTGTCGAAATTATGCACAACAAAC 57.496 33.333 0.00 0.00 0.00 2.93
3859 11636 5.848406 ACAGAGCCTTAATCAGCATACTAC 58.152 41.667 0.00 0.00 0.00 2.73
4054 11832 3.606153 GCACATTCGAAACACACACTACC 60.606 47.826 0.00 0.00 0.00 3.18
4111 11889 5.675575 GCATGACCTGAGCATTCTAAAACAG 60.676 44.000 0.00 0.00 0.00 3.16
4122 11900 1.241165 CACAAAGCATGACCTGAGCA 58.759 50.000 0.00 0.00 0.00 4.26
4206 11984 1.205055 GTAGGGAAAGTCCTCCAGGG 58.795 60.000 0.00 0.00 38.30 4.45
4243 12021 2.427506 ACCTTCGTCTTGCAGGAATTC 58.572 47.619 0.00 0.00 0.00 2.17
4310 12418 2.288395 CCAAACAATGGCAGGTGAAGAC 60.288 50.000 7.87 0.00 43.80 3.01
4323 12431 3.448934 TGGAATACATGGCCCAAACAAT 58.551 40.909 0.00 0.00 0.00 2.71
4352 12460 3.659444 GCGTTTCTCGTTGTGAATTTCAG 59.341 43.478 0.00 0.00 42.13 3.02
4355 12463 3.684103 TGCGTTTCTCGTTGTGAATTT 57.316 38.095 0.00 0.00 42.13 1.82
4364 12472 1.225855 TGCTTTCATGCGTTTCTCGT 58.774 45.000 0.00 0.00 42.13 4.18
4433 12541 5.273208 TCCAGAACTCTTCTTGCCTACTAT 58.727 41.667 0.00 0.00 38.11 2.12
4472 12585 4.321745 GCTCAAATCAAAGCACATACAACG 59.678 41.667 0.00 0.00 38.42 4.10
4499 12775 5.435686 TTGGACAGCATTTAGACCATACT 57.564 39.130 0.00 0.00 0.00 2.12
4529 12805 5.222213 ACATGGATCTCTCAAAAGTTTCCCT 60.222 40.000 0.00 0.00 0.00 4.20
4556 12832 9.688091 TCCTACATAGAGTCCTATTGATACATC 57.312 37.037 0.00 0.00 33.47 3.06


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

AutoCloner maintained by Alex Coulton.