Multiple sequence alignment - TraesCS5D01G429300

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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 TraesCS5D01G429300 chr5D 100.000 2573 0 0 1 2573 486822374 486819802 0.000000e+00 4752
1 TraesCS5D01G429300 chr3D 95.672 2195 59 16 249 2411 284994361 284996551 0.000000e+00 3494
2 TraesCS5D01G429300 chr3D 95.800 1619 43 11 808 2411 453177516 453175908 0.000000e+00 2590
3 TraesCS5D01G429300 chr3D 88.481 2205 153 56 249 2411 79621258 79619113 0.000000e+00 2571
4 TraesCS5D01G429300 chr3D 91.453 936 41 17 250 1156 83487421 83488346 0.000000e+00 1249
5 TraesCS5D01G429300 chr3D 95.732 164 7 0 2408 2571 83489882 83490045 5.460000e-67 265
6 TraesCS5D01G429300 chr3D 95.732 164 7 0 2408 2571 285003628 285003791 5.460000e-67 265
7 TraesCS5D01G429300 chrUn 94.619 2193 51 18 250 2411 22359594 22361750 0.000000e+00 3334
8 TraesCS5D01G429300 chrUn 96.341 164 6 0 2408 2571 22364030 22364193 1.170000e-68 270
9 TraesCS5D01G429300 chr1D 96.187 1626 39 12 790 2411 482330148 482331754 0.000000e+00 2638
10 TraesCS5D01G429300 chr1D 94.899 1627 49 10 808 2411 206977846 206979461 0.000000e+00 2514
11 TraesCS5D01G429300 chr1D 89.639 637 27 5 249 855 1816972 1817599 0.000000e+00 774
12 TraesCS5D01G429300 chr6D 95.617 1620 44 12 808 2411 454506180 454504572 0.000000e+00 2573
13 TraesCS5D01G429300 chr2D 95.182 1619 57 10 794 2411 50038696 50037098 0.000000e+00 2538
14 TraesCS5D01G429300 chr2D 94.856 1633 54 12 796 2411 128970951 128969332 0.000000e+00 2523
15 TraesCS5D01G429300 chr2D 94.617 613 26 4 250 860 125435970 125435363 0.000000e+00 942
16 TraesCS5D01G429300 chr2D 89.225 529 26 6 250 748 585391070 585391597 1.300000e-177 632
17 TraesCS5D01G429300 chr2D 90.789 152 14 0 855 1006 324176504 324176655 1.210000e-48 204
18 TraesCS5D01G429300 chr1B 88.525 1281 100 15 714 1967 620554006 620555266 0.000000e+00 1507
19 TraesCS5D01G429300 chr1B 92.060 1058 59 12 751 1806 3208226 3207192 0.000000e+00 1465
20 TraesCS5D01G429300 chr1B 85.393 356 41 11 250 600 636814486 636814137 2.430000e-95 359
21 TraesCS5D01G429300 chr1B 75.250 400 63 27 366 741 620553675 620554062 9.530000e-35 158
22 TraesCS5D01G429300 chr2A 90.926 1058 71 9 751 1806 726336960 726335926 0.000000e+00 1399
23 TraesCS5D01G429300 chr7D 89.509 896 25 12 238 1104 109148783 109149638 0.000000e+00 1070
24 TraesCS5D01G429300 chr7D 95.732 164 7 0 2408 2571 109166058 109166221 5.460000e-67 265
25 TraesCS5D01G429300 chr7B 90.468 598 37 5 721 1317 630811548 630812126 0.000000e+00 771
26 TraesCS5D01G429300 chr7B 94.667 150 8 0 2417 2566 630814864 630815013 1.540000e-57 233
27 TraesCS5D01G429300 chr2B 85.955 356 39 11 250 600 721355761 721356110 1.120000e-98 370
28 TraesCS5D01G429300 chr2B 91.613 155 11 2 2417 2571 525625344 525625496 2.010000e-51 213
29 TraesCS5D01G429300 chr4B 83.984 256 27 4 761 1002 601276044 601275789 1.540000e-57 233
30 TraesCS5D01G429300 chr5B 94.000 150 7 2 2417 2566 467435547 467435694 2.580000e-55 226
31 TraesCS5D01G429300 chr5B 85.976 164 18 4 851 1011 682242955 682242794 1.220000e-38 171
32 TraesCS5D01G429300 chr3B 90.968 155 12 2 2417 2571 642463018 642462866 9.330000e-50 207
33 TraesCS5D01G429300 chr6B 88.554 166 15 2 2408 2571 459163474 459163637 5.620000e-47 198


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 TraesCS5D01G429300 chr5D 486819802 486822374 2572 True 4752.0 4752 100.0000 1 2573 1 chr5D.!!$R1 2572
1 TraesCS5D01G429300 chr3D 284994361 284996551 2190 False 3494.0 3494 95.6720 249 2411 1 chr3D.!!$F1 2162
2 TraesCS5D01G429300 chr3D 453175908 453177516 1608 True 2590.0 2590 95.8000 808 2411 1 chr3D.!!$R2 1603
3 TraesCS5D01G429300 chr3D 79619113 79621258 2145 True 2571.0 2571 88.4810 249 2411 1 chr3D.!!$R1 2162
4 TraesCS5D01G429300 chr3D 83487421 83490045 2624 False 757.0 1249 93.5925 250 2571 2 chr3D.!!$F3 2321
5 TraesCS5D01G429300 chrUn 22359594 22364193 4599 False 1802.0 3334 95.4800 250 2571 2 chrUn.!!$F1 2321
6 TraesCS5D01G429300 chr1D 482330148 482331754 1606 False 2638.0 2638 96.1870 790 2411 1 chr1D.!!$F3 1621
7 TraesCS5D01G429300 chr1D 206977846 206979461 1615 False 2514.0 2514 94.8990 808 2411 1 chr1D.!!$F2 1603
8 TraesCS5D01G429300 chr1D 1816972 1817599 627 False 774.0 774 89.6390 249 855 1 chr1D.!!$F1 606
9 TraesCS5D01G429300 chr6D 454504572 454506180 1608 True 2573.0 2573 95.6170 808 2411 1 chr6D.!!$R1 1603
10 TraesCS5D01G429300 chr2D 50037098 50038696 1598 True 2538.0 2538 95.1820 794 2411 1 chr2D.!!$R1 1617
11 TraesCS5D01G429300 chr2D 128969332 128970951 1619 True 2523.0 2523 94.8560 796 2411 1 chr2D.!!$R3 1615
12 TraesCS5D01G429300 chr2D 125435363 125435970 607 True 942.0 942 94.6170 250 860 1 chr2D.!!$R2 610
13 TraesCS5D01G429300 chr2D 585391070 585391597 527 False 632.0 632 89.2250 250 748 1 chr2D.!!$F2 498
14 TraesCS5D01G429300 chr1B 3207192 3208226 1034 True 1465.0 1465 92.0600 751 1806 1 chr1B.!!$R1 1055
15 TraesCS5D01G429300 chr1B 620553675 620555266 1591 False 832.5 1507 81.8875 366 1967 2 chr1B.!!$F1 1601
16 TraesCS5D01G429300 chr2A 726335926 726336960 1034 True 1399.0 1399 90.9260 751 1806 1 chr2A.!!$R1 1055
17 TraesCS5D01G429300 chr7D 109148783 109149638 855 False 1070.0 1070 89.5090 238 1104 1 chr7D.!!$F1 866
18 TraesCS5D01G429300 chr7B 630811548 630815013 3465 False 502.0 771 92.5675 721 2566 2 chr7B.!!$F1 1845

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
84 85 0.033011 GCCAGTAGTGAGGGAGAGGA 60.033 60.0 0.0 0.0 0.0 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2008 4589 1.037579 TGCATCGACGGAGGATGACT 61.038 55.0 14.34 0.0 43.07 3.41 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
29 30 3.283684 CAACGTGGAAGCCCGCAA 61.284 61.111 0.00 0.00 43.08 4.85
30 31 3.284449 AACGTGGAAGCCCGCAAC 61.284 61.111 0.00 0.00 43.08 4.17
33 34 3.670377 GTGGAAGCCCGCAACCAC 61.670 66.667 15.61 15.61 44.23 4.16
34 35 4.196778 TGGAAGCCCGCAACCACA 62.197 61.111 1.67 0.00 34.29 4.17
35 36 3.670377 GGAAGCCCGCAACCACAC 61.670 66.667 0.00 0.00 0.00 3.82
36 37 4.025401 GAAGCCCGCAACCACACG 62.025 66.667 0.00 0.00 0.00 4.49
37 38 4.555709 AAGCCCGCAACCACACGA 62.556 61.111 0.00 0.00 0.00 4.35
38 39 4.988598 AGCCCGCAACCACACGAG 62.989 66.667 0.00 0.00 0.00 4.18
40 41 4.308458 CCCGCAACCACACGAGGA 62.308 66.667 0.00 0.00 0.00 3.71
41 42 2.738521 CCGCAACCACACGAGGAG 60.739 66.667 0.00 0.00 0.00 3.69
42 43 3.414700 CGCAACCACACGAGGAGC 61.415 66.667 0.00 0.00 0.00 4.70
43 44 2.280797 GCAACCACACGAGGAGCA 60.281 61.111 0.00 0.00 34.80 4.26
44 45 1.891919 GCAACCACACGAGGAGCAA 60.892 57.895 0.00 0.00 34.80 3.91
45 46 1.845809 GCAACCACACGAGGAGCAAG 61.846 60.000 0.00 0.00 34.80 4.01
46 47 1.071471 AACCACACGAGGAGCAAGG 59.929 57.895 0.00 0.00 0.00 3.61
47 48 2.046892 CCACACGAGGAGCAAGGG 60.047 66.667 0.00 0.00 0.00 3.95
48 49 2.583441 CCACACGAGGAGCAAGGGA 61.583 63.158 0.00 0.00 0.00 4.20
49 50 1.079543 CACACGAGGAGCAAGGGAG 60.080 63.158 0.00 0.00 0.00 4.30
50 51 2.125350 CACGAGGAGCAAGGGAGC 60.125 66.667 0.00 0.00 0.00 4.70
51 52 2.604686 ACGAGGAGCAAGGGAGCA 60.605 61.111 0.00 0.00 36.85 4.26
52 53 1.992277 ACGAGGAGCAAGGGAGCAT 60.992 57.895 0.00 0.00 36.85 3.79
53 54 1.523258 CGAGGAGCAAGGGAGCATG 60.523 63.158 0.00 0.00 36.85 4.06
54 55 1.823041 GAGGAGCAAGGGAGCATGC 60.823 63.158 10.51 10.51 42.87 4.06
55 56 2.044650 GGAGCAAGGGAGCATGCA 60.045 61.111 21.98 0.00 44.95 3.96
56 57 1.679977 GGAGCAAGGGAGCATGCAA 60.680 57.895 21.98 0.00 44.95 4.08
57 58 1.664321 GGAGCAAGGGAGCATGCAAG 61.664 60.000 21.98 3.64 44.95 4.01
58 59 0.964358 GAGCAAGGGAGCATGCAAGT 60.964 55.000 21.98 0.00 44.95 3.16
59 60 1.214589 GCAAGGGAGCATGCAAGTG 59.785 57.895 21.98 11.09 42.12 3.16
60 61 1.530013 GCAAGGGAGCATGCAAGTGT 61.530 55.000 21.98 0.00 42.12 3.55
61 62 0.524862 CAAGGGAGCATGCAAGTGTC 59.475 55.000 21.98 7.97 0.00 3.67
62 63 0.957395 AAGGGAGCATGCAAGTGTCG 60.957 55.000 21.98 0.00 0.00 4.35
63 64 2.482374 GGAGCATGCAAGTGTCGC 59.518 61.111 21.98 0.00 0.00 5.19
64 65 2.482374 GAGCATGCAAGTGTCGCC 59.518 61.111 21.98 0.00 0.00 5.54
65 66 3.372676 GAGCATGCAAGTGTCGCCG 62.373 63.158 21.98 0.00 0.00 6.46
67 68 4.465512 CATGCAAGTGTCGCCGCC 62.466 66.667 0.00 0.00 0.00 6.13
71 72 2.048597 CAAGTGTCGCCGCCAGTA 60.049 61.111 0.00 0.00 0.00 2.74
72 73 2.094659 CAAGTGTCGCCGCCAGTAG 61.095 63.158 0.00 0.00 0.00 2.57
73 74 2.571216 AAGTGTCGCCGCCAGTAGT 61.571 57.895 0.00 0.00 0.00 2.73
74 75 2.765250 AAGTGTCGCCGCCAGTAGTG 62.765 60.000 0.00 0.00 0.00 2.74
75 76 2.986979 TGTCGCCGCCAGTAGTGA 60.987 61.111 0.00 0.00 0.00 3.41
76 77 2.202623 GTCGCCGCCAGTAGTGAG 60.203 66.667 0.00 0.00 0.00 3.51
77 78 3.449227 TCGCCGCCAGTAGTGAGG 61.449 66.667 0.00 3.48 0.00 3.86
78 79 4.514577 CGCCGCCAGTAGTGAGGG 62.515 72.222 12.12 7.93 0.00 4.30
79 80 3.075005 GCCGCCAGTAGTGAGGGA 61.075 66.667 10.12 0.00 0.00 4.20
80 81 3.082579 GCCGCCAGTAGTGAGGGAG 62.083 68.421 10.12 0.00 0.00 4.30
81 82 1.379977 CCGCCAGTAGTGAGGGAGA 60.380 63.158 0.00 0.00 0.00 3.71
82 83 1.388065 CCGCCAGTAGTGAGGGAGAG 61.388 65.000 0.00 0.00 0.00 3.20
83 84 1.388065 CGCCAGTAGTGAGGGAGAGG 61.388 65.000 0.00 0.00 0.00 3.69
84 85 0.033011 GCCAGTAGTGAGGGAGAGGA 60.033 60.000 0.00 0.00 0.00 3.71
85 86 1.619977 GCCAGTAGTGAGGGAGAGGAA 60.620 57.143 0.00 0.00 0.00 3.36
86 87 2.104170 CCAGTAGTGAGGGAGAGGAAC 58.896 57.143 0.00 0.00 0.00 3.62
87 88 1.746220 CAGTAGTGAGGGAGAGGAACG 59.254 57.143 0.00 0.00 0.00 3.95
88 89 0.456628 GTAGTGAGGGAGAGGAACGC 59.543 60.000 0.00 0.00 0.00 4.84
89 90 0.331954 TAGTGAGGGAGAGGAACGCT 59.668 55.000 0.00 0.00 44.68 5.07
90 91 1.216710 GTGAGGGAGAGGAACGCTG 59.783 63.158 0.00 0.00 39.71 5.18
91 92 1.984570 TGAGGGAGAGGAACGCTGG 60.985 63.158 0.00 0.00 39.71 4.85
92 93 1.682684 GAGGGAGAGGAACGCTGGA 60.683 63.158 0.00 0.00 39.71 3.86
93 94 1.671901 GAGGGAGAGGAACGCTGGAG 61.672 65.000 0.00 0.00 39.71 3.86
94 95 1.682684 GGGAGAGGAACGCTGGAGA 60.683 63.158 0.00 0.00 39.71 3.71
95 96 1.671901 GGGAGAGGAACGCTGGAGAG 61.672 65.000 0.00 0.00 39.71 3.20
96 97 1.671901 GGAGAGGAACGCTGGAGAGG 61.672 65.000 0.00 0.00 39.71 3.69
97 98 1.671901 GAGAGGAACGCTGGAGAGGG 61.672 65.000 0.00 0.00 39.71 4.30
98 99 1.985116 GAGGAACGCTGGAGAGGGT 60.985 63.158 0.00 0.00 46.90 4.34
102 103 2.526873 ACGCTGGAGAGGGTTGGT 60.527 61.111 0.00 0.00 42.52 3.67
103 104 2.046892 CGCTGGAGAGGGTTGGTG 60.047 66.667 0.00 0.00 0.00 4.17
104 105 2.352805 GCTGGAGAGGGTTGGTGG 59.647 66.667 0.00 0.00 0.00 4.61
105 106 2.352805 CTGGAGAGGGTTGGTGGC 59.647 66.667 0.00 0.00 0.00 5.01
106 107 3.612247 CTGGAGAGGGTTGGTGGCG 62.612 68.421 0.00 0.00 0.00 5.69
136 137 2.753055 GGAGACCAGTCAAGGAACTC 57.247 55.000 0.00 0.00 38.49 3.01
137 138 1.276705 GGAGACCAGTCAAGGAACTCC 59.723 57.143 0.00 12.17 42.80 3.85
148 149 2.630889 AGGAACTCCTCATCACCAGA 57.369 50.000 0.00 0.00 44.77 3.86
149 150 3.127791 AGGAACTCCTCATCACCAGAT 57.872 47.619 0.00 0.00 44.77 2.90
156 157 3.817787 CATCACCAGATGGCACGG 58.182 61.111 0.00 0.00 46.33 4.94
157 158 1.078214 CATCACCAGATGGCACGGT 60.078 57.895 0.00 0.00 46.33 4.83
158 159 1.091771 CATCACCAGATGGCACGGTC 61.092 60.000 0.00 0.00 46.33 4.79
159 160 2.578163 ATCACCAGATGGCACGGTCG 62.578 60.000 0.00 0.48 39.32 4.79
160 161 4.760047 ACCAGATGGCACGGTCGC 62.760 66.667 0.00 0.00 39.32 5.19
171 172 3.484547 CGGTCGCCGTTAACCTGC 61.485 66.667 9.69 2.38 42.73 4.85
172 173 2.357760 GGTCGCCGTTAACCTGCA 60.358 61.111 13.38 0.00 32.54 4.41
173 174 2.388232 GGTCGCCGTTAACCTGCAG 61.388 63.158 6.78 6.78 32.54 4.41
174 175 2.047655 TCGCCGTTAACCTGCAGG 60.048 61.111 31.60 31.60 42.17 4.85
175 176 3.124921 CGCCGTTAACCTGCAGGG 61.125 66.667 35.42 18.09 40.27 4.45
186 187 3.471620 TGCAGGGTGTGGAGAGTC 58.528 61.111 0.00 0.00 0.00 3.36
187 188 2.217038 TGCAGGGTGTGGAGAGTCC 61.217 63.158 0.00 0.00 36.96 3.85
188 189 2.960688 GCAGGGTGTGGAGAGTCCC 61.961 68.421 0.00 0.00 40.16 4.46
189 190 1.536418 CAGGGTGTGGAGAGTCCCA 60.536 63.158 0.00 0.00 42.12 4.37
190 191 0.911525 CAGGGTGTGGAGAGTCCCAT 60.912 60.000 3.97 0.00 42.12 4.00
191 192 0.911525 AGGGTGTGGAGAGTCCCATG 60.912 60.000 3.97 0.00 42.12 3.66
192 193 1.078143 GGTGTGGAGAGTCCCATGC 60.078 63.158 3.97 1.44 38.66 4.06
193 194 1.078143 GTGTGGAGAGTCCCATGCC 60.078 63.158 3.97 0.00 38.66 4.40
194 195 1.538629 TGTGGAGAGTCCCATGCCA 60.539 57.895 3.97 0.00 38.66 4.92
195 196 1.133181 TGTGGAGAGTCCCATGCCAA 61.133 55.000 3.97 0.00 38.66 4.52
196 197 0.038166 GTGGAGAGTCCCATGCCAAA 59.962 55.000 3.97 0.00 38.66 3.28
197 198 0.329261 TGGAGAGTCCCATGCCAAAG 59.671 55.000 0.00 0.00 35.03 2.77
198 199 1.034292 GGAGAGTCCCATGCCAAAGC 61.034 60.000 0.00 0.00 40.48 3.51
220 221 2.872028 CGCAGCAAAGGACAACAAC 58.128 52.632 0.00 0.00 0.00 3.32
221 222 0.381801 CGCAGCAAAGGACAACAACT 59.618 50.000 0.00 0.00 0.00 3.16
222 223 1.843992 GCAGCAAAGGACAACAACTG 58.156 50.000 0.00 0.00 0.00 3.16
223 224 1.405105 GCAGCAAAGGACAACAACTGA 59.595 47.619 0.00 0.00 0.00 3.41
224 225 2.035066 GCAGCAAAGGACAACAACTGAT 59.965 45.455 0.00 0.00 0.00 2.90
225 226 3.635331 CAGCAAAGGACAACAACTGATG 58.365 45.455 0.00 0.00 0.00 3.07
226 227 3.316029 CAGCAAAGGACAACAACTGATGA 59.684 43.478 0.00 0.00 0.00 2.92
227 228 3.567164 AGCAAAGGACAACAACTGATGAG 59.433 43.478 0.00 0.00 0.00 2.90
228 229 3.316308 GCAAAGGACAACAACTGATGAGT 59.684 43.478 0.00 0.00 0.00 3.41
229 230 4.790766 GCAAAGGACAACAACTGATGAGTG 60.791 45.833 0.00 0.00 30.61 3.51
230 231 3.131709 AGGACAACAACTGATGAGTGG 57.868 47.619 0.00 0.00 30.61 4.00
231 232 2.154462 GGACAACAACTGATGAGTGGG 58.846 52.381 0.00 0.00 30.61 4.61
232 233 2.487265 GGACAACAACTGATGAGTGGGT 60.487 50.000 0.00 0.00 30.61 4.51
233 234 2.549754 GACAACAACTGATGAGTGGGTG 59.450 50.000 2.79 2.79 45.47 4.61
234 235 1.267806 CAACAACTGATGAGTGGGTGC 59.732 52.381 0.00 0.00 33.91 5.01
235 236 0.767375 ACAACTGATGAGTGGGTGCT 59.233 50.000 0.00 0.00 30.61 4.40
236 237 1.977854 ACAACTGATGAGTGGGTGCTA 59.022 47.619 0.00 0.00 30.61 3.49
237 238 2.289694 ACAACTGATGAGTGGGTGCTAC 60.290 50.000 0.00 0.00 30.61 3.58
238 239 1.644509 ACTGATGAGTGGGTGCTACA 58.355 50.000 0.00 0.00 0.00 2.74
239 240 1.552337 ACTGATGAGTGGGTGCTACAG 59.448 52.381 0.00 0.00 0.00 2.74
240 241 1.827344 CTGATGAGTGGGTGCTACAGA 59.173 52.381 0.00 0.00 0.00 3.41
241 242 1.827344 TGATGAGTGGGTGCTACAGAG 59.173 52.381 0.00 0.00 0.00 3.35
242 243 1.827969 GATGAGTGGGTGCTACAGAGT 59.172 52.381 0.00 0.00 0.00 3.24
243 244 1.717032 TGAGTGGGTGCTACAGAGTT 58.283 50.000 0.00 0.00 0.00 3.01
244 245 2.047061 TGAGTGGGTGCTACAGAGTTT 58.953 47.619 0.00 0.00 0.00 2.66
245 246 2.037251 TGAGTGGGTGCTACAGAGTTTC 59.963 50.000 0.00 0.00 0.00 2.78
246 247 1.000955 AGTGGGTGCTACAGAGTTTCG 59.999 52.381 0.00 0.00 0.00 3.46
247 248 0.320374 TGGGTGCTACAGAGTTTCGG 59.680 55.000 0.00 0.00 0.00 4.30
315 317 6.564557 AAGGACTACCCGTGGATAAATTTA 57.435 37.500 0.00 0.00 40.87 1.40
641 706 0.977627 TCCCATGACAGCGACCTGAT 60.978 55.000 0.00 0.00 41.77 2.90
685 752 0.542805 TGGATGCTGATGTGCTGCTA 59.457 50.000 0.00 0.00 41.53 3.49
696 765 0.321298 GTGCTGCTACTTTTCCCGGA 60.321 55.000 0.73 0.00 0.00 5.14
742 839 2.095461 GGGAATCACTCCTGCTTTTCC 58.905 52.381 0.00 0.00 44.68 3.13
791 888 3.821033 GCTTGTTCTATTTGAGTGGGTGT 59.179 43.478 0.00 0.00 0.00 4.16
1239 1495 6.147164 CGGTATGCTTTAACCATCACGAATAT 59.853 38.462 0.00 0.00 35.35 1.28
1241 1497 8.995220 GGTATGCTTTAACCATCACGAATATAA 58.005 33.333 0.00 0.00 35.73 0.98
1317 1573 0.105593 CTCCGCCTCTGTGCATGTAT 59.894 55.000 0.00 0.00 0.00 2.29
1575 3703 1.595993 CGAAAGGAGGCTCGTGAGGA 61.596 60.000 10.92 0.00 0.00 3.71
1697 3829 8.851541 TCCTGTGGTAGTATTTTAAATTTCGT 57.148 30.769 0.00 0.00 0.00 3.85
1810 3947 3.567530 TCAGTTGTACGTGTCGTAATGG 58.432 45.455 0.00 0.00 43.95 3.16
1875 4342 5.010719 TCCCTCCACTAATATCGAACATCAC 59.989 44.000 0.00 0.00 0.00 3.06
1953 4534 9.968743 GAGTACAAACTAATAATGCAAGTACAC 57.031 33.333 0.00 0.00 35.56 2.90
2146 4727 1.347707 ACTCTTGCCCTTTGACGATGA 59.652 47.619 0.00 0.00 0.00 2.92
2158 4739 1.345089 TGACGATGAAGAACCCGGAAA 59.655 47.619 0.73 0.00 0.00 3.13
2464 7328 2.686715 GCAGAGAGTAGAAGAGGAGGCT 60.687 54.545 0.00 0.00 0.00 4.58
2566 7430 2.444624 CGTGTGAGTGATTCCCGCG 61.445 63.158 0.00 0.00 0.00 6.46
2571 7435 3.665675 GAGTGATTCCCGCGGTGCT 62.666 63.158 26.12 11.92 0.00 4.40
2572 7436 3.499737 GTGATTCCCGCGGTGCTG 61.500 66.667 26.12 8.83 0.00 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 3.283684 TTGCGGGCTTCCACGTTG 61.284 61.111 0.00 0.00 0.00 4.10
13 14 3.284449 GTTGCGGGCTTCCACGTT 61.284 61.111 0.00 0.00 0.00 3.99
16 17 3.670377 GTGGTTGCGGGCTTCCAC 61.670 66.667 16.81 16.81 42.40 4.02
17 18 4.196778 TGTGGTTGCGGGCTTCCA 62.197 61.111 3.98 3.98 0.00 3.53
18 19 3.670377 GTGTGGTTGCGGGCTTCC 61.670 66.667 0.00 0.00 0.00 3.46
19 20 4.025401 CGTGTGGTTGCGGGCTTC 62.025 66.667 0.00 0.00 0.00 3.86
20 21 4.555709 TCGTGTGGTTGCGGGCTT 62.556 61.111 0.00 0.00 0.00 4.35
21 22 4.988598 CTCGTGTGGTTGCGGGCT 62.989 66.667 0.00 0.00 0.00 5.19
23 24 4.308458 TCCTCGTGTGGTTGCGGG 62.308 66.667 0.00 0.00 0.00 6.13
24 25 2.738521 CTCCTCGTGTGGTTGCGG 60.739 66.667 0.00 0.00 0.00 5.69
25 26 3.414700 GCTCCTCGTGTGGTTGCG 61.415 66.667 0.00 0.00 0.00 4.85
26 27 1.845809 CTTGCTCCTCGTGTGGTTGC 61.846 60.000 0.00 0.00 0.00 4.17
27 28 1.230635 CCTTGCTCCTCGTGTGGTTG 61.231 60.000 0.00 0.00 0.00 3.77
28 29 1.071471 CCTTGCTCCTCGTGTGGTT 59.929 57.895 0.00 0.00 0.00 3.67
29 30 2.743718 CCTTGCTCCTCGTGTGGT 59.256 61.111 0.00 0.00 0.00 4.16
30 31 2.046892 CCCTTGCTCCTCGTGTGG 60.047 66.667 0.00 0.00 0.00 4.17
31 32 1.079543 CTCCCTTGCTCCTCGTGTG 60.080 63.158 0.00 0.00 0.00 3.82
32 33 2.948720 GCTCCCTTGCTCCTCGTGT 61.949 63.158 0.00 0.00 0.00 4.49
33 34 2.125350 GCTCCCTTGCTCCTCGTG 60.125 66.667 0.00 0.00 0.00 4.35
34 35 1.992277 ATGCTCCCTTGCTCCTCGT 60.992 57.895 0.00 0.00 0.00 4.18
35 36 1.523258 CATGCTCCCTTGCTCCTCG 60.523 63.158 0.00 0.00 0.00 4.63
36 37 1.823041 GCATGCTCCCTTGCTCCTC 60.823 63.158 11.37 0.00 38.64 3.71
37 38 2.146146 TTGCATGCTCCCTTGCTCCT 62.146 55.000 20.33 0.00 41.32 3.69
38 39 1.664321 CTTGCATGCTCCCTTGCTCC 61.664 60.000 20.33 0.00 41.32 4.70
39 40 0.964358 ACTTGCATGCTCCCTTGCTC 60.964 55.000 20.33 0.00 41.32 4.26
40 41 1.076192 ACTTGCATGCTCCCTTGCT 59.924 52.632 20.33 0.00 41.32 3.91
41 42 1.214589 CACTTGCATGCTCCCTTGC 59.785 57.895 20.33 0.00 41.18 4.01
42 43 0.524862 GACACTTGCATGCTCCCTTG 59.475 55.000 20.33 10.98 0.00 3.61
43 44 0.957395 CGACACTTGCATGCTCCCTT 60.957 55.000 20.33 0.00 0.00 3.95
44 45 1.376424 CGACACTTGCATGCTCCCT 60.376 57.895 20.33 0.00 0.00 4.20
45 46 3.044059 GCGACACTTGCATGCTCCC 62.044 63.158 20.33 0.00 0.00 4.30
46 47 2.482374 GCGACACTTGCATGCTCC 59.518 61.111 20.33 0.74 0.00 4.70
47 48 2.482374 GGCGACACTTGCATGCTC 59.518 61.111 20.33 6.53 0.00 4.26
48 49 3.425713 CGGCGACACTTGCATGCT 61.426 61.111 20.33 0.00 0.00 3.79
50 51 4.465512 GGCGGCGACACTTGCATG 62.466 66.667 12.98 0.00 0.00 4.06
54 55 2.048597 TACTGGCGGCGACACTTG 60.049 61.111 13.60 4.75 0.00 3.16
55 56 2.261671 CTACTGGCGGCGACACTT 59.738 61.111 13.60 3.85 0.00 3.16
56 57 2.989824 ACTACTGGCGGCGACACT 60.990 61.111 13.60 5.52 0.00 3.55
57 58 2.809601 CACTACTGGCGGCGACAC 60.810 66.667 13.60 0.00 0.00 3.67
58 59 2.986979 TCACTACTGGCGGCGACA 60.987 61.111 17.61 17.61 0.00 4.35
59 60 2.202623 CTCACTACTGGCGGCGAC 60.203 66.667 12.98 9.31 0.00 5.19
60 61 3.449227 CCTCACTACTGGCGGCGA 61.449 66.667 12.98 0.00 0.00 5.54
61 62 4.514577 CCCTCACTACTGGCGGCG 62.515 72.222 0.51 0.51 0.00 6.46
62 63 3.075005 TCCCTCACTACTGGCGGC 61.075 66.667 0.00 0.00 0.00 6.53
63 64 1.379977 TCTCCCTCACTACTGGCGG 60.380 63.158 0.00 0.00 0.00 6.13
64 65 1.388065 CCTCTCCCTCACTACTGGCG 61.388 65.000 0.00 0.00 0.00 5.69
65 66 0.033011 TCCTCTCCCTCACTACTGGC 60.033 60.000 0.00 0.00 0.00 4.85
66 67 2.104170 GTTCCTCTCCCTCACTACTGG 58.896 57.143 0.00 0.00 0.00 4.00
67 68 1.746220 CGTTCCTCTCCCTCACTACTG 59.254 57.143 0.00 0.00 0.00 2.74
68 69 1.956159 GCGTTCCTCTCCCTCACTACT 60.956 57.143 0.00 0.00 0.00 2.57
69 70 0.456628 GCGTTCCTCTCCCTCACTAC 59.543 60.000 0.00 0.00 0.00 2.73
70 71 0.331954 AGCGTTCCTCTCCCTCACTA 59.668 55.000 0.00 0.00 0.00 2.74
71 72 1.077625 AGCGTTCCTCTCCCTCACT 59.922 57.895 0.00 0.00 0.00 3.41
72 73 1.216710 CAGCGTTCCTCTCCCTCAC 59.783 63.158 0.00 0.00 0.00 3.51
73 74 1.984570 CCAGCGTTCCTCTCCCTCA 60.985 63.158 0.00 0.00 0.00 3.86
74 75 1.671901 CTCCAGCGTTCCTCTCCCTC 61.672 65.000 0.00 0.00 0.00 4.30
75 76 1.684049 CTCCAGCGTTCCTCTCCCT 60.684 63.158 0.00 0.00 0.00 4.20
76 77 1.671901 CTCTCCAGCGTTCCTCTCCC 61.672 65.000 0.00 0.00 0.00 4.30
77 78 1.671901 CCTCTCCAGCGTTCCTCTCC 61.672 65.000 0.00 0.00 0.00 3.71
78 79 1.671901 CCCTCTCCAGCGTTCCTCTC 61.672 65.000 0.00 0.00 0.00 3.20
79 80 1.684049 CCCTCTCCAGCGTTCCTCT 60.684 63.158 0.00 0.00 0.00 3.69
80 81 1.545706 AACCCTCTCCAGCGTTCCTC 61.546 60.000 0.00 0.00 0.00 3.71
81 82 1.536662 AACCCTCTCCAGCGTTCCT 60.537 57.895 0.00 0.00 0.00 3.36
82 83 1.376037 CAACCCTCTCCAGCGTTCC 60.376 63.158 0.00 0.00 0.00 3.62
83 84 1.376037 CCAACCCTCTCCAGCGTTC 60.376 63.158 0.00 0.00 0.00 3.95
84 85 2.147387 ACCAACCCTCTCCAGCGTT 61.147 57.895 0.00 0.00 0.00 4.84
85 86 2.526873 ACCAACCCTCTCCAGCGT 60.527 61.111 0.00 0.00 0.00 5.07
86 87 2.046892 CACCAACCCTCTCCAGCG 60.047 66.667 0.00 0.00 0.00 5.18
87 88 2.352805 CCACCAACCCTCTCCAGC 59.647 66.667 0.00 0.00 0.00 4.85
88 89 2.352805 GCCACCAACCCTCTCCAG 59.647 66.667 0.00 0.00 0.00 3.86
89 90 3.636231 CGCCACCAACCCTCTCCA 61.636 66.667 0.00 0.00 0.00 3.86
107 108 3.612247 CTGGTCTCCCAACCCAGCG 62.612 68.421 0.00 0.00 41.27 5.18
108 109 2.352805 CTGGTCTCCCAACCCAGC 59.647 66.667 0.00 0.00 41.27 4.85
110 111 0.696143 TTGACTGGTCTCCCAACCCA 60.696 55.000 2.38 0.00 41.27 4.51
111 112 0.036875 CTTGACTGGTCTCCCAACCC 59.963 60.000 2.38 0.00 41.27 4.11
112 113 0.036875 CCTTGACTGGTCTCCCAACC 59.963 60.000 2.38 0.00 41.27 3.77
113 114 1.056660 TCCTTGACTGGTCTCCCAAC 58.943 55.000 2.38 0.00 41.27 3.77
114 115 1.420138 GTTCCTTGACTGGTCTCCCAA 59.580 52.381 2.38 0.00 41.27 4.12
115 116 1.056660 GTTCCTTGACTGGTCTCCCA 58.943 55.000 2.38 0.00 38.87 4.37
116 117 1.276705 GAGTTCCTTGACTGGTCTCCC 59.723 57.143 2.38 0.00 0.00 4.30
117 118 1.276705 GGAGTTCCTTGACTGGTCTCC 59.723 57.143 2.38 0.00 39.63 3.71
118 119 2.252714 AGGAGTTCCTTGACTGGTCTC 58.747 52.381 0.00 0.00 46.09 3.36
119 120 2.407340 AGGAGTTCCTTGACTGGTCT 57.593 50.000 0.00 0.00 46.09 3.85
140 141 1.221840 GACCGTGCCATCTGGTGAT 59.778 57.895 0.00 0.00 35.75 3.06
141 142 2.662596 GACCGTGCCATCTGGTGA 59.337 61.111 0.00 0.00 35.75 4.02
142 143 2.815211 CGACCGTGCCATCTGGTG 60.815 66.667 0.00 0.00 35.75 4.17
143 144 4.760047 GCGACCGTGCCATCTGGT 62.760 66.667 0.00 0.00 39.12 4.00
155 156 2.357760 TGCAGGTTAACGGCGACC 60.358 61.111 16.62 11.61 43.71 4.79
156 157 2.388232 CCTGCAGGTTAACGGCGAC 61.388 63.158 25.53 0.00 43.71 5.19
157 158 2.047655 CCTGCAGGTTAACGGCGA 60.048 61.111 25.53 0.00 43.71 5.54
158 159 3.124921 CCCTGCAGGTTAACGGCG 61.125 66.667 30.63 4.80 43.71 6.46
167 168 2.177594 GACTCTCCACACCCTGCAGG 62.178 65.000 26.87 26.87 43.78 4.85
168 169 1.294780 GACTCTCCACACCCTGCAG 59.705 63.158 6.78 6.78 0.00 4.41
169 170 2.217038 GGACTCTCCACACCCTGCA 61.217 63.158 0.00 0.00 36.28 4.41
170 171 2.665603 GGACTCTCCACACCCTGC 59.334 66.667 0.00 0.00 36.28 4.85
171 172 0.911525 ATGGGACTCTCCACACCCTG 60.912 60.000 0.00 0.00 42.49 4.45
172 173 0.911525 CATGGGACTCTCCACACCCT 60.912 60.000 0.00 0.00 42.49 4.34
173 174 1.604378 CATGGGACTCTCCACACCC 59.396 63.158 0.00 0.00 39.97 4.61
174 175 1.078143 GCATGGGACTCTCCACACC 60.078 63.158 0.00 0.00 39.97 4.16
175 176 1.078143 GGCATGGGACTCTCCACAC 60.078 63.158 0.00 0.00 39.97 3.82
176 177 1.133181 TTGGCATGGGACTCTCCACA 61.133 55.000 0.00 0.00 39.97 4.17
177 178 0.038166 TTTGGCATGGGACTCTCCAC 59.962 55.000 0.00 0.00 39.97 4.02
178 179 0.329261 CTTTGGCATGGGACTCTCCA 59.671 55.000 0.00 0.00 38.64 3.86
179 180 1.034292 GCTTTGGCATGGGACTCTCC 61.034 60.000 0.00 0.00 38.54 3.71
180 181 0.322816 TGCTTTGGCATGGGACTCTC 60.323 55.000 0.00 0.00 44.28 3.20
181 182 1.769665 TGCTTTGGCATGGGACTCT 59.230 52.632 0.00 0.00 44.28 3.24
182 183 4.421365 TGCTTTGGCATGGGACTC 57.579 55.556 0.00 0.00 44.28 3.36
191 192 4.728102 TGCTGCGCATGCTTTGGC 62.728 61.111 25.02 17.94 43.34 4.52
192 193 1.623081 CTTTGCTGCGCATGCTTTGG 61.623 55.000 25.02 9.34 43.34 3.28
193 194 1.623081 CCTTTGCTGCGCATGCTTTG 61.623 55.000 25.02 16.57 43.34 2.77
194 195 1.373748 CCTTTGCTGCGCATGCTTT 60.374 52.632 25.02 0.00 43.34 3.51
195 196 2.260434 CCTTTGCTGCGCATGCTT 59.740 55.556 25.02 0.00 43.34 3.91
196 197 2.674033 TCCTTTGCTGCGCATGCT 60.674 55.556 25.02 0.00 43.34 3.79
197 198 2.505557 GTCCTTTGCTGCGCATGC 60.506 61.111 12.24 17.56 38.76 4.06
198 199 1.005294 GTTGTCCTTTGCTGCGCATG 61.005 55.000 12.24 6.51 38.76 4.06
199 200 1.286880 GTTGTCCTTTGCTGCGCAT 59.713 52.632 12.24 0.00 38.76 4.73
200 201 1.661498 TTGTTGTCCTTTGCTGCGCA 61.661 50.000 10.98 10.98 36.47 6.09
201 202 1.065600 TTGTTGTCCTTTGCTGCGC 59.934 52.632 0.00 0.00 0.00 6.09
202 203 0.381801 AGTTGTTGTCCTTTGCTGCG 59.618 50.000 0.00 0.00 0.00 5.18
203 204 1.405105 TCAGTTGTTGTCCTTTGCTGC 59.595 47.619 0.00 0.00 0.00 5.25
204 205 3.316029 TCATCAGTTGTTGTCCTTTGCTG 59.684 43.478 0.00 0.00 0.00 4.41
205 206 3.554934 TCATCAGTTGTTGTCCTTTGCT 58.445 40.909 0.00 0.00 0.00 3.91
206 207 3.316308 ACTCATCAGTTGTTGTCCTTTGC 59.684 43.478 0.00 0.00 0.00 3.68
207 208 4.261322 CCACTCATCAGTTGTTGTCCTTTG 60.261 45.833 0.00 0.00 0.00 2.77
208 209 3.885297 CCACTCATCAGTTGTTGTCCTTT 59.115 43.478 0.00 0.00 0.00 3.11
209 210 3.480470 CCACTCATCAGTTGTTGTCCTT 58.520 45.455 0.00 0.00 0.00 3.36
210 211 2.224621 CCCACTCATCAGTTGTTGTCCT 60.225 50.000 0.00 0.00 0.00 3.85
211 212 2.154462 CCCACTCATCAGTTGTTGTCC 58.846 52.381 0.00 0.00 0.00 4.02
212 213 2.549754 CACCCACTCATCAGTTGTTGTC 59.450 50.000 0.00 0.00 0.00 3.18
213 214 2.575532 CACCCACTCATCAGTTGTTGT 58.424 47.619 0.00 0.00 0.00 3.32
214 215 1.267806 GCACCCACTCATCAGTTGTTG 59.732 52.381 0.00 0.00 0.00 3.33
215 216 1.143684 AGCACCCACTCATCAGTTGTT 59.856 47.619 0.00 0.00 0.00 2.83
216 217 0.767375 AGCACCCACTCATCAGTTGT 59.233 50.000 0.00 0.00 0.00 3.32
217 218 2.289631 TGTAGCACCCACTCATCAGTTG 60.290 50.000 0.00 0.00 0.00 3.16
218 219 1.977854 TGTAGCACCCACTCATCAGTT 59.022 47.619 0.00 0.00 0.00 3.16
219 220 1.552337 CTGTAGCACCCACTCATCAGT 59.448 52.381 0.00 0.00 0.00 3.41
220 221 1.827344 TCTGTAGCACCCACTCATCAG 59.173 52.381 0.00 0.00 0.00 2.90
221 222 1.827344 CTCTGTAGCACCCACTCATCA 59.173 52.381 0.00 0.00 0.00 3.07
222 223 1.827969 ACTCTGTAGCACCCACTCATC 59.172 52.381 0.00 0.00 0.00 2.92
223 224 1.944177 ACTCTGTAGCACCCACTCAT 58.056 50.000 0.00 0.00 0.00 2.90
224 225 1.717032 AACTCTGTAGCACCCACTCA 58.283 50.000 0.00 0.00 0.00 3.41
225 226 2.689646 GAAACTCTGTAGCACCCACTC 58.310 52.381 0.00 0.00 0.00 3.51
226 227 1.000955 CGAAACTCTGTAGCACCCACT 59.999 52.381 0.00 0.00 0.00 4.00
227 228 1.429463 CGAAACTCTGTAGCACCCAC 58.571 55.000 0.00 0.00 0.00 4.61
228 229 0.320374 CCGAAACTCTGTAGCACCCA 59.680 55.000 0.00 0.00 0.00 4.51
229 230 0.391263 CCCGAAACTCTGTAGCACCC 60.391 60.000 0.00 0.00 0.00 4.61
230 231 0.391263 CCCCGAAACTCTGTAGCACC 60.391 60.000 0.00 0.00 0.00 5.01
231 232 0.606604 TCCCCGAAACTCTGTAGCAC 59.393 55.000 0.00 0.00 0.00 4.40
232 233 1.568504 ATCCCCGAAACTCTGTAGCA 58.431 50.000 0.00 0.00 0.00 3.49
233 234 2.693267 AATCCCCGAAACTCTGTAGC 57.307 50.000 0.00 0.00 0.00 3.58
399 429 1.064825 AGTTGGGATTCCTGTTCGGT 58.935 50.000 2.01 0.00 0.00 4.69
406 436 1.831736 CGGTGAGTAGTTGGGATTCCT 59.168 52.381 2.01 0.00 0.00 3.36
602 654 0.461516 ATCAGCGCCATCAGTGTCAG 60.462 55.000 2.29 0.00 0.00 3.51
603 655 0.036105 AATCAGCGCCATCAGTGTCA 60.036 50.000 2.29 0.00 0.00 3.58
604 656 0.654683 GAATCAGCGCCATCAGTGTC 59.345 55.000 2.29 0.00 0.00 3.67
641 706 1.355796 CGCCGTTGGAATTAGCGTCA 61.356 55.000 0.00 0.00 41.78 4.35
685 752 2.375509 AGGAGTGATTTCCGGGAAAAGT 59.624 45.455 24.83 13.01 42.29 2.66
696 765 5.136105 ACAGAAGAAAAGCAGGAGTGATTT 58.864 37.500 0.00 0.00 44.18 2.17
742 839 0.461961 GGAGTGATTCCCGGACAGAG 59.538 60.000 0.73 0.00 40.37 3.35
778 875 0.889186 GCCGTCACACCCACTCAAAT 60.889 55.000 0.00 0.00 0.00 2.32
779 876 1.525077 GCCGTCACACCCACTCAAA 60.525 57.895 0.00 0.00 0.00 2.69
791 888 4.680237 CCTTCCGCAGTGCCGTCA 62.680 66.667 10.11 0.00 0.00 4.35
937 1113 1.218047 CGAGGATGGCTGGACGAAA 59.782 57.895 0.00 0.00 0.00 3.46
1317 1573 3.193903 TCTCCGTGTCAATCCAACGATAA 59.806 43.478 0.00 0.00 39.64 1.75
1575 3703 3.515562 TCTTTCTTTCTCTGCCTCTCCT 58.484 45.455 0.00 0.00 0.00 3.69
1618 3750 1.451028 ATCGCCAGCTTCTTCTGCC 60.451 57.895 0.00 0.00 32.87 4.85
1953 4534 5.484715 TCCAGTTCTACCGTTTAATTCAGG 58.515 41.667 0.00 0.00 0.00 3.86
2008 4589 1.037579 TGCATCGACGGAGGATGACT 61.038 55.000 14.34 0.00 43.07 3.41
2158 4739 0.392706 TGATATCTTCATGCCGCCGT 59.607 50.000 3.98 0.00 0.00 5.68
2481 7345 7.979537 CCTTTTATATAGTATGCGTATGCTCCA 59.020 37.037 7.46 0.00 43.34 3.86


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

AutoCloner maintained by Alex Coulton.