Multiple sequence alignment - TraesCS2A01G165100

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS2A01G165100 chr2A 100.000 3354 0 0 1 3354 117404900 117401547 0.000000e+00 6194
1 TraesCS2A01G165100 chr2B 94.985 2672 83 11 717 3354 166612694 166610040 0.000000e+00 4145
2 TraesCS2A01G165100 chr2D 95.034 2537 88 16 345 2852 115959921 115957394 0.000000e+00 3952
3 TraesCS2A01G165100 chr2D 94.737 114 6 0 248 361 115960805 115960692 9.560000e-41 178
4 TraesCS2A01G165100 chr3B 85.751 386 53 2 1188 1573 467068558 467068175 1.120000e-109 407
5 TraesCS2A01G165100 chr6A 84.422 398 58 4 1188 1583 580187120 580187515 4.060000e-104 388
6 TraesCS2A01G165100 chr6A 89.113 248 26 1 1 247 45650393 45650640 1.170000e-79 307
7 TraesCS2A01G165100 chr7A 84.171 398 59 4 1188 1583 64595519 64595124 1.890000e-102 383
8 TraesCS2A01G165100 chr4B 91.538 260 11 1 1 249 633957688 633957947 6.890000e-92 348
9 TraesCS2A01G165100 chr4B 90.385 260 13 1 1 248 90454983 90455242 6.940000e-87 331
10 TraesCS2A01G165100 chr7B 90.769 260 12 1 1 248 876629 876370 1.490000e-88 337
11 TraesCS2A01G165100 chr1B 90.189 265 14 1 1 253 678293087 678292823 5.360000e-88 335
12 TraesCS2A01G165100 chr1B 90.000 260 14 1 1 248 681725818 681726077 3.230000e-85 326
13 TraesCS2A01G165100 chr1B 94.186 172 10 0 1 172 226912441 226912612 2.570000e-66 263
14 TraesCS2A01G165100 chr5B 90.385 260 13 1 1 248 250231365 250231106 6.940000e-87 331
15 TraesCS2A01G165100 chr5B 87.956 274 21 2 1 263 412263692 412263964 2.510000e-81 313
16 TraesCS2A01G165100 chr5B 88.000 275 20 3 1 263 689861957 689862230 2.510000e-81 313
17 TraesCS2A01G165100 chr3A 88.686 274 19 2 1 263 99251796 99252068 1.160000e-84 324
18 TraesCS2A01G165100 chr3A 87.956 274 21 3 1 263 692490640 692490912 2.510000e-81 313
19 TraesCS2A01G165100 chr5D 89.272 261 14 3 1 248 345933480 345933739 6.990000e-82 315
20 TraesCS2A01G165100 chrUn 89.020 255 14 4 1 243 46119525 46119777 1.510000e-78 303
21 TraesCS2A01G165100 chr3D 88.462 260 18 2 1 248 562172983 562172724 1.510000e-78 303


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 TraesCS2A01G165100 chr2A 117401547 117404900 3353 True 6194 6194 100.0000 1 3354 1 chr2A.!!$R1 3353
1 TraesCS2A01G165100 chr2B 166610040 166612694 2654 True 4145 4145 94.9850 717 3354 1 chr2B.!!$R1 2637
2 TraesCS2A01G165100 chr2D 115957394 115960805 3411 True 2065 3952 94.8855 248 2852 2 chr2D.!!$R1 2604

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
74 75 0.196888 TATCCATCCTCCCAGGCCAT 59.803 55.0 5.01 0.0 34.61 4.40 F
247 248 0.241213 GCCTCCAAAACGCCTTTCTC 59.759 55.0 0.00 0.0 0.00 2.87 F
1667 2458 0.749649 CTAAGCCCGCTGATCTGAGT 59.250 55.0 3.42 0.0 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1999 2793 4.635223 TCTTGAATTCTCAGTGTGTCCAG 58.365 43.478 7.05 0.0 31.69 3.86 R
2147 2941 0.462759 CCCTCAGGAACGGCAGATTC 60.463 60.000 0.00 0.0 33.47 2.52 R
3258 4092 0.250234 CAGAGAAAGGGATGCGGTGA 59.750 55.000 0.00 0.0 0.00 4.02 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
45 46 8.926715 AAAAGACAAATCTGAGGTTGTTTAAC 57.073 30.769 9.94 0.00 38.07 2.01
46 47 7.639113 AAGACAAATCTGAGGTTGTTTAACA 57.361 32.000 9.94 0.00 38.07 2.41
47 48 7.027778 AGACAAATCTGAGGTTGTTTAACAC 57.972 36.000 0.00 0.00 38.07 3.32
48 49 6.601613 AGACAAATCTGAGGTTGTTTAACACA 59.398 34.615 0.00 0.00 38.07 3.72
49 50 7.285401 AGACAAATCTGAGGTTGTTTAACACAT 59.715 33.333 0.00 0.00 38.07 3.21
50 51 7.202526 ACAAATCTGAGGTTGTTTAACACATG 58.797 34.615 0.00 0.00 38.58 3.21
51 52 7.068103 ACAAATCTGAGGTTGTTTAACACATGA 59.932 33.333 0.00 0.00 38.58 3.07
52 53 7.765695 AATCTGAGGTTGTTTAACACATGAT 57.234 32.000 0.00 0.00 38.58 2.45
53 54 8.862325 AATCTGAGGTTGTTTAACACATGATA 57.138 30.769 0.00 0.00 38.58 2.15
54 55 7.667043 TCTGAGGTTGTTTAACACATGATAC 57.333 36.000 0.00 0.00 38.58 2.24
55 56 7.450074 TCTGAGGTTGTTTAACACATGATACT 58.550 34.615 0.00 0.00 38.58 2.12
56 57 8.590204 TCTGAGGTTGTTTAACACATGATACTA 58.410 33.333 0.00 0.00 38.58 1.82
57 58 9.383519 CTGAGGTTGTTTAACACATGATACTAT 57.616 33.333 0.00 0.00 38.58 2.12
58 59 9.378551 TGAGGTTGTTTAACACATGATACTATC 57.621 33.333 0.00 0.00 38.58 2.08
59 60 8.732746 AGGTTGTTTAACACATGATACTATCC 57.267 34.615 0.00 0.00 38.58 2.59
60 61 8.325787 AGGTTGTTTAACACATGATACTATCCA 58.674 33.333 0.00 0.00 38.58 3.41
61 62 9.120538 GGTTGTTTAACACATGATACTATCCAT 57.879 33.333 0.00 0.00 38.58 3.41
63 64 8.902540 TGTTTAACACATGATACTATCCATCC 57.097 34.615 0.00 0.00 0.00 3.51
64 65 8.713971 TGTTTAACACATGATACTATCCATCCT 58.286 33.333 0.00 0.00 0.00 3.24
65 66 9.209175 GTTTAACACATGATACTATCCATCCTC 57.791 37.037 0.00 0.00 0.00 3.71
66 67 6.365970 AACACATGATACTATCCATCCTCC 57.634 41.667 0.00 0.00 0.00 4.30
67 68 4.780021 ACACATGATACTATCCATCCTCCC 59.220 45.833 0.00 0.00 0.00 4.30
68 69 4.779489 CACATGATACTATCCATCCTCCCA 59.221 45.833 0.00 0.00 0.00 4.37
69 70 5.028802 ACATGATACTATCCATCCTCCCAG 58.971 45.833 0.00 0.00 0.00 4.45
70 71 4.066578 TGATACTATCCATCCTCCCAGG 57.933 50.000 0.00 0.00 36.46 4.45
71 72 2.327325 TACTATCCATCCTCCCAGGC 57.673 55.000 0.00 0.00 34.61 4.85
72 73 0.474660 ACTATCCATCCTCCCAGGCC 60.475 60.000 0.00 0.00 34.61 5.19
73 74 0.474466 CTATCCATCCTCCCAGGCCA 60.474 60.000 5.01 0.00 34.61 5.36
74 75 0.196888 TATCCATCCTCCCAGGCCAT 59.803 55.000 5.01 0.00 34.61 4.40
75 76 1.432852 ATCCATCCTCCCAGGCCATG 61.433 60.000 5.01 0.00 34.61 3.66
76 77 2.080536 CCATCCTCCCAGGCCATGA 61.081 63.158 5.01 0.00 34.61 3.07
77 78 1.648302 CCATCCTCCCAGGCCATGAA 61.648 60.000 5.01 0.00 34.61 2.57
78 79 0.481567 CATCCTCCCAGGCCATGAAT 59.518 55.000 5.01 0.00 34.61 2.57
79 80 1.133262 CATCCTCCCAGGCCATGAATT 60.133 52.381 5.01 0.00 34.61 2.17
80 81 1.009997 TCCTCCCAGGCCATGAATTT 58.990 50.000 5.01 0.00 34.61 1.82
81 82 1.117150 CCTCCCAGGCCATGAATTTG 58.883 55.000 5.01 0.00 0.00 2.32
82 83 1.620524 CCTCCCAGGCCATGAATTTGT 60.621 52.381 5.01 0.00 0.00 2.83
83 84 1.753073 CTCCCAGGCCATGAATTTGTC 59.247 52.381 5.01 0.00 0.00 3.18
84 85 1.358787 TCCCAGGCCATGAATTTGTCT 59.641 47.619 5.01 0.00 0.00 3.41
85 86 2.181975 CCCAGGCCATGAATTTGTCTT 58.818 47.619 5.01 0.00 0.00 3.01
86 87 2.568509 CCCAGGCCATGAATTTGTCTTT 59.431 45.455 5.01 0.00 0.00 2.52
87 88 3.008266 CCCAGGCCATGAATTTGTCTTTT 59.992 43.478 5.01 0.00 0.00 2.27
88 89 4.505390 CCCAGGCCATGAATTTGTCTTTTT 60.505 41.667 5.01 0.00 0.00 1.94
106 107 3.462483 TTTTGTAGAGGTCGCAACTCA 57.538 42.857 4.40 0.00 37.43 3.41
107 108 3.462483 TTTGTAGAGGTCGCAACTCAA 57.538 42.857 4.40 0.00 37.43 3.02
108 109 2.724977 TGTAGAGGTCGCAACTCAAG 57.275 50.000 4.40 0.00 37.43 3.02
109 110 1.272490 TGTAGAGGTCGCAACTCAAGG 59.728 52.381 4.40 0.00 37.43 3.61
110 111 1.272769 GTAGAGGTCGCAACTCAAGGT 59.727 52.381 4.40 0.00 37.43 3.50
111 112 1.629043 AGAGGTCGCAACTCAAGGTA 58.371 50.000 4.40 0.00 37.43 3.08
112 113 2.180276 AGAGGTCGCAACTCAAGGTAT 58.820 47.619 4.40 0.00 37.43 2.73
113 114 2.567615 AGAGGTCGCAACTCAAGGTATT 59.432 45.455 4.40 0.00 37.43 1.89
114 115 3.008049 AGAGGTCGCAACTCAAGGTATTT 59.992 43.478 4.40 0.00 37.43 1.40
115 116 3.335579 AGGTCGCAACTCAAGGTATTTC 58.664 45.455 0.00 0.00 0.00 2.17
116 117 3.071479 GGTCGCAACTCAAGGTATTTCA 58.929 45.455 0.00 0.00 0.00 2.69
117 118 3.689649 GGTCGCAACTCAAGGTATTTCAT 59.310 43.478 0.00 0.00 0.00 2.57
118 119 4.201822 GGTCGCAACTCAAGGTATTTCATC 60.202 45.833 0.00 0.00 0.00 2.92
119 120 4.391830 GTCGCAACTCAAGGTATTTCATCA 59.608 41.667 0.00 0.00 0.00 3.07
120 121 5.065218 GTCGCAACTCAAGGTATTTCATCAT 59.935 40.000 0.00 0.00 0.00 2.45
121 122 5.065090 TCGCAACTCAAGGTATTTCATCATG 59.935 40.000 0.00 0.00 0.00 3.07
122 123 5.065090 CGCAACTCAAGGTATTTCATCATGA 59.935 40.000 0.00 0.00 0.00 3.07
123 124 6.403527 CGCAACTCAAGGTATTTCATCATGAA 60.404 38.462 0.00 0.00 34.03 2.57
124 125 7.486647 GCAACTCAAGGTATTTCATCATGAAT 58.513 34.615 0.00 0.00 36.11 2.57
125 126 7.977853 GCAACTCAAGGTATTTCATCATGAATT 59.022 33.333 0.00 0.16 36.11 2.17
126 127 9.865321 CAACTCAAGGTATTTCATCATGAATTT 57.135 29.630 0.00 0.00 36.11 1.82
138 139 9.761504 TTTCATCATGAATTTTTACACACATGT 57.238 25.926 0.00 0.00 38.32 3.21
139 140 9.194271 TTCATCATGAATTTTTACACACATGTG 57.806 29.630 24.25 24.25 40.52 3.21
160 161 7.234661 TGTGAGTAACATCCTTACATACACA 57.765 36.000 0.00 0.00 35.60 3.72
161 162 7.094631 TGTGAGTAACATCCTTACATACACAC 58.905 38.462 0.00 0.00 38.05 3.82
162 163 7.094631 GTGAGTAACATCCTTACATACACACA 58.905 38.462 0.00 0.00 37.72 3.72
163 164 7.764443 GTGAGTAACATCCTTACATACACACAT 59.236 37.037 0.00 0.00 37.72 3.21
164 165 8.973182 TGAGTAACATCCTTACATACACACATA 58.027 33.333 0.00 0.00 0.00 2.29
165 166 9.982651 GAGTAACATCCTTACATACACACATAT 57.017 33.333 0.00 0.00 0.00 1.78
223 224 6.790232 TTTTAAATAAAGGCCTCCATGGAG 57.210 37.500 31.69 31.69 41.63 3.86
224 225 2.371658 AATAAAGGCCTCCATGGAGC 57.628 50.000 32.97 26.44 40.69 4.70
225 226 1.527457 ATAAAGGCCTCCATGGAGCT 58.473 50.000 32.97 23.24 40.69 4.09
226 227 0.839946 TAAAGGCCTCCATGGAGCTC 59.160 55.000 32.97 25.21 40.69 4.09
227 228 2.262774 AAAGGCCTCCATGGAGCTCG 62.263 60.000 32.97 21.57 40.69 5.03
228 229 4.247380 GGCCTCCATGGAGCTCGG 62.247 72.222 32.97 22.55 40.69 4.63
229 230 4.925861 GCCTCCATGGAGCTCGGC 62.926 72.222 32.97 27.64 40.69 5.54
230 231 4.247380 CCTCCATGGAGCTCGGCC 62.247 72.222 32.97 0.00 40.69 6.13
231 232 3.160047 CTCCATGGAGCTCGGCCT 61.160 66.667 28.45 0.00 35.31 5.19
232 233 3.157252 TCCATGGAGCTCGGCCTC 61.157 66.667 11.44 0.00 0.00 4.70
238 239 3.579685 GAGCTCGGCCTCCAAAAC 58.420 61.111 0.00 0.00 0.00 2.43
239 240 2.358737 AGCTCGGCCTCCAAAACG 60.359 61.111 0.00 0.00 0.00 3.60
240 241 4.103103 GCTCGGCCTCCAAAACGC 62.103 66.667 0.00 0.00 0.00 4.84
241 242 3.431725 CTCGGCCTCCAAAACGCC 61.432 66.667 0.00 0.00 39.41 5.68
242 243 3.901797 CTCGGCCTCCAAAACGCCT 62.902 63.158 0.00 0.00 40.70 5.52
243 244 2.983592 CGGCCTCCAAAACGCCTT 60.984 61.111 0.00 0.00 40.70 4.35
244 245 2.561037 CGGCCTCCAAAACGCCTTT 61.561 57.895 0.00 0.00 40.70 3.11
245 246 1.289066 GGCCTCCAAAACGCCTTTC 59.711 57.895 0.00 0.00 39.70 2.62
246 247 1.179174 GGCCTCCAAAACGCCTTTCT 61.179 55.000 0.00 0.00 39.70 2.52
247 248 0.241213 GCCTCCAAAACGCCTTTCTC 59.759 55.000 0.00 0.00 0.00 2.87
248 249 1.897560 CCTCCAAAACGCCTTTCTCT 58.102 50.000 0.00 0.00 0.00 3.10
249 250 2.230660 CCTCCAAAACGCCTTTCTCTT 58.769 47.619 0.00 0.00 0.00 2.85
250 251 2.623416 CCTCCAAAACGCCTTTCTCTTT 59.377 45.455 0.00 0.00 0.00 2.52
251 252 3.068165 CCTCCAAAACGCCTTTCTCTTTT 59.932 43.478 0.00 0.00 0.00 2.27
252 253 4.441495 CCTCCAAAACGCCTTTCTCTTTTT 60.441 41.667 0.00 0.00 0.00 1.94
290 291 6.477742 TGCGAACAAGAATTCATCTTAATCG 58.522 36.000 8.44 14.98 46.80 3.34
292 293 6.625310 GCGAACAAGAATTCATCTTAATCGAC 59.375 38.462 19.88 12.04 46.80 4.20
319 320 7.415541 GCATAATCAAAATGCTCCTAGTTGTCA 60.416 37.037 0.93 0.00 45.05 3.58
320 321 8.627403 CATAATCAAAATGCTCCTAGTTGTCAT 58.373 33.333 0.00 0.00 0.00 3.06
443 1231 9.443323 TTCTTAATTCGATTCCAACTTCATACA 57.557 29.630 0.00 0.00 0.00 2.29
505 1293 4.377635 GCAACAATTTAGGCACATGCTTTG 60.378 41.667 3.48 3.81 41.70 2.77
510 1298 5.720371 ATTTAGGCACATGCTTTGTACAA 57.280 34.783 3.59 3.59 41.70 2.41
530 1318 8.637986 TGTACAAATTCCTGTTTCTTTATGCTT 58.362 29.630 0.00 0.00 0.00 3.91
565 1353 6.485313 TCAAAGATTTCAAAGAGGCGTCTTAA 59.515 34.615 21.14 12.75 42.59 1.85
586 1374 5.703978 AACATTAACACATTGCTAGCACA 57.296 34.783 19.17 9.50 0.00 4.57
609 1397 6.660521 ACATTAGCATGATCAAAGTGGAAGAA 59.339 34.615 0.00 0.00 34.11 2.52
630 1418 6.005823 AGAATCATGTCTGAAAATGTGGTCA 58.994 36.000 0.00 0.00 34.37 4.02
635 1423 6.770303 TCATGTCTGAAAATGTGGTCAGTAAA 59.230 34.615 0.00 0.00 41.69 2.01
667 1455 4.448210 TCCGTTAGATGTGGAATAAAGCC 58.552 43.478 0.00 0.00 0.00 4.35
696 1484 4.030134 ACGAACCGTTAGAATAGAGCTG 57.970 45.455 0.00 0.00 36.35 4.24
752 1540 5.837586 TGGTATTGTAACCGTTACGAAAC 57.162 39.130 14.12 11.56 42.91 2.78
753 1541 5.292765 TGGTATTGTAACCGTTACGAAACA 58.707 37.500 14.12 9.07 42.91 2.83
757 1545 8.439286 GGTATTGTAACCGTTACGAAACAAATA 58.561 33.333 14.12 9.45 38.98 1.40
807 1595 5.209818 TCGCTGTAAATAGGGGTGATTAG 57.790 43.478 0.00 0.00 0.00 1.73
812 1600 7.228706 CGCTGTAAATAGGGGTGATTAGAAATT 59.771 37.037 0.00 0.00 0.00 1.82
813 1601 9.569122 GCTGTAAATAGGGGTGATTAGAAATTA 57.431 33.333 0.00 0.00 0.00 1.40
854 1643 8.721019 TTTTAACGGTGGTCTATATAAACAGG 57.279 34.615 0.00 0.00 0.00 4.00
929 1718 1.109920 ACACTCACCAGCTGTCTCGT 61.110 55.000 13.81 0.00 0.00 4.18
1667 2458 0.749649 CTAAGCCCGCTGATCTGAGT 59.250 55.000 3.42 0.00 0.00 3.41
1674 2465 1.066303 CCGCTGATCTGAGTACTGACC 59.934 57.143 0.00 0.00 0.00 4.02
1791 2582 5.067805 GGGAATAATGTTGGAGTTGGACATC 59.932 44.000 0.00 0.00 33.16 3.06
1999 2793 4.456911 TGATTGGAGTGAAAATGCAGAGAC 59.543 41.667 0.00 0.00 30.98 3.36
2090 2884 1.591183 GCATTTTGGTGCGGATGGT 59.409 52.632 0.00 0.00 35.10 3.55
2146 2940 9.749340 ATCAGATGATATAATGGAGAATTTGCA 57.251 29.630 0.00 0.00 32.01 4.08
2147 2941 9.227777 TCAGATGATATAATGGAGAATTTGCAG 57.772 33.333 0.00 0.00 0.00 4.41
2148 2942 9.227777 CAGATGATATAATGGAGAATTTGCAGA 57.772 33.333 0.00 0.00 0.00 4.26
2288 3082 1.534595 CTGCTCCTTTGCTGTCACTTC 59.465 52.381 0.00 0.00 0.00 3.01
2338 3132 8.151596 TGTTAGTCTTATGTTGTGTGGTAATCA 58.848 33.333 0.00 0.00 0.00 2.57
2478 3273 2.552315 CGAAGCAAAGCAACTTAGGGAA 59.448 45.455 0.00 0.00 0.00 3.97
2498 3293 6.378280 AGGGAACTTATGGTGAAGCAAATAAG 59.622 38.462 0.00 0.00 37.44 1.73
2569 3364 5.477510 TGTAAGGCCATTGTTTGCAATTAG 58.522 37.500 5.01 0.00 42.91 1.73
2589 3384 4.701651 AGCTCCTGATTGCATGATTCTA 57.298 40.909 0.00 0.00 0.00 2.10
2598 3393 6.500910 TGATTGCATGATTCTATTTGCACTC 58.499 36.000 0.00 7.03 44.16 3.51
2706 3501 2.790433 TCACCAGCCTTATTGTTGTCC 58.210 47.619 0.00 0.00 0.00 4.02
2817 3631 7.377766 ACATCAGAAAAGCACATTATTACGT 57.622 32.000 0.00 0.00 0.00 3.57
2821 3635 9.691362 ATCAGAAAAGCACATTATTACGTTTTT 57.309 25.926 0.00 0.00 0.00 1.94
2854 3674 7.672351 TTTTTGTAAAACTGTGAAGCGTATG 57.328 32.000 0.00 0.00 0.00 2.39
2861 3681 2.813754 ACTGTGAAGCGTATGCAAATGT 59.186 40.909 10.11 0.00 46.23 2.71
2926 3746 1.340248 GCTCGTAGGTGGCTATAGCAA 59.660 52.381 25.53 12.91 44.36 3.91
2927 3747 2.223971 GCTCGTAGGTGGCTATAGCAAA 60.224 50.000 25.53 10.94 44.36 3.68
2928 3748 3.740141 GCTCGTAGGTGGCTATAGCAAAA 60.740 47.826 25.53 8.37 44.36 2.44
2929 3749 4.439057 CTCGTAGGTGGCTATAGCAAAAA 58.561 43.478 25.53 5.86 44.36 1.94
2962 3782 7.568199 ACAGTAACTAAATGTCAGTTTGCTT 57.432 32.000 0.00 0.00 37.42 3.91
3060 3894 8.350722 CAGTCAATGAGCTGCATTTTATAATCT 58.649 33.333 1.02 0.00 44.68 2.40
3095 3929 6.086371 GCTTTAAGTTGTGTTTTCGTATGCTC 59.914 38.462 0.00 0.00 0.00 4.26
3116 3950 8.319057 TGCTCCTATCAGGAAGTTTAATAGAA 57.681 34.615 0.00 0.00 45.28 2.10
3153 3987 5.687166 AATGGTCCATAGAACCGTCTAAA 57.313 39.130 4.33 0.00 39.81 1.85
3224 4058 8.328758 TGGTAATTTCCAGAGATGTATTGAACT 58.671 33.333 0.00 0.00 33.19 3.01
3225 4059 9.178758 GGTAATTTCCAGAGATGTATTGAACTT 57.821 33.333 0.00 0.00 0.00 2.66
3237 4071 9.979578 AGATGTATTGAACTTTTTATGCAACAA 57.020 25.926 0.00 0.00 0.00 2.83
3258 4092 5.418840 ACAAATTCTTGTCCTGAAACTGTGT 59.581 36.000 0.00 0.00 42.25 3.72
3262 4096 2.325583 TGTCCTGAAACTGTGTCACC 57.674 50.000 0.00 0.00 0.00 4.02
3264 4098 0.531974 TCCTGAAACTGTGTCACCGC 60.532 55.000 0.00 0.00 0.00 5.68
3301 4135 5.760253 GTGTGGTTCATCATATCCTCGAATT 59.240 40.000 0.00 0.00 0.00 2.17
3304 4138 4.756642 GGTTCATCATATCCTCGAATTGCA 59.243 41.667 0.00 0.00 0.00 4.08
3311 4145 2.028420 TCCTCGAATTGCATGGACTG 57.972 50.000 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 9.366216 GTTAAACAACCTCAGATTTGTCTTTTT 57.634 29.630 0.00 0.00 34.82 1.94
20 21 8.527810 TGTTAAACAACCTCAGATTTGTCTTTT 58.472 29.630 0.00 0.00 34.82 2.27
21 22 7.973944 GTGTTAAACAACCTCAGATTTGTCTTT 59.026 33.333 0.00 0.00 34.82 2.52
22 23 7.122055 TGTGTTAAACAACCTCAGATTTGTCTT 59.878 33.333 0.00 0.66 34.82 3.01
23 24 6.601613 TGTGTTAAACAACCTCAGATTTGTCT 59.398 34.615 0.00 0.00 34.82 3.41
24 25 6.791303 TGTGTTAAACAACCTCAGATTTGTC 58.209 36.000 0.00 0.00 34.82 3.18
25 26 6.767524 TGTGTTAAACAACCTCAGATTTGT 57.232 33.333 0.00 0.00 37.55 2.83
26 27 7.424803 TCATGTGTTAAACAACCTCAGATTTG 58.575 34.615 0.00 0.00 43.61 2.32
27 28 7.581213 TCATGTGTTAAACAACCTCAGATTT 57.419 32.000 0.00 0.00 43.61 2.17
28 29 7.765695 ATCATGTGTTAAACAACCTCAGATT 57.234 32.000 0.00 0.00 43.61 2.40
29 30 8.103305 AGTATCATGTGTTAAACAACCTCAGAT 58.897 33.333 0.00 0.00 43.61 2.90
30 31 7.450074 AGTATCATGTGTTAAACAACCTCAGA 58.550 34.615 0.00 0.00 43.61 3.27
31 32 7.672983 AGTATCATGTGTTAAACAACCTCAG 57.327 36.000 0.00 0.00 43.61 3.35
32 33 9.378551 GATAGTATCATGTGTTAAACAACCTCA 57.621 33.333 5.21 0.00 43.61 3.86
33 34 8.827677 GGATAGTATCATGTGTTAAACAACCTC 58.172 37.037 12.19 0.00 43.61 3.85
34 35 8.325787 TGGATAGTATCATGTGTTAAACAACCT 58.674 33.333 12.19 0.00 43.61 3.50
35 36 8.500753 TGGATAGTATCATGTGTTAAACAACC 57.499 34.615 12.19 0.00 43.61 3.77
37 38 9.337396 GGATGGATAGTATCATGTGTTAAACAA 57.663 33.333 12.19 0.00 43.61 2.83
38 39 8.713971 AGGATGGATAGTATCATGTGTTAAACA 58.286 33.333 12.19 0.00 44.79 2.83
39 40 9.209175 GAGGATGGATAGTATCATGTGTTAAAC 57.791 37.037 12.19 0.00 0.00 2.01
40 41 8.375506 GGAGGATGGATAGTATCATGTGTTAAA 58.624 37.037 12.19 0.00 0.00 1.52
41 42 7.038302 GGGAGGATGGATAGTATCATGTGTTAA 60.038 40.741 12.19 0.00 0.00 2.01
42 43 6.440647 GGGAGGATGGATAGTATCATGTGTTA 59.559 42.308 12.19 0.00 0.00 2.41
43 44 5.249393 GGGAGGATGGATAGTATCATGTGTT 59.751 44.000 12.19 0.00 0.00 3.32
44 45 4.780021 GGGAGGATGGATAGTATCATGTGT 59.220 45.833 12.19 0.00 0.00 3.72
45 46 4.779489 TGGGAGGATGGATAGTATCATGTG 59.221 45.833 12.19 0.00 0.00 3.21
46 47 5.028678 TGGGAGGATGGATAGTATCATGT 57.971 43.478 12.19 0.00 0.00 3.21
47 48 4.408270 CCTGGGAGGATGGATAGTATCATG 59.592 50.000 12.19 0.00 37.67 3.07
48 49 4.629122 CCTGGGAGGATGGATAGTATCAT 58.371 47.826 12.19 4.03 37.67 2.45
49 50 3.823061 GCCTGGGAGGATGGATAGTATCA 60.823 52.174 12.19 0.00 37.67 2.15
50 51 2.769095 GCCTGGGAGGATGGATAGTATC 59.231 54.545 1.11 1.11 37.67 2.24
51 52 2.563134 GGCCTGGGAGGATGGATAGTAT 60.563 54.545 0.00 0.00 37.67 2.12
52 53 1.203313 GGCCTGGGAGGATGGATAGTA 60.203 57.143 0.00 0.00 37.67 1.82
53 54 0.474660 GGCCTGGGAGGATGGATAGT 60.475 60.000 0.00 0.00 37.67 2.12
54 55 0.474466 TGGCCTGGGAGGATGGATAG 60.474 60.000 3.32 0.00 37.67 2.08
55 56 0.196888 ATGGCCTGGGAGGATGGATA 59.803 55.000 3.32 0.00 37.67 2.59
56 57 1.072380 ATGGCCTGGGAGGATGGAT 60.072 57.895 3.32 0.00 37.67 3.41
57 58 2.080536 CATGGCCTGGGAGGATGGA 61.081 63.158 3.32 0.00 37.67 3.41
58 59 1.648302 TTCATGGCCTGGGAGGATGG 61.648 60.000 3.32 0.00 37.67 3.51
59 60 0.481567 ATTCATGGCCTGGGAGGATG 59.518 55.000 3.32 0.00 37.67 3.51
60 61 1.238615 AATTCATGGCCTGGGAGGAT 58.761 50.000 3.32 0.00 37.67 3.24
61 62 1.009997 AAATTCATGGCCTGGGAGGA 58.990 50.000 3.32 0.00 37.67 3.71
62 63 1.117150 CAAATTCATGGCCTGGGAGG 58.883 55.000 3.32 0.00 38.80 4.30
63 64 1.753073 GACAAATTCATGGCCTGGGAG 59.247 52.381 3.32 0.00 0.00 4.30
64 65 1.358787 AGACAAATTCATGGCCTGGGA 59.641 47.619 3.32 0.00 0.00 4.37
65 66 1.856629 AGACAAATTCATGGCCTGGG 58.143 50.000 3.32 0.00 0.00 4.45
66 67 3.967332 AAAGACAAATTCATGGCCTGG 57.033 42.857 3.32 0.00 0.00 4.45
85 86 3.799366 TGAGTTGCGACCTCTACAAAAA 58.201 40.909 0.00 0.00 0.00 1.94
86 87 3.462483 TGAGTTGCGACCTCTACAAAA 57.538 42.857 0.00 0.00 0.00 2.44
87 88 3.390135 CTTGAGTTGCGACCTCTACAAA 58.610 45.455 0.00 0.00 0.00 2.83
88 89 2.288825 CCTTGAGTTGCGACCTCTACAA 60.289 50.000 0.00 0.09 0.00 2.41
89 90 1.272490 CCTTGAGTTGCGACCTCTACA 59.728 52.381 0.00 0.00 0.00 2.74
90 91 1.272769 ACCTTGAGTTGCGACCTCTAC 59.727 52.381 0.00 0.00 0.00 2.59
91 92 1.629043 ACCTTGAGTTGCGACCTCTA 58.371 50.000 0.00 0.00 0.00 2.43
92 93 1.629043 TACCTTGAGTTGCGACCTCT 58.371 50.000 0.00 0.00 0.00 3.69
93 94 2.674796 ATACCTTGAGTTGCGACCTC 57.325 50.000 0.00 0.00 0.00 3.85
94 95 3.244422 TGAAATACCTTGAGTTGCGACCT 60.244 43.478 0.00 0.00 0.00 3.85
95 96 3.071479 TGAAATACCTTGAGTTGCGACC 58.929 45.455 0.00 0.00 0.00 4.79
96 97 4.391830 TGATGAAATACCTTGAGTTGCGAC 59.608 41.667 0.00 0.00 0.00 5.19
97 98 4.574892 TGATGAAATACCTTGAGTTGCGA 58.425 39.130 0.00 0.00 0.00 5.10
98 99 4.944962 TGATGAAATACCTTGAGTTGCG 57.055 40.909 0.00 0.00 0.00 4.85
99 100 6.441093 TCATGATGAAATACCTTGAGTTGC 57.559 37.500 0.00 0.00 0.00 4.17
100 101 9.865321 AAATTCATGATGAAATACCTTGAGTTG 57.135 29.630 12.36 0.00 40.12 3.16
112 113 9.761504 ACATGTGTGTAAAAATTCATGATGAAA 57.238 25.926 12.36 0.00 37.02 2.69
113 114 9.194271 CACATGTGTGTAAAAATTCATGATGAA 57.806 29.630 18.03 10.65 39.72 2.57
114 115 8.574737 TCACATGTGTGTAAAAATTCATGATGA 58.425 29.630 24.63 0.00 45.76 2.92
115 116 8.745464 TCACATGTGTGTAAAAATTCATGATG 57.255 30.769 24.63 0.00 45.76 3.07
116 117 8.579006 ACTCACATGTGTGTAAAAATTCATGAT 58.421 29.630 27.36 2.52 45.76 2.45
117 118 7.939782 ACTCACATGTGTGTAAAAATTCATGA 58.060 30.769 27.36 2.56 45.76 3.07
118 119 9.676195 TTACTCACATGTGTGTAAAAATTCATG 57.324 29.630 34.46 6.73 42.74 3.07
119 120 9.677567 GTTACTCACATGTGTGTAAAAATTCAT 57.322 29.630 36.47 16.17 45.27 2.57
120 121 8.678199 TGTTACTCACATGTGTGTAAAAATTCA 58.322 29.630 36.47 29.49 45.27 2.57
121 122 9.677567 ATGTTACTCACATGTGTGTAAAAATTC 57.322 29.630 36.47 28.02 45.12 2.17
122 123 9.677567 GATGTTACTCACATGTGTGTAAAAATT 57.322 29.630 36.47 25.21 46.96 1.82
123 124 8.296713 GGATGTTACTCACATGTGTGTAAAAAT 58.703 33.333 36.47 32.19 46.96 1.82
124 125 7.500892 AGGATGTTACTCACATGTGTGTAAAAA 59.499 33.333 36.47 30.24 46.96 1.94
125 126 6.995686 AGGATGTTACTCACATGTGTGTAAAA 59.004 34.615 36.47 33.81 46.96 1.52
126 127 6.530120 AGGATGTTACTCACATGTGTGTAAA 58.470 36.000 36.47 28.98 46.96 2.01
127 128 6.109156 AGGATGTTACTCACATGTGTGTAA 57.891 37.500 33.60 33.60 46.96 2.41
128 129 5.738619 AGGATGTTACTCACATGTGTGTA 57.261 39.130 28.21 28.21 46.96 2.90
129 130 4.623932 AGGATGTTACTCACATGTGTGT 57.376 40.909 30.01 30.01 46.96 3.72
130 131 5.931724 TGTAAGGATGTTACTCACATGTGTG 59.068 40.000 24.63 23.70 46.96 3.82
131 132 6.109156 TGTAAGGATGTTACTCACATGTGT 57.891 37.500 24.63 9.87 46.96 3.72
132 133 7.763985 TGTATGTAAGGATGTTACTCACATGTG 59.236 37.037 20.18 20.18 46.96 3.21
133 134 7.764443 GTGTATGTAAGGATGTTACTCACATGT 59.236 37.037 0.00 0.00 46.96 3.21
134 135 7.763985 TGTGTATGTAAGGATGTTACTCACATG 59.236 37.037 0.00 0.00 46.96 3.21
136 137 7.094631 GTGTGTATGTAAGGATGTTACTCACA 58.905 38.462 0.00 12.36 40.71 3.58
137 138 7.094631 TGTGTGTATGTAAGGATGTTACTCAC 58.905 38.462 0.00 0.00 37.59 3.51
138 139 7.234661 TGTGTGTATGTAAGGATGTTACTCA 57.765 36.000 0.00 0.00 0.00 3.41
139 140 9.982651 ATATGTGTGTATGTAAGGATGTTACTC 57.017 33.333 0.00 0.00 0.00 2.59
199 200 6.351796 GCTCCATGGAGGCCTTTATTTAAAAA 60.352 38.462 36.92 0.41 42.19 1.94
200 201 5.128663 GCTCCATGGAGGCCTTTATTTAAAA 59.871 40.000 36.92 0.77 42.19 1.52
201 202 4.649218 GCTCCATGGAGGCCTTTATTTAAA 59.351 41.667 36.92 1.17 42.19 1.52
202 203 4.079212 AGCTCCATGGAGGCCTTTATTTAA 60.079 41.667 36.92 1.84 42.19 1.52
203 204 3.463329 AGCTCCATGGAGGCCTTTATTTA 59.537 43.478 36.92 2.30 42.19 1.40
204 205 2.245806 AGCTCCATGGAGGCCTTTATTT 59.754 45.455 36.92 13.14 42.19 1.40
205 206 1.855599 AGCTCCATGGAGGCCTTTATT 59.144 47.619 36.92 13.75 42.19 1.40
206 207 1.423161 GAGCTCCATGGAGGCCTTTAT 59.577 52.381 36.92 16.48 42.19 1.40
207 208 0.839946 GAGCTCCATGGAGGCCTTTA 59.160 55.000 36.92 4.58 42.19 1.85
208 209 1.611965 GAGCTCCATGGAGGCCTTT 59.388 57.895 36.92 17.10 42.19 3.11
209 210 2.739996 CGAGCTCCATGGAGGCCTT 61.740 63.158 36.92 17.72 42.19 4.35
210 211 3.160047 CGAGCTCCATGGAGGCCT 61.160 66.667 36.92 27.78 42.19 5.19
211 212 4.247380 CCGAGCTCCATGGAGGCC 62.247 72.222 36.92 23.97 42.19 5.19
212 213 4.925861 GCCGAGCTCCATGGAGGC 62.926 72.222 36.92 29.82 42.19 4.70
213 214 4.247380 GGCCGAGCTCCATGGAGG 62.247 72.222 36.92 25.05 42.19 4.30
214 215 3.160047 AGGCCGAGCTCCATGGAG 61.160 66.667 33.73 33.73 44.56 3.86
215 216 3.157252 GAGGCCGAGCTCCATGGA 61.157 66.667 15.27 15.27 0.00 3.41
216 217 4.247380 GGAGGCCGAGCTCCATGG 62.247 72.222 4.97 4.97 39.45 3.66
217 218 3.473647 TGGAGGCCGAGCTCCATG 61.474 66.667 8.47 0.00 44.02 3.66
219 220 2.525124 TTTTGGAGGCCGAGCTCCA 61.525 57.895 8.47 7.35 46.84 3.86
220 221 2.041115 GTTTTGGAGGCCGAGCTCC 61.041 63.158 8.47 0.00 40.05 4.70
221 222 2.391389 CGTTTTGGAGGCCGAGCTC 61.391 63.158 2.73 2.73 0.00 4.09
222 223 2.358737 CGTTTTGGAGGCCGAGCT 60.359 61.111 0.00 0.00 0.00 4.09
223 224 4.103103 GCGTTTTGGAGGCCGAGC 62.103 66.667 0.00 0.00 33.08 5.03
228 229 0.241213 GAGAAAGGCGTTTTGGAGGC 59.759 55.000 5.76 0.00 38.40 4.70
229 230 1.897560 AGAGAAAGGCGTTTTGGAGG 58.102 50.000 5.76 0.00 0.00 4.30
230 231 3.990318 AAAGAGAAAGGCGTTTTGGAG 57.010 42.857 5.76 0.00 0.00 3.86
231 232 4.729227 AAAAAGAGAAAGGCGTTTTGGA 57.271 36.364 5.76 0.00 0.00 3.53
251 252 5.654317 TGTTCGCATCGTAGTAACAAAAA 57.346 34.783 0.00 0.00 0.00 1.94
252 253 5.462729 TCTTGTTCGCATCGTAGTAACAAAA 59.537 36.000 0.00 0.00 38.98 2.44
320 321 9.941325 AACTTCATATGTTATTGAATGCCAAAA 57.059 25.926 1.90 0.00 38.43 2.44
409 1197 9.110502 GTTGGAATCGAATTAAGAAGGTAGATT 57.889 33.333 0.00 0.00 0.00 2.40
443 1231 7.656412 TGTCATGTTAAATTAGCACACAATGT 58.344 30.769 0.00 0.00 0.00 2.71
505 1293 9.476202 AAAGCATAAAGAAACAGGAATTTGTAC 57.524 29.630 0.00 0.00 0.00 2.90
510 1298 6.424812 GTGCAAAGCATAAAGAAACAGGAATT 59.575 34.615 0.00 0.00 41.91 2.17
530 1318 8.489990 TCTTTGAAATCTTTGAATTTGTGCAA 57.510 26.923 0.00 0.00 0.00 4.08
565 1353 5.902613 ATGTGCTAGCAATGTGTTAATGT 57.097 34.783 21.29 0.00 0.00 2.71
586 1374 7.558807 TGATTCTTCCACTTTGATCATGCTAAT 59.441 33.333 0.00 0.00 0.00 1.73
609 1397 5.319453 ACTGACCACATTTTCAGACATGAT 58.681 37.500 0.00 0.00 41.65 2.45
635 1423 7.414222 TCCACATCTAACGGAGTACTATTTT 57.586 36.000 0.00 0.00 45.00 1.82
654 1442 4.612943 GTTTTCAACGGCTTTATTCCACA 58.387 39.130 0.00 0.00 0.00 4.17
728 1516 6.426328 TGTTTCGTAACGGTTACAATACCAAT 59.574 34.615 25.71 0.00 38.12 3.16
813 1601 9.379791 CACCGTTAAAAATATTTCCTCTCTACT 57.620 33.333 0.10 0.00 0.00 2.57
814 1602 8.610035 CCACCGTTAAAAATATTTCCTCTCTAC 58.390 37.037 0.10 0.00 0.00 2.59
854 1643 1.039856 GAGCATCTCTCTCACCCTCC 58.960 60.000 0.00 0.00 38.78 4.30
929 1718 3.572584 GCTTAAGACCTTCTCGTTTCGA 58.427 45.455 6.67 0.00 0.00 3.71
1999 2793 4.635223 TCTTGAATTCTCAGTGTGTCCAG 58.365 43.478 7.05 0.00 31.69 3.86
2090 2884 4.592351 ACATCCAAATCAAACCCAATGTCA 59.408 37.500 0.00 0.00 0.00 3.58
2146 2940 0.539051 CCTCAGGAACGGCAGATTCT 59.461 55.000 0.00 0.00 0.00 2.40
2147 2941 0.462759 CCCTCAGGAACGGCAGATTC 60.463 60.000 0.00 0.00 33.47 2.52
2148 2942 0.909610 TCCCTCAGGAACGGCAGATT 60.910 55.000 0.00 0.00 40.08 2.40
2150 2944 2.119611 TCCCTCAGGAACGGCAGA 59.880 61.111 0.00 0.00 40.08 4.26
2288 3082 5.747565 TGACAGACACGAAATTAAAAGCAG 58.252 37.500 0.00 0.00 0.00 4.24
2338 3132 3.389329 CAGCTACCCATAGACACAGGATT 59.611 47.826 0.00 0.00 0.00 3.01
2478 3273 5.016173 TGCCTTATTTGCTTCACCATAAGT 58.984 37.500 0.00 0.00 30.28 2.24
2569 3364 5.961396 AATAGAATCATGCAATCAGGAGC 57.039 39.130 0.00 0.00 36.37 4.70
2589 3384 7.445402 ACTTTGTGTAGTATGAAGAGTGCAAAT 59.555 33.333 0.00 0.00 0.00 2.32
2854 3674 1.724654 CGTGACCAGCGTAACATTTGC 60.725 52.381 0.00 0.00 0.00 3.68
2861 3681 0.598158 GTTCCACGTGACCAGCGTAA 60.598 55.000 19.30 0.00 40.90 3.18
2866 3686 2.519377 TAACTGTTCCACGTGACCAG 57.481 50.000 19.30 19.99 0.00 4.00
2952 3772 5.827797 AGTCCACATAAAAGAAGCAAACTGA 59.172 36.000 0.00 0.00 0.00 3.41
2962 3782 7.074653 ACAGAACCTAAGTCCACATAAAAGA 57.925 36.000 0.00 0.00 0.00 2.52
3060 3894 9.699703 AAAACACAACTTAAAGCTAACTTGAAA 57.300 25.926 0.00 0.00 35.85 2.69
3073 3907 5.761234 AGGAGCATACGAAAACACAACTTAA 59.239 36.000 0.00 0.00 0.00 1.85
3123 3957 6.887545 ACGGTTCTATGGACCATTTTTATGAA 59.112 34.615 13.40 5.64 0.00 2.57
3133 3967 5.486735 TTTTTAGACGGTTCTATGGACCA 57.513 39.130 0.00 0.00 34.15 4.02
3153 3987 9.986833 GTTTCAATTAAACTTTGCAGACAATTT 57.013 25.926 0.00 0.00 43.52 1.82
3207 4041 8.461222 TGCATAAAAAGTTCAATACATCTCTGG 58.539 33.333 0.00 0.00 0.00 3.86
3237 4071 5.066505 GTGACACAGTTTCAGGACAAGAATT 59.933 40.000 0.00 0.00 0.00 2.17
3240 4074 3.531538 GTGACACAGTTTCAGGACAAGA 58.468 45.455 0.00 0.00 0.00 3.02
3241 4075 2.614057 GGTGACACAGTTTCAGGACAAG 59.386 50.000 8.08 0.00 0.00 3.16
3258 4092 0.250234 CAGAGAAAGGGATGCGGTGA 59.750 55.000 0.00 0.00 0.00 4.02
3262 4096 1.081892 CACACAGAGAAAGGGATGCG 58.918 55.000 0.00 0.00 0.00 4.73
3264 4098 2.867109 ACCACACAGAGAAAGGGATG 57.133 50.000 0.00 0.00 0.00 3.51
3301 4135 0.250234 GCCAGTAGACAGTCCATGCA 59.750 55.000 0.00 0.00 0.00 3.96
3304 4138 4.074970 CAAAAAGCCAGTAGACAGTCCAT 58.925 43.478 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.