Multiple sequence alignment - TraesCS2A01G263700

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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 TraesCS2A01G263700 chr2A 100.000 2399 0 0 1 2399 418807945 418810343 0.000000e+00 4431.0
1 TraesCS2A01G263700 chr2A 90.588 170 3 2 286 443 418814853 418815021 1.870000e-51 213.0
2 TraesCS2A01G263700 chr2A 86.458 192 6 1 283 454 610205169 610205360 2.430000e-45 193.0
3 TraesCS2A01G263700 chr2A 90.833 120 10 1 341 459 192215267 192215386 2.470000e-35 159.0
4 TraesCS2A01G263700 chr2A 77.376 221 21 15 349 543 762400152 762399935 1.170000e-18 104.0
5 TraesCS2A01G263700 chr2A 85.870 92 6 5 286 371 633527793 633527703 9.130000e-15 91.6
6 TraesCS2A01G263700 chr5A 97.460 2126 42 1 286 2399 693605835 693607960 0.000000e+00 3616.0
7 TraesCS2A01G263700 chr5A 82.922 527 46 25 593 1094 669593436 669592929 3.660000e-118 435.0
8 TraesCS2A01G263700 chr5A 91.716 169 2 1 286 442 693612501 693612669 8.630000e-55 224.0
9 TraesCS2A01G263700 chr3A 97.791 2037 43 2 363 2399 13830805 13828771 0.000000e+00 3511.0
10 TraesCS2A01G263700 chr3A 86.486 111 8 4 286 390 556283758 556283649 5.420000e-22 115.0
11 TraesCS2A01G263700 chr6A 97.591 2034 49 0 366 2399 14150432 14148399 0.000000e+00 3485.0
12 TraesCS2A01G263700 chr6A 87.231 697 76 10 1699 2388 583032618 583033308 0.000000e+00 782.0
13 TraesCS2A01G263700 chr6A 87.006 177 3 6 286 442 14143833 14143657 5.270000e-42 182.0
14 TraesCS2A01G263700 chr6A 83.582 201 11 5 281 459 524319334 524319534 4.100000e-38 169.0
15 TraesCS2A01G263700 chr6A 87.629 97 4 4 286 374 14157576 14157480 3.260000e-19 106.0
16 TraesCS2A01G263700 chr6B 94.625 1600 70 6 812 2399 342808014 342806419 0.000000e+00 2464.0
17 TraesCS2A01G263700 chr5B 94.552 1597 75 3 812 2399 271155262 271156855 0.000000e+00 2457.0
18 TraesCS2A01G263700 chr2B 94.019 836 48 2 665 1498 299000704 298999869 0.000000e+00 1266.0
19 TraesCS2A01G263700 chr2B 91.859 823 58 6 1577 2399 155140268 155139455 0.000000e+00 1140.0
20 TraesCS2A01G263700 chr2B 94.833 600 24 2 1497 2096 298999240 298998648 0.000000e+00 929.0
21 TraesCS2A01G263700 chr2B 84.076 628 57 24 286 881 155156110 155155494 1.240000e-157 566.0
22 TraesCS2A01G263700 chr2B 82.955 528 45 26 592 1094 728615511 728616018 3.660000e-118 435.0
23 TraesCS2A01G263700 chr2B 88.963 299 17 5 1 286 384396788 384396493 2.930000e-94 355.0
24 TraesCS2A01G263700 chr2B 86.735 294 30 6 1224 1517 155142153 155141869 3.850000e-83 318.0
25 TraesCS2A01G263700 chr2B 91.250 80 7 0 1510 1589 155140609 155140530 2.520000e-20 110.0
26 TraesCS2A01G263700 chr1D 87.773 687 78 6 1705 2388 386796666 386795983 0.000000e+00 798.0
27 TraesCS2A01G263700 chr1D 100.000 55 0 0 286 340 425540844 425540790 4.220000e-18 102.0
28 TraesCS2A01G263700 chr7B 83.144 528 44 26 592 1094 93325760 93325253 7.870000e-120 440.0
29 TraesCS2A01G263700 chr7B 82.922 527 46 25 593 1094 517843254 517843761 3.660000e-118 435.0
30 TraesCS2A01G263700 chr7B 82.732 527 47 25 593 1094 107641091 107640584 1.700000e-116 429.0
31 TraesCS2A01G263700 chr4B 82.353 527 49 27 593 1094 175557662 175557155 3.690000e-113 418.0
32 TraesCS2A01G263700 chr2D 88.772 285 19 4 10 286 316321644 316321365 1.060000e-88 337.0
33 TraesCS2A01G263700 chr7D 85.876 177 5 1 286 442 616520936 616521112 1.140000e-38 171.0
34 TraesCS2A01G263700 chr7A 83.663 202 12 10 282 462 119771416 119771215 1.140000e-38 171.0
35 TraesCS2A01G263700 chr7A 88.571 140 12 4 349 487 688669898 688670034 1.480000e-37 167.0
36 TraesCS2A01G263700 chr7A 100.000 56 0 0 285 340 661610825 661610770 1.170000e-18 104.0
37 TraesCS2A01G263700 chrUn 93.750 80 5 0 408 487 34423413 34423492 1.160000e-23 121.0


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 TraesCS2A01G263700 chr2A 418807945 418810343 2398 False 4431.000000 4431 100.000 1 2399 1 chr2A.!!$F2 2398
1 TraesCS2A01G263700 chr5A 693605835 693607960 2125 False 3616.000000 3616 97.460 286 2399 1 chr5A.!!$F1 2113
2 TraesCS2A01G263700 chr5A 669592929 669593436 507 True 435.000000 435 82.922 593 1094 1 chr5A.!!$R1 501
3 TraesCS2A01G263700 chr3A 13828771 13830805 2034 True 3511.000000 3511 97.791 363 2399 1 chr3A.!!$R1 2036
4 TraesCS2A01G263700 chr6A 14148399 14150432 2033 True 3485.000000 3485 97.591 366 2399 1 chr6A.!!$R2 2033
5 TraesCS2A01G263700 chr6A 583032618 583033308 690 False 782.000000 782 87.231 1699 2388 1 chr6A.!!$F2 689
6 TraesCS2A01G263700 chr6B 342806419 342808014 1595 True 2464.000000 2464 94.625 812 2399 1 chr6B.!!$R1 1587
7 TraesCS2A01G263700 chr5B 271155262 271156855 1593 False 2457.000000 2457 94.552 812 2399 1 chr5B.!!$F1 1587
8 TraesCS2A01G263700 chr2B 298998648 299000704 2056 True 1097.500000 1266 94.426 665 2096 2 chr2B.!!$R4 1431
9 TraesCS2A01G263700 chr2B 155155494 155156110 616 True 566.000000 566 84.076 286 881 1 chr2B.!!$R1 595
10 TraesCS2A01G263700 chr2B 155139455 155142153 2698 True 522.666667 1140 89.948 1224 2399 3 chr2B.!!$R3 1175
11 TraesCS2A01G263700 chr2B 728615511 728616018 507 False 435.000000 435 82.955 592 1094 1 chr2B.!!$F1 502
12 TraesCS2A01G263700 chr1D 386795983 386796666 683 True 798.000000 798 87.773 1705 2388 1 chr1D.!!$R1 683
13 TraesCS2A01G263700 chr7B 93325253 93325760 507 True 440.000000 440 83.144 592 1094 1 chr7B.!!$R1 502
14 TraesCS2A01G263700 chr7B 517843254 517843761 507 False 435.000000 435 82.922 593 1094 1 chr7B.!!$F1 501
15 TraesCS2A01G263700 chr7B 107640584 107641091 507 True 429.000000 429 82.732 593 1094 1 chr7B.!!$R2 501
16 TraesCS2A01G263700 chr4B 175557155 175557662 507 True 418.000000 418 82.353 593 1094 1 chr4B.!!$R1 501

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
40 41 0.034380 GGGGGTCCTTTCAAGCTACC 60.034 60.0 0.0 0.0 32.69 3.18 F
41 42 0.992695 GGGGTCCTTTCAAGCTACCT 59.007 55.0 0.0 0.0 33.49 3.08 F
88 89 1.009829 GCACGAATCAGCTCGGAAAT 58.990 50.0 0.0 0.0 43.22 2.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1140 1198 0.679640 TGGCCGCCTCATCGAAAAAT 60.680 50.000 11.61 0.0 0.00 1.82 R
1216 1274 4.555709 ACCGTGTTTGCTGCCGGA 62.556 61.111 18.73 0.0 43.01 5.14 R
2005 4247 4.705507 AGTGACACGATGTAGACCTTACAT 59.294 41.667 0.00 0.0 40.50 2.29 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
20 21 4.337060 CGAGTGCGTGACCGACCA 62.337 66.667 0.00 0.00 35.63 4.02
21 22 2.430921 GAGTGCGTGACCGACCAG 60.431 66.667 0.00 0.00 35.63 4.00
36 37 1.304464 CCAGGGGGTCCTTTCAAGC 60.304 63.158 0.00 0.00 42.67 4.01
37 38 1.770324 CAGGGGGTCCTTTCAAGCT 59.230 57.895 0.00 0.00 42.67 3.74
38 39 0.991920 CAGGGGGTCCTTTCAAGCTA 59.008 55.000 0.00 0.00 42.67 3.32
39 40 0.992695 AGGGGGTCCTTTCAAGCTAC 59.007 55.000 0.00 0.00 41.56 3.58
40 41 0.034380 GGGGGTCCTTTCAAGCTACC 60.034 60.000 0.00 0.00 32.69 3.18
41 42 0.992695 GGGGTCCTTTCAAGCTACCT 59.007 55.000 0.00 0.00 33.49 3.08
42 43 1.340114 GGGGTCCTTTCAAGCTACCTG 60.340 57.143 0.00 0.00 33.49 4.00
43 44 1.454201 GGTCCTTTCAAGCTACCTGC 58.546 55.000 0.00 0.00 43.29 4.85
44 45 1.271379 GGTCCTTTCAAGCTACCTGCA 60.271 52.381 0.00 0.00 45.94 4.41
45 46 2.504367 GTCCTTTCAAGCTACCTGCAA 58.496 47.619 0.00 0.00 45.94 4.08
46 47 2.226674 GTCCTTTCAAGCTACCTGCAAC 59.773 50.000 0.00 0.00 45.94 4.17
47 48 2.158682 TCCTTTCAAGCTACCTGCAACA 60.159 45.455 0.00 0.00 45.94 3.33
48 49 2.622942 CCTTTCAAGCTACCTGCAACAA 59.377 45.455 0.00 0.00 45.94 2.83
49 50 3.304928 CCTTTCAAGCTACCTGCAACAAG 60.305 47.826 0.00 0.00 45.94 3.16
50 51 1.238439 TCAAGCTACCTGCAACAAGC 58.762 50.000 5.86 5.86 45.94 4.01
59 60 3.286751 GCAACAAGCACCCGCAGA 61.287 61.111 0.00 0.00 44.79 4.26
60 61 2.639286 CAACAAGCACCCGCAGAC 59.361 61.111 0.00 0.00 42.27 3.51
61 62 2.972505 AACAAGCACCCGCAGACG 60.973 61.111 0.00 0.00 42.27 4.18
79 80 4.833561 CACGCGCGCACGAATCAG 62.834 66.667 32.58 14.51 43.93 2.90
82 83 4.565704 GCGCGCACGAATCAGCTC 62.566 66.667 29.10 0.00 43.93 4.09
83 84 4.257376 CGCGCACGAATCAGCTCG 62.257 66.667 8.75 0.00 43.93 5.03
84 85 3.918220 GCGCACGAATCAGCTCGG 61.918 66.667 0.30 0.00 43.22 4.63
85 86 2.202610 CGCACGAATCAGCTCGGA 60.203 61.111 0.00 0.00 43.22 4.55
86 87 1.805539 CGCACGAATCAGCTCGGAA 60.806 57.895 0.00 0.00 43.22 4.30
87 88 1.351430 CGCACGAATCAGCTCGGAAA 61.351 55.000 0.00 0.00 43.22 3.13
88 89 1.009829 GCACGAATCAGCTCGGAAAT 58.990 50.000 0.00 0.00 43.22 2.17
89 90 2.201732 GCACGAATCAGCTCGGAAATA 58.798 47.619 0.00 0.00 43.22 1.40
90 91 2.802816 GCACGAATCAGCTCGGAAATAT 59.197 45.455 0.00 0.00 43.22 1.28
91 92 3.120854 GCACGAATCAGCTCGGAAATATC 60.121 47.826 0.00 0.00 43.22 1.63
92 93 4.302455 CACGAATCAGCTCGGAAATATCT 58.698 43.478 0.00 0.00 43.22 1.98
93 94 5.461526 CACGAATCAGCTCGGAAATATCTA 58.538 41.667 0.00 0.00 43.22 1.98
94 95 6.096036 CACGAATCAGCTCGGAAATATCTAT 58.904 40.000 0.00 0.00 43.22 1.98
95 96 7.251281 CACGAATCAGCTCGGAAATATCTATA 58.749 38.462 0.00 0.00 43.22 1.31
96 97 7.219154 CACGAATCAGCTCGGAAATATCTATAC 59.781 40.741 0.00 0.00 43.22 1.47
97 98 7.094334 ACGAATCAGCTCGGAAATATCTATACA 60.094 37.037 0.00 0.00 43.22 2.29
98 99 7.430793 CGAATCAGCTCGGAAATATCTATACAG 59.569 40.741 0.00 0.00 35.14 2.74
99 100 7.946381 ATCAGCTCGGAAATATCTATACAGA 57.054 36.000 0.00 0.00 34.56 3.41
100 101 7.761038 TCAGCTCGGAAATATCTATACAGAA 57.239 36.000 0.00 0.00 33.50 3.02
101 102 8.178313 TCAGCTCGGAAATATCTATACAGAAA 57.822 34.615 0.00 0.00 33.50 2.52
102 103 8.638873 TCAGCTCGGAAATATCTATACAGAAAA 58.361 33.333 0.00 0.00 33.50 2.29
103 104 8.920665 CAGCTCGGAAATATCTATACAGAAAAG 58.079 37.037 0.00 0.00 33.50 2.27
104 105 8.861086 AGCTCGGAAATATCTATACAGAAAAGA 58.139 33.333 0.00 0.00 33.50 2.52
105 106 9.477484 GCTCGGAAATATCTATACAGAAAAGAA 57.523 33.333 0.00 0.00 33.50 2.52
119 120 9.799106 ATACAGAAAAGAAGAAGAGGAAAATCA 57.201 29.630 0.00 0.00 0.00 2.57
120 121 8.164058 ACAGAAAAGAAGAAGAGGAAAATCAG 57.836 34.615 0.00 0.00 0.00 2.90
121 122 7.777440 ACAGAAAAGAAGAAGAGGAAAATCAGT 59.223 33.333 0.00 0.00 0.00 3.41
122 123 8.628280 CAGAAAAGAAGAAGAGGAAAATCAGTT 58.372 33.333 0.00 0.00 0.00 3.16
123 124 9.194972 AGAAAAGAAGAAGAGGAAAATCAGTTT 57.805 29.630 0.00 0.00 0.00 2.66
124 125 9.809096 GAAAAGAAGAAGAGGAAAATCAGTTTT 57.191 29.630 0.00 0.00 40.13 2.43
125 126 9.591792 AAAAGAAGAAGAGGAAAATCAGTTTTG 57.408 29.630 0.00 0.00 37.65 2.44
126 127 7.888250 AGAAGAAGAGGAAAATCAGTTTTGT 57.112 32.000 0.00 0.00 37.65 2.83
127 128 8.980481 AGAAGAAGAGGAAAATCAGTTTTGTA 57.020 30.769 0.00 0.00 37.65 2.41
128 129 9.579932 AGAAGAAGAGGAAAATCAGTTTTGTAT 57.420 29.630 0.00 0.00 37.65 2.29
129 130 9.617975 GAAGAAGAGGAAAATCAGTTTTGTATG 57.382 33.333 0.00 0.00 37.65 2.39
130 131 8.115490 AGAAGAGGAAAATCAGTTTTGTATGG 57.885 34.615 0.00 0.00 37.65 2.74
131 132 6.840780 AGAGGAAAATCAGTTTTGTATGGG 57.159 37.500 0.00 0.00 37.65 4.00
132 133 5.185828 AGAGGAAAATCAGTTTTGTATGGGC 59.814 40.000 0.00 0.00 37.65 5.36
133 134 5.086621 AGGAAAATCAGTTTTGTATGGGCT 58.913 37.500 0.00 0.00 37.65 5.19
134 135 5.185828 AGGAAAATCAGTTTTGTATGGGCTC 59.814 40.000 0.00 0.00 37.65 4.70
135 136 5.047377 GGAAAATCAGTTTTGTATGGGCTCA 60.047 40.000 0.00 0.00 37.65 4.26
136 137 6.351286 GGAAAATCAGTTTTGTATGGGCTCAT 60.351 38.462 3.57 3.57 37.65 2.90
137 138 6.610075 AAATCAGTTTTGTATGGGCTCATT 57.390 33.333 3.29 0.00 34.96 2.57
138 139 6.610075 AATCAGTTTTGTATGGGCTCATTT 57.390 33.333 3.29 0.00 34.96 2.32
139 140 5.389859 TCAGTTTTGTATGGGCTCATTTG 57.610 39.130 3.29 0.00 34.96 2.32
140 141 5.076182 TCAGTTTTGTATGGGCTCATTTGA 58.924 37.500 3.29 0.00 34.96 2.69
141 142 5.716228 TCAGTTTTGTATGGGCTCATTTGAT 59.284 36.000 3.29 0.00 34.96 2.57
142 143 6.211184 TCAGTTTTGTATGGGCTCATTTGATT 59.789 34.615 3.29 0.00 34.96 2.57
143 144 6.875195 CAGTTTTGTATGGGCTCATTTGATTT 59.125 34.615 3.29 0.00 34.96 2.17
144 145 6.875195 AGTTTTGTATGGGCTCATTTGATTTG 59.125 34.615 3.29 0.00 34.96 2.32
145 146 4.389890 TGTATGGGCTCATTTGATTTGC 57.610 40.909 3.29 0.00 34.96 3.68
146 147 3.768215 TGTATGGGCTCATTTGATTTGCA 59.232 39.130 3.29 0.00 34.96 4.08
147 148 3.536956 ATGGGCTCATTTGATTTGCAG 57.463 42.857 0.00 0.00 0.00 4.41
148 149 2.527497 TGGGCTCATTTGATTTGCAGA 58.473 42.857 0.00 0.00 0.00 4.26
149 150 2.898612 TGGGCTCATTTGATTTGCAGAA 59.101 40.909 0.00 0.00 0.00 3.02
150 151 3.516300 TGGGCTCATTTGATTTGCAGAAT 59.484 39.130 0.00 0.00 0.00 2.40
151 152 4.020039 TGGGCTCATTTGATTTGCAGAATT 60.020 37.500 0.00 0.00 0.00 2.17
152 153 4.569564 GGGCTCATTTGATTTGCAGAATTC 59.430 41.667 0.00 0.00 0.00 2.17
153 154 5.416947 GGCTCATTTGATTTGCAGAATTCT 58.583 37.500 0.88 0.88 0.00 2.40
154 155 6.406177 GGGCTCATTTGATTTGCAGAATTCTA 60.406 38.462 7.86 0.00 0.00 2.10
155 156 7.037438 GGCTCATTTGATTTGCAGAATTCTAA 58.963 34.615 7.86 0.00 0.00 2.10
156 157 7.546667 GGCTCATTTGATTTGCAGAATTCTAAA 59.453 33.333 7.86 6.75 0.00 1.85
157 158 8.928733 GCTCATTTGATTTGCAGAATTCTAAAA 58.071 29.630 7.86 12.09 0.00 1.52
160 161 9.815936 CATTTGATTTGCAGAATTCTAAAAACC 57.184 29.630 7.86 3.74 0.00 3.27
161 162 9.783081 ATTTGATTTGCAGAATTCTAAAAACCT 57.217 25.926 7.86 0.00 0.00 3.50
163 164 9.912634 TTGATTTGCAGAATTCTAAAAACCTAG 57.087 29.630 7.86 0.00 0.00 3.02
164 165 8.522830 TGATTTGCAGAATTCTAAAAACCTAGG 58.477 33.333 7.86 7.41 0.00 3.02
165 166 8.650143 ATTTGCAGAATTCTAAAAACCTAGGA 57.350 30.769 17.98 0.00 0.00 2.94
166 167 8.472007 TTTGCAGAATTCTAAAAACCTAGGAA 57.528 30.769 17.98 0.00 0.00 3.36
167 168 8.650143 TTGCAGAATTCTAAAAACCTAGGAAT 57.350 30.769 17.98 0.02 0.00 3.01
168 169 9.747898 TTGCAGAATTCTAAAAACCTAGGAATA 57.252 29.630 17.98 1.77 0.00 1.75
169 170 9.747898 TGCAGAATTCTAAAAACCTAGGAATAA 57.252 29.630 17.98 0.01 0.00 1.40
207 208 9.882996 ATATGATAGAAATGCATGTACAAAACG 57.117 29.630 0.00 0.00 0.00 3.60
208 209 6.550843 TGATAGAAATGCATGTACAAAACGG 58.449 36.000 0.00 0.00 0.00 4.44
209 210 6.372937 TGATAGAAATGCATGTACAAAACGGA 59.627 34.615 0.00 0.00 0.00 4.69
210 211 5.046910 AGAAATGCATGTACAAAACGGAG 57.953 39.130 0.00 0.00 0.00 4.63
211 212 3.848272 AATGCATGTACAAAACGGAGG 57.152 42.857 0.00 0.00 0.00 4.30
212 213 1.529226 TGCATGTACAAAACGGAGGG 58.471 50.000 0.00 0.00 0.00 4.30
213 214 1.072489 TGCATGTACAAAACGGAGGGA 59.928 47.619 0.00 0.00 0.00 4.20
214 215 2.290641 TGCATGTACAAAACGGAGGGAT 60.291 45.455 0.00 0.00 0.00 3.85
215 216 2.752903 GCATGTACAAAACGGAGGGATT 59.247 45.455 0.00 0.00 0.00 3.01
216 217 3.181500 GCATGTACAAAACGGAGGGATTC 60.181 47.826 0.00 0.00 0.00 2.52
217 218 4.261801 CATGTACAAAACGGAGGGATTCT 58.738 43.478 0.00 0.00 0.00 2.40
218 219 5.424757 CATGTACAAAACGGAGGGATTCTA 58.575 41.667 0.00 0.00 0.00 2.10
219 220 5.687166 TGTACAAAACGGAGGGATTCTAT 57.313 39.130 0.00 0.00 0.00 1.98
220 221 6.795144 TGTACAAAACGGAGGGATTCTATA 57.205 37.500 0.00 0.00 0.00 1.31
221 222 7.185318 TGTACAAAACGGAGGGATTCTATAA 57.815 36.000 0.00 0.00 0.00 0.98
222 223 7.622713 TGTACAAAACGGAGGGATTCTATAAA 58.377 34.615 0.00 0.00 0.00 1.40
223 224 6.997239 ACAAAACGGAGGGATTCTATAAAC 57.003 37.500 0.00 0.00 0.00 2.01
224 225 6.718294 ACAAAACGGAGGGATTCTATAAACT 58.282 36.000 0.00 0.00 0.00 2.66
225 226 7.173032 ACAAAACGGAGGGATTCTATAAACTT 58.827 34.615 0.00 0.00 0.00 2.66
226 227 7.668469 ACAAAACGGAGGGATTCTATAAACTTT 59.332 33.333 0.00 0.00 0.00 2.66
227 228 7.860918 AAACGGAGGGATTCTATAAACTTTC 57.139 36.000 0.00 0.00 0.00 2.62
228 229 6.555463 ACGGAGGGATTCTATAAACTTTCA 57.445 37.500 0.00 0.00 0.00 2.69
229 230 7.138054 ACGGAGGGATTCTATAAACTTTCAT 57.862 36.000 0.00 0.00 0.00 2.57
230 231 6.992715 ACGGAGGGATTCTATAAACTTTCATG 59.007 38.462 0.00 0.00 0.00 3.07
231 232 6.992715 CGGAGGGATTCTATAAACTTTCATGT 59.007 38.462 0.00 0.00 0.00 3.21
232 233 7.499232 CGGAGGGATTCTATAAACTTTCATGTT 59.501 37.037 0.00 0.00 0.00 2.71
233 234 9.190317 GGAGGGATTCTATAAACTTTCATGTTT 57.810 33.333 0.00 0.00 42.10 2.83
273 274 9.601810 AAGAAAAATACAAAAATCCTACTCCCT 57.398 29.630 0.00 0.00 0.00 4.20
274 275 9.601810 AGAAAAATACAAAAATCCTACTCCCTT 57.398 29.630 0.00 0.00 0.00 3.95
275 276 9.856488 GAAAAATACAAAAATCCTACTCCCTTC 57.144 33.333 0.00 0.00 0.00 3.46
276 277 7.625828 AAATACAAAAATCCTACTCCCTTCG 57.374 36.000 0.00 0.00 0.00 3.79
277 278 4.903045 ACAAAAATCCTACTCCCTTCGA 57.097 40.909 0.00 0.00 0.00 3.71
278 279 5.437191 ACAAAAATCCTACTCCCTTCGAT 57.563 39.130 0.00 0.00 0.00 3.59
279 280 5.429130 ACAAAAATCCTACTCCCTTCGATC 58.571 41.667 0.00 0.00 0.00 3.69
280 281 4.691326 AAAATCCTACTCCCTTCGATCC 57.309 45.455 0.00 0.00 0.00 3.36
281 282 3.330126 AATCCTACTCCCTTCGATCCA 57.670 47.619 0.00 0.00 0.00 3.41
282 283 2.840640 TCCTACTCCCTTCGATCCAA 57.159 50.000 0.00 0.00 0.00 3.53
283 284 3.110293 TCCTACTCCCTTCGATCCAAA 57.890 47.619 0.00 0.00 0.00 3.28
284 285 2.764572 TCCTACTCCCTTCGATCCAAAC 59.235 50.000 0.00 0.00 0.00 2.93
390 409 9.930693 GGTATAAATACCCTATTCTTCAGTCAG 57.069 37.037 7.80 0.00 45.62 3.51
709 739 4.899239 GACCTCCCGCATCAGCCG 62.899 72.222 0.00 0.00 37.52 5.52
854 891 7.554118 GGATCAGAAGAAAACATACAAGATCCA 59.446 37.037 0.00 0.00 44.38 3.41
934 978 5.252547 TCAATCAGGTGATTCAATTCCGAA 58.747 37.500 2.07 0.00 42.41 4.30
937 981 6.780457 ATCAGGTGATTCAATTCCGAATTT 57.220 33.333 3.48 0.00 35.74 1.82
1140 1198 4.175337 GCACTCCGGGCCTGCATA 62.175 66.667 5.85 0.00 0.00 3.14
1245 1303 4.111016 CACGGTGTCTCGCGGCTA 62.111 66.667 6.13 0.00 0.00 3.93
1246 1304 3.138798 ACGGTGTCTCGCGGCTAT 61.139 61.111 6.13 0.00 0.00 2.97
2005 4247 7.759489 AATTTTGCAGACTATCCACTGTTAA 57.241 32.000 0.00 0.00 36.62 2.01
2153 4396 2.360483 CTGCGAGATCTACACCACATCT 59.640 50.000 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 4.337060 TGGTCGGTCACGCACTCG 62.337 66.667 0.00 0.00 40.69 4.18
4 5 2.430921 CTGGTCGGTCACGCACTC 60.431 66.667 0.00 0.00 40.69 3.51
5 6 3.991051 CCTGGTCGGTCACGCACT 61.991 66.667 0.00 0.00 40.69 4.40
18 19 1.304464 GCTTGAAAGGACCCCCTGG 60.304 63.158 0.00 0.00 43.48 4.45
19 20 0.991920 TAGCTTGAAAGGACCCCCTG 59.008 55.000 0.00 0.00 43.48 4.45
21 22 0.034380 GGTAGCTTGAAAGGACCCCC 60.034 60.000 0.00 0.00 0.00 5.40
22 23 0.992695 AGGTAGCTTGAAAGGACCCC 59.007 55.000 0.00 0.00 0.00 4.95
23 24 1.950954 GCAGGTAGCTTGAAAGGACCC 60.951 57.143 0.00 0.00 41.15 4.46
24 25 1.271379 TGCAGGTAGCTTGAAAGGACC 60.271 52.381 0.00 0.00 45.94 4.46
25 26 2.185004 TGCAGGTAGCTTGAAAGGAC 57.815 50.000 0.00 0.00 45.94 3.85
26 27 2.158682 TGTTGCAGGTAGCTTGAAAGGA 60.159 45.455 0.00 0.00 45.94 3.36
27 28 2.229792 TGTTGCAGGTAGCTTGAAAGG 58.770 47.619 0.00 0.00 45.94 3.11
28 29 3.854784 GCTTGTTGCAGGTAGCTTGAAAG 60.855 47.826 0.00 0.00 45.94 2.62
29 30 2.034558 GCTTGTTGCAGGTAGCTTGAAA 59.965 45.455 0.00 0.00 45.94 2.69
30 31 1.608590 GCTTGTTGCAGGTAGCTTGAA 59.391 47.619 0.00 0.00 45.94 2.69
31 32 1.238439 GCTTGTTGCAGGTAGCTTGA 58.762 50.000 0.00 0.00 45.94 3.02
32 33 3.780925 GCTTGTTGCAGGTAGCTTG 57.219 52.632 0.00 0.00 45.94 4.01
42 43 3.286751 TCTGCGGGTGCTTGTTGC 61.287 61.111 0.00 0.00 43.34 4.17
43 44 2.639286 GTCTGCGGGTGCTTGTTG 59.361 61.111 0.00 0.00 43.34 3.33
44 45 2.972505 CGTCTGCGGGTGCTTGTT 60.973 61.111 0.00 0.00 43.34 2.83
62 63 4.833561 CTGATTCGTGCGCGCGTG 62.834 66.667 38.29 21.19 38.14 5.34
65 66 4.565704 GAGCTGATTCGTGCGCGC 62.566 66.667 27.26 27.26 38.14 6.86
66 67 4.257376 CGAGCTGATTCGTGCGCG 62.257 66.667 14.79 14.79 44.55 6.86
67 68 3.918220 CCGAGCTGATTCGTGCGC 61.918 66.667 0.00 0.00 38.88 6.09
68 69 1.351430 TTTCCGAGCTGATTCGTGCG 61.351 55.000 0.00 0.00 38.88 5.34
69 70 1.009829 ATTTCCGAGCTGATTCGTGC 58.990 50.000 0.00 0.00 38.88 5.34
70 71 4.302455 AGATATTTCCGAGCTGATTCGTG 58.698 43.478 0.00 0.00 38.88 4.35
71 72 4.592485 AGATATTTCCGAGCTGATTCGT 57.408 40.909 0.00 0.00 38.88 3.85
72 73 7.251281 TGTATAGATATTTCCGAGCTGATTCG 58.749 38.462 0.00 0.00 40.18 3.34
73 74 8.462811 TCTGTATAGATATTTCCGAGCTGATTC 58.537 37.037 0.00 0.00 0.00 2.52
74 75 8.354711 TCTGTATAGATATTTCCGAGCTGATT 57.645 34.615 0.00 0.00 0.00 2.57
75 76 7.946381 TCTGTATAGATATTTCCGAGCTGAT 57.054 36.000 0.00 0.00 0.00 2.90
76 77 7.761038 TTCTGTATAGATATTTCCGAGCTGA 57.239 36.000 0.00 0.00 31.81 4.26
77 78 8.818141 TTTTCTGTATAGATATTTCCGAGCTG 57.182 34.615 0.00 0.00 31.81 4.24
78 79 8.861086 TCTTTTCTGTATAGATATTTCCGAGCT 58.139 33.333 0.00 0.00 31.81 4.09
79 80 9.477484 TTCTTTTCTGTATAGATATTTCCGAGC 57.523 33.333 0.00 0.00 31.81 5.03
93 94 9.799106 TGATTTTCCTCTTCTTCTTTTCTGTAT 57.201 29.630 0.00 0.00 0.00 2.29
94 95 9.277783 CTGATTTTCCTCTTCTTCTTTTCTGTA 57.722 33.333 0.00 0.00 0.00 2.74
95 96 7.777440 ACTGATTTTCCTCTTCTTCTTTTCTGT 59.223 33.333 0.00 0.00 0.00 3.41
96 97 8.164058 ACTGATTTTCCTCTTCTTCTTTTCTG 57.836 34.615 0.00 0.00 0.00 3.02
97 98 8.759481 AACTGATTTTCCTCTTCTTCTTTTCT 57.241 30.769 0.00 0.00 0.00 2.52
98 99 9.809096 AAAACTGATTTTCCTCTTCTTCTTTTC 57.191 29.630 0.00 0.00 32.29 2.29
99 100 9.591792 CAAAACTGATTTTCCTCTTCTTCTTTT 57.408 29.630 0.00 0.00 35.79 2.27
100 101 8.753133 ACAAAACTGATTTTCCTCTTCTTCTTT 58.247 29.630 0.00 0.00 35.79 2.52
101 102 8.298729 ACAAAACTGATTTTCCTCTTCTTCTT 57.701 30.769 0.00 0.00 35.79 2.52
102 103 7.888250 ACAAAACTGATTTTCCTCTTCTTCT 57.112 32.000 0.00 0.00 35.79 2.85
103 104 9.617975 CATACAAAACTGATTTTCCTCTTCTTC 57.382 33.333 0.00 0.00 35.79 2.87
104 105 8.579863 CCATACAAAACTGATTTTCCTCTTCTT 58.420 33.333 0.00 0.00 35.79 2.52
105 106 7.177392 CCCATACAAAACTGATTTTCCTCTTCT 59.823 37.037 0.00 0.00 35.79 2.85
106 107 7.315890 CCCATACAAAACTGATTTTCCTCTTC 58.684 38.462 0.00 0.00 35.79 2.87
107 108 6.295292 GCCCATACAAAACTGATTTTCCTCTT 60.295 38.462 0.00 0.00 35.79 2.85
108 109 5.185828 GCCCATACAAAACTGATTTTCCTCT 59.814 40.000 0.00 0.00 35.79 3.69
109 110 5.185828 AGCCCATACAAAACTGATTTTCCTC 59.814 40.000 0.00 0.00 35.79 3.71
110 111 5.086621 AGCCCATACAAAACTGATTTTCCT 58.913 37.500 0.00 0.00 35.79 3.36
111 112 5.047377 TGAGCCCATACAAAACTGATTTTCC 60.047 40.000 0.00 0.00 35.79 3.13
112 113 6.024552 TGAGCCCATACAAAACTGATTTTC 57.975 37.500 0.00 0.00 35.79 2.29
113 114 6.610075 ATGAGCCCATACAAAACTGATTTT 57.390 33.333 0.00 0.00 38.61 1.82
114 115 6.610075 AATGAGCCCATACAAAACTGATTT 57.390 33.333 0.00 0.00 31.59 2.17
115 116 6.211184 TCAAATGAGCCCATACAAAACTGATT 59.789 34.615 0.00 0.00 31.59 2.57
116 117 5.716228 TCAAATGAGCCCATACAAAACTGAT 59.284 36.000 0.00 0.00 31.59 2.90
117 118 5.076182 TCAAATGAGCCCATACAAAACTGA 58.924 37.500 0.00 0.00 31.59 3.41
118 119 5.389859 TCAAATGAGCCCATACAAAACTG 57.610 39.130 0.00 0.00 31.59 3.16
119 120 6.610075 AATCAAATGAGCCCATACAAAACT 57.390 33.333 0.00 0.00 31.59 2.66
120 121 6.402442 GCAAATCAAATGAGCCCATACAAAAC 60.402 38.462 0.00 0.00 31.59 2.43
121 122 5.642919 GCAAATCAAATGAGCCCATACAAAA 59.357 36.000 0.00 0.00 31.59 2.44
122 123 5.177326 GCAAATCAAATGAGCCCATACAAA 58.823 37.500 0.00 0.00 31.59 2.83
123 124 4.222366 TGCAAATCAAATGAGCCCATACAA 59.778 37.500 0.00 0.00 31.59 2.41
124 125 3.768215 TGCAAATCAAATGAGCCCATACA 59.232 39.130 0.00 0.00 31.59 2.29
125 126 4.098349 TCTGCAAATCAAATGAGCCCATAC 59.902 41.667 0.00 0.00 31.59 2.39
126 127 4.279982 TCTGCAAATCAAATGAGCCCATA 58.720 39.130 0.00 0.00 31.59 2.74
127 128 3.101437 TCTGCAAATCAAATGAGCCCAT 58.899 40.909 0.00 0.00 33.66 4.00
128 129 2.527497 TCTGCAAATCAAATGAGCCCA 58.473 42.857 0.00 0.00 0.00 5.36
129 130 3.598019 TTCTGCAAATCAAATGAGCCC 57.402 42.857 0.00 0.00 0.00 5.19
130 131 5.416947 AGAATTCTGCAAATCAAATGAGCC 58.583 37.500 7.30 0.00 0.00 4.70
131 132 8.470040 TTTAGAATTCTGCAAATCAAATGAGC 57.530 30.769 18.47 0.00 0.00 4.26
134 135 9.815936 GGTTTTTAGAATTCTGCAAATCAAATG 57.184 29.630 18.47 0.00 0.00 2.32
135 136 9.783081 AGGTTTTTAGAATTCTGCAAATCAAAT 57.217 25.926 18.47 0.00 0.00 2.32
137 138 9.912634 CTAGGTTTTTAGAATTCTGCAAATCAA 57.087 29.630 18.47 0.00 0.00 2.57
138 139 8.522830 CCTAGGTTTTTAGAATTCTGCAAATCA 58.477 33.333 18.47 7.12 0.00 2.57
139 140 8.739972 TCCTAGGTTTTTAGAATTCTGCAAATC 58.260 33.333 18.47 15.22 0.00 2.17
140 141 8.650143 TCCTAGGTTTTTAGAATTCTGCAAAT 57.350 30.769 18.47 5.62 0.00 2.32
141 142 8.472007 TTCCTAGGTTTTTAGAATTCTGCAAA 57.528 30.769 18.47 13.24 0.00 3.68
142 143 8.650143 ATTCCTAGGTTTTTAGAATTCTGCAA 57.350 30.769 18.47 7.92 0.00 4.08
143 144 9.747898 TTATTCCTAGGTTTTTAGAATTCTGCA 57.252 29.630 18.47 1.55 0.00 4.41
181 182 9.882996 CGTTTTGTACATGCATTTCTATCATAT 57.117 29.630 0.00 0.00 0.00 1.78
182 183 8.341903 CCGTTTTGTACATGCATTTCTATCATA 58.658 33.333 0.00 0.00 0.00 2.15
183 184 7.066887 TCCGTTTTGTACATGCATTTCTATCAT 59.933 33.333 0.00 0.00 0.00 2.45
184 185 6.372937 TCCGTTTTGTACATGCATTTCTATCA 59.627 34.615 0.00 0.00 0.00 2.15
185 186 6.781138 TCCGTTTTGTACATGCATTTCTATC 58.219 36.000 0.00 0.00 0.00 2.08
186 187 6.183360 CCTCCGTTTTGTACATGCATTTCTAT 60.183 38.462 0.00 0.00 0.00 1.98
187 188 5.123186 CCTCCGTTTTGTACATGCATTTCTA 59.877 40.000 0.00 0.00 0.00 2.10
188 189 4.082787 CCTCCGTTTTGTACATGCATTTCT 60.083 41.667 0.00 0.00 0.00 2.52
189 190 4.165779 CCTCCGTTTTGTACATGCATTTC 58.834 43.478 0.00 0.00 0.00 2.17
190 191 3.056891 CCCTCCGTTTTGTACATGCATTT 60.057 43.478 0.00 0.00 0.00 2.32
191 192 2.491693 CCCTCCGTTTTGTACATGCATT 59.508 45.455 0.00 0.00 0.00 3.56
192 193 2.091541 CCCTCCGTTTTGTACATGCAT 58.908 47.619 0.00 0.00 0.00 3.96
193 194 1.072489 TCCCTCCGTTTTGTACATGCA 59.928 47.619 0.00 0.00 0.00 3.96
194 195 1.816074 TCCCTCCGTTTTGTACATGC 58.184 50.000 0.00 0.00 0.00 4.06
195 196 4.261801 AGAATCCCTCCGTTTTGTACATG 58.738 43.478 0.00 0.00 0.00 3.21
196 197 4.569719 AGAATCCCTCCGTTTTGTACAT 57.430 40.909 0.00 0.00 0.00 2.29
197 198 5.687166 ATAGAATCCCTCCGTTTTGTACA 57.313 39.130 0.00 0.00 0.00 2.90
198 199 7.767659 AGTTTATAGAATCCCTCCGTTTTGTAC 59.232 37.037 0.00 0.00 0.00 2.90
199 200 7.854337 AGTTTATAGAATCCCTCCGTTTTGTA 58.146 34.615 0.00 0.00 0.00 2.41
200 201 6.718294 AGTTTATAGAATCCCTCCGTTTTGT 58.282 36.000 0.00 0.00 0.00 2.83
201 202 7.625828 AAGTTTATAGAATCCCTCCGTTTTG 57.374 36.000 0.00 0.00 0.00 2.44
202 203 7.886446 TGAAAGTTTATAGAATCCCTCCGTTTT 59.114 33.333 0.00 0.00 0.00 2.43
203 204 7.399634 TGAAAGTTTATAGAATCCCTCCGTTT 58.600 34.615 0.00 0.00 0.00 3.60
204 205 6.954232 TGAAAGTTTATAGAATCCCTCCGTT 58.046 36.000 0.00 0.00 0.00 4.44
205 206 6.555463 TGAAAGTTTATAGAATCCCTCCGT 57.445 37.500 0.00 0.00 0.00 4.69
206 207 6.992715 ACATGAAAGTTTATAGAATCCCTCCG 59.007 38.462 0.00 0.00 0.00 4.63
207 208 8.753497 AACATGAAAGTTTATAGAATCCCTCC 57.247 34.615 0.00 0.00 0.00 4.30
247 248 9.601810 AGGGAGTAGGATTTTTGTATTTTTCTT 57.398 29.630 0.00 0.00 0.00 2.52
248 249 9.601810 AAGGGAGTAGGATTTTTGTATTTTTCT 57.398 29.630 0.00 0.00 0.00 2.52
249 250 9.856488 GAAGGGAGTAGGATTTTTGTATTTTTC 57.144 33.333 0.00 0.00 0.00 2.29
250 251 8.520351 CGAAGGGAGTAGGATTTTTGTATTTTT 58.480 33.333 0.00 0.00 0.00 1.94
251 252 7.886446 TCGAAGGGAGTAGGATTTTTGTATTTT 59.114 33.333 0.00 0.00 0.00 1.82
252 253 7.399634 TCGAAGGGAGTAGGATTTTTGTATTT 58.600 34.615 0.00 0.00 0.00 1.40
253 254 6.954232 TCGAAGGGAGTAGGATTTTTGTATT 58.046 36.000 0.00 0.00 0.00 1.89
254 255 6.555463 TCGAAGGGAGTAGGATTTTTGTAT 57.445 37.500 0.00 0.00 0.00 2.29
255 256 6.407752 GGATCGAAGGGAGTAGGATTTTTGTA 60.408 42.308 0.00 0.00 0.00 2.41
256 257 4.903045 TCGAAGGGAGTAGGATTTTTGT 57.097 40.909 0.00 0.00 0.00 2.83
257 258 4.816925 GGATCGAAGGGAGTAGGATTTTTG 59.183 45.833 0.00 0.00 0.00 2.44
258 259 4.473559 TGGATCGAAGGGAGTAGGATTTTT 59.526 41.667 0.00 0.00 0.00 1.94
259 260 4.037927 TGGATCGAAGGGAGTAGGATTTT 58.962 43.478 0.00 0.00 0.00 1.82
260 261 3.654273 TGGATCGAAGGGAGTAGGATTT 58.346 45.455 0.00 0.00 0.00 2.17
261 262 3.330126 TGGATCGAAGGGAGTAGGATT 57.670 47.619 0.00 0.00 0.00 3.01
262 263 3.330126 TTGGATCGAAGGGAGTAGGAT 57.670 47.619 0.00 0.00 0.00 3.24
263 264 2.764572 GTTTGGATCGAAGGGAGTAGGA 59.235 50.000 0.00 0.00 0.00 2.94
264 265 2.766828 AGTTTGGATCGAAGGGAGTAGG 59.233 50.000 0.00 0.00 0.00 3.18
265 266 3.195825 ACAGTTTGGATCGAAGGGAGTAG 59.804 47.826 0.00 0.00 0.00 2.57
266 267 3.170717 ACAGTTTGGATCGAAGGGAGTA 58.829 45.455 0.00 0.00 0.00 2.59
267 268 1.978580 ACAGTTTGGATCGAAGGGAGT 59.021 47.619 0.00 0.00 0.00 3.85
268 269 2.770164 ACAGTTTGGATCGAAGGGAG 57.230 50.000 0.00 0.00 0.00 4.30
269 270 4.564821 CCTTAACAGTTTGGATCGAAGGGA 60.565 45.833 0.00 0.00 0.00 4.20
270 271 3.689649 CCTTAACAGTTTGGATCGAAGGG 59.310 47.826 0.00 0.00 0.00 3.95
271 272 4.575885 TCCTTAACAGTTTGGATCGAAGG 58.424 43.478 0.00 0.00 34.71 3.46
272 273 6.743575 AATCCTTAACAGTTTGGATCGAAG 57.256 37.500 16.37 2.89 38.25 3.79
273 274 8.801882 ATTAATCCTTAACAGTTTGGATCGAA 57.198 30.769 16.37 14.25 38.25 3.71
274 275 8.801882 AATTAATCCTTAACAGTTTGGATCGA 57.198 30.769 16.37 10.83 38.25 3.59
305 306 7.226720 ACAACCGACCTAAGCATTGATTATTAG 59.773 37.037 0.00 0.00 0.00 1.73
390 409 5.376854 AATGGATTGAACAGTAACTGCAC 57.623 39.130 0.00 0.00 34.37 4.57
450 471 1.073923 CTCCAGGTTAGGGCAAAGTGT 59.926 52.381 0.00 0.00 0.00 3.55
854 891 5.591643 GTTTTGTACGAGATGTGTCACAT 57.408 39.130 18.45 18.45 42.43 3.21
934 978 9.765795 GATGCACTAGAGGTTAGTATAACAAAT 57.234 33.333 0.00 0.00 0.00 2.32
937 981 6.544931 ACGATGCACTAGAGGTTAGTATAACA 59.455 38.462 0.00 0.00 0.00 2.41
1140 1198 0.679640 TGGCCGCCTCATCGAAAAAT 60.680 50.000 11.61 0.00 0.00 1.82
1180 1238 4.988598 CGGACGTTGGCCACTGCT 62.989 66.667 3.88 0.00 37.74 4.24
1216 1274 4.555709 ACCGTGTTTGCTGCCGGA 62.556 61.111 18.73 0.00 43.01 5.14
2001 4243 7.008992 GTGACACGATGTAGACCTTACATTAAC 59.991 40.741 0.00 0.00 38.18 2.01
2005 4247 4.705507 AGTGACACGATGTAGACCTTACAT 59.294 41.667 0.00 0.00 40.50 2.29
2153 4396 7.038302 AGGATAACACTTTGAAGATAGTCACCA 60.038 37.037 0.00 0.00 0.00 4.17


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

AutoCloner maintained by Alex Coulton.