Multiple sequence alignment - TraesCS3B01G279000

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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 TraesCS3B01G279000 chr3B 100.000 3755 0 0 1 3755 448783451 448779697 0.000000e+00 6935
1 TraesCS3B01G279000 chr2B 97.197 1962 37 9 1805 3755 40314954 40313000 0.000000e+00 3302
2 TraesCS3B01G279000 chr2B 95.363 1186 36 4 202 1370 40317097 40315914 0.000000e+00 1868
3 TraesCS3B01G279000 chr5B 97.044 1962 41 7 1805 3755 493690323 493688368 0.000000e+00 3286
4 TraesCS3B01G279000 chr5B 95.639 1628 51 9 202 1812 493692710 493691086 0.000000e+00 2595
5 TraesCS3B01G279000 chr7B 97.044 1962 39 9 1805 3755 195785993 195784040 0.000000e+00 3284
6 TraesCS3B01G279000 chr7B 93.255 682 27 4 202 866 195787334 195786655 0.000000e+00 987
7 TraesCS3B01G279000 chr1A 96.993 1962 39 10 1805 3755 96435273 96433321 0.000000e+00 3278
8 TraesCS3B01G279000 chr1A 93.548 682 25 4 202 866 96436614 96435935 0.000000e+00 998
9 TraesCS3B01G279000 chr1A 95.098 612 25 3 3144 3755 34344784 34345390 0.000000e+00 959
10 TraesCS3B01G279000 chr5D 96.589 1964 46 9 1805 3755 505355056 505353101 0.000000e+00 3236
11 TraesCS3B01G279000 chr5D 93.413 835 29 10 198 1012 505356602 505355774 0.000000e+00 1214
12 TraesCS3B01G279000 chr6B 95.084 1953 72 8 1813 3755 616357583 616359521 0.000000e+00 3053
13 TraesCS3B01G279000 chr5A 91.662 1979 123 17 1805 3755 307219980 307221944 0.000000e+00 2702
14 TraesCS3B01G279000 chr5A 81.661 289 40 9 199 484 307217210 307217488 1.050000e-55 228
15 TraesCS3B01G279000 chr4B 91.460 1979 129 14 1805 3755 301786169 301784203 0.000000e+00 2682
16 TraesCS3B01G279000 chr4B 86.829 1640 168 33 202 1812 301869487 301867867 0.000000e+00 1788
17 TraesCS3B01G279000 chr4B 86.792 1643 167 34 202 1812 301901514 301899890 0.000000e+00 1786
18 TraesCS3B01G279000 chr4B 86.524 1640 173 33 202 1812 301788555 301786935 0.000000e+00 1760
19 TraesCS3B01G279000 chr4B 86.280 1640 176 33 202 1812 301707679 301706060 0.000000e+00 1736
20 TraesCS3B01G279000 chr4A 94.782 1629 61 8 202 1812 731916772 731915150 0.000000e+00 2516
21 TraesCS3B01G279000 chr4A 90.388 1238 102 9 2528 3755 578769505 578770735 0.000000e+00 1611
22 TraesCS3B01G279000 chr4D 94.424 1632 54 10 203 1812 25467229 25468845 0.000000e+00 2475
23 TraesCS3B01G279000 chr2D 95.532 1298 45 8 1805 3091 34034957 34036252 0.000000e+00 2063
24 TraesCS3B01G279000 chr6A 94.713 1305 55 9 1804 3096 29789591 29788289 0.000000e+00 2015
25 TraesCS3B01G279000 chr7A 86.957 1633 187 19 198 1812 555085701 555087325 0.000000e+00 1812
26 TraesCS3B01G279000 chr7A 94.955 1011 25 6 202 1195 692012511 692013512 0.000000e+00 1561
27 TraesCS3B01G279000 chr7A 97.409 656 17 0 3100 3755 692014650 692015305 0.000000e+00 1118
28 TraesCS3B01G279000 chr7A 91.200 500 32 5 2706 3195 664365423 664365920 0.000000e+00 669
29 TraesCS3B01G279000 chrUn 86.646 1640 171 33 202 1812 315979343 315980963 0.000000e+00 1772
30 TraesCS3B01G279000 chr3A 92.683 82 6 0 119 200 468007710 468007629 6.590000e-23 119


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 TraesCS3B01G279000 chr3B 448779697 448783451 3754 True 6935.0 6935 100.0000 1 3755 1 chr3B.!!$R1 3754
1 TraesCS3B01G279000 chr2B 40313000 40317097 4097 True 2585.0 3302 96.2800 202 3755 2 chr2B.!!$R1 3553
2 TraesCS3B01G279000 chr5B 493688368 493692710 4342 True 2940.5 3286 96.3415 202 3755 2 chr5B.!!$R1 3553
3 TraesCS3B01G279000 chr7B 195784040 195787334 3294 True 2135.5 3284 95.1495 202 3755 2 chr7B.!!$R1 3553
4 TraesCS3B01G279000 chr1A 96433321 96436614 3293 True 2138.0 3278 95.2705 202 3755 2 chr1A.!!$R1 3553
5 TraesCS3B01G279000 chr1A 34344784 34345390 606 False 959.0 959 95.0980 3144 3755 1 chr1A.!!$F1 611
6 TraesCS3B01G279000 chr5D 505353101 505356602 3501 True 2225.0 3236 95.0010 198 3755 2 chr5D.!!$R1 3557
7 TraesCS3B01G279000 chr6B 616357583 616359521 1938 False 3053.0 3053 95.0840 1813 3755 1 chr6B.!!$F1 1942
8 TraesCS3B01G279000 chr5A 307217210 307221944 4734 False 1465.0 2702 86.6615 199 3755 2 chr5A.!!$F1 3556
9 TraesCS3B01G279000 chr4B 301784203 301788555 4352 True 2221.0 2682 88.9920 202 3755 2 chr4B.!!$R4 3553
10 TraesCS3B01G279000 chr4B 301867867 301869487 1620 True 1788.0 1788 86.8290 202 1812 1 chr4B.!!$R2 1610
11 TraesCS3B01G279000 chr4B 301899890 301901514 1624 True 1786.0 1786 86.7920 202 1812 1 chr4B.!!$R3 1610
12 TraesCS3B01G279000 chr4B 301706060 301707679 1619 True 1736.0 1736 86.2800 202 1812 1 chr4B.!!$R1 1610
13 TraesCS3B01G279000 chr4A 731915150 731916772 1622 True 2516.0 2516 94.7820 202 1812 1 chr4A.!!$R1 1610
14 TraesCS3B01G279000 chr4A 578769505 578770735 1230 False 1611.0 1611 90.3880 2528 3755 1 chr4A.!!$F1 1227
15 TraesCS3B01G279000 chr4D 25467229 25468845 1616 False 2475.0 2475 94.4240 203 1812 1 chr4D.!!$F1 1609
16 TraesCS3B01G279000 chr2D 34034957 34036252 1295 False 2063.0 2063 95.5320 1805 3091 1 chr2D.!!$F1 1286
17 TraesCS3B01G279000 chr6A 29788289 29789591 1302 True 2015.0 2015 94.7130 1804 3096 1 chr6A.!!$R1 1292
18 TraesCS3B01G279000 chr7A 555085701 555087325 1624 False 1812.0 1812 86.9570 198 1812 1 chr7A.!!$F1 1614
19 TraesCS3B01G279000 chr7A 692012511 692015305 2794 False 1339.5 1561 96.1820 202 3755 2 chr7A.!!$F3 3553
20 TraesCS3B01G279000 chrUn 315979343 315980963 1620 False 1772.0 1772 86.6460 202 1812 1 chrUn.!!$F1 1610

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
635 1053 0.039074 CCTATCCAGGCGACGCTTAG 60.039 60.0 20.77 5.25 34.35 2.18 F
960 1383 1.555967 GGCTCAACCTCTCTCTCTGT 58.444 55.0 0.00 0.00 34.51 3.41 F
1347 1922 2.159057 GGGTGGCCATTTGATCATCAAC 60.159 50.0 9.72 0.00 35.89 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1537 2112 1.623811 ACTATCGGAACCAACACTGCT 59.376 47.619 0.0 0.0 0.00 4.24 R
2317 3999 2.799412 CACTCTCACTCACTTCTGCAAC 59.201 50.000 0.0 0.0 0.00 4.17 R
2957 4652 5.611374 TGAAAGTAGAGCTAGTGCAGTTTT 58.389 37.500 0.0 0.0 42.74 2.43 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
21 22 3.689347 TGCATTCATGTAGAGCCTTTGT 58.311 40.909 0.00 0.00 0.00 2.83
22 23 3.691118 TGCATTCATGTAGAGCCTTTGTC 59.309 43.478 0.00 0.00 0.00 3.18
23 24 3.065925 GCATTCATGTAGAGCCTTTGTCC 59.934 47.826 0.00 0.00 0.00 4.02
24 25 4.521146 CATTCATGTAGAGCCTTTGTCCT 58.479 43.478 0.00 0.00 0.00 3.85
25 26 5.674525 CATTCATGTAGAGCCTTTGTCCTA 58.325 41.667 0.00 0.00 0.00 2.94
26 27 5.957771 TTCATGTAGAGCCTTTGTCCTAT 57.042 39.130 0.00 0.00 0.00 2.57
27 28 7.445121 CATTCATGTAGAGCCTTTGTCCTATA 58.555 38.462 0.00 0.00 0.00 1.31
28 29 6.656632 TCATGTAGAGCCTTTGTCCTATAG 57.343 41.667 0.00 0.00 0.00 1.31
29 30 6.136857 TCATGTAGAGCCTTTGTCCTATAGT 58.863 40.000 0.00 0.00 0.00 2.12
30 31 6.611642 TCATGTAGAGCCTTTGTCCTATAGTT 59.388 38.462 0.00 0.00 0.00 2.24
31 32 6.466885 TGTAGAGCCTTTGTCCTATAGTTC 57.533 41.667 0.00 0.00 0.00 3.01
32 33 6.195700 TGTAGAGCCTTTGTCCTATAGTTCT 58.804 40.000 0.00 0.00 0.00 3.01
33 34 7.351952 TGTAGAGCCTTTGTCCTATAGTTCTA 58.648 38.462 0.00 0.00 0.00 2.10
34 35 7.837689 TGTAGAGCCTTTGTCCTATAGTTCTAA 59.162 37.037 0.00 0.00 0.00 2.10
35 36 7.922699 AGAGCCTTTGTCCTATAGTTCTAAT 57.077 36.000 0.00 0.00 0.00 1.73
36 37 7.958088 AGAGCCTTTGTCCTATAGTTCTAATC 58.042 38.462 0.00 0.00 0.00 1.75
37 38 7.787424 AGAGCCTTTGTCCTATAGTTCTAATCT 59.213 37.037 0.00 0.00 0.00 2.40
38 39 9.080097 GAGCCTTTGTCCTATAGTTCTAATCTA 57.920 37.037 0.00 0.00 0.00 1.98
39 40 8.862085 AGCCTTTGTCCTATAGTTCTAATCTAC 58.138 37.037 0.00 0.00 0.00 2.59
40 41 8.639761 GCCTTTGTCCTATAGTTCTAATCTACA 58.360 37.037 0.00 0.00 0.00 2.74
45 46 9.877222 TGTCCTATAGTTCTAATCTACAATCCA 57.123 33.333 0.00 0.00 0.00 3.41
87 88 8.528044 AACAAGGTTATGTTTCCACTTTAGAA 57.472 30.769 0.00 0.00 40.52 2.10
88 89 8.528044 ACAAGGTTATGTTTCCACTTTAGAAA 57.472 30.769 0.00 0.00 0.00 2.52
89 90 8.973182 ACAAGGTTATGTTTCCACTTTAGAAAA 58.027 29.630 0.00 0.00 35.13 2.29
90 91 9.981114 CAAGGTTATGTTTCCACTTTAGAAAAT 57.019 29.630 0.00 0.00 35.13 1.82
92 93 9.588096 AGGTTATGTTTCCACTTTAGAAAATCT 57.412 29.630 0.00 0.00 35.13 2.40
93 94 9.841880 GGTTATGTTTCCACTTTAGAAAATCTC 57.158 33.333 0.00 0.00 35.13 2.75
94 95 9.841880 GTTATGTTTCCACTTTAGAAAATCTCC 57.158 33.333 0.00 0.00 35.13 3.71
95 96 9.581289 TTATGTTTCCACTTTAGAAAATCTCCA 57.419 29.630 0.00 0.00 35.13 3.86
96 97 7.889873 TGTTTCCACTTTAGAAAATCTCCAA 57.110 32.000 0.00 0.00 35.13 3.53
97 98 8.477419 TGTTTCCACTTTAGAAAATCTCCAAT 57.523 30.769 0.00 0.00 35.13 3.16
98 99 8.359642 TGTTTCCACTTTAGAAAATCTCCAATG 58.640 33.333 0.00 0.00 35.13 2.82
99 100 8.360390 GTTTCCACTTTAGAAAATCTCCAATGT 58.640 33.333 0.00 0.00 35.13 2.71
100 101 9.581289 TTTCCACTTTAGAAAATCTCCAATGTA 57.419 29.630 0.00 0.00 30.48 2.29
101 102 8.792830 TCCACTTTAGAAAATCTCCAATGTAG 57.207 34.615 0.00 0.00 0.00 2.74
102 103 8.602424 TCCACTTTAGAAAATCTCCAATGTAGA 58.398 33.333 0.00 0.00 0.00 2.59
103 104 9.401058 CCACTTTAGAAAATCTCCAATGTAGAT 57.599 33.333 0.00 0.00 35.17 1.98
112 113 8.753497 AAATCTCCAATGTAGATTAGGAAACC 57.247 34.615 1.46 0.00 41.68 3.27
113 114 7.698163 ATCTCCAATGTAGATTAGGAAACCT 57.302 36.000 0.00 0.00 37.71 3.50
114 115 6.889198 TCTCCAATGTAGATTAGGAAACCTG 58.111 40.000 0.00 0.00 34.61 4.00
115 116 6.672218 TCTCCAATGTAGATTAGGAAACCTGA 59.328 38.462 0.00 0.00 34.61 3.86
116 117 7.348274 TCTCCAATGTAGATTAGGAAACCTGAT 59.652 37.037 0.00 0.00 34.61 2.90
117 118 7.872138 TCCAATGTAGATTAGGAAACCTGATT 58.128 34.615 0.00 0.00 34.61 2.57
118 119 7.993183 TCCAATGTAGATTAGGAAACCTGATTC 59.007 37.037 0.00 0.00 34.61 2.52
119 120 7.995488 CCAATGTAGATTAGGAAACCTGATTCT 59.005 37.037 0.00 0.00 34.61 2.40
123 124 8.204836 TGTAGATTAGGAAACCTGATTCTAAGC 58.795 37.037 0.00 0.00 34.61 3.09
124 125 7.200434 AGATTAGGAAACCTGATTCTAAGCA 57.800 36.000 0.00 0.00 34.61 3.91
125 126 7.278875 AGATTAGGAAACCTGATTCTAAGCAG 58.721 38.462 0.98 0.98 41.86 4.24
135 136 6.360844 CTGATTCTAAGCAGGTCATTTGAG 57.639 41.667 0.00 0.00 38.70 3.02
136 137 6.053632 TGATTCTAAGCAGGTCATTTGAGA 57.946 37.500 0.00 0.00 0.00 3.27
137 138 6.475504 TGATTCTAAGCAGGTCATTTGAGAA 58.524 36.000 0.00 0.00 0.00 2.87
138 139 6.596888 TGATTCTAAGCAGGTCATTTGAGAAG 59.403 38.462 0.00 0.00 0.00 2.85
139 140 5.489792 TCTAAGCAGGTCATTTGAGAAGT 57.510 39.130 0.00 0.00 0.00 3.01
140 141 5.240891 TCTAAGCAGGTCATTTGAGAAGTG 58.759 41.667 0.00 0.00 0.00 3.16
141 142 2.787994 AGCAGGTCATTTGAGAAGTGG 58.212 47.619 0.00 0.00 0.00 4.00
142 143 2.373169 AGCAGGTCATTTGAGAAGTGGA 59.627 45.455 0.00 0.00 0.00 4.02
143 144 2.485814 GCAGGTCATTTGAGAAGTGGAC 59.514 50.000 0.00 0.00 0.00 4.02
144 145 3.743521 CAGGTCATTTGAGAAGTGGACA 58.256 45.455 0.00 0.00 0.00 4.02
145 146 3.499918 CAGGTCATTTGAGAAGTGGACAC 59.500 47.826 0.00 0.00 0.00 3.67
146 147 3.392616 AGGTCATTTGAGAAGTGGACACT 59.607 43.478 0.00 0.00 44.94 3.55
147 148 3.499918 GGTCATTTGAGAAGTGGACACTG 59.500 47.826 5.63 0.00 41.58 3.66
148 149 4.380531 GTCATTTGAGAAGTGGACACTGA 58.619 43.478 5.63 0.00 41.58 3.41
149 150 4.999950 GTCATTTGAGAAGTGGACACTGAT 59.000 41.667 5.63 0.00 41.58 2.90
150 151 6.166279 GTCATTTGAGAAGTGGACACTGATA 58.834 40.000 5.63 0.00 41.58 2.15
151 152 6.650807 GTCATTTGAGAAGTGGACACTGATAA 59.349 38.462 5.63 0.00 41.58 1.75
152 153 6.650807 TCATTTGAGAAGTGGACACTGATAAC 59.349 38.462 5.63 0.00 41.58 1.89
153 154 5.545063 TTGAGAAGTGGACACTGATAACA 57.455 39.130 5.63 0.81 41.58 2.41
154 155 5.745312 TGAGAAGTGGACACTGATAACAT 57.255 39.130 5.63 0.00 41.58 2.71
155 156 5.724328 TGAGAAGTGGACACTGATAACATC 58.276 41.667 5.63 0.00 41.58 3.06
156 157 5.245977 TGAGAAGTGGACACTGATAACATCA 59.754 40.000 5.63 1.16 41.58 3.07
157 158 6.070596 TGAGAAGTGGACACTGATAACATCAT 60.071 38.462 5.63 0.00 41.58 2.45
158 159 6.111382 AGAAGTGGACACTGATAACATCATG 58.889 40.000 5.63 0.00 41.58 3.07
159 160 5.426689 AGTGGACACTGATAACATCATGT 57.573 39.130 3.82 0.00 40.75 3.21
160 161 5.423015 AGTGGACACTGATAACATCATGTC 58.577 41.667 3.82 15.67 41.60 3.06
161 162 5.046376 AGTGGACACTGATAACATCATGTCA 60.046 40.000 20.56 11.82 42.68 3.58
162 163 5.819379 GTGGACACTGATAACATCATGTCAT 59.181 40.000 20.56 0.00 42.68 3.06
163 164 5.818857 TGGACACTGATAACATCATGTCATG 59.181 40.000 20.56 6.47 42.68 3.07
164 165 5.277683 GGACACTGATAACATCATGTCATGC 60.278 44.000 20.56 0.00 42.68 4.06
165 166 5.434408 ACACTGATAACATCATGTCATGCT 58.566 37.500 8.03 0.00 38.85 3.79
166 167 5.884232 ACACTGATAACATCATGTCATGCTT 59.116 36.000 8.03 2.36 38.85 3.91
167 168 7.049754 ACACTGATAACATCATGTCATGCTTA 58.950 34.615 8.03 4.36 38.85 3.09
168 169 7.226128 ACACTGATAACATCATGTCATGCTTAG 59.774 37.037 8.03 0.77 38.85 2.18
169 170 7.440255 CACTGATAACATCATGTCATGCTTAGA 59.560 37.037 8.03 0.00 38.85 2.10
170 171 7.989170 ACTGATAACATCATGTCATGCTTAGAA 59.011 33.333 8.03 0.00 38.85 2.10
171 172 8.913487 TGATAACATCATGTCATGCTTAGAAT 57.087 30.769 8.03 0.00 33.59 2.40
172 173 8.996271 TGATAACATCATGTCATGCTTAGAATC 58.004 33.333 8.03 7.26 33.59 2.52
173 174 8.913487 ATAACATCATGTCATGCTTAGAATCA 57.087 30.769 8.03 0.00 0.00 2.57
174 175 7.634671 AACATCATGTCATGCTTAGAATCAA 57.365 32.000 8.03 0.00 0.00 2.57
175 176 7.260558 ACATCATGTCATGCTTAGAATCAAG 57.739 36.000 8.03 0.00 0.00 3.02
184 185 4.308899 GCTTAGAATCAAGCTCGTAGGA 57.691 45.455 9.18 0.00 46.04 2.94
185 186 4.295051 GCTTAGAATCAAGCTCGTAGGAG 58.705 47.826 8.10 8.10 46.04 3.69
186 187 4.202070 GCTTAGAATCAAGCTCGTAGGAGT 60.202 45.833 13.65 0.00 46.04 3.85
187 188 5.008811 GCTTAGAATCAAGCTCGTAGGAGTA 59.991 44.000 13.65 0.00 46.04 2.59
188 189 4.904253 AGAATCAAGCTCGTAGGAGTAC 57.096 45.455 13.65 0.00 42.53 2.73
189 190 4.528920 AGAATCAAGCTCGTAGGAGTACT 58.471 43.478 13.65 0.00 42.53 2.73
190 191 5.682659 AGAATCAAGCTCGTAGGAGTACTA 58.317 41.667 13.65 0.00 42.53 1.82
191 192 6.300703 AGAATCAAGCTCGTAGGAGTACTAT 58.699 40.000 13.65 1.51 42.53 2.12
192 193 6.428771 AGAATCAAGCTCGTAGGAGTACTATC 59.571 42.308 13.65 6.32 42.53 2.08
193 194 5.032327 TCAAGCTCGTAGGAGTACTATCA 57.968 43.478 13.65 0.00 42.53 2.15
194 195 5.434408 TCAAGCTCGTAGGAGTACTATCAA 58.566 41.667 13.65 0.00 42.53 2.57
195 196 6.062749 TCAAGCTCGTAGGAGTACTATCAAT 58.937 40.000 13.65 0.00 42.53 2.57
196 197 6.205076 TCAAGCTCGTAGGAGTACTATCAATC 59.795 42.308 13.65 0.00 42.53 2.67
200 201 7.388500 AGCTCGTAGGAGTACTATCAATCTTAC 59.612 40.741 13.65 0.00 42.53 2.34
269 270 2.036346 GCCATCCAACAAAGCTTCAGTT 59.964 45.455 0.00 5.36 0.00 3.16
328 329 1.672854 CCATCGCCGTTAGTCTCCCA 61.673 60.000 0.00 0.00 0.00 4.37
396 402 2.489938 ACCCTCGCTGCAGATTAAAA 57.510 45.000 20.43 0.00 0.00 1.52
397 403 2.790433 ACCCTCGCTGCAGATTAAAAA 58.210 42.857 20.43 0.00 0.00 1.94
433 443 2.583441 CCCGCACCTGACTCTCCAA 61.583 63.158 0.00 0.00 0.00 3.53
635 1053 0.039074 CCTATCCAGGCGACGCTTAG 60.039 60.000 20.77 5.25 34.35 2.18
862 1283 2.639347 TGCTCTTCCCAAGATCAACTCA 59.361 45.455 0.00 0.00 36.82 3.41
960 1383 1.555967 GGCTCAACCTCTCTCTCTGT 58.444 55.000 0.00 0.00 34.51 3.41
1119 1679 5.011840 TGGCAGTGAATCAAAAATCAATGGA 59.988 36.000 0.00 0.00 40.81 3.41
1128 1688 9.649167 GAATCAAAAATCAATGGAGATTCAACT 57.351 29.630 0.00 0.00 39.53 3.16
1327 1902 7.013274 TGTTTGACTGTTTTGAGAAGAATAGGG 59.987 37.037 0.00 0.00 0.00 3.53
1347 1922 2.159057 GGGTGGCCATTTGATCATCAAC 60.159 50.000 9.72 0.00 35.89 3.18
1537 2112 6.846505 AGATGAGGAGGACCAATACTCAATTA 59.153 38.462 0.00 0.00 41.03 1.40
2038 3719 7.766219 ATAGCATACTTAAACAAGTACCACG 57.234 36.000 0.00 0.00 38.01 4.94
2091 3772 5.892348 ACCTCCTCAAAAGTGGATTATGTT 58.108 37.500 0.00 0.00 0.00 2.71
2106 3787 9.816354 GTGGATTATGTTACAAATAATTTGGCT 57.184 29.630 0.00 0.00 44.81 4.75
2317 3999 9.939802 TTGAATATGAGAGAATAGATGACATGG 57.060 33.333 0.00 0.00 0.00 3.66
2881 4565 6.712547 ACTCATGTAGGGACAAAAGAAAGAAG 59.287 38.462 0.00 0.00 39.59 2.85
2910 4596 8.303876 ACCCATTACAAAAGCTATTTGTACAAG 58.696 33.333 22.63 17.39 42.49 3.16
2911 4597 8.303876 CCCATTACAAAAGCTATTTGTACAAGT 58.696 33.333 22.63 8.67 42.49 3.16
2912 4598 9.128107 CCATTACAAAAGCTATTTGTACAAGTG 57.872 33.333 22.63 18.94 42.49 3.16
2913 4599 9.891828 CATTACAAAAGCTATTTGTACAAGTGA 57.108 29.630 22.63 13.72 42.49 3.41
2957 4652 7.732025 TCTACTTCTGTGTCCAAGTGAAAATA 58.268 34.615 0.00 0.00 34.60 1.40
3102 4817 9.811995 TTATATTCTGTGAGTGTACCATTGTAC 57.188 33.333 0.13 0.13 46.22 2.90
3196 4911 0.459489 AAGAAGAGAGCTGCGCCTAG 59.541 55.000 4.18 0.00 0.00 3.02
3461 5179 9.113838 CTTGAGTATATTACTTTGTTGCTGGAT 57.886 33.333 0.00 0.00 39.59 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.065925 GGACAAAGGCTCTACATGAATGC 59.934 47.826 0.00 0.00 0.00 3.56
2 3 4.521146 AGGACAAAGGCTCTACATGAATG 58.479 43.478 0.00 0.00 0.00 2.67
3 4 4.851639 AGGACAAAGGCTCTACATGAAT 57.148 40.909 0.00 0.00 0.00 2.57
4 5 5.957771 ATAGGACAAAGGCTCTACATGAA 57.042 39.130 0.00 0.00 0.00 2.57
5 6 6.136857 ACTATAGGACAAAGGCTCTACATGA 58.863 40.000 0.00 0.00 0.00 3.07
6 7 6.412362 ACTATAGGACAAAGGCTCTACATG 57.588 41.667 4.43 0.00 0.00 3.21
7 8 6.841755 AGAACTATAGGACAAAGGCTCTACAT 59.158 38.462 4.43 0.00 0.00 2.29
8 9 6.195700 AGAACTATAGGACAAAGGCTCTACA 58.804 40.000 4.43 0.00 0.00 2.74
9 10 6.718522 AGAACTATAGGACAAAGGCTCTAC 57.281 41.667 4.43 0.00 0.00 2.59
10 11 9.080097 GATTAGAACTATAGGACAAAGGCTCTA 57.920 37.037 4.43 0.00 0.00 2.43
11 12 7.787424 AGATTAGAACTATAGGACAAAGGCTCT 59.213 37.037 4.43 0.00 0.00 4.09
12 13 7.958088 AGATTAGAACTATAGGACAAAGGCTC 58.042 38.462 4.43 0.00 0.00 4.70
13 14 7.922699 AGATTAGAACTATAGGACAAAGGCT 57.077 36.000 4.43 0.00 0.00 4.58
14 15 8.639761 TGTAGATTAGAACTATAGGACAAAGGC 58.360 37.037 4.43 0.00 0.00 4.35
19 20 9.877222 TGGATTGTAGATTAGAACTATAGGACA 57.123 33.333 4.43 0.00 0.00 4.02
52 53 9.974980 GGAAACATAACCTTGTTTTTCTTATGA 57.025 29.630 4.28 0.00 46.84 2.15
53 54 9.757227 TGGAAACATAACCTTGTTTTTCTTATG 57.243 29.630 4.28 0.00 46.84 1.90
54 55 9.758651 GTGGAAACATAACCTTGTTTTTCTTAT 57.241 29.630 4.28 0.00 46.84 1.73
55 56 8.973182 AGTGGAAACATAACCTTGTTTTTCTTA 58.027 29.630 4.28 0.00 46.84 2.10
56 57 7.847096 AGTGGAAACATAACCTTGTTTTTCTT 58.153 30.769 4.28 0.00 46.84 2.52
57 58 7.418337 AGTGGAAACATAACCTTGTTTTTCT 57.582 32.000 4.28 2.02 46.84 2.52
58 59 8.487313 AAAGTGGAAACATAACCTTGTTTTTC 57.513 30.769 4.28 2.13 46.84 2.29
59 60 9.594478 CTAAAGTGGAAACATAACCTTGTTTTT 57.406 29.630 4.28 0.00 46.84 1.94
60 61 8.973182 TCTAAAGTGGAAACATAACCTTGTTTT 58.027 29.630 4.28 0.00 46.84 2.43
62 63 8.528044 TTCTAAAGTGGAAACATAACCTTGTT 57.472 30.769 0.00 0.00 46.14 2.83
63 64 8.528044 TTTCTAAAGTGGAAACATAACCTTGT 57.472 30.769 0.00 0.00 46.14 3.16
64 65 9.981114 ATTTTCTAAAGTGGAAACATAACCTTG 57.019 29.630 0.00 0.00 46.14 3.61
66 67 9.588096 AGATTTTCTAAAGTGGAAACATAACCT 57.412 29.630 0.00 0.00 46.14 3.50
67 68 9.841880 GAGATTTTCTAAAGTGGAAACATAACC 57.158 33.333 0.00 0.00 46.14 2.85
68 69 9.841880 GGAGATTTTCTAAAGTGGAAACATAAC 57.158 33.333 0.00 0.00 46.14 1.89
69 70 9.581289 TGGAGATTTTCTAAAGTGGAAACATAA 57.419 29.630 0.00 0.00 46.14 1.90
70 71 9.581289 TTGGAGATTTTCTAAAGTGGAAACATA 57.419 29.630 0.00 0.00 46.14 2.29
71 72 8.477419 TTGGAGATTTTCTAAAGTGGAAACAT 57.523 30.769 0.00 0.00 46.14 2.71
72 73 7.889873 TTGGAGATTTTCTAAAGTGGAAACA 57.110 32.000 0.00 0.00 33.22 2.83
73 74 8.360390 ACATTGGAGATTTTCTAAAGTGGAAAC 58.640 33.333 0.00 0.00 33.22 2.78
74 75 8.477419 ACATTGGAGATTTTCTAAAGTGGAAA 57.523 30.769 0.00 0.00 28.78 3.13
75 76 9.231297 CTACATTGGAGATTTTCTAAAGTGGAA 57.769 33.333 0.00 0.00 31.33 3.53
76 77 8.602424 TCTACATTGGAGATTTTCTAAAGTGGA 58.398 33.333 0.00 0.00 34.70 4.02
77 78 8.792830 TCTACATTGGAGATTTTCTAAAGTGG 57.207 34.615 0.00 0.00 31.81 4.00
86 87 9.190317 GGTTTCCTAATCTACATTGGAGATTTT 57.810 33.333 25.40 9.29 40.04 1.82
87 88 8.560903 AGGTTTCCTAATCTACATTGGAGATTT 58.439 33.333 25.40 12.33 40.04 2.17
88 89 7.995488 CAGGTTTCCTAATCTACATTGGAGATT 59.005 37.037 24.07 24.07 44.13 2.40
89 90 7.348274 TCAGGTTTCCTAATCTACATTGGAGAT 59.652 37.037 5.50 5.50 35.08 2.75
90 91 6.672218 TCAGGTTTCCTAATCTACATTGGAGA 59.328 38.462 0.00 0.00 29.64 3.71
91 92 6.889198 TCAGGTTTCCTAATCTACATTGGAG 58.111 40.000 0.00 0.00 29.64 3.86
92 93 6.884472 TCAGGTTTCCTAATCTACATTGGA 57.116 37.500 0.00 0.00 29.64 3.53
93 94 7.995488 AGAATCAGGTTTCCTAATCTACATTGG 59.005 37.037 0.00 0.00 29.64 3.16
94 95 8.970859 AGAATCAGGTTTCCTAATCTACATTG 57.029 34.615 0.00 0.00 29.64 2.82
97 98 8.204836 GCTTAGAATCAGGTTTCCTAATCTACA 58.795 37.037 0.00 0.00 29.64 2.74
98 99 8.204836 TGCTTAGAATCAGGTTTCCTAATCTAC 58.795 37.037 0.00 0.00 29.64 2.59
99 100 8.319057 TGCTTAGAATCAGGTTTCCTAATCTA 57.681 34.615 0.00 0.00 29.64 1.98
100 101 7.200434 TGCTTAGAATCAGGTTTCCTAATCT 57.800 36.000 0.00 0.00 29.64 2.40
101 102 6.484977 CCTGCTTAGAATCAGGTTTCCTAATC 59.515 42.308 4.31 0.00 43.66 1.75
102 103 6.360618 CCTGCTTAGAATCAGGTTTCCTAAT 58.639 40.000 4.31 0.00 43.66 1.73
103 104 5.745227 CCTGCTTAGAATCAGGTTTCCTAA 58.255 41.667 4.31 0.00 43.66 2.69
104 105 5.359194 CCTGCTTAGAATCAGGTTTCCTA 57.641 43.478 4.31 0.00 43.66 2.94
105 106 4.227864 CCTGCTTAGAATCAGGTTTCCT 57.772 45.455 4.31 0.00 43.66 3.36
112 113 6.111382 TCTCAAATGACCTGCTTAGAATCAG 58.889 40.000 0.00 0.00 0.00 2.90
113 114 6.053632 TCTCAAATGACCTGCTTAGAATCA 57.946 37.500 0.00 0.00 0.00 2.57
114 115 6.597280 ACTTCTCAAATGACCTGCTTAGAATC 59.403 38.462 0.00 0.00 0.00 2.52
115 116 6.373774 CACTTCTCAAATGACCTGCTTAGAAT 59.626 38.462 0.00 0.00 0.00 2.40
116 117 5.702670 CACTTCTCAAATGACCTGCTTAGAA 59.297 40.000 0.00 0.00 0.00 2.10
117 118 5.240891 CACTTCTCAAATGACCTGCTTAGA 58.759 41.667 0.00 0.00 0.00 2.10
118 119 4.394300 CCACTTCTCAAATGACCTGCTTAG 59.606 45.833 0.00 0.00 0.00 2.18
119 120 4.041567 TCCACTTCTCAAATGACCTGCTTA 59.958 41.667 0.00 0.00 0.00 3.09
120 121 3.152341 CCACTTCTCAAATGACCTGCTT 58.848 45.455 0.00 0.00 0.00 3.91
121 122 2.373169 TCCACTTCTCAAATGACCTGCT 59.627 45.455 0.00 0.00 0.00 4.24
122 123 2.485814 GTCCACTTCTCAAATGACCTGC 59.514 50.000 0.00 0.00 0.00 4.85
123 124 3.499918 GTGTCCACTTCTCAAATGACCTG 59.500 47.826 0.00 0.00 0.00 4.00
124 125 3.392616 AGTGTCCACTTCTCAAATGACCT 59.607 43.478 0.00 0.00 38.83 3.85
125 126 3.499918 CAGTGTCCACTTCTCAAATGACC 59.500 47.826 0.00 0.00 40.20 4.02
126 127 4.380531 TCAGTGTCCACTTCTCAAATGAC 58.619 43.478 0.00 0.00 40.20 3.06
127 128 4.687901 TCAGTGTCCACTTCTCAAATGA 57.312 40.909 0.00 0.00 40.20 2.57
128 129 6.427853 TGTTATCAGTGTCCACTTCTCAAATG 59.572 38.462 0.00 0.00 40.20 2.32
129 130 6.533730 TGTTATCAGTGTCCACTTCTCAAAT 58.466 36.000 0.00 0.00 40.20 2.32
130 131 5.924356 TGTTATCAGTGTCCACTTCTCAAA 58.076 37.500 0.00 0.00 40.20 2.69
131 132 5.545063 TGTTATCAGTGTCCACTTCTCAA 57.455 39.130 0.00 0.00 40.20 3.02
132 133 5.245977 TGATGTTATCAGTGTCCACTTCTCA 59.754 40.000 0.00 0.00 40.20 3.27
133 134 5.724328 TGATGTTATCAGTGTCCACTTCTC 58.276 41.667 0.00 0.00 40.20 2.87
134 135 5.745312 TGATGTTATCAGTGTCCACTTCT 57.255 39.130 0.00 0.00 40.20 2.85
135 136 5.877012 ACATGATGTTATCAGTGTCCACTTC 59.123 40.000 0.00 0.00 43.53 3.01
136 137 5.809001 ACATGATGTTATCAGTGTCCACTT 58.191 37.500 0.00 0.00 43.53 3.16
137 138 5.046376 TGACATGATGTTATCAGTGTCCACT 60.046 40.000 19.56 0.00 43.53 4.00
138 139 5.178061 TGACATGATGTTATCAGTGTCCAC 58.822 41.667 19.56 0.00 43.53 4.02
139 140 5.419239 TGACATGATGTTATCAGTGTCCA 57.581 39.130 19.56 11.92 43.53 4.02
140 141 5.277683 GCATGACATGATGTTATCAGTGTCC 60.278 44.000 19.76 9.77 43.53 4.02
141 142 5.526479 AGCATGACATGATGTTATCAGTGTC 59.474 40.000 19.76 17.62 43.53 3.67
142 143 5.434408 AGCATGACATGATGTTATCAGTGT 58.566 37.500 19.76 0.00 43.53 3.55
143 144 6.373186 AAGCATGACATGATGTTATCAGTG 57.627 37.500 19.76 0.00 43.53 3.66
144 145 7.503549 TCTAAGCATGACATGATGTTATCAGT 58.496 34.615 19.76 0.00 43.53 3.41
145 146 7.958053 TCTAAGCATGACATGATGTTATCAG 57.042 36.000 19.76 4.84 43.53 2.90
146 147 8.913487 ATTCTAAGCATGACATGATGTTATCA 57.087 30.769 19.76 0.00 44.55 2.15
147 148 8.996271 TGATTCTAAGCATGACATGATGTTATC 58.004 33.333 19.76 13.41 0.00 1.75
148 149 8.913487 TGATTCTAAGCATGACATGATGTTAT 57.087 30.769 19.76 0.00 0.00 1.89
149 150 8.735692 TTGATTCTAAGCATGACATGATGTTA 57.264 30.769 19.76 11.25 0.00 2.41
150 151 7.634671 TTGATTCTAAGCATGACATGATGTT 57.365 32.000 19.76 10.73 0.00 2.71
151 152 7.260558 CTTGATTCTAAGCATGACATGATGT 57.739 36.000 19.76 0.00 0.00 3.06
164 165 5.508200 ACTCCTACGAGCTTGATTCTAAG 57.492 43.478 8.31 0.10 40.03 2.18
165 166 6.120905 AGTACTCCTACGAGCTTGATTCTAA 58.879 40.000 8.31 0.00 40.03 2.10
166 167 5.682659 AGTACTCCTACGAGCTTGATTCTA 58.317 41.667 8.31 0.00 40.03 2.10
167 168 4.528920 AGTACTCCTACGAGCTTGATTCT 58.471 43.478 8.31 0.00 40.03 2.40
168 169 4.904253 AGTACTCCTACGAGCTTGATTC 57.096 45.455 8.31 0.00 40.03 2.52
169 170 6.062749 TGATAGTACTCCTACGAGCTTGATT 58.937 40.000 8.31 0.00 40.03 2.57
170 171 5.622180 TGATAGTACTCCTACGAGCTTGAT 58.378 41.667 8.31 0.00 40.03 2.57
171 172 5.032327 TGATAGTACTCCTACGAGCTTGA 57.968 43.478 8.31 0.00 40.03 3.02
172 173 5.752892 TTGATAGTACTCCTACGAGCTTG 57.247 43.478 0.00 0.00 40.03 4.01
173 174 6.300703 AGATTGATAGTACTCCTACGAGCTT 58.699 40.000 0.00 0.00 40.03 3.74
174 175 5.871834 AGATTGATAGTACTCCTACGAGCT 58.128 41.667 0.00 0.00 40.03 4.09
175 176 6.563222 AAGATTGATAGTACTCCTACGAGC 57.437 41.667 0.00 0.00 40.03 5.03
176 177 7.598118 TCGTAAGATTGATAGTACTCCTACGAG 59.402 40.741 0.00 0.00 45.01 4.18
177 178 7.436933 TCGTAAGATTGATAGTACTCCTACGA 58.563 38.462 0.00 3.09 45.01 3.43
178 179 7.649370 TCGTAAGATTGATAGTACTCCTACG 57.351 40.000 0.00 0.57 45.01 3.51
195 196 8.255206 TGGTATAGAAGCAATTTTCTCGTAAGA 58.745 33.333 0.00 0.00 38.35 2.10
196 197 8.420374 TGGTATAGAAGCAATTTTCTCGTAAG 57.580 34.615 0.00 0.00 38.35 2.34
200 201 6.420903 TCGATGGTATAGAAGCAATTTTCTCG 59.579 38.462 0.00 0.00 39.48 4.04
328 329 7.054124 TGACAAGAAAACAGAGACTTGGTAAT 58.946 34.615 0.00 0.00 42.39 1.89
433 443 1.299926 GTGCGTTGAGTCGTGGTCT 60.300 57.895 0.00 0.00 0.00 3.85
798 1219 3.358076 CTCTCCACCTCGCCGGAAC 62.358 68.421 5.05 0.00 36.31 3.62
832 1253 2.792947 GGGAAGAGCATCGGCCGTA 61.793 63.158 27.15 12.70 42.67 4.02
960 1383 6.540914 CCCGAGAAATTACCTAGCACAAATAA 59.459 38.462 0.00 0.00 0.00 1.40
1128 1688 6.252995 ACCCTCAATAATCTGCCAACTAAAA 58.747 36.000 0.00 0.00 0.00 1.52
1327 1902 2.762327 AGTTGATGATCAAATGGCCACC 59.238 45.455 8.16 0.00 38.22 4.61
1537 2112 1.623811 ACTATCGGAACCAACACTGCT 59.376 47.619 0.00 0.00 0.00 4.24
2091 3772 7.946207 TGAAACACTCAGCCAAATTATTTGTA 58.054 30.769 15.40 0.00 38.98 2.41
2106 3787 3.882888 GGATCCAGTTGTTGAAACACTCA 59.117 43.478 6.95 0.00 38.92 3.41
2317 3999 2.799412 CACTCTCACTCACTTCTGCAAC 59.201 50.000 0.00 0.00 0.00 4.17
2863 4547 5.831525 GGGTTTCTTCTTTCTTTTGTCCCTA 59.168 40.000 0.00 0.00 0.00 3.53
2881 4565 9.135843 GTACAAATAGCTTTTGTAATGGGTTTC 57.864 33.333 23.62 12.69 43.77 2.78
2957 4652 5.611374 TGAAAGTAGAGCTAGTGCAGTTTT 58.389 37.500 0.00 0.00 42.74 2.43


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

AutoCloner maintained by Alex Coulton.