Multiple sequence alignment - TraesCS2D01G501200

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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 TraesCS2D01G501200 chr2D 100.000 6360 0 0 1 6360 595506306 595512665 0.000000e+00 11745.0
1 TraesCS2D01G501200 chr2D 82.076 1869 274 42 3562 5386 595430310 595432161 0.000000e+00 1539.0
2 TraesCS2D01G501200 chr2D 80.865 1850 249 49 3563 5366 595438101 595439891 0.000000e+00 1358.0
3 TraesCS2D01G501200 chr2D 82.781 1539 214 24 2029 3558 595428744 595430240 0.000000e+00 1327.0
4 TraesCS2D01G501200 chr2D 84.327 1225 162 15 2341 3558 595436829 595438030 0.000000e+00 1171.0
5 TraesCS2D01G501200 chr2D 78.219 932 181 16 2362 3287 594833522 594834437 1.540000e-160 577.0
6 TraesCS2D01G501200 chr2D 89.197 361 33 5 1596 1956 595428374 595428728 4.520000e-121 446.0
7 TraesCS2D01G501200 chr2D 95.431 197 3 2 1 192 43781740 43781935 6.190000e-80 309.0
8 TraesCS2D01G501200 chr2D 86.574 216 20 5 1197 1405 595427937 595428150 4.960000e-56 230.0
9 TraesCS2D01G501200 chr2D 75.974 308 55 7 5077 5365 597631243 597631550 2.390000e-29 141.0
10 TraesCS2D01G501200 chr2B 97.500 4680 86 14 726 5390 723428138 723432801 0.000000e+00 7965.0
11 TraesCS2D01G501200 chr2B 80.401 1847 270 31 3563 5386 723134009 723135786 0.000000e+00 1321.0
12 TraesCS2D01G501200 chr2B 80.011 1851 266 48 3563 5366 723332312 723334105 0.000000e+00 1273.0
13 TraesCS2D01G501200 chr2B 84.000 1225 166 17 2341 3558 723331040 723332241 0.000000e+00 1149.0
14 TraesCS2D01G501200 chr2B 80.637 1539 237 32 2029 3558 723132452 723133938 0.000000e+00 1134.0
15 TraesCS2D01G501200 chr2B 83.591 1164 178 9 2401 3558 723298335 723299491 0.000000e+00 1079.0
16 TraesCS2D01G501200 chr2B 82.368 1157 179 13 4248 5386 723301707 723302856 0.000000e+00 983.0
17 TraesCS2D01G501200 chr2B 95.208 480 17 3 193 671 723427655 723428129 0.000000e+00 754.0
18 TraesCS2D01G501200 chr2B 76.309 1165 201 37 4256 5386 122266654 122265531 2.590000e-153 553.0
19 TraesCS2D01G501200 chr2B 80.027 731 104 32 3563 4265 723299562 723300278 2.650000e-138 503.0
20 TraesCS2D01G501200 chr2B 84.746 295 45 0 1664 1958 723132135 723132429 4.820000e-76 296.0
21 TraesCS2D01G501200 chr2B 86.777 242 32 0 1596 1837 723266390 723266631 2.920000e-68 270.0
22 TraesCS2D01G501200 chr2B 86.294 197 21 6 1213 1405 723265972 723266166 6.460000e-50 209.0
23 TraesCS2D01G501200 chr2B 75.325 308 57 7 5077 5365 726226737 726227044 5.170000e-26 130.0
24 TraesCS2D01G501200 chr2A 97.333 1800 46 2 3593 5390 729569369 729571168 0.000000e+00 3057.0
25 TraesCS2D01G501200 chr2A 94.821 1506 48 12 679 2171 729566595 729568083 0.000000e+00 2322.0
26 TraesCS2D01G501200 chr2A 97.022 1276 20 5 2170 3445 729568121 729569378 0.000000e+00 2130.0
27 TraesCS2D01G501200 chr2A 87.288 1888 196 16 3535 5390 727611360 727613235 0.000000e+00 2117.0
28 TraesCS2D01G501200 chr2A 86.753 1940 188 31 1644 3580 727609484 727611357 0.000000e+00 2095.0
29 TraesCS2D01G501200 chr2A 82.834 1870 248 34 3563 5386 729561394 729563236 0.000000e+00 1607.0
30 TraesCS2D01G501200 chr2A 80.574 1848 267 32 3562 5386 729532044 729533822 0.000000e+00 1339.0
31 TraesCS2D01G501200 chr2A 84.336 1213 160 15 2341 3546 729560122 729561311 0.000000e+00 1160.0
32 TraesCS2D01G501200 chr2A 80.132 1520 229 32 2029 3539 729530500 729531955 0.000000e+00 1066.0
33 TraesCS2D01G501200 chr2A 82.500 960 140 12 4448 5386 729527437 729528389 0.000000e+00 817.0
34 TraesCS2D01G501200 chr2A 94.104 424 16 4 193 610 729566183 729566603 2.500000e-178 636.0
35 TraesCS2D01G501200 chr2A 85.522 297 43 0 1664 1960 729530183 729530479 1.720000e-80 311.0
36 TraesCS2D01G501200 chr2A 75.974 308 55 7 5077 5365 732281002 732280695 2.390000e-29 141.0
37 TraesCS2D01G501200 chr6D 98.966 967 9 1 5395 6360 446752197 446753163 0.000000e+00 1729.0
38 TraesCS2D01G501200 chr6D 98.567 977 12 2 5385 6360 452381412 452382387 0.000000e+00 1725.0
39 TraesCS2D01G501200 chr6D 98.656 967 12 1 5395 6360 14527325 14526359 0.000000e+00 1712.0
40 TraesCS2D01G501200 chr4D 98.966 967 9 1 5395 6360 112198909 112199875 0.000000e+00 1729.0
41 TraesCS2D01G501200 chr4D 98.759 967 11 1 5395 6360 455012012 455011046 0.000000e+00 1718.0
42 TraesCS2D01G501200 chr7D 98.762 969 10 2 5393 6360 585326505 585327472 0.000000e+00 1722.0
43 TraesCS2D01G501200 chr7D 98.759 967 11 1 5395 6360 8272611 8271645 0.000000e+00 1718.0
44 TraesCS2D01G501200 chr7D 98.656 967 11 2 5395 6360 12136129 12137094 0.000000e+00 1712.0
45 TraesCS2D01G501200 chr7D 97.436 195 4 1 1 195 613372462 613372269 1.320000e-86 331.0
46 TraesCS2D01G501200 chr7D 94.330 194 9 2 1 193 57789199 57789391 4.820000e-76 296.0
47 TraesCS2D01G501200 chr1D 98.657 968 11 2 5395 6360 494034026 494034993 0.000000e+00 1714.0
48 TraesCS2D01G501200 chr3D 97.409 193 4 1 1 193 9071923 9072114 1.710000e-85 327.0
49 TraesCS2D01G501200 chr3D 97.409 193 4 1 1 193 602821634 602821443 1.710000e-85 327.0
50 TraesCS2D01G501200 chr3D 96.891 193 5 1 1 193 143151945 143151754 7.950000e-84 322.0
51 TraesCS2D01G501200 chr5D 96.373 193 6 1 1 193 435681929 435682120 3.700000e-82 316.0
52 TraesCS2D01G501200 chr5B 94.211 190 8 3 7 195 110044088 110043901 2.900000e-73 287.0
53 TraesCS2D01G501200 chr5B 92.821 195 11 3 2 195 109902141 109901949 4.860000e-71 279.0
54 TraesCS2D01G501200 chrUn 88.732 71 7 1 4679 4749 31527557 31527488 1.140000e-12 86.1


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 TraesCS2D01G501200 chr2D 595506306 595512665 6359 False 11745.000000 11745 100.000000 1 6360 1 chr2D.!!$F3 6359
1 TraesCS2D01G501200 chr2D 595436829 595439891 3062 False 1264.500000 1358 82.596000 2341 5366 2 chr2D.!!$F6 3025
2 TraesCS2D01G501200 chr2D 595427937 595432161 4224 False 885.500000 1539 85.157000 1197 5386 4 chr2D.!!$F5 4189
3 TraesCS2D01G501200 chr2D 594833522 594834437 915 False 577.000000 577 78.219000 2362 3287 1 chr2D.!!$F2 925
4 TraesCS2D01G501200 chr2B 723427655 723432801 5146 False 4359.500000 7965 96.354000 193 5390 2 chr2B.!!$F6 5197
5 TraesCS2D01G501200 chr2B 723331040 723334105 3065 False 1211.000000 1273 82.005500 2341 5366 2 chr2B.!!$F5 3025
6 TraesCS2D01G501200 chr2B 723132135 723135786 3651 False 917.000000 1321 81.928000 1664 5386 3 chr2B.!!$F2 3722
7 TraesCS2D01G501200 chr2B 723298335 723302856 4521 False 855.000000 1079 81.995333 2401 5386 3 chr2B.!!$F4 2985
8 TraesCS2D01G501200 chr2B 122265531 122266654 1123 True 553.000000 553 76.309000 4256 5386 1 chr2B.!!$R1 1130
9 TraesCS2D01G501200 chr2B 723265972 723266631 659 False 239.500000 270 86.535500 1213 1837 2 chr2B.!!$F3 624
10 TraesCS2D01G501200 chr2A 727609484 727613235 3751 False 2106.000000 2117 87.020500 1644 5390 2 chr2A.!!$F1 3746
11 TraesCS2D01G501200 chr2A 729560122 729571168 11046 False 1818.666667 3057 91.741667 193 5390 6 chr2A.!!$F3 5197
12 TraesCS2D01G501200 chr2A 729527437 729533822 6385 False 883.250000 1339 82.182000 1664 5386 4 chr2A.!!$F2 3722
13 TraesCS2D01G501200 chr6D 446752197 446753163 966 False 1729.000000 1729 98.966000 5395 6360 1 chr6D.!!$F1 965
14 TraesCS2D01G501200 chr6D 452381412 452382387 975 False 1725.000000 1725 98.567000 5385 6360 1 chr6D.!!$F2 975
15 TraesCS2D01G501200 chr6D 14526359 14527325 966 True 1712.000000 1712 98.656000 5395 6360 1 chr6D.!!$R1 965
16 TraesCS2D01G501200 chr4D 112198909 112199875 966 False 1729.000000 1729 98.966000 5395 6360 1 chr4D.!!$F1 965
17 TraesCS2D01G501200 chr4D 455011046 455012012 966 True 1718.000000 1718 98.759000 5395 6360 1 chr4D.!!$R1 965
18 TraesCS2D01G501200 chr7D 585326505 585327472 967 False 1722.000000 1722 98.762000 5393 6360 1 chr7D.!!$F3 967
19 TraesCS2D01G501200 chr7D 8271645 8272611 966 True 1718.000000 1718 98.759000 5395 6360 1 chr7D.!!$R1 965
20 TraesCS2D01G501200 chr7D 12136129 12137094 965 False 1712.000000 1712 98.656000 5395 6360 1 chr7D.!!$F1 965
21 TraesCS2D01G501200 chr1D 494034026 494034993 967 False 1714.000000 1714 98.657000 5395 6360 1 chr1D.!!$F1 965

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
720 722 0.035739 TACCTTTCGGGCACTGGTTC 59.964 55.0 0.0 0.0 39.10 3.62 F
1287 1306 0.108615 CGCTGGGAGTTCGAAGACAT 60.109 55.0 0.0 0.0 34.32 3.06 F
2720 11985 0.030101 CCGGTTCGTGCAATTGTGTT 59.970 50.0 7.4 0.0 0.00 3.32 F
4052 13414 1.032657 CACGAGGAGATGGAGGACGT 61.033 60.0 0.0 0.0 0.00 4.34 F
4764 15609 2.171237 TGTCTGGTGGCATATTGGAGAG 59.829 50.0 0.0 0.0 0.00 3.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1594 1613 0.028110 GCTTCGAATTCCGGCATGAC 59.972 55.000 0.00 0.0 39.14 3.06 R
2887 12152 0.260816 ATAGTGGCCTGGACCGACTA 59.739 55.000 3.32 0.0 31.99 2.59 R
4708 15553 1.070601 GGGCCAGTCAAGTGCAAAAAT 59.929 47.619 4.39 0.0 0.00 1.82 R
4963 15808 1.588674 CCTTTACAACACGAGCACCA 58.411 50.000 0.00 0.0 0.00 4.17 R
6133 16987 7.362487 CCATGGCACTATGTATAACAAACAACA 60.362 37.037 0.00 0.0 0.00 3.33 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
17 18 3.621520 GTCGACGCTTCGGTTTGT 58.378 55.556 13.04 0.00 45.90 2.83
19 20 2.127758 CGACGCTTCGGTTTGTGC 60.128 61.111 4.41 0.00 41.89 4.57
22 23 2.326550 CGCTTCGGTTTGTGCGTT 59.673 55.556 0.00 0.00 42.93 4.84
23 24 2.003443 CGCTTCGGTTTGTGCGTTG 61.003 57.895 0.00 0.00 42.93 4.10
24 25 1.657181 GCTTCGGTTTGTGCGTTGG 60.657 57.895 0.00 0.00 0.00 3.77
26 27 0.041312 CTTCGGTTTGTGCGTTGGAG 60.041 55.000 0.00 0.00 0.00 3.86
28 29 2.903547 CGGTTTGTGCGTTGGAGGG 61.904 63.158 0.00 0.00 0.00 4.30
30 31 1.652563 GTTTGTGCGTTGGAGGGAC 59.347 57.895 0.00 0.00 0.00 4.46
32 33 3.818121 TTGTGCGTTGGAGGGACGG 62.818 63.158 0.00 0.00 40.66 4.79
46 47 4.903010 ACGGGCGCTTCACACGTT 62.903 61.111 7.64 0.00 33.54 3.99
47 48 4.072088 CGGGCGCTTCACACGTTC 62.072 66.667 7.64 0.00 0.00 3.95
48 49 4.072088 GGGCGCTTCACACGTTCG 62.072 66.667 7.64 0.00 0.00 3.95
49 50 3.335534 GGCGCTTCACACGTTCGT 61.336 61.111 7.64 0.00 0.00 3.85
51 52 2.844146 CGCTTCACACGTTCGTCC 59.156 61.111 0.00 0.00 0.00 4.79
52 53 1.947146 CGCTTCACACGTTCGTCCA 60.947 57.895 0.00 0.00 0.00 4.02
53 54 1.853319 GCTTCACACGTTCGTCCAG 59.147 57.895 0.00 0.00 0.00 3.86
56 57 2.198406 CTTCACACGTTCGTCCAGAAA 58.802 47.619 0.00 0.00 41.10 2.52
58 59 2.619147 TCACACGTTCGTCCAGAAAAA 58.381 42.857 0.00 0.00 41.10 1.94
80 81 6.500684 AAAAGAAAATCAGATAAGCGCTCA 57.499 33.333 12.06 0.00 0.00 4.26
82 83 6.500684 AAGAAAATCAGATAAGCGCTCAAA 57.499 33.333 12.06 0.00 0.00 2.69
84 85 7.792374 AGAAAATCAGATAAGCGCTCAAATA 57.208 32.000 12.06 0.00 0.00 1.40
85 86 7.859598 AGAAAATCAGATAAGCGCTCAAATAG 58.140 34.615 12.06 0.00 0.00 1.73
94 95 1.011794 GCTCAAATAGCGCTCGTGC 60.012 57.895 16.34 10.21 42.53 5.34
110 111 2.050077 GCGTTTGCAAGCCCAGTC 60.050 61.111 7.78 0.00 42.15 3.51
111 112 2.252260 CGTTTGCAAGCCCAGTCG 59.748 61.111 7.78 0.00 0.00 4.18
112 113 2.050077 GTTTGCAAGCCCAGTCGC 60.050 61.111 1.15 0.00 0.00 5.19
113 114 2.203337 TTTGCAAGCCCAGTCGCT 60.203 55.556 0.00 0.00 42.22 4.93
119 120 2.663196 AGCCCAGTCGCTTACACC 59.337 61.111 0.00 0.00 34.73 4.16
122 123 2.654877 CCAGTCGCTTACACCGGT 59.345 61.111 0.00 0.00 0.00 5.28
123 124 1.736645 CCAGTCGCTTACACCGGTG 60.737 63.158 32.83 32.83 0.00 4.94
124 125 2.048503 AGTCGCTTACACCGGTGC 60.049 61.111 34.26 19.39 0.00 5.01
125 126 2.048503 GTCGCTTACACCGGTGCT 60.049 61.111 34.26 22.43 0.00 4.40
128 129 2.388232 CGCTTACACCGGTGCTTCC 61.388 63.158 34.26 18.61 0.00 3.46
129 130 2.038837 GCTTACACCGGTGCTTCCC 61.039 63.158 34.26 15.08 0.00 3.97
131 132 2.814913 CTTACACCGGTGCTTCCCCC 62.815 65.000 34.26 0.00 0.00 5.40
132 133 3.857521 TACACCGGTGCTTCCCCCT 62.858 63.158 34.26 14.75 0.00 4.79
135 136 1.848895 ACCGGTGCTTCCCCCTAAA 60.849 57.895 6.12 0.00 0.00 1.85
136 137 1.212250 ACCGGTGCTTCCCCCTAAAT 61.212 55.000 6.12 0.00 0.00 1.40
138 139 1.213430 CCGGTGCTTCCCCCTAAATTA 59.787 52.381 0.00 0.00 0.00 1.40
139 140 2.357361 CCGGTGCTTCCCCCTAAATTAA 60.357 50.000 0.00 0.00 0.00 1.40
141 142 3.958147 CGGTGCTTCCCCCTAAATTAATT 59.042 43.478 0.00 0.00 0.00 1.40
146 147 7.311046 GGTGCTTCCCCCTAAATTAATTTTCTT 60.311 37.037 18.14 0.00 0.00 2.52
148 149 8.664992 TGCTTCCCCCTAAATTAATTTTCTTTT 58.335 29.630 18.14 0.00 0.00 2.27
149 150 9.515226 GCTTCCCCCTAAATTAATTTTCTTTTT 57.485 29.630 18.14 0.00 0.00 1.94
159 160 8.912112 AATTAATTTTCTTTTTAACGCAAGCG 57.088 26.923 13.50 13.50 46.03 4.68
170 171 2.930168 CGCAAGCGTCCAAATAAGC 58.070 52.632 6.25 0.00 34.35 3.09
171 172 0.857311 CGCAAGCGTCCAAATAAGCG 60.857 55.000 6.25 0.00 37.91 4.68
174 175 2.407616 GCGTCCAAATAAGCGCCC 59.592 61.111 2.29 0.00 43.52 6.13
175 176 2.707039 CGTCCAAATAAGCGCCCG 59.293 61.111 2.29 0.00 0.00 6.13
176 177 2.104253 CGTCCAAATAAGCGCCCGT 61.104 57.895 2.29 0.00 0.00 5.28
177 178 1.427819 GTCCAAATAAGCGCCCGTG 59.572 57.895 2.29 0.00 0.00 4.94
178 179 2.102161 CCAAATAAGCGCCCGTGC 59.898 61.111 2.29 0.00 0.00 5.34
180 181 1.433064 CAAATAAGCGCCCGTGCAT 59.567 52.632 2.29 0.00 37.32 3.96
181 182 0.179140 CAAATAAGCGCCCGTGCATT 60.179 50.000 2.29 0.00 37.32 3.56
182 183 0.179140 AAATAAGCGCCCGTGCATTG 60.179 50.000 2.29 0.00 37.32 2.82
184 185 2.884997 ATAAGCGCCCGTGCATTGGA 62.885 55.000 2.29 0.00 37.32 3.53
190 191 2.484062 CCCGTGCATTGGAGATGCC 61.484 63.158 9.37 0.25 43.94 4.40
191 192 2.484062 CCGTGCATTGGAGATGCCC 61.484 63.158 8.36 0.00 43.94 5.36
195 196 2.378038 GTGCATTGGAGATGCCCTTAA 58.622 47.619 8.36 0.00 43.94 1.85
208 209 5.475909 AGATGCCCTTAAATATGACATGCAG 59.524 40.000 0.00 0.00 0.00 4.41
287 288 3.619038 GGCAACTAGATGTACTGAACAGC 59.381 47.826 0.00 0.00 45.09 4.40
326 327 5.530915 CCTTTGAACATACTGTGGAAACTCA 59.469 40.000 0.00 0.00 0.00 3.41
401 402 8.578448 TTGATGAAGACCATTGATAATTGTGA 57.422 30.769 0.00 0.00 35.17 3.58
402 403 8.217131 TGATGAAGACCATTGATAATTGTGAG 57.783 34.615 0.00 0.00 35.17 3.51
404 405 6.720309 TGAAGACCATTGATAATTGTGAGGA 58.280 36.000 0.00 0.00 0.00 3.71
543 544 9.781425 AATTATAGAGATGGATGGAGATGTACT 57.219 33.333 0.00 0.00 0.00 2.73
545 546 9.688091 TTATAGAGATGGATGGAGATGTACTAC 57.312 37.037 0.00 0.00 0.00 2.73
626 627 0.547712 TAGGGCTGCCTTCCACTTCT 60.548 55.000 19.68 6.84 0.00 2.85
643 644 8.089625 TCCACTTCTAATAATTGATCACCTCA 57.910 34.615 0.00 0.00 0.00 3.86
680 682 9.878599 AAAATATATTAAGAAACGAATGCGAGG 57.121 29.630 0.00 0.00 41.64 4.63
681 683 8.603242 AATATATTAAGAAACGAATGCGAGGT 57.397 30.769 0.00 0.00 41.64 3.85
682 684 9.701098 AATATATTAAGAAACGAATGCGAGGTA 57.299 29.630 0.00 0.00 41.64 3.08
683 685 5.713822 ATTAAGAAACGAATGCGAGGTAC 57.286 39.130 0.00 0.00 41.64 3.34
685 687 4.445452 AAGAAACGAATGCGAGGTACTA 57.555 40.909 0.00 0.00 41.55 1.82
700 702 6.273825 CGAGGTACTAGCATTAAACAGATGT 58.726 40.000 0.00 0.00 41.55 3.06
701 703 6.757010 CGAGGTACTAGCATTAAACAGATGTT 59.243 38.462 0.00 0.00 41.55 2.71
702 704 7.919091 CGAGGTACTAGCATTAAACAGATGTTA 59.081 37.037 0.00 0.00 41.55 2.41
704 706 7.985752 AGGTACTAGCATTAAACAGATGTTACC 59.014 37.037 0.00 0.00 36.02 2.85
705 707 7.985752 GGTACTAGCATTAAACAGATGTTACCT 59.014 37.037 0.00 0.00 37.25 3.08
706 708 9.379791 GTACTAGCATTAAACAGATGTTACCTT 57.620 33.333 0.00 0.00 37.25 3.50
708 710 8.947115 ACTAGCATTAAACAGATGTTACCTTTC 58.053 33.333 0.00 0.00 37.25 2.62
710 712 6.027749 GCATTAAACAGATGTTACCTTTCGG 58.972 40.000 0.00 0.00 37.25 4.30
711 713 6.551736 CATTAAACAGATGTTACCTTTCGGG 58.448 40.000 0.00 0.00 37.25 5.14
712 714 2.109425 ACAGATGTTACCTTTCGGGC 57.891 50.000 0.00 0.00 39.10 6.13
713 715 1.349688 ACAGATGTTACCTTTCGGGCA 59.650 47.619 0.00 0.00 39.10 5.36
714 716 1.737793 CAGATGTTACCTTTCGGGCAC 59.262 52.381 0.00 0.00 39.10 5.01
715 717 1.628846 AGATGTTACCTTTCGGGCACT 59.371 47.619 0.00 0.00 39.10 4.40
716 718 1.737793 GATGTTACCTTTCGGGCACTG 59.262 52.381 0.00 0.00 39.10 3.66
717 719 0.250553 TGTTACCTTTCGGGCACTGG 60.251 55.000 0.00 0.00 39.10 4.00
718 720 0.250597 GTTACCTTTCGGGCACTGGT 60.251 55.000 0.00 0.00 39.10 4.00
719 721 0.475044 TTACCTTTCGGGCACTGGTT 59.525 50.000 0.00 0.00 39.10 3.67
720 722 0.035739 TACCTTTCGGGCACTGGTTC 59.964 55.000 0.00 0.00 39.10 3.62
721 723 2.325082 CCTTTCGGGCACTGGTTCG 61.325 63.158 0.00 0.00 33.92 3.95
722 724 1.597027 CTTTCGGGCACTGGTTCGT 60.597 57.895 0.00 0.00 33.92 3.85
723 725 1.566018 CTTTCGGGCACTGGTTCGTC 61.566 60.000 0.00 0.00 33.92 4.20
724 726 2.035237 TTTCGGGCACTGGTTCGTCT 62.035 55.000 0.00 0.00 33.92 4.18
733 735 0.319555 CTGGTTCGTCTCCGCTTTGA 60.320 55.000 0.00 0.00 0.00 2.69
753 755 5.047566 TGACCAGTTCCTCATTTGAGAAA 57.952 39.130 9.15 0.00 44.74 2.52
773 775 0.323360 TCAATTCCAAGAAGCCCCCG 60.323 55.000 0.00 0.00 0.00 5.73
791 793 1.206578 GCCGAATGTGTGTGGAACG 59.793 57.895 0.00 0.00 42.39 3.95
857 859 1.215173 ACATATGTGTGGTGGATGGGG 59.785 52.381 7.78 0.00 37.14 4.96
1119 1123 1.079543 CTGAGCGGAGAGTTGGGTG 60.080 63.158 0.00 0.00 0.00 4.61
1287 1306 0.108615 CGCTGGGAGTTCGAAGACAT 60.109 55.000 0.00 0.00 34.32 3.06
1390 1409 1.333619 CCGGTTGGATCGGCAATAAAG 59.666 52.381 0.00 0.00 41.07 1.85
1435 1454 2.573341 GATTCGCGACGAGGACGACA 62.573 60.000 9.15 0.00 42.66 4.35
1474 1493 1.355066 GCTTTCGACAGGAAGGAGCG 61.355 60.000 0.00 0.00 33.80 5.03
1592 1611 2.009774 GCACAGATTGGTTAGCGACAT 58.990 47.619 0.00 0.00 0.00 3.06
1593 1612 2.030946 GCACAGATTGGTTAGCGACATC 59.969 50.000 0.00 0.00 0.00 3.06
1594 1613 2.282555 CACAGATTGGTTAGCGACATCG 59.717 50.000 0.00 0.00 43.27 3.84
1987 3074 1.541672 GAGGAGGAGGAGGAGGAGG 59.458 68.421 0.00 0.00 0.00 4.30
1988 3075 0.996762 GAGGAGGAGGAGGAGGAGGA 60.997 65.000 0.00 0.00 0.00 3.71
1991 3078 2.018086 AGGAGGAGGAGGAGGAGGG 61.018 68.421 0.00 0.00 0.00 4.30
1992 3079 2.612251 GAGGAGGAGGAGGAGGGG 59.388 72.222 0.00 0.00 0.00 4.79
2392 3485 2.030893 GCTCTTTACACATTGCACAGCA 60.031 45.455 0.00 0.00 36.47 4.41
2577 3673 3.007182 ACACATTGCCAAATCCTTGAAGG 59.993 43.478 4.45 4.45 34.14 3.46
2720 11985 0.030101 CCGGTTCGTGCAATTGTGTT 59.970 50.000 7.40 0.00 0.00 3.32
3478 12749 1.264288 GACTTTGCAACTCCGTGGAAG 59.736 52.381 0.00 0.00 29.97 3.46
3574 12911 2.632512 ACCCATTTCAAAATTGGCGACT 59.367 40.909 5.69 0.00 35.25 4.18
3645 12983 5.335897 CGATGTTGAATTGTTGAGGATTGGT 60.336 40.000 0.00 0.00 0.00 3.67
3743 13099 3.057315 CCGCTGGTCAATTTCTCAATGTT 60.057 43.478 0.00 0.00 0.00 2.71
3897 13259 4.152045 CAGCTAGTCTCAACAGAAGCAAAG 59.848 45.833 0.00 0.00 33.06 2.77
3954 13316 2.564771 GCATGCTATTGCTCCACACTA 58.435 47.619 11.37 0.00 39.57 2.74
4011 13373 1.075212 TGGGTGCCAGATTTGACATCA 59.925 47.619 0.00 0.00 0.00 3.07
4044 13406 3.551046 CGATAAGGGAACACGAGGAGATG 60.551 52.174 0.00 0.00 0.00 2.90
4052 13414 1.032657 CACGAGGAGATGGAGGACGT 61.033 60.000 0.00 0.00 0.00 4.34
4151 13513 4.580995 TGAAAACTGGGAATTTAGTCGCAA 59.419 37.500 0.00 0.00 39.66 4.85
4194 13556 4.324267 ACCCAAGTGAGTAAATGTGCTAC 58.676 43.478 0.00 0.00 0.00 3.58
4550 15381 3.379372 GCTGAAGGTATACGGTGTAGTCA 59.621 47.826 0.00 0.00 0.00 3.41
4764 15609 2.171237 TGTCTGGTGGCATATTGGAGAG 59.829 50.000 0.00 0.00 0.00 3.20
4963 15808 1.899814 TCAGTCCAAGCCACTATCGTT 59.100 47.619 0.00 0.00 0.00 3.85
5322 16173 4.951715 TGTTGAAAGCCAGCATGATATCTT 59.048 37.500 3.98 0.00 39.69 2.40
5390 16242 3.202906 TGCCCGTCATGAAGCTTTATAC 58.797 45.455 3.03 2.82 0.00 1.47
5391 16243 3.202906 GCCCGTCATGAAGCTTTATACA 58.797 45.455 3.03 0.00 0.00 2.29
5392 16244 3.815401 GCCCGTCATGAAGCTTTATACAT 59.185 43.478 3.03 0.00 0.00 2.29
5393 16245 4.994852 GCCCGTCATGAAGCTTTATACATA 59.005 41.667 3.03 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 1.657181 CCAACGCACAAACCGAAGC 60.657 57.895 0.00 0.00 0.00 3.86
7 8 0.041312 CTCCAACGCACAAACCGAAG 60.041 55.000 0.00 0.00 0.00 3.79
8 9 1.440938 CCTCCAACGCACAAACCGAA 61.441 55.000 0.00 0.00 0.00 4.30
10 11 2.637025 CCTCCAACGCACAAACCG 59.363 61.111 0.00 0.00 0.00 4.44
12 13 1.652563 GTCCCTCCAACGCACAAAC 59.347 57.895 0.00 0.00 0.00 2.93
13 14 1.890041 CGTCCCTCCAACGCACAAA 60.890 57.895 0.00 0.00 32.84 2.83
15 16 4.308458 CCGTCCCTCCAACGCACA 62.308 66.667 0.00 0.00 38.77 4.57
30 31 4.072088 GAACGTGTGAAGCGCCCG 62.072 66.667 2.29 0.00 0.00 6.13
32 33 3.277742 GACGAACGTGTGAAGCGCC 62.278 63.158 2.29 0.00 0.00 6.53
33 34 2.167918 GACGAACGTGTGAAGCGC 59.832 61.111 0.00 0.00 0.00 5.92
34 35 1.876453 CTGGACGAACGTGTGAAGCG 61.876 60.000 4.19 0.00 0.00 4.68
35 36 0.596600 TCTGGACGAACGTGTGAAGC 60.597 55.000 4.19 0.00 0.00 3.86
38 39 2.296831 TTTTCTGGACGAACGTGTGA 57.703 45.000 4.19 0.00 0.00 3.58
56 57 6.913170 TGAGCGCTTATCTGATTTTCTTTTT 58.087 32.000 13.26 0.00 0.00 1.94
58 59 6.500684 TTGAGCGCTTATCTGATTTTCTTT 57.499 33.333 13.26 0.00 0.00 2.52
62 63 6.433766 GCTATTTGAGCGCTTATCTGATTTT 58.566 36.000 13.26 0.00 42.62 1.82
63 64 5.995055 GCTATTTGAGCGCTTATCTGATTT 58.005 37.500 13.26 0.00 42.62 2.17
64 65 5.604010 GCTATTTGAGCGCTTATCTGATT 57.396 39.130 13.26 0.00 42.62 2.57
88 89 2.427410 GGCTTGCAAACGCACGAG 60.427 61.111 12.19 0.00 39.71 4.18
90 91 4.263209 TGGGCTTGCAAACGCACG 62.263 61.111 14.82 0.00 39.71 5.34
91 92 2.355009 CTGGGCTTGCAAACGCAC 60.355 61.111 14.82 10.52 39.71 5.34
92 93 2.832661 ACTGGGCTTGCAAACGCA 60.833 55.556 17.35 17.35 37.72 5.24
93 94 2.050077 GACTGGGCTTGCAAACGC 60.050 61.111 9.76 9.76 0.00 4.84
94 95 2.252260 CGACTGGGCTTGCAAACG 59.748 61.111 0.00 0.00 0.00 3.60
111 112 2.038837 GGGAAGCACCGGTGTAAGC 61.039 63.158 33.92 20.85 40.11 3.09
112 113 1.376812 GGGGAAGCACCGGTGTAAG 60.377 63.158 33.92 11.07 40.11 2.34
113 114 2.751688 GGGGAAGCACCGGTGTAA 59.248 61.111 33.92 0.00 40.11 2.41
115 116 3.857521 TAGGGGGAAGCACCGGTGT 62.858 63.158 33.92 17.27 40.11 4.16
117 118 1.212250 ATTTAGGGGGAAGCACCGGT 61.212 55.000 0.00 0.00 40.11 5.28
118 119 0.033503 AATTTAGGGGGAAGCACCGG 60.034 55.000 0.00 0.00 40.11 5.28
119 120 2.721425 TAATTTAGGGGGAAGCACCG 57.279 50.000 0.00 0.00 40.11 4.94
122 123 7.806680 AAGAAAATTAATTTAGGGGGAAGCA 57.193 32.000 13.68 0.00 0.00 3.91
123 124 9.515226 AAAAAGAAAATTAATTTAGGGGGAAGC 57.485 29.630 13.68 0.00 0.00 3.86
135 136 8.067780 ACGCTTGCGTTAAAAAGAAAATTAAT 57.932 26.923 15.19 0.00 0.00 1.40
136 137 7.306109 GGACGCTTGCGTTAAAAAGAAAATTAA 60.306 33.333 21.49 0.00 0.00 1.40
138 139 5.051307 GGACGCTTGCGTTAAAAAGAAAATT 60.051 36.000 21.49 0.00 0.00 1.82
139 140 4.443063 GGACGCTTGCGTTAAAAAGAAAAT 59.557 37.500 21.49 0.00 0.00 1.82
141 142 3.181499 TGGACGCTTGCGTTAAAAAGAAA 60.181 39.130 21.49 0.00 0.00 2.52
146 147 2.846039 TTTGGACGCTTGCGTTAAAA 57.154 40.000 21.49 19.56 0.00 1.52
148 149 3.668491 GCTTATTTGGACGCTTGCGTTAA 60.668 43.478 21.49 16.17 0.00 2.01
149 150 2.159626 GCTTATTTGGACGCTTGCGTTA 60.160 45.455 21.49 11.38 0.00 3.18
150 151 1.401018 GCTTATTTGGACGCTTGCGTT 60.401 47.619 21.49 8.19 0.00 4.84
153 154 2.930168 CGCTTATTTGGACGCTTGC 58.070 52.632 0.00 0.00 0.00 4.01
158 159 2.104253 ACGGGCGCTTATTTGGACG 61.104 57.895 7.64 1.11 0.00 4.79
159 160 1.427819 CACGGGCGCTTATTTGGAC 59.572 57.895 7.64 0.00 0.00 4.02
160 161 2.403378 GCACGGGCGCTTATTTGGA 61.403 57.895 7.64 0.00 0.00 3.53
161 162 2.003658 ATGCACGGGCGCTTATTTGG 62.004 55.000 4.58 0.00 45.35 3.28
163 164 0.179140 CAATGCACGGGCGCTTATTT 60.179 50.000 4.58 0.00 45.35 1.40
164 165 1.433064 CAATGCACGGGCGCTTATT 59.567 52.632 4.58 0.00 45.35 1.40
165 166 2.480610 CCAATGCACGGGCGCTTAT 61.481 57.895 4.58 0.00 45.35 1.73
166 167 3.130819 CCAATGCACGGGCGCTTA 61.131 61.111 4.58 0.00 45.35 3.09
170 171 2.514592 ATCTCCAATGCACGGGCG 60.515 61.111 4.58 0.00 45.35 6.13
171 172 3.113745 CATCTCCAATGCACGGGC 58.886 61.111 0.34 0.34 41.68 6.13
173 174 2.484062 GGGCATCTCCAATGCACGG 61.484 63.158 11.69 0.00 46.21 4.94
174 175 3.113745 GGGCATCTCCAATGCACG 58.886 61.111 11.69 0.00 46.21 5.34
176 177 2.824689 TTAAGGGCATCTCCAATGCA 57.175 45.000 11.69 0.00 46.21 3.96
177 178 5.477984 TCATATTTAAGGGCATCTCCAATGC 59.522 40.000 1.40 1.40 43.85 3.56
178 179 6.491062 TGTCATATTTAAGGGCATCTCCAATG 59.509 38.462 0.00 0.00 36.21 2.82
180 181 6.012337 TGTCATATTTAAGGGCATCTCCAA 57.988 37.500 0.00 0.00 36.21 3.53
181 182 5.645056 TGTCATATTTAAGGGCATCTCCA 57.355 39.130 0.00 0.00 36.21 3.86
182 183 5.105997 GCATGTCATATTTAAGGGCATCTCC 60.106 44.000 0.00 0.00 0.00 3.71
184 185 5.387788 TGCATGTCATATTTAAGGGCATCT 58.612 37.500 0.00 0.00 0.00 2.90
185 186 5.242393 ACTGCATGTCATATTTAAGGGCATC 59.758 40.000 0.00 0.00 0.00 3.91
190 191 9.643693 AAAGAAAACTGCATGTCATATTTAAGG 57.356 29.630 0.00 0.00 0.00 2.69
195 196 9.545105 TTGAAAAAGAAAACTGCATGTCATATT 57.455 25.926 0.00 0.00 0.00 1.28
326 327 7.633193 TGTTTGGTAAAATACACAAGACACT 57.367 32.000 0.00 0.00 0.00 3.55
365 366 8.343366 CAATGGTCTTCATCAATATGACAAGAG 58.657 37.037 4.58 0.00 41.87 2.85
462 463 3.960755 TCTCGTAGGCATATCCATATGGG 59.039 47.826 21.78 6.64 40.31 4.00
543 544 3.858812 GTGTGTGTGTCACTACGTTTGTA 59.141 43.478 4.27 0.00 46.27 2.41
544 545 2.669434 GTGTGTGTGTCACTACGTTTGT 59.331 45.455 4.27 0.00 46.27 2.83
545 546 2.029970 GGTGTGTGTGTCACTACGTTTG 59.970 50.000 4.27 0.00 46.27 2.93
569 570 4.621068 TTCTCGCCATTTTGCTAAGATG 57.379 40.909 0.00 0.00 0.00 2.90
658 660 8.355169 AGTACCTCGCATTCGTTTCTTAATATA 58.645 33.333 0.00 0.00 36.96 0.86
676 678 6.273825 ACATCTGTTTAATGCTAGTACCTCG 58.726 40.000 0.00 0.00 0.00 4.63
680 682 8.943909 AGGTAACATCTGTTTAATGCTAGTAC 57.056 34.615 0.20 0.00 39.31 2.73
681 683 9.953565 AAAGGTAACATCTGTTTAATGCTAGTA 57.046 29.630 0.20 0.00 39.31 1.82
682 684 8.863872 AAAGGTAACATCTGTTTAATGCTAGT 57.136 30.769 0.20 0.00 39.31 2.57
683 685 8.116753 CGAAAGGTAACATCTGTTTAATGCTAG 58.883 37.037 0.20 0.00 39.31 3.42
684 686 7.970384 CGAAAGGTAACATCTGTTTAATGCTA 58.030 34.615 0.20 0.00 39.31 3.49
685 687 6.842163 CGAAAGGTAACATCTGTTTAATGCT 58.158 36.000 0.20 0.00 39.31 3.79
704 706 1.566018 GACGAACCAGTGCCCGAAAG 61.566 60.000 0.00 0.00 0.00 2.62
705 707 1.595929 GACGAACCAGTGCCCGAAA 60.596 57.895 0.00 0.00 0.00 3.46
706 708 2.029964 GACGAACCAGTGCCCGAA 59.970 61.111 0.00 0.00 0.00 4.30
708 710 2.432628 GAGACGAACCAGTGCCCG 60.433 66.667 0.00 0.00 0.00 6.13
721 723 1.149148 GAACTGGTCAAAGCGGAGAC 58.851 55.000 0.00 0.00 0.00 3.36
722 724 0.034896 GGAACTGGTCAAAGCGGAGA 59.965 55.000 0.00 0.00 0.00 3.71
723 725 0.035458 AGGAACTGGTCAAAGCGGAG 59.965 55.000 0.00 0.00 37.18 4.63
724 726 0.034896 GAGGAACTGGTCAAAGCGGA 59.965 55.000 0.00 0.00 41.55 5.54
733 735 5.634118 TGATTTCTCAAATGAGGAACTGGT 58.366 37.500 6.29 0.00 42.06 4.00
753 755 1.686115 CGGGGGCTTCTTGGAATTGAT 60.686 52.381 0.00 0.00 0.00 2.57
773 775 1.206578 CGTTCCACACACATTCGGC 59.793 57.895 0.00 0.00 0.00 5.54
791 793 2.445438 CCGCCGAACGCTTCTCTTC 61.445 63.158 0.00 0.00 41.76 2.87
845 847 2.690840 ACTATCTACCCCATCCACCAC 58.309 52.381 0.00 0.00 0.00 4.16
883 885 0.867746 TGCTCATGCACTCGAAACAC 59.132 50.000 0.00 0.00 45.31 3.32
1119 1123 0.251608 TGTTAGGGGGAAGGCAAAGC 60.252 55.000 0.00 0.00 0.00 3.51
1170 1174 2.014857 GGGGAGAACACGCTATTTTCC 58.985 52.381 0.00 0.00 0.00 3.13
1199 1208 4.293626 CCGCCGCCGCTATTTTCG 62.294 66.667 0.00 0.00 0.00 3.46
1287 1306 2.525629 TCGGACTTGCCACTCCCA 60.526 61.111 0.00 0.00 35.94 4.37
1390 1409 2.432123 GGGCTCCATCGATTCCCC 59.568 66.667 0.00 0.00 0.00 4.81
1435 1454 0.549169 TCCCCTCCGGTTTCCATCTT 60.549 55.000 0.00 0.00 0.00 2.40
1474 1493 4.162690 ATTCAGGGACTCGCCGCC 62.163 66.667 0.00 0.00 34.60 6.13
1592 1611 0.108567 TTCGAATTCCGGCATGACGA 60.109 50.000 25.84 2.81 39.14 4.20
1593 1612 0.301687 CTTCGAATTCCGGCATGACG 59.698 55.000 15.88 15.88 39.14 4.35
1594 1613 0.028110 GCTTCGAATTCCGGCATGAC 59.972 55.000 0.00 0.00 39.14 3.06
1870 2957 1.480954 GAAGTCTGGGTCCATTCGCTA 59.519 52.381 0.00 0.00 0.00 4.26
1991 3078 2.949705 GATTCCTTCCCTGCCGCTCC 62.950 65.000 0.00 0.00 0.00 4.70
1992 3079 1.524849 GATTCCTTCCCTGCCGCTC 60.525 63.158 0.00 0.00 0.00 5.03
2194 3287 2.161211 GGAATCAGCTTGCTTGAGACAC 59.839 50.000 0.00 0.00 0.00 3.67
2392 3485 1.077787 TTCATTCGGGATGCGGCTT 60.078 52.632 0.00 0.00 35.64 4.35
2508 3604 0.615331 ATGACGGTCCACAGCATCTT 59.385 50.000 5.55 0.00 0.00 2.40
2720 11985 7.441157 GGATTTCGATGTAAACAGTATCCATCA 59.559 37.037 0.00 0.00 33.23 3.07
2887 12152 0.260816 ATAGTGGCCTGGACCGACTA 59.739 55.000 3.32 0.00 31.99 2.59
3478 12749 6.771188 TTTCAACTTCAGAAGATTCGAGTC 57.229 37.500 17.56 0.00 0.00 3.36
3574 12911 3.449737 CCTCCAGTTTCCATCTTACCGTA 59.550 47.826 0.00 0.00 0.00 4.02
3645 12983 4.451096 GTCTTCAACATTCTGCCTTCGTTA 59.549 41.667 0.00 0.00 0.00 3.18
3743 13099 4.040339 TGTTTCTGACAGATCTGGCTACAA 59.960 41.667 28.52 15.34 39.96 2.41
3897 13259 4.739046 AAGCATGCATATCGCTAGAAAC 57.261 40.909 21.98 0.00 43.06 2.78
4011 13373 2.338809 TCCCTTATCGATCCCATTGCT 58.661 47.619 0.00 0.00 0.00 3.91
4044 13406 2.826725 CCTATCCTTATCCACGTCCTCC 59.173 54.545 0.00 0.00 0.00 4.30
4052 13414 5.285401 TCACAACCTTCCTATCCTTATCCA 58.715 41.667 0.00 0.00 0.00 3.41
4151 13513 2.760092 TCTTCAAAGCTGCCAAAGTTGT 59.240 40.909 0.00 0.00 0.00 3.32
4194 13556 7.147143 AGCATACTAACTACGACCATATCAG 57.853 40.000 0.00 0.00 0.00 2.90
4550 15381 1.867233 GTCAACAACATCTCGTGCAGT 59.133 47.619 0.00 0.00 0.00 4.40
4708 15553 1.070601 GGGCCAGTCAAGTGCAAAAAT 59.929 47.619 4.39 0.00 0.00 1.82
4764 15609 5.648092 AGGTGGACTTCAATAGTAACATTGC 59.352 40.000 0.00 0.00 37.17 3.56
4963 15808 1.588674 CCTTTACAACACGAGCACCA 58.411 50.000 0.00 0.00 0.00 4.17
5322 16173 2.434336 GGCGCTATATATCCCATCACCA 59.566 50.000 7.64 0.00 0.00 4.17
5393 16245 8.141909 GCTTGACATTTAACCCTTTTTCTACTT 58.858 33.333 0.00 0.00 0.00 2.24
6127 16981 9.089601 CACTATGTATAACAAACAACATACGGA 57.910 33.333 0.00 0.00 34.54 4.69
6133 16987 7.362487 CCATGGCACTATGTATAACAAACAACA 60.362 37.037 0.00 0.00 0.00 3.33


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

AutoCloner maintained by Alex Coulton.