Multiple sequence alignment - TraesCS7D01G241900

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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 TraesCS7D01G241900 chr7D 100.000 2349 0 0 2850 5198 205952241 205949893 0.000000e+00 4338.0
1 TraesCS7D01G241900 chr7D 100.000 2289 0 0 1 2289 205955090 205952802 0.000000e+00 4228.0
2 TraesCS7D01G241900 chr7D 97.602 1126 26 1 2850 3975 533623820 533622696 0.000000e+00 1929.0
3 TraesCS7D01G241900 chr7D 86.111 108 14 1 1 107 498600348 498600455 1.180000e-21 115.0
4 TraesCS7D01G241900 chr7D 100.000 53 0 0 55 107 394256730 394256782 1.190000e-16 99.0
5 TraesCS7D01G241900 chr7A 94.313 2110 84 12 109 2188 218266571 218264468 0.000000e+00 3199.0
6 TraesCS7D01G241900 chr7A 94.074 810 35 6 3973 4781 218264484 218263687 0.000000e+00 1218.0
7 TraesCS7D01G241900 chr7A 97.037 135 4 0 5064 5198 218263692 218263558 1.460000e-55 228.0
8 TraesCS7D01G241900 chr7A 73.205 571 141 11 4626 5190 693206199 693206763 4.110000e-46 196.0
9 TraesCS7D01G241900 chr7B 94.540 2088 72 15 128 2188 196275669 196277741 0.000000e+00 3186.0
10 TraesCS7D01G241900 chr7B 94.529 658 25 7 3975 4630 196277727 196278375 0.000000e+00 1005.0
11 TraesCS7D01G241900 chr7B 95.957 371 15 0 4721 5091 196278370 196278740 2.070000e-168 603.0
12 TraesCS7D01G241900 chr7B 94.444 108 5 1 1 107 437763220 437763327 1.160000e-36 165.0
13 TraesCS7D01G241900 chr7B 92.157 102 7 1 1 101 52614346 52614447 5.430000e-30 143.0
14 TraesCS7D01G241900 chr7B 98.507 67 1 0 5132 5198 196278737 196278803 9.140000e-23 119.0
15 TraesCS7D01G241900 chr3D 97.691 1126 25 1 2850 3975 15905255 15906379 0.000000e+00 1934.0
16 TraesCS7D01G241900 chr3D 90.724 787 65 7 4419 5198 592869095 592868310 0.000000e+00 1042.0
17 TraesCS7D01G241900 chr3D 90.724 787 65 7 4419 5198 592874836 592874051 0.000000e+00 1042.0
18 TraesCS7D01G241900 chr3D 85.714 84 12 0 24 107 607576261 607576344 7.170000e-14 89.8
19 TraesCS7D01G241900 chr2D 97.150 1123 27 2 2853 3975 5433299 5432182 0.000000e+00 1892.0
20 TraesCS7D01G241900 chr2D 72.355 586 137 19 4620 5196 548977386 548976817 1.500000e-35 161.0
21 TraesCS7D01G241900 chr2D 84.615 91 14 0 17 107 141017206 141017116 1.990000e-14 91.6
22 TraesCS7D01G241900 chr2D 83.951 81 13 0 27 107 650930910 650930830 1.550000e-10 78.7
23 TraesCS7D01G241900 chr1D 96.359 1126 41 0 2850 3975 9086321 9085196 0.000000e+00 1853.0
24 TraesCS7D01G241900 chr5A 96.007 1127 36 6 2853 3975 547164406 547163285 0.000000e+00 1823.0
25 TraesCS7D01G241900 chr6B 95.741 1127 45 3 2850 3975 607120713 607121837 0.000000e+00 1812.0
26 TraesCS7D01G241900 chr5B 95.575 1130 45 4 2850 3975 640284202 640285330 0.000000e+00 1805.0
27 TraesCS7D01G241900 chr1A 95.567 1128 47 2 2850 3975 482800715 482801841 0.000000e+00 1803.0
28 TraesCS7D01G241900 chr4A 95.471 1126 47 3 2853 3975 735689281 735688157 0.000000e+00 1794.0
29 TraesCS7D01G241900 chrUn 94.437 701 39 0 4498 5198 214045089 214044389 0.000000e+00 1079.0
30 TraesCS7D01G241900 chrUn 94.437 701 39 0 4498 5198 240299996 240300696 0.000000e+00 1079.0
31 TraesCS7D01G241900 chrUn 90.597 787 66 7 4419 5198 45773614 45772829 0.000000e+00 1037.0
32 TraesCS7D01G241900 chrUn 86.076 79 11 0 28 106 83321889 83321967 9.270000e-13 86.1
33 TraesCS7D01G241900 chr2A 75.300 583 126 14 4620 5193 764770487 764771060 3.990000e-66 263.0
34 TraesCS7D01G241900 chr2B 85.714 77 11 0 31 107 569265256 569265332 1.200000e-11 82.4


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 TraesCS7D01G241900 chr7D 205949893 205955090 5197 True 4283.000000 4338 100.000000 1 5198 2 chr7D.!!$R2 5197
1 TraesCS7D01G241900 chr7D 533622696 533623820 1124 True 1929.000000 1929 97.602000 2850 3975 1 chr7D.!!$R1 1125
2 TraesCS7D01G241900 chr7A 218263558 218266571 3013 True 1548.333333 3199 95.141333 109 5198 3 chr7A.!!$R1 5089
3 TraesCS7D01G241900 chr7B 196275669 196278803 3134 False 1228.250000 3186 95.883250 128 5198 4 chr7B.!!$F3 5070
4 TraesCS7D01G241900 chr3D 15905255 15906379 1124 False 1934.000000 1934 97.691000 2850 3975 1 chr3D.!!$F1 1125
5 TraesCS7D01G241900 chr3D 592868310 592869095 785 True 1042.000000 1042 90.724000 4419 5198 1 chr3D.!!$R1 779
6 TraesCS7D01G241900 chr3D 592874051 592874836 785 True 1042.000000 1042 90.724000 4419 5198 1 chr3D.!!$R2 779
7 TraesCS7D01G241900 chr2D 5432182 5433299 1117 True 1892.000000 1892 97.150000 2853 3975 1 chr2D.!!$R1 1122
8 TraesCS7D01G241900 chr1D 9085196 9086321 1125 True 1853.000000 1853 96.359000 2850 3975 1 chr1D.!!$R1 1125
9 TraesCS7D01G241900 chr5A 547163285 547164406 1121 True 1823.000000 1823 96.007000 2853 3975 1 chr5A.!!$R1 1122
10 TraesCS7D01G241900 chr6B 607120713 607121837 1124 False 1812.000000 1812 95.741000 2850 3975 1 chr6B.!!$F1 1125
11 TraesCS7D01G241900 chr5B 640284202 640285330 1128 False 1805.000000 1805 95.575000 2850 3975 1 chr5B.!!$F1 1125
12 TraesCS7D01G241900 chr1A 482800715 482801841 1126 False 1803.000000 1803 95.567000 2850 3975 1 chr1A.!!$F1 1125
13 TraesCS7D01G241900 chr4A 735688157 735689281 1124 True 1794.000000 1794 95.471000 2853 3975 1 chr4A.!!$R1 1122
14 TraesCS7D01G241900 chrUn 214044389 214045089 700 True 1079.000000 1079 94.437000 4498 5198 1 chrUn.!!$R2 700
15 TraesCS7D01G241900 chrUn 240299996 240300696 700 False 1079.000000 1079 94.437000 4498 5198 1 chrUn.!!$F2 700
16 TraesCS7D01G241900 chrUn 45772829 45773614 785 True 1037.000000 1037 90.597000 4419 5198 1 chrUn.!!$R1 779
17 TraesCS7D01G241900 chr2A 764770487 764771060 573 False 263.000000 263 75.300000 4620 5193 1 chr2A.!!$F1 573

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
78 79 0.037605 GTGGGATCGGTCGACTGTTT 60.038 55.0 23.27 12.66 0.00 2.83 F
79 80 0.037697 TGGGATCGGTCGACTGTTTG 60.038 55.0 23.27 5.27 0.00 2.93 F
80 81 0.245539 GGGATCGGTCGACTGTTTGA 59.754 55.0 23.27 5.09 0.00 2.69 F
981 1011 0.380378 TTGCGGCACTGTTTTGACTC 59.620 50.0 0.05 0.00 0.00 3.36 F
1558 1588 0.106669 TAGCTGCCGAGAGAAGCCTA 60.107 55.0 0.00 0.00 40.21 3.93 F
2193 2241 0.325203 TATCCCTTGCTTTTGGCCCC 60.325 55.0 0.00 0.00 40.92 5.80 F
2232 2280 0.459759 CCCGCTCTCGTTAGGGTTTC 60.460 60.0 0.00 0.00 39.05 2.78 F
2234 2282 0.459759 CGCTCTCGTTAGGGTTTCCC 60.460 60.0 0.00 0.00 45.90 3.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1209 1239 0.038166 ACCGAATGATGCCCAGTTGT 59.962 50.000 0.00 0.0 0.00 3.32 R
1212 1242 0.180406 GGTACCGAATGATGCCCAGT 59.820 55.000 0.00 0.0 0.00 4.00 R
1470 1500 1.873591 CAGTTTGTCTTGAACCCCTCG 59.126 52.381 0.00 0.0 0.00 4.63 R
2213 2261 0.459759 GAAACCCTAACGAGAGCGGG 60.460 60.000 0.00 0.0 43.17 6.13 R
3547 3597 0.481128 TTTCTCCCAACCTCCAACCC 59.519 55.000 0.00 0.0 0.00 4.11 R
3978 4033 2.031120 TGGACACAGAAAAAGCAAGGG 58.969 47.619 0.00 0.0 0.00 3.95 R
4190 4245 2.353704 CCACGTGCCTCAAGTTAGATGA 60.354 50.000 10.91 0.0 0.00 2.92 R
4314 4369 5.932303 GCTTACAGACAGGTTTCAGTAATCA 59.068 40.000 0.00 0.0 29.96 2.57 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
18 19 2.421220 TTCCCAAAACCGGAACTGC 58.579 52.632 9.46 0.00 34.40 4.40
19 20 1.110518 TTCCCAAAACCGGAACTGCC 61.111 55.000 9.46 0.00 34.40 4.85
20 21 1.530655 CCCAAAACCGGAACTGCCT 60.531 57.895 9.46 0.00 0.00 4.75
21 22 0.250989 CCCAAAACCGGAACTGCCTA 60.251 55.000 9.46 0.00 0.00 3.93
22 23 0.879090 CCAAAACCGGAACTGCCTAC 59.121 55.000 9.46 0.00 0.00 3.18
23 24 1.600023 CAAAACCGGAACTGCCTACA 58.400 50.000 9.46 0.00 0.00 2.74
44 45 4.176752 GGAGATGGTCCGGCCCAC 62.177 72.222 6.24 0.36 37.31 4.61
45 46 3.083997 GAGATGGTCCGGCCCACT 61.084 66.667 6.24 6.32 37.31 4.00
46 47 2.610859 AGATGGTCCGGCCCACTT 60.611 61.111 6.24 0.00 37.31 3.16
47 48 2.198304 GAGATGGTCCGGCCCACTTT 62.198 60.000 6.24 0.00 37.31 2.66
48 49 0.912487 AGATGGTCCGGCCCACTTTA 60.912 55.000 6.24 0.00 37.31 1.85
49 50 0.182775 GATGGTCCGGCCCACTTTAT 59.817 55.000 6.24 0.00 37.31 1.40
50 51 0.182775 ATGGTCCGGCCCACTTTATC 59.817 55.000 6.24 0.00 37.31 1.75
51 52 1.523032 GGTCCGGCCCACTTTATCG 60.523 63.158 0.00 0.00 0.00 2.92
52 53 2.178235 GTCCGGCCCACTTTATCGC 61.178 63.158 0.00 0.00 0.00 4.58
53 54 3.269347 CCGGCCCACTTTATCGCG 61.269 66.667 0.00 0.00 0.00 5.87
54 55 3.937062 CGGCCCACTTTATCGCGC 61.937 66.667 0.00 0.00 0.00 6.86
55 56 3.583086 GGCCCACTTTATCGCGCC 61.583 66.667 0.00 0.00 0.00 6.53
56 57 3.583086 GCCCACTTTATCGCGCCC 61.583 66.667 0.00 0.00 0.00 6.13
57 58 2.900337 CCCACTTTATCGCGCCCC 60.900 66.667 0.00 0.00 0.00 5.80
58 59 2.189521 CCACTTTATCGCGCCCCT 59.810 61.111 0.00 0.00 0.00 4.79
59 60 2.180204 CCACTTTATCGCGCCCCTG 61.180 63.158 0.00 0.00 0.00 4.45
60 61 1.449601 CACTTTATCGCGCCCCTGT 60.450 57.895 0.00 0.00 0.00 4.00
61 62 1.449601 ACTTTATCGCGCCCCTGTG 60.450 57.895 0.00 0.00 0.00 3.66
62 63 2.124901 TTTATCGCGCCCCTGTGG 60.125 61.111 0.00 0.00 37.09 4.17
73 74 2.494918 CCTGTGGGATCGGTCGAC 59.505 66.667 7.13 7.13 33.58 4.20
74 75 2.052690 CCTGTGGGATCGGTCGACT 61.053 63.158 16.46 0.00 33.58 4.18
75 76 1.139734 CTGTGGGATCGGTCGACTG 59.860 63.158 18.66 18.66 0.00 3.51
76 77 1.595993 CTGTGGGATCGGTCGACTGT 61.596 60.000 23.27 11.31 0.00 3.55
77 78 1.183030 TGTGGGATCGGTCGACTGTT 61.183 55.000 23.27 15.78 0.00 3.16
78 79 0.037605 GTGGGATCGGTCGACTGTTT 60.038 55.000 23.27 12.66 0.00 2.83
79 80 0.037697 TGGGATCGGTCGACTGTTTG 60.038 55.000 23.27 5.27 0.00 2.93
80 81 0.245539 GGGATCGGTCGACTGTTTGA 59.754 55.000 23.27 5.09 0.00 2.69
81 82 1.347320 GGATCGGTCGACTGTTTGAC 58.653 55.000 23.27 11.16 35.57 3.18
82 83 0.982673 GATCGGTCGACTGTTTGACG 59.017 55.000 23.27 12.50 37.04 4.35
83 84 1.007336 ATCGGTCGACTGTTTGACGC 61.007 55.000 23.27 0.00 37.04 5.19
84 85 1.947146 CGGTCGACTGTTTGACGCA 60.947 57.895 16.54 0.00 37.04 5.24
85 86 1.853319 GGTCGACTGTTTGACGCAG 59.147 57.895 16.46 0.00 37.04 5.18
86 87 0.596600 GGTCGACTGTTTGACGCAGA 60.597 55.000 16.46 0.00 37.04 4.26
87 88 0.778815 GTCGACTGTTTGACGCAGAG 59.221 55.000 8.70 0.00 37.40 3.35
88 89 0.666374 TCGACTGTTTGACGCAGAGA 59.334 50.000 0.00 0.00 37.40 3.10
89 90 1.056103 CGACTGTTTGACGCAGAGAG 58.944 55.000 0.00 0.00 37.40 3.20
90 91 0.787183 GACTGTTTGACGCAGAGAGC 59.213 55.000 0.00 0.00 37.40 4.09
101 102 1.576356 GCAGAGAGCGTCAAATAGGG 58.424 55.000 0.00 0.00 0.00 3.53
102 103 1.134670 GCAGAGAGCGTCAAATAGGGT 60.135 52.381 0.00 0.00 0.00 4.34
103 104 2.678190 GCAGAGAGCGTCAAATAGGGTT 60.678 50.000 0.00 0.00 0.00 4.11
104 105 3.600388 CAGAGAGCGTCAAATAGGGTTT 58.400 45.455 0.00 0.00 0.00 3.27
105 106 4.003648 CAGAGAGCGTCAAATAGGGTTTT 58.996 43.478 0.00 0.00 0.00 2.43
106 107 4.093556 CAGAGAGCGTCAAATAGGGTTTTC 59.906 45.833 0.00 0.00 0.00 2.29
107 108 4.020128 AGAGAGCGTCAAATAGGGTTTTCT 60.020 41.667 0.00 0.00 0.00 2.52
108 109 4.003648 AGAGCGTCAAATAGGGTTTTCTG 58.996 43.478 0.00 0.00 0.00 3.02
109 110 2.488153 AGCGTCAAATAGGGTTTTCTGC 59.512 45.455 0.00 0.00 0.00 4.26
110 111 2.727916 GCGTCAAATAGGGTTTTCTGCG 60.728 50.000 0.00 0.00 0.00 5.18
111 112 2.739913 CGTCAAATAGGGTTTTCTGCGA 59.260 45.455 0.00 0.00 0.00 5.10
112 113 3.187637 CGTCAAATAGGGTTTTCTGCGAA 59.812 43.478 0.00 0.00 0.00 4.70
113 114 4.319911 CGTCAAATAGGGTTTTCTGCGAAA 60.320 41.667 0.00 0.55 0.00 3.46
144 145 4.477975 CGTCCCTGTCCGCTCGAC 62.478 72.222 0.00 0.00 42.33 4.20
146 147 4.671590 TCCCTGTCCGCTCGACCA 62.672 66.667 0.00 0.00 41.18 4.02
255 263 3.314331 CTCGGTGGTGGGTGAGCT 61.314 66.667 0.00 0.00 0.00 4.09
346 361 5.047377 GCAGAAGAAGGTATCCTATCTCCAG 60.047 48.000 0.00 0.00 31.13 3.86
397 412 8.635983 GCTTGAAAATCCGAGTAAAAATTGTAC 58.364 33.333 0.00 0.00 0.00 2.90
502 522 3.009033 TCAGACGGGGTCATTTCTTCATT 59.991 43.478 0.00 0.00 34.60 2.57
645 665 6.873605 TCTGAATTTCGGGTACTGCATATATG 59.126 38.462 8.45 8.45 32.53 1.78
919 949 1.938577 CTGAATCTCGTGCAGGAATGG 59.061 52.381 10.76 0.00 0.00 3.16
981 1011 0.380378 TTGCGGCACTGTTTTGACTC 59.620 50.000 0.05 0.00 0.00 3.36
999 1029 2.421314 CGCACAGACACTCCACCA 59.579 61.111 0.00 0.00 0.00 4.17
1089 1119 1.728672 CGGAGAGTACCTTCGAGCC 59.271 63.158 6.26 0.00 46.85 4.70
1095 1125 1.183676 AGTACCTTCGAGCCGGTGTT 61.184 55.000 1.90 0.00 34.76 3.32
1102 1132 2.434359 GAGCCGGTGTTCCTTCGG 60.434 66.667 1.90 0.00 45.84 4.30
1131 1161 2.632602 TTTCCCAGCTTGGTTGCGGA 62.633 55.000 3.35 0.00 35.17 5.54
1154 1184 6.367422 GGATACAGAAGTTCTTCAAGTGTGAG 59.633 42.308 1.56 0.00 34.49 3.51
1470 1500 1.816835 TCGATATCACAGGGATACGGC 59.183 52.381 3.12 0.00 41.17 5.68
1489 1519 1.814248 GCGAGGGGTTCAAGACAAACT 60.814 52.381 0.00 0.00 0.00 2.66
1558 1588 0.106669 TAGCTGCCGAGAGAAGCCTA 60.107 55.000 0.00 0.00 40.21 3.93
1637 1667 9.683069 ATTCAAAACTAGCACTTGTTATTTCAG 57.317 29.630 0.00 0.00 0.00 3.02
1664 1694 9.524496 TTATCATATTTATCATTTCTGGCTGCT 57.476 29.630 0.00 0.00 0.00 4.24
1709 1745 7.201920 GCCTAGACTATGTCTGGACTTTATTGA 60.202 40.741 11.71 0.00 42.49 2.57
1872 1916 7.329717 ACGAGAAACTCAAAATATGACTCTGTC 59.670 37.037 0.00 0.00 33.47 3.51
1907 1951 4.821805 CACTCTTGTTGTTTACACCATCCT 59.178 41.667 0.00 0.00 36.21 3.24
1914 1958 7.406031 TGTTGTTTACACCATCCTTTGTAAA 57.594 32.000 3.40 3.40 42.93 2.01
2073 2120 3.828451 AGTTGCCAACTTGCTATTCATGT 59.172 39.130 3.74 0.00 39.04 3.21
2152 2200 7.663493 TGACACAATTATGTTGTATCTTGACCA 59.337 33.333 0.00 0.00 37.82 4.02
2188 2236 6.698008 TGTCATGTATATCCCTTGCTTTTG 57.302 37.500 0.00 0.00 0.00 2.44
2189 2237 5.593909 TGTCATGTATATCCCTTGCTTTTGG 59.406 40.000 0.00 0.00 0.00 3.28
2190 2238 4.584325 TCATGTATATCCCTTGCTTTTGGC 59.416 41.667 0.00 0.00 42.22 4.52
2191 2239 3.295973 TGTATATCCCTTGCTTTTGGCC 58.704 45.455 0.00 0.00 40.92 5.36
2192 2240 1.793414 ATATCCCTTGCTTTTGGCCC 58.207 50.000 0.00 0.00 40.92 5.80
2193 2241 0.325203 TATCCCTTGCTTTTGGCCCC 60.325 55.000 0.00 0.00 40.92 5.80
2194 2242 3.694538 CCCTTGCTTTTGGCCCCG 61.695 66.667 0.00 0.00 40.92 5.73
2195 2243 4.377708 CCTTGCTTTTGGCCCCGC 62.378 66.667 0.00 0.00 40.92 6.13
2196 2244 3.305516 CTTGCTTTTGGCCCCGCT 61.306 61.111 0.00 0.00 40.92 5.52
2197 2245 3.286915 CTTGCTTTTGGCCCCGCTC 62.287 63.158 0.00 0.00 40.92 5.03
2200 2248 4.366684 CTTTTGGCCCCGCTCCCT 62.367 66.667 0.00 0.00 0.00 4.20
2201 2249 4.360405 TTTTGGCCCCGCTCCCTC 62.360 66.667 0.00 0.00 0.00 4.30
2226 2274 4.570663 CCGCCCCGCTCTCGTTAG 62.571 72.222 0.00 0.00 0.00 2.34
2227 2275 4.570663 CGCCCCGCTCTCGTTAGG 62.571 72.222 0.00 0.00 0.00 2.69
2228 2276 4.222847 GCCCCGCTCTCGTTAGGG 62.223 72.222 0.00 0.00 43.41 3.53
2229 2277 2.758737 CCCCGCTCTCGTTAGGGT 60.759 66.667 0.00 0.00 42.26 4.34
2230 2278 2.356780 CCCCGCTCTCGTTAGGGTT 61.357 63.158 0.00 0.00 42.26 4.11
2231 2279 1.595357 CCCGCTCTCGTTAGGGTTT 59.405 57.895 0.00 0.00 39.05 3.27
2232 2280 0.459759 CCCGCTCTCGTTAGGGTTTC 60.460 60.000 0.00 0.00 39.05 2.78
2233 2281 0.459759 CCGCTCTCGTTAGGGTTTCC 60.460 60.000 3.90 0.00 0.00 3.13
2234 2282 0.459759 CGCTCTCGTTAGGGTTTCCC 60.460 60.000 0.00 0.00 45.90 3.97
3505 3555 1.077858 TGGCGCATATTGGCAGACA 60.078 52.632 10.83 0.00 36.93 3.41
3531 3581 2.203070 GGTGGAGCGCGATGGATT 60.203 61.111 12.10 0.00 0.00 3.01
3547 3597 0.673644 GATTGTCTGGGGTCGTGGTG 60.674 60.000 0.00 0.00 0.00 4.17
3745 3796 1.032014 TCTTGAAGGTGTTGCTTGGC 58.968 50.000 0.00 0.00 0.00 4.52
3979 4034 5.762825 GGAAACCCTTTTTCGGTATATCC 57.237 43.478 0.00 0.00 31.69 2.59
3980 4035 4.581824 GGAAACCCTTTTTCGGTATATCCC 59.418 45.833 0.00 0.00 31.69 3.85
3981 4036 5.443283 GAAACCCTTTTTCGGTATATCCCT 58.557 41.667 0.00 0.00 31.69 4.20
3982 4037 5.461516 AACCCTTTTTCGGTATATCCCTT 57.538 39.130 0.00 0.00 31.69 3.95
3983 4038 4.788679 ACCCTTTTTCGGTATATCCCTTG 58.211 43.478 0.00 0.00 0.00 3.61
3984 4039 3.568430 CCCTTTTTCGGTATATCCCTTGC 59.432 47.826 0.00 0.00 0.00 4.01
3985 4040 4.461198 CCTTTTTCGGTATATCCCTTGCT 58.539 43.478 0.00 0.00 0.00 3.91
3986 4041 4.887655 CCTTTTTCGGTATATCCCTTGCTT 59.112 41.667 0.00 0.00 0.00 3.91
3987 4042 5.359860 CCTTTTTCGGTATATCCCTTGCTTT 59.640 40.000 0.00 0.00 0.00 3.51
3988 4043 6.127451 CCTTTTTCGGTATATCCCTTGCTTTT 60.127 38.462 0.00 0.00 0.00 2.27
4075 4130 3.065233 CACTGCTGCAGTCTTTTTACACA 59.935 43.478 30.96 0.00 43.43 3.72
4076 4131 3.885297 ACTGCTGCAGTCTTTTTACACAT 59.115 39.130 28.49 2.02 41.21 3.21
4077 4132 5.049474 CACTGCTGCAGTCTTTTTACACATA 60.049 40.000 30.96 0.00 43.43 2.29
4078 4133 5.707298 ACTGCTGCAGTCTTTTTACACATAT 59.293 36.000 28.49 0.88 41.21 1.78
4079 4134 6.128172 ACTGCTGCAGTCTTTTTACACATATC 60.128 38.462 28.49 0.00 41.21 1.63
4080 4135 5.704978 TGCTGCAGTCTTTTTACACATATCA 59.295 36.000 16.64 0.00 0.00 2.15
4081 4136 6.128200 TGCTGCAGTCTTTTTACACATATCAG 60.128 38.462 16.64 0.00 0.00 2.90
4180 4235 7.432350 CTAGGAAGGATTGTGAAAGATATGC 57.568 40.000 0.00 0.00 0.00 3.14
4190 4245 5.687780 TGTGAAAGATATGCCTGATGATGT 58.312 37.500 0.00 0.00 0.00 3.06
4212 4267 0.320421 TCTAACTTGAGGCACGTGGC 60.320 55.000 32.77 32.77 43.74 5.01
4459 4522 5.229423 GCACCAGCTTCATTAATTGAAACA 58.771 37.500 0.00 0.00 43.64 2.83
4638 4702 4.350368 TGTCTCAACTTGCCTCATTGTA 57.650 40.909 0.00 0.00 0.00 2.41
4706 4770 3.316308 GCAACTTCTTTGGCTTCTTCAGA 59.684 43.478 0.00 0.00 35.51 3.27
4763 4827 5.753921 CGAAGAGTTTGTCTTGGTTTACTCT 59.246 40.000 0.00 0.00 46.21 3.24
4835 4899 6.891908 ACACATGGCTTCTTCCTTGTTAATAT 59.108 34.615 0.00 0.00 41.01 1.28
4899 4963 1.007038 GAGTCGCCGTGTGTGGTAA 60.007 57.895 0.00 0.00 0.00 2.85
4905 4969 1.403116 CGCCGTGTGTGGTAATACTCA 60.403 52.381 0.00 0.00 0.00 3.41
5002 5066 6.032717 GCTCCAAAATCTGATACTTTTGCTC 58.967 40.000 8.67 0.00 39.75 4.26
5128 5192 4.894798 GCTATTCTTAGCCGATCTTTCG 57.105 45.455 0.00 0.00 44.29 3.46
5130 5194 4.619336 GCTATTCTTAGCCGATCTTTCGAG 59.381 45.833 0.00 0.00 43.36 4.04
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 0.250989 TAGGCAGTTCCGGTTTTGGG 60.251 55.000 0.00 0.00 40.77 4.12
6 7 0.605589 GCTGTAGGCAGTTCCGGTTT 60.606 55.000 0.00 0.00 44.32 3.27
7 8 1.003718 GCTGTAGGCAGTTCCGGTT 60.004 57.895 0.00 0.00 44.32 4.44
9 10 2.509336 CGCTGTAGGCAGTTCCGG 60.509 66.667 0.00 0.00 44.32 5.14
11 12 2.125106 CCCGCTGTAGGCAGTTCC 60.125 66.667 0.00 0.00 44.32 3.62
12 13 1.153549 CTCCCGCTGTAGGCAGTTC 60.154 63.158 0.00 0.00 44.32 3.01
13 14 0.978146 ATCTCCCGCTGTAGGCAGTT 60.978 55.000 0.00 0.00 44.32 3.16
14 15 1.381872 ATCTCCCGCTGTAGGCAGT 60.382 57.895 0.00 0.00 44.32 4.40
15 16 1.068753 CATCTCCCGCTGTAGGCAG 59.931 63.158 0.00 0.00 45.23 4.85
16 17 2.434843 CCATCTCCCGCTGTAGGCA 61.435 63.158 0.00 0.00 41.91 4.75
17 18 2.370647 GACCATCTCCCGCTGTAGGC 62.371 65.000 0.00 0.00 37.64 3.93
18 19 1.742768 GACCATCTCCCGCTGTAGG 59.257 63.158 0.00 0.00 0.00 3.18
19 20 1.742768 GGACCATCTCCCGCTGTAG 59.257 63.158 0.00 0.00 31.83 2.74
20 21 2.125326 CGGACCATCTCCCGCTGTA 61.125 63.158 0.00 0.00 39.22 2.74
21 22 3.461773 CGGACCATCTCCCGCTGT 61.462 66.667 0.00 0.00 39.22 4.40
22 23 4.227134 CCGGACCATCTCCCGCTG 62.227 72.222 0.00 0.00 44.07 5.18
27 28 4.176752 GTGGGCCGGACCATCTCC 62.177 72.222 36.84 17.12 43.59 3.71
28 29 2.198304 AAAGTGGGCCGGACCATCTC 62.198 60.000 36.84 21.32 43.59 2.75
29 30 0.912487 TAAAGTGGGCCGGACCATCT 60.912 55.000 36.84 27.81 43.59 2.90
30 31 0.182775 ATAAAGTGGGCCGGACCATC 59.817 55.000 36.84 25.90 43.59 3.51
31 32 0.182775 GATAAAGTGGGCCGGACCAT 59.817 55.000 36.84 20.93 43.59 3.55
32 33 1.605453 GATAAAGTGGGCCGGACCA 59.395 57.895 30.39 30.39 42.05 4.02
33 34 1.523032 CGATAAAGTGGGCCGGACC 60.523 63.158 23.70 23.70 37.93 4.46
34 35 2.178235 GCGATAAAGTGGGCCGGAC 61.178 63.158 5.05 0.00 0.00 4.79
35 36 2.188469 GCGATAAAGTGGGCCGGA 59.812 61.111 5.05 0.00 0.00 5.14
36 37 3.269347 CGCGATAAAGTGGGCCGG 61.269 66.667 0.00 0.00 0.00 6.13
37 38 3.937062 GCGCGATAAAGTGGGCCG 61.937 66.667 12.10 0.00 38.02 6.13
39 40 3.583086 GGGCGCGATAAAGTGGGC 61.583 66.667 12.10 0.00 42.67 5.36
40 41 2.900337 GGGGCGCGATAAAGTGGG 60.900 66.667 12.10 0.00 0.00 4.61
41 42 2.180204 CAGGGGCGCGATAAAGTGG 61.180 63.158 12.10 0.00 0.00 4.00
42 43 1.449601 ACAGGGGCGCGATAAAGTG 60.450 57.895 12.10 0.58 0.00 3.16
43 44 1.449601 CACAGGGGCGCGATAAAGT 60.450 57.895 12.10 0.00 0.00 2.66
44 45 2.180204 CCACAGGGGCGCGATAAAG 61.180 63.158 12.10 0.00 0.00 1.85
45 46 2.124901 CCACAGGGGCGCGATAAA 60.125 61.111 12.10 0.00 0.00 1.40
55 56 2.758327 TCGACCGATCCCACAGGG 60.758 66.667 0.00 0.00 46.11 4.45
56 57 2.052690 AGTCGACCGATCCCACAGG 61.053 63.158 13.01 0.00 0.00 4.00
57 58 1.139734 CAGTCGACCGATCCCACAG 59.860 63.158 13.01 0.00 0.00 3.66
58 59 1.183030 AACAGTCGACCGATCCCACA 61.183 55.000 13.01 0.00 0.00 4.17
59 60 0.037605 AAACAGTCGACCGATCCCAC 60.038 55.000 13.01 0.00 0.00 4.61
60 61 0.037697 CAAACAGTCGACCGATCCCA 60.038 55.000 13.01 0.00 0.00 4.37
61 62 0.245539 TCAAACAGTCGACCGATCCC 59.754 55.000 13.01 0.00 0.00 3.85
62 63 1.347320 GTCAAACAGTCGACCGATCC 58.653 55.000 13.01 0.00 0.00 3.36
63 64 0.982673 CGTCAAACAGTCGACCGATC 59.017 55.000 13.01 0.00 0.00 3.69
64 65 1.007336 GCGTCAAACAGTCGACCGAT 61.007 55.000 13.01 0.00 0.00 4.18
65 66 1.659335 GCGTCAAACAGTCGACCGA 60.659 57.895 13.01 0.00 0.00 4.69
66 67 1.876453 CTGCGTCAAACAGTCGACCG 61.876 60.000 13.01 4.15 0.00 4.79
67 68 0.596600 TCTGCGTCAAACAGTCGACC 60.597 55.000 13.01 0.00 36.50 4.79
68 69 0.778815 CTCTGCGTCAAACAGTCGAC 59.221 55.000 7.70 7.70 36.50 4.20
69 70 0.666374 TCTCTGCGTCAAACAGTCGA 59.334 50.000 0.00 0.00 36.50 4.20
70 71 1.056103 CTCTCTGCGTCAAACAGTCG 58.944 55.000 0.00 0.00 36.50 4.18
71 72 0.787183 GCTCTCTGCGTCAAACAGTC 59.213 55.000 0.00 0.00 36.50 3.51
72 73 2.906047 GCTCTCTGCGTCAAACAGT 58.094 52.632 0.00 0.00 36.50 3.55
82 83 1.134670 ACCCTATTTGACGCTCTCTGC 60.135 52.381 0.00 0.00 38.57 4.26
83 84 2.969628 ACCCTATTTGACGCTCTCTG 57.030 50.000 0.00 0.00 0.00 3.35
84 85 3.983044 AAACCCTATTTGACGCTCTCT 57.017 42.857 0.00 0.00 0.00 3.10
85 86 4.093556 CAGAAAACCCTATTTGACGCTCTC 59.906 45.833 0.00 0.00 0.00 3.20
86 87 4.003648 CAGAAAACCCTATTTGACGCTCT 58.996 43.478 0.00 0.00 0.00 4.09
87 88 3.426292 GCAGAAAACCCTATTTGACGCTC 60.426 47.826 0.00 0.00 0.00 5.03
88 89 2.488153 GCAGAAAACCCTATTTGACGCT 59.512 45.455 0.00 0.00 0.00 5.07
89 90 2.727916 CGCAGAAAACCCTATTTGACGC 60.728 50.000 0.00 0.00 0.00 5.19
90 91 2.739913 TCGCAGAAAACCCTATTTGACG 59.260 45.455 0.00 0.00 0.00 4.35
91 92 4.759516 TTCGCAGAAAACCCTATTTGAC 57.240 40.909 0.00 0.00 45.90 3.18
92 93 4.825085 AGTTTCGCAGAAAACCCTATTTGA 59.175 37.500 5.51 0.00 45.90 2.69
93 94 5.121221 AGTTTCGCAGAAAACCCTATTTG 57.879 39.130 5.51 0.00 45.90 2.32
94 95 4.217767 GGAGTTTCGCAGAAAACCCTATTT 59.782 41.667 5.51 0.00 45.90 1.40
95 96 3.756963 GGAGTTTCGCAGAAAACCCTATT 59.243 43.478 5.51 0.00 45.90 1.73
96 97 3.344515 GGAGTTTCGCAGAAAACCCTAT 58.655 45.455 5.51 0.00 45.90 2.57
97 98 2.551504 GGGAGTTTCGCAGAAAACCCTA 60.552 50.000 23.33 0.21 45.90 3.53
98 99 1.605753 GGAGTTTCGCAGAAAACCCT 58.394 50.000 5.51 0.55 45.90 4.34
99 100 0.596577 GGGAGTTTCGCAGAAAACCC 59.403 55.000 19.95 19.95 45.90 4.11
100 101 0.596577 GGGGAGTTTCGCAGAAAACC 59.403 55.000 5.51 10.63 45.90 3.27
101 102 1.535896 GAGGGGAGTTTCGCAGAAAAC 59.464 52.381 5.51 2.52 45.90 2.43
102 103 1.876416 CGAGGGGAGTTTCGCAGAAAA 60.876 52.381 5.51 0.00 45.90 2.29
103 104 0.320421 CGAGGGGAGTTTCGCAGAAA 60.320 55.000 0.55 0.55 45.90 2.52
104 105 1.292223 CGAGGGGAGTTTCGCAGAA 59.708 57.895 0.00 0.00 45.90 3.02
105 106 2.970639 CGAGGGGAGTTTCGCAGA 59.029 61.111 0.00 0.00 0.00 4.26
327 342 6.688554 ACTTTCTGGAGATAGGATACCTTCT 58.311 40.000 0.00 0.00 34.61 2.85
346 361 1.959226 TGGGCACGAGCGAACTTTC 60.959 57.895 0.00 0.00 43.41 2.62
387 402 5.103687 GTGTTGGGTGTTCGTACAATTTTT 58.896 37.500 0.00 0.00 35.69 1.94
397 412 1.778027 GAACGGGTGTTGGGTGTTCG 61.778 60.000 0.00 0.00 38.78 3.95
502 522 5.017294 TGTATCATGCGTAGGATTGACAA 57.983 39.130 5.87 0.00 35.32 3.18
645 665 4.927425 TGCATACTTGAGGTTTACGAGAAC 59.073 41.667 0.00 0.00 0.00 3.01
744 767 6.396829 AGAAGGAAAATCTTGTGGAGTTTG 57.603 37.500 0.00 0.00 41.45 2.93
981 1011 2.357517 GGTGGAGTGTCTGTGCGG 60.358 66.667 0.00 0.00 0.00 5.69
1102 1132 2.440247 CTGGGAAATGGGGGCGAC 60.440 66.667 0.00 0.00 0.00 5.19
1131 1161 5.698545 GCTCACACTTGAAGAACTTCTGTAT 59.301 40.000 14.31 2.37 40.14 2.29
1154 1184 2.829741 AGGAACAGAAGTGAGACAGC 57.170 50.000 0.00 0.00 0.00 4.40
1209 1239 0.038166 ACCGAATGATGCCCAGTTGT 59.962 50.000 0.00 0.00 0.00 3.32
1212 1242 0.180406 GGTACCGAATGATGCCCAGT 59.820 55.000 0.00 0.00 0.00 4.00
1470 1500 1.873591 CAGTTTGTCTTGAACCCCTCG 59.126 52.381 0.00 0.00 0.00 4.63
1558 1588 4.463891 CCAACAGCAAATAATCAACTCCCT 59.536 41.667 0.00 0.00 0.00 4.20
1637 1667 9.565213 GCAGCCAGAAATGATAAATATGATAAC 57.435 33.333 0.00 0.00 0.00 1.89
1645 1675 6.830324 TCAGTTAGCAGCCAGAAATGATAAAT 59.170 34.615 0.00 0.00 29.91 1.40
1664 1694 8.108364 GTCTAGGCTACTATAATCCCTCAGTTA 58.892 40.741 0.00 0.00 0.00 2.24
1709 1745 5.614308 TCTTATATGCACTGCTAGCACATT 58.386 37.500 20.51 12.68 45.95 2.71
1819 1863 6.028131 TCTTCCTAGATGGCAATGGATATCT 58.972 40.000 2.05 0.00 35.26 1.98
1978 2025 3.211045 AGTGCCAATACAACTTCGTGTT 58.789 40.909 0.00 0.00 39.92 3.32
2073 2120 5.875224 TCACAGGTCCATGAAATGTTTCTA 58.125 37.500 6.99 0.00 44.81 2.10
2152 2200 7.287696 GGATATACATGACAAGGAAAAACCCAT 59.712 37.037 0.00 0.00 40.05 4.00
2209 2257 4.570663 CTAACGAGAGCGGGGCGG 62.571 72.222 0.00 0.00 43.17 6.13
2210 2258 4.570663 CCTAACGAGAGCGGGGCG 62.571 72.222 0.00 0.00 43.17 6.13
2211 2259 4.222847 CCCTAACGAGAGCGGGGC 62.223 72.222 0.00 0.00 43.17 5.80
2212 2260 1.896122 AAACCCTAACGAGAGCGGGG 61.896 60.000 0.00 0.00 43.17 5.73
2213 2261 0.459759 GAAACCCTAACGAGAGCGGG 60.460 60.000 0.00 0.00 43.17 6.13
2214 2262 0.459759 GGAAACCCTAACGAGAGCGG 60.460 60.000 0.00 0.00 43.17 5.52
2215 2263 3.046280 GGAAACCCTAACGAGAGCG 57.954 57.895 0.00 0.00 44.79 5.03
3132 3182 0.926293 CCCAAAAGGGCCCAGATCTA 59.074 55.000 27.56 0.00 34.21 1.98
3505 3555 1.450312 GCGCTCCACCATACTTGCT 60.450 57.895 0.00 0.00 0.00 3.91
3531 3581 3.238497 CCACCACGACCCCAGACA 61.238 66.667 0.00 0.00 0.00 3.41
3547 3597 0.481128 TTTCTCCCAACCTCCAACCC 59.519 55.000 0.00 0.00 0.00 4.11
3745 3796 3.722295 ACCACGAAACGCCGCATG 61.722 61.111 0.00 0.00 0.00 4.06
3975 4030 4.079253 GGACACAGAAAAAGCAAGGGATA 58.921 43.478 0.00 0.00 0.00 2.59
3976 4031 2.893489 GGACACAGAAAAAGCAAGGGAT 59.107 45.455 0.00 0.00 0.00 3.85
3977 4032 2.306847 GGACACAGAAAAAGCAAGGGA 58.693 47.619 0.00 0.00 0.00 4.20
3978 4033 2.031120 TGGACACAGAAAAAGCAAGGG 58.969 47.619 0.00 0.00 0.00 3.95
3979 4034 5.183713 TCATATGGACACAGAAAAAGCAAGG 59.816 40.000 2.13 0.00 0.00 3.61
3980 4035 6.258230 TCATATGGACACAGAAAAAGCAAG 57.742 37.500 2.13 0.00 0.00 4.01
3981 4036 6.647334 TTCATATGGACACAGAAAAAGCAA 57.353 33.333 2.13 0.00 0.00 3.91
3982 4037 6.839124 ATTCATATGGACACAGAAAAAGCA 57.161 33.333 2.13 0.00 0.00 3.91
3983 4038 7.542025 AGAATTCATATGGACACAGAAAAAGC 58.458 34.615 8.44 0.00 0.00 3.51
3986 4041 9.739276 AGTTAGAATTCATATGGACACAGAAAA 57.261 29.630 8.44 0.00 0.00 2.29
4190 4245 2.353704 CCACGTGCCTCAAGTTAGATGA 60.354 50.000 10.91 0.00 0.00 2.92
4314 4369 5.932303 GCTTACAGACAGGTTTCAGTAATCA 59.068 40.000 0.00 0.00 29.96 2.57
4389 4444 9.630098 TTGCTATCAAAAATAAAAGAGCTCTTG 57.370 29.630 29.09 14.93 36.12 3.02
4427 4483 2.129555 GAAGCTGGTGCCCTTCCTGA 62.130 60.000 0.00 0.00 40.80 3.86
4459 4522 9.197306 GTAACCTGATTGATACCCCTTTTATTT 57.803 33.333 0.00 0.00 0.00 1.40
4470 4533 3.181469 TGCCTCGGTAACCTGATTGATAC 60.181 47.826 0.00 0.00 0.00 2.24
4638 4702 3.117851 GCTTAAAGGGTGAAGATAGGCCT 60.118 47.826 11.78 11.78 0.00 5.19
4706 4770 0.250513 GCAAGTCATCGAGGAAGGGT 59.749 55.000 0.00 0.00 0.00 4.34
4763 4827 6.592994 CAGTCTAACTGCTGAATTCATCTTGA 59.407 38.462 8.96 0.00 39.62 3.02
4835 4899 0.764271 TGGTGTCATGCTTGTGGAGA 59.236 50.000 0.00 0.00 0.00 3.71
4899 4963 8.506083 ACTTTTGGATATTTGGATCCTGAGTAT 58.494 33.333 14.23 8.19 45.07 2.12
4905 4969 6.745857 AGGAACTTTTGGATATTTGGATCCT 58.254 36.000 14.23 0.00 40.82 3.24
5002 5066 4.395231 TGTACTACTTGACGATCACCTCAG 59.605 45.833 0.00 0.00 0.00 3.35
5128 5192 1.137872 CACTCCACTATCAGTGCCCTC 59.862 57.143 0.64 0.00 44.63 4.30
5130 5194 3.768633 CACTCCACTATCAGTGCCC 57.231 57.895 0.64 0.00 44.63 5.36


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

AutoCloner maintained by Alex Coulton.