Multiple sequence alignment - TraesCS6B01G222700

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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 TraesCS6B01G222700 chr6B 100.000 3453 0 0 1 3453 325034136 325037588 0.000000e+00 6377
1 TraesCS6B01G222700 chr6B 99.291 3243 20 2 212 3453 365709306 365712546 0.000000e+00 5858
2 TraesCS6B01G222700 chr2A 99.229 3242 24 1 213 3453 351419579 351422820 0.000000e+00 5847
3 TraesCS6B01G222700 chr2A 98.859 3242 21 2 213 3453 642924699 642921473 0.000000e+00 5768
4 TraesCS6B01G222700 chr7A 98.520 3243 30 4 213 3453 176256562 176259788 0.000000e+00 5707
5 TraesCS6B01G222700 chr5B 98.304 3243 37 4 213 3453 161074846 161078072 0.000000e+00 5668
6 TraesCS6B01G222700 chr5A 99.218 2812 20 2 643 3453 547620693 547617883 0.000000e+00 5070
7 TraesCS6B01G222700 chr5A 93.308 777 16 6 213 987 422075408 422074666 0.000000e+00 1114
8 TraesCS6B01G222700 chr2B 99.446 2529 12 2 926 3453 669227498 669230025 0.000000e+00 4591
9 TraesCS6B01G222700 chr2B 96.535 606 6 1 212 817 669226923 669227513 0.000000e+00 989
10 TraesCS6B01G222700 chr4A 99.129 2526 21 1 929 3453 548525503 548522978 0.000000e+00 4542
11 TraesCS6B01G222700 chr4A 94.878 781 20 5 209 987 548526251 548525489 0.000000e+00 1203
12 TraesCS6B01G222700 chr1A 99.129 2526 21 1 929 3453 80308178 80305653 0.000000e+00 4542
13 TraesCS6B01G222700 chr4B 95.478 774 17 5 213 984 439195477 439196234 0.000000e+00 1219
14 TraesCS6B01G222700 chr6A 95.646 758 16 5 213 969 466092189 466092930 0.000000e+00 1201
15 TraesCS6B01G222700 chr6A 82.474 194 7 3 46 212 250715306 250715113 9.990000e-31 145
16 TraesCS6B01G222700 chr2D 87.514 865 61 26 213 1068 33017492 33018318 0.000000e+00 955
17 TraesCS6B01G222700 chr6D 85.586 222 5 2 18 212 200490878 200491099 1.260000e-49 207


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 TraesCS6B01G222700 chr6B 325034136 325037588 3452 False 6377.0 6377 100.0000 1 3453 1 chr6B.!!$F1 3452
1 TraesCS6B01G222700 chr6B 365709306 365712546 3240 False 5858.0 5858 99.2910 212 3453 1 chr6B.!!$F2 3241
2 TraesCS6B01G222700 chr2A 351419579 351422820 3241 False 5847.0 5847 99.2290 213 3453 1 chr2A.!!$F1 3240
3 TraesCS6B01G222700 chr2A 642921473 642924699 3226 True 5768.0 5768 98.8590 213 3453 1 chr2A.!!$R1 3240
4 TraesCS6B01G222700 chr7A 176256562 176259788 3226 False 5707.0 5707 98.5200 213 3453 1 chr7A.!!$F1 3240
5 TraesCS6B01G222700 chr5B 161074846 161078072 3226 False 5668.0 5668 98.3040 213 3453 1 chr5B.!!$F1 3240
6 TraesCS6B01G222700 chr5A 547617883 547620693 2810 True 5070.0 5070 99.2180 643 3453 1 chr5A.!!$R2 2810
7 TraesCS6B01G222700 chr5A 422074666 422075408 742 True 1114.0 1114 93.3080 213 987 1 chr5A.!!$R1 774
8 TraesCS6B01G222700 chr2B 669226923 669230025 3102 False 2790.0 4591 97.9905 212 3453 2 chr2B.!!$F1 3241
9 TraesCS6B01G222700 chr4A 548522978 548526251 3273 True 2872.5 4542 97.0035 209 3453 2 chr4A.!!$R1 3244
10 TraesCS6B01G222700 chr1A 80305653 80308178 2525 True 4542.0 4542 99.1290 929 3453 1 chr1A.!!$R1 2524
11 TraesCS6B01G222700 chr4B 439195477 439196234 757 False 1219.0 1219 95.4780 213 984 1 chr4B.!!$F1 771
12 TraesCS6B01G222700 chr6A 466092189 466092930 741 False 1201.0 1201 95.6460 213 969 1 chr6A.!!$F1 756
13 TraesCS6B01G222700 chr2D 33017492 33018318 826 False 955.0 955 87.5140 213 1068 1 chr2D.!!$F1 855

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
90 91 0.032403 TTTGCATGTGTCAAGCTGGC 59.968 50.0 0.00 0.0 0.0 4.85 F
97 98 0.036022 GTGTCAAGCTGGCCTTCTCT 59.964 55.0 3.32 0.0 0.0 3.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1898 1961 1.411977 CTGAGTATCCACCTCTGCCTG 59.588 57.143 0.0 0.0 0.0 4.85 R
2923 2987 2.524569 AGCCCCAAAAATGTTGTTCG 57.475 45.000 0.0 0.0 0.0 3.95 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
25 26 7.547285 TTTGCGTTTTCTCGAAAATATTCTG 57.453 32.000 7.95 0.00 41.64 3.02
26 27 5.627172 TGCGTTTTCTCGAAAATATTCTGG 58.373 37.500 7.95 0.00 41.64 3.86
27 28 5.028375 GCGTTTTCTCGAAAATATTCTGGG 58.972 41.667 7.95 0.00 41.64 4.45
28 29 5.163794 GCGTTTTCTCGAAAATATTCTGGGA 60.164 40.000 7.95 0.00 41.64 4.37
29 30 6.622028 GCGTTTTCTCGAAAATATTCTGGGAA 60.622 38.462 7.95 0.00 41.64 3.97
30 31 7.472543 CGTTTTCTCGAAAATATTCTGGGAAT 58.527 34.615 7.95 0.00 41.64 3.01
31 32 7.429340 CGTTTTCTCGAAAATATTCTGGGAATG 59.571 37.037 7.95 0.00 41.64 2.67
32 33 6.377327 TTCTCGAAAATATTCTGGGAATGC 57.623 37.500 3.37 0.00 33.17 3.56
33 34 5.684704 TCTCGAAAATATTCTGGGAATGCT 58.315 37.500 3.37 0.00 33.17 3.79
34 35 6.122277 TCTCGAAAATATTCTGGGAATGCTT 58.878 36.000 3.37 0.00 33.17 3.91
35 36 6.603201 TCTCGAAAATATTCTGGGAATGCTTT 59.397 34.615 3.37 3.17 33.17 3.51
36 37 6.563422 TCGAAAATATTCTGGGAATGCTTTG 58.437 36.000 3.37 0.00 33.17 2.77
37 38 6.376864 TCGAAAATATTCTGGGAATGCTTTGA 59.623 34.615 3.37 1.76 33.17 2.69
38 39 6.473455 CGAAAATATTCTGGGAATGCTTTGAC 59.527 38.462 3.37 2.58 33.17 3.18
39 40 7.486407 AAAATATTCTGGGAATGCTTTGACT 57.514 32.000 3.37 0.00 0.00 3.41
40 41 8.593945 AAAATATTCTGGGAATGCTTTGACTA 57.406 30.769 3.37 0.00 0.00 2.59
41 42 7.573968 AATATTCTGGGAATGCTTTGACTAC 57.426 36.000 3.37 0.00 0.00 2.73
42 43 3.350219 TCTGGGAATGCTTTGACTACC 57.650 47.619 0.00 0.00 0.00 3.18
43 44 2.912956 TCTGGGAATGCTTTGACTACCT 59.087 45.455 0.00 0.00 0.00 3.08
44 45 3.055094 TCTGGGAATGCTTTGACTACCTC 60.055 47.826 0.00 0.00 0.00 3.85
45 46 2.642311 TGGGAATGCTTTGACTACCTCA 59.358 45.455 0.00 0.00 0.00 3.86
46 47 3.073798 TGGGAATGCTTTGACTACCTCAA 59.926 43.478 0.00 0.00 37.08 3.02
47 48 3.691609 GGGAATGCTTTGACTACCTCAAG 59.308 47.826 0.00 0.00 40.12 3.02
48 49 3.127721 GGAATGCTTTGACTACCTCAAGC 59.872 47.826 0.00 0.00 40.12 4.01
49 50 2.928801 TGCTTTGACTACCTCAAGCA 57.071 45.000 1.34 1.34 40.12 3.91
50 51 3.207265 TGCTTTGACTACCTCAAGCAA 57.793 42.857 3.00 0.00 40.12 3.91
51 52 3.550820 TGCTTTGACTACCTCAAGCAAA 58.449 40.909 3.00 0.00 40.12 3.68
52 53 3.315191 TGCTTTGACTACCTCAAGCAAAC 59.685 43.478 3.00 0.00 40.12 2.93
53 54 3.315191 GCTTTGACTACCTCAAGCAAACA 59.685 43.478 0.00 0.00 40.12 2.83
54 55 4.022849 GCTTTGACTACCTCAAGCAAACAT 60.023 41.667 0.00 0.00 40.12 2.71
55 56 5.437289 TTTGACTACCTCAAGCAAACATG 57.563 39.130 0.00 0.00 40.12 3.21
56 57 3.411446 TGACTACCTCAAGCAAACATGG 58.589 45.455 0.00 0.00 0.00 3.66
57 58 2.749621 GACTACCTCAAGCAAACATGGG 59.250 50.000 0.00 0.00 0.00 4.00
58 59 1.474077 CTACCTCAAGCAAACATGGGC 59.526 52.381 0.00 0.00 0.00 5.36
59 60 0.469705 ACCTCAAGCAAACATGGGCA 60.470 50.000 0.00 0.00 0.00 5.36
60 61 0.680618 CCTCAAGCAAACATGGGCAA 59.319 50.000 0.00 0.00 0.00 4.52
61 62 1.337447 CCTCAAGCAAACATGGGCAAG 60.337 52.381 0.00 0.00 0.00 4.01
62 63 0.680618 TCAAGCAAACATGGGCAAGG 59.319 50.000 0.00 0.00 0.00 3.61
63 64 0.320946 CAAGCAAACATGGGCAAGGG 60.321 55.000 0.00 0.00 0.00 3.95
64 65 0.763986 AAGCAAACATGGGCAAGGGT 60.764 50.000 0.00 0.00 0.00 4.34
65 66 0.114168 AGCAAACATGGGCAAGGGTA 59.886 50.000 0.00 0.00 0.00 3.69
66 67 0.972883 GCAAACATGGGCAAGGGTAA 59.027 50.000 0.00 0.00 0.00 2.85
67 68 1.337728 GCAAACATGGGCAAGGGTAAC 60.338 52.381 0.00 0.00 0.00 2.50
68 69 1.967066 CAAACATGGGCAAGGGTAACA 59.033 47.619 0.00 0.00 39.74 2.41
69 70 2.366916 CAAACATGGGCAAGGGTAACAA 59.633 45.455 0.00 0.00 39.74 2.83
70 71 2.390225 ACATGGGCAAGGGTAACAAA 57.610 45.000 0.00 0.00 39.74 2.83
71 72 2.901291 ACATGGGCAAGGGTAACAAAT 58.099 42.857 0.00 0.00 39.74 2.32
72 73 3.247162 ACATGGGCAAGGGTAACAAATT 58.753 40.909 0.00 0.00 39.74 1.82
73 74 3.650461 ACATGGGCAAGGGTAACAAATTT 59.350 39.130 0.00 0.00 39.74 1.82
74 75 3.760580 TGGGCAAGGGTAACAAATTTG 57.239 42.857 16.67 16.67 39.74 2.32
75 76 2.224402 TGGGCAAGGGTAACAAATTTGC 60.224 45.455 18.12 1.15 42.43 3.68
76 77 2.224402 GGGCAAGGGTAACAAATTTGCA 60.224 45.455 18.12 3.54 44.33 4.08
77 78 3.558958 GGGCAAGGGTAACAAATTTGCAT 60.559 43.478 18.12 9.89 44.33 3.96
78 79 3.436359 GGCAAGGGTAACAAATTTGCATG 59.564 43.478 18.12 5.95 44.33 4.06
79 80 4.064388 GCAAGGGTAACAAATTTGCATGT 58.936 39.130 18.12 4.05 42.63 3.21
80 81 4.083908 GCAAGGGTAACAAATTTGCATGTG 60.084 41.667 18.12 8.37 42.63 3.21
81 82 4.953940 AGGGTAACAAATTTGCATGTGT 57.046 36.364 18.12 0.00 31.37 3.72
82 83 4.881920 AGGGTAACAAATTTGCATGTGTC 58.118 39.130 18.12 2.82 28.32 3.67
83 84 4.343526 AGGGTAACAAATTTGCATGTGTCA 59.656 37.500 18.12 0.00 28.32 3.58
84 85 5.053145 GGGTAACAAATTTGCATGTGTCAA 58.947 37.500 18.12 0.00 28.32 3.18
85 86 5.177327 GGGTAACAAATTTGCATGTGTCAAG 59.823 40.000 18.12 0.00 28.32 3.02
86 87 4.799419 AACAAATTTGCATGTGTCAAGC 57.201 36.364 18.12 0.00 28.32 4.01
87 88 4.062677 ACAAATTTGCATGTGTCAAGCT 57.937 36.364 18.12 0.00 0.00 3.74
88 89 3.805422 ACAAATTTGCATGTGTCAAGCTG 59.195 39.130 18.12 0.00 0.00 4.24
89 90 2.736144 ATTTGCATGTGTCAAGCTGG 57.264 45.000 0.00 0.00 0.00 4.85
90 91 0.032403 TTTGCATGTGTCAAGCTGGC 59.968 50.000 0.00 0.00 0.00 4.85
91 92 1.808531 TTGCATGTGTCAAGCTGGCC 61.809 55.000 0.00 0.00 0.00 5.36
92 93 1.975407 GCATGTGTCAAGCTGGCCT 60.975 57.895 3.32 0.00 0.00 5.19
93 94 1.530013 GCATGTGTCAAGCTGGCCTT 61.530 55.000 3.32 0.00 0.00 4.35
94 95 0.524862 CATGTGTCAAGCTGGCCTTC 59.475 55.000 3.32 0.00 0.00 3.46
95 96 0.403271 ATGTGTCAAGCTGGCCTTCT 59.597 50.000 3.32 0.00 0.00 2.85
96 97 0.250467 TGTGTCAAGCTGGCCTTCTC 60.250 55.000 3.32 0.00 0.00 2.87
97 98 0.036022 GTGTCAAGCTGGCCTTCTCT 59.964 55.000 3.32 0.00 0.00 3.10
98 99 1.276421 GTGTCAAGCTGGCCTTCTCTA 59.724 52.381 3.32 0.00 0.00 2.43
99 100 2.093235 GTGTCAAGCTGGCCTTCTCTAT 60.093 50.000 3.32 0.00 0.00 1.98
100 101 2.093288 TGTCAAGCTGGCCTTCTCTATG 60.093 50.000 3.32 0.00 0.00 2.23
101 102 2.093235 GTCAAGCTGGCCTTCTCTATGT 60.093 50.000 3.32 0.00 0.00 2.29
102 103 3.133003 GTCAAGCTGGCCTTCTCTATGTA 59.867 47.826 3.32 0.00 0.00 2.29
103 104 3.386078 TCAAGCTGGCCTTCTCTATGTAG 59.614 47.826 3.32 0.00 0.00 2.74
104 105 2.324541 AGCTGGCCTTCTCTATGTAGG 58.675 52.381 3.32 0.00 36.44 3.18
113 114 6.339587 CCTTCTCTATGTAGGCTTAGGAAG 57.660 45.833 0.00 4.49 34.34 3.46
114 115 5.245075 CCTTCTCTATGTAGGCTTAGGAAGG 59.755 48.000 17.83 17.83 39.59 3.46
115 116 4.742012 TCTCTATGTAGGCTTAGGAAGGG 58.258 47.826 0.00 0.00 0.00 3.95
116 117 3.835395 CTCTATGTAGGCTTAGGAAGGGG 59.165 52.174 0.00 0.00 0.00 4.79
117 118 2.889522 ATGTAGGCTTAGGAAGGGGA 57.110 50.000 0.00 0.00 0.00 4.81
118 119 2.653543 TGTAGGCTTAGGAAGGGGAA 57.346 50.000 0.00 0.00 0.00 3.97
119 120 2.478292 TGTAGGCTTAGGAAGGGGAAG 58.522 52.381 0.00 0.00 0.00 3.46
120 121 1.769465 GTAGGCTTAGGAAGGGGAAGG 59.231 57.143 0.00 0.00 0.00 3.46
121 122 0.121402 AGGCTTAGGAAGGGGAAGGT 59.879 55.000 0.00 0.00 0.00 3.50
122 123 0.256177 GGCTTAGGAAGGGGAAGGTG 59.744 60.000 0.00 0.00 0.00 4.00
123 124 0.256177 GCTTAGGAAGGGGAAGGTGG 59.744 60.000 0.00 0.00 0.00 4.61
124 125 1.670059 CTTAGGAAGGGGAAGGTGGT 58.330 55.000 0.00 0.00 0.00 4.16
125 126 1.560146 CTTAGGAAGGGGAAGGTGGTC 59.440 57.143 0.00 0.00 0.00 4.02
126 127 0.797579 TAGGAAGGGGAAGGTGGTCT 59.202 55.000 0.00 0.00 0.00 3.85
127 128 0.797579 AGGAAGGGGAAGGTGGTCTA 59.202 55.000 0.00 0.00 0.00 2.59
128 129 1.205055 GGAAGGGGAAGGTGGTCTAG 58.795 60.000 0.00 0.00 0.00 2.43
129 130 1.205055 GAAGGGGAAGGTGGTCTAGG 58.795 60.000 0.00 0.00 0.00 3.02
130 131 0.797579 AAGGGGAAGGTGGTCTAGGA 59.202 55.000 0.00 0.00 0.00 2.94
131 132 1.027815 AGGGGAAGGTGGTCTAGGAT 58.972 55.000 0.00 0.00 0.00 3.24
132 133 2.233178 AGGGGAAGGTGGTCTAGGATA 58.767 52.381 0.00 0.00 0.00 2.59
133 134 2.180308 AGGGGAAGGTGGTCTAGGATAG 59.820 54.545 0.00 0.00 41.04 2.08
134 135 1.972075 GGGAAGGTGGTCTAGGATAGC 59.028 57.143 0.00 0.00 38.99 2.97
135 136 2.426561 GGGAAGGTGGTCTAGGATAGCT 60.427 54.545 0.00 0.00 38.99 3.32
136 137 3.310193 GGAAGGTGGTCTAGGATAGCTT 58.690 50.000 0.00 5.56 38.99 3.74
137 138 3.712218 GGAAGGTGGTCTAGGATAGCTTT 59.288 47.826 0.00 0.00 38.99 3.51
138 139 4.443598 GGAAGGTGGTCTAGGATAGCTTTG 60.444 50.000 0.00 0.00 38.99 2.77
139 140 3.041946 AGGTGGTCTAGGATAGCTTTGG 58.958 50.000 0.00 0.00 38.99 3.28
140 141 2.104963 GGTGGTCTAGGATAGCTTTGGG 59.895 54.545 0.00 0.00 38.99 4.12
141 142 2.772515 GTGGTCTAGGATAGCTTTGGGT 59.227 50.000 0.00 0.00 38.99 4.51
142 143 2.771943 TGGTCTAGGATAGCTTTGGGTG 59.228 50.000 0.00 0.00 38.99 4.61
143 144 3.039011 GGTCTAGGATAGCTTTGGGTGA 58.961 50.000 0.00 0.00 38.99 4.02
144 145 3.648545 GGTCTAGGATAGCTTTGGGTGAT 59.351 47.826 0.00 0.00 38.99 3.06
145 146 4.838986 GGTCTAGGATAGCTTTGGGTGATA 59.161 45.833 0.00 0.00 38.99 2.15
146 147 5.307196 GGTCTAGGATAGCTTTGGGTGATAA 59.693 44.000 0.00 0.00 38.99 1.75
147 148 6.183361 GGTCTAGGATAGCTTTGGGTGATAAA 60.183 42.308 0.00 0.00 38.99 1.40
148 149 7.280356 GTCTAGGATAGCTTTGGGTGATAAAA 58.720 38.462 0.00 0.00 38.99 1.52
149 150 7.442666 GTCTAGGATAGCTTTGGGTGATAAAAG 59.557 40.741 0.00 0.00 38.99 2.27
150 151 5.449553 AGGATAGCTTTGGGTGATAAAAGG 58.550 41.667 0.00 0.00 34.60 3.11
151 152 4.584743 GGATAGCTTTGGGTGATAAAAGGG 59.415 45.833 0.00 0.00 34.60 3.95
152 153 2.179427 AGCTTTGGGTGATAAAAGGGC 58.821 47.619 0.00 0.00 34.60 5.19
153 154 2.179427 GCTTTGGGTGATAAAAGGGCT 58.821 47.619 0.00 0.00 34.60 5.19
154 155 3.011257 AGCTTTGGGTGATAAAAGGGCTA 59.989 43.478 0.00 0.00 34.60 3.93
155 156 3.767131 GCTTTGGGTGATAAAAGGGCTAA 59.233 43.478 0.00 0.00 34.60 3.09
156 157 4.405680 GCTTTGGGTGATAAAAGGGCTAAT 59.594 41.667 0.00 0.00 34.60 1.73
157 158 5.682212 GCTTTGGGTGATAAAAGGGCTAATG 60.682 44.000 0.00 0.00 34.60 1.90
158 159 4.601406 TGGGTGATAAAAGGGCTAATGT 57.399 40.909 0.00 0.00 0.00 2.71
159 160 4.277476 TGGGTGATAAAAGGGCTAATGTG 58.723 43.478 0.00 0.00 0.00 3.21
160 161 3.068165 GGGTGATAAAAGGGCTAATGTGC 59.932 47.826 0.00 0.00 0.00 4.57
169 170 2.493547 GCTAATGTGCCTGGAACCC 58.506 57.895 1.39 0.00 0.00 4.11
170 171 0.323360 GCTAATGTGCCTGGAACCCA 60.323 55.000 1.39 0.00 0.00 4.51
179 180 3.636231 TGGAACCCAGGCAGACGG 61.636 66.667 0.00 0.00 0.00 4.79
180 181 3.637273 GGAACCCAGGCAGACGGT 61.637 66.667 0.00 0.00 0.00 4.83
181 182 2.358737 GAACCCAGGCAGACGGTG 60.359 66.667 0.00 0.00 0.00 4.94
182 183 3.168528 AACCCAGGCAGACGGTGT 61.169 61.111 0.00 0.00 0.00 4.16
183 184 3.178540 AACCCAGGCAGACGGTGTC 62.179 63.158 0.00 0.00 0.00 3.67
184 185 3.314331 CCCAGGCAGACGGTGTCT 61.314 66.667 0.00 0.00 44.21 3.41
194 195 1.546476 AGACGGTGTCTGACTTCATCC 59.454 52.381 9.51 3.54 41.76 3.51
195 196 1.546476 GACGGTGTCTGACTTCATCCT 59.454 52.381 9.51 0.00 0.00 3.24
196 197 1.273606 ACGGTGTCTGACTTCATCCTG 59.726 52.381 9.51 0.00 0.00 3.86
197 198 1.546029 CGGTGTCTGACTTCATCCTGA 59.454 52.381 9.51 0.00 0.00 3.86
198 199 2.416566 CGGTGTCTGACTTCATCCTGAG 60.417 54.545 9.51 0.00 0.00 3.35
199 200 2.615869 GTGTCTGACTTCATCCTGAGC 58.384 52.381 9.51 0.00 0.00 4.26
200 201 2.028658 GTGTCTGACTTCATCCTGAGCA 60.029 50.000 9.51 0.00 0.00 4.26
201 202 2.634453 TGTCTGACTTCATCCTGAGCAA 59.366 45.455 9.51 0.00 0.00 3.91
202 203 3.260740 GTCTGACTTCATCCTGAGCAAG 58.739 50.000 0.00 0.00 0.00 4.01
1044 1107 1.672356 GGCTTTGGAGAAGCTCGCA 60.672 57.895 10.21 0.00 42.62 5.10
1502 1565 2.403132 GAACTGCAGGCTCTGTGGGT 62.403 60.000 19.93 0.00 33.43 4.51
2923 2987 1.940613 GGACAATGGAACGGAGTATGC 59.059 52.381 0.00 0.00 45.00 3.14
3023 3087 0.601841 GAGTGGCCGAACGGAAGAAA 60.602 55.000 17.63 0.00 37.50 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.273381 CCAGAATATTTTCGAGAAAACGCAAAT 59.727 33.333 12.51 0.00 42.32 2.32
1 2 6.580791 CCAGAATATTTTCGAGAAAACGCAAA 59.419 34.615 12.51 0.00 42.32 3.68
2 3 6.083630 CCAGAATATTTTCGAGAAAACGCAA 58.916 36.000 12.51 1.31 42.32 4.85
3 4 5.391523 CCCAGAATATTTTCGAGAAAACGCA 60.392 40.000 12.51 3.14 42.32 5.24
4 5 5.028375 CCCAGAATATTTTCGAGAAAACGC 58.972 41.667 12.51 4.05 42.32 4.84
5 6 6.417191 TCCCAGAATATTTTCGAGAAAACG 57.583 37.500 12.51 0.00 42.32 3.60
6 7 7.220875 GCATTCCCAGAATATTTTCGAGAAAAC 59.779 37.037 12.51 1.73 42.32 2.43
7 8 7.122650 AGCATTCCCAGAATATTTTCGAGAAAA 59.877 33.333 12.61 12.61 43.48 2.29
8 9 6.603201 AGCATTCCCAGAATATTTTCGAGAAA 59.397 34.615 0.00 0.00 36.93 2.52
9 10 6.122277 AGCATTCCCAGAATATTTTCGAGAA 58.878 36.000 0.00 0.00 36.93 2.87
10 11 5.684704 AGCATTCCCAGAATATTTTCGAGA 58.315 37.500 0.00 0.00 36.93 4.04
11 12 6.382869 AAGCATTCCCAGAATATTTTCGAG 57.617 37.500 0.00 0.00 36.93 4.04
12 13 6.376864 TCAAAGCATTCCCAGAATATTTTCGA 59.623 34.615 0.00 0.00 36.93 3.71
13 14 6.473455 GTCAAAGCATTCCCAGAATATTTTCG 59.527 38.462 0.00 0.00 36.93 3.46
14 15 7.550712 AGTCAAAGCATTCCCAGAATATTTTC 58.449 34.615 0.00 0.00 0.00 2.29
15 16 7.486407 AGTCAAAGCATTCCCAGAATATTTT 57.514 32.000 0.00 0.00 0.00 1.82
16 17 7.068716 GGTAGTCAAAGCATTCCCAGAATATTT 59.931 37.037 0.00 0.00 0.00 1.40
17 18 6.547510 GGTAGTCAAAGCATTCCCAGAATATT 59.452 38.462 0.00 0.00 0.00 1.28
18 19 6.064717 GGTAGTCAAAGCATTCCCAGAATAT 58.935 40.000 0.00 0.00 0.00 1.28
19 20 5.191722 AGGTAGTCAAAGCATTCCCAGAATA 59.808 40.000 0.00 0.00 0.00 1.75
20 21 4.018050 AGGTAGTCAAAGCATTCCCAGAAT 60.018 41.667 0.00 0.00 0.00 2.40
21 22 3.330701 AGGTAGTCAAAGCATTCCCAGAA 59.669 43.478 0.00 0.00 0.00 3.02
22 23 2.912956 AGGTAGTCAAAGCATTCCCAGA 59.087 45.455 0.00 0.00 0.00 3.86
23 24 3.274288 GAGGTAGTCAAAGCATTCCCAG 58.726 50.000 0.00 0.00 0.00 4.45
24 25 2.642311 TGAGGTAGTCAAAGCATTCCCA 59.358 45.455 0.00 0.00 29.64 4.37
25 26 3.350219 TGAGGTAGTCAAAGCATTCCC 57.650 47.619 0.00 0.00 29.64 3.97
26 27 3.127721 GCTTGAGGTAGTCAAAGCATTCC 59.872 47.826 1.57 0.00 44.83 3.01
27 28 3.753272 TGCTTGAGGTAGTCAAAGCATTC 59.247 43.478 4.91 0.00 44.83 2.67
28 29 3.754965 TGCTTGAGGTAGTCAAAGCATT 58.245 40.909 4.91 0.00 44.83 3.56
29 30 3.423539 TGCTTGAGGTAGTCAAAGCAT 57.576 42.857 4.91 0.00 44.83 3.79
30 31 2.928801 TGCTTGAGGTAGTCAAAGCA 57.071 45.000 4.91 4.91 44.83 3.91
31 32 3.315191 TGTTTGCTTGAGGTAGTCAAAGC 59.685 43.478 0.00 0.00 44.83 3.51
32 33 5.455392 CATGTTTGCTTGAGGTAGTCAAAG 58.545 41.667 0.00 0.00 44.83 2.77
33 34 4.278170 CCATGTTTGCTTGAGGTAGTCAAA 59.722 41.667 0.00 0.00 44.83 2.69
34 35 3.820467 CCATGTTTGCTTGAGGTAGTCAA 59.180 43.478 0.00 0.00 43.26 3.18
35 36 3.411446 CCATGTTTGCTTGAGGTAGTCA 58.589 45.455 0.00 0.00 0.00 3.41
36 37 2.749621 CCCATGTTTGCTTGAGGTAGTC 59.250 50.000 0.00 0.00 0.00 2.59
37 38 2.795329 CCCATGTTTGCTTGAGGTAGT 58.205 47.619 0.00 0.00 0.00 2.73
38 39 1.474077 GCCCATGTTTGCTTGAGGTAG 59.526 52.381 0.00 0.00 0.00 3.18
39 40 1.202989 TGCCCATGTTTGCTTGAGGTA 60.203 47.619 0.00 0.00 0.00 3.08
40 41 0.469705 TGCCCATGTTTGCTTGAGGT 60.470 50.000 0.00 0.00 0.00 3.85
41 42 0.680618 TTGCCCATGTTTGCTTGAGG 59.319 50.000 0.00 0.00 0.00 3.86
42 43 1.337447 CCTTGCCCATGTTTGCTTGAG 60.337 52.381 0.00 0.00 0.00 3.02
43 44 0.680618 CCTTGCCCATGTTTGCTTGA 59.319 50.000 0.00 0.00 0.00 3.02
44 45 0.320946 CCCTTGCCCATGTTTGCTTG 60.321 55.000 0.00 0.00 0.00 4.01
45 46 0.763986 ACCCTTGCCCATGTTTGCTT 60.764 50.000 0.00 0.00 0.00 3.91
46 47 0.114168 TACCCTTGCCCATGTTTGCT 59.886 50.000 0.00 0.00 0.00 3.91
47 48 0.972883 TTACCCTTGCCCATGTTTGC 59.027 50.000 0.00 0.00 0.00 3.68
48 49 1.967066 TGTTACCCTTGCCCATGTTTG 59.033 47.619 0.00 0.00 0.00 2.93
49 50 2.390225 TGTTACCCTTGCCCATGTTT 57.610 45.000 0.00 0.00 0.00 2.83
50 51 2.390225 TTGTTACCCTTGCCCATGTT 57.610 45.000 0.00 0.00 0.00 2.71
51 52 2.390225 TTTGTTACCCTTGCCCATGT 57.610 45.000 0.00 0.00 0.00 3.21
52 53 3.979101 AATTTGTTACCCTTGCCCATG 57.021 42.857 0.00 0.00 0.00 3.66
53 54 3.558958 GCAAATTTGTTACCCTTGCCCAT 60.559 43.478 19.03 0.00 37.10 4.00
54 55 2.224402 GCAAATTTGTTACCCTTGCCCA 60.224 45.455 19.03 0.00 37.10 5.36
55 56 2.224402 TGCAAATTTGTTACCCTTGCCC 60.224 45.455 19.03 0.00 41.29 5.36
56 57 3.118905 TGCAAATTTGTTACCCTTGCC 57.881 42.857 19.03 0.00 41.29 4.52
57 58 4.064388 ACATGCAAATTTGTTACCCTTGC 58.936 39.130 19.03 3.15 42.12 4.01
58 59 5.055812 ACACATGCAAATTTGTTACCCTTG 58.944 37.500 19.03 11.95 0.00 3.61
59 60 5.163364 TGACACATGCAAATTTGTTACCCTT 60.163 36.000 19.03 0.00 0.00 3.95
60 61 4.343526 TGACACATGCAAATTTGTTACCCT 59.656 37.500 19.03 0.00 0.00 4.34
61 62 4.626042 TGACACATGCAAATTTGTTACCC 58.374 39.130 19.03 3.17 0.00 3.69
62 63 5.333263 GCTTGACACATGCAAATTTGTTACC 60.333 40.000 19.03 3.53 35.13 2.85
63 64 5.463061 AGCTTGACACATGCAAATTTGTTAC 59.537 36.000 19.03 3.88 37.06 2.50
64 65 5.462729 CAGCTTGACACATGCAAATTTGTTA 59.537 36.000 19.03 9.50 37.06 2.41
65 66 4.271533 CAGCTTGACACATGCAAATTTGTT 59.728 37.500 19.03 5.12 37.06 2.83
66 67 3.805422 CAGCTTGACACATGCAAATTTGT 59.195 39.130 19.03 0.00 37.06 2.83
67 68 3.185594 CCAGCTTGACACATGCAAATTTG 59.814 43.478 14.03 14.03 37.06 2.32
68 69 3.395639 CCAGCTTGACACATGCAAATTT 58.604 40.909 11.07 0.00 37.06 1.82
69 70 2.868839 GCCAGCTTGACACATGCAAATT 60.869 45.455 11.07 0.00 37.06 1.82
70 71 1.337447 GCCAGCTTGACACATGCAAAT 60.337 47.619 11.07 0.00 37.06 2.32
71 72 0.032403 GCCAGCTTGACACATGCAAA 59.968 50.000 11.07 0.00 37.06 3.68
72 73 1.661480 GCCAGCTTGACACATGCAA 59.339 52.632 11.07 0.00 37.06 4.08
73 74 2.270257 GGCCAGCTTGACACATGCA 61.270 57.895 0.00 0.00 37.06 3.96
74 75 1.530013 AAGGCCAGCTTGACACATGC 61.530 55.000 5.01 0.00 35.22 4.06
75 76 0.524862 GAAGGCCAGCTTGACACATG 59.475 55.000 5.01 0.00 0.00 3.21
76 77 0.403271 AGAAGGCCAGCTTGACACAT 59.597 50.000 5.01 0.00 0.00 3.21
77 78 0.250467 GAGAAGGCCAGCTTGACACA 60.250 55.000 5.01 0.00 0.00 3.72
78 79 0.036022 AGAGAAGGCCAGCTTGACAC 59.964 55.000 5.01 0.00 0.00 3.67
79 80 1.644509 TAGAGAAGGCCAGCTTGACA 58.355 50.000 5.01 0.00 0.00 3.58
80 81 2.093235 ACATAGAGAAGGCCAGCTTGAC 60.093 50.000 5.01 0.00 0.00 3.18
81 82 2.191400 ACATAGAGAAGGCCAGCTTGA 58.809 47.619 5.01 0.00 0.00 3.02
82 83 2.706339 ACATAGAGAAGGCCAGCTTG 57.294 50.000 5.01 0.00 0.00 4.01
83 84 2.703007 CCTACATAGAGAAGGCCAGCTT 59.297 50.000 5.01 0.00 0.00 3.74
84 85 2.324541 CCTACATAGAGAAGGCCAGCT 58.675 52.381 5.01 0.00 0.00 4.24
85 86 2.829741 CCTACATAGAGAAGGCCAGC 57.170 55.000 5.01 0.00 0.00 4.85
90 91 5.245075 CCTTCCTAAGCCTACATAGAGAAGG 59.755 48.000 0.00 0.00 37.72 3.46
91 92 5.245075 CCCTTCCTAAGCCTACATAGAGAAG 59.755 48.000 0.00 0.00 31.41 2.85
92 93 5.148502 CCCTTCCTAAGCCTACATAGAGAA 58.851 45.833 0.00 0.00 0.00 2.87
93 94 4.449376 CCCCTTCCTAAGCCTACATAGAGA 60.449 50.000 0.00 0.00 0.00 3.10
94 95 3.835395 CCCCTTCCTAAGCCTACATAGAG 59.165 52.174 0.00 0.00 0.00 2.43
95 96 3.469771 TCCCCTTCCTAAGCCTACATAGA 59.530 47.826 0.00 0.00 0.00 1.98
96 97 3.858135 TCCCCTTCCTAAGCCTACATAG 58.142 50.000 0.00 0.00 0.00 2.23
97 98 4.232091 CTTCCCCTTCCTAAGCCTACATA 58.768 47.826 0.00 0.00 0.00 2.29
98 99 2.889522 TCCCCTTCCTAAGCCTACAT 57.110 50.000 0.00 0.00 0.00 2.29
99 100 2.478292 CTTCCCCTTCCTAAGCCTACA 58.522 52.381 0.00 0.00 0.00 2.74
100 101 1.769465 CCTTCCCCTTCCTAAGCCTAC 59.231 57.143 0.00 0.00 0.00 3.18
101 102 1.368558 ACCTTCCCCTTCCTAAGCCTA 59.631 52.381 0.00 0.00 0.00 3.93
102 103 0.121402 ACCTTCCCCTTCCTAAGCCT 59.879 55.000 0.00 0.00 0.00 4.58
103 104 0.256177 CACCTTCCCCTTCCTAAGCC 59.744 60.000 0.00 0.00 0.00 4.35
104 105 0.256177 CCACCTTCCCCTTCCTAAGC 59.744 60.000 0.00 0.00 0.00 3.09
105 106 1.560146 GACCACCTTCCCCTTCCTAAG 59.440 57.143 0.00 0.00 0.00 2.18
106 107 1.153565 AGACCACCTTCCCCTTCCTAA 59.846 52.381 0.00 0.00 0.00 2.69
107 108 0.797579 AGACCACCTTCCCCTTCCTA 59.202 55.000 0.00 0.00 0.00 2.94
108 109 0.797579 TAGACCACCTTCCCCTTCCT 59.202 55.000 0.00 0.00 0.00 3.36
109 110 1.205055 CTAGACCACCTTCCCCTTCC 58.795 60.000 0.00 0.00 0.00 3.46
110 111 1.205055 CCTAGACCACCTTCCCCTTC 58.795 60.000 0.00 0.00 0.00 3.46
111 112 0.797579 TCCTAGACCACCTTCCCCTT 59.202 55.000 0.00 0.00 0.00 3.95
112 113 1.027815 ATCCTAGACCACCTTCCCCT 58.972 55.000 0.00 0.00 0.00 4.79
113 114 2.610873 CTATCCTAGACCACCTTCCCC 58.389 57.143 0.00 0.00 0.00 4.81
114 115 1.972075 GCTATCCTAGACCACCTTCCC 59.028 57.143 0.00 0.00 0.00 3.97
115 116 2.965562 AGCTATCCTAGACCACCTTCC 58.034 52.381 0.00 0.00 0.00 3.46
116 117 4.443598 CCAAAGCTATCCTAGACCACCTTC 60.444 50.000 0.00 0.00 0.00 3.46
117 118 3.456277 CCAAAGCTATCCTAGACCACCTT 59.544 47.826 0.00 0.00 0.00 3.50
118 119 3.041946 CCAAAGCTATCCTAGACCACCT 58.958 50.000 0.00 0.00 0.00 4.00
119 120 2.104963 CCCAAAGCTATCCTAGACCACC 59.895 54.545 0.00 0.00 0.00 4.61
120 121 2.772515 ACCCAAAGCTATCCTAGACCAC 59.227 50.000 0.00 0.00 0.00 4.16
121 122 2.771943 CACCCAAAGCTATCCTAGACCA 59.228 50.000 0.00 0.00 0.00 4.02
122 123 3.039011 TCACCCAAAGCTATCCTAGACC 58.961 50.000 0.00 0.00 0.00 3.85
123 124 4.965200 ATCACCCAAAGCTATCCTAGAC 57.035 45.455 0.00 0.00 0.00 2.59
124 125 7.420214 CCTTTTATCACCCAAAGCTATCCTAGA 60.420 40.741 0.00 0.00 0.00 2.43
125 126 6.712547 CCTTTTATCACCCAAAGCTATCCTAG 59.287 42.308 0.00 0.00 0.00 3.02
126 127 6.410388 CCCTTTTATCACCCAAAGCTATCCTA 60.410 42.308 0.00 0.00 0.00 2.94
127 128 5.449553 CCTTTTATCACCCAAAGCTATCCT 58.550 41.667 0.00 0.00 0.00 3.24
128 129 4.584743 CCCTTTTATCACCCAAAGCTATCC 59.415 45.833 0.00 0.00 0.00 2.59
129 130 4.038042 GCCCTTTTATCACCCAAAGCTATC 59.962 45.833 0.00 0.00 0.00 2.08
130 131 3.960755 GCCCTTTTATCACCCAAAGCTAT 59.039 43.478 0.00 0.00 0.00 2.97
131 132 3.011257 AGCCCTTTTATCACCCAAAGCTA 59.989 43.478 0.00 0.00 0.00 3.32
132 133 2.179427 GCCCTTTTATCACCCAAAGCT 58.821 47.619 0.00 0.00 0.00 3.74
133 134 2.179427 AGCCCTTTTATCACCCAAAGC 58.821 47.619 0.00 0.00 0.00 3.51
134 135 5.422012 ACATTAGCCCTTTTATCACCCAAAG 59.578 40.000 0.00 0.00 0.00 2.77
135 136 5.186797 CACATTAGCCCTTTTATCACCCAAA 59.813 40.000 0.00 0.00 0.00 3.28
136 137 4.709397 CACATTAGCCCTTTTATCACCCAA 59.291 41.667 0.00 0.00 0.00 4.12
137 138 4.277476 CACATTAGCCCTTTTATCACCCA 58.723 43.478 0.00 0.00 0.00 4.51
138 139 3.068165 GCACATTAGCCCTTTTATCACCC 59.932 47.826 0.00 0.00 0.00 4.61
139 140 4.307443 GCACATTAGCCCTTTTATCACC 57.693 45.455 0.00 0.00 0.00 4.02
151 152 0.323360 TGGGTTCCAGGCACATTAGC 60.323 55.000 0.00 0.00 0.00 3.09
152 153 3.976704 TGGGTTCCAGGCACATTAG 57.023 52.632 0.00 0.00 0.00 1.73
162 163 3.636231 CCGTCTGCCTGGGTTCCA 61.636 66.667 0.00 0.00 0.00 3.53
163 164 3.637273 ACCGTCTGCCTGGGTTCC 61.637 66.667 0.00 0.00 0.00 3.62
164 165 2.358737 CACCGTCTGCCTGGGTTC 60.359 66.667 0.00 0.00 29.82 3.62
165 166 3.168528 ACACCGTCTGCCTGGGTT 61.169 61.111 0.00 0.00 29.82 4.11
166 167 3.626924 GACACCGTCTGCCTGGGT 61.627 66.667 0.00 0.00 33.37 4.51
167 168 3.314331 AGACACCGTCTGCCTGGG 61.314 66.667 0.00 0.00 41.76 4.45
174 175 1.546476 GGATGAAGTCAGACACCGTCT 59.454 52.381 2.66 0.00 44.44 4.18
175 176 1.546476 AGGATGAAGTCAGACACCGTC 59.454 52.381 2.66 4.79 0.00 4.79
176 177 1.273606 CAGGATGAAGTCAGACACCGT 59.726 52.381 2.66 0.00 39.69 4.83
177 178 1.546029 TCAGGATGAAGTCAGACACCG 59.454 52.381 2.66 0.00 45.97 4.94
189 190 9.962289 AACACTTTTGTACCTTGCTCAGGATGA 62.962 40.741 9.32 0.00 39.21 2.92
190 191 7.905870 AACACTTTTGTACCTTGCTCAGGATG 61.906 42.308 9.32 0.00 39.21 3.51
191 192 5.923988 AACACTTTTGTACCTTGCTCAGGAT 60.924 40.000 9.32 0.00 39.21 3.24
192 193 4.627741 AACACTTTTGTACCTTGCTCAGGA 60.628 41.667 9.32 0.00 39.21 3.86
193 194 3.632145 AACACTTTTGTACCTTGCTCAGG 59.368 43.478 1.19 1.19 41.56 3.86
194 195 4.335315 TCAACACTTTTGTACCTTGCTCAG 59.665 41.667 0.00 0.00 33.55 3.35
195 196 4.265893 TCAACACTTTTGTACCTTGCTCA 58.734 39.130 0.00 0.00 33.55 4.26
196 197 4.893424 TCAACACTTTTGTACCTTGCTC 57.107 40.909 0.00 0.00 33.55 4.26
197 198 4.142249 GGTTCAACACTTTTGTACCTTGCT 60.142 41.667 5.75 0.00 37.04 3.91
198 199 4.109766 GGTTCAACACTTTTGTACCTTGC 58.890 43.478 5.75 0.00 37.04 4.01
199 200 4.347813 CGGTTCAACACTTTTGTACCTTG 58.652 43.478 10.06 0.00 37.61 3.61
200 201 3.379057 CCGGTTCAACACTTTTGTACCTT 59.621 43.478 10.06 0.00 37.61 3.50
201 202 2.946990 CCGGTTCAACACTTTTGTACCT 59.053 45.455 10.06 0.00 37.61 3.08
202 203 2.684374 ACCGGTTCAACACTTTTGTACC 59.316 45.455 0.00 3.41 36.77 3.34
203 204 5.445845 CATACCGGTTCAACACTTTTGTAC 58.554 41.667 15.04 0.00 33.55 2.90
204 205 4.515944 CCATACCGGTTCAACACTTTTGTA 59.484 41.667 15.04 0.00 33.55 2.41
205 206 3.316868 CCATACCGGTTCAACACTTTTGT 59.683 43.478 15.04 0.00 37.67 2.83
206 207 3.305064 CCCATACCGGTTCAACACTTTTG 60.305 47.826 15.04 0.00 0.00 2.44
207 208 2.888414 CCCATACCGGTTCAACACTTTT 59.112 45.455 15.04 0.00 0.00 2.27
1502 1565 3.199946 GGGATCACAGTTATCCTGGTCAA 59.800 47.826 12.68 0.00 46.06 3.18
1898 1961 1.411977 CTGAGTATCCACCTCTGCCTG 59.588 57.143 0.00 0.00 0.00 4.85
2923 2987 2.524569 AGCCCCAAAAATGTTGTTCG 57.475 45.000 0.00 0.00 0.00 3.95
3023 3087 1.873591 GCAACCTCAAGAACATGACGT 59.126 47.619 0.00 0.00 0.00 4.34


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

AutoCloner maintained by Alex Coulton.