Multiple sequence alignment - TraesCS5D01G559500

Loading Multiple Alignment...

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 TraesCS5D01G559500 chr5D 100.000 2117 0 0 1 2117 560872363 560874479 0.000000e+00 3910.0
1 TraesCS5D01G559500 chr5D 98.338 1925 29 3 194 2117 6201193 6199271 0.000000e+00 3374.0
2 TraesCS5D01G559500 chr5D 97.974 1925 34 5 194 2117 329162265 329164185 0.000000e+00 3334.0
3 TraesCS5D01G559500 chr1D 98.442 1925 29 1 194 2117 254498085 254500009 0.000000e+00 3387.0
4 TraesCS5D01G559500 chr1D 93.102 1928 86 27 194 2117 244483961 244482077 0.000000e+00 2780.0
5 TraesCS5D01G559500 chr1A 97.141 1924 49 5 194 2117 168450479 168448562 0.000000e+00 3243.0
6 TraesCS5D01G559500 chr4D 96.985 1924 55 3 194 2117 19916583 19918503 0.000000e+00 3229.0
7 TraesCS5D01G559500 chr7A 95.057 1922 89 6 194 2113 352193936 352192019 0.000000e+00 3018.0
8 TraesCS5D01G559500 chr6B 97.272 1393 36 2 194 1585 22426032 22427423 0.000000e+00 2361.0
9 TraesCS5D01G559500 chr3B 97.934 1113 19 4 1007 2117 201515580 201516690 0.000000e+00 1925.0
10 TraesCS5D01G559500 chr3B 96.496 1170 13 5 194 1362 201513214 201514356 0.000000e+00 1908.0
11 TraesCS5D01G559500 chr3B 95.354 495 20 3 1623 2117 524777564 524777073 0.000000e+00 784.0
12 TraesCS5D01G559500 chr3B 94.118 85 5 0 1541 1625 152335335 152335419 1.700000e-26 130.0
13 TraesCS5D01G559500 chr7B 95.565 496 22 0 1622 2117 102632114 102631619 0.000000e+00 795.0
14 TraesCS5D01G559500 chr7D 98.925 372 4 0 1588 1959 231542486 231542115 0.000000e+00 665.0
15 TraesCS5D01G559500 chr7D 97.927 193 3 1 1 193 18065054 18064863 1.210000e-87 333.0
16 TraesCS5D01G559500 chr7D 97.927 193 3 1 1 193 77818740 77818549 1.210000e-87 333.0
17 TraesCS5D01G559500 chr7D 97.927 193 3 1 1 193 608915577 608915768 1.210000e-87 333.0
18 TraesCS5D01G559500 chrUn 97.927 193 3 1 1 193 24405253 24405444 1.210000e-87 333.0
19 TraesCS5D01G559500 chrUn 97.409 193 5 0 1 193 442764431 442764239 1.570000e-86 329.0
20 TraesCS5D01G559500 chr3D 97.927 193 3 1 1 193 30684144 30683953 1.210000e-87 333.0
21 TraesCS5D01G559500 chr6D 97.409 193 5 0 1 193 22627666 22627858 1.570000e-86 329.0
22 TraesCS5D01G559500 chr6D 97.423 194 4 1 1 193 313572141 313572334 1.570000e-86 329.0
23 TraesCS5D01G559500 chr6D 97.409 193 5 0 1 193 444906735 444906543 1.570000e-86 329.0
24 TraesCS5D01G559500 chr2B 94.231 52 3 0 1508 1559 113026823 113026772 1.740000e-11 80.5


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 TraesCS5D01G559500 chr5D 560872363 560874479 2116 False 3910.0 3910 100.000 1 2117 1 chr5D.!!$F2 2116
1 TraesCS5D01G559500 chr5D 6199271 6201193 1922 True 3374.0 3374 98.338 194 2117 1 chr5D.!!$R1 1923
2 TraesCS5D01G559500 chr5D 329162265 329164185 1920 False 3334.0 3334 97.974 194 2117 1 chr5D.!!$F1 1923
3 TraesCS5D01G559500 chr1D 254498085 254500009 1924 False 3387.0 3387 98.442 194 2117 1 chr1D.!!$F1 1923
4 TraesCS5D01G559500 chr1D 244482077 244483961 1884 True 2780.0 2780 93.102 194 2117 1 chr1D.!!$R1 1923
5 TraesCS5D01G559500 chr1A 168448562 168450479 1917 True 3243.0 3243 97.141 194 2117 1 chr1A.!!$R1 1923
6 TraesCS5D01G559500 chr4D 19916583 19918503 1920 False 3229.0 3229 96.985 194 2117 1 chr4D.!!$F1 1923
7 TraesCS5D01G559500 chr7A 352192019 352193936 1917 True 3018.0 3018 95.057 194 2113 1 chr7A.!!$R1 1919
8 TraesCS5D01G559500 chr6B 22426032 22427423 1391 False 2361.0 2361 97.272 194 1585 1 chr6B.!!$F1 1391
9 TraesCS5D01G559500 chr3B 201513214 201516690 3476 False 1916.5 1925 97.215 194 2117 2 chr3B.!!$F2 1923

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
132 133 0.035739 TTAGTCCCGGTTCTTGTGGC 59.964 55.0 0.00 0.0 0.0 5.01 F
141 142 0.035739 GTTCTTGTGGCTAACCGGGA 59.964 55.0 6.32 0.0 39.7 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1057 1598 3.700038 GGTGGTTCTCGGAAGAAGATAGA 59.300 47.826 0.0 0.0 42.14 1.98 R
1979 3565 4.511454 GGCAAACAAAATTGGAAGGAAGAC 59.489 41.667 0.0 0.0 0.00 3.01 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 3.220447 TTAGTCCCGGTTCGCAAAG 57.780 52.632 0.00 0.00 0.00 2.77
19 20 0.320946 TTAGTCCCGGTTCGCAAAGG 60.321 55.000 0.00 0.00 0.00 3.11
20 21 2.791501 TAGTCCCGGTTCGCAAAGGC 62.792 60.000 0.00 0.00 0.00 4.35
23 24 2.983592 CCGGTTCGCAAAGGCCTT 60.984 61.111 13.78 13.78 36.38 4.35
24 25 2.561037 CCGGTTCGCAAAGGCCTTT 61.561 57.895 25.47 25.47 36.38 3.11
25 26 1.362355 CGGTTCGCAAAGGCCTTTT 59.638 52.632 28.42 11.04 36.38 2.27
27 28 0.104120 GGTTCGCAAAGGCCTTTTGT 59.896 50.000 28.42 4.95 46.35 2.83
28 29 1.487482 GTTCGCAAAGGCCTTTTGTC 58.513 50.000 28.42 17.91 46.35 3.18
29 30 0.387565 TTCGCAAAGGCCTTTTGTCC 59.612 50.000 28.42 14.97 46.35 4.02
30 31 1.006220 CGCAAAGGCCTTTTGTCCC 60.006 57.895 28.42 12.65 46.35 4.46
31 32 1.006220 GCAAAGGCCTTTTGTCCCG 60.006 57.895 28.42 16.47 46.35 5.14
32 33 1.665442 CAAAGGCCTTTTGTCCCGG 59.335 57.895 28.42 11.40 41.02 5.73
33 34 2.207229 AAAGGCCTTTTGTCCCGGC 61.207 57.895 25.47 0.00 43.03 6.13
34 35 2.656698 AAAGGCCTTTTGTCCCGGCT 62.657 55.000 25.47 0.00 43.29 5.52
35 36 3.373565 GGCCTTTTGTCCCGGCTG 61.374 66.667 0.00 0.00 43.29 4.85
36 37 2.597510 GCCTTTTGTCCCGGCTGT 60.598 61.111 0.00 0.00 40.62 4.40
37 38 2.919494 GCCTTTTGTCCCGGCTGTG 61.919 63.158 0.00 0.00 40.62 3.66
38 39 2.644992 CTTTTGTCCCGGCTGTGC 59.355 61.111 0.00 0.00 0.00 4.57
39 40 2.124109 TTTTGTCCCGGCTGTGCA 60.124 55.556 0.00 0.00 0.00 4.57
40 41 1.733402 CTTTTGTCCCGGCTGTGCAA 61.733 55.000 0.00 0.00 0.00 4.08
41 42 2.010582 TTTTGTCCCGGCTGTGCAAC 62.011 55.000 0.00 0.00 37.35 4.17
42 43 4.947147 TGTCCCGGCTGTGCAACC 62.947 66.667 0.00 0.00 34.36 3.77
48 49 4.643387 GGCTGTGCAACCGGGACT 62.643 66.667 6.32 0.00 38.87 3.85
49 50 2.345991 GCTGTGCAACCGGGACTA 59.654 61.111 6.32 0.00 38.87 2.59
50 51 1.302192 GCTGTGCAACCGGGACTAA 60.302 57.895 6.32 0.00 38.87 2.24
51 52 0.887387 GCTGTGCAACCGGGACTAAA 60.887 55.000 6.32 0.00 38.87 1.85
52 53 1.821216 CTGTGCAACCGGGACTAAAT 58.179 50.000 6.32 0.00 38.87 1.40
53 54 2.937873 GCTGTGCAACCGGGACTAAATA 60.938 50.000 6.32 0.00 38.87 1.40
54 55 3.541632 CTGTGCAACCGGGACTAAATAT 58.458 45.455 6.32 0.00 38.87 1.28
55 56 3.275143 TGTGCAACCGGGACTAAATATG 58.725 45.455 6.32 0.00 38.87 1.78
56 57 2.032924 GTGCAACCGGGACTAAATATGC 59.967 50.000 6.32 2.60 34.56 3.14
57 58 1.263217 GCAACCGGGACTAAATATGCG 59.737 52.381 6.32 0.00 0.00 4.73
58 59 1.263217 CAACCGGGACTAAATATGCGC 59.737 52.381 6.32 0.00 0.00 6.09
59 60 0.599204 ACCGGGACTAAATATGCGCG 60.599 55.000 6.32 0.00 36.61 6.86
60 61 0.319211 CCGGGACTAAATATGCGCGA 60.319 55.000 12.10 0.00 38.72 5.87
61 62 0.782384 CGGGACTAAATATGCGCGAC 59.218 55.000 12.10 0.88 38.72 5.19
62 63 1.602165 CGGGACTAAATATGCGCGACT 60.602 52.381 12.10 0.00 38.72 4.18
63 64 2.351060 CGGGACTAAATATGCGCGACTA 60.351 50.000 12.10 0.00 38.72 2.59
64 65 3.645884 GGGACTAAATATGCGCGACTAA 58.354 45.455 12.10 0.00 0.00 2.24
65 66 4.053295 GGGACTAAATATGCGCGACTAAA 58.947 43.478 12.10 0.00 0.00 1.85
66 67 4.150098 GGGACTAAATATGCGCGACTAAAG 59.850 45.833 12.10 0.00 0.00 1.85
67 68 4.980434 GGACTAAATATGCGCGACTAAAGA 59.020 41.667 12.10 0.00 0.00 2.52
68 69 5.107951 GGACTAAATATGCGCGACTAAAGAC 60.108 44.000 12.10 0.00 0.00 3.01
69 70 4.743644 ACTAAATATGCGCGACTAAAGACC 59.256 41.667 12.10 0.00 0.00 3.85
70 71 2.150397 ATATGCGCGACTAAAGACCC 57.850 50.000 12.10 0.00 0.00 4.46
71 72 0.103572 TATGCGCGACTAAAGACCCC 59.896 55.000 12.10 0.00 0.00 4.95
72 73 1.614241 ATGCGCGACTAAAGACCCCT 61.614 55.000 12.10 0.00 0.00 4.79
73 74 1.518792 GCGCGACTAAAGACCCCTC 60.519 63.158 12.10 0.00 0.00 4.30
74 75 1.141234 CGCGACTAAAGACCCCTCC 59.859 63.158 0.00 0.00 0.00 4.30
75 76 1.521141 GCGACTAAAGACCCCTCCC 59.479 63.158 0.00 0.00 0.00 4.30
76 77 1.969200 GCGACTAAAGACCCCTCCCC 61.969 65.000 0.00 0.00 0.00 4.81
77 78 0.325390 CGACTAAAGACCCCTCCCCT 60.325 60.000 0.00 0.00 0.00 4.79
78 79 1.900337 CGACTAAAGACCCCTCCCCTT 60.900 57.143 0.00 0.00 0.00 3.95
79 80 2.276391 GACTAAAGACCCCTCCCCTTT 58.724 52.381 0.00 0.00 34.81 3.11
80 81 3.457836 GACTAAAGACCCCTCCCCTTTA 58.542 50.000 0.00 0.00 32.92 1.85
82 83 2.452923 AAAGACCCCTCCCCTTTAGT 57.547 50.000 0.00 0.00 0.00 2.24
83 84 1.968278 AAGACCCCTCCCCTTTAGTC 58.032 55.000 0.00 0.00 0.00 2.59
84 85 0.325390 AGACCCCTCCCCTTTAGTCG 60.325 60.000 0.00 0.00 0.00 4.18
85 86 1.969200 GACCCCTCCCCTTTAGTCGC 61.969 65.000 0.00 0.00 0.00 5.19
86 87 2.499685 CCCTCCCCTTTAGTCGCG 59.500 66.667 0.00 0.00 0.00 5.87
87 88 2.202892 CCTCCCCTTTAGTCGCGC 60.203 66.667 0.00 0.00 0.00 6.86
88 89 2.202892 CTCCCCTTTAGTCGCGCC 60.203 66.667 0.00 0.00 0.00 6.53
89 90 2.682494 TCCCCTTTAGTCGCGCCT 60.682 61.111 0.00 0.00 0.00 5.52
90 91 2.202892 CCCCTTTAGTCGCGCCTC 60.203 66.667 0.00 0.00 0.00 4.70
91 92 2.722201 CCCCTTTAGTCGCGCCTCT 61.722 63.158 0.00 2.63 0.00 3.69
92 93 1.218316 CCCTTTAGTCGCGCCTCTT 59.782 57.895 0.00 0.00 0.00 2.85
93 94 0.458669 CCCTTTAGTCGCGCCTCTTA 59.541 55.000 0.00 0.00 0.00 2.10
94 95 1.557651 CCTTTAGTCGCGCCTCTTAC 58.442 55.000 0.00 0.00 0.00 2.34
95 96 1.189403 CTTTAGTCGCGCCTCTTACG 58.811 55.000 0.00 0.00 0.00 3.18
96 97 0.804364 TTTAGTCGCGCCTCTTACGA 59.196 50.000 0.00 0.00 0.00 3.43
97 98 0.804364 TTAGTCGCGCCTCTTACGAA 59.196 50.000 0.00 0.00 37.60 3.85
98 99 0.097674 TAGTCGCGCCTCTTACGAAC 59.902 55.000 0.00 0.00 37.60 3.95
99 100 2.157073 GTCGCGCCTCTTACGAACC 61.157 63.158 0.00 0.00 37.60 3.62
100 101 3.245315 CGCGCCTCTTACGAACCG 61.245 66.667 0.00 0.00 0.00 4.44
101 102 3.551915 GCGCCTCTTACGAACCGC 61.552 66.667 0.00 0.00 33.61 5.68
103 104 2.180017 GCCTCTTACGAACCGCGA 59.820 61.111 8.23 0.00 44.57 5.87
104 105 2.157073 GCCTCTTACGAACCGCGAC 61.157 63.158 8.23 0.00 44.57 5.19
105 106 1.505353 CCTCTTACGAACCGCGACT 59.495 57.895 8.23 0.00 44.57 4.18
106 107 0.729116 CCTCTTACGAACCGCGACTA 59.271 55.000 8.23 0.00 44.57 2.59
107 108 1.131126 CCTCTTACGAACCGCGACTAA 59.869 52.381 8.23 0.00 44.57 2.24
108 109 2.414559 CCTCTTACGAACCGCGACTAAA 60.415 50.000 8.23 0.00 44.57 1.85
109 110 2.844804 CTCTTACGAACCGCGACTAAAG 59.155 50.000 8.23 3.58 44.57 1.85
110 111 1.916000 CTTACGAACCGCGACTAAAGG 59.084 52.381 8.23 0.00 44.57 3.11
111 112 0.881118 TACGAACCGCGACTAAAGGT 59.119 50.000 8.23 0.00 44.57 3.50
117 118 3.391506 ACCGCGACTAAAGGTTTTAGT 57.608 42.857 8.23 12.60 37.89 2.24
118 119 3.320626 ACCGCGACTAAAGGTTTTAGTC 58.679 45.455 22.65 22.65 44.44 2.59
119 120 2.669924 CCGCGACTAAAGGTTTTAGTCC 59.330 50.000 24.79 19.02 44.84 3.85
120 121 2.669924 CGCGACTAAAGGTTTTAGTCCC 59.330 50.000 24.79 18.96 44.84 4.46
121 122 2.669924 GCGACTAAAGGTTTTAGTCCCG 59.330 50.000 24.79 19.25 44.84 5.14
122 123 3.256558 CGACTAAAGGTTTTAGTCCCGG 58.743 50.000 24.79 14.05 44.84 5.73
123 124 3.306294 CGACTAAAGGTTTTAGTCCCGGT 60.306 47.826 24.79 3.47 44.84 5.28
124 125 4.645535 GACTAAAGGTTTTAGTCCCGGTT 58.354 43.478 22.26 0.00 42.97 4.44
125 126 4.645535 ACTAAAGGTTTTAGTCCCGGTTC 58.354 43.478 0.00 0.00 29.89 3.62
126 127 3.870538 AAAGGTTTTAGTCCCGGTTCT 57.129 42.857 0.00 0.15 0.00 3.01
127 128 3.870538 AAGGTTTTAGTCCCGGTTCTT 57.129 42.857 0.00 0.00 0.00 2.52
128 129 3.136009 AGGTTTTAGTCCCGGTTCTTG 57.864 47.619 0.00 0.00 0.00 3.02
129 130 2.440627 AGGTTTTAGTCCCGGTTCTTGT 59.559 45.455 0.00 0.00 0.00 3.16
130 131 2.551032 GGTTTTAGTCCCGGTTCTTGTG 59.449 50.000 0.00 0.00 0.00 3.33
131 132 2.551032 GTTTTAGTCCCGGTTCTTGTGG 59.449 50.000 0.00 0.00 0.00 4.17
132 133 0.035739 TTAGTCCCGGTTCTTGTGGC 59.964 55.000 0.00 0.00 0.00 5.01
133 134 0.834687 TAGTCCCGGTTCTTGTGGCT 60.835 55.000 0.00 0.00 0.00 4.75
134 135 0.834687 AGTCCCGGTTCTTGTGGCTA 60.835 55.000 0.00 0.00 0.00 3.93
135 136 0.035739 GTCCCGGTTCTTGTGGCTAA 59.964 55.000 0.00 0.00 0.00 3.09
136 137 0.035739 TCCCGGTTCTTGTGGCTAAC 59.964 55.000 0.00 0.00 0.00 2.34
137 138 0.958876 CCCGGTTCTTGTGGCTAACC 60.959 60.000 0.00 0.00 39.44 2.85
139 140 2.551644 GGTTCTTGTGGCTAACCGG 58.448 57.895 0.00 0.00 39.70 5.28
140 141 0.958876 GGTTCTTGTGGCTAACCGGG 60.959 60.000 6.32 0.00 39.70 5.73
141 142 0.035739 GTTCTTGTGGCTAACCGGGA 59.964 55.000 6.32 0.00 39.70 5.14
142 143 0.035739 TTCTTGTGGCTAACCGGGAC 59.964 55.000 6.32 0.00 39.70 4.46
143 144 0.834687 TCTTGTGGCTAACCGGGACT 60.835 55.000 6.32 0.00 39.70 3.85
144 145 0.899720 CTTGTGGCTAACCGGGACTA 59.100 55.000 6.32 0.00 39.70 2.59
145 146 1.276989 CTTGTGGCTAACCGGGACTAA 59.723 52.381 6.32 0.00 39.70 2.24
146 147 1.350071 TGTGGCTAACCGGGACTAAA 58.650 50.000 6.32 0.00 39.70 1.85
147 148 1.276989 TGTGGCTAACCGGGACTAAAG 59.723 52.381 6.32 0.00 39.70 1.85
148 149 0.906775 TGGCTAACCGGGACTAAAGG 59.093 55.000 6.32 0.00 39.70 3.11
149 150 0.463295 GGCTAACCGGGACTAAAGGC 60.463 60.000 6.32 1.99 0.00 4.35
150 151 0.463295 GCTAACCGGGACTAAAGGCC 60.463 60.000 6.32 0.00 0.00 5.19
151 152 0.179702 CTAACCGGGACTAAAGGCCC 59.820 60.000 11.29 11.29 41.11 5.80
155 156 2.588439 GGGACTAAAGGCCCGTCC 59.412 66.667 18.06 18.06 45.02 4.79
163 164 3.723245 AGGCCCGTCCTTTAGTCC 58.277 61.111 0.00 0.00 44.75 3.85
164 165 1.993948 AGGCCCGTCCTTTAGTCCC 60.994 63.158 0.00 0.00 44.75 4.46
165 166 2.186125 GCCCGTCCTTTAGTCCCG 59.814 66.667 0.00 0.00 0.00 5.14
166 167 2.897972 CCCGTCCTTTAGTCCCGG 59.102 66.667 0.00 0.00 38.39 5.73
167 168 1.986210 CCCGTCCTTTAGTCCCGGT 60.986 63.158 0.00 0.00 36.98 5.28
168 169 1.547472 CCCGTCCTTTAGTCCCGGTT 61.547 60.000 0.00 0.00 36.98 4.44
169 170 0.108472 CCGTCCTTTAGTCCCGGTTC 60.108 60.000 0.00 0.00 34.10 3.62
170 171 0.893447 CGTCCTTTAGTCCCGGTTCT 59.107 55.000 0.00 0.15 0.00 3.01
171 172 1.135170 CGTCCTTTAGTCCCGGTTCTC 60.135 57.143 0.00 0.00 0.00 2.87
172 173 1.135170 GTCCTTTAGTCCCGGTTCTCG 60.135 57.143 0.00 0.00 38.88 4.04
173 174 0.893447 CCTTTAGTCCCGGTTCTCGT 59.107 55.000 0.00 0.00 37.11 4.18
174 175 1.403780 CCTTTAGTCCCGGTTCTCGTG 60.404 57.143 0.00 0.00 37.11 4.35
175 176 0.604578 TTTAGTCCCGGTTCTCGTGG 59.395 55.000 0.00 0.00 37.11 4.94
176 177 1.880819 TTAGTCCCGGTTCTCGTGGC 61.881 60.000 0.00 0.00 37.11 5.01
177 178 2.776370 TAGTCCCGGTTCTCGTGGCT 62.776 60.000 0.00 0.00 37.11 4.75
178 179 2.036098 TCCCGGTTCTCGTGGCTA 59.964 61.111 0.00 0.00 37.11 3.93
179 180 1.607178 TCCCGGTTCTCGTGGCTAA 60.607 57.895 0.00 0.00 37.11 3.09
180 181 1.447314 CCCGGTTCTCGTGGCTAAC 60.447 63.158 0.00 0.00 37.11 2.34
181 182 1.447314 CCGGTTCTCGTGGCTAACC 60.447 63.158 0.00 0.00 39.44 2.85
182 183 4.180496 GGTTCTCGTGGCTAACCG 57.820 61.111 0.00 0.00 39.70 4.44
183 184 1.447314 GGTTCTCGTGGCTAACCGG 60.447 63.158 0.00 0.00 39.70 5.28
184 185 1.447314 GTTCTCGTGGCTAACCGGG 60.447 63.158 6.32 0.00 39.70 5.73
185 186 1.607178 TTCTCGTGGCTAACCGGGA 60.607 57.895 6.32 0.00 39.70 5.14
186 187 1.880819 TTCTCGTGGCTAACCGGGAC 61.881 60.000 6.32 0.00 39.70 4.46
187 188 2.283388 TCGTGGCTAACCGGGACT 60.283 61.111 6.32 0.00 39.70 3.85
188 189 1.001020 TCGTGGCTAACCGGGACTA 60.001 57.895 6.32 0.00 39.70 2.59
189 190 0.611618 TCGTGGCTAACCGGGACTAA 60.612 55.000 6.32 0.00 39.70 2.24
190 191 0.247185 CGTGGCTAACCGGGACTAAA 59.753 55.000 6.32 0.00 39.70 1.85
191 192 1.738030 CGTGGCTAACCGGGACTAAAG 60.738 57.143 6.32 0.00 39.70 1.85
192 193 0.906775 TGGCTAACCGGGACTAAAGG 59.093 55.000 6.32 0.00 39.70 3.11
336 337 5.437060 GAATAGCTGTTGGATGGTTAGGAA 58.563 41.667 0.00 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.320946 CCTTTGCGAACCGGGACTAA 60.321 55.000 6.32 0.00 0.00 2.24
1 2 1.294138 CCTTTGCGAACCGGGACTA 59.706 57.895 6.32 0.00 0.00 2.59
2 3 2.032071 CCTTTGCGAACCGGGACT 59.968 61.111 6.32 0.00 0.00 3.85
3 4 3.733960 GCCTTTGCGAACCGGGAC 61.734 66.667 6.32 0.00 0.00 4.46
6 7 2.082629 AAAAGGCCTTTGCGAACCGG 62.083 55.000 31.02 0.00 38.85 5.28
7 8 0.939106 CAAAAGGCCTTTGCGAACCG 60.939 55.000 31.02 10.08 38.17 4.44
8 9 2.899153 CAAAAGGCCTTTGCGAACC 58.101 52.632 31.02 0.00 38.17 3.62
15 16 2.207229 GCCGGGACAAAAGGCCTTT 61.207 57.895 25.47 25.47 44.80 3.11
16 17 2.600470 GCCGGGACAAAAGGCCTT 60.600 61.111 13.78 13.78 44.80 4.35
20 21 2.919494 GCACAGCCGGGACAAAAGG 61.919 63.158 2.18 0.00 0.00 3.11
21 22 1.733402 TTGCACAGCCGGGACAAAAG 61.733 55.000 2.18 0.00 0.00 2.27
22 23 1.754621 TTGCACAGCCGGGACAAAA 60.755 52.632 2.18 0.00 0.00 2.44
23 24 2.124109 TTGCACAGCCGGGACAAA 60.124 55.556 2.18 0.00 0.00 2.83
24 25 2.904866 GTTGCACAGCCGGGACAA 60.905 61.111 2.18 0.00 0.00 3.18
25 26 4.947147 GGTTGCACAGCCGGGACA 62.947 66.667 2.18 0.00 0.00 4.02
31 32 2.741486 TTAGTCCCGGTTGCACAGCC 62.741 60.000 0.00 0.00 0.00 4.85
32 33 0.887387 TTTAGTCCCGGTTGCACAGC 60.887 55.000 0.00 0.00 0.00 4.40
33 34 1.821216 ATTTAGTCCCGGTTGCACAG 58.179 50.000 0.00 0.00 0.00 3.66
34 35 3.275143 CATATTTAGTCCCGGTTGCACA 58.725 45.455 0.00 0.00 0.00 4.57
35 36 2.032924 GCATATTTAGTCCCGGTTGCAC 59.967 50.000 0.00 0.00 0.00 4.57
36 37 2.294074 GCATATTTAGTCCCGGTTGCA 58.706 47.619 0.00 0.00 0.00 4.08
37 38 1.263217 CGCATATTTAGTCCCGGTTGC 59.737 52.381 0.00 0.00 0.00 4.17
38 39 1.263217 GCGCATATTTAGTCCCGGTTG 59.737 52.381 0.30 0.00 0.00 3.77
39 40 1.589803 GCGCATATTTAGTCCCGGTT 58.410 50.000 0.30 0.00 0.00 4.44
40 41 0.599204 CGCGCATATTTAGTCCCGGT 60.599 55.000 8.75 0.00 0.00 5.28
41 42 0.319211 TCGCGCATATTTAGTCCCGG 60.319 55.000 8.75 0.00 0.00 5.73
42 43 0.782384 GTCGCGCATATTTAGTCCCG 59.218 55.000 8.75 0.00 0.00 5.14
43 44 2.150397 AGTCGCGCATATTTAGTCCC 57.850 50.000 8.75 0.00 0.00 4.46
44 45 4.980434 TCTTTAGTCGCGCATATTTAGTCC 59.020 41.667 8.75 0.00 0.00 3.85
45 46 5.107951 GGTCTTTAGTCGCGCATATTTAGTC 60.108 44.000 8.75 0.00 0.00 2.59
46 47 4.743644 GGTCTTTAGTCGCGCATATTTAGT 59.256 41.667 8.75 0.00 0.00 2.24
47 48 4.150098 GGGTCTTTAGTCGCGCATATTTAG 59.850 45.833 8.75 0.00 0.00 1.85
48 49 4.053295 GGGTCTTTAGTCGCGCATATTTA 58.947 43.478 8.75 0.00 0.00 1.40
49 50 2.870411 GGGTCTTTAGTCGCGCATATTT 59.130 45.455 8.75 0.00 0.00 1.40
50 51 2.480845 GGGTCTTTAGTCGCGCATATT 58.519 47.619 8.75 0.00 0.00 1.28
51 52 1.270147 GGGGTCTTTAGTCGCGCATAT 60.270 52.381 8.75 0.00 0.00 1.78
52 53 0.103572 GGGGTCTTTAGTCGCGCATA 59.896 55.000 8.75 0.00 0.00 3.14
53 54 1.153429 GGGGTCTTTAGTCGCGCAT 60.153 57.895 8.75 0.00 0.00 4.73
54 55 2.221906 GAGGGGTCTTTAGTCGCGCA 62.222 60.000 8.75 0.00 0.00 6.09
55 56 1.518792 GAGGGGTCTTTAGTCGCGC 60.519 63.158 0.00 0.00 0.00 6.86
56 57 1.141234 GGAGGGGTCTTTAGTCGCG 59.859 63.158 0.00 0.00 0.00 5.87
57 58 1.521141 GGGAGGGGTCTTTAGTCGC 59.479 63.158 0.00 0.00 0.00 5.19
58 59 0.325390 AGGGGAGGGGTCTTTAGTCG 60.325 60.000 0.00 0.00 0.00 4.18
59 60 1.968278 AAGGGGAGGGGTCTTTAGTC 58.032 55.000 0.00 0.00 0.00 2.59
60 61 2.452923 AAAGGGGAGGGGTCTTTAGT 57.547 50.000 0.00 0.00 0.00 2.24
61 62 3.455177 GACTAAAGGGGAGGGGTCTTTAG 59.545 52.174 16.01 16.01 41.02 1.85
62 63 3.457836 GACTAAAGGGGAGGGGTCTTTA 58.542 50.000 0.00 0.00 0.00 1.85
63 64 2.276391 GACTAAAGGGGAGGGGTCTTT 58.724 52.381 0.00 0.00 0.00 2.52
64 65 1.900337 CGACTAAAGGGGAGGGGTCTT 60.900 57.143 0.00 0.00 0.00 3.01
65 66 0.325390 CGACTAAAGGGGAGGGGTCT 60.325 60.000 0.00 0.00 0.00 3.85
66 67 1.969200 GCGACTAAAGGGGAGGGGTC 61.969 65.000 0.00 0.00 0.00 4.46
67 68 1.993948 GCGACTAAAGGGGAGGGGT 60.994 63.158 0.00 0.00 0.00 4.95
68 69 2.908796 GCGACTAAAGGGGAGGGG 59.091 66.667 0.00 0.00 0.00 4.79
69 70 2.499685 CGCGACTAAAGGGGAGGG 59.500 66.667 0.00 0.00 0.00 4.30
70 71 2.202892 GCGCGACTAAAGGGGAGG 60.203 66.667 12.10 0.00 0.00 4.30
71 72 2.202892 GGCGCGACTAAAGGGGAG 60.203 66.667 12.10 0.00 0.00 4.30
72 73 2.682494 AGGCGCGACTAAAGGGGA 60.682 61.111 16.12 0.00 0.00 4.81
73 74 2.202892 GAGGCGCGACTAAAGGGG 60.203 66.667 18.29 0.00 0.00 4.79
74 75 0.458669 TAAGAGGCGCGACTAAAGGG 59.541 55.000 18.29 0.00 0.00 3.95
75 76 1.557651 GTAAGAGGCGCGACTAAAGG 58.442 55.000 18.29 0.00 0.00 3.11
76 77 1.189403 CGTAAGAGGCGCGACTAAAG 58.811 55.000 18.29 1.48 43.02 1.85
77 78 0.804364 TCGTAAGAGGCGCGACTAAA 59.196 50.000 18.29 0.00 45.01 1.85
78 79 2.470156 TCGTAAGAGGCGCGACTAA 58.530 52.632 18.29 0.00 45.01 2.24
79 80 4.206958 TCGTAAGAGGCGCGACTA 57.793 55.556 18.29 0.00 45.01 2.59
90 91 1.916000 CCTTTAGTCGCGGTTCGTAAG 59.084 52.381 6.13 3.09 39.67 2.34
91 92 1.269448 ACCTTTAGTCGCGGTTCGTAA 59.731 47.619 6.13 0.00 39.67 3.18
92 93 0.881118 ACCTTTAGTCGCGGTTCGTA 59.119 50.000 6.13 0.00 39.67 3.43
93 94 0.032540 AACCTTTAGTCGCGGTTCGT 59.967 50.000 6.13 0.00 36.32 3.85
94 95 1.142474 AAACCTTTAGTCGCGGTTCG 58.858 50.000 6.13 0.00 39.97 3.95
95 96 3.742882 ACTAAAACCTTTAGTCGCGGTTC 59.257 43.478 6.13 0.00 39.97 3.62
96 97 3.732212 ACTAAAACCTTTAGTCGCGGTT 58.268 40.909 6.13 0.00 42.52 4.44
97 98 3.320626 GACTAAAACCTTTAGTCGCGGT 58.679 45.455 18.53 0.00 40.74 5.68
98 99 3.985912 GACTAAAACCTTTAGTCGCGG 57.014 47.619 18.53 0.00 40.74 6.46
99 100 2.669924 GGGACTAAAACCTTTAGTCGCG 59.330 50.000 26.73 0.00 47.00 5.87
102 103 4.277515 ACCGGGACTAAAACCTTTAGTC 57.722 45.455 22.57 22.57 46.16 2.59
103 104 4.349048 AGAACCGGGACTAAAACCTTTAGT 59.651 41.667 6.32 10.76 37.89 2.24
104 105 4.903054 AGAACCGGGACTAAAACCTTTAG 58.097 43.478 6.32 4.91 0.00 1.85
105 106 4.980339 AGAACCGGGACTAAAACCTTTA 57.020 40.909 6.32 0.00 0.00 1.85
106 107 3.870538 AGAACCGGGACTAAAACCTTT 57.129 42.857 6.32 0.00 0.00 3.11
107 108 3.117776 ACAAGAACCGGGACTAAAACCTT 60.118 43.478 6.32 0.00 0.00 3.50
108 109 2.440627 ACAAGAACCGGGACTAAAACCT 59.559 45.455 6.32 0.00 0.00 3.50
109 110 2.551032 CACAAGAACCGGGACTAAAACC 59.449 50.000 6.32 0.00 0.00 3.27
110 111 2.551032 CCACAAGAACCGGGACTAAAAC 59.449 50.000 6.32 0.00 0.00 2.43
111 112 2.853705 CCACAAGAACCGGGACTAAAA 58.146 47.619 6.32 0.00 0.00 1.52
112 113 1.543871 GCCACAAGAACCGGGACTAAA 60.544 52.381 6.32 0.00 0.00 1.85
113 114 0.035739 GCCACAAGAACCGGGACTAA 59.964 55.000 6.32 0.00 0.00 2.24
114 115 0.834687 AGCCACAAGAACCGGGACTA 60.835 55.000 6.32 0.00 0.00 2.59
115 116 0.834687 TAGCCACAAGAACCGGGACT 60.835 55.000 6.32 0.73 0.00 3.85
116 117 0.035739 TTAGCCACAAGAACCGGGAC 59.964 55.000 6.32 0.00 0.00 4.46
117 118 0.035739 GTTAGCCACAAGAACCGGGA 59.964 55.000 6.32 0.00 0.00 5.14
118 119 0.958876 GGTTAGCCACAAGAACCGGG 60.959 60.000 6.32 0.00 33.75 5.73
119 120 2.551644 GGTTAGCCACAAGAACCGG 58.448 57.895 0.00 0.00 33.75 5.28
121 122 0.958876 CCCGGTTAGCCACAAGAACC 60.959 60.000 0.00 0.00 39.44 3.62
122 123 0.035739 TCCCGGTTAGCCACAAGAAC 59.964 55.000 0.00 0.00 34.09 3.01
123 124 0.035739 GTCCCGGTTAGCCACAAGAA 59.964 55.000 0.00 0.00 34.09 2.52
124 125 0.834687 AGTCCCGGTTAGCCACAAGA 60.835 55.000 0.00 0.00 34.09 3.02
125 126 0.899720 TAGTCCCGGTTAGCCACAAG 59.100 55.000 0.00 0.00 34.09 3.16
126 127 1.350071 TTAGTCCCGGTTAGCCACAA 58.650 50.000 0.00 0.00 34.09 3.33
127 128 1.276989 CTTTAGTCCCGGTTAGCCACA 59.723 52.381 0.00 0.00 34.09 4.17
128 129 1.406477 CCTTTAGTCCCGGTTAGCCAC 60.406 57.143 0.00 0.00 34.09 5.01
129 130 0.906775 CCTTTAGTCCCGGTTAGCCA 59.093 55.000 0.00 0.00 34.09 4.75
130 131 0.463295 GCCTTTAGTCCCGGTTAGCC 60.463 60.000 0.00 0.00 0.00 3.93
131 132 0.463295 GGCCTTTAGTCCCGGTTAGC 60.463 60.000 0.00 0.00 0.00 3.09
132 133 0.179702 GGGCCTTTAGTCCCGGTTAG 59.820 60.000 0.84 0.00 32.00 2.34
133 134 2.299975 GGGCCTTTAGTCCCGGTTA 58.700 57.895 0.84 0.00 32.00 2.85
134 135 3.084304 GGGCCTTTAGTCCCGGTT 58.916 61.111 0.84 0.00 32.00 4.44
138 139 2.588439 GGACGGGCCTTTAGTCCC 59.412 66.667 21.39 9.76 46.40 4.46
147 148 2.588439 GGGACTAAAGGACGGGCC 59.412 66.667 0.00 0.00 0.00 5.80
148 149 2.186125 CGGGACTAAAGGACGGGC 59.814 66.667 0.00 0.00 0.00 6.13
149 150 2.897972 CCGGGACTAAAGGACGGG 59.102 66.667 0.00 0.00 40.79 5.28
151 152 0.893447 AGAACCGGGACTAAAGGACG 59.107 55.000 6.32 0.00 0.00 4.79
152 153 1.135170 CGAGAACCGGGACTAAAGGAC 60.135 57.143 6.32 0.00 33.91 3.85
153 154 1.180029 CGAGAACCGGGACTAAAGGA 58.820 55.000 6.32 0.00 33.91 3.36
154 155 0.893447 ACGAGAACCGGGACTAAAGG 59.107 55.000 6.32 0.00 43.93 3.11
155 156 1.403780 CCACGAGAACCGGGACTAAAG 60.404 57.143 6.32 2.68 46.66 1.85
156 157 0.604578 CCACGAGAACCGGGACTAAA 59.395 55.000 6.32 0.00 46.66 1.85
157 158 1.880819 GCCACGAGAACCGGGACTAA 61.881 60.000 6.32 0.00 46.66 2.24
158 159 2.345760 GCCACGAGAACCGGGACTA 61.346 63.158 6.32 0.00 46.66 2.59
159 160 2.776370 TAGCCACGAGAACCGGGACT 62.776 60.000 6.32 4.01 46.66 3.85
160 161 1.880819 TTAGCCACGAGAACCGGGAC 61.881 60.000 6.32 0.00 46.66 4.46
161 162 1.607178 TTAGCCACGAGAACCGGGA 60.607 57.895 6.32 0.00 46.66 5.14
162 163 1.447314 GTTAGCCACGAGAACCGGG 60.447 63.158 6.32 0.00 43.93 5.73
163 164 1.447314 GGTTAGCCACGAGAACCGG 60.447 63.158 0.00 0.00 43.93 5.28
164 165 4.180496 GGTTAGCCACGAGAACCG 57.820 61.111 0.00 0.00 45.44 4.44
165 166 1.447314 CCGGTTAGCCACGAGAACC 60.447 63.158 0.00 0.00 39.44 3.62
166 167 1.447314 CCCGGTTAGCCACGAGAAC 60.447 63.158 0.00 0.00 34.09 3.01
167 168 1.607178 TCCCGGTTAGCCACGAGAA 60.607 57.895 0.00 0.00 34.09 2.87
168 169 2.036098 TCCCGGTTAGCCACGAGA 59.964 61.111 0.00 0.00 34.09 4.04
169 170 1.033746 TAGTCCCGGTTAGCCACGAG 61.034 60.000 0.00 0.00 34.09 4.18
170 171 0.611618 TTAGTCCCGGTTAGCCACGA 60.612 55.000 0.00 0.00 34.09 4.35
171 172 0.247185 TTTAGTCCCGGTTAGCCACG 59.753 55.000 0.00 0.00 34.09 4.94
172 173 1.406477 CCTTTAGTCCCGGTTAGCCAC 60.406 57.143 0.00 0.00 34.09 5.01
173 174 0.906775 CCTTTAGTCCCGGTTAGCCA 59.093 55.000 0.00 0.00 34.09 4.75
174 175 1.197812 TCCTTTAGTCCCGGTTAGCC 58.802 55.000 0.00 0.00 0.00 3.93
175 176 2.699321 AGATCCTTTAGTCCCGGTTAGC 59.301 50.000 0.00 0.00 0.00 3.09
176 177 5.597594 ACTAAGATCCTTTAGTCCCGGTTAG 59.402 44.000 0.00 0.00 39.10 2.34
177 178 5.522641 ACTAAGATCCTTTAGTCCCGGTTA 58.477 41.667 0.00 0.00 39.10 2.85
178 179 4.359996 ACTAAGATCCTTTAGTCCCGGTT 58.640 43.478 0.00 0.00 39.10 4.44
179 180 3.991683 ACTAAGATCCTTTAGTCCCGGT 58.008 45.455 0.00 0.00 39.10 5.28
180 181 5.354842 AAACTAAGATCCTTTAGTCCCGG 57.645 43.478 7.60 0.00 41.70 5.73
181 182 7.723324 TGATAAACTAAGATCCTTTAGTCCCG 58.277 38.462 7.60 0.00 41.70 5.14
182 183 8.925338 TCTGATAAACTAAGATCCTTTAGTCCC 58.075 37.037 7.60 0.95 41.70 4.46
185 186 9.825109 GCTTCTGATAAACTAAGATCCTTTAGT 57.175 33.333 2.35 2.35 43.77 2.24
188 189 9.171877 CAAGCTTCTGATAAACTAAGATCCTTT 57.828 33.333 0.00 0.00 0.00 3.11
189 190 7.772757 CCAAGCTTCTGATAAACTAAGATCCTT 59.227 37.037 0.00 0.00 0.00 3.36
190 191 7.092668 ACCAAGCTTCTGATAAACTAAGATCCT 60.093 37.037 0.00 0.00 0.00 3.24
191 192 7.051000 ACCAAGCTTCTGATAAACTAAGATCC 58.949 38.462 0.00 0.00 0.00 3.36
192 193 7.984617 AGACCAAGCTTCTGATAAACTAAGATC 59.015 37.037 0.00 0.00 0.00 2.75
403 405 5.536916 TCATCTACCAAAACAACCGGAAATT 59.463 36.000 9.46 0.00 0.00 1.82
1056 1597 4.202070 GGTGGTTCTCGGAAGAAGATAGAG 60.202 50.000 0.00 0.00 42.14 2.43
1057 1598 3.700038 GGTGGTTCTCGGAAGAAGATAGA 59.300 47.826 0.00 0.00 42.14 1.98
1473 2015 5.067805 ACTTTCCCATATTCCGAATTCAAGC 59.932 40.000 6.22 0.00 0.00 4.01
1979 3565 4.511454 GGCAAACAAAATTGGAAGGAAGAC 59.489 41.667 0.00 0.00 0.00 3.01
2064 3650 4.562082 TCTTCGAATAAGAACCGCTTGAA 58.438 39.130 0.00 0.00 37.42 2.69


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

AutoCloner maintained by Alex Coulton.