Multiple sequence alignment - TraesCS3A01G177100

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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 TraesCS3A01G177100 chr3A 100.000 3427 0 0 880 4306 199147806 199144380 0.000000e+00 6329.0
1 TraesCS3A01G177100 chr3A 100.000 471 0 0 1 471 199148685 199148215 0.000000e+00 870.0
2 TraesCS3A01G177100 chr3B 97.641 3433 74 4 880 4306 243768190 243771621 0.000000e+00 5884.0
3 TraesCS3A01G177100 chr3B 91.549 284 7 7 193 471 243767753 243768024 4.070000e-100 375.0
4 TraesCS3A01G177100 chr3B 89.130 138 13 2 3071 3206 611485418 611485281 2.060000e-38 171.0
5 TraesCS3A01G177100 chr3D 97.856 3172 58 7 897 4059 168493316 168496486 0.000000e+00 5472.0
6 TraesCS3A01G177100 chr3D 94.071 253 14 1 4055 4306 168498234 168498486 2.430000e-102 383.0
7 TraesCS3A01G177100 chr3D 90.444 293 0 7 193 471 168492700 168492978 1.140000e-95 361.0
8 TraesCS3A01G177100 chr3D 95.361 194 9 0 1 194 569120447 569120640 4.180000e-80 309.0
9 TraesCS3A01G177100 chr1D 84.389 442 46 6 2102 2540 183748240 183747819 3.100000e-111 412.0
10 TraesCS3A01G177100 chr1D 89.855 138 12 2 3071 3206 183747803 183747666 4.430000e-40 176.0
11 TraesCS3A01G177100 chr4B 93.814 194 12 0 1 194 96442866 96443059 4.210000e-75 292.0
12 TraesCS3A01G177100 chr4B 88.112 143 14 2 46 187 460793538 460793398 2.660000e-37 167.0
13 TraesCS3A01G177100 chr5A 90.968 155 13 1 3008 3162 401376198 401376351 1.570000e-49 207.0
14 TraesCS3A01G177100 chr6A 91.216 148 12 1 3015 3162 87361648 87361502 2.630000e-47 200.0
15 TraesCS3A01G177100 chr5B 82.915 199 29 4 1 197 297828734 297828539 1.590000e-39 174.0
16 TraesCS3A01G177100 chr1A 85.470 117 17 0 2959 3075 171080758 171080874 5.850000e-24 122.0
17 TraesCS3A01G177100 chr1A 100.000 28 0 0 3283 3310 410465736 410465763 8.000000e-03 52.8
18 TraesCS3A01G177100 chr7D 94.286 35 2 0 3276 3310 374643569 374643603 2.000000e-03 54.7


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 TraesCS3A01G177100 chr3A 199144380 199148685 4305 True 3599.5 6329 100.000000 1 4306 2 chr3A.!!$R1 4305
1 TraesCS3A01G177100 chr3B 243767753 243771621 3868 False 3129.5 5884 94.595000 193 4306 2 chr3B.!!$F1 4113
2 TraesCS3A01G177100 chr3D 168492700 168498486 5786 False 2072.0 5472 94.123667 193 4306 3 chr3D.!!$F2 4113
3 TraesCS3A01G177100 chr1D 183747666 183748240 574 True 294.0 412 87.122000 2102 3206 2 chr1D.!!$R1 1104

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
107 108 0.034337 TTTTACGCGCTGGAGTTCCT 59.966 50.0 5.73 0.00 36.82 3.36 F
122 123 0.039618 TTCCTGACCTCCAAATGGCC 59.960 55.0 0.00 0.00 34.44 5.36 F
143 144 0.106519 GGCCCATGTGCATCTACCTT 60.107 55.0 1.71 0.00 0.00 3.50 F
331 346 0.169230 AACGAGCGCTCTGTAGTCTG 59.831 55.0 32.88 18.03 0.00 3.51 F
1928 1943 0.394192 CTGCTCGATGAGGCCCATAA 59.606 55.0 0.00 0.00 35.17 1.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1311 1326 1.144936 GCATCTCCCCTTCACCTCG 59.855 63.158 0.00 0.0 0.00 4.63 R
1941 1956 1.290324 GCAACCTCTCTGACTCGCA 59.710 57.895 0.00 0.0 0.00 5.10 R
2314 2332 0.312102 GCCTGACCAGCTTTTGTGAC 59.688 55.000 0.00 0.0 0.00 3.67 R
2348 2366 4.554973 GCTGACTCATTGCGTGAAAAATAC 59.445 41.667 0.00 0.0 36.14 1.89 R
3917 3945 1.139163 GCCAAAAACATTGGTCAGCG 58.861 50.000 8.84 0.0 41.53 5.18 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 3.981308 ACGTTTCAGCCCGATTGG 58.019 55.556 0.00 0.00 37.09 3.16
18 19 1.072505 ACGTTTCAGCCCGATTGGT 59.927 52.632 0.00 0.00 36.04 3.67
19 20 0.322322 ACGTTTCAGCCCGATTGGTA 59.678 50.000 0.00 0.00 36.04 3.25
20 21 1.006832 CGTTTCAGCCCGATTGGTAG 58.993 55.000 0.00 0.00 36.04 3.18
21 22 1.379527 GTTTCAGCCCGATTGGTAGG 58.620 55.000 0.00 0.00 36.04 3.18
22 23 0.988832 TTTCAGCCCGATTGGTAGGT 59.011 50.000 0.00 0.00 36.04 3.08
23 24 0.988832 TTCAGCCCGATTGGTAGGTT 59.011 50.000 0.00 0.00 36.04 3.50
24 25 0.539986 TCAGCCCGATTGGTAGGTTC 59.460 55.000 0.00 0.00 36.04 3.62
25 26 0.541863 CAGCCCGATTGGTAGGTTCT 59.458 55.000 0.00 0.00 36.04 3.01
26 27 1.760613 CAGCCCGATTGGTAGGTTCTA 59.239 52.381 0.00 0.00 36.04 2.10
27 28 2.040178 AGCCCGATTGGTAGGTTCTAG 58.960 52.381 0.00 0.00 36.04 2.43
28 29 2.037144 GCCCGATTGGTAGGTTCTAGA 58.963 52.381 0.00 0.00 36.04 2.43
29 30 2.223994 GCCCGATTGGTAGGTTCTAGAC 60.224 54.545 0.00 0.00 36.04 2.59
30 31 3.297736 CCCGATTGGTAGGTTCTAGACT 58.702 50.000 0.00 0.00 0.00 3.24
31 32 3.705072 CCCGATTGGTAGGTTCTAGACTT 59.295 47.826 0.00 0.00 0.00 3.01
32 33 4.202131 CCCGATTGGTAGGTTCTAGACTTC 60.202 50.000 0.00 0.00 0.00 3.01
33 34 4.497674 CCGATTGGTAGGTTCTAGACTTCG 60.498 50.000 0.00 0.00 0.00 3.79
34 35 3.863142 TTGGTAGGTTCTAGACTTCGC 57.137 47.619 0.00 0.00 0.00 4.70
35 36 1.741706 TGGTAGGTTCTAGACTTCGCG 59.258 52.381 0.00 0.00 0.00 5.87
36 37 2.012673 GGTAGGTTCTAGACTTCGCGA 58.987 52.381 3.71 3.71 0.00 5.87
37 38 2.421424 GGTAGGTTCTAGACTTCGCGAA 59.579 50.000 22.01 22.01 0.00 4.70
38 39 3.066481 GGTAGGTTCTAGACTTCGCGAAT 59.934 47.826 23.67 12.59 0.00 3.34
39 40 3.152261 AGGTTCTAGACTTCGCGAATG 57.848 47.619 23.67 17.98 0.00 2.67
40 41 2.159226 AGGTTCTAGACTTCGCGAATGG 60.159 50.000 23.67 14.35 0.00 3.16
41 42 2.194271 GTTCTAGACTTCGCGAATGGG 58.806 52.381 23.67 13.57 0.00 4.00
42 43 1.758936 TCTAGACTTCGCGAATGGGA 58.241 50.000 23.67 13.03 34.90 4.37
43 44 1.404391 TCTAGACTTCGCGAATGGGAC 59.596 52.381 23.67 11.24 36.70 4.46
44 45 0.099968 TAGACTTCGCGAATGGGACG 59.900 55.000 23.67 12.00 36.70 4.79
45 46 1.445582 GACTTCGCGAATGGGACGT 60.446 57.895 23.67 15.43 41.33 4.34
46 47 1.411493 GACTTCGCGAATGGGACGTC 61.411 60.000 23.67 19.86 44.82 4.34
47 48 1.445410 CTTCGCGAATGGGACGTCA 60.445 57.895 23.67 0.00 36.70 4.35
48 49 1.683790 CTTCGCGAATGGGACGTCAC 61.684 60.000 23.67 15.66 36.70 3.67
49 50 3.541831 CGCGAATGGGACGTCACG 61.542 66.667 18.91 14.42 0.00 4.35
50 51 2.126228 GCGAATGGGACGTCACGA 60.126 61.111 18.91 5.08 0.00 4.35
51 52 2.158959 GCGAATGGGACGTCACGAG 61.159 63.158 18.91 7.55 0.00 4.18
52 53 1.211969 CGAATGGGACGTCACGAGT 59.788 57.895 18.91 3.77 0.00 4.18
53 54 0.388134 CGAATGGGACGTCACGAGTT 60.388 55.000 18.91 10.21 0.00 3.01
54 55 1.347320 GAATGGGACGTCACGAGTTC 58.653 55.000 18.91 15.14 0.00 3.01
55 56 0.388134 AATGGGACGTCACGAGTTCG 60.388 55.000 18.91 0.00 46.33 3.95
56 57 1.239296 ATGGGACGTCACGAGTTCGA 61.239 55.000 18.91 0.00 43.02 3.71
57 58 1.239296 TGGGACGTCACGAGTTCGAT 61.239 55.000 18.91 0.00 43.02 3.59
58 59 0.729116 GGGACGTCACGAGTTCGATA 59.271 55.000 18.91 0.00 43.02 2.92
59 60 1.332997 GGGACGTCACGAGTTCGATAT 59.667 52.381 18.91 0.00 43.02 1.63
60 61 2.601741 GGGACGTCACGAGTTCGATATC 60.602 54.545 18.91 0.00 43.02 1.63
61 62 2.287373 GGACGTCACGAGTTCGATATCT 59.713 50.000 18.91 0.00 43.02 1.98
62 63 3.281601 GACGTCACGAGTTCGATATCTG 58.718 50.000 11.55 0.00 43.02 2.90
63 64 2.031807 ACGTCACGAGTTCGATATCTGG 59.968 50.000 2.91 0.00 43.02 3.86
64 65 2.386249 GTCACGAGTTCGATATCTGGC 58.614 52.381 8.72 0.00 43.02 4.85
65 66 1.337071 TCACGAGTTCGATATCTGGCC 59.663 52.381 8.72 0.00 43.02 5.36
66 67 1.067060 CACGAGTTCGATATCTGGCCA 59.933 52.381 4.71 4.71 43.02 5.36
67 68 1.067212 ACGAGTTCGATATCTGGCCAC 59.933 52.381 0.00 0.00 43.02 5.01
68 69 1.603172 CGAGTTCGATATCTGGCCACC 60.603 57.143 0.00 0.00 43.02 4.61
69 70 1.412710 GAGTTCGATATCTGGCCACCA 59.587 52.381 0.00 0.00 0.00 4.17
70 71 1.139058 AGTTCGATATCTGGCCACCAC 59.861 52.381 0.00 0.00 0.00 4.16
71 72 0.104120 TTCGATATCTGGCCACCACG 59.896 55.000 0.00 3.94 0.00 4.94
72 73 1.040893 TCGATATCTGGCCACCACGT 61.041 55.000 0.00 0.00 0.00 4.49
73 74 0.179084 CGATATCTGGCCACCACGTT 60.179 55.000 0.00 0.00 0.00 3.99
74 75 1.742411 CGATATCTGGCCACCACGTTT 60.742 52.381 0.00 0.00 0.00 3.60
75 76 2.482316 CGATATCTGGCCACCACGTTTA 60.482 50.000 0.00 0.00 0.00 2.01
76 77 3.740115 GATATCTGGCCACCACGTTTAT 58.260 45.455 0.00 0.00 0.00 1.40
77 78 2.507407 ATCTGGCCACCACGTTTATT 57.493 45.000 0.00 0.00 0.00 1.40
78 79 2.279935 TCTGGCCACCACGTTTATTT 57.720 45.000 0.00 0.00 0.00 1.40
79 80 2.588620 TCTGGCCACCACGTTTATTTT 58.411 42.857 0.00 0.00 0.00 1.82
80 81 2.959707 TCTGGCCACCACGTTTATTTTT 59.040 40.909 0.00 0.00 0.00 1.94
81 82 3.056304 CTGGCCACCACGTTTATTTTTG 58.944 45.455 0.00 0.00 0.00 2.44
82 83 2.224066 TGGCCACCACGTTTATTTTTGG 60.224 45.455 0.00 0.00 35.06 3.28
83 84 1.795872 GCCACCACGTTTATTTTTGGC 59.204 47.619 0.00 0.00 41.19 4.52
84 85 2.055100 CCACCACGTTTATTTTTGGCG 58.945 47.619 0.00 0.00 31.76 5.69
85 86 2.287668 CCACCACGTTTATTTTTGGCGA 60.288 45.455 0.00 0.00 31.76 5.54
86 87 3.570559 CACCACGTTTATTTTTGGCGAT 58.429 40.909 0.00 0.00 31.76 4.58
87 88 3.984633 CACCACGTTTATTTTTGGCGATT 59.015 39.130 0.00 0.00 31.76 3.34
88 89 4.446051 CACCACGTTTATTTTTGGCGATTT 59.554 37.500 0.00 0.00 31.76 2.17
89 90 5.050702 CACCACGTTTATTTTTGGCGATTTT 60.051 36.000 0.00 0.00 31.76 1.82
90 91 5.524281 ACCACGTTTATTTTTGGCGATTTTT 59.476 32.000 0.00 0.00 31.76 1.94
106 107 0.869730 TTTTTACGCGCTGGAGTTCC 59.130 50.000 5.73 0.00 0.00 3.62
107 108 0.034337 TTTTACGCGCTGGAGTTCCT 59.966 50.000 5.73 0.00 36.82 3.36
108 109 0.669318 TTTACGCGCTGGAGTTCCTG 60.669 55.000 5.73 0.13 37.93 3.86
109 110 1.529152 TTACGCGCTGGAGTTCCTGA 61.529 55.000 5.73 0.00 37.15 3.86
110 111 2.209064 TACGCGCTGGAGTTCCTGAC 62.209 60.000 5.73 0.13 37.15 3.51
111 112 2.435059 GCGCTGGAGTTCCTGACC 60.435 66.667 0.00 0.00 37.15 4.02
112 113 2.948720 GCGCTGGAGTTCCTGACCT 61.949 63.158 0.00 0.00 37.15 3.85
113 114 1.216710 CGCTGGAGTTCCTGACCTC 59.783 63.158 9.01 0.00 37.15 3.85
114 115 1.599576 GCTGGAGTTCCTGACCTCC 59.400 63.158 9.01 3.93 37.15 4.30
115 116 1.194781 GCTGGAGTTCCTGACCTCCA 61.195 60.000 12.24 12.24 42.95 3.86
116 117 1.352083 CTGGAGTTCCTGACCTCCAA 58.648 55.000 13.56 0.32 44.27 3.53
117 118 1.699634 CTGGAGTTCCTGACCTCCAAA 59.300 52.381 13.56 0.00 44.27 3.28
118 119 2.307098 CTGGAGTTCCTGACCTCCAAAT 59.693 50.000 13.56 0.00 44.27 2.32
119 120 2.040278 TGGAGTTCCTGACCTCCAAATG 59.960 50.000 10.64 0.00 42.32 2.32
120 121 2.619074 GGAGTTCCTGACCTCCAAATGG 60.619 54.545 5.92 0.00 36.11 3.16
121 122 1.177401 GTTCCTGACCTCCAAATGGC 58.823 55.000 0.00 0.00 34.44 4.40
122 123 0.039618 TTCCTGACCTCCAAATGGCC 59.960 55.000 0.00 0.00 34.44 5.36
123 124 1.380380 CCTGACCTCCAAATGGCCC 60.380 63.158 0.00 0.00 34.44 5.80
124 125 1.750399 CTGACCTCCAAATGGCCCG 60.750 63.158 0.00 0.00 34.44 6.13
125 126 2.440247 GACCTCCAAATGGCCCGG 60.440 66.667 0.00 0.00 34.44 5.73
126 127 4.759205 ACCTCCAAATGGCCCGGC 62.759 66.667 0.00 0.00 34.44 6.13
138 139 4.511246 CCCGGCCCATGTGCATCT 62.511 66.667 1.71 0.00 0.00 2.90
139 140 2.510411 CCGGCCCATGTGCATCTA 59.490 61.111 1.71 0.00 0.00 1.98
140 141 1.893808 CCGGCCCATGTGCATCTAC 60.894 63.158 1.71 0.00 0.00 2.59
141 142 1.893808 CGGCCCATGTGCATCTACC 60.894 63.158 1.71 0.00 0.00 3.18
142 143 1.533711 GGCCCATGTGCATCTACCT 59.466 57.895 1.71 0.00 0.00 3.08
143 144 0.106519 GGCCCATGTGCATCTACCTT 60.107 55.000 1.71 0.00 0.00 3.50
144 145 1.312815 GCCCATGTGCATCTACCTTC 58.687 55.000 0.00 0.00 0.00 3.46
145 146 1.586422 CCCATGTGCATCTACCTTCG 58.414 55.000 0.00 0.00 0.00 3.79
146 147 1.586422 CCATGTGCATCTACCTTCGG 58.414 55.000 0.00 0.00 0.00 4.30
147 148 0.940126 CATGTGCATCTACCTTCGGC 59.060 55.000 0.00 0.00 0.00 5.54
148 149 0.530650 ATGTGCATCTACCTTCGGCG 60.531 55.000 0.00 0.00 0.00 6.46
149 150 1.141019 GTGCATCTACCTTCGGCGA 59.859 57.895 4.99 4.99 0.00 5.54
150 151 0.459585 GTGCATCTACCTTCGGCGAA 60.460 55.000 22.33 22.33 0.00 4.70
151 152 0.459585 TGCATCTACCTTCGGCGAAC 60.460 55.000 19.83 6.95 0.00 3.95
152 153 1.480219 GCATCTACCTTCGGCGAACG 61.480 60.000 19.83 17.31 46.11 3.95
153 154 1.226888 ATCTACCTTCGGCGAACGC 60.227 57.895 19.83 10.81 43.86 4.84
154 155 1.940883 ATCTACCTTCGGCGAACGCA 61.941 55.000 19.83 4.75 44.11 5.24
155 156 2.431260 TACCTTCGGCGAACGCAC 60.431 61.111 19.83 9.12 44.11 5.34
156 157 3.919973 TACCTTCGGCGAACGCACC 62.920 63.158 19.83 3.68 44.11 5.01
158 159 3.041940 CTTCGGCGAACGCACCTT 61.042 61.111 19.83 0.00 44.11 3.50
159 160 3.011760 CTTCGGCGAACGCACCTTC 62.012 63.158 19.83 2.28 44.11 3.46
167 168 3.315796 ACGCACCTTCGTTTGACG 58.684 55.556 0.00 0.00 44.19 4.35
168 169 2.127758 CGCACCTTCGTTTGACGC 60.128 61.111 0.00 0.00 42.21 5.19
169 170 2.594962 CGCACCTTCGTTTGACGCT 61.595 57.895 0.00 0.00 42.21 5.07
170 171 1.279527 CGCACCTTCGTTTGACGCTA 61.280 55.000 0.00 0.00 42.21 4.26
171 172 0.863144 GCACCTTCGTTTGACGCTAA 59.137 50.000 0.00 0.00 42.21 3.09
172 173 1.398071 GCACCTTCGTTTGACGCTAAC 60.398 52.381 0.00 0.00 42.21 2.34
184 185 4.861883 GCTAACGAGCGTCAGACA 57.138 55.556 0.41 0.00 39.39 3.41
185 186 2.643044 GCTAACGAGCGTCAGACAG 58.357 57.895 0.41 0.00 39.39 3.51
186 187 0.798771 GCTAACGAGCGTCAGACAGG 60.799 60.000 0.41 0.00 39.39 4.00
187 188 0.179161 CTAACGAGCGTCAGACAGGG 60.179 60.000 0.41 0.00 0.00 4.45
188 189 1.592400 TAACGAGCGTCAGACAGGGG 61.592 60.000 0.41 0.00 0.00 4.79
189 190 4.135153 CGAGCGTCAGACAGGGGG 62.135 72.222 0.41 0.00 0.00 5.40
190 191 2.997897 GAGCGTCAGACAGGGGGT 60.998 66.667 0.41 0.00 0.00 4.95
217 218 3.307480 GCTTACTAATCGTGCCCCCATAT 60.307 47.826 0.00 0.00 0.00 1.78
218 219 4.081309 GCTTACTAATCGTGCCCCCATATA 60.081 45.833 0.00 0.00 0.00 0.86
327 342 1.687494 GGCAAACGAGCGCTCTGTAG 61.687 60.000 32.88 24.88 34.64 2.74
328 343 1.009389 GCAAACGAGCGCTCTGTAGT 61.009 55.000 32.88 21.19 0.00 2.73
329 344 0.985549 CAAACGAGCGCTCTGTAGTC 59.014 55.000 32.88 8.20 0.00 2.59
330 345 0.882474 AAACGAGCGCTCTGTAGTCT 59.118 50.000 32.88 15.21 0.00 3.24
331 346 0.169230 AACGAGCGCTCTGTAGTCTG 59.831 55.000 32.88 18.03 0.00 3.51
332 347 0.956410 ACGAGCGCTCTGTAGTCTGT 60.956 55.000 32.88 18.68 0.00 3.41
333 348 1.007580 CGAGCGCTCTGTAGTCTGTA 58.992 55.000 32.88 0.00 0.00 2.74
1134 1149 1.669760 CAAGTTCAGGCCGGCGTTA 60.670 57.895 21.08 9.35 0.00 3.18
1311 1326 2.870372 GCGTTGATGCTGGTGGAC 59.130 61.111 0.00 0.00 0.00 4.02
1764 1779 3.459598 AGGATGCTAAGCCAAATACCTCA 59.540 43.478 0.00 0.00 32.71 3.86
1851 1866 4.427312 GTGATGAAATGGAACTTGATGGC 58.573 43.478 0.00 0.00 0.00 4.40
1854 1869 4.314522 TGAAATGGAACTTGATGGCCTA 57.685 40.909 3.32 0.00 0.00 3.93
1872 1887 6.905736 TGGCCTATATCCAAACTTAATGACA 58.094 36.000 3.32 0.00 0.00 3.58
1928 1943 0.394192 CTGCTCGATGAGGCCCATAA 59.606 55.000 0.00 0.00 35.17 1.90
1941 1956 7.732222 TGAGGCCCATAAAATATTTGAAAGT 57.268 32.000 0.00 0.00 0.00 2.66
2314 2332 7.161773 AGTTACTCCATTTTGATTCATGGTG 57.838 36.000 5.01 5.35 40.90 4.17
2348 2366 1.819288 TCAGGCTAGAGAAACGTCCAG 59.181 52.381 0.00 0.00 0.00 3.86
2574 2592 4.645956 CTTACATGCTTTCTGAAGAAGCG 58.354 43.478 8.96 0.30 35.21 4.68
3087 3105 1.949525 GCAATGGAGGCGTATCACATT 59.050 47.619 0.00 0.00 32.43 2.71
3272 3291 5.482163 TCAGGATCTTGTATTGTGACACA 57.518 39.130 3.56 3.56 0.00 3.72
3273 3292 5.237815 TCAGGATCTTGTATTGTGACACAC 58.762 41.667 8.05 0.00 34.56 3.82
3322 3343 3.169099 ACTGAGTTGATCTGGCTGTACT 58.831 45.455 0.00 0.00 0.00 2.73
3479 3502 5.794894 TCTGGTAAGGTTCTGATCTTCAAC 58.205 41.667 0.00 0.00 0.00 3.18
3801 3829 3.222603 ACTTCCCTTCATTGGTGTTGTC 58.777 45.455 0.00 0.00 0.00 3.18
3806 3834 3.255642 CCCTTCATTGGTGTTGTCGAAAT 59.744 43.478 0.00 0.00 0.00 2.17
3852 3880 0.817634 TTCACTCCAAACAGGCACCG 60.818 55.000 0.00 0.00 37.29 4.94
3917 3945 8.718102 TGATAAATAGTTGAGTTTGGTAGCTC 57.282 34.615 0.00 0.00 0.00 4.09
4085 5865 8.579850 AATGTTGAAAGTTAGCCAGATCATAA 57.420 30.769 0.00 0.00 0.00 1.90
4086 5866 7.615582 TGTTGAAAGTTAGCCAGATCATAAG 57.384 36.000 0.00 0.00 0.00 1.73
4112 5892 7.323052 TGATATGCTCCTCTAGACTTCTCTA 57.677 40.000 0.00 0.00 0.00 2.43
4114 5894 3.799366 TGCTCCTCTAGACTTCTCTACG 58.201 50.000 0.00 0.00 0.00 3.51
4125 5905 5.048507 AGACTTCTCTACGTTGGTGTTTTC 58.951 41.667 0.00 0.00 0.00 2.29
4126 5906 4.761975 ACTTCTCTACGTTGGTGTTTTCA 58.238 39.130 0.00 0.00 0.00 2.69
4160 5941 5.935789 CCTGTGAAATTCCTGCATTTGAAAT 59.064 36.000 0.00 0.00 0.00 2.17
4288 6069 5.142061 TCTCTTGCCGTGTAAAGTTGATA 57.858 39.130 0.00 0.00 0.00 2.15
4294 6075 5.726397 TGCCGTGTAAAGTTGATAGTACAT 58.274 37.500 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.322322 TACCAATCGGGCTGAAACGT 59.678 50.000 0.00 0.00 42.05 3.99
1 2 1.006832 CTACCAATCGGGCTGAAACG 58.993 55.000 0.00 0.00 42.05 3.60
2 3 1.339727 ACCTACCAATCGGGCTGAAAC 60.340 52.381 0.00 0.00 42.05 2.78
3 4 0.988832 ACCTACCAATCGGGCTGAAA 59.011 50.000 0.00 0.00 42.05 2.69
4 5 0.988832 AACCTACCAATCGGGCTGAA 59.011 50.000 0.00 0.00 42.05 3.02
5 6 0.539986 GAACCTACCAATCGGGCTGA 59.460 55.000 0.00 0.00 42.05 4.26
6 7 0.541863 AGAACCTACCAATCGGGCTG 59.458 55.000 0.00 0.00 42.05 4.85
7 8 2.040178 CTAGAACCTACCAATCGGGCT 58.960 52.381 0.00 0.00 42.05 5.19
8 9 2.037144 TCTAGAACCTACCAATCGGGC 58.963 52.381 0.00 0.00 42.05 6.13
9 10 3.297736 AGTCTAGAACCTACCAATCGGG 58.702 50.000 0.00 0.00 44.81 5.14
10 11 4.497674 CGAAGTCTAGAACCTACCAATCGG 60.498 50.000 0.00 0.00 38.77 4.18
11 12 4.599047 CGAAGTCTAGAACCTACCAATCG 58.401 47.826 0.00 0.00 0.00 3.34
12 13 4.361420 GCGAAGTCTAGAACCTACCAATC 58.639 47.826 0.00 0.00 0.00 2.67
13 14 3.181489 CGCGAAGTCTAGAACCTACCAAT 60.181 47.826 0.00 0.00 0.00 3.16
14 15 2.163010 CGCGAAGTCTAGAACCTACCAA 59.837 50.000 0.00 0.00 0.00 3.67
15 16 1.741706 CGCGAAGTCTAGAACCTACCA 59.258 52.381 0.00 0.00 0.00 3.25
16 17 2.012673 TCGCGAAGTCTAGAACCTACC 58.987 52.381 6.20 0.00 0.00 3.18
17 18 3.754188 TTCGCGAAGTCTAGAACCTAC 57.246 47.619 19.38 0.00 0.00 3.18
18 19 3.066342 CCATTCGCGAAGTCTAGAACCTA 59.934 47.826 27.20 0.00 0.00 3.08
19 20 2.159226 CCATTCGCGAAGTCTAGAACCT 60.159 50.000 27.20 2.84 0.00 3.50
20 21 2.194271 CCATTCGCGAAGTCTAGAACC 58.806 52.381 27.20 0.00 0.00 3.62
21 22 2.159282 TCCCATTCGCGAAGTCTAGAAC 60.159 50.000 27.20 0.00 0.00 3.01
22 23 2.097036 TCCCATTCGCGAAGTCTAGAA 58.903 47.619 27.20 0.74 0.00 2.10
23 24 1.404391 GTCCCATTCGCGAAGTCTAGA 59.596 52.381 27.20 15.32 0.00 2.43
24 25 1.841450 GTCCCATTCGCGAAGTCTAG 58.159 55.000 27.20 13.32 0.00 2.43
25 26 0.099968 CGTCCCATTCGCGAAGTCTA 59.900 55.000 27.20 9.98 0.00 2.59
26 27 1.153823 CGTCCCATTCGCGAAGTCT 60.154 57.895 27.20 7.74 0.00 3.24
27 28 1.411493 GACGTCCCATTCGCGAAGTC 61.411 60.000 27.20 21.58 31.91 3.01
28 29 1.445582 GACGTCCCATTCGCGAAGT 60.446 57.895 27.20 17.60 0.00 3.01
29 30 1.445410 TGACGTCCCATTCGCGAAG 60.445 57.895 27.20 17.68 0.00 3.79
30 31 1.735198 GTGACGTCCCATTCGCGAA 60.735 57.895 25.66 25.66 0.00 4.70
31 32 2.126228 GTGACGTCCCATTCGCGA 60.126 61.111 14.12 3.71 0.00 5.87
32 33 3.541831 CGTGACGTCCCATTCGCG 61.542 66.667 14.12 0.00 39.17 5.87
33 34 2.126228 TCGTGACGTCCCATTCGC 60.126 61.111 14.12 0.00 0.00 4.70
34 35 0.388134 AACTCGTGACGTCCCATTCG 60.388 55.000 14.12 10.00 0.00 3.34
35 36 1.347320 GAACTCGTGACGTCCCATTC 58.653 55.000 14.12 6.27 0.00 2.67
36 37 0.388134 CGAACTCGTGACGTCCCATT 60.388 55.000 14.12 0.06 34.11 3.16
37 38 1.211969 CGAACTCGTGACGTCCCAT 59.788 57.895 14.12 0.00 34.11 4.00
38 39 1.239296 ATCGAACTCGTGACGTCCCA 61.239 55.000 14.12 0.00 40.80 4.37
39 40 0.729116 TATCGAACTCGTGACGTCCC 59.271 55.000 14.12 0.00 40.80 4.46
40 41 2.287373 AGATATCGAACTCGTGACGTCC 59.713 50.000 14.12 3.43 40.80 4.79
41 42 3.281601 CAGATATCGAACTCGTGACGTC 58.718 50.000 9.11 9.11 40.80 4.34
42 43 2.031807 CCAGATATCGAACTCGTGACGT 59.968 50.000 4.40 0.00 40.80 4.34
43 44 2.640831 CCAGATATCGAACTCGTGACG 58.359 52.381 0.00 0.00 40.80 4.35
44 45 2.386249 GCCAGATATCGAACTCGTGAC 58.614 52.381 0.00 0.00 40.80 3.67
45 46 1.337071 GGCCAGATATCGAACTCGTGA 59.663 52.381 0.00 0.00 40.80 4.35
46 47 1.067060 TGGCCAGATATCGAACTCGTG 59.933 52.381 0.00 0.00 40.80 4.35
47 48 1.067212 GTGGCCAGATATCGAACTCGT 59.933 52.381 5.11 0.00 40.80 4.18
48 49 1.603172 GGTGGCCAGATATCGAACTCG 60.603 57.143 5.11 0.00 41.45 4.18
49 50 1.412710 TGGTGGCCAGATATCGAACTC 59.587 52.381 5.11 0.00 0.00 3.01
50 51 1.139058 GTGGTGGCCAGATATCGAACT 59.861 52.381 5.11 0.00 32.34 3.01
51 52 1.583054 GTGGTGGCCAGATATCGAAC 58.417 55.000 5.11 0.00 32.34 3.95
52 53 0.104120 CGTGGTGGCCAGATATCGAA 59.896 55.000 5.11 0.00 32.34 3.71
53 54 1.040893 ACGTGGTGGCCAGATATCGA 61.041 55.000 5.11 0.00 32.34 3.59
54 55 0.179084 AACGTGGTGGCCAGATATCG 60.179 55.000 5.11 9.93 32.34 2.92
55 56 2.038387 AAACGTGGTGGCCAGATATC 57.962 50.000 5.11 0.00 32.34 1.63
56 57 3.857157 ATAAACGTGGTGGCCAGATAT 57.143 42.857 5.11 0.00 32.34 1.63
57 58 3.637911 AATAAACGTGGTGGCCAGATA 57.362 42.857 5.11 0.00 32.34 1.98
58 59 2.507407 AATAAACGTGGTGGCCAGAT 57.493 45.000 5.11 0.00 32.34 2.90
59 60 2.279935 AAATAAACGTGGTGGCCAGA 57.720 45.000 5.11 0.00 32.34 3.86
60 61 3.056304 CAAAAATAAACGTGGTGGCCAG 58.944 45.455 5.11 0.00 32.34 4.85
61 62 2.224066 CCAAAAATAAACGTGGTGGCCA 60.224 45.455 0.00 0.00 0.00 5.36
62 63 2.409012 CCAAAAATAAACGTGGTGGCC 58.591 47.619 0.00 0.00 0.00 5.36
63 64 1.795872 GCCAAAAATAAACGTGGTGGC 59.204 47.619 0.00 0.00 42.88 5.01
64 65 2.055100 CGCCAAAAATAAACGTGGTGG 58.945 47.619 0.00 0.00 37.88 4.61
65 66 3.001395 TCGCCAAAAATAAACGTGGTG 57.999 42.857 0.00 0.00 41.96 4.17
66 67 3.926821 ATCGCCAAAAATAAACGTGGT 57.073 38.095 0.00 0.00 33.43 4.16
67 68 5.583969 AAAATCGCCAAAAATAAACGTGG 57.416 34.783 0.00 0.00 0.00 4.94
87 88 0.869730 GGAACTCCAGCGCGTAAAAA 59.130 50.000 8.43 0.00 35.64 1.94
88 89 0.034337 AGGAACTCCAGCGCGTAAAA 59.966 50.000 8.43 0.00 38.89 1.52
89 90 0.669318 CAGGAACTCCAGCGCGTAAA 60.669 55.000 8.43 0.00 34.60 2.01
90 91 1.080093 CAGGAACTCCAGCGCGTAA 60.080 57.895 8.43 0.00 34.60 3.18
91 92 1.974875 TCAGGAACTCCAGCGCGTA 60.975 57.895 8.43 0.00 34.60 4.42
92 93 3.303135 TCAGGAACTCCAGCGCGT 61.303 61.111 8.43 0.00 34.60 6.01
93 94 2.811317 GTCAGGAACTCCAGCGCG 60.811 66.667 0.00 0.00 34.60 6.86
94 95 2.435059 GGTCAGGAACTCCAGCGC 60.435 66.667 0.00 0.00 34.60 5.92
95 96 1.216710 GAGGTCAGGAACTCCAGCG 59.783 63.158 2.86 0.00 39.20 5.18
100 101 2.716217 CCATTTGGAGGTCAGGAACTC 58.284 52.381 5.77 5.77 44.27 3.01
101 102 1.272147 GCCATTTGGAGGTCAGGAACT 60.272 52.381 0.00 0.00 36.54 3.01
102 103 1.177401 GCCATTTGGAGGTCAGGAAC 58.823 55.000 0.00 0.00 37.39 3.62
103 104 0.039618 GGCCATTTGGAGGTCAGGAA 59.960 55.000 0.00 0.00 37.39 3.36
104 105 1.691219 GGCCATTTGGAGGTCAGGA 59.309 57.895 0.00 0.00 37.39 3.86
105 106 1.380380 GGGCCATTTGGAGGTCAGG 60.380 63.158 4.39 0.00 37.39 3.86
106 107 1.750399 CGGGCCATTTGGAGGTCAG 60.750 63.158 4.39 0.00 37.39 3.51
107 108 2.354729 CGGGCCATTTGGAGGTCA 59.645 61.111 4.39 0.00 37.39 4.02
108 109 2.440247 CCGGGCCATTTGGAGGTC 60.440 66.667 4.39 0.00 37.39 3.85
109 110 4.759205 GCCGGGCCATTTGGAGGT 62.759 66.667 8.12 0.00 37.39 3.85
121 122 3.118768 TAGATGCACATGGGCCGGG 62.119 63.158 19.33 0.00 0.00 5.73
122 123 1.893808 GTAGATGCACATGGGCCGG 60.894 63.158 19.33 0.00 0.00 6.13
123 124 1.893808 GGTAGATGCACATGGGCCG 60.894 63.158 19.33 0.00 0.00 6.13
124 125 0.106519 AAGGTAGATGCACATGGGCC 60.107 55.000 19.33 2.11 0.00 5.80
125 126 1.312815 GAAGGTAGATGCACATGGGC 58.687 55.000 14.67 14.67 0.00 5.36
126 127 1.586422 CGAAGGTAGATGCACATGGG 58.414 55.000 0.00 0.00 0.00 4.00
150 151 2.877974 GCGTCAAACGAAGGTGCGT 61.878 57.895 3.28 0.00 46.05 5.24
151 152 1.279527 TAGCGTCAAACGAAGGTGCG 61.280 55.000 3.28 0.00 46.05 5.34
152 153 0.863144 TTAGCGTCAAACGAAGGTGC 59.137 50.000 3.28 0.00 46.05 5.01
153 154 2.572173 GTTAGCGTCAAACGAAGGTG 57.428 50.000 3.28 0.00 46.05 4.00
167 168 0.798771 CCTGTCTGACGCTCGTTAGC 60.799 60.000 9.00 5.76 45.86 3.09
168 169 0.179161 CCCTGTCTGACGCTCGTTAG 60.179 60.000 7.73 7.73 33.68 2.34
169 170 1.592400 CCCCTGTCTGACGCTCGTTA 61.592 60.000 2.98 0.00 0.00 3.18
170 171 2.651361 CCCTGTCTGACGCTCGTT 59.349 61.111 2.98 0.00 0.00 3.85
171 172 3.374402 CCCCTGTCTGACGCTCGT 61.374 66.667 2.98 0.00 0.00 4.18
172 173 4.135153 CCCCCTGTCTGACGCTCG 62.135 72.222 2.98 0.00 0.00 5.03
173 174 2.997897 ACCCCCTGTCTGACGCTC 60.998 66.667 2.98 0.00 0.00 5.03
174 175 2.997897 GACCCCCTGTCTGACGCT 60.998 66.667 2.98 0.00 41.03 5.07
175 176 4.083862 GGACCCCCTGTCTGACGC 62.084 72.222 2.98 0.00 43.89 5.19
176 177 3.391382 GGGACCCCCTGTCTGACG 61.391 72.222 0.00 0.00 43.89 4.35
188 189 0.749049 ACGATTAGTAAGCGGGGACC 59.251 55.000 23.03 0.00 45.98 4.46
189 190 1.849097 CACGATTAGTAAGCGGGGAC 58.151 55.000 23.03 0.00 45.98 4.46
190 191 0.103572 GCACGATTAGTAAGCGGGGA 59.896 55.000 22.94 0.00 45.19 4.81
191 192 0.878961 GGCACGATTAGTAAGCGGGG 60.879 60.000 22.94 15.59 45.19 5.73
269 270 2.341101 CCAAGCAGAGCTGGCCAAG 61.341 63.158 7.01 1.85 39.62 3.61
327 342 2.303175 CTAGGAGAGCAGGGTACAGAC 58.697 57.143 0.00 0.00 0.00 3.51
328 343 1.215673 CCTAGGAGAGCAGGGTACAGA 59.784 57.143 1.05 0.00 0.00 3.41
329 344 1.063567 ACCTAGGAGAGCAGGGTACAG 60.064 57.143 17.98 0.00 36.15 2.74
330 345 1.008403 ACCTAGGAGAGCAGGGTACA 58.992 55.000 17.98 0.00 36.15 2.90
331 346 2.162264 AACCTAGGAGAGCAGGGTAC 57.838 55.000 17.98 0.00 36.15 3.34
332 347 2.942604 AAACCTAGGAGAGCAGGGTA 57.057 50.000 17.98 0.00 36.15 3.69
333 348 2.046280 AAAACCTAGGAGAGCAGGGT 57.954 50.000 17.98 0.00 36.15 4.34
1103 1118 3.899981 AACTTGAGCCGCCGCATGA 62.900 57.895 0.00 0.00 37.52 3.07
1311 1326 1.144936 GCATCTCCCCTTCACCTCG 59.855 63.158 0.00 0.00 0.00 4.63
1872 1887 6.126478 ACAGCCTATCCACCATTATGTTAACT 60.126 38.462 7.22 0.00 0.00 2.24
1928 1943 6.650807 TCTCTGACTCGCACTTTCAAATATTT 59.349 34.615 0.00 0.00 0.00 1.40
1941 1956 1.290324 GCAACCTCTCTGACTCGCA 59.710 57.895 0.00 0.00 0.00 5.10
2314 2332 0.312102 GCCTGACCAGCTTTTGTGAC 59.688 55.000 0.00 0.00 0.00 3.67
2348 2366 4.554973 GCTGACTCATTGCGTGAAAAATAC 59.445 41.667 0.00 0.00 36.14 1.89
2605 2623 7.701539 AGCCATCTATGAGAGAACTATACAG 57.298 40.000 0.00 0.00 37.85 2.74
3087 3105 4.514066 GCCCTTAGACGAGTTTCTTCAAAA 59.486 41.667 0.00 0.00 0.00 2.44
3322 3343 2.722094 AGTGACCAAGAAGCACAAACA 58.278 42.857 0.00 0.00 35.08 2.83
3443 3465 5.098663 ACCTTACCAGAATCAAGGGAACTA 58.901 41.667 4.73 0.00 42.65 2.24
3555 3578 4.096984 GGTTCAAATCATCAGCTTACCTGG 59.903 45.833 0.00 0.00 42.05 4.45
3730 3755 6.149633 GCTAACTTTCGTCATTTCAAATGGT 58.850 36.000 10.30 0.00 0.00 3.55
3801 3829 6.371548 TCACAGGAACTTCATAGGAAATTTCG 59.628 38.462 11.95 0.00 34.60 3.46
3806 3834 7.176690 GGAATTTCACAGGAACTTCATAGGAAA 59.823 37.037 8.95 4.94 41.76 3.13
3852 3880 6.860080 ACTCCATTGTTCAAATCATGTGATC 58.140 36.000 0.00 0.00 32.75 2.92
3917 3945 1.139163 GCCAAAAACATTGGTCAGCG 58.861 50.000 8.84 0.00 41.53 5.18
4086 5866 6.886459 AGAGAAGTCTAGAGGAGCATATCATC 59.114 42.308 0.00 0.00 39.06 2.92
4112 5892 6.036626 GGAATTTTCAATGAAAACACCAACGT 59.963 34.615 25.86 9.68 42.98 3.99
4114 5894 7.065683 ACAGGAATTTTCAATGAAAACACCAAC 59.934 33.333 29.09 16.84 42.98 3.77
4125 5905 7.360607 GCAGGAATTTCACAGGAATTTTCAATG 60.361 37.037 0.00 0.00 31.85 2.82
4126 5906 6.652062 GCAGGAATTTCACAGGAATTTTCAAT 59.348 34.615 0.00 0.00 31.85 2.57
4219 6000 4.202010 GGACAGCAAGCTAACAAACTCAAA 60.202 41.667 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.