Multiple sequence alignment - TraesCS4D01G245100

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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 TraesCS4D01G245100 chr4D 100.000 3081 0 0 1 3081 410305118 410308198 0.000000e+00 5690
1 TraesCS4D01G245100 chr4D 92.153 2842 166 27 262 3081 132439452 132436646 0.000000e+00 3960
2 TraesCS4D01G245100 chr4D 97.297 259 7 0 1 259 254700924 254700666 1.010000e-119 440
3 TraesCS4D01G245100 chr4D 97.297 259 7 0 1 259 479821881 479822139 1.010000e-119 440
4 TraesCS4D01G245100 chr2A 95.330 2848 101 9 258 3081 755097031 755094192 0.000000e+00 4494
5 TraesCS4D01G245100 chr2A 95.148 2844 107 11 262 3081 755104801 755101965 0.000000e+00 4458
6 TraesCS4D01G245100 chr2A 95.153 2847 90 11 259 3081 618956014 618958836 0.000000e+00 4449
7 TraesCS4D01G245100 chr2A 93.137 816 46 5 262 1071 471763301 471764112 0.000000e+00 1188
8 TraesCS4D01G245100 chr2A 97.080 274 8 0 1066 1339 471774443 471774716 2.160000e-126 462
9 TraesCS4D01G245100 chr5A 95.323 2844 103 11 262 3081 257553567 257556404 0.000000e+00 4488
10 TraesCS4D01G245100 chr5A 95.265 2851 100 17 258 3081 302990423 302993265 0.000000e+00 4484
11 TraesCS4D01G245100 chr5B 96.024 2289 74 4 809 3081 236069779 236067492 0.000000e+00 3707
12 TraesCS4D01G245100 chr7D 95.114 2108 82 9 262 2356 235511587 235509488 0.000000e+00 3302
13 TraesCS4D01G245100 chr7D 96.578 1841 47 3 1256 3081 72315541 72313702 0.000000e+00 3037
14 TraesCS4D01G245100 chr7A 82.064 2074 348 19 998 3062 60710782 60708724 0.000000e+00 1748
15 TraesCS4D01G245100 chr4A 90.655 1038 60 13 262 1290 740666874 740667883 0.000000e+00 1345
16 TraesCS4D01G245100 chr6B 90.656 610 43 6 262 862 674204911 674204307 0.000000e+00 798
17 TraesCS4D01G245100 chr5D 97.683 259 6 0 1 259 116237140 116237398 2.180000e-121 446
18 TraesCS4D01G245100 chr5D 97.297 259 7 0 1 259 221426121 221425863 1.010000e-119 440
19 TraesCS4D01G245100 chr3D 97.683 259 6 0 1 259 41629967 41629709 2.180000e-121 446
20 TraesCS4D01G245100 chr3D 97.683 259 6 0 1 259 381355273 381355531 2.180000e-121 446
21 TraesCS4D01G245100 chr2D 97.683 259 6 0 1 259 273912836 273912578 2.180000e-121 446
22 TraesCS4D01G245100 chr6D 97.297 259 7 0 1 259 426521367 426521109 1.010000e-119 440
23 TraesCS4D01G245100 chr1A 97.297 259 7 0 1 259 373516296 373516554 1.010000e-119 440


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 TraesCS4D01G245100 chr4D 410305118 410308198 3080 False 5690 5690 100.000 1 3081 1 chr4D.!!$F1 3080
1 TraesCS4D01G245100 chr4D 132436646 132439452 2806 True 3960 3960 92.153 262 3081 1 chr4D.!!$R1 2819
2 TraesCS4D01G245100 chr2A 755094192 755097031 2839 True 4494 4494 95.330 258 3081 1 chr2A.!!$R1 2823
3 TraesCS4D01G245100 chr2A 755101965 755104801 2836 True 4458 4458 95.148 262 3081 1 chr2A.!!$R2 2819
4 TraesCS4D01G245100 chr2A 618956014 618958836 2822 False 4449 4449 95.153 259 3081 1 chr2A.!!$F3 2822
5 TraesCS4D01G245100 chr2A 471763301 471764112 811 False 1188 1188 93.137 262 1071 1 chr2A.!!$F1 809
6 TraesCS4D01G245100 chr5A 257553567 257556404 2837 False 4488 4488 95.323 262 3081 1 chr5A.!!$F1 2819
7 TraesCS4D01G245100 chr5A 302990423 302993265 2842 False 4484 4484 95.265 258 3081 1 chr5A.!!$F2 2823
8 TraesCS4D01G245100 chr5B 236067492 236069779 2287 True 3707 3707 96.024 809 3081 1 chr5B.!!$R1 2272
9 TraesCS4D01G245100 chr7D 235509488 235511587 2099 True 3302 3302 95.114 262 2356 1 chr7D.!!$R2 2094
10 TraesCS4D01G245100 chr7D 72313702 72315541 1839 True 3037 3037 96.578 1256 3081 1 chr7D.!!$R1 1825
11 TraesCS4D01G245100 chr7A 60708724 60710782 2058 True 1748 1748 82.064 998 3062 1 chr7A.!!$R1 2064
12 TraesCS4D01G245100 chr4A 740666874 740667883 1009 False 1345 1345 90.655 262 1290 1 chr4A.!!$F1 1028
13 TraesCS4D01G245100 chr6B 674204307 674204911 604 True 798 798 90.656 262 862 1 chr6B.!!$R1 600

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
93 94 0.389948 GGTCGGTTCAGCTGTCGATT 60.390 55.000 23.53 0.00 34.13 3.34 F
96 97 1.000394 TCGGTTCAGCTGTCGATTTGA 60.000 47.619 14.67 1.36 0.00 2.69 F
890 917 1.065854 GGTGTGGCTGCAGACTTAGAT 60.066 52.381 22.80 0.00 0.00 1.98 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1159 1187 1.610363 TGCGCACCTTCCAAATAACA 58.390 45.000 5.66 0.0 0.00 2.41 R
1552 1593 2.293122 CCTCGCTCTCATCCTTACTCTG 59.707 54.545 0.00 0.0 0.00 3.35 R
2377 2435 1.574526 TAGCCAGCTGCCCCTTGAAT 61.575 55.000 8.66 0.0 42.71 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
47 48 6.921914 AGTTGAACTAGCTATTTCAGTACGT 58.078 36.000 21.41 9.30 33.36 3.57
48 49 6.807230 AGTTGAACTAGCTATTTCAGTACGTG 59.193 38.462 21.41 0.00 33.36 4.49
49 50 5.647589 TGAACTAGCTATTTCAGTACGTGG 58.352 41.667 19.40 0.00 0.00 4.94
50 51 5.184479 TGAACTAGCTATTTCAGTACGTGGT 59.816 40.000 19.40 0.00 0.00 4.16
51 52 5.656213 ACTAGCTATTTCAGTACGTGGTT 57.344 39.130 0.00 0.00 0.00 3.67
52 53 5.408356 ACTAGCTATTTCAGTACGTGGTTG 58.592 41.667 0.00 0.00 0.00 3.77
53 54 3.596214 AGCTATTTCAGTACGTGGTTGG 58.404 45.455 0.00 0.00 0.00 3.77
54 55 2.095372 GCTATTTCAGTACGTGGTTGGC 59.905 50.000 0.00 0.00 0.00 4.52
55 56 2.264005 ATTTCAGTACGTGGTTGGCA 57.736 45.000 0.00 0.00 0.00 4.92
56 57 2.039818 TTTCAGTACGTGGTTGGCAA 57.960 45.000 0.00 0.00 0.00 4.52
57 58 2.264005 TTCAGTACGTGGTTGGCAAT 57.736 45.000 1.92 0.00 0.00 3.56
58 59 3.404224 TTCAGTACGTGGTTGGCAATA 57.596 42.857 1.92 0.00 0.00 1.90
59 60 3.404224 TCAGTACGTGGTTGGCAATAA 57.596 42.857 1.92 0.00 0.00 1.40
60 61 3.945346 TCAGTACGTGGTTGGCAATAAT 58.055 40.909 1.92 0.00 0.00 1.28
61 62 4.328536 TCAGTACGTGGTTGGCAATAATT 58.671 39.130 1.92 0.00 0.00 1.40
62 63 4.155099 TCAGTACGTGGTTGGCAATAATTG 59.845 41.667 1.92 0.00 0.00 2.32
63 64 3.442273 AGTACGTGGTTGGCAATAATTGG 59.558 43.478 1.92 0.00 0.00 3.16
64 65 1.548269 ACGTGGTTGGCAATAATTGGG 59.452 47.619 1.92 0.00 0.00 4.12
65 66 1.134848 CGTGGTTGGCAATAATTGGGG 60.135 52.381 1.92 0.00 0.00 4.96
66 67 2.183679 GTGGTTGGCAATAATTGGGGA 58.816 47.619 1.92 0.00 0.00 4.81
67 68 2.569404 GTGGTTGGCAATAATTGGGGAA 59.431 45.455 1.92 0.00 0.00 3.97
68 69 3.008485 GTGGTTGGCAATAATTGGGGAAA 59.992 43.478 1.92 0.00 0.00 3.13
69 70 3.652869 TGGTTGGCAATAATTGGGGAAAA 59.347 39.130 1.92 0.00 0.00 2.29
70 71 4.290722 TGGTTGGCAATAATTGGGGAAAAT 59.709 37.500 1.92 0.00 0.00 1.82
71 72 5.222213 TGGTTGGCAATAATTGGGGAAAATT 60.222 36.000 1.92 0.00 34.24 1.82
72 73 5.714333 GGTTGGCAATAATTGGGGAAAATTT 59.286 36.000 1.92 0.00 32.16 1.82
73 74 6.210385 GGTTGGCAATAATTGGGGAAAATTTT 59.790 34.615 1.92 2.28 32.16 1.82
74 75 6.830873 TGGCAATAATTGGGGAAAATTTTG 57.169 33.333 8.47 0.00 32.16 2.44
75 76 5.713861 TGGCAATAATTGGGGAAAATTTTGG 59.286 36.000 8.47 0.00 32.16 3.28
76 77 5.714333 GGCAATAATTGGGGAAAATTTTGGT 59.286 36.000 8.47 0.00 32.16 3.67
77 78 6.127758 GGCAATAATTGGGGAAAATTTTGGTC 60.128 38.462 8.47 0.00 32.16 4.02
78 79 6.403092 GCAATAATTGGGGAAAATTTTGGTCG 60.403 38.462 8.47 0.00 32.16 4.79
79 80 3.694043 ATTGGGGAAAATTTTGGTCGG 57.306 42.857 8.47 0.00 0.00 4.79
80 81 2.089600 TGGGGAAAATTTTGGTCGGT 57.910 45.000 8.47 0.00 0.00 4.69
81 82 2.399580 TGGGGAAAATTTTGGTCGGTT 58.600 42.857 8.47 0.00 0.00 4.44
82 83 2.365941 TGGGGAAAATTTTGGTCGGTTC 59.634 45.455 8.47 0.00 0.00 3.62
83 84 2.365941 GGGGAAAATTTTGGTCGGTTCA 59.634 45.455 8.47 0.00 0.00 3.18
84 85 3.554129 GGGGAAAATTTTGGTCGGTTCAG 60.554 47.826 8.47 0.00 0.00 3.02
85 86 3.057019 GGAAAATTTTGGTCGGTTCAGC 58.943 45.455 8.47 0.00 0.00 4.26
86 87 3.243737 GGAAAATTTTGGTCGGTTCAGCT 60.244 43.478 8.47 0.00 0.00 4.24
87 88 3.369546 AAATTTTGGTCGGTTCAGCTG 57.630 42.857 7.63 7.63 0.00 4.24
88 89 1.981256 ATTTTGGTCGGTTCAGCTGT 58.019 45.000 14.67 0.00 0.00 4.40
89 90 1.305201 TTTTGGTCGGTTCAGCTGTC 58.695 50.000 14.67 8.29 0.00 3.51
90 91 0.878523 TTTGGTCGGTTCAGCTGTCG 60.879 55.000 14.67 15.72 0.00 4.35
91 92 1.740332 TTGGTCGGTTCAGCTGTCGA 61.740 55.000 14.67 17.66 0.00 4.20
92 93 1.215647 GGTCGGTTCAGCTGTCGAT 59.784 57.895 23.53 0.00 34.13 3.59
93 94 0.389948 GGTCGGTTCAGCTGTCGATT 60.390 55.000 23.53 0.00 34.13 3.34
94 95 1.429463 GTCGGTTCAGCTGTCGATTT 58.571 50.000 23.53 0.00 34.13 2.17
95 96 1.126846 GTCGGTTCAGCTGTCGATTTG 59.873 52.381 23.53 7.82 34.13 2.32
96 97 1.000394 TCGGTTCAGCTGTCGATTTGA 60.000 47.619 14.67 1.36 0.00 2.69
97 98 1.798223 CGGTTCAGCTGTCGATTTGAA 59.202 47.619 14.67 0.00 0.00 2.69
98 99 2.411547 CGGTTCAGCTGTCGATTTGAAC 60.412 50.000 14.67 18.15 45.29 3.18
99 100 2.808543 GGTTCAGCTGTCGATTTGAACT 59.191 45.455 14.67 2.38 45.32 3.01
100 101 3.364366 GGTTCAGCTGTCGATTTGAACTG 60.364 47.826 14.67 11.70 45.32 3.16
101 102 3.111853 TCAGCTGTCGATTTGAACTGT 57.888 42.857 14.67 0.00 0.00 3.55
102 103 3.466836 TCAGCTGTCGATTTGAACTGTT 58.533 40.909 14.67 0.00 0.00 3.16
103 104 3.876914 TCAGCTGTCGATTTGAACTGTTT 59.123 39.130 14.67 0.00 0.00 2.83
104 105 3.970610 CAGCTGTCGATTTGAACTGTTTG 59.029 43.478 5.25 0.00 0.00 2.93
105 106 3.627577 AGCTGTCGATTTGAACTGTTTGT 59.372 39.130 0.00 0.00 0.00 2.83
106 107 4.814234 AGCTGTCGATTTGAACTGTTTGTA 59.186 37.500 0.00 0.00 0.00 2.41
107 108 5.470098 AGCTGTCGATTTGAACTGTTTGTAT 59.530 36.000 0.00 0.00 0.00 2.29
108 109 6.649141 AGCTGTCGATTTGAACTGTTTGTATA 59.351 34.615 0.00 0.00 0.00 1.47
109 110 7.172532 AGCTGTCGATTTGAACTGTTTGTATAA 59.827 33.333 0.00 0.00 0.00 0.98
110 111 7.801315 GCTGTCGATTTGAACTGTTTGTATAAA 59.199 33.333 0.00 0.00 0.00 1.40
111 112 9.825972 CTGTCGATTTGAACTGTTTGTATAAAT 57.174 29.630 0.00 0.00 31.47 1.40
124 125 9.262472 CTGTTTGTATAAATTAAGAACGACTGC 57.738 33.333 0.00 0.00 0.00 4.40
125 126 8.995220 TGTTTGTATAAATTAAGAACGACTGCT 58.005 29.630 0.00 0.00 0.00 4.24
126 127 9.821662 GTTTGTATAAATTAAGAACGACTGCTT 57.178 29.630 0.00 0.00 0.00 3.91
135 136 9.817809 AATTAAGAACGACTGCTTAATCTATGA 57.182 29.630 0.00 0.00 43.04 2.15
136 137 9.817809 ATTAAGAACGACTGCTTAATCTATGAA 57.182 29.630 0.00 0.00 41.14 2.57
137 138 9.817809 TTAAGAACGACTGCTTAATCTATGAAT 57.182 29.630 0.00 0.00 33.12 2.57
138 139 7.706281 AGAACGACTGCTTAATCTATGAATG 57.294 36.000 0.00 0.00 0.00 2.67
139 140 7.492524 AGAACGACTGCTTAATCTATGAATGA 58.507 34.615 0.00 0.00 0.00 2.57
140 141 7.981789 AGAACGACTGCTTAATCTATGAATGAA 59.018 33.333 0.00 0.00 0.00 2.57
141 142 8.492673 AACGACTGCTTAATCTATGAATGAAA 57.507 30.769 0.00 0.00 0.00 2.69
142 143 8.668510 ACGACTGCTTAATCTATGAATGAAAT 57.331 30.769 0.00 0.00 0.00 2.17
143 144 8.768955 ACGACTGCTTAATCTATGAATGAAATC 58.231 33.333 0.00 0.00 0.00 2.17
144 145 8.986847 CGACTGCTTAATCTATGAATGAAATCT 58.013 33.333 0.00 0.00 0.00 2.40
190 191 8.567285 AGTTGCAAAAATTAGATACTGCTAGT 57.433 30.769 0.00 0.00 0.00 2.57
191 192 8.454106 AGTTGCAAAAATTAGATACTGCTAGTG 58.546 33.333 0.00 0.00 0.00 2.74
192 193 8.450964 GTTGCAAAAATTAGATACTGCTAGTGA 58.549 33.333 0.00 0.00 0.00 3.41
193 194 8.737168 TGCAAAAATTAGATACTGCTAGTGAT 57.263 30.769 0.00 0.00 0.00 3.06
194 195 9.177608 TGCAAAAATTAGATACTGCTAGTGATT 57.822 29.630 0.00 0.00 0.00 2.57
203 204 8.655651 AGATACTGCTAGTGATTTTTAGCTTC 57.344 34.615 0.00 0.00 42.13 3.86
204 205 8.260818 AGATACTGCTAGTGATTTTTAGCTTCA 58.739 33.333 0.00 0.00 42.13 3.02
205 206 8.970859 ATACTGCTAGTGATTTTTAGCTTCAT 57.029 30.769 0.00 0.00 42.13 2.57
207 208 8.970859 ACTGCTAGTGATTTTTAGCTTCATAT 57.029 30.769 0.00 0.00 42.13 1.78
208 209 9.401058 ACTGCTAGTGATTTTTAGCTTCATATT 57.599 29.630 0.00 0.00 42.13 1.28
220 221 7.969387 TTAGCTTCATATTTTGACAAATCGC 57.031 32.000 0.50 0.00 34.29 4.58
221 222 5.953183 AGCTTCATATTTTGACAAATCGCA 58.047 33.333 0.50 0.00 34.29 5.10
222 223 6.032094 AGCTTCATATTTTGACAAATCGCAG 58.968 36.000 0.50 0.00 34.29 5.18
223 224 5.801947 GCTTCATATTTTGACAAATCGCAGT 59.198 36.000 0.50 0.00 34.29 4.40
224 225 6.237384 GCTTCATATTTTGACAAATCGCAGTG 60.237 38.462 0.50 0.00 34.29 3.66
225 226 6.252967 TCATATTTTGACAAATCGCAGTGT 57.747 33.333 0.50 0.00 34.29 3.55
226 227 6.676950 TCATATTTTGACAAATCGCAGTGTT 58.323 32.000 0.50 0.00 34.29 3.32
227 228 7.811653 TCATATTTTGACAAATCGCAGTGTTA 58.188 30.769 0.50 0.00 34.29 2.41
228 229 7.748683 TCATATTTTGACAAATCGCAGTGTTAC 59.251 33.333 0.50 0.00 34.29 2.50
229 230 4.884458 TTTGACAAATCGCAGTGTTACA 57.116 36.364 0.00 0.00 0.00 2.41
230 231 4.466567 TTGACAAATCGCAGTGTTACAG 57.533 40.909 0.00 0.00 0.00 2.74
231 232 2.805671 TGACAAATCGCAGTGTTACAGG 59.194 45.455 0.00 0.00 0.00 4.00
232 233 2.151202 ACAAATCGCAGTGTTACAGGG 58.849 47.619 0.00 0.00 0.00 4.45
233 234 2.224426 ACAAATCGCAGTGTTACAGGGA 60.224 45.455 0.00 0.00 31.75 4.20
234 235 2.094762 AATCGCAGTGTTACAGGGAC 57.905 50.000 0.00 0.00 30.11 4.46
235 236 1.267121 ATCGCAGTGTTACAGGGACT 58.733 50.000 0.00 0.00 43.88 3.85
250 251 4.993705 AGGGACTGACAAATCTTACCAA 57.006 40.909 0.00 0.00 37.18 3.67
251 252 5.319043 AGGGACTGACAAATCTTACCAAA 57.681 39.130 0.00 0.00 37.18 3.28
252 253 5.892348 AGGGACTGACAAATCTTACCAAAT 58.108 37.500 0.00 0.00 37.18 2.32
253 254 6.314917 AGGGACTGACAAATCTTACCAAATT 58.685 36.000 0.00 0.00 37.18 1.82
254 255 6.209391 AGGGACTGACAAATCTTACCAAATTG 59.791 38.462 0.00 0.00 37.18 2.32
255 256 6.015434 GGGACTGACAAATCTTACCAAATTGT 60.015 38.462 0.00 0.00 36.96 2.71
256 257 7.433680 GGACTGACAAATCTTACCAAATTGTT 58.566 34.615 0.00 0.00 34.59 2.83
320 321 8.467598 GGTTCCTTATTTTACCCTGAAGAAATC 58.532 37.037 0.00 0.00 0.00 2.17
454 456 2.182516 AGTAGCTAGCCCACAAGGAT 57.817 50.000 12.13 0.00 38.24 3.24
768 782 2.969238 GGCGCGACTATGCAGCAT 60.969 61.111 12.10 13.73 36.55 3.79
769 783 1.664649 GGCGCGACTATGCAGCATA 60.665 57.895 12.10 14.59 36.55 3.14
773 787 1.794701 CGCGACTATGCAGCATATGTT 59.205 47.619 15.69 3.48 34.15 2.71
890 917 1.065854 GGTGTGGCTGCAGACTTAGAT 60.066 52.381 22.80 0.00 0.00 1.98
926 953 6.159299 TCCACAATTTCTCTTCAAATGCAA 57.841 33.333 0.00 0.00 0.00 4.08
1159 1187 4.982241 ATTATAGTGCAGTACCAGCCAT 57.018 40.909 2.64 0.00 0.00 4.40
1172 1200 3.099141 ACCAGCCATGTTATTTGGAAGG 58.901 45.455 0.00 0.00 36.26 3.46
1214 1242 6.677781 TGATGAAGTTCTGAAAACGTTTCT 57.322 33.333 15.01 2.78 0.00 2.52
1431 1459 3.065786 CGGAGAATGAACATGTTGGGATG 59.934 47.826 17.58 0.00 0.00 3.51
1552 1593 1.691434 GTGAGGATGGGAGTGAGGATC 59.309 57.143 0.00 0.00 0.00 3.36
1784 1840 5.327737 TGTAGGTTCAGGGGTTGTAAAAT 57.672 39.130 0.00 0.00 0.00 1.82
2003 2061 7.517614 AGAAGGAAAAAGAAGGTGAAGAATC 57.482 36.000 0.00 0.00 0.00 2.52
2078 2136 4.917906 ACTCTAGGAGCAAAGGAATTGT 57.082 40.909 0.00 0.00 41.32 2.71
2325 2383 0.183731 CCTTGCATAGAGGGGTTCCC 59.816 60.000 0.00 0.00 45.90 3.97
2377 2435 1.072806 AGCACATTCTTGACAGGCAGA 59.927 47.619 0.00 0.00 0.00 4.26
2433 2491 9.363401 CATTGATGGCCATAATTGGATATATCT 57.637 33.333 20.84 0.00 46.92 1.98
2485 2544 5.288804 ACAAACGAGAATTGGATTTGGTTG 58.711 37.500 0.00 0.00 35.12 3.77
2489 2548 4.766891 ACGAGAATTGGATTTGGTTGATGT 59.233 37.500 0.00 0.00 0.00 3.06
2501 2560 8.416329 GGATTTGGTTGATGTAATTGCTAAGAT 58.584 33.333 0.00 0.00 0.00 2.40
2583 2642 2.136026 AGGGGTGAAAGAAGTGTTCCT 58.864 47.619 0.00 0.00 0.00 3.36
2661 2720 1.826720 CCATGGGAAGGTGTTTGATGG 59.173 52.381 2.85 0.00 0.00 3.51
2813 2872 7.497249 GGAGTCAATTCTCAACTATATGCAAGT 59.503 37.037 0.00 0.00 36.30 3.16
2851 2910 3.149196 CAACCTGGCTGAGAGCTTTAAA 58.851 45.455 0.00 0.00 41.99 1.52
2900 2959 5.005740 TGAACTTGGATGACCTCTTTGATG 58.994 41.667 0.00 0.00 37.04 3.07
2902 2961 5.246981 ACTTGGATGACCTCTTTGATGAA 57.753 39.130 0.00 0.00 37.04 2.57
2909 2968 3.196469 TGACCTCTTTGATGAAGCGAGAT 59.804 43.478 0.00 0.00 35.24 2.75
2915 2974 6.293298 CCTCTTTGATGAAGCGAGATAATTGG 60.293 42.308 0.00 0.00 35.24 3.16
3051 3110 4.262678 GGTAGAAAGCTCAGAAGAAGTGGT 60.263 45.833 0.00 0.00 0.00 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 8.684520 ACGTACTGAAATAGCTAGTTCAACTAT 58.315 33.333 30.02 20.11 39.41 2.12
22 23 7.966753 CACGTACTGAAATAGCTAGTTCAACTA 59.033 37.037 30.02 21.03 39.41 2.24
23 24 6.807230 CACGTACTGAAATAGCTAGTTCAACT 59.193 38.462 30.02 21.85 39.41 3.16
24 25 6.034683 CCACGTACTGAAATAGCTAGTTCAAC 59.965 42.308 30.02 25.12 39.41 3.18
25 26 6.097356 CCACGTACTGAAATAGCTAGTTCAA 58.903 40.000 30.02 18.07 39.41 2.69
26 27 5.184479 ACCACGTACTGAAATAGCTAGTTCA 59.816 40.000 28.96 28.96 37.87 3.18
27 28 5.648572 ACCACGTACTGAAATAGCTAGTTC 58.351 41.667 23.55 23.55 0.00 3.01
28 29 5.656213 ACCACGTACTGAAATAGCTAGTT 57.344 39.130 6.06 6.06 0.00 2.24
29 30 5.408356 CAACCACGTACTGAAATAGCTAGT 58.592 41.667 0.00 0.00 0.00 2.57
30 31 4.804139 CCAACCACGTACTGAAATAGCTAG 59.196 45.833 0.00 0.00 0.00 3.42
31 32 4.751060 CCAACCACGTACTGAAATAGCTA 58.249 43.478 0.00 0.00 0.00 3.32
32 33 3.596214 CCAACCACGTACTGAAATAGCT 58.404 45.455 0.00 0.00 0.00 3.32
33 34 2.095372 GCCAACCACGTACTGAAATAGC 59.905 50.000 0.00 0.00 0.00 2.97
34 35 3.331150 TGCCAACCACGTACTGAAATAG 58.669 45.455 0.00 0.00 0.00 1.73
35 36 3.404224 TGCCAACCACGTACTGAAATA 57.596 42.857 0.00 0.00 0.00 1.40
36 37 2.264005 TGCCAACCACGTACTGAAAT 57.736 45.000 0.00 0.00 0.00 2.17
37 38 2.039818 TTGCCAACCACGTACTGAAA 57.960 45.000 0.00 0.00 0.00 2.69
38 39 2.264005 ATTGCCAACCACGTACTGAA 57.736 45.000 0.00 0.00 0.00 3.02
39 40 3.404224 TTATTGCCAACCACGTACTGA 57.596 42.857 0.00 0.00 0.00 3.41
40 41 4.411327 CAATTATTGCCAACCACGTACTG 58.589 43.478 0.00 0.00 0.00 2.74
41 42 3.442273 CCAATTATTGCCAACCACGTACT 59.558 43.478 0.00 0.00 0.00 2.73
42 43 3.428316 CCCAATTATTGCCAACCACGTAC 60.428 47.826 0.00 0.00 0.00 3.67
43 44 2.755655 CCCAATTATTGCCAACCACGTA 59.244 45.455 0.00 0.00 0.00 3.57
44 45 1.548269 CCCAATTATTGCCAACCACGT 59.452 47.619 0.00 0.00 0.00 4.49
45 46 1.134848 CCCCAATTATTGCCAACCACG 60.135 52.381 0.00 0.00 0.00 4.94
46 47 2.183679 TCCCCAATTATTGCCAACCAC 58.816 47.619 0.00 0.00 0.00 4.16
47 48 2.630889 TCCCCAATTATTGCCAACCA 57.369 45.000 0.00 0.00 0.00 3.67
48 49 3.990959 TTTCCCCAATTATTGCCAACC 57.009 42.857 0.00 0.00 0.00 3.77
49 50 6.832520 AAATTTTCCCCAATTATTGCCAAC 57.167 33.333 0.00 0.00 0.00 3.77
50 51 6.210185 CCAAAATTTTCCCCAATTATTGCCAA 59.790 34.615 0.00 0.00 0.00 4.52
51 52 5.713861 CCAAAATTTTCCCCAATTATTGCCA 59.286 36.000 0.00 0.00 0.00 4.92
52 53 5.714333 ACCAAAATTTTCCCCAATTATTGCC 59.286 36.000 0.00 0.00 0.00 4.52
53 54 6.403092 CGACCAAAATTTTCCCCAATTATTGC 60.403 38.462 0.00 0.00 0.00 3.56
54 55 6.093357 CCGACCAAAATTTTCCCCAATTATTG 59.907 38.462 0.00 0.00 0.00 1.90
55 56 6.176896 CCGACCAAAATTTTCCCCAATTATT 58.823 36.000 0.00 0.00 0.00 1.40
56 57 5.249622 ACCGACCAAAATTTTCCCCAATTAT 59.750 36.000 0.00 0.00 0.00 1.28
57 58 4.593634 ACCGACCAAAATTTTCCCCAATTA 59.406 37.500 0.00 0.00 0.00 1.40
58 59 3.392947 ACCGACCAAAATTTTCCCCAATT 59.607 39.130 0.00 0.00 0.00 2.32
59 60 2.976185 ACCGACCAAAATTTTCCCCAAT 59.024 40.909 0.00 0.00 0.00 3.16
60 61 2.399580 ACCGACCAAAATTTTCCCCAA 58.600 42.857 0.00 0.00 0.00 4.12
61 62 2.089600 ACCGACCAAAATTTTCCCCA 57.910 45.000 0.00 0.00 0.00 4.96
62 63 2.365941 TGAACCGACCAAAATTTTCCCC 59.634 45.455 0.00 0.00 0.00 4.81
63 64 3.649073 CTGAACCGACCAAAATTTTCCC 58.351 45.455 0.00 0.00 0.00 3.97
64 65 3.057019 GCTGAACCGACCAAAATTTTCC 58.943 45.455 0.00 0.00 0.00 3.13
65 66 3.735746 CAGCTGAACCGACCAAAATTTTC 59.264 43.478 8.42 0.00 0.00 2.29
66 67 3.132111 ACAGCTGAACCGACCAAAATTTT 59.868 39.130 23.35 0.00 0.00 1.82
67 68 2.693074 ACAGCTGAACCGACCAAAATTT 59.307 40.909 23.35 0.00 0.00 1.82
68 69 2.293399 GACAGCTGAACCGACCAAAATT 59.707 45.455 23.35 0.00 0.00 1.82
69 70 1.880027 GACAGCTGAACCGACCAAAAT 59.120 47.619 23.35 0.00 0.00 1.82
70 71 1.305201 GACAGCTGAACCGACCAAAA 58.695 50.000 23.35 0.00 0.00 2.44
71 72 0.878523 CGACAGCTGAACCGACCAAA 60.879 55.000 23.35 0.00 0.00 3.28
72 73 1.300620 CGACAGCTGAACCGACCAA 60.301 57.895 23.35 0.00 0.00 3.67
73 74 1.532604 ATCGACAGCTGAACCGACCA 61.533 55.000 23.35 5.59 33.69 4.02
74 75 0.389948 AATCGACAGCTGAACCGACC 60.390 55.000 23.35 0.00 33.69 4.79
75 76 1.126846 CAAATCGACAGCTGAACCGAC 59.873 52.381 23.35 3.47 33.69 4.79
76 77 1.000394 TCAAATCGACAGCTGAACCGA 60.000 47.619 23.35 23.72 35.43 4.69
77 78 1.428448 TCAAATCGACAGCTGAACCG 58.572 50.000 23.35 19.45 0.00 4.44
78 79 2.808543 AGTTCAAATCGACAGCTGAACC 59.191 45.455 23.35 8.06 45.67 3.62
79 80 3.248602 ACAGTTCAAATCGACAGCTGAAC 59.751 43.478 23.35 11.79 45.15 3.18
80 81 3.466836 ACAGTTCAAATCGACAGCTGAA 58.533 40.909 23.35 5.64 0.00 3.02
81 82 3.111853 ACAGTTCAAATCGACAGCTGA 57.888 42.857 23.35 0.00 0.00 4.26
82 83 3.885484 AACAGTTCAAATCGACAGCTG 57.115 42.857 13.48 13.48 0.00 4.24
83 84 3.627577 ACAAACAGTTCAAATCGACAGCT 59.372 39.130 0.00 0.00 0.00 4.24
84 85 3.952535 ACAAACAGTTCAAATCGACAGC 58.047 40.909 0.00 0.00 0.00 4.40
85 86 9.825972 ATTTATACAAACAGTTCAAATCGACAG 57.174 29.630 0.00 0.00 0.00 3.51
98 99 9.262472 GCAGTCGTTCTTAATTTATACAAACAG 57.738 33.333 0.00 0.00 0.00 3.16
99 100 8.995220 AGCAGTCGTTCTTAATTTATACAAACA 58.005 29.630 0.00 0.00 0.00 2.83
100 101 9.821662 AAGCAGTCGTTCTTAATTTATACAAAC 57.178 29.630 0.00 0.00 0.00 2.93
109 110 9.817809 TCATAGATTAAGCAGTCGTTCTTAATT 57.182 29.630 8.17 0.00 42.35 1.40
110 111 9.817809 TTCATAGATTAAGCAGTCGTTCTTAAT 57.182 29.630 6.87 6.87 43.94 1.40
111 112 9.817809 ATTCATAGATTAAGCAGTCGTTCTTAA 57.182 29.630 0.00 0.00 38.61 1.85
112 113 9.249457 CATTCATAGATTAAGCAGTCGTTCTTA 57.751 33.333 0.00 0.00 0.00 2.10
113 114 7.981789 TCATTCATAGATTAAGCAGTCGTTCTT 59.018 33.333 0.00 0.00 0.00 2.52
114 115 7.492524 TCATTCATAGATTAAGCAGTCGTTCT 58.507 34.615 0.00 0.00 0.00 3.01
115 116 7.700322 TCATTCATAGATTAAGCAGTCGTTC 57.300 36.000 0.00 0.00 0.00 3.95
116 117 8.492673 TTTCATTCATAGATTAAGCAGTCGTT 57.507 30.769 0.00 0.00 0.00 3.85
117 118 8.668510 ATTTCATTCATAGATTAAGCAGTCGT 57.331 30.769 0.00 0.00 0.00 4.34
118 119 8.986847 AGATTTCATTCATAGATTAAGCAGTCG 58.013 33.333 0.00 0.00 0.00 4.18
164 165 9.667107 ACTAGCAGTATCTAATTTTTGCAACTA 57.333 29.630 0.00 0.00 34.17 2.24
165 166 8.454106 CACTAGCAGTATCTAATTTTTGCAACT 58.546 33.333 0.00 0.00 34.17 3.16
166 167 8.450964 TCACTAGCAGTATCTAATTTTTGCAAC 58.549 33.333 0.00 0.00 34.17 4.17
167 168 8.560355 TCACTAGCAGTATCTAATTTTTGCAA 57.440 30.769 0.00 0.00 34.17 4.08
168 169 8.737168 ATCACTAGCAGTATCTAATTTTTGCA 57.263 30.769 0.00 0.00 34.17 4.08
177 178 9.751542 GAAGCTAAAAATCACTAGCAGTATCTA 57.248 33.333 4.10 0.00 42.51 1.98
178 179 8.260818 TGAAGCTAAAAATCACTAGCAGTATCT 58.739 33.333 4.10 0.00 42.51 1.98
179 180 8.425577 TGAAGCTAAAAATCACTAGCAGTATC 57.574 34.615 4.10 0.00 42.51 2.24
180 181 8.970859 ATGAAGCTAAAAATCACTAGCAGTAT 57.029 30.769 4.10 0.00 42.51 2.12
182 183 8.970859 ATATGAAGCTAAAAATCACTAGCAGT 57.029 30.769 4.10 0.00 42.51 4.40
194 195 8.859156 GCGATTTGTCAAAATATGAAGCTAAAA 58.141 29.630 1.31 0.00 40.50 1.52
195 196 8.026026 TGCGATTTGTCAAAATATGAAGCTAAA 58.974 29.630 1.31 0.00 40.50 1.85
196 197 7.534282 TGCGATTTGTCAAAATATGAAGCTAA 58.466 30.769 1.31 0.00 40.50 3.09
197 198 7.082700 TGCGATTTGTCAAAATATGAAGCTA 57.917 32.000 1.31 0.00 40.50 3.32
198 199 5.953183 TGCGATTTGTCAAAATATGAAGCT 58.047 33.333 1.31 0.00 40.50 3.74
199 200 5.801947 ACTGCGATTTGTCAAAATATGAAGC 59.198 36.000 1.31 1.98 40.50 3.86
200 201 6.803320 ACACTGCGATTTGTCAAAATATGAAG 59.197 34.615 1.31 0.00 40.50 3.02
201 202 6.676950 ACACTGCGATTTGTCAAAATATGAA 58.323 32.000 1.31 0.00 40.50 2.57
202 203 6.252967 ACACTGCGATTTGTCAAAATATGA 57.747 33.333 1.31 0.00 36.10 2.15
203 204 6.932901 AACACTGCGATTTGTCAAAATATG 57.067 33.333 1.31 0.00 36.10 1.78
204 205 7.589395 TGTAACACTGCGATTTGTCAAAATAT 58.411 30.769 1.31 0.00 36.10 1.28
205 206 6.960468 TGTAACACTGCGATTTGTCAAAATA 58.040 32.000 1.31 0.00 36.10 1.40
206 207 5.826586 TGTAACACTGCGATTTGTCAAAAT 58.173 33.333 1.31 0.00 38.74 1.82
207 208 5.236655 TGTAACACTGCGATTTGTCAAAA 57.763 34.783 1.31 0.00 0.00 2.44
208 209 4.260990 CCTGTAACACTGCGATTTGTCAAA 60.261 41.667 0.00 0.00 0.00 2.69
209 210 3.249799 CCTGTAACACTGCGATTTGTCAA 59.750 43.478 0.00 0.00 0.00 3.18
210 211 2.805671 CCTGTAACACTGCGATTTGTCA 59.194 45.455 0.00 0.00 0.00 3.58
211 212 2.159627 CCCTGTAACACTGCGATTTGTC 59.840 50.000 0.00 0.00 0.00 3.18
212 213 2.151202 CCCTGTAACACTGCGATTTGT 58.849 47.619 0.00 0.00 0.00 2.83
213 214 2.159627 GTCCCTGTAACACTGCGATTTG 59.840 50.000 0.00 0.00 0.00 2.32
214 215 2.038557 AGTCCCTGTAACACTGCGATTT 59.961 45.455 0.00 0.00 0.00 2.17
215 216 1.623811 AGTCCCTGTAACACTGCGATT 59.376 47.619 0.00 0.00 0.00 3.34
216 217 1.066858 CAGTCCCTGTAACACTGCGAT 60.067 52.381 0.00 0.00 31.62 4.58
217 218 0.317160 CAGTCCCTGTAACACTGCGA 59.683 55.000 0.00 0.00 31.62 5.10
218 219 0.317160 TCAGTCCCTGTAACACTGCG 59.683 55.000 0.00 0.00 37.95 5.18
219 220 1.070134 TGTCAGTCCCTGTAACACTGC 59.930 52.381 0.00 0.00 37.95 4.40
220 221 3.469008 TTGTCAGTCCCTGTAACACTG 57.531 47.619 0.00 0.00 39.18 3.66
221 222 4.348168 AGATTTGTCAGTCCCTGTAACACT 59.652 41.667 0.00 0.00 32.61 3.55
222 223 4.642429 AGATTTGTCAGTCCCTGTAACAC 58.358 43.478 0.00 0.00 32.61 3.32
223 224 4.974645 AGATTTGTCAGTCCCTGTAACA 57.025 40.909 0.00 0.00 32.61 2.41
224 225 5.642491 GGTAAGATTTGTCAGTCCCTGTAAC 59.358 44.000 0.00 0.00 32.61 2.50
225 226 5.308497 TGGTAAGATTTGTCAGTCCCTGTAA 59.692 40.000 0.00 0.00 32.61 2.41
226 227 4.841813 TGGTAAGATTTGTCAGTCCCTGTA 59.158 41.667 0.00 0.00 32.61 2.74
227 228 3.650942 TGGTAAGATTTGTCAGTCCCTGT 59.349 43.478 0.00 0.00 32.61 4.00
228 229 4.286297 TGGTAAGATTTGTCAGTCCCTG 57.714 45.455 0.00 0.00 0.00 4.45
229 230 4.993705 TTGGTAAGATTTGTCAGTCCCT 57.006 40.909 0.00 0.00 0.00 4.20
230 231 6.015434 ACAATTTGGTAAGATTTGTCAGTCCC 60.015 38.462 0.78 0.00 0.00 4.46
231 232 6.981722 ACAATTTGGTAAGATTTGTCAGTCC 58.018 36.000 0.78 0.00 0.00 3.85
232 233 8.755018 CAAACAATTTGGTAAGATTTGTCAGTC 58.245 33.333 0.78 0.00 37.01 3.51
233 234 8.647143 CAAACAATTTGGTAAGATTTGTCAGT 57.353 30.769 0.78 0.00 37.01 3.41
252 253 9.528018 GTCAAATAAGAAATTCTCACCAAACAA 57.472 29.630 0.00 0.00 0.00 2.83
253 254 8.690884 TGTCAAATAAGAAATTCTCACCAAACA 58.309 29.630 0.00 0.00 0.00 2.83
254 255 8.968242 GTGTCAAATAAGAAATTCTCACCAAAC 58.032 33.333 0.00 0.00 0.00 2.93
255 256 8.912988 AGTGTCAAATAAGAAATTCTCACCAAA 58.087 29.630 0.00 0.00 0.00 3.28
256 257 8.463930 AGTGTCAAATAAGAAATTCTCACCAA 57.536 30.769 0.00 0.00 0.00 3.67
260 261 9.793259 AAGGTAGTGTCAAATAAGAAATTCTCA 57.207 29.630 0.00 0.00 0.00 3.27
357 359 1.274596 GACGGCGATGTCACGTAATT 58.725 50.000 16.62 0.00 41.40 1.40
358 360 0.526954 GGACGGCGATGTCACGTAAT 60.527 55.000 16.62 0.00 41.40 1.89
454 456 2.413837 GCTAGCGACTCTGGTCAAAAA 58.586 47.619 0.00 0.00 42.21 1.94
563 568 2.486504 CGCCACCGTACGAGCTAA 59.513 61.111 18.76 0.00 0.00 3.09
832 847 4.028490 CGCCCACCCTTGTAGCCA 62.028 66.667 0.00 0.00 0.00 4.75
837 864 3.256960 ATCCACGCCCACCCTTGT 61.257 61.111 0.00 0.00 0.00 3.16
890 917 1.217916 TTGTGGAAGGAACTCACCCA 58.782 50.000 0.00 0.00 38.49 4.51
926 953 3.413105 ACCTGCTCCTCCTTCTAATCT 57.587 47.619 0.00 0.00 0.00 2.40
1159 1187 1.610363 TGCGCACCTTCCAAATAACA 58.390 45.000 5.66 0.00 0.00 2.41
1172 1200 3.186909 TCATAGTAGTGAACATGCGCAC 58.813 45.455 14.90 0.00 35.30 5.34
1260 1288 4.569943 TCTGCACCATCTTTGACTTAGAC 58.430 43.478 0.00 0.00 0.00 2.59
1342 1370 6.186957 TGTTCTTAGGTTGGATATGCACATT 58.813 36.000 0.00 0.00 0.00 2.71
1431 1459 9.784531 TCCTTCAAATACATATTCTCTTCATCC 57.215 33.333 0.00 0.00 0.00 3.51
1552 1593 2.293122 CCTCGCTCTCATCCTTACTCTG 59.707 54.545 0.00 0.00 0.00 3.35
1743 1796 2.299013 ACATGGTGCACTCTTCTTCGTA 59.701 45.455 17.98 0.00 0.00 3.43
1747 1800 3.340814 CCTACATGGTGCACTCTTCTT 57.659 47.619 17.98 0.00 0.00 2.52
1784 1840 8.937835 TCCATGGACAATTATCTTCATCTCTTA 58.062 33.333 11.44 0.00 0.00 2.10
2003 2061 7.348080 TCTCACATATCCAGTACTTAGTTGG 57.652 40.000 0.00 0.00 0.00 3.77
2078 2136 5.650266 TGTGGTGTTCTTTAAGCTTCTTTCA 59.350 36.000 0.00 0.00 0.00 2.69
2377 2435 1.574526 TAGCCAGCTGCCCCTTGAAT 61.575 55.000 8.66 0.00 42.71 2.57
2428 2486 8.383175 TCAAAGACTCCAAAACTAACCAGATAT 58.617 33.333 0.00 0.00 0.00 1.63
2433 2491 7.013274 CAGAATCAAAGACTCCAAAACTAACCA 59.987 37.037 0.00 0.00 0.00 3.67
2485 2544 7.497249 CCTATGGCCTATCTTAGCAATTACATC 59.503 40.741 3.32 0.00 0.00 3.06
2489 2548 7.402941 TGATCCTATGGCCTATCTTAGCAATTA 59.597 37.037 3.32 0.00 0.00 1.40
2501 2560 3.074390 CCATTTGGTGATCCTATGGCCTA 59.926 47.826 3.32 0.00 38.62 3.93
2561 2620 1.609072 GAACACTTCTTTCACCCCTGC 59.391 52.381 0.00 0.00 0.00 4.85
2583 2642 2.464796 TTCCCTATGTTCCGCCTCTA 57.535 50.000 0.00 0.00 0.00 2.43
2720 2779 4.467795 AGCTAGCTTTGTTGTCTCCATAGA 59.532 41.667 12.68 0.00 0.00 1.98
2813 2872 6.469410 CCAGGTTGTTGGTTACATAGTCTAA 58.531 40.000 0.00 0.00 36.44 2.10
2851 2910 5.279456 GGACTTGTGGTGCTTAATCCAATTT 60.279 40.000 0.00 0.00 35.38 1.82
2900 2959 9.979270 CAATATCATAACCAATTATCTCGCTTC 57.021 33.333 0.00 0.00 0.00 3.86
2902 2961 8.939929 CACAATATCATAACCAATTATCTCGCT 58.060 33.333 0.00 0.00 0.00 4.93
2909 2968 7.993758 TCGGTTCCACAATATCATAACCAATTA 59.006 33.333 0.00 0.00 36.92 1.40
2915 2974 6.053005 TCCTTCGGTTCCACAATATCATAAC 58.947 40.000 0.00 0.00 0.00 1.89
3051 3110 4.980573 ACCACCTAATGCAGTTACTTCAA 58.019 39.130 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.