Multiple sequence alignment - TraesCS7A01G462100

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 TraesCS7A01G462100 chr7A 100.000 3398 0 0 1 3398 658706917 658703520 0.000000e+00 6276
1 TraesCS7A01G462100 chr7A 97.343 3237 67 4 176 3398 576403313 576406544 0.000000e+00 5483
2 TraesCS7A01G462100 chr7A 97.143 175 5 0 1 175 727192390 727192564 2.560000e-76 296
3 TraesCS7A01G462100 chr4A 97.015 2714 62 5 697 3395 628881991 628884700 0.000000e+00 4545
4 TraesCS7A01G462100 chr4A 94.769 325 13 3 697 1017 628889866 628889542 1.410000e-138 503
5 TraesCS7A01G462100 chr4A 91.608 143 12 0 470 612 715634096 715633954 7.440000e-47 198
6 TraesCS7A01G462100 chr4A 94.286 70 4 0 612 681 715621692 715621623 1.290000e-19 108
7 TraesCS7A01G462100 chr5A 96.394 2718 74 7 696 3398 697625372 697628080 0.000000e+00 4455
8 TraesCS7A01G462100 chr5A 90.255 2155 114 45 697 2795 78443874 78441760 0.000000e+00 2728
9 TraesCS7A01G462100 chr5A 93.846 325 16 3 697 1017 697642232 697641908 1.420000e-133 486
10 TraesCS7A01G462100 chr2A 96.356 2717 63 8 697 3398 752883172 752880477 0.000000e+00 4436
11 TraesCS7A01G462100 chr2A 95.385 1972 85 5 695 2664 739802159 739804126 0.000000e+00 3133
12 TraesCS7A01G462100 chr2A 96.089 179 7 0 1 179 626282691 626282513 3.320000e-75 292
13 TraesCS7A01G462100 chr2A 94.652 187 9 1 1 186 766800557 766800371 4.290000e-74 289
14 TraesCS7A01G462100 chr2A 93.651 189 12 0 1 189 131532838 131533026 2.000000e-72 283
15 TraesCS7A01G462100 chr2A 93.651 189 12 0 1 189 131553362 131553550 2.000000e-72 283
16 TraesCS7A01G462100 chr1A 96.283 2717 65 12 697 3398 13813934 13811239 0.000000e+00 4425
17 TraesCS7A01G462100 chr1A 96.102 2719 67 11 697 3398 34337446 34340142 0.000000e+00 4397
18 TraesCS7A01G462100 chr1A 95.668 2724 81 13 691 3398 566074881 566072179 0.000000e+00 4342
19 TraesCS7A01G462100 chr1A 95.082 183 8 1 1 183 274537724 274537543 1.540000e-73 287
20 TraesCS7A01G462100 chr6A 95.376 2725 77 12 697 3398 71102124 71099426 0.000000e+00 4289
21 TraesCS7A01G462100 chr6A 95.580 181 7 1 1 181 35885117 35884938 4.290000e-74 289
22 TraesCS7A01G462100 chr5D 94.950 2713 76 10 697 3398 356119496 356116834 0.000000e+00 4194
23 TraesCS7A01G462100 chr5D 94.118 2737 94 26 696 3398 52374528 52371825 0.000000e+00 4100
24 TraesCS7A01G462100 chr7D 94.652 2730 77 10 697 3398 538836051 538838739 0.000000e+00 4169
25 TraesCS7A01G462100 chr7D 92.985 2737 82 33 696 3398 426837237 426834577 0.000000e+00 3890
26 TraesCS7A01G462100 chr7D 96.179 602 23 0 2797 3398 445243613 445244214 0.000000e+00 985
27 TraesCS7A01G462100 chr7D 93.233 399 22 2 303 696 569232265 569231867 1.760000e-162 582
28 TraesCS7A01G462100 chr7D 92.473 93 7 0 219 311 569233556 569233464 2.130000e-27 134
29 TraesCS7A01G462100 chr4D 94.453 2740 72 10 696 3398 392724847 392722151 0.000000e+00 4145
30 TraesCS7A01G462100 chr4D 86.413 1288 111 31 697 1938 428621339 428622608 0.000000e+00 1351
31 TraesCS7A01G462100 chr4D 78.414 454 73 17 985 1427 108842555 108842994 4.320000e-69 272
32 TraesCS7A01G462100 chr3D 95.080 2134 53 10 696 2795 52842441 52844556 0.000000e+00 3312
33 TraesCS7A01G462100 chr2B 92.822 1226 68 4 1585 2792 629732798 629731575 0.000000e+00 1759
34 TraesCS7A01G462100 chr1B 96.571 175 6 0 1 175 322054496 322054670 1.190000e-74 291
35 TraesCS7A01G462100 chr3A 94.624 186 8 2 1 185 566863057 566862873 1.540000e-73 287


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 TraesCS7A01G462100 chr7A 658703520 658706917 3397 True 6276 6276 100.000 1 3398 1 chr7A.!!$R1 3397
1 TraesCS7A01G462100 chr7A 576403313 576406544 3231 False 5483 5483 97.343 176 3398 1 chr7A.!!$F1 3222
2 TraesCS7A01G462100 chr4A 628881991 628884700 2709 False 4545 4545 97.015 697 3395 1 chr4A.!!$F1 2698
3 TraesCS7A01G462100 chr5A 697625372 697628080 2708 False 4455 4455 96.394 696 3398 1 chr5A.!!$F1 2702
4 TraesCS7A01G462100 chr5A 78441760 78443874 2114 True 2728 2728 90.255 697 2795 1 chr5A.!!$R1 2098
5 TraesCS7A01G462100 chr2A 752880477 752883172 2695 True 4436 4436 96.356 697 3398 1 chr2A.!!$R2 2701
6 TraesCS7A01G462100 chr2A 739802159 739804126 1967 False 3133 3133 95.385 695 2664 1 chr2A.!!$F3 1969
7 TraesCS7A01G462100 chr1A 13811239 13813934 2695 True 4425 4425 96.283 697 3398 1 chr1A.!!$R1 2701
8 TraesCS7A01G462100 chr1A 34337446 34340142 2696 False 4397 4397 96.102 697 3398 1 chr1A.!!$F1 2701
9 TraesCS7A01G462100 chr1A 566072179 566074881 2702 True 4342 4342 95.668 691 3398 1 chr1A.!!$R3 2707
10 TraesCS7A01G462100 chr6A 71099426 71102124 2698 True 4289 4289 95.376 697 3398 1 chr6A.!!$R2 2701
11 TraesCS7A01G462100 chr5D 356116834 356119496 2662 True 4194 4194 94.950 697 3398 1 chr5D.!!$R2 2701
12 TraesCS7A01G462100 chr5D 52371825 52374528 2703 True 4100 4100 94.118 696 3398 1 chr5D.!!$R1 2702
13 TraesCS7A01G462100 chr7D 538836051 538838739 2688 False 4169 4169 94.652 697 3398 1 chr7D.!!$F2 2701
14 TraesCS7A01G462100 chr7D 426834577 426837237 2660 True 3890 3890 92.985 696 3398 1 chr7D.!!$R1 2702
15 TraesCS7A01G462100 chr7D 445243613 445244214 601 False 985 985 96.179 2797 3398 1 chr7D.!!$F1 601
16 TraesCS7A01G462100 chr7D 569231867 569233556 1689 True 358 582 92.853 219 696 2 chr7D.!!$R2 477
17 TraesCS7A01G462100 chr4D 392722151 392724847 2696 True 4145 4145 94.453 696 3398 1 chr4D.!!$R1 2702
18 TraesCS7A01G462100 chr4D 428621339 428622608 1269 False 1351 1351 86.413 697 1938 1 chr4D.!!$F2 1241
19 TraesCS7A01G462100 chr3D 52842441 52844556 2115 False 3312 3312 95.080 696 2795 1 chr3D.!!$F1 2099
20 TraesCS7A01G462100 chr2B 629731575 629732798 1223 True 1759 1759 92.822 1585 2792 1 chr2B.!!$R1 1207


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
125 126 0.042581 TGATCTGTGGGGCCAGTCTA 59.957 55.000 4.39 0.00 34.02 2.59 F
149 150 0.109412 CCGACAGGAGTAACGACCAC 60.109 60.000 0.00 0.00 41.02 4.16 F
153 154 0.389948 CAGGAGTAACGACCACTGGC 60.390 60.000 0.00 0.00 0.00 4.85 F
598 599 0.539986 GGGGTCGAGTTGGATGCTAA 59.460 55.000 0.00 0.00 0.00 3.09 F
638 639 1.756538 CAATTTGAGTATGGGGGCCAC 59.243 52.381 4.39 0.17 35.80 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1305 2268 1.541588 GATTCAACCACAAGCCCACTC 59.458 52.381 0.0 0.0 0.00 3.51 R
1577 2661 6.183347 AGATGTTCCCTAAATTCAGTTCCTG 58.817 40.000 0.0 0.0 0.00 3.86 R
2194 3313 6.054295 CAGCCTTCAGTAGCTTAGAAATGAT 58.946 40.000 0.0 0.0 37.18 2.45 R
2203 3322 1.352083 TGACCAGCCTTCAGTAGCTT 58.648 50.000 0.0 0.0 37.18 3.74 R
3034 4356 4.438797 GCTACATCAAATGCAAACATAGCG 59.561 41.667 0.0 0.0 34.62 4.26 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
22 23 4.351874 AGTTAAGTGTGCTTAGCTTGGA 57.648 40.909 5.60 0.00 43.24 3.53
23 24 4.319177 AGTTAAGTGTGCTTAGCTTGGAG 58.681 43.478 5.60 0.00 43.24 3.86
24 25 2.938956 AAGTGTGCTTAGCTTGGAGT 57.061 45.000 5.60 0.00 32.27 3.85
25 26 5.011738 AGTTAAGTGTGCTTAGCTTGGAGTA 59.988 40.000 5.60 0.00 43.24 2.59
26 27 3.601443 AGTGTGCTTAGCTTGGAGTAG 57.399 47.619 5.60 0.00 0.00 2.57
27 28 2.900546 AGTGTGCTTAGCTTGGAGTAGT 59.099 45.455 5.60 0.00 0.00 2.73
28 29 2.996621 GTGTGCTTAGCTTGGAGTAGTG 59.003 50.000 5.60 0.00 0.00 2.74
29 30 2.632996 TGTGCTTAGCTTGGAGTAGTGT 59.367 45.455 5.60 0.00 0.00 3.55
30 31 3.254892 GTGCTTAGCTTGGAGTAGTGTC 58.745 50.000 5.60 0.00 0.00 3.67
31 32 2.897326 TGCTTAGCTTGGAGTAGTGTCA 59.103 45.455 5.60 0.00 0.00 3.58
32 33 3.056536 TGCTTAGCTTGGAGTAGTGTCAG 60.057 47.826 5.60 0.00 0.00 3.51
33 34 3.677424 GCTTAGCTTGGAGTAGTGTCAGG 60.677 52.174 0.00 0.00 0.00 3.86
34 35 2.310779 AGCTTGGAGTAGTGTCAGGA 57.689 50.000 0.00 0.00 0.00 3.86
35 36 2.826488 AGCTTGGAGTAGTGTCAGGAT 58.174 47.619 0.00 0.00 0.00 3.24
36 37 2.499289 AGCTTGGAGTAGTGTCAGGATG 59.501 50.000 0.00 0.00 37.54 3.51
37 38 2.419297 GCTTGGAGTAGTGTCAGGATGG 60.419 54.545 0.00 0.00 36.16 3.51
38 39 1.866015 TGGAGTAGTGTCAGGATGGG 58.134 55.000 0.00 0.00 36.16 4.00
39 40 1.078823 TGGAGTAGTGTCAGGATGGGT 59.921 52.381 0.00 0.00 36.16 4.51
40 41 1.482593 GGAGTAGTGTCAGGATGGGTG 59.517 57.143 0.00 0.00 36.16 4.61
41 42 2.457598 GAGTAGTGTCAGGATGGGTGA 58.542 52.381 0.00 0.00 36.16 4.02
42 43 2.166664 GAGTAGTGTCAGGATGGGTGAC 59.833 54.545 0.00 0.00 43.97 3.67
55 56 4.324991 GTGACCGGCCGGGAAGTT 62.325 66.667 44.99 26.86 39.97 2.66
56 57 4.323477 TGACCGGCCGGGAAGTTG 62.323 66.667 44.99 21.06 39.97 3.16
65 66 3.647771 GGGAAGTTGCTCCCGGGT 61.648 66.667 22.86 0.00 45.81 5.28
66 67 2.359975 GGAAGTTGCTCCCGGGTG 60.360 66.667 22.86 20.53 0.00 4.61
67 68 3.056328 GAAGTTGCTCCCGGGTGC 61.056 66.667 35.31 35.31 35.46 5.01
80 81 4.357947 GGTGCGCACGAGTGAGGA 62.358 66.667 32.35 1.86 0.00 3.71
81 82 3.106407 GTGCGCACGAGTGAGGAC 61.106 66.667 26.77 14.42 43.08 3.85
82 83 4.700365 TGCGCACGAGTGAGGACG 62.700 66.667 5.66 2.25 0.00 4.79
83 84 4.400109 GCGCACGAGTGAGGACGA 62.400 66.667 0.30 0.00 0.00 4.20
84 85 2.254350 CGCACGAGTGAGGACGAA 59.746 61.111 7.50 0.00 0.00 3.85
85 86 1.797933 CGCACGAGTGAGGACGAAG 60.798 63.158 7.50 0.00 0.00 3.79
98 99 2.986311 ACGAAGTGCGCAGAAAAGA 58.014 47.368 12.22 0.00 46.04 2.52
99 100 0.582005 ACGAAGTGCGCAGAAAAGAC 59.418 50.000 12.22 0.00 46.04 3.01
100 101 0.861837 CGAAGTGCGCAGAAAAGACT 59.138 50.000 12.22 0.00 0.00 3.24
101 102 2.058798 CGAAGTGCGCAGAAAAGACTA 58.941 47.619 12.22 0.00 0.00 2.59
102 103 2.091277 CGAAGTGCGCAGAAAAGACTAG 59.909 50.000 12.22 0.00 0.00 2.57
103 104 2.821991 AGTGCGCAGAAAAGACTAGT 57.178 45.000 12.22 0.00 0.00 2.57
104 105 3.936372 AGTGCGCAGAAAAGACTAGTA 57.064 42.857 12.22 0.00 0.00 1.82
105 106 4.457834 AGTGCGCAGAAAAGACTAGTAT 57.542 40.909 12.22 0.00 0.00 2.12
106 107 4.822026 AGTGCGCAGAAAAGACTAGTATT 58.178 39.130 12.22 0.00 0.00 1.89
107 108 4.627467 AGTGCGCAGAAAAGACTAGTATTG 59.373 41.667 12.22 0.00 0.00 1.90
108 109 4.625742 GTGCGCAGAAAAGACTAGTATTGA 59.374 41.667 12.22 0.00 0.00 2.57
109 110 5.292101 GTGCGCAGAAAAGACTAGTATTGAT 59.708 40.000 12.22 0.00 0.00 2.57
110 111 5.520288 TGCGCAGAAAAGACTAGTATTGATC 59.480 40.000 5.66 5.93 0.00 2.92
111 112 5.751028 GCGCAGAAAAGACTAGTATTGATCT 59.249 40.000 0.30 8.07 0.00 2.75
112 113 6.292061 GCGCAGAAAAGACTAGTATTGATCTG 60.292 42.308 26.54 26.54 34.47 2.90
113 114 6.754209 CGCAGAAAAGACTAGTATTGATCTGT 59.246 38.462 28.67 6.17 34.16 3.41
114 115 7.253917 CGCAGAAAAGACTAGTATTGATCTGTG 60.254 40.741 28.67 28.07 35.17 3.66
115 116 7.010923 GCAGAAAAGACTAGTATTGATCTGTGG 59.989 40.741 28.67 15.98 34.16 4.17
116 117 7.493971 CAGAAAAGACTAGTATTGATCTGTGGG 59.506 40.741 24.47 10.26 30.53 4.61
117 118 5.878406 AAGACTAGTATTGATCTGTGGGG 57.122 43.478 1.03 0.00 0.00 4.96
118 119 3.643792 AGACTAGTATTGATCTGTGGGGC 59.356 47.826 0.00 0.00 0.00 5.80
119 120 2.706190 ACTAGTATTGATCTGTGGGGCC 59.294 50.000 0.00 0.00 0.00 5.80
120 121 1.595311 AGTATTGATCTGTGGGGCCA 58.405 50.000 4.39 0.00 0.00 5.36
121 122 1.492176 AGTATTGATCTGTGGGGCCAG 59.508 52.381 4.39 0.00 0.00 4.85
122 123 1.212935 GTATTGATCTGTGGGGCCAGT 59.787 52.381 4.39 0.00 34.02 4.00
123 124 0.257039 ATTGATCTGTGGGGCCAGTC 59.743 55.000 4.39 0.00 34.02 3.51
124 125 0.842030 TTGATCTGTGGGGCCAGTCT 60.842 55.000 4.39 0.00 34.02 3.24
125 126 0.042581 TGATCTGTGGGGCCAGTCTA 59.957 55.000 4.39 0.00 34.02 2.59
126 127 0.755686 GATCTGTGGGGCCAGTCTAG 59.244 60.000 4.39 0.00 34.02 2.43
127 128 0.339859 ATCTGTGGGGCCAGTCTAGA 59.660 55.000 4.39 1.35 34.02 2.43
128 129 0.339859 TCTGTGGGGCCAGTCTAGAT 59.660 55.000 4.39 0.00 34.02 1.98
129 130 0.755686 CTGTGGGGCCAGTCTAGATC 59.244 60.000 4.39 0.00 0.00 2.75
130 131 0.691078 TGTGGGGCCAGTCTAGATCC 60.691 60.000 4.39 0.00 0.00 3.36
131 132 1.074471 TGGGGCCAGTCTAGATCCC 60.074 63.158 4.39 11.66 36.25 3.85
132 133 2.210711 GGGGCCAGTCTAGATCCCG 61.211 68.421 4.39 0.00 37.85 5.14
133 134 1.152525 GGGCCAGTCTAGATCCCGA 60.153 63.158 4.39 0.00 0.00 5.14
134 135 1.465200 GGGCCAGTCTAGATCCCGAC 61.465 65.000 4.39 4.30 0.00 4.79
135 136 0.755698 GGCCAGTCTAGATCCCGACA 60.756 60.000 12.79 0.00 32.68 4.35
136 137 0.671251 GCCAGTCTAGATCCCGACAG 59.329 60.000 12.79 6.21 32.68 3.51
137 138 1.323412 CCAGTCTAGATCCCGACAGG 58.677 60.000 12.79 10.58 31.81 4.00
146 147 2.559785 TCCCGACAGGAGTAACGAC 58.440 57.895 0.00 0.00 40.93 4.34
147 148 0.962356 TCCCGACAGGAGTAACGACC 60.962 60.000 0.00 0.00 40.93 4.79
148 149 1.246056 CCCGACAGGAGTAACGACCA 61.246 60.000 0.00 0.00 41.02 4.02
149 150 0.109412 CCGACAGGAGTAACGACCAC 60.109 60.000 0.00 0.00 41.02 4.16
150 151 0.879765 CGACAGGAGTAACGACCACT 59.120 55.000 0.00 0.00 0.00 4.00
151 152 1.401148 CGACAGGAGTAACGACCACTG 60.401 57.143 0.00 0.00 36.43 3.66
152 153 0.966920 ACAGGAGTAACGACCACTGG 59.033 55.000 0.00 0.00 35.30 4.00
153 154 0.389948 CAGGAGTAACGACCACTGGC 60.390 60.000 0.00 0.00 0.00 4.85
154 155 1.445582 GGAGTAACGACCACTGGCG 60.446 63.158 9.51 9.51 0.00 5.69
155 156 1.445582 GAGTAACGACCACTGGCGG 60.446 63.158 13.99 0.00 0.00 6.13
156 157 2.433664 GTAACGACCACTGGCGGG 60.434 66.667 13.99 0.00 0.00 6.13
157 158 2.918802 TAACGACCACTGGCGGGT 60.919 61.111 13.99 0.00 42.61 5.28
158 159 3.229156 TAACGACCACTGGCGGGTG 62.229 63.158 13.99 0.48 39.19 4.61
161 162 4.250305 GACCACTGGCGGGTGTGT 62.250 66.667 0.00 1.76 39.19 3.72
162 163 4.250305 ACCACTGGCGGGTGTGTC 62.250 66.667 0.00 0.00 37.23 3.67
171 172 3.881104 GGGTGTGTCCGGGGTGTT 61.881 66.667 0.00 0.00 37.00 3.32
172 173 2.518709 GGGTGTGTCCGGGGTGTTA 61.519 63.158 0.00 0.00 37.00 2.41
173 174 1.301953 GGTGTGTCCGGGGTGTTAC 60.302 63.158 0.00 0.00 0.00 2.50
174 175 1.446791 GTGTGTCCGGGGTGTTACA 59.553 57.895 0.00 0.00 0.00 2.41
387 388 3.684788 AGGATTGTTTTTCGGTCAGATCG 59.315 43.478 0.00 0.00 0.00 3.69
451 452 1.404583 GCAGGCAGGCGAAATTTCATT 60.405 47.619 17.99 0.04 0.00 2.57
488 489 3.404869 TCAATCTTCTGGAGAGCCCTA 57.595 47.619 0.00 0.00 37.93 3.53
521 522 3.587840 CCTCCAAGGGTCCACCAA 58.412 61.111 0.00 0.00 43.89 3.67
556 557 1.867233 CGCACATAACAGCCATCCTAC 59.133 52.381 0.00 0.00 0.00 3.18
598 599 0.539986 GGGGTCGAGTTGGATGCTAA 59.460 55.000 0.00 0.00 0.00 3.09
616 617 2.624316 AAATGCTTGCTGTGTCATCG 57.376 45.000 0.00 0.00 0.00 3.84
627 628 2.485426 CTGTGTCATCGGCAATTTGAGT 59.515 45.455 0.00 0.00 0.00 3.41
633 634 2.051334 TCGGCAATTTGAGTATGGGG 57.949 50.000 0.00 0.00 0.00 4.96
638 639 1.756538 CAATTTGAGTATGGGGGCCAC 59.243 52.381 4.39 0.17 35.80 5.01
1237 1924 7.097192 TCTTCCATGTAGTTCTTATGTGTGAC 58.903 38.462 0.00 0.00 0.00 3.67
1305 2268 4.253685 ACACGGTGATAGATCCAAGTTTG 58.746 43.478 16.29 0.00 0.00 2.93
1429 2488 4.212716 TGGATGTGCTACTACGGTAAGAT 58.787 43.478 0.00 0.00 0.00 2.40
1513 2572 9.467258 AACATTGATATTCTTGTTGTTTCAGTG 57.533 29.630 0.00 0.00 31.45 3.66
1577 2661 7.331934 TGTTCATGTGTTAGCTAAATCTCTGAC 59.668 37.037 7.99 4.08 0.00 3.51
2194 3313 4.029520 AGAGAAGAAGAAGCTGGAGCATA 58.970 43.478 0.65 0.00 45.16 3.14
2203 3322 6.430962 AGAAGCTGGAGCATATCATTTCTA 57.569 37.500 0.65 0.00 45.16 2.10
2815 4131 8.738199 TTATACAGTTCAACTACTGACGAAAG 57.262 34.615 10.46 0.00 46.72 2.62
3034 4356 0.716108 CGTCGTCTTCATGCACCTTC 59.284 55.000 0.00 0.00 0.00 3.46
3038 4360 1.735700 CGTCTTCATGCACCTTCGCTA 60.736 52.381 0.00 0.00 0.00 4.26
3083 4405 0.613572 TGGAGTGACATAGCGGTGGA 60.614 55.000 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.714632 TCCAAGCTAAGCACACTTAACTT 58.285 39.130 0.00 0.00 42.71 2.66
2 3 4.065789 ACTCCAAGCTAAGCACACTTAAC 58.934 43.478 0.00 0.00 37.91 2.01
4 5 4.527038 ACTACTCCAAGCTAAGCACACTTA 59.473 41.667 0.00 0.00 37.33 2.24
5 6 2.938956 ACTCCAAGCTAAGCACACTT 57.061 45.000 0.00 0.00 40.07 3.16
6 7 2.900546 ACTACTCCAAGCTAAGCACACT 59.099 45.455 0.00 0.00 0.00 3.55
7 8 2.996621 CACTACTCCAAGCTAAGCACAC 59.003 50.000 0.00 0.00 0.00 3.82
8 9 2.632996 ACACTACTCCAAGCTAAGCACA 59.367 45.455 0.00 0.00 0.00 4.57
9 10 3.254892 GACACTACTCCAAGCTAAGCAC 58.745 50.000 0.00 0.00 0.00 4.40
10 11 2.897326 TGACACTACTCCAAGCTAAGCA 59.103 45.455 0.00 0.00 0.00 3.91
11 12 3.516615 CTGACACTACTCCAAGCTAAGC 58.483 50.000 0.00 0.00 0.00 3.09
12 13 3.764434 TCCTGACACTACTCCAAGCTAAG 59.236 47.826 0.00 0.00 0.00 2.18
13 14 3.774734 TCCTGACACTACTCCAAGCTAA 58.225 45.455 0.00 0.00 0.00 3.09
14 15 3.451402 TCCTGACACTACTCCAAGCTA 57.549 47.619 0.00 0.00 0.00 3.32
15 16 2.310779 TCCTGACACTACTCCAAGCT 57.689 50.000 0.00 0.00 0.00 3.74
16 17 2.419297 CCATCCTGACACTACTCCAAGC 60.419 54.545 0.00 0.00 0.00 4.01
17 18 2.169352 CCCATCCTGACACTACTCCAAG 59.831 54.545 0.00 0.00 0.00 3.61
18 19 2.187958 CCCATCCTGACACTACTCCAA 58.812 52.381 0.00 0.00 0.00 3.53
19 20 1.078823 ACCCATCCTGACACTACTCCA 59.921 52.381 0.00 0.00 0.00 3.86
20 21 1.482593 CACCCATCCTGACACTACTCC 59.517 57.143 0.00 0.00 0.00 3.85
21 22 2.166664 GTCACCCATCCTGACACTACTC 59.833 54.545 0.00 0.00 38.36 2.59
22 23 2.180276 GTCACCCATCCTGACACTACT 58.820 52.381 0.00 0.00 38.36 2.57
23 24 1.207329 GGTCACCCATCCTGACACTAC 59.793 57.143 1.29 0.00 39.97 2.73
24 25 1.568504 GGTCACCCATCCTGACACTA 58.431 55.000 1.29 0.00 39.97 2.74
25 26 1.544825 CGGTCACCCATCCTGACACT 61.545 60.000 0.00 0.00 39.97 3.55
26 27 1.079127 CGGTCACCCATCCTGACAC 60.079 63.158 0.00 0.00 39.97 3.67
27 28 2.290287 CCGGTCACCCATCCTGACA 61.290 63.158 0.00 0.00 39.97 3.58
28 29 2.584608 CCGGTCACCCATCCTGAC 59.415 66.667 0.00 0.00 37.84 3.51
29 30 3.399181 GCCGGTCACCCATCCTGA 61.399 66.667 1.90 0.00 0.00 3.86
30 31 4.489771 GGCCGGTCACCCATCCTG 62.490 72.222 0.00 0.00 0.00 3.86
38 39 4.324991 AACTTCCCGGCCGGTCAC 62.325 66.667 40.52 0.00 0.00 3.67
39 40 4.323477 CAACTTCCCGGCCGGTCA 62.323 66.667 40.52 25.50 0.00 4.02
49 50 2.359975 CACCCGGGAGCAACTTCC 60.360 66.667 32.02 0.00 36.46 3.46
50 51 3.056328 GCACCCGGGAGCAACTTC 61.056 66.667 34.66 6.62 0.00 3.01
63 64 4.357947 TCCTCACTCGTGCGCACC 62.358 66.667 33.23 16.56 0.00 5.01
64 65 3.106407 GTCCTCACTCGTGCGCAC 61.106 66.667 30.42 30.42 0.00 5.34
65 66 4.700365 CGTCCTCACTCGTGCGCA 62.700 66.667 5.66 5.66 0.00 6.09
66 67 3.891586 TTCGTCCTCACTCGTGCGC 62.892 63.158 0.00 0.00 0.00 6.09
67 68 1.797933 CTTCGTCCTCACTCGTGCG 60.798 63.158 0.00 0.00 0.00 5.34
68 69 1.004277 CACTTCGTCCTCACTCGTGC 61.004 60.000 0.00 0.00 0.00 5.34
69 70 1.004277 GCACTTCGTCCTCACTCGTG 61.004 60.000 0.00 0.00 0.00 4.35
70 71 1.286260 GCACTTCGTCCTCACTCGT 59.714 57.895 0.00 0.00 0.00 4.18
71 72 1.797933 CGCACTTCGTCCTCACTCG 60.798 63.158 0.00 0.00 0.00 4.18
72 73 2.089349 GCGCACTTCGTCCTCACTC 61.089 63.158 0.30 0.00 41.07 3.51
73 74 2.049063 GCGCACTTCGTCCTCACT 60.049 61.111 0.30 0.00 41.07 3.41
74 75 2.355837 TGCGCACTTCGTCCTCAC 60.356 61.111 5.66 0.00 41.07 3.51
75 76 2.049156 CTGCGCACTTCGTCCTCA 60.049 61.111 5.66 0.00 41.07 3.86
76 77 0.944311 TTTCTGCGCACTTCGTCCTC 60.944 55.000 5.66 0.00 41.07 3.71
77 78 0.531974 TTTTCTGCGCACTTCGTCCT 60.532 50.000 5.66 0.00 41.07 3.85
78 79 0.110644 CTTTTCTGCGCACTTCGTCC 60.111 55.000 5.66 0.00 41.07 4.79
79 80 0.859232 TCTTTTCTGCGCACTTCGTC 59.141 50.000 5.66 0.00 41.07 4.20
80 81 0.582005 GTCTTTTCTGCGCACTTCGT 59.418 50.000 5.66 0.00 41.07 3.85
81 82 0.861837 AGTCTTTTCTGCGCACTTCG 59.138 50.000 5.66 0.00 42.12 3.79
82 83 3.060602 ACTAGTCTTTTCTGCGCACTTC 58.939 45.455 5.66 0.00 0.00 3.01
83 84 3.113260 ACTAGTCTTTTCTGCGCACTT 57.887 42.857 5.66 0.00 0.00 3.16
84 85 2.821991 ACTAGTCTTTTCTGCGCACT 57.178 45.000 5.66 2.15 0.00 4.40
85 86 4.625742 TCAATACTAGTCTTTTCTGCGCAC 59.374 41.667 5.66 0.00 0.00 5.34
86 87 4.816392 TCAATACTAGTCTTTTCTGCGCA 58.184 39.130 10.98 10.98 0.00 6.09
87 88 5.751028 AGATCAATACTAGTCTTTTCTGCGC 59.249 40.000 0.00 0.00 0.00 6.09
88 89 6.754209 ACAGATCAATACTAGTCTTTTCTGCG 59.246 38.462 20.08 7.76 33.16 5.18
89 90 7.010923 CCACAGATCAATACTAGTCTTTTCTGC 59.989 40.741 20.08 1.61 33.16 4.26
90 91 7.493971 CCCACAGATCAATACTAGTCTTTTCTG 59.506 40.741 19.27 19.27 35.40 3.02
91 92 7.365117 CCCCACAGATCAATACTAGTCTTTTCT 60.365 40.741 0.00 0.00 0.00 2.52
92 93 6.763610 CCCCACAGATCAATACTAGTCTTTTC 59.236 42.308 0.00 0.00 0.00 2.29
93 94 6.653989 CCCCACAGATCAATACTAGTCTTTT 58.346 40.000 0.00 0.00 0.00 2.27
94 95 5.396884 GCCCCACAGATCAATACTAGTCTTT 60.397 44.000 0.00 0.00 0.00 2.52
95 96 4.101741 GCCCCACAGATCAATACTAGTCTT 59.898 45.833 0.00 0.00 0.00 3.01
96 97 3.643792 GCCCCACAGATCAATACTAGTCT 59.356 47.826 0.00 0.00 0.00 3.24
97 98 3.244249 GGCCCCACAGATCAATACTAGTC 60.244 52.174 0.00 0.00 0.00 2.59
98 99 2.706190 GGCCCCACAGATCAATACTAGT 59.294 50.000 0.00 0.00 0.00 2.57
99 100 2.705658 TGGCCCCACAGATCAATACTAG 59.294 50.000 0.00 0.00 0.00 2.57
100 101 2.705658 CTGGCCCCACAGATCAATACTA 59.294 50.000 0.00 0.00 40.97 1.82
101 102 1.492176 CTGGCCCCACAGATCAATACT 59.508 52.381 0.00 0.00 40.97 2.12
102 103 1.212935 ACTGGCCCCACAGATCAATAC 59.787 52.381 0.00 0.00 40.97 1.89
103 104 1.490490 GACTGGCCCCACAGATCAATA 59.510 52.381 0.00 0.00 40.97 1.90
104 105 0.257039 GACTGGCCCCACAGATCAAT 59.743 55.000 0.00 0.00 40.97 2.57
105 106 0.842030 AGACTGGCCCCACAGATCAA 60.842 55.000 0.00 0.00 40.97 2.57
106 107 0.042581 TAGACTGGCCCCACAGATCA 59.957 55.000 0.00 0.00 40.97 2.92
107 108 0.755686 CTAGACTGGCCCCACAGATC 59.244 60.000 0.00 0.00 40.97 2.75
108 109 0.339859 TCTAGACTGGCCCCACAGAT 59.660 55.000 0.00 0.00 40.97 2.90
109 110 0.339859 ATCTAGACTGGCCCCACAGA 59.660 55.000 0.00 0.00 40.97 3.41
110 111 0.755686 GATCTAGACTGGCCCCACAG 59.244 60.000 0.00 0.00 44.03 3.66
111 112 0.691078 GGATCTAGACTGGCCCCACA 60.691 60.000 0.00 0.00 0.00 4.17
112 113 1.411651 GGGATCTAGACTGGCCCCAC 61.412 65.000 0.00 0.00 34.10 4.61
113 114 1.074471 GGGATCTAGACTGGCCCCA 60.074 63.158 0.00 0.00 34.10 4.96
114 115 2.210711 CGGGATCTAGACTGGCCCC 61.211 68.421 0.00 9.76 35.30 5.80
115 116 1.152525 TCGGGATCTAGACTGGCCC 60.153 63.158 0.00 3.13 35.40 5.80
116 117 0.755698 TGTCGGGATCTAGACTGGCC 60.756 60.000 17.40 0.00 38.16 5.36
117 118 0.671251 CTGTCGGGATCTAGACTGGC 59.329 60.000 17.40 0.00 38.16 4.85
118 119 1.323412 CCTGTCGGGATCTAGACTGG 58.677 60.000 22.00 22.00 45.39 4.00
119 120 2.226330 CTCCTGTCGGGATCTAGACTG 58.774 57.143 17.40 16.40 44.15 3.51
120 121 1.847737 ACTCCTGTCGGGATCTAGACT 59.152 52.381 17.40 0.00 44.15 3.24
121 122 2.351706 ACTCCTGTCGGGATCTAGAC 57.648 55.000 0.00 12.16 44.15 2.59
122 123 3.743584 CGTTACTCCTGTCGGGATCTAGA 60.744 52.174 0.00 0.00 44.15 2.43
123 124 2.548904 CGTTACTCCTGTCGGGATCTAG 59.451 54.545 0.00 0.00 44.15 2.43
124 125 2.171237 TCGTTACTCCTGTCGGGATCTA 59.829 50.000 0.00 0.00 44.15 1.98
125 126 1.064906 TCGTTACTCCTGTCGGGATCT 60.065 52.381 0.00 0.00 44.15 2.75
126 127 1.065251 GTCGTTACTCCTGTCGGGATC 59.935 57.143 0.00 0.00 44.15 3.36
127 128 1.101331 GTCGTTACTCCTGTCGGGAT 58.899 55.000 0.00 0.00 44.15 3.85
128 129 0.962356 GGTCGTTACTCCTGTCGGGA 60.962 60.000 0.00 0.00 42.77 5.14
129 130 1.246056 TGGTCGTTACTCCTGTCGGG 61.246 60.000 0.00 0.00 0.00 5.14
130 131 0.109412 GTGGTCGTTACTCCTGTCGG 60.109 60.000 0.00 0.00 0.00 4.79
131 132 0.879765 AGTGGTCGTTACTCCTGTCG 59.120 55.000 0.00 0.00 0.00 4.35
132 133 1.067776 CCAGTGGTCGTTACTCCTGTC 60.068 57.143 0.00 0.00 0.00 3.51
133 134 0.966920 CCAGTGGTCGTTACTCCTGT 59.033 55.000 0.00 0.00 0.00 4.00
134 135 0.389948 GCCAGTGGTCGTTACTCCTG 60.390 60.000 11.74 0.00 0.00 3.86
135 136 1.874345 CGCCAGTGGTCGTTACTCCT 61.874 60.000 11.74 0.00 0.00 3.69
136 137 1.445582 CGCCAGTGGTCGTTACTCC 60.446 63.158 11.74 0.00 0.00 3.85
137 138 1.445582 CCGCCAGTGGTCGTTACTC 60.446 63.158 19.84 0.00 0.00 2.59
138 139 2.654877 CCGCCAGTGGTCGTTACT 59.345 61.111 19.84 0.00 0.00 2.24
139 140 2.433664 CCCGCCAGTGGTCGTTAC 60.434 66.667 19.84 0.00 0.00 2.50
140 141 2.918802 ACCCGCCAGTGGTCGTTA 60.919 61.111 19.84 0.00 0.00 3.18
141 142 4.619227 CACCCGCCAGTGGTCGTT 62.619 66.667 19.84 7.92 32.46 3.85
144 145 4.250305 ACACACCCGCCAGTGGTC 62.250 66.667 11.74 2.09 42.28 4.02
145 146 4.250305 GACACACCCGCCAGTGGT 62.250 66.667 11.74 1.28 42.28 4.16
154 155 2.518709 TAACACCCCGGACACACCC 61.519 63.158 0.73 0.00 34.64 4.61
155 156 1.301953 GTAACACCCCGGACACACC 60.302 63.158 0.73 0.00 0.00 4.16
156 157 0.601841 CTGTAACACCCCGGACACAC 60.602 60.000 0.73 0.00 0.00 3.82
157 158 0.759812 TCTGTAACACCCCGGACACA 60.760 55.000 0.73 0.00 0.00 3.72
158 159 0.320160 GTCTGTAACACCCCGGACAC 60.320 60.000 0.73 0.00 37.03 3.67
159 160 0.759812 TGTCTGTAACACCCCGGACA 60.760 55.000 0.73 0.00 42.97 4.02
160 161 2.051941 TGTCTGTAACACCCCGGAC 58.948 57.895 0.73 0.00 37.46 4.79
161 162 4.623308 TGTCTGTAACACCCCGGA 57.377 55.556 0.73 0.00 31.20 5.14
168 169 2.545113 GCGTGAGAAGGTGTCTGTAACA 60.545 50.000 0.00 0.00 36.41 2.41
169 170 2.059541 GCGTGAGAAGGTGTCTGTAAC 58.940 52.381 0.00 0.00 36.41 2.50
170 171 1.335597 CGCGTGAGAAGGTGTCTGTAA 60.336 52.381 0.00 0.00 36.41 2.41
171 172 0.240145 CGCGTGAGAAGGTGTCTGTA 59.760 55.000 0.00 0.00 36.41 2.74
172 173 1.007271 CGCGTGAGAAGGTGTCTGT 60.007 57.895 0.00 0.00 36.41 3.41
173 174 0.730834 CTCGCGTGAGAAGGTGTCTG 60.731 60.000 21.40 0.00 45.57 3.51
174 175 1.173444 ACTCGCGTGAGAAGGTGTCT 61.173 55.000 31.50 4.24 45.57 3.41
387 388 1.137479 TGCACGTACACCCTATAAGCC 59.863 52.381 0.00 0.00 0.00 4.35
451 452 7.784073 AGAAGATTGATCTATCCTCTTGTCTCA 59.216 37.037 12.72 0.00 35.76 3.27
488 489 2.225343 TGGAGGGCACTGAATTTTCCAT 60.225 45.455 0.00 0.00 0.00 3.41
556 557 6.418956 CCAATTCGTACAATATTCCTGAACG 58.581 40.000 0.00 0.00 0.00 3.95
598 599 0.806868 CCGATGACACAGCAAGCATT 59.193 50.000 0.00 0.00 0.00 3.56
616 617 0.752658 GCCCCCATACTCAAATTGCC 59.247 55.000 0.00 0.00 0.00 4.52
627 628 1.089123 AGAAAAAGGTGGCCCCCATA 58.911 50.000 7.14 0.00 35.28 2.74
633 634 2.049156 GCGCAGAAAAAGGTGGCC 60.049 61.111 0.30 0.00 0.00 5.36
638 639 0.665369 CCTTGCAGCGCAGAAAAAGG 60.665 55.000 11.47 12.20 40.61 3.11
1237 1924 4.183865 CCCATATATATCAGCCACACACG 58.816 47.826 0.00 0.00 0.00 4.49
1305 2268 1.541588 GATTCAACCACAAGCCCACTC 59.458 52.381 0.00 0.00 0.00 3.51
1429 2488 8.908903 ACATGAAAACCACTAACAATTAGTTGA 58.091 29.630 4.81 0.00 43.70 3.18
1513 2572 9.997482 TTGTACTTCAATTTTCAGTAAACAGAC 57.003 29.630 0.00 0.00 0.00 3.51
1577 2661 6.183347 AGATGTTCCCTAAATTCAGTTCCTG 58.817 40.000 0.00 0.00 0.00 3.86
2194 3313 6.054295 CAGCCTTCAGTAGCTTAGAAATGAT 58.946 40.000 0.00 0.00 37.18 2.45
2203 3322 1.352083 TGACCAGCCTTCAGTAGCTT 58.648 50.000 0.00 0.00 37.18 3.74
3034 4356 4.438797 GCTACATCAAATGCAAACATAGCG 59.561 41.667 0.00 0.00 34.62 4.26
3038 4360 5.636121 CACAAGCTACATCAAATGCAAACAT 59.364 36.000 0.00 0.00 38.49 2.71
3069 4391 1.218047 GCAGTCCACCGCTATGTCA 59.782 57.895 0.00 0.00 0.00 3.58
3094 4416 4.764771 GATGCTGGGCAGGGGCAA 62.765 66.667 0.00 0.00 43.65 4.52



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

AutoCloner maintained by Alex Coulton.