Multiple sequence alignment - TraesCS2B01G280700

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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 TraesCS2B01G280700 chr2B 100.000 2477 0 0 1 2477 387144527 387147003 0.000000e+00 4575.0
1 TraesCS2B01G280700 chr2B 94.550 844 44 2 669 1510 768546188 768547031 0.000000e+00 1303.0
2 TraesCS2B01G280700 chr2B 91.126 293 26 0 2185 2477 306905217 306904925 4.960000e-107 398.0
3 TraesCS2B01G280700 chr2B 83.516 91 9 6 39 126 488279417 488279504 2.040000e-11 80.5
4 TraesCS2B01G280700 chr7B 98.088 837 16 0 669 1505 663194823 663193987 0.000000e+00 1458.0
5 TraesCS2B01G280700 chr7B 97.947 828 17 0 669 1496 131367633 131368460 0.000000e+00 1435.0
6 TraesCS2B01G280700 chr7B 97.491 837 20 1 669 1505 428933640 428934475 0.000000e+00 1428.0
7 TraesCS2B01G280700 chr7B 97.252 837 22 1 669 1505 45326651 45327486 0.000000e+00 1417.0
8 TraesCS2B01G280700 chr7B 95.579 837 36 1 669 1504 713392412 713393248 0.000000e+00 1339.0
9 TraesCS2B01G280700 chr4B 97.857 840 15 1 669 1505 647595244 647596083 0.000000e+00 1448.0
10 TraesCS2B01G280700 chr5B 95.171 849 29 3 669 1506 184286791 184287638 0.000000e+00 1330.0
11 TraesCS2B01G280700 chr5B 86.047 86 8 4 38 121 585840025 585839942 3.390000e-14 89.8
12 TraesCS2B01G280700 chr2A 93.810 840 52 0 669 1508 728564363 728565202 0.000000e+00 1264.0
13 TraesCS2B01G280700 chr7D 92.319 677 50 2 1505 2179 156121828 156121152 0.000000e+00 961.0
14 TraesCS2B01G280700 chr7D 90.749 681 56 6 1505 2179 17370563 17369884 0.000000e+00 902.0
15 TraesCS2B01G280700 chr7D 90.970 299 27 0 2174 2472 399446480 399446778 1.070000e-108 403.0
16 TraesCS2B01G280700 chr7D 91.186 295 26 0 2183 2477 17369811 17369517 3.840000e-108 401.0
17 TraesCS2B01G280700 chr7D 81.915 94 11 6 46 135 112238108 112238017 9.500000e-10 75.0
18 TraesCS2B01G280700 chr6D 92.330 678 47 5 1505 2179 430012082 430011407 0.000000e+00 959.0
19 TraesCS2B01G280700 chr6D 91.433 677 56 2 1505 2179 156559342 156558666 0.000000e+00 928.0
20 TraesCS2B01G280700 chr6D 92.149 484 34 4 184 665 156559813 156559332 0.000000e+00 680.0
21 TraesCS2B01G280700 chr6D 91.476 481 39 2 185 663 430012554 430012074 0.000000e+00 660.0
22 TraesCS2B01G280700 chr6D 91.864 295 22 1 2183 2477 430011317 430011025 6.380000e-111 411.0
23 TraesCS2B01G280700 chr5A 91.988 674 52 2 1505 2176 1386946 1387619 0.000000e+00 944.0
24 TraesCS2B01G280700 chr5A 89.300 486 51 1 178 662 1386468 1386953 2.110000e-170 608.0
25 TraesCS2B01G280700 chr7A 92.101 671 50 3 1508 2176 172201160 172201829 0.000000e+00 942.0
26 TraesCS2B01G280700 chr7A 91.639 299 24 1 2180 2477 172201921 172202219 1.770000e-111 412.0
27 TraesCS2B01G280700 chr3A 91.888 678 50 5 1505 2179 731741941 731742616 0.000000e+00 942.0
28 TraesCS2B01G280700 chr3A 89.027 483 51 2 185 665 731741469 731741951 4.560000e-167 597.0
29 TraesCS2B01G280700 chr3A 92.414 290 22 0 2185 2474 731742711 731743000 4.930000e-112 414.0
30 TraesCS2B01G280700 chr3A 83.529 85 10 4 46 127 606027979 606027896 2.640000e-10 76.8
31 TraesCS2B01G280700 chr3D 91.876 677 50 5 1505 2178 600857701 600857027 0.000000e+00 941.0
32 TraesCS2B01G280700 chr3D 89.234 483 48 4 185 665 600858171 600857691 3.520000e-168 601.0
33 TraesCS2B01G280700 chr3D 92.177 294 19 2 2185 2477 600855203 600854913 1.770000e-111 412.0
34 TraesCS2B01G280700 chr5D 90.990 677 58 3 1505 2179 55834093 55833418 0.000000e+00 909.0
35 TraesCS2B01G280700 chr5D 90.756 476 41 3 183 656 293160423 293160897 1.250000e-177 632.0
36 TraesCS2B01G280700 chr5D 88.843 484 53 1 181 663 556926426 556925943 5.900000e-166 593.0
37 TraesCS2B01G280700 chr5D 88.683 486 54 1 181 665 55834568 55834083 2.120000e-165 592.0
38 TraesCS2B01G280700 chr5D 83.908 87 10 3 36 121 78406654 78406571 2.040000e-11 80.5
39 TraesCS2B01G280700 chr1A 91.250 480 39 3 185 663 175176180 175175703 0.000000e+00 651.0
40 TraesCS2B01G280700 chr1D 78.056 679 140 9 806 1481 294747560 294748232 1.060000e-113 420.0
41 TraesCS2B01G280700 chrUn 92.491 293 21 1 2185 2477 290175233 290174942 3.810000e-113 418.0
42 TraesCS2B01G280700 chrUn 85.714 77 9 2 46 121 57796666 57796591 2.040000e-11 80.5
43 TraesCS2B01G280700 chr4D 91.000 300 26 1 2176 2475 469070615 469070317 1.070000e-108 403.0
44 TraesCS2B01G280700 chr2D 93.846 65 4 0 121 185 318584653 318584717 5.640000e-17 99.0
45 TraesCS2B01G280700 chr3B 81.739 115 19 2 10 123 788248227 788248340 7.290000e-16 95.3
46 TraesCS2B01G280700 chr3B 87.013 77 8 2 46 121 736430218 736430293 4.390000e-13 86.1
47 TraesCS2B01G280700 chr4A 85.000 80 9 3 43 121 503628354 503628431 7.340000e-11 78.7


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 TraesCS2B01G280700 chr2B 387144527 387147003 2476 False 4575.000000 4575 100.000000 1 2477 1 chr2B.!!$F1 2476
1 TraesCS2B01G280700 chr2B 768546188 768547031 843 False 1303.000000 1303 94.550000 669 1510 1 chr2B.!!$F3 841
2 TraesCS2B01G280700 chr7B 663193987 663194823 836 True 1458.000000 1458 98.088000 669 1505 1 chr7B.!!$R1 836
3 TraesCS2B01G280700 chr7B 131367633 131368460 827 False 1435.000000 1435 97.947000 669 1496 1 chr7B.!!$F2 827
4 TraesCS2B01G280700 chr7B 428933640 428934475 835 False 1428.000000 1428 97.491000 669 1505 1 chr7B.!!$F3 836
5 TraesCS2B01G280700 chr7B 45326651 45327486 835 False 1417.000000 1417 97.252000 669 1505 1 chr7B.!!$F1 836
6 TraesCS2B01G280700 chr7B 713392412 713393248 836 False 1339.000000 1339 95.579000 669 1504 1 chr7B.!!$F4 835
7 TraesCS2B01G280700 chr4B 647595244 647596083 839 False 1448.000000 1448 97.857000 669 1505 1 chr4B.!!$F1 836
8 TraesCS2B01G280700 chr5B 184286791 184287638 847 False 1330.000000 1330 95.171000 669 1506 1 chr5B.!!$F1 837
9 TraesCS2B01G280700 chr2A 728564363 728565202 839 False 1264.000000 1264 93.810000 669 1508 1 chr2A.!!$F1 839
10 TraesCS2B01G280700 chr7D 156121152 156121828 676 True 961.000000 961 92.319000 1505 2179 1 chr7D.!!$R2 674
11 TraesCS2B01G280700 chr7D 17369517 17370563 1046 True 651.500000 902 90.967500 1505 2477 2 chr7D.!!$R3 972
12 TraesCS2B01G280700 chr6D 156558666 156559813 1147 True 804.000000 928 91.791000 184 2179 2 chr6D.!!$R1 1995
13 TraesCS2B01G280700 chr6D 430011025 430012554 1529 True 676.666667 959 91.890000 185 2477 3 chr6D.!!$R2 2292
14 TraesCS2B01G280700 chr5A 1386468 1387619 1151 False 776.000000 944 90.644000 178 2176 2 chr5A.!!$F1 1998
15 TraesCS2B01G280700 chr7A 172201160 172202219 1059 False 677.000000 942 91.870000 1508 2477 2 chr7A.!!$F1 969
16 TraesCS2B01G280700 chr3A 731741469 731743000 1531 False 651.000000 942 91.109667 185 2474 3 chr3A.!!$F1 2289
17 TraesCS2B01G280700 chr3D 600854913 600858171 3258 True 651.333333 941 91.095667 185 2477 3 chr3D.!!$R1 2292
18 TraesCS2B01G280700 chr5D 55833418 55834568 1150 True 750.500000 909 89.836500 181 2179 2 chr5D.!!$R3 1998
19 TraesCS2B01G280700 chr1D 294747560 294748232 672 False 420.000000 420 78.056000 806 1481 1 chr1D.!!$F1 675

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
476 478 0.039256 CCCAACGGTTGCACTCAATG 60.039 55.0 15.31 0.0 34.29 2.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2399 4246 0.105224 TTCGGTTTTGACGAGCCTGA 59.895 50.0 0.0 0.0 41.81 3.86 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
35 36 9.609950 TGGTTTATGTAAATTTAACTAACACGC 57.390 29.630 0.00 0.00 0.00 5.34
36 37 9.830294 GGTTTATGTAAATTTAACTAACACGCT 57.170 29.630 0.00 0.00 0.00 5.07
46 47 9.811995 AATTTAACTAACACGCTATGTATCTCA 57.188 29.630 0.00 0.00 42.31 3.27
47 48 9.982651 ATTTAACTAACACGCTATGTATCTCAT 57.017 29.630 0.00 0.00 42.31 2.90
51 52 9.982651 AACTAACACGCTATGTATCTCATAAAT 57.017 29.630 0.00 0.00 42.31 1.40
52 53 9.982651 ACTAACACGCTATGTATCTCATAAATT 57.017 29.630 0.00 0.00 42.31 1.82
80 81 8.449251 TGAAAATTCATATCAATCCATCGTCA 57.551 30.769 0.00 0.00 31.01 4.35
81 82 8.562052 TGAAAATTCATATCAATCCATCGTCAG 58.438 33.333 0.00 0.00 31.01 3.51
82 83 8.681486 AAAATTCATATCAATCCATCGTCAGA 57.319 30.769 0.00 0.00 0.00 3.27
83 84 8.681486 AAATTCATATCAATCCATCGTCAGAA 57.319 30.769 0.00 0.00 0.00 3.02
84 85 8.859236 AATTCATATCAATCCATCGTCAGAAT 57.141 30.769 0.00 0.00 0.00 2.40
85 86 9.948964 AATTCATATCAATCCATCGTCAGAATA 57.051 29.630 0.00 0.00 0.00 1.75
86 87 8.992835 TTCATATCAATCCATCGTCAGAATAG 57.007 34.615 0.00 0.00 0.00 1.73
87 88 8.353423 TCATATCAATCCATCGTCAGAATAGA 57.647 34.615 0.00 0.00 0.00 1.98
88 89 8.246871 TCATATCAATCCATCGTCAGAATAGAC 58.753 37.037 0.00 0.00 35.19 2.59
94 95 4.014065 GTCAGAATAGACGGGCGC 57.986 61.111 0.00 0.00 0.00 6.53
95 96 1.141019 GTCAGAATAGACGGGCGCA 59.859 57.895 10.83 0.00 0.00 6.09
96 97 0.872021 GTCAGAATAGACGGGCGCAG 60.872 60.000 10.83 4.90 0.00 5.18
114 115 3.863543 CAACGCGCGCCATCATGA 61.864 61.111 32.58 0.00 0.00 3.07
115 116 2.896854 AACGCGCGCCATCATGAT 60.897 55.556 32.58 1.18 0.00 2.45
116 117 2.885676 AACGCGCGCCATCATGATC 61.886 57.895 32.58 0.00 0.00 2.92
117 118 3.040175 CGCGCGCCATCATGATCT 61.040 61.111 27.72 0.00 0.00 2.75
118 119 1.734117 CGCGCGCCATCATGATCTA 60.734 57.895 27.72 0.00 0.00 1.98
119 120 1.681025 CGCGCGCCATCATGATCTAG 61.681 60.000 27.72 1.87 0.00 2.43
120 121 0.668706 GCGCGCCATCATGATCTAGT 60.669 55.000 23.24 0.00 0.00 2.57
121 122 1.788258 CGCGCCATCATGATCTAGTT 58.212 50.000 4.86 0.00 0.00 2.24
122 123 2.138320 CGCGCCATCATGATCTAGTTT 58.862 47.619 4.86 0.00 0.00 2.66
123 124 3.317150 CGCGCCATCATGATCTAGTTTA 58.683 45.455 4.86 0.00 0.00 2.01
124 125 3.928992 CGCGCCATCATGATCTAGTTTAT 59.071 43.478 4.86 0.00 0.00 1.40
125 126 4.389992 CGCGCCATCATGATCTAGTTTATT 59.610 41.667 4.86 0.00 0.00 1.40
126 127 5.106948 CGCGCCATCATGATCTAGTTTATTT 60.107 40.000 4.86 0.00 0.00 1.40
127 128 6.082338 GCGCCATCATGATCTAGTTTATTTG 58.918 40.000 4.86 0.00 0.00 2.32
128 129 6.073058 GCGCCATCATGATCTAGTTTATTTGA 60.073 38.462 4.86 0.00 0.00 2.69
129 130 7.293745 CGCCATCATGATCTAGTTTATTTGAC 58.706 38.462 4.86 0.00 0.00 3.18
130 131 7.041848 CGCCATCATGATCTAGTTTATTTGACA 60.042 37.037 4.86 0.00 0.00 3.58
131 132 8.623903 GCCATCATGATCTAGTTTATTTGACAA 58.376 33.333 4.86 0.00 0.00 3.18
136 137 9.294030 CATGATCTAGTTTATTTGACAAAAGCC 57.706 33.333 4.41 0.00 0.00 4.35
137 138 8.635765 TGATCTAGTTTATTTGACAAAAGCCT 57.364 30.769 4.41 1.99 0.00 4.58
138 139 8.730680 TGATCTAGTTTATTTGACAAAAGCCTC 58.269 33.333 4.41 0.00 0.00 4.70
139 140 8.635765 ATCTAGTTTATTTGACAAAAGCCTCA 57.364 30.769 4.41 0.00 0.00 3.86
140 141 8.635765 TCTAGTTTATTTGACAAAAGCCTCAT 57.364 30.769 4.41 0.00 0.00 2.90
141 142 8.514594 TCTAGTTTATTTGACAAAAGCCTCATG 58.485 33.333 4.41 0.00 0.00 3.07
142 143 7.054491 AGTTTATTTGACAAAAGCCTCATGT 57.946 32.000 4.41 0.00 0.00 3.21
143 144 8.177119 AGTTTATTTGACAAAAGCCTCATGTA 57.823 30.769 4.41 0.00 0.00 2.29
144 145 8.082242 AGTTTATTTGACAAAAGCCTCATGTAC 58.918 33.333 4.41 0.00 0.00 2.90
145 146 7.517614 TTATTTGACAAAAGCCTCATGTACA 57.482 32.000 4.41 0.00 0.00 2.90
146 147 5.843673 TTTGACAAAAGCCTCATGTACAA 57.156 34.783 0.00 0.00 0.00 2.41
147 148 5.437289 TTGACAAAAGCCTCATGTACAAG 57.563 39.130 0.00 0.00 0.00 3.16
148 149 4.460263 TGACAAAAGCCTCATGTACAAGT 58.540 39.130 0.00 0.00 0.00 3.16
149 150 4.515191 TGACAAAAGCCTCATGTACAAGTC 59.485 41.667 0.00 0.00 0.00 3.01
150 151 4.718961 ACAAAAGCCTCATGTACAAGTCT 58.281 39.130 0.00 0.00 0.00 3.24
151 152 4.757149 ACAAAAGCCTCATGTACAAGTCTC 59.243 41.667 0.00 0.00 0.00 3.36
152 153 4.899352 AAAGCCTCATGTACAAGTCTCT 57.101 40.909 0.00 0.00 0.00 3.10
153 154 4.464069 AAGCCTCATGTACAAGTCTCTC 57.536 45.455 0.00 0.00 0.00 3.20
154 155 3.707316 AGCCTCATGTACAAGTCTCTCT 58.293 45.455 0.00 0.00 0.00 3.10
155 156 3.446873 AGCCTCATGTACAAGTCTCTCTG 59.553 47.826 0.00 0.00 0.00 3.35
156 157 3.445450 GCCTCATGTACAAGTCTCTCTGA 59.555 47.826 0.00 0.00 0.00 3.27
157 158 4.099266 GCCTCATGTACAAGTCTCTCTGAT 59.901 45.833 0.00 0.00 0.00 2.90
158 159 5.735922 GCCTCATGTACAAGTCTCTCTGATC 60.736 48.000 0.00 0.00 0.00 2.92
159 160 5.221224 CCTCATGTACAAGTCTCTCTGATCC 60.221 48.000 0.00 0.00 0.00 3.36
160 161 5.514169 TCATGTACAAGTCTCTCTGATCCT 58.486 41.667 0.00 0.00 0.00 3.24
161 162 5.954752 TCATGTACAAGTCTCTCTGATCCTT 59.045 40.000 0.00 0.00 0.00 3.36
162 163 5.906113 TGTACAAGTCTCTCTGATCCTTC 57.094 43.478 0.00 0.00 0.00 3.46
163 164 5.575157 TGTACAAGTCTCTCTGATCCTTCT 58.425 41.667 0.00 0.00 0.00 2.85
164 165 6.722328 TGTACAAGTCTCTCTGATCCTTCTA 58.278 40.000 0.00 0.00 0.00 2.10
165 166 6.826231 TGTACAAGTCTCTCTGATCCTTCTAG 59.174 42.308 0.00 0.00 0.00 2.43
166 167 4.644685 ACAAGTCTCTCTGATCCTTCTAGC 59.355 45.833 0.00 0.00 0.00 3.42
167 168 4.796110 AGTCTCTCTGATCCTTCTAGCT 57.204 45.455 0.00 0.00 0.00 3.32
168 169 4.464008 AGTCTCTCTGATCCTTCTAGCTG 58.536 47.826 0.00 0.00 0.00 4.24
169 170 4.079787 AGTCTCTCTGATCCTTCTAGCTGT 60.080 45.833 0.00 0.00 0.00 4.40
170 171 5.131977 AGTCTCTCTGATCCTTCTAGCTGTA 59.868 44.000 0.00 0.00 0.00 2.74
171 172 6.003950 GTCTCTCTGATCCTTCTAGCTGTAT 58.996 44.000 0.00 0.00 0.00 2.29
172 173 6.149474 GTCTCTCTGATCCTTCTAGCTGTATC 59.851 46.154 0.00 0.00 0.00 2.24
173 174 5.946486 TCTCTGATCCTTCTAGCTGTATCA 58.054 41.667 0.00 0.00 0.00 2.15
174 175 6.551085 TCTCTGATCCTTCTAGCTGTATCAT 58.449 40.000 0.00 0.00 0.00 2.45
175 176 7.009550 TCTCTGATCCTTCTAGCTGTATCATT 58.990 38.462 0.00 0.00 0.00 2.57
176 177 8.166726 TCTCTGATCCTTCTAGCTGTATCATTA 58.833 37.037 0.00 0.00 0.00 1.90
244 245 4.872124 TCAATCGATGCATGTAGCCATATC 59.128 41.667 2.46 0.00 44.83 1.63
292 294 9.739276 TCTTAAGATCCAAAGAAGCTCATAAAA 57.261 29.630 0.00 0.00 0.00 1.52
293 295 9.780413 CTTAAGATCCAAAGAAGCTCATAAAAC 57.220 33.333 0.00 0.00 0.00 2.43
350 352 2.029380 CCACATCCGGCGATATAGAACA 60.029 50.000 9.30 0.00 0.00 3.18
471 473 1.227853 GTCTCCCAACGGTTGCACT 60.228 57.895 15.31 0.00 0.00 4.40
476 478 0.039256 CCCAACGGTTGCACTCAATG 60.039 55.000 15.31 0.00 34.29 2.82
494 496 5.132502 TCAATGACCAAAAGCTCTCTGAAA 58.867 37.500 0.00 0.00 0.00 2.69
515 517 1.751351 TCCGCATGAGTGAGTAAGGAG 59.249 52.381 0.00 0.00 0.00 3.69
537 539 3.123804 CACATACGGATCCAAGCTGTAC 58.876 50.000 13.41 0.00 30.52 2.90
640 642 5.760253 AGAAAAGTGCACATATTCCTATCCG 59.240 40.000 21.04 0.00 0.00 4.18
641 643 4.955811 AAGTGCACATATTCCTATCCGA 57.044 40.909 21.04 0.00 0.00 4.55
642 644 4.955811 AGTGCACATATTCCTATCCGAA 57.044 40.909 21.04 0.00 0.00 4.30
643 645 5.489792 AGTGCACATATTCCTATCCGAAT 57.510 39.130 21.04 0.00 36.45 3.34
644 646 6.605471 AGTGCACATATTCCTATCCGAATA 57.395 37.500 21.04 0.00 38.69 1.75
645 647 7.187824 AGTGCACATATTCCTATCCGAATAT 57.812 36.000 21.04 0.00 43.22 1.28
656 658 9.823647 ATTCCTATCCGAATATGTTTAGCTATG 57.176 33.333 0.00 0.00 30.59 2.23
657 659 8.362464 TCCTATCCGAATATGTTTAGCTATGT 57.638 34.615 0.00 0.00 0.00 2.29
658 660 8.251026 TCCTATCCGAATATGTTTAGCTATGTG 58.749 37.037 0.00 0.00 0.00 3.21
659 661 8.035394 CCTATCCGAATATGTTTAGCTATGTGT 58.965 37.037 0.00 0.00 0.00 3.72
662 664 8.757164 TCCGAATATGTTTAGCTATGTGTATG 57.243 34.615 0.00 0.00 0.00 2.39
663 665 8.364894 TCCGAATATGTTTAGCTATGTGTATGT 58.635 33.333 0.00 0.00 0.00 2.29
664 666 8.648097 CCGAATATGTTTAGCTATGTGTATGTC 58.352 37.037 0.00 0.00 0.00 3.06
665 667 9.411801 CGAATATGTTTAGCTATGTGTATGTCT 57.588 33.333 0.00 0.00 0.00 3.41
679 681 7.703058 TGTGTATGTCTATTCTGTCAGAAGA 57.297 36.000 19.64 14.66 37.69 2.87
925 942 3.409636 ACTATCCTCCATGGGGATTAGGA 59.590 47.826 29.04 24.38 43.91 2.94
961 978 0.396417 TGTAAATGCCCATTCCCCGG 60.396 55.000 0.00 0.00 0.00 5.73
1183 1200 8.506168 TCTAAGGTTTGGATTATTACTTGCAG 57.494 34.615 0.00 0.00 0.00 4.41
1666 1683 6.861144 TCATTTTGATCACAGAAACAACACA 58.139 32.000 0.00 0.00 0.00 3.72
1791 1814 2.942804 TCCAAATGTGCAAAGACCTCA 58.057 42.857 0.00 0.00 0.00 3.86
1863 1887 2.690786 TCCATTCGTGGTTAACTTCCG 58.309 47.619 5.42 5.76 0.00 4.30
1945 1969 0.178975 AAGCATTCCAACGTTCCCCA 60.179 50.000 0.00 0.00 0.00 4.96
1948 1972 0.601057 CATTCCAACGTTCCCCAACC 59.399 55.000 0.00 0.00 0.00 3.77
1975 1999 9.411848 AGGGATCTCCTAAATTGGATATTAAGT 57.588 33.333 1.23 0.00 45.98 2.24
2057 2081 4.906747 AAGGGATATTGCAAAGCCAAAA 57.093 36.364 1.71 0.00 0.00 2.44
2181 4022 2.143925 CTTCCAAAAGGGTGAGTCGAC 58.856 52.381 7.70 7.70 38.11 4.20
2213 4054 2.223665 GCCATTTGCTAAGCAGACATCC 60.224 50.000 0.00 0.00 40.61 3.51
2324 4171 1.337167 GGCCTCATCACTTTGCCAAAC 60.337 52.381 0.00 0.00 41.76 2.93
2325 4172 1.340889 GCCTCATCACTTTGCCAAACA 59.659 47.619 0.00 0.00 0.00 2.83
2372 4219 4.895297 TCTTTTTCGTATCCCTACCGGTAT 59.105 41.667 16.25 3.44 0.00 2.73
2399 4246 7.386851 TCAAAGAAAGATAGAAGGAACATCGT 58.613 34.615 0.00 0.00 0.00 3.73
2460 4307 2.235155 TCCGTAAGACATTAGCTTGCCA 59.765 45.455 0.00 0.00 43.02 4.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 9.609950 GCGTGTTAGTTAAATTTACATAAACCA 57.390 29.630 0.00 0.00 0.00 3.67
10 11 9.830294 AGCGTGTTAGTTAAATTTACATAAACC 57.170 29.630 0.00 0.00 0.00 3.27
20 21 9.811995 TGAGATACATAGCGTGTTAGTTAAATT 57.188 29.630 3.14 0.00 42.29 1.82
21 22 9.982651 ATGAGATACATAGCGTGTTAGTTAAAT 57.017 29.630 3.14 0.00 42.29 1.40
25 26 9.982651 ATTTATGAGATACATAGCGTGTTAGTT 57.017 29.630 3.14 0.00 41.64 2.24
26 27 9.982651 AATTTATGAGATACATAGCGTGTTAGT 57.017 29.630 3.14 0.00 41.64 2.24
55 56 8.449251 TGACGATGGATTGATATGAATTTTCA 57.551 30.769 0.00 0.00 42.14 2.69
56 57 8.777413 TCTGACGATGGATTGATATGAATTTTC 58.223 33.333 0.00 0.00 0.00 2.29
57 58 8.681486 TCTGACGATGGATTGATATGAATTTT 57.319 30.769 0.00 0.00 0.00 1.82
58 59 8.681486 TTCTGACGATGGATTGATATGAATTT 57.319 30.769 0.00 0.00 0.00 1.82
59 60 8.859236 ATTCTGACGATGGATTGATATGAATT 57.141 30.769 0.00 0.00 0.00 2.17
60 61 9.597170 CTATTCTGACGATGGATTGATATGAAT 57.403 33.333 0.00 0.00 0.00 2.57
61 62 8.806146 TCTATTCTGACGATGGATTGATATGAA 58.194 33.333 0.00 0.00 0.00 2.57
62 63 8.246871 GTCTATTCTGACGATGGATTGATATGA 58.753 37.037 0.00 0.00 0.00 2.15
63 64 8.404889 GTCTATTCTGACGATGGATTGATATG 57.595 38.462 0.00 0.00 0.00 1.78
77 78 0.872021 CTGCGCCCGTCTATTCTGAC 60.872 60.000 4.18 0.00 0.00 3.51
78 79 1.437573 CTGCGCCCGTCTATTCTGA 59.562 57.895 4.18 0.00 0.00 3.27
79 80 2.240500 GCTGCGCCCGTCTATTCTG 61.241 63.158 4.18 0.00 0.00 3.02
80 81 2.107141 GCTGCGCCCGTCTATTCT 59.893 61.111 4.18 0.00 0.00 2.40
81 82 1.813753 TTGCTGCGCCCGTCTATTC 60.814 57.895 4.18 0.00 0.00 1.75
82 83 2.106683 GTTGCTGCGCCCGTCTATT 61.107 57.895 4.18 0.00 0.00 1.73
83 84 2.511600 GTTGCTGCGCCCGTCTAT 60.512 61.111 4.18 0.00 0.00 1.98
97 98 3.172099 ATCATGATGGCGCGCGTTG 62.172 57.895 32.35 16.86 0.00 4.10
98 99 2.885676 GATCATGATGGCGCGCGTT 61.886 57.895 32.35 15.25 0.00 4.84
99 100 2.420466 TAGATCATGATGGCGCGCGT 62.420 55.000 32.35 16.88 0.00 6.01
100 101 1.681025 CTAGATCATGATGGCGCGCG 61.681 60.000 28.44 28.44 0.00 6.86
101 102 0.668706 ACTAGATCATGATGGCGCGC 60.669 55.000 25.94 25.94 0.00 6.86
102 103 1.788258 AACTAGATCATGATGGCGCG 58.212 50.000 14.30 0.00 0.00 6.86
103 104 5.869753 AATAAACTAGATCATGATGGCGC 57.130 39.130 14.30 0.00 0.00 6.53
104 105 7.041848 TGTCAAATAAACTAGATCATGATGGCG 60.042 37.037 14.30 3.12 0.00 5.69
105 106 8.158169 TGTCAAATAAACTAGATCATGATGGC 57.842 34.615 14.30 0.00 0.00 4.40
110 111 9.294030 GGCTTTTGTCAAATAAACTAGATCATG 57.706 33.333 0.00 0.00 0.00 3.07
111 112 9.247861 AGGCTTTTGTCAAATAAACTAGATCAT 57.752 29.630 0.00 0.00 0.00 2.45
112 113 8.635765 AGGCTTTTGTCAAATAAACTAGATCA 57.364 30.769 0.00 0.00 0.00 2.92
113 114 8.730680 TGAGGCTTTTGTCAAATAAACTAGATC 58.269 33.333 0.00 0.00 0.00 2.75
114 115 8.635765 TGAGGCTTTTGTCAAATAAACTAGAT 57.364 30.769 0.00 0.00 0.00 1.98
115 116 8.514594 CATGAGGCTTTTGTCAAATAAACTAGA 58.485 33.333 0.00 0.00 0.00 2.43
116 117 8.299570 ACATGAGGCTTTTGTCAAATAAACTAG 58.700 33.333 0.00 0.00 0.00 2.57
117 118 8.177119 ACATGAGGCTTTTGTCAAATAAACTA 57.823 30.769 0.00 0.00 0.00 2.24
118 119 7.054491 ACATGAGGCTTTTGTCAAATAAACT 57.946 32.000 0.00 0.00 0.00 2.66
119 120 7.865385 TGTACATGAGGCTTTTGTCAAATAAAC 59.135 33.333 0.00 0.33 0.00 2.01
120 121 7.946207 TGTACATGAGGCTTTTGTCAAATAAA 58.054 30.769 0.00 0.00 0.00 1.40
121 122 7.517614 TGTACATGAGGCTTTTGTCAAATAA 57.482 32.000 0.00 0.00 0.00 1.40
122 123 7.230510 ACTTGTACATGAGGCTTTTGTCAAATA 59.769 33.333 15.13 0.00 0.00 1.40
123 124 6.040842 ACTTGTACATGAGGCTTTTGTCAAAT 59.959 34.615 15.13 0.90 0.00 2.32
124 125 5.359576 ACTTGTACATGAGGCTTTTGTCAAA 59.640 36.000 15.13 0.00 0.00 2.69
125 126 4.887071 ACTTGTACATGAGGCTTTTGTCAA 59.113 37.500 15.13 9.54 0.00 3.18
126 127 4.460263 ACTTGTACATGAGGCTTTTGTCA 58.540 39.130 15.13 3.69 0.00 3.58
127 128 4.757149 AGACTTGTACATGAGGCTTTTGTC 59.243 41.667 15.13 0.00 0.00 3.18
128 129 4.718961 AGACTTGTACATGAGGCTTTTGT 58.281 39.130 15.13 8.13 0.00 2.83
129 130 4.999950 AGAGACTTGTACATGAGGCTTTTG 59.000 41.667 15.13 0.00 29.39 2.44
130 131 5.012561 AGAGAGACTTGTACATGAGGCTTTT 59.987 40.000 15.13 2.48 29.39 2.27
131 132 4.530161 AGAGAGACTTGTACATGAGGCTTT 59.470 41.667 15.13 4.52 29.39 3.51
132 133 4.081752 CAGAGAGACTTGTACATGAGGCTT 60.082 45.833 15.13 1.15 29.39 4.35
133 134 3.446873 CAGAGAGACTTGTACATGAGGCT 59.553 47.826 15.13 9.18 32.78 4.58
134 135 3.445450 TCAGAGAGACTTGTACATGAGGC 59.555 47.826 15.13 3.98 0.00 4.70
135 136 5.221224 GGATCAGAGAGACTTGTACATGAGG 60.221 48.000 15.13 0.63 0.00 3.86
136 137 5.593909 AGGATCAGAGAGACTTGTACATGAG 59.406 44.000 15.13 4.42 0.00 2.90
137 138 5.514169 AGGATCAGAGAGACTTGTACATGA 58.486 41.667 15.13 4.98 0.00 3.07
138 139 5.850557 AGGATCAGAGAGACTTGTACATG 57.149 43.478 7.18 7.18 0.00 3.21
139 140 6.194235 AGAAGGATCAGAGAGACTTGTACAT 58.806 40.000 0.00 0.00 0.00 2.29
140 141 5.575157 AGAAGGATCAGAGAGACTTGTACA 58.425 41.667 0.00 0.00 0.00 2.90
141 142 6.238648 GCTAGAAGGATCAGAGAGACTTGTAC 60.239 46.154 0.00 0.00 0.00 2.90
142 143 5.825679 GCTAGAAGGATCAGAGAGACTTGTA 59.174 44.000 0.00 0.00 0.00 2.41
143 144 4.644685 GCTAGAAGGATCAGAGAGACTTGT 59.355 45.833 0.00 0.00 0.00 3.16
144 145 4.889409 AGCTAGAAGGATCAGAGAGACTTG 59.111 45.833 0.00 0.00 0.00 3.16
145 146 4.889409 CAGCTAGAAGGATCAGAGAGACTT 59.111 45.833 0.00 0.00 0.00 3.01
146 147 4.079787 ACAGCTAGAAGGATCAGAGAGACT 60.080 45.833 0.00 0.00 0.00 3.24
147 148 4.207165 ACAGCTAGAAGGATCAGAGAGAC 58.793 47.826 0.00 0.00 0.00 3.36
148 149 4.518278 ACAGCTAGAAGGATCAGAGAGA 57.482 45.455 0.00 0.00 0.00 3.10
149 150 6.003326 TGATACAGCTAGAAGGATCAGAGAG 58.997 44.000 5.84 0.00 0.00 3.20
150 151 5.946486 TGATACAGCTAGAAGGATCAGAGA 58.054 41.667 5.84 0.00 0.00 3.10
151 152 6.839124 ATGATACAGCTAGAAGGATCAGAG 57.161 41.667 13.24 0.00 0.00 3.35
152 153 7.947332 AGTAATGATACAGCTAGAAGGATCAGA 59.053 37.037 13.24 4.14 34.29 3.27
153 154 8.121305 AGTAATGATACAGCTAGAAGGATCAG 57.879 38.462 13.24 0.00 34.29 2.90
154 155 7.947332 AGAGTAATGATACAGCTAGAAGGATCA 59.053 37.037 10.96 10.96 34.29 2.92
155 156 8.348285 AGAGTAATGATACAGCTAGAAGGATC 57.652 38.462 0.00 0.00 34.29 3.36
156 157 9.989296 ATAGAGTAATGATACAGCTAGAAGGAT 57.011 33.333 0.00 0.00 34.29 3.24
209 210 1.102978 TCGATTGATGCAGAGGTCGA 58.897 50.000 11.44 11.44 35.97 4.20
273 275 6.428385 CTCGTTTTATGAGCTTCTTTGGAT 57.572 37.500 0.00 0.00 0.00 3.41
292 294 3.637998 TTTCTTTCGACTACTGCTCGT 57.362 42.857 0.00 0.00 32.77 4.18
293 295 6.308282 ACTTATTTTCTTTCGACTACTGCTCG 59.692 38.462 0.00 0.00 0.00 5.03
350 352 0.110486 ACCGGATGTGGCACTTTTCT 59.890 50.000 19.83 0.00 0.00 2.52
476 478 3.126000 CGGATTTCAGAGAGCTTTTGGTC 59.874 47.826 0.00 0.00 46.50 4.02
494 496 2.363680 CTCCTTACTCACTCATGCGGAT 59.636 50.000 0.00 0.00 0.00 4.18
515 517 0.940126 CAGCTTGGATCCGTATGTGC 59.060 55.000 7.39 4.93 0.00 4.57
645 647 9.750125 CAGAATAGACATACACATAGCTAAACA 57.250 33.333 0.00 0.00 0.00 2.83
646 648 9.751542 ACAGAATAGACATACACATAGCTAAAC 57.248 33.333 0.00 0.00 0.00 2.01
647 649 9.967346 GACAGAATAGACATACACATAGCTAAA 57.033 33.333 0.00 0.00 0.00 1.85
648 650 9.131791 TGACAGAATAGACATACACATAGCTAA 57.868 33.333 0.00 0.00 0.00 3.09
649 651 8.691661 TGACAGAATAGACATACACATAGCTA 57.308 34.615 0.00 0.00 0.00 3.32
650 652 7.503902 TCTGACAGAATAGACATACACATAGCT 59.496 37.037 1.64 0.00 0.00 3.32
651 653 7.652727 TCTGACAGAATAGACATACACATAGC 58.347 38.462 1.64 0.00 0.00 2.97
652 654 9.676195 CTTCTGACAGAATAGACATACACATAG 57.324 37.037 18.04 0.00 33.13 2.23
653 655 9.408648 TCTTCTGACAGAATAGACATACACATA 57.591 33.333 18.04 0.00 33.13 2.29
654 656 8.194104 GTCTTCTGACAGAATAGACATACACAT 58.806 37.037 23.60 0.00 42.48 3.21
655 657 7.539436 GTCTTCTGACAGAATAGACATACACA 58.461 38.462 23.60 0.00 42.48 3.72
656 658 7.979115 GTCTTCTGACAGAATAGACATACAC 57.021 40.000 23.60 4.74 42.48 2.90
925 942 9.418045 GGCATTTACATAGTTTGTTGTTATTGT 57.582 29.630 0.00 0.00 39.87 2.71
1183 1200 1.599240 GATTGCATCCCGCCCTCTC 60.599 63.158 0.00 0.00 41.33 3.20
1603 1620 6.084925 TCTTTCTCGAATGTTCTCTTACGAC 58.915 40.000 0.00 0.00 0.00 4.34
1613 1630 7.360101 CGATTAAACACCTCTTTCTCGAATGTT 60.360 37.037 0.00 0.00 0.00 2.71
1680 1697 8.477419 AAGATAACTTGGTGAAAAGGAATTGA 57.523 30.769 0.00 0.00 34.80 2.57
1791 1814 1.864669 ATTGATTCCGGGCCATTGTT 58.135 45.000 4.39 0.00 0.00 2.83
1823 1847 5.494724 TGGAATCTTCTCAGTGAAATCCAG 58.505 41.667 0.00 0.00 37.21 3.86
1863 1887 3.364023 CGATTAGGCGGATACAATTCGTC 59.636 47.826 0.00 0.00 0.00 4.20
1975 1999 4.877251 GCCACGGTATTAAACTTGATACCA 59.123 41.667 18.37 0.00 45.23 3.25
1993 2017 0.389391 AGGAGGATTATGTCGCCACG 59.611 55.000 0.00 0.00 0.00 4.94
2035 2059 4.906747 TTTGGCTTTGCAATATCCCTTT 57.093 36.364 0.00 0.00 0.00 3.11
2036 2060 4.835678 CTTTTGGCTTTGCAATATCCCTT 58.164 39.130 0.00 0.00 0.00 3.95
2057 2081 0.401105 ACATGGCTAGGGGAGATGCT 60.401 55.000 0.00 0.00 0.00 3.79
2277 4121 6.609212 AGAAGAAGTACAGATTGGCTAGATGA 59.391 38.462 0.00 0.00 0.00 2.92
2324 4171 7.437748 ACTTGACTTCTATAGATCCCGATTTG 58.562 38.462 2.58 0.00 0.00 2.32
2325 4172 7.507616 AGACTTGACTTCTATAGATCCCGATTT 59.492 37.037 2.58 0.00 0.00 2.17
2360 4207 5.248934 TCTTTCTTTGAAATACCGGTAGGGA 59.751 40.000 20.91 0.00 43.47 4.20
2372 4219 8.721478 CGATGTTCCTTCTATCTTTCTTTGAAA 58.279 33.333 0.00 0.00 0.00 2.69
2399 4246 0.105224 TTCGGTTTTGACGAGCCTGA 59.895 50.000 0.00 0.00 41.81 3.86


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

AutoCloner maintained by Alex Coulton.