Multiple sequence alignment - TraesCS3B01G003400

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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 TraesCS3B01G003400 chr3B 100.000 4166 0 0 1 4166 2321937 2326102 0.000000e+00 7694.0
1 TraesCS3B01G003400 chr3B 98.753 3368 13 6 283 3649 2131232 2127893 0.000000e+00 5960.0
2 TraesCS3B01G003400 chr3B 81.967 488 80 6 1940 2425 2256529 2256048 1.390000e-109 407.0
3 TraesCS3B01G003400 chr3B 80.725 524 90 7 1907 2425 2109712 2109195 8.390000e-107 398.0
4 TraesCS3B01G003400 chr3B 89.720 214 22 0 64 277 29726893 29726680 1.480000e-69 274.0
5 TraesCS3B01G003400 chr3B 80.435 276 42 9 1443 1710 2145421 2145150 2.540000e-47 200.0
6 TraesCS3B01G003400 chr3B 80.488 246 26 12 974 1218 2257396 2257172 7.160000e-38 169.0
7 TraesCS3B01G003400 chr3B 91.139 79 7 0 3096 3174 2169579 2169501 1.580000e-19 108.0
8 TraesCS3B01G003400 chr3B 93.617 47 3 0 841 887 2110709 2110663 2.080000e-08 71.3
9 TraesCS3B01G003400 chr3D 89.334 1772 158 15 1893 3645 3098283 3096524 0.000000e+00 2196.0
10 TraesCS3B01G003400 chr3D 89.787 705 45 8 546 1240 3100011 3099324 0.000000e+00 878.0
11 TraesCS3B01G003400 chr3D 97.059 510 15 0 3657 4166 578206542 578206033 0.000000e+00 859.0
12 TraesCS3B01G003400 chr3D 82.061 825 120 22 2159 2976 3151921 3151118 0.000000e+00 678.0
13 TraesCS3B01G003400 chr3D 91.045 335 22 3 912 1245 3155080 3154753 2.950000e-121 446.0
14 TraesCS3B01G003400 chr3D 79.213 712 81 33 565 1245 3181797 3181122 2.300000e-117 433.0
15 TraesCS3B01G003400 chr3D 88.315 368 15 8 1351 1714 3152974 3152631 2.320000e-112 416.0
16 TraesCS3B01G003400 chr3D 81.967 488 79 7 1940 2425 3073689 3073209 5.010000e-109 405.0
17 TraesCS3B01G003400 chr3D 89.062 320 27 3 1298 1612 3099052 3098736 1.400000e-104 390.0
18 TraesCS3B01G003400 chr3D 74.508 914 168 38 2578 3449 3053500 3052610 1.860000e-88 337.0
19 TraesCS3B01G003400 chr3D 95.960 198 8 0 1687 1884 3098709 3098512 5.200000e-84 322.0
20 TraesCS3B01G003400 chr3D 80.435 276 27 17 974 1242 3085831 3085576 7.110000e-43 185.0
21 TraesCS3B01G003400 chr3D 78.986 276 48 7 3010 3285 3072691 3072426 3.310000e-41 180.0
22 TraesCS3B01G003400 chr3D 85.185 189 10 6 350 520 3155619 3155431 1.190000e-40 178.0
23 TraesCS3B01G003400 chr3D 82.353 170 10 9 369 520 3100251 3100084 3.380000e-26 130.0
24 TraesCS3B01G003400 chr3D 82.209 163 16 10 1 150 511887103 511887265 1.220000e-25 128.0
25 TraesCS3B01G003400 chr3D 92.000 75 6 0 3096 3170 3196784 3196710 5.700000e-19 106.0
26 TraesCS3B01G003400 chr3A 85.419 1063 117 25 1886 2924 206526 205478 0.000000e+00 1070.0
27 TraesCS3B01G003400 chr3A 97.036 506 15 0 3661 4166 623196671 623196166 0.000000e+00 852.0
28 TraesCS3B01G003400 chr3A 83.844 588 88 7 3061 3645 205036 204453 1.690000e-153 553.0
29 TraesCS3B01G003400 chr3A 83.218 578 85 9 1301 1876 207397 206830 1.720000e-143 520.0
30 TraesCS3B01G003400 chr3A 82.377 488 79 6 1940 2425 131440 130958 6.440000e-113 418.0
31 TraesCS3B01G003400 chr3A 88.604 351 23 4 546 896 208204 207871 1.080000e-110 411.0
32 TraesCS3B01G003400 chr3A 85.979 378 48 2 921 1294 207887 207511 2.330000e-107 399.0
33 TraesCS3B01G003400 chr3A 79.849 531 95 10 1901 2428 141541 141020 1.090000e-100 377.0
34 TraesCS3B01G003400 chr3A 78.555 443 73 12 3009 3449 140340 139918 5.310000e-69 272.0
35 TraesCS3B01G003400 chr3A 85.022 227 19 9 315 528 208489 208265 2.520000e-52 217.0
36 TraesCS3B01G003400 chr3A 76.494 251 41 14 3096 3338 398129 397889 2.030000e-23 121.0
37 TraesCS3B01G003400 chr2B 97.647 510 11 1 3658 4166 17850146 17849637 0.000000e+00 874.0
38 TraesCS3B01G003400 chr7A 97.053 509 14 1 3658 4166 647148192 647148699 0.000000e+00 856.0
39 TraesCS3B01G003400 chr6D 93.957 513 24 6 3657 4166 354364645 354364137 0.000000e+00 769.0
40 TraesCS3B01G003400 chr6D 97.952 293 6 0 3874 4166 39586581 39586289 3.720000e-140 508.0
41 TraesCS3B01G003400 chr6D 97.727 44 1 0 1 44 100387274 100387317 4.470000e-10 76.8
42 TraesCS3B01G003400 chr1B 90.217 368 30 4 3657 4023 114603727 114604089 3.770000e-130 475.0
43 TraesCS3B01G003400 chr4B 78.214 739 141 17 1999 2727 653429739 653429011 4.910000e-124 455.0
44 TraesCS3B01G003400 chr4B 79.279 222 24 12 981 1195 653431838 653431632 7.260000e-28 135.0
45 TraesCS3B01G003400 chr4B 78.924 223 25 12 980 1195 653009321 653009528 9.400000e-27 132.0
46 TraesCS3B01G003400 chr4B 79.755 163 20 5 1 150 581081246 581081084 5.700000e-19 106.0
47 TraesCS3B01G003400 chr4B 100.000 30 0 0 314 343 595707021 595706992 5.820000e-04 56.5
48 TraesCS3B01G003400 chr4D 94.118 289 16 1 3657 3944 506215814 506216102 4.940000e-119 438.0
49 TraesCS3B01G003400 chr4A 87.413 286 27 6 1 277 709617886 709618171 1.870000e-83 320.0
50 TraesCS3B01G003400 chr7B 83.566 286 38 4 1 277 699563706 699563421 4.130000e-65 259.0
51 TraesCS3B01G003400 chr6A 92.632 95 5 1 45 137 17575091 17575185 7.260000e-28 135.0
52 TraesCS3B01G003400 chrUn 78.829 222 25 12 981 1195 126953973 126953767 3.380000e-26 130.0
53 TraesCS3B01G003400 chr5D 82.317 164 14 11 1 150 396441538 396441700 1.220000e-25 128.0
54 TraesCS3B01G003400 chr1D 81.595 163 17 10 1 150 32440167 32440329 5.660000e-24 122.0
55 TraesCS3B01G003400 chr1D 97.727 44 1 0 1 44 10696019 10696062 4.470000e-10 76.8
56 TraesCS3B01G003400 chr7D 80.982 163 18 10 1 150 13346103 13346265 2.630000e-22 117.0
57 TraesCS3B01G003400 chr7D 95.455 44 2 0 1 44 591203072 591203029 2.080000e-08 71.3
58 TraesCS3B01G003400 chr5A 78.607 201 25 11 998 1195 690561077 690561262 2.630000e-22 117.0
59 TraesCS3B01G003400 chr1A 97.674 43 1 0 1 43 128632051 128632009 1.610000e-09 75.0
60 TraesCS3B01G003400 chr6B 100.000 29 0 0 315 343 57394005 57393977 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 TraesCS3B01G003400 chr3B 2321937 2326102 4165 False 7694.000000 7694 100.000000 1 4166 1 chr3B.!!$F1 4165
1 TraesCS3B01G003400 chr3B 2127893 2131232 3339 True 5960.000000 5960 98.753000 283 3649 1 chr3B.!!$R1 3366
2 TraesCS3B01G003400 chr3B 2256048 2257396 1348 True 288.000000 407 81.227500 974 2425 2 chr3B.!!$R6 1451
3 TraesCS3B01G003400 chr3B 2109195 2110709 1514 True 234.650000 398 87.171000 841 2425 2 chr3B.!!$R5 1584
4 TraesCS3B01G003400 chr3D 578206033 578206542 509 True 859.000000 859 97.059000 3657 4166 1 chr3D.!!$R5 509
5 TraesCS3B01G003400 chr3D 3096524 3100251 3727 True 783.200000 2196 89.299200 369 3645 5 chr3D.!!$R7 3276
6 TraesCS3B01G003400 chr3D 3181122 3181797 675 True 433.000000 433 79.213000 565 1245 1 chr3D.!!$R3 680
7 TraesCS3B01G003400 chr3D 3151118 3155619 4501 True 429.500000 678 86.651500 350 2976 4 chr3D.!!$R8 2626
8 TraesCS3B01G003400 chr3D 3052610 3053500 890 True 337.000000 337 74.508000 2578 3449 1 chr3D.!!$R1 871
9 TraesCS3B01G003400 chr3D 3072426 3073689 1263 True 292.500000 405 80.476500 1940 3285 2 chr3D.!!$R6 1345
10 TraesCS3B01G003400 chr3A 623196166 623196671 505 True 852.000000 852 97.036000 3661 4166 1 chr3A.!!$R3 505
11 TraesCS3B01G003400 chr3A 204453 208489 4036 True 528.333333 1070 85.347667 315 3645 6 chr3A.!!$R5 3330
12 TraesCS3B01G003400 chr3A 139918 141541 1623 True 324.500000 377 79.202000 1901 3449 2 chr3A.!!$R4 1548
13 TraesCS3B01G003400 chr2B 17849637 17850146 509 True 874.000000 874 97.647000 3658 4166 1 chr2B.!!$R1 508
14 TraesCS3B01G003400 chr7A 647148192 647148699 507 False 856.000000 856 97.053000 3658 4166 1 chr7A.!!$F1 508
15 TraesCS3B01G003400 chr6D 354364137 354364645 508 True 769.000000 769 93.957000 3657 4166 1 chr6D.!!$R2 509
16 TraesCS3B01G003400 chr4B 653429011 653431838 2827 True 295.000000 455 78.746500 981 2727 2 chr4B.!!$R3 1746

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
136 137 0.033228 CCGCCTCAGATGAGATCCAC 59.967 60.0 11.44 0.0 44.74 4.02 F
385 387 0.035739 AATGGCGAGGTACAAACGGT 59.964 50.0 0.00 0.0 0.00 4.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2629 6607 4.039124 AGCCAACGTTCCAAAATGAAAGAT 59.961 37.50 0.0 0.0 0.0 2.40 R
3533 8109 5.821516 TGTATTTTGTTGGGGCTATAACG 57.178 39.13 0.0 0.0 0.0 3.18 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
23 24 4.082523 CACCACCGCCGTCCATCT 62.083 66.667 0.00 0.00 0.00 2.90
24 25 3.771160 ACCACCGCCGTCCATCTC 61.771 66.667 0.00 0.00 0.00 2.75
25 26 3.770040 CCACCGCCGTCCATCTCA 61.770 66.667 0.00 0.00 0.00 3.27
26 27 2.202797 CACCGCCGTCCATCTCAG 60.203 66.667 0.00 0.00 0.00 3.35
27 28 3.461773 ACCGCCGTCCATCTCAGG 61.462 66.667 0.00 0.00 0.00 3.86
28 29 4.227134 CCGCCGTCCATCTCAGGG 62.227 72.222 0.00 0.00 0.00 4.45
29 30 4.899239 CGCCGTCCATCTCAGGGC 62.899 72.222 0.00 0.00 40.73 5.19
30 31 4.554036 GCCGTCCATCTCAGGGCC 62.554 72.222 0.00 0.00 38.62 5.80
31 32 4.227134 CCGTCCATCTCAGGGCCG 62.227 72.222 0.00 0.00 0.00 6.13
32 33 4.899239 CGTCCATCTCAGGGCCGC 62.899 72.222 0.00 0.00 0.00 6.53
33 34 4.554036 GTCCATCTCAGGGCCGCC 62.554 72.222 0.00 0.00 0.00 6.13
59 60 3.948719 GGTTCAGCCACCACCGGA 61.949 66.667 9.46 0.00 36.73 5.14
60 61 2.668550 GTTCAGCCACCACCGGAC 60.669 66.667 9.46 0.00 0.00 4.79
61 62 4.308458 TTCAGCCACCACCGGACG 62.308 66.667 9.46 0.00 0.00 4.79
105 106 3.744719 CCTTCGGGTCGCACGAGA 61.745 66.667 4.51 0.00 41.81 4.04
106 107 2.202492 CTTCGGGTCGCACGAGAG 60.202 66.667 4.51 2.95 41.81 3.20
107 108 3.685214 CTTCGGGTCGCACGAGAGG 62.685 68.421 4.51 0.00 41.81 3.69
108 109 4.710167 TCGGGTCGCACGAGAGGA 62.710 66.667 0.01 0.00 35.12 3.71
109 110 4.180946 CGGGTCGCACGAGAGGAG 62.181 72.222 0.00 0.00 0.00 3.69
110 111 4.500116 GGGTCGCACGAGAGGAGC 62.500 72.222 0.00 0.00 0.00 4.70
111 112 4.500116 GGTCGCACGAGAGGAGCC 62.500 72.222 0.00 0.00 33.48 4.70
112 113 4.838486 GTCGCACGAGAGGAGCCG 62.838 72.222 0.00 0.00 33.48 5.52
129 130 4.166888 GCCTGCCGCCTCAGATGA 62.167 66.667 1.76 0.00 36.19 2.92
130 131 2.108566 CCTGCCGCCTCAGATGAG 59.891 66.667 2.72 2.72 41.71 2.90
131 132 2.429767 CCTGCCGCCTCAGATGAGA 61.430 63.158 11.44 0.00 44.74 3.27
132 133 1.747145 CTGCCGCCTCAGATGAGAT 59.253 57.895 11.44 0.00 44.74 2.75
133 134 0.319727 CTGCCGCCTCAGATGAGATC 60.320 60.000 11.44 2.31 44.74 2.75
134 135 1.005156 GCCGCCTCAGATGAGATCC 60.005 63.158 11.44 0.00 44.74 3.36
135 136 1.752358 GCCGCCTCAGATGAGATCCA 61.752 60.000 11.44 0.00 44.74 3.41
136 137 0.033228 CCGCCTCAGATGAGATCCAC 59.967 60.000 11.44 0.00 44.74 4.02
137 138 0.749049 CGCCTCAGATGAGATCCACA 59.251 55.000 11.44 0.00 44.74 4.17
138 139 1.343789 CGCCTCAGATGAGATCCACAT 59.656 52.381 11.44 3.17 44.74 3.21
139 140 2.609984 CGCCTCAGATGAGATCCACATC 60.610 54.545 17.43 17.43 44.74 3.06
140 141 2.367894 GCCTCAGATGAGATCCACATCA 59.632 50.000 23.29 8.57 44.74 3.07
141 142 3.008157 GCCTCAGATGAGATCCACATCAT 59.992 47.826 23.29 12.31 44.74 2.45
146 147 3.672808 GATGAGATCCACATCATCCACC 58.327 50.000 19.17 0.00 43.92 4.61
147 148 1.770658 TGAGATCCACATCATCCACCC 59.229 52.381 0.00 0.00 0.00 4.61
148 149 0.761187 AGATCCACATCATCCACCCG 59.239 55.000 0.00 0.00 0.00 5.28
149 150 0.886490 GATCCACATCATCCACCCGC 60.886 60.000 0.00 0.00 0.00 6.13
150 151 2.665008 ATCCACATCATCCACCCGCG 62.665 60.000 0.00 0.00 0.00 6.46
151 152 2.186644 CACATCATCCACCCGCGA 59.813 61.111 8.23 0.00 0.00 5.87
152 153 2.173669 CACATCATCCACCCGCGAC 61.174 63.158 8.23 0.00 0.00 5.19
153 154 2.588877 CATCATCCACCCGCGACC 60.589 66.667 8.23 0.00 0.00 4.79
154 155 3.080765 ATCATCCACCCGCGACCA 61.081 61.111 8.23 0.00 0.00 4.02
155 156 3.385749 ATCATCCACCCGCGACCAC 62.386 63.158 8.23 0.00 0.00 4.16
175 176 2.436115 GGCAGACCCAACGTAGCC 60.436 66.667 0.00 0.00 38.24 3.93
176 177 2.345991 GCAGACCCAACGTAGCCA 59.654 61.111 0.00 0.00 0.00 4.75
177 178 2.033194 GCAGACCCAACGTAGCCAC 61.033 63.158 0.00 0.00 0.00 5.01
178 179 1.375523 CAGACCCAACGTAGCCACC 60.376 63.158 0.00 0.00 0.00 4.61
179 180 1.839747 AGACCCAACGTAGCCACCA 60.840 57.895 0.00 0.00 0.00 4.17
180 181 1.670083 GACCCAACGTAGCCACCAC 60.670 63.158 0.00 0.00 0.00 4.16
181 182 2.359478 CCCAACGTAGCCACCACC 60.359 66.667 0.00 0.00 0.00 4.61
182 183 2.747686 CCAACGTAGCCACCACCT 59.252 61.111 0.00 0.00 0.00 4.00
183 184 1.375523 CCAACGTAGCCACCACCTC 60.376 63.158 0.00 0.00 0.00 3.85
184 185 1.736645 CAACGTAGCCACCACCTCG 60.737 63.158 0.00 0.00 0.00 4.63
185 186 3.584868 AACGTAGCCACCACCTCGC 62.585 63.158 0.00 0.00 0.00 5.03
187 188 3.755628 GTAGCCACCACCTCGCGA 61.756 66.667 9.26 9.26 0.00 5.87
188 189 3.755628 TAGCCACCACCTCGCGAC 61.756 66.667 3.71 0.00 0.00 5.19
191 192 4.293648 CCACCACCTCGCGACACA 62.294 66.667 3.71 0.00 0.00 3.72
192 193 3.036084 CACCACCTCGCGACACAC 61.036 66.667 3.71 0.00 0.00 3.82
193 194 3.533105 ACCACCTCGCGACACACA 61.533 61.111 3.71 0.00 0.00 3.72
194 195 2.734723 CCACCTCGCGACACACAG 60.735 66.667 3.71 0.00 0.00 3.66
195 196 2.734723 CACCTCGCGACACACAGG 60.735 66.667 3.71 6.48 0.00 4.00
196 197 4.664677 ACCTCGCGACACACAGGC 62.665 66.667 3.71 0.00 0.00 4.85
262 263 4.849310 GCCGCCGAAGCCCACATA 62.849 66.667 0.00 0.00 34.57 2.29
263 264 2.895372 CCGCCGAAGCCCACATAC 60.895 66.667 0.00 0.00 34.57 2.39
264 265 3.261951 CGCCGAAGCCCACATACG 61.262 66.667 0.00 0.00 34.57 3.06
265 266 2.125269 GCCGAAGCCCACATACGT 60.125 61.111 0.00 0.00 0.00 3.57
266 267 2.171725 GCCGAAGCCCACATACGTC 61.172 63.158 0.00 0.00 0.00 4.34
267 268 1.520787 CCGAAGCCCACATACGTCC 60.521 63.158 0.00 0.00 0.00 4.79
268 269 1.876714 CGAAGCCCACATACGTCCG 60.877 63.158 0.00 0.00 0.00 4.79
269 270 1.520787 GAAGCCCACATACGTCCGG 60.521 63.158 0.00 0.00 0.00 5.14
270 271 3.675619 AAGCCCACATACGTCCGGC 62.676 63.158 0.00 0.00 37.71 6.13
273 274 4.508128 CCACATACGTCCGGCGCT 62.508 66.667 16.48 7.98 46.11 5.92
274 275 2.954868 CACATACGTCCGGCGCTC 60.955 66.667 16.48 0.00 46.11 5.03
275 276 4.203076 ACATACGTCCGGCGCTCC 62.203 66.667 16.48 0.00 46.11 4.70
276 277 3.900892 CATACGTCCGGCGCTCCT 61.901 66.667 16.48 2.06 46.11 3.69
277 278 3.900892 ATACGTCCGGCGCTCCTG 61.901 66.667 16.48 0.00 46.11 3.86
279 280 3.974835 TACGTCCGGCGCTCCTGTA 62.975 63.158 16.48 1.51 46.11 2.74
280 281 4.849329 CGTCCGGCGCTCCTGTAC 62.849 72.222 7.64 0.00 0.00 2.90
281 282 4.509737 GTCCGGCGCTCCTGTACC 62.510 72.222 7.64 0.00 0.00 3.34
296 297 6.585695 TCCTGTACCGATCCATATTAGTTC 57.414 41.667 0.00 0.00 0.00 3.01
298 299 6.433404 TCCTGTACCGATCCATATTAGTTCTC 59.567 42.308 0.00 0.00 0.00 2.87
308 310 5.105106 TCCATATTAGTTCTCGCTCAAACCA 60.105 40.000 0.00 0.00 0.00 3.67
312 314 2.851195 AGTTCTCGCTCAAACCAATGT 58.149 42.857 0.00 0.00 0.00 2.71
313 315 3.214328 AGTTCTCGCTCAAACCAATGTT 58.786 40.909 0.00 0.00 35.82 2.71
321 323 2.788786 CTCAAACCAATGTTGCGACAAC 59.211 45.455 11.67 13.54 39.66 3.32
334 336 4.577834 TGCGACAACTAATATGGATCGA 57.422 40.909 0.00 0.00 0.00 3.59
343 345 7.289317 ACAACTAATATGGATCGAAGGGAGTAA 59.711 37.037 0.00 0.00 0.00 2.24
385 387 0.035739 AATGGCGAGGTACAAACGGT 59.964 50.000 0.00 0.00 0.00 4.83
457 499 5.834169 TGTATCGATCGTGCTTAACCAATA 58.166 37.500 15.94 0.00 0.00 1.90
3649 8227 7.095774 GCTATCACTAATTTGTATGGTACGGTG 60.096 40.741 0.00 0.00 0.00 4.94
3650 8228 6.040209 TCACTAATTTGTATGGTACGGTGT 57.960 37.500 0.00 0.00 0.00 4.16
3651 8229 7.167924 TCACTAATTTGTATGGTACGGTGTA 57.832 36.000 0.00 0.00 0.00 2.90
3652 8230 7.259882 TCACTAATTTGTATGGTACGGTGTAG 58.740 38.462 0.00 0.00 0.00 2.74
3653 8231 6.019318 CACTAATTTGTATGGTACGGTGTAGC 60.019 42.308 0.00 0.00 0.00 3.58
3654 8232 3.957591 TTTGTATGGTACGGTGTAGCA 57.042 42.857 10.80 10.80 0.00 3.49
3655 8233 3.513680 TTGTATGGTACGGTGTAGCAG 57.486 47.619 13.42 0.00 0.00 4.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 4.082523 AGATGGACGGCGGTGGTG 62.083 66.667 13.24 0.00 0.00 4.17
7 8 3.771160 GAGATGGACGGCGGTGGT 61.771 66.667 13.24 0.00 0.00 4.16
8 9 3.723235 CTGAGATGGACGGCGGTGG 62.723 68.421 13.24 0.00 0.00 4.61
9 10 2.202797 CTGAGATGGACGGCGGTG 60.203 66.667 13.24 0.00 0.00 4.94
10 11 3.461773 CCTGAGATGGACGGCGGT 61.462 66.667 13.24 0.00 0.00 5.68
11 12 4.227134 CCCTGAGATGGACGGCGG 62.227 72.222 13.24 0.00 0.00 6.13
12 13 4.899239 GCCCTGAGATGGACGGCG 62.899 72.222 4.80 4.80 0.00 6.46
13 14 4.554036 GGCCCTGAGATGGACGGC 62.554 72.222 0.00 0.00 38.96 5.68
16 17 4.554036 GGCGGCCCTGAGATGGAC 62.554 72.222 8.12 0.00 0.00 4.02
42 43 3.948719 TCCGGTGGTGGCTGAACC 61.949 66.667 0.00 0.00 40.94 3.62
43 44 2.668550 GTCCGGTGGTGGCTGAAC 60.669 66.667 0.00 0.00 0.00 3.18
44 45 4.308458 CGTCCGGTGGTGGCTGAA 62.308 66.667 0.00 0.00 0.00 3.02
89 90 2.202492 CTCTCGTGCGACCCGAAG 60.202 66.667 0.00 0.00 33.34 3.79
90 91 3.744719 CCTCTCGTGCGACCCGAA 61.745 66.667 0.00 0.00 33.34 4.30
91 92 4.710167 TCCTCTCGTGCGACCCGA 62.710 66.667 0.00 0.00 0.00 5.14
92 93 4.180946 CTCCTCTCGTGCGACCCG 62.181 72.222 0.00 0.00 0.00 5.28
93 94 4.500116 GCTCCTCTCGTGCGACCC 62.500 72.222 0.00 0.00 0.00 4.46
94 95 4.500116 GGCTCCTCTCGTGCGACC 62.500 72.222 0.00 0.00 0.00 4.79
95 96 4.838486 CGGCTCCTCTCGTGCGAC 62.838 72.222 0.00 0.00 0.00 5.19
99 100 4.504916 CAGGCGGCTCCTCTCGTG 62.505 72.222 9.32 0.00 45.52 4.35
112 113 4.166888 TCATCTGAGGCGGCAGGC 62.167 66.667 13.08 1.08 44.19 4.85
113 114 1.756408 ATCTCATCTGAGGCGGCAGG 61.756 60.000 13.08 0.06 42.30 4.85
114 115 0.319727 GATCTCATCTGAGGCGGCAG 60.320 60.000 13.08 0.00 42.30 4.85
115 116 1.744639 GATCTCATCTGAGGCGGCA 59.255 57.895 13.08 0.00 42.30 5.69
116 117 1.005156 GGATCTCATCTGAGGCGGC 60.005 63.158 0.00 0.00 42.30 6.53
117 118 0.033228 GTGGATCTCATCTGAGGCGG 59.967 60.000 7.33 0.00 42.30 6.13
118 119 0.749049 TGTGGATCTCATCTGAGGCG 59.251 55.000 7.33 0.00 42.30 5.52
119 120 2.367894 TGATGTGGATCTCATCTGAGGC 59.632 50.000 22.00 0.84 42.30 4.70
120 121 4.322877 GGATGATGTGGATCTCATCTGAGG 60.323 50.000 22.00 0.00 44.62 3.86
121 122 4.283722 TGGATGATGTGGATCTCATCTGAG 59.716 45.833 22.00 0.56 44.62 3.35
122 123 4.040095 GTGGATGATGTGGATCTCATCTGA 59.960 45.833 22.00 10.87 44.62 3.27
123 124 4.316645 GTGGATGATGTGGATCTCATCTG 58.683 47.826 22.00 0.00 44.62 2.90
124 125 3.327172 GGTGGATGATGTGGATCTCATCT 59.673 47.826 22.00 13.27 44.62 2.90
125 126 3.558746 GGGTGGATGATGTGGATCTCATC 60.559 52.174 17.87 17.87 44.54 2.92
126 127 2.374504 GGGTGGATGATGTGGATCTCAT 59.625 50.000 0.00 0.00 34.86 2.90
127 128 1.770658 GGGTGGATGATGTGGATCTCA 59.229 52.381 0.00 0.00 0.00 3.27
128 129 1.270518 CGGGTGGATGATGTGGATCTC 60.271 57.143 0.00 0.00 0.00 2.75
129 130 0.761187 CGGGTGGATGATGTGGATCT 59.239 55.000 0.00 0.00 0.00 2.75
130 131 0.886490 GCGGGTGGATGATGTGGATC 60.886 60.000 0.00 0.00 0.00 3.36
131 132 1.149174 GCGGGTGGATGATGTGGAT 59.851 57.895 0.00 0.00 0.00 3.41
132 133 2.589540 GCGGGTGGATGATGTGGA 59.410 61.111 0.00 0.00 0.00 4.02
133 134 2.896854 CGCGGGTGGATGATGTGG 60.897 66.667 0.00 0.00 0.00 4.17
134 135 2.173669 GTCGCGGGTGGATGATGTG 61.174 63.158 6.13 0.00 0.00 3.21
135 136 2.186903 GTCGCGGGTGGATGATGT 59.813 61.111 6.13 0.00 0.00 3.06
136 137 2.588877 GGTCGCGGGTGGATGATG 60.589 66.667 6.13 0.00 0.00 3.07
137 138 3.080765 TGGTCGCGGGTGGATGAT 61.081 61.111 6.13 0.00 0.00 2.45
138 139 4.077184 GTGGTCGCGGGTGGATGA 62.077 66.667 6.13 0.00 0.00 2.92
158 159 2.436115 GGCTACGTTGGGTCTGCC 60.436 66.667 0.00 0.00 39.87 4.85
159 160 2.033194 GTGGCTACGTTGGGTCTGC 61.033 63.158 0.00 0.00 0.00 4.26
160 161 1.375523 GGTGGCTACGTTGGGTCTG 60.376 63.158 0.00 0.00 0.00 3.51
161 162 1.839747 TGGTGGCTACGTTGGGTCT 60.840 57.895 0.00 0.00 0.00 3.85
162 163 1.670083 GTGGTGGCTACGTTGGGTC 60.670 63.158 0.00 0.00 0.00 4.46
163 164 2.428622 GTGGTGGCTACGTTGGGT 59.571 61.111 0.00 0.00 0.00 4.51
164 165 2.359478 GGTGGTGGCTACGTTGGG 60.359 66.667 0.00 0.00 0.00 4.12
165 166 1.375523 GAGGTGGTGGCTACGTTGG 60.376 63.158 0.00 0.00 0.00 3.77
166 167 1.736645 CGAGGTGGTGGCTACGTTG 60.737 63.158 0.00 0.00 0.00 4.10
167 168 2.654877 CGAGGTGGTGGCTACGTT 59.345 61.111 0.00 0.00 0.00 3.99
168 169 4.065281 GCGAGGTGGTGGCTACGT 62.065 66.667 0.00 0.00 0.00 3.57
170 171 3.755628 TCGCGAGGTGGTGGCTAC 61.756 66.667 3.71 0.00 0.00 3.58
171 172 3.755628 GTCGCGAGGTGGTGGCTA 61.756 66.667 10.24 0.00 0.00 3.93
174 175 4.293648 TGTGTCGCGAGGTGGTGG 62.294 66.667 10.24 0.00 0.00 4.61
175 176 3.036084 GTGTGTCGCGAGGTGGTG 61.036 66.667 10.24 0.00 0.00 4.17
176 177 3.499929 CTGTGTGTCGCGAGGTGGT 62.500 63.158 10.24 0.00 0.00 4.16
177 178 2.734723 CTGTGTGTCGCGAGGTGG 60.735 66.667 10.24 0.00 0.00 4.61
178 179 2.734723 CCTGTGTGTCGCGAGGTG 60.735 66.667 10.24 0.00 0.00 4.00
179 180 4.664677 GCCTGTGTGTCGCGAGGT 62.665 66.667 10.24 0.00 0.00 3.85
245 246 4.849310 TATGTGGGCTTCGGCGGC 62.849 66.667 7.21 2.69 42.91 6.53
246 247 2.895372 GTATGTGGGCTTCGGCGG 60.895 66.667 7.21 0.00 42.91 6.13
247 248 3.261951 CGTATGTGGGCTTCGGCG 61.262 66.667 0.00 0.00 42.91 6.46
248 249 2.125269 ACGTATGTGGGCTTCGGC 60.125 61.111 0.00 0.00 40.88 5.54
249 250 1.520787 GGACGTATGTGGGCTTCGG 60.521 63.158 0.00 0.00 0.00 4.30
250 251 1.876714 CGGACGTATGTGGGCTTCG 60.877 63.158 0.00 0.00 0.00 3.79
251 252 1.520787 CCGGACGTATGTGGGCTTC 60.521 63.158 0.00 0.00 0.00 3.86
252 253 2.582436 CCGGACGTATGTGGGCTT 59.418 61.111 0.00 0.00 0.00 4.35
253 254 4.157120 GCCGGACGTATGTGGGCT 62.157 66.667 5.05 0.00 39.84 5.19
256 257 4.508128 AGCGCCGGACGTATGTGG 62.508 66.667 5.05 0.00 46.11 4.17
257 258 2.954868 GAGCGCCGGACGTATGTG 60.955 66.667 5.05 0.00 46.11 3.21
258 259 4.203076 GGAGCGCCGGACGTATGT 62.203 66.667 5.05 0.00 46.11 2.29
259 260 3.900892 AGGAGCGCCGGACGTATG 61.901 66.667 5.05 0.00 46.11 2.39
260 261 3.900892 CAGGAGCGCCGGACGTAT 61.901 66.667 5.05 1.46 46.11 3.06
261 262 3.974835 TACAGGAGCGCCGGACGTA 62.975 63.158 14.42 5.40 46.11 3.57
264 265 4.509737 GGTACAGGAGCGCCGGAC 62.510 72.222 14.42 9.27 39.96 4.79
271 272 3.963428 AATATGGATCGGTACAGGAGC 57.037 47.619 0.00 0.00 0.00 4.70
272 273 6.434652 AGAACTAATATGGATCGGTACAGGAG 59.565 42.308 0.00 0.00 0.00 3.69
273 274 6.312529 AGAACTAATATGGATCGGTACAGGA 58.687 40.000 0.00 0.00 0.00 3.86
274 275 6.591750 AGAACTAATATGGATCGGTACAGG 57.408 41.667 0.00 0.00 0.00 4.00
275 276 6.315551 CGAGAACTAATATGGATCGGTACAG 58.684 44.000 0.00 0.00 0.00 2.74
276 277 5.335426 GCGAGAACTAATATGGATCGGTACA 60.335 44.000 0.00 0.00 0.00 2.90
277 278 5.094134 GCGAGAACTAATATGGATCGGTAC 58.906 45.833 0.00 0.00 0.00 3.34
278 279 5.008331 AGCGAGAACTAATATGGATCGGTA 58.992 41.667 0.00 0.00 37.61 4.02
279 280 3.827302 AGCGAGAACTAATATGGATCGGT 59.173 43.478 0.00 0.00 34.94 4.69
280 281 4.082733 TGAGCGAGAACTAATATGGATCGG 60.083 45.833 0.00 0.00 0.00 4.18
281 282 5.048153 TGAGCGAGAACTAATATGGATCG 57.952 43.478 0.00 0.00 0.00 3.69
296 297 1.689959 GCAACATTGGTTTGAGCGAG 58.310 50.000 0.00 0.00 34.21 5.03
298 299 0.040514 TCGCAACATTGGTTTGAGCG 60.041 50.000 0.00 0.00 41.95 5.03
308 310 6.292865 CGATCCATATTAGTTGTCGCAACATT 60.293 38.462 19.82 9.79 34.73 2.71
312 314 4.939271 TCGATCCATATTAGTTGTCGCAA 58.061 39.130 0.00 0.00 0.00 4.85
313 315 4.577834 TCGATCCATATTAGTTGTCGCA 57.422 40.909 0.00 0.00 0.00 5.10
321 323 7.469537 ACTTACTCCCTTCGATCCATATTAG 57.530 40.000 0.00 0.00 0.00 1.73
334 336 6.195600 TCACCACAATAAACTTACTCCCTT 57.804 37.500 0.00 0.00 0.00 3.95
343 345 4.887071 TGTTGCTCTTCACCACAATAAACT 59.113 37.500 0.00 0.00 0.00 2.66
385 387 0.846427 AGTGGGAGCTGGGATTTCCA 60.846 55.000 0.00 0.00 44.79 3.53
457 499 2.573869 CAGCGTGGACGTGGATCT 59.426 61.111 0.00 0.00 42.22 2.75
2629 6607 4.039124 AGCCAACGTTCCAAAATGAAAGAT 59.961 37.500 0.00 0.00 0.00 2.40
3533 8109 5.821516 TGTATTTTGTTGGGGCTATAACG 57.178 39.130 0.00 0.00 0.00 3.18
3649 8227 3.851128 GGGGTCGGGAGCTGCTAC 61.851 72.222 2.38 2.38 0.00 3.58


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

AutoCloner maintained by Alex Coulton.