Multiple sequence alignment - TraesCS7D01G107800

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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 TraesCS7D01G107800 chr7D 100.000 2278 0 0 638 2915 64736590 64734313 0.000000e+00 4207.0
1 TraesCS7D01G107800 chr7D 81.225 1273 186 34 674 1925 64700917 64699677 0.000000e+00 977.0
2 TraesCS7D01G107800 chr7D 77.628 666 139 8 1236 1899 64467519 64466862 2.110000e-106 396.0
3 TraesCS7D01G107800 chr7D 100.000 212 0 0 1 212 64737227 64737016 2.720000e-105 392.0
4 TraesCS7D01G107800 chr7D 89.121 239 18 7 638 872 64468142 64467908 1.020000e-74 291.0
5 TraesCS7D01G107800 chr7D 78.979 333 58 8 638 962 65776826 65777154 1.760000e-52 217.0
6 TraesCS7D01G107800 chr7D 88.000 75 3 2 2685 2753 64704167 64704241 1.860000e-12 84.2
7 TraesCS7D01G107800 chr7B 95.492 1686 49 7 638 2306 6374960 6373285 0.000000e+00 2667.0
8 TraesCS7D01G107800 chr7B 79.572 1263 186 40 674 1925 6181649 6180448 0.000000e+00 837.0
9 TraesCS7D01G107800 chr7B 92.405 237 14 3 638 872 6034670 6034436 4.650000e-88 335.0
10 TraesCS7D01G107800 chr7B 95.652 161 1 1 2755 2915 6372815 6372661 1.340000e-63 254.0
11 TraesCS7D01G107800 chr7B 88.500 200 22 1 680 878 7541561 7541760 1.040000e-59 241.0
12 TraesCS7D01G107800 chr7B 96.154 130 5 0 2336 2465 6372944 6372815 2.280000e-51 213.0
13 TraesCS7D01G107800 chr7B 84.828 145 13 8 1775 1918 7544446 7544582 1.410000e-28 137.0
14 TraesCS7D01G107800 chr7B 82.524 103 12 6 2372 2473 6234052 6234149 5.180000e-13 86.1
15 TraesCS7D01G107800 chr7B 86.667 75 3 3 2685 2753 6234605 6234678 3.120000e-10 76.8
16 TraesCS7D01G107800 chr7A 95.471 1678 62 5 638 2301 68901871 68900194 0.000000e+00 2665.0
17 TraesCS7D01G107800 chr7A 83.452 562 79 10 1377 1925 68862410 68861850 7.210000e-141 510.0
18 TraesCS7D01G107800 chr7A 93.066 274 4 5 2409 2668 68890707 68890435 1.270000e-103 387.0
19 TraesCS7D01G107800 chr7A 98.140 215 4 0 2701 2915 68889721 68889507 2.740000e-100 375.0
20 TraesCS7D01G107800 chr7A 90.123 243 16 8 638 876 68320755 68320517 2.820000e-80 309.0
21 TraesCS7D01G107800 chr7A 76.325 604 117 16 790 1387 68863455 68862872 1.700000e-77 300.0
22 TraesCS7D01G107800 chr7A 76.667 210 49 0 1236 1445 68320121 68319912 1.840000e-22 117.0
23 TraesCS7D01G107800 chr7A 87.209 86 5 1 2302 2381 68890785 68890700 3.090000e-15 93.5
24 TraesCS7D01G107800 chr7A 88.000 75 3 3 2685 2753 68880583 68880657 1.860000e-12 84.2
25 TraesCS7D01G107800 chr7A 100.000 30 0 0 2444 2473 68880098 68880127 4.060000e-04 56.5
26 TraesCS7D01G107800 chr6B 76.495 1221 222 41 638 1843 43144853 43146023 3.210000e-169 604.0
27 TraesCS7D01G107800 chr6B 86.957 230 22 6 638 863 42860658 42860883 4.820000e-63 252.0
28 TraesCS7D01G107800 chrUn 76.965 1094 215 26 760 1843 93879956 93881022 9.000000e-165 590.0
29 TraesCS7D01G107800 chrUn 79.775 534 94 10 1314 1843 93939530 93940053 2.740000e-100 375.0
30 TraesCS7D01G107800 chr6A 75.630 1231 221 49 640 1843 24705531 24706709 3.310000e-149 538.0
31 TraesCS7D01G107800 chr2D 79.259 135 17 7 2416 2542 614848267 614848398 1.860000e-12 84.2
32 TraesCS7D01G107800 chr2B 79.259 135 17 7 2416 2542 749233765 749233896 1.860000e-12 84.2


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 TraesCS7D01G107800 chr7D 64734313 64737227 2914 True 2299.500000 4207 100.0000 1 2915 2 chr7D.!!$R3 2914
1 TraesCS7D01G107800 chr7D 64699677 64700917 1240 True 977.000000 977 81.2250 674 1925 1 chr7D.!!$R1 1251
2 TraesCS7D01G107800 chr7D 64466862 64468142 1280 True 343.500000 396 83.3745 638 1899 2 chr7D.!!$R2 1261
3 TraesCS7D01G107800 chr7B 6372661 6374960 2299 True 1044.666667 2667 95.7660 638 2915 3 chr7B.!!$R3 2277
4 TraesCS7D01G107800 chr7B 6180448 6181649 1201 True 837.000000 837 79.5720 674 1925 1 chr7B.!!$R2 1251
5 TraesCS7D01G107800 chr7A 68900194 68901871 1677 True 2665.000000 2665 95.4710 638 2301 1 chr7A.!!$R1 1663
6 TraesCS7D01G107800 chr7A 68861850 68863455 1605 True 405.000000 510 79.8885 790 1925 2 chr7A.!!$R3 1135
7 TraesCS7D01G107800 chr7A 68889507 68890785 1278 True 285.166667 387 92.8050 2302 2915 3 chr7A.!!$R4 613
8 TraesCS7D01G107800 chr7A 68319912 68320755 843 True 213.000000 309 83.3950 638 1445 2 chr7A.!!$R2 807
9 TraesCS7D01G107800 chr6B 43144853 43146023 1170 False 604.000000 604 76.4950 638 1843 1 chr6B.!!$F2 1205
10 TraesCS7D01G107800 chrUn 93879956 93881022 1066 False 590.000000 590 76.9650 760 1843 1 chrUn.!!$F1 1083
11 TraesCS7D01G107800 chrUn 93939530 93940053 523 False 375.000000 375 79.7750 1314 1843 1 chrUn.!!$F2 529
12 TraesCS7D01G107800 chr6A 24705531 24706709 1178 False 538.000000 538 75.6300 640 1843 1 chr6A.!!$F1 1203

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
138 139 0.035343 GCCTTAGACGGGCCTTCTTT 60.035 55.0 18.52 0.0 43.49 2.52 F
145 146 0.036294 ACGGGCCTTCTTTGTAGAGC 60.036 55.0 0.84 0.0 0.00 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1191 1363 0.032952 ACTGGCTAACGAAGAACGCA 59.967 50.000 0.0 0.0 46.94 5.24 R
2087 2781 1.133823 ACTTGCCAGACCATGTTCACA 60.134 47.619 0.0 0.0 0.00 3.58 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
38 39 5.880054 AAAAAGATGATGAACAGTACCGG 57.120 39.130 0.00 0.00 0.00 5.28
39 40 4.553330 AAAGATGATGAACAGTACCGGT 57.447 40.909 13.98 13.98 0.00 5.28
40 41 4.553330 AAGATGATGAACAGTACCGGTT 57.447 40.909 15.04 0.00 0.00 4.44
41 42 4.553330 AGATGATGAACAGTACCGGTTT 57.447 40.909 15.04 0.00 0.00 3.27
42 43 4.504858 AGATGATGAACAGTACCGGTTTC 58.495 43.478 15.04 11.51 0.00 2.78
43 44 4.223032 AGATGATGAACAGTACCGGTTTCT 59.777 41.667 15.04 9.53 0.00 2.52
44 45 3.921677 TGATGAACAGTACCGGTTTCTC 58.078 45.455 15.04 10.25 0.00 2.87
45 46 3.576982 TGATGAACAGTACCGGTTTCTCT 59.423 43.478 15.04 3.76 0.00 3.10
46 47 4.039973 TGATGAACAGTACCGGTTTCTCTT 59.960 41.667 15.04 6.04 0.00 2.85
47 48 4.411256 TGAACAGTACCGGTTTCTCTTT 57.589 40.909 15.04 7.42 0.00 2.52
48 49 4.773013 TGAACAGTACCGGTTTCTCTTTT 58.227 39.130 15.04 6.16 0.00 2.27
49 50 5.187687 TGAACAGTACCGGTTTCTCTTTTT 58.812 37.500 15.04 2.66 0.00 1.94
73 74 5.859205 TTTTAGGGGTAGTACCGATTCTC 57.141 43.478 13.27 0.00 39.83 2.87
74 75 1.978454 AGGGGTAGTACCGATTCTCG 58.022 55.000 13.27 0.00 39.83 4.04
92 93 4.577246 GAGGCCGGCGCTCTACAG 62.577 72.222 27.75 0.00 34.44 2.74
96 97 4.514577 CCGGCGCTCTACAGTGGG 62.515 72.222 7.64 0.00 0.00 4.61
98 99 3.775654 GGCGCTCTACAGTGGGCT 61.776 66.667 7.64 0.00 43.81 5.19
99 100 2.202810 GCGCTCTACAGTGGGCTC 60.203 66.667 0.00 0.00 41.98 4.70
100 101 3.006756 GCGCTCTACAGTGGGCTCA 62.007 63.158 0.00 0.00 41.98 4.26
101 102 1.819229 CGCTCTACAGTGGGCTCAT 59.181 57.895 0.00 0.00 0.00 2.90
102 103 0.249238 CGCTCTACAGTGGGCTCATC 60.249 60.000 0.00 0.00 0.00 2.92
103 104 0.105778 GCTCTACAGTGGGCTCATCC 59.894 60.000 0.00 0.00 0.00 3.51
114 115 2.629336 GGCTCATCCCTCGAAAAGAT 57.371 50.000 0.00 0.00 0.00 2.40
115 116 2.488952 GGCTCATCCCTCGAAAAGATC 58.511 52.381 0.00 0.00 0.00 2.75
116 117 2.103941 GGCTCATCCCTCGAAAAGATCT 59.896 50.000 0.00 0.00 0.00 2.75
117 118 3.322254 GGCTCATCCCTCGAAAAGATCTA 59.678 47.826 0.00 0.00 0.00 1.98
118 119 4.555262 GCTCATCCCTCGAAAAGATCTAG 58.445 47.826 0.00 0.00 0.00 2.43
119 120 4.560513 GCTCATCCCTCGAAAAGATCTAGG 60.561 50.000 0.00 0.00 40.04 3.02
120 121 3.322254 TCATCCCTCGAAAAGATCTAGGC 59.678 47.826 0.00 0.00 39.22 3.93
121 122 2.040178 TCCCTCGAAAAGATCTAGGCC 58.960 52.381 0.00 0.00 39.22 5.19
122 123 2.043227 CCCTCGAAAAGATCTAGGCCT 58.957 52.381 11.78 11.78 39.22 5.19
123 124 2.436173 CCCTCGAAAAGATCTAGGCCTT 59.564 50.000 12.58 0.00 39.22 4.35
124 125 3.641906 CCCTCGAAAAGATCTAGGCCTTA 59.358 47.826 12.58 0.00 39.22 2.69
125 126 4.262249 CCCTCGAAAAGATCTAGGCCTTAG 60.262 50.000 12.58 6.74 39.22 2.18
126 127 4.585162 CCTCGAAAAGATCTAGGCCTTAGA 59.415 45.833 12.58 12.53 42.44 2.10
127 128 5.508320 CCTCGAAAAGATCTAGGCCTTAGAC 60.508 48.000 12.58 0.45 41.10 2.59
128 129 4.036498 TCGAAAAGATCTAGGCCTTAGACG 59.964 45.833 12.58 10.31 41.10 4.18
129 130 4.623002 GAAAAGATCTAGGCCTTAGACGG 58.377 47.826 12.58 0.00 41.10 4.79
130 131 2.296073 AGATCTAGGCCTTAGACGGG 57.704 55.000 12.58 0.00 41.10 5.28
136 137 3.310652 GCCTTAGACGGGCCTTCT 58.689 61.111 17.43 17.43 43.49 2.85
137 138 1.602771 GCCTTAGACGGGCCTTCTT 59.397 57.895 18.52 2.71 43.49 2.52
138 139 0.035343 GCCTTAGACGGGCCTTCTTT 60.035 55.000 18.52 0.00 43.49 2.52
139 140 1.739067 CCTTAGACGGGCCTTCTTTG 58.261 55.000 18.52 10.80 0.00 2.77
140 141 1.003233 CCTTAGACGGGCCTTCTTTGT 59.997 52.381 18.52 0.00 0.00 2.83
141 142 2.235402 CCTTAGACGGGCCTTCTTTGTA 59.765 50.000 18.52 0.00 0.00 2.41
142 143 3.522553 CTTAGACGGGCCTTCTTTGTAG 58.477 50.000 18.52 7.21 0.00 2.74
143 144 1.640917 AGACGGGCCTTCTTTGTAGA 58.359 50.000 6.74 0.00 0.00 2.59
144 145 1.550976 AGACGGGCCTTCTTTGTAGAG 59.449 52.381 6.74 0.00 0.00 2.43
145 146 0.036294 ACGGGCCTTCTTTGTAGAGC 60.036 55.000 0.84 0.00 0.00 4.09
146 147 0.744771 CGGGCCTTCTTTGTAGAGCC 60.745 60.000 0.84 0.00 39.72 4.70
147 148 0.328258 GGGCCTTCTTTGTAGAGCCA 59.672 55.000 0.84 0.00 41.34 4.75
148 149 1.064389 GGGCCTTCTTTGTAGAGCCAT 60.064 52.381 0.84 0.00 41.34 4.40
149 150 2.293170 GGCCTTCTTTGTAGAGCCATC 58.707 52.381 0.00 0.00 40.03 3.51
150 151 2.092699 GGCCTTCTTTGTAGAGCCATCT 60.093 50.000 0.00 0.00 40.03 2.90
151 152 3.134804 GGCCTTCTTTGTAGAGCCATCTA 59.865 47.826 0.00 0.00 40.03 1.98
159 160 3.629438 GTAGAGCCATCTACGAAGTCC 57.371 52.381 0.00 0.00 46.31 3.85
160 161 1.025812 AGAGCCATCTACGAAGTCCG 58.974 55.000 0.00 0.00 43.93 4.79
161 162 1.022735 GAGCCATCTACGAAGTCCGA 58.977 55.000 0.00 0.00 43.93 4.55
162 163 1.404391 GAGCCATCTACGAAGTCCGAA 59.596 52.381 0.00 0.00 43.93 4.30
163 164 1.134560 AGCCATCTACGAAGTCCGAAC 59.865 52.381 0.00 0.00 43.93 3.95
164 165 1.801765 GCCATCTACGAAGTCCGAACC 60.802 57.143 0.00 0.00 43.93 3.62
165 166 1.533338 CCATCTACGAAGTCCGAACCG 60.533 57.143 0.00 0.00 43.93 4.44
184 185 4.351054 CCCAGCGCTCCAAACCCT 62.351 66.667 7.13 0.00 0.00 4.34
185 186 3.058160 CCAGCGCTCCAAACCCTG 61.058 66.667 7.13 0.00 0.00 4.45
189 190 2.747855 CGCTCCAAACCCTGGCTC 60.748 66.667 0.00 0.00 45.98 4.70
190 191 2.361737 GCTCCAAACCCTGGCTCC 60.362 66.667 0.00 0.00 45.98 4.70
191 192 2.356667 CTCCAAACCCTGGCTCCC 59.643 66.667 0.00 0.00 45.98 4.30
192 193 2.451493 TCCAAACCCTGGCTCCCA 60.451 61.111 0.00 0.00 45.98 4.37
193 194 2.080336 CTCCAAACCCTGGCTCCCAA 62.080 60.000 0.00 0.00 45.98 4.12
194 195 1.908299 CCAAACCCTGGCTCCCAAC 60.908 63.158 0.00 0.00 38.76 3.77
195 196 1.908299 CAAACCCTGGCTCCCAACC 60.908 63.158 0.00 0.00 30.80 3.77
196 197 2.091283 AAACCCTGGCTCCCAACCT 61.091 57.895 0.00 0.00 30.80 3.50
197 198 1.664956 AAACCCTGGCTCCCAACCTT 61.665 55.000 0.00 0.00 30.80 3.50
198 199 1.664956 AACCCTGGCTCCCAACCTTT 61.665 55.000 0.00 0.00 30.80 3.11
199 200 1.304464 CCCTGGCTCCCAACCTTTC 60.304 63.158 0.00 0.00 30.80 2.62
200 201 1.770324 CCTGGCTCCCAACCTTTCT 59.230 57.895 0.00 0.00 30.80 2.52
201 202 0.113190 CCTGGCTCCCAACCTTTCTT 59.887 55.000 0.00 0.00 30.80 2.52
202 203 1.539157 CTGGCTCCCAACCTTTCTTC 58.461 55.000 0.00 0.00 30.80 2.87
203 204 0.250727 TGGCTCCCAACCTTTCTTCG 60.251 55.000 0.00 0.00 0.00 3.79
204 205 1.587043 GGCTCCCAACCTTTCTTCGC 61.587 60.000 0.00 0.00 0.00 4.70
205 206 0.606673 GCTCCCAACCTTTCTTCGCT 60.607 55.000 0.00 0.00 0.00 4.93
206 207 1.160137 CTCCCAACCTTTCTTCGCTG 58.840 55.000 0.00 0.00 0.00 5.18
207 208 0.472471 TCCCAACCTTTCTTCGCTGT 59.528 50.000 0.00 0.00 0.00 4.40
208 209 0.875059 CCCAACCTTTCTTCGCTGTC 59.125 55.000 0.00 0.00 0.00 3.51
209 210 0.875059 CCAACCTTTCTTCGCTGTCC 59.125 55.000 0.00 0.00 0.00 4.02
210 211 0.875059 CAACCTTTCTTCGCTGTCCC 59.125 55.000 0.00 0.00 0.00 4.46
211 212 0.250770 AACCTTTCTTCGCTGTCCCC 60.251 55.000 0.00 0.00 0.00 4.81
667 668 2.753966 CGCCCCATCAAGCAAGACG 61.754 63.158 0.00 0.00 0.00 4.18
748 750 0.390472 CTTTCCACCTCACGGAGAGC 60.390 60.000 2.84 0.00 43.31 4.09
812 823 2.922503 TCTGCAAGTCCTGGGCGA 60.923 61.111 0.00 0.00 33.76 5.54
832 843 3.781770 GACCATCTCCGAGCGGCTG 62.782 68.421 7.50 0.00 34.68 4.85
887 898 4.291047 TCGCGAGGACGAGTACTT 57.709 55.556 3.71 0.00 42.66 2.24
888 899 2.084844 TCGCGAGGACGAGTACTTC 58.915 57.895 3.71 0.00 42.66 3.01
889 900 1.062206 CGCGAGGACGAGTACTTCC 59.938 63.158 0.00 5.57 42.66 3.46
890 901 1.367599 CGCGAGGACGAGTACTTCCT 61.368 60.000 14.81 14.81 45.52 3.36
901 912 3.547746 GAGTACTTCCTCGATCTCCTGT 58.452 50.000 0.00 0.00 0.00 4.00
902 913 3.949113 GAGTACTTCCTCGATCTCCTGTT 59.051 47.826 0.00 0.00 0.00 3.16
903 914 3.949113 AGTACTTCCTCGATCTCCTGTTC 59.051 47.826 0.00 0.00 0.00 3.18
904 915 2.104170 ACTTCCTCGATCTCCTGTTCC 58.896 52.381 0.00 0.00 0.00 3.62
905 916 2.291930 ACTTCCTCGATCTCCTGTTCCT 60.292 50.000 0.00 0.00 0.00 3.36
906 917 1.769026 TCCTCGATCTCCTGTTCCTG 58.231 55.000 0.00 0.00 0.00 3.86
907 918 0.103937 CCTCGATCTCCTGTTCCTGC 59.896 60.000 0.00 0.00 0.00 4.85
908 919 0.103937 CTCGATCTCCTGTTCCTGCC 59.896 60.000 0.00 0.00 0.00 4.85
909 920 1.144936 CGATCTCCTGTTCCTGCCC 59.855 63.158 0.00 0.00 0.00 5.36
910 921 1.144936 GATCTCCTGTTCCTGCCCG 59.855 63.158 0.00 0.00 0.00 6.13
911 922 1.306141 ATCTCCTGTTCCTGCCCGA 60.306 57.895 0.00 0.00 0.00 5.14
912 923 1.617947 ATCTCCTGTTCCTGCCCGAC 61.618 60.000 0.00 0.00 0.00 4.79
913 924 2.203788 TCCTGTTCCTGCCCGACT 60.204 61.111 0.00 0.00 0.00 4.18
914 925 1.831652 CTCCTGTTCCTGCCCGACTT 61.832 60.000 0.00 0.00 0.00 3.01
915 926 0.543410 TCCTGTTCCTGCCCGACTTA 60.543 55.000 0.00 0.00 0.00 2.24
1155 1243 4.785453 CCCCGGCACAGGCTTCTC 62.785 72.222 0.00 0.00 40.87 2.87
1536 2201 0.320683 TGCTCACACCAGATGAACCG 60.321 55.000 0.00 0.00 0.00 4.44
1551 2216 2.282462 CCGCTTTGCCCCAAGACT 60.282 61.111 0.00 0.00 0.00 3.24
1932 2618 8.023021 TGCTCTAGGTATGTACAATCAGATTT 57.977 34.615 0.00 0.00 0.00 2.17
2041 2735 2.105528 CGGGCATTGCATTGCTCC 59.894 61.111 27.32 24.08 40.11 4.70
2081 2775 4.014406 GGAGGGTGGTTTATTCGAACAAT 58.986 43.478 0.00 0.00 0.00 2.71
2084 2778 5.778862 AGGGTGGTTTATTCGAACAATTTG 58.221 37.500 0.00 0.00 0.00 2.32
2085 2779 4.387559 GGGTGGTTTATTCGAACAATTTGC 59.612 41.667 0.00 0.00 0.00 3.68
2086 2780 4.985409 GGTGGTTTATTCGAACAATTTGCA 59.015 37.500 0.00 0.00 0.00 4.08
2087 2781 5.637387 GGTGGTTTATTCGAACAATTTGCAT 59.363 36.000 0.00 0.00 0.00 3.96
2229 2925 5.649782 AAAGCTTCATCCTTAACACCATG 57.350 39.130 0.00 0.00 0.00 3.66
2340 3042 3.945304 CTAACACCGCCCACGACCC 62.945 68.421 0.00 0.00 43.93 4.46
2423 3430 3.156293 CAACATTGTGATGAGTTGGGGA 58.844 45.455 0.00 0.00 38.09 4.81
2462 3469 6.843676 CTGTTTTCAGTTCATTCGCTAATG 57.156 37.500 4.61 4.61 41.78 1.90
2504 3511 9.777297 ATAAAAGGAAAACAATTATGTGCTGTT 57.223 25.926 0.00 0.00 40.46 3.16
2545 3555 7.193377 AGGAAATTGCAATTTTGTGAATGAC 57.807 32.000 32.09 18.47 38.64 3.06
2625 3646 4.599041 TGGAGCTAATGTGTAGCCATTTT 58.401 39.130 1.81 0.00 41.25 1.82
2689 3843 2.224621 ACCAACTGTCATGAACTGGGAG 60.225 50.000 14.67 1.77 0.00 4.30
2717 4419 7.430441 TCAAATACTACCTTTTTGCCAGTTTC 58.570 34.615 0.00 0.00 31.88 2.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 5.313712 ACCGGTACTGTTCATCATCTTTTT 58.686 37.500 4.49 0.00 0.00 1.94
17 18 4.906618 ACCGGTACTGTTCATCATCTTTT 58.093 39.130 4.49 0.00 0.00 2.27
18 19 4.553330 ACCGGTACTGTTCATCATCTTT 57.447 40.909 4.49 0.00 0.00 2.52
19 20 4.553330 AACCGGTACTGTTCATCATCTT 57.447 40.909 8.00 0.00 26.78 2.40
20 21 4.223032 AGAAACCGGTACTGTTCATCATCT 59.777 41.667 8.00 0.00 33.88 2.90
21 22 4.504858 AGAAACCGGTACTGTTCATCATC 58.495 43.478 8.00 0.00 33.88 2.92
22 23 4.223032 AGAGAAACCGGTACTGTTCATCAT 59.777 41.667 8.00 0.00 33.88 2.45
23 24 3.576982 AGAGAAACCGGTACTGTTCATCA 59.423 43.478 8.00 0.00 33.88 3.07
24 25 4.189639 AGAGAAACCGGTACTGTTCATC 57.810 45.455 8.00 7.67 33.88 2.92
25 26 4.618920 AAGAGAAACCGGTACTGTTCAT 57.381 40.909 8.00 0.00 33.88 2.57
26 27 4.411256 AAAGAGAAACCGGTACTGTTCA 57.589 40.909 19.04 0.00 33.88 3.18
27 28 5.746307 AAAAAGAGAAACCGGTACTGTTC 57.254 39.130 19.04 14.42 33.88 3.18
50 51 6.225981 GAGAATCGGTACTACCCCTAAAAA 57.774 41.667 0.00 0.00 33.75 1.94
51 52 5.859205 GAGAATCGGTACTACCCCTAAAA 57.141 43.478 0.00 0.00 33.75 1.52
75 76 4.577246 CTGTAGAGCGCCGGCCTC 62.577 72.222 27.77 27.77 41.24 4.70
79 80 4.514577 CCCACTGTAGAGCGCCGG 62.515 72.222 2.29 0.00 0.00 6.13
81 82 3.724914 GAGCCCACTGTAGAGCGCC 62.725 68.421 2.29 0.00 0.00 6.53
82 83 2.202810 GAGCCCACTGTAGAGCGC 60.203 66.667 0.00 0.00 0.00 5.92
83 84 0.249238 GATGAGCCCACTGTAGAGCG 60.249 60.000 0.00 0.00 0.00 5.03
84 85 0.105778 GGATGAGCCCACTGTAGAGC 59.894 60.000 0.00 0.00 0.00 4.09
95 96 2.103941 AGATCTTTTCGAGGGATGAGCC 59.896 50.000 0.00 0.00 0.00 4.70
96 97 3.467374 AGATCTTTTCGAGGGATGAGC 57.533 47.619 0.00 0.00 0.00 4.26
97 98 4.560513 GCCTAGATCTTTTCGAGGGATGAG 60.561 50.000 0.00 0.00 44.94 2.90
98 99 3.322254 GCCTAGATCTTTTCGAGGGATGA 59.678 47.826 0.00 0.00 44.94 2.92
99 100 3.556004 GGCCTAGATCTTTTCGAGGGATG 60.556 52.174 0.00 0.00 44.94 3.51
100 101 2.635427 GGCCTAGATCTTTTCGAGGGAT 59.365 50.000 0.00 0.00 44.94 3.85
101 102 2.040178 GGCCTAGATCTTTTCGAGGGA 58.960 52.381 0.00 0.00 44.94 4.20
102 103 2.043227 AGGCCTAGATCTTTTCGAGGG 58.957 52.381 1.29 0.00 44.94 4.30
103 104 3.828875 AAGGCCTAGATCTTTTCGAGG 57.171 47.619 5.16 1.77 46.89 4.63
104 105 5.525199 GTCTAAGGCCTAGATCTTTTCGAG 58.475 45.833 5.16 0.00 38.91 4.04
105 106 4.036498 CGTCTAAGGCCTAGATCTTTTCGA 59.964 45.833 5.16 0.00 38.91 3.71
106 107 4.291783 CGTCTAAGGCCTAGATCTTTTCG 58.708 47.826 5.16 4.70 38.91 3.46
107 108 4.501743 CCCGTCTAAGGCCTAGATCTTTTC 60.502 50.000 5.16 0.00 38.91 2.29
108 109 3.388350 CCCGTCTAAGGCCTAGATCTTTT 59.612 47.826 5.16 0.00 38.91 2.27
109 110 2.966516 CCCGTCTAAGGCCTAGATCTTT 59.033 50.000 5.16 0.00 38.91 2.52
110 111 2.599677 CCCGTCTAAGGCCTAGATCTT 58.400 52.381 5.16 0.00 38.91 2.40
111 112 1.824045 GCCCGTCTAAGGCCTAGATCT 60.824 57.143 5.16 0.00 45.16 2.75
112 113 0.604073 GCCCGTCTAAGGCCTAGATC 59.396 60.000 5.16 4.16 45.16 2.75
113 114 2.748018 GCCCGTCTAAGGCCTAGAT 58.252 57.895 5.16 0.00 45.16 1.98
114 115 4.272245 GCCCGTCTAAGGCCTAGA 57.728 61.111 5.16 6.77 45.16 2.43
120 121 1.003233 ACAAAGAAGGCCCGTCTAAGG 59.997 52.381 6.97 3.23 0.00 2.69
121 122 2.474410 ACAAAGAAGGCCCGTCTAAG 57.526 50.000 6.97 5.74 0.00 2.18
122 123 3.167485 TCTACAAAGAAGGCCCGTCTAA 58.833 45.455 6.97 0.00 0.00 2.10
123 124 2.758979 CTCTACAAAGAAGGCCCGTCTA 59.241 50.000 6.97 0.00 0.00 2.59
124 125 1.550976 CTCTACAAAGAAGGCCCGTCT 59.449 52.381 0.00 0.00 0.00 4.18
125 126 2.007547 GCTCTACAAAGAAGGCCCGTC 61.008 57.143 0.00 0.00 0.00 4.79
126 127 0.036294 GCTCTACAAAGAAGGCCCGT 60.036 55.000 0.00 0.00 0.00 5.28
127 128 0.744771 GGCTCTACAAAGAAGGCCCG 60.745 60.000 0.00 0.00 37.19 6.13
128 129 0.328258 TGGCTCTACAAAGAAGGCCC 59.672 55.000 0.00 0.00 40.67 5.80
129 130 2.092699 AGATGGCTCTACAAAGAAGGCC 60.093 50.000 0.00 0.00 41.38 5.19
130 131 3.274095 AGATGGCTCTACAAAGAAGGC 57.726 47.619 0.00 0.00 0.00 4.35
140 141 2.158856 TCGGACTTCGTAGATGGCTCTA 60.159 50.000 0.00 0.00 39.92 2.43
141 142 1.025812 CGGACTTCGTAGATGGCTCT 58.974 55.000 0.00 0.00 39.92 4.09
142 143 1.022735 TCGGACTTCGTAGATGGCTC 58.977 55.000 0.00 0.00 39.92 4.70
143 144 1.134560 GTTCGGACTTCGTAGATGGCT 59.865 52.381 0.00 0.00 39.92 4.75
144 145 1.557651 GTTCGGACTTCGTAGATGGC 58.442 55.000 0.00 0.00 39.21 4.40
145 146 1.533338 CGGTTCGGACTTCGTAGATGG 60.533 57.143 0.00 0.00 40.32 3.51
146 147 1.823828 CGGTTCGGACTTCGTAGATG 58.176 55.000 0.00 0.00 40.32 2.90
167 168 4.351054 AGGGTTTGGAGCGCTGGG 62.351 66.667 18.48 0.00 0.00 4.45
168 169 3.058160 CAGGGTTTGGAGCGCTGG 61.058 66.667 18.48 0.00 41.38 4.85
177 178 1.908299 GGTTGGGAGCCAGGGTTTG 60.908 63.158 0.00 0.00 33.81 2.93
178 179 1.664956 AAGGTTGGGAGCCAGGGTTT 61.665 55.000 0.00 0.00 33.81 3.27
179 180 1.664956 AAAGGTTGGGAGCCAGGGTT 61.665 55.000 0.00 0.00 33.81 4.11
180 181 2.081585 GAAAGGTTGGGAGCCAGGGT 62.082 60.000 0.00 0.00 33.81 4.34
181 182 1.304464 GAAAGGTTGGGAGCCAGGG 60.304 63.158 0.00 0.00 33.81 4.45
182 183 0.113190 AAGAAAGGTTGGGAGCCAGG 59.887 55.000 0.00 0.00 33.81 4.45
183 184 1.539157 GAAGAAAGGTTGGGAGCCAG 58.461 55.000 0.00 0.00 33.81 4.85
184 185 0.250727 CGAAGAAAGGTTGGGAGCCA 60.251 55.000 0.00 0.00 0.00 4.75
185 186 1.587043 GCGAAGAAAGGTTGGGAGCC 61.587 60.000 0.00 0.00 0.00 4.70
186 187 0.606673 AGCGAAGAAAGGTTGGGAGC 60.607 55.000 0.00 0.00 0.00 4.70
187 188 1.160137 CAGCGAAGAAAGGTTGGGAG 58.840 55.000 0.00 0.00 0.00 4.30
188 189 0.472471 ACAGCGAAGAAAGGTTGGGA 59.528 50.000 0.00 0.00 0.00 4.37
189 190 0.875059 GACAGCGAAGAAAGGTTGGG 59.125 55.000 0.00 0.00 0.00 4.12
190 191 0.875059 GGACAGCGAAGAAAGGTTGG 59.125 55.000 0.00 0.00 0.00 3.77
191 192 0.875059 GGGACAGCGAAGAAAGGTTG 59.125 55.000 0.00 0.00 0.00 3.77
192 193 0.250770 GGGGACAGCGAAGAAAGGTT 60.251 55.000 0.00 0.00 0.00 3.50
193 194 1.375326 GGGGACAGCGAAGAAAGGT 59.625 57.895 0.00 0.00 0.00 3.50
194 195 4.303257 GGGGACAGCGAAGAAAGG 57.697 61.111 0.00 0.00 0.00 3.11
650 651 3.056313 GCGTCTTGCTTGATGGGGC 62.056 63.158 0.00 0.00 41.73 5.80
748 750 2.664185 CTGATGCGGCGGAGGATG 60.664 66.667 9.78 0.00 0.00 3.51
812 823 3.518998 CCGCTCGGAGATGGTCGT 61.519 66.667 9.69 0.00 37.50 4.34
880 891 3.547746 ACAGGAGATCGAGGAAGTACTC 58.452 50.000 0.00 0.00 0.00 2.59
881 892 3.655615 ACAGGAGATCGAGGAAGTACT 57.344 47.619 0.00 0.00 0.00 2.73
882 893 3.067040 GGAACAGGAGATCGAGGAAGTAC 59.933 52.174 0.00 0.00 0.00 2.73
883 894 3.053544 AGGAACAGGAGATCGAGGAAGTA 60.054 47.826 0.00 0.00 0.00 2.24
884 895 2.104170 GGAACAGGAGATCGAGGAAGT 58.896 52.381 0.00 0.00 0.00 3.01
885 896 2.100584 CAGGAACAGGAGATCGAGGAAG 59.899 54.545 0.00 0.00 0.00 3.46
886 897 2.103373 CAGGAACAGGAGATCGAGGAA 58.897 52.381 0.00 0.00 0.00 3.36
887 898 1.769026 CAGGAACAGGAGATCGAGGA 58.231 55.000 0.00 0.00 0.00 3.71
888 899 0.103937 GCAGGAACAGGAGATCGAGG 59.896 60.000 0.00 0.00 0.00 4.63
889 900 0.103937 GGCAGGAACAGGAGATCGAG 59.896 60.000 0.00 0.00 0.00 4.04
890 901 1.330655 GGGCAGGAACAGGAGATCGA 61.331 60.000 0.00 0.00 0.00 3.59
891 902 1.144936 GGGCAGGAACAGGAGATCG 59.855 63.158 0.00 0.00 0.00 3.69
892 903 1.144936 CGGGCAGGAACAGGAGATC 59.855 63.158 0.00 0.00 0.00 2.75
893 904 1.306141 TCGGGCAGGAACAGGAGAT 60.306 57.895 0.00 0.00 0.00 2.75
894 905 2.119611 TCGGGCAGGAACAGGAGA 59.880 61.111 0.00 0.00 0.00 3.71
895 906 1.831652 AAGTCGGGCAGGAACAGGAG 61.832 60.000 0.00 0.00 0.00 3.69
896 907 0.543410 TAAGTCGGGCAGGAACAGGA 60.543 55.000 0.00 0.00 0.00 3.86
897 908 0.108138 CTAAGTCGGGCAGGAACAGG 60.108 60.000 0.00 0.00 0.00 4.00
898 909 0.895530 TCTAAGTCGGGCAGGAACAG 59.104 55.000 0.00 0.00 0.00 3.16
899 910 0.895530 CTCTAAGTCGGGCAGGAACA 59.104 55.000 0.00 0.00 0.00 3.18
900 911 0.460459 GCTCTAAGTCGGGCAGGAAC 60.460 60.000 0.00 0.00 0.00 3.62
901 912 1.898154 GCTCTAAGTCGGGCAGGAA 59.102 57.895 0.00 0.00 0.00 3.36
902 913 2.415608 CGCTCTAAGTCGGGCAGGA 61.416 63.158 0.00 0.00 0.00 3.86
903 914 2.105128 CGCTCTAAGTCGGGCAGG 59.895 66.667 0.00 0.00 0.00 4.85
904 915 2.583593 GCGCTCTAAGTCGGGCAG 60.584 66.667 0.00 0.00 38.74 4.85
905 916 4.143333 GGCGCTCTAAGTCGGGCA 62.143 66.667 7.64 0.00 40.41 5.36
910 921 4.493747 ACGGCGGCGCTCTAAGTC 62.494 66.667 32.57 12.04 0.00 3.01
911 922 4.796231 CACGGCGGCGCTCTAAGT 62.796 66.667 32.57 19.61 0.00 2.24
1155 1243 1.019278 CCCTGACCGTCGGTTGAATG 61.019 60.000 19.95 7.16 35.25 2.67
1191 1363 0.032952 ACTGGCTAACGAAGAACGCA 59.967 50.000 0.00 0.00 46.94 5.24
1536 2201 2.019984 CTGATAGTCTTGGGGCAAAGC 58.980 52.381 0.00 0.00 0.00 3.51
1551 2216 2.145397 ACACCTCGAAGCCTCTGATA 57.855 50.000 0.00 0.00 0.00 2.15
1609 2274 2.496817 GTCATCGGCGAGCCTCTT 59.503 61.111 17.22 0.00 0.00 2.85
1932 2618 3.787785 TCGAACTGCAACTTACACTCAA 58.212 40.909 0.00 0.00 0.00 3.02
2041 2735 1.411246 TCCCGATACAAAGGACCGATG 59.589 52.381 0.00 0.00 0.00 3.84
2086 2780 2.165167 CTTGCCAGACCATGTTCACAT 58.835 47.619 0.00 0.00 36.96 3.21
2087 2781 1.133823 ACTTGCCAGACCATGTTCACA 60.134 47.619 0.00 0.00 0.00 3.58
2229 2925 1.737816 CTAGCACCATGCCCATTGC 59.262 57.895 0.00 0.00 46.52 3.56
2340 3042 4.082523 AGTGATGGCGGTGGTCGG 62.083 66.667 0.00 0.00 39.69 4.79
2382 3389 2.680841 TGCACCGCCAAAACATAGTATC 59.319 45.455 0.00 0.00 0.00 2.24
2423 3430 3.550437 AACAGTGACAAGAGCTGAGTT 57.450 42.857 0.00 0.00 34.60 3.01
2462 3469 8.652810 TTCCTTTTATAACCACGATAACTAGC 57.347 34.615 0.00 0.00 0.00 3.42
2545 3555 6.758416 TGTCTTCTATGATTCTGATTTCCACG 59.242 38.462 0.00 0.00 0.00 4.94
2582 3603 5.182380 TCCAATTATTCAAACTTCCACGGAC 59.818 40.000 0.00 0.00 0.00 4.79
2625 3646 7.437748 CACACACCATTTTTATTAAGGGAACA 58.562 34.615 0.00 0.00 33.34 3.18
2689 3843 6.206829 ACTGGCAAAAAGGTAGTATTTGAGTC 59.793 38.462 1.95 0.00 36.41 3.36


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

AutoCloner maintained by Alex Coulton.