Multiple sequence alignment - TraesCS7B01G036500

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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 TraesCS7B01G036500 chr7B 100.000 4110 0 0 1 4110 35313990 35309881 0.000000e+00 7590
1 TraesCS7B01G036500 chr7B 90.616 3037 223 27 252 3268 35513437 35510443 0.000000e+00 3973
2 TraesCS7B01G036500 chr7B 88.462 182 17 3 1 181 554172229 554172051 2.490000e-52 217
3 TraesCS7B01G036500 chr7B 85.000 200 25 4 4 203 563740389 563740195 9.010000e-47 198
4 TraesCS7B01G036500 chr7D 91.121 3942 262 39 199 4099 87212663 87208769 0.000000e+00 5260
5 TraesCS7B01G036500 chr7D 91.826 3756 237 24 364 4103 86800998 86797297 0.000000e+00 5171
6 TraesCS7B01G036500 chr7D 90.334 3807 287 35 199 3973 86768718 86764961 0.000000e+00 4916
7 TraesCS7B01G036500 chr7D 90.823 3683 257 37 461 4103 86924492 86920851 0.000000e+00 4854
8 TraesCS7B01G036500 chr7D 88.351 2232 193 28 199 2406 86927492 86925304 0.000000e+00 2619
9 TraesCS7B01G036500 chr7D 86.769 2154 242 26 199 2328 86298504 86296370 0.000000e+00 2359
10 TraesCS7B01G036500 chr7A 90.742 3910 271 37 223 4100 88014544 88010694 0.000000e+00 5131
11 TraesCS7B01G036500 chr7A 90.361 3932 291 34 199 4100 88127847 88123974 0.000000e+00 5081
12 TraesCS7B01G036500 chr7A 90.183 3942 292 46 199 4099 88442093 88438206 0.000000e+00 5048
13 TraesCS7B01G036500 chr7A 89.519 3931 305 36 199 4100 88178594 88174742 0.000000e+00 4878
14 TraesCS7B01G036500 chr7A 92.314 3435 203 31 708 4103 87456919 87453507 0.000000e+00 4824
15 TraesCS7B01G036500 chr7A 88.781 2362 209 26 199 2545 88323891 88321571 0.000000e+00 2843
16 TraesCS7B01G036500 chr7A 92.165 1455 90 12 2555 3998 88320596 88319155 0.000000e+00 2034
17 TraesCS7B01G036500 chr7A 90.702 484 30 9 201 680 87457388 87456916 7.500000e-177 630
18 TraesCS7B01G036500 chr7A 88.889 189 16 3 2 189 208123133 208122949 1.150000e-55 228
19 TraesCS7B01G036500 chr3D 87.562 201 18 4 1 200 426169387 426169193 4.130000e-55 226
20 TraesCS7B01G036500 chr3D 88.649 185 17 3 16 200 426169624 426169444 5.350000e-54 222
21 TraesCS7B01G036500 chr5B 86.935 199 20 2 1 199 455518546 455518738 6.920000e-53 219
22 TraesCS7B01G036500 chr4D 86.500 200 20 6 2 201 12693270 12693078 3.220000e-51 213
23 TraesCS7B01G036500 chr6A 87.027 185 19 3 16 200 149953424 149953245 1.940000e-48 204
24 TraesCS7B01G036500 chr3B 86.224 196 18 6 1 195 702675122 702675309 1.940000e-48 204


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 TraesCS7B01G036500 chr7B 35309881 35313990 4109 True 7590.0 7590 100.000 1 4110 1 chr7B.!!$R1 4109
1 TraesCS7B01G036500 chr7B 35510443 35513437 2994 True 3973.0 3973 90.616 252 3268 1 chr7B.!!$R2 3016
2 TraesCS7B01G036500 chr7D 87208769 87212663 3894 True 5260.0 5260 91.121 199 4099 1 chr7D.!!$R4 3900
3 TraesCS7B01G036500 chr7D 86797297 86800998 3701 True 5171.0 5171 91.826 364 4103 1 chr7D.!!$R3 3739
4 TraesCS7B01G036500 chr7D 86764961 86768718 3757 True 4916.0 4916 90.334 199 3973 1 chr7D.!!$R2 3774
5 TraesCS7B01G036500 chr7D 86920851 86927492 6641 True 3736.5 4854 89.587 199 4103 2 chr7D.!!$R5 3904
6 TraesCS7B01G036500 chr7D 86296370 86298504 2134 True 2359.0 2359 86.769 199 2328 1 chr7D.!!$R1 2129
7 TraesCS7B01G036500 chr7A 88010694 88014544 3850 True 5131.0 5131 90.742 223 4100 1 chr7A.!!$R1 3877
8 TraesCS7B01G036500 chr7A 88123974 88127847 3873 True 5081.0 5081 90.361 199 4100 1 chr7A.!!$R2 3901
9 TraesCS7B01G036500 chr7A 88438206 88442093 3887 True 5048.0 5048 90.183 199 4099 1 chr7A.!!$R4 3900
10 TraesCS7B01G036500 chr7A 88174742 88178594 3852 True 4878.0 4878 89.519 199 4100 1 chr7A.!!$R3 3901
11 TraesCS7B01G036500 chr7A 87453507 87457388 3881 True 2727.0 4824 91.508 201 4103 2 chr7A.!!$R6 3902
12 TraesCS7B01G036500 chr7A 88319155 88323891 4736 True 2438.5 2843 90.473 199 3998 2 chr7A.!!$R7 3799

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
157 158 0.034896 GCAAGGTTGGACGAAGGAGA 59.965 55.0 0.00 0.00 0.00 3.71 F
161 162 0.037232 GGTTGGACGAAGGAGAGGTG 60.037 60.0 0.00 0.00 0.00 4.00 F
1399 4192 0.254154 TGGGGTAGGAGAGGAGGAGA 60.254 60.0 0.00 0.00 0.00 3.71 F
2837 6639 0.323302 TGACACCGAGCTATTGGCAA 59.677 50.0 0.68 0.68 44.79 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1229 1266 0.421904 AGTAACATGGGTCCCCTCCT 59.578 55.000 5.13 0.0 36.94 3.69 R
1455 4251 1.138036 CTCACCCGTCAACGCGATA 59.862 57.895 15.93 0.0 38.18 2.92 R
2880 6682 1.425066 AGCTTGGGTCATTGTTGAGGA 59.575 47.619 0.00 0.0 30.85 3.71 R
3894 7738 3.134804 CCAATCGTACCCCTGATCTCTTT 59.865 47.826 0.00 0.0 0.00 2.52 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
62 63 9.618890 TGAGACAATTGATTCTATTTTAGGGAG 57.381 33.333 13.59 0.00 0.00 4.30
63 64 9.838339 GAGACAATTGATTCTATTTTAGGGAGA 57.162 33.333 13.59 0.00 0.00 3.71
71 72 9.578576 TGATTCTATTTTAGGGAGAATTGATGG 57.421 33.333 0.00 0.00 39.46 3.51
72 73 8.946797 ATTCTATTTTAGGGAGAATTGATGGG 57.053 34.615 0.00 0.00 36.71 4.00
73 74 7.705912 TCTATTTTAGGGAGAATTGATGGGA 57.294 36.000 0.00 0.00 0.00 4.37
74 75 7.749666 TCTATTTTAGGGAGAATTGATGGGAG 58.250 38.462 0.00 0.00 0.00 4.30
75 76 6.596869 ATTTTAGGGAGAATTGATGGGAGA 57.403 37.500 0.00 0.00 0.00 3.71
76 77 6.401537 TTTTAGGGAGAATTGATGGGAGAA 57.598 37.500 0.00 0.00 0.00 2.87
77 78 6.401537 TTTAGGGAGAATTGATGGGAGAAA 57.598 37.500 0.00 0.00 0.00 2.52
78 79 6.596869 TTAGGGAGAATTGATGGGAGAAAT 57.403 37.500 0.00 0.00 0.00 2.17
79 80 7.705912 TTAGGGAGAATTGATGGGAGAAATA 57.294 36.000 0.00 0.00 0.00 1.40
80 81 6.596869 AGGGAGAATTGATGGGAGAAATAA 57.403 37.500 0.00 0.00 0.00 1.40
81 82 6.985225 AGGGAGAATTGATGGGAGAAATAAA 58.015 36.000 0.00 0.00 0.00 1.40
82 83 7.421684 AGGGAGAATTGATGGGAGAAATAAAA 58.578 34.615 0.00 0.00 0.00 1.52
83 84 8.069979 AGGGAGAATTGATGGGAGAAATAAAAT 58.930 33.333 0.00 0.00 0.00 1.82
84 85 8.363390 GGGAGAATTGATGGGAGAAATAAAATC 58.637 37.037 0.00 0.00 0.00 2.17
85 86 8.917088 GGAGAATTGATGGGAGAAATAAAATCA 58.083 33.333 0.00 0.00 0.00 2.57
92 93 8.698210 TGATGGGAGAAATAAAATCAAAGATGG 58.302 33.333 0.00 0.00 0.00 3.51
93 94 7.422465 TGGGAGAAATAAAATCAAAGATGGG 57.578 36.000 0.00 0.00 0.00 4.00
94 95 7.188381 TGGGAGAAATAAAATCAAAGATGGGA 58.812 34.615 0.00 0.00 0.00 4.37
95 96 7.342799 TGGGAGAAATAAAATCAAAGATGGGAG 59.657 37.037 0.00 0.00 0.00 4.30
96 97 7.201947 GGGAGAAATAAAATCAAAGATGGGAGG 60.202 40.741 0.00 0.00 0.00 4.30
97 98 7.561356 GGAGAAATAAAATCAAAGATGGGAGGA 59.439 37.037 0.00 0.00 0.00 3.71
98 99 8.899887 AGAAATAAAATCAAAGATGGGAGGAA 57.100 30.769 0.00 0.00 0.00 3.36
99 100 9.325248 AGAAATAAAATCAAAGATGGGAGGAAA 57.675 29.630 0.00 0.00 0.00 3.13
100 101 9.942850 GAAATAAAATCAAAGATGGGAGGAAAA 57.057 29.630 0.00 0.00 0.00 2.29
144 145 7.875327 AAAATGGAACGTATATAAGCAAGGT 57.125 32.000 0.00 0.00 0.00 3.50
145 146 7.875327 AAATGGAACGTATATAAGCAAGGTT 57.125 32.000 0.00 0.00 0.00 3.50
146 147 6.861065 ATGGAACGTATATAAGCAAGGTTG 57.139 37.500 0.00 0.00 0.00 3.77
147 148 5.120399 TGGAACGTATATAAGCAAGGTTGG 58.880 41.667 0.00 0.00 0.00 3.77
148 149 5.104859 TGGAACGTATATAAGCAAGGTTGGA 60.105 40.000 0.00 0.00 0.00 3.53
149 150 5.235831 GGAACGTATATAAGCAAGGTTGGAC 59.764 44.000 0.00 0.00 0.00 4.02
150 151 4.365723 ACGTATATAAGCAAGGTTGGACG 58.634 43.478 0.00 0.00 0.00 4.79
151 152 4.098349 ACGTATATAAGCAAGGTTGGACGA 59.902 41.667 12.93 0.00 0.00 4.20
152 153 5.045215 CGTATATAAGCAAGGTTGGACGAA 58.955 41.667 0.00 0.00 0.00 3.85
153 154 5.175126 CGTATATAAGCAAGGTTGGACGAAG 59.825 44.000 0.00 0.00 0.00 3.79
154 155 2.178912 TAAGCAAGGTTGGACGAAGG 57.821 50.000 0.00 0.00 0.00 3.46
155 156 0.472471 AAGCAAGGTTGGACGAAGGA 59.528 50.000 0.00 0.00 0.00 3.36
156 157 0.035458 AGCAAGGTTGGACGAAGGAG 59.965 55.000 0.00 0.00 0.00 3.69
157 158 0.034896 GCAAGGTTGGACGAAGGAGA 59.965 55.000 0.00 0.00 0.00 3.71
158 159 1.941668 GCAAGGTTGGACGAAGGAGAG 60.942 57.143 0.00 0.00 0.00 3.20
159 160 0.977395 AAGGTTGGACGAAGGAGAGG 59.023 55.000 0.00 0.00 0.00 3.69
160 161 0.178929 AGGTTGGACGAAGGAGAGGT 60.179 55.000 0.00 0.00 0.00 3.85
161 162 0.037232 GGTTGGACGAAGGAGAGGTG 60.037 60.000 0.00 0.00 0.00 4.00
162 163 0.966920 GTTGGACGAAGGAGAGGTGA 59.033 55.000 0.00 0.00 0.00 4.02
163 164 1.343465 GTTGGACGAAGGAGAGGTGAA 59.657 52.381 0.00 0.00 0.00 3.18
164 165 1.712056 TGGACGAAGGAGAGGTGAAA 58.288 50.000 0.00 0.00 0.00 2.69
165 166 2.257207 TGGACGAAGGAGAGGTGAAAT 58.743 47.619 0.00 0.00 0.00 2.17
166 167 2.028112 TGGACGAAGGAGAGGTGAAATG 60.028 50.000 0.00 0.00 0.00 2.32
167 168 2.233922 GGACGAAGGAGAGGTGAAATGA 59.766 50.000 0.00 0.00 0.00 2.57
168 169 3.516615 GACGAAGGAGAGGTGAAATGAG 58.483 50.000 0.00 0.00 0.00 2.90
169 170 3.165875 ACGAAGGAGAGGTGAAATGAGA 58.834 45.455 0.00 0.00 0.00 3.27
170 171 3.578716 ACGAAGGAGAGGTGAAATGAGAA 59.421 43.478 0.00 0.00 0.00 2.87
171 172 3.929610 CGAAGGAGAGGTGAAATGAGAAC 59.070 47.826 0.00 0.00 0.00 3.01
172 173 3.990959 AGGAGAGGTGAAATGAGAACC 57.009 47.619 0.00 0.00 0.00 3.62
174 175 3.913163 AGGAGAGGTGAAATGAGAACCTT 59.087 43.478 0.00 0.00 44.42 3.50
175 176 5.094387 AGGAGAGGTGAAATGAGAACCTTA 58.906 41.667 0.00 0.00 44.42 2.69
176 177 5.046231 AGGAGAGGTGAAATGAGAACCTTAC 60.046 44.000 0.00 0.00 44.42 2.34
177 178 4.822026 AGAGGTGAAATGAGAACCTTACG 58.178 43.478 0.00 0.00 44.42 3.18
178 179 4.283722 AGAGGTGAAATGAGAACCTTACGT 59.716 41.667 0.00 0.00 44.42 3.57
179 180 4.969484 AGGTGAAATGAGAACCTTACGTT 58.031 39.130 0.00 0.00 41.65 3.99
180 181 5.374071 AGGTGAAATGAGAACCTTACGTTT 58.626 37.500 0.00 0.00 41.65 3.60
181 182 6.527423 AGGTGAAATGAGAACCTTACGTTTA 58.473 36.000 0.00 0.00 41.65 2.01
182 183 7.166167 AGGTGAAATGAGAACCTTACGTTTAT 58.834 34.615 0.00 0.00 41.65 1.40
183 184 7.664318 AGGTGAAATGAGAACCTTACGTTTATT 59.336 33.333 0.00 0.00 41.65 1.40
184 185 8.294577 GGTGAAATGAGAACCTTACGTTTATTT 58.705 33.333 0.00 0.00 33.74 1.40
185 186 9.673454 GTGAAATGAGAACCTTACGTTTATTTT 57.327 29.630 0.00 0.00 33.74 1.82
250 251 7.011295 CACAATTGATTGGCCCATGTATTAAAC 59.989 37.037 13.59 0.00 41.96 2.01
255 257 6.897966 TGATTGGCCCATGTATTAAACCTTTA 59.102 34.615 0.00 0.00 0.00 1.85
260 262 7.008332 GGCCCATGTATTAAACCTTTATACCT 58.992 38.462 0.00 0.00 0.00 3.08
333 335 3.567797 GCGCTCGATGTGGGAAGC 61.568 66.667 0.00 0.00 0.00 3.86
356 360 7.955918 AGCAGTCACCAAAATTAAGAGAAAAT 58.044 30.769 0.00 0.00 0.00 1.82
385 396 2.944129 ACCTTTGCTGGTAATGTGTGT 58.056 42.857 0.00 0.00 38.79 3.72
414 428 9.147732 CATATATGTAGCCTAGTTATCATGGGA 57.852 37.037 4.43 0.00 0.00 4.37
458 472 5.735892 GCATTTATCGCACATATGTATGCAG 59.264 40.000 23.28 14.14 42.17 4.41
488 502 4.080975 TCCATTGATGCATGTGTCACTAGA 60.081 41.667 2.46 0.00 0.00 2.43
623 641 8.458052 CAAGATGCGTGTTCTATCTATCTAGAT 58.542 37.037 10.73 10.73 44.69 1.98
625 643 7.826744 AGATGCGTGTTCTATCTATCTAGATCA 59.173 37.037 8.95 0.00 41.85 2.92
799 824 3.686016 TGTTCCTCAAAGGGTCATAAGC 58.314 45.455 0.00 0.00 35.59 3.09
961 995 9.593134 GCTATAACCCATCTTCATAGTTCATAG 57.407 37.037 0.00 0.00 0.00 2.23
993 1030 5.664294 TTCTATAGCGTTCAACTACCCAA 57.336 39.130 0.00 0.00 0.00 4.12
1107 1144 2.236741 TGTACGACGACAACGATGAG 57.763 50.000 0.00 0.00 42.66 2.90
1113 1150 3.172050 CGACGACAACGATGAGAAGAAT 58.828 45.455 0.00 0.00 42.66 2.40
1211 1248 2.083774 TGTTGATCTCGCCATGGAAAC 58.916 47.619 18.40 7.85 0.00 2.78
1229 1266 3.558931 AACACATATGATCCAGCGGAA 57.441 42.857 10.38 0.00 34.34 4.30
1387 4176 3.254657 TGCGAATGAAAACTTTGGGGTAG 59.745 43.478 0.00 0.00 0.00 3.18
1390 4179 4.156008 CGAATGAAAACTTTGGGGTAGGAG 59.844 45.833 0.00 0.00 0.00 3.69
1391 4180 5.321927 GAATGAAAACTTTGGGGTAGGAGA 58.678 41.667 0.00 0.00 0.00 3.71
1392 4181 4.367039 TGAAAACTTTGGGGTAGGAGAG 57.633 45.455 0.00 0.00 0.00 3.20
1399 4192 0.254154 TGGGGTAGGAGAGGAGGAGA 60.254 60.000 0.00 0.00 0.00 3.71
1455 4251 1.831106 TGTGCAATGGAGGATACGAGT 59.169 47.619 0.00 0.00 46.39 4.18
1490 4286 2.203070 GGCACCGCTGATGGTAGG 60.203 66.667 0.00 0.00 41.38 3.18
1676 4476 9.284968 ACATATACTAATAAAGAATGGTGTGCC 57.715 33.333 0.00 0.00 0.00 5.01
1696 4496 7.975616 GTGTGCCAATTTATTATGTGAGAACAT 59.024 33.333 0.00 0.00 0.00 2.71
1856 4658 8.483307 AATAGATTTTCATTTCATTGTGCACC 57.517 30.769 15.69 0.00 0.00 5.01
1954 4774 5.684704 ACAATACTTCCAATGATCGACCAT 58.315 37.500 0.00 0.00 0.00 3.55
1959 4779 5.496556 ACTTCCAATGATCGACCATTTGTA 58.503 37.500 1.00 0.00 34.77 2.41
1960 4780 5.943416 ACTTCCAATGATCGACCATTTGTAA 59.057 36.000 1.00 0.00 34.77 2.41
2011 4831 5.061920 AGAGGAACACAAGTTAGTCGATC 57.938 43.478 0.00 0.00 38.30 3.69
2027 4847 8.725148 GTTAGTCGATCCCTATATTCTTCGTTA 58.275 37.037 0.00 0.00 0.00 3.18
2144 4964 7.822575 GCAACGATATTGCACTTTACTAATC 57.177 36.000 6.75 0.00 44.34 1.75
2149 4969 8.912658 ACGATATTGCACTTTACTAATCGTATG 58.087 33.333 8.09 0.00 44.33 2.39
2226 5059 4.853924 TTGATGAACTTTCTTTCTGCCC 57.146 40.909 0.00 0.00 0.00 5.36
2270 5105 7.910683 GGACTTTGATTAGAAAATAGAAAGGCG 59.089 37.037 0.00 0.00 35.40 5.52
2272 5107 7.393515 ACTTTGATTAGAAAATAGAAAGGCGGT 59.606 33.333 0.00 0.00 33.14 5.68
2277 5113 9.499585 GATTAGAAAATAGAAAGGCGGTTAAAC 57.500 33.333 0.00 0.00 0.00 2.01
2281 5117 2.943036 AGAAAGGCGGTTAAACAGGA 57.057 45.000 0.00 0.00 0.00 3.86
2312 5148 3.133362 TCCAATATGGTACGTCTTGTCCC 59.867 47.826 0.00 0.00 39.03 4.46
2313 5149 3.118555 CCAATATGGTACGTCTTGTCCCA 60.119 47.826 0.00 0.00 41.33 4.37
2314 5150 4.509616 CAATATGGTACGTCTTGTCCCAA 58.490 43.478 0.00 0.00 40.35 4.12
2315 5151 5.123227 CAATATGGTACGTCTTGTCCCAAT 58.877 41.667 0.00 0.00 40.35 3.16
2316 5152 2.754946 TGGTACGTCTTGTCCCAATC 57.245 50.000 0.00 0.00 32.93 2.67
2317 5153 1.972075 TGGTACGTCTTGTCCCAATCA 59.028 47.619 0.00 0.00 32.93 2.57
2318 5154 2.569853 TGGTACGTCTTGTCCCAATCAT 59.430 45.455 0.00 0.00 32.93 2.45
2319 5155 3.195661 GGTACGTCTTGTCCCAATCATC 58.804 50.000 0.00 0.00 0.00 2.92
2320 5156 2.403252 ACGTCTTGTCCCAATCATCC 57.597 50.000 0.00 0.00 0.00 3.51
2379 5215 9.832445 TCATTTCGCTATAGAAAAATAGAGGTT 57.168 29.630 3.21 0.00 42.52 3.50
2476 5313 9.217336 TGATATACATGCATTCTATCCCATACT 57.783 33.333 0.00 0.00 0.00 2.12
2579 6381 4.990426 GGTGCTTCAATAAAACAACTGCAT 59.010 37.500 0.00 0.00 0.00 3.96
2776 6578 7.397221 TCAAGAGAATAGAGAAAAAGGCATCA 58.603 34.615 0.00 0.00 0.00 3.07
2837 6639 0.323302 TGACACCGAGCTATTGGCAA 59.677 50.000 0.68 0.68 44.79 4.52
2880 6682 1.407618 GCAAACCCTTTCTTTCACCGT 59.592 47.619 0.00 0.00 0.00 4.83
3105 6910 6.757947 TCAGCTTATTTTTATCTTGGCAATGC 59.242 34.615 0.00 0.00 0.00 3.56
3127 6932 6.283694 TGCATGAACAAGATGTAGTAGATCC 58.716 40.000 0.00 0.00 0.00 3.36
3128 6933 5.403766 GCATGAACAAGATGTAGTAGATCCG 59.596 44.000 0.00 0.00 0.00 4.18
3129 6934 4.933330 TGAACAAGATGTAGTAGATCCGC 58.067 43.478 3.74 0.00 0.00 5.54
3154 6959 1.859302 TGGGCCATGTTTGGAATACC 58.141 50.000 0.00 0.00 46.92 2.73
3221 7026 1.136891 GGCAACAAGACATTATGGCCC 59.863 52.381 0.00 0.00 34.17 5.80
3226 7031 2.158682 ACAAGACATTATGGCCCGCATA 60.159 45.455 0.00 0.00 0.00 3.14
3390 7218 6.055231 TGTTGTATTACCATATGAAAGCGC 57.945 37.500 3.65 0.00 0.00 5.92
3451 7280 8.534333 TCATAATTTGCCTACATTACGAGATC 57.466 34.615 0.00 0.00 0.00 2.75
3628 7462 1.407258 TGTTGGCTCTTCCCGTTTTTG 59.593 47.619 0.00 0.00 0.00 2.44
3640 7474 0.040425 CGTTTTTGGTCCAAGAGCCG 60.040 55.000 4.09 3.48 0.00 5.52
3894 7738 8.868522 ATTTGTGTCTTTGAGAATGGAGAATA 57.131 30.769 0.00 0.00 0.00 1.75
4065 7913 7.870509 TCAGAATGGGTCATTTCATAAGAAG 57.129 36.000 0.00 0.00 33.90 2.85
4082 7930 8.677300 TCATAAGAAGCATTGGATAGTGTTTTC 58.323 33.333 0.00 0.00 0.00 2.29
4086 7934 7.175104 AGAAGCATTGGATAGTGTTTTCCTTA 58.825 34.615 0.00 0.00 32.95 2.69
4103 7951 5.772393 TCCTTACCTTCTTTTGGCTCATA 57.228 39.130 0.00 0.00 0.00 2.15
4104 7952 6.327386 TCCTTACCTTCTTTTGGCTCATAT 57.673 37.500 0.00 0.00 0.00 1.78
4105 7953 6.357367 TCCTTACCTTCTTTTGGCTCATATC 58.643 40.000 0.00 0.00 0.00 1.63
4106 7954 5.532779 CCTTACCTTCTTTTGGCTCATATCC 59.467 44.000 0.00 0.00 0.00 2.59
4107 7955 4.591321 ACCTTCTTTTGGCTCATATCCA 57.409 40.909 0.00 0.00 0.00 3.41
4108 7956 4.530875 ACCTTCTTTTGGCTCATATCCAG 58.469 43.478 0.00 0.00 34.66 3.86
4109 7957 4.018050 ACCTTCTTTTGGCTCATATCCAGT 60.018 41.667 0.00 0.00 34.66 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 9.618890 CTCCCTAAAATAGAATCAATTGTCTCA 57.381 33.333 5.13 0.00 0.00 3.27
37 38 9.838339 TCTCCCTAAAATAGAATCAATTGTCTC 57.162 33.333 5.13 3.56 0.00 3.36
45 46 9.578576 CCATCAATTCTCCCTAAAATAGAATCA 57.421 33.333 0.00 0.00 38.65 2.57
46 47 9.018582 CCCATCAATTCTCCCTAAAATAGAATC 57.981 37.037 0.00 0.00 38.65 2.52
47 48 8.736675 TCCCATCAATTCTCCCTAAAATAGAAT 58.263 33.333 0.00 0.00 40.74 2.40
48 49 8.113114 TCCCATCAATTCTCCCTAAAATAGAA 57.887 34.615 0.00 0.00 34.00 2.10
49 50 7.572485 TCTCCCATCAATTCTCCCTAAAATAGA 59.428 37.037 0.00 0.00 0.00 1.98
50 51 7.749666 TCTCCCATCAATTCTCCCTAAAATAG 58.250 38.462 0.00 0.00 0.00 1.73
51 52 7.705912 TCTCCCATCAATTCTCCCTAAAATA 57.294 36.000 0.00 0.00 0.00 1.40
52 53 6.596869 TCTCCCATCAATTCTCCCTAAAAT 57.403 37.500 0.00 0.00 0.00 1.82
53 54 6.401537 TTCTCCCATCAATTCTCCCTAAAA 57.598 37.500 0.00 0.00 0.00 1.52
54 55 6.401537 TTTCTCCCATCAATTCTCCCTAAA 57.598 37.500 0.00 0.00 0.00 1.85
55 56 6.596869 ATTTCTCCCATCAATTCTCCCTAA 57.403 37.500 0.00 0.00 0.00 2.69
56 57 7.705912 TTATTTCTCCCATCAATTCTCCCTA 57.294 36.000 0.00 0.00 0.00 3.53
57 58 6.596869 TTATTTCTCCCATCAATTCTCCCT 57.403 37.500 0.00 0.00 0.00 4.20
58 59 7.660030 TTTTATTTCTCCCATCAATTCTCCC 57.340 36.000 0.00 0.00 0.00 4.30
59 60 8.917088 TGATTTTATTTCTCCCATCAATTCTCC 58.083 33.333 0.00 0.00 0.00 3.71
66 67 8.698210 CCATCTTTGATTTTATTTCTCCCATCA 58.302 33.333 0.00 0.00 0.00 3.07
67 68 8.146412 CCCATCTTTGATTTTATTTCTCCCATC 58.854 37.037 0.00 0.00 0.00 3.51
68 69 7.845800 TCCCATCTTTGATTTTATTTCTCCCAT 59.154 33.333 0.00 0.00 0.00 4.00
69 70 7.188381 TCCCATCTTTGATTTTATTTCTCCCA 58.812 34.615 0.00 0.00 0.00 4.37
70 71 7.201947 CCTCCCATCTTTGATTTTATTTCTCCC 60.202 40.741 0.00 0.00 0.00 4.30
71 72 7.561356 TCCTCCCATCTTTGATTTTATTTCTCC 59.439 37.037 0.00 0.00 0.00 3.71
72 73 8.525290 TCCTCCCATCTTTGATTTTATTTCTC 57.475 34.615 0.00 0.00 0.00 2.87
73 74 8.899887 TTCCTCCCATCTTTGATTTTATTTCT 57.100 30.769 0.00 0.00 0.00 2.52
74 75 9.942850 TTTTCCTCCCATCTTTGATTTTATTTC 57.057 29.630 0.00 0.00 0.00 2.17
119 120 8.288689 ACCTTGCTTATATACGTTCCATTTTT 57.711 30.769 0.00 0.00 0.00 1.94
120 121 7.875327 ACCTTGCTTATATACGTTCCATTTT 57.125 32.000 0.00 0.00 0.00 1.82
121 122 7.201785 CCAACCTTGCTTATATACGTTCCATTT 60.202 37.037 0.00 0.00 0.00 2.32
122 123 6.262273 CCAACCTTGCTTATATACGTTCCATT 59.738 38.462 0.00 0.00 0.00 3.16
123 124 5.763204 CCAACCTTGCTTATATACGTTCCAT 59.237 40.000 0.00 0.00 0.00 3.41
124 125 5.104859 TCCAACCTTGCTTATATACGTTCCA 60.105 40.000 0.00 0.00 0.00 3.53
125 126 5.235831 GTCCAACCTTGCTTATATACGTTCC 59.764 44.000 0.00 0.00 0.00 3.62
126 127 5.051240 CGTCCAACCTTGCTTATATACGTTC 60.051 44.000 0.00 0.00 0.00 3.95
127 128 4.807304 CGTCCAACCTTGCTTATATACGTT 59.193 41.667 0.00 0.00 0.00 3.99
128 129 4.098349 TCGTCCAACCTTGCTTATATACGT 59.902 41.667 0.00 0.00 0.00 3.57
129 130 4.613944 TCGTCCAACCTTGCTTATATACG 58.386 43.478 0.00 0.00 0.00 3.06
130 131 5.465724 CCTTCGTCCAACCTTGCTTATATAC 59.534 44.000 0.00 0.00 0.00 1.47
131 132 5.364446 TCCTTCGTCCAACCTTGCTTATATA 59.636 40.000 0.00 0.00 0.00 0.86
132 133 4.163458 TCCTTCGTCCAACCTTGCTTATAT 59.837 41.667 0.00 0.00 0.00 0.86
133 134 3.516300 TCCTTCGTCCAACCTTGCTTATA 59.484 43.478 0.00 0.00 0.00 0.98
134 135 2.304761 TCCTTCGTCCAACCTTGCTTAT 59.695 45.455 0.00 0.00 0.00 1.73
135 136 1.695242 TCCTTCGTCCAACCTTGCTTA 59.305 47.619 0.00 0.00 0.00 3.09
136 137 0.472471 TCCTTCGTCCAACCTTGCTT 59.528 50.000 0.00 0.00 0.00 3.91
137 138 0.035458 CTCCTTCGTCCAACCTTGCT 59.965 55.000 0.00 0.00 0.00 3.91
138 139 0.034896 TCTCCTTCGTCCAACCTTGC 59.965 55.000 0.00 0.00 0.00 4.01
139 140 1.338200 CCTCTCCTTCGTCCAACCTTG 60.338 57.143 0.00 0.00 0.00 3.61
140 141 0.977395 CCTCTCCTTCGTCCAACCTT 59.023 55.000 0.00 0.00 0.00 3.50
141 142 0.178929 ACCTCTCCTTCGTCCAACCT 60.179 55.000 0.00 0.00 0.00 3.50
142 143 0.037232 CACCTCTCCTTCGTCCAACC 60.037 60.000 0.00 0.00 0.00 3.77
143 144 0.966920 TCACCTCTCCTTCGTCCAAC 59.033 55.000 0.00 0.00 0.00 3.77
144 145 1.712056 TTCACCTCTCCTTCGTCCAA 58.288 50.000 0.00 0.00 0.00 3.53
145 146 1.712056 TTTCACCTCTCCTTCGTCCA 58.288 50.000 0.00 0.00 0.00 4.02
146 147 2.233922 TCATTTCACCTCTCCTTCGTCC 59.766 50.000 0.00 0.00 0.00 4.79
147 148 3.193691 TCTCATTTCACCTCTCCTTCGTC 59.806 47.826 0.00 0.00 0.00 4.20
148 149 3.165875 TCTCATTTCACCTCTCCTTCGT 58.834 45.455 0.00 0.00 0.00 3.85
149 150 3.876274 TCTCATTTCACCTCTCCTTCG 57.124 47.619 0.00 0.00 0.00 3.79
150 151 4.019771 AGGTTCTCATTTCACCTCTCCTTC 60.020 45.833 0.00 0.00 35.99 3.46
151 152 3.913163 AGGTTCTCATTTCACCTCTCCTT 59.087 43.478 0.00 0.00 35.99 3.36
152 153 3.525862 AGGTTCTCATTTCACCTCTCCT 58.474 45.455 0.00 0.00 35.99 3.69
153 154 3.990959 AGGTTCTCATTTCACCTCTCC 57.009 47.619 0.00 0.00 35.99 3.71
154 155 4.865365 CGTAAGGTTCTCATTTCACCTCTC 59.135 45.833 0.00 0.00 40.23 3.20
155 156 4.283722 ACGTAAGGTTCTCATTTCACCTCT 59.716 41.667 0.00 0.00 40.23 3.69
156 157 4.566987 ACGTAAGGTTCTCATTTCACCTC 58.433 43.478 0.00 0.00 40.23 3.85
157 158 4.618920 ACGTAAGGTTCTCATTTCACCT 57.381 40.909 0.00 0.00 43.17 4.00
214 215 7.014134 TGGGCCAATCAATTGTGTATGTATAAG 59.986 37.037 2.13 0.00 36.06 1.73
215 216 6.836007 TGGGCCAATCAATTGTGTATGTATAA 59.164 34.615 2.13 0.00 36.06 0.98
216 217 6.368805 TGGGCCAATCAATTGTGTATGTATA 58.631 36.000 2.13 0.00 36.06 1.47
221 222 4.032310 ACATGGGCCAATCAATTGTGTAT 58.968 39.130 11.89 0.00 36.06 2.29
250 251 7.639113 TTAATGGCACTTCAAGGTATAAAGG 57.361 36.000 0.00 0.00 0.00 3.11
255 257 6.096846 GGTCATTTAATGGCACTTCAAGGTAT 59.903 38.462 11.79 0.00 36.36 2.73
260 262 6.350110 GCTTAGGTCATTTAATGGCACTTCAA 60.350 38.462 11.79 0.00 36.36 2.69
364 368 4.093472 ACACACATTACCAGCAAAGGTA 57.907 40.909 0.00 0.00 43.08 3.08
365 369 2.944129 ACACACATTACCAGCAAAGGT 58.056 42.857 1.10 1.10 45.72 3.50
366 370 4.699735 TGATACACACATTACCAGCAAAGG 59.300 41.667 0.00 0.00 0.00 3.11
434 448 5.630061 TGCATACATATGTGCGATAAATGC 58.370 37.500 22.18 22.18 45.45 3.56
435 449 6.834876 ACTGCATACATATGTGCGATAAATG 58.165 36.000 18.81 12.47 45.45 2.32
436 450 8.546597 TTACTGCATACATATGTGCGATAAAT 57.453 30.769 18.81 0.00 45.45 1.40
437 451 7.954788 TTACTGCATACATATGTGCGATAAA 57.045 32.000 18.81 5.19 45.45 1.40
438 452 7.954788 TTTACTGCATACATATGTGCGATAA 57.045 32.000 18.81 12.52 45.45 1.75
439 453 7.655732 AGTTTTACTGCATACATATGTGCGATA 59.344 33.333 18.81 7.70 45.45 2.92
440 454 6.483307 AGTTTTACTGCATACATATGTGCGAT 59.517 34.615 18.81 8.60 45.45 4.58
441 455 5.815222 AGTTTTACTGCATACATATGTGCGA 59.185 36.000 18.81 0.00 45.45 5.10
442 456 6.048073 AGTTTTACTGCATACATATGTGCG 57.952 37.500 18.81 9.98 45.45 5.34
458 472 5.713025 ACACATGCATCAATGGAGTTTTAC 58.287 37.500 0.00 0.00 31.46 2.01
488 502 5.476945 GGATATATCCATTCGGTTTTGGCTT 59.523 40.000 24.41 0.00 46.38 4.35
623 641 8.632679 GGCCTATTGAGTATTCATCAATTTTGA 58.367 33.333 6.50 0.00 43.20 2.69
625 643 8.636213 CAGGCCTATTGAGTATTCATCAATTTT 58.364 33.333 3.98 0.00 43.20 1.82
634 652 2.802816 CACGCAGGCCTATTGAGTATTC 59.197 50.000 3.98 0.00 0.00 1.75
725 744 9.814899 ACATTGTGTCTTTGTTTGATTGATTTA 57.185 25.926 0.00 0.00 0.00 1.40
762 787 6.662755 TGAGGAACATGCCAAACTATTCTAT 58.337 36.000 0.00 0.00 0.00 1.98
961 995 7.868415 AGTTGAACGCTATAGAATTATGAGGAC 59.132 37.037 3.21 0.00 0.00 3.85
993 1030 6.239829 GGTTGACTATTGGATCCATGAGAGAT 60.240 42.308 23.70 13.33 0.00 2.75
1044 1081 2.017623 GCAATGAGTGAGCATGCCTCT 61.018 52.381 15.66 11.91 41.35 3.69
1107 1144 7.063544 ACGATGTAGTTGTGCTTCTTATTCTTC 59.936 37.037 0.00 0.00 0.00 2.87
1113 1150 5.128992 TCACGATGTAGTTGTGCTTCTTA 57.871 39.130 0.00 0.00 41.28 2.10
1211 1248 2.037641 TCCTTCCGCTGGATCATATGTG 59.962 50.000 1.90 0.00 0.00 3.21
1212 1249 2.301296 CTCCTTCCGCTGGATCATATGT 59.699 50.000 1.90 0.00 32.56 2.29
1229 1266 0.421904 AGTAACATGGGTCCCCTCCT 59.578 55.000 5.13 0.00 36.94 3.69
1288 1325 5.197682 GGTAGCTCATAGTTACCGTTGAT 57.802 43.478 4.50 0.00 41.19 2.57
1387 4176 2.834549 TGATTGTTGTCTCCTCCTCTCC 59.165 50.000 0.00 0.00 0.00 3.71
1390 4179 3.198635 TCCATGATTGTTGTCTCCTCCTC 59.801 47.826 0.00 0.00 0.00 3.71
1391 4180 3.054802 GTCCATGATTGTTGTCTCCTCCT 60.055 47.826 0.00 0.00 0.00 3.69
1392 4181 3.274288 GTCCATGATTGTTGTCTCCTCC 58.726 50.000 0.00 0.00 0.00 4.30
1399 4192 7.664552 ATCCATTATTGTCCATGATTGTTGT 57.335 32.000 0.00 0.00 0.00 3.32
1455 4251 1.138036 CTCACCCGTCAACGCGATA 59.862 57.895 15.93 0.00 38.18 2.92
1459 4255 4.980805 TGCCTCACCCGTCAACGC 62.981 66.667 0.00 0.00 38.18 4.84
1490 4286 1.956477 ACACCTCCATCTTGTTGTTGC 59.044 47.619 0.00 0.00 0.00 4.17
1563 4362 2.225727 GTGTTCCTCATCGGTCCAAAAC 59.774 50.000 0.00 0.00 0.00 2.43
1670 4470 7.312154 TGTTCTCACATAATAAATTGGCACAC 58.688 34.615 0.00 0.00 39.29 3.82
1696 4496 8.510243 ACAATATCATCACAAACATAAGCTGA 57.490 30.769 0.00 0.00 0.00 4.26
1732 4534 3.385193 TGACAGTGTCCATGTGTACAG 57.615 47.619 20.43 0.00 0.00 2.74
1856 4658 1.961394 TCCCGATTCTTGTATCCTCCG 59.039 52.381 0.00 0.00 0.00 4.63
1873 4693 2.141312 GAGCCTCCTCCATCTTCCC 58.859 63.158 0.00 0.00 31.68 3.97
1954 4774 3.210232 TCGTTGATGTGGGGTTACAAA 57.790 42.857 0.00 0.00 33.69 2.83
1959 4779 2.358322 ACTTTCGTTGATGTGGGGTT 57.642 45.000 0.00 0.00 0.00 4.11
1960 4780 2.358322 AACTTTCGTTGATGTGGGGT 57.642 45.000 0.00 0.00 30.67 4.95
2080 4900 6.751425 TGCCTCATAAAATTAATTTGCAGACG 59.249 34.615 14.04 7.48 32.27 4.18
2248 5082 7.696992 ACCGCCTTTCTATTTTCTAATCAAA 57.303 32.000 0.00 0.00 0.00 2.69
2256 5090 6.072342 TCCTGTTTAACCGCCTTTCTATTTTC 60.072 38.462 0.00 0.00 0.00 2.29
2277 5113 8.289618 CGTACCATATTGGAATTTAATGTCCTG 58.710 37.037 0.00 0.00 40.96 3.86
2281 5117 8.974060 AGACGTACCATATTGGAATTTAATGT 57.026 30.769 0.00 0.00 40.96 2.71
2312 5148 6.459670 TGATCTGTTTGATTGGGATGATTG 57.540 37.500 0.00 0.00 35.14 2.67
2313 5149 7.670605 ATTGATCTGTTTGATTGGGATGATT 57.329 32.000 0.00 0.00 35.14 2.57
2314 5150 8.636213 GTTATTGATCTGTTTGATTGGGATGAT 58.364 33.333 0.00 0.00 35.14 2.45
2315 5151 7.068593 GGTTATTGATCTGTTTGATTGGGATGA 59.931 37.037 0.00 0.00 35.14 2.92
2316 5152 7.069085 AGGTTATTGATCTGTTTGATTGGGATG 59.931 37.037 0.00 0.00 35.14 3.51
2317 5153 7.128077 AGGTTATTGATCTGTTTGATTGGGAT 58.872 34.615 0.00 0.00 35.14 3.85
2318 5154 6.493166 AGGTTATTGATCTGTTTGATTGGGA 58.507 36.000 0.00 0.00 35.14 4.37
2319 5155 6.780457 AGGTTATTGATCTGTTTGATTGGG 57.220 37.500 0.00 0.00 35.14 4.12
2476 5313 8.910666 CACATGCTTATTTTTGTTGATTTACGA 58.089 29.630 0.00 0.00 0.00 3.43
2611 6413 9.132521 CTGTGGACATAATGTTCAAAAGAATTC 57.867 33.333 0.00 0.00 37.66 2.17
2776 6578 2.699954 CTGTAACGCTTTGTCCCTGAT 58.300 47.619 0.00 0.00 0.00 2.90
2823 6625 4.630894 TTATTTGTTGCCAATAGCTCGG 57.369 40.909 0.00 0.00 44.23 4.63
2837 6639 5.681639 CCGAGGGGAAGAACTATTATTTGT 58.318 41.667 0.00 0.00 34.06 2.83
2852 6654 2.420466 GAAAGGGTTTGCCGAGGGGA 62.420 60.000 0.00 0.00 34.06 4.81
2880 6682 1.425066 AGCTTGGGTCATTGTTGAGGA 59.575 47.619 0.00 0.00 30.85 3.71
3105 6910 5.403766 GCGGATCTACTACATCTTGTTCATG 59.596 44.000 0.00 0.00 0.00 3.07
3154 6959 2.753043 GGGACACATGCCTGGCTG 60.753 66.667 21.03 16.96 32.31 4.85
3365 7190 7.138736 GCGCTTTCATATGGTAATACAACAAT 58.861 34.615 0.00 0.00 0.00 2.71
3390 7218 3.424829 GCCACGTATTGAGACAACATGTG 60.425 47.826 0.00 7.77 0.00 3.21
3451 7280 2.609350 CTTTTTCATGGGGTGATTGCG 58.391 47.619 0.00 0.00 36.54 4.85
3530 7359 6.238648 AGGTCTGATTTTCAAGTAATTCGGT 58.761 36.000 0.00 0.00 0.00 4.69
3628 7462 0.822164 TTACTAGCGGCTCTTGGACC 59.178 55.000 5.39 0.00 0.00 4.46
3640 7474 9.716507 CAACACCACACAATATTAATTACTAGC 57.283 33.333 0.00 0.00 0.00 3.42
3740 7584 6.884832 AGTGACGGTGAAATATGAAATCCTA 58.115 36.000 0.00 0.00 0.00 2.94
3879 7723 8.209584 CCTGATCTCTTTATTCTCCATTCTCAA 58.790 37.037 0.00 0.00 0.00 3.02
3894 7738 3.134804 CCAATCGTACCCCTGATCTCTTT 59.865 47.826 0.00 0.00 0.00 2.52
3942 7786 4.017867 ACCTAGGTCTCTAGAGCAAGAACT 60.018 45.833 15.35 8.58 44.35 3.01
4008 7855 9.520515 TTCATCTACTAATTTCTTCTTTTGGCT 57.479 29.630 0.00 0.00 0.00 4.75
4065 7913 5.652452 AGGTAAGGAAAACACTATCCAATGC 59.348 40.000 0.00 0.00 38.23 3.56
4082 7930 5.532779 GGATATGAGCCAAAAGAAGGTAAGG 59.467 44.000 0.00 0.00 0.00 2.69
4086 7934 4.018050 ACTGGATATGAGCCAAAAGAAGGT 60.018 41.667 0.00 0.00 34.44 3.50


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

AutoCloner maintained by Alex Coulton.