Multiple sequence alignment - TraesCS6A01G257100

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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 TraesCS6A01G257100 chr6A 100.000 3516 0 0 1 3516 479403664 479407179 0.000000e+00 6493
1 TraesCS6A01G257100 chr6A 97.859 3270 48 4 261 3516 88095284 88098545 0.000000e+00 5631
2 TraesCS6A01G257100 chr6A 92.308 91 4 2 186 276 88095282 88095369 3.680000e-25 126
3 TraesCS6A01G257100 chr6A 93.182 88 3 2 262 346 479403852 479403939 3.680000e-25 126
4 TraesCS6A01G257100 chr6A 93.182 88 3 2 189 276 479403925 479404009 3.680000e-25 126
5 TraesCS6A01G257100 chr7A 98.075 3273 45 4 261 3516 671188854 671192125 0.000000e+00 5679
6 TraesCS6A01G257100 chr7A 94.516 620 24 2 255 864 163373942 163373323 0.000000e+00 948
7 TraesCS6A01G257100 chr7A 82.287 446 79 0 3067 3512 208088990 208089435 1.530000e-103 387
8 TraesCS6A01G257100 chr7A 93.478 92 3 2 185 276 671188851 671188939 2.200000e-27 134
9 TraesCS6A01G257100 chr7A 92.473 93 4 2 184 276 163373939 163373850 2.850000e-26 130
10 TraesCS6A01G257100 chr5B 98.260 3218 40 2 315 3516 522908154 522904937 0.000000e+00 5618
11 TraesCS6A01G257100 chr7D 97.703 2917 49 9 608 3516 28369167 28366261 0.000000e+00 5000
12 TraesCS6A01G257100 chr7D 92.113 355 17 3 262 607 28383197 28382845 1.130000e-134 490
13 TraesCS6A01G257100 chr7D 92.222 90 3 3 187 276 28383199 28383114 1.330000e-24 124
14 TraesCS6A01G257100 chr7B 88.109 2338 236 24 1205 3516 133496924 133494603 0.000000e+00 2739
15 TraesCS6A01G257100 chr5D 89.173 2152 208 13 1371 3516 245298147 245300279 0.000000e+00 2660
16 TraesCS6A01G257100 chr4A 86.016 1895 212 26 1205 3064 281409988 281411864 0.000000e+00 1982
17 TraesCS6A01G257100 chr4A 93.873 457 28 0 3060 3516 281416891 281417347 0.000000e+00 689
18 TraesCS6A01G257100 chr4A 91.429 105 7 1 85 189 716296337 716296235 3.660000e-30 143
19 TraesCS6A01G257100 chr1A 99.122 1025 9 0 2492 3516 549415506 549416530 0.000000e+00 1844
20 TraesCS6A01G257100 chr1A 95.455 792 21 1 261 1037 549414716 549415507 0.000000e+00 1249
21 TraesCS6A01G257100 chr2D 79.727 878 103 40 462 1315 14463046 14463872 1.830000e-157 566
22 TraesCS6A01G257100 chr2D 87.313 134 11 5 266 396 14462863 14462993 7.860000e-32 148
23 TraesCS6A01G257100 chr5A 98.942 189 0 1 1 189 261711690 261711504 1.560000e-88 337


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 TraesCS6A01G257100 chr6A 479403664 479407179 3515 False 2248.333333 6493 95.454667 1 3516 3 chr6A.!!$F2 3515
1 TraesCS6A01G257100 chr6A 88095282 88098545 3263 False 2878.500000 5631 95.083500 186 3516 2 chr6A.!!$F1 3330
2 TraesCS6A01G257100 chr7A 671188851 671192125 3274 False 2906.500000 5679 95.776500 185 3516 2 chr7A.!!$F2 3331
3 TraesCS6A01G257100 chr7A 163373323 163373942 619 True 539.000000 948 93.494500 184 864 2 chr7A.!!$R1 680
4 TraesCS6A01G257100 chr5B 522904937 522908154 3217 True 5618.000000 5618 98.260000 315 3516 1 chr5B.!!$R1 3201
5 TraesCS6A01G257100 chr7D 28366261 28369167 2906 True 5000.000000 5000 97.703000 608 3516 1 chr7D.!!$R1 2908
6 TraesCS6A01G257100 chr7B 133494603 133496924 2321 True 2739.000000 2739 88.109000 1205 3516 1 chr7B.!!$R1 2311
7 TraesCS6A01G257100 chr5D 245298147 245300279 2132 False 2660.000000 2660 89.173000 1371 3516 1 chr5D.!!$F1 2145
8 TraesCS6A01G257100 chr4A 281409988 281411864 1876 False 1982.000000 1982 86.016000 1205 3064 1 chr4A.!!$F1 1859
9 TraesCS6A01G257100 chr1A 549414716 549416530 1814 False 1546.500000 1844 97.288500 261 3516 2 chr1A.!!$F1 3255
10 TraesCS6A01G257100 chr2D 14462863 14463872 1009 False 357.000000 566 83.520000 266 1315 2 chr2D.!!$F1 1049

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
61 62 0.035630 CTCCTGGCCCTCTTTGACAG 60.036 60.000 0.00 0.0 0.0 3.51 F
647 673 0.252479 CCTTCTGCTCAGCTGGTCAT 59.748 55.000 15.13 0.0 0.0 3.06 F
732 762 0.984230 ACTCCAAAAGCCAGATCCGA 59.016 50.000 0.00 0.0 0.0 4.55 F
1813 1884 6.039829 CCCTTTTATGAAGAATTAGCTCCACC 59.960 42.308 0.00 0.0 0.0 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1146 1187 4.799949 CAGGGCACAAATGATATTTGTTCG 59.200 41.667 15.14 8.24 40.30 3.95 R
2071 2142 1.990563 GTAAACCACATGTCCGACTCG 59.009 52.381 0.00 0.00 0.00 4.18 R
2179 2250 5.009010 AGTGTCATGTTTCTCCATTTGTGTC 59.991 40.000 0.00 0.00 0.00 3.67 R
3278 3356 2.225267 CCATGGTTTTCAAGTACCCCCT 60.225 50.000 2.57 0.00 33.34 4.79 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
40 41 8.384607 GAGAATACCATTCTCAACCTAATTCC 57.615 38.462 19.29 0.00 43.25 3.01
41 42 7.872138 AGAATACCATTCTCAACCTAATTCCA 58.128 34.615 0.00 0.00 0.00 3.53
42 43 7.775561 AGAATACCATTCTCAACCTAATTCCAC 59.224 37.037 0.00 0.00 0.00 4.02
43 44 5.520748 ACCATTCTCAACCTAATTCCACT 57.479 39.130 0.00 0.00 0.00 4.00
44 45 5.501156 ACCATTCTCAACCTAATTCCACTC 58.499 41.667 0.00 0.00 0.00 3.51
45 46 4.884164 CCATTCTCAACCTAATTCCACTCC 59.116 45.833 0.00 0.00 0.00 3.85
46 47 5.339530 CCATTCTCAACCTAATTCCACTCCT 60.340 44.000 0.00 0.00 0.00 3.69
47 48 4.826274 TCTCAACCTAATTCCACTCCTG 57.174 45.455 0.00 0.00 0.00 3.86
48 49 3.519510 TCTCAACCTAATTCCACTCCTGG 59.480 47.826 0.00 0.00 39.23 4.45
49 50 2.026262 TCAACCTAATTCCACTCCTGGC 60.026 50.000 0.00 0.00 37.49 4.85
50 51 0.919710 ACCTAATTCCACTCCTGGCC 59.080 55.000 0.00 0.00 37.49 5.36
51 52 0.183731 CCTAATTCCACTCCTGGCCC 59.816 60.000 0.00 0.00 37.49 5.80
52 53 1.216990 CTAATTCCACTCCTGGCCCT 58.783 55.000 0.00 0.00 37.49 5.19
53 54 1.141858 CTAATTCCACTCCTGGCCCTC 59.858 57.143 0.00 0.00 37.49 4.30
54 55 0.551131 AATTCCACTCCTGGCCCTCT 60.551 55.000 0.00 0.00 37.49 3.69
55 56 0.551131 ATTCCACTCCTGGCCCTCTT 60.551 55.000 0.00 0.00 37.49 2.85
56 57 0.772124 TTCCACTCCTGGCCCTCTTT 60.772 55.000 0.00 0.00 37.49 2.52
57 58 1.001641 CCACTCCTGGCCCTCTTTG 60.002 63.158 0.00 0.00 0.00 2.77
58 59 1.492133 CCACTCCTGGCCCTCTTTGA 61.492 60.000 0.00 0.00 0.00 2.69
59 60 0.322008 CACTCCTGGCCCTCTTTGAC 60.322 60.000 0.00 0.00 0.00 3.18
60 61 0.768221 ACTCCTGGCCCTCTTTGACA 60.768 55.000 0.00 0.00 0.00 3.58
61 62 0.035630 CTCCTGGCCCTCTTTGACAG 60.036 60.000 0.00 0.00 0.00 3.51
62 63 0.473694 TCCTGGCCCTCTTTGACAGA 60.474 55.000 0.00 0.00 0.00 3.41
63 64 0.401738 CCTGGCCCTCTTTGACAGAA 59.598 55.000 0.00 0.00 0.00 3.02
64 65 1.612726 CCTGGCCCTCTTTGACAGAAG 60.613 57.143 0.00 0.00 0.00 2.85
65 66 1.349026 CTGGCCCTCTTTGACAGAAGA 59.651 52.381 0.00 0.00 34.63 2.87
66 67 1.988107 TGGCCCTCTTTGACAGAAGAT 59.012 47.619 0.00 0.00 35.27 2.40
67 68 3.181329 TGGCCCTCTTTGACAGAAGATA 58.819 45.455 0.00 0.00 35.27 1.98
68 69 3.587061 TGGCCCTCTTTGACAGAAGATAA 59.413 43.478 0.00 0.00 35.27 1.75
69 70 4.228210 TGGCCCTCTTTGACAGAAGATAAT 59.772 41.667 0.00 0.00 35.27 1.28
70 71 4.819088 GGCCCTCTTTGACAGAAGATAATC 59.181 45.833 0.00 0.00 35.27 1.75
71 72 5.431765 GCCCTCTTTGACAGAAGATAATCA 58.568 41.667 2.04 0.00 35.27 2.57
72 73 6.060788 GCCCTCTTTGACAGAAGATAATCAT 58.939 40.000 2.04 0.00 35.27 2.45
73 74 6.545298 GCCCTCTTTGACAGAAGATAATCATT 59.455 38.462 2.04 0.00 35.27 2.57
74 75 7.255070 GCCCTCTTTGACAGAAGATAATCATTC 60.255 40.741 2.04 0.00 35.27 2.67
75 76 7.772292 CCCTCTTTGACAGAAGATAATCATTCA 59.228 37.037 2.04 0.00 35.27 2.57
76 77 9.170734 CCTCTTTGACAGAAGATAATCATTCAA 57.829 33.333 2.04 0.00 35.27 2.69
92 93 7.781324 ATCATTCAAAAACTACATTGGTCCT 57.219 32.000 0.00 0.00 0.00 3.85
93 94 8.877864 ATCATTCAAAAACTACATTGGTCCTA 57.122 30.769 0.00 0.00 0.00 2.94
94 95 8.877864 TCATTCAAAAACTACATTGGTCCTAT 57.122 30.769 0.00 0.00 0.00 2.57
95 96 8.739039 TCATTCAAAAACTACATTGGTCCTATG 58.261 33.333 11.29 11.29 0.00 2.23
96 97 8.522830 CATTCAAAAACTACATTGGTCCTATGT 58.477 33.333 20.55 20.55 39.44 2.29
97 98 7.681939 TCAAAAACTACATTGGTCCTATGTC 57.318 36.000 20.37 0.00 37.42 3.06
98 99 6.657541 TCAAAAACTACATTGGTCCTATGTCC 59.342 38.462 20.37 0.00 37.42 4.02
99 100 6.388619 AAAACTACATTGGTCCTATGTCCT 57.611 37.500 20.37 6.18 37.42 3.85
100 101 6.388619 AAACTACATTGGTCCTATGTCCTT 57.611 37.500 20.37 11.14 37.42 3.36
101 102 6.388619 AACTACATTGGTCCTATGTCCTTT 57.611 37.500 20.37 10.55 37.42 3.11
102 103 5.745227 ACTACATTGGTCCTATGTCCTTTG 58.255 41.667 20.37 10.48 37.42 2.77
103 104 4.657814 ACATTGGTCCTATGTCCTTTGT 57.342 40.909 12.58 0.00 30.65 2.83
104 105 4.998051 ACATTGGTCCTATGTCCTTTGTT 58.002 39.130 12.58 0.00 30.65 2.83
105 106 5.393866 ACATTGGTCCTATGTCCTTTGTTT 58.606 37.500 12.58 0.00 30.65 2.83
106 107 5.838521 ACATTGGTCCTATGTCCTTTGTTTT 59.161 36.000 12.58 0.00 30.65 2.43
107 108 6.015434 ACATTGGTCCTATGTCCTTTGTTTTC 60.015 38.462 12.58 0.00 30.65 2.29
108 109 5.319043 TGGTCCTATGTCCTTTGTTTTCT 57.681 39.130 0.00 0.00 0.00 2.52
109 110 5.701224 TGGTCCTATGTCCTTTGTTTTCTT 58.299 37.500 0.00 0.00 0.00 2.52
110 111 6.843752 TGGTCCTATGTCCTTTGTTTTCTTA 58.156 36.000 0.00 0.00 0.00 2.10
111 112 6.713450 TGGTCCTATGTCCTTTGTTTTCTTAC 59.287 38.462 0.00 0.00 0.00 2.34
112 113 6.713450 GGTCCTATGTCCTTTGTTTTCTTACA 59.287 38.462 0.00 0.00 0.00 2.41
113 114 7.308408 GGTCCTATGTCCTTTGTTTTCTTACAC 60.308 40.741 0.00 0.00 0.00 2.90
114 115 7.227910 GTCCTATGTCCTTTGTTTTCTTACACA 59.772 37.037 0.00 0.00 0.00 3.72
115 116 7.942341 TCCTATGTCCTTTGTTTTCTTACACAT 59.058 33.333 0.00 0.00 0.00 3.21
116 117 8.023128 CCTATGTCCTTTGTTTTCTTACACATG 58.977 37.037 0.00 0.00 0.00 3.21
117 118 6.767524 TGTCCTTTGTTTTCTTACACATGT 57.232 33.333 0.00 0.00 0.00 3.21
118 119 6.559810 TGTCCTTTGTTTTCTTACACATGTG 58.440 36.000 24.25 24.25 0.00 3.21
119 120 5.977129 GTCCTTTGTTTTCTTACACATGTGG 59.023 40.000 28.64 12.14 34.19 4.17
120 121 5.888724 TCCTTTGTTTTCTTACACATGTGGA 59.111 36.000 28.64 19.57 34.19 4.02
121 122 6.549364 TCCTTTGTTTTCTTACACATGTGGAT 59.451 34.615 28.64 12.23 34.19 3.41
122 123 6.642131 CCTTTGTTTTCTTACACATGTGGATG 59.358 38.462 28.64 22.24 35.49 3.51
123 124 6.951062 TTGTTTTCTTACACATGTGGATGA 57.049 33.333 28.64 24.10 33.36 2.92
124 125 6.558771 TGTTTTCTTACACATGTGGATGAG 57.441 37.500 28.64 16.28 30.54 2.90
125 126 5.048782 TGTTTTCTTACACATGTGGATGAGC 60.049 40.000 28.64 19.42 30.54 4.26
126 127 3.979101 TCTTACACATGTGGATGAGCA 57.021 42.857 28.64 4.97 33.36 4.26
127 128 3.865446 TCTTACACATGTGGATGAGCAG 58.135 45.455 28.64 14.83 33.36 4.24
128 129 3.261643 TCTTACACATGTGGATGAGCAGT 59.738 43.478 28.64 7.84 33.36 4.40
129 130 2.574006 ACACATGTGGATGAGCAGTT 57.426 45.000 28.64 1.52 33.36 3.16
130 131 2.156917 ACACATGTGGATGAGCAGTTG 58.843 47.619 28.64 0.10 33.36 3.16
131 132 2.224597 ACACATGTGGATGAGCAGTTGA 60.225 45.455 28.64 0.00 33.36 3.18
132 133 2.161012 CACATGTGGATGAGCAGTTGAC 59.839 50.000 18.51 0.00 33.36 3.18
133 134 2.224597 ACATGTGGATGAGCAGTTGACA 60.225 45.455 0.00 0.00 33.36 3.58
134 135 1.882912 TGTGGATGAGCAGTTGACAC 58.117 50.000 0.00 0.00 0.00 3.67
135 136 1.140652 TGTGGATGAGCAGTTGACACA 59.859 47.619 0.00 0.00 35.29 3.72
136 137 2.221169 GTGGATGAGCAGTTGACACAA 58.779 47.619 0.00 0.00 0.00 3.33
137 138 2.816087 GTGGATGAGCAGTTGACACAAT 59.184 45.455 0.00 0.00 0.00 2.71
138 139 3.254166 GTGGATGAGCAGTTGACACAATT 59.746 43.478 0.00 0.00 0.00 2.32
139 140 3.890756 TGGATGAGCAGTTGACACAATTT 59.109 39.130 0.00 0.00 0.00 1.82
140 141 4.341806 TGGATGAGCAGTTGACACAATTTT 59.658 37.500 0.00 0.00 0.00 1.82
141 142 4.919754 GGATGAGCAGTTGACACAATTTTC 59.080 41.667 0.00 0.00 0.00 2.29
142 143 4.305989 TGAGCAGTTGACACAATTTTCC 57.694 40.909 0.00 0.00 0.00 3.13
143 144 3.953612 TGAGCAGTTGACACAATTTTCCT 59.046 39.130 0.00 0.00 0.00 3.36
144 145 5.129634 TGAGCAGTTGACACAATTTTCCTA 58.870 37.500 0.00 0.00 0.00 2.94
145 146 5.769662 TGAGCAGTTGACACAATTTTCCTAT 59.230 36.000 0.00 0.00 0.00 2.57
146 147 6.265196 TGAGCAGTTGACACAATTTTCCTATT 59.735 34.615 0.00 0.00 0.00 1.73
147 148 6.449698 AGCAGTTGACACAATTTTCCTATTG 58.550 36.000 0.00 0.00 40.53 1.90
148 149 6.040842 AGCAGTTGACACAATTTTCCTATTGT 59.959 34.615 0.00 0.00 46.73 2.71
149 150 6.363357 GCAGTTGACACAATTTTCCTATTGTC 59.637 38.462 0.00 0.00 44.64 3.18
150 151 6.578545 CAGTTGACACAATTTTCCTATTGTCG 59.421 38.462 0.00 0.00 44.64 4.35
151 152 5.621197 TGACACAATTTTCCTATTGTCGG 57.379 39.130 0.00 0.00 44.64 4.79
152 153 5.067273 TGACACAATTTTCCTATTGTCGGT 58.933 37.500 0.00 0.00 44.64 4.69
153 154 6.231951 TGACACAATTTTCCTATTGTCGGTA 58.768 36.000 0.00 0.00 44.64 4.02
154 155 6.882140 TGACACAATTTTCCTATTGTCGGTAT 59.118 34.615 0.00 0.00 44.64 2.73
155 156 7.065324 TGACACAATTTTCCTATTGTCGGTATC 59.935 37.037 0.00 0.00 44.64 2.24
156 157 6.882140 ACACAATTTTCCTATTGTCGGTATCA 59.118 34.615 0.00 0.00 44.64 2.15
157 158 7.556275 ACACAATTTTCCTATTGTCGGTATCAT 59.444 33.333 0.00 0.00 44.64 2.45
158 159 7.857389 CACAATTTTCCTATTGTCGGTATCATG 59.143 37.037 0.00 0.00 44.64 3.07
159 160 7.556275 ACAATTTTCCTATTGTCGGTATCATGT 59.444 33.333 0.00 0.00 43.39 3.21
160 161 8.405531 CAATTTTCCTATTGTCGGTATCATGTT 58.594 33.333 0.00 0.00 32.17 2.71
161 162 6.918892 TTTCCTATTGTCGGTATCATGTTG 57.081 37.500 0.00 0.00 0.00 3.33
162 163 5.607939 TCCTATTGTCGGTATCATGTTGT 57.392 39.130 0.00 0.00 0.00 3.32
163 164 6.718522 TCCTATTGTCGGTATCATGTTGTA 57.281 37.500 0.00 0.00 0.00 2.41
164 165 7.297936 TCCTATTGTCGGTATCATGTTGTAT 57.702 36.000 0.00 0.00 0.00 2.29
165 166 7.151976 TCCTATTGTCGGTATCATGTTGTATG 58.848 38.462 0.00 0.00 0.00 2.39
166 167 6.368791 CCTATTGTCGGTATCATGTTGTATGG 59.631 42.308 0.00 0.00 0.00 2.74
167 168 3.462982 TGTCGGTATCATGTTGTATGGC 58.537 45.455 0.00 0.00 0.00 4.40
168 169 3.133901 TGTCGGTATCATGTTGTATGGCT 59.866 43.478 0.00 0.00 0.00 4.75
169 170 4.342665 TGTCGGTATCATGTTGTATGGCTA 59.657 41.667 0.00 0.00 0.00 3.93
170 171 4.684703 GTCGGTATCATGTTGTATGGCTAC 59.315 45.833 0.00 0.00 0.00 3.58
171 172 4.587262 TCGGTATCATGTTGTATGGCTACT 59.413 41.667 0.00 0.00 0.00 2.57
172 173 4.923871 CGGTATCATGTTGTATGGCTACTC 59.076 45.833 0.00 0.00 0.00 2.59
173 174 5.508994 CGGTATCATGTTGTATGGCTACTCA 60.509 44.000 0.00 0.00 0.00 3.41
174 175 6.467677 GGTATCATGTTGTATGGCTACTCAT 58.532 40.000 0.00 0.00 0.00 2.90
175 176 6.936900 GGTATCATGTTGTATGGCTACTCATT 59.063 38.462 0.00 0.00 0.00 2.57
176 177 7.118390 GGTATCATGTTGTATGGCTACTCATTC 59.882 40.741 0.00 0.00 0.00 2.67
177 178 6.239217 TCATGTTGTATGGCTACTCATTCT 57.761 37.500 0.00 0.00 0.00 2.40
178 179 6.051074 TCATGTTGTATGGCTACTCATTCTG 58.949 40.000 0.00 0.00 0.00 3.02
179 180 5.675684 TGTTGTATGGCTACTCATTCTGA 57.324 39.130 0.00 0.00 0.00 3.27
228 229 9.486123 TCATGGGATTTTTGTAGGATTTTCATA 57.514 29.630 0.00 0.00 0.00 2.15
229 230 9.754382 CATGGGATTTTTGTAGGATTTTCATAG 57.246 33.333 0.00 0.00 0.00 2.23
230 231 8.305046 TGGGATTTTTGTAGGATTTTCATAGG 57.695 34.615 0.00 0.00 0.00 2.57
231 232 8.119246 TGGGATTTTTGTAGGATTTTCATAGGA 58.881 33.333 0.00 0.00 0.00 2.94
232 233 9.147732 GGGATTTTTGTAGGATTTTCATAGGAT 57.852 33.333 0.00 0.00 0.00 3.24
292 293 7.043565 CCTTTGATTCATGGGATTTTTGTAGG 58.956 38.462 0.00 0.00 0.00 3.18
303 304 9.713684 ATGGGATTTTTGTAGGATTTTCATAGA 57.286 29.630 0.00 0.00 0.00 1.98
445 446 2.183679 AGCTCTCGGAAAGAATCCTGT 58.816 47.619 0.00 0.00 46.98 4.00
446 447 2.569404 AGCTCTCGGAAAGAATCCTGTT 59.431 45.455 0.00 0.00 46.98 3.16
522 545 3.402110 TCTCACAAGACACATCGCAAAT 58.598 40.909 0.00 0.00 0.00 2.32
647 673 0.252479 CCTTCTGCTCAGCTGGTCAT 59.748 55.000 15.13 0.00 0.00 3.06
681 707 2.774234 CCTCCTTGCTTCTATTCCTCCA 59.226 50.000 0.00 0.00 0.00 3.86
732 762 0.984230 ACTCCAAAAGCCAGATCCGA 59.016 50.000 0.00 0.00 0.00 4.55
1813 1884 6.039829 CCCTTTTATGAAGAATTAGCTCCACC 59.960 42.308 0.00 0.00 0.00 4.61
1918 1989 7.566760 TTGATTGTTCTAAGCAAGTCTTTGA 57.433 32.000 0.00 0.00 36.36 2.69
2179 2250 1.821332 GCAAGCCCCTCCAAGATCG 60.821 63.158 0.00 0.00 0.00 3.69
2328 2399 2.315155 AGAAGCTAGAGGACCCCTACAA 59.685 50.000 0.00 0.00 31.76 2.41
3278 3356 7.309744 CCAGCATCTACAAGGTAAAATTTTCCA 60.310 37.037 6.72 0.00 0.00 3.53
3489 3567 0.885879 TGTACCATCTATAGCGCCGG 59.114 55.000 2.29 0.00 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 7.993183 TGGAATTAGGTTGAGAATGGTATTCTC 59.007 37.037 19.56 19.56 43.85 2.87
16 17 7.775561 GTGGAATTAGGTTGAGAATGGTATTCT 59.224 37.037 3.86 3.86 0.00 2.40
17 18 7.775561 AGTGGAATTAGGTTGAGAATGGTATTC 59.224 37.037 0.00 0.00 0.00 1.75
18 19 7.643123 AGTGGAATTAGGTTGAGAATGGTATT 58.357 34.615 0.00 0.00 0.00 1.89
19 20 7.213178 AGTGGAATTAGGTTGAGAATGGTAT 57.787 36.000 0.00 0.00 0.00 2.73
20 21 6.352737 GGAGTGGAATTAGGTTGAGAATGGTA 60.353 42.308 0.00 0.00 0.00 3.25
21 22 5.501156 GAGTGGAATTAGGTTGAGAATGGT 58.499 41.667 0.00 0.00 0.00 3.55
22 23 4.884164 GGAGTGGAATTAGGTTGAGAATGG 59.116 45.833 0.00 0.00 0.00 3.16
23 24 5.587844 CAGGAGTGGAATTAGGTTGAGAATG 59.412 44.000 0.00 0.00 0.00 2.67
24 25 5.749462 CAGGAGTGGAATTAGGTTGAGAAT 58.251 41.667 0.00 0.00 0.00 2.40
25 26 5.165961 CAGGAGTGGAATTAGGTTGAGAA 57.834 43.478 0.00 0.00 0.00 2.87
26 27 4.826274 CAGGAGTGGAATTAGGTTGAGA 57.174 45.455 0.00 0.00 0.00 3.27
40 41 0.322008 GTCAAAGAGGGCCAGGAGTG 60.322 60.000 6.18 0.00 0.00 3.51
41 42 0.768221 TGTCAAAGAGGGCCAGGAGT 60.768 55.000 6.18 0.00 0.00 3.85
42 43 0.035630 CTGTCAAAGAGGGCCAGGAG 60.036 60.000 6.18 0.00 0.00 3.69
43 44 0.473694 TCTGTCAAAGAGGGCCAGGA 60.474 55.000 6.18 0.00 0.00 3.86
44 45 0.401738 TTCTGTCAAAGAGGGCCAGG 59.598 55.000 6.18 0.00 35.91 4.45
45 46 1.349026 TCTTCTGTCAAAGAGGGCCAG 59.651 52.381 6.18 0.00 35.91 4.85
46 47 1.434188 TCTTCTGTCAAAGAGGGCCA 58.566 50.000 6.18 0.00 35.91 5.36
47 48 2.797177 ATCTTCTGTCAAAGAGGGCC 57.203 50.000 0.00 0.00 38.60 5.80
48 49 5.431765 TGATTATCTTCTGTCAAAGAGGGC 58.568 41.667 0.00 0.00 38.60 5.19
49 50 7.772292 TGAATGATTATCTTCTGTCAAAGAGGG 59.228 37.037 0.00 0.00 38.60 4.30
50 51 8.728337 TGAATGATTATCTTCTGTCAAAGAGG 57.272 34.615 0.00 0.00 38.60 3.69
66 67 9.308000 AGGACCAATGTAGTTTTTGAATGATTA 57.692 29.630 0.00 0.00 0.00 1.75
67 68 8.193953 AGGACCAATGTAGTTTTTGAATGATT 57.806 30.769 0.00 0.00 0.00 2.57
68 69 7.781324 AGGACCAATGTAGTTTTTGAATGAT 57.219 32.000 0.00 0.00 0.00 2.45
69 70 8.739039 CATAGGACCAATGTAGTTTTTGAATGA 58.261 33.333 0.00 0.00 0.00 2.57
70 71 8.522830 ACATAGGACCAATGTAGTTTTTGAATG 58.477 33.333 0.00 0.00 35.82 2.67
71 72 8.650143 ACATAGGACCAATGTAGTTTTTGAAT 57.350 30.769 0.00 0.00 35.82 2.57
72 73 7.175990 GGACATAGGACCAATGTAGTTTTTGAA 59.824 37.037 0.00 0.00 37.69 2.69
73 74 6.657541 GGACATAGGACCAATGTAGTTTTTGA 59.342 38.462 0.00 0.00 37.69 2.69
74 75 6.659242 AGGACATAGGACCAATGTAGTTTTTG 59.341 38.462 0.00 0.00 37.69 2.44
75 76 6.790319 AGGACATAGGACCAATGTAGTTTTT 58.210 36.000 0.00 0.00 37.69 1.94
76 77 6.388619 AGGACATAGGACCAATGTAGTTTT 57.611 37.500 0.00 0.00 37.69 2.43
77 78 6.388619 AAGGACATAGGACCAATGTAGTTT 57.611 37.500 0.00 0.00 37.69 2.66
78 79 6.180472 CAAAGGACATAGGACCAATGTAGTT 58.820 40.000 0.00 0.00 37.69 2.24
79 80 5.250774 ACAAAGGACATAGGACCAATGTAGT 59.749 40.000 0.00 0.00 37.69 2.73
80 81 5.745227 ACAAAGGACATAGGACCAATGTAG 58.255 41.667 0.00 0.00 37.69 2.74
81 82 5.772393 ACAAAGGACATAGGACCAATGTA 57.228 39.130 0.00 0.00 37.69 2.29
82 83 4.657814 ACAAAGGACATAGGACCAATGT 57.342 40.909 0.00 0.17 40.23 2.71
83 84 5.982890 AAACAAAGGACATAGGACCAATG 57.017 39.130 0.00 0.00 0.00 2.82
84 85 6.314917 AGAAAACAAAGGACATAGGACCAAT 58.685 36.000 0.00 0.00 0.00 3.16
85 86 5.701224 AGAAAACAAAGGACATAGGACCAA 58.299 37.500 0.00 0.00 0.00 3.67
86 87 5.319043 AGAAAACAAAGGACATAGGACCA 57.681 39.130 0.00 0.00 0.00 4.02
87 88 6.713450 TGTAAGAAAACAAAGGACATAGGACC 59.287 38.462 0.00 0.00 0.00 4.46
88 89 7.227910 TGTGTAAGAAAACAAAGGACATAGGAC 59.772 37.037 0.00 0.00 0.00 3.85
89 90 7.284074 TGTGTAAGAAAACAAAGGACATAGGA 58.716 34.615 0.00 0.00 0.00 2.94
90 91 7.504924 TGTGTAAGAAAACAAAGGACATAGG 57.495 36.000 0.00 0.00 0.00 2.57
91 92 8.567948 ACATGTGTAAGAAAACAAAGGACATAG 58.432 33.333 0.00 0.00 0.00 2.23
92 93 8.349245 CACATGTGTAAGAAAACAAAGGACATA 58.651 33.333 18.03 0.00 0.00 2.29
93 94 7.202526 CACATGTGTAAGAAAACAAAGGACAT 58.797 34.615 18.03 0.00 0.00 3.06
94 95 6.405286 CCACATGTGTAAGAAAACAAAGGACA 60.405 38.462 23.79 0.00 0.00 4.02
95 96 5.977129 CCACATGTGTAAGAAAACAAAGGAC 59.023 40.000 23.79 0.00 0.00 3.85
96 97 5.888724 TCCACATGTGTAAGAAAACAAAGGA 59.111 36.000 23.79 6.40 0.00 3.36
97 98 6.142818 TCCACATGTGTAAGAAAACAAAGG 57.857 37.500 23.79 4.02 0.00 3.11
98 99 7.424803 TCATCCACATGTGTAAGAAAACAAAG 58.575 34.615 23.79 4.49 0.00 2.77
99 100 7.340122 TCATCCACATGTGTAAGAAAACAAA 57.660 32.000 23.79 0.00 0.00 2.83
100 101 6.514870 GCTCATCCACATGTGTAAGAAAACAA 60.515 38.462 23.79 0.90 0.00 2.83
101 102 5.048782 GCTCATCCACATGTGTAAGAAAACA 60.049 40.000 23.79 0.92 0.00 2.83
102 103 5.048782 TGCTCATCCACATGTGTAAGAAAAC 60.049 40.000 23.79 10.59 0.00 2.43
103 104 5.069318 TGCTCATCCACATGTGTAAGAAAA 58.931 37.500 23.79 6.60 0.00 2.29
104 105 4.650734 TGCTCATCCACATGTGTAAGAAA 58.349 39.130 23.79 6.90 0.00 2.52
105 106 4.256110 CTGCTCATCCACATGTGTAAGAA 58.744 43.478 23.79 9.29 0.00 2.52
106 107 3.261643 ACTGCTCATCCACATGTGTAAGA 59.738 43.478 23.79 14.53 0.00 2.10
107 108 3.603532 ACTGCTCATCCACATGTGTAAG 58.396 45.455 23.79 15.21 0.00 2.34
108 109 3.701205 ACTGCTCATCCACATGTGTAA 57.299 42.857 23.79 12.38 0.00 2.41
109 110 3.007831 TCAACTGCTCATCCACATGTGTA 59.992 43.478 23.79 9.60 0.00 2.90
110 111 2.156917 CAACTGCTCATCCACATGTGT 58.843 47.619 23.79 3.99 0.00 3.72
111 112 2.161012 GTCAACTGCTCATCCACATGTG 59.839 50.000 19.31 19.31 0.00 3.21
112 113 2.224597 TGTCAACTGCTCATCCACATGT 60.225 45.455 0.00 0.00 0.00 3.21
113 114 2.161012 GTGTCAACTGCTCATCCACATG 59.839 50.000 0.00 0.00 0.00 3.21
114 115 2.224597 TGTGTCAACTGCTCATCCACAT 60.225 45.455 0.00 0.00 0.00 3.21
115 116 1.140652 TGTGTCAACTGCTCATCCACA 59.859 47.619 0.00 0.00 0.00 4.17
116 117 1.882912 TGTGTCAACTGCTCATCCAC 58.117 50.000 0.00 0.00 0.00 4.02
117 118 2.636647 TTGTGTCAACTGCTCATCCA 57.363 45.000 0.00 0.00 0.00 3.41
118 119 4.510038 AAATTGTGTCAACTGCTCATCC 57.490 40.909 0.00 0.00 0.00 3.51
119 120 4.919754 GGAAAATTGTGTCAACTGCTCATC 59.080 41.667 0.00 0.00 0.00 2.92
120 121 4.586001 AGGAAAATTGTGTCAACTGCTCAT 59.414 37.500 0.00 0.00 0.00 2.90
121 122 3.953612 AGGAAAATTGTGTCAACTGCTCA 59.046 39.130 0.00 0.00 0.00 4.26
122 123 4.574599 AGGAAAATTGTGTCAACTGCTC 57.425 40.909 0.00 0.00 0.00 4.26
123 124 6.040842 ACAATAGGAAAATTGTGTCAACTGCT 59.959 34.615 1.63 0.00 45.90 4.24
124 125 6.215845 ACAATAGGAAAATTGTGTCAACTGC 58.784 36.000 1.63 0.00 45.90 4.40
134 135 7.930217 ACATGATACCGACAATAGGAAAATTG 58.070 34.615 0.00 0.00 41.65 2.32
135 136 8.405531 CAACATGATACCGACAATAGGAAAATT 58.594 33.333 0.00 0.00 0.00 1.82
136 137 7.556275 ACAACATGATACCGACAATAGGAAAAT 59.444 33.333 0.00 0.00 0.00 1.82
137 138 6.882140 ACAACATGATACCGACAATAGGAAAA 59.118 34.615 0.00 0.00 0.00 2.29
138 139 6.411376 ACAACATGATACCGACAATAGGAAA 58.589 36.000 0.00 0.00 0.00 3.13
139 140 5.984725 ACAACATGATACCGACAATAGGAA 58.015 37.500 0.00 0.00 0.00 3.36
140 141 5.607939 ACAACATGATACCGACAATAGGA 57.392 39.130 0.00 0.00 0.00 2.94
141 142 6.368791 CCATACAACATGATACCGACAATAGG 59.631 42.308 0.00 0.00 0.00 2.57
142 143 6.128553 GCCATACAACATGATACCGACAATAG 60.129 42.308 0.00 0.00 0.00 1.73
143 144 5.699001 GCCATACAACATGATACCGACAATA 59.301 40.000 0.00 0.00 0.00 1.90
144 145 4.515191 GCCATACAACATGATACCGACAAT 59.485 41.667 0.00 0.00 0.00 2.71
145 146 3.874543 GCCATACAACATGATACCGACAA 59.125 43.478 0.00 0.00 0.00 3.18
146 147 3.133901 AGCCATACAACATGATACCGACA 59.866 43.478 0.00 0.00 0.00 4.35
147 148 3.728845 AGCCATACAACATGATACCGAC 58.271 45.455 0.00 0.00 0.00 4.79
148 149 4.587262 AGTAGCCATACAACATGATACCGA 59.413 41.667 0.00 0.00 34.07 4.69
149 150 4.883083 AGTAGCCATACAACATGATACCG 58.117 43.478 0.00 0.00 34.07 4.02
150 151 5.853936 TGAGTAGCCATACAACATGATACC 58.146 41.667 0.00 0.00 34.07 2.73
151 152 7.875041 AGAATGAGTAGCCATACAACATGATAC 59.125 37.037 0.00 0.00 34.11 2.24
152 153 7.874528 CAGAATGAGTAGCCATACAACATGATA 59.125 37.037 0.00 0.00 39.69 2.15
153 154 6.709397 CAGAATGAGTAGCCATACAACATGAT 59.291 38.462 0.00 0.00 39.69 2.45
154 155 6.051074 CAGAATGAGTAGCCATACAACATGA 58.949 40.000 0.00 0.00 39.69 3.07
155 156 6.051074 TCAGAATGAGTAGCCATACAACATG 58.949 40.000 0.00 0.00 42.56 3.21
156 157 6.239217 TCAGAATGAGTAGCCATACAACAT 57.761 37.500 0.00 0.00 42.56 2.71
157 158 5.675684 TCAGAATGAGTAGCCATACAACA 57.324 39.130 0.00 0.00 42.56 3.33
171 172 7.125507 AAGGAGCTCTTAGAAATCTCAGAATGA 59.874 37.037 14.64 0.00 36.93 2.57
172 173 6.819284 AGGAGCTCTTAGAAATCTCAGAATG 58.181 40.000 14.64 0.00 37.54 2.67
173 174 7.436320 AAGGAGCTCTTAGAAATCTCAGAAT 57.564 36.000 14.64 0.00 33.14 2.40
174 175 6.865834 AAGGAGCTCTTAGAAATCTCAGAA 57.134 37.500 14.64 0.00 33.14 3.02
175 176 6.438741 TCAAAGGAGCTCTTAGAAATCTCAGA 59.561 38.462 14.64 0.00 34.78 3.27
176 177 6.638610 TCAAAGGAGCTCTTAGAAATCTCAG 58.361 40.000 14.64 0.00 34.78 3.35
177 178 6.611613 TCAAAGGAGCTCTTAGAAATCTCA 57.388 37.500 14.64 0.00 34.78 3.27
178 179 7.768120 TGAATCAAAGGAGCTCTTAGAAATCTC 59.232 37.037 14.64 5.26 34.78 2.75
179 180 7.628234 TGAATCAAAGGAGCTCTTAGAAATCT 58.372 34.615 14.64 0.00 34.78 2.40
180 181 7.856145 TGAATCAAAGGAGCTCTTAGAAATC 57.144 36.000 14.64 10.81 34.78 2.17
181 182 7.284944 CCATGAATCAAAGGAGCTCTTAGAAAT 59.715 37.037 14.64 2.15 34.78 2.17
182 183 6.600822 CCATGAATCAAAGGAGCTCTTAGAAA 59.399 38.462 14.64 0.00 34.78 2.52
183 184 6.118170 CCATGAATCAAAGGAGCTCTTAGAA 58.882 40.000 14.64 0.00 34.78 2.10
187 188 3.267812 TCCCATGAATCAAAGGAGCTCTT 59.732 43.478 14.64 2.08 37.28 2.85
248 249 3.177228 AGGAGCTCTAGCAGAGGAAAAA 58.823 45.455 14.64 0.00 42.54 1.94
249 250 2.826488 AGGAGCTCTAGCAGAGGAAAA 58.174 47.619 14.64 0.00 42.54 2.29
250 251 2.541233 AGGAGCTCTAGCAGAGGAAA 57.459 50.000 14.64 0.00 42.54 3.13
251 252 2.499289 CAAAGGAGCTCTAGCAGAGGAA 59.501 50.000 14.64 0.00 42.54 3.36
252 253 2.106566 CAAAGGAGCTCTAGCAGAGGA 58.893 52.381 14.64 0.00 42.54 3.71
253 254 2.106566 TCAAAGGAGCTCTAGCAGAGG 58.893 52.381 14.64 0.00 42.54 3.69
254 255 4.141981 TGAATCAAAGGAGCTCTAGCAGAG 60.142 45.833 14.64 8.34 45.04 3.35
255 256 3.771479 TGAATCAAAGGAGCTCTAGCAGA 59.229 43.478 14.64 6.30 45.16 4.26
256 257 4.134379 TGAATCAAAGGAGCTCTAGCAG 57.866 45.455 14.64 0.62 45.16 4.24
257 258 4.449131 CATGAATCAAAGGAGCTCTAGCA 58.551 43.478 14.64 1.78 45.16 3.49
258 259 3.814283 CCATGAATCAAAGGAGCTCTAGC 59.186 47.826 14.64 0.00 42.49 3.42
259 260 4.102210 TCCCATGAATCAAAGGAGCTCTAG 59.898 45.833 14.64 1.36 0.00 2.43
495 518 4.627467 GCGATGTGTCTTGTGAGAAGTTAT 59.373 41.667 0.00 0.00 32.66 1.89
681 707 4.475016 ACCTTGTTGCTGGACTTCCTATAT 59.525 41.667 0.00 0.00 36.82 0.86
732 762 1.925255 TCATGGGAAGCAAAGGAGGAT 59.075 47.619 0.00 0.00 0.00 3.24
1072 1103 5.607939 TTACCACGTGATGATCCAATAGT 57.392 39.130 19.30 3.95 0.00 2.12
1146 1187 4.799949 CAGGGCACAAATGATATTTGTTCG 59.200 41.667 15.14 8.24 40.30 3.95
1918 1989 7.068348 TCAGCATAACGACCTAGAGAATAGTTT 59.932 37.037 0.00 0.00 0.00 2.66
2071 2142 1.990563 GTAAACCACATGTCCGACTCG 59.009 52.381 0.00 0.00 0.00 4.18
2084 2155 9.273016 CTCAAGTTCTTCATCTAAAGTAAACCA 57.727 33.333 0.00 0.00 0.00 3.67
2179 2250 5.009010 AGTGTCATGTTTCTCCATTTGTGTC 59.991 40.000 0.00 0.00 0.00 3.67
2226 2297 5.600069 TCATGGAAGTCATCAGTAGCACTAT 59.400 40.000 0.00 0.00 32.92 2.12
2328 2399 6.691754 TTGTTGTGATACACTTGTTGATGT 57.308 33.333 0.00 0.00 35.11 3.06
3278 3356 2.225267 CCATGGTTTTCAAGTACCCCCT 60.225 50.000 2.57 0.00 33.34 4.79


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

AutoCloner maintained by Alex Coulton.