Multiple sequence alignment - TraesCS4D01G308900

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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 TraesCS4D01G308900 chr4D 100.000 1628 0 0 849 2476 477006951 477008578 0.000000e+00 3007
1 TraesCS4D01G308900 chr4D 100.000 536 0 0 1 536 477006103 477006638 0.000000e+00 990
2 TraesCS4D01G308900 chr4D 85.034 147 13 1 28 165 476884991 476884845 9.230000e-30 141
3 TraesCS4D01G308900 chr4B 94.424 1632 61 10 849 2465 601191858 601193474 0.000000e+00 2483
4 TraesCS4D01G308900 chr4B 93.182 352 15 7 187 536 601191516 601191860 2.200000e-140 508
5 TraesCS4D01G308900 chr4B 90.860 186 13 2 2050 2235 420713696 420713515 1.900000e-61 246
6 TraesCS4D01G308900 chr4A 91.794 1304 83 13 909 2205 683769227 683770513 0.000000e+00 1794
7 TraesCS4D01G308900 chr4A 93.315 359 8 8 169 512 683768382 683768739 1.310000e-142 516
8 TraesCS4D01G308900 chr4A 89.785 186 15 3 2050 2235 688269069 688268888 4.120000e-58 235
9 TraesCS4D01G308900 chr1B 79.953 429 49 26 2050 2466 41251103 41250700 5.210000e-72 281
10 TraesCS4D01G308900 chr6B 78.454 427 59 21 2050 2466 677435293 677434890 5.290000e-62 248
11 TraesCS4D01G308900 chr6B 90.860 186 13 2 2050 2235 165278764 165278583 1.900000e-61 246
12 TraesCS4D01G308900 chr6B 85.143 175 15 3 1 165 60118320 60118493 4.230000e-38 169
13 TraesCS4D01G308900 chr7B 88.710 186 17 2 2050 2235 724776415 724776596 8.910000e-55 224
14 TraesCS4D01G308900 chr6A 86.705 173 12 6 1 163 582805282 582805111 5.440000e-42 182
15 TraesCS4D01G308900 chr6A 82.166 157 16 7 19 165 582809345 582809499 9.300000e-25 124
16 TraesCS4D01G308900 chr2B 86.127 173 13 3 1 163 231244666 231244837 2.530000e-40 176
17 TraesCS4D01G308900 chr2B 85.795 176 14 3 1 166 326311036 326310862 2.530000e-40 176
18 TraesCS4D01G308900 chr2B 85.065 154 11 4 20 163 231238941 231238790 1.980000e-31 147
19 TraesCS4D01G308900 chr1D 88.732 142 15 1 21 162 471098865 471099005 3.270000e-39 172
20 TraesCS4D01G308900 chr1D 83.234 167 16 4 19 174 471097804 471097639 2.570000e-30 143
21 TraesCS4D01G308900 chr5B 85.549 173 14 3 1 163 3572599 3572770 1.180000e-38 171
22 TraesCS4D01G308900 chr5B 85.799 169 12 4 12 170 3568776 3568610 4.230000e-38 169
23 TraesCS4D01G308900 chr5B 84.416 77 10 2 1 76 280458222 280458297 9.500000e-10 75
24 TraesCS4D01G308900 chr2A 84.971 173 15 3 1 163 617846222 617846051 5.480000e-37 165
25 TraesCS4D01G308900 chr2A 85.802 162 12 3 12 163 617850409 617850569 7.090000e-36 161
26 TraesCS4D01G308900 chr2D 83.439 157 16 2 19 166 630778986 630778831 1.190000e-28 137


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 TraesCS4D01G308900 chr4D 477006103 477008578 2475 False 1998.5 3007 100.0000 1 2476 2 chr4D.!!$F1 2475
1 TraesCS4D01G308900 chr4B 601191516 601193474 1958 False 1495.5 2483 93.8030 187 2465 2 chr4B.!!$F1 2278
2 TraesCS4D01G308900 chr4A 683768382 683770513 2131 False 1155.0 1794 92.5545 169 2205 2 chr4A.!!$F1 2036

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
147 148 0.517316 GGCGCAAGTTCAAGTACCTG 59.483 55.0 10.83 0.0 41.68 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1554 1675 0.108585 ACCAGACAAACCAGTGCGAT 59.891 50.0 0.0 0.0 0.0 4.58 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
17 18 4.409218 TACGTGGCGCTCGTGGAC 62.409 66.667 29.52 6.09 41.62 4.02
23 24 4.357947 GCGCTCGTGGACTGGTCA 62.358 66.667 0.00 0.00 0.00 4.02
24 25 2.338620 CGCTCGTGGACTGGTCAA 59.661 61.111 3.10 0.00 0.00 3.18
25 26 1.300620 CGCTCGTGGACTGGTCAAA 60.301 57.895 3.10 0.00 0.00 2.69
26 27 1.557443 CGCTCGTGGACTGGTCAAAC 61.557 60.000 3.10 0.38 0.00 2.93
27 28 1.228657 GCTCGTGGACTGGTCAAACC 61.229 60.000 3.10 0.00 39.22 3.27
28 29 0.944311 CTCGTGGACTGGTCAAACCG 60.944 60.000 3.10 0.00 42.58 4.44
37 38 3.781162 GTCAAACCGGCGGCGTAC 61.781 66.667 30.09 15.50 0.00 3.67
49 50 4.320971 GCGTACCGGCTCTGTATG 57.679 61.111 0.00 0.00 0.00 2.39
50 51 1.436336 GCGTACCGGCTCTGTATGT 59.564 57.895 0.00 0.00 0.00 2.29
51 52 0.870307 GCGTACCGGCTCTGTATGTG 60.870 60.000 0.00 0.00 0.00 3.21
52 53 0.736636 CGTACCGGCTCTGTATGTGA 59.263 55.000 0.00 0.00 0.00 3.58
53 54 1.133598 CGTACCGGCTCTGTATGTGAA 59.866 52.381 0.00 0.00 0.00 3.18
54 55 2.416296 CGTACCGGCTCTGTATGTGAAA 60.416 50.000 0.00 0.00 0.00 2.69
55 56 2.094762 ACCGGCTCTGTATGTGAAAC 57.905 50.000 0.00 0.00 37.35 2.78
72 73 7.520119 TGTGAAACAGTGATCGTATAATCAC 57.480 36.000 8.84 8.84 45.67 3.06
73 74 6.252655 TGTGAAACAGTGATCGTATAATCACG 59.747 38.462 10.50 8.76 45.67 4.35
74 75 8.051168 TGTGAAACAGTGATCGTATAATCACGT 61.051 37.037 10.50 9.22 45.67 4.49
78 79 4.233123 GTGATCGTATAATCACGTCCCA 57.767 45.455 2.55 0.00 44.30 4.37
79 80 4.806330 GTGATCGTATAATCACGTCCCAT 58.194 43.478 2.55 0.00 44.30 4.00
80 81 4.857588 GTGATCGTATAATCACGTCCCATC 59.142 45.833 2.55 0.00 44.30 3.51
81 82 3.547649 TCGTATAATCACGTCCCATCG 57.452 47.619 0.00 0.00 42.51 3.84
82 83 2.880268 TCGTATAATCACGTCCCATCGT 59.120 45.455 0.00 0.00 45.10 3.73
83 84 4.064388 TCGTATAATCACGTCCCATCGTA 58.936 43.478 0.00 0.00 42.27 3.43
84 85 4.083855 TCGTATAATCACGTCCCATCGTAC 60.084 45.833 0.00 0.00 42.27 3.67
85 86 4.319694 CGTATAATCACGTCCCATCGTACA 60.320 45.833 0.00 0.00 42.27 2.90
86 87 4.866508 ATAATCACGTCCCATCGTACAT 57.133 40.909 0.00 0.00 42.27 2.29
87 88 5.970317 ATAATCACGTCCCATCGTACATA 57.030 39.130 0.00 0.00 42.27 2.29
88 89 3.917329 ATCACGTCCCATCGTACATAG 57.083 47.619 0.00 0.00 42.27 2.23
89 90 2.646930 TCACGTCCCATCGTACATAGT 58.353 47.619 0.00 0.00 42.27 2.12
90 91 2.356695 TCACGTCCCATCGTACATAGTG 59.643 50.000 0.00 0.00 42.27 2.74
91 92 2.356695 CACGTCCCATCGTACATAGTGA 59.643 50.000 0.00 0.00 42.27 3.41
92 93 2.357009 ACGTCCCATCGTACATAGTGAC 59.643 50.000 0.00 0.00 42.35 3.67
93 94 2.287427 CGTCCCATCGTACATAGTGACC 60.287 54.545 0.00 0.00 0.00 4.02
94 95 1.951602 TCCCATCGTACATAGTGACCG 59.048 52.381 0.00 0.00 0.00 4.79
95 96 1.679680 CCCATCGTACATAGTGACCGT 59.320 52.381 0.00 0.00 0.00 4.83
96 97 2.880268 CCCATCGTACATAGTGACCGTA 59.120 50.000 0.00 0.00 0.00 4.02
97 98 3.504906 CCCATCGTACATAGTGACCGTAT 59.495 47.826 0.00 0.00 0.00 3.06
98 99 4.022589 CCCATCGTACATAGTGACCGTATT 60.023 45.833 0.00 0.00 0.00 1.89
99 100 5.508489 CCCATCGTACATAGTGACCGTATTT 60.508 44.000 0.00 0.00 0.00 1.40
100 101 5.628193 CCATCGTACATAGTGACCGTATTTC 59.372 44.000 0.00 0.00 0.00 2.17
101 102 6.436261 CATCGTACATAGTGACCGTATTTCT 58.564 40.000 0.00 0.00 0.00 2.52
102 103 7.308169 CCATCGTACATAGTGACCGTATTTCTA 60.308 40.741 0.00 0.00 0.00 2.10
103 104 7.552458 TCGTACATAGTGACCGTATTTCTAA 57.448 36.000 0.00 0.00 0.00 2.10
104 105 7.633621 TCGTACATAGTGACCGTATTTCTAAG 58.366 38.462 0.00 0.00 0.00 2.18
105 106 7.280876 TCGTACATAGTGACCGTATTTCTAAGT 59.719 37.037 0.00 0.00 0.00 2.24
106 107 8.551205 CGTACATAGTGACCGTATTTCTAAGTA 58.449 37.037 0.00 0.00 0.00 2.24
107 108 9.657121 GTACATAGTGACCGTATTTCTAAGTAC 57.343 37.037 0.00 0.00 32.72 2.73
108 109 8.284945 ACATAGTGACCGTATTTCTAAGTACA 57.715 34.615 0.00 0.00 0.00 2.90
109 110 8.742777 ACATAGTGACCGTATTTCTAAGTACAA 58.257 33.333 0.00 0.00 0.00 2.41
110 111 9.745880 CATAGTGACCGTATTTCTAAGTACAAT 57.254 33.333 0.00 0.00 0.00 2.71
111 112 9.745880 ATAGTGACCGTATTTCTAAGTACAATG 57.254 33.333 0.00 0.00 0.00 2.82
112 113 7.833786 AGTGACCGTATTTCTAAGTACAATGA 58.166 34.615 0.00 0.00 0.00 2.57
113 114 7.758528 AGTGACCGTATTTCTAAGTACAATGAC 59.241 37.037 0.00 0.00 0.00 3.06
114 115 7.009907 GTGACCGTATTTCTAAGTACAATGACC 59.990 40.741 0.00 0.00 0.00 4.02
115 116 6.938507 ACCGTATTTCTAAGTACAATGACCA 58.061 36.000 0.00 0.00 0.00 4.02
116 117 7.388437 ACCGTATTTCTAAGTACAATGACCAA 58.612 34.615 0.00 0.00 0.00 3.67
117 118 7.879160 ACCGTATTTCTAAGTACAATGACCAAA 59.121 33.333 0.00 0.00 0.00 3.28
118 119 8.173130 CCGTATTTCTAAGTACAATGACCAAAC 58.827 37.037 0.00 0.00 0.00 2.93
119 120 8.173130 CGTATTTCTAAGTACAATGACCAAACC 58.827 37.037 0.00 0.00 0.00 3.27
120 121 9.005777 GTATTTCTAAGTACAATGACCAAACCA 57.994 33.333 0.00 0.00 0.00 3.67
121 122 7.883391 TTTCTAAGTACAATGACCAAACCAA 57.117 32.000 0.00 0.00 0.00 3.67
122 123 7.504924 TTCTAAGTACAATGACCAAACCAAG 57.495 36.000 0.00 0.00 0.00 3.61
123 124 4.584327 AAGTACAATGACCAAACCAAGC 57.416 40.909 0.00 0.00 0.00 4.01
124 125 3.832527 AGTACAATGACCAAACCAAGCT 58.167 40.909 0.00 0.00 0.00 3.74
125 126 3.821033 AGTACAATGACCAAACCAAGCTC 59.179 43.478 0.00 0.00 0.00 4.09
126 127 1.608590 ACAATGACCAAACCAAGCTCG 59.391 47.619 0.00 0.00 0.00 5.03
127 128 0.598065 AATGACCAAACCAAGCTCGC 59.402 50.000 0.00 0.00 0.00 5.03
128 129 1.577328 ATGACCAAACCAAGCTCGCG 61.577 55.000 0.00 0.00 0.00 5.87
129 130 2.966309 GACCAAACCAAGCTCGCGG 61.966 63.158 6.13 0.00 0.00 6.46
130 131 4.404654 CCAAACCAAGCTCGCGGC 62.405 66.667 6.13 9.11 42.19 6.53
140 141 3.711842 CTCGCGGCGCAAGTTCAA 61.712 61.111 32.61 6.40 41.68 2.69
141 142 3.635734 CTCGCGGCGCAAGTTCAAG 62.636 63.158 32.61 12.84 41.68 3.02
142 143 4.012895 CGCGGCGCAAGTTCAAGT 62.013 61.111 32.61 0.00 41.68 3.16
143 144 2.663478 CGCGGCGCAAGTTCAAGTA 61.663 57.895 32.61 0.00 41.68 2.24
144 145 1.154469 GCGGCGCAAGTTCAAGTAC 60.154 57.895 29.21 0.00 41.68 2.73
145 146 1.495951 CGGCGCAAGTTCAAGTACC 59.504 57.895 10.83 0.00 41.68 3.34
146 147 0.949105 CGGCGCAAGTTCAAGTACCT 60.949 55.000 10.83 0.00 41.68 3.08
147 148 0.517316 GGCGCAAGTTCAAGTACCTG 59.483 55.000 10.83 0.00 41.68 4.00
148 149 1.226746 GCGCAAGTTCAAGTACCTGT 58.773 50.000 0.30 0.00 41.68 4.00
149 150 2.409975 GCGCAAGTTCAAGTACCTGTA 58.590 47.619 0.30 0.00 41.68 2.74
150 151 2.412089 GCGCAAGTTCAAGTACCTGTAG 59.588 50.000 0.30 0.00 41.68 2.74
151 152 3.650139 CGCAAGTTCAAGTACCTGTAGT 58.350 45.455 0.00 0.00 0.00 2.73
152 153 3.428870 CGCAAGTTCAAGTACCTGTAGTG 59.571 47.826 0.00 0.00 0.00 2.74
153 154 4.377897 GCAAGTTCAAGTACCTGTAGTGT 58.622 43.478 0.00 0.00 0.00 3.55
154 155 5.535333 GCAAGTTCAAGTACCTGTAGTGTA 58.465 41.667 0.00 0.00 0.00 2.90
155 156 6.164176 GCAAGTTCAAGTACCTGTAGTGTAT 58.836 40.000 0.00 0.00 0.00 2.29
156 157 6.649557 GCAAGTTCAAGTACCTGTAGTGTATT 59.350 38.462 0.00 0.00 0.00 1.89
157 158 7.172703 GCAAGTTCAAGTACCTGTAGTGTATTT 59.827 37.037 0.00 0.00 0.00 1.40
158 159 9.052759 CAAGTTCAAGTACCTGTAGTGTATTTT 57.947 33.333 0.00 0.00 0.00 1.82
160 161 9.702494 AGTTCAAGTACCTGTAGTGTATTTTAC 57.298 33.333 0.00 0.00 0.00 2.01
161 162 9.702494 GTTCAAGTACCTGTAGTGTATTTTACT 57.298 33.333 0.00 0.00 0.00 2.24
162 163 9.918630 TTCAAGTACCTGTAGTGTATTTTACTC 57.081 33.333 0.00 0.00 0.00 2.59
163 164 9.081204 TCAAGTACCTGTAGTGTATTTTACTCA 57.919 33.333 0.00 0.00 0.00 3.41
164 165 9.701098 CAAGTACCTGTAGTGTATTTTACTCAA 57.299 33.333 0.00 0.00 0.00 3.02
205 208 1.225855 CGACGAGAGAGAGATGGAGG 58.774 60.000 0.00 0.00 0.00 4.30
412 423 3.308866 CCCGCTCCGTTTTAAATAGACAG 59.691 47.826 0.00 0.00 0.00 3.51
449 462 3.566210 CACCCCACCCCAACTCGT 61.566 66.667 0.00 0.00 0.00 4.18
531 547 1.204113 CCCCTCTCAGCTCCAAGGTT 61.204 60.000 4.54 0.00 0.00 3.50
877 893 4.910585 CCTCCCCCGCGAAATCCG 62.911 72.222 8.23 0.00 42.21 4.18
924 1027 2.355108 CCGTTGATTGATCTGGTGGTCT 60.355 50.000 0.00 0.00 0.00 3.85
935 1042 2.076863 CTGGTGGTCTGTTCGGATTTC 58.923 52.381 0.00 0.00 0.00 2.17
964 1071 2.703007 TGGTTTGGGGATTTGTTCTTGG 59.297 45.455 0.00 0.00 0.00 3.61
1121 1241 1.436983 GCGGATGGCGAAACCCTAAG 61.437 60.000 0.00 0.00 37.83 2.18
1126 1246 2.477845 TGGCGAAACCCTAAGTAACC 57.522 50.000 0.00 0.00 37.83 2.85
1538 1659 0.396435 GAAAACCCCAGGCCCTTTTG 59.604 55.000 0.00 0.00 0.00 2.44
1572 1693 0.798776 GATCGCACTGGTTTGTCTGG 59.201 55.000 0.00 0.00 0.00 3.86
1670 1794 7.957002 AGTCTGTGTTATTATCCTGGATACTG 58.043 38.462 15.88 10.04 37.61 2.74
1691 1815 5.412594 ACTGTTGAATGCTACCTGTTATGTG 59.587 40.000 0.00 0.00 0.00 3.21
1705 1829 4.905429 TGTTATGTGATGCTGGTACTGTT 58.095 39.130 0.00 0.00 0.00 3.16
1706 1830 4.694982 TGTTATGTGATGCTGGTACTGTTG 59.305 41.667 0.00 0.00 0.00 3.33
1715 1839 3.447586 TGCTGGTACTGTTGGTAGATCTC 59.552 47.826 0.00 0.00 0.00 2.75
1718 1842 2.699321 GGTACTGTTGGTAGATCTCCCC 59.301 54.545 0.00 0.83 0.00 4.81
1776 1901 7.624077 ACTGTTATCTGGTTCCTTAGATTAGGT 59.376 37.037 0.00 0.00 36.63 3.08
1781 1906 7.361457 TCTGGTTCCTTAGATTAGGTGTATG 57.639 40.000 0.00 0.00 36.63 2.39
1809 1934 9.671279 TGTTCATGTGATAGTGAATCTTATGTT 57.329 29.630 0.00 0.00 36.79 2.71
1821 1946 8.270744 AGTGAATCTTATGTTTAGCAAGAGGAT 58.729 33.333 0.00 0.00 32.16 3.24
1822 1947 8.897752 GTGAATCTTATGTTTAGCAAGAGGATT 58.102 33.333 0.00 0.00 32.16 3.01
1830 1955 1.831580 AGCAAGAGGATTTGGAGCAC 58.168 50.000 0.00 0.00 0.00 4.40
1832 1957 1.471684 GCAAGAGGATTTGGAGCACTG 59.528 52.381 0.00 0.00 0.00 3.66
1844 1969 2.779430 TGGAGCACTGGTTATGGATGAT 59.221 45.455 0.00 0.00 0.00 2.45
1853 1978 4.910195 TGGTTATGGATGATCTATGCACC 58.090 43.478 12.32 12.32 40.11 5.01
1901 2026 4.766373 TGCATGTTTGGTACATCATCAACT 59.234 37.500 0.00 0.00 45.71 3.16
1922 2047 7.814587 TCAACTGTATCATGTTAGTCTGAAGTG 59.185 37.037 0.00 0.00 0.00 3.16
1926 2051 7.666623 TGTATCATGTTAGTCTGAAGTGACAA 58.333 34.615 0.00 0.00 39.27 3.18
1993 2118 7.814107 GTCCACATTTGTTAACATCATCAACAT 59.186 33.333 9.56 0.00 32.57 2.71
1996 2121 9.194271 CACATTTGTTAACATCATCAACATTGA 57.806 29.630 9.56 0.00 42.14 2.57
2055 2180 1.882623 GGAGGAACTTGCCTTGTCTTG 59.117 52.381 0.00 0.00 41.55 3.02
2113 2239 6.873605 AGTTGCTATGCGATGCTGTTATAATA 59.126 34.615 0.00 0.00 0.00 0.98
2245 2371 3.073650 AGAGCAAATGGAACTCTGGACTT 59.926 43.478 0.00 0.00 0.00 3.01
2252 2378 4.771114 TGGAACTCTGGACTTTCAAAGA 57.229 40.909 3.49 0.00 0.00 2.52
2273 2399 6.290294 AGAATTATCACAGGCAAAAATGCT 57.710 33.333 0.40 0.00 34.73 3.79
2275 2401 2.642139 ATCACAGGCAAAAATGCTCG 57.358 45.000 0.40 0.00 34.73 5.03
2286 2412 4.508052 CAAAAATGCTCGTCTTTTTGCAC 58.492 39.130 7.35 0.00 42.20 4.57
2295 2421 7.406553 TGCTCGTCTTTTTGCACATTATATAC 58.593 34.615 0.00 0.00 0.00 1.47
2299 2425 7.011950 TCGTCTTTTTGCACATTATATACCCTG 59.988 37.037 0.00 0.00 0.00 4.45
2304 2430 2.939640 GCACATTATATACCCTGGGCCG 60.940 54.545 14.08 0.00 31.83 6.13
2364 2490 7.450014 TGTTGAATGTCCAGTACCATTGTAAAT 59.550 33.333 0.51 0.00 31.67 1.40
2408 2534 4.642885 TCACAGGAAGTAAAAACAACTGGG 59.357 41.667 0.00 0.00 0.00 4.45
2423 2549 1.242076 CTGGGGTTCTGCAGAGTTTG 58.758 55.000 17.43 3.08 0.00 2.93
2465 2591 1.879380 TCACCATGCTGCTTTGTGTAC 59.121 47.619 15.97 0.00 0.00 2.90
2466 2592 0.874390 ACCATGCTGCTTTGTGTACG 59.126 50.000 0.00 0.00 0.00 3.67
2467 2593 0.874390 CCATGCTGCTTTGTGTACGT 59.126 50.000 0.00 0.00 0.00 3.57
2468 2594 1.266718 CCATGCTGCTTTGTGTACGTT 59.733 47.619 0.00 0.00 0.00 3.99
2469 2595 2.287547 CCATGCTGCTTTGTGTACGTTT 60.288 45.455 0.00 0.00 0.00 3.60
2470 2596 3.058570 CCATGCTGCTTTGTGTACGTTTA 60.059 43.478 0.00 0.00 0.00 2.01
2471 2597 3.870723 TGCTGCTTTGTGTACGTTTAG 57.129 42.857 0.00 0.00 0.00 1.85
2472 2598 2.032377 TGCTGCTTTGTGTACGTTTAGC 60.032 45.455 0.00 0.00 0.00 3.09
2473 2599 2.032377 GCTGCTTTGTGTACGTTTAGCA 60.032 45.455 0.00 10.73 37.14 3.49
2474 2600 3.364964 GCTGCTTTGTGTACGTTTAGCAT 60.365 43.478 11.37 0.00 37.91 3.79
2475 2601 4.783242 CTGCTTTGTGTACGTTTAGCATT 58.217 39.130 11.37 0.00 37.91 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.409218 GTCCACGAGCGCCACGTA 62.409 66.667 24.91 11.80 42.07 3.57
6 7 3.858868 TTGACCAGTCCACGAGCGC 62.859 63.158 0.00 0.00 0.00 5.92
7 8 1.300620 TTTGACCAGTCCACGAGCG 60.301 57.895 0.00 0.00 0.00 5.03
8 9 1.228657 GGTTTGACCAGTCCACGAGC 61.229 60.000 0.00 0.00 38.42 5.03
9 10 0.944311 CGGTTTGACCAGTCCACGAG 60.944 60.000 0.00 0.00 38.47 4.18
10 11 1.068417 CGGTTTGACCAGTCCACGA 59.932 57.895 0.00 0.00 38.47 4.35
11 12 1.959226 CCGGTTTGACCAGTCCACG 60.959 63.158 0.00 0.00 38.47 4.94
12 13 2.258726 GCCGGTTTGACCAGTCCAC 61.259 63.158 1.90 0.00 38.47 4.02
13 14 2.112297 GCCGGTTTGACCAGTCCA 59.888 61.111 1.90 0.00 38.47 4.02
14 15 3.047877 CGCCGGTTTGACCAGTCC 61.048 66.667 1.90 0.00 38.47 3.85
15 16 3.047877 CCGCCGGTTTGACCAGTC 61.048 66.667 1.90 0.00 38.47 3.51
20 21 3.781162 GTACGCCGCCGGTTTGAC 61.781 66.667 4.45 0.00 39.22 3.18
34 35 2.928116 GTTTCACATACAGAGCCGGTAC 59.072 50.000 1.90 0.00 0.00 3.34
35 36 2.563620 TGTTTCACATACAGAGCCGGTA 59.436 45.455 1.90 0.00 0.00 4.02
36 37 1.346395 TGTTTCACATACAGAGCCGGT 59.654 47.619 1.90 0.00 0.00 5.28
37 38 2.002586 CTGTTTCACATACAGAGCCGG 58.997 52.381 0.00 0.00 44.52 6.13
38 39 2.413112 CACTGTTTCACATACAGAGCCG 59.587 50.000 9.74 0.00 44.52 5.52
39 40 3.664107 TCACTGTTTCACATACAGAGCC 58.336 45.455 9.74 0.00 44.52 4.70
40 41 4.032217 CGATCACTGTTTCACATACAGAGC 59.968 45.833 9.74 0.00 44.52 4.09
41 42 5.164233 ACGATCACTGTTTCACATACAGAG 58.836 41.667 9.74 2.48 44.52 3.35
42 43 5.134202 ACGATCACTGTTTCACATACAGA 57.866 39.130 9.74 0.00 44.52 3.41
43 44 8.628882 TTATACGATCACTGTTTCACATACAG 57.371 34.615 0.00 0.00 46.56 2.74
44 45 9.244799 GATTATACGATCACTGTTTCACATACA 57.755 33.333 0.00 0.00 0.00 2.29
45 46 9.244799 TGATTATACGATCACTGTTTCACATAC 57.755 33.333 0.00 0.00 31.35 2.39
58 59 4.379082 CGATGGGACGTGATTATACGATCA 60.379 45.833 0.00 1.36 46.46 2.92
59 60 4.096311 CGATGGGACGTGATTATACGATC 58.904 47.826 0.00 0.00 46.46 3.69
60 61 3.504906 ACGATGGGACGTGATTATACGAT 59.495 43.478 0.00 0.00 46.46 3.73
61 62 2.880268 ACGATGGGACGTGATTATACGA 59.120 45.455 0.00 0.00 46.46 3.43
63 64 5.112220 TGTACGATGGGACGTGATTATAC 57.888 43.478 0.00 0.00 46.02 1.47
64 65 5.970317 ATGTACGATGGGACGTGATTATA 57.030 39.130 0.00 0.00 46.02 0.98
65 66 4.866508 ATGTACGATGGGACGTGATTAT 57.133 40.909 0.00 0.00 46.02 1.28
66 67 4.823442 ACTATGTACGATGGGACGTGATTA 59.177 41.667 0.00 0.00 46.02 1.75
67 68 3.635373 ACTATGTACGATGGGACGTGATT 59.365 43.478 0.00 0.00 46.02 2.57
68 69 3.004419 CACTATGTACGATGGGACGTGAT 59.996 47.826 0.00 0.00 46.02 3.06
69 70 2.356695 CACTATGTACGATGGGACGTGA 59.643 50.000 0.00 0.00 46.02 4.35
70 71 2.356695 TCACTATGTACGATGGGACGTG 59.643 50.000 0.00 0.00 46.02 4.49
72 73 2.287427 GGTCACTATGTACGATGGGACG 60.287 54.545 0.00 0.00 39.31 4.79
73 74 2.287427 CGGTCACTATGTACGATGGGAC 60.287 54.545 5.86 5.86 0.00 4.46
74 75 1.951602 CGGTCACTATGTACGATGGGA 59.048 52.381 0.00 0.00 0.00 4.37
75 76 1.679680 ACGGTCACTATGTACGATGGG 59.320 52.381 0.00 0.00 0.00 4.00
76 77 4.761235 ATACGGTCACTATGTACGATGG 57.239 45.455 0.00 0.00 0.00 3.51
77 78 6.436261 AGAAATACGGTCACTATGTACGATG 58.564 40.000 0.00 0.00 0.00 3.84
78 79 6.630444 AGAAATACGGTCACTATGTACGAT 57.370 37.500 0.00 0.00 0.00 3.73
79 80 7.280876 ACTTAGAAATACGGTCACTATGTACGA 59.719 37.037 0.00 0.00 0.00 3.43
80 81 7.412853 ACTTAGAAATACGGTCACTATGTACG 58.587 38.462 0.00 0.00 0.00 3.67
81 82 9.657121 GTACTTAGAAATACGGTCACTATGTAC 57.343 37.037 0.00 0.00 37.44 2.90
82 83 9.394767 TGTACTTAGAAATACGGTCACTATGTA 57.605 33.333 0.00 0.00 0.00 2.29
83 84 8.284945 TGTACTTAGAAATACGGTCACTATGT 57.715 34.615 0.00 0.00 0.00 2.29
84 85 9.745880 ATTGTACTTAGAAATACGGTCACTATG 57.254 33.333 0.00 0.00 0.00 2.23
85 86 9.745880 CATTGTACTTAGAAATACGGTCACTAT 57.254 33.333 0.00 0.00 0.00 2.12
86 87 8.959548 TCATTGTACTTAGAAATACGGTCACTA 58.040 33.333 0.00 0.00 0.00 2.74
87 88 7.758528 GTCATTGTACTTAGAAATACGGTCACT 59.241 37.037 0.00 0.00 0.00 3.41
88 89 7.009907 GGTCATTGTACTTAGAAATACGGTCAC 59.990 40.741 0.00 0.00 0.00 3.67
89 90 7.037438 GGTCATTGTACTTAGAAATACGGTCA 58.963 38.462 0.00 0.00 0.00 4.02
90 91 7.037438 TGGTCATTGTACTTAGAAATACGGTC 58.963 38.462 0.00 0.00 0.00 4.79
91 92 6.938507 TGGTCATTGTACTTAGAAATACGGT 58.061 36.000 0.00 0.00 0.00 4.83
92 93 7.837202 TTGGTCATTGTACTTAGAAATACGG 57.163 36.000 0.00 0.00 0.00 4.02
93 94 8.173130 GGTTTGGTCATTGTACTTAGAAATACG 58.827 37.037 0.00 0.00 0.00 3.06
94 95 9.005777 TGGTTTGGTCATTGTACTTAGAAATAC 57.994 33.333 0.00 0.00 0.00 1.89
95 96 9.575868 TTGGTTTGGTCATTGTACTTAGAAATA 57.424 29.630 0.00 0.00 0.00 1.40
96 97 8.472007 TTGGTTTGGTCATTGTACTTAGAAAT 57.528 30.769 0.00 0.00 0.00 2.17
97 98 7.469456 GCTTGGTTTGGTCATTGTACTTAGAAA 60.469 37.037 0.00 0.00 0.00 2.52
98 99 6.016610 GCTTGGTTTGGTCATTGTACTTAGAA 60.017 38.462 0.00 0.00 0.00 2.10
99 100 5.472137 GCTTGGTTTGGTCATTGTACTTAGA 59.528 40.000 0.00 0.00 0.00 2.10
100 101 5.473504 AGCTTGGTTTGGTCATTGTACTTAG 59.526 40.000 0.00 0.00 0.00 2.18
101 102 5.381757 AGCTTGGTTTGGTCATTGTACTTA 58.618 37.500 0.00 0.00 0.00 2.24
102 103 4.215109 AGCTTGGTTTGGTCATTGTACTT 58.785 39.130 0.00 0.00 0.00 2.24
103 104 3.821033 GAGCTTGGTTTGGTCATTGTACT 59.179 43.478 0.00 0.00 32.79 2.73
104 105 3.364964 CGAGCTTGGTTTGGTCATTGTAC 60.365 47.826 0.00 0.00 32.79 2.90
105 106 2.811431 CGAGCTTGGTTTGGTCATTGTA 59.189 45.455 0.00 0.00 32.79 2.41
106 107 1.608590 CGAGCTTGGTTTGGTCATTGT 59.391 47.619 0.00 0.00 32.79 2.71
107 108 1.666888 GCGAGCTTGGTTTGGTCATTG 60.667 52.381 2.37 0.00 32.79 2.82
108 109 0.598065 GCGAGCTTGGTTTGGTCATT 59.402 50.000 2.37 0.00 32.79 2.57
109 110 1.577328 CGCGAGCTTGGTTTGGTCAT 61.577 55.000 0.00 0.00 32.79 3.06
110 111 2.250939 CGCGAGCTTGGTTTGGTCA 61.251 57.895 0.00 0.00 32.79 4.02
111 112 2.556287 CGCGAGCTTGGTTTGGTC 59.444 61.111 0.00 0.00 0.00 4.02
112 113 2.978010 CCGCGAGCTTGGTTTGGT 60.978 61.111 8.23 0.00 0.00 3.67
113 114 4.404654 GCCGCGAGCTTGGTTTGG 62.405 66.667 8.23 0.00 38.99 3.28
114 115 4.741781 CGCCGCGAGCTTGGTTTG 62.742 66.667 8.23 0.00 40.39 2.93
123 124 3.635734 CTTGAACTTGCGCCGCGAG 62.636 63.158 24.24 24.24 44.94 5.03
124 125 3.711842 CTTGAACTTGCGCCGCGA 61.712 61.111 18.91 0.15 0.00 5.87
125 126 2.663478 TACTTGAACTTGCGCCGCG 61.663 57.895 8.83 8.83 0.00 6.46
126 127 1.154469 GTACTTGAACTTGCGCCGC 60.154 57.895 4.18 0.00 0.00 6.53
127 128 0.949105 AGGTACTTGAACTTGCGCCG 60.949 55.000 4.18 0.00 27.25 6.46
128 129 0.517316 CAGGTACTTGAACTTGCGCC 59.483 55.000 4.18 0.00 34.60 6.53
129 130 1.226746 ACAGGTACTTGAACTTGCGC 58.773 50.000 12.54 0.00 34.60 6.09
130 131 3.428870 CACTACAGGTACTTGAACTTGCG 59.571 47.826 12.54 0.00 34.60 4.85
131 132 4.377897 ACACTACAGGTACTTGAACTTGC 58.622 43.478 12.54 0.00 34.60 4.01
132 133 8.603242 AAATACACTACAGGTACTTGAACTTG 57.397 34.615 12.54 5.69 34.60 3.16
134 135 9.702494 GTAAAATACACTACAGGTACTTGAACT 57.298 33.333 12.54 0.00 34.60 3.01
135 136 9.702494 AGTAAAATACACTACAGGTACTTGAAC 57.298 33.333 12.54 0.00 34.60 3.18
136 137 9.918630 GAGTAAAATACACTACAGGTACTTGAA 57.081 33.333 12.54 0.00 34.60 2.69
137 138 9.081204 TGAGTAAAATACACTACAGGTACTTGA 57.919 33.333 12.54 0.00 34.60 3.02
138 139 9.701098 TTGAGTAAAATACACTACAGGTACTTG 57.299 33.333 2.98 2.98 34.60 3.16
143 144 8.967664 TGTTTTGAGTAAAATACACTACAGGT 57.032 30.769 0.00 0.00 38.01 4.00
151 152 9.677567 GCAGAGAATTGTTTTGAGTAAAATACA 57.322 29.630 0.00 0.00 38.01 2.29
152 153 9.899226 AGCAGAGAATTGTTTTGAGTAAAATAC 57.101 29.630 0.00 0.00 38.01 1.89
154 155 8.084684 GGAGCAGAGAATTGTTTTGAGTAAAAT 58.915 33.333 0.00 0.00 38.01 1.82
155 156 7.425606 GGAGCAGAGAATTGTTTTGAGTAAAA 58.574 34.615 0.00 0.00 33.57 1.52
156 157 6.016276 GGGAGCAGAGAATTGTTTTGAGTAAA 60.016 38.462 0.00 0.00 0.00 2.01
157 158 5.473504 GGGAGCAGAGAATTGTTTTGAGTAA 59.526 40.000 0.00 0.00 0.00 2.24
158 159 5.003804 GGGAGCAGAGAATTGTTTTGAGTA 58.996 41.667 0.00 0.00 0.00 2.59
159 160 3.823304 GGGAGCAGAGAATTGTTTTGAGT 59.177 43.478 0.00 0.00 0.00 3.41
160 161 3.120060 CGGGAGCAGAGAATTGTTTTGAG 60.120 47.826 0.00 0.00 0.00 3.02
161 162 2.813754 CGGGAGCAGAGAATTGTTTTGA 59.186 45.455 0.00 0.00 0.00 2.69
162 163 3.207474 CGGGAGCAGAGAATTGTTTTG 57.793 47.619 0.00 0.00 0.00 2.44
205 208 0.730840 CGGAAATCTAACCGTTGGGC 59.269 55.000 0.00 0.00 43.53 5.36
247 250 4.572571 TGGGCTGGGTTTCGCGTT 62.573 61.111 5.77 0.00 0.00 4.84
412 423 4.699522 GGTGGGGGAGCGTGTGTC 62.700 72.222 0.00 0.00 0.00 3.67
880 896 1.370437 CTGATCCAGCGGAGGGATG 59.630 63.158 5.71 0.00 45.05 3.51
901 1004 2.239654 ACCACCAGATCAATCAACGGAT 59.760 45.455 0.00 0.00 34.43 4.18
904 1007 2.674852 CAGACCACCAGATCAATCAACG 59.325 50.000 0.00 0.00 0.00 4.10
924 1027 4.651778 ACCATTTCAGAGAAATCCGAACA 58.348 39.130 2.20 0.00 0.00 3.18
935 1042 4.284234 ACAAATCCCCAAACCATTTCAGAG 59.716 41.667 0.00 0.00 0.00 3.35
964 1071 3.781770 CTCGATCGAGGCCCTGCAC 62.782 68.421 32.81 0.00 38.51 4.57
995 1102 1.619057 TGGATCTGGCCCATGTCCA 60.619 57.895 11.95 11.95 36.66 4.02
1121 1241 0.792031 CGGCCGTGTTAGTTGGTTAC 59.208 55.000 19.50 0.00 0.00 2.50
1126 1246 0.719465 GACATCGGCCGTGTTAGTTG 59.281 55.000 27.15 14.01 0.00 3.16
1307 1427 1.672356 CCACTCGTTCTGCAAGGGG 60.672 63.158 0.00 0.00 0.00 4.79
1503 1624 0.481128 TTTCAGGAGTTCCAACCCCC 59.519 55.000 0.28 0.00 38.89 5.40
1538 1659 2.062519 GCGATCGCCCTTTTAGAGATC 58.937 52.381 29.48 0.00 35.61 2.75
1554 1675 0.108585 ACCAGACAAACCAGTGCGAT 59.891 50.000 0.00 0.00 0.00 4.58
1572 1693 3.997021 CACCAACACAACTAGATCCTGAC 59.003 47.826 0.00 0.00 0.00 3.51
1670 1794 6.489675 CATCACATAACAGGTAGCATTCAAC 58.510 40.000 0.00 0.00 0.00 3.18
1691 1815 3.887621 TCTACCAACAGTACCAGCATC 57.112 47.619 0.00 0.00 0.00 3.91
1705 1829 1.216930 TCATCACGGGGAGATCTACCA 59.783 52.381 25.87 5.15 34.34 3.25
1706 1830 1.996798 TCATCACGGGGAGATCTACC 58.003 55.000 16.60 16.60 0.00 3.18
1715 1839 2.168521 ACACTAACAGATCATCACGGGG 59.831 50.000 0.00 0.00 0.00 5.73
1718 1842 6.256539 AGCATTAACACTAACAGATCATCACG 59.743 38.462 0.00 0.00 0.00 4.35
1776 1901 6.293004 TCACTATCACATGAACACCATACA 57.707 37.500 0.00 0.00 33.31 2.29
1781 1906 6.992063 AAGATTCACTATCACATGAACACC 57.008 37.500 0.00 0.00 37.64 4.16
1809 1934 3.009473 AGTGCTCCAAATCCTCTTGCTAA 59.991 43.478 0.00 0.00 0.00 3.09
1821 1946 3.010027 TCATCCATAACCAGTGCTCCAAA 59.990 43.478 0.00 0.00 0.00 3.28
1822 1947 2.575735 TCATCCATAACCAGTGCTCCAA 59.424 45.455 0.00 0.00 0.00 3.53
1830 1955 4.940046 GGTGCATAGATCATCCATAACCAG 59.060 45.833 0.00 0.00 0.00 4.00
1832 1957 3.935203 CGGTGCATAGATCATCCATAACC 59.065 47.826 0.00 0.00 0.00 2.85
1844 1969 2.430248 TAGTCTGGACGGTGCATAGA 57.570 50.000 1.88 0.00 36.20 1.98
1853 1978 2.673368 GAGGTGCATTTTAGTCTGGACG 59.327 50.000 0.00 0.00 34.86 4.79
1882 2007 7.164803 TGATACAGTTGATGATGTACCAAACA 58.835 34.615 0.00 0.00 43.86 2.83
1901 2026 7.227049 TGTCACTTCAGACTAACATGATACA 57.773 36.000 0.00 0.00 39.27 2.29
1993 2118 4.083537 GCGAATTACCAGTGTCACAATCAA 60.084 41.667 5.62 0.00 0.00 2.57
1996 2121 3.407698 TGCGAATTACCAGTGTCACAAT 58.592 40.909 5.62 0.00 0.00 2.71
2055 2180 4.702131 AGAGTGCCAATGATAACAAAGACC 59.298 41.667 0.00 0.00 0.00 3.85
2113 2239 9.047947 AGATAATTACAGGAAGTTCTACCAGTT 57.952 33.333 2.25 0.00 0.00 3.16
2245 2371 8.991026 CATTTTTGCCTGTGATAATTCTTTGAA 58.009 29.630 0.00 0.00 0.00 2.69
2252 2378 5.104374 CGAGCATTTTTGCCTGTGATAATT 58.896 37.500 0.00 0.00 34.90 1.40
2273 2399 7.011950 CAGGGTATATAATGTGCAAAAAGACGA 59.988 37.037 0.00 0.00 0.00 4.20
2275 2401 7.425606 CCAGGGTATATAATGTGCAAAAAGAC 58.574 38.462 0.00 0.00 0.00 3.01
2286 2412 1.913419 ACCGGCCCAGGGTATATAATG 59.087 52.381 7.55 0.00 35.58 1.90
2295 2421 3.809013 ATGCTAACCGGCCCAGGG 61.809 66.667 0.00 0.00 35.02 4.45
2299 2425 1.823899 CCTTCATGCTAACCGGCCC 60.824 63.158 0.00 0.00 0.00 5.80
2304 2430 3.265791 CAGTGACTCCTTCATGCTAACC 58.734 50.000 0.00 0.00 36.32 2.85
2364 2490 6.208402 TGTGACAGCAATATAGCTTTGGAAAA 59.792 34.615 0.00 0.00 43.70 2.29
2408 2534 2.550180 GTCCTTCAAACTCTGCAGAACC 59.450 50.000 18.85 0.00 0.00 3.62
2423 2549 1.334869 CACTTGCACAACCTGTCCTTC 59.665 52.381 0.00 0.00 0.00 3.46


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

AutoCloner maintained by Alex Coulton.