Multiple sequence alignment - TraesCS2D01G217000

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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 TraesCS2D01G217000 chr2D 100.000 4900 0 0 1 4900 180089612 180084713 0.000000e+00 9049
1 TraesCS2D01G217000 chr2D 88.734 1580 174 4 2259 3836 639396713 639398290 0.000000e+00 1929
2 TraesCS2D01G217000 chr2D 86.663 1642 211 7 2259 3896 639667251 639668888 0.000000e+00 1812
3 TraesCS2D01G217000 chr2D 83.266 741 110 8 1347 2086 639666404 639667131 0.000000e+00 669
4 TraesCS2D01G217000 chr2D 96.933 163 5 0 1 163 449715552 449715714 1.740000e-69 274
5 TraesCS2D01G217000 chr2D 89.340 197 14 5 1 194 70626478 70626670 1.760000e-59 241
6 TraesCS2D01G217000 chr2D 78.261 253 25 20 996 1248 639393581 639393803 8.560000e-28 135
7 TraesCS2D01G217000 chr2B 94.735 3875 139 29 254 4116 236778560 236774739 0.000000e+00 5965
8 TraesCS2D01G217000 chr2B 87.910 1646 182 10 2259 3899 798318257 798316624 0.000000e+00 1921
9 TraesCS2D01G217000 chr2B 86.768 1640 213 4 2259 3896 798614319 798612682 0.000000e+00 1823
10 TraesCS2D01G217000 chr2B 84.980 739 106 3 1348 2085 798615175 798614441 0.000000e+00 745
11 TraesCS2D01G217000 chr2B 84.595 740 109 5 1344 2082 798723291 798724026 0.000000e+00 730
12 TraesCS2D01G217000 chr2B 98.052 154 3 0 1 154 206744714 206744867 8.080000e-68 268
13 TraesCS2D01G217000 chr2A 93.917 3995 125 44 168 4116 194425348 194421426 0.000000e+00 5923
14 TraesCS2D01G217000 chr2A 87.912 1638 198 0 2259 3896 765040534 765042171 0.000000e+00 1929
15 TraesCS2D01G217000 chr2A 85.210 737 104 5 1347 2082 765039668 765040400 0.000000e+00 752
16 TraesCS2D01G217000 chr7D 89.356 1569 164 2 2259 3824 638473426 638474994 0.000000e+00 1969
17 TraesCS2D01G217000 chr7D 90.590 797 60 6 4115 4900 212213052 212212260 0.000000e+00 1042
18 TraesCS2D01G217000 chr7D 83.919 740 111 5 1347 2085 638470777 638471509 0.000000e+00 701
19 TraesCS2D01G217000 chr7D 96.835 158 5 0 1 158 119052232 119052075 1.050000e-66 265
20 TraesCS2D01G217000 chr7D 89.209 139 15 0 1117 1255 638558638 638558776 1.810000e-39 174
21 TraesCS2D01G217000 chr7D 86.719 128 8 5 1121 1248 638470229 638470347 3.080000e-27 134
22 TraesCS2D01G217000 chr7A 89.293 1569 165 2 2259 3824 727431545 727429977 0.000000e+00 1964
23 TraesCS2D01G217000 chr7A 85.190 736 101 5 1347 2081 727433897 727433169 0.000000e+00 749
24 TraesCS2D01G217000 chr7A 81.013 158 16 8 1124 1281 727434223 727434080 4.010000e-21 113
25 TraesCS2D01G217000 chr4B 90.211 807 65 6 4107 4900 75535324 75536129 0.000000e+00 1040
26 TraesCS2D01G217000 chr7B 90.339 797 65 5 4115 4900 581380046 581380841 0.000000e+00 1035
27 TraesCS2D01G217000 chr7B 97.484 159 4 0 3 161 670256636 670256478 6.250000e-69 272
28 TraesCS2D01G217000 chr7B 81.421 183 20 9 1099 1281 734252901 734252733 2.380000e-28 137
29 TraesCS2D01G217000 chr6D 89.962 797 68 8 4115 4900 412058025 412057230 0.000000e+00 1018
30 TraesCS2D01G217000 chr5B 89.750 800 66 11 4115 4900 706763435 706762638 0.000000e+00 1009
31 TraesCS2D01G217000 chr5B 97.436 156 4 0 1 156 67024764 67024609 2.910000e-67 267
32 TraesCS2D01G217000 chr3A 89.824 796 68 8 4116 4900 729702527 729703320 0.000000e+00 1009
33 TraesCS2D01G217000 chr3B 89.335 797 70 10 4115 4900 3135259 3136051 0.000000e+00 987
34 TraesCS2D01G217000 chr1D 89.223 798 72 7 4115 4900 16205577 16204782 0.000000e+00 985
35 TraesCS2D01G217000 chr1D 97.468 158 4 0 1 158 268934762 268934919 2.250000e-68 270
36 TraesCS2D01G217000 chr4D 89.335 797 66 10 4115 4900 405476470 405475682 0.000000e+00 983
37 TraesCS2D01G217000 chr5D 98.089 157 3 0 1 157 465701713 465701557 1.740000e-69 274
38 TraesCS2D01G217000 chr6B 97.468 158 3 1 1 158 526727572 526727728 8.080000e-68 268
39 TraesCS2D01G217000 chrUn 88.321 137 16 0 1119 1255 88119324 88119188 1.090000e-36 165
40 TraesCS2D01G217000 chrUn 88.321 137 16 0 1119 1255 88974600 88974464 1.090000e-36 165
41 TraesCS2D01G217000 chr1A 71.760 733 161 31 1387 2082 95314096 95313373 1.090000e-36 165


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 TraesCS2D01G217000 chr2D 180084713 180089612 4899 True 9049.000000 9049 100.000000 1 4900 1 chr2D.!!$R1 4899
1 TraesCS2D01G217000 chr2D 639666404 639668888 2484 False 1240.500000 1812 84.964500 1347 3896 2 chr2D.!!$F4 2549
2 TraesCS2D01G217000 chr2D 639393581 639398290 4709 False 1032.000000 1929 83.497500 996 3836 2 chr2D.!!$F3 2840
3 TraesCS2D01G217000 chr2B 236774739 236778560 3821 True 5965.000000 5965 94.735000 254 4116 1 chr2B.!!$R1 3862
4 TraesCS2D01G217000 chr2B 798316624 798318257 1633 True 1921.000000 1921 87.910000 2259 3899 1 chr2B.!!$R2 1640
5 TraesCS2D01G217000 chr2B 798612682 798615175 2493 True 1284.000000 1823 85.874000 1348 3896 2 chr2B.!!$R3 2548
6 TraesCS2D01G217000 chr2B 798723291 798724026 735 False 730.000000 730 84.595000 1344 2082 1 chr2B.!!$F2 738
7 TraesCS2D01G217000 chr2A 194421426 194425348 3922 True 5923.000000 5923 93.917000 168 4116 1 chr2A.!!$R1 3948
8 TraesCS2D01G217000 chr2A 765039668 765042171 2503 False 1340.500000 1929 86.561000 1347 3896 2 chr2A.!!$F1 2549
9 TraesCS2D01G217000 chr7D 212212260 212213052 792 True 1042.000000 1042 90.590000 4115 4900 1 chr7D.!!$R2 785
10 TraesCS2D01G217000 chr7D 638470229 638474994 4765 False 934.666667 1969 86.664667 1121 3824 3 chr7D.!!$F2 2703
11 TraesCS2D01G217000 chr7A 727429977 727434223 4246 True 942.000000 1964 85.165333 1124 3824 3 chr7A.!!$R1 2700
12 TraesCS2D01G217000 chr4B 75535324 75536129 805 False 1040.000000 1040 90.211000 4107 4900 1 chr4B.!!$F1 793
13 TraesCS2D01G217000 chr7B 581380046 581380841 795 False 1035.000000 1035 90.339000 4115 4900 1 chr7B.!!$F1 785
14 TraesCS2D01G217000 chr6D 412057230 412058025 795 True 1018.000000 1018 89.962000 4115 4900 1 chr6D.!!$R1 785
15 TraesCS2D01G217000 chr5B 706762638 706763435 797 True 1009.000000 1009 89.750000 4115 4900 1 chr5B.!!$R2 785
16 TraesCS2D01G217000 chr3A 729702527 729703320 793 False 1009.000000 1009 89.824000 4116 4900 1 chr3A.!!$F1 784
17 TraesCS2D01G217000 chr3B 3135259 3136051 792 False 987.000000 987 89.335000 4115 4900 1 chr3B.!!$F1 785
18 TraesCS2D01G217000 chr1D 16204782 16205577 795 True 985.000000 985 89.223000 4115 4900 1 chr1D.!!$R1 785
19 TraesCS2D01G217000 chr4D 405475682 405476470 788 True 983.000000 983 89.335000 4115 4900 1 chr4D.!!$R1 785

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
178 179 0.182299 TAATGCGGATGGGTGATGCA 59.818 50.000 0.00 0.00 40.23 3.96 F
597 611 1.002430 GGCATGGAGGCATATCTTCGA 59.998 52.381 0.00 0.00 43.51 3.71 F
1310 1697 1.131218 CATGCTGTTCTCGTGCGTG 59.869 57.895 0.00 0.00 37.37 5.34 F
1952 2359 0.577269 GCCAACGATCTGATGCGTAC 59.423 55.000 12.94 5.57 40.23 3.67 F
3248 6838 0.319405 CGTACAACCTCTTCCCCGTT 59.681 55.000 0.00 0.00 0.00 4.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1580 1987 0.038526 GGTCGACTGTGGTGACGAAT 60.039 55.000 16.46 0.0 36.15 3.34 R
1703 2110 1.372997 CTCGTAGTGCACCAGCGTT 60.373 57.895 14.63 0.0 46.23 4.84 R
3230 6820 1.622312 AGAACGGGGAAGAGGTTGTAC 59.378 52.381 0.00 0.0 0.00 2.90 R
3332 6925 1.715585 GAACATGCCGATCACGTGG 59.284 57.895 17.00 0.0 37.88 4.94 R
4117 7712 1.672356 GCACGGCTGTTGGAGATGT 60.672 57.895 0.00 0.0 0.00 3.06 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
18 19 3.950869 ACTAAAAACGGAGCCCTCC 57.049 52.632 4.19 4.19 46.18 4.30
19 20 0.327259 ACTAAAAACGGAGCCCTCCC 59.673 55.000 8.68 0.00 46.96 4.30
41 42 2.440980 GCCCTTGCCAGGATCCAC 60.441 66.667 15.82 3.31 44.19 4.02
42 43 2.276740 CCCTTGCCAGGATCCACC 59.723 66.667 15.82 1.73 44.19 4.61
43 44 2.124570 CCTTGCCAGGATCCACCG 60.125 66.667 15.82 1.33 44.19 4.94
44 45 2.825836 CTTGCCAGGATCCACCGC 60.826 66.667 15.82 12.41 44.74 5.68
45 46 4.776322 TTGCCAGGATCCACCGCG 62.776 66.667 15.82 0.00 44.74 6.46
49 50 4.899239 CAGGATCCACCGCGCCTC 62.899 72.222 15.82 0.00 44.74 4.70
52 53 4.241555 GATCCACCGCGCCTCCAT 62.242 66.667 0.00 0.00 0.00 3.41
53 54 4.552365 ATCCACCGCGCCTCCATG 62.552 66.667 0.00 0.00 0.00 3.66
72 73 4.475444 CCCTAGGGCCACCGGAGA 62.475 72.222 16.90 0.00 43.47 3.71
73 74 3.155167 CCTAGGGCCACCGGAGAC 61.155 72.222 9.46 0.00 43.47 3.36
110 111 4.415332 GCCGGCGAGAGACACGAA 62.415 66.667 12.58 0.00 41.50 3.85
111 112 2.504244 CCGGCGAGAGACACGAAC 60.504 66.667 9.30 0.00 41.50 3.95
112 113 2.504244 CGGCGAGAGACACGAACC 60.504 66.667 0.00 0.00 41.50 3.62
113 114 2.126031 GGCGAGAGACACGAACCC 60.126 66.667 0.00 0.00 40.66 4.11
114 115 2.637383 GGCGAGAGACACGAACCCT 61.637 63.158 0.00 0.00 40.66 4.34
115 116 1.310933 GGCGAGAGACACGAACCCTA 61.311 60.000 0.00 0.00 40.66 3.53
116 117 0.524862 GCGAGAGACACGAACCCTAA 59.475 55.000 0.00 0.00 0.00 2.69
117 118 1.731750 GCGAGAGACACGAACCCTAAC 60.732 57.143 0.00 0.00 0.00 2.34
118 119 1.811359 CGAGAGACACGAACCCTAACT 59.189 52.381 0.00 0.00 0.00 2.24
119 120 2.228343 CGAGAGACACGAACCCTAACTT 59.772 50.000 0.00 0.00 0.00 2.66
120 121 3.305199 CGAGAGACACGAACCCTAACTTT 60.305 47.826 0.00 0.00 0.00 2.66
121 122 4.236147 GAGAGACACGAACCCTAACTTTC 58.764 47.826 0.00 0.00 0.00 2.62
122 123 3.896272 AGAGACACGAACCCTAACTTTCT 59.104 43.478 0.00 0.00 0.00 2.52
123 124 4.344390 AGAGACACGAACCCTAACTTTCTT 59.656 41.667 0.00 0.00 0.00 2.52
124 125 5.032327 AGACACGAACCCTAACTTTCTTT 57.968 39.130 0.00 0.00 0.00 2.52
125 126 5.055144 AGACACGAACCCTAACTTTCTTTC 58.945 41.667 0.00 0.00 0.00 2.62
126 127 5.032327 ACACGAACCCTAACTTTCTTTCT 57.968 39.130 0.00 0.00 0.00 2.52
127 128 5.434408 ACACGAACCCTAACTTTCTTTCTT 58.566 37.500 0.00 0.00 0.00 2.52
128 129 5.296035 ACACGAACCCTAACTTTCTTTCTTG 59.704 40.000 0.00 0.00 0.00 3.02
129 130 5.526111 CACGAACCCTAACTTTCTTTCTTGA 59.474 40.000 0.00 0.00 0.00 3.02
130 131 6.037830 CACGAACCCTAACTTTCTTTCTTGAA 59.962 38.462 0.00 0.00 0.00 2.69
131 132 6.260271 ACGAACCCTAACTTTCTTTCTTGAAG 59.740 38.462 0.00 0.00 36.67 3.02
132 133 6.293462 CGAACCCTAACTTTCTTTCTTGAAGG 60.293 42.308 0.00 0.00 35.98 3.46
133 134 6.262056 ACCCTAACTTTCTTTCTTGAAGGA 57.738 37.500 0.00 0.00 35.98 3.36
134 135 6.299922 ACCCTAACTTTCTTTCTTGAAGGAG 58.700 40.000 0.00 0.00 35.98 3.69
135 136 5.707764 CCCTAACTTTCTTTCTTGAAGGAGG 59.292 44.000 0.00 0.00 35.98 4.30
136 137 6.465894 CCCTAACTTTCTTTCTTGAAGGAGGA 60.466 42.308 0.00 0.00 35.98 3.71
137 138 6.652900 CCTAACTTTCTTTCTTGAAGGAGGAG 59.347 42.308 0.00 2.31 35.98 3.69
138 139 4.979335 ACTTTCTTTCTTGAAGGAGGAGG 58.021 43.478 0.00 0.00 35.98 4.30
139 140 4.660771 ACTTTCTTTCTTGAAGGAGGAGGA 59.339 41.667 0.00 0.00 35.98 3.71
140 141 4.899352 TTCTTTCTTGAAGGAGGAGGAG 57.101 45.455 0.00 0.00 35.98 3.69
141 142 3.177228 TCTTTCTTGAAGGAGGAGGAGG 58.823 50.000 0.00 0.00 35.98 4.30
142 143 3.177228 CTTTCTTGAAGGAGGAGGAGGA 58.823 50.000 0.00 0.00 0.00 3.71
143 144 2.541233 TCTTGAAGGAGGAGGAGGAG 57.459 55.000 0.00 0.00 0.00 3.69
144 145 1.007721 TCTTGAAGGAGGAGGAGGAGG 59.992 57.143 0.00 0.00 0.00 4.30
145 146 0.618968 TTGAAGGAGGAGGAGGAGGC 60.619 60.000 0.00 0.00 0.00 4.70
146 147 2.042435 AAGGAGGAGGAGGAGGCG 60.042 66.667 0.00 0.00 0.00 5.52
147 148 3.687828 AAGGAGGAGGAGGAGGCGG 62.688 68.421 0.00 0.00 0.00 6.13
148 149 4.144727 GGAGGAGGAGGAGGCGGA 62.145 72.222 0.00 0.00 0.00 5.54
149 150 2.520741 GAGGAGGAGGAGGCGGAG 60.521 72.222 0.00 0.00 0.00 4.63
166 167 3.987404 GCCCTGGCTATAATGCGG 58.013 61.111 0.00 0.00 38.26 5.69
170 171 1.679944 CCCTGGCTATAATGCGGATGG 60.680 57.143 0.00 0.00 0.00 3.51
177 178 1.538047 ATAATGCGGATGGGTGATGC 58.462 50.000 0.00 0.00 0.00 3.91
178 179 0.182299 TAATGCGGATGGGTGATGCA 59.818 50.000 0.00 0.00 40.23 3.96
196 197 2.810852 TGCATTTATCGCACACAGTTCA 59.189 40.909 0.00 0.00 33.55 3.18
223 224 6.460537 CGCTAGGGTGTATGTTAGATGTGTTA 60.461 42.308 0.00 0.00 0.00 2.41
277 278 3.839293 ACGTCTCCTTCTTTTCGATGAG 58.161 45.455 0.00 0.00 0.00 2.90
279 280 3.610242 CGTCTCCTTCTTTTCGATGAGTG 59.390 47.826 0.00 0.00 0.00 3.51
416 427 2.914941 ACGGTAGTTTGATTAGGGGGTT 59.085 45.455 0.00 0.00 0.00 4.11
417 428 4.103342 ACGGTAGTTTGATTAGGGGGTTA 58.897 43.478 0.00 0.00 0.00 2.85
525 538 2.405061 TTCATGCGCACACACCTTGC 62.405 55.000 14.90 0.00 36.57 4.01
543 557 3.188159 TGCCAACACTAAGTCGTTCTT 57.812 42.857 1.98 1.98 39.89 2.52
574 588 2.443255 TCCTTCCAGCTGGTTTTCTTCT 59.557 45.455 31.58 0.00 36.34 2.85
586 600 2.205022 TTTCTTCTGTGGCATGGAGG 57.795 50.000 0.00 0.00 0.00 4.30
596 610 1.446907 GGCATGGAGGCATATCTTCG 58.553 55.000 0.00 0.00 43.51 3.79
597 611 1.002430 GGCATGGAGGCATATCTTCGA 59.998 52.381 0.00 0.00 43.51 3.71
628 642 4.222114 ACTAACTGTAAGCGTACACGTTC 58.778 43.478 21.19 0.00 42.22 3.95
637 651 2.494870 AGCGTACACGTTCTCCCTAAAT 59.505 45.455 3.44 0.00 42.22 1.40
656 670 7.391554 CCCTAAATATGTCACTCCATACCAATG 59.608 40.741 0.00 0.00 30.47 2.82
664 678 5.410746 GTCACTCCATACCAATGCAGATATG 59.589 44.000 0.00 0.00 0.00 1.78
671 691 6.531594 CCATACCAATGCAGATATGTACTACG 59.468 42.308 0.00 0.00 0.00 3.51
673 693 6.644248 ACCAATGCAGATATGTACTACGTA 57.356 37.500 0.00 0.00 0.00 3.57
768 788 3.363970 CGTCAGAACTCGGAAAATGGTTG 60.364 47.826 0.00 0.00 0.00 3.77
876 901 2.360350 CTGGCAGCCGATGGTTGT 60.360 61.111 7.03 0.00 36.29 3.32
933 958 2.236959 ATAAACCCCCGCCTGGCAAT 62.237 55.000 20.29 0.00 0.00 3.56
957 982 1.597663 CTGGTCGACACGAAAAAGCTT 59.402 47.619 18.91 0.00 37.72 3.74
1277 1302 2.514592 GCGCCATTCTAGCCTGCA 60.515 61.111 0.00 0.00 0.00 4.41
1306 1693 3.598678 CATGCATGCTGTTCTCGTG 57.401 52.632 20.33 0.00 0.00 4.35
1310 1697 1.131218 CATGCTGTTCTCGTGCGTG 59.869 57.895 0.00 0.00 37.37 5.34
1580 1987 2.421314 CTGCCGGGCATCGACATA 59.579 61.111 24.10 0.00 42.43 2.29
1649 2056 3.963374 TGAACACCATCCTCTCTATCCTG 59.037 47.826 0.00 0.00 0.00 3.86
1952 2359 0.577269 GCCAACGATCTGATGCGTAC 59.423 55.000 12.94 5.57 40.23 3.67
1964 2371 1.321743 GATGCGTACAACTCGAGCAAG 59.678 52.381 13.61 5.01 41.37 4.01
2248 5837 9.091255 CAATTAAAACAAGCTTTGAATTAACGC 57.909 29.630 0.00 0.00 34.01 4.84
2414 6004 4.729595 GTTATAACCACCAAAAGAAGGCG 58.270 43.478 4.11 0.00 0.00 5.52
2546 6136 1.375908 GTGCTTCATGCTCGACCCA 60.376 57.895 0.00 0.00 43.37 4.51
2987 6577 1.004200 GGACGTGGTGACCGGATTT 60.004 57.895 9.46 0.00 0.00 2.17
3230 6820 2.047274 ACGGTGTTCATCCTGGCG 60.047 61.111 0.00 0.00 0.00 5.69
3248 6838 0.319405 CGTACAACCTCTTCCCCGTT 59.681 55.000 0.00 0.00 0.00 4.44
3287 6880 2.114616 CAGTTCTACATCCAGAGGCCT 58.885 52.381 3.86 3.86 0.00 5.19
3794 7387 0.903924 TGTTGGTCATGGCCATTGGG 60.904 55.000 22.11 5.17 38.48 4.12
4109 7704 6.529220 AGAACAACTCTAGCAAACTTGAGAT 58.471 36.000 10.72 0.00 45.33 2.75
4110 7705 6.995091 AGAACAACTCTAGCAAACTTGAGATT 59.005 34.615 10.72 3.46 45.33 2.40
4117 7712 8.535335 ACTCTAGCAAACTTGAGATTATCAGAA 58.465 33.333 10.72 0.00 45.33 3.02
4196 7791 2.202260 GAGTTTTTACGCGGCGCC 60.202 61.111 27.87 19.07 0.00 6.53
4237 7832 2.172419 GCAAAGTTTAGCGCGCGA 59.828 55.556 37.18 19.65 0.00 5.87
4324 7926 4.552166 ACACAACCAAGAAGATCAAACG 57.448 40.909 0.00 0.00 0.00 3.60
4457 8059 1.091771 ATGATGCTCTTTGTCGGCCG 61.092 55.000 22.12 22.12 0.00 6.13
4465 8067 1.228003 TTTGTCGGCCGTTCCATGT 60.228 52.632 27.15 0.00 34.01 3.21
4533 8135 3.069289 GCACATCGAATGGCATGATAGA 58.931 45.455 0.00 0.00 33.60 1.98
4675 8284 1.672363 CAAGCGTGCATGATGTACCAT 59.328 47.619 10.93 0.00 28.65 3.55
4691 8300 6.000246 TGTACCATAGCATCTTTTGATCCA 58.000 37.500 0.00 0.00 36.97 3.41
4763 8373 5.010415 CCAAAAGCTCTCTCCACATCTTTTT 59.990 40.000 0.00 0.00 33.19 1.94
4770 8380 4.532126 TCTCTCCACATCTTTTTCTAGCCA 59.468 41.667 0.00 0.00 0.00 4.75
4813 8423 7.996098 AATCAAGATTTTTCTTACCTTCCGA 57.004 32.000 0.00 0.00 0.00 4.55
4889 8499 7.116948 GCAAGATAGTAGCCATAGTTGTATGTG 59.883 40.741 0.00 0.00 35.15 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 2.440980 GTGGATCCTGGCAAGGGC 60.441 66.667 14.23 0.00 44.62 5.19
25 26 2.276740 GGTGGATCCTGGCAAGGG 59.723 66.667 14.23 0.00 44.62 3.95
26 27 2.124570 CGGTGGATCCTGGCAAGG 60.125 66.667 14.23 0.00 46.06 3.61
27 28 2.825836 GCGGTGGATCCTGGCAAG 60.826 66.667 14.23 0.00 0.00 4.01
28 29 4.776322 CGCGGTGGATCCTGGCAA 62.776 66.667 14.23 0.00 0.00 4.52
32 33 4.899239 GAGGCGCGGTGGATCCTG 62.899 72.222 14.23 4.04 0.00 3.86
35 36 4.241555 ATGGAGGCGCGGTGGATC 62.242 66.667 8.83 0.00 0.00 3.36
36 37 4.552365 CATGGAGGCGCGGTGGAT 62.552 66.667 8.83 0.00 0.00 3.41
55 56 4.475444 TCTCCGGTGGCCCTAGGG 62.475 72.222 24.89 24.89 38.57 3.53
56 57 3.155167 GTCTCCGGTGGCCCTAGG 61.155 72.222 0.06 0.06 0.00 3.02
57 58 3.528370 CGTCTCCGGTGGCCCTAG 61.528 72.222 0.00 0.00 0.00 3.02
58 59 4.051167 TCGTCTCCGGTGGCCCTA 62.051 66.667 0.00 0.00 33.95 3.53
68 69 3.827898 CAGGTCCGCCTCGTCTCC 61.828 72.222 0.00 0.00 44.97 3.71
69 70 4.500116 GCAGGTCCGCCTCGTCTC 62.500 72.222 0.00 0.00 44.97 3.36
93 94 4.415332 TTCGTGTCTCTCGCCGGC 62.415 66.667 19.07 19.07 0.00 6.13
94 95 2.504244 GTTCGTGTCTCTCGCCGG 60.504 66.667 0.00 0.00 0.00 6.13
95 96 2.504244 GGTTCGTGTCTCTCGCCG 60.504 66.667 0.00 0.00 0.00 6.46
96 97 1.310933 TAGGGTTCGTGTCTCTCGCC 61.311 60.000 0.00 0.00 0.00 5.54
97 98 0.524862 TTAGGGTTCGTGTCTCTCGC 59.475 55.000 0.00 0.00 0.00 5.03
98 99 1.811359 AGTTAGGGTTCGTGTCTCTCG 59.189 52.381 0.00 0.00 0.00 4.04
99 100 3.938289 AAGTTAGGGTTCGTGTCTCTC 57.062 47.619 0.00 0.00 0.00 3.20
100 101 3.896272 AGAAAGTTAGGGTTCGTGTCTCT 59.104 43.478 0.00 0.00 0.00 3.10
101 102 4.254402 AGAAAGTTAGGGTTCGTGTCTC 57.746 45.455 0.00 0.00 0.00 3.36
102 103 4.684484 AAGAAAGTTAGGGTTCGTGTCT 57.316 40.909 0.00 0.00 0.00 3.41
103 104 5.055144 AGAAAGAAAGTTAGGGTTCGTGTC 58.945 41.667 0.00 0.00 0.00 3.67
104 105 5.032327 AGAAAGAAAGTTAGGGTTCGTGT 57.968 39.130 0.00 0.00 0.00 4.49
105 106 5.526111 TCAAGAAAGAAAGTTAGGGTTCGTG 59.474 40.000 0.00 0.00 0.00 4.35
106 107 5.677567 TCAAGAAAGAAAGTTAGGGTTCGT 58.322 37.500 0.00 0.00 0.00 3.85
107 108 6.293462 CCTTCAAGAAAGAAAGTTAGGGTTCG 60.293 42.308 0.00 0.00 37.12 3.95
108 109 6.771267 TCCTTCAAGAAAGAAAGTTAGGGTTC 59.229 38.462 0.00 0.00 37.12 3.62
109 110 6.669631 TCCTTCAAGAAAGAAAGTTAGGGTT 58.330 36.000 0.00 0.00 37.12 4.11
110 111 6.262056 TCCTTCAAGAAAGAAAGTTAGGGT 57.738 37.500 0.00 0.00 37.12 4.34
111 112 5.707764 CCTCCTTCAAGAAAGAAAGTTAGGG 59.292 44.000 0.00 0.00 37.12 3.53
112 113 6.534634 TCCTCCTTCAAGAAAGAAAGTTAGG 58.465 40.000 0.00 0.00 37.12 2.69
113 114 6.652900 CCTCCTCCTTCAAGAAAGAAAGTTAG 59.347 42.308 0.00 0.00 37.12 2.34
114 115 6.329197 TCCTCCTCCTTCAAGAAAGAAAGTTA 59.671 38.462 0.00 0.00 37.12 2.24
115 116 5.132816 TCCTCCTCCTTCAAGAAAGAAAGTT 59.867 40.000 0.00 0.00 37.12 2.66
116 117 4.660771 TCCTCCTCCTTCAAGAAAGAAAGT 59.339 41.667 0.00 0.00 37.12 2.66
117 118 5.234466 TCCTCCTCCTTCAAGAAAGAAAG 57.766 43.478 0.00 0.00 37.12 2.62
118 119 4.042187 CCTCCTCCTCCTTCAAGAAAGAAA 59.958 45.833 0.00 0.00 37.12 2.52
119 120 3.584848 CCTCCTCCTCCTTCAAGAAAGAA 59.415 47.826 0.00 0.00 37.12 2.52
120 121 3.177228 CCTCCTCCTCCTTCAAGAAAGA 58.823 50.000 0.00 0.00 37.12 2.52
121 122 3.177228 TCCTCCTCCTCCTTCAAGAAAG 58.823 50.000 0.00 0.00 34.52 2.62
122 123 3.177228 CTCCTCCTCCTCCTTCAAGAAA 58.823 50.000 0.00 0.00 0.00 2.52
123 124 2.560841 CCTCCTCCTCCTCCTTCAAGAA 60.561 54.545 0.00 0.00 0.00 2.52
124 125 1.007721 CCTCCTCCTCCTCCTTCAAGA 59.992 57.143 0.00 0.00 0.00 3.02
125 126 1.494960 CCTCCTCCTCCTCCTTCAAG 58.505 60.000 0.00 0.00 0.00 3.02
126 127 0.618968 GCCTCCTCCTCCTCCTTCAA 60.619 60.000 0.00 0.00 0.00 2.69
127 128 1.002274 GCCTCCTCCTCCTCCTTCA 59.998 63.158 0.00 0.00 0.00 3.02
128 129 2.131067 CGCCTCCTCCTCCTCCTTC 61.131 68.421 0.00 0.00 0.00 3.46
129 130 2.042435 CGCCTCCTCCTCCTCCTT 60.042 66.667 0.00 0.00 0.00 3.36
130 131 4.150454 CCGCCTCCTCCTCCTCCT 62.150 72.222 0.00 0.00 0.00 3.69
131 132 4.144727 TCCGCCTCCTCCTCCTCC 62.145 72.222 0.00 0.00 0.00 4.30
132 133 2.520741 CTCCGCCTCCTCCTCCTC 60.521 72.222 0.00 0.00 0.00 3.71
133 134 4.851214 GCTCCGCCTCCTCCTCCT 62.851 72.222 0.00 0.00 0.00 3.69
149 150 0.035056 ATCCGCATTATAGCCAGGGC 60.035 55.000 0.97 0.97 42.33 5.19
150 151 1.679944 CCATCCGCATTATAGCCAGGG 60.680 57.143 0.00 0.00 0.00 4.45
151 152 1.679944 CCCATCCGCATTATAGCCAGG 60.680 57.143 0.00 0.00 0.00 4.45
152 153 1.003580 ACCCATCCGCATTATAGCCAG 59.996 52.381 0.00 0.00 0.00 4.85
153 154 1.064003 ACCCATCCGCATTATAGCCA 58.936 50.000 0.00 0.00 0.00 4.75
154 155 1.003118 TCACCCATCCGCATTATAGCC 59.997 52.381 0.00 0.00 0.00 3.93
155 156 2.472695 TCACCCATCCGCATTATAGC 57.527 50.000 0.00 0.00 0.00 2.97
156 157 2.679837 GCATCACCCATCCGCATTATAG 59.320 50.000 0.00 0.00 0.00 1.31
157 158 2.039613 TGCATCACCCATCCGCATTATA 59.960 45.455 0.00 0.00 0.00 0.98
158 159 1.202915 TGCATCACCCATCCGCATTAT 60.203 47.619 0.00 0.00 0.00 1.28
159 160 0.182299 TGCATCACCCATCCGCATTA 59.818 50.000 0.00 0.00 0.00 1.90
160 161 0.468585 ATGCATCACCCATCCGCATT 60.469 50.000 0.00 0.00 40.26 3.56
161 162 0.468585 AATGCATCACCCATCCGCAT 60.469 50.000 0.00 0.00 44.84 4.73
162 163 0.683828 AAATGCATCACCCATCCGCA 60.684 50.000 0.00 0.00 36.95 5.69
163 164 1.317613 TAAATGCATCACCCATCCGC 58.682 50.000 0.00 0.00 0.00 5.54
164 165 2.160219 CGATAAATGCATCACCCATCCG 59.840 50.000 0.00 0.00 0.00 4.18
165 166 2.095059 GCGATAAATGCATCACCCATCC 60.095 50.000 0.00 0.00 0.00 3.51
166 167 2.553602 TGCGATAAATGCATCACCCATC 59.446 45.455 0.00 0.00 37.44 3.51
170 171 2.097304 TGTGTGCGATAAATGCATCACC 59.903 45.455 0.00 0.00 45.34 4.02
177 178 3.840209 CGTTGAACTGTGTGCGATAAATG 59.160 43.478 0.00 0.00 0.00 2.32
178 179 3.666902 GCGTTGAACTGTGTGCGATAAAT 60.667 43.478 0.00 0.00 0.00 1.40
196 197 4.404715 ACATCTAACATACACCCTAGCGTT 59.595 41.667 0.00 0.00 0.00 4.84
223 224 7.444629 CACTAATGCAGAATGGTGCTATTAT 57.555 36.000 0.00 0.00 44.32 1.28
525 538 2.729882 CCGAAGAACGACTTAGTGTTGG 59.270 50.000 0.00 0.00 45.77 3.77
543 557 0.611714 GCTGGAAGGAAAGGTACCGA 59.388 55.000 6.18 0.00 0.00 4.69
574 588 1.142936 AGATATGCCTCCATGCCACA 58.857 50.000 0.00 0.00 32.85 4.17
586 600 4.728534 AGTAGAAGCGATCGAAGATATGC 58.271 43.478 21.57 2.06 45.12 3.14
594 608 5.503683 GCTTACAGTTAGTAGAAGCGATCGA 60.504 44.000 21.57 0.00 33.51 3.59
595 609 4.671516 GCTTACAGTTAGTAGAAGCGATCG 59.328 45.833 11.69 11.69 33.51 3.69
628 642 6.270000 TGGTATGGAGTGACATATTTAGGGAG 59.730 42.308 0.00 0.00 35.91 4.30
637 651 4.408596 TCTGCATTGGTATGGAGTGACATA 59.591 41.667 6.56 0.00 46.77 2.29
706 726 7.807907 CGACAAAAACTCACCTGCTATATTTTT 59.192 33.333 0.00 0.00 0.00 1.94
707 727 7.305474 CGACAAAAACTCACCTGCTATATTTT 58.695 34.615 0.00 0.00 0.00 1.82
708 728 6.128007 CCGACAAAAACTCACCTGCTATATTT 60.128 38.462 0.00 0.00 0.00 1.40
709 729 5.354234 CCGACAAAAACTCACCTGCTATATT 59.646 40.000 0.00 0.00 0.00 1.28
710 730 4.876107 CCGACAAAAACTCACCTGCTATAT 59.124 41.667 0.00 0.00 0.00 0.86
711 731 4.250464 CCGACAAAAACTCACCTGCTATA 58.750 43.478 0.00 0.00 0.00 1.31
712 732 3.074412 CCGACAAAAACTCACCTGCTAT 58.926 45.455 0.00 0.00 0.00 2.97
784 804 3.323243 CACTTTTATTCCGTCTGGTCGT 58.677 45.455 0.00 0.00 36.30 4.34
933 958 2.804697 TTTTCGTGTCGACCAGATGA 57.195 45.000 14.12 2.42 34.89 2.92
957 982 0.979709 CCCTGACAGCTGATCTCCCA 60.980 60.000 23.35 7.06 0.00 4.37
1316 1703 3.044305 AGCCGTGTTCAGAAGCGC 61.044 61.111 0.00 0.00 0.00 5.92
1318 1705 1.862806 GACAGCCGTGTTCAGAAGC 59.137 57.895 0.00 0.00 36.88 3.86
1319 1706 2.145225 CGACAGCCGTGTTCAGAAG 58.855 57.895 0.00 0.00 36.88 2.85
1580 1987 0.038526 GGTCGACTGTGGTGACGAAT 60.039 55.000 16.46 0.00 36.15 3.34
1703 2110 1.372997 CTCGTAGTGCACCAGCGTT 60.373 57.895 14.63 0.00 46.23 4.84
1841 2248 2.885266 CCTCATGAATTCTCCAGCCATG 59.115 50.000 7.05 1.06 36.78 3.66
1847 2254 5.250082 CCTATGATCCCTCATGAATTCTCCA 59.750 44.000 7.05 0.00 42.19 3.86
1952 2359 3.032017 TCTCCTTTCTTGCTCGAGTTG 57.968 47.619 15.13 4.77 0.00 3.16
1964 2371 2.000447 GCACGTACACCATCTCCTTTC 59.000 52.381 0.00 0.00 0.00 2.62
2107 2582 5.425217 AGACAGAGATCTCTCACTAGACTCA 59.575 44.000 22.69 0.00 45.21 3.41
2108 2583 5.918608 AGACAGAGATCTCTCACTAGACTC 58.081 45.833 22.69 6.00 45.21 3.36
2109 2584 5.957771 AGACAGAGATCTCTCACTAGACT 57.042 43.478 22.69 13.15 45.21 3.24
2222 5793 9.091255 GCGTTAATTCAAAGCTTGTTTTAATTG 57.909 29.630 0.00 0.00 38.44 2.32
2223 5794 8.001549 CGCGTTAATTCAAAGCTTGTTTTAATT 58.998 29.630 0.00 5.04 39.22 1.40
2248 5837 5.577164 CCTAGTATGACCTGTGAGAAAAACG 59.423 44.000 0.00 0.00 0.00 3.60
2414 6004 2.824041 ATCACGTTCATGGCGCCC 60.824 61.111 26.77 6.80 0.00 6.13
2447 6037 2.202878 GGCGCGTTGGAGAGCATA 60.203 61.111 8.43 0.00 38.70 3.14
2546 6136 2.354305 GTGTTCTGACCGTCGCGT 60.354 61.111 5.77 0.00 0.00 6.01
2855 6445 3.103911 GCCTCGTCGACCAACACG 61.104 66.667 10.58 0.00 37.36 4.49
2933 6523 2.989824 ACCCACCCGACGTCTCTG 60.990 66.667 14.70 5.56 0.00 3.35
3059 6649 2.456119 GCGCTCGGTGAGGTTGATG 61.456 63.158 0.00 0.00 0.00 3.07
3177 6767 1.641577 GACATGTTGAGGTAGGCGAC 58.358 55.000 0.00 0.00 0.00 5.19
3230 6820 1.622312 AGAACGGGGAAGAGGTTGTAC 59.378 52.381 0.00 0.00 0.00 2.90
3248 6838 3.183130 CTCGGAGAAGAGCCAGAGA 57.817 57.895 0.00 0.00 34.09 3.10
3287 6880 2.087501 ACATGATGTACGTGCCGAAA 57.912 45.000 0.00 0.00 38.94 3.46
3332 6925 1.715585 GAACATGCCGATCACGTGG 59.284 57.895 17.00 0.00 37.88 4.94
4051 7646 2.867975 GCACAAGCTGCACTTCAATTTT 59.132 40.909 1.02 0.00 46.29 1.82
4052 7647 2.476821 GCACAAGCTGCACTTCAATTT 58.523 42.857 1.02 0.00 46.29 1.82
4053 7648 2.144482 GCACAAGCTGCACTTCAATT 57.856 45.000 1.02 0.00 46.29 2.32
4054 7649 3.879912 GCACAAGCTGCACTTCAAT 57.120 47.368 1.02 0.00 46.29 2.57
4081 7676 7.272978 TCAAGTTTGCTAGAGTTGTTCTTACT 58.727 34.615 0.00 0.00 37.36 2.24
4109 7704 4.517285 GGCTGTTGGAGATGTTCTGATAA 58.483 43.478 0.00 0.00 0.00 1.75
4110 7705 3.430790 CGGCTGTTGGAGATGTTCTGATA 60.431 47.826 0.00 0.00 0.00 2.15
4117 7712 1.672356 GCACGGCTGTTGGAGATGT 60.672 57.895 0.00 0.00 0.00 3.06
4407 8009 5.637810 TGCGTTTGGTTTTGTATTGTTGAAA 59.362 32.000 0.00 0.00 0.00 2.69
4421 8023 3.724508 TCATGATTTGTGCGTTTGGTT 57.275 38.095 0.00 0.00 0.00 3.67
4423 8025 2.346244 GCATCATGATTTGTGCGTTTGG 59.654 45.455 5.16 0.00 0.00 3.28
4457 8059 2.739932 CGAGGAGTGATGGACATGGAAC 60.740 54.545 0.00 0.00 0.00 3.62
4465 8067 2.736670 TCTCATCGAGGAGTGATGGA 57.263 50.000 24.89 3.70 42.73 3.41
4533 8135 2.060980 TGGCCCGTTTTGTTGCCTT 61.061 52.632 0.00 0.00 44.32 4.35
4582 8184 3.776969 TCAGTATGAGCTCTTGGGACATT 59.223 43.478 16.19 0.00 42.56 2.71
4675 8284 9.466497 ACTAGATTTTTGGATCAAAAGATGCTA 57.534 29.630 3.38 4.88 42.91 3.49
4691 8300 4.527038 TGTGAGAGGACCGACTAGATTTTT 59.473 41.667 0.00 0.00 0.00 1.94
4763 8373 3.461773 GCTCAGGCGGTGGCTAGA 61.462 66.667 0.00 0.00 36.44 2.43
4770 8380 2.360350 CCACAATGCTCAGGCGGT 60.360 61.111 0.00 0.00 42.25 5.68
4842 8452 3.750371 CGGATGGCATCTACCCAAAATA 58.250 45.455 25.48 0.00 35.67 1.40
4844 8454 2.021723 GCGGATGGCATCTACCCAAAA 61.022 52.381 25.48 0.00 42.87 2.44


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

AutoCloner maintained by Alex Coulton.