Multiple sequence alignment - TraesCS5A01G450400

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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 TraesCS5A01G450400 chr5A 100.000 2998 0 0 1 2998 632255159 632252162 0.000000e+00 5537
1 TraesCS5A01G450400 chr3B 98.556 1801 22 4 1202 2998 23367223 23369023 0.000000e+00 3179
2 TraesCS5A01G450400 chr3B 98.075 883 14 1 285 1164 23366341 23367223 0.000000e+00 1533
3 TraesCS5A01G450400 chr3B 99.333 300 2 0 2699 2998 23346228 23346527 7.310000e-151 544
4 TraesCS5A01G450400 chr2A 98.109 1798 31 3 1202 2998 54192146 54193941 0.000000e+00 3129
5 TraesCS5A01G450400 chr2A 89.518 1555 133 14 1449 2998 5661904 5663433 0.000000e+00 1941
6 TraesCS5A01G450400 chr2A 97.955 880 17 1 285 1164 54191268 54192146 0.000000e+00 1524
7 TraesCS5A01G450400 chr4A 90.240 2039 160 16 498 2499 659683937 659685973 0.000000e+00 2627
8 TraesCS5A01G450400 chr4A 89.990 2038 164 20 498 2497 659654170 659656205 0.000000e+00 2597
9 TraesCS5A01G450400 chr4A 89.653 1556 130 12 1449 2998 668366283 668367813 0.000000e+00 1953
10 TraesCS5A01G450400 chr4A 95.085 468 22 1 2387 2854 659656207 659656673 0.000000e+00 736
11 TraesCS5A01G450400 chr4A 86.068 646 57 17 364 977 659567987 659568631 0.000000e+00 664
12 TraesCS5A01G450400 chr4A 92.647 204 15 0 2387 2590 659685973 659686176 8.130000e-76 294
13 TraesCS5A01G450400 chr4A 90.968 155 11 1 2840 2994 659658209 659658360 3.920000e-49 206
14 TraesCS5A01G450400 chr4A 94.737 95 5 0 2904 2998 659699842 659699936 6.700000e-32 148
15 TraesCS5A01G450400 chrUn 89.582 1555 130 22 1449 2998 85473979 85472452 0.000000e+00 1945
16 TraesCS5A01G450400 chr7B 99.655 290 1 0 1 290 117214100 117214389 5.690000e-147 531
17 TraesCS5A01G450400 chr7B 100.000 285 0 0 1 285 117217094 117216810 7.360000e-146 527
18 TraesCS5A01G450400 chr7B 100.000 285 0 0 1 285 126230201 126230485 7.360000e-146 527
19 TraesCS5A01G450400 chr7B 100.000 284 0 0 1 284 122773386 122773669 2.650000e-145 525
20 TraesCS5A01G450400 chr3A 100.000 285 0 0 1 285 26153401 26153685 7.360000e-146 527
21 TraesCS5A01G450400 chr6D 100.000 284 0 0 1 284 431858417 431858700 2.650000e-145 525
22 TraesCS5A01G450400 chr6A 100.000 284 0 0 1 284 73783334 73783051 2.650000e-145 525
23 TraesCS5A01G450400 chr3D 100.000 284 0 0 1 284 39859770 39860053 2.650000e-145 525
24 TraesCS5A01G450400 chr3D 100.000 284 0 0 1 284 39895806 39896089 2.650000e-145 525
25 TraesCS5A01G450400 chr1D 89.362 141 15 0 498 638 416215385 416215525 8.540000e-41 178


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 TraesCS5A01G450400 chr5A 632252162 632255159 2997 True 5537.000000 5537 100.000000 1 2998 1 chr5A.!!$R1 2997
1 TraesCS5A01G450400 chr3B 23366341 23369023 2682 False 2356.000000 3179 98.315500 285 2998 2 chr3B.!!$F2 2713
2 TraesCS5A01G450400 chr2A 54191268 54193941 2673 False 2326.500000 3129 98.032000 285 2998 2 chr2A.!!$F2 2713
3 TraesCS5A01G450400 chr2A 5661904 5663433 1529 False 1941.000000 1941 89.518000 1449 2998 1 chr2A.!!$F1 1549
4 TraesCS5A01G450400 chr4A 668366283 668367813 1530 False 1953.000000 1953 89.653000 1449 2998 1 chr4A.!!$F3 1549
5 TraesCS5A01G450400 chr4A 659683937 659686176 2239 False 1460.500000 2627 91.443500 498 2590 2 chr4A.!!$F5 2092
6 TraesCS5A01G450400 chr4A 659654170 659658360 4190 False 1179.666667 2597 92.014333 498 2994 3 chr4A.!!$F4 2496
7 TraesCS5A01G450400 chr4A 659567987 659568631 644 False 664.000000 664 86.068000 364 977 1 chr4A.!!$F1 613
8 TraesCS5A01G450400 chrUn 85472452 85473979 1527 True 1945.000000 1945 89.582000 1449 2998 1 chrUn.!!$R1 1549

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
262 263 0.035056 CAGTTGGACCACCCTGGATC 60.035 60.0 11.12 0.0 40.96 3.36 F
409 410 0.174845 CGCGGTCTGGAAATCTACCA 59.825 55.0 0.00 0.0 35.96 3.25 F
1186 1222 0.762418 TTTTCTCCCTCGGACTGCAA 59.238 50.0 0.00 0.0 0.00 4.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1288 1324 0.250513 ACCCTTCCGCATCACTCTTC 59.749 55.0 0.0 0.0 0.00 2.87 R
1370 1408 0.933097 CCTCCGTGCAGAAATCATCG 59.067 55.0 0.0 0.0 0.00 3.84 R
2703 2905 1.961793 TGCAGTTTTTACACGGCTCT 58.038 45.0 0.0 0.0 38.54 4.09 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
20 21 3.287867 AAAGATACTCCCTCCGTACGA 57.712 47.619 18.76 1.79 0.00 3.43
21 22 3.287867 AAGATACTCCCTCCGTACGAA 57.712 47.619 18.76 0.00 0.00 3.85
22 23 3.287867 AGATACTCCCTCCGTACGAAA 57.712 47.619 18.76 3.28 0.00 3.46
23 24 3.624777 AGATACTCCCTCCGTACGAAAA 58.375 45.455 18.76 0.48 0.00 2.29
24 25 4.019174 AGATACTCCCTCCGTACGAAAAA 58.981 43.478 18.76 0.00 0.00 1.94
25 26 2.738013 ACTCCCTCCGTACGAAAAAG 57.262 50.000 18.76 9.67 0.00 2.27
26 27 1.966354 ACTCCCTCCGTACGAAAAAGT 59.034 47.619 18.76 10.30 0.00 2.66
27 28 2.366590 ACTCCCTCCGTACGAAAAAGTT 59.633 45.455 18.76 0.00 0.00 2.66
28 29 3.181462 ACTCCCTCCGTACGAAAAAGTTT 60.181 43.478 18.76 0.00 0.00 2.66
29 30 3.132925 TCCCTCCGTACGAAAAAGTTTG 58.867 45.455 18.76 0.00 0.00 2.93
30 31 2.874086 CCCTCCGTACGAAAAAGTTTGT 59.126 45.455 18.76 0.00 35.43 2.83
31 32 3.059393 CCCTCCGTACGAAAAAGTTTGTC 60.059 47.826 18.76 0.00 33.20 3.18
32 33 3.059393 CCTCCGTACGAAAAAGTTTGTCC 60.059 47.826 18.76 0.00 33.20 4.02
33 34 2.871633 TCCGTACGAAAAAGTTTGTCCC 59.128 45.455 18.76 0.00 33.20 4.46
34 35 2.613133 CCGTACGAAAAAGTTTGTCCCA 59.387 45.455 18.76 0.00 33.20 4.37
35 36 3.065095 CCGTACGAAAAAGTTTGTCCCAA 59.935 43.478 18.76 0.00 33.20 4.12
36 37 4.276460 CGTACGAAAAAGTTTGTCCCAAG 58.724 43.478 10.44 0.00 33.20 3.61
37 38 4.201841 CGTACGAAAAAGTTTGTCCCAAGT 60.202 41.667 10.44 0.00 33.20 3.16
38 39 4.794278 ACGAAAAAGTTTGTCCCAAGTT 57.206 36.364 0.00 0.00 0.00 2.66
39 40 5.142061 ACGAAAAAGTTTGTCCCAAGTTT 57.858 34.783 0.00 0.00 0.00 2.66
40 41 4.926832 ACGAAAAAGTTTGTCCCAAGTTTG 59.073 37.500 0.00 0.00 0.00 2.93
41 42 4.926832 CGAAAAAGTTTGTCCCAAGTTTGT 59.073 37.500 0.00 0.00 0.00 2.83
42 43 5.061684 CGAAAAAGTTTGTCCCAAGTTTGTC 59.938 40.000 0.00 0.00 0.00 3.18
43 44 4.465632 AAAGTTTGTCCCAAGTTTGTCC 57.534 40.909 0.00 0.00 0.00 4.02
44 45 2.384828 AGTTTGTCCCAAGTTTGTCCC 58.615 47.619 0.00 0.00 0.00 4.46
45 46 2.024369 AGTTTGTCCCAAGTTTGTCCCT 60.024 45.455 0.00 0.00 0.00 4.20
46 47 2.358322 TTGTCCCAAGTTTGTCCCTC 57.642 50.000 0.00 0.00 0.00 4.30
47 48 1.217916 TGTCCCAAGTTTGTCCCTCA 58.782 50.000 0.00 0.00 0.00 3.86
48 49 1.566703 TGTCCCAAGTTTGTCCCTCAA 59.433 47.619 0.00 0.00 0.00 3.02
49 50 2.024846 TGTCCCAAGTTTGTCCCTCAAA 60.025 45.455 0.00 0.00 42.79 2.69
50 51 3.230976 GTCCCAAGTTTGTCCCTCAAAT 58.769 45.455 0.00 0.00 45.88 2.32
51 52 4.141135 TGTCCCAAGTTTGTCCCTCAAATA 60.141 41.667 0.00 0.00 45.88 1.40
52 53 4.459337 GTCCCAAGTTTGTCCCTCAAATAG 59.541 45.833 0.00 0.00 45.88 1.73
53 54 4.352595 TCCCAAGTTTGTCCCTCAAATAGA 59.647 41.667 0.00 0.00 45.88 1.98
54 55 5.015178 TCCCAAGTTTGTCCCTCAAATAGAT 59.985 40.000 0.00 0.00 45.88 1.98
55 56 5.126061 CCCAAGTTTGTCCCTCAAATAGATG 59.874 44.000 0.00 0.00 45.88 2.90
56 57 5.711976 CCAAGTTTGTCCCTCAAATAGATGT 59.288 40.000 0.00 0.00 45.88 3.06
57 58 6.884295 CCAAGTTTGTCCCTCAAATAGATGTA 59.116 38.462 0.00 0.00 45.88 2.29
58 59 7.557719 CCAAGTTTGTCCCTCAAATAGATGTAT 59.442 37.037 0.00 0.00 45.88 2.29
59 60 8.616076 CAAGTTTGTCCCTCAAATAGATGTATC 58.384 37.037 0.00 0.00 45.88 2.24
60 61 8.095452 AGTTTGTCCCTCAAATAGATGTATCT 57.905 34.615 0.00 0.00 45.88 1.98
61 62 9.213777 AGTTTGTCCCTCAAATAGATGTATCTA 57.786 33.333 4.22 4.22 45.88 1.98
64 65 8.956446 TGTCCCTCAAATAGATGTATCTATCA 57.044 34.615 13.26 4.06 46.49 2.15
65 66 8.807118 TGTCCCTCAAATAGATGTATCTATCAC 58.193 37.037 13.26 4.95 46.49 3.06
66 67 9.030452 GTCCCTCAAATAGATGTATCTATCACT 57.970 37.037 13.26 0.00 46.49 3.41
76 77 8.879342 AGATGTATCTATCACTAACTTGTTGC 57.121 34.615 0.00 0.00 34.85 4.17
77 78 8.700051 AGATGTATCTATCACTAACTTGTTGCT 58.300 33.333 0.00 0.00 34.85 3.91
78 79 9.967346 GATGTATCTATCACTAACTTGTTGCTA 57.033 33.333 0.00 0.00 0.00 3.49
79 80 9.973450 ATGTATCTATCACTAACTTGTTGCTAG 57.027 33.333 0.00 0.00 0.00 3.42
80 81 9.185680 TGTATCTATCACTAACTTGTTGCTAGA 57.814 33.333 0.00 0.00 0.00 2.43
84 85 9.185680 TCTATCACTAACTTGTTGCTAGATACA 57.814 33.333 0.00 0.00 0.00 2.29
85 86 9.973450 CTATCACTAACTTGTTGCTAGATACAT 57.027 33.333 0.00 0.00 0.00 2.29
86 87 8.879342 ATCACTAACTTGTTGCTAGATACATC 57.121 34.615 0.00 0.00 0.00 3.06
87 88 8.067751 TCACTAACTTGTTGCTAGATACATCT 57.932 34.615 0.00 0.00 40.86 2.90
88 89 9.185680 TCACTAACTTGTTGCTAGATACATCTA 57.814 33.333 0.00 0.00 38.32 1.98
89 90 9.973450 CACTAACTTGTTGCTAGATACATCTAT 57.027 33.333 0.00 0.00 38.60 1.98
93 94 9.890629 AACTTGTTGCTAGATACATCTATTTGA 57.109 29.630 0.00 0.00 38.60 2.69
94 95 9.539825 ACTTGTTGCTAGATACATCTATTTGAG 57.460 33.333 0.00 0.00 38.60 3.02
95 96 8.893219 TTGTTGCTAGATACATCTATTTGAGG 57.107 34.615 0.00 0.00 38.60 3.86
96 97 7.445121 TGTTGCTAGATACATCTATTTGAGGG 58.555 38.462 0.00 0.00 38.60 4.30
97 98 7.290014 TGTTGCTAGATACATCTATTTGAGGGA 59.710 37.037 0.00 0.00 38.60 4.20
98 99 7.233389 TGCTAGATACATCTATTTGAGGGAC 57.767 40.000 0.00 0.00 38.60 4.46
99 100 6.782494 TGCTAGATACATCTATTTGAGGGACA 59.218 38.462 0.00 0.00 38.60 4.02
100 101 7.290014 TGCTAGATACATCTATTTGAGGGACAA 59.710 37.037 0.00 0.00 38.60 3.18
101 102 7.816995 GCTAGATACATCTATTTGAGGGACAAG 59.183 40.741 0.00 0.00 38.60 3.16
102 103 7.682787 AGATACATCTATTTGAGGGACAAGT 57.317 36.000 0.00 0.00 36.19 3.16
103 104 8.095452 AGATACATCTATTTGAGGGACAAGTT 57.905 34.615 0.00 0.00 36.19 2.66
104 105 8.552296 AGATACATCTATTTGAGGGACAAGTTT 58.448 33.333 0.00 0.00 36.19 2.66
105 106 9.178758 GATACATCTATTTGAGGGACAAGTTTT 57.821 33.333 0.00 0.00 39.77 2.43
106 107 7.839680 ACATCTATTTGAGGGACAAGTTTTT 57.160 32.000 0.00 0.00 39.77 1.94
123 124 2.754946 TTTTTGGACGGAGCGAGTAT 57.245 45.000 0.00 0.00 0.00 2.12
124 125 2.754946 TTTTGGACGGAGCGAGTATT 57.245 45.000 0.00 0.00 0.00 1.89
125 126 3.872511 TTTTGGACGGAGCGAGTATTA 57.127 42.857 0.00 0.00 0.00 0.98
126 127 4.395959 TTTTGGACGGAGCGAGTATTAT 57.604 40.909 0.00 0.00 0.00 1.28
127 128 5.518848 TTTTGGACGGAGCGAGTATTATA 57.481 39.130 0.00 0.00 0.00 0.98
128 129 4.761235 TTGGACGGAGCGAGTATTATAG 57.239 45.455 0.00 0.00 0.00 1.31
129 130 4.011966 TGGACGGAGCGAGTATTATAGA 57.988 45.455 0.00 0.00 0.00 1.98
130 131 4.392047 TGGACGGAGCGAGTATTATAGAA 58.608 43.478 0.00 0.00 0.00 2.10
131 132 4.823442 TGGACGGAGCGAGTATTATAGAAA 59.177 41.667 0.00 0.00 0.00 2.52
132 133 5.475909 TGGACGGAGCGAGTATTATAGAAAT 59.524 40.000 0.00 0.00 0.00 2.17
133 134 5.800941 GGACGGAGCGAGTATTATAGAAATG 59.199 44.000 0.00 0.00 0.00 2.32
134 135 6.328641 ACGGAGCGAGTATTATAGAAATGT 57.671 37.500 0.00 0.00 0.00 2.71
135 136 6.746120 ACGGAGCGAGTATTATAGAAATGTT 58.254 36.000 0.00 0.00 0.00 2.71
136 137 6.641314 ACGGAGCGAGTATTATAGAAATGTTG 59.359 38.462 0.00 0.00 0.00 3.33
137 138 6.400091 CGGAGCGAGTATTATAGAAATGTTGC 60.400 42.308 0.00 0.00 0.00 4.17
138 139 6.423905 GGAGCGAGTATTATAGAAATGTTGCA 59.576 38.462 0.00 0.00 0.00 4.08
139 140 7.042051 GGAGCGAGTATTATAGAAATGTTGCAA 60.042 37.037 0.00 0.00 0.00 4.08
140 141 8.208718 AGCGAGTATTATAGAAATGTTGCAAA 57.791 30.769 0.00 0.00 0.00 3.68
141 142 8.673711 AGCGAGTATTATAGAAATGTTGCAAAA 58.326 29.630 0.00 0.00 0.00 2.44
142 143 9.284594 GCGAGTATTATAGAAATGTTGCAAAAA 57.715 29.630 0.00 0.00 0.00 1.94
149 150 9.912634 TTATAGAAATGTTGCAAAAAGAAGAGG 57.087 29.630 0.00 0.00 0.00 3.69
150 151 5.604565 AGAAATGTTGCAAAAAGAAGAGGG 58.395 37.500 0.00 0.00 0.00 4.30
151 152 5.129320 AGAAATGTTGCAAAAAGAAGAGGGT 59.871 36.000 0.00 0.00 0.00 4.34
152 153 5.357742 AATGTTGCAAAAAGAAGAGGGTT 57.642 34.783 0.00 0.00 0.00 4.11
153 154 4.122143 TGTTGCAAAAAGAAGAGGGTTG 57.878 40.909 0.00 0.00 0.00 3.77
154 155 3.118811 TGTTGCAAAAAGAAGAGGGTTGG 60.119 43.478 0.00 0.00 0.00 3.77
155 156 3.025322 TGCAAAAAGAAGAGGGTTGGA 57.975 42.857 0.00 0.00 0.00 3.53
156 157 2.958355 TGCAAAAAGAAGAGGGTTGGAG 59.042 45.455 0.00 0.00 0.00 3.86
157 158 3.222603 GCAAAAAGAAGAGGGTTGGAGA 58.777 45.455 0.00 0.00 0.00 3.71
158 159 3.004839 GCAAAAAGAAGAGGGTTGGAGAC 59.995 47.826 0.00 0.00 0.00 3.36
159 160 4.207165 CAAAAAGAAGAGGGTTGGAGACA 58.793 43.478 0.00 0.00 39.83 3.41
160 161 4.731313 AAAAGAAGAGGGTTGGAGACAT 57.269 40.909 0.00 0.00 42.32 3.06
161 162 4.731313 AAAGAAGAGGGTTGGAGACATT 57.269 40.909 0.00 0.00 42.32 2.71
162 163 3.710209 AGAAGAGGGTTGGAGACATTG 57.290 47.619 0.00 0.00 42.32 2.82
163 164 2.087646 GAAGAGGGTTGGAGACATTGC 58.912 52.381 0.00 0.00 42.32 3.56
164 165 1.067295 AGAGGGTTGGAGACATTGCA 58.933 50.000 0.00 0.00 42.32 4.08
165 166 1.637553 AGAGGGTTGGAGACATTGCAT 59.362 47.619 0.00 0.00 42.32 3.96
166 167 2.019984 GAGGGTTGGAGACATTGCATC 58.980 52.381 0.00 0.00 42.32 3.91
167 168 1.106285 GGGTTGGAGACATTGCATCC 58.894 55.000 0.00 0.00 42.32 3.51
168 169 1.341383 GGGTTGGAGACATTGCATCCT 60.341 52.381 4.96 0.00 42.32 3.24
169 170 2.450476 GGTTGGAGACATTGCATCCTT 58.550 47.619 4.96 0.00 42.32 3.36
170 171 2.827921 GGTTGGAGACATTGCATCCTTT 59.172 45.455 4.96 0.00 42.32 3.11
171 172 3.259123 GGTTGGAGACATTGCATCCTTTT 59.741 43.478 4.96 0.00 42.32 2.27
172 173 4.462483 GGTTGGAGACATTGCATCCTTTTA 59.538 41.667 4.96 0.00 42.32 1.52
173 174 5.127682 GGTTGGAGACATTGCATCCTTTTAT 59.872 40.000 4.96 0.00 42.32 1.40
174 175 6.351286 GGTTGGAGACATTGCATCCTTTTATT 60.351 38.462 4.96 0.00 42.32 1.40
175 176 6.211587 TGGAGACATTGCATCCTTTTATTG 57.788 37.500 4.96 0.00 34.04 1.90
176 177 5.951148 TGGAGACATTGCATCCTTTTATTGA 59.049 36.000 4.96 0.00 34.04 2.57
177 178 6.608405 TGGAGACATTGCATCCTTTTATTGAT 59.392 34.615 4.96 0.00 34.04 2.57
178 179 7.124599 TGGAGACATTGCATCCTTTTATTGATT 59.875 33.333 4.96 0.00 34.04 2.57
179 180 7.983484 GGAGACATTGCATCCTTTTATTGATTT 59.017 33.333 0.00 0.00 0.00 2.17
180 181 8.712285 AGACATTGCATCCTTTTATTGATTTG 57.288 30.769 0.00 0.00 0.00 2.32
181 182 8.316214 AGACATTGCATCCTTTTATTGATTTGT 58.684 29.630 0.00 0.00 0.00 2.83
182 183 8.259049 ACATTGCATCCTTTTATTGATTTGTG 57.741 30.769 0.00 0.00 0.00 3.33
183 184 6.724694 TTGCATCCTTTTATTGATTTGTGC 57.275 33.333 0.00 0.00 0.00 4.57
184 185 6.040209 TGCATCCTTTTATTGATTTGTGCT 57.960 33.333 0.00 0.00 0.00 4.40
185 186 6.465948 TGCATCCTTTTATTGATTTGTGCTT 58.534 32.000 0.00 0.00 0.00 3.91
186 187 6.935771 TGCATCCTTTTATTGATTTGTGCTTT 59.064 30.769 0.00 0.00 0.00 3.51
187 188 7.444792 TGCATCCTTTTATTGATTTGTGCTTTT 59.555 29.630 0.00 0.00 0.00 2.27
188 189 7.747357 GCATCCTTTTATTGATTTGTGCTTTTG 59.253 33.333 0.00 0.00 0.00 2.44
189 190 8.991026 CATCCTTTTATTGATTTGTGCTTTTGA 58.009 29.630 0.00 0.00 0.00 2.69
190 191 9.729281 ATCCTTTTATTGATTTGTGCTTTTGAT 57.271 25.926 0.00 0.00 0.00 2.57
224 225 9.793252 ATATTCAAAAGATAGCATGTTGTGTTC 57.207 29.630 0.00 0.00 0.00 3.18
225 226 6.882610 TCAAAAGATAGCATGTTGTGTTCT 57.117 33.333 0.00 0.00 0.00 3.01
226 227 7.275888 TCAAAAGATAGCATGTTGTGTTCTT 57.724 32.000 0.00 0.00 0.00 2.52
227 228 7.140705 TCAAAAGATAGCATGTTGTGTTCTTG 58.859 34.615 0.00 0.79 0.00 3.02
228 229 6.639632 AAAGATAGCATGTTGTGTTCTTGT 57.360 33.333 0.00 0.00 0.00 3.16
229 230 5.869753 AGATAGCATGTTGTGTTCTTGTC 57.130 39.130 0.00 0.00 0.00 3.18
230 231 4.697352 AGATAGCATGTTGTGTTCTTGTCC 59.303 41.667 0.00 0.00 0.00 4.02
231 232 2.653726 AGCATGTTGTGTTCTTGTCCA 58.346 42.857 0.00 0.00 0.00 4.02
232 233 3.023119 AGCATGTTGTGTTCTTGTCCAA 58.977 40.909 0.00 0.00 0.00 3.53
233 234 3.446873 AGCATGTTGTGTTCTTGTCCAAA 59.553 39.130 0.00 0.00 0.00 3.28
234 235 4.081752 AGCATGTTGTGTTCTTGTCCAAAA 60.082 37.500 0.00 0.00 0.00 2.44
235 236 4.629200 GCATGTTGTGTTCTTGTCCAAAAA 59.371 37.500 0.00 0.00 0.00 1.94
254 255 4.385358 AAAATTGTGTCAGTTGGACCAC 57.615 40.909 0.00 0.00 46.38 4.16
255 256 1.981256 ATTGTGTCAGTTGGACCACC 58.019 50.000 0.00 0.00 46.38 4.61
256 257 0.106918 TTGTGTCAGTTGGACCACCC 60.107 55.000 0.00 0.00 46.38 4.61
257 258 0.986019 TGTGTCAGTTGGACCACCCT 60.986 55.000 0.00 0.00 46.38 4.34
258 259 0.535102 GTGTCAGTTGGACCACCCTG 60.535 60.000 12.34 12.34 46.38 4.45
259 260 1.073199 GTCAGTTGGACCACCCTGG 59.927 63.158 16.64 0.00 45.02 4.45
260 261 1.074090 TCAGTTGGACCACCCTGGA 60.074 57.895 16.64 5.08 40.96 3.86
261 262 0.475632 TCAGTTGGACCACCCTGGAT 60.476 55.000 16.64 0.00 40.96 3.41
262 263 0.035056 CAGTTGGACCACCCTGGATC 60.035 60.000 11.12 0.00 40.96 3.36
263 264 1.078426 GTTGGACCACCCTGGATCG 60.078 63.158 0.00 0.00 40.96 3.69
264 265 1.229368 TTGGACCACCCTGGATCGA 60.229 57.895 0.00 0.00 40.96 3.59
265 266 0.838554 TTGGACCACCCTGGATCGAA 60.839 55.000 0.00 0.00 40.96 3.71
266 267 0.838554 TGGACCACCCTGGATCGAAA 60.839 55.000 0.00 0.00 40.96 3.46
267 268 0.546598 GGACCACCCTGGATCGAAAT 59.453 55.000 0.00 0.00 40.96 2.17
268 269 1.475213 GGACCACCCTGGATCGAAATC 60.475 57.143 0.00 0.00 40.96 2.17
277 278 1.784525 GGATCGAAATCCTGGCTACG 58.215 55.000 0.00 0.00 46.97 3.51
278 279 1.140816 GATCGAAATCCTGGCTACGC 58.859 55.000 0.00 0.00 0.00 4.42
340 341 5.932619 ACAGTTATGATACACCTGCAGTA 57.067 39.130 13.81 0.00 0.00 2.74
409 410 0.174845 CGCGGTCTGGAAATCTACCA 59.825 55.000 0.00 0.00 35.96 3.25
817 853 9.125026 GTTGAGTTGATGGGAGTCATATTATTT 57.875 33.333 0.00 0.00 35.97 1.40
1029 1065 6.313519 TGCTTTGGTTAGACCTTCTCATAT 57.686 37.500 0.00 0.00 39.58 1.78
1106 1142 5.116180 TCGCAGGAGACGAATCAATAATTT 58.884 37.500 0.00 0.00 36.44 1.82
1186 1222 0.762418 TTTTCTCCCTCGGACTGCAA 59.238 50.000 0.00 0.00 0.00 4.08
1188 1224 1.544825 TTCTCCCTCGGACTGCAAGG 61.545 60.000 0.00 0.00 39.30 3.61
1199 1235 1.913722 CTGCAAGGATGGAGGAGCT 59.086 57.895 0.00 0.00 40.99 4.09
1633 1671 1.271543 TGAAGTAGCTGCATGGCTTGT 60.272 47.619 5.70 0.00 42.97 3.16
1711 1750 1.615384 GCCTTGGAAGCCAGATTCTGT 60.615 52.381 12.54 0.00 33.81 3.41
1806 1845 3.390967 TCATGTGAAAGAGGTCTTGGACA 59.609 43.478 6.56 6.56 36.12 4.02
2185 2229 3.181489 CGATTACGGTGCTAGGAGAAACT 60.181 47.826 0.00 0.00 35.72 2.66
2703 2905 6.779049 TGGGCTAAGAAGGTACTCGATTATTA 59.221 38.462 0.00 0.00 38.49 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.287867 TCGTACGGAGGGAGTATCTTT 57.712 47.619 16.52 0.00 33.73 2.52
1 2 3.287867 TTCGTACGGAGGGAGTATCTT 57.712 47.619 16.52 0.00 33.73 2.40
2 3 3.287867 TTTCGTACGGAGGGAGTATCT 57.712 47.619 16.52 0.00 33.73 1.98
3 4 4.142293 ACTTTTTCGTACGGAGGGAGTATC 60.142 45.833 16.52 0.00 0.00 2.24
4 5 3.766051 ACTTTTTCGTACGGAGGGAGTAT 59.234 43.478 16.52 0.00 0.00 2.12
5 6 3.157087 ACTTTTTCGTACGGAGGGAGTA 58.843 45.455 16.52 0.00 0.00 2.59
6 7 1.966354 ACTTTTTCGTACGGAGGGAGT 59.034 47.619 16.52 8.90 0.00 3.85
7 8 2.738013 ACTTTTTCGTACGGAGGGAG 57.262 50.000 16.52 8.26 0.00 4.30
8 9 3.132925 CAAACTTTTTCGTACGGAGGGA 58.867 45.455 16.52 0.00 0.00 4.20
9 10 2.874086 ACAAACTTTTTCGTACGGAGGG 59.126 45.455 16.52 3.28 0.00 4.30
10 11 3.059393 GGACAAACTTTTTCGTACGGAGG 60.059 47.826 16.52 5.20 0.00 4.30
11 12 3.059393 GGGACAAACTTTTTCGTACGGAG 60.059 47.826 16.52 10.80 0.00 4.63
12 13 2.871633 GGGACAAACTTTTTCGTACGGA 59.128 45.455 16.52 2.84 0.00 4.69
13 14 2.613133 TGGGACAAACTTTTTCGTACGG 59.387 45.455 16.52 0.68 31.92 4.02
14 15 3.948196 TGGGACAAACTTTTTCGTACG 57.052 42.857 9.53 9.53 31.92 3.67
24 25 7.809906 TTGAGGGACAAACTTGGGACAAACT 62.810 44.000 0.00 0.00 38.59 2.66
25 26 5.651632 TTGAGGGACAAACTTGGGACAAAC 61.652 45.833 0.00 0.00 38.59 2.93
26 27 3.564571 TTGAGGGACAAACTTGGGACAAA 60.565 43.478 0.00 0.00 38.59 2.83
27 28 2.024846 TTGAGGGACAAACTTGGGACAA 60.025 45.455 0.00 0.00 38.59 3.18
28 29 1.217916 TGAGGGACAAACTTGGGACA 58.782 50.000 0.00 0.00 0.00 4.02
29 30 2.358322 TTGAGGGACAAACTTGGGAC 57.642 50.000 0.00 0.00 35.39 4.46
35 36 9.213777 TAGATACATCTATTTGAGGGACAAACT 57.786 33.333 0.00 0.00 42.79 2.66
38 39 9.379770 TGATAGATACATCTATTTGAGGGACAA 57.620 33.333 11.99 0.00 46.98 3.18
39 40 8.807118 GTGATAGATACATCTATTTGAGGGACA 58.193 37.037 11.99 2.36 46.98 4.02
40 41 9.030452 AGTGATAGATACATCTATTTGAGGGAC 57.970 37.037 11.99 0.18 46.98 4.46
50 51 9.967346 GCAACAAGTTAGTGATAGATACATCTA 57.033 33.333 1.54 1.54 43.00 1.98
51 52 8.700051 AGCAACAAGTTAGTGATAGATACATCT 58.300 33.333 0.00 0.00 40.86 2.90
52 53 8.879342 AGCAACAAGTTAGTGATAGATACATC 57.121 34.615 0.00 0.00 0.00 3.06
53 54 9.973450 CTAGCAACAAGTTAGTGATAGATACAT 57.027 33.333 4.89 0.00 0.00 2.29
54 55 9.185680 TCTAGCAACAAGTTAGTGATAGATACA 57.814 33.333 8.23 0.00 33.25 2.29
58 59 9.185680 TGTATCTAGCAACAAGTTAGTGATAGA 57.814 33.333 12.69 12.69 33.25 1.98
59 60 9.973450 ATGTATCTAGCAACAAGTTAGTGATAG 57.027 33.333 4.60 4.60 33.25 2.08
60 61 9.967346 GATGTATCTAGCAACAAGTTAGTGATA 57.033 33.333 1.73 0.00 33.25 2.15
61 62 8.700051 AGATGTATCTAGCAACAAGTTAGTGAT 58.300 33.333 1.73 0.00 34.85 3.06
62 63 8.067751 AGATGTATCTAGCAACAAGTTAGTGA 57.932 34.615 1.73 0.00 34.85 3.41
63 64 9.973450 ATAGATGTATCTAGCAACAAGTTAGTG 57.027 33.333 7.57 0.00 42.20 2.74
67 68 9.890629 TCAAATAGATGTATCTAGCAACAAGTT 57.109 29.630 7.57 0.00 42.20 2.66
68 69 9.539825 CTCAAATAGATGTATCTAGCAACAAGT 57.460 33.333 7.57 0.00 42.20 3.16
69 70 8.986847 CCTCAAATAGATGTATCTAGCAACAAG 58.013 37.037 7.57 1.72 42.20 3.16
70 71 7.933577 CCCTCAAATAGATGTATCTAGCAACAA 59.066 37.037 7.57 0.00 42.20 2.83
71 72 7.290014 TCCCTCAAATAGATGTATCTAGCAACA 59.710 37.037 7.57 0.24 42.20 3.33
72 73 7.600752 GTCCCTCAAATAGATGTATCTAGCAAC 59.399 40.741 7.57 0.00 42.20 4.17
73 74 7.290014 TGTCCCTCAAATAGATGTATCTAGCAA 59.710 37.037 7.57 0.00 42.20 3.91
74 75 6.782494 TGTCCCTCAAATAGATGTATCTAGCA 59.218 38.462 7.57 0.00 42.20 3.49
75 76 7.233389 TGTCCCTCAAATAGATGTATCTAGC 57.767 40.000 7.57 0.00 42.20 3.42
76 77 8.865090 ACTTGTCCCTCAAATAGATGTATCTAG 58.135 37.037 7.57 0.00 36.19 2.43
77 78 8.783660 ACTTGTCCCTCAAATAGATGTATCTA 57.216 34.615 4.22 4.22 36.64 1.98
78 79 7.682787 ACTTGTCCCTCAAATAGATGTATCT 57.317 36.000 0.00 0.00 36.97 1.98
79 80 8.738645 AAACTTGTCCCTCAAATAGATGTATC 57.261 34.615 0.00 0.00 35.48 2.24
80 81 9.533831 AAAAACTTGTCCCTCAAATAGATGTAT 57.466 29.630 0.00 0.00 35.48 2.29
81 82 8.934023 AAAAACTTGTCCCTCAAATAGATGTA 57.066 30.769 0.00 0.00 35.48 2.29
82 83 7.839680 AAAAACTTGTCCCTCAAATAGATGT 57.160 32.000 0.00 0.00 35.48 3.06
104 105 2.754946 ATACTCGCTCCGTCCAAAAA 57.245 45.000 0.00 0.00 0.00 1.94
105 106 2.754946 AATACTCGCTCCGTCCAAAA 57.245 45.000 0.00 0.00 0.00 2.44
106 107 4.823442 TCTATAATACTCGCTCCGTCCAAA 59.177 41.667 0.00 0.00 0.00 3.28
107 108 4.392047 TCTATAATACTCGCTCCGTCCAA 58.608 43.478 0.00 0.00 0.00 3.53
108 109 4.011966 TCTATAATACTCGCTCCGTCCA 57.988 45.455 0.00 0.00 0.00 4.02
109 110 5.368256 TTTCTATAATACTCGCTCCGTCC 57.632 43.478 0.00 0.00 0.00 4.79
110 111 6.380190 ACATTTCTATAATACTCGCTCCGTC 58.620 40.000 0.00 0.00 0.00 4.79
111 112 6.328641 ACATTTCTATAATACTCGCTCCGT 57.671 37.500 0.00 0.00 0.00 4.69
112 113 6.400091 GCAACATTTCTATAATACTCGCTCCG 60.400 42.308 0.00 0.00 0.00 4.63
113 114 6.423905 TGCAACATTTCTATAATACTCGCTCC 59.576 38.462 0.00 0.00 0.00 4.70
114 115 7.408132 TGCAACATTTCTATAATACTCGCTC 57.592 36.000 0.00 0.00 0.00 5.03
115 116 7.786178 TTGCAACATTTCTATAATACTCGCT 57.214 32.000 0.00 0.00 0.00 4.93
116 117 8.835467 TTTTGCAACATTTCTATAATACTCGC 57.165 30.769 0.00 0.00 0.00 5.03
123 124 9.912634 CCTCTTCTTTTTGCAACATTTCTATAA 57.087 29.630 0.00 0.00 0.00 0.98
124 125 8.522830 CCCTCTTCTTTTTGCAACATTTCTATA 58.477 33.333 0.00 0.00 0.00 1.31
125 126 7.015584 ACCCTCTTCTTTTTGCAACATTTCTAT 59.984 33.333 0.00 0.00 0.00 1.98
126 127 6.323739 ACCCTCTTCTTTTTGCAACATTTCTA 59.676 34.615 0.00 0.00 0.00 2.10
127 128 5.129320 ACCCTCTTCTTTTTGCAACATTTCT 59.871 36.000 0.00 0.00 0.00 2.52
128 129 5.359756 ACCCTCTTCTTTTTGCAACATTTC 58.640 37.500 0.00 0.00 0.00 2.17
129 130 5.357742 ACCCTCTTCTTTTTGCAACATTT 57.642 34.783 0.00 0.00 0.00 2.32
130 131 5.118286 CAACCCTCTTCTTTTTGCAACATT 58.882 37.500 0.00 0.00 0.00 2.71
131 132 4.443315 CCAACCCTCTTCTTTTTGCAACAT 60.443 41.667 0.00 0.00 0.00 2.71
132 133 3.118811 CCAACCCTCTTCTTTTTGCAACA 60.119 43.478 0.00 0.00 0.00 3.33
133 134 3.132111 TCCAACCCTCTTCTTTTTGCAAC 59.868 43.478 0.00 0.00 0.00 4.17
134 135 3.370104 TCCAACCCTCTTCTTTTTGCAA 58.630 40.909 0.00 0.00 0.00 4.08
135 136 2.958355 CTCCAACCCTCTTCTTTTTGCA 59.042 45.455 0.00 0.00 0.00 4.08
136 137 3.004839 GTCTCCAACCCTCTTCTTTTTGC 59.995 47.826 0.00 0.00 0.00 3.68
137 138 4.207165 TGTCTCCAACCCTCTTCTTTTTG 58.793 43.478 0.00 0.00 0.00 2.44
138 139 4.519906 TGTCTCCAACCCTCTTCTTTTT 57.480 40.909 0.00 0.00 0.00 1.94
139 140 4.731313 ATGTCTCCAACCCTCTTCTTTT 57.269 40.909 0.00 0.00 0.00 2.27
140 141 4.401925 CAATGTCTCCAACCCTCTTCTTT 58.598 43.478 0.00 0.00 0.00 2.52
141 142 3.812167 GCAATGTCTCCAACCCTCTTCTT 60.812 47.826 0.00 0.00 0.00 2.52
142 143 2.290577 GCAATGTCTCCAACCCTCTTCT 60.291 50.000 0.00 0.00 0.00 2.85
143 144 2.087646 GCAATGTCTCCAACCCTCTTC 58.912 52.381 0.00 0.00 0.00 2.87
144 145 1.425066 TGCAATGTCTCCAACCCTCTT 59.575 47.619 0.00 0.00 0.00 2.85
145 146 1.067295 TGCAATGTCTCCAACCCTCT 58.933 50.000 0.00 0.00 0.00 3.69
146 147 2.019984 GATGCAATGTCTCCAACCCTC 58.980 52.381 0.00 0.00 0.00 4.30
147 148 1.341383 GGATGCAATGTCTCCAACCCT 60.341 52.381 0.00 0.00 0.00 4.34
148 149 1.106285 GGATGCAATGTCTCCAACCC 58.894 55.000 0.00 0.00 0.00 4.11
149 150 2.134789 AGGATGCAATGTCTCCAACC 57.865 50.000 6.09 0.00 0.00 3.77
150 151 4.525912 AAAAGGATGCAATGTCTCCAAC 57.474 40.909 6.09 0.00 0.00 3.77
151 152 6.436847 TCAATAAAAGGATGCAATGTCTCCAA 59.563 34.615 6.09 0.00 0.00 3.53
152 153 5.951148 TCAATAAAAGGATGCAATGTCTCCA 59.049 36.000 6.09 0.00 0.00 3.86
153 154 6.455360 TCAATAAAAGGATGCAATGTCTCC 57.545 37.500 0.00 0.00 0.00 3.71
154 155 8.814235 CAAATCAATAAAAGGATGCAATGTCTC 58.186 33.333 0.00 0.00 0.00 3.36
155 156 8.316214 ACAAATCAATAAAAGGATGCAATGTCT 58.684 29.630 0.00 0.00 0.00 3.41
156 157 8.385111 CACAAATCAATAAAAGGATGCAATGTC 58.615 33.333 0.00 0.00 0.00 3.06
157 158 7.148373 GCACAAATCAATAAAAGGATGCAATGT 60.148 33.333 0.00 0.00 0.00 2.71
158 159 7.065324 AGCACAAATCAATAAAAGGATGCAATG 59.935 33.333 0.00 0.00 0.00 2.82
159 160 7.107542 AGCACAAATCAATAAAAGGATGCAAT 58.892 30.769 0.00 0.00 0.00 3.56
160 161 6.465948 AGCACAAATCAATAAAAGGATGCAA 58.534 32.000 0.00 0.00 0.00 4.08
161 162 6.040209 AGCACAAATCAATAAAAGGATGCA 57.960 33.333 0.00 0.00 0.00 3.96
162 163 6.973229 AAGCACAAATCAATAAAAGGATGC 57.027 33.333 0.00 0.00 0.00 3.91
163 164 8.991026 TCAAAAGCACAAATCAATAAAAGGATG 58.009 29.630 0.00 0.00 0.00 3.51
164 165 9.729281 ATCAAAAGCACAAATCAATAAAAGGAT 57.271 25.926 0.00 0.00 0.00 3.24
198 199 9.793252 GAACACAACATGCTATCTTTTGAATAT 57.207 29.630 0.00 0.00 0.00 1.28
199 200 9.013229 AGAACACAACATGCTATCTTTTGAATA 57.987 29.630 0.00 0.00 0.00 1.75
200 201 7.889469 AGAACACAACATGCTATCTTTTGAAT 58.111 30.769 0.00 0.00 0.00 2.57
201 202 7.275888 AGAACACAACATGCTATCTTTTGAA 57.724 32.000 0.00 0.00 0.00 2.69
202 203 6.882610 AGAACACAACATGCTATCTTTTGA 57.117 33.333 0.00 0.00 0.00 2.69
203 204 6.919662 ACAAGAACACAACATGCTATCTTTTG 59.080 34.615 0.00 0.00 30.63 2.44
204 205 7.042797 ACAAGAACACAACATGCTATCTTTT 57.957 32.000 0.00 0.00 30.63 2.27
205 206 6.294176 GGACAAGAACACAACATGCTATCTTT 60.294 38.462 0.00 0.00 30.63 2.52
206 207 5.182001 GGACAAGAACACAACATGCTATCTT 59.818 40.000 0.00 0.00 32.27 2.40
207 208 4.697352 GGACAAGAACACAACATGCTATCT 59.303 41.667 0.00 0.00 0.00 1.98
208 209 4.455533 TGGACAAGAACACAACATGCTATC 59.544 41.667 0.00 0.00 0.00 2.08
209 210 4.397420 TGGACAAGAACACAACATGCTAT 58.603 39.130 0.00 0.00 0.00 2.97
210 211 3.814625 TGGACAAGAACACAACATGCTA 58.185 40.909 0.00 0.00 0.00 3.49
211 212 2.653726 TGGACAAGAACACAACATGCT 58.346 42.857 0.00 0.00 0.00 3.79
212 213 3.435105 TTGGACAAGAACACAACATGC 57.565 42.857 0.00 0.00 0.00 4.06
232 233 4.382577 GGTGGTCCAACTGACACAATTTTT 60.383 41.667 0.00 0.00 46.38 1.94
233 234 3.132111 GGTGGTCCAACTGACACAATTTT 59.868 43.478 0.00 0.00 46.38 1.82
234 235 2.693074 GGTGGTCCAACTGACACAATTT 59.307 45.455 0.00 0.00 46.38 1.82
235 236 2.306847 GGTGGTCCAACTGACACAATT 58.693 47.619 0.00 0.00 46.38 2.32
236 237 1.478654 GGGTGGTCCAACTGACACAAT 60.479 52.381 6.92 0.00 46.38 2.71
237 238 0.106918 GGGTGGTCCAACTGACACAA 60.107 55.000 6.92 0.00 46.38 3.33
238 239 0.986019 AGGGTGGTCCAACTGACACA 60.986 55.000 6.92 0.00 46.38 3.72
239 240 0.535102 CAGGGTGGTCCAACTGACAC 60.535 60.000 16.33 0.00 46.38 3.67
240 241 1.705002 CCAGGGTGGTCCAACTGACA 61.705 60.000 20.95 0.00 46.38 3.58
241 242 1.073199 CCAGGGTGGTCCAACTGAC 59.927 63.158 20.95 0.51 43.67 3.51
242 243 0.475632 ATCCAGGGTGGTCCAACTGA 60.476 55.000 20.95 10.53 39.03 3.41
243 244 0.035056 GATCCAGGGTGGTCCAACTG 60.035 60.000 6.92 11.87 39.03 3.16
244 245 1.553690 CGATCCAGGGTGGTCCAACT 61.554 60.000 6.92 0.00 39.03 3.16
245 246 1.078426 CGATCCAGGGTGGTCCAAC 60.078 63.158 0.00 0.00 39.03 3.77
246 247 0.838554 TTCGATCCAGGGTGGTCCAA 60.839 55.000 0.00 0.00 39.03 3.53
247 248 0.838554 TTTCGATCCAGGGTGGTCCA 60.839 55.000 0.00 0.00 39.03 4.02
248 249 0.546598 ATTTCGATCCAGGGTGGTCC 59.453 55.000 0.00 0.00 39.03 4.46
249 250 1.475213 GGATTTCGATCCAGGGTGGTC 60.475 57.143 0.00 0.00 40.43 4.02
250 251 0.546598 GGATTTCGATCCAGGGTGGT 59.453 55.000 0.00 0.00 40.43 4.16
251 252 0.839946 AGGATTTCGATCCAGGGTGG 59.160 55.000 7.77 0.00 43.14 4.61
252 253 1.475751 CCAGGATTTCGATCCAGGGTG 60.476 57.143 8.31 0.00 41.97 4.61
253 254 0.839946 CCAGGATTTCGATCCAGGGT 59.160 55.000 8.31 0.00 41.97 4.34
254 255 0.536006 GCCAGGATTTCGATCCAGGG 60.536 60.000 15.93 12.89 44.76 4.45
255 256 0.471617 AGCCAGGATTTCGATCCAGG 59.528 55.000 11.23 11.23 46.64 4.45
256 257 2.760374 GTAGCCAGGATTTCGATCCAG 58.240 52.381 7.77 0.00 43.14 3.86
257 258 1.068588 CGTAGCCAGGATTTCGATCCA 59.931 52.381 7.77 0.00 43.14 3.41
258 259 1.784525 CGTAGCCAGGATTTCGATCC 58.215 55.000 0.00 0.00 41.02 3.36
273 274 2.373938 GCTACAAGCAGTGGCGTAG 58.626 57.895 2.18 0.00 45.00 3.51
274 275 4.590487 GCTACAAGCAGTGGCGTA 57.410 55.556 2.18 0.00 45.00 4.42
278 279 2.472695 TTGTAGGCTACAAGCAGTGG 57.527 50.000 30.85 0.00 44.75 4.00
340 341 8.198807 ACCAAGTAAGTACAGGTAAACAGTAT 57.801 34.615 0.00 0.00 35.84 2.12
409 410 3.624777 CACAGAAGCATTATTCCCAGGT 58.375 45.455 0.00 0.00 0.00 4.00
491 495 3.668141 TGTCCCATCAACCAGCAATAT 57.332 42.857 0.00 0.00 0.00 1.28
1012 1048 6.661805 AGCTAGCTATATGAGAAGGTCTAACC 59.338 42.308 17.69 0.00 38.99 2.85
1029 1065 1.852633 TGGCACTCAGAAGCTAGCTA 58.147 50.000 19.70 0.34 0.00 3.32
1186 1222 1.428912 CCTCTCTAGCTCCTCCATCCT 59.571 57.143 0.00 0.00 0.00 3.24
1188 1224 1.256812 GCCTCTCTAGCTCCTCCATC 58.743 60.000 0.00 0.00 0.00 3.51
1199 1235 2.415608 CCGCGGAACTGCCTCTCTA 61.416 63.158 24.07 0.00 0.00 2.43
1288 1324 0.250513 ACCCTTCCGCATCACTCTTC 59.749 55.000 0.00 0.00 0.00 2.87
1370 1408 0.933097 CCTCCGTGCAGAAATCATCG 59.067 55.000 0.00 0.00 0.00 3.84
1633 1671 8.153221 TGATTTAGGTACCTTGTTAGGATTGA 57.847 34.615 22.11 0.00 45.05 2.57
1711 1750 1.111277 TGGCGATTCTCCTTCATCGA 58.889 50.000 5.76 0.00 44.18 3.59
1806 1845 2.030027 TCAGACATCAAGGGACCACT 57.970 50.000 0.00 0.00 0.00 4.00
2185 2229 8.154856 GCCACCTATATTGTGAATTACTCCTTA 58.845 37.037 6.64 0.00 35.74 2.69
2703 2905 1.961793 TGCAGTTTTTACACGGCTCT 58.038 45.000 0.00 0.00 38.54 4.09


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

AutoCloner maintained by Alex Coulton.