Multiple sequence alignment - TraesCS5A01G103600

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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 TraesCS5A01G103600 chr5A 100.000 2447 0 0 1 2447 162146257 162143811 0.000000e+00 4519
1 TraesCS5A01G103600 chr4A 96.177 2171 82 1 278 2447 350191680 350189510 0.000000e+00 3548
2 TraesCS5A01G103600 chr4A 94.374 711 37 3 275 983 350159835 350160544 0.000000e+00 1088
3 TraesCS5A01G103600 chr4A 92.105 646 39 3 277 921 280930583 280931217 0.000000e+00 900
4 TraesCS5A01G103600 chr4A 91.931 347 22 3 275 620 295191248 295190907 4.730000e-132 481
5 TraesCS5A01G103600 chr6D 98.818 1607 18 1 842 2447 430466784 430465178 0.000000e+00 2861
6 TraesCS5A01G103600 chr6D 95.588 340 15 0 275 614 430467131 430466792 1.650000e-151 545
7 TraesCS5A01G103600 chr6D 95.000 340 17 0 275 614 370001242 370000903 3.580000e-148 534
8 TraesCS5A01G103600 chr6D 99.273 275 2 0 2 276 430484718 430484444 4.700000e-137 497
9 TraesCS5A01G103600 chr6D 92.375 341 20 4 500 834 153952982 153953322 4.730000e-132 481
10 TraesCS5A01G103600 chr3D 98.817 1606 19 0 842 2447 202625480 202623875 0.000000e+00 2861
11 TraesCS5A01G103600 chr7B 98.007 1606 32 0 842 2447 742965082 742966687 0.000000e+00 2789
12 TraesCS5A01G103600 chr7B 97.581 1612 39 0 836 2447 52951952 52950341 0.000000e+00 2761
13 TraesCS5A01G103600 chr4D 97.758 1606 35 1 842 2447 97361819 97363423 0.000000e+00 2765
14 TraesCS5A01G103600 chr4D 95.882 340 14 0 275 614 97361472 97361811 3.560000e-153 551
15 TraesCS5A01G103600 chr3B 97.634 1606 38 0 842 2447 92237791 92239396 0.000000e+00 2756
16 TraesCS5A01G103600 chr3B 97.634 1606 38 0 842 2447 201583761 201582156 0.000000e+00 2756
17 TraesCS5A01G103600 chr3B 92.176 409 21 6 517 915 575858275 575857868 3.530000e-158 568
18 TraesCS5A01G103600 chr3B 99.275 276 2 0 1 276 92264819 92264544 1.310000e-137 499
19 TraesCS5A01G103600 chr1D 97.509 1606 40 0 842 2447 350977670 350979275 0.000000e+00 2745
20 TraesCS5A01G103600 chr1D 95.000 340 17 0 275 614 350977323 350977662 3.580000e-148 534
21 TraesCS5A01G103600 chr1D 98.913 276 3 0 1 276 141341576 141341851 6.080000e-136 494
22 TraesCS5A01G103600 chrUn 95.588 340 15 0 275 614 414475821 414475482 1.650000e-151 545
23 TraesCS5A01G103600 chrUn 99.275 276 2 0 1 276 223703969 223704244 1.310000e-137 499
24 TraesCS5A01G103600 chr6B 99.275 276 2 0 1 276 128915079 128914804 1.310000e-137 499
25 TraesCS5A01G103600 chr4B 99.275 276 2 0 1 276 495539808 495540083 1.310000e-137 499
26 TraesCS5A01G103600 chr2A 99.275 276 2 0 1 276 735139755 735139480 1.310000e-137 499
27 TraesCS5A01G103600 chr1B 99.275 276 2 0 1 276 683731179 683731454 1.310000e-137 499
28 TraesCS5A01G103600 chr1A 98.913 276 3 0 1 276 278503792 278503517 6.080000e-136 494


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 TraesCS5A01G103600 chr5A 162143811 162146257 2446 True 4519.0 4519 100.0000 1 2447 1 chr5A.!!$R1 2446
1 TraesCS5A01G103600 chr4A 350189510 350191680 2170 True 3548.0 3548 96.1770 278 2447 1 chr4A.!!$R2 2169
2 TraesCS5A01G103600 chr4A 350159835 350160544 709 False 1088.0 1088 94.3740 275 983 1 chr4A.!!$F2 708
3 TraesCS5A01G103600 chr4A 280930583 280931217 634 False 900.0 900 92.1050 277 921 1 chr4A.!!$F1 644
4 TraesCS5A01G103600 chr6D 430465178 430467131 1953 True 1703.0 2861 97.2030 275 2447 2 chr6D.!!$R3 2172
5 TraesCS5A01G103600 chr3D 202623875 202625480 1605 True 2861.0 2861 98.8170 842 2447 1 chr3D.!!$R1 1605
6 TraesCS5A01G103600 chr7B 742965082 742966687 1605 False 2789.0 2789 98.0070 842 2447 1 chr7B.!!$F1 1605
7 TraesCS5A01G103600 chr7B 52950341 52951952 1611 True 2761.0 2761 97.5810 836 2447 1 chr7B.!!$R1 1611
8 TraesCS5A01G103600 chr4D 97361472 97363423 1951 False 1658.0 2765 96.8200 275 2447 2 chr4D.!!$F1 2172
9 TraesCS5A01G103600 chr3B 92237791 92239396 1605 False 2756.0 2756 97.6340 842 2447 1 chr3B.!!$F1 1605
10 TraesCS5A01G103600 chr3B 201582156 201583761 1605 True 2756.0 2756 97.6340 842 2447 1 chr3B.!!$R2 1605
11 TraesCS5A01G103600 chr1D 350977323 350979275 1952 False 1639.5 2745 96.2545 275 2447 2 chr1D.!!$F2 2172

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
232 233 0.032217 ACCATTATTGCAGGGGTGGG 60.032 55.0 12.83 3.74 0.00 4.61 F
339 340 0.033504 GGAGAGTTGCTCGTGTTGGA 59.966 55.0 0.00 0.00 44.91 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1238 1240 1.697432 AGGTTTGTTGTCGATCCCTGA 59.303 47.619 0.0 0.0 0.00 3.86 R
1996 2001 2.163818 TGAGCGAAAGGTTACACCAG 57.836 50.000 0.0 0.0 45.11 4.00 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
25 26 6.558771 ACGAAGTGATTCATCATGTTCAAA 57.441 33.333 12.14 0.00 42.51 2.69
26 27 6.373779 ACGAAGTGATTCATCATGTTCAAAC 58.626 36.000 12.14 0.00 42.51 2.93
27 28 6.017192 ACGAAGTGATTCATCATGTTCAAACA 60.017 34.615 0.00 0.00 42.51 2.83
28 29 7.308770 ACGAAGTGATTCATCATGTTCAAACAT 60.309 33.333 2.53 2.53 45.97 2.71
39 40 3.701241 TGTTCAAACATGAACCTTTCGC 58.299 40.909 16.54 0.00 45.41 4.70
40 41 3.380004 TGTTCAAACATGAACCTTTCGCT 59.620 39.130 16.54 0.00 45.41 4.93
41 42 3.896648 TCAAACATGAACCTTTCGCTC 57.103 42.857 0.00 0.00 0.00 5.03
42 43 3.210227 TCAAACATGAACCTTTCGCTCA 58.790 40.909 0.00 0.00 0.00 4.26
43 44 3.820467 TCAAACATGAACCTTTCGCTCAT 59.180 39.130 0.00 0.00 0.00 2.90
44 45 4.278170 TCAAACATGAACCTTTCGCTCATT 59.722 37.500 0.00 0.00 0.00 2.57
45 46 3.837213 ACATGAACCTTTCGCTCATTG 57.163 42.857 0.00 0.00 0.00 2.82
46 47 2.489329 ACATGAACCTTTCGCTCATTGG 59.511 45.455 0.00 0.00 0.00 3.16
47 48 1.533625 TGAACCTTTCGCTCATTGGG 58.466 50.000 0.00 0.00 0.00 4.12
48 49 0.811281 GAACCTTTCGCTCATTGGGG 59.189 55.000 0.00 0.00 0.00 4.96
49 50 0.404040 AACCTTTCGCTCATTGGGGA 59.596 50.000 0.00 0.00 0.00 4.81
50 51 0.322546 ACCTTTCGCTCATTGGGGAC 60.323 55.000 0.00 0.00 0.00 4.46
51 52 1.369091 CCTTTCGCTCATTGGGGACG 61.369 60.000 0.00 0.00 0.00 4.79
52 53 1.369091 CTTTCGCTCATTGGGGACGG 61.369 60.000 0.00 0.00 0.00 4.79
53 54 2.119484 TTTCGCTCATTGGGGACGGT 62.119 55.000 0.00 0.00 0.00 4.83
54 55 2.046314 CGCTCATTGGGGACGGTT 60.046 61.111 0.00 0.00 0.00 4.44
55 56 1.674322 CGCTCATTGGGGACGGTTT 60.674 57.895 0.00 0.00 0.00 3.27
56 57 0.391927 CGCTCATTGGGGACGGTTTA 60.392 55.000 0.00 0.00 0.00 2.01
57 58 1.745827 CGCTCATTGGGGACGGTTTAT 60.746 52.381 0.00 0.00 0.00 1.40
58 59 2.484065 CGCTCATTGGGGACGGTTTATA 60.484 50.000 0.00 0.00 0.00 0.98
59 60 3.547746 GCTCATTGGGGACGGTTTATAA 58.452 45.455 0.00 0.00 0.00 0.98
60 61 3.949113 GCTCATTGGGGACGGTTTATAAA 59.051 43.478 0.00 0.00 0.00 1.40
61 62 4.583073 GCTCATTGGGGACGGTTTATAAAT 59.417 41.667 0.31 0.00 0.00 1.40
62 63 5.278315 GCTCATTGGGGACGGTTTATAAATC 60.278 44.000 0.31 0.00 0.00 2.17
63 64 5.756918 TCATTGGGGACGGTTTATAAATCA 58.243 37.500 9.11 0.00 0.00 2.57
64 65 6.369629 TCATTGGGGACGGTTTATAAATCAT 58.630 36.000 9.11 0.00 0.00 2.45
65 66 6.488683 TCATTGGGGACGGTTTATAAATCATC 59.511 38.462 9.11 2.70 0.00 2.92
66 67 5.375283 TGGGGACGGTTTATAAATCATCA 57.625 39.130 6.85 0.00 0.00 3.07
67 68 5.756918 TGGGGACGGTTTATAAATCATCAA 58.243 37.500 6.85 0.00 0.00 2.57
68 69 6.188407 TGGGGACGGTTTATAAATCATCAAA 58.812 36.000 6.85 0.00 0.00 2.69
69 70 6.836527 TGGGGACGGTTTATAAATCATCAAAT 59.163 34.615 6.85 0.00 0.00 2.32
70 71 7.343316 TGGGGACGGTTTATAAATCATCAAATT 59.657 33.333 6.85 0.00 0.00 1.82
71 72 7.865889 GGGGACGGTTTATAAATCATCAAATTC 59.134 37.037 6.85 0.00 0.00 2.17
72 73 7.865889 GGGACGGTTTATAAATCATCAAATTCC 59.134 37.037 6.85 0.00 0.00 3.01
73 74 7.865889 GGACGGTTTATAAATCATCAAATTCCC 59.134 37.037 6.85 0.00 0.00 3.97
74 75 8.299990 ACGGTTTATAAATCATCAAATTCCCA 57.700 30.769 9.11 0.00 0.00 4.37
75 76 8.194769 ACGGTTTATAAATCATCAAATTCCCAC 58.805 33.333 9.11 0.00 0.00 4.61
76 77 8.194104 CGGTTTATAAATCATCAAATTCCCACA 58.806 33.333 9.11 0.00 0.00 4.17
77 78 9.883142 GGTTTATAAATCATCAAATTCCCACAA 57.117 29.630 3.49 0.00 0.00 3.33
81 82 8.967664 ATAAATCATCAAATTCCCACAAATGG 57.032 30.769 0.00 0.00 46.81 3.16
94 95 4.445452 CACAAATGGAATGAGAAGTGGG 57.555 45.455 0.00 0.00 0.00 4.61
95 96 3.828451 CACAAATGGAATGAGAAGTGGGT 59.172 43.478 0.00 0.00 0.00 4.51
96 97 4.082125 ACAAATGGAATGAGAAGTGGGTC 58.918 43.478 0.00 0.00 0.00 4.46
97 98 3.372440 AATGGAATGAGAAGTGGGTCC 57.628 47.619 0.00 0.00 0.00 4.46
98 99 1.741028 TGGAATGAGAAGTGGGTCCA 58.259 50.000 0.00 0.00 32.80 4.02
99 100 2.278245 TGGAATGAGAAGTGGGTCCAT 58.722 47.619 0.00 0.00 30.27 3.41
100 101 2.025981 TGGAATGAGAAGTGGGTCCATG 60.026 50.000 0.00 0.00 30.27 3.66
101 102 2.025887 GGAATGAGAAGTGGGTCCATGT 60.026 50.000 0.00 0.00 0.00 3.21
102 103 3.199946 GGAATGAGAAGTGGGTCCATGTA 59.800 47.826 0.00 0.00 0.00 2.29
103 104 4.324254 GGAATGAGAAGTGGGTCCATGTAA 60.324 45.833 0.00 0.00 0.00 2.41
104 105 4.927267 ATGAGAAGTGGGTCCATGTAAA 57.073 40.909 0.00 0.00 0.00 2.01
105 106 4.927267 TGAGAAGTGGGTCCATGTAAAT 57.073 40.909 0.00 0.00 0.00 1.40
106 107 4.588899 TGAGAAGTGGGTCCATGTAAATG 58.411 43.478 0.00 0.00 0.00 2.32
107 108 4.288366 TGAGAAGTGGGTCCATGTAAATGA 59.712 41.667 0.00 0.00 0.00 2.57
108 109 5.044919 TGAGAAGTGGGTCCATGTAAATGAT 60.045 40.000 0.00 0.00 0.00 2.45
109 110 5.440610 AGAAGTGGGTCCATGTAAATGATC 58.559 41.667 0.00 0.00 0.00 2.92
110 111 3.808728 AGTGGGTCCATGTAAATGATCG 58.191 45.455 0.00 0.00 0.00 3.69
111 112 3.454447 AGTGGGTCCATGTAAATGATCGA 59.546 43.478 0.00 0.00 0.00 3.59
112 113 3.809832 GTGGGTCCATGTAAATGATCGAG 59.190 47.826 0.00 0.00 0.00 4.04
113 114 3.709141 TGGGTCCATGTAAATGATCGAGA 59.291 43.478 0.00 0.00 0.00 4.04
114 115 4.058817 GGGTCCATGTAAATGATCGAGAC 58.941 47.826 0.00 0.00 0.00 3.36
115 116 4.058817 GGTCCATGTAAATGATCGAGACC 58.941 47.826 0.00 0.00 34.97 3.85
116 117 4.202264 GGTCCATGTAAATGATCGAGACCT 60.202 45.833 9.77 0.00 38.55 3.85
117 118 4.985409 GTCCATGTAAATGATCGAGACCTC 59.015 45.833 0.00 0.00 0.00 3.85
127 128 2.600388 CGAGACCTCGCAAACAACA 58.400 52.632 6.49 0.00 46.50 3.33
128 129 0.934496 CGAGACCTCGCAAACAACAA 59.066 50.000 6.49 0.00 46.50 2.83
129 130 1.332904 CGAGACCTCGCAAACAACAAC 60.333 52.381 6.49 0.00 46.50 3.32
130 131 0.655733 AGACCTCGCAAACAACAACG 59.344 50.000 0.00 0.00 0.00 4.10
131 132 0.375803 GACCTCGCAAACAACAACGT 59.624 50.000 0.00 0.00 0.00 3.99
132 133 0.806241 ACCTCGCAAACAACAACGTT 59.194 45.000 0.00 0.00 0.00 3.99
133 134 1.202098 ACCTCGCAAACAACAACGTTC 60.202 47.619 0.00 0.00 0.00 3.95
134 135 1.462791 CTCGCAAACAACAACGTTCC 58.537 50.000 0.00 0.00 0.00 3.62
135 136 1.063469 CTCGCAAACAACAACGTTCCT 59.937 47.619 0.00 0.00 0.00 3.36
136 137 1.469308 TCGCAAACAACAACGTTCCTT 59.531 42.857 0.00 0.00 0.00 3.36
137 138 1.843753 CGCAAACAACAACGTTCCTTC 59.156 47.619 0.00 0.00 0.00 3.46
138 139 2.190161 GCAAACAACAACGTTCCTTCC 58.810 47.619 0.00 0.00 0.00 3.46
139 140 2.804647 CAAACAACAACGTTCCTTCCC 58.195 47.619 0.00 0.00 0.00 3.97
140 141 1.395635 AACAACAACGTTCCTTCCCC 58.604 50.000 0.00 0.00 0.00 4.81
141 142 0.256464 ACAACAACGTTCCTTCCCCA 59.744 50.000 0.00 0.00 0.00 4.96
142 143 1.133606 ACAACAACGTTCCTTCCCCAT 60.134 47.619 0.00 0.00 0.00 4.00
143 144 2.106857 ACAACAACGTTCCTTCCCCATA 59.893 45.455 0.00 0.00 0.00 2.74
144 145 3.245122 ACAACAACGTTCCTTCCCCATAT 60.245 43.478 0.00 0.00 0.00 1.78
145 146 2.999331 ACAACGTTCCTTCCCCATATG 58.001 47.619 0.00 0.00 0.00 1.78
146 147 2.297701 CAACGTTCCTTCCCCATATGG 58.702 52.381 15.41 15.41 0.00 2.74
147 148 1.887797 ACGTTCCTTCCCCATATGGA 58.112 50.000 24.00 0.41 37.39 3.41
148 149 1.768870 ACGTTCCTTCCCCATATGGAG 59.231 52.381 24.00 10.59 35.37 3.86
149 150 1.768870 CGTTCCTTCCCCATATGGAGT 59.231 52.381 24.00 0.00 35.37 3.85
150 151 2.172717 CGTTCCTTCCCCATATGGAGTT 59.827 50.000 24.00 0.00 35.37 3.01
151 152 3.744530 CGTTCCTTCCCCATATGGAGTTC 60.745 52.174 24.00 4.70 35.37 3.01
152 153 2.047061 TCCTTCCCCATATGGAGTTCG 58.953 52.381 24.00 5.64 35.37 3.95
153 154 1.072331 CCTTCCCCATATGGAGTTCGG 59.928 57.143 24.00 14.89 35.37 4.30
154 155 1.072331 CTTCCCCATATGGAGTTCGGG 59.928 57.143 24.00 14.16 35.37 5.14
155 156 0.266453 TCCCCATATGGAGTTCGGGA 59.734 55.000 24.00 16.26 39.44 5.14
156 157 0.396811 CCCCATATGGAGTTCGGGAC 59.603 60.000 24.00 0.00 39.44 4.46
157 158 0.396811 CCCATATGGAGTTCGGGACC 59.603 60.000 24.00 0.00 39.44 4.46
158 159 0.396811 CCATATGGAGTTCGGGACCC 59.603 60.000 17.49 0.00 37.39 4.46
159 160 1.128200 CATATGGAGTTCGGGACCCA 58.872 55.000 12.15 0.00 34.47 4.51
160 161 1.488812 CATATGGAGTTCGGGACCCAA 59.511 52.381 12.15 1.06 33.93 4.12
161 162 1.200519 TATGGAGTTCGGGACCCAAG 58.799 55.000 12.15 0.00 33.93 3.61
162 163 1.562672 ATGGAGTTCGGGACCCAAGG 61.563 60.000 12.15 0.00 33.93 3.61
163 164 2.669240 GAGTTCGGGACCCAAGGG 59.331 66.667 12.15 2.91 42.03 3.95
164 165 3.623703 GAGTTCGGGACCCAAGGGC 62.624 68.421 12.15 0.00 39.32 5.19
165 166 3.961414 GTTCGGGACCCAAGGGCA 61.961 66.667 12.15 0.00 39.32 5.36
166 167 3.179339 TTCGGGACCCAAGGGCAA 61.179 61.111 12.15 0.00 39.32 4.52
167 168 2.543797 TTCGGGACCCAAGGGCAAT 61.544 57.895 12.15 0.00 39.32 3.56
168 169 2.440247 CGGGACCCAAGGGCAATC 60.440 66.667 12.15 0.00 39.32 2.67
169 170 2.440247 GGGACCCAAGGGCAATCG 60.440 66.667 5.33 0.00 39.32 3.34
170 171 2.355115 GGACCCAAGGGCAATCGT 59.645 61.111 4.70 0.00 39.32 3.73
171 172 1.304134 GGACCCAAGGGCAATCGTT 60.304 57.895 4.70 0.00 39.32 3.85
172 173 1.595093 GGACCCAAGGGCAATCGTTG 61.595 60.000 4.70 0.00 40.00 4.10
173 174 0.608035 GACCCAAGGGCAATCGTTGA 60.608 55.000 4.70 0.00 42.11 3.18
174 175 0.609131 ACCCAAGGGCAATCGTTGAG 60.609 55.000 4.70 0.00 42.11 3.02
175 176 0.609131 CCCAAGGGCAATCGTTGAGT 60.609 55.000 0.00 0.00 42.11 3.41
176 177 0.523072 CCAAGGGCAATCGTTGAGTG 59.477 55.000 2.51 0.00 42.11 3.51
177 178 1.522668 CAAGGGCAATCGTTGAGTGA 58.477 50.000 0.00 0.00 42.11 3.41
178 179 1.879380 CAAGGGCAATCGTTGAGTGAA 59.121 47.619 0.00 0.00 42.11 3.18
179 180 1.523758 AGGGCAATCGTTGAGTGAAC 58.476 50.000 0.00 0.00 28.30 3.18
180 181 1.072331 AGGGCAATCGTTGAGTGAACT 59.928 47.619 0.00 0.00 31.70 3.01
181 182 1.197721 GGGCAATCGTTGAGTGAACTG 59.802 52.381 0.00 0.00 31.70 3.16
182 183 1.873591 GGCAATCGTTGAGTGAACTGT 59.126 47.619 0.00 0.00 31.70 3.55
183 184 3.064207 GGCAATCGTTGAGTGAACTGTA 58.936 45.455 0.00 0.00 31.70 2.74
184 185 3.684788 GGCAATCGTTGAGTGAACTGTAT 59.315 43.478 0.00 0.00 31.70 2.29
185 186 4.201724 GGCAATCGTTGAGTGAACTGTATC 60.202 45.833 0.00 0.00 31.70 2.24
186 187 4.627467 GCAATCGTTGAGTGAACTGTATCT 59.373 41.667 0.00 0.00 31.70 1.98
187 188 5.120830 GCAATCGTTGAGTGAACTGTATCTT 59.879 40.000 0.00 0.00 31.70 2.40
188 189 6.310467 GCAATCGTTGAGTGAACTGTATCTTA 59.690 38.462 0.00 0.00 31.70 2.10
189 190 7.010552 GCAATCGTTGAGTGAACTGTATCTTAT 59.989 37.037 0.00 0.00 31.70 1.73
190 191 8.873830 CAATCGTTGAGTGAACTGTATCTTATT 58.126 33.333 0.00 0.00 31.70 1.40
191 192 8.635877 ATCGTTGAGTGAACTGTATCTTATTC 57.364 34.615 0.00 0.00 31.70 1.75
192 193 7.599171 TCGTTGAGTGAACTGTATCTTATTCA 58.401 34.615 0.00 0.00 31.70 2.57
193 194 8.251026 TCGTTGAGTGAACTGTATCTTATTCAT 58.749 33.333 0.00 0.00 33.85 2.57
194 195 9.516314 CGTTGAGTGAACTGTATCTTATTCATA 57.484 33.333 0.00 0.00 33.85 2.15
210 211 9.998106 TCTTATTCATATTAGTTGACCTAAGCC 57.002 33.333 0.00 0.00 38.99 4.35
211 212 8.827177 TTATTCATATTAGTTGACCTAAGCCG 57.173 34.615 0.00 0.00 38.99 5.52
212 213 4.628074 TCATATTAGTTGACCTAAGCCGC 58.372 43.478 0.00 0.00 38.99 6.53
213 214 4.100344 TCATATTAGTTGACCTAAGCCGCA 59.900 41.667 0.00 0.00 38.99 5.69
214 215 2.088950 TTAGTTGACCTAAGCCGCAC 57.911 50.000 0.00 0.00 31.89 5.34
215 216 0.248289 TAGTTGACCTAAGCCGCACC 59.752 55.000 0.00 0.00 0.00 5.01
216 217 1.302192 GTTGACCTAAGCCGCACCA 60.302 57.895 0.00 0.00 0.00 4.17
217 218 0.676782 GTTGACCTAAGCCGCACCAT 60.677 55.000 0.00 0.00 0.00 3.55
218 219 0.037590 TTGACCTAAGCCGCACCATT 59.962 50.000 0.00 0.00 0.00 3.16
219 220 0.906066 TGACCTAAGCCGCACCATTA 59.094 50.000 0.00 0.00 0.00 1.90
220 221 1.488812 TGACCTAAGCCGCACCATTAT 59.511 47.619 0.00 0.00 0.00 1.28
221 222 2.092646 TGACCTAAGCCGCACCATTATT 60.093 45.455 0.00 0.00 0.00 1.40
222 223 2.290641 GACCTAAGCCGCACCATTATTG 59.709 50.000 0.00 0.00 0.00 1.90
223 224 1.001378 CCTAAGCCGCACCATTATTGC 60.001 52.381 0.00 0.00 36.57 3.56
224 225 1.675483 CTAAGCCGCACCATTATTGCA 59.325 47.619 0.00 0.00 40.20 4.08
225 226 0.457035 AAGCCGCACCATTATTGCAG 59.543 50.000 0.00 0.00 40.20 4.41
226 227 1.066257 GCCGCACCATTATTGCAGG 59.934 57.895 0.00 0.00 40.20 4.85
227 228 1.735360 CCGCACCATTATTGCAGGG 59.265 57.895 0.00 0.00 40.20 4.45
228 229 1.735360 CGCACCATTATTGCAGGGG 59.265 57.895 0.00 0.00 40.20 4.79
229 230 1.037030 CGCACCATTATTGCAGGGGT 61.037 55.000 0.00 0.00 40.20 4.95
231 232 1.113788 CACCATTATTGCAGGGGTGG 58.886 55.000 13.36 10.96 44.06 4.61
232 233 0.032217 ACCATTATTGCAGGGGTGGG 60.032 55.000 12.83 3.74 0.00 4.61
233 234 0.760189 CCATTATTGCAGGGGTGGGG 60.760 60.000 0.00 0.00 0.00 4.96
234 235 1.075301 ATTATTGCAGGGGTGGGGC 60.075 57.895 0.00 0.00 0.00 5.80
235 236 1.593166 ATTATTGCAGGGGTGGGGCT 61.593 55.000 0.00 0.00 0.00 5.19
236 237 2.223464 TTATTGCAGGGGTGGGGCTC 62.223 60.000 0.00 0.00 0.00 4.70
254 255 3.752339 GGCCTCCGAACCGTACGT 61.752 66.667 15.21 0.00 0.00 3.57
255 256 2.505557 GCCTCCGAACCGTACGTG 60.506 66.667 15.21 8.32 0.00 4.49
256 257 2.180017 CCTCCGAACCGTACGTGG 59.820 66.667 15.21 10.32 0.00 4.94
257 258 2.180017 CTCCGAACCGTACGTGGG 59.820 66.667 15.21 7.54 0.00 4.61
258 259 2.282110 TCCGAACCGTACGTGGGA 60.282 61.111 15.21 9.92 0.00 4.37
259 260 2.126346 CCGAACCGTACGTGGGAC 60.126 66.667 15.21 6.85 0.00 4.46
261 262 2.953821 GAACCGTACGTGGGACGA 59.046 61.111 15.21 0.00 46.05 4.20
262 263 1.154150 GAACCGTACGTGGGACGAG 60.154 63.158 15.21 4.06 46.05 4.18
263 264 1.856265 GAACCGTACGTGGGACGAGT 61.856 60.000 15.21 4.63 46.05 4.18
264 265 1.455383 AACCGTACGTGGGACGAGTT 61.455 55.000 15.21 9.79 46.05 3.01
265 266 1.286880 CCGTACGTGGGACGAGTTT 59.713 57.895 15.21 0.00 46.05 2.66
266 267 0.730494 CCGTACGTGGGACGAGTTTC 60.730 60.000 15.21 0.00 46.05 2.78
267 268 0.239347 CGTACGTGGGACGAGTTTCT 59.761 55.000 7.22 0.00 46.05 2.52
268 269 1.694639 GTACGTGGGACGAGTTTCTG 58.305 55.000 0.00 0.00 46.05 3.02
269 270 0.038892 TACGTGGGACGAGTTTCTGC 60.039 55.000 0.00 0.00 46.05 4.26
270 271 2.027625 CGTGGGACGAGTTTCTGCC 61.028 63.158 0.00 0.00 46.05 4.85
271 272 1.371558 GTGGGACGAGTTTCTGCCT 59.628 57.895 0.00 0.00 0.00 4.75
272 273 0.670854 GTGGGACGAGTTTCTGCCTC 60.671 60.000 0.00 0.00 0.00 4.70
273 274 1.118965 TGGGACGAGTTTCTGCCTCA 61.119 55.000 0.00 0.00 0.00 3.86
331 332 2.007547 GCTAAACCGGGAGAGTTGCTC 61.008 57.143 6.32 0.00 43.17 4.26
339 340 0.033504 GGAGAGTTGCTCGTGTTGGA 59.966 55.000 0.00 0.00 44.91 3.53
572 573 3.629058 ACGCTCTAGTGTATGCATTACG 58.371 45.455 3.54 0.00 36.94 3.18
628 629 0.802222 AATGTCATGTCGCGACTCGG 60.802 55.000 36.27 25.25 39.05 4.63
685 686 1.134936 TGCTACAATCGCTTTAGCCGA 60.135 47.619 9.24 0.00 37.95 5.54
824 826 6.861065 TCTAATTGTTGAGTGTGAAGTTCC 57.139 37.500 0.00 0.00 0.00 3.62
1119 1121 1.975660 AAACTTTTCACCGCCTAGCA 58.024 45.000 0.00 0.00 0.00 3.49
1238 1240 6.575244 TTATGATGTTCCTGGGATTGTAGT 57.425 37.500 0.00 0.00 0.00 2.73
1248 1250 2.317040 GGGATTGTAGTCAGGGATCGA 58.683 52.381 0.00 0.00 0.00 3.59
1295 1297 1.682854 CCTTGGAGCAGCTTTCAAACA 59.317 47.619 0.00 0.00 0.00 2.83
1568 1572 1.419720 GGCCTTCCTCATACTCCCCC 61.420 65.000 0.00 0.00 0.00 5.40
1593 1597 6.485984 CCTTCATTCATAGAGTTGGAGGAATG 59.514 42.308 0.00 0.00 41.64 2.67
1759 1763 3.655486 TCGCCTTATTTCGTTTGACTCA 58.345 40.909 0.00 0.00 0.00 3.41
1946 1951 1.077005 TGTGCTTTTTCCCCTATGCCT 59.923 47.619 0.00 0.00 0.00 4.75
1973 1978 8.168725 CCTATTGGTACTAGTGGAGTAGGATTA 58.831 40.741 5.39 0.00 41.47 1.75
2050 2055 2.753452 CAATTGAAGCATCTGAGGCTGT 59.247 45.455 18.30 8.04 41.66 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.142838 TGAACATGATGAATCACTTCGTGC 60.143 41.667 0.00 0.00 40.83 5.34
1 2 5.535043 TGAACATGATGAATCACTTCGTG 57.465 39.130 0.00 4.92 42.01 4.35
2 3 6.017192 TGTTTGAACATGATGAATCACTTCGT 60.017 34.615 0.00 0.00 40.03 3.85
3 4 6.372981 TGTTTGAACATGATGAATCACTTCG 58.627 36.000 0.00 0.00 40.03 3.79
20 21 3.629855 TGAGCGAAAGGTTCATGTTTGAA 59.370 39.130 0.00 0.00 45.11 2.69
21 22 3.210227 TGAGCGAAAGGTTCATGTTTGA 58.790 40.909 0.00 0.00 45.11 2.69
22 23 3.624326 TGAGCGAAAGGTTCATGTTTG 57.376 42.857 0.00 0.00 45.11 2.93
23 24 4.549458 CAATGAGCGAAAGGTTCATGTTT 58.451 39.130 0.00 0.00 44.67 2.83
24 25 3.057315 CCAATGAGCGAAAGGTTCATGTT 60.057 43.478 0.00 0.00 44.67 2.71
25 26 2.489329 CCAATGAGCGAAAGGTTCATGT 59.511 45.455 0.00 0.00 44.67 3.21
26 27 2.159338 CCCAATGAGCGAAAGGTTCATG 60.159 50.000 0.00 0.00 44.67 3.07
28 29 1.533625 CCCAATGAGCGAAAGGTTCA 58.466 50.000 0.00 0.00 45.11 3.18
29 30 0.811281 CCCCAATGAGCGAAAGGTTC 59.189 55.000 0.00 0.00 45.11 3.62
30 31 0.404040 TCCCCAATGAGCGAAAGGTT 59.596 50.000 0.00 0.00 45.11 3.50
32 33 1.369091 CGTCCCCAATGAGCGAAAGG 61.369 60.000 0.00 0.00 0.00 3.11
33 34 1.369091 CCGTCCCCAATGAGCGAAAG 61.369 60.000 0.00 0.00 0.00 2.62
34 35 1.376683 CCGTCCCCAATGAGCGAAA 60.377 57.895 0.00 0.00 0.00 3.46
35 36 2.119484 AACCGTCCCCAATGAGCGAA 62.119 55.000 0.00 0.00 0.00 4.70
36 37 2.119484 AAACCGTCCCCAATGAGCGA 62.119 55.000 0.00 0.00 0.00 4.93
37 38 0.391927 TAAACCGTCCCCAATGAGCG 60.392 55.000 0.00 0.00 0.00 5.03
38 39 2.052782 ATAAACCGTCCCCAATGAGC 57.947 50.000 0.00 0.00 0.00 4.26
39 40 5.825679 TGATTTATAAACCGTCCCCAATGAG 59.174 40.000 0.00 0.00 0.00 2.90
40 41 5.756918 TGATTTATAAACCGTCCCCAATGA 58.243 37.500 0.00 0.00 0.00 2.57
41 42 6.264292 TGATGATTTATAAACCGTCCCCAATG 59.736 38.462 8.97 0.00 0.00 2.82
42 43 6.369629 TGATGATTTATAAACCGTCCCCAAT 58.630 36.000 8.97 0.00 0.00 3.16
43 44 5.756918 TGATGATTTATAAACCGTCCCCAA 58.243 37.500 8.97 0.00 0.00 4.12
44 45 5.375283 TGATGATTTATAAACCGTCCCCA 57.625 39.130 8.97 0.00 0.00 4.96
45 46 6.702716 TTTGATGATTTATAAACCGTCCCC 57.297 37.500 8.97 0.00 0.00 4.81
46 47 7.865889 GGAATTTGATGATTTATAAACCGTCCC 59.134 37.037 8.97 0.07 0.00 4.46
47 48 7.865889 GGGAATTTGATGATTTATAAACCGTCC 59.134 37.037 8.97 3.14 0.00 4.79
48 49 8.410141 TGGGAATTTGATGATTTATAAACCGTC 58.590 33.333 4.98 4.98 0.00 4.79
49 50 8.194769 GTGGGAATTTGATGATTTATAAACCGT 58.805 33.333 0.00 0.00 0.00 4.83
50 51 8.194104 TGTGGGAATTTGATGATTTATAAACCG 58.806 33.333 0.00 0.00 0.00 4.44
51 52 9.883142 TTGTGGGAATTTGATGATTTATAAACC 57.117 29.630 0.00 0.00 0.00 3.27
56 57 8.770322 TCCATTTGTGGGAATTTGATGATTTAT 58.230 29.630 0.00 0.00 0.00 1.40
57 58 8.143673 TCCATTTGTGGGAATTTGATGATTTA 57.856 30.769 0.00 0.00 0.00 1.40
58 59 7.018487 TCCATTTGTGGGAATTTGATGATTT 57.982 32.000 0.00 0.00 0.00 2.17
59 60 6.623979 TCCATTTGTGGGAATTTGATGATT 57.376 33.333 0.00 0.00 0.00 2.57
60 61 6.623979 TTCCATTTGTGGGAATTTGATGAT 57.376 33.333 0.00 0.00 39.44 2.45
70 71 4.081406 CACTTCTCATTCCATTTGTGGGA 58.919 43.478 0.00 0.00 0.00 4.37
71 72 3.194116 CCACTTCTCATTCCATTTGTGGG 59.806 47.826 0.00 0.00 39.75 4.61
72 73 3.194116 CCCACTTCTCATTCCATTTGTGG 59.806 47.826 0.00 0.00 42.16 4.17
73 74 3.828451 ACCCACTTCTCATTCCATTTGTG 59.172 43.478 0.00 0.00 0.00 3.33
74 75 4.082125 GACCCACTTCTCATTCCATTTGT 58.918 43.478 0.00 0.00 0.00 2.83
75 76 3.445096 GGACCCACTTCTCATTCCATTTG 59.555 47.826 0.00 0.00 0.00 2.32
76 77 3.075882 TGGACCCACTTCTCATTCCATTT 59.924 43.478 0.00 0.00 0.00 2.32
77 78 2.649312 TGGACCCACTTCTCATTCCATT 59.351 45.455 0.00 0.00 0.00 3.16
78 79 2.278245 TGGACCCACTTCTCATTCCAT 58.722 47.619 0.00 0.00 0.00 3.41
79 80 1.741028 TGGACCCACTTCTCATTCCA 58.259 50.000 0.00 0.00 0.00 3.53
80 81 2.025887 ACATGGACCCACTTCTCATTCC 60.026 50.000 0.00 0.00 0.00 3.01
81 82 3.356529 ACATGGACCCACTTCTCATTC 57.643 47.619 0.00 0.00 0.00 2.67
82 83 4.927267 TTACATGGACCCACTTCTCATT 57.073 40.909 0.00 0.00 0.00 2.57
83 84 4.927267 TTTACATGGACCCACTTCTCAT 57.073 40.909 0.00 0.00 0.00 2.90
84 85 4.288366 TCATTTACATGGACCCACTTCTCA 59.712 41.667 0.00 0.00 0.00 3.27
85 86 4.843728 TCATTTACATGGACCCACTTCTC 58.156 43.478 0.00 0.00 0.00 2.87
86 87 4.927267 TCATTTACATGGACCCACTTCT 57.073 40.909 0.00 0.00 0.00 2.85
87 88 4.273480 CGATCATTTACATGGACCCACTTC 59.727 45.833 0.00 0.00 0.00 3.01
88 89 4.080582 TCGATCATTTACATGGACCCACTT 60.081 41.667 0.00 0.00 0.00 3.16
89 90 3.454447 TCGATCATTTACATGGACCCACT 59.546 43.478 0.00 0.00 0.00 4.00
90 91 3.804036 TCGATCATTTACATGGACCCAC 58.196 45.455 0.00 0.00 0.00 4.61
91 92 3.709141 TCTCGATCATTTACATGGACCCA 59.291 43.478 0.00 0.00 0.00 4.51
92 93 4.058817 GTCTCGATCATTTACATGGACCC 58.941 47.826 0.00 0.00 0.00 4.46
93 94 4.058817 GGTCTCGATCATTTACATGGACC 58.941 47.826 0.00 0.00 32.71 4.46
94 95 4.950050 AGGTCTCGATCATTTACATGGAC 58.050 43.478 0.00 0.00 0.00 4.02
95 96 5.201713 GAGGTCTCGATCATTTACATGGA 57.798 43.478 0.00 0.00 0.00 3.41
110 111 1.332904 CGTTGTTGTTTGCGAGGTCTC 60.333 52.381 0.00 0.00 0.00 3.36
111 112 0.655733 CGTTGTTGTTTGCGAGGTCT 59.344 50.000 0.00 0.00 0.00 3.85
112 113 0.375803 ACGTTGTTGTTTGCGAGGTC 59.624 50.000 0.00 0.00 0.00 3.85
113 114 0.806241 AACGTTGTTGTTTGCGAGGT 59.194 45.000 0.00 0.00 0.00 3.85
114 115 1.462791 GAACGTTGTTGTTTGCGAGG 58.537 50.000 5.00 0.00 30.75 4.63
115 116 1.063469 AGGAACGTTGTTGTTTGCGAG 59.937 47.619 5.00 0.00 30.75 5.03
116 117 1.088306 AGGAACGTTGTTGTTTGCGA 58.912 45.000 5.00 0.00 30.75 5.10
117 118 1.843753 GAAGGAACGTTGTTGTTTGCG 59.156 47.619 5.00 0.00 30.75 4.85
118 119 2.190161 GGAAGGAACGTTGTTGTTTGC 58.810 47.619 5.00 0.00 30.75 3.68
119 120 2.480587 GGGGAAGGAACGTTGTTGTTTG 60.481 50.000 5.00 0.00 30.75 2.93
120 121 1.752498 GGGGAAGGAACGTTGTTGTTT 59.248 47.619 5.00 0.00 30.75 2.83
121 122 1.341187 TGGGGAAGGAACGTTGTTGTT 60.341 47.619 5.00 0.00 34.02 2.83
122 123 0.256464 TGGGGAAGGAACGTTGTTGT 59.744 50.000 5.00 0.00 0.00 3.32
123 124 1.616159 ATGGGGAAGGAACGTTGTTG 58.384 50.000 5.00 0.00 0.00 3.33
124 125 3.352648 CATATGGGGAAGGAACGTTGTT 58.647 45.455 5.00 0.00 0.00 2.83
125 126 2.356741 CCATATGGGGAAGGAACGTTGT 60.357 50.000 14.52 0.00 0.00 3.32
126 127 2.092646 TCCATATGGGGAAGGAACGTTG 60.093 50.000 21.78 0.00 37.22 4.10
127 128 2.172717 CTCCATATGGGGAAGGAACGTT 59.827 50.000 17.53 0.00 38.16 3.99
128 129 1.768870 CTCCATATGGGGAAGGAACGT 59.231 52.381 17.53 0.00 38.16 3.99
129 130 1.768870 ACTCCATATGGGGAAGGAACG 59.231 52.381 28.98 5.26 38.16 3.95
130 131 3.744530 CGAACTCCATATGGGGAAGGAAC 60.745 52.174 28.98 10.62 38.16 3.62
131 132 2.438021 CGAACTCCATATGGGGAAGGAA 59.562 50.000 28.98 2.56 38.16 3.36
132 133 2.047061 CGAACTCCATATGGGGAAGGA 58.953 52.381 28.98 3.35 38.16 3.36
133 134 1.072331 CCGAACTCCATATGGGGAAGG 59.928 57.143 28.98 21.46 38.16 3.46
134 135 1.072331 CCCGAACTCCATATGGGGAAG 59.928 57.143 28.98 17.14 38.16 3.46
135 136 1.136828 CCCGAACTCCATATGGGGAA 58.863 55.000 28.98 4.95 38.16 3.97
136 137 0.266453 TCCCGAACTCCATATGGGGA 59.734 55.000 28.98 18.56 40.81 4.81
137 138 0.396811 GTCCCGAACTCCATATGGGG 59.603 60.000 20.77 20.77 42.91 4.96
138 139 0.396811 GGTCCCGAACTCCATATGGG 59.603 60.000 21.78 14.30 41.43 4.00
139 140 0.396811 GGGTCCCGAACTCCATATGG 59.603 60.000 16.25 16.25 0.00 2.74
140 141 1.128200 TGGGTCCCGAACTCCATATG 58.872 55.000 2.65 0.00 0.00 1.78
141 142 1.768870 CTTGGGTCCCGAACTCCATAT 59.231 52.381 2.65 0.00 31.03 1.78
142 143 1.200519 CTTGGGTCCCGAACTCCATA 58.799 55.000 2.65 0.00 31.03 2.74
143 144 1.562672 CCTTGGGTCCCGAACTCCAT 61.563 60.000 2.65 0.00 31.03 3.41
144 145 2.221299 CCTTGGGTCCCGAACTCCA 61.221 63.158 2.65 0.00 0.00 3.86
145 146 2.669240 CCTTGGGTCCCGAACTCC 59.331 66.667 2.65 0.00 0.00 3.85
146 147 2.669240 CCCTTGGGTCCCGAACTC 59.331 66.667 2.65 0.00 0.00 3.01
147 148 3.647771 GCCCTTGGGTCCCGAACT 61.648 66.667 2.65 0.00 0.00 3.01
148 149 2.781431 ATTGCCCTTGGGTCCCGAAC 62.781 60.000 2.65 0.00 0.00 3.95
149 150 2.493273 GATTGCCCTTGGGTCCCGAA 62.493 60.000 2.65 0.00 0.00 4.30
150 151 2.938798 ATTGCCCTTGGGTCCCGA 60.939 61.111 2.65 0.00 0.00 5.14
151 152 2.440247 GATTGCCCTTGGGTCCCG 60.440 66.667 2.65 0.00 0.00 5.14
152 153 2.440247 CGATTGCCCTTGGGTCCC 60.440 66.667 0.00 0.00 0.00 4.46
153 154 1.304134 AACGATTGCCCTTGGGTCC 60.304 57.895 7.61 0.00 0.00 4.46
154 155 0.608035 TCAACGATTGCCCTTGGGTC 60.608 55.000 7.61 0.69 0.00 4.46
155 156 0.609131 CTCAACGATTGCCCTTGGGT 60.609 55.000 7.61 0.00 0.00 4.51
156 157 0.609131 ACTCAACGATTGCCCTTGGG 60.609 55.000 0.32 0.32 0.00 4.12
157 158 0.523072 CACTCAACGATTGCCCTTGG 59.477 55.000 0.00 0.00 0.00 3.61
158 159 1.522668 TCACTCAACGATTGCCCTTG 58.477 50.000 0.00 0.00 0.00 3.61
159 160 1.880027 GTTCACTCAACGATTGCCCTT 59.120 47.619 0.00 0.00 0.00 3.95
160 161 1.072331 AGTTCACTCAACGATTGCCCT 59.928 47.619 0.00 0.00 40.32 5.19
161 162 1.197721 CAGTTCACTCAACGATTGCCC 59.802 52.381 0.00 0.00 40.32 5.36
162 163 1.873591 ACAGTTCACTCAACGATTGCC 59.126 47.619 0.00 0.00 40.32 4.52
163 164 4.627467 AGATACAGTTCACTCAACGATTGC 59.373 41.667 0.00 0.00 40.32 3.56
164 165 6.712241 AAGATACAGTTCACTCAACGATTG 57.288 37.500 0.00 0.00 40.32 2.67
165 166 9.088512 GAATAAGATACAGTTCACTCAACGATT 57.911 33.333 0.00 0.00 40.32 3.34
166 167 8.251026 TGAATAAGATACAGTTCACTCAACGAT 58.749 33.333 0.00 0.00 40.32 3.73
167 168 7.599171 TGAATAAGATACAGTTCACTCAACGA 58.401 34.615 0.00 0.00 40.32 3.85
168 169 7.812309 TGAATAAGATACAGTTCACTCAACG 57.188 36.000 0.00 0.00 40.32 4.10
184 185 9.998106 GGCTTAGGTCAACTAATATGAATAAGA 57.002 33.333 11.16 0.00 40.71 2.10
185 186 8.926710 CGGCTTAGGTCAACTAATATGAATAAG 58.073 37.037 0.00 0.00 40.71 1.73
186 187 7.386848 GCGGCTTAGGTCAACTAATATGAATAA 59.613 37.037 0.00 0.00 40.71 1.40
187 188 6.872020 GCGGCTTAGGTCAACTAATATGAATA 59.128 38.462 0.00 0.00 40.71 1.75
188 189 5.701290 GCGGCTTAGGTCAACTAATATGAAT 59.299 40.000 0.00 0.00 40.71 2.57
189 190 5.054477 GCGGCTTAGGTCAACTAATATGAA 58.946 41.667 0.00 0.00 40.71 2.57
190 191 4.100344 TGCGGCTTAGGTCAACTAATATGA 59.900 41.667 0.00 0.00 40.71 2.15
191 192 4.211374 GTGCGGCTTAGGTCAACTAATATG 59.789 45.833 0.00 0.00 40.71 1.78
192 193 4.377897 GTGCGGCTTAGGTCAACTAATAT 58.622 43.478 0.00 0.00 40.71 1.28
193 194 3.431207 GGTGCGGCTTAGGTCAACTAATA 60.431 47.826 0.00 0.00 40.71 0.98
194 195 2.629051 GTGCGGCTTAGGTCAACTAAT 58.371 47.619 0.00 0.00 40.71 1.73
195 196 1.338389 GGTGCGGCTTAGGTCAACTAA 60.338 52.381 0.00 0.00 39.31 2.24
196 197 0.248289 GGTGCGGCTTAGGTCAACTA 59.752 55.000 0.00 0.00 0.00 2.24
197 198 1.003718 GGTGCGGCTTAGGTCAACT 60.004 57.895 0.00 0.00 0.00 3.16
198 199 0.676782 ATGGTGCGGCTTAGGTCAAC 60.677 55.000 0.00 0.00 0.00 3.18
199 200 0.037590 AATGGTGCGGCTTAGGTCAA 59.962 50.000 0.00 0.00 0.00 3.18
200 201 0.906066 TAATGGTGCGGCTTAGGTCA 59.094 50.000 0.00 0.00 0.00 4.02
201 202 2.256117 ATAATGGTGCGGCTTAGGTC 57.744 50.000 0.00 0.00 0.00 3.85
202 203 2.297701 CAATAATGGTGCGGCTTAGGT 58.702 47.619 0.00 0.00 0.00 3.08
203 204 1.001378 GCAATAATGGTGCGGCTTAGG 60.001 52.381 0.00 0.00 31.20 2.69
204 205 1.675483 TGCAATAATGGTGCGGCTTAG 59.325 47.619 0.00 0.00 45.27 2.18
205 206 1.675483 CTGCAATAATGGTGCGGCTTA 59.325 47.619 0.00 0.00 45.27 3.09
206 207 0.457035 CTGCAATAATGGTGCGGCTT 59.543 50.000 0.00 0.00 45.27 4.35
207 208 1.386525 CCTGCAATAATGGTGCGGCT 61.387 55.000 0.00 0.00 45.33 5.52
208 209 1.066257 CCTGCAATAATGGTGCGGC 59.934 57.895 0.00 0.00 45.33 6.53
209 210 1.735360 CCCTGCAATAATGGTGCGG 59.265 57.895 0.00 0.00 45.27 5.69
210 211 1.037030 ACCCCTGCAATAATGGTGCG 61.037 55.000 0.00 0.00 45.27 5.34
211 212 0.461135 CACCCCTGCAATAATGGTGC 59.539 55.000 6.78 0.00 39.95 5.01
212 213 1.113788 CCACCCCTGCAATAATGGTG 58.886 55.000 10.98 10.98 44.79 4.17
213 214 0.032217 CCCACCCCTGCAATAATGGT 60.032 55.000 6.11 0.00 0.00 3.55
214 215 0.760189 CCCCACCCCTGCAATAATGG 60.760 60.000 0.00 0.00 0.00 3.16
215 216 1.402107 GCCCCACCCCTGCAATAATG 61.402 60.000 0.00 0.00 0.00 1.90
216 217 1.075301 GCCCCACCCCTGCAATAAT 60.075 57.895 0.00 0.00 0.00 1.28
217 218 2.223464 GAGCCCCACCCCTGCAATAA 62.223 60.000 0.00 0.00 0.00 1.40
218 219 2.616893 AGCCCCACCCCTGCAATA 60.617 61.111 0.00 0.00 0.00 1.90
219 220 4.066139 GAGCCCCACCCCTGCAAT 62.066 66.667 0.00 0.00 0.00 3.56
237 238 3.752339 ACGTACGGTTCGGAGGCC 61.752 66.667 21.06 0.00 0.00 5.19
238 239 2.505557 CACGTACGGTTCGGAGGC 60.506 66.667 21.06 0.00 0.00 4.70
239 240 2.180017 CCACGTACGGTTCGGAGG 59.820 66.667 21.06 8.90 0.00 4.30
240 241 2.180017 CCCACGTACGGTTCGGAG 59.820 66.667 21.06 3.91 0.00 4.63
241 242 2.282110 TCCCACGTACGGTTCGGA 60.282 61.111 21.06 14.57 0.00 4.55
242 243 2.126346 GTCCCACGTACGGTTCGG 60.126 66.667 21.06 13.53 0.00 4.30
243 244 2.502510 CGTCCCACGTACGGTTCG 60.503 66.667 21.06 12.33 36.74 3.95
244 245 1.154150 CTCGTCCCACGTACGGTTC 60.154 63.158 21.06 4.37 43.14 3.62
245 246 1.455383 AACTCGTCCCACGTACGGTT 61.455 55.000 21.06 8.26 43.14 4.44
246 247 1.455383 AAACTCGTCCCACGTACGGT 61.455 55.000 21.06 1.70 43.14 4.83
247 248 0.730494 GAAACTCGTCCCACGTACGG 60.730 60.000 21.06 8.46 43.14 4.02
248 249 0.239347 AGAAACTCGTCCCACGTACG 59.761 55.000 15.01 15.01 43.14 3.67
249 250 1.694639 CAGAAACTCGTCCCACGTAC 58.305 55.000 0.00 0.00 43.14 3.67
250 251 0.038892 GCAGAAACTCGTCCCACGTA 60.039 55.000 0.00 0.00 43.14 3.57
251 252 1.300697 GCAGAAACTCGTCCCACGT 60.301 57.895 0.00 0.00 43.14 4.49
252 253 2.027625 GGCAGAAACTCGTCCCACG 61.028 63.158 0.00 0.00 44.19 4.94
253 254 0.670854 GAGGCAGAAACTCGTCCCAC 60.671 60.000 0.00 0.00 0.00 4.61
254 255 1.118965 TGAGGCAGAAACTCGTCCCA 61.119 55.000 0.00 0.00 37.79 4.37
255 256 0.250513 ATGAGGCAGAAACTCGTCCC 59.749 55.000 0.00 0.00 37.79 4.46
256 257 2.482142 CCTATGAGGCAGAAACTCGTCC 60.482 54.545 0.00 0.00 37.79 4.79
257 258 2.482142 CCCTATGAGGCAGAAACTCGTC 60.482 54.545 0.00 0.00 37.79 4.20
258 259 1.482593 CCCTATGAGGCAGAAACTCGT 59.517 52.381 0.00 0.00 37.79 4.18
259 260 2.231215 CCCTATGAGGCAGAAACTCG 57.769 55.000 0.00 0.00 37.79 4.18
269 270 3.242867 TCATTCCACTAGCCCTATGAGG 58.757 50.000 0.00 0.00 34.30 3.86
270 271 3.260380 CCTCATTCCACTAGCCCTATGAG 59.740 52.174 14.12 14.12 38.96 2.90
271 272 3.242867 CCTCATTCCACTAGCCCTATGA 58.757 50.000 0.00 0.00 0.00 2.15
272 273 2.289945 GCCTCATTCCACTAGCCCTATG 60.290 54.545 0.00 0.00 0.00 2.23
273 274 1.981495 GCCTCATTCCACTAGCCCTAT 59.019 52.381 0.00 0.00 0.00 2.57
331 332 2.719046 GCGAAACTTTGAATCCAACACG 59.281 45.455 0.00 0.00 30.88 4.49
339 340 4.455877 CCTTGGTAGAGCGAAACTTTGAAT 59.544 41.667 0.00 0.00 0.00 2.57
476 477 9.023962 TCTCTTATAACCAAACATTGCAAAGAT 57.976 29.630 8.96 0.00 0.00 2.40
572 573 4.418392 CATGACAAAATGCTAGTTGCCTC 58.582 43.478 0.00 0.00 42.00 4.70
628 629 6.683974 TTGATTTAGCTCCTTCTAACATGC 57.316 37.500 0.00 0.00 0.00 4.06
685 686 3.492102 TCACACCTTTCTGCTAAGCTT 57.508 42.857 3.48 3.48 0.00 3.74
824 826 7.741216 TCCAACGAAACGAATATTTTTAGAACG 59.259 33.333 0.00 0.00 0.00 3.95
1093 1095 7.094118 TGCTAGGCGGTGAAAAGTTTTATAAAT 60.094 33.333 0.00 0.00 0.00 1.40
1119 1121 2.054687 TTACATCGCGTTCAGTTCGT 57.945 45.000 5.77 0.00 0.00 3.85
1238 1240 1.697432 AGGTTTGTTGTCGATCCCTGA 59.303 47.619 0.00 0.00 0.00 3.86
1248 1250 5.048991 CCAACGAATAGCTAAGGTTTGTTGT 60.049 40.000 24.25 2.76 41.98 3.32
1295 1297 6.651975 AGCTTATCCTGTAGCTTATACGTT 57.348 37.500 0.00 0.00 45.03 3.99
1568 1572 5.620738 TCCTCCAACTCTATGAATGAAGG 57.379 43.478 0.00 0.00 0.00 3.46
1759 1763 5.946942 TGAAGTAGATTTCTCAGCTCCAT 57.053 39.130 0.00 0.00 0.00 3.41
1946 1951 5.673574 TCCTACTCCACTAGTACCAATAGGA 59.326 44.000 13.91 13.91 39.80 2.94
1973 1978 6.015010 CAGCTATAGGTTCTGTATTACAGGCT 60.015 42.308 20.83 15.81 45.94 4.58
1996 2001 2.163818 TGAGCGAAAGGTTACACCAG 57.836 50.000 0.00 0.00 45.11 4.00
2050 2055 5.959618 ATGTCGTGTATCCTCGATTGATA 57.040 39.130 1.73 1.73 38.65 2.15


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

AutoCloner maintained by Alex Coulton.