Multiple sequence alignment - TraesCS2D01G099400

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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 TraesCS2D01G099400 chr2D 100.000 3863 0 0 1 3863 51194123 51190261 0.000000e+00 7134.0
1 TraesCS2D01G099400 chr2A 91.010 3682 193 63 186 3796 52666884 52663270 0.000000e+00 4839.0
2 TraesCS2D01G099400 chr2A 94.545 55 3 0 3809 3863 52663229 52663175 6.880000e-13 86.1
3 TraesCS2D01G099400 chr2B 91.160 3303 157 54 191 3447 80123372 80120159 0.000000e+00 4357.0
4 TraesCS2D01G099400 chr2B 86.667 225 19 9 3573 3796 80120042 80119828 4.990000e-59 239.0
5 TraesCS2D01G099400 chr2B 88.298 188 17 4 1 184 80168657 80168471 1.810000e-53 220.0
6 TraesCS2D01G099400 chr4B 83.575 828 112 22 1177 1998 384292788 384291979 0.000000e+00 754.0
7 TraesCS2D01G099400 chr4A 83.495 824 118 17 1178 1998 168792300 168793108 0.000000e+00 752.0
8 TraesCS2D01G099400 chr4D 83.051 826 120 16 1177 1998 308371491 308370682 0.000000e+00 732.0


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 TraesCS2D01G099400 chr2D 51190261 51194123 3862 True 7134.00 7134 100.0000 1 3863 1 chr2D.!!$R1 3862
1 TraesCS2D01G099400 chr2A 52663175 52666884 3709 True 2462.55 4839 92.7775 186 3863 2 chr2A.!!$R1 3677
2 TraesCS2D01G099400 chr2B 80119828 80123372 3544 True 2298.00 4357 88.9135 191 3796 2 chr2B.!!$R2 3605
3 TraesCS2D01G099400 chr4B 384291979 384292788 809 True 754.00 754 83.5750 1177 1998 1 chr4B.!!$R1 821
4 TraesCS2D01G099400 chr4A 168792300 168793108 808 False 752.00 752 83.4950 1178 1998 1 chr4A.!!$F1 820
5 TraesCS2D01G099400 chr4D 308370682 308371491 809 True 732.00 732 83.0510 1177 1998 1 chr4D.!!$R1 821

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
48 49 0.034186 TTTATCTGCTGCCCACCCTG 60.034 55.0 0.00 0.00 0.00 4.45 F
64 65 0.106519 CCTGAGGGGTTAAGGGCATG 60.107 60.0 0.00 0.00 0.00 4.06 F
65 66 0.106519 CTGAGGGGTTAAGGGCATGG 60.107 60.0 0.00 0.00 0.00 3.66 F
783 841 0.179100 AACTCTGATCCATGTCCGCG 60.179 55.0 0.00 0.00 0.00 6.46 F
870 929 0.310854 CCGTGCTCACTTTTGTTCCC 59.689 55.0 0.00 0.00 0.00 3.97 F
2682 2781 0.451628 CGAACAACGTGATGCAGCAG 60.452 55.0 4.06 1.97 37.22 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1008 1071 2.040464 ATCATCGCCACCCCTCCT 60.040 61.111 0.00 0.00 0.00 3.69 R
2223 2304 1.008079 GAAGTCGACGTCGGTGGTT 60.008 57.895 35.05 22.63 40.29 3.67 R
2224 2305 2.188829 TGAAGTCGACGTCGGTGGT 61.189 57.895 35.05 19.23 40.29 4.16 R
2539 2632 1.048160 TACATGCTCATCAGCCCGGA 61.048 55.000 0.73 0.00 46.26 5.14 R
2775 2874 2.932234 CGCTGACAGGTCGAACCCT 61.932 63.158 4.26 0.00 39.75 4.34 R
3541 3670 0.248539 GCCTGTACGACGTCAGATCC 60.249 60.000 17.16 10.56 34.02 3.36 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
19 20 1.770294 TCTGTTTTGGGTGTTGGGTC 58.230 50.000 0.00 0.00 0.00 4.46
20 21 1.006043 TCTGTTTTGGGTGTTGGGTCA 59.994 47.619 0.00 0.00 0.00 4.02
21 22 2.038659 CTGTTTTGGGTGTTGGGTCAT 58.961 47.619 0.00 0.00 0.00 3.06
22 23 1.759445 TGTTTTGGGTGTTGGGTCATG 59.241 47.619 0.00 0.00 0.00 3.07
23 24 2.035632 GTTTTGGGTGTTGGGTCATGA 58.964 47.619 0.00 0.00 0.00 3.07
24 25 1.993956 TTTGGGTGTTGGGTCATGAG 58.006 50.000 0.00 0.00 0.00 2.90
25 26 0.850100 TTGGGTGTTGGGTCATGAGT 59.150 50.000 0.00 0.00 0.00 3.41
26 27 0.850100 TGGGTGTTGGGTCATGAGTT 59.150 50.000 0.00 0.00 0.00 3.01
27 28 1.216678 TGGGTGTTGGGTCATGAGTTT 59.783 47.619 0.00 0.00 0.00 2.66
28 29 2.443632 TGGGTGTTGGGTCATGAGTTTA 59.556 45.455 0.00 0.00 0.00 2.01
29 30 3.075283 TGGGTGTTGGGTCATGAGTTTAT 59.925 43.478 0.00 0.00 0.00 1.40
30 31 4.086457 GGGTGTTGGGTCATGAGTTTATT 58.914 43.478 0.00 0.00 0.00 1.40
31 32 4.526650 GGGTGTTGGGTCATGAGTTTATTT 59.473 41.667 0.00 0.00 0.00 1.40
32 33 5.712917 GGGTGTTGGGTCATGAGTTTATTTA 59.287 40.000 0.00 0.00 0.00 1.40
33 34 6.379988 GGGTGTTGGGTCATGAGTTTATTTAT 59.620 38.462 0.00 0.00 0.00 1.40
34 35 7.416326 GGGTGTTGGGTCATGAGTTTATTTATC 60.416 40.741 0.00 0.00 0.00 1.75
35 36 7.339466 GGTGTTGGGTCATGAGTTTATTTATCT 59.661 37.037 0.00 0.00 0.00 1.98
36 37 8.184192 GTGTTGGGTCATGAGTTTATTTATCTG 58.816 37.037 0.00 0.00 0.00 2.90
37 38 6.942532 TGGGTCATGAGTTTATTTATCTGC 57.057 37.500 0.00 0.00 0.00 4.26
38 39 6.662755 TGGGTCATGAGTTTATTTATCTGCT 58.337 36.000 0.00 0.00 0.00 4.24
39 40 6.543465 TGGGTCATGAGTTTATTTATCTGCTG 59.457 38.462 0.00 0.00 0.00 4.41
40 41 6.433766 GGTCATGAGTTTATTTATCTGCTGC 58.566 40.000 0.00 0.00 0.00 5.25
41 42 6.433766 GTCATGAGTTTATTTATCTGCTGCC 58.566 40.000 0.00 0.00 0.00 4.85
42 43 5.532406 TCATGAGTTTATTTATCTGCTGCCC 59.468 40.000 0.00 0.00 0.00 5.36
43 44 4.854173 TGAGTTTATTTATCTGCTGCCCA 58.146 39.130 0.00 0.00 0.00 5.36
44 45 4.640201 TGAGTTTATTTATCTGCTGCCCAC 59.360 41.667 0.00 0.00 0.00 4.61
45 46 3.954258 AGTTTATTTATCTGCTGCCCACC 59.046 43.478 0.00 0.00 0.00 4.61
46 47 2.656947 TATTTATCTGCTGCCCACCC 57.343 50.000 0.00 0.00 0.00 4.61
47 48 0.929244 ATTTATCTGCTGCCCACCCT 59.071 50.000 0.00 0.00 0.00 4.34
48 49 0.034186 TTTATCTGCTGCCCACCCTG 60.034 55.000 0.00 0.00 0.00 4.45
49 50 0.913934 TTATCTGCTGCCCACCCTGA 60.914 55.000 0.00 0.00 0.00 3.86
50 51 1.340399 TATCTGCTGCCCACCCTGAG 61.340 60.000 0.00 0.00 0.00 3.35
51 52 4.421515 CTGCTGCCCACCCTGAGG 62.422 72.222 0.00 0.00 40.04 3.86
62 63 3.835134 CCTGAGGGGTTAAGGGCA 58.165 61.111 0.00 0.00 0.00 5.36
63 64 2.321720 CCTGAGGGGTTAAGGGCAT 58.678 57.895 0.00 0.00 0.00 4.40
64 65 0.106519 CCTGAGGGGTTAAGGGCATG 60.107 60.000 0.00 0.00 0.00 4.06
65 66 0.106519 CTGAGGGGTTAAGGGCATGG 60.107 60.000 0.00 0.00 0.00 3.66
66 67 0.849094 TGAGGGGTTAAGGGCATGGT 60.849 55.000 0.00 0.00 0.00 3.55
67 68 0.395724 GAGGGGTTAAGGGCATGGTG 60.396 60.000 0.00 0.00 0.00 4.17
68 69 0.849094 AGGGGTTAAGGGCATGGTGA 60.849 55.000 0.00 0.00 0.00 4.02
69 70 0.395724 GGGGTTAAGGGCATGGTGAG 60.396 60.000 0.00 0.00 0.00 3.51
70 71 0.331616 GGGTTAAGGGCATGGTGAGT 59.668 55.000 0.00 0.00 0.00 3.41
71 72 1.562475 GGGTTAAGGGCATGGTGAGTA 59.438 52.381 0.00 0.00 0.00 2.59
72 73 2.174854 GGGTTAAGGGCATGGTGAGTAT 59.825 50.000 0.00 0.00 0.00 2.12
73 74 3.372675 GGGTTAAGGGCATGGTGAGTATT 60.373 47.826 0.00 0.00 0.00 1.89
74 75 4.278310 GGTTAAGGGCATGGTGAGTATTT 58.722 43.478 0.00 0.00 0.00 1.40
75 76 4.709886 GGTTAAGGGCATGGTGAGTATTTT 59.290 41.667 0.00 0.00 0.00 1.82
76 77 5.394115 GGTTAAGGGCATGGTGAGTATTTTG 60.394 44.000 0.00 0.00 0.00 2.44
77 78 2.738743 AGGGCATGGTGAGTATTTTGG 58.261 47.619 0.00 0.00 0.00 3.28
78 79 1.756538 GGGCATGGTGAGTATTTTGGG 59.243 52.381 0.00 0.00 0.00 4.12
79 80 1.756538 GGCATGGTGAGTATTTTGGGG 59.243 52.381 0.00 0.00 0.00 4.96
80 81 1.756538 GCATGGTGAGTATTTTGGGGG 59.243 52.381 0.00 0.00 0.00 5.40
81 82 2.888069 GCATGGTGAGTATTTTGGGGGT 60.888 50.000 0.00 0.00 0.00 4.95
82 83 3.440127 CATGGTGAGTATTTTGGGGGTT 58.560 45.455 0.00 0.00 0.00 4.11
83 84 3.621682 TGGTGAGTATTTTGGGGGTTT 57.378 42.857 0.00 0.00 0.00 3.27
84 85 3.930035 TGGTGAGTATTTTGGGGGTTTT 58.070 40.909 0.00 0.00 0.00 2.43
85 86 5.076057 TGGTGAGTATTTTGGGGGTTTTA 57.924 39.130 0.00 0.00 0.00 1.52
86 87 5.464984 TGGTGAGTATTTTGGGGGTTTTAA 58.535 37.500 0.00 0.00 0.00 1.52
87 88 5.903589 TGGTGAGTATTTTGGGGGTTTTAAA 59.096 36.000 0.00 0.00 0.00 1.52
88 89 6.386050 TGGTGAGTATTTTGGGGGTTTTAAAA 59.614 34.615 0.00 0.00 0.00 1.52
89 90 7.092578 TGGTGAGTATTTTGGGGGTTTTAAAAA 60.093 33.333 1.31 0.00 0.00 1.94
90 91 7.442969 GGTGAGTATTTTGGGGGTTTTAAAAAG 59.557 37.037 1.31 0.00 0.00 2.27
91 92 8.205512 GTGAGTATTTTGGGGGTTTTAAAAAGA 58.794 33.333 1.31 0.00 0.00 2.52
92 93 8.939932 TGAGTATTTTGGGGGTTTTAAAAAGAT 58.060 29.630 1.31 0.00 0.00 2.40
93 94 9.787435 GAGTATTTTGGGGGTTTTAAAAAGATT 57.213 29.630 1.31 0.00 0.00 2.40
96 97 7.555306 TTTTGGGGGTTTTAAAAAGATTTCG 57.445 32.000 1.31 0.00 0.00 3.46
97 98 5.873146 TGGGGGTTTTAAAAAGATTTCGT 57.127 34.783 1.31 0.00 0.00 3.85
98 99 6.236558 TGGGGGTTTTAAAAAGATTTCGTT 57.763 33.333 1.31 0.00 0.00 3.85
99 100 7.357429 TGGGGGTTTTAAAAAGATTTCGTTA 57.643 32.000 1.31 0.00 0.00 3.18
100 101 7.964624 TGGGGGTTTTAAAAAGATTTCGTTAT 58.035 30.769 1.31 0.00 0.00 1.89
101 102 9.086758 TGGGGGTTTTAAAAAGATTTCGTTATA 57.913 29.630 1.31 0.00 0.00 0.98
102 103 9.577110 GGGGGTTTTAAAAAGATTTCGTTATAG 57.423 33.333 1.31 0.00 0.00 1.31
103 104 9.577110 GGGGTTTTAAAAAGATTTCGTTATAGG 57.423 33.333 1.31 0.00 0.00 2.57
104 105 9.577110 GGGTTTTAAAAAGATTTCGTTATAGGG 57.423 33.333 1.31 0.00 0.00 3.53
105 106 9.577110 GGTTTTAAAAAGATTTCGTTATAGGGG 57.423 33.333 1.31 0.00 0.00 4.79
106 107 9.577110 GTTTTAAAAAGATTTCGTTATAGGGGG 57.423 33.333 1.31 0.00 0.00 5.40
107 108 8.882557 TTTAAAAAGATTTCGTTATAGGGGGT 57.117 30.769 0.00 0.00 0.00 4.95
108 109 9.972106 TTTAAAAAGATTTCGTTATAGGGGGTA 57.028 29.630 0.00 0.00 0.00 3.69
109 110 9.617523 TTAAAAAGATTTCGTTATAGGGGGTAG 57.382 33.333 0.00 0.00 0.00 3.18
110 111 5.820404 AAGATTTCGTTATAGGGGGTAGG 57.180 43.478 0.00 0.00 0.00 3.18
111 112 5.083953 AGATTTCGTTATAGGGGGTAGGA 57.916 43.478 0.00 0.00 0.00 2.94
112 113 4.837298 AGATTTCGTTATAGGGGGTAGGAC 59.163 45.833 0.00 0.00 0.00 3.85
113 114 2.683211 TCGTTATAGGGGGTAGGACC 57.317 55.000 0.00 0.00 37.60 4.46
125 126 2.934887 GGTAGGACCCTAGAGAGTGAC 58.065 57.143 0.00 0.00 30.04 3.67
126 127 2.241685 GGTAGGACCCTAGAGAGTGACA 59.758 54.545 0.00 0.00 30.04 3.58
127 128 3.308976 GGTAGGACCCTAGAGAGTGACAA 60.309 52.174 0.00 0.00 30.04 3.18
128 129 3.767309 AGGACCCTAGAGAGTGACAAT 57.233 47.619 0.00 0.00 0.00 2.71
129 130 4.067944 AGGACCCTAGAGAGTGACAATT 57.932 45.455 0.00 0.00 0.00 2.32
130 131 4.027437 AGGACCCTAGAGAGTGACAATTC 58.973 47.826 0.00 0.00 0.00 2.17
131 132 3.133183 GGACCCTAGAGAGTGACAATTCC 59.867 52.174 0.00 0.00 0.00 3.01
132 133 3.769844 GACCCTAGAGAGTGACAATTCCA 59.230 47.826 0.00 0.00 0.00 3.53
133 134 4.366267 ACCCTAGAGAGTGACAATTCCAT 58.634 43.478 0.00 0.00 0.00 3.41
134 135 4.163078 ACCCTAGAGAGTGACAATTCCATG 59.837 45.833 0.00 0.00 0.00 3.66
135 136 4.444022 CCCTAGAGAGTGACAATTCCATGG 60.444 50.000 4.97 4.97 0.00 3.66
136 137 4.163078 CCTAGAGAGTGACAATTCCATGGT 59.837 45.833 12.58 0.00 0.00 3.55
137 138 5.363868 CCTAGAGAGTGACAATTCCATGGTA 59.636 44.000 12.58 1.50 0.00 3.25
138 139 5.762179 AGAGAGTGACAATTCCATGGTAA 57.238 39.130 12.58 5.35 0.00 2.85
139 140 6.126863 AGAGAGTGACAATTCCATGGTAAA 57.873 37.500 12.58 0.00 0.00 2.01
140 141 6.725364 AGAGAGTGACAATTCCATGGTAAAT 58.275 36.000 12.58 1.81 0.00 1.40
141 142 6.600822 AGAGAGTGACAATTCCATGGTAAATG 59.399 38.462 12.58 10.46 0.00 2.32
142 143 6.484288 AGAGTGACAATTCCATGGTAAATGA 58.516 36.000 12.58 0.00 0.00 2.57
143 144 6.947733 AGAGTGACAATTCCATGGTAAATGAA 59.052 34.615 12.58 0.00 0.00 2.57
144 145 7.451255 AGAGTGACAATTCCATGGTAAATGAAA 59.549 33.333 12.58 0.00 0.00 2.69
145 146 8.137745 AGTGACAATTCCATGGTAAATGAAAT 57.862 30.769 12.58 0.00 0.00 2.17
146 147 8.596293 AGTGACAATTCCATGGTAAATGAAATT 58.404 29.630 12.58 5.58 38.98 1.82
147 148 9.868277 GTGACAATTCCATGGTAAATGAAATTA 57.132 29.630 12.58 0.00 33.67 1.40
149 150 9.533253 GACAATTCCATGGTAAATGAAATTAGG 57.467 33.333 12.58 0.88 33.67 2.69
150 151 9.265862 ACAATTCCATGGTAAATGAAATTAGGA 57.734 29.630 12.58 0.00 33.67 2.94
151 152 9.754382 CAATTCCATGGTAAATGAAATTAGGAG 57.246 33.333 12.58 0.00 33.67 3.69
152 153 6.959639 TCCATGGTAAATGAAATTAGGAGC 57.040 37.500 12.58 0.00 33.67 4.70
153 154 6.672593 TCCATGGTAAATGAAATTAGGAGCT 58.327 36.000 12.58 0.00 33.67 4.09
154 155 6.772716 TCCATGGTAAATGAAATTAGGAGCTC 59.227 38.462 12.58 4.71 33.67 4.09
155 156 6.774656 CCATGGTAAATGAAATTAGGAGCTCT 59.225 38.462 14.64 2.18 33.67 4.09
156 157 7.255381 CCATGGTAAATGAAATTAGGAGCTCTG 60.255 40.741 14.64 0.00 33.67 3.35
157 158 5.590259 TGGTAAATGAAATTAGGAGCTCTGC 59.410 40.000 14.64 0.00 33.67 4.26
158 159 5.825151 GGTAAATGAAATTAGGAGCTCTGCT 59.175 40.000 14.64 5.67 37.23 4.24
159 160 6.017523 GGTAAATGAAATTAGGAGCTCTGCTC 60.018 42.308 14.64 10.74 45.44 4.26
171 172 4.833478 AGCTCTGCTCCTCAATTAAGAA 57.167 40.909 0.00 0.00 30.62 2.52
172 173 5.171339 AGCTCTGCTCCTCAATTAAGAAA 57.829 39.130 0.00 0.00 30.62 2.52
173 174 5.564550 AGCTCTGCTCCTCAATTAAGAAAA 58.435 37.500 0.00 0.00 30.62 2.29
174 175 5.414144 AGCTCTGCTCCTCAATTAAGAAAAC 59.586 40.000 0.00 0.00 30.62 2.43
175 176 5.414144 GCTCTGCTCCTCAATTAAGAAAACT 59.586 40.000 0.00 0.00 0.00 2.66
176 177 6.595716 GCTCTGCTCCTCAATTAAGAAAACTA 59.404 38.462 0.00 0.00 0.00 2.24
177 178 7.281999 GCTCTGCTCCTCAATTAAGAAAACTAT 59.718 37.037 0.00 0.00 0.00 2.12
178 179 9.171877 CTCTGCTCCTCAATTAAGAAAACTATT 57.828 33.333 0.00 0.00 0.00 1.73
179 180 9.520515 TCTGCTCCTCAATTAAGAAAACTATTT 57.479 29.630 0.00 0.00 0.00 1.40
268 269 2.473376 CGCCGTAAATTTTCAGTCGGTC 60.473 50.000 0.00 1.02 40.05 4.79
271 273 3.422603 CCGTAAATTTTCAGTCGGTCGTG 60.423 47.826 0.00 0.00 34.38 4.35
325 330 0.601046 CACACACTCACGCCATCACT 60.601 55.000 0.00 0.00 0.00 3.41
335 340 3.799753 CCATCACTAGGCACGCAC 58.200 61.111 0.00 0.00 0.00 5.34
406 438 1.002134 ACCCGGATGGCTCAACTTG 60.002 57.895 0.73 0.00 37.83 3.16
407 439 2.409870 CCCGGATGGCTCAACTTGC 61.410 63.158 0.73 0.00 0.00 4.01
408 440 1.675310 CCGGATGGCTCAACTTGCA 60.675 57.895 0.00 0.00 0.00 4.08
409 441 1.651240 CCGGATGGCTCAACTTGCAG 61.651 60.000 0.00 0.00 0.00 4.41
492 530 2.048222 CACTCGCCGCTCTTTCCA 60.048 61.111 0.00 0.00 0.00 3.53
503 541 2.613977 CGCTCTTTCCACATCTCCTGTT 60.614 50.000 0.00 0.00 35.29 3.16
504 542 3.416156 GCTCTTTCCACATCTCCTGTTT 58.584 45.455 0.00 0.00 35.29 2.83
505 543 3.438434 GCTCTTTCCACATCTCCTGTTTC 59.562 47.826 0.00 0.00 35.29 2.78
506 544 4.006319 CTCTTTCCACATCTCCTGTTTCC 58.994 47.826 0.00 0.00 35.29 3.13
520 558 3.853698 TTTCCTTCCGCCCCCAACG 62.854 63.158 0.00 0.00 0.00 4.10
544 582 1.682684 TGTTCCTCCTCGCCTCCTC 60.683 63.158 0.00 0.00 0.00 3.71
579 630 0.323360 CCTCATCCGCCAAGGGAAAA 60.323 55.000 0.00 0.00 40.09 2.29
611 662 2.246469 ACCAGAGATGCAGCGATAGAT 58.754 47.619 0.00 0.00 39.76 1.98
612 663 2.230992 ACCAGAGATGCAGCGATAGATC 59.769 50.000 0.00 0.00 39.76 2.75
613 664 2.230750 CCAGAGATGCAGCGATAGATCA 59.769 50.000 0.00 0.00 39.76 2.92
615 666 4.097589 CCAGAGATGCAGCGATAGATCATA 59.902 45.833 0.00 0.00 39.76 2.15
616 667 5.036090 CAGAGATGCAGCGATAGATCATAC 58.964 45.833 0.00 0.00 39.76 2.39
617 668 4.949238 AGAGATGCAGCGATAGATCATACT 59.051 41.667 0.00 0.00 39.76 2.12
618 669 4.996344 AGATGCAGCGATAGATCATACTG 58.004 43.478 0.00 0.00 39.76 2.74
619 670 4.462132 AGATGCAGCGATAGATCATACTGT 59.538 41.667 0.00 0.00 39.76 3.55
620 671 5.649831 AGATGCAGCGATAGATCATACTGTA 59.350 40.000 0.00 0.00 39.76 2.74
621 672 5.302357 TGCAGCGATAGATCATACTGTAG 57.698 43.478 0.00 0.00 39.76 2.74
622 673 5.003804 TGCAGCGATAGATCATACTGTAGA 58.996 41.667 0.00 0.00 39.76 2.59
623 674 5.649831 TGCAGCGATAGATCATACTGTAGAT 59.350 40.000 0.00 0.00 39.76 1.98
656 707 3.486383 TCAATTTCACTTTTCGCCTCCT 58.514 40.909 0.00 0.00 0.00 3.69
657 708 3.502211 TCAATTTCACTTTTCGCCTCCTC 59.498 43.478 0.00 0.00 0.00 3.71
658 709 2.930826 TTTCACTTTTCGCCTCCTCT 57.069 45.000 0.00 0.00 0.00 3.69
659 710 2.930826 TTCACTTTTCGCCTCCTCTT 57.069 45.000 0.00 0.00 0.00 2.85
660 711 2.457366 TCACTTTTCGCCTCCTCTTC 57.543 50.000 0.00 0.00 0.00 2.87
661 712 1.691976 TCACTTTTCGCCTCCTCTTCA 59.308 47.619 0.00 0.00 0.00 3.02
662 713 1.801178 CACTTTTCGCCTCCTCTTCAC 59.199 52.381 0.00 0.00 0.00 3.18
663 714 1.071605 CTTTTCGCCTCCTCTTCACG 58.928 55.000 0.00 0.00 0.00 4.35
664 715 0.391597 TTTTCGCCTCCTCTTCACGT 59.608 50.000 0.00 0.00 0.00 4.49
665 716 1.250328 TTTCGCCTCCTCTTCACGTA 58.750 50.000 0.00 0.00 0.00 3.57
666 717 0.524862 TTCGCCTCCTCTTCACGTAC 59.475 55.000 0.00 0.00 0.00 3.67
667 718 0.607217 TCGCCTCCTCTTCACGTACA 60.607 55.000 0.00 0.00 0.00 2.90
668 719 0.456312 CGCCTCCTCTTCACGTACAC 60.456 60.000 0.00 0.00 0.00 2.90
669 720 0.601558 GCCTCCTCTTCACGTACACA 59.398 55.000 0.00 0.00 0.00 3.72
670 721 1.000506 GCCTCCTCTTCACGTACACAA 59.999 52.381 0.00 0.00 0.00 3.33
692 743 0.609131 CCAACCAAGATCCCGCTTGT 60.609 55.000 0.00 0.00 42.84 3.16
695 746 1.995376 ACCAAGATCCCGCTTGTTTT 58.005 45.000 0.00 0.00 42.84 2.43
696 747 1.613437 ACCAAGATCCCGCTTGTTTTG 59.387 47.619 0.00 0.00 42.84 2.44
698 749 0.603065 AAGATCCCGCTTGTTTTGCC 59.397 50.000 0.00 0.00 0.00 4.52
775 833 0.391661 GGCTCGCAAACTCTGATCCA 60.392 55.000 0.00 0.00 0.00 3.41
782 840 1.667724 CAAACTCTGATCCATGTCCGC 59.332 52.381 0.00 0.00 0.00 5.54
783 841 0.179100 AACTCTGATCCATGTCCGCG 60.179 55.000 0.00 0.00 0.00 6.46
784 842 1.323271 ACTCTGATCCATGTCCGCGT 61.323 55.000 4.92 0.00 0.00 6.01
785 843 0.596083 CTCTGATCCATGTCCGCGTC 60.596 60.000 4.92 0.00 0.00 5.19
786 844 1.592669 CTGATCCATGTCCGCGTCC 60.593 63.158 4.92 0.00 0.00 4.79
787 845 2.658593 GATCCATGTCCGCGTCCG 60.659 66.667 4.92 0.00 0.00 4.79
788 846 4.891727 ATCCATGTCCGCGTCCGC 62.892 66.667 4.92 0.68 37.85 5.54
868 927 1.940613 AGTCCGTGCTCACTTTTGTTC 59.059 47.619 0.00 0.00 0.00 3.18
870 929 0.310854 CCGTGCTCACTTTTGTTCCC 59.689 55.000 0.00 0.00 0.00 3.97
975 1034 2.748058 ATTGCTTGCTTCGGGGTCGT 62.748 55.000 0.00 0.00 37.69 4.34
976 1035 3.119096 GCTTGCTTCGGGGTCGTC 61.119 66.667 0.00 0.00 37.69 4.20
977 1036 2.809601 CTTGCTTCGGGGTCGTCG 60.810 66.667 0.00 0.00 37.69 5.12
1008 1071 1.383109 AGCGGTGGAGATGATGGGA 60.383 57.895 0.00 0.00 0.00 4.37
2085 2166 2.516460 AGCTCCGGCGAGTACGAT 60.516 61.111 9.30 0.00 44.37 3.73
2121 2202 2.586357 GAGGCCGCGAACCAGATC 60.586 66.667 18.56 5.69 0.00 2.75
2191 2272 3.122150 TCGAGCAACGAGTTCATGG 57.878 52.632 2.09 0.00 46.45 3.66
2223 2304 1.806542 GCGCTGATGAAGGAAGAAACA 59.193 47.619 0.00 0.00 0.00 2.83
2224 2305 2.226437 GCGCTGATGAAGGAAGAAACAA 59.774 45.455 0.00 0.00 0.00 2.83
2225 2306 3.814945 CGCTGATGAAGGAAGAAACAAC 58.185 45.455 0.00 0.00 0.00 3.32
2234 2315 1.292992 GAAGAAACAACCACCGACGT 58.707 50.000 0.00 0.00 0.00 4.34
2395 2488 4.697756 GCAGCGCCCACCAGTACA 62.698 66.667 2.29 0.00 0.00 2.90
2681 2780 1.569003 CGAACAACGTGATGCAGCA 59.431 52.632 0.00 0.00 37.22 4.41
2682 2781 0.451628 CGAACAACGTGATGCAGCAG 60.452 55.000 4.06 1.97 37.22 4.24
2683 2782 0.727122 GAACAACGTGATGCAGCAGC 60.727 55.000 4.06 2.87 42.57 5.25
2882 2981 3.288092 GAACAACCAAGAAGGAACCACT 58.712 45.455 0.00 0.00 41.22 4.00
2883 2982 4.080243 TGAACAACCAAGAAGGAACCACTA 60.080 41.667 0.00 0.00 41.22 2.74
2884 2983 3.816994 ACAACCAAGAAGGAACCACTAC 58.183 45.455 0.00 0.00 41.22 2.73
2915 3017 4.939052 TGTAGCTCTAGGCCATTAGAAC 57.061 45.455 5.01 0.00 43.05 3.01
3036 3138 4.285807 TCACACCGAAATCAAACTGTTG 57.714 40.909 0.00 0.00 35.95 3.33
3130 3235 2.096335 ACCAAAACACCGACGAACTTTC 59.904 45.455 0.00 0.00 0.00 2.62
3137 3243 0.598158 CCGACGAACTTTCCCGTTCA 60.598 55.000 0.00 0.00 42.57 3.18
3193 3300 0.514691 GAAGACTCAGCAAAGCGTGG 59.485 55.000 0.00 0.00 0.00 4.94
3330 3446 3.321648 ACATGCTCGCCAGGGACA 61.322 61.111 0.00 0.00 0.00 4.02
3347 3463 2.046892 ACCATGACAGCGACTGGC 60.047 61.111 10.80 8.46 40.49 4.85
3437 3562 1.301716 GCTGCTGACTTTGACGGGA 60.302 57.895 0.00 0.00 0.00 5.14
3470 3599 2.519013 AGGAAAGGATGGTTTCTGTGC 58.481 47.619 0.00 0.00 36.76 4.57
3476 3605 2.489329 AGGATGGTTTCTGTGCAATTCG 59.511 45.455 0.00 0.00 0.00 3.34
3495 3624 1.472480 CGCGGGGATTTCAGTTGAATT 59.528 47.619 0.00 0.00 33.54 2.17
3509 3638 7.979115 TCAGTTGAATTCGGTTAAGTTTTTG 57.021 32.000 0.04 0.00 0.00 2.44
3510 3639 6.474102 TCAGTTGAATTCGGTTAAGTTTTTGC 59.526 34.615 0.04 0.00 0.00 3.68
3511 3640 6.254589 CAGTTGAATTCGGTTAAGTTTTTGCA 59.745 34.615 0.04 0.00 0.00 4.08
3512 3641 6.475402 AGTTGAATTCGGTTAAGTTTTTGCAG 59.525 34.615 0.04 0.00 0.00 4.41
3515 3644 5.722021 ATTCGGTTAAGTTTTTGCAGGAT 57.278 34.783 0.00 0.00 0.00 3.24
3516 3645 5.523438 TTCGGTTAAGTTTTTGCAGGATT 57.477 34.783 0.00 0.00 0.00 3.01
3518 3647 5.908341 TCGGTTAAGTTTTTGCAGGATTTT 58.092 33.333 0.00 0.00 0.00 1.82
3519 3648 7.040473 TCGGTTAAGTTTTTGCAGGATTTTA 57.960 32.000 0.00 0.00 0.00 1.52
3520 3649 6.919115 TCGGTTAAGTTTTTGCAGGATTTTAC 59.081 34.615 0.00 0.00 0.00 2.01
3521 3650 6.144886 CGGTTAAGTTTTTGCAGGATTTTACC 59.855 38.462 0.00 0.00 0.00 2.85
3523 3652 4.251543 AGTTTTTGCAGGATTTTACCGG 57.748 40.909 0.00 0.00 34.73 5.28
3524 3653 3.006430 AGTTTTTGCAGGATTTTACCGGG 59.994 43.478 6.32 0.00 34.73 5.73
3525 3654 2.588464 TTTGCAGGATTTTACCGGGA 57.412 45.000 6.32 0.00 34.73 5.14
3527 3656 2.341846 TGCAGGATTTTACCGGGATC 57.658 50.000 6.32 3.56 34.73 3.36
3528 3657 1.133915 TGCAGGATTTTACCGGGATCC 60.134 52.381 6.32 12.95 39.70 3.36
3530 3659 2.851195 CAGGATTTTACCGGGATCCAG 58.149 52.381 22.37 9.92 41.43 3.86
3531 3660 2.172717 CAGGATTTTACCGGGATCCAGT 59.827 50.000 22.37 12.86 41.43 4.00
3532 3661 2.850568 AGGATTTTACCGGGATCCAGTT 59.149 45.455 22.37 0.00 41.43 3.16
3533 3662 4.042174 AGGATTTTACCGGGATCCAGTTA 58.958 43.478 22.37 0.00 41.43 2.24
3534 3663 4.102681 AGGATTTTACCGGGATCCAGTTAG 59.897 45.833 22.37 0.00 41.43 2.34
3535 3664 4.102054 GGATTTTACCGGGATCCAGTTAGA 59.898 45.833 15.23 0.00 39.30 2.10
3536 3665 4.476628 TTTTACCGGGATCCAGTTAGAC 57.523 45.455 15.23 0.00 0.00 2.59
3537 3666 3.393426 TTACCGGGATCCAGTTAGACT 57.607 47.619 15.23 0.00 0.00 3.24
3538 3667 1.486211 ACCGGGATCCAGTTAGACTG 58.514 55.000 15.23 1.14 45.53 3.51
3539 3668 1.273098 ACCGGGATCCAGTTAGACTGT 60.273 52.381 15.23 0.00 44.50 3.55
3540 3669 1.831736 CCGGGATCCAGTTAGACTGTT 59.168 52.381 15.23 0.00 44.50 3.16
3541 3670 2.418746 CCGGGATCCAGTTAGACTGTTG 60.419 54.545 15.23 0.00 44.50 3.33
3542 3671 2.418746 CGGGATCCAGTTAGACTGTTGG 60.419 54.545 15.23 0.00 44.50 3.77
3543 3672 2.838202 GGGATCCAGTTAGACTGTTGGA 59.162 50.000 15.23 0.96 44.50 3.53
3550 3679 4.169508 CAGTTAGACTGTTGGATCTGACG 58.830 47.826 0.00 0.00 41.19 4.35
3577 3721 1.883926 AGGCAAACATAAACGGACACC 59.116 47.619 0.00 0.00 0.00 4.16
3602 3746 4.346127 TCAGATTCAGGGACCATCATGTAG 59.654 45.833 0.00 0.00 0.00 2.74
3648 3792 8.514594 CATTTGATGAGTGGTTTCTAAGCTAAA 58.485 33.333 0.00 0.00 0.00 1.85
3660 3804 5.614324 TCTAAGCTAAATGGCTAAGCAGA 57.386 39.130 0.00 0.00 42.24 4.26
3672 3816 0.535335 TAAGCAGACTTAGGCCACCG 59.465 55.000 5.01 0.00 37.33 4.94
3724 3873 1.269998 CGAGATCCACCTAATCCGACC 59.730 57.143 0.00 0.00 0.00 4.79
3745 3895 3.450817 CCCTTAAAATAAAGCACCCCTGG 59.549 47.826 0.00 0.00 0.00 4.45
3753 3903 2.746277 GCACCCCTGGTTAGCACG 60.746 66.667 0.00 0.00 31.02 5.34
3759 3909 0.034896 CCCTGGTTAGCACGTCTGTT 59.965 55.000 0.00 0.00 0.00 3.16
3760 3910 1.542547 CCCTGGTTAGCACGTCTGTTT 60.543 52.381 0.00 0.00 0.00 2.83
3762 3912 2.479837 CTGGTTAGCACGTCTGTTTGA 58.520 47.619 0.00 0.00 0.00 2.69
3763 3913 2.869801 CTGGTTAGCACGTCTGTTTGAA 59.130 45.455 0.00 0.00 0.00 2.69
3764 3914 2.869801 TGGTTAGCACGTCTGTTTGAAG 59.130 45.455 0.00 0.00 0.00 3.02
3765 3915 3.128349 GGTTAGCACGTCTGTTTGAAGA 58.872 45.455 0.00 0.00 0.00 2.87
3766 3916 3.746492 GGTTAGCACGTCTGTTTGAAGAT 59.254 43.478 0.00 0.00 0.00 2.40
3767 3917 4.213482 GGTTAGCACGTCTGTTTGAAGATT 59.787 41.667 0.00 0.00 0.00 2.40
3796 3946 3.921119 TTCTGATGAAACACATGCCAC 57.079 42.857 0.00 0.00 39.56 5.01
3797 3947 3.144657 TCTGATGAAACACATGCCACT 57.855 42.857 0.00 0.00 39.56 4.00
3801 3951 3.752747 TGATGAAACACATGCCACTAGTG 59.247 43.478 16.34 16.34 39.56 2.74
3802 3952 3.483808 TGAAACACATGCCACTAGTGA 57.516 42.857 24.68 5.51 37.05 3.41
3804 3954 5.159273 TGAAACACATGCCACTAGTGATA 57.841 39.130 24.68 12.52 37.05 2.15
3805 3955 5.178061 TGAAACACATGCCACTAGTGATAG 58.822 41.667 24.68 12.74 37.05 2.08
3807 3957 5.620738 AACACATGCCACTAGTGATAGAT 57.379 39.130 24.68 7.19 37.05 1.98
3808 3958 6.731292 AACACATGCCACTAGTGATAGATA 57.269 37.500 24.68 4.07 37.05 1.98
3809 3959 6.731292 ACACATGCCACTAGTGATAGATAA 57.269 37.500 24.68 1.92 37.05 1.75
3811 3961 7.739825 ACACATGCCACTAGTGATAGATAAAT 58.260 34.615 24.68 3.13 37.05 1.40
3812 3962 7.875041 ACACATGCCACTAGTGATAGATAAATC 59.125 37.037 24.68 1.16 37.05 2.17
3813 3963 7.874528 CACATGCCACTAGTGATAGATAAATCA 59.125 37.037 24.68 6.22 35.33 2.57
3814 3964 8.093307 ACATGCCACTAGTGATAGATAAATCAG 58.907 37.037 24.68 3.62 36.57 2.90
3815 3965 7.603180 TGCCACTAGTGATAGATAAATCAGT 57.397 36.000 24.68 0.00 41.39 3.41
3816 3966 8.706322 TGCCACTAGTGATAGATAAATCAGTA 57.294 34.615 24.68 0.00 39.63 2.74
3860 4038 0.882927 CGACGTGCAAAAGGGAGGAA 60.883 55.000 0.00 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.006043 TGACCCAACACCCAAAACAGA 59.994 47.619 0.00 0.00 0.00 3.41
1 2 1.479709 TGACCCAACACCCAAAACAG 58.520 50.000 0.00 0.00 0.00 3.16
2 3 1.759445 CATGACCCAACACCCAAAACA 59.241 47.619 0.00 0.00 0.00 2.83
3 4 2.035632 TCATGACCCAACACCCAAAAC 58.964 47.619 0.00 0.00 0.00 2.43
4 5 2.315176 CTCATGACCCAACACCCAAAA 58.685 47.619 0.00 0.00 0.00 2.44
5 6 1.216678 ACTCATGACCCAACACCCAAA 59.783 47.619 0.00 0.00 0.00 3.28
6 7 0.850100 ACTCATGACCCAACACCCAA 59.150 50.000 0.00 0.00 0.00 4.12
7 8 0.850100 AACTCATGACCCAACACCCA 59.150 50.000 0.00 0.00 0.00 4.51
8 9 1.995376 AAACTCATGACCCAACACCC 58.005 50.000 0.00 0.00 0.00 4.61
9 10 5.722021 AAATAAACTCATGACCCAACACC 57.278 39.130 0.00 0.00 0.00 4.16
10 11 8.184192 CAGATAAATAAACTCATGACCCAACAC 58.816 37.037 0.00 0.00 0.00 3.32
11 12 7.148086 GCAGATAAATAAACTCATGACCCAACA 60.148 37.037 0.00 0.00 0.00 3.33
12 13 7.067494 AGCAGATAAATAAACTCATGACCCAAC 59.933 37.037 0.00 0.00 0.00 3.77
13 14 7.067372 CAGCAGATAAATAAACTCATGACCCAA 59.933 37.037 0.00 0.00 0.00 4.12
14 15 6.543465 CAGCAGATAAATAAACTCATGACCCA 59.457 38.462 0.00 0.00 0.00 4.51
15 16 6.514048 GCAGCAGATAAATAAACTCATGACCC 60.514 42.308 0.00 0.00 0.00 4.46
16 17 6.433766 GCAGCAGATAAATAAACTCATGACC 58.566 40.000 0.00 0.00 0.00 4.02
17 18 6.433766 GGCAGCAGATAAATAAACTCATGAC 58.566 40.000 0.00 0.00 0.00 3.06
18 19 5.532406 GGGCAGCAGATAAATAAACTCATGA 59.468 40.000 0.00 0.00 0.00 3.07
19 20 5.300034 TGGGCAGCAGATAAATAAACTCATG 59.700 40.000 0.00 0.00 0.00 3.07
20 21 5.300286 GTGGGCAGCAGATAAATAAACTCAT 59.700 40.000 0.00 0.00 0.00 2.90
21 22 4.640201 GTGGGCAGCAGATAAATAAACTCA 59.360 41.667 0.00 0.00 0.00 3.41
22 23 4.036852 GGTGGGCAGCAGATAAATAAACTC 59.963 45.833 0.00 0.00 0.00 3.01
23 24 3.954258 GGTGGGCAGCAGATAAATAAACT 59.046 43.478 0.00 0.00 0.00 2.66
24 25 3.068165 GGGTGGGCAGCAGATAAATAAAC 59.932 47.826 0.00 0.00 0.00 2.01
25 26 3.052944 AGGGTGGGCAGCAGATAAATAAA 60.053 43.478 0.00 0.00 0.00 1.40
26 27 2.513738 AGGGTGGGCAGCAGATAAATAA 59.486 45.455 0.00 0.00 0.00 1.40
27 28 2.135189 AGGGTGGGCAGCAGATAAATA 58.865 47.619 0.00 0.00 0.00 1.40
28 29 0.929244 AGGGTGGGCAGCAGATAAAT 59.071 50.000 0.00 0.00 0.00 1.40
29 30 0.034186 CAGGGTGGGCAGCAGATAAA 60.034 55.000 0.00 0.00 0.00 1.40
30 31 0.913934 TCAGGGTGGGCAGCAGATAA 60.914 55.000 0.00 0.00 0.00 1.75
31 32 1.306911 TCAGGGTGGGCAGCAGATA 60.307 57.895 0.00 0.00 0.00 1.98
32 33 2.611800 TCAGGGTGGGCAGCAGAT 60.612 61.111 0.00 0.00 0.00 2.90
33 34 3.324930 CTCAGGGTGGGCAGCAGA 61.325 66.667 0.00 0.00 0.00 4.26
34 35 4.421515 CCTCAGGGTGGGCAGCAG 62.422 72.222 0.00 0.00 0.00 4.24
45 46 0.106519 CATGCCCTTAACCCCTCAGG 60.107 60.000 0.00 0.00 43.78 3.86
46 47 0.106519 CCATGCCCTTAACCCCTCAG 60.107 60.000 0.00 0.00 0.00 3.35
47 48 0.849094 ACCATGCCCTTAACCCCTCA 60.849 55.000 0.00 0.00 0.00 3.86
48 49 0.395724 CACCATGCCCTTAACCCCTC 60.396 60.000 0.00 0.00 0.00 4.30
49 50 0.849094 TCACCATGCCCTTAACCCCT 60.849 55.000 0.00 0.00 0.00 4.79
50 51 0.395724 CTCACCATGCCCTTAACCCC 60.396 60.000 0.00 0.00 0.00 4.95
51 52 0.331616 ACTCACCATGCCCTTAACCC 59.668 55.000 0.00 0.00 0.00 4.11
52 53 3.577805 ATACTCACCATGCCCTTAACC 57.422 47.619 0.00 0.00 0.00 2.85
53 54 5.394115 CCAAAATACTCACCATGCCCTTAAC 60.394 44.000 0.00 0.00 0.00 2.01
54 55 4.709397 CCAAAATACTCACCATGCCCTTAA 59.291 41.667 0.00 0.00 0.00 1.85
55 56 4.277476 CCAAAATACTCACCATGCCCTTA 58.723 43.478 0.00 0.00 0.00 2.69
56 57 3.099141 CCAAAATACTCACCATGCCCTT 58.901 45.455 0.00 0.00 0.00 3.95
57 58 2.624029 CCCAAAATACTCACCATGCCCT 60.624 50.000 0.00 0.00 0.00 5.19
58 59 1.756538 CCCAAAATACTCACCATGCCC 59.243 52.381 0.00 0.00 0.00 5.36
59 60 1.756538 CCCCAAAATACTCACCATGCC 59.243 52.381 0.00 0.00 0.00 4.40
60 61 1.756538 CCCCCAAAATACTCACCATGC 59.243 52.381 0.00 0.00 0.00 4.06
61 62 3.100207 ACCCCCAAAATACTCACCATG 57.900 47.619 0.00 0.00 0.00 3.66
62 63 3.845109 AACCCCCAAAATACTCACCAT 57.155 42.857 0.00 0.00 0.00 3.55
63 64 3.621682 AAACCCCCAAAATACTCACCA 57.378 42.857 0.00 0.00 0.00 4.17
64 65 6.422344 TTTAAAACCCCCAAAATACTCACC 57.578 37.500 0.00 0.00 0.00 4.02
65 66 8.205512 TCTTTTTAAAACCCCCAAAATACTCAC 58.794 33.333 0.00 0.00 0.00 3.51
66 67 8.320338 TCTTTTTAAAACCCCCAAAATACTCA 57.680 30.769 0.00 0.00 0.00 3.41
67 68 9.787435 AATCTTTTTAAAACCCCCAAAATACTC 57.213 29.630 0.00 0.00 0.00 2.59
70 71 9.274206 CGAAATCTTTTTAAAACCCCCAAAATA 57.726 29.630 0.00 0.00 0.00 1.40
71 72 7.776030 ACGAAATCTTTTTAAAACCCCCAAAAT 59.224 29.630 0.00 0.00 0.00 1.82
72 73 7.110810 ACGAAATCTTTTTAAAACCCCCAAAA 58.889 30.769 0.00 0.00 0.00 2.44
73 74 6.651086 ACGAAATCTTTTTAAAACCCCCAAA 58.349 32.000 0.00 0.00 0.00 3.28
74 75 6.236558 ACGAAATCTTTTTAAAACCCCCAA 57.763 33.333 0.00 0.00 0.00 4.12
75 76 5.873146 ACGAAATCTTTTTAAAACCCCCA 57.127 34.783 0.00 0.00 0.00 4.96
76 77 9.577110 CTATAACGAAATCTTTTTAAAACCCCC 57.423 33.333 0.00 0.00 0.00 5.40
77 78 9.577110 CCTATAACGAAATCTTTTTAAAACCCC 57.423 33.333 0.00 0.00 0.00 4.95
78 79 9.577110 CCCTATAACGAAATCTTTTTAAAACCC 57.423 33.333 0.00 0.00 0.00 4.11
79 80 9.577110 CCCCTATAACGAAATCTTTTTAAAACC 57.423 33.333 0.00 0.00 0.00 3.27
80 81 9.577110 CCCCCTATAACGAAATCTTTTTAAAAC 57.423 33.333 0.00 0.00 0.00 2.43
81 82 9.311676 ACCCCCTATAACGAAATCTTTTTAAAA 57.688 29.630 0.00 0.00 0.00 1.52
82 83 8.882557 ACCCCCTATAACGAAATCTTTTTAAA 57.117 30.769 0.00 0.00 0.00 1.52
83 84 9.617523 CTACCCCCTATAACGAAATCTTTTTAA 57.382 33.333 0.00 0.00 0.00 1.52
84 85 8.212995 CCTACCCCCTATAACGAAATCTTTTTA 58.787 37.037 0.00 0.00 0.00 1.52
85 86 7.058525 CCTACCCCCTATAACGAAATCTTTTT 58.941 38.462 0.00 0.00 0.00 1.94
86 87 6.387807 TCCTACCCCCTATAACGAAATCTTTT 59.612 38.462 0.00 0.00 0.00 2.27
87 88 5.907079 TCCTACCCCCTATAACGAAATCTTT 59.093 40.000 0.00 0.00 0.00 2.52
88 89 5.306419 GTCCTACCCCCTATAACGAAATCTT 59.694 44.000 0.00 0.00 0.00 2.40
89 90 4.837298 GTCCTACCCCCTATAACGAAATCT 59.163 45.833 0.00 0.00 0.00 2.40
90 91 4.020751 GGTCCTACCCCCTATAACGAAATC 60.021 50.000 0.00 0.00 30.04 2.17
91 92 3.906218 GGTCCTACCCCCTATAACGAAAT 59.094 47.826 0.00 0.00 30.04 2.17
92 93 3.308401 GGTCCTACCCCCTATAACGAAA 58.692 50.000 0.00 0.00 30.04 3.46
93 94 2.962859 GGTCCTACCCCCTATAACGAA 58.037 52.381 0.00 0.00 30.04 3.85
94 95 2.683211 GGTCCTACCCCCTATAACGA 57.317 55.000 0.00 0.00 30.04 3.85
105 106 2.241685 TGTCACTCTCTAGGGTCCTACC 59.758 54.545 0.00 0.00 37.60 3.18
106 107 3.648507 TGTCACTCTCTAGGGTCCTAC 57.351 52.381 0.00 0.00 0.00 3.18
107 108 4.883021 ATTGTCACTCTCTAGGGTCCTA 57.117 45.455 0.00 0.00 0.00 2.94
108 109 3.767309 ATTGTCACTCTCTAGGGTCCT 57.233 47.619 0.00 0.00 0.00 3.85
109 110 3.133183 GGAATTGTCACTCTCTAGGGTCC 59.867 52.174 0.00 0.00 0.00 4.46
110 111 3.769844 TGGAATTGTCACTCTCTAGGGTC 59.230 47.826 0.00 0.00 0.00 4.46
111 112 3.791320 TGGAATTGTCACTCTCTAGGGT 58.209 45.455 0.00 0.00 0.00 4.34
112 113 4.444022 CCATGGAATTGTCACTCTCTAGGG 60.444 50.000 5.56 0.00 0.00 3.53
113 114 4.163078 ACCATGGAATTGTCACTCTCTAGG 59.837 45.833 21.47 0.00 0.00 3.02
114 115 5.350504 ACCATGGAATTGTCACTCTCTAG 57.649 43.478 21.47 0.00 0.00 2.43
115 116 6.867519 TTACCATGGAATTGTCACTCTCTA 57.132 37.500 21.47 0.00 0.00 2.43
116 117 5.762179 TTACCATGGAATTGTCACTCTCT 57.238 39.130 21.47 0.00 0.00 3.10
117 118 6.599244 TCATTTACCATGGAATTGTCACTCTC 59.401 38.462 21.47 0.00 0.00 3.20
118 119 6.484288 TCATTTACCATGGAATTGTCACTCT 58.516 36.000 21.47 0.00 0.00 3.24
119 120 6.757897 TCATTTACCATGGAATTGTCACTC 57.242 37.500 21.47 0.00 0.00 3.51
120 121 7.537596 TTTCATTTACCATGGAATTGTCACT 57.462 32.000 21.47 0.00 0.00 3.41
121 122 8.776376 AATTTCATTTACCATGGAATTGTCAC 57.224 30.769 21.47 0.00 36.25 3.67
123 124 9.533253 CCTAATTTCATTTACCATGGAATTGTC 57.467 33.333 21.47 0.00 37.66 3.18
124 125 9.265862 TCCTAATTTCATTTACCATGGAATTGT 57.734 29.630 21.47 0.00 37.66 2.71
125 126 9.754382 CTCCTAATTTCATTTACCATGGAATTG 57.246 33.333 21.47 14.01 37.66 2.32
126 127 8.424133 GCTCCTAATTTCATTTACCATGGAATT 58.576 33.333 21.47 13.98 39.69 2.17
127 128 7.786464 AGCTCCTAATTTCATTTACCATGGAAT 59.214 33.333 21.47 5.71 0.00 3.01
128 129 7.125391 AGCTCCTAATTTCATTTACCATGGAA 58.875 34.615 21.47 2.96 0.00 3.53
129 130 6.672593 AGCTCCTAATTTCATTTACCATGGA 58.327 36.000 21.47 0.00 0.00 3.41
130 131 6.774656 AGAGCTCCTAATTTCATTTACCATGG 59.225 38.462 11.19 11.19 0.00 3.66
131 132 7.646314 CAGAGCTCCTAATTTCATTTACCATG 58.354 38.462 10.93 0.00 0.00 3.66
132 133 6.264067 GCAGAGCTCCTAATTTCATTTACCAT 59.736 38.462 10.93 0.00 0.00 3.55
133 134 5.590259 GCAGAGCTCCTAATTTCATTTACCA 59.410 40.000 10.93 0.00 0.00 3.25
134 135 5.825151 AGCAGAGCTCCTAATTTCATTTACC 59.175 40.000 10.93 0.00 30.62 2.85
135 136 6.934048 AGCAGAGCTCCTAATTTCATTTAC 57.066 37.500 10.93 0.00 30.62 2.01
150 151 4.833478 TTCTTAATTGAGGAGCAGAGCT 57.167 40.909 0.00 0.00 43.88 4.09
151 152 5.414144 AGTTTTCTTAATTGAGGAGCAGAGC 59.586 40.000 0.00 0.00 0.00 4.09
152 153 8.729805 ATAGTTTTCTTAATTGAGGAGCAGAG 57.270 34.615 0.00 0.00 0.00 3.35
153 154 9.520515 AAATAGTTTTCTTAATTGAGGAGCAGA 57.479 29.630 0.00 0.00 0.00 4.26
208 209 2.673368 CGGCCTACTCTTAAAGTGCAAG 59.327 50.000 0.00 0.00 39.11 4.01
250 251 3.717830 CACGACCGACTGAAAATTTACG 58.282 45.455 0.00 0.00 0.00 3.18
256 257 1.484227 CGTGCACGACCGACTGAAAA 61.484 55.000 34.93 0.00 43.02 2.29
271 273 1.372128 CTTTTGCTCAAGGGCGTGC 60.372 57.895 0.00 0.00 34.52 5.34
302 304 2.588877 GGCGTGAGTGTGTGTGCT 60.589 61.111 0.00 0.00 0.00 4.40
304 306 0.879839 TGATGGCGTGAGTGTGTGTG 60.880 55.000 0.00 0.00 0.00 3.82
305 307 0.880278 GTGATGGCGTGAGTGTGTGT 60.880 55.000 0.00 0.00 0.00 3.72
306 308 0.601046 AGTGATGGCGTGAGTGTGTG 60.601 55.000 0.00 0.00 0.00 3.82
307 309 0.966179 TAGTGATGGCGTGAGTGTGT 59.034 50.000 0.00 0.00 0.00 3.72
325 330 3.716539 GATGCTCCGTGCGTGCCTA 62.717 63.158 0.00 0.00 46.63 3.93
333 338 2.815211 CGTGGTGGATGCTCCGTG 60.815 66.667 0.63 0.00 40.17 4.94
335 340 2.815211 CACGTGGTGGATGCTCCG 60.815 66.667 7.95 0.00 40.17 4.63
492 530 1.339151 GCGGAAGGAAACAGGAGATGT 60.339 52.381 0.00 0.00 46.97 3.06
503 541 4.338710 CGTTGGGGGCGGAAGGAA 62.339 66.667 0.00 0.00 0.00 3.36
505 543 3.853698 TTTCGTTGGGGGCGGAAGG 62.854 63.158 0.00 0.00 0.00 3.46
506 544 2.281900 TTTCGTTGGGGGCGGAAG 60.282 61.111 0.00 0.00 0.00 3.46
520 558 1.289800 GGCGAGGAGGAACACGTTTC 61.290 60.000 0.00 0.00 0.00 2.78
547 585 1.643310 GATGAGGAGGATGAGGAGGG 58.357 60.000 0.00 0.00 0.00 4.30
579 630 0.761187 TCTCTGGTTGCTCTGCTTGT 59.239 50.000 0.00 0.00 0.00 3.16
632 683 4.156739 GGAGGCGAAAAGTGAAATTGATCT 59.843 41.667 0.00 0.00 0.00 2.75
637 688 3.756117 AGAGGAGGCGAAAAGTGAAATT 58.244 40.909 0.00 0.00 0.00 1.82
656 707 3.810941 GGTTGGATTTGTGTACGTGAAGA 59.189 43.478 0.00 0.00 0.00 2.87
657 708 3.562141 TGGTTGGATTTGTGTACGTGAAG 59.438 43.478 0.00 0.00 0.00 3.02
658 709 3.542648 TGGTTGGATTTGTGTACGTGAA 58.457 40.909 0.00 0.00 0.00 3.18
659 710 3.195471 TGGTTGGATTTGTGTACGTGA 57.805 42.857 0.00 0.00 0.00 4.35
660 711 3.562141 TCTTGGTTGGATTTGTGTACGTG 59.438 43.478 0.00 0.00 0.00 4.49
661 712 3.811083 TCTTGGTTGGATTTGTGTACGT 58.189 40.909 0.00 0.00 0.00 3.57
662 713 4.142687 GGATCTTGGTTGGATTTGTGTACG 60.143 45.833 0.00 0.00 0.00 3.67
663 714 4.157840 GGGATCTTGGTTGGATTTGTGTAC 59.842 45.833 0.00 0.00 0.00 2.90
664 715 4.340617 GGGATCTTGGTTGGATTTGTGTA 58.659 43.478 0.00 0.00 0.00 2.90
665 716 3.165071 GGGATCTTGGTTGGATTTGTGT 58.835 45.455 0.00 0.00 0.00 3.72
666 717 2.164219 CGGGATCTTGGTTGGATTTGTG 59.836 50.000 0.00 0.00 0.00 3.33
667 718 2.446435 CGGGATCTTGGTTGGATTTGT 58.554 47.619 0.00 0.00 0.00 2.83
668 719 1.134946 GCGGGATCTTGGTTGGATTTG 59.865 52.381 0.00 0.00 0.00 2.32
669 720 1.005924 AGCGGGATCTTGGTTGGATTT 59.994 47.619 0.00 0.00 0.00 2.17
670 721 0.625849 AGCGGGATCTTGGTTGGATT 59.374 50.000 0.00 0.00 0.00 3.01
698 749 0.519175 CGCAATCGACAAGCCGAAAG 60.519 55.000 0.00 0.00 42.22 2.62
707 758 2.431771 CCGTGACCGCAATCGACA 60.432 61.111 0.00 0.00 38.10 4.35
782 840 2.089854 CAAGAAATGGAGGCGGACG 58.910 57.895 0.00 0.00 0.00 4.79
792 850 3.065510 CAGAGCAGAGCATCCAAGAAATG 59.934 47.826 0.00 0.00 33.66 2.32
793 851 3.280295 CAGAGCAGAGCATCCAAGAAAT 58.720 45.455 0.00 0.00 33.66 2.17
868 927 0.600255 AGCAACACGACGAAGAAGGG 60.600 55.000 0.00 0.00 0.00 3.95
870 929 1.657538 GCAAGCAACACGACGAAGAAG 60.658 52.381 0.00 0.00 0.00 2.85
1008 1071 2.040464 ATCATCGCCACCCCTCCT 60.040 61.111 0.00 0.00 0.00 3.69
2223 2304 1.008079 GAAGTCGACGTCGGTGGTT 60.008 57.895 35.05 22.63 40.29 3.67
2224 2305 2.188829 TGAAGTCGACGTCGGTGGT 61.189 57.895 35.05 19.23 40.29 4.16
2225 2306 1.728426 GTGAAGTCGACGTCGGTGG 60.728 63.158 35.05 10.02 40.29 4.61
2234 2315 3.998672 GGGCGTGGGTGAAGTCGA 61.999 66.667 0.00 0.00 0.00 4.20
2499 2592 2.815647 GGCAGGCCGAAGTCGAAG 60.816 66.667 1.43 0.00 43.02 3.79
2539 2632 1.048160 TACATGCTCATCAGCCCGGA 61.048 55.000 0.73 0.00 46.26 5.14
2689 2788 3.805307 GCTCTGCTGCTGCTGCTG 61.805 66.667 27.67 26.32 40.48 4.41
2775 2874 2.932234 CGCTGACAGGTCGAACCCT 61.932 63.158 4.26 0.00 39.75 4.34
2872 2971 5.045578 ACATGCTAATCAGTAGTGGTTCCTT 60.046 40.000 0.00 0.00 31.78 3.36
2915 3017 4.327982 TCGAGAATGGAAGCCTTATGAG 57.672 45.455 0.00 0.00 0.00 2.90
3062 3166 4.895668 TTTAAGGTGGATGAACGTAGGT 57.104 40.909 0.00 0.00 0.00 3.08
3130 3235 1.066587 GAGCGAGGAGATGAACGGG 59.933 63.158 0.00 0.00 0.00 5.28
3137 3243 2.701587 CTCTCACGAGCGAGGAGAT 58.298 57.895 15.20 0.00 37.09 2.75
3215 3322 1.810030 GAGAGCGGGTGTAAAGCCG 60.810 63.158 19.40 19.40 0.00 5.52
3330 3446 2.046892 GCCAGTCGCTGTCATGGT 60.047 61.111 0.00 0.00 35.17 3.55
3437 3562 1.156736 CTTTCCTTCGCCGTGTTGAT 58.843 50.000 0.00 0.00 0.00 2.57
3470 3599 1.094785 ACTGAAATCCCCGCGAATTG 58.905 50.000 8.23 0.00 0.00 2.32
3476 3605 2.477863 CGAATTCAACTGAAATCCCCGC 60.478 50.000 6.22 0.00 37.61 6.13
3495 3624 5.523438 AAATCCTGCAAAAACTTAACCGA 57.477 34.783 0.00 0.00 0.00 4.69
3509 3638 1.133915 TGGATCCCGGTAAAATCCTGC 60.134 52.381 9.90 0.00 39.78 4.85
3510 3639 2.172717 ACTGGATCCCGGTAAAATCCTG 59.827 50.000 9.90 19.05 41.98 3.86
3511 3640 2.488836 ACTGGATCCCGGTAAAATCCT 58.511 47.619 9.90 2.67 41.98 3.24
3512 3641 3.292492 AACTGGATCCCGGTAAAATCC 57.708 47.619 9.90 12.94 43.15 3.01
3515 3644 4.081309 CAGTCTAACTGGATCCCGGTAAAA 60.081 45.833 9.90 0.00 43.15 1.52
3516 3645 3.449737 CAGTCTAACTGGATCCCGGTAAA 59.550 47.826 9.90 0.00 43.15 2.01
3518 3647 2.662866 CAGTCTAACTGGATCCCGGTA 58.337 52.381 9.90 4.83 43.15 4.02
3519 3648 1.486211 CAGTCTAACTGGATCCCGGT 58.514 55.000 9.90 3.60 46.37 5.28
3530 3659 4.167268 GACGTCAGATCCAACAGTCTAAC 58.833 47.826 11.55 0.00 0.00 2.34
3531 3660 3.119955 CGACGTCAGATCCAACAGTCTAA 60.120 47.826 17.16 0.00 0.00 2.10
3532 3661 2.418976 CGACGTCAGATCCAACAGTCTA 59.581 50.000 17.16 0.00 0.00 2.59
3533 3662 1.200252 CGACGTCAGATCCAACAGTCT 59.800 52.381 17.16 0.00 0.00 3.24
3534 3663 1.068472 ACGACGTCAGATCCAACAGTC 60.068 52.381 17.16 0.50 0.00 3.51
3535 3664 0.959553 ACGACGTCAGATCCAACAGT 59.040 50.000 17.16 0.00 0.00 3.55
3536 3665 2.095415 TGTACGACGTCAGATCCAACAG 60.095 50.000 17.16 0.00 0.00 3.16
3537 3666 1.881324 TGTACGACGTCAGATCCAACA 59.119 47.619 17.16 0.00 0.00 3.33
3538 3667 2.516923 CTGTACGACGTCAGATCCAAC 58.483 52.381 17.16 4.41 34.02 3.77
3539 3668 1.471287 CCTGTACGACGTCAGATCCAA 59.529 52.381 17.16 0.00 34.02 3.53
3540 3669 1.092348 CCTGTACGACGTCAGATCCA 58.908 55.000 17.16 3.49 34.02 3.41
3541 3670 0.248539 GCCTGTACGACGTCAGATCC 60.249 60.000 17.16 10.56 34.02 3.36
3542 3671 0.450583 TGCCTGTACGACGTCAGATC 59.549 55.000 17.16 15.13 34.02 2.75
3543 3672 0.885879 TTGCCTGTACGACGTCAGAT 59.114 50.000 17.16 2.63 34.02 2.90
3544 3673 0.669619 TTTGCCTGTACGACGTCAGA 59.330 50.000 17.16 0.00 34.02 3.27
3550 3679 3.423907 CCGTTTATGTTTGCCTGTACGAC 60.424 47.826 0.00 0.00 0.00 4.34
3577 3721 1.482182 TGATGGTCCCTGAATCTGACG 59.518 52.381 0.00 0.00 0.00 4.35
3602 3746 1.068434 GTCTACAGAGGCATCTCCAGC 59.932 57.143 0.00 0.00 40.83 4.85
3660 3804 0.541863 CCAGATTCGGTGGCCTAAGT 59.458 55.000 3.32 0.00 0.00 2.24
3724 3873 4.093743 ACCAGGGGTGCTTTATTTTAAGG 58.906 43.478 0.00 0.00 32.98 2.69
3745 3895 4.992381 ATCTTCAAACAGACGTGCTAAC 57.008 40.909 0.00 0.00 0.00 2.34
3753 3903 5.757850 ACCAACTGAATCTTCAAACAGAC 57.242 39.130 0.00 0.00 36.64 3.51
3759 3909 6.772233 TCATCAGAAACCAACTGAATCTTCAA 59.228 34.615 0.00 0.00 45.44 2.69
3760 3910 6.298361 TCATCAGAAACCAACTGAATCTTCA 58.702 36.000 0.00 0.00 45.44 3.02
3762 3912 7.587037 TTTCATCAGAAACCAACTGAATCTT 57.413 32.000 0.00 0.00 45.44 2.40
3797 3947 8.504815 GCGTGTCTACTGATTTATCTATCACTA 58.495 37.037 0.00 0.00 31.51 2.74
3801 3951 6.804295 CAGGCGTGTCTACTGATTTATCTATC 59.196 42.308 0.00 0.00 34.21 2.08
3802 3952 6.265649 ACAGGCGTGTCTACTGATTTATCTAT 59.734 38.462 6.15 0.00 36.17 1.98
3804 3954 4.402793 ACAGGCGTGTCTACTGATTTATCT 59.597 41.667 6.15 0.00 36.17 1.98
3805 3955 4.683832 ACAGGCGTGTCTACTGATTTATC 58.316 43.478 6.15 0.00 36.17 1.75
3807 3957 4.530710 AACAGGCGTGTCTACTGATTTA 57.469 40.909 13.21 0.00 35.08 1.40
3808 3958 3.402628 AACAGGCGTGTCTACTGATTT 57.597 42.857 13.21 0.00 35.08 2.17
3809 3959 3.067106 CAAACAGGCGTGTCTACTGATT 58.933 45.455 13.21 0.00 35.08 2.57
3811 3961 1.684450 TCAAACAGGCGTGTCTACTGA 59.316 47.619 13.21 10.34 35.08 3.41
3812 3962 2.148916 TCAAACAGGCGTGTCTACTG 57.851 50.000 13.21 8.27 35.08 2.74
3813 3963 2.364324 TCTTCAAACAGGCGTGTCTACT 59.636 45.455 13.21 0.00 35.08 2.57
3814 3964 2.750948 TCTTCAAACAGGCGTGTCTAC 58.249 47.619 13.21 0.00 35.08 2.59
3815 3965 3.678056 ATCTTCAAACAGGCGTGTCTA 57.322 42.857 13.21 0.00 35.08 2.59
3816 3966 2.550830 ATCTTCAAACAGGCGTGTCT 57.449 45.000 13.21 0.00 35.08 3.41
3817 3967 2.095718 GGAATCTTCAAACAGGCGTGTC 60.096 50.000 13.21 0.00 35.08 3.67


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

AutoCloner maintained by Alex Coulton.