Multiple sequence alignment - TraesCS3D01G427000

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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 TraesCS3D01G427000 chr3D 100.000 2255 0 0 1 2255 540158998 540156744 0.000000e+00 4165.0
1 TraesCS3D01G427000 chr3B 93.999 1833 55 22 462 2255 716302997 716301181 0.000000e+00 2724.0
2 TraesCS3D01G427000 chr3B 86.878 221 22 5 1 217 716305531 716305314 8.050000e-60 241.0
3 TraesCS3D01G427000 chr3B 100.000 35 0 0 2147 2181 716301231 716301197 5.200000e-07 65.8
4 TraesCS3D01G427000 chr3A 92.651 1279 55 16 342 1603 675290691 675289435 0.000000e+00 1805.0
5 TraesCS3D01G427000 chr3A 88.186 237 24 3 1702 1934 63180535 63180771 1.710000e-71 279.0
6 TraesCS3D01G427000 chr3A 87.712 236 23 5 1699 1931 501225638 501225870 1.030000e-68 270.0
7 TraesCS3D01G427000 chr3A 84.588 279 36 4 1934 2207 675266906 675266630 1.030000e-68 270.0
8 TraesCS3D01G427000 chr3A 85.542 249 27 5 1685 1930 33422440 33422682 3.720000e-63 252.0
9 TraesCS3D01G427000 chr3A 88.983 118 9 3 1587 1701 675279234 675279118 2.330000e-30 143.0
10 TraesCS3D01G427000 chr3A 88.136 118 10 4 1587 1701 675267060 675266944 1.090000e-28 137.0
11 TraesCS3D01G427000 chr3A 87.288 118 11 4 1587 1701 675233284 675233168 5.050000e-27 132.0
12 TraesCS3D01G427000 chr3A 87.288 118 11 4 1587 1701 675245694 675245578 5.050000e-27 132.0
13 TraesCS3D01G427000 chr4D 89.076 238 20 5 1702 1934 51076340 51076104 7.880000e-75 291.0
14 TraesCS3D01G427000 chr4D 80.676 207 38 2 1050 1255 446749516 446749311 2.320000e-35 159.0
15 TraesCS3D01G427000 chr7B 87.719 228 25 3 1705 1930 256020135 256019909 1.720000e-66 263.0
16 TraesCS3D01G427000 chr4B 86.864 236 27 4 1702 1934 447455463 447455229 6.180000e-66 261.0
17 TraesCS3D01G427000 chr4B 81.159 207 37 2 1050 1255 558753848 558753643 4.980000e-37 165.0
18 TraesCS3D01G427000 chr5D 86.250 240 30 3 1695 1931 44622974 44623213 7.990000e-65 257.0
19 TraesCS3D01G427000 chr1D 86.066 244 26 7 1699 1934 320384660 320384417 2.870000e-64 255.0
20 TraesCS3D01G427000 chr1A 82.500 240 23 7 616 836 186369619 186369380 2.290000e-45 193.0
21 TraesCS3D01G427000 chr6A 87.730 163 20 0 1101 1263 560649259 560649421 8.220000e-45 191.0
22 TraesCS3D01G427000 chr6D 87.135 171 14 2 1101 1263 418176462 418176632 1.060000e-43 187.0
23 TraesCS3D01G427000 chr4A 80.193 207 39 2 1050 1255 21025198 21025403 1.080000e-33 154.0
24 TraesCS3D01G427000 chr7D 89.831 118 11 1 1425 1542 61751714 61751598 1.400000e-32 150.0


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 TraesCS3D01G427000 chr3D 540156744 540158998 2254 True 4165.0 4165 100.0000 1 2255 1 chr3D.!!$R1 2254
1 TraesCS3D01G427000 chr3B 716301181 716302997 1816 True 1394.9 2724 96.9995 462 2255 2 chr3B.!!$R2 1793
2 TraesCS3D01G427000 chr3A 675289435 675290691 1256 True 1805.0 1805 92.6510 342 1603 1 chr3A.!!$R4 1261

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
936 984 0.039764 ACAGGTCGGATCAGAGGTCA 59.96 55.0 0.0 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1816 1872 1.786937 ACATGGCAACTTTGTCCCAA 58.213 45.0 0.0 0.0 37.61 4.12 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
24 25 6.707440 AATTTTGTCACTGTACAATGACCA 57.293 33.333 28.90 18.93 43.84 4.02
25 26 6.899393 ATTTTGTCACTGTACAATGACCAT 57.101 33.333 28.90 17.72 43.84 3.55
26 27 5.940192 TTTGTCACTGTACAATGACCATC 57.060 39.130 28.90 9.83 43.84 3.51
27 28 3.937814 TGTCACTGTACAATGACCATCC 58.062 45.455 28.90 9.49 43.84 3.51
28 29 3.270877 GTCACTGTACAATGACCATCCC 58.729 50.000 23.54 0.68 39.49 3.85
29 30 3.055094 GTCACTGTACAATGACCATCCCT 60.055 47.826 23.54 0.00 39.49 4.20
30 31 4.161565 GTCACTGTACAATGACCATCCCTA 59.838 45.833 23.54 0.00 39.49 3.53
31 32 4.968719 TCACTGTACAATGACCATCCCTAT 59.031 41.667 2.21 0.00 0.00 2.57
32 33 6.041637 GTCACTGTACAATGACCATCCCTATA 59.958 42.308 23.54 0.00 39.49 1.31
33 34 6.613679 TCACTGTACAATGACCATCCCTATAA 59.386 38.462 2.21 0.00 0.00 0.98
34 35 7.292356 TCACTGTACAATGACCATCCCTATAAT 59.708 37.037 2.21 0.00 0.00 1.28
35 36 7.388776 CACTGTACAATGACCATCCCTATAATG 59.611 40.741 0.00 0.00 0.00 1.90
36 37 6.237901 TGTACAATGACCATCCCTATAATGC 58.762 40.000 0.00 0.00 0.00 3.56
37 38 4.666512 ACAATGACCATCCCTATAATGCC 58.333 43.478 0.00 0.00 0.00 4.40
38 39 4.019174 CAATGACCATCCCTATAATGCCC 58.981 47.826 0.00 0.00 0.00 5.36
39 40 3.004126 TGACCATCCCTATAATGCCCT 57.996 47.619 0.00 0.00 0.00 5.19
40 41 2.912956 TGACCATCCCTATAATGCCCTC 59.087 50.000 0.00 0.00 0.00 4.30
41 42 2.239907 GACCATCCCTATAATGCCCTCC 59.760 54.545 0.00 0.00 0.00 4.30
42 43 2.157786 ACCATCCCTATAATGCCCTCCT 60.158 50.000 0.00 0.00 0.00 3.69
43 44 3.080619 ACCATCCCTATAATGCCCTCCTA 59.919 47.826 0.00 0.00 0.00 2.94
44 45 3.456277 CCATCCCTATAATGCCCTCCTAC 59.544 52.174 0.00 0.00 0.00 3.18
45 46 3.935240 TCCCTATAATGCCCTCCTACA 57.065 47.619 0.00 0.00 0.00 2.74
46 47 3.517612 TCCCTATAATGCCCTCCTACAC 58.482 50.000 0.00 0.00 0.00 2.90
47 48 3.116512 TCCCTATAATGCCCTCCTACACA 60.117 47.826 0.00 0.00 0.00 3.72
48 49 3.008049 CCCTATAATGCCCTCCTACACAC 59.992 52.174 0.00 0.00 0.00 3.82
49 50 3.008049 CCTATAATGCCCTCCTACACACC 59.992 52.174 0.00 0.00 0.00 4.16
50 51 1.209621 TAATGCCCTCCTACACACCC 58.790 55.000 0.00 0.00 0.00 4.61
51 52 0.550147 AATGCCCTCCTACACACCCT 60.550 55.000 0.00 0.00 0.00 4.34
52 53 1.274703 ATGCCCTCCTACACACCCTG 61.275 60.000 0.00 0.00 0.00 4.45
53 54 2.990479 CCCTCCTACACACCCTGC 59.010 66.667 0.00 0.00 0.00 4.85
54 55 1.613630 CCCTCCTACACACCCTGCT 60.614 63.158 0.00 0.00 0.00 4.24
55 56 0.325296 CCCTCCTACACACCCTGCTA 60.325 60.000 0.00 0.00 0.00 3.49
56 57 1.568504 CCTCCTACACACCCTGCTAA 58.431 55.000 0.00 0.00 0.00 3.09
57 58 1.207329 CCTCCTACACACCCTGCTAAC 59.793 57.143 0.00 0.00 0.00 2.34
58 59 2.180276 CTCCTACACACCCTGCTAACT 58.820 52.381 0.00 0.00 0.00 2.24
59 60 2.567615 CTCCTACACACCCTGCTAACTT 59.432 50.000 0.00 0.00 0.00 2.66
60 61 2.976882 TCCTACACACCCTGCTAACTTT 59.023 45.455 0.00 0.00 0.00 2.66
61 62 3.074412 CCTACACACCCTGCTAACTTTG 58.926 50.000 0.00 0.00 0.00 2.77
62 63 2.729028 ACACACCCTGCTAACTTTGT 57.271 45.000 0.00 0.00 0.00 2.83
63 64 3.849563 ACACACCCTGCTAACTTTGTA 57.150 42.857 0.00 0.00 0.00 2.41
64 65 3.740115 ACACACCCTGCTAACTTTGTAG 58.260 45.455 0.00 0.00 0.00 2.74
65 66 3.135895 ACACACCCTGCTAACTTTGTAGT 59.864 43.478 0.00 0.00 35.68 2.73
66 67 3.498397 CACACCCTGCTAACTTTGTAGTG 59.502 47.826 0.00 0.00 34.01 2.74
67 68 3.389983 ACACCCTGCTAACTTTGTAGTGA 59.610 43.478 0.00 0.00 34.01 3.41
68 69 3.997021 CACCCTGCTAACTTTGTAGTGAG 59.003 47.826 0.00 0.00 36.12 3.51
69 70 3.646637 ACCCTGCTAACTTTGTAGTGAGT 59.353 43.478 0.00 0.00 35.54 3.41
70 71 4.836736 ACCCTGCTAACTTTGTAGTGAGTA 59.163 41.667 0.00 0.00 35.54 2.59
71 72 5.169295 CCCTGCTAACTTTGTAGTGAGTAC 58.831 45.833 0.00 0.00 35.54 2.73
72 73 5.279306 CCCTGCTAACTTTGTAGTGAGTACA 60.279 44.000 0.00 0.00 40.06 2.90
82 83 6.665992 TTGTAGTGAGTACAAAGGATGAGT 57.334 37.500 10.26 0.00 46.60 3.41
83 84 6.665992 TGTAGTGAGTACAAAGGATGAGTT 57.334 37.500 0.00 0.00 38.78 3.01
84 85 7.770366 TGTAGTGAGTACAAAGGATGAGTTA 57.230 36.000 0.00 0.00 38.78 2.24
85 86 7.600065 TGTAGTGAGTACAAAGGATGAGTTAC 58.400 38.462 0.00 0.00 38.78 2.50
86 87 6.919775 AGTGAGTACAAAGGATGAGTTACT 57.080 37.500 0.00 0.00 0.00 2.24
87 88 6.926313 AGTGAGTACAAAGGATGAGTTACTC 58.074 40.000 5.27 5.27 36.44 2.59
88 89 6.722129 AGTGAGTACAAAGGATGAGTTACTCT 59.278 38.462 13.86 0.00 36.67 3.24
89 90 7.233757 AGTGAGTACAAAGGATGAGTTACTCTT 59.766 37.037 13.86 7.21 36.67 2.85
90 91 8.521176 GTGAGTACAAAGGATGAGTTACTCTTA 58.479 37.037 13.86 0.00 36.67 2.10
91 92 8.521176 TGAGTACAAAGGATGAGTTACTCTTAC 58.479 37.037 13.86 8.10 36.67 2.34
92 93 8.653036 AGTACAAAGGATGAGTTACTCTTACT 57.347 34.615 13.86 10.36 31.29 2.24
93 94 9.091220 AGTACAAAGGATGAGTTACTCTTACTT 57.909 33.333 16.94 16.94 39.49 2.24
94 95 9.708092 GTACAAAGGATGAGTTACTCTTACTTT 57.292 33.333 24.18 24.18 44.36 2.66
98 99 8.608844 AAGGATGAGTTACTCTTACTTTGTTG 57.391 34.615 16.94 0.00 35.98 3.33
99 100 7.736893 AGGATGAGTTACTCTTACTTTGTTGT 58.263 34.615 13.86 0.00 26.11 3.32
100 101 8.211629 AGGATGAGTTACTCTTACTTTGTTGTT 58.788 33.333 13.86 0.00 26.11 2.83
101 102 8.283291 GGATGAGTTACTCTTACTTTGTTGTTG 58.717 37.037 13.86 0.00 0.00 3.33
102 103 8.732746 ATGAGTTACTCTTACTTTGTTGTTGT 57.267 30.769 13.86 0.00 0.00 3.32
103 104 8.556213 TGAGTTACTCTTACTTTGTTGTTGTT 57.444 30.769 13.86 0.00 0.00 2.83
104 105 9.005777 TGAGTTACTCTTACTTTGTTGTTGTTT 57.994 29.630 13.86 0.00 0.00 2.83
105 106 9.486857 GAGTTACTCTTACTTTGTTGTTGTTTC 57.513 33.333 4.94 0.00 0.00 2.78
106 107 8.173130 AGTTACTCTTACTTTGTTGTTGTTTCG 58.827 33.333 0.00 0.00 0.00 3.46
107 108 6.730960 ACTCTTACTTTGTTGTTGTTTCGA 57.269 33.333 0.00 0.00 0.00 3.71
108 109 6.540205 ACTCTTACTTTGTTGTTGTTTCGAC 58.460 36.000 0.00 0.00 0.00 4.20
109 110 6.148150 ACTCTTACTTTGTTGTTGTTTCGACA 59.852 34.615 0.00 0.00 0.00 4.35
110 111 6.900189 TCTTACTTTGTTGTTGTTTCGACAA 58.100 32.000 0.00 0.00 39.17 3.18
111 112 7.531716 TCTTACTTTGTTGTTGTTTCGACAAT 58.468 30.769 5.95 0.00 39.53 2.71
112 113 8.666573 TCTTACTTTGTTGTTGTTTCGACAATA 58.333 29.630 5.95 1.47 39.53 1.90
113 114 9.445786 CTTACTTTGTTGTTGTTTCGACAATAT 57.554 29.630 5.95 0.00 39.53 1.28
114 115 7.678194 ACTTTGTTGTTGTTTCGACAATATG 57.322 32.000 5.95 3.54 39.53 1.78
115 116 7.254852 ACTTTGTTGTTGTTTCGACAATATGT 58.745 30.769 5.95 4.01 39.53 2.29
116 117 8.399425 ACTTTGTTGTTGTTTCGACAATATGTA 58.601 29.630 5.95 0.00 39.53 2.29
117 118 8.549777 TTTGTTGTTGTTTCGACAATATGTAC 57.450 30.769 5.95 0.00 39.53 2.90
118 119 7.247929 TGTTGTTGTTTCGACAATATGTACA 57.752 32.000 0.00 0.00 39.53 2.90
119 120 7.694886 TGTTGTTGTTTCGACAATATGTACAA 58.305 30.769 0.00 0.00 39.53 2.41
120 121 8.346300 TGTTGTTGTTTCGACAATATGTACAAT 58.654 29.630 0.00 0.00 39.53 2.71
121 122 8.626576 GTTGTTGTTTCGACAATATGTACAATG 58.373 33.333 0.00 2.25 39.53 2.82
122 123 7.866729 TGTTGTTTCGACAATATGTACAATGT 58.133 30.769 0.00 5.81 31.79 2.71
123 124 7.800847 TGTTGTTTCGACAATATGTACAATGTG 59.199 33.333 14.66 8.71 31.79 3.21
124 125 7.428282 TGTTTCGACAATATGTACAATGTGT 57.572 32.000 14.66 11.42 0.00 3.72
125 126 8.535690 TGTTTCGACAATATGTACAATGTGTA 57.464 30.769 14.66 0.00 0.00 2.90
126 127 9.157104 TGTTTCGACAATATGTACAATGTGTAT 57.843 29.630 14.66 0.00 35.05 2.29
127 128 9.420966 GTTTCGACAATATGTACAATGTGTATG 57.579 33.333 14.66 8.47 35.05 2.39
128 129 8.934507 TTCGACAATATGTACAATGTGTATGA 57.065 30.769 14.66 10.12 35.05 2.15
129 130 9.541143 TTCGACAATATGTACAATGTGTATGAT 57.459 29.630 14.66 0.00 35.05 2.45
139 140 9.981114 TGTACAATGTGTATGATATGTCCTTAG 57.019 33.333 0.00 0.00 35.05 2.18
153 154 4.142609 GTCCTTAGACATGAGAATGCCA 57.857 45.455 0.00 0.00 42.99 4.92
154 155 4.712476 GTCCTTAGACATGAGAATGCCAT 58.288 43.478 0.00 0.00 42.99 4.40
155 156 5.858381 GTCCTTAGACATGAGAATGCCATA 58.142 41.667 0.00 0.00 42.99 2.74
156 157 6.471146 GTCCTTAGACATGAGAATGCCATAT 58.529 40.000 0.00 0.00 42.99 1.78
157 158 6.370994 GTCCTTAGACATGAGAATGCCATATG 59.629 42.308 0.00 0.00 42.99 1.78
158 159 6.043590 TCCTTAGACATGAGAATGCCATATGT 59.956 38.462 0.00 0.00 34.91 2.29
159 160 7.235399 TCCTTAGACATGAGAATGCCATATGTA 59.765 37.037 0.00 0.00 32.58 2.29
160 161 7.332926 CCTTAGACATGAGAATGCCATATGTAC 59.667 40.741 0.00 0.00 32.58 2.90
161 162 5.555017 AGACATGAGAATGCCATATGTACC 58.445 41.667 0.00 0.00 32.58 3.34
162 163 4.655963 ACATGAGAATGCCATATGTACCC 58.344 43.478 0.00 0.00 30.79 3.69
163 164 4.352001 ACATGAGAATGCCATATGTACCCT 59.648 41.667 0.00 0.00 30.79 4.34
164 165 5.163055 ACATGAGAATGCCATATGTACCCTT 60.163 40.000 0.00 0.00 30.79 3.95
165 166 5.387113 TGAGAATGCCATATGTACCCTTT 57.613 39.130 1.24 0.00 0.00 3.11
166 167 5.376625 TGAGAATGCCATATGTACCCTTTC 58.623 41.667 1.24 2.30 0.00 2.62
167 168 5.132648 TGAGAATGCCATATGTACCCTTTCT 59.867 40.000 1.24 6.42 0.00 2.52
168 169 6.328934 TGAGAATGCCATATGTACCCTTTCTA 59.671 38.462 1.24 0.00 0.00 2.10
169 170 7.017551 TGAGAATGCCATATGTACCCTTTCTAT 59.982 37.037 1.24 0.00 0.00 1.98
170 171 8.449423 AGAATGCCATATGTACCCTTTCTATA 57.551 34.615 1.24 0.00 0.00 1.31
171 172 9.062367 AGAATGCCATATGTACCCTTTCTATAT 57.938 33.333 1.24 0.00 0.00 0.86
175 176 8.210946 TGCCATATGTACCCTTTCTATATATGC 58.789 37.037 1.24 0.00 30.17 3.14
176 177 8.210946 GCCATATGTACCCTTTCTATATATGCA 58.789 37.037 1.24 0.00 30.17 3.96
181 182 9.672673 ATGTACCCTTTCTATATATGCATGAAC 57.327 33.333 10.16 0.00 0.00 3.18
182 183 8.655901 TGTACCCTTTCTATATATGCATGAACA 58.344 33.333 10.16 0.00 0.00 3.18
183 184 9.672673 GTACCCTTTCTATATATGCATGAACAT 57.327 33.333 10.16 0.00 0.00 2.71
192 193 9.675553 CTATATATGCATGAACATAAAACGTCG 57.324 33.333 10.16 0.00 36.17 5.12
193 194 2.845486 TGCATGAACATAAAACGTCGC 58.155 42.857 0.00 0.00 0.00 5.19
194 195 2.224314 TGCATGAACATAAAACGTCGCA 59.776 40.909 0.00 0.00 0.00 5.10
195 196 2.588106 GCATGAACATAAAACGTCGCAC 59.412 45.455 0.00 0.00 0.00 5.34
197 198 2.125685 TGAACATAAAACGTCGCACGA 58.874 42.857 14.18 0.00 46.05 4.35
198 199 2.097299 TGAACATAAAACGTCGCACGAC 60.097 45.455 13.02 13.02 46.05 4.34
199 200 1.774639 ACATAAAACGTCGCACGACT 58.225 45.000 19.74 4.93 46.05 4.18
200 201 2.932498 ACATAAAACGTCGCACGACTA 58.068 42.857 19.74 6.93 46.05 2.59
201 202 3.307674 ACATAAAACGTCGCACGACTAA 58.692 40.909 19.74 2.66 46.05 2.24
202 203 3.735240 ACATAAAACGTCGCACGACTAAA 59.265 39.130 19.74 2.98 46.05 1.85
203 204 4.208873 ACATAAAACGTCGCACGACTAAAA 59.791 37.500 19.74 3.62 46.05 1.52
204 205 3.654952 AAAACGTCGCACGACTAAAAA 57.345 38.095 19.74 0.00 46.05 1.94
205 206 2.916735 AACGTCGCACGACTAAAAAG 57.083 45.000 19.74 6.77 46.05 2.27
206 207 0.505655 ACGTCGCACGACTAAAAAGC 59.494 50.000 19.74 0.00 46.05 3.51
207 208 0.782384 CGTCGCACGACTAAAAAGCT 59.218 50.000 19.74 0.00 46.05 3.74
208 209 1.980844 CGTCGCACGACTAAAAAGCTA 59.019 47.619 19.74 0.00 46.05 3.32
209 210 2.597305 CGTCGCACGACTAAAAAGCTAT 59.403 45.455 19.74 0.00 46.05 2.97
210 211 3.060363 CGTCGCACGACTAAAAAGCTATT 59.940 43.478 19.74 0.00 46.05 1.73
211 212 4.323751 GTCGCACGACTAAAAAGCTATTG 58.676 43.478 15.56 0.00 41.57 1.90
212 213 3.091417 CGCACGACTAAAAAGCTATTGC 58.909 45.455 0.00 0.00 40.05 3.56
213 214 3.424302 CGCACGACTAAAAAGCTATTGCA 60.424 43.478 1.12 0.00 42.74 4.08
214 215 4.662145 GCACGACTAAAAAGCTATTGCAT 58.338 39.130 1.12 0.00 42.74 3.96
215 216 5.095490 GCACGACTAAAAAGCTATTGCATT 58.905 37.500 1.12 0.00 42.74 3.56
216 217 5.228012 GCACGACTAAAAAGCTATTGCATTC 59.772 40.000 1.12 0.00 42.74 2.67
217 218 6.546395 CACGACTAAAAAGCTATTGCATTCT 58.454 36.000 1.12 0.00 42.74 2.40
218 219 6.684555 CACGACTAAAAAGCTATTGCATTCTC 59.315 38.462 1.12 0.00 42.74 2.87
219 220 6.595716 ACGACTAAAAAGCTATTGCATTCTCT 59.404 34.615 1.12 0.00 42.74 3.10
220 221 7.119846 ACGACTAAAAAGCTATTGCATTCTCTT 59.880 33.333 1.12 0.00 42.74 2.85
221 222 7.965107 CGACTAAAAAGCTATTGCATTCTCTTT 59.035 33.333 1.12 0.00 42.74 2.52
222 223 9.631452 GACTAAAAAGCTATTGCATTCTCTTTT 57.369 29.630 1.12 11.65 42.74 2.27
223 224 9.987272 ACTAAAAAGCTATTGCATTCTCTTTTT 57.013 25.926 22.57 22.57 42.61 1.94
225 226 8.667076 AAAAAGCTATTGCATTCTCTTTTTGT 57.333 26.923 20.53 8.35 40.23 2.83
226 227 8.667076 AAAAGCTATTGCATTCTCTTTTTGTT 57.333 26.923 1.12 0.00 42.74 2.83
227 228 8.667076 AAAGCTATTGCATTCTCTTTTTGTTT 57.333 26.923 1.12 0.00 42.74 2.83
228 229 9.762933 AAAGCTATTGCATTCTCTTTTTGTTTA 57.237 25.926 1.12 0.00 42.74 2.01
229 230 9.933723 AAGCTATTGCATTCTCTTTTTGTTTAT 57.066 25.926 1.12 0.00 42.74 1.40
234 235 8.532977 TTGCATTCTCTTTTTGTTTATAAGGC 57.467 30.769 0.00 0.00 0.00 4.35
235 236 7.665690 TGCATTCTCTTTTTGTTTATAAGGCA 58.334 30.769 0.00 0.00 0.00 4.75
236 237 8.313292 TGCATTCTCTTTTTGTTTATAAGGCAT 58.687 29.630 0.00 0.00 0.00 4.40
237 238 8.598075 GCATTCTCTTTTTGTTTATAAGGCATG 58.402 33.333 0.00 0.00 0.00 4.06
238 239 9.643693 CATTCTCTTTTTGTTTATAAGGCATGT 57.356 29.630 0.00 0.00 0.00 3.21
253 254 8.978874 ATAAGGCATGTATGTTTAGAATGTGA 57.021 30.769 0.00 0.00 0.00 3.58
254 255 7.701539 AAGGCATGTATGTTTAGAATGTGAA 57.298 32.000 0.00 0.00 0.00 3.18
255 256 7.886629 AGGCATGTATGTTTAGAATGTGAAT 57.113 32.000 0.00 0.00 0.00 2.57
256 257 7.934457 AGGCATGTATGTTTAGAATGTGAATC 58.066 34.615 0.00 0.00 0.00 2.52
257 258 7.013655 AGGCATGTATGTTTAGAATGTGAATCC 59.986 37.037 0.00 0.00 0.00 3.01
258 259 7.201812 GGCATGTATGTTTAGAATGTGAATCCA 60.202 37.037 0.00 0.00 0.00 3.41
259 260 8.190122 GCATGTATGTTTAGAATGTGAATCCAA 58.810 33.333 0.00 0.00 0.00 3.53
290 291 9.309516 AGTATAATACACGGACAAGTACATTTG 57.690 33.333 0.00 0.00 0.00 2.32
291 292 5.873179 AATACACGGACAAGTACATTTGG 57.127 39.130 0.00 0.00 32.32 3.28
292 293 1.877443 ACACGGACAAGTACATTTGGC 59.123 47.619 0.00 0.00 35.26 4.52
293 294 2.151202 CACGGACAAGTACATTTGGCT 58.849 47.619 0.00 0.00 36.31 4.75
294 295 2.552315 CACGGACAAGTACATTTGGCTT 59.448 45.455 0.00 0.00 36.31 4.35
295 296 3.004315 CACGGACAAGTACATTTGGCTTT 59.996 43.478 0.00 0.00 36.31 3.51
296 297 3.252458 ACGGACAAGTACATTTGGCTTTC 59.748 43.478 0.00 0.00 36.31 2.62
297 298 3.666902 CGGACAAGTACATTTGGCTTTCG 60.667 47.826 0.00 0.00 36.31 3.46
298 299 3.365969 GGACAAGTACATTTGGCTTTCGG 60.366 47.826 0.00 0.00 36.31 4.30
299 300 2.556622 ACAAGTACATTTGGCTTTCGGG 59.443 45.455 0.00 0.00 32.32 5.14
300 301 2.556622 CAAGTACATTTGGCTTTCGGGT 59.443 45.455 0.00 0.00 0.00 5.28
301 302 2.159382 AGTACATTTGGCTTTCGGGTG 58.841 47.619 0.00 0.00 0.00 4.61
302 303 1.883926 GTACATTTGGCTTTCGGGTGT 59.116 47.619 0.00 0.00 0.00 4.16
303 304 2.279935 ACATTTGGCTTTCGGGTGTA 57.720 45.000 0.00 0.00 0.00 2.90
304 305 2.802719 ACATTTGGCTTTCGGGTGTAT 58.197 42.857 0.00 0.00 0.00 2.29
305 306 3.958018 ACATTTGGCTTTCGGGTGTATA 58.042 40.909 0.00 0.00 0.00 1.47
306 307 4.532834 ACATTTGGCTTTCGGGTGTATAT 58.467 39.130 0.00 0.00 0.00 0.86
307 308 4.338118 ACATTTGGCTTTCGGGTGTATATG 59.662 41.667 0.00 0.00 0.00 1.78
308 309 1.961793 TGGCTTTCGGGTGTATATGC 58.038 50.000 0.00 0.00 0.00 3.14
309 310 1.210722 TGGCTTTCGGGTGTATATGCA 59.789 47.619 0.00 0.00 0.00 3.96
310 311 1.873591 GGCTTTCGGGTGTATATGCAG 59.126 52.381 0.00 0.00 0.00 4.41
311 312 1.264288 GCTTTCGGGTGTATATGCAGC 59.736 52.381 13.85 13.85 36.26 5.25
312 313 2.838736 CTTTCGGGTGTATATGCAGCT 58.161 47.619 20.11 0.00 37.09 4.24
313 314 2.238942 TTCGGGTGTATATGCAGCTG 57.761 50.000 21.64 21.64 42.67 4.24
314 315 0.392706 TCGGGTGTATATGCAGCTGG 59.607 55.000 25.39 16.35 41.89 4.85
315 316 0.106708 CGGGTGTATATGCAGCTGGT 59.893 55.000 20.37 0.00 38.99 4.00
316 317 1.343142 CGGGTGTATATGCAGCTGGTA 59.657 52.381 20.37 0.00 38.99 3.25
317 318 2.028112 CGGGTGTATATGCAGCTGGTAT 60.028 50.000 20.37 4.00 38.99 2.73
318 319 3.338249 GGGTGTATATGCAGCTGGTATG 58.662 50.000 20.11 0.00 37.09 2.39
319 320 3.007940 GGGTGTATATGCAGCTGGTATGA 59.992 47.826 20.11 0.00 37.09 2.15
320 321 4.504864 GGGTGTATATGCAGCTGGTATGAA 60.505 45.833 20.11 0.00 37.09 2.57
321 322 5.063204 GGTGTATATGCAGCTGGTATGAAA 58.937 41.667 17.12 0.00 34.39 2.69
322 323 5.530915 GGTGTATATGCAGCTGGTATGAAAA 59.469 40.000 17.12 0.00 34.39 2.29
323 324 6.039270 GGTGTATATGCAGCTGGTATGAAAAA 59.961 38.462 17.12 0.00 34.39 1.94
324 325 7.134815 GTGTATATGCAGCTGGTATGAAAAAG 58.865 38.462 17.12 0.00 0.00 2.27
325 326 7.012327 GTGTATATGCAGCTGGTATGAAAAAGA 59.988 37.037 17.12 0.00 0.00 2.52
326 327 7.720957 TGTATATGCAGCTGGTATGAAAAAGAT 59.279 33.333 17.12 0.00 0.00 2.40
327 328 9.219603 GTATATGCAGCTGGTATGAAAAAGATA 57.780 33.333 17.12 0.00 0.00 1.98
328 329 8.696043 ATATGCAGCTGGTATGAAAAAGATAA 57.304 30.769 17.12 0.00 0.00 1.75
329 330 7.592885 ATGCAGCTGGTATGAAAAAGATAAT 57.407 32.000 17.12 0.00 0.00 1.28
330 331 7.408756 TGCAGCTGGTATGAAAAAGATAATT 57.591 32.000 17.12 0.00 0.00 1.40
331 332 7.839907 TGCAGCTGGTATGAAAAAGATAATTT 58.160 30.769 17.12 0.00 0.00 1.82
332 333 8.965819 TGCAGCTGGTATGAAAAAGATAATTTA 58.034 29.630 17.12 0.00 0.00 1.40
333 334 9.237846 GCAGCTGGTATGAAAAAGATAATTTAC 57.762 33.333 17.12 0.00 0.00 2.01
390 394 9.865321 ACTTCTTTAAAACAAACTTAACCTTCC 57.135 29.630 0.00 0.00 0.00 3.46
391 395 8.914328 TTCTTTAAAACAAACTTAACCTTCCG 57.086 30.769 0.00 0.00 0.00 4.30
402 406 4.746611 ACTTAACCTTCCGTTTTACTCGTG 59.253 41.667 0.00 0.00 35.79 4.35
432 438 6.644347 ACCTTACTCATTCAAATCGTGATCT 58.356 36.000 0.00 0.00 35.70 2.75
445 451 4.690184 TCGTGATCTGCGTTAACTAGAA 57.310 40.909 11.80 0.00 0.00 2.10
448 454 5.515270 TCGTGATCTGCGTTAACTAGAATTG 59.485 40.000 11.80 5.16 0.00 2.32
522 531 4.239304 CAATGCAGCATCTGTAAAAAGCA 58.761 39.130 8.77 0.00 33.43 3.91
775 818 4.020128 CAGTTCTTGTACCCTTCCTTAGCT 60.020 45.833 0.00 0.00 0.00 3.32
936 984 0.039764 ACAGGTCGGATCAGAGGTCA 59.960 55.000 0.00 0.00 0.00 4.02
951 999 0.388649 GGTCAGAGCACGTGTACAGG 60.389 60.000 18.38 13.84 0.00 4.00
953 1001 1.538512 GTCAGAGCACGTGTACAGGTA 59.461 52.381 19.99 1.85 0.00 3.08
998 1046 3.955291 CGAGAGGATCATCGCTTGT 57.045 52.632 9.40 0.00 37.82 3.16
1008 1056 1.078709 CATCGCTTGTCATGAACGGT 58.921 50.000 0.00 0.00 0.00 4.83
1743 1798 5.413309 AATTCGGATTTTAACCATGGCAA 57.587 34.783 13.04 3.06 0.00 4.52
1777 1833 0.746204 TGGCAACTTGAGTTCACGCA 60.746 50.000 6.91 0.00 35.83 5.24
1880 1937 4.793071 TCGTGTCAACTAAAATTGCCATG 58.207 39.130 0.00 0.00 0.00 3.66
1920 1977 5.116069 ACATGCTTAAAATCCGAACGTTT 57.884 34.783 0.46 0.00 0.00 3.60
1924 1981 3.828786 CTTAAAATCCGAACGTTTGGGG 58.171 45.455 30.12 18.60 32.26 4.96
1931 1988 2.152830 CCGAACGTTTGGGGTTTATCA 58.847 47.619 24.79 0.00 0.00 2.15
1939 1996 1.974028 TGGGGTTTATCAGGCCACTA 58.026 50.000 5.01 0.00 0.00 2.74
2121 2178 9.872757 TTTTTATATATTTGAAATCTCGGCGAC 57.127 29.630 4.99 0.00 0.00 5.19
2212 2269 7.878036 AGTACGGCAAACACTTTATACATTTT 58.122 30.769 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.809546 TGGTCATTGTACAGTGACAAAATTA 57.190 32.000 37.05 20.66 46.07 1.40
1 2 6.707440 TGGTCATTGTACAGTGACAAAATT 57.293 33.333 37.05 0.00 46.07 1.82
2 3 6.071952 GGATGGTCATTGTACAGTGACAAAAT 60.072 38.462 37.05 29.31 46.07 1.82
3 4 5.240623 GGATGGTCATTGTACAGTGACAAAA 59.759 40.000 37.05 27.03 46.07 2.44
4 5 4.759693 GGATGGTCATTGTACAGTGACAAA 59.240 41.667 37.05 28.87 46.07 2.83
5 6 4.323417 GGATGGTCATTGTACAGTGACAA 58.677 43.478 37.05 31.85 46.07 3.18
6 7 3.307410 GGGATGGTCATTGTACAGTGACA 60.307 47.826 37.05 27.56 46.07 3.58
7 8 3.055094 AGGGATGGTCATTGTACAGTGAC 60.055 47.826 32.36 32.36 44.30 3.67
8 9 3.181329 AGGGATGGTCATTGTACAGTGA 58.819 45.455 16.33 16.33 0.00 3.41
9 10 3.634397 AGGGATGGTCATTGTACAGTG 57.366 47.619 11.91 11.91 0.00 3.66
10 11 7.453393 CATTATAGGGATGGTCATTGTACAGT 58.547 38.462 0.00 0.00 0.00 3.55
11 12 6.372659 GCATTATAGGGATGGTCATTGTACAG 59.627 42.308 0.00 0.00 0.00 2.74
12 13 6.237901 GCATTATAGGGATGGTCATTGTACA 58.762 40.000 0.00 0.00 0.00 2.90
13 14 5.648092 GGCATTATAGGGATGGTCATTGTAC 59.352 44.000 0.00 0.00 0.00 2.90
14 15 5.280985 GGGCATTATAGGGATGGTCATTGTA 60.281 44.000 0.00 0.00 0.00 2.41
15 16 4.509122 GGGCATTATAGGGATGGTCATTGT 60.509 45.833 0.00 0.00 0.00 2.71
16 17 4.019174 GGGCATTATAGGGATGGTCATTG 58.981 47.826 0.00 0.00 0.00 2.82
17 18 3.925370 AGGGCATTATAGGGATGGTCATT 59.075 43.478 0.00 0.00 0.00 2.57
18 19 3.525199 GAGGGCATTATAGGGATGGTCAT 59.475 47.826 0.00 0.00 0.00 3.06
19 20 2.912956 GAGGGCATTATAGGGATGGTCA 59.087 50.000 0.00 0.00 0.00 4.02
20 21 2.239907 GGAGGGCATTATAGGGATGGTC 59.760 54.545 0.00 0.00 0.00 4.02
21 22 2.157786 AGGAGGGCATTATAGGGATGGT 60.158 50.000 0.00 0.00 0.00 3.55
22 23 2.566746 AGGAGGGCATTATAGGGATGG 58.433 52.381 0.00 0.00 0.00 3.51
23 24 4.080863 GTGTAGGAGGGCATTATAGGGATG 60.081 50.000 0.00 0.00 0.00 3.51
24 25 4.104831 GTGTAGGAGGGCATTATAGGGAT 58.895 47.826 0.00 0.00 0.00 3.85
25 26 3.116512 TGTGTAGGAGGGCATTATAGGGA 60.117 47.826 0.00 0.00 0.00 4.20
26 27 3.008049 GTGTGTAGGAGGGCATTATAGGG 59.992 52.174 0.00 0.00 0.00 3.53
27 28 3.008049 GGTGTGTAGGAGGGCATTATAGG 59.992 52.174 0.00 0.00 0.00 2.57
28 29 3.008049 GGGTGTGTAGGAGGGCATTATAG 59.992 52.174 0.00 0.00 0.00 1.31
29 30 2.976882 GGGTGTGTAGGAGGGCATTATA 59.023 50.000 0.00 0.00 0.00 0.98
30 31 1.774856 GGGTGTGTAGGAGGGCATTAT 59.225 52.381 0.00 0.00 0.00 1.28
31 32 1.209621 GGGTGTGTAGGAGGGCATTA 58.790 55.000 0.00 0.00 0.00 1.90
32 33 0.550147 AGGGTGTGTAGGAGGGCATT 60.550 55.000 0.00 0.00 0.00 3.56
33 34 1.082954 AGGGTGTGTAGGAGGGCAT 59.917 57.895 0.00 0.00 0.00 4.40
34 35 1.918293 CAGGGTGTGTAGGAGGGCA 60.918 63.158 0.00 0.00 0.00 5.36
35 36 2.990479 CAGGGTGTGTAGGAGGGC 59.010 66.667 0.00 0.00 0.00 5.19
36 37 0.325296 TAGCAGGGTGTGTAGGAGGG 60.325 60.000 0.00 0.00 0.00 4.30
37 38 1.207329 GTTAGCAGGGTGTGTAGGAGG 59.793 57.143 0.00 0.00 0.00 4.30
38 39 2.180276 AGTTAGCAGGGTGTGTAGGAG 58.820 52.381 0.00 0.00 0.00 3.69
39 40 2.320681 AGTTAGCAGGGTGTGTAGGA 57.679 50.000 0.00 0.00 0.00 2.94
40 41 3.074412 CAAAGTTAGCAGGGTGTGTAGG 58.926 50.000 0.00 0.00 0.00 3.18
41 42 3.740115 ACAAAGTTAGCAGGGTGTGTAG 58.260 45.455 0.00 0.00 0.00 2.74
42 43 3.849563 ACAAAGTTAGCAGGGTGTGTA 57.150 42.857 0.00 0.00 0.00 2.90
43 44 2.729028 ACAAAGTTAGCAGGGTGTGT 57.271 45.000 0.00 0.00 0.00 3.72
44 45 3.498397 CACTACAAAGTTAGCAGGGTGTG 59.502 47.826 0.00 0.00 31.97 3.82
45 46 3.389983 TCACTACAAAGTTAGCAGGGTGT 59.610 43.478 0.00 0.00 31.97 4.16
46 47 3.997021 CTCACTACAAAGTTAGCAGGGTG 59.003 47.826 0.00 0.00 31.97 4.61
47 48 3.646637 ACTCACTACAAAGTTAGCAGGGT 59.353 43.478 0.00 0.00 31.25 4.34
48 49 4.273148 ACTCACTACAAAGTTAGCAGGG 57.727 45.455 0.00 0.00 31.25 4.45
49 50 5.779922 TGTACTCACTACAAAGTTAGCAGG 58.220 41.667 0.00 0.00 31.25 4.85
50 51 7.709269 TTTGTACTCACTACAAAGTTAGCAG 57.291 36.000 2.26 0.00 46.19 4.24
59 60 6.665992 ACTCATCCTTTGTACTCACTACAA 57.334 37.500 0.00 0.00 42.57 2.41
60 61 6.665992 AACTCATCCTTTGTACTCACTACA 57.334 37.500 0.00 0.00 33.18 2.74
61 62 7.828712 AGTAACTCATCCTTTGTACTCACTAC 58.171 38.462 0.00 0.00 0.00 2.73
62 63 7.889073 AGAGTAACTCATCCTTTGTACTCACTA 59.111 37.037 10.35 0.00 36.20 2.74
63 64 6.722129 AGAGTAACTCATCCTTTGTACTCACT 59.278 38.462 10.35 0.00 36.20 3.41
64 65 6.926313 AGAGTAACTCATCCTTTGTACTCAC 58.074 40.000 10.35 0.00 36.20 3.51
65 66 7.540474 AAGAGTAACTCATCCTTTGTACTCA 57.460 36.000 10.35 0.00 36.20 3.41
66 67 8.741841 AGTAAGAGTAACTCATCCTTTGTACTC 58.258 37.037 0.00 0.00 34.55 2.59
67 68 8.653036 AGTAAGAGTAACTCATCCTTTGTACT 57.347 34.615 0.00 0.00 32.06 2.73
68 69 9.708092 AAAGTAAGAGTAACTCATCCTTTGTAC 57.292 33.333 0.00 0.00 32.06 2.90
69 70 9.706691 CAAAGTAAGAGTAACTCATCCTTTGTA 57.293 33.333 13.80 0.00 36.66 2.41
70 71 8.211629 ACAAAGTAAGAGTAACTCATCCTTTGT 58.788 33.333 18.52 18.52 42.07 2.83
71 72 8.608844 ACAAAGTAAGAGTAACTCATCCTTTG 57.391 34.615 17.64 17.64 41.08 2.77
72 73 9.057089 CAACAAAGTAAGAGTAACTCATCCTTT 57.943 33.333 0.00 0.00 32.06 3.11
73 74 8.211629 ACAACAAAGTAAGAGTAACTCATCCTT 58.788 33.333 0.00 0.00 32.06 3.36
74 75 7.736893 ACAACAAAGTAAGAGTAACTCATCCT 58.263 34.615 0.00 0.00 32.06 3.24
75 76 7.964604 ACAACAAAGTAAGAGTAACTCATCC 57.035 36.000 0.00 0.00 32.06 3.51
76 77 8.827677 ACAACAACAAAGTAAGAGTAACTCATC 58.172 33.333 0.00 0.00 32.06 2.92
77 78 8.732746 ACAACAACAAAGTAAGAGTAACTCAT 57.267 30.769 0.00 0.00 32.06 2.90
78 79 8.556213 AACAACAACAAAGTAAGAGTAACTCA 57.444 30.769 0.00 0.00 32.06 3.41
79 80 9.486857 GAAACAACAACAAAGTAAGAGTAACTC 57.513 33.333 0.00 0.00 0.00 3.01
80 81 8.173130 CGAAACAACAACAAAGTAAGAGTAACT 58.827 33.333 0.00 0.00 0.00 2.24
81 82 8.170553 TCGAAACAACAACAAAGTAAGAGTAAC 58.829 33.333 0.00 0.00 0.00 2.50
82 83 8.170553 GTCGAAACAACAACAAAGTAAGAGTAA 58.829 33.333 0.00 0.00 0.00 2.24
83 84 7.331440 TGTCGAAACAACAACAAAGTAAGAGTA 59.669 33.333 0.00 0.00 30.70 2.59
84 85 6.148150 TGTCGAAACAACAACAAAGTAAGAGT 59.852 34.615 0.00 0.00 30.70 3.24
85 86 6.539324 TGTCGAAACAACAACAAAGTAAGAG 58.461 36.000 0.00 0.00 30.70 2.85
86 87 6.483385 TGTCGAAACAACAACAAAGTAAGA 57.517 33.333 0.00 0.00 30.70 2.10
100 101 7.428282 ACACATTGTACATATTGTCGAAACA 57.572 32.000 0.00 0.00 0.00 2.83
101 102 9.420966 CATACACATTGTACATATTGTCGAAAC 57.579 33.333 0.00 0.00 35.42 2.78
102 103 9.372369 TCATACACATTGTACATATTGTCGAAA 57.628 29.630 0.00 0.00 35.42 3.46
103 104 8.934507 TCATACACATTGTACATATTGTCGAA 57.065 30.769 0.00 0.00 35.42 3.71
113 114 9.981114 CTAAGGACATATCATACACATTGTACA 57.019 33.333 0.00 0.00 35.42 2.90
116 117 8.704668 TGTCTAAGGACATATCATACACATTGT 58.295 33.333 0.00 0.00 46.19 2.71
132 133 4.142609 TGGCATTCTCATGTCTAAGGAC 57.857 45.455 0.00 0.00 42.42 3.85
133 134 6.043590 ACATATGGCATTCTCATGTCTAAGGA 59.956 38.462 4.78 0.00 35.84 3.36
134 135 6.236409 ACATATGGCATTCTCATGTCTAAGG 58.764 40.000 4.78 0.00 35.84 2.69
135 136 7.332926 GGTACATATGGCATTCTCATGTCTAAG 59.667 40.741 15.00 0.00 35.84 2.18
136 137 7.161404 GGTACATATGGCATTCTCATGTCTAA 58.839 38.462 15.00 0.00 35.84 2.10
137 138 6.295859 GGGTACATATGGCATTCTCATGTCTA 60.296 42.308 15.00 0.00 35.84 2.59
138 139 5.513788 GGGTACATATGGCATTCTCATGTCT 60.514 44.000 15.00 0.00 35.84 3.41
139 140 4.697352 GGGTACATATGGCATTCTCATGTC 59.303 45.833 15.00 8.59 35.34 3.06
140 141 4.352001 AGGGTACATATGGCATTCTCATGT 59.648 41.667 15.67 15.67 34.40 3.21
141 142 4.914983 AGGGTACATATGGCATTCTCATG 58.085 43.478 4.78 5.82 0.00 3.07
142 143 5.589367 AAGGGTACATATGGCATTCTCAT 57.411 39.130 4.78 0.00 0.00 2.90
143 144 5.132648 AGAAAGGGTACATATGGCATTCTCA 59.867 40.000 4.78 0.00 0.00 3.27
144 145 5.625150 AGAAAGGGTACATATGGCATTCTC 58.375 41.667 4.78 0.00 0.00 2.87
145 146 5.653255 AGAAAGGGTACATATGGCATTCT 57.347 39.130 4.78 5.38 0.00 2.40
149 150 8.210946 GCATATATAGAAAGGGTACATATGGCA 58.789 37.037 7.80 0.00 0.00 4.92
150 151 8.210946 TGCATATATAGAAAGGGTACATATGGC 58.789 37.037 7.80 0.00 0.00 4.40
155 156 9.672673 GTTCATGCATATATAGAAAGGGTACAT 57.327 33.333 0.00 0.00 0.00 2.29
156 157 8.655901 TGTTCATGCATATATAGAAAGGGTACA 58.344 33.333 0.00 0.00 0.00 2.90
157 158 9.672673 ATGTTCATGCATATATAGAAAGGGTAC 57.327 33.333 0.00 0.00 0.00 3.34
166 167 9.675553 CGACGTTTTATGTTCATGCATATATAG 57.324 33.333 0.00 0.00 32.16 1.31
167 168 8.166066 GCGACGTTTTATGTTCATGCATATATA 58.834 33.333 0.00 0.00 32.16 0.86
168 169 7.015289 GCGACGTTTTATGTTCATGCATATAT 58.985 34.615 0.00 0.00 32.16 0.86
169 170 6.018669 TGCGACGTTTTATGTTCATGCATATA 60.019 34.615 0.00 0.00 32.16 0.86
170 171 5.204833 GCGACGTTTTATGTTCATGCATAT 58.795 37.500 0.00 0.00 32.16 1.78
171 172 4.093556 TGCGACGTTTTATGTTCATGCATA 59.906 37.500 0.00 0.00 0.00 3.14
172 173 3.120025 TGCGACGTTTTATGTTCATGCAT 60.120 39.130 0.00 0.00 0.00 3.96
173 174 2.224314 TGCGACGTTTTATGTTCATGCA 59.776 40.909 0.00 0.00 0.00 3.96
174 175 2.588106 GTGCGACGTTTTATGTTCATGC 59.412 45.455 0.00 0.00 0.00 4.06
175 176 2.832178 CGTGCGACGTTTTATGTTCATG 59.168 45.455 0.00 0.00 36.74 3.07
176 177 2.732500 TCGTGCGACGTTTTATGTTCAT 59.267 40.909 8.22 0.00 43.14 2.57
177 178 2.097299 GTCGTGCGACGTTTTATGTTCA 60.097 45.455 9.00 0.00 43.14 3.18
178 179 2.479328 GTCGTGCGACGTTTTATGTTC 58.521 47.619 9.00 0.00 43.14 3.18
179 180 2.565367 GTCGTGCGACGTTTTATGTT 57.435 45.000 9.00 0.00 43.14 2.71
189 190 4.323751 CAATAGCTTTTTAGTCGTGCGAC 58.676 43.478 15.92 15.92 44.86 5.19
190 191 3.181524 GCAATAGCTTTTTAGTCGTGCGA 60.182 43.478 0.00 0.00 37.91 5.10
191 192 3.091417 GCAATAGCTTTTTAGTCGTGCG 58.909 45.455 0.00 0.00 37.91 5.34
192 193 4.078363 TGCAATAGCTTTTTAGTCGTGC 57.922 40.909 0.00 0.00 42.74 5.34
193 194 6.546395 AGAATGCAATAGCTTTTTAGTCGTG 58.454 36.000 0.00 0.00 42.74 4.35
194 195 6.595716 AGAGAATGCAATAGCTTTTTAGTCGT 59.404 34.615 0.00 0.00 42.74 4.34
195 196 7.009568 AGAGAATGCAATAGCTTTTTAGTCG 57.990 36.000 0.00 0.00 42.74 4.18
196 197 9.631452 AAAAGAGAATGCAATAGCTTTTTAGTC 57.369 29.630 12.19 0.00 42.74 2.59
197 198 9.987272 AAAAAGAGAATGCAATAGCTTTTTAGT 57.013 25.926 21.48 7.73 38.29 2.24
199 200 9.762933 ACAAAAAGAGAATGCAATAGCTTTTTA 57.237 25.926 21.96 0.00 38.15 1.52
200 201 8.667076 ACAAAAAGAGAATGCAATAGCTTTTT 57.333 26.923 19.14 19.14 39.45 1.94
201 202 8.667076 AACAAAAAGAGAATGCAATAGCTTTT 57.333 26.923 12.19 12.19 42.74 2.27
202 203 8.667076 AAACAAAAAGAGAATGCAATAGCTTT 57.333 26.923 0.00 0.00 42.74 3.51
203 204 9.933723 ATAAACAAAAAGAGAATGCAATAGCTT 57.066 25.926 0.00 0.00 42.74 3.74
208 209 9.154847 GCCTTATAAACAAAAAGAGAATGCAAT 57.845 29.630 0.00 0.00 0.00 3.56
209 210 8.147058 TGCCTTATAAACAAAAAGAGAATGCAA 58.853 29.630 0.00 0.00 0.00 4.08
210 211 7.665690 TGCCTTATAAACAAAAAGAGAATGCA 58.334 30.769 0.00 0.00 0.00 3.96
211 212 8.598075 CATGCCTTATAAACAAAAAGAGAATGC 58.402 33.333 0.00 0.00 0.00 3.56
212 213 9.643693 ACATGCCTTATAAACAAAAAGAGAATG 57.356 29.630 0.00 0.00 0.00 2.67
228 229 8.978874 TCACATTCTAAACATACATGCCTTAT 57.021 30.769 0.00 0.00 0.00 1.73
229 230 8.800370 TTCACATTCTAAACATACATGCCTTA 57.200 30.769 0.00 0.00 0.00 2.69
230 231 7.701539 TTCACATTCTAAACATACATGCCTT 57.298 32.000 0.00 0.00 0.00 4.35
231 232 7.013655 GGATTCACATTCTAAACATACATGCCT 59.986 37.037 0.00 0.00 0.00 4.75
232 233 7.141363 GGATTCACATTCTAAACATACATGCC 58.859 38.462 0.00 0.00 0.00 4.40
233 234 7.706159 TGGATTCACATTCTAAACATACATGC 58.294 34.615 0.00 0.00 0.00 4.06
264 265 9.309516 CAAATGTACTTGTCCGTGTATTATACT 57.690 33.333 3.92 0.00 0.00 2.12
265 266 8.545420 CCAAATGTACTTGTCCGTGTATTATAC 58.455 37.037 0.00 0.00 0.00 1.47
266 267 7.225145 GCCAAATGTACTTGTCCGTGTATTATA 59.775 37.037 0.00 0.00 0.00 0.98
267 268 6.037830 GCCAAATGTACTTGTCCGTGTATTAT 59.962 38.462 0.00 0.00 0.00 1.28
268 269 5.352016 GCCAAATGTACTTGTCCGTGTATTA 59.648 40.000 0.00 0.00 0.00 0.98
269 270 4.155280 GCCAAATGTACTTGTCCGTGTATT 59.845 41.667 0.00 0.00 0.00 1.89
270 271 3.687698 GCCAAATGTACTTGTCCGTGTAT 59.312 43.478 0.00 0.00 0.00 2.29
271 272 3.068560 GCCAAATGTACTTGTCCGTGTA 58.931 45.455 0.00 0.00 0.00 2.90
272 273 1.877443 GCCAAATGTACTTGTCCGTGT 59.123 47.619 0.00 0.00 0.00 4.49
273 274 2.151202 AGCCAAATGTACTTGTCCGTG 58.849 47.619 0.00 0.00 0.00 4.94
274 275 2.561478 AGCCAAATGTACTTGTCCGT 57.439 45.000 0.00 0.00 0.00 4.69
275 276 3.666902 CGAAAGCCAAATGTACTTGTCCG 60.667 47.826 0.00 0.00 0.00 4.79
276 277 3.365969 CCGAAAGCCAAATGTACTTGTCC 60.366 47.826 0.00 0.00 0.00 4.02
277 278 3.365969 CCCGAAAGCCAAATGTACTTGTC 60.366 47.826 0.00 0.00 0.00 3.18
278 279 2.556622 CCCGAAAGCCAAATGTACTTGT 59.443 45.455 0.00 0.00 0.00 3.16
279 280 2.556622 ACCCGAAAGCCAAATGTACTTG 59.443 45.455 0.00 0.00 0.00 3.16
280 281 2.556622 CACCCGAAAGCCAAATGTACTT 59.443 45.455 0.00 0.00 0.00 2.24
281 282 2.159382 CACCCGAAAGCCAAATGTACT 58.841 47.619 0.00 0.00 0.00 2.73
282 283 1.883926 ACACCCGAAAGCCAAATGTAC 59.116 47.619 0.00 0.00 0.00 2.90
283 284 2.279935 ACACCCGAAAGCCAAATGTA 57.720 45.000 0.00 0.00 0.00 2.29
284 285 2.279935 TACACCCGAAAGCCAAATGT 57.720 45.000 0.00 0.00 0.00 2.71
285 286 4.792704 GCATATACACCCGAAAGCCAAATG 60.793 45.833 0.00 0.00 0.00 2.32
286 287 3.317993 GCATATACACCCGAAAGCCAAAT 59.682 43.478 0.00 0.00 0.00 2.32
287 288 2.685897 GCATATACACCCGAAAGCCAAA 59.314 45.455 0.00 0.00 0.00 3.28
288 289 2.294074 GCATATACACCCGAAAGCCAA 58.706 47.619 0.00 0.00 0.00 4.52
289 290 1.210722 TGCATATACACCCGAAAGCCA 59.789 47.619 0.00 0.00 0.00 4.75
290 291 1.873591 CTGCATATACACCCGAAAGCC 59.126 52.381 0.00 0.00 0.00 4.35
291 292 1.264288 GCTGCATATACACCCGAAAGC 59.736 52.381 0.00 0.00 0.00 3.51
292 293 2.545526 CAGCTGCATATACACCCGAAAG 59.454 50.000 0.00 0.00 0.00 2.62
293 294 2.560504 CAGCTGCATATACACCCGAAA 58.439 47.619 0.00 0.00 0.00 3.46
294 295 1.202639 CCAGCTGCATATACACCCGAA 60.203 52.381 8.66 0.00 0.00 4.30
295 296 0.392706 CCAGCTGCATATACACCCGA 59.607 55.000 8.66 0.00 0.00 5.14
296 297 0.106708 ACCAGCTGCATATACACCCG 59.893 55.000 8.66 0.00 0.00 5.28
297 298 3.007940 TCATACCAGCTGCATATACACCC 59.992 47.826 8.66 0.00 0.00 4.61
298 299 4.271696 TCATACCAGCTGCATATACACC 57.728 45.455 8.66 0.00 0.00 4.16
299 300 6.618287 TTTTCATACCAGCTGCATATACAC 57.382 37.500 8.66 0.00 0.00 2.90
300 301 7.053498 TCTTTTTCATACCAGCTGCATATACA 58.947 34.615 8.66 0.00 0.00 2.29
301 302 7.496529 TCTTTTTCATACCAGCTGCATATAC 57.503 36.000 8.66 0.00 0.00 1.47
302 303 9.791801 TTATCTTTTTCATACCAGCTGCATATA 57.208 29.630 8.66 0.00 0.00 0.86
303 304 8.696043 TTATCTTTTTCATACCAGCTGCATAT 57.304 30.769 8.66 5.53 0.00 1.78
304 305 8.696043 ATTATCTTTTTCATACCAGCTGCATA 57.304 30.769 8.66 3.03 0.00 3.14
305 306 7.592885 ATTATCTTTTTCATACCAGCTGCAT 57.407 32.000 8.66 0.05 0.00 3.96
306 307 7.408756 AATTATCTTTTTCATACCAGCTGCA 57.591 32.000 8.66 0.00 0.00 4.41
307 308 9.237846 GTAAATTATCTTTTTCATACCAGCTGC 57.762 33.333 8.66 0.00 0.00 5.25
368 372 8.692110 AACGGAAGGTTAAGTTTGTTTTAAAG 57.308 30.769 0.00 0.00 37.00 1.85
402 406 9.113876 CACGATTTGAATGAGTAAGGTTTTTAC 57.886 33.333 0.00 0.00 0.00 2.01
410 416 6.417327 GCAGATCACGATTTGAATGAGTAAG 58.583 40.000 1.95 0.00 37.92 2.34
432 438 4.927425 GTGACTCCAATTCTAGTTAACGCA 59.073 41.667 0.00 0.00 0.00 5.24
522 531 0.036294 GCTCCCGTTTTCCTACTGCT 60.036 55.000 0.00 0.00 0.00 4.24
614 626 0.445829 GAAAAGAAGCCGAGCAGAGC 59.554 55.000 0.00 0.00 0.00 4.09
936 984 2.195741 TCTACCTGTACACGTGCTCT 57.804 50.000 17.22 0.00 0.00 4.09
951 999 1.892474 CTCCAGGCTCCAGCTATCTAC 59.108 57.143 0.00 0.00 41.70 2.59
953 1001 0.471591 CCTCCAGGCTCCAGCTATCT 60.472 60.000 0.00 0.00 41.70 1.98
994 1042 1.131126 GATGCCACCGTTCATGACAAG 59.869 52.381 0.00 0.00 0.00 3.16
996 1044 1.018752 CGATGCCACCGTTCATGACA 61.019 55.000 0.00 0.00 0.00 3.58
998 1046 1.449423 CCGATGCCACCGTTCATGA 60.449 57.895 0.00 0.00 0.00 3.07
1318 1366 4.305956 AGGCAAACAGGGGCAGGG 62.306 66.667 0.00 0.00 0.00 4.45
1319 1367 2.993264 CAGGCAAACAGGGGCAGG 60.993 66.667 0.00 0.00 0.00 4.85
1320 1368 1.402107 AAACAGGCAAACAGGGGCAG 61.402 55.000 0.00 0.00 0.00 4.85
1321 1369 1.382420 AAACAGGCAAACAGGGGCA 60.382 52.632 0.00 0.00 0.00 5.36
1322 1370 1.069596 CAAACAGGCAAACAGGGGC 59.930 57.895 0.00 0.00 0.00 5.80
1323 1371 1.341080 ATCAAACAGGCAAACAGGGG 58.659 50.000 0.00 0.00 0.00 4.79
1578 1632 1.165270 CCCGGTAGCACTTTCCAAAG 58.835 55.000 0.00 0.00 41.73 2.77
1721 1776 5.413309 TTGCCATGGTTAAAATCCGAATT 57.587 34.783 14.67 0.00 0.00 2.17
1722 1777 5.453198 GGATTGCCATGGTTAAAATCCGAAT 60.453 40.000 23.20 6.86 37.58 3.34
1739 1794 3.189285 CCATGAAAAATGTCGGATTGCC 58.811 45.455 0.00 0.00 0.00 4.52
1743 1798 3.511146 AGTTGCCATGAAAAATGTCGGAT 59.489 39.130 0.00 0.00 0.00 4.18
1777 1833 6.993902 AGAAAATTGCCATGTTTGTCAATCTT 59.006 30.769 0.00 0.00 0.00 2.40
1812 1868 3.191078 TGGCAACTTTGTCCCAATTTG 57.809 42.857 0.00 0.00 37.61 2.32
1813 1869 3.136260 ACATGGCAACTTTGTCCCAATTT 59.864 39.130 0.00 0.00 37.61 1.82
1816 1872 1.786937 ACATGGCAACTTTGTCCCAA 58.213 45.000 0.00 0.00 37.61 4.12
1817 1873 1.786937 AACATGGCAACTTTGTCCCA 58.213 45.000 0.00 0.00 33.40 4.37
1818 1874 2.908688 AAACATGGCAACTTTGTCCC 57.091 45.000 0.00 0.00 33.40 4.46
1820 1876 6.312672 AGTTGTTAAAACATGGCAACTTTGTC 59.687 34.615 0.00 0.00 44.79 3.18
1822 1878 6.660887 AGTTGTTAAAACATGGCAACTTTG 57.339 33.333 0.00 0.00 44.79 2.77
1853 1910 4.783242 CAATTTTAGTTGACACGAGGTGG 58.217 43.478 0.42 0.00 37.94 4.61
1890 1947 4.336433 CGGATTTTAAGCATGTCATCCTGT 59.664 41.667 0.00 0.00 0.00 4.00
1920 1977 1.843851 CTAGTGGCCTGATAAACCCCA 59.156 52.381 3.32 0.00 0.00 4.96
1924 1981 4.058817 CGATTCCTAGTGGCCTGATAAAC 58.941 47.826 3.32 0.00 0.00 2.01
1931 1988 1.807814 AATCCGATTCCTAGTGGCCT 58.192 50.000 3.32 0.00 0.00 5.19
1939 1996 5.982890 AAATGTGTGAAAATCCGATTCCT 57.017 34.783 0.00 0.00 0.00 3.36
1977 2034 7.822822 AGCCACTTCTAATACTAAAATGTCGTT 59.177 33.333 0.00 0.00 0.00 3.85
2051 2108 3.057033 AGCCTCTTTGTGAAATGCATGTC 60.057 43.478 10.16 10.16 0.00 3.06
2121 2178 8.125728 TCCAAAATTGAGTTTTAAAGCTTTCG 57.874 30.769 16.57 0.00 37.93 3.46
2186 2243 8.550710 AAATGTATAAAGTGTTTGCCGTACTA 57.449 30.769 0.00 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.