Multiple sequence alignment - TraesCS1D01G177100

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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 TraesCS1D01G177100 chr1D 100.000 3113 0 0 1 3113 252476564 252479676 0.000000e+00 5749.0
1 TraesCS1D01G177100 chr1D 94.118 187 11 0 1 187 251841603 251841789 5.080000e-73 285.0
2 TraesCS1D01G177100 chr1D 95.028 181 8 1 1 180 249725300 249725480 1.830000e-72 283.0
3 TraesCS1D01G177100 chr1A 94.010 2304 94 14 840 3113 323192885 323190596 0.000000e+00 3450.0
4 TraesCS1D01G177100 chr1B 94.623 2083 85 10 840 2899 361016540 361014462 0.000000e+00 3201.0
5 TraesCS1D01G177100 chr1B 96.380 221 7 1 2893 3113 361014303 361014084 2.280000e-96 363.0
6 TraesCS1D01G177100 chr1B 95.556 180 7 1 1 180 171371958 171371780 1.410000e-73 287.0
7 TraesCS1D01G177100 chr1B 80.843 261 31 14 189 435 539882760 539882505 1.470000e-43 187.0
8 TraesCS1D01G177100 chr1B 80.534 262 31 13 189 435 531638052 531637796 1.910000e-42 183.0
9 TraesCS1D01G177100 chr1B 79.926 269 37 10 180 435 316264320 316264584 6.860000e-42 182.0
10 TraesCS1D01G177100 chr2D 91.842 380 25 3 463 840 628656230 628655855 2.750000e-145 525.0
11 TraesCS1D01G177100 chr2D 96.111 180 7 0 1 180 137060356 137060535 8.440000e-76 294.0
12 TraesCS1D01G177100 chr2D 84.543 317 21 14 179 468 628657364 628657049 3.930000e-74 289.0
13 TraesCS1D01G177100 chr2D 95.000 180 9 0 1 180 478355883 478355704 1.830000e-72 283.0
14 TraesCS1D01G177100 chr2D 85.906 149 16 3 492 639 73103597 73103453 1.500000e-33 154.0
15 TraesCS1D01G177100 chr2A 91.901 284 19 3 557 840 758709141 758709420 8.090000e-106 394.0
16 TraesCS1D01G177100 chr2A 83.713 307 23 10 183 462 758707969 758708275 6.620000e-67 265.0
17 TraesCS1D01G177100 chr2A 87.248 149 14 3 492 639 71670031 71669887 6.910000e-37 165.0
18 TraesCS1D01G177100 chr3D 96.667 180 6 0 1 180 304756484 304756305 1.810000e-77 300.0
19 TraesCS1D01G177100 chr3D 95.556 180 8 0 1 180 67346332 67346511 3.930000e-74 289.0
20 TraesCS1D01G177100 chr3D 94.086 186 11 0 1 186 421577286 421577471 1.830000e-72 283.0
21 TraesCS1D01G177100 chr7D 95.000 180 9 0 1 180 489661395 489661574 1.830000e-72 283.0
22 TraesCS1D01G177100 chr2B 80.843 261 31 12 189 435 773432731 773432476 1.470000e-43 187.0
23 TraesCS1D01G177100 chr2B 80.000 270 35 12 180 435 403095435 403095699 6.860000e-42 182.0
24 TraesCS1D01G177100 chr2B 87.143 140 13 3 492 630 110483865 110483730 1.500000e-33 154.0
25 TraesCS1D01G177100 chr5B 80.385 260 33 14 189 435 438028742 438028488 6.860000e-42 182.0
26 TraesCS1D01G177100 chr5B 82.432 148 17 8 687 830 88341692 88341550 1.520000e-23 121.0
27 TraesCS1D01G177100 chr4B 79.630 270 36 12 180 435 666625204 666625468 3.190000e-40 176.0
28 TraesCS1D01G177100 chr6B 78.889 270 38 12 180 435 306974248 306974512 6.910000e-37 165.0
29 TraesCS1D01G177100 chr6B 78.010 191 37 5 654 841 88310031 88310219 7.050000e-22 115.0
30 TraesCS1D01G177100 chr4A 78.486 251 39 9 197 435 713375280 713375033 1.930000e-32 150.0
31 TraesCS1D01G177100 chr4A 96.970 33 1 0 811 843 739081455 739081423 4.340000e-04 56.5
32 TraesCS1D01G177100 chr7B 86.777 121 12 3 228 345 616482190 616482071 7.000000e-27 132.0
33 TraesCS1D01G177100 chr6A 80.488 164 26 5 654 814 37834455 37834615 1.520000e-23 121.0
34 TraesCS1D01G177100 chr7A 96.875 32 1 0 809 840 186527716 186527685 2.000000e-03 54.7


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 TraesCS1D01G177100 chr1D 252476564 252479676 3112 False 5749.0 5749 100.0000 1 3113 1 chr1D.!!$F3 3112
1 TraesCS1D01G177100 chr1A 323190596 323192885 2289 True 3450.0 3450 94.0100 840 3113 1 chr1A.!!$R1 2273
2 TraesCS1D01G177100 chr1B 361014084 361016540 2456 True 1782.0 3201 95.5015 840 3113 2 chr1B.!!$R4 2273
3 TraesCS1D01G177100 chr2D 628655855 628657364 1509 True 407.0 525 88.1925 179 840 2 chr2D.!!$R3 661
4 TraesCS1D01G177100 chr2A 758707969 758709420 1451 False 329.5 394 87.8070 183 840 2 chr2A.!!$F1 657

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
59 60 0.025001 GTTTGATGTCGTCGCCATCG 59.975 55.0 11.27 0.0 41.28 3.84 F
159 160 0.097150 TCTCTGATTCGACTGTCGCG 59.903 55.0 24.37 0.0 40.21 5.87 F
177 178 0.107508 CGATTGGACCATCCTGCAGT 60.108 55.0 13.81 0.0 37.46 4.40 F
1824 2762 0.035458 AGAAGTTCAGCCAGTTCCGG 59.965 55.0 5.50 0.0 0.00 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1758 2696 0.390860 AGCTCAGAAACTCGTGTGCT 59.609 50.000 0.00 0.00 38.39 4.40 R
1815 2753 0.951558 CAAACCACTTCCGGAACTGG 59.048 55.000 30.48 30.48 32.65 4.00 R
1896 2834 1.017387 CTGTATGCCGCTTTCCCTTC 58.983 55.000 0.00 0.00 0.00 3.46 R
2778 3723 7.272978 GTGCCTATCAACTTAATCAGGACTTA 58.727 38.462 0.00 0.00 0.00 2.24 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
17 18 4.847255 GTTTGCCACTCATCGCAC 57.153 55.556 0.00 0.00 33.97 5.34
18 19 1.948508 GTTTGCCACTCATCGCACA 59.051 52.632 0.00 0.00 33.97 4.57
19 20 0.385974 GTTTGCCACTCATCGCACAC 60.386 55.000 0.00 0.00 33.97 3.82
20 21 1.840630 TTTGCCACTCATCGCACACG 61.841 55.000 0.00 0.00 42.01 4.49
21 22 4.152625 GCCACTCATCGCACACGC 62.153 66.667 0.00 0.00 39.84 5.34
22 23 2.738139 CCACTCATCGCACACGCA 60.738 61.111 0.00 0.00 39.84 5.24
23 24 2.316867 CCACTCATCGCACACGCAA 61.317 57.895 0.00 0.00 39.84 4.85
24 25 1.569003 CACTCATCGCACACGCAAA 59.431 52.632 0.00 0.00 39.84 3.68
25 26 0.166597 CACTCATCGCACACGCAAAT 59.833 50.000 0.00 0.00 39.84 2.32
26 27 0.443869 ACTCATCGCACACGCAAATC 59.556 50.000 0.00 0.00 39.84 2.17
27 28 0.723414 CTCATCGCACACGCAAATCT 59.277 50.000 0.00 0.00 39.84 2.40
28 29 1.926510 CTCATCGCACACGCAAATCTA 59.073 47.619 0.00 0.00 39.84 1.98
29 30 2.342179 TCATCGCACACGCAAATCTAA 58.658 42.857 0.00 0.00 39.84 2.10
30 31 2.935849 TCATCGCACACGCAAATCTAAT 59.064 40.909 0.00 0.00 39.84 1.73
31 32 4.116238 TCATCGCACACGCAAATCTAATA 58.884 39.130 0.00 0.00 39.84 0.98
32 33 4.749598 TCATCGCACACGCAAATCTAATAT 59.250 37.500 0.00 0.00 39.84 1.28
33 34 4.451379 TCGCACACGCAAATCTAATATG 57.549 40.909 0.00 0.00 39.84 1.78
34 35 4.116238 TCGCACACGCAAATCTAATATGA 58.884 39.130 0.00 0.00 39.84 2.15
35 36 4.568760 TCGCACACGCAAATCTAATATGAA 59.431 37.500 0.00 0.00 39.84 2.57
36 37 4.666176 CGCACACGCAAATCTAATATGAAC 59.334 41.667 0.00 0.00 38.40 3.18
37 38 4.970003 GCACACGCAAATCTAATATGAACC 59.030 41.667 0.00 0.00 38.36 3.62
38 39 5.197549 CACACGCAAATCTAATATGAACCG 58.802 41.667 0.00 0.00 0.00 4.44
39 40 4.873827 ACACGCAAATCTAATATGAACCGT 59.126 37.500 0.00 0.00 0.00 4.83
40 41 5.197549 CACGCAAATCTAATATGAACCGTG 58.802 41.667 0.00 0.00 36.79 4.94
41 42 4.873827 ACGCAAATCTAATATGAACCGTGT 59.126 37.500 0.00 0.00 0.00 4.49
42 43 5.353123 ACGCAAATCTAATATGAACCGTGTT 59.647 36.000 0.00 0.00 0.00 3.32
43 44 6.128117 ACGCAAATCTAATATGAACCGTGTTT 60.128 34.615 0.00 0.00 0.00 2.83
44 45 6.194508 CGCAAATCTAATATGAACCGTGTTTG 59.805 38.462 0.00 0.00 0.00 2.93
45 46 7.247728 GCAAATCTAATATGAACCGTGTTTGA 58.752 34.615 0.00 0.00 0.00 2.69
46 47 7.915397 GCAAATCTAATATGAACCGTGTTTGAT 59.085 33.333 0.00 0.00 0.00 2.57
47 48 9.225201 CAAATCTAATATGAACCGTGTTTGATG 57.775 33.333 0.00 0.00 0.00 3.07
48 49 8.506168 AATCTAATATGAACCGTGTTTGATGT 57.494 30.769 0.00 0.00 0.00 3.06
49 50 7.534085 TCTAATATGAACCGTGTTTGATGTC 57.466 36.000 0.00 0.00 0.00 3.06
50 51 4.857871 ATATGAACCGTGTTTGATGTCG 57.142 40.909 0.00 0.00 0.00 4.35
51 52 1.942677 TGAACCGTGTTTGATGTCGT 58.057 45.000 0.00 0.00 0.00 4.34
52 53 1.862201 TGAACCGTGTTTGATGTCGTC 59.138 47.619 0.00 0.00 0.00 4.20
53 54 0.856641 AACCGTGTTTGATGTCGTCG 59.143 50.000 0.00 0.00 0.00 5.12
54 55 1.129809 CCGTGTTTGATGTCGTCGC 59.870 57.895 0.00 0.00 0.00 5.19
55 56 1.129809 CGTGTTTGATGTCGTCGCC 59.870 57.895 0.00 0.00 0.00 5.54
56 57 1.553195 CGTGTTTGATGTCGTCGCCA 61.553 55.000 0.00 0.00 0.00 5.69
57 58 0.796312 GTGTTTGATGTCGTCGCCAT 59.204 50.000 0.00 0.00 0.00 4.40
58 59 1.075542 TGTTTGATGTCGTCGCCATC 58.924 50.000 9.26 9.26 39.32 3.51
59 60 0.025001 GTTTGATGTCGTCGCCATCG 59.975 55.000 11.27 0.00 41.28 3.84
60 61 1.692148 TTTGATGTCGTCGCCATCGC 61.692 55.000 11.27 0.00 41.28 4.58
61 62 2.582226 GATGTCGTCGCCATCGCA 60.582 61.111 0.00 0.00 35.26 5.10
62 63 2.125713 ATGTCGTCGCCATCGCAA 60.126 55.556 0.00 0.00 35.26 4.85
63 64 1.692148 GATGTCGTCGCCATCGCAAA 61.692 55.000 0.00 0.00 35.26 3.68
64 65 1.966493 ATGTCGTCGCCATCGCAAAC 61.966 55.000 0.00 0.00 35.26 2.93
65 66 3.474904 TCGTCGCCATCGCAAACG 61.475 61.111 1.60 1.60 42.26 3.60
66 67 3.773630 CGTCGCCATCGCAAACGT 61.774 61.111 0.10 0.00 38.39 3.99
67 68 2.554272 GTCGCCATCGCAAACGTT 59.446 55.556 0.00 0.00 41.18 3.99
68 69 1.082366 GTCGCCATCGCAAACGTTT 60.082 52.632 7.96 7.96 41.18 3.60
69 70 0.659123 GTCGCCATCGCAAACGTTTT 60.659 50.000 11.66 0.00 41.18 2.43
70 71 0.658829 TCGCCATCGCAAACGTTTTG 60.659 50.000 11.66 7.13 41.18 2.44
71 72 1.486801 GCCATCGCAAACGTTTTGC 59.513 52.632 11.66 16.47 41.18 3.68
72 73 1.211818 GCCATCGCAAACGTTTTGCA 61.212 50.000 24.71 16.49 45.14 4.08
73 74 1.417372 CCATCGCAAACGTTTTGCAT 58.583 45.000 24.71 17.47 45.14 3.96
74 75 1.386412 CCATCGCAAACGTTTTGCATC 59.614 47.619 24.71 9.01 45.14 3.91
75 76 2.318578 CATCGCAAACGTTTTGCATCT 58.681 42.857 24.71 12.42 45.14 2.90
76 77 2.483583 TCGCAAACGTTTTGCATCTT 57.516 40.000 24.71 0.00 45.14 2.40
77 78 2.803451 TCGCAAACGTTTTGCATCTTT 58.197 38.095 24.71 0.00 45.14 2.52
78 79 3.182967 TCGCAAACGTTTTGCATCTTTT 58.817 36.364 24.71 0.00 45.14 2.27
79 80 3.614616 TCGCAAACGTTTTGCATCTTTTT 59.385 34.783 24.71 0.00 45.14 1.94
106 107 5.691815 CGGTTTTATTACATCACCGTTTGT 58.308 37.500 0.82 0.00 44.40 2.83
107 108 5.566016 CGGTTTTATTACATCACCGTTTGTG 59.434 40.000 0.82 0.00 44.40 3.33
118 119 3.492421 ACCGTTTGTGATTGATGCATC 57.508 42.857 20.14 20.14 0.00 3.91
119 120 2.164219 ACCGTTTGTGATTGATGCATCC 59.836 45.455 23.67 9.24 0.00 3.51
120 121 2.480073 CCGTTTGTGATTGATGCATCCC 60.480 50.000 23.67 13.07 0.00 3.85
121 122 2.164017 CGTTTGTGATTGATGCATCCCA 59.836 45.455 23.67 15.38 0.00 4.37
122 123 3.514645 GTTTGTGATTGATGCATCCCAC 58.485 45.455 23.67 24.39 0.00 4.61
123 124 2.510928 TGTGATTGATGCATCCCACA 57.489 45.000 27.86 27.86 32.38 4.17
124 125 2.093890 TGTGATTGATGCATCCCACAC 58.906 47.619 27.86 26.85 30.99 3.82
125 126 2.093890 GTGATTGATGCATCCCACACA 58.906 47.619 26.80 17.38 0.00 3.72
126 127 2.098607 GTGATTGATGCATCCCACACAG 59.901 50.000 26.80 0.00 0.00 3.66
127 128 2.291089 TGATTGATGCATCCCACACAGT 60.291 45.455 23.67 1.27 0.00 3.55
128 129 2.291209 TTGATGCATCCCACACAGTT 57.709 45.000 23.67 0.00 0.00 3.16
129 130 2.291209 TGATGCATCCCACACAGTTT 57.709 45.000 23.67 0.00 0.00 2.66
130 131 2.161855 TGATGCATCCCACACAGTTTC 58.838 47.619 23.67 0.00 0.00 2.78
131 132 1.131126 GATGCATCCCACACAGTTTCG 59.869 52.381 16.23 0.00 0.00 3.46
132 133 0.179032 TGCATCCCACACAGTTTCGT 60.179 50.000 0.00 0.00 0.00 3.85
133 134 0.517316 GCATCCCACACAGTTTCGTC 59.483 55.000 0.00 0.00 0.00 4.20
134 135 1.877637 CATCCCACACAGTTTCGTCA 58.122 50.000 0.00 0.00 0.00 4.35
135 136 2.217750 CATCCCACACAGTTTCGTCAA 58.782 47.619 0.00 0.00 0.00 3.18
136 137 2.404923 TCCCACACAGTTTCGTCAAA 57.595 45.000 0.00 0.00 0.00 2.69
137 138 2.285083 TCCCACACAGTTTCGTCAAAG 58.715 47.619 0.00 0.00 0.00 2.77
138 139 1.333619 CCCACACAGTTTCGTCAAAGG 59.666 52.381 0.00 0.00 0.00 3.11
139 140 1.333619 CCACACAGTTTCGTCAAAGGG 59.666 52.381 0.00 0.00 0.00 3.95
140 141 2.014128 CACACAGTTTCGTCAAAGGGT 58.986 47.619 0.00 0.00 0.00 4.34
141 142 2.031683 CACACAGTTTCGTCAAAGGGTC 59.968 50.000 0.00 0.00 0.00 4.46
142 143 2.093128 ACACAGTTTCGTCAAAGGGTCT 60.093 45.455 0.00 0.00 0.00 3.85
143 144 2.544267 CACAGTTTCGTCAAAGGGTCTC 59.456 50.000 0.00 0.00 0.00 3.36
144 145 2.434702 ACAGTTTCGTCAAAGGGTCTCT 59.565 45.455 0.00 0.00 0.00 3.10
145 146 2.802816 CAGTTTCGTCAAAGGGTCTCTG 59.197 50.000 0.00 0.00 0.00 3.35
146 147 2.698797 AGTTTCGTCAAAGGGTCTCTGA 59.301 45.455 0.00 0.00 0.00 3.27
147 148 3.325135 AGTTTCGTCAAAGGGTCTCTGAT 59.675 43.478 0.00 0.00 0.00 2.90
148 149 4.065789 GTTTCGTCAAAGGGTCTCTGATT 58.934 43.478 0.00 0.00 0.00 2.57
149 150 3.594603 TCGTCAAAGGGTCTCTGATTC 57.405 47.619 0.00 0.00 0.00 2.52
150 151 2.094700 TCGTCAAAGGGTCTCTGATTCG 60.095 50.000 0.00 0.00 0.00 3.34
151 152 2.094700 CGTCAAAGGGTCTCTGATTCGA 60.095 50.000 0.00 0.00 0.00 3.71
152 153 3.254892 GTCAAAGGGTCTCTGATTCGAC 58.745 50.000 0.00 0.00 0.00 4.20
153 154 3.056465 GTCAAAGGGTCTCTGATTCGACT 60.056 47.826 0.00 0.00 0.00 4.18
154 155 3.056536 TCAAAGGGTCTCTGATTCGACTG 60.057 47.826 0.00 0.00 0.00 3.51
155 156 2.223803 AGGGTCTCTGATTCGACTGT 57.776 50.000 0.00 0.00 0.00 3.55
156 157 2.096248 AGGGTCTCTGATTCGACTGTC 58.904 52.381 0.00 0.00 0.00 3.51
157 158 1.202200 GGGTCTCTGATTCGACTGTCG 60.202 57.143 23.33 23.33 42.10 4.35
158 159 1.540407 GTCTCTGATTCGACTGTCGC 58.460 55.000 24.37 11.82 40.21 5.19
159 160 0.097150 TCTCTGATTCGACTGTCGCG 59.903 55.000 24.37 0.00 40.21 5.87
160 161 0.097150 CTCTGATTCGACTGTCGCGA 59.903 55.000 24.37 3.71 40.21 5.87
161 162 0.733150 TCTGATTCGACTGTCGCGAT 59.267 50.000 24.37 19.27 40.21 4.58
162 163 1.132453 TCTGATTCGACTGTCGCGATT 59.868 47.619 24.37 9.19 40.21 3.34
163 164 1.253800 CTGATTCGACTGTCGCGATTG 59.746 52.381 24.37 11.11 40.21 2.67
164 165 0.572590 GATTCGACTGTCGCGATTGG 59.427 55.000 24.37 8.27 40.21 3.16
165 166 0.172578 ATTCGACTGTCGCGATTGGA 59.827 50.000 24.37 3.88 40.21 3.53
166 167 0.731514 TTCGACTGTCGCGATTGGAC 60.732 55.000 24.37 0.00 40.21 4.02
167 168 2.158959 CGACTGTCGCGATTGGACC 61.159 63.158 17.94 0.00 33.46 4.46
168 169 1.080093 GACTGTCGCGATTGGACCA 60.080 57.895 14.06 2.89 33.46 4.02
169 170 0.460284 GACTGTCGCGATTGGACCAT 60.460 55.000 14.06 0.00 33.46 3.55
170 171 0.460284 ACTGTCGCGATTGGACCATC 60.460 55.000 14.06 0.00 33.46 3.51
171 172 1.153449 TGTCGCGATTGGACCATCC 60.153 57.895 14.06 0.00 36.96 3.51
172 173 1.144057 GTCGCGATTGGACCATCCT 59.856 57.895 14.06 0.00 37.46 3.24
173 174 1.143838 TCGCGATTGGACCATCCTG 59.856 57.895 3.71 0.00 37.46 3.86
174 175 2.537560 CGCGATTGGACCATCCTGC 61.538 63.158 0.00 0.00 37.46 4.85
175 176 1.451927 GCGATTGGACCATCCTGCA 60.452 57.895 0.00 0.00 37.46 4.41
176 177 1.442526 GCGATTGGACCATCCTGCAG 61.443 60.000 6.78 6.78 37.46 4.41
177 178 0.107508 CGATTGGACCATCCTGCAGT 60.108 55.000 13.81 0.00 37.46 4.40
178 179 1.138859 CGATTGGACCATCCTGCAGTA 59.861 52.381 13.81 0.00 37.46 2.74
179 180 2.804572 CGATTGGACCATCCTGCAGTAG 60.805 54.545 13.81 1.47 37.46 2.57
180 181 0.253044 TTGGACCATCCTGCAGTAGC 59.747 55.000 13.81 0.00 37.46 3.58
181 182 1.227380 GGACCATCCTGCAGTAGCG 60.227 63.158 13.81 0.00 46.23 4.26
203 204 5.502220 GCGAGTGGTACTTTTAAAAACACGA 60.502 40.000 17.74 7.57 32.98 4.35
207 208 7.190871 AGTGGTACTTTTAAAAACACGACATG 58.809 34.615 19.62 0.00 32.98 3.21
224 225 5.106555 ACGACATGGTGATGAAAATGTCTTC 60.107 40.000 11.57 0.00 44.30 2.87
225 226 5.122869 CGACATGGTGATGAAAATGTCTTCT 59.877 40.000 11.57 0.00 44.30 2.85
226 227 6.313658 CGACATGGTGATGAAAATGTCTTCTA 59.686 38.462 11.57 0.00 44.30 2.10
256 270 6.908825 TGCGAAGTTATGTTCTAATTTGCTT 58.091 32.000 0.00 0.00 0.00 3.91
311 325 6.991938 AGTTGTGCCTTTTTAATTAGCATGA 58.008 32.000 0.00 0.00 35.62 3.07
350 364 5.027293 AGCTTTGAACTGAAATTTTGCCT 57.973 34.783 0.00 0.00 0.00 4.75
374 388 9.039870 CCTTCTTGTTCAATGACTATCTATGAC 57.960 37.037 0.00 0.00 0.00 3.06
377 391 8.200120 TCTTGTTCAATGACTATCTATGACCTG 58.800 37.037 0.00 0.00 0.00 4.00
378 392 7.660030 TGTTCAATGACTATCTATGACCTGA 57.340 36.000 0.00 0.00 0.00 3.86
381 395 8.986847 GTTCAATGACTATCTATGACCTGAATG 58.013 37.037 0.00 0.00 0.00 2.67
382 396 8.482852 TCAATGACTATCTATGACCTGAATGA 57.517 34.615 0.00 0.00 0.00 2.57
383 397 8.363390 TCAATGACTATCTATGACCTGAATGAC 58.637 37.037 0.00 0.00 0.00 3.06
384 398 6.319141 TGACTATCTATGACCTGAATGACG 57.681 41.667 0.00 0.00 0.00 4.35
410 438 4.855340 TCCTGAATTACATTGGTCTTCCC 58.145 43.478 0.00 0.00 0.00 3.97
415 443 6.364701 TGAATTACATTGGTCTTCCCTATGG 58.635 40.000 7.51 0.00 46.88 2.74
418 446 3.189606 ACATTGGTCTTCCCTATGGTGA 58.810 45.455 7.51 0.00 46.88 4.02
432 460 0.960286 TGGTGATTGTGCACACATGG 59.040 50.000 21.56 0.00 41.52 3.66
448 476 3.706055 TGGCACACAAGAGTCCTTC 57.294 52.632 0.00 0.00 0.00 3.46
467 1385 7.124448 AGTCCTTCTCTACTTTATTTCATCGGT 59.876 37.037 0.00 0.00 0.00 4.69
470 1388 7.549488 CCTTCTCTACTTTATTTCATCGGTGTT 59.451 37.037 0.00 0.00 0.00 3.32
484 1402 3.547746 TCGGTGTTAAAGAGGCAAGTTT 58.452 40.909 0.00 0.00 0.00 2.66
523 1441 2.159653 CCTGCAATCTTTGTAGACGTGC 60.160 50.000 0.00 2.53 44.85 5.34
536 1454 2.317685 GACGTGCGAGCTCTCTCTCC 62.318 65.000 12.85 0.00 37.19 3.71
541 1459 2.489275 CGAGCTCTCTCTCCCTGCC 61.489 68.421 12.85 0.00 37.19 4.85
555 1473 5.271598 TCTCCCTGCCATGTAATTTTGAAT 58.728 37.500 0.00 0.00 0.00 2.57
671 1589 3.686016 ACAAATATGGTCGCTGGAGTTT 58.314 40.909 0.00 0.00 0.00 2.66
680 1598 3.428589 GGTCGCTGGAGTTTTAGTCGTAT 60.429 47.826 0.00 0.00 0.00 3.06
851 1773 6.460399 GCACGATTACTAGTCTCCAGAAAGAT 60.460 42.308 0.00 0.00 0.00 2.40
870 1792 2.916502 TATCTCGGCGCCGCATTTGT 62.917 55.000 42.78 25.19 39.59 2.83
916 1838 1.499007 AGCCCTTGGTTGGAGAAAGAA 59.501 47.619 0.00 0.00 0.00 2.52
1278 2216 2.647875 CCGCTCTCCCTATCGCTG 59.352 66.667 0.00 0.00 0.00 5.18
1317 2255 2.185350 CTTGCCGTCGCATCCTCT 59.815 61.111 0.00 0.00 46.67 3.69
1326 2264 4.593864 GCATCCTCTCCCGACGCC 62.594 72.222 0.00 0.00 0.00 5.68
1363 2301 3.785859 GCCTCCTCGCCATGTCCA 61.786 66.667 0.00 0.00 0.00 4.02
1377 2315 3.000819 TCCACATCCCGCTCCGTT 61.001 61.111 0.00 0.00 0.00 4.44
1474 2412 4.148825 CCCACCTCTTCCGCCTCG 62.149 72.222 0.00 0.00 0.00 4.63
1521 2459 1.208358 CGTTCTACACCTCGTCGCA 59.792 57.895 0.00 0.00 0.00 5.10
1586 2524 0.801067 CCGGAGAAGTACGCTTTCCG 60.801 60.000 17.64 17.64 44.82 4.30
1751 2689 0.545646 AAGATGGAGAAGAGGGCAGC 59.454 55.000 0.00 0.00 0.00 5.25
1758 2696 0.691078 AGAAGAGGGCAGCCGGAATA 60.691 55.000 5.05 0.00 0.00 1.75
1782 2720 1.795286 CACGAGTTTCTGAGCTTGACC 59.205 52.381 0.00 0.00 0.00 4.02
1797 2735 2.225382 TGACCGTGGAGAAGATGGTA 57.775 50.000 0.00 0.00 32.55 3.25
1815 2753 2.093921 GGTAGAGGTGGAGAAGTTCAGC 60.094 54.545 5.50 0.00 0.00 4.26
1824 2762 0.035458 AGAAGTTCAGCCAGTTCCGG 59.965 55.000 5.50 0.00 0.00 5.14
1872 2810 3.132289 TCAGGGACGTATTCTTGGATCAC 59.868 47.826 0.00 0.00 0.00 3.06
1896 2834 2.036733 TGGGATATTTTACCTCTCGGCG 59.963 50.000 0.00 0.00 0.00 6.46
1914 2852 0.742990 CGAAGGGAAAGCGGCATACA 60.743 55.000 1.45 0.00 0.00 2.29
1977 2915 2.289002 GCCTAATGATGTTTCAGAGGCG 59.711 50.000 13.03 0.00 46.64 5.52
2037 2975 1.531739 GCCTTGGGAACGCCAATTCA 61.532 55.000 0.00 0.00 35.15 2.57
2046 2984 2.766345 ACGCCAATTCAAATGCCAAT 57.234 40.000 0.00 0.00 0.00 3.16
2067 3005 1.985473 TGTCTTCAAGTGCCAATGCT 58.015 45.000 0.00 0.00 38.71 3.79
2143 3081 0.390866 ATCTGTGAAGCTGCAGGACG 60.391 55.000 17.12 0.00 33.81 4.79
2180 3118 5.508489 GGTTGTGCAATTCATGGATATCCTG 60.508 44.000 22.35 16.75 36.82 3.86
2249 3190 2.315925 ATGTTAGTGGTGCAGATCCG 57.684 50.000 0.00 0.00 0.00 4.18
2252 3193 2.764010 TGTTAGTGGTGCAGATCCGTAT 59.236 45.455 0.00 0.00 0.00 3.06
2356 3297 0.392336 CTCCCTGAGCTAGGCATGTC 59.608 60.000 0.00 0.00 45.89 3.06
2357 3298 0.031716 TCCCTGAGCTAGGCATGTCT 60.032 55.000 4.63 4.63 45.89 3.41
2417 3358 9.035890 TGATCGGTAATGTATCTTTATCCTGAT 57.964 33.333 0.00 0.00 0.00 2.90
2544 3488 5.946972 TGAGTTTTGTTTCAGTTCCTTGGTA 59.053 36.000 0.00 0.00 0.00 3.25
2566 3510 6.304683 GGTATTGCTTATTGTTGTTTCGTCAC 59.695 38.462 0.00 0.00 0.00 3.67
2630 3574 6.071728 GCTAACCTAGACCAACAACTACAGTA 60.072 42.308 0.00 0.00 0.00 2.74
2687 3631 5.059161 GCAGGATAATTGTGTAGATGCAGA 58.941 41.667 0.00 0.00 0.00 4.26
3100 4217 3.354089 ACACGAAAAAGTCCTTGCATG 57.646 42.857 0.00 0.00 0.00 4.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.385974 GTGTGCGATGAGTGGCAAAC 60.386 55.000 0.00 0.00 40.87 2.93
1 2 1.840630 CGTGTGCGATGAGTGGCAAA 61.841 55.000 0.00 0.00 40.87 3.68
2 3 2.316867 CGTGTGCGATGAGTGGCAA 61.317 57.895 0.00 0.00 40.87 4.52
3 4 2.738139 CGTGTGCGATGAGTGGCA 60.738 61.111 0.00 0.00 41.33 4.92
14 15 4.970003 GGTTCATATTAGATTTGCGTGTGC 59.030 41.667 0.00 0.00 43.20 4.57
15 16 5.197549 CGGTTCATATTAGATTTGCGTGTG 58.802 41.667 0.00 0.00 0.00 3.82
16 17 4.873827 ACGGTTCATATTAGATTTGCGTGT 59.126 37.500 0.00 0.00 0.00 4.49
17 18 5.197549 CACGGTTCATATTAGATTTGCGTG 58.802 41.667 0.00 0.00 0.00 5.34
18 19 4.873827 ACACGGTTCATATTAGATTTGCGT 59.126 37.500 0.00 0.00 0.00 5.24
19 20 5.403897 ACACGGTTCATATTAGATTTGCG 57.596 39.130 0.00 0.00 0.00 4.85
20 21 7.247728 TCAAACACGGTTCATATTAGATTTGC 58.752 34.615 0.00 0.00 0.00 3.68
21 22 9.225201 CATCAAACACGGTTCATATTAGATTTG 57.775 33.333 0.00 0.00 0.00 2.32
22 23 8.956426 ACATCAAACACGGTTCATATTAGATTT 58.044 29.630 0.00 0.00 0.00 2.17
23 24 8.506168 ACATCAAACACGGTTCATATTAGATT 57.494 30.769 0.00 0.00 0.00 2.40
24 25 7.042725 CGACATCAAACACGGTTCATATTAGAT 60.043 37.037 0.00 0.00 0.00 1.98
25 26 6.254804 CGACATCAAACACGGTTCATATTAGA 59.745 38.462 0.00 0.00 0.00 2.10
26 27 6.035650 ACGACATCAAACACGGTTCATATTAG 59.964 38.462 0.00 0.00 0.00 1.73
27 28 5.870433 ACGACATCAAACACGGTTCATATTA 59.130 36.000 0.00 0.00 0.00 0.98
28 29 4.693566 ACGACATCAAACACGGTTCATATT 59.306 37.500 0.00 0.00 0.00 1.28
29 30 4.250464 ACGACATCAAACACGGTTCATAT 58.750 39.130 0.00 0.00 0.00 1.78
30 31 3.655486 ACGACATCAAACACGGTTCATA 58.345 40.909 0.00 0.00 0.00 2.15
31 32 2.478894 GACGACATCAAACACGGTTCAT 59.521 45.455 0.00 0.00 0.00 2.57
32 33 1.862201 GACGACATCAAACACGGTTCA 59.138 47.619 0.00 0.00 0.00 3.18
33 34 1.136721 CGACGACATCAAACACGGTTC 60.137 52.381 0.00 0.00 0.00 3.62
34 35 0.856641 CGACGACATCAAACACGGTT 59.143 50.000 0.00 0.00 0.00 4.44
35 36 1.554042 GCGACGACATCAAACACGGT 61.554 55.000 0.00 0.00 0.00 4.83
36 37 1.129809 GCGACGACATCAAACACGG 59.870 57.895 0.00 0.00 0.00 4.94
37 38 1.129809 GGCGACGACATCAAACACG 59.870 57.895 0.00 0.00 0.00 4.49
38 39 0.796312 ATGGCGACGACATCAAACAC 59.204 50.000 11.28 0.00 0.00 3.32
39 40 1.075542 GATGGCGACGACATCAAACA 58.924 50.000 33.52 0.00 46.49 2.83
40 41 3.877801 GATGGCGACGACATCAAAC 57.122 52.632 33.52 11.36 46.49 2.93
44 45 1.692148 TTTGCGATGGCGACGACATC 61.692 55.000 29.94 29.94 44.03 3.06
45 46 1.739929 TTTGCGATGGCGACGACAT 60.740 52.632 17.96 17.96 44.10 3.06
46 47 2.356433 TTTGCGATGGCGACGACA 60.356 55.556 5.51 5.51 44.10 4.35
47 48 2.095843 GTTTGCGATGGCGACGAC 59.904 61.111 0.00 0.00 44.10 4.34
50 51 0.659123 AAAACGTTTGCGATGGCGAC 60.659 50.000 15.46 0.00 44.10 5.19
51 52 0.658829 CAAAACGTTTGCGATGGCGA 60.659 50.000 15.46 0.00 44.10 5.54
52 53 1.766176 CAAAACGTTTGCGATGGCG 59.234 52.632 15.46 0.00 44.10 5.69
53 54 1.486801 GCAAAACGTTTGCGATGGC 59.513 52.632 15.46 8.10 42.00 4.40
76 77 6.856938 CGGTGATGTAATAAAACCGTCAAAAA 59.143 34.615 4.44 0.00 46.66 1.94
77 78 6.372185 CGGTGATGTAATAAAACCGTCAAAA 58.628 36.000 4.44 0.00 46.66 2.44
78 79 5.929278 CGGTGATGTAATAAAACCGTCAAA 58.071 37.500 4.44 0.00 46.66 2.69
79 80 5.533533 CGGTGATGTAATAAAACCGTCAA 57.466 39.130 4.44 0.00 46.66 3.18
98 99 2.164219 GGATGCATCAATCACAAACGGT 59.836 45.455 27.25 0.00 0.00 4.83
99 100 2.480073 GGGATGCATCAATCACAAACGG 60.480 50.000 27.25 0.00 29.82 4.44
100 101 2.164017 TGGGATGCATCAATCACAAACG 59.836 45.455 27.25 0.00 37.03 3.60
101 102 3.056678 TGTGGGATGCATCAATCACAAAC 60.057 43.478 30.09 17.31 41.55 2.93
102 103 3.056678 GTGTGGGATGCATCAATCACAAA 60.057 43.478 32.01 19.02 41.55 2.83
103 104 2.492881 GTGTGGGATGCATCAATCACAA 59.507 45.455 32.01 21.42 41.55 3.33
104 105 2.093890 GTGTGGGATGCATCAATCACA 58.906 47.619 29.27 29.27 37.64 3.58
105 106 2.093890 TGTGTGGGATGCATCAATCAC 58.906 47.619 27.25 26.68 0.00 3.06
106 107 2.291089 ACTGTGTGGGATGCATCAATCA 60.291 45.455 27.25 18.34 0.00 2.57
107 108 2.372264 ACTGTGTGGGATGCATCAATC 58.628 47.619 27.25 16.13 0.00 2.67
108 109 2.519771 ACTGTGTGGGATGCATCAAT 57.480 45.000 27.25 0.00 0.00 2.57
109 110 2.291209 AACTGTGTGGGATGCATCAA 57.709 45.000 27.25 12.78 0.00 2.57
110 111 2.161855 GAAACTGTGTGGGATGCATCA 58.838 47.619 27.25 6.50 0.00 3.07
111 112 1.131126 CGAAACTGTGTGGGATGCATC 59.869 52.381 18.81 18.81 0.00 3.91
112 113 1.167851 CGAAACTGTGTGGGATGCAT 58.832 50.000 0.00 0.00 0.00 3.96
113 114 0.179032 ACGAAACTGTGTGGGATGCA 60.179 50.000 0.00 0.00 0.00 3.96
114 115 0.517316 GACGAAACTGTGTGGGATGC 59.483 55.000 0.00 0.00 0.00 3.91
115 116 1.877637 TGACGAAACTGTGTGGGATG 58.122 50.000 0.00 0.00 0.00 3.51
116 117 2.631160 TTGACGAAACTGTGTGGGAT 57.369 45.000 0.00 0.00 0.00 3.85
117 118 2.285083 CTTTGACGAAACTGTGTGGGA 58.715 47.619 0.00 0.00 0.00 4.37
118 119 1.333619 CCTTTGACGAAACTGTGTGGG 59.666 52.381 0.00 0.00 0.00 4.61
119 120 1.333619 CCCTTTGACGAAACTGTGTGG 59.666 52.381 0.00 0.00 0.00 4.17
120 121 2.014128 ACCCTTTGACGAAACTGTGTG 58.986 47.619 0.00 0.00 0.00 3.82
121 122 2.093128 AGACCCTTTGACGAAACTGTGT 60.093 45.455 0.00 0.00 0.00 3.72
122 123 2.544267 GAGACCCTTTGACGAAACTGTG 59.456 50.000 0.00 0.00 0.00 3.66
123 124 2.434702 AGAGACCCTTTGACGAAACTGT 59.565 45.455 0.00 0.00 0.00 3.55
124 125 2.802816 CAGAGACCCTTTGACGAAACTG 59.197 50.000 0.00 0.00 0.00 3.16
125 126 2.698797 TCAGAGACCCTTTGACGAAACT 59.301 45.455 0.00 0.00 0.00 2.66
126 127 3.107642 TCAGAGACCCTTTGACGAAAC 57.892 47.619 0.00 0.00 0.00 2.78
127 128 4.315803 GAATCAGAGACCCTTTGACGAAA 58.684 43.478 0.00 0.00 27.56 3.46
128 129 3.614150 CGAATCAGAGACCCTTTGACGAA 60.614 47.826 0.00 0.00 27.56 3.85
129 130 2.094700 CGAATCAGAGACCCTTTGACGA 60.095 50.000 0.00 0.00 27.56 4.20
130 131 2.094700 TCGAATCAGAGACCCTTTGACG 60.095 50.000 0.00 0.00 27.56 4.35
131 132 3.056465 AGTCGAATCAGAGACCCTTTGAC 60.056 47.826 0.00 0.00 38.08 3.18
132 133 3.056536 CAGTCGAATCAGAGACCCTTTGA 60.057 47.826 0.00 0.00 38.08 2.69
133 134 3.257393 CAGTCGAATCAGAGACCCTTTG 58.743 50.000 0.00 0.00 38.08 2.77
134 135 2.900546 ACAGTCGAATCAGAGACCCTTT 59.099 45.455 0.00 0.00 38.08 3.11
135 136 2.494073 GACAGTCGAATCAGAGACCCTT 59.506 50.000 0.00 0.00 38.08 3.95
136 137 2.096248 GACAGTCGAATCAGAGACCCT 58.904 52.381 0.00 0.00 38.08 4.34
137 138 1.202200 CGACAGTCGAATCAGAGACCC 60.202 57.143 18.63 0.00 43.74 4.46
138 139 1.795889 GCGACAGTCGAATCAGAGACC 60.796 57.143 27.29 0.51 43.74 3.85
139 140 1.540407 GCGACAGTCGAATCAGAGAC 58.460 55.000 27.29 1.28 43.74 3.36
140 141 0.097150 CGCGACAGTCGAATCAGAGA 59.903 55.000 27.29 0.00 43.74 3.10
141 142 0.097150 TCGCGACAGTCGAATCAGAG 59.903 55.000 27.29 7.79 43.74 3.35
142 143 0.733150 ATCGCGACAGTCGAATCAGA 59.267 50.000 27.29 15.67 43.74 3.27
143 144 1.253800 CAATCGCGACAGTCGAATCAG 59.746 52.381 27.29 11.11 43.74 2.90
144 145 1.268265 CAATCGCGACAGTCGAATCA 58.732 50.000 27.29 6.59 43.74 2.57
145 146 0.572590 CCAATCGCGACAGTCGAATC 59.427 55.000 27.29 8.05 43.74 2.52
146 147 0.172578 TCCAATCGCGACAGTCGAAT 59.827 50.000 27.29 15.38 43.74 3.34
147 148 0.731514 GTCCAATCGCGACAGTCGAA 60.732 55.000 27.29 13.70 43.74 3.71
148 149 1.154093 GTCCAATCGCGACAGTCGA 60.154 57.895 27.29 7.00 43.74 4.20
149 150 2.158959 GGTCCAATCGCGACAGTCG 61.159 63.158 19.10 19.10 43.89 4.18
150 151 0.460284 ATGGTCCAATCGCGACAGTC 60.460 55.000 12.93 0.27 31.55 3.51
151 152 0.460284 GATGGTCCAATCGCGACAGT 60.460 55.000 12.93 0.00 31.55 3.55
152 153 1.154205 GGATGGTCCAATCGCGACAG 61.154 60.000 12.93 6.83 36.28 3.51
153 154 1.153449 GGATGGTCCAATCGCGACA 60.153 57.895 12.93 3.60 36.28 4.35
154 155 1.144057 AGGATGGTCCAATCGCGAC 59.856 57.895 12.93 0.00 39.61 5.19
155 156 1.143838 CAGGATGGTCCAATCGCGA 59.856 57.895 13.09 13.09 39.61 5.87
156 157 2.537560 GCAGGATGGTCCAATCGCG 61.538 63.158 0.00 0.00 39.61 5.87
157 158 1.442526 CTGCAGGATGGTCCAATCGC 61.443 60.000 5.57 0.00 39.61 4.58
158 159 0.107508 ACTGCAGGATGGTCCAATCG 60.108 55.000 19.93 0.00 39.61 3.34
159 160 2.843701 CTACTGCAGGATGGTCCAATC 58.156 52.381 19.93 0.00 39.61 2.67
160 161 1.133976 GCTACTGCAGGATGGTCCAAT 60.134 52.381 19.93 0.00 39.61 3.16
161 162 0.253044 GCTACTGCAGGATGGTCCAA 59.747 55.000 19.93 0.00 39.61 3.53
162 163 1.907739 GCTACTGCAGGATGGTCCA 59.092 57.895 19.93 0.00 39.61 4.02
163 164 1.227380 CGCTACTGCAGGATGGTCC 60.227 63.158 19.93 0.00 39.64 4.46
164 165 0.249238 CTCGCTACTGCAGGATGGTC 60.249 60.000 19.93 0.00 39.64 4.02
165 166 0.972983 ACTCGCTACTGCAGGATGGT 60.973 55.000 19.93 6.11 39.64 3.55
166 167 0.529337 CACTCGCTACTGCAGGATGG 60.529 60.000 19.93 4.20 39.64 3.51
167 168 0.529337 CCACTCGCTACTGCAGGATG 60.529 60.000 19.93 3.84 39.64 3.51
168 169 0.972983 ACCACTCGCTACTGCAGGAT 60.973 55.000 19.93 0.00 39.64 3.24
169 170 0.323087 TACCACTCGCTACTGCAGGA 60.323 55.000 19.93 9.06 39.64 3.86
170 171 0.179134 GTACCACTCGCTACTGCAGG 60.179 60.000 19.93 1.57 39.64 4.85
171 172 0.811915 AGTACCACTCGCTACTGCAG 59.188 55.000 13.48 13.48 39.64 4.41
172 173 1.254026 AAGTACCACTCGCTACTGCA 58.746 50.000 0.00 0.00 39.64 4.41
173 174 2.365408 AAAGTACCACTCGCTACTGC 57.635 50.000 0.00 0.00 0.00 4.40
174 175 6.774354 TTTTAAAAGTACCACTCGCTACTG 57.226 37.500 0.00 0.00 0.00 2.74
175 176 6.762661 TGTTTTTAAAAGTACCACTCGCTACT 59.237 34.615 0.14 0.00 0.00 2.57
176 177 6.847792 GTGTTTTTAAAAGTACCACTCGCTAC 59.152 38.462 0.14 0.00 0.00 3.58
177 178 6.292274 CGTGTTTTTAAAAGTACCACTCGCTA 60.292 38.462 9.75 0.00 0.00 4.26
178 179 5.502869 CGTGTTTTTAAAAGTACCACTCGCT 60.503 40.000 9.75 0.00 0.00 4.93
179 180 4.667504 CGTGTTTTTAAAAGTACCACTCGC 59.332 41.667 9.75 0.00 0.00 5.03
180 181 5.898061 GTCGTGTTTTTAAAAGTACCACTCG 59.102 40.000 13.78 13.78 0.00 4.18
181 182 6.774084 TGTCGTGTTTTTAAAAGTACCACTC 58.226 36.000 0.14 0.00 0.00 3.51
203 204 9.857656 ATATAGAAGACATTTTCATCACCATGT 57.142 29.630 0.00 0.00 32.41 3.21
231 245 6.908825 AGCAAATTAGAACATAACTTCGCAA 58.091 32.000 0.00 0.00 0.00 4.85
279 293 7.597288 ATTAAAAAGGCACAACTCTTAACCT 57.403 32.000 0.00 0.00 0.00 3.50
311 325 8.624776 GTTCAAAGCTAGCCTGATGTATAAATT 58.375 33.333 12.13 0.00 0.00 1.82
319 333 3.603532 TCAGTTCAAAGCTAGCCTGATG 58.396 45.455 12.13 10.74 0.00 3.07
350 364 8.762645 AGGTCATAGATAGTCATTGAACAAGAA 58.237 33.333 0.00 0.00 0.00 2.52
374 388 0.250234 TCAGGAAGGCGTCATTCAGG 59.750 55.000 2.23 0.00 0.00 3.86
377 391 3.938963 TGTAATTCAGGAAGGCGTCATTC 59.061 43.478 2.23 0.00 0.00 2.67
378 392 3.950397 TGTAATTCAGGAAGGCGTCATT 58.050 40.909 2.23 0.00 0.00 2.57
381 395 3.065371 CCAATGTAATTCAGGAAGGCGTC 59.935 47.826 0.00 0.00 31.22 5.19
382 396 3.016736 CCAATGTAATTCAGGAAGGCGT 58.983 45.455 0.00 0.00 31.22 5.68
383 397 3.016736 ACCAATGTAATTCAGGAAGGCG 58.983 45.455 0.00 0.00 31.22 5.52
384 398 4.273318 AGACCAATGTAATTCAGGAAGGC 58.727 43.478 0.00 0.00 31.22 4.35
410 438 3.181494 CCATGTGTGCACAATCACCATAG 60.181 47.826 23.59 9.63 45.41 2.23
415 443 0.314618 TGCCATGTGTGCACAATCAC 59.685 50.000 23.59 9.86 45.41 3.06
467 1385 6.147164 CAGTATCGAAACTTGCCTCTTTAACA 59.853 38.462 0.00 0.00 0.00 2.41
470 1388 4.630069 GCAGTATCGAAACTTGCCTCTTTA 59.370 41.667 0.00 0.00 0.00 1.85
484 1402 0.815213 GGCATTGGCAGCAGTATCGA 60.815 55.000 5.17 0.00 43.71 3.59
523 1441 2.489275 GGCAGGGAGAGAGAGCTCG 61.489 68.421 8.37 0.00 45.98 5.03
586 1504 9.645128 TCAACCAAACATCCATCTCATTATATT 57.355 29.630 0.00 0.00 0.00 1.28
659 1577 2.061740 ACGACTAAAACTCCAGCGAC 57.938 50.000 0.00 0.00 0.00 5.19
797 1717 7.448588 GCAAATGCACGTATTATTGATTGAA 57.551 32.000 0.00 0.00 41.59 2.69
875 1797 2.188161 GTCGCCAAACCCAACCGAA 61.188 57.895 0.00 0.00 0.00 4.30
876 1798 2.592287 GTCGCCAAACCCAACCGA 60.592 61.111 0.00 0.00 0.00 4.69
877 1799 4.020378 CGTCGCCAAACCCAACCG 62.020 66.667 0.00 0.00 0.00 4.44
878 1800 2.125202 CTTCGTCGCCAAACCCAACC 62.125 60.000 0.00 0.00 0.00 3.77
916 1838 2.123428 GCTCCAAATGGATGCGGCT 61.123 57.895 1.93 0.00 44.46 5.52
1363 2301 2.683933 AGGAACGGAGCGGGATGT 60.684 61.111 0.00 0.00 0.00 3.06
1521 2459 1.830408 CTCCTCCTTCGCCGGATCT 60.830 63.158 5.05 0.00 31.43 2.75
1615 2553 2.483889 CCTTCTTCCGATACTCCTTGGC 60.484 54.545 0.00 0.00 0.00 4.52
1751 2689 1.659098 GAAACTCGTGTGCTATTCCGG 59.341 52.381 0.00 0.00 0.00 5.14
1758 2696 0.390860 AGCTCAGAAACTCGTGTGCT 59.609 50.000 0.00 0.00 38.39 4.40
1782 2720 2.099921 CACCTCTACCATCTTCTCCACG 59.900 54.545 0.00 0.00 0.00 4.94
1797 2735 0.980423 GGCTGAACTTCTCCACCTCT 59.020 55.000 0.00 0.00 0.00 3.69
1815 2753 0.951558 CAAACCACTTCCGGAACTGG 59.048 55.000 30.48 30.48 32.65 4.00
1824 2762 1.076332 CGTCGATCCCAAACCACTTC 58.924 55.000 0.00 0.00 0.00 3.01
1872 2810 4.273148 CGAGAGGTAAAATATCCCAGGG 57.727 50.000 0.00 0.00 0.00 4.45
1896 2834 1.017387 CTGTATGCCGCTTTCCCTTC 58.983 55.000 0.00 0.00 0.00 3.46
2037 2975 5.413499 GCACTTGAAGACATATTGGCATTT 58.587 37.500 0.00 0.00 0.00 2.32
2046 2984 3.441222 CAGCATTGGCACTTGAAGACATA 59.559 43.478 0.00 0.00 44.61 2.29
2067 3005 1.207811 TCATCGCTCTCTTTGGCATCA 59.792 47.619 0.00 0.00 0.00 3.07
2209 3147 0.471591 TTTGCCATCCAAGTTGGGCT 60.472 50.000 21.85 7.05 46.53 5.19
2249 3190 6.791887 AACATCCATCGTCATCATCAATAC 57.208 37.500 0.00 0.00 0.00 1.89
2252 3193 5.430886 AGAAACATCCATCGTCATCATCAA 58.569 37.500 0.00 0.00 0.00 2.57
2356 3297 5.201713 TGAACTTCACTCTTGACCTACAG 57.798 43.478 0.00 0.00 0.00 2.74
2357 3298 4.649674 ACTGAACTTCACTCTTGACCTACA 59.350 41.667 0.00 0.00 0.00 2.74
2417 3358 7.903995 ACATGAGCTTTCAAAACTTTTTCAA 57.096 28.000 0.00 0.00 0.00 2.69
2544 3488 5.914635 CAGTGACGAAACAACAATAAGCAAT 59.085 36.000 0.00 0.00 0.00 3.56
2566 3510 3.624861 GTCCTTCATTAGGCATGTCACAG 59.375 47.826 0.00 0.00 44.37 3.66
2687 3631 9.657419 CCAATAACAATTCAAAGCTTTCCTTAT 57.343 29.630 9.23 2.02 32.20 1.73
2778 3723 7.272978 GTGCCTATCAACTTAATCAGGACTTA 58.727 38.462 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.