Multiple sequence alignment - TraesCS3D01G167500

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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 TraesCS3D01G167500 chr3D 100.000 4690 0 0 1 4690 141664295 141659606 0.000000e+00 8661.0
1 TraesCS3D01G167500 chr3D 92.308 182 13 1 3 184 609019263 609019443 1.670000e-64 257.0
2 TraesCS3D01G167500 chr3D 79.070 129 17 6 1574 1697 141662599 141662722 3.890000e-11 80.5
3 TraesCS3D01G167500 chr3D 90.196 51 4 1 583 632 581014558 581014508 1.090000e-06 65.8
4 TraesCS3D01G167500 chr3D 94.872 39 1 1 4342 4379 378055454 378055492 5.070000e-05 60.2
5 TraesCS3D01G167500 chr3B 94.558 2242 86 23 2263 4486 203646512 203644289 0.000000e+00 3432.0
6 TraesCS3D01G167500 chr3B 92.650 898 35 20 829 1699 203655087 203654194 0.000000e+00 1264.0
7 TraesCS3D01G167500 chr3B 96.435 561 18 2 1707 2267 203652950 203652392 0.000000e+00 924.0
8 TraesCS3D01G167500 chr3B 96.875 192 6 0 4499 4690 203644172 203643981 5.850000e-84 322.0
9 TraesCS3D01G167500 chr3B 84.797 296 41 3 181 476 203655662 203655371 1.280000e-75 294.0
10 TraesCS3D01G167500 chr3B 87.978 183 19 3 4 185 527381417 527381597 3.680000e-51 213.0
11 TraesCS3D01G167500 chr3B 78.740 127 17 7 1576 1697 203654198 203654319 5.030000e-10 76.8
12 TraesCS3D01G167500 chr3B 97.059 34 1 0 588 621 777652905 777652938 1.820000e-04 58.4
13 TraesCS3D01G167500 chr3A 92.510 1255 61 15 1509 2757 160081254 160080027 0.000000e+00 1766.0
14 TraesCS3D01G167500 chr3A 93.046 1136 57 18 2966 4085 160077168 160076039 0.000000e+00 1640.0
15 TraesCS3D01G167500 chr3A 86.618 1091 75 39 321 1370 160082552 160081492 0.000000e+00 1140.0
16 TraesCS3D01G167500 chr3A 92.832 572 26 7 4124 4690 160076042 160075481 0.000000e+00 815.0
17 TraesCS3D01G167500 chr3A 95.833 216 8 1 2756 2970 160079865 160079650 9.660000e-92 348.0
18 TraesCS3D01G167500 chr3A 88.971 136 14 1 181 316 160293117 160292983 2.900000e-37 167.0
19 TraesCS3D01G167500 chr7B 88.178 1032 78 23 2764 3768 642275870 642274856 0.000000e+00 1190.0
20 TraesCS3D01G167500 chr7B 90.761 552 43 6 2219 2764 642276666 642276117 0.000000e+00 730.0
21 TraesCS3D01G167500 chr7B 90.037 271 22 3 996 1266 642277150 642276885 3.470000e-91 346.0
22 TraesCS3D01G167500 chr7B 89.404 151 13 3 2036 2184 642276882 642276733 2.230000e-43 187.0
23 TraesCS3D01G167500 chr7B 100.000 31 0 0 4343 4373 728627202 728627172 1.820000e-04 58.4
24 TraesCS3D01G167500 chr7A 86.406 1074 84 24 2764 3825 670754517 670753494 0.000000e+00 1118.0
25 TraesCS3D01G167500 chr7A 88.679 424 38 6 2219 2635 670755231 670754811 4.190000e-140 508.0
26 TraesCS3D01G167500 chr7A 86.920 237 24 7 1031 1266 670755756 670755526 4.660000e-65 259.0
27 TraesCS3D01G167500 chr7A 100.000 29 0 0 4344 4372 701033023 701033051 2.000000e-03 54.7
28 TraesCS3D01G167500 chr7D 90.048 834 60 16 2771 3591 578489197 578488374 0.000000e+00 1059.0
29 TraesCS3D01G167500 chr7D 90.545 550 46 3 2219 2764 578489814 578489267 0.000000e+00 723.0
30 TraesCS3D01G167500 chr7D 89.091 275 19 5 996 1266 578490298 578490031 9.730000e-87 331.0
31 TraesCS3D01G167500 chr7D 83.871 186 20 6 2036 2221 578490028 578489853 8.070000e-38 169.0
32 TraesCS3D01G167500 chr6D 92.090 177 13 1 3 178 140104236 140104412 1.010000e-61 248.0
33 TraesCS3D01G167500 chr6D 89.831 177 13 4 3 178 336531949 336532121 6.110000e-54 222.0
34 TraesCS3D01G167500 chr6D 100.000 29 0 0 4345 4373 52011185 52011213 2.000000e-03 54.7
35 TraesCS3D01G167500 chr4B 89.944 179 17 1 4 181 43736004 43736182 3.650000e-56 230.0
36 TraesCS3D01G167500 chr4B 100.000 28 0 0 4345 4372 661192494 661192521 8.000000e-03 52.8
37 TraesCS3D01G167500 chrUn 88.235 187 20 2 3 187 22531664 22531478 6.110000e-54 222.0
38 TraesCS3D01G167500 chr2D 88.333 180 20 1 3 181 469007498 469007319 1.020000e-51 215.0
39 TraesCS3D01G167500 chr1B 86.432 199 23 4 3 200 41445615 41445810 1.020000e-51 215.0
40 TraesCS3D01G167500 chr1B 86.364 88 6 5 541 625 432610691 432610775 1.800000e-14 91.6
41 TraesCS3D01G167500 chr1B 100.000 30 0 0 4344 4373 155655573 155655602 6.560000e-04 56.5
42 TraesCS3D01G167500 chr6B 88.202 178 18 3 3 178 285227616 285227440 4.760000e-50 209.0
43 TraesCS3D01G167500 chr1D 86.364 88 6 5 541 625 319684025 319684109 1.800000e-14 91.6
44 TraesCS3D01G167500 chr1D 100.000 29 0 0 4342 4370 493609771 493609799 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 TraesCS3D01G167500 chr3D 141659606 141664295 4689 True 8661.000000 8661 100.00000 1 4690 1 chr3D.!!$R1 4689
1 TraesCS3D01G167500 chr3B 203643981 203646512 2531 True 1877.000000 3432 95.71650 2263 4690 2 chr3B.!!$R1 2427
2 TraesCS3D01G167500 chr3B 203652392 203655662 3270 True 827.333333 1264 91.29400 181 2267 3 chr3B.!!$R2 2086
3 TraesCS3D01G167500 chr3A 160075481 160082552 7071 True 1141.800000 1766 92.16780 321 4690 5 chr3A.!!$R2 4369
4 TraesCS3D01G167500 chr7B 642274856 642277150 2294 True 613.250000 1190 89.59500 996 3768 4 chr7B.!!$R2 2772
5 TraesCS3D01G167500 chr7A 670753494 670755756 2262 True 628.333333 1118 87.33500 1031 3825 3 chr7A.!!$R1 2794
6 TraesCS3D01G167500 chr7D 578488374 578490298 1924 True 570.500000 1059 88.38875 996 3591 4 chr7D.!!$R1 2595

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
152 153 0.030504 TTGTGCCATGTTGCTTCGTG 59.969 50.0 0.00 0.00 0.00 4.35 F
532 552 0.037046 GCTCATGGGGTGCCTTTTTG 60.037 55.0 0.00 0.00 0.00 2.44 F
875 967 0.250081 GGACCGGAGATGCCTCAATC 60.250 60.0 9.46 0.00 41.20 2.67 F
876 968 0.598680 GACCGGAGATGCCTCAATCG 60.599 60.0 9.46 0.00 41.20 3.34 F
2485 4120 0.676782 GCTTCCAACACGGCAGGTAT 60.677 55.0 0.00 0.00 33.14 2.73 F
3035 7516 1.597742 TGACTTGGCAAGTGAGAAGC 58.402 50.0 35.57 20.41 43.03 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1292 1415 0.755686 AAGATGAGATGCGAGGGACC 59.244 55.000 0.00 0.00 0.00 4.46 R
2164 3756 2.629617 CCCCTTTCTTTTCACATGCTGT 59.370 45.455 0.00 0.00 0.00 4.40 R
2573 4215 4.386867 TCCTGATTCTCACGGTATGAAC 57.613 45.455 0.00 0.00 36.69 3.18 R
2935 4918 5.564550 AGCAAACTTCTATGGTCTGTCATT 58.435 37.500 0.00 0.00 0.00 2.57 R
3670 8164 0.383949 GGAAAAGTGGCTGCGACAAA 59.616 50.000 17.03 0.00 0.00 2.83 R
4530 9140 0.820871 CTACCCTGAGCAGACTGGTC 59.179 60.000 24.56 24.56 44.54 4.02 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
69 70 9.921637 ATGAGATAAAACATTTTTAAGCCGAAA 57.078 25.926 0.00 0.00 0.00 3.46
70 71 9.751542 TGAGATAAAACATTTTTAAGCCGAAAA 57.248 25.926 0.00 0.00 0.00 2.29
72 73 8.984764 AGATAAAACATTTTTAAGCCGAAAACC 58.015 29.630 0.00 0.00 0.00 3.27
73 74 6.986904 AAAACATTTTTAAGCCGAAAACCA 57.013 29.167 0.00 0.00 0.00 3.67
74 75 6.986904 AAACATTTTTAAGCCGAAAACCAA 57.013 29.167 0.00 0.00 0.00 3.67
75 76 6.986904 AACATTTTTAAGCCGAAAACCAAA 57.013 29.167 0.00 0.00 0.00 3.28
76 77 6.986904 ACATTTTTAAGCCGAAAACCAAAA 57.013 29.167 0.00 0.00 0.00 2.44
77 78 7.379098 ACATTTTTAAGCCGAAAACCAAAAA 57.621 28.000 0.00 0.00 31.65 1.94
78 79 7.990917 ACATTTTTAAGCCGAAAACCAAAAAT 58.009 26.923 0.00 0.00 36.51 1.82
79 80 9.110502 ACATTTTTAAGCCGAAAACCAAAAATA 57.889 25.926 0.00 0.00 35.15 1.40
83 84 9.549078 TTTTAAGCCGAAAACCAAAAATATTCT 57.451 25.926 0.00 0.00 0.00 2.40
84 85 8.527567 TTAAGCCGAAAACCAAAAATATTCTG 57.472 30.769 0.00 0.00 0.00 3.02
85 86 4.929211 AGCCGAAAACCAAAAATATTCTGC 59.071 37.500 0.00 0.00 32.56 4.26
86 87 4.929211 GCCGAAAACCAAAAATATTCTGCT 59.071 37.500 0.00 0.00 30.63 4.24
87 88 5.163963 GCCGAAAACCAAAAATATTCTGCTG 60.164 40.000 0.00 0.00 30.63 4.41
88 89 6.155827 CCGAAAACCAAAAATATTCTGCTGA 58.844 36.000 0.00 0.00 0.00 4.26
89 90 6.813152 CCGAAAACCAAAAATATTCTGCTGAT 59.187 34.615 0.00 0.00 0.00 2.90
90 91 7.201461 CCGAAAACCAAAAATATTCTGCTGATG 60.201 37.037 0.00 0.00 0.00 3.07
91 92 7.329226 CGAAAACCAAAAATATTCTGCTGATGT 59.671 33.333 0.00 0.00 0.00 3.06
92 93 8.538409 AAAACCAAAAATATTCTGCTGATGTC 57.462 30.769 0.00 0.00 0.00 3.06
93 94 6.839124 ACCAAAAATATTCTGCTGATGTCA 57.161 33.333 0.00 0.00 0.00 3.58
94 95 7.414222 ACCAAAAATATTCTGCTGATGTCAT 57.586 32.000 0.00 0.00 0.00 3.06
95 96 7.486647 ACCAAAAATATTCTGCTGATGTCATC 58.513 34.615 5.83 5.83 0.00 2.92
96 97 7.341256 ACCAAAAATATTCTGCTGATGTCATCT 59.659 33.333 13.90 0.00 0.00 2.90
97 98 7.648112 CCAAAAATATTCTGCTGATGTCATCTG 59.352 37.037 13.90 13.85 0.00 2.90
98 99 7.876936 AAAATATTCTGCTGATGTCATCTGT 57.123 32.000 17.91 4.02 0.00 3.41
99 100 7.876936 AAATATTCTGCTGATGTCATCTGTT 57.123 32.000 17.91 3.54 0.00 3.16
100 101 7.876936 AATATTCTGCTGATGTCATCTGTTT 57.123 32.000 17.91 5.08 0.00 2.83
101 102 7.876936 ATATTCTGCTGATGTCATCTGTTTT 57.123 32.000 17.91 5.35 0.00 2.43
102 103 5.366829 TTCTGCTGATGTCATCTGTTTTG 57.633 39.130 17.91 8.45 0.00 2.44
103 104 4.644498 TCTGCTGATGTCATCTGTTTTGA 58.356 39.130 17.91 10.08 0.00 2.69
104 105 5.250982 TCTGCTGATGTCATCTGTTTTGAT 58.749 37.500 17.91 0.00 0.00 2.57
105 106 5.123344 TCTGCTGATGTCATCTGTTTTGATG 59.877 40.000 17.91 0.00 43.66 3.07
106 107 4.763279 TGCTGATGTCATCTGTTTTGATGT 59.237 37.500 17.91 0.00 43.03 3.06
107 108 5.093457 GCTGATGTCATCTGTTTTGATGTG 58.907 41.667 17.91 0.00 43.03 3.21
108 109 5.632244 TGATGTCATCTGTTTTGATGTGG 57.368 39.130 13.90 0.00 43.03 4.17
109 110 3.921119 TGTCATCTGTTTTGATGTGGC 57.079 42.857 0.00 0.00 43.03 5.01
110 111 3.220940 TGTCATCTGTTTTGATGTGGCA 58.779 40.909 0.00 0.00 43.03 4.92
111 112 3.635836 TGTCATCTGTTTTGATGTGGCAA 59.364 39.130 0.00 0.00 43.03 4.52
112 113 4.099113 TGTCATCTGTTTTGATGTGGCAAA 59.901 37.500 0.00 0.00 43.03 3.68
113 114 5.049167 GTCATCTGTTTTGATGTGGCAAAA 58.951 37.500 0.00 0.00 43.31 2.44
114 115 5.697633 GTCATCTGTTTTGATGTGGCAAAAT 59.302 36.000 0.00 0.00 45.96 1.82
115 116 5.697178 TCATCTGTTTTGATGTGGCAAAATG 59.303 36.000 0.00 0.00 45.96 2.32
116 117 5.273674 TCTGTTTTGATGTGGCAAAATGA 57.726 34.783 0.00 0.00 45.96 2.57
117 118 5.668471 TCTGTTTTGATGTGGCAAAATGAA 58.332 33.333 0.00 0.00 45.96 2.57
118 119 6.289834 TCTGTTTTGATGTGGCAAAATGAAT 58.710 32.000 0.00 0.00 45.96 2.57
119 120 6.203145 TCTGTTTTGATGTGGCAAAATGAATG 59.797 34.615 0.00 0.00 45.96 2.67
120 121 6.053650 TGTTTTGATGTGGCAAAATGAATGA 58.946 32.000 0.00 0.00 45.96 2.57
121 122 6.711194 TGTTTTGATGTGGCAAAATGAATGAT 59.289 30.769 0.00 0.00 45.96 2.45
122 123 7.876582 TGTTTTGATGTGGCAAAATGAATGATA 59.123 29.630 0.00 0.00 45.96 2.15
123 124 7.830940 TTTGATGTGGCAAAATGAATGATAC 57.169 32.000 0.00 0.00 35.03 2.24
124 125 6.778834 TGATGTGGCAAAATGAATGATACT 57.221 33.333 0.00 0.00 0.00 2.12
125 126 6.566141 TGATGTGGCAAAATGAATGATACTG 58.434 36.000 0.00 0.00 0.00 2.74
126 127 5.327616 TGTGGCAAAATGAATGATACTGG 57.672 39.130 0.00 0.00 0.00 4.00
127 128 5.015515 TGTGGCAAAATGAATGATACTGGA 58.984 37.500 0.00 0.00 0.00 3.86
128 129 5.125900 TGTGGCAAAATGAATGATACTGGAG 59.874 40.000 0.00 0.00 0.00 3.86
129 130 4.646040 TGGCAAAATGAATGATACTGGAGG 59.354 41.667 0.00 0.00 0.00 4.30
130 131 4.646492 GGCAAAATGAATGATACTGGAGGT 59.354 41.667 0.00 0.00 0.00 3.85
131 132 5.450965 GGCAAAATGAATGATACTGGAGGTG 60.451 44.000 0.00 0.00 0.00 4.00
132 133 5.126061 GCAAAATGAATGATACTGGAGGTGT 59.874 40.000 0.00 0.00 0.00 4.16
133 134 6.350445 GCAAAATGAATGATACTGGAGGTGTT 60.350 38.462 0.00 0.00 0.00 3.32
134 135 7.605449 CAAAATGAATGATACTGGAGGTGTTT 58.395 34.615 0.00 0.00 0.00 2.83
135 136 6.764308 AATGAATGATACTGGAGGTGTTTG 57.236 37.500 0.00 0.00 0.00 2.93
136 137 5.241403 TGAATGATACTGGAGGTGTTTGT 57.759 39.130 0.00 0.00 0.00 2.83
137 138 5.003160 TGAATGATACTGGAGGTGTTTGTG 58.997 41.667 0.00 0.00 0.00 3.33
138 139 2.778299 TGATACTGGAGGTGTTTGTGC 58.222 47.619 0.00 0.00 0.00 4.57
139 140 2.084546 GATACTGGAGGTGTTTGTGCC 58.915 52.381 0.00 0.00 0.00 5.01
140 141 0.840617 TACTGGAGGTGTTTGTGCCA 59.159 50.000 0.00 0.00 0.00 4.92
141 142 0.185901 ACTGGAGGTGTTTGTGCCAT 59.814 50.000 0.00 0.00 0.00 4.40
142 143 0.599558 CTGGAGGTGTTTGTGCCATG 59.400 55.000 0.00 0.00 0.00 3.66
143 144 0.106268 TGGAGGTGTTTGTGCCATGT 60.106 50.000 0.00 0.00 0.00 3.21
144 145 1.039856 GGAGGTGTTTGTGCCATGTT 58.960 50.000 0.00 0.00 0.00 2.71
145 146 1.269726 GGAGGTGTTTGTGCCATGTTG 60.270 52.381 0.00 0.00 0.00 3.33
146 147 0.104671 AGGTGTTTGTGCCATGTTGC 59.895 50.000 0.00 0.00 0.00 4.17
147 148 0.104671 GGTGTTTGTGCCATGTTGCT 59.895 50.000 0.00 0.00 0.00 3.91
148 149 1.473080 GGTGTTTGTGCCATGTTGCTT 60.473 47.619 0.00 0.00 0.00 3.91
149 150 1.860326 GTGTTTGTGCCATGTTGCTTC 59.140 47.619 0.00 0.00 0.00 3.86
150 151 1.130955 GTTTGTGCCATGTTGCTTCG 58.869 50.000 0.00 0.00 0.00 3.79
151 152 0.743688 TTTGTGCCATGTTGCTTCGT 59.256 45.000 0.00 0.00 0.00 3.85
152 153 0.030504 TTGTGCCATGTTGCTTCGTG 59.969 50.000 0.00 0.00 0.00 4.35
153 154 1.730547 GTGCCATGTTGCTTCGTGC 60.731 57.895 0.00 0.00 43.25 5.34
154 155 2.126346 GCCATGTTGCTTCGTGCC 60.126 61.111 0.00 0.00 42.00 5.01
155 156 2.918345 GCCATGTTGCTTCGTGCCA 61.918 57.895 0.00 0.00 42.00 4.92
156 157 1.081242 CCATGTTGCTTCGTGCCAC 60.081 57.895 0.00 0.00 42.00 5.01
158 159 4.155950 TGTTGCTTCGTGCCACAT 57.844 50.000 0.00 0.00 41.54 3.21
159 160 1.653667 TGTTGCTTCGTGCCACATG 59.346 52.632 0.00 0.00 41.54 3.21
160 161 1.100463 TGTTGCTTCGTGCCACATGT 61.100 50.000 0.00 0.00 41.54 3.21
161 162 0.661187 GTTGCTTCGTGCCACATGTG 60.661 55.000 19.31 19.31 42.00 3.21
162 163 1.100463 TTGCTTCGTGCCACATGTGT 61.100 50.000 23.79 0.00 42.00 3.72
163 164 1.081906 GCTTCGTGCCACATGTGTG 60.082 57.895 23.79 15.96 45.23 3.82
175 176 4.481930 CACATGTGTGGACGTTAACATT 57.518 40.909 18.03 0.00 42.10 2.71
176 177 4.854399 CACATGTGTGGACGTTAACATTT 58.146 39.130 18.03 0.00 42.10 2.32
177 178 4.674662 CACATGTGTGGACGTTAACATTTG 59.325 41.667 18.03 9.94 42.10 2.32
178 179 4.336993 ACATGTGTGGACGTTAACATTTGT 59.663 37.500 6.39 10.43 30.98 2.83
179 180 4.280101 TGTGTGGACGTTAACATTTGTG 57.720 40.909 6.39 0.00 0.00 3.33
185 186 7.432838 GTGTGGACGTTAACATTTGTGTAAAAT 59.567 33.333 6.39 0.00 0.00 1.82
187 188 9.448294 GTGGACGTTAACATTTGTGTAAAATTA 57.552 29.630 6.39 0.00 0.00 1.40
211 212 3.569701 GGTCCAAAGACTTGCAATGAAGA 59.430 43.478 0.00 0.00 43.05 2.87
220 221 2.787473 TGCAATGAAGACCGAGGAAT 57.213 45.000 0.00 0.00 0.00 3.01
223 224 4.584874 TGCAATGAAGACCGAGGAATAAA 58.415 39.130 0.00 0.00 0.00 1.40
259 260 5.568392 AGATTGAGGAGAAAAGACTTGCAT 58.432 37.500 0.00 0.00 0.00 3.96
264 265 4.077822 AGGAGAAAAGACTTGCATTGGAG 58.922 43.478 0.00 0.00 0.00 3.86
267 268 4.464008 AGAAAAGACTTGCATTGGAGACA 58.536 39.130 0.00 0.00 39.83 3.41
274 275 3.181440 ACTTGCATTGGAGACAGAGGAAA 60.181 43.478 0.00 0.00 44.54 3.13
276 277 3.415212 TGCATTGGAGACAGAGGAAAAG 58.585 45.455 0.00 0.00 44.54 2.27
277 278 3.072915 TGCATTGGAGACAGAGGAAAAGA 59.927 43.478 0.00 0.00 44.54 2.52
280 281 5.555017 CATTGGAGACAGAGGAAAAGAAGA 58.445 41.667 0.00 0.00 44.54 2.87
283 284 4.408921 TGGAGACAGAGGAAAAGAAGAACA 59.591 41.667 0.00 0.00 35.01 3.18
291 292 3.891977 AGGAAAAGAAGAACAAAGAGGGC 59.108 43.478 0.00 0.00 0.00 5.19
293 294 2.930826 AAGAAGAACAAAGAGGGCGA 57.069 45.000 0.00 0.00 0.00 5.54
295 296 1.416401 AGAAGAACAAAGAGGGCGACA 59.584 47.619 0.00 0.00 0.00 4.35
296 297 2.158813 AGAAGAACAAAGAGGGCGACAA 60.159 45.455 0.00 0.00 0.00 3.18
301 302 1.073923 ACAAAGAGGGCGACAAAGGAT 59.926 47.619 0.00 0.00 0.00 3.24
303 304 0.108138 AAGAGGGCGACAAAGGATCG 60.108 55.000 0.00 0.00 42.55 3.69
319 320 4.564041 AGGATCGTGCTATCATGTTCATC 58.436 43.478 0.00 0.00 32.28 2.92
345 346 3.308688 CCAAACAAGATGGATGAGAGGGT 60.309 47.826 0.00 0.00 40.56 4.34
348 349 3.184628 ACAAGATGGATGAGAGGGTGAA 58.815 45.455 0.00 0.00 0.00 3.18
362 363 5.650283 AGAGGGTGAAACAATATTGGGAAA 58.350 37.500 19.37 0.20 39.98 3.13
369 370 5.417266 TGAAACAATATTGGGAAATCGCTCA 59.583 36.000 19.37 5.73 0.00 4.26
408 427 3.424703 AGTTAGTTAGTAGTGGTGGCGA 58.575 45.455 0.00 0.00 0.00 5.54
409 428 4.021916 AGTTAGTTAGTAGTGGTGGCGAT 58.978 43.478 0.00 0.00 0.00 4.58
410 429 2.961526 AGTTAGTAGTGGTGGCGATG 57.038 50.000 0.00 0.00 0.00 3.84
411 430 2.453521 AGTTAGTAGTGGTGGCGATGA 58.546 47.619 0.00 0.00 0.00 2.92
427 446 0.400213 ATGACAATGGTGGTGACGGT 59.600 50.000 0.00 0.00 0.00 4.83
444 463 2.356913 TGACGATGGCACGTGTGG 60.357 61.111 18.38 0.95 46.52 4.17
449 468 2.281484 ATGGCACGTGTGGGTGAC 60.281 61.111 18.38 0.00 46.42 3.67
451 470 2.281484 GGCACGTGTGGGTGACAT 60.281 61.111 18.38 0.00 45.52 3.06
531 551 0.471591 TGCTCATGGGGTGCCTTTTT 60.472 50.000 0.00 0.00 35.15 1.94
532 552 0.037046 GCTCATGGGGTGCCTTTTTG 60.037 55.000 0.00 0.00 0.00 2.44
533 553 1.631405 CTCATGGGGTGCCTTTTTGA 58.369 50.000 0.00 0.00 0.00 2.69
534 554 1.273327 CTCATGGGGTGCCTTTTTGAC 59.727 52.381 0.00 0.00 0.00 3.18
535 555 1.133199 TCATGGGGTGCCTTTTTGACT 60.133 47.619 0.00 0.00 0.00 3.41
536 556 1.273327 CATGGGGTGCCTTTTTGACTC 59.727 52.381 0.00 0.00 0.00 3.36
537 557 0.260230 TGGGGTGCCTTTTTGACTCA 59.740 50.000 0.00 0.00 0.00 3.41
873 965 0.982852 ATGGACCGGAGATGCCTCAA 60.983 55.000 9.46 0.00 41.20 3.02
874 966 0.982852 TGGACCGGAGATGCCTCAAT 60.983 55.000 9.46 0.00 41.20 2.57
875 967 0.250081 GGACCGGAGATGCCTCAATC 60.250 60.000 9.46 0.00 41.20 2.67
876 968 0.598680 GACCGGAGATGCCTCAATCG 60.599 60.000 9.46 0.00 41.20 3.34
914 1019 1.816224 GCTCGTGGAATTAAGCCCAAA 59.184 47.619 0.69 0.00 33.69 3.28
938 1044 1.635487 CTCCCCAGGTCCATGAGAAAA 59.365 52.381 0.00 0.00 0.00 2.29
939 1045 1.354368 TCCCCAGGTCCATGAGAAAAC 59.646 52.381 0.00 0.00 0.00 2.43
940 1046 1.075374 CCCCAGGTCCATGAGAAAACA 59.925 52.381 0.00 0.00 0.00 2.83
941 1047 2.162681 CCCAGGTCCATGAGAAAACAC 58.837 52.381 0.00 0.00 0.00 3.32
942 1048 1.806542 CCAGGTCCATGAGAAAACACG 59.193 52.381 0.00 0.00 0.00 4.49
943 1049 1.197721 CAGGTCCATGAGAAAACACGC 59.802 52.381 0.00 0.00 0.00 5.34
944 1050 1.202758 AGGTCCATGAGAAAACACGCA 60.203 47.619 0.00 0.00 0.00 5.24
945 1051 1.812571 GGTCCATGAGAAAACACGCAT 59.187 47.619 0.00 0.00 0.00 4.73
947 1053 3.492313 GTCCATGAGAAAACACGCATTC 58.508 45.455 0.00 0.00 0.00 2.67
948 1054 3.189287 GTCCATGAGAAAACACGCATTCT 59.811 43.478 0.00 0.00 38.56 2.40
955 1061 0.884704 AAACACGCATTCTCGCCACT 60.885 50.000 0.00 0.00 0.00 4.00
1233 1356 3.641436 ACATCATGAAGCACCGAGGTATA 59.359 43.478 0.00 0.00 0.00 1.47
1292 1415 2.521465 TGCTGCACAAACCCCCTG 60.521 61.111 0.00 0.00 0.00 4.45
1426 1703 5.465935 GTGGTTTCTTCAACAACTTGTGAA 58.534 37.500 0.00 1.74 36.47 3.18
1518 1795 1.540267 TTGCCCCGGATTTGTGTTAG 58.460 50.000 0.73 0.00 0.00 2.34
1720 3240 5.638596 TGTGTTCTTCATAGCTTAGACGA 57.361 39.130 0.00 0.00 0.00 4.20
1743 3263 6.535150 CGAAGTTATGTCATCTCTTTTAGCCA 59.465 38.462 0.00 0.00 0.00 4.75
1750 3270 7.149569 TGTCATCTCTTTTAGCCATTGAAAG 57.850 36.000 0.00 0.00 0.00 2.62
1998 3518 7.620880 AGTAGGTTATGTGTGAGAATAGCAAA 58.379 34.615 0.00 0.00 0.00 3.68
2116 3636 7.959651 CCTTCATTTATCGAGAACAAGTGAAAG 59.040 37.037 0.00 0.00 30.61 2.62
2164 3756 8.466798 GCAGCCTTTCCTTTATCATTTAACTTA 58.533 33.333 0.00 0.00 0.00 2.24
2192 3784 5.746990 TGTGAAAAGAAAGGGGAAAAACA 57.253 34.783 0.00 0.00 0.00 2.83
2285 3919 6.203338 TGAGAACATTTCTTTTACGGTGGTAC 59.797 38.462 0.00 0.00 40.87 3.34
2485 4120 0.676782 GCTTCCAACACGGCAGGTAT 60.677 55.000 0.00 0.00 33.14 2.73
2573 4215 7.687941 ATCTTGGTCTATTTTGGTACTGTTG 57.312 36.000 0.00 0.00 0.00 3.33
2984 7461 6.311723 ACTTGGTTGAATTACTTTTATCGCG 58.688 36.000 0.00 0.00 0.00 5.87
3035 7516 1.597742 TGACTTGGCAAGTGAGAAGC 58.402 50.000 35.57 20.41 43.03 3.86
3095 7576 5.593502 ACTAACTGATACTGGTACCTAGTGC 59.406 44.000 20.68 14.83 0.00 4.40
3186 7671 5.109903 CGAAGCACTTGGTAGCTAAACTAT 58.890 41.667 0.00 0.00 40.90 2.12
3670 8164 5.070714 AGCATCTATGATCTTGCTGAGAACT 59.929 40.000 0.00 0.00 43.44 3.01
3706 8200 2.350899 TCCAAAATCTTGCATGCACG 57.649 45.000 22.58 19.83 0.00 5.34
3846 8341 1.367346 TGAGATGTTAGCAACCCCCA 58.633 50.000 0.00 0.00 0.00 4.96
3847 8342 1.922447 TGAGATGTTAGCAACCCCCAT 59.078 47.619 0.00 0.00 0.00 4.00
3899 8394 5.703876 CTTGGTCTTTCTAACCTGCATTTC 58.296 41.667 0.00 0.00 37.69 2.17
3900 8395 4.724399 TGGTCTTTCTAACCTGCATTTCA 58.276 39.130 0.00 0.00 37.69 2.69
3951 8449 2.091278 GCTGTAGCTATCCTCGTGGGA 61.091 57.143 3.23 2.97 42.64 4.37
3964 8462 3.763897 CCTCGTGGGAATTTTCCTGATTT 59.236 43.478 9.13 0.00 46.72 2.17
3967 8465 4.458989 TCGTGGGAATTTTCCTGATTTCTG 59.541 41.667 9.13 0.00 46.72 3.02
4006 8508 1.664873 TTGCAATGCAAAGACCCCG 59.335 52.632 19.21 0.00 45.96 5.73
4009 8511 0.388520 GCAATGCAAAGACCCCGAAC 60.389 55.000 0.00 0.00 0.00 3.95
4011 8513 0.250553 AATGCAAAGACCCCGAACGA 60.251 50.000 0.00 0.00 0.00 3.85
4092 8597 4.517285 ACCTCGCATGTAAATGTCTCATT 58.483 39.130 0.00 0.00 0.00 2.57
4095 8600 6.037172 ACCTCGCATGTAAATGTCTCATTAAC 59.963 38.462 0.00 0.00 0.00 2.01
4118 8623 7.964545 ACATTGTTTTTAGACGACAAGTTTC 57.035 32.000 0.00 0.00 36.80 2.78
4119 8624 6.970613 ACATTGTTTTTAGACGACAAGTTTCC 59.029 34.615 0.00 0.00 36.80 3.13
4162 8667 4.819105 ACCAAGAATAACGAGATCACCA 57.181 40.909 0.00 0.00 0.00 4.17
4174 8679 7.687941 AACGAGATCACCACTTTCATTTTAT 57.312 32.000 0.00 0.00 0.00 1.40
4322 8827 4.416620 TGCAAAAACTGGACGTTTAACAG 58.583 39.130 0.00 0.00 44.77 3.16
4339 8844 4.792521 AACAGCACCTAACTCAGTCTAG 57.207 45.455 0.00 0.00 0.00 2.43
4429 8935 6.609616 ACCTTTTGATTTGGAACCTTCTGTTA 59.390 34.615 0.00 0.00 37.29 2.41
4438 8944 7.921786 TTGGAACCTTCTGTTATGTTATCTG 57.078 36.000 0.00 0.00 37.29 2.90
4439 8945 7.252612 TGGAACCTTCTGTTATGTTATCTGA 57.747 36.000 0.00 0.00 37.29 3.27
4440 8946 7.861629 TGGAACCTTCTGTTATGTTATCTGAT 58.138 34.615 0.00 0.00 37.29 2.90
4441 8947 8.328758 TGGAACCTTCTGTTATGTTATCTGATT 58.671 33.333 0.00 0.00 37.29 2.57
4442 8948 9.832445 GGAACCTTCTGTTATGTTATCTGATTA 57.168 33.333 0.00 0.00 37.29 1.75
4530 9140 5.991328 ATACATGTTCGGACAATAGCTTG 57.009 39.130 2.30 0.00 39.66 4.01
4559 9169 1.482593 GCTCAGGGTAGCTGTACATGT 59.517 52.381 2.69 2.69 39.50 3.21
4593 9207 5.939296 TGCTCTTGATTGTGTGTATCATGAA 59.061 36.000 0.00 0.00 36.41 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 9.921637 TTTCGGCTTAAAAATGTTTTATCTCAT 57.078 25.926 0.00 0.00 0.00 2.90
44 45 9.751542 TTTTCGGCTTAAAAATGTTTTATCTCA 57.248 25.926 0.00 0.00 0.00 3.27
46 47 8.984764 GGTTTTCGGCTTAAAAATGTTTTATCT 58.015 29.630 0.00 0.00 30.53 1.98
47 48 8.766151 TGGTTTTCGGCTTAAAAATGTTTTATC 58.234 29.630 0.00 0.00 30.53 1.75
48 49 8.664211 TGGTTTTCGGCTTAAAAATGTTTTAT 57.336 26.923 0.00 0.00 30.53 1.40
49 50 8.488651 TTGGTTTTCGGCTTAAAAATGTTTTA 57.511 26.923 0.00 0.00 30.53 1.52
50 51 6.986904 TGGTTTTCGGCTTAAAAATGTTTT 57.013 29.167 0.00 0.00 30.53 2.43
51 52 6.986904 TTGGTTTTCGGCTTAAAAATGTTT 57.013 29.167 0.00 0.00 30.53 2.83
52 53 6.986904 TTTGGTTTTCGGCTTAAAAATGTT 57.013 29.167 0.00 0.00 30.53 2.71
53 54 6.986904 TTTTGGTTTTCGGCTTAAAAATGT 57.013 29.167 0.00 0.00 30.53 2.71
57 58 9.549078 AGAATATTTTTGGTTTTCGGCTTAAAA 57.451 25.926 0.00 0.00 0.00 1.52
58 59 8.983724 CAGAATATTTTTGGTTTTCGGCTTAAA 58.016 29.630 0.00 0.00 0.00 1.52
59 60 7.117092 GCAGAATATTTTTGGTTTTCGGCTTAA 59.883 33.333 0.00 0.00 35.53 1.85
60 61 6.588373 GCAGAATATTTTTGGTTTTCGGCTTA 59.412 34.615 0.00 0.00 35.53 3.09
61 62 5.408299 GCAGAATATTTTTGGTTTTCGGCTT 59.592 36.000 0.00 0.00 35.53 4.35
62 63 4.929211 GCAGAATATTTTTGGTTTTCGGCT 59.071 37.500 0.00 0.00 35.53 5.52
63 64 4.929211 AGCAGAATATTTTTGGTTTTCGGC 59.071 37.500 0.00 0.00 37.64 5.54
64 65 6.155827 TCAGCAGAATATTTTTGGTTTTCGG 58.844 36.000 3.67 0.00 0.00 4.30
65 66 7.329226 ACATCAGCAGAATATTTTTGGTTTTCG 59.671 33.333 3.67 0.00 0.00 3.46
66 67 8.538409 ACATCAGCAGAATATTTTTGGTTTTC 57.462 30.769 3.67 0.00 0.00 2.29
67 68 8.149647 TGACATCAGCAGAATATTTTTGGTTTT 58.850 29.630 3.67 0.00 0.00 2.43
68 69 7.669427 TGACATCAGCAGAATATTTTTGGTTT 58.331 30.769 3.67 0.00 0.00 3.27
69 70 7.230849 TGACATCAGCAGAATATTTTTGGTT 57.769 32.000 3.67 0.00 0.00 3.67
70 71 6.839124 TGACATCAGCAGAATATTTTTGGT 57.161 33.333 0.00 0.00 0.00 3.67
71 72 7.648112 CAGATGACATCAGCAGAATATTTTTGG 59.352 37.037 17.57 0.00 34.14 3.28
72 73 8.188799 ACAGATGACATCAGCAGAATATTTTTG 58.811 33.333 17.57 4.44 34.14 2.44
73 74 8.289939 ACAGATGACATCAGCAGAATATTTTT 57.710 30.769 17.57 0.00 34.14 1.94
74 75 7.876936 ACAGATGACATCAGCAGAATATTTT 57.123 32.000 17.57 0.00 34.14 1.82
75 76 7.876936 AACAGATGACATCAGCAGAATATTT 57.123 32.000 17.57 0.00 34.14 1.40
76 77 7.876936 AAACAGATGACATCAGCAGAATATT 57.123 32.000 17.57 0.00 34.14 1.28
77 78 7.555195 TCAAAACAGATGACATCAGCAGAATAT 59.445 33.333 17.57 0.00 34.14 1.28
78 79 6.880529 TCAAAACAGATGACATCAGCAGAATA 59.119 34.615 17.57 0.00 34.14 1.75
79 80 5.708697 TCAAAACAGATGACATCAGCAGAAT 59.291 36.000 17.57 0.00 34.14 2.40
80 81 5.065235 TCAAAACAGATGACATCAGCAGAA 58.935 37.500 17.57 0.00 34.14 3.02
81 82 4.644498 TCAAAACAGATGACATCAGCAGA 58.356 39.130 17.57 5.01 34.14 4.26
82 83 5.106277 ACATCAAAACAGATGACATCAGCAG 60.106 40.000 17.57 6.89 46.51 4.24
83 84 4.763279 ACATCAAAACAGATGACATCAGCA 59.237 37.500 17.57 0.00 46.51 4.41
84 85 5.093457 CACATCAAAACAGATGACATCAGC 58.907 41.667 17.57 0.00 46.51 4.26
85 86 5.637809 CCACATCAAAACAGATGACATCAG 58.362 41.667 17.57 11.95 46.51 2.90
86 87 4.082625 GCCACATCAAAACAGATGACATCA 60.083 41.667 17.57 0.00 46.51 3.07
87 88 4.082625 TGCCACATCAAAACAGATGACATC 60.083 41.667 7.39 7.39 46.51 3.06
88 89 3.827876 TGCCACATCAAAACAGATGACAT 59.172 39.130 10.59 0.00 46.51 3.06
89 90 3.220940 TGCCACATCAAAACAGATGACA 58.779 40.909 10.59 3.70 46.51 3.58
90 91 3.921119 TGCCACATCAAAACAGATGAC 57.079 42.857 10.59 1.45 46.51 3.06
91 92 4.933505 TTTGCCACATCAAAACAGATGA 57.066 36.364 10.59 0.00 46.51 2.92
92 93 5.697178 TCATTTTGCCACATCAAAACAGATG 59.303 36.000 4.11 2.62 45.28 2.90
93 94 5.856156 TCATTTTGCCACATCAAAACAGAT 58.144 33.333 4.11 0.00 45.28 2.90
94 95 5.273674 TCATTTTGCCACATCAAAACAGA 57.726 34.783 4.11 3.73 45.28 3.41
95 96 5.987777 TTCATTTTGCCACATCAAAACAG 57.012 34.783 4.11 1.77 45.28 3.16
96 97 6.053650 TCATTCATTTTGCCACATCAAAACA 58.946 32.000 4.11 0.00 45.28 2.83
97 98 6.542574 TCATTCATTTTGCCACATCAAAAC 57.457 33.333 4.11 0.00 45.28 2.43
98 99 8.095792 AGTATCATTCATTTTGCCACATCAAAA 58.904 29.630 4.45 4.45 46.14 2.44
99 100 7.546316 CAGTATCATTCATTTTGCCACATCAAA 59.454 33.333 0.00 0.00 34.47 2.69
100 101 7.036829 CAGTATCATTCATTTTGCCACATCAA 58.963 34.615 0.00 0.00 0.00 2.57
101 102 6.406065 CCAGTATCATTCATTTTGCCACATCA 60.406 38.462 0.00 0.00 0.00 3.07
102 103 5.981315 CCAGTATCATTCATTTTGCCACATC 59.019 40.000 0.00 0.00 0.00 3.06
103 104 5.657745 TCCAGTATCATTCATTTTGCCACAT 59.342 36.000 0.00 0.00 0.00 3.21
104 105 5.015515 TCCAGTATCATTCATTTTGCCACA 58.984 37.500 0.00 0.00 0.00 4.17
105 106 5.450965 CCTCCAGTATCATTCATTTTGCCAC 60.451 44.000 0.00 0.00 0.00 5.01
106 107 4.646040 CCTCCAGTATCATTCATTTTGCCA 59.354 41.667 0.00 0.00 0.00 4.92
107 108 4.646492 ACCTCCAGTATCATTCATTTTGCC 59.354 41.667 0.00 0.00 0.00 4.52
108 109 5.126061 ACACCTCCAGTATCATTCATTTTGC 59.874 40.000 0.00 0.00 0.00 3.68
109 110 6.764308 ACACCTCCAGTATCATTCATTTTG 57.236 37.500 0.00 0.00 0.00 2.44
110 111 7.233348 ACAAACACCTCCAGTATCATTCATTTT 59.767 33.333 0.00 0.00 0.00 1.82
111 112 6.721208 ACAAACACCTCCAGTATCATTCATTT 59.279 34.615 0.00 0.00 0.00 2.32
112 113 6.151648 CACAAACACCTCCAGTATCATTCATT 59.848 38.462 0.00 0.00 0.00 2.57
113 114 5.649395 CACAAACACCTCCAGTATCATTCAT 59.351 40.000 0.00 0.00 0.00 2.57
114 115 5.003160 CACAAACACCTCCAGTATCATTCA 58.997 41.667 0.00 0.00 0.00 2.57
115 116 4.142600 GCACAAACACCTCCAGTATCATTC 60.143 45.833 0.00 0.00 0.00 2.67
116 117 3.758554 GCACAAACACCTCCAGTATCATT 59.241 43.478 0.00 0.00 0.00 2.57
117 118 3.347216 GCACAAACACCTCCAGTATCAT 58.653 45.455 0.00 0.00 0.00 2.45
118 119 2.552155 GGCACAAACACCTCCAGTATCA 60.552 50.000 0.00 0.00 0.00 2.15
119 120 2.084546 GGCACAAACACCTCCAGTATC 58.915 52.381 0.00 0.00 0.00 2.24
120 121 1.423541 TGGCACAAACACCTCCAGTAT 59.576 47.619 0.00 0.00 31.92 2.12
121 122 0.840617 TGGCACAAACACCTCCAGTA 59.159 50.000 0.00 0.00 31.92 2.74
122 123 1.612513 TGGCACAAACACCTCCAGT 59.387 52.632 0.00 0.00 31.92 4.00
123 124 4.577152 TGGCACAAACACCTCCAG 57.423 55.556 0.00 0.00 31.92 3.86
133 134 3.857810 GCACGAAGCAACATGGCACAA 62.858 52.381 0.00 0.00 43.65 3.33
134 135 2.405061 GCACGAAGCAACATGGCACA 62.405 55.000 0.00 0.00 44.40 4.57
135 136 1.730547 GCACGAAGCAACATGGCAC 60.731 57.895 0.00 0.00 44.79 5.01
136 137 2.644418 GCACGAAGCAACATGGCA 59.356 55.556 0.00 0.00 44.79 4.92
138 139 1.081242 GTGGCACGAAGCAACATGG 60.081 57.895 0.00 0.00 46.95 3.66
139 140 4.539152 GTGGCACGAAGCAACATG 57.461 55.556 0.00 0.00 46.95 3.21
145 146 1.081906 CACACATGTGGCACGAAGC 60.082 57.895 28.64 0.00 42.10 3.86
154 155 4.481930 AATGTTAACGTCCACACATGTG 57.518 40.909 24.25 24.25 45.23 3.21
155 156 4.336993 ACAAATGTTAACGTCCACACATGT 59.663 37.500 0.00 0.00 30.15 3.21
156 157 4.674662 CACAAATGTTAACGTCCACACATG 59.325 41.667 0.00 7.02 30.15 3.21
157 158 4.336993 ACACAAATGTTAACGTCCACACAT 59.663 37.500 0.00 0.00 34.46 3.21
158 159 3.690139 ACACAAATGTTAACGTCCACACA 59.310 39.130 0.00 0.00 34.46 3.72
159 160 4.281525 ACACAAATGTTAACGTCCACAC 57.718 40.909 0.00 0.00 34.46 3.82
160 161 6.432607 TTTACACAAATGTTAACGTCCACA 57.567 33.333 0.00 2.49 40.48 4.17
161 162 7.917720 ATTTTACACAAATGTTAACGTCCAC 57.082 32.000 0.00 0.00 40.48 4.02
170 171 9.892130 TTTGGACCTTAATTTTACACAAATGTT 57.108 25.926 0.00 0.00 40.48 2.71
171 172 9.541143 CTTTGGACCTTAATTTTACACAAATGT 57.459 29.630 0.00 0.00 43.30 2.71
172 173 9.757227 TCTTTGGACCTTAATTTTACACAAATG 57.243 29.630 0.00 0.00 0.00 2.32
173 174 9.758651 GTCTTTGGACCTTAATTTTACACAAAT 57.241 29.630 0.00 0.00 36.53 2.32
174 175 8.973182 AGTCTTTGGACCTTAATTTTACACAAA 58.027 29.630 0.00 0.00 43.05 2.83
175 176 8.528044 AGTCTTTGGACCTTAATTTTACACAA 57.472 30.769 0.00 0.00 43.05 3.33
176 177 8.410141 CAAGTCTTTGGACCTTAATTTTACACA 58.590 33.333 0.00 0.00 43.05 3.72
177 178 7.381408 GCAAGTCTTTGGACCTTAATTTTACAC 59.619 37.037 0.00 0.00 43.05 2.90
178 179 7.068839 TGCAAGTCTTTGGACCTTAATTTTACA 59.931 33.333 0.00 0.00 43.05 2.41
179 180 7.430441 TGCAAGTCTTTGGACCTTAATTTTAC 58.570 34.615 0.00 0.00 43.05 2.01
185 186 5.136828 TCATTGCAAGTCTTTGGACCTTAA 58.863 37.500 4.94 0.00 43.05 1.85
187 188 3.565307 TCATTGCAAGTCTTTGGACCTT 58.435 40.909 4.94 0.00 43.05 3.50
211 212 5.012768 TCCTCTTGTTCTTTTATTCCTCGGT 59.987 40.000 0.00 0.00 0.00 4.69
220 221 7.745717 TCCTCAATCTTCCTCTTGTTCTTTTA 58.254 34.615 0.00 0.00 0.00 1.52
223 224 5.545723 TCTCCTCAATCTTCCTCTTGTTCTT 59.454 40.000 0.00 0.00 0.00 2.52
259 260 5.104527 TGTTCTTCTTTTCCTCTGTCTCCAA 60.105 40.000 0.00 0.00 0.00 3.53
264 265 6.017523 CCTCTTTGTTCTTCTTTTCCTCTGTC 60.018 42.308 0.00 0.00 0.00 3.51
267 268 5.380900 CCCTCTTTGTTCTTCTTTTCCTCT 58.619 41.667 0.00 0.00 0.00 3.69
274 275 2.158813 TGTCGCCCTCTTTGTTCTTCTT 60.159 45.455 0.00 0.00 0.00 2.52
276 277 1.878953 TGTCGCCCTCTTTGTTCTTC 58.121 50.000 0.00 0.00 0.00 2.87
277 278 2.341846 TTGTCGCCCTCTTTGTTCTT 57.658 45.000 0.00 0.00 0.00 2.52
280 281 1.133915 TCCTTTGTCGCCCTCTTTGTT 60.134 47.619 0.00 0.00 0.00 2.83
283 284 1.676014 CGATCCTTTGTCGCCCTCTTT 60.676 52.381 0.00 0.00 31.85 2.52
291 292 2.809446 TGATAGCACGATCCTTTGTCG 58.191 47.619 0.00 0.00 44.26 4.35
293 294 4.142609 ACATGATAGCACGATCCTTTGT 57.857 40.909 0.00 0.00 0.00 2.83
295 296 4.769688 TGAACATGATAGCACGATCCTTT 58.230 39.130 0.00 0.00 0.00 3.11
296 297 4.406648 TGAACATGATAGCACGATCCTT 57.593 40.909 0.00 0.00 0.00 3.36
301 302 3.708563 TCGATGAACATGATAGCACGA 57.291 42.857 0.00 0.67 0.00 4.35
303 304 4.309933 TGGATCGATGAACATGATAGCAC 58.690 43.478 0.54 0.00 0.00 4.40
345 346 5.417266 TGAGCGATTTCCCAATATTGTTTCA 59.583 36.000 14.25 2.50 0.00 2.69
348 349 5.593909 TCATGAGCGATTTCCCAATATTGTT 59.406 36.000 14.25 0.00 0.00 2.83
362 363 2.299582 CCAAGATCTCCTCATGAGCGAT 59.700 50.000 17.76 18.87 41.18 4.58
369 370 2.203584 ACTTGGCCAAGATCTCCTCAT 58.796 47.619 44.50 21.27 40.79 2.90
408 427 0.400213 ACCGTCACCACCATTGTCAT 59.600 50.000 0.00 0.00 0.00 3.06
409 428 0.533978 CACCGTCACCACCATTGTCA 60.534 55.000 0.00 0.00 0.00 3.58
410 429 0.250124 TCACCGTCACCACCATTGTC 60.250 55.000 0.00 0.00 0.00 3.18
411 430 0.534203 GTCACCGTCACCACCATTGT 60.534 55.000 0.00 0.00 0.00 2.71
427 446 2.356913 CCACACGTGCCATCGTCA 60.357 61.111 17.22 0.00 42.27 4.35
440 459 4.078537 CAATTACAAGGATGTCACCCACA 58.921 43.478 0.00 0.00 41.05 4.17
444 463 6.732154 CATCATCAATTACAAGGATGTCACC 58.268 40.000 0.00 0.00 41.05 4.02
449 468 6.264744 AGAAGGCATCATCAATTACAAGGATG 59.735 38.462 0.00 0.00 39.75 3.51
451 470 5.591472 CAGAAGGCATCATCAATTACAAGGA 59.409 40.000 0.00 0.00 0.00 3.36
506 526 0.037975 GCACCCCATGAGCAAGTTTG 60.038 55.000 0.00 0.00 0.00 2.93
507 527 1.187567 GGCACCCCATGAGCAAGTTT 61.188 55.000 0.00 0.00 0.00 2.66
514 534 1.273327 GTCAAAAAGGCACCCCATGAG 59.727 52.381 0.00 0.00 0.00 2.90
519 539 1.408969 TTGAGTCAAAAAGGCACCCC 58.591 50.000 2.20 0.00 0.00 4.95
520 540 3.535280 TTTTGAGTCAAAAAGGCACCC 57.465 42.857 25.15 0.00 39.85 4.61
564 586 9.271828 ACGAGCATACACATAATTCATTCATTA 57.728 29.630 0.00 0.00 0.00 1.90
565 587 8.158169 ACGAGCATACACATAATTCATTCATT 57.842 30.769 0.00 0.00 0.00 2.57
580 602 7.926018 ACATCATAATTCAACTACGAGCATACA 59.074 33.333 0.00 0.00 0.00 2.29
581 603 8.217115 CACATCATAATTCAACTACGAGCATAC 58.783 37.037 0.00 0.00 0.00 2.39
630 661 7.056800 CACAAACTTAAACAATCAATTCGCAC 58.943 34.615 0.00 0.00 0.00 5.34
861 953 3.938963 TGTTTAACGATTGAGGCATCTCC 59.061 43.478 0.00 0.00 39.23 3.71
873 965 2.475111 CAGTGTGACGCTGTTTAACGAT 59.525 45.455 17.48 0.00 37.23 3.73
874 966 1.855978 CAGTGTGACGCTGTTTAACGA 59.144 47.619 17.48 0.00 37.23 3.85
875 967 1.656429 GCAGTGTGACGCTGTTTAACG 60.656 52.381 24.97 0.72 43.09 3.18
876 968 1.597663 AGCAGTGTGACGCTGTTTAAC 59.402 47.619 24.97 9.85 43.09 2.01
914 1019 2.128226 ATGGACCTGGGGAGGCTT 59.872 61.111 0.00 0.00 0.00 4.35
938 1044 2.029288 CAGTGGCGAGAATGCGTGT 61.029 57.895 0.00 0.00 35.06 4.49
939 1045 2.743752 CCAGTGGCGAGAATGCGTG 61.744 63.158 0.00 0.00 35.06 5.34
940 1046 2.434884 CCAGTGGCGAGAATGCGT 60.435 61.111 0.00 0.00 35.06 5.24
941 1047 3.869272 GCCAGTGGCGAGAATGCG 61.869 66.667 20.55 0.00 39.62 4.73
987 1093 1.909986 AGAAGGGTGGGAAGAGTTAGC 59.090 52.381 0.00 0.00 0.00 3.09
1087 1208 4.637489 CCCCATCGCTCGCTCGAG 62.637 72.222 8.45 8.45 42.14 4.04
1233 1356 1.305381 AGGGAGCACGGAGTAGCTT 60.305 57.895 0.00 0.00 41.61 3.74
1292 1415 0.755686 AAGATGAGATGCGAGGGACC 59.244 55.000 0.00 0.00 0.00 4.46
1377 1503 4.907875 CCAACCTCCTCTCCCATCTTAATA 59.092 45.833 0.00 0.00 0.00 0.98
1504 1781 5.621197 TTTCACATCTAACACAAATCCGG 57.379 39.130 0.00 0.00 0.00 5.14
1505 1782 7.060979 CACATTTTCACATCTAACACAAATCCG 59.939 37.037 0.00 0.00 0.00 4.18
1518 1795 4.241590 TGCCAACTCACATTTTCACATC 57.758 40.909 0.00 0.00 0.00 3.06
1703 1987 7.997482 ACATAACTTCGTCTAAGCTATGAAGA 58.003 34.615 19.31 10.90 42.88 2.87
1720 3240 8.680903 CAATGGCTAAAAGAGATGACATAACTT 58.319 33.333 0.00 0.00 0.00 2.66
1740 3260 4.501071 ACTTGCATGATTCTTTCAATGGC 58.499 39.130 6.60 0.00 38.03 4.40
1743 3263 7.977853 GTGGAATACTTGCATGATTCTTTCAAT 59.022 33.333 6.60 0.00 38.03 2.57
1750 3270 7.712639 TCTTAGAGTGGAATACTTGCATGATTC 59.287 37.037 6.60 10.35 40.53 2.52
1998 3518 8.428852 ACAAAAACAGGGTATTAAAGAAGCAAT 58.571 29.630 0.00 0.00 0.00 3.56
2116 3636 7.354751 TGCCAATACCCCAAATAACTTATTC 57.645 36.000 0.00 0.00 0.00 1.75
2164 3756 2.629617 CCCCTTTCTTTTCACATGCTGT 59.370 45.455 0.00 0.00 0.00 4.40
2249 3883 6.232581 AGAAATGTTCTCATACCCTCTCAG 57.767 41.667 0.00 0.00 34.07 3.35
2285 3919 7.814587 GTCCACAGAATAAATTTCAGGGAAAAG 59.185 37.037 0.00 0.00 35.11 2.27
2573 4215 4.386867 TCCTGATTCTCACGGTATGAAC 57.613 45.455 0.00 0.00 36.69 3.18
2935 4918 5.564550 AGCAAACTTCTATGGTCTGTCATT 58.435 37.500 0.00 0.00 0.00 2.57
2979 7456 4.702612 AGATGGAGTACTCATATTCGCGAT 59.297 41.667 23.91 2.60 0.00 4.58
3035 7516 2.189594 TTCCCTGAGAATGTGTGCTG 57.810 50.000 0.00 0.00 0.00 4.41
3186 7671 4.635765 CAGGACAAATAAGCATTCGGAAGA 59.364 41.667 0.00 0.00 39.20 2.87
3670 8164 0.383949 GGAAAAGTGGCTGCGACAAA 59.616 50.000 17.03 0.00 0.00 2.83
3706 8200 5.715434 TTAGCAGTGTGTTTTAAATCCCC 57.285 39.130 0.00 0.00 0.00 4.81
3751 8246 4.307032 AATGGTCAATACTGCCTCAAGT 57.693 40.909 0.00 0.00 0.00 3.16
3820 8315 4.036027 GGGTTGCTAACATCTCATCACATG 59.964 45.833 0.00 0.00 0.00 3.21
3822 8317 3.609853 GGGTTGCTAACATCTCATCACA 58.390 45.455 0.00 0.00 0.00 3.58
3826 8321 1.922447 TGGGGGTTGCTAACATCTCAT 59.078 47.619 0.00 0.00 0.00 2.90
3830 8325 2.435372 TCATGGGGGTTGCTAACATC 57.565 50.000 0.00 0.00 0.00 3.06
3847 8342 9.269453 CATCATATTCTAGCAGAAACAAGATCA 57.731 33.333 0.00 0.00 37.82 2.92
3997 8499 2.554370 TTTGATCGTTCGGGGTCTTT 57.446 45.000 0.00 0.00 0.00 2.52
4006 8508 2.487762 TGCAAGACCCATTTGATCGTTC 59.512 45.455 0.00 0.00 0.00 3.95
4009 8511 2.684374 TGATGCAAGACCCATTTGATCG 59.316 45.455 0.00 0.00 0.00 3.69
4011 8513 3.433343 TGTGATGCAAGACCCATTTGAT 58.567 40.909 0.00 0.00 0.00 2.57
4071 8576 6.037062 TGTTAATGAGACATTTACATGCGAGG 59.963 38.462 10.71 0.00 33.05 4.63
4092 8597 9.493206 GAAACTTGTCGTCTAAAAACAATGTTA 57.507 29.630 0.00 0.00 32.85 2.41
4095 8600 7.165812 CAGGAAACTTGTCGTCTAAAAACAATG 59.834 37.037 0.00 0.00 40.21 2.82
4108 8613 7.323656 GTGTTATGATTTTCAGGAAACTTGTCG 59.676 37.037 0.00 0.00 40.21 4.35
4118 8623 9.703892 TGGTTAAAATGTGTTATGATTTTCAGG 57.296 29.630 0.00 0.00 34.42 3.86
4162 8667 5.264395 CCTCCCTCACCATAAAATGAAAGT 58.736 41.667 0.00 0.00 0.00 2.66
4174 8679 1.289160 CTTTGATCCCTCCCTCACCA 58.711 55.000 0.00 0.00 0.00 4.17
4228 8733 6.012858 TGGAATAGCATATTTAGGTAGTGGGG 60.013 42.308 0.00 0.00 0.00 4.96
4268 8773 3.529533 TGTTGATTTGCAGTTTGGTTGG 58.470 40.909 0.00 0.00 0.00 3.77
4322 8827 7.998580 AGTATTTACTAGACTGAGTTAGGTGC 58.001 38.462 0.00 0.00 34.13 5.01
4339 8844 5.382664 TTTGGGATGGAGGGAGTATTTAC 57.617 43.478 0.00 0.00 0.00 2.01
4400 8906 3.641436 AGGTTCCAAATCAAAAGGTGTCC 59.359 43.478 0.00 0.00 0.00 4.02
4495 9105 5.342433 CGAACATGTATTCCAATGCACATT 58.658 37.500 0.00 0.00 33.87 2.71
4505 9115 5.057149 AGCTATTGTCCGAACATGTATTCC 58.943 41.667 0.00 0.00 34.73 3.01
4530 9140 0.820871 CTACCCTGAGCAGACTGGTC 59.179 60.000 24.56 24.56 44.54 4.02
4559 9169 5.882000 ACACAATCAAGAGCACATATTAGCA 59.118 36.000 0.00 0.00 0.00 3.49
4593 9207 2.664402 AGCAAGGTCCAGTGTTCAAT 57.336 45.000 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.