Multiple sequence alignment - TraesCS5D01G265400

Loading Multiple Alignment...

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 TraesCS5D01G265400 chr5D 100.000 5040 0 0 1 5040 369723625 369728664 0.000000e+00 9308
1 TraesCS5D01G265400 chr5B 93.952 4861 183 48 253 5040 439065816 439070638 0.000000e+00 7245
2 TraesCS5D01G265400 chr5B 85.714 196 17 7 4658 4843 385609821 385609627 3.980000e-46 196
3 TraesCS5D01G265400 chr5A 93.873 4456 181 53 254 4682 472282748 472287138 0.000000e+00 6632
4 TraesCS5D01G265400 chr5A 87.879 99 5 5 1 96 487808157 487808251 5.330000e-20 110
5 TraesCS5D01G265400 chr2D 82.054 847 124 21 1589 2424 518600965 518600136 0.000000e+00 697
6 TraesCS5D01G265400 chr2D 78.901 455 68 16 2630 3077 518600023 518599590 2.970000e-72 283
7 TraesCS5D01G265400 chr2D 88.660 97 8 3 1 96 522752238 522752332 1.150000e-21 115
8 TraesCS5D01G265400 chr2D 87.629 97 7 4 1 95 223550815 223550722 1.920000e-19 108
9 TraesCS5D01G265400 chr2B 81.818 847 126 21 1589 2424 610694667 610693838 0.000000e+00 686
10 TraesCS5D01G265400 chr2B 85.774 239 28 2 2630 2868 610693725 610693493 1.080000e-61 248
11 TraesCS5D01G265400 chr2B 84.074 270 29 4 4658 4913 721107631 721107362 1.080000e-61 248
12 TraesCS5D01G265400 chr2A 81.110 847 132 21 1589 2424 662747066 662746237 0.000000e+00 652
13 TraesCS5D01G265400 chr2A 80.624 449 64 15 2630 3077 662746124 662745698 4.870000e-85 326
14 TraesCS5D01G265400 chr1A 74.917 602 125 17 1820 2411 10159826 10159241 8.380000e-63 252
15 TraesCS5D01G265400 chr1D 74.751 602 126 17 1820 2411 8925803 8925218 3.900000e-61 246
16 TraesCS5D01G265400 chr1D 85.906 149 17 4 4894 5040 42254630 42254776 6.760000e-34 156
17 TraesCS5D01G265400 chr1D 80.795 151 27 2 4890 5040 107251444 107251296 3.190000e-22 117
18 TraesCS5D01G265400 chr1D 86.735 98 10 2 1 96 441286389 441286293 6.900000e-19 106
19 TraesCS5D01G265400 chr6B 86.082 194 19 7 4657 4843 366569309 366569501 8.560000e-48 202
20 TraesCS5D01G265400 chr6B 79.348 276 53 4 3752 4025 492193049 492193322 1.850000e-44 191
21 TraesCS5D01G265400 chr6A 80.072 276 51 4 3752 4025 467046352 467046625 8.560000e-48 202
22 TraesCS5D01G265400 chr4B 80.072 276 51 4 3752 4025 633933112 633932839 8.560000e-48 202
23 TraesCS5D01G265400 chr4B 80.072 276 51 4 3752 4025 634076604 634076331 8.560000e-48 202
24 TraesCS5D01G265400 chr4B 85.787 197 17 7 4657 4843 154925842 154926037 1.110000e-46 198
25 TraesCS5D01G265400 chr6D 85.714 196 17 7 4658 4843 100582063 100582257 3.980000e-46 196
26 TraesCS5D01G265400 chr6D 79.710 276 52 4 3752 4025 328332464 328332737 3.980000e-46 196
27 TraesCS5D01G265400 chr1B 85.641 195 17 7 4658 4842 118893091 118893284 1.430000e-45 195
28 TraesCS5D01G265400 chr3B 85.000 200 19 7 4654 4843 539052747 539052549 5.150000e-45 193
29 TraesCS5D01G265400 chr3B 84.653 202 19 8 4658 4849 234499621 234499422 1.850000e-44 191
30 TraesCS5D01G265400 chr3B 83.537 164 17 3 4879 5040 368104498 368104343 1.460000e-30 145
31 TraesCS5D01G265400 chr7B 84.397 141 19 2 4891 5030 428470690 428470552 8.800000e-28 135
32 TraesCS5D01G265400 chr7D 80.864 162 26 3 4816 4977 332258308 332258464 6.850000e-24 122
33 TraesCS5D01G265400 chr7D 88.542 96 11 0 1 96 513211579 513211674 3.190000e-22 117
34 TraesCS5D01G265400 chr7D 88.542 96 9 2 1 96 51830924 51831017 1.150000e-21 115
35 TraesCS5D01G265400 chr3A 89.583 96 10 0 1 96 46569186 46569091 6.850000e-24 122
36 TraesCS5D01G265400 chr3D 90.698 86 6 1 13 96 114387121 114387036 4.120000e-21 113
37 TraesCS5D01G265400 chr3D 87.755 98 7 4 1 96 83492047 83491953 5.330000e-20 110


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 TraesCS5D01G265400 chr5D 369723625 369728664 5039 False 9308 9308 100.0000 1 5040 1 chr5D.!!$F1 5039
1 TraesCS5D01G265400 chr5B 439065816 439070638 4822 False 7245 7245 93.9520 253 5040 1 chr5B.!!$F1 4787
2 TraesCS5D01G265400 chr5A 472282748 472287138 4390 False 6632 6632 93.8730 254 4682 1 chr5A.!!$F1 4428
3 TraesCS5D01G265400 chr2D 518599590 518600965 1375 True 490 697 80.4775 1589 3077 2 chr2D.!!$R2 1488
4 TraesCS5D01G265400 chr2B 610693493 610694667 1174 True 467 686 83.7960 1589 2868 2 chr2B.!!$R2 1279
5 TraesCS5D01G265400 chr2A 662745698 662747066 1368 True 489 652 80.8670 1589 3077 2 chr2A.!!$R1 1488
6 TraesCS5D01G265400 chr1A 10159241 10159826 585 True 252 252 74.9170 1820 2411 1 chr1A.!!$R1 591
7 TraesCS5D01G265400 chr1D 8925218 8925803 585 True 246 246 74.7510 1820 2411 1 chr1D.!!$R1 591

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
200 201 0.108585 GGTGGACTGAGACTTGGCAA 59.891 55.000 0.00 0.00 0.00 4.52 F
408 412 0.179073 CATCCACCATGGGTCGAGTC 60.179 60.000 18.09 0.00 38.32 3.36 F
518 528 0.398664 AATAGGCCACCCTAGCTCGT 60.399 55.000 5.01 0.00 46.56 4.18 F
519 529 0.828343 ATAGGCCACCCTAGCTCGTC 60.828 60.000 5.01 0.00 46.56 4.20 F
940 992 1.081376 GTACGCCGATCGATCCAGG 60.081 63.158 18.66 16.14 41.67 4.45 F
2884 2967 0.748450 AGCATTCCATTCCGCCATTG 59.252 50.000 0.00 0.00 0.00 2.82 F
3054 3151 0.250467 GCAGAACAGGGTGAGCAAGA 60.250 55.000 0.00 0.00 0.00 3.02 F
3832 3933 0.320683 TCGATGACACCAACAGGCTG 60.321 55.000 14.16 14.16 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1413 1478 1.670590 CCGCATCTCCTCCATCTCC 59.329 63.158 0.00 0.00 0.00 3.71 R
2052 2129 2.596631 GCCATGCGGATGAGCCAT 60.597 61.111 19.50 0.00 35.94 4.40 R
2724 2807 0.176449 TGATCTGCTCGTCCATGGTG 59.824 55.000 12.58 6.00 0.00 4.17 R
2884 2967 1.153958 GTTGCAAGCAAGGATCGGC 60.154 57.895 7.88 0.00 36.52 5.54 R
3054 3151 1.122019 ACCCAGTTCTTGAGCGACCT 61.122 55.000 0.00 0.00 0.00 3.85 R
3871 3972 0.179045 CGAACCTCATCCCCATGTCC 60.179 60.000 0.00 0.00 0.00 4.02 R
3940 4041 0.660595 GCATCCGGTACTCGATGTCG 60.661 60.000 18.05 0.00 42.43 4.35 R
4635 4745 3.049674 TCTTTGCTTCAGCGGCCG 61.050 61.111 24.05 24.05 45.83 6.13 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
26 27 5.615925 ACTTAACCAAGTCTCAGTCAAGT 57.384 39.130 0.00 0.00 41.25 3.16
27 28 5.360591 ACTTAACCAAGTCTCAGTCAAGTG 58.639 41.667 0.00 0.00 41.25 3.16
28 29 5.128827 ACTTAACCAAGTCTCAGTCAAGTGA 59.871 40.000 0.00 0.00 41.25 3.41
29 30 4.696479 AACCAAGTCTCAGTCAAGTGAT 57.304 40.909 0.00 0.00 0.00 3.06
30 31 5.808366 AACCAAGTCTCAGTCAAGTGATA 57.192 39.130 0.00 0.00 0.00 2.15
31 32 6.365970 AACCAAGTCTCAGTCAAGTGATAT 57.634 37.500 0.00 0.00 0.00 1.63
32 33 7.482169 AACCAAGTCTCAGTCAAGTGATATA 57.518 36.000 0.00 0.00 0.00 0.86
33 34 7.106439 ACCAAGTCTCAGTCAAGTGATATAG 57.894 40.000 0.00 0.00 0.00 1.31
34 35 6.665680 ACCAAGTCTCAGTCAAGTGATATAGT 59.334 38.462 0.00 0.00 0.00 2.12
35 36 7.834681 ACCAAGTCTCAGTCAAGTGATATAGTA 59.165 37.037 0.00 0.00 0.00 1.82
36 37 8.855110 CCAAGTCTCAGTCAAGTGATATAGTAT 58.145 37.037 0.00 0.00 0.00 2.12
89 90 8.778358 AGAGAATTTTTATACGAATCTCCATGC 58.222 33.333 0.00 0.00 0.00 4.06
90 91 8.450578 AGAATTTTTATACGAATCTCCATGCA 57.549 30.769 0.00 0.00 0.00 3.96
91 92 8.902806 AGAATTTTTATACGAATCTCCATGCAA 58.097 29.630 0.00 0.00 0.00 4.08
92 93 9.515020 GAATTTTTATACGAATCTCCATGCAAA 57.485 29.630 0.00 0.00 0.00 3.68
93 94 9.868277 AATTTTTATACGAATCTCCATGCAAAA 57.132 25.926 0.00 0.00 0.00 2.44
95 96 9.515020 TTTTTATACGAATCTCCATGCAAAATC 57.485 29.630 0.00 0.00 0.00 2.17
96 97 8.450578 TTTATACGAATCTCCATGCAAAATCT 57.549 30.769 0.00 0.00 0.00 2.40
97 98 4.889832 ACGAATCTCCATGCAAAATCTC 57.110 40.909 0.00 0.00 0.00 2.75
98 99 4.264253 ACGAATCTCCATGCAAAATCTCA 58.736 39.130 0.00 0.00 0.00 3.27
99 100 4.334759 ACGAATCTCCATGCAAAATCTCAG 59.665 41.667 0.00 0.00 0.00 3.35
100 101 4.334759 CGAATCTCCATGCAAAATCTCAGT 59.665 41.667 0.00 0.00 0.00 3.41
101 102 5.578005 AATCTCCATGCAAAATCTCAGTG 57.422 39.130 0.00 0.00 0.00 3.66
102 103 3.349927 TCTCCATGCAAAATCTCAGTGG 58.650 45.455 0.00 0.00 0.00 4.00
103 104 3.009363 TCTCCATGCAAAATCTCAGTGGA 59.991 43.478 0.00 0.00 33.58 4.02
104 105 3.084039 TCCATGCAAAATCTCAGTGGAC 58.916 45.455 0.00 0.00 29.89 4.02
105 106 3.087031 CCATGCAAAATCTCAGTGGACT 58.913 45.455 0.00 0.00 0.00 3.85
106 107 3.119602 CCATGCAAAATCTCAGTGGACTG 60.120 47.826 0.00 0.00 45.08 3.51
117 118 2.513753 CAGTGGACTGAGACTGAGACT 58.486 52.381 0.04 0.00 46.59 3.24
118 119 2.890311 CAGTGGACTGAGACTGAGACTT 59.110 50.000 0.04 0.00 46.59 3.01
119 120 2.890311 AGTGGACTGAGACTGAGACTTG 59.110 50.000 0.00 0.00 0.00 3.16
120 121 2.029470 GTGGACTGAGACTGAGACTTGG 60.029 54.545 0.00 0.00 0.00 3.61
121 122 1.067213 GGACTGAGACTGAGACTTGGC 60.067 57.143 0.00 0.00 0.00 4.52
122 123 1.615883 GACTGAGACTGAGACTTGGCA 59.384 52.381 0.00 0.00 0.00 4.92
123 124 2.036475 GACTGAGACTGAGACTTGGCAA 59.964 50.000 0.00 0.00 0.00 4.52
124 125 2.435805 ACTGAGACTGAGACTTGGCAAA 59.564 45.455 0.00 0.00 0.00 3.68
125 126 3.118261 ACTGAGACTGAGACTTGGCAAAA 60.118 43.478 0.00 0.00 0.00 2.44
126 127 3.206150 TGAGACTGAGACTTGGCAAAAC 58.794 45.455 0.00 0.00 0.00 2.43
127 128 3.118261 TGAGACTGAGACTTGGCAAAACT 60.118 43.478 0.00 3.36 0.00 2.66
128 129 3.209410 AGACTGAGACTTGGCAAAACTG 58.791 45.455 0.00 0.00 0.00 3.16
129 130 2.945668 GACTGAGACTTGGCAAAACTGT 59.054 45.455 0.00 0.00 0.00 3.55
130 131 3.356290 ACTGAGACTTGGCAAAACTGTT 58.644 40.909 0.00 0.00 0.00 3.16
131 132 3.378427 ACTGAGACTTGGCAAAACTGTTC 59.622 43.478 0.00 0.00 0.00 3.18
132 133 3.620488 TGAGACTTGGCAAAACTGTTCT 58.380 40.909 0.00 0.00 0.00 3.01
133 134 4.016444 TGAGACTTGGCAAAACTGTTCTT 58.984 39.130 0.00 0.00 0.00 2.52
134 135 5.189928 TGAGACTTGGCAAAACTGTTCTTA 58.810 37.500 0.00 0.00 0.00 2.10
135 136 5.827797 TGAGACTTGGCAAAACTGTTCTTAT 59.172 36.000 0.00 0.00 0.00 1.73
136 137 6.995686 TGAGACTTGGCAAAACTGTTCTTATA 59.004 34.615 0.00 0.00 0.00 0.98
137 138 7.041372 TGAGACTTGGCAAAACTGTTCTTATAC 60.041 37.037 0.00 0.00 0.00 1.47
138 139 5.997385 ACTTGGCAAAACTGTTCTTATACG 58.003 37.500 0.00 0.00 0.00 3.06
139 140 5.761234 ACTTGGCAAAACTGTTCTTATACGA 59.239 36.000 0.00 0.00 0.00 3.43
140 141 6.261381 ACTTGGCAAAACTGTTCTTATACGAA 59.739 34.615 0.00 0.00 0.00 3.85
141 142 6.811253 TGGCAAAACTGTTCTTATACGAAT 57.189 33.333 0.00 0.00 0.00 3.34
142 143 7.209471 TGGCAAAACTGTTCTTATACGAATT 57.791 32.000 0.00 0.00 0.00 2.17
143 144 7.653647 TGGCAAAACTGTTCTTATACGAATTT 58.346 30.769 0.00 0.00 0.00 1.82
144 145 8.138712 TGGCAAAACTGTTCTTATACGAATTTT 58.861 29.630 0.00 0.00 0.00 1.82
145 146 8.974408 GGCAAAACTGTTCTTATACGAATTTTT 58.026 29.630 0.00 0.65 0.00 1.94
174 175 9.577110 ACGAATTTTTATACAGAGACATAACGA 57.423 29.630 0.00 0.00 0.00 3.85
184 185 3.427243 GAGACATAACGAAGTCTCGGTG 58.573 50.000 6.80 0.00 46.84 4.94
185 186 2.163815 AGACATAACGAAGTCTCGGTGG 59.836 50.000 0.00 0.00 46.84 4.61
186 187 2.163010 GACATAACGAAGTCTCGGTGGA 59.837 50.000 0.00 0.00 46.84 4.02
187 188 2.094854 ACATAACGAAGTCTCGGTGGAC 60.095 50.000 0.00 0.00 46.84 4.02
188 189 1.901591 TAACGAAGTCTCGGTGGACT 58.098 50.000 0.00 0.00 46.84 3.85
189 190 0.314302 AACGAAGTCTCGGTGGACTG 59.686 55.000 7.22 0.00 45.37 3.51
190 191 2.089050 AACGAAGTCTCGGTGGACTGA 61.089 52.381 7.22 0.00 45.37 3.41
191 192 3.963053 AACGAAGTCTCGGTGGACTGAG 61.963 54.545 9.06 9.06 45.37 3.35
197 198 2.351777 TCGGTGGACTGAGACTTGG 58.648 57.895 0.00 0.00 0.00 3.61
198 199 1.374758 CGGTGGACTGAGACTTGGC 60.375 63.158 0.00 0.00 0.00 4.52
199 200 1.754745 GGTGGACTGAGACTTGGCA 59.245 57.895 0.00 0.00 0.00 4.92
200 201 0.108585 GGTGGACTGAGACTTGGCAA 59.891 55.000 0.00 0.00 0.00 4.52
201 202 1.476833 GGTGGACTGAGACTTGGCAAA 60.477 52.381 0.00 0.00 0.00 3.68
202 203 2.297701 GTGGACTGAGACTTGGCAAAA 58.702 47.619 0.00 0.00 0.00 2.44
203 204 2.033424 GTGGACTGAGACTTGGCAAAAC 59.967 50.000 0.00 0.00 0.00 2.43
204 205 2.092429 TGGACTGAGACTTGGCAAAACT 60.092 45.455 0.00 3.36 0.00 2.66
205 206 2.291741 GGACTGAGACTTGGCAAAACTG 59.708 50.000 0.00 0.00 0.00 3.16
206 207 2.945668 GACTGAGACTTGGCAAAACTGT 59.054 45.455 0.00 0.00 0.00 3.55
207 208 3.356290 ACTGAGACTTGGCAAAACTGTT 58.644 40.909 0.00 0.00 0.00 3.16
208 209 3.378427 ACTGAGACTTGGCAAAACTGTTC 59.622 43.478 0.00 0.00 0.00 3.18
209 210 3.620488 TGAGACTTGGCAAAACTGTTCT 58.380 40.909 0.00 0.00 0.00 3.01
210 211 4.016444 TGAGACTTGGCAAAACTGTTCTT 58.984 39.130 0.00 0.00 0.00 2.52
211 212 4.462483 TGAGACTTGGCAAAACTGTTCTTT 59.538 37.500 0.00 0.00 0.00 2.52
212 213 4.998788 AGACTTGGCAAAACTGTTCTTTC 58.001 39.130 0.00 0.00 0.00 2.62
213 214 4.706962 AGACTTGGCAAAACTGTTCTTTCT 59.293 37.500 0.00 0.00 0.00 2.52
214 215 5.185828 AGACTTGGCAAAACTGTTCTTTCTT 59.814 36.000 0.00 0.00 0.00 2.52
215 216 5.793817 ACTTGGCAAAACTGTTCTTTCTTT 58.206 33.333 0.00 0.00 0.00 2.52
216 217 5.869344 ACTTGGCAAAACTGTTCTTTCTTTC 59.131 36.000 0.00 0.00 0.00 2.62
217 218 5.659440 TGGCAAAACTGTTCTTTCTTTCT 57.341 34.783 0.00 0.00 0.00 2.52
218 219 6.036577 TGGCAAAACTGTTCTTTCTTTCTT 57.963 33.333 0.00 0.00 0.00 2.52
219 220 6.463360 TGGCAAAACTGTTCTTTCTTTCTTT 58.537 32.000 0.00 0.00 0.00 2.52
220 221 6.934083 TGGCAAAACTGTTCTTTCTTTCTTTT 59.066 30.769 0.00 0.00 0.00 2.27
221 222 7.443879 TGGCAAAACTGTTCTTTCTTTCTTTTT 59.556 29.630 0.00 0.00 0.00 1.94
222 223 7.746034 GGCAAAACTGTTCTTTCTTTCTTTTTG 59.254 33.333 0.00 0.00 35.49 2.44
223 224 8.282592 GCAAAACTGTTCTTTCTTTCTTTTTGT 58.717 29.630 0.00 0.00 35.07 2.83
227 228 9.764363 AACTGTTCTTTCTTTCTTTTTGTTTCT 57.236 25.926 0.00 0.00 0.00 2.52
228 229 9.764363 ACTGTTCTTTCTTTCTTTTTGTTTCTT 57.236 25.926 0.00 0.00 0.00 2.52
231 232 9.318041 GTTCTTTCTTTCTTTTTGTTTCTTTGC 57.682 29.630 0.00 0.00 0.00 3.68
232 233 8.028540 TCTTTCTTTCTTTTTGTTTCTTTGCC 57.971 30.769 0.00 0.00 0.00 4.52
233 234 7.877612 TCTTTCTTTCTTTTTGTTTCTTTGCCT 59.122 29.630 0.00 0.00 0.00 4.75
234 235 7.977789 TTCTTTCTTTTTGTTTCTTTGCCTT 57.022 28.000 0.00 0.00 0.00 4.35
235 236 7.977789 TCTTTCTTTTTGTTTCTTTGCCTTT 57.022 28.000 0.00 0.00 0.00 3.11
236 237 8.389779 TCTTTCTTTTTGTTTCTTTGCCTTTT 57.610 26.923 0.00 0.00 0.00 2.27
237 238 8.845227 TCTTTCTTTTTGTTTCTTTGCCTTTTT 58.155 25.926 0.00 0.00 0.00 1.94
307 308 0.969894 ACGGTTTGGTCTCCTCTCTG 59.030 55.000 0.00 0.00 0.00 3.35
353 354 9.282569 CATGGATTTTATGTTGAAAAGGGAAAA 57.717 29.630 0.00 0.00 32.06 2.29
376 380 2.686816 CGGTTTGATGTGCGGGACC 61.687 63.158 0.00 0.00 0.00 4.46
377 381 1.602323 GGTTTGATGTGCGGGACCA 60.602 57.895 0.00 0.00 0.00 4.02
378 382 1.579429 GTTTGATGTGCGGGACCAC 59.421 57.895 0.00 0.00 36.28 4.16
391 395 3.196040 GACCACATCCACCATGCAT 57.804 52.632 0.00 0.00 35.65 3.96
393 397 0.396139 ACCACATCCACCATGCATCC 60.396 55.000 0.00 0.00 35.65 3.51
394 398 0.396001 CCACATCCACCATGCATCCA 60.396 55.000 0.00 0.00 35.65 3.41
395 399 0.742505 CACATCCACCATGCATCCAC 59.257 55.000 0.00 0.00 35.65 4.02
396 400 0.396139 ACATCCACCATGCATCCACC 60.396 55.000 0.00 0.00 35.65 4.61
397 401 0.396001 CATCCACCATGCATCCACCA 60.396 55.000 0.00 0.00 0.00 4.17
402 406 4.690849 CATGCATCCACCATGGGT 57.309 55.556 18.09 0.00 38.32 4.51
404 408 1.152902 ATGCATCCACCATGGGTCG 60.153 57.895 18.09 3.74 38.32 4.79
406 410 1.524621 GCATCCACCATGGGTCGAG 60.525 63.158 18.09 4.00 38.32 4.04
407 411 1.907739 CATCCACCATGGGTCGAGT 59.092 57.895 18.09 0.00 38.32 4.18
408 412 0.179073 CATCCACCATGGGTCGAGTC 60.179 60.000 18.09 0.00 38.32 3.36
409 413 1.676678 ATCCACCATGGGTCGAGTCG 61.677 60.000 18.09 6.09 38.32 4.18
410 414 2.348104 CCACCATGGGTCGAGTCGA 61.348 63.158 18.09 12.09 31.02 4.20
411 415 1.139734 CACCATGGGTCGAGTCGAG 59.860 63.158 17.12 5.53 36.23 4.04
412 416 1.304217 ACCATGGGTCGAGTCGAGT 60.304 57.895 17.12 6.24 36.23 4.18
414 418 1.062685 CATGGGTCGAGTCGAGTCG 59.937 63.158 31.83 31.83 41.51 4.18
415 419 1.078637 ATGGGTCGAGTCGAGTCGA 60.079 57.895 34.99 34.99 46.52 4.20
429 433 2.748647 TCGAGTCGACCGCATCCA 60.749 61.111 12.09 0.00 0.00 3.41
430 434 2.579787 CGAGTCGACCGCATCCAC 60.580 66.667 13.01 0.00 0.00 4.02
467 475 1.270907 AGCACCAAGAGACGAGGAAT 58.729 50.000 0.00 0.00 0.00 3.01
474 482 3.119291 CAAGAGACGAGGAATGGAATCG 58.881 50.000 0.00 0.00 42.04 3.34
475 483 1.067821 AGAGACGAGGAATGGAATCGC 59.932 52.381 0.00 0.00 40.02 4.58
484 492 0.462047 AATGGAATCGCCGAGACCAC 60.462 55.000 15.25 0.00 40.66 4.16
488 496 0.876342 GAATCGCCGAGACCACATCC 60.876 60.000 0.00 0.00 0.00 3.51
510 520 1.382557 CCCCCAAAATAGGCCACCC 60.383 63.158 5.01 0.00 0.00 4.61
513 523 1.133482 CCCCAAAATAGGCCACCCTAG 60.133 57.143 5.01 0.00 46.56 3.02
514 524 1.692411 CCAAAATAGGCCACCCTAGC 58.308 55.000 5.01 0.00 46.56 3.42
516 526 2.576615 CAAAATAGGCCACCCTAGCTC 58.423 52.381 5.01 0.00 46.56 4.09
518 528 0.398664 AATAGGCCACCCTAGCTCGT 60.399 55.000 5.01 0.00 46.56 4.18
519 529 0.828343 ATAGGCCACCCTAGCTCGTC 60.828 60.000 5.01 0.00 46.56 4.20
520 530 2.219449 TAGGCCACCCTAGCTCGTCA 62.219 60.000 5.01 0.00 42.87 4.35
521 531 2.184579 GCCACCCTAGCTCGTCAC 59.815 66.667 0.00 0.00 0.00 3.67
522 532 2.893398 CCACCCTAGCTCGTCACC 59.107 66.667 0.00 0.00 0.00 4.02
523 533 1.982395 CCACCCTAGCTCGTCACCA 60.982 63.158 0.00 0.00 0.00 4.17
540 550 1.893808 CACTCACCACCACCACTGC 60.894 63.158 0.00 0.00 0.00 4.40
541 551 2.072487 ACTCACCACCACCACTGCT 61.072 57.895 0.00 0.00 0.00 4.24
542 552 1.598962 CTCACCACCACCACTGCTG 60.599 63.158 0.00 0.00 0.00 4.41
543 553 2.192979 CACCACCACCACTGCTGT 59.807 61.111 0.00 0.00 0.00 4.40
544 554 2.188829 CACCACCACCACTGCTGTG 61.189 63.158 16.20 16.20 43.45 3.66
545 555 3.289834 CCACCACCACTGCTGTGC 61.290 66.667 17.57 0.00 42.54 4.57
546 556 2.516695 CACCACCACTGCTGTGCA 60.517 61.111 17.57 0.00 42.54 4.57
700 715 1.985159 GATATATGCCACCCCACTCCA 59.015 52.381 0.00 0.00 0.00 3.86
742 765 1.880340 CTCGCCGGAGCAGATCAAC 60.880 63.158 5.05 0.00 39.83 3.18
764 797 2.122413 AGGTCAGGCTGGGTGACA 60.122 61.111 15.73 0.00 45.24 3.58
776 809 2.048127 GTGACAGACACTCCCGCC 60.048 66.667 0.00 0.00 45.13 6.13
777 810 3.311110 TGACAGACACTCCCGCCC 61.311 66.667 0.00 0.00 0.00 6.13
778 811 4.436998 GACAGACACTCCCGCCCG 62.437 72.222 0.00 0.00 0.00 6.13
940 992 1.081376 GTACGCCGATCGATCCAGG 60.081 63.158 18.66 16.14 41.67 4.45
2884 2967 0.748450 AGCATTCCATTCCGCCATTG 59.252 50.000 0.00 0.00 0.00 2.82
3054 3151 0.250467 GCAGAACAGGGTGAGCAAGA 60.250 55.000 0.00 0.00 0.00 3.02
3167 3264 2.677003 CCACATGGCCAACGTCGTC 61.677 63.158 10.96 0.00 0.00 4.20
3329 3426 1.450312 CCTCTTCGTCATGCACCCC 60.450 63.158 0.00 0.00 0.00 4.95
3403 3500 4.125703 CCTGTTGATTCTACCTGATCTGC 58.874 47.826 0.00 0.00 0.00 4.26
3406 3503 3.051940 TGATTCTACCTGATCTGCCCT 57.948 47.619 0.00 0.00 0.00 5.19
3407 3504 2.702478 TGATTCTACCTGATCTGCCCTG 59.298 50.000 0.00 0.00 0.00 4.45
3408 3505 0.833287 TTCTACCTGATCTGCCCTGC 59.167 55.000 0.00 0.00 0.00 4.85
3409 3506 0.325577 TCTACCTGATCTGCCCTGCA 60.326 55.000 0.00 0.00 36.92 4.41
3688 3785 0.538057 CCCTTGCTCCTTGCTCAACA 60.538 55.000 0.00 0.00 43.37 3.33
3692 3789 2.574006 TGCTCCTTGCTCAACAGAAT 57.426 45.000 0.00 0.00 43.37 2.40
3739 3840 5.834742 TCATGAGCAATATTAAGCCCATGTT 59.165 36.000 16.64 0.00 44.30 2.71
3799 3900 1.571773 GGTACCCTGGCTCCATGGTT 61.572 60.000 18.71 6.04 41.11 3.67
3832 3933 0.320683 TCGATGACACCAACAGGCTG 60.321 55.000 14.16 14.16 0.00 4.85
3871 3972 0.883833 GGCACACCATCAACTTCCAG 59.116 55.000 0.00 0.00 35.26 3.86
3904 4005 1.545706 GGTTCGACAGGAGGGAGCTT 61.546 60.000 0.00 0.00 0.00 3.74
4058 4159 7.851822 TTTTGAAATTCGCTATGAACACTTC 57.148 32.000 0.00 0.00 40.00 3.01
4209 4310 7.849804 TTTACACAGAATTAGAATCAGCTCC 57.150 36.000 0.00 0.00 0.00 4.70
4216 4317 7.833183 ACAGAATTAGAATCAGCTCCAATTCTT 59.167 33.333 16.55 4.08 41.33 2.52
4276 4381 1.226888 GGCACCGAGTAAGGCGTAG 60.227 63.158 0.00 0.00 33.69 3.51
4287 4392 2.622064 AAGGCGTAGATCATCCAACC 57.378 50.000 0.00 0.00 0.00 3.77
4377 4482 7.675619 AGAATGGGACCTTTATTGACTCAAAAT 59.324 33.333 0.00 0.00 0.00 1.82
4402 4507 1.169661 ATCGAGGCAAAACAACCGCA 61.170 50.000 0.00 0.00 0.00 5.69
4482 4587 4.214119 TCATGCTTCACACACTCTAAAAGC 59.786 41.667 0.00 0.00 39.55 3.51
4525 4630 8.105197 GGGAAAGGAAGAAAACATAAGGTACTA 58.895 37.037 0.00 0.00 38.49 1.82
4635 4745 1.902938 AAAGAAGCTCCTTGTGCTCC 58.097 50.000 0.00 0.00 40.22 4.70
4685 4795 1.281867 CATGTAGTCCCCATGTGTGGT 59.718 52.381 0.00 0.00 44.48 4.16
4777 4888 6.455647 AGCAATGCATGAAGAATATTGGATG 58.544 36.000 8.35 0.00 31.28 3.51
4812 4923 6.299141 ACCCGTCAAGATAAAGATATGCATT 58.701 36.000 3.54 0.00 0.00 3.56
4890 5001 6.569179 TTCCATATGTGATGCATGATGAAG 57.431 37.500 2.46 0.00 38.47 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 5.601662 TCACTTGACTGAGACTTGGTTAAG 58.398 41.667 9.86 9.86 39.86 1.85
6 7 5.607939 TCACTTGACTGAGACTTGGTTAA 57.392 39.130 0.00 0.00 0.00 2.01
7 8 5.808366 ATCACTTGACTGAGACTTGGTTA 57.192 39.130 0.00 0.00 0.00 2.85
8 9 4.696479 ATCACTTGACTGAGACTTGGTT 57.304 40.909 0.00 0.00 0.00 3.67
9 10 6.665680 ACTATATCACTTGACTGAGACTTGGT 59.334 38.462 0.00 0.00 0.00 3.67
10 11 7.106439 ACTATATCACTTGACTGAGACTTGG 57.894 40.000 0.00 0.00 0.00 3.61
63 64 8.778358 GCATGGAGATTCGTATAAAAATTCTCT 58.222 33.333 0.00 0.00 0.00 3.10
64 65 8.559536 TGCATGGAGATTCGTATAAAAATTCTC 58.440 33.333 0.00 0.00 0.00 2.87
65 66 8.450578 TGCATGGAGATTCGTATAAAAATTCT 57.549 30.769 0.00 0.00 0.00 2.40
66 67 9.515020 TTTGCATGGAGATTCGTATAAAAATTC 57.485 29.630 0.00 0.00 0.00 2.17
67 68 9.868277 TTTTGCATGGAGATTCGTATAAAAATT 57.132 25.926 0.00 0.00 0.00 1.82
69 70 9.515020 GATTTTGCATGGAGATTCGTATAAAAA 57.485 29.630 0.00 0.00 0.00 1.94
70 71 8.902806 AGATTTTGCATGGAGATTCGTATAAAA 58.097 29.630 0.00 0.00 0.00 1.52
71 72 8.450578 AGATTTTGCATGGAGATTCGTATAAA 57.549 30.769 0.00 0.00 0.00 1.40
72 73 7.714813 TGAGATTTTGCATGGAGATTCGTATAA 59.285 33.333 0.00 0.00 0.00 0.98
73 74 7.216494 TGAGATTTTGCATGGAGATTCGTATA 58.784 34.615 0.00 0.00 0.00 1.47
74 75 6.057533 TGAGATTTTGCATGGAGATTCGTAT 58.942 36.000 0.00 0.00 0.00 3.06
75 76 5.427378 TGAGATTTTGCATGGAGATTCGTA 58.573 37.500 0.00 0.00 0.00 3.43
76 77 4.264253 TGAGATTTTGCATGGAGATTCGT 58.736 39.130 0.00 0.00 0.00 3.85
77 78 4.334759 ACTGAGATTTTGCATGGAGATTCG 59.665 41.667 0.00 0.00 0.00 3.34
78 79 5.450137 CCACTGAGATTTTGCATGGAGATTC 60.450 44.000 0.00 0.00 0.00 2.52
79 80 4.401519 CCACTGAGATTTTGCATGGAGATT 59.598 41.667 0.00 0.00 0.00 2.40
80 81 3.952323 CCACTGAGATTTTGCATGGAGAT 59.048 43.478 0.00 0.00 0.00 2.75
81 82 3.009363 TCCACTGAGATTTTGCATGGAGA 59.991 43.478 0.00 0.00 31.25 3.71
82 83 3.128242 GTCCACTGAGATTTTGCATGGAG 59.872 47.826 0.18 0.00 35.49 3.86
83 84 3.084039 GTCCACTGAGATTTTGCATGGA 58.916 45.455 0.00 0.00 32.39 3.41
84 85 3.087031 AGTCCACTGAGATTTTGCATGG 58.913 45.455 0.00 0.00 0.00 3.66
85 86 4.092771 CAGTCCACTGAGATTTTGCATG 57.907 45.455 0.00 0.00 46.59 4.06
97 98 2.513753 AGTCTCAGTCTCAGTCCACTG 58.486 52.381 0.00 0.00 45.08 3.66
98 99 2.890311 CAAGTCTCAGTCTCAGTCCACT 59.110 50.000 0.00 0.00 0.00 4.00
99 100 2.029470 CCAAGTCTCAGTCTCAGTCCAC 60.029 54.545 0.00 0.00 0.00 4.02
100 101 2.242926 CCAAGTCTCAGTCTCAGTCCA 58.757 52.381 0.00 0.00 0.00 4.02
101 102 1.067213 GCCAAGTCTCAGTCTCAGTCC 60.067 57.143 0.00 0.00 0.00 3.85
102 103 1.615883 TGCCAAGTCTCAGTCTCAGTC 59.384 52.381 0.00 0.00 0.00 3.51
103 104 1.709578 TGCCAAGTCTCAGTCTCAGT 58.290 50.000 0.00 0.00 0.00 3.41
104 105 2.827800 TTGCCAAGTCTCAGTCTCAG 57.172 50.000 0.00 0.00 0.00 3.35
105 106 3.118261 AGTTTTGCCAAGTCTCAGTCTCA 60.118 43.478 0.00 0.00 0.00 3.27
106 107 3.249559 CAGTTTTGCCAAGTCTCAGTCTC 59.750 47.826 0.00 0.00 0.00 3.36
107 108 3.209410 CAGTTTTGCCAAGTCTCAGTCT 58.791 45.455 0.00 0.00 0.00 3.24
108 109 2.945668 ACAGTTTTGCCAAGTCTCAGTC 59.054 45.455 0.00 0.00 0.00 3.51
109 110 3.004752 ACAGTTTTGCCAAGTCTCAGT 57.995 42.857 0.00 0.00 0.00 3.41
110 111 3.629398 AGAACAGTTTTGCCAAGTCTCAG 59.371 43.478 0.00 0.00 0.00 3.35
111 112 3.620488 AGAACAGTTTTGCCAAGTCTCA 58.380 40.909 0.00 0.00 0.00 3.27
112 113 4.639135 AAGAACAGTTTTGCCAAGTCTC 57.361 40.909 0.00 0.00 0.00 3.36
113 114 6.073222 CGTATAAGAACAGTTTTGCCAAGTCT 60.073 38.462 0.00 0.00 0.00 3.24
114 115 6.073440 TCGTATAAGAACAGTTTTGCCAAGTC 60.073 38.462 0.00 0.00 0.00 3.01
115 116 5.761234 TCGTATAAGAACAGTTTTGCCAAGT 59.239 36.000 0.00 0.00 0.00 3.16
116 117 6.236017 TCGTATAAGAACAGTTTTGCCAAG 57.764 37.500 0.00 0.00 0.00 3.61
117 118 6.621316 TTCGTATAAGAACAGTTTTGCCAA 57.379 33.333 0.00 0.00 0.00 4.52
118 119 6.811253 ATTCGTATAAGAACAGTTTTGCCA 57.189 33.333 3.08 0.00 32.39 4.92
119 120 8.515473 AAAATTCGTATAAGAACAGTTTTGCC 57.485 30.769 3.08 0.00 32.39 4.52
148 149 9.577110 TCGTTATGTCTCTGTATAAAAATTCGT 57.423 29.630 0.00 0.00 0.00 3.85
164 165 2.163815 CCACCGAGACTTCGTTATGTCT 59.836 50.000 0.00 0.00 45.28 3.41
165 166 2.163010 TCCACCGAGACTTCGTTATGTC 59.837 50.000 0.00 0.00 45.28 3.06
166 167 2.094854 GTCCACCGAGACTTCGTTATGT 60.095 50.000 0.00 0.00 45.28 2.29
167 168 2.163815 AGTCCACCGAGACTTCGTTATG 59.836 50.000 0.00 0.00 44.83 1.90
168 169 2.163815 CAGTCCACCGAGACTTCGTTAT 59.836 50.000 0.63 0.00 44.83 1.89
169 170 1.538512 CAGTCCACCGAGACTTCGTTA 59.461 52.381 0.63 0.00 44.83 3.18
170 171 0.314302 CAGTCCACCGAGACTTCGTT 59.686 55.000 0.63 0.00 44.83 3.85
171 172 0.536687 TCAGTCCACCGAGACTTCGT 60.537 55.000 0.63 0.00 44.83 3.85
172 173 0.169230 CTCAGTCCACCGAGACTTCG 59.831 60.000 0.63 0.00 44.83 3.79
173 174 1.535833 TCTCAGTCCACCGAGACTTC 58.464 55.000 0.63 0.00 44.83 3.01
174 175 3.747735 TCTCAGTCCACCGAGACTT 57.252 52.632 0.63 0.00 44.83 3.01
177 178 1.248486 CAAGTCTCAGTCCACCGAGA 58.752 55.000 0.00 0.00 35.93 4.04
178 179 0.244994 CCAAGTCTCAGTCCACCGAG 59.755 60.000 0.00 0.00 0.00 4.63
179 180 1.816863 GCCAAGTCTCAGTCCACCGA 61.817 60.000 0.00 0.00 0.00 4.69
180 181 1.374758 GCCAAGTCTCAGTCCACCG 60.375 63.158 0.00 0.00 0.00 4.94
181 182 0.108585 TTGCCAAGTCTCAGTCCACC 59.891 55.000 0.00 0.00 0.00 4.61
182 183 1.967319 TTTGCCAAGTCTCAGTCCAC 58.033 50.000 0.00 0.00 0.00 4.02
183 184 2.092429 AGTTTTGCCAAGTCTCAGTCCA 60.092 45.455 0.00 0.00 0.00 4.02
184 185 2.291741 CAGTTTTGCCAAGTCTCAGTCC 59.708 50.000 0.00 0.00 0.00 3.85
185 186 2.945668 ACAGTTTTGCCAAGTCTCAGTC 59.054 45.455 0.00 0.00 0.00 3.51
186 187 3.004752 ACAGTTTTGCCAAGTCTCAGT 57.995 42.857 0.00 0.00 0.00 3.41
187 188 3.629398 AGAACAGTTTTGCCAAGTCTCAG 59.371 43.478 0.00 0.00 0.00 3.35
188 189 3.620488 AGAACAGTTTTGCCAAGTCTCA 58.380 40.909 0.00 0.00 0.00 3.27
189 190 4.639135 AAGAACAGTTTTGCCAAGTCTC 57.361 40.909 0.00 0.00 0.00 3.36
190 191 4.706962 AGAAAGAACAGTTTTGCCAAGTCT 59.293 37.500 0.00 0.00 0.00 3.24
191 192 4.998788 AGAAAGAACAGTTTTGCCAAGTC 58.001 39.130 0.00 0.00 0.00 3.01
192 193 5.405935 AAGAAAGAACAGTTTTGCCAAGT 57.594 34.783 0.00 0.00 0.00 3.16
193 194 6.101997 AGAAAGAAAGAACAGTTTTGCCAAG 58.898 36.000 0.00 0.00 0.00 3.61
194 195 6.036577 AGAAAGAAAGAACAGTTTTGCCAA 57.963 33.333 0.00 0.00 0.00 4.52
195 196 5.659440 AGAAAGAAAGAACAGTTTTGCCA 57.341 34.783 0.00 0.00 0.00 4.92
196 197 6.968131 AAAGAAAGAAAGAACAGTTTTGCC 57.032 33.333 0.00 0.00 0.00 4.52
197 198 8.282592 ACAAAAAGAAAGAAAGAACAGTTTTGC 58.717 29.630 0.00 0.00 37.08 3.68
201 202 9.764363 AGAAACAAAAAGAAAGAAAGAACAGTT 57.236 25.926 0.00 0.00 0.00 3.16
202 203 9.764363 AAGAAACAAAAAGAAAGAAAGAACAGT 57.236 25.926 0.00 0.00 0.00 3.55
205 206 9.318041 GCAAAGAAACAAAAAGAAAGAAAGAAC 57.682 29.630 0.00 0.00 0.00 3.01
206 207 8.503196 GGCAAAGAAACAAAAAGAAAGAAAGAA 58.497 29.630 0.00 0.00 0.00 2.52
207 208 7.877612 AGGCAAAGAAACAAAAAGAAAGAAAGA 59.122 29.630 0.00 0.00 0.00 2.52
208 209 8.032952 AGGCAAAGAAACAAAAAGAAAGAAAG 57.967 30.769 0.00 0.00 0.00 2.62
209 210 7.977789 AGGCAAAGAAACAAAAAGAAAGAAA 57.022 28.000 0.00 0.00 0.00 2.52
210 211 7.977789 AAGGCAAAGAAACAAAAAGAAAGAA 57.022 28.000 0.00 0.00 0.00 2.52
211 212 7.977789 AAAGGCAAAGAAACAAAAAGAAAGA 57.022 28.000 0.00 0.00 0.00 2.52
246 247 4.747605 GCGATGGCCAAAGAAAACTAAAAA 59.252 37.500 10.96 0.00 0.00 1.94
247 248 4.303282 GCGATGGCCAAAGAAAACTAAAA 58.697 39.130 10.96 0.00 0.00 1.52
248 249 3.610585 CGCGATGGCCAAAGAAAACTAAA 60.611 43.478 10.96 0.00 35.02 1.85
249 250 2.095466 CGCGATGGCCAAAGAAAACTAA 60.095 45.455 10.96 0.00 35.02 2.24
250 251 1.466950 CGCGATGGCCAAAGAAAACTA 59.533 47.619 10.96 0.00 35.02 2.24
251 252 0.240945 CGCGATGGCCAAAGAAAACT 59.759 50.000 10.96 0.00 35.02 2.66
353 354 0.030101 CCGCACATCAAACCGTTGTT 59.970 50.000 0.00 0.00 36.07 2.83
376 380 0.742505 GTGGATGCATGGTGGATGTG 59.257 55.000 2.46 0.00 34.14 3.21
377 381 0.396139 GGTGGATGCATGGTGGATGT 60.396 55.000 2.46 0.00 34.14 3.06
378 382 0.396001 TGGTGGATGCATGGTGGATG 60.396 55.000 2.46 0.00 34.84 3.51
379 383 0.559205 ATGGTGGATGCATGGTGGAT 59.441 50.000 2.46 0.00 0.00 3.41
380 384 0.396001 CATGGTGGATGCATGGTGGA 60.396 55.000 2.46 0.00 0.00 4.02
381 385 1.396607 CCATGGTGGATGCATGGTGG 61.397 60.000 2.46 0.00 40.96 4.61
382 386 1.396607 CCCATGGTGGATGCATGGTG 61.397 60.000 11.73 0.00 43.11 4.17
383 387 1.075822 CCCATGGTGGATGCATGGT 60.076 57.895 11.73 0.00 43.11 3.55
384 388 1.075822 ACCCATGGTGGATGCATGG 60.076 57.895 11.73 0.00 40.96 3.66
385 389 1.449726 CGACCCATGGTGGATGCATG 61.450 60.000 11.73 0.00 40.96 4.06
386 390 1.152902 CGACCCATGGTGGATGCAT 60.153 57.895 11.73 0.00 40.96 3.96
387 391 2.256072 CTCGACCCATGGTGGATGCA 62.256 60.000 11.73 0.00 40.96 3.96
388 392 1.524621 CTCGACCCATGGTGGATGC 60.525 63.158 11.73 0.00 40.96 3.91
391 395 2.348104 CGACTCGACCCATGGTGGA 61.348 63.158 11.73 3.74 40.96 4.02
393 397 1.139734 CTCGACTCGACCCATGGTG 59.860 63.158 11.73 4.77 35.25 4.17
394 398 1.304217 ACTCGACTCGACCCATGGT 60.304 57.895 11.73 0.00 39.44 3.55
395 399 1.433879 GACTCGACTCGACCCATGG 59.566 63.158 4.14 4.14 0.00 3.66
396 400 1.062685 CGACTCGACTCGACCCATG 59.937 63.158 8.56 0.00 35.58 3.66
397 401 1.078637 TCGACTCGACTCGACCCAT 60.079 57.895 12.30 0.00 37.76 4.00
400 404 1.709182 GACTCGACTCGACTCGACC 59.291 63.158 12.30 5.12 37.76 4.79
401 405 1.069924 TCGACTCGACTCGACTCGAC 61.070 60.000 21.74 4.52 42.54 4.20
402 406 1.211190 TCGACTCGACTCGACTCGA 59.789 57.895 21.74 21.74 44.07 4.04
412 416 2.748647 TGGATGCGGTCGACTCGA 60.749 61.111 24.32 13.04 0.00 4.04
414 418 2.202756 GGTGGATGCGGTCGACTC 60.203 66.667 16.46 8.39 36.01 3.36
415 419 2.359169 ATGGTGGATGCGGTCGACT 61.359 57.895 16.46 0.00 36.01 4.18
416 420 2.173669 CATGGTGGATGCGGTCGAC 61.174 63.158 7.13 7.13 35.08 4.20
417 421 2.186644 CATGGTGGATGCGGTCGA 59.813 61.111 0.00 0.00 0.00 4.20
444 448 0.605589 CTCGTCTCTTGGTGCTTCCT 59.394 55.000 0.80 0.00 37.07 3.36
445 449 0.390472 CCTCGTCTCTTGGTGCTTCC 60.390 60.000 0.00 0.00 0.00 3.46
467 475 1.613317 ATGTGGTCTCGGCGATTCCA 61.613 55.000 22.73 22.73 34.01 3.53
474 482 2.125106 GGTGGATGTGGTCTCGGC 60.125 66.667 0.00 0.00 0.00 5.54
475 483 2.584608 GGGTGGATGTGGTCTCGG 59.415 66.667 0.00 0.00 0.00 4.63
497 507 1.141053 CGAGCTAGGGTGGCCTATTTT 59.859 52.381 3.32 0.00 0.00 1.82
507 517 0.966370 GAGTGGTGACGAGCTAGGGT 60.966 60.000 0.00 0.00 0.00 4.34
510 520 0.171455 GGTGAGTGGTGACGAGCTAG 59.829 60.000 0.00 0.00 0.00 3.42
512 522 1.832608 TGGTGAGTGGTGACGAGCT 60.833 57.895 0.00 0.00 0.00 4.09
513 523 1.664965 GTGGTGAGTGGTGACGAGC 60.665 63.158 0.00 0.00 0.00 5.03
514 524 1.006102 GGTGGTGAGTGGTGACGAG 60.006 63.158 0.00 0.00 0.00 4.18
516 526 1.594293 GTGGTGGTGAGTGGTGACG 60.594 63.158 0.00 0.00 0.00 4.35
518 528 1.690985 TGGTGGTGGTGAGTGGTGA 60.691 57.895 0.00 0.00 0.00 4.02
519 529 1.525995 GTGGTGGTGGTGAGTGGTG 60.526 63.158 0.00 0.00 0.00 4.17
520 530 1.692749 AGTGGTGGTGGTGAGTGGT 60.693 57.895 0.00 0.00 0.00 4.16
521 531 1.227943 CAGTGGTGGTGGTGAGTGG 60.228 63.158 0.00 0.00 0.00 4.00
522 532 1.893808 GCAGTGGTGGTGGTGAGTG 60.894 63.158 0.00 0.00 0.00 3.51
523 533 2.072487 AGCAGTGGTGGTGGTGAGT 61.072 57.895 0.00 0.00 31.51 3.41
540 550 3.862402 GCTAGCTGCGCTGCACAG 61.862 66.667 35.70 30.33 40.10 3.66
575 585 3.490348 AGGAAATCAAGTTGGGACTGTG 58.510 45.455 2.34 0.00 35.91 3.66
700 715 1.122019 AAGTGGAAGCTGTCGAGGGT 61.122 55.000 0.00 0.00 0.00 4.34
742 765 4.087892 CCCAGCCTGACCTGACGG 62.088 72.222 0.00 0.00 34.77 4.79
780 813 3.322466 AACGGGCAGTGGAGGGAG 61.322 66.667 0.00 0.00 0.00 4.30
781 814 3.636231 CAACGGGCAGTGGAGGGA 61.636 66.667 0.00 0.00 0.00 4.20
999 1064 4.855105 TTCCGCGGAAGATCCATG 57.145 55.556 35.81 0.13 35.91 3.66
1138 1203 4.087892 GGAGAAGGAGCTGGCGCA 62.088 66.667 10.83 0.00 39.10 6.09
1413 1478 1.670590 CCGCATCTCCTCCATCTCC 59.329 63.158 0.00 0.00 0.00 3.71
2052 2129 2.596631 GCCATGCGGATGAGCCAT 60.597 61.111 19.50 0.00 35.94 4.40
2724 2807 0.176449 TGATCTGCTCGTCCATGGTG 59.824 55.000 12.58 6.00 0.00 4.17
2884 2967 1.153958 GTTGCAAGCAAGGATCGGC 60.154 57.895 7.88 0.00 36.52 5.54
3054 3151 1.122019 ACCCAGTTCTTGAGCGACCT 61.122 55.000 0.00 0.00 0.00 3.85
3167 3264 3.071459 GAACACGATGAGCGCCACG 62.071 63.158 2.29 7.72 46.04 4.94
3242 3339 4.778415 GCGACGAGGAGCTGCGAA 62.778 66.667 0.00 0.00 0.00 4.70
3329 3426 3.011789 CGATCGCCGACGTCGAAG 61.012 66.667 37.65 28.30 41.83 3.79
3408 3505 1.843368 ATCAGTGCAACCCTTGGATG 58.157 50.000 0.00 0.00 37.80 3.51
3409 3506 2.173519 CAATCAGTGCAACCCTTGGAT 58.826 47.619 0.00 0.00 37.80 3.41
3688 3785 4.122046 GTGAGTTTTGGCAGCAAAATTCT 58.878 39.130 17.87 11.19 39.74 2.40
3692 3789 3.608316 AAGTGAGTTTTGGCAGCAAAA 57.392 38.095 0.00 0.00 0.00 2.44
3705 3802 8.565896 TTAATATTGCTCATGACAAAGTGAGT 57.434 30.769 12.60 1.78 42.91 3.41
3739 3840 6.876789 TGTCAAGGTAGCTGAAATTCGAAATA 59.123 34.615 0.00 0.00 0.00 1.40
3832 3933 2.554032 CCGGCACCAGATGGATATTTTC 59.446 50.000 5.72 0.00 38.94 2.29
3871 3972 0.179045 CGAACCTCATCCCCATGTCC 60.179 60.000 0.00 0.00 0.00 4.02
3904 4005 8.724113 AGATCTTCATCATCTCTTGGAGAATA 57.276 34.615 1.26 0.00 42.27 1.75
3940 4041 0.660595 GCATCCGGTACTCGATGTCG 60.661 60.000 18.05 0.00 42.43 4.35
4058 4159 8.808529 CAACTTTACTCCACAATCTAACTATCG 58.191 37.037 0.00 0.00 0.00 2.92
4276 4381 1.211457 AGGCTCACAGGTTGGATGATC 59.789 52.381 0.00 0.00 0.00 2.92
4287 4392 4.463879 CCGGGCAGAGGCTCACAG 62.464 72.222 18.26 7.26 42.15 3.66
4377 4482 0.882484 TGTTTTGCCTCGATGCGACA 60.882 50.000 8.19 9.60 0.00 4.35
4402 4507 4.278419 GCAAAGGTTGGTTGTGAACTCTAT 59.722 41.667 0.00 0.00 0.00 1.98
4482 4587 5.449588 CCTTTCCCTGAATCATGTCGATTTG 60.450 44.000 0.00 0.00 44.65 2.32
4525 4630 8.463607 GTTTAGTACTCTTTAGATCAGTGCTCT 58.536 37.037 0.00 1.52 35.14 4.09
4635 4745 3.049674 TCTTTGCTTCAGCGGCCG 61.050 61.111 24.05 24.05 45.83 6.13
4710 4820 6.668541 ACATCTCAATGAAACATTAGTCCG 57.331 37.500 0.00 0.00 36.67 4.79
4755 4865 6.988522 TCCATCCAATATTCTTCATGCATTG 58.011 36.000 0.00 0.00 0.00 2.82
4777 4888 3.343617 TCTTGACGGGTTTCATCAATCC 58.656 45.455 0.00 0.00 32.16 3.01
4812 4923 7.148086 GGAATTGCTATTCATTACCAACACTCA 60.148 37.037 20.07 0.00 41.62 3.41
4879 4990 4.173290 TCCATCCAATCTTCATCATGCA 57.827 40.909 0.00 0.00 0.00 3.96
4886 4997 7.152942 TCATTCCTAATCCATCCAATCTTCA 57.847 36.000 0.00 0.00 0.00 3.02
4890 5001 7.771927 ACATTCATTCCTAATCCATCCAATC 57.228 36.000 0.00 0.00 0.00 2.67
4922 5033 7.228590 TCAATGATCTTGATGCATATCTTGGA 58.771 34.615 0.00 0.00 34.31 3.53
4986 5097 3.904800 TGATGCCTCGGAGTTCATTTA 57.095 42.857 4.02 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.