Multiple sequence alignment - TraesCS5D01G285600

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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 TraesCS5D01G285600 chr5D 100.000 2270 0 0 1 2270 386068386 386066117 0.000000e+00 4193.0
1 TraesCS5D01G285600 chr5D 92.359 602 34 4 720 1321 386036130 386035541 0.000000e+00 846.0
2 TraesCS5D01G285600 chr5D 82.895 988 72 37 1338 2260 386057733 386056778 0.000000e+00 798.0
3 TraesCS5D01G285600 chr5D 92.081 543 33 7 786 1325 386058317 386057782 0.000000e+00 756.0
4 TraesCS5D01G285600 chr5D 86.707 662 33 27 687 1321 385978847 385978214 0.000000e+00 684.0
5 TraesCS5D01G285600 chr5D 92.378 328 23 2 1902 2228 386035243 386034917 1.230000e-127 466.0
6 TraesCS5D01G285600 chr5D 89.831 177 10 6 324 499 386087923 386087754 1.060000e-53 220.0
7 TraesCS5D01G285600 chr5D 95.181 83 4 0 1 83 386087190 386087108 5.090000e-27 132.0
8 TraesCS5D01G285600 chr5B 94.726 1934 62 8 324 2234 463945754 463943838 0.000000e+00 2970.0
9 TraesCS5D01G285600 chr5B 88.065 620 33 17 731 1343 463912641 463912056 0.000000e+00 697.0
10 TraesCS5D01G285600 chr5B 89.222 501 41 7 1772 2270 463918210 463917721 4.140000e-172 614.0
11 TraesCS5D01G285600 chr5B 88.960 471 43 4 1794 2263 463937376 463936914 7.030000e-160 573.0
12 TraesCS5D01G285600 chr5B 84.861 502 39 12 1740 2224 463911922 463911441 2.640000e-129 472.0
13 TraesCS5D01G285600 chr5B 100.000 42 0 0 2229 2270 463941280 463941239 6.720000e-11 78.7
14 TraesCS5D01G285600 chr5A 93.353 1685 57 19 622 2270 488009250 488007585 0.000000e+00 2440.0
15 TraesCS5D01G285600 chr5A 88.296 675 49 15 687 1339 487918974 487918308 0.000000e+00 782.0
16 TraesCS5D01G285600 chr5A 85.946 740 59 25 786 1502 487985127 487984410 0.000000e+00 749.0
17 TraesCS5D01G285600 chr5A 87.676 641 60 7 687 1321 487949283 487948656 0.000000e+00 728.0
18 TraesCS5D01G285600 chr5A 89.159 535 42 9 1704 2229 487940230 487939703 0.000000e+00 652.0
19 TraesCS5D01G285600 chr5A 84.591 636 52 20 697 1321 487941128 487940528 6.980000e-165 590.0
20 TraesCS5D01G285600 chr5A 86.422 545 44 9 1731 2270 487984159 487983640 9.100000e-159 569.0
21 TraesCS5D01G285600 chr5A 85.931 462 43 9 1772 2228 487918171 487917727 7.340000e-130 473.0
22 TraesCS5D01G285600 chr5A 87.574 338 24 7 1 324 495584189 495583856 2.130000e-100 375.0
23 TraesCS5D01G285600 chr5A 88.479 217 21 3 2054 2270 487924112 487923900 2.240000e-65 259.0
24 TraesCS5D01G285600 chr5A 89.326 178 16 2 324 499 488010181 488010005 1.060000e-53 220.0
25 TraesCS5D01G285600 chr5A 89.091 110 6 2 720 823 487925190 487925081 5.090000e-27 132.0
26 TraesCS5D01G285600 chr5A 97.368 38 1 0 618 655 487949313 487949276 5.230000e-07 65.8
27 TraesCS5D01G285600 chr1D 92.262 336 13 2 1 323 46489177 46489512 4.420000e-127 464.0
28 TraesCS5D01G285600 chr1D 91.098 337 17 6 1 324 46464791 46465127 5.750000e-121 444.0
29 TraesCS5D01G285600 chr1D 89.286 336 23 2 1 323 49514332 49513997 2.100000e-110 409.0
30 TraesCS5D01G285600 chr6B 89.053 338 21 7 1 324 716326343 716326008 2.720000e-109 405.0
31 TraesCS5D01G285600 chr3A 87.574 338 23 8 1 324 356619466 356619134 7.660000e-100 374.0
32 TraesCS5D01G285600 chr3A 87.574 338 23 8 1 324 356624351 356624019 7.660000e-100 374.0
33 TraesCS5D01G285600 chr3A 87.537 337 24 7 1 323 681112824 681112492 7.660000e-100 374.0
34 TraesCS5D01G285600 chr3A 87.278 338 25 7 1 324 681117710 681117377 9.900000e-99 370.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G285600 chr5D 386066117 386068386 2269 True 4193.000000 4193 100.0000 1 2270 1 chr5D.!!$R2 2269
1 TraesCS5D01G285600 chr5D 386056778 386058317 1539 True 777.000000 798 87.4880 786 2260 2 chr5D.!!$R4 1474
2 TraesCS5D01G285600 chr5D 385978214 385978847 633 True 684.000000 684 86.7070 687 1321 1 chr5D.!!$R1 634
3 TraesCS5D01G285600 chr5D 386034917 386036130 1213 True 656.000000 846 92.3685 720 2228 2 chr5D.!!$R3 1508
4 TraesCS5D01G285600 chr5B 463936914 463945754 8840 True 1207.233333 2970 94.5620 324 2270 3 chr5B.!!$R3 1946
5 TraesCS5D01G285600 chr5B 463911441 463912641 1200 True 584.500000 697 86.4630 731 2224 2 chr5B.!!$R2 1493
6 TraesCS5D01G285600 chr5A 488007585 488010181 2596 True 1330.000000 2440 91.3395 324 2270 2 chr5A.!!$R7 1946
7 TraesCS5D01G285600 chr5A 487983640 487985127 1487 True 659.000000 749 86.1840 786 2270 2 chr5A.!!$R6 1484
8 TraesCS5D01G285600 chr5A 487917727 487918974 1247 True 627.500000 782 87.1135 687 2228 2 chr5A.!!$R2 1541
9 TraesCS5D01G285600 chr5A 487939703 487941128 1425 True 621.000000 652 86.8750 697 2229 2 chr5A.!!$R4 1532
10 TraesCS5D01G285600 chr5A 487948656 487949313 657 True 396.900000 728 92.5220 618 1321 2 chr5A.!!$R5 703

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
114 115 0.034337 TCCTACCTTTGTGCCACGAC 59.966 55.0 0.0 0.0 0.0 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1458 2325 0.595095 CTGGAGCAGAAACAGCCAAC 59.405 55.0 0.0 0.0 32.44 3.77 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 4.115401 GGAAAGACTCCATGGATTTTGC 57.885 45.455 16.63 16.57 44.67 3.68
25 26 3.511146 GGAAAGACTCCATGGATTTTGCA 59.489 43.478 16.63 0.00 44.67 4.08
26 27 4.161001 GGAAAGACTCCATGGATTTTGCAT 59.839 41.667 16.63 0.00 44.67 3.96
27 28 4.996788 AAGACTCCATGGATTTTGCATC 57.003 40.909 16.63 4.81 0.00 3.91
28 29 2.947652 AGACTCCATGGATTTTGCATCG 59.052 45.455 16.63 2.31 0.00 3.84
29 30 1.406539 ACTCCATGGATTTTGCATCGC 59.593 47.619 16.63 0.00 0.00 4.58
30 31 0.381445 TCCATGGATTTTGCATCGCG 59.619 50.000 11.44 0.00 0.00 5.87
31 32 0.101040 CCATGGATTTTGCATCGCGT 59.899 50.000 5.56 0.00 0.00 6.01
32 33 1.193644 CATGGATTTTGCATCGCGTG 58.806 50.000 5.77 5.06 0.00 5.34
54 55 3.680789 CAAAACTTGCGACTTTTCTCGT 58.319 40.909 0.00 0.00 35.99 4.18
55 56 4.095610 CAAAACTTGCGACTTTTCTCGTT 58.904 39.130 0.00 0.00 35.99 3.85
56 57 4.351131 AAACTTGCGACTTTTCTCGTTT 57.649 36.364 0.00 0.00 35.99 3.60
57 58 5.473796 AAACTTGCGACTTTTCTCGTTTA 57.526 34.783 0.00 0.00 35.99 2.01
58 59 5.668558 AACTTGCGACTTTTCTCGTTTAT 57.331 34.783 0.00 0.00 35.99 1.40
59 60 5.668558 ACTTGCGACTTTTCTCGTTTATT 57.331 34.783 0.00 0.00 35.99 1.40
60 61 5.676953 ACTTGCGACTTTTCTCGTTTATTC 58.323 37.500 0.00 0.00 35.99 1.75
61 62 5.465724 ACTTGCGACTTTTCTCGTTTATTCT 59.534 36.000 0.00 0.00 35.99 2.40
62 63 5.917541 TGCGACTTTTCTCGTTTATTCTT 57.082 34.783 0.00 0.00 35.99 2.52
63 64 5.912528 TGCGACTTTTCTCGTTTATTCTTC 58.087 37.500 0.00 0.00 35.99 2.87
64 65 5.107220 TGCGACTTTTCTCGTTTATTCTTCC 60.107 40.000 0.00 0.00 35.99 3.46
65 66 5.120363 GCGACTTTTCTCGTTTATTCTTCCT 59.880 40.000 0.00 0.00 35.99 3.36
66 67 6.670214 GCGACTTTTCTCGTTTATTCTTCCTC 60.670 42.308 0.00 0.00 35.99 3.71
67 68 6.586844 CGACTTTTCTCGTTTATTCTTCCTCT 59.413 38.462 0.00 0.00 0.00 3.69
68 69 7.754027 CGACTTTTCTCGTTTATTCTTCCTCTA 59.246 37.037 0.00 0.00 0.00 2.43
69 70 9.589111 GACTTTTCTCGTTTATTCTTCCTCTAT 57.411 33.333 0.00 0.00 0.00 1.98
70 71 9.945904 ACTTTTCTCGTTTATTCTTCCTCTATT 57.054 29.630 0.00 0.00 0.00 1.73
77 78 9.555727 TCGTTTATTCTTCCTCTATTTATTGGG 57.444 33.333 0.00 0.00 0.00 4.12
78 79 9.338622 CGTTTATTCTTCCTCTATTTATTGGGT 57.661 33.333 0.00 0.00 0.00 4.51
93 94 2.967270 GGGTACCGTGACAGGTAGT 58.033 57.895 5.65 0.00 46.40 2.73
94 95 1.260544 GGGTACCGTGACAGGTAGTT 58.739 55.000 5.65 0.00 46.40 2.24
95 96 1.620323 GGGTACCGTGACAGGTAGTTT 59.380 52.381 5.65 0.00 46.40 2.66
96 97 2.353109 GGGTACCGTGACAGGTAGTTTC 60.353 54.545 5.65 0.00 46.40 2.78
97 98 2.353109 GGTACCGTGACAGGTAGTTTCC 60.353 54.545 0.00 2.32 46.40 3.13
98 99 1.713297 ACCGTGACAGGTAGTTTCCT 58.287 50.000 0.00 0.00 43.89 3.36
99 100 2.880443 ACCGTGACAGGTAGTTTCCTA 58.120 47.619 0.00 0.00 43.89 2.94
100 101 2.560105 ACCGTGACAGGTAGTTTCCTAC 59.440 50.000 0.00 0.00 43.89 3.18
110 111 3.746940 GTAGTTTCCTACCTTTGTGCCA 58.253 45.455 0.00 0.00 38.09 4.92
111 112 2.583143 AGTTTCCTACCTTTGTGCCAC 58.417 47.619 0.00 0.00 0.00 5.01
112 113 1.265905 GTTTCCTACCTTTGTGCCACG 59.734 52.381 0.00 0.00 0.00 4.94
113 114 0.759959 TTCCTACCTTTGTGCCACGA 59.240 50.000 0.00 0.00 0.00 4.35
114 115 0.034337 TCCTACCTTTGTGCCACGAC 59.966 55.000 0.00 0.00 0.00 4.34
115 116 0.953960 CCTACCTTTGTGCCACGACC 60.954 60.000 0.00 0.00 0.00 4.79
116 117 0.953960 CTACCTTTGTGCCACGACCC 60.954 60.000 0.00 0.00 0.00 4.46
117 118 1.412453 TACCTTTGTGCCACGACCCT 61.412 55.000 0.00 0.00 0.00 4.34
118 119 2.260869 CCTTTGTGCCACGACCCTG 61.261 63.158 0.00 0.00 0.00 4.45
119 120 1.227823 CTTTGTGCCACGACCCTGA 60.228 57.895 0.00 0.00 0.00 3.86
120 121 1.507141 CTTTGTGCCACGACCCTGAC 61.507 60.000 0.00 0.00 0.00 3.51
121 122 2.951475 TTTGTGCCACGACCCTGACC 62.951 60.000 0.00 0.00 0.00 4.02
122 123 3.936203 GTGCCACGACCCTGACCA 61.936 66.667 0.00 0.00 0.00 4.02
123 124 3.936203 TGCCACGACCCTGACCAC 61.936 66.667 0.00 0.00 0.00 4.16
124 125 3.626924 GCCACGACCCTGACCACT 61.627 66.667 0.00 0.00 0.00 4.00
125 126 2.657237 CCACGACCCTGACCACTC 59.343 66.667 0.00 0.00 0.00 3.51
126 127 2.258591 CACGACCCTGACCACTCG 59.741 66.667 0.00 0.00 0.00 4.18
127 128 2.203451 ACGACCCTGACCACTCGT 60.203 61.111 0.00 0.00 34.59 4.18
128 129 2.258591 CGACCCTGACCACTCGTG 59.741 66.667 0.00 0.00 0.00 4.35
129 130 2.048127 GACCCTGACCACTCGTGC 60.048 66.667 0.00 0.00 0.00 5.34
130 131 3.591254 GACCCTGACCACTCGTGCC 62.591 68.421 0.00 0.00 0.00 5.01
131 132 3.625897 CCCTGACCACTCGTGCCA 61.626 66.667 0.00 0.00 0.00 4.92
132 133 2.665000 CCTGACCACTCGTGCCAT 59.335 61.111 0.00 0.00 0.00 4.40
133 134 1.448540 CCTGACCACTCGTGCCATC 60.449 63.158 0.00 0.00 0.00 3.51
134 135 1.448540 CTGACCACTCGTGCCATCC 60.449 63.158 0.00 0.00 0.00 3.51
135 136 2.125106 GACCACTCGTGCCATCCC 60.125 66.667 0.00 0.00 0.00 3.85
136 137 2.927856 ACCACTCGTGCCATCCCA 60.928 61.111 0.00 0.00 0.00 4.37
137 138 2.436646 CCACTCGTGCCATCCCAC 60.437 66.667 0.00 0.00 0.00 4.61
143 144 3.890674 GTGCCATCCCACGAGTTC 58.109 61.111 0.00 0.00 0.00 3.01
144 145 2.100631 GTGCCATCCCACGAGTTCG 61.101 63.158 0.00 0.00 46.33 3.95
145 146 3.195698 GCCATCCCACGAGTTCGC 61.196 66.667 0.73 0.00 44.43 4.70
146 147 2.885644 CCATCCCACGAGTTCGCG 60.886 66.667 0.00 0.00 44.43 5.87
147 148 2.126071 CATCCCACGAGTTCGCGT 60.126 61.111 5.77 0.00 46.88 6.01
148 149 2.158959 CATCCCACGAGTTCGCGTC 61.159 63.158 5.77 0.31 43.59 5.19
149 150 3.678717 ATCCCACGAGTTCGCGTCG 62.679 63.158 15.00 15.00 43.59 5.12
154 155 2.202260 CGAGTTCGCGTCGTGCTA 60.202 61.111 5.77 0.00 43.27 3.49
155 156 1.794785 CGAGTTCGCGTCGTGCTAA 60.795 57.895 5.77 0.00 43.27 3.09
156 157 1.332180 CGAGTTCGCGTCGTGCTAAA 61.332 55.000 5.77 0.00 43.27 1.85
157 158 0.090843 GAGTTCGCGTCGTGCTAAAC 59.909 55.000 5.77 0.00 43.27 2.01
158 159 1.129209 GTTCGCGTCGTGCTAAACC 59.871 57.895 5.77 0.00 43.27 3.27
159 160 1.300003 TTCGCGTCGTGCTAAACCA 60.300 52.632 5.77 0.00 43.27 3.67
160 161 1.550659 TTCGCGTCGTGCTAAACCAC 61.551 55.000 5.77 0.00 43.27 4.16
161 162 2.858158 GCGTCGTGCTAAACCACC 59.142 61.111 0.00 0.00 41.73 4.61
162 163 2.674084 GCGTCGTGCTAAACCACCC 61.674 63.158 0.00 0.00 41.73 4.61
163 164 2.377310 CGTCGTGCTAAACCACCCG 61.377 63.158 0.00 0.00 32.10 5.28
164 165 1.005867 GTCGTGCTAAACCACCCGA 60.006 57.895 0.00 0.00 32.10 5.14
165 166 1.012486 GTCGTGCTAAACCACCCGAG 61.012 60.000 0.00 0.00 32.10 4.63
166 167 2.388232 CGTGCTAAACCACCCGAGC 61.388 63.158 0.00 0.00 35.43 5.03
167 168 1.003718 GTGCTAAACCACCCGAGCT 60.004 57.895 0.00 0.00 35.89 4.09
168 169 0.248289 GTGCTAAACCACCCGAGCTA 59.752 55.000 0.00 0.00 35.89 3.32
169 170 0.978151 TGCTAAACCACCCGAGCTAA 59.022 50.000 0.00 0.00 35.89 3.09
170 171 1.348366 TGCTAAACCACCCGAGCTAAA 59.652 47.619 0.00 0.00 35.89 1.85
171 172 1.736126 GCTAAACCACCCGAGCTAAAC 59.264 52.381 0.00 0.00 32.04 2.01
172 173 1.997606 CTAAACCACCCGAGCTAAACG 59.002 52.381 0.00 0.00 0.00 3.60
173 174 1.232621 AAACCACCCGAGCTAAACGC 61.233 55.000 0.00 0.00 39.57 4.84
174 175 2.047655 CCACCCGAGCTAAACGCA 60.048 61.111 0.00 0.00 42.61 5.24
175 176 1.449601 CCACCCGAGCTAAACGCAT 60.450 57.895 0.00 0.00 42.61 4.73
176 177 1.705337 CCACCCGAGCTAAACGCATG 61.705 60.000 0.00 0.00 42.61 4.06
177 178 1.449601 ACCCGAGCTAAACGCATGG 60.450 57.895 0.00 0.00 42.61 3.66
178 179 2.180204 CCCGAGCTAAACGCATGGG 61.180 63.158 8.44 8.44 45.20 4.00
179 180 2.709475 CGAGCTAAACGCATGGGC 59.291 61.111 10.10 0.00 42.61 5.36
180 181 1.815421 CGAGCTAAACGCATGGGCT 60.815 57.895 10.10 0.00 42.61 5.19
181 182 0.529773 CGAGCTAAACGCATGGGCTA 60.530 55.000 10.10 0.97 42.61 3.93
182 183 1.663695 GAGCTAAACGCATGGGCTAA 58.336 50.000 10.10 0.00 42.61 3.09
183 184 2.222027 GAGCTAAACGCATGGGCTAAT 58.778 47.619 10.10 0.00 42.61 1.73
184 185 1.949525 AGCTAAACGCATGGGCTAATG 59.050 47.619 10.10 0.00 42.61 1.90
185 186 1.676006 GCTAAACGCATGGGCTAATGT 59.324 47.619 10.10 0.00 38.92 2.71
186 187 2.541588 GCTAAACGCATGGGCTAATGTG 60.542 50.000 10.10 11.13 42.52 3.21
187 188 1.832883 AAACGCATGGGCTAATGTGA 58.167 45.000 10.10 0.00 39.87 3.58
188 189 2.057137 AACGCATGGGCTAATGTGAT 57.943 45.000 10.10 6.33 39.87 3.06
189 190 1.311859 ACGCATGGGCTAATGTGATG 58.688 50.000 10.10 0.00 39.87 3.07
190 191 1.311859 CGCATGGGCTAATGTGATGT 58.688 50.000 0.00 0.00 39.87 3.06
191 192 1.002142 CGCATGGGCTAATGTGATGTG 60.002 52.381 0.00 0.00 39.87 3.21
192 193 1.338973 GCATGGGCTAATGTGATGTGG 59.661 52.381 0.00 0.00 36.96 4.17
193 194 2.658285 CATGGGCTAATGTGATGTGGT 58.342 47.619 0.00 0.00 0.00 4.16
194 195 2.418368 TGGGCTAATGTGATGTGGTC 57.582 50.000 0.00 0.00 0.00 4.02
195 196 1.632920 TGGGCTAATGTGATGTGGTCA 59.367 47.619 0.00 0.00 0.00 4.02
206 207 3.507597 TGTGGTCACATCGTGCTAC 57.492 52.632 0.00 0.00 36.21 3.58
207 208 0.676736 TGTGGTCACATCGTGCTACA 59.323 50.000 0.00 0.00 36.21 2.74
208 209 1.336795 TGTGGTCACATCGTGCTACAG 60.337 52.381 0.00 0.00 36.21 2.74
209 210 0.246360 TGGTCACATCGTGCTACAGG 59.754 55.000 0.00 0.00 32.98 4.00
210 211 1.084370 GGTCACATCGTGCTACAGGC 61.084 60.000 0.00 0.00 42.22 4.85
211 212 1.084370 GTCACATCGTGCTACAGGCC 61.084 60.000 0.00 0.00 40.92 5.19
212 213 1.815421 CACATCGTGCTACAGGCCC 60.815 63.158 0.00 0.00 40.92 5.80
213 214 2.290287 ACATCGTGCTACAGGCCCA 61.290 57.895 0.00 0.00 40.92 5.36
214 215 1.146930 CATCGTGCTACAGGCCCAT 59.853 57.895 0.00 0.00 40.92 4.00
215 216 1.146930 ATCGTGCTACAGGCCCATG 59.853 57.895 0.00 0.00 40.92 3.66
216 217 2.947938 ATCGTGCTACAGGCCCATGC 62.948 60.000 0.00 0.00 40.92 4.06
217 218 2.045045 GTGCTACAGGCCCATGCA 60.045 61.111 0.00 2.11 40.92 3.96
218 219 2.117156 GTGCTACAGGCCCATGCAG 61.117 63.158 0.00 0.00 40.92 4.41
219 220 3.214845 GCTACAGGCCCATGCAGC 61.215 66.667 0.00 0.00 40.13 5.25
226 227 3.440151 GCCCATGCAGCCTACATG 58.560 61.111 0.00 0.00 43.67 3.21
227 228 2.853290 GCCCATGCAGCCTACATGC 61.853 63.158 0.00 0.00 42.89 4.06
236 237 4.241999 CCTACATGCAAGGCGCGC 62.242 66.667 25.94 25.94 46.97 6.86
237 238 3.498834 CTACATGCAAGGCGCGCA 61.499 61.111 34.42 12.78 46.97 6.09
238 239 3.037992 CTACATGCAAGGCGCGCAA 62.038 57.895 34.42 12.80 46.97 4.85
239 240 2.526091 CTACATGCAAGGCGCGCAAA 62.526 55.000 34.42 13.19 46.97 3.68
240 241 2.134968 TACATGCAAGGCGCGCAAAA 62.135 50.000 34.42 13.59 46.97 2.44
241 242 2.431260 ATGCAAGGCGCGCAAAAG 60.431 55.556 34.42 19.73 46.97 2.27
242 243 3.211564 ATGCAAGGCGCGCAAAAGT 62.212 52.632 34.42 10.97 46.97 2.66
243 244 3.099574 GCAAGGCGCGCAAAAGTC 61.100 61.111 34.42 14.51 0.00 3.01
244 245 2.796617 CAAGGCGCGCAAAAGTCG 60.797 61.111 34.42 9.46 0.00 4.18
252 253 3.050275 GCAAAAGTCGCGGGCTCT 61.050 61.111 6.13 0.00 0.00 4.09
253 254 2.617274 GCAAAAGTCGCGGGCTCTT 61.617 57.895 6.13 3.61 0.00 2.85
254 255 1.207593 CAAAAGTCGCGGGCTCTTG 59.792 57.895 6.13 4.74 0.00 3.02
255 256 2.617274 AAAAGTCGCGGGCTCTTGC 61.617 57.895 6.13 0.00 38.76 4.01
268 269 3.820777 GCTCTTGCCAGACAAACTAAG 57.179 47.619 0.00 0.00 37.96 2.18
269 270 2.095516 GCTCTTGCCAGACAAACTAAGC 60.096 50.000 0.00 0.00 37.96 3.09
270 271 3.406764 CTCTTGCCAGACAAACTAAGCT 58.593 45.455 0.00 0.00 37.96 3.74
271 272 3.141398 TCTTGCCAGACAAACTAAGCTG 58.859 45.455 0.00 0.00 37.96 4.24
278 279 5.499139 CAGACAAACTAAGCTGGAAACAA 57.501 39.130 0.00 0.00 42.06 2.83
279 280 5.890334 CAGACAAACTAAGCTGGAAACAAA 58.110 37.500 0.00 0.00 42.06 2.83
280 281 5.743872 CAGACAAACTAAGCTGGAAACAAAC 59.256 40.000 0.00 0.00 42.06 2.93
281 282 5.652452 AGACAAACTAAGCTGGAAACAAACT 59.348 36.000 0.00 0.00 42.06 2.66
282 283 6.826741 AGACAAACTAAGCTGGAAACAAACTA 59.173 34.615 0.00 0.00 42.06 2.24
283 284 7.338449 AGACAAACTAAGCTGGAAACAAACTAA 59.662 33.333 0.00 0.00 42.06 2.24
284 285 7.255569 ACAAACTAAGCTGGAAACAAACTAAC 58.744 34.615 0.00 0.00 42.06 2.34
285 286 7.122204 ACAAACTAAGCTGGAAACAAACTAACT 59.878 33.333 0.00 0.00 42.06 2.24
286 287 8.617809 CAAACTAAGCTGGAAACAAACTAACTA 58.382 33.333 0.00 0.00 42.06 2.24
287 288 7.725818 ACTAAGCTGGAAACAAACTAACTAC 57.274 36.000 0.00 0.00 42.06 2.73
288 289 7.506971 ACTAAGCTGGAAACAAACTAACTACT 58.493 34.615 0.00 0.00 42.06 2.57
289 290 6.619801 AAGCTGGAAACAAACTAACTACTG 57.380 37.500 0.00 0.00 42.06 2.74
290 291 4.515567 AGCTGGAAACAAACTAACTACTGC 59.484 41.667 0.00 0.00 42.06 4.40
291 292 4.610680 GCTGGAAACAAACTAACTACTGCG 60.611 45.833 0.00 0.00 42.06 5.18
292 293 4.695396 TGGAAACAAACTAACTACTGCGA 58.305 39.130 0.00 0.00 37.44 5.10
293 294 4.748102 TGGAAACAAACTAACTACTGCGAG 59.252 41.667 0.00 0.00 37.44 5.03
294 295 4.748600 GGAAACAAACTAACTACTGCGAGT 59.251 41.667 0.00 0.00 0.00 4.18
295 296 5.235831 GGAAACAAACTAACTACTGCGAGTT 59.764 40.000 4.20 4.20 42.35 3.01
296 297 6.238293 GGAAACAAACTAACTACTGCGAGTTT 60.238 38.462 4.08 0.00 41.60 2.66
297 298 7.042523 GGAAACAAACTAACTACTGCGAGTTTA 60.043 37.037 4.08 0.00 39.50 2.01
298 299 7.958053 AACAAACTAACTACTGCGAGTTTAT 57.042 32.000 4.08 0.00 39.50 1.40
299 300 7.958053 ACAAACTAACTACTGCGAGTTTATT 57.042 32.000 4.08 0.00 39.50 1.40
300 301 8.015409 ACAAACTAACTACTGCGAGTTTATTC 57.985 34.615 4.08 0.00 39.50 1.75
301 302 7.871463 ACAAACTAACTACTGCGAGTTTATTCT 59.129 33.333 4.08 0.00 39.50 2.40
302 303 8.709646 CAAACTAACTACTGCGAGTTTATTCTT 58.290 33.333 4.08 0.00 39.50 2.52
303 304 9.918630 AAACTAACTACTGCGAGTTTATTCTTA 57.081 29.630 4.08 0.00 39.67 2.10
304 305 8.908172 ACTAACTACTGCGAGTTTATTCTTAC 57.092 34.615 4.08 0.00 40.22 2.34
305 306 7.972832 ACTAACTACTGCGAGTTTATTCTTACC 59.027 37.037 4.08 0.00 40.22 2.85
306 307 5.338365 ACTACTGCGAGTTTATTCTTACCG 58.662 41.667 0.00 0.00 0.00 4.02
307 308 4.445452 ACTGCGAGTTTATTCTTACCGA 57.555 40.909 0.00 0.00 0.00 4.69
308 309 4.171754 ACTGCGAGTTTATTCTTACCGAC 58.828 43.478 0.00 0.00 0.00 4.79
309 310 4.082354 ACTGCGAGTTTATTCTTACCGACT 60.082 41.667 0.00 0.00 0.00 4.18
310 311 5.124457 ACTGCGAGTTTATTCTTACCGACTA 59.876 40.000 0.00 0.00 0.00 2.59
311 312 5.575957 TGCGAGTTTATTCTTACCGACTAG 58.424 41.667 0.00 0.00 0.00 2.57
312 313 5.355071 TGCGAGTTTATTCTTACCGACTAGA 59.645 40.000 0.00 0.00 0.00 2.43
313 314 6.039047 TGCGAGTTTATTCTTACCGACTAGAT 59.961 38.462 0.00 0.00 0.00 1.98
314 315 6.916932 GCGAGTTTATTCTTACCGACTAGATT 59.083 38.462 0.00 0.00 0.00 2.40
315 316 8.072567 GCGAGTTTATTCTTACCGACTAGATTA 58.927 37.037 0.00 0.00 0.00 1.75
316 317 9.596677 CGAGTTTATTCTTACCGACTAGATTAG 57.403 37.037 0.00 0.00 0.00 1.73
317 318 9.396938 GAGTTTATTCTTACCGACTAGATTAGC 57.603 37.037 0.00 0.00 0.00 3.09
318 319 9.134055 AGTTTATTCTTACCGACTAGATTAGCT 57.866 33.333 0.00 0.00 0.00 3.32
322 323 7.870509 TTCTTACCGACTAGATTAGCTAACA 57.129 36.000 8.70 0.00 0.00 2.41
340 341 2.089980 ACAAGATGTTGCTGATCTGCC 58.910 47.619 20.39 7.84 37.14 4.85
343 344 0.745845 GATGTTGCTGATCTGCCGGT 60.746 55.000 20.39 5.52 0.00 5.28
361 362 3.490419 CCGGTGTAGTGTAGGTTCTATGC 60.490 52.174 0.00 0.00 0.00 3.14
374 375 4.656112 AGGTTCTATGCTAGGTGCTAACAT 59.344 41.667 0.00 0.00 43.37 2.71
458 459 3.782656 AACTCGCTCTTTTCCCCTTTA 57.217 42.857 0.00 0.00 0.00 1.85
473 476 3.939592 CCCCTTTATCGTTTCCTTCTGAC 59.060 47.826 0.00 0.00 0.00 3.51
494 497 5.690409 TGACGAATCTCTTGAACAGTTGTAC 59.310 40.000 0.00 0.00 0.00 2.90
575 578 6.205784 TGAGCACGGTTCAAGAAAATAAAAG 58.794 36.000 0.00 0.00 0.00 2.27
580 584 8.234546 GCACGGTTCAAGAAAATAAAAGATAGA 58.765 33.333 0.00 0.00 0.00 1.98
584 588 8.739972 GGTTCAAGAAAATAAAAGATAGAGCCA 58.260 33.333 0.00 0.00 0.00 4.75
590 594 2.990066 AAAAGATAGAGCCAGGGTCG 57.010 50.000 13.16 0.00 35.00 4.79
604 608 2.222013 GGTCGGGGACTGGGTTTCT 61.222 63.158 0.00 0.00 33.92 2.52
658 1321 1.278238 GTTGACGTGGATCGATGGTC 58.722 55.000 0.54 5.63 42.86 4.02
665 1328 1.069358 GTGGATCGATGGTCCTCCTTC 59.931 57.143 0.54 0.00 36.68 3.46
1321 2064 6.293004 ACCTGATCCTTGTCTCTTTTCTAG 57.707 41.667 0.00 0.00 0.00 2.43
1324 2067 7.093684 ACCTGATCCTTGTCTCTTTTCTAGTAC 60.094 40.741 0.00 0.00 0.00 2.73
1326 2069 8.190326 TGATCCTTGTCTCTTTTCTAGTACAA 57.810 34.615 0.00 0.00 33.20 2.41
1387 2213 5.696270 TGTCATAATAAAGGTAGAGCATGCG 59.304 40.000 13.01 0.00 0.00 4.73
1458 2325 2.785681 GCTTGTCAATGCTGTCGATTCG 60.786 50.000 0.00 0.00 0.00 3.34
1561 2467 2.887152 GGAACCTTGAACATGAACAGCT 59.113 45.455 0.00 0.00 0.00 4.24
1610 2516 3.944055 TGCGCTAATCTTAGAGATCCC 57.056 47.619 9.73 0.00 32.89 3.85
1611 2517 3.501349 TGCGCTAATCTTAGAGATCCCT 58.499 45.455 9.73 0.00 32.89 4.20
1612 2518 3.898123 TGCGCTAATCTTAGAGATCCCTT 59.102 43.478 9.73 0.00 32.89 3.95
1613 2519 4.345257 TGCGCTAATCTTAGAGATCCCTTT 59.655 41.667 9.73 0.00 32.89 3.11
1653 2563 3.228453 CTGCATAAGGCTGGGAATTGAT 58.772 45.455 0.00 0.00 45.15 2.57
2224 3246 6.808321 ACTTGTGCTGGTAGAATATTCCTA 57.192 37.500 11.92 1.77 0.00 2.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.717119 CAAAATCCATGGAGTCTTTCCTTG 58.283 41.667 21.33 13.43 46.92 3.61
2 3 3.766051 GCAAAATCCATGGAGTCTTTCCT 59.234 43.478 21.33 0.00 46.92 3.36
3 4 3.511146 TGCAAAATCCATGGAGTCTTTCC 59.489 43.478 21.33 10.16 46.98 3.13
4 5 4.789012 TGCAAAATCCATGGAGTCTTTC 57.211 40.909 21.33 9.61 0.00 2.62
6 7 3.379372 CGATGCAAAATCCATGGAGTCTT 59.621 43.478 21.33 11.54 0.00 3.01
7 8 2.947652 CGATGCAAAATCCATGGAGTCT 59.052 45.455 21.33 0.00 0.00 3.24
8 9 2.542411 GCGATGCAAAATCCATGGAGTC 60.542 50.000 21.33 6.51 0.00 3.36
9 10 1.406539 GCGATGCAAAATCCATGGAGT 59.593 47.619 21.33 15.80 0.00 3.85
11 12 0.381445 CGCGATGCAAAATCCATGGA 59.619 50.000 18.88 18.88 0.00 3.41
12 13 0.101040 ACGCGATGCAAAATCCATGG 59.899 50.000 15.93 4.97 0.00 3.66
13 14 1.193644 CACGCGATGCAAAATCCATG 58.806 50.000 15.93 0.00 0.00 3.66
14 15 3.628005 CACGCGATGCAAAATCCAT 57.372 47.368 15.93 0.00 0.00 3.41
33 34 3.680789 ACGAGAAAAGTCGCAAGTTTTG 58.319 40.909 0.00 0.00 44.06 2.44
34 35 4.351131 AACGAGAAAAGTCGCAAGTTTT 57.649 36.364 0.00 0.00 44.06 2.43
35 36 4.351131 AAACGAGAAAAGTCGCAAGTTT 57.649 36.364 0.00 0.00 44.06 2.66
36 37 5.668558 ATAAACGAGAAAAGTCGCAAGTT 57.331 34.783 0.00 0.00 44.06 2.66
37 38 5.465724 AGAATAAACGAGAAAAGTCGCAAGT 59.534 36.000 0.00 0.00 44.06 3.16
38 39 5.916969 AGAATAAACGAGAAAAGTCGCAAG 58.083 37.500 0.00 0.00 44.06 4.01
39 40 5.917541 AGAATAAACGAGAAAAGTCGCAA 57.082 34.783 0.00 0.00 44.06 4.85
40 41 5.107220 GGAAGAATAAACGAGAAAAGTCGCA 60.107 40.000 0.00 0.00 44.06 5.10
41 42 5.120363 AGGAAGAATAAACGAGAAAAGTCGC 59.880 40.000 0.00 0.00 44.06 5.19
42 43 6.586844 AGAGGAAGAATAAACGAGAAAAGTCG 59.413 38.462 0.00 0.00 45.76 4.18
43 44 7.892778 AGAGGAAGAATAAACGAGAAAAGTC 57.107 36.000 0.00 0.00 0.00 3.01
44 45 9.945904 AATAGAGGAAGAATAAACGAGAAAAGT 57.054 29.630 0.00 0.00 0.00 2.66
51 52 9.555727 CCCAATAAATAGAGGAAGAATAAACGA 57.444 33.333 0.00 0.00 0.00 3.85
52 53 9.338622 ACCCAATAAATAGAGGAAGAATAAACG 57.661 33.333 0.00 0.00 0.00 3.60
56 57 8.591072 CGGTACCCAATAAATAGAGGAAGAATA 58.409 37.037 6.25 0.00 0.00 1.75
57 58 7.072076 ACGGTACCCAATAAATAGAGGAAGAAT 59.928 37.037 6.25 0.00 0.00 2.40
58 59 6.384886 ACGGTACCCAATAAATAGAGGAAGAA 59.615 38.462 6.25 0.00 0.00 2.52
59 60 5.901276 ACGGTACCCAATAAATAGAGGAAGA 59.099 40.000 6.25 0.00 0.00 2.87
60 61 5.989777 CACGGTACCCAATAAATAGAGGAAG 59.010 44.000 6.25 0.00 0.00 3.46
61 62 5.662208 TCACGGTACCCAATAAATAGAGGAA 59.338 40.000 6.25 0.00 0.00 3.36
62 63 5.069516 GTCACGGTACCCAATAAATAGAGGA 59.930 44.000 6.25 0.00 0.00 3.71
63 64 5.163385 TGTCACGGTACCCAATAAATAGAGG 60.163 44.000 6.25 0.00 0.00 3.69
64 65 5.909477 TGTCACGGTACCCAATAAATAGAG 58.091 41.667 6.25 0.00 0.00 2.43
65 66 5.163385 CCTGTCACGGTACCCAATAAATAGA 60.163 44.000 6.25 0.00 0.00 1.98
66 67 5.054477 CCTGTCACGGTACCCAATAAATAG 58.946 45.833 6.25 0.00 0.00 1.73
67 68 4.470664 ACCTGTCACGGTACCCAATAAATA 59.529 41.667 6.25 0.00 34.94 1.40
68 69 3.264964 ACCTGTCACGGTACCCAATAAAT 59.735 43.478 6.25 0.00 34.94 1.40
69 70 2.638855 ACCTGTCACGGTACCCAATAAA 59.361 45.455 6.25 0.00 34.94 1.40
70 71 2.259012 ACCTGTCACGGTACCCAATAA 58.741 47.619 6.25 0.00 34.94 1.40
71 72 1.941377 ACCTGTCACGGTACCCAATA 58.059 50.000 6.25 0.00 34.94 1.90
72 73 1.829222 CTACCTGTCACGGTACCCAAT 59.171 52.381 6.25 0.00 38.49 3.16
73 74 1.259609 CTACCTGTCACGGTACCCAA 58.740 55.000 6.25 0.00 38.49 4.12
74 75 0.112995 ACTACCTGTCACGGTACCCA 59.887 55.000 6.25 0.00 38.49 4.51
75 76 1.260544 AACTACCTGTCACGGTACCC 58.739 55.000 6.25 0.00 38.49 3.69
76 77 2.353109 GGAAACTACCTGTCACGGTACC 60.353 54.545 0.16 0.16 38.49 3.34
77 78 2.560105 AGGAAACTACCTGTCACGGTAC 59.440 50.000 0.00 0.00 40.61 3.34
78 79 2.880443 AGGAAACTACCTGTCACGGTA 58.120 47.619 0.00 0.00 40.61 4.02
79 80 1.713297 AGGAAACTACCTGTCACGGT 58.287 50.000 0.00 0.00 40.61 4.83
90 91 3.746940 GTGGCACAAAGGTAGGAAACTA 58.253 45.455 13.86 0.00 44.16 2.24
91 92 2.583143 GTGGCACAAAGGTAGGAAACT 58.417 47.619 13.86 0.00 44.16 2.66
92 93 1.265905 CGTGGCACAAAGGTAGGAAAC 59.734 52.381 19.09 0.00 44.16 2.78
93 94 1.141254 TCGTGGCACAAAGGTAGGAAA 59.859 47.619 19.09 0.00 44.16 3.13
94 95 0.759959 TCGTGGCACAAAGGTAGGAA 59.240 50.000 19.09 0.00 44.16 3.36
95 96 0.034337 GTCGTGGCACAAAGGTAGGA 59.966 55.000 19.09 0.68 44.16 2.94
96 97 0.953960 GGTCGTGGCACAAAGGTAGG 60.954 60.000 19.09 0.00 44.16 3.18
97 98 0.953960 GGGTCGTGGCACAAAGGTAG 60.954 60.000 19.09 0.00 44.16 3.18
98 99 1.071814 GGGTCGTGGCACAAAGGTA 59.928 57.895 19.09 0.00 44.16 3.08
99 100 2.203294 GGGTCGTGGCACAAAGGT 60.203 61.111 19.09 0.00 44.16 3.50
100 101 2.113139 AGGGTCGTGGCACAAAGG 59.887 61.111 19.09 0.71 44.16 3.11
101 102 1.227823 TCAGGGTCGTGGCACAAAG 60.228 57.895 19.09 1.11 44.16 2.77
102 103 1.525077 GTCAGGGTCGTGGCACAAA 60.525 57.895 19.09 1.54 44.16 2.83
103 104 2.110213 GTCAGGGTCGTGGCACAA 59.890 61.111 19.09 0.00 44.16 3.33
104 105 3.936203 GGTCAGGGTCGTGGCACA 61.936 66.667 19.09 1.83 0.00 4.57
105 106 3.936203 TGGTCAGGGTCGTGGCAC 61.936 66.667 7.79 7.79 0.00 5.01
106 107 3.936203 GTGGTCAGGGTCGTGGCA 61.936 66.667 0.00 0.00 0.00 4.92
107 108 3.591254 GAGTGGTCAGGGTCGTGGC 62.591 68.421 0.00 0.00 0.00 5.01
108 109 2.657237 GAGTGGTCAGGGTCGTGG 59.343 66.667 0.00 0.00 0.00 4.94
109 110 2.258591 CGAGTGGTCAGGGTCGTG 59.741 66.667 0.00 0.00 0.00 4.35
110 111 2.203451 ACGAGTGGTCAGGGTCGT 60.203 61.111 0.00 0.00 40.70 4.34
111 112 2.258591 CACGAGTGGTCAGGGTCG 59.741 66.667 0.00 0.00 38.40 4.79
112 113 2.048127 GCACGAGTGGTCAGGGTC 60.048 66.667 5.32 0.00 0.00 4.46
113 114 3.626924 GGCACGAGTGGTCAGGGT 61.627 66.667 5.32 0.00 0.00 4.34
114 115 2.859273 GATGGCACGAGTGGTCAGGG 62.859 65.000 5.32 0.00 0.00 4.45
115 116 1.448540 GATGGCACGAGTGGTCAGG 60.449 63.158 5.32 0.00 0.00 3.86
116 117 1.448540 GGATGGCACGAGTGGTCAG 60.449 63.158 5.32 0.00 0.00 3.51
117 118 2.662596 GGATGGCACGAGTGGTCA 59.337 61.111 5.32 0.00 0.00 4.02
118 119 2.125106 GGGATGGCACGAGTGGTC 60.125 66.667 5.32 0.00 0.00 4.02
119 120 2.927856 TGGGATGGCACGAGTGGT 60.928 61.111 5.32 0.00 0.00 4.16
120 121 2.436646 GTGGGATGGCACGAGTGG 60.437 66.667 5.32 0.00 0.00 4.00
121 122 2.815211 CGTGGGATGGCACGAGTG 60.815 66.667 0.00 0.00 46.46 3.51
122 123 2.994995 TCGTGGGATGGCACGAGT 60.995 61.111 0.00 0.00 46.91 4.18
125 126 2.047274 AACTCGTGGGATGGCACG 60.047 61.111 0.00 0.00 45.09 5.34
126 127 2.100631 CGAACTCGTGGGATGGCAC 61.101 63.158 0.00 0.00 34.11 5.01
127 128 2.264480 CGAACTCGTGGGATGGCA 59.736 61.111 0.00 0.00 34.11 4.92
128 129 3.195698 GCGAACTCGTGGGATGGC 61.196 66.667 0.51 0.00 42.22 4.40
129 130 2.885644 CGCGAACTCGTGGGATGG 60.886 66.667 0.00 0.00 45.14 3.51
144 145 2.674084 GGGTGGTTTAGCACGACGC 61.674 63.158 6.04 0.00 39.36 5.19
145 146 2.377310 CGGGTGGTTTAGCACGACG 61.377 63.158 11.35 11.35 34.98 5.12
146 147 1.005867 TCGGGTGGTTTAGCACGAC 60.006 57.895 6.04 1.64 33.41 4.34
147 148 1.290955 CTCGGGTGGTTTAGCACGA 59.709 57.895 6.04 1.13 0.00 4.35
148 149 2.388232 GCTCGGGTGGTTTAGCACG 61.388 63.158 6.04 0.00 35.05 5.34
149 150 0.248289 TAGCTCGGGTGGTTTAGCAC 59.752 55.000 3.55 3.55 37.44 4.40
150 151 0.978151 TTAGCTCGGGTGGTTTAGCA 59.022 50.000 0.00 0.00 37.44 3.49
151 152 1.736126 GTTTAGCTCGGGTGGTTTAGC 59.264 52.381 0.00 0.00 35.16 3.09
152 153 1.997606 CGTTTAGCTCGGGTGGTTTAG 59.002 52.381 0.00 0.00 0.00 1.85
153 154 1.940752 GCGTTTAGCTCGGGTGGTTTA 60.941 52.381 0.00 0.00 44.04 2.01
154 155 1.232621 GCGTTTAGCTCGGGTGGTTT 61.233 55.000 0.00 0.00 44.04 3.27
155 156 1.670083 GCGTTTAGCTCGGGTGGTT 60.670 57.895 0.00 0.00 44.04 3.67
156 157 2.047560 GCGTTTAGCTCGGGTGGT 60.048 61.111 0.00 0.00 44.04 4.16
159 160 2.869503 CCCATGCGTTTAGCTCGGGT 62.870 60.000 0.00 0.00 46.42 5.28
166 167 2.942376 TCACATTAGCCCATGCGTTTAG 59.058 45.455 0.00 0.00 44.33 1.85
167 168 2.992593 TCACATTAGCCCATGCGTTTA 58.007 42.857 0.00 0.00 44.33 2.01
168 169 1.832883 TCACATTAGCCCATGCGTTT 58.167 45.000 0.00 0.00 44.33 3.60
169 170 1.677576 CATCACATTAGCCCATGCGTT 59.322 47.619 0.00 0.00 44.33 4.84
170 171 1.311859 CATCACATTAGCCCATGCGT 58.688 50.000 0.00 0.00 44.33 5.24
171 172 1.002142 CACATCACATTAGCCCATGCG 60.002 52.381 0.00 0.00 44.33 4.73
172 173 1.338973 CCACATCACATTAGCCCATGC 59.661 52.381 0.00 0.00 37.95 4.06
173 174 2.620115 GACCACATCACATTAGCCCATG 59.380 50.000 0.00 0.00 0.00 3.66
174 175 2.241941 TGACCACATCACATTAGCCCAT 59.758 45.455 0.00 0.00 29.99 4.00
175 176 1.632920 TGACCACATCACATTAGCCCA 59.367 47.619 0.00 0.00 29.99 5.36
176 177 2.418368 TGACCACATCACATTAGCCC 57.582 50.000 0.00 0.00 29.99 5.19
188 189 0.676736 TGTAGCACGATGTGACCACA 59.323 50.000 5.22 5.22 46.44 4.17
189 190 1.350193 CTGTAGCACGATGTGACCAC 58.650 55.000 0.24 0.00 35.23 4.16
190 191 0.246360 CCTGTAGCACGATGTGACCA 59.754 55.000 0.24 0.00 35.23 4.02
191 192 1.084370 GCCTGTAGCACGATGTGACC 61.084 60.000 0.24 0.00 42.97 4.02
192 193 1.084370 GGCCTGTAGCACGATGTGAC 61.084 60.000 0.00 0.00 46.50 3.67
193 194 1.218047 GGCCTGTAGCACGATGTGA 59.782 57.895 0.00 0.00 46.50 3.58
194 195 1.815421 GGGCCTGTAGCACGATGTG 60.815 63.158 0.84 0.00 46.50 3.21
195 196 2.584608 GGGCCTGTAGCACGATGT 59.415 61.111 0.84 0.00 46.50 3.06
201 202 2.273123 CTGCATGGGCCTGTAGCA 59.727 61.111 4.53 8.78 46.50 3.49
202 203 3.214845 GCTGCATGGGCCTGTAGC 61.215 66.667 22.42 22.42 45.38 3.58
203 204 2.517875 GGCTGCATGGGCCTGTAG 60.518 66.667 4.53 10.63 45.57 2.74
209 210 2.853290 GCATGTAGGCTGCATGGGC 61.853 63.158 35.76 24.23 42.72 5.36
210 211 1.454295 TGCATGTAGGCTGCATGGG 60.454 57.895 35.76 19.55 44.30 4.00
211 212 4.246053 TGCATGTAGGCTGCATGG 57.754 55.556 35.76 22.54 44.30 3.66
219 220 4.241999 GCGCGCCTTGCATGTAGG 62.242 66.667 23.24 10.63 46.97 3.18
220 221 2.526091 TTTGCGCGCCTTGCATGTAG 62.526 55.000 30.77 0.00 46.97 2.74
221 222 2.134968 TTTTGCGCGCCTTGCATGTA 62.135 50.000 30.77 2.53 46.97 2.29
222 223 3.496875 TTTTGCGCGCCTTGCATGT 62.497 52.632 30.77 0.00 46.97 3.21
223 224 2.722731 CTTTTGCGCGCCTTGCATG 61.723 57.895 30.77 8.35 46.97 4.06
224 225 2.431260 CTTTTGCGCGCCTTGCAT 60.431 55.556 30.77 0.00 46.97 3.96
225 226 3.822403 GACTTTTGCGCGCCTTGCA 62.822 57.895 30.77 6.23 46.97 4.08
226 227 3.099574 GACTTTTGCGCGCCTTGC 61.100 61.111 30.77 9.38 41.47 4.01
227 228 2.796617 CGACTTTTGCGCGCCTTG 60.797 61.111 30.77 17.99 0.00 3.61
228 229 4.683334 GCGACTTTTGCGCGCCTT 62.683 61.111 30.77 7.77 45.27 4.35
235 236 2.617274 AAGAGCCCGCGACTTTTGC 61.617 57.895 8.23 0.00 0.00 3.68
236 237 1.207593 CAAGAGCCCGCGACTTTTG 59.792 57.895 8.23 12.61 0.00 2.44
237 238 2.617274 GCAAGAGCCCGCGACTTTT 61.617 57.895 8.23 3.05 33.58 2.27
238 239 3.050275 GCAAGAGCCCGCGACTTT 61.050 61.111 8.23 0.00 33.58 2.66
248 249 2.095516 GCTTAGTTTGTCTGGCAAGAGC 60.096 50.000 0.00 0.96 38.47 4.09
249 250 3.188048 CAGCTTAGTTTGTCTGGCAAGAG 59.812 47.826 0.00 0.00 38.47 2.85
250 251 3.141398 CAGCTTAGTTTGTCTGGCAAGA 58.859 45.455 0.00 0.00 38.47 3.02
251 252 2.227388 CCAGCTTAGTTTGTCTGGCAAG 59.773 50.000 0.00 0.00 39.53 4.01
252 253 2.158682 TCCAGCTTAGTTTGTCTGGCAA 60.159 45.455 2.44 0.00 44.27 4.52
253 254 1.419762 TCCAGCTTAGTTTGTCTGGCA 59.580 47.619 2.44 0.00 44.27 4.92
254 255 2.185004 TCCAGCTTAGTTTGTCTGGC 57.815 50.000 2.44 0.00 44.27 4.85
255 256 3.882888 TGTTTCCAGCTTAGTTTGTCTGG 59.117 43.478 0.92 0.92 45.59 3.86
256 257 5.499139 TTGTTTCCAGCTTAGTTTGTCTG 57.501 39.130 0.00 0.00 0.00 3.51
257 258 5.652452 AGTTTGTTTCCAGCTTAGTTTGTCT 59.348 36.000 0.00 0.00 0.00 3.41
258 259 5.891451 AGTTTGTTTCCAGCTTAGTTTGTC 58.109 37.500 0.00 0.00 0.00 3.18
259 260 5.914898 AGTTTGTTTCCAGCTTAGTTTGT 57.085 34.783 0.00 0.00 0.00 2.83
260 261 7.480810 AGTTAGTTTGTTTCCAGCTTAGTTTG 58.519 34.615 0.00 0.00 0.00 2.93
261 262 7.640597 AGTTAGTTTGTTTCCAGCTTAGTTT 57.359 32.000 0.00 0.00 0.00 2.66
262 263 7.991460 AGTAGTTAGTTTGTTTCCAGCTTAGTT 59.009 33.333 0.00 0.00 0.00 2.24
263 264 7.441458 CAGTAGTTAGTTTGTTTCCAGCTTAGT 59.559 37.037 0.00 0.00 0.00 2.24
264 265 7.571428 GCAGTAGTTAGTTTGTTTCCAGCTTAG 60.571 40.741 0.00 0.00 0.00 2.18
265 266 6.204108 GCAGTAGTTAGTTTGTTTCCAGCTTA 59.796 38.462 0.00 0.00 0.00 3.09
266 267 5.008712 GCAGTAGTTAGTTTGTTTCCAGCTT 59.991 40.000 0.00 0.00 0.00 3.74
267 268 4.515567 GCAGTAGTTAGTTTGTTTCCAGCT 59.484 41.667 0.00 0.00 0.00 4.24
268 269 4.610680 CGCAGTAGTTAGTTTGTTTCCAGC 60.611 45.833 0.00 0.00 0.00 4.85
269 270 4.748102 TCGCAGTAGTTAGTTTGTTTCCAG 59.252 41.667 0.00 0.00 0.00 3.86
270 271 4.695396 TCGCAGTAGTTAGTTTGTTTCCA 58.305 39.130 0.00 0.00 0.00 3.53
271 272 4.748600 ACTCGCAGTAGTTAGTTTGTTTCC 59.251 41.667 0.00 0.00 0.00 3.13
272 273 5.902051 ACTCGCAGTAGTTAGTTTGTTTC 57.098 39.130 0.00 0.00 0.00 2.78
273 274 6.673154 AAACTCGCAGTAGTTAGTTTGTTT 57.327 33.333 0.00 0.00 39.89 2.83
274 275 7.958053 ATAAACTCGCAGTAGTTAGTTTGTT 57.042 32.000 9.03 0.00 41.11 2.83
275 276 7.871463 AGAATAAACTCGCAGTAGTTAGTTTGT 59.129 33.333 9.03 0.86 41.11 2.83
276 277 8.240883 AGAATAAACTCGCAGTAGTTAGTTTG 57.759 34.615 9.03 0.00 41.11 2.93
277 278 8.828688 AAGAATAAACTCGCAGTAGTTAGTTT 57.171 30.769 0.00 0.00 42.91 2.66
278 279 9.351570 GTAAGAATAAACTCGCAGTAGTTAGTT 57.648 33.333 0.00 0.00 38.76 2.24
279 280 7.972832 GGTAAGAATAAACTCGCAGTAGTTAGT 59.027 37.037 0.00 0.00 38.76 2.24
280 281 7.165483 CGGTAAGAATAAACTCGCAGTAGTTAG 59.835 40.741 0.00 0.00 38.76 2.34
281 282 6.968904 CGGTAAGAATAAACTCGCAGTAGTTA 59.031 38.462 0.00 0.00 38.76 2.24
282 283 5.803967 CGGTAAGAATAAACTCGCAGTAGTT 59.196 40.000 0.00 0.00 41.46 2.24
283 284 5.124457 TCGGTAAGAATAAACTCGCAGTAGT 59.876 40.000 0.00 0.00 0.00 2.73
284 285 5.454877 GTCGGTAAGAATAAACTCGCAGTAG 59.545 44.000 0.00 0.00 0.00 2.57
285 286 5.124457 AGTCGGTAAGAATAAACTCGCAGTA 59.876 40.000 0.00 0.00 0.00 2.74
286 287 4.082354 AGTCGGTAAGAATAAACTCGCAGT 60.082 41.667 0.00 0.00 0.00 4.40
287 288 4.421948 AGTCGGTAAGAATAAACTCGCAG 58.578 43.478 0.00 0.00 0.00 5.18
288 289 4.445452 AGTCGGTAAGAATAAACTCGCA 57.555 40.909 0.00 0.00 0.00 5.10
289 290 5.814783 TCTAGTCGGTAAGAATAAACTCGC 58.185 41.667 0.00 0.00 0.00 5.03
290 291 9.596677 CTAATCTAGTCGGTAAGAATAAACTCG 57.403 37.037 0.00 0.00 0.00 4.18
291 292 9.396938 GCTAATCTAGTCGGTAAGAATAAACTC 57.603 37.037 0.00 0.00 0.00 3.01
292 293 9.134055 AGCTAATCTAGTCGGTAAGAATAAACT 57.866 33.333 0.00 0.00 0.00 2.66
296 297 9.565090 TGTTAGCTAATCTAGTCGGTAAGAATA 57.435 33.333 9.88 0.00 0.00 1.75
297 298 8.461249 TGTTAGCTAATCTAGTCGGTAAGAAT 57.539 34.615 9.88 0.00 0.00 2.40
298 299 7.870509 TGTTAGCTAATCTAGTCGGTAAGAA 57.129 36.000 9.88 0.00 0.00 2.52
299 300 7.772292 TCTTGTTAGCTAATCTAGTCGGTAAGA 59.228 37.037 9.88 4.04 0.00 2.10
300 301 7.928103 TCTTGTTAGCTAATCTAGTCGGTAAG 58.072 38.462 9.88 2.05 0.00 2.34
301 302 7.870509 TCTTGTTAGCTAATCTAGTCGGTAA 57.129 36.000 9.88 0.00 0.00 2.85
302 303 7.501559 ACATCTTGTTAGCTAATCTAGTCGGTA 59.498 37.037 9.88 0.00 0.00 4.02
303 304 6.321690 ACATCTTGTTAGCTAATCTAGTCGGT 59.678 38.462 9.88 7.26 0.00 4.69
304 305 6.740110 ACATCTTGTTAGCTAATCTAGTCGG 58.260 40.000 9.88 6.79 0.00 4.79
305 306 7.306283 GCAACATCTTGTTAGCTAATCTAGTCG 60.306 40.741 9.88 7.89 38.77 4.18
306 307 7.708752 AGCAACATCTTGTTAGCTAATCTAGTC 59.291 37.037 9.88 0.00 38.77 2.59
307 308 7.493971 CAGCAACATCTTGTTAGCTAATCTAGT 59.506 37.037 9.88 1.86 40.24 2.57
308 309 7.708322 TCAGCAACATCTTGTTAGCTAATCTAG 59.292 37.037 9.88 9.64 40.24 2.43
309 310 7.555965 TCAGCAACATCTTGTTAGCTAATCTA 58.444 34.615 9.88 0.00 40.24 1.98
310 311 6.409704 TCAGCAACATCTTGTTAGCTAATCT 58.590 36.000 9.88 0.00 40.24 2.40
311 312 6.668541 TCAGCAACATCTTGTTAGCTAATC 57.331 37.500 9.88 4.43 40.24 1.75
312 313 7.012138 CAGATCAGCAACATCTTGTTAGCTAAT 59.988 37.037 9.88 7.90 40.24 1.73
313 314 6.314648 CAGATCAGCAACATCTTGTTAGCTAA 59.685 38.462 0.86 0.86 40.24 3.09
314 315 5.814188 CAGATCAGCAACATCTTGTTAGCTA 59.186 40.000 13.20 0.00 40.24 3.32
315 316 4.634883 CAGATCAGCAACATCTTGTTAGCT 59.365 41.667 0.00 0.00 41.67 3.32
316 317 4.730035 GCAGATCAGCAACATCTTGTTAGC 60.730 45.833 5.05 0.70 38.77 3.09
317 318 4.201891 GGCAGATCAGCAACATCTTGTTAG 60.202 45.833 12.54 0.00 38.77 2.34
318 319 3.691118 GGCAGATCAGCAACATCTTGTTA 59.309 43.478 12.54 0.00 38.77 2.41
319 320 2.490903 GGCAGATCAGCAACATCTTGTT 59.509 45.455 12.54 0.00 42.08 2.83
320 321 2.089980 GGCAGATCAGCAACATCTTGT 58.910 47.619 12.54 0.00 35.83 3.16
321 322 1.063616 CGGCAGATCAGCAACATCTTG 59.936 52.381 12.54 0.00 35.83 3.02
322 323 1.376543 CGGCAGATCAGCAACATCTT 58.623 50.000 12.54 0.00 35.83 2.40
340 341 3.380637 AGCATAGAACCTACACTACACCG 59.619 47.826 0.00 0.00 0.00 4.94
343 344 5.593095 CACCTAGCATAGAACCTACACTACA 59.407 44.000 0.00 0.00 42.77 2.74
361 362 3.684788 AGCGAAAACATGTTAGCACCTAG 59.315 43.478 25.27 9.84 0.00 3.02
374 375 1.804151 GTGCACTATGGAGCGAAAACA 59.196 47.619 10.32 0.00 31.76 2.83
458 459 4.158764 AGAGATTCGTCAGAAGGAAACGAT 59.841 41.667 0.00 0.00 44.04 3.73
473 476 6.771188 AAGTACAACTGTTCAAGAGATTCG 57.229 37.500 0.00 0.00 0.00 3.34
575 578 2.210711 CCCCGACCCTGGCTCTATC 61.211 68.421 0.00 0.00 0.00 2.08
584 588 3.805151 AAACCCAGTCCCCGACCCT 62.805 63.158 0.00 0.00 32.18 4.34
604 608 1.885887 GCACTGCATCCACAGGTTAAA 59.114 47.619 0.00 0.00 42.21 1.52
655 1318 4.493747 CGCGGACGAAGGAGGACC 62.494 72.222 0.00 0.00 43.93 4.46
835 1524 0.529773 TGTGGCTCGAATGGTATCGC 60.530 55.000 0.00 0.00 42.44 4.58
836 1525 1.860950 CTTGTGGCTCGAATGGTATCG 59.139 52.381 0.00 0.00 44.04 2.92
902 1597 1.571215 TTGATGACTGCTGTGCTGCG 61.571 55.000 0.00 0.00 35.36 5.18
914 1609 5.220931 GCTCTGATGGTTATGGTTTGATGAC 60.221 44.000 0.00 0.00 0.00 3.06
984 1715 0.103208 ACATCTCGAACTGGATCGGC 59.897 55.000 5.50 0.00 42.92 5.54
996 1727 2.417924 CCTTGACCCAGAAGACATCTCG 60.418 54.545 0.00 0.00 35.73 4.04
1387 2213 2.260481 GACAACGTCAACCTAGCTAGC 58.740 52.381 15.74 6.62 32.09 3.42
1458 2325 0.595095 CTGGAGCAGAAACAGCCAAC 59.405 55.000 0.00 0.00 32.44 3.77
1561 2467 1.138337 GCAAATTGTGCGTGCATGAA 58.862 45.000 10.93 0.00 45.10 2.57
1585 2491 4.244425 TCTCTAAGATTAGCGCATCCAC 57.756 45.455 11.47 0.00 0.00 4.02
1610 2516 3.254892 GGACGCAGGAACTCTAAGAAAG 58.745 50.000 0.00 0.00 34.60 2.62
1611 2517 2.028385 GGGACGCAGGAACTCTAAGAAA 60.028 50.000 0.00 0.00 34.60 2.52
1612 2518 1.549170 GGGACGCAGGAACTCTAAGAA 59.451 52.381 0.00 0.00 34.60 2.52
1613 2519 1.183549 GGGACGCAGGAACTCTAAGA 58.816 55.000 0.00 0.00 34.60 2.10
1653 2563 1.846007 AAGGGTGTGCAAAACAGACA 58.154 45.000 0.00 0.00 44.26 3.41
1857 2820 8.215926 TCCTGAAAAGAAAAATACAACGAGAA 57.784 30.769 0.00 0.00 0.00 2.87


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

AutoCloner maintained by Alex Coulton.