Multiple sequence alignment - TraesCS5D01G053400

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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 TraesCS5D01G053400 chr5D 100.000 2439 0 0 1 2439 50991873 50989435 0.000000e+00 4505.0
1 TraesCS5D01G053400 chr5D 91.940 1005 64 8 654 1644 460222219 460223220 0.000000e+00 1391.0
2 TraesCS5D01G053400 chr5D 86.860 449 47 2 216 652 460221730 460222178 2.180000e-135 492.0
3 TraesCS5D01G053400 chr5D 84.324 185 15 9 2221 2404 51246880 51246709 4.170000e-38 169.0
4 TraesCS5D01G053400 chr5D 83.784 185 16 9 2221 2404 51323490 51323319 1.940000e-36 163.0
5 TraesCS5D01G053400 chr5D 95.349 43 2 0 2397 2439 51246701 51246659 4.350000e-08 69.4
6 TraesCS5D01G053400 chr5D 91.837 49 3 1 2392 2439 51323317 51323269 1.570000e-07 67.6
7 TraesCS5D01G053400 chr2B 82.672 1160 121 37 216 1337 223140628 223141745 0.000000e+00 955.0
8 TraesCS5D01G053400 chr1B 85.234 833 110 8 1000 1822 502774648 502775477 0.000000e+00 845.0
9 TraesCS5D01G053400 chr1B 86.161 672 54 10 677 1337 411182776 411182133 0.000000e+00 689.0
10 TraesCS5D01G053400 chr1B 81.707 328 36 6 1819 2146 411182004 411181701 4.030000e-63 252.0
11 TraesCS5D01G053400 chr6A 84.597 831 116 7 1000 1819 563488595 563489424 0.000000e+00 815.0
12 TraesCS5D01G053400 chr2A 84.710 811 111 9 1023 1822 556949122 556949930 0.000000e+00 798.0
13 TraesCS5D01G053400 chr2A 84.464 811 113 7 1023 1822 291666057 291666865 0.000000e+00 787.0
14 TraesCS5D01G053400 chr7A 83.832 835 122 8 1000 1822 106410296 106409463 0.000000e+00 782.0
15 TraesCS5D01G053400 chr2D 84.257 794 111 12 1026 1808 80029958 80030748 0.000000e+00 761.0
16 TraesCS5D01G053400 chr7D 82.912 831 130 7 1000 1819 199528785 199529614 0.000000e+00 737.0
17 TraesCS5D01G053400 chr4B 82.402 841 131 13 1000 1826 168270919 168270082 0.000000e+00 717.0
18 TraesCS5D01G053400 chr5B 86.095 676 56 9 673 1337 529379349 529378701 0.000000e+00 693.0
19 TraesCS5D01G053400 chr5B 94.118 204 10 2 1 203 54198317 54198115 2.360000e-80 309.0
20 TraesCS5D01G053400 chr5B 87.895 190 19 3 2221 2409 54197824 54197638 1.140000e-53 220.0
21 TraesCS5D01G053400 chr5B 96.341 82 3 0 2147 2228 54197925 54197844 4.230000e-28 135.0
22 TraesCS5D01G053400 chr4A 82.222 315 44 4 225 527 743999944 744000258 6.690000e-66 261.0
23 TraesCS5D01G053400 chr5A 82.105 190 20 10 2221 2409 40475614 40475438 1.510000e-32 150.0
24 TraesCS5D01G053400 chr5A 94.872 78 4 0 64 141 40624193 40624116 3.290000e-24 122.0
25 TraesCS5D01G053400 chr5A 97.015 67 2 0 1 67 40625320 40625254 1.980000e-21 113.0


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 TraesCS5D01G053400 chr5D 50989435 50991873 2438 True 4505.000000 4505 100.000000 1 2439 1 chr5D.!!$R1 2438
1 TraesCS5D01G053400 chr5D 460221730 460223220 1490 False 941.500000 1391 89.400000 216 1644 2 chr5D.!!$F1 1428
2 TraesCS5D01G053400 chr2B 223140628 223141745 1117 False 955.000000 955 82.672000 216 1337 1 chr2B.!!$F1 1121
3 TraesCS5D01G053400 chr1B 502774648 502775477 829 False 845.000000 845 85.234000 1000 1822 1 chr1B.!!$F1 822
4 TraesCS5D01G053400 chr1B 411181701 411182776 1075 True 470.500000 689 83.934000 677 2146 2 chr1B.!!$R1 1469
5 TraesCS5D01G053400 chr6A 563488595 563489424 829 False 815.000000 815 84.597000 1000 1819 1 chr6A.!!$F1 819
6 TraesCS5D01G053400 chr2A 556949122 556949930 808 False 798.000000 798 84.710000 1023 1822 1 chr2A.!!$F2 799
7 TraesCS5D01G053400 chr2A 291666057 291666865 808 False 787.000000 787 84.464000 1023 1822 1 chr2A.!!$F1 799
8 TraesCS5D01G053400 chr7A 106409463 106410296 833 True 782.000000 782 83.832000 1000 1822 1 chr7A.!!$R1 822
9 TraesCS5D01G053400 chr2D 80029958 80030748 790 False 761.000000 761 84.257000 1026 1808 1 chr2D.!!$F1 782
10 TraesCS5D01G053400 chr7D 199528785 199529614 829 False 737.000000 737 82.912000 1000 1819 1 chr7D.!!$F1 819
11 TraesCS5D01G053400 chr4B 168270082 168270919 837 True 717.000000 717 82.402000 1000 1826 1 chr4B.!!$R1 826
12 TraesCS5D01G053400 chr5B 529378701 529379349 648 True 693.000000 693 86.095000 673 1337 1 chr5B.!!$R1 664
13 TraesCS5D01G053400 chr5B 54197638 54198317 679 True 221.333333 309 92.784667 1 2409 3 chr5B.!!$R2 2408

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
129 130 0.03467 AGAGCTGTTTGATCTGGGGC 60.035 55.0 0.0 0.0 40.31 5.8 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2037 2214 0.038892 AGTTGTCGCACGGTCGTATT 60.039 50.0 0.0 0.0 0.0 1.89 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
86 87 4.864704 AAAACAGCCGGTAAACATCAAT 57.135 36.364 1.90 0.00 0.00 2.57
88 89 2.091541 ACAGCCGGTAAACATCAATGG 58.908 47.619 1.90 0.00 0.00 3.16
94 95 3.119990 CCGGTAAACATCAATGGTGTGAC 60.120 47.826 0.00 1.55 0.00 3.67
95 96 3.751175 CGGTAAACATCAATGGTGTGACT 59.249 43.478 0.00 0.00 0.00 3.41
96 97 4.378356 CGGTAAACATCAATGGTGTGACTG 60.378 45.833 0.00 3.21 0.00 3.51
97 98 4.518970 GGTAAACATCAATGGTGTGACTGT 59.481 41.667 0.00 0.00 0.00 3.55
98 99 4.572985 AAACATCAATGGTGTGACTGTG 57.427 40.909 0.00 0.00 0.00 3.66
99 100 3.213206 ACATCAATGGTGTGACTGTGT 57.787 42.857 0.00 0.00 0.00 3.72
100 101 2.880268 ACATCAATGGTGTGACTGTGTG 59.120 45.455 0.00 0.00 0.00 3.82
101 102 2.708216 TCAATGGTGTGACTGTGTGT 57.292 45.000 0.00 0.00 0.00 3.72
102 103 2.997980 TCAATGGTGTGACTGTGTGTT 58.002 42.857 0.00 0.00 0.00 3.32
103 104 2.682352 TCAATGGTGTGACTGTGTGTTG 59.318 45.455 0.00 0.00 0.00 3.33
104 105 2.418368 ATGGTGTGACTGTGTGTTGT 57.582 45.000 0.00 0.00 0.00 3.32
105 106 3.552132 ATGGTGTGACTGTGTGTTGTA 57.448 42.857 0.00 0.00 0.00 2.41
106 107 2.899976 TGGTGTGACTGTGTGTTGTAG 58.100 47.619 0.00 0.00 0.00 2.74
107 108 1.597663 GGTGTGACTGTGTGTTGTAGC 59.402 52.381 0.00 0.00 0.00 3.58
108 109 1.597663 GTGTGACTGTGTGTTGTAGCC 59.402 52.381 0.00 0.00 0.00 3.93
109 110 1.226746 GTGACTGTGTGTTGTAGCCC 58.773 55.000 0.00 0.00 0.00 5.19
110 111 0.833949 TGACTGTGTGTTGTAGCCCA 59.166 50.000 0.00 0.00 0.00 5.36
111 112 1.202639 TGACTGTGTGTTGTAGCCCAG 60.203 52.381 0.00 0.00 0.00 4.45
112 113 1.070134 GACTGTGTGTTGTAGCCCAGA 59.930 52.381 0.00 0.00 0.00 3.86
113 114 1.070758 ACTGTGTGTTGTAGCCCAGAG 59.929 52.381 0.00 0.00 0.00 3.35
114 115 0.250295 TGTGTGTTGTAGCCCAGAGC 60.250 55.000 0.00 0.00 44.25 4.09
124 125 3.566130 GCCCAGAGCTGTTTGATCT 57.434 52.632 0.00 0.00 42.94 2.75
129 130 0.034670 AGAGCTGTTTGATCTGGGGC 60.035 55.000 0.00 0.00 40.31 5.80
130 131 0.034670 GAGCTGTTTGATCTGGGGCT 60.035 55.000 0.00 0.00 0.00 5.19
131 132 0.407139 AGCTGTTTGATCTGGGGCTT 59.593 50.000 0.00 0.00 0.00 4.35
132 133 1.203100 AGCTGTTTGATCTGGGGCTTT 60.203 47.619 0.00 0.00 0.00 3.51
133 134 1.067354 GCTGTTTGATCTGGGGCTTTG 60.067 52.381 0.00 0.00 0.00 2.77
134 135 2.242043 CTGTTTGATCTGGGGCTTTGT 58.758 47.619 0.00 0.00 0.00 2.83
135 136 3.420893 CTGTTTGATCTGGGGCTTTGTA 58.579 45.455 0.00 0.00 0.00 2.41
136 137 3.420893 TGTTTGATCTGGGGCTTTGTAG 58.579 45.455 0.00 0.00 0.00 2.74
137 138 2.755103 GTTTGATCTGGGGCTTTGTAGG 59.245 50.000 0.00 0.00 0.00 3.18
138 139 0.918983 TGATCTGGGGCTTTGTAGGG 59.081 55.000 0.00 0.00 0.00 3.53
139 140 0.919710 GATCTGGGGCTTTGTAGGGT 59.080 55.000 0.00 0.00 0.00 4.34
140 141 0.625849 ATCTGGGGCTTTGTAGGGTG 59.374 55.000 0.00 0.00 0.00 4.61
141 142 0.474854 TCTGGGGCTTTGTAGGGTGA 60.475 55.000 0.00 0.00 0.00 4.02
142 143 0.404040 CTGGGGCTTTGTAGGGTGAA 59.596 55.000 0.00 0.00 0.00 3.18
143 144 1.005924 CTGGGGCTTTGTAGGGTGAAT 59.994 52.381 0.00 0.00 0.00 2.57
144 145 2.241176 CTGGGGCTTTGTAGGGTGAATA 59.759 50.000 0.00 0.00 0.00 1.75
145 146 2.856231 TGGGGCTTTGTAGGGTGAATAT 59.144 45.455 0.00 0.00 0.00 1.28
146 147 4.048600 TGGGGCTTTGTAGGGTGAATATA 58.951 43.478 0.00 0.00 0.00 0.86
147 148 4.479056 TGGGGCTTTGTAGGGTGAATATAA 59.521 41.667 0.00 0.00 0.00 0.98
148 149 5.044030 TGGGGCTTTGTAGGGTGAATATAAA 60.044 40.000 0.00 0.00 0.00 1.40
149 150 6.075315 GGGGCTTTGTAGGGTGAATATAAAT 58.925 40.000 0.00 0.00 0.00 1.40
150 151 6.553476 GGGGCTTTGTAGGGTGAATATAAATT 59.447 38.462 0.00 0.00 0.00 1.82
151 152 7.255836 GGGGCTTTGTAGGGTGAATATAAATTC 60.256 40.741 0.00 0.00 41.69 2.17
165 166 9.540538 TGAATATAAATTCAAGGGGAAACTGAA 57.459 29.630 0.00 0.00 46.64 3.02
170 171 7.806409 AAATTCAAGGGGAAACTGAAAAATG 57.194 32.000 0.00 0.00 39.39 2.32
171 172 4.953940 TCAAGGGGAAACTGAAAAATGG 57.046 40.909 0.00 0.00 0.00 3.16
172 173 4.294347 TCAAGGGGAAACTGAAAAATGGT 58.706 39.130 0.00 0.00 0.00 3.55
173 174 5.459505 TCAAGGGGAAACTGAAAAATGGTA 58.540 37.500 0.00 0.00 0.00 3.25
174 175 6.081356 TCAAGGGGAAACTGAAAAATGGTAT 58.919 36.000 0.00 0.00 0.00 2.73
175 176 6.014669 TCAAGGGGAAACTGAAAAATGGTATG 60.015 38.462 0.00 0.00 0.00 2.39
176 177 4.777366 AGGGGAAACTGAAAAATGGTATGG 59.223 41.667 0.00 0.00 0.00 2.74
177 178 4.775253 GGGGAAACTGAAAAATGGTATGGA 59.225 41.667 0.00 0.00 0.00 3.41
178 179 5.425217 GGGGAAACTGAAAAATGGTATGGAT 59.575 40.000 0.00 0.00 0.00 3.41
179 180 6.406961 GGGGAAACTGAAAAATGGTATGGATC 60.407 42.308 0.00 0.00 0.00 3.36
180 181 6.154363 GGGAAACTGAAAAATGGTATGGATCA 59.846 38.462 0.00 0.00 0.00 2.92
181 182 7.260603 GGAAACTGAAAAATGGTATGGATCAG 58.739 38.462 0.00 0.00 38.91 2.90
182 183 6.780457 AACTGAAAAATGGTATGGATCAGG 57.220 37.500 0.00 0.00 37.67 3.86
183 184 6.078456 ACTGAAAAATGGTATGGATCAGGA 57.922 37.500 0.00 0.00 37.67 3.86
184 185 6.676558 ACTGAAAAATGGTATGGATCAGGAT 58.323 36.000 0.00 0.00 37.67 3.24
185 186 6.774656 ACTGAAAAATGGTATGGATCAGGATC 59.225 38.462 0.55 0.55 37.67 3.36
186 187 6.671605 TGAAAAATGGTATGGATCAGGATCA 58.328 36.000 11.12 0.00 39.54 2.92
187 188 7.299896 TGAAAAATGGTATGGATCAGGATCAT 58.700 34.615 11.12 5.77 39.54 2.45
188 189 7.785985 TGAAAAATGGTATGGATCAGGATCATT 59.214 33.333 11.12 0.00 39.54 2.57
189 190 7.771927 AAAATGGTATGGATCAGGATCATTC 57.228 36.000 11.12 2.15 39.54 2.67
190 191 4.916041 TGGTATGGATCAGGATCATTCC 57.084 45.455 11.12 9.70 42.96 3.01
191 192 3.588842 TGGTATGGATCAGGATCATTCCC 59.411 47.826 11.12 6.11 43.76 3.97
192 193 3.369892 GGTATGGATCAGGATCATTCCCG 60.370 52.174 11.12 0.00 43.76 5.14
193 194 1.059098 TGGATCAGGATCATTCCCGG 58.941 55.000 11.12 0.00 43.76 5.73
194 195 1.352083 GGATCAGGATCATTCCCGGA 58.648 55.000 0.73 0.00 43.76 5.14
195 196 1.277557 GGATCAGGATCATTCCCGGAG 59.722 57.143 0.73 0.00 43.76 4.63
196 197 0.689623 ATCAGGATCATTCCCGGAGC 59.310 55.000 0.73 0.00 43.76 4.70
197 198 0.690744 TCAGGATCATTCCCGGAGCA 60.691 55.000 0.73 0.00 43.76 4.26
198 199 0.250209 CAGGATCATTCCCGGAGCAG 60.250 60.000 0.73 0.00 43.76 4.24
199 200 1.599240 GGATCATTCCCGGAGCAGC 60.599 63.158 0.73 0.00 35.84 5.25
200 201 1.958205 GATCATTCCCGGAGCAGCG 60.958 63.158 0.73 0.00 0.00 5.18
201 202 2.369257 GATCATTCCCGGAGCAGCGA 62.369 60.000 0.73 0.00 0.00 4.93
202 203 1.971505 ATCATTCCCGGAGCAGCGAA 61.972 55.000 0.73 0.00 0.00 4.70
203 204 1.524621 CATTCCCGGAGCAGCGAAT 60.525 57.895 0.73 0.00 0.00 3.34
204 205 1.524621 ATTCCCGGAGCAGCGAATG 60.525 57.895 0.73 0.00 0.00 2.67
205 206 1.971505 ATTCCCGGAGCAGCGAATGA 61.972 55.000 0.73 0.00 0.00 2.57
206 207 2.852495 TTCCCGGAGCAGCGAATGAC 62.852 60.000 0.73 0.00 0.00 3.06
207 208 2.185350 CCGGAGCAGCGAATGACT 59.815 61.111 0.00 0.00 0.00 3.41
208 209 1.437573 CCGGAGCAGCGAATGACTA 59.562 57.895 0.00 0.00 0.00 2.59
209 210 0.179111 CCGGAGCAGCGAATGACTAA 60.179 55.000 0.00 0.00 0.00 2.24
210 211 1.203928 CGGAGCAGCGAATGACTAAG 58.796 55.000 0.00 0.00 0.00 2.18
211 212 0.933796 GGAGCAGCGAATGACTAAGC 59.066 55.000 0.00 0.00 0.00 3.09
212 213 1.472376 GGAGCAGCGAATGACTAAGCT 60.472 52.381 0.00 0.00 41.07 3.74
218 219 4.188247 AGCGAATGACTAAGCTGTAACA 57.812 40.909 0.00 0.00 38.67 2.41
276 277 8.931385 TGTAATTACCGAACTAGTAAATGACC 57.069 34.615 13.01 0.00 33.63 4.02
281 282 2.858344 CGAACTAGTAAATGACCAGCGG 59.142 50.000 0.00 0.00 0.00 5.52
335 347 0.249398 CTGGCCGCTGTTACTAACCT 59.751 55.000 0.00 0.00 0.00 3.50
342 354 2.352030 CGCTGTTACTAACCTCGTCCAA 60.352 50.000 0.00 0.00 0.00 3.53
503 516 1.324005 GCTCCTGTAGCCTCCTTCGT 61.324 60.000 0.00 0.00 46.25 3.85
553 566 0.176680 CAATCCCTCACACCTCTCCG 59.823 60.000 0.00 0.00 0.00 4.63
558 571 1.185618 CCTCACACCTCTCCGACCAA 61.186 60.000 0.00 0.00 0.00 3.67
570 583 1.487142 TCCGACCAAGAAAACCACTCA 59.513 47.619 0.00 0.00 0.00 3.41
574 587 0.951558 CCAAGAAAACCACTCACCGG 59.048 55.000 0.00 0.00 0.00 5.28
632 653 2.471084 ATCCTCCCCACCAAGGACGA 62.471 60.000 0.00 0.00 44.26 4.20
634 655 1.913762 CTCCCCACCAAGGACGACT 60.914 63.158 0.00 0.00 41.22 4.18
636 657 1.003718 CCCCACCAAGGACGACTTC 60.004 63.158 0.00 0.00 41.22 3.01
646 667 1.605971 GGACGACTTCCCACTCTCCC 61.606 65.000 0.00 0.00 38.70 4.30
648 669 2.711922 CGACTTCCCACTCTCCCCG 61.712 68.421 0.00 0.00 0.00 5.73
649 670 1.609794 GACTTCCCACTCTCCCCGT 60.610 63.158 0.00 0.00 0.00 5.28
651 672 2.284405 TTCCCACTCTCCCCGTCC 60.284 66.667 0.00 0.00 0.00 4.79
695 756 2.242572 CGCATCATCGTGAGCCCTG 61.243 63.158 0.00 0.00 0.00 4.45
717 778 0.193574 TCTCCACCCTTCTCCCTGTT 59.806 55.000 0.00 0.00 0.00 3.16
758 819 5.997385 TGCGAATTTGGAAGAAGTAAGAAC 58.003 37.500 0.00 0.00 0.00 3.01
772 833 5.593679 AGTAAGAACGCCTCAGCTAAATA 57.406 39.130 0.00 0.00 36.60 1.40
804 865 8.212995 ACAATTGGACTTGATTGAAATCCTTTT 58.787 29.630 10.83 0.00 36.87 2.27
981 1046 4.082026 AGCTGGTTTCTCATAATTTGGCAC 60.082 41.667 0.00 0.00 0.00 5.01
982 1047 4.747810 CTGGTTTCTCATAATTTGGCACC 58.252 43.478 0.00 0.00 0.00 5.01
1021 1086 0.947244 GGATACAGCTGGGCATTTCG 59.053 55.000 19.93 0.00 0.00 3.46
1053 1118 2.045242 ATGCCTCACAGCCAGCAG 60.045 61.111 0.00 0.00 38.89 4.24
1217 1296 5.183713 CCATTTGATCCTTTGTGTAGCTCAA 59.816 40.000 0.00 0.00 0.00 3.02
1273 1352 7.434307 GCAATGATGAAGAAAATCAATGTCGAT 59.566 33.333 0.00 0.00 37.30 3.59
1298 1377 7.523293 AAATATTTGATATCGGCATTGGTCA 57.477 32.000 0.00 0.00 0.00 4.02
1303 1382 1.436195 TATCGGCATTGGTCAAGCGC 61.436 55.000 0.00 0.00 0.00 5.92
1388 1497 1.272760 TGAGTTGTTTGTGGGGGTTGT 60.273 47.619 0.00 0.00 0.00 3.32
1436 1610 4.202121 GCAAAGATGATGCATCATGGTCTT 60.202 41.667 39.76 32.72 46.84 3.01
1495 1669 5.806502 TGAACAACACATGAAGCAAAAGAAG 59.193 36.000 0.00 0.00 0.00 2.85
1619 1796 3.567164 CCGAGAGATTAATTGGCATGCTT 59.433 43.478 18.92 6.78 0.00 3.91
1623 1800 5.443283 AGAGATTAATTGGCATGCTTGAGA 58.557 37.500 18.92 0.07 0.00 3.27
1630 1807 3.306917 TGGCATGCTTGAGAAATTGTG 57.693 42.857 18.92 0.00 0.00 3.33
1645 1822 7.665559 TGAGAAATTGTGCTAGAAATACTTGGT 59.334 33.333 0.00 0.00 0.00 3.67
1647 1824 8.299570 AGAAATTGTGCTAGAAATACTTGGTTG 58.700 33.333 0.00 0.00 0.00 3.77
1648 1825 7.759489 AATTGTGCTAGAAATACTTGGTTGA 57.241 32.000 0.00 0.00 0.00 3.18
1706 1883 6.742644 GCCAGCTATGTATCTCCAGTTTATGT 60.743 42.308 0.00 0.00 0.00 2.29
1711 1888 9.413048 GCTATGTATCTCCAGTTTATGTAGAAC 57.587 37.037 0.00 0.00 0.00 3.01
1719 1896 4.750098 CCAGTTTATGTAGAACATAGGGCG 59.250 45.833 0.52 0.00 41.56 6.13
1720 1897 4.750098 CAGTTTATGTAGAACATAGGGCGG 59.250 45.833 0.52 0.00 41.56 6.13
1722 1899 0.033504 ATGTAGAACATAGGGCGGCG 59.966 55.000 0.51 0.51 36.99 6.46
1788 1965 0.038892 CAGTTGAGCATGGGTGTTGC 60.039 55.000 0.00 0.00 40.45 4.17
1789 1966 0.467844 AGTTGAGCATGGGTGTTGCA 60.468 50.000 0.00 0.00 42.62 4.08
1808 1985 7.540055 GTGTTGCAAAGGAGAGATTAGAAATTG 59.460 37.037 0.00 0.00 0.00 2.32
1811 1988 6.379133 TGCAAAGGAGAGATTAGAAATTGCAT 59.621 34.615 5.35 0.00 43.77 3.96
1832 2009 5.484715 CATGGCCTTTGTTCTTGAATTCAT 58.515 37.500 9.40 0.00 0.00 2.57
1836 2013 4.624452 GCCTTTGTTCTTGAATTCATCTGC 59.376 41.667 9.40 1.67 0.00 4.26
1840 2017 5.618056 TGTTCTTGAATTCATCTGCAGAC 57.382 39.130 20.97 5.61 0.00 3.51
1846 2023 7.755591 TCTTGAATTCATCTGCAGACATTAAC 58.244 34.615 20.97 10.34 0.00 2.01
1848 2025 7.080353 TGAATTCATCTGCAGACATTAACAG 57.920 36.000 20.97 1.98 0.00 3.16
1852 2029 5.419542 TCATCTGCAGACATTAACAGGTAC 58.580 41.667 20.97 0.00 0.00 3.34
1899 2076 9.574516 AAACTGATTTACTATTGACTCAAGGTT 57.425 29.630 0.00 0.00 0.00 3.50
1900 2077 8.553459 ACTGATTTACTATTGACTCAAGGTTG 57.447 34.615 0.00 0.00 0.00 3.77
1902 2079 9.388506 CTGATTTACTATTGACTCAAGGTTGAT 57.611 33.333 0.00 0.00 36.46 2.57
1903 2080 9.739276 TGATTTACTATTGACTCAAGGTTGATT 57.261 29.630 0.00 0.00 36.46 2.57
1927 2104 5.353394 TTTGGCGACCTATTAGTTCTCAT 57.647 39.130 0.00 0.00 0.00 2.90
1935 2112 7.326547 GCGACCTATTAGTTCTCATAAACTAGC 59.673 40.741 0.00 0.00 41.45 3.42
1943 2120 7.772332 AGTTCTCATAAACTAGCAATTACCG 57.228 36.000 0.00 0.00 37.71 4.02
2022 2199 9.921637 CCATTGAATAGATTAGGTAGAAGACTC 57.078 37.037 0.00 0.00 0.00 3.36
2026 2203 9.475620 TGAATAGATTAGGTAGAAGACTCAACA 57.524 33.333 0.00 0.00 0.00 3.33
2030 2207 7.616313 AGATTAGGTAGAAGACTCAACAAAGG 58.384 38.462 0.00 0.00 0.00 3.11
2031 2208 6.989155 TTAGGTAGAAGACTCAACAAAGGA 57.011 37.500 0.00 0.00 0.00 3.36
2032 2209 5.476091 AGGTAGAAGACTCAACAAAGGAG 57.524 43.478 0.00 0.00 38.36 3.69
2033 2210 5.148502 AGGTAGAAGACTCAACAAAGGAGA 58.851 41.667 0.00 0.00 36.26 3.71
2034 2211 5.782845 AGGTAGAAGACTCAACAAAGGAGAT 59.217 40.000 0.00 0.00 36.26 2.75
2035 2212 5.872070 GGTAGAAGACTCAACAAAGGAGATG 59.128 44.000 0.00 0.00 36.26 2.90
2036 2213 4.322567 AGAAGACTCAACAAAGGAGATGC 58.677 43.478 0.00 0.00 36.26 3.91
2037 2214 3.777106 AGACTCAACAAAGGAGATGCA 57.223 42.857 0.00 0.00 36.26 3.96
2038 2215 4.090761 AGACTCAACAAAGGAGATGCAA 57.909 40.909 0.00 0.00 36.26 4.08
2039 2216 4.660168 AGACTCAACAAAGGAGATGCAAT 58.340 39.130 0.00 0.00 36.26 3.56
2040 2217 5.809001 AGACTCAACAAAGGAGATGCAATA 58.191 37.500 0.00 0.00 36.26 1.90
2041 2218 5.645497 AGACTCAACAAAGGAGATGCAATAC 59.355 40.000 0.00 0.00 36.26 1.89
2042 2219 4.393062 ACTCAACAAAGGAGATGCAATACG 59.607 41.667 0.00 0.00 36.26 3.06
2043 2220 4.574892 TCAACAAAGGAGATGCAATACGA 58.425 39.130 0.00 0.00 0.00 3.43
2044 2221 4.391830 TCAACAAAGGAGATGCAATACGAC 59.608 41.667 0.00 0.00 0.00 4.34
2053 2230 2.089936 GCAATACGACCGTGCGACA 61.090 57.895 5.20 0.00 34.83 4.35
2062 2239 1.389106 GACCGTGCGACAACTTACATC 59.611 52.381 0.00 0.00 0.00 3.06
2064 2241 0.365523 CGTGCGACAACTTACATCCG 59.634 55.000 0.00 0.00 0.00 4.18
2090 2267 3.771479 ACTGCAGGTCAAGTAGATGATCA 59.229 43.478 19.93 0.00 32.68 2.92
2092 2269 5.600069 ACTGCAGGTCAAGTAGATGATCATA 59.400 40.000 19.93 0.00 32.68 2.15
2102 2279 6.581171 AGTAGATGATCATAATGACGAGCA 57.419 37.500 8.54 0.00 31.17 4.26
2103 2280 6.619744 AGTAGATGATCATAATGACGAGCAG 58.380 40.000 8.54 0.00 29.94 4.24
2105 2282 2.759191 TGATCATAATGACGAGCAGCC 58.241 47.619 0.00 0.00 0.00 4.85
2111 2288 2.842394 AATGACGAGCAGCCGGTGAG 62.842 60.000 1.90 0.00 0.00 3.51
2113 2290 3.282745 GACGAGCAGCCGGTGAGAA 62.283 63.158 1.90 0.00 0.00 2.87
2116 2293 1.869690 GAGCAGCCGGTGAGAAAAC 59.130 57.895 1.90 0.00 0.00 2.43
2117 2294 0.884704 GAGCAGCCGGTGAGAAAACA 60.885 55.000 1.90 0.00 0.00 2.83
2120 2297 1.021202 CAGCCGGTGAGAAAACACAA 58.979 50.000 1.90 0.00 41.88 3.33
2131 2308 6.092807 GGTGAGAAAACACAACTCCTATGATC 59.907 42.308 0.00 0.00 41.88 2.92
2210 2387 7.867909 TCAAGCTATTCTAGTACAAATCCATCG 59.132 37.037 0.00 0.00 0.00 3.84
2211 2388 6.692486 AGCTATTCTAGTACAAATCCATCGG 58.308 40.000 0.00 0.00 0.00 4.18
2229 2433 3.291584 TCGGCTGACTTCAGATGTATCT 58.708 45.455 10.54 0.00 46.59 1.98
2244 2449 7.458409 AGATGTATCTGAGCAAAACAAACAT 57.542 32.000 0.00 0.00 35.42 2.71
2254 2459 8.846943 TGAGCAAAACAAACATCTTCTCTATA 57.153 30.769 0.00 0.00 0.00 1.31
2281 2486 3.242870 ACTCTTGCTTGCTTTCTTGAACG 60.243 43.478 0.00 0.00 0.00 3.95
2312 2517 5.456265 GTTCCTTTTGAGAGAATTGACAGC 58.544 41.667 0.00 0.00 0.00 4.40
2335 2540 2.436824 GCCTCGGCAGTTTCTCCC 60.437 66.667 2.41 0.00 41.49 4.30
2338 2543 1.544825 CCTCGGCAGTTTCTCCCTGA 61.545 60.000 0.00 0.00 31.38 3.86
2340 2545 0.984230 TCGGCAGTTTCTCCCTGAAT 59.016 50.000 0.00 0.00 34.24 2.57
2341 2546 1.089920 CGGCAGTTTCTCCCTGAATG 58.910 55.000 0.00 0.00 34.24 2.67
2347 2552 2.135903 TTTCTCCCTGAATGGCGCCA 62.136 55.000 34.80 34.80 34.24 5.69
2359 2564 2.325082 GGCGCCACATCGTGTTTCT 61.325 57.895 24.80 0.00 0.00 2.52
2361 2566 1.565156 GCGCCACATCGTGTTTCTGA 61.565 55.000 0.00 0.00 0.00 3.27
2362 2567 1.078709 CGCCACATCGTGTTTCTGAT 58.921 50.000 0.00 0.00 0.00 2.90
2363 2568 1.464608 CGCCACATCGTGTTTCTGATT 59.535 47.619 0.00 0.00 0.00 2.57
2364 2569 2.474526 CGCCACATCGTGTTTCTGATTC 60.475 50.000 0.00 0.00 0.00 2.52
2374 2579 5.856986 TCGTGTTTCTGATTCGTCTTCTTAG 59.143 40.000 0.00 0.00 0.00 2.18
2376 2581 6.032985 CGTGTTTCTGATTCGTCTTCTTAGAG 59.967 42.308 0.00 0.00 0.00 2.43
2389 2594 5.927689 GTCTTCTTAGAGGATGCATCATCTG 59.072 44.000 40.14 29.11 46.20 2.90
2399 2604 1.133699 TGCATCATCTGGATTCCCCAC 60.134 52.381 0.00 0.00 40.82 4.61
2414 2619 3.006672 CCACAGGTGGTTCACTGTC 57.993 57.895 10.34 0.00 45.53 3.51
2415 2620 0.535102 CCACAGGTGGTTCACTGTCC 60.535 60.000 10.34 0.00 45.53 4.02
2416 2621 0.180171 CACAGGTGGTTCACTGTCCA 59.820 55.000 0.00 0.00 34.40 4.02
2417 2622 0.916086 ACAGGTGGTTCACTGTCCAA 59.084 50.000 0.00 0.00 35.38 3.53
2418 2623 1.494721 ACAGGTGGTTCACTGTCCAAT 59.505 47.619 0.00 0.00 35.38 3.16
2419 2624 1.881973 CAGGTGGTTCACTGTCCAATG 59.118 52.381 0.00 0.00 35.38 2.82
2420 2625 1.494721 AGGTGGTTCACTGTCCAATGT 59.505 47.619 0.00 0.00 35.38 2.71
2421 2626 1.608590 GGTGGTTCACTGTCCAATGTG 59.391 52.381 0.00 0.00 35.38 3.21
2422 2627 1.001378 GTGGTTCACTGTCCAATGTGC 60.001 52.381 0.00 0.00 35.38 4.57
2423 2628 0.598065 GGTTCACTGTCCAATGTGCC 59.402 55.000 0.00 0.00 34.49 5.01
2424 2629 1.609208 GTTCACTGTCCAATGTGCCT 58.391 50.000 0.00 0.00 34.49 4.75
2425 2630 1.267806 GTTCACTGTCCAATGTGCCTG 59.732 52.381 0.00 0.00 34.49 4.85
2426 2631 0.890542 TCACTGTCCAATGTGCCTGC 60.891 55.000 0.00 0.00 34.49 4.85
2427 2632 1.151221 ACTGTCCAATGTGCCTGCA 59.849 52.632 0.00 0.00 0.00 4.41
2428 2633 0.251474 ACTGTCCAATGTGCCTGCAT 60.251 50.000 0.00 0.00 0.00 3.96
2429 2634 0.454600 CTGTCCAATGTGCCTGCATC 59.545 55.000 0.00 0.00 0.00 3.91
2430 2635 0.038599 TGTCCAATGTGCCTGCATCT 59.961 50.000 0.00 0.00 0.00 2.90
2431 2636 0.454600 GTCCAATGTGCCTGCATCTG 59.545 55.000 0.00 0.00 0.00 2.90
2432 2637 1.141019 CCAATGTGCCTGCATCTGC 59.859 57.895 0.00 0.00 42.50 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
74 75 4.518970 ACAGTCACACCATTGATGTTTACC 59.481 41.667 0.00 0.00 0.00 2.85
86 87 2.899976 CTACAACACACAGTCACACCA 58.100 47.619 0.00 0.00 0.00 4.17
88 89 1.597663 GGCTACAACACACAGTCACAC 59.402 52.381 0.00 0.00 0.00 3.82
94 95 1.800805 CTCTGGGCTACAACACACAG 58.199 55.000 0.00 0.00 0.00 3.66
95 96 0.250295 GCTCTGGGCTACAACACACA 60.250 55.000 0.00 0.00 38.06 3.72
96 97 2.544726 GCTCTGGGCTACAACACAC 58.455 57.895 0.00 0.00 38.06 3.82
106 107 1.093159 CAGATCAAACAGCTCTGGGC 58.907 55.000 0.00 0.00 36.95 5.36
109 110 1.747709 CCCCAGATCAAACAGCTCTG 58.252 55.000 0.00 0.00 39.60 3.35
110 111 0.034670 GCCCCAGATCAAACAGCTCT 60.035 55.000 0.00 0.00 0.00 4.09
111 112 0.034670 AGCCCCAGATCAAACAGCTC 60.035 55.000 0.00 0.00 0.00 4.09
112 113 0.407139 AAGCCCCAGATCAAACAGCT 59.593 50.000 0.00 0.00 0.00 4.24
113 114 1.067354 CAAAGCCCCAGATCAAACAGC 60.067 52.381 0.00 0.00 0.00 4.40
114 115 2.242043 ACAAAGCCCCAGATCAAACAG 58.758 47.619 0.00 0.00 0.00 3.16
115 116 2.380064 ACAAAGCCCCAGATCAAACA 57.620 45.000 0.00 0.00 0.00 2.83
116 117 2.755103 CCTACAAAGCCCCAGATCAAAC 59.245 50.000 0.00 0.00 0.00 2.93
117 118 2.291540 CCCTACAAAGCCCCAGATCAAA 60.292 50.000 0.00 0.00 0.00 2.69
118 119 1.284785 CCCTACAAAGCCCCAGATCAA 59.715 52.381 0.00 0.00 0.00 2.57
119 120 0.918983 CCCTACAAAGCCCCAGATCA 59.081 55.000 0.00 0.00 0.00 2.92
120 121 0.919710 ACCCTACAAAGCCCCAGATC 59.080 55.000 0.00 0.00 0.00 2.75
121 122 0.625849 CACCCTACAAAGCCCCAGAT 59.374 55.000 0.00 0.00 0.00 2.90
122 123 0.474854 TCACCCTACAAAGCCCCAGA 60.475 55.000 0.00 0.00 0.00 3.86
123 124 0.404040 TTCACCCTACAAAGCCCCAG 59.596 55.000 0.00 0.00 0.00 4.45
124 125 1.080638 ATTCACCCTACAAAGCCCCA 58.919 50.000 0.00 0.00 0.00 4.96
125 126 3.595190 ATATTCACCCTACAAAGCCCC 57.405 47.619 0.00 0.00 0.00 5.80
126 127 7.286775 TGAATTTATATTCACCCTACAAAGCCC 59.713 37.037 4.67 0.00 43.93 5.19
127 128 8.232913 TGAATTTATATTCACCCTACAAAGCC 57.767 34.615 4.67 0.00 43.93 4.35
139 140 9.540538 TTCAGTTTCCCCTTGAATTTATATTCA 57.459 29.630 4.67 4.67 46.38 2.57
144 145 9.506018 CATTTTTCAGTTTCCCCTTGAATTTAT 57.494 29.630 0.00 0.00 31.54 1.40
145 146 7.936301 CCATTTTTCAGTTTCCCCTTGAATTTA 59.064 33.333 0.00 0.00 31.54 1.40
146 147 6.772233 CCATTTTTCAGTTTCCCCTTGAATTT 59.228 34.615 0.00 0.00 31.54 1.82
147 148 6.126507 ACCATTTTTCAGTTTCCCCTTGAATT 60.127 34.615 0.00 0.00 31.54 2.17
148 149 5.369404 ACCATTTTTCAGTTTCCCCTTGAAT 59.631 36.000 0.00 0.00 31.54 2.57
149 150 4.719273 ACCATTTTTCAGTTTCCCCTTGAA 59.281 37.500 0.00 0.00 0.00 2.69
150 151 4.294347 ACCATTTTTCAGTTTCCCCTTGA 58.706 39.130 0.00 0.00 0.00 3.02
151 152 4.687901 ACCATTTTTCAGTTTCCCCTTG 57.312 40.909 0.00 0.00 0.00 3.61
152 153 5.248248 CCATACCATTTTTCAGTTTCCCCTT 59.752 40.000 0.00 0.00 0.00 3.95
153 154 4.777366 CCATACCATTTTTCAGTTTCCCCT 59.223 41.667 0.00 0.00 0.00 4.79
154 155 4.775253 TCCATACCATTTTTCAGTTTCCCC 59.225 41.667 0.00 0.00 0.00 4.81
155 156 5.993748 TCCATACCATTTTTCAGTTTCCC 57.006 39.130 0.00 0.00 0.00 3.97
156 157 7.169158 TGATCCATACCATTTTTCAGTTTCC 57.831 36.000 0.00 0.00 0.00 3.13
157 158 7.122650 TCCTGATCCATACCATTTTTCAGTTTC 59.877 37.037 0.00 0.00 0.00 2.78
158 159 6.953520 TCCTGATCCATACCATTTTTCAGTTT 59.046 34.615 0.00 0.00 0.00 2.66
159 160 6.493166 TCCTGATCCATACCATTTTTCAGTT 58.507 36.000 0.00 0.00 0.00 3.16
160 161 6.078456 TCCTGATCCATACCATTTTTCAGT 57.922 37.500 0.00 0.00 0.00 3.41
161 162 6.774170 TGATCCTGATCCATACCATTTTTCAG 59.226 38.462 4.76 0.00 37.02 3.02
162 163 6.671605 TGATCCTGATCCATACCATTTTTCA 58.328 36.000 4.76 0.00 37.02 2.69
163 164 7.771927 ATGATCCTGATCCATACCATTTTTC 57.228 36.000 4.76 0.00 37.02 2.29
164 165 7.234166 GGAATGATCCTGATCCATACCATTTTT 59.766 37.037 4.76 0.00 42.93 1.94
165 166 6.723052 GGAATGATCCTGATCCATACCATTTT 59.277 38.462 4.76 0.00 42.93 1.82
166 167 6.251471 GGAATGATCCTGATCCATACCATTT 58.749 40.000 4.76 0.00 42.93 2.32
167 168 5.281401 GGGAATGATCCTGATCCATACCATT 60.281 44.000 4.76 0.00 45.77 3.16
168 169 4.229123 GGGAATGATCCTGATCCATACCAT 59.771 45.833 4.76 0.00 45.77 3.55
169 170 3.588842 GGGAATGATCCTGATCCATACCA 59.411 47.826 4.76 0.00 45.77 3.25
170 171 4.227864 GGGAATGATCCTGATCCATACC 57.772 50.000 4.76 0.60 45.77 2.73
180 181 2.049627 GCTGCTCCGGGAATGATCCT 62.050 60.000 0.00 0.00 45.77 3.24
181 182 1.599240 GCTGCTCCGGGAATGATCC 60.599 63.158 0.00 0.00 45.77 3.36
182 183 1.958205 CGCTGCTCCGGGAATGATC 60.958 63.158 0.00 0.00 0.00 2.92
183 184 1.971505 TTCGCTGCTCCGGGAATGAT 61.972 55.000 0.00 0.00 31.89 2.45
184 185 1.971505 ATTCGCTGCTCCGGGAATGA 61.972 55.000 0.00 0.00 42.63 2.57
185 186 1.524621 ATTCGCTGCTCCGGGAATG 60.525 57.895 0.00 0.00 42.63 2.67
186 187 1.524621 CATTCGCTGCTCCGGGAAT 60.525 57.895 0.00 0.00 44.33 3.01
187 188 2.125147 CATTCGCTGCTCCGGGAA 60.125 61.111 0.00 0.00 39.66 3.97
188 189 3.074369 TCATTCGCTGCTCCGGGA 61.074 61.111 0.00 0.00 0.00 5.14
189 190 2.016393 TAGTCATTCGCTGCTCCGGG 62.016 60.000 0.00 0.00 0.00 5.73
190 191 0.179111 TTAGTCATTCGCTGCTCCGG 60.179 55.000 0.00 0.00 0.00 5.14
191 192 1.203928 CTTAGTCATTCGCTGCTCCG 58.796 55.000 0.00 0.00 0.00 4.63
192 193 0.933796 GCTTAGTCATTCGCTGCTCC 59.066 55.000 0.00 0.00 0.00 4.70
193 194 1.592081 CAGCTTAGTCATTCGCTGCTC 59.408 52.381 0.00 0.00 42.66 4.26
194 195 1.649664 CAGCTTAGTCATTCGCTGCT 58.350 50.000 0.00 0.00 42.66 4.24
197 198 3.927142 GTGTTACAGCTTAGTCATTCGCT 59.073 43.478 0.00 0.00 0.00 4.93
198 199 3.062234 GGTGTTACAGCTTAGTCATTCGC 59.938 47.826 7.35 0.00 0.00 4.70
199 200 3.303495 CGGTGTTACAGCTTAGTCATTCG 59.697 47.826 12.77 0.00 0.00 3.34
200 201 4.491676 TCGGTGTTACAGCTTAGTCATTC 58.508 43.478 12.77 0.00 0.00 2.67
201 202 4.530710 TCGGTGTTACAGCTTAGTCATT 57.469 40.909 12.77 0.00 0.00 2.57
202 203 4.737855 ATCGGTGTTACAGCTTAGTCAT 57.262 40.909 12.77 0.00 0.00 3.06
203 204 4.530710 AATCGGTGTTACAGCTTAGTCA 57.469 40.909 12.77 0.00 0.00 3.41
204 205 5.857822 AAAATCGGTGTTACAGCTTAGTC 57.142 39.130 12.77 0.00 0.00 2.59
266 267 4.079253 ACAATTTCCGCTGGTCATTTACT 58.921 39.130 0.00 0.00 0.00 2.24
276 277 6.747280 CCTTACTATTTTCACAATTTCCGCTG 59.253 38.462 0.00 0.00 0.00 5.18
281 282 6.464834 CGCGTCCTTACTATTTTCACAATTTC 59.535 38.462 0.00 0.00 0.00 2.17
342 354 2.618053 GCTAACAATAGCGACCACACT 58.382 47.619 0.00 0.00 44.70 3.55
471 484 2.516225 GGAGCACCATTACCGCCC 60.516 66.667 0.00 0.00 35.97 6.13
473 486 0.177141 TACAGGAGCACCATTACCGC 59.823 55.000 2.07 0.00 38.94 5.68
527 540 1.580059 GTGTGAGGGATTGGGGAGTA 58.420 55.000 0.00 0.00 0.00 2.59
553 566 1.602377 CGGTGAGTGGTTTTCTTGGTC 59.398 52.381 0.00 0.00 0.00 4.02
558 571 1.597027 CGCCGGTGAGTGGTTTTCT 60.597 57.895 10.20 0.00 0.00 2.52
582 595 2.585247 CCGGATTCGAACGGGAGC 60.585 66.667 17.06 0.00 46.08 4.70
632 653 1.609794 GACGGGGAGAGTGGGAAGT 60.610 63.158 0.00 0.00 0.00 3.01
634 655 2.284405 GGACGGGGAGAGTGGGAA 60.284 66.667 0.00 0.00 0.00 3.97
671 706 1.474648 CTCACGATGATGCGGTCACG 61.475 60.000 0.00 10.16 40.28 4.35
695 756 0.041982 AGGGAGAAGGGTGGAGAGAC 59.958 60.000 0.00 0.00 0.00 3.36
717 778 5.514274 TCGCATGACAGACACATATTAGA 57.486 39.130 0.00 0.00 0.00 2.10
758 819 5.484173 TGTGAATTTATTTAGCTGAGGCG 57.516 39.130 0.00 0.00 44.37 5.52
772 833 8.961294 TTTCAATCAAGTCCAATTGTGAATTT 57.039 26.923 4.43 0.00 35.02 1.82
821 882 9.066892 TCAAACAGTGAAGCATTAGTCTAATTT 57.933 29.630 2.12 0.00 31.51 1.82
981 1046 2.906691 TTGCCAACAATGTTTCCTGG 57.093 45.000 0.00 0.00 0.00 4.45
1016 1081 5.451798 GGCATCCATAACAAATCACCGAAAT 60.452 40.000 0.00 0.00 0.00 2.17
1021 1086 3.953612 TGAGGCATCCATAACAAATCACC 59.046 43.478 0.00 0.00 0.00 4.02
1053 1118 9.002600 ACATTTTCCCAAGCTTTTGATATTTTC 57.997 29.630 0.00 0.00 0.00 2.29
1217 1296 8.037723 TGGTAAAAACCTAGGTTCTCTAAAGT 57.962 34.615 27.24 6.50 37.35 2.66
1273 1352 8.628630 TGACCAATGCCGATATCAAATATTTA 57.371 30.769 0.00 0.00 0.00 1.40
1303 1382 0.107703 TATTTGTCTCAGGCCGCCAG 60.108 55.000 13.15 3.23 0.00 4.85
1388 1497 7.284489 GCCAATAAGTTGTTTACCATGGATAGA 59.716 37.037 21.47 0.00 33.36 1.98
1436 1610 4.382685 CCCAAGCGACCTCTCAATTAACTA 60.383 45.833 0.00 0.00 0.00 2.24
1495 1669 4.574599 AATATTGCCATCGCCTTTTCTC 57.425 40.909 0.00 0.00 0.00 2.87
1559 1736 1.805943 CATCACATGGAAGCGTTCACA 59.194 47.619 0.00 0.00 0.00 3.58
1619 1796 7.665559 ACCAAGTATTTCTAGCACAATTTCTCA 59.334 33.333 0.00 0.00 0.00 3.27
1623 1800 8.177119 TCAACCAAGTATTTCTAGCACAATTT 57.823 30.769 0.00 0.00 0.00 1.82
1630 1807 6.151144 ACACCATTCAACCAAGTATTTCTAGC 59.849 38.462 0.00 0.00 0.00 3.42
1679 1856 3.246301 ACTGGAGATACATAGCTGGCAT 58.754 45.455 0.00 0.00 0.00 4.40
1706 1883 0.103572 GTTCGCCGCCCTATGTTCTA 59.896 55.000 0.00 0.00 0.00 2.10
1711 1888 1.592669 CTCTGTTCGCCGCCCTATG 60.593 63.158 0.00 0.00 0.00 2.23
1712 1889 0.754217 TACTCTGTTCGCCGCCCTAT 60.754 55.000 0.00 0.00 0.00 2.57
1719 1896 3.139077 CCCCAATTATACTCTGTTCGCC 58.861 50.000 0.00 0.00 0.00 5.54
1720 1897 4.058817 CTCCCCAATTATACTCTGTTCGC 58.941 47.826 0.00 0.00 0.00 4.70
1722 1899 5.036117 TGCTCCCCAATTATACTCTGTTC 57.964 43.478 0.00 0.00 0.00 3.18
1788 1965 7.201145 CCATGCAATTTCTAATCTCTCCTTTG 58.799 38.462 0.00 0.00 0.00 2.77
1789 1966 6.183360 GCCATGCAATTTCTAATCTCTCCTTT 60.183 38.462 0.00 0.00 0.00 3.11
1808 1985 2.818130 TTCAAGAACAAAGGCCATGC 57.182 45.000 5.01 0.00 0.00 4.06
1811 1988 4.834496 AGATGAATTCAAGAACAAAGGCCA 59.166 37.500 13.09 0.00 0.00 5.36
1832 2009 3.508402 TCGTACCTGTTAATGTCTGCAGA 59.492 43.478 13.74 13.74 0.00 4.26
1836 2013 8.714179 TGTTTATTTCGTACCTGTTAATGTCTG 58.286 33.333 0.00 0.00 0.00 3.51
1877 2054 9.739276 AATCAACCTTGAGTCAATAGTAAATCA 57.261 29.630 5.91 0.00 41.08 2.57
1903 2080 5.553123 TGAGAACTAATAGGTCGCCAAAAA 58.447 37.500 6.61 0.00 36.93 1.94
1918 2095 8.689061 TCGGTAATTGCTAGTTTATGAGAACTA 58.311 33.333 0.00 0.00 40.24 2.24
1920 2097 7.766219 TCGGTAATTGCTAGTTTATGAGAAC 57.234 36.000 0.00 0.00 0.00 3.01
1968 2145 8.621532 ACAAGTGTACATTGTACAGATGATTT 57.378 30.769 30.00 17.22 39.06 2.17
1977 2154 6.370442 TCAATGGCTACAAGTGTACATTGTAC 59.630 38.462 21.83 18.13 41.17 2.90
2022 2199 4.437390 GGTCGTATTGCATCTCCTTTGTTG 60.437 45.833 0.00 0.00 0.00 3.33
2023 2200 3.689649 GGTCGTATTGCATCTCCTTTGTT 59.310 43.478 0.00 0.00 0.00 2.83
2024 2201 3.270877 GGTCGTATTGCATCTCCTTTGT 58.729 45.455 0.00 0.00 0.00 2.83
2025 2202 2.285220 CGGTCGTATTGCATCTCCTTTG 59.715 50.000 0.00 0.00 0.00 2.77
2026 2203 2.093658 ACGGTCGTATTGCATCTCCTTT 60.094 45.455 0.00 0.00 0.00 3.11
2027 2204 1.480954 ACGGTCGTATTGCATCTCCTT 59.519 47.619 0.00 0.00 0.00 3.36
2028 2205 1.112113 ACGGTCGTATTGCATCTCCT 58.888 50.000 0.00 0.00 0.00 3.69
2029 2206 1.209128 CACGGTCGTATTGCATCTCC 58.791 55.000 0.00 0.00 0.00 3.71
2030 2207 0.577269 GCACGGTCGTATTGCATCTC 59.423 55.000 0.00 0.00 36.22 2.75
2031 2208 1.145759 CGCACGGTCGTATTGCATCT 61.146 55.000 0.00 0.00 35.93 2.90
2032 2209 1.143373 TCGCACGGTCGTATTGCATC 61.143 55.000 0.00 0.00 35.93 3.91
2033 2210 1.153726 TCGCACGGTCGTATTGCAT 60.154 52.632 0.00 0.00 35.93 3.96
2034 2211 2.089936 GTCGCACGGTCGTATTGCA 61.090 57.895 0.00 0.00 35.93 4.08
2035 2212 1.619526 TTGTCGCACGGTCGTATTGC 61.620 55.000 0.00 0.00 0.00 3.56
2036 2213 0.092351 GTTGTCGCACGGTCGTATTG 59.908 55.000 0.00 0.00 0.00 1.90
2037 2214 0.038892 AGTTGTCGCACGGTCGTATT 60.039 50.000 0.00 0.00 0.00 1.89
2038 2215 0.038892 AAGTTGTCGCACGGTCGTAT 60.039 50.000 0.00 0.00 0.00 3.06
2039 2216 0.590682 TAAGTTGTCGCACGGTCGTA 59.409 50.000 0.00 0.00 0.00 3.43
2040 2217 0.936297 GTAAGTTGTCGCACGGTCGT 60.936 55.000 0.00 0.00 0.00 4.34
2041 2218 0.935831 TGTAAGTTGTCGCACGGTCG 60.936 55.000 0.00 0.00 0.00 4.79
2042 2219 1.389106 GATGTAAGTTGTCGCACGGTC 59.611 52.381 0.00 0.00 0.00 4.79
2043 2220 1.425412 GATGTAAGTTGTCGCACGGT 58.575 50.000 0.00 0.00 0.00 4.83
2044 2221 0.719465 GGATGTAAGTTGTCGCACGG 59.281 55.000 0.00 0.00 0.00 4.94
2053 2230 2.989422 GCAGTTTGCGGATGTAAGTT 57.011 45.000 0.00 0.00 31.71 2.66
2064 2241 2.494059 TCTACTTGACCTGCAGTTTGC 58.506 47.619 13.81 0.00 45.29 3.68
2090 2267 0.530650 CACCGGCTGCTCGTCATTAT 60.531 55.000 0.00 0.00 0.00 1.28
2092 2269 2.434884 CACCGGCTGCTCGTCATT 60.435 61.111 0.00 0.00 0.00 2.57
2102 2279 1.021968 GTTGTGTTTTCTCACCGGCT 58.978 50.000 0.00 0.00 37.51 5.52
2103 2280 1.002792 GAGTTGTGTTTTCTCACCGGC 60.003 52.381 0.00 0.00 37.51 6.13
2105 2282 2.561569 AGGAGTTGTGTTTTCTCACCG 58.438 47.619 0.00 0.00 37.51 4.94
2111 2288 6.910536 ATCGATCATAGGAGTTGTGTTTTC 57.089 37.500 0.00 0.00 0.00 2.29
2113 2290 5.586243 CCAATCGATCATAGGAGTTGTGTTT 59.414 40.000 0.00 0.00 0.00 2.83
2116 2293 4.509230 CACCAATCGATCATAGGAGTTGTG 59.491 45.833 0.00 0.00 0.00 3.33
2117 2294 4.405680 TCACCAATCGATCATAGGAGTTGT 59.594 41.667 0.00 0.00 0.00 3.32
2120 2297 4.590647 ACATCACCAATCGATCATAGGAGT 59.409 41.667 0.00 0.00 0.00 3.85
2131 2308 1.003545 GCCATTCGACATCACCAATCG 60.004 52.381 0.00 0.00 37.20 3.34
2229 2433 7.750229 ATAGAGAAGATGTTTGTTTTGCTCA 57.250 32.000 0.00 0.00 0.00 4.26
2244 2449 7.469870 GCAAGCAAGAGTGATCTATAGAGAAGA 60.470 40.741 8.70 0.00 34.61 2.87
2254 2459 4.018484 AGAAAGCAAGCAAGAGTGATCT 57.982 40.909 0.00 0.00 0.00 2.75
2264 2469 0.316937 CGCGTTCAAGAAAGCAAGCA 60.317 50.000 18.11 0.00 44.17 3.91
2281 2486 2.742589 CTCTCAAAAGGAACCTTACCGC 59.257 50.000 6.53 0.00 34.84 5.68
2320 2525 0.321671 TTCAGGGAGAAACTGCCGAG 59.678 55.000 3.86 1.96 46.84 4.63
2323 2528 1.467920 CCATTCAGGGAGAAACTGCC 58.532 55.000 1.10 1.10 42.52 4.85
2335 2540 2.108514 ACGATGTGGCGCCATTCAG 61.109 57.895 35.23 25.33 33.86 3.02
2338 2543 1.523154 AAACACGATGTGGCGCCATT 61.523 50.000 35.23 23.72 37.94 3.16
2340 2545 2.593148 AAACACGATGTGGCGCCA 60.593 55.556 29.03 29.03 37.94 5.69
2341 2546 2.175811 GAAACACGATGTGGCGCC 59.824 61.111 22.73 22.73 37.94 6.53
2347 2552 3.914312 AGACGAATCAGAAACACGATGT 58.086 40.909 0.00 0.00 0.00 3.06
2359 2564 4.402474 TGCATCCTCTAAGAAGACGAATCA 59.598 41.667 0.00 0.00 0.00 2.57
2361 2566 5.069648 TGATGCATCCTCTAAGAAGACGAAT 59.930 40.000 23.67 0.00 0.00 3.34
2362 2567 4.402474 TGATGCATCCTCTAAGAAGACGAA 59.598 41.667 23.67 0.00 0.00 3.85
2363 2568 3.954258 TGATGCATCCTCTAAGAAGACGA 59.046 43.478 23.67 0.00 0.00 4.20
2364 2569 4.313277 TGATGCATCCTCTAAGAAGACG 57.687 45.455 23.67 0.00 0.00 4.18
2374 2579 3.345414 GGAATCCAGATGATGCATCCTC 58.655 50.000 23.67 22.03 41.36 3.71
2376 2581 2.444421 GGGAATCCAGATGATGCATCC 58.556 52.381 23.67 9.46 41.36 3.51
2399 2604 1.881973 CATTGGACAGTGAACCACCTG 59.118 52.381 11.89 9.51 35.81 4.00
2405 2610 1.267806 CAGGCACATTGGACAGTGAAC 59.732 52.381 0.00 0.00 37.97 3.18
2409 2614 0.251474 ATGCAGGCACATTGGACAGT 60.251 50.000 0.00 0.00 0.00 3.55
2410 2615 0.454600 GATGCAGGCACATTGGACAG 59.545 55.000 0.00 0.00 0.00 3.51
2411 2616 0.038599 AGATGCAGGCACATTGGACA 59.961 50.000 0.00 0.00 0.00 4.02
2412 2617 0.454600 CAGATGCAGGCACATTGGAC 59.545 55.000 0.00 0.00 0.00 4.02
2413 2618 1.317431 GCAGATGCAGGCACATTGGA 61.317 55.000 0.00 0.00 41.59 3.53
2414 2619 1.141019 GCAGATGCAGGCACATTGG 59.859 57.895 0.00 0.00 41.59 3.16
2415 2620 4.806571 GCAGATGCAGGCACATTG 57.193 55.556 0.00 0.00 41.59 2.82


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

AutoCloner maintained by Alex Coulton.