Multiple sequence alignment - TraesCS6B01G105000

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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 TraesCS6B01G105000 chr6B 100.000 2264 0 0 1 2264 84603378 84605641 0.000000e+00 4181
1 TraesCS6B01G105000 chr6B 96.130 1292 37 1 973 2264 181110591 181109313 0.000000e+00 2097
2 TraesCS6B01G105000 chr6B 96.157 1145 43 1 973 2116 599877073 599878217 0.000000e+00 1869
3 TraesCS6B01G105000 chr6B 96.129 620 23 1 354 973 26500507 26499889 0.000000e+00 1011
4 TraesCS6B01G105000 chr6B 95.231 629 28 2 346 973 599874264 599874891 0.000000e+00 994
5 TraesCS6B01G105000 chr5B 96.983 1160 34 1 973 2131 506966514 506967673 0.000000e+00 1947
6 TraesCS6B01G105000 chr5B 96.513 1147 36 4 973 2116 584815957 584814812 0.000000e+00 1893
7 TraesCS6B01G105000 chr5B 95.554 1147 48 3 973 2116 234884633 234883487 0.000000e+00 1832
8 TraesCS6B01G105000 chr5B 95.520 625 27 1 349 973 709188959 709188336 0.000000e+00 998
9 TraesCS6B01G105000 chr5B 95.040 625 30 1 349 973 64272916 64273539 0.000000e+00 981
10 TraesCS6B01G105000 chr5B 99.237 131 1 0 2134 2264 535136386 535136516 1.050000e-58 237
11 TraesCS6B01G105000 chr5B 98.473 131 2 0 2134 2264 709184597 709184467 4.860000e-57 231
12 TraesCS6B01G105000 chr5B 97.710 131 3 0 2134 2264 506967725 506967855 2.260000e-55 226
13 TraesCS6B01G105000 chr5B 95.495 111 5 0 1 111 590180520 590180410 6.430000e-41 178
14 TraesCS6B01G105000 chr5B 93.860 114 7 0 1 114 585336471 585336358 2.990000e-39 172
15 TraesCS6B01G105000 chr4B 96.894 1159 33 2 973 2131 551061007 551062162 0.000000e+00 1938
16 TraesCS6B01G105000 chr4B 95.840 625 25 1 349 973 310254937 310255560 0.000000e+00 1009
17 TraesCS6B01G105000 chr4B 95.687 626 25 2 349 973 396487588 396488212 0.000000e+00 1005
18 TraesCS6B01G105000 chr4B 95.056 627 30 1 347 973 551057137 551057762 0.000000e+00 985
19 TraesCS6B01G105000 chr4B 98.473 131 2 0 2134 2264 551062289 551062419 4.860000e-57 231
20 TraesCS6B01G105000 chr3B 96.441 1152 35 4 973 2118 604265070 604263919 0.000000e+00 1895
21 TraesCS6B01G105000 chr3B 98.473 131 2 0 2134 2264 420918872 420918742 4.860000e-57 231
22 TraesCS6B01G105000 chr3B 93.860 114 7 0 1 114 13773185 13773072 2.990000e-39 172
23 TraesCS6B01G105000 chr3B 94.231 104 5 1 2029 2131 760825838 760825735 8.370000e-35 158
24 TraesCS6B01G105000 chr2B 95.812 1146 46 2 973 2116 549353818 549354963 0.000000e+00 1849
25 TraesCS6B01G105000 chr2B 96.266 1098 37 4 973 2068 454450197 454451292 0.000000e+00 1797
26 TraesCS6B01G105000 chr2B 95.360 625 28 1 349 973 549350318 549350941 0.000000e+00 992
27 TraesCS6B01G105000 chr2B 86.486 259 12 12 2029 2264 454451136 454451394 1.720000e-66 263
28 TraesCS6B01G105000 chr1B 95.680 625 21 5 353 973 571425300 571424678 0.000000e+00 1000
29 TraesCS6B01G105000 chr1B 98.473 131 2 0 2134 2264 571420290 571420160 4.860000e-57 231
30 TraesCS6B01G105000 chrUn 86.486 259 12 12 2029 2264 480940928 480941186 1.720000e-66 263
31 TraesCS6B01G105000 chrUn 87.591 137 14 3 1 135 62406596 62406461 3.010000e-34 156
32 TraesCS6B01G105000 chr6A 97.710 131 3 0 2134 2264 23006919 23007049 2.260000e-55 226
33 TraesCS6B01G105000 chr3D 95.495 111 5 0 1 111 463681615 463681505 6.430000e-41 178
34 TraesCS6B01G105000 chr2A 94.595 111 6 0 1 111 42015841 42015951 2.990000e-39 172
35 TraesCS6B01G105000 chr1D 94.595 111 6 0 1 111 459867522 459867412 2.990000e-39 172
36 TraesCS6B01G105000 chr6D 94.545 110 6 0 1 110 377864084 377864193 1.080000e-38 171
37 TraesCS6B01G105000 chr7B 93.103 116 7 1 1 116 747358733 747358619 3.870000e-38 169


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 TraesCS6B01G105000 chr6B 84603378 84605641 2263 False 4181.000000 4181 100.000000 1 2264 1 chr6B.!!$F1 2263
1 TraesCS6B01G105000 chr6B 181109313 181110591 1278 True 2097.000000 2097 96.130000 973 2264 1 chr6B.!!$R2 1291
2 TraesCS6B01G105000 chr6B 599874264 599878217 3953 False 1431.500000 1869 95.694000 346 2116 2 chr6B.!!$F2 1770
3 TraesCS6B01G105000 chr6B 26499889 26500507 618 True 1011.000000 1011 96.129000 354 973 1 chr6B.!!$R1 619
4 TraesCS6B01G105000 chr5B 584814812 584815957 1145 True 1893.000000 1893 96.513000 973 2116 1 chr5B.!!$R2 1143
5 TraesCS6B01G105000 chr5B 234883487 234884633 1146 True 1832.000000 1832 95.554000 973 2116 1 chr5B.!!$R1 1143
6 TraesCS6B01G105000 chr5B 506966514 506967855 1341 False 1086.500000 1947 97.346500 973 2264 2 chr5B.!!$F3 1291
7 TraesCS6B01G105000 chr5B 64272916 64273539 623 False 981.000000 981 95.040000 349 973 1 chr5B.!!$F1 624
8 TraesCS6B01G105000 chr5B 709184467 709188959 4492 True 614.500000 998 96.996500 349 2264 2 chr5B.!!$R5 1915
9 TraesCS6B01G105000 chr4B 551057137 551062419 5282 False 1051.333333 1938 96.807667 347 2264 3 chr4B.!!$F3 1917
10 TraesCS6B01G105000 chr4B 310254937 310255560 623 False 1009.000000 1009 95.840000 349 973 1 chr4B.!!$F1 624
11 TraesCS6B01G105000 chr4B 396487588 396488212 624 False 1005.000000 1005 95.687000 349 973 1 chr4B.!!$F2 624
12 TraesCS6B01G105000 chr3B 604263919 604265070 1151 True 1895.000000 1895 96.441000 973 2118 1 chr3B.!!$R3 1145
13 TraesCS6B01G105000 chr2B 549350318 549354963 4645 False 1420.500000 1849 95.586000 349 2116 2 chr2B.!!$F2 1767
14 TraesCS6B01G105000 chr2B 454450197 454451394 1197 False 1030.000000 1797 91.376000 973 2264 2 chr2B.!!$F1 1291
15 TraesCS6B01G105000 chr1B 571424678 571425300 622 True 1000.000000 1000 95.680000 353 973 1 chr1B.!!$R2 620

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
68 69 0.178301 TGGTGTTCGTTGTACTGCCA 59.822 50.0 0.0 0.0 0.0 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1585 4840 1.071471 CCTTCCTGTCACGTGCCTT 59.929 57.895 11.67 0.0 0.0 4.35 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
19 20 2.616634 TAGTCGTCGCTAGGTGATCT 57.383 50.000 0.00 0.00 0.00 2.75
20 21 2.616634 AGTCGTCGCTAGGTGATCTA 57.383 50.000 0.00 0.00 0.00 1.98
21 22 2.211806 AGTCGTCGCTAGGTGATCTAC 58.788 52.381 0.00 0.00 0.00 2.59
22 23 1.070710 GTCGTCGCTAGGTGATCTACG 60.071 57.143 0.00 0.00 0.00 3.51
23 24 0.235144 CGTCGCTAGGTGATCTACGG 59.765 60.000 0.00 0.00 0.00 4.02
24 25 1.590932 GTCGCTAGGTGATCTACGGA 58.409 55.000 0.00 0.00 0.00 4.69
25 26 2.152830 GTCGCTAGGTGATCTACGGAT 58.847 52.381 0.00 0.00 34.45 4.18
26 27 2.160022 GTCGCTAGGTGATCTACGGATC 59.840 54.545 0.00 0.00 46.20 3.36
27 28 2.038689 TCGCTAGGTGATCTACGGATCT 59.961 50.000 7.39 0.00 46.18 2.75
28 29 2.160615 CGCTAGGTGATCTACGGATCTG 59.839 54.545 0.00 0.00 46.18 2.90
29 30 2.490115 GCTAGGTGATCTACGGATCTGG 59.510 54.545 6.47 0.00 46.18 3.86
30 31 3.811098 GCTAGGTGATCTACGGATCTGGA 60.811 52.174 6.47 0.00 46.18 3.86
31 32 3.534357 AGGTGATCTACGGATCTGGAT 57.466 47.619 6.47 0.00 46.18 3.41
32 33 3.161067 AGGTGATCTACGGATCTGGATG 58.839 50.000 6.47 0.00 46.18 3.51
33 34 2.894126 GGTGATCTACGGATCTGGATGT 59.106 50.000 6.47 0.00 46.18 3.06
34 35 4.079970 GGTGATCTACGGATCTGGATGTA 58.920 47.826 6.47 0.00 46.18 2.29
35 36 4.523173 GGTGATCTACGGATCTGGATGTAA 59.477 45.833 6.47 0.00 46.18 2.41
36 37 5.186021 GGTGATCTACGGATCTGGATGTAAT 59.814 44.000 6.47 0.00 46.18 1.89
37 38 6.295349 GGTGATCTACGGATCTGGATGTAATT 60.295 42.308 6.47 0.00 46.18 1.40
38 39 7.155328 GTGATCTACGGATCTGGATGTAATTT 58.845 38.462 6.47 0.00 46.18 1.82
39 40 7.657761 GTGATCTACGGATCTGGATGTAATTTT 59.342 37.037 6.47 0.00 46.18 1.82
40 41 8.210946 TGATCTACGGATCTGGATGTAATTTTT 58.789 33.333 6.47 0.00 46.18 1.94
41 42 9.706691 GATCTACGGATCTGGATGTAATTTTTA 57.293 33.333 6.47 0.00 43.55 1.52
61 62 9.974980 ATTTTTATTATTTCTGGTGTTCGTTGT 57.025 25.926 0.00 0.00 0.00 3.32
63 64 9.881529 TTTTATTATTTCTGGTGTTCGTTGTAC 57.118 29.630 0.00 0.00 0.00 2.90
64 65 8.836268 TTATTATTTCTGGTGTTCGTTGTACT 57.164 30.769 0.00 0.00 0.00 2.73
65 66 6.533819 TTATTTCTGGTGTTCGTTGTACTG 57.466 37.500 0.00 0.00 0.00 2.74
66 67 1.860676 TCTGGTGTTCGTTGTACTGC 58.139 50.000 0.00 0.00 0.00 4.40
67 68 0.865769 CTGGTGTTCGTTGTACTGCC 59.134 55.000 0.00 0.00 0.00 4.85
68 69 0.178301 TGGTGTTCGTTGTACTGCCA 59.822 50.000 0.00 0.00 0.00 4.92
69 70 1.202710 TGGTGTTCGTTGTACTGCCAT 60.203 47.619 0.00 0.00 0.00 4.40
70 71 2.037381 TGGTGTTCGTTGTACTGCCATA 59.963 45.455 0.00 0.00 0.00 2.74
71 72 3.068560 GGTGTTCGTTGTACTGCCATAA 58.931 45.455 0.00 0.00 0.00 1.90
72 73 3.687698 GGTGTTCGTTGTACTGCCATAAT 59.312 43.478 0.00 0.00 0.00 1.28
73 74 4.155280 GGTGTTCGTTGTACTGCCATAATT 59.845 41.667 0.00 0.00 0.00 1.40
74 75 5.086058 GTGTTCGTTGTACTGCCATAATTG 58.914 41.667 0.00 0.00 0.00 2.32
75 76 4.998033 TGTTCGTTGTACTGCCATAATTGA 59.002 37.500 0.00 0.00 0.00 2.57
76 77 5.470437 TGTTCGTTGTACTGCCATAATTGAA 59.530 36.000 0.00 0.00 0.00 2.69
77 78 5.794687 TCGTTGTACTGCCATAATTGAAG 57.205 39.130 0.00 0.00 0.00 3.02
78 79 5.483811 TCGTTGTACTGCCATAATTGAAGA 58.516 37.500 0.00 0.00 0.00 2.87
79 80 5.935206 TCGTTGTACTGCCATAATTGAAGAA 59.065 36.000 0.00 0.00 0.00 2.52
80 81 6.092122 TCGTTGTACTGCCATAATTGAAGAAG 59.908 38.462 0.00 0.00 0.00 2.85
81 82 6.092122 CGTTGTACTGCCATAATTGAAGAAGA 59.908 38.462 0.00 0.00 0.00 2.87
82 83 7.360861 CGTTGTACTGCCATAATTGAAGAAGAA 60.361 37.037 0.00 0.00 0.00 2.52
83 84 8.462016 GTTGTACTGCCATAATTGAAGAAGAAT 58.538 33.333 0.00 0.00 0.00 2.40
84 85 9.679661 TTGTACTGCCATAATTGAAGAAGAATA 57.320 29.630 0.00 0.00 0.00 1.75
85 86 9.330063 TGTACTGCCATAATTGAAGAAGAATAG 57.670 33.333 0.00 0.00 0.00 1.73
86 87 9.547753 GTACTGCCATAATTGAAGAAGAATAGA 57.452 33.333 0.00 0.00 0.00 1.98
88 89 9.282569 ACTGCCATAATTGAAGAAGAATAGATC 57.717 33.333 0.00 0.00 0.00 2.75
89 90 8.315391 TGCCATAATTGAAGAAGAATAGATCG 57.685 34.615 0.00 0.00 0.00 3.69
90 91 7.388776 TGCCATAATTGAAGAAGAATAGATCGG 59.611 37.037 0.00 0.00 0.00 4.18
91 92 7.604164 GCCATAATTGAAGAAGAATAGATCGGA 59.396 37.037 0.00 0.00 0.00 4.55
92 93 9.494271 CCATAATTGAAGAAGAATAGATCGGAA 57.506 33.333 0.00 0.00 0.00 4.30
96 97 9.454859 AATTGAAGAAGAATAGATCGGAAGTTT 57.545 29.630 0.00 0.00 0.00 2.66
97 98 8.848474 TTGAAGAAGAATAGATCGGAAGTTTT 57.152 30.769 0.00 0.00 0.00 2.43
98 99 8.480643 TGAAGAAGAATAGATCGGAAGTTTTC 57.519 34.615 0.00 0.00 0.00 2.29
99 100 8.314751 TGAAGAAGAATAGATCGGAAGTTTTCT 58.685 33.333 0.00 0.00 0.00 2.52
100 101 9.157104 GAAGAAGAATAGATCGGAAGTTTTCTT 57.843 33.333 9.68 9.68 43.55 2.52
101 102 8.485976 AGAAGAATAGATCGGAAGTTTTCTTG 57.514 34.615 11.56 0.00 40.61 3.02
102 103 6.670077 AGAATAGATCGGAAGTTTTCTTGC 57.330 37.500 0.00 0.00 43.33 4.01
103 104 6.173339 AGAATAGATCGGAAGTTTTCTTGCA 58.827 36.000 0.00 0.00 46.34 4.08
104 105 6.655003 AGAATAGATCGGAAGTTTTCTTGCAA 59.345 34.615 0.00 0.00 46.34 4.08
105 106 6.817765 ATAGATCGGAAGTTTTCTTGCAAA 57.182 33.333 0.00 0.00 46.34 3.68
106 107 5.514274 AGATCGGAAGTTTTCTTGCAAAA 57.486 34.783 0.00 0.00 46.34 2.44
107 108 5.901552 AGATCGGAAGTTTTCTTGCAAAAA 58.098 33.333 0.00 1.75 46.34 1.94
130 131 6.566197 AAAAGAGTACAAGGCATTCTCTTG 57.434 37.500 12.54 6.28 42.27 3.02
131 132 3.604582 AGAGTACAAGGCATTCTCTTGC 58.395 45.455 0.00 0.00 43.79 4.01
138 139 3.247033 GCATTCTCTTGCCAATCGC 57.753 52.632 0.00 0.00 36.60 4.58
139 140 0.248784 GCATTCTCTTGCCAATCGCC 60.249 55.000 0.00 0.00 36.60 5.54
140 141 1.097232 CATTCTCTTGCCAATCGCCA 58.903 50.000 0.00 0.00 36.24 5.69
141 142 1.679680 CATTCTCTTGCCAATCGCCAT 59.320 47.619 0.00 0.00 36.24 4.40
142 143 1.097232 TTCTCTTGCCAATCGCCATG 58.903 50.000 0.00 0.00 36.24 3.66
143 144 1.065273 CTCTTGCCAATCGCCATGC 59.935 57.895 0.00 0.00 36.24 4.06
154 155 3.813596 GCCATGCGTAGAACCCTG 58.186 61.111 0.00 0.00 0.00 4.45
155 156 2.472909 GCCATGCGTAGAACCCTGC 61.473 63.158 0.00 0.00 0.00 4.85
156 157 1.819632 CCATGCGTAGAACCCTGCC 60.820 63.158 0.00 0.00 0.00 4.85
157 158 2.173669 CATGCGTAGAACCCTGCCG 61.174 63.158 0.00 0.00 0.00 5.69
158 159 3.385749 ATGCGTAGAACCCTGCCGG 62.386 63.158 0.00 0.00 37.81 6.13
159 160 3.766691 GCGTAGAACCCTGCCGGA 61.767 66.667 5.05 0.00 34.64 5.14
160 161 2.975536 CGTAGAACCCTGCCGGAA 59.024 61.111 5.05 0.00 34.64 4.30
161 162 1.294138 CGTAGAACCCTGCCGGAAA 59.706 57.895 5.05 0.00 34.64 3.13
162 163 0.320946 CGTAGAACCCTGCCGGAAAA 60.321 55.000 5.05 0.00 34.64 2.29
163 164 1.878948 CGTAGAACCCTGCCGGAAAAA 60.879 52.381 5.05 0.00 34.64 1.94
181 182 3.420839 AAAAAGAAACCTGCAGTCACG 57.579 42.857 13.81 0.00 0.00 4.35
182 183 1.308998 AAAGAAACCTGCAGTCACGG 58.691 50.000 13.81 0.00 0.00 4.94
183 184 1.166531 AAGAAACCTGCAGTCACGGC 61.167 55.000 13.81 0.00 0.00 5.68
184 185 2.954753 GAAACCTGCAGTCACGGCG 61.955 63.158 13.81 4.80 0.00 6.46
185 186 4.988598 AACCTGCAGTCACGGCGG 62.989 66.667 13.81 1.02 37.39 6.13
187 188 4.457496 CCTGCAGTCACGGCGGAT 62.457 66.667 10.74 0.00 40.08 4.18
188 189 2.887568 CTGCAGTCACGGCGGATC 60.888 66.667 13.24 0.04 40.08 3.36
189 190 4.451150 TGCAGTCACGGCGGATCC 62.451 66.667 13.24 0.00 0.00 3.36
201 202 3.252484 GGATCCGTTTCCGCGTCG 61.252 66.667 4.92 4.29 0.00 5.12
202 203 3.910104 GATCCGTTTCCGCGTCGC 61.910 66.667 7.29 7.29 0.00 5.19
221 222 4.963428 GGAATACGCCCCGCCGAG 62.963 72.222 0.00 0.00 0.00 4.63
232 233 4.441695 CGCCGAGCTTCTGCAGGA 62.442 66.667 15.13 3.47 42.74 3.86
233 234 2.511145 GCCGAGCTTCTGCAGGAG 60.511 66.667 18.48 18.48 42.74 3.69
234 235 2.511145 CCGAGCTTCTGCAGGAGC 60.511 66.667 35.74 35.74 42.74 4.70
235 236 2.884685 CGAGCTTCTGCAGGAGCG 60.885 66.667 35.65 22.07 46.23 5.03
236 237 2.575993 GAGCTTCTGCAGGAGCGA 59.424 61.111 35.65 4.79 46.23 4.93
237 238 1.079543 GAGCTTCTGCAGGAGCGAA 60.080 57.895 35.65 12.78 46.23 4.70
238 239 1.079266 AGCTTCTGCAGGAGCGAAG 60.079 57.895 35.65 21.75 45.48 3.79
239 240 1.375268 GCTTCTGCAGGAGCGAAGT 60.375 57.895 30.68 0.00 45.01 3.01
240 241 1.633852 GCTTCTGCAGGAGCGAAGTG 61.634 60.000 30.68 0.46 45.01 3.16
241 242 0.320247 CTTCTGCAGGAGCGAAGTGT 60.320 55.000 15.13 0.00 46.23 3.55
242 243 0.319900 TTCTGCAGGAGCGAAGTGTC 60.320 55.000 15.13 0.00 46.23 3.67
256 257 2.162716 GTGTCGTCCACATGAAGGC 58.837 57.895 0.00 0.00 43.92 4.35
257 258 1.003839 TGTCGTCCACATGAAGGCC 60.004 57.895 0.00 0.00 0.00 5.19
258 259 2.100631 GTCGTCCACATGAAGGCCG 61.101 63.158 0.00 2.55 0.00 6.13
259 260 3.499737 CGTCCACATGAAGGCCGC 61.500 66.667 0.00 0.00 0.00 6.53
260 261 2.045926 GTCCACATGAAGGCCGCT 60.046 61.111 0.00 0.00 0.00 5.52
261 262 2.109126 GTCCACATGAAGGCCGCTC 61.109 63.158 0.00 0.00 0.00 5.03
262 263 2.046023 CCACATGAAGGCCGCTCA 60.046 61.111 12.34 12.34 0.00 4.26
263 264 1.452651 CCACATGAAGGCCGCTCAT 60.453 57.895 15.46 15.46 33.73 2.90
264 265 1.442526 CCACATGAAGGCCGCTCATC 61.443 60.000 17.67 4.83 30.99 2.92
265 266 1.153086 ACATGAAGGCCGCTCATCC 60.153 57.895 17.67 0.00 30.99 3.51
266 267 1.153107 CATGAAGGCCGCTCATCCA 60.153 57.895 17.67 1.63 30.99 3.41
267 268 0.536687 CATGAAGGCCGCTCATCCAT 60.537 55.000 17.67 3.70 30.99 3.41
268 269 0.536687 ATGAAGGCCGCTCATCCATG 60.537 55.000 15.46 0.00 0.00 3.66
269 270 1.146930 GAAGGCCGCTCATCCATGA 59.853 57.895 0.00 0.00 35.16 3.07
270 271 0.464373 GAAGGCCGCTCATCCATGAA 60.464 55.000 0.00 0.00 36.18 2.57
271 272 0.749454 AAGGCCGCTCATCCATGAAC 60.749 55.000 0.00 0.00 36.18 3.18
272 273 2.189499 GGCCGCTCATCCATGAACC 61.189 63.158 0.00 0.00 36.18 3.62
273 274 1.451927 GCCGCTCATCCATGAACCA 60.452 57.895 0.00 0.00 36.18 3.67
274 275 0.820891 GCCGCTCATCCATGAACCAT 60.821 55.000 0.00 0.00 36.18 3.55
275 276 0.949397 CCGCTCATCCATGAACCATG 59.051 55.000 0.00 0.00 41.10 3.66
276 277 1.671979 CGCTCATCCATGAACCATGT 58.328 50.000 0.00 0.00 39.94 3.21
277 278 2.019249 CGCTCATCCATGAACCATGTT 58.981 47.619 0.00 0.00 39.94 2.71
278 279 3.205338 CGCTCATCCATGAACCATGTTA 58.795 45.455 0.00 0.00 39.94 2.41
279 280 3.817084 CGCTCATCCATGAACCATGTTAT 59.183 43.478 0.00 0.00 39.94 1.89
280 281 4.996758 CGCTCATCCATGAACCATGTTATA 59.003 41.667 0.00 0.00 39.94 0.98
281 282 5.645067 CGCTCATCCATGAACCATGTTATAT 59.355 40.000 0.00 0.00 39.94 0.86
282 283 6.183360 CGCTCATCCATGAACCATGTTATATC 60.183 42.308 0.00 0.00 39.94 1.63
283 284 6.183360 GCTCATCCATGAACCATGTTATATCG 60.183 42.308 0.00 0.00 39.94 2.92
284 285 6.768483 TCATCCATGAACCATGTTATATCGT 58.232 36.000 0.00 0.00 39.94 3.73
285 286 6.650390 TCATCCATGAACCATGTTATATCGTG 59.350 38.462 0.00 0.00 39.94 4.35
286 287 6.168270 TCCATGAACCATGTTATATCGTGA 57.832 37.500 0.00 0.00 39.94 4.35
287 288 6.768483 TCCATGAACCATGTTATATCGTGAT 58.232 36.000 0.00 0.00 39.94 3.06
288 289 6.873605 TCCATGAACCATGTTATATCGTGATC 59.126 38.462 0.00 4.11 39.94 2.92
289 290 6.650390 CCATGAACCATGTTATATCGTGATCA 59.350 38.462 0.00 0.00 39.94 2.92
290 291 7.335171 CCATGAACCATGTTATATCGTGATCAT 59.665 37.037 0.00 13.22 39.94 2.45
291 292 7.656707 TGAACCATGTTATATCGTGATCATG 57.343 36.000 8.74 8.74 34.41 3.07
294 295 4.333649 CCATGTTATATCGTGATCATGGGC 59.666 45.833 14.91 0.00 44.64 5.36
295 296 3.937814 TGTTATATCGTGATCATGGGCC 58.062 45.455 14.91 0.00 0.00 5.80
296 297 2.930040 GTTATATCGTGATCATGGGCCG 59.070 50.000 14.91 5.72 0.00 6.13
297 298 0.391661 ATATCGTGATCATGGGCCGC 60.392 55.000 14.91 0.00 0.00 6.53
298 299 1.753368 TATCGTGATCATGGGCCGCA 61.753 55.000 14.91 0.00 0.00 5.69
299 300 3.274586 CGTGATCATGGGCCGCAG 61.275 66.667 7.06 0.00 0.00 5.18
300 301 3.589881 GTGATCATGGGCCGCAGC 61.590 66.667 0.00 0.00 38.76 5.25
301 302 4.112433 TGATCATGGGCCGCAGCA 62.112 61.111 0.00 0.00 42.56 4.41
302 303 2.596631 GATCATGGGCCGCAGCAT 60.597 61.111 0.00 0.00 42.56 3.79
303 304 2.910479 ATCATGGGCCGCAGCATG 60.910 61.111 12.16 12.16 42.56 4.06
333 334 3.408389 CGTGAGCGTGACTCTCATT 57.592 52.632 8.65 0.00 46.41 2.57
334 335 1.702886 CGTGAGCGTGACTCTCATTT 58.297 50.000 8.65 0.00 46.41 2.32
335 336 1.651138 CGTGAGCGTGACTCTCATTTC 59.349 52.381 8.65 0.00 46.41 2.17
336 337 2.677199 GTGAGCGTGACTCTCATTTCA 58.323 47.619 8.65 0.00 46.41 2.69
337 338 2.410053 GTGAGCGTGACTCTCATTTCAC 59.590 50.000 8.65 0.00 46.41 3.18
338 339 2.035832 TGAGCGTGACTCTCATTTCACA 59.964 45.455 0.39 0.00 46.41 3.58
339 340 2.665537 GAGCGTGACTCTCATTTCACAG 59.334 50.000 0.00 0.00 41.98 3.66
340 341 1.127582 GCGTGACTCTCATTTCACAGC 59.872 52.381 2.90 3.47 41.98 4.40
341 342 2.407090 CGTGACTCTCATTTCACAGCA 58.593 47.619 2.90 0.00 41.98 4.41
342 343 2.802247 CGTGACTCTCATTTCACAGCAA 59.198 45.455 2.90 0.00 41.98 3.91
343 344 3.363378 CGTGACTCTCATTTCACAGCAAC 60.363 47.826 2.90 0.00 41.98 4.17
344 345 2.802247 TGACTCTCATTTCACAGCAACG 59.198 45.455 0.00 0.00 0.00 4.10
345 346 1.532868 ACTCTCATTTCACAGCAACGC 59.467 47.619 0.00 0.00 0.00 4.84
346 347 0.512518 TCTCATTTCACAGCAACGCG 59.487 50.000 3.53 3.53 0.00 6.01
347 348 0.512518 CTCATTTCACAGCAACGCGA 59.487 50.000 15.93 0.00 0.00 5.87
400 401 4.559862 AACAAAATCGAGATCTGACCCT 57.440 40.909 0.00 0.00 0.00 4.34
469 470 2.125269 GGCGGTAGGATTGCGTGT 60.125 61.111 0.00 0.00 0.00 4.49
509 510 1.302192 GGTAGGCACTTTGACGGCA 60.302 57.895 0.00 0.00 41.75 5.69
543 544 1.798735 CAGCCGCTGATGTGGAAAG 59.201 57.895 15.74 0.00 46.34 2.62
589 590 2.743553 GTAGGTTACTGGAGCCTACCA 58.256 52.381 19.26 0.00 45.38 3.25
673 674 0.764890 CCACCACCACTCTTCTTCCA 59.235 55.000 0.00 0.00 0.00 3.53
718 722 0.933700 CTCCTCTTCCCCCTCTCTCT 59.066 60.000 0.00 0.00 0.00 3.10
765 771 4.533311 ACTCCATTTGCTTGGGATTTCATT 59.467 37.500 1.84 0.00 37.37 2.57
766 772 5.721000 ACTCCATTTGCTTGGGATTTCATTA 59.279 36.000 1.84 0.00 37.37 1.90
964 970 2.507058 GTGTTAGGGTTAGGGTTAGGGG 59.493 54.545 0.00 0.00 0.00 4.79
969 975 2.115973 AGGGTTAGGGTTAGGGGTGTTA 59.884 50.000 0.00 0.00 0.00 2.41
1095 4350 3.208747 TCTTTGGACAAGGTGAAGGAC 57.791 47.619 0.00 0.00 0.00 3.85
1118 4373 1.876156 GGATGTGAAGATTCCGCCATC 59.124 52.381 0.00 0.00 0.00 3.51
1164 4419 1.117142 AGGAGTCCACCGACCGAAAA 61.117 55.000 12.86 0.00 40.12 2.29
1219 4474 4.669206 TGCCCCAATTATGCTTACAATG 57.331 40.909 0.00 0.00 0.00 2.82
1418 4673 2.235016 AGATTGTTTTAGGCGCCAACA 58.765 42.857 31.54 26.48 0.00 3.33
1485 4740 2.303022 TCAAAAAGAGAGGATGGAGCGT 59.697 45.455 0.00 0.00 0.00 5.07
1487 4742 3.810310 AAAAGAGAGGATGGAGCGTAG 57.190 47.619 0.00 0.00 0.00 3.51
1585 4840 1.210478 GCAAGGCACAAGAGGAGGATA 59.790 52.381 0.00 0.00 0.00 2.59
1792 5047 5.291614 GTGAAGATGTTTGCAATGTGTTGTT 59.708 36.000 0.00 0.00 37.65 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.616634 AGATCACCTAGCGACGACTA 57.383 50.000 0.00 0.00 0.00 2.59
4 5 0.235144 CCGTAGATCACCTAGCGACG 59.765 60.000 0.00 0.00 41.49 5.12
5 6 1.590932 TCCGTAGATCACCTAGCGAC 58.409 55.000 0.00 0.00 0.00 5.19
6 7 2.563261 ATCCGTAGATCACCTAGCGA 57.437 50.000 0.00 0.00 0.00 4.93
35 36 9.974980 ACAACGAACACCAGAAATAATAAAAAT 57.025 25.926 0.00 0.00 0.00 1.82
37 38 9.881529 GTACAACGAACACCAGAAATAATAAAA 57.118 29.630 0.00 0.00 0.00 1.52
38 39 9.275398 AGTACAACGAACACCAGAAATAATAAA 57.725 29.630 0.00 0.00 0.00 1.40
39 40 8.714179 CAGTACAACGAACACCAGAAATAATAA 58.286 33.333 0.00 0.00 0.00 1.40
40 41 7.148540 GCAGTACAACGAACACCAGAAATAATA 60.149 37.037 0.00 0.00 0.00 0.98
41 42 6.348213 GCAGTACAACGAACACCAGAAATAAT 60.348 38.462 0.00 0.00 0.00 1.28
42 43 5.049954 GCAGTACAACGAACACCAGAAATAA 60.050 40.000 0.00 0.00 0.00 1.40
43 44 4.449743 GCAGTACAACGAACACCAGAAATA 59.550 41.667 0.00 0.00 0.00 1.40
44 45 3.250040 GCAGTACAACGAACACCAGAAAT 59.750 43.478 0.00 0.00 0.00 2.17
45 46 2.610374 GCAGTACAACGAACACCAGAAA 59.390 45.455 0.00 0.00 0.00 2.52
46 47 2.206750 GCAGTACAACGAACACCAGAA 58.793 47.619 0.00 0.00 0.00 3.02
47 48 1.539496 GGCAGTACAACGAACACCAGA 60.539 52.381 0.00 0.00 0.00 3.86
48 49 0.865769 GGCAGTACAACGAACACCAG 59.134 55.000 0.00 0.00 0.00 4.00
49 50 0.178301 TGGCAGTACAACGAACACCA 59.822 50.000 0.00 0.00 0.00 4.17
50 51 1.519408 ATGGCAGTACAACGAACACC 58.481 50.000 0.00 0.00 0.00 4.16
51 52 4.939509 ATTATGGCAGTACAACGAACAC 57.060 40.909 0.00 0.00 0.00 3.32
52 53 4.998033 TCAATTATGGCAGTACAACGAACA 59.002 37.500 0.00 0.00 0.00 3.18
53 54 5.539582 TCAATTATGGCAGTACAACGAAC 57.460 39.130 0.00 0.00 0.00 3.95
54 55 5.935206 TCTTCAATTATGGCAGTACAACGAA 59.065 36.000 0.00 0.00 0.00 3.85
55 56 5.483811 TCTTCAATTATGGCAGTACAACGA 58.516 37.500 0.00 0.00 0.00 3.85
56 57 5.794687 TCTTCAATTATGGCAGTACAACG 57.205 39.130 0.00 0.00 0.00 4.10
57 58 7.377766 TCTTCTTCAATTATGGCAGTACAAC 57.622 36.000 0.00 0.00 0.00 3.32
58 59 7.994425 TTCTTCTTCAATTATGGCAGTACAA 57.006 32.000 0.00 0.00 0.00 2.41
59 60 9.330063 CTATTCTTCTTCAATTATGGCAGTACA 57.670 33.333 0.00 0.00 0.00 2.90
60 61 9.547753 TCTATTCTTCTTCAATTATGGCAGTAC 57.452 33.333 0.00 0.00 0.00 2.73
62 63 9.282569 GATCTATTCTTCTTCAATTATGGCAGT 57.717 33.333 0.00 0.00 0.00 4.40
63 64 8.441608 CGATCTATTCTTCTTCAATTATGGCAG 58.558 37.037 0.00 0.00 0.00 4.85
64 65 7.388776 CCGATCTATTCTTCTTCAATTATGGCA 59.611 37.037 0.00 0.00 0.00 4.92
65 66 7.604164 TCCGATCTATTCTTCTTCAATTATGGC 59.396 37.037 0.00 0.00 0.00 4.40
66 67 9.494271 TTCCGATCTATTCTTCTTCAATTATGG 57.506 33.333 0.00 0.00 0.00 2.74
70 71 9.454859 AAACTTCCGATCTATTCTTCTTCAATT 57.545 29.630 0.00 0.00 0.00 2.32
71 72 9.454859 AAAACTTCCGATCTATTCTTCTTCAAT 57.545 29.630 0.00 0.00 0.00 2.57
72 73 8.848474 AAAACTTCCGATCTATTCTTCTTCAA 57.152 30.769 0.00 0.00 0.00 2.69
73 74 8.314751 AGAAAACTTCCGATCTATTCTTCTTCA 58.685 33.333 0.00 0.00 0.00 3.02
74 75 8.710835 AGAAAACTTCCGATCTATTCTTCTTC 57.289 34.615 0.00 0.00 0.00 2.87
75 76 8.940952 CAAGAAAACTTCCGATCTATTCTTCTT 58.059 33.333 0.00 0.00 34.43 2.52
76 77 7.065204 GCAAGAAAACTTCCGATCTATTCTTCT 59.935 37.037 0.00 0.00 34.43 2.85
77 78 7.148407 TGCAAGAAAACTTCCGATCTATTCTTC 60.148 37.037 0.00 0.00 34.43 2.87
78 79 6.655003 TGCAAGAAAACTTCCGATCTATTCTT 59.345 34.615 0.00 0.00 36.41 2.52
79 80 6.173339 TGCAAGAAAACTTCCGATCTATTCT 58.827 36.000 0.00 0.00 0.00 2.40
80 81 6.422776 TGCAAGAAAACTTCCGATCTATTC 57.577 37.500 0.00 0.00 0.00 1.75
81 82 6.817765 TTGCAAGAAAACTTCCGATCTATT 57.182 33.333 0.00 0.00 0.00 1.73
82 83 6.817765 TTTGCAAGAAAACTTCCGATCTAT 57.182 33.333 0.00 0.00 0.00 1.98
83 84 6.627395 TTTTGCAAGAAAACTTCCGATCTA 57.373 33.333 0.00 0.00 0.00 1.98
84 85 5.514274 TTTTGCAAGAAAACTTCCGATCT 57.486 34.783 0.00 0.00 0.00 2.75
106 107 6.515696 GCAAGAGAATGCCTTGTACTCTTTTT 60.516 38.462 0.00 0.00 43.17 1.94
107 108 5.048434 GCAAGAGAATGCCTTGTACTCTTTT 60.048 40.000 0.00 0.00 43.17 2.27
108 109 4.457257 GCAAGAGAATGCCTTGTACTCTTT 59.543 41.667 0.00 0.00 43.17 2.52
109 110 4.006319 GCAAGAGAATGCCTTGTACTCTT 58.994 43.478 0.00 0.00 44.99 2.85
110 111 3.604582 GCAAGAGAATGCCTTGTACTCT 58.395 45.455 0.00 0.00 42.11 3.24
120 121 0.248784 GGCGATTGGCAAGAGAATGC 60.249 55.000 5.96 3.06 46.16 3.56
121 122 3.932459 GGCGATTGGCAAGAGAATG 57.068 52.632 5.96 0.00 46.16 2.67
137 138 2.472909 GCAGGGTTCTACGCATGGC 61.473 63.158 0.00 0.00 32.95 4.40
138 139 1.819632 GGCAGGGTTCTACGCATGG 60.820 63.158 0.00 0.00 32.95 3.66
139 140 2.173669 CGGCAGGGTTCTACGCATG 61.174 63.158 0.00 0.00 32.95 4.06
140 141 2.186903 CGGCAGGGTTCTACGCAT 59.813 61.111 0.00 0.00 32.95 4.73
141 142 4.077184 CCGGCAGGGTTCTACGCA 62.077 66.667 0.00 0.00 32.95 5.24
142 143 2.791501 TTTCCGGCAGGGTTCTACGC 62.792 60.000 2.05 0.00 38.33 4.42
143 144 0.320946 TTTTCCGGCAGGGTTCTACG 60.321 55.000 2.05 0.00 38.33 3.51
144 145 1.900245 TTTTTCCGGCAGGGTTCTAC 58.100 50.000 2.05 0.00 38.33 2.59
161 162 2.099098 CCGTGACTGCAGGTTTCTTTTT 59.901 45.455 19.93 0.00 0.00 1.94
162 163 1.676006 CCGTGACTGCAGGTTTCTTTT 59.324 47.619 19.93 0.00 0.00 2.27
163 164 1.308998 CCGTGACTGCAGGTTTCTTT 58.691 50.000 19.93 0.00 0.00 2.52
164 165 1.166531 GCCGTGACTGCAGGTTTCTT 61.167 55.000 19.93 0.00 0.00 2.52
165 166 1.598130 GCCGTGACTGCAGGTTTCT 60.598 57.895 19.93 0.00 0.00 2.52
166 167 2.946762 GCCGTGACTGCAGGTTTC 59.053 61.111 19.93 7.30 0.00 2.78
167 168 2.972505 CGCCGTGACTGCAGGTTT 60.973 61.111 19.93 0.00 0.00 3.27
168 169 4.988598 CCGCCGTGACTGCAGGTT 62.989 66.667 19.93 0.00 0.00 3.50
170 171 4.457496 ATCCGCCGTGACTGCAGG 62.457 66.667 19.93 0.79 0.00 4.85
171 172 2.887568 GATCCGCCGTGACTGCAG 60.888 66.667 13.48 13.48 0.00 4.41
172 173 4.451150 GGATCCGCCGTGACTGCA 62.451 66.667 0.00 0.00 0.00 4.41
204 205 4.963428 CTCGGCGGGGCGTATTCC 62.963 72.222 14.35 0.00 0.00 3.01
215 216 4.441695 TCCTGCAGAAGCTCGGCG 62.442 66.667 17.39 0.00 40.49 6.46
216 217 2.511145 CTCCTGCAGAAGCTCGGC 60.511 66.667 17.39 0.00 42.74 5.54
217 218 2.511145 GCTCCTGCAGAAGCTCGG 60.511 66.667 18.89 0.00 42.74 4.63
218 219 2.825726 TTCGCTCCTGCAGAAGCTCG 62.826 60.000 23.32 8.48 42.74 5.03
219 220 1.079543 TTCGCTCCTGCAGAAGCTC 60.080 57.895 23.32 0.00 42.74 4.09
220 221 1.079266 CTTCGCTCCTGCAGAAGCT 60.079 57.895 23.32 0.00 40.17 3.74
221 222 1.375268 ACTTCGCTCCTGCAGAAGC 60.375 57.895 16.04 16.04 44.95 3.86
222 223 0.320247 ACACTTCGCTCCTGCAGAAG 60.320 55.000 17.39 13.07 45.69 2.85
223 224 0.319900 GACACTTCGCTCCTGCAGAA 60.320 55.000 17.39 0.00 39.64 3.02
224 225 1.290324 GACACTTCGCTCCTGCAGA 59.710 57.895 17.39 0.00 39.64 4.26
225 226 2.091112 CGACACTTCGCTCCTGCAG 61.091 63.158 6.78 6.78 38.71 4.41
226 227 2.049156 CGACACTTCGCTCCTGCA 60.049 61.111 0.00 0.00 38.71 4.41
239 240 1.003839 GGCCTTCATGTGGACGACA 60.004 57.895 10.79 0.00 39.53 4.35
240 241 3.890674 GGCCTTCATGTGGACGAC 58.109 61.111 10.79 0.00 0.00 4.34
243 244 2.045926 AGCGGCCTTCATGTGGAC 60.046 61.111 0.00 7.35 0.00 4.02
244 245 1.913951 ATGAGCGGCCTTCATGTGGA 61.914 55.000 16.26 0.00 34.14 4.02
245 246 1.442526 GATGAGCGGCCTTCATGTGG 61.443 60.000 20.48 0.00 35.50 4.17
246 247 1.442526 GGATGAGCGGCCTTCATGTG 61.443 60.000 20.48 0.00 35.50 3.21
247 248 1.153086 GGATGAGCGGCCTTCATGT 60.153 57.895 20.48 2.75 35.50 3.21
248 249 0.536687 ATGGATGAGCGGCCTTCATG 60.537 55.000 20.48 0.00 35.50 3.07
249 250 0.536687 CATGGATGAGCGGCCTTCAT 60.537 55.000 16.79 16.79 37.96 2.57
250 251 1.153107 CATGGATGAGCGGCCTTCA 60.153 57.895 8.99 8.99 0.00 3.02
251 252 0.464373 TTCATGGATGAGCGGCCTTC 60.464 55.000 0.00 0.00 38.19 3.46
252 253 0.749454 GTTCATGGATGAGCGGCCTT 60.749 55.000 0.00 0.00 38.19 4.35
253 254 1.153086 GTTCATGGATGAGCGGCCT 60.153 57.895 0.00 0.00 38.19 5.19
254 255 2.189499 GGTTCATGGATGAGCGGCC 61.189 63.158 0.00 0.00 38.69 6.13
255 256 0.820891 ATGGTTCATGGATGAGCGGC 60.821 55.000 0.00 0.00 38.69 6.53
256 257 0.949397 CATGGTTCATGGATGAGCGG 59.051 55.000 0.00 0.00 38.69 5.52
257 258 1.671979 ACATGGTTCATGGATGAGCG 58.328 50.000 11.85 0.00 45.16 5.03
258 259 6.183360 CGATATAACATGGTTCATGGATGAGC 60.183 42.308 11.85 0.00 45.16 4.26
259 260 6.875726 ACGATATAACATGGTTCATGGATGAG 59.124 38.462 11.85 4.74 45.16 2.90
260 261 6.650390 CACGATATAACATGGTTCATGGATGA 59.350 38.462 11.85 0.00 45.16 2.92
261 262 6.650390 TCACGATATAACATGGTTCATGGATG 59.350 38.462 11.85 0.00 45.16 3.51
262 263 6.768483 TCACGATATAACATGGTTCATGGAT 58.232 36.000 11.85 7.51 45.16 3.41
263 264 6.168270 TCACGATATAACATGGTTCATGGA 57.832 37.500 11.85 1.09 45.16 3.41
264 265 6.650390 TGATCACGATATAACATGGTTCATGG 59.350 38.462 11.85 0.00 45.16 3.66
265 266 7.656707 TGATCACGATATAACATGGTTCATG 57.343 36.000 6.37 6.37 46.18 3.07
266 267 7.335171 CCATGATCACGATATAACATGGTTCAT 59.665 37.037 0.00 0.00 45.23 2.57
267 268 6.650390 CCATGATCACGATATAACATGGTTCA 59.350 38.462 0.00 0.00 45.23 3.18
268 269 7.065216 CCATGATCACGATATAACATGGTTC 57.935 40.000 0.00 0.00 45.23 3.62
272 273 4.333649 GGCCCATGATCACGATATAACATG 59.666 45.833 0.00 0.00 36.10 3.21
273 274 4.517285 GGCCCATGATCACGATATAACAT 58.483 43.478 0.00 0.00 0.00 2.71
274 275 3.616317 CGGCCCATGATCACGATATAACA 60.616 47.826 0.00 0.00 0.00 2.41
275 276 2.930040 CGGCCCATGATCACGATATAAC 59.070 50.000 0.00 0.00 0.00 1.89
276 277 2.676750 GCGGCCCATGATCACGATATAA 60.677 50.000 0.00 0.00 0.00 0.98
277 278 1.134818 GCGGCCCATGATCACGATATA 60.135 52.381 0.00 0.00 0.00 0.86
278 279 0.391661 GCGGCCCATGATCACGATAT 60.392 55.000 0.00 0.00 0.00 1.63
279 280 1.005037 GCGGCCCATGATCACGATA 60.005 57.895 0.00 0.00 0.00 2.92
280 281 2.281070 GCGGCCCATGATCACGAT 60.281 61.111 0.00 0.00 0.00 3.73
281 282 3.738429 CTGCGGCCCATGATCACGA 62.738 63.158 0.00 0.00 0.00 4.35
282 283 3.274586 CTGCGGCCCATGATCACG 61.275 66.667 0.00 0.00 0.00 4.35
283 284 3.589881 GCTGCGGCCCATGATCAC 61.590 66.667 6.12 0.00 0.00 3.06
284 285 3.424780 ATGCTGCGGCCCATGATCA 62.425 57.895 16.57 0.00 37.74 2.92
285 286 2.596631 ATGCTGCGGCCCATGATC 60.597 61.111 16.57 0.00 37.74 2.92
286 287 2.910479 CATGCTGCGGCCCATGAT 60.910 61.111 16.57 0.00 40.92 2.45
296 297 3.015799 CATATCATGCGCATGCTGC 57.984 52.632 39.11 22.12 43.34 5.25
306 307 1.190984 GTCACGCTCACGCATATCATG 59.809 52.381 0.00 0.00 45.53 3.07
307 308 1.067669 AGTCACGCTCACGCATATCAT 59.932 47.619 0.00 0.00 45.53 2.45
308 309 0.455815 AGTCACGCTCACGCATATCA 59.544 50.000 0.00 0.00 45.53 2.15
309 310 1.124462 GAGTCACGCTCACGCATATC 58.876 55.000 0.00 0.00 45.53 1.63
310 311 0.741326 AGAGTCACGCTCACGCATAT 59.259 50.000 0.00 0.00 46.47 1.78
311 312 0.098905 GAGAGTCACGCTCACGCATA 59.901 55.000 3.27 0.00 46.47 3.14
312 313 1.153939 GAGAGTCACGCTCACGCAT 60.154 57.895 3.27 0.00 46.47 4.73
313 314 1.866853 ATGAGAGTCACGCTCACGCA 61.867 55.000 14.05 0.00 42.43 5.24
314 315 0.734253 AATGAGAGTCACGCTCACGC 60.734 55.000 14.05 0.00 42.43 5.34
315 316 1.651138 GAAATGAGAGTCACGCTCACG 59.349 52.381 14.05 0.00 42.43 4.35
316 317 2.410053 GTGAAATGAGAGTCACGCTCAC 59.590 50.000 14.05 2.04 42.43 3.51
317 318 2.035832 TGTGAAATGAGAGTCACGCTCA 59.964 45.455 14.12 14.12 45.83 4.26
318 319 2.665537 CTGTGAAATGAGAGTCACGCTC 59.334 50.000 0.76 0.76 45.83 5.03
319 320 2.681706 CTGTGAAATGAGAGTCACGCT 58.318 47.619 0.00 0.00 45.83 5.07
320 321 1.127582 GCTGTGAAATGAGAGTCACGC 59.872 52.381 0.00 0.00 45.83 5.34
321 322 2.407090 TGCTGTGAAATGAGAGTCACG 58.593 47.619 0.00 0.00 45.83 4.35
322 323 3.363378 CGTTGCTGTGAAATGAGAGTCAC 60.363 47.826 0.00 0.00 43.66 3.67
323 324 2.802247 CGTTGCTGTGAAATGAGAGTCA 59.198 45.455 0.00 0.00 0.00 3.41
324 325 2.412065 GCGTTGCTGTGAAATGAGAGTC 60.412 50.000 0.00 0.00 0.00 3.36
325 326 1.532868 GCGTTGCTGTGAAATGAGAGT 59.467 47.619 0.00 0.00 0.00 3.24
326 327 1.463034 CGCGTTGCTGTGAAATGAGAG 60.463 52.381 0.00 0.00 0.00 3.20
327 328 0.512518 CGCGTTGCTGTGAAATGAGA 59.487 50.000 0.00 0.00 0.00 3.27
328 329 0.512518 TCGCGTTGCTGTGAAATGAG 59.487 50.000 5.77 0.00 0.00 2.90
329 330 0.512518 CTCGCGTTGCTGTGAAATGA 59.487 50.000 5.77 0.00 0.00 2.57
330 331 0.453282 CCTCGCGTTGCTGTGAAATG 60.453 55.000 5.77 0.00 0.00 2.32
331 332 1.868997 CCTCGCGTTGCTGTGAAAT 59.131 52.632 5.77 0.00 0.00 2.17
332 333 2.892334 GCCTCGCGTTGCTGTGAAA 61.892 57.895 5.77 0.00 0.00 2.69
333 334 3.345808 GCCTCGCGTTGCTGTGAA 61.346 61.111 5.77 0.00 0.00 3.18
336 337 4.927782 TTGGCCTCGCGTTGCTGT 62.928 61.111 18.86 0.00 0.00 4.40
337 338 2.476534 AATTTGGCCTCGCGTTGCTG 62.477 55.000 18.86 1.53 0.00 4.41
338 339 1.805428 AAATTTGGCCTCGCGTTGCT 61.805 50.000 18.86 0.53 0.00 3.91
339 340 1.344226 GAAATTTGGCCTCGCGTTGC 61.344 55.000 5.77 10.22 0.00 4.17
340 341 1.065031 CGAAATTTGGCCTCGCGTTG 61.065 55.000 5.77 0.00 0.00 4.10
341 342 1.209127 CGAAATTTGGCCTCGCGTT 59.791 52.632 5.77 0.00 0.00 4.84
342 343 1.964373 ACGAAATTTGGCCTCGCGT 60.964 52.632 5.77 6.11 36.03 6.01
343 344 1.511887 CACGAAATTTGGCCTCGCG 60.512 57.895 10.94 0.00 36.03 5.87
344 345 0.039527 AACACGAAATTTGGCCTCGC 60.040 50.000 10.94 0.00 36.03 5.03
345 346 2.415697 AAACACGAAATTTGGCCTCG 57.584 45.000 3.32 7.10 38.53 4.63
346 347 3.489416 GTCAAAACACGAAATTTGGCCTC 59.511 43.478 3.32 0.00 35.62 4.70
347 348 3.453424 GTCAAAACACGAAATTTGGCCT 58.547 40.909 3.32 0.00 35.62 5.19
389 390 3.383698 TTCCGAACTAGGGTCAGATCT 57.616 47.619 0.00 0.00 0.00 2.75
424 425 1.605451 GGCGGTAGGCAAAAGGGTT 60.605 57.895 0.00 0.00 46.16 4.11
469 470 0.892358 CGTAGGCTATGGCGGTAGGA 60.892 60.000 5.81 0.00 39.81 2.94
498 499 1.157870 CCGTCAGTTGCCGTCAAAGT 61.158 55.000 0.00 0.00 33.37 2.66
535 536 2.598787 CGGTAGGCCCCTTTCCACA 61.599 63.158 0.00 0.00 0.00 4.17
589 590 0.759436 CTACCGCCAGAGGGTATGGT 60.759 60.000 0.00 0.00 39.22 3.55
673 674 1.276421 CACGGGGAAGAAGATGAGTGT 59.724 52.381 0.00 0.00 0.00 3.55
765 771 2.503765 TGAAAATGCTCCGGATCCACTA 59.496 45.455 13.41 0.00 0.00 2.74
766 772 1.281867 TGAAAATGCTCCGGATCCACT 59.718 47.619 13.41 0.00 0.00 4.00
969 975 8.706322 ACAACAAATAAAGATGTTAAGTCCCT 57.294 30.769 0.00 0.00 37.66 4.20
1095 4350 1.672881 GGCGGAATCTTCACATCCTTG 59.327 52.381 0.00 0.00 0.00 3.61
1118 4373 1.955778 TGCAAACATCTCCACACCAAG 59.044 47.619 0.00 0.00 0.00 3.61
1164 4419 2.290323 CCTTCCTTCGGTCCATGACTTT 60.290 50.000 0.00 0.00 32.47 2.66
1219 4474 1.495951 CGTTAGTTGGAAGCGCACC 59.504 57.895 11.47 13.74 0.00 5.01
1418 4673 3.541632 TGAAACCTTTCTTCGAACAGCT 58.458 40.909 0.00 0.00 38.02 4.24
1485 4740 2.361992 TCCTCCTCGCGTTGCCTA 60.362 61.111 5.77 0.00 0.00 3.93
1487 4742 3.708220 CTCTCCTCCTCGCGTTGCC 62.708 68.421 5.77 0.00 0.00 4.52
1585 4840 1.071471 CCTTCCTGTCACGTGCCTT 59.929 57.895 11.67 0.00 0.00 4.35
1850 5105 3.068590 CCCACTTTTCTTCACAGCACAAT 59.931 43.478 0.00 0.00 0.00 2.71
1960 5215 4.569180 CCCCCTACCGCCATGCAG 62.569 72.222 0.00 0.00 0.00 4.41


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

AutoCloner maintained by Alex Coulton.