Multiple sequence alignment - TraesCS5B01G476900

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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 TraesCS5B01G476900 chr5B 100.000 3524 0 0 1 3524 649400488 649404011 0.000000e+00 6508.0
1 TraesCS5B01G476900 chr5D 92.491 2304 142 22 825 3120 516815998 516818278 0.000000e+00 3267.0
2 TraesCS5B01G476900 chr5D 95.025 402 16 1 3113 3510 516818213 516818614 2.310000e-176 628.0
3 TraesCS5B01G476900 chr5D 91.549 355 25 4 267 616 516815442 516815796 5.290000e-133 484.0
4 TraesCS5B01G476900 chr5A 92.266 1849 121 14 1674 3520 644134064 644135892 0.000000e+00 2603.0
5 TraesCS5B01G476900 chr5A 84.966 725 60 25 215 902 644132433 644133145 0.000000e+00 689.0
6 TraesCS5B01G476900 chr5A 82.609 115 11 8 889 996 644133165 644133277 3.750000e-15 93.5
7 TraesCS5B01G476900 chr5A 94.915 59 3 0 3113 3171 644135434 644135492 3.750000e-15 93.5
8 TraesCS5B01G476900 chr1B 87.766 1267 120 26 1958 3216 34730809 34729570 0.000000e+00 1448.0
9 TraesCS5B01G476900 chr1B 86.508 252 34 0 1715 1966 34731588 34731337 9.630000e-71 278.0
10 TraesCS5B01G476900 chr1B 83.774 265 36 2 3161 3425 34729574 34729317 9.770000e-61 244.0
11 TraesCS5B01G476900 chr1B 76.344 465 69 25 1327 1764 97812022 97811572 9.910000e-51 211.0
12 TraesCS5B01G476900 chr1B 88.542 96 11 0 3420 3515 34727984 34727889 2.220000e-22 117.0


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 TraesCS5B01G476900 chr5B 649400488 649404011 3523 False 6508.000000 6508 100.000000 1 3524 1 chr5B.!!$F1 3523
1 TraesCS5B01G476900 chr5D 516815442 516818614 3172 False 1459.666667 3267 93.021667 267 3510 3 chr5D.!!$F1 3243
2 TraesCS5B01G476900 chr5A 644132433 644135892 3459 False 869.750000 2603 88.689000 215 3520 4 chr5A.!!$F1 3305
3 TraesCS5B01G476900 chr1B 34727889 34731588 3699 True 521.750000 1448 86.647500 1715 3515 4 chr1B.!!$R2 1800

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
195 196 0.043053 CGCATAATTCACAGCGTCCG 60.043 55.0 0.0 0.0 44.67 4.79 F
754 810 0.107643 GGCTCTTCCCACTATCTGGC 59.892 60.0 0.0 0.0 39.01 4.85 F
1479 1804 0.248377 GAAATGCCGATGCTCTGTGC 60.248 55.0 0.0 0.0 43.25 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1251 1548 0.102844 GAGCAGAGCAGAGAAGCGAT 59.897 55.0 0.00 0.0 40.15 4.58 R
1905 2242 0.105039 GGCTTATGTCCTCCTCCACG 59.895 60.0 0.00 0.0 0.00 4.94 R
3210 4149 0.163788 GTTGACGACAACGCAGATGG 59.836 55.0 14.57 0.0 45.06 3.51 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
36 37 9.214957 TGTTTGTCATACTTTATAGAACTGTGG 57.785 33.333 0.00 0.00 0.00 4.17
37 38 7.843490 TTGTCATACTTTATAGAACTGTGGC 57.157 36.000 0.00 0.00 0.00 5.01
38 39 6.346096 TGTCATACTTTATAGAACTGTGGCC 58.654 40.000 0.00 0.00 0.00 5.36
39 40 6.156256 TGTCATACTTTATAGAACTGTGGCCT 59.844 38.462 3.32 0.00 0.00 5.19
40 41 7.048512 GTCATACTTTATAGAACTGTGGCCTT 58.951 38.462 3.32 0.00 0.00 4.35
41 42 7.553044 GTCATACTTTATAGAACTGTGGCCTTT 59.447 37.037 3.32 0.00 0.00 3.11
42 43 8.107095 TCATACTTTATAGAACTGTGGCCTTTT 58.893 33.333 3.32 0.00 0.00 2.27
43 44 8.739972 CATACTTTATAGAACTGTGGCCTTTTT 58.260 33.333 3.32 0.00 0.00 1.94
66 67 9.720769 TTTTTAGTAAAATTCGATGAGGAGTCT 57.279 29.630 8.84 0.00 0.00 3.24
67 68 8.928270 TTTAGTAAAATTCGATGAGGAGTCTC 57.072 34.615 0.00 0.00 40.36 3.36
68 69 5.583495 AGTAAAATTCGATGAGGAGTCTCG 58.417 41.667 0.00 0.00 42.79 4.04
69 70 4.457834 AAAATTCGATGAGGAGTCTCGT 57.542 40.909 0.00 0.00 42.79 4.18
70 71 4.457834 AAATTCGATGAGGAGTCTCGTT 57.542 40.909 0.00 0.00 42.79 3.85
71 72 2.921634 TTCGATGAGGAGTCTCGTTG 57.078 50.000 0.00 0.00 42.79 4.10
72 73 1.822506 TCGATGAGGAGTCTCGTTGT 58.177 50.000 0.00 0.00 42.79 3.32
73 74 2.160205 TCGATGAGGAGTCTCGTTGTT 58.840 47.619 0.00 0.00 42.79 2.83
74 75 2.557056 TCGATGAGGAGTCTCGTTGTTT 59.443 45.455 0.00 0.00 42.79 2.83
75 76 3.754850 TCGATGAGGAGTCTCGTTGTTTA 59.245 43.478 0.00 0.00 42.79 2.01
76 77 4.216902 TCGATGAGGAGTCTCGTTGTTTAA 59.783 41.667 0.00 0.00 42.79 1.52
77 78 5.103000 CGATGAGGAGTCTCGTTGTTTAAT 58.897 41.667 0.00 0.00 42.79 1.40
78 79 5.230306 CGATGAGGAGTCTCGTTGTTTAATC 59.770 44.000 0.00 0.00 42.79 1.75
79 80 5.723672 TGAGGAGTCTCGTTGTTTAATCT 57.276 39.130 0.00 0.00 42.79 2.40
80 81 6.097915 TGAGGAGTCTCGTTGTTTAATCTT 57.902 37.500 0.00 0.00 42.79 2.40
81 82 6.522054 TGAGGAGTCTCGTTGTTTAATCTTT 58.478 36.000 0.00 0.00 42.79 2.52
82 83 6.990349 TGAGGAGTCTCGTTGTTTAATCTTTT 59.010 34.615 0.00 0.00 42.79 2.27
83 84 7.497909 TGAGGAGTCTCGTTGTTTAATCTTTTT 59.502 33.333 0.00 0.00 42.79 1.94
84 85 7.639945 AGGAGTCTCGTTGTTTAATCTTTTTG 58.360 34.615 0.00 0.00 0.00 2.44
85 86 7.282450 AGGAGTCTCGTTGTTTAATCTTTTTGT 59.718 33.333 0.00 0.00 0.00 2.83
86 87 7.586664 GGAGTCTCGTTGTTTAATCTTTTTGTC 59.413 37.037 0.00 0.00 0.00 3.18
87 88 7.981142 AGTCTCGTTGTTTAATCTTTTTGTCA 58.019 30.769 0.00 0.00 0.00 3.58
88 89 8.122952 AGTCTCGTTGTTTAATCTTTTTGTCAG 58.877 33.333 0.00 0.00 0.00 3.51
89 90 6.910433 TCTCGTTGTTTAATCTTTTTGTCAGC 59.090 34.615 0.00 0.00 0.00 4.26
90 91 6.791303 TCGTTGTTTAATCTTTTTGTCAGCT 58.209 32.000 0.00 0.00 0.00 4.24
91 92 7.921787 TCGTTGTTTAATCTTTTTGTCAGCTA 58.078 30.769 0.00 0.00 0.00 3.32
92 93 8.399425 TCGTTGTTTAATCTTTTTGTCAGCTAA 58.601 29.630 0.00 0.00 0.00 3.09
93 94 9.015577 CGTTGTTTAATCTTTTTGTCAGCTAAA 57.984 29.630 0.00 0.00 0.00 1.85
95 96 8.865590 TGTTTAATCTTTTTGTCAGCTAAACC 57.134 30.769 0.00 0.00 30.53 3.27
96 97 8.470805 TGTTTAATCTTTTTGTCAGCTAAACCA 58.529 29.630 0.00 0.00 30.53 3.67
97 98 9.308318 GTTTAATCTTTTTGTCAGCTAAACCAA 57.692 29.630 0.00 0.00 0.00 3.67
102 103 9.643693 ATCTTTTTGTCAGCTAAACCAATAATG 57.356 29.630 0.00 0.00 0.00 1.90
103 104 8.637986 TCTTTTTGTCAGCTAAACCAATAATGT 58.362 29.630 0.00 0.00 0.00 2.71
104 105 9.906660 CTTTTTGTCAGCTAAACCAATAATGTA 57.093 29.630 0.00 0.00 0.00 2.29
105 106 9.685828 TTTTTGTCAGCTAAACCAATAATGTAC 57.314 29.630 0.00 0.00 0.00 2.90
106 107 6.656314 TGTCAGCTAAACCAATAATGTACG 57.344 37.500 0.00 0.00 0.00 3.67
107 108 6.399743 TGTCAGCTAAACCAATAATGTACGA 58.600 36.000 0.00 0.00 0.00 3.43
108 109 6.533723 TGTCAGCTAAACCAATAATGTACGAG 59.466 38.462 0.00 0.00 0.00 4.18
109 110 5.522460 TCAGCTAAACCAATAATGTACGAGC 59.478 40.000 0.00 0.00 0.00 5.03
110 111 4.814771 AGCTAAACCAATAATGTACGAGCC 59.185 41.667 0.00 0.00 0.00 4.70
111 112 4.573201 GCTAAACCAATAATGTACGAGCCA 59.427 41.667 0.00 0.00 0.00 4.75
112 113 4.957759 AAACCAATAATGTACGAGCCAC 57.042 40.909 0.00 0.00 0.00 5.01
113 114 3.620427 ACCAATAATGTACGAGCCACA 57.380 42.857 0.00 0.00 0.00 4.17
114 115 4.150897 ACCAATAATGTACGAGCCACAT 57.849 40.909 0.00 0.00 38.25 3.21
115 116 3.876914 ACCAATAATGTACGAGCCACATG 59.123 43.478 0.00 0.00 36.74 3.21
116 117 3.876914 CCAATAATGTACGAGCCACATGT 59.123 43.478 0.00 0.00 36.74 3.21
117 118 4.024893 CCAATAATGTACGAGCCACATGTC 60.025 45.833 0.00 0.00 36.74 3.06
118 119 2.760634 AATGTACGAGCCACATGTCA 57.239 45.000 0.00 0.00 36.74 3.58
119 120 2.988010 ATGTACGAGCCACATGTCAT 57.012 45.000 0.00 0.00 35.33 3.06
120 121 4.400529 AATGTACGAGCCACATGTCATA 57.599 40.909 0.00 0.00 36.74 2.15
121 122 3.436700 TGTACGAGCCACATGTCATAG 57.563 47.619 0.00 0.00 0.00 2.23
122 123 3.020984 TGTACGAGCCACATGTCATAGA 58.979 45.455 0.00 0.00 0.00 1.98
123 124 3.445805 TGTACGAGCCACATGTCATAGAA 59.554 43.478 0.00 0.00 0.00 2.10
124 125 3.170791 ACGAGCCACATGTCATAGAAG 57.829 47.619 0.00 0.00 0.00 2.85
125 126 1.863454 CGAGCCACATGTCATAGAAGC 59.137 52.381 0.00 0.00 0.00 3.86
126 127 2.482664 CGAGCCACATGTCATAGAAGCT 60.483 50.000 0.00 0.00 0.00 3.74
127 128 3.243535 CGAGCCACATGTCATAGAAGCTA 60.244 47.826 0.00 0.00 0.00 3.32
128 129 4.560311 CGAGCCACATGTCATAGAAGCTAT 60.560 45.833 0.00 0.00 0.00 2.97
129 130 5.335976 CGAGCCACATGTCATAGAAGCTATA 60.336 44.000 0.00 0.00 0.00 1.31
130 131 5.788450 AGCCACATGTCATAGAAGCTATAC 58.212 41.667 0.00 0.00 0.00 1.47
131 132 5.305386 AGCCACATGTCATAGAAGCTATACA 59.695 40.000 0.00 0.00 0.00 2.29
132 133 6.013898 AGCCACATGTCATAGAAGCTATACAT 60.014 38.462 0.00 0.00 0.00 2.29
133 134 6.652481 GCCACATGTCATAGAAGCTATACATT 59.348 38.462 0.00 0.00 0.00 2.71
134 135 7.173907 GCCACATGTCATAGAAGCTATACATTT 59.826 37.037 0.00 0.00 0.00 2.32
135 136 8.501580 CCACATGTCATAGAAGCTATACATTTG 58.498 37.037 0.00 0.00 0.00 2.32
136 137 9.264719 CACATGTCATAGAAGCTATACATTTGA 57.735 33.333 0.00 0.00 30.40 2.69
137 138 9.836864 ACATGTCATAGAAGCTATACATTTGAA 57.163 29.630 0.00 0.00 0.00 2.69
173 174 8.997621 ACTATGTATTCGACACTACAATTTGT 57.002 30.769 7.30 7.30 42.17 2.83
174 175 8.869897 ACTATGTATTCGACACTACAATTTGTG 58.130 33.333 12.30 5.10 42.17 3.33
175 176 7.899178 ATGTATTCGACACTACAATTTGTGA 57.101 32.000 12.30 0.00 42.17 3.58
176 177 7.112528 TGTATTCGACACTACAATTTGTGAC 57.887 36.000 12.30 3.72 37.59 3.67
178 179 2.473609 TCGACACTACAATTTGTGACGC 59.526 45.455 12.30 0.00 45.96 5.19
179 180 2.219903 CGACACTACAATTTGTGACGCA 59.780 45.455 12.30 0.00 42.58 5.24
180 181 3.120683 CGACACTACAATTTGTGACGCAT 60.121 43.478 12.30 0.00 42.58 4.73
181 182 4.090786 CGACACTACAATTTGTGACGCATA 59.909 41.667 12.30 0.00 42.58 3.14
182 183 5.388994 CGACACTACAATTTGTGACGCATAA 60.389 40.000 12.30 0.00 42.58 1.90
183 184 6.494893 ACACTACAATTTGTGACGCATAAT 57.505 33.333 12.30 0.00 37.59 1.28
184 185 6.908825 ACACTACAATTTGTGACGCATAATT 58.091 32.000 12.30 0.00 37.59 1.40
185 186 7.021196 ACACTACAATTTGTGACGCATAATTC 58.979 34.615 12.30 0.00 37.59 2.17
186 187 7.020602 CACTACAATTTGTGACGCATAATTCA 58.979 34.615 12.30 0.00 36.38 2.57
187 188 7.007367 CACTACAATTTGTGACGCATAATTCAC 59.993 37.037 12.30 0.00 42.18 3.18
194 195 3.806257 CGCATAATTCACAGCGTCC 57.194 52.632 0.00 0.00 44.67 4.79
195 196 0.043053 CGCATAATTCACAGCGTCCG 60.043 55.000 0.00 0.00 44.67 4.79
196 197 1.006832 GCATAATTCACAGCGTCCGT 58.993 50.000 0.00 0.00 0.00 4.69
197 198 1.004927 GCATAATTCACAGCGTCCGTC 60.005 52.381 0.00 0.00 0.00 4.79
198 199 2.267426 CATAATTCACAGCGTCCGTCA 58.733 47.619 0.00 0.00 0.00 4.35
199 200 2.442212 TAATTCACAGCGTCCGTCAA 57.558 45.000 0.00 0.00 0.00 3.18
200 201 1.588674 AATTCACAGCGTCCGTCAAA 58.411 45.000 0.00 0.00 0.00 2.69
201 202 0.865769 ATTCACAGCGTCCGTCAAAC 59.134 50.000 0.00 0.00 0.00 2.93
202 203 0.179094 TTCACAGCGTCCGTCAAACT 60.179 50.000 0.00 0.00 0.00 2.66
203 204 0.596600 TCACAGCGTCCGTCAAACTC 60.597 55.000 0.00 0.00 0.00 3.01
204 205 1.660575 ACAGCGTCCGTCAAACTCG 60.661 57.895 0.00 0.00 0.00 4.18
211 212 4.966005 CGTCAAACTCGGAGCTCA 57.034 55.556 17.19 0.00 0.00 4.26
212 213 2.435741 CGTCAAACTCGGAGCTCAC 58.564 57.895 17.19 4.01 0.00 3.51
213 214 1.337817 CGTCAAACTCGGAGCTCACG 61.338 60.000 17.19 16.35 0.00 4.35
216 217 1.272490 TCAAACTCGGAGCTCACGATT 59.728 47.619 22.06 16.16 39.89 3.34
219 220 0.739561 ACTCGGAGCTCACGATTACC 59.260 55.000 22.06 1.20 39.89 2.85
245 246 6.699575 GGTGTATGAACCAAGCAGAAATAT 57.300 37.500 0.00 0.00 40.22 1.28
247 248 8.220755 GGTGTATGAACCAAGCAGAAATATTA 57.779 34.615 0.00 0.00 40.22 0.98
270 272 6.964677 AATATTGTTACTATCGTCGTCGTG 57.035 37.500 1.33 0.00 38.33 4.35
273 275 2.159667 TGTTACTATCGTCGTCGTGGTG 60.160 50.000 1.33 0.00 38.33 4.17
295 297 0.308684 GGACGTCGACCATACGCATA 59.691 55.000 10.58 0.00 44.04 3.14
383 396 4.617645 CCGAGTTCGAAAACAAACAAACAA 59.382 37.500 0.00 0.00 43.02 2.83
384 397 5.219951 CCGAGTTCGAAAACAAACAAACAAG 60.220 40.000 0.00 0.00 43.02 3.16
419 443 2.348666 GTCATCATCCAGGAAACGAACG 59.651 50.000 0.00 0.00 0.00 3.95
426 450 1.069906 CCAGGAAACGAACGAGCAAAG 60.070 52.381 0.14 0.00 0.00 2.77
450 479 4.277239 TGGCGAAGTCAACATCGG 57.723 55.556 9.47 0.00 42.02 4.18
558 590 0.955178 CGCTCTCACCGACCATATCT 59.045 55.000 0.00 0.00 0.00 1.98
559 591 1.068885 CGCTCTCACCGACCATATCTC 60.069 57.143 0.00 0.00 0.00 2.75
560 592 1.271102 GCTCTCACCGACCATATCTCC 59.729 57.143 0.00 0.00 0.00 3.71
561 593 1.537638 CTCTCACCGACCATATCTCCG 59.462 57.143 0.00 0.00 0.00 4.63
616 651 2.203070 GTCCGCCGCCTGATGATT 60.203 61.111 0.00 0.00 0.00 2.57
619 654 2.898840 CGCCGCCTGATGATTGCT 60.899 61.111 0.00 0.00 0.00 3.91
623 660 0.530650 CCGCCTGATGATTGCTACGT 60.531 55.000 0.00 0.00 0.00 3.57
630 667 5.559035 GCCTGATGATTGCTACGTGAAATAC 60.559 44.000 0.00 0.00 0.00 1.89
641 678 1.201877 CGTGAAATACGCCAAGGAACG 60.202 52.381 0.00 0.00 46.92 3.95
669 720 0.390603 TCACCGGTATTTGCAGGACG 60.391 55.000 6.87 0.00 0.00 4.79
705 761 4.003788 CGTCCGAAGCACCCAGGT 62.004 66.667 0.00 0.00 0.00 4.00
754 810 0.107643 GGCTCTTCCCACTATCTGGC 59.892 60.000 0.00 0.00 39.01 4.85
756 812 0.390860 CTCTTCCCACTATCTGGCGG 59.609 60.000 0.00 0.00 39.01 6.13
818 877 8.765219 CGTGTACCGTATATTAACTGTAGTAGT 58.235 37.037 0.00 0.00 42.89 2.73
941 1033 4.127040 CGCTCTGCCTCTGCGTCT 62.127 66.667 0.00 0.00 44.00 4.18
942 1034 2.508887 GCTCTGCCTCTGCGTCTG 60.509 66.667 0.00 0.00 41.78 3.51
943 1035 2.508887 CTCTGCCTCTGCGTCTGC 60.509 66.667 0.00 0.00 41.78 4.26
944 1036 4.074526 TCTGCCTCTGCGTCTGCC 62.075 66.667 0.00 0.00 41.78 4.85
945 1037 4.079850 CTGCCTCTGCGTCTGCCT 62.080 66.667 0.00 0.00 41.78 4.75
1034 1141 4.200283 CGGCAGCTCCTCCTCGTC 62.200 72.222 0.00 0.00 0.00 4.20
1041 1148 1.304952 CTCCTCCTCGTCCTCCACT 59.695 63.158 0.00 0.00 0.00 4.00
1042 1149 0.750182 CTCCTCCTCGTCCTCCACTC 60.750 65.000 0.00 0.00 0.00 3.51
1077 1184 2.888863 CGTGCTCACCTCCTCCTC 59.111 66.667 0.00 0.00 0.00 3.71
1163 1460 3.202706 GCCCGGATCGAAGCCAAC 61.203 66.667 0.73 0.00 0.00 3.77
1165 1462 1.815421 CCCGGATCGAAGCCAACTG 60.815 63.158 0.73 0.00 0.00 3.16
1181 1478 1.062525 CTGGCGCCGTTTTAGATGC 59.937 57.895 23.90 0.00 0.00 3.91
1183 1480 2.407616 GCGCCGTTTTAGATGCCC 59.592 61.111 0.00 0.00 0.00 5.36
1257 1554 2.749044 CCACTGGCTGCATCGCTT 60.749 61.111 0.50 0.00 0.00 4.68
1275 1572 0.975135 TTCTCTGCTCTGCTCTGCTT 59.025 50.000 0.00 0.00 0.00 3.91
1288 1590 2.034687 TGCTTTGCTCCAGGGCTC 59.965 61.111 0.00 0.00 0.00 4.70
1314 1616 1.219522 ACGCGTTTACTGCAGTGTCC 61.220 55.000 29.57 14.54 0.00 4.02
1342 1644 6.766467 GTCTTTTTCTTCAGGAGTTCAGGTTA 59.234 38.462 0.00 0.00 0.00 2.85
1347 1649 6.282199 TCTTCAGGAGTTCAGGTTACATAC 57.718 41.667 0.00 0.00 0.00 2.39
1354 1656 5.479306 GAGTTCAGGTTACATACTGCAGAA 58.521 41.667 23.35 0.00 34.76 3.02
1355 1657 5.865085 AGTTCAGGTTACATACTGCAGAAA 58.135 37.500 23.35 8.48 34.76 2.52
1385 1687 3.753272 GCAAGGTTTCTGCAGTAGATTCA 59.247 43.478 14.67 0.00 34.80 2.57
1422 1724 1.339535 TGTTGCATAAGGGATGACGCA 60.340 47.619 0.00 0.00 37.82 5.24
1467 1772 4.097589 AGCTAGAGCAAGAAATGAAATGCC 59.902 41.667 4.01 0.00 45.16 4.40
1479 1804 0.248377 GAAATGCCGATGCTCTGTGC 60.248 55.000 0.00 0.00 43.25 4.57
1486 1811 1.703438 CGATGCTCTGTGCTTCCTGC 61.703 60.000 10.69 0.00 41.21 4.85
1557 1883 2.517959 ACAAGTGATGGTGATGGGTTG 58.482 47.619 0.00 0.00 0.00 3.77
1668 2005 6.628919 TCATGCTACTGAATTCCATCATTG 57.371 37.500 2.27 0.00 0.00 2.82
1677 2014 7.934457 ACTGAATTCCATCATTGTTACTATGC 58.066 34.615 2.27 0.00 0.00 3.14
1689 2026 3.189080 TGTTACTATGCTTGCTTGCTGTG 59.811 43.478 3.47 0.00 0.00 3.66
1825 2162 0.676466 CAAGGTTGGCATAGCGGACA 60.676 55.000 0.00 0.00 0.00 4.02
1842 2179 1.228063 CATCCAGGATGAAGCCGGG 60.228 63.158 23.71 0.00 42.09 5.73
1890 2227 1.447838 CCCCGATGTCCTGTTCGTG 60.448 63.158 0.00 0.00 33.60 4.35
1905 2242 3.702555 GTGCACTGCGACGTCACC 61.703 66.667 17.16 6.31 0.00 4.02
2004 2877 1.165270 GCATTACAGGCGACAAGGTT 58.835 50.000 0.00 0.00 0.00 3.50
2111 2984 1.518352 CGCGTGTCATGATCCCGAA 60.518 57.895 13.61 0.00 0.00 4.30
2157 3030 1.229428 CGAGTGTTGCCAGTGTCATT 58.771 50.000 0.00 0.00 0.00 2.57
2268 3141 2.424705 TACGGGTGAACTGCGTGTCC 62.425 60.000 0.00 0.00 0.00 4.02
2271 3144 2.668550 GTGAACTGCGTGTCCCCC 60.669 66.667 0.00 0.00 0.00 5.40
2307 3180 1.159713 CGCTCTCCATGCCGCATTTA 61.160 55.000 2.16 0.00 0.00 1.40
2313 3186 1.326213 CCATGCCGCATTTACCCCAA 61.326 55.000 2.16 0.00 0.00 4.12
2316 3189 1.379309 GCCGCATTTACCCCAAGGA 60.379 57.895 0.00 0.00 36.73 3.36
2322 3195 2.648059 CATTTACCCCAAGGAGAGCAG 58.352 52.381 0.00 0.00 36.73 4.24
2439 3320 3.456431 CTACCTGGCGAGCGACGAG 62.456 68.421 0.00 0.40 45.77 4.18
2484 3365 2.884207 GTGGTCGACGGCGGATTC 60.884 66.667 12.58 0.00 38.28 2.52
2487 3368 2.884207 GTCGACGGCGGATTCACC 60.884 66.667 12.58 0.00 38.28 4.02
2490 3371 2.202892 GACGGCGGATTCACCTCC 60.203 66.667 13.24 0.00 39.96 4.30
2702 3584 7.905604 TGATATTACTCTGTTGAACCTGTTG 57.094 36.000 0.00 0.00 0.00 3.33
2704 3586 2.348411 ACTCTGTTGAACCTGTTGGG 57.652 50.000 0.00 0.00 41.89 4.12
2812 3695 5.126869 TGAGCTTCAACATTTGAGTTGGAAA 59.873 36.000 6.95 0.00 46.74 3.13
2879 3763 7.406799 TGTGCGTGTATATGATAACTGAATG 57.593 36.000 0.00 0.00 0.00 2.67
2898 3782 7.094634 ACTGAATGTGTGTACAGAAATGGATTC 60.095 37.037 0.00 0.19 40.79 2.52
2916 3800 4.457257 GGATTCCCAGAGCTGTTATAATGC 59.543 45.833 0.00 5.59 0.00 3.56
2921 3805 3.246226 CCAGAGCTGTTATAATGCGTGTC 59.754 47.826 0.00 2.26 0.00 3.67
2940 3824 6.382608 CGTGTCTAGTTCAGAAGAATCTTGA 58.617 40.000 0.00 0.00 35.92 3.02
2941 3825 6.306837 CGTGTCTAGTTCAGAAGAATCTTGAC 59.693 42.308 0.00 0.00 37.68 3.18
3221 4160 1.409064 TCTAGCCTACCATCTGCGTTG 59.591 52.381 0.00 0.00 0.00 4.10
3341 4280 1.986757 AGCTGAGATGGCGTCACCT 60.987 57.895 9.78 0.00 40.22 4.00
3425 5701 0.583438 CGTTATGCCGAGCAATCAGG 59.417 55.000 2.68 0.00 43.62 3.86
3500 5776 2.414481 CAGCAAATCTCCTTCAGACACG 59.586 50.000 0.00 0.00 32.26 4.49
3515 5791 1.265635 GACACGGCAATGCTTGTGTTA 59.734 47.619 27.35 0.00 43.57 2.41
3516 5792 1.885887 ACACGGCAATGCTTGTGTTAT 59.114 42.857 23.50 8.33 42.02 1.89
3517 5793 2.295909 ACACGGCAATGCTTGTGTTATT 59.704 40.909 23.50 8.05 42.02 1.40
3518 5794 2.662637 CACGGCAATGCTTGTGTTATTG 59.337 45.455 18.17 0.00 35.47 1.90
3523 5799 4.850859 CAATGCTTGTGTTATTGCATGG 57.149 40.909 0.00 0.00 44.15 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 9.214957 CCACAGTTCTATAAAGTATGACAAACA 57.785 33.333 0.00 0.00 0.00 2.83
11 12 8.175716 GCCACAGTTCTATAAAGTATGACAAAC 58.824 37.037 0.00 0.00 0.00 2.93
12 13 7.335924 GGCCACAGTTCTATAAAGTATGACAAA 59.664 37.037 0.00 0.00 0.00 2.83
13 14 6.821665 GGCCACAGTTCTATAAAGTATGACAA 59.178 38.462 0.00 0.00 0.00 3.18
14 15 6.156256 AGGCCACAGTTCTATAAAGTATGACA 59.844 38.462 5.01 0.00 0.00 3.58
15 16 6.583562 AGGCCACAGTTCTATAAAGTATGAC 58.416 40.000 5.01 0.00 0.00 3.06
16 17 6.808321 AGGCCACAGTTCTATAAAGTATGA 57.192 37.500 5.01 0.00 0.00 2.15
17 18 7.865706 AAAGGCCACAGTTCTATAAAGTATG 57.134 36.000 5.01 0.00 0.00 2.39
18 19 8.879427 AAAAAGGCCACAGTTCTATAAAGTAT 57.121 30.769 5.01 0.00 0.00 2.12
40 41 9.720769 AGACTCCTCATCGAATTTTACTAAAAA 57.279 29.630 0.00 0.00 38.87 1.94
41 42 9.367444 GAGACTCCTCATCGAATTTTACTAAAA 57.633 33.333 0.00 0.00 39.24 1.52
42 43 7.701078 CGAGACTCCTCATCGAATTTTACTAAA 59.299 37.037 0.00 0.00 39.39 1.85
43 44 7.148120 ACGAGACTCCTCATCGAATTTTACTAA 60.148 37.037 0.30 0.00 39.39 2.24
44 45 6.318144 ACGAGACTCCTCATCGAATTTTACTA 59.682 38.462 0.30 0.00 39.39 1.82
45 46 5.125739 ACGAGACTCCTCATCGAATTTTACT 59.874 40.000 0.30 0.00 39.39 2.24
46 47 5.341617 ACGAGACTCCTCATCGAATTTTAC 58.658 41.667 0.30 0.00 39.39 2.01
47 48 5.578005 ACGAGACTCCTCATCGAATTTTA 57.422 39.130 0.30 0.00 39.39 1.52
48 49 4.457834 ACGAGACTCCTCATCGAATTTT 57.542 40.909 0.30 0.00 39.39 1.82
49 50 4.177026 CAACGAGACTCCTCATCGAATTT 58.823 43.478 0.30 0.00 39.39 1.82
50 51 3.193691 ACAACGAGACTCCTCATCGAATT 59.806 43.478 0.30 0.00 39.39 2.17
51 52 2.755655 ACAACGAGACTCCTCATCGAAT 59.244 45.455 0.30 0.00 39.39 3.34
52 53 2.160205 ACAACGAGACTCCTCATCGAA 58.840 47.619 0.30 0.00 39.39 3.71
53 54 1.822506 ACAACGAGACTCCTCATCGA 58.177 50.000 0.30 0.00 39.39 3.59
54 55 2.638556 AACAACGAGACTCCTCATCG 57.361 50.000 0.00 0.00 39.39 3.84
55 56 6.334202 AGATTAAACAACGAGACTCCTCATC 58.666 40.000 0.00 0.00 39.39 2.92
56 57 6.287589 AGATTAAACAACGAGACTCCTCAT 57.712 37.500 0.00 0.00 39.39 2.90
57 58 5.723672 AGATTAAACAACGAGACTCCTCA 57.276 39.130 0.00 0.00 39.39 3.86
58 59 7.422878 AAAAGATTAAACAACGAGACTCCTC 57.577 36.000 0.00 0.00 36.08 3.71
59 60 7.282450 ACAAAAAGATTAAACAACGAGACTCCT 59.718 33.333 0.00 0.00 0.00 3.69
60 61 7.415229 ACAAAAAGATTAAACAACGAGACTCC 58.585 34.615 0.00 0.00 0.00 3.85
61 62 8.120465 TGACAAAAAGATTAAACAACGAGACTC 58.880 33.333 0.00 0.00 0.00 3.36
62 63 7.981142 TGACAAAAAGATTAAACAACGAGACT 58.019 30.769 0.00 0.00 0.00 3.24
63 64 7.097006 GCTGACAAAAAGATTAAACAACGAGAC 60.097 37.037 0.00 0.00 0.00 3.36
64 65 6.910433 GCTGACAAAAAGATTAAACAACGAGA 59.090 34.615 0.00 0.00 0.00 4.04
65 66 6.912591 AGCTGACAAAAAGATTAAACAACGAG 59.087 34.615 0.00 0.00 0.00 4.18
66 67 6.791303 AGCTGACAAAAAGATTAAACAACGA 58.209 32.000 0.00 0.00 0.00 3.85
67 68 8.555166 TTAGCTGACAAAAAGATTAAACAACG 57.445 30.769 0.00 0.00 0.00 4.10
69 70 9.308318 GGTTTAGCTGACAAAAAGATTAAACAA 57.692 29.630 0.00 0.00 33.01 2.83
70 71 8.470805 TGGTTTAGCTGACAAAAAGATTAAACA 58.529 29.630 0.00 0.00 33.01 2.83
71 72 8.865590 TGGTTTAGCTGACAAAAAGATTAAAC 57.134 30.769 0.00 0.00 31.89 2.01
76 77 9.643693 CATTATTGGTTTAGCTGACAAAAAGAT 57.356 29.630 0.00 0.00 0.00 2.40
77 78 8.637986 ACATTATTGGTTTAGCTGACAAAAAGA 58.362 29.630 0.00 0.00 0.00 2.52
78 79 8.816640 ACATTATTGGTTTAGCTGACAAAAAG 57.183 30.769 0.00 0.00 0.00 2.27
79 80 9.685828 GTACATTATTGGTTTAGCTGACAAAAA 57.314 29.630 0.00 0.00 0.00 1.94
80 81 8.018520 CGTACATTATTGGTTTAGCTGACAAAA 58.981 33.333 0.00 0.00 0.00 2.44
81 82 7.388224 TCGTACATTATTGGTTTAGCTGACAAA 59.612 33.333 0.00 0.00 0.00 2.83
82 83 6.874664 TCGTACATTATTGGTTTAGCTGACAA 59.125 34.615 0.00 0.00 0.00 3.18
83 84 6.399743 TCGTACATTATTGGTTTAGCTGACA 58.600 36.000 0.00 0.00 0.00 3.58
84 85 6.509677 GCTCGTACATTATTGGTTTAGCTGAC 60.510 42.308 0.00 0.00 0.00 3.51
85 86 5.522460 GCTCGTACATTATTGGTTTAGCTGA 59.478 40.000 0.00 0.00 0.00 4.26
86 87 5.277345 GGCTCGTACATTATTGGTTTAGCTG 60.277 44.000 0.00 0.00 0.00 4.24
87 88 4.814771 GGCTCGTACATTATTGGTTTAGCT 59.185 41.667 0.00 0.00 0.00 3.32
88 89 4.573201 TGGCTCGTACATTATTGGTTTAGC 59.427 41.667 0.00 0.00 0.00 3.09
89 90 5.583061 TGTGGCTCGTACATTATTGGTTTAG 59.417 40.000 0.00 0.00 0.00 1.85
90 91 5.489249 TGTGGCTCGTACATTATTGGTTTA 58.511 37.500 0.00 0.00 0.00 2.01
91 92 4.328536 TGTGGCTCGTACATTATTGGTTT 58.671 39.130 0.00 0.00 0.00 3.27
92 93 3.945346 TGTGGCTCGTACATTATTGGTT 58.055 40.909 0.00 0.00 0.00 3.67
93 94 3.620427 TGTGGCTCGTACATTATTGGT 57.380 42.857 0.00 0.00 0.00 3.67
94 95 3.876914 ACATGTGGCTCGTACATTATTGG 59.123 43.478 0.00 0.00 36.67 3.16
95 96 4.570369 TGACATGTGGCTCGTACATTATTG 59.430 41.667 1.15 0.00 36.67 1.90
96 97 4.765273 TGACATGTGGCTCGTACATTATT 58.235 39.130 1.15 0.00 36.67 1.40
97 98 4.400529 TGACATGTGGCTCGTACATTAT 57.599 40.909 1.15 0.00 36.67 1.28
98 99 3.878160 TGACATGTGGCTCGTACATTA 57.122 42.857 1.15 0.00 36.67 1.90
99 100 2.760634 TGACATGTGGCTCGTACATT 57.239 45.000 1.15 0.00 36.67 2.71
100 101 2.988010 ATGACATGTGGCTCGTACAT 57.012 45.000 1.15 0.00 39.23 2.29
101 102 3.020984 TCTATGACATGTGGCTCGTACA 58.979 45.455 1.15 0.00 0.00 2.90
102 103 3.710326 TCTATGACATGTGGCTCGTAC 57.290 47.619 1.15 0.00 0.00 3.67
103 104 3.490933 GCTTCTATGACATGTGGCTCGTA 60.491 47.826 1.15 0.00 0.00 3.43
104 105 2.739932 GCTTCTATGACATGTGGCTCGT 60.740 50.000 1.15 0.00 0.00 4.18
105 106 1.863454 GCTTCTATGACATGTGGCTCG 59.137 52.381 1.15 0.00 0.00 5.03
106 107 3.191078 AGCTTCTATGACATGTGGCTC 57.809 47.619 1.15 0.00 0.00 4.70
107 108 4.970860 ATAGCTTCTATGACATGTGGCT 57.029 40.909 1.15 4.00 0.00 4.75
108 109 5.541845 TGTATAGCTTCTATGACATGTGGC 58.458 41.667 1.15 0.00 0.00 5.01
109 110 8.501580 CAAATGTATAGCTTCTATGACATGTGG 58.498 37.037 1.15 0.00 31.62 4.17
110 111 9.264719 TCAAATGTATAGCTTCTATGACATGTG 57.735 33.333 1.15 13.36 34.98 3.21
111 112 9.836864 TTCAAATGTATAGCTTCTATGACATGT 57.163 29.630 0.00 0.00 0.00 3.21
148 149 8.869897 CACAAATTGTAGTGTCGAATACATAGT 58.130 33.333 0.00 2.92 41.10 2.12
149 150 9.083080 TCACAAATTGTAGTGTCGAATACATAG 57.917 33.333 0.00 2.47 41.10 2.23
150 151 8.865978 GTCACAAATTGTAGTGTCGAATACATA 58.134 33.333 0.00 1.38 41.10 2.29
151 152 7.411480 CGTCACAAATTGTAGTGTCGAATACAT 60.411 37.037 15.19 0.00 45.43 2.29
152 153 6.129035 CGTCACAAATTGTAGTGTCGAATACA 60.129 38.462 15.19 3.60 45.43 2.29
153 154 6.231365 CGTCACAAATTGTAGTGTCGAATAC 58.769 40.000 15.19 0.00 45.43 1.89
154 155 5.164031 GCGTCACAAATTGTAGTGTCGAATA 60.164 40.000 20.65 0.00 45.43 1.75
155 156 4.377022 GCGTCACAAATTGTAGTGTCGAAT 60.377 41.667 20.65 0.00 45.43 3.34
156 157 3.060138 GCGTCACAAATTGTAGTGTCGAA 60.060 43.478 20.65 0.00 45.43 3.71
157 158 2.473609 GCGTCACAAATTGTAGTGTCGA 59.526 45.455 20.65 0.00 45.43 4.20
158 159 2.219903 TGCGTCACAAATTGTAGTGTCG 59.780 45.455 15.65 15.65 45.38 4.35
159 160 3.870723 TGCGTCACAAATTGTAGTGTC 57.129 42.857 0.00 1.28 37.07 3.67
160 161 5.933187 TTATGCGTCACAAATTGTAGTGT 57.067 34.783 0.00 0.00 37.07 3.55
161 162 7.007367 GTGAATTATGCGTCACAAATTGTAGTG 59.993 37.037 0.00 0.00 43.02 2.74
162 163 7.021196 GTGAATTATGCGTCACAAATTGTAGT 58.979 34.615 0.00 0.00 43.02 2.73
163 164 7.423274 GTGAATTATGCGTCACAAATTGTAG 57.577 36.000 0.00 0.00 43.02 2.74
172 173 2.077155 CGCTGTGAATTATGCGTCAC 57.923 50.000 0.00 0.00 43.66 3.67
177 178 1.004927 GACGGACGCTGTGAATTATGC 60.005 52.381 0.00 0.00 0.00 3.14
178 179 2.267426 TGACGGACGCTGTGAATTATG 58.733 47.619 0.00 0.00 0.00 1.90
179 180 2.665649 TGACGGACGCTGTGAATTAT 57.334 45.000 0.00 0.00 0.00 1.28
180 181 2.442212 TTGACGGACGCTGTGAATTA 57.558 45.000 0.00 0.00 0.00 1.40
181 182 1.263217 GTTTGACGGACGCTGTGAATT 59.737 47.619 0.00 0.00 0.00 2.17
182 183 0.865769 GTTTGACGGACGCTGTGAAT 59.134 50.000 0.00 0.00 0.00 2.57
183 184 0.179094 AGTTTGACGGACGCTGTGAA 60.179 50.000 0.00 0.00 0.00 3.18
184 185 0.596600 GAGTTTGACGGACGCTGTGA 60.597 55.000 0.00 0.00 0.00 3.58
185 186 1.853319 GAGTTTGACGGACGCTGTG 59.147 57.895 0.00 0.00 0.00 3.66
186 187 1.660575 CGAGTTTGACGGACGCTGT 60.661 57.895 0.00 0.00 0.00 4.40
187 188 3.147294 CGAGTTTGACGGACGCTG 58.853 61.111 0.00 0.00 0.00 5.18
194 195 1.337817 CGTGAGCTCCGAGTTTGACG 61.338 60.000 12.15 7.92 0.00 4.35
195 196 0.039437 TCGTGAGCTCCGAGTTTGAC 60.039 55.000 19.22 5.09 0.00 3.18
196 197 0.888619 ATCGTGAGCTCCGAGTTTGA 59.111 50.000 24.61 8.96 37.81 2.69
197 198 1.714794 AATCGTGAGCTCCGAGTTTG 58.285 50.000 24.61 4.58 37.81 2.93
198 199 2.416972 GGTAATCGTGAGCTCCGAGTTT 60.417 50.000 24.83 19.02 37.81 2.66
199 200 1.134560 GGTAATCGTGAGCTCCGAGTT 59.865 52.381 24.83 20.45 37.81 3.01
200 201 0.739561 GGTAATCGTGAGCTCCGAGT 59.260 55.000 24.61 24.16 37.81 4.18
201 202 0.317103 CGGTAATCGTGAGCTCCGAG 60.317 60.000 24.61 12.09 40.29 4.63
202 203 1.725665 CGGTAATCGTGAGCTCCGA 59.274 57.895 23.38 23.38 40.29 4.55
203 204 4.303853 CGGTAATCGTGAGCTCCG 57.696 61.111 12.15 14.33 0.00 4.63
212 213 2.861935 GGTTCATACACCACGGTAATCG 59.138 50.000 0.00 0.00 45.88 3.34
213 214 3.864243 TGGTTCATACACCACGGTAATC 58.136 45.455 0.00 0.00 42.27 1.75
222 223 6.699575 ATATTTCTGCTTGGTTCATACACC 57.300 37.500 0.00 0.00 37.34 4.16
259 261 2.257371 CACCACCACGACGACGAT 59.743 61.111 15.32 0.00 42.66 3.73
261 263 3.968568 TCCACCACCACGACGACG 61.969 66.667 5.58 5.58 45.75 5.12
270 272 1.597797 TATGGTCGACGTCCACCACC 61.598 60.000 33.11 21.56 45.61 4.61
273 275 1.226491 CGTATGGTCGACGTCCACC 60.226 63.158 23.71 23.71 37.81 4.61
295 297 8.394971 TCGGAAATGATGACAGCATTATTTAT 57.605 30.769 18.63 3.40 45.29 1.40
335 337 3.646534 TGATGGCTCATCTTCCTCACTA 58.353 45.455 13.94 0.00 41.06 2.74
403 427 0.721718 GCTCGTTCGTTTCCTGGATG 59.278 55.000 0.00 0.00 0.00 3.51
404 428 0.320374 TGCTCGTTCGTTTCCTGGAT 59.680 50.000 0.00 0.00 0.00 3.41
419 443 2.183555 GCCATGGCTGCTTTGCTC 59.816 61.111 29.98 0.00 38.26 4.26
426 450 2.334946 TTGACTTCGCCATGGCTGC 61.335 57.895 33.07 17.56 39.32 5.25
450 479 4.351054 CACACCAGGCCCACCCTC 62.351 72.222 0.00 0.00 44.09 4.30
534 566 1.741770 GGTCGGTGAGAGCGCAAAT 60.742 57.895 11.47 0.00 39.21 2.32
602 637 1.595109 TAGCAATCATCAGGCGGCG 60.595 57.895 0.51 0.51 0.00 6.46
623 660 0.800012 GCGTTCCTTGGCGTATTTCA 59.200 50.000 0.00 0.00 0.00 2.69
630 667 4.697756 TCAGGGCGTTCCTTGGCG 62.698 66.667 0.00 0.00 45.47 5.69
641 678 1.972660 AATACCGGTGAGCTCAGGGC 61.973 60.000 26.23 12.83 42.19 5.19
690 741 3.319198 GGACCTGGGTGCTTCGGA 61.319 66.667 4.01 0.00 33.56 4.55
705 761 5.452496 GCTGTGAGCTAATTAGACATCAGGA 60.452 44.000 16.85 5.75 38.45 3.86
822 881 9.708092 GTTGTTGACTAAGGAAGAGTAATTAGT 57.292 33.333 0.00 0.00 40.29 2.24
823 882 9.706691 TGTTGTTGACTAAGGAAGAGTAATTAG 57.293 33.333 0.00 0.00 0.00 1.73
938 1030 2.716017 CGTGGGGAGAGAGGCAGAC 61.716 68.421 0.00 0.00 0.00 3.51
939 1031 2.363018 CGTGGGGAGAGAGGCAGA 60.363 66.667 0.00 0.00 0.00 4.26
940 1032 2.363018 TCGTGGGGAGAGAGGCAG 60.363 66.667 0.00 0.00 0.00 4.85
941 1033 2.680352 GTCGTGGGGAGAGAGGCA 60.680 66.667 0.00 0.00 0.00 4.75
942 1034 3.827898 CGTCGTGGGGAGAGAGGC 61.828 72.222 0.00 0.00 0.00 4.70
943 1035 3.827898 GCGTCGTGGGGAGAGAGG 61.828 72.222 0.00 0.00 0.00 3.69
944 1036 3.827898 GGCGTCGTGGGGAGAGAG 61.828 72.222 0.00 0.00 0.00 3.20
1032 1139 4.459089 GGCGCTGGAGTGGAGGAC 62.459 72.222 7.64 0.00 0.00 3.85
1060 1167 2.716017 GGAGGAGGAGGTGAGCACG 61.716 68.421 0.00 0.00 0.00 5.34
1077 1184 1.282653 GGGGAAAGGGAGGAAGAGGG 61.283 65.000 0.00 0.00 0.00 4.30
1115 1412 1.227060 CTGCCGCGACAGATCATGA 60.227 57.895 18.32 0.00 40.25 3.07
1147 1444 1.815421 CAGTTGGCTTCGATCCGGG 60.815 63.158 0.00 0.00 0.00 5.73
1163 1460 1.062525 GCATCTAAAACGGCGCCAG 59.937 57.895 28.98 21.29 0.00 4.85
1165 1462 2.407616 GGCATCTAAAACGGCGCC 59.592 61.111 19.07 19.07 0.00 6.53
1181 1478 2.737881 CCATTGCAGGGCCATTGGG 61.738 63.158 6.18 0.00 34.29 4.12
1183 1480 2.188469 GCCATTGCAGGGCCATTG 59.812 61.111 18.06 3.11 45.87 2.82
1240 1537 2.749044 AAGCGATGCAGCCAGTGG 60.749 61.111 4.20 4.20 38.01 4.00
1242 1539 1.449246 GAGAAGCGATGCAGCCAGT 60.449 57.895 0.00 0.00 38.01 4.00
1248 1545 0.459759 CAGAGCAGAGAAGCGATGCA 60.460 55.000 0.00 0.00 42.45 3.96
1251 1548 0.102844 GAGCAGAGCAGAGAAGCGAT 59.897 55.000 0.00 0.00 40.15 4.58
1257 1554 0.975135 AAAGCAGAGCAGAGCAGAGA 59.025 50.000 0.00 0.00 0.00 3.10
1275 1572 1.681666 CTTCTGAGCCCTGGAGCAA 59.318 57.895 9.36 0.00 34.23 3.91
1288 1590 0.451135 GCAGTAAACGCGTGCTTCTG 60.451 55.000 14.98 19.24 34.23 3.02
1314 1616 4.570772 TGAACTCCTGAAGAAAAAGACACG 59.429 41.667 0.00 0.00 0.00 4.49
1354 1656 0.105504 AGAAACCTTGCCCTGCCTTT 60.106 50.000 0.00 0.00 0.00 3.11
1355 1657 0.829182 CAGAAACCTTGCCCTGCCTT 60.829 55.000 0.00 0.00 0.00 4.35
1364 1666 5.947228 TTGAATCTACTGCAGAAACCTTG 57.053 39.130 23.35 0.00 36.67 3.61
1422 1724 2.125512 GACGGAGCATCAAGGCGT 60.126 61.111 0.00 0.00 39.27 5.68
1479 1804 0.386478 GTCAAAAGCAGCGCAGGAAG 60.386 55.000 11.47 0.00 0.00 3.46
1486 1811 0.317269 CCACACTGTCAAAAGCAGCG 60.317 55.000 0.00 0.00 37.47 5.18
1491 1816 2.564771 TCTGCTCCACACTGTCAAAAG 58.435 47.619 0.00 0.00 0.00 2.27
1557 1883 1.342174 CATGAGCCCCCATTGTAATGC 59.658 52.381 0.00 0.00 35.08 3.56
1668 2005 3.436704 TCACAGCAAGCAAGCATAGTAAC 59.563 43.478 3.19 0.00 36.85 2.50
1677 2014 3.734231 CAGTCAAATTCACAGCAAGCAAG 59.266 43.478 0.00 0.00 0.00 4.01
1689 2026 5.981915 AGAGAAAAGCAAAGCAGTCAAATTC 59.018 36.000 0.00 0.00 0.00 2.17
1813 2150 1.302033 CCTGGATGTCCGCTATGCC 60.302 63.158 0.00 0.00 39.43 4.40
1825 2162 3.125376 GCCCGGCTTCATCCTGGAT 62.125 63.158 2.57 2.57 32.82 3.41
1905 2242 0.105039 GGCTTATGTCCTCCTCCACG 59.895 60.000 0.00 0.00 0.00 4.94
1944 2281 1.152830 GAGGGTGCCAAACTTCCCA 59.847 57.895 0.00 0.00 42.12 4.37
1946 2283 1.072505 TCGAGGGTGCCAAACTTCC 59.927 57.895 0.00 0.00 0.00 3.46
2073 2946 2.815211 GCGTGCTTCATGCCGAGA 60.815 61.111 0.00 0.00 40.14 4.04
2111 2984 3.690460 GACACAATGGATCCCTTCTTGT 58.310 45.455 9.90 10.82 0.00 3.16
2121 2994 0.321210 TCGCCAACGACACAATGGAT 60.321 50.000 0.00 0.00 45.12 3.41
2157 3030 4.037413 TGAGGCCCCATCCCTCCA 62.037 66.667 0.00 0.00 46.69 3.86
2307 3180 1.204113 CCTTCTGCTCTCCTTGGGGT 61.204 60.000 0.00 0.00 0.00 4.95
2313 3186 1.202330 CATCACCCTTCTGCTCTCCT 58.798 55.000 0.00 0.00 0.00 3.69
2316 3189 0.252479 CTGCATCACCCTTCTGCTCT 59.748 55.000 0.00 0.00 36.84 4.09
2322 3195 0.393537 CCCTCACTGCATCACCCTTC 60.394 60.000 0.00 0.00 0.00 3.46
2439 3320 2.962253 GCGCTGATGTACCTCGCC 60.962 66.667 0.00 0.00 39.91 5.54
2484 3365 1.586154 GGTTGCCATTCACGGAGGTG 61.586 60.000 0.00 0.00 45.78 4.00
2487 3368 0.321564 TCAGGTTGCCATTCACGGAG 60.322 55.000 0.00 0.00 0.00 4.63
2490 3371 0.523072 CCTTCAGGTTGCCATTCACG 59.477 55.000 0.00 0.00 0.00 4.35
2701 3583 1.142060 CACAAGGTCCTAACACACCCA 59.858 52.381 0.00 0.00 32.45 4.51
2702 3584 1.142262 ACACAAGGTCCTAACACACCC 59.858 52.381 0.00 0.00 32.45 4.61
2704 3586 4.444536 TGTTACACAAGGTCCTAACACAC 58.555 43.478 0.00 0.00 0.00 3.82
2709 3591 6.182507 ACTGAATGTTACACAAGGTCCTAA 57.817 37.500 0.00 0.00 0.00 2.69
2710 3592 5.818678 ACTGAATGTTACACAAGGTCCTA 57.181 39.130 0.00 0.00 0.00 2.94
2784 3666 4.454678 ACTCAAATGTTGAAGCTCACTGA 58.545 39.130 0.00 0.00 39.58 3.41
2879 3763 4.331968 TGGGAATCCATTTCTGTACACAC 58.668 43.478 0.09 0.00 38.32 3.82
2898 3782 2.545526 CACGCATTATAACAGCTCTGGG 59.454 50.000 9.33 4.24 34.19 4.45
2905 3789 6.972901 TCTGAACTAGACACGCATTATAACAG 59.027 38.462 0.00 0.00 0.00 3.16
2916 3800 6.306837 GTCAAGATTCTTCTGAACTAGACACG 59.693 42.308 0.00 0.00 34.43 4.49
2921 3805 6.696411 ACCTGTCAAGATTCTTCTGAACTAG 58.304 40.000 0.00 0.00 34.71 2.57
2982 3869 1.668151 GCCTTTCTTGGCGTCGACT 60.668 57.895 14.70 0.00 43.74 4.18
3033 3921 4.437794 GCATATCTGTTGTGTGGTGTCATG 60.438 45.833 0.00 0.00 0.00 3.07
3070 3958 9.202273 GATAATTGCAGTGTCTATTTAGAGAGG 57.798 37.037 0.00 0.00 32.01 3.69
3100 3988 4.831107 TGACAGCAGCAATGATGTACTTA 58.169 39.130 0.00 0.00 38.65 2.24
3101 3989 3.678289 TGACAGCAGCAATGATGTACTT 58.322 40.909 0.00 0.00 38.65 2.24
3102 3990 3.268330 CTGACAGCAGCAATGATGTACT 58.732 45.455 0.00 0.00 38.65 2.73
3103 3991 3.670311 CTGACAGCAGCAATGATGTAC 57.330 47.619 0.00 0.00 38.65 2.90
3126 4014 4.748892 TGCAGTGTCTATTTAGAGAGCAC 58.251 43.478 0.00 0.00 32.01 4.40
3210 4149 0.163788 GTTGACGACAACGCAGATGG 59.836 55.000 14.57 0.00 45.06 3.51
3341 4280 4.756642 GTGGACAGAACACATTCAGAATCA 59.243 41.667 0.00 0.00 38.67 2.57


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

AutoCloner maintained by Alex Coulton.