Multiple sequence alignment - TraesCS7A01G172400

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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 TraesCS7A01G172400 chr7A 100.000 3187 0 0 1 3187 127077028 127073842 0.000000e+00 5886
1 TraesCS7A01G172400 chr7D 90.445 2407 118 46 799 3178 124877739 124875418 0.000000e+00 3068
2 TraesCS7A01G172400 chr7D 85.079 630 47 22 192 809 124879049 124878455 1.640000e-167 599
3 TraesCS7A01G172400 chr7B 88.634 2270 145 48 449 2668 86808301 86806095 0.000000e+00 2658
4 TraesCS7A01G172400 chr7B 90.495 505 22 10 2693 3180 86806103 86805608 0.000000e+00 643
5 TraesCS7A01G172400 chr7B 90.099 101 8 2 215 314 86808601 86808502 2.580000e-26 130


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 TraesCS7A01G172400 chr7A 127073842 127077028 3186 True 5886.000000 5886 100.000000 1 3187 1 chr7A.!!$R1 3186
1 TraesCS7A01G172400 chr7D 124875418 124879049 3631 True 1833.500000 3068 87.762000 192 3178 2 chr7D.!!$R1 2986
2 TraesCS7A01G172400 chr7B 86805608 86808601 2993 True 1143.666667 2658 89.742667 215 3180 3 chr7B.!!$R1 2965

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
164 165 0.101759 CGTCGGCGGGAGATAAGAAA 59.898 55.0 7.21 0.0 0.0 2.52 F
926 1765 0.179045 GGCGCTCTCTCTCTCTCTCT 60.179 60.0 7.64 0.0 0.0 3.10 F
1856 2701 0.107831 AAGCACAAACGCAGGAGGTA 59.892 50.0 0.00 0.0 0.0 3.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1132 1971 0.037326 TGCTTCCTCATCTTCGCGTT 60.037 50.0 5.77 0.0 0.00 4.84 R
2039 2891 0.101399 CGATAGAGCGACTGCCAAGT 59.899 55.0 0.00 0.0 44.31 3.16 R
2743 3623 0.670546 TTCGCCGCAAAAGAGAGAGG 60.671 55.0 0.00 0.0 0.00 3.69 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
17 18 2.581354 CCTCGCCCTCCTGAACAG 59.419 66.667 0.00 0.00 0.00 3.16
33 34 6.633500 CTGAACAGGAATCAAACCTAAACA 57.367 37.500 0.00 0.00 35.84 2.83
34 35 6.633500 TGAACAGGAATCAAACCTAAACAG 57.367 37.500 0.00 0.00 35.84 3.16
35 36 6.361433 TGAACAGGAATCAAACCTAAACAGA 58.639 36.000 0.00 0.00 35.84 3.41
36 37 6.262273 TGAACAGGAATCAAACCTAAACAGAC 59.738 38.462 0.00 0.00 35.84 3.51
37 38 5.941788 ACAGGAATCAAACCTAAACAGACT 58.058 37.500 0.00 0.00 35.84 3.24
38 39 7.074653 ACAGGAATCAAACCTAAACAGACTA 57.925 36.000 0.00 0.00 35.84 2.59
39 40 7.514721 ACAGGAATCAAACCTAAACAGACTAA 58.485 34.615 0.00 0.00 35.84 2.24
40 41 7.996644 ACAGGAATCAAACCTAAACAGACTAAA 59.003 33.333 0.00 0.00 35.84 1.85
41 42 8.846211 CAGGAATCAAACCTAAACAGACTAAAA 58.154 33.333 0.00 0.00 35.84 1.52
42 43 9.416284 AGGAATCAAACCTAAACAGACTAAAAA 57.584 29.630 0.00 0.00 35.84 1.94
62 63 6.506500 AAAAACACCTAGAGATGAAGCATG 57.493 37.500 0.00 0.00 0.00 4.06
63 64 5.426689 AAACACCTAGAGATGAAGCATGA 57.573 39.130 0.00 0.00 0.00 3.07
64 65 4.669206 ACACCTAGAGATGAAGCATGAG 57.331 45.455 0.00 0.00 0.00 2.90
65 66 3.181467 ACACCTAGAGATGAAGCATGAGC 60.181 47.826 0.00 0.00 42.56 4.26
66 67 2.368221 ACCTAGAGATGAAGCATGAGCC 59.632 50.000 0.00 0.00 43.56 4.70
67 68 2.609984 CCTAGAGATGAAGCATGAGCCG 60.610 54.545 0.00 0.00 43.56 5.52
68 69 0.829333 AGAGATGAAGCATGAGCCGT 59.171 50.000 0.00 0.00 43.56 5.68
69 70 1.202510 AGAGATGAAGCATGAGCCGTC 60.203 52.381 0.00 0.00 43.56 4.79
70 71 0.179062 AGATGAAGCATGAGCCGTCC 60.179 55.000 0.00 0.00 43.56 4.79
71 72 1.153086 ATGAAGCATGAGCCGTCCC 60.153 57.895 0.00 0.00 43.56 4.46
72 73 2.892425 GAAGCATGAGCCGTCCCG 60.892 66.667 0.00 0.00 43.56 5.14
90 91 3.747579 CTGGCAAGGGGCTGGGAT 61.748 66.667 0.00 0.00 44.01 3.85
91 92 3.728292 CTGGCAAGGGGCTGGGATC 62.728 68.421 0.00 0.00 44.01 3.36
92 93 4.529731 GGCAAGGGGCTGGGATCC 62.530 72.222 1.92 1.92 44.01 3.36
93 94 3.743017 GCAAGGGGCTGGGATCCA 61.743 66.667 15.23 0.00 40.25 3.41
94 95 3.078843 GCAAGGGGCTGGGATCCAT 62.079 63.158 15.23 0.00 40.25 3.41
95 96 1.152368 CAAGGGGCTGGGATCCATC 59.848 63.158 15.23 1.09 30.82 3.51
96 97 2.455565 AAGGGGCTGGGATCCATCG 61.456 63.158 15.23 1.73 30.82 3.84
97 98 4.650377 GGGGCTGGGATCCATCGC 62.650 72.222 15.23 12.07 39.87 4.58
98 99 3.877450 GGGCTGGGATCCATCGCA 61.877 66.667 15.23 6.20 45.80 5.10
99 100 2.592861 GGCTGGGATCCATCGCAC 60.593 66.667 15.23 3.44 43.59 5.34
100 101 2.592861 GCTGGGATCCATCGCACC 60.593 66.667 15.23 0.00 43.59 5.01
101 102 3.112205 GCTGGGATCCATCGCACCT 62.112 63.158 15.23 0.00 43.59 4.00
102 103 1.528824 CTGGGATCCATCGCACCTT 59.471 57.895 15.23 0.00 43.59 3.50
103 104 0.533755 CTGGGATCCATCGCACCTTC 60.534 60.000 15.23 0.00 43.59 3.46
104 105 1.595382 GGGATCCATCGCACCTTCG 60.595 63.158 15.23 0.00 39.31 3.79
105 106 1.144057 GGATCCATCGCACCTTCGT 59.856 57.895 6.95 0.00 0.00 3.85
106 107 1.154205 GGATCCATCGCACCTTCGTG 61.154 60.000 6.95 0.00 43.35 4.35
107 108 0.179111 GATCCATCGCACCTTCGTGA 60.179 55.000 0.00 0.00 43.14 4.35
108 109 0.460284 ATCCATCGCACCTTCGTGAC 60.460 55.000 0.00 0.00 43.14 3.67
109 110 2.100631 CCATCGCACCTTCGTGACC 61.101 63.158 0.00 0.00 43.14 4.02
110 111 2.100631 CATCGCACCTTCGTGACCC 61.101 63.158 0.00 0.00 43.14 4.46
111 112 2.283529 ATCGCACCTTCGTGACCCT 61.284 57.895 0.00 0.00 43.14 4.34
112 113 1.827399 ATCGCACCTTCGTGACCCTT 61.827 55.000 0.00 0.00 43.14 3.95
113 114 1.180456 TCGCACCTTCGTGACCCTTA 61.180 55.000 0.00 0.00 43.14 2.69
114 115 0.320073 CGCACCTTCGTGACCCTTAA 60.320 55.000 0.00 0.00 43.14 1.85
115 116 1.439679 GCACCTTCGTGACCCTTAAG 58.560 55.000 0.00 0.00 43.14 1.85
116 117 1.944430 GCACCTTCGTGACCCTTAAGG 60.944 57.143 15.14 15.14 43.14 2.69
117 118 0.323957 ACCTTCGTGACCCTTAAGGC 59.676 55.000 16.70 4.03 41.87 4.35
118 119 0.323629 CCTTCGTGACCCTTAAGGCA 59.676 55.000 16.70 6.86 40.58 4.75
119 120 1.271163 CCTTCGTGACCCTTAAGGCAA 60.271 52.381 16.70 0.31 40.58 4.52
120 121 2.618045 CCTTCGTGACCCTTAAGGCAAT 60.618 50.000 16.70 3.35 40.58 3.56
121 122 3.370103 CCTTCGTGACCCTTAAGGCAATA 60.370 47.826 16.70 0.00 40.58 1.90
122 123 3.536956 TCGTGACCCTTAAGGCAATAG 57.463 47.619 16.70 4.57 40.58 1.73
123 124 2.169769 TCGTGACCCTTAAGGCAATAGG 59.830 50.000 16.70 3.82 40.58 2.57
124 125 2.169769 CGTGACCCTTAAGGCAATAGGA 59.830 50.000 16.70 0.00 40.58 2.94
125 126 3.741388 CGTGACCCTTAAGGCAATAGGAG 60.741 52.174 16.70 2.31 40.58 3.69
126 127 3.454812 GTGACCCTTAAGGCAATAGGAGA 59.545 47.826 16.70 0.00 40.58 3.71
127 128 3.454812 TGACCCTTAAGGCAATAGGAGAC 59.545 47.826 16.70 1.23 40.58 3.36
128 129 2.434702 ACCCTTAAGGCAATAGGAGACG 59.565 50.000 16.70 0.29 40.58 4.18
129 130 2.698797 CCCTTAAGGCAATAGGAGACGA 59.301 50.000 16.70 0.00 0.00 4.20
130 131 3.243907 CCCTTAAGGCAATAGGAGACGAG 60.244 52.174 16.70 0.00 0.00 4.18
131 132 3.637229 CCTTAAGGCAATAGGAGACGAGA 59.363 47.826 9.00 0.00 0.00 4.04
132 133 4.500035 CCTTAAGGCAATAGGAGACGAGAC 60.500 50.000 9.00 0.00 0.00 3.36
133 134 2.145397 AGGCAATAGGAGACGAGACA 57.855 50.000 0.00 0.00 0.00 3.41
134 135 2.028130 AGGCAATAGGAGACGAGACAG 58.972 52.381 0.00 0.00 0.00 3.51
135 136 2.025155 GGCAATAGGAGACGAGACAGA 58.975 52.381 0.00 0.00 0.00 3.41
136 137 2.625790 GGCAATAGGAGACGAGACAGAT 59.374 50.000 0.00 0.00 0.00 2.90
137 138 3.305064 GGCAATAGGAGACGAGACAGATC 60.305 52.174 0.00 0.00 0.00 2.75
138 139 3.316588 GCAATAGGAGACGAGACAGATCA 59.683 47.826 0.00 0.00 0.00 2.92
139 140 4.202060 GCAATAGGAGACGAGACAGATCAA 60.202 45.833 0.00 0.00 0.00 2.57
140 141 5.277825 CAATAGGAGACGAGACAGATCAAC 58.722 45.833 0.00 0.00 0.00 3.18
141 142 1.740585 AGGAGACGAGACAGATCAACG 59.259 52.381 0.00 0.00 34.57 4.10
142 143 1.202200 GGAGACGAGACAGATCAACGG 60.202 57.143 0.00 0.00 33.34 4.44
143 144 0.171455 AGACGAGACAGATCAACGGC 59.829 55.000 0.00 0.00 35.89 5.68
144 145 0.109272 GACGAGACAGATCAACGGCA 60.109 55.000 0.00 0.00 35.78 5.69
145 146 0.388649 ACGAGACAGATCAACGGCAC 60.389 55.000 0.00 0.00 33.34 5.01
159 160 3.896133 GCACGTCGGCGGGAGATA 61.896 66.667 19.76 0.00 45.97 1.98
160 161 2.802792 CACGTCGGCGGGAGATAA 59.197 61.111 16.39 0.00 45.97 1.75
161 162 1.299165 CACGTCGGCGGGAGATAAG 60.299 63.158 16.39 0.00 45.97 1.73
162 163 1.452651 ACGTCGGCGGGAGATAAGA 60.453 57.895 16.39 0.00 43.45 2.10
163 164 1.033746 ACGTCGGCGGGAGATAAGAA 61.034 55.000 16.39 0.00 43.45 2.52
164 165 0.101759 CGTCGGCGGGAGATAAGAAA 59.898 55.000 7.21 0.00 0.00 2.52
165 166 1.568606 GTCGGCGGGAGATAAGAAAC 58.431 55.000 7.21 0.00 0.00 2.78
166 167 0.462789 TCGGCGGGAGATAAGAAACC 59.537 55.000 7.21 0.00 0.00 3.27
167 168 0.532196 CGGCGGGAGATAAGAAACCC 60.532 60.000 0.00 0.00 39.02 4.11
168 169 0.837940 GGCGGGAGATAAGAAACCCT 59.162 55.000 0.00 0.00 40.12 4.34
169 170 1.212195 GGCGGGAGATAAGAAACCCTT 59.788 52.381 0.00 0.00 40.12 3.95
170 171 2.289565 GCGGGAGATAAGAAACCCTTG 58.710 52.381 0.00 0.00 40.12 3.61
171 172 2.093128 GCGGGAGATAAGAAACCCTTGA 60.093 50.000 0.00 0.00 40.12 3.02
172 173 3.433740 GCGGGAGATAAGAAACCCTTGAT 60.434 47.826 0.00 0.00 40.12 2.57
173 174 4.130118 CGGGAGATAAGAAACCCTTGATG 58.870 47.826 0.00 0.00 40.12 3.07
174 175 4.384208 CGGGAGATAAGAAACCCTTGATGT 60.384 45.833 0.00 0.00 40.12 3.06
175 176 5.126779 GGGAGATAAGAAACCCTTGATGTC 58.873 45.833 0.00 0.00 39.28 3.06
176 177 5.104318 GGGAGATAAGAAACCCTTGATGTCT 60.104 44.000 0.00 0.00 39.28 3.41
177 178 6.418946 GGAGATAAGAAACCCTTGATGTCTT 58.581 40.000 0.00 0.00 36.34 3.01
178 179 7.365652 GGGAGATAAGAAACCCTTGATGTCTTA 60.366 40.741 0.00 0.00 39.28 2.10
179 180 8.047310 GGAGATAAGAAACCCTTGATGTCTTAA 58.953 37.037 0.00 0.00 35.16 1.85
180 181 9.103861 GAGATAAGAAACCCTTGATGTCTTAAG 57.896 37.037 0.00 0.00 35.16 1.85
181 182 8.049721 AGATAAGAAACCCTTGATGTCTTAAGG 58.950 37.037 1.85 0.00 42.46 2.69
253 254 3.643237 CCCACTGTAATCTAGAGACCCA 58.357 50.000 0.00 0.00 0.00 4.51
282 283 2.548057 CACTTGCAACTTATCGTGTGGT 59.452 45.455 0.00 0.00 0.00 4.16
284 285 3.630312 ACTTGCAACTTATCGTGTGGTTT 59.370 39.130 0.00 0.00 0.00 3.27
314 315 9.659830 TTTCTTTTCGAAAAAGCTTATAGTGTC 57.340 29.630 22.67 0.00 38.62 3.67
315 316 7.803724 TCTTTTCGAAAAAGCTTATAGTGTCC 58.196 34.615 22.67 0.00 0.00 4.02
316 317 6.490566 TTTCGAAAAAGCTTATAGTGTCCC 57.509 37.500 8.44 0.00 0.00 4.46
317 318 4.510571 TCGAAAAAGCTTATAGTGTCCCC 58.489 43.478 0.00 0.00 0.00 4.81
318 319 4.224370 TCGAAAAAGCTTATAGTGTCCCCT 59.776 41.667 0.00 0.00 0.00 4.79
319 320 4.332819 CGAAAAAGCTTATAGTGTCCCCTG 59.667 45.833 0.00 0.00 0.00 4.45
320 321 3.283259 AAAGCTTATAGTGTCCCCTGC 57.717 47.619 0.00 0.00 0.00 4.85
321 322 1.879575 AGCTTATAGTGTCCCCTGCA 58.120 50.000 0.00 0.00 0.00 4.41
322 323 2.196595 AGCTTATAGTGTCCCCTGCAA 58.803 47.619 0.00 0.00 0.00 4.08
323 324 2.576191 AGCTTATAGTGTCCCCTGCAAA 59.424 45.455 0.00 0.00 0.00 3.68
324 325 3.010138 AGCTTATAGTGTCCCCTGCAAAA 59.990 43.478 0.00 0.00 0.00 2.44
388 396 6.890663 TTTTTGAAAGAAGTTCAGTGCATG 57.109 33.333 5.50 0.00 46.85 4.06
404 412 7.761409 TCAGTGCATGGTAAAAATATTCAGTC 58.239 34.615 0.00 0.00 0.00 3.51
632 733 4.740822 ACGCCACAAGCCCATCCC 62.741 66.667 0.00 0.00 38.78 3.85
684 785 2.864378 GAACCCCAACCGTCCGATCC 62.864 65.000 0.00 0.00 0.00 3.36
701 802 3.925090 CATCCCCTCGCCGGTACC 61.925 72.222 1.90 0.16 0.00 3.34
749 851 2.199236 GTTACAGCGGCAGTACCATAC 58.801 52.381 4.61 0.00 39.03 2.39
887 1726 1.519898 CGCGCCGGGTATTTGTACT 60.520 57.895 2.18 0.00 0.00 2.73
921 1760 1.943116 TTGCTGGCGCTCTCTCTCTC 61.943 60.000 7.64 0.00 36.97 3.20
922 1761 2.120909 GCTGGCGCTCTCTCTCTCT 61.121 63.158 7.64 0.00 0.00 3.10
923 1762 2.024918 CTGGCGCTCTCTCTCTCTC 58.975 63.158 7.64 0.00 0.00 3.20
924 1763 0.464373 CTGGCGCTCTCTCTCTCTCT 60.464 60.000 7.64 0.00 0.00 3.10
925 1764 0.463654 TGGCGCTCTCTCTCTCTCTC 60.464 60.000 7.64 0.00 0.00 3.20
926 1765 0.179045 GGCGCTCTCTCTCTCTCTCT 60.179 60.000 7.64 0.00 0.00 3.10
927 1766 1.221414 GCGCTCTCTCTCTCTCTCTC 58.779 60.000 0.00 0.00 0.00 3.20
928 1767 1.202580 GCGCTCTCTCTCTCTCTCTCT 60.203 57.143 0.00 0.00 0.00 3.10
929 1768 2.748605 CGCTCTCTCTCTCTCTCTCTC 58.251 57.143 0.00 0.00 0.00 3.20
930 1769 2.363680 CGCTCTCTCTCTCTCTCTCTCT 59.636 54.545 0.00 0.00 0.00 3.10
931 1770 3.551863 CGCTCTCTCTCTCTCTCTCTCTC 60.552 56.522 0.00 0.00 0.00 3.20
932 1771 3.244044 GCTCTCTCTCTCTCTCTCTCTCC 60.244 56.522 0.00 0.00 0.00 3.71
933 1772 4.222336 CTCTCTCTCTCTCTCTCTCTCCT 58.778 52.174 0.00 0.00 0.00 3.69
934 1773 4.219115 TCTCTCTCTCTCTCTCTCTCCTC 58.781 52.174 0.00 0.00 0.00 3.71
935 1774 4.078922 TCTCTCTCTCTCTCTCTCTCCTCT 60.079 50.000 0.00 0.00 0.00 3.69
947 1786 0.462937 TCTCCTCTCTCTCGGAAGCG 60.463 60.000 0.00 0.00 0.00 4.68
983 1822 0.237498 CAAAGCGACGGGTTCTTTCC 59.763 55.000 0.00 0.00 32.40 3.13
1017 1856 1.166531 GGATGGGGAAGTACATGCGC 61.167 60.000 0.00 0.00 0.00 6.09
1024 1863 0.179189 GAAGTACATGCGCAAGTGCC 60.179 55.000 27.10 17.07 41.68 5.01
1026 1865 3.124270 TACATGCGCAAGTGCCGG 61.124 61.111 27.10 0.00 41.68 6.13
1304 2143 2.444895 GGATCAGCTCCGGGGACT 60.445 66.667 4.80 0.00 33.29 3.85
1305 2144 2.066999 GGATCAGCTCCGGGGACTT 61.067 63.158 4.80 0.00 33.29 3.01
1348 2187 4.918201 CGGGGCTGCCGGATTCTC 62.918 72.222 13.40 0.00 0.00 2.87
1464 2303 2.266055 GAAGCGGAGGTGAGTGGG 59.734 66.667 0.00 0.00 39.47 4.61
1490 2329 1.482593 CACTGCCCTAGAATTCTCCGT 59.517 52.381 12.24 0.00 0.00 4.69
1491 2330 2.693591 CACTGCCCTAGAATTCTCCGTA 59.306 50.000 12.24 0.00 0.00 4.02
1549 2389 7.608153 TGAATTACGAGATTTGGTTCTGACTA 58.392 34.615 0.00 0.00 0.00 2.59
1655 2499 1.202663 CCTCCTCTCTCGATACCGACA 60.203 57.143 0.00 0.00 40.30 4.35
1687 2531 9.412460 TCTGCTGAATTATCCATTGTTTTCTAT 57.588 29.630 0.00 0.00 0.00 1.98
1693 2537 9.884465 GAATTATCCATTGTTTTCTATTCTCCG 57.116 33.333 0.00 0.00 0.00 4.63
1709 2553 0.902531 TCCGGGGTGATCTTGAGTTC 59.097 55.000 0.00 0.00 0.00 3.01
1710 2554 0.905357 CCGGGGTGATCTTGAGTTCT 59.095 55.000 0.00 0.00 0.00 3.01
1711 2555 1.279271 CCGGGGTGATCTTGAGTTCTT 59.721 52.381 0.00 0.00 0.00 2.52
1716 2561 3.339141 GGTGATCTTGAGTTCTTGACCC 58.661 50.000 0.00 0.00 0.00 4.46
1743 2588 5.596836 TTGCTTCTGAATTTGACCTGTTT 57.403 34.783 0.00 0.00 0.00 2.83
1746 2591 5.126869 TGCTTCTGAATTTGACCTGTTTGAA 59.873 36.000 0.00 0.00 0.00 2.69
1856 2701 0.107831 AAGCACAAACGCAGGAGGTA 59.892 50.000 0.00 0.00 0.00 3.08
2018 2870 5.772521 AGTGGAAATTACAATTGAGCACAC 58.227 37.500 13.59 10.92 0.00 3.82
2019 2871 5.301551 AGTGGAAATTACAATTGAGCACACA 59.698 36.000 13.59 0.13 0.00 3.72
2020 2872 5.982516 GTGGAAATTACAATTGAGCACACAA 59.017 36.000 13.59 0.00 0.00 3.33
2022 2874 6.183360 TGGAAATTACAATTGAGCACACAAGT 60.183 34.615 13.59 0.00 33.22 3.16
2025 2877 6.875948 ATTACAATTGAGCACACAAGTACA 57.124 33.333 13.59 0.00 33.22 2.90
2028 2880 4.580167 ACAATTGAGCACACAAGTACACAT 59.420 37.500 13.59 0.00 33.22 3.21
2029 2881 5.762711 ACAATTGAGCACACAAGTACACATA 59.237 36.000 13.59 0.00 33.22 2.29
2030 2882 5.862924 ATTGAGCACACAAGTACACATAC 57.137 39.130 0.00 0.00 33.22 2.39
2031 2883 3.313690 TGAGCACACAAGTACACATACG 58.686 45.455 0.00 0.00 36.33 3.06
2032 2884 3.243602 TGAGCACACAAGTACACATACGT 60.244 43.478 0.00 0.00 36.33 3.57
2033 2885 3.314553 AGCACACAAGTACACATACGTC 58.685 45.455 0.00 0.00 36.33 4.34
2035 2887 3.739300 GCACACAAGTACACATACGTCTT 59.261 43.478 0.00 0.00 36.33 3.01
2036 2888 4.376008 GCACACAAGTACACATACGTCTTG 60.376 45.833 8.79 8.79 40.54 3.02
2037 2889 4.149922 CACACAAGTACACATACGTCTTGG 59.850 45.833 13.44 6.77 39.49 3.61
2039 2891 3.243941 ACAAGTACACATACGTCTTGGCA 60.244 43.478 13.44 0.00 39.49 4.92
2054 2909 2.358003 GCACTTGGCAGTCGCTCT 60.358 61.111 0.00 0.00 43.97 4.09
2059 2914 1.211818 CTTGGCAGTCGCTCTATCGC 61.212 60.000 0.00 0.00 38.60 4.58
2105 2961 2.813042 GTGCTCTCGCTGCCTCAC 60.813 66.667 0.00 0.00 36.97 3.51
2192 3057 3.386237 GCCACCGTCTGAGGCTCT 61.386 66.667 16.72 0.00 44.92 4.09
2282 3147 1.519455 GAGACGCTGATCCAACCCG 60.519 63.158 0.00 0.00 0.00 5.28
2313 3179 7.041712 GGAAAACAGTAAAGAGAAAGAGGAGTG 60.042 40.741 0.00 0.00 0.00 3.51
2365 3232 2.682836 GCCTAGAGCTAGCTATGCAAC 58.317 52.381 21.96 6.44 38.99 4.17
2367 3234 3.648009 CCTAGAGCTAGCTATGCAACAC 58.352 50.000 21.96 4.91 31.95 3.32
2369 3236 4.520874 CCTAGAGCTAGCTATGCAACACTA 59.479 45.833 21.96 12.72 31.95 2.74
2370 3237 4.582701 AGAGCTAGCTATGCAACACTAG 57.417 45.455 19.38 13.22 36.11 2.57
2374 3241 4.582701 CTAGCTATGCAACACTAGCTCT 57.417 45.455 20.04 3.95 45.82 4.09
2375 3242 3.451141 AGCTATGCAACACTAGCTCTC 57.549 47.619 12.74 0.00 45.82 3.20
2376 3243 3.030291 AGCTATGCAACACTAGCTCTCT 58.970 45.455 12.74 0.00 45.82 3.10
2377 3244 3.068024 AGCTATGCAACACTAGCTCTCTC 59.932 47.826 12.74 0.00 45.82 3.20
2378 3245 3.068024 GCTATGCAACACTAGCTCTCTCT 59.932 47.826 9.34 0.00 37.85 3.10
2386 3257 1.774856 ACTAGCTCTCTCTCTCTCCCC 59.225 57.143 0.00 0.00 0.00 4.81
2393 3264 2.316067 TCTCTCTCTCTCCCCATCCAAA 59.684 50.000 0.00 0.00 0.00 3.28
2405 3276 5.803552 TCCCCATCCAAATTGTTCAAATTC 58.196 37.500 0.00 0.00 0.00 2.17
2409 3280 5.062558 CCATCCAAATTGTTCAAATTCGCTC 59.937 40.000 0.00 0.00 0.00 5.03
2411 3282 4.038522 TCCAAATTGTTCAAATTCGCTCCA 59.961 37.500 0.00 0.00 0.00 3.86
2429 3300 5.236478 CGCTCCAGTTTTTAACTTCTTCTGA 59.764 40.000 0.00 0.00 40.46 3.27
2509 3382 2.548480 CTCCTGTTTCCGTTTCCAGTTC 59.452 50.000 0.00 0.00 0.00 3.01
2511 3384 0.658897 TGTTTCCGTTTCCAGTTCGC 59.341 50.000 0.00 0.00 0.00 4.70
2711 3588 2.939022 GCACAGTCACGCTTGTCC 59.061 61.111 0.00 0.00 0.00 4.02
2743 3623 1.702491 CCGGCGATTTTTCTCCCGTC 61.702 60.000 9.30 0.00 37.37 4.79
2749 3633 2.166664 CGATTTTTCTCCCGTCCTCTCT 59.833 50.000 0.00 0.00 0.00 3.10
2750 3634 3.735514 CGATTTTTCTCCCGTCCTCTCTC 60.736 52.174 0.00 0.00 0.00 3.20
2751 3635 2.606751 TTTTCTCCCGTCCTCTCTCT 57.393 50.000 0.00 0.00 0.00 3.10
2781 3665 1.605058 AACAGCGCTCCGTCCTGTAT 61.605 55.000 7.13 0.00 0.00 2.29
2782 3666 0.750546 ACAGCGCTCCGTCCTGTATA 60.751 55.000 7.13 0.00 0.00 1.47
2783 3667 0.598562 CAGCGCTCCGTCCTGTATAT 59.401 55.000 7.13 0.00 0.00 0.86
2785 3669 2.423892 CAGCGCTCCGTCCTGTATATAT 59.576 50.000 7.13 0.00 0.00 0.86
2786 3670 3.626217 CAGCGCTCCGTCCTGTATATATA 59.374 47.826 7.13 0.00 0.00 0.86
2787 3671 4.276183 CAGCGCTCCGTCCTGTATATATAT 59.724 45.833 7.13 0.00 0.00 0.86
2788 3672 5.469084 CAGCGCTCCGTCCTGTATATATATA 59.531 44.000 7.13 0.00 0.00 0.86
2789 3673 6.149640 CAGCGCTCCGTCCTGTATATATATAT 59.850 42.308 7.13 10.10 0.00 0.86
2813 3704 2.301583 AGAGAGGAAGCTTTGTCTGTCC 59.698 50.000 14.45 3.46 0.00 4.02
2816 3707 1.149148 GGAAGCTTTGTCTGTCCGTC 58.851 55.000 0.00 0.00 0.00 4.79
2876 3767 1.210155 CCGCCAGCTAAACAAGTGC 59.790 57.895 0.00 0.00 0.00 4.40
2905 3796 2.035066 GCGAAATGATTTGGGATCTGGG 59.965 50.000 0.00 0.00 0.00 4.45
2973 3864 3.721706 GCAGGGGGTGGTGGAGAG 61.722 72.222 0.00 0.00 0.00 3.20
2976 3867 4.348495 GGGGGTGGTGGAGAGGGA 62.348 72.222 0.00 0.00 0.00 4.20
3074 3966 0.387929 TCTACCGATGATTCGTGGGC 59.612 55.000 6.82 0.00 43.97 5.36
3129 4030 2.057922 CAAGAGGGGGTATATGCTGGT 58.942 52.381 0.00 0.00 0.00 4.00
3142 4043 1.102809 TGCTGGTCTTTGGCAGTGTG 61.103 55.000 0.00 0.00 0.00 3.82
3180 4081 2.768833 TCCGTGCGTATGCTACTAAG 57.231 50.000 8.69 0.00 43.34 2.18
3181 4082 2.019249 TCCGTGCGTATGCTACTAAGT 58.981 47.619 8.69 0.00 43.34 2.24
3182 4083 3.205338 TCCGTGCGTATGCTACTAAGTA 58.795 45.455 8.69 0.00 43.34 2.24
3183 4084 3.002656 TCCGTGCGTATGCTACTAAGTAC 59.997 47.826 8.69 0.00 43.34 2.73
3184 4085 2.962834 CGTGCGTATGCTACTAAGTACG 59.037 50.000 8.69 3.20 43.34 3.67
3185 4086 3.544834 CGTGCGTATGCTACTAAGTACGT 60.545 47.826 8.69 0.00 41.26 3.57
3186 4087 4.318050 CGTGCGTATGCTACTAAGTACGTA 60.318 45.833 8.69 0.00 41.26 3.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.581354 CTGTTCAGGAGGGCGAGG 59.419 66.667 0.00 0.00 0.00 4.63
1 2 1.544825 TTCCTGTTCAGGAGGGCGAG 61.545 60.000 18.99 0.00 39.43 5.03
2 3 0.909610 ATTCCTGTTCAGGAGGGCGA 60.910 55.000 18.99 7.06 39.43 5.54
3 4 0.462759 GATTCCTGTTCAGGAGGGCG 60.463 60.000 18.99 0.00 39.43 6.13
4 5 0.620556 TGATTCCTGTTCAGGAGGGC 59.379 55.000 18.99 13.50 39.43 5.19
5 6 3.084786 GTTTGATTCCTGTTCAGGAGGG 58.915 50.000 18.99 0.00 39.43 4.30
6 7 3.084786 GGTTTGATTCCTGTTCAGGAGG 58.915 50.000 18.99 0.00 39.43 4.30
7 8 4.026356 AGGTTTGATTCCTGTTCAGGAG 57.974 45.455 18.99 0.00 39.43 3.69
8 9 5.576563 TTAGGTTTGATTCCTGTTCAGGA 57.423 39.130 16.47 16.47 36.60 3.86
9 10 5.534654 TGTTTAGGTTTGATTCCTGTTCAGG 59.465 40.000 12.20 12.20 36.60 3.86
10 11 6.486657 TCTGTTTAGGTTTGATTCCTGTTCAG 59.513 38.462 0.00 0.00 36.60 3.02
11 12 6.262273 GTCTGTTTAGGTTTGATTCCTGTTCA 59.738 38.462 0.00 0.00 36.60 3.18
12 13 6.486993 AGTCTGTTTAGGTTTGATTCCTGTTC 59.513 38.462 0.00 0.00 36.60 3.18
13 14 6.365520 AGTCTGTTTAGGTTTGATTCCTGTT 58.634 36.000 0.00 0.00 36.60 3.16
14 15 5.941788 AGTCTGTTTAGGTTTGATTCCTGT 58.058 37.500 0.00 0.00 36.60 4.00
15 16 7.979444 TTAGTCTGTTTAGGTTTGATTCCTG 57.021 36.000 0.00 0.00 36.60 3.86
16 17 8.990163 TTTTAGTCTGTTTAGGTTTGATTCCT 57.010 30.769 0.00 0.00 38.91 3.36
39 40 6.240894 TCATGCTTCATCTCTAGGTGTTTTT 58.759 36.000 0.00 0.00 0.00 1.94
40 41 5.809001 TCATGCTTCATCTCTAGGTGTTTT 58.191 37.500 0.00 0.00 0.00 2.43
41 42 5.426504 CTCATGCTTCATCTCTAGGTGTTT 58.573 41.667 0.00 0.00 0.00 2.83
42 43 4.682859 GCTCATGCTTCATCTCTAGGTGTT 60.683 45.833 0.00 0.00 36.03 3.32
43 44 3.181467 GCTCATGCTTCATCTCTAGGTGT 60.181 47.826 0.00 0.00 36.03 4.16
44 45 3.391965 GCTCATGCTTCATCTCTAGGTG 58.608 50.000 0.00 0.00 36.03 4.00
45 46 2.368221 GGCTCATGCTTCATCTCTAGGT 59.632 50.000 0.00 0.00 39.59 3.08
46 47 2.609984 CGGCTCATGCTTCATCTCTAGG 60.610 54.545 0.00 0.00 39.59 3.02
47 48 2.035704 ACGGCTCATGCTTCATCTCTAG 59.964 50.000 0.00 0.00 39.59 2.43
48 49 2.034878 ACGGCTCATGCTTCATCTCTA 58.965 47.619 0.00 0.00 39.59 2.43
49 50 0.829333 ACGGCTCATGCTTCATCTCT 59.171 50.000 0.00 0.00 39.59 3.10
50 51 1.216122 GACGGCTCATGCTTCATCTC 58.784 55.000 0.00 0.00 39.59 2.75
51 52 0.179062 GGACGGCTCATGCTTCATCT 60.179 55.000 0.00 0.00 39.59 2.90
52 53 1.162800 GGGACGGCTCATGCTTCATC 61.163 60.000 0.00 0.00 39.59 2.92
53 54 1.153086 GGGACGGCTCATGCTTCAT 60.153 57.895 0.00 0.00 39.59 2.57
54 55 2.268920 GGGACGGCTCATGCTTCA 59.731 61.111 0.00 0.00 39.59 3.02
73 74 3.728292 GATCCCAGCCCCTTGCCAG 62.728 68.421 0.00 0.00 42.71 4.85
74 75 3.743017 GATCCCAGCCCCTTGCCA 61.743 66.667 0.00 0.00 42.71 4.92
75 76 4.529731 GGATCCCAGCCCCTTGCC 62.530 72.222 0.00 0.00 42.71 4.52
76 77 2.990994 GATGGATCCCAGCCCCTTGC 62.991 65.000 9.90 0.00 36.75 4.01
77 78 1.152368 GATGGATCCCAGCCCCTTG 59.848 63.158 9.90 0.00 36.75 3.61
78 79 2.455565 CGATGGATCCCAGCCCCTT 61.456 63.158 9.90 0.00 36.45 3.95
79 80 2.851102 CGATGGATCCCAGCCCCT 60.851 66.667 9.90 0.00 36.45 4.79
80 81 4.650377 GCGATGGATCCCAGCCCC 62.650 72.222 9.90 0.00 36.45 5.80
81 82 3.877450 TGCGATGGATCCCAGCCC 61.877 66.667 9.90 0.00 36.45 5.19
82 83 2.592861 GTGCGATGGATCCCAGCC 60.593 66.667 9.90 3.08 36.45 4.85
83 84 2.592861 GGTGCGATGGATCCCAGC 60.593 66.667 9.90 12.47 36.75 4.85
84 85 0.533755 GAAGGTGCGATGGATCCCAG 60.534 60.000 9.90 1.27 36.75 4.45
85 86 1.526887 GAAGGTGCGATGGATCCCA 59.473 57.895 9.90 0.00 38.19 4.37
86 87 1.595382 CGAAGGTGCGATGGATCCC 60.595 63.158 9.90 0.00 0.00 3.85
87 88 1.144057 ACGAAGGTGCGATGGATCC 59.856 57.895 4.20 4.20 34.83 3.36
88 89 0.179111 TCACGAAGGTGCGATGGATC 60.179 55.000 0.00 0.00 44.03 3.36
89 90 0.460284 GTCACGAAGGTGCGATGGAT 60.460 55.000 0.00 0.00 44.03 3.41
90 91 1.080093 GTCACGAAGGTGCGATGGA 60.080 57.895 0.00 0.00 44.03 3.41
91 92 2.100631 GGTCACGAAGGTGCGATGG 61.101 63.158 0.00 0.00 44.03 3.51
92 93 2.100631 GGGTCACGAAGGTGCGATG 61.101 63.158 0.00 0.00 44.03 3.84
93 94 1.827399 AAGGGTCACGAAGGTGCGAT 61.827 55.000 0.00 0.00 44.03 4.58
94 95 1.180456 TAAGGGTCACGAAGGTGCGA 61.180 55.000 0.00 0.00 44.03 5.10
95 96 0.320073 TTAAGGGTCACGAAGGTGCG 60.320 55.000 0.00 0.00 44.03 5.34
96 97 1.439679 CTTAAGGGTCACGAAGGTGC 58.560 55.000 0.00 0.00 44.03 5.01
97 98 1.944430 GCCTTAAGGGTCACGAAGGTG 60.944 57.143 23.06 0.00 38.57 4.00
98 99 0.323957 GCCTTAAGGGTCACGAAGGT 59.676 55.000 23.06 0.00 38.57 3.50
99 100 0.323629 TGCCTTAAGGGTCACGAAGG 59.676 55.000 23.06 4.81 39.03 3.46
100 101 2.178912 TTGCCTTAAGGGTCACGAAG 57.821 50.000 23.06 0.00 37.43 3.79
101 102 2.871096 ATTGCCTTAAGGGTCACGAA 57.129 45.000 23.06 0.00 37.43 3.85
102 103 2.169769 CCTATTGCCTTAAGGGTCACGA 59.830 50.000 23.06 6.46 37.43 4.35
103 104 2.169769 TCCTATTGCCTTAAGGGTCACG 59.830 50.000 23.06 4.87 37.43 4.35
104 105 3.454812 TCTCCTATTGCCTTAAGGGTCAC 59.545 47.826 23.06 6.77 37.43 3.67
105 106 3.454812 GTCTCCTATTGCCTTAAGGGTCA 59.545 47.826 23.06 10.53 37.43 4.02
106 107 3.492829 CGTCTCCTATTGCCTTAAGGGTC 60.493 52.174 23.06 7.88 37.43 4.46
107 108 2.434702 CGTCTCCTATTGCCTTAAGGGT 59.565 50.000 23.06 0.00 37.43 4.34
108 109 2.698797 TCGTCTCCTATTGCCTTAAGGG 59.301 50.000 23.06 5.72 35.18 3.95
109 110 3.637229 TCTCGTCTCCTATTGCCTTAAGG 59.363 47.826 17.81 17.81 38.53 2.69
110 111 4.098044 TGTCTCGTCTCCTATTGCCTTAAG 59.902 45.833 0.00 0.00 0.00 1.85
111 112 4.021229 TGTCTCGTCTCCTATTGCCTTAA 58.979 43.478 0.00 0.00 0.00 1.85
112 113 3.628008 TGTCTCGTCTCCTATTGCCTTA 58.372 45.455 0.00 0.00 0.00 2.69
113 114 2.428890 CTGTCTCGTCTCCTATTGCCTT 59.571 50.000 0.00 0.00 0.00 4.35
114 115 2.028130 CTGTCTCGTCTCCTATTGCCT 58.972 52.381 0.00 0.00 0.00 4.75
115 116 2.025155 TCTGTCTCGTCTCCTATTGCC 58.975 52.381 0.00 0.00 0.00 4.52
116 117 3.316588 TGATCTGTCTCGTCTCCTATTGC 59.683 47.826 0.00 0.00 0.00 3.56
117 118 5.277825 GTTGATCTGTCTCGTCTCCTATTG 58.722 45.833 0.00 0.00 0.00 1.90
118 119 4.035792 CGTTGATCTGTCTCGTCTCCTATT 59.964 45.833 0.00 0.00 0.00 1.73
119 120 3.562141 CGTTGATCTGTCTCGTCTCCTAT 59.438 47.826 0.00 0.00 0.00 2.57
120 121 2.937149 CGTTGATCTGTCTCGTCTCCTA 59.063 50.000 0.00 0.00 0.00 2.94
121 122 1.740585 CGTTGATCTGTCTCGTCTCCT 59.259 52.381 0.00 0.00 0.00 3.69
122 123 1.202200 CCGTTGATCTGTCTCGTCTCC 60.202 57.143 0.00 0.00 0.00 3.71
123 124 1.795889 GCCGTTGATCTGTCTCGTCTC 60.796 57.143 0.00 0.00 0.00 3.36
124 125 0.171455 GCCGTTGATCTGTCTCGTCT 59.829 55.000 0.00 0.00 0.00 4.18
125 126 0.109272 TGCCGTTGATCTGTCTCGTC 60.109 55.000 0.00 0.00 0.00 4.20
126 127 0.388649 GTGCCGTTGATCTGTCTCGT 60.389 55.000 0.00 0.00 0.00 4.18
127 128 1.406219 CGTGCCGTTGATCTGTCTCG 61.406 60.000 0.00 0.00 0.00 4.04
128 129 0.388649 ACGTGCCGTTGATCTGTCTC 60.389 55.000 0.00 0.00 36.35 3.36
129 130 0.388649 GACGTGCCGTTGATCTGTCT 60.389 55.000 0.00 0.00 41.37 3.41
130 131 1.674611 CGACGTGCCGTTGATCTGTC 61.675 60.000 8.74 0.00 43.17 3.51
131 132 1.733041 CGACGTGCCGTTGATCTGT 60.733 57.895 8.74 0.00 43.17 3.41
132 133 2.444624 CCGACGTGCCGTTGATCTG 61.445 63.158 14.32 0.00 43.17 2.90
133 134 2.126071 CCGACGTGCCGTTGATCT 60.126 61.111 14.32 0.00 43.17 2.75
134 135 3.849953 GCCGACGTGCCGTTGATC 61.850 66.667 14.32 0.00 43.17 2.92
142 143 3.420214 TTATCTCCCGCCGACGTGC 62.420 63.158 0.00 0.00 37.70 5.34
143 144 1.299165 CTTATCTCCCGCCGACGTG 60.299 63.158 0.00 0.00 37.70 4.49
144 145 1.033746 TTCTTATCTCCCGCCGACGT 61.034 55.000 0.00 0.00 37.70 4.34
145 146 0.101759 TTTCTTATCTCCCGCCGACG 59.898 55.000 0.00 0.00 39.67 5.12
146 147 1.568606 GTTTCTTATCTCCCGCCGAC 58.431 55.000 0.00 0.00 0.00 4.79
147 148 0.462789 GGTTTCTTATCTCCCGCCGA 59.537 55.000 0.00 0.00 0.00 5.54
148 149 0.532196 GGGTTTCTTATCTCCCGCCG 60.532 60.000 0.00 0.00 0.00 6.46
149 150 0.837940 AGGGTTTCTTATCTCCCGCC 59.162 55.000 0.00 0.00 44.13 6.13
150 151 2.093128 TCAAGGGTTTCTTATCTCCCGC 60.093 50.000 0.00 0.00 44.13 6.13
151 152 3.906720 TCAAGGGTTTCTTATCTCCCG 57.093 47.619 0.00 0.00 44.13 5.14
152 153 5.104318 AGACATCAAGGGTTTCTTATCTCCC 60.104 44.000 0.00 0.00 40.16 4.30
153 154 5.995446 AGACATCAAGGGTTTCTTATCTCC 58.005 41.667 0.00 0.00 33.68 3.71
154 155 9.103861 CTTAAGACATCAAGGGTTTCTTATCTC 57.896 37.037 0.00 0.00 33.68 2.75
155 156 8.049721 CCTTAAGACATCAAGGGTTTCTTATCT 58.950 37.037 3.36 0.00 38.12 1.98
156 157 8.214721 CCTTAAGACATCAAGGGTTTCTTATC 57.785 38.462 3.36 0.00 38.12 1.75
211 212 1.726791 CTTGATCTCGGTTGGTTGTCG 59.273 52.381 0.00 0.00 0.00 4.35
221 222 0.824109 TACAGTGGGCTTGATCTCGG 59.176 55.000 0.00 0.00 0.00 4.63
253 254 4.551990 CGATAAGTTGCAAGTGTCGTTTGT 60.552 41.667 23.69 5.44 0.00 2.83
291 292 7.021790 GGGACACTATAAGCTTTTTCGAAAAG 58.978 38.462 21.53 16.55 0.00 2.27
298 299 4.017126 GCAGGGGACACTATAAGCTTTTT 58.983 43.478 3.20 0.00 0.00 1.94
299 300 3.010138 TGCAGGGGACACTATAAGCTTTT 59.990 43.478 3.20 0.00 0.00 2.27
300 301 2.576191 TGCAGGGGACACTATAAGCTTT 59.424 45.455 3.20 0.00 0.00 3.51
301 302 2.196595 TGCAGGGGACACTATAAGCTT 58.803 47.619 3.48 3.48 0.00 3.74
302 303 1.879575 TGCAGGGGACACTATAAGCT 58.120 50.000 0.00 0.00 0.00 3.74
303 304 2.710096 TTGCAGGGGACACTATAAGC 57.290 50.000 0.00 0.00 0.00 3.09
343 344 8.911247 AAAAATAACCAGCGAATAAGTTCATC 57.089 30.769 0.00 0.00 33.86 2.92
382 390 8.986477 AAAGACTGAATATTTTTACCATGCAC 57.014 30.769 0.00 0.00 0.00 4.57
447 541 7.553760 TGCTGAATGCTTCACTGAATATTCTTA 59.446 33.333 16.24 0.00 43.37 2.10
453 547 4.142534 GCTTGCTGAATGCTTCACTGAATA 60.143 41.667 0.00 0.00 43.37 1.75
632 733 1.463553 AAAAACTTGGCCCCTCGCAG 61.464 55.000 0.00 0.00 40.31 5.18
684 785 3.925090 GGTACCGGCGAGGGGATG 61.925 72.222 9.30 0.00 46.96 3.51
711 812 2.259204 GGCGCACTACACGGTACA 59.741 61.111 10.83 0.00 0.00 2.90
712 813 2.877582 CGGCGCACTACACGGTAC 60.878 66.667 10.83 0.00 0.00 3.34
836 1675 3.480225 ATTCGGATCGGACGGTCGC 62.480 63.158 1.88 0.00 0.00 5.19
837 1676 1.370172 GATTCGGATCGGACGGTCG 60.370 63.158 1.88 0.00 0.00 4.79
839 1678 2.842256 CGGATTCGGATCGGACGGT 61.842 63.158 5.32 0.00 35.30 4.83
872 1711 2.981997 CGGAGTACAAATACCCGGC 58.018 57.895 0.00 0.00 39.52 6.13
887 1726 1.449601 GCAAATTCGCTCCTCCGGA 60.450 57.895 2.93 2.93 0.00 5.14
909 1748 2.363680 AGAGAGAGAGAGAGAGAGAGCG 59.636 54.545 0.00 0.00 0.00 5.03
921 1760 2.036475 CCGAGAGAGAGGAGAGAGAGAG 59.964 59.091 0.00 0.00 0.00 3.20
922 1761 2.039418 CCGAGAGAGAGGAGAGAGAGA 58.961 57.143 0.00 0.00 0.00 3.10
923 1762 2.039418 TCCGAGAGAGAGGAGAGAGAG 58.961 57.143 0.00 0.00 31.95 3.20
924 1763 2.168458 TCCGAGAGAGAGGAGAGAGA 57.832 55.000 0.00 0.00 31.95 3.10
925 1764 2.838736 CTTCCGAGAGAGAGGAGAGAG 58.161 57.143 0.00 0.00 37.88 3.20
926 1765 1.134220 GCTTCCGAGAGAGAGGAGAGA 60.134 57.143 0.00 0.00 37.88 3.10
927 1766 1.308998 GCTTCCGAGAGAGAGGAGAG 58.691 60.000 0.00 0.00 37.88 3.20
928 1767 0.462937 CGCTTCCGAGAGAGAGGAGA 60.463 60.000 0.00 0.00 37.88 3.71
929 1768 0.746563 ACGCTTCCGAGAGAGAGGAG 60.747 60.000 0.00 0.00 37.88 3.69
930 1769 1.027255 CACGCTTCCGAGAGAGAGGA 61.027 60.000 0.00 0.00 38.29 3.71
931 1770 1.431440 CACGCTTCCGAGAGAGAGG 59.569 63.158 0.00 0.00 38.29 3.69
932 1771 1.226547 GCACGCTTCCGAGAGAGAG 60.227 63.158 0.00 0.00 38.29 3.20
933 1772 2.878429 GCACGCTTCCGAGAGAGA 59.122 61.111 0.00 0.00 38.29 3.10
934 1773 2.578178 CGCACGCTTCCGAGAGAG 60.578 66.667 0.00 0.00 38.29 3.20
935 1774 4.116328 CCGCACGCTTCCGAGAGA 62.116 66.667 0.00 0.00 38.29 3.10
1132 1971 0.037326 TGCTTCCTCATCTTCGCGTT 60.037 50.000 5.77 0.00 0.00 4.84
1416 2255 3.127352 CTCTCTAGCCGCCACGTCC 62.127 68.421 0.00 0.00 0.00 4.79
1469 2308 1.757118 CGGAGAATTCTAGGGCAGTGA 59.243 52.381 8.25 0.00 0.00 3.41
1470 2309 1.482593 ACGGAGAATTCTAGGGCAGTG 59.517 52.381 8.25 0.00 0.00 3.66
1471 2310 1.867363 ACGGAGAATTCTAGGGCAGT 58.133 50.000 8.25 0.00 0.00 4.40
1472 2311 4.402056 TTTACGGAGAATTCTAGGGCAG 57.598 45.455 8.25 0.00 0.00 4.85
1490 2329 0.595567 CGATCGACCGGCCGAATTTA 60.596 55.000 30.73 8.30 42.22 1.40
1491 2330 1.881252 CGATCGACCGGCCGAATTT 60.881 57.895 30.73 7.60 42.22 1.82
1501 2340 2.373938 CAGAAACTGCCGATCGACC 58.626 57.895 18.66 7.76 0.00 4.79
1512 2352 3.664107 TCGTAATTCAGCAGCAGAAACT 58.336 40.909 4.09 0.00 0.00 2.66
1549 2389 0.179062 GCCTGCTGATCGACCAAGAT 60.179 55.000 0.00 0.00 0.00 2.40
1687 2531 1.195115 CTCAAGATCACCCCGGAGAA 58.805 55.000 0.73 0.00 0.00 2.87
1693 2537 3.339141 GTCAAGAACTCAAGATCACCCC 58.661 50.000 0.00 0.00 0.00 4.95
1709 2553 1.001378 CAGAAGCAAAACCGGGTCAAG 60.001 52.381 6.32 0.00 0.00 3.02
1710 2554 1.028905 CAGAAGCAAAACCGGGTCAA 58.971 50.000 6.32 0.00 0.00 3.18
1711 2555 0.181587 TCAGAAGCAAAACCGGGTCA 59.818 50.000 6.32 0.00 0.00 4.02
1716 2561 3.735746 GGTCAAATTCAGAAGCAAAACCG 59.264 43.478 0.00 0.00 0.00 4.44
1743 2588 3.053693 CCCTCCTGGATTACCACAATTCA 60.054 47.826 0.00 0.00 41.77 2.57
1746 2591 2.780010 CTCCCTCCTGGATTACCACAAT 59.220 50.000 0.00 0.00 44.07 2.71
1788 2633 2.125147 TCGCTCAAATCTGCCGGG 60.125 61.111 2.18 0.00 0.00 5.73
1793 2638 1.066573 ACTCCAGGTCGCTCAAATCTG 60.067 52.381 0.00 0.00 0.00 2.90
1856 2701 2.025418 GTCGTCGTTGTTGCCGGAT 61.025 57.895 5.05 0.00 0.00 4.18
1892 2737 0.818296 TCTCGCCTCCAAGTCTAAGC 59.182 55.000 0.00 0.00 0.00 3.09
2018 2870 3.122948 GTGCCAAGACGTATGTGTACTTG 59.877 47.826 7.65 7.65 38.02 3.16
2019 2871 3.006537 AGTGCCAAGACGTATGTGTACTT 59.993 43.478 0.00 0.00 0.00 2.24
2020 2872 2.561419 AGTGCCAAGACGTATGTGTACT 59.439 45.455 0.00 0.00 0.00 2.73
2022 2874 3.322369 CAAGTGCCAAGACGTATGTGTA 58.678 45.455 0.00 0.00 0.00 2.90
2025 2877 1.808411 CCAAGTGCCAAGACGTATGT 58.192 50.000 0.00 0.00 0.00 2.29
2028 2880 0.602638 CTGCCAAGTGCCAAGACGTA 60.603 55.000 0.00 0.00 40.16 3.57
2029 2881 1.893808 CTGCCAAGTGCCAAGACGT 60.894 57.895 0.00 0.00 40.16 4.34
2030 2882 1.845809 GACTGCCAAGTGCCAAGACG 61.846 60.000 0.00 0.00 40.16 4.18
2031 2883 1.845809 CGACTGCCAAGTGCCAAGAC 61.846 60.000 0.00 0.00 40.16 3.01
2032 2884 1.597854 CGACTGCCAAGTGCCAAGA 60.598 57.895 0.00 0.00 40.16 3.02
2033 2885 2.949106 CGACTGCCAAGTGCCAAG 59.051 61.111 0.00 0.00 40.16 3.61
2035 2887 4.254709 AGCGACTGCCAAGTGCCA 62.255 61.111 0.00 0.00 44.31 4.92
2036 2888 2.507110 TAGAGCGACTGCCAAGTGCC 62.507 60.000 0.00 0.00 44.31 5.01
2037 2889 0.460987 ATAGAGCGACTGCCAAGTGC 60.461 55.000 0.00 0.00 44.31 4.40
2039 2891 0.101399 CGATAGAGCGACTGCCAAGT 59.899 55.000 0.00 0.00 44.31 3.16
2105 2961 1.060713 CGTCGAAGTTGTACCTGCAG 58.939 55.000 6.78 6.78 0.00 4.41
2190 3046 3.181504 CGTCATTTTGCATCATGCTCAGA 60.182 43.478 11.84 0.00 45.31 3.27
2192 3057 2.159352 CCGTCATTTTGCATCATGCTCA 60.159 45.455 11.84 0.00 45.31 4.26
2282 3147 7.480810 TCTTTCTCTTTACTGTTTTCCTTTGC 58.519 34.615 0.00 0.00 0.00 3.68
2357 3224 4.580167 AGAGAGAGAGCTAGTGTTGCATAG 59.420 45.833 0.00 0.00 0.00 2.23
2358 3225 4.531854 AGAGAGAGAGCTAGTGTTGCATA 58.468 43.478 0.00 0.00 0.00 3.14
2364 3231 2.172717 GGGAGAGAGAGAGAGCTAGTGT 59.827 54.545 0.00 0.00 0.00 3.55
2365 3232 2.487265 GGGGAGAGAGAGAGAGCTAGTG 60.487 59.091 0.00 0.00 0.00 2.74
2367 3234 1.774254 TGGGGAGAGAGAGAGAGCTAG 59.226 57.143 0.00 0.00 0.00 3.42
2369 3236 1.145738 GATGGGGAGAGAGAGAGAGCT 59.854 57.143 0.00 0.00 0.00 4.09
2370 3237 1.620822 GATGGGGAGAGAGAGAGAGC 58.379 60.000 0.00 0.00 0.00 4.09
2371 3238 1.498576 TGGATGGGGAGAGAGAGAGAG 59.501 57.143 0.00 0.00 0.00 3.20
2372 3239 1.613241 TGGATGGGGAGAGAGAGAGA 58.387 55.000 0.00 0.00 0.00 3.10
2373 3240 2.468301 TTGGATGGGGAGAGAGAGAG 57.532 55.000 0.00 0.00 0.00 3.20
2374 3241 2.948889 TTTGGATGGGGAGAGAGAGA 57.051 50.000 0.00 0.00 0.00 3.10
2375 3242 3.201708 ACAATTTGGATGGGGAGAGAGAG 59.798 47.826 0.78 0.00 0.00 3.20
2376 3243 3.192944 ACAATTTGGATGGGGAGAGAGA 58.807 45.455 0.78 0.00 0.00 3.10
2377 3244 3.659183 ACAATTTGGATGGGGAGAGAG 57.341 47.619 0.78 0.00 0.00 3.20
2378 3245 3.333381 TGAACAATTTGGATGGGGAGAGA 59.667 43.478 0.78 0.00 0.00 3.10
2386 3257 5.062558 GGAGCGAATTTGAACAATTTGGATG 59.937 40.000 0.78 0.00 0.00 3.51
2393 3264 4.853924 AACTGGAGCGAATTTGAACAAT 57.146 36.364 0.00 0.00 0.00 2.71
2405 3276 5.236478 TCAGAAGAAGTTAAAAACTGGAGCG 59.764 40.000 0.00 0.00 41.91 5.03
2429 3300 6.723977 TGGCCTAGTGAATGAAAGGTAAAAAT 59.276 34.615 3.32 0.00 0.00 1.82
2435 3308 2.615493 CGTGGCCTAGTGAATGAAAGGT 60.615 50.000 3.32 0.00 0.00 3.50
2436 3309 2.009774 CGTGGCCTAGTGAATGAAAGG 58.990 52.381 3.32 0.00 0.00 3.11
2438 3311 1.948611 GCCGTGGCCTAGTGAATGAAA 60.949 52.381 3.32 0.00 34.56 2.69
2440 3313 1.220749 GCCGTGGCCTAGTGAATGA 59.779 57.895 3.32 0.00 34.56 2.57
2441 3314 2.173669 CGCCGTGGCCTAGTGAATG 61.174 63.158 3.32 0.00 37.98 2.67
2442 3315 1.686325 ATCGCCGTGGCCTAGTGAAT 61.686 55.000 3.32 0.00 37.98 2.57
2629 3506 4.586618 TGCGAGAGAAGCAGAAGC 57.413 55.556 0.00 0.00 40.01 3.86
2634 3511 6.341316 AGAATAAAATACTGCGAGAGAAGCA 58.659 36.000 0.00 0.00 42.04 3.91
2743 3623 0.670546 TTCGCCGCAAAAGAGAGAGG 60.671 55.000 0.00 0.00 0.00 3.69
2749 3633 1.008995 GCTGTTTCGCCGCAAAAGA 60.009 52.632 0.00 0.00 0.00 2.52
2750 3634 2.356796 CGCTGTTTCGCCGCAAAAG 61.357 57.895 0.00 0.00 0.00 2.27
2751 3635 2.352915 CGCTGTTTCGCCGCAAAA 60.353 55.556 0.00 0.00 0.00 2.44
2785 3669 8.001875 ACAGACAAAGCTTCCTCTCTCTATATA 58.998 37.037 0.00 0.00 0.00 0.86
2786 3670 6.838612 ACAGACAAAGCTTCCTCTCTCTATAT 59.161 38.462 0.00 0.00 0.00 0.86
2787 3671 6.191315 ACAGACAAAGCTTCCTCTCTCTATA 58.809 40.000 0.00 0.00 0.00 1.31
2788 3672 5.022787 ACAGACAAAGCTTCCTCTCTCTAT 58.977 41.667 0.00 0.00 0.00 1.98
2789 3673 4.411927 ACAGACAAAGCTTCCTCTCTCTA 58.588 43.478 0.00 0.00 0.00 2.43
2876 3767 3.796178 CCCAAATCATTTCGCCGTAATTG 59.204 43.478 0.00 0.00 0.00 2.32
2905 3796 4.424566 CATGTGCGTGCCCAAGCC 62.425 66.667 3.86 0.00 38.69 4.35
2976 3867 2.366972 CATTCCTCCCTCCCCCGT 60.367 66.667 0.00 0.00 0.00 5.28
3074 3966 2.203070 GCACGTGCCCCTATCTGG 60.203 66.667 30.12 0.00 34.31 3.86
3129 4030 1.072806 AGCATCTCACACTGCCAAAGA 59.927 47.619 0.00 0.00 39.22 2.52
3142 4043 4.693095 ACGGAAAGAAAGAAGAAGCATCTC 59.307 41.667 0.00 0.00 33.77 2.75


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

AutoCloner maintained by Alex Coulton.