Multiple sequence alignment - TraesCS7B01G278800

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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 TraesCS7B01G278800 chr7B 100.000 4062 0 0 1 4062 511061371 511065432 0.000000e+00 7502
1 TraesCS7B01G278800 chr7D 93.264 3474 134 36 653 4062 484361342 484364779 0.000000e+00 5027
2 TraesCS7B01G278800 chr7D 83.453 278 32 9 299 566 484360904 484361177 3.140000e-61 246
3 TraesCS7B01G278800 chr7A 94.552 3194 115 20 908 4062 552678993 552682166 0.000000e+00 4879
4 TraesCS7B01G278800 chr7A 90.155 193 5 2 653 831 552678395 552678587 5.250000e-59 239
5 TraesCS7B01G278800 chr7A 78.388 273 32 8 299 566 552677966 552678216 7.030000e-33 152
6 TraesCS7B01G278800 chr6D 77.032 1772 358 35 1307 3052 155542104 155543852 0.000000e+00 972
7 TraesCS7B01G278800 chr6B 76.949 1770 363 34 1307 3052 278539918 278541666 0.000000e+00 966
8 TraesCS7B01G278800 chr6A 76.637 1772 365 34 1307 3052 209267068 209268816 0.000000e+00 933


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 TraesCS7B01G278800 chr7B 511061371 511065432 4061 False 7502.000000 7502 100.000000 1 4062 1 chr7B.!!$F1 4061
1 TraesCS7B01G278800 chr7D 484360904 484364779 3875 False 2636.500000 5027 88.358500 299 4062 2 chr7D.!!$F1 3763
2 TraesCS7B01G278800 chr7A 552677966 552682166 4200 False 1756.666667 4879 87.698333 299 4062 3 chr7A.!!$F1 3763
3 TraesCS7B01G278800 chr6D 155542104 155543852 1748 False 972.000000 972 77.032000 1307 3052 1 chr6D.!!$F1 1745
4 TraesCS7B01G278800 chr6B 278539918 278541666 1748 False 966.000000 966 76.949000 1307 3052 1 chr6B.!!$F1 1745
5 TraesCS7B01G278800 chr6A 209267068 209268816 1748 False 933.000000 933 76.637000 1307 3052 1 chr6A.!!$F1 1745

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
141 142 0.037605 ACCGGACCTCGCAGTAAAAG 60.038 55.0 9.46 0.0 37.59 2.27 F
142 143 0.245539 CCGGACCTCGCAGTAAAAGA 59.754 55.0 0.00 0.0 37.59 2.52 F
833 951 0.398696 ACATAAGAACCACCACCGCA 59.601 50.0 0.00 0.0 0.00 5.69 F
2422 2905 0.315251 GCAGCCCAAAGTTCAAGACC 59.685 55.0 0.00 0.0 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1101 1566 0.534877 AATCAGCACAACGCACCAGA 60.535 50.000 0.00 0.00 46.13 3.86 R
1879 2362 1.975407 GGCAACACCAGAGCATGCT 60.975 57.895 22.92 22.92 38.86 3.79 R
2575 3058 1.205655 CCGCTCAGGTCAAGATTCTCA 59.794 52.381 0.00 0.00 34.51 3.27 R
3495 4009 0.108138 CGGATCAAAGAACCGGAGCT 60.108 55.000 9.46 0.63 42.82 4.09 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
25 26 8.782339 CCTTAATTTTTCTGAAAATGCAGGAT 57.218 30.769 15.63 3.47 42.97 3.24
26 27 8.662141 CCTTAATTTTTCTGAAAATGCAGGATG 58.338 33.333 15.63 3.52 42.97 3.51
27 28 9.426837 CTTAATTTTTCTGAAAATGCAGGATGA 57.573 29.630 15.63 0.00 42.97 2.92
28 29 9.947433 TTAATTTTTCTGAAAATGCAGGATGAT 57.053 25.926 15.63 1.50 42.97 2.45
29 30 7.843490 ATTTTTCTGAAAATGCAGGATGATG 57.157 32.000 15.63 0.00 42.37 3.07
30 31 5.988310 TTTCTGAAAATGCAGGATGATGT 57.012 34.783 0.00 0.00 39.69 3.06
31 32 5.988310 TTCTGAAAATGCAGGATGATGTT 57.012 34.783 0.00 0.00 39.69 2.71
32 33 5.319140 TCTGAAAATGCAGGATGATGTTG 57.681 39.130 0.00 0.00 39.69 3.33
33 34 4.158949 TCTGAAAATGCAGGATGATGTTGG 59.841 41.667 0.00 0.00 39.69 3.77
34 35 3.196039 TGAAAATGCAGGATGATGTTGGG 59.804 43.478 0.00 0.00 39.69 4.12
35 36 1.784358 AATGCAGGATGATGTTGGGG 58.216 50.000 0.00 0.00 39.69 4.96
36 37 0.632835 ATGCAGGATGATGTTGGGGT 59.367 50.000 0.00 0.00 39.69 4.95
37 38 0.409092 TGCAGGATGATGTTGGGGTT 59.591 50.000 0.00 0.00 39.69 4.11
38 39 1.106285 GCAGGATGATGTTGGGGTTC 58.894 55.000 0.00 0.00 39.69 3.62
39 40 1.616725 GCAGGATGATGTTGGGGTTCA 60.617 52.381 0.00 0.00 39.69 3.18
40 41 2.372264 CAGGATGATGTTGGGGTTCAG 58.628 52.381 0.00 0.00 39.69 3.02
41 42 1.285962 AGGATGATGTTGGGGTTCAGG 59.714 52.381 0.00 0.00 0.00 3.86
42 43 1.284785 GGATGATGTTGGGGTTCAGGA 59.715 52.381 0.00 0.00 0.00 3.86
43 44 2.291540 GGATGATGTTGGGGTTCAGGAA 60.292 50.000 0.00 0.00 0.00 3.36
44 45 2.286365 TGATGTTGGGGTTCAGGAAC 57.714 50.000 3.58 3.58 40.45 3.62
45 46 1.496857 TGATGTTGGGGTTCAGGAACA 59.503 47.619 13.62 0.00 42.85 3.18
46 47 2.109834 TGATGTTGGGGTTCAGGAACAT 59.890 45.455 13.62 0.00 42.85 2.71
47 48 1.993956 TGTTGGGGTTCAGGAACATG 58.006 50.000 13.62 0.00 42.85 3.21
48 49 1.216678 TGTTGGGGTTCAGGAACATGT 59.783 47.619 13.62 0.00 42.85 3.21
49 50 2.316108 GTTGGGGTTCAGGAACATGTT 58.684 47.619 11.78 11.78 42.85 2.71
50 51 3.117474 TGTTGGGGTTCAGGAACATGTTA 60.117 43.478 11.95 0.00 42.85 2.41
51 52 3.885976 TGGGGTTCAGGAACATGTTAA 57.114 42.857 11.95 0.00 42.85 2.01
52 53 4.186077 TGGGGTTCAGGAACATGTTAAA 57.814 40.909 11.95 1.24 42.85 1.52
53 54 4.547671 TGGGGTTCAGGAACATGTTAAAA 58.452 39.130 11.95 0.88 42.85 1.52
54 55 4.342665 TGGGGTTCAGGAACATGTTAAAAC 59.657 41.667 11.95 12.48 42.85 2.43
55 56 4.342665 GGGGTTCAGGAACATGTTAAAACA 59.657 41.667 11.95 0.00 42.85 2.83
56 57 5.163395 GGGGTTCAGGAACATGTTAAAACAA 60.163 40.000 11.95 0.00 42.85 2.83
57 58 6.463755 GGGGTTCAGGAACATGTTAAAACAAT 60.464 38.462 11.95 0.00 42.85 2.71
58 59 6.645003 GGGTTCAGGAACATGTTAAAACAATC 59.355 38.462 11.95 1.67 42.85 2.67
59 60 7.206687 GGTTCAGGAACATGTTAAAACAATCA 58.793 34.615 11.95 0.00 42.85 2.57
60 61 7.872483 GGTTCAGGAACATGTTAAAACAATCAT 59.128 33.333 11.95 0.00 42.85 2.45
61 62 8.915654 GTTCAGGAACATGTTAAAACAATCATC 58.084 33.333 11.95 0.00 43.03 2.92
62 63 8.408043 TCAGGAACATGTTAAAACAATCATCT 57.592 30.769 11.95 0.00 43.03 2.90
63 64 8.514594 TCAGGAACATGTTAAAACAATCATCTC 58.485 33.333 11.95 0.00 43.03 2.75
64 65 8.517878 CAGGAACATGTTAAAACAATCATCTCT 58.482 33.333 11.95 0.00 43.03 3.10
65 66 9.082313 AGGAACATGTTAAAACAATCATCTCTT 57.918 29.630 11.95 0.00 43.03 2.85
66 67 9.132521 GGAACATGTTAAAACAATCATCTCTTG 57.867 33.333 11.95 0.00 43.03 3.02
67 68 8.524870 AACATGTTAAAACAATCATCTCTTGC 57.475 30.769 9.97 0.00 43.03 4.01
68 69 7.092716 ACATGTTAAAACAATCATCTCTTGCC 58.907 34.615 0.00 0.00 43.03 4.52
69 70 6.024552 TGTTAAAACAATCATCTCTTGCCC 57.975 37.500 0.00 0.00 35.67 5.36
70 71 5.047377 TGTTAAAACAATCATCTCTTGCCCC 60.047 40.000 0.00 0.00 35.67 5.80
71 72 3.463048 AAACAATCATCTCTTGCCCCT 57.537 42.857 0.00 0.00 0.00 4.79
72 73 3.463048 AACAATCATCTCTTGCCCCTT 57.537 42.857 0.00 0.00 0.00 3.95
73 74 3.463048 ACAATCATCTCTTGCCCCTTT 57.537 42.857 0.00 0.00 0.00 3.11
74 75 3.782992 ACAATCATCTCTTGCCCCTTTT 58.217 40.909 0.00 0.00 0.00 2.27
75 76 4.162651 ACAATCATCTCTTGCCCCTTTTT 58.837 39.130 0.00 0.00 0.00 1.94
76 77 4.020839 ACAATCATCTCTTGCCCCTTTTTG 60.021 41.667 0.00 0.00 0.00 2.44
77 78 3.243359 TCATCTCTTGCCCCTTTTTGT 57.757 42.857 0.00 0.00 0.00 2.83
78 79 2.892852 TCATCTCTTGCCCCTTTTTGTG 59.107 45.455 0.00 0.00 0.00 3.33
79 80 1.703411 TCTCTTGCCCCTTTTTGTGG 58.297 50.000 0.00 0.00 0.00 4.17
80 81 1.216678 TCTCTTGCCCCTTTTTGTGGA 59.783 47.619 0.00 0.00 0.00 4.02
81 82 2.038659 CTCTTGCCCCTTTTTGTGGAA 58.961 47.619 0.00 0.00 0.00 3.53
82 83 2.634453 CTCTTGCCCCTTTTTGTGGAAT 59.366 45.455 0.00 0.00 0.00 3.01
83 84 3.831911 CTCTTGCCCCTTTTTGTGGAATA 59.168 43.478 0.00 0.00 0.00 1.75
84 85 4.424842 TCTTGCCCCTTTTTGTGGAATAT 58.575 39.130 0.00 0.00 0.00 1.28
85 86 4.466015 TCTTGCCCCTTTTTGTGGAATATC 59.534 41.667 0.00 0.00 0.00 1.63
86 87 4.059773 TGCCCCTTTTTGTGGAATATCT 57.940 40.909 0.00 0.00 0.00 1.98
87 88 4.424842 TGCCCCTTTTTGTGGAATATCTT 58.575 39.130 0.00 0.00 0.00 2.40
88 89 4.466015 TGCCCCTTTTTGTGGAATATCTTC 59.534 41.667 0.00 0.00 0.00 2.87
103 104 8.675040 GGAATATCTTCCTTATTAATTTGCGC 57.325 34.615 0.00 0.00 46.44 6.09
104 105 8.515414 GGAATATCTTCCTTATTAATTTGCGCT 58.485 33.333 9.73 0.00 46.44 5.92
105 106 9.899226 GAATATCTTCCTTATTAATTTGCGCTT 57.101 29.630 9.73 0.00 0.00 4.68
106 107 9.899226 AATATCTTCCTTATTAATTTGCGCTTC 57.101 29.630 9.73 0.00 0.00 3.86
107 108 6.751514 TCTTCCTTATTAATTTGCGCTTCA 57.248 33.333 9.73 0.00 0.00 3.02
108 109 7.333528 TCTTCCTTATTAATTTGCGCTTCAT 57.666 32.000 9.73 0.00 0.00 2.57
109 110 7.417612 TCTTCCTTATTAATTTGCGCTTCATC 58.582 34.615 9.73 0.00 0.00 2.92
110 111 5.747565 TCCTTATTAATTTGCGCTTCATCG 58.252 37.500 9.73 0.00 0.00 3.84
111 112 5.295787 TCCTTATTAATTTGCGCTTCATCGT 59.704 36.000 9.73 0.00 0.00 3.73
112 113 5.396362 CCTTATTAATTTGCGCTTCATCGTG 59.604 40.000 9.73 0.00 0.00 4.35
113 114 2.823196 TAATTTGCGCTTCATCGTGG 57.177 45.000 9.73 0.00 0.00 4.94
114 115 0.881118 AATTTGCGCTTCATCGTGGT 59.119 45.000 9.73 0.00 0.00 4.16
115 116 0.881118 ATTTGCGCTTCATCGTGGTT 59.119 45.000 9.73 0.00 0.00 3.67
116 117 0.665835 TTTGCGCTTCATCGTGGTTT 59.334 45.000 9.73 0.00 0.00 3.27
117 118 1.514003 TTGCGCTTCATCGTGGTTTA 58.486 45.000 9.73 0.00 0.00 2.01
118 119 1.732941 TGCGCTTCATCGTGGTTTAT 58.267 45.000 9.73 0.00 0.00 1.40
119 120 2.080693 TGCGCTTCATCGTGGTTTATT 58.919 42.857 9.73 0.00 0.00 1.40
120 121 2.486203 TGCGCTTCATCGTGGTTTATTT 59.514 40.909 9.73 0.00 0.00 1.40
121 122 3.098636 GCGCTTCATCGTGGTTTATTTC 58.901 45.455 0.00 0.00 0.00 2.17
122 123 3.425625 GCGCTTCATCGTGGTTTATTTCA 60.426 43.478 0.00 0.00 0.00 2.69
123 124 4.088648 CGCTTCATCGTGGTTTATTTCAC 58.911 43.478 0.00 0.00 0.00 3.18
124 125 4.412207 GCTTCATCGTGGTTTATTTCACC 58.588 43.478 0.00 0.00 34.52 4.02
125 126 4.647964 CTTCATCGTGGTTTATTTCACCG 58.352 43.478 0.00 0.00 37.07 4.94
126 127 3.004171 TCATCGTGGTTTATTTCACCGG 58.996 45.455 0.00 0.00 37.07 5.28
127 128 2.835580 TCGTGGTTTATTTCACCGGA 57.164 45.000 9.46 0.00 37.07 5.14
128 129 2.415776 TCGTGGTTTATTTCACCGGAC 58.584 47.619 9.46 0.00 37.07 4.79
129 130 1.465777 CGTGGTTTATTTCACCGGACC 59.534 52.381 9.46 2.38 37.07 4.46
130 131 2.786777 GTGGTTTATTTCACCGGACCT 58.213 47.619 9.46 0.00 37.07 3.85
131 132 2.745821 GTGGTTTATTTCACCGGACCTC 59.254 50.000 9.46 0.00 37.07 3.85
132 133 2.004733 GGTTTATTTCACCGGACCTCG 58.995 52.381 9.46 0.00 38.88 4.63
133 134 1.395954 GTTTATTTCACCGGACCTCGC 59.604 52.381 9.46 0.00 37.59 5.03
134 135 0.609151 TTATTTCACCGGACCTCGCA 59.391 50.000 9.46 0.00 37.59 5.10
135 136 0.174845 TATTTCACCGGACCTCGCAG 59.825 55.000 9.46 0.00 37.59 5.18
136 137 1.827399 ATTTCACCGGACCTCGCAGT 61.827 55.000 9.46 0.00 37.59 4.40
137 138 1.180456 TTTCACCGGACCTCGCAGTA 61.180 55.000 9.46 0.00 37.59 2.74
138 139 1.180456 TTCACCGGACCTCGCAGTAA 61.180 55.000 9.46 0.00 37.59 2.24
139 140 1.180456 TCACCGGACCTCGCAGTAAA 61.180 55.000 9.46 0.00 37.59 2.01
140 141 0.320073 CACCGGACCTCGCAGTAAAA 60.320 55.000 9.46 0.00 37.59 1.52
141 142 0.037605 ACCGGACCTCGCAGTAAAAG 60.038 55.000 9.46 0.00 37.59 2.27
142 143 0.245539 CCGGACCTCGCAGTAAAAGA 59.754 55.000 0.00 0.00 37.59 2.52
143 144 1.134788 CCGGACCTCGCAGTAAAAGAT 60.135 52.381 0.00 0.00 37.59 2.40
144 145 2.618053 CGGACCTCGCAGTAAAAGATT 58.382 47.619 0.00 0.00 0.00 2.40
145 146 2.603560 CGGACCTCGCAGTAAAAGATTC 59.396 50.000 0.00 0.00 0.00 2.52
146 147 2.937149 GGACCTCGCAGTAAAAGATTCC 59.063 50.000 0.00 0.00 0.00 3.01
147 148 3.369576 GGACCTCGCAGTAAAAGATTCCT 60.370 47.826 0.00 0.00 0.00 3.36
148 149 4.254492 GACCTCGCAGTAAAAGATTCCTT 58.746 43.478 0.00 0.00 0.00 3.36
149 150 5.416271 ACCTCGCAGTAAAAGATTCCTTA 57.584 39.130 0.00 0.00 31.15 2.69
150 151 5.801380 ACCTCGCAGTAAAAGATTCCTTAA 58.199 37.500 0.00 0.00 31.15 1.85
151 152 6.235664 ACCTCGCAGTAAAAGATTCCTTAAA 58.764 36.000 0.00 0.00 31.15 1.52
152 153 6.371825 ACCTCGCAGTAAAAGATTCCTTAAAG 59.628 38.462 0.00 0.00 31.15 1.85
153 154 6.178239 TCGCAGTAAAAGATTCCTTAAAGC 57.822 37.500 0.00 0.00 31.15 3.51
154 155 5.123344 TCGCAGTAAAAGATTCCTTAAAGCC 59.877 40.000 0.00 0.00 31.15 4.35
155 156 5.123979 CGCAGTAAAAGATTCCTTAAAGCCT 59.876 40.000 0.00 0.00 31.15 4.58
156 157 6.349363 CGCAGTAAAAGATTCCTTAAAGCCTT 60.349 38.462 0.00 0.00 31.15 4.35
157 158 7.378966 GCAGTAAAAGATTCCTTAAAGCCTTT 58.621 34.615 0.00 0.00 31.15 3.11
158 159 7.329471 GCAGTAAAAGATTCCTTAAAGCCTTTG 59.671 37.037 0.00 0.00 31.15 2.77
159 160 7.814587 CAGTAAAAGATTCCTTAAAGCCTTTGG 59.185 37.037 0.00 0.00 31.15 3.28
160 161 5.152623 AAAGATTCCTTAAAGCCTTTGGC 57.847 39.130 0.00 0.00 39.53 4.52
161 162 4.592778 AAAGATTCCTTAAAGCCTTTGGCA 59.407 37.500 11.38 0.00 40.79 4.92
162 163 5.249163 AAAGATTCCTTAAAGCCTTTGGCAT 59.751 36.000 11.38 0.00 40.79 4.40
163 164 6.798367 AAAGATTCCTTAAAGCCTTTGGCATG 60.798 38.462 11.38 0.00 40.79 4.06
164 165 9.107233 AAAGATTCCTTAAAGCCTTTGGCATGT 62.107 37.037 11.38 0.00 40.79 3.21
172 173 2.373540 CCTTTGGCATGTCATTGTGG 57.626 50.000 0.00 0.00 0.00 4.17
173 174 1.619827 CCTTTGGCATGTCATTGTGGT 59.380 47.619 0.00 0.00 0.00 4.16
174 175 2.353011 CCTTTGGCATGTCATTGTGGTC 60.353 50.000 0.00 0.00 0.00 4.02
175 176 2.291209 TTGGCATGTCATTGTGGTCT 57.709 45.000 0.00 0.00 0.00 3.85
176 177 3.431673 TTGGCATGTCATTGTGGTCTA 57.568 42.857 0.00 0.00 0.00 2.59
177 178 3.650281 TGGCATGTCATTGTGGTCTAT 57.350 42.857 0.00 0.00 0.00 1.98
178 179 3.966979 TGGCATGTCATTGTGGTCTATT 58.033 40.909 0.00 0.00 0.00 1.73
179 180 3.947196 TGGCATGTCATTGTGGTCTATTC 59.053 43.478 0.00 0.00 0.00 1.75
180 181 3.947196 GGCATGTCATTGTGGTCTATTCA 59.053 43.478 0.00 0.00 0.00 2.57
181 182 4.398988 GGCATGTCATTGTGGTCTATTCAA 59.601 41.667 0.00 0.00 0.00 2.69
182 183 5.068198 GGCATGTCATTGTGGTCTATTCAAT 59.932 40.000 0.00 0.00 32.93 2.57
183 184 6.204359 GCATGTCATTGTGGTCTATTCAATC 58.796 40.000 0.00 0.00 30.74 2.67
184 185 6.732154 CATGTCATTGTGGTCTATTCAATCC 58.268 40.000 0.00 0.00 30.74 3.01
185 186 4.875536 TGTCATTGTGGTCTATTCAATCCG 59.124 41.667 0.00 0.00 30.74 4.18
186 187 5.116180 GTCATTGTGGTCTATTCAATCCGA 58.884 41.667 0.00 0.00 30.74 4.55
187 188 5.006746 GTCATTGTGGTCTATTCAATCCGAC 59.993 44.000 0.00 0.00 30.74 4.79
188 189 3.536956 TGTGGTCTATTCAATCCGACC 57.463 47.619 10.51 10.51 44.76 4.79
189 190 3.104512 TGTGGTCTATTCAATCCGACCT 58.895 45.455 15.98 0.00 44.79 3.85
190 191 3.517901 TGTGGTCTATTCAATCCGACCTT 59.482 43.478 15.98 0.00 44.79 3.50
191 192 3.871594 GTGGTCTATTCAATCCGACCTTG 59.128 47.826 15.98 0.00 44.79 3.61
192 193 3.772572 TGGTCTATTCAATCCGACCTTGA 59.227 43.478 15.98 0.00 44.79 3.02
193 194 4.408921 TGGTCTATTCAATCCGACCTTGAT 59.591 41.667 15.98 0.00 44.79 2.57
194 195 4.991687 GGTCTATTCAATCCGACCTTGATC 59.008 45.833 10.26 0.00 42.02 2.92
195 196 5.221541 GGTCTATTCAATCCGACCTTGATCT 60.222 44.000 10.26 0.00 42.02 2.75
196 197 6.015350 GGTCTATTCAATCCGACCTTGATCTA 60.015 42.308 10.26 0.00 42.02 1.98
197 198 7.434492 GTCTATTCAATCCGACCTTGATCTAA 58.566 38.462 0.00 0.00 32.94 2.10
198 199 7.926555 GTCTATTCAATCCGACCTTGATCTAAA 59.073 37.037 0.00 0.00 32.94 1.85
199 200 8.144478 TCTATTCAATCCGACCTTGATCTAAAG 58.856 37.037 0.00 0.00 32.94 1.85
200 201 5.932619 TCAATCCGACCTTGATCTAAAGA 57.067 39.130 0.00 0.00 0.00 2.52
201 202 6.485830 TCAATCCGACCTTGATCTAAAGAT 57.514 37.500 0.00 0.00 37.51 2.40
202 203 6.889198 TCAATCCGACCTTGATCTAAAGATT 58.111 36.000 0.00 0.00 34.37 2.40
203 204 6.986817 TCAATCCGACCTTGATCTAAAGATTC 59.013 38.462 0.00 0.00 34.37 2.52
204 205 5.277857 TCCGACCTTGATCTAAAGATTCC 57.722 43.478 0.00 0.00 34.37 3.01
205 206 4.714802 TCCGACCTTGATCTAAAGATTCCA 59.285 41.667 0.00 0.00 34.37 3.53
206 207 5.188948 TCCGACCTTGATCTAAAGATTCCAA 59.811 40.000 0.00 0.00 34.37 3.53
207 208 5.880332 CCGACCTTGATCTAAAGATTCCAAA 59.120 40.000 0.00 0.00 34.37 3.28
208 209 6.374333 CCGACCTTGATCTAAAGATTCCAAAA 59.626 38.462 0.00 0.00 34.37 2.44
209 210 7.414540 CCGACCTTGATCTAAAGATTCCAAAAG 60.415 40.741 0.00 0.00 34.37 2.27
210 211 7.334421 CGACCTTGATCTAAAGATTCCAAAAGA 59.666 37.037 0.00 0.00 34.37 2.52
211 212 8.940397 ACCTTGATCTAAAGATTCCAAAAGAA 57.060 30.769 0.00 0.00 39.32 2.52
289 290 9.405587 TGAGTCGAAAACAAATGAATATTTTCC 57.594 29.630 0.00 0.00 37.63 3.13
290 291 9.405587 GAGTCGAAAACAAATGAATATTTTCCA 57.594 29.630 0.00 0.00 37.63 3.53
291 292 9.757227 AGTCGAAAACAAATGAATATTTTCCAA 57.243 25.926 0.00 0.00 37.63 3.53
302 303 5.248020 TGAATATTTTCCAAACATGGCCACT 59.752 36.000 8.16 0.00 0.00 4.00
313 314 4.169059 ACATGGCCACTTGCTCATTATA 57.831 40.909 8.16 0.00 40.92 0.98
404 414 4.746611 TCATCGATCAATTGAGAATCCACG 59.253 41.667 14.54 10.05 0.00 4.94
417 427 1.967319 ATCCACGCGCCAGATAAAAT 58.033 45.000 5.73 0.00 0.00 1.82
443 453 8.314751 TCCTTCTATTTTTGTTTGTTTTGTCCA 58.685 29.630 0.00 0.00 0.00 4.02
477 489 5.949354 TCCTGTCGGGATTGTTTTTCATAAT 59.051 36.000 0.00 0.00 39.58 1.28
498 510 1.143183 GCATGCTTGCTTCCCCATG 59.857 57.895 16.80 0.00 45.77 3.66
501 513 2.101783 CATGCTTGCTTCCCCATGTAA 58.898 47.619 0.00 0.00 32.51 2.41
513 525 6.127366 GCTTCCCCATGTAATCTTTCAAATCA 60.127 38.462 0.00 0.00 0.00 2.57
514 526 7.418254 GCTTCCCCATGTAATCTTTCAAATCAT 60.418 37.037 0.00 0.00 0.00 2.45
515 527 7.350744 TCCCCATGTAATCTTTCAAATCATG 57.649 36.000 0.00 0.00 0.00 3.07
526 538 4.327982 TTCAAATCATGGAAACCGCAAA 57.672 36.364 0.00 0.00 0.00 3.68
538 550 3.914426 AACCGCAAATCCATCTAGACT 57.086 42.857 0.00 0.00 0.00 3.24
540 552 4.592485 ACCGCAAATCCATCTAGACTAG 57.408 45.455 2.81 2.81 0.00 2.57
543 555 3.986572 CGCAAATCCATCTAGACTAGCAG 59.013 47.826 4.47 0.00 0.00 4.24
546 558 3.541242 ATCCATCTAGACTAGCAGCCT 57.459 47.619 4.47 0.00 0.00 4.58
553 565 1.577736 AGACTAGCAGCCTGGTTCAT 58.422 50.000 0.00 0.00 32.39 2.57
589 657 2.985311 TGAAATGAAAAGGCCCCCAAAT 59.015 40.909 0.00 0.00 0.00 2.32
603 671 2.429610 CCCCAAATCTCCAAATCAGCAG 59.570 50.000 0.00 0.00 0.00 4.24
605 673 2.159142 CCAAATCTCCAAATCAGCAGCC 60.159 50.000 0.00 0.00 0.00 4.85
606 674 2.494471 CAAATCTCCAAATCAGCAGCCA 59.506 45.455 0.00 0.00 0.00 4.75
607 675 2.054232 ATCTCCAAATCAGCAGCCAG 57.946 50.000 0.00 0.00 0.00 4.85
608 676 0.986527 TCTCCAAATCAGCAGCCAGA 59.013 50.000 0.00 0.00 0.00 3.86
609 677 1.065636 TCTCCAAATCAGCAGCCAGAG 60.066 52.381 0.00 0.00 0.00 3.35
610 678 0.986527 TCCAAATCAGCAGCCAGAGA 59.013 50.000 0.00 0.00 0.00 3.10
611 679 1.065636 TCCAAATCAGCAGCCAGAGAG 60.066 52.381 0.00 0.00 0.00 3.20
613 681 1.065636 CAAATCAGCAGCCAGAGAGGA 60.066 52.381 0.00 0.00 41.22 3.71
614 682 1.283347 AATCAGCAGCCAGAGAGGAA 58.717 50.000 0.00 0.00 41.22 3.36
615 683 1.283347 ATCAGCAGCCAGAGAGGAAA 58.717 50.000 0.00 0.00 41.22 3.13
616 684 1.059098 TCAGCAGCCAGAGAGGAAAA 58.941 50.000 0.00 0.00 41.22 2.29
769 887 2.734755 ATCCCGGCAAATCTTCATCA 57.265 45.000 0.00 0.00 0.00 3.07
833 951 0.398696 ACATAAGAACCACCACCGCA 59.601 50.000 0.00 0.00 0.00 5.69
850 973 4.212797 ACCCCAAACCCACCACCG 62.213 66.667 0.00 0.00 0.00 4.94
875 998 3.429580 CCCCACCCCATTCCTCCC 61.430 72.222 0.00 0.00 0.00 4.30
878 1001 3.809013 CACCCCATTCCTCCCCCG 61.809 72.222 0.00 0.00 0.00 5.73
881 1004 3.878667 CCCATTCCTCCCCCGCTC 61.879 72.222 0.00 0.00 0.00 5.03
882 1005 3.878667 CCATTCCTCCCCCGCTCC 61.879 72.222 0.00 0.00 0.00 4.70
883 1006 2.770048 CATTCCTCCCCCGCTCCT 60.770 66.667 0.00 0.00 0.00 3.69
884 1007 2.446802 ATTCCTCCCCCGCTCCTC 60.447 66.667 0.00 0.00 0.00 3.71
885 1008 4.798682 TTCCTCCCCCGCTCCTCC 62.799 72.222 0.00 0.00 0.00 4.30
893 1016 4.806339 CCGCTCCTCCTCCCCCTT 62.806 72.222 0.00 0.00 0.00 3.95
894 1017 3.157949 CGCTCCTCCTCCCCCTTC 61.158 72.222 0.00 0.00 0.00 3.46
895 1018 2.770475 GCTCCTCCTCCCCCTTCC 60.770 72.222 0.00 0.00 0.00 3.46
966 1413 5.404366 GCCCGATTGATTGATTGATTGATTG 59.596 40.000 0.00 0.00 0.00 2.67
968 1415 6.419710 CCCGATTGATTGATTGATTGATTGTG 59.580 38.462 0.00 0.00 0.00 3.33
991 1438 1.737355 GCAGCAGCTCCTCGATCTCT 61.737 60.000 0.00 0.00 37.91 3.10
1008 1455 4.161295 TTCCTCGCCATGCCTCCG 62.161 66.667 0.00 0.00 0.00 4.63
1030 1477 2.098233 CACGATTGCCGCGGTAAGT 61.098 57.895 31.59 22.51 43.32 2.24
1055 1503 2.294512 GGCCCCGAATTGAATTGAGATC 59.705 50.000 0.00 0.00 0.00 2.75
1059 1507 3.059325 CCCGAATTGAATTGAGATCGAGC 60.059 47.826 0.00 0.00 32.38 5.03
1060 1508 3.362401 CCGAATTGAATTGAGATCGAGCG 60.362 47.826 0.00 0.00 32.38 5.03
1061 1509 3.539756 GAATTGAATTGAGATCGAGCGC 58.460 45.455 0.00 0.00 0.00 5.92
1062 1510 2.299993 TTGAATTGAGATCGAGCGCT 57.700 45.000 11.27 11.27 0.00 5.92
1063 1511 2.299993 TGAATTGAGATCGAGCGCTT 57.700 45.000 13.26 0.00 0.00 4.68
1064 1512 1.929169 TGAATTGAGATCGAGCGCTTG 59.071 47.619 19.15 19.15 0.00 4.01
1101 1566 2.422093 GCCGGAGATCTGGAGGATTTTT 60.422 50.000 5.05 0.00 45.36 1.94
1110 1575 1.202879 TGGAGGATTTTTCTGGTGCGT 60.203 47.619 0.00 0.00 0.00 5.24
1171 1636 3.636231 CTTGTCCTGGACCCGGCA 61.636 66.667 23.42 1.92 0.00 5.69
1879 2362 2.542020 TGAAGACGCTGACCATTGAA 57.458 45.000 0.00 0.00 0.00 2.69
2422 2905 0.315251 GCAGCCCAAAGTTCAAGACC 59.685 55.000 0.00 0.00 0.00 3.85
2533 3016 1.303561 GCAGTGCCCAGGATTCACA 60.304 57.895 2.85 0.00 33.44 3.58
2575 3058 2.273538 GCATGATCTGCCCTCATCTT 57.726 50.000 0.00 0.00 45.66 2.40
2668 3151 1.076024 AGTGGGCTGGTTCATGTTGAT 59.924 47.619 0.00 0.00 0.00 2.57
2677 3160 4.567971 TGGTTCATGTTGATTTGAATGGC 58.432 39.130 0.00 0.00 34.60 4.40
3134 3620 1.751351 CCTCATAGCAGAGTCGGTTCA 59.249 52.381 0.00 0.00 33.75 3.18
3173 3664 0.251787 ATGGTGGGCTTCCTTTGTCC 60.252 55.000 0.00 0.00 0.00 4.02
3327 3818 1.985159 TGCCCTTGTGATTACAGTCCT 59.015 47.619 0.00 0.00 38.23 3.85
3405 3905 6.483640 GTCAGTTGTGTCTTCTTTTCCAGTAT 59.516 38.462 0.00 0.00 0.00 2.12
3495 4009 1.890489 TGTGCCTGTCGTAGAAGCTTA 59.110 47.619 0.00 0.00 39.69 3.09
3508 4022 2.303311 AGAAGCTTAGCTCCGGTTCTTT 59.697 45.455 18.49 4.28 43.20 2.52
3568 4082 2.051334 TGGTTGTTCCAGTTCCAGTG 57.949 50.000 0.00 0.00 41.93 3.66
3626 4148 4.752879 CGTCGGCGGTGGATGGTT 62.753 66.667 7.21 0.00 0.00 3.67
3650 4172 1.279496 TTCTGCAGCATCTGTAGGGT 58.721 50.000 9.47 0.00 42.85 4.34
3770 4292 1.140804 GGTTTTTGCAGGCGTGTGT 59.859 52.632 8.40 0.00 0.00 3.72
3841 4364 3.751175 TCCGTCCAAGTTCTATGCTTTTG 59.249 43.478 0.00 0.00 0.00 2.44
3903 4426 7.770366 TCCTTGTACTGTGTCTAAATGTCTA 57.230 36.000 0.00 0.00 0.00 2.59
3976 4508 3.429141 CCTTGGCAGCTGCGTGAG 61.429 66.667 31.19 25.32 43.26 3.51
3986 4518 4.377841 GGCAGCTGCGTGAGATATATTTTC 60.378 45.833 31.19 8.58 43.26 2.29
3995 4527 6.096036 CGTGAGATATATTTTCGGCTCTGAT 58.904 40.000 0.00 0.00 0.00 2.90
3996 4528 6.034363 CGTGAGATATATTTTCGGCTCTGATG 59.966 42.308 0.00 0.00 0.00 3.07
3997 4529 7.093354 GTGAGATATATTTTCGGCTCTGATGA 58.907 38.462 0.00 0.00 0.00 2.92
4006 4538 4.685169 TCGGCTCTGATGAATTTTGTTC 57.315 40.909 0.00 0.00 0.00 3.18
4012 4544 6.145048 GGCTCTGATGAATTTTGTTCAAGTTG 59.855 38.462 0.00 0.00 31.55 3.16
4016 4548 9.119418 TCTGATGAATTTTGTTCAAGTTGTAGA 57.881 29.630 2.11 0.00 31.55 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.662141 CATCCTGCATTTTCAGAAAAATTAAGG 58.338 33.333 12.38 15.08 41.96 2.69
1 2 9.426837 TCATCCTGCATTTTCAGAAAAATTAAG 57.573 29.630 12.38 7.87 41.96 1.85
2 3 9.947433 ATCATCCTGCATTTTCAGAAAAATTAA 57.053 25.926 12.38 0.00 41.96 1.40
3 4 9.373603 CATCATCCTGCATTTTCAGAAAAATTA 57.626 29.630 12.38 1.50 41.96 1.40
4 5 7.881232 ACATCATCCTGCATTTTCAGAAAAATT 59.119 29.630 12.38 0.00 41.96 1.82
5 6 7.391620 ACATCATCCTGCATTTTCAGAAAAAT 58.608 30.769 12.38 1.13 44.12 1.82
6 7 6.761312 ACATCATCCTGCATTTTCAGAAAAA 58.239 32.000 12.38 0.00 38.66 1.94
7 8 6.349243 ACATCATCCTGCATTTTCAGAAAA 57.651 33.333 10.80 10.80 36.19 2.29
8 9 5.988310 ACATCATCCTGCATTTTCAGAAA 57.012 34.783 0.00 0.00 36.19 2.52
9 10 5.336929 CCAACATCATCCTGCATTTTCAGAA 60.337 40.000 0.00 0.00 36.19 3.02
10 11 4.158949 CCAACATCATCCTGCATTTTCAGA 59.841 41.667 0.00 0.00 36.19 3.27
11 12 4.430007 CCAACATCATCCTGCATTTTCAG 58.570 43.478 0.00 0.00 0.00 3.02
12 13 3.196039 CCCAACATCATCCTGCATTTTCA 59.804 43.478 0.00 0.00 0.00 2.69
13 14 3.431207 CCCCAACATCATCCTGCATTTTC 60.431 47.826 0.00 0.00 0.00 2.29
14 15 2.502538 CCCCAACATCATCCTGCATTTT 59.497 45.455 0.00 0.00 0.00 1.82
15 16 2.112998 CCCCAACATCATCCTGCATTT 58.887 47.619 0.00 0.00 0.00 2.32
16 17 1.007479 ACCCCAACATCATCCTGCATT 59.993 47.619 0.00 0.00 0.00 3.56
17 18 0.632835 ACCCCAACATCATCCTGCAT 59.367 50.000 0.00 0.00 0.00 3.96
18 19 0.409092 AACCCCAACATCATCCTGCA 59.591 50.000 0.00 0.00 0.00 4.41
19 20 1.106285 GAACCCCAACATCATCCTGC 58.894 55.000 0.00 0.00 0.00 4.85
20 21 2.372264 CTGAACCCCAACATCATCCTG 58.628 52.381 0.00 0.00 0.00 3.86
21 22 1.285962 CCTGAACCCCAACATCATCCT 59.714 52.381 0.00 0.00 0.00 3.24
22 23 1.284785 TCCTGAACCCCAACATCATCC 59.715 52.381 0.00 0.00 0.00 3.51
23 24 2.755103 GTTCCTGAACCCCAACATCATC 59.245 50.000 0.00 0.00 35.36 2.92
24 25 2.109834 TGTTCCTGAACCCCAACATCAT 59.890 45.455 7.51 0.00 40.46 2.45
25 26 1.496857 TGTTCCTGAACCCCAACATCA 59.503 47.619 7.51 0.00 40.46 3.07
26 27 2.286365 TGTTCCTGAACCCCAACATC 57.714 50.000 7.51 0.00 40.46 3.06
27 28 2.158325 ACATGTTCCTGAACCCCAACAT 60.158 45.455 7.51 0.00 39.52 2.71
28 29 1.216678 ACATGTTCCTGAACCCCAACA 59.783 47.619 7.51 0.00 40.46 3.33
29 30 1.995376 ACATGTTCCTGAACCCCAAC 58.005 50.000 7.51 0.00 40.46 3.77
30 31 2.765689 AACATGTTCCTGAACCCCAA 57.234 45.000 4.92 0.00 40.46 4.12
31 32 3.885976 TTAACATGTTCCTGAACCCCA 57.114 42.857 15.85 0.00 40.46 4.96
32 33 4.342665 TGTTTTAACATGTTCCTGAACCCC 59.657 41.667 15.85 0.00 35.83 4.95
33 34 5.523438 TGTTTTAACATGTTCCTGAACCC 57.477 39.130 15.85 0.00 35.83 4.11
34 35 7.206687 TGATTGTTTTAACATGTTCCTGAACC 58.793 34.615 15.85 0.00 38.95 3.62
35 36 8.816640 ATGATTGTTTTAACATGTTCCTGAAC 57.183 30.769 15.85 14.88 38.95 3.18
36 37 8.859090 AGATGATTGTTTTAACATGTTCCTGAA 58.141 29.630 15.85 0.27 38.95 3.02
37 38 8.408043 AGATGATTGTTTTAACATGTTCCTGA 57.592 30.769 15.85 0.00 38.95 3.86
38 39 8.517878 AGAGATGATTGTTTTAACATGTTCCTG 58.482 33.333 15.85 0.00 38.95 3.86
39 40 8.641498 AGAGATGATTGTTTTAACATGTTCCT 57.359 30.769 15.85 0.00 38.95 3.36
40 41 9.132521 CAAGAGATGATTGTTTTAACATGTTCC 57.867 33.333 15.85 2.58 38.95 3.62
41 42 8.642020 GCAAGAGATGATTGTTTTAACATGTTC 58.358 33.333 15.85 0.75 38.95 3.18
42 43 7.599998 GGCAAGAGATGATTGTTTTAACATGTT 59.400 33.333 16.68 16.68 38.95 2.71
43 44 7.092716 GGCAAGAGATGATTGTTTTAACATGT 58.907 34.615 0.00 0.00 38.95 3.21
44 45 6.532657 GGGCAAGAGATGATTGTTTTAACATG 59.467 38.462 0.00 0.00 38.95 3.21
45 46 6.351286 GGGGCAAGAGATGATTGTTTTAACAT 60.351 38.462 0.00 0.00 38.95 2.71
46 47 5.047377 GGGGCAAGAGATGATTGTTTTAACA 60.047 40.000 0.00 0.00 37.08 2.41
47 48 5.185828 AGGGGCAAGAGATGATTGTTTTAAC 59.814 40.000 0.00 0.00 0.00 2.01
48 49 5.332743 AGGGGCAAGAGATGATTGTTTTAA 58.667 37.500 0.00 0.00 0.00 1.52
49 50 4.934356 AGGGGCAAGAGATGATTGTTTTA 58.066 39.130 0.00 0.00 0.00 1.52
50 51 3.782992 AGGGGCAAGAGATGATTGTTTT 58.217 40.909 0.00 0.00 0.00 2.43
51 52 3.463048 AGGGGCAAGAGATGATTGTTT 57.537 42.857 0.00 0.00 0.00 2.83
52 53 3.463048 AAGGGGCAAGAGATGATTGTT 57.537 42.857 0.00 0.00 0.00 2.83
53 54 3.463048 AAAGGGGCAAGAGATGATTGT 57.537 42.857 0.00 0.00 0.00 2.71
54 55 4.020839 ACAAAAAGGGGCAAGAGATGATTG 60.021 41.667 0.00 0.00 0.00 2.67
55 56 4.020839 CACAAAAAGGGGCAAGAGATGATT 60.021 41.667 0.00 0.00 0.00 2.57
56 57 3.512724 CACAAAAAGGGGCAAGAGATGAT 59.487 43.478 0.00 0.00 0.00 2.45
57 58 2.892852 CACAAAAAGGGGCAAGAGATGA 59.107 45.455 0.00 0.00 0.00 2.92
58 59 2.028748 CCACAAAAAGGGGCAAGAGATG 60.029 50.000 0.00 0.00 30.89 2.90
59 60 2.158325 TCCACAAAAAGGGGCAAGAGAT 60.158 45.455 0.00 0.00 42.23 2.75
60 61 1.216678 TCCACAAAAAGGGGCAAGAGA 59.783 47.619 0.00 0.00 42.23 3.10
61 62 1.703411 TCCACAAAAAGGGGCAAGAG 58.297 50.000 0.00 0.00 42.23 2.85
62 63 2.166907 TTCCACAAAAAGGGGCAAGA 57.833 45.000 0.00 0.00 42.23 3.02
63 64 4.467438 AGATATTCCACAAAAAGGGGCAAG 59.533 41.667 0.00 0.00 42.23 4.01
64 65 4.424842 AGATATTCCACAAAAAGGGGCAA 58.575 39.130 0.00 0.00 42.23 4.52
65 66 4.059773 AGATATTCCACAAAAAGGGGCA 57.940 40.909 0.00 0.00 42.23 5.36
66 67 4.141937 GGAAGATATTCCACAAAAAGGGGC 60.142 45.833 14.34 0.00 42.23 5.80
67 68 5.272402 AGGAAGATATTCCACAAAAAGGGG 58.728 41.667 20.86 0.00 44.73 4.79
68 69 6.857437 AAGGAAGATATTCCACAAAAAGGG 57.143 37.500 20.86 0.00 43.54 3.95
76 77 9.612620 CGCAAATTAATAAGGAAGATATTCCAC 57.387 33.333 20.86 0.00 43.54 4.02
77 78 8.296713 GCGCAAATTAATAAGGAAGATATTCCA 58.703 33.333 20.86 1.63 43.54 3.53
78 79 8.515414 AGCGCAAATTAATAAGGAAGATATTCC 58.485 33.333 11.33 11.33 41.42 3.01
79 80 9.899226 AAGCGCAAATTAATAAGGAAGATATTC 57.101 29.630 11.47 0.00 0.00 1.75
80 81 9.899226 GAAGCGCAAATTAATAAGGAAGATATT 57.101 29.630 11.47 0.00 0.00 1.28
81 82 9.066892 TGAAGCGCAAATTAATAAGGAAGATAT 57.933 29.630 11.47 0.00 0.00 1.63
82 83 8.445275 TGAAGCGCAAATTAATAAGGAAGATA 57.555 30.769 11.47 0.00 0.00 1.98
83 84 7.333528 TGAAGCGCAAATTAATAAGGAAGAT 57.666 32.000 11.47 0.00 0.00 2.40
84 85 6.751514 TGAAGCGCAAATTAATAAGGAAGA 57.248 33.333 11.47 0.00 0.00 2.87
85 86 6.358030 CGATGAAGCGCAAATTAATAAGGAAG 59.642 38.462 11.47 0.00 0.00 3.46
86 87 6.183360 ACGATGAAGCGCAAATTAATAAGGAA 60.183 34.615 11.47 0.00 33.86 3.36
87 88 5.295787 ACGATGAAGCGCAAATTAATAAGGA 59.704 36.000 11.47 0.00 33.86 3.36
88 89 5.396362 CACGATGAAGCGCAAATTAATAAGG 59.604 40.000 11.47 0.00 33.86 2.69
89 90 5.396362 CCACGATGAAGCGCAAATTAATAAG 59.604 40.000 11.47 0.00 33.86 1.73
90 91 5.163703 ACCACGATGAAGCGCAAATTAATAA 60.164 36.000 11.47 0.00 33.86 1.40
91 92 4.334203 ACCACGATGAAGCGCAAATTAATA 59.666 37.500 11.47 0.00 33.86 0.98
92 93 3.128589 ACCACGATGAAGCGCAAATTAAT 59.871 39.130 11.47 0.00 33.86 1.40
93 94 2.486203 ACCACGATGAAGCGCAAATTAA 59.514 40.909 11.47 0.00 33.86 1.40
94 95 2.080693 ACCACGATGAAGCGCAAATTA 58.919 42.857 11.47 0.00 33.86 1.40
95 96 0.881118 ACCACGATGAAGCGCAAATT 59.119 45.000 11.47 0.00 33.86 1.82
96 97 0.881118 AACCACGATGAAGCGCAAAT 59.119 45.000 11.47 0.00 33.86 2.32
97 98 0.665835 AAACCACGATGAAGCGCAAA 59.334 45.000 11.47 0.00 33.86 3.68
98 99 1.514003 TAAACCACGATGAAGCGCAA 58.486 45.000 11.47 0.00 33.86 4.85
99 100 1.732941 ATAAACCACGATGAAGCGCA 58.267 45.000 11.47 0.00 33.86 6.09
100 101 2.825086 AATAAACCACGATGAAGCGC 57.175 45.000 0.00 0.00 33.86 5.92
101 102 4.088648 GTGAAATAAACCACGATGAAGCG 58.911 43.478 0.00 0.00 37.29 4.68
102 103 4.412207 GGTGAAATAAACCACGATGAAGC 58.588 43.478 0.00 0.00 37.65 3.86
103 104 4.436852 CCGGTGAAATAAACCACGATGAAG 60.437 45.833 0.00 0.00 37.57 3.02
104 105 3.437395 CCGGTGAAATAAACCACGATGAA 59.563 43.478 0.00 0.00 37.57 2.57
105 106 3.004171 CCGGTGAAATAAACCACGATGA 58.996 45.455 0.00 0.00 37.57 2.92
106 107 3.004171 TCCGGTGAAATAAACCACGATG 58.996 45.455 0.00 0.00 37.57 3.84
107 108 3.004862 GTCCGGTGAAATAAACCACGAT 58.995 45.455 0.00 0.00 37.57 3.73
108 109 2.415776 GTCCGGTGAAATAAACCACGA 58.584 47.619 0.00 0.00 37.57 4.35
109 110 1.465777 GGTCCGGTGAAATAAACCACG 59.534 52.381 0.00 0.00 37.57 4.94
110 111 2.745821 GAGGTCCGGTGAAATAAACCAC 59.254 50.000 0.00 0.00 37.57 4.16
111 112 2.613474 CGAGGTCCGGTGAAATAAACCA 60.613 50.000 0.00 0.00 37.57 3.67
112 113 2.004733 CGAGGTCCGGTGAAATAAACC 58.995 52.381 0.00 0.00 33.91 3.27
113 114 1.395954 GCGAGGTCCGGTGAAATAAAC 59.604 52.381 0.00 0.00 39.04 2.01
114 115 1.002201 TGCGAGGTCCGGTGAAATAAA 59.998 47.619 0.00 0.00 39.04 1.40
115 116 0.609151 TGCGAGGTCCGGTGAAATAA 59.391 50.000 0.00 0.00 39.04 1.40
116 117 0.174845 CTGCGAGGTCCGGTGAAATA 59.825 55.000 0.00 0.00 39.04 1.40
117 118 1.079127 CTGCGAGGTCCGGTGAAAT 60.079 57.895 0.00 0.00 39.04 2.17
118 119 1.180456 TACTGCGAGGTCCGGTGAAA 61.180 55.000 0.00 0.00 39.04 2.69
119 120 1.180456 TTACTGCGAGGTCCGGTGAA 61.180 55.000 0.00 0.00 39.04 3.18
120 121 1.180456 TTTACTGCGAGGTCCGGTGA 61.180 55.000 0.00 0.00 39.04 4.02
121 122 0.320073 TTTTACTGCGAGGTCCGGTG 60.320 55.000 0.00 0.00 39.04 4.94
122 123 0.037605 CTTTTACTGCGAGGTCCGGT 60.038 55.000 0.00 0.00 39.04 5.28
123 124 0.245539 TCTTTTACTGCGAGGTCCGG 59.754 55.000 0.00 0.00 39.04 5.14
124 125 2.295253 ATCTTTTACTGCGAGGTCCG 57.705 50.000 0.00 0.00 42.21 4.79
125 126 2.937149 GGAATCTTTTACTGCGAGGTCC 59.063 50.000 0.00 0.00 0.00 4.46
126 127 3.863041 AGGAATCTTTTACTGCGAGGTC 58.137 45.455 0.00 0.00 0.00 3.85
127 128 3.983044 AGGAATCTTTTACTGCGAGGT 57.017 42.857 0.00 0.00 0.00 3.85
128 129 6.675728 GCTTTAAGGAATCTTTTACTGCGAGG 60.676 42.308 0.00 0.00 34.59 4.63
129 130 6.251549 GCTTTAAGGAATCTTTTACTGCGAG 58.748 40.000 0.00 0.00 34.59 5.03
130 131 5.123344 GGCTTTAAGGAATCTTTTACTGCGA 59.877 40.000 0.00 0.00 34.59 5.10
131 132 5.123979 AGGCTTTAAGGAATCTTTTACTGCG 59.876 40.000 0.00 0.00 34.59 5.18
132 133 6.516739 AGGCTTTAAGGAATCTTTTACTGC 57.483 37.500 0.00 0.00 34.59 4.40
133 134 7.814587 CCAAAGGCTTTAAGGAATCTTTTACTG 59.185 37.037 12.95 0.00 34.59 2.74
134 135 7.525526 GCCAAAGGCTTTAAGGAATCTTTTACT 60.526 37.037 17.86 0.00 46.69 2.24
135 136 6.590292 GCCAAAGGCTTTAAGGAATCTTTTAC 59.410 38.462 17.86 0.00 46.69 2.01
136 137 6.697395 GCCAAAGGCTTTAAGGAATCTTTTA 58.303 36.000 17.86 0.00 46.69 1.52
137 138 5.551233 GCCAAAGGCTTTAAGGAATCTTTT 58.449 37.500 17.86 0.00 46.69 2.27
138 139 5.152623 GCCAAAGGCTTTAAGGAATCTTT 57.847 39.130 17.86 0.00 46.69 2.52
139 140 4.808414 GCCAAAGGCTTTAAGGAATCTT 57.192 40.909 17.86 0.00 46.69 2.40
153 154 1.619827 ACCACAATGACATGCCAAAGG 59.380 47.619 0.00 0.00 0.00 3.11
154 155 2.559668 AGACCACAATGACATGCCAAAG 59.440 45.455 0.00 0.00 0.00 2.77
155 156 2.596346 AGACCACAATGACATGCCAAA 58.404 42.857 0.00 0.00 0.00 3.28
156 157 2.291209 AGACCACAATGACATGCCAA 57.709 45.000 0.00 0.00 0.00 4.52
157 158 3.650281 ATAGACCACAATGACATGCCA 57.350 42.857 0.00 0.00 0.00 4.92
158 159 3.947196 TGAATAGACCACAATGACATGCC 59.053 43.478 0.00 0.00 0.00 4.40
159 160 5.565592 TTGAATAGACCACAATGACATGC 57.434 39.130 0.00 0.00 0.00 4.06
160 161 6.512253 CGGATTGAATAGACCACAATGACATG 60.512 42.308 0.00 0.00 34.94 3.21
161 162 5.528690 CGGATTGAATAGACCACAATGACAT 59.471 40.000 0.00 0.00 34.94 3.06
162 163 4.875536 CGGATTGAATAGACCACAATGACA 59.124 41.667 0.00 0.00 34.94 3.58
163 164 5.006746 GTCGGATTGAATAGACCACAATGAC 59.993 44.000 0.00 0.00 34.94 3.06
164 165 5.116180 GTCGGATTGAATAGACCACAATGA 58.884 41.667 0.00 0.00 34.94 2.57
165 166 5.409643 GTCGGATTGAATAGACCACAATG 57.590 43.478 0.00 0.00 34.94 2.82
172 173 5.848406 AGATCAAGGTCGGATTGAATAGAC 58.152 41.667 0.00 5.13 39.92 2.59
173 174 7.597288 TTAGATCAAGGTCGGATTGAATAGA 57.403 36.000 0.00 0.00 39.92 1.98
174 175 8.144478 TCTTTAGATCAAGGTCGGATTGAATAG 58.856 37.037 0.00 0.00 39.92 1.73
175 176 8.018537 TCTTTAGATCAAGGTCGGATTGAATA 57.981 34.615 0.00 0.00 39.92 1.75
176 177 6.889198 TCTTTAGATCAAGGTCGGATTGAAT 58.111 36.000 0.00 0.00 39.92 2.57
177 178 6.294361 TCTTTAGATCAAGGTCGGATTGAA 57.706 37.500 0.00 0.00 39.92 2.69
178 179 5.932619 TCTTTAGATCAAGGTCGGATTGA 57.067 39.130 0.00 0.00 40.72 2.57
179 180 6.203723 GGAATCTTTAGATCAAGGTCGGATTG 59.796 42.308 0.00 0.00 32.75 2.67
180 181 6.126768 TGGAATCTTTAGATCAAGGTCGGATT 60.127 38.462 0.00 0.00 32.75 3.01
181 182 5.366768 TGGAATCTTTAGATCAAGGTCGGAT 59.633 40.000 0.00 0.00 32.75 4.18
182 183 4.714802 TGGAATCTTTAGATCAAGGTCGGA 59.285 41.667 0.00 0.00 32.75 4.55
183 184 5.023533 TGGAATCTTTAGATCAAGGTCGG 57.976 43.478 0.00 0.00 32.75 4.79
184 185 6.985188 TTTGGAATCTTTAGATCAAGGTCG 57.015 37.500 0.00 0.00 32.75 4.79
185 186 8.567285 TCTTTTGGAATCTTTAGATCAAGGTC 57.433 34.615 0.00 0.00 32.75 3.85
186 187 8.940397 TTCTTTTGGAATCTTTAGATCAAGGT 57.060 30.769 0.00 0.00 32.75 3.50
201 202 9.267084 GCATTACCTTTTGTAATTCTTTTGGAA 57.733 29.630 0.00 0.00 45.78 3.53
202 203 7.875554 GGCATTACCTTTTGTAATTCTTTTGGA 59.124 33.333 0.00 0.00 45.78 3.53
203 204 8.028540 GGCATTACCTTTTGTAATTCTTTTGG 57.971 34.615 0.00 0.00 45.78 3.28
263 264 9.405587 GGAAAATATTCATTTGTTTTCGACTCA 57.594 29.630 0.00 0.00 39.97 3.41
264 265 9.405587 TGGAAAATATTCATTTGTTTTCGACTC 57.594 29.630 0.00 0.00 39.97 3.36
265 266 9.757227 TTGGAAAATATTCATTTGTTTTCGACT 57.243 25.926 0.00 0.00 39.97 4.18
272 273 8.513774 GCCATGTTTGGAAAATATTCATTTGTT 58.486 29.630 0.00 0.00 46.92 2.83
273 274 7.121020 GGCCATGTTTGGAAAATATTCATTTGT 59.879 33.333 0.00 0.00 46.92 2.83
274 275 7.120873 TGGCCATGTTTGGAAAATATTCATTTG 59.879 33.333 0.00 0.00 46.92 2.32
275 276 7.121020 GTGGCCATGTTTGGAAAATATTCATTT 59.879 33.333 9.72 0.00 46.92 2.32
276 277 6.598850 GTGGCCATGTTTGGAAAATATTCATT 59.401 34.615 9.72 0.00 46.92 2.57
277 278 6.070078 AGTGGCCATGTTTGGAAAATATTCAT 60.070 34.615 9.72 0.00 46.92 2.57
278 279 5.248020 AGTGGCCATGTTTGGAAAATATTCA 59.752 36.000 9.72 0.00 46.92 2.57
279 280 5.733676 AGTGGCCATGTTTGGAAAATATTC 58.266 37.500 9.72 0.00 46.92 1.75
280 281 5.760484 AGTGGCCATGTTTGGAAAATATT 57.240 34.783 9.72 0.00 46.92 1.28
281 282 5.490159 CAAGTGGCCATGTTTGGAAAATAT 58.510 37.500 9.72 0.00 46.92 1.28
282 283 4.802248 GCAAGTGGCCATGTTTGGAAAATA 60.802 41.667 21.67 0.00 46.92 1.40
283 284 3.742385 CAAGTGGCCATGTTTGGAAAAT 58.258 40.909 9.72 0.00 46.92 1.82
284 285 2.744494 GCAAGTGGCCATGTTTGGAAAA 60.744 45.455 21.67 0.00 46.92 2.29
285 286 1.202627 GCAAGTGGCCATGTTTGGAAA 60.203 47.619 21.67 0.00 46.92 3.13
286 287 0.392336 GCAAGTGGCCATGTTTGGAA 59.608 50.000 21.67 0.00 46.92 3.53
287 288 0.469705 AGCAAGTGGCCATGTTTGGA 60.470 50.000 21.67 0.00 46.92 3.53
288 289 0.037975 GAGCAAGTGGCCATGTTTGG 60.038 55.000 21.67 7.34 46.50 3.28
289 290 0.675083 TGAGCAAGTGGCCATGTTTG 59.325 50.000 9.72 15.46 46.50 2.93
290 291 1.636148 ATGAGCAAGTGGCCATGTTT 58.364 45.000 9.72 0.74 46.50 2.83
291 292 1.636148 AATGAGCAAGTGGCCATGTT 58.364 45.000 9.72 0.76 46.50 2.71
292 293 2.512692 TAATGAGCAAGTGGCCATGT 57.487 45.000 9.72 0.00 46.50 3.21
293 294 4.392047 TCTATAATGAGCAAGTGGCCATG 58.608 43.478 9.72 5.05 46.50 3.66
294 295 4.712051 TCTATAATGAGCAAGTGGCCAT 57.288 40.909 9.72 0.00 46.50 4.40
295 296 4.454678 CTTCTATAATGAGCAAGTGGCCA 58.545 43.478 0.00 0.00 46.50 5.36
296 297 3.817647 CCTTCTATAATGAGCAAGTGGCC 59.182 47.826 0.00 0.00 46.50 5.36
297 298 4.455606 ACCTTCTATAATGAGCAAGTGGC 58.544 43.478 0.00 0.00 45.30 5.01
354 364 6.372937 CCAAAACTTTTGCCTTCACCTTTAAA 59.627 34.615 8.53 0.00 0.00 1.52
362 372 2.499289 TGAGCCAAAACTTTTGCCTTCA 59.501 40.909 8.53 8.44 29.82 3.02
404 414 5.948992 AATAGAAGGATTTTATCTGGCGC 57.051 39.130 0.00 0.00 0.00 6.53
417 427 8.314751 TGGACAAAACAAACAAAAATAGAAGGA 58.685 29.630 0.00 0.00 0.00 3.36
454 464 5.637006 TTATGAAAAACAATCCCGACAGG 57.363 39.130 0.00 0.00 37.24 4.00
455 465 7.411804 GCAAATTATGAAAAACAATCCCGACAG 60.412 37.037 0.00 0.00 0.00 3.51
458 468 6.459066 TGCAAATTATGAAAAACAATCCCGA 58.541 32.000 0.00 0.00 0.00 5.14
459 469 6.718454 TGCAAATTATGAAAAACAATCCCG 57.282 33.333 0.00 0.00 0.00 5.14
498 510 6.253512 GCGGTTTCCATGATTTGAAAGATTAC 59.746 38.462 0.00 0.00 31.55 1.89
501 513 4.220382 TGCGGTTTCCATGATTTGAAAGAT 59.780 37.500 0.00 0.00 31.55 2.40
514 526 2.214376 AGATGGATTTGCGGTTTCCA 57.786 45.000 0.00 0.00 43.37 3.53
515 527 3.312697 GTCTAGATGGATTTGCGGTTTCC 59.687 47.826 0.00 0.00 0.00 3.13
526 538 3.164268 CAGGCTGCTAGTCTAGATGGAT 58.836 50.000 11.27 0.00 0.00 3.41
538 550 3.495331 TGAAAAATGAACCAGGCTGCTA 58.505 40.909 9.56 0.00 0.00 3.49
540 552 2.818130 TGAAAAATGAACCAGGCTGC 57.182 45.000 9.56 0.00 0.00 5.25
543 555 3.876320 TGCTTTTGAAAAATGAACCAGGC 59.124 39.130 0.00 0.00 0.00 4.85
546 558 7.621428 TCAAATGCTTTTGAAAAATGAACCA 57.379 28.000 21.62 0.00 46.26 3.67
579 647 1.123077 GATTTGGAGATTTGGGGGCC 58.877 55.000 0.00 0.00 0.00 5.80
589 657 0.986527 TCTGGCTGCTGATTTGGAGA 59.013 50.000 0.00 0.00 0.00 3.71
623 713 0.683179 GCACAGGGGTGGGGTATTTC 60.683 60.000 0.00 0.00 45.38 2.17
769 887 3.432186 GTTGCTCGCCCAACTTGT 58.568 55.556 9.76 0.00 41.36 3.16
807 925 2.916269 TGGTGGTTCTTATGTGGATGGA 59.084 45.455 0.00 0.00 0.00 3.41
833 951 4.212797 CGGTGGTGGGTTTGGGGT 62.213 66.667 0.00 0.00 0.00 4.95
878 1001 2.770475 GGAAGGGGGAGGAGGAGC 60.770 72.222 0.00 0.00 0.00 4.70
879 1002 2.040359 GGGAAGGGGGAGGAGGAG 60.040 72.222 0.00 0.00 0.00 3.69
880 1003 3.707189 GGGGAAGGGGGAGGAGGA 61.707 72.222 0.00 0.00 0.00 3.71
881 1004 2.883316 ATTGGGGAAGGGGGAGGAGG 62.883 65.000 0.00 0.00 0.00 4.30
882 1005 0.926220 AATTGGGGAAGGGGGAGGAG 60.926 60.000 0.00 0.00 0.00 3.69
883 1006 0.481607 AAATTGGGGAAGGGGGAGGA 60.482 55.000 0.00 0.00 0.00 3.71
884 1007 0.417437 AAAATTGGGGAAGGGGGAGG 59.583 55.000 0.00 0.00 0.00 4.30
885 1008 2.342406 AAAAATTGGGGAAGGGGGAG 57.658 50.000 0.00 0.00 0.00 4.30
966 1413 4.385405 AGGAGCTGCTGCGACCAC 62.385 66.667 26.10 11.67 45.42 4.16
991 1438 4.161295 CGGAGGCATGGCGAGGAA 62.161 66.667 14.30 0.00 0.00 3.36
1030 1477 2.024846 TCAATTCAATTCGGGGCCCTTA 60.025 45.455 24.38 8.65 0.00 2.69
1060 1508 1.208642 GAAGCACCGCACAAACAAGC 61.209 55.000 0.00 0.00 0.00 4.01
1061 1509 0.929824 CGAAGCACCGCACAAACAAG 60.930 55.000 0.00 0.00 0.00 3.16
1062 1510 1.063327 CGAAGCACCGCACAAACAA 59.937 52.632 0.00 0.00 0.00 2.83
1063 1511 2.712539 CGAAGCACCGCACAAACA 59.287 55.556 0.00 0.00 0.00 2.83
1076 1524 1.361993 CTCCAGATCTCCGGCGAAG 59.638 63.158 9.30 0.00 0.00 3.79
1101 1566 0.534877 AATCAGCACAACGCACCAGA 60.535 50.000 0.00 0.00 46.13 3.86
1110 1575 3.865011 ACACACACAAAATCAGCACAA 57.135 38.095 0.00 0.00 0.00 3.33
1171 1636 4.891727 CCGCCGAACATAGCCGCT 62.892 66.667 0.00 0.00 0.00 5.52
1714 2197 4.365111 GGCACATCCCACAGGGCA 62.365 66.667 0.00 0.00 43.94 5.36
1879 2362 1.975407 GGCAACACCAGAGCATGCT 60.975 57.895 22.92 22.92 38.86 3.79
2422 2905 4.310769 CAGTACACTTCACCAAAGAGAGG 58.689 47.826 0.00 0.00 38.44 3.69
2575 3058 1.205655 CCGCTCAGGTCAAGATTCTCA 59.794 52.381 0.00 0.00 34.51 3.27
2668 3151 2.679837 GAGATTCTCGCAGCCATTCAAA 59.320 45.455 0.00 0.00 0.00 2.69
2710 3193 2.111043 CCGTGTGCCTTCACCAGT 59.889 61.111 0.00 0.00 42.46 4.00
2733 3216 1.673923 CGAGGCTCAGATGTGCAAGAA 60.674 52.381 15.95 0.00 36.36 2.52
2764 3247 8.032952 CAAACAGACTTGCATCAGTTATCTTA 57.967 34.615 0.00 0.00 29.13 2.10
3134 3620 1.897398 GACTCAAACGCGCAACCGAT 61.897 55.000 5.73 0.00 36.29 4.18
3351 3842 1.625818 AGCTCCCACACAGGACTTAAG 59.374 52.381 0.00 0.00 41.22 1.85
3352 3843 1.623811 GAGCTCCCACACAGGACTTAA 59.376 52.381 0.87 0.00 41.22 1.85
3353 3844 1.267121 GAGCTCCCACACAGGACTTA 58.733 55.000 0.87 0.00 41.22 2.24
3495 4009 0.108138 CGGATCAAAGAACCGGAGCT 60.108 55.000 9.46 0.63 42.82 4.09
3508 4022 2.092323 CAGACACCTAGACACGGATCA 58.908 52.381 0.00 0.00 0.00 2.92
3568 4082 2.034305 ACACACTACAGACCGTGAAGAC 59.966 50.000 0.00 0.00 35.23 3.01
3650 4172 2.354729 CCGGGGACATCAGGCAAA 59.645 61.111 0.00 0.00 0.00 3.68
3751 4273 1.140589 CACACGCCTGCAAAAACCA 59.859 52.632 0.00 0.00 0.00 3.67
3770 4292 3.020274 TGCAAAGGTTACAGCACTCAAA 58.980 40.909 0.00 0.00 31.05 2.69
3841 4364 1.604604 TCACAAGGTTGCAGGTAAGC 58.395 50.000 0.00 0.00 0.00 3.09
3903 4426 1.303309 GCAGCAGCTCCGACAATATT 58.697 50.000 0.00 0.00 37.91 1.28
3964 4496 4.665142 CGAAAATATATCTCACGCAGCTGC 60.665 45.833 29.12 29.12 37.78 5.25
3967 4499 3.423645 GCCGAAAATATATCTCACGCAGC 60.424 47.826 0.00 0.00 0.00 5.25
3972 4504 7.093354 TCATCAGAGCCGAAAATATATCTCAC 58.907 38.462 0.00 0.00 0.00 3.51
3986 4518 4.424061 TGAACAAAATTCATCAGAGCCG 57.576 40.909 0.00 0.00 0.00 5.52
3995 4527 7.066887 TCAGCTCTACAACTTGAACAAAATTCA 59.933 33.333 0.00 0.00 0.00 2.57
3996 4528 7.417612 TCAGCTCTACAACTTGAACAAAATTC 58.582 34.615 0.00 0.00 0.00 2.17
3997 4529 7.333528 TCAGCTCTACAACTTGAACAAAATT 57.666 32.000 0.00 0.00 0.00 1.82
4006 4538 6.304356 TGTTTCAATCAGCTCTACAACTTG 57.696 37.500 0.00 0.00 0.00 3.16
4012 4544 4.083271 GGGTGTTGTTTCAATCAGCTCTAC 60.083 45.833 0.00 0.00 0.00 2.59
4016 4548 1.608590 CGGGTGTTGTTTCAATCAGCT 59.391 47.619 0.00 0.00 0.00 4.24


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

AutoCloner maintained by Alex Coulton.