Multiple sequence alignment - TraesCS6A01G240400

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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 TraesCS6A01G240400 chr6A 100.000 2774 0 0 1 2774 451658958 451661731 0.000000e+00 5123.0
1 TraesCS6A01G240400 chr6D 88.472 1917 96 44 295 2128 314055417 314057291 0.000000e+00 2200.0
2 TraesCS6A01G240400 chr6D 93.931 379 20 3 2134 2510 314057335 314057712 1.110000e-158 569.0
3 TraesCS6A01G240400 chr6D 89.370 254 17 8 2525 2770 314084480 314084731 7.460000e-81 311.0
4 TraesCS6A01G240400 chr6D 97.701 87 2 0 1 87 317085051 317085137 1.720000e-32 150.0
5 TraesCS6A01G240400 chr6B 86.051 1950 94 81 294 2128 512449045 512447159 0.000000e+00 1930.0
6 TraesCS6A01G240400 chr6B 87.538 650 43 15 2139 2752 512447110 512446463 0.000000e+00 717.0
7 TraesCS6A01G240400 chr6B 95.556 45 0 2 253 297 512449107 512449065 1.380000e-08 71.3
8 TraesCS6A01G240400 chr2D 89.226 297 29 3 1095 1388 492676495 492676791 4.360000e-98 368.0
9 TraesCS6A01G240400 chr2A 88.514 296 31 3 1095 1387 637984682 637984977 3.400000e-94 355.0
10 TraesCS6A01G240400 chr2B 88.176 296 32 3 1095 1387 578605270 578605565 1.580000e-92 350.0
11 TraesCS6A01G240400 chr4D 81.313 198 30 7 1106 1301 457075096 457075288 1.330000e-33 154.0
12 TraesCS6A01G240400 chr4D 96.552 87 3 0 1 87 441497594 441497508 8.010000e-31 145.0
13 TraesCS6A01G240400 chr5D 97.701 87 2 0 1 87 11290210 11290124 1.720000e-32 150.0
14 TraesCS6A01G240400 chr5D 97.701 87 2 0 1 87 398792051 398791965 1.720000e-32 150.0
15 TraesCS6A01G240400 chr5A 97.701 87 2 0 1 87 372935949 372935863 1.720000e-32 150.0
16 TraesCS6A01G240400 chr5A 96.552 87 3 0 1 87 372956656 372956570 8.010000e-31 145.0
17 TraesCS6A01G240400 chr7D 96.552 87 3 0 1 87 607622435 607622349 8.010000e-31 145.0
18 TraesCS6A01G240400 chr5B 96.552 87 3 0 1 87 278791804 278791890 8.010000e-31 145.0
19 TraesCS6A01G240400 chr1D 95.455 88 4 0 1 88 253092745 253092658 1.040000e-29 141.0


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 TraesCS6A01G240400 chr6A 451658958 451661731 2773 False 5123.0 5123 100.0000 1 2774 1 chr6A.!!$F1 2773
1 TraesCS6A01G240400 chr6D 314055417 314057712 2295 False 1384.5 2200 91.2015 295 2510 2 chr6D.!!$F3 2215
2 TraesCS6A01G240400 chr6B 512446463 512449107 2644 True 906.1 1930 89.7150 253 2752 3 chr6B.!!$R1 2499

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
683 761 0.031449 GAGGATCTCGCACTACAGCC 59.969 60.0 0.0 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1824 1984 0.105039 CCGGATCAACCAGCTAGACC 59.895 60.0 0.0 0.0 38.9 3.85 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 2.922740 TTGTGGTCCACCTTGTACTC 57.077 50.000 19.57 0.00 36.82 2.59
20 21 1.053424 TGTGGTCCACCTTGTACTCC 58.947 55.000 19.57 0.00 36.82 3.85
21 22 1.053424 GTGGTCCACCTTGTACTCCA 58.947 55.000 11.30 0.00 36.82 3.86
22 23 1.628846 GTGGTCCACCTTGTACTCCAT 59.371 52.381 11.30 0.00 36.82 3.41
23 24 2.835764 GTGGTCCACCTTGTACTCCATA 59.164 50.000 11.30 0.00 36.82 2.74
24 25 3.454812 GTGGTCCACCTTGTACTCCATAT 59.545 47.826 11.30 0.00 36.82 1.78
25 26 4.652421 GTGGTCCACCTTGTACTCCATATA 59.348 45.833 11.30 0.00 36.82 0.86
26 27 5.307196 GTGGTCCACCTTGTACTCCATATAT 59.693 44.000 11.30 0.00 36.82 0.86
27 28 6.495872 GTGGTCCACCTTGTACTCCATATATA 59.504 42.308 11.30 0.00 36.82 0.86
28 29 6.495872 TGGTCCACCTTGTACTCCATATATAC 59.504 42.308 0.00 0.00 36.82 1.47
29 30 6.349944 GGTCCACCTTGTACTCCATATATACG 60.350 46.154 0.00 0.00 0.00 3.06
30 31 6.208204 GTCCACCTTGTACTCCATATATACGT 59.792 42.308 0.00 0.00 0.00 3.57
31 32 6.208007 TCCACCTTGTACTCCATATATACGTG 59.792 42.308 0.00 0.00 0.00 4.49
32 33 5.862323 CACCTTGTACTCCATATATACGTGC 59.138 44.000 0.00 0.00 0.00 5.34
33 34 5.093457 CCTTGTACTCCATATATACGTGCG 58.907 45.833 0.00 0.00 0.00 5.34
34 35 4.087510 TGTACTCCATATATACGTGCGC 57.912 45.455 0.00 0.00 0.00 6.09
35 36 3.754850 TGTACTCCATATATACGTGCGCT 59.245 43.478 9.73 0.00 0.00 5.92
36 37 4.937015 TGTACTCCATATATACGTGCGCTA 59.063 41.667 9.73 0.00 0.00 4.26
37 38 5.587443 TGTACTCCATATATACGTGCGCTAT 59.413 40.000 9.73 0.17 0.00 2.97
38 39 4.921547 ACTCCATATATACGTGCGCTATG 58.078 43.478 9.73 6.27 0.00 2.23
39 40 3.702330 TCCATATATACGTGCGCTATGC 58.298 45.455 9.73 0.00 46.70 3.14
48 49 3.717899 GCGCTATGCACCGATCAA 58.282 55.556 0.00 0.00 45.45 2.57
49 50 2.238353 GCGCTATGCACCGATCAAT 58.762 52.632 0.00 0.00 45.45 2.57
50 51 1.428448 GCGCTATGCACCGATCAATA 58.572 50.000 0.00 0.00 45.45 1.90
51 52 1.126846 GCGCTATGCACCGATCAATAC 59.873 52.381 0.00 0.00 45.45 1.89
52 53 2.403259 CGCTATGCACCGATCAATACA 58.597 47.619 0.00 0.00 0.00 2.29
53 54 2.995939 CGCTATGCACCGATCAATACAT 59.004 45.455 0.00 0.00 0.00 2.29
54 55 3.061295 CGCTATGCACCGATCAATACATC 59.939 47.826 0.00 0.00 0.00 3.06
55 56 3.061295 GCTATGCACCGATCAATACATCG 59.939 47.826 0.00 0.00 44.45 3.84
56 57 2.595124 TGCACCGATCAATACATCGT 57.405 45.000 2.46 0.00 43.53 3.73
57 58 2.200899 TGCACCGATCAATACATCGTG 58.799 47.619 2.46 2.71 43.53 4.35
58 59 2.159170 TGCACCGATCAATACATCGTGA 60.159 45.455 2.46 0.00 43.53 4.35
59 60 2.863740 GCACCGATCAATACATCGTGAA 59.136 45.455 2.46 0.00 43.53 3.18
60 61 3.060272 GCACCGATCAATACATCGTGAAG 60.060 47.826 2.46 0.00 43.53 3.02
61 62 3.060272 CACCGATCAATACATCGTGAAGC 60.060 47.826 2.46 0.00 43.53 3.86
62 63 3.123050 CCGATCAATACATCGTGAAGCA 58.877 45.455 2.46 0.00 43.53 3.91
63 64 3.742882 CCGATCAATACATCGTGAAGCAT 59.257 43.478 2.46 0.00 43.53 3.79
64 65 4.143242 CCGATCAATACATCGTGAAGCATC 60.143 45.833 2.46 0.00 43.53 3.91
65 66 4.432115 CGATCAATACATCGTGAAGCATCG 60.432 45.833 0.00 0.00 40.72 3.84
66 67 2.539688 TCAATACATCGTGAAGCATCGC 59.460 45.455 0.00 0.00 0.00 4.58
67 68 1.502231 ATACATCGTGAAGCATCGCC 58.498 50.000 0.00 0.00 32.24 5.54
68 69 0.174617 TACATCGTGAAGCATCGCCA 59.825 50.000 0.00 0.00 32.24 5.69
69 70 0.673333 ACATCGTGAAGCATCGCCAA 60.673 50.000 0.00 0.00 32.24 4.52
70 71 0.447406 CATCGTGAAGCATCGCCAAA 59.553 50.000 0.00 0.00 32.24 3.28
71 72 1.135717 CATCGTGAAGCATCGCCAAAA 60.136 47.619 0.00 0.00 32.24 2.44
72 73 0.237235 TCGTGAAGCATCGCCAAAAC 59.763 50.000 0.00 0.00 32.24 2.43
73 74 0.040514 CGTGAAGCATCGCCAAAACA 60.041 50.000 0.00 0.00 32.24 2.83
74 75 1.401409 CGTGAAGCATCGCCAAAACAT 60.401 47.619 0.00 0.00 32.24 2.71
75 76 2.676076 GTGAAGCATCGCCAAAACATT 58.324 42.857 0.00 0.00 0.00 2.71
76 77 2.663119 GTGAAGCATCGCCAAAACATTC 59.337 45.455 0.00 0.00 0.00 2.67
77 78 1.913403 GAAGCATCGCCAAAACATTCG 59.087 47.619 0.00 0.00 0.00 3.34
78 79 0.881118 AGCATCGCCAAAACATTCGT 59.119 45.000 0.00 0.00 0.00 3.85
79 80 1.269448 AGCATCGCCAAAACATTCGTT 59.731 42.857 0.00 0.00 36.73 3.85
81 82 2.090503 GCATCGCCAAAACATTCGTTTC 59.909 45.455 0.00 0.00 44.65 2.78
82 83 2.409152 TCGCCAAAACATTCGTTTCC 57.591 45.000 0.00 0.00 44.65 3.13
83 84 1.676529 TCGCCAAAACATTCGTTTCCA 59.323 42.857 0.00 0.00 44.65 3.53
84 85 2.099263 TCGCCAAAACATTCGTTTCCAA 59.901 40.909 0.00 0.00 44.65 3.53
85 86 2.217620 CGCCAAAACATTCGTTTCCAAC 59.782 45.455 0.00 0.00 44.65 3.77
86 87 3.190874 GCCAAAACATTCGTTTCCAACA 58.809 40.909 0.00 0.00 44.65 3.33
87 88 3.245048 GCCAAAACATTCGTTTCCAACAG 59.755 43.478 0.00 0.00 44.65 3.16
88 89 4.677584 CCAAAACATTCGTTTCCAACAGA 58.322 39.130 0.00 0.00 44.65 3.41
89 90 4.502645 CCAAAACATTCGTTTCCAACAGAC 59.497 41.667 0.00 0.00 44.65 3.51
90 91 5.339990 CAAAACATTCGTTTCCAACAGACT 58.660 37.500 0.00 0.00 44.65 3.24
91 92 4.813296 AACATTCGTTTCCAACAGACTC 57.187 40.909 0.00 0.00 28.09 3.36
92 93 3.804036 ACATTCGTTTCCAACAGACTCA 58.196 40.909 0.00 0.00 0.00 3.41
93 94 4.389374 ACATTCGTTTCCAACAGACTCAT 58.611 39.130 0.00 0.00 0.00 2.90
94 95 4.821805 ACATTCGTTTCCAACAGACTCATT 59.178 37.500 0.00 0.00 0.00 2.57
95 96 5.049405 ACATTCGTTTCCAACAGACTCATTC 60.049 40.000 0.00 0.00 0.00 2.67
96 97 3.057019 TCGTTTCCAACAGACTCATTCG 58.943 45.455 0.00 0.00 0.00 3.34
97 98 2.411547 CGTTTCCAACAGACTCATTCGC 60.412 50.000 0.00 0.00 0.00 4.70
98 99 1.808411 TTCCAACAGACTCATTCGCC 58.192 50.000 0.00 0.00 0.00 5.54
99 100 0.684535 TCCAACAGACTCATTCGCCA 59.315 50.000 0.00 0.00 0.00 5.69
100 101 1.081892 CCAACAGACTCATTCGCCAG 58.918 55.000 0.00 0.00 0.00 4.85
101 102 0.445436 CAACAGACTCATTCGCCAGC 59.555 55.000 0.00 0.00 0.00 4.85
102 103 0.322975 AACAGACTCATTCGCCAGCT 59.677 50.000 0.00 0.00 0.00 4.24
103 104 0.322975 ACAGACTCATTCGCCAGCTT 59.677 50.000 0.00 0.00 0.00 3.74
104 105 0.725686 CAGACTCATTCGCCAGCTTG 59.274 55.000 0.00 0.00 0.00 4.01
105 106 1.023513 AGACTCATTCGCCAGCTTGC 61.024 55.000 0.00 0.00 0.00 4.01
106 107 1.002868 ACTCATTCGCCAGCTTGCT 60.003 52.632 8.31 0.00 0.00 3.91
107 108 1.023513 ACTCATTCGCCAGCTTGCTC 61.024 55.000 8.31 0.00 0.00 4.26
108 109 0.743701 CTCATTCGCCAGCTTGCTCT 60.744 55.000 8.31 0.00 0.00 4.09
109 110 0.321919 TCATTCGCCAGCTTGCTCTT 60.322 50.000 8.31 0.00 0.00 2.85
110 111 0.524862 CATTCGCCAGCTTGCTCTTT 59.475 50.000 8.31 0.00 0.00 2.52
111 112 0.524862 ATTCGCCAGCTTGCTCTTTG 59.475 50.000 8.31 0.00 0.00 2.77
112 113 2.126580 CGCCAGCTTGCTCTTTGC 60.127 61.111 8.31 0.00 43.25 3.68
126 127 5.508124 GCTCTTTGCACTCTATATAAGCG 57.492 43.478 0.00 0.00 42.31 4.68
127 128 4.387256 GCTCTTTGCACTCTATATAAGCGG 59.613 45.833 0.00 0.00 42.31 5.52
128 129 5.773575 CTCTTTGCACTCTATATAAGCGGA 58.226 41.667 0.00 0.00 0.00 5.54
129 130 6.346477 TCTTTGCACTCTATATAAGCGGAT 57.654 37.500 0.00 0.00 0.00 4.18
130 131 6.759272 TCTTTGCACTCTATATAAGCGGATT 58.241 36.000 0.00 0.00 0.00 3.01
131 132 7.892609 TCTTTGCACTCTATATAAGCGGATTA 58.107 34.615 0.00 0.00 0.00 1.75
132 133 8.364894 TCTTTGCACTCTATATAAGCGGATTAA 58.635 33.333 0.00 0.00 0.00 1.40
133 134 9.155975 CTTTGCACTCTATATAAGCGGATTAAT 57.844 33.333 0.00 0.00 0.00 1.40
135 136 9.803315 TTGCACTCTATATAAGCGGATTAATAG 57.197 33.333 0.00 0.56 0.00 1.73
136 137 8.967918 TGCACTCTATATAAGCGGATTAATAGT 58.032 33.333 11.39 0.00 0.00 2.12
137 138 9.453325 GCACTCTATATAAGCGGATTAATAGTC 57.547 37.037 11.39 0.00 0.00 2.59
138 139 9.953697 CACTCTATATAAGCGGATTAATAGTCC 57.046 37.037 11.39 0.00 0.00 3.85
139 140 9.696572 ACTCTATATAAGCGGATTAATAGTCCA 57.303 33.333 2.74 0.00 35.41 4.02
144 145 4.755266 AGCGGATTAATAGTCCAACTGT 57.245 40.909 2.74 0.00 35.41 3.55
145 146 4.694339 AGCGGATTAATAGTCCAACTGTC 58.306 43.478 2.74 0.00 35.41 3.51
146 147 3.808174 GCGGATTAATAGTCCAACTGTCC 59.192 47.826 2.74 0.00 35.41 4.02
147 148 4.682320 GCGGATTAATAGTCCAACTGTCCA 60.682 45.833 2.74 0.00 35.41 4.02
148 149 5.424757 CGGATTAATAGTCCAACTGTCCAA 58.575 41.667 2.74 0.00 35.41 3.53
149 150 5.293569 CGGATTAATAGTCCAACTGTCCAAC 59.706 44.000 2.74 0.00 35.41 3.77
150 151 6.415573 GGATTAATAGTCCAACTGTCCAACT 58.584 40.000 0.00 0.00 35.76 3.16
151 152 6.316390 GGATTAATAGTCCAACTGTCCAACTG 59.684 42.308 0.00 0.00 35.76 3.16
152 153 4.974645 AATAGTCCAACTGTCCAACTGA 57.025 40.909 0.00 0.00 0.00 3.41
153 154 5.505181 AATAGTCCAACTGTCCAACTGAT 57.495 39.130 0.00 0.00 0.00 2.90
154 155 3.131709 AGTCCAACTGTCCAACTGATG 57.868 47.619 0.00 0.00 0.00 3.07
168 169 5.786401 CAACTGATGGACTAGTGTTAAGC 57.214 43.478 0.00 0.00 0.00 3.09
169 170 5.237815 CAACTGATGGACTAGTGTTAAGCA 58.762 41.667 0.00 0.00 0.00 3.91
170 171 5.483685 ACTGATGGACTAGTGTTAAGCAA 57.516 39.130 0.00 0.00 0.00 3.91
171 172 5.238583 ACTGATGGACTAGTGTTAAGCAAC 58.761 41.667 0.00 0.00 35.06 4.17
172 173 4.575885 TGATGGACTAGTGTTAAGCAACC 58.424 43.478 0.00 0.00 33.41 3.77
173 174 3.412237 TGGACTAGTGTTAAGCAACCC 57.588 47.619 0.00 0.00 33.41 4.11
174 175 2.976882 TGGACTAGTGTTAAGCAACCCT 59.023 45.455 0.00 0.00 33.41 4.34
175 176 4.161876 TGGACTAGTGTTAAGCAACCCTA 58.838 43.478 0.00 0.00 33.41 3.53
176 177 4.781087 TGGACTAGTGTTAAGCAACCCTAT 59.219 41.667 0.00 0.00 33.41 2.57
177 178 5.959594 TGGACTAGTGTTAAGCAACCCTATA 59.040 40.000 0.00 0.00 33.41 1.31
178 179 6.614087 TGGACTAGTGTTAAGCAACCCTATAT 59.386 38.462 0.00 0.00 33.41 0.86
179 180 7.785985 TGGACTAGTGTTAAGCAACCCTATATA 59.214 37.037 0.00 0.00 33.41 0.86
180 181 8.087136 GGACTAGTGTTAAGCAACCCTATATAC 58.913 40.741 0.00 0.00 33.41 1.47
181 182 8.543293 ACTAGTGTTAAGCAACCCTATATACA 57.457 34.615 0.00 0.00 33.41 2.29
182 183 8.639761 ACTAGTGTTAAGCAACCCTATATACAG 58.360 37.037 0.00 0.00 33.41 2.74
183 184 7.670605 AGTGTTAAGCAACCCTATATACAGA 57.329 36.000 0.00 0.00 33.41 3.41
184 185 8.263854 AGTGTTAAGCAACCCTATATACAGAT 57.736 34.615 0.00 0.00 33.41 2.90
185 186 9.375974 AGTGTTAAGCAACCCTATATACAGATA 57.624 33.333 0.00 0.00 33.41 1.98
186 187 9.991906 GTGTTAAGCAACCCTATATACAGATAA 57.008 33.333 0.00 0.00 33.41 1.75
191 192 9.561069 AAGCAACCCTATATACAGATAAAACTG 57.439 33.333 0.00 0.00 42.78 3.16
192 193 8.157476 AGCAACCCTATATACAGATAAAACTGG 58.843 37.037 0.00 0.00 41.59 4.00
193 194 8.154856 GCAACCCTATATACAGATAAAACTGGA 58.845 37.037 0.00 0.00 41.59 3.86
200 201 8.773404 ATATACAGATAAAACTGGATAACGCC 57.227 34.615 0.00 0.00 43.90 5.68
201 202 4.839121 ACAGATAAAACTGGATAACGCCA 58.161 39.130 0.00 0.00 41.59 5.69
202 203 4.634443 ACAGATAAAACTGGATAACGCCAC 59.366 41.667 0.00 0.00 41.59 5.01
203 204 4.634004 CAGATAAAACTGGATAACGCCACA 59.366 41.667 0.00 0.00 34.64 4.17
204 205 5.123186 CAGATAAAACTGGATAACGCCACAA 59.877 40.000 0.00 0.00 34.64 3.33
205 206 5.708230 AGATAAAACTGGATAACGCCACAAA 59.292 36.000 0.00 0.00 33.52 2.83
206 207 3.636282 AAACTGGATAACGCCACAAAC 57.364 42.857 0.00 0.00 33.52 2.93
207 208 1.530323 ACTGGATAACGCCACAAACC 58.470 50.000 0.00 0.00 33.52 3.27
208 209 0.808755 CTGGATAACGCCACAAACCC 59.191 55.000 0.00 0.00 33.52 4.11
209 210 0.110678 TGGATAACGCCACAAACCCA 59.889 50.000 0.00 0.00 31.66 4.51
210 211 1.249407 GGATAACGCCACAAACCCAA 58.751 50.000 0.00 0.00 0.00 4.12
211 212 1.201414 GGATAACGCCACAAACCCAAG 59.799 52.381 0.00 0.00 0.00 3.61
212 213 2.156098 GATAACGCCACAAACCCAAGA 58.844 47.619 0.00 0.00 0.00 3.02
213 214 1.310904 TAACGCCACAAACCCAAGAC 58.689 50.000 0.00 0.00 0.00 3.01
214 215 1.388837 AACGCCACAAACCCAAGACC 61.389 55.000 0.00 0.00 0.00 3.85
215 216 1.528309 CGCCACAAACCCAAGACCT 60.528 57.895 0.00 0.00 0.00 3.85
216 217 1.515521 CGCCACAAACCCAAGACCTC 61.516 60.000 0.00 0.00 0.00 3.85
217 218 1.515521 GCCACAAACCCAAGACCTCG 61.516 60.000 0.00 0.00 0.00 4.63
218 219 0.179029 CCACAAACCCAAGACCTCGT 60.179 55.000 0.00 0.00 0.00 4.18
219 220 1.675552 CACAAACCCAAGACCTCGTT 58.324 50.000 0.00 0.00 0.00 3.85
220 221 1.333619 CACAAACCCAAGACCTCGTTG 59.666 52.381 0.00 0.00 0.00 4.10
221 222 0.310854 CAAACCCAAGACCTCGTTGC 59.689 55.000 0.00 0.00 0.00 4.17
222 223 0.822121 AAACCCAAGACCTCGTTGCC 60.822 55.000 0.00 0.00 0.00 4.52
223 224 1.705997 AACCCAAGACCTCGTTGCCT 61.706 55.000 0.00 0.00 0.00 4.75
224 225 1.376037 CCCAAGACCTCGTTGCCTC 60.376 63.158 0.00 0.00 0.00 4.70
225 226 1.371183 CCAAGACCTCGTTGCCTCA 59.629 57.895 0.00 0.00 0.00 3.86
226 227 0.036010 CCAAGACCTCGTTGCCTCAT 60.036 55.000 0.00 0.00 0.00 2.90
227 228 1.611673 CCAAGACCTCGTTGCCTCATT 60.612 52.381 0.00 0.00 0.00 2.57
228 229 1.466167 CAAGACCTCGTTGCCTCATTG 59.534 52.381 0.00 0.00 0.00 2.82
229 230 0.036010 AGACCTCGTTGCCTCATTGG 60.036 55.000 0.00 0.00 39.35 3.16
238 239 2.586245 CCTCATTGGCAGGAGCGA 59.414 61.111 11.49 0.00 43.41 4.93
239 240 1.078214 CCTCATTGGCAGGAGCGAA 60.078 57.895 11.49 0.00 42.72 4.70
241 242 0.942962 CTCATTGGCAGGAGCGAATC 59.057 55.000 5.48 0.00 44.48 2.52
242 243 0.252761 TCATTGGCAGGAGCGAATCA 59.747 50.000 0.00 0.00 44.48 2.57
243 244 0.379669 CATTGGCAGGAGCGAATCAC 59.620 55.000 0.00 0.00 44.48 3.06
244 245 0.035152 ATTGGCAGGAGCGAATCACA 60.035 50.000 0.00 0.00 44.48 3.58
245 246 0.250684 TTGGCAGGAGCGAATCACAA 60.251 50.000 0.00 0.00 43.41 3.33
246 247 0.250684 TGGCAGGAGCGAATCACAAA 60.251 50.000 0.00 0.00 43.41 2.83
247 248 0.169009 GGCAGGAGCGAATCACAAAC 59.831 55.000 0.00 0.00 43.41 2.93
248 249 0.874390 GCAGGAGCGAATCACAAACA 59.126 50.000 0.00 0.00 0.00 2.83
249 250 1.135859 GCAGGAGCGAATCACAAACAG 60.136 52.381 0.00 0.00 0.00 3.16
250 251 1.466167 CAGGAGCGAATCACAAACAGG 59.534 52.381 0.00 0.00 0.00 4.00
251 252 1.072331 AGGAGCGAATCACAAACAGGT 59.928 47.619 0.00 0.00 0.00 4.00
252 253 1.880027 GGAGCGAATCACAAACAGGTT 59.120 47.619 0.00 0.00 0.00 3.50
253 254 3.071479 GGAGCGAATCACAAACAGGTTA 58.929 45.455 0.00 0.00 0.00 2.85
254 255 3.120304 GGAGCGAATCACAAACAGGTTAC 60.120 47.826 0.00 0.00 0.00 2.50
255 256 3.472652 AGCGAATCACAAACAGGTTACA 58.527 40.909 0.00 0.00 0.00 2.41
256 257 3.880490 AGCGAATCACAAACAGGTTACAA 59.120 39.130 0.00 0.00 0.00 2.41
257 258 4.336993 AGCGAATCACAAACAGGTTACAAA 59.663 37.500 0.00 0.00 0.00 2.83
268 269 3.942748 ACAGGTTACAAACAACACACGAT 59.057 39.130 0.00 0.00 0.00 3.73
329 353 2.047844 CAGCTGGAGGGACACGTG 60.048 66.667 15.48 15.48 0.00 4.49
333 363 3.916392 CTGGAGGGACACGTGACGC 62.916 68.421 25.01 24.05 0.00 5.19
363 393 5.606348 ATCGAACTGGAGATAAGCTCTTT 57.394 39.130 0.00 0.00 43.43 2.52
366 396 6.931838 TCGAACTGGAGATAAGCTCTTTTAA 58.068 36.000 0.00 0.00 43.43 1.52
389 419 5.063180 TCTAGCTTTAACGACGATCCAAA 57.937 39.130 0.00 0.00 0.00 3.28
404 434 4.502282 CGATCCAAAGACGAAGAGAAGATG 59.498 45.833 0.00 0.00 0.00 2.90
429 459 3.039252 TGGAATTCTCCTCTCCTCTCC 57.961 52.381 5.23 0.00 42.94 3.71
433 463 3.884037 ATTCTCCTCTCCTCTCCTCTC 57.116 52.381 0.00 0.00 0.00 3.20
434 464 2.587060 TCTCCTCTCCTCTCCTCTCT 57.413 55.000 0.00 0.00 0.00 3.10
435 465 2.858644 TCTCCTCTCCTCTCCTCTCTT 58.141 52.381 0.00 0.00 0.00 2.85
436 466 2.777692 TCTCCTCTCCTCTCCTCTCTTC 59.222 54.545 0.00 0.00 0.00 2.87
522 552 2.436115 CGAGAAAACGGGGAGCCC 60.436 66.667 0.00 0.00 41.09 5.19
538 568 4.263572 CCCCCAGGCAACGTGACA 62.264 66.667 0.00 0.00 46.39 3.58
539 569 2.203280 CCCCAGGCAACGTGACAA 60.203 61.111 0.00 0.00 46.39 3.18
558 588 4.844420 CCACCTCGGCATCTCTTC 57.156 61.111 0.00 0.00 0.00 2.87
578 619 2.586357 GGAGAAGCCGTGCCGATC 60.586 66.667 0.00 0.00 0.00 3.69
620 664 2.666596 CTACAGCGATTGGCCTCCCC 62.667 65.000 3.32 0.00 45.17 4.81
683 761 0.031449 GAGGATCTCGCACTACAGCC 59.969 60.000 0.00 0.00 0.00 4.85
688 766 2.125147 TCGCACTACAGCCATGCC 60.125 61.111 0.00 0.00 35.91 4.40
692 770 4.838152 ACTACAGCCATGCCCGCG 62.838 66.667 0.00 0.00 0.00 6.46
928 1020 3.807538 GCCACAGATGCACGCCTG 61.808 66.667 10.08 10.08 36.53 4.85
929 1021 3.129502 CCACAGATGCACGCCTGG 61.130 66.667 14.57 3.37 34.85 4.45
930 1022 2.359107 CACAGATGCACGCCTGGT 60.359 61.111 14.57 1.58 34.85 4.00
944 1036 4.610714 TGGTGCACGCGCTACCAA 62.611 61.111 22.36 9.95 42.53 3.67
966 1058 2.147150 GCTTGGTTCAGTGGAGTTCTC 58.853 52.381 0.00 0.00 0.00 2.87
967 1059 2.408050 CTTGGTTCAGTGGAGTTCTCG 58.592 52.381 0.00 0.00 0.00 4.04
979 1071 2.416162 GGAGTTCTCGCTCTGACGATTT 60.416 50.000 0.00 0.00 42.02 2.17
1012 1110 1.515954 TCCGAAATGGAGAGCGACC 59.484 57.895 0.00 0.00 43.74 4.79
1449 1569 3.598668 GTCGTCGATCATTACAGATACGC 59.401 47.826 0.00 0.00 32.70 4.42
1575 1704 1.444553 CGAGGTGGACGACAAGAGC 60.445 63.158 0.00 0.00 0.00 4.09
1594 1723 0.307453 CAACAACGTTAGCAGCTGCA 59.693 50.000 38.24 22.31 45.16 4.41
1672 1804 1.108776 GGGCTGGTACGAGTATGACA 58.891 55.000 6.75 0.00 0.00 3.58
1701 1833 0.744414 CGTATGGGGTTGACCTGCAG 60.744 60.000 6.78 6.78 40.03 4.41
1781 1913 1.081242 CAGTGGCATGAACCAACGC 60.081 57.895 0.00 0.00 42.70 4.84
1789 1921 2.723209 CATGAACCAACGCTGCATATG 58.277 47.619 0.00 0.00 0.00 1.78
1812 1966 4.598062 CATACATCTGTGTACGTCGATGT 58.402 43.478 15.78 15.78 45.82 3.06
1824 1984 0.110056 GTCGATGTTGTTGCTGGCTG 60.110 55.000 0.00 0.00 0.00 4.85
1909 2075 2.171840 CAGATAGGTAGGGATCCCACG 58.828 57.143 32.69 10.55 38.92 4.94
2002 2176 1.482182 CTCTGGGATTCATGTCCGTGA 59.518 52.381 0.00 0.00 39.26 4.35
2044 2222 2.257371 GCGTGTCTGGCGACTGTA 59.743 61.111 10.03 0.00 40.86 2.74
2049 2227 0.240145 TGTCTGGCGACTGTAACTCG 59.760 55.000 10.03 0.00 40.86 4.18
2090 2268 3.228878 CGCCGACGAAAAATATACACC 57.771 47.619 0.00 0.00 43.93 4.16
2093 2271 3.242511 GCCGACGAAAAATATACACCCAC 60.243 47.826 0.00 0.00 0.00 4.61
2094 2272 4.186159 CCGACGAAAAATATACACCCACT 58.814 43.478 0.00 0.00 0.00 4.00
2095 2273 4.033587 CCGACGAAAAATATACACCCACTG 59.966 45.833 0.00 0.00 0.00 3.66
2102 2280 4.783560 AATATACACCCACTGGTTACCC 57.216 45.455 0.00 0.00 44.75 3.69
2114 2292 3.446516 ACTGGTTACCCATAGAGAACGTC 59.553 47.826 0.00 0.00 40.90 4.34
2128 2306 1.940613 GAACGTCTTTCACCAGTTGCT 59.059 47.619 0.00 0.00 33.94 3.91
2129 2307 1.299541 ACGTCTTTCACCAGTTGCTG 58.700 50.000 0.00 0.00 0.00 4.41
2130 2308 1.299541 CGTCTTTCACCAGTTGCTGT 58.700 50.000 0.00 0.00 0.00 4.40
2131 2309 1.003545 CGTCTTTCACCAGTTGCTGTG 60.004 52.381 0.00 0.00 0.00 3.66
2132 2310 2.017049 GTCTTTCACCAGTTGCTGTGT 58.983 47.619 0.00 0.00 0.00 3.72
2163 2381 2.159156 CGTGCTATTACTGTGGCCTGTA 60.159 50.000 3.32 1.75 0.00 2.74
2276 2495 1.312815 GTCTGTTGCTGCTTTGGACT 58.687 50.000 0.00 0.00 0.00 3.85
2343 2562 1.544759 GGGGCCAAAGACGAGAAAGAA 60.545 52.381 4.39 0.00 0.00 2.52
2357 2576 1.336755 GAAAGAAGCAGCGGGAAAACA 59.663 47.619 0.00 0.00 0.00 2.83
2408 2627 1.223417 GGACGGTTCGGCGAGAAAAA 61.223 55.000 10.46 0.00 41.10 1.94
2467 2695 2.295349 GTGGAAACGACTCACTCACCTA 59.705 50.000 0.00 0.00 0.00 3.08
2518 2746 2.794910 GAGCGCGCAGATGTTCTAATTA 59.205 45.455 35.10 0.00 0.00 1.40
2519 2747 3.393800 AGCGCGCAGATGTTCTAATTAT 58.606 40.909 35.10 2.61 0.00 1.28
2566 2804 6.272792 TGGTTATTTCTTTACTCCTGGGTGTA 59.727 38.462 0.00 0.00 0.00 2.90
2567 2805 7.170277 GGTTATTTCTTTACTCCTGGGTGTAA 58.830 38.462 9.39 9.39 33.88 2.41
2596 2834 4.513692 CACCTCGTGGACAGTAAATTTGAA 59.486 41.667 11.17 0.00 37.04 2.69
2643 2894 9.769093 ACATCAATATACTCAAACGTTTTAAGC 57.231 29.630 11.66 0.00 0.00 3.09
2663 2914 3.071479 GCGATTTGAGGAGGTTTACACA 58.929 45.455 0.00 0.00 0.00 3.72
2669 2920 5.828299 TTGAGGAGGTTTACACACAAAAG 57.172 39.130 0.00 0.00 0.00 2.27
2672 2923 6.126409 TGAGGAGGTTTACACACAAAAGAAT 58.874 36.000 0.00 0.00 0.00 2.40
2683 2934 4.736793 CACACAAAAGAATTCACTGCTCAC 59.263 41.667 8.44 0.00 0.00 3.51
2736 2987 9.173021 TGTGTATAATCACCTAGAAACATTTGG 57.827 33.333 0.00 0.00 37.51 3.28
2744 2995 4.956075 ACCTAGAAACATTTGGGCCTATTG 59.044 41.667 4.53 6.71 0.00 1.90
2745 2996 4.956075 CCTAGAAACATTTGGGCCTATTGT 59.044 41.667 4.53 7.43 0.00 2.71
2747 2998 5.151297 AGAAACATTTGGGCCTATTGTTG 57.849 39.130 22.53 8.04 31.34 3.33
2748 2999 4.837860 AGAAACATTTGGGCCTATTGTTGA 59.162 37.500 22.53 0.00 31.34 3.18
2749 3000 4.535526 AACATTTGGGCCTATTGTTGAC 57.464 40.909 21.62 0.00 0.00 3.18
2750 3001 3.505386 ACATTTGGGCCTATTGTTGACA 58.495 40.909 4.53 0.00 0.00 3.58
2753 3004 5.163258 ACATTTGGGCCTATTGTTGACAAAA 60.163 36.000 4.53 0.00 39.55 2.44
2754 3005 5.359194 TTTGGGCCTATTGTTGACAAAAA 57.641 34.783 4.53 0.00 39.55 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.053424 GGAGTACAAGGTGGACCACA 58.947 55.000 25.75 1.93 38.89 4.17
2 3 1.053424 TGGAGTACAAGGTGGACCAC 58.947 55.000 16.86 16.86 38.89 4.16
3 4 2.038863 ATGGAGTACAAGGTGGACCA 57.961 50.000 0.00 0.00 38.89 4.02
4 5 6.349944 CGTATATATGGAGTACAAGGTGGACC 60.350 46.154 0.00 0.00 29.22 4.46
5 6 6.208204 ACGTATATATGGAGTACAAGGTGGAC 59.792 42.308 6.89 0.00 0.00 4.02
6 7 6.208007 CACGTATATATGGAGTACAAGGTGGA 59.792 42.308 6.89 0.00 0.00 4.02
7 8 6.387465 CACGTATATATGGAGTACAAGGTGG 58.613 44.000 6.89 0.00 0.00 4.61
8 9 5.862323 GCACGTATATATGGAGTACAAGGTG 59.138 44.000 6.89 0.00 0.00 4.00
9 10 5.335426 CGCACGTATATATGGAGTACAAGGT 60.335 44.000 6.89 0.00 0.00 3.50
10 11 5.093457 CGCACGTATATATGGAGTACAAGG 58.907 45.833 6.89 0.00 0.00 3.61
11 12 4.557690 GCGCACGTATATATGGAGTACAAG 59.442 45.833 0.30 0.00 0.00 3.16
12 13 4.216902 AGCGCACGTATATATGGAGTACAA 59.783 41.667 11.47 0.00 0.00 2.41
13 14 3.754850 AGCGCACGTATATATGGAGTACA 59.245 43.478 11.47 0.00 0.00 2.90
14 15 4.352600 AGCGCACGTATATATGGAGTAC 57.647 45.455 11.47 0.00 0.00 2.73
15 16 5.505159 GCATAGCGCACGTATATATGGAGTA 60.505 44.000 11.47 0.00 41.79 2.59
16 17 4.733815 GCATAGCGCACGTATATATGGAGT 60.734 45.833 11.47 0.00 41.79 3.85
17 18 3.731216 GCATAGCGCACGTATATATGGAG 59.269 47.826 11.47 0.43 41.79 3.86
18 19 3.702330 GCATAGCGCACGTATATATGGA 58.298 45.455 11.47 0.00 41.79 3.41
31 32 1.126846 GTATTGATCGGTGCATAGCGC 59.873 52.381 0.00 0.00 46.67 5.92
33 34 3.061295 CGATGTATTGATCGGTGCATAGC 59.939 47.826 0.00 0.00 41.29 2.97
34 35 4.830015 CGATGTATTGATCGGTGCATAG 57.170 45.455 0.00 0.00 41.29 2.23
43 44 4.665142 GCGATGCTTCACGATGTATTGATC 60.665 45.833 0.08 0.00 0.00 2.92
44 45 3.185188 GCGATGCTTCACGATGTATTGAT 59.815 43.478 0.08 0.00 0.00 2.57
45 46 2.539688 GCGATGCTTCACGATGTATTGA 59.460 45.455 0.08 0.00 0.00 2.57
46 47 2.348872 GGCGATGCTTCACGATGTATTG 60.349 50.000 0.08 0.00 0.00 1.90
47 48 1.867233 GGCGATGCTTCACGATGTATT 59.133 47.619 0.08 0.00 0.00 1.89
48 49 1.202521 TGGCGATGCTTCACGATGTAT 60.203 47.619 0.08 0.00 0.00 2.29
49 50 0.174617 TGGCGATGCTTCACGATGTA 59.825 50.000 0.08 0.00 0.00 2.29
50 51 0.673333 TTGGCGATGCTTCACGATGT 60.673 50.000 0.08 0.00 0.00 3.06
51 52 0.447406 TTTGGCGATGCTTCACGATG 59.553 50.000 0.08 0.00 0.00 3.84
52 53 1.135689 GTTTTGGCGATGCTTCACGAT 60.136 47.619 0.08 0.00 0.00 3.73
53 54 0.237235 GTTTTGGCGATGCTTCACGA 59.763 50.000 0.08 0.00 0.00 4.35
54 55 0.040514 TGTTTTGGCGATGCTTCACG 60.041 50.000 0.08 0.00 0.00 4.35
55 56 2.352503 ATGTTTTGGCGATGCTTCAC 57.647 45.000 0.08 0.00 0.00 3.18
56 57 2.668001 CGAATGTTTTGGCGATGCTTCA 60.668 45.455 0.08 0.00 0.00 3.02
57 58 1.913403 CGAATGTTTTGGCGATGCTTC 59.087 47.619 0.00 0.00 0.00 3.86
58 59 1.269448 ACGAATGTTTTGGCGATGCTT 59.731 42.857 0.00 0.00 0.00 3.91
59 60 0.881118 ACGAATGTTTTGGCGATGCT 59.119 45.000 0.00 0.00 0.00 3.79
60 61 1.696988 AACGAATGTTTTGGCGATGC 58.303 45.000 0.00 0.00 33.53 3.91
78 79 2.151202 GGCGAATGAGTCTGTTGGAAA 58.849 47.619 0.00 0.00 0.00 3.13
79 80 1.071542 TGGCGAATGAGTCTGTTGGAA 59.928 47.619 0.00 0.00 0.00 3.53
80 81 0.684535 TGGCGAATGAGTCTGTTGGA 59.315 50.000 0.00 0.00 0.00 3.53
81 82 1.081892 CTGGCGAATGAGTCTGTTGG 58.918 55.000 0.00 0.00 0.00 3.77
82 83 0.445436 GCTGGCGAATGAGTCTGTTG 59.555 55.000 0.00 0.00 0.00 3.33
83 84 0.322975 AGCTGGCGAATGAGTCTGTT 59.677 50.000 0.00 0.00 0.00 3.16
84 85 0.322975 AAGCTGGCGAATGAGTCTGT 59.677 50.000 0.00 0.00 0.00 3.41
85 86 0.725686 CAAGCTGGCGAATGAGTCTG 59.274 55.000 0.00 0.00 0.00 3.51
86 87 1.023513 GCAAGCTGGCGAATGAGTCT 61.024 55.000 0.00 0.00 0.00 3.24
87 88 1.023513 AGCAAGCTGGCGAATGAGTC 61.024 55.000 7.63 0.00 39.27 3.36
88 89 1.002868 AGCAAGCTGGCGAATGAGT 60.003 52.632 7.63 0.00 39.27 3.41
89 90 0.743701 AGAGCAAGCTGGCGAATGAG 60.744 55.000 7.63 0.00 39.27 2.90
90 91 0.321919 AAGAGCAAGCTGGCGAATGA 60.322 50.000 7.63 0.00 39.27 2.57
91 92 0.524862 AAAGAGCAAGCTGGCGAATG 59.475 50.000 7.63 0.00 39.27 2.67
92 93 0.524862 CAAAGAGCAAGCTGGCGAAT 59.475 50.000 7.63 0.00 39.27 3.34
93 94 1.951510 CAAAGAGCAAGCTGGCGAA 59.048 52.632 7.63 0.00 39.27 4.70
94 95 2.620112 GCAAAGAGCAAGCTGGCGA 61.620 57.895 7.63 0.00 44.79 5.54
95 96 2.126580 GCAAAGAGCAAGCTGGCG 60.127 61.111 7.63 0.00 44.79 5.69
104 105 4.387256 CCGCTTATATAGAGTGCAAAGAGC 59.613 45.833 0.00 0.00 45.96 4.09
105 106 5.773575 TCCGCTTATATAGAGTGCAAAGAG 58.226 41.667 0.00 0.00 0.00 2.85
106 107 5.784578 TCCGCTTATATAGAGTGCAAAGA 57.215 39.130 0.00 0.00 0.00 2.52
107 108 8.534333 TTAATCCGCTTATATAGAGTGCAAAG 57.466 34.615 0.00 0.00 0.00 2.77
109 110 9.803315 CTATTAATCCGCTTATATAGAGTGCAA 57.197 33.333 0.00 0.00 0.00 4.08
110 111 8.967918 ACTATTAATCCGCTTATATAGAGTGCA 58.032 33.333 0.00 0.00 0.00 4.57
111 112 9.453325 GACTATTAATCCGCTTATATAGAGTGC 57.547 37.037 0.00 0.00 0.00 4.40
112 113 9.953697 GGACTATTAATCCGCTTATATAGAGTG 57.046 37.037 0.00 0.00 0.00 3.51
113 114 9.696572 TGGACTATTAATCCGCTTATATAGAGT 57.303 33.333 0.00 0.00 39.30 3.24
118 119 8.594550 ACAGTTGGACTATTAATCCGCTTATAT 58.405 33.333 0.00 0.00 39.30 0.86
119 120 7.959175 ACAGTTGGACTATTAATCCGCTTATA 58.041 34.615 0.00 0.00 39.30 0.98
120 121 6.827727 ACAGTTGGACTATTAATCCGCTTAT 58.172 36.000 0.00 0.00 39.30 1.73
121 122 6.229936 ACAGTTGGACTATTAATCCGCTTA 57.770 37.500 0.00 0.00 39.30 3.09
122 123 5.099042 ACAGTTGGACTATTAATCCGCTT 57.901 39.130 0.00 0.00 39.30 4.68
123 124 4.443034 GGACAGTTGGACTATTAATCCGCT 60.443 45.833 0.00 0.00 39.30 5.52
124 125 3.808174 GGACAGTTGGACTATTAATCCGC 59.192 47.826 0.00 0.00 39.30 5.54
125 126 5.018539 TGGACAGTTGGACTATTAATCCG 57.981 43.478 0.00 0.00 39.30 4.18
126 127 6.316390 CAGTTGGACAGTTGGACTATTAATCC 59.684 42.308 0.00 0.00 36.70 3.01
127 128 7.103641 TCAGTTGGACAGTTGGACTATTAATC 58.896 38.462 0.00 0.00 0.00 1.75
128 129 7.016153 TCAGTTGGACAGTTGGACTATTAAT 57.984 36.000 0.00 0.00 0.00 1.40
129 130 6.428083 TCAGTTGGACAGTTGGACTATTAA 57.572 37.500 0.00 0.00 0.00 1.40
130 131 6.406370 CATCAGTTGGACAGTTGGACTATTA 58.594 40.000 0.00 0.00 0.00 0.98
131 132 4.974645 TCAGTTGGACAGTTGGACTATT 57.025 40.909 0.00 0.00 0.00 1.73
132 133 4.836825 CATCAGTTGGACAGTTGGACTAT 58.163 43.478 0.00 0.00 0.00 2.12
133 134 4.271696 CATCAGTTGGACAGTTGGACTA 57.728 45.455 0.00 0.00 0.00 2.59
134 135 3.131709 CATCAGTTGGACAGTTGGACT 57.868 47.619 0.00 0.00 0.00 3.85
146 147 5.237815 TGCTTAACACTAGTCCATCAGTTG 58.762 41.667 0.00 0.00 0.00 3.16
147 148 5.483685 TGCTTAACACTAGTCCATCAGTT 57.516 39.130 0.00 0.00 0.00 3.16
148 149 5.238583 GTTGCTTAACACTAGTCCATCAGT 58.761 41.667 0.00 0.00 0.00 3.41
149 150 4.631813 GGTTGCTTAACACTAGTCCATCAG 59.368 45.833 0.00 0.00 0.00 2.90
150 151 4.564821 GGGTTGCTTAACACTAGTCCATCA 60.565 45.833 0.00 0.00 0.00 3.07
151 152 3.939592 GGGTTGCTTAACACTAGTCCATC 59.060 47.826 0.00 0.00 0.00 3.51
152 153 3.587506 AGGGTTGCTTAACACTAGTCCAT 59.412 43.478 0.00 0.00 34.01 3.41
153 154 2.976882 AGGGTTGCTTAACACTAGTCCA 59.023 45.455 0.00 0.00 34.01 4.02
154 155 3.697619 AGGGTTGCTTAACACTAGTCC 57.302 47.619 0.00 0.00 34.01 3.85
155 156 8.636213 TGTATATAGGGTTGCTTAACACTAGTC 58.364 37.037 8.00 0.90 41.48 2.59
156 157 8.543293 TGTATATAGGGTTGCTTAACACTAGT 57.457 34.615 8.00 0.00 41.48 2.57
157 158 8.857098 TCTGTATATAGGGTTGCTTAACACTAG 58.143 37.037 8.00 0.00 41.48 2.57
158 159 8.771521 TCTGTATATAGGGTTGCTTAACACTA 57.228 34.615 4.78 4.78 42.29 2.74
159 160 7.670605 TCTGTATATAGGGTTGCTTAACACT 57.329 36.000 0.27 0.27 40.10 3.55
160 161 9.991906 TTATCTGTATATAGGGTTGCTTAACAC 57.008 33.333 0.00 0.00 0.00 3.32
165 166 9.561069 CAGTTTTATCTGTATATAGGGTTGCTT 57.439 33.333 0.00 0.00 0.00 3.91
166 167 8.157476 CCAGTTTTATCTGTATATAGGGTTGCT 58.843 37.037 0.00 0.00 34.02 3.91
167 168 8.154856 TCCAGTTTTATCTGTATATAGGGTTGC 58.845 37.037 0.00 0.00 34.02 4.17
174 175 9.865321 GGCGTTATCCAGTTTTATCTGTATATA 57.135 33.333 0.00 0.00 34.02 0.86
175 176 8.372459 TGGCGTTATCCAGTTTTATCTGTATAT 58.628 33.333 0.00 0.00 34.02 0.86
176 177 7.654520 GTGGCGTTATCCAGTTTTATCTGTATA 59.345 37.037 0.00 0.00 36.67 1.47
177 178 6.482308 GTGGCGTTATCCAGTTTTATCTGTAT 59.518 38.462 0.00 0.00 36.67 2.29
178 179 5.813672 GTGGCGTTATCCAGTTTTATCTGTA 59.186 40.000 0.00 0.00 36.67 2.74
179 180 4.634443 GTGGCGTTATCCAGTTTTATCTGT 59.366 41.667 0.00 0.00 36.67 3.41
180 181 4.634004 TGTGGCGTTATCCAGTTTTATCTG 59.366 41.667 0.00 0.00 36.67 2.90
181 182 4.839121 TGTGGCGTTATCCAGTTTTATCT 58.161 39.130 0.00 0.00 36.67 1.98
182 183 5.554822 TTGTGGCGTTATCCAGTTTTATC 57.445 39.130 0.00 0.00 36.67 1.75
183 184 5.336134 GGTTTGTGGCGTTATCCAGTTTTAT 60.336 40.000 0.00 0.00 36.67 1.40
184 185 4.023021 GGTTTGTGGCGTTATCCAGTTTTA 60.023 41.667 0.00 0.00 36.67 1.52
185 186 3.243602 GGTTTGTGGCGTTATCCAGTTTT 60.244 43.478 0.00 0.00 36.67 2.43
186 187 2.295070 GGTTTGTGGCGTTATCCAGTTT 59.705 45.455 0.00 0.00 36.67 2.66
187 188 1.883926 GGTTTGTGGCGTTATCCAGTT 59.116 47.619 0.00 0.00 36.67 3.16
188 189 1.530323 GGTTTGTGGCGTTATCCAGT 58.470 50.000 0.00 0.00 36.67 4.00
189 190 0.808755 GGGTTTGTGGCGTTATCCAG 59.191 55.000 0.00 0.00 36.67 3.86
190 191 0.110678 TGGGTTTGTGGCGTTATCCA 59.889 50.000 0.00 0.00 0.00 3.41
191 192 1.201414 CTTGGGTTTGTGGCGTTATCC 59.799 52.381 0.00 0.00 0.00 2.59
192 193 2.095415 GTCTTGGGTTTGTGGCGTTATC 60.095 50.000 0.00 0.00 0.00 1.75
193 194 1.883926 GTCTTGGGTTTGTGGCGTTAT 59.116 47.619 0.00 0.00 0.00 1.89
194 195 1.310904 GTCTTGGGTTTGTGGCGTTA 58.689 50.000 0.00 0.00 0.00 3.18
195 196 1.388837 GGTCTTGGGTTTGTGGCGTT 61.389 55.000 0.00 0.00 0.00 4.84
196 197 1.826487 GGTCTTGGGTTTGTGGCGT 60.826 57.895 0.00 0.00 0.00 5.68
197 198 1.515521 GAGGTCTTGGGTTTGTGGCG 61.516 60.000 0.00 0.00 0.00 5.69
198 199 1.515521 CGAGGTCTTGGGTTTGTGGC 61.516 60.000 0.00 0.00 0.00 5.01
199 200 0.179029 ACGAGGTCTTGGGTTTGTGG 60.179 55.000 0.00 0.00 0.00 4.17
200 201 1.333619 CAACGAGGTCTTGGGTTTGTG 59.666 52.381 0.00 0.00 0.00 3.33
201 202 1.675552 CAACGAGGTCTTGGGTTTGT 58.324 50.000 0.00 0.00 0.00 2.83
202 203 0.310854 GCAACGAGGTCTTGGGTTTG 59.689 55.000 0.00 0.00 0.00 2.93
203 204 0.822121 GGCAACGAGGTCTTGGGTTT 60.822 55.000 0.00 0.00 0.00 3.27
204 205 1.228154 GGCAACGAGGTCTTGGGTT 60.228 57.895 0.00 0.00 0.00 4.11
205 206 2.113243 GAGGCAACGAGGTCTTGGGT 62.113 60.000 0.00 0.00 46.39 4.51
206 207 1.376037 GAGGCAACGAGGTCTTGGG 60.376 63.158 0.00 0.00 46.39 4.12
207 208 0.036010 ATGAGGCAACGAGGTCTTGG 60.036 55.000 0.00 0.00 46.39 3.61
208 209 1.466167 CAATGAGGCAACGAGGTCTTG 59.534 52.381 0.00 0.00 46.39 3.02
209 210 1.611673 CCAATGAGGCAACGAGGTCTT 60.612 52.381 0.00 0.00 46.39 3.01
210 211 0.036010 CCAATGAGGCAACGAGGTCT 60.036 55.000 0.00 0.00 46.39 3.85
211 212 2.471255 CCAATGAGGCAACGAGGTC 58.529 57.895 0.00 0.00 46.39 3.85
212 213 4.722193 CCAATGAGGCAACGAGGT 57.278 55.556 0.00 0.00 46.39 3.85
221 222 0.465097 ATTCGCTCCTGCCAATGAGG 60.465 55.000 0.00 0.00 41.84 3.86
222 223 0.942962 GATTCGCTCCTGCCAATGAG 59.057 55.000 0.00 0.00 30.42 2.90
223 224 0.252761 TGATTCGCTCCTGCCAATGA 59.747 50.000 0.00 0.00 30.42 2.57
224 225 0.379669 GTGATTCGCTCCTGCCAATG 59.620 55.000 0.00 0.00 30.42 2.82
225 226 0.035152 TGTGATTCGCTCCTGCCAAT 60.035 50.000 0.00 0.00 32.86 3.16
226 227 0.250684 TTGTGATTCGCTCCTGCCAA 60.251 50.000 0.00 0.00 35.36 4.52
227 228 0.250684 TTTGTGATTCGCTCCTGCCA 60.251 50.000 0.00 0.00 35.36 4.92
228 229 0.169009 GTTTGTGATTCGCTCCTGCC 59.831 55.000 0.00 0.00 35.36 4.85
229 230 0.874390 TGTTTGTGATTCGCTCCTGC 59.126 50.000 0.00 0.00 0.00 4.85
230 231 1.466167 CCTGTTTGTGATTCGCTCCTG 59.534 52.381 0.00 0.00 0.00 3.86
231 232 1.072331 ACCTGTTTGTGATTCGCTCCT 59.928 47.619 0.00 0.00 0.00 3.69
232 233 1.523758 ACCTGTTTGTGATTCGCTCC 58.476 50.000 0.00 0.00 0.00 4.70
233 234 3.496884 TGTAACCTGTTTGTGATTCGCTC 59.503 43.478 0.00 0.00 0.00 5.03
234 235 3.472652 TGTAACCTGTTTGTGATTCGCT 58.527 40.909 0.00 0.00 0.00 4.93
235 236 3.889196 TGTAACCTGTTTGTGATTCGC 57.111 42.857 0.00 0.00 0.00 4.70
236 237 5.574082 TGTTTGTAACCTGTTTGTGATTCG 58.426 37.500 0.00 0.00 0.00 3.34
237 238 6.809196 TGTTGTTTGTAACCTGTTTGTGATTC 59.191 34.615 0.00 0.00 0.00 2.52
238 239 6.588373 GTGTTGTTTGTAACCTGTTTGTGATT 59.412 34.615 0.00 0.00 0.00 2.57
239 240 6.096695 GTGTTGTTTGTAACCTGTTTGTGAT 58.903 36.000 0.00 0.00 0.00 3.06
240 241 5.009710 TGTGTTGTTTGTAACCTGTTTGTGA 59.990 36.000 0.00 0.00 0.00 3.58
241 242 5.117897 GTGTGTTGTTTGTAACCTGTTTGTG 59.882 40.000 0.00 0.00 0.00 3.33
242 243 5.224135 GTGTGTTGTTTGTAACCTGTTTGT 58.776 37.500 0.00 0.00 0.00 2.83
243 244 4.322274 CGTGTGTTGTTTGTAACCTGTTTG 59.678 41.667 0.00 0.00 0.00 2.93
244 245 4.215827 TCGTGTGTTGTTTGTAACCTGTTT 59.784 37.500 0.00 0.00 0.00 2.83
245 246 3.752222 TCGTGTGTTGTTTGTAACCTGTT 59.248 39.130 0.00 0.00 0.00 3.16
246 247 3.336468 TCGTGTGTTGTTTGTAACCTGT 58.664 40.909 0.00 0.00 0.00 4.00
247 248 4.545823 ATCGTGTGTTGTTTGTAACCTG 57.454 40.909 0.00 0.00 0.00 4.00
248 249 5.570234 AAATCGTGTGTTGTTTGTAACCT 57.430 34.783 0.00 0.00 0.00 3.50
249 250 6.635166 AAAAATCGTGTGTTGTTTGTAACC 57.365 33.333 0.00 0.00 0.00 2.85
329 353 1.509162 GTTCGATTGGCGTTGCGTC 60.509 57.895 0.00 0.00 41.80 5.19
333 363 0.443869 CTCCAGTTCGATTGGCGTTG 59.556 55.000 10.75 0.15 41.80 4.10
363 393 6.798482 TGGATCGTCGTTAAAGCTAGATTAA 58.202 36.000 0.00 0.00 0.00 1.40
366 396 4.913335 TGGATCGTCGTTAAAGCTAGAT 57.087 40.909 0.00 0.00 0.00 1.98
377 407 1.538512 TCTTCGTCTTTGGATCGTCGT 59.461 47.619 0.00 0.00 0.00 4.34
378 408 2.159558 TCTCTTCGTCTTTGGATCGTCG 60.160 50.000 0.00 0.00 0.00 5.12
379 409 3.489180 TCTCTTCGTCTTTGGATCGTC 57.511 47.619 0.00 0.00 0.00 4.20
389 419 3.131933 CCATGGACATCTTCTCTTCGTCT 59.868 47.826 5.56 0.00 0.00 4.18
404 434 3.044894 AGGAGAGGAGAATTCCATGGAC 58.955 50.000 15.91 2.84 46.64 4.02
429 459 2.103934 CGGCTCGGCAGAAGAGAG 59.896 66.667 0.00 0.00 37.93 3.20
498 528 2.680913 CCCGTTTTCTCGCTGGCTG 61.681 63.158 0.00 0.00 0.00 4.85
522 552 2.203280 TTGTCACGTTGCCTGGGG 60.203 61.111 0.00 0.00 0.00 4.96
526 556 2.186826 GTGGCTTGTCACGTTGCCT 61.187 57.895 12.35 0.00 45.11 4.75
527 557 2.331451 GTGGCTTGTCACGTTGCC 59.669 61.111 0.00 0.00 45.10 4.52
528 558 2.117941 GAGGTGGCTTGTCACGTTGC 62.118 60.000 2.14 0.00 38.46 4.17
529 559 1.831389 CGAGGTGGCTTGTCACGTTG 61.831 60.000 2.14 1.89 38.46 4.10
530 560 1.594293 CGAGGTGGCTTGTCACGTT 60.594 57.895 2.14 0.00 38.46 3.99
531 561 2.029073 CGAGGTGGCTTGTCACGT 59.971 61.111 0.00 0.00 38.46 4.49
532 562 2.738521 CCGAGGTGGCTTGTCACG 60.739 66.667 0.00 0.00 38.46 4.35
622 666 2.740826 AACGATGCCACGGTTCCG 60.741 61.111 9.81 9.81 37.61 4.30
623 667 1.231958 TTCAACGATGCCACGGTTCC 61.232 55.000 0.00 0.00 37.61 3.62
714 792 1.227089 CGAGATCGACTTGGGCCTG 60.227 63.158 4.53 0.00 43.02 4.85
778 864 3.467119 CGTACAGGTGTCGCGCAC 61.467 66.667 20.56 20.56 46.97 5.34
927 1019 4.610714 TTGGTAGCGCGTGCACCA 62.611 61.111 29.15 29.15 44.80 4.17
928 1020 3.308878 CTTTGGTAGCGCGTGCACC 62.309 63.158 24.79 25.42 46.23 5.01
929 1021 2.173382 CTTTGGTAGCGCGTGCAC 59.827 61.111 24.79 17.92 46.23 4.57
930 1022 3.722295 GCTTTGGTAGCGCGTGCA 61.722 61.111 24.79 6.35 46.23 4.57
942 1034 2.301346 ACTCCACTGAACCAAGCTTTG 58.699 47.619 0.00 0.00 0.00 2.77
943 1035 2.736670 ACTCCACTGAACCAAGCTTT 57.263 45.000 0.00 0.00 0.00 3.51
944 1036 2.173569 AGAACTCCACTGAACCAAGCTT 59.826 45.455 0.00 0.00 0.00 3.74
966 1058 1.781429 CGGTATCAAATCGTCAGAGCG 59.219 52.381 0.00 0.00 0.00 5.03
967 1059 1.523095 GCGGTATCAAATCGTCAGAGC 59.477 52.381 0.00 0.00 0.00 4.09
1071 1169 1.924320 GCTGCTGCTGCTGAAGGAAG 61.924 60.000 23.39 9.16 40.01 3.46
1110 1214 4.436998 AACCGCCGCTTCCTCTCG 62.437 66.667 0.00 0.00 0.00 4.04
1457 1577 0.815213 ACGACGCCATTAGCATGCAT 60.815 50.000 21.98 7.68 44.04 3.96
1471 1591 2.500442 GCACATCGAGCAGACGACG 61.500 63.158 0.00 0.00 44.84 5.12
1560 1689 0.531974 TGTTGCTCTTGTCGTCCACC 60.532 55.000 0.00 0.00 0.00 4.61
1575 1704 0.307453 TGCAGCTGCTAACGTTGTTG 59.693 50.000 36.61 3.38 42.66 3.33
1594 1723 0.387202 CTCTCATCCTTCGCCACGAT 59.613 55.000 0.00 0.00 35.23 3.73
1672 1804 2.674754 CCCATACGCCAGGTGGTT 59.325 61.111 4.64 0.00 37.57 3.67
1781 1913 5.164022 CGTACACAGATGTATGCATATGCAG 60.164 44.000 32.10 20.06 46.66 4.41
1812 1966 0.606401 GCTAGACCAGCCAGCAACAA 60.606 55.000 0.00 0.00 45.23 2.83
1824 1984 0.105039 CCGGATCAACCAGCTAGACC 59.895 60.000 0.00 0.00 38.90 3.85
1909 2075 1.203994 AGATTTCATGGCTGCTTGCAC 59.796 47.619 0.00 0.00 45.15 4.57
1964 2130 3.889044 TCGACGGAGCAGATCGCC 61.889 66.667 0.00 0.00 44.04 5.54
1965 2131 2.652496 GTCGACGGAGCAGATCGC 60.652 66.667 0.00 1.92 42.91 4.58
1966 2132 1.010574 GAGTCGACGGAGCAGATCG 60.011 63.158 10.46 0.00 37.20 3.69
2002 2176 4.165779 CGCGTGATTCTTAAGCCATTTTT 58.834 39.130 0.00 0.00 0.00 1.94
2039 2217 2.037144 AGGAACCACACGAGTTACAGT 58.963 47.619 0.00 0.00 29.85 3.55
2044 2222 0.249322 CGACAGGAACCACACGAGTT 60.249 55.000 0.00 0.00 0.00 3.01
2049 2227 3.712881 GCGCGACAGGAACCACAC 61.713 66.667 12.10 0.00 0.00 3.82
2095 2273 5.107824 GAAAGACGTTCTCTATGGGTAACC 58.892 45.833 0.00 0.00 45.33 2.85
2102 2280 4.810790 ACTGGTGAAAGACGTTCTCTATG 58.189 43.478 2.80 0.00 37.13 2.23
2114 2292 2.684881 AGAACACAGCAACTGGTGAAAG 59.315 45.455 15.40 7.38 45.66 2.62
2343 2562 3.030652 CGTTGTTTTCCCGCTGCT 58.969 55.556 0.00 0.00 0.00 4.24
2408 2627 1.237285 GCCACGCATCCACAACTTCT 61.237 55.000 0.00 0.00 0.00 2.85
2445 2673 1.068741 GGTGAGTGAGTCGTTTCCACT 59.931 52.381 0.00 0.00 43.11 4.00
2492 2720 3.260483 CATCTGCGCGCTCCTCAC 61.260 66.667 33.29 0.86 0.00 3.51
2497 2725 1.212616 ATTAGAACATCTGCGCGCTC 58.787 50.000 33.29 19.96 0.00 5.03
2544 2782 7.170277 GGTTACACCCAGGAGTAAAGAAATAA 58.830 38.462 8.09 0.00 34.15 1.40
2545 2783 6.272792 TGGTTACACCCAGGAGTAAAGAAATA 59.727 38.462 8.09 0.00 37.50 1.40
2546 2784 5.073965 TGGTTACACCCAGGAGTAAAGAAAT 59.926 40.000 8.09 0.00 37.50 2.17
2549 2787 3.325716 GTGGTTACACCCAGGAGTAAAGA 59.674 47.826 8.09 0.00 41.84 2.52
2550 2788 3.671716 GTGGTTACACCCAGGAGTAAAG 58.328 50.000 8.09 0.00 41.84 1.85
2574 2812 4.345859 TCAAATTTACTGTCCACGAGGT 57.654 40.909 0.00 0.00 35.89 3.85
2611 2856 8.317891 ACGTTTGAGTATATTGATGTCACAAA 57.682 30.769 0.00 0.00 33.44 2.83
2625 2870 7.577979 TCAAATCGCTTAAAACGTTTGAGTAT 58.422 30.769 15.46 10.46 36.54 2.12
2626 2871 6.946165 TCAAATCGCTTAAAACGTTTGAGTA 58.054 32.000 15.46 8.80 36.54 2.59
2628 2873 5.339611 CCTCAAATCGCTTAAAACGTTTGAG 59.660 40.000 25.13 25.13 45.39 3.02
2630 2875 5.209240 TCCTCAAATCGCTTAAAACGTTTG 58.791 37.500 15.46 3.22 35.17 2.93
2641 2892 3.244422 TGTGTAAACCTCCTCAAATCGCT 60.244 43.478 0.00 0.00 0.00 4.93
2643 2894 4.062293 TGTGTGTAAACCTCCTCAAATCG 58.938 43.478 0.00 0.00 0.00 3.34
2663 2914 5.179045 CTGTGAGCAGTGAATTCTTTTGT 57.821 39.130 7.05 0.00 37.92 2.83
2683 2934 9.472361 AGAGAAACAAAATGATGATGAAAACTG 57.528 29.630 0.00 0.00 0.00 3.16
2717 2968 3.769300 GGCCCAAATGTTTCTAGGTGATT 59.231 43.478 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.