Multiple sequence alignment - TraesCS3B01G237100

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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 TraesCS3B01G237100 chr3B 100.000 1867 0 0 1001 2867 371978729 371976863 0.000000e+00 3448.0
1 TraesCS3B01G237100 chr3B 100.000 611 0 0 1 611 371979729 371979119 0.000000e+00 1129.0
2 TraesCS3B01G237100 chr3A 94.673 1896 63 17 1001 2864 360518363 360516474 0.000000e+00 2907.0
3 TraesCS3B01G237100 chr3A 88.350 206 16 5 409 611 360518641 360518441 1.030000e-59 241.0
4 TraesCS3B01G237100 chr3D 94.549 1706 34 18 1001 2669 278801734 278803417 0.000000e+00 2580.0
5 TraesCS3B01G237100 chr3D 92.424 198 14 1 231 428 278801239 278801435 6.050000e-72 281.0
6 TraesCS3B01G237100 chr3D 87.444 223 17 1 1 223 278782932 278783143 2.210000e-61 246.0
7 TraesCS3B01G237100 chr3D 91.061 179 13 3 435 611 278801482 278801659 3.690000e-59 239.0
8 TraesCS3B01G237100 chr3D 94.268 157 7 2 2712 2867 278803401 278803556 3.690000e-59 239.0
9 TraesCS3B01G237100 chr3D 89.130 46 4 1 555 600 278801411 278801455 3.990000e-04 56.5


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 TraesCS3B01G237100 chr3B 371976863 371979729 2866 True 2288.5 3448 100.0000 1 2867 2 chr3B.!!$R1 2866
1 TraesCS3B01G237100 chr3A 360516474 360518641 2167 True 1574.0 2907 91.5115 409 2864 2 chr3A.!!$R1 2455
2 TraesCS3B01G237100 chr3D 278801239 278803556 2317 False 679.1 2580 92.2864 231 2867 5 chr3D.!!$F2 2636

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
498 539 0.034089 AAGGGGGAAATCCTCGCAAG 60.034 55.0 0.0 0.0 42.27 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2391 2479 0.457509 CACGCACAAAACCAACAGCA 60.458 50.0 0.0 0.0 0.0 4.41 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
22 23 5.956068 TTTCATCAACATGAATGTCCGAA 57.044 34.783 0.00 1.13 46.36 4.30
23 24 5.550232 TTCATCAACATGAATGTCCGAAG 57.450 39.130 0.00 0.00 42.99 3.79
24 25 3.940852 TCATCAACATGAATGTCCGAAGG 59.059 43.478 0.00 0.00 42.71 3.46
44 45 8.813643 CGAAGGATATAACCGAAAGATAAACT 57.186 34.615 0.00 0.00 34.73 2.66
45 46 8.913656 CGAAGGATATAACCGAAAGATAAACTC 58.086 37.037 0.00 0.00 34.73 3.01
46 47 9.760077 GAAGGATATAACCGAAAGATAAACTCA 57.240 33.333 0.00 0.00 34.73 3.41
48 49 9.930693 AGGATATAACCGAAAGATAAACTCATC 57.069 33.333 0.00 0.00 34.73 2.92
49 50 9.706691 GGATATAACCGAAAGATAAACTCATCA 57.293 33.333 0.00 0.00 0.00 3.07
51 52 5.779806 AACCGAAAGATAAACTCATCACG 57.220 39.130 0.00 0.00 0.00 4.35
52 53 5.068234 ACCGAAAGATAAACTCATCACGA 57.932 39.130 0.00 0.00 0.00 4.35
54 55 4.026475 CCGAAAGATAAACTCATCACGAGC 60.026 45.833 0.00 0.00 46.63 5.03
55 56 4.800993 CGAAAGATAAACTCATCACGAGCT 59.199 41.667 0.00 0.00 46.63 4.09
56 57 5.289675 CGAAAGATAAACTCATCACGAGCTT 59.710 40.000 0.00 0.00 46.63 3.74
57 58 6.414408 AAAGATAAACTCATCACGAGCTTG 57.586 37.500 0.00 0.00 46.63 4.01
58 59 5.078411 AGATAAACTCATCACGAGCTTGT 57.922 39.130 0.00 0.00 46.63 3.16
59 60 5.105752 AGATAAACTCATCACGAGCTTGTC 58.894 41.667 2.72 0.00 46.63 3.18
60 61 2.086054 AACTCATCACGAGCTTGTCC 57.914 50.000 2.72 0.00 46.63 4.02
61 62 1.261480 ACTCATCACGAGCTTGTCCT 58.739 50.000 2.72 0.00 46.63 3.85
62 63 1.620819 ACTCATCACGAGCTTGTCCTT 59.379 47.619 2.72 0.00 46.63 3.36
63 64 1.998315 CTCATCACGAGCTTGTCCTTG 59.002 52.381 2.72 2.49 34.18 3.61
64 65 1.081892 CATCACGAGCTTGTCCTTGG 58.918 55.000 2.72 0.00 0.00 3.61
65 66 0.674895 ATCACGAGCTTGTCCTTGGC 60.675 55.000 2.72 0.00 0.00 4.52
66 67 2.032681 ACGAGCTTGTCCTTGGCC 59.967 61.111 0.00 0.00 0.00 5.36
67 68 2.747855 CGAGCTTGTCCTTGGCCC 60.748 66.667 0.00 0.00 0.00 5.80
68 69 2.436109 GAGCTTGTCCTTGGCCCA 59.564 61.111 0.00 0.00 0.00 5.36
69 70 1.000396 GAGCTTGTCCTTGGCCCAT 60.000 57.895 0.00 0.00 0.00 4.00
70 71 1.304713 AGCTTGTCCTTGGCCCATG 60.305 57.895 0.00 0.00 0.00 3.66
71 72 1.304381 GCTTGTCCTTGGCCCATGA 60.304 57.895 0.00 0.00 0.00 3.07
72 73 0.899717 GCTTGTCCTTGGCCCATGAA 60.900 55.000 0.00 0.00 0.00 2.57
73 74 1.856629 CTTGTCCTTGGCCCATGAAT 58.143 50.000 0.00 0.00 0.00 2.57
74 75 2.181975 CTTGTCCTTGGCCCATGAATT 58.818 47.619 0.00 0.00 0.00 2.17
75 76 1.559368 TGTCCTTGGCCCATGAATTG 58.441 50.000 0.00 0.00 0.00 2.32
76 77 0.176449 GTCCTTGGCCCATGAATTGC 59.824 55.000 0.00 0.00 0.00 3.56
77 78 0.252148 TCCTTGGCCCATGAATTGCA 60.252 50.000 0.00 0.00 0.00 4.08
78 79 0.614294 CCTTGGCCCATGAATTGCAA 59.386 50.000 0.00 0.00 0.00 4.08
79 80 1.676615 CCTTGGCCCATGAATTGCAAC 60.677 52.381 0.00 0.00 0.00 4.17
80 81 0.324285 TTGGCCCATGAATTGCAACC 59.676 50.000 0.00 0.00 0.00 3.77
81 82 0.835115 TGGCCCATGAATTGCAACCA 60.835 50.000 0.00 3.17 0.00 3.67
82 83 0.542805 GGCCCATGAATTGCAACCAT 59.457 50.000 0.00 5.77 0.00 3.55
83 84 1.761784 GGCCCATGAATTGCAACCATA 59.238 47.619 13.74 0.00 0.00 2.74
84 85 2.224113 GGCCCATGAATTGCAACCATAG 60.224 50.000 13.74 8.40 0.00 2.23
85 86 2.694628 GCCCATGAATTGCAACCATAGA 59.305 45.455 13.74 0.00 0.00 1.98
86 87 3.491447 GCCCATGAATTGCAACCATAGAC 60.491 47.826 13.74 5.14 0.00 2.59
87 88 3.068590 CCCATGAATTGCAACCATAGACC 59.931 47.826 13.74 0.00 0.00 3.85
88 89 3.956199 CCATGAATTGCAACCATAGACCT 59.044 43.478 13.74 0.00 0.00 3.85
89 90 5.132502 CCATGAATTGCAACCATAGACCTA 58.867 41.667 13.74 0.00 0.00 3.08
90 91 5.240183 CCATGAATTGCAACCATAGACCTAG 59.760 44.000 13.74 3.17 0.00 3.02
91 92 4.199310 TGAATTGCAACCATAGACCTAGC 58.801 43.478 0.00 0.00 0.00 3.42
92 93 3.931907 ATTGCAACCATAGACCTAGCA 57.068 42.857 0.00 0.00 0.00 3.49
93 94 3.931907 TTGCAACCATAGACCTAGCAT 57.068 42.857 0.00 0.00 0.00 3.79
94 95 3.475566 TGCAACCATAGACCTAGCATC 57.524 47.619 0.00 0.00 0.00 3.91
95 96 2.771372 TGCAACCATAGACCTAGCATCA 59.229 45.455 0.00 0.00 0.00 3.07
96 97 3.392285 TGCAACCATAGACCTAGCATCAT 59.608 43.478 0.00 0.00 0.00 2.45
97 98 4.141413 TGCAACCATAGACCTAGCATCATT 60.141 41.667 0.00 0.00 0.00 2.57
98 99 4.214971 GCAACCATAGACCTAGCATCATTG 59.785 45.833 0.00 0.00 0.00 2.82
99 100 5.371526 CAACCATAGACCTAGCATCATTGT 58.628 41.667 0.00 0.00 0.00 2.71
100 101 5.636903 ACCATAGACCTAGCATCATTGTT 57.363 39.130 0.00 0.00 0.00 2.83
101 102 5.371526 ACCATAGACCTAGCATCATTGTTG 58.628 41.667 0.00 0.00 0.00 3.33
102 103 5.104360 ACCATAGACCTAGCATCATTGTTGT 60.104 40.000 0.00 0.00 0.00 3.32
103 104 5.237996 CCATAGACCTAGCATCATTGTTGTG 59.762 44.000 0.00 0.00 0.00 3.33
104 105 3.012518 AGACCTAGCATCATTGTTGTGC 58.987 45.455 0.00 0.00 39.10 4.57
105 106 2.094675 ACCTAGCATCATTGTTGTGCC 58.905 47.619 7.47 0.00 39.62 5.01
106 107 2.291153 ACCTAGCATCATTGTTGTGCCT 60.291 45.455 7.47 0.00 39.62 4.75
107 108 2.098607 CCTAGCATCATTGTTGTGCCTG 59.901 50.000 7.47 3.00 39.62 4.85
108 109 1.913778 AGCATCATTGTTGTGCCTGA 58.086 45.000 7.47 0.00 39.62 3.86
109 110 2.241160 AGCATCATTGTTGTGCCTGAA 58.759 42.857 7.47 0.00 39.62 3.02
110 111 2.230508 AGCATCATTGTTGTGCCTGAAG 59.769 45.455 7.47 0.00 39.62 3.02
111 112 2.229543 GCATCATTGTTGTGCCTGAAGA 59.770 45.455 0.00 0.00 32.88 2.87
112 113 3.119245 GCATCATTGTTGTGCCTGAAGAT 60.119 43.478 0.00 0.00 32.88 2.40
113 114 4.096833 GCATCATTGTTGTGCCTGAAGATA 59.903 41.667 0.00 0.00 32.88 1.98
114 115 5.575957 CATCATTGTTGTGCCTGAAGATAC 58.424 41.667 0.00 0.00 0.00 2.24
115 116 4.650734 TCATTGTTGTGCCTGAAGATACA 58.349 39.130 0.00 0.00 0.00 2.29
116 117 5.069318 TCATTGTTGTGCCTGAAGATACAA 58.931 37.500 0.00 0.00 0.00 2.41
117 118 5.711506 TCATTGTTGTGCCTGAAGATACAAT 59.288 36.000 0.00 0.00 35.72 2.71
118 119 6.209192 TCATTGTTGTGCCTGAAGATACAATT 59.791 34.615 0.00 0.00 35.72 2.32
119 120 7.392953 TCATTGTTGTGCCTGAAGATACAATTA 59.607 33.333 0.00 0.00 35.72 1.40
120 121 7.517614 TTGTTGTGCCTGAAGATACAATTAA 57.482 32.000 0.00 0.00 35.72 1.40
121 122 6.908825 TGTTGTGCCTGAAGATACAATTAAC 58.091 36.000 0.00 0.00 35.72 2.01
122 123 6.072175 TGTTGTGCCTGAAGATACAATTAACC 60.072 38.462 0.00 0.00 35.72 2.85
123 124 5.565509 TGTGCCTGAAGATACAATTAACCA 58.434 37.500 0.00 0.00 0.00 3.67
124 125 5.414454 TGTGCCTGAAGATACAATTAACCAC 59.586 40.000 0.00 0.00 0.00 4.16
125 126 5.414454 GTGCCTGAAGATACAATTAACCACA 59.586 40.000 0.00 0.00 0.00 4.17
126 127 6.007076 TGCCTGAAGATACAATTAACCACAA 58.993 36.000 0.00 0.00 0.00 3.33
127 128 6.663093 TGCCTGAAGATACAATTAACCACAAT 59.337 34.615 0.00 0.00 0.00 2.71
128 129 7.831690 TGCCTGAAGATACAATTAACCACAATA 59.168 33.333 0.00 0.00 0.00 1.90
129 130 8.129211 GCCTGAAGATACAATTAACCACAATAC 58.871 37.037 0.00 0.00 0.00 1.89
130 131 9.173021 CCTGAAGATACAATTAACCACAATACA 57.827 33.333 0.00 0.00 0.00 2.29
138 139 8.940768 ACAATTAACCACAATACAATATTGGC 57.059 30.769 19.37 0.00 33.56 4.52
139 140 7.704472 ACAATTAACCACAATACAATATTGGCG 59.296 33.333 19.37 7.16 33.56 5.69
140 141 7.575414 ATTAACCACAATACAATATTGGCGA 57.425 32.000 19.37 5.06 33.56 5.54
141 142 5.906113 AACCACAATACAATATTGGCGAA 57.094 34.783 19.37 2.87 33.56 4.70
142 143 6.463995 AACCACAATACAATATTGGCGAAT 57.536 33.333 19.37 0.00 33.56 3.34
143 144 6.072112 ACCACAATACAATATTGGCGAATC 57.928 37.500 19.37 0.00 33.56 2.52
144 145 5.827797 ACCACAATACAATATTGGCGAATCT 59.172 36.000 19.37 0.00 33.56 2.40
145 146 6.017109 ACCACAATACAATATTGGCGAATCTC 60.017 38.462 19.37 0.00 33.56 2.75
146 147 6.017192 CCACAATACAATATTGGCGAATCTCA 60.017 38.462 19.37 0.00 33.56 3.27
147 148 7.416817 CACAATACAATATTGGCGAATCTCAA 58.583 34.615 19.37 0.00 33.56 3.02
148 149 7.376866 CACAATACAATATTGGCGAATCTCAAC 59.623 37.037 19.37 0.00 33.56 3.18
149 150 7.066887 ACAATACAATATTGGCGAATCTCAACA 59.933 33.333 19.37 0.00 33.56 3.33
150 151 5.895636 ACAATATTGGCGAATCTCAACAA 57.104 34.783 19.37 0.00 0.00 2.83
151 152 5.883661 ACAATATTGGCGAATCTCAACAAG 58.116 37.500 19.37 0.00 0.00 3.16
152 153 5.647658 ACAATATTGGCGAATCTCAACAAGA 59.352 36.000 19.37 0.00 38.72 3.02
172 173 7.621428 CAAGATTTTCTTGCAAGATAGGAGA 57.379 36.000 28.89 11.01 46.03 3.71
173 174 8.048534 CAAGATTTTCTTGCAAGATAGGAGAA 57.951 34.615 28.89 16.36 46.03 2.87
174 175 8.684520 CAAGATTTTCTTGCAAGATAGGAGAAT 58.315 33.333 28.89 19.44 46.03 2.40
175 176 8.820153 AGATTTTCTTGCAAGATAGGAGAATT 57.180 30.769 28.89 14.93 34.49 2.17
176 177 8.901793 AGATTTTCTTGCAAGATAGGAGAATTC 58.098 33.333 28.89 21.12 34.49 2.17
177 178 7.396540 TTTTCTTGCAAGATAGGAGAATTCC 57.603 36.000 28.89 0.00 38.11 3.01
178 179 5.698741 TCTTGCAAGATAGGAGAATTCCA 57.301 39.130 25.16 0.00 46.64 3.53
179 180 5.678583 TCTTGCAAGATAGGAGAATTCCAG 58.321 41.667 25.16 0.00 46.64 3.86
180 181 5.426509 TCTTGCAAGATAGGAGAATTCCAGA 59.573 40.000 25.16 0.00 46.64 3.86
181 182 5.287674 TGCAAGATAGGAGAATTCCAGAG 57.712 43.478 0.65 0.00 46.64 3.35
182 183 4.064388 GCAAGATAGGAGAATTCCAGAGC 58.936 47.826 0.65 0.00 46.64 4.09
183 184 4.444022 GCAAGATAGGAGAATTCCAGAGCA 60.444 45.833 0.65 0.00 46.64 4.26
184 185 5.678583 CAAGATAGGAGAATTCCAGAGCAA 58.321 41.667 0.65 0.00 46.64 3.91
185 186 6.297582 CAAGATAGGAGAATTCCAGAGCAAT 58.702 40.000 0.65 0.00 46.64 3.56
186 187 7.448420 CAAGATAGGAGAATTCCAGAGCAATA 58.552 38.462 0.65 0.00 46.64 1.90
187 188 7.623999 AGATAGGAGAATTCCAGAGCAATAA 57.376 36.000 0.65 0.00 46.64 1.40
188 189 8.038862 AGATAGGAGAATTCCAGAGCAATAAA 57.961 34.615 0.65 0.00 46.64 1.40
189 190 8.497745 AGATAGGAGAATTCCAGAGCAATAAAA 58.502 33.333 0.65 0.00 46.64 1.52
190 191 9.294614 GATAGGAGAATTCCAGAGCAATAAAAT 57.705 33.333 0.65 0.00 46.64 1.82
191 192 7.968014 AGGAGAATTCCAGAGCAATAAAATT 57.032 32.000 0.65 0.00 46.64 1.82
192 193 8.005192 AGGAGAATTCCAGAGCAATAAAATTC 57.995 34.615 0.65 0.00 46.64 2.17
193 194 7.069208 AGGAGAATTCCAGAGCAATAAAATTCC 59.931 37.037 0.65 0.00 46.64 3.01
194 195 7.117285 AGAATTCCAGAGCAATAAAATTCCC 57.883 36.000 0.65 0.00 34.98 3.97
195 196 6.899631 AGAATTCCAGAGCAATAAAATTCCCT 59.100 34.615 0.65 0.00 34.98 4.20
196 197 5.920193 TTCCAGAGCAATAAAATTCCCTG 57.080 39.130 0.00 0.00 0.00 4.45
197 198 5.191727 TCCAGAGCAATAAAATTCCCTGA 57.808 39.130 0.00 0.00 0.00 3.86
198 199 5.579047 TCCAGAGCAATAAAATTCCCTGAA 58.421 37.500 0.00 0.00 0.00 3.02
199 200 5.653769 TCCAGAGCAATAAAATTCCCTGAAG 59.346 40.000 0.00 0.00 0.00 3.02
200 201 5.420104 CCAGAGCAATAAAATTCCCTGAAGT 59.580 40.000 0.00 0.00 0.00 3.01
201 202 6.603201 CCAGAGCAATAAAATTCCCTGAAGTA 59.397 38.462 0.00 0.00 0.00 2.24
202 203 7.415653 CCAGAGCAATAAAATTCCCTGAAGTAC 60.416 40.741 0.00 0.00 0.00 2.73
203 204 7.121168 CAGAGCAATAAAATTCCCTGAAGTACA 59.879 37.037 0.00 0.00 0.00 2.90
204 205 7.121315 AGAGCAATAAAATTCCCTGAAGTACAC 59.879 37.037 0.00 0.00 0.00 2.90
205 206 6.719370 AGCAATAAAATTCCCTGAAGTACACA 59.281 34.615 0.00 0.00 0.00 3.72
206 207 6.806739 GCAATAAAATTCCCTGAAGTACACAC 59.193 38.462 0.00 0.00 0.00 3.82
207 208 7.312899 CAATAAAATTCCCTGAAGTACACACC 58.687 38.462 0.00 0.00 0.00 4.16
208 209 3.434940 AATTCCCTGAAGTACACACCC 57.565 47.619 0.00 0.00 0.00 4.61
209 210 1.809133 TTCCCTGAAGTACACACCCA 58.191 50.000 0.00 0.00 0.00 4.51
210 211 1.809133 TCCCTGAAGTACACACCCAA 58.191 50.000 0.00 0.00 0.00 4.12
211 212 1.418637 TCCCTGAAGTACACACCCAAC 59.581 52.381 0.00 0.00 0.00 3.77
212 213 1.508632 CCTGAAGTACACACCCAACG 58.491 55.000 0.00 0.00 0.00 4.10
213 214 1.069513 CCTGAAGTACACACCCAACGA 59.930 52.381 0.00 0.00 0.00 3.85
214 215 2.404215 CTGAAGTACACACCCAACGAG 58.596 52.381 0.00 0.00 0.00 4.18
215 216 1.145803 GAAGTACACACCCAACGAGC 58.854 55.000 0.00 0.00 0.00 5.03
216 217 0.466543 AAGTACACACCCAACGAGCA 59.533 50.000 0.00 0.00 0.00 4.26
217 218 0.685097 AGTACACACCCAACGAGCAT 59.315 50.000 0.00 0.00 0.00 3.79
218 219 1.897133 AGTACACACCCAACGAGCATA 59.103 47.619 0.00 0.00 0.00 3.14
219 220 1.997606 GTACACACCCAACGAGCATAC 59.002 52.381 0.00 0.00 0.00 2.39
220 221 0.394938 ACACACCCAACGAGCATACA 59.605 50.000 0.00 0.00 0.00 2.29
221 222 0.796312 CACACCCAACGAGCATACAC 59.204 55.000 0.00 0.00 0.00 2.90
222 223 0.394938 ACACCCAACGAGCATACACA 59.605 50.000 0.00 0.00 0.00 3.72
223 224 1.003118 ACACCCAACGAGCATACACAT 59.997 47.619 0.00 0.00 0.00 3.21
224 225 2.235155 ACACCCAACGAGCATACACATA 59.765 45.455 0.00 0.00 0.00 2.29
225 226 3.118408 ACACCCAACGAGCATACACATAT 60.118 43.478 0.00 0.00 0.00 1.78
226 227 4.100344 ACACCCAACGAGCATACACATATA 59.900 41.667 0.00 0.00 0.00 0.86
227 228 4.447724 CACCCAACGAGCATACACATATAC 59.552 45.833 0.00 0.00 0.00 1.47
228 229 4.100344 ACCCAACGAGCATACACATATACA 59.900 41.667 0.00 0.00 0.00 2.29
229 230 5.053811 CCCAACGAGCATACACATATACAA 58.946 41.667 0.00 0.00 0.00 2.41
353 354 6.913170 TCTTGAGCATCTGAATTTAAACCAC 58.087 36.000 0.00 0.00 34.92 4.16
354 355 5.295431 TGAGCATCTGAATTTAAACCACG 57.705 39.130 0.00 0.00 34.92 4.94
357 358 6.150976 TGAGCATCTGAATTTAAACCACGAAT 59.849 34.615 0.00 0.00 34.92 3.34
372 373 4.943705 ACCACGAATATTTCAACAGAGCAT 59.056 37.500 0.00 0.00 0.00 3.79
374 375 5.065090 CCACGAATATTTCAACAGAGCATCA 59.935 40.000 0.00 0.00 37.82 3.07
382 383 4.430137 TCAACAGAGCATCATTCAAAGC 57.570 40.909 0.00 0.00 37.82 3.51
395 396 6.164408 TCATTCAAAGCACATTAGTACGTG 57.836 37.500 0.00 0.00 36.18 4.49
396 397 5.699001 TCATTCAAAGCACATTAGTACGTGT 59.301 36.000 0.00 0.00 35.51 4.49
397 398 6.869388 TCATTCAAAGCACATTAGTACGTGTA 59.131 34.615 0.00 0.00 35.51 2.90
406 407 6.347079 GCACATTAGTACGTGTAAGAAAAGCA 60.347 38.462 0.00 0.00 35.51 3.91
460 501 9.696917 CATAACAAAGCAAAAAGATAAAGAGGT 57.303 29.630 0.00 0.00 0.00 3.85
468 509 7.928167 AGCAAAAAGATAAAGAGGTTGAAAAGG 59.072 33.333 0.00 0.00 0.00 3.11
493 534 7.069578 GGAACTAATAAAAAGGGGGAAATCCTC 59.930 40.741 0.00 0.00 35.78 3.71
498 539 0.034089 AAGGGGGAAATCCTCGCAAG 60.034 55.000 0.00 0.00 42.27 4.01
523 565 3.535561 AGCGAGTGACCATAGAAATTGG 58.464 45.455 0.00 0.00 40.26 3.16
525 567 3.873910 CGAGTGACCATAGAAATTGGGT 58.126 45.455 0.00 0.00 38.64 4.51
601 645 1.743623 CGTCCACTTATTGCGCCCA 60.744 57.895 4.18 0.00 0.00 5.36
602 646 1.302383 CGTCCACTTATTGCGCCCAA 61.302 55.000 4.18 0.00 35.01 4.12
1038 1082 4.016706 CCGTCCTCCAAGCCGGTT 62.017 66.667 1.90 0.00 35.78 4.44
1380 1424 2.577059 GTCACCTCCCGCATCGAA 59.423 61.111 0.00 0.00 0.00 3.71
1386 1430 0.461870 CCTCCCGCATCGAATTCACA 60.462 55.000 6.22 0.00 0.00 3.58
1982 2028 9.367160 TGATTTTATCTTCCTCTTGGTTTCTTT 57.633 29.630 0.00 0.00 34.23 2.52
1983 2029 9.631452 GATTTTATCTTCCTCTTGGTTTCTTTG 57.369 33.333 0.00 0.00 34.23 2.77
1998 2044 5.391416 GGTTTCTTTGCTTGCTACTCTCATC 60.391 44.000 0.00 0.00 0.00 2.92
2026 2072 5.444481 CCTTTCTTTGTCACAAGCAAAAACG 60.444 40.000 0.00 0.00 35.71 3.60
2036 2082 2.094762 AGCAAAAACGAGCCGAGTAT 57.905 45.000 1.50 0.00 0.00 2.12
2039 2085 1.084289 AAAAACGAGCCGAGTATGCC 58.916 50.000 1.50 0.00 0.00 4.40
2060 2118 3.058155 CCGCGTAGATCTATGCTACAGTT 60.058 47.826 33.43 0.00 43.85 3.16
2134 2200 1.271325 TGCAGCCGAGAAGAAATGGAA 60.271 47.619 0.00 0.00 0.00 3.53
2142 2208 4.390297 CCGAGAAGAAATGGAAGTGAACTC 59.610 45.833 0.00 0.00 0.00 3.01
2143 2209 4.390297 CGAGAAGAAATGGAAGTGAACTCC 59.610 45.833 0.00 0.00 0.00 3.85
2144 2210 5.308825 GAGAAGAAATGGAAGTGAACTCCA 58.691 41.667 0.00 0.00 37.99 3.86
2145 2211 5.312079 AGAAGAAATGGAAGTGAACTCCAG 58.688 41.667 0.00 0.00 36.92 3.86
2146 2212 4.713792 AGAAATGGAAGTGAACTCCAGT 57.286 40.909 0.00 0.00 36.92 4.00
2147 2213 5.825593 AGAAATGGAAGTGAACTCCAGTA 57.174 39.130 0.00 0.00 36.92 2.74
2148 2214 5.552178 AGAAATGGAAGTGAACTCCAGTAC 58.448 41.667 0.00 0.00 36.92 2.73
2151 2220 1.337821 GAAGTGAACTCCAGTACGCG 58.662 55.000 3.53 3.53 0.00 6.01
2158 2227 3.456431 CTCCAGTACGCGAGCGAGG 62.456 68.421 24.72 17.86 42.83 4.63
2237 2306 4.100279 TCCTTTTTGGTTTCTCTCCCTC 57.900 45.455 0.00 0.00 37.07 4.30
2256 2325 1.831736 TCCCGTTTCCTCAATCTCTCC 59.168 52.381 0.00 0.00 0.00 3.71
2266 2335 3.490348 CTCAATCTCTCCTCTCCTCTCC 58.510 54.545 0.00 0.00 0.00 3.71
2458 2555 3.636764 GAGAGGATGAGGGAGAGAGAAAC 59.363 52.174 0.00 0.00 0.00 2.78
2489 2586 0.962855 CTCTCGCTCCAGTCCAGTGA 60.963 60.000 0.00 0.00 0.00 3.41
2586 2695 4.273969 GTGGTAGTACAATCCGAGAGAGAG 59.726 50.000 2.06 0.00 0.00 3.20
2667 2837 2.002586 TCAGTGAGAATTGCTAAGCGC 58.997 47.619 0.00 0.00 39.77 5.92
2675 2845 2.047274 TGCTAAGCGCAGTGGACC 60.047 61.111 11.47 0.00 45.47 4.46
2676 2846 2.047274 GCTAAGCGCAGTGGACCA 60.047 61.111 11.47 0.00 38.92 4.02
2677 2847 2.391389 GCTAAGCGCAGTGGACCAC 61.391 63.158 17.43 17.43 38.92 4.16
2678 2848 2.048597 TAAGCGCAGTGGACCACG 60.049 61.111 18.93 14.38 39.64 4.94
2679 2849 2.765250 CTAAGCGCAGTGGACCACGT 62.765 60.000 18.93 4.93 39.64 4.49
2680 2850 4.969196 AGCGCAGTGGACCACGTG 62.969 66.667 18.93 19.14 39.64 4.49
2681 2851 4.961511 GCGCAGTGGACCACGTGA 62.962 66.667 24.56 0.00 39.64 4.35
2682 2852 2.734723 CGCAGTGGACCACGTGAG 60.735 66.667 19.30 14.43 39.64 3.51
2683 2853 2.357517 GCAGTGGACCACGTGAGG 60.358 66.667 19.30 3.18 39.64 3.86
2684 2854 3.138625 CAGTGGACCACGTGAGGT 58.861 61.111 19.30 7.32 46.82 3.85
2685 2855 1.300931 CAGTGGACCACGTGAGGTG 60.301 63.158 19.30 6.93 43.38 4.00
2686 2856 1.760875 AGTGGACCACGTGAGGTGT 60.761 57.895 19.30 5.92 45.52 4.16
2687 2857 1.594293 GTGGACCACGTGAGGTGTG 60.594 63.158 19.30 0.71 45.52 3.82
2688 2858 1.758906 TGGACCACGTGAGGTGTGA 60.759 57.895 19.30 0.00 45.52 3.58
2689 2859 1.331399 TGGACCACGTGAGGTGTGAA 61.331 55.000 19.30 0.00 45.52 3.18
2690 2860 0.034896 GGACCACGTGAGGTGTGAAT 59.965 55.000 19.30 0.00 45.52 2.57
2691 2861 1.148310 GACCACGTGAGGTGTGAATG 58.852 55.000 19.30 0.00 45.52 2.67
2692 2862 0.884704 ACCACGTGAGGTGTGAATGC 60.885 55.000 19.30 0.00 45.52 3.56
2693 2863 0.603707 CCACGTGAGGTGTGAATGCT 60.604 55.000 19.30 0.00 45.52 3.79
2694 2864 0.514255 CACGTGAGGTGTGAATGCTG 59.486 55.000 10.90 0.00 41.89 4.41
2695 2865 0.603707 ACGTGAGGTGTGAATGCTGG 60.604 55.000 0.00 0.00 0.00 4.85
2696 2866 1.300971 CGTGAGGTGTGAATGCTGGG 61.301 60.000 0.00 0.00 0.00 4.45
2697 2867 0.250901 GTGAGGTGTGAATGCTGGGT 60.251 55.000 0.00 0.00 0.00 4.51
2698 2868 1.003118 GTGAGGTGTGAATGCTGGGTA 59.997 52.381 0.00 0.00 0.00 3.69
2699 2869 1.003118 TGAGGTGTGAATGCTGGGTAC 59.997 52.381 0.00 0.00 0.00 3.34
2700 2870 0.036388 AGGTGTGAATGCTGGGTACG 60.036 55.000 0.00 0.00 0.00 3.67
2701 2871 1.644786 GGTGTGAATGCTGGGTACGC 61.645 60.000 2.35 2.35 0.00 4.42
2702 2872 1.739929 TGTGAATGCTGGGTACGCG 60.740 57.895 3.53 3.53 0.00 6.01
2703 2873 1.447140 GTGAATGCTGGGTACGCGA 60.447 57.895 15.93 0.00 0.00 5.87
2704 2874 1.447140 TGAATGCTGGGTACGCGAC 60.447 57.895 15.93 6.63 0.00 5.19
2718 2888 3.693245 CGACCTCGCCGAGATTTG 58.307 61.111 17.19 0.56 0.00 2.32
2719 2889 2.517450 CGACCTCGCCGAGATTTGC 61.517 63.158 17.19 0.00 0.00 3.68
2720 2890 1.153549 GACCTCGCCGAGATTTGCT 60.154 57.895 17.19 0.00 0.00 3.91
2721 2891 0.102481 GACCTCGCCGAGATTTGCTA 59.898 55.000 17.19 0.00 0.00 3.49
2722 2892 0.535335 ACCTCGCCGAGATTTGCTAA 59.465 50.000 17.19 0.00 0.00 3.09
2723 2893 1.212616 CCTCGCCGAGATTTGCTAAG 58.787 55.000 17.19 0.00 0.00 2.18
2724 2894 0.579156 CTCGCCGAGATTTGCTAAGC 59.421 55.000 8.82 0.00 0.00 3.09
2725 2895 1.145759 TCGCCGAGATTTGCTAAGCG 61.146 55.000 5.38 5.38 44.91 4.68
2747 2917 0.509929 CATGAGTCGCATACGCCATG 59.490 55.000 0.00 8.86 39.84 3.66
2817 2987 3.431725 GCAACGGAAGAAGCGGGG 61.432 66.667 0.00 0.00 0.00 5.73
2828 2998 0.603975 GAAGCGGGGTGATCATAGGC 60.604 60.000 0.00 0.59 0.00 3.93
2831 3001 1.300931 CGGGGTGATCATAGGCGTG 60.301 63.158 0.00 0.00 0.00 5.34
2852 3022 0.962356 GCAGGGCATGTGCAGTACTT 60.962 55.000 7.36 0.00 44.36 2.24
2853 3023 1.089920 CAGGGCATGTGCAGTACTTC 58.910 55.000 7.36 0.00 44.36 3.01
2854 3024 0.391661 AGGGCATGTGCAGTACTTCG 60.392 55.000 7.36 0.00 44.36 3.79
2856 3026 0.443869 GGCATGTGCAGTACTTCGTG 59.556 55.000 7.36 0.15 44.36 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.497730 ATCCTTCGGACATTCATGTTGATGAAA 61.498 37.037 11.51 0.00 42.13 2.69
1 2 7.080473 ATCCTTCGGACATTCATGTTGATGAA 61.080 38.462 11.51 0.00 42.60 2.57
2 3 3.940852 CCTTCGGACATTCATGTTGATGA 59.059 43.478 11.51 0.00 41.95 2.92
3 4 3.940852 TCCTTCGGACATTCATGTTGATG 59.059 43.478 5.59 5.48 41.95 3.07
4 5 4.220693 TCCTTCGGACATTCATGTTGAT 57.779 40.909 5.59 0.00 41.95 2.57
5 6 3.694043 TCCTTCGGACATTCATGTTGA 57.306 42.857 5.59 0.00 41.95 3.18
6 7 7.307989 GGTTATATCCTTCGGACATTCATGTTG 60.308 40.741 0.00 0.00 41.95 3.33
7 8 6.710744 GGTTATATCCTTCGGACATTCATGTT 59.289 38.462 0.00 0.00 41.95 2.71
8 9 6.231211 GGTTATATCCTTCGGACATTCATGT 58.769 40.000 0.00 0.00 45.16 3.21
9 10 5.348724 CGGTTATATCCTTCGGACATTCATG 59.651 44.000 0.00 0.00 32.98 3.07
10 11 5.245301 TCGGTTATATCCTTCGGACATTCAT 59.755 40.000 0.00 0.00 32.98 2.57
11 12 4.585581 TCGGTTATATCCTTCGGACATTCA 59.414 41.667 0.00 0.00 32.98 2.57
12 13 5.130292 TCGGTTATATCCTTCGGACATTC 57.870 43.478 0.00 0.00 32.98 2.67
13 14 5.540400 TTCGGTTATATCCTTCGGACATT 57.460 39.130 0.00 0.00 32.98 2.71
14 15 5.303589 TCTTTCGGTTATATCCTTCGGACAT 59.696 40.000 0.00 0.00 32.98 3.06
15 16 4.646040 TCTTTCGGTTATATCCTTCGGACA 59.354 41.667 0.00 0.00 32.98 4.02
16 17 5.192327 TCTTTCGGTTATATCCTTCGGAC 57.808 43.478 0.00 0.00 32.98 4.79
17 18 7.528996 TTATCTTTCGGTTATATCCTTCGGA 57.471 36.000 0.00 0.00 35.55 4.55
18 19 7.871463 AGTTTATCTTTCGGTTATATCCTTCGG 59.129 37.037 0.00 0.00 0.00 4.30
19 20 8.813643 AGTTTATCTTTCGGTTATATCCTTCG 57.186 34.615 0.00 0.00 0.00 3.79
20 21 9.760077 TGAGTTTATCTTTCGGTTATATCCTTC 57.240 33.333 0.00 0.00 0.00 3.46
22 23 9.930693 GATGAGTTTATCTTTCGGTTATATCCT 57.069 33.333 0.00 0.00 0.00 3.24
23 24 9.706691 TGATGAGTTTATCTTTCGGTTATATCC 57.293 33.333 0.00 0.00 0.00 2.59
25 26 9.193133 CGTGATGAGTTTATCTTTCGGTTATAT 57.807 33.333 0.00 0.00 0.00 0.86
26 27 8.407832 TCGTGATGAGTTTATCTTTCGGTTATA 58.592 33.333 0.00 0.00 0.00 0.98
27 28 7.262772 TCGTGATGAGTTTATCTTTCGGTTAT 58.737 34.615 0.00 0.00 0.00 1.89
28 29 6.623486 TCGTGATGAGTTTATCTTTCGGTTA 58.377 36.000 0.00 0.00 0.00 2.85
29 30 5.475719 TCGTGATGAGTTTATCTTTCGGTT 58.524 37.500 0.00 0.00 0.00 4.44
30 31 5.068234 TCGTGATGAGTTTATCTTTCGGT 57.932 39.130 0.00 0.00 0.00 4.69
31 32 5.627802 CTCGTGATGAGTTTATCTTTCGG 57.372 43.478 0.00 0.00 40.03 4.30
32 33 5.289675 AAGCTCGTGATGAGTTTATCTTTCG 59.710 40.000 1.71 0.00 45.12 3.46
33 34 6.091441 ACAAGCTCGTGATGAGTTTATCTTTC 59.909 38.462 3.41 0.00 45.18 2.62
34 35 5.934625 ACAAGCTCGTGATGAGTTTATCTTT 59.065 36.000 3.41 0.00 45.18 2.52
35 36 5.482908 ACAAGCTCGTGATGAGTTTATCTT 58.517 37.500 3.41 0.00 45.18 2.40
36 37 5.078411 ACAAGCTCGTGATGAGTTTATCT 57.922 39.130 3.41 0.00 45.18 1.98
37 38 4.268884 GGACAAGCTCGTGATGAGTTTATC 59.731 45.833 3.41 2.40 45.18 1.75
38 39 4.081420 AGGACAAGCTCGTGATGAGTTTAT 60.081 41.667 3.41 0.00 45.18 1.40
39 40 3.258372 AGGACAAGCTCGTGATGAGTTTA 59.742 43.478 3.41 0.00 45.18 2.01
44 45 1.338105 CCAAGGACAAGCTCGTGATGA 60.338 52.381 0.00 0.00 0.00 2.92
45 46 1.081892 CCAAGGACAAGCTCGTGATG 58.918 55.000 0.00 0.00 0.00 3.07
46 47 0.674895 GCCAAGGACAAGCTCGTGAT 60.675 55.000 0.00 0.00 0.00 3.06
47 48 1.301716 GCCAAGGACAAGCTCGTGA 60.302 57.895 0.00 0.00 0.00 4.35
48 49 2.328099 GGCCAAGGACAAGCTCGTG 61.328 63.158 0.00 0.00 0.00 4.35
49 50 2.032681 GGCCAAGGACAAGCTCGT 59.967 61.111 0.00 0.00 0.00 4.18
50 51 2.747855 GGGCCAAGGACAAGCTCG 60.748 66.667 4.39 0.00 0.00 5.03
51 52 1.000396 ATGGGCCAAGGACAAGCTC 60.000 57.895 11.89 0.00 0.00 4.09
52 53 1.304713 CATGGGCCAAGGACAAGCT 60.305 57.895 11.89 0.00 0.00 3.74
53 54 0.899717 TTCATGGGCCAAGGACAAGC 60.900 55.000 11.89 0.00 0.00 4.01
54 55 1.856629 ATTCATGGGCCAAGGACAAG 58.143 50.000 11.89 0.00 0.00 3.16
55 56 1.901159 CAATTCATGGGCCAAGGACAA 59.099 47.619 11.89 0.00 0.00 3.18
56 57 1.559368 CAATTCATGGGCCAAGGACA 58.441 50.000 11.89 3.34 0.00 4.02
57 58 0.176449 GCAATTCATGGGCCAAGGAC 59.824 55.000 11.89 0.00 0.00 3.85
58 59 0.252148 TGCAATTCATGGGCCAAGGA 60.252 50.000 11.89 9.01 0.00 3.36
59 60 0.614294 TTGCAATTCATGGGCCAAGG 59.386 50.000 11.89 6.22 0.00 3.61
60 61 1.676615 GGTTGCAATTCATGGGCCAAG 60.677 52.381 11.89 6.29 0.00 3.61
61 62 0.324285 GGTTGCAATTCATGGGCCAA 59.676 50.000 11.89 0.00 0.00 4.52
62 63 0.835115 TGGTTGCAATTCATGGGCCA 60.835 50.000 9.61 9.61 0.00 5.36
63 64 0.542805 ATGGTTGCAATTCATGGGCC 59.457 50.000 14.70 0.00 0.00 5.80
64 65 2.694628 TCTATGGTTGCAATTCATGGGC 59.305 45.455 21.12 0.67 0.00 5.36
65 66 3.068590 GGTCTATGGTTGCAATTCATGGG 59.931 47.826 21.12 15.50 0.00 4.00
66 67 3.956199 AGGTCTATGGTTGCAATTCATGG 59.044 43.478 21.12 19.06 0.00 3.66
67 68 5.278169 GCTAGGTCTATGGTTGCAATTCATG 60.278 44.000 21.12 13.97 0.00 3.07
68 69 4.823989 GCTAGGTCTATGGTTGCAATTCAT 59.176 41.667 18.02 18.02 0.00 2.57
69 70 4.199310 GCTAGGTCTATGGTTGCAATTCA 58.801 43.478 0.59 5.08 0.00 2.57
70 71 4.199310 TGCTAGGTCTATGGTTGCAATTC 58.801 43.478 0.59 0.00 0.00 2.17
71 72 4.235079 TGCTAGGTCTATGGTTGCAATT 57.765 40.909 0.59 0.00 0.00 2.32
72 73 3.931907 TGCTAGGTCTATGGTTGCAAT 57.068 42.857 0.59 0.00 0.00 3.56
73 74 3.199727 TGATGCTAGGTCTATGGTTGCAA 59.800 43.478 0.00 0.00 32.66 4.08
74 75 2.771372 TGATGCTAGGTCTATGGTTGCA 59.229 45.455 0.00 0.00 0.00 4.08
75 76 3.475566 TGATGCTAGGTCTATGGTTGC 57.524 47.619 0.00 0.00 0.00 4.17
76 77 5.371526 ACAATGATGCTAGGTCTATGGTTG 58.628 41.667 0.00 0.00 0.00 3.77
77 78 5.636903 ACAATGATGCTAGGTCTATGGTT 57.363 39.130 0.00 0.00 0.00 3.67
78 79 5.104360 ACAACAATGATGCTAGGTCTATGGT 60.104 40.000 0.00 0.00 0.00 3.55
79 80 5.237996 CACAACAATGATGCTAGGTCTATGG 59.762 44.000 0.00 0.00 0.00 2.74
80 81 5.277683 GCACAACAATGATGCTAGGTCTATG 60.278 44.000 0.00 0.00 36.40 2.23
81 82 4.818546 GCACAACAATGATGCTAGGTCTAT 59.181 41.667 0.00 0.00 36.40 1.98
82 83 4.191544 GCACAACAATGATGCTAGGTCTA 58.808 43.478 0.00 0.00 36.40 2.59
83 84 3.012518 GCACAACAATGATGCTAGGTCT 58.987 45.455 0.00 0.00 36.40 3.85
84 85 2.098117 GGCACAACAATGATGCTAGGTC 59.902 50.000 8.29 0.00 39.38 3.85
85 86 2.094675 GGCACAACAATGATGCTAGGT 58.905 47.619 8.29 0.00 39.38 3.08
86 87 2.098607 CAGGCACAACAATGATGCTAGG 59.901 50.000 8.29 0.00 39.38 3.02
87 88 3.011818 TCAGGCACAACAATGATGCTAG 58.988 45.455 8.29 0.00 39.38 3.42
88 89 3.070476 TCAGGCACAACAATGATGCTA 57.930 42.857 8.29 0.00 39.38 3.49
89 90 1.913778 TCAGGCACAACAATGATGCT 58.086 45.000 8.29 0.00 39.38 3.79
90 91 2.229543 TCTTCAGGCACAACAATGATGC 59.770 45.455 0.00 0.00 38.68 3.91
91 92 4.713824 ATCTTCAGGCACAACAATGATG 57.286 40.909 0.00 0.00 0.00 3.07
92 93 5.255687 TGTATCTTCAGGCACAACAATGAT 58.744 37.500 0.00 0.00 0.00 2.45
93 94 4.650734 TGTATCTTCAGGCACAACAATGA 58.349 39.130 0.00 0.00 0.00 2.57
94 95 5.375417 TTGTATCTTCAGGCACAACAATG 57.625 39.130 0.00 0.00 0.00 2.82
95 96 6.594788 AATTGTATCTTCAGGCACAACAAT 57.405 33.333 0.00 0.00 37.60 2.71
96 97 7.367285 GTTAATTGTATCTTCAGGCACAACAA 58.633 34.615 0.00 0.00 34.00 2.83
97 98 6.072175 GGTTAATTGTATCTTCAGGCACAACA 60.072 38.462 0.00 0.00 34.00 3.33
98 99 6.072175 TGGTTAATTGTATCTTCAGGCACAAC 60.072 38.462 0.00 0.00 34.00 3.32
99 100 6.007076 TGGTTAATTGTATCTTCAGGCACAA 58.993 36.000 0.00 0.00 35.53 3.33
100 101 5.414454 GTGGTTAATTGTATCTTCAGGCACA 59.586 40.000 0.00 0.00 0.00 4.57
101 102 5.414454 TGTGGTTAATTGTATCTTCAGGCAC 59.586 40.000 0.00 0.00 0.00 5.01
102 103 5.565509 TGTGGTTAATTGTATCTTCAGGCA 58.434 37.500 0.00 0.00 0.00 4.75
103 104 6.509418 TTGTGGTTAATTGTATCTTCAGGC 57.491 37.500 0.00 0.00 0.00 4.85
104 105 9.173021 TGTATTGTGGTTAATTGTATCTTCAGG 57.827 33.333 0.00 0.00 0.00 3.86
113 114 7.704472 CGCCAATATTGTATTGTGGTTAATTGT 59.296 33.333 14.25 0.00 0.00 2.71
114 115 7.918033 TCGCCAATATTGTATTGTGGTTAATTG 59.082 33.333 14.25 0.00 0.00 2.32
115 116 8.001881 TCGCCAATATTGTATTGTGGTTAATT 57.998 30.769 14.25 0.00 0.00 1.40
116 117 7.575414 TCGCCAATATTGTATTGTGGTTAAT 57.425 32.000 14.25 0.00 0.00 1.40
117 118 7.392494 TTCGCCAATATTGTATTGTGGTTAA 57.608 32.000 14.25 0.00 0.00 2.01
118 119 7.500892 AGATTCGCCAATATTGTATTGTGGTTA 59.499 33.333 14.25 0.00 0.00 2.85
119 120 5.906113 TTCGCCAATATTGTATTGTGGTT 57.094 34.783 14.25 0.00 0.00 3.67
120 121 5.827797 AGATTCGCCAATATTGTATTGTGGT 59.172 36.000 14.25 0.00 0.00 4.16
121 122 6.017192 TGAGATTCGCCAATATTGTATTGTGG 60.017 38.462 14.25 0.00 0.00 4.17
122 123 6.958255 TGAGATTCGCCAATATTGTATTGTG 58.042 36.000 14.25 5.79 0.00 3.33
123 124 7.066887 TGTTGAGATTCGCCAATATTGTATTGT 59.933 33.333 14.25 0.00 0.00 2.71
124 125 7.416817 TGTTGAGATTCGCCAATATTGTATTG 58.583 34.615 14.25 0.24 0.00 1.90
125 126 7.566760 TGTTGAGATTCGCCAATATTGTATT 57.433 32.000 14.25 0.00 0.00 1.89
126 127 7.498900 TCTTGTTGAGATTCGCCAATATTGTAT 59.501 33.333 14.25 2.63 0.00 2.29
127 128 6.821160 TCTTGTTGAGATTCGCCAATATTGTA 59.179 34.615 14.25 0.00 0.00 2.41
128 129 5.647658 TCTTGTTGAGATTCGCCAATATTGT 59.352 36.000 14.25 0.00 0.00 2.71
129 130 6.122850 TCTTGTTGAGATTCGCCAATATTG 57.877 37.500 8.58 8.58 0.00 1.90
130 131 6.949352 ATCTTGTTGAGATTCGCCAATATT 57.051 33.333 0.00 0.00 42.55 1.28
149 150 8.820153 ATTCTCCTATCTTGCAAGAAAATCTT 57.180 30.769 31.55 17.10 38.77 2.40
150 151 8.820153 AATTCTCCTATCTTGCAAGAAAATCT 57.180 30.769 31.55 17.81 38.77 2.40
151 152 8.134261 GGAATTCTCCTATCTTGCAAGAAAATC 58.866 37.037 31.55 20.60 37.39 2.17
152 153 7.616935 TGGAATTCTCCTATCTTGCAAGAAAAT 59.383 33.333 31.55 18.54 42.94 1.82
153 154 6.947733 TGGAATTCTCCTATCTTGCAAGAAAA 59.052 34.615 31.55 21.12 42.94 2.29
154 155 6.484288 TGGAATTCTCCTATCTTGCAAGAAA 58.516 36.000 31.55 20.27 42.94 2.52
155 156 6.065976 TGGAATTCTCCTATCTTGCAAGAA 57.934 37.500 31.55 19.21 42.94 2.52
156 157 5.426509 TCTGGAATTCTCCTATCTTGCAAGA 59.573 40.000 30.23 30.23 42.94 3.02
157 158 5.678583 TCTGGAATTCTCCTATCTTGCAAG 58.321 41.667 20.81 20.81 42.94 4.01
158 159 5.678583 CTCTGGAATTCTCCTATCTTGCAA 58.321 41.667 5.23 0.00 42.94 4.08
159 160 4.444022 GCTCTGGAATTCTCCTATCTTGCA 60.444 45.833 5.23 0.00 42.94 4.08
160 161 4.064388 GCTCTGGAATTCTCCTATCTTGC 58.936 47.826 5.23 0.00 42.94 4.01
161 162 5.287674 TGCTCTGGAATTCTCCTATCTTG 57.712 43.478 5.23 0.00 42.94 3.02
162 163 5.965033 TTGCTCTGGAATTCTCCTATCTT 57.035 39.130 5.23 0.00 42.94 2.40
163 164 7.623999 TTATTGCTCTGGAATTCTCCTATCT 57.376 36.000 5.23 0.00 42.94 1.98
164 165 8.682936 TTTTATTGCTCTGGAATTCTCCTATC 57.317 34.615 5.23 0.00 42.94 2.08
165 166 9.652114 AATTTTATTGCTCTGGAATTCTCCTAT 57.348 29.630 5.23 0.00 42.94 2.57
166 167 9.125026 GAATTTTATTGCTCTGGAATTCTCCTA 57.875 33.333 5.23 0.00 42.94 2.94
167 168 7.069208 GGAATTTTATTGCTCTGGAATTCTCCT 59.931 37.037 5.23 0.00 42.94 3.69
168 169 7.205992 GGAATTTTATTGCTCTGGAATTCTCC 58.794 38.462 5.23 0.00 42.81 3.71
169 170 7.069208 AGGGAATTTTATTGCTCTGGAATTCTC 59.931 37.037 5.23 9.62 35.34 2.87
170 171 6.899631 AGGGAATTTTATTGCTCTGGAATTCT 59.100 34.615 5.23 0.00 35.15 2.40
171 172 6.982724 CAGGGAATTTTATTGCTCTGGAATTC 59.017 38.462 0.00 0.00 34.44 2.17
172 173 6.669154 TCAGGGAATTTTATTGCTCTGGAATT 59.331 34.615 0.00 0.00 0.00 2.17
173 174 6.197168 TCAGGGAATTTTATTGCTCTGGAAT 58.803 36.000 0.00 0.00 0.00 3.01
174 175 5.579047 TCAGGGAATTTTATTGCTCTGGAA 58.421 37.500 0.00 0.00 0.00 3.53
175 176 5.191727 TCAGGGAATTTTATTGCTCTGGA 57.808 39.130 0.00 0.00 0.00 3.86
176 177 5.420104 ACTTCAGGGAATTTTATTGCTCTGG 59.580 40.000 0.00 0.00 0.00 3.86
177 178 6.521151 ACTTCAGGGAATTTTATTGCTCTG 57.479 37.500 0.00 0.00 0.00 3.35
178 179 7.121315 GTGTACTTCAGGGAATTTTATTGCTCT 59.879 37.037 0.00 0.00 0.00 4.09
179 180 7.094377 TGTGTACTTCAGGGAATTTTATTGCTC 60.094 37.037 0.00 0.00 0.00 4.26
180 181 6.719370 TGTGTACTTCAGGGAATTTTATTGCT 59.281 34.615 0.00 0.00 0.00 3.91
181 182 6.806739 GTGTGTACTTCAGGGAATTTTATTGC 59.193 38.462 0.00 0.00 0.00 3.56
182 183 7.312899 GGTGTGTACTTCAGGGAATTTTATTG 58.687 38.462 0.00 0.00 0.00 1.90
183 184 6.436218 GGGTGTGTACTTCAGGGAATTTTATT 59.564 38.462 0.00 0.00 0.00 1.40
184 185 5.949952 GGGTGTGTACTTCAGGGAATTTTAT 59.050 40.000 0.00 0.00 0.00 1.40
185 186 5.163077 TGGGTGTGTACTTCAGGGAATTTTA 60.163 40.000 0.00 0.00 0.00 1.52
186 187 4.149598 GGGTGTGTACTTCAGGGAATTTT 58.850 43.478 0.00 0.00 0.00 1.82
187 188 3.139397 TGGGTGTGTACTTCAGGGAATTT 59.861 43.478 0.00 0.00 0.00 1.82
188 189 2.714250 TGGGTGTGTACTTCAGGGAATT 59.286 45.455 0.00 0.00 0.00 2.17
189 190 2.344592 TGGGTGTGTACTTCAGGGAAT 58.655 47.619 0.00 0.00 0.00 3.01
190 191 1.809133 TGGGTGTGTACTTCAGGGAA 58.191 50.000 0.00 0.00 0.00 3.97
191 192 1.418637 GTTGGGTGTGTACTTCAGGGA 59.581 52.381 0.00 0.00 0.00 4.20
192 193 1.876416 CGTTGGGTGTGTACTTCAGGG 60.876 57.143 0.00 0.00 0.00 4.45
193 194 1.069513 TCGTTGGGTGTGTACTTCAGG 59.930 52.381 0.00 0.00 0.00 3.86
194 195 2.404215 CTCGTTGGGTGTGTACTTCAG 58.596 52.381 0.00 0.00 0.00 3.02
195 196 1.539496 GCTCGTTGGGTGTGTACTTCA 60.539 52.381 0.00 0.00 0.00 3.02
196 197 1.145803 GCTCGTTGGGTGTGTACTTC 58.854 55.000 0.00 0.00 0.00 3.01
197 198 0.466543 TGCTCGTTGGGTGTGTACTT 59.533 50.000 0.00 0.00 0.00 2.24
198 199 0.685097 ATGCTCGTTGGGTGTGTACT 59.315 50.000 0.00 0.00 0.00 2.73
199 200 1.997606 GTATGCTCGTTGGGTGTGTAC 59.002 52.381 0.00 0.00 0.00 2.90
200 201 1.619332 TGTATGCTCGTTGGGTGTGTA 59.381 47.619 0.00 0.00 0.00 2.90
201 202 0.394938 TGTATGCTCGTTGGGTGTGT 59.605 50.000 0.00 0.00 0.00 3.72
202 203 0.796312 GTGTATGCTCGTTGGGTGTG 59.204 55.000 0.00 0.00 0.00 3.82
203 204 0.394938 TGTGTATGCTCGTTGGGTGT 59.605 50.000 0.00 0.00 0.00 4.16
204 205 1.737838 ATGTGTATGCTCGTTGGGTG 58.262 50.000 0.00 0.00 0.00 4.61
205 206 3.838244 ATATGTGTATGCTCGTTGGGT 57.162 42.857 0.00 0.00 0.00 4.51
206 207 4.627058 TGTATATGTGTATGCTCGTTGGG 58.373 43.478 0.00 0.00 0.00 4.12
207 208 6.597262 TTTGTATATGTGTATGCTCGTTGG 57.403 37.500 0.00 0.00 0.00 3.77
208 209 9.502145 AAATTTTGTATATGTGTATGCTCGTTG 57.498 29.630 0.00 0.00 0.00 4.10
330 331 5.796935 CGTGGTTTAAATTCAGATGCTCAAG 59.203 40.000 0.00 0.00 0.00 3.02
353 354 7.412063 TGAATGATGCTCTGTTGAAATATTCG 58.588 34.615 0.00 0.00 0.00 3.34
354 355 9.577110 TTTGAATGATGCTCTGTTGAAATATTC 57.423 29.630 0.00 0.00 0.00 1.75
357 358 7.031372 GCTTTGAATGATGCTCTGTTGAAATA 58.969 34.615 0.00 0.00 0.00 1.40
364 365 3.151554 TGTGCTTTGAATGATGCTCTGT 58.848 40.909 0.00 0.00 0.00 3.41
372 373 5.699001 ACACGTACTAATGTGCTTTGAATGA 59.301 36.000 0.00 0.00 45.01 2.57
374 375 7.601130 TCTTACACGTACTAATGTGCTTTGAAT 59.399 33.333 0.00 0.00 45.01 2.57
382 383 7.007697 GTGCTTTTCTTACACGTACTAATGTG 58.992 38.462 0.00 1.65 46.30 3.21
443 484 7.926018 TCCTTTTCAACCTCTTTATCTTTTTGC 59.074 33.333 0.00 0.00 0.00 3.68
460 501 7.790314 TCCCCCTTTTTATTAGTTCCTTTTCAA 59.210 33.333 0.00 0.00 0.00 2.69
468 509 7.201794 CGAGGATTTCCCCCTTTTTATTAGTTC 60.202 40.741 0.00 0.00 36.42 3.01
498 539 5.803020 ATTTCTATGGTCACTCGCTTTTC 57.197 39.130 0.00 0.00 0.00 2.29
504 546 3.873910 ACCCAATTTCTATGGTCACTCG 58.126 45.455 0.00 0.00 36.14 4.18
523 565 1.308783 GCTTGCTGGTCTAGGCAACC 61.309 60.000 0.00 0.00 42.45 3.77
525 567 0.110295 TTGCTTGCTGGTCTAGGCAA 59.890 50.000 0.00 0.02 44.64 4.52
1380 1424 3.112075 CGCGCGGTCACTGTGAAT 61.112 61.111 24.84 0.00 0.00 2.57
1978 2024 3.261643 TGGATGAGAGTAGCAAGCAAAGA 59.738 43.478 0.00 0.00 0.00 2.52
1982 2028 2.103771 GGATGGATGAGAGTAGCAAGCA 59.896 50.000 0.00 0.00 0.00 3.91
1983 2029 2.368221 AGGATGGATGAGAGTAGCAAGC 59.632 50.000 0.00 0.00 0.00 4.01
1998 2044 3.318839 TGCTTGTGACAAAGAAAGGATGG 59.681 43.478 0.00 0.00 0.00 3.51
2026 2072 3.190323 TACGCGGCATACTCGGCTC 62.190 63.158 12.47 0.00 0.00 4.70
2036 2082 1.199327 GTAGCATAGATCTACGCGGCA 59.801 52.381 14.63 2.36 28.47 5.69
2039 2085 3.815337 ACTGTAGCATAGATCTACGCG 57.185 47.619 14.63 3.53 39.30 6.01
2042 2088 4.039245 TGCCCAACTGTAGCATAGATCTAC 59.961 45.833 4.10 0.00 37.50 2.59
2060 2118 2.423185 CGTTCTTGCAGAATTATGCCCA 59.577 45.455 21.56 8.09 45.91 5.36
2080 2138 3.119352 GGTGTGGTTAACTAGTACTCCCG 60.119 52.174 0.00 0.00 0.00 5.14
2083 2141 5.010415 ACTGTGGTGTGGTTAACTAGTACTC 59.990 44.000 0.00 1.95 0.00 2.59
2085 2151 4.986659 CACTGTGGTGTGGTTAACTAGTAC 59.013 45.833 5.42 1.94 38.54 2.73
2134 2200 0.522180 CTCGCGTACTGGAGTTCACT 59.478 55.000 5.77 0.00 0.00 3.41
2142 2208 4.554363 CCCTCGCTCGCGTACTGG 62.554 72.222 5.77 9.19 40.74 4.00
2143 2209 2.337749 AATCCCTCGCTCGCGTACTG 62.338 60.000 5.77 0.00 40.74 2.74
2144 2210 2.061182 GAATCCCTCGCTCGCGTACT 62.061 60.000 5.77 0.00 40.74 2.73
2145 2211 1.657794 GAATCCCTCGCTCGCGTAC 60.658 63.158 5.77 0.00 40.74 3.67
2146 2212 2.719979 GAATCCCTCGCTCGCGTA 59.280 61.111 5.77 0.00 40.74 4.42
2147 2213 4.554363 CGAATCCCTCGCTCGCGT 62.554 66.667 5.77 0.00 41.49 6.01
2237 2306 1.834263 AGGAGAGATTGAGGAAACGGG 59.166 52.381 0.00 0.00 0.00 5.28
2256 2325 2.126882 TGAGAGGAGAGGAGAGGAGAG 58.873 57.143 0.00 0.00 0.00 3.20
2266 2335 2.206536 GCCCCGGATGAGAGGAGAG 61.207 68.421 0.73 0.00 0.00 3.20
2340 2422 3.141398 CCACAGTTCACTACATGCTGTT 58.859 45.455 0.00 0.00 38.21 3.16
2391 2479 0.457509 CACGCACAAAACCAACAGCA 60.458 50.000 0.00 0.00 0.00 4.41
2392 2480 1.145162 CCACGCACAAAACCAACAGC 61.145 55.000 0.00 0.00 0.00 4.40
2393 2481 1.145162 GCCACGCACAAAACCAACAG 61.145 55.000 0.00 0.00 0.00 3.16
2394 2482 1.153745 GCCACGCACAAAACCAACA 60.154 52.632 0.00 0.00 0.00 3.33
2395 2483 2.227568 CGCCACGCACAAAACCAAC 61.228 57.895 0.00 0.00 0.00 3.77
2396 2484 2.103143 CGCCACGCACAAAACCAA 59.897 55.556 0.00 0.00 0.00 3.67
2398 2486 2.051345 CTCGCCACGCACAAAACC 60.051 61.111 0.00 0.00 0.00 3.27
2400 2488 3.959975 GCCTCGCCACGCACAAAA 61.960 61.111 0.00 0.00 0.00 2.44
2438 2535 2.360801 CGTTTCTCTCTCCCTCATCCTC 59.639 54.545 0.00 0.00 0.00 3.71
2458 2555 2.176055 CGAGAGTGACGTCCACCG 59.824 66.667 14.12 5.86 46.87 4.94
2515 2613 2.244252 TCACTTAGGACTAGGAGACCCC 59.756 54.545 0.00 0.00 30.10 4.95
2516 2614 3.666345 TCACTTAGGACTAGGAGACCC 57.334 52.381 0.00 0.00 30.10 4.46
2517 2615 4.342359 TGTTCACTTAGGACTAGGAGACC 58.658 47.826 0.00 0.00 0.00 3.85
2518 2616 5.011586 ACTGTTCACTTAGGACTAGGAGAC 58.988 45.833 0.00 0.00 0.00 3.36
2519 2617 5.010933 CACTGTTCACTTAGGACTAGGAGA 58.989 45.833 0.00 0.00 0.00 3.71
2667 2837 1.300931 CACCTCACGTGGTCCACTG 60.301 63.158 19.82 15.73 38.45 3.66
2668 2838 3.138625 CACCTCACGTGGTCCACT 58.861 61.111 19.82 4.41 38.45 4.00
2676 2846 0.603707 CCAGCATTCACACCTCACGT 60.604 55.000 0.00 0.00 0.00 4.49
2677 2847 1.300971 CCCAGCATTCACACCTCACG 61.301 60.000 0.00 0.00 0.00 4.35
2678 2848 0.250901 ACCCAGCATTCACACCTCAC 60.251 55.000 0.00 0.00 0.00 3.51
2679 2849 1.003118 GTACCCAGCATTCACACCTCA 59.997 52.381 0.00 0.00 0.00 3.86
2680 2850 1.739067 GTACCCAGCATTCACACCTC 58.261 55.000 0.00 0.00 0.00 3.85
2681 2851 0.036388 CGTACCCAGCATTCACACCT 60.036 55.000 0.00 0.00 0.00 4.00
2682 2852 1.644786 GCGTACCCAGCATTCACACC 61.645 60.000 0.00 0.00 34.19 4.16
2683 2853 1.794222 GCGTACCCAGCATTCACAC 59.206 57.895 0.00 0.00 34.19 3.82
2684 2854 1.739929 CGCGTACCCAGCATTCACA 60.740 57.895 0.00 0.00 34.19 3.58
2685 2855 1.447140 TCGCGTACCCAGCATTCAC 60.447 57.895 5.77 0.00 34.19 3.18
2686 2856 1.447140 GTCGCGTACCCAGCATTCA 60.447 57.895 5.77 0.00 34.19 2.57
2687 2857 2.171725 GGTCGCGTACCCAGCATTC 61.172 63.158 5.77 0.00 43.16 2.67
2688 2858 2.125269 GGTCGCGTACCCAGCATT 60.125 61.111 5.77 0.00 43.16 3.56
2701 2871 2.517450 GCAAATCTCGGCGAGGTCG 61.517 63.158 33.93 23.15 43.27 4.79
2702 2872 0.102481 TAGCAAATCTCGGCGAGGTC 59.898 55.000 33.93 17.37 34.54 3.85
2703 2873 0.535335 TTAGCAAATCTCGGCGAGGT 59.465 50.000 33.93 27.25 34.54 3.85
2704 2874 1.212616 CTTAGCAAATCTCGGCGAGG 58.787 55.000 33.93 20.09 34.54 4.63
2705 2875 0.579156 GCTTAGCAAATCTCGGCGAG 59.421 55.000 30.10 30.10 34.54 5.03
2706 2876 1.145759 CGCTTAGCAAATCTCGGCGA 61.146 55.000 10.14 10.14 43.50 5.54
2707 2877 1.273887 CGCTTAGCAAATCTCGGCG 59.726 57.895 4.70 0.00 38.66 6.46
2718 2888 2.353435 GCGACTCATGTGCGCTTAGC 62.353 60.000 21.06 0.00 46.53 3.09
2719 2889 1.633171 GCGACTCATGTGCGCTTAG 59.367 57.895 21.06 1.06 46.53 2.18
2720 2890 3.780693 GCGACTCATGTGCGCTTA 58.219 55.556 21.06 0.00 46.53 3.09
2724 2894 1.555066 CGTATGCGACTCATGTGCG 59.445 57.895 0.00 0.00 41.33 5.34
2725 2895 1.273887 GCGTATGCGACTCATGTGC 59.726 57.895 7.60 0.00 41.33 4.57
2747 2917 5.466728 ACAGATGATTATGTGACCGTTATGC 59.533 40.000 1.31 0.00 32.28 3.14
2817 2987 0.933097 CTGCACACGCCTATGATCAC 59.067 55.000 0.00 0.00 37.32 3.06
2828 2998 4.409218 GCACATGCCCTGCACACG 62.409 66.667 2.12 0.00 43.04 4.49
2831 3001 1.675310 TACTGCACATGCCCTGCAC 60.675 57.895 5.43 0.00 43.04 4.57


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

AutoCloner maintained by Alex Coulton.