Multiple sequence alignment - TraesCS7D01G038400

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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 TraesCS7D01G038400 chr7D 100.000 3698 0 0 1 3698 19555615 19559312 0.000000e+00 6830.0
1 TraesCS7D01G038400 chr7D 81.525 341 57 6 11 348 577929492 577929829 3.640000e-70 276.0
2 TraesCS7D01G038400 chr7D 78.834 326 63 5 25 348 531618169 531618490 8.040000e-52 215.0
3 TraesCS7D01G038400 chr7D 95.652 115 5 0 369 483 19559965 19559851 6.310000e-43 185.0
4 TraesCS7D01G038400 chr5D 98.151 2380 33 5 371 2749 532746000 532748369 0.000000e+00 4141.0
5 TraesCS7D01G038400 chr5D 94.005 417 16 6 2747 3163 532749543 532749950 1.130000e-174 623.0
6 TraesCS7D01G038400 chr5D 98.765 324 4 0 3159 3482 532749978 532750301 8.910000e-161 577.0
7 TraesCS7D01G038400 chr5D 99.539 217 1 0 3482 3698 532753894 532754110 2.680000e-106 396.0
8 TraesCS7D01G038400 chr5D 94.828 116 6 0 368 483 532754773 532754658 8.160000e-42 182.0
9 TraesCS7D01G038400 chr1B 86.598 2328 255 33 367 2688 420605857 420603581 0.000000e+00 2518.0
10 TraesCS7D01G038400 chr1B 92.208 77 6 0 2748 2824 420602059 420601983 3.900000e-20 110.0
11 TraesCS7D01G038400 chr1B 95.082 61 3 0 2685 2745 420603480 420603420 3.040000e-16 97.1
12 TraesCS7D01G038400 chr2A 85.684 950 134 1 1739 2688 762297659 762296712 0.000000e+00 1000.0
13 TraesCS7D01G038400 chr7B 85.158 950 141 0 1739 2688 571592455 571593404 0.000000e+00 974.0
14 TraesCS7D01G038400 chr7B 85.600 125 15 1 2747 2868 571594778 571594902 1.080000e-25 128.0
15 TraesCS7D01G038400 chr4A 85.158 950 141 0 1739 2688 690105345 690104396 0.000000e+00 974.0
16 TraesCS7D01G038400 chr4A 80.511 313 57 3 4 315 571712315 571712624 1.720000e-58 237.0
17 TraesCS7D01G038400 chr4A 86.400 125 14 1 2747 2868 690103022 690102898 2.320000e-27 134.0
18 TraesCS7D01G038400 chr3B 85.158 950 141 0 1739 2688 52926035 52926984 0.000000e+00 974.0
19 TraesCS7D01G038400 chr3B 95.798 119 5 0 2906 3024 667390120 667390002 3.770000e-45 193.0
20 TraesCS7D01G038400 chr3B 93.600 125 6 2 2900 3023 111679640 111679763 6.310000e-43 185.0
21 TraesCS7D01G038400 chr6A 85.053 950 142 0 1739 2688 584919620 584920569 0.000000e+00 968.0
22 TraesCS7D01G038400 chr6A 77.119 354 60 14 1 348 553008008 553008346 6.310000e-43 185.0
23 TraesCS7D01G038400 chr6A 85.600 125 15 1 2747 2868 584921943 584922067 1.080000e-25 128.0
24 TraesCS7D01G038400 chr6D 84.227 951 148 2 1739 2688 469086171 469085222 0.000000e+00 924.0
25 TraesCS7D01G038400 chr6B 83.912 951 151 2 1739 2688 63422641 63421692 0.000000e+00 907.0
26 TraesCS7D01G038400 chr2D 79.888 358 61 6 1 349 615125819 615126174 6.130000e-63 252.0
27 TraesCS7D01G038400 chr2D 78.413 315 58 7 35 348 49036158 49035853 2.910000e-46 196.0
28 TraesCS7D01G038400 chr2D 81.034 116 19 1 2756 2868 643472698 643472583 5.090000e-14 89.8
29 TraesCS7D01G038400 chr5B 80.702 285 46 7 1 281 335810762 335811041 2.890000e-51 213.0
30 TraesCS7D01G038400 chr5B 94.615 130 7 0 2894 3023 614065032 614065161 6.260000e-48 202.0
31 TraesCS7D01G038400 chr2B 96.667 120 3 1 2904 3023 47744739 47744621 8.100000e-47 198.0
32 TraesCS7D01G038400 chr2B 96.667 120 3 1 2904 3023 47774425 47774307 8.100000e-47 198.0
33 TraesCS7D01G038400 chr2B 95.833 120 4 1 2904 3023 47816392 47816274 3.770000e-45 193.0
34 TraesCS7D01G038400 chr2B 95.041 121 6 0 2903 3023 653603259 653603139 1.360000e-44 191.0
35 TraesCS7D01G038400 chr4B 96.581 117 4 0 2907 3023 171613923 171613807 1.050000e-45 195.0
36 TraesCS7D01G038400 chr5A 77.299 348 63 10 4 348 454394775 454395109 1.360000e-44 191.0
37 TraesCS7D01G038400 chr4D 76.676 343 62 10 4 343 7998107 7997780 1.370000e-39 174.0


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 TraesCS7D01G038400 chr7D 19555615 19559312 3697 False 6830.000000 6830 100.0000 1 3698 1 chr7D.!!$F1 3697
1 TraesCS7D01G038400 chr5D 532746000 532754110 8110 False 1434.250000 4141 97.6150 371 3698 4 chr5D.!!$F1 3327
2 TraesCS7D01G038400 chr1B 420601983 420605857 3874 True 908.366667 2518 91.2960 367 2824 3 chr1B.!!$R1 2457
3 TraesCS7D01G038400 chr2A 762296712 762297659 947 True 1000.000000 1000 85.6840 1739 2688 1 chr2A.!!$R1 949
4 TraesCS7D01G038400 chr7B 571592455 571594902 2447 False 551.000000 974 85.3790 1739 2868 2 chr7B.!!$F1 1129
5 TraesCS7D01G038400 chr4A 690102898 690105345 2447 True 554.000000 974 85.7790 1739 2868 2 chr4A.!!$R1 1129
6 TraesCS7D01G038400 chr3B 52926035 52926984 949 False 974.000000 974 85.1580 1739 2688 1 chr3B.!!$F1 949
7 TraesCS7D01G038400 chr6A 584919620 584922067 2447 False 548.000000 968 85.3265 1739 2868 2 chr6A.!!$F2 1129
8 TraesCS7D01G038400 chr6D 469085222 469086171 949 True 924.000000 924 84.2270 1739 2688 1 chr6D.!!$R1 949
9 TraesCS7D01G038400 chr6B 63421692 63422641 949 True 907.000000 907 83.9120 1739 2688 1 chr6B.!!$R1 949

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
98 99 0.037232 GTCATCCCTATACGCCCAGC 60.037 60.000 0.00 0.0 0.0 4.85 F
151 152 0.252012 AGGGAGGATATGAGGGCTCG 60.252 60.000 0.00 0.0 0.0 5.03 F
203 204 0.460284 CATGTAGGACGTGGCCTCAC 60.460 60.000 3.32 0.0 39.5 3.51 F
217 218 0.843984 CCTCACCCGGGACCATATTT 59.156 55.000 32.02 0.0 0.0 1.40 F
218 219 1.214424 CCTCACCCGGGACCATATTTT 59.786 52.381 32.02 0.0 0.0 1.82 F
629 630 2.025416 CCTTCTCTCCTGTCTCTCTCCA 60.025 54.545 0.00 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1370 1376 1.548269 CACTGTCTCCCTCTTCCTCAC 59.452 57.143 0.00 0.0 0.00 3.51 R
2141 2149 1.638529 AGCCCTGATCCTATCTTCGG 58.361 55.000 0.00 0.0 0.00 4.30 R
2294 2302 6.538742 GTGCTCATACTTTCTTGCTATAACCA 59.461 38.462 0.00 0.0 0.00 3.67 R
2309 2317 5.867903 AGCTCTTAAGATGTGCTCATACT 57.132 39.130 10.97 0.0 34.06 2.12 R
2694 2806 1.681166 CCCAGCCTTCACCTTGATCAG 60.681 57.143 0.00 0.0 0.00 2.90 R
3053 4557 4.407945 ACCACCAGTTCTGTTGTACTACTT 59.592 41.667 8.88 0.0 0.00 2.24 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 3.520862 TCCCATACGTCCGCGGAC 61.521 66.667 41.75 41.75 43.45 4.79
27 28 4.657824 CCGCGGACGTGTCTGGTT 62.658 66.667 24.07 0.00 37.70 3.67
28 29 2.256158 CGCGGACGTGTCTGGTTA 59.744 61.111 10.64 0.00 36.50 2.85
29 30 1.800315 CGCGGACGTGTCTGGTTAG 60.800 63.158 10.64 0.00 36.50 2.34
30 31 1.288127 GCGGACGTGTCTGGTTAGT 59.712 57.895 10.64 0.00 36.50 2.24
31 32 0.523072 GCGGACGTGTCTGGTTAGTA 59.477 55.000 10.64 0.00 36.50 1.82
32 33 1.068333 GCGGACGTGTCTGGTTAGTAA 60.068 52.381 10.64 0.00 36.50 2.24
33 34 2.589014 CGGACGTGTCTGGTTAGTAAC 58.411 52.381 4.32 4.32 32.43 2.50
43 44 2.955477 GGTTAGTAACCGGACAGGAG 57.045 55.000 16.22 0.00 45.00 3.69
44 45 2.450476 GGTTAGTAACCGGACAGGAGA 58.550 52.381 16.22 0.00 45.00 3.71
45 46 3.029570 GGTTAGTAACCGGACAGGAGAT 58.970 50.000 16.22 0.00 45.00 2.75
46 47 4.210331 GGTTAGTAACCGGACAGGAGATA 58.790 47.826 16.22 0.00 45.00 1.98
47 48 4.646492 GGTTAGTAACCGGACAGGAGATAA 59.354 45.833 16.22 0.00 45.00 1.75
48 49 5.127682 GGTTAGTAACCGGACAGGAGATAAA 59.872 44.000 16.22 0.00 45.00 1.40
49 50 6.351286 GGTTAGTAACCGGACAGGAGATAAAA 60.351 42.308 16.22 0.00 45.00 1.52
50 51 5.750352 AGTAACCGGACAGGAGATAAAAA 57.250 39.130 9.46 0.00 45.00 1.94
73 74 3.382083 AAATGTGACCCTATTGGACCC 57.618 47.619 0.00 0.00 38.00 4.46
74 75 1.222567 ATGTGACCCTATTGGACCCC 58.777 55.000 0.00 0.00 38.00 4.95
75 76 0.120377 TGTGACCCTATTGGACCCCT 59.880 55.000 0.00 0.00 38.00 4.79
76 77 1.296002 GTGACCCTATTGGACCCCTT 58.704 55.000 0.00 0.00 38.00 3.95
77 78 2.225934 TGTGACCCTATTGGACCCCTTA 60.226 50.000 0.00 0.00 38.00 2.69
78 79 3.053826 GTGACCCTATTGGACCCCTTAT 58.946 50.000 0.00 0.00 38.00 1.73
79 80 3.053077 TGACCCTATTGGACCCCTTATG 58.947 50.000 0.00 0.00 38.00 1.90
80 81 3.053826 GACCCTATTGGACCCCTTATGT 58.946 50.000 0.00 0.00 38.00 2.29
81 82 3.053826 ACCCTATTGGACCCCTTATGTC 58.946 50.000 0.00 0.00 38.00 3.06
82 83 3.053077 CCCTATTGGACCCCTTATGTCA 58.947 50.000 0.00 0.00 35.39 3.58
83 84 3.657727 CCCTATTGGACCCCTTATGTCAT 59.342 47.826 0.00 0.00 35.39 3.06
84 85 4.263506 CCCTATTGGACCCCTTATGTCATC 60.264 50.000 0.00 0.00 35.39 2.92
85 86 3.884037 ATTGGACCCCTTATGTCATCC 57.116 47.619 0.00 0.00 34.36 3.51
86 87 1.518367 TGGACCCCTTATGTCATCCC 58.482 55.000 0.00 0.00 34.36 3.85
87 88 1.010793 TGGACCCCTTATGTCATCCCT 59.989 52.381 0.00 0.00 34.36 4.20
88 89 2.251605 TGGACCCCTTATGTCATCCCTA 59.748 50.000 0.00 0.00 34.36 3.53
89 90 3.115962 TGGACCCCTTATGTCATCCCTAT 60.116 47.826 0.00 0.00 34.36 2.57
90 91 4.110592 TGGACCCCTTATGTCATCCCTATA 59.889 45.833 0.00 0.00 34.36 1.31
91 92 4.470304 GGACCCCTTATGTCATCCCTATAC 59.530 50.000 0.00 0.00 34.36 1.47
92 93 4.094476 ACCCCTTATGTCATCCCTATACG 58.906 47.826 0.00 0.00 0.00 3.06
93 94 3.118738 CCCCTTATGTCATCCCTATACGC 60.119 52.174 0.00 0.00 0.00 4.42
94 95 3.118738 CCCTTATGTCATCCCTATACGCC 60.119 52.174 0.00 0.00 0.00 5.68
95 96 3.118738 CCTTATGTCATCCCTATACGCCC 60.119 52.174 0.00 0.00 0.00 6.13
96 97 2.024176 ATGTCATCCCTATACGCCCA 57.976 50.000 0.00 0.00 0.00 5.36
97 98 1.338107 TGTCATCCCTATACGCCCAG 58.662 55.000 0.00 0.00 0.00 4.45
98 99 0.037232 GTCATCCCTATACGCCCAGC 60.037 60.000 0.00 0.00 0.00 4.85
99 100 1.192146 TCATCCCTATACGCCCAGCC 61.192 60.000 0.00 0.00 0.00 4.85
100 101 1.158705 ATCCCTATACGCCCAGCCT 59.841 57.895 0.00 0.00 0.00 4.58
101 102 1.194781 ATCCCTATACGCCCAGCCTG 61.195 60.000 0.00 0.00 0.00 4.85
102 103 2.140792 CCCTATACGCCCAGCCTGT 61.141 63.158 0.00 0.00 0.00 4.00
103 104 1.367840 CCTATACGCCCAGCCTGTC 59.632 63.158 0.00 0.00 0.00 3.51
104 105 1.367840 CTATACGCCCAGCCTGTCC 59.632 63.158 0.00 0.00 0.00 4.02
105 106 2.421877 CTATACGCCCAGCCTGTCCG 62.422 65.000 0.00 0.00 0.00 4.79
115 116 3.691342 CCTGTCCGCGAACCCTCA 61.691 66.667 8.23 0.00 0.00 3.86
116 117 2.579201 CTGTCCGCGAACCCTCAT 59.421 61.111 8.23 0.00 0.00 2.90
117 118 1.672854 CCTGTCCGCGAACCCTCATA 61.673 60.000 8.23 0.00 0.00 2.15
118 119 0.389391 CTGTCCGCGAACCCTCATAT 59.611 55.000 8.23 0.00 0.00 1.78
119 120 0.387929 TGTCCGCGAACCCTCATATC 59.612 55.000 8.23 0.00 0.00 1.63
120 121 0.319641 GTCCGCGAACCCTCATATCC 60.320 60.000 8.23 0.00 0.00 2.59
121 122 0.757561 TCCGCGAACCCTCATATCCA 60.758 55.000 8.23 0.00 0.00 3.41
122 123 0.321671 CCGCGAACCCTCATATCCAT 59.678 55.000 8.23 0.00 0.00 3.41
123 124 1.673033 CCGCGAACCCTCATATCCATC 60.673 57.143 8.23 0.00 0.00 3.51
124 125 1.273606 CGCGAACCCTCATATCCATCT 59.726 52.381 0.00 0.00 0.00 2.90
125 126 2.672478 CGCGAACCCTCATATCCATCTC 60.672 54.545 0.00 0.00 0.00 2.75
126 127 2.672478 GCGAACCCTCATATCCATCTCG 60.672 54.545 0.00 0.00 0.00 4.04
127 128 2.820197 CGAACCCTCATATCCATCTCGA 59.180 50.000 0.00 0.00 0.00 4.04
128 129 3.255888 CGAACCCTCATATCCATCTCGAA 59.744 47.826 0.00 0.00 0.00 3.71
129 130 4.081972 CGAACCCTCATATCCATCTCGAAT 60.082 45.833 0.00 0.00 0.00 3.34
130 131 4.815533 ACCCTCATATCCATCTCGAATG 57.184 45.455 0.00 0.00 0.00 2.67
131 132 4.163427 ACCCTCATATCCATCTCGAATGT 58.837 43.478 6.77 0.00 0.00 2.71
132 133 5.333581 ACCCTCATATCCATCTCGAATGTA 58.666 41.667 6.77 0.00 0.00 2.29
133 134 5.420421 ACCCTCATATCCATCTCGAATGTAG 59.580 44.000 6.77 0.00 0.00 2.74
134 135 5.163468 CCCTCATATCCATCTCGAATGTAGG 60.163 48.000 6.77 0.00 0.00 3.18
135 136 5.163468 CCTCATATCCATCTCGAATGTAGGG 60.163 48.000 6.77 0.00 0.00 3.53
136 137 5.580022 TCATATCCATCTCGAATGTAGGGA 58.420 41.667 6.77 0.00 0.00 4.20
137 138 5.654209 TCATATCCATCTCGAATGTAGGGAG 59.346 44.000 6.77 0.00 0.00 4.30
138 139 2.598565 TCCATCTCGAATGTAGGGAGG 58.401 52.381 6.77 0.00 0.00 4.30
139 140 2.177016 TCCATCTCGAATGTAGGGAGGA 59.823 50.000 6.77 0.00 0.00 3.71
140 141 3.169099 CCATCTCGAATGTAGGGAGGAT 58.831 50.000 6.77 0.00 0.00 3.24
141 142 4.044191 TCCATCTCGAATGTAGGGAGGATA 59.956 45.833 6.77 0.00 0.00 2.59
142 143 4.959210 CCATCTCGAATGTAGGGAGGATAT 59.041 45.833 6.77 0.00 0.00 1.63
143 144 5.163468 CCATCTCGAATGTAGGGAGGATATG 60.163 48.000 6.77 0.00 0.00 1.78
144 145 5.256806 TCTCGAATGTAGGGAGGATATGA 57.743 43.478 0.00 0.00 0.00 2.15
145 146 5.257262 TCTCGAATGTAGGGAGGATATGAG 58.743 45.833 0.00 0.00 0.00 2.90
146 147 4.344978 TCGAATGTAGGGAGGATATGAGG 58.655 47.826 0.00 0.00 0.00 3.86
147 148 3.449018 CGAATGTAGGGAGGATATGAGGG 59.551 52.174 0.00 0.00 0.00 4.30
148 149 2.327325 TGTAGGGAGGATATGAGGGC 57.673 55.000 0.00 0.00 0.00 5.19
149 150 1.795786 TGTAGGGAGGATATGAGGGCT 59.204 52.381 0.00 0.00 0.00 5.19
150 151 2.225394 TGTAGGGAGGATATGAGGGCTC 60.225 54.545 0.00 0.00 0.00 4.70
151 152 0.252012 AGGGAGGATATGAGGGCTCG 60.252 60.000 0.00 0.00 0.00 5.03
152 153 1.594310 GGAGGATATGAGGGCTCGC 59.406 63.158 0.00 0.00 0.00 5.03
153 154 1.214062 GAGGATATGAGGGCTCGCG 59.786 63.158 0.00 0.00 0.00 5.87
154 155 2.219325 GAGGATATGAGGGCTCGCGG 62.219 65.000 6.13 0.00 0.00 6.46
155 156 2.276116 GGATATGAGGGCTCGCGGA 61.276 63.158 6.13 0.00 0.00 5.54
156 157 1.080434 GATATGAGGGCTCGCGGAC 60.080 63.158 6.13 0.00 0.00 4.79
157 158 2.804368 GATATGAGGGCTCGCGGACG 62.804 65.000 6.13 0.00 42.01 4.79
193 194 3.071580 GCAGTCTGCCATGTAGGAC 57.928 57.895 14.27 0.00 41.22 3.85
194 195 0.807667 GCAGTCTGCCATGTAGGACG 60.808 60.000 14.27 0.00 41.22 4.79
195 196 0.532573 CAGTCTGCCATGTAGGACGT 59.467 55.000 0.00 0.00 41.22 4.34
196 197 0.532573 AGTCTGCCATGTAGGACGTG 59.467 55.000 0.00 0.00 41.22 4.49
201 202 4.835927 CATGTAGGACGTGGCCTC 57.164 61.111 3.32 0.00 39.50 4.70
202 203 1.897423 CATGTAGGACGTGGCCTCA 59.103 57.895 3.32 0.00 39.50 3.86
203 204 0.460284 CATGTAGGACGTGGCCTCAC 60.460 60.000 3.32 0.00 39.50 3.51
204 205 1.614241 ATGTAGGACGTGGCCTCACC 61.614 60.000 3.32 7.12 40.65 4.02
205 206 2.682494 TAGGACGTGGCCTCACCC 60.682 66.667 3.32 4.21 40.65 4.61
214 215 2.766651 GCCTCACCCGGGACCATA 60.767 66.667 32.02 6.14 0.00 2.74
215 216 2.147387 GCCTCACCCGGGACCATAT 61.147 63.158 32.02 0.00 0.00 1.78
216 217 1.705997 GCCTCACCCGGGACCATATT 61.706 60.000 32.02 0.00 0.00 1.28
217 218 0.843984 CCTCACCCGGGACCATATTT 59.156 55.000 32.02 0.00 0.00 1.40
218 219 1.214424 CCTCACCCGGGACCATATTTT 59.786 52.381 32.02 0.00 0.00 1.82
219 220 2.572290 CTCACCCGGGACCATATTTTC 58.428 52.381 32.02 0.00 0.00 2.29
220 221 2.172717 CTCACCCGGGACCATATTTTCT 59.827 50.000 32.02 0.00 0.00 2.52
221 222 2.171870 TCACCCGGGACCATATTTTCTC 59.828 50.000 32.02 0.00 0.00 2.87
222 223 2.172717 CACCCGGGACCATATTTTCTCT 59.827 50.000 32.02 0.00 0.00 3.10
223 224 2.850568 ACCCGGGACCATATTTTCTCTT 59.149 45.455 32.02 0.00 0.00 2.85
224 225 3.268595 ACCCGGGACCATATTTTCTCTTT 59.731 43.478 32.02 0.00 0.00 2.52
225 226 3.883489 CCCGGGACCATATTTTCTCTTTC 59.117 47.826 18.48 0.00 0.00 2.62
226 227 4.385310 CCCGGGACCATATTTTCTCTTTCT 60.385 45.833 18.48 0.00 0.00 2.52
227 228 5.193679 CCGGGACCATATTTTCTCTTTCTT 58.806 41.667 0.00 0.00 0.00 2.52
228 229 5.652452 CCGGGACCATATTTTCTCTTTCTTT 59.348 40.000 0.00 0.00 0.00 2.52
229 230 6.826741 CCGGGACCATATTTTCTCTTTCTTTA 59.173 38.462 0.00 0.00 0.00 1.85
230 231 7.502561 CCGGGACCATATTTTCTCTTTCTTTAT 59.497 37.037 0.00 0.00 0.00 1.40
231 232 8.903820 CGGGACCATATTTTCTCTTTCTTTATT 58.096 33.333 0.00 0.00 0.00 1.40
277 278 5.821516 TTTTTCACCAATCACGTACAAGT 57.178 34.783 0.00 0.00 0.00 3.16
278 279 4.804608 TTTCACCAATCACGTACAAGTG 57.195 40.909 0.00 0.00 43.11 3.16
290 291 7.289587 TCACGTACAAGTGATCAAACATATG 57.710 36.000 0.00 0.00 45.18 1.78
291 292 7.093992 TCACGTACAAGTGATCAAACATATGA 58.906 34.615 10.38 0.00 45.18 2.15
292 293 7.275560 TCACGTACAAGTGATCAAACATATGAG 59.724 37.037 10.38 0.00 45.18 2.90
293 294 6.535150 ACGTACAAGTGATCAAACATATGAGG 59.465 38.462 10.38 0.00 31.76 3.86
294 295 6.756542 CGTACAAGTGATCAAACATATGAGGA 59.243 38.462 10.38 4.04 31.76 3.71
295 296 7.043125 CGTACAAGTGATCAAACATATGAGGAG 60.043 40.741 10.38 0.00 31.76 3.69
296 297 6.950842 ACAAGTGATCAAACATATGAGGAGA 58.049 36.000 10.38 2.24 31.76 3.71
297 298 7.397221 ACAAGTGATCAAACATATGAGGAGAA 58.603 34.615 10.38 0.00 31.76 2.87
298 299 7.884877 ACAAGTGATCAAACATATGAGGAGAAA 59.115 33.333 10.38 0.00 31.76 2.52
299 300 8.733458 CAAGTGATCAAACATATGAGGAGAAAA 58.267 33.333 10.38 0.00 31.76 2.29
300 301 8.868522 AGTGATCAAACATATGAGGAGAAAAA 57.131 30.769 10.38 0.00 31.76 1.94
301 302 9.471702 AGTGATCAAACATATGAGGAGAAAAAT 57.528 29.630 10.38 0.00 31.76 1.82
302 303 9.512435 GTGATCAAACATATGAGGAGAAAAATG 57.488 33.333 10.38 0.00 31.76 2.32
303 304 9.465199 TGATCAAACATATGAGGAGAAAAATGA 57.535 29.630 10.38 0.00 31.76 2.57
304 305 9.947669 GATCAAACATATGAGGAGAAAAATGAG 57.052 33.333 10.38 0.00 31.76 2.90
305 306 8.284945 TCAAACATATGAGGAGAAAAATGAGG 57.715 34.615 10.38 0.00 0.00 3.86
306 307 8.108999 TCAAACATATGAGGAGAAAAATGAGGA 58.891 33.333 10.38 0.00 0.00 3.71
307 308 8.742777 CAAACATATGAGGAGAAAAATGAGGAA 58.257 33.333 10.38 0.00 0.00 3.36
308 309 9.484806 AAACATATGAGGAGAAAAATGAGGAAT 57.515 29.630 10.38 0.00 0.00 3.01
309 310 8.461249 ACATATGAGGAGAAAAATGAGGAATG 57.539 34.615 10.38 0.00 0.00 2.67
310 311 8.057623 ACATATGAGGAGAAAAATGAGGAATGT 58.942 33.333 10.38 0.00 0.00 2.71
311 312 6.770746 ATGAGGAGAAAAATGAGGAATGTG 57.229 37.500 0.00 0.00 0.00 3.21
312 313 5.012239 TGAGGAGAAAAATGAGGAATGTGG 58.988 41.667 0.00 0.00 0.00 4.17
313 314 5.003096 AGGAGAAAAATGAGGAATGTGGT 57.997 39.130 0.00 0.00 0.00 4.16
314 315 5.397360 AGGAGAAAAATGAGGAATGTGGTT 58.603 37.500 0.00 0.00 0.00 3.67
315 316 6.552008 AGGAGAAAAATGAGGAATGTGGTTA 58.448 36.000 0.00 0.00 0.00 2.85
316 317 7.184862 AGGAGAAAAATGAGGAATGTGGTTAT 58.815 34.615 0.00 0.00 0.00 1.89
317 318 7.123247 AGGAGAAAAATGAGGAATGTGGTTATG 59.877 37.037 0.00 0.00 0.00 1.90
318 319 7.093771 GGAGAAAAATGAGGAATGTGGTTATGT 60.094 37.037 0.00 0.00 0.00 2.29
319 320 7.605449 AGAAAAATGAGGAATGTGGTTATGTG 58.395 34.615 0.00 0.00 0.00 3.21
320 321 5.920193 AAATGAGGAATGTGGTTATGTGG 57.080 39.130 0.00 0.00 0.00 4.17
321 322 4.860802 ATGAGGAATGTGGTTATGTGGA 57.139 40.909 0.00 0.00 0.00 4.02
322 323 4.649267 TGAGGAATGTGGTTATGTGGAA 57.351 40.909 0.00 0.00 0.00 3.53
323 324 4.588899 TGAGGAATGTGGTTATGTGGAAG 58.411 43.478 0.00 0.00 0.00 3.46
324 325 4.288366 TGAGGAATGTGGTTATGTGGAAGA 59.712 41.667 0.00 0.00 0.00 2.87
325 326 5.222027 TGAGGAATGTGGTTATGTGGAAGAA 60.222 40.000 0.00 0.00 0.00 2.52
326 327 5.010282 AGGAATGTGGTTATGTGGAAGAAC 58.990 41.667 0.00 0.00 0.00 3.01
327 328 4.764823 GGAATGTGGTTATGTGGAAGAACA 59.235 41.667 0.00 0.00 0.00 3.18
328 329 5.242838 GGAATGTGGTTATGTGGAAGAACAA 59.757 40.000 0.00 0.00 32.81 2.83
329 330 6.239176 GGAATGTGGTTATGTGGAAGAACAAA 60.239 38.462 0.00 0.00 32.81 2.83
330 331 6.916360 ATGTGGTTATGTGGAAGAACAAAT 57.084 33.333 0.00 0.00 32.81 2.32
331 332 8.415950 AATGTGGTTATGTGGAAGAACAAATA 57.584 30.769 0.00 0.00 32.81 1.40
332 333 7.447374 TGTGGTTATGTGGAAGAACAAATAG 57.553 36.000 0.00 0.00 32.81 1.73
333 334 6.432783 TGTGGTTATGTGGAAGAACAAATAGG 59.567 38.462 0.00 0.00 32.81 2.57
334 335 6.657541 GTGGTTATGTGGAAGAACAAATAGGA 59.342 38.462 0.00 0.00 32.81 2.94
335 336 6.884295 TGGTTATGTGGAAGAACAAATAGGAG 59.116 38.462 0.00 0.00 32.81 3.69
336 337 6.884836 GGTTATGTGGAAGAACAAATAGGAGT 59.115 38.462 0.00 0.00 32.81 3.85
337 338 7.393515 GGTTATGTGGAAGAACAAATAGGAGTT 59.606 37.037 0.00 0.00 32.81 3.01
338 339 8.793592 GTTATGTGGAAGAACAAATAGGAGTTT 58.206 33.333 0.00 0.00 32.81 2.66
340 341 8.934023 ATGTGGAAGAACAAATAGGAGTTTAA 57.066 30.769 0.00 0.00 32.81 1.52
341 342 8.754991 TGTGGAAGAACAAATAGGAGTTTAAA 57.245 30.769 0.00 0.00 0.00 1.52
342 343 9.191479 TGTGGAAGAACAAATAGGAGTTTAAAA 57.809 29.630 0.00 0.00 0.00 1.52
345 346 9.639601 GGAAGAACAAATAGGAGTTTAAAATGG 57.360 33.333 0.00 0.00 0.00 3.16
348 349 8.512138 AGAACAAATAGGAGTTTAAAATGGACG 58.488 33.333 0.00 0.00 0.00 4.79
349 350 7.754851 ACAAATAGGAGTTTAAAATGGACGT 57.245 32.000 0.00 0.00 0.00 4.34
350 351 8.173542 ACAAATAGGAGTTTAAAATGGACGTT 57.826 30.769 0.00 0.00 0.00 3.99
351 352 8.635328 ACAAATAGGAGTTTAAAATGGACGTTT 58.365 29.630 0.00 0.00 0.00 3.60
356 357 7.654568 AGGAGTTTAAAATGGACGTTTAAAGG 58.345 34.615 6.36 6.36 39.72 3.11
357 358 6.864685 GGAGTTTAAAATGGACGTTTAAAGGG 59.135 38.462 12.21 0.00 39.72 3.95
358 359 7.350744 AGTTTAAAATGGACGTTTAAAGGGT 57.649 32.000 12.21 2.45 39.72 4.34
359 360 7.428020 AGTTTAAAATGGACGTTTAAAGGGTC 58.572 34.615 12.21 10.86 39.72 4.46
368 369 7.870509 GGACGTTTAAAGGGTCCTATTTATT 57.129 36.000 22.44 0.00 45.34 1.40
369 370 8.962884 GGACGTTTAAAGGGTCCTATTTATTA 57.037 34.615 22.44 0.00 45.34 0.98
629 630 2.025416 CCTTCTCTCCTGTCTCTCTCCA 60.025 54.545 0.00 0.00 0.00 3.86
682 685 2.987821 GTCTCTTCAGTTTCAGGTACGC 59.012 50.000 0.00 0.00 0.00 4.42
1018 1024 2.437281 AGCATGGATCCGAGTGAGAAAT 59.563 45.455 7.39 0.00 0.00 2.17
1200 1206 5.371115 TGAAGCTTTATTTCTTGGTTCCG 57.629 39.130 0.00 0.00 36.47 4.30
1575 1581 5.360591 ACTTTTAGAGTTGAGTGTGGACAG 58.639 41.667 0.00 0.00 33.92 3.51
1712 1718 6.931840 GGAAGAGAAGAACATAACAGTGAGTT 59.068 38.462 0.00 0.00 44.27 3.01
2022 2030 3.556423 GCAAGTACCCCAGGTATAATCCG 60.556 52.174 0.00 0.00 40.54 4.18
2141 2149 7.441017 AGGAGTATAATCTTCATGAAGTCAGC 58.559 38.462 29.80 17.74 39.38 4.26
2294 2302 7.712639 CAGATACAATCACCTTGTTACTGCTAT 59.287 37.037 0.00 0.00 45.98 2.97
2694 2806 6.016777 AGCTGCTTTGTGCTATTGGATATTAC 60.017 38.462 0.00 0.00 43.37 1.89
2895 4399 5.510430 TCCTGATTGTCTACTGCTTCTCTA 58.490 41.667 0.00 0.00 0.00 2.43
2918 4422 5.764432 AGTCTAATTAGTACTCCCTCCGTT 58.236 41.667 12.19 0.00 0.00 4.44
2945 4449 8.620416 CGGAAATACTTGTCATTGAAATGGATA 58.380 33.333 3.31 0.00 37.03 2.59
3039 4543 8.429641 GGAGGGAGTATGTTAAATTAGATGTCA 58.570 37.037 0.00 0.00 0.00 3.58
3040 4544 9.482627 GAGGGAGTATGTTAAATTAGATGTCAG 57.517 37.037 0.00 0.00 0.00 3.51
3041 4545 8.993424 AGGGAGTATGTTAAATTAGATGTCAGT 58.007 33.333 0.00 0.00 0.00 3.41
3115 4625 7.712204 TCTTAAGTCAGTATGGTCATGTACA 57.288 36.000 0.00 0.00 36.16 2.90
3192 4734 4.853924 AGGTGTTTCTAAAATGGCACTG 57.146 40.909 0.00 0.00 0.00 3.66
3224 4766 8.322828 TCTGTACTGGGTGCTTTTGTTATATTA 58.677 33.333 0.00 0.00 0.00 0.98
3281 4823 8.282592 TGAATGCTTTTATTATAACTAGCTGCG 58.717 33.333 14.96 0.00 0.00 5.18
3694 8829 5.299028 CACACAAAATAGCCACAGCCATATA 59.701 40.000 0.00 0.00 41.25 0.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.520862 GTCCGCGGACGTATGGGA 61.521 66.667 39.77 8.07 37.70 4.37
10 11 3.271706 TAACCAGACACGTCCGCGG 62.272 63.158 22.12 22.12 43.45 6.46
11 12 1.800315 CTAACCAGACACGTCCGCG 60.800 63.158 0.00 0.00 44.93 6.46
12 13 0.523072 TACTAACCAGACACGTCCGC 59.477 55.000 0.00 0.00 0.00 5.54
13 14 2.589014 GTTACTAACCAGACACGTCCG 58.411 52.381 0.00 0.00 0.00 4.79
25 26 5.841957 TTATCTCCTGTCCGGTTACTAAC 57.158 43.478 0.00 0.00 0.00 2.34
26 27 6.855763 TTTTATCTCCTGTCCGGTTACTAA 57.144 37.500 0.00 0.00 0.00 2.24
27 28 6.855763 TTTTTATCTCCTGTCCGGTTACTA 57.144 37.500 0.00 0.00 0.00 1.82
28 29 5.750352 TTTTTATCTCCTGTCCGGTTACT 57.250 39.130 0.00 0.00 0.00 2.24
51 52 4.093743 GGGTCCAATAGGGTCACATTTTT 58.906 43.478 0.00 0.00 38.11 1.94
52 53 3.565670 GGGGTCCAATAGGGTCACATTTT 60.566 47.826 0.00 0.00 38.11 1.82
53 54 2.024369 GGGGTCCAATAGGGTCACATTT 60.024 50.000 0.00 0.00 38.11 2.32
54 55 1.569072 GGGGTCCAATAGGGTCACATT 59.431 52.381 0.00 0.00 38.11 2.71
55 56 1.222567 GGGGTCCAATAGGGTCACAT 58.777 55.000 0.00 0.00 38.11 3.21
56 57 0.120377 AGGGGTCCAATAGGGTCACA 59.880 55.000 0.00 0.00 38.11 3.58
57 58 1.296002 AAGGGGTCCAATAGGGTCAC 58.704 55.000 0.00 0.00 38.11 3.67
58 59 2.974285 TAAGGGGTCCAATAGGGTCA 57.026 50.000 0.00 0.00 38.11 4.02
59 60 3.053826 ACATAAGGGGTCCAATAGGGTC 58.946 50.000 0.00 0.00 38.11 4.46
60 61 3.053826 GACATAAGGGGTCCAATAGGGT 58.946 50.000 0.00 0.00 38.11 4.34
61 62 3.053077 TGACATAAGGGGTCCAATAGGG 58.947 50.000 0.00 0.00 34.36 3.53
62 63 4.263506 GGATGACATAAGGGGTCCAATAGG 60.264 50.000 0.00 0.00 34.36 2.57
63 64 4.263506 GGGATGACATAAGGGGTCCAATAG 60.264 50.000 0.00 0.00 34.36 1.73
64 65 3.655777 GGGATGACATAAGGGGTCCAATA 59.344 47.826 0.00 0.00 34.36 1.90
65 66 2.447047 GGGATGACATAAGGGGTCCAAT 59.553 50.000 0.00 0.00 34.36 3.16
66 67 1.850345 GGGATGACATAAGGGGTCCAA 59.150 52.381 0.00 0.00 34.36 3.53
67 68 1.010793 AGGGATGACATAAGGGGTCCA 59.989 52.381 0.00 0.00 34.36 4.02
68 69 1.821088 AGGGATGACATAAGGGGTCC 58.179 55.000 0.00 0.00 34.36 4.46
69 70 4.159879 CGTATAGGGATGACATAAGGGGTC 59.840 50.000 0.00 0.00 35.83 4.46
70 71 4.094476 CGTATAGGGATGACATAAGGGGT 58.906 47.826 0.00 0.00 0.00 4.95
71 72 3.118738 GCGTATAGGGATGACATAAGGGG 60.119 52.174 0.00 0.00 0.00 4.79
72 73 3.118738 GGCGTATAGGGATGACATAAGGG 60.119 52.174 0.00 0.00 0.00 3.95
73 74 3.118738 GGGCGTATAGGGATGACATAAGG 60.119 52.174 0.00 0.00 0.00 2.69
74 75 3.513912 TGGGCGTATAGGGATGACATAAG 59.486 47.826 0.00 0.00 0.00 1.73
75 76 3.512496 TGGGCGTATAGGGATGACATAA 58.488 45.455 0.00 0.00 0.00 1.90
76 77 3.096852 CTGGGCGTATAGGGATGACATA 58.903 50.000 0.00 0.00 0.00 2.29
77 78 1.902508 CTGGGCGTATAGGGATGACAT 59.097 52.381 0.00 0.00 0.00 3.06
78 79 1.338107 CTGGGCGTATAGGGATGACA 58.662 55.000 0.00 0.00 0.00 3.58
79 80 0.037232 GCTGGGCGTATAGGGATGAC 60.037 60.000 0.00 0.00 0.00 3.06
80 81 1.192146 GGCTGGGCGTATAGGGATGA 61.192 60.000 0.00 0.00 0.00 2.92
81 82 1.194781 AGGCTGGGCGTATAGGGATG 61.195 60.000 0.00 0.00 0.00 3.51
82 83 1.158705 AGGCTGGGCGTATAGGGAT 59.841 57.895 0.00 0.00 0.00 3.85
83 84 1.837051 CAGGCTGGGCGTATAGGGA 60.837 63.158 6.61 0.00 0.00 4.20
84 85 2.100879 GACAGGCTGGGCGTATAGGG 62.101 65.000 20.34 0.00 0.00 3.53
85 86 1.367840 GACAGGCTGGGCGTATAGG 59.632 63.158 20.34 0.00 0.00 2.57
86 87 1.367840 GGACAGGCTGGGCGTATAG 59.632 63.158 20.34 0.00 0.00 1.31
87 88 2.495409 CGGACAGGCTGGGCGTATA 61.495 63.158 20.34 0.00 0.00 1.47
88 89 3.849951 CGGACAGGCTGGGCGTAT 61.850 66.667 20.34 0.00 0.00 3.06
98 99 1.672854 TATGAGGGTTCGCGGACAGG 61.673 60.000 21.18 0.00 0.00 4.00
99 100 0.389391 ATATGAGGGTTCGCGGACAG 59.611 55.000 21.18 0.00 0.00 3.51
100 101 0.387929 GATATGAGGGTTCGCGGACA 59.612 55.000 21.18 0.00 0.00 4.02
101 102 0.319641 GGATATGAGGGTTCGCGGAC 60.320 60.000 9.70 9.70 0.00 4.79
102 103 0.757561 TGGATATGAGGGTTCGCGGA 60.758 55.000 6.13 0.00 0.00 5.54
103 104 0.321671 ATGGATATGAGGGTTCGCGG 59.678 55.000 6.13 0.00 0.00 6.46
104 105 1.273606 AGATGGATATGAGGGTTCGCG 59.726 52.381 0.00 0.00 0.00 5.87
105 106 2.672478 CGAGATGGATATGAGGGTTCGC 60.672 54.545 0.00 0.00 0.00 4.70
106 107 2.820197 TCGAGATGGATATGAGGGTTCG 59.180 50.000 0.00 0.00 0.00 3.95
107 108 4.873746 TTCGAGATGGATATGAGGGTTC 57.126 45.455 0.00 0.00 0.00 3.62
108 109 4.594920 ACATTCGAGATGGATATGAGGGTT 59.405 41.667 10.82 0.00 0.00 4.11
109 110 4.163427 ACATTCGAGATGGATATGAGGGT 58.837 43.478 10.82 0.00 0.00 4.34
110 111 4.815533 ACATTCGAGATGGATATGAGGG 57.184 45.455 10.82 0.00 0.00 4.30
111 112 5.163468 CCCTACATTCGAGATGGATATGAGG 60.163 48.000 10.82 7.21 0.00 3.86
112 113 5.654209 TCCCTACATTCGAGATGGATATGAG 59.346 44.000 10.82 0.59 0.00 2.90
113 114 5.580022 TCCCTACATTCGAGATGGATATGA 58.420 41.667 10.82 0.22 0.00 2.15
114 115 5.163468 CCTCCCTACATTCGAGATGGATATG 60.163 48.000 10.82 1.95 0.00 1.78
115 116 4.959210 CCTCCCTACATTCGAGATGGATAT 59.041 45.833 10.82 0.00 0.00 1.63
116 117 4.044191 TCCTCCCTACATTCGAGATGGATA 59.956 45.833 10.82 0.00 0.00 2.59
117 118 3.169099 CCTCCCTACATTCGAGATGGAT 58.831 50.000 10.82 0.00 0.00 3.41
118 119 2.177016 TCCTCCCTACATTCGAGATGGA 59.823 50.000 10.82 3.40 0.00 3.41
119 120 2.598565 TCCTCCCTACATTCGAGATGG 58.401 52.381 10.82 0.47 0.00 3.51
120 121 5.654209 TCATATCCTCCCTACATTCGAGATG 59.346 44.000 6.18 6.18 0.00 2.90
121 122 5.832221 TCATATCCTCCCTACATTCGAGAT 58.168 41.667 0.00 0.00 0.00 2.75
122 123 5.256806 TCATATCCTCCCTACATTCGAGA 57.743 43.478 0.00 0.00 0.00 4.04
123 124 4.400884 CCTCATATCCTCCCTACATTCGAG 59.599 50.000 0.00 0.00 0.00 4.04
124 125 4.344978 CCTCATATCCTCCCTACATTCGA 58.655 47.826 0.00 0.00 0.00 3.71
125 126 3.449018 CCCTCATATCCTCCCTACATTCG 59.551 52.174 0.00 0.00 0.00 3.34
126 127 3.198853 GCCCTCATATCCTCCCTACATTC 59.801 52.174 0.00 0.00 0.00 2.67
127 128 3.181390 AGCCCTCATATCCTCCCTACATT 60.181 47.826 0.00 0.00 0.00 2.71
128 129 2.388563 AGCCCTCATATCCTCCCTACAT 59.611 50.000 0.00 0.00 0.00 2.29
129 130 1.795786 AGCCCTCATATCCTCCCTACA 59.204 52.381 0.00 0.00 0.00 2.74
130 131 2.462723 GAGCCCTCATATCCTCCCTAC 58.537 57.143 0.00 0.00 0.00 3.18
131 132 1.006043 CGAGCCCTCATATCCTCCCTA 59.994 57.143 0.00 0.00 0.00 3.53
132 133 0.252012 CGAGCCCTCATATCCTCCCT 60.252 60.000 0.00 0.00 0.00 4.20
133 134 1.893919 GCGAGCCCTCATATCCTCCC 61.894 65.000 0.00 0.00 0.00 4.30
134 135 1.594310 GCGAGCCCTCATATCCTCC 59.406 63.158 0.00 0.00 0.00 4.30
135 136 1.214062 CGCGAGCCCTCATATCCTC 59.786 63.158 0.00 0.00 0.00 3.71
136 137 2.279069 CCGCGAGCCCTCATATCCT 61.279 63.158 8.23 0.00 0.00 3.24
137 138 2.262915 CCGCGAGCCCTCATATCC 59.737 66.667 8.23 0.00 0.00 2.59
138 139 1.080434 GTCCGCGAGCCCTCATATC 60.080 63.158 8.23 0.00 0.00 1.63
139 140 2.920645 CGTCCGCGAGCCCTCATAT 61.921 63.158 8.23 0.00 41.33 1.78
140 141 3.592814 CGTCCGCGAGCCCTCATA 61.593 66.667 8.23 0.00 41.33 2.15
175 176 0.807667 CGTCCTACATGGCAGACTGC 60.808 60.000 19.55 19.55 44.08 4.40
176 177 0.532573 ACGTCCTACATGGCAGACTG 59.467 55.000 0.00 0.00 35.26 3.51
177 178 0.532573 CACGTCCTACATGGCAGACT 59.467 55.000 0.00 0.00 35.26 3.24
178 179 0.460284 CCACGTCCTACATGGCAGAC 60.460 60.000 0.00 0.00 35.26 3.51
179 180 1.897423 CCACGTCCTACATGGCAGA 59.103 57.895 0.00 0.00 35.26 4.26
180 181 4.521075 CCACGTCCTACATGGCAG 57.479 61.111 0.00 0.00 35.26 4.85
183 184 1.144057 GAGGCCACGTCCTACATGG 59.856 63.158 5.01 0.00 36.38 3.66
184 185 0.460284 GTGAGGCCACGTCCTACATG 60.460 60.000 5.01 0.00 36.38 3.21
185 186 1.614241 GGTGAGGCCACGTCCTACAT 61.614 60.000 5.01 0.00 44.09 2.29
186 187 2.280552 GGTGAGGCCACGTCCTACA 61.281 63.158 5.01 0.00 44.09 2.74
187 188 2.577593 GGTGAGGCCACGTCCTAC 59.422 66.667 5.01 0.00 44.09 3.18
188 189 2.682494 GGGTGAGGCCACGTCCTA 60.682 66.667 5.01 0.00 44.09 2.94
197 198 1.705997 AATATGGTCCCGGGTGAGGC 61.706 60.000 22.86 6.79 0.00 4.70
198 199 0.843984 AAATATGGTCCCGGGTGAGG 59.156 55.000 22.86 0.00 0.00 3.86
199 200 2.172717 AGAAAATATGGTCCCGGGTGAG 59.827 50.000 22.86 0.00 0.00 3.51
200 201 2.171870 GAGAAAATATGGTCCCGGGTGA 59.828 50.000 22.86 5.77 0.00 4.02
201 202 2.172717 AGAGAAAATATGGTCCCGGGTG 59.827 50.000 22.86 0.00 0.00 4.61
202 203 2.488836 AGAGAAAATATGGTCCCGGGT 58.511 47.619 22.86 2.78 0.00 5.28
203 204 3.577805 AAGAGAAAATATGGTCCCGGG 57.422 47.619 16.85 16.85 0.00 5.73
204 205 4.781934 AGAAAGAGAAAATATGGTCCCGG 58.218 43.478 0.00 0.00 0.00 5.73
205 206 6.759497 AAAGAAAGAGAAAATATGGTCCCG 57.241 37.500 0.00 0.00 0.00 5.14
255 256 5.354513 TCACTTGTACGTGATTGGTGAAAAA 59.645 36.000 0.00 0.00 38.89 1.94
256 257 4.876679 TCACTTGTACGTGATTGGTGAAAA 59.123 37.500 0.00 0.00 38.89 2.29
257 258 4.443621 TCACTTGTACGTGATTGGTGAAA 58.556 39.130 0.00 0.00 38.89 2.69
258 259 4.061357 TCACTTGTACGTGATTGGTGAA 57.939 40.909 0.00 0.00 38.89 3.18
259 260 3.737032 TCACTTGTACGTGATTGGTGA 57.263 42.857 0.00 3.78 38.89 4.02
266 267 7.093992 TCATATGTTTGATCACTTGTACGTGA 58.906 34.615 0.00 6.13 46.82 4.35
267 268 7.289587 TCATATGTTTGATCACTTGTACGTG 57.710 36.000 0.00 0.00 36.25 4.49
268 269 6.535150 CCTCATATGTTTGATCACTTGTACGT 59.465 38.462 1.90 0.00 0.00 3.57
269 270 6.756542 TCCTCATATGTTTGATCACTTGTACG 59.243 38.462 1.90 0.00 0.00 3.67
270 271 7.981789 TCTCCTCATATGTTTGATCACTTGTAC 59.018 37.037 1.90 0.00 0.00 2.90
271 272 8.078060 TCTCCTCATATGTTTGATCACTTGTA 57.922 34.615 1.90 0.00 0.00 2.41
272 273 6.950842 TCTCCTCATATGTTTGATCACTTGT 58.049 36.000 1.90 0.00 0.00 3.16
273 274 7.854557 TTCTCCTCATATGTTTGATCACTTG 57.145 36.000 1.90 0.00 0.00 3.16
274 275 8.868522 TTTTCTCCTCATATGTTTGATCACTT 57.131 30.769 1.90 0.00 0.00 3.16
275 276 8.868522 TTTTTCTCCTCATATGTTTGATCACT 57.131 30.769 1.90 0.00 0.00 3.41
276 277 9.512435 CATTTTTCTCCTCATATGTTTGATCAC 57.488 33.333 1.90 0.00 0.00 3.06
277 278 9.465199 TCATTTTTCTCCTCATATGTTTGATCA 57.535 29.630 1.90 0.00 0.00 2.92
278 279 9.947669 CTCATTTTTCTCCTCATATGTTTGATC 57.052 33.333 1.90 0.00 0.00 2.92
279 280 8.910944 CCTCATTTTTCTCCTCATATGTTTGAT 58.089 33.333 1.90 0.00 0.00 2.57
280 281 8.108999 TCCTCATTTTTCTCCTCATATGTTTGA 58.891 33.333 1.90 0.00 0.00 2.69
281 282 8.284945 TCCTCATTTTTCTCCTCATATGTTTG 57.715 34.615 1.90 0.00 0.00 2.93
282 283 8.884124 TTCCTCATTTTTCTCCTCATATGTTT 57.116 30.769 1.90 0.00 0.00 2.83
283 284 8.910944 CATTCCTCATTTTTCTCCTCATATGTT 58.089 33.333 1.90 0.00 0.00 2.71
284 285 8.057623 ACATTCCTCATTTTTCTCCTCATATGT 58.942 33.333 1.90 0.00 0.00 2.29
285 286 8.350722 CACATTCCTCATTTTTCTCCTCATATG 58.649 37.037 0.00 0.00 0.00 1.78
286 287 7.504911 CCACATTCCTCATTTTTCTCCTCATAT 59.495 37.037 0.00 0.00 0.00 1.78
287 288 6.830324 CCACATTCCTCATTTTTCTCCTCATA 59.170 38.462 0.00 0.00 0.00 2.15
288 289 5.655532 CCACATTCCTCATTTTTCTCCTCAT 59.344 40.000 0.00 0.00 0.00 2.90
289 290 5.012239 CCACATTCCTCATTTTTCTCCTCA 58.988 41.667 0.00 0.00 0.00 3.86
290 291 5.012893 ACCACATTCCTCATTTTTCTCCTC 58.987 41.667 0.00 0.00 0.00 3.71
291 292 5.003096 ACCACATTCCTCATTTTTCTCCT 57.997 39.130 0.00 0.00 0.00 3.69
292 293 5.728637 AACCACATTCCTCATTTTTCTCC 57.271 39.130 0.00 0.00 0.00 3.71
293 294 7.756722 CACATAACCACATTCCTCATTTTTCTC 59.243 37.037 0.00 0.00 0.00 2.87
294 295 7.309990 CCACATAACCACATTCCTCATTTTTCT 60.310 37.037 0.00 0.00 0.00 2.52
295 296 6.813152 CCACATAACCACATTCCTCATTTTTC 59.187 38.462 0.00 0.00 0.00 2.29
296 297 6.496565 TCCACATAACCACATTCCTCATTTTT 59.503 34.615 0.00 0.00 0.00 1.94
297 298 6.015918 TCCACATAACCACATTCCTCATTTT 58.984 36.000 0.00 0.00 0.00 1.82
298 299 5.579047 TCCACATAACCACATTCCTCATTT 58.421 37.500 0.00 0.00 0.00 2.32
299 300 5.191727 TCCACATAACCACATTCCTCATT 57.808 39.130 0.00 0.00 0.00 2.57
300 301 4.860802 TCCACATAACCACATTCCTCAT 57.139 40.909 0.00 0.00 0.00 2.90
301 302 4.288366 TCTTCCACATAACCACATTCCTCA 59.712 41.667 0.00 0.00 0.00 3.86
302 303 4.843728 TCTTCCACATAACCACATTCCTC 58.156 43.478 0.00 0.00 0.00 3.71
303 304 4.927267 TCTTCCACATAACCACATTCCT 57.073 40.909 0.00 0.00 0.00 3.36
304 305 4.764823 TGTTCTTCCACATAACCACATTCC 59.235 41.667 0.00 0.00 0.00 3.01
305 306 5.957842 TGTTCTTCCACATAACCACATTC 57.042 39.130 0.00 0.00 0.00 2.67
306 307 6.723298 TTTGTTCTTCCACATAACCACATT 57.277 33.333 0.00 0.00 0.00 2.71
307 308 6.916360 ATTTGTTCTTCCACATAACCACAT 57.084 33.333 0.00 0.00 0.00 3.21
308 309 6.432783 CCTATTTGTTCTTCCACATAACCACA 59.567 38.462 0.00 0.00 0.00 4.17
309 310 6.657541 TCCTATTTGTTCTTCCACATAACCAC 59.342 38.462 0.00 0.00 0.00 4.16
310 311 6.785076 TCCTATTTGTTCTTCCACATAACCA 58.215 36.000 0.00 0.00 0.00 3.67
311 312 6.884836 ACTCCTATTTGTTCTTCCACATAACC 59.115 38.462 0.00 0.00 0.00 2.85
312 313 7.923414 ACTCCTATTTGTTCTTCCACATAAC 57.077 36.000 0.00 0.00 0.00 1.89
313 314 8.934023 AAACTCCTATTTGTTCTTCCACATAA 57.066 30.769 0.00 0.00 0.00 1.90
315 316 8.934023 TTAAACTCCTATTTGTTCTTCCACAT 57.066 30.769 0.00 0.00 0.00 3.21
316 317 8.754991 TTTAAACTCCTATTTGTTCTTCCACA 57.245 30.769 0.00 0.00 0.00 4.17
319 320 9.639601 CCATTTTAAACTCCTATTTGTTCTTCC 57.360 33.333 0.00 0.00 0.00 3.46
322 323 8.512138 CGTCCATTTTAAACTCCTATTTGTTCT 58.488 33.333 0.00 0.00 0.00 3.01
323 324 8.294577 ACGTCCATTTTAAACTCCTATTTGTTC 58.705 33.333 0.00 0.00 0.00 3.18
324 325 8.173542 ACGTCCATTTTAAACTCCTATTTGTT 57.826 30.769 0.00 0.00 0.00 2.83
325 326 7.754851 ACGTCCATTTTAAACTCCTATTTGT 57.245 32.000 0.00 0.00 0.00 2.83
330 331 8.785946 CCTTTAAACGTCCATTTTAAACTCCTA 58.214 33.333 0.00 0.00 34.81 2.94
331 332 7.255695 CCCTTTAAACGTCCATTTTAAACTCCT 60.256 37.037 0.00 0.00 34.81 3.69
332 333 6.864685 CCCTTTAAACGTCCATTTTAAACTCC 59.135 38.462 0.00 0.00 34.81 3.85
333 334 7.428020 ACCCTTTAAACGTCCATTTTAAACTC 58.572 34.615 0.00 0.00 34.81 3.01
334 335 7.350744 ACCCTTTAAACGTCCATTTTAAACT 57.649 32.000 0.00 0.00 34.81 2.66
335 336 6.642131 GGACCCTTTAAACGTCCATTTTAAAC 59.358 38.462 18.68 0.00 44.60 2.01
336 337 6.747125 GGACCCTTTAAACGTCCATTTTAAA 58.253 36.000 18.68 0.00 44.60 1.52
337 338 6.330004 GGACCCTTTAAACGTCCATTTTAA 57.670 37.500 18.68 0.00 44.60 1.52
338 339 5.963176 GGACCCTTTAAACGTCCATTTTA 57.037 39.130 18.68 0.00 44.60 1.52
339 340 4.859304 GGACCCTTTAAACGTCCATTTT 57.141 40.909 18.68 0.00 44.60 1.82
344 345 7.870509 AATAAATAGGACCCTTTAAACGTCC 57.129 36.000 16.92 16.92 45.40 4.79
466 467 2.203209 CCAGCCGGGATTAGCCAC 60.203 66.667 2.18 0.00 40.01 5.01
615 616 3.464720 ACAGATTGGAGAGAGACAGGA 57.535 47.619 0.00 0.00 0.00 3.86
629 630 2.706190 CGGGGGAGAATAGGAACAGATT 59.294 50.000 0.00 0.00 0.00 2.40
902 907 4.978099 AGAACCACACAGAAATCTCACAT 58.022 39.130 0.00 0.00 0.00 3.21
1018 1024 4.097135 TCCAAAGTGAAAGCGAACATTCAA 59.903 37.500 0.00 0.00 35.44 2.69
1200 1206 5.405935 AGCCATTTGACAATTCTAAACCC 57.594 39.130 0.00 0.00 0.00 4.11
1370 1376 1.548269 CACTGTCTCCCTCTTCCTCAC 59.452 57.143 0.00 0.00 0.00 3.51
1575 1581 5.006844 CAGAGCATCAATCATCTGTGAACTC 59.993 44.000 0.00 0.00 35.99 3.01
1584 1590 4.069300 TCCTGTCAGAGCATCAATCATC 57.931 45.455 0.00 0.00 37.82 2.92
1585 1591 4.452825 CTTCCTGTCAGAGCATCAATCAT 58.547 43.478 0.00 0.00 37.82 2.45
1712 1718 4.579753 TGCTTGAATCACTGTCATGTTCAA 59.420 37.500 5.58 5.58 36.69 2.69
2022 2030 6.633856 ACAAAACATTGGAATATCTGCCTTC 58.366 36.000 0.00 0.00 0.00 3.46
2141 2149 1.638529 AGCCCTGATCCTATCTTCGG 58.361 55.000 0.00 0.00 0.00 4.30
2294 2302 6.538742 GTGCTCATACTTTCTTGCTATAACCA 59.461 38.462 0.00 0.00 0.00 3.67
2309 2317 5.867903 AGCTCTTAAGATGTGCTCATACT 57.132 39.130 10.97 0.00 34.06 2.12
2694 2806 1.681166 CCCAGCCTTCACCTTGATCAG 60.681 57.143 0.00 0.00 0.00 2.90
2778 4279 5.069516 TGCTTCTGCTTGATCTTTTCCTTTT 59.930 36.000 0.00 0.00 40.48 2.27
2895 4399 5.385628 ACGGAGGGAGTACTAATTAGACT 57.614 43.478 19.38 16.13 0.00 3.24
2918 4422 6.657117 TCCATTTCAATGACAAGTATTTCCGA 59.343 34.615 0.81 0.00 38.70 4.55
2983 4487 9.473007 TGGAAATACTTGTCATCAAAATGGATA 57.527 29.630 0.00 0.00 33.42 2.59
3047 4551 7.069085 ACCAGTTCTGTTGTACTACTTTCTGTA 59.931 37.037 8.88 0.00 0.00 2.74
3048 4552 6.127140 ACCAGTTCTGTTGTACTACTTTCTGT 60.127 38.462 8.88 0.00 0.00 3.41
3049 4553 6.201044 CACCAGTTCTGTTGTACTACTTTCTG 59.799 42.308 8.88 10.62 0.00 3.02
3050 4554 6.281405 CACCAGTTCTGTTGTACTACTTTCT 58.719 40.000 8.88 0.50 0.00 2.52
3051 4555 5.465724 CCACCAGTTCTGTTGTACTACTTTC 59.534 44.000 8.88 0.00 0.00 2.62
3052 4556 5.104652 ACCACCAGTTCTGTTGTACTACTTT 60.105 40.000 8.88 0.00 0.00 2.66
3053 4557 4.407945 ACCACCAGTTCTGTTGTACTACTT 59.592 41.667 8.88 0.00 0.00 2.24
3115 4625 2.438021 ACAGTGACACACATAACCACCT 59.562 45.455 8.59 0.00 36.74 4.00
3192 4734 2.162681 AGCACCCAGTACAGATTTTGC 58.837 47.619 0.00 0.00 0.00 3.68
3224 4766 7.386299 GCATTCTGTAGTAGTATTAAGCAGCAT 59.614 37.037 0.00 0.00 0.00 3.79
3244 4786 9.880157 ATAATAAAAGCATTCAGTTTGCATTCT 57.120 25.926 0.00 0.00 42.62 2.40
3281 4823 4.681744 TCAGTGAACTTTTGGTTGCATTC 58.318 39.130 0.00 0.00 38.41 2.67


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

AutoCloner maintained by Alex Coulton.