Multiple sequence alignment - TraesCS3D01G297200

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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 TraesCS3D01G297200 chr3D 100.000 3866 0 0 1 3866 410974297 410970432 0.000000e+00 7140.0
1 TraesCS3D01G297200 chr3D 97.573 206 4 1 1 206 241199655 241199451 6.150000e-93 351.0
2 TraesCS3D01G297200 chr3D 83.871 62 6 4 848 907 609740945 609740886 5.400000e-04 56.5
3 TraesCS3D01G297200 chr3A 96.090 2967 94 15 879 3832 540683059 540686016 0.000000e+00 4817.0
4 TraesCS3D01G297200 chr3A 91.680 649 46 4 200 843 540682415 540683060 0.000000e+00 893.0
5 TraesCS3D01G297200 chr3B 96.326 2259 68 4 1019 3265 537310290 537308035 0.000000e+00 3698.0
6 TraesCS3D01G297200 chr3B 93.069 606 35 4 3267 3866 537301580 537300976 0.000000e+00 880.0
7 TraesCS3D01G297200 chr1D 98.068 207 4 0 1 207 176405645 176405439 1.020000e-95 361.0
8 TraesCS3D01G297200 chr1D 98.500 200 3 0 1 200 168942034 168941835 1.710000e-93 353.0
9 TraesCS3D01G297200 chr1D 96.667 210 7 0 1 210 152738575 152738784 2.210000e-92 350.0
10 TraesCS3D01G297200 chr1D 95.775 213 8 1 1 212 179750010 179750222 3.700000e-90 342.0
11 TraesCS3D01G297200 chr1D 91.667 48 2 2 848 894 261881899 261881853 8.970000e-07 65.8
12 TraesCS3D01G297200 chr4D 98.039 204 4 0 1 204 291955546 291955343 4.750000e-94 355.0
13 TraesCS3D01G297200 chr4D 96.667 210 5 2 1 208 208572550 208572759 7.950000e-92 348.0
14 TraesCS3D01G297200 chrUn 98.010 201 4 0 1 201 105790393 105790193 2.210000e-92 350.0
15 TraesCS3D01G297200 chr2D 96.635 208 7 0 1 208 269800671 269800878 2.860000e-91 346.0
16 TraesCS3D01G297200 chr4A 92.000 50 3 1 840 888 477883531 477883580 6.930000e-08 69.4
17 TraesCS3D01G297200 chr4A 84.127 63 5 5 854 914 614617345 614617286 5.400000e-04 56.5
18 TraesCS3D01G297200 chr5B 85.714 63 7 2 837 897 465013690 465013628 8.970000e-07 65.8
19 TraesCS3D01G297200 chr7B 85.246 61 6 3 848 908 92964046 92963989 4.170000e-05 60.2
20 TraesCS3D01G297200 chr7D 85.965 57 4 4 848 902 494673627 494673573 1.500000e-04 58.4
21 TraesCS3D01G297200 chr7A 86.207 58 3 5 848 902 133087734 133087679 1.500000e-04 58.4
22 TraesCS3D01G297200 chr5D 81.944 72 8 5 845 914 553875636 553875704 5.400000e-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 TraesCS3D01G297200 chr3D 410970432 410974297 3865 True 7140 7140 100.000 1 3866 1 chr3D.!!$R2 3865
1 TraesCS3D01G297200 chr3A 540682415 540686016 3601 False 2855 4817 93.885 200 3832 2 chr3A.!!$F1 3632
2 TraesCS3D01G297200 chr3B 537308035 537310290 2255 True 3698 3698 96.326 1019 3265 1 chr3B.!!$R2 2246
3 TraesCS3D01G297200 chr3B 537300976 537301580 604 True 880 880 93.069 3267 3866 1 chr3B.!!$R1 599

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
613 619 0.036388 TCGATGAACCTTGTGAGCCC 60.036 55.000 0.0 0.0 0.00 5.19 F
883 889 0.324091 TGGGACGGAGGGAGTAAGTC 60.324 60.000 0.0 0.0 0.00 3.01 F
885 891 0.679321 GGACGGAGGGAGTAAGTCGT 60.679 60.000 0.0 0.0 33.04 4.34 F
886 892 1.407437 GGACGGAGGGAGTAAGTCGTA 60.407 57.143 0.0 0.0 33.04 3.43 F
2100 2107 1.477014 GCTGGGTTAGTTATGGAGGGC 60.477 57.143 0.0 0.0 0.00 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2100 2107 0.318869 TGCAAGCAAAAGCATCACGG 60.319 50.000 0.00 0.0 35.51 4.94 R
2622 2629 0.106217 CACCCTCTCTCTCCTCCTCC 60.106 65.000 0.00 0.0 0.00 4.30 R
2776 2783 4.019858 ACAATCTCTCGATTCTCCACAGA 58.980 43.478 0.00 0.0 37.77 3.41 R
2847 2854 7.390718 AGAGTTTGTTACCAATATTCCAGACAC 59.609 37.037 0.00 0.0 0.00 3.67 R
2947 2966 0.322816 GCAGAATTCCAGGACAGGCA 60.323 55.000 0.65 0.0 0.00 4.75 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
18 19 3.461843 GTTCTTCGTTTGCCTGCAG 57.538 52.632 6.78 6.78 0.00 4.41
19 20 0.040067 GTTCTTCGTTTGCCTGCAGG 60.040 55.000 29.34 29.34 38.53 4.85
20 21 0.179032 TTCTTCGTTTGCCTGCAGGA 60.179 50.000 37.21 18.42 37.39 3.86
21 22 0.179032 TCTTCGTTTGCCTGCAGGAA 60.179 50.000 37.21 25.79 37.39 3.36
22 23 0.667993 CTTCGTTTGCCTGCAGGAAA 59.332 50.000 37.21 30.49 37.39 3.13
23 24 0.383949 TTCGTTTGCCTGCAGGAAAC 59.616 50.000 37.21 33.04 37.39 2.78
24 25 0.749818 TCGTTTGCCTGCAGGAAACA 60.750 50.000 34.59 25.01 36.20 2.83
25 26 0.318107 CGTTTGCCTGCAGGAAACAG 60.318 55.000 34.59 28.08 36.20 3.16
26 27 1.032014 GTTTGCCTGCAGGAAACAGA 58.968 50.000 37.21 15.05 37.32 3.41
27 28 1.032014 TTTGCCTGCAGGAAACAGAC 58.968 50.000 37.21 16.86 37.32 3.51
28 29 0.823356 TTGCCTGCAGGAAACAGACC 60.823 55.000 37.21 16.08 37.32 3.85
29 30 1.073897 GCCTGCAGGAAACAGACCT 59.926 57.895 37.21 0.00 37.32 3.85
30 31 0.538287 GCCTGCAGGAAACAGACCTT 60.538 55.000 37.21 0.00 37.32 3.50
31 32 1.528129 CCTGCAGGAAACAGACCTTC 58.472 55.000 29.88 0.00 37.32 3.46
32 33 1.151668 CTGCAGGAAACAGACCTTCG 58.848 55.000 5.57 0.00 37.32 3.79
33 34 0.468226 TGCAGGAAACAGACCTTCGT 59.532 50.000 0.00 0.00 35.35 3.85
34 35 0.868406 GCAGGAAACAGACCTTCGTG 59.132 55.000 0.00 1.88 40.15 4.35
35 36 1.512926 CAGGAAACAGACCTTCGTGG 58.487 55.000 0.00 0.00 42.93 4.94
45 46 3.935993 CCTTCGTGGTCAGGTTGAT 57.064 52.632 0.00 0.00 0.00 2.57
46 47 1.726853 CCTTCGTGGTCAGGTTGATC 58.273 55.000 0.00 0.00 0.00 2.92
47 48 1.350193 CTTCGTGGTCAGGTTGATCG 58.650 55.000 0.00 0.00 27.66 3.69
48 49 0.677288 TTCGTGGTCAGGTTGATCGT 59.323 50.000 0.00 0.00 27.66 3.73
49 50 0.038618 TCGTGGTCAGGTTGATCGTG 60.039 55.000 0.00 0.00 27.66 4.35
50 51 1.626654 CGTGGTCAGGTTGATCGTGC 61.627 60.000 0.00 0.00 27.66 5.34
51 52 0.320771 GTGGTCAGGTTGATCGTGCT 60.321 55.000 0.00 0.00 27.66 4.40
52 53 0.037326 TGGTCAGGTTGATCGTGCTC 60.037 55.000 0.00 0.00 27.66 4.26
53 54 0.741221 GGTCAGGTTGATCGTGCTCC 60.741 60.000 0.00 0.00 32.68 4.70
54 55 1.078759 GTCAGGTTGATCGTGCTCCG 61.079 60.000 0.00 0.00 38.13 4.63
55 56 1.811266 CAGGTTGATCGTGCTCCGG 60.811 63.158 0.00 0.00 37.11 5.14
56 57 2.264794 GGTTGATCGTGCTCCGGT 59.735 61.111 0.00 0.00 37.11 5.28
57 58 2.100631 GGTTGATCGTGCTCCGGTG 61.101 63.158 0.00 0.00 37.11 4.94
58 59 1.374252 GTTGATCGTGCTCCGGTGT 60.374 57.895 0.00 0.00 37.11 4.16
59 60 1.374125 TTGATCGTGCTCCGGTGTG 60.374 57.895 0.00 0.00 37.11 3.82
60 61 2.509336 GATCGTGCTCCGGTGTGG 60.509 66.667 0.00 0.00 37.11 4.17
61 62 3.296709 GATCGTGCTCCGGTGTGGT 62.297 63.158 0.00 0.00 39.52 4.16
62 63 3.296709 ATCGTGCTCCGGTGTGGTC 62.297 63.158 0.00 0.00 39.52 4.02
63 64 4.293648 CGTGCTCCGGTGTGGTCA 62.294 66.667 0.00 0.00 39.52 4.02
64 65 2.110213 GTGCTCCGGTGTGGTCAA 59.890 61.111 0.00 0.00 39.52 3.18
65 66 1.302511 GTGCTCCGGTGTGGTCAAT 60.303 57.895 0.00 0.00 39.52 2.57
66 67 0.036765 GTGCTCCGGTGTGGTCAATA 60.037 55.000 0.00 0.00 39.52 1.90
67 68 0.687920 TGCTCCGGTGTGGTCAATAA 59.312 50.000 0.00 0.00 39.52 1.40
68 69 1.084289 GCTCCGGTGTGGTCAATAAC 58.916 55.000 0.00 0.00 39.52 1.89
80 81 4.680171 GGTCAATAACCTTTCGGAGTTG 57.320 45.455 0.00 0.00 45.45 3.16
81 82 3.439129 GGTCAATAACCTTTCGGAGTTGG 59.561 47.826 0.00 0.00 45.45 3.77
82 83 4.070009 GTCAATAACCTTTCGGAGTTGGT 58.930 43.478 0.00 0.00 0.00 3.67
83 84 4.517832 GTCAATAACCTTTCGGAGTTGGTT 59.482 41.667 13.20 13.20 44.03 3.67
84 85 5.009310 GTCAATAACCTTTCGGAGTTGGTTT 59.991 40.000 13.67 3.76 42.14 3.27
85 86 6.205270 GTCAATAACCTTTCGGAGTTGGTTTA 59.795 38.462 13.67 4.69 42.14 2.01
86 87 6.428771 TCAATAACCTTTCGGAGTTGGTTTAG 59.571 38.462 13.67 7.24 42.14 1.85
87 88 2.501261 ACCTTTCGGAGTTGGTTTAGC 58.499 47.619 0.00 0.00 0.00 3.09
88 89 1.463444 CCTTTCGGAGTTGGTTTAGCG 59.537 52.381 0.00 0.00 0.00 4.26
89 90 2.409975 CTTTCGGAGTTGGTTTAGCGA 58.590 47.619 0.00 0.00 0.00 4.93
90 91 2.754946 TTCGGAGTTGGTTTAGCGAT 57.245 45.000 0.00 0.00 0.00 4.58
91 92 2.754946 TCGGAGTTGGTTTAGCGATT 57.245 45.000 0.00 0.00 0.00 3.34
92 93 2.343101 TCGGAGTTGGTTTAGCGATTG 58.657 47.619 0.00 0.00 0.00 2.67
93 94 1.202031 CGGAGTTGGTTTAGCGATTGC 60.202 52.381 0.00 0.00 43.24 3.56
103 104 3.261951 GCGATTGCTAAGGCGCGA 61.262 61.111 12.10 0.00 42.25 5.87
104 105 2.621000 CGATTGCTAAGGCGCGAC 59.379 61.111 12.10 7.34 42.25 5.19
105 106 2.621000 GATTGCTAAGGCGCGACG 59.379 61.111 12.10 0.00 42.25 5.12
106 107 2.125673 ATTGCTAAGGCGCGACGT 60.126 55.556 12.10 8.51 42.25 4.34
107 108 2.078958 GATTGCTAAGGCGCGACGTC 62.079 60.000 12.10 5.18 42.25 4.34
108 109 4.789075 TGCTAAGGCGCGACGTCC 62.789 66.667 12.10 0.00 42.25 4.79
109 110 4.493747 GCTAAGGCGCGACGTCCT 62.494 66.667 12.10 2.98 35.62 3.85
110 111 2.278013 CTAAGGCGCGACGTCCTC 60.278 66.667 12.10 0.88 33.75 3.71
111 112 4.170062 TAAGGCGCGACGTCCTCG 62.170 66.667 12.10 17.31 45.97 4.63
121 122 2.174107 CGTCCTCGCACGTTCGTA 59.826 61.111 7.61 0.00 34.95 3.43
122 123 1.862147 CGTCCTCGCACGTTCGTAG 60.862 63.158 7.61 3.99 34.95 3.51
123 124 1.208614 GTCCTCGCACGTTCGTAGT 59.791 57.895 7.61 0.00 0.00 2.73
124 125 0.792356 GTCCTCGCACGTTCGTAGTC 60.792 60.000 7.61 0.00 0.00 2.59
125 126 1.862147 CCTCGCACGTTCGTAGTCG 60.862 63.158 7.61 3.03 38.55 4.18
126 127 1.862147 CTCGCACGTTCGTAGTCGG 60.862 63.158 7.61 0.00 37.69 4.79
127 128 2.174107 CGCACGTTCGTAGTCGGA 59.826 61.111 0.00 0.00 37.69 4.55
128 129 1.226211 CGCACGTTCGTAGTCGGAT 60.226 57.895 0.00 0.00 37.69 4.18
129 130 1.192436 CGCACGTTCGTAGTCGGATC 61.192 60.000 0.00 0.00 37.69 3.36
130 131 1.192436 GCACGTTCGTAGTCGGATCG 61.192 60.000 0.00 0.00 37.69 3.69
131 132 0.095935 CACGTTCGTAGTCGGATCGT 59.904 55.000 0.00 0.00 37.96 3.73
132 133 0.371645 ACGTTCGTAGTCGGATCGTC 59.628 55.000 0.00 0.00 35.14 4.20
133 134 0.371301 CGTTCGTAGTCGGATCGTCA 59.629 55.000 0.00 0.00 37.69 4.35
134 135 1.201954 CGTTCGTAGTCGGATCGTCAA 60.202 52.381 0.00 0.00 37.69 3.18
135 136 2.725759 CGTTCGTAGTCGGATCGTCAAA 60.726 50.000 0.00 0.00 37.69 2.69
136 137 2.819422 TCGTAGTCGGATCGTCAAAG 57.181 50.000 0.00 0.00 37.69 2.77
137 138 2.079158 TCGTAGTCGGATCGTCAAAGT 58.921 47.619 0.00 0.00 37.69 2.66
138 139 2.094894 TCGTAGTCGGATCGTCAAAGTC 59.905 50.000 0.00 0.00 37.69 3.01
139 140 2.438583 GTAGTCGGATCGTCAAAGTCG 58.561 52.381 0.00 0.00 0.00 4.18
140 141 1.162698 AGTCGGATCGTCAAAGTCGA 58.837 50.000 0.00 0.00 41.45 4.20
141 142 1.135746 AGTCGGATCGTCAAAGTCGAC 60.136 52.381 7.70 7.70 44.69 4.20
142 143 1.135746 GTCGGATCGTCAAAGTCGACT 60.136 52.381 13.58 13.58 42.20 4.18
143 144 1.538512 TCGGATCGTCAAAGTCGACTT 59.461 47.619 24.93 24.93 40.07 3.01
144 145 1.912110 CGGATCGTCAAAGTCGACTTC 59.088 52.381 29.82 17.01 40.07 3.01
145 146 2.260481 GGATCGTCAAAGTCGACTTCC 58.740 52.381 29.82 20.81 40.07 3.46
146 147 2.094649 GGATCGTCAAAGTCGACTTCCT 60.095 50.000 29.82 13.85 40.07 3.36
147 148 2.701073 TCGTCAAAGTCGACTTCCTC 57.299 50.000 29.82 19.95 34.61 3.71
148 149 1.268899 TCGTCAAAGTCGACTTCCTCC 59.731 52.381 29.82 16.73 34.61 4.30
149 150 1.000607 CGTCAAAGTCGACTTCCTCCA 60.001 52.381 29.82 10.35 34.61 3.86
150 151 2.545113 CGTCAAAGTCGACTTCCTCCAA 60.545 50.000 29.82 10.09 34.61 3.53
151 152 3.463944 GTCAAAGTCGACTTCCTCCAAA 58.536 45.455 29.82 8.78 34.61 3.28
152 153 3.875134 GTCAAAGTCGACTTCCTCCAAAA 59.125 43.478 29.82 7.81 34.61 2.44
153 154 3.875134 TCAAAGTCGACTTCCTCCAAAAC 59.125 43.478 29.82 0.00 34.61 2.43
154 155 2.150397 AGTCGACTTCCTCCAAAACG 57.850 50.000 13.58 0.00 0.00 3.60
155 156 1.684983 AGTCGACTTCCTCCAAAACGA 59.315 47.619 13.58 0.00 0.00 3.85
156 157 2.299297 AGTCGACTTCCTCCAAAACGAT 59.701 45.455 13.58 0.00 0.00 3.73
157 158 3.508793 AGTCGACTTCCTCCAAAACGATA 59.491 43.478 13.58 0.00 0.00 2.92
158 159 3.858238 GTCGACTTCCTCCAAAACGATAG 59.142 47.826 8.70 0.00 46.19 2.08
159 160 2.603560 CGACTTCCTCCAAAACGATAGC 59.396 50.000 0.00 0.00 42.67 2.97
160 161 2.937149 GACTTCCTCCAAAACGATAGCC 59.063 50.000 0.00 0.00 42.67 3.93
161 162 2.304761 ACTTCCTCCAAAACGATAGCCA 59.695 45.455 0.00 0.00 42.67 4.75
162 163 2.396590 TCCTCCAAAACGATAGCCAC 57.603 50.000 0.00 0.00 42.67 5.01
163 164 1.065709 TCCTCCAAAACGATAGCCACC 60.066 52.381 0.00 0.00 42.67 4.61
164 165 1.339631 CCTCCAAAACGATAGCCACCA 60.340 52.381 0.00 0.00 42.67 4.17
165 166 2.643551 CTCCAAAACGATAGCCACCAT 58.356 47.619 0.00 0.00 42.67 3.55
166 167 2.614057 CTCCAAAACGATAGCCACCATC 59.386 50.000 0.00 0.00 42.67 3.51
167 168 2.238646 TCCAAAACGATAGCCACCATCT 59.761 45.455 0.00 0.00 42.67 2.90
168 169 2.614057 CCAAAACGATAGCCACCATCTC 59.386 50.000 0.00 0.00 42.67 2.75
169 170 3.270027 CAAAACGATAGCCACCATCTCA 58.730 45.455 0.00 0.00 42.67 3.27
170 171 3.845781 AAACGATAGCCACCATCTCAT 57.154 42.857 0.00 0.00 42.67 2.90
171 172 3.393089 AACGATAGCCACCATCTCATC 57.607 47.619 0.00 0.00 42.67 2.92
172 173 1.270826 ACGATAGCCACCATCTCATCG 59.729 52.381 0.00 0.00 40.68 3.84
173 174 1.541588 CGATAGCCACCATCTCATCGA 59.458 52.381 0.00 0.00 37.95 3.59
174 175 2.029918 CGATAGCCACCATCTCATCGAA 60.030 50.000 0.00 0.00 37.95 3.71
175 176 3.552890 CGATAGCCACCATCTCATCGAAA 60.553 47.826 0.00 0.00 37.95 3.46
176 177 2.322355 AGCCACCATCTCATCGAAAG 57.678 50.000 0.00 0.00 0.00 2.62
178 179 1.936547 GCCACCATCTCATCGAAAGAC 59.063 52.381 3.25 0.00 46.97 3.01
179 180 2.196749 CCACCATCTCATCGAAAGACG 58.803 52.381 3.25 0.00 46.97 4.18
191 192 2.538449 TCGAAAGACGAGACAACTTTGC 59.462 45.455 0.00 0.00 46.45 3.68
192 193 2.348591 CGAAAGACGAGACAACTTTGCC 60.349 50.000 0.00 0.00 45.77 4.52
193 194 2.622064 AAGACGAGACAACTTTGCCT 57.378 45.000 0.00 0.00 0.00 4.75
194 195 2.156343 AGACGAGACAACTTTGCCTC 57.844 50.000 0.00 0.00 34.78 4.70
195 196 1.689273 AGACGAGACAACTTTGCCTCT 59.311 47.619 4.12 0.00 35.80 3.69
196 197 2.891580 AGACGAGACAACTTTGCCTCTA 59.108 45.455 4.12 0.00 35.80 2.43
197 198 3.511934 AGACGAGACAACTTTGCCTCTAT 59.488 43.478 4.12 0.00 35.80 1.98
198 199 3.851098 ACGAGACAACTTTGCCTCTATC 58.149 45.455 4.12 0.00 35.80 2.08
210 211 1.689273 GCCTCTATCAGTTCGGGATGT 59.311 52.381 0.00 0.00 0.00 3.06
226 227 3.627237 GGGATGTAAGGGCATCTCCAAAA 60.627 47.826 6.11 0.00 43.41 2.44
250 251 2.158638 ACCACTGCATTTGCCCATTTTT 60.159 40.909 0.00 0.00 41.18 1.94
282 284 5.926542 CGTTATACCATGGTATCCAAGTGAG 59.073 44.000 35.39 17.54 41.12 3.51
287 289 1.580059 TGGTATCCAAGTGAGTCCCC 58.420 55.000 0.00 0.00 0.00 4.81
288 290 1.203376 TGGTATCCAAGTGAGTCCCCA 60.203 52.381 0.00 0.00 0.00 4.96
300 302 1.351017 GAGTCCCCACTTGTCCATCAA 59.649 52.381 0.00 0.00 30.63 2.57
309 311 6.463614 CCCCACTTGTCCATCAATTTTGTTTA 60.464 38.462 0.00 0.00 35.35 2.01
343 346 4.661222 TGCAGTCTATTTGTTCCATTCCA 58.339 39.130 0.00 0.00 0.00 3.53
438 441 3.807622 ACATAGTGTTCCAAGTTCACACG 59.192 43.478 0.00 0.00 44.64 4.49
440 443 2.550978 AGTGTTCCAAGTTCACACGAG 58.449 47.619 0.00 0.00 44.64 4.18
451 454 6.201517 CAAGTTCACACGAGTTGAATCAAAT 58.798 36.000 0.00 0.00 0.00 2.32
538 541 3.055747 TGGTACGCACAGTATTGATCCAA 60.056 43.478 0.00 0.00 37.69 3.53
555 558 3.541632 TCCAATTCTATTGGTTCGCCTC 58.458 45.455 15.89 0.00 40.40 4.70
571 577 1.139654 GCCTCCATGATGCTAGTGTCA 59.860 52.381 0.00 2.38 0.00 3.58
583 589 5.468540 TGCTAGTGTCAGTAAACATGACT 57.531 39.130 0.00 0.00 45.87 3.41
598 604 6.824305 AACATGACTTTTGAAATCCTCGAT 57.176 33.333 0.00 0.00 0.00 3.59
599 605 6.187125 ACATGACTTTTGAAATCCTCGATG 57.813 37.500 0.00 0.00 0.00 3.84
613 619 0.036388 TCGATGAACCTTGTGAGCCC 60.036 55.000 0.00 0.00 0.00 5.19
616 622 0.610232 ATGAACCTTGTGAGCCCAGC 60.610 55.000 0.00 0.00 0.00 4.85
642 648 1.403679 TGGTCTTTGTTGCCTTTCACG 59.596 47.619 0.00 0.00 0.00 4.35
653 659 1.263217 GCCTTTCACGTCAACGACAAT 59.737 47.619 9.88 0.00 43.02 2.71
682 688 4.111577 TCTCTCTCTCCCTCTTTCTCTCT 58.888 47.826 0.00 0.00 0.00 3.10
684 690 5.911178 TCTCTCTCTCCCTCTTTCTCTCTAT 59.089 44.000 0.00 0.00 0.00 1.98
698 704 8.826765 TCTTTCTCTCTATTTGGGTTGTATCTT 58.173 33.333 0.00 0.00 0.00 2.40
708 714 3.118038 TGGGTTGTATCTTCATGTAGCCC 60.118 47.826 4.23 4.23 0.00 5.19
736 742 3.181428 CCTTTCACCCTTCTTTTCCTCCT 60.181 47.826 0.00 0.00 0.00 3.69
737 743 4.474394 CTTTCACCCTTCTTTTCCTCCTT 58.526 43.478 0.00 0.00 0.00 3.36
738 744 3.790089 TCACCCTTCTTTTCCTCCTTC 57.210 47.619 0.00 0.00 0.00 3.46
756 762 3.944015 CCTTCCTCTCTTATTGCACTTGG 59.056 47.826 0.00 0.00 0.00 3.61
790 796 9.616634 CATGGGAAAATATTCGTCATTCTATTG 57.383 33.333 0.00 0.00 36.36 1.90
799 805 9.915629 ATATTCGTCATTCTATTGTTCTACCTC 57.084 33.333 0.00 0.00 0.00 3.85
852 858 9.385902 CACAATCAAATATAATACTCCAAAGCG 57.614 33.333 0.00 0.00 0.00 4.68
853 859 8.076178 ACAATCAAATATAATACTCCAAAGCGC 58.924 33.333 0.00 0.00 0.00 5.92
854 860 7.986085 ATCAAATATAATACTCCAAAGCGCT 57.014 32.000 2.64 2.64 0.00 5.92
855 861 7.421530 TCAAATATAATACTCCAAAGCGCTC 57.578 36.000 12.06 0.00 0.00 5.03
856 862 7.217200 TCAAATATAATACTCCAAAGCGCTCT 58.783 34.615 12.06 0.00 0.00 4.09
857 863 7.715249 TCAAATATAATACTCCAAAGCGCTCTT 59.285 33.333 12.06 4.51 0.00 2.85
858 864 8.988934 CAAATATAATACTCCAAAGCGCTCTTA 58.011 33.333 12.06 0.00 31.02 2.10
859 865 9.726438 AAATATAATACTCCAAAGCGCTCTTAT 57.274 29.630 12.06 6.97 31.02 1.73
865 871 8.709386 ATACTCCAAAGCGCTCTTATATTATG 57.291 34.615 12.06 0.00 31.02 1.90
866 872 5.934625 ACTCCAAAGCGCTCTTATATTATGG 59.065 40.000 12.06 8.44 31.02 2.74
867 873 5.245531 TCCAAAGCGCTCTTATATTATGGG 58.754 41.667 12.06 0.00 31.02 4.00
868 874 5.012664 TCCAAAGCGCTCTTATATTATGGGA 59.987 40.000 12.06 0.05 31.02 4.37
869 875 5.122396 CCAAAGCGCTCTTATATTATGGGAC 59.878 44.000 12.06 0.00 31.02 4.46
870 876 4.111375 AGCGCTCTTATATTATGGGACG 57.889 45.455 2.64 0.00 0.00 4.79
871 877 3.119101 AGCGCTCTTATATTATGGGACGG 60.119 47.826 2.64 0.00 0.00 4.79
872 878 3.119245 GCGCTCTTATATTATGGGACGGA 60.119 47.826 0.00 0.00 0.00 4.69
873 879 4.673441 CGCTCTTATATTATGGGACGGAG 58.327 47.826 0.00 0.00 0.00 4.63
874 880 4.440250 CGCTCTTATATTATGGGACGGAGG 60.440 50.000 0.00 0.00 0.00 4.30
875 881 4.141914 GCTCTTATATTATGGGACGGAGGG 60.142 50.000 0.00 0.00 0.00 4.30
876 882 5.269991 CTCTTATATTATGGGACGGAGGGA 58.730 45.833 0.00 0.00 0.00 4.20
877 883 5.269991 TCTTATATTATGGGACGGAGGGAG 58.730 45.833 0.00 0.00 0.00 4.30
878 884 3.562108 ATATTATGGGACGGAGGGAGT 57.438 47.619 0.00 0.00 0.00 3.85
879 885 4.687262 ATATTATGGGACGGAGGGAGTA 57.313 45.455 0.00 0.00 0.00 2.59
880 886 2.852714 TTATGGGACGGAGGGAGTAA 57.147 50.000 0.00 0.00 0.00 2.24
881 887 2.376695 TATGGGACGGAGGGAGTAAG 57.623 55.000 0.00 0.00 0.00 2.34
882 888 0.338814 ATGGGACGGAGGGAGTAAGT 59.661 55.000 0.00 0.00 0.00 2.24
883 889 0.324091 TGGGACGGAGGGAGTAAGTC 60.324 60.000 0.00 0.00 0.00 3.01
884 890 1.382692 GGGACGGAGGGAGTAAGTCG 61.383 65.000 0.00 0.00 33.04 4.18
885 891 0.679321 GGACGGAGGGAGTAAGTCGT 60.679 60.000 0.00 0.00 33.04 4.34
886 892 1.407437 GGACGGAGGGAGTAAGTCGTA 60.407 57.143 0.00 0.00 33.04 3.43
887 893 2.570135 GACGGAGGGAGTAAGTCGTAT 58.430 52.381 0.00 0.00 0.00 3.06
888 894 2.290093 GACGGAGGGAGTAAGTCGTATG 59.710 54.545 0.00 0.00 0.00 2.39
889 895 2.295885 CGGAGGGAGTAAGTCGTATGT 58.704 52.381 0.00 0.00 0.00 2.29
890 896 2.033049 CGGAGGGAGTAAGTCGTATGTG 59.967 54.545 0.00 0.00 0.00 3.21
1013 1019 2.443255 AGTTCACCATGTTGAGAAGGGT 59.557 45.455 0.00 0.00 0.00 4.34
1027 1033 4.101585 TGAGAAGGGTATATCTGGTTGCTG 59.898 45.833 0.00 0.00 0.00 4.41
1098 1105 9.498039 AAAGGGAATATTCAATTCCTCAATTCT 57.502 29.630 17.07 2.12 45.21 2.40
1406 1413 1.873903 CGCTATTGCCTTCTACCGCAT 60.874 52.381 0.00 0.00 34.35 4.73
1647 1654 2.949447 AGAAGTGTTGTGGCTTGGAAT 58.051 42.857 0.00 0.00 0.00 3.01
1707 1714 2.828877 CGGGCGATTGAGGTGTATAAA 58.171 47.619 0.00 0.00 0.00 1.40
1721 1728 2.434336 TGTATAAAGAGATGCAGGCGGT 59.566 45.455 0.00 0.00 0.00 5.68
1792 1799 3.958860 AGGCTGGTGCACTGGACC 61.959 66.667 17.98 12.70 41.91 4.46
1809 1816 2.358737 CTGGGGCGTGAAGTGGAC 60.359 66.667 0.00 0.00 0.00 4.02
1811 1818 2.358737 GGGGCGTGAAGTGGACAG 60.359 66.667 0.00 0.00 0.00 3.51
1845 1852 5.624159 TCTGAAAGAATGGACATCAGTGTT 58.376 37.500 0.00 0.00 42.31 3.32
1866 1873 2.175878 TTCTTGGCTCTGCTCTTGTC 57.824 50.000 0.00 0.00 0.00 3.18
2100 2107 1.477014 GCTGGGTTAGTTATGGAGGGC 60.477 57.143 0.00 0.00 0.00 5.19
2202 2209 1.611936 GGAAGGGCTGGACTTCTTGAC 60.612 57.143 0.00 0.00 42.96 3.18
2223 2230 5.743398 TGACGAAGCAATGCAATTTATAAGC 59.257 36.000 8.35 0.00 31.22 3.09
2355 2362 1.962807 CTCGAGCCTGAGAATCCATCT 59.037 52.381 0.00 0.00 42.61 2.90
2622 2629 5.070770 AGTCAGTTCTGCATGAGTTAGAG 57.929 43.478 0.00 0.00 0.00 2.43
2776 2783 4.769688 TCTCGCCATCAAGTTTATGTCAT 58.230 39.130 0.00 0.00 0.00 3.06
2847 2854 5.345741 CCATTTTAAAGATGGCAAGTGTTCG 59.654 40.000 13.13 0.00 37.81 3.95
2947 2966 8.621532 AATGAACAACTACATTCACATACACT 57.378 30.769 0.00 0.00 37.64 3.55
3045 3065 4.279671 TGTGGGGTGATTTTTGTGATACAC 59.720 41.667 0.00 0.00 34.56 2.90
3124 3144 3.258872 TGGGTCCAATGCTTCTCATTTTG 59.741 43.478 0.00 0.00 42.48 2.44
3168 3188 4.976731 CGACCTACATATTTCTGAACTCCG 59.023 45.833 0.00 0.00 0.00 4.63
3244 3264 2.586258 TGCTAGCTCATCCGAAAGAC 57.414 50.000 17.23 0.00 0.00 3.01
3252 3272 3.367910 GCTCATCCGAAAGACTGAAGAGT 60.368 47.826 0.00 0.00 32.80 3.24
3342 3362 1.952296 GGTCCTCAATAATGCCTGCAG 59.048 52.381 6.78 6.78 0.00 4.41
3399 3423 7.008440 TGAAGCAAATTCATCTGTCTAATCG 57.992 36.000 0.00 0.00 43.09 3.34
3495 3519 2.037136 GTGCCTGACTCATTGCGCT 61.037 57.895 9.73 0.00 0.00 5.92
3548 3572 4.404507 TCGACTACATTTGAAGCTTTGC 57.595 40.909 0.00 0.00 0.00 3.68
3586 3610 1.199615 TGGTGAGTGGTGACTGACAA 58.800 50.000 0.00 0.00 38.01 3.18
3639 3664 0.605589 ACTGCTAAACGGCCAAGACC 60.606 55.000 2.24 0.00 0.00 3.85
3656 3681 6.151817 GCCAAGACCAGAAGATTATTGAGTTT 59.848 38.462 0.00 0.00 0.00 2.66
3731 3757 2.265367 TCAATGGAGACTGCCCTTGTA 58.735 47.619 0.00 0.00 35.72 2.41
3768 3794 6.039270 TGGACTTACTTTGTCATTGTCCTTTG 59.961 38.462 0.00 0.00 41.93 2.77
3783 3809 6.636454 TGTCCTTTGGGAAGTACATTATCT 57.364 37.500 0.00 0.00 44.15 1.98
3787 3813 7.393515 GTCCTTTGGGAAGTACATTATCTTTGT 59.606 37.037 0.00 0.00 44.15 2.83
3788 3814 7.610305 TCCTTTGGGAAGTACATTATCTTTGTC 59.390 37.037 0.00 0.00 38.93 3.18
3789 3815 7.393234 CCTTTGGGAAGTACATTATCTTTGTCA 59.607 37.037 0.00 0.00 33.58 3.58
3791 3817 7.016153 TGGGAAGTACATTATCTTTGTCACT 57.984 36.000 0.00 0.00 0.00 3.41
3793 3819 7.390440 TGGGAAGTACATTATCTTTGTCACTTG 59.610 37.037 0.00 0.00 0.00 3.16
3794 3820 7.244192 GGAAGTACATTATCTTTGTCACTTGC 58.756 38.462 0.00 0.00 30.51 4.01
3795 3821 7.094805 GGAAGTACATTATCTTTGTCACTTGCA 60.095 37.037 0.00 0.00 33.98 4.08
3796 3822 7.744087 AGTACATTATCTTTGTCACTTGCAA 57.256 32.000 0.00 0.00 0.00 4.08
3797 3823 8.340618 AGTACATTATCTTTGTCACTTGCAAT 57.659 30.769 0.00 0.00 0.00 3.56
3835 3861 4.097437 GCTTTCATCAGAGCAAATCATGGA 59.903 41.667 0.00 0.00 38.73 3.41
3859 3885 1.216178 GCACCATCACCAACATGGC 59.784 57.895 0.00 0.00 44.32 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.040067 CCTGCAGGCAAACGAAGAAC 60.040 55.000 22.33 0.00 0.00 3.01
1 2 0.179032 TCCTGCAGGCAAACGAAGAA 60.179 50.000 28.91 3.28 34.44 2.52
2 3 0.179032 TTCCTGCAGGCAAACGAAGA 60.179 50.000 28.91 4.13 34.44 2.87
3 4 0.667993 TTTCCTGCAGGCAAACGAAG 59.332 50.000 28.91 0.67 34.44 3.79
4 5 0.383949 GTTTCCTGCAGGCAAACGAA 59.616 50.000 28.89 17.56 31.12 3.85
5 6 0.749818 TGTTTCCTGCAGGCAAACGA 60.750 50.000 32.36 25.04 37.69 3.85
6 7 0.318107 CTGTTTCCTGCAGGCAAACG 60.318 55.000 32.36 26.95 37.69 3.60
7 8 1.032014 TCTGTTTCCTGCAGGCAAAC 58.968 50.000 32.26 32.26 36.57 2.93
8 9 1.032014 GTCTGTTTCCTGCAGGCAAA 58.968 50.000 28.91 23.49 38.36 3.68
9 10 0.823356 GGTCTGTTTCCTGCAGGCAA 60.823 55.000 28.91 21.69 40.08 4.52
10 11 1.228245 GGTCTGTTTCCTGCAGGCA 60.228 57.895 28.91 15.88 40.08 4.75
11 12 0.538287 AAGGTCTGTTTCCTGCAGGC 60.538 55.000 28.91 14.89 37.81 4.85
12 13 1.528129 GAAGGTCTGTTTCCTGCAGG 58.472 55.000 27.87 27.87 35.27 4.85
13 14 1.151668 CGAAGGTCTGTTTCCTGCAG 58.848 55.000 6.78 6.78 35.27 4.41
14 15 0.468226 ACGAAGGTCTGTTTCCTGCA 59.532 50.000 0.00 0.00 35.27 4.41
15 16 0.868406 CACGAAGGTCTGTTTCCTGC 59.132 55.000 0.00 0.00 35.27 4.85
16 17 1.512926 CCACGAAGGTCTGTTTCCTG 58.487 55.000 0.00 0.00 35.27 3.86
27 28 1.726853 GATCAACCTGACCACGAAGG 58.273 55.000 0.00 0.00 45.67 3.46
28 29 1.336887 ACGATCAACCTGACCACGAAG 60.337 52.381 0.00 0.00 0.00 3.79
29 30 0.677288 ACGATCAACCTGACCACGAA 59.323 50.000 0.00 0.00 0.00 3.85
30 31 0.038618 CACGATCAACCTGACCACGA 60.039 55.000 0.00 0.00 0.00 4.35
31 32 1.626654 GCACGATCAACCTGACCACG 61.627 60.000 0.00 0.00 0.00 4.94
32 33 0.320771 AGCACGATCAACCTGACCAC 60.321 55.000 0.00 0.00 0.00 4.16
33 34 0.037326 GAGCACGATCAACCTGACCA 60.037 55.000 0.00 0.00 0.00 4.02
34 35 0.741221 GGAGCACGATCAACCTGACC 60.741 60.000 0.00 0.00 0.00 4.02
35 36 2.755929 GGAGCACGATCAACCTGAC 58.244 57.895 0.00 0.00 0.00 3.51
46 47 3.687060 TATTGACCACACCGGAGCACG 62.687 57.143 9.46 0.00 43.80 5.34
47 48 0.036765 TATTGACCACACCGGAGCAC 60.037 55.000 9.46 0.00 38.63 4.40
48 49 0.687920 TTATTGACCACACCGGAGCA 59.312 50.000 9.46 0.00 38.63 4.26
49 50 1.084289 GTTATTGACCACACCGGAGC 58.916 55.000 9.46 0.00 38.63 4.70
69 70 2.409975 TCGCTAAACCAACTCCGAAAG 58.590 47.619 0.00 0.00 0.00 2.62
70 71 2.529780 TCGCTAAACCAACTCCGAAA 57.470 45.000 0.00 0.00 0.00 3.46
71 72 2.739913 CAATCGCTAAACCAACTCCGAA 59.260 45.455 0.00 0.00 0.00 4.30
72 73 2.343101 CAATCGCTAAACCAACTCCGA 58.657 47.619 0.00 0.00 0.00 4.55
73 74 1.202031 GCAATCGCTAAACCAACTCCG 60.202 52.381 0.00 0.00 34.30 4.63
74 75 2.544480 GCAATCGCTAAACCAACTCC 57.456 50.000 0.00 0.00 34.30 3.85
86 87 3.261951 TCGCGCCTTAGCAATCGC 61.262 61.111 0.00 0.00 43.62 4.58
87 88 2.621000 GTCGCGCCTTAGCAATCG 59.379 61.111 0.00 0.00 39.83 3.34
88 89 2.078958 GACGTCGCGCCTTAGCAATC 62.079 60.000 0.00 0.00 39.83 2.67
89 90 2.125673 ACGTCGCGCCTTAGCAAT 60.126 55.556 0.00 0.00 39.83 3.56
90 91 2.807895 GACGTCGCGCCTTAGCAA 60.808 61.111 0.00 0.00 39.83 3.91
91 92 4.789075 GGACGTCGCGCCTTAGCA 62.789 66.667 9.92 0.00 39.83 3.49
92 93 4.493747 AGGACGTCGCGCCTTAGC 62.494 66.667 9.92 0.00 31.65 3.09
93 94 2.278013 GAGGACGTCGCGCCTTAG 60.278 66.667 9.92 0.00 34.66 2.18
94 95 4.170062 CGAGGACGTCGCGCCTTA 62.170 66.667 14.88 0.00 43.03 2.69
104 105 1.862147 CTACGAACGTGCGAGGACG 60.862 63.158 25.68 15.20 45.09 4.79
105 106 0.792356 GACTACGAACGTGCGAGGAC 60.792 60.000 25.68 10.94 34.83 3.85
106 107 1.499056 GACTACGAACGTGCGAGGA 59.501 57.895 25.68 6.35 34.83 3.71
107 108 1.862147 CGACTACGAACGTGCGAGG 60.862 63.158 25.68 16.50 42.66 4.63
108 109 1.862147 CCGACTACGAACGTGCGAG 60.862 63.158 25.68 17.49 42.66 5.03
109 110 1.638388 ATCCGACTACGAACGTGCGA 61.638 55.000 25.68 5.35 42.66 5.10
110 111 1.192436 GATCCGACTACGAACGTGCG 61.192 60.000 16.06 16.06 42.66 5.34
111 112 1.192436 CGATCCGACTACGAACGTGC 61.192 60.000 10.14 0.00 42.66 5.34
112 113 0.095935 ACGATCCGACTACGAACGTG 59.904 55.000 10.14 3.19 42.66 4.49
113 114 0.371645 GACGATCCGACTACGAACGT 59.628 55.000 5.03 5.03 42.66 3.99
114 115 0.371301 TGACGATCCGACTACGAACG 59.629 55.000 0.00 0.00 42.66 3.95
115 116 2.532531 TTGACGATCCGACTACGAAC 57.467 50.000 0.00 0.00 42.66 3.95
116 117 2.485426 ACTTTGACGATCCGACTACGAA 59.515 45.455 0.00 0.00 42.66 3.85
117 118 2.079158 ACTTTGACGATCCGACTACGA 58.921 47.619 0.00 0.00 42.66 3.43
118 119 2.438583 GACTTTGACGATCCGACTACG 58.561 52.381 0.00 0.00 39.43 3.51
119 120 2.094894 TCGACTTTGACGATCCGACTAC 59.905 50.000 0.00 0.00 34.85 2.73
120 121 2.094894 GTCGACTTTGACGATCCGACTA 59.905 50.000 8.70 0.00 41.88 2.59
121 122 1.135746 GTCGACTTTGACGATCCGACT 60.136 52.381 8.70 0.00 41.88 4.18
122 123 1.135746 AGTCGACTTTGACGATCCGAC 60.136 52.381 13.58 0.00 43.70 4.79
123 124 1.162698 AGTCGACTTTGACGATCCGA 58.837 50.000 13.58 0.00 43.70 4.55
124 125 1.912110 GAAGTCGACTTTGACGATCCG 59.088 52.381 30.22 0.00 43.70 4.18
125 126 2.094649 AGGAAGTCGACTTTGACGATCC 60.095 50.000 30.22 23.77 43.86 3.36
126 127 3.172824 GAGGAAGTCGACTTTGACGATC 58.827 50.000 30.22 16.32 43.70 3.69
127 128 2.094649 GGAGGAAGTCGACTTTGACGAT 60.095 50.000 30.22 13.51 43.70 3.73
128 129 1.268899 GGAGGAAGTCGACTTTGACGA 59.731 52.381 30.22 0.00 43.70 4.20
129 130 1.000607 TGGAGGAAGTCGACTTTGACG 60.001 52.381 30.22 0.00 43.70 4.35
130 131 2.814280 TGGAGGAAGTCGACTTTGAC 57.186 50.000 30.22 22.21 36.11 3.18
131 132 3.830744 TTTGGAGGAAGTCGACTTTGA 57.169 42.857 30.22 11.12 36.11 2.69
132 133 3.303132 CGTTTTGGAGGAAGTCGACTTTG 60.303 47.826 30.22 8.07 36.11 2.77
133 134 2.870411 CGTTTTGGAGGAAGTCGACTTT 59.130 45.455 30.22 16.87 36.11 2.66
134 135 2.101917 TCGTTTTGGAGGAAGTCGACTT 59.898 45.455 30.12 30.12 39.23 3.01
135 136 1.684983 TCGTTTTGGAGGAAGTCGACT 59.315 47.619 13.58 13.58 0.00 4.18
136 137 2.144482 TCGTTTTGGAGGAAGTCGAC 57.856 50.000 7.70 7.70 0.00 4.20
137 138 3.675228 GCTATCGTTTTGGAGGAAGTCGA 60.675 47.826 0.00 0.00 0.00 4.20
138 139 2.603560 GCTATCGTTTTGGAGGAAGTCG 59.396 50.000 0.00 0.00 0.00 4.18
139 140 2.937149 GGCTATCGTTTTGGAGGAAGTC 59.063 50.000 0.00 0.00 0.00 3.01
140 141 2.304761 TGGCTATCGTTTTGGAGGAAGT 59.695 45.455 0.00 0.00 0.00 3.01
141 142 2.678336 GTGGCTATCGTTTTGGAGGAAG 59.322 50.000 0.00 0.00 0.00 3.46
142 143 2.617021 GGTGGCTATCGTTTTGGAGGAA 60.617 50.000 0.00 0.00 0.00 3.36
143 144 1.065709 GGTGGCTATCGTTTTGGAGGA 60.066 52.381 0.00 0.00 0.00 3.71
144 145 1.339631 TGGTGGCTATCGTTTTGGAGG 60.340 52.381 0.00 0.00 0.00 4.30
145 146 2.107950 TGGTGGCTATCGTTTTGGAG 57.892 50.000 0.00 0.00 0.00 3.86
146 147 2.238646 AGATGGTGGCTATCGTTTTGGA 59.761 45.455 0.00 0.00 0.00 3.53
147 148 2.614057 GAGATGGTGGCTATCGTTTTGG 59.386 50.000 0.00 0.00 0.00 3.28
148 149 3.270027 TGAGATGGTGGCTATCGTTTTG 58.730 45.455 0.00 0.00 0.00 2.44
149 150 3.627395 TGAGATGGTGGCTATCGTTTT 57.373 42.857 0.00 0.00 0.00 2.43
150 151 3.733337 GATGAGATGGTGGCTATCGTTT 58.267 45.455 0.00 0.00 0.00 3.60
151 152 2.288457 CGATGAGATGGTGGCTATCGTT 60.288 50.000 0.00 0.00 34.43 3.85
152 153 1.270826 CGATGAGATGGTGGCTATCGT 59.729 52.381 0.00 0.00 34.43 3.73
153 154 1.541588 TCGATGAGATGGTGGCTATCG 59.458 52.381 0.00 0.00 38.86 2.92
154 155 3.667497 TTCGATGAGATGGTGGCTATC 57.333 47.619 0.00 0.00 0.00 2.08
155 156 3.643320 TCTTTCGATGAGATGGTGGCTAT 59.357 43.478 0.00 0.00 0.00 2.97
156 157 3.031013 TCTTTCGATGAGATGGTGGCTA 58.969 45.455 0.00 0.00 0.00 3.93
157 158 1.833630 TCTTTCGATGAGATGGTGGCT 59.166 47.619 0.00 0.00 0.00 4.75
158 159 1.936547 GTCTTTCGATGAGATGGTGGC 59.063 52.381 2.78 0.00 0.00 5.01
159 160 2.159240 TCGTCTTTCGATGAGATGGTGG 60.159 50.000 14.84 1.06 44.01 4.61
160 161 3.150848 TCGTCTTTCGATGAGATGGTG 57.849 47.619 14.84 3.22 44.01 4.17
170 171 2.538449 GCAAAGTTGTCTCGTCTTTCGA 59.462 45.455 0.00 0.00 46.83 3.71
171 172 2.348591 GGCAAAGTTGTCTCGTCTTTCG 60.349 50.000 0.00 0.00 41.41 3.46
172 173 2.872858 AGGCAAAGTTGTCTCGTCTTTC 59.127 45.455 0.00 0.00 39.25 2.62
173 174 2.919228 AGGCAAAGTTGTCTCGTCTTT 58.081 42.857 0.00 0.00 39.25 2.52
174 175 2.622064 AGGCAAAGTTGTCTCGTCTT 57.378 45.000 0.00 0.00 39.25 3.01
181 182 4.092091 CGAACTGATAGAGGCAAAGTTGTC 59.908 45.833 0.00 0.00 31.45 3.18
182 183 3.997021 CGAACTGATAGAGGCAAAGTTGT 59.003 43.478 0.00 0.00 31.45 3.32
183 184 3.372206 CCGAACTGATAGAGGCAAAGTTG 59.628 47.826 0.00 0.00 31.45 3.16
184 185 3.600388 CCGAACTGATAGAGGCAAAGTT 58.400 45.455 0.00 0.00 33.91 2.66
185 186 2.093447 CCCGAACTGATAGAGGCAAAGT 60.093 50.000 0.00 0.00 0.00 2.66
186 187 2.168521 TCCCGAACTGATAGAGGCAAAG 59.831 50.000 0.00 0.00 0.00 2.77
187 188 2.184533 TCCCGAACTGATAGAGGCAAA 58.815 47.619 0.00 0.00 0.00 3.68
188 189 1.860641 TCCCGAACTGATAGAGGCAA 58.139 50.000 0.00 0.00 0.00 4.52
189 190 1.688735 CATCCCGAACTGATAGAGGCA 59.311 52.381 0.00 0.00 0.00 4.75
190 191 1.689273 ACATCCCGAACTGATAGAGGC 59.311 52.381 0.00 0.00 0.00 4.70
191 192 4.021894 CCTTACATCCCGAACTGATAGAGG 60.022 50.000 0.00 0.00 0.00 3.69
192 193 4.021894 CCCTTACATCCCGAACTGATAGAG 60.022 50.000 0.00 0.00 0.00 2.43
193 194 3.895656 CCCTTACATCCCGAACTGATAGA 59.104 47.826 0.00 0.00 0.00 1.98
194 195 3.555168 GCCCTTACATCCCGAACTGATAG 60.555 52.174 0.00 0.00 0.00 2.08
195 196 2.367567 GCCCTTACATCCCGAACTGATA 59.632 50.000 0.00 0.00 0.00 2.15
196 197 1.141053 GCCCTTACATCCCGAACTGAT 59.859 52.381 0.00 0.00 0.00 2.90
197 198 0.539986 GCCCTTACATCCCGAACTGA 59.460 55.000 0.00 0.00 0.00 3.41
198 199 0.251916 TGCCCTTACATCCCGAACTG 59.748 55.000 0.00 0.00 0.00 3.16
226 227 0.835941 TGGGCAAATGCAGTGGTTTT 59.164 45.000 7.80 0.00 44.36 2.43
250 251 2.572556 ACCATGGTATAACGTGTCCCAA 59.427 45.455 18.10 0.00 0.00 4.12
255 256 5.129815 ACTTGGATACCATGGTATAACGTGT 59.870 40.000 32.68 24.52 40.93 4.49
256 257 5.465390 CACTTGGATACCATGGTATAACGTG 59.535 44.000 32.68 28.63 40.93 4.49
257 258 5.364446 TCACTTGGATACCATGGTATAACGT 59.636 40.000 32.68 23.82 40.93 3.99
258 259 5.849510 TCACTTGGATACCATGGTATAACG 58.150 41.667 32.68 23.28 40.93 3.18
259 260 6.827727 ACTCACTTGGATACCATGGTATAAC 58.172 40.000 32.68 27.20 40.93 1.89
282 284 2.514458 ATTGATGGACAAGTGGGGAC 57.486 50.000 0.00 0.00 42.02 4.46
334 336 7.130681 AGTTGTTTTATTTGGTGGAATGGAA 57.869 32.000 0.00 0.00 0.00 3.53
404 407 7.517614 TGGAACACTATGTTGCTTGATTTTA 57.482 32.000 13.33 0.00 46.83 1.52
409 412 4.460263 ACTTGGAACACTATGTTGCTTGA 58.540 39.130 13.33 1.13 46.83 3.02
422 425 2.675844 CAACTCGTGTGAACTTGGAACA 59.324 45.455 0.00 0.00 0.00 3.18
538 541 3.136443 TCATGGAGGCGAACCAATAGAAT 59.864 43.478 5.38 0.00 40.93 2.40
555 558 5.178061 TGTTTACTGACACTAGCATCATGG 58.822 41.667 0.00 0.00 0.00 3.66
571 577 7.444183 TCGAGGATTTCAAAAGTCATGTTTACT 59.556 33.333 0.00 0.00 0.00 2.24
583 589 5.534654 ACAAGGTTCATCGAGGATTTCAAAA 59.465 36.000 0.00 0.00 0.00 2.44
598 604 1.228245 GCTGGGCTCACAAGGTTCA 60.228 57.895 0.00 0.00 0.00 3.18
599 605 0.538287 AAGCTGGGCTCACAAGGTTC 60.538 55.000 0.00 0.00 38.25 3.62
613 619 2.466846 CAACAAAGACCAAGCAAGCTG 58.533 47.619 0.00 0.00 0.00 4.24
616 622 1.410153 AGGCAACAAAGACCAAGCAAG 59.590 47.619 0.00 0.00 41.41 4.01
642 648 1.003233 AGAAGGGGGATTGTCGTTGAC 59.997 52.381 0.00 0.00 0.00 3.18
653 659 0.556380 AGGGAGAGAGAGAAGGGGGA 60.556 60.000 0.00 0.00 0.00 4.81
682 688 6.770785 GGCTACATGAAGATACAACCCAAATA 59.229 38.462 0.00 0.00 0.00 1.40
684 690 4.947388 GGCTACATGAAGATACAACCCAAA 59.053 41.667 0.00 0.00 0.00 3.28
698 704 5.007682 GTGAAAGGTTTAAGGGCTACATGA 58.992 41.667 0.00 0.00 0.00 3.07
708 714 6.323996 AGGAAAAGAAGGGTGAAAGGTTTAAG 59.676 38.462 0.00 0.00 0.00 1.85
736 742 3.587061 TCCCAAGTGCAATAAGAGAGGAA 59.413 43.478 0.00 0.00 0.00 3.36
737 743 3.055094 GTCCCAAGTGCAATAAGAGAGGA 60.055 47.826 0.00 0.00 0.00 3.71
738 744 3.274288 GTCCCAAGTGCAATAAGAGAGG 58.726 50.000 0.00 0.00 0.00 3.69
756 762 4.559300 CGAATATTTTCCCATGCATGGTCC 60.559 45.833 37.30 17.16 46.65 4.46
778 784 9.400638 GAATAGAGGTAGAACAATAGAATGACG 57.599 37.037 0.00 0.00 0.00 4.35
843 849 5.352569 CCCATAATATAAGAGCGCTTTGGAG 59.647 44.000 13.26 4.81 35.56 3.86
844 850 5.012664 TCCCATAATATAAGAGCGCTTTGGA 59.987 40.000 13.26 2.17 35.56 3.53
845 851 5.122396 GTCCCATAATATAAGAGCGCTTTGG 59.878 44.000 13.26 8.63 35.56 3.28
846 852 5.163953 CGTCCCATAATATAAGAGCGCTTTG 60.164 44.000 13.26 0.00 35.56 2.77
847 853 4.929808 CGTCCCATAATATAAGAGCGCTTT 59.070 41.667 13.26 1.42 35.56 3.51
848 854 4.495422 CGTCCCATAATATAAGAGCGCTT 58.505 43.478 13.26 8.09 38.15 4.68
850 856 3.119245 TCCGTCCCATAATATAAGAGCGC 60.119 47.826 0.00 0.00 0.00 5.92
851 857 4.440250 CCTCCGTCCCATAATATAAGAGCG 60.440 50.000 0.00 0.00 0.00 5.03
852 858 4.141914 CCCTCCGTCCCATAATATAAGAGC 60.142 50.000 0.00 0.00 0.00 4.09
853 859 5.269991 TCCCTCCGTCCCATAATATAAGAG 58.730 45.833 0.00 0.00 0.00 2.85
854 860 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
855 861 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
856 862 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
857 863 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
858 864 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
859 865 4.140853 ACTTACTCCCTCCGTCCCATAATA 60.141 45.833 0.00 0.00 0.00 0.98
860 866 3.240302 CTTACTCCCTCCGTCCCATAAT 58.760 50.000 0.00 0.00 0.00 1.28
861 867 2.023695 ACTTACTCCCTCCGTCCCATAA 60.024 50.000 0.00 0.00 0.00 1.90
862 868 1.572415 ACTTACTCCCTCCGTCCCATA 59.428 52.381 0.00 0.00 0.00 2.74
863 869 0.338814 ACTTACTCCCTCCGTCCCAT 59.661 55.000 0.00 0.00 0.00 4.00
864 870 0.324091 GACTTACTCCCTCCGTCCCA 60.324 60.000 0.00 0.00 0.00 4.37
865 871 1.382692 CGACTTACTCCCTCCGTCCC 61.383 65.000 0.00 0.00 0.00 4.46
866 872 0.679321 ACGACTTACTCCCTCCGTCC 60.679 60.000 0.00 0.00 0.00 4.79
867 873 2.029838 TACGACTTACTCCCTCCGTC 57.970 55.000 0.00 0.00 0.00 4.79
868 874 2.295885 CATACGACTTACTCCCTCCGT 58.704 52.381 0.00 0.00 0.00 4.69
869 875 2.033049 CACATACGACTTACTCCCTCCG 59.967 54.545 0.00 0.00 0.00 4.63
870 876 3.022406 ACACATACGACTTACTCCCTCC 58.978 50.000 0.00 0.00 0.00 4.30
871 877 4.715527 AACACATACGACTTACTCCCTC 57.284 45.455 0.00 0.00 0.00 4.30
872 878 6.594788 TTAAACACATACGACTTACTCCCT 57.405 37.500 0.00 0.00 0.00 4.20
873 879 7.838771 ATTTAAACACATACGACTTACTCCC 57.161 36.000 0.00 0.00 0.00 4.30
933 939 7.692460 TCAATAAGACTTGAATTGTGCAGAT 57.308 32.000 9.49 0.00 32.35 2.90
936 942 9.195411 GAATTTCAATAAGACTTGAATTGTGCA 57.805 29.630 9.49 0.00 42.87 4.57
937 943 8.650714 GGAATTTCAATAAGACTTGAATTGTGC 58.349 33.333 9.49 0.00 42.87 4.57
938 944 9.143631 GGGAATTTCAATAAGACTTGAATTGTG 57.856 33.333 9.49 0.00 42.87 3.33
942 948 7.454380 TGTGGGGAATTTCAATAAGACTTGAAT 59.546 33.333 0.00 0.00 42.87 2.57
943 949 6.780031 TGTGGGGAATTTCAATAAGACTTGAA 59.220 34.615 0.00 0.00 41.97 2.69
944 950 6.310941 TGTGGGGAATTTCAATAAGACTTGA 58.689 36.000 0.00 0.00 33.42 3.02
945 951 6.588719 TGTGGGGAATTTCAATAAGACTTG 57.411 37.500 0.00 0.00 0.00 3.16
946 952 7.610580 TTTGTGGGGAATTTCAATAAGACTT 57.389 32.000 0.00 0.00 0.00 3.01
947 953 7.610580 TTTTGTGGGGAATTTCAATAAGACT 57.389 32.000 0.00 0.00 0.00 3.24
991 997 2.816087 CCCTTCTCAACATGGTGAACTG 59.184 50.000 15.67 3.35 0.00 3.16
992 998 2.443255 ACCCTTCTCAACATGGTGAACT 59.557 45.455 15.67 0.00 0.00 3.01
1013 1019 4.119862 GTTCGCTTCAGCAACCAGATATA 58.880 43.478 0.00 0.00 42.21 0.86
1027 1033 2.033194 CGGTGGAAGGGTTCGCTTC 61.033 63.158 17.39 17.39 0.00 3.86
1555 1562 0.440371 GAGTACAGCACAAGAAGCGC 59.560 55.000 0.00 0.00 37.01 5.92
1572 1579 2.281761 AGTTGGCCGCACTTGGAG 60.282 61.111 0.00 0.00 0.00 3.86
1647 1654 3.342377 TCGTACCCAGAAATCATTGCA 57.658 42.857 0.00 0.00 0.00 4.08
1691 1698 5.985530 TGCATCTCTTTATACACCTCAATCG 59.014 40.000 0.00 0.00 0.00 3.34
1695 1702 4.443457 GCCTGCATCTCTTTATACACCTCA 60.443 45.833 0.00 0.00 0.00 3.86
1707 1714 1.220206 CTTCACCGCCTGCATCTCT 59.780 57.895 0.00 0.00 0.00 3.10
1792 1799 2.358737 GTCCACTTCACGCCCCAG 60.359 66.667 0.00 0.00 0.00 4.45
1809 1816 7.017645 CCATTCTTTCAGAAACAATACGTCTG 58.982 38.462 0.00 0.00 37.82 3.51
1811 1818 7.015877 GTCCATTCTTTCAGAAACAATACGTC 58.984 38.462 0.00 0.00 37.82 4.34
1845 1852 2.880890 GACAAGAGCAGAGCCAAGAAAA 59.119 45.455 0.00 0.00 0.00 2.29
1866 1873 1.473677 CCACACCTGGCATACATGTTG 59.526 52.381 2.30 3.61 0.00 3.33
1935 1942 2.465860 TGGAAGTCCATGTAACCACG 57.534 50.000 0.00 0.00 42.01 4.94
2100 2107 0.318869 TGCAAGCAAAAGCATCACGG 60.319 50.000 0.00 0.00 35.51 4.94
2149 2156 5.537300 ACCATAGAACAATAGTGCTCGAT 57.463 39.130 0.00 0.00 34.64 3.59
2202 2209 4.969395 TCGCTTATAAATTGCATTGCTTCG 59.031 37.500 10.49 0.00 0.00 3.79
2223 2230 2.898705 GGCTCTCCAGGCATATAATCG 58.101 52.381 0.00 0.00 44.88 3.34
2622 2629 0.106217 CACCCTCTCTCTCCTCCTCC 60.106 65.000 0.00 0.00 0.00 4.30
2776 2783 4.019858 ACAATCTCTCGATTCTCCACAGA 58.980 43.478 0.00 0.00 37.77 3.41
2847 2854 7.390718 AGAGTTTGTTACCAATATTCCAGACAC 59.609 37.037 0.00 0.00 0.00 3.67
2947 2966 0.322816 GCAGAATTCCAGGACAGGCA 60.323 55.000 0.65 0.00 0.00 4.75
3045 3065 7.041848 TCGTATTTTGATGCAATATCAGGACTG 60.042 37.037 0.00 0.00 0.00 3.51
3124 3144 2.416431 GCTGGAATTGTGGATGTTCAGC 60.416 50.000 0.00 0.00 0.00 4.26
3168 3188 7.068716 AGCATCCTGACCCTTTAAATTATGTTC 59.931 37.037 0.00 0.00 0.00 3.18
3244 3264 2.297315 TGCACTGTACCTCACTCTTCAG 59.703 50.000 0.00 0.00 0.00 3.02
3252 3272 1.407299 GGATGCATGCACTGTACCTCA 60.407 52.381 25.37 0.00 0.00 3.86
3342 3362 0.678048 GGACTTGATGTGCCCTCACC 60.678 60.000 0.00 0.00 42.46 4.02
3387 3411 3.554544 CCTGCTGCATCGATTAGACAGAT 60.555 47.826 20.24 0.00 0.00 2.90
3399 3423 3.192001 TCAAAGAATCAACCTGCTGCATC 59.808 43.478 1.31 0.00 0.00 3.91
3495 3519 5.173774 GCTTTTGCATGATAATTCTCCGA 57.826 39.130 0.00 0.00 46.58 4.55
3548 3572 2.426024 CCAATGTGGGCAATCTTCAGAG 59.574 50.000 0.00 0.00 32.67 3.35
3639 3664 9.166173 TGGTACATGAAACTCAATAATCTTCTG 57.834 33.333 0.00 0.00 0.00 3.02
3656 3681 8.670135 CAACGGAATATAAAGTTTGGTACATGA 58.330 33.333 0.00 0.00 39.30 3.07
3731 3757 4.357918 AGTAAGTCCATGCTCACAAGTT 57.642 40.909 0.00 0.00 0.00 2.66
3768 3794 7.626452 GCAAGTGACAAAGATAATGTACTTCCC 60.626 40.741 0.00 0.00 29.93 3.97
3793 3819 1.535437 GCTGGTAGCATGCAAGATTGC 60.535 52.381 21.98 10.60 46.98 3.56
3794 3820 2.022195 AGCTGGTAGCATGCAAGATTG 58.978 47.619 21.98 6.36 45.56 2.67
3795 3821 2.431954 AGCTGGTAGCATGCAAGATT 57.568 45.000 21.98 0.16 45.56 2.40
3796 3822 2.431954 AAGCTGGTAGCATGCAAGAT 57.568 45.000 21.98 7.55 45.56 2.40
3797 3823 2.086869 GAAAGCTGGTAGCATGCAAGA 58.913 47.619 21.98 1.02 45.56 3.02
3835 3861 0.823356 GTTGGTGATGGTGCTGGTGT 60.823 55.000 0.00 0.00 0.00 4.16


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

AutoCloner maintained by Alex Coulton.